	10-fTHF	uc031sbp.1	O75891	OTTHUMG00000125551	ENST00000393434.2:c.1993A>T	chr3.hg19:g.125833489T>A	ENSP00000377083:p.Ser665Cys	68.0	0.0		63.0	27.0	NM_001270364	B4DG36|E9PBX3|Q68CS1	Missense_Mutation	SNP	ENST00000393434.2	hg19	CCDS3034.1	.	.	.	.	.	.	.	.	.	.	T	16.48	3.135527	0.56828	.	.	ENSG00000144908	ENST00000273450;ENST00000472186;ENST00000452905;ENST00000393434	T;T;T;T	0.09350	2.99;2.99;2.99;2.99	4.14	4.14	0.48551	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.146153	0.64402	D	0.000012	T	0.40546	0.1121	H	0.96080	3.765	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.79784	0.971;0.993;0.973	T	0.46176	-0.9210	10	0.87932	D	0	.	6.134	0.20221	0.0:0.1142:0.0:0.8858	.	564;200;665	E9PBX3;Q6ZV71;O75891	.;.;AL1L1_HUMAN	C	675;665;564;665	ENSP00000273450:S675C;ENSP00000420293:S665C;ENSP00000395881:S564C;ENSP00000377083:S665C	ENSP00000273450:S675C	S	-	1	0	ALDH1L1	127316179	1.000000	0.71417	0.396000	0.26296	0.705000	0.40729	3.937000	0.56575	1.732000	0.51606	0.402000	0.26972	AGT	.	.		0.617	ALDH1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354391.1	NM_012190		A	125833489	T	A	125833489	3	1	235	1	0	0	0	0	1	0	0	0	494	1609	56	4	739	4	ALDH1L1	3	125833489	Missense_Mutation	SNP	T	TCGA-DD-AAW2-01A-11D-A40P-10	73108832	125833489	72188941	29	32715										
STX18	53407	hgsc.bcm.edu	37	chr4	4426917	4426917	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	tcatcaaacaagctgttcatTtcaccaattagtcgctgatt	5	10	4	1			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr4:4426917T>C	ENST00000306200.2	-	8	798	c.735A>G	c.(733-735)gaA>gaG	p.E245E	STX18_ENST00000505286.1_Silent_p.E245E	NM_016930.2	NP_058626.1	Q9P2W9	STX18_HUMAN	syntaxin 18	245	t-SNARE coiled-coil homology.				ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	5				UCEC - Uterine corpus endometrioid carcinoma (64;0.0534)		AGCTGTTCATTTCACCAATTA	0.413																																					p.E245E		Atlas-SNP	.											.	STX18	16	.	0			c.A735G						.						160	132	141					4																	4426917		2203	4300	6503	SO:0001819	synonymous_variant	53407	exon8			GTTCATTTCACCA	AB028741	CCDS3377.1	4p16.3-p16.2	2013-09-23			ENSG00000168818	ENSG00000168818			15942	protein-coding gene	gene with protein product		606046				10788491	Standard	NM_016930		Approved	Ufe1	uc003gic.3	Q9P2W9	OTTHUMG00000090331	ENST00000306200.2:c.735A>G	chr4.hg19:g.4426917T>C		73.0	0.0		94.0	4.0	NM_016930	Q596L3|Q5TZP5	Silent	SNP	ENST00000306200.2	hg19	CCDS3377.1																																																																																			.	.		0.413	STX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206696.1			C	4426917	T	C	4426917	2	2	235	1	0	0	0	0	0	0	0	1	15356	1838	64	2		2	STX18	4	4426917	Silent	SNP	T	TCGA-DD-AAW2-01A-11D-A40P-10		4426917	186727359	30	32716										
WDR1	9948	hgsc.bcm.edu	37	chr4	10079384	10079384	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	cgccgccactcaccgagtagCcgtcagcaacgctgaacact	9	17	2	1			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr4:10079384C>A	ENST00000499869.2	-	13	1755	c.1562G>T	c.(1561-1563)gGc>gTc	p.G521V	WDR1_ENST00000382452.2_Missense_Mutation_p.G521V|WDR1_ENST00000382451.2_Missense_Mutation_p.G381V|WDR1_ENST00000515743.1_5'UTR|WDR1_ENST00000502702.1_Missense_Mutation_p.G381V|MIR3138_ENST00000585238.1_RNA			O75083	WDR1_HUMAN	WD repeat domain 1	521					blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|sensory perception of sound (GO:0007605)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)				endometrium(3)|lung(5)|ovary(2)|pancreas(1)|urinary_tract(1)	12				STAD - Stomach adenocarcinoma(129;0.000703)|Colorectal(103;0.0057)|LUSC - Lung squamous cell carcinoma(721;0.0232)		CACCGAGTAGCCGTCAGCAAC	0.667																																					p.G521V		Atlas-SNP	.											.	WDR1	93	.	0			c.G1562T						.						17	20	19					4																	10079384		2149	4224	6373	SO:0001583	missense	9948	exon13			GAGTAGCCGTCAG	AF020260	CCDS54739.1, CCDS54740.1	4p16.1	2013-01-09			ENSG00000071127	ENSG00000071127		"WD repeat domain containing"	12754	protein-coding gene	gene with protein product		604734				10036186	Standard	NM_017491		Approved		uc021xlv.1	O75083	OTTHUMG00000160253	ENST00000499869.2:c.1562G>T	chr4.hg19:g.10079384C>A	ENSP00000427687:p.Gly521Val	100.0	0.0		165.0	63.0	NM_017491	A8K6E9|A8MPU4|O75313|Q8N6E5|Q9UG05|Q9UG78|Q9UQE0	Missense_Mutation	SNP	ENST00000499869.2	hg19	CCDS54740.1	.	.	.	.	.	.	.	.	.	.	C	12.31	1.900449	0.33535	.	.	ENSG00000071127	ENST00000499869;ENST00000382452;ENST00000382451;ENST00000502702;ENST00000439733	T;T;T;T	0.57436	0.4;0.4;0.59;0.59	5.85	4.12	0.48240	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.200800	0.51477	D	0.000088	T	0.53222	0.1783	M	0.83312	2.635	0.80722	D	1	P;P	0.41947	0.634;0.766	B;B	0.37198	0.165;0.243	T	0.58423	-0.7639	10	0.66056	D	0.02	-21.513	10.2261	0.43227	0.1363:0.7937:0.0:0.07	.	381;521	O75083-3;O75083	.;WDR1_HUMAN	V	521;521;381;381;356	ENSP00000427687:G521V;ENSP00000371890:G521V;ENSP00000371889:G381V;ENSP00000426725:G381V	ENSP00000371889:G381V	G	-	2	0	WDR1	9688482	1.000000	0.71417	0.803000	0.32268	0.598000	0.36846	2.193000	0.42658	0.813000	0.34350	0.655000	0.94253	GGC	.	.		0.667	WDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359877.1			A	10079384	C	A	10079384	3	1	235	1	0	0	0	0	1	0	0	0	17287	739	26	3	270	3	WDR1	4	10079384	Missense_Mutation	SNP	C	TCGA-DD-AAW2-01A-11D-A40P-10	5652467	10079384	181074892	31	32717										
CCDC149	91050	hgsc.bcm.edu	37	chr4	24839840	24839840	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	ctcatgggctgcaaagtgtcGcacgccgattgcttcgtctc	11	13	2	0	rs377438836		TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr4:24839840G>A	ENST00000389609.4	-	6	570	c.427C>T	c.(427-429)Cga>Tga	p.R143*	CCDC149_ENST00000502801.1_Intron|CCDC149_ENST00000504487.1_Nonsense_Mutation_p.R143*|CCDC149_ENST00000428116.2_Intron	NM_173463.4	NP_775734.2	Q6ZUS6	CC149_HUMAN	coiled-coil domain containing 149	88										cervix(1)|endometrium(1)|large_intestine(2)|lung(3)	7		Breast(46;0.173)				GCAAAGTGTCGCACGCCGATT	0.478																																					p.R143X		Atlas-SNP	.											.	CCDC149	41	.	0			c.C427T						.	G	stop/ARG,stop/ARG	1,4405	2.1+/-5.4	0,1,2202	169	152	157		427,427	5	1	4		157	0,8600		0,0,4300	no	stop-gained,stop-gained	CCDC149	NM_001130726.2,NM_173463.4	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	143/530,143/530	24839840	1,13005	2203	4300	6503	SO:0001587	stop_gained	91050	exon6			AGTGTCGCACGCC		CCDS33967.1, CCDS47036.1, CCDS33967.2	4p15.2	2008-03-03				ENSG00000181982			25405	protein-coding gene	gene with protein product						17457313	Standard	NM_173463		Approved	DKFZp761B107	uc003grc.3	Q6ZUS6		ENST00000389609.4:c.427C>T	chr4.hg19:g.24839840G>A	ENSP00000374260:p.Arg143*	77.0	0.0		118.0	5.0	NM_173463	A6NJE7|B4DK90|B4DZG3|G5EA04|Q6NW41|Q8N3K8	Nonsense_Mutation	SNP	ENST00000389609.4	hg19	CCDS33967.2	.	.	.	.	.	.	.	.	.	.	G	37	6.215628	0.97385	2.27E-4	0.0	ENSG00000181982	ENST00000504487;ENST00000389609;ENST00000382116;ENST00000503881	.	.	.	5.82	4.96	0.65561	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-23.7498	15.8605	0.79017	0.0:0.0:0.8594:0.1406	.	.	.	.	X	143;143;67;88	.	ENSP00000371550:R67X	R	-	1	2	CCDC149	24448938	1.000000	0.71417	0.983000	0.44433	0.857000	0.48899	6.535000	0.73838	1.394000	0.46624	0.591000	0.81541	CGA	.	.		0.478	CCDC149-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000360157.1	NM_173463		A	24839840	G	A	24839840	4	1	235	1	0	0	0	0	0	1	0	0	2785	1095	38	1	1198	1	CCDC149	4	24839840	Nonsense_Mutation	SNP	G	TCGA-DD-AAW2-01A-11D-A40P-10	14760456	24839840	166314436	32	32718										
PDGFRA	5156	hgsc.bcm.edu	37	chr4	55139876	55139876	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	tccttggagctgagaaccgaGagctgaagctggtggctccc	14	11	0	3			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr4:55139876G>A	ENST00000257290.5	+	10	1868	c.1537G>A	c.(1537-1539)Gag>Aag	p.E513K	FIP1L1_ENST00000507166.1_Intron	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	513	Ig-like C2-type 5.				adrenal gland development (GO:0030325)|cardiac myofibril assembly (GO:0055003)|cell activation (GO:0001775)|cell chemotaxis (GO:0060326)|cellular response to amino acid stimulus (GO:0071230)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|epidermal growth factor receptor signaling pathway (GO:0007173)|estrogen metabolic process (GO:0008210)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hematopoietic progenitor cell differentiation (GO:0002244)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|Leydig cell differentiation (GO:0033327)|lung development (GO:0030324)|luteinization (GO:0001553)|male genitalia development (GO:0030539)|metanephric glomerular capillary formation (GO:0072277)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet aggregation (GO:0070527)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-alpha signaling pathway (GO:0035790)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of chemotaxis (GO:0050920)|regulation of mesenchymal stem cell differentiation (GO:2000739)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction involved in regulation of gene expression (GO:0023019)|viral process (GO:0016032)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet-derived growth factor alpha-receptor activity (GO:0005018)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|autonomic_ganglia(1)|bone(1)|breast(4)|central_nervous_system(17)|cervix(1)|endometrium(4)|eye(1)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(22)|kidney(6)|large_intestine(26)|liver(4)|lung(48)|ovary(4)|prostate(6)|skin(11)|small_intestine(49)|soft_tissue(727)|stomach(32)|urinary_tract(1)	967	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sunitinib(DB01268)	TGAGAACCGAGAGCTGAAGCT	0.577			"Mis, O, T"	FIP1L1	"GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"				Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	TSP Lung(21;0.16)																											p.E513K	Pancreas(151;208 1913 7310 23853 37092)	Atlas-SNP	.		Dom	yes		4	4q11-q13	5156	"platelet-derived growth factor, alpha-receptor"		"L, M, O"	.	PDGFRA	1583	.	0			c.G1537A						.						57	59	58					4																	55139876		2203	4300	6503	SO:0001583	missense	5156	exon10	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	AACCGAGAGCTGA	D50001	CCDS3495.1	4q12	2014-09-17			ENSG00000134853	ENSG00000134853		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	8803	protein-coding gene	gene with protein product		173490					Standard	NM_006206		Approved	CD140a, PDGFR2	uc003han.4	P16234	OTTHUMG00000128699	ENST00000257290.5:c.1537G>A	chr4.hg19:g.55139876G>A	ENSP00000257290:p.Glu513Lys	41.0	0.0		46.0	4.0	NM_006206	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Missense_Mutation	SNP	ENST00000257290.5	hg19	CCDS3495.1	.	.	.	.	.	.	.	.	.	.	G	33	5.229952	0.95173	.	.	ENSG00000134853	ENST00000257290	T	0.75589	-0.95	5.9	5.9	0.94986	Immunoglobulin-like fold (1);	0.000000	0.32273	U	0.006328	D	0.86151	0.5864	M	0.77820	2.39	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.85130	0.979;0.997	T	0.81057	-0.1105	10	0.15952	T	0.53	.	20.2789	0.98501	0.0:0.0:1.0:0.0	.	513;513	P16234-3;P16234	.;PGFRA_HUMAN	K	513	ENSP00000257290:E513K	ENSP00000257290:E513K	E	+	1	0	PDGFRA	54834633	1.000000	0.71417	0.998000	0.56505	0.669000	0.39330	8.662000	0.91130	2.788000	0.95919	0.650000	0.86243	GAG	.	.		0.577	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206		A	55139876	G	A	55139876	3	1	235	1	0	0	0	0	1	0	0	0	11670	943	33	3	1571	3	PDGFRA	4	55139876	Missense_Mutation	SNP	G	TCGA-DD-AAW2-01A-11D-A40P-10	30300036	55139876	136014400	33	32719										
ALB	213	hgsc.bcm.edu	37	chr4	74275115	74275115	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	gacatccttacttttatgccCcggaactccttttctttgct	5	13	1	0			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr4:74275115C>G	ENST00000503124.1	+	3	283	c.76C>G	c.(76-78)Ccg>Gcg	p.P26A	ALB_ENST00000415165.2_Intron|ALB_ENST00000509063.1_Missense_Mutation_p.P176A|ALB_ENST00000401494.3_Missense_Mutation_p.P61A|ALB_ENST00000505649.1_3'UTR|ALB_ENST00000295897.4_Missense_Mutation_p.P176A			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CTTTTATGCCCCGGAACTCCT	0.353																																					p.P176A		Atlas-SNP	.											.	ALB	132	.	0			c.C526G						.						69	74	72					4																	74275115		2203	4299	6502	SO:0001583	missense	213	exon5			TATGCCCCGGAAC	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.76C>G	chr4.hg19:g.74275115C>G	ENSP00000421027:p.Pro26Ala	203.0	0.0		239.0	104.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000503124.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.7|22.7	4.328345|4.328345	0.81690|0.81690	.|.	.|.	ENSG00000163631|ENSG00000163631	ENST00000441319;ENST00000295897;ENST00000503124;ENST00000509063;ENST00000401494;ENST00000430202|ENST00000511370	T;T;T;T;T|.	0.73258|.	-0.73;-0.73;-0.73;-0.73;-0.73|.	5.55|5.55	5.55|5.55	0.83447|0.83447	Serum albumin-like (1);Serum albumin, N-terminal (3);|.	0.133283|0.133283	0.52532|0.52532	D|D	0.000066|0.000066	D|D	0.84306|0.84306	0.5443|0.5443	M|M	0.88906|0.88906	2.99|2.99	0.53005|0.53005	D|D	0.999967|0.999967	D;P;P;D|.	0.89917|.	1.0;0.955;0.916;0.986|.	D;P;P;P|.	0.83275|.	0.996;0.57;0.784;0.827|.	D|D	0.85964|0.85964	0.1472|0.1472	10|6	0.87932|.	D|.	0|.	-21.472|-21.472	18.2485|18.2485	0.89995|0.89995	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	61;26;176;176|.	B7WNR0;D6RHD5;A6NBZ8;P02768|.	.;.;.;ALBU_HUMAN|.	A|R	178;176;26;176;61;185|20	ENSP00000392541:P178A;ENSP00000295897:P176A;ENSP00000421027:P26A;ENSP00000422784:P176A;ENSP00000384695:P61A|.	ENSP00000295897:P176A|.	P|P	+|+	1|2	0|0	ALB|ALB	74493979|74493979	0.977000|0.977000	0.34250|0.34250	0.998000|0.998000	0.56505|0.56505	0.916000|0.916000	0.54674|0.54674	3.066000|3.066000	0.50002|0.50002	2.894000|2.894000	0.99253|0.99253	0.591000|0.591000	0.81541|0.81541	CCG|CCC	.	.		0.353	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		G	74275115	C	G	74275115	3	3	235	1	0	0	0	0	1	0	0	0	486	623	22	4	544	4	ALB	4	74275115	Missense_Mutation	SNP	C	TCGA-DD-AAW2-01A-11D-A40P-10	19135239	74275115	116879161	34	32720										
MYOZ2	51778	hgsc.bcm.edu	37	chr4	120079231	120079231	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	gaagtaacttggaaggtggtTcgcagcaagcccccttgact	12	10	0	1			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr4:120079231T>A	ENST00000307128.5	+	4	514	c.301T>A	c.(301-303)Tcg>Acg	p.S101T		NM_016599.4	NP_057683.1			myozenin 2											endometrium(1)|large_intestine(6)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	16						GGAAGGTGGTTCGCAGCAAGC	0.458																																					p.S101T		Atlas-SNP	.											MYOZ2,NS,malignant_melanoma,0,1	MYOZ2	34	.	0			c.T301A						.						160	152	155					4																	120079231		2203	4300	6503	SO:0001583	missense	51778	exon4			GGTGGTTCGCAGC	AF249873	CCDS3711.1	4q26-q27	2014-09-17	2002-01-07	2002-01-11	ENSG00000172399	ENSG00000172399			1330	protein-coding gene	gene with protein product		605602	"chromosome 4 open reading frame 5"	C4orf5		8619474, 9110174	Standard	NM_016599		Approved	CS-1	uc003icp.4	Q9NPC6	OTTHUMG00000132968	ENST00000307128.5:c.301T>A	chr4.hg19:g.120079231T>A	ENSP00000306997:p.Ser101Thr	133.0	1.0		162.0	69.0	NM_016599		Missense_Mutation	SNP	ENST00000307128.5	hg19	CCDS3711.1	.	.	.	.	.	.	.	.	.	.	T	11.17	1.560723	0.27827	.	.	ENSG00000172399	ENST00000307128	T	0.64085	-0.08	5.55	5.55	0.83447	.	0.340145	0.30464	N	0.009561	T	0.46367	0.1389	L	0.38531	1.155	0.09310	N	1	B	0.30563	0.285	B	0.30251	0.113	T	0.32666	-0.9898	10	0.20046	T	0.44	-9.7478	5.9555	0.19271	0.0:0.2042:0.0:0.7958	.	101	Q9NPC6	MYOZ2_HUMAN	T	101	ENSP00000306997:S101T	ENSP00000306997:S101T	S	+	1	0	MYOZ2	120298679	0.216000	0.23585	0.798000	0.32154	0.985000	0.73830	2.064000	0.41432	2.108000	0.64289	0.533000	0.62120	TCG	.	.		0.458	MYOZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256526.2			A	120079231	T	A	120079231	3	1	235	1	0	0	0	0	1	0	0	0	10105	1783	62	4	311	4	MYOZ2	4	120079231	Missense_Mutation	SNP	T	TCGA-DD-AAW2-01A-11D-A40P-10	45804116	120079231	71075045	35	32721										
DDX60L	91351	hgsc.bcm.edu	37	chr4	169369922	169369922	+	Frame_Shift_Del	DEL	C	C	-													0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	cttaaaatgaaatattcacaCcacttgttctgaaaattaaa							TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr4:169369922delC	ENST00000511577.1	-	9	1252	c.1005delG	c.(1003-1005)tggfs	p.W335fs	DDX60L_ENST00000505890.1_Frame_Shift_Del_p.W335fs|DDX60L_ENST00000260184.7_Frame_Shift_Del_p.W335fs			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	335							ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		AATATTCACACCACTTGTTCT	0.328																																					p.C336fs		Atlas-INDEL	.											.	DDX60L	116	.	0			c.1006delT						.						43	40	41					4																	169369922		1814	4062	5876	SO:0001589	frameshift_variant	91351	exon9			.	AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.1005delG	chr4.hg19:g.169369922delC	ENSP00000422423:p.Trp335fs	377.0	0.0		376.0	176.0	NM_001012967	Q96ND6	Frame_Shift_Del	DEL	ENST00000511577.1	hg19																																																																																				.	.		0.328	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967		-	169369922	C	-	169369922	7	5	235	1	0	1	0	1	0	0	0	0	4381	508	18	0	4235	0	DDX60L	4	169369922	Frame_Shift_Del	DEL	C	TCGA-DD-AAW2-01A-11D-A40P-10	49290691	169369922	21784354	36	32722										
FAT1	2195	hgsc.bcm.edu	37	chr4	187524333	187524333	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	acactcatgtgcagtaccttTgcagagacacaccgctgccc	8	15	1	1			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr4:187524333T>G	ENST00000441802.2	-	19	11556	c.11347A>C	c.(11347-11349)Aaa>Caa	p.K3783Q		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	3783					actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						GCAGTACCTTTGCAGAGACAC	0.483										HNSCC(5;0.00058)																											p.K3783Q	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.A11347C						.						51	50	51					4																	187524333		2036	4187	6223	SO:0001583	missense	2195	exon19			TACCTTTGCAGAG	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.11347A>C	chr4.hg19:g.187524333T>G	ENSP00000406229:p.Lys3783Gln	83.0	0.0		139.0	55.0	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	hg19	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	T	9.519	1.107704	0.20714	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.42513	0.97	4.41	0.312	0.15837	.	0.413094	0.28052	N	0.016800	T	0.29684	0.0741	L	0.41573	1.285	0.37503	D	0.916859	B	0.02656	0.0	B	0.12156	0.007	T	0.21177	-1.0253	10	0.13853	T	0.58	.	12.3299	0.55033	0.0:0.0:0.4089:0.5911	.	3783	Q14517	FAT1_HUMAN	Q	3783;3785	ENSP00000406229:K3783Q	ENSP00000260147:K3785Q	K	-	1	0	FAT1	187761327	0.993000	0.37304	0.983000	0.44433	0.660000	0.38997	0.511000	0.22739	-0.005000	0.14395	-0.429000	0.05907	AAA	.	.		0.483	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		G	187524333	T	G	187524333	3	3	235	1	0	0	0	0	1	0	0	0	5697	1821	63	5	2455	5	FAT1	4	187524333	Missense_Mutation	SNP	T	TCGA-DD-AAW2-01A-11D-A40P-10	18154411	187524333	3629943	37	32723										
NAIP	4671	hgsc.bcm.edu	37	chr5	70308645	70308645	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	cttctagttcctttgccaacTgaactgcatctaggcccaga	7	13	2	2			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr5:70308645T>A	ENST00000517649.1	-	4	388	c.98A>T	c.(97-99)cAg>cTg	p.Q33L	NAIP_ENST00000523981.1_Intron|NAIP_ENST00000503719.2_Intron|NAIP_ENST00000194097.4_Missense_Mutation_p.Q33L|NAIP_ENST00000508426.2_Missense_Mutation_p.Q33L	NM_004536.2	NP_004527.2	Q13075	BIRC1_HUMAN	NLR family, apoptosis inhibitory protein	33					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|metal ion binding (GO:0046872)			central_nervous_system(1)	1		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)		CTTTGCCAACTGAACTGCATC	0.478																																					p.Q33L		Atlas-SNP	.											.	NAIP	38	.	0			c.A98T						.						122	112	115					5																	70308645		2202	4296	6498	SO:0001583	missense	4671	exon4			GCCAACTGAACTG	U19251	CCDS4009.1, CCDS43327.1	5q13.2	2010-06-16	2006-12-08	2006-12-08	ENSG00000249437	ENSG00000249437		"Baculoviral IAP repeat containing", "Nucleotide-binding domain and leucine rich repeat containing"	7634	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and BIR domain containing 1", "NLR family, BIR domain containing 1"	600355	"baculoviral IAP repeat-containing 1"	BIRC1		7813013	Standard	NM_022892		Approved	NLRB1	uc003jyj.1	Q13075	OTTHUMG00000163318	ENST00000517649.1:c.98A>T	chr5.hg19:g.70308645T>A	ENSP00000428657:p.Gln33Leu	89.0	0.0		147.0	89.0	NM_004536	B9EG72|E9PHD1|O75857|Q13730|Q59GI6|Q8TDZ4|Q99796	Missense_Mutation	SNP	ENST00000517649.1	hg19	CCDS4009.1	.	.	.	.	.	.	.	.	.	.	t	9.817	1.184803	0.21870	.	.	ENSG00000249437	ENST00000517649;ENST00000194097;ENST00000508426	T;T;T	0.76060	-0.99;-0.99;-0.99	3.25	0.72	0.18214	.	2.505560	0.02342	U	0.075009	T	0.59702	0.2213	L	0.29908	0.895	0.09310	N	1	B;P	0.34462	0.255;0.454	B;B	0.26614	0.071;0.057	T	0.52533	-0.8563	10	0.72032	D	0.01	.	3.0408	0.06138	0.0:0.247:0.2274:0.5256	.	33;33	E7EQW0;Q13075	.;BIRC1_HUMAN	L	33	ENSP00000428657:Q33L;ENSP00000443944:Q33L;ENSP00000429545:Q33L	ENSP00000443944:Q33L	Q	-	2	0	NAIP	70344401	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.010000	0.12743	0.146000	0.19002	-0.495000	0.04643	CAG	.	.		0.478	NAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372649.6	NM_004536		A	70308645	T	A	70308645	3	1	235	1	0	0	0	0	1	0	0	0	10156	1580	55	4	4169	4	NAIP	5	70308645	Missense_Mutation	SNP	T	TCGA-DD-AAW2-01A-11D-A40P-10		70308645	110606615	38	32724										
TRPC7	57113	hgsc.bcm.edu	37	chr5	135651445	135651445	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	ctacaaaatccttgcattgcAtagataacttcctgtaatcg	5	10	0	1			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr5:135651445A>C	ENST00000513104.1	-	3	1085	c.803T>G	c.(802-804)aTg>aGg	p.M268R	TRPC7-AS2_ENST00000513958.1_RNA|TRPC7_ENST00000426057.2_Intron|TRPC7_ENST00000355180.3_Intron	NM_020389.2	NP_065122.1	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel, subfamily C, member 7	268					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|manganese ion transport (GO:0006828)|platelet activation (GO:0030168)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(3)	46			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CTTGCATTGCATAGATAACTT	0.483																																					p.M268R		Atlas-SNP	.											.	TRPC7	126	.	0			c.T803G						.						68	70	69					5																	135651445		2073	4232	6305	SO:0001583	missense	57113	exon3			CATTGCATAGATA	AJ272034	CCDS47267.1, CCDS47267.2, CCDS54905.1, CCDS54906.1	5q31.2	2011-12-14			ENSG00000069018	ENSG00000069018		"Voltage-gated ion channels / Transient receptor potential cation channels"	20754	protein-coding gene	gene with protein product						11805119, 16382100	Standard	NM_020389		Approved		uc003lbn.2	Q9HCX4	OTTHUMG00000162035	ENST00000513104.1:c.803T>G	chr5.hg19:g.135651445A>C	ENSP00000426070:p.Met268Arg	100.0	0.0		181.0	14.0	NM_020389	A1A4Z4|F5H5U9|Q70T26|Q8IWP7	Missense_Mutation	SNP	ENST00000513104.1	hg19	CCDS47267.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.60|16.60	3.167790|3.167790	0.57476|0.57476	.|.	.|.	ENSG00000069018|ENSG00000069018	ENST00000513104;ENST00000265193|ENST00000502753	T|.	0.61392|.	0.11|.	5.64|5.64	5.64|5.64	0.86602|0.86602	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.56171|.	0.1967|.	L|L	0.28740|0.28740	0.885|0.885	0.80722|0.80722	D|D	1|1	B;B|.	0.33883|.	0.43;0.006|.	B;B|.	0.33846|.	0.171;0.01|.	T|.	0.52064|.	-0.8625|.	10|.	0.02654|.	T|.	1|.	-34.974|-34.974	16.0238|16.0238	0.80522|0.80522	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	268;268|.	Q70T25;Q9HCX4|.	.;TRPC7_HUMAN|.	R|X	268|267	ENSP00000426070:M268R|.	ENSP00000265193:M268R|.	M|Y	-|-	2|3	0|2	TRPC7|TRPC7	135679344|135679344	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.072000|5.072000	0.64389|0.64389	2.367000|2.367000	0.80283|0.80283	0.528000|0.528000	0.53228|0.53228	ATG|TAT	.	.		0.483	TRPC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366975.1	NM_020389		C	135651445	A	C	135651445	3	2	235	1	0	0	0	0	1	0	0	0	16599	217	8	5	1825	5	TRPC7	5	135651445	Missense_Mutation	SNP	A	TCGA-DD-AAW2-01A-11D-A40P-10	65342800	135651445	45263815	39	32725										
PCDHB3	56132	hgsc.bcm.edu	37	chr5	140480412	140480412	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	actaagggtagaggaactggCcgcgaggggggcccaagttg	18	8	0	1			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr5:140480412C>T	ENST00000231130.2	+	1	179	c.179C>T	c.(178-180)gCc>gTc	p.A60V	AC005754.7_ENST00000607216.1_RNA	NM_018937.2	NP_061760.1	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3	60	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	72			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GAGGAACTGGCCGCGAGGGGG	0.507																																					p.A60V		Atlas-SNP	.											.	PCDHB3	208	.	0			c.C179T						.						59	70	67					5																	140480412		2203	4300	6503	SO:0001583	missense	56132	exon1			AACTGGCCGCGAG	AF152496	CCDS4245.1	5q31	2010-01-26			ENSG00000113205	ENSG00000113205		"Cadherins / Protocadherins : Clustered"	8688	other	protocadherin		606329				10380929	Standard	NM_018937		Approved	PCDH-BETA3	uc003lio.3	Q9Y5E6	OTTHUMG00000129622	ENST00000231130.2:c.179C>T	chr5.hg19:g.140480412C>T	ENSP00000231130:p.Ala60Val	125.0	0.0		255.0	62.0	NM_018937	B2R8P2	Missense_Mutation	SNP	ENST00000231130.2	hg19	CCDS4245.1	.	.	.	.	.	.	.	.	.	.	C	10.58	1.391001	0.25118	.	.	ENSG00000113205	ENST00000231130	T	0.41065	1.01	4.61	2.77	0.32553	Cadherin, N-terminal (1);Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.42630	0.1211	L	0.58302	1.8	0.09310	N	1	B	0.18610	0.029	B	0.30251	0.113	T	0.44772	-0.9306	9	0.59425	D	0.04	.	10.5778	0.45238	0.0:0.7718:0.0:0.2282	.	60	Q9Y5E6	PCDB3_HUMAN	V	60	ENSP00000231130:A60V	ENSP00000231130:A60V	A	+	2	0	PCDHB3	140460596	0.000000	0.05858	0.142000	0.22268	0.832000	0.47134	0.295000	0.19065	1.046000	0.40249	0.655000	0.94253	GCC	.	.		0.507	PCDHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251817.2	NM_018937		T	140480412	C	T	140480412	3	4	235	1	0	0	0	0	1	0	0	0	11552	739	26	3	181	3	PCDHB3	5	140480412	Missense_Mutation	SNP	C	TCGA-DD-AAW2-01A-11D-A40P-10	4828967	140480412	40434848	40	32726										
NKX2-5	1482	hgsc.bcm.edu	37	chr5	172661932	172661932	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	gcccagcgtaggcctctggcTtgaaggcggccagcatgcag	15	13	1	1			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr5:172661932T>A	ENST00000329198.4	-	1	428	c.155A>T	c.(154-156)aAg>aTg	p.K52M	NKX2-5_ENST00000424406.2_Missense_Mutation_p.K52M|NKX2-5_ENST00000521848.1_Missense_Mutation_p.K52M	NM_001166175.1|NM_001166176.1|NM_004387.3	NP_001159647.1|NP_001159648.1|NP_004378.1	P52952	NKX25_HUMAN	NK2 homeobox 5	52	Ala/Pro-rich.				adult heart development (GO:0007512)|apoptotic process involved in heart morphogenesis (GO:0003278)|atrial cardiac muscle cell development (GO:0055014)|atrial septum morphogenesis (GO:0060413)|atrioventricular node cell development (GO:0060928)|atrioventricular node cell fate commitment (GO:0060929)|BMP signaling pathway (GO:0030509)|bundle of His development (GO:0003166)|canonical Wnt signaling pathway (GO:0060070)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle contraction (GO:0060048)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac ventricle formation (GO:0003211)|cell differentiation (GO:0030154)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|heart trabecula formation (GO:0060347)|hemopoiesis (GO:0030097)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|pharyngeal system development (GO:0060037)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of cell proliferation (GO:0008284)|positive regulation of heart contraction (GO:0045823)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription via serum response element binding (GO:0010735)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of voltage-gated calcium channel activity (GO:1901387)|proepicardium development (GO:0003342)|pulmonary myocardium development (GO:0003350)|Purkinje myocyte differentiation (GO:0003168)|regulation of cardiac muscle cell proliferation (GO:0060043)|regulation of cardiac muscle contraction (GO:0055117)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|sarcomere organization (GO:0045214)|septum secundum development (GO:0003285)|spleen development (GO:0048536)|thyroid gland development (GO:0030878)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell development (GO:0055015)|ventricular cardiac myofibril assembly (GO:0055005)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|serum response element binding (GO:0010736)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(7)|prostate(1)	12	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			GGCCTCTGGCTTGAAGGCGGC	0.736																																					p.K52M	Esophageal Squamous(72;810 1219 2387 13420 44943)	Atlas-SNP	.											.	NKX2-5	42	.	0			c.A155T						.						8	12	11					5																	172661932		2088	4175	6263	SO:0001583	missense	1482	exon1			TCTGGCTTGAAGG	AB021133	CCDS4387.1, CCDS54949.1, CCDS54950.1	5q34	2014-09-17	2011-06-01	2002-10-04	ENSG00000183072	ENSG00000183072		"Homeoboxes / ANTP class : NKL subclass"	2488	protein-coding gene	gene with protein product	"tinman paralog (Drosophila)"	600584	"cardiac-specific homeo box", "NK2 transcription factor related, locus 5 (Drosophila)"	CSX, NKX2E		7665173, 8900537	Standard	NM_004387		Approved	CSX1, NKX2.5, NKX4-1	uc003mcm.2	P52952	OTTHUMG00000130522	ENST00000329198.4:c.155A>T	chr5.hg19:g.172661932T>A	ENSP00000327758:p.Lys52Met	100.0	0.0		212.0	128.0	NM_004387	A8K3K0|B4DNB6|E9PBU6	Missense_Mutation	SNP	ENST00000329198.4	hg19	CCDS4387.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.150426	0.78001	.	.	ENSG00000183072	ENST00000329198;ENST00000424406;ENST00000521848;ENST00000517440	D;D;D;D	0.91945	-2.76;-2.84;-2.94;-2.89	5.01	3.82	0.43975	.	0.397263	0.18720	N	0.133025	D	0.92896	0.7740	L	0.59436	1.845	0.51233	D	0.999912	D;D;B	0.61697	0.99;0.98;0.441	P;P;B	0.57152	0.814;0.58;0.087	D	0.90168	0.4233	10	0.33141	T	0.24	.	11.309	0.49353	0.1366:0.0:0.0:0.8634	.	52;52;52	B4DNB6;E5RH49;P52952	.;.;NKX25_HUMAN	M	52	ENSP00000327758:K52M;ENSP00000395378:K52M;ENSP00000427906:K52M;ENSP00000429905:K52M	ENSP00000327758:K52M	K	-	2	0	NKX2-5	172594538	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	5.697000	0.68295	0.821000	0.34540	0.379000	0.24179	AAG	.	.		0.736	NKX2-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252942.2			A	172661932	T	A	172661932	3	1	235	1	0	0	0	0	1	0	0	0	10462	1609	56	4	962	4	NKX2-5	5	172661932	Missense_Mutation	SNP	T	TCGA-DD-AAW2-01A-11D-A40P-10	32181520	172661932	8253328	41	32727										
FOXF2	2295	hgsc.bcm.edu	37	chr6	1391085	1391085	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	gggggcgtcggtgcggccggGggcggcggcggcggcgacta	25	11	0	0	rs58230522|rs147426137|rs111257067|rs397731476	byFrequency	TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr6:1391085G>C	ENST00000259806.1	+	1	1017	c.903G>C	c.(901-903)ggG>ggC	p.G301G		NM_001452.1	NP_001443.1	Q12947	FOXF2_HUMAN	forkhead box F2	301	Poly-Gly.				embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digestive tract development (GO:0048566)|epithelial to mesenchymal transition (GO:0001837)|establishment of planar polarity of embryonic epithelium (GO:0042249)|extracellular matrix organization (GO:0030198)|genitalia development (GO:0048806)|negative regulation of transcription, DNA-templated (GO:0045892)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			large_intestine(2)|lung(5)|prostate(1)	8	Ovarian(93;0.0733)	all_lung(73;0.0713)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.095)		gtgcggccgggggcggcggcg	0.746																																					p.G301G		Atlas-SNP	.											.	FOXF2	28	.	0			c.G903C						.						1	2	1					6																	1391085		586	1494	2080	SO:0001819	synonymous_variant	2295	exon1			GGCCGGGGGCGGC	U13220	CCDS4472.1	6p25.3	2008-04-10			ENSG00000137273	ENSG00000137273		"Forkhead boxes"	3810	protein-coding gene	gene with protein product		603250		FKHL6		9799607, 7957066	Standard	NM_001452		Approved	FREAC2	uc003mtm.3	Q12947	OTTHUMG00000016243	ENST00000259806.1:c.903G>C	chr6.hg19:g.1391085G>C		22.0	0.0		80.0	14.0	NM_001452	Q5TGJ1|Q9UQ85	Silent	SNP	ENST00000259806.1	hg19	CCDS4472.1																																																																																			.	.		0.746	FOXF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043558.1			C	1391085	G	C	1391085	2	2	235	1	0	0	0	0	0	0	0	1	6014	1219	43	4		4	FOXF2	6	1391085	Silent	SNP	G	TCGA-DD-AAW2-01A-11D-A40P-10		1391085	169723982	42	32728										
FOXC1	2296	hgsc.bcm.edu	37	chr6	1612042	1612042	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	ggcggcggcggcggcggcggGggaggccaggaggccggcca	25	12	0	0			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr6:1612042G>C	ENST00000380874.2	+	1	1362	c.1362G>C	c.(1360-1362)ggG>ggC	p.G454G		NM_001453.2	NP_001444.2	Q12948	FOXC1_HUMAN	forkhead box C1	454	Poly-Gly.				artery morphogenesis (GO:0048844)|blood vessel remodeling (GO:0001974)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|cardiac muscle cell proliferation (GO:0060038)|collagen fibril organization (GO:0030199)|embryonic heart tube development (GO:0035050)|eye development (GO:0001654)|germ cell migration (GO:0008354)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|lacrimal gland development (GO:0032808)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process involved in outflow tract morphogenesis (GO:1902257)|negative regulation of mitotic cell cycle (GO:0045930)|neural crest cell development (GO:0014032)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|ovarian follicle development (GO:0001541)|paraxial mesoderm formation (GO:0048341)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood vessel size (GO:0050880)|regulation of organ growth (GO:0046620)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|somitogenesis (GO:0001756)|ureteric bud development (GO:0001657)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	8	Ovarian(93;0.0733)	all_cancers(2;4.45e-07)|all_epithelial(2;4.33e-05)|all_lung(73;0.0713)|all_hematologic(90;0.0895)		Epithelial(2;0.0904)|OV - Ovarian serous cystadenocarcinoma(45;0.095)|all cancers(2;0.168)		gcggcggcggGGGAGGCCAGG	0.751																																					p.G454G	Pancreas(133;719 1821 3197 26645 35015)	Atlas-SNP	.											.	FOXC1	19	.	0			c.G1362C						.						1	1	1					6																	1612042		591	1329	1920	SO:0001819	synonymous_variant	2296	exon1			CGGCGGGGGAGGC	AF048693	CCDS4473.1	6p25	2008-04-10			ENSG00000054598	ENSG00000054598		"Forkhead boxes"	3800	protein-coding gene	gene with protein product		601090		FKHL7, IRID1		7957066, 9620769	Standard	NM_001453		Approved	FREAC3, ARA, IGDA, IHG1	uc003mtp.3	Q12948	OTTHUMG00000016182	ENST00000380874.2:c.1362G>C	chr6.hg19:g.1612042G>C		132.0	0.0		512.0	24.0	NM_001453	Q86UP7|Q9BYM1|Q9NUE5|Q9UDD0|Q9UP06	Silent	SNP	ENST00000380874.2	hg19	CCDS4473.1																																																																																			.	.		0.751	FOXC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043450.1			C	1612042	G	C	1612042	2	2	235	1	0	0	0	0	0	0	0	1	6002	1219	43	4		4	FOXC1	6	1612042	Silent	SNP	G	TCGA-DD-AAW2-01A-11D-A40P-10	220957	1612042	169503025	43	32729										
LYRM4	57128	hgsc.bcm.edu	37	chr6	5109701	5109701	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	ctcaatgatcagcttgtcagTtgaatacagttggccaatgt	9	8	3	2			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr6:5109701T>C	ENST00000330636.4	-	3	437	c.232A>G	c.(232-234)Act>Gct	p.T78A	LYRM4_ENST00000464010.1_3'UTR|LYRM4_ENST00000606472.1_5'Flank|LYRM4_ENST00000468929.1_Silent_p.Q37Q	NM_020408.4	NP_065141.3	Q9HD34	LYRM4_HUMAN	LYR motif containing 4	78					small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)				endometrium(1)	1	Ovarian(93;0.11)	all_hematologic(90;0.0901)				AGCTTGTCAGTTGAATACAGT	0.562																																					p.T78A	NSCLC(130;1006 2426 17608 36797)	Atlas-SNP	.											.	LYRM4	5	.	0			c.A232G						.						136	125	129					6																	5109701		2203	4300	6503	SO:0001583	missense	57128	exon3			TGTCAGTTGAATA	AF258559	CCDS4493.1, CCDS54961.1	6p25.1	2008-02-05	2006-09-19	2006-09-19	ENSG00000214113	ENSG00000214113		"LYR motif containing"	21365	protein-coding gene	gene with protein product		613311	"chromosome 6 open reading frame 149"	C6orf149			Standard	XM_005249239		Approved	CGI-203, ISD11	uc021ykw.1	Q9HD34	OTTHUMG00000014173	ENST00000330636.4:c.232A>G	chr6.hg19:g.5109701T>C	ENSP00000418787:p.Thr78Ala	134.0	0.0		406.0	55.0	NM_020408	A8K543|Q5XKP1	Missense_Mutation	SNP	ENST00000330636.4	hg19	CCDS4493.1	.	.	.	.	.	.	.	.	.	.	T	7.176	0.588654	0.13812	.	.	ENSG00000214113	ENST00000330636	T	0.41400	1.0	5.42	3.01	0.34805	.	0.973282	0.08253	U	0.974336	T	0.05777	0.0151	.	.	.	0.19300	N	0.999977	B	0.18166	0.026	B	0.12156	0.007	T	0.36407	-0.9749	9	0.06099	T	0.92	.	7.1482	0.25595	0.0:0.1836:0.0:0.8164	.	78	Q9HD34	LYRM4_HUMAN	A	78	ENSP00000418787:T78A	ENSP00000418787:T78A	T	-	1	0	LYRM4	5054700	0.812000	0.29077	0.023000	0.16930	0.977000	0.68977	1.331000	0.33793	0.908000	0.36671	0.533000	0.62120	ACT	.	.		0.562	LYRM4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353461.3	NM_020408		C	5109701	T	C	5109701	3	2	235	1	0	0	0	0	1	0	0	0	9130	1725	60	2	47	2	LYRM4	6	5109701	Missense_Mutation	SNP	T	TCGA-DD-AAW2-01A-11D-A40P-10	3497659	5109701	166005366	44	32730										
HIST1H2AE	3012	hgsc.bcm.edu	37	chr6	26217396	26217396	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	tctgacggccgagatcttagAgctagctggcaacgcggctc	13	12	2	3			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr6:26217396A>T	ENST00000303910.2	+	1	232	c.194A>T	c.(193-195)gAg>gTg	p.E65V	HIST1H2BG_ENST00000244601.3_5'Flank	NM_021052.2	NP_066390.1	P04908	H2A1B_HUMAN	histone cluster 1, H2ae	65						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(2)	10		all_hematologic(11;0.196)				GAGATCTTAGAGCTAGCTGGC	0.602																																					p.E65V		Atlas-SNP	.											.	HIST1H2AE	25	.	0			c.A194T						.						56	57	56					6																	26217396		2203	4300	6503	SO:0001583	missense	3012	exon1			TCTTAGAGCTAGC	M60752	CCDS4595.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000168274	ENSG00000277075		"Histones / Replication-dependent"	4724	protein-coding gene	gene with protein product		602786	"H2A histone family, member A", "histone 1, H2ae"	H2AFA		9119399, 1916825, 12408966	Standard	NM_021052		Approved	H2A/a, H2A.1	uc003nha.1	P04908	OTTHUMG00000014440	ENST00000303910.2:c.194A>T	chr6.hg19:g.26217396A>T	ENSP00000303373:p.Glu65Val	114.0	0.0		394.0	301.0	NM_021052	P28001|Q76P63	Missense_Mutation	SNP	ENST00000303910.2	hg19	CCDS4595.1	.	.	.	.	.	.	.	.	.	.	.	12.37	1.918180	0.33815	.	.	ENSG00000168274	ENST00000303910	T	0.72505	-0.66	4.07	4.07	0.47477	.	0.000000	0.34314	U	0.004071	D	0.90625	0.7060	H	0.99958	5.055	0.50632	D	0.999888	.	.	.	.	.	.	D	0.93878	0.7168	8	0.87932	D	0	.	12.6507	0.56759	1.0:0.0:0.0:0.0	.	.	.	.	V	65	ENSP00000303373:E65V	ENSP00000303373:E65V	E	+	2	0	HIST1H2AE	26325375	1.000000	0.71417	1.000000	0.80357	0.019000	0.09904	8.908000	0.92640	1.834000	0.53371	0.528000	0.53228	GAG	.	.		0.602	HIST1H2AE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040103.1	NM_021052		T	26217396	A	T	26217396	3	4	235	1	0	0	0	0	1	0	0	0	7141	304	11	4	196	4	HIST1H2AE	6	26217396	Missense_Mutation	SNP	A	TCGA-DD-AAW2-01A-11D-A40P-10	21107695	26217396	144897671	45	32731										
TTBK1	84630	hgsc.bcm.edu	37	chr6	43222808	43222808	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	ctcggaatgtggccgggtttCgaggaacggttcgctatgcc	15	10	0	0			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr6:43222808C>T	ENST00000259750.4	+	7	681	c.598C>T	c.(598-600)Cga>Tga	p.R200*	TTBK1_ENST00000304139.5_Nonsense_Mutation_p.R149*	NM_032538.1	NP_115927.1	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	200	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(10)|liver(1)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)			GGCCGGGTTTCGAGGAACGGT	0.607																																					p.R200X		Atlas-SNP	.											.	TTBK1	124	.	0			c.C598T						.						146	110	122					6																	43222808		2203	4300	6503	SO:0001587	stop_gained	84630	exon7			GGGTTTCGAGGAA	AB058758	CCDS34455.1	6p21.1	2008-02-05			ENSG00000146216	ENSG00000146216			19140	protein-coding gene	gene with protein product						11347906	Standard	XM_006715229		Approved	KIAA1855	uc003ouq.1	Q5TCY1	OTTHUMG00000014725	ENST00000259750.4:c.598C>T	chr6.hg19:g.43222808C>T	ENSP00000259750:p.Arg200*	91.0	0.0		332.0	55.0	NM_032538	A2A2U5|Q2L6C6|Q6ZNH0|Q8N444|Q96JH2	Nonsense_Mutation	SNP	ENST00000259750.4	hg19	CCDS34455.1	.	.	.	.	.	.	.	.	.	.	C	37	6.600649	0.97697	.	.	ENSG00000146216	ENST00000393984;ENST00000259750;ENST00000304139	.	.	.	4.83	4.83	0.62350	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.6948	0.85332	0.0:1.0:0.0:0.0	.	.	.	.	X	149;200;149	.	ENSP00000259750:R200X	R	+	1	2	TTBK1	43330786	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.543000	0.60684	2.242000	0.73789	0.655000	0.94253	CGA	.	.		0.607	TTBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040584.3			T	43222808	C	T	43222808	4	4	235	1	0	0	0	0	0	1	0	0	16691	876	31	1	620	1	TTBK1	6	43222808	Nonsense_Mutation	SNP	C	TCGA-DD-AAW2-01A-11D-A40P-10	17005412	43222808	127892259	46	32732										
DOPEY1	23033	hgsc.bcm.edu	37	chr6	83819950	83819950	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	ctgctgtgcgtttacctggaAtcacgtatgttcttgcccat	9	11	2	0			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr6:83819950A>G	ENST00000349129.2	+	6	858	c.598A>G	c.(598-600)Atc>Gtc	p.I200V	DOPEY1_ENST00000369739.3_Missense_Mutation_p.I200V|DOPEY1_ENST00000237163.5_Missense_Mutation_p.I200V|DOPEY1_ENST00000536812.1_Missense_Mutation_p.I200V	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	200					protein transport (GO:0015031)					breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(16)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	67		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		TTTACCTGGAATCACGTATGT	0.428																																					p.I200V		Atlas-SNP	.											.	DOPEY1	190	.	0			c.A598G						.						191	170	177					6																	83819950		2203	4300	6503	SO:0001583	missense	23033	exon6			CCTGGAATCACGT	AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097			21194	protein-coding gene	gene with protein product			"KIAA1117"	KIAA1117		16301316, 16303751, 10931277	Standard	NM_015018		Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365	ENST00000349129.2:c.598A>G	chr6.hg19:g.83819950A>G	ENSP00000195654:p.Ile200Val	137.0	1.0		86.0	64.0	NM_015018	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Missense_Mutation	SNP	ENST00000349129.2	hg19	CCDS4996.1	.	.	.	.	.	.	.	.	.	.	A	11.56	1.675843	0.29783	.	.	ENSG00000083097	ENST00000349129;ENST00000237163;ENST00000536812;ENST00000369739	T;T;T	0.23754	1.9;1.9;1.89	5.73	5.73	0.89815	Dopey, N-terminal (1);	0.059716	0.64402	D	0.000001	T	0.13500	0.0327	L	0.41027	1.25	0.46167	D	0.998901	B;B;B	0.14438	0.007;0.01;0.01	B;B;B	0.17098	0.012;0.017;0.017	T	0.02639	-1.1130	10	0.41790	T	0.15	.	16.3123	0.82883	1.0:0.0:0.0:0.0	.	200;200;200	E1P545;B2RWN9;Q5JWR5	.;.;DOP1_HUMAN	V	200	ENSP00000195654:I200V;ENSP00000237163:I200V;ENSP00000358754:I200V	ENSP00000237163:I200V	I	+	1	0	DOPEY1	83876669	1.000000	0.71417	1.000000	0.80357	0.679000	0.39708	6.862000	0.75484	2.308000	0.77769	0.533000	0.62120	ATC	.	.		0.428	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018		G	83819950	A	G	83819950	3	3	235	1	0	0	0	0	1	0	0	0	4709	101	4	2	612	2	DOPEY1	6	83819950	Missense_Mutation	SNP	A	TCGA-DD-AAW2-01A-11D-A40P-10	40597142	83819950	87295117	47	32733										
FBXL18	80028	hgsc.bcm.edu	37	chr7	5540596	5540605	+	Frame_Shift_Del	DEL	GCGCGGTCGG	GCGCGGTCGG	-													0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	gcatggccggctgggcgggcGcgcggtcggcgcgcggcgcg							TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	GCGCGGTCGG	GCGCGGTCGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr7:5540596_5540605delGCGCGGTCGG	ENST00000382368.3	-	3	1418_1427	c.1295_1304delCCGACCGCGC	c.(1294-1305)gccgaccgcgcgfs	p.ADRA432fs	FBXL18_ENST00000453700.3_Frame_Shift_Del_p.ADRA432fs	NM_024963.4	NP_079239.3	Q96ME1	FXL18_HUMAN	F-box and leucine-rich repeat protein 18	432									FBXL18/RNF216(2)	central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)	21		Ovarian(82;0.0607)		UCEC - Uterine corpus endometrioid carcinoma (126;0.181)|OV - Ovarian serous cystadenocarcinoma(56;3.64e-13)		ctgggcgggcgcgcggtcggcgcgcggcgc	0.743																																					p.432_435del		Atlas-INDEL	.											.	FBXL18	99	.	0			c.1296_1305del						.																																			SO:0001589	frameshift_variant	80028	exon3			.	AK057042	CCDS43546.1	7p22.2	2011-06-09			ENSG00000155034	ENSG00000155034		"F-boxes / Leucine-rich repeats"	21874	protein-coding gene	gene with protein product		609084					Standard	NM_024963		Approved	FLJ11467, Fbl18	uc003son.4	Q96ME1	OTTHUMG00000151832	ENST00000382368.3:c.1295_1304delCCGACCGCGC	chr7.hg19:g.5540596_5540605delGCGCGGTCGG	ENSP00000371805:p.Ala432fs	37.0	0.0		73.0	24.0	NM_024963	Q9BR90|Q9BTC7|Q9HAK7	Frame_Shift_Del	DEL	ENST00000382368.3	hg19	CCDS43546.1																																																																																			.	.		0.743	FBXL18-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324093.1	NM_024963		-	5540605	GCGCGGTCGG	-	5540596	7	5	235	1	0	1	0	1	0	0	0	0	5722	1087	38	0	864	0	FBXL18	7	5540596	Frame_Shift_Del	DEL	GCGCGGTCGG	TCGA-DD-AAW2-01A-11D-A40P-10		5540596	153598067	48	32734										
RAPGEF5	9771	hgsc.bcm.edu	37	chr7	22179655	22179655	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	aggctcacctcccaggtctgCgacagtcgactgacagaagc	11	14	2	2			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr7:22179655C>T	ENST00000401957.2	-	11	1603	c.1356G>A	c.(1354-1356)tcG>tcA	p.S452S	RAPGEF5_ENST00000344041.6_Silent_p.S602S			Q92565	RPGF5_HUMAN	Rap guanine nucleotide exchange factor (GEF) 5	452	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				nervous system development (GO:0007399)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|small GTPase mediated signal transduction (GO:0007264)	nucleus (GO:0005634)	GTP-dependent protein binding (GO:0030742)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(2)|ovary(1)	6						CCCAGGTCTGCGACAGTCGAC	0.413																																					p.S602S		Atlas-SNP	.											.	RAPGEF5	96	.	0			c.G1806A						.						31	32	31					7																	22179655		1892	4117	6009	SO:0001819	synonymous_variant	9771	exon21			GGTCTGCGACAGT	D87467	CCDS55093.1	7p15.3	2004-03-01			ENSG00000136237	ENSG00000136237			16862	protein-coding gene	gene with protein product	"M-Ras-regulated GEF"	609527				9039502, 10486569	Standard	NM_012294		Approved	KIAA0277, GFR, MR-GEF	uc003svg.3	Q92565	OTTHUMG00000152525	ENST00000401957.2:c.1356G>A	chr7.hg19:g.22179655C>T		271.0	0.0		440.0	118.0	NM_012294	A4D140|Q8IXU5	Silent	SNP	ENST00000401957.2	hg19																																																																																				.	.		0.413	RAPGEF5-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000326590.2	NM_012294		T	22179655	C	T	22179655	2	4	235	1	0	0	0	0	0	0	0	1	13062	755	27	1		1	RAPGEF5	7	22179655	Silent	SNP	C	TCGA-DD-AAW2-01A-11D-A40P-10	16639059	22179655	136959008	49	32735										
CDK13	8621	hgsc.bcm.edu	37	chr7	40133994	40133994	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	caggatgaccccaaaagagaAggtgggattgattatcaagc	12	7	1	3			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr7:40133994A>G	ENST00000181839.4	+	14	4559	c.3954A>G	c.(3952-3954)gaA>gaG	p.E1318E	CDK13_ENST00000340829.5_Silent_p.E1258E	NM_003718.4|NM_031267.3	NP_003709.3|NP_112557.2	Q14004	CDK13_HUMAN	cyclin-dependent kinase 13	1318					alternative mRNA splicing, via spliceosome (GO:0000380)|hemopoiesis (GO:0030097)|multicellular organismal development (GO:0007275)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|positive regulation of cell proliferation (GO:0008284)|regulation of mitosis (GO:0007088)|viral process (GO:0016032)	cyclin K-CDK13 complex (GO:0002945)|extracellular space (GO:0005615)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(2)|prostate(2)|skin(5)|stomach(2)|urinary_tract(1)	49						CCAAAAGAGAAGGTGGGATTG	0.493																																					p.E1318E		Atlas-SNP	.											.	CDK13	114	.	0			c.A3954G						.						130	126	128					7																	40133994		2203	4300	6503	SO:0001819	synonymous_variant	8621	exon14			AAGAGAAGGTGGG	M80629	CCDS5461.1, CCDS5462.1	7p14.1	2011-11-08	2009-12-16	2009-12-16	ENSG00000065883	ENSG00000065883		"Cyclin-dependent kinases"	1733	protein-coding gene	gene with protein product	"cholinesterase-related cell division controller"	603309	"cell division cycle 2-like 5 (cholinesterase-related cell division controller)"	CDC2L5		1731328, 19884882	Standard	NM_003718		Approved	CHED, CDC2L, KIAA1791	uc003thh.4	Q14004	OTTHUMG00000023726	ENST00000181839.4:c.3954A>G	chr7.hg19:g.40133994A>G		63.0	0.0		147.0	39.0	NM_003718	Q53G78|Q6DKQ9|Q75MH4|Q75MH5|Q96JN4|Q9H4A0|Q9H4A1|Q9UDR4	Silent	SNP	ENST00000181839.4	hg19	CCDS5461.1																																																																																			.	.		0.493	CDK13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250726.2	NM_003718		G	40133994	A	G	40133994	2	3	235	1	0	0	0	0	0	0	0	1	3131	69	3	2		2	CDK13	7	40133994	Silent	SNP	A	TCGA-DD-AAW2-01A-11D-A40P-10	17954339	40133994	119004669	50	32736										
COBL	23242	hgsc.bcm.edu	37	chr7	51095425	51095425	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	tcaccttgcgtagtctgtccTtccctcccgcagagtggatg	10	14	2	1			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr7:51095425T>C	ENST00000265136.7	-	10	3533	c.3368A>G	c.(3367-3369)aAg>aGg	p.K1123R	COBL_ENST00000395542.2_Missense_Mutation_p.K1205R	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	1123	WH2 1. {ECO:0000255|PROSITE- ProRule:PRU00406}.				actin filament network formation (GO:0051639)|actin filament polymerization (GO:0030041)|collateral sprouting in absence of injury (GO:0048669)|digestive tract development (GO:0048565)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|liver development (GO:0001889)|neural tube closure (GO:0001843)|notochord development (GO:0030903)|positive regulation of dendrite development (GO:1900006)|somite specification (GO:0001757)	actin filament (GO:0005884)|axon (GO:0030424)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic growth cone (GO:0044294)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)			NS(2)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(26)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Glioma(55;0.08)					TAGTCTGTCCTTCCCTCCCGC	0.567																																					p.K1123R	NSCLC(189;2119 2138 12223 30818 34679)	Atlas-SNP	.											.	COBL	167	.	0			c.A3368G						.						106	92	96					7																	51095425		2203	4300	6503	SO:0001583	missense	23242	exon10			CTGTCCTTCCCTC	AB014533	CCDS34637.1, CCDS75601.1, CCDS75602.1	7p12.2-p12.1	2012-12-07	2012-12-07		ENSG00000106078	ENSG00000106078			22199	protein-coding gene	gene with protein product		610317	"cordon-bleu homolog (mouse)"				Standard	NM_015198		Approved	KIAA0633	uc003tpr.4	O75128	OTTHUMG00000155999	ENST00000265136.7:c.3368A>G	chr7.hg19:g.51095425T>C	ENSP00000265136:p.Lys1123Arg	82.0	0.0		156.0	30.0	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Missense_Mutation	SNP	ENST00000265136.7	hg19	CCDS34637.1	.	.	.	.	.	.	.	.	.	.	T	7.010	0.556676	0.13436	.	.	ENSG00000106078	ENST00000265136;ENST00000445054;ENST00000431948;ENST00000395542	T;T;T;T	0.59906	0.23;0.23;0.23;0.23	5.27	0.0736	0.14391	Actin-binding WH2 (3);	0.325435	0.22233	N	0.062783	T	0.30572	0.0769	N	0.12182	0.205	0.22199	N	0.999296	B;B;B;B;B	0.27997	0.082;0.082;0.1;0.197;0.122	B;B;B;B;B	0.28916	0.058;0.058;0.096;0.062;0.056	T	0.17018	-1.0383	10	0.18276	T	0.48	.	5.1978	0.15246	0.0:0.2352:0.1416:0.6232	.	1123;1180;1123;1205;665	O75128-3;O75128-7;O75128;O75128-2;O75128-6	.;.;COBL_HUMAN;.;.	R	1123;1015;1008;1205	ENSP00000265136:K1123R;ENSP00000401204:K1015R;ENSP00000413498:K1008R;ENSP00000378912:K1205R	ENSP00000265136:K1123R	K	-	2	0	COBL	51062919	0.994000	0.37717	0.170000	0.22879	0.412000	0.31113	1.401000	0.34589	-0.224000	0.09928	0.460000	0.39030	AAG	.	.		0.567	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198		C	51095425	T	C	51095425	3	2	235	1	0	0	0	0	1	0	0	0	3655	1609	56	2	433	2	COBL	7	51095425	Missense_Mutation	SNP	T	TCGA-DD-AAW2-01A-11D-A40P-10	10961431	51095425	108043238	51	32737										
SAMD9	54809	hgsc.bcm.edu	37	chr7	92734707	92734707	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	tgtctttgactccaaaatgaAtagtgccattggtacgtgaa	9	7	1	3			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr7:92734707A>G	ENST00000379958.2	-	3	973	c.704T>C	c.(703-705)aTt>aCt	p.I235T		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	235						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			TCCAAAATGAATAGTGCCATT	0.393																																					p.I235T		Atlas-SNP	.											.	SAMD9	239	.	0			c.T704C						.						134	128	130					7																	92734707		2203	4300	6503	SO:0001583	missense	54809	exon2			AAATGAATAGTGC	AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"Sterile alpha motif (SAM) domain containing"	1348	protein-coding gene	gene with protein product		610456	"chromosome 7 open reading frame 5"	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.704T>C	chr7.hg19:g.92734707A>G	ENSP00000369292:p.Ile235Thr	88.0	0.0		172.0	46.0	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Missense_Mutation	SNP	ENST00000379958.2	hg19	CCDS34680.1	.	.	.	.	.	.	.	.	.	.	A	19.94	3.919098	0.73098	.	.	ENSG00000205413	ENST00000379958;ENST00000446617	T;T	0.16324	2.35;2.35	4.39	4.39	0.52855	.	0.000000	0.64402	D	0.000008	T	0.37892	0.1020	M	0.61703	1.905	0.40974	D	0.98472	D	0.89917	1.0	D	0.83275	0.996	T	0.27640	-1.0068	10	0.87932	D	0	.	12.837	0.57780	1.0:0.0:0.0:0.0	.	235	Q5K651	SAMD9_HUMAN	T	235	ENSP00000369292:I235T;ENSP00000414529:I235T	ENSP00000369292:I235T	I	-	2	0	SAMD9	92572643	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.733000	0.91539	1.976000	0.57569	0.491000	0.48974	ATT	.	.		0.393	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654		G	92734707	A	G	92734707	3	3	235	1	0	0	0	0	1	0	0	0	13841	101	4	2	4069	2	SAMD9	7	92734707	Missense_Mutation	SNP	A	TCGA-DD-AAW2-01A-11D-A40P-10	41639282	92734707	66403956	52	32738										
NOS3	4846	hgsc.bcm.edu	37	chr7	150695672	150695672	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	cgctgccctggccgaggagaCttccgaatctggaacagcca	12	14	1	1			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr7:150695672C>A	ENST00000484524.1	+	6	720	c.720C>A	c.(718-720)gaC>gaA	p.D240E	NOS3_ENST00000297494.3_Missense_Mutation_p.D240E|NOS3_ENST00000461406.1_Missense_Mutation_p.D34E|NOS3_ENST00000467517.1_Missense_Mutation_p.D240E	NM_001160111.1	NP_001153583.1	P60323	NANO3_HUMAN	nitric oxide synthase 3 (endothelial cell)	3					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|oogenesis (GO:0048477)|regulation of cell cycle (GO:0051726)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(11)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	50	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GCCGAGGAGACTTCCGAATCT	0.667																																					p.D240E		Atlas-SNP	.											.	NOS3	131	.	0			c.C720A						.						21	19	20					7																	150695672		2178	4278	6456	SO:0001583	missense	4846	exon6			AGGAGACTTCCGA		CCDS5912.1, CCDS55182.1, CCDS55183.1	7q36	2007-02-15			ENSG00000164867	ENSG00000164867	1.14.13.39		7876	protein-coding gene	gene with protein product	"endothelial nitric oxide synthase"	163729				1379542	Standard	NM_000603		Approved	ECNOS, eNOS	uc003wif.3	P29474	OTTHUMG00000158343	ENST00000484524.1:c.720C>A	chr7.hg19:g.150695672C>A	ENSP00000420215:p.Asp240Glu	75.0	0.0		137.0	44.0	NM_001160111	Q495E5	Missense_Mutation	SNP	ENST00000484524.1	hg19	CCDS55182.1	.	.	.	.	.	.	.	.	.	.	c	20.6	4.025959	0.75390	.	.	ENSG00000164867	ENST00000297494;ENST00000461406;ENST00000484524;ENST00000467517	T;T;T;T	0.34275	1.37;1.37;1.37;1.37	4.9	3.06	0.35304	Nitric oxide synthase, oxygenase domain (3);	0.000000	0.64402	D	0.000011	T	0.48874	0.1524	L	0.56124	1.755	0.39030	D	0.95992	B;B;D;D;B	0.65815	0.006;0.006;0.993;0.995;0.153	B;B;D;D;B	0.79784	0.039;0.039;0.993;0.982;0.132	T	0.51212	-0.8734	10	0.66056	D	0.02	-11.1048	6.5113	0.22224	0.0:0.7143:0.0:0.2857	.	240;240;240;34;240	A0S0A6;E9PFR2;A0S0A8;E7ESA7;P29474	.;.;.;.;NOS3_HUMAN	E	240;34;240;240	ENSP00000297494:D240E;ENSP00000417143:D34E;ENSP00000420215:D240E;ENSP00000420551:D240E	ENSP00000297494:D240E	D	+	3	2	NOS3	150326605	0.967000	0.33354	0.999000	0.59377	0.824000	0.46624	0.201000	0.17276	1.192000	0.43071	0.471000	0.43371	GAC	.	.		0.667	NOS3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351550.1	NM_000603		A	150695672	C	A	150695672	3	1	235	1	0	0	0	0	1	0	0	0	10553	564	20	3	742	3	NOS3	7	150695672	Missense_Mutation	SNP	C	TCGA-DD-AAW2-01A-11D-A40P-10	57960965	150695672	8442991	53	32739										
WDR60	55112	hgsc.bcm.edu	37	chr7	158718939	158718939	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	gcagtagaacctatctcaacGtccgtccacaaaaagcagag	8	12	1	2			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr7:158718939G>T	ENST00000407559.3	+	18	2477	c.2319G>T	c.(2317-2319)acG>acT	p.T773T		NM_018051.4	NP_060521.4	Q8WVS4	WDR60_HUMAN	WD repeat domain 60	773					cell projection organization (GO:0030030)	cilium (GO:0005929)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(3)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(4)|lung(16)|ovary(2)	35	Ovarian(565;0.152)	all_cancers(7;1.25e-09)|all_epithelial(9;0.000894)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)|STAD - Stomach adenocarcinoma(7;0.18)		CTATCTCAACGTCCGTCCACA	0.433																																					p.T773T		Atlas-SNP	.											.	WDR60	94	.	0			c.G2319T						.						85	80	82					7																	158718939		1904	4123	6027	SO:0001819	synonymous_variant	55112	exon18			CTCAACGTCCGTC		CCDS47757.1	7q36.3	2013-11-15			ENSG00000126870	ENSG00000126870		"WD repeat domain containing"	21862	protein-coding gene	gene with protein product		615462				23910462	Standard	NM_018051		Approved	FLJ10300, FAP163	uc003woe.4	Q8WVS4	OTTHUMG00000151443	ENST00000407559.3:c.2319G>T	chr7.hg19:g.158718939G>T		163.0	0.0		251.0	76.0	NM_018051	Q9NW58	Silent	SNP	ENST00000407559.3	hg19	CCDS47757.1																																																																																			.	.		0.433	WDR60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322668.1	NM_018051		T	158718939	G	T	158718939	2	4	235	1	0	0	0	0	0	0	0	1	17326	1132	40	1		1	WDR60	7	158718939	Silent	SNP	G	TCGA-DD-AAW2-01A-11D-A40P-10	8023267	158718939	419724	54	32740										
FRMPD1	22844	hgsc.bcm.edu	37	chr9	37708463	37708463	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	atgaacaatgagcctgctgaAgacctttcctgggaacgagc	11	10	0	4			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr9:37708463A>C	ENST00000539465.1	+	4	920	c.327A>C	c.(325-327)gaA>gaC	p.E109D	RP11-613M10.9_ENST00000540557.1_Intron|FRMPD1_ENST00000377765.3_Missense_Mutation_p.E109D			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	109	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		AGCCTGCTGAAGACCTTTCCT	0.443																																					p.E109D		Atlas-SNP	.											.	FRMPD1	237	.	0			c.A327C						.						127	116	120					9																	37708463		2203	4300	6503	SO:0001583	missense	22844	exon4			TGCTGAAGACCTT	AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.327A>C	chr9.hg19:g.37708463A>C	ENSP00000444411:p.Glu109Asp	56.0	0.0		85.0	34.0	NM_014907	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	hg19	CCDS6612.1	.	.	.	.	.	.	.	.	.	.	A	14.86	2.660429	0.47572	.	.	ENSG00000070601	ENST00000377765;ENST00000539465	T;T	0.30182	1.54;1.54	5.91	5.91	0.95273	PDZ/DHR/GLGF (4);	0.314836	0.36303	N	0.002664	T	0.26521	0.0648	L	0.37630	1.12	0.80722	D	1	B	0.28605	0.217	B	0.30855	0.121	T	0.05338	-1.0891	10	0.33141	T	0.24	-7.7796	12.7269	0.57176	1.0:0.0:0.0:0.0	.	109	Q5SYB0	FRPD1_HUMAN	D	109	ENSP00000366995:E109D;ENSP00000444411:E109D	ENSP00000366995:E109D	E	+	3	2	FRMPD1	37698463	1.000000	0.71417	0.997000	0.53966	0.676000	0.39594	1.665000	0.37449	2.262000	0.75019	0.528000	0.53228	GAA	.	.		0.443	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907		C	37708463	A	C	37708463	3	2	235	1	0	0	0	0	1	0	0	0	6065	69	3	5	337	5	FRMPD1	9	37708463	Missense_Mutation	SNP	A	TCGA-DD-AAW2-01A-11D-A40P-10		37708463	103504968	55	32741										
FBP1	2203	hgsc.bcm.edu	37	chr9	97367847	97367847	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	acataccgggccccataaggAgctgaattatcctgcaagtt	9	11	0	1			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr9:97367847A>T	ENST00000375326.4	-	6	913	c.717T>A	c.(715-717)gcT>gcA	p.A239A	FBP1_ENST00000415431.1_Silent_p.A239A	NM_000507.3	NP_000498.2	P09467	F16P1_HUMAN	fructose-1,6-bisphosphatase 1	239					carbohydrate metabolic process (GO:0005975)|cellular response to drug (GO:0035690)|cellular response to magnesium ion (GO:0071286)|dephosphorylation (GO:0016311)|fructose 6-phosphate metabolic process (GO:0006002)|fructose metabolic process (GO:0006000)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|negative regulation of cell growth (GO:0030308)|negative regulation of glycolytic process (GO:0045820)|negative regulation of Ras protein signal transduction (GO:0046580)|protein homotetramerization (GO:0051289)|regulation of gluconeogenesis (GO:0006111)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	AMP binding (GO:0016208)|fructose 1,6-bisphosphate 1-phosphatase activity (GO:0042132)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|monosaccharide binding (GO:0048029)			kidney(1)|liver(1)|lung(1)	3		Acute lymphoblastic leukemia(62;0.136)			Adenosine monophosphate(DB00131)	CCCCATAAGGAGCTGAATTAT	0.463																																					p.A239A	Ovarian(142;590 2466 25593 44496)	Atlas-SNP	.											.	FBP1	13	.	0			c.T717A						.						44	42	43					9																	97367847		2203	4300	6503	SO:0001819	synonymous_variant	2203	exon6			ATAAGGAGCTGAA	M19922	CCDS6712.1	9q22.3	2012-08-13			ENSG00000165140	ENSG00000165140	3.1.3.11		3606	protein-coding gene	gene with protein product		611570		FBP		8387495	Standard	NM_000507		Approved		uc004auw.4	P09467	OTTHUMG00000020268	ENST00000375326.4:c.717T>A	chr9.hg19:g.97367847A>T		61.0	0.0		84.0	28.0	NM_000507	O75571|Q53F94|Q96E46	Silent	SNP	ENST00000375326.4	hg19	CCDS6712.1																																																																																			.	.		0.463	FBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053187.1	NM_000507		T	97367847	A	T	97367847	2	4	235	1	0	0	0	0	0	0	0	1	5713	291	11	4		4	FBP1	9	97367847	Silent	SNP	A	TCGA-DD-AAW2-01A-11D-A40P-10	59659384	97367847	43845584	56	32742										
CACNA1B	774	hgsc.bcm.edu	37	chr9	141008886	141008886	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	tgatgatattcgacttctacAagcagaacaaaaccaccaga	6	10	1	4			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr9:141008886A>G	ENST00000371372.1	+	41	5738	c.5593A>G	c.(5593-5595)Aag>Gag	p.K1865E	CACNA1B_ENST00000371363.1_Missense_Mutation_p.K1863E|CACNA1B_ENST00000371355.4_Missense_Mutation_p.K1866E|CACNA1B_ENST00000371357.1_Missense_Mutation_p.K1864E|CACNA1B_ENST00000277551.2_Missense_Mutation_p.K1865E|CACNA1B_ENST00000277549.5_Missense_Mutation_p.K1059E	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	1865					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	CGACTTCTACAAGCAGAACAA	0.527																																					p.K1865E		Atlas-SNP	.											.	CACNA1B	266	.	0			c.A5593G						.						52	48	49					9																	141008886		1922	4130	6052	SO:0001583	missense	774	exon40			TTCTACAAGCAGA	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.5593A>G	chr9.hg19:g.141008886A>G	ENSP00000360423:p.Lys1865Glu	72.0	0.0		111.0	51.0	NM_001243812	B1AQK5	Missense_Mutation	SNP	ENST00000371372.1	hg19	CCDS59522.1	.	.	.	.	.	.	.	.	.	.	A	31	5.067602	0.93898	.	.	ENSG00000148408	ENST00000371372;ENST00000277551;ENST00000277549;ENST00000371363;ENST00000371357;ENST00000371355	T;T;T;T;T;T	0.71817	-0.6;-0.6;-0.6;-0.6;-0.6;-0.6	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	D	0.82337	0.5015	M	0.63843	1.955	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.76071	0.987;0.987	D	0.84226	0.0464	10	0.87932	D	0	.	15.9983	0.80268	1.0:0.0:0.0:0.0	.	1864;1863	B1AQK7;B1AQK6	.;.	E	1865;1865;1059;1863;1864;1866	ENSP00000360423:K1865E;ENSP00000277551:K1865E;ENSP00000277549:K1059E;ENSP00000360414:K1863E;ENSP00000360408:K1864E;ENSP00000360406:K1866E	ENSP00000277549:K1059E	K	+	1	0	CACNA1B	140128707	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.910000	0.69931	2.171000	0.68590	0.533000	0.62120	AAG	.	.		0.527	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718		G	141008886	A	G	141008886	3	3	235	1	0	0	0	0	1	0	0	0	2541	131	5	2	5751	2	CACNA1B	9	141008886	Missense_Mutation	SNP	A	TCGA-DD-AAW2-01A-11D-A40P-10	43641039	141008886	204545	57	32743										
MMS19	64210	hgsc.bcm.edu	37	chr10	99219816	99219816	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	tcctcaccttggggagcagcAtggaagccctggaccaaagc	12	13	1	0			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr10:99219816A>G	ENST00000438925.2	-	26	2978	c.2643T>C	c.(2641-2643)caT>caC	p.H881H	MMS19_ENST00000327238.10_Silent_p.H783H|MMS19_ENST00000370782.2_Silent_p.H881H|MMS19_ENST00000327277.7_3'UTR|MMS19_ENST00000355839.6_Silent_p.H838H	NM_022362.4	NP_071757.4	Q96T76	MMS19_HUMAN	MMS19 nucleotide excision repair homolog (S. cerevisiae)	881					cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|iron-sulfur cluster assembly (GO:0016226)|nucleotide-excision repair (GO:0006289)|phosphorelay signal transduction system (GO:0000160)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	CIA complex (GO:0097361)|cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|membrane (GO:0016020)|MMXD complex (GO:0071817)|nucleus (GO:0005634)|spindle (GO:0005819)	estrogen receptor binding (GO:0030331)|protein binding, bridging (GO:0030674)|receptor signaling complex scaffold activity (GO:0030159)|transcription coactivator activity (GO:0003713)			endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|stomach(1)	16		Colorectal(252;0.0846)		Epithelial(162;3.33e-10)|all cancers(201;2.74e-08)		GGGGAGCAGCATGGAAGCCCT	0.537								Direct reversal of damage																													p.H881H		Atlas-SNP	.											.	MMS19	36	.	0			c.T2643C						.						96	92	94					10																	99219816		2203	4300	6503	SO:0001819	synonymous_variant	64210	exon26			AGCAGCATGGAAG	AF007151	CCDS7464.1, CCDS73177.1	10q24-q25	2007-08-15	2007-08-15	2007-08-15	ENSG00000155229	ENSG00000155229			13824	protein-coding gene	gene with protein product	"MET18 homolog (S. cerevisiae)"	614777		MMS19L		11071939	Standard	NM_022362		Approved	MET18, hMMS19	uc001kns.4	Q96T76	OTTHUMG00000018857	ENST00000438925.2:c.2643T>C	chr10.hg19:g.99219816A>G		136.0	0.0		143.0	55.0	NM_022362	B0QZ75|B3KPE5|B4DQX2|B4E2I3|D3DR55|F8W9Y2|Q17RZ8|Q5T455|Q66K82|Q7L4W8|Q969Z1|Q96DF1|Q96MR1|Q96RK5|Q96SK1|Q9BUE2|Q9BYS9	Silent	SNP	ENST00000438925.2	hg19	CCDS7464.1	.	.	.	.	.	.	.	.	.	.	A	7.438	0.640150	0.14386	.	.	ENSG00000155229	ENST00000434538	.	.	.	5.65	2.03	0.26663	.	.	.	.	.	T	0.57315	0.2045	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50329	-0.8841	4	.	.	.	.	8.4545	0.32890	0.6422:0.0:0.3578:0.0	.	.	.	.	T	456	.	.	M	-	2	0	MMS19	99209806	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.364000	0.34171	0.437000	0.26423	0.482000	0.46254	ATG	.	.		0.537	MMS19-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049706.2			G	99219816	A	G	99219816	2	3	235	1	0	0	0	0	0	0	0	1	9681	214	8	2		2	MMS19	10	99219816	Silent	SNP	A	TCGA-DD-AAW2-01A-11D-A40P-10		99219816	36314931	58	32744										
MMP21	118856	hgsc.bcm.edu	37	chr10	127456123	127456123	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	gggactccttgaagaagtaaAttaacttctgtcttcggtca	9	8	3	2			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr10:127456123A>G	ENST00000368808.3	-	6	1387	c.1388T>C	c.(1387-1389)aTt>aCt	p.I463T		NM_147191.1	NP_671724.1	Q8N119	MMP21_HUMAN	matrix metallopeptidase 21	463					hematopoietic progenitor cell differentiation (GO:0002244)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|urinary_tract(1)	16		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)			Marimastat(DB00786)	GAAGAAGTAAATTAACTTCTG	0.418																																					p.I463T		Atlas-SNP	.											.	MMP21	46	.	0			c.T1388C						.						109	107	107					10																	127456123		2203	4300	6503	SO:0001583	missense	118856	exon6			AAGTAAATTAACT	AF331526	CCDS7647.1	10q26.3	2008-07-28	2005-08-08		ENSG00000154485	ENSG00000154485			14357	protein-coding gene	gene with protein product		608416	"matrix metalloproteinase 21"			11255011	Standard	NM_147191		Approved		uc001liu.3	Q8N119	OTTHUMG00000019235	ENST00000368808.3:c.1388T>C	chr10.hg19:g.127456123A>G	ENSP00000357798:p.Ile463Thr	85.0	0.0		121.0	46.0	NM_147191	Q5VZP9|Q8NG02	Missense_Mutation	SNP	ENST00000368808.3	hg19	CCDS7647.1	.	.	.	.	.	.	.	.	.	.	A	15.71	2.912747	0.52439	.	.	ENSG00000154485	ENST00000368808	T	0.02121	4.44	5.75	5.75	0.90469	Hemopexin/matrixin (2);	0.000000	0.85682	D	0.000000	T	0.03915	0.0110	L	0.37561	1.115	0.53688	D	0.99997	D	0.53312	0.959	P	0.53313	0.723	T	0.47086	-0.9144	10	0.02654	T	1	-19.6822	14.0066	0.64468	1.0:0.0:0.0:0.0	.	463	Q8N119	MMP21_HUMAN	T	463	ENSP00000357798:I463T	ENSP00000357798:I463T	I	-	2	0	MMP21	127446113	1.000000	0.71417	0.977000	0.42913	0.533000	0.34776	5.951000	0.70273	2.195000	0.70347	0.533000	0.62120	ATT	.	.		0.418	MMP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050928.1			G	127456123	A	G	127456123	3	3	235	1	0	0	0	0	1	0	0	0	9669	101	4	2	329	2	MMP21	10	127456123	Missense_Mutation	SNP	A	TCGA-DD-AAW2-01A-11D-A40P-10	28236307	127456123	8078624	59	32745										
DOCK1	1793	hgsc.bcm.edu	37	chr10	128835982	128835982	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	attgtcattttctgtttccaGtggaccttctggggctcttg	10	9	4	0			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr10:128835982G>A	ENST00000280333.6	+	19	1958		c.e19-1			NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1						apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		TCTGTTTCCAGTGGACCTTCT	0.443																																					.		Atlas-SNP	.											.	DOCK1	188	.	0			c.1850-1G>A						.						57	51	53					10																	128835982		1873	4103	5976	SO:0001630	splice_region_variant	1793	exon19			TTTCCAGTGGACC	D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"DOwnstream of CrK"	601403	"dedicator of cyto-kinesis 1"			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.1850-1G>A	chr10.hg19:g.128835982G>A		60.0	0.0		89.0	37.0	NM_001380	A9Z1Z5	Splice_Site	SNP	ENST00000280333.6	hg19		.	.	.	.	.	.	.	.	.	.	G	22.2	4.256376	0.80246	.	.	ENSG00000150760	ENST00000280333	.	.	.	4.73	4.73	0.59995	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.9241	0.88977	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DOCK1	128725972	1.000000	0.71417	0.998000	0.56505	0.856000	0.48823	9.339000	0.96797	2.456000	0.83038	0.462000	0.41574	.	.	.		0.443	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380	Intron	A	128835982	G	A	128835982	5	1	235	1	0	0	0	0	0	0	1	0	4686	1043	36	3	1923	3	DOCK1	10	128835982	Splice_Site	SNP	G	TCGA-DD-AAW2-01A-11D-A40P-10	1379859	128835982	6698765	60	32746										
MKI67	4288	hgsc.bcm.edu	37	chr10	129914021	129914021	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	gtagtgggaacagacttcaaTtctccataacggctcactaa	8	10	3	1			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr10:129914021T>A	ENST00000368654.3	-	7	1026	c.651A>T	c.(649-651)gaA>gaT	p.E217D	MKI67_ENST00000368653.3_Intron	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	217					cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				CAGACTTCAATTCTCCATAAC	0.393																																					p.E217D		Atlas-SNP	.											.	MKI67	363	.	0			c.A651T						.						91	90	90					10																	129914021		2203	4300	6503	SO:0001583	missense	4288	exon7			CTTCAATTCTCCA	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 105"	176741	"antigen identified by monoclonal antibody Ki-67"			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.651A>T	chr10.hg19:g.129914021T>A	ENSP00000357643:p.Glu217Asp	49.0	0.0		61.0	31.0	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	hg19	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	T	12.90	2.077529	0.36662	.	.	ENSG00000148773	ENST00000368654;ENST00000537609	T	0.22945	1.93	3.69	-1.77	0.07982	.	1.628700	0.03650	N	0.240821	T	0.14743	0.0356	N	0.17082	0.46	0.09310	N	1	B	0.24618	0.107	B	0.19946	0.027	T	0.20306	-1.0279	9	.	.	.	.	6.5656	0.22511	0.0:0.0917:0.4518:0.4565	.	217	P46013	KI67_HUMAN	D	217	ENSP00000357643:E217D	.	E	-	3	2	MKI67	129804011	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.305000	0.19254	-0.318000	0.08665	0.533000	0.62120	GAA	.	.		0.393	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		A	129914021	T	A	129914021	3	1	235	1	0	0	0	0	1	0	0	0	9607	1490	52	4	9155	4	MKI67	10	129914021	Missense_Mutation	SNP	T	TCGA-DD-AAW2-01A-11D-A40P-10	1078039	129914021	5620726	61	32747										
EPS8L2	64787	hgsc.bcm.edu	37	chr11	721563	721563	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	ccctgaccccctctgaccccAgcaaatcctcaactgcgccc	5	22	2	2	rs111293076		TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr11:721563A>T	ENST00000533256.1	+	11	1143		c.e11-1		EPS8L2_ENST00000318562.8_Splice_Site|EPS8L2_ENST00000530636.1_Splice_Site|EPS8L2_ENST00000526198.1_Splice_Site|AP006621.9_ENST00000527021.2_RNA			Q9H6S3	ES8L2_HUMAN	EPS8-like 2						positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	actin binding (GO:0003779)			NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|pancreas(1)|prostate(2)|soft_tissue(1)|urinary_tract(1)	13		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;4.37e-27)|Epithelial(43;2.81e-26)|OV - Ovarian serous cystadenocarcinoma(40;1.33e-20)|BRCA - Breast invasive adenocarcinoma(625;4.29e-05)|Lung(200;0.0582)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CTCTGACCCCAGCAAATCCTC	0.652																																					.		Atlas-SNP	.											.	EPS8L2	42	.	0			c.769-2A>T						.						20	25	23					11																	721563		2184	4276	6460	SO:0001630	splice_region_variant	64787	exon10			GACCCCAGCAAAT	AF318331	CCDS31328.1	11p15.5	2008-02-05				ENSG00000177106			21296	protein-coding gene	gene with protein product		614988				12620401	Standard	NM_022772		Approved	FLJ21935, FLJ22171, MGC3088	uc001lqt.3	Q9H6S3		ENST00000533256.1:c.769-1A>T	chr11.hg19:g.721563A>T		154.0	0.0		247.0	118.0	NM_022772	B3KSX1|B7ZKL3|Q53GM8|Q8WYW7|Q96K06|Q9H6K9	Splice_Site	SNP	ENST00000533256.1	hg19	CCDS31328.1	.	.	.	.	.	.	.	.	.	.	A	15.47	2.842242	0.51057	.	.	ENSG00000177106	ENST00000318562;ENST00000533256;ENST00000530636;ENST00000526198	.	.	.	3.57	3.57	0.40892	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.404	0.26981	0.8055:0.0:0.0:0.1945	.	.	.	.	.	-1	.	.	.	+	.	.	EPS8L2	711563	1.000000	0.71417	0.928000	0.36995	0.749000	0.42624	6.698000	0.74608	1.628000	0.50416	0.451000	0.29950	.	.	T|1.000		0.652	EPS8L2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382344.1	NM_022772	Intron	T	721563	A	T	721563	5	4	235	1	0	0	0	0	0	0	1	0	5198	202	7	4	801	4	EPS8L2	11	721563	Splice_Site	SNP	A	TCGA-DD-AAW2-01A-11D-A40P-10		721563	134284953	62	32748										
SMPD1	6609	hgsc.bcm.edu	37	chr11	6411942	6411942	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	tggatgggcctggtgctggcGctggcgctggcgctggcgct	20	11	0	0	rs550365194|rs550067660	byFrequency	TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr11:6411942G>C	ENST00000342245.4	+	1	282	c.114G>C	c.(112-114)gcG>gcC	p.A38A	SMPD1_ENST00000527275.1_Silent_p.A38A|SMPD1_ENST00000299397.3_Silent_p.A38A|SMPD1_ENST00000356761.2_Silent_p.A38A|SMPD1_ENST00000533196.1_3'UTR	NM_000543.4|NM_001007593.2	NP_000534.3|NP_001007594.2	P17405	ASM_HUMAN	sphingomyelin phosphodiesterase 1, acid lysosomal	38					cell death (GO:0008219)|ceramide biosynthetic process (GO:0046513)|glycosphingolipid metabolic process (GO:0006687)|negative regulation of MAP kinase activity (GO:0043407)|nervous system development (GO:0007399)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein dephosphorylation (GO:0035307)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)|sphingomyelin metabolic process (GO:0006684)|termination of signal transduction (GO:0023021)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lamellar body (GO:0042599)|lysosomal lumen (GO:0043202)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(3)	23		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;4.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	Amlodipine(DB00381)|Chlorpromazine(DB00477)|Desipramine(DB01151)	tggtgctggcgctggcgctgg	0.706																																					p.A38A		Atlas-SNP	.											.	SMPD1	108	.	0			c.G114C						.						13	17	16					11																	6411942		2189	4262	6451	SO:0001819	synonymous_variant	6609	exon1			GCTGGCGCTGGCG	AB209775	CCDS31409.1, CCDS44531.1, CCDS31409.2	11p15.4-p15.1	2010-04-28	2008-02-04		ENSG00000166311	ENSG00000166311	3.1.4.12		11120	protein-coding gene	gene with protein product	"acid sphingomyelinase"	607608				1711683	Standard	NM_000543		Approved	ASM	uc001mcw.3	P17405	OTTHUMG00000165453	ENST00000342245.4:c.114G>C	chr11.hg19:g.6411942G>C		32.0	0.0		83.0	7.0	NM_000543	A8K8M3|E9PKS3|P17406|Q13811|Q16837|Q16841	Silent	SNP	ENST00000342245.4	hg19	CCDS44531.1																																																																																			.	.		0.706	SMPD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384205.1	NM_000543		C	6411942	G	C	6411942	2	2	235	1	0	0	0	0	0	0	0	1	14819	1074	38	4		4	SMPD1	11	6411942	Silent	SNP	G	TCGA-DD-AAW2-01A-11D-A40P-10	5690379	6411942	128594574	63	32749										
OR5M11	219487	hgsc.bcm.edu	37	chr11	56310580	56310580	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	gggcgtgtgaaggcgagagtCcagtctcattaacattatca	12	8	2	2			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr11:56310580C>T	ENST00000528616.2	-	1	177	c.154G>A	c.(154-156)Gac>Aac	p.D52N		NM_001005245.1	NP_001005245.1	Q96RB7	OR5MB_HUMAN	olfactory receptor, family 5, subfamily M, member 11	52						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.D52Y(1)		central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(14)	18						AGGCGAGAGTCCAGTCTCATT	0.468																																					p.D52N		Atlas-SNP	.											OR5M11,NS,carcinoma,0,1	OR5M11	60	.	1	Substitution - Missense(1)	lung(1)	c.G154A						.						154	154	154					11																	56310580		2168	4280	6448	SO:0001583	missense	219487	exon1			GAGAGTCCAGTCT	AP002517	CCDS53629.1	11q11	2012-08-09				ENSG00000255223		"GPCR / Class A : Olfactory receptors"	15291	protein-coding gene	gene with protein product							Standard	NM_001005245		Approved	OR11-199	uc010rjl.2	Q96RB7		ENST00000528616.2:c.154G>A	chr11.hg19:g.56310580C>T	ENSP00000432417:p.Asp52Asn	92.0	0.0		140.0	69.0	NM_001005245	B2RNL5|B2RNL7	Missense_Mutation	SNP	ENST00000528616.2	hg19	CCDS53629.1	.	.	.	.	.	.	.	.	.	.	C	4.361	0.066493	0.08388	.	.	ENSG00000255223	ENST00000528616	T	0.02837	4.14	5.1	2.26	0.28386	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.04588	0.0125	M	0.73319	2.225	0.09310	N	1	B	0.10296	0.003	B	0.10450	0.005	T	0.36016	-0.9765	9	0.30078	T	0.28	.	7.739	0.28831	0.0:0.6718:0.0:0.3282	.	52	Q96RB7	OR5MB_HUMAN	N	52	ENSP00000432417:D52N	ENSP00000432417:D52N	D	-	1	0	OR5M11	56067156	0.000000	0.05858	0.695000	0.30226	0.061000	0.15899	-0.087000	0.11215	0.362000	0.24319	-0.162000	0.13425	GAC	.	.		0.468	OR5M11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391608.1	NM_001005245		T	56310580	C	T	56310580	3	4	235	1	0	0	0	0	1	0	0	0	11183	855	30	3	766	3	OR5M11	11	56310580	Missense_Mutation	SNP	C	TCGA-DD-AAW2-01A-11D-A40P-10	49898638	56310580	78695936	64	32750										
OR9G1	390174	hgsc.bcm.edu	37	chr11	56468039	56468039	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	ctgcctccacacacccatgtAttttttcactggaaatctgt	5	13	2	0			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr11:56468039A>G	ENST00000312153.1	+	1	176	c.176A>G	c.(175-177)tAt>tGt	p.Y59C		NM_001005213.1	NP_001005213.1	Q8NH87	OR9G1_HUMAN	olfactory receptor, family 9, subfamily G, member 1	59						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|kidney(1)|lung(25)|stomach(2)|upper_aerodigestive_tract(1)	31						ACACCCATGTATTTTTTCACT	0.473																																					p.Y59C		Atlas-SNP	.											.	.	.	.	0			c.A176G						.						116	102	107					11																	56468039		2201	4296	6497	SO:0001583	missense	504191	exon1			CCATGTATTTTTT	AB065500	CCDS31536.1	11q11	2012-08-09			ENSG00000174914	ENSG00000174914		"GPCR / Class A : Olfactory receptors"	15319	protein-coding gene	gene with protein product				OR9G5			Standard	NM_001005213		Approved			Q8NH87	OTTHUMG00000167112	ENST00000312153.1:c.176A>G	chr11.hg19:g.56468039A>G	ENSP00000309012:p.Tyr59Cys	77.0	0.0		68.0	16.0	NM_001013358	Q6IEU9|Q8NGQ0	Missense_Mutation	SNP	ENST00000312153.1	hg19	CCDS31536.1	.	.	.	.	.	.	.	.	.	.	A	15.73	2.918447	0.52546	.	.	ENSG00000174914	ENST00000312153	T	0.15718	2.4	4.54	4.54	0.55810	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47852	D	0.000208	T	0.52403	0.1732	H	0.94964	3.605	0.48135	D	0.999595	D	0.89917	1.0	D	0.76071	0.987	T	0.67268	-0.5713	10	0.87932	D	0	-26.0348	13.988	0.64348	1.0:0.0:0.0:0.0	.	59	Q8NH87	OR9G1_HUMAN	C	59	ENSP00000309012:Y59C	ENSP00000309012:Y59C	Y	+	2	0	OR9G1	56224615	1.000000	0.71417	1.000000	0.80357	0.406000	0.30931	5.099000	0.64554	2.013000	0.59113	0.477000	0.44152	TAT	.	.		0.473	OR9G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393253.1	NM_001005213		G	56468039	A	G	56468039	3	3	235	1	0	0	0	0	1	0	0	0	11259	449	16	2	178	2	OR9G1	11	56468039	Missense_Mutation	SNP	A	TCGA-DD-AAW2-01A-11D-A40P-10	157459	56468039	78538477	65	32751										
HRASLS5	117245	hgsc.bcm.edu	37	chr11	63257813	63257813	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	cccacggattcttctaattcAaggggggaaatgctatttag	10	8	3	0			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr11:63257813A>G	ENST00000301790.4	-	2	330	c.171T>C	c.(169-171)ctT>ctC	p.L57L	HRASLS5_ENST00000540857.1_Intron|HRASLS5_ENST00000539221.1_Silent_p.L57L			Q96KN8	HRSL5_HUMAN	HRAS-like suppressor family, member 5	57							transferase activity, transferring acyl groups (GO:0016746)			endometrium(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|urinary_tract(1)	14						CTTCTAATTCAAGGGGGGAAA	0.557																																					p.L57L		Atlas-SNP	.											.	HRASLS5	28	.	0			c.T171C						.						145	159	154					11																	63257813		2201	4298	6499	SO:0001819	synonymous_variant	117245	exon2			TAATTCAAGGGGG	AJ416558	CCDS8044.1, CCDS53646.1, CCDS53647.1	11q13.2	2006-08-16			ENSG00000168004	ENSG00000168004			24978	protein-coding gene	gene with protein product		611474					Standard	NM_001146729		Approved	HRLP5	uc001nwy.2	Q96KN8	OTTHUMG00000167806	ENST00000301790.4:c.171T>C	chr11.hg19:g.63257813A>G		32.0	0.0		59.0	21.0	NM_001146728	B7X6T1|F5GZ87|F5H4Y9	Silent	SNP	ENST00000301790.4	hg19	CCDS8044.1																																																																																			.	.		0.557	HRASLS5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396375.1	NM_054108		G	63257813	A	G	63257813	2	3	235	1	0	0	0	0	0	0	0	1	7360	117	5	2		2	HRASLS5	11	63257813	Silent	SNP	A	TCGA-DD-AAW2-01A-11D-A40P-10	6789774	63257813	71748703	66	32752										
CATSPER1	117144	hgsc.bcm.edu	37	chr11	65790380	65790380	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	catgacggtgttgaggcagaCaacgaagaagatgaaagttt	13	5	0	6			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr11:65790380C>A	ENST00000312106.5	-	2	1506	c.1369G>T	c.(1369-1371)Gtc>Ttc	p.V457F		NM_053054.3	NP_444282.3	Q8NEC5	CTSR1_HUMAN	cation channel, sperm associated 1	457					calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|fusion of sperm to egg plasma membrane (GO:0007342)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|regulation of calcium ion transport (GO:0051924)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|central_nervous_system(1)|endometrium(9)|kidney(3)|large_intestine(6)|liver(3)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44						TTGAGGCAGACAACGAAGAAG	0.557											OREG0021092	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V457F		Atlas-SNP	.											.	CATSPER1	101	.	0			c.G1369T						.						104	99	101					11																	65790380		2201	4296	6497	SO:0001583	missense	117144	exon2			GGCAGACAACGAA	AF407333	CCDS8127.1	11q12.1	2011-07-05			ENSG00000175294	ENSG00000175294		"Voltage-gated ion channels / Cation channels, sperm associated"	17116	protein-coding gene	gene with protein product		606389				11675491, 11595941, 16382101	Standard	NM_053054		Approved	CATSPER	uc001ogt.3	Q8NEC5	OTTHUMG00000166668	ENST00000312106.5:c.1369G>T	chr11.hg19:g.65790380C>A	ENSP00000309052:p.Val457Phe	94.0	0.0	1086	88.0	37.0	NM_053054	Q96P76	Missense_Mutation	SNP	ENST00000312106.5	hg19	CCDS8127.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.033169	0.75504	.	.	ENSG00000175294	ENST00000312106	D	0.97831	-4.56	5.62	-2.72	0.05968	.	0.613850	0.12427	N	0.469938	D	0.97272	0.9108	L	0.46157	1.445	0.21355	N	0.999717	D	0.63880	0.993	D	0.67900	0.954	D	0.93655	0.6976	10	0.87932	D	0	-18.652	10.8032	0.46502	0.0:0.3494:0.0:0.6506	.	457	Q8NEC5	CTSR1_HUMAN	F	457	ENSP00000309052:V457F	ENSP00000309052:V457F	V	-	1	0	CATSPER1	65546956	0.309000	0.24518	0.003000	0.11579	0.114000	0.19823	0.411000	0.21115	-0.904000	0.03876	-0.471000	0.05019	GTC	.	.		0.557	CATSPER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391055.1	NM_053054		A	65790380	C	A	65790380	3	1	235	1	0	0	0	0	1	0	0	0	2689	478	17	3	1017	3	CATSPER1	11	65790380	Missense_Mutation	SNP	C	TCGA-DD-AAW2-01A-11D-A40P-10	2532567	65790380	69216136	67	32753										
PICALM	8301	hgsc.bcm.edu	37	chr11	85722082	85722082	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	agacagtttacctctgcaacTttgaggaactctgagattct	8	9	3	3			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr11:85722082T>G	ENST00000393346.3	-	7	904	c.756A>C	c.(754-756)aaA>aaC	p.K252N	PICALM_ENST00000532317.1_Missense_Mutation_p.K252N|PICALM_ENST00000526033.1_Missense_Mutation_p.K252N|PICALM_ENST00000528398.1_Missense_Mutation_p.K201N|PICALM_ENST00000356360.5_Missense_Mutation_p.K252N			Q13492	PICAL_HUMAN	phosphatidylinositol binding clathrin assembly protein	252	Interaction with FAM64A.				axonogenesis (GO:0007409)|cargo loading into vesicle (GO:0035459)|cell proliferation (GO:0008283)|clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|hemopoiesis (GO:0030097)|iron ion homeostasis (GO:0055072)|iron ion import into cell (GO:0097459)|negative regulation of gene expression (GO:0010629)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of receptor-mediated endocytosis (GO:0048261)|positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902961)|positive regulation of beta-amyloid formation (GO:1902004)|positive regulation of neuron death (GO:1901216)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902959)|regulation of endocytosis (GO:0030100)|regulation of protein localization (GO:0032880)|synaptic vesicle maturation (GO:0016188)|vesicle-mediated transport (GO:0016192)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neurofibrillary tangle (GO:0097418)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|vesicle (GO:0031982)	1-phosphatidylinositol binding (GO:0005545)|clathrin adaptor activity (GO:0035615)|clathrin binding (GO:0030276)|clathrin heavy chain binding (GO:0032050)			endometrium(1)|kidney(2)|large_intestine(2)|liver(1)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	19		Acute lymphoblastic leukemia(157;7.42e-07)|all_hematologic(158;0.00092)				CCTCTGCAACTTTGAGGAACT	0.338			T	"MLLT10, MLL"	"TALL, AML, "																																p.K252N		Atlas-SNP	.		Dom	yes		11	11q14	8301	phosphatidylinositol binding clathrin assembly protein (CALM)		L	.	PICALM	82	.	0			c.A756C						.						126	110	115					11																	85722082		2202	4298	6500	SO:0001583	missense	8301	exon7			TGCAACTTTGAGG	BC048259	CCDS8272.1, CCDS31653.1, CCDS55783.1, CCDS55784.1	11q14	2008-02-01			ENSG00000073921	ENSG00000073921			15514	protein-coding gene	gene with protein product		603025				8643484	Standard	NM_001206947		Approved	CALM, CLTH	uc001pbm.3	Q13492	OTTHUMG00000166981	ENST00000393346.3:c.756A>C	chr11.hg19:g.85722082T>G	ENSP00000377015:p.Lys252Asn	92.0	0.0		93.0	39.0	NM_007166	B4DTM3|E9PN05|F8VPG7|O60700|Q4LE54|Q6GMQ6|Q86XZ9	Missense_Mutation	SNP	ENST00000393346.3	hg19	CCDS8272.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.387462	0.82902	.	.	ENSG00000073921	ENST00000532317;ENST00000526033;ENST00000447890;ENST00000393346;ENST00000528398;ENST00000356360	T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92	5.48	4.34	0.51931	ANTH (1);Clathrin adaptor, phosphoinositide-binding, GAT-like (1);	0.000000	0.85682	D	0.000000	T	0.64918	0.2642	M	0.83692	2.655	0.80722	D	1	D;D;P;D	0.89917	1.0;0.99;0.551;0.996	D;D;P;D	0.87578	0.998;0.951;0.51;0.971	T	0.68792	-0.5315	9	.	.	.	-21.1179	11.9695	0.53055	0.0:0.0713:0.0:0.9287	.	201;252;252;252	E9PN05;F8VPG7;Q13492;Q13492-3	.;.;PICAL_HUMAN;.	N	252;252;252;252;201;252	ENSP00000436958:K252N;ENSP00000433846:K252N;ENSP00000377015:K252N;ENSP00000434884:K201N;ENSP00000348718:K252N	.	K	-	3	2	PICALM	85399730	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.539000	0.53604	2.197000	0.70478	0.533000	0.62120	AAA	.	.		0.338	PICALM-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392224.1	NM_007166		G	85722082	T	G	85722082	3	3	235	1	0	0	0	0	1	0	0	0	11889	1606	56	5	1286	5	PICALM	11	85722082	Missense_Mutation	SNP	T	TCGA-DD-AAW2-01A-11D-A40P-10	19931702	85722082	49284434	68	32754										
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	103156996	103156996	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	ttttttagattgctctccccAgtctttatcagaccctctgc	5	13	4	2			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr11:103156996A>G	ENST00000375735.2	+	74	11047	c.10903A>G	c.(10903-10905)Agt>Ggt	p.S3635G	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.S3642G|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3635					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		TGCTCTCCCCAGTCTTTATCA	0.338																																					p.S3642G		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.A10924G						.						200	203	202					11																	103156996		1865	4114	5979	SO:0001583	missense	79659	exon75			CTCCCCAGTCTTT	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.10903A>G	chr11.hg19:g.103156996A>G	ENSP00000364887:p.Ser3635Gly	53.0	0.0		70.0	27.0	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	hg19	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	A	10.26	1.301971	0.23736	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.07800	3.16;3.16	5.41	-0.903	0.10534	Dynein heavy chain (1);	0.787654	0.10472	U	0.670691	T	0.06280	0.0162	L	0.36672	1.1	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41610	-0.9499	10	0.26408	T	0.33	.	6.6822	0.23127	0.3711:0.0:0.494:0.1349	.	3635;3642	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	G	3635;3642	ENSP00000364887:S3635G;ENSP00000381167:S3642G	ENSP00000364887:S3635G	S	+	1	0	DYNC2H1	102662206	0.003000	0.15002	0.203000	0.23512	0.953000	0.61014	-0.019000	0.12546	0.032000	0.15435	0.533000	0.62120	AGT	.	.		0.338	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		G	103156996	A	G	103156996	3	3	235	1	0	0	0	0	1	0	0	0	4848	188	7	2	11222	2	DYNC2H1	11	103156996	Missense_Mutation	SNP	A	TCGA-DD-AAW2-01A-11D-A40P-10	17434914	103156996	31849520	69	32755										
NCAM1	4684	hgsc.bcm.edu	37	chr11	113142501	113142501	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	ggaaagatgagtccaaggagCccatcgtggaggttcgaacg	15	8	0	2			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr11:113142501C>A	ENST00000316851.7	+	17	2329	c.2329C>A	c.(2329-2331)Ccc>Acc	p.P777T	NCAM1-AS1_ENST00000526229.1_RNA|NCAM1-AS1_ENST00000533638.1_RNA|NCAM1_ENST00000397957.4_3'UTR	NM_001242607.1|NM_181351.4	NP_001229536.1|NP_851996.2	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1	787					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		GTCCAAGGAGCCCATCGTGGA	0.592																																					p.P813T		Atlas-SNP	.											.	NCAM1	372	.	0			c.C2437A						.						69	79	76					11																	113142501		2058	4160	6218	SO:0001583	missense	4684	exon20			AAGGAGCCCATCG		CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000316851.7:c.2329C>A	chr11.hg19:g.113142501C>A	ENSP00000318472:p.Pro777Thr	68.0	0.0		69.0	34.0	NM_001242607	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Missense_Mutation	SNP	ENST00000316851.7	hg19		.	.	.	.	.	.	.	.	.	.	C	25.9	4.682760	0.88542	.	.	ENSG00000149294	ENST00000531044;ENST00000316851;ENST00000433634	T	0.48201	0.82	5.83	5.83	0.93111	.	0.000000	0.85682	U	0.000000	T	0.72882	0.3516	.	.	.	0.80722	D	1	D;D;D	0.89917	1.0;0.988;0.995	D;P;P	0.87578	0.998;0.799;0.728	T	0.74870	-0.3517	9	0.72032	D	0.01	-24.8787	20.1152	0.97926	0.0:1.0:0.0:0.0	.	659;777;787	E9PLH7;P13591-1;P13591	.;.;NCAM1_HUMAN	T	659;777;242	ENSP00000318472:P777T	ENSP00000318472:P777T	P	+	1	0	NCAM1	112647711	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	6.070000	0.71220	2.750000	0.94351	0.655000	0.94253	CCC	.	.		0.592	NCAM1-201	KNOWN	basic	protein_coding	protein_coding		NM_000615		A	113142501	C	A	113142501	3	1	235	1	0	0	0	0	1	0	0	0	10211	739	26	3	2631	3	NCAM1	11	113142501	Missense_Mutation	SNP	C	TCGA-DD-AAW2-01A-11D-A40P-10	9985505	113142501	21864015	70	32756										
WNT5B	81029	hgsc.bcm.edu	37	chr12	1755095	1755095	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	aggagaagtacgacagcgcgGccgccatgcgcgtcacccgc	14	15	1	1			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr12:1755095G>C	ENST00000397196.2	+	5	989	c.757G>C	c.(757-759)Gcc>Ccc	p.A253P	WNT5B_ENST00000537031.1_Missense_Mutation_p.A253P|WNT5B_ENST00000542408.1_3'UTR|WNT5B_ENST00000310594.3_Missense_Mutation_p.A253P|WNT5B_ENST00000545747.1_3'UTR	NM_032642.2	NP_116031.1	Q9H1J7	WNT5B_HUMAN	wingless-type MMTV integration site family, member 5B	253					cell fate commitment (GO:0045165)|cellular response to retinoic acid (GO:0071300)|chondrocyte differentiation (GO:0002062)|fat cell differentiation (GO:0045444)|lens fiber cell development (GO:0070307)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|neuron differentiation (GO:0030182)|positive regulation of cell migration (GO:0030335)|positive regulation of fat cell differentiation (GO:0045600)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor binding (GO:0005102)			skin(1)	1	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00109)			CGACAGCGCGGCCGCCATGCG	0.697																																					p.A253P		Atlas-SNP	.											.	WNT5B	27	.	0			c.G757C						.						26	29	28					12																	1755095		2202	4299	6501	SO:0001583	missense	81029	exon5			AGCGCGGCCGCCA	AB060966	CCDS8510.1	12p13.3	2008-07-07			ENSG00000111186	ENSG00000111186		"Wingless-type MMTV integration sites"	16265	protein-coding gene	gene with protein product		606361				11445850	Standard	NM_030775		Approved		uc001qjk.3	Q9H1J7	OTTHUMG00000090375	ENST00000397196.2:c.757G>C	chr12.hg19:g.1755095G>C	ENSP00000380379:p.Ala253Pro	32.0	0.0		44.0	14.0	NM_032642	A8K315|D3DUP9|Q96S49|Q9BV04	Missense_Mutation	SNP	ENST00000397196.2	hg19	CCDS8510.1	.	.	.	.	.	.	.	.	.	.	G	19.62	3.862399	0.71949	.	.	ENSG00000111186	ENST00000537031;ENST00000310594;ENST00000397196;ENST00000543071	T;T;T;T	0.76578	-1.03;-1.03;-1.03;-1.03	5.14	5.14	0.70334	.	0.048696	0.85682	D	0.000000	D	0.86628	0.5978	M	0.69358	2.11	0.80722	D	1	D	0.60160	0.987	D	0.65573	0.936	D	0.86836	0.2014	10	0.54805	T	0.06	.	18.8	0.92013	0.0:0.0:1.0:0.0	.	253	Q9H1J7	WNT5B_HUMAN	P	253	ENSP00000439312:A253P;ENSP00000308887:A253P;ENSP00000380379:A253P;ENSP00000442348:A253P	ENSP00000308887:A253P	A	+	1	0	WNT5B	1625356	1.000000	0.71417	0.463000	0.27130	0.531000	0.34715	7.652000	0.83633	2.668000	0.90789	0.650000	0.86243	GCC	.	.		0.697	WNT5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206747.2			C	1755095	G	C	1755095	3	2	235	1	0	0	0	0	1	0	0	0	17407	1203	42	4	771	4	WNT5B	12	1755095	Missense_Mutation	SNP	G	TCGA-DD-AAW2-01A-11D-A40P-10		1755095	132096800	71	32757										
MLF2	8079	hgsc.bcm.edu	37	chr12	6859471	6859472	+	Splice_Site	DNP	CC	CC	AG													0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	gcctccagctgtcatgtgttCctgaggacagggtaggtagg							TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr12:6859471_6859472CC>AG	ENST00000203630.5	-	6	915	c.271_271GG>CT	c.(271-273)GGga>CTgga	p.G91L	MLF2_ENST00000539187.1_Splice_Site_p.G91L|MLF2_ENST00000435120.1_Splice_Site_p.G91L|MLF2_ENST00000564181.1_5'Flank|MLF2_ENST00000542154.1_Splice_Site_p.G91L			Q15773	MLF2_HUMAN	myeloid leukemia factor 2	91					defense response (GO:0006952)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				kidney(2)|large_intestine(3)|lung(4)	9						GTCATGTGTTCCTGAGGACAGG	0.545																																					p.E91X|.		Atlas-SNP	.											.	MLF2	26	.	0			c.G271T|c.271-1G>C						.																																			SO:0001630	splice_region_variant	8079	exon6|exon7			TGTGTTCCTGAGG|GTGTTCCTGAGGA	U57342	CCDS8559.1	12p13.31	2014-09-11			ENSG00000089693	ENSG00000089693			7126	protein-coding gene	gene with protein product		601401				8661158	Standard	NM_005439		Approved	NTN4	uc010sfi.2	Q15773	OTTHUMG00000168717	ENST00000203630.5:c.271_271delinsAG	chr12.hg19:g.6859471_6859472delinsAG		48.0	0.0		51.0	23.0|22.0	NM_005439		Nonsense_Mutation|Splice_Site	SNP	ENST00000203630.5	hg19	CCDS8559.1																																																																																			.	.		0.545	MLF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400733.2		Missense_Mutation	AG	6859472	CC	AG	6859471	5	1	235	1	0	0	0	0	0	0	1	0	9625	869	30	3	487	3	MLF2	12	6859471	Splice_Site	DNP	CC	TCGA-DD-AAW2-01A-11D-A40P-10	5104376	6859471	126992424	72	32758										
A2ML1	144568	hgsc.bcm.edu	37	chr12	9004828	9004828	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	tcagactgacctggctaaatCgcatgagtaccagctagaat	9	10	1	4			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr12:9004828C>T	ENST00000299698.7	+	20	2666	c.2486C>T	c.(2485-2487)tCg>tTg	p.S829L	A2ML1_ENST00000539547.1_Missense_Mutation_p.S338L	NM_001282424.1|NM_144670.4	NP_001269353.1|NP_653271			alpha-2-macroglobulin-like 1											NS(2)|breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(2)|lung(36)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	80						CTGGCTAAATCGCATGAGTAC	0.498																																					p.S829L		Atlas-SNP	.											.	A2ML1	199	.	0			c.C2486T						.						248	234	239					12																	9004828		1939	4164	6103	SO:0001583	missense	144568	exon20			CTAAATCGCATGA	AK057908	CCDS8596.2, CCDS73439.1	12p13	2010-12-14	2005-09-01	2005-09-01	ENSG00000166535	ENSG00000166535			23336	protein-coding gene	gene with protein product		610627	"C3 and PZP-like, alpha-2-macroglobulin domain containing 9"	CPAMD9		16298998	Standard	NM_144670		Approved	FLJ25179	uc001quz.5	A8K2U0	OTTHUMG00000128499	ENST00000299698.7:c.2486C>T	chr12.hg19:g.9004828C>T	ENSP00000299698:p.Ser829Leu	92.0	0.0		97.0	8.0	NM_144670		Missense_Mutation	SNP	ENST00000299698.7	hg19	CCDS8596.2	.	.	.	.	.	.	.	.	.	.	C	16.43	3.122517	0.56613	.	.	ENSG00000166535	ENST00000299698;ENST00000539161;ENST00000541459;ENST00000539547	T;T;T	0.16597	2.33;2.33;2.33	3.08	3.08	0.35506	.	0.652197	0.12736	N	0.443418	T	0.41558	0.1164	M	0.91612	3.225	0.09310	N	1	D	0.64830	0.994	P	0.53062	0.717	T	0.38607	-0.9653	10	0.54805	T	0.06	.	13.9246	0.63955	0.0:1.0:0.0:0.0	.	829	A8K2U0	A2ML1_HUMAN	L	829;829;379;338	ENSP00000299698:S829L;ENSP00000443174:S379L;ENSP00000438292:S338L	ENSP00000299698:S829L	S	+	2	0	A2ML1	8896095	0.005000	0.15991	0.009000	0.14445	0.001000	0.01503	0.951000	0.29135	2.025000	0.59659	0.442000	0.29010	TCG	.	.		0.498	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250304.3	NM_144670		T	9004828	C	T	9004828	3	4	235	1	0	0	0	0	1	0	0	0	5	893	31	1	2564	1	A2ML1	12	9004828	Missense_Mutation	SNP	C	TCGA-DD-AAW2-01A-11D-A40P-10	2145357	9004828	124847067	73	32759										
NCKAP1L	3071	hgsc.bcm.edu	37	chr12	54917217	54917223	+	Frame_Shift_Del	DEL	AAGAACA	AAGAACA	-													0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	ccactacaatcagcaaagccAagaacaagaaaaccaggaag					rs146187661	byFrequency	TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	AAGAACA	AAGAACA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr12:54917217_54917223delAAGAACA	ENST00000293373.6	+	19	1997_2003	c.1918_1924delAAGAACA	c.(1918-1926)aagaacaagfs	p.KNK640fs	NCKAP1L_ENST00000545638.2_Frame_Shift_Del_p.KNK590fs	NM_005337.4	NP_005328.2	P55160	NCKPL_HUMAN	NCK-associated protein 1-like	640					actin polymerization-dependent cell motility (GO:0070358)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|chemotaxis (GO:0006935)|cortical actin cytoskeleton organization (GO:0030866)|erythrocyte development (GO:0048821)|maintenance of cell polarity (GO:0030011)|myeloid cell homeostasis (GO:0002262)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of myosin-light-chain-phosphatase activity (GO:0035509)|neutrophil chemotaxis (GO:0030593)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of CD8-positive, alpha-beta T cell differentiation (GO:0043378)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of lymphocyte differentiation (GO:0045621)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of T cell proliferation (GO:0042102)|protein complex assembly (GO:0006461)|response to drug (GO:0042493)|T cell homeostasis (GO:0043029)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|SCAR complex (GO:0031209)	protein complex binding (GO:0032403)|protein kinase activator activity (GO:0030295)|Rac GTPase activator activity (GO:0030675)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(37)|ovary(3)|prostate(3)|skin(3)|stomach(2)	80						CAGCAAAGCCAAGAACAAGAAAACCAG	0.498																																					p.639_641del		Atlas-INDEL	.											.	NCKAP1L	180	.	0			c.1917_1923del						.																																			SO:0001589	frameshift_variant	3071	exon19			.	AI924363	CCDS31813.1, CCDS53799.1	12q13.1	2005-10-11	2005-10-11	2005-10-11		ENSG00000123338			4862	protein-coding gene	gene with protein product		141180	"hematopoietic protein 1"	HEM1		1932118	Standard	NM_005337		Approved		uc001sgc.4	P55160	OTTHUMG00000169843	ENST00000293373.6:c.1918_1924delAAGAACA	chr12.hg19:g.54917217_54917223delAAGAACA	ENSP00000293373:p.Lys640fs	182.0	0.0		210.0	64.0	NM_005337	B4DUT5|Q52LW0	Frame_Shift_Del	DEL	ENST00000293373.6	hg19	CCDS31813.1																																																																																			.	.		0.498	NCKAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406195.1	NM_005337		-	54917223	AAGAACA	-	54917217	7	5	235	1	0	1	0	1	0	0	0	0	10231	131	5	0	1992	0	NCKAP1L	12	54917217	Frame_Shift_Del	DEL	AAGAACA	TCGA-DD-AAW2-01A-11D-A40P-10	45912389	54917217	78934678	74	32760										
PDE1B	5153	hgsc.bcm.edu	37	chr12	54969802	54969802	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	tcgacttcattgtggagcccAcattctctgtgctgactgac	9	12	2	2			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr12:54969802A>T	ENST00000243052.3	+	13	1730	c.1294A>T	c.(1294-1296)Aca>Tca	p.T432S	PDE1B_ENST00000394277.3_3'UTR|PPP1R1A_ENST00000547431.1_3'UTR|PDE1B_ENST00000550620.1_Missense_Mutation_p.T412S|PDE1B_ENST00000538346.1_Missense_Mutation_p.T391S	NM_000924.3	NP_000915.1	Q01064	PDE1B_HUMAN	phosphodiesterase 1B, calmodulin-dependent	432	Catalytic. {ECO:0000250}.				activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cGMP catabolic process (GO:0046069)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|monocyte differentiation (GO:0030224)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of dopamine metabolic process (GO:0042053)|regulation of neurotransmitter levels (GO:0001505)|response to amphetamine (GO:0001975)|serotonin metabolic process (GO:0042428)|signal transduction (GO:0007165)|visual learning (GO:0008542)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|calcium- and calmodulin-regulated 3',5'-cyclic-GMP phosphodiesterase activity (GO:0048101)|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)			endometrium(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(4)	31					Bepridil(DB01244)|Caffeine(DB00201)|Felodipine(DB01023)|Nicardipine(DB00622)	TGTGGAGCCCACATTCTCTGT	0.547																																					p.T432S		Atlas-SNP	.											.	PDE1B	76	.	0			c.A1294T						.						146	142	144					12																	54969802		2203	4300	6503	SO:0001583	missense	5153	exon13			GAGCCCACATTCT	U56976	CCDS8882.1, CCDS53800.1, CCDS73477.1	12q13	2008-03-18				ENSG00000123360	3.1.4.17	"Phosphodiesterases"	8775	protein-coding gene	gene with protein product		171891		PDES1B		8855339, 9419816	Standard	NM_000924		Approved		uc001sgd.2	Q01064	OTTHUMG00000169844	ENST00000243052.3:c.1294A>T	chr12.hg19:g.54969802A>T	ENSP00000243052:p.Thr432Ser	72.0	0.0		59.0	23.0	NM_000924	Q92825|Q96KP3	Missense_Mutation	SNP	ENST00000243052.3	hg19	CCDS8882.1	.	.	.	.	.	.	.	.	.	.	A	16.37	3.104221	0.56291	.	.	ENSG00000123360	ENST00000243052;ENST00000538346;ENST00000550620	D;D;D	0.81821	-1.54;-1.54;-1.54	4.95	4.95	0.65309	5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.000000	0.85682	D	0.000000	T	0.74336	0.3703	N	0.13198	0.31	0.80722	D	1	P;B	0.38110	0.618;0.443	P;P	0.50378	0.584;0.639	T	0.69822	-0.5041	10	0.14252	T	0.57	.	12.8837	0.58032	1.0:0.0:0.0:0.0	.	412;432	Q01064-2;Q01064	.;PDE1B_HUMAN	S	432;391;412	ENSP00000243052:T432S;ENSP00000442559:T391S;ENSP00000448519:T412S	ENSP00000243052:T432S	T	+	1	0	PDE1B	53256069	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	9.115000	0.94336	1.984000	0.57885	0.533000	0.62120	ACA	.	.		0.547	PDE1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406203.1			T	54969802	A	T	54969802	3	4	235	1	0	0	0	0	1	0	0	0	11643	159	6	4	1397	4	PDE1B	12	54969802	Missense_Mutation	SNP	A	TCGA-DD-AAW2-01A-11D-A40P-10	52585	54969802	78882093	75	32761										
PAN2	9924	hgsc.bcm.edu	37	chr12	56720131	56720131	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	tggtgcggggattgggcgcaTagccaatgaagcccaccttc	14	11	0	1			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr12:56720131T>A	ENST00000425394.2	-	8	1701	c.1325A>T	c.(1324-1326)tAt>tTt	p.Y442F	PAN2_ENST00000257931.5_Missense_Mutation_p.Y442F|PAN2_ENST00000440411.3_Missense_Mutation_p.Y442F|PAN2_ENST00000548043.1_Missense_Mutation_p.Y442F	NM_001127460.2	NP_001120932	Q9HBH5	RDH14_HUMAN	PAN2 poly(A) specific ribonuclease subunit	0					osteoblast differentiation (GO:0001649)	endoplasmic reticulum (GO:0005783)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	41					Vitamin A(DB00162)	ATTGGGCGCATAGCCAATGAA	0.547																																					p.Y442F		Atlas-SNP	.											.	PAN2	107	.	0			c.A1325T						.						50	43	45					12																	56720131		2203	4300	6503	SO:0001583	missense	9924	exon8			GGCGCATAGCCAA	AB014610	CCDS8915.1, CCDS44922.1, CCDS53802.1	12q13.2	2014-03-27	2014-03-27	2008-01-08		ENSG00000135473		"Ubiquitin-specific peptidases"	20074	protein-coding gene	gene with protein product	"PAN2 homolog, PABP1 dependent poly A specific ribonuclease subunit (S. cerevisiae)"		"ubiquitin specific protease 52", "ubiquitin specific peptidase 52", "PAN2 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)"	USP52		12838346, 14583602	Standard	NM_014871		Approved	KIAA0710, hPAN2	uc001skx.3	Q504Q3	OTTHUMG00000170412	ENST00000425394.2:c.1325A>T	chr12.hg19:g.56720131T>A	ENSP00000401721:p.Tyr442Phe	74.0	0.0		120.0	48.0	NM_014871		Missense_Mutation	SNP	ENST00000425394.2	hg19	CCDS44922.1	.	.	.	.	.	.	.	.	.	.	t	34	5.303289	0.95601	.	.	ENSG00000135473	ENST00000425394;ENST00000440411;ENST00000257931;ENST00000548043	T;T;T;T	0.33438	1.43;1.44;1.41;1.43	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.53384	0.1793	M	0.69358	2.11	0.58432	D	0.999999	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.87578	0.998;0.955;0.997	T	0.55592	-0.8117	10	0.56958	D	0.05	-13.1945	14.2558	0.66051	0.0:0.0:0.0:1.0	.	442;442;442	Q504Q3-3;Q504Q3-2;Q504Q3	.;.;PAN2_HUMAN	F	442	ENSP00000401721:Y442F;ENSP00000388231:Y442F;ENSP00000257931:Y442F;ENSP00000449861:Y442F	ENSP00000257931:Y442F	Y	-	2	0	PAN2	55006398	1.000000	0.71417	0.980000	0.43619	0.939000	0.58152	7.873000	0.87193	2.071000	0.62044	0.473000	0.43528	TAT	.	.		0.547	PAN2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409024.1	NM_014871		A	56720131	T	A	56720131	3	1	235	1	0	0	0	0	1	0	0	0	11423	1406	49	4	2359	4	PAN2	12	56720131	Missense_Mutation	SNP	T	TCGA-DD-AAW2-01A-11D-A40P-10	1750329	56720131	77131764	76	32762										
LRIG3	121227	hgsc.bcm.edu	37	chr12	59307787	59307787	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	agagaagtgtaatatttgccGagactggtcccagatttgga	12	6	0	3			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr12:59307787G>A	ENST00000320743.3	-	3	645	c.359C>T	c.(358-360)tCg>tTg	p.S120L	LRIG3_ENST00000379141.4_Missense_Mutation_p.S60L	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3	120					otolith morphogenesis (GO:0032474)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)			LRIG3/ROS1(2)	breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(12)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48			GBM - Glioblastoma multiforme(1;1.17e-18)			AATATTTGCCGAGACTGGTCC	0.388			T	ROS1	NSCLC																																p.S120L		Atlas-SNP	.		Dom	yes		12	12q14.1	121227	leucine-rich repeats and immunoglobulin-like domains 3		E	.	LRIG3	120	.	0			c.C359T						.						107	108	108					12																	59307787		2203	4300	6503	SO:0001583	missense	121227	exon3			TTTGCCGAGACTG	AY505340	CCDS8960.1, CCDS44933.1	12q13.2	2013-01-11				ENSG00000139263		"Immunoglobulin superfamily / I-set domain containing"	30991	protein-coding gene	gene with protein product		608870					Standard	NM_153377		Approved	FLJ90440, KIAA3016	uc001sqr.4	Q6UXM1	OTTHUMG00000169940	ENST00000320743.3:c.359C>T	chr12.hg19:g.59307787G>A	ENSP00000326759:p.Ser120Leu	51.0	0.0		68.0	22.0	NM_153377	Q6UXL7|Q8NC72	Missense_Mutation	SNP	ENST00000320743.3	hg19	CCDS8960.1	.	.	.	.	.	.	.	.	.	.	G	13.76	2.334663	0.41297	.	.	ENSG00000139263	ENST00000379141;ENST00000320743;ENST00000552267	T;T;T	0.40756	2.06;2.12;1.02	5.85	5.85	0.93711	.	0.260402	0.20444	N	0.092226	T	0.44201	0.1282	M	0.66939	2.045	0.43698	D	0.996155	B;B	0.32781	0.001;0.384	B;B	0.24974	0.007;0.057	T	0.32771	-0.9894	9	.	.	.	.	20.1731	0.98165	0.0:0.0:1.0:0.0	.	60;120	Q6UXM1-2;Q6UXM1	.;LRIG3_HUMAN	L	60;120;27	ENSP00000368436:S60L;ENSP00000326759:S120L;ENSP00000449109:S27L	.	S	-	2	0	LRIG3	57594054	1.000000	0.71417	0.446000	0.26920	0.093000	0.18481	7.552000	0.82192	2.768000	0.95171	0.655000	0.94253	TCG	.	.		0.388	LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406623.1	NM_153377		A	59307787	G	A	59307787	3	1	235	1	0	0	0	0	1	0	0	0	8955	1059	37	1	3068	1	LRIG3	12	59307787	Missense_Mutation	SNP	G	TCGA-DD-AAW2-01A-11D-A40P-10	2587656	59307787	74544108	77	32763										
C12orf43	64897	hgsc.bcm.edu	37	chr12	121448715	121448715	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	cgttgccatcttgttcatgcTcattcaccttatgcctacga	6	13	4	0			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr12:121448715T>A	ENST00000288757.3	-	3	225	c.203A>T	c.(202-204)gAg>gTg	p.E68V	C12orf43_ENST00000537817.1_Missense_Mutation_p.E69V|C12orf43_ENST00000366211.2_Missense_Mutation_p.E26V|C12orf43_ENST00000536407.2_Missense_Mutation_p.E68V|C12orf43_ENST00000539736.1_Missense_Mutation_p.E68V|C12orf43_ENST00000445832.3_Missense_Mutation_p.E38V	NM_022895.1	NP_075046.1	Q96C57	CL043_HUMAN	chromosome 12 open reading frame 43	68										cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)	14	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					TTGTTCATGCTCATTCACCTT	0.542																																					p.E68V		Atlas-SNP	.											.	C12orf43	30	.	0			c.A203T						.						220	186	197					12																	121448715		2203	4300	6503	SO:0001583	missense	64897	exon3			TCATGCTCATTCA	AK022510	CCDS66486.1, CCDS66487.1	12q24.31	2012-05-30			ENSG00000157895	ENSG00000157895			25719	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_001286195		Approved	FLJ12448	uc001tzh.1	Q96C57	OTTHUMG00000169150	ENST00000288757.3:c.203A>T	chr12.hg19:g.121448715T>A	ENSP00000288757:p.Glu68Val	118.0	0.0		147.0	56.0	NM_022895	Q53HF0|Q9H9Z7	Missense_Mutation	SNP	ENST00000288757.3	hg19	CCDS9210.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	17.23|17.23|17.23	3.336842|3.336842|3.336842	0.60963|0.60963|0.60963	.|.|.	.|.|.	ENSG00000157895|ENSG00000157895|ENSG00000157895	ENST00000445832;ENST00000288757;ENST00000537817;ENST00000366211;ENST00000539736;ENST00000535367|ENST00000546272|ENST00000536407	T;T;T;T|.|.	0.47177|.|.	0.85;0.85;0.85;0.85|.|.	5.53|5.53|5.53	5.53|5.53|5.53	0.82687|0.82687|0.82687	.|.|.	0.595405|.|.	0.19292|.|.	N|.|.	0.117871|.|.	T|T|.	0.47801|0.47801|.	0.1465|0.1465|.	M|M|M	0.64997|0.64997|0.64997	1.995|1.995|1.995	0.26468|0.26468|0.26468	N|N|N	0.975334|0.975334|0.975334	D;D;D;D;D|.|.	0.67145|.|.	0.996;0.996;0.996;0.996;0.996|.|.	P;P;P;P;P|.|.	0.62298|.|.	0.857;0.857;0.9;0.773;0.9|.|.	T|T|.	0.47459|0.47459|.	-0.9116|-0.9116|.	10|5|.	0.72032|.|.	D|.|.	0.01|.|.	-16.1759|-16.1759|-16.1759	8.2172|8.2172|8.2172	0.31519|0.31519|0.31519	0.0:0.153:0.0:0.847|0.0:0.153:0.0:0.847|0.0:0.153:0.0:0.847	.|.|.	68;26;69;68;68|.|.	G5EA44;F6TFQ5;F5H7W8;B4DWJ9;Q96C57|.|.	.;.;.;.;CL043_HUMAN|.|.	V|C|C	38;68;69;26;68;22|21|72	ENSP00000409788:E38V;ENSP00000288757:E68V;ENSP00000442224:E69V;ENSP00000437803:E68V|.|.	ENSP00000288757:E68V|.|.	E|S|X	-|-|-	2|1|3	0|0|0	C12orf43|C12orf43|C12orf43	119933098|119933098|119933098	0.970000|0.970000|0.970000	0.33590|0.33590|0.33590	0.807000|0.807000|0.807000	0.32361|0.32361|0.32361	0.710000|0.710000|0.710000	0.40934|0.40934|0.40934	2.059000|2.059000|2.059000	0.41384|0.41384|0.41384	2.112000|2.112000|2.112000	0.64535|0.64535|0.64535	0.460000|0.460000|0.460000	0.39030|0.39030|0.39030	GAG|AGC|TGA	.	.		0.542	C12orf43-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_022895		A	121448715	T	A	121448715	3	1	235	1	0	0	0	0	1	0	0	0	1691	1551	54	4	601	4	C12orf43	12	121448715	Missense_Mutation	SNP	T	TCGA-DD-AAW2-01A-11D-A40P-10	62140928	121448715	12403180	78	32764										
SCARB1	949	hgsc.bcm.edu	37	chr12	125299561	125299561	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	acgatgtagtcgctctccgaGccgtgggacttggagggctg	16	10	1	0			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr12:125299561G>A	ENST00000415380.2	-	3	509	c.384C>T	c.(382-384)ggC>ggT	p.G128G	SCARB1_ENST00000535005.1_5'UTR|SCARB1_ENST00000339570.5_Silent_p.G128G|SCARB1_ENST00000544327.1_Silent_p.G74G|SCARB1_ENST00000376788.1_Intron|SCARB1_ENST00000540495.1_Silent_p.G91G|SCARB1_ENST00000261693.6_Silent_p.G128G|SCARB1_ENST00000546215.1_Silent_p.G128G|SCARB1_ENST00000541205.1_Silent_p.G87G			Q8WTV0	SCRB1_HUMAN	scavenger receptor class B, member 1	128					adhesion of symbiont to host (GO:0044406)|androgen biosynthetic process (GO:0006702)|blood vessel endothelial cell migration (GO:0043534)|cell adhesion (GO:0007155)|cholesterol catabolic process (GO:0006707)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|detection of lipopolysaccharide (GO:0032497)|endothelial cell proliferation (GO:0001935)|high-density lipoprotein particle clearance (GO:0034384)|high-density lipoprotein particle remodeling (GO:0034375)|lipopolysaccharide transport (GO:0015920)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|recognition of apoptotic cell (GO:0043654)|regulation of phagocytosis (GO:0050764)|regulation of phosphatidylcholine catabolic process (GO:0010899)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)|viral process (GO:0016032)|wound healing (GO:0042060)	caveola (GO:0005901)|cell surface (GO:0009986)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein binding (GO:0034185)|high-density lipoprotein particle binding (GO:0008035)|high-density lipoprotein particle receptor activity (GO:0070506)|lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|prostate(1)	17	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000116)|Epithelial(86;0.000415)|all cancers(50;0.00395)	Phosphatidylserine(DB00144)	CGCTCTCCGAGCCGTGGGACT	0.607																																					p.G128G		Atlas-SNP	.											.	SCARB1	40	.	0			c.C384T						.						295	216	243					12																	125299561		2203	4300	6503	SO:0001819	synonymous_variant	949	exon3			CTCCGAGCCGTGG	Z22555	CCDS9259.1, CCDS45008.1	12q24.32	2008-08-05	2002-09-06	2002-09-06	ENSG00000073060	ENSG00000073060			1664	protein-coding gene	gene with protein product		601040	"CD36 antigen (collagen type I receptor, thrombospondin receptor)-like 1"	CD36L1		7689561	Standard	NM_001082959		Approved	SRB1, CLA-1, CLA1, SR-BI	uc001ugm.4	Q8WTV0	OTTHUMG00000168544	ENST00000415380.2:c.384C>T	chr12.hg19:g.125299561G>A		82.0	0.0		123.0	5.0	NM_005505	F8W8N0|Q14016|Q52LZ5|Q6KFX4	Silent	SNP	ENST00000415380.2	hg19																																																																																				.	.		0.607	SCARB1-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000400165.1	NM_005505		A	125299561	G	A	125299561	2	1	235	1	0	0	0	0	0	0	0	1	13896	958	34	3		3	SCARB1	12	125299561	Silent	SNP	G	TCGA-DD-AAW2-01A-11D-A40P-10	3850846	125299561	8552334	79	32765										
ATP12A	479	hgsc.bcm.edu	37	chr13	25255721	25255721	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	aaaccccagaaatttactccGtggagctcagcggaactaag	9	11	1	1			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr13:25255721G>A	ENST00000381946.3	+	2	198	c.31G>A	c.(31-33)Gtg>Atg	p.V11M	ATP12A_ENST00000218548.6_Missense_Mutation_p.V11M			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	11					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		AATTTACTCCGTGGAGCTCAG	0.517																																					p.V11M	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-SNP	.											.	ATP12A	172	.	0			c.G31A						.						64	66	66					13																	25255721		2203	4300	6503	SO:0001583	missense	479	exon2			TACTCCGTGGAGC	L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"ATPases / P-type"	13816	protein-coding gene	gene with protein product	"ATPase, Na+K+ transporting, alpha-1 polypeptide-like", "potassium-transporting ATPase alpha chain 2", "proton pump", "non-gastric H(+)/K(+) ATPase alpha subunit", "sodium/potassium ATPase, alpha polypeptide-like"	182360	"ATPase, Na+/K+ transporting, alpha polypeptide-like 1"	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.31G>A	chr13.hg19:g.25255721G>A	ENSP00000371372:p.Val11Met	225.0	0.0		261.0	14.0	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Missense_Mutation	SNP	ENST00000381946.3	hg19	CCDS31948.1	.	.	.	.	.	.	.	.	.	.	G	15.07	2.723645	0.48728	.	.	ENSG00000075673	ENST00000218548;ENST00000381946	D;D	0.93659	-3.26;-3.26	5.21	4.29	0.51040	.	4.421500	0.00604	N	0.000384	D	0.92241	0.7539	N	0.08118	0	0.38326	D	0.943652	D;D	0.64830	0.994;0.977	P;P	0.58928	0.848;0.483	D	0.85080	0.0945	10	0.66056	D	0.02	.	10.5599	0.45140	0.1008:0.0:0.8992:0.0	.	11;11	P54707-2;P54707	.;AT12A_HUMAN	M	11	ENSP00000218548:V11M;ENSP00000371372:V11M	ENSP00000218548:V11M	V	+	1	0	ATP12A	24153721	0.983000	0.35010	0.996000	0.52242	0.264000	0.26372	1.860000	0.39428	2.716000	0.92895	0.650000	0.86243	GTG	.	.		0.517	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676		A	25255721	G	A	25255721	3	1	235	1	0	0	0	0	1	0	0	0	1122	1145	40	1	37	1	ATP12A	13	25255721	Missense_Mutation	SNP	G	TCGA-DD-AAW2-01A-11D-A40P-10		25255721	89914157	80	32766										
KLHL1	57626	hgsc.bcm.edu	37	chr13	70314528	70314528	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	agaaaaaaatttacttacttGccattcaatgctgctacacc	4	10	1	1			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr13:70314528G>T	ENST00000377844.4	-	8	2559	c.1800C>A	c.(1798-1800)ggC>ggA	p.G600G	KLHL1_ENST00000545028.1_Silent_p.G407G	NM_020866.2	NP_065917.1	Q9NR64	KLHL1_HUMAN	kelch-like family member 1	600					actin cytoskeleton organization (GO:0030036)|adult walking behavior (GO:0007628)|cerebellar Purkinje cell layer development (GO:0021680)|dendrite development (GO:0016358)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	actin binding (GO:0003779)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(56)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	84		Breast(118;0.000162)		COAD - Colon adenocarcinoma(199;0.000193)|GBM - Glioblastoma multiforme(99;0.000211)		TTACTTACTTGCCATTCAATG	0.313																																					p.G600G		Atlas-SNP	.											.	KLHL1	164	.	0			c.C1800A						.						57	51	53					13																	70314528		2203	4299	6502	SO:0001819	synonymous_variant	57626	exon8			TTACTTGCCATTC	AB040923	CCDS9445.1, CCDS73582.1	13q21	2013-01-30	2013-01-30		ENSG00000150361	ENSG00000150361		"Kelch-like", "BTB/POZ domain containing"	6352	protein-coding gene	gene with protein product	"Kelch-like protein 1", "Mayven-related protein 2"	605332	"kelch (Drosophila)-like 1", "kelch-like 1 (Drosophila)"			10888605	Standard	NM_020866		Approved	KIAA1490, MRP2, FLJ30047	uc001vip.3	Q9NR64	OTTHUMG00000017056	ENST00000377844.4:c.1800C>A	chr13.hg19:g.70314528G>T		56.0	0.0		51.0	34.0	NM_020866	A8K5X0|Q5VZ64|Q9H4X4|Q9NR65|Q9P238	Silent	SNP	ENST00000377844.4	hg19	CCDS9445.1																																																																																			.	.		0.313	KLHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045231.3	NM_020866		T	70314528	G	T	70314528	2	4	235	1	0	0	0	0	0	0	0	1	8374	1306	46	3		3	KLHL1	13	70314528	Silent	SNP	G	TCGA-DD-AAW2-01A-11D-A40P-10	45058807	70314528	44855350	81	32767										
MYO16	23026	hgsc.bcm.edu	37	chr13	109644729	109644729	+	Frame_Shift_Del	DEL	A	A	-													0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	attgttttgtttcagcatgcAgacattggatattggaatat							TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr13:109644729delA	ENST00000357550.2	+	20	2350	c.2309delA	c.(2308-2310)cagfs	p.Q770fs	MYO16_ENST00000251041.5_Frame_Shift_Del_p.Q770fs|MYO16_ENST00000457511.2_Frame_Shift_Del_p.Q282fs|MYO16_ENST00000356711.2_Frame_Shift_Del_p.Q770fs	NM_001198950.1	NP_001185879.1			myosin XVI											NS(3)|breast(4)|central_nervous_system(2)|endometrium(10)|kidney(8)|large_intestine(27)|lung(51)|ovary(9)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	121	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			TTCAGCATGCAGACATTGGAT	0.338																																					p.Q792fs		Atlas-INDEL	.											.	MYO16	285	.	0			c.2374delC						.						177	166	170					13																	109644729		2202	4299	6501	SO:0001589	frameshift_variant	23026	exon21			.		CCDS32008.1, CCDS73598.1	13q33.3	2014-06-12			ENSG00000041515	ENSG00000041515		"Myosins / Myosin superfamily : Class XVI", "Ankyrin repeat domain containing"	29822	protein-coding gene	gene with protein product	"neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 3", "protein phosphatase 1, regulatory subunit 107"	615479				11588169, 17029291, 21946561	Standard	NM_001198950		Approved	MYR8, KIAA0865, Myo16b, NYAP3, PPP1R107	uc001vqt.1	Q9Y6X6	OTTHUMG00000017333	ENST00000357550.2:c.2309delA	chr13.hg19:g.109644729delA	ENSP00000350160:p.Gln770fs	79.0	0.0		85.0	37.0	NM_001198950		Frame_Shift_Del	DEL	ENST00000357550.2	hg19	CCDS32008.1																																																																																			.	.		0.338	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011		-	109644729	A	-	109644729	7	5	235	1	0	1	0	1	0	0	0	0	10073	188	7	0	2387	0	MYO16	13	109644729	Frame_Shift_Del	DEL	A	TCGA-DD-AAW2-01A-11D-A40P-10	39330201	109644729	5525149	82	32768										
RTN1	6252	hgsc.bcm.edu	37	chr14	60212848	60212848	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	cctcctcgggtctggttatgTcaatgtatttataggcctct	9	10	3	0			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr14:60212848T>A	ENST00000267484.5	-	2	928	c.593A>T	c.(592-594)gAc>gTc	p.D198V		NM_021136.2	NP_066959.1	Q16799	RTN1_HUMAN	reticulon 1	198					neuron differentiation (GO:0030182)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)		p.D198G(1)		central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(30)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(108;0.0968)		TCTGGTTATGTCAATGTATTT	0.448																																					p.D198V		Atlas-SNP	.											RTN1,NS,carcinoma,0,1	RTN1	139	.	1	Substitution - Missense(1)	kidney(1)	c.A593T						.						230	225	227					14																	60212848		2203	4300	6503	SO:0001583	missense	6252	exon2			GTTATGTCAATGT	L10333	CCDS9740.1, CCDS9741.1	14q21-q22	2008-08-29			ENSG00000139970	ENSG00000139970			10467	protein-coding gene	gene with protein product		600865	"neuroendocrine-specific protein"	NSP		8275708	Standard	NM_206852		Approved		uc001xen.1	Q16799	OTTHUMG00000028947	ENST00000267484.5:c.593A>T	chr14.hg19:g.60212848T>A	ENSP00000267484:p.Asp198Val	108.0	0.0		107.0	26.0	NM_021136	Q16800|Q16801|Q5BKZ4|Q9BQ59	Missense_Mutation	SNP	ENST00000267484.5	hg19	CCDS9740.1	.	.	.	.	.	.	.	.	.	.	T	19.92	3.917192	0.73098	.	.	ENSG00000139970	ENST00000267484;ENST00000433623	T	0.39592	1.07	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.66557	0.2801	M	0.77103	2.36	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.71111	-0.4687	10	0.87932	D	0	.	15.9506	0.79830	0.0:0.0:0.0:1.0	.	198	Q16799	RTN1_HUMAN	V	198;124	ENSP00000267484:D198V	ENSP00000267484:D198V	D	-	2	0	RTN1	59282601	1.000000	0.71417	0.992000	0.48379	0.839000	0.47603	5.887000	0.69751	2.171000	0.68590	0.455000	0.32223	GAC	.	.		0.448	RTN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000072278.2			A	60212848	T	A	60212848	3	1	235	1	0	0	0	0	1	0	0	0	13740	1667	58	4	1834	4	RTN1	14	60212848	Missense_Mutation	SNP	T	TCGA-DD-AAW2-01A-11D-A40P-10		60212848	47136692	83	32769										
OR4M2	390538	hgsc.bcm.edu	37	chr15	22368845	22368845	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	gacttctttgtggagaggaaGataatttcttttgatggatg	12	3	2	3			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr15:22368845G>C	ENST00000332663.2	+	1	368	c.270G>C	c.(268-270)aaG>aaC	p.K90N	RP11-69H14.6_ENST00000558896.1_RNA	NM_001004719.2	NP_001004719.2	Q8NGB6	OR4M2_HUMAN	olfactory receptor, family 4, subfamily M, member 2	90						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|endometrium(2)|kidney(4)|large_intestine(6)|lung(38)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	63		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		TGGAGAGGAAGATAATTTCTT	0.438																																					p.K90N		Atlas-SNP	.											.	OR4M2	140	.	0			c.G270C						.						344	292	309					15																	22368845		2203	4300	6503	SO:0001583	missense	390538	exon1			GAGGAAGATAATT	AC060768	CCDS32172.1	15q11.2	2013-09-23			ENSG00000182974	ENSG00000182974		"GPCR / Class A : Olfactory receptors"	15373	protein-coding gene	gene with protein product							Standard	NM_001004719		Approved		uc010tzu.2	Q8NGB6	OTTHUMG00000171738	ENST00000332663.2:c.270G>C	chr15.hg19:g.22368845G>C	ENSP00000329467:p.Lys90Asn	180.0	0.0		175.0	55.0	NM_001004719	B9EH16|Q6IEY2	Missense_Mutation	SNP	ENST00000332663.2	hg19	CCDS32172.1	.	.	.	.	.	.	.	.	.	.	.	13.71	2.317630	0.40996	.	.	ENSG00000182974	ENST00000332663	T	0.38240	1.15	2.5	2.5	0.30297	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49305	D	0.000142	T	0.55784	0.1942	M	0.76170	2.325	0.09310	N	1	D	0.89917	1.0	D	0.76071	0.987	T	0.43686	-0.9376	10	0.66056	D	0.02	-11.6614	10.8078	0.46529	0.0:0.0:1.0:0.0	.	90	Q8NGB6	OR4M2_HUMAN	N	90	ENSP00000329467:K90N	ENSP00000329467:K90N	K	+	3	2	OR4M2	19870209	0.004000	0.15560	0.953000	0.39169	0.939000	0.58152	-0.116000	0.10724	1.422000	0.47177	0.448000	0.29417	AAG	.	.		0.438	OR4M2-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414921.1			C	22368845	G	C	22368845	3	2	235	1	0	0	0	0	1	0	0	0	11085	933	33	4	272	4	OR4M2	15	22368845	Missense_Mutation	SNP	G	TCGA-DD-AAW2-01A-11D-A40P-10		22368845	80162547	84	32770										
APBA2	321	hgsc.bcm.edu	37	chr15	29346270	29346270	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	agccccgcgccagaggaacaGgagtgccacaaccacagccc	11	17	0	1			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr15:29346270G>A	ENST00000558402.1	+	5	782	c.183G>A	c.(181-183)caG>caA	p.Q61Q	APBA2_ENST00000558330.1_Silent_p.Q61Q|APBA2_ENST00000558259.1_Silent_p.Q61Q|APBA2_ENST00000561069.1_Silent_p.Q61Q|APBA2_ENST00000411764.1_Silent_p.Q61Q			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	61					in utero embryonic development (GO:0001701)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|liver(2)|lung(33)|stomach(1)|urinary_tract(1)	59		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		CAGAGGAACAGGAGTGCCACA	0.657																																					p.Q61Q		Atlas-SNP	.											.	APBA2	132	.	0			c.G183A						.						71	82	78					15																	29346270		2203	4300	6503	SO:0001819	synonymous_variant	321	exon3			GGAACAGGAGTGC	AB014719	CCDS10022.1, CCDS45197.1	15q11-q12	2008-07-18	2008-07-18		ENSG00000034053	ENSG00000034053			579	protein-coding gene	gene with protein product		602712	"X11-like", "amyloid beta (A4) precursor protein-binding, family A, member 2 (X11-like)"	X11L, MINT2		8955346	Standard	NM_005503		Approved	D15S1518E, LIN-10, MGC:14091, HsT16821	uc001zck.3	Q99767	OTTHUMG00000129255	ENST00000558402.1:c.183G>A	chr15.hg19:g.29346270G>A		129.0	0.0		221.0	110.0	NM_005503	E9PGI4|O60571|Q5XKC0	Silent	SNP	ENST00000558402.1	hg19	CCDS10022.1																																																																																			.	.		0.657	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503		A	29346270	G	A	29346270	2	1	235	1	0	0	0	0	0	0	0	1	757	991	35	3		3	APBA2	15	29346270	Silent	SNP	G	TCGA-DD-AAW2-01A-11D-A40P-10	6977425	29346270	73185122	85	32771										
C15orf23	90417	hgsc.bcm.edu	37	chr15	40675151	40675151	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	ggaagtttctatttgaaaccCaggcggccgacttagccggt	12	10	1	1			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr15:40675151C>T	ENST00000249776.8	+	1	230	c.115C>T	c.(115-117)Cag>Tag	p.Q39*	KNSTRN_ENST00000416151.2_Nonsense_Mutation_p.Q39*|KNSTRN_ENST00000608100.1_5'UTR|KNSTRN_ENST00000448395.2_Nonsense_Mutation_p.Q39*	NM_033286.3	NP_150628.3			kinetochore-localized astrin/SPAG5 binding protein																		ATTTGAAACCCAGGCGGCCGA	0.592																																					p.Q39X		Atlas-SNP	.											.	.	.	.	0			c.C115T						.						53	59	57					15																	40675151		1852	4094	5946	SO:0001587	stop_gained	90417	exon1			GAAACCCAGGCGG	AK027408	CCDS42021.1, CCDS45226.1, CCDS45227.1	15q15.1	2013-01-17	2012-12-04	2012-12-04	ENSG00000128944	ENSG00000128944			30767	protein-coding gene	gene with protein product	"small kinetochore-associated protein", "kinetochore-localized astrin-binding protein", "TRAF4 associated factor 1"	614718	"chromosome 15 open reading frame 23"	C15orf23		12477932	Standard	NM_033286		Approved	FLJ14502, SKAP, kinastrin, TRAF4AF1	uc001zll.3	Q9Y448	OTTHUMG00000172454	ENST00000249776.8:c.115C>T	chr15.hg19:g.40675151C>T	ENSP00000249776:p.Gln39*	63.0	0.0		105.0	42.0	NM_033286		Nonsense_Mutation	SNP	ENST00000249776.8	hg19	CCDS42021.1	.	.	.	.	.	.	.	.	.	.	C	16.16	3.043118	0.55003	.	.	ENSG00000128944	ENST00000249776;ENST00000416151;ENST00000448395	.	.	.	4.77	0.634	0.17718	.	1.943820	0.02223	N	0.064168	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.21540	T	0.41	-1.5582	14.7288	0.69365	0.0:0.4704:0.5296:0.0	.	.	.	.	X	39	.	ENSP00000249776:Q39X	Q	+	1	0	C15orf23	38462443	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-0.133000	0.10451	0.036000	0.15547	-0.128000	0.14901	CAG	.	.		0.592	KNSTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418636.1	NM_001142761		T	40675151	C	T	40675151	4	4	235	1	0	0	0	0	0	1	0	0	1787	595	21	3	117	3	C15orf23	15	40675151	Nonsense_Mutation	SNP	C	TCGA-DD-AAW2-01A-11D-A40P-10	11328881	40675151	61856241	86	32772										
SPG11	80208	hgsc.bcm.edu	37	chr15	44876651	44876651	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	agaagctgctttgcttgaaaTtgaatttttcttaaaattct	6	5	2	3			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr15:44876651T>C	ENST00000261866.7	-	30	5243	c.5227A>G	c.(5227-5229)Att>Gtt	p.I1743V	SPG11_ENST00000535302.2_Missense_Mutation_p.I1743V|SPG11_ENST00000558319.1_Missense_Mutation_p.I1743V|SPG11_ENST00000427534.2_Missense_Mutation_p.I1743V|SPG11_ENST00000558253.1_5'Flank	NM_025137.3	NP_079413.3	Q96JI7	SPTCS_HUMAN	spastic paraplegia 11 (autosomal recessive)	1743					cell death (GO:0008219)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	72		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		TTGCTTGAAATTGAATTTTTC	0.438																																					p.I1743V		Atlas-SNP	.											.	SPG11	207	.	0			c.A5227G						.						49	55	53					15																	44876651		2198	4298	6496	SO:0001583	missense	80208	exon30			TTGAAATTGAATT		CCDS10112.1, CCDS53939.1	15q13-q15	2007-11-13			ENSG00000104133	ENSG00000104133			11226	protein-coding gene	gene with protein product	"spatacsin"	610844	"KIAA1840"	KIAA1840		10408536, 17322883	Standard	NM_001160227		Approved	FLJ21439	uc001ztx.3	Q96JI7	OTTHUMG00000131199	ENST00000261866.7:c.5227A>G	chr15.hg19:g.44876651T>C	ENSP00000261866:p.Ile1743Val	103.0	0.0		92.0	50.0	NM_025137	A8KAX9|B9EK60|F5H3N6|Q4VC11|Q58G86|Q69YG6|Q6NW01|Q8N270|Q8TBU9|Q9H734	Missense_Mutation	SNP	ENST00000261866.7	hg19	CCDS10112.1	.	.	.	.	.	.	.	.	.	.	T	1.527	-0.545263	0.04024	.	.	ENSG00000104133	ENST00000261866;ENST00000535302;ENST00000427534	T;T;T	0.74106	-0.81;-0.55;-0.55	5.74	-1.91	0.07641	.	0.538736	0.20039	N	0.100560	T	0.52709	0.1751	N	0.26130	0.795	0.80722	D	1	B;B;B;B	0.10296	0.003;0.002;0.003;0.003	B;B;B;B	0.09377	0.003;0.004;0.003;0.003	T	0.47711	-0.9096	10	0.05620	T	0.96	.	11.9132	0.52751	0.0:0.5039:0.0:0.4961	.	1743;1743;1743;1743	C4B7M2;F5H3N6;C4B7M4;Q96JI7	.;.;.;SPTCS_HUMAN	V	1743	ENSP00000261866:I1743V;ENSP00000445278:I1743V;ENSP00000396110:I1743V	ENSP00000261866:I1743V	I	-	1	0	SPG11	42663943	0.528000	0.26314	0.969000	0.41365	0.310000	0.27922	0.030000	0.13688	-0.360000	0.08138	0.455000	0.32223	ATT	.	.		0.438	SPG11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253927.1			C	44876651	T	C	44876651	3	2	235	1	0	0	0	0	1	0	0	0	15056	1493	52	2	2148	2	SPG11	15	44876651	Missense_Mutation	SNP	T	TCGA-DD-AAW2-01A-11D-A40P-10	4201500	44876651	57654741	87	32773										
DUOX2	50506	hgsc.bcm.edu	37	chr15	45404147	45404147	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	tcaccacgtcggaaagaacaTggtagcctgcgggcatgggg	15	10	1	1			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr15:45404147T>C	ENST00000603300.1	-	5	534	c.332A>G	c.(331-333)cAt>cGt	p.H111R	DUOXA2_ENST00000323030.5_5'Flank|DUOX2_ENST00000389039.6_Missense_Mutation_p.H111R	NM_014080.4	NP_054799.4	Q9NRD8	DUOX2_HUMAN	dual oxidase 2	111	Peroxidase-like; mediates peroxidase activity. {ECO:0000250}.				adenohypophysis morphogenesis (GO:0048855)|bone mineralization (GO:0030282)|cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|fertilization (GO:0009566)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|inner ear development (GO:0048839)|multicellular organism growth (GO:0035264)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|response to virus (GO:0009615)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|peroxidase activity (GO:0004601)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	63		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		GGAAAGAACATGGTAGCCTGC	0.642																																					p.H111R		Atlas-SNP	.											.	DUOX2	137	.	0			c.A332G						.						27	27	27					15																	45404147		2198	4298	6496	SO:0001583	missense	50506	exon5			AGAACATGGTAGC	AF181972	CCDS10117.1	15q15.3-q21	2013-01-10			ENSG00000140279	ENSG00000140279		"EF-hand domain containing"	13273	protein-coding gene	gene with protein product	"dual oxidase-like domains 2", "nicotinamide adenine dinucleotide phosphate oxidase", "flavoprotein NADPH oxidase", "NADPH thyroid oxidase 2", "NADH/NADPH thyroid oxidase p138-tox", "NADPH oxidase/peroxidase DUOX2"	606759				10601291, 10806195	Standard	NM_014080		Approved	P138-TOX, P138(TOX), THOX2, LNOX2	uc010bea.3	Q9NRD8	OTTHUMG00000131355	ENST00000603300.1:c.332A>G	chr15.hg19:g.45404147T>C	ENSP00000475084:p.His111Arg	156.0	0.0		191.0	90.0	NM_014080	A8MQ13|D2XI64|Q9NR02|Q9UHF9	Missense_Mutation	SNP	ENST00000603300.1	hg19	CCDS10117.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.294574	0.81025	.	.	ENSG00000140279	ENST00000389039	.	.	.	5.22	4.06	0.47325	.	0.000000	0.85682	D	0.000000	T	0.78991	0.4371	M	0.87038	2.855	0.80722	D	1	D	0.58970	0.984	D	0.65684	0.937	T	0.80334	-0.1426	9	0.56958	D	0.05	-27.9211	11.3871	0.49791	0.0:0.0:0.1517:0.8483	.	111	Q9NRD8	DUOX2_HUMAN	R	111	.	ENSP00000373691:H111R	H	-	2	0	DUOX2	43191439	1.000000	0.71417	1.000000	0.80357	0.863000	0.49368	7.980000	0.88113	0.800000	0.34041	0.459000	0.35465	CAT	.	.		0.642	DUOX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_014080		C	45404147	T	C	45404147	3	2	235	1	0	0	0	0	1	0	0	0	4803	1464	51	2	4434	2	DUOX2	15	45404147	Missense_Mutation	SNP	T	TCGA-DD-AAW2-01A-11D-A40P-10	527496	45404147	57127245	88	32774										
CRTC3	64784	hgsc.bcm.edu	37	chr15	91181991	91181991	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	catctttgaccaacttcttcCcagatgtgggttttgaccag	8	11	2	3			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr15:91181991C>T	ENST00000268184.6	+	13	1496	c.1492C>T	c.(1492-1494)Cca>Tca	p.P498S	CRTC3_ENST00000420329.2_Missense_Mutation_p.P498S|RP11-387D10.2_ENST00000559531.1_RNA			Q6UUV7	CRTC3_HUMAN	CREB regulated transcription coactivator 3	498					energy homeostasis (GO:0097009)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of lipid catabolic process (GO:0050995)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cAMP response element binding protein binding (GO:0008140)		CRTC3/MAML2(26)	breast(1)|endometrium(4)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|urinary_tract(1)	20	Melanoma(11;0.00551)|Lung NSC(78;0.0931)|all_lung(78;0.163)		BRCA - Breast invasive adenocarcinoma(143;0.0745)			CAACTTCTTCCCAGATGTGGG	0.522			T	MAML2	salivary gland mucoepidermoid																																p.P498S		Atlas-SNP	.		Dom	yes		15	15q26.1	64784	CREB regulated transcription coactivator 3		E	.	CRTC3	47	.	0			c.C1492T						.						126	114	118					15																	91181991		2198	4298	6496	SO:0001583	missense	64784	exon13			TTCTTCCCAGATG		CCDS32331.1, CCDS45348.1	15q26.1	2005-11-24				ENSG00000140577			26148	protein-coding gene	gene with protein product		608986				14536081, 14506290	Standard	NM_022769		Approved	FLJ21868	uc002bpp.4	Q6UUV7		ENST00000268184.6:c.1492C>T	chr15.hg19:g.91181991C>T	ENSP00000268184:p.Pro498Ser	87.0	0.0		93.0	40.0	NM_022769	Q6DK61|Q6DK62|Q8NF38|Q9H6U2	Missense_Mutation	SNP	ENST00000268184.6	hg19	CCDS32331.1	.	.	.	.	.	.	.	.	.	.	C	8.575	0.880977	0.17467	.	.	ENSG00000140577	ENST00000437186;ENST00000268184;ENST00000420329	T;T	0.11277	2.8;2.79	5.46	4.54	0.55810	.	0.763029	0.13278	N	0.399945	T	0.08088	0.0202	L	0.35414	1.06	0.28992	N	0.888007	B;B	0.09022	0.001;0.002	B;B	0.10450	0.002;0.005	T	0.31110	-0.9955	10	0.06625	T	0.88	-4.4159	10.3229	0.43777	0.0:0.9111:0.0:0.0889	.	498;498	Q6UUV7;Q6UUV7-3	CRTC3_HUMAN;.	S	462;498;498	ENSP00000268184:P498S;ENSP00000416573:P498S	ENSP00000268184:P498S	P	+	1	0	CRTC3	88982995	0.902000	0.30710	0.940000	0.37924	0.788000	0.44548	1.938000	0.40203	1.545000	0.49373	0.591000	0.81541	CCA	.	.		0.522	CRTC3-001	KNOWN	NAGNAG_splice_site|non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417716.2	NM_022769		T	91181991	C	T	91181991	3	4	235	1	0	0	0	0	1	0	0	0	3903	623	22	3	1542	3	CRTC3	15	91181991	Missense_Mutation	SNP	C	TCGA-DD-AAW2-01A-11D-A40P-10	45777844	91181991	11349401	89	32775										
BTBD12	84464	hgsc.bcm.edu	37	chr16	3647563	3647563	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	ctgctggcaggaagtggtggCgtgctagacaattccacttc	13	10	0	1			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr16:3647563C>A	ENST00000294008.3	-	7	2140	c.1500G>T	c.(1498-1500)acG>acT	p.T500T		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	500	Interaction with SLX4IP, ERCC4 and MSH2.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						GAAGTGGTGGCGTGCTAGACA	0.572								Direct reversal of damage																													p.T500T		Atlas-SNP	.											.	SLX4	173	.	0			c.G1500T						.						78	76	77					16																	3647563		2197	4300	6497	SO:0001819	synonymous_variant	84464	exon7			TGGTGGCGTGCTA	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"Fanconi anemia, complementation groups", "BTB/POZ domain containing"	23845	protein-coding gene	gene with protein product	"Fanconi anemia, complementation group P"	613278	"BTB (POZ) domain containing 12", "SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.1500G>T	chr16.hg19:g.3647563C>A		92.0	0.0		111.0	53.0	NM_032444	Q69YT8|Q8TF15|Q96JP1	Silent	SNP	ENST00000294008.3	hg19	CCDS10506.2																																																																																			.	.		0.572	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444		A	3647563	C	A	3647563	2	1	235	1	0	0	0	0	0	0	0	1	1542	755	27	1		1	BTBD12	16	3647563	Silent	SNP	C	TCGA-DD-AAW2-01A-11D-A40P-10		3647563	86707190	90	32776										
SPNS1	83985	hgsc.bcm.edu	37	chr16	28986482	28986482	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	cccccgggaccatggccgggTccgacaccgcgcccttcctc	11	21	0	0			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr16:28986482T>C	ENST00000311008.11	+	1	387	c.10T>C	c.(10-12)Tcc>Ccc	p.S4P	RP11-264B17.3_ENST00000569969.1_RNA|SPNS1_ENST00000334536.8_Missense_Mutation_p.S4P|SPNS1_ENST00000352260.7_Missense_Mutation_p.S4P|SPNS1_ENST00000565975.1_Missense_Mutation_p.S49P|RP11-264B17.4_ENST00000567209.1_RNA|SPNS1_ENST00000323081.8_Intron	NM_032038.2	NP_114427.1	Q9H2V7	SPNS1_HUMAN	spinster homolog 1 (Drosophila)	4					lipid transport (GO:0006869)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrial inner membrane (GO:0005743)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)|urinary_tract(1)	21						CATGGCCGGGTCCGACACCGC	0.736																																					p.S4P		Atlas-SNP	.											.	SPNS1	47	.	0			c.T10C						.						2	3	3					16																	28986482		1626	3333	4959	SO:0001583	missense	83985	exon1			GCCGGGTCCGACA	BC006156	CCDS10646.1, CCDS45452.1, CCDS45453.1, CCDS45454.1	16p11.2	2007-04-12			ENSG00000169682	ENSG00000169682			30621	protein-coding gene	gene with protein product		612583				11340170, 12815463	Standard	NM_032038		Approved	HSpin1, nrs, SPINL, PP2030, SPIN1, LAT	uc010vdi.1	Q9H2V7	OTTHUMG00000131762	ENST00000311008.11:c.10T>C	chr16.hg19:g.28986482T>C	ENSP00000309945:p.Ser4Pro	42.0	0.0		39.0	17.0	NM_001142451	B5MDM9|Q6P182|Q71RB5|Q7L541|Q86VU7|Q8N953|Q8TCS5|Q9BRN5	Missense_Mutation	SNP	ENST00000311008.11	hg19	CCDS10646.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.451786	0.84209	.	.	ENSG00000169682	ENST00000311008;ENST00000334536;ENST00000352260	T;T;T	0.33865	1.8;1.41;1.39	4.27	1.94	0.25998	.	0.265993	0.31709	N	0.007195	T	0.30510	0.0767	N	0.08118	0	0.29604	N	0.847475	B;D;D;B	0.57899	0.001;0.967;0.981;0.0	B;D;D;B	0.68621	0.002;0.91;0.959;0.002	T	0.08994	-1.0695	10	0.62326	D	0.03	.	3.7767	0.08663	0.0:0.1159:0.2247:0.6594	.	4;4;4;4	Q9H2V7-3;Q9H2V7;Q9H2V7-2;Q9H2V7-5	.;SPNS1_HUMAN;.;.	P	4	ENSP00000309945:S4P;ENSP00000335494:S4P;ENSP00000306050:S4P	ENSP00000309945:S4P	S	+	1	0	SPNS1	28893983	0.999000	0.42202	1.000000	0.80357	0.932000	0.56968	0.608000	0.24223	0.734000	0.32515	0.459000	0.35465	TCC	.	.		0.736	SPNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254690.2	NM_032038		C	28986482	T	C	28986482	3	2	235	1	0	0	0	0	1	0	0	0	15089	1667	58	2	12	2	SPNS1	16	28986482	Missense_Mutation	SNP	T	TCGA-DD-AAW2-01A-11D-A40P-10	25338919	28986482	61368271	91	32777										
TMCO7	79613	hgsc.bcm.edu	37	chr16	68894026	68894026	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	tgaaggaaaccatgatccgcCttgcagctaatttcaatcca	7	11	1	2			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr16:68894026C>T	ENST00000261778.1	+	2	346	c.334C>T	c.(334-336)Ctt>Ttt	p.L112F		NM_024562.1	NP_078838.1	Q9C0B7	TNG6_HUMAN	transport and golgi organization 6 homolog (Drosophila)	112						integral component of membrane (GO:0016021)											CATGATCCGCCTTGCAGCTAA	0.473																																					p.L112F		Atlas-SNP	.											.	.	.	.	0			c.C334T						.						191	184	187					16																	68894026		1954	4154	6108	SO:0001583	missense	79613	exon2			ATCCGCCTTGCAG		CCDS45516.1	16q22.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000103047	ENSG00000103047			25749	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 7"	TMCO7		11214970	Standard	NM_024562		Approved	FLJ12688, KIAA1746	uc002ewi.4	Q9C0B7	OTTHUMG00000176743	ENST00000261778.1:c.334C>T	chr16.hg19:g.68894026C>T	ENSP00000261778:p.Leu112Phe	114.0	0.0		114.0	47.0	NM_024562	Q569F9|Q9H9K1	Missense_Mutation	SNP	ENST00000261778.1	hg19	CCDS45516.1	.	.	.	.	.	.	.	.	.	.	C	13.95	2.390203	0.42410	.	.	ENSG00000103047	ENST00000261778	.	.	.	5.41	5.41	0.78517	.	.	.	.	.	T	0.76169	0.3950	M	0.72118	2.19	0.41450	D	0.987974	D	0.76494	0.999	D	0.85130	0.997	T	0.77373	-0.2612	8	0.52906	T	0.07	-5.1723	11.475	0.50293	0.0:0.9166:0.0:0.0834	.	112	Q9C0B7	TMCO7_HUMAN	F	112	.	ENSP00000261778:L112F	L	+	1	0	TMCO7	67451527	0.813000	0.29090	0.729000	0.30791	0.213000	0.24496	1.496000	0.35638	2.548000	0.85928	0.561000	0.74099	CTT	.	.		0.473	TANGO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433471.2	XM_928235.2		T	68894026	C	T	68894026	3	4	235	1	0	0	0	0	1	0	0	0	16016	681	24	3	340	3	TMCO7	16	68894026	Missense_Mutation	SNP	C	TCGA-DD-AAW2-01A-11D-A40P-10	39907544	68894026	21460727	92	32778										
NQO1	1728	hgsc.bcm.edu	37	chr16	69752318	69752318	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	gggattgaagttcatggcatAgaggtccgactccaccacct	11	11	1	2			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr16:69752318A>C	ENST00000320623.5	-	2	638	c.127T>G	c.(127-129)Tat>Gat	p.Y43D	NQO1_ENST00000379047.3_Missense_Mutation_p.Y43D|NQO1_ENST00000561500.1_Missense_Mutation_p.Y43D|NQO1_ENST00000379046.2_Missense_Mutation_p.Y43D|NQO1_ENST00000439109.2_Missense_Mutation_p.Y43D|NQO1_ENST00000564043.1_Missense_Mutation_p.Y22D	NM_000903.2	NP_000894.1	P15559	NQO1_HUMAN	NAD(P)H dehydrogenase, quinone 1	43					aging (GO:0007568)|cellular nitrogen compound metabolic process (GO:0034641)|negative regulation of catalytic activity (GO:0043086)|nitric oxide biosynthetic process (GO:0006809)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cellular amino acid metabolic process (GO:0006521)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to nutrient (GO:0007584)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|synaptic transmission, cholinergic (GO:0007271)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|NAD(P)H dehydrogenase (quinone) activity (GO:0003955)|poly(A) RNA binding (GO:0044822)|superoxide dismutase activity (GO:0004784)			autonomic_ganglia(1)|large_intestine(2)|lung(5)|prostate(1)|stomach(1)	10					Carboplatin(DB00958)|Cisplatin(DB00515)|Dicoumarol(DB00266)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|Menadione(DB00170)|Oxaliplatin(DB00526)|Vitamin E(DB00163)	TTCATGGCATAGAGGTCCGAC	0.507																																					p.Y43D		Atlas-SNP	.											.	NQO1	21	.	0			c.T127G						.						124	115	118					16																	69752318		2198	4300	6498	SO:0001583	missense	1728	exon2			TGGCATAGAGGTC	M81600	CCDS10883.1, CCDS32471.1, CCDS32472.1, CCDS67067.1	16q12-q22	2012-10-02	2001-11-30	2001-12-07	ENSG00000181019	ENSG00000181019	1.6.5.2		2874	protein-coding gene	gene with protein product		125860	"diaphorase (NADH/NADPH) (cytochrome b-5 reductase)"	NMOR1, DIA4		2843525	Standard	NM_001286137		Approved	DHQU, QR1, DTD	uc002exp.3	P15559	OTTHUMG00000137575	ENST00000320623.5:c.127T>G	chr16.hg19:g.69752318A>C	ENSP00000319788:p.Tyr43Asp	85.0	0.0		97.0	46.0	NM_000903	B2R5Y9|B4DNM7|B7ZAD1|Q86UK1	Missense_Mutation	SNP	ENST00000320623.5	hg19	CCDS10883.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.447327	0.84101	.	.	ENSG00000181019	ENST00000320623;ENST00000379047;ENST00000379046;ENST00000439109	T;T;T;T	0.10192	2.9;2.9;2.9;2.9	6.02	4.92	0.64577	Flavodoxin-like fold (1);	0.053569	0.85682	D	0.000000	T	0.39384	0.1076	M	0.90705	3.14	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;0.999;1.0	T	0.43278	-0.9401	9	.	.	.	-6.4844	12.3394	0.55085	0.8732:0.0:0.0:0.1268	.	43;43;43;43	B4DLR8;B4DNM7;B7ZAD1;P15559	.;.;.;NQO1_HUMAN	D	43	ENSP00000319788:Y43D;ENSP00000368335:Y43D;ENSP00000368334:Y43D;ENSP00000398330:Y43D	.	Y	-	1	0	NQO1	68309819	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.624000	0.90961	1.071000	0.40834	0.533000	0.62120	TAT	.	.		0.507	NQO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268956.2			C	69752318	A	C	69752318	3	2	235	1	0	0	0	0	1	0	0	0	10620	420	15	5	717	5	NQO1	16	69752318	Missense_Mutation	SNP	A	TCGA-DD-AAW2-01A-11D-A40P-10	858292	69752318	20602435	93	32779										
FA2H	79152	hgsc.bcm.edu	37	chr16	74752917	74752917	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	ggccgtgcatgacgaagtgcAgcatgatgaggtaatagctg	15	7	0	3			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr16:74752917A>T	ENST00000219368.3	-	5	824	c.755T>A	c.(754-756)cTg>cAg	p.L252Q	FA2H_ENST00000544337.1_Missense_Mutation_p.L39Q	NM_024306.4	NP_077282.3	Q7L5A8	FA2H_HUMAN	fatty acid 2-hydroxylase	252					cell death (GO:0008219)|central nervous system myelin maintenance (GO:0032286)|fatty acid biosynthetic process (GO:0006633)|lipid modification (GO:0030258)|peripheral nervous system myelin maintenance (GO:0032287)|regulation of cell proliferation (GO:0042127)|regulation of hair cycle (GO:0042634)|sebaceous gland cell differentiation (GO:0001949)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	fatty acid alpha-hydroxylase activity (GO:0080132)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			endometrium(2)|large_intestine(4)|lung(3)|skin(1)	10						GACGAAGTGCAGCATGATGAG	0.632																																					p.L252Q		Atlas-SNP	.											.	FA2H	21	.	0			c.T755A						.						65	61	62					16																	74752917		2198	4300	6498	SO:0001583	missense	79152	exon5			AAGTGCAGCATGA	BC002679	CCDS10911.1	16q23	2013-03-04	2003-10-29	2003-10-31	ENSG00000103089	ENSG00000103089		"Fatty acid hydroxylase domain containing"	21197	protein-coding gene	gene with protein product	"fatty acid hydroxylase"	611026	"fatty acid hydroxylase domain containing 1", "spastic paraplegia 35 (autosomal recessive)"	FAXDC1, SPG35		20104589	Standard	NM_024306		Approved	FAAH, FLJ25287	uc002fde.2	Q7L5A8	OTTHUMG00000137603	ENST00000219368.3:c.755T>A	chr16.hg19:g.74752917A>T	ENSP00000219368:p.Leu252Gln	66.0	0.0		81.0	32.0	NM_024306	B7Z8T6|O75213|Q96DK1|Q9H1A5	Missense_Mutation	SNP	ENST00000219368.3	hg19	CCDS10911.1	.	.	.	.	.	.	.	.	.	.	A	29.6	5.023649	0.93462	.	.	ENSG00000103089	ENST00000219368;ENST00000544337	D;D	0.85556	-2.0;-2.0	5.36	5.36	0.76844	Fatty acid hydroxylase (1);	0.201690	0.43919	D	0.000507	D	0.94102	0.8109	M	0.94021	3.485	0.80722	D	1	D	0.89917	1.0	D	0.72075	0.976	D	0.95546	0.8616	10	0.87932	D	0	-6.0E-4	15.3568	0.74434	1.0:0.0:0.0:0.0	.	252	Q7L5A8	FA2H_HUMAN	Q	252;39	ENSP00000219368:L252Q;ENSP00000442334:L39Q	ENSP00000219368:L252Q	L	-	2	0	FA2H	73310418	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.297000	0.96120	2.030000	0.59900	0.459000	0.35465	CTG	.	.		0.632	FA2H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269015.2	NM_024306		T	74752917	A	T	74752917	3	4	235	1	0	0	0	0	1	0	0	0	5357	188	7	4	375	4	FA2H	16	74752917	Missense_Mutation	SNP	A	TCGA-DD-AAW2-01A-11D-A40P-10	5000599	74752917	15601836	94	32780										
SPEM1	374768	hgsc.bcm.edu	37	chr17	7324364	7324364	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	ctcccacacgctgtgctcacTgcccagtagcttgggctcct	9	17	1	0			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr17:7324364T>A	ENST00000323675.3	+	3	395	c.370T>A	c.(370-372)Tgc>Agc	p.C124S	RP11-104H15.7_ENST00000575310.1_RNA	NM_199339.2	NP_955371.2	Q8N4L4	SPEM1_HUMAN	spermatid maturation 1	124					sperm individualization (GO:0007291)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	12		Prostate(122;0.173)				CTGTGCTCACTGCCCAGTAGC	0.607																																					p.C124S		Atlas-SNP	.											.	SPEM1	41	.	0			c.T370A						.						64	69	67					17																	7324364		2136	4240	6376	SO:0001583	missense	374768	exon3			GCTCACTGCCCAG	AK097400	CCDS42254.1	17p13.1	2011-12-12	2008-02-04	2008-02-04	ENSG00000181323	ENSG00000181323			32429	protein-coding gene	gene with protein product		615116	"chromosome 17 open reading frame 83"	C17orf83		17426145, 20558241, 21184802	Standard	NM_199339		Approved	FLJ40081	uc002ggv.3	Q8N4L4		ENST00000323675.3:c.370T>A	chr17.hg19:g.7324364T>A	ENSP00000315554:p.Cys124Ser	69.0	0.0		106.0	53.0	NM_199339		Missense_Mutation	SNP	ENST00000323675.3	hg19	CCDS42254.1	.	.	.	.	.	.	.	.	.	.	T	12.58	1.981441	0.34942	.	.	ENSG00000181323	ENST00000323383;ENST00000323675	.	.	.	5.55	-4.19	0.03835	.	1.737370	0.02984	N	0.145997	T	0.17916	0.0430	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.09122	-1.0689	9	0.17369	T	0.5	0.2299	0.966	0.01406	0.232:0.3529:0.1139:0.3012	.	124	Q8N4L4	SPEM1_HUMAN	S	73;124	.	ENSP00000315511:C73S	C	+	1	0	SPEM1	7265088	0.000000	0.05858	0.002000	0.10522	0.148000	0.21650	-0.095000	0.11077	-0.226000	0.09899	-0.177000	0.13119	TGC	.	.		0.607	SPEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440932.1	NM_199339		A	7324364	T	A	7324364	3	1	235	1	0	0	0	0	1	0	0	0	15052	1580	55	4	380	4	SPEM1	17	7324364	Missense_Mutation	SNP	T	TCGA-DD-AAW2-01A-11D-A40P-10		7324364	73870846	95	32781										
EME1	146956	hgsc.bcm.edu	37	chr17	48457826	48457826	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	ctggaaatggccagtgcagtTgtgaatgcctatccctcccc	10	13	0	1			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr17:48457826T>C	ENST00000338165.4	+	8	1582	c.1500T>C	c.(1498-1500)gtT>gtC	p.V500V	EME1_ENST00000511648.2_Silent_p.V513V|EME1_ENST00000393271.2_Silent_p.V513V	NM_152463.2	NP_689676.2	Q96AY2	EME1_HUMAN	essential meiotic structure-specific endonuclease 1	500					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cytoplasm (GO:0005737)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(4)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	19	Breast(11;5.62e-19)		BRCA - Breast invasive adenocarcinoma(22;2.43e-08)			CCAGTGCAGTTGTGAATGCCT	0.607								Direct reversal of damage;Homologous recombination																													p.V513V		Atlas-SNP	.											.	EME1	39	.	0			c.T1539C						.						93	75	81					17																	48457826		2203	4300	6503	SO:0001819	synonymous_variant	146956	exon8			TGCAGTTGTGAAT	BC016470	CCDS11565.1, CCDS54141.1	17q21.33	2013-07-03	2013-07-03			ENSG00000154920			24965	protein-coding gene	gene with protein product	"SLX2 structure-specific endonuclease subunit homolog A (S. cerevisiae)"	610885	"essential meiotic endonuclease 1 homolog 1 (S. pombe)"			12721304	Standard	NM_001166131		Approved	FLJ31364, MMS4L, SLX2A	uc010dbp.2	Q96AY2		ENST00000338165.4:c.1500T>C	chr17.hg19:g.48457826T>C		67.0	0.0		84.0	34.0	NM_001166131	Q96N62	Silent	SNP	ENST00000338165.4	hg19	CCDS11565.1	.	.	.	.	.	.	.	.	.	.	T	7.818	0.717179	0.15372	.	.	ENSG00000154920	ENST00000510246	.	.	.	6.06	2.61	0.31194	.	.	.	.	.	T	0.53465	0.1798	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40869	-0.9540	4	.	.	.	-26.1322	5.4971	0.16809	0.0:0.1978:0.2484:0.5539	.	.	.	.	R	312	.	.	C	+	1	0	EME1	45812825	0.981000	0.34729	0.863000	0.33907	0.694000	0.40290	0.119000	0.15626	0.167000	0.19631	0.533000	0.62120	TGT	.	.		0.607	EME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367118.3	NM_152463		C	48457826	T	C	48457826	2	2	235	1	0	0	0	0	0	0	0	1	5090	1799	63	2		2	EME1	17	48457826	Silent	SNP	T	TCGA-DD-AAW2-01A-11D-A40P-10	41133462	48457826	32737384	96	32782										
GRIN2C	2905	hgsc.bcm.edu	37	chr17	72838940	72838940	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	tgcgccaagcgcctgcaggcCgagtggccgtcggggcgggc	19	14	0	0			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr17:72838940C>G	ENST00000293190.5	-	13	3482	c.3336G>C	c.(3334-3336)tcG>tcC	p.S1112S		NM_000835.3	NP_000826.2	Q14957	NMDE3_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2C	1112					directional locomotion (GO:0033058)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of protein catabolic process (GO:0042177)|neuromuscular process controlling balance (GO:0050885)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|response to wounding (GO:0009611)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	33	all_lung(278;0.172)|Lung NSC(278;0.207)				Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GCCTGCAGGCCGAGTGGCCGT	0.761																																					p.S1112S		Atlas-SNP	.											.	GRIN2C	144	.	0			c.G3336C						.						1	2	2					17																	72838940		752	1936	2688	SO:0001819	synonymous_variant	2905	exon13			GCAGGCCGAGTGG		CCDS32724.1, CCDS62330.1	17q25.1	2012-08-29			ENSG00000161509	ENSG00000161509		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4587	protein-coding gene	gene with protein product		138254		NMDAR2C		9480759	Standard	NM_001278553		Approved	GluN2C	uc002jlt.1	Q14957	OTTHUMG00000044524	ENST00000293190.5:c.3336G>C	chr17.hg19:g.72838940C>G		19.0	0.0		51.0	23.0	NM_000835	B2RTT1	Silent	SNP	ENST00000293190.5	hg19	CCDS32724.1																																																																																			.	.		0.761	GRIN2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103824.1			G	72838940	C	G	72838940	2	3	235	1	0	0	0	0	0	0	0	1	6790	639	23	4		4	GRIN2C	17	72838940	Silent	SNP	C	TCGA-DD-AAW2-01A-11D-A40P-10	24381114	72838940	8356270	97	32783										
FOXK2	3607	hgsc.bcm.edu	37	chr17	80529707	80529707	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	atttatacacacatcactaaAaattatccctactacaggac	2	11	1	0			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr17:80529707A>C	ENST00000335255.5	+	4	1044	c.870A>C	c.(868-870)aaA>aaC	p.K290N		NM_004514.3	NP_004505.2	Q01167	FOXK2_HUMAN	forkhead box K2	290					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|urinary_tract(1)	17	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)			ACATCACTAAAAATTATCCCT	0.488																																					p.K290N		Atlas-SNP	.											.	FOXK2	46	.	0			c.A870C						.						67	59	62					17																	80529707		2203	4300	6503	SO:0001583	missense	3607	exon4			CACTAAAAATTAT	U58196	CCDS11813.1	17q25	2006-12-15	2004-03-09	2004-03-10	ENSG00000141568	ENSG00000141568		"Forkhead boxes"	6036	protein-coding gene	gene with protein product		147685	"interleukin enhancer binding factor 1"	ILF, ILF1		3260003	Standard	NM_004514		Approved		uc002kfn.3	Q01167	OTTHUMG00000140374	ENST00000335255.5:c.870A>C	chr17.hg19:g.80529707A>C	ENSP00000335677:p.Lys290Asn	128.0	0.0		148.0	52.0	NM_004514	A6NEP5|Q13622|Q13623|Q13624	Missense_Mutation	SNP	ENST00000335255.5	hg19	CCDS11813.1	.	.	.	.	.	.	.	.	.	.	A	19.58	3.853657	0.71719	.	.	ENSG00000141568	ENST00000535184;ENST00000335255;ENST00000335241;ENST00000531030;ENST00000526383	D;D;D	0.95518	-3.73;-3.73;-3.73	5.64	-3.3	0.05003	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (4);	0.000000	0.85682	D	0.000000	D	0.94594	0.8258	L	0.31065	0.9	0.58432	D	0.999991	D;D;D	0.89917	1.0;0.968;0.96	D;D;P	0.85130	0.997;0.943;0.905	D	0.91623	0.5312	10	0.72032	D	0.01	.	12.4947	0.55921	0.5508:0.0:0.4492:0.0	.	290;290;290	Q01167-3;Q01167;Q01167-2	.;FOXK2_HUMAN;.	N	286;290;290;101;170	ENSP00000335677:K290N;ENSP00000433167:K101N;ENSP00000432663:K170N	ENSP00000334321:K290N	K	+	3	2	FOXK2	78122996	1.000000	0.71417	0.036000	0.18154	0.713000	0.41058	0.969000	0.29370	-0.744000	0.04778	0.528000	0.53228	AAA	.	.		0.488	FOXK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277099.2	NM_181430		C	80529707	A	C	80529707	3	2	235	1	0	0	0	0	1	0	0	0	6023	11	1	5	884	5	FOXK2	17	80529707	Missense_Mutation	SNP	A	TCGA-DD-AAW2-01A-11D-A40P-10	7690767	80529707	665503	98	32784										
TXNDC2	84203	hgsc.bcm.edu	37	chr18	9886755	9886755	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	gatgacctacccaagtcctcAgcaaacaccagccatcccaa	5	17	1	1			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr18:9886755A>C	ENST00000306084.6	+	2	478	c.279A>C	c.(277-279)tcA>tcC	p.S93S	TXNDC2_ENST00000357775.5_Silent_p.S26S|TXNDC2_ENST00000536353.2_Silent_p.S26S|TXNDC2_ENST00000426718.3_3'UTR	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN	thioredoxin domain containing 2 (spermatozoa)	93					cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|glycerol ether metabolic process (GO:0006662)|multicellular organismal development (GO:0007275)|oxidation-reduction process (GO:0055114)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)	nutrient reservoir activity (GO:0045735)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)|thioredoxin-disulfide reductase activity (GO:0004791)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|skin(7)|urinary_tract(1)	31						CCAAGTCCTCAGCAAACACCA	0.572																																					p.S93S		Atlas-SNP	.											.	TXNDC2	168	.	0			c.A279C						.						169	108	129					18																	9886755		2203	4300	6503	SO:0001819	synonymous_variant	84203	exon2			GTCCTCAGCAAAC	AF080095	CCDS11846.1, CCDS42414.1	18p11.31-p11.2	2009-03-11	2009-03-11	2007-08-16	ENSG00000168454	ENSG00000168454			16470	protein-coding gene	gene with protein product	"sperm-specific thioredoxin 1"					11230166, 11399755	Standard	NM_001098529		Approved	SPTRX1	uc002koi.4	Q86VQ3	OTTHUMG00000131602	ENST00000306084.6:c.279A>C	chr18.hg19:g.9886755A>C		128.0	0.0		164.0	12.0	NM_001098529	A5YM73|Q8N7U4|Q96RX3|Q9H0L8	Silent	SNP	ENST00000306084.6	hg19	CCDS42414.1																																																																																			.	.		0.572	TXNDC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254487.1			C	9886755	A	C	9886755	2	2	235	1	0	0	0	0	0	0	0	1	16812	175	7	5		5	TXNDC2	18	9886755	Silent	SNP	A	TCGA-DD-AAW2-01A-11D-A40P-10		9886755	68190493	99	32785										
RIOK3	8780	hgsc.bcm.edu	37	chr18	21053404	21053404	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	tccacttagcatggaggatgAaaaggaagatagtaaagtta	11	4	0	2			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr18:21053404A>G	ENST00000339486.3	+	8	1444	c.827A>G	c.(826-828)gAa>gGa	p.E276G	RIOK3_ENST00000577501.1_Missense_Mutation_p.E276G|RIOK3_ENST00000581585.1_Missense_Mutation_p.E260G	NM_003831.3	NP_003822.2	O14730	RIOK3_HUMAN	RIO kinase 3	276	Protein kinase.				chromosome segregation (GO:0007059)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|kidney(3)|large_intestine(1)|lung(3)|ovary(2)	10	all_cancers(21;0.000106)|all_epithelial(16;6.74e-07)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0202)|Ovarian(20;0.127)					ATGGAGGATGAAAAGGAAGAT	0.303																																					p.E276G		Atlas-SNP	.											.	RIOK3	42	.	0			c.A827G						.						39	38	38					18																	21053404		2203	4298	6501	SO:0001583	missense	8780	exon8			AGGATGAAAAGGA	AF013591	CCDS11877.1	18q11.2	2012-12-10	2012-12-10	2003-06-25	ENSG00000101782	ENSG00000101782			11451	protein-coding gene	gene with protein product		603579	"sudD (suppressor of bimD6, Aspergillus nidulans) homolog", "RIO kinase 3 (yeast)"	SUDD		9602165	Standard	NM_003831		Approved		uc002kui.4	O14730	OTTHUMG00000131813	ENST00000339486.3:c.827A>G	chr18.hg19:g.21053404A>G	ENSP00000341874:p.Glu276Gly	249.0	0.0		297.0	133.0	NM_003831	Q8IXN9	Missense_Mutation	SNP	ENST00000339486.3	hg19	CCDS11877.1	.	.	.	.	.	.	.	.	.	.	A	10.65	1.410784	0.25465	.	.	ENSG00000101782	ENST00000339486	T	0.07908	3.15	4.86	-0.302	0.12796	RIO kinase (1);Protein kinase-like domain (1);RIO-like kinase (1);	0.388002	0.28171	N	0.016336	T	0.04227	0.0117	L	0.29908	0.895	0.28808	N	0.898395	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.33599	-0.9862	10	0.21014	T	0.42	-11.1858	1.5643	0.02601	0.3836:0.2586:0.2433:0.1146	.	260;276;276	B4E1Q4;O14730-2;O14730	.;.;RIOK3_HUMAN	G	276	ENSP00000341874:E276G	ENSP00000341874:E276G	E	+	2	0	RIOK3	19307402	0.994000	0.37717	0.999000	0.59377	0.985000	0.73830	0.431000	0.21444	0.050000	0.15949	0.477000	0.44152	GAA	.	.		0.303	RIOK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254756.1	NM_003831		G	21053404	A	G	21053404	3	3	235	1	0	0	0	0	1	0	0	0	13394	246	9	2	857	2	RIOK3	18	21053404	Missense_Mutation	SNP	A	TCGA-DD-AAW2-01A-11D-A40P-10	11166649	21053404	57023844	100	32786										
DTNA	1837	hgsc.bcm.edu	37	chr18	32418754	32418754	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	gacaggctagctgatgaacaTgttctcatcgggttgtatgt	12	7	1	2			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr18:32418754T>G	ENST00000399113.3	+	12	1218	c.1218T>G	c.(1216-1218)caT>caG	p.H406Q	DTNA_ENST00000599844.1_Intron|DTNA_ENST00000556414.3_Intron|DTNA_ENST00000597674.1_Intron|DTNA_ENST00000399121.5_Intron|DTNA_ENST00000601125.1_Intron|DTNA_ENST00000444659.1_Missense_Mutation_p.H406Q|DTNA_ENST00000283365.9_Intron|DTNA_ENST00000348997.5_Missense_Mutation_p.H403Q|DTNA_ENST00000598142.1_Intron|DTNA_ENST00000399097.3_Intron|DTNA_ENST00000269192.7_Missense_Mutation_p.H115Q|DTNA_ENST00000595022.1_Intron|DTNA_ENST00000596745.1_Intron|DTNA_ENST00000269191.6_Missense_Mutation_p.H406Q|DTNA_ENST00000598774.1_Intron|DTNA_ENST00000598334.1_Intron|DTNA_ENST00000597599.1_Intron|DTNA_ENST00000591182.1_Intron|DTNA_ENST00000269190.7_Missense_Mutation_p.H407Q			Q9Y4J8	DTNA_HUMAN	dystrobrevin, alpha	406	Syntrophin-binding region.				neuromuscular synaptic transmission (GO:0007274)|signal transduction (GO:0007165)|striated muscle contraction (GO:0006941)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(2)|lung(19)|prostate(1)|upper_aerodigestive_tract(1)	29						CTGATGAACATGTTCTCATCG	0.493																																					p.H406Q		Atlas-SNP	.											.	DTNA	321	.	0			c.T1218G						.						177	135	149					18																	32418754		2203	4300	6503	SO:0001583	missense	1837	exon12			TGAACATGTTCTC	U84540	CCDS11908.1, CCDS11909.1, CCDS42426.1, CCDS45848.1, CCDS56060.1, CCDS56061.1, CCDS56062.1, CCDS56063.1, CCDS59309.1, CCDS59310.1, CCDS59311.1, CCDS59312.1, CCDS59313.1, CCDS59314.1	18q12	2014-09-17			ENSG00000134769	ENSG00000134769			3057	protein-coding gene	gene with protein product	"dystrophin-related protein 3"	601239				8081380, 15834686	Standard	NM_001390		Approved	D18S892E, DTN, DTN-1, DTN-2, DTN-3, DRP3	uc010dmn.1	Q9Y4J8	OTTHUMG00000132309	ENST00000399113.3:c.1218T>G	chr18.hg19:g.32418754T>G	ENSP00000382064:p.His406Gln	128.0	0.0		139.0	56.0	NM_001390	A8K541|A8MSZ0|A8MUY4|B4DGS6|B4DIR0|B4DIU8|M0QYX6|M0R397|O15332|O15333|O75697|Q13197|Q13198|Q13199|Q13498|Q13499|Q13500|Q59GK7|Q9BS59	Missense_Mutation	SNP	ENST00000399113.3	hg19	CCDS59311.1	.	.	.	.	.	.	.	.	.	.	T	18.31	3.595096	0.66219	.	.	ENSG00000134769	ENST00000269190;ENST00000348997;ENST00000399121;ENST00000444659;ENST00000269191;ENST00000399113;ENST00000269192	T;T;T;T;T	0.27256	1.68;1.88;1.69;1.85;1.69	5.95	4.8	0.61643	.	0.000000	0.85682	D	0.000000	T	0.46425	0.1392	M	0.70275	2.135	0.80722	D	1	D;D;D;D	0.71674	0.991;0.998;0.991;0.997	D;D;P;D	0.78314	0.958;0.986;0.849;0.991	T	0.45338	-0.9268	10	0.66056	D	0.02	-16.978	9.0993	0.36658	0.0:0.138:0.0:0.862	.	115;406;406;403	B4DIR0;Q9Y4J8;Q9Y4J8-3;Q9Y4J8-4	.;DTNA_HUMAN;.;.	Q	407;403;406;406;406;406;115	ENSP00000269190:H407Q;ENSP00000336682:H403Q;ENSP00000405819:H406Q;ENSP00000269191:H406Q;ENSP00000382064:H406Q	ENSP00000269190:H407Q	H	+	3	2	DTNA	30672752	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.898000	0.48672	2.272000	0.75746	0.460000	0.39030	CAT	.	.		0.493	DTNA-005	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255422.2	NM_001390		G	32418754	T	G	32418754	3	3	235	1	0	0	0	0	1	0	0	0	4790	1461	51	5	1299	5	DTNA	18	32418754	Missense_Mutation	SNP	T	TCGA-DD-AAW2-01A-11D-A40P-10	11365350	32418754	45658494	101	32787										
ZNF397	100101467	hgsc.bcm.edu	37	chr18	32834231	32834231	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	ccaaagcttcttcagctatcCgttgggaatgtgtttctcca	8	11	3	0			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr18:32834231C>A	ENST00000420878.3	-	5	1123	c.668G>T	c.(667-669)cGg>cTg	p.R223L	ZSCAN30_ENST00000333206.5_Missense_Mutation_p.R223L|ZNF397_ENST00000592264.1_Intron|ZNF397_ENST00000261333.6_Missense_Mutation_p.R228S|ZNF397_ENST00000355632.4_Missense_Mutation_p.R198S|ZNF397_ENST00000589420.1_3'UTR	NM_001166012.1	NP_001159484.1	Q86W11	ZSC30_HUMAN	zinc finger and SCAN domain containing 30	223					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R228S(1)|p.R223L(1)		large_intestine(5)|lung(3)|urinary_tract(1)	9						TTCAGCTATCCGTTGGGAATG	0.468																																					p.R228S		Atlas-SNP	.											ZSCAN30,colon,carcinoma,0,2	ZNF397	51	.	2	Substitution - Missense(2)	lung(2)	c.C682A						.						159	150	153					18																	32834231		2203	4300	6503	SO:0001583	missense	84307	exon5			GCTATCCGTTGGG	AY234408	CCDS42427.1, CCDS74207.1	18q12.2	2013-01-08	2010-07-23	2010-07-23	ENSG00000186814	ENSG00000186814		"-", "Zinc fingers, C2H2-type"	33517	protein-coding gene	gene with protein product			"zinc finger protein 397 opposite strand", "ZNF397 opposite strand"	ZNF397OS		12801647	Standard	NM_001166012		Approved	ZNF917	uc002kym.3	Q86W11		ENST00000420878.3:c.668G>T	chr18.hg19:g.32834231C>A	ENSP00000392371:p.Arg223Leu	109.0	1.0		117.0	48.0	NM_032347	B4E0N0|Q6ZNB3|Q96PN3	Missense_Mutation	SNP	ENST00000420878.3	hg19	CCDS42427.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	8.880|8.880	0.951460|0.951460	0.18431|0.18431	.|.	.|.	ENSG00000186814|ENSG00000186812	ENST00000420878;ENST00000333206;ENST00000360932|ENST00000261333;ENST00000355632	T;T|T;T	0.06768|0.02944	3.26;3.26|4.23;4.1	4.21|4.21	4.21|4.21	0.49690|0.49690	.|.	0.529775|0.529775	0.14290|0.14290	N|N	0.328959|0.328959	T|T	0.02047|0.02047	0.0064|0.0064	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	B|B;B	0.06786|0.02656	0.001|0.0;0.0	B|B;B	0.01281|0.01281	0.0|0.0;0.0	T|T	0.47209|0.47209	-0.9135|-0.9135	9|9	0.27785|0.12103	T|T	0.31|0.63	.|.	8.1344|8.1344	0.31046|0.31046	0.0:0.0984:0.0:0.9016|0.0:0.0984:0.0:0.9016	.|.	223|198;228	Q86W11|Q96K65;Q8NF99-2	ZSC30_HUMAN|.;.	L|S	223;223;158|228;198	ENSP00000392371:R223L;ENSP00000329738:R223L|ENSP00000261333:R228S;ENSP00000347850:R198S	ENSP00000329738:R223L|ENSP00000261333:R228S	R|R	-|+	2|1	0|0	ZSCAN30|ZNF397	31088229|31088229	0.017000|0.017000	0.18338|0.18338	0.141000|0.141000	0.22245|0.22245	0.070000|0.070000	0.16714|0.16714	0.926000|0.926000	0.28804|0.28804	0.766000|0.766000	0.33244|0.33244	-0.268000|-0.268000	0.10319|0.10319	CGG|CGT	.	.		0.468	ZSCAN30-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442510.1	NM_001112734		A	32834231	C	A	32834231	3	1	235	1	0	0	0	0	1	0	0	0	17898	652	23	1	1655	1	ZNF397	18	32834231	Missense_Mutation	SNP	C	TCGA-DD-AAW2-01A-11D-A40P-10	415477	32834231	45243017	102	32788										
ZNRF4	148066	hgsc.bcm.edu	37	chr19	5456638	5456638	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	ggacccctccctaccgggccAccggccccccatctgggcca	10	22	1	0			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr19:5456638A>T	ENST00000222033.4	+	1	1213	c.1136A>T	c.(1135-1137)cAc>cTc	p.H379L		NM_181710.3	NP_859061.3	Q8WWF5	ZNRF4_HUMAN	zinc and ring finger 4	379						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			NS(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (162;0.0002)		CTACCGGGCCACCGGCCCCCC	0.677																																					p.H379L		Atlas-SNP	.											.	ZNRF4	59	.	0			c.A1136T						.						44	52	50					19																	5456638		1977	4151	6128	SO:0001583	missense	148066	exon1			CGGGCCACCGGCC	AK098722	CCDS42475.1	19p13.3	2013-01-09				ENSG00000105428		"RING-type (C3HC4) zinc fingers"	17726	protein-coding gene	gene with protein product		612063					Standard	NM_181710		Approved	spzn, Ssrzf1, RNF204	uc002mca.4	Q8WWF5		ENST00000222033.4:c.1136A>T	chr19.hg19:g.5456638A>T	ENSP00000222033:p.His379Leu	58.0	0.0		107.0	45.0	NM_181710	A8K886|O75866	Missense_Mutation	SNP	ENST00000222033.4	hg19	CCDS42475.1	.	.	.	.	.	.	.	.	.	.	A	5.548	0.286016	0.10513	.	.	ENSG00000105428	ENST00000222033	T	0.04234	3.67	3.47	-0.104	0.13605	.	0.295799	0.32134	U	0.006522	T	0.03434	0.0099	L	0.27053	0.805	0.28196	N	0.927536	P	0.50943	0.94	P	0.44732	0.459	T	0.45469	-0.9259	10	0.17832	T	0.49	-14.1544	6.5764	0.22569	0.6462:0.0:0.3538:0.0	.	379	Q8WWF5	ZNRF4_HUMAN	L	379	ENSP00000222033:H379L	ENSP00000222033:H379L	H	+	2	0	ZNRF4	5407638	0.000000	0.05858	0.183000	0.23137	0.058000	0.15608	-0.458000	0.06737	-0.235000	0.09767	0.459000	0.35465	CAC	.	.		0.677	ZNRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450924.1	NM_181710		T	5456638	A	T	5456638	3	4	235	1	0	0	0	0	1	0	0	0	18229	159	6	4	1138	4	ZNRF4	19	5456638	Missense_Mutation	SNP	A	TCGA-DD-AAW2-01A-11D-A40P-10		5456638	53672345	103	32789										
MLLT1	4298	hgsc.bcm.edu	37	chr19	6213406	6213406	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	tccggtgtagctccaccagcTcatccgtgtaggcctgggga	13	13	1	0			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr19:6213406T>C	ENST00000252674.7	-	11	1656	c.1493A>G	c.(1492-1494)gAg>gGg	p.E498G	MLLT1_ENST00000585588.1_5'UTR|CTC-503J8.6_ENST00000586154.1_lincRNA	NM_005934.3	NP_005925.2	Q03111	ENL_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 1	498					negative regulation of protein kinase activity (GO:0006469)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	DNA binding (GO:0003677)			endometrium(3)|kidney(3)|large_intestine(2)|lung(5)|prostate(2)|skin(2)	17						CTCCACCAGCTCATCCGTGTA	0.701			T	MLL	AL																																p.E498G		Atlas-SNP	.		Dom	yes		19	19p13.3	4298	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 1 (ENL)"		L	.	MLLT1	47	.	0			c.A1493G						.						42	50	47					19																	6213406		2200	4287	6487	SO:0001583	missense	4298	exon11			ACCAGCTCATCCG		CCDS12160.1	19p13.3	2012-10-04	2001-11-28		ENSG00000130382	ENSG00000130382			7134	protein-coding gene	gene with protein product		159556	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 1"				Standard	XM_005259561		Approved	ENL, LTG19, YEATS1	uc002mek.3	Q03111	OTTHUMG00000180757	ENST00000252674.7:c.1493A>G	chr19.hg19:g.6213406T>C	ENSP00000252674:p.Glu498Gly	49.0	0.0		72.0	29.0	NM_005934	Q14768	Missense_Mutation	SNP	ENST00000252674.7	hg19	CCDS12160.1	.	.	.	.	.	.	.	.	.	.	t	15.57	2.873518	0.51695	.	.	ENSG00000130382	ENST00000252674	.	.	.	4.16	4.16	0.48862	.	0.124124	0.51477	N	0.000082	T	0.63177	0.2489	M	0.78049	2.395	0.49213	D	0.999765	P	0.52316	0.952	P	0.49140	0.601	T	0.68006	-0.5523	9	0.87932	D	0	-14.3704	8.3814	0.32474	0.1755:0.0:0.0:0.8245	.	498	Q03111	ENL_HUMAN	G	498	.	ENSP00000252674:E498G	E	-	2	0	MLLT1	6164406	1.000000	0.71417	0.508000	0.27688	0.677000	0.39632	5.933000	0.70130	1.514000	0.48869	0.478000	0.44815	GAG	.	.		0.701	MLLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452909.1	NM_005934		C	6213406	T	C	6213406	3	2	235	1	0	0	0	0	1	0	0	0	9634	1551	54	2	194	2	MLLT1	19	6213406	Missense_Mutation	SNP	T	TCGA-DD-AAW2-01A-11D-A40P-10	756768	6213406	52915577	104	32790										
MUC16	94025	hgsc.bcm.edu	37	chr19	9083038	9083038	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	gagacttggacagtgaggaaGatgctgtgcttgcatctgag	15	6	1	4			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr19:9083038G>A	ENST00000397910.4	-	1	8980	c.8777C>T	c.(8776-8778)tCt>tTt	p.S2926F		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2927	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CAGTGAGGAAGATGCTGTGCT	0.458																																					p.S2926F		Atlas-SNP	.											.	MUC16	4315	.	0			c.C8777T						.						105	96	99					19																	9083038		1933	4136	6069	SO:0001583	missense	94025	exon1			GAGGAAGATGCTG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.8777C>T	chr19.hg19:g.9083038G>A	ENSP00000381008:p.Ser2926Phe	143.0	0.0		203.0	93.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	6.177	0.400786	0.11696	.	.	ENSG00000181143	ENST00000397910	T	0.02737	4.18	0.773	0.773	0.18516	.	.	.	.	.	T	0.03095	0.0091	N	0.08118	0	.	.	.	D	0.58268	0.982	P	0.56700	0.804	T	0.44937	-0.9295	8	0.87932	D	0	.	4.823	0.13400	0.0:0.0:1.0:0.0	.	2926	B5ME49	.	F	2926	ENSP00000381008:S2926F	ENSP00000381008:S2926F	S	-	2	0	MUC16	8944038	0.017000	0.18338	0.005000	0.12908	0.629000	0.37895	0.337000	0.19841	0.680000	0.31366	0.313000	0.20887	TCT	.	.		0.458	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9083038	G	A	9083038	3	1	235	1	0	0	0	0	1	0	0	0	9982	942	33	3	35082	3	MUC16	19	9083038	Missense_Mutation	SNP	G	TCGA-DD-AAW2-01A-11D-A40P-10	2869632	9083038	50045945	105	32791										
ZNF181	339318	hgsc.bcm.edu	37	chr19	35231867	35231867	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	attaaagaagaacttaccaaAaaagtcagttataaaaaatg	5	4	1	2			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr19:35231867A>G	ENST00000492450.1	+	4	670	c.581A>G	c.(580-582)aAa>aGa	p.K194R	ZNF181_ENST00000392232.3_Missense_Mutation_p.K238R|ZNF181_ENST00000459757.2_Missense_Mutation_p.K193R			Q2M3W8	ZN181_HUMAN	zinc finger protein 181	194					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(6)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|skin(1)	22	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			AACTTACCAAAAAAGTCAGTT	0.343																																					p.K194R		Atlas-SNP	.											.	ZNF181	65	.	0			c.A581G						.						43	50	48					19																	35231867		2191	4292	6483	SO:0001583	missense	339318	exon4			TACCAAAAAAGTC	BC104759, H54888	CCDS32990.2, CCDS46043.1	19q13.13	2013-01-08	2006-04-27		ENSG00000197841	ENSG00000197841		"Zinc fingers, C2H2-type", "-"	12971	protein-coding gene	gene with protein product		606741	"zinc finger protein 181 (HHZ181)"				Standard	NM_001029997		Approved	HHZ181, MGC44316	uc002nvu.3	Q2M3W8	OTTHUMG00000157508	ENST00000492450.1:c.581A>G	chr19.hg19:g.35231867A>G	ENSP00000420727:p.Lys194Arg	343.0	1.0		420.0	195.0	NM_001029997	B7ZKX3|Q49A75	Missense_Mutation	SNP	ENST00000492450.1	hg19	CCDS32990.2	.	.	.	.	.	.	.	.	.	.	A	0.114	-1.134773	0.01742	.	.	ENSG00000197841	ENST00000392232;ENST00000425140;ENST00000492450;ENST00000459757	T;T;T	0.06687	3.27;3.37;3.33	2.89	0.667	0.17907	.	.	.	.	.	T	0.13114	0.0318	L	0.40543	1.245	0.09310	N	1	B;P	0.52842	0.089;0.956	B;D	0.65010	0.051;0.931	T	0.26189	-1.0110	9	0.19590	T	0.45	.	4.4584	0.11654	0.6002:0.2189:0.0:0.1809	.	193;194	B7ZKX3;Q2M3W8	.;ZN181_HUMAN	R	238;193;194;193	ENSP00000376065:K238R;ENSP00000420727:K194R;ENSP00000419435:K193R	ENSP00000376065:K238R	K	+	2	0	ZNF181	39923707	0.000000	0.05858	0.001000	0.08648	0.050000	0.14768	-0.078000	0.11375	0.077000	0.16863	0.402000	0.26972	AAA	.	.		0.343	ZNF181-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349005.3	NM_001029997		G	35231867	A	G	35231867	3	3	235	1	0	0	0	0	1	0	0	0	17764	14	1	2	595	2	ZNF181	19	35231867	Missense_Mutation	SNP	A	TCGA-DD-AAW2-01A-11D-A40P-10	26148829	35231867	23897116	106	32792										
PTH2	113091	hgsc.bcm.edu	37	chr19	49926536	49926536	+	Missense_Mutation	SNP	G	G	C													0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	gccccagggcaccaccagcaGcagcagcagcagcagcagca					rs371950649		TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr19:49926536G>C	ENST00000270631.1	-	1	162	c.61C>G	c.(61-63)Ctg>Gtg	p.L21V	CTD-3148I10.1_ENST00000576655.1_5'Flank	NM_178449.3	NP_848544.1	Q96A98	TIP39_HUMAN	parathyroid hormone 2	21					neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|skin(1)	6				OV - Ovarian serous cystadenocarcinoma(262;0.0015)|GBM - Glioblastoma multiforme(486;0.044)|Lung(386;0.0785)|LUSC - Lung squamous cell carcinoma(496;0.0836)		ACCACcagcagcagcagcagc	0.687																																					p.L21V		Atlas-SNP	.											.	PTH2	20	.	0			c.C61G						.						11	15	14					19																	49926536		2186	4273	6459	SO:0001583	missense	113091	exon1			CCAGCAGCAGCAG	AY037555	CCDS12763.1	19q13.33	2013-02-28				ENSG00000142538		"Endogenous ligands"	30828	protein-coding gene	gene with protein product	"tuberoinfundibular 39 residues"	608386				11861531	Standard	NM_178449		Approved	TIP39	uc002pnn.1	Q96A98		ENST00000270631.1:c.61C>G	chr19.hg19:g.49926536G>C	ENSP00000270631:p.Leu21Val	51.0	0.0		129.0	12.0	NM_178449	Q96DJ4	Missense_Mutation	SNP	ENST00000270631.1	hg19	CCDS12763.1	.	.	.	.	.	.	.	.	.	.	g	1.896	-0.454359	0.04540	.	.	ENSG00000142538	ENST00000270631	.	.	.	4.24	2.06	0.26882	.	0.116151	0.35436	U	0.003207	T	0.46580	0.1400	L	0.27053	0.805	0.09310	N	1	D	0.71674	0.998	D	0.73708	0.981	T	0.36237	-0.9756	9	0.87932	D	0	-4.0206	9.5665	0.39402	0.1978:0.0:0.8022:0.0	.	21	Q96A98	TIP39_HUMAN	V	21	.	ENSP00000270631:L21V	L	-	1	2	PTH2	54618348	0.089000	0.21612	0.003000	0.11579	0.024000	0.10985	0.799000	0.27028	0.056000	0.16144	-1.634000	0.00779	CTG	.	.		0.687	PTH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465366.1	NM_178449		C	49926536	G	C	49926536	3	2	235	1	0	0	0	0	1	0	0	0	12772	962	34	4	249	4	PTH2	19	49926536	Missense_Mutation	SNP	G	TCGA-DD-AAW2-01A-11D-A40P-10	14694669	49926536	9202447	107	32793	170	2								
PTH2	113091	hgsc.bcm.edu	37	chr19	49926539	49926539	+	Missense_Mutation	SNP	G	G	C													0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	ccagggcaccaccagcagcaGcagcagcagcagcagcagcc					rs371950649		TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr19:49926539G>C	ENST00000270631.1	-	1	159	c.58C>G	c.(58-60)Ctg>Gtg	p.L20V	CTD-3148I10.1_ENST00000576655.1_5'Flank	NM_178449.3	NP_848544.1	Q96A98	TIP39_HUMAN	parathyroid hormone 2	20					neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|skin(1)	6				OV - Ovarian serous cystadenocarcinoma(262;0.0015)|GBM - Glioblastoma multiforme(486;0.044)|Lung(386;0.0785)|LUSC - Lung squamous cell carcinoma(496;0.0836)		ACcagcagcagcagcagcagc	0.687																																					p.L20V		Atlas-SNP	.											.	PTH2	20	.	0			c.C58G						.						11	14	13					19																	49926539		2184	4260	6444	SO:0001583	missense	113091	exon1			GCAGCAGCAGCAG	AY037555	CCDS12763.1	19q13.33	2013-02-28				ENSG00000142538		"Endogenous ligands"	30828	protein-coding gene	gene with protein product	"tuberoinfundibular 39 residues"	608386				11861531	Standard	NM_178449		Approved	TIP39	uc002pnn.1	Q96A98		ENST00000270631.1:c.58C>G	chr19.hg19:g.49926539G>C	ENSP00000270631:p.Leu20Val	48.0	0.0		123.0	14.0	NM_178449	Q96DJ4	Missense_Mutation	SNP	ENST00000270631.1	hg19	CCDS12763.1	.	.	.	.	.	.	.	.	.	.	g	12.98	2.101872	0.37048	.	.	ENSG00000142538	ENST00000270631	.	.	.	3.93	3.93	0.45458	.	0.148013	0.39544	U	0.001330	T	0.48660	0.1512	L	0.27053	0.805	0.24833	N	0.992511	D	0.71674	0.998	D	0.73708	0.981	T	0.36359	-0.9751	9	0.87932	D	0	.	11.8501	0.52407	0.0:0.0:1.0:0.0	.	20	Q96A98	TIP39_HUMAN	V	20	.	ENSP00000270631:L20V	L	-	1	2	PTH2	54618351	0.064000	0.20934	0.867000	0.34043	0.174000	0.22865	1.881000	0.39638	1.921000	0.55644	0.457000	0.33378	CTG	.	.		0.687	PTH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465366.1	NM_178449		C	49926539	G	C	49926539	3	2	235	1	0	0	0	0	1	0	0	0	12772	962	34	4	252	4	PTH2	19	49926539	Missense_Mutation	SNP	G	TCGA-DD-AAW2-01A-11D-A40P-10	3	49926539	9202444	108	32794	170	2								
LILRA5	353514	hgsc.bcm.edu	37	chr19	54822602	54822602	+	Intron	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	cccctttttgtctttcttagCaggggctgccctgcctgtaa	9	13	2	0			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr19:54822602C>G	ENST00000301219.3	-	5	832				LILRA5_ENST00000346508.3_Intron|LILRA5_ENST00000446712.3_Missense_Mutation_p.C253S|LILRA5_ENST00000432233.3_Missense_Mutation_p.C265S|AC008984.2_ENST00000507363.1_RNA	NM_021250.2	NP_067073.1	A6NI73	LIRA5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 5						innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	20	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TCTTTCTTAGCAGGGGCTGCC	0.517																																					p.C265S		Atlas-SNP	.											.	LILRA5	49	.	0			c.G794C						.						33	35	34					19																	54822602		1327	2308	3635	SO:0001627	intron_variant	353514	exon5			TCTTAGCAGGGGC	AF212842	CCDS12888.1, CCDS12889.1	19q13.4	2013-01-11	2005-05-13	2005-05-13	ENSG00000187116	ENSG00000187116		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	16309	protein-coding gene	gene with protein product		606047		LILRB7		10941842	Standard	NM_181986		Approved	ILT11, LIR9, CD85, CD85f	uc002qfe.3	A6NI73	OTTHUMG00000065357	ENST00000301219.3:c.712+81G>C	chr19.hg19:g.54822602C>G		68.0	0.0		91.0	10.0	NM_181879	A6NHI3	Missense_Mutation	SNP	ENST00000301219.3	hg19	CCDS12888.1	.	.	.	.	.	.	.	.	.	.	C	4.309	0.056564	0.08291	.	.	ENSG00000187116	ENST00000446712;ENST00000432233	T;T	0.00520	6.85;6.94	1.27	-0.71	0.11234	.	.	.	.	.	T	0.00356	0.0011	.	.	.	0.09310	N	1	B;B	0.17038	0.02;0.019	B;B	0.12156	0.007;0.003	T	0.41413	-0.9510	8	0.87932	D	0	.	5.512	0.16886	0.0:0.4866:0.5134:0.0	.	253;265	A6NI73-4;A6NI73-3	.;.	S	253;265	ENSP00000389499:C253S;ENSP00000404236:C265S	ENSP00000404236:C265S	C	-	2	0	LILRA5	59514414	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	-2.074000	0.01375	-0.056000	0.13221	0.430000	0.28490	TGC	.	.		0.517	LILRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140231.1	NM_181985		G	54822602	C	G	54822602	1	3	235	0	1	0	0	0	0	0	0	0	8797	710	25	4		4	LILRA5	19	54822602	Intron	SNP	C	TCGA-DD-AAW2-01A-11D-A40P-10	4896063	54822602	4306381	109	32795										
NOP56	10528	hgsc.bcm.edu	37	chr20	2635441	2635441	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	gtgaagggtctgaccgatctGtcagcttgtaaagcacagct	12	9	3	2	rs140571524		TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr20:2635441G>A	ENST00000329276.5	+	5	933	c.417G>A	c.(415-417)ctG>ctA	p.L139L	SNORA51_ENST00000606420.1_RNA|MIR1292_ENST00000408135.1_RNA|SNORD57_ENST00000448188.1_RNA|SNORD110_ENST00000408189.1_RNA|SNORD86_ENST00000391196.1_RNA|SNORD56_ENST00000413522.1_RNA	NM_006392.3	NP_006383.2	O00567	NOP56_HUMAN	NOP56 ribonucleoprotein	139					cell death (GO:0008219)|rRNA processing (GO:0006364)	box C/D snoRNP complex (GO:0031428)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|snoRNA binding (GO:0030515)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25						TGACCGATCTGTCAGCTTGTA	0.517																																					p.L139L		Atlas-SNP	.											.	NOP56	73	.	0			c.G417A						.						170	167	168					20																	2635441		2203	4300	6503	SO:0001819	synonymous_variant	10528	exon5			CGATCTGTCAGCT	Y12065	CCDS13030.1	20p13	2012-12-10	2012-12-10	2009-01-13	ENSG00000101361	ENSG00000101361			15911	protein-coding gene	gene with protein product	"spinocerebellar ataxia 36"	614154	"nucleolar protein 5A (56kD with KKE/D repeat)", "nucleolar protein 5A (56kDa with KKE/D repeat)", "NOP56 ribonucleoprotein homolog (yeast)"	NOL5A		9372940, 21683323	Standard	NR_027700		Approved	SCA36	uc002wgh.3	O00567	OTTHUMG00000031703	ENST00000329276.5:c.417G>A	chr20.hg19:g.2635441G>A		55.0	0.0		72.0	28.0	NM_006392	Q2M3T6|Q9NQ05	Silent	SNP	ENST00000329276.5	hg19	CCDS13030.1																																																																																			.	G|1.000;T|0.000		0.517	NOP56-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077631.2	NM_006392		A	2635441	G	A	2635441	2	1	235	1	0	0	0	0	0	0	0	1	10548	1364	48	3		3	NOP56	20	2635441	Silent	SNP	G	TCGA-DD-AAW2-01A-11D-A40P-10		2635441	60390079	110	32796										
RRP1B	23076	hgsc.bcm.edu	37	chr21	45107430	45107430	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	ttgtgtagaggaagaggacaGtgaaagcagtcttcaaaaga	13	4	2	4			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr21:45107430G>A	ENST00000340648.4	+	13	1292	c.1175G>A	c.(1174-1176)aGt>aAt	p.S392N		NM_015056.2	NP_055871.1	Q14684	RRP1B_HUMAN	ribosomal RNA processing 1B	392					negative regulation of phosphatase activity (GO:0010923)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|euchromatin (GO:0000791)|heterochromatin (GO:0000792)|nucleolus (GO:0005730)|nucleus (GO:0005634)|preribosome, small subunit precursor (GO:0030688)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(3)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(1)	21				STAD - Stomach adenocarcinoma(101;0.178)		GAAGAGGACAGTGAAAGCAGT	0.522																																					p.S392N		Atlas-SNP	.											.	RRP1B	51	.	0			c.G1175A						.						66	78	74					21																	45107430		2122	4177	6299	SO:0001583	missense	23076	exon13			AGGACAGTGAAAG	AK124620	CCDS33577.1	21q22.3	2014-06-13	2013-07-02	2007-03-26	ENSG00000160208	ENSG00000160208			23818	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 136"	610654	"KIAA0179", "ribosomal RNA processing 1 homolog B (S. cerevisiae)"	KIAA0179			Standard	NM_015056		Approved	Nnp1, RRP1, PPP1R136	uc002zdk.3	Q14684	OTTHUMG00000086872	ENST00000340648.4:c.1175G>A	chr21.hg19:g.45107430G>A	ENSP00000339145:p.Ser392Asn	22.0	0.0		29.0	16.0	NM_015056	Q8TBZ4	Missense_Mutation	SNP	ENST00000340648.4	hg19	CCDS33577.1	.	.	.	.	.	.	.	.	.	.	G	9.516	1.107103	0.20714	.	.	ENSG00000160208	ENST00000340648	T	0.02032	4.49	4.17	0.876	0.19138	.	0.809018	0.11744	N	0.533722	T	0.02342	0.0072	L	0.43152	1.355	0.09310	N	1	B	0.19331	0.035	B	0.17098	0.017	T	0.43861	-0.9365	10	0.87932	D	0	-0.0476	3.3812	0.07255	0.3914:0.2042:0.4044:0.0	.	392	Q14684	RRP1B_HUMAN	N	392	ENSP00000339145:S392N	ENSP00000339145:S392N	S	+	2	0	RRP1B	43931858	0.000000	0.05858	0.000000	0.03702	0.114000	0.19823	0.346000	0.19997	0.439000	0.26476	0.561000	0.74099	AGT	.	.		0.522	RRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195651.1	NM_015056		A	45107430	G	A	45107430	3	1	235	1	0	0	0	0	1	0	0	0	13703	1029	36	3	1225	3	RRP1B	21	45107430	Missense_Mutation	SNP	G	TCGA-DD-AAW2-01A-11D-A40P-10		45107430	3022465	111	32797										
AIRE	326	hgsc.bcm.edu	37	chr21	45707002	45707002	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	agcagccctgactccaagggGcaccgccagcccaggtaccc	11	18	0	1			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr21:45707002G>T	ENST00000291582.5	+	3	576	c.449G>T	c.(448-450)gGc>gTc	p.G150V		NM_000383.3	NP_000374.1	O43918	AIRE_HUMAN	autoimmune regulator	150					humoral immune response (GO:0006959)|immune response (GO:0006955)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|transcription regulatory region DNA binding (GO:0044212)|translation regulator activity (GO:0045182)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|skin(2)|urinary_tract(1)	14				Colorectal(79;0.0806)		ACTCCAAGGGGCACCGCCAGC	0.711									Autoimmune PolyEndocrinopathy Candidiasis Ectodermal Dystrophy																												p.G150V		Atlas-SNP	.											.	AIRE	61	.	0			c.G449T						.						16	22	20					21																	45707002		2155	4222	6377	SO:0001583	missense	326	exon3	Familial Cancer Database	APECED	CAAGGGGCACCGC	AB006684	CCDS13706.1	21q22.3	2014-09-17	2007-06-20		ENSG00000160224	ENSG00000160224		"Zinc fingers, PHD-type"	360	protein-coding gene	gene with protein product	"autoimmune polyendocrinopathy candidiasis ectodermal dystrophy"	607358	"autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy)"	APECED		9398840	Standard	NM_000383		Approved	PGA1, APS1	uc002zei.3	O43918	OTTHUMG00000086921	ENST00000291582.5:c.449G>T	chr21.hg19:g.45707002G>T	ENSP00000291582:p.Gly150Val	102.0	0.0		150.0	40.0	NM_000383	B2RP50|O43922|O43932|O75745	Missense_Mutation	SNP	ENST00000291582.5	hg19	CCDS13706.1	.	.	.	.	.	.	.	.	.	.	G	0.020	-1.435265	0.01108	.	.	ENSG00000160224	ENST00000291582	D	0.94613	-3.47	3.8	1.82	0.25136	.	0.759894	0.11472	N	0.560676	D	0.87573	0.6211	N	0.22421	0.69	0.23879	N	0.996583	B	0.18461	0.028	B	0.12837	0.008	T	0.75039	-0.3458	10	0.26408	T	0.33	-28.9906	6.7098	0.23270	0.0:0.1974:0.5991:0.2035	.	150	O43918	AIRE_HUMAN	V	150	ENSP00000291582:G150V	ENSP00000291582:G150V	G	+	2	0	AIRE	44531430	0.000000	0.05858	0.292000	0.24919	0.018000	0.09664	0.144000	0.16135	0.295000	0.22570	0.543000	0.68304	GGC	.	.		0.711	AIRE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195842.2			T	45707002	G	T	45707002	3	4	235	1	0	0	0	0	1	0	0	0	437	1203	42	3	459	3	AIRE	21	45707002	Missense_Mutation	SNP	G	TCGA-DD-AAW2-01A-11D-A40P-10	599572	45707002	2422893	112	32798										
PIWIL3	440822	hgsc.bcm.edu	37	chr22	25155853	25155853	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	caccttgagactgtgctcctCctcctgctcctcctcttgct	6	18	1	1			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr22:25155853C>T	ENST00000332271.5	-	3	622	c.206G>A	c.(205-207)gGa>gAa	p.G69E	PIWIL3_ENST00000532537.2_5'UTR|PIWIL3_ENST00000533313.1_5'UTR|PIWIL3_ENST00000527701.1_5'UTR	NM_001008496.3|NM_001255975.1	NP_001008496.2|NP_001242904.1	Q7Z3Z3	PIWL3_HUMAN	piwi-like RNA-mediated gene silencing 3	69					cell differentiation (GO:0030154)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	RNA binding (GO:0003723)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(15)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50						CTGTGCTCCTCCTCCTGCTCC	0.582																																					p.G69E		Atlas-SNP	.											.	PIWIL3	115	.	0			c.G206A						.						431	420	424					22																	25155853		2203	4300	6503	SO:0001583	missense	440822	exon3			GCTCCTCCTCCTG	AB079368	CCDS33623.1	22q11.23	2013-02-15	2013-02-15		ENSG00000184571	ENSG00000184571		"Argonaute/PIWI family"	18443	protein-coding gene	gene with protein product		610314	"piwi-like 3 (Drosophila)"			12906857	Standard	NM_001008496		Approved	HIWI3	uc003abd.2	Q7Z3Z3	OTTHUMG00000150788	ENST00000332271.5:c.206G>A	chr22.hg19:g.25155853C>T	ENSP00000330031:p.Gly69Glu	39.0	0.0		70.0	35.0	NM_001008496		Missense_Mutation	SNP	ENST00000332271.5	hg19	CCDS33623.1	.	.	.	.	.	.	.	.	.	.	C	6.241	0.412595	0.11812	.	.	ENSG00000184571	ENST00000332271	T	0.03982	3.74	2.32	0.113	0.14631	.	251.269000	0.02277	U	0.068982	T	0.02267	0.0070	N	0.08118	0	0.09310	N	0.999999	B;P	0.40731	0.141;0.728	B;B	0.37601	0.021;0.254	T	0.35943	-0.9768	10	0.02654	T	1	-0.842	3.4604	0.07531	0.0:0.5657:0.2712:0.1631	.	69;69	B4DYF7;Q7Z3Z3	.;PIWL3_HUMAN	E	69	ENSP00000330031:G69E	ENSP00000330031:G69E	G	-	2	0	PIWIL3	23485853	0.004000	0.15560	0.000000	0.03702	0.001000	0.01503	0.171000	0.16685	0.102000	0.17638	0.385000	0.25706	GGA	.	.		0.582	PIWIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320084.2	NM_001008496		T	25155853	C	T	25155853	3	4	235	1	0	0	0	0	1	0	0	0	11968	855	30	3	2518	3	PIWIL3	22	25155853	Missense_Mutation	SNP	C	TCGA-DD-AAW2-01A-11D-A40P-10		25155853	26148713	113	32799										
TAB1	10454	hgsc.bcm.edu	37	chr22	39817945	39817945	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	ggggttgtacaaggccctagAggcagcccatgggcctgggc	17	11	0	1			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chr22:39817945A>T	ENST00000216160.6	+	8	952	c.890A>T	c.(889-891)gAg>gTg	p.E297V	TAB1_ENST00000331454.3_Missense_Mutation_p.E297V	NM_006116.2	NP_006107.1	Q15750	TAB1_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 1	297	PP2C-like.				activation of MAPK activity (GO:0000187)|activation of MAPKKK activity (GO:0000185)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart morphogenesis (GO:0003007)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|lung development (GO:0030324)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|protein complex (GO:0043234)	catalytic activity (GO:0003824)|enzyme activator activity (GO:0008047)|kinase activator activity (GO:0019209)			breast(1)|endometrium(2)|large_intestine(2)|lung(8)|urinary_tract(1)	14						AAGGCCCTAGAGGCAGCCCAT	0.637																																					p.E297V		Atlas-SNP	.											.	TAB1	36	.	0			c.A890T						.						59	56	57					22																	39817945		2203	4300	6503	SO:0001583	missense	10454	exon8			CCCTAGAGGCAGC	U49928	CCDS13992.1, CCDS13993.1	22q13.1	2010-02-05	2010-02-05	2010-02-05	ENSG00000100324	ENSG00000100324			18157	protein-coding gene	gene with protein product	"TAK1-binding protein 1", "mitogen-activated protein kinase kinase kinase 7 interacting protein 1"	602615	"mitogen-activated protein kinase kinase kinase 7 interacting protein 1"	MAP3K7IP1		8638164, 10187861	Standard	NM_153497		Approved		uc003axt.3	Q15750	OTTHUMG00000151102	ENST00000216160.6:c.890A>T	chr22.hg19:g.39817945A>T	ENSP00000216160:p.Glu297Val	101.0	0.0		118.0	51.0	NM_153497	Q2PP09|Q8IZW2	Missense_Mutation	SNP	ENST00000216160.6	hg19	CCDS13993.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.527637	0.85706	.	.	ENSG00000100324	ENST00000216160;ENST00000331454	T;T	0.10099	2.91;2.91	5.26	5.26	0.73747	Protein phosphatase 2C-like (4);	0.000000	0.85682	D	0.000000	T	0.32763	0.0840	M	0.70595	2.14	0.80722	D	1	D;D;D	0.89917	0.996;1.0;1.0	P;D;D	0.91635	0.892;0.999;0.998	T	0.02877	-1.1099	10	0.52906	T	0.07	-12.6493	15.4812	0.75528	1.0:0.0:0.0:0.0	.	297;297;441	Q15750-2;Q15750;Q59FT7	.;TAB1_HUMAN;.	V	297	ENSP00000216160:E297V;ENSP00000333049:E297V	ENSP00000216160:E297V	E	+	2	0	TAB1	38147891	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	8.525000	0.90583	2.118000	0.64928	0.533000	0.62120	GAG	.	.		0.637	TAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321313.1	NM_153497		T	39817945	A	T	39817945	3	4	235	1	0	0	0	0	1	0	0	0	15510	304	11	4	920	4	TAB1	22	39817945	Missense_Mutation	SNP	A	TCGA-DD-AAW2-01A-11D-A40P-10	14662092	39817945	11486621	114	32800										
ACE2	59272	hgsc.bcm.edu	37	chrX	15609834	15609834	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	ctctacagatcagcaaacttAcgatttgctcttgccatctc	5	13	4	1			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chrX:15609834A>G	ENST00000252519.3	-	4	686		c.e4+1		ACE2_ENST00000427411.1_Splice_Site			Q9BYF1	ACE2_HUMAN	angiotensin I converting enzyme 2						angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|angiotensin-mediated drinking behavior (GO:0003051)|cellular protein metabolic process (GO:0044267)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|receptor biosynthetic process (GO:0032800)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of cell proliferation (GO:0042127)|regulation of cytokine production (GO:0001817)|regulation of inflammatory response (GO:0050727)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)|response to virus (GO:0009615)|viral entry into host cell (GO:0046718)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	carboxypeptidase activity (GO:0004180)|endopeptidase activity (GO:0004175)|glycoprotein binding (GO:0001948)|peptide hormone binding (GO:0017046)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(10)|lung(10)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	32	Hepatocellular(33;0.183)				Lisinopril(DB00722)|Moexipril(DB00691)	CAGCAAACTTACGATTTGCTC	0.493																																					.		Atlas-SNP	.											.	ACE2	87	.	0			c.583+2T>C						.						234	220	225					X																	15609834		2203	4300	6503	SO:0001630	splice_region_variant	59272	exon6			AAACTTACGATTT	AF291820	CCDS14169.1	Xp22	2013-06-12	2013-06-12		ENSG00000130234	ENSG00000130234	3.4.17.23		13557	protein-coding gene	gene with protein product	"peptidyl-dipeptidase A"	300335	"angiotensin I converting enzyme (peptidyl-dipeptidase A) 2"			10969042	Standard	NM_021804		Approved		uc004cxb.2	Q9BYF1	OTTHUMG00000021177	ENST00000252519.3:c.583+1T>C	chrX.hg19:g.15609834A>G		53.0	0.0		121.0	110.0	NM_021804	C7ECU1|Q6UWP0|Q86WT0|Q9NRA7|Q9UFZ6	Splice_Site	SNP	ENST00000252519.3	hg19	CCDS14169.1	.	.	.	.	.	.	.	.	.	.	A	13.01	2.109965	0.37242	.	.	ENSG00000130234	ENST00000252519;ENST00000427411	.	.	.	5.84	4.64	0.57946	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.5295	0.50599	0.8638:0.0:0.0:0.1362	.	.	.	.	.	-1	.	.	.	-	.	.	ACE2	15519755	1.000000	0.71417	0.099000	0.21106	0.386000	0.30323	8.220000	0.89772	0.874000	0.35823	0.483000	0.47432	.	.	.		0.493	ACE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055867.1		Intron	G	15609834	A	G	15609834	5	3	235	1	0	0	0	0	0	0	1	0	137	405	14	2	1892	2	ACE2	23	15609834	Splice_Site	SNP	A	TCGA-DD-AAW2-01A-11D-A40P-10		15609834	139660726	115	32801										
KDM5C	8242	hgsc.bcm.edu	37	chrX	53230776	53230776	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0260869565217391	3	1	0.717914438502674	1.01704545454545	0.625874125874126	1	1	0	acgccgctcttcttgcaccaTgatgaacatctccttatgca	6	14	3	2			TCGA-DD-AAW2-01A-11D-A40P-10	TCGA-DD-AAW2-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91d7e3b8-5b43-4687-82e3-fd0f5f872589	8038b7be-ceb3-48e7-a9a2-b55e0e60721f	g.chrX:53230776T>C	ENST00000375401.3	-	14	2549	c.2017A>G	c.(2017-2019)Atg>Gtg	p.M673V	KDM5C_ENST00000404049.3_Missense_Mutation_p.M672V|KDM5C_ENST00000375383.3_Missense_Mutation_p.M632V|KDM5C_ENST00000465402.1_5'UTR|KDM5C_ENST00000452825.3_Missense_Mutation_p.M606V|KDM5C_ENST00000375379.3_Missense_Mutation_p.M673V	NM_001282622.1|NM_004187.3	NP_001269551.1|NP_004178.2	P41229	KDM5C_HUMAN	lysine (K)-specific demethylase 5C	673					histone H3-K4 demethylation (GO:0034720)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-K4 specific) (GO:0032453)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(30)|large_intestine(9)|lung(17)|oesophagus(1)|ovary(6)|prostate(1)|salivary_gland(1)|skin(1)|upper_aerodigestive_tract(2)	82						TCTTGCACCATGATGAACATC	0.567			"N, F, S"		clear cell renal carcinoma																																p.M673V		Atlas-SNP	.		Rec	yes		X	Xp11.22-p11.21	8242	lysine (K)-specific demethylase 5C (JARID1C)		E	.	KDM5C	385	.	0			c.A2017G						.						90	83	85					X																	53230776		2203	4300	6503	SO:0001583	missense	8242	exon14			GCACCATGATGAA	Z29650	CCDS14351.1, CCDS55417.1, CCDS65269.1	Xp11.22-p11.21	2014-01-31	2009-04-06	2009-04-06	ENSG00000126012	ENSG00000126012		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	11114	protein-coding gene	gene with protein product		314690	"Jumonji, AT rich interactive domain 1C (RBP2-like)", "Smcy homolog, X-linked (mouse)", "jumonji, AT rich interactive domain 1C", "mental retardation, X-linked 13"	SMCX, JARID1C, MRX13		7951230, 8162017, 19826449	Standard	NM_004187		Approved	DXS1272E, XE169	uc004drz.3	P41229	OTTHUMG00000021606	ENST00000375401.3:c.2017A>G	chrX.hg19:g.53230776T>C	ENSP00000364550:p.Met673Val	77.0	0.0		142.0	6.0	NM_004187	B0QZ44|B4E3I2|F5H3T1|Q5JUX3|Q5JUX4|Q5JUX5|Q7Z5S5	Missense_Mutation	SNP	ENST00000375401.3	hg19	CCDS14351.1	.	.	.	.	.	.	.	.	.	.	T	14.54	2.565255	0.45694	.	.	ENSG00000126012	ENST00000452825;ENST00000375401;ENST00000404049;ENST00000375379;ENST00000375383	D;D;D;D;D	0.86769	-2.17;-1.88;-1.88;-1.88;-2.02	5.58	5.58	0.84498	.	0.091914	0.85682	D	0.000000	D	0.82981	0.5155	L	0.54965	1.715	0.37150	D	0.902132	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.003;0.001;0.002	T	0.81709	-0.0809	10	0.72032	D	0.01	-19.3333	8.1293	0.31018	0.1817:0.0:0.0:0.8183	.	606;672;673	F5H3T1;B0QZ44;P41229	.;.;KDM5C_HUMAN	V	606;673;672;673;632	ENSP00000445176:M606V;ENSP00000364550:M673V;ENSP00000385394:M672V;ENSP00000364528:M673V;ENSP00000364532:M632V	ENSP00000364528:M673V	M	-	1	0	KDM5C	53247501	0.997000	0.39634	1.000000	0.80357	0.996000	0.88848	0.675000	0.25232	1.864000	0.54056	0.486000	0.48141	ATG	.	.		0.567	KDM5C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056737.2	NM_004187		C	53230776	T	C	53230776	3	2	235	1	0	0	0	0	1	0	0	0	8144	1464	51	2	2815	2	KDM5C	23	53230776	Missense_Mutation	SNP	T	TCGA-DD-AAW2-01A-11D-A40P-10	37620942	53230776	102039784	116	32802										
PIK3CD	5293	hgsc.bcm.edu	37	chr1	9778944	9778944	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	tcgagaaagccaagaaggctCgctccaccaagaagaagtcc	10	12	0	4			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr1:9778944C>T	ENST00000377346.4	+	9	1408	c.1213C>T	c.(1213-1215)Cgc>Tgc	p.R405C	PIK3CD_ENST00000536656.1_Missense_Mutation_p.R370C|PIK3CD_ENST00000361110.2_Missense_Mutation_p.R370C|PIK3CD_ENST00000543390.1_Missense_Mutation_p.R72C	NM_005026.3	NP_005017.3	O00329	PK3CD_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta	405	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00880}.				adaptive immune response (GO:0002250)|B cell activation (GO:0042113)|B cell chemotaxis (GO:0035754)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|cytokine production (GO:0001816)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell chemotaxis (GO:0002551)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|natural killer cell activation (GO:0030101)|natural killer cell chemotaxis (GO:0035747)|natural killer cell differentiation (GO:0001779)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein phosphorylation (GO:0006468)|respiratory burst involved in defense response (GO:0002679)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|mast cell granule (GO:0042629)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(12)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31	all_lung(157;0.222)	all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0231)|Colorectal(212;7.52e-08)|COAD - Colon adenocarcinoma(227;1.78e-05)|Kidney(185;0.000322)|KIRC - Kidney renal clear cell carcinoma(229;0.00114)|BRCA - Breast invasive adenocarcinoma(304;0.0021)|STAD - Stomach adenocarcinoma(132;0.00395)|READ - Rectum adenocarcinoma(331;0.0419)	Caffeine(DB00201)	CAAGAAGGCTCGCTCCACCAA	0.637																																					p.R405C		Atlas-SNP	.											.	PIK3CD	86	.	0			c.C1213T						.						58	56	57					1																	9778944		2203	4300	6503	SO:0001583	missense	5293	exon9			AAGGCTCGCTCCA		CCDS104.1	1p36.2	2014-09-17	2012-07-13		ENSG00000171608	ENSG00000171608	2.7.1.153		8977	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase, catalytic, delta polypeptide", "phosphoinositide-3-kinase C"	602839	"phosphoinositide-3-kinase, catalytic, delta polypeptide"			9113989, 9455486	Standard	NM_005026		Approved	p110D	uc001aqb.4	O00329	OTTHUMG00000001450	ENST00000377346.4:c.1213C>T	chr1.hg19:g.9778944C>T	ENSP00000366563:p.Arg405Cys	65.0	0.0		57.0	20.0	NM_005026	A6NCG0|G1FFP1|O15445|Q5SR49	Missense_Mutation	SNP	ENST00000377346.4	hg19	CCDS104.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.368120	0.82463	.	.	ENSG00000171608	ENST00000536656;ENST00000377346;ENST00000361110;ENST00000360563;ENST00000543390	T;T;T;T	0.70986	-0.53;-0.53;-0.53;-0.53	5.35	5.35	0.76521	C2 calcium/lipid-binding domain, CaLB (1);Phosphoinositide 3-kinase, C2 (2);	0.113763	0.64402	D	0.000014	T	0.75206	0.3818	L	0.29908	0.895	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79784	0.973;0.993;0.987	T	0.76471	-0.2947	10	0.54805	T	0.06	-34.6236	13.1212	0.59327	0.1597:0.8402:0.0:0.0	.	405;370;405	B7ZM44;Q5SR50;O00329	.;.;PK3CD_HUMAN	C	370;405;370;370;72	ENSP00000446444:R370C;ENSP00000366563:R405C;ENSP00000354410:R370C;ENSP00000443811:R72C	ENSP00000353766:R370C	R	+	1	0	PIK3CD	9701531	0.871000	0.30034	0.954000	0.39281	0.947000	0.59692	1.712000	0.37940	2.499000	0.84300	0.563000	0.77884	CGC	.	.		0.637	PIK3CD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004235.1	NM_005026		T	9778944	C	T	9778944	3	4	236	1	0	0	0	0	1	0	0	0	11924	884	31	1	1239	1	PIK3CD	1	9778944	Missense_Mutation	SNP	C	TCGA-DD-AAW3-01A-11D-A40P-10		9778944	239471677	1	32803										
C1orf175	374977	hgsc.bcm.edu	37	chr1	55158176	55158177	+	Missense_Mutation	DNP	GG	GG	AC													0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	cgtttctggaggaccagggtGgctgggagctcatggagcag					rs537957753	byFrequency	TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr1:55158176_55158177GG>AC	ENST00000421030.2	+	16	3076_3077	c.2791_2792GG>AC	c.(2791-2793)GGc>ACc	p.G931T	MROH7_ENST00000545244.1_Missense_Mutation_p.G499T|MROH7_ENST00000339553.5_Missense_Mutation_p.G931T|MROH7_ENST00000409996.1_Missense_Mutation_p.G499T|MROH7_ENST00000395690.2_Missense_Mutation_p.G931T|MROH7-TTC4_ENST00000414150.2_Missense_Mutation_p.G931T|MROH7_ENST00000454855.2_Missense_Mutation_p.G449T	NM_001039464.2	NP_001034553	Q68CQ1	MROH7_HUMAN	maestro heat-like repeat family member 7	931						extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											GGACCAGGGTGGCTGGGAGCTC	0.594																																					p.G931S|p.G931A		Atlas-SNP	.											.	.	.	.	0			c.G2791A|c.G2792C						.																																			SO:0001583	missense	374977	exon16			CAGGGTGGCTGGG|AGGGTGGCTGGGA	AL832492	CCDS41342.2	1p32.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000184313	ENSG00000184313		"maestro heat-like repeat containing"	24802	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 175", "HEAT repeat containing 8"	C1orf175, HEATR8		12477932	Standard	NM_001039464		Approved	FLJ46354	uc010ooe.1	Q68CQ1	OTTHUMG00000009890	Exception_encountered	chr1.hg19:g.55158176_55158177delinsAC	ENSP00000396622:p.Gly931Thr	45.0|46.0	0.0		72.0|73.0	30.0	NM_001039464	A0AUX8|Q5TA99|Q6ZP40|Q6ZRH6|Q8N311|Q8NA14	Missense_Mutation	SNP	ENST00000421030.2	hg19	CCDS41342.2																																																																																			.	.		0.594	MROH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346978.1	NM_198547		AC	55158177	GG	AC	55158176	3	1	236	1	0	0	0	0	1	0	0	0	2018	1348	47	3	2845	3	C1orf175	1	55158176	Missense_Mutation	DNP	GG	TCGA-DD-AAW3-01A-11D-A40P-10	45379232	55158176	194092445	2	32804										
PTBP2	58155	hgsc.bcm.edu	37	chr1	97250726	97250726	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	ataaaagtagggattatactCgacctgatcttccatctggg	9	8	2	1			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr1:97250726C>T	ENST00000426398.2	+	8	863	c.820C>T	c.(820-822)Cga>Tga	p.R274*	PTBP2_ENST00000541987.1_Nonsense_Mutation_p.R243*|PTBP2_ENST00000370198.1_Nonsense_Mutation_p.R274*|PTBP2_ENST00000370197.1_Nonsense_Mutation_p.R274*|PTBP2_ENST00000609116.1_Nonsense_Mutation_p.R274*|PTBP2_ENST00000394184.3_Nonsense_Mutation_p.R285*|PTBP2_ENST00000482253.1_3'UTR	NM_021190.2	NP_067013.1	Q9UKA9	PTBP2_HUMAN	polypyrimidine tract binding protein 2	274					mRNA splice site selection (GO:0006376)|negative regulation of RNA splicing (GO:0033119)|regulation of neural precursor cell proliferation (GO:2000177)	spliceosomal complex (GO:0005681)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(15)|skin(1)	26		all_epithelial(167;2.95e-05)|all_lung(203;0.000396)|Lung NSC(277;0.00171)		all cancers(265;0.0582)|Epithelial(280;0.0716)|Colorectal(170;0.0879)|KIRC - Kidney renal clear cell carcinoma(1967;0.202)		GGATTATACTCGACCTGATCT	0.383																																					p.R274X		Atlas-SNP	.											.	PTBP2	62	.	0			c.C820T						.						127	122	123					1																	97250726		2203	4300	6503	SO:0001587	stop_gained	58155	exon8			TATACTCGACCTG	AB051232	CCDS754.1, CCDS72828.1, CCDS72829.1, CCDS72830.1	1p21.3	2013-07-16			ENSG00000117569	ENSG00000117569		"RNA binding motif (RRM) containing"	17662	protein-coding gene	gene with protein product		608449				11003644	Standard	XM_005271084		Approved	brPTB, nPTB, PTB, PTBLP	uc001drq.3	Q9UKA9	OTTHUMG00000010685	ENST00000426398.2:c.820C>T	chr1.hg19:g.97250726C>T	ENSP00000412788:p.Arg274*	90.0	0.0		83.0	30.0	NM_021190	Q8N0Z1|Q8N160|Q8NFB0|Q8NFB1|Q969N9|Q96Q76	Nonsense_Mutation	SNP	ENST00000426398.2	hg19	CCDS754.1	.	.	.	.	.	.	.	.	.	.	C	39	7.749179	0.98468	.	.	ENSG00000117569	ENST00000236228;ENST00000370198;ENST00000370197;ENST00000426398;ENST00000394184;ENST00000541987;ENST00000394176	.	.	.	5.57	4.66	0.58398	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.1846	0.65598	0.0:0.928:0.0:0.072	.	.	.	.	X	274;274;274;274;285;243;264	.	ENSP00000236228:R274X	R	+	1	2	PTBP2	97023314	1.000000	0.71417	0.999000	0.59377	0.951000	0.60555	3.524000	0.53495	1.362000	0.46000	0.591000	0.81541	CGA	.	.		0.383	PTBP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029453.1			T	97250726	C	T	97250726	4	4	236	1	0	0	0	0	0	1	0	0	12738	876	31	1	850	1	PTBP2	1	97250726	Nonsense_Mutation	SNP	C	TCGA-DD-AAW3-01A-11D-A40P-10	42092550	97250726	151999895	3	32805										
SYT6	148281	hgsc.bcm.edu	37	chr1	114680598	114680598	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	tgctggtgggctgctctgctGctggtggaagctcattgcca	15	10	2	0			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr1:114680598G>A	ENST00000610222.1	-	3	736	c.590C>T	c.(589-591)gCa>gTa	p.A197V	SYT6_ENST00000393296.1_Missense_Mutation_p.A197V|SYT6_ENST00000609117.1_Missense_Mutation_p.A112V|SYT6_ENST00000369547.1_Missense_Mutation_p.A112V|SYT6_ENST00000607941.1_Missense_Mutation_p.A112V			Q5T7P8	SYT6_HUMAN	synaptotagmin VI	197					acrosomal vesicle exocytosis (GO:0060478)	cell junction (GO:0030054)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|integral component of membrane (GO:0016021)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	clathrin binding (GO:0030276)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|syntaxin binding (GO:0019905)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(3)|large_intestine(10)|lung(14)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37	Lung SC(450;0.184)	all_cancers(81;4.41e-08)|all_epithelial(167;5.18e-08)|all_lung(203;1.58e-05)|Lung NSC(69;2.82e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CTGCTCTGCTGCTGGTGGAAG	0.597																																					p.A112V		Atlas-SNP	.											.	SYT6	66	.	0			c.C335T						.						80	69	73					1																	114680598		2203	4300	6503	SO:0001583	missense	148281	exon3			TCTGCTGCTGGTG		CCDS871.1	1p13.1	2013-01-21			ENSG00000134207	ENSG00000134207		"Synaptotagmins"	18638	protein-coding gene	gene with protein product		607718				11543631	Standard	NM_205848		Approved		uc021orz.1	Q5T7P8	OTTHUMG00000011755	ENST00000610222.1:c.590C>T	chr1.hg19:g.114680598G>A	ENSP00000476396:p.Ala197Val	45.0	0.0		56.0	27.0	NM_205848	B1AMB8|B3KPK1	Missense_Mutation	SNP	ENST00000610222.1	hg19		.	.	.	.	.	.	.	.	.	.	G	5.713	0.316132	0.10789	.	.	ENSG00000134207	ENST00000369547;ENST00000393296;ENST00000369546;ENST00000369545	T;T;T;T	0.58358	0.34;0.35;0.34;0.35	5.38	2.41	0.29592	.	0.350509	0.29093	N	0.013173	T	0.12135	0.0295	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.15464	-1.0436	10	0.33141	T	0.24	.	1.8167	0.03102	0.2673:0.1358:0.4576:0.1393	.	197	Q5T7P8	SYT6_HUMAN	V	112;197;112;197	ENSP00000358560:A112V;ENSP00000376974:A197V;ENSP00000358559:A112V;ENSP00000358558:A197V	ENSP00000358558:A197V	A	-	2	0	SYT6	114482121	0.274000	0.24191	0.008000	0.14137	0.420000	0.31355	1.326000	0.33735	0.609000	0.30018	0.655000	0.94253	GCA	.	.		0.597	SYT6-004	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000314819.2	NM_205848		A	114680598	G	A	114680598	3	1	236	1	0	0	0	0	1	0	0	0	15493	1319	46	3	962	3	SYT6	1	114680598	Missense_Mutation	SNP	G	TCGA-DD-AAW3-01A-11D-A40P-10	17429872	114680598	134570023	4	32806										
AMPD1	270	hgsc.bcm.edu	37	chr1	115222318	115222318	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	ggaacttcaggcgccggtggGtataggtcttactgtgaaaa	14	7	2	1			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr1:115222318G>A	ENST00000520113.2	-	7	893	c.878C>T	c.(877-879)aCc>aTc	p.T293I	AMPD1_ENST00000353928.6_Missense_Mutation_p.T260I|AMPD1_ENST00000369538.3_Missense_Mutation_p.T289I			P23109	AMPD1_HUMAN	adenosine monophosphate deaminase 1	293					IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(3)|pancreas(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	45	all_epithelial(7;7.83e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	Adenosine monophosphate(DB00131)	GCGCCGGTGGGTATAGGTCTT	0.413																																					p.T293I		Atlas-SNP	.											.	AMPD1	223	.	0			c.C878T						.						90	98	95					1																	115222318		2203	4300	6503	SO:0001583	missense	270	exon7			CGGTGGGTATAGG	M60092	CCDS876.1, CCDS876.2, CCDS53349.1	1p13	2010-02-10	2010-02-10		ENSG00000116748	ENSG00000116748	3.5.4.6		468	protein-coding gene	gene with protein product	"AMPD isoform M", "skeletal muscle AMPD"	102770	"adenosine monophosphate deaminase 1 (isoform M)"			1400401	Standard	NM_001172626		Approved	MAD, MADA	uc001efe.2	P23109	OTTHUMG00000011892	ENST00000520113.2:c.878C>T	chr1.hg19:g.115222318G>A	ENSP00000430075:p.Thr293Ile	114.0	0.0		114.0	52.0	NM_000036	A8K5N4|B2RAM1|F2Z3B3|Q5TF00|Q5TF02	Missense_Mutation	SNP	ENST00000520113.2	hg19	CCDS876.2	.	.	.	.	.	.	.	.	.	.	G	15.99	2.995677	0.54147	.	.	ENSG00000116748	ENST00000520113;ENST00000369538;ENST00000353928	D;D;D	0.86097	-2.07;-2.07;-2.07	5.63	5.63	0.86233	.	0.334724	0.38381	N	0.001701	T	0.78502	0.4293	M	0.62723	1.935	0.34864	D	0.742917	P;B	0.35383	0.498;0.042	B;B	0.33620	0.167;0.04	T	0.83320	-0.0018	10	0.87932	D	0	-2.9922	15.465	0.75394	0.0:0.2525:0.7475:0.0	.	289;260	Q5TF02;P23109	.;AMPD1_HUMAN	I	293;289;260	ENSP00000430075:T293I;ENSP00000358551:T289I;ENSP00000316520:T260I	ENSP00000316520:T260I	T	-	2	0	AMPD1	115023841	1.000000	0.71417	0.934000	0.37439	0.982000	0.71751	3.907000	0.56348	2.826000	0.97356	0.655000	0.94253	ACC	.	.		0.413	AMPD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032860.4			A	115222318	G	A	115222318	3	1	236	1	0	0	0	0	1	0	0	0	585	1261	44	3	1504	3	AMPD1	1	115222318	Missense_Mutation	SNP	G	TCGA-DD-AAW3-01A-11D-A40P-10	541720	115222318	134028303	5	32807										
FLG	2312	hgsc.bcm.edu	37	chr1	152283840	152283840	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	tggtgggatccctgccttccTcctctccttgaccccgggtg	11	16	1	1			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr1:152283840T>A	ENST00000368799.1	-	3	3557	c.3522A>T	c.(3520-3522)ggA>ggT	p.G1174G	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1174	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCTGCCTTCCTCCTCTCCTTG	0.602									Ichthyosis																												p.G1174G		Atlas-SNP	.											.	FLG	900	.	0			c.A3522T						.						323	363	349					1																	152283840		2203	4300	6503	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CCTTCCTCCTCTC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.3522A>T	chr1.hg19:g.152283840T>A		76.0	0.0		119.0	65.0	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	hg19	CCDS30860.1																																																																																			.	.		0.602	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152283840	T	A	152283840	2	1	236	1	0	0	0	0	0	0	0	1	5930	1538	54	4		4	FLG	1	152283840	Silent	SNP	T	TCGA-DD-AAW3-01A-11D-A40P-10	37061522	152283840	96966781	6	32808										
CCT3	7203	hgsc.bcm.edu	37	chr1	156303356	156303356	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	accaagaataattactgatgTggtcccatctccaacctctt	5	12	2	2			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr1:156303356T>A	ENST00000295688.3	-	5	566	c.286A>T	c.(286-288)Aca>Tca	p.T96S	CCT3_ENST00000368256.3_5'UTR|CCT3_ENST00000472765.2_Missense_Mutation_p.T51S|CCT3_ENST00000368259.2_Missense_Mutation_p.T58S|CCT3_ENST00000368261.3_Missense_Mutation_p.T51S	NM_005998.4	NP_005989.3	P49368	TCPG_HUMAN	chaperonin containing TCP1, subunit 3 (gamma)	96					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			endometrium(4)|large_intestine(1)|liver(1)|lung(11)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	22	Hepatocellular(266;0.158)					ATTACTGATGTGGTCCCATCT	0.403																																					p.T96S		Atlas-SNP	.											.	CCT3	61	.	0			c.A286T						.						133	135	135					1																	156303356		2203	4300	6503	SO:0001583	missense	7203	exon5			CTGATGTGGTCCC	BC008019	CCDS1140.2, CCDS30888.1	1q23	2011-09-02			ENSG00000163468	ENSG00000163468		"Heat Shock Proteins / Chaperonins"	1616	protein-coding gene	gene with protein product		600114		TRIC5		8110840	Standard	NM_005998		Approved	Cctg	uc001fol.2	P49368	OTTHUMG00000024061	ENST00000295688.3:c.286A>T	chr1.hg19:g.156303356T>A	ENSP00000295688:p.Thr96Ser	36.0	0.0		60.0	38.0	NM_005998	A6NE14|Q5SZY1|Q9BR64	Missense_Mutation	SNP	ENST00000295688.3	hg19	CCDS1140.2	.	.	.	.	.	.	.	.	.	.	T	31	5.077699	0.94000	.	.	ENSG00000163468	ENST00000295688;ENST00000368259;ENST00000368261;ENST00000472765;ENST00000413555;ENST00000496684;ENST00000533194;ENST00000446905;ENST00000478640;ENST00000415548	D;D;D;D;D;D;D;D;D;D	0.92858	-1.72;-1.72;-1.72;-1.72;-1.72;-1.72;-1.72;-1.72;-1.72;-3.12	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	D	0.97324	0.9125	H	0.98178	4.165	0.58432	D	0.99999	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.87578	0.997;0.998;0.99	D	0.98444	1.0588	10	0.87932	D	0	-10.3319	12.6112	0.56552	0.0:0.0:0.0:1.0	.	58;96;96	P49368-2;E9PAQ6;P49368	.;.;TCPG_HUMAN	S	96;58;51;51;120;96;17;82;75;96	ENSP00000295688:T96S;ENSP00000357242:T58S;ENSP00000357244:T51S;ENSP00000431543:T51S;ENSP00000413308:T120S;ENSP00000434232:T96S;ENSP00000434481:T17S;ENSP00000388799:T82S;ENSP00000435026:T75S;ENSP00000413431:T96S	ENSP00000295688:T96S	T	-	1	0	CCT3	154569980	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.394000	0.79862	2.234000	0.73211	0.528000	0.53228	ACA	.	.		0.403	CCT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060602.3	NM_005998		A	156303356	T	A	156303356	3	1	236	1	0	0	0	0	1	0	0	0	2956	1696	59	4	1391	4	CCT3	1	156303356	Missense_Mutation	SNP	T	TCGA-DD-AAW3-01A-11D-A40P-10	4019516	156303356	92947265	7	32809										
PRCC	5546	hgsc.bcm.edu	37	chr1	156737670	156737670	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	tacatctgggcccgctttagGgggcttgttcgcttctctcc	11	13	2	0			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr1:156737670G>C	ENST00000271526.4	+	1	379	c.107G>C	c.(106-108)gGg>gCg	p.G36A	PRCC_ENST00000353233.3_Missense_Mutation_p.G36A|HDGF_ENST00000465180.1_5'Flank|PRCC_ENST00000491853.1_Intron	NM_005973.4	NP_005964.3	Q92733	PRCC_HUMAN	papillary renal cell carcinoma (translocation-associated)	36	Mediates interaction with MAD2L2.				mitotic cell cycle checkpoint (GO:0007093)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)			PRCC/TFE3(25)	breast(1)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(1)|liver(1)|lung(5)|upper_aerodigestive_tract(1)	15	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CCCGCTTTAGGGGGCTTGTTC	0.677			T	TFE3	papillary renal																																p.G36A		Atlas-SNP	.		Dom	yes		1	1q21.1	5546	papillary renal cell carcinoma (translocation-associated)		E	.	PRCC	39	.	0			c.G107C						.						17	15	16					1																	156737670		2200	4298	6498	SO:0001583	missense	5546	exon1			CTTTAGGGGGCTT	X99720	CCDS1157.1	1q21.1	2008-02-05			ENSG00000143294	ENSG00000143294			9343	protein-coding gene	gene with protein product		179755				8872474	Standard	NM_005973		Approved	RCCP1	uc001fqa.3	Q92733	OTTHUMG00000041294	ENST00000271526.4:c.107G>C	chr1.hg19:g.156737670G>C	ENSP00000271526:p.Gly36Ala	181.0	0.0		226.0	58.0	NM_005973	A8K1F7|O00665|O00724|Q5SZ06	Missense_Mutation	SNP	ENST00000271526.4	hg19	CCDS1157.1	.	.	.	.	.	.	.	.	.	.	G	15.46	2.839359	0.51057	.	.	ENSG00000143294	ENST00000271526;ENST00000353233	T;T	0.42513	0.97;0.97	5.55	5.55	0.83447	.	0.054551	0.64402	D	0.000001	T	0.26521	0.0648	L	0.53249	1.67	0.41931	D	0.99056	P;P	0.46784	0.884;0.884	B;B	0.43838	0.433;0.337	T	0.06516	-1.0822	10	0.07813	T	0.8	-10.7178	16.3527	0.83220	0.0:0.0:1.0:0.0	.	36;36	A6NG79;Q92733	.;PRCC_HUMAN	A	36	ENSP00000271526:G36A;ENSP00000339300:G36A	ENSP00000271526:G36A	G	+	2	0	PRCC	155004294	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	4.795000	0.62489	2.885000	0.99019	0.655000	0.94253	GGG	.	.		0.677	PRCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098941.2	NM_005973		C	156737670	G	C	156737670	3	2	236	1	0	0	0	0	1	0	0	0	12459	1232	43	4	109	4	PRCC	1	156737670	Missense_Mutation	SNP	G	TCGA-DD-AAW3-01A-11D-A40P-10	434314	156737670	92512951	8	32810										
SLC9A11	284525	hgsc.bcm.edu	37	chr1	173556888	173556888	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	taggcaagattgcaaatcccAtgaatctttattgaatttta	6	6	1	3			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr1:173556888A>T	ENST00000367714.3	-	5	861	c.439T>A	c.(439-441)Tgg>Agg	p.W147R	SLC9C2_ENST00000536496.1_Missense_Mutation_p.W45R|RP3-436N22.3_ENST00000431459.1_RNA	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	147					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)										TGCAAATCCCATGAATCTTTA	0.333																																					p.W147R		Atlas-SNP	.											.	.	.	.	0			c.T439A						.						117	118	117					1																	173556888		2203	4299	6502	SO:0001583	missense	284525	exon5			AATCCCATGAATC	AK128104	CCDS1308.1	1q25.1	2013-07-18	2013-07-18	2012-03-22	ENSG00000162753	ENSG00000162753		"Solute carriers"	28664	protein-coding gene	gene with protein product			"solute carrier family 9, isoform 11", "solute carrier family 9, member 11", "solute carrier family 9, member C2"	SLC9A11			Standard	NM_178527		Approved	MGC43026	uc001giz.2	Q5TAH2	OTTHUMG00000034800	ENST00000367714.3:c.439T>A	chr1.hg19:g.173556888A>T	ENSP00000356687:p.Trp147Arg	102.0	0.0		128.0	61.0	NM_178527	Q86UF3	Missense_Mutation	SNP	ENST00000367714.3	hg19	CCDS1308.1	.	.	.	.	.	.	.	.	.	.	A	16.20	3.054827	0.55325	.	.	ENSG00000162753	ENST00000367714;ENST00000536496	T;T	0.06142	3.34;3.34	5.59	5.59	0.84812	Cation/H+ exchanger (1);	0.000000	0.53938	D	0.000046	T	0.11495	0.0280	L	0.54323	1.7	0.31595	N	0.653435	D	0.89917	1.0	D	0.97110	1.0	T	0.01464	-1.1348	10	0.66056	D	0.02	-9.1585	12.153	0.54059	1.0:0.0:0.0:0.0	.	147	Q5TAH2	S9A11_HUMAN	R	147;45	ENSP00000356687:W147R;ENSP00000445437:W45R	ENSP00000356687:W147R	W	-	1	0	SLC9A11	171823511	0.996000	0.38824	0.917000	0.36280	0.379000	0.30106	4.446000	0.60014	2.137000	0.66172	0.482000	0.46254	TGG	.	.		0.333	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527		T	173556888	A	T	173556888	3	4	236	1	0	0	0	0	1	0	0	0	14726	217	8	4	3031	4	SLC9A11	1	173556888	Missense_Mutation	SNP	A	TCGA-DD-AAW3-01A-11D-A40P-10	16819218	173556888	75693733	9	32811										
KCNT2	343450	hgsc.bcm.edu	37	chr1	196398776	196398776	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	agcttggaggaccatgtttcAggagtgacatccccgaagcc	12	11	1	1			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr1:196398776A>T	ENST00000294725.9	-	9	1665	c.750T>A	c.(748-750)ccT>ccA	p.P250P	KCNT2_ENST00000367433.5_Silent_p.P250P|KCNT2_ENST00000451324.2_Intron|KCNT2_ENST00000609185.1_Silent_p.P250P|KCNT2_ENST00000367431.4_Silent_p.P250P|KCNT2_ENST00000498426.1_5'UTR			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	250					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(16)|lung(43)|ovary(5)|pancreas(1)|prostate(1)|skin(11)|stomach(2)|upper_aerodigestive_tract(1)	97						ACCATGTTTCAGGAGTGACAT	0.408																																					p.P250P		Atlas-SNP	.											.	KCNT2	243	.	0			c.T750A						.						118	103	108					1																	196398776		2203	4300	6503	SO:0001819	synonymous_variant	343450	exon9			TGTTTCAGGAGTG	BX647852, AY359444, AK127807	CCDS1384.1, CCDS72994.1, CCDS72995.1	1q31.3	2012-07-05			ENSG00000162687	ENSG00000162687		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18866	protein-coding gene	gene with protein product	"sodium and chloride activated ATP sensitive potassium channel"	610044				16382103	Standard	NM_198503		Approved	KCa4.2, SLICK, SLO2.1	uc001gtd.1	Q6UVM3	OTTHUMG00000035611	ENST00000294725.9:c.750T>A	chr1.hg19:g.196398776A>T		418.0	0.0		595.0	360.0	NM_198503	Q3SY59|Q5VTN1|Q6ZMT3	Silent	SNP	ENST00000294725.9	hg19	CCDS1384.1																																																																																			.	.		0.408	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503		T	196398776	A	T	196398776	2	4	236	1	0	0	0	0	0	0	0	1	8101	175	7	4		4	KCNT2	1	196398776	Silent	SNP	A	TCGA-DD-AAW3-01A-11D-A40P-10	22841888	196398776	52851845	10	32812										
RYR2	6262	hgsc.bcm.edu	37	chr1	237804207	237804207	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	ttcatgaaagtgacacagagGaggaggaagatgacactatc	12	6	1	5			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr1:237804207G>T	ENST00000366574.2	+	47	7443	c.7126G>T	c.(7126-7128)Gag>Tag	p.E2376*	RYR2_ENST00000360064.6_Nonsense_Mutation_p.E2374*|RYR2_ENST00000542537.1_Nonsense_Mutation_p.E2360*	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	2376	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TGACACAGAGGAGGAGGAAGA	0.433																																					p.E2376X		Atlas-SNP	.											.	RYR2	1273	.	0			c.G7126T						.						143	136	138					1																	237804207		2041	4212	6253	SO:0001587	stop_gained	6262	exon47			ACAGAGGAGGAGG	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.7126G>T	chr1.hg19:g.237804207G>T	ENSP00000355533:p.Glu2376*	54.0	0.0		80.0	54.0	NM_001035	Q15411|Q546N8|Q5T3P2	Nonsense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	G	48	14.281882	0.99788	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	.	.	.	5.84	4.92	0.64577	.	0.079351	0.47093	D	0.000249	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	-10.7054	15.3501	0.74376	0.0678:0.0:0.9322:0.0	.	.	.	.	X	2376;2374;2360	.	ENSP00000353174:E2374X	E	+	1	0	RYR2	235870830	1.000000	0.71417	0.969000	0.41365	0.562000	0.35680	7.635000	0.83286	2.779000	0.95612	0.591000	0.81541	GAG	.	.		0.433	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		T	237804207	G	T	237804207	4	4	236	1	0	0	0	0	0	1	0	0	13784	1175	41	3	7312	3	RYR2	1	237804207	Nonsense_Mutation	SNP	G	TCGA-DD-AAW3-01A-11D-A40P-10	41405431	237804207	11446414	11	32813										
OR14C36	127066	hgsc.bcm.edu	37	chr1	248512967	248512967	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	agaaataagcaaataaaggtGgccatcaagaaaatcatgaa	8	5	2	3			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr1:248512967G>A	ENST00000317861.1	+	1	891	c.891G>A	c.(889-891)gtG>gtA	p.V297V		NM_001001918.1	NP_001001918.1	Q8NHC7	O14CZ_HUMAN	olfactory receptor, family 14, subfamily C, member 36	297						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|liver(2)|lung(20)|ovary(2)|prostate(3)|skin(7)|upper_aerodigestive_tract(2)	43						AAATAAAGGTGGCCATCAAGA	0.383																																					p.V297V		Atlas-SNP	.											.	OR14C36	113	.	0			c.G891A						.						64	79	74					1																	248512967		2148	4170	6318	SO:0001819	synonymous_variant	127066	exon1			AAAGGTGGCCATC	BK004466	CCDS31112.1	1q44	2012-08-09	2008-04-02	2008-04-02	ENSG00000177174	ENSG00000177174		"GPCR / Class A : Olfactory receptors"	15026	protein-coding gene	gene with protein product			"olfactory receptor, family 5, subfamily BF, member 1"	OR5BF1			Standard	NM_001001918		Approved		uc010pzl.2	Q8NHC7	OTTHUMG00000040463	ENST00000317861.1:c.891G>A	chr1.hg19:g.248512967G>A		94.0	0.0		119.0	24.0	NM_001001918	Q6IEZ6	Silent	SNP	ENST00000317861.1	hg19	CCDS31112.1																																																																																			.	.		0.383	OR14C36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097359.1	NM_001001918		A	248512967	G	A	248512967	2	1	236	1	0	0	0	0	0	0	0	1	10955	1335	47	3		3	OR14C36	1	248512967	Silent	SNP	G	TCGA-DD-AAW3-01A-11D-A40P-10	10708760	248512967	737654	12	32814										
DDX1	1653	hgsc.bcm.edu	37	chr2	15758310	15758310	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	ttgtttctcatgcaggatggGcttctttctcaaggttattc	9	8	3	0			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr2:15758310G>T	ENST00000381341.2	+	17	1511	c.1122G>T	c.(1120-1122)ggG>ggT	p.G374G	DDX1_ENST00000233084.3_Silent_p.G374G			Q92499	DDX1_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 1	374	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.|Necessary for interaction with RELA.				ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|multicellular organismal development (GO:0007275)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translational initiation (GO:0006446)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|spliceosomal complex assembly (GO:0000245)|transcription, DNA-templated (GO:0006351)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	cleavage body (GO:0071920)|cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|tRNA-splicing ligase complex (GO:0072669)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA/RNA helicase activity (GO:0033677)|double-stranded RNA binding (GO:0003725)|exonuclease activity (GO:0004527)|nuclease activity (GO:0004518)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|transcription cofactor activity (GO:0003712)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(13)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)	all_epithelial(98;2.96e-07)|Acute lymphoblastic leukemia(84;4.24e-05)|Ovarian(717;0.0694)	GBM - Glioblastoma multiforme(3;0.00969)	Epithelial(75;4.35e-05)|OV - Ovarian serous cystadenocarcinoma(76;0.133)		TGCAGGATGGGCTTCTTTCTC	0.289																																					p.G374G		Atlas-SNP	.											.	DDX1	70	.	0			c.G1122T						.						125	143	137					2																	15758310		2203	4299	6502	SO:0001819	synonymous_variant	1653	exon16			GGATGGGCTTCTT	X70649	CCDS1686.1	2p24	2012-02-23	2012-02-23		ENSG00000079785	ENSG00000079785		"DEAD-boxes"	2734	protein-coding gene	gene with protein product		601257	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 1", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 1"			1552844, 19058135	Standard	NM_004939		Approved	DBP-RB	uc002rce.4	Q92499	OTTHUMG00000090593	ENST00000381341.2:c.1122G>T	chr2.hg19:g.15758310G>T		212.0	0.0		186.0	73.0	NM_004939	B4DME8|B4DPN6	Silent	SNP	ENST00000381341.2	hg19	CCDS1686.1																																																																																			.	.		0.289	DDX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207141.2	NM_004939		T	15758310	G	T	15758310	2	4	236	1	0	0	0	0	0	0	0	1	4343	1190	42	3		3	DDX1	2	15758310	Silent	SNP	G	TCGA-DD-AAW3-01A-11D-A40P-10		15758310	227441063	13	32815										
OTOF	9381	hgsc.bcm.edu	37	chr2	26702479	26702479	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	gctccttccggggccgaggcCgctggggccgggacaggcca	18	15	0	0	rs142370721		TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr2:26702479C>T	ENST00000272371.2	-	17	2081	c.1955G>A	c.(1954-1956)cGg>cAg	p.R652Q	OTOF_ENST00000402415.3_5'Flank|OTOF_ENST00000338581.6_5'Flank|OTOF_ENST00000403946.3_Missense_Mutation_p.R652Q|OTOF_ENST00000339598.3_5'Flank	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	652					membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			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)					GGGCCGAGGCCGCTGGGGCCG	0.642													C|||	1	0.000199681	0	0	5008	,	,		18849	0		0	False		,,,				2504	0.001				p.R652Q	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											.	OTOF	524	.	0			c.G1955A						.	C	GLN/ARG	1,4397	2.1+/-5.4	0,1,2198	31	35	34		1955	3.8	0.8	2	dbSNP_134	34	0,8598		0,0,4299	no	missense	OTOF	NM_194248.2	43	0,1,6497	TT,TC,CC		0.0,0.0227,0.0077	benign	652/1998	26702479	1,12995	2199	4299	6498	SO:0001583	missense	9381	exon17			CGAGGCCGCTGGG	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"fer-1-like family member 2"	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.1955G>A	chr2.hg19:g.26702479C>T	ENSP00000272371:p.Arg652Gln	102.0	0.0		90.0	33.0	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Missense_Mutation	SNP	ENST00000272371.2	hg19	CCDS1725.1	.	.	.	.	.	.	.	.	.	.	C	8.707	0.911027	0.17833	2.27E-4	0.0	ENSG00000115155	ENST00000272371;ENST00000403946	T;T	0.79845	-1.31;-1.31	4.63	3.75	0.43078	.	0.000000	0.22692	U	0.056801	T	0.58409	0.2120	N	0.12182	0.205	0.09310	N	1	B	0.32620	0.378	B	0.19148	0.024	T	0.43782	-0.9370	10	0.17832	T	0.49	-13.8053	10.2866	0.43570	0.0:0.9014:0.0:0.0986	.	652	Q9HC10	OTOF_HUMAN	Q	652	ENSP00000272371:R652Q;ENSP00000385255:R652Q	ENSP00000272371:R652Q	R	-	2	0	OTOF	26555983	0.925000	0.31364	0.822000	0.32727	0.015000	0.08874	2.440000	0.44855	0.914000	0.36822	0.561000	0.74099	CGG	.	C|1.000;T|0.000		0.642	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3			T	26702479	C	T	26702479	3	4	236	1	0	0	0	0	1	0	0	0	11312	652	23	1	4487	1	OTOF	2	26702479	Missense_Mutation	SNP	C	TCGA-DD-AAW3-01A-11D-A40P-10	10944169	26702479	216496894	14	32816										
TTC7A	57217	hgsc.bcm.edu	37	chr2	47278963	47278963	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	gactatgccctcttcggtccTgaagcagggccccatgcagc	11	15	1	1			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr2:47278963T>A	ENST00000319190.5	+	18	2464	c.2096T>A	c.(2095-2097)cTg>cAg	p.L699Q	TTC7A_ENST00000409245.1_Missense_Mutation_p.L665Q|TTC7A_ENST00000394850.2_Missense_Mutation_p.L723Q|TTC7A_ENST00000263737.6_Missense_Mutation_p.L345Q	NM_020458.2	NP_065191.2	Q9ULT0	TTC7A_HUMAN	tetratricopeptide repeat domain 7A	699					cellular iron ion homeostasis (GO:0006879)|hemopoiesis (GO:0030097)					breast(4)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			TCTTCGGTCCTGAAGCAGGGC	0.657																																					p.L699Q		Atlas-SNP	.											.	TTC7A	80	.	0			c.T2096A						.						38	37	37					2																	47278963		2203	4300	6503	SO:0001583	missense	57217	exon18			CGGTCCTGAAGCA	AB032966	CCDS33193.1, CCDS74510.1, CCDS74511.1	2p16.3	2013-01-10	2004-06-02	2004-06-02	ENSG00000068724	ENSG00000068724		"Tetratricopeptide (TTC) repeat domain containing"	19750	protein-coding gene	gene with protein product		609332	"tetratricopeptide repeat domain 7"	TTC7		10574461	Standard	XM_005264439		Approved	KIAA1140	uc002rvo.3	Q9ULT0	OTTHUMG00000153121	ENST00000319190.5:c.2096T>A	chr2.hg19:g.47278963T>A	ENSP00000316699:p.Leu699Gln	95.0	0.0		106.0	39.0	NM_020458	Q6PIX4|Q8ND67|Q9BUS3	Missense_Mutation	SNP	ENST00000319190.5	hg19	CCDS33193.1	.	.	.	.	.	.	.	.	.	.	T	11.68	1.709502	0.30322	.	.	ENSG00000068724	ENST00000409245;ENST00000319190;ENST00000394850;ENST00000263737;ENST00000434093	T;T;T;T	0.32515	1.87;1.88;1.49;1.45	5.18	5.18	0.71444	.	0.434081	0.25619	N	0.029426	T	0.12902	0.0313	N	0.03608	-0.345	0.80722	D	1	B;B;B;B	0.26195	0.144;0.013;0.087;0.022	B;B;B;B	0.20955	0.032;0.01;0.02;0.022	T	0.13872	-1.0493	10	0.29301	T	0.29	-8.4471	8.7474	0.34594	0.0:0.0851:0.0:0.9149	.	723;665;699;665	Q2T9J9;B3KPK7;Q9ULT0;G5E9G4	.;.;TTC7A_HUMAN;.	Q	665;699;723;345;526	ENSP00000386307:L665Q;ENSP00000316699:L699Q;ENSP00000378320:L723Q;ENSP00000263737:L345Q	ENSP00000263737:L345Q	L	+	2	0	TTC7A	47132467	0.994000	0.37717	0.953000	0.39169	0.984000	0.73092	1.574000	0.36482	2.172000	0.68678	0.533000	0.62120	CTG	.	.		0.657	TTC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329667.2	XM_372927		A	47278963	T	A	47278963	3	1	236	1	0	0	0	0	1	0	0	0	16727	1580	55	4	2166	4	TTC7A	2	47278963	Missense_Mutation	SNP	T	TCGA-DD-AAW3-01A-11D-A40P-10	20576484	47278963	195920410	15	32817										
KIAA1310	55683	hgsc.bcm.edu	37	chr2	97274685	97274685	+	Silent	SNP	T	T	C													0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	gggacttcaaaggccaagtcTctgcgggccacatcgcgggg							TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr2:97274685T>C	ENST00000431828.1	-	13	1576	c.1500A>G	c.(1498-1500)agA>agG	p.R500R	KANSL3_ENST00000599854.1_Silent_p.R413R|KANSL3_ENST00000487070.1_5'UTR|KANSL3_ENST00000440133.1_Silent_p.R294R|KANSL3_ENST00000441706.2_Silent_p.R413R			Q9P2N6	KANL3_HUMAN	KAT8 regulatory NSL complex subunit 3	500					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											AGGCCAAGTCTCTGCGGGCCA	0.617																																					p.R500R		Atlas-SNP	.											.	.	.	.	0			c.A1500G						.						14	17	16					2																	97274685		1897	4122	6019	SO:0001819	synonymous_variant	55683	exon13			CAAGTCTCTGCGG	BC063792	CCDS46361.1	2q11.2	2011-10-31	2011-10-31	2011-10-31	ENSG00000114982	ENSG00000114982			25473	protein-coding gene	gene with protein product			"KIAA1310"	KIAA1310			Standard	NM_001115016		Approved	FLJ10081, Rcd1, NSL3	uc002swn.5	Q9P2N6	OTTHUMG00000155249	ENST00000431828.1:c.1500A>G	chr2.hg19:g.97274685T>C		109.0	0.0		103.0	7.0	NM_001115016	A1L184|D3DXH3|D3DXH4|Q05BU4|Q6P3X2|Q6PJH6|Q86T19|Q96L64|Q9H0C9|Q9H8C9|Q9HAP8|Q9NWE5	Silent	SNP	ENST00000431828.1	hg19	CCDS46361.1																																																																																			.	.		0.617	KANSL3-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339040.2	NM_017991		C	97274685	T	C	97274685	2	2	236	1	0	0	0	0	0	0	0	1	8231	1548	54	2		2	KIAA1310	2	97274685	Silent	SNP	T	TCGA-DD-AAW3-01A-11D-A40P-10	49995722	97274685	145924688	16	32818	171	2								
KIAA1310	55683	hgsc.bcm.edu	37	chr2	97274687	97274687	+	Missense_Mutation	SNP	T	T	C													0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	gacttcaaaggccaagtctcTgcgggccacatcgcggggct							TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr2:97274687T>C	ENST00000431828.1	-	13	1574	c.1498A>G	c.(1498-1500)Aga>Gga	p.R500G	KANSL3_ENST00000599854.1_Missense_Mutation_p.R413G|KANSL3_ENST00000487070.1_5'UTR|KANSL3_ENST00000440133.1_Missense_Mutation_p.R294G|KANSL3_ENST00000441706.2_Missense_Mutation_p.R413G			Q9P2N6	KANL3_HUMAN	KAT8 regulatory NSL complex subunit 3	500					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											GCCAAGTCTCTGCGGGCCACA	0.617																																					p.R500G		Atlas-SNP	.											.	.	.	.	0			c.A1498G						.						14	17	16					2																	97274687		1899	4122	6021	SO:0001583	missense	55683	exon13			AGTCTCTGCGGGC	BC063792	CCDS46361.1	2q11.2	2011-10-31	2011-10-31	2011-10-31	ENSG00000114982	ENSG00000114982			25473	protein-coding gene	gene with protein product			"KIAA1310"	KIAA1310			Standard	NM_001115016		Approved	FLJ10081, Rcd1, NSL3	uc002swn.5	Q9P2N6	OTTHUMG00000155249	ENST00000431828.1:c.1498A>G	chr2.hg19:g.97274687T>C	ENSP00000396749:p.Arg500Gly	110.0	0.0		102.0	6.0	NM_001115016	A1L184|D3DXH3|D3DXH4|Q05BU4|Q6P3X2|Q6PJH6|Q86T19|Q96L64|Q9H0C9|Q9H8C9|Q9HAP8|Q9NWE5	Missense_Mutation	SNP	ENST00000431828.1	hg19	CCDS46361.1	.	.	.	.	.	.	.	.	.	.	T	19.60	3.857290	0.71834	.	.	ENSG00000114982	ENST00000354204;ENST00000447759;ENST00000431828;ENST00000441706;ENST00000440133;ENST00000444759	T;T	0.69175	0.43;-0.38	5.44	1.78	0.24846	.	0.000000	0.85682	D	0.000000	T	0.71358	0.3330	L	0.38175	1.15	0.80722	D	1	D;D;D;D	0.89917	0.999;0.989;1.0;0.999	D;D;D;D	0.83275	0.991;0.978;0.996;0.994	T	0.68488	-0.5395	10	0.42905	T	0.14	.	12.3585	0.55188	0.0:0.0:0.5105:0.4895	.	294;500;413;388	B4E1W4;Q9P2N6-3;Q9P2N6-5;Q9P2N6-6	.;.;.;.	G	413;388;500;413;294;294	ENSP00000396749:R500G;ENSP00000406207:R294G	ENSP00000346144:R413G	R	-	1	2	KIAA1310	96638414	1.000000	0.71417	0.973000	0.42090	0.915000	0.54546	1.925000	0.40074	0.344000	0.23847	0.460000	0.39030	AGA	.	.		0.617	KANSL3-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339040.2	NM_017991		C	97274687	T	C	97274687	3	2	236	1	0	0	0	0	1	0	0	0	8231	1588	55	2	1174	2	KIAA1310	2	97274687	Missense_Mutation	SNP	T	TCGA-DD-AAW3-01A-11D-A40P-10	2	97274687	145924686	17	32819	171	2								
LRP1B	53353	hgsc.bcm.edu	37	chr2	141459290	141459290	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	attctttcaagagtgctgacCtttctctcttactcggttaa	6	10	4	2			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr2:141459290C>T	ENST00000389484.3	-	40	7398	c.6427G>A	c.(6427-6429)Ggg>Agg	p.G2143R		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2143	EGF-like 9. {ECO:0000255|PROSITE- ProRule:PRU00076}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		GAGTGCTGACCTTTCTCTCTT	0.348										TSP Lung(27;0.18)																											p.G2143R	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.G6427A						.						87	83	84					2																	141459290		2203	4299	6502	SO:0001630	splice_region_variant	53353	exon40			GCTGACCTTTCTC	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.6427+1G>A	chr2.hg19:g.141459290C>T		63.0	0.0		54.0	21.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.423085	0.83559	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.90385	-2.66	4.58	4.58	0.56647	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	U	0.000000	D	0.95815	0.8638	M	0.86740	2.835	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.96133	0.9094	9	.	.	.	.	17.5696	0.87931	0.0:1.0:0.0:0.0	.	2143	Q9NZR2	LRP1B_HUMAN	R	2143;2081	ENSP00000374135:G2143R	.	G	-	1	0	LRP1B	141175760	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	7.539000	0.82063	2.360000	0.80028	0.467000	0.42956	GGG	.	.		0.348	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	Missense_Mutation	T	141459290	C	T	141459290	5	4	236	1	0	0	0	0	0	0	1	0	8964	695	24	3	7580	3	LRP1B	2	141459290	Splice_Site	SNP	C	TCGA-DD-AAW3-01A-11D-A40P-10	44184603	141459290	101740083	18	32820										
BAZ2B	29994	hgsc.bcm.edu	37	chr2	160231234	160231234	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	ttcaatctgtttttccagctCttcaacacttgctgcttggt	6	11	4	0			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr2:160231234C>A	ENST00000392783.2	-	26	4531	c.4036G>T	c.(4036-4038)Gag>Tag	p.E1346*	BAZ2B_ENST00000343439.5_Nonsense_Mutation_p.E1246*|BAZ2B_ENST00000355831.2_Nonsense_Mutation_p.E1312*|BAZ2B_ENST00000392782.1_Nonsense_Mutation_p.E1310*	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	1346					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						TTTTCCAGCTCTTCAACACTT	0.294																																					p.E1346X		Atlas-SNP	.											.	BAZ2B	196	.	0			c.G4036T						.						123	114	117					2																	160231234		1832	4085	5917	SO:0001587	stop_gained	29994	exon26			CCAGCTCTTCAAC	AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636		"Zinc fingers, PHD-type"	963	protein-coding gene	gene with protein product		605683				10662543	Standard	XM_005246488		Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.4036G>T	chr2.hg19:g.160231234C>A	ENSP00000376534:p.Glu1346*	36.0	0.0		39.0	11.0	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Nonsense_Mutation	SNP	ENST00000392783.2	hg19	CCDS2209.2	.	.	.	.	.	.	.	.	.	.	C	46	12.453254	0.99669	.	.	ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831;ENST00000343439	.	.	.	5.07	5.07	0.68467	.	0.000000	0.37348	U	0.002124	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-12.788	18.4517	0.90705	0.0:1.0:0.0:0.0	.	.	.	.	X	1310;1346;1312;1246	.	ENSP00000339670:E1246X	E	-	1	0	BAZ2B	159939480	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.087000	0.76893	2.345000	0.79718	0.591000	0.81541	GAG	.	.		0.294	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2			A	160231234	C	A	160231234	4	1	236	1	0	0	0	0	0	1	0	0	1332	922	32	3	2518	3	BAZ2B	2	160231234	Nonsense_Mutation	SNP	C	TCGA-DD-AAW3-01A-11D-A40P-10	18771944	160231234	82968139	19	32821										
LRP2	4036	hgsc.bcm.edu	37	chr2	170101205	170101205	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	aaccagctcaaaacttactgCagttcttttcatcagatcca	4	12	4	1			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr2:170101205C>A	ENST00000263816.3	-	22	3713	c.3428G>T	c.(3427-3429)tGc>tTc	p.C1143F	LRP2_ENST00000443831.1_Missense_Mutation_p.C1006F	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1143	LDL-receptor class A 10. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	AAACTTACTGCAGTTCTTTTC	0.433																																					p.C1143F		Atlas-SNP	.											.	LRP2	751	.	0			c.G3428T						.						136	131	133					2																	170101205		2203	4300	6503	SO:0001583	missense	4036	exon22			TTACTGCAGTTCT		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.3428G>T	chr2.hg19:g.170101205C>A	ENSP00000263816:p.Cys1143Phe	48.0	0.0		39.0	14.0	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	hg19	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	C	14.85	2.659432	0.47467	.	.	ENSG00000081479	ENST00000263816;ENST00000443831	D;D	0.99919	-8.0;-8.0	5.93	5.93	0.95920	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.99953	0.9980	H	0.99435	4.565	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.99939	1.1392	10	0.14252	T	0.57	.	20.3368	0.98748	0.0:1.0:0.0:0.0	.	1006;1143	E9PC35;P98164	.;LRP2_HUMAN	F	1143;1006	ENSP00000263816:C1143F;ENSP00000409813:C1006F	ENSP00000263816:C1143F	C	-	2	0	LRP2	169809451	1.000000	0.71417	0.871000	0.34182	0.952000	0.60782	7.760000	0.85248	2.805000	0.96524	0.655000	0.94253	TGC	.	.		0.433	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		A	170101205	C	A	170101205	3	1	236	1	0	0	0	0	1	0	0	0	8965	710	25	3	10771	3	LRP2	2	170101205	Missense_Mutation	SNP	C	TCGA-DD-AAW3-01A-11D-A40P-10	9869971	170101205	73098168	20	32822										
TTN	7273	hgsc.bcm.edu	37	chr2	179427083	179427083	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	atactcttctcctgcagttaAgccagatatagttgcttcta	6	10	3	1			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr2:179427083A>G	ENST00000591111.1	-	276	79077	c.78853T>C	c.(78853-78855)Tta>Cta	p.L26285L	TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000589042.1_Silent_p.L27926L|TTN_ENST00000342992.6_Silent_p.L25358L|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Silent_p.L19053L|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000359218.5_Silent_p.L18986L|TTN_ENST00000460472.2_Silent_p.L18861L|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592600.1_RNA			Q8WZ42	TITIN_HUMAN	titin	26285	Fibronectin type-III 91. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCTGCAGTTAAGCCAGATATA	0.428																																					p.L27926L		Atlas-SNP	.											.	TTN	18412	.	0			c.T83776C						.						134	129	131					2																	179427083		1926	4136	6062	SO:0001819	synonymous_variant	7273	exon326			CAGTTAAGCCAGA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.78853T>C	chr2.hg19:g.179427083A>G		67.0	0.0		62.0	29.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179427083	A	G	179427083	2	3	236	1	0	0	0	0	0	0	0	1	16750	69	3	2		2	TTN	2	179427083	Silent	SNP	A	TCGA-DD-AAW3-01A-11D-A40P-10	9325878	179427083	63772290	21	32823										
CDK15	65061	hgsc.bcm.edu	37	chr2	202698631	202698631	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	accaccaacacgttcttcacAgggacctgaaacctcagaac	6	15	3	2			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr2:202698631A>G	ENST00000374598.4	+	7	667	c.667A>G	c.(667-669)Agg>Ggg	p.R223G	CDK15_ENST00000434439.1_Missense_Mutation_p.R223G|CDK15_ENST00000410091.3_Missense_Mutation_p.R172G|CDK15_ENST00000260967.2_Missense_Mutation_p.R172G|CDK15_ENST00000488419.1_3'UTR|CDK15_ENST00000450471.2_Missense_Mutation_p.R223G			Q96Q40	CDK15_HUMAN	cyclin-dependent kinase 15	223	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|metal ion binding (GO:0046872)			breast(3)|endometrium(2)|kidney(5)|large_intestine(1)|lung(14)|ovary(1)	26					Adenosine triphosphate(DB00171)	CGTTCTTCACAGGGACCTGAA	0.498																																					p.R223G		Atlas-SNP	.											.	CDK15	66	.	0			c.A667G						.						171	148	155					2																	202698631		2203	4300	6503	SO:0001583	missense	65061	exon7			CTTCACAGGGACC	AB053308	CCDS2350.1, CCDS58746.1, CCDS58747.1	2q33.2	2011-11-08	2009-12-16	2009-12-16	ENSG00000138395	ENSG00000138395		"Cyclin-dependent kinases"	14434	protein-coding gene	gene with protein product			"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 7", "PFTAIRE protein kinase 2"	ALS2CR7, PFTK2		11586298, 16236519, 19884882	Standard	NM_139158		Approved	PFTAIRE2	uc002uyt.3	Q96Q40	OTTHUMG00000132838	ENST00000374598.4:c.667A>G	chr2.hg19:g.202698631A>G	ENSP00000363726:p.Arg223Gly	95.0	0.0		73.0	29.0	NM_001261435	A8K8R9|B8ZZX0|C9J1N8|C9K003|F8W6H8|Q4ZG86|Q53TV1|Q6ZMR9|Q8IUP1	Missense_Mutation	SNP	ENST00000374598.4	hg19		.	.	.	.	.	.	.	.	.	.	A	21.1	4.099900	0.76983	.	.	ENSG00000138395	ENST00000410091;ENST00000260967;ENST00000450471;ENST00000434439;ENST00000374598	T;T;T;T;T	0.64991	-0.13;-0.13;-0.13;-0.13;-0.13	5.47	4.36	0.52297	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.82337	0.5015	M	0.93978	3.48	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.85906	0.1437	10	0.87932	D	0	-15.225	10.6141	0.45441	0.5839:0.4161:0.0:0.0	.	202;223;223	Q96Q40-2;Q96Q40;F8W6H8	.;CDK15_HUMAN;.	G	172;172;223;223;223	ENSP00000386901:R172G;ENSP00000260967:R172G;ENSP00000406472:R223G;ENSP00000412775:R223G;ENSP00000363726:R223G	ENSP00000260967:R172G	R	+	1	2	CDK15	202406876	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.295000	0.59049	2.068000	0.61886	0.454000	0.30748	AGG	.	.		0.498	CDK15-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000336053.2			G	202698631	A	G	202698631	3	3	236	1	0	0	0	0	1	0	0	0	3133	179	7	2	536	2	CDK15	2	202698631	Missense_Mutation	SNP	A	TCGA-DD-AAW3-01A-11D-A40P-10	23271548	202698631	40500742	22	32824										
FAM117B	150864	hgsc.bcm.edu	37	chr2	203630340	203630341	+	Frame_Shift_Ins	INS	-	-	A													0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	gcctgacagtcaccactggcINSatgacaaccactctgctgca							TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr2:203630340_203630341insA	ENST00000392238.2	+	8	1623_1624	c.1623_1624insA	c.(1624-1626)atgfs	p.M542fs	FAM117B_ENST00000303116.6_Frame_Shift_Ins_p.M298fs			Q6P1L5	F117B_HUMAN	family with sequence similarity 117, member B	542										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)	17						TCACCACTGGCATGACAACCAC	0.554																																					p.G541fs		Atlas-INDEL	.											.	FAM117B	73	.	0			c.1623_1624insA						.																																			SO:0001589	frameshift_variant	150864	exon8			.	AB053315	CCDS33362.1, CCDS33362.2	2q33	2008-08-18	2008-08-18	2008-08-18	ENSG00000138439	ENSG00000138439			14440	protein-coding gene	gene with protein product			"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 13"	ALS2CR13		11586298	Standard	NM_173511		Approved	FLJ38771	uc010zhx.2	Q6P1L5	OTTHUMG00000154550	ENST00000392238.2:c.1624dupA	chr2.hg19:g.203630341_203630341dupA	ENSP00000376071:p.Met542fs	83.0	0.0		62.0	29.0	NM_173511	Q53QZ5|Q585T9|Q8N8W1|Q96Q34	Frame_Shift_Ins	INS	ENST00000392238.2	hg19	CCDS33362.2																																																																																			.	.		0.554	FAM117B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335888.3	NM_173511		A	203630341	-	A	203630340	7	5	236	1	0	1	1	0	0	0	0	0	5415	697	25	0	1653	0	FAM117B	2	203630340	Frame_Shift_Ins	INS	-	TCGA-DD-AAW3-01A-11D-A40P-10	931709	203630340	39569033	23	32825										
SUSD5	26032	hgsc.bcm.edu	37	chr3	33195306	33195306	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	ggacactgctcccagcaccaGgcaagcctgtggttggcaca	12	14	0	0			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr3:33195306G>A	ENST00000309558.3	-	5	1235	c.818C>T	c.(817-819)cCt>cTt	p.P273L		NM_015551.1	NP_056366.1	O60279	SUSD5_HUMAN	sushi domain containing 5	273					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	hyaluronic acid binding (GO:0005540)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24						CCCAGCACCAGGCAAGCCTGT	0.557																																					p.P273L		Atlas-SNP	.											.	SUSD5	53	.	0			c.C818T						.						48	48	48					3																	33195306		1903	4120	6023	SO:0001583	missense	26032	exon5			GCACCAGGCAAGC	AB011099	CCDS46787.1	3p23	2014-02-12	2006-01-13		ENSG00000173705	ENSG00000173705			29061	protein-coding gene	gene with protein product							Standard	NM_015551		Approved	KIAA0527	uc003cfo.1	O60279	OTTHUMG00000155829	ENST00000309558.3:c.818C>T	chr3.hg19:g.33195306G>A	ENSP00000308727:p.Pro273Leu	49.0	0.0		54.0	42.0	NM_015551		Missense_Mutation	SNP	ENST00000309558.3	hg19	CCDS46787.1	.	.	.	.	.	.	.	.	.	.	G	11.68	1.709800	0.30322	.	.	ENSG00000173705	ENST00000309558	T	0.07327	3.2	6.02	4.24	0.50183	.	0.484707	0.23035	N	0.052684	T	0.06917	0.0176	L	0.29908	0.895	0.09310	N	0.999997	B	0.29508	0.246	B	0.26094	0.066	T	0.28839	-1.0031	10	0.39692	T	0.17	-6.0917	10.7109	0.45982	0.1472:0.0:0.8528:0.0	.	273	O60279	SUSD5_HUMAN	L	273	ENSP00000308727:P273L	ENSP00000308727:P273L	P	-	2	0	SUSD5	33170310	0.697000	0.27767	0.019000	0.16419	0.091000	0.18340	3.539000	0.53604	0.888000	0.36160	0.655000	0.94253	CCT	.	.		0.557	SUSD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341902.1	XM_171054		A	33195306	G	A	33195306	3	1	236	1	0	0	0	0	1	0	0	0	15426	1000	35	3	1075	3	SUSD5	3	33195306	Missense_Mutation	SNP	G	TCGA-DD-AAW3-01A-11D-A40P-10		33195306	164827124	24	32826										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266136	41266136	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	gtgccactaccacagctcctTctctgagtggtaaaggcaat	9	12	1	1	rs121913407		TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr3:41266136T>C	ENST00000349496.5	+	3	413	c.133T>C	c.(133-135)Tct>Cct	p.S45P	CTNNB1_ENST00000396185.3_Missense_Mutation_p.S45P|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S45P|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S38P|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S45P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	45			Missing (in colorectal cancer). {ECO:0000269|PubMed:9065402}.|S -> F (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> P (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S45P(168)|p.A5_A80del(53)|p.S45del(50)|p.S45A(11)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.S45_G48del(1)|p.Q28_Q61del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.S45_L46del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.P44_N51del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.T40_L46del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.S45E(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.S45T(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.T42_K49>Q(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CACAGCTCCTTCTCTGAGTGG	0.502		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S45P	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,carcinoma,0,1	CTNNB1	4904	.	355	Substitution - Missense(181)|Deletion - In frame(149)|Complex - deletion inframe(18)|Unknown(7)	liver(151)|kidney(53)|soft_tissue(47)|large_intestine(37)|adrenal_gland(28)|endometrium(9)|stomach(7)|skin(6)|pituitary(3)|prostate(3)|thyroid(2)|small_intestine(2)|bone(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)	c.T133C						.						84	74	78					3																	41266136		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	GCTCCTTCTCTGA	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.133T>C	chr3.hg19:g.41266136T>C	ENSP00000344456:p.Ser45Pro	107.0	1.0		108.0	90.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.440246	0.83993	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.65903	0.2736	M	0.65677	2.01	0.80722	D	1	D	0.60575	0.988	P	0.62649	0.905	T	0.69083	-0.5239	10	0.87932	D	0	-13.6823	16.3453	0.83126	0.0:0.0:0.0:1.0	.	45	P35222	CTNB1_HUMAN	P	38;45;45;45;45;38;45;45;45	ENSP00000400508:S38P;ENSP00000385604:S45P;ENSP00000412219:S45P;ENSP00000379486:S45P;ENSP00000344456:S45P;ENSP00000411226:S38P;ENSP00000379488:S45P;ENSP00000409302:S45P;ENSP00000401599:S45P	ENSP00000344456:S45P	S	+	1	0	CTNNB1	41241140	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.261000	0.74972	0.533000	0.62120	TCT	.	.		0.502	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266136	T	C	41266136	3	2	236	1	0	0	0	0	1	0	0	0	4018	1783	62	2	139	2	CTNNB1	3	41266136	Missense_Mutation	SNP	T	TCGA-DD-AAW3-01A-11D-A40P-10	8070830	41266136	156756294	25	32827										
TMEM110	375346	hgsc.bcm.edu	37	chr3	52877737	52877737	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	aaatgcaacatggcactgacGttgacaaagaaggggacgat	12	7	0	3			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr3:52877737G>A	ENST00000355083.5	-	6	763	c.618C>T	c.(616-618)aaC>aaT	p.N206N	TMEM110-MUSTN1_ENST00000504329.1_Splice_Site_p.N206N|TMEM110_ENST00000464769.1_5'Flank	NM_198563.2	NP_940965.1	Q86TL2	TM110_HUMAN	transmembrane protein 110	206						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(1)|lung(2)	4				BRCA - Breast invasive adenocarcinoma(193;7.72e-05)|Kidney(197;0.000777)|KIRC - Kidney renal clear cell carcinoma(197;0.000915)|OV - Ovarian serous cystadenocarcinoma(275;0.0541)		TGGCACTGACGTTGACAAAGA	0.502																																					p.N206N		Atlas-SNP	.											.	.	.	.	0			c.C618T						.						183	160	168					3																	52877737		2203	4300	6503	SO:0001630	splice_region_variant	100526772	exon6			ACTGACGTTGACA	BC047015	CCDS2866.1	3p21.1	2010-08-13			ENSG00000213533	ENSG00000213533			30526	protein-coding gene	gene with protein product						12477932	Standard	NM_198563		Approved	MGC52022		Q86TL2	OTTHUMG00000150346	ENST00000355083.5:c.618+1C>T	chr3.hg19:g.52877737G>A		51.0	0.0		47.0	39.0	NM_001198974		Silent	SNP	ENST00000355083.5	hg19	CCDS2866.1																																																																																			.	.		0.502	TMEM110-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352949.2	NM_198563	Silent	A	52877737	G	A	52877737	5	1	236	1	0	0	0	0	0	0	1	0	16042	1159	40	1	278	1	TMEM110	3	52877737	Splice_Site	SNP	G	TCGA-DD-AAW3-01A-11D-A40P-10	11611601	52877737	145144693	26	32828										
CBLB	868	hgsc.bcm.edu	37	chr3	105404274	105404274	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	tcctctactgggtctcttgtTttctctgaaagagaatttgc	8	9	3	2			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr3:105404274T>C	ENST00000264122.4	-	14	2412	c.2091A>G	c.(2089-2091)aaA>aaG	p.K697K	CBLB_ENST00000405772.1_Silent_p.K697K|CBLB_ENST00000394027.3_Silent_p.K719K|CBLB_ENST00000403724.1_Silent_p.K697K	NM_170662.3	NP_733762.2	Q13191	CBLB_HUMAN	Cbl proto-oncogene B, E3 ubiquitin protein ligase	697	Pro-rich.				cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of alpha-beta T cell proliferation (GO:0046642)|negative regulation of T cell receptor signaling pathway (GO:0050860)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of T cell anergy (GO:0002669)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(2)|urinary_tract(2)	49						GGTCTCTTGTTTTCTCTGAAA	0.383			Mis S		AML																																p.K697K	GBM(93;588 1337 9788 29341 43499)	Atlas-SNP	.		Rec	yes		3	3q13.11	868	Cas-Br-M (murine) ecotropic retroviral transforming sequence b		L	.	CBLB	118	.	0			c.A2091G						.						139	134	136					3																	105404274		2203	4300	6503	SO:0001819	synonymous_variant	868	exon14			TCTTGTTTTCTCT	U26710	CCDS2948.1	3q	2013-07-09	2013-07-09		ENSG00000114423	ENSG00000114423		"RING-type (C3HC4) zinc fingers"	1542	protein-coding gene	gene with protein product		604491	"Cas-Br-M (murine) ectropic retroviral transforming sequence b", "Cas-Br-M (murine) ecotropic retroviral transforming sequence b"			7784085	Standard	XM_005247853		Approved	RNF56, Cbl-b	uc003dwc.3	Q13191	OTTHUMG00000150654	ENST00000264122.4:c.2091A>G	chr3.hg19:g.105404274T>C		99.0	0.0		65.0	30.0	NM_170662	A8K9S7|B7WNM4|Q13192|Q13193|Q3LIC0|Q63Z43|Q8IVC5	Silent	SNP	ENST00000264122.4	hg19	CCDS2948.1																																																																																			.	.		0.383	CBLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319417.2	NM_170662		C	105404274	T	C	105404274	2	2	236	1	0	0	0	0	0	0	0	1	2703	1838	64	2		2	CBLB	3	105404274	Silent	SNP	T	TCGA-DD-AAW3-01A-11D-A40P-10	52526537	105404274	92618156	27	32829										
MORC1	27136	hgsc.bcm.edu	37	chr3	108819341	108819341	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	gatcgtccaaagtaaatgatGtctgaagcttcctctgtaat	8	8	2	2			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr3:108819341G>A	ENST00000483760.1	-	5	280	c.237C>T	c.(235-237)gaC>gaT	p.D79D	MORC1_ENST00000232603.5_Silent_p.D79D|MORC1-AS1_ENST00000480826.1_RNA					MORC family CW-type zinc finger 1											breast(7)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(47)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	105						AGTAAATGATGTCTGAAGCTT	0.438																																					p.D79D		Atlas-SNP	.											.	MORC1	211	.	0			c.C237T						.						160	160	160					3																	108819341		2203	4300	6503	SO:0001819	synonymous_variant	27136	exon5			AATGATGTCTGAA	AF084946	CCDS2955.1	3q13	2011-10-26	2005-06-15	2005-06-15	ENSG00000114487	ENSG00000114487			7198	protein-coding gene	gene with protein product	"cancer/testis antigen 33"	603205	"microrchidia (mouse) homolog", "microrchidia homolog (mouse)"	MORC		10369865	Standard	NM_014429		Approved	ZCW6, CT33	uc003dxl.3	Q86VD1	OTTHUMG00000159209	ENST00000483760.1:c.237C>T	chr3.hg19:g.108819341G>A		90.0	0.0		102.0	44.0	NM_014429		Silent	SNP	ENST00000483760.1	hg19																																																																																				.	.		0.438	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1			A	108819341	G	A	108819341	2	1	236	1	0	0	0	0	0	0	0	1	9710	1368	48	3		3	MORC1	3	108819341	Silent	SNP	G	TCGA-DD-AAW3-01A-11D-A40P-10	3415067	108819341	89203089	28	32830										
TRH	7200	hgsc.bcm.edu	37	chr3	129696007	129696007	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	ccagggagctgaggaaaagcGgcagcaccctggtcggcggg	18	11	0	1	rs149654673		TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr3:129696007G>A	ENST00000302649.3	+	3	1204	c.677G>A	c.(676-678)cGg>cAg	p.R226Q	TRH_ENST00000507066.1_Missense_Mutation_p.R222Q	NM_007117.3	NP_009048.1	P20396	TRH_HUMAN	thyrotropin-releasing hormone	226					adult walking behavior (GO:0007628)|cell-cell signaling (GO:0007267)|eating behavior (GO:0042755)|histamine metabolic process (GO:0001692)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of feeding behavior (GO:2000252)|negative regulation of glutamate secretion (GO:0014050)|positive regulation of gamma-aminobutyric acid secretion (GO:0014054)|positive regulation of insulin secretion (GO:0032024)|response to cold (GO:0009409)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)	thyrotropin-releasing hormone activity (GO:0008437)			NS(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)	14						GAGGAAAAGCGGCAGCACCCT	0.632																																					p.R226Q	Esophageal Squamous(60;321 1330 17401 41911)	Atlas-SNP	.											.	TRH	30	.	0			c.G677A						.	G	GLN/ARG	3,4399		0,3,2198	24	26	25		677	3.5	1	3	dbSNP_134	25	2,8574		0,2,4286	yes	missense	TRH	NM_007117.3	43	0,5,6484	AA,AG,GG		0.0233,0.0682,0.0385	benign	226/243	129696007	5,12973	2201	4288	6489	SO:0001583	missense	7200	exon3			AAAAGCGGCAGCA		CCDS3066.1	3q13.3-q21	2013-02-28				ENSG00000170893		"Endogenous ligands"	12298	protein-coding gene	gene with protein product	"prothyroliberin"	613879				2126343, 1900134	Standard	NM_007117		Approved		uc003enc.4	P20396		ENST00000302649.3:c.677G>A	chr3.hg19:g.129696007G>A	ENSP00000303452:p.Arg226Gln	39.0	0.0		36.0	12.0	NM_007117	B2R8R1|Q2TB83	Missense_Mutation	SNP	ENST00000302649.3	hg19	CCDS3066.1	.	.	.	.	.	.	.	.	.	.	G	9.152	1.016595	0.19355	6.82E-4	2.33E-4	ENSG00000170893	ENST00000302649;ENST00000507066	T;T	0.57107	0.42;0.44	4.34	3.47	0.39725	.	0.139469	0.46442	D	0.000286	T	0.37073	0.0990	L	0.27053	0.805	0.34790	D	0.735581	B	0.18863	0.031	B	0.10450	0.005	T	0.43782	-0.9370	10	0.56958	D	0.05	-7.6057	8.7081	0.34367	0.1093:0.0:0.8907:0.0	.	226	P20396	TRH_HUMAN	Q	226;222	ENSP00000303452:R226Q;ENSP00000426522:R222Q	ENSP00000303452:R226Q	R	+	2	0	TRH	131178697	0.994000	0.37717	0.983000	0.44433	0.003000	0.03518	1.287000	0.33284	0.948000	0.37687	-0.244000	0.11960	CGG	.	G|1.000;A|0.000		0.632	TRH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356592.1	NM_007117		A	129696007	G	A	129696007	3	1	236	1	0	0	0	0	1	0	0	0	16493	1116	39	1	683	1	TRH	3	129696007	Missense_Mutation	SNP	G	TCGA-DD-AAW3-01A-11D-A40P-10	20876666	129696007	68326423	29	32831										
TP63	8626	hgsc.bcm.edu	37	chr3	189584586	189584586	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	gtaccttatgagccaccccaGgtaaaaagcaaaaaaccaaa	6	11	0	1			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr3:189584586G>A	ENST00000264731.3	+	6	971	c.882G>A	c.(880-882)caG>caA	p.Q294Q	TP63_ENST00000437221.1_Splice_Site_p.Q200Q|TP63_ENST00000449992.1_Splice_Site_p.Q115Q|TP63_ENST00000320472.5_Splice_Site_p.Q294Q|TP63_ENST00000354600.5_Splice_Site_p.Q200Q|TP63_ENST00000392460.3_Splice_Site_p.Q294Q|TP63_ENST00000382063.4_Splice_Site_p.Q209Q|TP63_ENST00000392461.3_Splice_Site_p.Q200Q|TP63_ENST00000456148.1_Splice_Site_p.Q200Q|TP63_ENST00000440651.2_Splice_Site_p.Q294Q|TP63_ENST00000418709.2_Splice_Site_p.Q294Q|TP63_ENST00000392463.2_Splice_Site_p.Q200Q	NM_001114978.1|NM_003722.4	NP_001108450.1|NP_003713.3	Q9H3D4	P63_HUMAN	tumor protein p63	294					apoptotic process (GO:0006915)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|cloacal septation (GO:0060197)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|ectoderm and mesoderm interaction (GO:0007499)|embryonic limb morphogenesis (GO:0030326)|epidermal cell division (GO:0010481)|epithelial cell development (GO:0002064)|establishment of planar polarity (GO:0001736)|establishment of skin barrier (GO:0061436)|female genitalia morphogenesis (GO:0048807)|hair follicle morphogenesis (GO:0031069)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|keratinocyte differentiation (GO:0030216)|keratinocyte proliferation (GO:0043616)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organismal aging (GO:0010259)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular senescence (GO:2000773)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of mesoderm development (GO:2000381)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|polarized epithelial cell differentiation (GO:0030859)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell cycle G1/S phase transition (GO:1902808)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-anal tail morphogenesis (GO:0036342)|prostatic bud formation (GO:0060513)|protein homotetramerization (GO:0051289)|proximal/distal pattern formation (GO:0009954)|regulation of epidermal cell division (GO:0010482)|regulation of neuron apoptotic process (GO:0043523)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|skeletal system development (GO:0001501)|smooth muscle tissue development (GO:0048745)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|sympathetic nervous system development (GO:0048485)|urinary bladder development (GO:0060157)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region DNA binding (GO:0044212)|WW domain binding (GO:0050699)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(5)|large_intestine(12)|lung(15)|ovary(2)|skin(9)|upper_aerodigestive_tract(6)	61	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)		AGCCACCCCAGGTAAAAAGCA	0.443										HNSCC(45;0.13)																											p.Q294Q		Atlas-SNP	.											.	TP63	187	.	0			c.G882A						.						74	65	68					3																	189584586		2203	4300	6503	SO:0001630	splice_region_variant	8626	exon6			ACCCCAGGTAAAA	AB010153	CCDS3293.1, CCDS46976.1, CCDS46977.1, CCDS46978.1, CCDS46979.1, CCDS46980.1	3q27-q29	2014-09-17			ENSG00000073282	ENSG00000073282			15979	protein-coding gene	gene with protein product		603273	"tumor protein p73-like", "tumor protein p53-like", "tumor protein p53-competing protein"	TP73L, TP53L, TP53CP		9774969, 9662378, 11181441, 11181451	Standard	NM_003722		Approved	p51, SHFM4, EEC3, p63, p73L, OFC8, KET, p73H, NBP, p53CP	uc003fry.2	Q9H3D4	OTTHUMG00000156313	ENST00000264731.3:c.882+1G>A	chr3.hg19:g.189584586G>A		185.0	0.0		172.0	63.0	NM_001114979	O75080|O75195|O75922|O76078|Q6VEG2|Q6VEG3|Q6VEG4|Q6VFJ1|Q6VFJ2|Q6VFJ3|Q6VH20|Q7LDI3|Q7LDI4|Q7LDI5|Q96KR0|Q9H3D2|Q9H3D3|Q9H3P8|Q9NPH7|Q9P1B4|Q9P1B5|Q9P1B6|Q9P1B7|Q9UBV9|Q9UE10|Q9UP26|Q9UP27|Q9UP28|Q9UP74	Silent	SNP	ENST00000264731.3	hg19	CCDS3293.1																																																																																			.	.		0.443	TP63-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000343865.1	NM_003722	Silent	A	189584586	G	A	189584586	5	1	236	1	0	0	0	0	0	0	1	0	16407	1014	35	3	950	3	TP63	3	189584586	Splice_Site	SNP	G	TCGA-DD-AAW3-01A-11D-A40P-10	59888579	189584586	8437844	30	32832										
TRAM1L1	133022	hgsc.bcm.edu	37	chr4	118005493	118005493	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	gtctactctatttgaagtttCcactcccactccgttttctg	5	13	3	1			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr4:118005493C>A	ENST00000310754.4	-	1	1243	c.1057G>T	c.(1057-1059)Gaa>Taa	p.E353*		NM_152402.2	NP_689615.2	Q8N609	TR1L1_HUMAN	translocation associated membrane protein 1-like 1	353					protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22						TTTGAAGTTTCCACTCCCACT	0.398																																					p.E353X		Atlas-SNP	.											.	TRAM1L1	55	.	0			c.G1057T						.						155	160	158					4																	118005493		2203	4300	6503	SO:0001587	stop_gained	133022	exon1			AAGTTTCCACTCC	AK074617	CCDS3707.1	4q26	2008-02-05			ENSG00000174599	ENSG00000174599			28371	protein-coding gene	gene with protein product						12477932	Standard	NM_152402		Approved	MGC26568	uc003ibv.4	Q8N609	OTTHUMG00000132956	ENST00000310754.4:c.1057G>T	chr4.hg19:g.118005493C>A	ENSP00000309402:p.Glu353*	97.0	0.0		84.0	31.0	NM_152402	Q8N2L7	Nonsense_Mutation	SNP	ENST00000310754.4	hg19	CCDS3707.1	.	.	.	.	.	.	.	.	.	.	C	18.46	3.628645	0.67015	.	.	ENSG00000174599	ENST00000310754	.	.	.	0.225	0.225	0.15325	.	0.394016	0.24217	U	0.040464	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06236	T	0.91	-13.609	6.2336	0.20750	0.0:0.9997:0.0:3.0E-4	.	.	.	.	X	353	.	ENSP00000309402:E353X	E	-	1	0	TRAM1L1	118224941	0.048000	0.20356	0.174000	0.22961	0.651000	0.38670	0.765000	0.26546	0.300000	0.22699	0.305000	0.20034	GAA	.	.		0.398	TRAM1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256513.1	NM_152402		A	118005493	C	A	118005493	4	1	236	1	0	0	0	0	0	1	0	0	16467	864	30	3	56	3	TRAM1L1	4	118005493	Nonsense_Mutation	SNP	C	TCGA-DD-AAW3-01A-11D-A40P-10		118005493	73148783	31	32833										
PCDH18	54510	hgsc.bcm.edu	37	chr4	138451631	138451631	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	cacaaaagtgatctgactcaCttcttcatgatcaaagattc	5	10	5	4			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr4:138451631C>A	ENST00000344876.4	-	1	1998	c.1612G>T	c.(1612-1614)Gtg>Ttg	p.V538L	PCDH18_ENST00000412923.2_Missense_Mutation_p.V538L|PCDH18_ENST00000510305.1_Intron|PCDH18_ENST00000511115.1_Intron|PCDH18_ENST00000507846.1_Missense_Mutation_p.V318L	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	538	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				brain development (GO:0007420)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(27)|lung(21)|ovary(2)|pancreas(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86	all_hematologic(180;0.24)					ATCTGACTCACTTCTTCATGA	0.418																																					p.V538L		Atlas-SNP	.											.	PCDH18	229	.	0			c.G1612T						.						123	123	123					4																	138451631		2203	4300	6503	SO:0001583	missense	54510	exon1			GACTCACTTCTTC	AL137471	CCDS34064.1, CCDS75193.1	4q28.3	2010-01-26			ENSG00000189184	ENSG00000189184		"Cadherins / Protocadherins : Non-clustered"	14268	protein-coding gene	gene with protein product		608287				10835267, 11549318	Standard	XM_005263070		Approved	KIAA1562, PCDH68L	uc003ihe.4	Q9HCL0	OTTHUMG00000161348	ENST00000344876.4:c.1612G>T	chr4.hg19:g.138451631C>A	ENSP00000355082:p.Val538Leu	77.0	0.0		76.0	30.0	NM_019035	A8K7K3|B7ZKT1|Q52LS2	Missense_Mutation	SNP	ENST00000344876.4	hg19	CCDS34064.1	.	.	.	.	.	.	.	.	.	.	C	12.01	1.808482	0.31961	.	.	ENSG00000189184	ENST00000344876;ENST00000412923;ENST00000507846	T;T;T	0.51071	0.72;0.72;0.72	5.93	5.93	0.95920	Cadherin (5);Cadherin-like (1);	0.000000	0.39020	N	0.001492	T	0.43389	0.1245	N	0.02865	-0.47	0.80722	D	1	D;B;D	0.89917	1.0;0.067;1.0	D;B;D	0.87578	0.998;0.108;0.998	T	0.36016	-0.9765	10	0.02654	T	1	.	20.3437	0.98782	0.0:1.0:0.0:0.0	.	318;538;538	D6RIG4;Q9HCL0-2;Q9HCL0	.;.;PCD18_HUMAN	L	538;538;318	ENSP00000355082:V538L;ENSP00000390688:V538L;ENSP00000425903:V318L	ENSP00000355082:V538L	V	-	1	0	PCDH18	138671081	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	4.196000	0.58407	2.802000	0.96397	0.563000	0.77884	GTG	.	.		0.418	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035		A	138451631	C	A	138451631	3	1	236	1	0	0	0	0	1	0	0	0	11522	565	20	3	1811	3	PCDH18	4	138451631	Missense_Mutation	SNP	C	TCGA-DD-AAW3-01A-11D-A40P-10	20446138	138451631	52702645	32	32834										
KIAA1430	57587	hgsc.bcm.edu	37	chr4	186111951	186111951	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	atcactgctttcctctccatCtgtgtagtaatcatcttcac	4	13	6	0			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr4:186111951C>A	ENST00000458385.2	-	2	519	c.400G>T	c.(400-402)Gat>Tat	p.D134Y	KIAA1430_ENST00000514798.1_Missense_Mutation_p.D134Y|KIAA1430_ENST00000296775.6_Missense_Mutation_p.D134Y	NM_020827.1	NP_065878.1	Q9P2B7	K1430_HUMAN		134										endometrium(3)|kidney(2)|large_intestine(5)|upper_aerodigestive_tract(1)	11		all_lung(41;1.19e-13)|Lung NSC(41;3.16e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00872)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;9.44e-26)|Epithelial(43;2.64e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.66e-11)|Colorectal(24;6.03e-05)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.000331)|COAD - Colon adenocarcinoma(29;0.000427)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00924)|READ - Rectum adenocarcinoma(43;0.165)		TCCTCTCCATCTGTGTAGTAA	0.348																																					p.D134Y		Atlas-SNP	.											.	KIAA1430	55	.	0			c.G400T						.						74	70	71					4																	186111951		1905	4113	6018	SO:0001583	missense	57587	exon2			CTCCATCTGTGTA																												ENST00000458385.2:c.400G>T	chr4.hg19:g.186111951C>A	ENSP00000409964:p.Asp134Tyr	81.0	0.0		90.0	43.0	NM_020827	B3KRP7|D3DP60|Q05CU1|Q4W5M4|Q8N6E7|Q9UF45	Missense_Mutation	SNP	ENST00000458385.2	hg19	CCDS47168.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.008982	0.75046	.	.	ENSG00000164323	ENST00000458385;ENST00000514798;ENST00000296775;ENST00000503223	T;T;T;T	0.48201	0.82;0.82;0.82;0.82	5.37	5.37	0.77165	.	0.417324	0.25089	N	0.033226	T	0.67655	0.2916	M	0.61703	1.905	0.45676	D	0.998592	D;D	0.89917	1.0;0.998	D;P	0.71870	0.975;0.879	T	0.68938	-0.5277	10	0.66056	D	0.02	-23.3418	19.469	0.94954	0.0:1.0:0.0:0.0	.	134;134	Q9P2B7-2;Q9P2B7	.;K1430_HUMAN	Y	134	ENSP00000409964:D134Y;ENSP00000423312:D134Y;ENSP00000296775:D134Y;ENSP00000420832:D134Y	ENSP00000296775:D134Y	D	-	1	0	KIAA1430	186348945	1.000000	0.71417	0.994000	0.49952	0.865000	0.49528	5.721000	0.68477	2.649000	0.89929	0.655000	0.94253	GAT	.	.		0.348	KIAA1430-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000360717.2			A	186111951	C	A	186111951	3	1	236	1	0	0	0	0	1	0	0	0	8241	913	32	3	1214	3	KIAA1430	4	186111951	Missense_Mutation	SNP	C	TCGA-DD-AAW3-01A-11D-A40P-10	47660320	186111951	5042325	33	32835										
DHX29	54505	hgsc.bcm.edu	37	chr5	54581616	54581616	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	acccaatcaatcagaaattgTttgggagattttccagtcca	7	9	2	2			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr5:54581616T>C	ENST00000251636.5	-	9	1288	c.1140A>G	c.(1138-1140)aaA>aaG	p.K380K	RP11-506H20.1_ENST00000506435.1_RNA	NM_019030.2	NP_061903.2	Q7Z478	DHX29_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 29	380						eukaryotic 43S preinitiation complex (GO:0016282)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|translation initiation factor activity (GO:0003743)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|lung(6)|ovary(4)|prostate(1)|skin(3)|urinary_tract(2)	46		Lung NSC(810;4.08e-05)|Breast(144;0.0544)|Prostate(74;0.183)				TCAGAAATTGTTTGGGAGATT	0.353																																					p.K380K		Atlas-SNP	.											.	DHX29	116	.	0			c.A1140G						.						67	70	69					5																	54581616		2203	4300	6503	SO:0001819	synonymous_variant	54505	exon9			AAATTGTTTGGGA	AY036974	CCDS34158.1	5q11.2	2008-02-05	2003-06-13	2003-06-20	ENSG00000067248	ENSG00000067248		"DEAH-boxes"	15815	protein-coding gene	gene with protein product		612720	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 29"	DDX29			Standard	XM_005248544		Approved		uc003jpx.3	Q7Z478	OTTHUMG00000162313	ENST00000251636.5:c.1140A>G	chr5.hg19:g.54581616T>C		144.0	0.0		136.0	48.0	NM_019030	O75549|Q63HN0|Q63HN3|Q8IWW2|Q8N3A1|Q9UMH2	Silent	SNP	ENST00000251636.5	hg19	CCDS34158.1																																																																																			.	.		0.353	DHX29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368532.1	NM_019030		C	54581616	T	C	54581616	2	2	236	1	0	0	0	0	0	0	0	1	4505	1722	60	2		2	DHX29	5	54581616	Silent	SNP	T	TCGA-DD-AAW3-01A-11D-A40P-10		54581616	126333644	34	32836										
CENPH	64946	hgsc.bcm.edu	37	chr5	68492921	68492921	+	Frame_Shift_Del	DEL	T	T	-													0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	taaaaaaaacctggagaaaaTtagcagacagtctaggtatg							TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr5:68492921delT	ENST00000283006.2	+	5	443	c.356delT	c.(355-357)attfs	p.I119fs	CENPH_ENST00000515001.1_Intron	NM_022909.3	NP_075060.1			centromere protein H											kidney(15)|large_intestine(2)|lung(3)	20		Lung NSC(167;5.51e-05)|Prostate(74;0.00634)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.41e-56)|Epithelial(20;1.29e-52)|all cancers(19;3.15e-48)|Lung(70;0.0178)		CTGGAGAAAATTAGCAGACAG	0.318																																					p.I119fs		Atlas-INDEL	.											.	CENPH	28	.	0			c.355delA						.						48	51	50					5																	68492921		2203	4299	6502	SO:0001589	frameshift_variant	64946	exon5			.	AB035124	CCDS3998.1	5p15.2	2013-11-05			ENSG00000153044	ENSG00000153044			17268	protein-coding gene	gene with protein product		605607				11092768, 15502821	Standard	NM_022909		Approved		uc003jvp.3	Q9H3R5	OTTHUMG00000097816	ENST00000283006.2:c.356delT	chr5.hg19:g.68492921delT	ENSP00000283006:p.Ile119fs	260.0	0.0		247.0	110.0	NM_022909		Frame_Shift_Del	DEL	ENST00000283006.2	hg19	CCDS3998.1																																																																																			.	.		0.318	CENPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215083.1			-	68492921	T	-	68492921	7	5	236	1	0	1	0	1	0	0	0	0	3234	1493	52	0	374	0	CENPH	5	68492921	Frame_Shift_Del	DEL	T	TCGA-DD-AAW3-01A-11D-A40P-10	13911305	68492921	112422339	35	32837										
IQGAP2	10788	hgsc.bcm.edu	37	chr5	75886316	75886316	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	taacactaagaaacccaaatGcggttttaactttagtggat	7	7	0	1			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr5:75886316G>A	ENST00000274364.6	+	8	1021	c.724G>A	c.(724-726)Gcg>Acg	p.A242T	IQGAP2_ENST00000379730.3_5'UTR	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	242					negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		AAACCCAAATGCGGTTTTAAC	0.383																																					p.A242T		Atlas-SNP	.											.	IQGAP2	186	.	0			c.G724A						.						92	92	92					5																	75886316		2203	4300	6503	SO:0001583	missense	10788	exon8			CCAAATGCGGTTT	U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.724G>A	chr5.hg19:g.75886316G>A	ENSP00000274364:p.Ala242Thr	131.0	0.0		130.0	51.0	NM_006633	A8K4V1|B7Z8A4|J3KR91	Missense_Mutation	SNP	ENST00000274364.6	hg19	CCDS34188.1	.	.	.	.	.	.	.	.	.	.	G	35	5.457558	0.96240	.	.	ENSG00000145703	ENST00000274364;ENST00000514350;ENST00000505766	T;T;T	0.51574	3.28;0.7;3.28	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.69682	0.3138	M	0.82716	2.605	0.80722	D	1	D	0.56035	0.974	P	0.58210	0.835	T	0.73522	-0.3956	10	0.72032	D	0.01	-23.1046	19.8594	0.96778	0.0:0.0:1.0:0.0	.	242	Q13576	IQGA2_HUMAN	T	242;215;192	ENSP00000274364:A242T;ENSP00000423672:A215T;ENSP00000421097:A192T	ENSP00000274364:A242T	A	+	1	0	IQGAP2	75922072	1.000000	0.71417	0.952000	0.39060	0.879000	0.50718	9.592000	0.98245	2.691000	0.91804	0.650000	0.86243	GCG	.	.		0.383	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633		A	75886316	G	A	75886316	3	1	236	1	0	0	0	0	1	0	0	0	7824	1319	46	3	754	3	IQGAP2	5	75886316	Missense_Mutation	SNP	G	TCGA-DD-AAW3-01A-11D-A40P-10	7393395	75886316	105028944	36	32838										
UNC5CL	222643	hgsc.bcm.edu	37	chr6	40998166	40998166	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	gccccaggtgggaggccagtCtgcgccagtcattgccggtg	16	13	2	0	rs533058060		TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr6:40998166C>T	ENST00000373164.1	-	7	1355	c.1295G>A	c.(1294-1296)aGa>aAa	p.R432K	UNC5CL_ENST00000470102.1_5'UTR|UNC5CL_ENST00000244565.3_Missense_Mutation_p.R432K			Q8IV45	UN5CL_HUMAN	unc-5 homolog C (C. elegans)-like	432	Death. {ECO:0000255|PROSITE- ProRule:PRU00064}.		R -> G (in dbSNP:rs742493). {ECO:0000269|PubMed:14769797, ECO:0000269|PubMed:15489334}.		positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of JNK cascade (GO:0046330)|proteolysis (GO:0006508)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	peptidase activity (GO:0008233)			endometrium(1)|kidney(3)|large_intestine(3)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	13	Ovarian(28;0.0418)|Colorectal(47;0.196)					GGAGGCCAGTCTGCGCCAGTC	0.587																																					p.R432K		Atlas-SNP	.											.	UNC5CL	52	.	0			c.G1295A						.						87	80	82					6																	40998166		2203	4300	6503	SO:0001583	missense	222643	exon8			GCCAGTCTGCGCC	BC035284	CCDS4847.1	6p21.1	2013-10-15			ENSG00000124602	ENSG00000124602			21203	protein-coding gene	gene with protein product	"ZU5 and death domain containing"					14769797	Standard	NM_173561		Approved	MGC34763, ZUD	uc003opi.3	Q8IV45	OTTHUMG00000014665	ENST00000373164.1:c.1295G>A	chr6.hg19:g.40998166C>T	ENSP00000362258:p.Arg432Lys	87.0	0.0		194.0	22.0	NM_173561	Q5TGU1	Missense_Mutation	SNP	ENST00000373164.1	hg19	CCDS4847.1	.	.	.	.	.	.	.	.	.	.	C	3.741	-0.053527	0.07362	.	.	ENSG00000124602	ENST00000244565;ENST00000373164	D;D	0.85013	-1.93;-1.93	4.64	2.78	0.32641	Death (3);DEATH-like (2);	0.000000	0.42420	D	0.000719	T	0.41834	0.1176	N	0.08118	0	0.09310	N	1	B	0.12630	0.006	B	0.12156	0.007	T	0.42481	-0.9449	10	0.06099	T	0.92	-13.9955	7.6946	0.28587	0.0:0.7978:0.0:0.2022	.	432	Q8IV45	UN5CL_HUMAN	K	432	ENSP00000244565:R432K;ENSP00000362258:R432K	ENSP00000244565:R432K	R	-	2	0	UNC5CL	41106144	0.050000	0.20438	0.018000	0.16275	0.961000	0.63080	1.027000	0.30115	1.140000	0.42260	0.655000	0.94253	AGA	.	.		0.587	UNC5CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040491.1	NM_173561		T	40998166	C	T	40998166	3	4	236	1	0	0	0	0	1	0	0	0	17009	913	32	3	269	3	UNC5CL	6	40998166	Missense_Mutation	SNP	C	TCGA-DD-AAW3-01A-11D-A40P-10		40998166	130116901	37	32839										
GCLC	2729	hgsc.bcm.edu	37	chr6	53364926	53364926	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	cttccatgttttcaaggtaaGagttcagaattgggatcagt	10	6	3	2			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr6:53364926G>T	ENST00000229416.6	-	15	2102	c.1619C>A	c.(1618-1620)tCt>tAt	p.S540Y		NM_001197115.1|NM_001498.3	NP_001184044.1|NP_001489.1	P48506	GSH1_HUMAN	glutamate-cysteine ligase, catalytic subunit	540					apoptotic mitochondrial changes (GO:0008637)|cell redox homeostasis (GO:0045454)|cellular nitrogen compound metabolic process (GO:0034641)|cysteine metabolic process (GO:0006534)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|L-ascorbic acid metabolic process (GO:0019852)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|regulation of blood vessel size (GO:0050880)|regulation of mitochondrial depolarization (GO:0051900)|response to arsenic-containing substance (GO:0046685)|response to heat (GO:0009408)|response to hormone (GO:0009725)|response to nitrosative stress (GO:0051409)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|glutamate-cysteine ligase complex (GO:0017109)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|coenzyme binding (GO:0050662)|glutamate binding (GO:0016595)|glutamate-cysteine ligase activity (GO:0004357)|magnesium ion binding (GO:0000287)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22	Lung NSC(77;0.0137)				L-Cysteine(DB00151)|Vitamin E(DB00163)	TTCAAGGTAAGAGTTCAGAAT	0.433																																					p.S540Y		Atlas-SNP	.											.	GCLC	58	.	0			c.C1619A						.						133	125	127					6																	53364926		2203	4300	6503	SO:0001583	missense	2729	exon15			AGGTAAGAGTTCA	M90656	CCDS4952.1, CCDS75471.1	6p12	2008-02-05				ENSG00000001084	6.3.2.2		4311	protein-coding gene	gene with protein product		606857		GLCLC, GLCL		1350904	Standard	NM_001498		Approved	GCS	uc003pbw.2	P48506		ENST00000229416.6:c.1619C>A	chr6.hg19:g.53364926G>T	ENSP00000229416:p.Ser540Tyr	93.0	0.0		214.0	49.0	NM_001498	Q14399	Missense_Mutation	SNP	ENST00000229416.6	hg19	CCDS4952.1	.	.	.	.	.	.	.	.	.	.	G	18.85	3.710712	0.68730	.	.	ENSG00000001084	ENST00000229416	T	0.74526	-0.85	5.77	2.95	0.34219	.	0.306839	0.41396	D	0.000885	T	0.80444	0.4624	M	0.84683	2.71	0.80722	D	1	P	0.42620	0.785	P	0.53224	0.721	D	0.83985	0.0334	10	0.72032	D	0.01	.	17.2211	0.86957	0.0:0.3539:0.6461:0.0	.	540	P48506	GSH1_HUMAN	Y	540	ENSP00000229416:S540Y	ENSP00000229416:S540Y	S	-	2	0	GCLC	53472885	1.000000	0.71417	0.717000	0.30585	0.942000	0.58702	3.334000	0.52097	0.412000	0.25729	-0.150000	0.13652	TCT	.	.		0.433	GCLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359710.2			T	53364926	G	T	53364926	3	4	236	1	0	0	0	0	1	0	0	0	6303	942	33	3	302	3	GCLC	6	53364926	Missense_Mutation	SNP	G	TCGA-DD-AAW3-01A-11D-A40P-10	12366760	53364926	117750141	38	32840										
DST	667	hgsc.bcm.edu	37	chr6	56481993	56481993	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	cagtcacagtgtgcctaagcCcttggaatttaaattcatca	7	10	3	0			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr6:56481993C>T	ENST00000370765.6	-	24	6379	c.6272G>A	c.(6271-6273)gGg>gAg	p.G2091E	DST_ENST00000244364.6_Intron|DST_ENST00000312431.6_Intron|DST_ENST00000370754.5_Intron|DST_ENST00000446842.2_Intron|DST_ENST00000361203.3_Intron|DST_ENST00000370788.2_Intron|DST_ENST00000421834.2_Intron|DST_ENST00000370769.4_Intron	NM_001723.5	NP_001714.1	Q03001	DYST_HUMAN	dystonin	0					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			GTGCCTAAGCCCTTGGAATTT	0.458																																					p.G2091E		Atlas-SNP	.											.	DST	1427	.	0			c.G6272A						.						130	128	129					6																	56481993		2203	4300	6503	SO:0001583	missense	667	exon24			CTAAGCCCTTGGA	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000370765.6:c.6272G>A	chr6.hg19:g.56481993C>T	ENSP00000359801:p.Gly2091Glu	50.0	0.0		119.0	23.0	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000370765.6	hg19	CCDS4959.1	.	.	.	.	.	.	.	.	.	.	C	17.85	3.489319	0.64074	.	.	ENSG00000151914	ENST00000370765	T	0.70045	-0.45	5.77	5.77	0.91146	.	.	.	.	.	T	0.77765	0.4179	.	.	.	0.18873	N	0.999984	D	0.89917	1.0	D	0.83275	0.996	T	0.70350	-0.4896	7	0.25106	T	0.35	.	20.3472	0.98799	0.0:1.0:0.0:0.0	.	2091	Q03001-3	.	E	2091	ENSP00000359801:G2091E	ENSP00000359801:G2091E	G	-	2	0	DST	56589952	0.999000	0.42202	0.999000	0.59377	0.979000	0.70002	3.033000	0.49743	2.890000	0.99128	0.650000	0.86243	GGG	.	.		0.458	DST-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041027.2	NM_001723		T	56481993	C	T	56481993	3	4	236	1	0	0	0	0	1	0	0	0	4785	623	22	3	14127	3	DST	6	56481993	Missense_Mutation	SNP	C	TCGA-DD-AAW3-01A-11D-A40P-10	3117067	56481993	114633074	39	32841										
OPRM1	4988	hgsc.bcm.edu	37	chr6	154360440	154360440	+	5'Flank	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	tcctgcagcggtgcggggcaGgtgatgagcctctgtgaact	16	10	1	3			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr6:154360440G>T	ENST00000330432.7	+	0	0				OPRM1_ENST00000524163.1_5'Flank|OPRM1_ENST00000452687.2_5'Flank|OPRM1_ENST00000419506.2_5'Flank|OPRM1_ENST00000428397.2_5'Flank|OPRM1_ENST00000520708.1_Intron|OPRM1_ENST00000229768.5_5'Flank|OPRM1_ENST00000434900.2_Splice_Site_p.A49S|OPRM1_ENST00000518759.1_Intron|OPRM1_ENST00000435918.2_5'Flank|OPRM1_ENST00000414028.2_5'Flank|OPRM1_ENST00000337049.4_5'Flank|OPRM1_ENST00000360422.4_5'Flank	NM_000914.3	NP_000905.3	P35372	OPRM_HUMAN	opioid receptor, mu 1						adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavioral response to ethanol (GO:0048149)|calcium ion transmembrane transport (GO:0070588)|cellular response to stress (GO:0033554)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|locomotory behavior (GO:0007626)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of Wnt protein secretion (GO:0061358)|neuropeptide signaling pathway (GO:0007218)|opioid receptor signaling pathway (GO:0038003)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neurogenesis (GO:0050769)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-endorphin receptor activity (GO:0004979)|G-protein alpha-subunit binding (GO:0001965)|G-protein coupled receptor activity (GO:0004930)|morphine receptor activity (GO:0038047)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(15)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	33		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;9.26e-11)|BRCA - Breast invasive adenocarcinoma(81;0.0154)	Alfentanil(DB00802)|Alvimopan(DB06274)|Amitriptyline(DB00321)|Anileridine(DB00913)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dezocine(DB01209)|Diphenoxylate(DB01081)|Ethylmorphine(DB01466)|Fentanyl(DB00813)|Heroin(DB01452)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levallorphan(DB00504)|Levomethadyl Acetate(DB01227)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Methadyl Acetate(DB01433)|Methylnaltrexone(DB06800)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Ondansetron(DB00904)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Pentazocine(DB00652)|Pethidine(DB00454)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	GTGCGGGGCAGGTGATGAGCC	0.622																																					p.A49S		Atlas-SNP	.											.	OPRM1	241	.	0			c.G145T						.						71	68	69					6																	154360440		692	1591	2283	SO:0001631	upstream_gene_variant	4988	exon2			GGGGCAGGTGATG	L29301	CCDS43517.1, CCDS43518.1, CCDS47503.1, CCDS47504.1, CCDS47505.1, CCDS47506.1, CCDS47507.1, CCDS47508.1, CCDS55071.1, CCDS55068.1, CCDS55069.1, CCDS55070.1	6q24-q25	2012-08-08			ENSG00000112038	ENSG00000112038		"GPCR / Class A : Opioid receptors"	8156	protein-coding gene	gene with protein product		600018					Standard	NM_001145285		Approved	MOR1	uc003qpo.1	P35372	OTTHUMG00000015870		chr6.hg19:g.154360440G>T	Exception_encountered	80.0	0.0		52.0	40.0	NM_001145279	B0FXJ1|B2R9S7|B8Q1L7|B8Q1L8|B8Q1L9|E7EWZ3|G8XRH6|G8XRH8|Q12930|Q4VWM1|Q4VWM2|Q4VWM3|Q4VWM4|Q4VWM6|Q4VWX6|Q5TDA1|Q6UPP1|Q6UQ80|Q7Z2D8|Q86V80|Q8IWW3|Q8IWW4|Q9UCZ4|Q9UN57	Missense_Mutation	SNP	ENST00000330432.7	hg19	CCDS55070.1	.	.	.	.	.	.	.	.	.	.	G	10.14	1.267847	0.23136	.	.	ENSG00000112038	ENST00000434900	T	0.72505	-0.66	5.48	0.339	0.15979	.	.	.	.	.	T	0.23649	0.0572	N	0.08118	0	0.22001	N	0.999426	B	0.12013	0.005	B	0.12156	0.007	T	0.20009	-1.0288	9	0.56958	D	0.05	.	3.4842	0.07614	0.0784:0.2559:0.3686:0.2971	.	49	P35372-10	.	S	49	ENSP00000394624:A49S	ENSP00000394624:A49S	A	+	1	0	OPRM1	154402133	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	1.166000	0.31834	-0.243000	0.09653	-0.885000	0.02943	GCC	.	.		0.622	OPRM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042786.2	NM_000914		T	154360440	G	T	154360440	1	4	236	0	1	0	0	0	0	0	0	0	10896	1014	35	3		3	OPRM1	6	154360440	5'Flank	SNP	G	TCGA-DD-AAW3-01A-11D-A40P-10	97878447	154360440	16754627	40	32842										
PCLO	27445	hgsc.bcm.edu	37	chr7	82585150	82585157	+	Frame_Shift_Del	DEL	AGTCTGTC	AGTCTGTC	-													0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	ccttgacctatcttcaggtgAgtctgtcaggctttccattt							TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	AGTCTGTC	AGTCTGTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr7:82585150_82585157delAGTCTGTC	ENST00000333891.9	-	5	5449_5456	c.5112_5119delGACAGACT	c.(5110-5121)ctgacagactcafs	p.TDS1705fs	PCLO_ENST00000423517.2_Frame_Shift_Del_p.TDS1705fs	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TCTTCAGGTGAGTCTGTCAGGCTTTCCA	0.433																																					p.1705_1707del		Atlas-INDEL	.											.	PCLO	1506	.	0			c.5113_5120del						.																																			SO:0001589	frameshift_variant	27445	exon5			.	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.5112_5119delGACAGACT	chr7.hg19:g.82585150_82585157delAGTCTGTC	ENSP00000334319:p.Thr1705fs	97.0	0.0		130.0	23.0	NM_014510		Frame_Shift_Del	DEL	ENST00000333891.9	hg19	CCDS47630.1																																																																																			.	.		0.433	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		-	82585157	AGTCTGTC	-	82585150	7	5	236	1	0	1	0	1	0	0	0	0	11592	304	11	0	10410	0	PCLO	7	82585150	Frame_Shift_Del	DEL	AGTCTGTC	TCGA-DD-AAW3-01A-11D-A40P-10		82585150	76553513	41	32843										
ASZ1	136991	hgsc.bcm.edu	37	chr7	117003700	117003700	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	gaaaagaagaaaaccgaatcCgcatatggtaatagctgtcc	9	8	0	2			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr7:117003700C>T	ENST00000284629.2	-	13	1440	c.1378G>A	c.(1378-1380)Gga>Aga	p.G460R		NM_130768.2	NP_570124.1			ankyrin repeat, SAM and basic leucine zipper domain containing 1											breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(3)|skin(1)	24	Lung NSC(10;0.00156)|all_lung(10;0.00175)		STAD - Stomach adenocarcinoma(10;0.000512)			AAACCGAATCCGCATATGGTA	0.323																																					p.G460R		Atlas-SNP	.											.	ASZ1	56	.	0			c.G1378A						.						114	113	113					7																	117003700		2203	4299	6502	SO:0001583	missense	136991	exon13			CGAATCCGCATAT	AF461259	CCDS5772.1	7q31.2	2013-01-10	2005-03-15	2004-07-16	ENSG00000154438	ENSG00000154438		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	1350	protein-coding gene	gene with protein product		605797	"ankyrin-like 1"	C7orf7, ANKL1		12040005, 11279520	Standard	NM_130768		Approved	Orf3, GASZ, ALP1, CT1.19	uc003vjb.2	Q8WWH4	OTTHUMG00000064565	ENST00000284629.2:c.1378G>A	chr7.hg19:g.117003700C>T	ENSP00000284629:p.Gly460Arg	83.0	0.0		93.0	16.0	NM_130768		Missense_Mutation	SNP	ENST00000284629.2	hg19	CCDS5772.1	.	.	.	.	.	.	.	.	.	.	C	16.91	3.254029	0.59212	.	.	ENSG00000154438	ENST00000284629	T	0.74947	-0.89	5.23	5.23	0.72850	.	0.056344	0.64402	D	0.000001	D	0.83261	0.5216	L	0.59436	1.845	0.52501	D	0.999957	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.992	D	0.84862	0.0820	10	0.87932	D	0	2.3198	14.2861	0.66247	0.0:1.0:0.0:0.0	.	451;460	B7ZM20;Q8WWH4	.;ASZ1_HUMAN	R	460	ENSP00000284629:G460R	ENSP00000284629:G460R	G	-	1	0	ASZ1	116790936	0.997000	0.39634	0.998000	0.56505	0.435000	0.31806	4.401000	0.59716	2.440000	0.82611	0.591000	0.81541	GGA	.	.		0.323	ASZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000138907.7	NM_130768		T	117003700	C	T	117003700	3	4	236	1	0	0	0	0	1	0	0	0	1069	661	23	1	53	1	ASZ1	7	117003700	Missense_Mutation	SNP	C	TCGA-DD-AAW3-01A-11D-A40P-10	34418550	117003700	42134963	42	32844										
FAM40B	57464	hgsc.bcm.edu	37	chr7	129102863	129102863	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	ctctaccagggaatgctgtaCagccttccgcagtatatggt	10	11	1	0			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr7:129102863C>T	ENST00000249344.2	+	14	1573	c.1533C>T	c.(1531-1533)taC>taT	p.Y511Y	STRIP2_ENST00000435494.2_Silent_p.Y511Y	NM_020704.2	NP_065755.1	Q9ULQ0	STRP2_HUMAN	striatin interacting protein 2	511					cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)											GAATGCTGTACAGCCTTCCGC	0.507																																					p.Y511Y		Atlas-SNP	.											.	.	.	.	0			c.C1533T						.						97	86	90					7																	129102863		2203	4300	6503	SO:0001819	synonymous_variant	57464	exon14			GCTGTACAGCCTT	AB032996	CCDS34752.1, CCDS47709.1	7q32.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000128578	ENSG00000128578			22209	protein-coding gene	gene with protein product	"FAR11 factor arrest 11 homolog B (yeast)"		"family with sequence similarity 40, member B"	FAM40B		22782902, 22298706, 18782753	Standard	NM_020704		Approved	KIAA1170, FAR11B	uc011koy.2	Q9ULQ0	OTTHUMG00000157695	ENST00000249344.2:c.1533C>T	chr7.hg19:g.129102863C>T		65.0	0.0		64.0	14.0	NM_020704	Q8WUZ4	Silent	SNP	ENST00000249344.2	hg19	CCDS34752.1																																																																																			.	.		0.507	STRIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349418.1	NM_001134336		T	129102863	C	T	129102863	2	4	236	1	0	0	0	0	0	0	0	1	5569	489	17	3		3	FAM40B	7	129102863	Silent	SNP	C	TCGA-DD-AAW3-01A-11D-A40P-10	12099163	129102863	30035800	43	32845										
MKLN1	4289	hgsc.bcm.edu	37	chr7	131122635	131122635	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	gcgttacttggattcctctgTgaggaacagcaaatctctga	10	9	2	2			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr7:131122635T>C	ENST00000352689.6	+	10	1092	c.1052T>C	c.(1051-1053)gTg>gCg	p.V351A	MKLN1_ENST00000421797.2_Missense_Mutation_p.V259A	NM_013255.4	NP_037387.2	Q9UL63	MKLN1_HUMAN	muskelin 1, intracellular mediator containing kelch motifs	351					signal transduction (GO:0007165)	cytoplasm (GO:0005737)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	28	Melanoma(18;0.162)					GATTCCTCTGTGAGGAACAGC	0.433																																					p.V351A		Atlas-SNP	.											.	MKLN1	67	.	0			c.T1052C						.						237	225	229					7																	131122635		2203	4300	6503	SO:0001583	missense	4289	exon10			CCTCTGTGAGGAA	AF047489	CCDS34754.1	7q32	2008-07-18			ENSG00000128585	ENSG00000128585			7109	protein-coding gene	gene with protein product		605623				10640805	Standard	NM_001145354		Approved	TWA2	uc011kpm.2	Q9UL63	OTTHUMG00000154880	ENST00000352689.6:c.1052T>C	chr7.hg19:g.131122635T>C	ENSP00000323527:p.Val351Ala	112.0	0.0		149.0	31.0	NM_013255	A4D1M8|A6NG43|Q9NSK4|Q9NUS8	Missense_Mutation	SNP	ENST00000352689.6	hg19	CCDS34754.1	.	.	.	.	.	.	.	.	.	.	T	14.73	2.622137	0.46840	.	.	ENSG00000128585	ENST00000421797;ENST00000352689	T;T	0.44482	1.93;0.92	5.83	5.83	0.93111	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.27419	0.0673	N	0.14661	0.345	0.80722	D	1	B;B;B	0.15473	0.007;0.013;0.013	B;B;B	0.12156	0.007;0.003;0.003	T	0.10154	-1.0642	10	0.16896	T	0.51	-14.1727	15.3799	0.74648	0.0:0.0:0.0:1.0	.	351;328;259	Q9UL63;B4DG30;C9J7E8	MKLN1_HUMAN;.;.	A	259;351	ENSP00000398094:V259A;ENSP00000323527:V351A	ENSP00000323527:V351A	V	+	2	0	MKLN1	130773175	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.040000	0.89188	2.230000	0.72887	0.454000	0.30748	GTG	.	.		0.433	MKLN1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000337473.4	NM_013255		C	131122635	T	C	131122635	3	2	236	1	0	0	0	0	1	0	0	0	9612	1696	59	2	1123	2	MKLN1	7	131122635	Missense_Mutation	SNP	T	TCGA-DD-AAW3-01A-11D-A40P-10	2019772	131122635	28016028	44	32846										
RUNX1T1	862	hgsc.bcm.edu	37	chr8	92982954	92982954	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	cgcctgccgtttggcctcggCgaccgtgcgctccatcttgg	13	16	1	0			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr8:92982954C>T	ENST00000523629.1	-	11	1925	c.1471G>A	c.(1471-1473)Gcc>Acc	p.A491T	RUNX1T1_ENST00000436581.2_Missense_Mutation_p.A502T|RUNX1T1_ENST00000265814.3_Missense_Mutation_p.A491T|RUNX1T1_ENST00000396218.1_Missense_Mutation_p.A464T|RUNX1T1_ENST00000422361.2_Missense_Mutation_p.A454T|RUNX1T1_ENST00000520724.1_Missense_Mutation_p.A454T|RUNX1T1_ENST00000360348.2_Missense_Mutation_p.A454T|RUNX1T1_ENST00000518844.1_Missense_Mutation_p.A464T	NM_001198626.1|NM_001198630.1|NM_001198633.1|NM_175634.2	NP_001185555.1|NP_001185559.1|NP_001185562.1|NP_783552.1	Q06455	MTG8_HUMAN	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	491					fat cell differentiation (GO:0045444)|generation of precursor metabolites and energy (GO:0006091)|regulation of DNA binding (GO:0051101)|transcription, DNA-templated (GO:0006351)	nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A491T(2)|p.A454T(2)|p.A502T(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(54)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	86			BRCA - Breast invasive adenocarcinoma(11;0.0141)			TTGGCCTCGGCGACCGTGCGC	0.602																																					p.A550T		Atlas-SNP	.											RUNX1T1_ENST00000436581,NS,carcinoma,0,5	RUNX1T1	516	.	5	Substitution - Missense(5)	lung(3)|large_intestine(2)	c.G1648A						.						71	61	64					8																	92982954		2203	4300	6503	SO:0001583	missense	862	exon11			CCTCGGCGACCGT	D43638	CCDS6256.1, CCDS6257.1, CCDS47891.1, CCDS56544.1, CCDS75766.1, CCDS75767.1	8q22	2007-01-29	2005-01-20	2005-01-22	ENSG00000079102	ENSG00000079102		"Zinc fingers, MYND-type"	1535	protein-coding gene	gene with protein product		133435	"core-binding factor, runt domain, alpha subunit 2; translocated to, 1; cyclin D-related"	AML1T1, CBFA2T1		1391946, 9790752	Standard	NM_004349		Approved	CDR, ETO, MTG8, ZMYND2	uc011lgi.2	Q06455	OTTHUMG00000164066	ENST00000523629.1:c.1471G>A	chr8.hg19:g.92982954C>T	ENSP00000428543:p.Ala491Thr	67.0	0.0		124.0	26.0	NM_001198679	B7Z4P4|E7EPN4|O14784|Q06456|Q14873|Q16239|Q16346|Q16347|Q6IBL1|Q6NXH1|Q7Z4J5|Q92479|Q9BRZ0	Missense_Mutation	SNP	ENST00000523629.1	hg19	CCDS6256.1	.	.	.	.	.	.	.	.	.	.	C	32	5.157358	0.94686	.	.	ENSG00000079102	ENST00000523629;ENST00000396218;ENST00000265814;ENST00000360348;ENST00000422361;ENST00000520724;ENST00000436581;ENST00000518844	T;T;T;T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96;0.96;0.96;0.96	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.67154	0.2863	M	0.83603	2.65	0.58432	D	0.999996	D;D;D;D	0.67145	0.994;0.996;0.995;0.984	P;P;P;P	0.62184	0.82;0.899;0.838;0.773	T	0.68062	-0.5508	10	0.48119	T	0.1	-15.9301	19.9981	0.97395	0.0:1.0:0.0:0.0	.	502;454;491;464	E7EPN4;Q7Z4J5;Q06455;Q06455-2	.;.;MTG8_HUMAN;.	T	491;464;491;454;454;454;502;464	ENSP00000428543:A491T;ENSP00000379520:A464T;ENSP00000265814:A491T;ENSP00000353504:A454T;ENSP00000390137:A454T;ENSP00000428742:A454T;ENSP00000402257:A502T;ENSP00000430728:A464T	ENSP00000265814:A491T	A	-	1	0	RUNX1T1	93052130	1.000000	0.71417	0.954000	0.39281	0.838000	0.47535	5.999000	0.70665	2.729000	0.93468	0.655000	0.94253	GCC	.	.		0.602	RUNX1T1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377045.3	NM_004349, NM_175635		T	92982954	C	T	92982954	3	4	236	1	0	0	0	0	1	0	0	0	13762	768	27	1	351	1	RUNX1T1	8	92982954	Missense_Mutation	SNP	C	TCGA-DD-AAW3-01A-11D-A40P-10		92982954	53381068	45	32847										
MAL2	114569	hgsc.bcm.edu	37	chr8	120220776	120220776	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	cgtgtccttcccgccgccccGgggtcaccctgcccgccggc	12	22	1	0	rs398009582|rs71302978		TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr8:120220776G>C	ENST00000276681.6	+	1	167	c.65G>C	c.(64-66)cGg>cCg	p.R22P	MAL2_ENST00000521748.1_3'UTR	NM_052886.2	NP_443118.1	Q969L2	MAL2_HUMAN	mal, T-cell differentiation protein 2 (gene/pseudogene)	22						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)						all_cancers(13;1.91e-26)|Lung NSC(37;8.61e-08)|Ovarian(258;0.018)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.000967)			CCGCCGCCCCGGGGTCACCCT	0.771																																					.		Atlas-SNP	.											.	.	.	.	0			c.64+1G>C						.						1	1	1					8																	120220776		184	483	667	SO:0001630	splice_region_variant	114569	exon1			CGCCCCGGGGTCA	AL117612	CCDS75780.1	8q23	2011-01-26	2011-01-26			ENSG00000147676			13634	protein-coding gene	gene with protein product	"MAL proteolipid protein 2"	609684				11549320	Standard	NM_052886		Approved		uc003yop.3	Q969L2		ENST00000276681.6:c.66+1G>C	chr8.hg19:g.120220776G>C		34.0	0.0		81.0	13.0	NM_052886	B2R520|Q6ZMD9	Splice_Site	SNP	ENST00000276681.6	hg19																																																																																				.	.		0.771	MAL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052886	Missense_Mutation	C	120220776	G	C	120220776	5	2	236	1	0	0	0	0	0	0	1	0	9209	1116	39	4	67	4	MAL2	8	120220776	Splice_Site	SNP	G	TCGA-DD-AAW3-01A-11D-A40P-10	27237822	120220776	26143246	46	32848										
HSF1	3297	hgsc.bcm.edu	37	chr8	145533250	145533250	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	cgtggccaggagcagctcctTgagaacatcaagaggaaagt	13	9	1	2			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr8:145533250T>A	ENST00000528838.1	+	3	496	c.336T>A	c.(334-336)ctT>ctA	p.L112L	HSF1_ENST00000400780.4_Silent_p.L47L	NM_005526.2	NP_005517.1	Q00613	HSF1_HUMAN	heat shock transcription factor 1	112					cellular response to heat (GO:0034605)|defense response (GO:0006952)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|female meiotic division (GO:0007143)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of tumor necrosis factor production (GO:0032720)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of spindle checkpoint (GO:0090231)|response to lipopolysaccharide (GO:0032496)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|pronucleus (GO:0045120)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding (GO:0001162)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(1)|lung(3)|prostate(3)|skin(1)|urinary_tract(2)	11	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.94e-40)|Epithelial(56;1.12e-39)|all cancers(56;9.11e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0547)|Colorectal(110;0.055)			AGCAGCTCCTTGAGAACATCA	0.642																																					p.L112L		Atlas-SNP	.											.	HSF1	29	.	0			c.T336A						.						121	118	119					8																	145533250		2203	4296	6499	SO:0001819	synonymous_variant	3297	exon3			GCTCCTTGAGAAC	M64673	CCDS6419.1	8q24.3	2014-04-10			ENSG00000185122	ENSG00000185122			5224	protein-coding gene	gene with protein product		140580				1871105	Standard	NM_005526		Approved	HSTF1	uc003zbt.4	Q00613	OTTHUMG00000174604	ENST00000528838.1:c.336T>A	chr8.hg19:g.145533250T>A		172.0	0.0		353.0	250.0	NM_005526	A8K4L0|A8MW26|Q53XT4	Silent	SNP	ENST00000528838.1	hg19	CCDS6419.1																																																																																			.	.		0.642	HSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382053.1	NM_005526		A	145533250	T	A	145533250	2	1	236	1	0	0	0	0	0	0	0	1	7404	1799	63	4		4	HSF1	8	145533250	Silent	SNP	T	TCGA-DD-AAW3-01A-11D-A40P-10	25312474	145533250	830772	47	32849										
CDKN2A	1029	hgsc.bcm.edu	37	chr9	21971190	21971190	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	agcagctccgccactcgggcGctgcccatcatcatgacctg	10	17	2	1			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr9:21971190G>T	ENST00000304494.5	-	2	438	c.168C>A	c.(166-168)agC>agA	p.S56R	CDKN2A_ENST00000498124.1_Missense_Mutation_p.S56R|CDKN2A_ENST00000578845.2_Missense_Mutation_p.S5R|CDKN2A_ENST00000479692.2_Missense_Mutation_p.S5R|CDKN2A_ENST00000530628.2_Missense_Mutation_p.R71S|CDKN2A_ENST00000579755.1_Missense_Mutation_p.R71S|CDKN2A_ENST00000446177.1_Missense_Mutation_p.S56R|CDKN2A_ENST00000497750.1_Missense_Mutation_p.S5R|CDKN2A_ENST00000579122.1_Missense_Mutation_p.S56R|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000494262.1_Missense_Mutation_p.S5R|CDKN2A_ENST00000361570.3_Missense_Mutation_p.R112S|CDKN2A_ENST00000498628.2_Missense_Mutation_p.S5R	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	56			S -> I (possible polymorphism).		cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular senescence (GO:2000774)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|Ras protein signal transduction (GO:0007265)|replicative senescence (GO:0090399)|senescence-associated heterochromatin focus assembly (GO:0035986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|senescence-associated heterochromatin focus (GO:0035985)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.0?(1315)|p.?(45)|p.M53_R58del(3)|p.M54fs*61(2)|p.A57fs*63(2)|p.0(1)|p.V28_V51del(1)|p.A57fs*62(1)|p.G55fs*86(1)|p.S56fs*90(1)|p.S114fs*>61(1)		NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		CCACTCGGGCGCTGCCCATCA	0.687		17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)																											p.R71S		Atlas-SNP	.											CDKN2A_ENST00000361570,NS,carcinoma,+1,1	CDKN2A	4810	.	1373	Whole gene deletion(1316)|Unknown(45)|Deletion - Frameshift(5)|Deletion - In frame(4)|Insertion - Frameshift(3)	haematopoietic_and_lymphoid_tissue(283)|skin(177)|central_nervous_system(167)|lung(146)|urinary_tract(92)|bone(74)|soft_tissue(57)|upper_aerodigestive_tract(56)|pleura(51)|oesophagus(50)|ovary(37)|kidney(32)|breast(32)|pancreas(30)|thyroid(13)|NS(12)|biliary_tract(12)|stomach(12)|autonomic_ganglia(7)|meninges(7)|large_intestine(6)|liver(6)|salivary_gland(4)|thymus(4)|vulva(2)|endometrium(2)|prostate(2)	c.C211A						.						7	9	8					9																	21971190		2052	4098	6150	SO:0001583	missense	1029	exon2			TCGGGCGCTGCCC	L27211	CCDS6510.1, CCDS6511.1, CCDS6511.2, CCDS56565.1	9p21	2014-09-17	2012-03-08		ENSG00000147889	ENSG00000147889			1787	protein-coding gene	gene with protein product		600160	"cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)"	CDKN2, MLM		8152487, 7606716	Standard	NM_058195		Approved	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf	uc003zpk.3	P42771	OTTHUMG00000019686	ENST00000304494.5:c.168C>A	chr9.hg19:g.21971190G>T	ENSP00000307101:p.Ser56Arg	42.0	0.0		39.0	17.0	NM_058195	A5X2G7|D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	Missense_Mutation	SNP	ENST00000304494.5	hg19	CCDS6510.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.997|8.997	0.979147|0.979147	0.18812|0.18812	.|.	.|.	ENSG00000147889|ENSG00000147889	ENST00000361570;ENST00000530628|ENST00000304494;ENST00000446177	T;T|T;T	0.78816|0.64991	-1.21;-1.15|-0.13;-0.13	5.79|5.79	3.64|3.64	0.41730|0.41730	.|Ankyrin repeat-containing domain (4);	0.577489|.	0.14579|.	N|.	0.310962|.	T|T	0.64080|0.64080	0.2566|0.2566	N|N	0.24115|0.24115	0.695|0.695	0.21950|0.21950	N|N	0.999459|0.999459	B|D	0.16802|0.89917	0.019|1.0	B|D	0.12156|0.68039	0.007|0.955	T|T	0.53151|0.53151	-0.8479|-0.8479	10|9	0.44086|0.49607	T|T	0.13|0.09	-13.3999|-13.3999	10.119|10.119	0.42609|0.42609	0.2392:0.0:0.7608:0.0|0.2392:0.0:0.7608:0.0	.|.	112|56	Q8N726|P42771	CD2A2_HUMAN|CD2A1_HUMAN	S|R	112;71|56	ENSP00000355153:R112S;ENSP00000432664:R71S|ENSP00000307101:S56R;ENSP00000394932:S56R	ENSP00000355153:R112S|ENSP00000307101:S56R	R|S	-|-	1|3	0|2	CDKN2A|CDKN2A	21961190|21961190	0.983000|0.983000	0.35010|0.35010	0.488000|0.488000	0.27440|0.27440	0.368000|0.368000	0.29767|0.29767	3.981000|3.981000	0.56902|0.56902	1.454000|1.454000	0.47793|0.47793	-0.263000|-0.263000	0.10527|0.10527	CGC|AGC	.	.		0.687	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	NM_000077		T	21971190	G	T	21971190	3	4	236	1	0	0	0	0	1	0	0	0	3163	1087	38	1	310	1	CDKN2A	9	21971190	Missense_Mutation	SNP	G	TCGA-DD-AAW3-01A-11D-A40P-10		21971190	119242241	48	32850										
C9orf131	138724	hgsc.bcm.edu	37	chr9	35044496	35044497	+	Frame_Shift_Del	DEL	CA	CA	-													0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	tgggagtcttgtctgattctCagtctattgtaggggaaatg							TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr9:35044496_35044497delCA	ENST00000312292.5	+	2	1917_1918	c.1870_1871delCA	c.(1870-1872)cagfs	p.Q624fs	C9orf131_ENST00000421362.2_Frame_Shift_Del_p.Q576fs|C9orf131_ENST00000354479.5_Frame_Shift_Del_p.Q551fs|FLJ00273_ENST00000595331.1_5'Flank	NM_001040410.1|NM_203299.2	NP_001035500.1|NP_976044.2	Q5VYM1	CI131_HUMAN	chromosome 9 open reading frame 131	624										cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(23)|prostate(2)|skin(2)|stomach(1)	39	all_epithelial(49;0.22)		LUSC - Lung squamous cell carcinoma(32;0.00117)|Lung(28;0.00309)			GTCTGATTCTCAGTCTATTGTA	0.49																																					p.623_624del		Atlas-INDEL	.											.	C9orf131	71	.	0			c.1869_1870del						.																																			SO:0001589	frameshift_variant	138724	exon2			.	BC045643	CCDS6572.2, CCDS47961.1, CCDS47962.1	9p13.3	2008-02-05			ENSG00000174038	ENSG00000174038			31418	protein-coding gene	gene with protein product							Standard	NM_001287391		Approved	MGC41945	uc003zvw.3	Q5VYM1	OTTHUMG00000019853	ENST00000312292.5:c.1870_1871delCA	chr9.hg19:g.35044496_35044497delCA	ENSP00000308279:p.Gln624fs	98.0	0.0		59.0	25.0	NM_203299	A6NLE6|E9PB26|Q86XC6|Q9UF74	Frame_Shift_Del	DEL	ENST00000312292.5	hg19	CCDS6572.2																																																																																			.	.		0.49	C9orf131-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052283.5	NM_203299		-	35044497	CA	-	35044496	7	5	236	1	0	1	0	1	0	0	0	0	2459	827	29	0	1892	0	C9orf131	9	35044496	Frame_Shift_Del	DEL	CA	TCGA-DD-AAW3-01A-11D-A40P-10	13073306	35044496	106168935	49	32851										
KIAA1529	100499483	hgsc.bcm.edu	37	chr9	100105806	100105806	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	tgccaagttcatagaacaagTgacaattccatcgagactaa	7	9	1	3			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr9:100105806T>C	ENST00000357054.1	+	33	3943	c.3008T>C	c.(3007-3009)gTg>gCg	p.V1003A	CCDC180_ENST00000529487.1_Missense_Mutation_p.V864A|CCDC180_ENST00000395220.1_3'UTR|CCDC180_ENST00000375202.2_Missense_Mutation_p.V864A|CCDC180_ENST00000411667.2_Missense_Mutation_p.V861A|CCDC180_ENST00000460482.2_3'UTR|RP11-23J9.4_ENST00000534123.1_RNA			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	1003						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											ATAGAACAAGTGACAATTCCA	0.378																																					p.V864A		Atlas-SNP	.											.	.	.	.	0			c.T2591C						.						82	78	79					9																	100105806		2203	4300	6503	SO:0001583	missense	0	exon19			AACAAGTGACAAT	AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"Behcet's Disease Associated Gene 1"		"KIAA1529", "chromosome 9 open reading frame 174"	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.3008T>C	chr9.hg19:g.100105806T>C	ENSP00000349562:p.Val1003Ala	57.0	0.0		59.0	20.0	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Missense_Mutation	SNP	ENST00000357054.1	hg19		.	.	.	.	.	.	.	.	.	.	T	11.21	1.570755	0.28003	.	.	ENSG00000197816	ENST00000357054;ENST00000375202;ENST00000411667;ENST00000541524;ENST00000529487	T;T;T;T	0.19250	2.81;2.82;2.16;2.82	5.39	3.05	0.35203	.	0.249082	0.33127	N	0.005243	T	0.12860	0.0312	L	0.32530	0.975	0.09310	N	1	B;B;P	0.36144	0.087;0.42;0.539	B;B;B	0.37650	0.063;0.255;0.17	T	0.21348	-1.0248	10	0.06757	T	0.87	-13.5431	7.2665	0.26232	0.0:0.1774:0.0:0.8226	.	887;1003;1003	Q86Y65;B7ZMG3;Q9P1Z9	.;.;CI174_HUMAN	A	1003;864;861;887;864	ENSP00000349562:V1003A;ENSP00000364348:V864A;ENSP00000414000:V861A;ENSP00000434727:V864A	ENSP00000349562:V1003A	V	+	2	0	C9orf174	99145627	0.669000	0.27502	0.135000	0.22099	0.038000	0.13279	0.812000	0.27211	0.441000	0.26529	-0.256000	0.11100	GTG	.	.		0.378	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893		C	100105806	T	C	100105806	3	2	236	1	0	0	0	0	1	0	0	0	8249	1696	59	2	3094	2	KIAA1529	9	100105806	Missense_Mutation	SNP	T	TCGA-DD-AAW3-01A-11D-A40P-10	65061310	100105806	41107625	50	32852										
ACTL7B	10880	hgsc.bcm.edu	37	chr9	111617761	111617761	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	ctggggctgagcggagggtcGgagaccagcacagcgtgctc	18	11	0	2			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr9:111617761G>A	ENST00000374667.3	-	1	1478	c.450C>T	c.(448-450)tcC>tcT	p.S150S		NM_006686.3	NP_006677.1	Q9Y614	ACL7B_HUMAN	actin-like 7B	150						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	structural constituent of cytoskeleton (GO:0005200)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						GCGGAGGGTCGGAGACCAGCA	0.627																																					p.S150S		Atlas-SNP	.											.	ACTL7B	57	.	0			c.C450T						.						59	44	49					9																	111617761		2203	4300	6503	SO:0001819	synonymous_variant	10880	exon1			AGGGTCGGAGACC	BC033789	CCDS6771.1	9q31	2009-05-15			ENSG00000148156	ENSG00000148156			162	protein-coding gene	gene with protein product		604304				10373328, 12907721	Standard	NM_006686		Approved	Tact1	uc004bdi.3	Q9Y614	OTTHUMG00000020462	ENST00000374667.3:c.450C>T	chr9.hg19:g.111617761G>A		64.0	0.0		53.0	16.0	NM_006686	B2R9Q2|Q5JSV1	Silent	SNP	ENST00000374667.3	hg19	CCDS6771.1																																																																																			.	.		0.627	ACTL7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053571.1	NM_006686		A	111617761	G	A	111617761	2	1	236	1	0	0	0	0	0	0	0	1	201	1103	39	1		1	ACTL7B	9	111617761	Silent	SNP	G	TCGA-DD-AAW3-01A-11D-A40P-10	11511955	111617761	29595670	51	32853										
GPSM1	26086	hgsc.bcm.edu	37	chr9	139234263	139234263	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	gccaagaagcacctgcagatCtcccaggaggtgagccaggc	13	13	1	3			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr9:139234263C>T	ENST00000440944.1	+	8	1294	c.1074C>T	c.(1072-1074)atC>atT	p.I358I	GPSM1_ENST00000392945.3_Silent_p.I358I	NM_001145638.1	NP_001139110	Q86YR5	GPSM1_HUMAN	G-protein signaling modulator 1	358	Mediates association with membranes. {ECO:0000250}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	GDP-dissociation inhibitor activity (GO:0005092)			biliary_tract(1)|endometrium(1)|kidney(2)|lung(4)|upper_aerodigestive_tract(1)	9		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.39e-06)|Epithelial(140;3.24e-06)		ACCTGCAGATCTCCCAGGAGG	0.711																																					p.I358I		Atlas-SNP	.											.	GPSM1	50	.	0			c.C1074T						.						28	29	29					9																	139234263		1822	3480	5302	SO:0001819	synonymous_variant	26086	exon8			GCAGATCTCCCAG	AI272212	CCDS6996.2, CCDS48055.1, CCDS48056.1	9q34.3	2013-01-10	2010-06-24		ENSG00000160360	ENSG00000160360		"Tetratricopeptide (TTC) repeat domain containing"	17858	protein-coding gene	gene with protein product	"AGS3 homolog (C. elegans)"	609491	"G-protein signalling modulator 1 (AGS3-like, C. elegans)"			11278352, 10969064	Standard	NM_001145639		Approved	AGS3, DKFZP727I051	uc004chd.2	Q86YR5	OTTHUMG00000020930	ENST00000440944.1:c.1074C>T	chr9.hg19:g.139234263C>T		63.0	0.0		55.0	27.0	NM_015597	A9Z1X4|B1B0W3|Q86SR5|Q969T1|Q9UFS8	Silent	SNP	ENST00000440944.1	hg19	CCDS48055.1																																																																																			.	.		0.711	GPSM1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015597		T	139234263	C	T	139234263	2	4	236	1	0	0	0	0	0	0	0	1	6743	903	32	3		3	GPSM1	9	139234263	Silent	SNP	C	TCGA-DD-AAW3-01A-11D-A40P-10	27616502	139234263	1979168	52	32854										
ABCA2	20	hgsc.bcm.edu	37	chr9	139902954	139902954	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	aagtgcccggagctccgtggGggcagaccggggccggagca	19	12	0	1			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr9:139902954G>T	ENST00000371605.3	-	47	7333	c.7186C>A	c.(7186-7188)Ccc>Acc	p.P2396T	ABCA2_ENST00000341511.6_Missense_Mutation_p.P2397T|ABCA2_ENST00000265662.5_Missense_Mutation_p.P2397T			Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 2	2396					ATP catabolic process (GO:0006200)|cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|regulation of intracellular cholesterol transport (GO:0032383)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|nucleotide binding (GO:0000166)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|liver(1)|lung(25)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	41	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		AGCTCCGTGGGGGCAGACCGG	0.682																																					p.P2427T		Atlas-SNP	.											.	ABCA2	113	.	0			c.C7279A						.						13	16	15					9																	139902954		1972	4151	6123	SO:0001583	missense	20	exon48			CCGTGGGGGCAGA	U18235	CCDS43909.1	9q34	2012-03-14			ENSG00000107331	ENSG00000107331		"ATP binding cassette transporters / subfamily A"	32	protein-coding gene	gene with protein product		600047		ABC2		8088782	Standard	NM_212533		Approved		uc022bpy.1	Q9BZC7	OTTHUMG00000020958	ENST00000371605.3:c.7186C>A	chr9.hg19:g.139902954G>T	ENSP00000360666:p.Pro2396Thr	60.0	0.0		61.0	23.0	NM_212533	A6NED5|Q5SPY5|Q5W9G5|Q76MW7|Q9HC28	Missense_Mutation	SNP	ENST00000371605.3	hg19		.	.	.	.	.	.	.	.	.	.	G	11.41	1.629176	0.28978	.	.	ENSG00000107331	ENST00000265662;ENST00000371605;ENST00000355090;ENST00000341511;ENST00000490486;ENST00000448336	D;D;D;D;D	0.86865	-2.18;-2.18;-2.18;-1.75;-1.72	4.06	3.13	0.36017	.	0.583672	0.15862	U	0.240980	T	0.79167	0.4400	N	0.24115	0.695	0.40152	D	0.976961	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.73329	-0.4017	10	0.48119	T	0.1	.	12.8377	0.57782	0.0:0.0:0.8353:0.1647	.	2396;2427	Q9BZC7;E7ETC3	ABCA2_HUMAN;.	T	2397;2396;2427;2397;156;146	ENSP00000265662:P2397T;ENSP00000360666:P2396T;ENSP00000344155:P2397T;ENSP00000420360:P156T;ENSP00000406741:P146T	ENSP00000265662:P2397T	P	-	1	0	ABCA2	139022775	0.979000	0.34478	0.489000	0.27452	0.448000	0.32197	1.156000	0.31712	0.877000	0.35895	0.313000	0.20887	CCC	.	.		0.682	ABCA2-202	KNOWN	basic	protein_coding	protein_coding		NM_001606		T	139902954	G	T	139902954	3	4	236	1	0	0	0	0	1	0	0	0	32	1232	43	3	129	3	ABCA2	9	139902954	Missense_Mutation	SNP	G	TCGA-DD-AAW3-01A-11D-A40P-10	668691	139902954	1310477	53	32855										
FUT7	2529	hgsc.bcm.edu	37	chr9	139925353	139925353	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	gaaagccgccagctctcgggCtgagccaaagtcatccacat	10	14	2	1	rs547445437		TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr9:139925353C>T	ENST00000314412.6	-	2	1856	c.838G>A	c.(838-840)Gcc>Acc	p.A280T	ABCA2_ENST00000492260.1_5'Flank|ABCA2_ENST00000341511.6_5'Flank|ABCA2_ENST00000371605.3_5'Flank|ABCA2_ENST00000265662.5_5'Flank|C9orf139_ENST00000314330.2_Intron	NM_004479.3	NP_004470.1	Q11130	FUT7_HUMAN	fucosyltransferase 7 (alpha (1,3) fucosyltransferase)	280					CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|leukocyte migration involved in immune response (GO:0002522)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			NS(1)|endometrium(1)|lung(4)|ovary(1)|skin(1)	8	all_cancers(76;0.0893)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.96e-05)|Epithelial(140;0.000486)		AGCTCTCGGGCTGAGCCAAAG	0.637																																					p.A280T		Atlas-SNP	.											.	FUT7	24	.	0			c.G838A						.						49	52	51					9																	139925353		2201	4295	6496	SO:0001583	missense	2529	exon2			CTCGGGCTGAGCC	X78031, AB012668	CCDS7022.1	9q34.3	2013-02-26			ENSG00000180549	ENSG00000180549		"Fucosyltransferases"	4018	protein-coding gene	gene with protein product		602030				8207002, 8182079	Standard	NM_004479		Approved		uc004ckq.2	Q11130	OTTHUMG00000020964	ENST00000314412.6:c.838G>A	chr9.hg19:g.139925353C>T	ENSP00000318142:p.Ala280Thr	43.0	0.0		65.0	26.0	NM_004479	B2R7U7|Q6DK54	Missense_Mutation	SNP	ENST00000314412.6	hg19	CCDS7022.1	.	.	.	.	.	.	.	.	.	.	c	9.723	1.160111	0.21454	.	.	ENSG00000180549	ENST00000314412	T	0.26223	1.75	4.37	4.37	0.52481	.	0.354005	0.24143	U	0.041148	T	0.20820	0.0501	L	0.31752	0.955	0.27989	N	0.935726	B	0.29766	0.256	B	0.32393	0.145	T	0.11275	-1.0594	10	0.31617	T	0.26	-18.2707	14.499	0.67709	0.0:1.0:0.0:0.0	.	280	Q11130	FUT7_HUMAN	T	280	ENSP00000318142:A280T	ENSP00000318142:A280T	A	-	1	0	FUT7	139045174	0.000000	0.05858	0.745000	0.31077	0.023000	0.10783	-0.310000	0.08135	2.252000	0.74401	0.552000	0.68991	GCC	.	.		0.637	FUT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055220.1	NM_004479		T	139925353	C	T	139925353	3	4	236	1	0	0	0	0	1	0	0	0	6117	797	28	3	194	3	FUT7	9	139925353	Missense_Mutation	SNP	C	TCGA-DD-AAW3-01A-11D-A40P-10	22399	139925353	1288078	54	32856										
RASGEF1A	221002	hgsc.bcm.edu	37	chr10	43691966	43691966	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	tttccatgtggttctcgggaCcctcactttcaaaggaggcg	11	11	3	0			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr10:43691966C>T	ENST00000395809.1	-	12	3885	c.1379G>A	c.(1378-1380)gGt>gAt	p.G460D	RASGEF1A_ENST00000395810.1_Missense_Mutation_p.G460D|RASGEF1A_ENST00000374459.1_Missense_Mutation_p.G468D			Q8N9B8	RGF1A_HUMAN	RasGEF domain family, member 1A	460	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				cell migration (GO:0016477)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	Ras guanyl-nucleotide exchange factor activity (GO:0005088)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(2)	11						GTTCTCGGGACCCTCACTTTC	0.572																																					p.G460D		Atlas-SNP	.											.	RASGEF1A	66	.	0			c.G1379A						.						156	142	147					10																	43691966		2203	4300	6503	SO:0001583	missense	221002	exon12			TCGGGACCCTCAC	AK095136	CCDS7202.2, CCDS60517.1	10q11.21	2006-01-11			ENSG00000198915	ENSG00000198915			24246	protein-coding gene	gene with protein product		614531				12477932	Standard	XM_005271808		Approved	CG4853, FLJ37817	uc001jap.1	Q8N9B8	OTTHUMG00000018025	ENST00000395809.1:c.1379G>A	chr10.hg19:g.43691966C>T	ENSP00000379154:p.Gly460Asp	50.0	0.0		59.0	21.0	NM_145313	Q8TBF1	Missense_Mutation	SNP	ENST00000395809.1	hg19	CCDS7202.2	.	.	.	.	.	.	.	.	.	.	C	29.3	4.995664	0.93167	.	.	ENSG00000198915	ENST00000374459;ENST00000395810;ENST00000395809	T;T;T	0.29655	1.56;1.56;1.56	5.14	5.14	0.70334	Guanine-nucleotide dissociation stimulator CDC25 (2);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.64402	D	0.000001	T	0.40595	0.1123	L	0.51422	1.61	0.80722	D	1	P;P	0.45672	0.645;0.864	B;P	0.47981	0.231;0.563	T	0.25152	-1.0140	10	0.56958	D	0.05	.	18.9656	0.92695	0.0:1.0:0.0:0.0	.	460;468	Q8N9B8;Q8N9B8-2	RGF1A_HUMAN;.	D	468;460;460	ENSP00000363583:G468D;ENSP00000379155:G460D;ENSP00000379154:G460D	ENSP00000363583:G468D	G	-	2	0	RASGEF1A	43011972	1.000000	0.71417	0.992000	0.48379	0.949000	0.60115	7.403000	0.79983	2.550000	0.86006	0.462000	0.41574	GGT	.	.		0.572	RASGEF1A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000313989.1	NM_145313		T	43691966	C	T	43691966	3	4	236	1	0	0	0	0	1	0	0	0	13084	507	18	3	74	3	RASGEF1A	10	43691966	Missense_Mutation	SNP	C	TCGA-DD-AAW3-01A-11D-A40P-10		43691966	91842781	55	32857										
JMJD1C	221037	hgsc.bcm.edu	37	chr10	64952883	64952883	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	gcatgcacagagaaattttaTtactgtgattaagaacattc	7	6	0	3			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr10:64952883T>C	ENST00000399262.2	-	16	6109	c.5891A>G	c.(5890-5892)aAt>aGt	p.N1964S	JMJD1C_ENST00000542921.1_Missense_Mutation_p.N1782S|JMJD1C_ENST00000399251.1_3'UTR|JMJD1C_ENST00000402544.1_Intron	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	1964					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					AGAAATTTTATTACTGTGATT	0.353																																					p.N1964S		Atlas-SNP	.											.	JMJD1C	347	.	0			c.A5891G						.						75	67	69					10																	64952883		1855	4101	5956	SO:0001583	missense	221037	exon16			ATTTTATTACTGT	L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"thyroid hormone receptor interactor 8"	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.5891A>G	chr10.hg19:g.64952883T>C	ENSP00000382204:p.Asn1964Ser	20.0	0.0		17.0	6.0	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Missense_Mutation	SNP	ENST00000399262.2	hg19	CCDS41532.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.75|12.75	2.030144|2.030144	0.35797|0.35797	.|.	.|.	ENSG00000171988|ENSG00000171988	ENST00000327520|ENST00000399262;ENST00000542921	.|T;T	.|0.50001	.|0.76;0.77	5.67|5.67	3.31|3.31	0.37934|0.37934	.|.	.|0.048027	.|0.85682	.|D	.|0.000000	T|T	0.39009|0.39009	0.1062|0.1062	L|L	0.58101|0.58101	1.795|1.795	0.80722|0.80722	D|D	1|1	.|B;B	.|0.30793	.|0.052;0.295	.|B;B	.|0.23852	.|0.031;0.049	T|T	0.18335|0.18335	-1.0340|-1.0340	5|10	.|0.27082	.|T	.|0.32	-10.3947|-10.3947	10.073|10.073	0.42345|0.42345	0.0:0.1406:0.0:0.8594|0.0:0.1406:0.0:0.8594	.|.	.|1505;1964	.|A6PW35;Q15652	.|.;JHD2C_HUMAN	V|S	511|1964;1782	.|ENSP00000382204:N1964S;ENSP00000444682:N1782S	.|ENSP00000382204:N1964S	I|N	-|-	1|2	0|0	JMJD1C|JMJD1C	64622889|64622889	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.878000|0.878000	0.50629|0.50629	3.212000|3.212000	0.51145|0.51145	0.982000|0.982000	0.38575|0.38575	0.528000|0.528000	0.53228|0.53228	ATA|AAT	.	.		0.353	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241		C	64952883	T	C	64952883	3	2	236	1	0	0	0	0	1	0	0	0	7959	1493	52	2	1775	2	JMJD1C	10	64952883	Missense_Mutation	SNP	T	TCGA-DD-AAW3-01A-11D-A40P-10	21260917	64952883	70581864	56	32858										
C10orf27	219793	hgsc.bcm.edu	37	chr10	72536989	72536989	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	actctgctggccctggtgagAtctgcggcggccgacagccc	14	15	2	1			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr10:72536989A>G	ENST00000299290.1	-	7	999	c.610T>C	c.(610-612)Tct>Cct	p.S204P	TBATA_ENST00000456372.2_Missense_Mutation_p.S204P	NM_152710.2	NP_689923	Q96M53	TBATA_HUMAN	thymus, brain and testes associated	204					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|nucleus (GO:0005634)											CCCTGGTGAGATCTGCGGCGG	0.632																																					p.S204P		Atlas-SNP	.											.	.	.	.	0			c.T610C						.						61	64	63					10																	72536989		2203	4300	6503	SO:0001583	missense	219793	exon7			GGTGAGATCTGCG	AK057382	CCDS7308.1	10q22.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000166220	ENSG00000166220			23511	protein-coding gene	gene with protein product		612640	"chromosome 10 open reading frame 27"	C10orf27		20937703	Standard	NM_152710		Approved	FLJ32820, spatial	uc001jrj.1	Q96M53	OTTHUMG00000018413	ENST00000299290.1:c.610T>C	chr10.hg19:g.72536989A>G	ENSP00000299290:p.Ser204Pro	40.0	0.0		38.0	12.0	NM_152710	A4QPA8|B2RPQ2|Q5T4G2	Missense_Mutation	SNP	ENST00000299290.1	hg19	CCDS7308.1	.	.	.	.	.	.	.	.	.	.	A	9.941	1.217434	0.22373	.	.	ENSG00000166220	ENST00000299290;ENST00000536955;ENST00000456372	T;T	0.19394	2.15;2.15	4.66	0.438	0.16560	.	0.536654	0.14140	N	0.338743	T	0.30978	0.0782	M	0.75264	2.295	0.09310	N	1	D;B;B;B	0.64830	0.994;0.004;0.004;0.019	P;B;B;B	0.52957	0.714;0.007;0.011;0.011	T	0.11641	-1.0579	10	0.66056	D	0.02	-11.2433	5.6987	0.17871	0.5189:0.3238:0.0:0.1573	.	224;203;205;204	B7Z8G0;B7ZMN4;B7ZMN5;Q96M53	.;.;.;SPATL_HUMAN	P	204;222;204	ENSP00000299290:S204P;ENSP00000400224:S204P	ENSP00000299290:S204P	S	-	1	0	C10orf27	72206995	0.216000	0.23585	0.003000	0.11579	0.001000	0.01503	0.811000	0.27198	0.208000	0.20626	-0.501000	0.04562	TCT	.	.		0.632	TBATA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048519.1	NM_152710		G	72536989	A	G	72536989	3	3	236	1	0	0	0	0	1	0	0	0	1602	333	12	2	465	2	C10orf27	10	72536989	Missense_Mutation	SNP	A	TCGA-DD-AAW3-01A-11D-A40P-10	7584106	72536989	62997758	57	32859										
PTEN	5728	hgsc.bcm.edu	37	chr10	89685287	89685287	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	aaggtttttggattcaaagcAtaaaaaccattacaagatat	6	5	1	1	rs398123316		TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr10:89685287A>T	ENST00000371953.3	+	3	1539	c.182A>T	c.(181-183)cAt>cTt	p.H61L		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	61	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.		H -> D (in VATER). {ECO:0000269|PubMed:11748304}.|H -> R (loss of phosphatase activity towards Ins(1,3,4,5)P4).		activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.H61R(8)|p.?(6)|p.R55fs*1(5)|p.Y27fs*1(2)|p.H61L(1)|p.V54fs*29(1)|p.R55_L70>S(1)|p.F56fs*2(1)|p.H61P(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		GATTCAAAGCATAAAAACCAT	0.259		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																											p.H61L		Atlas-SNP	.	yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	PTEN,NS,carcinoma,0,10	PTEN	3652	.	63	Whole gene deletion(37)|Substitution - Missense(10)|Deletion - Frameshift(9)|Unknown(6)|Complex - deletion inframe(1)	central_nervous_system(18)|prostate(16)|lung(8)|skin(7)|haematopoietic_and_lymphoid_tissue(5)|ovary(3)|urinary_tract(2)|breast(2)|soft_tissue(1)|endometrium(1)	c.A182T	GRCh37	CI022298	PTEN	I		.						35	36	36					10																	89685287		2184	4274	6458	SO:0001583	missense	5728	exon3	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	CAAAGCATAAAAA	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.182A>T	chr10.hg19:g.89685287A>T	ENSP00000361021:p.His61Leu	1343.0	1.0		1334.0	544.0	NM_000314	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	hg19	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.546993	0.86022	.	.	ENSG00000171862	ENST00000371953	D	0.98602	-5.02	5.46	5.46	0.80206	Phosphatase tensin type (1);	0.000000	0.85682	D	0.000000	D	0.99202	0.9723	M	0.93594	3.435	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99170	1.0864	9	.	.	.	-10.6657	15.5246	0.75894	1.0:0.0:0.0:0.0	.	61	P60484	PTEN_HUMAN	L	61	ENSP00000361021:H61L	.	H	+	2	0	PTEN	89675267	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.668000	0.91158	2.072000	0.62099	0.533000	0.62120	CAT	.	.		0.259	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		T	89685287	A	T	89685287	3	4	236	1	0	0	0	0	1	0	0	0	12750	217	8	4	192	4	PTEN	10	89685287	Missense_Mutation	SNP	A	TCGA-DD-AAW3-01A-11D-A40P-10	17148298	89685287	45849460	58	32860										
CHUK	1147	hgsc.bcm.edu	37	chr10	101967049	101967049	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	gcccttcatatacagttttaCttttatcaaacaaataaacc	2	10	2	0			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr10:101967049C>T	ENST00000370397.7	-	11	1255	c.1169G>A	c.(1168-1170)aGt>aAt	p.S390N		NM_001278.3	NP_001269.3	O15111	IKKA_HUMAN	conserved helix-loop-helix ubiquitous kinase	390					anatomical structure morphogenesis (GO:0009653)|cellular response to tumor necrosis factor (GO:0071356)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|morphogenesis of an epithelial sheet (GO:0002011)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hydroperoxide (GO:0033194)|response to lipopolysaccharide (GO:0032496)|response to toxic substance (GO:0009636)|response to virus (GO:0009615)|Rho protein signal transduction (GO:0007266)|skeletal muscle contraction (GO:0003009)|striated muscle cell differentiation (GO:0051146)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|scaffold protein binding (GO:0097110)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(9)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	27		Colorectal(252;0.117)		Epithelial(162;2.05e-10)|all cancers(201;1.91e-08)	Acetylcysteine(DB06151)|Aminosalicylic Acid(DB00233)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	TACAGTTTTACTTTTATCAAA	0.333																																					p.S390N	Ovarian(159;52 1904 10536 35305 37148)	Atlas-SNP	.											.	CHUK	71	.	0			c.G1169A						.						65	65	65					10																	101967049		2202	4295	6497	SO:0001583	missense	1147	exon11			GTTTTACTTTTAT	AF009225	CCDS7488.1	10q24-q25	2008-08-01			ENSG00000213341	ENSG00000213341			1974	protein-coding gene	gene with protein product		600664		TCF16		7558004, 16902410	Standard	XR_246062		Approved	IKK1, IKK-alpha, IkBKA, NFKBIKA, IKKA	uc001kqp.3	O15111	OTTHUMG00000018899	ENST00000370397.7:c.1169G>A	chr10.hg19:g.101967049C>T	ENSP00000359424:p.Ser390Asn	75.0	0.0		59.0	13.0	NM_001278	O14666|Q13132|Q5W0I4|Q92467	Missense_Mutation	SNP	ENST00000370397.7	hg19	CCDS7488.1	.	.	.	.	.	.	.	.	.	.	C	19.30	3.800210	0.70567	.	.	ENSG00000213341	ENST00000370397	T	0.56103	0.48	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	T	0.69780	0.3149	L	0.58810	1.83	0.80722	D	1	D	0.69078	0.997	D	0.75484	0.986	T	0.69921	-0.5014	10	0.56958	D	0.05	-11.411	17.2953	0.87169	0.0:1.0:0.0:0.0	.	390	O15111	IKKA_HUMAN	N	390	ENSP00000359424:S390N	ENSP00000359424:S390N	S	-	2	0	CHUK	101957039	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.814000	0.86154	2.678000	0.91216	0.650000	0.86243	AGT	.	.		0.333	CHUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049836.1	NM_001278		T	101967049	C	T	101967049	3	4	236	1	0	0	0	0	1	0	0	0	3418	565	20	3	1112	3	CHUK	10	101967049	Missense_Mutation	SNP	C	TCGA-DD-AAW3-01A-11D-A40P-10	12281762	101967049	33567698	59	32861										
SORCS3	22986	hgsc.bcm.edu	37	chr10	107022244	107022244	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	caaagagctggacacgcgggTcataggtacatgctcctgct	12	11	1	1	rs367891062		TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr10:107022244T>C	ENST00000369701.3	+	26	3826	c.3599T>C	c.(3598-3600)gTc>gCc	p.V1200A		NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	1200					learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		GACACGCGGGTCATAGGTACA	0.532																																					p.V1200A	NSCLC(116;1497 1690 7108 13108 14106)	Atlas-SNP	.											.	SORCS3	282	.	0			c.T3599C						.	T	ALA/VAL	0,4406		0,0,2203	60	47	51		3599	5.8	1	10		51	1,8599	1.2+/-3.3	0,1,4299	no	missense	SORCS3	NM_014978.1	64	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	benign	1200/1223	107022244	1,13005	2203	4300	6503	SO:0001583	missense	22986	exon26			CGCGGGTCATAGG	AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.3599T>C	chr10.hg19:g.107022244T>C	ENSP00000358715:p.Val1200Ala	62.0	0.0		59.0	28.0	NM_014978	Q5VXF9|Q9NQJ2	Missense_Mutation	SNP	ENST00000369701.3	hg19	CCDS7558.1	.	.	.	.	.	.	.	.	.	.	T	13.15	2.150713	0.37923	0.0	1.16E-4	ENSG00000156395	ENST00000369701	T	0.14144	2.53	5.84	5.84	0.93424	.	0.334249	0.31909	N	0.006878	T	0.13114	0.0318	L	0.36672	1.1	0.35142	D	0.768993	B	0.14805	0.011	B	0.12156	0.007	T	0.14980	-1.0453	9	.	.	.	.	16.2322	0.82352	0.0:0.0:0.0:1.0	.	1200	Q9UPU3	SORC3_HUMAN	A	1200	ENSP00000358715:V1200A	.	V	+	2	0	SORCS3	107012234	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	1.978000	0.40598	2.233000	0.73108	0.454000	0.30748	GTC	.	.		0.532	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978		C	107022244	T	C	107022244	3	2	236	1	0	0	0	0	1	0	0	0	14947	1667	58	2	3701	2	SORCS3	10	107022244	Missense_Mutation	SNP	T	TCGA-DD-AAW3-01A-11D-A40P-10	5055195	107022244	28512503	60	32862										
FAM45A	404636	hgsc.bcm.edu	37	chr10	120879889	120879890	+	Frame_Shift_Ins	INS	-	-	A													0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	ggaatggaaactgttatcttINSacacacagcactgatgctaa							TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr10:120879889_120879890insA	ENST00000361432.2	+	5	544_545	c.518_519insA	c.(517-522)ttacacfs	p.H174fs	FAM45A_ENST00000535029.1_Intron|FAM45A_ENST00000544016.1_Frame_Shift_Ins_p.H23fs|FAM45A_ENST00000489988.1_3'UTR	NM_207009.2	NP_996892.1	Q8TCE6	FA45A_HUMAN	family with sequence similarity 45, member A	174										breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(2)|urinary_tract(1)	14		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0293)		ACTGTTATCTTACACACAGCAC	0.347																																					p.L173fs		Atlas-INDEL	.											.	FAM45A	30	.	0			c.518_519insA						.																																			SO:0001589	frameshift_variant	404636	exon5			.	AF168713	CCDS7609.1	10q25	2008-09-04			ENSG00000119979	ENSG00000119979			31793	protein-coding gene	gene with protein product							Standard	NM_207009		Approved			Q8TCE6	OTTHUMG00000019143	ENST00000361432.2:c.519dupA	chr10.hg19:g.120879890_120879890dupA	ENSP00000354688:p.His174fs	289.0	0.0		240.0	100.0	NM_207009	B1AMV6|B4DDC3|D3DRC8|Q9NXW4	Frame_Shift_Ins	INS	ENST00000361432.2	hg19	CCDS7609.1																																																																																			.	.		0.347	FAM45A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050623.1	NM_207009		A	120879890	-	A	120879889	7	5	236	1	0	1	1	0	0	0	0	0	5572	1764	61	0	536	0	FAM45A	10	120879889	Frame_Shift_Ins	INS	-	TCGA-DD-AAW3-01A-11D-A40P-10	13857645	120879889	14654858	61	32863										
COPB1	1315	hgsc.bcm.edu	37	chr11	14512195	14512195	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	agaaaatcatgtatcagttcAggagcatcaggtataagatg	10	5	4	2			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr11:14512195A>G	ENST00000249923.3	-	5	822	c.522T>C	c.(520-522)ccT>ccC	p.P174P	COPB1_ENST00000439561.2_Silent_p.P174P	NM_016451.4	NP_057535.1	P53618	COPB_HUMAN	coatomer protein complex, subunit beta 1	174					COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|viral process (GO:0016032)	COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi-associated vesicle (GO:0005798)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	36						GTATCAGTTCAGGAGCATCAG	0.323																																					p.P174P		Atlas-SNP	.											.	COPB1	81	.	0			c.T522C						.						88	76	80					11																	14512195		2200	4292	6492	SO:0001819	synonymous_variant	1315	exon5			CAGTTCAGGAGCA	BC037280	CCDS7815.1	11p15.2	2011-05-20	2006-06-30	2006-06-30	ENSG00000129083	ENSG00000129083			2231	protein-coding gene	gene with protein product		600959	"coatomer protein complex, subunit beta"	COPB		7982906	Standard	NM_016451		Approved		uc001mlg.2	P53618	OTTHUMG00000165824	ENST00000249923.3:c.522T>C	chr11.hg19:g.14512195A>G		170.0	0.0		153.0	53.0	NM_001144062	D3DQX0|Q6GTT7|Q9NTK2|Q9UNW7	Silent	SNP	ENST00000249923.3	hg19	CCDS7815.1																																																																																			.	.		0.323	COPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386410.1	NM_016451		G	14512195	A	G	14512195	2	3	236	1	0	0	0	0	0	0	0	1	3730	175	7	2		2	COPB1	11	14512195	Silent	SNP	A	TCGA-DD-AAW3-01A-11D-A40P-10		14512195	120494321	62	32864										
OR8H2	390151	hgsc.bcm.edu	37	chr11	55872580	55872580	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	ccttatgggactgacactttCtgaagagatccagatggctc	10	10	1	4			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr11:55872580C>T	ENST00000313503.1	+	1	62	c.62C>T	c.(61-63)tCt>tTt	p.S21F		NM_001005200.1	NP_001005200.1	Q8N162	OR8H2_HUMAN	olfactory receptor, family 8, subfamily H, member 2	21						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(38)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	61	Esophageal squamous(21;0.00693)					CTGACACTTTCTGAAGAGATC	0.423										HNSCC(53;0.14)																											p.S21F		Atlas-SNP	.											.	OR8H2	117	.	0			c.C62T						.						238	230	232					11																	55872580		2201	4296	6497	SO:0001583	missense	390151	exon1			CACTTTCTGAAGA	AB065657	CCDS31518.1	11q11	2012-08-09			ENSG00000181767	ENSG00000181767		"GPCR / Class A : Olfactory receptors"	15308	protein-coding gene	gene with protein product							Standard	NM_001005200		Approved		uc010riy.2	Q8N162	OTTHUMG00000166832	ENST00000313503.1:c.62C>T	chr11.hg19:g.55872580C>T	ENSP00000323982:p.Ser21Phe	88.0	0.0		76.0	32.0	NM_001005200	Q6IFC1	Missense_Mutation	SNP	ENST00000313503.1	hg19	CCDS31518.1	.	.	.	.	.	.	.	.	.	.	c	3.756	-0.050546	0.07407	.	.	ENSG00000181767	ENST00000313503	T	0.01099	5.34	3.74	1.81	0.25067	.	0.135646	0.34700	N	0.003756	T	0.01189	0.0039	L	0.43598	1.365	0.09310	N	1	B	0.24043	0.096	B	0.23018	0.043	T	0.45556	-0.9253	10	0.46703	T	0.11	.	5.6885	0.17817	0.1589:0.6551:0.0:0.186	.	21	Q8N162	OR8H2_HUMAN	F	21	ENSP00000323982:S21F	ENSP00000323982:S21F	S	+	2	0	OR8H2	55629156	0.000000	0.05858	0.002000	0.10522	0.004000	0.04260	-0.275000	0.08525	0.866000	0.35629	0.440000	0.28878	TCT	.	.		0.423	OR8H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391540.1	NM_001005200		T	55872580	C	T	55872580	3	4	236	1	0	0	0	0	1	0	0	0	11247	913	32	3	64	3	OR8H2	11	55872580	Missense_Mutation	SNP	C	TCGA-DD-AAW3-01A-11D-A40P-10	41360385	55872580	79133936	63	32865										
OR5T3	390154	hgsc.bcm.edu	37	chr11	56019703	56019703	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	ccactttcacaggctataacCtttataacctgcaagtaaaa	4	11	1	0			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr11:56019703C>T	ENST00000303059.3	+	1	28	c.28C>T	c.(28-30)Ctt>Ttt	p.L10F		NM_001004747.1	NP_001004747.1	Q8NGG3	OR5T3_HUMAN	olfactory receptor, family 5, subfamily T, member 3	10						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(23)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	39	Esophageal squamous(21;0.00448)					AGGCTATAACCTTTATAACCT	0.353																																					p.L10F		Atlas-SNP	.											.	OR5T3	98	.	0			c.C28T						.						60	57	58					11																	56019703		2199	4295	6494	SO:0001583	missense	390154	exon1			TATAACCTTTATA	AB065837	CCDS31524.1	11q11	2012-08-09			ENSG00000172489	ENSG00000172489		"GPCR / Class A : Olfactory receptors"	15297	protein-coding gene	gene with protein product							Standard	NM_001004747		Approved	OR5T3Q	uc010rjd.2	Q8NGG3	OTTHUMG00000166852	ENST00000303059.3:c.28C>T	chr11.hg19:g.56019703C>T	ENSP00000305403:p.Leu10Phe	64.0	0.0		55.0	19.0	NM_001004747	Q6IFC7	Missense_Mutation	SNP	ENST00000303059.3	hg19	CCDS31524.1	.	.	.	.	.	.	.	.	.	.	C	9.450	1.090394	0.20471	.	.	ENSG00000172489	ENST00000303059	T	0.00007	9.66	4.7	-7.43	0.01383	.	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.11665	-1.0578	9	0.66056	D	0.02	.	5.8558	0.18718	0.3431:0.4707:0.0:0.1862	.	10	Q8NGG3	OR5T3_HUMAN	F	10	ENSP00000305403:L10F	ENSP00000305403:L10F	L	+	1	0	OR5T3	55776279	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.271000	0.00532	-1.389000	0.02090	-1.020000	0.02445	CTT	.	.		0.353	OR5T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391599.1	NM_001004747		T	56019703	C	T	56019703	3	4	236	1	0	0	0	0	1	0	0	0	11192	681	24	3	30	3	OR5T3	11	56019703	Missense_Mutation	SNP	C	TCGA-DD-AAW3-01A-11D-A40P-10	147123	56019703	78986813	64	32866										
AHNAK	79026	hgsc.bcm.edu	37	chr11	62293842	62293842	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	ctttccctctggtccttcaaTgttaacatcagggccttcaa	6	13	4	0			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr11:62293842T>C	ENST00000378024.4	-	5	8321	c.8047A>G	c.(8047-8049)Att>Gtt	p.I2683V	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	2683					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				GGTCCTTCAATGTTAACATCA	0.483																																					p.I2683V		Atlas-SNP	.											.	AHNAK	532	.	0			c.A8047G						.						163	164	164					11																	62293842		2202	4299	6501	SO:0001583	missense	79026	exon5			CTTCAATGTTAAC	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.8047A>G	chr11.hg19:g.62293842T>C	ENSP00000367263:p.Ile2683Val	85.0	0.0		101.0	42.0	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	hg19	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	t	5.912	0.352398	0.11182	.	.	ENSG00000124942	ENST00000244934;ENST00000378024	T	0.01347	4.99	4.65	-0.928	0.10448	.	.	.	.	.	T	0.01254	0.0041	L	0.28400	0.85	0.09310	N	1	B	0.25955	0.138	B	0.29785	0.107	T	0.47749	-0.9093	9	0.32370	T	0.25	-5.9575	3.7706	0.08640	0.1239:0.0737:0.3838:0.4186	.	2683	Q09666	AHNK_HUMAN	V	772;2683	ENSP00000367263:I2683V	ENSP00000244934:I772V	I	-	1	0	AHNAK	62050418	.	.	0.000000	0.03702	0.002000	0.02628	.	.	-0.480000	0.06803	0.392000	0.25879	ATT	.	.		0.483	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		C	62293842	T	C	62293842	3	2	236	1	0	0	0	0	1	0	0	0	414	1464	51	2	9745	2	AHNAK	11	62293842	Missense_Mutation	SNP	T	TCGA-DD-AAW3-01A-11D-A40P-10	6274139	62293842	72712674	65	32867										
PIH1D2	120379	hgsc.bcm.edu	37	chr11	111941928	111941928	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	ttcatggccatctgaattaaCtgattttttttcacttggtc	6	8	3	2			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr11:111941928C>A	ENST00000280350.4	-	4	603	c.381G>T	c.(379-381)caG>caT	p.Q127H	PIH1D2_ENST00000530641.1_Missense_Mutation_p.Q127H|C11orf57_ENST00000420986.2_5'Flank|PIH1D2_ENST00000532211.1_Missense_Mutation_p.Q127H|PIH1D2_ENST00000431456.1_Missense_Mutation_p.Q127H|PIH1D2_ENST00000521853.2_5'UTR|PIH1D2_ENST00000528775.1_Missense_Mutation_p.Q127H	NM_138789.3	NP_620144.1	Q8WWB5	PIHD2_HUMAN	PIH1 domain containing 2	127										endometrium(2)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	11		all_cancers(61;1.09e-14)|all_epithelial(67;7.64e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;3.19e-07)|BRCA - Breast invasive adenocarcinoma(274;6.17e-07)|all cancers(92;6.18e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0508)		TCTGAATTAACTGATTTTTTT	0.373																																					p.Q127H		Atlas-SNP	.											.	PIH1D2	24	.	0			c.G381T						.						175	168	171					11																	111941928		2201	4297	6498	SO:0001583	missense	120379	exon4			AATTAACTGATTT	BC019238	CCDS8355.1, CCDS44730.1	11q23.1	2007-01-31			ENSG00000150773	ENSG00000150773			25210	protein-coding gene	gene with protein product						12477932	Standard	NM_138789		Approved		uc001pmp.4	Q8WWB5	OTTHUMG00000166925	ENST00000280350.4:c.381G>T	chr11.hg19:g.111941928C>A	ENSP00000280350:p.Gln127His	52.0	0.0		57.0	29.0	NM_001082619	B4DU48|E9PD82	Missense_Mutation	SNP	ENST00000280350.4	hg19	CCDS8355.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	1.037|1.037	-0.680063|-0.680063	0.03353|0.03353	.|.	.|.	ENSG00000150773|ENSG00000150773	ENST00000528775;ENST00000431456;ENST00000532211;ENST00000280350;ENST00000530641;ENST00000525744|ENST00000525072	T;T;T;T;T;T|.	0.17854|.	2.25;2.25;2.25;2.25;2.25;2.25|.	5.9|5.9	-4.06|-4.06	0.03986|0.03986	.|.	0.706089|.	0.14818|.	N|.	0.296636|.	T|T	0.42988|0.42988	0.1227|0.1227	L|L	0.54323|0.54323	1.7|1.7	0.29794|0.29794	N|N	0.832949|0.832949	B;P;B|.	0.35684|.	0.164;0.515;0.16|.	B;B;B|.	0.34138|.	0.126;0.176;0.119|.	T|T	0.51942|0.51942	-0.8641|-0.8641	10|5	0.14252|.	T|.	0.57|.	-0.7436|-0.7436	7.4158|7.4158	0.27044|0.27044	0.1853:0.6243:0.0925:0.0978|0.1853:0.6243:0.0925:0.0978	.|.	127;127;127|.	B4DU48;E9PD82;Q8WWB5|.	.;.;PIHD2_HUMAN|.	H|F	127;127;127;127;127;92|83	ENSP00000434275:Q127H;ENSP00000388209:Q127H;ENSP00000431841:Q127H;ENSP00000280350:Q127H;ENSP00000431147:Q127H;ENSP00000433297:Q92H|.	ENSP00000280350:Q127H|.	Q|V	-|-	3|1	2|0	PIH1D2|PIH1D2	111447138|111447138	0.677000|0.677000	0.27577|0.27577	0.166000|0.166000	0.22797|0.22797	0.301000|0.301000	0.27625|0.27625	-0.422000|-0.422000	0.07043|0.07043	-0.318000|-0.318000	0.08665|0.08665	-0.282000|-0.282000	0.10007|0.10007	CAG|GTT	.	.		0.373	PIH1D2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391916.1	NM_138789		A	111941928	C	A	111941928	3	1	236	1	0	0	0	0	1	0	0	0	11916	564	20	3	636	3	PIH1D2	11	111941928	Missense_Mutation	SNP	C	TCGA-DD-AAW3-01A-11D-A40P-10	49648086	111941928	23064588	66	32868										
KCNJ1	3758	hgsc.bcm.edu	37	chr11	128709552	128709552	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	taagaaggctcttcctgagaTtagccactcggattaggagg	12	8	1	2			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr11:128709552T>C	ENST00000392664.2	-	2	760	c.644A>G	c.(643-645)aAt>aGt	p.N215S	KCNJ1_ENST00000392666.1_Missense_Mutation_p.N196S|KCNJ1_ENST00000440599.2_Missense_Mutation_p.N196S|KCNJ1_ENST00000324036.3_Missense_Mutation_p.N196S|KCNJ1_ENST00000392665.2_Missense_Mutation_p.N196S	NM_000220.4	NP_000211.1	P48048	KCNJ1_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 1	215					cardiovascular system development (GO:0072358)|excretion (GO:0007588)|kidney development (GO:0001822)|post-embryonic development (GO:0009791)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of G-protein activated inward rectifier potassium channel activity (GO:1900128)|renal sodium ion absorption (GO:0070294)|synaptic transmission (GO:0007268)|tissue homeostasis (GO:0001894)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|inward rectifier potassium channel activity (GO:0005242)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			breast(2)|endometrium(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)	23	all_hematologic(175;0.0641)	all_lung(97;4.89e-06)|Lung NSC(97;9.34e-06)|Breast(109;0.00123)|all_hematologic(192;0.00793)|Renal(330;0.0112)|all_neural(223;0.0189)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;4.05e-06)|LUSC - Lung squamous cell carcinoma(976;0.008)|Lung(977;0.00942)	Bethanidine(DB00217)|Glimepiride(DB00222)|Glyburide(DB01016)|Glycodiazine(DB01382)|Minoxidil(DB00350)|Tolazamide(DB00839)|Tolbutamide(DB01124)|Yohimbine(DB01392)	CTTCCTGAGATTAGCCACTCG	0.473																																					p.N215S		Atlas-SNP	.											.	KCNJ1	68	.	0			c.A644G						.						86	88	87					11																	128709552		2199	4290	6489	SO:0001583	missense	3758	exon2			CTGAGATTAGCCA	BC063109	CCDS8476.1, CCDS8477.1	11q24	2011-07-05			ENSG00000151704	ENSG00000151704		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6255	protein-coding gene	gene with protein product		600359				7680431, 8190102, 16382105	Standard	NM_153765		Approved	Kir1.1, ROMK1	uc001qeo.2	P48048	OTTHUMG00000048247	ENST00000392664.2:c.644A>G	chr11.hg19:g.128709552T>C	ENSP00000376432:p.Asn215Ser	71.0	0.0		72.0	32.0	NM_000220	B2RMR4|Q6LD67	Missense_Mutation	SNP	ENST00000392664.2	hg19	CCDS8476.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.209756	0.79240	.	.	ENSG00000151704	ENST00000392665;ENST00000392666;ENST00000440599;ENST00000324036;ENST00000392664	D;D;D;D;D	0.94758	-3.51;-3.51;-3.51;-3.51;-3.51	5.71	5.71	0.89125	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.000000	0.85682	D	0.000000	D	0.97885	0.9305	M	0.92784	3.345	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.98962	1.0798	10	0.87932	D	0	.	15.992	0.80214	0.0:0.0:0.0:1.0	.	215	P48048	IRK1_HUMAN	S	196;196;196;196;215	ENSP00000376433:N196S;ENSP00000376434:N196S;ENSP00000406320:N196S;ENSP00000316233:N196S;ENSP00000376432:N215S	ENSP00000316233:N196S	N	-	2	0	KCNJ1	128214762	1.000000	0.71417	0.971000	0.41717	0.968000	0.65278	8.026000	0.88783	2.173000	0.68751	0.421000	0.28195	AAT	.	.		0.473	KCNJ1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386233.1	NM_000220		C	128709552	T	C	128709552	3	2	236	1	0	0	0	0	1	0	0	0	8052	1493	52	2	535	2	KCNJ1	11	128709552	Missense_Mutation	SNP	T	TCGA-DD-AAW3-01A-11D-A40P-10	16767624	128709552	6296964	67	32869										
VWF	7450	hgsc.bcm.edu	37	chr12	6128399	6128399	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	tggacgtagcggacaaagttCcgggacatccgttggggctc	15	10	0	0	rs63749069		TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr12:6128399C>A	ENST00000261405.5	-	28	4439	c.4185G>T	c.(4183-4185)cgG>cgT	p.R1395R		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	1395	VWFA 1; binding site for platelet glycoprotein Ib. {ECO:0000255|PROSITE- ProRule:PRU00219}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	GGACAAAGTTCCGGGACATCC	0.582																																					p.R1395R		Atlas-SNP	.											.	VWF	338	.	0			c.G4185T						.						45	51	49					12																	6128399		2203	4297	6500	SO:0001819	synonymous_variant	7450	exon28			AAAGTTCCGGGAC		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"Endogenous ligands"	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.4185G>T	chr12.hg19:g.6128399C>A		40.0	0.0		42.0	15.0	NM_000552	Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	hg19	CCDS8539.1																																																																																			.	.		0.582	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		A	6128399	C	A	6128399	2	1	236	1	0	0	0	0	0	0	0	1	17261	842	30	3		3	VWF	12	6128399	Silent	SNP	C	TCGA-DD-AAW3-01A-11D-A40P-10		6128399	127723496	68	32870										
CLSTN3	9746	hgsc.bcm.edu	37	chr12	7288407	7288407	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	gaccccaccccagggaacatTgagaacacagagaagctgca	10	13	0	2			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr12:7288407T>A	ENST00000266546.6	+	5	1050	c.600T>A	c.(598-600)atT>atA	p.I200I	CLSTN3_ENST00000537408.1_Silent_p.I212I	NM_014718.3	NP_055533.2	Q9BQT9	CSTN3_HUMAN	calsyntenin 3	200	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(7)|prostate(1)|skin(1)	33						CAGGGAACATTGAGAACACAG	0.547																																					p.I200I		Atlas-SNP	.											.	CLSTN3	84	.	0			c.T600A						.						108	98	101					12																	7288407		2203	4300	6503	SO:0001819	synonymous_variant	9746	exon5			GAACATTGAGAAC	AB018269	CCDS8575.1	12p13.31	2011-07-01			ENSG00000139182	ENSG00000139182		"Cadherins / Cadherin-related"	18371	protein-coding gene	gene with protein product	"cadherin-related family member 14"	611324				12498782	Standard	NM_014718		Approved	CSTN3, KIAA0726, CDHR14	uc001qsr.3	Q9BQT9	OTTHUMG00000168167	ENST00000266546.6:c.600T>A	chr12.hg19:g.7288407T>A		64.0	0.0		53.0	26.0	NM_014718	D3DUT6|O94831|Q2T9J5|Q5UE57	Silent	SNP	ENST00000266546.6	hg19	CCDS8575.1																																																																																			.	.		0.547	CLSTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398560.2	NM_014718		A	7288407	T	A	7288407	2	1	236	1	0	0	0	0	0	0	0	1	3565	1800	63	4		4	CLSTN3	12	7288407	Silent	SNP	T	TCGA-DD-AAW3-01A-11D-A40P-10	1160008	7288407	126563488	69	32871										
KRT86	3892	hgsc.bcm.edu	37	chr12	52699514	52699514	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	ccgcaccaaggaggagatcaAcgagctgaaccgcatgatcc	11	13	1	3	rs373358594		TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr12:52699514A>T	ENST00000423955.2	+	8	1146	c.968A>T	c.(967-969)aAc>aTc	p.N323I	RP11-845M18.6_ENST00000552441.1_RNA|KRT86_ENST00000544024.1_Missense_Mutation_p.N323I|KRT86_ENST00000293525.5_Missense_Mutation_p.N323I			O43790	KRT86_HUMAN	keratin 86	323	Coil 2.|Rod.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(1)|cervix(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(357;0.189)		GAGGAGATCAACGAGCTGAAC	0.597																																					p.N323I		Atlas-SNP	.											.	KRT86	33	.	0			c.A968T						.						128	113	118					12																	52699514		2203	4300	6503	SO:0001583	missense	3892	exon6			AGATCAACGAGCT	X99142	CCDS41785.1	12q13	2013-01-16	2006-07-17	2006-07-17		ENSG00000170442		"-", "Intermediate filaments type II, keratins (basic)"	6463	protein-coding gene	gene with protein product	"hard keratin type II 6"	601928	"keratin, hair, basic, 6 (monilethrix)"	KRTHB6		9241275, 16831889	Standard	NM_002284		Approved	MNX, Hb6	uc001sad.3	O43790		ENST00000423955.2:c.968A>T	chr12.hg19:g.52699514A>T	ENSP00000444533:p.Asn323Ile	111.0	0.0		105.0	40.0	NM_002284	P78387	Missense_Mutation	SNP	ENST00000423955.2	hg19	CCDS41785.1	.	.	.	.	.	.	.	.	.	.	A	18.21	3.573534	0.65765	.	.	ENSG00000170442;ENSG00000170442;ENSG00000170442;ENSG00000258832	ENST00000544024;ENST00000423955;ENST00000293525;ENST00000553310	T;T;T	0.78126	-1.15;-1.15;-1.15	4.73	4.73	0.59995	Filament (1);	0.000000	0.47455	U	0.000230	T	0.81659	0.4869	M	0.64170	1.965	0.24475	N	0.994378	P	0.40211	0.707	P	0.52598	0.703	T	0.75345	-0.3350	10	0.72032	D	0.01	.	9.4167	0.38525	0.7567:0.2433:0.0:0.0	.	323	O43790	KRT86_HUMAN	I	323	ENSP00000443169:N323I;ENSP00000444533:N323I;ENSP00000293525:N323I	ENSP00000293525:N323I	N	+	2	0	AC021066.1;KRT86	50985781	0.085000	0.21516	0.994000	0.49952	0.961000	0.63080	1.035000	0.30216	1.781000	0.52344	0.413000	0.27773	AAC	.	.		0.597	KRT86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404911.1	NM_002284		T	52699514	A	T	52699514	3	4	236	1	0	0	0	0	1	0	0	0	8509	43	2	4	990	4	KRT86	12	52699514	Missense_Mutation	SNP	A	TCGA-DD-AAW3-01A-11D-A40P-10	45411107	52699514	81152381	70	32872										
MFSD5	84975	hgsc.bcm.edu	37	chr12	53646678	53646678	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	ggcctcctgcctggggctggAactgtcaagatgccgggcta	15	12	1	1			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr12:53646678A>G	ENST00000329548.4	+	2	250	c.59A>G	c.(58-60)gAa>gGa	p.E20G	MFSD5_ENST00000534842.1_Missense_Mutation_p.E127G	NM_032889.4	NP_116278.3	Q6N075	MFSD5_HUMAN	major facilitator superfamily domain containing 5	20					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|skin(3)|urinary_tract(1)	16						CTGGGGCTGGAACTGTCAAGA	0.602																																					p.E127G		Atlas-SNP	.											.	MFSD5	40	.	0			c.A380G						.						77	84	81					12																	53646678		2203	4300	6503	SO:0001583	missense	84975	exon2			GGCTGGAACTGTC	AK097576	CCDS8851.1, CCDS53796.1	12q13.13	2012-03-09			ENSG00000182544	ENSG00000182544			28156	protein-coding gene	gene with protein product							Standard	NM_032889		Approved	MGC11308	uc001sch.2	Q6N075	OTTHUMG00000170028	ENST00000329548.4:c.59A>G	chr12.hg19:g.53646678A>G	ENSP00000332624:p.Glu20Gly	65.0	0.0		65.0	31.0	NM_001170790	G3V1N7|Q6NW04|Q8N7W8|Q8NCK0|Q96IA5	Missense_Mutation	SNP	ENST00000329548.4	hg19	CCDS8851.1	.	.	.	.	.	.	.	.	.	.	A	15.25	2.778806	0.49891	.	.	ENSG00000182544	ENST00000551660;ENST00000534842;ENST00000328704;ENST00000329548	.	.	.	4.3	4.3	0.51218	.	0.000000	0.85682	D	0.000000	T	0.65954	0.2741	M	0.76170	2.325	0.58432	D	0.999991	B;B	0.32350	0.2;0.366	B;B	0.39094	0.29;0.157	T	0.70128	-0.4957	9	0.59425	D	0.04	-5.2353	12.5639	0.56297	1.0:0.0:0.0:0.0	.	20;127	Q6N075;G3V1N7	MFSD5_HUMAN;.	G	127;127;127;20	.	ENSP00000331231:E127G	E	+	2	0	MFSD5	51932945	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	8.147000	0.89628	1.817000	0.53016	0.459000	0.35465	GAA	.	.		0.602	MFSD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406896.1	NM_032889		G	53646678	A	G	53646678	3	3	236	1	0	0	0	0	1	0	0	0	9543	246	9	2	386	2	MFSD5	12	53646678	Missense_Mutation	SNP	A	TCGA-DD-AAW3-01A-11D-A40P-10	947164	53646678	80205217	71	32873										
IKZF4	64375	hgsc.bcm.edu	37	chr12	56429110	56429110	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	tccggggggagcataaggtgGgctagcaacctctccctctc	13	13	2	0			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr12:56429110G>A	ENST00000262032.5	+	12	2120	c.1753G>A	c.(1753-1755)Ggc>Agc	p.G585S	IKZF4_ENST00000547791.1_Missense_Mutation_p.G540S|IKZF4_ENST00000547167.1_Missense_Mutation_p.G585S|RP11-603J24.4_ENST00000551846.1_RNA|IKZF4_ENST00000431367.2_Missense_Mutation_p.G483S			Q9H2S9	IKZF4_HUMAN	IKAROS family zinc finger 4 (Eos)	585					negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|lung(3)|ovary(1)|prostate(1)	8			UCEC - Uterine corpus endometrioid carcinoma (6;0.025)|OV - Ovarian serous cystadenocarcinoma(18;0.123)			GCATAAGGTGGGCTAGCAACC	0.537																																					p.G585S		Atlas-SNP	.											.	IKZF4	71	.	0			c.G1753A						.						137	138	137					12																	56429110		2128	4235	6363	SO:0001583	missense	64375	exon8			AAGGTGGGCTAGC	AF230809	CCDS44917.1	12q13	2013-01-08	2006-08-25	2006-08-25		ENSG00000123411		"Zinc fingers, C2H2-type", "IKAROS zinc fingers"	13179	protein-coding gene	gene with protein product		606239	"zinc finger protein, subfamily 1A, 4 (Eos)"	ZNFN1A4		10978333	Standard	NM_022465		Approved	Eos	uc001sjc.1	Q9H2S9		ENST00000262032.5:c.1753G>A	chr12.hg19:g.56429110G>A	ENSP00000262032:p.Gly585Ser	37.0	0.0		49.0	16.0	NM_022465	Q96JP3	Missense_Mutation	SNP	ENST00000262032.5	hg19	CCDS44917.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.027025	0.75390	.	.	ENSG00000123411	ENST00000262032;ENST00000431367;ENST00000547167;ENST00000547791	T;T;T;T	0.15718	2.4;2.66;2.4;2.54	4.74	4.74	0.60224	.	0.282883	0.25347	N	0.031330	T	0.29458	0.0734	L	0.27053	0.805	0.44006	D	0.996716	D;D;D;D	0.89917	1.0;0.999;1.0;0.999	D;D;D;D	0.87578	0.998;0.998;0.998;0.997	T	0.04522	-1.0945	10	0.87932	D	0	-5.1608	14.7469	0.69494	0.0:0.0:1.0:0.0	.	483;540;544;585	G5E9S4;F8VPL6;Q9H2S9-2;Q9H2S9	.;.;.;IKZF4_HUMAN	S	585;483;585;540	ENSP00000262032:G585S;ENSP00000412101:G483S;ENSP00000448419:G585S;ENSP00000450020:G540S	ENSP00000262032:G585S	G	+	1	0	IKZF4	54715377	1.000000	0.71417	1.000000	0.80357	0.815000	0.46073	3.234000	0.51320	2.453000	0.82957	0.313000	0.20887	GGC	.	.		0.537	IKZF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407590.1	NM_022465		A	56429110	G	A	56429110	3	1	236	1	0	0	0	0	1	0	0	0	7626	1232	43	3	1783	3	IKZF4	12	56429110	Missense_Mutation	SNP	G	TCGA-DD-AAW3-01A-11D-A40P-10	2782432	56429110	77422785	72	32874										
SLC26A10	65012	hgsc.bcm.edu	37	chr12	58015473	58015473	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	ctcatcgcccctgccctcagAcgctggcctccttgctgact	8	19	2	2			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr12:58015473A>G	ENST00000320442.4	+	4	867	c.556A>G	c.(556-558)Acg>Gcg	p.T186A	SLC26A10_ENST00000379218.2_Splice_Site_p.T186A|AC025165.8_ENST00000593846.1_RNA	NM_133489.2	NP_597996.2	Q8NG04	S2610_HUMAN	solute carrier family 26, member 10	186						integral component of membrane (GO:0016021)	antiporter activity (GO:0015297)|sulfate transmembrane transporter activity (GO:0015116)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(7)	19	Melanoma(17;0.122)					CTGCCCTCAGACGCTGGCCTC	0.701											OREG0021948	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T186A		Atlas-SNP	.											.	SLC26A10	89	.	0			c.A556G						.						10	11	11					12																	58015473		2193	4291	6484	SO:0001630	splice_region_variant	65012	exon4			CCTCAGACGCTGG		CCDS8949.2	12q13	2013-07-18			ENSG00000135502	ENSG00000135502		"Solute carriers"	14470	protein-coding gene	gene with protein product							Standard	NM_133489		Approved		uc001spe.3	Q8NG04	OTTHUMG00000128505	ENST00000320442.4:c.556-1A>G	chr12.hg19:g.58015473A>G		67.0	0.0	1027	46.0	20.0	NM_133489	A6NMJ2|B6ZDQ3|Q6ZWI7	Missense_Mutation	SNP	ENST00000320442.4	hg19	CCDS8949.2	.	.	.	.	.	.	.	.	.	.	.	20.2	3.942556	0.73672	.	.	ENSG00000135502	ENST00000320442;ENST00000379218	D;D	0.92199	-2.99;-2.99	3.89	3.89	0.44902	Sulphate transporter (1);	.	.	.	.	D	0.93406	0.7897	M	0.71871	2.18	0.43242	D	0.995152	D	0.53885	0.963	P	0.57204	0.815	D	0.92534	0.6036	8	.	.	.	.	9.3146	0.37926	1.0:0.0:0.0:0.0	.	186	Q8NG04	S2610_HUMAN	A	186	ENSP00000320217:T186A;ENSP00000368520:T186A	.	T	+	1	0	SLC26A10	56301740	1.000000	0.71417	1.000000	0.80357	0.445000	0.32107	4.464000	0.60134	1.785000	0.52413	0.454000	0.30748	ACG	.	.		0.701	SLC26A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250311.2		Missense_Mutation	G	58015473	A	G	58015473	5	3	236	1	0	0	0	0	0	0	1	0	14530	289	10	2	570	2	SLC26A10	12	58015473	Splice_Site	SNP	A	TCGA-DD-AAW3-01A-11D-A40P-10	1586363	58015473	75836422	73	32875										
GIT2	9815	hgsc.bcm.edu	37	chr12	110370863	110370863	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	gtacgcacactggatgacctGctgcgtgaccagctgaacgt	12	12	0	3			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr12:110370863G>C	ENST00000355312.3	-	20	2199	c.2200C>G	c.(2200-2202)Cag>Gag	p.Q734E	GIT2_ENST00000360185.4_Missense_Mutation_p.Q684E|GIT2_ENST00000551209.1_Missense_Mutation_p.Q683E|GIT2_ENST00000354574.4_Missense_Mutation_p.Q656E|GIT2_ENST00000553118.1_Missense_Mutation_p.Q606E|GIT2_ENST00000361006.5_Missense_Mutation_p.Q704E|GIT2_ENST00000548655.1_5'Flank|GIT2_ENST00000457474.2_Missense_Mutation_p.Q656E|GIT2_ENST00000343646.5_Missense_Mutation_p.Q624E|GIT2_ENST00000356259.4_Missense_Mutation_p.Q621E|TCHP_ENST00000550780.1_3'UTR|GIT2_ENST00000338373.5_Missense_Mutation_p.Q636E	NM_057169.3	NP_476510.1	Q14161	GIT2_HUMAN	G protein-coupled receptor kinase interacting ArfGAP 2	734					behavioral response to pain (GO:0048266)|regulation of ARF GTPase activity (GO:0032312)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(8)|skin(4)	27						TGGATGACCTGCTGCGTGACC	0.592																																					p.Q734E		Atlas-SNP	.											.	GIT2	81	.	0			c.C2200G						.						155	124	135					12																	110370863		2203	4300	6503	SO:0001583	missense	9815	exon20			TGACCTGCTGCGT	AF124491	CCDS9138.1, CCDS9139.1, CCDS44968.1, CCDS44969.1, CCDS55884.1	12q24.1	2013-01-10	2008-09-05			ENSG00000139436		"ADP-ribosylation factor GTPase activating proteins", "Ankyrin repeat domain containing"	4273	protein-coding gene	gene with protein product		608564	"G protein-coupled receptor kinase interactor 2"			9826657, 10896954	Standard	NM_139201		Approved	KIAA0148	uc001tps.2	Q14161	OTTHUMG00000169313	ENST00000355312.3:c.2200C>G	chr12.hg19:g.110370863G>C	ENSP00000347464:p.Gln734Glu	66.0	0.0		53.0	23.0	NM_057169	Q86U59|Q96CI2|Q9BV91|Q9Y5V2	Missense_Mutation	SNP	ENST00000355312.3	hg19	CCDS9138.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.021747	0.75275	.	.	ENSG00000139436	ENST00000355312;ENST00000360185;ENST00000354574;ENST00000338373;ENST00000343646;ENST00000356259;ENST00000457474;ENST00000361006;ENST00000553118;ENST00000551209;ENST00000552978	T;T;T;T;T;T;T;T;T;T	0.75938	-0.8;-0.95;-0.77;-0.69;-0.9;-0.67;-0.74;-0.78;-0.8;-0.98	5.53	5.53	0.82687	G protein-coupled receptor kinase-interacting protein 1 C term (1);	0.000000	0.85682	D	0.000000	D	0.83243	0.5212	L	0.56199	1.76	0.42362	D	0.992419	D;D;P;D;P	0.76494	0.997;0.997;0.943;0.999;0.514	D;D;P;D;B	0.85130	0.926;0.926;0.546;0.997;0.276	T	0.79727	-0.1682	10	0.25106	T	0.35	.	18.4469	0.90688	0.0:0.0:1.0:0.0	.	656;656;606;734;704	Q14161-10;F8WAK2;Q14161-11;Q14161;Q14161-5	.;.;.;GIT2_HUMAN;.	E	734;684;656;636;624;621;656;704;606;683;120	ENSP00000347464:Q734E;ENSP00000353312:Q684E;ENSP00000346585:Q656E;ENSP00000340342:Q636E;ENSP00000340938:Q624E;ENSP00000348595:Q621E;ENSP00000391813:Q656E;ENSP00000354282:Q704E;ENSP00000447465:Q606E;ENSP00000448832:Q683E	ENSP00000340342:Q636E	Q	-	1	0	GIT2	108855246	1.000000	0.71417	1.000000	0.80357	0.618000	0.37518	9.869000	0.99810	2.593000	0.87608	0.455000	0.32223	CAG	.	.		0.592	GIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403407.1	NM_057169		C	110370863	G	C	110370863	3	2	236	1	0	0	0	0	1	0	0	0	6405	1328	46	4	83	4	GIT2	12	110370863	Missense_Mutation	SNP	G	TCGA-DD-AAW3-01A-11D-A40P-10	52355390	110370863	23481032	74	32876										
PIWIL1	9271	hgsc.bcm.edu	37	chr12	130832690	130832690	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	caacaaattggacgaaattaTtataacccaaatgacccaat	4	9	0	1			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr12:130832690T>C	ENST00000245255.3	+	7	968	c.696T>C	c.(694-696)taT>taC	p.Y232Y		NM_001190971.1|NM_004764.4	NP_001177900.1|NP_004755.2	Q96J94	PIWL1_HUMAN	piwi-like RNA-mediated gene silencing 1	232					gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|mRNA cap binding complex (GO:0005845)|P granule (GO:0043186)|polysome (GO:0005844)	mRNA binding (GO:0003729)|piRNA binding (GO:0034584)|single-stranded RNA binding (GO:0003727)			breast(6)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(26)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	57	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.02e-06)|Epithelial(86;3.85e-05)|all cancers(50;4.65e-05)		GACGAAATTATTATAACCCAA	0.328																																					p.Y232Y		Atlas-SNP	.											.	PIWIL1	157	.	0			c.T696C						.						87	84	85					12																	130832690		2203	4300	6503	SO:0001819	synonymous_variant	9271	exon7			AAATTATTATAAC	AF104260	CCDS9268.1	12q24.33	2014-01-21	2013-02-15		ENSG00000125207	ENSG00000125207		"Argonaute/PIWI family"	9007	protein-coding gene	gene with protein product		605571	"piwi (Drosophila)-like 1", "piwi-like 1 (Drosophila)"			9851978, 12906857	Standard	NM_004764		Approved	PIWI, HIWI, CT80.1	uc001uik.3	Q96J94	OTTHUMG00000168382	ENST00000245255.3:c.696T>C	chr12.hg19:g.130832690T>C		103.0	0.0		65.0	28.0	NM_004764	A4F266|O95404|Q8NA60|Q8TBY5|Q96JD5	Silent	SNP	ENST00000245255.3	hg19	CCDS9268.1																																																																																			.	.		0.328	PIWIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399510.1			C	130832690	T	C	130832690	2	2	236	1	0	0	0	0	0	0	0	1	11966	1500	52	2		2	PIWIL1	12	130832690	Silent	SNP	T	TCGA-DD-AAW3-01A-11D-A40P-10	20461827	130832690	3019205	75	32877										
RNF17	56163	hgsc.bcm.edu	37	chr13	25367348	25367348	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	ttgcaacctgagacaaatgaTgtacatttagaagcaaaaaa	7	6	0	3			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr13:25367348T>C	ENST00000255324.5	+	10	1156	c.1104T>C	c.(1102-1104)gaT>gaC	p.D368D	RNF17_ENST00000381921.1_Silent_p.D368D|RNF17_ENST00000255325.6_Silent_p.D368D|RNF17_ENST00000255326.4_3'UTR	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	368					multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(3)|skin(6)	36		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)		AGACAAATGATGTACATTTAG	0.448																																					p.D368D		Atlas-SNP	.											.	RNF17	259	.	0			c.T1104C						.						169	158	162					13																	25367348		2203	4300	6503	SO:0001819	synonymous_variant	56163	exon10			AAATGATGTACAT	AF285602, AK001907	CCDS9308.2	13q12.13	2013-01-23			ENSG00000132972	ENSG00000132972		"RING-type (C3HC4) zinc fingers", "Tudor domain containing"	10060	protein-coding gene	gene with protein product	"spermatogenesis associated 23"	605793	"tudor domain containing 4"	TDRD4		11279525	Standard	NM_001184993		Approved	Mmip-2, SPATA23, FLJ11045	uc001upr.3	Q9BXT8	OTTHUMG00000016589	ENST00000255324.5:c.1104T>C	chr13.hg19:g.25367348T>C		115.0	0.0		101.0	42.0	NM_001184993	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Silent	SNP	ENST00000255324.5	hg19	CCDS9308.2																																																																																			.	.		0.448	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994		C	25367348	T	C	25367348	2	2	236	1	0	0	0	0	0	0	0	1	13476	1461	51	2		2	RNF17	13	25367348	Silent	SNP	T	TCGA-DD-AAW3-01A-11D-A40P-10		25367348	89802530	76	32878										
HMGB1	3146	hgsc.bcm.edu	37	chr13	31035522	31035522	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	catcatcatcttcttcttcaTcttcatcttcttcatcttcc	0	15	12	0	rs55678359		TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr13:31035522T>A	ENST00000405805.1	-	5	1560	c.620A>T	c.(619-621)gAt>gTt	p.D207V	HMGB1_ENST00000399489.1_3'UTR|HMGB1_ENST00000468384.1_5'Flank|HMGB1_ENST00000339872.4_Missense_Mutation_p.D207V|HMGB1_ENST00000341423.5_Missense_Mutation_p.D207V|HMGB1_ENST00000399494.1_Missense_Mutation_p.D207V			P09429	HMGB1_HUMAN	high mobility group box 1	207	Asp/Glu-rich (acidic).				apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|base-excision repair, DNA ligation (GO:0006288)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|dendritic cell chemotaxis (GO:0002407)|DNA ligation involved in DNA repair (GO:0051103)|DNA recombination (GO:0006310)|DNA topological change (GO:0006265)|inflammatory response to antigenic stimulus (GO:0002437)|innate immune response (GO:0045087)|myeloid dendritic cell activation (GO:0001773)|negative regulation of apoptotic cell clearance (GO:2000426)|negative regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0017055)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron projection development (GO:0031175)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|V(D)J recombination (GO:0033151)	cell surface (GO:0009986)|condensed chromosome (GO:0000793)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chemoattractant activity (GO:0042056)|cytokine activity (GO:0005125)|damaged DNA binding (GO:0003684)|DNA binding, bending (GO:0008301)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|RAGE receptor binding (GO:0050786)|repressing transcription factor binding (GO:0070491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription factor binding (GO:0008134)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(1)|ovary(1)	8		Lung SC(185;0.0257)		all cancers(112;0.072)|OV - Ovarian serous cystadenocarcinoma(117;0.177)|Lung(94;0.216)|GBM - Glioblastoma multiforme(144;0.232)		ttcttcttcatcttcatcttc	0.398																																					p.D207V		Atlas-SNP	.											.	HMGB1	21	.	0			c.A620T						.						17	20	19					13																	31035522		1871	4092	5963	SO:0001583	missense	3146	exon5			TCTTCATCTTCAT	D63874	CCDS9335.1	13q12	2011-07-01	2011-04-05	2002-08-16	ENSG00000189403	ENSG00000189403		"High-mobility group / Canonical"	4983	protein-coding gene	gene with protein product	"high mobility group box 1", "Sulfoglucuronyl carbohydrate binding protein", "Amphoterin", "high mobility group protein 1"	163905	"high-mobility group (nonhistone chromosomal) protein 1", "high-mobility group box 1"	HMG1		8661151, 11279268	Standard	NM_002128		Approved	HMG3, SBP-1, DKFZp686A04236	uc001usx.3	P09429	OTTHUMG00000016670	ENST00000405805.1:c.620A>T	chr13.hg19:g.31035522T>A	ENSP00000384678:p.Asp207Val	58.0	0.0		66.0	29.0	NM_002128	A5D8W9|Q14321|Q5T7C3|Q6IBE1	Missense_Mutation	SNP	ENST00000405805.1	hg19	CCDS9335.1	.	.	.	.	.	.	.	.	.	.	T	9.476	1.096774	0.20552	.	.	ENSG00000189403	ENST00000405805;ENST00000339872;ENST00000341423;ENST00000399494	T;T;T;T	0.72282	-0.64;-0.64;-0.64;-0.64	5.72	5.72	0.89469	Armadillo-like helical (1);	0.870387	0.09605	N	0.779737	T	0.55609	0.1931	N	0.08118	0	0.80722	D	1	P;P	0.41313	0.745;0.535	B;B	0.36608	0.229;0.151	T	0.60068	-0.7335	10	0.87932	D	0	.	15.9816	0.80114	0.0:0.0:0.0:1.0	.	168;207	B3KQ05;P09429	.;HMGB1_HUMAN	V	207	ENSP00000384678:D207V;ENSP00000343040:D207V;ENSP00000345347:D207V;ENSP00000382417:D207V	ENSP00000343040:D207V	D	-	2	0	HMGB1	29933522	1.000000	0.71417	0.995000	0.50966	0.998000	0.95712	7.386000	0.79775	2.180000	0.69256	0.519000	0.50382	GAT	.	.		0.398	HMGB1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303998.2	NM_002128		A	31035522	T	A	31035522	3	1	236	1	0	0	0	0	1	0	0	0	7234	1435	50	4	31	4	HMGB1	13	31035522	Missense_Mutation	SNP	T	TCGA-DD-AAW3-01A-11D-A40P-10	5668174	31035522	84134356	77	32879										
ITM2B	9445	hgsc.bcm.edu	37	chr13	48807572	48807572	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	agcccaagagcggcgaggagGcgctcatcatcccccccgac	12	17	2	1			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr13:48807572G>T	ENST00000378565.5	+	1	279	c.76G>T	c.(76-78)Gcg>Tcg	p.A26S	ITM2B_ENST00000378549.5_Missense_Mutation_p.A26S	NM_021999.4	NP_068839.1	Q9Y287	ITM2B_HUMAN	integral membrane protein 2B	26					extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|nervous system development (GO:0007399)	endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle membrane (GO:0030660)|integral component of organelle membrane (GO:0031301)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|beta-amyloid binding (GO:0001540)			endometrium(1)|large_intestine(2)|lung(3)	6		all_cancers(8;2.2e-31)|all_epithelial(8;6.77e-15)|all_lung(13;9.67e-07)|all_hematologic(8;9.72e-06)|Lung NSC(96;8.3e-05)|Breast(56;0.000141)|Acute lymphoblastic leukemia(8;0.00045)|Prostate(109;0.000669)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;1.97e-06)		CGGCGAGGAGGCGCTCATCAT	0.721																																					p.A26S		Atlas-SNP	.											.	ITM2B	24	.	0			c.G76T						.						10	9	9					13																	48807572		2141	4219	6360	SO:0001583	missense	9445	exon1			GAGGAGGCGCTCA	AF092128	CCDS9409.1	13q14.2	2012-10-10			ENSG00000136156	ENSG00000136156		"BRICHOS domain containing"	6174	protein-coding gene	gene with protein product	"BRICHOS domain containing 2B"	603904				9795190	Standard	NM_021999		Approved	BRI, E25B, E3-16, BRICD2B	uc001vbz.3	Q9Y287	OTTHUMG00000016894	ENST00000378565.5:c.76G>T	chr13.hg19:g.48807572G>T	ENSP00000367828:p.Ala26Ser	113.0	0.0		150.0	63.0	NM_021999	Q5W0A3|Q96B24|Q9NYH1	Missense_Mutation	SNP	ENST00000378565.5	hg19	CCDS9409.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.188503	0.78789	.	.	ENSG00000136156	ENST00000378565;ENST00000378549	T;T	0.30981	1.54;1.51	5.04	5.04	0.67666	.	0.169236	0.37906	N	0.001896	T	0.25680	0.0625	L	0.39898	1.24	0.35016	D	0.757332	B	0.22346	0.068	B	0.13407	0.009	T	0.23190	-1.0195	10	0.29301	T	0.29	-3.3056	13.8841	0.63698	0.0:0.0:1.0:0.0	.	26	Q9Y287	ITM2B_HUMAN	S	26	ENSP00000367828:A26S;ENSP00000367811:A26S	ENSP00000367811:A26S	A	+	1	0	ITM2B	47705573	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.966000	0.63715	2.333000	0.79357	0.561000	0.74099	GCG	.	.		0.721	ITM2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044870.3	NM_021999		T	48807572	G	T	48807572	3	4	236	1	0	0	0	0	1	0	0	0	7922	1203	42	3	78	3	ITM2B	13	48807572	Missense_Mutation	SNP	G	TCGA-DD-AAW3-01A-11D-A40P-10	17772050	48807572	66362306	78	32880										
ING1	3621	hgsc.bcm.edu	37	chr13	111368119	111368119	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	gggtgcggggcgagtctcccGctggcctcctccccattggc	15	16	1	0			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr13:111368119G>T	ENST00000375774.3	+	1	791	c.329G>T	c.(328-330)cGc>cTc	p.R110L	ING1_ENST00000338450.7_Intron|ING1_ENST00000333219.7_Intron|ING1_ENST00000375775.3_Intron|ING1_ENST00000464141.1_Intron|CARS2_ENST00000535398.1_5'Flank	NM_005537.4	NP_005528.3	Q9UK53	ING1_HUMAN	inhibitor of growth family, member 1	110					cell cycle (GO:0007049)|chromatin modification (GO:0016568)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell death (GO:0010941)	nucleus (GO:0005634)	methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(6)|lung(1)|ovary(1)	12	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.188)			CGAGTCTCCCGCTGGCCTCCT	0.692																																					p.R110L		Atlas-SNP	.											.	ING1	106	.	0			c.G329T						.						11	13	12					13																	111368119		2161	4213	6374	SO:0001583	missense	3621	exon1			TCTCCCGCTGGCC		CCDS9515.1, CCDS9516.1, CCDS9517.1, CCDS9518.1	13q34	2013-01-28			ENSG00000153487	ENSG00000153487		"Zinc fingers, PHD-type"	6062	protein-coding gene	gene with protein product	"inhibitor of growth 1", "tumor suppressor ING1", "growth inhibitor ING1", "growth inhibitory protein ING1"	601566				8944021, 9186514	Standard	NM_198219		Approved	p33ING1, p33ING1b, p24ING1c, p33, p47, p47ING1a	uc001vri.3	Q9UK53	OTTHUMG00000017346	ENST00000375774.3:c.329G>T	chr13.hg19:g.111368119G>T	ENSP00000364929:p.Arg110Leu	26.0	0.0		25.0	9.0	NM_005537	O00532|O43658|Q53ZR3|Q5T9G8|Q5T9G9|Q5T9H0|Q5T9H1|Q9H007|Q9HD98|Q9HD99|Q9NS83|Q9P0U6|Q9UBC6|Q9UIJ1|Q9UIJ2|Q9UIJ3|Q9UIJ4|Q9UK52	Missense_Mutation	SNP	ENST00000375774.3	hg19	CCDS9517.1	.	.	.	.	.	.	.	.	.	.	G	11.12	1.544859	0.27563	.	.	ENSG00000153487	ENST00000375774	T	0.55052	0.54	2.6	0.696	0.18075	.	.	.	.	.	T	0.31420	0.0796	N	0.14661	0.345	0.09310	N	1	B	0.12013	0.005	B	0.12156	0.007	T	0.21621	-1.0240	9	0.59425	D	0.04	-0.2528	4.9415	0.13967	0.0:0.2385:0.5168:0.2448	.	110	Q9UK53	ING1_HUMAN	L	110	ENSP00000364929:R110L	ENSP00000364929:R110L	R	+	2	0	ING1	110166120	0.000000	0.05858	0.003000	0.11579	0.045000	0.14185	-0.883000	0.04170	0.004000	0.14682	-0.310000	0.09108	CGC	.	.		0.692	ING1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045770.2	NM_005537		T	111368119	G	T	111368119	3	4	236	1	0	0	0	0	1	0	0	0	7744	1087	38	1	479	1	ING1	13	111368119	Missense_Mutation	SNP	G	TCGA-DD-AAW3-01A-11D-A40P-10	62560547	111368119	3801759	79	32881										
PCK2	5106	hgsc.bcm.edu	37	chr14	24572747	24572747	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	atcatgcacgacccatttgcCatgcggcccttttttggcta	8	13	1	0			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr14:24572747C>T	ENST00000216780.4	+	10	1765	c.1497C>T	c.(1495-1497)gcC>gcT	p.A499A	NRL_ENST00000561028.1_Intron|PCK2_ENST00000558096.1_Silent_p.A333A|PCK2_ENST00000545054.2_Silent_p.A365A|PCK2_ENST00000559250.1_Intron|PCK2_ENST00000561286.1_Silent_p.A365A	NM_004563.2	NP_004554.2	Q16822	PCKGM_HUMAN	phosphoenolpyruvate carboxykinase 2 (mitochondrial)	499					carbohydrate metabolic process (GO:0005975)|cellular response to glucose stimulus (GO:0071333)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|NADH oxidation (GO:0006116)|oxaloacetate metabolic process (GO:0006107)|positive regulation of insulin secretion (GO:0032024)|pyruvate metabolic process (GO:0006090)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|metal ion binding (GO:0046872)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)|phosphoenolpyruvate carboxykinase activity (GO:0004611)			breast(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	18				GBM - Glioblastoma multiforme(265;0.0184)		ACCCATTTGCCATGCGGCCCT	0.572																																					p.A499A		Atlas-SNP	.											.	PCK2	66	.	0			c.C1497T						.						74	75	75					14																	24572747		2203	4300	6503	SO:0001819	synonymous_variant	5106	exon10			ATTTGCCATGCGG	AK129934	CCDS9609.1, CCDS41928.1	14q12	2006-06-09			ENSG00000100889	ENSG00000100889	4.1.1.32		8725	protein-coding gene	gene with protein product		614095				8645161, 9657976	Standard	XM_005267726		Approved	PEPCK, PEPCK2	uc001wlt.3	Q16822	OTTHUMG00000028791	ENST00000216780.4:c.1497C>T	chr14.hg19:g.24572747C>T		102.0	0.0		90.0	43.0	NM_004563	O43253|Q86U01|Q9BV62	Silent	SNP	ENST00000216780.4	hg19	CCDS9609.1																																																																																			.	.		0.572	PCK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071900.3	NM_001018073		T	24572747	C	T	24572747	2	4	236	1	0	0	0	0	0	0	0	1	11591	581	21	3		3	PCK2	14	24572747	Silent	SNP	C	TCGA-DD-AAW3-01A-11D-A40P-10		24572747	82776793	80	32882										
ATP10A	57194	hgsc.bcm.edu	37	chr15	25928550	25928550	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	gacgagaagagcagattaaaGaagattagataccactggtc	11	6	0	6			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr15:25928550G>T	ENST00000356865.6	-	17	3486	c.3375C>A	c.(3373-3375)ttC>ttA	p.F1125L		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	1125					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			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)		GCAGATTAAAGAAGATTAGAT	0.502																																					p.F1125L		Atlas-SNP	.											.	ATP10A	270	.	0			c.C3375A						.						85	82	83					15																	25928550		2203	4300	6503	SO:0001583	missense	57194	exon17			ATTAAAGAAGATT	AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.3375C>A	chr15.hg19:g.25928550G>T	ENSP00000349325:p.Phe1125Leu	178.0	0.0		175.0	79.0	NM_024490	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	hg19	CCDS32178.1	.	.	.	.	.	.	.	.	.	.	G	15.25	2.777985	0.49786	.	.	ENSG00000206190	ENST00000356865	D	0.87887	-2.31	4.81	4.81	0.61882	.	0.046306	0.85682	N	0.000000	T	0.79185	0.4403	N	0.25890	0.77	0.52501	D	0.999954	B	0.11235	0.004	B	0.14578	0.011	T	0.73694	-0.3902	10	0.07644	T	0.81	-23.3633	17.8828	0.88845	0.0:0.0:1.0:0.0	.	1125	O60312	AT10A_HUMAN	L	1125	ENSP00000349325:F1125L	ENSP00000349325:F1125L	F	-	3	2	ATP10A	23479643	1.000000	0.71417	0.999000	0.59377	0.816000	0.46133	7.493000	0.81493	2.205000	0.71048	0.655000	0.94253	TTC	.	.		0.502	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		T	25928550	G	T	25928550	3	4	236	1	0	0	0	0	1	0	0	0	1116	933	33	3	1144	3	ATP10A	15	25928550	Missense_Mutation	SNP	G	TCGA-DD-AAW3-01A-11D-A40P-10		25928550	76602842	81	32883										
NOP10	55505	hgsc.bcm.edu	37	chr15	34635263	34635263	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	ccctgctcgttgaggtaataCtggagaaacatgatcgctta	10	9	0	3			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr15:34635263C>A	ENST00000328848.4	-	1	115	c.12G>T	c.(10-12)caG>caT	p.Q4H	NUTM1_ENST00000333756.4_5'Flank|NUTM1_ENST00000438749.3_5'Flank|NUTM1_ENST00000537011.1_5'Flank|NOP10_ENST00000557912.1_Missense_Mutation_p.Q4H	NM_018648.3	NP_061118.1	Q9NPE3	NOP10_HUMAN	NOP10 ribonucleoprotein	4					pseudouridine synthesis (GO:0001522)|rRNA processing (GO:0006364)	box H/ACA RNP complex (GO:0072588)|nucleus (GO:0005634)|small nucleolar ribonucleoprotein complex (GO:0005732)	snoRNA binding (GO:0030515)			lung(1)|ovary(1)	2						TGAGGTAATACTGGAGAAACA	0.522											OREG0023034	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q4H		Atlas-SNP	.											.	NOP10	8	.	0			c.G12T						.						226	176	193					15																	34635263		2201	4298	6499	SO:0001583	missense	55505	exon1			GTAATACTGGAGA	AB043103	CCDS10037.1	15q14-q15	2014-09-17	2012-12-10	2008-10-13	ENSG00000182117	ENSG00000182117			14378	protein-coding gene	gene with protein product	"homolog of yeast Nop10p"	606471	"nucleolar protein family A, member 3 (H/ACA small nucleolar RNPs)", "NOP10 ribonucleoprotein homolog (yeast)"	NOLA3		11074001, 9843512	Standard	NM_018648		Approved	NOP10P, MGC70651	uc001zie.1	Q9NPE3	OTTHUMG00000129440	ENST00000328848.4:c.12G>T	chr15.hg19:g.34635263C>A	ENSP00000332198:p.Gln4His	87.0	0.0	849	81.0	36.0	NM_018648		Missense_Mutation	SNP	ENST00000328848.4	hg19	CCDS10037.1	.	.	.	.	.	.	.	.	.	.	C	15.37	2.814900	0.50527	.	.	ENSG00000182117	ENST00000328848	T	0.77489	-1.1	5.04	3.13	0.36017	.	0.208582	0.45361	D	0.000362	T	0.68650	0.3024	.	.	.	0.49483	D	0.999799	B	0.02656	0.0	B	0.06405	0.002	T	0.64287	-0.6443	9	0.59425	D	0.04	.	10.0238	0.42059	0.0:0.8317:0.0:0.1683	.	4	Q9NPE3	NOP10_HUMAN	H	4	ENSP00000332198:Q4H	ENSP00000332198:Q4H	Q	-	3	2	NOP10	32422555	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.646000	0.37249	0.684000	0.31448	0.655000	0.94253	CAG	.	.		0.522	NOP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251602.2	NM_018648		A	34635263	C	A	34635263	3	1	236	1	0	0	0	0	1	0	0	0	10544	564	20	3	190	3	NOP10	15	34635263	Missense_Mutation	SNP	C	TCGA-DD-AAW3-01A-11D-A40P-10	8706713	34635263	67896129	82	32884										
SPG11	80208	hgsc.bcm.edu	37	chr15	44859685	44859685	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	tgcctcgtggttctcgccaaTctcccggcacatgctgaagc	10	15	2	1			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr15:44859685T>C	ENST00000261866.7	-	36	6707	c.6691A>G	c.(6691-6693)Att>Gtt	p.I2231V	SPG11_ENST00000535302.2_Missense_Mutation_p.I2118V|SPG11_ENST00000427534.2_Missense_Mutation_p.I2231V	NM_025137.3	NP_079413.3	Q96JI7	SPTCS_HUMAN	spastic paraplegia 11 (autosomal recessive)	2231					cell death (GO:0008219)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	72		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		TTCTCGCCAATCTCCCGGCAC	0.542																																					p.I2231V		Atlas-SNP	.											.	SPG11	207	.	0			c.A6691G						.						82	71	75					15																	44859685		2198	4298	6496	SO:0001583	missense	80208	exon36			CGCCAATCTCCCG		CCDS10112.1, CCDS53939.1	15q13-q15	2007-11-13			ENSG00000104133	ENSG00000104133			11226	protein-coding gene	gene with protein product	"spatacsin"	610844	"KIAA1840"	KIAA1840		10408536, 17322883	Standard	NM_001160227		Approved	FLJ21439	uc001ztx.3	Q96JI7	OTTHUMG00000131199	ENST00000261866.7:c.6691A>G	chr15.hg19:g.44859685T>C	ENSP00000261866:p.Ile2231Val	57.0	0.0		51.0	25.0	NM_025137	A8KAX9|B9EK60|F5H3N6|Q4VC11|Q58G86|Q69YG6|Q6NW01|Q8N270|Q8TBU9|Q9H734	Missense_Mutation	SNP	ENST00000261866.7	hg19	CCDS10112.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.287000	0.80803	.	.	ENSG00000104133	ENST00000261866;ENST00000535302;ENST00000427534	T;T;T	0.80994	-1.44;-1.06;-1.31	6.14	6.14	0.99180	.	0.044927	0.85682	D	0.000000	D	0.89739	0.6802	M	0.77103	2.36	0.80722	D	1	D;D;D;D	0.89917	1.0;0.996;1.0;1.0	D;D;D;D	0.85130	0.997;0.994;0.997;0.997	D	0.89546	0.3796	10	0.46703	T	0.11	.	16.7723	0.85541	0.0:0.0:0.0:1.0	.	2231;2118;2231;2231	C4B7M2;F5H3N6;C4B7M4;Q96JI7	.;.;.;SPTCS_HUMAN	V	2231;2118;2231	ENSP00000261866:I2231V;ENSP00000445278:I2118V;ENSP00000396110:I2231V	ENSP00000261866:I2231V	I	-	1	0	SPG11	42646977	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	7.988000	0.88194	2.360000	0.80028	0.519000	0.50382	ATT	.	.		0.542	SPG11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253927.1			C	44859685	T	C	44859685	3	2	236	1	0	0	0	0	1	0	0	0	15056	1435	50	2	660	2	SPG11	15	44859685	Missense_Mutation	SNP	T	TCGA-DD-AAW3-01A-11D-A40P-10	10224422	44859685	57671707	83	32885										
SEMA4B	10509	hgsc.bcm.edu	37	chr15	90764627	90764627	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	ctctacactggaacagtcagCagcttccaagggaatgaccc	9	13	2	1			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr15:90764627C>T	ENST00000411539.2	+	6	884	c.624C>T	c.(622-624)agC>agT	p.S208S	SEMA4B_ENST00000332496.6_Silent_p.S208S|SEMA4B_ENST00000379122.3_Silent_p.S203S	NM_198925.2	NP_945119.1	Q9NPR2	SEM4B_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B	203	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)	receptor activity (GO:0004872)			NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)	12	Melanoma(11;0.00551)|Lung NSC(78;0.0125)|all_lung(78;0.0272)		BRCA - Breast invasive adenocarcinoma(143;0.0107)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.217)			GAACAGTCAGCAGCTTCCAAG	0.602											OREG0023469	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S208S		Atlas-SNP	.											.	SEMA4B	51	.	0			c.C624T						.						26	28	27					15																	90764627		1978	4158	6136	SO:0001819	synonymous_variant	10509	exon7			AGTCAGCAGCTTC	AB051532	CCDS45347.1	15q25	2008-07-18						"Semaphorins"	10730	protein-coding gene	gene with protein product				SEMAC		7748561	Standard	NM_020210		Approved	SemC, KIAA1745, MGC131831	uc002boz.3	Q9NPR2		ENST00000411539.2:c.624C>T	chr15.hg19:g.90764627C>T		62.0	0.0	1277	69.0	26.0	NM_020210	Q6UXE3|Q8WVP9|Q96FK5|Q9C0B8|Q9H691|Q9NPM8|Q9NPN0	Silent	SNP	ENST00000411539.2	hg19	CCDS45347.1																																																																																			.	.		0.602	SEMA4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416810.1	NM_198925		T	90764627	C	T	90764627	2	4	236	1	0	0	0	0	0	0	0	1	14047	709	25	3		3	SEMA4B	15	90764627	Silent	SNP	C	TCGA-DD-AAW3-01A-11D-A40P-10	45904942	90764627	11766765	84	32886										
MAPK8IP3	23162	hgsc.bcm.edu	37	chr16	1816360	1816360	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	cccgggcctctcacagagcaCgtcttcactgacccagcccc	8	20	3	2			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr16:1816360C>T	ENST00000250894.4	+	22	2923	c.2766C>T	c.(2764-2766)caC>caT	p.H922H	MAPK8IP3_ENST00000356010.5_Silent_p.H916H	NM_015133.3	NP_055948.2	Q9UPT6	JIP3_HUMAN	mitogen-activated protein kinase 8 interacting protein 3	922					activation of JUN kinase activity (GO:0007257)|axon guidance (GO:0007411)|forebrain development (GO:0030900)|in utero embryonic development (GO:0001701)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|positive regulation of neuron differentiation (GO:0045666)|post-embryonic development (GO:0009791)|protein localization (GO:0008104)|regulation of gene expression (GO:0010468)|regulation of JNK cascade (GO:0046328)|respiratory gaseous exchange (GO:0007585)|vesicle-mediated transport (GO:0016192)	axolemma (GO:0030673)|dendrite (GO:0030425)|Golgi membrane (GO:0000139)|smooth endoplasmic reticulum (GO:0005790)	kinesin binding (GO:0019894)|MAP-kinase scaffold activity (GO:0005078)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(20)|ovary(1)|prostate(2)|skin(2)|urinary_tract(3)	42						TCACAGAGCACGTCTTCACTG	0.692																																					p.H922H		Atlas-SNP	.											.	MAPK8IP3	164	.	0			c.C2766T						.						26	37	33					16																	1816360		2049	4180	6229	SO:0001819	synonymous_variant	23162	exon22			AGAGCACGTCTTC	AB028989	CCDS10442.2, CCDS45379.1	16p13.3	2009-11-23			ENSG00000138834	ENSG00000138834			6884	protein-coding gene	gene with protein product	"homolog of Drosophila Sunday driver 2"	605431				10523642, 10629060	Standard	XM_005255187		Approved	KIAA1066, JSAP1, JIP3, syd	uc002cmk.3	Q9UPT6	OTTHUMG00000128637	ENST00000250894.4:c.2766C>T	chr16.hg19:g.1816360C>T		104.0	0.0		112.0	11.0	NM_015133	A2A2B3|A7E2B3|Q96RY4|Q9H4I4|Q9H7P1|Q9NUG0	Silent	SNP	ENST00000250894.4	hg19	CCDS10442.2																																																																																			.	.		0.692	MAPK8IP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250508.2	NM_001040439		T	1816360	C	T	1816360	2	4	236	1	0	0	0	0	0	0	0	1	9295	535	19	1		1	MAPK8IP3	16	1816360	Silent	SNP	C	TCGA-DD-AAW3-01A-11D-A40P-10		1816360	88538393	85	32887										
FAM92B	339145	hgsc.bcm.edu	37	chr16	85132897	85132897	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	gactaaacctgccatgattgGcatgaggatgttcagggtct	12	8	2	2			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr16:85132897G>A	ENST00000539556.1	-	9	964	c.809C>T	c.(808-810)gCc>gTc	p.A270V		NM_198491.1	NP_940893.1	Q6ZTR7	FA92B_HUMAN	family with sequence similarity 92, member B	270										breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	16						gccatgattggcatgaggatg	0.547																																					p.A270V		Atlas-SNP	.											.	FAM92B	29	.	0			c.C809T						.						136	106	116					16																	85132897		2198	4300	6498	SO:0001583	missense	339145	exon8			TGATTGGCATGAG		CCDS32500.1	16q24.1	2005-09-22				ENSG00000153789			24781	protein-coding gene	gene with protein product						12477932	Standard	NM_198491		Approved	FLJ44299	uc021tlz.1	Q6ZTR7		ENST00000539556.1:c.809C>T	chr16.hg19:g.85132897G>A	ENSP00000443411:p.Ala270Val	87.0	0.0		61.0	28.0	NM_198491		Missense_Mutation	SNP	ENST00000539556.1	hg19	CCDS32500.1	.	.	.	.	.	.	.	.	.	.	G	8.286	0.816552	0.16607	.	.	ENSG00000153789	ENST00000393246;ENST00000539556	T	0.35605	1.3	1.33	0.342	0.15996	.	16.395400	0.01771	N	0.031201	T	0.20455	0.0492	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.26744	-1.0094	10	0.87932	D	0	-1.9737	3.6117	0.08062	0.2602:0.0:0.7398:0.0	.	270	Q6ZTR7	FA92B_HUMAN	V	270	ENSP00000443411:A270V	ENSP00000376937:A270V	A	-	2	0	FAM92B	83690398	0.001000	0.12720	0.006000	0.13384	0.038000	0.13279	0.082000	0.14847	0.147000	0.19030	0.491000	0.48974	GCC	.	.		0.547	FAM92B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_198491		A	85132897	G	A	85132897	3	1	236	1	0	0	0	0	1	0	0	0	5661	1203	42	3	109	3	FAM92B	16	85132897	Missense_Mutation	SNP	G	TCGA-DD-AAW3-01A-11D-A40P-10	83316537	85132897	5221856	86	32888										
GLP2R	9340	hgsc.bcm.edu	37	chr17	9729508	9729508	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	tctctccttccacaggaagtGctctctctgggcccctggga	10	15	3	0			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr17:9729508G>A	ENST00000262441.5	+	1	641	c.128G>A	c.(127-129)tGc>tAc	p.C43Y	GLP2R_ENST00000574745.1_Intron	NM_004246.1	NP_004237.1	O95838	GLP2R_HUMAN	glucagon-like peptide 2 receptor	43					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|positive regulation of cell proliferation (GO:0008284)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|glucagon receptor activity (GO:0004967)			endometrium(4)|large_intestine(7)|lung(22)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	44					Glucagon recombinant(DB00040)|Teduglutide(DB08900)	CACAGGAAGTGCTCTCTCTGG	0.572																																					p.C43Y		Atlas-SNP	.											.	GLP2R	90	.	0			c.G128A						.						41	41	41					17																	9729508		2203	4300	6503	SO:0001583	missense	9340	exon1			GGAAGTGCTCTCT	AF105367	CCDS11150.1	17p13.3	2012-08-10			ENSG00000065325	ENSG00000065325		"GPCR / Class B : Glucagon receptors"	4325	protein-coding gene	gene with protein product		603659				9990065	Standard	NM_004246		Approved		uc002gmd.1	O95838	OTTHUMG00000130269	ENST00000262441.5:c.128G>A	chr17.hg19:g.9729508G>A	ENSP00000262441:p.Cys43Tyr	44.0	0.0		35.0	9.0	NM_004246	Q4VAT3	Missense_Mutation	SNP	ENST00000262441.5	hg19	CCDS11150.1	.	.	.	.	.	.	.	.	.	.	G	5.696	0.312991	0.10789	.	.	ENSG00000065325	ENST00000396206;ENST00000304773;ENST00000262441	T	0.55413	0.52	4.06	-4.54	0.03452	.	1.382700	0.05238	N	0.511683	T	0.26412	0.0645	N	0.08118	0	0.09310	N	1	B	0.18461	0.028	B	0.12156	0.007	T	0.13710	-1.0499	10	0.44086	T	0.13	.	2.9793	0.05948	0.096:0.3993:0.2079:0.2968	.	43	O95838	GLP2R_HUMAN	Y	43;18;43	ENSP00000262441:C43Y	ENSP00000262441:C43Y	C	+	2	0	GLP2R	9670233	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.381000	0.07417	-0.511000	0.06514	-0.878000	0.02970	TGC	.	.		0.572	GLP2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252601.4			A	9729508	G	A	9729508	3	1	236	1	0	0	0	0	1	0	0	0	6461	1319	46	3	130	3	GLP2R	17	9729508	Missense_Mutation	SNP	G	TCGA-DD-AAW3-01A-11D-A40P-10		9729508	71465702	87	32889										
TTC19	54902	hgsc.bcm.edu	37	chr17	15930009	15930023	+	Splice_Site	DEL	GCACAGAGGTAGGTA	GCACAGAGGTAGGTA	-													0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	aatctagctgcagttttgatGcacagaggtaggtagcaatg					rs189614332	byFrequency	TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	GCACAGAGGTAGGTA	GCACAGAGGTAGGTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr17:15930009_15930023delGCACAGAGGTAGGTA	ENST00000261647.5	+	9	1456_1463	c.987_994delGCACAGAGGTAGGTA	c.(985-996)atgcacagaggt>atgt	p.HRG330del	TTC19_ENST00000486880.2_Splice_Site_p.HRG451del|TTC19_ENST00000497842.2_3'UTR	NM_001271420.1|NM_017775.3	NP_001258349.1|NP_060245.3	Q6DKK2	TTC19_HUMAN	tetratricopeptide repeat domain 19	330					cytokinesis (GO:0000910)|mitochondrial respiratory chain complex III assembly (GO:0034551)	centrosome (GO:0005813)|midbody (GO:0030496)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)				central_nervous_system(1)|lung(2)|skin(1)|stomach(1)	5				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		CAGTTTTGATGCACAGAGGTAGGTAGCAATGTAAA	0.423																																					p.329_332del		Atlas-INDEL	.											.	TTC19	10	.	0			c.986_994del						.																																			SO:0001630	splice_region_variant	54902	exon9			.	AK094819	CCDS11174.1, CCDS11174.2	17p11.2	2013-01-11			ENSG00000011295	ENSG00000011295		"Tetratricopeptide (TTC) repeat domain containing"	26006	protein-coding gene	gene with protein product		613814					Standard	NM_017775		Approved	FLJ20343, MGC19520	uc002gph.3	Q6DKK2	OTTHUMG00000059306	ENST00000261647.5:c.994+1GCACAGAGGTAGGTA>-	chr17.hg19:g.15930009_15930023delGCACAGAGGTAGGTA		94.0	0.0		79.0	15.0	NM_017775	A8MZ52|B3KP62|B4DN65|Q2M248|Q7L3U8|Q9H6G3|Q9NXB2	In_Frame_Del	DEL	ENST00000261647.5	hg19	CCDS11174.2																																																																																			.	.		0.423	TTC19-001	NOVEL	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000131725.6	NM_017775	In_Frame_Del	-	15930023	GCACAGAGGTAGGTA	-	15930009	8	5	236	1	0	1	0	1	0	0	1	0	16701	1319	46	0	1384	0	TTC19	17	15930009	Splice_Site	DEL	GCACAGAGGTAGGTA	TCGA-DD-AAW3-01A-11D-A40P-10	6200501	15930009	65265201	88	32890										
FZD2	2535	hgsc.bcm.edu	37	chr17	42635670	42635675	+	In_Frame_Del	DEL	TCAAGG	TCAAGG	-													0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	cttccactgcccgcgcgtccTcaaggtgccatcctatctca					rs566397443	byFrequency	TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	TCAAGG	TCAAGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr17:42635670_42635675delTCAAGG	ENST00000315323.3	+	1	746_751	c.614_619delTCAAGG	c.(613-621)ctcaaggtg>ctg	p.KV206del		NM_001466.3	NP_001457.1	Q14332	FZD2_HUMAN	frizzled class receptor 2	206					axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cell-cell signaling (GO:0007267)|cochlea morphogenesis (GO:0090103)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hard palate development (GO:0060022)|inner ear receptor cell development (GO:0060119)|membranous septum morphogenesis (GO:0003149)|muscular septum morphogenesis (GO:0003150)|neuron differentiation (GO:0030182)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of cGMP metabolic process (GO:0030825)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|sensory perception of smell (GO:0007608)|vasculature development (GO:0001944)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	apical part of cell (GO:0045177)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(8)	33		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.189)		CCGCGCGTCCTCAAGGTGCCATCCTA	0.699																																					p.205_206del		Atlas-INDEL	.											.	FZD2	81	.	0			c.613_618del						.																																			SO:0001651	inframe_deletion	2535	exon1			.	L37882	CCDS11484.1	17q21.1	2014-01-29	2014-01-29			ENSG00000180340		"GPCR / Class F : Frizzled receptors"	4040	protein-coding gene	gene with protein product		600667	"frizzled (Drosophila) homolog 2", "frizzled homolog 2 (Drosophila)", "frizzled 2, seven transmembrane spanning receptor", "frizzled family receptor 2"			7558010, 9813155	Standard	NM_001466		Approved		uc002igx.2	Q14332		ENST00000315323.3:c.614_619delTCAAGG	chr17.hg19:g.42635670_42635675delTCAAGG	ENSP00000323901:p.Lys206_Val207del	49.0	0.0		35.0	11.0	NM_001466	Q0VG82	In_Frame_Del	DEL	ENST00000315323.3	hg19	CCDS11484.1																																																																																			.	.		0.699	FZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457806.1	NM_001466		-	42635675	TCAAGG	-	42635670	7	5	236	1	0	1	0	1	0	0	0	0	6138	1551	54	0	616	0	FZD2	17	42635670	In_Frame_Del	DEL	TCAAGG	TCGA-DD-AAW3-01A-11D-A40P-10	26705661	42635670	38559540	89	32891										
C19orf20	91978	hgsc.bcm.edu	37	chr19	519025	519025	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	gggacggccaagcccccgagGaggtggtggcgccgctgctg	19	13	0	0			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr19:519025G>A	ENST00000359315.5	+	2	683	c.475G>A	c.(475-477)Gag>Aag	p.E159K		NM_033513.2	NP_277048.2	Q6ZTW0	TPGS1_HUMAN	tubulin polyglutamylase complex subunit 1	159					adult behavior (GO:0030534)|multicellular organismal development (GO:0007275)|protein polyglutamylation (GO:0018095)|sperm axoneme assembly (GO:0007288)|synaptic transmission (GO:0007268)|vesicle localization (GO:0051648)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)	tubulin-glutamic acid ligase activity (GO:0070740)										AGCCCCCGAGGAGGTGGTGGC	0.731																																					p.E159K		Atlas-SNP	.											.	.	.	.	0			c.G475A						.						5	8	7					19																	519025		2004	4048	6052	SO:0001583	missense	91978	exon2			CCCGAGGAGGTGG	BC009520	CCDS42454.1	19p13.3	2011-11-23	2011-11-23	2011-11-23	ENSG00000141933	ENSG00000141933			25058	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 20"	C19orf20		11441184, 12972506	Standard	NM_033513		Approved	GTRGEO22, PGs1	uc002lou.3	Q6ZTW0		ENST00000359315.5:c.475G>A	chr19.hg19:g.519025G>A	ENSP00000352265:p.Glu159Lys	38.0	0.0		46.0	23.0	NM_033513	Q96GE2	Missense_Mutation	SNP	ENST00000359315.5	hg19	CCDS42454.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.293582	0.80914	.	.	ENSG00000141933	ENST00000359315;ENST00000388800	T	0.16743	2.32	4.24	3.11	0.35812	.	0.469643	0.17205	U	0.182972	T	0.13500	0.0327	L	0.29908	0.895	0.32558	N	0.531466	P	0.40731	0.728	B	0.40285	0.325	T	0.11767	-1.0574	10	0.33940	T	0.23	-18.4087	11.4992	0.50426	0.0:0.0:0.8197:0.1803	.	159	Q6ZTW0	TPGS1_HUMAN	K	159	ENSP00000352265:E159K	ENSP00000352265:E159K	E	+	1	0	C19orf20	470025	1.000000	0.71417	0.999000	0.59377	0.768000	0.43524	3.040000	0.49799	1.929000	0.55896	0.450000	0.29827	GAG	.	.		0.731	TPGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451887.2	NM_033513		A	519025	G	A	519025	3	1	236	1	0	0	0	0	1	0	0	0	1914	1175	41	3	481	3	C19orf20	19	519025	Missense_Mutation	SNP	G	TCGA-DD-AAW3-01A-11D-A40P-10		519025	58609958	90	32892										
ADAMTS10	81794	hgsc.bcm.edu	37	chr19	8661267	8661267	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	gacgctgcagcttctctcgcGctcacacattccgcccaccg	8	19	2	0			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr19:8661267G>A	ENST00000597188.1	-	10	1384	c.1114C>T	c.(1114-1116)Cgc>Tgc	p.R372C	ADAMTS10_ENST00000596709.1_5'Flank|ADAMTS10_ENST00000270328.4_Missense_Mutation_p.R372C	NM_030957.2	NP_112219.3	Q9H324	ATS10_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 10	372	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					extracellular matrix (GO:0031012)|microfibril (GO:0001527)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(16)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(3)|skin(10)|urinary_tract(1)	53						CTTCTCTCGCGCTCACACATT	0.662																																					p.R372C		Atlas-SNP	.											.	ADAMTS10	132	.	0			c.C1114T						.						40	35	36					19																	8661267		2203	4300	6503	SO:0001583	missense	81794	exon10			TCTCGCGCTCACA	AF163762	CCDS12206.1, CCDS62529.1	19p13.2	2014-08-12	2005-08-19		ENSG00000142303	ENSG00000142303		"ADAM metallopeptidases with thrombospondin type 1 motif"	13201	protein-coding gene	gene with protein product		608990	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 10"				Standard	XM_005272499		Approved	ADAM-TS10	uc002mkj.1	Q9H324	OTTHUMG00000182216	ENST00000597188.1:c.1114C>T	chr19.hg19:g.8661267G>A	ENSP00000471851:p.Arg372Cys	44.0	0.0		43.0	6.0	NM_030957	M0QZE4	Missense_Mutation	SNP	ENST00000597188.1	hg19	CCDS12206.1	.	.	.	.	.	.	.	.	.	.	G	12.74	2.028095	0.35797	.	.	ENSG00000142303	ENST00000270328;ENST00000393912	D	0.86956	-2.19	4.76	2.53	0.30540	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.159568	0.40908	D	0.000995	D	0.89860	0.6837	L	0.49126	1.545	0.58432	D	0.999992	D;D	0.76494	0.998;0.999	P;D	0.64877	0.892;0.93	D	0.89664	0.3879	10	0.87932	D	0	.	12.8281	0.57731	0.0:0.0:0.5787:0.4213	.	126;372	Q59FE5;Q9H324	.;ATS10_HUMAN	C	372;126	ENSP00000270328:R372C	ENSP00000270328:R372C	R	-	1	0	ADAMTS10	8567267	1.000000	0.71417	0.910000	0.35882	0.036000	0.12997	5.917000	0.69989	0.570000	0.29347	-0.538000	0.04264	CGC	.	.		0.662	ADAMTS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460085.3	NM_030957		A	8661267	G	A	8661267	3	1	236	1	0	0	0	0	1	0	0	0	256	1087	38	1	2265	1	ADAMTS10	19	8661267	Missense_Mutation	SNP	G	TCGA-DD-AAW3-01A-11D-A40P-10	8142242	8661267	50467716	91	32893										
ZNF878	729747	hgsc.bcm.edu	37	chr19	12154963	12154963	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	atccatagggtttctctcctGtgtgagttcgtatgtgcttt	10	8	1	1			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr19:12154963G>A	ENST00000547628.1	-	4	1390	c.1253C>T	c.(1252-1254)aCa>aTa	p.T418I	CTD-2006C1.2_ENST00000591898.1_RNA|CTD-2006C1.2_ENST00000591838.1_RNA|CTD-2006C1.2_ENST00000476474.1_RNA|CTD-2006C1.10_ENST00000547473.1_Intron|ZNF878_ENST00000602107.1_Missense_Mutation_p.T465I	NM_001080404.2	NP_001073873.2	C9JN71	ZN878_HUMAN	zinc finger protein 878	418					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			cervix(1)|endometrium(1)|kidney(1)|lung(4)|urinary_tract(1)	8						TTTCTCTCCTGTGTGAGTTCG	0.438																																					p.T418I		Atlas-SNP	.											.	ZNF878	172	.	0			c.C1253T						.						70	74	73					19																	12154963		2201	4300	6501	SO:0001583	missense	729747	exon4			TCTCCTGTGTGAG		CCDS45984.1, CCDS45984.2	19p13.2	2013-01-08				ENSG00000257446		"Zinc fingers, C2H2-type", "-"	37246	protein-coding gene	gene with protein product							Standard	NM_001080404		Approved		uc021upl.1	C9JN71		ENST00000547628.1:c.1253C>T	chr19.hg19:g.12154963G>A	ENSP00000447931:p.Thr418Ile	57.0	0.0		47.0	22.0	NM_001080404		Missense_Mutation	SNP	ENST00000547628.1	hg19	CCDS45984.2	.	.	.	.	.	.	.	.	.	.	G	18.65	3.668635	0.67814	.	.	ENSG00000257446;ENSG00000232371	ENST00000547628;ENST00000440730	T	0.25749	1.78	1.3	0.0242	0.14140	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.41650	0.1168	L	0.61036	1.89	0.30315	N	0.788124	D	0.76494	0.999	D	0.68621	0.959	T	0.39683	-0.9602	9	0.72032	D	0.01	.	7.9262	0.29876	0.0:0.259:0.7409:0.0	.	418	C9JN71	ZN878_HUMAN	I	418;465	ENSP00000447931:T418I	ENSP00000447931:T418I	T	-	2	0	AC022415.4;ZNF878	12015963	0.854000	0.29725	0.002000	0.10522	0.918000	0.54935	2.253000	0.43205	-0.149000	0.11215	0.313000	0.20887	ACA	.	.		0.438	ZNF878-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403723.1	NM_001080404		A	12154963	G	A	12154963	3	1	236	1	0	0	0	0	1	0	0	0	18211	1377	48	3	346	3	ZNF878	19	12154963	Missense_Mutation	SNP	G	TCGA-DD-AAW3-01A-11D-A40P-10	3493696	12154963	46974020	92	32894										
POP4	10775	hgsc.bcm.edu	37	chr19	30099579	30099579	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	cccaggtgtgatctaccatgCattgtctcagaaagaggcga	11	10	2	3			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr19:30099579C>T	ENST00000585603.1	+	2	2325	c.23C>T	c.(22-24)gCa>gTa	p.A8V	POP4_ENST00000591824.1_3'UTR|POP4_ENST00000392279.3_Missense_Mutation_p.H2Y|POP4_ENST00000221770.3_5'UTR			O95707	RPP29_HUMAN	processing of precursor 4, ribonuclease P/MRP subunit (S. cerevisiae)	8					mRNA cleavage (GO:0006379)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA processing (GO:0006364)|tRNA processing (GO:0008033)	nucleolar ribonuclease P complex (GO:0005655)|ribonuclease MRP complex (GO:0000172)|ribonuclease P complex (GO:0030677)	ribonuclease P activity (GO:0004526)|ribonuclease P RNA binding (GO:0033204)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|lung(4)	6	Ovarian(5;0.000567)|Breast(6;0.0602)|Esophageal squamous(110;0.239)		UCEC - Uterine corpus endometrioid carcinoma (4;2.65e-06)|STAD - Stomach adenocarcinoma(5;1.7e-06)|Lung(7;0.0623)|LUAD - Lung adenocarcinoma(5;0.0989)|BRCA - Breast invasive adenocarcinoma(6;0.225)			ATCTACCATGCATTGTCTCAG	0.443																																					p.A8V	Melanoma(89;1165 1449 14085 34436 43672)	Atlas-SNP	.											.	POP4	20	.	0			c.C23T						.						158	157	157					19																	30099579		2203	4300	6503	SO:0001583	missense	10775	exon2			ACCATGCATTGTC	BC006098	CCDS12416.1	19q13.11	2012-05-21				ENSG00000105171			30081	protein-coding gene	gene with protein product		606114				10352175, 10024167	Standard	NM_006627		Approved	RPP29	uc002nsf.2	O95707		ENST00000585603.1:c.23C>T	chr19.hg19:g.30099579C>T	ENSP00000465213:p.Ala8Val	59.0	0.0		42.0	18.0	NM_006627	Q5XKL7|Q6FHW9|Q9UQQ3	Missense_Mutation	SNP	ENST00000585603.1	hg19	CCDS12416.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.52|11.52	1.662680|1.662680	0.29515|0.29515	.|.	.|.	ENSG00000105171|ENSG00000105171	ENST00000221770|ENST00000392279	.|.	.|.	.|.	4.93|4.93	3.87|3.87	0.44632|0.44632	.|.	0.495975|.	0.21944|.	N|.	0.066828|.	T|T	0.41259|0.41259	0.1151|0.1151	M|M	0.68952|0.68952	2.095|2.095	0.09310|0.09310	N|N	0.999998|0.999998	B|B	0.24258|0.14012	0.1|0.009	B|B	0.21708|0.14578	0.036|0.011	T|T	0.44498|0.44498	-0.9324|-0.9324	9|8	0.52906|0.02654	T|T	0.07|1	-6.8732|-6.8732	11.2339|11.2339	0.48929|0.48929	0.0:0.815:0.185:0.0|0.0:0.815:0.185:0.0	.|.	8|2	O95707|A8MYC1	RPP29_HUMAN|.	V|Y	8|2	.|.	ENSP00000221770:A8V|ENSP00000376104:H2Y	A|H	+|+	2|1	0|0	POP4|POP4	34791419|34791419	0.394000|0.394000	0.25246|0.25246	0.560000|0.560000	0.28344|0.28344	0.352000|0.352000	0.29268|0.29268	0.660000|0.660000	0.25009|0.25009	1.399000|1.399000	0.46721|0.46721	0.655000|0.655000	0.94253|0.94253	GCA|CAT	.	.		0.443	POP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458710.1	NM_006627		T	30099579	C	T	30099579	3	4	236	1	0	0	0	0	1	0	0	0	12261	710	25	3	29	3	POP4	19	30099579	Missense_Mutation	SNP	C	TCGA-DD-AAW3-01A-11D-A40P-10	17944616	30099579	29029404	93	32895										
CEBPA	1050	hgsc.bcm.edu	37	chr19	33792753	33792753	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	cgggtgcgggtgcgggtgcgAgggcggcggcggcggcggcg	27	10	0	0			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr19:33792753A>G	ENST00000498907.2	-	1	717	c.568T>C	c.(568-570)Tcg>Ccg	p.S190P	CTD-2540B15.11_ENST00000589932.1_RNA|CTD-2540B15.7_ENST00000587312.1_RNA|CEBPA-AS1_ENST00000592982.2_RNA	NM_004364.3	NP_004355.2	P49715	CEBPA_HUMAN	CCAAT/enhancer binding protein (C/EBP), alpha	190					acute-phase response (GO:0006953)|brown fat cell differentiation (GO:0050873)|cell maturation (GO:0048469)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|cholesterol metabolic process (GO:0008203)|cytokine-mediated signaling pathway (GO:0019221)|embryonic placenta development (GO:0001892)|generation of precursor metabolites and energy (GO:0006091)|inner ear development (GO:0048839)|liver development (GO:0001889)|lung development (GO:0030324)|macrophage differentiation (GO:0030225)|mitochondrion organization (GO:0007005)|myeloid cell differentiation (GO:0030099)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ regeneration (GO:0031100)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|response to glucocorticoid (GO:0051384)|response to vitamin B2 (GO:0033274)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|urea cycle (GO:0000050)|viral process (GO:0016032)|white fat cell differentiation (GO:0050872)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|Rb-E2F complex (GO:0035189)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S190fs*131(1)|p.P185_P197del(1)|p.S190_P198del(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(912)|lung(5)|prostate(1)|stomach(1)	920	Esophageal squamous(110;0.137)					TGCGGGTGCGAGggcggcggc	0.751			"Mis, N, F"		"AML, MDS"				Acute Myeloid Leukemia, Familial, associated with CEBPA germline mutation																												p.S190P		Atlas-SNP	.		Dom	yes		19	19q13.1	1050	"CCAAT/enhancer binding protein (C/EBP), alpha"		L	.	CEBPA	986	.	3	Deletion - In frame(2)|Insertion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(3)	c.T568C						.						1	1	1					19																	33792753		457	1100	1557	SO:0001583	missense	1050	exon1	Familial Cancer Database	Familial AML	GGTGCGAGGGCGG	M37197	CCDS54243.1	19q13.1	2014-09-17				ENSG00000245848		"basic leucine zipper proteins"	1833	protein-coding gene	gene with protein product		116897		CEBP		1535333, 1840554	Standard	NM_004364		Approved	C/EBP-alpha	uc002nun.3	P49715		ENST00000498907.2:c.568T>C	chr19.hg19:g.33792753A>G	ENSP00000427514:p.Ser190Pro	71.0	0.0		129.0	12.0	NM_004364	A7LNP2|P78319|Q05CA4	Missense_Mutation	SNP	ENST00000498907.2	hg19	CCDS54243.1	.	.	.	.	.	.	.	.	.	.	A	1.858	-0.463433	0.04476	.	.	ENSG00000245848	ENST00000498907	T	0.18174	2.23	2.47	1.39	0.22231	.	.	.	.	.	T	0.07548	0.0190	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38134	-0.9675	9	0.29301	T	0.29	.	5.1081	0.14794	0.1886:0.0:0.8114:0.0	.	190	P49715	CEBPA_HUMAN	P	190	ENSP00000427514:S190P	ENSP00000427514:S190P	S	-	1	0	CEBPA	38484593	0.969000	0.33509	0.085000	0.20634	0.154000	0.21943	-0.452000	0.06787	0.068000	0.16574	0.055000	0.15244	TCG	.	.		0.751	CEBPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365012.1	NM_004364		G	33792753	A	G	33792753	3	3	236	1	0	0	0	0	1	0	0	0	3201	304	11	2	512	2	CEBPA	19	33792753	Missense_Mutation	SNP	A	TCGA-DD-AAW3-01A-11D-A40P-10	3693174	33792753	25336230	94	32896										
FGF21	26291	hgsc.bcm.edu	37	chr19	49259647	49259647	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	ggcagcggtacctctacacaGatgatgcccagcagacagaa	11	12	1	4			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr19:49259647G>A	ENST00000593756.1	+	2	726	c.154G>A	c.(154-156)Gat>Aat	p.D52N	FUT1_ENST00000310160.3_5'Flank|FGF21_ENST00000222157.3_Missense_Mutation_p.D52N|FUT1_ENST00000601931.1_5'Flank			Q9NSA1	FGF21_HUMAN	fibroblast growth factor 21	52					cell-cell signaling (GO:0007267)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of glucose import (GO:0046326)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|regulation of low-density lipoprotein particle clearance (GO:0010988)|signal transduction (GO:0007165)	extracellular region (GO:0005576)				breast(1)|cervix(2)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	8		all_lung(116;1.7e-06)|all_epithelial(76;3.52e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000348)|Epithelial(262;0.019)|GBM - Glioblastoma multiforme(486;0.022)		CCTCTACACAGATGATGCCCA	0.647																																					p.D52N		Atlas-SNP	.											.	FGF21	21	.	0			c.G154A						.						43	40	41					19																	49259647		2203	4300	6503	SO:0001583	missense	26291	exon1			TACACAGATGATG	AB021975	CCDS12734.1	19q13.33	2012-09-20			ENSG00000105550	ENSG00000105550			3678	protein-coding gene	gene with protein product		609436				10858549	Standard	XM_005258731		Approved		uc002pko.1	Q9NSA1		ENST00000593756.1:c.154G>A	chr19.hg19:g.49259647G>A	ENSP00000471477:p.Asp52Asn	44.0	0.0		46.0	18.0	NM_019113	Q8N683	Missense_Mutation	SNP	ENST00000593756.1	hg19	CCDS12734.1	.	.	.	.	.	.	.	.	.	.	G	19.60	3.857445	0.71834	.	.	ENSG00000105550	ENST00000222157	D	0.85773	-2.03	4.77	4.77	0.60923	.	0.143969	0.42964	D	0.000623	T	0.80934	0.4719	N	0.17800	0.525	0.47862	D	0.999533	P	0.52577	0.954	P	0.57057	0.812	T	0.75690	-0.3230	10	0.05620	T	0.96	-26.9537	13.5102	0.61508	0.0:0.0:1.0:0.0	.	52	Q9NSA1	FGF21_HUMAN	N	52	ENSP00000222157:D52N	ENSP00000222157:D52N	D	+	1	0	FGF21	53951459	0.986000	0.35501	0.726000	0.30738	0.954000	0.61252	4.701000	0.61810	2.664000	0.90586	0.561000	0.74099	GAT	.	.		0.647	FGF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466200.1			A	49259647	G	A	49259647	3	1	236	1	0	0	0	0	1	0	0	0	5858	942	33	3	156	3	FGF21	19	49259647	Missense_Mutation	SNP	G	TCGA-DD-AAW3-01A-11D-A40P-10	15466894	49259647	9869336	95	32897										
RUVBL2	10856	hgsc.bcm.edu	37	chr19	49506571	49506571	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	tccggggactggggctggacGatgccttggagcctcggcag	18	11	0	0			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr19:49506571G>A	ENST00000595090.1	+	3	567	c.103G>A	c.(103-105)Gat>Aat	p.D35N	RUVBL2_ENST00000413176.2_De_novo_Start_OutOfFrame|RUVBL2_ENST00000601968.1_De_novo_Start_OutOfFrame	NM_006666.1	NP_006657.1	Q9Y230	RUVB2_HUMAN	RuvB-like AAA ATPase 2	35					ATP catabolic process (GO:0006200)|cellular response to estradiol stimulus (GO:0071392)|cellular response to UV (GO:0034644)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|establishment of protein localization to chromatin (GO:0071169)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|negative regulation of estrogen receptor binding (GO:0071899)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein folding (GO:0006457)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)|transcriptional activation by promoter-enhancer looping (GO:0071733)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Ino80 complex (GO:0031011)|intracellular (GO:0005622)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|NuA4 histone acetyltransferase complex (GO:0035267)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|ATP-dependent DNA helicase activity (GO:0004003)|chromatin DNA binding (GO:0031490)|damaged DNA binding (GO:0003684)|DNA helicase activity (GO:0003678)|identical protein binding (GO:0042802)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|unfolded protein binding (GO:0051082)			large_intestine(1)|upper_aerodigestive_tract(1)	2		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000449)|OV - Ovarian serous cystadenocarcinoma(262;0.000555)|GBM - Glioblastoma multiforme(486;0.00585)|Epithelial(262;0.047)		GGGGCTGGACGATGCCTTGGA	0.607																																					p.D35N		Atlas-SNP	.											.	RUVBL2	31	.	0			c.G103A						.						75	80	79					19																	49506571		1975	4142	6117	SO:0001583	missense	10856	exon3			CTGGACGATGCCT	AF155138	CCDS42588.1	19q13.3	2013-09-12	2013-09-12					"INO80 complex subunits", "ATPases / AAA-type"	10475	protein-coding gene	gene with protein product	"reptin", "INO80 complex subunit J"	604788	"RuvB (E coli homolog)-like 2", "RuvB-like 2 (E. coli)"			10428817, 10998447	Standard	XM_005258426		Approved	RVB2, TIP48, TIP49b, Reptin52, ECP51, TIH2, INO80J, Rvb2	uc002plr.1	Q9Y230		ENST00000595090.1:c.103G>A	chr19.hg19:g.49506571G>A	ENSP00000473172:p.Asp35Asn	93.0	0.0		83.0	39.0	NM_006666	B3KQ59|E7ETE5|Q6FIB9|Q6PK27|Q9Y361	Missense_Mutation	SNP	ENST00000595090.1	hg19	CCDS42588.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.590485	0.86851	.	.	ENSG00000183207	ENST00000221413	T	0.47869	0.83	4.96	4.96	0.65561	TIP49, C-terminal (1);	0.000000	0.85682	U	0.000000	T	0.65196	0.2668	M	0.84683	2.71	0.80722	D	1	D;D	0.56968	0.977;0.978	P;P	0.53146	0.659;0.719	T	0.72377	-0.4312	10	0.62326	D	0.03	-21.2525	16.0913	0.81091	0.0:0.0:1.0:0.0	.	35;35	B4DW30;Q9Y230	.;RUVB2_HUMAN	N	35	ENSP00000221413:D35N	ENSP00000221413:D35N	D	+	1	0	RUVBL2	54198383	1.000000	0.71417	0.984000	0.44739	0.706000	0.40770	8.274000	0.89889	2.480000	0.83734	0.561000	0.74099	GAT	.	.		0.607	RUVBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466235.1			A	49506571	G	A	49506571	3	1	236	1	0	0	0	0	1	0	0	0	13768	1058	37	1	113	1	RUVBL2	19	49506571	Missense_Mutation	SNP	G	TCGA-DD-AAW3-01A-11D-A40P-10	246924	49506571	9622412	96	32898										
SIGLEC5	8778	hgsc.bcm.edu	37	chr19	52130954	52130954	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	aggagcatctgcagtgcagaCcctcagcctcccaggagcag	12	14	2	1			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr19:52130954C>T	ENST00000534261.2	-	7	1442	c.1043G>A	c.(1042-1044)gGt>gAt	p.G348D	SIGLEC5_ENST00000429354.3_Missense_Mutation_p.G348D|SIGLEC5_ENST00000570106.2_Missense_Mutation_p.G348D|SIGLEC5_ENST00000599649.1_Missense_Mutation_p.G348D|SIGLEC5_ENST00000222107.4_Missense_Mutation_p.G348D			O15389	SIGL5_HUMAN	sialic acid binding Ig-like lectin 5	348					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(9)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27		all_neural(266;0.0726)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0218)		GCAGTGCAGACCCTCAGCCTC	0.647																																					p.G348D		Atlas-SNP	.											.	SIGLEC5	67	.	0			c.G1043A						.						11	13	12					19																	52130954		2182	4283	6465	SO:0001583	missense	8778	exon6			TGCAGACCCTCAG	U71383	CCDS33088.1	19q13.41	2013-01-29			ENSG00000105501	ENSG00000105501		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10874	protein-coding gene	gene with protein product		604200		CD33L2		10343116	Standard	NM_003830		Approved	OB-BP2, SIGLEC-5, CD170	uc002pxe.4	O15389	OTTHUMG00000165510	ENST00000534261.2:c.1043G>A	chr19.hg19:g.52130954C>T	ENSP00000473238:p.Gly348Asp	30.0	0.0		44.0	19.0	NM_003830		Missense_Mutation	SNP	ENST00000534261.2	hg19	CCDS33088.1	.	.	.	.	.	.	.	.	.	.	C	4.700	0.130223	0.08981	.	.	ENSG00000105501	ENST00000222107;ENST00000429354	D;D	0.85629	-2.01;-2.01	3.86	0.0684	0.14369	.	45.634200	0.00465	U	0.000118	D	0.84388	0.5461	M	0.65975	2.015	0.09310	N	1	B	0.23442	0.085	B	0.29598	0.104	T	0.64193	-0.6465	10	0.49607	T	0.09	.	6.1484	0.20298	0.38:0.4349:0.1851:0.0	.	348	O15389	SIGL5_HUMAN	D	348	ENSP00000222107:G348D;ENSP00000415200:G348D	ENSP00000222107:G348D	G	-	2	0	SIGLEC5	56822766	0.000000	0.05858	0.001000	0.08648	0.145000	0.21501	-0.674000	0.05233	0.015000	0.14971	0.551000	0.68910	GGT	.	.		0.647	SIGLEC5-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466897.2	NM_003830		T	52130954	C	T	52130954	3	4	236	1	0	0	0	0	1	0	0	0	14326	507	18	3	628	3	SIGLEC5	19	52130954	Missense_Mutation	SNP	C	TCGA-DD-AAW3-01A-11D-A40P-10	2624383	52130954	6998029	97	32899										
SIGLEC1	6614	hgsc.bcm.edu	37	chr20	3674951	3674951	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	agacaccctcatcctccagcAtagccccgtggatctccaga	7	17	2	2			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr20:3674951A>T	ENST00000344754.4	-	12	3172	c.3173T>A	c.(3172-3174)aTg>aAg	p.M1058K	SIGLEC1_ENST00000202578.4_Missense_Mutation_p.M1058K	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	1058	Ig-like C2-type 10.				cell-matrix adhesion (GO:0007160)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of T cell apoptotic process (GO:0070234)|single organismal cell-cell adhesion (GO:0016337)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|liver(2)|lung(24)|ovary(3)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)	70						ATCCTCCAGCATAGCCCCGTG	0.627																																					p.M1058K		Atlas-SNP	.											.	SIGLEC1	210	.	0			c.T3173A						.						95	82	87					20																	3674951		2200	4297	6497	SO:0001583	missense	6614	exon12			TCCAGCATAGCCC	AF230073	CCDS13060.1	20p13	2013-01-29	2006-01-19	2006-01-19	ENSG00000088827	ENSG00000088827		"CD molecules", "Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	11127	protein-coding gene	gene with protein product		600751	"sialoadhesin"	SN		8530048	Standard	XM_006723610		Approved	SIGLEC-1, CD169, FLJ00051, FLJ00055, FLJ00073, FLJ32150, dJ1009E24.1, sialoadhesin	uc002wja.3	Q9BZZ2	OTTHUMG00000031757	ENST00000344754.4:c.3173T>A	chr20.hg19:g.3674951A>T	ENSP00000341141:p.Met1058Lys	102.0	0.0		92.0	44.0	NM_023068	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Missense_Mutation	SNP	ENST00000344754.4	hg19	CCDS13060.1	.	.	.	.	.	.	.	.	.	.	A	5.896	0.349345	0.11182	.	.	ENSG00000088827	ENST00000344754;ENST00000202578	T;T	0.63913	-0.07;-0.07	5.15	-7.42	0.01388	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.119980	0.06933	N	0.811492	T	0.25717	0.0626	N	0.04508	-0.205	0.09310	N	1	B;B	0.23735	0.02;0.09	B;B	0.21360	0.034;0.033	T	0.26916	-1.0089	10	0.06365	T	0.9	.	3.2747	0.06894	0.2953:0.4247:0.1763:0.1036	.	1058;1058	Q9BZZ2;Q9BZZ2-3	SN_HUMAN;.	K	1058	ENSP00000341141:M1058K;ENSP00000202578:M1058K	ENSP00000202578:M1058K	M	-	2	0	SIGLEC1	3622951	0.000000	0.05858	0.001000	0.08648	0.288000	0.27193	-0.575000	0.05861	-1.092000	0.03062	0.459000	0.35465	ATG	.	.		0.627	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068		T	3674951	A	T	3674951	3	4	236	1	0	0	0	0	1	0	0	0	14320	217	8	4	1996	4	SIGLEC1	20	3674951	Missense_Mutation	SNP	A	TCGA-DD-AAW3-01A-11D-A40P-10		3674951	59350569	98	32900										
CST11	140880	hgsc.bcm.edu	37	chr20	23432513	23432513	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	tctggcttttggcaggtggtCcactgcatttccacattcag	10	11	2	0			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr20:23432513C>A	ENST00000377009.3	-	2	306	c.273G>T	c.(271-273)tgG>tgT	p.W91C	CST11_ENST00000377007.3_Intron	NM_130794.1	NP_570612.1	Q9H112	CST11_HUMAN	cystatin 11	91					defense response to bacterium (GO:0042742)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			kidney(2)|large_intestine(1)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	14	Colorectal(13;0.0431)|Lung NSC(19;0.235)					GGCAGGTGGTCCACTGCATTT	0.557																																					p.W91C		Atlas-SNP	.											.	CST11	27	.	0			c.G273T						.						125	106	113					20																	23432513		2203	4300	6503	SO:0001583	missense	140880	exon2			GGTGGTCCACTGC	AL096677	CCDS13154.1, CCDS13155.1	20p11.21	2012-08-14			ENSG00000125831	ENSG00000125831			15959	protein-coding gene	gene with protein product		609731		CST8L		20565543	Standard	NM_080830		Approved	dJ322G13.6, CTES2	uc002wtf.1	Q9H112	OTTHUMG00000032060	ENST00000377009.3:c.273G>T	chr20.hg19:g.23432513C>A	ENSP00000366208:p.Trp91Cys	61.0	0.0		62.0	32.0	NM_130794	Q0VAF2|Q0VAF3|Q8WXU5|Q8WXU6|Q9H113	Missense_Mutation	SNP	ENST00000377009.3	hg19	CCDS13155.1	.	.	.	.	.	.	.	.	.	.	C	6.518	0.463782	0.12402	.	.	ENSG00000125831	ENST00000377009	T	0.12361	2.69	4.1	-1.38	0.09027	Proteinase inhibitor I25, cystatin (2);	0.124783	0.51477	D	0.000089	T	0.05593	0.0147	N	0.08118	0	0.20638	N	0.99988	B	0.09022	0.002	B	0.06405	0.002	T	0.24977	-1.0145	10	0.87932	D	0	-10.8155	5.9538	0.19261	0.0:0.5011:0.2594:0.2395	.	91	Q9H112	CST11_HUMAN	C	91	ENSP00000366208:W91C	ENSP00000366208:W91C	W	-	3	0	CST11	23380513	0.232000	0.23762	0.027000	0.17364	0.008000	0.06430	-0.114000	0.10757	-0.474000	0.06862	-1.128000	0.01989	TGG	.	.		0.557	CST11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078314.1	NM_130794		A	23432513	C	A	23432513	3	1	236	1	0	0	0	0	1	0	0	0	3973	856	30	3	151	3	CST11	20	23432513	Missense_Mutation	SNP	C	TCGA-DD-AAW3-01A-11D-A40P-10	19757562	23432513	39593007	99	32901										
SDC4	6385	hgsc.bcm.edu	37	chr20	43964503	43964503	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	ctcatcgtctggtagggctcCggagaagtatcggccttcta	12	11	3	1			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chr20:43964503C>T	ENST00000372733.3	-	2	157	c.118G>A	c.(118-120)Gga>Aga	p.G40R	SDC4_ENST00000537976.1_Intron	NM_002999.3	NP_002990.2	P31431	SDC4_HUMAN	syndecan 4	40					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stress fiber assembly (GO:0051496)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|costamere (GO:0043034)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	thrombospondin receptor activity (GO:0070053)		SDC4/ROS1(7)	NS(1)|breast(1)|endometrium(1)|large_intestine(2)	5		Myeloproliferative disorder(115;0.0122)				GGTAGGGCTCCGGAGAAGTAT	0.562			T	ROS1	NSCLC																																p.G40R		Atlas-SNP	.		Dom	yes		20	20q12	6385	syndecan 4		E	.	SDC4	16	.	0			c.G118A						.						69	65	67					20																	43964503		2203	4300	6503	SO:0001583	missense	6385	exon2			GGGCTCCGGAGAA	X67016, D13292	CCDS13350.1	20q12	2010-03-25	2007-02-15		ENSG00000124145	ENSG00000124145		"Proteoglycans / Cell Surface : Syndecans"	10661	protein-coding gene	gene with protein product	"syndecan proteoglycan 4"	600017	"syndecan 4 (amphiglycan, ryudocan)"			7916598, 1500433	Standard	NM_002999		Approved	SYND4, amphiglycan, ryudocan	uc002xnu.3	P31431	OTTHUMG00000033083	ENST00000372733.3:c.118G>A	chr20.hg19:g.43964503C>T	ENSP00000361818:p.Gly40Arg	44.0	0.0		37.0	14.0	NM_002999	O00773|Q16833|Q53FN9|Q6FGN3	Missense_Mutation	SNP	ENST00000372733.3	hg19	CCDS13350.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.977135	0.74360	.	.	ENSG00000124145	ENST00000372733	T	0.41758	0.99	4.79	4.79	0.61399	.	0.000000	0.85682	D	0.000000	T	0.62527	0.2435	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.64943	-0.6288	10	0.56958	D	0.05	-16.4399	13.6844	0.62506	0.0:1.0:0.0:0.0	.	40	P31431	SDC4_HUMAN	R	40	ENSP00000361818:G40R	ENSP00000361818:G40R	G	-	1	0	SDC4	43397917	0.992000	0.36948	0.998000	0.56505	0.746000	0.42486	4.003000	0.57061	2.376000	0.81061	0.561000	0.74099	GGA	.	.		0.562	SDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080515.1	NM_002999		T	43964503	C	T	43964503	3	4	236	1	0	0	0	0	1	0	0	0	13969	661	23	1	494	1	SDC4	20	43964503	Missense_Mutation	SNP	C	TCGA-DD-AAW3-01A-11D-A40P-10	20531990	43964503	19061017	100	32902										
RPS6KA3	6197	hgsc.bcm.edu	37	chrX	20222202	20222203	+	Frame_Shift_Ins	INS	-	-	T													0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	cctagcatcagagcctgagaINStttttttaactaagaaaacc							TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chrX:20222202_20222203insT	ENST00000379565.3	-	4	469_470	c.262_263insA	c.(262-264)atcfs	p.I88fs	RPS6KA3_ENST00000540702.1_Frame_Shift_Ins_p.I60fs|RPS6KA3_ENST00000544447.1_Frame_Shift_Ins_p.I60fs|RPS6KA3_ENST00000379548.4_Frame_Shift_Ins_p.I59fs	NM_004586.2	NP_004577.1	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 3	88	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|central nervous system development (GO:0007417)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(14)|lung(7)|ovary(1)|stomach(1)	41					Acetylsalicylic acid(DB00945)	AGAGCCTGAGATTTTTTTAACT	0.332																																					p.I88fs		Atlas-INDEL	.											.	RPS6KA3	110	.	0			c.263_264insA	GRCh37	CD982930|CI021234	RPS6KA3	D|I		.																																			SO:0001589	frameshift_variant	6197	exon4			.	U08316	CCDS14197.1	Xp22.2-p22.1	2013-06-03	2002-08-29		ENSG00000177189	ENSG00000177189			10432	protein-coding gene	gene with protein product		300075	"ribosomal protein S6 kinase, 90kD, polypeptide 3", "mental retardation, X-linked 19", "Coffin-Lowry syndrome"	MRX19, CLS		8141249, 11896450, 16879200	Standard	XM_005274573		Approved	RSK, RSK2, HU-3	uc004czu.3	P51812	OTTHUMG00000021231	ENST00000379565.3:c.263dupA	chrX.hg19:g.20222209_20222209dupT	ENSP00000368884:p.Ile88fs	107.0	0.0		112.0	32.0	NM_004586	B2R9V4|Q4VAP3|Q59H26|Q5JPK8|Q7Z3Z7	Frame_Shift_Ins	INS	ENST00000379565.3	hg19	CCDS14197.1																																																																																			.	.		0.332	RPS6KA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056011.3	NM_004586		T	20222203	-	T	20222202	7	5	236	1	0	1	1	0	0	0	0	0	13667	333	12	0	2035	0	RPS6KA3	23	20222202	Frame_Shift_Ins	INS	-	TCGA-DD-AAW3-01A-11D-A40P-10		20222202	135048358	101	32903										
DMD	1756	hgsc.bcm.edu	37	chrX	32235165	32235165	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	aaacgccgccatttctcaacAgatctgtcaaatcgcctgca	6	14	3	1			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chrX:32235165A>T	ENST00000357033.4	-	44	6512	c.6306T>A	c.(6304-6306)tcT>tcA	p.S2102S	DMD_ENST00000378677.2_Silent_p.S2098S	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	2102					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				ATTTCTCAACAGATCTGTCAA	0.328																																					p.S2102S		Atlas-SNP	.											.	DMD	2127	.	0			c.T6306A						.						45	41	42					X																	32235165		2202	4297	6499	SO:0001819	synonymous_variant	1756	exon44			CTCAACAGATCTG	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.6306T>A	chrX.hg19:g.32235165A>T		174.0	0.0		202.0	176.0	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Silent	SNP	ENST00000357033.4	hg19	CCDS14233.1																																																																																			.	.		0.328	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		T	32235165	A	T	32235165	2	4	236	1	0	0	0	0	0	0	0	1	4582	175	7	4		4	DMD	23	32235165	Silent	SNP	A	TCGA-DD-AAW3-01A-11D-A40P-10	12012963	32235165	123035395	102	32904										
MAGEC3	139081	hgsc.bcm.edu	37	chrX	140926121	140926121	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	catgctgctgccctgccactGggtgttggatgccaccttca	11	14	1	0			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chrX:140926121G>C	ENST00000298296.1	+	1	20	c.20G>C	c.(19-21)tGg>tCg	p.W7S		NM_138702.1	NP_619647.1	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3	7										NS(2)|breast(3)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|liver(1)|lung(32)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(2)	69	Acute lymphoblastic leukemia(192;6.56e-05)					CCCTGCCACTGGGTGTTGGAT	0.522																																					p.W7S		Atlas-SNP	.											.	MAGEC3	228	.	0			c.G20C						.						83	57	66					X																	140926121		2203	4300	6503	SO:0001583	missense	139081	exon1			GCCACTGGGTGTT	AF490508	CCDS14676.1, CCDS14677.1	Xq27.2	2009-03-25			ENSG00000165509	ENSG00000165509			23798	protein-coding gene	gene with protein product	"cancer/testis antigen family 7, member 2"	300469				10861452	Standard	NM_138702		Approved	HCA2, MAGE-C3, CT7.2	uc011mwp.2	Q8TD91	OTTHUMG00000022570	ENST00000298296.1:c.20G>C	chrX.hg19:g.140926121G>C	ENSP00000298296:p.Trp7Ser	89.0	0.0		86.0	76.0	NM_138702	Q3SYA7|Q5JZ43|Q9BZ80	Missense_Mutation	SNP	ENST00000298296.1	hg19	CCDS14676.1	.	.	.	.	.	.	.	.	.	.	G	6.044	0.376436	0.11466	.	.	ENSG00000165509	ENST00000298296	T	0.08634	3.07	0.427	0.427	0.16489	.	.	.	.	.	T	0.08223	0.0205	N	0.08118	0	0.09310	N	1	D	0.55605	0.972	P	0.56700	0.804	T	0.34800	-0.9814	8	0.87932	D	0	.	.	.	.	.	7	Q8TD91	MAGC3_HUMAN	S	7	ENSP00000298296:W7S	ENSP00000298296:W7S	W	+	2	0	MAGEC3	140753787	0.348000	0.24861	0.027000	0.17364	0.028000	0.11728	0.364000	0.20325	0.417000	0.25871	0.422000	0.28245	TGG	.	.		0.522	MAGEC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058606.1	NM_138702		C	140926121	G	C	140926121	3	2	236	1	0	0	0	0	1	0	0	0	9191	1357	47	4	22	4	MAGEC3	23	140926121	Missense_Mutation	SNP	G	TCGA-DD-AAW3-01A-11D-A40P-10	108690956	140926121	14344439	103	32905										
NLGN4Y	22829	hgsc.bcm.edu	37	chrY	16942170	16942170	+	3'UTR	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0388349514563107	4	1	0.657690738474092	0	0.725146198830409	0.076923076923077	0.551775147928995	0	cccccgccgtggccaccgccGacctgcacgcgcagtacggc	12	21	0	0			TCGA-DD-AAW3-01A-11D-A40P-10	TCGA-DD-AAW3-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	07d529e0-2ba2-49d7-b348-2ef3d52cc0ce	e3ae1920-aeb7-4aa2-b8c2-f83450414f08	g.chrY:16942170G>T	ENST00000476359.1	+	0	1917							Q8NFZ3	NLGNY_HUMAN	neuroligin 4, Y-linked						learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)			large_intestine(3)|lung(7)|prostate(2)|skin(2)	14						GGCCACCGCCGACCTGCACGC	0.617																																					p.D458Y		Atlas-SNP	.											.	NLGN4Y	44	.	0			c.G1372T						.																																			SO:0001624	3_prime_UTR_variant	22829	exon5			ACCGCCGACCTGC		CCDS14788.1, CCDS55553.1, CCDS56619.1	Yq11.221	2013-09-20	2004-05-21		ENSG00000165246	ENSG00000165246			15529	protein-coding gene	gene with protein product		400028	"neuroligin 4, Y linked"			10231032	Standard	NM_014893		Approved	KIAA0951	uc004ftg.2	Q8NFZ3	OTTHUMG00000036618	ENST00000476359.1:c.*1914G>T	chrY.hg19:g.16942170G>T		157.0	0.0		149.0	119.0	NM_014893	F5H6W0|Q14D08|Q7Z3T5|Q8N5B6|Q9Y2F8	Missense_Mutation	SNP	ENST00000476359.1	hg19																																																																																				.	.		0.617	NLGN4Y-004	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000089064.2	NM_014893		T	16942170	G	T	16942170	1	4	236	0	1	0	0	0	0	0	0	0	10474	1058	37	1		1	NLGN4Y	24	16942170	3'UTR	SNP	G	TCGA-DD-AAW3-01A-11D-A40P-10		16942170	42431396	104	32906										
TAS1R3	83756	hgsc.bcm.edu	37	chr1	1268035	1268035	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gcgctgcccgcagtgtgactGcatcacgctgcagaacgtga	13	13	1	3			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:1268035G>T	ENST00000339381.5	+	3	1156	c.1124G>T	c.(1123-1125)tGc>tTc	p.C375F		NM_152228.1	NP_689414	Q7RTX0	TS1R3_HUMAN	taste receptor, type 1, member 3	375					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			kidney(2)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.88e-21)|Colorectal(212;0.000157)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00251)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.146)		CAGTGTGACTGCATCACGCTG	0.647																																					p.C375F		Atlas-SNP	.											.	TAS1R3	39	.	0			c.G1124T						.						25	23	23					1																	1268035		2192	4295	6487	SO:0001583	missense	83756	exon3			GTGACTGCATCAC	AC026283	CCDS30556.1	1p36	2012-08-22			ENSG00000169962	ENSG00000169962		"Taste receptors / Type 1", "GPCR / Unclassified : Taste receptors"	15661	protein-coding gene	gene with protein product		605865				11319557	Standard	XM_006710939		Approved	T1R3	uc010nyk.2	Q7RTX0	OTTHUMG00000003071	ENST00000339381.5:c.1124G>T	chr1.hg19:g.1268035G>T	ENSP00000344411:p.Cys375Phe	57.0	0.0		52.0	13.0	NM_152228	Q5TA49|Q8NGW9	Missense_Mutation	SNP	ENST00000339381.5	hg19	CCDS30556.1	.	.	.	.	.	.	.	.	.	.	G	0.014	-1.591994	0.00864	.	.	ENSG00000169962	ENST00000339381	D	0.85861	-2.04	4.71	-5.38	0.02673	Extracellular ligand-binding receptor (1);	1.852440	0.04610	U	0.400039	T	0.66934	0.2840	N	0.08118	0	0.09310	N	1	B	0.19445	0.036	B	0.10450	0.005	T	0.54603	-0.8269	10	0.22109	T	0.4	.	8.0053	0.30321	0.3924:0.132:0.4756:0.0	.	375	Q7RTX0	TS1R3_HUMAN	F	375	ENSP00000344411:C375F	ENSP00000344411:C375F	C	+	2	0	TAS1R3	1257898	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.588000	0.23924	-0.779000	0.04560	-1.036000	0.02392	TGC	.	.		0.647	TAS1R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008493.1			T	1268035	G	T	1268035	3	4	237	1	0	0	0	0	1	0	0	0	15579	1319	46	3	1134	3	TAS1R3	1	1268035	Missense_Mutation	SNP	G	TCGA-ED-A459-01A-11D-A25V-10		1268035	247982586	1	32907										
GPR153	387509	hgsc.bcm.edu	37	chr1	6314095	6314095	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gaagcggcagccatgggtgtAgaagcgctcgctggtgtcgt	17	9	0	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:6314095A>C	ENST00000377893.2	-	3	728	c.469T>G	c.(469-471)Tac>Gac	p.Y157D		NM_207370.2	NP_997253.2	Q6NV75	GP153_HUMAN	G protein-coupled receptor 153	157						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|liver(1)|lung(7)|skin(1)	14	Ovarian(185;0.0634)	all_cancers(23;8.07e-33)|all_epithelial(116;4.45e-18)|all_lung(118;1.09e-06)|all_neural(13;3.68e-06)|Lung NSC(185;1.52e-05)|all_hematologic(16;2.39e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00475)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;1.91e-37)|GBM - Glioblastoma multiforme(13;4.87e-29)|OV - Ovarian serous cystadenocarcinoma(86;3.03e-19)|Colorectal(212;1.33e-07)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(365;0.00109)|STAD - Stomach adenocarcinoma(132;0.00313)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.246)		CCATGGGTGTAGAAGCGCTCG	0.637																																					p.Y157D		Atlas-SNP	.											.	GPR153	44	.	0			c.T469G						.						56	61	59					1																	6314095		2201	4298	6499	SO:0001583	missense	387509	exon3			GGGTGTAGAAGCG	AY255529	CCDS64.1	1p36.31	2012-08-21			ENSG00000158292	ENSG00000158292		"GPCR / Class A : Orphans"	23618	protein-coding gene	gene with protein product		614269				12679517	Standard	NM_207370		Approved	PGR1	uc001amp.2	Q6NV75	OTTHUMG00000001272	ENST00000377893.2:c.469T>G	chr1.hg19:g.6314095A>C	ENSP00000367125:p.Tyr157Asp	207.0	0.0		177.0	37.0	NM_207370	Q5TGR5|Q6AHW8|Q86SP8	Missense_Mutation	SNP	ENST00000377893.2	hg19	CCDS64.1	.	.	.	.	.	.	.	.	.	.	A	19.60	3.858451	0.71834	.	.	ENSG00000158292	ENST00000377893	T	0.34667	1.35	4.9	4.9	0.64082	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.48150	0.1484	L	0.34521	1.04	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	T	0.46925	-0.9156	10	0.51188	T	0.08	-39.2472	13.3635	0.60669	1.0:0.0:0.0:0.0	.	157	Q6NV75	GP153_HUMAN	D	157	ENSP00000367125:Y157D	ENSP00000367125:Y157D	Y	-	1	0	GPR153	6236682	1.000000	0.71417	1.000000	0.80357	0.722000	0.41435	9.265000	0.95647	1.833000	0.53350	0.460000	0.39030	TAC	.	.		0.637	GPR153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003717.2			C	6314095	A	C	6314095	3	2	237	1	0	0	0	0	1	0	0	0	6667	420	15	5	1376	5	GPR153	1	6314095	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	5046060	6314095	242936526	2	32908										
CA6	765	hgsc.bcm.edu	37	chr1	9027785	9027785	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	aggaacctccagcactactaCacctaccatggctcactcac	5	17	2	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:9027785C>A	ENST00000377443.2	+	6	643	c.639C>A	c.(637-639)taC>taA	p.Y213*	CA6_ENST00000377442.2_Nonsense_Mutation_p.Y153*|CA6_ENST00000476083.1_3'UTR|CA6_ENST00000377436.3_Nonsense_Mutation_p.Y213*	NM_001215.3	NP_001206.2	P23280	CAH6_HUMAN	carbonic anhydrase VI	213					bicarbonate transport (GO:0015701)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|skin(5)	16	Ovarian(185;0.112)|all_lung(157;0.143)	all_epithelial(116;1.02e-19)|all_lung(118;3.6e-06)|Lung NSC(185;7.94e-06)|Renal(390;0.000147)|Breast(348;0.00123)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.9e-07)|COAD - Colon adenocarcinoma(227;8.28e-05)|Kidney(185;0.000268)|KIRC - Kidney renal clear cell carcinoma(229;0.000971)|STAD - Stomach adenocarcinoma(132;0.00184)|BRCA - Breast invasive adenocarcinoma(304;0.00192)|READ - Rectum adenocarcinoma(331;0.0649)	Mafenide(DB06795)|Zonisamide(DB00909)	AGCACTACTACACCTACCATG	0.517																																					p.Y213X		Atlas-SNP	.											.	CA6	47	.	0			c.C639A						.						192	144	160					1																	9027785		2203	4300	6503	SO:0001587	stop_gained	765	exon6			CTACTACACCTAC	M57892	CCDS30578.1, CCDS57970.1, CCDS57971.1	1p36.2	2008-02-05			ENSG00000131686	ENSG00000131686	4.2.1.1	"Carbonic anhydrases"	1380	protein-coding gene	gene with protein product		114780				9691177	Standard	NM_001215		Approved		uc031plc.1	P23280	OTTHUMG00000001763	ENST00000377443.2:c.639C>A	chr1.hg19:g.9027785C>A	ENSP00000366662:p.Tyr213*	632.0	1.0		902.0	250.0	NM_001270500	E7EMQ1|Q5FBW3|Q5FC00|Q96QX8|Q9UF03	Nonsense_Mutation	SNP	ENST00000377443.2	hg19	CCDS30578.1	.	.	.	.	.	.	.	.	.	.	C	9.159	1.018118	0.19355	.	.	ENSG00000131686	ENST00000549778;ENST00000377443;ENST00000377436;ENST00000377442	.	.	.	5.31	2.22	0.28083	.	0.364504	0.32563	N	0.005924	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.9474	0.24526	0.0:0.6794:0.0:0.3206	.	.	.	.	X	181;213;213;153	.	ENSP00000366654:Y213X	Y	+	3	2	CA6	8950372	1.000000	0.71417	0.989000	0.46669	0.006000	0.05464	0.944000	0.29043	0.159000	0.19401	-0.258000	0.10820	TAC	.	.		0.517	CA6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000004911.1			A	9027785	C	A	9027785	4	1	237	1	0	0	0	0	0	1	0	0	2523	489	17	3	661	3	CA6	1	9027785	Nonsense_Mutation	SNP	C	TCGA-ED-A459-01A-11D-A25V-10	2713690	9027785	240222836	3	32909										
KIF1B	23095	hgsc.bcm.edu	37	chr1	10408722	10408722	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	cctagggcatccagcgaaggAtcacagtgaccattatccat	9	12	1	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:10408722A>T	ENST00000377086.1	+	37	4082	c.3880A>T	c.(3880-3882)Atc>Ttc	p.I1294F	KIF1B_ENST00000377081.1_Missense_Mutation_p.I1294F|KIF1B_ENST00000465635.1_3'UTR|KIF1B_ENST00000263934.6_Missense_Mutation_p.I1248F			O60333	KIF1B_HUMAN	kinesin family member 1B	1294					anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		CCAGCGAAGGATCACAGTGAC	0.478																																					p.I1248F		Atlas-SNP	.											.	KIF1B	242	.	0			c.A3742T						.						136	105	115					1																	10408722		2203	4300	6503	SO:0001583	missense	23095	exon35			CGAAGGATCACAG	AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"Kinesins", "Pleckstrin homology (PH) domain containing"	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.3880A>T	chr1.hg19:g.10408722A>T	ENSP00000366290:p.Ile1294Phe	253.0	0.0		368.0	115.0	NM_015074	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Missense_Mutation	SNP	ENST00000377086.1	hg19		.	.	.	.	.	.	.	.	.	.	A	25.8	4.673574	0.88445	.	.	ENSG00000054523	ENST00000355249;ENST00000263934;ENST00000377086;ENST00000377081	T;T;T	0.81415	-1.41;-1.49;-1.49	5.52	4.39	0.52855	.	0.000000	0.85682	D	0.000000	D	0.89887	0.6845	M	0.87269	2.87	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.976;1.0;0.96	D;D;D;D;D;D	0.91635	0.996;0.999;0.999;0.949;0.99;0.948	D	0.90376	0.4384	10	0.87932	D	0	.	11.3155	0.49390	0.9289:0.0:0.0711:0.0	.	1280;1254;1294;1268;1294;1248	Q4R9M9;Q4R9M7;Q4VXC4;Q4R9M8;O60333;O60333-2	.;.;.;.;KIF1B_HUMAN;.	F	1294;1248;1294;1294	ENSP00000263934:I1248F;ENSP00000366290:I1294F;ENSP00000366284:I1294F	ENSP00000263934:I1248F	I	+	1	0	KIF1B	10331309	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.335000	0.72949	0.932000	0.37266	0.533000	0.62120	ATC	.	.		0.478	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1			T	10408722	A	T	10408722	3	4	237	1	0	0	0	0	1	0	0	0	8293	333	12	4	5365	4	KIF1B	1	10408722	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	1380937	10408722	238841899	4	32910										
VPS13D	55187	hgsc.bcm.edu	37	chr1	12313850	12313850	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tattgggatgtcgattgcacTttactgggggatttgcctca	12	7	1	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:12313850T>A	ENST00000358136.3	+	7	766	c.636T>A	c.(634-636)acT>acA	p.T212T	VPS13D_ENST00000356315.4_Silent_p.T212T	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		TCGATTGCACTTTACTGGGGG	0.443																																					p.T212T		Atlas-SNP	.											.	VPS13D	316	.	0			c.T636A						.						207	188	195					1																	12313850		2203	4300	6503	SO:0001819	synonymous_variant	55187	exon7			TTGCACTTTACTG	AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"vacuolar protein sorting 13D (yeast)"				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.636T>A	chr1.hg19:g.12313850T>A		247.0	0.0		332.0	109.0	NM_015378		Silent	SNP	ENST00000358136.3	hg19	CCDS30588.1																																																																																			.	.		0.443	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		A	12313850	T	A	12313850	2	1	237	1	0	0	0	0	0	0	0	1	17207	1596	56	4		4	VPS13D	1	12313850	Silent	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	1905128	12313850	236936771	5	32911										
FBXO42	54455	hgsc.bcm.edu	37	chr1	16578144	16578145	+	Frame_Shift_Del	DEL	TG	TG	-													0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ccatgcttcttactggagacTgagagcggtactctcgggtt							TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:16578144_16578145delTG	ENST00000375592.3	-	10	1390_1391	c.1174_1175delCA	c.(1174-1176)cagfs	p.Q392fs		NM_018994.1	NP_061867.1	Q6P3S6	FBX42_HUMAN	F-box protein 42	392										autonomic_ganglia(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	26		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00475)|all_lung(284;0.00671)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0193)|Colorectal(212;3.16e-07)|COAD - Colon adenocarcinoma(227;1.46e-05)|BRCA - Breast invasive adenocarcinoma(304;4.37e-05)|Kidney(64;0.000246)|KIRC - Kidney renal clear cell carcinoma(64;0.00336)|STAD - Stomach adenocarcinoma(313;0.0139)|READ - Rectum adenocarcinoma(331;0.0693)		TACTGGAGACTGAGAGCGGTAC	0.569																																					p.392_392del		Atlas-Indel,Pindel	.											.	FBXO42	53	.	0			c.1175_1176del						.																																			SO:0001589	frameshift_variant	54455	exon10			.	BC063864	CCDS30613.1	1p36.23-p36.11	2008-02-05			ENSG00000037637	ENSG00000037637		"F-boxes /  "other""	29249	protein-coding gene	gene with protein product		609109				10718198	Standard	XM_006710698		Approved	KIAA1332, Fbx42	uc001ayg.3	Q6P3S6	OTTHUMG00000002218	ENST00000375592.3:c.1174_1175delCA	chr1.hg19:g.16578144_16578145delTG	ENSP00000364742:p.Gln392fs	201.0	0.0		239.0	29.0	NM_018994	B3KP30|Q5TEU8|Q86XI0|Q8N3N4|Q8N5F8|Q9BRM0|Q9P2L4	Frame_Shift_Del	DEL	ENST00000375592.3	hg19	CCDS30613.1																																																																																			.	.		0.569	FBXO42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006285.1			-	16578145	TG	-	16578144	7	5	237	1	0	1	0	1	0	0	0	0	5759	1580	55	0	982	0	FBXO42	1	16578144	Frame_Shift_Del	DEL	TG	TCGA-ED-A459-01A-11D-A25V-10	4264294	16578144	232672477	6	32912										
UBR4	23352	hgsc.bcm.edu	37	chr1	19480377	19480377	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	agcacaccaagccagggtggTtcatcacctcagaccactgg	10	14	3	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:19480377T>A	ENST00000375254.3	-	45	6542	c.6515A>T	c.(6514-6516)aAc>aTc	p.N2172I	UBR4_ENST00000375267.2_Missense_Mutation_p.N2172I|UBR4_ENST00000375217.2_Missense_Mutation_p.N2172I|UBR4_ENST00000375226.2_Missense_Mutation_p.N2172I	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	2172					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		GCCAGGGTGGTTCATCACCTC	0.493																																					p.N2172I		Atlas-SNP	.											.	UBR4	415	.	0			c.A6515T						.						104	97	100					1																	19480377		2203	4300	6503	SO:0001583	missense	23352	exon45			GGGTGGTTCATCA	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.6515A>T	chr1.hg19:g.19480377T>A	ENSP00000364403:p.Asn2172Ile	476.0	2.0		430.0	245.0	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	hg19	CCDS189.1	.	.	.	.	.	.	.	.	.	.	T	29.8	5.035890	0.93630	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000417040;ENST00000419533	T;T;T;T	0.25749	1.79;1.79;1.78;1.78	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.44477	0.1295	L	0.48642	1.525	0.80722	D	1	D;D	0.65815	0.993;0.995	P;D	0.75484	0.905;0.986	T	0.36407	-0.9749	10	0.72032	D	0.01	.	14.6112	0.68517	0.0:0.0:0.0:1.0	.	2173;2172	Q5T4S7-5;Q5T4S7	.;UBR4_HUMAN	I	2172;2172;2172;2172;882;1389	ENSP00000364403:N2172I;ENSP00000364416:N2172I;ENSP00000364365:N2172I;ENSP00000364374:N2172I	ENSP00000364365:N2172I	N	-	2	0	UBR4	19352964	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.330000	0.79181	2.243000	0.73865	0.482000	0.46254	AAC	.	.		0.493	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		A	19480377	T	A	19480377	3	1	237	1	0	0	0	0	1	0	0	0	16919	1725	60	4	9284	4	UBR4	1	19480377	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	2902233	19480377	229770244	7	32913										
EPHB2	2048	hgsc.bcm.edu	37	chr1	23222044	23222044	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ggcctggtcttcctcattgcTgtggttgtcatcgccatcgt	11	12	3	0	rs141173528		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:23222044T>A	ENST00000400191.3	+	8	1689	c.1671T>A	c.(1669-1671)gcT>gcA	p.A557A	EPHB2_ENST00000374627.1_Silent_p.A552A|EPHB2_ENST00000374630.3_Silent_p.A557A|EPHB2_ENST00000374632.3_Silent_p.A557A|EPHB2_ENST00000465676.1_3'UTR	NM_004442.6|NM_017449.3	NP_004433.2|NP_059145.2	P29323	EPHB2_HUMAN	EPH receptor B2	557					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|camera-type eye morphogenesis (GO:0048593)|central nervous system projection neuron axonogenesis (GO:0021952)|commissural neuron axon guidance (GO:0071679)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|ephrin receptor signaling pathway (GO:0048013)|inner ear morphogenesis (GO:0042472)|learning (GO:0007612)|negative regulation of axonogenesis (GO:0050771)|nervous system development (GO:0007399)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse assembly (GO:0051965)|regulation of body fluid levels (GO:0050878)|retinal ganglion cell axon guidance (GO:0031290)|urogenital system development (GO:0001655)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|protein tyrosine kinase activity (GO:0004713)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(8)|stomach(1)|urinary_tract(1)	56		Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153)		TCCTCATTGCTGTGGTTGTCA	0.582																																					p.A557A		Atlas-SNP	.											.	EPHB2	257	.	0			c.T1671A						.						128	110	116					1																	23222044		2203	4300	6503	SO:0001819	synonymous_variant	2048	exon8			CATTGCTGTGGTT	AF025304	CCDS229.2, CCDS230.1	1p36.1-p35	2014-09-17	2004-10-28		ENSG00000133216	ENSG00000133216	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3393	protein-coding gene	gene with protein product		600997	"EphB2"	DRT, ERK, EPHT3		1648701	Standard	NM_017449		Approved	Hek5, Tyro5	uc001bge.3	P29323	OTTHUMG00000002881	ENST00000400191.3:c.1671T>A	chr1.hg19:g.23222044T>A		181.0	0.0		113.0	18.0	NM_004442	O43477|Q5T0U6|Q5T0U7|Q5T0U8	Silent	SNP	ENST00000400191.3	hg19																																																																																				.	T|1.000;C|0.000		0.582	EPHB2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000008060.2	NM_017449		A	23222044	T	A	23222044	2	1	237	1	0	0	0	0	0	0	0	1	5177	1567	55	4		4	EPHB2	1	23222044	Silent	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	3741667	23222044	226028577	8	32914										
FAM54B	56181	hgsc.bcm.edu	37	chr1	26158452	26158452	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	aggaagaccctgctgtgcttAtctctgaggtcctaaggagg	13	9	1	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:26158452A>G	ENST00000374301.3	+	7	1122	c.814A>G	c.(814-816)Atc>Gtc	p.I272V	MTFR1L_ENST00000524618.1_Missense_Mutation_p.I175V|AUNIP_ENST00000538789.1_3'UTR|MTFR1L_ENST00000374303.2_Missense_Mutation_p.I272V|MTFR1L_ENST00000374307.5_Missense_Mutation_p.I260V|MTFR1L_ENST00000374300.3_Missense_Mutation_p.I272V|RP1-317E23.7_ENST00000606617.1_RNA|AUNIP_ENST00000481602.1_5'Flank|MTFR1L_ENST00000474295.1_3'UTR|MTFR1L_ENST00000469815.1_3'UTR|MTFR1L_ENST00000466284.1_3'UTR	NM_019557.5	NP_062457.3	Q9H019	MFR1L_HUMAN	mitochondrial fission regulator 1-like	272																	TGCTGTGCTTATCTCTGAGGT	0.423																																					p.I272V		Atlas-SNP	.											.	.	.	.	0			c.A814G						.						226	224	224					1																	26158452		1906	4106	6012	SO:0001583	missense	56181	exon7			GTGCTTATCTCTG		CCDS41284.1, CCDS44089.1	1p36.11	2012-11-30	2012-11-29	2012-11-29	ENSG00000117640	ENSG00000117640			28836	protein-coding gene	gene with protein product			"family with sequence similarity 54, member B"	FAM54B		8619474, 9110174	Standard	NM_019557		Approved		uc001bkq.4	Q9H019	OTTHUMG00000007377	ENST00000374301.3:c.814A>G	chr1.hg19:g.26158452A>G	ENSP00000363419:p.Ile272Val	145.0	0.0		128.0	9.0	NM_001099625	A6NCB4|B7WNV5|D3DPJ4|Q63HP1|Q7Z2S7|Q9NUI7	Missense_Mutation	SNP	ENST00000374301.3	hg19	CCDS41284.1	.	.	.	.	.	.	.	.	.	.	A	25.6	4.649922	0.87958	.	.	ENSG00000117640	ENST00000374303;ENST00000524618;ENST00000374307;ENST00000374301;ENST00000374300	T;T;T;T	0.59502	0.4;0.26;0.4;0.4	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.66446	0.2790	L	0.29908	0.895	0.80722	D	1	D;D;D	0.59357	0.985;0.978;0.963	D;D;P	0.67725	0.952;0.953;0.898	T	0.69198	-0.5208	10	0.72032	D	0.01	-7.8421	16.8222	0.85835	1.0:0.0:0.0:0.0	.	305;260;272	B4DRE5;Q9H019-3;Q9H019	.;.;FA54B_HUMAN	V	272;175;260;272;272	ENSP00000363421:I272V;ENSP00000363426:I260V;ENSP00000363419:I272V;ENSP00000363418:I272V	ENSP00000363418:I272V	I	+	1	0	FAM54B	26031039	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	8.448000	0.90335	2.371000	0.80710	0.533000	0.62120	ATC	.	.		0.423	MTFR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019319.1	NM_019557		G	26158452	A	G	26158452	3	3	237	1	0	0	0	0	1	0	0	0	5591	449	16	2	836	2	FAM54B	1	26158452	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	2936408	26158452	223092169	9	32915										
PIK3R3	8503	hgsc.bcm.edu	37	chr1	46531740	46531740	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	accaacctgggatgttctagTatattcttcatacagcctat	6	10	3	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:46531740T>C	ENST00000262741.5	-	5	1296	c.607A>G	c.(607-609)Act>Gct	p.T203A	PIK3R3_ENST00000540385.1_Missense_Mutation_p.T249A|PIK3R3_ENST00000420542.1_Missense_Mutation_p.T203A|PIK3R3_ENST00000354242.4_Missense_Mutation_p.T203A|PIK3R3_ENST00000423209.1_Missense_Mutation_p.T203A|PIK3R3_ENST00000372006.1_Missense_Mutation_p.T203A|PIK3R3_ENST00000340332.6_Missense_Mutation_p.T167A	NM_003629.3	NP_003620.3	Q92569	P55G_HUMAN	phosphoinositide-3-kinase, regulatory subunit 3 (gamma)	203					insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)			endometrium(1)|large_intestine(5)|lung(6)|prostate(2)	14	Acute lymphoblastic leukemia(166;0.155)				Isoprenaline(DB01064)	GATGTTCTAGTATATTCTTCA	0.318																																					p.T203A		Atlas-SNP	.											.	PIK3R3	41	.	0			c.A607G						.						176	161	166					1																	46531740		2203	4292	6495	SO:0001583	missense	8503	exon6			TTCTAGTATATTC	BC021622	CCDS529.1	1p34.1	2013-02-14	2008-02-04		ENSG00000117461	ENSG00000117461		"SH2 domain containing"	8981	protein-coding gene	gene with protein product		606076				9524259	Standard	NM_003629		Approved	p55	uc001cpb.4	Q92569	OTTHUMG00000008096	ENST00000262741.5:c.607A>G	chr1.hg19:g.46531740T>C	ENSP00000262741:p.Thr203Ala	75.0	0.0		116.0	14.0	NM_001114172	B2R9C1|D3DQ12|O60482|Q5T4P1|Q5T4P2	Missense_Mutation	SNP	ENST00000262741.5	hg19	CCDS529.1	.	.	.	.	.	.	.	.	.	.	T	17.48	3.400605	0.62177	.	.	ENSG00000117461	ENST00000372006;ENST00000262741;ENST00000420542;ENST00000354242;ENST00000340332;ENST00000540385;ENST00000423209;ENST00000425892	T;T;T;T;D;T;T;T	0.85556	-1.29;-1.29;-1.29;-1.43;-2.0;-1.27;-1.43;0.97	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.82199	0.4985	L	0.58583	1.82	0.80722	D	1	B;P;B;B	0.36974	0.081;0.576;0.06;0.39	B;B;B;B	0.32928	0.021;0.155;0.031;0.054	T	0.83341	-0.0008	10	0.52906	T	0.07	.	15.4406	0.75178	0.0:0.0:0.0:1.0	.	249;236;203;203	F6TDL0;Q7Z3W2;Q92569-2;Q92569	.;.;.;P55G_HUMAN	A	203;203;203;203;167;249;203;203	ENSP00000361075:T203A;ENSP00000262741:T203A;ENSP00000412546:T203A;ENSP00000346188:T203A;ENSP00000342484:T167A;ENSP00000439913:T249A;ENSP00000391431:T203A;ENSP00000416647:T203A	ENSP00000262741:T203A	T	-	1	0	PIK3R3	46304327	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	7.698000	0.84413	2.055000	0.61198	0.477000	0.44152	ACT	.	.		0.318	PIK3R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022171.1	NM_003629		C	46531740	T	C	46531740	3	2	237	1	0	0	0	0	1	0	0	0	11929	1638	57	2	802	2	PIK3R3	1	46531740	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	20373288	46531740	202718881	10	32916										
ZCCHC11	23318	hgsc.bcm.edu	37	chr1	52943444	52943444	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gttaaaatatcttgtatccgTacacatatgacatattcctc	4	9	1	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:52943444T>A	ENST00000371544.3	-	12	2221	c.1959A>T	c.(1957-1959)gtA>gtT	p.V653V	ZCCHC11_ENST00000257177.4_Silent_p.V653V|ZCCHC11_ENST00000371541.1_5'UTR	NM_001009881.2|NM_015269.2	NP_001009881.1|NP_056084.1	Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11	653	PAP-associated 1.				cytokine production (GO:0001816)|miRNA catabolic process (GO:0010587)|miRNA metabolic process (GO:0010586)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|pre-miRNA processing (GO:0031054)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|RNA 3'-end processing (GO:0031123)|stem cell maintenance (GO:0019827)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(17)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	58						CTTGTATCCGTACACATATGA	0.358																																					p.V653V		Atlas-SNP	.											.	ZCCHC11	151	.	0			c.A1959T						.						107	108	108					1																	52943444		2203	4300	6503	SO:0001819	synonymous_variant	23318	exon12			TATCCGTACACAT	D83776	CCDS30715.1, CCDS30716.1	1p32.3	2014-03-05			ENSG00000134744	ENSG00000134744		"Zinc fingers, CCHC domain containing"	28981	protein-coding gene	gene with protein product	"TUTase4"	613692				8724849, 12239557	Standard	NM_015269		Approved	KIAA0191, PAPD3, TUT4	uc001cty.2	Q5TAX3	OTTHUMG00000008200	ENST00000371544.3:c.1959A>T	chr1.hg19:g.52943444T>A		103.0	0.0		122.0	11.0	NM_015269	A2RRP0|B7Z8J5|D3DQ35|Q12764|Q5TAX2|Q5TAX4|Q86XZ3	Silent	SNP	ENST00000371544.3	hg19	CCDS30716.1																																																																																			.	.		0.358	ZCCHC11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022462.1	XM_038288		A	52943444	T	A	52943444	2	1	237	1	0	0	0	0	0	0	0	1	17595	1625	57	4		4	ZCCHC11	1	52943444	Silent	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	6411704	52943444	196307177	11	32917										
TMEM48	55706	hgsc.bcm.edu	37	chr1	54272140	54272140	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ctatttaacacttttggaagGcactcatctgacccttctgc	6	12	3	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:54272140G>T	ENST00000371429.3	-	9	1540	c.942C>A	c.(940-942)tgC>tgA	p.C314*	NDC1_ENST00000537333.1_5'UTR|NDC1_ENST00000234725.8_Nonsense_Mutation_p.C199*|NDC1_ENST00000540001.1_Nonsense_Mutation_p.C314*	NM_001168551.1|NM_018087.4	NP_001162023.1|NP_060557.3	Q9BTX1	NDC1_HUMAN	NDC1 transmembrane nucleoporin	314					mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore distribution (GO:0031081)|protein transport (GO:0015031)|spermatogenesis (GO:0007283)|synapsis (GO:0007129)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)										CTTTTGGAAGGCACTCATCTG	0.348																																					p.C314X		Atlas-SNP	.											.	TMEM48	47	.	0			c.C942A						.						97	96	96					1																	54272140		2203	4300	6503	SO:0001587	stop_gained	55706	exon9			TGGAAGGCACTCA	AL354613	CCDS583.1	1p32.3	2014-01-28	2013-05-23	2013-05-23	ENSG00000058804	ENSG00000058804			25525	protein-coding gene	gene with protein product	"nuclear division cycle 1 homolog (S. cerevisiae)"	610115	"transmembrane protein 48"	TMEM48		16779818, 12958361	Standard	NR_033142		Approved	FLJ10407, NET3		Q9BTX1	OTTHUMG00000008073	ENST00000371429.3:c.942C>A	chr1.hg19:g.54272140G>T	ENSP00000360483:p.Cys314*	87.0	0.0		92.0	4.0	NM_018087	B4DHA3|B4DQQ5|G3XA81|Q8NB76|Q9H9T6|Q9NSG3|Q9NSG4|Q9NVZ7	Nonsense_Mutation	SNP	ENST00000371429.3	hg19	CCDS583.1	.	.	.	.	.	.	.	.	.	.	G	38	6.979130	0.97979	.	.	ENSG00000058804	ENST00000371429;ENST00000360494;ENST00000540001;ENST00000234725	.	.	.	5.04	4.12	0.48240	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09843	T	0.71	.	10.3319	0.43827	0.1602:0.0:0.8398:0.0	.	.	.	.	X	314;314;314;199	.	ENSP00000234725:C199X	C	-	3	2	TMEM48	54044728	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.073000	0.41519	1.352000	0.45808	0.579000	0.79373	TGC	.	.		0.348	NDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022101.1	NM_018087		T	54272140	G	T	54272140	4	4	237	1	0	0	0	0	0	1	0	0	16187	1195	42	3	1122	3	TMEM48	1	54272140	Nonsense_Mutation	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	1328696	54272140	194978481	12	32918										
C1orf175	374977	hgsc.bcm.edu	37	chr1	55130862	55130862	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gcctttgatgaagtgacctcAtgcctggtgaaggtgccaga	13	9	1	5			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:55130862A>G	ENST00000421030.2	+	4	1539	c.1254A>G	c.(1252-1254)tcA>tcG	p.S418S	MROH7_ENST00000409996.1_5'UTR|MROH7_ENST00000395690.2_Silent_p.S418S|MROH7_ENST00000339553.5_Silent_p.S418S|MROH7_ENST00000454855.2_5'UTR|MROH7-TTC4_ENST00000414150.2_Silent_p.S418S|MROH7_ENST00000545244.1_5'UTR	NM_001039464.2	NP_001034553	Q68CQ1	MROH7_HUMAN	maestro heat-like repeat family member 7	418						extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											AAGTGACCTCATGCCTGGTGA	0.527																																					p.S418S		Atlas-SNP	.											.	.	.	.	0			c.A1254G						.						104	108	107					1																	55130862		2116	4236	6352	SO:0001819	synonymous_variant	374977	exon4			GACCTCATGCCTG	AL832492	CCDS41342.2	1p32.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000184313	ENSG00000184313		"maestro heat-like repeat containing"	24802	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 175", "HEAT repeat containing 8"	C1orf175, HEATR8		12477932	Standard	NM_001039464		Approved	FLJ46354	uc010ooe.1	Q68CQ1	OTTHUMG00000009890	ENST00000421030.2:c.1254A>G	chr1.hg19:g.55130862A>G		256.0	1.0		361.0	145.0	NM_001039464	A0AUX8|Q5TA99|Q6ZP40|Q6ZRH6|Q8N311|Q8NA14	Silent	SNP	ENST00000421030.2	hg19	CCDS41342.2																																																																																			.	.		0.527	MROH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346978.1	NM_198547		G	55130862	A	G	55130862	2	3	237	1	0	0	0	0	0	0	0	1	2018	204	8	2		2	C1orf175	1	55130862	Silent	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	858722	55130862	194119759	13	32919										
LEPR	3953	hgsc.bcm.edu	37	chr1	66081748	66081748	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gatatgtgataaaccatcatActtcctgcaatggaacatgg	8	8	1	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:66081748A>T	ENST00000349533.6	+	15	2238	c.2053A>T	c.(2053-2055)Act>Tct	p.T685S	LEPR_ENST00000371059.3_Missense_Mutation_p.T685S|LEPR_ENST00000344610.8_Missense_Mutation_p.T685S|LEPR_ENST00000406510.3_Intron|LEPR_ENST00000371058.1_Missense_Mutation_p.T685S|LEPR_ENST00000371060.3_Missense_Mutation_p.T685S	NM_002303.5	NP_002294.2	O15243	OBRG_HUMAN	leptin receptor	0					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(22)|skin(2)	36				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		AAACCATCATACTTCCTGCAA	0.413																																					p.T685S		Atlas-SNP	.											.	LEPR	284	.	0			c.A2053T						.						139	125	130					1																	66081748		2203	4300	6503	SO:0001583	missense	3953	exon15			CATCATACTTCCT	U43168	CCDS631.1, CCDS30740.1, CCDS30741.1, CCDS55604.1	1p31	2014-09-17			ENSG00000116678	ENSG00000116678		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6554	protein-coding gene	gene with protein product		601007				8548812, 8812446	Standard	NM_001003680		Approved	OBR, CD295	uc001dci.3	P48357	OTTHUMG00000009115	ENST00000349533.6:c.2053A>T	chr1.hg19:g.66081748A>T	ENSP00000330393:p.Thr685Ser	161.0	0.0		257.0	13.0	NM_001003680	Q6FHL5	Missense_Mutation	SNP	ENST00000349533.6	hg19	CCDS631.1	.	.	.	.	.	.	.	.	.	.	A	14.45	2.539579	0.45176	.	.	ENSG00000116678	ENST00000344610;ENST00000349533;ENST00000371060;ENST00000371059;ENST00000371058	T;T;T;T;T	0.38887	1.11;1.11;1.11;1.11;1.11	5.37	5.37	0.77165	Fibronectin, type III (2);	0.230349	0.44483	D	0.000451	T	0.53481	0.1799	M	0.75447	2.3	0.80722	D	1	D;D;D	0.69078	0.994;0.997;0.991	D;D;D	0.74348	0.963;0.983;0.919	T	0.52555	-0.8560	10	0.26408	T	0.33	-18.9545	15.3683	0.74541	1.0:0.0:0.0:0.0	.	685;685;685	P48357;P48357-2;P48357-3	LEPR_HUMAN;.;.	S	685	ENSP00000340884:T685S;ENSP00000330393:T685S;ENSP00000360099:T685S;ENSP00000360098:T685S;ENSP00000360097:T685S	ENSP00000340884:T685S	T	+	1	0	LEPR	65854336	0.978000	0.34361	0.076000	0.20297	0.045000	0.14185	6.384000	0.73177	2.045000	0.60652	0.533000	0.62120	ACT	.	.		0.413	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303		T	66081748	A	T	66081748	3	4	237	1	0	0	0	0	1	0	0	0	8737	391	14	4	2103	4	LEPR	1	66081748	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	10950886	66081748	183168873	14	32920										
ZNF326	284695	hgsc.bcm.edu	37	chr1	90473063	90473063	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	aatagccttgactctttcggAggtagaaaccagggcgggtc	13	9	1	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:90473063A>T	ENST00000340281.4	+	5	512	c.369A>T	c.(367-369)ggA>ggT	p.G123G	ZNF326_ENST00000455342.2_Intron|ZNF326_ENST00000370447.3_Intron	NM_182976.2	NP_892021.1	Q5BKZ1	ZN326_HUMAN	zinc finger protein 326	123	Gly-rich.|Mediates transcriptional activation. {ECO:0000250}.				mRNA processing (GO:0006397)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, elongation (GO:0032784)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	DBIRD complex (GO:0044609)|nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(7)|ovary(1)	25		all_lung(203;0.0116)|Lung NSC(277;0.0417)		all cancers(265;0.00728)|Epithelial(280;0.0265)		ACTCTTTCGGAGGTAGAAACC	0.498																																					p.G123G		Atlas-SNP	.											.	ZNF326	60	.	0			c.A369T						.						139	148	145					1																	90473063		2203	4300	6503	SO:0001819	synonymous_variant	284695	exon5			TTTCGGAGGTAGA	BC013102	CCDS727.1, CCDS728.1	1p22	2012-04-19			ENSG00000162664	ENSG00000162664		"Zinc fingers, C2H2-type"	14104	protein-coding gene	gene with protein product	"ZNF-protein interacting with nuclear mRNPs and DBC1"	614601				22446626	Standard	NM_182976		Approved	Zfp326, ZAN75, FLJ20403, ZIRD	uc001dnq.2	Q5BKZ1	OTTHUMG00000010675	ENST00000340281.4:c.369A>T	chr1.hg19:g.90473063A>T		151.0	0.0		228.0	19.0	NM_182976	A8MYX1|B4DLN0|B4E179|Q5VW93|Q5VW94|Q5VW96|Q5VW97|Q6NSA2|Q7Z638|Q7Z6C2	Silent	SNP	ENST00000340281.4	hg19	CCDS727.1																																																																																			.	.		0.498	ZNF326-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029428.2	NM_181781		T	90473063	A	T	90473063	2	4	237	1	0	0	0	0	0	0	0	1	17861	291	11	4		4	ZNF326	1	90473063	Silent	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	24391315	90473063	158777558	15	32921										
FRRS1	391059	hgsc.bcm.edu	37	chr1	100174554	100174554	+	3'UTR	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gtttgatgataattatcactTggcctgcaaaagccaaggtc	9	8	1	2	rs553200347		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:100174554T>A	ENST00000414213.1	-	0	2410				FRRS1_ENST00000287474.5_Missense_Mutation_p.Q594L|FRRS1_ENST00000492943.1_5'Flank			Q6ZNA5	FRRS1_HUMAN	ferric-chelate reductase 1							integral component of membrane (GO:0016021)	ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(12)|pancreas(1)|skin(1)|urinary_tract(1)	26		all_epithelial(167;2.09e-06)|all_lung(203;0.000435)|Lung NSC(277;0.00201)		Epithelial(280;0.0718)|all cancers(265;0.126)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.206)		AATTATCACTTGGCCTGCAAA	0.403																																					p.Q594L		Atlas-SNP	.											.	FRRS1	50	.	0			c.A1781T						.						73	74	74					1																	100174554		2203	4300	6503	SO:0001624	3_prime_UTR_variant	391059	exon17			ATCACTTGGCCTG	AK131302	CCDS30780.1	1p21.3	2009-11-30	2006-02-22	2006-02-22	ENSG00000156869	ENSG00000156869			27622	protein-coding gene	gene with protein product		611578	"stromal cell derived factor receptor 2 homolog (mouse)"	SDFR2			Standard	NM_001013660		Approved	SDR2	uc001dsh.1	Q6ZNA5	OTTHUMG00000010768	ENST00000414213.1:c.*30A>T	chr1.hg19:g.100174554T>A		77.0	0.0		120.0	48.0	NM_001013660	A6NLN7	Missense_Mutation	SNP	ENST00000414213.1	hg19		.	.	.	.	.	.	.	.	.	.	T	12.89	2.074439	0.36566	.	.	ENSG00000156869	ENST00000287474	.	.	.	5.67	-0.88	0.10610	.	3.411090	0.00597	N	0.000362	T	0.12135	0.0295	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.22103	-1.0226	8	0.87932	D	0	24.6037	3.05	0.06166	0.2873:0.2354:0.0:0.4773	.	594	Q6ZNA5-2	.	L	594	.	ENSP00000287474:Q594L	Q	-	2	0	FRRS1	99947142	0.005000	0.15991	0.002000	0.10522	0.062000	0.15995	0.105000	0.15333	-0.415000	0.07484	-0.341000	0.08007	CAA	.	.		0.403	FRRS1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001013660		A	100174554	T	A	100174554	1	1	237	0	1	0	0	0	0	0	0	0	6068	1812	63	4		4	FRRS1	1	100174554	3'UTR	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	9701491	100174554	149076067	16	32922										
SLC6A17	388662	hgsc.bcm.edu	37	chr1	110709579	110709579	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	agaacagcaaagtgacccagCgtgagcacagcagtgagcat	12	10	0	4			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:110709579C>A	ENST00000331565.4	+	2	513	c.28C>A	c.(28-30)Cgt>Agt	p.R10S	RP5-1028L10.1_ENST00000430098.1_RNA|RP5-1028L10.1_ENST00000418579.1_RNA|RP5-1028L10.1_ENST00000443008.1_RNA	NM_001010898.2	NP_001010898.1	Q9H1V8	S6A17_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 17	10					alanine transport (GO:0032328)|glycine transport (GO:0015816)|leucine transport (GO:0015820)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|synaptic vesicle (GO:0008021)	neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37		all_cancers(81;9.9e-06)|all_epithelial(167;3.24e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0282)|Epithelial(280;0.0372)|all cancers(265;0.0378)|Colorectal(144;0.0438)|LUSC - Lung squamous cell carcinoma(189;0.151)|COAD - Colon adenocarcinoma(174;0.151)		AGTGACCCAGCGTGAGCACAG	0.577																																					p.R10S		Atlas-SNP	.											.	SLC6A17	86	.	0			c.C28A						.						58	52	54					1																	110709579		2203	4300	6503	SO:0001583	missense	388662	exon2			ACCCAGCGTGAGC		CCDS30799.1	1p13.2	2013-07-19	2013-07-19		ENSG00000197106	ENSG00000197106		"Solute carriers"	31399	protein-coding gene	gene with protein product		610299	"solute carrier family 6 (neurotransmitter transporter), member 17", "solute carrier family 6, member 17"				Standard	NM_001010898		Approved		uc009wfq.3	Q9H1V8	OTTHUMG00000011761	ENST00000331565.4:c.28C>A	chr1.hg19:g.110709579C>A	ENSP00000330199:p.Arg10Ser	296.0	0.0		366.0	163.0	NM_001010898	A6NEA8|A8K1R7|B9EIR5|Q5T5Q9	Missense_Mutation	SNP	ENST00000331565.4	hg19	CCDS30799.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.149428	0.78001	.	.	ENSG00000197106	ENST00000331565;ENST00000450985	T	0.75589	-0.95	4.31	4.31	0.51392	.	0.060060	0.64402	D	0.000004	T	0.67297	0.2878	M	0.67397	2.05	0.49582	D	0.999809	P	0.43287	0.802	B	0.41466	0.358	T	0.73704	-0.3899	10	0.51188	T	0.08	.	16.9598	0.86269	0.0:1.0:0.0:0.0	.	10	Q9H1V8	S6A17_HUMAN	S	10	ENSP00000330199:R10S	ENSP00000330199:R10S	R	+	1	0	SLC6A17	110511102	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.457000	0.53007	2.221000	0.72209	0.563000	0.77884	CGT	.	.		0.577	SLC6A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032550.2	XM_371280		A	110709579	C	A	110709579	3	1	237	1	0	0	0	0	1	0	0	0	14695	768	27	1	30	1	SLC6A17	1	110709579	Missense_Mutation	SNP	C	TCGA-ED-A459-01A-11D-A25V-10	10535025	110709579	138541042	17	32923										
MTMR11	10903	hgsc.bcm.edu	37	chr1	149904191	149904191	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	catcgtgttccttccagggcTgaaagccatttatcctcagc	8	13	1	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:149904191T>A	ENST00000439741.2	-	11	1267	c.1017A>T	c.(1015-1017)tcA>tcT	p.S339S	MTMR11_ENST00000406732.3_Silent_p.S311S|MTMR11_ENST00000361405.6_Intron|MTMR11_ENST00000369140.3_Silent_p.S267S|MTMR11_ENST00000492824.1_5'UTR	NM_001145862.1	NP_001139334.1	A4FU01	MTMRB_HUMAN	myotubularin related protein 11	339	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.						phosphatase activity (GO:0016791)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(13)|prostate(2)|stomach(1)|urinary_tract(4)	34	Breast(34;0.0009)|Ovarian(49;0.0377)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)			CTTCCAGGGCTGAAAGCCATT	0.443																																					p.S339S		Atlas-SNP	.											.	MTMR11	136	.	0			c.A1017T						.						175	167	170					1																	149904191		2203	4300	6503	SO:0001819	synonymous_variant	10903	exon11			CAGGGCTGAAAGC	AK097000	CCDS72901.1, CCDS72902.1	1q12-q21	2011-06-09			ENSG00000014914	ENSG00000014914		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	24307	protein-coding gene	gene with protein product	"cisplatin resistance associated"					12495846	Standard	NM_181873		Approved	CRA	uc001etl.4	A4FU01	OTTHUMG00000012207	ENST00000439741.2:c.1017A>T	chr1.hg19:g.149904191T>A		99.0	0.0		162.0	13.0	NM_001145862	B3KUE4|B4DJI6|B4DQF5|B4E3Q6|Q3ZCP7|Q5SZ62|Q6P2Q8|Q99752|Q99753	Silent	SNP	ENST00000439741.2	hg19	CCDS53360.1																																																																																			.	.		0.443	MTMR11-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_181873		A	149904191	T	A	149904191	2	1	237	1	0	0	0	0	0	0	0	1	9949	1567	55	4		4	MTMR11	1	149904191	Silent	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	39194612	149904191	99346430	18	32924										
ADAM15	8751	hgsc.bcm.edu	37	chr1	155030505	155030505	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ctcctatgcccagcagtgccAgtcactttggggacctggag	12	13	1	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:155030505A>T	ENST00000356955.2	+	14	1696	c.1595A>T	c.(1594-1596)cAg>cTg	p.Q532L	ADAM15_ENST00000447332.3_Missense_Mutation_p.Q516L|ADAM15_ENST00000271836.6_Missense_Mutation_p.Q532L|ADAM15_ENST00000359280.4_Missense_Mutation_p.Q532L|ADAM15_ENST00000472434.1_3'UTR|ADAM15_ENST00000368413.1_Missense_Mutation_p.Q238L|ADAM15_ENST00000368412.3_Missense_Mutation_p.Q532L|ADAM15_ENST00000355956.2_Missense_Mutation_p.Q532L|ADAM15_ENST00000368410.2_Missense_Mutation_p.Q238L|ADAM15_ENST00000449910.2_Missense_Mutation_p.Q532L|ADAM15_ENST00000360674.4_Missense_Mutation_p.Q532L|ADAM15_ENST00000531455.1_Missense_Mutation_p.Q542L	NM_207197.2	NP_997080.1	Q13444	ADA15_HUMAN	ADAM metallopeptidase domain 15	532	Cys-rich.				angiogenesis (GO:0001525)|cardiac epithelial to mesenchymal transition (GO:0060317)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of receptor binding (GO:1900121)|protein kinase C signaling (GO:0070528)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(5)|urinary_tract(1)	39	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)			CAGCAGTGCCAGTCACTTTGG	0.637																																					p.Q542L		Atlas-SNP	.											.	ADAM15	92	.	0			c.A1625T						.						66	65	65					1																	155030505		2203	4300	6503	SO:0001583	missense	8751	exon14			AGTGCCAGTCACT	U46005	CCDS1084.1, CCDS1085.1, CCDS1086.1, CCDS1087.1, CCDS1088.1, CCDS44236.1, CCDS58031.1, CCDS58032.1, CCDS60282.1	1q21.3	2008-02-05	2007-06-04		ENSG00000143537	ENSG00000143537		"ADAM metallopeptidase domain containing"	193	protein-coding gene	gene with protein product	"metargidin"	605548	"a disintegrin and metalloproteinase domain 15 (metargidin)"			9516430	Standard	NM_003815		Approved	MDC15	uc001fgr.2	Q13444	OTTHUMG00000013898	ENST00000356955.2:c.1595A>T	chr1.hg19:g.155030505A>T	ENSP00000349436:p.Gln532Leu	80.0	0.0		69.0	5.0	NM_001261464	B3KQU5|B4DLB5|B4DMH8|E9PN65|Q13493|Q53XQ0|Q5SR68|Q5SR69|Q6R267|Q71S61|Q71S62|Q71S63|Q71S64|Q71S65|Q71S66|Q71S67|Q71S68|Q71S69|Q96C78|U3KQL5	Missense_Mutation	SNP	ENST00000356955.2	hg19	CCDS1087.1	.	.	.	.	.	.	.	.	.	.	A	13.20	2.167177	0.38315	.	.	ENSG00000143537	ENST00000356955;ENST00000449910;ENST00000359280;ENST00000360674;ENST00000368412;ENST00000355956;ENST00000368410;ENST00000271836;ENST00000368413;ENST00000531455	T;T;T;T;T;T;T;T;T;T	0.23348	1.91;1.91;1.91;1.91;1.91;1.91;1.91;1.91;1.91;1.91	5.4	4.28	0.50868	ADAM, cysteine-rich (2);	0.000000	0.42548	D	0.000683	T	0.32346	0.0826	M	0.76328	2.33	0.45607	D	0.998546	D;D;B;D;P;D;D;D;D;D;D	0.89917	0.999;0.999;0.198;0.995;0.741;1.0;1.0;1.0;0.99;0.996;1.0	D;D;B;D;P;D;D;D;D;D;D	0.87578	0.988;0.988;0.192;0.996;0.622;0.979;0.979;0.986;0.92;0.998;0.988	T	0.15925	-1.0420	10	0.26408	T	0.33	.	7.8003	0.29170	0.9081:0.0:0.0919:0.0	.	542;549;516;532;532;532;532;532;532;532;529	E9PN65;B7Z390;B4DMH8;Q13444-10;Q13444-2;Q13444-4;Q13444-5;Q13444-3;Q13444-9;Q13444;Q59GF2	.;.;.;.;.;.;.;.;.;ADA15_HUMAN;.	L	532;532;532;532;532;532;238;532;238;542	ENSP00000349436:Q532L;ENSP00000403843:Q532L;ENSP00000352226:Q532L;ENSP00000353892:Q532L;ENSP00000357397:Q532L;ENSP00000348227:Q532L;ENSP00000357395:Q238L;ENSP00000271836:Q532L;ENSP00000357398:Q238L;ENSP00000432927:Q542L	ENSP00000271836:Q532L	Q	+	2	0	ADAM15	153297129	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.514000	0.45503	1.075000	0.40932	0.533000	0.62120	CAG	.	.		0.637	ADAM15-019	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387168.1	NM_003815		T	155030505	A	T	155030505	3	4	237	1	0	0	0	0	1	0	0	0	237	188	7	4	1649	4	ADAM15	1	155030505	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	5126314	155030505	94220116	19	32925										
ARHGEF2	9181	hgsc.bcm.edu	37	chr1	155931649	155931649	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	cgtccacattggacagcagcTccttcactagccccagtgct	8	16	1	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:155931649T>A	ENST00000361247.4	-	11	1370	c.1271A>T	c.(1270-1272)gAg>gTg	p.E424V	ARHGEF2_ENST00000462460.2_Missense_Mutation_p.E469V|ARHGEF2_ENST00000313667.4_Missense_Mutation_p.E423V|ARHGEF2_ENST00000368316.1_Missense_Mutation_p.E396V|ARHGEF2_ENST00000368315.4_Missense_Mutation_p.E425V|ARHGEF2_ENST00000477754.2_Intron|ARHGEF2_ENST00000313695.7_Missense_Mutation_p.E396V	NM_001162383.1|NM_001162384.1	NP_001155855.1|NP_001155856.1	Q92974	ARHG2_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 2	424	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin filament organization (GO:0007015)|apoptotic signaling pathway (GO:0097190)|cell morphogenesis (GO:0000902)|cellular hyperosmotic response (GO:0071474)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to tumor necrosis factor (GO:0071356)|establishment of mitotic spindle orientation (GO:0000132)|innate immune response (GO:0045087)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress (GO:1902219)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of necroptotic process (GO:0060546)|negative regulation of neurogenesis (GO:0050768)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cell proliferation (GO:0042127)|regulation of Rho protein signal transduction (GO:0035023)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)|vesicle (GO:0031982)	microtubule binding (GO:0008017)|Rac GTPase binding (GO:0048365)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho GTPase binding (GO:0017048)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(4)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|skin(2)	40	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					GGACAGCAGCTCCTTCACTAG	0.607																																					p.E424V	Melanoma(178;35 2768 6610 28839)	Atlas-SNP	.											.	ARHGEF2	81	.	0			c.A1271T						.						80	78	79					1																	155931649		2203	4300	6503	SO:0001583	missense	9181	exon11			AGCAGCTCCTTCA	AB014551	CCDS1125.1, CCDS53375.1, CCDS53376.1	1q21-q22	2013-01-10	2009-06-12		ENSG00000116584	ENSG00000116584		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	682	protein-coding gene	gene with protein product		607560	"rho/rac guanine nucleotide exchange factor (GEF) 2"			9857026, 9734811	Standard	NM_004723		Approved	LFP40, GEF-H1, KIAA0651, P40	uc001fmt.2	Q92974	OTTHUMG00000017464	ENST00000361247.4:c.1271A>T	chr1.hg19:g.155931649T>A	ENSP00000354837:p.Glu424Val	231.0	0.0		312.0	35.0	NM_001162383	D3DVA6|O75142|Q15079|Q5VY92|Q8TDA3|Q8WUG4|Q9H023	Missense_Mutation	SNP	ENST00000361247.4	hg19	CCDS53376.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.326302	0.81580	.	.	ENSG00000116584	ENST00000313695;ENST00000361247;ENST00000368315;ENST00000368316;ENST00000435736;ENST00000543433;ENST00000313667	T;T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17;-0.17	4.86	4.86	0.63082	Dbl homology (DH) domain (5);	0.138147	0.33075	N	0.005303	T	0.73682	0.3618	M	0.83603	2.65	0.46061	D	0.998841	P;P;D;P	0.67145	0.789;0.87;0.996;0.923	P;P;D;P	0.68039	0.643;0.758;0.955;0.644	T	0.78677	-0.2111	10	0.72032	D	0.01	-25.5843	12.7091	0.57080	0.0:0.0:0.0:1.0	.	469;468;424;423	B7Z977;D3DVA5;Q92974;Q92974-2	.;.;ARHG2_HUMAN;.	V	396;424;425;396;469;397;423	ENSP00000315325:E396V;ENSP00000354837:E424V;ENSP00000357298:E425V;ENSP00000357299:E396V;ENSP00000314787:E423V	ENSP00000314787:E423V	E	-	2	0	ARHGEF2	154198273	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	5.540000	0.67205	2.162000	0.67917	0.482000	0.46254	GAG	.	.		0.607	ARHGEF2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046204.2	NM_004723		A	155931649	T	A	155931649	3	1	237	1	0	0	0	0	1	0	0	0	903	1551	54	4	1737	4	ARHGEF2	1	155931649	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	901144	155931649	93318972	20	32926										
SMG5	23381	hgsc.bcm.edu	37	chr1	156230352	156230352	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gtcctctgggagcagaaggcTagaggggaggtcaggcagtt	18	7	2	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:156230352T>A	ENST00000361813.5	-	15	2317	c.2173A>T	c.(2173-2175)Agc>Tgc	p.S725C	SMG5_ENST00000368267.5_Intron	NM_015327.2	NP_056142.2	Q9UPR3	SMG5_HUMAN	SMG5 nonsense mediated mRNA decay factor	725					gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	protein phosphatase 2A binding (GO:0051721)			NS(1)|breast(3)|endometrium(8)|kidney(2)|large_intestine(7)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	48	Hepatocellular(266;0.158)					AGCAGAAGGCTAGAGGGGAGG	0.577																																					p.S725C		Atlas-SNP	.											.	SMG5	98	.	0			c.A2173T						.						83	70	74					1																	156230352		2203	4300	6503	SO:0001583	missense	23381	exon15			GAAGGCTAGAGGG	AB029012	CCDS1137.1	1q21	2013-07-02	2013-07-02		ENSG00000198952	ENSG00000198952			24644	protein-coding gene	gene with protein product	"EST1 telomerase component homolog B (S. cerevisiae)"	610962	"smg-5 homolog, nonsense mediated mRNA decay factor (C. elegans)"			12676087, 12699629	Standard	NM_015327		Approved	KIAA1089, LPTS-RP1, LPTSRP1, RP11-54H19.7, SMG-5, EST1B	uc001foc.4	Q9UPR3	OTTHUMG00000017491	ENST00000361813.5:c.2173A>T	chr1.hg19:g.156230352T>A	ENSP00000355261:p.Ser725Cys	236.0	0.0		289.0	18.0	NM_015327	D3DVB7|Q5QJE7|Q659C7|Q8IXC0|Q8IY09|Q96IJ7	Missense_Mutation	SNP	ENST00000361813.5	hg19	CCDS1137.1	.	.	.	.	.	.	.	.	.	.	T	16.85	3.235373	0.58886	.	.	ENSG00000198952	ENST00000361813	T	0.33865	1.39	5.36	4.23	0.50019	.	0.379369	0.28772	N	0.014192	T	0.20981	0.0505	N	0.22421	0.69	0.80722	D	1	P	0.52061	0.95	P	0.56474	0.799	T	0.05632	-1.0873	10	0.39692	T	0.17	-7.092	6.1766	0.20447	0.1957:0.0:0.1229:0.6813	.	725	Q9UPR3	SMG5_HUMAN	C	725	ENSP00000355261:S725C	ENSP00000355261:S725C	S	-	1	0	SMG5	154496976	0.975000	0.34042	0.965000	0.40720	0.764000	0.43329	0.540000	0.23191	1.047000	0.40274	0.459000	0.35465	AGC	.	.		0.577	SMG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046308.1	NM_015327		A	156230352	T	A	156230352	3	1	237	1	0	0	0	0	1	0	0	0	14811	1522	53	4	909	4	SMG5	1	156230352	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	298703	156230352	93020269	21	32927										
OR6Y1	391112	hgsc.bcm.edu	37	chr1	158517532	158517532	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	atagcggtcaaaggccatgaTagcaagaaggatgtactcag	12	7	2	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:158517532T>A	ENST00000302617.3	-	1	363	c.364A>T	c.(364-366)Atc>Ttc	p.I122F		NM_001005189.1	NP_001005189.1	Q8NGX8	OR6Y1_HUMAN	olfactory receptor, family 6, subfamily Y, member 1	122						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|kidney(1)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30	all_hematologic(112;0.0378)					AAGGCCATGATAGCAAGAAGG	0.463																																					p.I122F		Atlas-SNP	.											.	OR6Y1	73	.	0			c.A364T						.						129	112	117					1																	158517532		2202	4300	6502	SO:0001583	missense	391112	exon1			CCATGATAGCAAG	BK004192	CCDS30899.1	1q23.1	2012-08-09			ENSG00000197532	ENSG00000197532		"GPCR / Class A : Olfactory receptors"	14823	protein-coding gene	gene with protein product				OR6Y2			Standard	NM_001005189		Approved		uc010pil.2	Q8NGX8	OTTHUMG00000019629	ENST00000302617.3:c.364A>T	chr1.hg19:g.158517532T>A	ENSP00000304807:p.Ile122Phe	255.0	0.0		414.0	39.0	NM_001005189	Q6IFS0	Missense_Mutation	SNP	ENST00000302617.3	hg19	CCDS30899.1	.	.	.	.	.	.	.	.	.	.	T	11.38	1.621977	0.28889	.	.	ENSG00000197532	ENST00000302617	T	0.01359	4.98	4.91	3.05	0.35203	GPCR, rhodopsin-like superfamily (1);	0.202846	0.24052	N	0.041990	T	0.00412	0.0013	N	0.16790	0.44	0.09310	N	1	B	0.33413	0.411	B	0.25405	0.06	T	0.49799	-0.8901	10	0.72032	D	0.01	.	8.5055	0.33184	0.0:0.7449:0.0:0.2551	.	122	Q8NGX8	OR6Y1_HUMAN	F	122	ENSP00000304807:I122F	ENSP00000304807:I122F	I	-	1	0	OR6Y1	156784156	0.004000	0.15560	0.007000	0.13788	0.849000	0.48306	1.803000	0.38863	0.780000	0.33566	-0.230000	0.12252	ATC	.	.		0.463	OR6Y1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051844.1	NM_001005189		A	158517532	T	A	158517532	3	1	237	1	0	0	0	0	1	0	0	0	11222	1406	49	4	615	4	OR6Y1	1	158517532	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	2287180	158517532	90733089	22	32928										
F5	2153	hgsc.bcm.edu	37	chr1	169521814	169521814	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ctttgagtgtgtctctgaccTgggctctgataataggaccc	11	10	2	3			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:169521814T>A	ENST00000367797.3	-	8	1478	c.1277A>T	c.(1276-1278)cAg>cTg	p.Q426L	F5_ENST00000367796.3_Missense_Mutation_p.Q426L|F5_ENST00000546081.1_Missense_Mutation_p.Q289L	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	426	F5/8 type A 2.|Plastocyanin-like 3.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	GTCTCTGACCTGGGCTCTGAT	0.343																																					p.Q426L		Atlas-SNP	.											.	F5	301	.	0			c.A1277T						.						123	120	121					1																	169521814		2203	4300	6503	SO:0001583	missense	2153	exon8			CTGACCTGGGCTC	M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.1277A>T	chr1.hg19:g.169521814T>A	ENSP00000356771:p.Gln426Leu	124.0	0.0		185.0	14.0	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	hg19	CCDS1281.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.578911	0.86645	.	.	ENSG00000198734	ENST00000367797;ENST00000367796;ENST00000546081	D;D;D	0.98968	-5.28;-5.28;-5.28	5.65	5.65	0.86999	Cupredoxin (2);	0.000000	0.85682	D	0.000000	D	0.99089	0.9687	M	0.84326	2.69	0.43267	D	0.995219	D	0.76494	0.999	D	0.83275	0.996	D	0.99851	1.1072	9	0.87932	D	0	-14.5758	16.1566	0.81673	0.0:0.0:0.0:1.0	.	426	P12259	FA5_HUMAN	L	426;426;289	ENSP00000356771:Q426L;ENSP00000356770:Q426L;ENSP00000439664:Q289L	ENSP00000356770:Q426L	Q	-	2	0	F5	167788438	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.420000	0.80191	2.268000	0.75426	0.533000	0.62120	CAG	.	.		0.343	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130		A	169521814	T	A	169521814	3	1	237	1	0	0	0	0	1	0	0	0	5350	1580	55	4	5469	4	F5	1	169521814	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	11004282	169521814	79728807	23	32929										
ASPM	259266	hgsc.bcm.edu	37	chr1	197108988	197108988	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gttttagaaattggagttctGaatattgataaatctaaaat	7	2	2	3			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:197108988G>T	ENST00000367409.4	-	4	2191	c.1935C>A	c.(1933-1935)ttC>ttA	p.F645L	ASPM_ENST00000294732.7_Missense_Mutation_p.F645L	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	645					developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						TTGGAGTTCTGAATATTGATA	0.303																																					p.F645L		Atlas-SNP	.											.	ASPM	444	.	0			c.C1935A						.						120	122	121					1																	197108988		2203	4300	6503	SO:0001583	missense	259266	exon4			AGTTCTGAATATT	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"microcephaly, primary autosomal recessive 5", "asp (abnormal spindle)-like, microcephaly associated (Drosophila)"	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.1935C>A	chr1.hg19:g.197108988G>T	ENSP00000356379:p.Phe645Leu	47.0	0.0		44.0	17.0	NM_001206846	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	hg19	CCDS1389.1	.	.	.	.	.	.	.	.	.	.	G	1.589	-0.529545	0.04112	.	.	ENSG00000066279	ENST00000367409;ENST00000294732	T;T	0.56103	0.48;1.76	5.79	-0.136	0.13473	.	0.724164	0.13219	N	0.404517	T	0.18299	0.0439	N	0.02539	-0.55	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.18335	-1.0340	10	0.11485	T	0.65	.	1.9633	0.03390	0.2746:0.1438:0.4079:0.1736	.	645;645	Q4G1H1;Q8IZT6	.;ASPM_HUMAN	L	645	ENSP00000356379:F645L;ENSP00000294732:F645L	ENSP00000294732:F645L	F	-	3	2	ASPM	195375611	0.000000	0.05858	0.015000	0.15790	0.017000	0.09413	-0.419000	0.07071	-0.125000	0.11703	-0.847000	0.03039	TTC	.	.		0.303	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136		T	197108988	G	T	197108988	3	4	237	1	0	0	0	0	1	0	0	0	1056	1281	45	3	8598	3	ASPM	1	197108988	Missense_Mutation	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	27587174	197108988	52141633	24	32930										
CR1	1378	hgsc.bcm.edu	37	chr1	207679331	207679331	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gagtttcccattgggacataTctgaactatgaatgccgccc	9	11	1	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:207679331T>A	ENST00000367049.4	+	2	204	c.204T>A	c.(202-204)taT>taA	p.Y68*	CR1_ENST00000367051.1_Nonsense_Mutation_p.Y68*|CR1_ENST00000367052.1_Nonsense_Mutation_p.Y68*|CR1_ENST00000367050.4_3'UTR|CR1_ENST00000400960.2_Nonsense_Mutation_p.Y68*|CR1_ENST00000367053.1_Nonsense_Mutation_p.Y68*	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	68	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						TTGGGACATATCTGAACTATG	0.468																																					p.Y68X		Atlas-SNP	.											.	CR1	354	.	0			c.T204A						.						172	160	164					1																	207679331		1850	4080	5930	SO:0001587	stop_gained	1378	exon2			GACATATCTGAAC	Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"CD molecules", "Blood group antigens", "Complement system"	2334	protein-coding gene	gene with protein product		120620	"complement component (3b/4b) receptor 1, including Knops blood group system"			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.204T>A	chr1.hg19:g.207679331T>A	ENSP00000356016:p.Tyr68*	332.0	0.0		444.0	33.0	NM_000573	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Nonsense_Mutation	SNP	ENST00000367049.4	hg19	CCDS44308.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.07|14.07	2.427113|2.427113	0.43122|0.43122	.|.	.|.	ENSG00000203710|ENSG00000203710	ENST00000529814|ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000534202;ENST00000367049	.|.	.|.	.|.	4.13|4.13	4.13|4.13	0.48395|0.48395	.|.	.|.	.|.	.|.	.|.	T|.	0.53738|.	0.1815|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.64245|.	-0.6453|.	3|.	.|0.37606	.|T	.|0.19	.|.	9.7248|9.7248	0.40324|0.40324	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|.	.|.	.|.	N|X	44|68	.|.	.|ENSP00000356016:Y68X	I|Y	+|+	2|3	0|2	CR1|CR1	205745954|205745954	0.017000|0.017000	0.18338|0.18338	0.049000|0.049000	0.19019|0.19019	0.001000|0.001000	0.01503|0.01503	3.058000|3.058000	0.49939|0.49939	1.868000|1.868000	0.54150|0.54150	0.482000|0.482000	0.46254|0.46254	ATC|TAT	.	.		0.468	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573		A	207679331	T	A	207679331	4	1	237	1	0	0	0	0	0	1	0	0	3842	1442	50	4	210	4	CR1	1	207679331	Nonsense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	10570343	207679331	41571290	25	32931										
RD3	343035	hgsc.bcm.edu	37	chr1	211652560	211652560	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ccactggcgcgtcagcttgtGggcctcctcttcctgcttca	10	16	3	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:211652560G>T	ENST00000367002.4	-	3	1569	c.406C>A	c.(406-408)Cac>Aac	p.H136N	RD3_ENST00000484910.1_5'UTR	NM_001164688.1|NM_183059.2	NP_001158160.1|NP_898882.1	Q7Z3Z2	RD3_HUMAN	retinal degeneration 3	136					response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)					central_nervous_system(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	10				OV - Ovarian serous cystadenocarcinoma(81;0.00284)|all cancers(67;0.0279)|Epithelial(68;0.0689)		GTCAGCTTGTGGGCCTCCTCT	0.687																																					p.H136N		Atlas-SNP	.											.	RD3	26	.	0			c.C406A						.						23	22	23					1																	211652560		2200	4299	6499	SO:0001583	missense	343035	exon3			GCTTGTGGGCCTC	AY191519	CCDS1498.1	1q32.3	2008-02-05	2006-11-13	2006-11-13	ENSG00000198570	ENSG00000198570			19689	protein-coding gene	gene with protein product		180040	"chromosome 1 open reading frame 36"	C1orf36		12914764	Standard	NM_183059		Approved	LCA12	uc001hin.2	Q7Z3Z2	OTTHUMG00000037002	ENST00000367002.4:c.406C>A	chr1.hg19:g.211652560G>T	ENSP00000355969:p.His136Asn	61.0	0.0		44.0	11.0	NM_183059	A8K595	Missense_Mutation	SNP	ENST00000367002.4	hg19	CCDS1498.1	.	.	.	.	.	.	.	.	.	.	G	14.07	2.426968	0.43122	.	.	ENSG00000198570	ENST00000367002	T	0.09163	3.01	4.33	3.25	0.37280	.	0.489617	0.23369	N	0.048933	T	0.07548	0.0190	N	0.22421	0.69	0.26407	N	0.976325	B	0.23990	0.095	B	0.24155	0.051	T	0.21075	-1.0256	10	0.45353	T	0.12	-16.4574	9.69	0.40123	0.0:0.0:0.5192:0.4808	.	136	Q7Z3Z2	RD3_HUMAN	N	136	ENSP00000355969:H136N	ENSP00000355969:H136N	H	-	1	0	RD3	209719183	1.000000	0.71417	0.975000	0.42487	0.809000	0.45718	3.898000	0.56281	2.131000	0.65755	0.555000	0.69702	CAC	.	.		0.687	RD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089837.1	NM_183059		T	211652560	G	T	211652560	3	4	237	1	0	0	0	0	1	0	0	0	13202	1348	47	3	185	3	RD3	1	211652560	Missense_Mutation	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	3973229	211652560	37598061	26	32932										
USH2A	7399	hgsc.bcm.edu	37	chr1	215972280	215972280	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ttgtacaccactccttcttcTccaccacaacactctaaatc	1	17	3	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:215972280T>C	ENST00000307340.3	-	50	10313	c.9927A>G	c.(9925-9927)ggA>ggG	p.G3309G	USH2A_ENST00000366943.2_Silent_p.G3309G	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3309					hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			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)		CTCCTTCTTCTCCACCACAAC	0.512										HNSCC(13;0.011)																											p.G3309G		Atlas-SNP	.											.	USH2A	1168	.	0			c.A9927G						.						178	151	160					1																	215972280		2203	4300	6503	SO:0001819	synonymous_variant	7399	exon50			TTCTTCTCCACCA	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.9927A>G	chr1.hg19:g.215972280T>C		284.0	0.0		410.0	168.0	NM_206933	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	hg19	CCDS31025.1																																																																																			.	.		0.512	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		C	215972280	T	C	215972280	2	2	237	1	0	0	0	0	0	0	0	1	17051	1538	54	2		2	USH2A	1	215972280	Silent	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	4319720	215972280	33278341	27	32933										
LGALS8	3964	hgsc.bcm.edu	37	chr1	236708178	236708178	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gggagaagaagagagaaataTtacctctttcccatttagtc	9	7	1	4			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:236708178T>C	ENST00000366584.4	+	9	1333	c.767T>C	c.(766-768)aTt>aCt	p.I256T	LGALS8_ENST00000526589.1_Missense_Mutation_p.I298T|LGALS8_ENST00000323938.6_Missense_Mutation_p.I229T|LGALS8_ENST00000450372.2_Missense_Mutation_p.I298T|LGALS8_ENST00000416919.2_Missense_Mutation_p.I239T|RP11-385F5.4_ENST00000433131.1_RNA|LGALS8_ENST00000525042.1_Missense_Mutation_p.I239T|LGALS8_ENST00000526634.1_Missense_Mutation_p.I256T|LGALS8_ENST00000352231.2_Missense_Mutation_p.I298T|LGALS8_ENST00000341872.6_Missense_Mutation_p.I256T|LGALS8_ENST00000527974.1_Missense_Mutation_p.I298T	NM_201544.2	NP_963838.1	O00214	LEG8_HUMAN	lectin, galactoside-binding, soluble, 8	256	Galectin 2. {ECO:0000255|PROSITE- ProRule:PRU00639}.				plasma cell differentiation (GO:0002317)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(5)	20	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.0253)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			GAGAGAAATATTACCTCTTTC	0.413																																					p.I298T		Atlas-SNP	.											.	LGALS8	42	.	0			c.T893C						.						87	89	88					1																	236708178		2203	4300	6503	SO:0001583	missense	3964	exon11			GAAATATTACCTC	X91790	CCDS1611.1, CCDS1612.1	1q43	2011-08-04	2008-07-25		ENSG00000116977	ENSG00000116977		"Lectins, galactoside-binding"	6569	protein-coding gene	gene with protein product	"galectin 8"	606099				7852431, 8692978	Standard	NM_201545		Approved	PCTA-1	uc001hxy.2	O00214	OTTHUMG00000039953	ENST00000366584.4:c.767T>C	chr1.hg19:g.236708178T>C	ENSP00000355543:p.Ile256Thr	105.0	0.0		136.0	50.0	NM_006499	O15215|Q5T3P5|Q5T3Q4|Q8TEV1|Q96B92|Q9BXC8|Q9H584|Q9H585|Q9UEZ6|Q9UP32|Q9UP33|Q9UP34	Missense_Mutation	SNP	ENST00000366584.4	hg19	CCDS1612.1	.	.	.	.	.	.	.	.	.	.	T	11.36	1.615985	0.28801	.	.	ENSG00000116977	ENST00000527974;ENST00000352231;ENST00000526589;ENST00000341872;ENST00000450372;ENST00000366584;ENST00000356238;ENST00000416919;ENST00000323938;ENST00000526634;ENST00000525042	T;T;T;T;T;T;T;T;T;T	0.04758	3.56;3.56;3.56;3.56;3.56;3.56;3.56;3.56;3.56;3.56	5.35	3.03	0.35002	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	0.266713	0.37178	N	0.002220	T	0.04363	0.0120	N	0.25992	0.78	0.09310	N	1	B;B;B	0.09022	0.0;0.0;0.002	B;B;B	0.19148	0.004;0.024;0.014	T	0.35126	-0.9801	10	0.62326	D	0.03	-8.274	10.0817	0.42393	0.0:0.1363:0.0:0.8637	.	239;256;298	F6V2D4;O00214;O00214-2	.;LEG8_HUMAN;.	T	298;298;298;256;298;256;297;239;229;256;239	ENSP00000431398:I298T;ENSP00000309576:I298T;ENSP00000435460:I298T;ENSP00000342139:I256T;ENSP00000408657:I298T;ENSP00000355543:I256T;ENSP00000410843:I239T;ENSP00000434860:I229T;ENSP00000437040:I256T;ENSP00000431884:I239T	ENSP00000434860:I229T	I	+	2	0	LGALS8	234774801	0.981000	0.34729	0.850000	0.33497	0.883000	0.51084	4.166000	0.58203	0.562000	0.29204	-0.274000	0.10170	ATT	.	.		0.413	LGALS8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000096365.2	NM_006499		C	236708178	T	C	236708178	3	2	237	1	0	0	0	0	1	0	0	0	8756	1493	52	2	927	2	LGALS8	1	236708178	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	20735898	236708178	12542443	28	32934										
RYR2	6262	hgsc.bcm.edu	37	chr1	237868576	237868576	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gcttttcctgtagcatttttGgaaactcatctggacaaaca	7	9	2	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:237868576G>A	ENST00000366574.2	+	67	9830	c.9513G>A	c.(9511-9513)ttG>ttA	p.L3171L	RYR2_ENST00000609119.1_3'UTR|RYR2_ENST00000542537.1_Silent_p.L3155L|RYR2_ENST00000360064.6_Silent_p.L3169L	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	3171					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TAGCATTTTTGGAAACTCATC	0.393																																					p.L3171L		Atlas-SNP	.											.	RYR2	1273	.	0			c.G9513A						.						116	107	110					1																	237868576		1881	4126	6007	SO:0001819	synonymous_variant	6262	exon67			ATTTTTGGAAACT	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.9513G>A	chr1.hg19:g.237868576G>A		133.0	0.0		155.0	47.0	NM_001035	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	hg19	CCDS55691.1																																																																																			.	.		0.393	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		A	237868576	G	A	237868576	2	1	237	1	0	0	0	0	0	0	0	1	13784	1339	47	3		3	RYR2	1	237868576	Silent	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	1160398	237868576	11382045	29	32935										
CEP170	9859	hgsc.bcm.edu	37	chr1	243354349	243354349	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ttttcaagtacactggaacaTcacttttaatgcttttagaa	5	7	2	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:243354349T>A	ENST00000366542.1	-	8	1130	c.1079A>T	c.(1078-1080)gAt>gTt	p.D360V	CEP170_ENST00000366543.1_Missense_Mutation_p.D360V|CEP170_ENST00000366544.1_Missense_Mutation_p.D360V	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	360						centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear membrane (GO:0031965)				NS(1)|breast(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	62	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			CACTGGAACATCACTTTTAAT	0.373																																					p.D360V		Atlas-SNP	.											.	CEP170	153	.	0			c.A1079T						.						25	24	24					1																	243354349		1829	4071	5900	SO:0001583	missense	9859	exon8			GGAACATCACTTT	AB022657	CCDS44337.1, CCDS44338.1, CCDS44339.1	1q44	2014-02-20	2006-01-12	2006-01-12	ENSG00000143702	ENSG00000143702			28920	protein-coding gene	gene with protein product	"KARP 1 binding protein", "XRCC5 binding protein"	613023	"KIAA0470"	KIAA0470		15616186	Standard	NM_014812		Approved	KAB, FAM68A	uc021plo.1	Q5SW79	OTTHUMG00000039862	ENST00000366542.1:c.1079A>T	chr1.hg19:g.243354349T>A	ENSP00000355500:p.Asp360Val	218.0	0.0		257.0	16.0	NM_001042405	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Missense_Mutation	SNP	ENST00000366542.1	hg19	CCDS44339.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.96|19.96	3.924033|3.924033	0.73213|0.73213	.|.	.|.	ENSG00000143702|ENSG00000143702	ENST00000366542;ENST00000366544;ENST00000366543;ENST00000424081|ENST00000336415	T;T;T|.	0.72942|.	-0.7;-0.56;-0.56|.	4.91|4.91	4.91|4.91	0.64330|0.64330	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72969|0.72969	0.3527|0.3527	M|M	0.72353|0.72353	2.195|2.195	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	0.999;1.0;0.999|.	T|T	0.73757|0.73757	-0.3882|-0.3882	10|5	0.87932|.	D|.	0|.	-16.166|-16.166	14.5724|14.5724	0.68220|0.68220	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	360;360;360|.	Q5SW79-3;Q5SW79-2;Q5SW79|.	.;.;CE170_HUMAN|.	V|L	360;360;360;258|262	ENSP00000355500:D360V;ENSP00000355502:D360V;ENSP00000355501:D360V|.	ENSP00000355500:D360V|.	D|M	-|-	2|1	0|0	CEP170|CEP170	241420972|241420972	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.694000|7.694000	0.84235|0.84235	1.853000|1.853000	0.53794|0.53794	0.374000|0.374000	0.22700|0.22700	GAT|ATG	.	.		0.373	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812		A	243354349	T	A	243354349	3	1	237	1	0	0	0	0	1	0	0	0	3252	1435	50	4	3757	4	CEP170	1	243354349	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	5485773	243354349	5896272	30	32936										
ALK	238	hgsc.bcm.edu	37	chr2	29416521	29416521	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gttggactgagagaatgccaTattcacgtgtcccccttcca	9	12	1	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr2:29416521T>C	ENST00000389048.3	-	29	5338	c.4432A>G	c.(4432-4434)Atg>Gtg	p.M1478V	ALK_ENST00000431873.1_Missense_Mutation_p.M308V	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	1478					activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	GAGAATGCCATATTCACGTGT	0.577			"T, Mis, A"	"NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"	"ALCL, NSCLC, Neuroblastoma"	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																												p.M1478V		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"L, E, M"	.	ALK	533	.	0			c.A4432G						.						111	113	112					2																	29416521		2203	4300	6503	SO:0001583	missense	238	exon29	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	ATGCCATATTCAC	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"CD molecules"	427	protein-coding gene	gene with protein product		105590	"anaplastic lymphoma kinase (Ki-1)"			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.4432A>G	chr2.hg19:g.29416521T>C	ENSP00000373700:p.Met1478Val	261.0	0.0		231.0	74.0	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Missense_Mutation	SNP	ENST00000389048.3	hg19	CCDS33172.1	.	.	.	.	.	.	.	.	.	.	t	9.190	1.025827	0.19512	.	.	ENSG00000171094	ENST00000389048;ENST00000431873	T;T	0.76316	-1.01;2.93	5.64	3.18	0.36537	.	0.000000	0.64402	U	0.000018	T	0.70902	0.3277	M	0.63428	1.95	0.24401	N	0.994708	B	0.06786	0.001	B	0.04013	0.001	T	0.57625	-0.7779	10	0.29301	T	0.29	.	8.7607	0.34672	0.0:0.067:0.1285:0.8045	.	1478	Q9UM73	ALK_HUMAN	V	1478;308	ENSP00000373700:M1478V;ENSP00000414027:M308V	ENSP00000373700:M1478V	M	-	1	0	ALK	29270025	1.000000	0.71417	0.967000	0.41034	0.349000	0.29174	1.855000	0.39378	0.390000	0.25115	0.454000	0.30748	ATG	.	.		0.577	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		C	29416521	T	C	29416521	3	2	237	1	0	0	0	0	1	0	0	0	525	1406	49	2	434	2	ALK	2	29416521	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10		29416521	213782852	31	32937										
HNRPLL	92906	hgsc.bcm.edu	37	chr2	38804603	38804603	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tttctaccttgacaacttacCatagccatcatgtctaaacg	4	12	3	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr2:38804603C>G	ENST00000449105.3	-	7	1213	c.874G>C	c.(874-876)Gga>Cga	p.G292R	HNRNPLL_ENST00000378915.3_Splice_Site_p.G258R|HNRNPLL_ENST00000409636.1_Splice_Site_p.G287R|HNRNPLL_ENST00000608859.1_Splice_Site_p.G292R|HNRNPLL_ENST00000409328.1_Splice_Site_p.G258R			Q8WVV9	HNRLL_HUMAN	heterogeneous nuclear ribonucleoprotein L-like	292					mRNA processing (GO:0006397)|positive regulation of RNA splicing (GO:0033120)	membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)										GACAACTTACCATAGCCATCA	0.398																																					p.G292R		Atlas-SNP	.											.	HNRPLL	19	.	0			c.G874C						.						169	153	158					2																	38804603		2203	4300	6503	SO:0001630	splice_region_variant	92906	exon7			ACTTACCATAGCC	BC008217	CCDS46261.1, CCDS1796.2	2p22	2014-02-10		2013-06-12	ENSG00000143889	ENSG00000143889		"RNA binding motif (RRM) containing"	25127	protein-coding gene	gene with protein product		611208		HNRPLL		18669861	Standard	NM_138394		Approved		uc021vgc.1	Q8WVV9	OTTHUMG00000102075	ENST00000449105.3:c.874+1G>C	chr2.hg19:g.38804603C>G		273.0	0.0		298.0	86.0	NM_138394	Q53T80|Q5JB51|Q5JB52|Q659B9|Q8IVH5|Q8IVH6|Q96HR5	Missense_Mutation	SNP	ENST00000449105.3	hg19		.	.	.	.	.	.	.	.	.	.	C	22.7	4.318637	0.81469	.	.	ENSG00000143889	ENST00000449105;ENST00000409636;ENST00000378915;ENST00000409328	.	.	.	6.03	6.03	0.97812	.	0.134395	0.48286	D	0.000194	T	0.74076	0.3669	L	0.40543	1.245	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.69157	-0.5219	8	.	.	.	-5.1667	20.5568	0.99304	0.0:1.0:0.0:0.0	.	287;292	C9J9G0;D6W592	.;.	R	292;287;258;258	.	.	G	-	1	0	HNRPLL	38658107	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.645000	0.74343	2.861000	0.98227	0.655000	0.94253	GGA	.	.		0.398	HNRNPLL-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000219887.2	NM_138394	Missense_Mutation	G	38804603	C	G	38804603	5	3	237	1	0	0	0	0	0	0	1	0	7286	608	21	4	782	4	HNRPLL	2	38804603	Splice_Site	SNP	C	TCGA-ED-A459-01A-11D-A25V-10	9388082	38804603	204394770	32	32938										
TMEM127	55654	hgsc.bcm.edu	37	chr2	96919803	96919803	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ctgctgctgctgggccaagaTgagttcagaagcccaataag	12	10	1	3			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr2:96919803T>C	ENST00000258439.3	-	4	716	c.460A>G	c.(460-462)Atc>Gtc	p.I154V	TMEM127_ENST00000435268.1_Missense_Mutation_p.I70V|TMEM127_ENST00000432959.1_Missense_Mutation_p.I154V	NM_001193304.2|NM_017849.3	NP_001180233.1|NP_060319.1	O75204	TM127_HUMAN	transmembrane protein 127	154					negative regulation of cell proliferation (GO:0008285)|negative regulation of TOR signaling (GO:0032007)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(1)|lung(1)|prostate(1)|stomach(1)	5						TGGGCCAAGATGAGTTCAGAA	0.537																																					p.I154V		Atlas-SNP	.											.	TMEM127	13	.	0			c.A460G						.						103	99	101					2																	96919803		2203	4300	6503	SO:0001583	missense	55654	exon4			CCAAGATGAGTTC	AK000514	CCDS2018.1	2q11.2	2014-09-17			ENSG00000135956	ENSG00000135956			26038	protein-coding gene	gene with protein product		613403				10493829	Standard	NM_017849		Approved	FLJ20507, FLJ22257	uc002svr.3	O75204	OTTHUMG00000130454	ENST00000258439.3:c.460A>G	chr2.hg19:g.96919803T>C	ENSP00000258439:p.Ile154Val	155.0	0.0		111.0	43.0	NM_001193304	D3DXH0	Missense_Mutation	SNP	ENST00000258439.3	hg19	CCDS2018.1	.	.	.	.	.	.	.	.	.	.	T	11.32	1.603311	0.28534	.	.	ENSG00000135956	ENST00000258439;ENST00000432959;ENST00000435268	D;D;D	0.95622	-3.76;-3.76;-2.93	6.06	6.06	0.98353	.	0.052153	0.64402	D	0.000001	D	0.90665	0.7072	N	0.14661	0.345	0.49582	D	0.999806	B	0.02656	0.0	B	0.04013	0.001	D	0.86602	0.1867	10	0.59425	D	0.04	-25.5181	15.5919	0.76537	0.0:0.0:0.0:1.0	.	154	O75204	TM127_HUMAN	V	154;154;70	ENSP00000258439:I154V;ENSP00000416660:I154V;ENSP00000411810:I70V	ENSP00000258439:I154V	I	-	1	0	TMEM127	96283530	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.660000	0.61511	2.324000	0.78689	0.533000	0.62120	ATC	.	.		0.537	TMEM127-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252845.3	NM_017849		C	96919803	T	C	96919803	3	2	237	1	0	0	0	0	1	0	0	0	16055	1464	51	2	260	2	TMEM127	2	96919803	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	58115200	96919803	146279570	33	32939										
MAP4K4	9448	hgsc.bcm.edu	37	chr2	102483701	102483701	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	caagtctgaaggctctccatCtcagcgcctggaaaatgcag	10	12	3	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr2:102483701C>G	ENST00000347699.4	+	19	2150	c.2150C>G	c.(2149-2151)tCt>tGt	p.S717C	MAP4K4_ENST00000324219.4_Missense_Mutation_p.S795C|MAP4K4_ENST00000302217.5_Missense_Mutation_p.S517C|MAP4K4_ENST00000350878.4_Missense_Mutation_p.S690C|MAP4K4_ENST00000350198.4_Missense_Mutation_p.S633C|MAP4K4_ENST00000425019.1_Missense_Mutation_p.S686C|MAP4K4_ENST00000413150.2_Missense_Mutation_p.S632C|MAP4K4_ENST00000456652.1_Missense_Mutation_p.S516C	NM_001242559.1|NM_145687.3	NP_001229488.1|NP_663720.1	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase kinase 4	717					intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of JNK cascade (GO:0046328)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						GGCTCTCCATCTCAGCGCCTG	0.438																																					p.S717C		Atlas-SNP	.											.	MAP4K4	111	.	0			c.C2150G						.						69	69	69					2																	102483701		1911	4132	6043	SO:0001583	missense	9448	exon19			CTCCATCTCAGCG	AF096300	CCDS56130.1, CCDS74546.1	2q11.2-q12	2011-06-09			ENSG00000071054	ENSG00000071054		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6866	protein-coding gene	gene with protein product	"HPK/GCK-like kinase", "hepatocyte progenitor kinase-like/germinal center kinase-like kinase"	604666				9890973, 9734811, 9135144	Standard	NM_004834		Approved	HGK, NIK, FLH21957	uc002tbf.3	O95819	OTTHUMG00000155394	ENST00000347699.4:c.2150C>G	chr2.hg19:g.102483701C>G	ENSP00000314363:p.Ser717Cys	153.0	0.0		135.0	35.0	NM_001242559	O75172|Q9NST7	Missense_Mutation	SNP	ENST00000347699.4	hg19	CCDS56130.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.30|19.30	3.801376|3.801376	0.70567|0.70567	.|.	.|.	ENSG00000071054|ENSG00000071054	ENST00000421882|ENST00000425019;ENST00000324219;ENST00000350198;ENST00000302217;ENST00000413150;ENST00000456652;ENST00000347699;ENST00000417294;ENST00000350878	.|T;T;T;T;T;T;T;T;T	.|0.12039	.|2.72;2.72;2.72;2.72;2.72;2.72;2.72;2.72;2.72	5.65|5.65	5.65|5.65	0.86999|0.86999	.|.	.|0.176739	.|0.49305	.|D	.|0.000146	T|T	0.30665|0.30665	0.0772|0.0772	L|L	0.36672|0.36672	1.1|1.1	0.51012|0.51012	D|D	0.9999|0.9999	.|P;P;P;P;D;D;D;D;D;D	.|0.76494	.|0.94;0.94;0.94;0.94;0.965;0.994;0.999;0.965;0.989;0.996	.|P;P;P;P;P;D;D;P;D;D	.|0.78314	.|0.635;0.635;0.635;0.635;0.73;0.922;0.991;0.73;0.916;0.947	T|T	0.00726|0.00726	-1.1592|-1.1592	5|10	.|0.51188	.|T	.|0.08	.|.	19.7244|19.7244	0.96157|0.96157	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|690;710;516;517;632;717;686;633;686;795	.|B7Z388;B7Z3V5;E7EX83;C9J840;O95819-4;O95819;E7EN19;G3XAA2;O95819-2;G5E948	.|.;.;.;.;.;M4K4_HUMAN;.;.;.;.	M|C	533|686;795;633;517;632;516;717;648;690	.|ENSP00000392830:S686C;ENSP00000313644:S795C;ENSP00000281111:S633C;ENSP00000303600:S517C;ENSP00000389752:S632C;ENSP00000387370:S516C;ENSP00000314363:S717C;ENSP00000409720:S648C;ENSP00000343658:S690C	.|ENSP00000303600:S517C	I|S	+|+	3|2	3|0	MAP4K4|MAP4K4	101850133|101850133	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	4.912000|4.912000	0.63335|0.63335	2.659000|2.659000	0.90383|0.90383	0.655000|0.655000	0.94253|0.94253	ATC|TCT	.	.		0.438	MAP4K4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339839.1	NM_004834		G	102483701	C	G	102483701	3	3	237	1	0	0	0	0	1	0	0	0	9271	913	32	4	2462	4	MAP4K4	2	102483701	Missense_Mutation	SNP	C	TCGA-ED-A459-01A-11D-A25V-10	5563898	102483701	140715672	34	32940										
MYO7B	4648	hgsc.bcm.edu	37	chr2	128334177	128334177	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ccctccctcccaggctcccgAggagcggaactaccatatct	8	18	1	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr2:128334177A>T	ENST00000409816.2	+	7	775	c.743A>T	c.(742-744)gAg>gTg	p.E248V	MYO7B_ENST00000389524.4_Missense_Mutation_p.E248V|MYO7B_ENST00000428314.1_Missense_Mutation_p.E248V			Q6PIF6	MYO7B_HUMAN	myosin VIIB	248	Myosin motor.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		CAGGCTCCCGAGGAGCGGAAC	0.627																																					p.E248V		Atlas-SNP	.											.	MYO7B	359	.	0			c.A743T						.						41	47	45					2																	128334177		2040	4195	6235	SO:0001583	missense	4648	exon8			CTCCCGAGGAGCG		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"Myosins / Myosin superfamily : Class VII"	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.743A>T	chr2.hg19:g.128334177A>T	ENSP00000386461:p.Glu248Val	52.0	0.0		53.0	12.0	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	hg19	CCDS46405.1	.	.	.	.	.	.	.	.	.	.	A	16.92	3.255896	0.59321	.	.	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000409816	T;T;T	0.72615	-0.67;-0.67;-0.67	4.94	4.94	0.65067	Myosin head, motor domain (2);	0.290858	0.31872	N	0.006934	T	0.78748	0.4332	M	0.71036	2.16	0.40794	D	0.983285	D	0.57899	0.981	P	0.60345	0.873	T	0.80331	-0.1427	10	0.51188	T	0.08	.	9.4397	0.38661	0.9196:0.0:0.0804:0.0	.	248	Q6PIF6	MYO7B_HUMAN	V	248	ENSP00000374175:E248V;ENSP00000415090:E248V;ENSP00000386461:E248V	ENSP00000374175:E248V	E	+	2	0	MYO7B	128050647	1.000000	0.71417	0.853000	0.33588	0.399000	0.30720	6.247000	0.72411	1.994000	0.58287	0.460000	0.39030	GAG	.	.		0.627	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001		T	128334177	A	T	128334177	3	4	237	1	0	0	0	0	1	0	0	0	10092	304	11	4	769	4	MYO7B	2	128334177	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	25850476	128334177	114865196	35	32941										
SCN1A	6323	hgsc.bcm.edu	37	chr2	166897947	166897947	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gttggaaaatttataccaacAgggtgggcatttctgcctgg	12	7	1	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr2:166897947A>T	ENST00000303395.4	-	13	2208	c.2209T>A	c.(2209-2211)Tgt>Agt	p.C737S	SCN1A_ENST00000375405.3_Missense_Mutation_p.C726S|AC010127.3_ENST00000595647.1_RNA|SCN1A_ENST00000409050.1_Missense_Mutation_p.C709S|SCN1A_ENST00000423058.2_Missense_Mutation_p.C737S|AC010127.3_ENST00000599041.1_RNA|AC010127.3_ENST00000595268.1_RNA			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	737					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TTATACCAACAGGGTGGGCAT	0.338																																					p.C737S		Atlas-SNP	.											.	SCN1A	641	.	0			c.T2209A						.						81	90	87					2																	166897947		2203	4300	6503	SO:0001583	missense	6323	exon13			ACCAACAGGGTGG	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10585	protein-coding gene	gene with protein product		182389	"febrile convulsions 3"	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.2209T>A	chr2.hg19:g.166897947A>T	ENSP00000303540:p.Cys737Ser	43.0	0.0		64.0	9.0	NM_001165963	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	hg19	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.578722	0.86645	.	.	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.96459	-4.02;-4.02;-3.99;-3.97	5.54	5.54	0.83059	.	0.000000	0.64402	D	0.000001	D	0.97489	0.9178	M	0.90425	3.115	0.80722	D	1	P;D;P	0.54207	0.943;0.965;0.94	P;B;P	0.49829	0.623;0.419;0.601	D	0.98239	1.0487	10	0.87932	D	0	.	15.9597	0.79918	1.0:0.0:0.0:0.0	.	726;709;737	P35498-2;E9PG49;P35498	.;.;SCN1A_HUMAN	S	737;737;726;709	ENSP00000407030:C737S;ENSP00000303540:C737S;ENSP00000364554:C726S;ENSP00000386312:C709S	ENSP00000303540:C737S	C	-	1	0	SCN1A	166606193	1.000000	0.71417	0.999000	0.59377	0.975000	0.68041	7.440000	0.80464	2.226000	0.72624	0.482000	0.46254	TGT	.	.		0.338	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		T	166897947	A	T	166897947	3	4	237	1	0	0	0	0	1	0	0	0	13929	188	7	4	3876	4	SCN1A	2	166897947	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	38563770	166897947	76301426	36	32942										
SCN9A	6335	hgsc.bcm.edu	37	chr2	167163108	167163108	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	catgatgagcatgctgaataAggtagcttagaatcaaggaa	11	5	1	4			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr2:167163108A>C	ENST00000409435.1	-	3	378	c.379T>G	c.(379-381)Tta>Gta	p.L127V	SCN9A_ENST00000303354.6_Missense_Mutation_p.L128V|SCN9A_ENST00000375387.4_Missense_Mutation_p.L128V|SCN9A_ENST00000409672.1_Splice_Site_p.L127V			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	127					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	ATGCTGAATAAGGTAGCTTAG	0.373																																					p.L127V		Atlas-SNP	.											.	SCN9A	296	.	0			c.T379G						.						65	64	65					2																	167163108		1936	4196	6132	SO:0001630	splice_region_variant	6335	exon4			TGAATAAGGTAGC	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10597	protein-coding gene	gene with protein product		603415	"sodium channel, voltage-gated, type IX, alpha polypeptide"			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.378-1T>G	chr2.hg19:g.167163108A>C		105.0	0.0		76.0	31.0	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Missense_Mutation	SNP	ENST00000409435.1	hg19	CCDS46441.1	.	.	.	.	.	.	.	.	.	.	a	12.90	2.075534	0.36662	.	.	ENSG00000169432	ENST00000409672;ENST00000375387;ENST00000303354;ENST00000409435	D;D;D;D	0.97480	-4.4;-4.4;-4.4;-4.4	5.96	3.59	0.41128	.	0.309084	0.23307	N	0.049614	D	0.95459	0.8525	M	0.75264	2.295	0.35953	D	0.834069	B	0.06786	0.001	B	0.13407	0.009	D	0.93250	0.6634	10	0.49607	T	0.09	.	8.8756	0.35343	0.7989:0.1352:0.0659:0.0	.	127	E7EUN6	.	V	127;128;128;127	ENSP00000386306:L127V;ENSP00000364536:L128V;ENSP00000304748:L128V;ENSP00000386330:L127V	ENSP00000304748:L128V	L	-	1	2	SCN9A	166871354	0.381000	0.25140	0.990000	0.47175	0.964000	0.63967	0.932000	0.28884	0.496000	0.27904	0.528000	0.53228	TTA	.	.		0.373	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977	Missense_Mutation	C	167163108	A	C	167163108	5	2	237	1	0	0	0	0	0	0	1	0	13940	86	3	5	5650	5	SCN9A	2	167163108	Splice_Site	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	265161	167163108	76036265	37	32943										
ITGA6	3655	hgsc.bcm.edu	37	chr2	173344405	173344405	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	aatattcagaaaaccatcacAgtaactcctaacagaattga	4	9	2	3			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr2:173344405A>T	ENST00000264106.6	+	11	1745	c.1542A>T	c.(1540-1542)acA>acT	p.T514T	ITGA6_ENST00000343713.4_Silent_p.T470T|ITGA6_ENST00000264107.7_Silent_p.T475T|AC093818.1_ENST00000442417.1_RNA|ITGA6_ENST00000409532.1_Silent_p.T356T|ITGA6_ENST00000375221.2_Silent_p.T514T|ITGA6_ENST00000409080.1_Silent_p.T475T			P23229	ITA6_HUMAN	integrin, alpha 6	514					amelogenesis (GO:0097186)|blood coagulation (GO:0007596)|brown fat cell differentiation (GO:0050873)|cell adhesion mediated by integrin (GO:0033627)|cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|cellular response to extracellular stimulus (GO:0031668)|cellular response to organic cyclic compound (GO:0071407)|digestive tract development (GO:0048565)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|nail development (GO:0035878)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|renal system development (GO:0072001)|single organismal cell-cell adhesion (GO:0016337)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|external side of plasma membrane (GO:0009897)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha6-beta4 complex (GO:0034676)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	44			OV - Ovarian serous cystadenocarcinoma(117;0.0979)			AAACCATCACAGTAACTCCTA	0.478																																					p.T475T		Atlas-SNP	.											.	ITGA6	171	.	0			c.A1425T						.						179	188	185					2																	173344405		2203	4300	6503	SO:0001819	synonymous_variant	3655	exon10			CATCACAGTAACT		CCDS2249.1, CCDS46451.1	2q31.1	2010-09-20			ENSG00000091409	ENSG00000091409		"CD molecules", "Integrins"	6142	protein-coding gene	gene with protein product		147556					Standard	NM_001079818		Approved	CD49f	uc002uhp.1	P23229	OTTHUMG00000132277	ENST00000264106.6:c.1542A>T	chr2.hg19:g.173344405A>T		111.0	0.0		85.0	31.0	NM_000210	B2RMU9|B4DG69|B4DKB8|C4AM96|G5E9H1|Q08443|Q0MRC7|Q14646|Q16508|Q53RX7|Q59HB7|Q86VL6|Q9UCT1|Q9UN03	Silent	SNP	ENST00000264106.6	hg19																																																																																				.	.		0.478	ITGA6-201	KNOWN	basic	protein_coding	protein_coding				T	173344405	A	T	173344405	2	4	237	1	0	0	0	0	0	0	0	1	7889	175	7	4		4	ITGA6	2	173344405	Silent	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	6181297	173344405	69854968	38	32944										
TTN	7273	hgsc.bcm.edu	37	chr2	179433349	179433349	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ttcttgtggtctgcttcagtGggagaccatctttagtccag	11	9	4	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr2:179433349G>A	ENST00000591111.1	-	276	72811	c.72587C>T	c.(72586-72588)cCa>cTa	p.P24196L	TTN_ENST00000359218.5_Missense_Mutation_p.P16897L|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.P16772L|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.P16964L|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.P25837L|TTN_ENST00000342992.6_Missense_Mutation_p.P23269L|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA			Q8WZ42	TITIN_HUMAN	titin	24196	Ig-like 121.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTGCTTCAGTGGGAGACCATC	0.418																																					p.P25837L		Atlas-SNP	.											TTN_ENST00000359218,right_upper_lobe,carcinoma,0,5	TTN	18412	.	0			c.C77510T						.						207	189	195					2																	179433349		1920	4146	6066	SO:0001583	missense	7273	exon326			TTCAGTGGGAGAC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.72587C>T	chr2.hg19:g.179433349G>A	ENSP00000465570:p.Pro24196Leu	279.0	1.0		295.0	27.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	10.60	1.396793	0.25205	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3	6.03	6.03	0.97812	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.63896	0.2550	L	0.41824	1.3	0.58432	D	0.999999	P;P;P;P	0.34462	0.454;0.454;0.454;0.454	B;B;B;B	0.34931	0.192;0.192;0.192;0.192	T	0.64939	-0.6289	9	0.87932	D	0	.	20.5666	0.99351	0.0:0.0:1.0:0.0	.	16772;16897;16964;24196	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	L	23269;16772;16964;16897;16770	ENSP00000343764:P23269L;ENSP00000434586:P16772L;ENSP00000340554:P16964L;ENSP00000352154:P16897L	ENSP00000340554:P16964L	P	-	2	0	TTN	179141595	1.000000	0.71417	0.901000	0.35422	0.774000	0.43823	3.386000	0.52492	2.854000	0.98071	0.655000	0.94253	CCA	.	.		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179433349	G	A	179433349	3	1	237	1	0	0	0	0	1	0	0	0	16750	1348	47	3	30617	3	TTN	2	179433349	Missense_Mutation	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	6088944	179433349	63766024	39	32945										
FN1	2335	hgsc.bcm.edu	37	chr2	216261912	216261912	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	agcactccagtgtcagggttTgcctccagatgcaagtttgt	11	10	1	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr2:216261912T>C	ENST00000359671.1	-	23	3817	c.3552A>G	c.(3550-3552)gcA>gcG	p.A1184A	FN1_ENST00000336916.4_Silent_p.A1184A|FN1_ENST00000346544.3_Silent_p.A1184A|FN1_ENST00000421182.1_Silent_p.A1184A|FN1_ENST00000345488.5_Silent_p.A1184A|FN1_ENST00000356005.4_Silent_p.A1184A|FN1_ENST00000446046.1_Silent_p.A1184A|FN1_ENST00000443816.1_Silent_p.A1184A|FN1_ENST00000357009.2_Silent_p.A1184A|FN1_ENST00000357867.4_Silent_p.A1184A|FN1_ENST00000354785.4_Silent_p.A1184A|FN1_ENST00000323926.6_Silent_p.A1184A|FN1_ENST00000432072.2_Silent_p.A1184A			P02751	FINC_HUMAN	fibronectin 1	1184	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316, ECO:0000255|PROSITE-ProRule:PRU00478, ECO:0000255|PROSITE-ProRule:PRU00479}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	TGTCAGGGTTTGCCTCCAGAT	0.473																																					p.A1184A		Atlas-SNP	.											.	FN1	521	.	0			c.A3552G						.						190	188	188					2																	216261912		2203	4300	6503	SO:0001819	synonymous_variant	2335	exon23			AGGGTTTGCCTCC		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"Fibronectin type III domain containing", "Endogenous ligands"	3778	protein-coding gene	gene with protein product	"migration-stimulating factor", "cold-insoluble globulin"	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.3552A>G	chr2.hg19:g.216261912T>C		82.0	0.0		72.0	15.0	NM_212476	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Silent	SNP	ENST00000359671.1	hg19																																																																																				.	.		0.473	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		C	216261912	T	C	216261912	2	2	237	1	0	0	0	0	0	0	0	1	5970	1799	63	2		2	FN1	2	216261912	Silent	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	36828563	216261912	26937461	40	32946										
CCDC108	255101	hgsc.bcm.edu	37	chr2	219897276	219897276	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tgagggatgaccgtgaagaaGaacttggtcttggggggcct	17	6	1	5			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr2:219897276G>A	ENST00000341552.5	-	6	644	c.561C>T	c.(559-561)ttC>ttT	p.F187F	CCDC108_ENST00000453220.1_Silent_p.F187F|CCDC108_ENST00000410037.1_Silent_p.F122F|CCDC108_ENST00000441968.1_Silent_p.F187F|CCDC108_ENST00000409865.3_Silent_p.F176F	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108	187						integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(1)|lung(34)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCGTGAAGAAGAACTTGGTCT	0.612																																					p.F187F		Atlas-SNP	.											.	CCDC108	208	.	0			c.C561T						.						59	49	53					2																	219897276		2202	4300	6502	SO:0001819	synonymous_variant	255101	exon6			GAAGAAGAACTTG	NM_194302, AL833882, AK127189	CCDS2430.2, CCDS2431.2, CCDS63125.1, CCDS63126.1	2q35	2008-02-05			ENSG00000181378	ENSG00000181378			25325	protein-coding gene	gene with protein product		614270				12477932	Standard	NM_194302		Approved	DKFZp434O0527, MGC35338	uc002vjl.2	Q6ZU64	OTTHUMG00000133013	ENST00000341552.5:c.561C>T	chr2.hg19:g.219897276G>A		252.0	0.0		200.0	55.0	NM_194302	A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Silent	SNP	ENST00000341552.5	hg19	CCDS2430.2																																																																																			.	.		0.612	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4	NM_194302		A	219897276	G	A	219897276	2	1	237	1	0	0	0	0	0	0	0	1	2745	933	33	3		3	CCDC108	2	219897276	Silent	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	3635364	219897276	23302097	41	32947										
SPEG	10290	hgsc.bcm.edu	37	chr2	220333737	220333737	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ctgctcagcccagctgtatgTagaagagccccggacagccg	12	14	1	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr2:220333737T>A	ENST00000312358.7	+	12	3590	c.3458T>A	c.(3457-3459)gTa>gAa	p.V1153E	SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	1153					cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		CAGCTGTATGTAGAAGAGCCC	0.662																																					p.V1153E		Atlas-SNP	.											.	SPEG	272	.	0			c.T3458A						.						35	43	41					2																	220333737		1976	4147	6123	SO:0001583	missense	10290	exon12			TGTATGTAGAAGA	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"Immunoglobulin superfamily / I-set domain containing"	16901	protein-coding gene	gene with protein product		615950	"aortic preferentially expressed gene 1"	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.3458T>A	chr2.hg19:g.220333737T>A	ENSP00000311684:p.Val1153Glu	106.0	0.0		80.0	9.0	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	hg19	CCDS42824.1	.	.	.	.	.	.	.	.	.	.	T	17.95	3.513685	0.64522	.	.	ENSG00000072195	ENST00000312358;ENST00000265327	D	0.86097	-2.07	4.77	4.77	0.60923	Immunoglobulin I-set (1);Immunoglobulin-like fold (1);	0.000000	0.37955	N	0.001864	D	0.95149	0.8428	H	0.97962	4.115	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	D	0.96857	0.9629	10	0.87932	D	0	.	14.4658	0.67482	0.0:0.0:0.0:1.0	.	1153	Q15772	SPEG_HUMAN	E	1153	ENSP00000311684:V1153E	ENSP00000265327:V1153E	V	+	2	0	SPEG	220041981	1.000000	0.71417	0.978000	0.43139	0.858000	0.48976	7.773000	0.85462	2.015000	0.59207	0.533000	0.62120	GTA	.	.		0.662	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		A	220333737	T	A	220333737	3	1	237	1	0	0	0	0	1	0	0	0	15051	1638	57	4	3516	4	SPEG	2	220333737	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	436461	220333737	22865636	42	32948										
NCL	4691	hgsc.bcm.edu	37	chr2	232326345	232326345	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gcagctgctgctttcatcgcTgctggttcaatttcatcttc	8	12	4	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr2:232326345T>A	ENST00000322723.4	-	3	759	c.519A>T	c.(517-519)gcA>gcT	p.A173A	SNORD82_ENST00000365530.1_RNA	NM_005381.2	NP_005372.2	P19338	NUCL_HUMAN	nucleolin	173					angiogenesis (GO:0001525)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)	cell cortex (GO:0005938)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)|telomeric DNA binding (GO:0042162)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(3)	35		Ovarian(221;1.34e-05)|Renal(207;0.0112)|Lung NSC(271;0.0339)|all_lung(227;0.0616)|all_hematologic(139;0.0748)|Hepatocellular(293;0.137)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.65e-111)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)|COAD - Colon adenocarcinoma(134;0.141)|STAD - Stomach adenocarcinoma(1183;0.18)		CTTTCATCGCTGCTGGTTCAA	0.512																																					p.A173A		Atlas-SNP	.											.	NCL	80	.	0			c.A519T						.						369	238	282					2																	232326345		2203	4300	6503	SO:0001819	synonymous_variant	4691	exon3			CATCGCTGCTGGT		CCDS33397.1	2q37.1	2013-09-19			ENSG00000115053	ENSG00000115053		"RNA binding motif (RRM) containing"	7667	protein-coding gene	gene with protein product		164035				2394707, 3409881	Standard	NM_005381		Approved	C23	uc002vru.3	P19338	OTTHUMG00000153866	ENST00000322723.4:c.519A>T	chr2.hg19:g.232326345T>A		277.0	0.0		213.0	18.0	NM_005381	Q53SK1|Q8NB06|Q9UCF0|Q9UDG1	Silent	SNP	ENST00000322723.4	hg19	CCDS33397.1																																																																																			.	.		0.512	NCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332731.1	NM_005381		A	232326345	T	A	232326345	2	1	237	1	0	0	0	0	0	0	0	1	10235	1567	55	4		4	NCL	2	232326345	Silent	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	11992608	232326345	10873028	43	32949										
TIMP4	7079	hgsc.bcm.edu	37	chr3	12195118	12195118	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tacagacataatgctgagccTggtaaccatagagctttcgt	9	9	0	3			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:12195118T>A	ENST00000287814.4	-	5	1082	c.572A>T	c.(571-573)cAg>cTg	p.Q191L	SYN2_ENST00000432424.2_RNA	NM_003256.3	NP_003247.1	Q99727	TIMP4_HUMAN	TIMP metallopeptidase inhibitor 4	191					central nervous system development (GO:0007417)|negative regulation of endopeptidase activity (GO:0010951)|ovulation cycle (GO:0042698)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to peptide hormone (GO:0043434)	extracellular space (GO:0005615)|sarcomere (GO:0030017)	metal ion binding (GO:0046872)|metalloendopeptidase inhibitor activity (GO:0008191)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	11						ATGCTGAGCCTGGTAACCATA	0.547																																					p.Q191L	Melanoma(199;1446 2144 30617 38794 51714)	Atlas-SNP	.											.	TIMP4	21	.	0			c.A572T						.						179	159	166					3																	12195118		2203	4300	6503	SO:0001583	missense	7079	exon5			TGAGCCTGGTAAC	U76456	CCDS2608.1	3p25	2005-10-31	2005-08-08		ENSG00000157150	ENSG00000157150			11823	protein-coding gene	gene with protein product		601915	"tissue inhibitor of metalloproteinase 4"			8939999, 9693046	Standard	NM_003256		Approved		uc003bwo.3	Q99727	OTTHUMG00000129763	ENST00000287814.4:c.572A>T	chr3.hg19:g.12195118T>A	ENSP00000287814:p.Gln191Leu	382.0	0.0		485.0	35.0	NM_003256	B2R7K6	Missense_Mutation	SNP	ENST00000287814.4	hg19	CCDS2608.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.846978	0.91277	.	.	ENSG00000157150	ENST00000287814	D	0.93859	-3.3	4.78	4.78	0.61160	Tissue inhibitor of metalloproteinases-like, OB-fold (1);	0.064005	0.64402	D	0.000004	D	0.96664	0.8911	M	0.84846	2.72	0.80722	D	1	D	0.76494	0.999	D	0.77004	0.989	D	0.97007	0.9733	10	0.56958	D	0.05	.	14.4922	0.67660	0.0:0.0:0.0:1.0	.	191	Q99727	TIMP4_HUMAN	L	191	ENSP00000287814:Q191L	ENSP00000287814:Q191L	Q	-	2	0	TIMP4	12170118	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.587000	0.82613	2.015000	0.59207	0.402000	0.26972	CAG	.	.		0.547	TIMP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251978.1	NM_003256		A	12195118	T	A	12195118	3	1	237	1	0	0	0	0	1	0	0	0	15935	1580	55	4	106	4	TIMP4	3	12195118	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10		12195118	185827312	44	32950										
TIMP4	7079	hgsc.bcm.edu	37	chr3	12198366	12198366	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ttggcttctagtttcacaccAcagagggaagagtcaaaagg	11	8	3	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:12198366A>G	ENST00000287814.4	-	3	816	c.306T>C	c.(304-306)tgT>tgC	p.C102C	SYN2_ENST00000432424.2_RNA	NM_003256.3	NP_003247.1	Q99727	TIMP4_HUMAN	TIMP metallopeptidase inhibitor 4	102	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				central nervous system development (GO:0007417)|negative regulation of endopeptidase activity (GO:0010951)|ovulation cycle (GO:0042698)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to peptide hormone (GO:0043434)	extracellular space (GO:0005615)|sarcomere (GO:0030017)	metal ion binding (GO:0046872)|metalloendopeptidase inhibitor activity (GO:0008191)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	11						GTTTCACACCACAGAGGGAAG	0.403																																					p.C102C	Melanoma(199;1446 2144 30617 38794 51714)	Atlas-SNP	.											.	TIMP4	21	.	0			c.T306C						.						126	115	119					3																	12198366		2203	4300	6503	SO:0001819	synonymous_variant	7079	exon3			CACACCACAGAGG	U76456	CCDS2608.1	3p25	2005-10-31	2005-08-08		ENSG00000157150	ENSG00000157150			11823	protein-coding gene	gene with protein product		601915	"tissue inhibitor of metalloproteinase 4"			8939999, 9693046	Standard	NM_003256		Approved		uc003bwo.3	Q99727	OTTHUMG00000129763	ENST00000287814.4:c.306T>C	chr3.hg19:g.12198366A>G		135.0	0.0		177.0	53.0	NM_003256	B2R7K6	Silent	SNP	ENST00000287814.4	hg19	CCDS2608.1																																																																																			.	.		0.403	TIMP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251978.1	NM_003256		G	12198366	A	G	12198366	2	3	237	1	0	0	0	0	0	0	0	1	15935	157	6	2		2	TIMP4	3	12198366	Silent	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	3248	12198366	185824064	45	32951										
CAND2	23066	hgsc.bcm.edu	37	chr3	12856693	12856693	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tgagctggaaggtgcgccggGcagctgccaagtgcatcgca	16	11	0	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:12856693G>T	ENST00000456430.2	+	8	1101	c.1060G>T	c.(1060-1062)Gca>Tca	p.A354S	CAND2_ENST00000295989.5_Missense_Mutation_p.A261S	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	354					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						GGTGCGCCGGGCAGCTGCCAA	0.602																																					p.A354S	GBM(43;676 868 1633 6395 37496)	Atlas-SNP	.											.	CAND2	138	.	0			c.G1060T						.						57	64	62					3																	12856693		2144	4252	6396	SO:0001583	missense	23066	exon8			CGCCGGGCAGCTG		CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"TBP interacting protein"	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.1060G>T	chr3.hg19:g.12856693G>T	ENSP00000387641:p.Ala354Ser	260.0	0.0		194.0	76.0	NM_001162499	B9EGM9|E9KL24	Missense_Mutation	SNP	ENST00000456430.2	hg19	CCDS54554.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.933132	0.73442	.	.	ENSG00000144712	ENST00000295989;ENST00000456430	T;T	0.10763	2.84;2.84	4.86	4.86	0.63082	Armadillo-like helical (1);Armadillo-type fold (1);	0.076940	0.51477	D	0.000096	T	0.17831	0.0428	L	0.33293	1	0.80722	D	1	B;D	0.61697	0.303;0.99	B;D	0.73380	0.145;0.98	T	0.07751	-1.0756	10	0.13108	T	0.6	-26.4464	10.7022	0.45934	0.0:0.0:0.8093:0.1907	.	354;261	O75155;O75155-2	CAND2_HUMAN;.	S	261;354	ENSP00000295989:A261S;ENSP00000387641:A354S	ENSP00000295989:A261S	A	+	1	0	CAND2	12831693	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	1.761000	0.38440	2.231000	0.72958	0.561000	0.74099	GCA	.	.		0.602	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617		T	12856693	G	T	12856693	3	4	237	1	0	0	0	0	1	0	0	0	2618	1203	42	3	1090	3	CAND2	3	12856693	Missense_Mutation	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	658327	12856693	185165737	46	32952										
MRPS25	64432	hgsc.bcm.edu	37	chr3	15093970	15093970	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	agtcctgggcatcggctttcAgagcggctttgtacttcccc	11	13	1	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:15093970A>T	ENST00000253686.2	-	4	640	c.500T>A	c.(499-501)cTg>cAg	p.L167Q	MRPS25_ENST00000444840.2_3'UTR|MRPS25_ENST00000449354.2_Intron|MRPS25_ENST00000496484.1_5'Flank	NM_022497.3	NP_071942.1	P82663	RT25_HUMAN	mitochondrial ribosomal protein S25	167						mitochondrion (GO:0005739)|ribosome (GO:0005840)				large_intestine(1)|lung(1)	2						ATCGGCTTTCAGAGCGGCTTT	0.597																																					p.L167Q		Atlas-SNP	.											.	MRPS25	14	.	0			c.T500A						.						169	148	155					3																	15093970		2203	4300	6503	SO:0001583	missense	64432	exon4			GCTTTCAGAGCGG	AB061208	CCDS2622.1	3p25	2012-09-13			ENSG00000131368	ENSG00000131368		"Mitochondrial ribosomal proteins / small subunits"	14511	protein-coding gene	gene with protein product	"mitochondrial 28S ribosomal protein S25"	611987				11279123	Standard	NM_022497		Approved	MRP-S25, FLJ00023, DKFZp313H0817, RPMS25	uc003bzl.3	P82663	OTTHUMG00000129836	ENST00000253686.2:c.500T>A	chr3.hg19:g.15093970A>T	ENSP00000253686:p.Leu167Gln	156.0	0.0		191.0	13.0	NM_022497	B4DFJ5|B4DQG6|Q9H7P5	Missense_Mutation	SNP	ENST00000253686.2	hg19	CCDS2622.1	.	.	.	.	.	.	.	.	.	.	A	15.72	2.916035	0.52546	.	.	ENSG00000131368	ENST00000253686	.	.	.	5.48	5.48	0.80851	.	0.169199	0.51477	D	0.000081	T	0.47451	0.1446	L	0.45581	1.43	0.80722	D	1	B	0.18741	0.03	B	0.12837	0.008	T	0.40251	-0.9573	9	0.22109	T	0.4	-29.3001	9.8852	0.41257	0.8474:0.0:0.0:0.1526	.	167	P82663	RT25_HUMAN	Q	167	.	ENSP00000253686:L167Q	L	-	2	0	MRPS25	15068974	0.585000	0.26774	0.070000	0.20053	0.034000	0.12701	2.063000	0.41423	2.079000	0.62486	0.402000	0.26972	CTG	.	.		0.597	MRPS25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252076.2	NM_022497		T	15093970	A	T	15093970	3	4	237	1	0	0	0	0	1	0	0	0	9845	188	7	4	25	4	MRPS25	3	15093970	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	2237277	15093970	182928460	47	32953										
SCN11A	11280	hgsc.bcm.edu	37	chr3	38945427	38945427	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ctccatggccaagaagacagTgttgatgatgatgcagatgg	13	7	0	6			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:38945427T>A	ENST00000302328.3	-	12	1969	c.1771A>T	c.(1771-1773)Act>Tct	p.T591S	SCN11A_ENST00000450244.1_Missense_Mutation_p.T591S|SCN11A_ENST00000444237.2_Missense_Mutation_p.T591S|SCN11A_ENST00000456224.3_Missense_Mutation_p.T591S	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	591					cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AAGAAGACAGTGTTGATGATG	0.433																																					p.T591S		Atlas-SNP	.											.	SCN11A	296	.	0			c.A1771T						.						143	124	130					3																	38945427		2203	4300	6503	SO:0001583	missense	11280	exon12			AGACAGTGTTGAT	AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10583	protein-coding gene	gene with protein product		604385	"sodium channel, voltage-gated, type XI, alpha polypeptide", "sodium channel, voltage-gated, type XII, alpha"	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.1771A>T	chr3.hg19:g.38945427T>A	ENSP00000307599:p.Thr591Ser	372.0	1.0		361.0	119.0	NM_014139	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Missense_Mutation	SNP	ENST00000302328.3	hg19	CCDS33737.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.976746	0.74360	.	.	ENSG00000168356	ENST00000302328;ENST00000450244;ENST00000456224;ENST00000444237	D;D;D;D	0.97378	-4.36;-4.36;-4.36;-4.36	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	D	0.98639	0.9544	M	0.90922	3.16	0.51767	D	0.999937	D	0.76494	0.999	D	0.80764	0.994	D	0.99320	1.0906	10	0.49607	T	0.09	.	14.5917	0.68371	0.0:0.0:0.0:1.0	.	591	Q9UI33	SCNBA_HUMAN	S	591	ENSP00000307599:T591S;ENSP00000400945:T591S;ENSP00000416757:T591S;ENSP00000408028:T591S	ENSP00000307599:T591S	T	-	1	0	SCN11A	38920431	1.000000	0.71417	0.989000	0.46669	0.945000	0.59286	7.993000	0.88291	2.124000	0.65301	0.477000	0.44152	ACT	.	.		0.433	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139		A	38945427	T	A	38945427	3	1	237	1	0	0	0	0	1	0	0	0	13928	1696	59	4	3664	4	SCN11A	3	38945427	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	23851457	38945427	159077003	48	32954										
NKTR	4820	hgsc.bcm.edu	37	chr3	42674105	42674105	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	cttaaaagtttttgagaaaaAaaggaagaaaccaactcatt	6	5	1	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:42674105A>G	ENST00000232978.8	+	9	751	c.563A>G	c.(562-564)aAa>aGa	p.K188R	RP4-613B23.1_ENST00000438017.1_RNA|RP4-613B23.1_ENST00000434363.1_RNA|RP4-613B23.1_ENST00000445452.1_RNA	NM_005385.3	NP_005376.2	P30414	NKTR_HUMAN	natural killer cell triggering receptor	188					protein folding (GO:0006457)	membrane (GO:0016020)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	41				KIRC - Kidney renal clear cell carcinoma(284;0.24)		TTTGAGAAAAAAAGGAAGAAA	0.323																																					p.K188R		Atlas-SNP	.											.	NKTR	116	.	0			c.A563G						.						36	38	37					3																	42674105		2203	4299	6502	SO:0001583	missense	4820	exon9			AGAAAAAAAGGAA		CCDS2702.1	3p22.1	2014-01-20	2014-01-20		ENSG00000114857	ENSG00000114857			7833	protein-coding gene	gene with protein product	"NK-tumor recognition protein", "natural-killer cells cyclophilin-related protein", "NK-TR protein"	161565	"natural killer-tumor recognition sequence"			8314596, 8144875	Standard	XM_005265173		Approved	p104	uc003clo.3	P30414	OTTHUMG00000133037	ENST00000232978.8:c.563A>G	chr3.hg19:g.42674105A>G	ENSP00000232978:p.Lys188Arg	70.0	0.0		86.0	25.0	NM_005385		Missense_Mutation	SNP	ENST00000232978.8	hg19	CCDS2702.1	.	.	.	.	.	.	.	.	.	.	A	25.7	4.660344	0.88154	.	.	ENSG00000114857	ENST00000232978	T	0.15487	2.42	5.83	5.83	0.93111	.	0.048674	0.85682	D	0.000000	T	0.40909	0.1136	M	0.64567	1.98	0.80722	D	1	D;D	0.89917	0.997;1.0	D;D	0.83275	0.985;0.996	T	0.15954	-1.0419	10	0.59425	D	0.04	-23.7897	16.1949	0.82021	1.0:0.0:0.0:0.0	.	68;188	Q59EC3;P30414	.;NKTR_HUMAN	R	188	ENSP00000232978:K188R	ENSP00000232978:K188R	K	+	2	0	NKTR	42649109	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.777000	0.75028	2.222000	0.72286	0.533000	0.62120	AAA	.	.		0.323	NKTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256642.2	NM_005385		G	42674105	A	G	42674105	3	3	237	1	0	0	0	0	1	0	0	0	10457	14	1	2	593	2	NKTR	3	42674105	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	3728678	42674105	155348325	49	32955										
NISCH	11188	hgsc.bcm.edu	37	chr3	52489713	52489713	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	agccgagccggccaaggaagCgcgcgtcgtgggctcggagc	18	13	0	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:52489713C>T	ENST00000479054.1	+	2	128	c.56C>T	c.(55-57)gCg>gTg	p.A19V	TNNC1_ENST00000232975.3_5'Flank|NISCH_ENST00000420808.2_Missense_Mutation_p.A19V|NISCH_ENST00000488380.1_Missense_Mutation_p.A19V|NISCH_ENST00000345716.4_Missense_Mutation_p.A19V			Q9Y2I1	NISCH_HUMAN	nischarin	19	Necessary for binding to phosphoinositide-3-P; not sufficient for targeting to endosomes.|PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				actin cytoskeleton organization (GO:0030036)|apoptotic process (GO:0006915)|glucose metabolic process (GO:0006006)|negative regulation of cell migration (GO:0030336)|norepinephrine secretion (GO:0048243)|Rac protein signal transduction (GO:0016601)|regulation of blood pressure (GO:0008217)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)|plasma membrane (GO:0005886)	G-protein coupled amine receptor activity (GO:0008227)|identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)			NS(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(9)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	33				BRCA - Breast invasive adenocarcinoma(193;1.93e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)|OV - Ovarian serous cystadenocarcinoma(275;0.0577)	Tizanidine(DB00697)	GCCAAGGAAGCGCGCGTCGTG	0.726																																					p.A19V		Atlas-SNP	.											.	NISCH	97	.	0			c.C56T						.						7	10	9					3																	52489713		2027	4089	6116	SO:0001583	missense	11188	exon1			AGGAAGCGCGCGT	AF082516	CCDS33767.1, CCDS63651.1, CCDS63652.1	3p21.1	2008-07-18			ENSG00000010322	ENSG00000010322			18006	protein-coding gene	gene with protein product	"imidazoline receptor candidate", "I-1 receptor candidate protein", "imidazoline receptor antisera selected"	615507				11912194, 10882231	Standard	NM_007184		Approved	KIAA0975, I-1, IRAS	uc003ded.4	Q9Y2I1	OTTHUMG00000158571	ENST00000479054.1:c.56C>T	chr3.hg19:g.52489713C>T	ENSP00000418232:p.Ala19Val	34.0	0.0		12.0	7.0	NM_001276293	C9J245|Q6PGP3|Q6PIB4|Q7L8M3|Q7Z2X6|Q9UES6|Q9UEU4|Q9UFW3	Missense_Mutation	SNP	ENST00000479054.1	hg19	CCDS33767.1	.	.	.	.	.	.	.	.	.	.	C	16.38	3.108295	0.56291	.	.	ENSG00000010322	ENST00000479054;ENST00000345716;ENST00000433196;ENST00000488380;ENST00000420808	T;T;T;T	0.07216	3.42;3.42;3.24;3.21	4.9	4.9	0.64082	Phox homologous domain (3);	0.060349	0.64402	D	0.000003	T	0.02380	0.0073	N	0.02181	-0.65	0.50467	D	0.999875	D;P	0.53619	0.961;0.806	B;B	0.38803	0.282;0.103	T	0.49969	-0.8882	10	0.02654	T	1	-23.1454	10.3167	0.43740	0.0:0.9082:0.0:0.0918	.	19;19	Q9Y2I1;C9J715	NISCH_HUMAN;.	V	19	ENSP00000418232:A19V;ENSP00000339958:A19V;ENSP00000417812:A19V;ENSP00000392484:A19V	ENSP00000339958:A19V	A	+	2	0	NISCH	52464753	1.000000	0.71417	0.999000	0.59377	0.786000	0.44442	2.593000	0.46180	2.268000	0.75426	0.655000	0.94253	GCG	.	.		0.726	NISCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351357.1	NM_007184		T	52489713	C	T	52489713	3	4	237	1	0	0	0	0	1	0	0	0	10441	768	27	1	58	1	NISCH	3	52489713	Missense_Mutation	SNP	C	TCGA-ED-A459-01A-11D-A25V-10	9815608	52489713	145532717	50	32956										
CHDH	55349	hgsc.bcm.edu	37	chr3	53857409	53857409	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tcctcggtgagcgggtagccGgcctgctgcgtggcctccag	16	14	0	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:53857409G>A	ENST00000315251.6	-	3	1064	c.627C>T	c.(625-627)gcC>gcT	p.A209A		NM_018397.4	NP_060867.2	Q8NE62	CHDH_HUMAN	choline dehydrogenase	209					glycine betaine biosynthetic process from choline (GO:0019285)	mitochondrial inner membrane (GO:0005743)	choline dehydrogenase activity (GO:0008812)|flavin adenine dinucleotide binding (GO:0050660)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	17		Hepatocellular(537;0.152)		BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)	Choline(DB00122)	GCGGGTAGCCGGCCTGCTGCG	0.652																																					p.A209A		Atlas-SNP	.											.	CHDH	34	.	0			c.C627T						.						37	39	38					3																	53857409		2202	4300	6502	SO:0001819	synonymous_variant	55349	exon3			GTAGCCGGCCTGC	AJ272267	CCDS2873.1	3p21	2004-11-24			ENSG00000016391	ENSG00000016391	1.1.99.1		24288	protein-coding gene	gene with protein product							Standard	NM_018397		Approved		uc003dgz.3	Q8NE62	OTTHUMG00000158281	ENST00000315251.6:c.627C>T	chr3.hg19:g.53857409G>A		143.0	0.0		99.0	11.0	NM_018397	Q9NY17	Silent	SNP	ENST00000315251.6	hg19	CCDS2873.1																																																																																			.	.		0.652	CHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350567.2	NM_018397		A	53857409	G	A	53857409	2	1	237	1	0	0	0	0	0	0	0	1	3335	1103	39	1		1	CHDH	3	53857409	Silent	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	1367696	53857409	144165021	51	32957										
CADPS	8618	hgsc.bcm.edu	37	chr3	62518735	62518735	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ggccaggactgaaccagcccTatataaagaataaaggagag	11	8	0	3			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:62518735T>A	ENST00000383710.4	-	13	2453		c.e13-2		CADPS_ENST00000357948.3_Splice_Site|CADPS_ENST00000283269.9_Splice_Site	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator						catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		GAACCAGCCCTATATAAAGAA	0.478																																					.		Atlas-SNP	.											.	CADPS	387	.	0			c.2104-2A>T						.						39	40	40					3																	62518735		2203	4300	6503	SO:0001630	splice_region_variant	8618	exon14			CAGCCCTATATAA	U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"Pleckstrin homology (PH) domain containing"	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.2104-2A>T	chr3.hg19:g.62518735T>A		71.0	0.0		90.0	7.0	NM_183394	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Splice_Site	SNP	ENST00000383710.4	hg19	CCDS46858.1	.	.	.	.	.	.	.	.	.	.	T	18.08	3.544072	0.65198	.	.	ENSG00000163618	ENST00000383709;ENST00000383710;ENST00000357948;ENST00000283269;ENST00000491424;ENST00000468271;ENST00000478434;ENST00000542833	.	.	.	5.77	5.77	0.91146	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0908	0.81090	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	CADPS	62493775	1.000000	0.71417	0.967000	0.41034	0.615000	0.37417	8.040000	0.89188	2.202000	0.70862	0.455000	0.32223	.	.	.		0.478	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394	Intron	A	62518735	T	A	62518735	5	1	237	1	0	0	0	0	0	0	1	0	2572	1536	53	4	2104	4	CADPS	3	62518735	Splice_Site	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	8661326	62518735	135503695	52	32958										
OR5H14	403273	hgsc.bcm.edu	37	chr3	97868315	97868315	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gtggaaaatacccctgttccTggcattcttggtaatatatc	8	9	1	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:97868315T>A	ENST00000437310.1	+	1	146	c.86T>A	c.(85-87)cTg>cAg	p.L29Q	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005514.1	NP_001005514.1	A6NHG9	O5H14_HUMAN	olfactory receptor, family 5, subfamily H, member 14	29						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	31						CCCCTGTTCCTGGCATTCTTG	0.418																																					p.L29Q		Atlas-SNP	.											.	OR5H14	56	.	0			c.T86A						.						90	95	93					3																	97868315		2202	4279	6481	SO:0001583	missense	403273	exon1			TGTTCCTGGCATT		CCDS33798.1	3q11.2	2013-09-23			ENSG00000236032	ENSG00000236032		"GPCR / Class A : Olfactory receptors"	31286	protein-coding gene	gene with protein product							Standard	NM_001005514		Approved		uc003dsg.1	A6NHG9	OTTHUMG00000160079	ENST00000437310.1:c.86T>A	chr3.hg19:g.97868315T>A	ENSP00000401706:p.Leu29Gln	256.0	0.0		291.0	18.0	NM_001005514	B9EH15	Missense_Mutation	SNP	ENST00000437310.1	hg19	CCDS33798.1	.	.	.	.	.	.	.	.	.	.	T	10.37	1.331239	0.24167	.	.	ENSG00000236032	ENST00000437310	T	0.00457	7.29	2.3	1.13	0.20643	.	0.000000	0.32819	N	0.005607	T	0.01387	0.0045	M	0.92122	3.275	0.09310	N	1	D	0.76494	0.999	D	0.69824	0.966	T	0.32161	-0.9917	10	0.62326	D	0.03	.	5.2077	0.15299	0.0:0.1723:0.0:0.8277	.	29	A6NHG9	O5H14_HUMAN	Q	29	ENSP00000401706:L29Q	ENSP00000401706:L29Q	L	+	2	0	OR5H14	99351005	0.027000	0.19231	0.649000	0.29536	0.386000	0.30323	2.309000	0.43699	1.052000	0.40392	0.164000	0.16699	CTG	.	.		0.418	OR5H14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359112.1			A	97868315	T	A	97868315	3	1	237	1	0	0	0	0	1	0	0	0	11169	1580	55	4	88	4	OR5H14	3	97868315	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	35349580	97868315	100154115	53	32959										
CEP97	79598	hgsc.bcm.edu	37	chr3	101451370	101451370	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ttaactgaattggaacagttGtcgattatgaacaatccttg	8	6	0	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:101451370G>A	ENST00000341893.3	+	6	1352	c.600G>A	c.(598-600)ttG>ttA	p.L200L	CEP97_ENST00000327230.4_Silent_p.L200L|CEP97_ENST00000494050.1_Silent_p.L200L			Q8IW35	CEP97_HUMAN	centrosomal protein 97kDa	200					cell projection organization (GO:0030030)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)				cervix(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	29						TGGAACAGTTGTCGATTATGA	0.418																																					p.L200L		Atlas-SNP	.											.	CEP97	122	.	0			c.G600A						.						136	121	126					3																	101451370		2203	4300	6503	SO:0001819	synonymous_variant	79598	exon6			ACAGTTGTCGATT	AL833269	CCDS2944.1	3q12.3	2014-02-20	2008-01-08	2008-01-08	ENSG00000182504	ENSG00000182504			26244	protein-coding gene	gene with protein product		615864	"leucine-rich repeats and IQ motif containing 2"	LRRIQ2		17719545, 18068367	Standard	NM_024548		Approved	FLJ23047	uc003dvk.1	Q8IW35	OTTHUMG00000159162	ENST00000341893.3:c.600G>A	chr3.hg19:g.101451370G>A		219.0	0.0		232.0	34.0	NM_024548	B5MDY8|Q8NA71|Q9H5T9	Silent	SNP	ENST00000341893.3	hg19	CCDS2944.1																																																																																			.	.		0.418	CEP97-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353597.2	NM_024548		A	101451370	G	A	101451370	2	1	237	1	0	0	0	0	0	0	0	1	3265	1368	48	3		3	CEP97	3	101451370	Silent	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	3583055	101451370	96571060	54	32960										
KALRN	8997	hgsc.bcm.edu	37	chr3	124048793	124048793	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	agacctagagctggcaatccAccaccaccagaccttgtatg	8	14	0	3			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:124048793A>T	ENST00000240874.3	+	8	1521	c.1364A>T	c.(1363-1365)cAc>cTc	p.H455L	KALRN_ENST00000460856.1_Missense_Mutation_p.H455L|KALRN_ENST00000360013.3_Missense_Mutation_p.H455L	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	455					apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						CTGGCAATCCACCACCACCAG	0.562																																					p.H455L		Atlas-SNP	.											.	KALRN	556	.	0			c.A1364T						.						150	124	133					3																	124048793		2203	4300	6503	SO:0001583	missense	8997	exon8			CAATCCACCACCA	U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	4814	protein-coding gene	gene with protein product	"serine/threonine kinase with Dbl and pleckstrin homology domains"	604605	"huntingtin-associated protein interacting protein (duo)"	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000240874.3:c.1364A>T	chr3.hg19:g.124048793A>T	ENSP00000240874:p.His455Leu	245.0	0.0		262.0	79.0	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Missense_Mutation	SNP	ENST00000240874.3	hg19	CCDS3027.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.2|21.2	4.115741|4.115741	0.77323|0.77323	.|.	.|.	ENSG00000160145|ENSG00000160145	ENST00000460856;ENST00000240874;ENST00000360013|ENST00000354186	T;T;T|.	0.40756|.	1.02;1.02;1.02|.	5.0|5.0	5.0|5.0	0.66597|0.66597	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.73094|0.73094	0.3543|0.3543	M|M	0.69823|0.69823	2.125|2.125	0.80722|0.80722	D|D	1|1	P;D;P|.	0.65815|.	0.895;0.995;0.936|.	P;D;P|.	0.72982|.	0.468;0.979;0.669|.	T|T	0.73633|0.73633	-0.3921|-0.3921	10|5	0.32370|.	T|.	0.25|.	.|.	15.1541|15.1541	0.72726|0.72726	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	455;455;455|.	C9IZQ6;O60229;O60229-2|.	.;KALRN_HUMAN;.|.	L|S	455|433	ENSP00000418611:H455L;ENSP00000240874:H455L;ENSP00000353109:H455L|.	ENSP00000240874:H455L|.	H|T	+|+	2|1	0|0	KALRN|KALRN	125531483|125531483	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.984000|0.984000	0.73092|0.73092	9.087000|9.087000	0.94110|0.94110	2.225000|2.225000	0.72522|0.72522	0.533000|0.533000	0.62120|0.62120	CAC|ACC	.	.		0.562	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947		T	124048793	A	T	124048793	3	4	237	1	0	0	0	0	1	0	0	0	7984	159	6	4	1394	4	KALRN	3	124048793	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	22597423	124048793	73973637	55	32961										
ITGB5	3693	hgsc.bcm.edu	37	chr3	124592297	124592297	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tcccccacctacatacctctTtggagcaccaggcacatttt	5	16	1	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:124592297T>A	ENST00000296181.4	-	2	448	c.152A>T	c.(151-153)aAa>aTa	p.K51I		NM_002213.3	NP_002204.2	P18084	ITB5_HUMAN	integrin, beta 5	51	PSI.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|epithelial cell-cell adhesion (GO:0090136)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|stress fiber assembly (GO:0043149)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alphav-beta5 complex (GO:0034684)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	30				GBM - Glioblastoma multiforme(114;0.163)		ACATACCTCTTTGGAGCACCA	0.483																																					p.K51I		Atlas-SNP	.											.	ITGB5	66	.	0			c.A152T						.						252	236	241					3																	124592297		2203	4300	6503	SO:0001583	missense	3693	exon2			ACCTCTTTGGAGC	J05633	CCDS3030.1	3q21.2	2010-03-23			ENSG00000082781	ENSG00000082781		"Integrins"	6160	protein-coding gene	gene with protein product		147561				2211615	Standard	NM_002213		Approved		uc003eho.3	P18084	OTTHUMG00000159432	ENST00000296181.4:c.152A>T	chr3.hg19:g.124592297T>A	ENSP00000296181:p.Lys51Ile	242.0	0.0		269.0	21.0	NM_002213	B0LPF8|B2RD70	Missense_Mutation	SNP	ENST00000296181.4	hg19	CCDS3030.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.055441	0.75960	.	.	ENSG00000082781	ENST00000296181	D	0.92965	-3.14	5.04	2.36	0.29203	Integrin beta subunit, N-terminal (2);	0.224693	0.47093	D	0.000258	D	0.92476	0.7611	M	0.67700	2.07	0.39505	D	0.968269	P	0.48016	0.904	P	0.54312	0.748	D	0.90475	0.4456	10	0.66056	D	0.02	.	6.8438	0.23977	0.0:0.2278:0.0:0.7722	.	51	P18084	ITB5_HUMAN	I	51	ENSP00000296181:K51I	ENSP00000296181:K51I	K	-	2	0	ITGB5	126074987	1.000000	0.71417	0.998000	0.56505	0.971000	0.66376	2.262000	0.43285	0.300000	0.22699	0.379000	0.24179	AAA	.	.		0.483	ITGB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355286.3	NM_002213		A	124592297	T	A	124592297	3	1	237	1	0	0	0	0	1	0	0	0	7907	1841	64	4	2303	4	ITGB5	3	124592297	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	543504	124592297	73430133	56	32962										
MGLL	11343	hgsc.bcm.edu	37	chr3	127441397	127441397	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ccatcctctccccttcgctcTgtccgtggccaactggaaag	8	17	2	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:127441397T>C	ENST00000434178.2	-	4	1141	c.245A>G	c.(244-246)cAg>cGg	p.Q82R	MGLL_ENST00000453507.2_Missense_Mutation_p.Q92R|MGLL_ENST00000398104.1_Missense_Mutation_p.Q82R|MGLL_ENST00000398101.3_Missense_Mutation_p.Q56R|MGLL_ENST00000265052.5_Missense_Mutation_p.Q92R			Q99685	MGLL_HUMAN	monoglyceride lipase	82					acylglycerol acyl-chain remodeling (GO:0036155)|acylglycerol catabolic process (GO:0046464)|arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|fatty acid biosynthetic process (GO:0006633)|glycerophospholipid biosynthetic process (GO:0046474)|inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|long term synaptic depression (GO:0060292)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|regulation of endocannabinoid signaling pathway (GO:2000124)|regulation of inflammatory response (GO:0050727)|regulation of sensory perception of pain (GO:0051930)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acylglycerol lipase activity (GO:0047372)|lipid binding (GO:0008289)|lysophospholipase activity (GO:0004622)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	6						CCCTTCGCTCTGTCCGTGGCC	0.542																																					p.Q92R		Atlas-SNP	.											.	MGLL	19	.	0			c.A275G						.						92	97	96					3																	127441397		2065	4224	6289	SO:0001583	missense	11343	exon4			TCGCTCTGTCCGT	BC000551	CCDS43148.1, CCDS46902.1, CCDS58852.1	3p13-q13.33	2014-03-14			ENSG00000074416	ENSG00000074416	3.1.1.23		17038	protein-coding gene	gene with protein product		609699				9495531	Standard	NM_007283		Approved	HU-K5, MGL	uc003ejx.4	Q99685	OTTHUMG00000159641	ENST00000434178.2:c.245A>G	chr3.hg19:g.127441397T>C	ENSP00000402798:p.Gln82Arg	245.0	0.0		329.0	120.0	NM_007283	B3KRC2|B7Z9D1|Q6IBG9|Q96AA5	Missense_Mutation	SNP	ENST00000434178.2	hg19	CCDS43148.1	.	.	.	.	.	.	.	.	.	.	T	11.52	1.663813	0.29515	.	.	ENSG00000074416	ENST00000434178;ENST00000265052;ENST00000398104;ENST00000398101;ENST00000487473;ENST00000536024;ENST00000453507;ENST00000484451;ENST00000493611	T;T;T;T;T;T;T	0.74315	-0.83;-0.83;-0.83;-0.83;-0.11;-0.11;-0.11	4.85	2.4	0.29515	Alpha/beta hydrolase fold-1 (1);	0.121894	0.56097	N	0.000023	T	0.50188	0.1601	N	0.11000	0.08	0.47245	D	0.999366	B;B;B;B;B	0.17465	0.01;0.019;0.022;0.004;0.003	B;B;B;B;B	0.31290	0.087;0.127;0.053;0.024;0.017	T	0.28490	-1.0042	10	0.06236	T	0.91	-12.7767	6.6136	0.22765	0.0:0.0836:0.1554:0.761	.	92;82;82;92;56	B7Z9D1;B2ZGL7;Q99685;B3KRC2;E7EWX8	.;.;MGLL_HUMAN;.;.	R	82;92;82;56;6;92;92;6;19	ENSP00000402798:Q82R;ENSP00000265052:Q92R;ENSP00000381176:Q82R;ENSP00000381173:Q56R;ENSP00000420125:Q6R;ENSP00000419340:Q6R;ENSP00000417689:Q19R	ENSP00000265052:Q92R	Q	-	2	0	MGLL	128924087	1.000000	0.71417	0.996000	0.52242	0.390000	0.30446	5.538000	0.67193	0.216000	0.20781	0.254000	0.18369	CAG	.	.		0.542	MGLL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356637.2	NM_007283		C	127441397	T	C	127441397	3	2	237	1	0	0	0	0	1	0	0	0	9565	1580	55	2	686	2	MGLL	3	127441397	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	2849100	127441397	70581033	57	32963										
CPNE4	131034	hgsc.bcm.edu	37	chr3	131418758	131418758	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ggagtgcctgcttaccgtgaTggaagatttccctgctgtgt	13	9	0	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:131418758T>A	ENST00000512055.1	-	8	2553	c.427A>T	c.(427-429)Atc>Ttc	p.I143F	CPNE4_ENST00000502818.1_Missense_Mutation_p.I161F|CPNE4_ENST00000512332.1_Missense_Mutation_p.I161F|CPNE4_ENST00000511604.1_Missense_Mutation_p.I143F|CPNE4_ENST00000429747.1_Missense_Mutation_p.I143F			Q96A23	CPNE4_HUMAN	copine IV	143	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.					extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|liver(1)|lung(16)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	39						CTTACCGTGATGGAAGATTTC	0.502																																					p.I143F		Atlas-SNP	.											.	CPNE4	112	.	0			c.A427T						.						74	66	69					3																	131418758		2203	4300	6503	SO:0001583	missense	131034	exon4			CCGTGATGGAAGA	H29499	CCDS3072.1, CCDS75010.1	3q22.1	2014-09-04			ENSG00000196353	ENSG00000196353			2317	protein-coding gene	gene with protein product	"copine 8"	604208				9430674, 12670487	Standard	XM_005247107		Approved	COPN4, CPN4	uc003eok.3	Q96A23	OTTHUMG00000159631	ENST00000512055.1:c.427A>T	chr3.hg19:g.131418758T>A	ENSP00000421705:p.Ile143Phe	97.0	0.0		133.0	9.0	NM_130808	D3DNC5|Q8TEX1	Missense_Mutation	SNP	ENST00000512055.1	hg19	CCDS3072.1	.	.	.	.	.	.	.	.	.	.	T	19.96	3.924203	0.73213	.	.	ENSG00000196353	ENST00000512055;ENST00000429747;ENST00000512332;ENST00000511604;ENST00000502818;ENST00000505881	T;T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95;0.95	5.32	5.32	0.75619	C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.65249	0.2673	M	0.84948	2.725	0.80722	D	1	D;D	0.56968	0.977;0.978	P;P	0.59825	0.854;0.864	T	0.72437	-0.4294	10	0.87932	D	0	-16.7256	15.5801	0.76428	0.0:0.0:0.0:1.0	.	161;143	Q96A23-2;Q96A23	.;CPNE4_HUMAN	F	143;143;161;143;161;143	ENSP00000421705:I143F;ENSP00000411904:I143F;ENSP00000424853:I161F;ENSP00000423811:I143F;ENSP00000421646:I161F;ENSP00000425506:I143F	ENSP00000411904:I143F	I	-	1	0	CPNE4	132901448	1.000000	0.71417	1.000000	0.80357	0.489000	0.33432	6.875000	0.75551	2.153000	0.67306	0.528000	0.53228	ATC	.	.		0.502	CPNE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356583.4	NM_130808		A	131418758	T	A	131418758	3	1	237	1	0	0	0	0	1	0	0	0	3816	1464	51	4	1298	4	CPNE4	3	131418758	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	3977361	131418758	66603672	58	32964										
ZIC4	84107	hgsc.bcm.edu	37	chr3	147108887	147108887	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	catgtgcttacgcagcgagcTggggtgcgtgtagcacttgt	15	9	0	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:147108887T>A	ENST00000383075.3	-	4	1347	c.835A>T	c.(835-837)Agc>Tgc	p.S279C	ZIC4_ENST00000473123.1_Missense_Mutation_p.S279C|ZIC4_ENST00000491672.1_Missense_Mutation_p.S73C|ZIC4_ENST00000472749.2_5'UTR|ZIC4_ENST00000484399.1_Missense_Mutation_p.S279C|ZIC4_ENST00000425731.3_Missense_Mutation_p.S317C|ZIC4_ENST00000525172.2_Missense_Mutation_p.S329C	NM_032153.5	NP_115529.2	Q8N9L1	ZIC4_HUMAN	Zic family member 4	279						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(34)|upper_aerodigestive_tract(4)	57						CGCAGCGAGCTGGGGTGCGTG	0.642																																					p.S329C		Atlas-SNP	.											.	ZIC4	174	.	0			c.A985T						.						40	46	44					3																	147108887		2203	4300	6503	SO:0001583	missense	84107	exon4			GCGAGCTGGGGTG	AF332509	CCDS43160.1, CCDS54652.1, CCDS54653.1, CCDS58857.1	3q24	2013-01-08	2003-02-21		ENSG00000174963	ENSG00000174963		"Zinc fingers, C2H2-type"	20393	protein-coding gene	gene with protein product		608948	"zinc finger protein of the cerebellum 4"				Standard	NM_001168378		Approved		uc011bno.2	Q8N9L1	OTTHUMG00000037281	ENST00000383075.3:c.835A>T	chr3.hg19:g.147108887T>A	ENSP00000372553:p.Ser279Cys	172.0	0.0		80.0	7.0	NM_001168378	A0AVA2|B2RMQ8|B4DF89|B7Z2L2|C9J7D5|J3KQG1|Q4G157|Q9BZ94	Missense_Mutation	SNP	ENST00000383075.3	hg19	CCDS43160.1	.	.	.	.	.	.	.	.	.	.	T	32	5.115585	0.94339	.	.	ENSG00000174963	ENST00000383075;ENST00000425731;ENST00000525172;ENST00000484399;ENST00000473123;ENST00000491672	T;T;T;T;T;T	0.58940	0.3;0.3;0.3;0.3;0.3;1.22	5.05	5.05	0.67936	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.56097	D	0.000037	T	0.71634	0.3363	L	0.52823	1.66	0.50171	D	0.999856	D;D	0.89917	0.999;1.0	D;D	0.97110	0.982;1.0	T	0.78257	-0.2274	9	0.87932	D	0	.	14.795	0.69870	0.0:0.0:0.0:1.0	.	329;279	B7Z2L2;Q8N9L1	.;ZIC4_HUMAN	C	279;317;329;279;279;73	ENSP00000372553:S279C;ENSP00000397695:S317C;ENSP00000435509:S329C;ENSP00000417855:S279C;ENSP00000420775:S279C;ENSP00000418277:S73C	ENSP00000372553:S279C	S	-	1	0	ZIC4	148591577	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.954000	0.87848	1.894000	0.54839	0.379000	0.24179	AGC	.	.		0.642	ZIC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355504.1			A	147108887	T	A	147108887	3	1	237	1	0	0	0	0	1	0	0	0	17696	1580	55	4	177	4	ZIC4	3	147108887	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	15690129	147108887	50913543	59	32965										
FAM194A	131831	hgsc.bcm.edu	37	chr3	150398678	150398678	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ttttatttgctcctcatagaTatagtcaatcagattttgga	6	6	3	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:150398678T>A	ENST00000295910.6	-	8	974	c.922A>T	c.(922-924)Atc>Ttc	p.I308F	FAM194A_ENST00000491361.1_Missense_Mutation_p.I162F	NM_152394.3	NP_689607.2														NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						TCCTCATAGATATAGTCAATC	0.423																																					p.I308F		Atlas-SNP	.											.	FAM194A	91	.	0			c.A922T						.						120	119	119					3																	150398678		2203	4300	6503	SO:0001583	missense	131831	exon8			CATAGATATAGTC																												ENST00000295910.6:c.922A>T	chr3.hg19:g.150398678T>A	ENSP00000295910:p.Ile308Phe	94.0	0.0		91.0	5.0	NM_152394		Missense_Mutation	SNP	ENST00000295910.6	hg19	CCDS3151.2	.	.	.	.	.	.	.	.	.	.	T	15.17	2.753964	0.49362	.	.	ENSG00000163645	ENST00000295910;ENST00000491361;ENST00000313811	T;T	0.16196	2.5;2.36	4.73	0.946	0.19549	.	0.208889	0.33327	N	0.005025	T	0.25419	0.0618	M	0.63843	1.955	0.09310	N	0.999996	D	0.57257	0.979	P	0.57244	0.816	T	0.07366	-1.0776	10	0.62326	D	0.03	-16.9773	3.9803	0.09492	0.0:0.192:0.1817:0.6263	.	308	Q7L0X2	F194A_HUMAN	F	308;162;266	ENSP00000295910:I308F;ENSP00000419366:I162F	ENSP00000295910:I308F	I	-	1	0	FAM194A	151881368	0.979000	0.34478	0.022000	0.16811	0.072000	0.16883	0.658000	0.24979	0.081000	0.16988	-1.106000	0.02097	ATC	.	.		0.423	FAM194A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257666.1			A	150398678	T	A	150398678	3	1	237	1	0	0	0	0	1	0	0	0	5531	1406	49	4	1097	4	FAM194A	3	150398678	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	3289791	150398678	47623752	60	32966										
KIAA0226	9711	hgsc.bcm.edu	37	chr3	197427705	197427705	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	acaaattggaactgctgctcTcggcattgctgctgtgactc	10	11	1	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:197427705T>A	ENST00000296343.5	-	7	1039	c.1040A>T	c.(1039-1041)gAg>gTg	p.E347V	KIAA0226_ENST00000467303.1_5'Flank|KIAA0226_ENST00000449205.1_Missense_Mutation_p.E347V|KIAA0226_ENST00000389665.5_Missense_Mutation_p.E347V|KIAA0226_ENST00000273582.5_Missense_Mutation_p.E287V	NM_014687.1	NP_055502.1	Q92622	RUBIC_HUMAN	KIAA0226	347	Ser-rich.				autophagy (GO:0006914)|cell death (GO:0008219)|endocytosis (GO:0006897)|negative regulation of autophagy (GO:0010507)|negative regulation of endocytosis (GO:0045806)	early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)				NS(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(143;8.26e-10)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.0446)		ACTGCTGCTCTCGGCATTGCT	0.607																																					p.E347V	Esophageal Squamous(3;167 355 3763 15924)	Atlas-SNP	.											.	KIAA0226	136	.	0			c.A1040T						.						55	59	58					3																	197427705		2041	4207	6248	SO:0001583	missense	9711	exon7			CTGCTCTCGGCAT	D86979	CCDS43195.1, CCDS46987.1	3q29	2011-08-09			ENSG00000145016	ENSG00000145016			28991	protein-coding gene	gene with protein product	"RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein"	613516				9039502, 19270693, 20826435	Standard	XM_005269374		Approved	rubicon, rundataxin	uc003fyc.2	Q92622	OTTHUMG00000155452	ENST00000296343.5:c.1040A>T	chr3.hg19:g.197427705T>A	ENSP00000296343:p.Glu347Val	189.0	0.0		178.0	18.0	NM_014687	Q96CK5	Missense_Mutation	SNP	ENST00000296343.5	hg19	CCDS43195.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.43|13.43	2.234821|2.234821	0.39498|0.39498	.|.	.|.	ENSG00000145016|ENSG00000145016	ENST00000273582;ENST00000296343;ENST00000389665;ENST00000449205|ENST00000415452	.|.	.|.	.|.	5.72|5.72	2.02|2.02	0.26589|0.26589	.|.	0.331648|.	0.27976|.	N|.	0.017083|.	T|.	0.21347|.	0.0514|.	N|N	0.19112|0.19112	0.55|0.55	0.26565|0.26565	N|N	0.973667|0.973667	P;P;P;P;P|.	0.47302|.	0.824;0.893;0.799;0.71;0.514|.	B;B;B;B;B|.	0.41571|.	0.345;0.36;0.217;0.281;0.05|.	T|.	0.24368|.	-1.0162|.	9|.	0.40728|.	T|.	0.16|.	.|.	5.0312|5.0312	0.14411|0.14411	0.0:0.222:0.1446:0.6335|0.0:0.222:0.1446:0.6335	.|.	347;180;347;287;347|.	E9PEM3;Q5HYI6;Q92622-3;Q92622-2;Q92622|.	.;.;.;.;RUBIC_HUMAN|.	V|X	287;347;347;347|106	.|.	ENSP00000273582:E287V|.	E|R	-|-	2|1	0|2	KIAA0226|KIAA0226	198912102|198912102	0.999000|0.999000	0.42202|0.42202	0.886000|0.886000	0.34754|0.34754	0.990000|0.990000	0.78478|0.78478	2.015000|2.015000	0.40961|0.40961	0.110000|0.110000	0.17919|0.17919	0.459000|0.459000	0.35465|0.35465	GAG|AGA	.	.		0.607	KIAA0226-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340184.1	XM_032901		A	197427705	T	A	197427705	3	1	237	1	0	0	0	0	1	0	0	0	8171	1551	54	4	1983	4	KIAA0226	3	197427705	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	47029027	197427705	594725	61	32967										
MAEA	10296	hgsc.bcm.edu	37	chr4	1332275	1332275	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tgtgtgcagccgctccctgaAcaagctggcgcagcccctgc	12	16	0	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr4:1332275A>T	ENST00000303400.4	+	8	1028	c.965A>T	c.(964-966)aAc>aTc	p.N322I	MAEA_ENST00000512289.1_3'UTR|MAEA_ENST00000514708.1_Missense_Mutation_p.N254I|MAEA_ENST00000452175.2_Missense_Mutation_p.N243I|MAEA_ENST00000505177.2_Missense_Mutation_p.N360I|MAEA_ENST00000264750.6_Missense_Mutation_p.N281I|MAEA_ENST00000505839.1_Missense_Mutation_p.N274I|MAEA_ENST00000510794.1_Missense_Mutation_p.N321I	NM_001017405.1	NP_001017405.1	Q7L5Y9	MAEA_HUMAN	macrophage erythroblast attacher	322					cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|cytoskeleton organization (GO:0007010)|enucleate erythrocyte development (GO:0048822)|erythrocyte maturation (GO:0043249)|negative regulation of myeloid cell apoptotic process (GO:0033033)|regulation of mitotic cell cycle (GO:0007346)	actomyosin contractile ring (GO:0005826)|cytoskeleton (GO:0005856)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(2)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(23;0.0201)		WF10(DB05389)	CGCTCCCTGAACAAGCTGGCG	0.617																																					p.N322I		Atlas-SNP	.											.	MAEA	39	.	0			c.A965T						.						55	52	53					4																	1332275		2203	4299	6502	SO:0001583	missense	10296	exon8			CCCTGAACAAGCT	AF084928	CCDS33936.1, CCDS33937.1, CCDS75090.1	4p16.3	2012-07-20			ENSG00000090316	ENSG00000090316			13731	protein-coding gene	gene with protein product	"GID complex subunit 9, FYV10 homolog (S. cerevisiae)"	606801				9763581	Standard	XM_005272243		Approved	EMP, GID9	uc003gda.3	Q7L5Y9	OTTHUMG00000160169	ENST00000303400.4:c.965A>T	chr4.hg19:g.1332275A>T	ENSP00000302830:p.Asn322Ile	112.0	0.0		102.0	7.0	NM_001017405	O95285|Q5JB54|Q6ZRD6|Q9BQ11|Q9H9V6|Q9H9Z4|Q9NW84	Missense_Mutation	SNP	ENST00000303400.4	hg19	CCDS33936.1	.	.	.	.	.	.	.	.	.	.	A	26.8	4.775632	0.90195	.	.	ENSG00000090316	ENST00000303400;ENST00000505177;ENST00000264750;ENST00000382947;ENST00000539495;ENST00000452175;ENST00000514708;ENST00000510794;ENST00000505839	T;T;T;T;T;T;T	0.11385	2.78;2.78;2.78;2.78;2.78;2.78;2.78	5.26	5.26	0.73747	.	0.079954	0.85682	D	0.000000	T	0.34542	0.0901	M	0.81614	2.55	0.80722	D	1	D;D;D;D;D;D	0.89917	0.999;1.0;0.988;0.999;0.997;0.97	D;D;P;D;D;P	0.80764	0.945;0.99;0.758;0.994;0.973;0.809	T	0.08827	-1.0703	10	0.37606	T	0.19	-32.9369	15.1708	0.72872	1.0:0.0:0.0:0.0	.	321;360;108;254;281;322	B4DVN3;E7ESC7;B3KRN7;D6RIB6;Q7L5Y9-3;Q7L5Y9	.;.;.;.;.;MAEA_HUMAN	I	322;360;281;254;301;243;254;321;274	ENSP00000302830:N322I;ENSP00000422215:N360I;ENSP00000264750:N281I;ENSP00000411415:N243I;ENSP00000427512:N254I;ENSP00000426807:N321I;ENSP00000424436:N274I	ENSP00000264750:N281I	N	+	2	0	MAEA	1322275	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.986000	0.93492	1.977000	0.57605	0.533000	0.62120	AAC	.	.		0.617	MAEA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359511.1	NM_005882		T	1332275	A	T	1332275	3	4	237	1	0	0	0	0	1	0	0	0	9162	43	2	4	995	4	MAEA	4	1332275	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10		1332275	189822001	62	32968										
CD38	952	hgsc.bcm.edu	37	chr4	15841652	15841652	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tgtttcttctattttagcacTtttgggagtgtggaagtcca	10	6	2	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr4:15841652T>G	ENST00000226279.3	+	6	800	c.663T>G	c.(661-663)acT>acG	p.T221T		NM_001775.2	NP_001766.2	P28907	CD38_HUMAN	CD38 molecule	221					apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|female pregnancy (GO:0007565)|long term synaptic depression (GO:0060292)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone resorption (GO:0045779)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell growth (GO:0030307)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of insulin secretion (GO:0032024)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vasoconstriction (GO:0045907)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hydroperoxide (GO:0033194)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	NAD(P)+ nucleosidase activity (GO:0050135)|NAD+ nucleosidase activity (GO:0003953)|phosphorus-oxygen lyase activity (GO:0016849)|transferase activity (GO:0016740)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|stomach(1)	14						ATTTTAGCACTTTTGGGAGTG	0.468																																					p.T221T		Atlas-SNP	.											.	CD38	36	.	0			c.T663G						.						215	234	228					4																	15841652		2203	4300	6503	SO:0001819	synonymous_variant	952	exon6			TAGCACTTTTGGG	D84276	CCDS3417.1	4p15.32	2010-05-04	2006-03-28		ENSG00000004468	ENSG00000004468	3.2.2.5	"CD molecules"	1667	protein-coding gene	gene with protein product	"ADP-ribosyl cyclase 1", "NAD(+) nucleosidase"	107270	"CD38 antigen (p45)"			9074508, 2319135	Standard	NM_001775		Approved		uc003gol.1	P28907	OTTHUMG00000048206	ENST00000226279.3:c.663T>G	chr4.hg19:g.15841652T>G		96.0	0.0		106.0	13.0	NM_001775	O00121|O00122|Q96HY4	Silent	SNP	ENST00000226279.3	hg19	CCDS3417.1																																																																																			.	.		0.468	CD38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250322.2	NM_001775		G	15841652	T	G	15841652	2	3	237	1	0	0	0	0	0	0	0	1	3011	1596	56	5		5	CD38	4	15841652	Silent	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	14509377	15841652	175312624	63	32969										
PPARGC1A	10891	hgsc.bcm.edu	37	chr4	23797512	23797512	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ccagagagtcatacttgctcTtggtggaagcagggtcaaag	13	8	3	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr4:23797512T>A	ENST00000264867.2	-	13	2449	c.2330A>T	c.(2329-2331)aAg>aTg	p.K777M	PPARGC1A_ENST00000509702.1_5'UTR	NM_013261.3	NP_037393.1	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 alpha	777	Mediates interaction with RNF34. {ECO:0000269|PubMed:22064484}.				androgen metabolic process (GO:0008209)|androgen receptor signaling pathway (GO:0030521)|brown fat cell differentiation (GO:0050873)|cellular glucose homeostasis (GO:0001678)|cellular respiration (GO:0045333)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|cellular response to nitrite (GO:0071250)|cellular response to oxidative stress (GO:0034599)|cellular response to thyroid hormone stimulus (GO:0097067)|cellular response to tumor necrosis factor (GO:0071356)|circadian regulation of gene expression (GO:0032922)|digestion (GO:0007586)|fatty acid oxidation (GO:0019395)|flavone metabolic process (GO:0051552)|galactose metabolic process (GO:0006012)|gluconeogenesis (GO:0006094)|mitochondrion organization (GO:0007005)|mRNA processing (GO:0006397)|negative regulation of glycolytic process (GO:0045820)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of receptor activity (GO:2000272)|positive regulation of ATP biosynthetic process (GO:2001171)|positive regulation of cellular respiration (GO:1901857)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of histone acetylation (GO:0035066)|positive regulation of mitochondrial DNA metabolic process (GO:1901860)|positive regulation of mitochondrion organization (GO:0010822)|positive regulation of muscle tissue development (GO:1901863)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|regulation of circadian rhythm (GO:0042752)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|response to cold (GO:0009409)|response to epinephrine (GO:0071871)|response to leucine (GO:0043201)|response to muscle activity (GO:0014850)|response to norepinephrine (GO:0071873)|response to starvation (GO:0042594)|response to statin (GO:0036273)|RNA splicing (GO:0008380)|temperature homeostasis (GO:0001659)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytosol (GO:0005829)|DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|liver(1)|lung(24)|ovary(3)|skin(5)	51		Breast(46;0.0503)				ATACTTGCTCTTGGTGGAAGC	0.428																																					p.K777M	Esophageal Squamous(29;694 744 13796 34866 44181)	Atlas-SNP	.											.	PPARGC1A	129	.	0			c.A2330T						.						113	111	112					4																	23797512		2203	4300	6503	SO:0001583	missense	10891	exon13			TTGCTCTTGGTGG	AF106698	CCDS3429.1	4p15.1	2013-02-12	2006-10-17	2004-02-04	ENSG00000109819	ENSG00000109819		"RNA binding motif (RRM) containing"	9237	protein-coding gene	gene with protein product		604517	"peroxisome proliferative activated receptor, gamma, coactivator 1", "peroxisome proliferative activated receptor, gamma, coactivator 1, alpha"	PPARGC1		10585775	Standard	NM_013261		Approved	PGC1, PGC1A	uc003gqs.3	Q9UBK2	OTTHUMG00000097747	ENST00000264867.2:c.2330A>T	chr4.hg19:g.23797512T>A	ENSP00000264867:p.Lys777Met	69.0	0.0		99.0	5.0	NM_013261	B7Z406|G8DM16|I3RTT5|I3RTT6|I3RTT7|I3RTT8|I3RTT9|Q3LIG1|Q4W5M7|Q9UN32	Missense_Mutation	SNP	ENST00000264867.2	hg19	CCDS3429.1	.	.	.	.	.	.	.	.	.	.	T	17.98	3.520719	0.64747	.	.	ENSG00000109819	ENST00000264867	T	0.28895	1.59	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.54515	0.1863	M	0.69358	2.11	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	T	0.58250	-0.7669	10	0.87932	D	0	-12.1653	15.7565	0.78030	0.0:0.0:0.0:1.0	.	777	Q9UBK2	PRGC1_HUMAN	M	777	ENSP00000264867:K777M	ENSP00000264867:K777M	K	-	2	0	PPARGC1A	23406610	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.655000	0.83696	2.177000	0.69029	0.533000	0.62120	AAG	.	.		0.428	PPARGC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214976.1	NM_013261		A	23797512	T	A	23797512	3	1	237	1	0	0	0	0	1	0	0	0	12309	1609	56	4	70	4	PPARGC1A	4	23797512	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	7955860	23797512	167356764	64	32970										
UGT2B7	7364	hgsc.bcm.edu	37	chr4	69962549	69962549	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gtcagaccttccaaaagataCattttggttatatttttcac	5	8	2	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr4:69962549C>A	ENST00000508661.1	+	1	338	c.311C>A	c.(310-312)aCa>aAa	p.T104K	UGT2B7_ENST00000509763.1_Intron|UGT2B7_ENST00000305231.7_Missense_Mutation_p.T104K			P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B7	104					androgen metabolic process (GO:0008209)|cellular glucuronidation (GO:0052695)|lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)			autonomic_ganglia(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38					Atorvastatin(DB01076)|Carbamazepine(DB00564)|Chenodeoxycholic acid(DB06777)|Codeine(DB00318)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Diclofenac(DB00586)|Epirubicin(DB00445)|Etodolac(DB00749)|Ezetimibe(DB00973)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naproxen(DB00788)|Oxazepam(DB00842)|Pitavastatin(DB08860)|Silodosin(DB06207)|Simvastatin(DB00641)|Suprofen(DB00870)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zidovudine(DB00495)	CCAAAAGATACATTTTGGTTA	0.299																																					p.T104K		Atlas-SNP	.											.	UGT2B7	79	.	0			c.C311A						.						46	48	48					4																	69962549		2196	4295	6491	SO:0001583	missense	7364	exon1			AAGATACATTTTG	BC030974	CCDS3526.1	4q13	2008-02-05	2005-07-20		ENSG00000171234	ENSG00000171234		"UDP glucuronosyltransferases"	12554	protein-coding gene	gene with protein product		600068	"UDP glycosyltransferase 2 family, polypeptide B7"			2159463, 7835904	Standard	NM_001074		Approved	UGT2B9	uc003heg.4	P16662	OTTHUMG00000129404	ENST00000508661.1:c.311C>A	chr4.hg19:g.69962549C>A	ENSP00000427659:p.Thr104Lys	67.0	0.0		66.0	28.0	NM_001074	B2R810|Q6GTW0	Missense_Mutation	SNP	ENST00000508661.1	hg19		.	.	.	.	.	.	.	.	.	.	C	10.02	1.237392	0.22711	.	.	ENSG00000171234	ENST00000305231;ENST00000508661	T;T	0.59638	0.25;0.25	2.54	2.54	0.30619	.	0.985432	0.08237	U	0.976560	T	0.65333	0.2681	M	0.67517	2.055	0.09310	N	1	P;B	0.34462	0.454;0.031	P;B	0.45794	0.493;0.082	T	0.57545	-0.7793	9	.	.	.	.	10.7765	0.46353	0.0:1.0:0.0:0.0	.	104;104	E9PBP8;P16662	.;UD2B7_HUMAN	K	104	ENSP00000304811:T104K;ENSP00000427659:T104K	.	T	+	2	0	UGT2B7	69997138	0.000000	0.05858	0.015000	0.15790	0.019000	0.09904	-0.722000	0.04958	1.408000	0.46895	0.313000	0.20887	ACA	.	.		0.299	UGT2B7-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000362103.1	NM_001074		A	69962549	C	A	69962549	3	1	237	1	0	0	0	0	1	0	0	0	16977	478	17	3	313	3	UGT2B7	4	69962549	Missense_Mutation	SNP	C	TCGA-ED-A459-01A-11D-A25V-10	46165037	69962549	121191727	65	32971										
ALPK1	80216	hgsc.bcm.edu	37	chr4	113353386	113353386	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ccaattcctctgtaagcggtAacatcctcttccctgtcctc	5	16	2	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr4:113353386A>G	ENST00000458497.1	+	11	2962	c.2683A>G	c.(2683-2685)Aac>Gac	p.N895D	ALPK1_ENST00000177648.9_Missense_Mutation_p.N895D|ALPK1_ENST00000504176.2_Missense_Mutation_p.N817D	NM_001102406.1|NM_025144.3	NP_001095876.1|NP_079420.3	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	895							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(20)|ovary(6)|prostate(2)|urinary_tract(1)	53		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		TGTAAGCGGTAACATCCTCTT	0.552																																					p.N895D		Atlas-SNP	.											.	ALPK1	125	.	0			c.A2683G						.						111	109	110					4																	113353386		2203	4300	6503	SO:0001583	missense	80216	exon11			AGCGGTAACATCC	AY044164	CCDS3697.1, CCDS58923.1	4q26	2008-02-05			ENSG00000073331	ENSG00000073331			20917	protein-coding gene	gene with protein product	"lymphocyte alpha-kinase"	607347				10021370, 10819331	Standard	NM_025144		Approved	Lak, FLJ22670, KIAA1527	uc003ian.4	Q96QP1	OTTHUMG00000132911	ENST00000458497.1:c.2683A>G	chr4.hg19:g.113353386A>G	ENSP00000398048:p.Asn895Asp	224.0	0.0		145.0	75.0	NM_001102406	B4E3G1|F5H138|Q68CI9|Q6P9F9|Q6ZNK4|Q9P201	Missense_Mutation	SNP	ENST00000458497.1	hg19	CCDS3697.1	.	.	.	.	.	.	.	.	.	.	A	14.57	2.574333	0.45902	.	.	ENSG00000073331	ENST00000458497;ENST00000177648;ENST00000504176	T;T;T	0.02472	4.35;4.35;4.28	5.03	-4.26	0.03755	.	1.382570	0.04233	N	0.335492	T	0.03178	0.0093	L	0.57536	1.79	0.09310	N	1	B;B;B	0.32467	0.372;0.255;0.031	B;B;B	0.30316	0.114;0.053;0.01	T	0.41395	-0.9511	10	0.52906	T	0.07	-0.2641	1.2056	0.01894	0.3977:0.2585:0.2189:0.1249	.	817;817;895	F5H138;B4E3G1;Q96QP1	.;.;ALPK1_HUMAN	D	895;895;817	ENSP00000398048:N895D;ENSP00000177648:N895D;ENSP00000426044:N817D	ENSP00000177648:N895D	N	+	1	0	ALPK1	113572835	0.000000	0.05858	0.000000	0.03702	0.119000	0.20118	-0.065000	0.11617	-0.509000	0.06532	0.533000	0.62120	AAC	.	.		0.552	ALPK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256421.2	NM_025144		G	113353386	A	G	113353386	3	3	237	1	0	0	0	0	1	0	0	0	544	362	13	2	2717	2	ALPK1	4	113353386	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	43390837	113353386	77800890	66	32972										
C4orf21	55345	hgsc.bcm.edu	37	chr4	113461976	113461976	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	actgtaatacataataccaaCcttgtacatctgggatttgt	6	8	1	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr4:113461976C>A	ENST00000505019.1	-	26	6036		c.e26+1		RP11-402J6.1_ENST00000504009.1_RNA	NM_018392.4	NP_060862.3	Q86YA3	ZGRF1_HUMAN								integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(6)|lung(21)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)		ATAATACCAACCTTGTACATC	0.318																																					.		Atlas-SNP	.											.	C4orf21	223	.	0			c.5910+1G>T						.						75	67	70					4																	113461976		2202	4299	6501	SO:0001630	splice_region_variant	55345	exon27			TACCAACCTTGTA																												ENST00000505019.1:c.5910+1G>T	chr4.hg19:g.113461976C>A		146.0	0.0		94.0	48.0	NM_018392	B3KQX2|B4DSN6|B4DYU8|E9PDE1|G5EA02|Q6ZU11|Q9NSW3|Q9NUJ4	Splice_Site	SNP	ENST00000505019.1	hg19		.	.	.	.	.	.	.	.	.	.	C	11.84	1.758574	0.31137	.	.	ENSG00000138658	ENST00000505019	.	.	.	5.81	5.81	0.92471	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.0782	0.97758	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	C4orf21	113681425	1.000000	0.71417	0.997000	0.53966	0.129000	0.20672	5.311000	0.65786	2.746000	0.94184	0.655000	0.94253	.	.	.		0.318	C4orf21-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000256413.1		Intron	A	113461976	C	A	113461976	5	1	237	1	0	0	0	0	0	0	1	0	2256	521	18	3	415	3	C4orf21	4	113461976	Splice_Site	SNP	C	TCGA-ED-A459-01A-11D-A25V-10	108590	113461976	77692300	67	32973										
ADAMTS12	81792	hgsc.bcm.edu	37	chr5	33648938	33648938	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tacacttacttctacttcctGgcagaaggtagcattgggtc	9	10	1	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr5:33648938G>A	ENST00000504830.1	-	9	1803	c.1468C>T	c.(1468-1470)Cag>Tag	p.Q490*	ADAMTS12_ENST00000352040.3_Nonsense_Mutation_p.Q490*|ADAMTS12_ENST00000504582.1_5'UTR	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	490	Disintegrin.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						TCTACTTCCTGGCAGAAGGTA	0.468										HNSCC(64;0.19)																											p.Q490X		Atlas-SNP	.											.	ADAMTS12	464	.	0			c.C1468T						.						134	128	130					5																	33648938		2203	4300	6503	SO:0001587	stop_gained	81792	exon9			CTTCCTGGCAGAA	AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"ADAM metallopeptidases with thrombospondin type 1 motif"	14605	protein-coding gene	gene with protein product		606184	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.1468C>T	chr5.hg19:g.33648938G>A	ENSP00000422554:p.Gln490*	179.0	0.0		219.0	80.0	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Nonsense_Mutation	SNP	ENST00000504830.1	hg19	CCDS34140.1	.	.	.	.	.	.	.	.	.	.	G	41	8.900709	0.98996	.	.	ENSG00000151388	ENST00000504830;ENST00000352040	.	.	.	5.6	5.6	0.85130	.	0.450232	0.25900	N	0.027561	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	.	14.1245	0.65210	0.0:0.2698:0.7302:0.0	.	.	.	.	X	490	.	ENSP00000344847:Q490X	Q	-	1	0	ADAMTS12	33684695	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	3.159000	0.50731	2.641000	0.89580	0.549000	0.68633	CAG	.	.		0.468	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		A	33648938	G	A	33648938	4	1	237	1	0	0	0	0	0	1	0	0	257	1357	47	3	3380	3	ADAMTS12	5	33648938	Nonsense_Mutation	SNP	G	TCGA-ED-A459-01A-11D-A25V-10		33648938	147266322	68	32974										
LIFR	3977	hgsc.bcm.edu	37	chr5	38490325	38490325	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	atatccaatcatggagcgtaAtaattgatatccttgatttc	6	7	1	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr5:38490325A>T	ENST00000263409.4	-	15	2296	c.2134T>A	c.(2134-2136)Tta>Ata	p.L712I	LIFR_ENST00000503088.1_5'Flank|LIFR_ENST00000453190.2_Missense_Mutation_p.L712I	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	712	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|leukemia inhibitory factor signaling pathway (GO:0048861)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|leukemia inhibitory factor receptor activity (GO:0004923)			NS(2)|breast(4)|endometrium(6)|kidney(2)|large_intestine(30)|liver(2)|lung(21)|ovary(3)|skin(5)|stomach(1)|urinary_tract(2)	78	all_lung(31;0.00021)					ATGGAGCGTAATAATTGATAT	0.313			T	PLAG1	salivary adenoma																																p.L712I	Melanoma(13;4 730 6426 9861 34751)	Atlas-SNP	.		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	.	LIFR	348	.	0			c.T2134A						.						98	108	105					5																	38490325		2202	4290	6492	SO:0001583	missense	3977	exon15			AGCGTAATAATTG	X61615	CCDS3927.1	5p13-p12	2013-02-11	2006-05-17		ENSG00000113594	ENSG00000113594		"CD molecules", "Fibronectin type III domain containing"	6597	protein-coding gene	gene with protein product		151443	"leukemia inhibitory factor receptor"			1915266	Standard	NM_001127671		Approved	CD118	uc003jli.2	P42702	OTTHUMG00000131138	ENST00000263409.4:c.2134T>A	chr5.hg19:g.38490325A>T	ENSP00000263409:p.Leu712Ile	129.0	0.0		148.0	20.0	NM_002310	Q6LCD9	Missense_Mutation	SNP	ENST00000263409.4	hg19	CCDS3927.1	.	.	.	.	.	.	.	.	.	.	A	18.81	3.702168	0.68501	.	.	ENSG00000113594	ENST00000263409;ENST00000453190	T;T	0.54279	0.58;0.58	6.05	-7.81	0.01210	Fibronectin, type III (1);	0.140763	0.49305	D	0.000150	T	0.56337	0.1978	M	0.80422	2.495	0.09310	N	0.999998	D	0.58268	0.982	P	0.48598	0.583	T	0.63305	-0.6667	10	0.13470	T	0.59	-16.8825	22.8685	0.99977	0.2868:0.0:0.7132:0.0	.	712	P42702	LIFR_HUMAN	I	712	ENSP00000263409:L712I;ENSP00000398368:L712I	ENSP00000263409:L712I	L	-	1	2	LIFR	38526082	0.000000	0.05858	0.003000	0.11579	0.953000	0.61014	-1.035000	0.03564	-1.854000	0.01163	-0.417000	0.06048	TTA	.	.		0.313	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310		T	38490325	A	T	38490325	3	4	237	1	0	0	0	0	1	0	0	0	8789	98	4	4	1183	4	LIFR	5	38490325	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	4841387	38490325	142424935	69	32975										
IL6ST	3572	hgsc.bcm.edu	37	chr5	55259982	55259990	+	In_Frame_Del	DEL	ACAGGATCA	ACAGGATCA	-													0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gtttataactacctttatatAcaggatcaaaattgatatga					rs183743555		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	ACAGGATCA	ACAGGATCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr5:55259982_55259990delACAGGATCA	ENST00000381298.2	-	6	954_962	c.642_650delTGATCCTGT	c.(640-651)tttgatcctgta>tta	p.214_217FDPV>L	IL6ST_ENST00000381286.3_Intron|IL6ST_ENST00000502326.3_In_Frame_Del_p.214_217FDPV>L|IL6ST_ENST00000381287.4_In_Frame_Del_p.214_217FDPV>L|IL6ST_ENST00000381294.3_In_Frame_Del_p.214_217FDPV>L|IL6ST_ENST00000536319.1_In_Frame_Del_p.214_217FDPV>L|IL6ST_ENST00000522633.2_In_Frame_Del_p.214_217FDPV>L|IL6ST_ENST00000577363.1_5'Flank|IL6ST_ENST00000381293.2_Intron|IL6ST_ENST00000336909.5_In_Frame_Del_p.214_217FDPV>L	NM_001190981.1|NM_002184.3|NM_175767.2	NP_001177910.1|NP_002175.2|NP_786943.1	P40189	IL6RB_HUMAN	interleukin 6 signal transducer	214	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|glycogen metabolic process (GO:0005977)|interleukin-27-mediated signaling pathway (GO:0070106)|interleukin-6-mediated signaling pathway (GO:0070102)|leukemia inhibitory factor signaling pathway (GO:0048861)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of Notch signaling pathway (GO:0008593)|response to cytokine (GO:0034097)|viral process (GO:0016032)	ciliary neurotrophic factor receptor complex (GO:0070110)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|interleukin-6 receptor complex (GO:0005896)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|oncostatin-M receptor complex (GO:0005900)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|interleukin-11 receptor activity (GO:0004921)|interleukin-27 receptor activity (GO:0045509)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(5)|kidney(5)|large_intestine(4)|liver(2)|lung(1)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)				ACCTTTATATACAGGATCAAAATTGATAT	0.301			O		hepatocellular ca																																p.215_217del		Atlas-Indel,Pindel	.		Dom	yes		5	5q11	3572	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"		E	.	IL6ST	75	.	0			c.643_651del						.																																			SO:0001651	inframe_deletion	3572	exon6			.	M57230	CCDS3971.1, CCDS47209.1, CCDS54856.1	5q11.2	2014-04-04	2014-04-04		ENSG00000134352	ENSG00000134352		"Interleukins and interleukin receptors", "CD molecules", "Fibronectin type III domain containing"	6021	protein-coding gene	gene with protein product	"gp130, oncostatin M receptor"	600694	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"			2261637	Standard	NM_002184		Approved	GP130, CD130	uc003jqq.3	P40189	OTTHUMG00000097043	ENST00000381298.2:c.642_650delTGATCCTGT	chr5.hg19:g.55259982_55259990delACAGGATCA	ENSP00000370698:p.Phe214_Val217delinsLeu	121.0	0.0		101.0	18.0	NM_001190981	A0N0L4|Q5FC04|Q9UQ41	In_Frame_Del	DEL	ENST00000381298.2	hg19	CCDS3971.1																																																																																			.	.		0.301	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184		-	55259990	ACAGGATCA	-	55259982	7	5	237	1	0	1	0	1	0	0	0	0	7712	391	14	0	2154	0	IL6ST	5	55259982	In_Frame_Del	DEL	ACAGGATCA	TCGA-ED-A459-01A-11D-A25V-10	16769657	55259982	125655278	70	32976										
MAN2A1	4124	hgsc.bcm.edu	37	chr5	109026191	109026191	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tgattttctcgctctacctgAtgctggaccggggtcactta	10	11	3	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr5:109026191A>G	ENST00000261483.4	+	1	1125	c.73A>G	c.(73-75)Atg>Gtg	p.M25V	CTC-332L22.1_ENST00000606424.1_lincRNA	NM_002372.2	NP_002363.2	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	25					cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|mannose metabolic process (GO:0006013)|mitochondrion organization (GO:0007005)|N-glycan processing (GO:0006491)|positive regulation of neurogenesis (GO:0050769)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)|retina morphogenesis in camera-type eye (GO:0060042)|vacuole organization (GO:0007033)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		GCTCTACCTGATGCTGGACCG	0.617																																					p.M25V		Atlas-SNP	.											.	MAN2A1	136	.	0			c.A73G						.						181	153	163					5																	109026191		2202	4300	6502	SO:0001583	missense	4124	exon1			TACCTGATGCTGG		CCDS34209.1	5q21.3	2013-09-20			ENSG00000112893	ENSG00000112893	3.2.1.114		6824	protein-coding gene	gene with protein product	"golgi integral membrane protein 7"	154582		MANA2		1757461, 15004235	Standard	NM_002372		Approved	GOLIM7	uc003kou.1	Q16706	OTTHUMG00000162834	ENST00000261483.4:c.73A>G	chr5.hg19:g.109026191A>G	ENSP00000261483:p.Met25Val	158.0	0.0		253.0	69.0	NM_002372	Q16767	Missense_Mutation	SNP	ENST00000261483.4	hg19	CCDS34209.1	.	.	.	.	.	.	.	.	.	.	A	15.70	2.909632	0.52439	.	.	ENSG00000112893	ENST00000261483	T	0.79454	-1.27	4.45	4.45	0.53987	.	0.000000	0.85682	D	0.000000	T	0.73337	0.3574	M	0.64567	1.98	0.58432	D	0.999997	B	0.28713	0.22	B	0.26864	0.074	T	0.71487	-0.4578	10	0.33940	T	0.23	-14.0474	12.9872	0.58598	1.0:0.0:0.0:0.0	.	25	Q16706	MA2A1_HUMAN	V	25	ENSP00000261483:M25V	ENSP00000261483:M25V	M	+	1	0	MAN2A1	109054090	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	6.853000	0.75435	1.739000	0.51704	0.460000	0.39030	ATG	.	.		0.617	MAN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370680.1			G	109026191	A	G	109026191	3	3	237	1	0	0	0	0	1	0	0	0	9223	333	12	2	75	2	MAN2A1	5	109026191	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	53766209	109026191	71889069	71	32977										
YTHDC2	64848	hgsc.bcm.edu	37	chr5	112889035	112889035	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tcatgcatcttctatacaatAtctgccatagttgtgatgct	6	9	4	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr5:112889035A>T	ENST00000161863.4	+	13	2059	c.1846A>T	c.(1846-1848)Atc>Ttc	p.I616F	YTHDC2_ENST00000515883.1_Missense_Mutation_p.I616F	NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	616	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|positive regulation by host of viral genome replication (GO:0044829)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)	endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA polymerase binding (GO:0070063)|RNA-dependent ATPase activity (GO:0008186)			NS(2)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(13)|lung(10)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		TCTATACAATATCTGCCATAG	0.323																																					p.I616F		Atlas-SNP	.											.	YTHDC2	118	.	0			c.A1846T						.						73	70	71					5																	112889035		2202	4299	6501	SO:0001583	missense	64848	exon13			TACAATATCTGCC	AK000915	CCDS4113.1	5q22.3	2008-02-05			ENSG00000047188	ENSG00000047188			24721	protein-coding gene	gene with protein product						12477932	Standard	NM_022828		Approved	FLJ2194, FLJ10053, DKFZp564A186	uc003kqn.3	Q9H6S0	OTTHUMG00000128837	ENST00000161863.4:c.1846A>T	chr5.hg19:g.112889035A>T	ENSP00000161863:p.Ile616Phe	79.0	0.0		112.0	7.0	NM_022828	B2RP66	Missense_Mutation	SNP	ENST00000161863.4	hg19	CCDS4113.1	.	.	.	.	.	.	.	.	.	.	A	17.60	3.428757	0.62844	.	.	ENSG00000047188	ENST00000161863;ENST00000515883;ENST00000511372	T;T	0.71461	0.9;-0.57	5.7	4.55	0.56014	Helicase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.77558	0.4148	H	0.96777	3.88	0.53005	D	0.999969	P	0.35272	0.493	B	0.26864	0.074	T	0.80266	-0.1454	10	0.87932	D	0	.	11.4557	0.50181	0.9295:0.0:0.0705:0.0	.	616	Q9H6S0	YTDC2_HUMAN	F	616;616;526	ENSP00000161863:I616F;ENSP00000423101:I616F	ENSP00000161863:I616F	I	+	1	0	YTHDC2	112916934	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.176000	0.77643	0.996000	0.38943	0.528000	0.53228	ATC	.	.		0.323	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828		T	112889035	A	T	112889035	3	4	237	1	0	0	0	0	1	0	0	0	17512	449	16	4	1896	4	YTHDC2	5	112889035	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	3862844	112889035	68026225	72	32978										
DDX46	9879	hgsc.bcm.edu	37	chr5	134117757	134117757	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tatgttgaagttccagaactAgcaaaaatgtctcaagaagg	9	6	1	3			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr5:134117757A>T	ENST00000354283.4	+	8	1161	c.1026A>T	c.(1024-1026)ctA>ctT	p.L342L	DDX46_ENST00000452510.2_Silent_p.L342L			Q7L014	DDX46_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	342					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TTCCAGAACTAGCAAAAATGT	0.343																																					p.L342L	Colon(13;391 453 4901 21675 24897)	Atlas-SNP	.											.	DDX46	77	.	0			c.A1026T						.						39	39	39					5																	134117757		2202	4298	6500	SO:0001819	synonymous_variant	9879	exon8			AGAACTAGCAAAA		CCDS34240.1, CCDS75306.1	5q31.1	2010-01-25			ENSG00000145833	ENSG00000145833		"DEAD-boxes"	18681	protein-coding gene	gene with protein product							Standard	XM_005272142		Approved	KIAA0801, FLJ25329, PRPF5, Prp5	uc003kzw.3	Q7L014	OTTHUMG00000163072	ENST00000354283.4:c.1026A>T	chr5.hg19:g.134117757A>T		177.0	0.0		202.0	13.0	NM_014829	O94894|Q96EI0|Q9Y658	Silent	SNP	ENST00000354283.4	hg19	CCDS34240.1																																																																																			.	.		0.343	DDX46-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371584.1	NM_014829		T	134117757	A	T	134117757	2	4	237	1	0	0	0	0	0	0	0	1	4366	407	15	4		4	DDX46	5	134117757	Silent	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	21228722	134117757	46797503	73	32979										
SPOCK1	6695	hgsc.bcm.edu	37	chr5	136324224	136324224	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gctcgtacttatccaggtagAtggcattgatctctgaaggg	12	8	1	3			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr5:136324224A>T	ENST00000394945.1	-	8	984	c.815T>A	c.(814-816)aTc>aAc	p.I272N	SPOCK1_ENST00000282223.7_Missense_Mutation_p.I272N|SPOCK1_ENST00000509978.1_5'UTR	NM_004598.3	NP_004589.1	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 1	272					cell adhesion (GO:0007155)|central nervous system neuron differentiation (GO:0021953)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron projection development (GO:0010977)|nervous system development (GO:0007399)|neurogenesis (GO:0022008)|neuron migration (GO:0001764)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|postsynaptic density (GO:0014069)|proteinaceous extracellular matrix (GO:0005578)|sarcoplasm (GO:0016528)	calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(2)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			ATCCAGGTAGATGGCATTGAT	0.488																																					p.I272N		Atlas-SNP	.											.	SPOCK1	58	.	0			c.T815A						.						172	153	160					5																	136324224		2203	4300	6503	SO:0001583	missense	6695	exon8			AGGTAGATGGCAT	AF231124	CCDS4191.1	5q31.2	2008-02-05	2005-11-04	2005-11-04	ENSG00000152377	ENSG00000152377			11251	protein-coding gene	gene with protein product		602264	"sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican)"	TIC1, SPOCK		9545645	Standard	NM_004598		Approved	testican-1	uc003lbp.3	Q08629	OTTHUMG00000129157	ENST00000394945.1:c.815T>A	chr5.hg19:g.136324224A>T	ENSP00000378401:p.Ile272Asn	349.0	0.0		395.0	137.0	NM_004598	B3KSW3|Q59EW0|Q8N630|Q9UCL8	Missense_Mutation	SNP	ENST00000394945.1	hg19	CCDS4191.1	.	.	.	.	.	.	.	.	.	.	A	28.5	4.928309	0.92389	.	.	ENSG00000152377	ENST00000394945;ENST00000282223	T;T	0.53640	0.61;0.61	6.06	6.06	0.98353	SPARC/Testican, calcium-binding domain (1);EF-hand-like domain (1);	0.054329	0.64402	D	0.000001	T	0.66228	0.2768	M	0.80183	2.485	0.58432	D	0.999999	P	0.50819	0.939	P	0.55455	0.776	T	0.71151	-0.4676	10	0.87932	D	0	.	15.7966	0.78416	1.0:0.0:0.0:0.0	.	272	Q08629	TICN1_HUMAN	N	272	ENSP00000378401:I272N;ENSP00000282223:I272N	ENSP00000282223:I272N	I	-	2	0	SPOCK1	136352123	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.335000	0.96500	2.315000	0.78130	0.533000	0.62120	ATC	.	.		0.488	SPOCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251222.1	NM_004598		T	136324224	A	T	136324224	3	4	237	1	0	0	0	0	1	0	0	0	15094	333	12	4	520	4	SPOCK1	5	136324224	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	2206467	136324224	44591036	74	32980										
PKD2L2	27039	hgsc.bcm.edu	37	chr5	137226191	137226191	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ggcttcgaaacataagttgcAttacagaaaggaagtagaaa	10	5	0	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr5:137226191A>G	ENST00000508883.1	+	2	79	c.53A>G	c.(52-54)cAt>cGt	p.H18R	PKD2L2_ENST00000350250.4_Intron|PKD2L2_ENST00000502810.1_Missense_Mutation_p.H18R|RP11-381K20.2_ENST00000514616.1_RNA|PKD2L2_ENST00000508638.1_Missense_Mutation_p.H18R|RP11-381K20.2_ENST00000508281.2_RNA|PKD2L2_ENST00000290431.5_Missense_Mutation_p.H18R			Q9NZM6	PK2L2_HUMAN	polycystic kidney disease 2-like 2	18					calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)	integral component of membrane (GO:0016021)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			breast(1)|endometrium(7)|kidney(4)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	28			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			CATAAGTTGCATTACAGAAAG	0.294																																					p.H18R		Atlas-SNP	.											.	PKD2L2	68	.	0			c.A53G						.						90	91	91					5																	137226191		1803	4069	5872	SO:0001583	missense	27039	exon2			AGTTGCATTACAG	AF118125	CCDS43367.1, CCDS58971.1, CCDS58972.1	5q31	2011-12-16			ENSG00000078795	ENSG00000078795		"Voltage-gated ion channels / Transient receptor potential cation channels"	9012	protein-coding gene	gene with protein product		604669				10602361	Standard	NM_014386		Approved	TRPP5	uc003lbw.1	Q9NZM6	OTTHUMG00000163306	ENST00000508883.1:c.53A>G	chr5.hg19:g.137226191A>G	ENSP00000424725:p.His18Arg	194.0	0.0		195.0	61.0	NM_001258448	A6NK98|B4DXD2|E9PC91|E9PDG4|Q86YB4|Q9UNJ0	Missense_Mutation	SNP	ENST00000508883.1	hg19		.	.	.	.	.	.	.	.	.	.	A	9.545	1.114460	0.20795	.	.	ENSG00000078795	ENST00000508638;ENST00000502810;ENST00000508883;ENST00000290431	T;T;T;T	0.70986	0.38;-0.53;-0.07;-0.08	5.8	1.83	0.25207	.	0.936760	0.08927	N	0.873599	T	0.52597	0.1744	L	0.29908	0.895	0.09310	N	0.999999	B;B;B	0.31581	0.002;0.329;0.008	B;B;B	0.22152	0.001;0.038;0.009	T	0.29212	-1.0019	10	0.16420	T	0.52	-1.1853	8.6922	0.34273	0.5786:0.3125:0.0:0.1089	.	18;18;18	Q9NZM6;E9PC91;Q9NZM6-5	PK2L2_HUMAN;.;.	R	18	ENSP00000423382:H18R;ENSP00000425513:H18R;ENSP00000424725:H18R;ENSP00000290431:H18R	ENSP00000290431:H18R	H	+	2	0	PKD2L2	137254090	0.000000	0.05858	0.917000	0.36280	0.801000	0.45260	-0.195000	0.09546	0.993000	0.38866	0.377000	0.23210	CAT	.	.		0.294	PKD2L2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372521.1	NM_014386		G	137226191	A	G	137226191	3	3	237	1	0	0	0	0	1	0	0	0	11977	217	8	2	59	2	PKD2L2	5	137226191	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	901967	137226191	43689069	75	32981										
DPYSL3	1809	hgsc.bcm.edu	37	chr5	146792244	146792244	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ctcccaggcaggtgaagatcTcatagagctgaaatagaaat	10	8	1	5			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr5:146792244T>A	ENST00000398514.3	-	6	919	c.548A>T	c.(547-549)gAg>gTg	p.E183V	DPYSL3_ENST00000343218.5_Missense_Mutation_p.E297V|DPYSL3_ENST00000534907.1_Intron	NM_001387.2	NP_001378.1	Q14195	DPYL3_HUMAN	dihydropyrimidinase-like 3	183					actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cell migration (GO:0030336)|negative regulation of neuron projection development (GO:0010977)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of neuron projection development (GO:0010976)|protein homooligomerization (GO:0051260)|pyrimidine nucleobase catabolic process (GO:0006208)|response to axon injury (GO:0048678)	cell body (GO:0044297)|cytosol (GO:0005829)|extracellular space (GO:0005615)|filamentous actin (GO:0031941)|growth cone (GO:0030426)|lamellipodium (GO:0030027)	chondroitin sulfate binding (GO:0035374)|hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)|SH3 domain binding (GO:0017124)			breast(2)|endometrium(1)|kidney(4)|large_intestine(6)|liver(1)|lung(9)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTGAAGATCTCATAGAGCTG	0.512																																					p.E297V		Atlas-SNP	.											.	DPYSL3	58	.	0			c.A890T						.						58	57	57					5																	146792244		1923	4121	6044	SO:0001583	missense	1809	exon6			AAGATCTCATAGA	D78014	CCDS43381.1, CCDS56387.1	5q32	2008-02-05							3015	protein-coding gene	gene with protein product		601168				8973361, 9115293	Standard	NM_001197294		Approved	DRP-3, ULIP, CRMP4	uc003loo.3	Q14195		ENST00000398514.3:c.548A>T	chr5.hg19:g.146792244T>A	ENSP00000381526:p.Glu183Val	114.0	0.0		112.0	11.0	NM_001197294	B3SXQ8|Q93012	Missense_Mutation	SNP	ENST00000398514.3	hg19	CCDS43381.1	.	.	.	.	.	.	.	.	.	.	T	28.5	4.928366	0.92389	.	.	ENSG00000113657	ENST00000398514;ENST00000343218	D;D	0.90955	-2.76;-2.76	6.02	6.02	0.97574	Amidohydrolase 1 (1);Metal-dependent hydrolase, composite domain (1);	0.109568	0.64402	D	0.000004	D	0.96463	0.8846	M	0.92604	3.325	0.80722	D	1	D;D	0.71674	0.998;0.993	D;P	0.76071	0.987;0.848	D	0.97201	0.9864	10	0.72032	D	0.01	-1.6788	16.5446	0.84426	0.0:0.0:0.0:1.0	.	297;183	B3SXQ8;Q14195	.;DPYL3_HUMAN	V	183;297	ENSP00000381526:E183V;ENSP00000343690:E297V	ENSP00000343690:E297V	E	-	2	0	DPYSL3	146772437	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	7.997000	0.88414	2.311000	0.77944	0.533000	0.62120	GAG	.	.		0.512	DPYSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373421.2	NM_001387		A	146792244	T	A	146792244	3	1	237	1	0	0	0	0	1	0	0	0	4750	1551	54	4	1200	4	DPYSL3	5	146792244	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	9566053	146792244	34123016	76	32982										
CCDC99	54908	hgsc.bcm.edu	37	chr5	169023605	169023605	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	acagatgaaagggtctcaaaCtgaatttgagcagcaggaac	11	7	1	4	rs145815866		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr5:169023605C>T	ENST00000265295.4	+	8	1211	c.932C>T	c.(931-933)aCt>aTt	p.T311I		NM_017785.4	NP_060255.3			spindle apparatus coiled-coil protein 1																		GGGTCTCAAACTGAATTTGAG	0.348																																					p.T311I		Atlas-SNP	.											.	.	.	.	0			c.C932T						.						82	86	85					5																	169023605		2203	4300	6503	SO:0001583	missense	54908	exon8			CTCAAACTGAATT	BC012568	CCDS4370.1	5q35.1	2012-09-27	2012-09-27	2012-09-27	ENSG00000040275	ENSG00000040275			26010	protein-coding gene	gene with protein product	"spindly homolog (Drosophila)"		"coiled-coil domain containing 99"	CCDC99		20427577	Standard	NM_017785		Approved	FLJ20364, hSpindly	uc003mae.4	Q96EA4	OTTHUMG00000130438	ENST00000265295.4:c.932C>T	chr5.hg19:g.169023605C>T	ENSP00000265295:p.Thr311Ile	207.0	0.0		226.0	70.0	NM_017785		Missense_Mutation	SNP	ENST00000265295.4	hg19	CCDS4370.1	.	.	.	.	.	.	.	.	.	.	C	15.53	2.861091	0.51482	.	.	ENSG00000040275	ENST00000265295;ENST00000274631	T	0.32023	1.47	5.7	5.7	0.88788	.	0.304797	0.38492	N	0.001673	T	0.44435	0.1293	L	0.54323	1.7	0.28765	N	0.900678	D;P;P	0.59767	0.986;0.773;0.573	P;B;B	0.55391	0.775;0.372;0.165	T	0.41413	-0.9510	10	0.56958	D	0.05	-4.1564	14.6759	0.68978	0.0:0.7347:0.2653:0.0	.	233;212;311	B4E393;Q96EA4-2;Q96EA4	.;.;SPDLY_HUMAN	I	311;212	ENSP00000265295:T311I	ENSP00000265295:T311I	T	+	2	0	CCDC99	168956183	1.000000	0.71417	0.916000	0.36221	0.970000	0.65996	3.958000	0.56737	2.665000	0.90641	0.655000	0.94253	ACT	.	C|1.000;G|0.000		0.348	SPDL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252829.2	NM_017785		T	169023605	C	T	169023605	3	4	237	1	0	0	0	0	1	0	0	0	2878	565	20	3	958	3	CCDC99	5	169023605	Missense_Mutation	SNP	C	TCGA-ED-A459-01A-11D-A25V-10	22231361	169023605	11891655	77	32983										
BTN2A2	10385	hgsc.bcm.edu	37	chr6	26392974	26392974	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gccgggtgggcgtcttcctgGactatgaagctggagatgtc	16	9	1	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr6:26392974G>T	ENST00000356709.4	+	8	1462	c.1351G>T	c.(1351-1353)Gac>Tac	p.D451Y	BTN2A2_ENST00000482536.1_Missense_Mutation_p.D241Y|BTN2A2_ENST00000432533.2_3'UTR|BTN2A2_ENST00000352867.2_Missense_Mutation_p.D335Y|BTN2A2_ENST00000469230.1_Intron|BTN2A2_ENST00000416795.2_Missense_Mutation_p.D451Y	NM_001197240.1|NM_006995.4	NP_001184169.1|NP_008926.2	Q8WVV5	BT2A2_HUMAN	butyrophilin, subfamily 2, member A2	451	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of cellular metabolic process (GO:0031324)|negative regulation of cytokine secretion (GO:0050710)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|large_intestine(5)|lung(13)	23						CGTCTTCCTGGACTATGAAGC	0.547																																					p.D451Y		Atlas-SNP	.											.	BTN2A2	87	.	0			c.G1351T						.						112	103	106					6																	26392974		2203	4298	6501	SO:0001583	missense	10385	exon8			TTCCTGGACTATG	U90550	CCDS4606.1, CCDS4607.1, CCDS56401.1, CCDS56402.1, CCDS56403.1	6p22.1	2014-01-14			ENSG00000124508	ENSG00000124508		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Butyrophilins"	1137	protein-coding gene	gene with protein product		613591				10354554, 9149941	Standard	NM_006995		Approved	BTF2, BT2.2, BTN2.2	uc003nhq.3	Q8WVV5	OTTHUMG00000014452	ENST00000356709.4:c.1351G>T	chr6.hg19:g.26392974G>T	ENSP00000349143:p.Asp451Tyr	397.0	1.0		408.0	134.0	NM_006995	A6NM84|B4DE97|B4DQ01|E9PH07|O00480	Missense_Mutation	SNP	ENST00000356709.4	hg19	CCDS4606.1	.	.	.	.	.	.	.	.	.	.	.	15.45	2.835821	0.50951	.	.	ENSG00000124508	ENST00000356709;ENST00000352867;ENST00000482536;ENST00000416795	D;D;D;D	0.81499	-1.5;-1.5;-1.5;-1.5	3.63	1.79	0.24919	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.113821	0.39615	N	0.001301	D	0.90762	0.7100	H	0.99197	4.465	0.35580	D	0.806183	D;D;D	0.89917	0.998;1.0;1.0	D;D;D	0.85130	0.938;0.986;0.997	D	0.88784	0.3273	10	0.87932	D	0	.	7.0519	0.25077	0.1049:0.1735:0.7216:0.0	.	241;335;451	E9PH07;A6NM84;Q8WVV5	.;.;BT2A2_HUMAN	Y	451;335;241;451	ENSP00000349143:D451Y;ENSP00000337117:D335Y;ENSP00000419451:D241Y;ENSP00000399308:D451Y	ENSP00000337117:D335Y	D	+	1	0	BTN2A2	26500953	1.000000	0.71417	0.705000	0.30386	0.634000	0.38068	4.649000	0.61433	0.165000	0.19558	-0.455000	0.05494	GAC	.	.		0.547	BTN2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040117.1			T	26392974	G	T	26392974	3	4	237	1	0	0	0	0	1	0	0	0	1563	1174	41	3	1377	3	BTN2A2	6	26392974	Missense_Mutation	SNP	G	TCGA-ED-A459-01A-11D-A25V-10		26392974	144722093	78	32984										
DPCR1	135656	hgsc.bcm.edu	37	chr6	30917142	30917142	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	atgagaacaacacaccatccCcagcagagcctacagaaaat	6	13	0	3			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr6:30917142C>T	ENST00000462446.1	+	2	929	c.901C>T	c.(901-903)Cca>Tca	p.P301S	HCG21_ENST00000419481.1_RNA|DPCR1_ENST00000304311.2_5'UTR			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	301	Thr-rich.					integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						CACACCATCCCCAGCAGAGCC	0.458																																					p.P301S		Atlas-SNP	.											.	DPCR1	99	.	0			c.C901T						.						86	82	83					6																	30917142		692	1591	2283	SO:0001583	missense	135656	exon2			CCATCCCCAGCAG	AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.901C>T	chr6.hg19:g.30917142C>T	ENSP00000417182:p.Pro301Ser	170.0	0.0		207.0	71.0	NM_080870	C9IZC0|Q658M7|Q8WYN2	Missense_Mutation	SNP	ENST00000462446.1	hg19	CCDS4692.2	.	.	.	.	.	.	.	.	.	.	c	0.015	-1.569991	0.00895	.	.	ENSG00000168631	ENST00000462446;ENST00000450344	T	0.45668	0.89	1.36	0.31	0.15825	.	.	.	.	.	T	0.08758	0.0217	L	0.28400	0.85	0.09310	N	0.999994	P	0.40282	0.711	B	0.38194	0.267	T	0.22173	-1.0224	9	0.07482	T	0.82	.	6.4298	0.21790	0.2897:0.7103:0.0:0.0	.	301	E9PEI6	.	S	301	ENSP00000417182:P301S	ENSP00000411741:P301S	P	+	1	0	DPCR1	31025121	0.000000	0.05858	0.006000	0.13384	0.078000	0.17371	0.938000	0.28965	0.091000	0.17302	0.175000	0.17021	CCA	.	.		0.458	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870		T	30917142	C	T	30917142	3	4	237	1	0	0	0	0	1	0	0	0	4714	623	22	3	907	3	DPCR1	6	30917142	Missense_Mutation	SNP	C	TCGA-ED-A459-01A-11D-A25V-10	4524168	30917142	140197925	79	32985										
TNF	7124	hgsc.bcm.edu	37	chr6	31544903	31544903	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ctccctccagcaaaccctcaAgctgaggggcagctccagtg	10	16	1	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr6:31544903A>T	ENST00000449264.2	+	4	466	c.291A>T	c.(289-291)caA>caT	p.Q97H		NM_000594.3	NP_000585.2	P01375	TNFA_HUMAN	tumor necrosis factor	97					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPK activity (GO:0000187)|activation of MAPKKK activity (GO:0000185)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|calcium-mediated signaling (GO:0019722)|cell activation (GO:0001775)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nicotine (GO:0071316)|cellular response to organic cyclic compound (GO:0071407)|chronic inflammatory response to antigenic stimulus (GO:0002439)|defense response to Gram-positive bacterium (GO:0050830)|embryonic digestive tract development (GO:0048566)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|glucose metabolic process (GO:0006006)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|JNK cascade (GO:0007254)|leukocyte tethering or rolling (GO:0050901)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MAPK cascade (GO:0000165)|necroptotic signaling pathway (GO:0097527)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of branching involved in lung morphogenesis (GO:0061048)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gene expression (GO:0010629)|negative regulation of glucose import (GO:0046325)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of L-glutamate transport (GO:0002037)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of lipid storage (GO:0010888)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|organ morphogenesis (GO:0009887)|osteoclast differentiation (GO:0030316)|positive regulation of apoptotic process (GO:0043065)|positive regulation of calcidiol 1-monooxygenase activity (GO:0060559)|positive regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000343)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of chemokine production (GO:0032722)|positive regulation of chronic inflammatory response to antigenic stimulus (GO:0002876)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fever generation (GO:0031622)|positive regulation of gene expression (GO:0010628)|positive regulation of hair follicle development (GO:0051798)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of mitosis (GO:0045840)|positive regulation of mononuclear cell migration (GO:0071677)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of podosome assembly (GO:0071803)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein complex disassembly (GO:0043243)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein localization to cell surface (GO:2000010)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein transport (GO:0051222)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of synaptic transmission (GO:0050806)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translational initiation by iron (GO:0045994)|positive regulation of vitamin D biosynthetic process (GO:0060557)|protein import into nucleus, translocation (GO:0000060)|protein kinase B signaling (GO:0043491)|receptor biosynthetic process (GO:0032800)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of immunoglobulin secretion (GO:0051023)|regulation of insulin secretion (GO:0050796)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to salt stress (GO:0009651)|response to virus (GO:0009615)|sequestering of triglyceride (GO:0030730)|skeletal muscle contraction (GO:0003009)|transformed cell apoptotic process (GO:0006927)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	cytokine activity (GO:0005125)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|transcription regulatory region DNA binding (GO:0044212)|tumor necrosis factor receptor binding (GO:0005164)			large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|skin(3)	8		Ovarian(999;0.00556)			Adalimumab(DB00051)|Amrinone(DB01427)|Certolizumab pegol(DB08904)|Chloroquine(DB00608)|Clenbuterol(DB01407)|Epinephrine(DB00668)|Etanercept(DB00005)|Glucosamine(DB01296)|golimumab(DB06674)|Infliximab(DB00065)|Pomalidomide(DB08910)|Pranlukast(DB01411)|Pseudoephedrine(DB00852)|Thalidomide(DB01041)	CAAACCCTCAAGCTGAGGGGC	0.637									Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of																												p.Q97H		Atlas-SNP	.											.	TNF	15	.	0			c.A291T						.						69	74	73					6																	31544903		1511	2709	4220	SO:0001583	missense	7124	exon4	Familial Cancer Database	incl.: Familial Head and Neck Cancer	CCCTCAAGCTGAG	X02910	CCDS4702.1	6p21.3	2013-05-22	2010-05-04		ENSG00000232810	ENSG00000232810		"Tumor necrosis factor (ligand) superfamily"	11892	protein-coding gene	gene with protein product	"TNF superfamily, member 2"	191160	"tumor necrosis factor (TNF superfamily, member 2)"	TNFA		2413547, 6392892	Standard	NM_000594		Approved	TNFSF2, DIF, TNF-alpha	uc003nui.4	P01375	OTTHUMG00000031194	ENST00000449264.2:c.291A>T	chr6.hg19:g.31544903A>T	ENSP00000398698:p.Gln97His	65.0	0.0		64.0	4.0	NM_000594	O43647|Q9P1Q2|Q9UIV3	Missense_Mutation	SNP	ENST00000449264.2	hg19	CCDS4702.1	.	.	.	.	.	.	.	.	.	.	A	5.959	0.360848	0.11296	.	.	ENSG00000232810	ENST00000449264	T	0.43688	0.94	5.41	-1.04	0.10068	Tumour necrosis factor (2);Tumour necrosis factor-like (2);	0.974983	0.08449	N	0.944165	T	0.19127	0.0459	M	0.77103	2.36	0.09310	N	1	B	0.27679	0.185	B	0.25884	0.064	T	0.39961	-0.9588	10	0.66056	D	0.02	.	1.414	0.02298	0.4253:0.2989:0.1307:0.1451	.	97	P01375	TNFA_HUMAN	H	97	ENSP00000398698:Q97H	ENSP00000398698:Q97H	Q	+	3	2	TNF	31652882	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-0.104000	0.10923	0.042000	0.15717	-0.460000	0.05396	CAA	.	.		0.637	TNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076390.2			T	31544903	A	T	31544903	3	4	237	1	0	0	0	0	1	0	0	0	16286	69	3	4	305	4	TNF	6	31544903	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	627761	31544903	139570164	80	32986										
RGL2	5863	hgsc.bcm.edu	37	chr6	33263466	33263466	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	cagatgggcagaggtgagaaTgtcctggccggtctctgtga	16	8	1	4	rs201427428	byFrequency	TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr6:33263466T>A	ENST00000497454.1	-	7	1334	c.839A>T	c.(838-840)cAt>cTt	p.H280L	RGL2_ENST00000444031.2_Missense_Mutation_p.H198L|RGL2_ENST00000437840.2_5'UTR|PFDN6_ENST00000463584.1_Intron	NM_001243738.1|NM_004761.4	NP_001230667.1|NP_004752.1	O15211	RGL2_HUMAN	ral guanine nucleotide dissociation stimulator-like 2	280	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)	intracellular (GO:0005622)	Ras guanyl-nucleotide exchange factor activity (GO:0005088)			breast(2)|cervix(2)|endometrium(7)|kidney(2)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	34						GAGGTGAGAATGTCCTGGCCG	0.547																																					p.H280L		Atlas-SNP	.											.	RGL2	58	.	0			c.A839T						.						51	53	52					6																	33263466		2203	4300	6503	SO:0001583	missense	5863	exon7			TGAGAATGTCCTG		CCDS4774.1	6p21.3	2010-02-17	2004-06-11	2004-06-16	ENSG00000237441	ENSG00000237441			9769	protein-coding gene	gene with protein product		602306	"RAB2, member RAS oncogene family-like"	RAB2L		8976381	Standard	NM_001243738		Approved	KE1.5, HKE1.5	uc003odv.3	O15211	OTTHUMG00000031072	ENST00000497454.1:c.839A>T	chr6.hg19:g.33263466T>A	ENSP00000420211:p.His280Leu	163.0	0.0		190.0	13.0	NM_004761	B4DG72|Q5STK0|Q9Y3F3	Missense_Mutation	SNP	ENST00000497454.1	hg19	CCDS4774.1	.	.	.	.	.	.	.	.	.	.	T	16.08	3.021312	0.54576	.	.	ENSG00000237441	ENST00000497454;ENST00000421215;ENST00000444031	T;T	0.28666	1.6;1.6	4.61	4.61	0.57282	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1);	0.199351	0.43260	D	0.000594	T	0.13072	0.0317	N	0.11698	0.16	0.39371	D	0.966088	P;P	0.48503	0.619;0.911	B;P	0.48488	0.137;0.579	T	0.03981	-1.0987	10	0.49607	T	0.09	.	10.3073	0.43689	0.0:0.0:0.0:1.0	.	198;280	B4DG72;O15211	.;RGL2_HUMAN	L	280;144;198	ENSP00000420211:H280L;ENSP00000403070:H198L	ENSP00000400083:H144L	H	-	2	0	RGL2	33371444	0.933000	0.31639	1.000000	0.80357	0.996000	0.88848	1.234000	0.32660	1.921000	0.55644	0.523000	0.50628	CAT	.	T|0.999;C|0.001		0.547	RGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076098.2			A	33263466	T	A	33263466	3	1	237	1	0	0	0	0	1	0	0	0	13292	1464	51	4	1542	4	RGL2	6	33263466	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	1718563	33263466	137851601	81	32987										
SYNGAP1	8831	hgsc.bcm.edu	37	chr6	33403036	33403036	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	cttggatgaagattccattaTcaagccagtgcacagctcca	8	11	1	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr6:33403036T>C	ENST00000418600.2	+	6	718	c.617T>C	c.(616-618)aTc>aCc	p.I206T	SYNGAP1_ENST00000428982.2_Missense_Mutation_p.I147T|SYNGAP1_ENST00000496374.1_3'UTR|SYNGAP1_ENST00000293748.5_Missense_Mutation_p.I206T	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	206	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				dendrite development (GO:0016358)|negative regulation of axonogenesis (GO:0050771)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|pattern specification process (GO:0007389)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|receptor clustering (GO:0043113)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of MAPK cascade (GO:0043408)|regulation of synapse structure and activity (GO:0050803)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Rab GTPase activator activity (GO:0005097)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(15)|ovary(7)|pancreas(1)|stomach(1)|urinary_tract(1)	43						GATTCCATTATCAAGCCAGTG	0.537																																					p.I206T		Atlas-SNP	.											.	SYNGAP1	202	.	0			c.T617C						.						106	95	99					6																	33403036		2203	4300	6503	SO:0001583	missense	8831	exon6			CCATTATCAAGCC	AB067525	CCDS34434.2	6p21.3	2010-06-25	2010-06-25		ENSG00000197283	ENSG00000197283			11497	protein-coding gene	gene with protein product		603384	"synaptic Ras GTPase activating protein 1 homolog (rat)"			9581761, 18323856	Standard	NM_006772		Approved	SYNGAP, RASA5, KIAA1938	uc011dri.2	Q96PV0	OTTHUMG00000031096	ENST00000418600.2:c.617T>C	chr6.hg19:g.33403036T>C	ENSP00000403636:p.Ile206Thr	147.0	0.0		176.0	50.0	NM_006772	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Missense_Mutation	SNP	ENST00000418600.2	hg19	CCDS34434.2	.	.	.	.	.	.	.	.	.	.	T	17.10	3.303239	0.60195	.	.	ENSG00000197283	ENST00000293748;ENST00000418600;ENST00000449372;ENST00000428982	T;T;T	0.25250	1.81;1.9;1.91	4.42	4.42	0.53409	Pleckstrin homology-type (1);Pleckstrin homology domain (1);	0.062978	0.64402	D	0.000005	T	0.27900	0.0687	M	0.68593	2.085	0.58432	D	0.999992	B;P;P	0.48694	0.421;0.557;0.914	B;B;P	0.52159	0.156;0.297;0.691	T	0.07790	-1.0754	10	0.87932	D	0	.	11.6525	0.51297	0.0:0.0:0.0:1.0	.	206;206;206	Q96PV0;Q96PV0-4;B7ZCA0	SYGP1_HUMAN;.;.	T	206;206;206;147	ENSP00000293748:I206T;ENSP00000403636:I206T;ENSP00000412475:I147T	ENSP00000293748:I206T	I	+	2	0	SYNGAP1	33511014	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.859000	0.86982	1.845000	0.53610	0.482000	0.46254	ATC	.	.		0.537	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407		C	33403036	T	C	33403036	3	2	237	1	0	0	0	0	1	0	0	0	15462	1435	50	2	639	2	SYNGAP1	6	33403036	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	139570	33403036	137712031	82	32988										
TAF8	129685	hgsc.bcm.edu	37	chr6	42036240	42036240	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ttcaccatcccctacctgacAgctcttcttccgtctgaact	4	17	4	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr6:42036240A>T	ENST00000372977.3	+	7	693	c.675A>T	c.(673-675)acA>acT	p.T225T	TAF8_ENST00000456846.2_Silent_p.T225T|TAF8_ENST00000465926.1_Splice_Site|TAF8_ENST00000372982.4_Silent_p.T225T|TAF8_ENST00000494547.1_Silent_p.T225T	NM_138572.2	NP_612639.2	Q7Z7C8	TAF8_HUMAN	TAF8 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 43kDa	225					cell differentiation (GO:0030154)|inner cell mass cell proliferation (GO:0001833)|maintenance of protein location in nucleus (GO:0051457)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fat cell differentiation (GO:0045598)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|transcription factor TFIID complex (GO:0005669)				endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)	6	Colorectal(47;0.196)		STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|Epithelial(12;0.00179)			CCTACCTGACAGCTCTTCTTC	0.507																																					p.T225T		Atlas-SNP	.											.	TAF8	25	.	0			c.A675T						.						259	258	258					6																	42036240		2045	4216	6261	SO:0001819	synonymous_variant	129685	exon7			CCTGACAGCTCTT	AK057383	CCDS43462.1	6p21.1	2008-10-23	2007-07-30	2007-07-30	ENSG00000137413	ENSG00000137413			17300	protein-coding gene	gene with protein product		609514	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 45/50kDa", "taube nuss homolog (mouse)"	TBN			Standard	NM_138572		Approved	FLJ32821, TAF(II)43	uc003ors.3	Q7Z7C8	OTTHUMG00000014692	ENST00000372977.3:c.675A>T	chr6.hg19:g.42036240A>T		221.0	0.0		302.0	20.0	NM_138572	Q5T0K1|Q8N4R9|Q96M52	Silent	SNP	ENST00000372977.3	hg19	CCDS43462.1	.	.	.	.	.	.	.	.	.	.	A	7.113	0.576351	0.13686	.	.	ENSG00000137413	ENST00000465926	.	.	.	6.06	-12.1	0.00011	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.8065	0.08779	0.1226:0.2962:0.3625:0.2187	.	.	.	.	.	-1	.	.	.	+	.	.	TAF8	42144218	0.000000	0.05858	0.020000	0.16555	0.999000	0.98932	-5.159000	0.00146	-3.750000	0.00111	0.533000	0.62120	.	.	.		0.507	TAF8-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000357901.1	NM_138572		T	42036240	A	T	42036240	2	4	237	1	0	0	0	0	0	0	0	1	15549	175	7	4		4	TAF8	6	42036240	Silent	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	8633204	42036240	129078827	83	32989										
AARS2	57505	hgsc.bcm.edu	37	chr6	44279864	44279864	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gcatttcaaagaaggtatgaTgggaaaggtctcgacccaca	11	8	2	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr6:44279864T>A	ENST00000244571.4	-	2	382	c.380A>T	c.(379-381)cAt>cTt	p.H127L	RP11-444E17.6_ENST00000505802.1_Intron	NM_020745.3	NP_065796			alanyl-tRNA synthetase 2, mitochondrial											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(2)|stomach(1)	34	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			GAAGGTATGATGGGAAAGGTC	0.502																																					p.H127L		Atlas-SNP	.											.	AARS2	77	.	0			c.A380T						.						200	167	179					6																	44279864		2203	4300	6503	SO:0001583	missense	57505	exon2			GTATGATGGGAAA	AB033096	CCDS34464.1	6p21.1	2012-10-26	2012-10-26	2007-02-23	ENSG00000124608	ENSG00000124608	6.1.1.7	"Aminoacyl tRNA synthetases / Class II"	21022	protein-coding gene	gene with protein product	"alanine tRNA ligase 2, mitochondrial"	612035	"alanyl-tRNA synthetase like", "alanyl-tRNA synthetase 2, mitochondrial (putative)"	AARSL		15779907, 21549344	Standard	NM_020745		Approved	KIAA1270, bA444E17.1	uc010jza.1	Q5JTZ9	OTTHUMG00000014766	ENST00000244571.4:c.380A>T	chr6.hg19:g.44279864T>A	ENSP00000244571:p.His127Leu	165.0	0.0		208.0	11.0	NM_020745		Missense_Mutation	SNP	ENST00000244571.4	hg19	CCDS34464.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.705725	0.89018	.	.	ENSG00000124608	ENST00000244571	D	0.97114	-4.25	4.9	4.9	0.64082	Alanyl-tRNA synthetase, class IIc, core domain (1);Alanyl-tRNA synthetase, class IIc, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.99086	0.9686	H	0.98446	4.235	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99104	1.0844	10	0.87932	D	0	-14.2778	14.698	0.69136	0.0:0.0:0.0:1.0	.	127	Q5JTZ9	SYAM_HUMAN	L	127	ENSP00000244571:H127L	ENSP00000244571:H127L	H	-	2	0	AARS2	44387842	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.868000	0.87116	2.054000	0.61138	0.358000	0.22013	CAT	.	.		0.502	AARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040741.2	NM_020745		A	44279864	T	A	44279864	3	1	237	1	0	0	0	0	1	0	0	0	20	1464	51	4	2661	4	AARS2	6	44279864	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	2243624	44279864	126835203	84	32990										
RIMS1	22999	hgsc.bcm.edu	37	chr6	72967855	72967855	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	taggtctagtgctagagaaaGtaaatctacaacattaactg	8	6	2	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr6:72967855G>T	ENST00000521978.1	+	17	2798	c.2798G>T	c.(2797-2799)aGt>aTt	p.S933I	RIMS1_ENST00000264839.7_Missense_Mutation_p.S933I|RIMS1_ENST00000538414.1_5'UTR|RIMS1_ENST00000348717.5_Missense_Mutation_p.S932I|RIMS1_ENST00000518273.1_Missense_Mutation_p.S933I|RIMS1_ENST00000517960.1_Missense_Mutation_p.S932I|RIMS1_ENST00000401910.3_Missense_Mutation_p.S406I|RIMS1_ENST00000522291.1_Missense_Mutation_p.S932I|RIMS1_ENST00000523963.1_Missense_Mutation_p.S407I|RIMS1_ENST00000425662.2_Missense_Mutation_p.S326I|RIMS1_ENST00000520567.1_Missense_Mutation_p.S932I|RIMS1_ENST00000517827.1_Missense_Mutation_p.S392I|RIMS1_ENST00000491071.2_Missense_Mutation_p.S933I	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	933					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				GCTAGAGAAAGTAAATCTACA	0.398																																					p.S933I		Atlas-SNP	.											.	RIMS1	278	.	0			c.G2798T						.						86	81	82					6																	72967855		1935	4131	6066	SO:0001583	missense	22999	exon17			GAGAAAGTAAATC	AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"Rab3-interacting molecule"	606629	"RAB3 interacting protein 2"	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.2798G>T	chr6.hg19:g.72967855G>T	ENSP00000428417:p.Ser933Ile	78.0	0.0		78.0	23.0	NM_014989	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Missense_Mutation	SNP	ENST00000521978.1	hg19	CCDS47449.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	13.06|13.06|13.06	2.125161|2.125161|2.125161	0.37533|0.37533|0.37533	.|.|.	.|.|.	ENSG00000079841|ENSG00000079841|ENSG00000079841	ENST00000517433|ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978;ENST00000401910;ENST00000523963;ENST00000425662;ENST00000453976;ENST00000517827;ENST00000370420|ENST00000522211	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T|.	.|0.18016|.	.|2.49;2.53;2.53;2.54;2.6;2.58;2.56;2.51;2.59;2.62;2.63;2.43;2.61;2.24|.	5.44|5.44|5.44	4.57|4.57|4.57	0.56435|0.56435|0.56435	.|.|.	.|0.065517|.	.|0.64402|.	.|D|.	.|0.000008|.	T|T|T	0.39937|0.39937|0.39937	0.1097|0.1097|0.1097	L|L|L	0.36672|0.36672|0.36672	1.1|1.1|1.1	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|B;B;P;D;B;D;B;P;P;B;P;P|.	.|0.60575|.	.|0.18;0.214;0.863;0.988;0.013;0.978;0.329;0.613;0.8;0.02;0.918;0.725|.	.|B;B;P;P;B;P;B;B;B;B;P;B|.	.|0.53722|.	.|0.065;0.094;0.451;0.675;0.009;0.733;0.077;0.269;0.276;0.028;0.451;0.248|.	T|T|T	0.32214|0.32214|0.32214	-0.9915|-0.9915|-0.9915	5|10|5	.|0.31617|.	.|T|.	.|0.26|.	-6.9858|-6.9858|-6.9858	11.2214|11.2214|11.2214	0.48857|0.48857|0.48857	0.1473:0.0:0.8527:0.0|0.1473:0.0:0.8527:0.0|0.1473:0.0:0.8527:0.0	.|.|.	.|392;407;933;392;406;932;185;933;932;186;933;933|.	.|B7Z3S3;E9PHF5;E9PHR1;B7Z9Z3;E9PF48;E7EX08;Q5JY22;E7ERQ1;E7ENC2;Q5JY21;C9JNW6;Q86UR5|.	.|.;.;.;.;.;.;.;.;.;.;.;RIMS1_HUMAN|.	N|I|L	506|933;933;933;932;933;932;933;932;933;932;932;933;406;407;326;326;392;158|24	.|ENSP00000430101:S933I;ENSP00000275037:S932I;ENSP00000264839:S933I;ENSP00000429959:S932I;ENSP00000430408:S933I;ENSP00000430502:S932I;ENSP00000430932:S932I;ENSP00000428417:S933I;ENSP00000385649:S406I;ENSP00000428328:S407I;ENSP00000411235:S326I;ENSP00000389503:S326I;ENSP00000428367:S392I;ENSP00000359448:S158I|.	.|ENSP00000264839:S933I|.	K|S|V	+|+|+	3|2|1	2|0|0	RIMS1|RIMS1|RIMS1	73024576|73024576|73024576	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.829000|0.829000|0.829000	0.46940|0.46940|0.46940	5.528000|5.528000|5.528000	0.67129|0.67129|0.67129	1.301000|1.301000|1.301000	0.44836|0.44836|0.44836	0.585000|0.585000|0.585000	0.79938|0.79938|0.79938	AAG|AGT|GTA	.	.		0.398	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1			T	72967855	G	T	72967855	3	4	237	1	0	0	0	0	1	0	0	0	13382	1029	36	3	3027	3	RIMS1	6	72967855	Missense_Mutation	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	28687991	72967855	98147212	85	32991										
RIMS1	22999	hgsc.bcm.edu	37	chr6	72967911	72967911	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gaacaactcatcaccgctcaCgttcagtatctcctcatcgc	5	16	6	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr6:72967911C>A	ENST00000521978.1	+	17	2854	c.2854C>A	c.(2854-2856)Cgt>Agt	p.R952S	RIMS1_ENST00000264839.7_Missense_Mutation_p.R952S|RIMS1_ENST00000538414.1_5'UTR|RIMS1_ENST00000348717.5_Missense_Mutation_p.R951S|RIMS1_ENST00000518273.1_Missense_Mutation_p.R952S|RIMS1_ENST00000517960.1_Missense_Mutation_p.R951S|RIMS1_ENST00000401910.3_Missense_Mutation_p.R425S|RIMS1_ENST00000522291.1_Missense_Mutation_p.R951S|RIMS1_ENST00000523963.1_Missense_Mutation_p.R426S|RIMS1_ENST00000425662.2_Missense_Mutation_p.R345S|RIMS1_ENST00000520567.1_Missense_Mutation_p.R951S|RIMS1_ENST00000517827.1_Missense_Mutation_p.R411S|RIMS1_ENST00000491071.2_Missense_Mutation_p.R952S	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	952					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				TCACCGCTCACGTTCAGTATC	0.463																																					p.R952S		Atlas-SNP	.											.	RIMS1	278	.	0			c.C2854A						.						93	89	90					6																	72967911		1994	4171	6165	SO:0001583	missense	22999	exon17			CGCTCACGTTCAG	AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"Rab3-interacting molecule"	606629	"RAB3 interacting protein 2"	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.2854C>A	chr6.hg19:g.72967911C>A	ENSP00000428417:p.Arg952Ser	122.0	0.0		121.0	30.0	NM_014989	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Missense_Mutation	SNP	ENST00000521978.1	hg19	CCDS47449.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	26.3|26.3|26.3	4.721823|4.721823|4.721823	0.89298|0.89298|0.89298	.|.|.	.|.|.	ENSG00000079841|ENSG00000079841|ENSG00000079841	ENST00000522211|ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978;ENST00000401910;ENST00000523963;ENST00000425662;ENST00000453976;ENST00000517827;ENST00000370420|ENST00000517433	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T|.	.|0.26810|.	.|1.93;2.31;2.06;2.31;2.12;2.02;2.13;1.81;1.94;2.07;2.3;2.27;2.26;1.71|.	5.19|5.19|5.19	5.19|5.19|5.19	0.71726|0.71726|0.71726	.|.|.	.|0.000000|.	.|0.64402|.	.|D|.	.|0.000016|.	T|T|T	0.65923|0.65923|0.65923	0.2738|0.2738|0.2738	L|L|L	0.60455|0.60455|0.60455	1.87|1.87|1.87	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|D;D;D;D;P;D;P;D;D;D;D;D|.	.|0.89917|.	.|0.957;0.993;0.998;0.998;0.956;1.0;0.76;0.978;0.995;0.997;0.999;0.998|.	.|P;D;D;D;P;D;B;P;D;D;D;D|.	.|0.87578|.	.|0.78;0.972;0.994;0.994;0.646;0.998;0.082;0.823;0.968;0.951;0.994;0.994|.	T|T|T	0.63910|0.63910|0.63910	-0.6530|-0.6530|-0.6530	5|10|5	.|0.66056|.	.|D|.	.|0.02|.	-14.3502|-14.3502|-14.3502	18.729|18.729|18.729	0.91728|0.91728|0.91728	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	.|411;426;952;411;425;951;204;952;951;205;952;952|.	.|B7Z3S3;E9PHF5;E9PHR1;B7Z9Z3;E9PF48;E7EX08;Q5JY22;E7ERQ1;E7ENC2;Q5JY21;C9JNW6;Q86UR5|.	.|.;.;.;.;.;.;.;.;.;.;.;RIMS1_HUMAN|.	Q|S|K	42|952;952;952;951;952;951;952;951;952;951;951;952;425;426;345;345;411;177|525	.|ENSP00000430101:R952S;ENSP00000275037:R951S;ENSP00000264839:R952S;ENSP00000429959:R951S;ENSP00000430408:R952S;ENSP00000430502:R951S;ENSP00000430932:R951S;ENSP00000428417:R952S;ENSP00000385649:R425S;ENSP00000428328:R426S;ENSP00000411235:R345S;ENSP00000389503:R345S;ENSP00000428367:R411S;ENSP00000359448:R177S|.	.|ENSP00000264839:R952S|.	H|R|T	+|+|+	3|1|2	2|0|0	RIMS1|RIMS1|RIMS1	73024632|73024632|73024632	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.893000|0.893000|0.893000	0.52053|0.52053|0.52053	7.607000|7.607000|7.607000	0.82883|0.82883|0.82883	2.434000|2.434000|2.434000	0.82447|0.82447|0.82447	0.585000|0.585000|0.585000	0.79938|0.79938|0.79938	CAC|CGT|ACG	.	.		0.463	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1			A	72967911	C	A	72967911	3	1	237	1	0	0	0	0	1	0	0	0	13382	536	19	1	3083	1	RIMS1	6	72967911	Missense_Mutation	SNP	C	TCGA-ED-A459-01A-11D-A25V-10	56	72967911	98147156	86	32992										
MDN1	23195	hgsc.bcm.edu	37	chr6	90380710	90380710	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gtactacggtgagttgctaaAgacatggtcaggaagaagag	14	5	1	4			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr6:90380710A>G	ENST00000369393.3	-	83	13999	c.13884T>C	c.(13882-13884)tcT>tcC	p.S4628S	RP1-122O8.7_ENST00000438877.1_RNA|MDN1_ENST00000468568.1_5'UTR|MDN1_ENST00000428876.1_Silent_p.S4628S			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	4628					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		GAGTTGCTAAAGACATGGTCA	0.532																																					p.S4628S		Atlas-SNP	.											.	MDN1	478	.	0			c.T13884C						.						102	91	95					6																	90380710		2203	4300	6503	SO:0001819	synonymous_variant	23195	exon83			TGCTAAAGACATG	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.13884T>C	chr6.hg19:g.90380710A>G		188.0	0.0		175.0	50.0	NM_014611	O15019|Q5T794	Silent	SNP	ENST00000369393.3	hg19	CCDS5024.1																																																																																			.	.		0.532	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			G	90380710	A	G	90380710	2	3	237	1	0	0	0	0	0	0	0	1	9424	59	3	2		2	MDN1	6	90380710	Silent	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	17412799	90380710	80734357	87	32993										
MDN1	23195	hgsc.bcm.edu	37	chr6	90381952	90381952	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gctgtgccatcctcaccgtaCgatttcagcctctccaacag	7	16	3	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr6:90381952C>A	ENST00000369393.3	-	82	13876	c.13761G>T	c.(13759-13761)tcG>tcT	p.S4587S	RP1-122O8.7_ENST00000438877.1_RNA|MDN1_ENST00000468568.1_5'UTR|MDN1_ENST00000428876.1_Silent_p.S4587S			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	4587					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		CCTCACCGTACGATTTCAGCC	0.468																																					p.S4587S		Atlas-SNP	.											.	MDN1	478	.	0			c.G13761T						.						122	109	114					6																	90381952		2203	4300	6503	SO:0001819	synonymous_variant	23195	exon82			ACCGTACGATTTC	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.13761G>T	chr6.hg19:g.90381952C>A		77.0	0.0		87.0	21.0	NM_014611	O15019|Q5T794	Silent	SNP	ENST00000369393.3	hg19	CCDS5024.1																																																																																			.	.		0.468	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			A	90381952	C	A	90381952	2	1	237	1	0	0	0	0	0	0	0	1	9424	523	19	1		1	MDN1	6	90381952	Silent	SNP	C	TCGA-ED-A459-01A-11D-A25V-10	1242	90381952	80733115	88	32994										
GRIK2	2898	hgsc.bcm.edu	37	chr6	102250278	102250278	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tgagaacagattttgatttgGatgtgatcagtctgaaggaa	12	3	2	5			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr6:102250278G>A	ENST00000421544.1	+	8	1658	c.1168G>A	c.(1168-1170)Gat>Aat	p.D390N	GRIK2_ENST00000413795.1_Missense_Mutation_p.D390N|GRIK2_ENST00000318991.6_Missense_Mutation_p.D390N|GRIK2_ENST00000369138.1_Missense_Mutation_p.D390N|GRIK2_ENST00000369134.4_Missense_Mutation_p.D341N|GRIK2_ENST00000369137.3_Missense_Mutation_p.D390N	NM_021956.4	NP_068775.1	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	390					behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|glutamate receptor signaling pathway (GO:0007215)|intracellular protein transport (GO:0006886)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuronal action potential (GO:0019228)|positive regulation of synaptic transmission (GO:0050806)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission (GO:0050804)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	TTTTGATTTGGATGTGATCAG	0.343																																					p.D390N		Atlas-SNP	.											.	GRIK2	487	.	0			c.G1168A						.						116	118	118					6																	102250278		2203	4299	6502	SO:0001583	missense	2898	exon8			GATTTGGATGTGA		CCDS5048.1, CCDS5049.1, CCDS55045.1	6q16.3	2012-08-29			ENSG00000164418	ENSG00000164418		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4580	protein-coding gene	gene with protein product		138244		GLUR6		8034316	Standard	NM_021956		Approved	GluK2, MRT6	uc003pqp.4	Q13002	OTTHUMG00000016328	ENST00000421544.1:c.1168G>A	chr6.hg19:g.102250278G>A	ENSP00000397026:p.Asp390Asn	104.0	0.0		112.0	29.0	NM_021956	A6NMY9|B5MCV0|D7RWZ3|D7RWZ4|D7RWZ5|D7RWZ6|D7RWZ7|Q8WWS1|Q96KS6|Q96KS7|Q96KS8	Missense_Mutation	SNP	ENST00000421544.1	hg19	CCDS5048.1	.	.	.	.	.	.	.	.	.	.	G	34	5.375248	0.95923	.	.	ENSG00000164418	ENST00000421544;ENST00000413795;ENST00000369138;ENST00000369137;ENST00000318991;ENST00000403289;ENST00000369134;ENST00000540076;ENST00000455610	D;D;D;D;D;D;D	0.83335	-1.71;-1.71;-1.71;-1.71;-1.71;-1.71;-1.71	5.61	5.61	0.85477	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.90786	0.7107	M	0.81682	2.555	0.54753	D	0.999989	D;D;D	0.76494	0.999;0.998;0.998	D;D;D	0.74674	0.984;0.983;0.972	D	0.91365	0.5115	10	0.87932	D	0	.	19.6406	0.95755	0.0:0.0:1.0:0.0	.	390;390;390	Q13002-5;Q13002;Q13002-2	.;GRIK2_HUMAN;.	N	390;390;390;390;390;390;341;352;103	ENSP00000397026:D390N;ENSP00000405596:D390N;ENSP00000358134:D390N;ENSP00000358133:D390N;ENSP00000313276:D390N;ENSP00000358130:D341N;ENSP00000391988:D103N	ENSP00000313276:D390N	D	+	1	0	GRIK2	102356971	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.398000	0.97281	2.633000	0.89246	0.544000	0.68410	GAT	.	.		0.343	GRIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043718.1			A	102250278	G	A	102250278	3	1	237	1	0	0	0	0	1	0	0	0	6783	1174	41	3	1198	3	GRIK2	6	102250278	Missense_Mutation	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	11868326	102250278	68864789	89	32995										
AMZ1	155185	hgsc.bcm.edu	37	chr7	2740227	2740227	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ggctcttcctggccgaggccTacaacccgcagaggacgctc	12	16	1	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr7:2740227T>A	ENST00000312371.4	+	2	510	c.142T>A	c.(142-144)Tac>Aac	p.Y48N	AMZ1_ENST00000407112.1_Missense_Mutation_p.Y48N	NM_133463.1	NP_597720.1	Q400G9	AMZ1_HUMAN	archaelysin family metallopeptidase 1	48							metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	16		Ovarian(82;0.0779)		OV - Ovarian serous cystadenocarcinoma(56;5.03e-14)		GGCCGAGGCCTACAACCCGCA	0.662																																					p.Y48N		Atlas-SNP	.											.	AMZ1	41	.	0			c.T142A						.						113	122	119					7																	2740227		2203	4300	6503	SO:0001583	missense	155185	exon2			GAGGCCTACAACC	AB075830	CCDS34589.1, CCDS64582.1	7p22.3	2008-01-17			ENSG00000174945	ENSG00000174945			22231	protein-coding gene	gene with protein product	"archaemetzincin-1"	615168				15972818	Standard	NM_133463		Approved	KIAA1950	uc003smr.1	Q400G9	OTTHUMG00000152111	ENST00000312371.4:c.142T>A	chr7.hg19:g.2740227T>A	ENSP00000308149:p.Tyr48Asn	92.0	0.0		45.0	5.0	NM_133463	B3KRS0|Q8TF51	Missense_Mutation	SNP	ENST00000312371.4	hg19	CCDS34589.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.242212	0.79912	.	.	ENSG00000174945	ENST00000312371;ENST00000407112	T;T	0.44881	1.3;0.91	4.34	4.34	0.51931	.	0.217682	0.31760	N	0.007109	T	0.61837	0.2379	M	0.70595	2.14	0.45946	D	0.998777	D;D	0.76494	0.999;0.998	D;D	0.83275	0.996;0.994	T	0.66135	-0.5999	10	0.87932	D	0	-43.205	12.1049	0.53807	0.0:0.0:0.0:1.0	.	48;48	B3KRS0;Q400G9	.;AMZ1_HUMAN	N	48	ENSP00000308149:Y48N;ENSP00000386020:Y48N	ENSP00000308149:Y48N	Y	+	1	0	AMZ1	2706753	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	5.290000	0.65661	1.603000	0.50134	0.459000	0.35465	TAC	.	.		0.662	AMZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325244.1	NM_133463		A	2740227	T	A	2740227	3	1	237	1	0	0	0	0	1	0	0	0	596	1522	53	4	144	4	AMZ1	7	2740227	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10		2740227	156398436	90	32996										
NPC1L1	29881	hgsc.bcm.edu	37	chr7	44578770	44578770	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	taggagccgtcaggatcaccTggttggttcggaagaagggg	17	7	2	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr7:44578770T>A	ENST00000289547.4	-	2	1281	c.1226A>T	c.(1225-1227)cAg>cTg	p.Q409L	NPC1L1_ENST00000381160.3_Missense_Mutation_p.Q409L|NPC1L1_ENST00000546276.1_Missense_Mutation_p.Q409L|NPC1L1_ENST00000423141.1_Missense_Mutation_p.Q409L	NM_013389.2	NP_037521.2	Q9UHC9	NPCL1_HUMAN	NPC1-like 1	409					cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intestinal cholesterol absorption (GO:0030299)|lipoprotein metabolic process (GO:0042157)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)	brush border membrane (GO:0031526)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|hedgehog receptor activity (GO:0008158)|myosin V binding (GO:0031489)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(7)|lung(27)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	57					Ezetimibe(DB00973)	CAGGATCACCTGGTTGGTTCG	0.597																																					p.Q409L		Atlas-SNP	.											.	NPC1L1	141	.	0			c.A1226T						.						83	93	89					7																	44578770		2203	4300	6503	SO:0001583	missense	29881	exon2			ATCACCTGGTTGG		CCDS5491.1, CCDS43575.1, CCDS75587.1	7p13	2012-11-15	2012-11-15		ENSG00000015520	ENSG00000015520			7898	protein-coding gene	gene with protein product		608010	"NPC1 (Niemann-Pick disease, type C1, gene)-like 1"			10783261	Standard	NM_013389		Approved		uc003tlb.3	Q9UHC9	OTTHUMG00000023691	ENST00000289547.4:c.1226A>T	chr7.hg19:g.44578770T>A	ENSP00000289547:p.Gln409Leu	193.0	0.0		226.0	15.0	NM_001101648	A4D2J7|B7ZLE6|D3DVK9|Q17RV5|Q6R3Q4|Q9UHC8	Missense_Mutation	SNP	ENST00000289547.4	hg19	CCDS5491.1	.	.	.	.	.	.	.	.	.	.	t	21.7	4.190787	0.78789	.	.	ENSG00000015520	ENST00000289547;ENST00000381160;ENST00000546276;ENST00000423141	D;D;D;D	0.92595	-3.07;-3.07;-3.07;-3.07	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	D	0.96765	0.8944	M	0.93241	3.395	0.54753	D	0.999984	D;P;D;P	0.76494	0.999;0.946;0.999;0.533	D;P;D;B	0.78314	0.978;0.509;0.991;0.133	D	0.97343	0.9958	10	0.62326	D	0.03	-24.8398	12.7308	0.57197	0.0:0.0:0.0:1.0	.	409;409;409;409	B7ZLE6;Q9UHC9-3;Q17RV5;D3DVK9	.;.;.;.	L	409	ENSP00000289547:Q409L;ENSP00000370552:Q409L;ENSP00000438033:Q409L;ENSP00000404670:Q409L	ENSP00000289547:Q409L	Q	-	2	0	NPC1L1	44545295	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.593000	0.82686	1.897000	0.54924	0.379000	0.24179	CAG	.	.		0.597	NPC1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251256.1	NM_013389		A	44578770	T	A	44578770	3	1	237	1	0	0	0	0	1	0	0	0	10580	1580	55	4	2929	4	NPC1L1	7	44578770	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	41838543	44578770	114559893	91	32997										
ZPBP	11055	hgsc.bcm.edu	37	chr7	50129226	50129226	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	aaaatatatttatgaataccTggaaaacttgttgatcccac	5	7	0	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr7:50129226T>A	ENST00000046087.2	-	2	276	c.207A>T	c.(205-207)ccA>ccT	p.P69P	ZPBP_ENST00000419417.1_Splice_Site_p.P69P	NM_001159878.1|NM_007009.2	NP_001153350.1|NP_008940.2	Q9BS86	ZPBP1_HUMAN	zona pellucida binding protein	69					acrosome assembly (GO:0001675)|binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|extracellular region (GO:0005576)|nucleus (GO:0005634)|zona pellucida receptor complex (GO:0002199)				NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(3)	29	Glioma(55;0.08)|all_neural(89;0.245)					TATGAATACCTGGAAAACTTG	0.308																																					p.P69P		Atlas-SNP	.											.	ZPBP	65	.	0			c.A207T						.						27	28	28					7																	50129226		2202	4297	6499	SO:0001630	splice_region_variant	11055	exon2			AATACCTGGAAAA	D17570	CCDS5509.1, CCDS55110.1	7p14.3	2013-01-11			ENSG00000042813	ENSG00000042813		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15662	protein-coding gene	gene with protein product		608498				9378618	Standard	NM_007009		Approved	SP38, ZPBP1	uc003tou.3	Q9BS86	OTTHUMG00000023528	ENST00000046087.2:c.208+1A>T	chr7.hg19:g.50129226T>A		97.0	0.0		103.0	10.0	NM_007009	A4D253|C9JPU1|Q15941|Q75KX9|Q75MI3	Silent	SNP	ENST00000046087.2	hg19	CCDS5509.1																																																																																			.	.		0.308	ZPBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251374.1	NM_007009	Silent	A	50129226	T	A	50129226	5	1	237	1	0	0	0	0	0	0	1	0	18234	1594	55	4	876	4	ZPBP	7	50129226	Splice_Site	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	5550456	50129226	109009437	92	32998										
FIS1	51024	hgsc.bcm.edu	37	chr7	100884160	100884160	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	agaagacgtaatcccgctgtTcctccttgctccctttgggc	9	14	0	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr7:100884160T>A	ENST00000223136.4	-	3	286	c.206A>T	c.(205-207)gAa>gTa	p.E69V	FIS1_ENST00000482199.1_5'UTR|FIS1_ENST00000474120.1_Silent_p.G14G|FIS1_ENST00000442303.1_Silent_p.G45G|CLDN15_ENST00000308344.5_5'Flank|CLDN15_ENST00000401528.1_5'Flank	NM_016068.2	NP_057152.2	Q9Y3D6	FIS1_HUMAN	fission 1 (mitochondrial outer membrane) homolog (S. cerevisiae)	69					calcium-mediated signaling using intracellular calcium source (GO:0035584)|mitochondrial fission (GO:0000266)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial fusion (GO:0008053)|mitochondrion degradation (GO:0000422)|mitochondrion morphogenesis (GO:0070584)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|peroxisome fission (GO:0016559)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein targeting to membrane (GO:0090314)|protein homooligomerization (GO:0051260)|protein targeting to mitochondrion (GO:0006626)|regulation of mitochondrion organization (GO:0010821)|release of cytochrome c from mitochondria (GO:0001836)	integral component of mitochondrial outer membrane (GO:0031307)|integral component of peroxisomal membrane (GO:0005779)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|protein complex (GO:0043234)	receptor binding (GO:0005102)			kidney(1)|large_intestine(2)|lung(1)	4	Lung NSC(181;0.168)|all_lung(186;0.215)					ATCCCGCTGTTCCTCCTTGCT	0.582																																					p.E69V		Atlas-SNP	.											FIS1,right_upper_lobe,carcinoma,0,1	FIS1	11	.	0			c.A206T						.						90	96	94					7																	100884160		2004	4159	6163	SO:0001583	missense	51024	exon3			CGCTGTTCCTCCT	AF151893	CCDS43626.1	7q22.1	2012-10-01	2006-04-04	2006-01-24	ENSG00000214253	ENSG00000214253			21689	protein-coding gene	gene with protein product	"CGI-135 protein"	609003	"tetratricopeptide repeat domain 11", "fission 1 (mitochondrial outer membrane) homolog (yeast)"	TTC11		14996942, 16010987	Standard	NM_016068		Approved	CGI-135, H_NH0132A01.6, Fis1	uc003uyj.4	Q9Y3D6	OTTHUMG00000157106	ENST00000223136.4:c.206A>T	chr7.hg19:g.100884160T>A	ENSP00000223136:p.Glu69Val	351.0	0.0		461.0	31.0	NM_016068	Q9BTP3	Missense_Mutation	SNP	ENST00000223136.4	hg19	CCDS43626.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.93|14.93	2.681473|2.681473	0.47991|0.47991	.|.	.|.	ENSG00000214253|ENSG00000214253	ENST00000223136|ENST00000435848	.|.	.|.	.|.	5.1|5.1	5.1|5.1	0.69264|0.69264	Tetratricopeptide-like helical (1);|.	0.087599|.	0.44902|.	U|.	0.000412|.	T|T	0.61776|0.61776	0.2374|0.2374	L|L	0.43923|0.43923	1.385|1.385	0.53688|0.53688	D|D	0.999979|0.999979	B|.	0.19583|.	0.037|.	B|.	0.21360|.	0.034|.	T|T	0.65565|0.65565	-0.6137|-0.6137	9|6	0.33940|0.87932	T|D	0.23|0	.|.	12.8187|12.8187	0.57679|0.57679	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	69|.	Q9Y3D6|.	FIS1_HUMAN|.	V|Y	69|59	.|.	ENSP00000223136:E69V|ENSP00000413500:N59Y	E|N	-|-	2|1	0|0	FIS1|FIS1	100670880|100670880	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.969000|0.969000	0.65631|0.65631	6.741000|6.741000	0.74837|0.74837	1.931000|1.931000	0.55961|0.55961	0.459000|0.459000	0.35465|0.35465	GAA|AAC	.	.		0.582	FIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347449.1	NM_016068		A	100884160	T	A	100884160	3	1	237	1	0	0	0	0	1	0	0	0	5905	1783	62	4	264	4	FIS1	7	100884160	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	50754934	100884160	58254503	93	32999										
PRKAR2B	5577	hgsc.bcm.edu	37	chr7	106781395	106781395	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tgacaacttttatgtaattgAtaggtaagttttgcccaacc	7	7	0	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr7:106781395A>T	ENST00000265717.4	+	5	843	c.584A>T	c.(583-585)gAt>gTt	p.D195V	PRKAR2B_ENST00000393613.2_3'UTR	NM_002736.2	NP_002727.2	P31323	KAP3_HUMAN	protein kinase, cAMP-dependent, regulatory, type II, beta	195					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fatty acid metabolic process (GO:0006631)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|mitotic cell cycle (GO:0000278)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	14						TATGTAATTGATAGGTAAGTT	0.348																																					p.D195V		Atlas-SNP	.											.	PRKAR2B	34	.	0			c.A584T						.						141	136	137					7																	106781395		2203	4299	6502	SO:0001583	missense	5577	exon5			TAATTGATAGGTA		CCDS5740.1	7q22.3	2010-04-22			ENSG00000005249	ENSG00000005249	2.7.11.1		9392	protein-coding gene	gene with protein product		176912		PRKAR2		1358799	Standard	NM_002736		Approved		uc003vdx.3	P31323	OTTHUMG00000137418	ENST00000265717.4:c.584A>T	chr7.hg19:g.106781395A>T	ENSP00000265717:p.Asp195Val	146.0	0.0		199.0	10.0	NM_002736	A4D0R9	Missense_Mutation	SNP	ENST00000265717.4	hg19	CCDS5740.1	.	.	.	.	.	.	.	.	.	.	A	26.4	4.729366	0.89390	.	.	ENSG00000005249	ENST00000265717;ENST00000543645;ENST00000539794	D	0.91740	-2.9	5.25	5.25	0.73442	Cyclic nucleotide-binding, conserved site (1);Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.043573	0.85682	D	0.000000	D	0.91952	0.7451	N	0.13327	0.33	0.80722	D	1	D	0.65815	0.995	D	0.72338	0.977	D	0.93780	0.7083	10	0.87932	D	0	-0.8069	15.4527	0.75285	1.0:0.0:0.0:0.0	.	195	P31323	KAP3_HUMAN	V	195;195;182	ENSP00000265717:D195V	ENSP00000265717:D195V	D	+	2	0	PRKAR2B	106568631	1.000000	0.71417	0.999000	0.59377	0.957000	0.61999	9.259000	0.95561	2.121000	0.65114	0.460000	0.39030	GAT	.	.		0.348	PRKAR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268386.1			T	106781395	A	T	106781395	3	4	237	1	0	0	0	0	1	0	0	0	12518	333	12	4	602	4	PRKAR2B	7	106781395	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	5897235	106781395	52357268	94	33000										
LRRN3	54674	hgsc.bcm.edu	37	chr7	110763113	110763113	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gactttccagtaaaccttacTggcctggatttatctcaaaa	6	10	1	0	rs151294396		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr7:110763113T>A	ENST00000422987.3	+	2	1116	c.285T>A	c.(283-285)acT>acA	p.T95T	IMMP2L_ENST00000450877.1_Intron|LRRN3_ENST00000308478.5_Silent_p.T95T|IMMP2L_ENST00000415362.1_Intron|IMMP2L_ENST00000437687.1_Intron|IMMP2L_ENST00000447215.1_Intron|LRRN3_ENST00000451085.1_Silent_p.T95T|IMMP2L_ENST00000452895.1_Intron|IMMP2L_ENST00000405709.2_Intron|IMMP2L_ENST00000489381.1_Intron|IMMP2L_ENST00000331762.3_Intron	NM_018334.4	NP_060804.3	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3	95					positive regulation of protein phosphorylation (GO:0001934)	clathrin adaptor complex (GO:0030131)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(15)|lung(20)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)		TAAACCTTACTGGCCTGGATT	0.373																																					p.T95T		Atlas-SNP	.											.	LRRN3	132	.	0			c.T285A						.						56	55	55					7																	110763113		2203	4299	6502	SO:0001819	synonymous_variant	54674	exon2			CCTTACTGGCCTG	AB060967	CCDS5754.1	7q31.1	2013-02-11			ENSG00000173114	ENSG00000173114		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	17200	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 5"					11549284	Standard	NM_001099660		Approved	NLRR3, FLJ11129, FIGLER5	uc003vfs.4	Q9H3W5	OTTHUMG00000155039	ENST00000422987.3:c.285T>A	chr7.hg19:g.110763113T>A		33.0	0.0		64.0	4.0	NM_018334	O43377|Q6I9V8|Q8IYQ6	Silent	SNP	ENST00000422987.3	hg19	CCDS5754.1																																																																																			.	T|1.000;C|0.000		0.373	LRRN3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338171.2	NM_018334		A	110763113	T	A	110763113	2	1	237	1	0	0	0	0	0	0	0	1	9045	1567	55	4		4	LRRN3	7	110763113	Silent	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	3981718	110763113	48375550	95	33001										
LRGUK	136332	hgsc.bcm.edu	37	chr7	133881819	133881819	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	acaccgtagaaggtatcgcaAgagatggtttggcaagctgt	13	7	0	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr7:133881819A>T	ENST00000285928.2	+	13	1576	c.1507A>T	c.(1507-1509)Aga>Tga	p.R503*		NM_144648.1	NP_653249.1	Q96M69	LRGUK_HUMAN	leucine-rich repeats and guanylate kinase domain containing	503	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)			breast(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(23)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	49						AGGTATCGCAAGAGATGGTTT	0.363																																					p.R503X		Atlas-SNP	.											.	LRGUK	113	.	0			c.A1507T						.						182	168	173					7																	133881819		2203	4300	6503	SO:0001587	stop_gained	136332	exon13			ATCGCAAGAGATG	AK057348	CCDS5830.1	7q33	2006-10-27			ENSG00000155530	ENSG00000155530			21964	protein-coding gene	gene with protein product							Standard	NM_144648		Approved	FLJ32786	uc003vrm.1	Q96M69	OTTHUMG00000155320	ENST00000285928.2:c.1507A>T	chr7.hg19:g.133881819A>T	ENSP00000285928:p.Arg503*	112.0	0.0		186.0	15.0	NM_144648	Q2M3I1	Nonsense_Mutation	SNP	ENST00000285928.2	hg19	CCDS5830.1	.	.	.	.	.	.	.	.	.	.	A	38	7.261324	0.98171	.	.	ENSG00000155530	ENST00000285928	.	.	.	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-27.9895	12.2884	0.54805	0.8586:0.1414:0.0:0.0	.	.	.	.	X	503	.	ENSP00000285928:R503X	R	+	1	2	LRGUK	133532359	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	3.931000	0.56529	2.254000	0.74563	0.524000	0.50904	AGA	.	.		0.363	LRGUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339442.1	NM_144648		T	133881819	A	T	133881819	4	4	237	1	0	0	0	0	0	1	0	0	8952	64	3	4	1557	4	LRGUK	7	133881819	Nonsense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	23118706	133881819	25256844	96	33002										
CNTNAP2	26047	hgsc.bcm.edu	37	chr7	147675070	147675071	+	Missense_Mutation	DNP	GC	GC	TT													0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gagcgtaggtcctctgcgctGccaaggagacagtaagtttg							TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr7:147675070_147675071GC>TT	ENST00000361727.3	+	15	2888_2889	c.2372_2373GC>TT	c.(2371-2373)tGC>tTT	p.C791F		NM_014141.5	NP_054860.1	Q9UHC6	CNTP2_HUMAN	contactin associated protein-like 2	791	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				adult behavior (GO:0030534)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|cerebral cortex development (GO:0021987)|clustering of voltage-gated potassium channels (GO:0045163)|learning (GO:0007612)|limbic system development (GO:0021761)|neuron projection development (GO:0031175)|neuron recognition (GO:0008038)|protein localization to juxtaparanode region of axon (GO:0071205)|social behavior (GO:0035176)|striatum development (GO:0021756)|superior temporal gyrus development (GO:0071109)|thalamus development (GO:0021794)|transmission of nerve impulse (GO:0019226)|vocalization behavior (GO:0071625)	axolemma (GO:0030673)|axon (GO:0030424)|cell surface (GO:0009986)|dendrite (GO:0030425)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|voltage-gated potassium channel complex (GO:0008076)	enzyme binding (GO:0019899)			NS(3)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(105)|ovary(9)|pancreas(2)|prostate(5)|skin(7)|stomach(3)|upper_aerodigestive_tract(6)|urinary_tract(3)	188	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			CCTCTGCGCTGCCAAGGAGACA	0.465										HNSCC(39;0.1)																											p.C791F|p.C791C		Atlas-SNP	.											.	CNTNAP2	392	.	0			c.G2372T|c.C2373T						.																																			SO:0001583	missense	26047	exon15			TGCGCTGCCAAGG|GCGCTGCCAAGGA	AF193613	CCDS5889.1	7q35	2008-02-04			ENSG00000174469	ENSG00000174469			13830	protein-coding gene	gene with protein product		604569				10624965, 10048485	Standard	NM_014141		Approved	Caspr2, KIAA0868, NRXN4	uc003weu.2	Q9UHC6	OTTHUMG00000152743	Exception_encountered	chr7.hg19:g.147675070_147675071delinsTT	ENSP00000354778:p.Cys791Phe	173.0|172.0	0.0		260.0|257.0	18.0|17.0	NM_014141	D3DWG2|Q14DG2|Q52LV1|Q5H9Q7|Q9UQ12	Missense_Mutation|Silent	SNP	ENST00000361727.3	hg19	CCDS5889.1																																																																																			.	.		0.465	CNTNAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327668.1			TT	147675071	GC	TT	147675070	3	4	237	1	0	0	0	0	1	0	0	0	3649	1319	46	3	2430	3	CNTNAP2	7	147675070	Missense_Mutation	DNP	GC	TCGA-ED-A459-01A-11D-A25V-10	13793251	147675070	11463593	97	33003										
MLL3	58508	hgsc.bcm.edu	37	chr7	151878935	151878935	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tggtttagtaaagtgatcacTggttccagctgctatagggc	12	7	1	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr7:151878935T>A	ENST00000262189.6	-	36	6228	c.6010A>T	c.(6010-6012)Agt>Tgt	p.S2004C	KMT2C_ENST00000355193.2_Missense_Mutation_p.S2004C	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	2004	Pro-rich.				histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										AAGTGATCACTGGTTCCAGCT	0.468																																					p.S2004C		Atlas-SNP	.											.	MLL3	1564	.	0			c.A6010T						.						140	143	142					7																	151878935		2203	4300	6503	SO:0001583	missense	58508	exon36			GATCACTGGTTCC	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.6010A>T	chr7.hg19:g.151878935T>A	ENSP00000262189:p.Ser2004Cys	120.0	0.0		248.0	66.0	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	hg19	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	T	12.37	1.917129	0.33815	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	T;T	0.44083	0.93;0.93	5.59	3.2	0.36748	.	0.474047	0.17146	U	0.185268	T	0.35451	0.0932	N	0.24115	0.695	0.80722	D	1	P;P	0.50272	0.89;0.933	B;P	0.49528	0.315;0.614	T	0.07462	-1.0771	10	0.59425	D	0.04	.	8.3035	0.32027	0.0:0.0689:0.1337:0.7973	.	2004;1065	Q8NEZ4;Q8NEZ4-2	MLL3_HUMAN;.	C	2004	ENSP00000262189:S2004C;ENSP00000347325:S2004C	ENSP00000262189:S2004C	S	-	1	0	MLL3	151509868	0.999000	0.42202	0.004000	0.12327	0.660000	0.38997	3.059000	0.49947	0.404000	0.25506	0.456000	0.33151	AGT	.	.		0.468	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			A	151878935	T	A	151878935	3	1	237	1	0	0	0	0	1	0	0	0	9631	1580	55	4	8821	4	MLL3	7	151878935	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	4203865	151878935	7259728	98	33004										
LMBR1	64327	hgsc.bcm.edu	37	chr7	156556491	156556491	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	aaatgcgggctcggattcccTgaaaaatagagtagaaatat	10	6	0	3			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr7:156556491T>A	ENST00000353442.5	-	6	660		c.e6-2		LMBR1_ENST00000354505.4_Splice_Site|LMBR1_ENST00000540390.1_Splice_Site|LMBR1_ENST00000359422.4_Splice_Site	NM_022458.3	NP_071903.2	Q8WVP7	LMBR1_HUMAN	limb development membrane protein 1						embryonic digit morphogenesis (GO:0042733)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	18	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.208)		TCGGATTCCCTGAAAAATAGA	0.368																																					.		Atlas-SNP	.											.	LMBR1	35	.	0			c.424-2A>T						.						73	70	71					7																	156556491		2203	4300	6503	SO:0001630	splice_region_variant	64327	exon7			ATTCCCTGAAAAA	AF107454	CCDS5945.1	7q36.3	2013-08-05	2013-08-05	2005-07-25	ENSG00000105983	ENSG00000105983			13243	protein-coding gene	gene with protein product		605522	"chromosome 7 open reading frame 2", "limb region 1 homolog (mouse)"	C7orf2		10329000, 11090342	Standard	NM_022458		Approved	ACHP, FLJ11665, ZRS	uc003wmw.4	Q8WVP7	OTTHUMG00000151510	ENST00000353442.5:c.424-2A>T	chr7.hg19:g.156556491T>A		90.0	0.0		159.0	7.0	NM_022458	A4D242|Q8N3E3|Q96QZ5|Q9H5N0|Q9HAG9|Q9UDN5|Q9Y6U2	Splice_Site	SNP	ENST00000353442.5	hg19	CCDS5945.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.082918	0.76642	.	.	ENSG00000105983	ENST00000353442;ENST00000415428;ENST00000354505;ENST00000540390;ENST00000347571	.	.	.	5.22	5.22	0.72569	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4307	0.75092	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	LMBR1	156249252	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.333000	0.79214	2.099000	0.63709	0.533000	0.62120	.	.	.		0.368	LMBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347939.3	NM_022458	Intron	A	156556491	T	A	156556491	5	1	237	1	0	0	0	0	0	0	1	0	8849	1594	55	4	1098	4	LMBR1	7	156556491	Splice_Site	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	4677556	156556491	2582172	99	33005										
TEX15	56154	hgsc.bcm.edu	37	chr8	30703652	30703652	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	aaaatgttttaattcgtcctTgggataatgaagagaaacac	8	5	0	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr8:30703652T>A	ENST00000256246.2	-	1	2956	c.2882A>T	c.(2881-2883)cAa>cTa	p.Q961L	TEX15_ENST00000523186.1_5'Flank	NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	961					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)					NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		AATTCGTCCTTGGGATAATGA	0.353																																					p.Q961L		Atlas-SNP	.											.	TEX15	350	.	0			c.A2882T						.						121	121	121					8																	30703652		2203	4299	6502	SO:0001583	missense	56154	exon1			CGTCCTTGGGATA	AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"cancer/testis antigen 42"	605795	"testis expressed sequence 15"			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.2882A>T	chr8.hg19:g.30703652T>A	ENSP00000256246:p.Gln961Leu	103.0	0.0		109.0	11.0	NM_031271		Missense_Mutation	SNP	ENST00000256246.2	hg19	CCDS6080.1	.	.	.	.	.	.	.	.	.	.	T	18.88	3.716496	0.68844	.	.	ENSG00000133863	ENST00000256246	T	0.11495	2.77	5.62	4.47	0.54385	.	0.285236	0.25386	N	0.031044	T	0.17831	0.0428	L	0.50333	1.59	0.32469	N	0.543097	D	0.57571	0.98	P	0.52856	0.711	T	0.14924	-1.0455	10	0.87932	D	0	.	9.3139	0.37921	0.0:0.0829:0.0:0.9171	.	961	Q9BXT5	TEX15_HUMAN	L	961	ENSP00000256246:Q961L	ENSP00000256246:Q961L	Q	-	2	0	TEX15	30823194	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.039000	0.49791	0.963000	0.38082	0.383000	0.25322	CAA	.	.		0.353	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			A	30703652	T	A	30703652	3	1	237	1	0	0	0	0	1	0	0	0	15794	1812	63	4	5503	4	TEX15	8	30703652	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10		30703652	115660370	100	33006										
RP1	6101	hgsc.bcm.edu	37	chr8	55541215	55541215	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	agtccagtgacttctgattgGtcagactatcggcctgacag	11	10	2	4			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr8:55541215G>A	ENST00000220676.1	+	4	4921	c.4773G>A	c.(4771-4773)tgG>tgA	p.W1591*		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	1591					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			CTTCTGATTGGTCAGACTATC	0.398																																					p.W1591X	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.G4773A						.						63	63	63					8																	55541215		2203	4300	6503	SO:0001587	stop_gained	6101	exon4			TGATTGGTCAGAC	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.4773G>A	chr8.hg19:g.55541215G>A	ENSP00000220676:p.Trp1591*	55.0	0.0		63.0	34.0	NM_006269		Nonsense_Mutation	SNP	ENST00000220676.1	hg19	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	G	43	10.195949	0.99357	.	.	ENSG00000104237	ENST00000220676	.	.	.	5.74	2.82	0.32997	.	0.278923	0.26255	N	0.025422	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.0459	7.2585	0.26189	0.0673:0.1242:0.6796:0.1289	.	.	.	.	X	1591	.	ENSP00000220676:W1591X	W	+	3	0	RP1	55703768	1.000000	0.71417	0.972000	0.41901	0.817000	0.46193	2.517000	0.45529	0.765000	0.33221	0.655000	0.94253	TGG	.	.		0.398	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		A	55541215	G	A	55541215	4	1	237	1	0	0	0	0	0	1	0	0	13547	1270	44	3	4783	3	RP1	8	55541215	Nonsense_Mutation	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	24837563	55541215	90822807	101	33007										
TRPA1	8989	hgsc.bcm.edu	37	chr8	72958812	72958812	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tttttttggtgaattctaatGgacattgaagatatttgaaa	8	2	1	4			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr8:72958812G>T	ENST00000262209.4	-	17	2204	c.1997C>A	c.(1996-1998)cCa>cAa	p.P666Q	RP11-383H13.1_ENST00000524152.1_Intron|RP11-383H13.1_ENST00000457356.4_Intron|RP11-383H13.1_ENST00000537896.1_Intron	NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	666					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	GAATTCTAATGGACATTGAAG	0.299																																					p.P666Q		Atlas-SNP	.											.	TRPA1	256	.	0			c.C1997A						.						140	150	147					8																	72958812		2203	4300	6503	SO:0001583	missense	8989	exon17			TCTAATGGACATT	Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	497	protein-coding gene	gene with protein product		604775	"ankyrin-like with transmembrane domains 1"	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.1997C>A	chr8.hg19:g.72958812G>T	ENSP00000262209:p.Pro666Gln	37.0	0.0		39.0	4.0	NM_007332	A6NIN6	Missense_Mutation	SNP	ENST00000262209.4	hg19	CCDS34908.1	.	.	.	.	.	.	.	.	.	.	G	15.35	2.807389	0.50421	.	.	ENSG00000104321	ENST00000523582;ENST00000262209	T;T	0.78126	-1.15;-1.15	4.89	4.89	0.63831	.	0.000000	0.85682	D	0.000000	D	0.87888	0.6291	M	0.76574	2.34	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.88096	0.2816	10	0.48119	T	0.1	-12.8801	18.3975	0.90504	0.0:0.0:1.0:0.0	.	666	O75762	TRPA1_HUMAN	Q	518;666	ENSP00000428151:P518Q;ENSP00000262209:P666Q	ENSP00000262209:P666Q	P	-	2	0	TRPA1	73121366	1.000000	0.71417	0.528000	0.27938	0.079000	0.17450	7.635000	0.83286	2.402000	0.81655	0.555000	0.69702	CCA	.	.		0.299	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332		T	72958812	G	T	72958812	3	4	237	1	0	0	0	0	1	0	0	0	16592	1348	47	3	1406	3	TRPA1	8	72958812	Missense_Mutation	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	17417597	72958812	73405210	102	33008										
SLC26A7	115111	hgsc.bcm.edu	37	chr8	92352644	92352644	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ttccacagaattccctcaccTagagctcccccgatgaacat	5	16	1	3	rs373170016		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr8:92352644T>A	ENST00000276609.3	+	8	1130	c.891T>A	c.(889-891)ccT>ccA	p.P297P	SLC26A7_ENST00000309536.2_Silent_p.P297P|SLC26A7_ENST00000523719.1_Silent_p.P297P	NM_001282356.1|NM_052832.2	NP_001269285.1|NP_439897.1			solute carrier family 26 (anion exchanger), member 7											breast(1)|cervix(1)|endometrium(4)|large_intestine(10)|lung(26)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	50			BRCA - Breast invasive adenocarcinoma(11;0.00802)			TTCCCTCACCTAGAGCTCCCC	0.458																																					p.P297P		Atlas-SNP	.											.	SLC26A7	207	.	0			c.T891A						.						113	102	106					8																	92352644		2203	4300	6503	SO:0001819	synonymous_variant	115111	exon8			CTCACCTAGAGCT	AF331521	CCDS6254.1, CCDS6255.1, CCDS75765.1	8q23	2013-07-18	2013-07-18		ENSG00000147606	ENSG00000147606		"Solute carriers"	14467	protein-coding gene	gene with protein product		608479	"solute carrier family 26, member 7"			11834742, 11829495, 16524946	Standard	NM_134266		Approved	SUT2	uc003yez.3	Q8TE54	OTTHUMG00000164062	ENST00000276609.3:c.891T>A	chr8.hg19:g.92352644T>A		152.0	0.0		219.0	13.0	NM_134266		Silent	SNP	ENST00000276609.3	hg19	CCDS6254.1	.	.	.	.	.	.	.	.	.	.	T	1.066	-0.671378	0.03403	.	.	ENSG00000147606	ENST00000520818	.	.	.	6.02	-6.47	0.01902	.	.	.	.	.	T	0.37679	0.1012	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40961	-0.9535	4	.	.	.	.	2.907	0.05723	0.3567:0.3614:0.166:0.1159	.	.	.	.	Q	165	.	.	L	+	2	0	SLC26A7	92421820	0.000000	0.05858	0.035000	0.18076	0.195000	0.23768	-0.989000	0.03736	-1.065000	0.03168	0.533000	0.62120	CTA	.	.		0.458	SLC26A7-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377011.1			A	92352644	T	A	92352644	2	1	237	1	0	0	0	0	0	0	0	1	14537	1509	53	4		4	SLC26A7	8	92352644	Silent	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	19393832	92352644	54011378	103	33009										
TRHR	7201	hgsc.bcm.edu	37	chr8	110099893	110099893	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	catggtagtcctggttgtcaTgagaaccaagcacatgagga	12	8	1	2	rs144587571		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr8:110099893T>C	ENST00000518632.1	+	2	503	c.152T>C	c.(151-153)aTg>aCg	p.M51T	TRHR_ENST00000311762.2_Missense_Mutation_p.M51T			P34981	TRFR_HUMAN	thyrotropin-releasing hormone receptor	51					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	thyrotropin-releasing hormone receptor activity (GO:0004997)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(12)|prostate(4)|skin(4)|urinary_tract(1)	37			OV - Ovarian serous cystadenocarcinoma(57;2.3e-11)			CTGGTTGTCATGAGAACCAAG	0.522																																					p.M51T		Atlas-SNP	.											.	TRHR	74	.	0			c.T152C						.						154	137	143					8																	110099893		2203	4300	6503	SO:0001583	missense	7201	exon1			TTGTCATGAGAAC		CCDS6311.1	8q23.1	2013-09-20			ENSG00000174417	ENSG00000174417			12299	protein-coding gene	gene with protein product		188545				8128317	Standard	NM_003301		Approved		uc003ymz.4	P34981	OTTHUMG00000164910	ENST00000518632.1:c.152T>C	chr8.hg19:g.110099893T>C	ENSP00000430711:p.Met51Thr	183.0	0.0		237.0	101.0	NM_003301	Q2M339	Missense_Mutation	SNP	ENST00000518632.1	hg19	CCDS6311.1	.	.	.	.	.	.	.	.	.	.	T	13.99	2.402429	0.42613	.	.	ENSG00000174417	ENST00000518632;ENST00000311762	T;T	0.35421	1.31;1.31	5.85	5.85	0.93711	GPCR, rhodopsin-like superfamily (1);	0.257307	0.45126	D	0.000391	T	0.20861	0.0502	N	0.04245	-0.25	0.40689	D	0.982372	B	0.02656	0.0	B	0.04013	0.001	T	0.06373	-1.0830	10	0.42905	T	0.14	-10.4335	15.4167	0.74974	0.0:0.0:0.0:1.0	.	51	P34981	TRFR_HUMAN	T	51	ENSP00000430711:M51T;ENSP00000309818:M51T	ENSP00000309818:M51T	M	+	2	0	TRHR	110169069	1.000000	0.71417	0.997000	0.53966	0.994000	0.84299	6.264000	0.72527	2.238000	0.73509	0.533000	0.62120	ATG	.	T|1.000;G|0.000		0.522	TRHR-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380892.1			C	110099893	T	C	110099893	3	2	237	1	0	0	0	0	1	0	0	0	16495	1464	51	2	154	2	TRHR	8	110099893	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	17747249	110099893	36264129	104	33010										
TSNARE1	203062	hgsc.bcm.edu	37	chr8	143425738	143425738	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	agtgctgggccccgccatccGgccatggggcccagcagccg	15	17	0	0	rs199897318		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr8:143425738G>A	ENST00000307180.3	-	4	451	c.334C>T	c.(334-336)Cgg>Tgg	p.R112W	TSNARE1_ENST00000520166.1_Missense_Mutation_p.R112W|TSNARE1_ENST00000519651.1_Intron|TSNARE1_ENST00000524325.1_Missense_Mutation_p.R112W	NM_145003.3	NP_659440.2	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1	112					intracellular protein transport (GO:0006886)|synaptic vesicle exocytosis (GO:0016079)	integral component of membrane (GO:0016021)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)			breast(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(6)|ovary(2)|stomach(2)|urinary_tract(1)	20	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					CCCGCCATCCGGCCATGGGGC	0.677													G|||	1	0.000199681	0	0.0014	5008	,	,		11782	0		0	False		,,,				2504	0				p.R112W		Atlas-SNP	.											TSNARE1,caecum,carcinoma,0,1	TSNARE1	59	.	0			c.C334T						.	G	TRP/ARG	3,4305		0,3,2151	7	10	9		334	-4.4	0	8		9	0,8446		0,0,4223	yes	missense	TSNARE1	NM_145003.3	101	0,3,6374	AA,AG,GG		0.0,0.0696,0.0235	probably-damaging	112/514	143425738	3,12751	2154	4223	6377	SO:0001583	missense	203062	exon4			CCATCCGGCCATG			8q24.3	2005-08-18							26437	protein-coding gene	gene with protein product						14702039	Standard	XM_005250828		Approved	FLJ31164	uc003ywk.3	Q96NA8		ENST00000307180.3:c.334C>T	chr8.hg19:g.143425738G>A	ENSP00000303437:p.Arg112Trp	83.0	0.0		65.0	3.0	NM_145003	B7ZLB0|Q14D03	Missense_Mutation	SNP	ENST00000307180.3	hg19	CCDS6384.1	.	.	.	.	.	.	.	.	.	.	G	10.78	1.447714	0.26074	6.96E-4	0.0	ENSG00000171045	ENST00000524325;ENST00000307180;ENST00000520166;ENST00000520462;ENST00000518720	T;T;T;T;T	0.24538	2.72;2.72;2.72;1.87;1.85	3.64	-4.4	0.03600	.	0.352416	0.14877	U	0.293184	T	0.19765	0.0475	L	0.27053	0.805	0.09310	N	1	D;D;D	0.69078	0.997;0.997;0.997	P;P;P	0.55999	0.789;0.789;0.789	T	0.11867	-1.0570	10	0.87932	D	0	-5.0028	1.1029	0.01687	0.2036:0.1252:0.3468:0.3244	.	112;112;112	B7ZLB0;Q96NA8;A0AVG3	.;TSNA1_HUMAN;.	W	112;112;112;112;128	ENSP00000428763:R112W;ENSP00000303437:R112W;ENSP00000427770:R112W;ENSP00000429626:R112W;ENSP00000430789:R128W	ENSP00000303437:R112W	R	-	1	2	TSNARE1	143423645	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.266000	0.08631	-0.513000	0.06496	-0.346000	0.07831	CGG	.	.		0.677	TSNARE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_145003		A	143425738	G	A	143425738	3	1	237	1	0	0	0	0	1	0	0	0	16645	1115	39	1	1247	1	TSNARE1	8	143425738	Missense_Mutation	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	33325845	143425738	2938284	105	33011										
TAF1L	138474	hgsc.bcm.edu	37	chr9	32630489	32630489	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ctgtttttctggagtggcagTggaaatatccaagacagaca	11	7	1	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr9:32630489T>C	ENST00000242310.4	-	1	5178	c.5089A>G	c.(5089-5091)Act>Gct	p.T1697A	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1697					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)			breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		GGAGTGGCAGTGGAAATATCC	0.478																																					p.T1697A		Atlas-SNP	.											.	TAF1L	382	.	0			c.A5089G						.						171	156	161					9																	32630489		2203	4300	6503	SO:0001583	missense	138474	exon1			TGGCAGTGGAAAT	AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.5089A>G	chr9.hg19:g.32630489T>C	ENSP00000418379:p.Thr1697Ala	281.0	0.0		215.0	36.0	NM_153809	Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	hg19	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	T	9.376	1.071662	0.20147	.	.	ENSG00000122728	ENST00000242310	T	0.06371	3.31	0.479	0.479	0.16796	.	0.621996	0.17394	N	0.175836	T	0.03434	0.0099	N	0.22421	0.69	0.18873	N	0.999983	B	0.02656	0.0	B	0.01281	0.0	T	0.45920	-0.9228	10	0.14656	T	0.56	.	5.1959	0.15236	0.0:1.0E-4:0.0:0.9999	.	1697	Q8IZX4	TAF1L_HUMAN	A	1697	ENSP00000418379:T1697A	ENSP00000418379:T1697A	T	-	1	0	TAF1L	32620489	1.000000	0.71417	0.971000	0.41717	0.194000	0.23727	0.684000	0.25364	0.426000	0.26116	0.164000	0.16699	ACT	.	.		0.478	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			C	32630489	T	C	32630489	3	2	237	1	0	0	0	0	1	0	0	0	15538	1696	59	2	395	2	TAF1L	9	32630489	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10		32630489	108582942	106	33012										
NOL6	65083	hgsc.bcm.edu	37	chr9	33466415	33466415	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gctggacggactggagttggTgggaacacctgtggaagaag	18	6	0	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr9:33466415T>A	ENST00000379471.2	-	17	2187	c.2100A>T	c.(2098-2100)ccA>ccT	p.P700P	NOL6_ENST00000464829.1_Intron|NOL6_ENST00000455041.2_Silent_p.P648P			Q9H6R4	NOL6_HUMAN	nucleolar protein 6 (RNA-associated)	700					rRNA processing (GO:0006364)	condensed nuclear chromosome (GO:0000794)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|skin(2)	27			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.152)		CTGGAGTTGGTGGGAACACCT	0.612											OREG0019137	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P700P		Atlas-SNP	.											.	NOL6	85	.	0			c.A2100T						.						88	84	86					9																	33466415		2203	4300	6503	SO:0001819	synonymous_variant	65083	exon17			AGTTGGTGGGAAC	AF361079	CCDS6543.1, CCDS6544.1	9p12	2013-02-22	2013-02-22		ENSG00000165271	ENSG00000165271			19910	protein-coding gene	gene with protein product		611532	"nucleolar protein family 6 (RNA-associated)"			11895476, 15590835	Standard	NM_022917		Approved	bA311H10.1, Nrap, FLJ21959, MGC14896, MGC14921, MGC20838, UTP22	uc003zsz.3	Q9H6R4	OTTHUMG00000000394	ENST00000379471.2:c.2100A>T	chr9.hg19:g.33466415T>A		186.0	0.0	840	169.0	72.0	NM_022917	Q5T5M3|Q5T5M4|Q7L4G6|Q8N6I0|Q8TEY9|Q8TEZ0|Q8TEZ1|Q9H675	Silent	SNP	ENST00000379471.2	hg19																																																																																				.	.		0.612	NOL6-005	NOVEL	non_canonical_TEC|basic	protein_coding	protein_coding	OTTHUMT00000001019.2	NM_022917		A	33466415	T	A	33466415	2	1	237	1	0	0	0	0	0	0	0	1	10534	1683	59	4		4	NOL6	9	33466415	Silent	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	835926	33466415	107747016	107	33013										
ZNF462	58499	hgsc.bcm.edu	37	chr9	109734475	109734475	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ctccggctacatccagagcaTcaggcgtcattaccgggaca	10	14	2	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr9:109734475T>A	ENST00000277225.5	+	8	6906	c.6617T>A	c.(6616-6618)aTc>aAc	p.I2206N	ZNF462_ENST00000457913.1_Missense_Mutation_p.I2266N|ZNF462_ENST00000441147.2_Missense_Mutation_p.I1112N|ZNF462_ENST00000542028.1_Missense_Mutation_p.I163N|RP11-508N12.2_ENST00000439901.1_RNA			Q96JM2	ZN462_HUMAN	zinc finger protein 462	2206					chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						ATCCAGAGCATCAGGCGTCAT	0.502																																					p.I2206N		Atlas-SNP	.											.	ZNF462	322	.	0			c.T6617A						.						97	92	94					9																	109734475		2203	4300	6503	SO:0001583	missense	58499	exon8			AGAGCATCAGGCG	AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"Zinc fingers, C2H2-type"	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.6617T>A	chr9.hg19:g.109734475T>A	ENSP00000277225:p.Ile2206Asn	323.0	0.0		229.0	16.0	NM_021224	Q5T0T4|Q8N408	Missense_Mutation	SNP	ENST00000277225.5	hg19	CCDS35096.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	28.0|28.0	4.878950|4.878950	0.91740|0.91740	.|.	.|.	ENSG00000148143|ENSG00000148143	ENST00000427098|ENST00000277225;ENST00000457913;ENST00000374686;ENST00000441147;ENST00000542028	.|T;T;T;T;T	.|0.28895	.|1.59;1.59;1.59;1.59;1.59	6.13|6.13	6.13|6.13	0.99165|0.99165	.|Zinc finger, C2H2-like (1);	.|0.062819	.|0.64402	.|D	.|0.000002	T|T	0.52041|0.52041	0.1710|0.1710	L|L	0.52905|0.52905	1.665|1.665	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.76494	.|0.998;0.999;0.998	.|P;D;P	.|0.71184	.|0.905;0.972;0.896	T|T	0.51965|0.51965	-0.8638|-0.8638	5|10	.|0.87932	.|D	.|0	.|.	16.8061|16.8061	0.85666|0.85666	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|2266;107;2206	.|Q96JM2-3;Q5T0T2;Q96JM2	.|.;.;ZN462_HUMAN	Q|N	107|2206;2266;1149;1112;163	.|ENSP00000277225:I2206N;ENSP00000414570:I2266N;ENSP00000363818:I1149N;ENSP00000397306:I1112N;ENSP00000439771:I163N	.|ENSP00000277225:I2206N	H|I	+|+	3|2	2|0	ZNF462|ZNF462	108774296|108774296	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.946000|0.946000	0.59487|0.59487	7.662000|7.662000	0.83803|0.83803	2.367000|2.367000	0.80283|0.80283	0.529000|0.529000	0.55759|0.55759	CAT|ATC	.	.		0.502	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224		A	109734475	T	A	109734475	3	1	237	1	0	0	0	0	1	0	0	0	17941	1435	50	4	6643	4	ZNF462	9	109734475	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	76268060	109734475	31478956	108	33014										
TNC	3371	hgsc.bcm.edu	37	chr9	117844994	117844994	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	attccggaagatgatctcccAggtttcaaaagcaatgtcta	8	9	3	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr9:117844994A>T	ENST00000350763.4	-	5	2635	c.2224T>A	c.(2224-2226)Tgg>Agg	p.W742R	TNC_ENST00000346706.3_Missense_Mutation_p.W742R|TNC_ENST00000340094.3_Missense_Mutation_p.W742R|TNC_ENST00000542877.1_Missense_Mutation_p.W742R|TNC_ENST00000423613.2_Missense_Mutation_p.W742R|TNC_ENST00000535648.1_Missense_Mutation_p.W742R|TNC_ENST00000537320.1_Missense_Mutation_p.W742R|TNC_ENST00000345230.3_Missense_Mutation_p.W742R|TNC_ENST00000341037.4_Missense_Mutation_p.W742R	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	742	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)			NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						ATGATCTCCCAGGTTTCAAAA	0.433																																					p.W742R		Atlas-SNP	.											.	TNC	282	.	0			c.T2224A						.						117	109	111					9																	117844994		2203	4300	6503	SO:0001583	missense	3371	exon5			TCTCCCAGGTTTC		CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	5318	protein-coding gene	gene with protein product	"hexabrachion (tenascin)"	187380	"hexabrachion (tenascin C, cytotactin)", "deafness, autosomal dominant 56"	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.2224T>A	chr9.hg19:g.117844994A>T	ENSP00000265131:p.Trp742Arg	198.0	0.0		146.0	61.0	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	ENST00000350763.4	hg19	CCDS6811.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.210080	0.79240	.	.	ENSG00000041982	ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000442945;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877	T;T;T;T;T;T;T;T;T	0.53857	0.6;0.61;0.6;0.61;0.61;0.61;0.61;0.61;0.61	5.88	5.88	0.94601	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.73916	0.3648	M	0.77103	2.36	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.77469	-0.2576	10	0.87932	D	0	.	16.268	0.82600	1.0:0.0:0.0:0.0	.	742;742	E9PC84;P24821	.;TENA_HUMAN	R	742	ENSP00000344400:W742R;ENSP00000438152:W742R;ENSP00000344555:W742R;ENSP00000345861:W742R;ENSP00000265131:W742R;ENSP00000339553:W742R;ENSP00000411406:W742R;ENSP00000443478:W742R;ENSP00000442242:W742R	ENSP00000344400:W742R	W	-	1	0	TNC	116884815	1.000000	0.71417	0.944000	0.38274	0.708000	0.40852	9.339000	0.96797	2.240000	0.73641	0.533000	0.62120	TGG	.	.		0.433	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160		T	117844994	A	T	117844994	3	4	237	1	0	0	0	0	1	0	0	0	16285	188	7	4	4477	4	TNC	9	117844994	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	8110519	117844994	23368437	109	33015										
LHX6	26468	hgsc.bcm.edu	37	chr9	124979380	124979380	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	cctcttgaggttctcaatcaTggtgtcgtagtggatgcggc	13	9	3	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr9:124979380T>A	ENST00000373755.2	-	4	670	c.562A>T	c.(562-564)Atg>Ttg	p.M188L	LHX6_ENST00000559895.1_Start_Codon_SNP_p.M1L|LHX6_ENST00000373754.2_Missense_Mutation_p.M188L|LHX6_ENST00000541397.2_Missense_Mutation_p.M206L|LHX6_ENST00000394319.4_Missense_Mutation_p.M217L|LHX6_ENST00000340587.3_Missense_Mutation_p.M217L	NM_001242334.1	NP_001229263.1	Q9UPM6	LHX6_HUMAN	LIM homeobox 6	188	Required for interaction with LDB1. {ECO:0000250}.				cell maturation (GO:0048469)|cerebral cortex GABAergic interneuron migration (GO:0021853)|cerebral cortex radially oriented cell migration (GO:0021799)|cerebral cortex tangential migration (GO:0021800)|forebrain neuron fate commitment (GO:0021877)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(5)	8						TTCTCAATCATGGTGTCGTAG	0.652																																					p.M217L		Atlas-SNP	.											.	LHX6	73	.	0			c.A649T						.						90	81	84					9																	124979380		2203	4300	6503	SO:0001583	missense	26468	exon5			CAATCATGGTGTC	AB031041	CCDS6837.2, CCDS6838.2, CCDS56583.1, CCDS56584.1, CCDS59144.1	9q33.2	2011-06-20			ENSG00000106852	ENSG00000106852		"Homeoboxes / LIM class"	21735	protein-coding gene	gene with protein product		608215				10393337	Standard	NM_014368		Approved	LHX6.1	uc004blx.4	Q9UPM6	OTTHUMG00000020601	ENST00000373755.2:c.562A>T	chr9.hg19:g.124979380T>A	ENSP00000362860:p.Met188Leu	200.0	0.0		126.0	8.0	NM_014368	A6PVQ1|A6PVQ2|A8K1B2|B7Z4D0|H0YN76|Q5T7S7|Q5T7S8|Q9NTK3|Q9UPM5	Missense_Mutation	SNP	ENST00000373755.2	hg19	CCDS56583.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.554457	0.86231	.	.	ENSG00000106852	ENST00000373755;ENST00000373754;ENST00000394319;ENST00000340587;ENST00000541397	D;D;D;D;D	0.85484	-1.99;-1.96;-1.89;-1.83;-1.89	5.87	5.87	0.94306	Zinc finger, LIM-type (2);	0.000000	0.85682	D	0.000000	T	0.78660	0.4318	N	0.26042	0.785	0.80722	D	1	B;B;B	0.27264	0.173;0.024;0.144	B;B;B	0.36186	0.071;0.029;0.219	T	0.72584	-0.4249	10	0.07482	T	0.82	.	15.45	0.75265	0.0:0.0:0.0:1.0	.	188;217;217	Q9UPM6;Q9UPM6-4;Q9UPM6-3	LHX6_HUMAN;.;.	L	188;188;217;217;206	ENSP00000362860:M188L;ENSP00000362859:M188L;ENSP00000377854:M217L;ENSP00000340137:M217L;ENSP00000441464:M206L	ENSP00000340137:M217L	M	-	1	0	LHX6	124019201	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.698000	0.84413	2.244000	0.73946	0.533000	0.62120	ATG	.	.		0.652	LHX6-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053924.2	NM_014368		A	124979380	T	A	124979380	3	1	237	1	0	0	0	0	1	0	0	0	8784	1464	51	4	612	4	LHX6	9	124979380	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	7134386	124979380	16234051	110	33016										
GLE1	2733	hgsc.bcm.edu	37	chr9	131287658	131287658	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gggaccagaggcccacaaagAgcccccagctcccagccagg	12	17	0	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr9:131287658A>G	ENST00000309971.4	+	7	1191	c.1085A>G	c.(1084-1086)gAg>gGg	p.E362G	GLE1_ENST00000539582.1_Missense_Mutation_p.E108G|GLE1_ENST00000494417.1_3'UTR|GLE1_ENST00000372770.4_Missense_Mutation_p.E362G	NM_001003722.1	NP_001003722.1	Q53GS7	GLE1_HUMAN	GLE1 RNA export mediator	362					mRNA export from nucleus (GO:0006406)|poly(A)+ mRNA export from nucleus (GO:0016973)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)|nuclear pore (GO:0005643)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	16						GCCCACAAAGAGCCCCCAGCT	0.537																																					p.E362G		Atlas-SNP	.											.	GLE1	42	.	0			c.A1085G						.						40	40	40					9																	131287658		2200	4299	6499	SO:0001583	missense	2733	exon7			ACAAAGAGCCCCC	AF058922	CCDS6904.1, CCDS35154.1	9q34.13	2014-09-17	2013-06-18	2007-10-04	ENSG00000119392	ENSG00000119392			4315	protein-coding gene	gene with protein product		603371	"GLE1 (yeast homolog)-like, RNA export mediator", "GLE1 RNA export mediator-like (yeast)", "GLE1 RNA export mediator (yeast)", "lethal congenital contracture syndrome 1", "GLE1 RNA export mediator homolog (yeast)"	GLE1L, LCCS1		9618489, 18204449	Standard	NM_001499		Approved	hGLE1	uc004bvj.3	Q53GS7	OTTHUMG00000020749	ENST00000309971.4:c.1085A>G	chr9.hg19:g.131287658A>G	ENSP00000308622:p.Glu362Gly	102.0	0.0		82.0	28.0	NM_001499	O75458|Q53GT9|Q5VVU1|Q8NCP6|Q9UFL6	Missense_Mutation	SNP	ENST00000309971.4	hg19	CCDS35154.1	.	.	.	.	.	.	.	.	.	.	A	10.00	1.233194	0.22626	.	.	ENSG00000119392	ENST00000309971;ENST00000372770;ENST00000539582	T;T;T	0.79247	-0.27;0.15;-1.25	5.59	1.79	0.24919	.	0.876442	0.10354	N	0.684813	T	0.67135	0.2861	L	0.43152	1.355	0.09310	N	1	B;B	0.31625	0.224;0.332	B;B	0.29598	0.055;0.104	T	0.52079	-0.8623	10	0.35671	T	0.21	-2.2002	7.1116	0.25392	0.6462:0.2797:0.0741:0.0	.	362;362	Q53GS7;Q53GS7-2	GLE1_HUMAN;.	G	362;362;108	ENSP00000308622:E362G;ENSP00000361856:E362G;ENSP00000438670:E108G	ENSP00000308622:E362G	E	+	2	0	GLE1	130327479	0.998000	0.40836	0.000000	0.03702	0.744000	0.42396	3.423000	0.52756	0.057000	0.16193	0.379000	0.24179	GAG	.	.		0.537	GLE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054456.1	NM_001003722		G	131287658	A	G	131287658	3	3	237	1	0	0	0	0	1	0	0	0	6443	304	11	2	1111	2	GLE1	9	131287658	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	6308278	131287658	9925773	111	33017										
CRAT	1384	hgsc.bcm.edu	37	chr9	131860591	131860591	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ggcttagcttctccgacttgGggaagtcttttccaaaatgg	11	9	2	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr9:131860591G>A	ENST00000318080.2	-	10	1559	c.1265C>T	c.(1264-1266)cCc>cTc	p.P422L	RP11-247A12.1_ENST00000434250.1_RNA	NM_000755.3|NM_001257363.1	NP_000746|NP_001244292.1	P43155	CACP_HUMAN	carnitine O-acetyltransferase	422					carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carnitine O-acetyltransferase activity (GO:0004092)|receptor binding (GO:0005102)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(2)	13				UCEC - Uterine corpus endometrioid carcinoma (4;0.0178)	L-Carnitine(DB00583)	CTCCGACTTGGGGAAGTCTTT	0.587																																					p.P422L		Atlas-SNP	.											.	CRAT	43	.	0			c.C1265T						.						87	85	86					9																	131860591		2203	4300	6503	SO:0001583	missense	1384	exon10			GACTTGGGGAAGT	X78706	CCDS6919.1	9q34.1	2010-04-27	2010-04-27		ENSG00000095321	ENSG00000095321	2.3.1.7		2342	protein-coding gene	gene with protein product		600184	"carnitine acetyltransferase"			7829107	Standard	NM_000755		Approved	CAT1	uc004bxh.3	P43155	OTTHUMG00000147343	ENST00000318080.2:c.1265C>T	chr9.hg19:g.131860591G>A	ENSP00000315013:p.Pro422Leu	202.0	0.0		179.0	28.0	NM_000755	Q5T952|Q9BW16	Missense_Mutation	SNP	ENST00000318080.2	hg19	CCDS6919.1	.	.	.	.	.	.	.	.	.	.	G	15.53	2.859754	0.51376	.	.	ENSG00000095321	ENST00000351352;ENST00000318080	D	0.87966	-2.32	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	D	0.89065	0.6609	L	0.35723	1.085	0.80722	D	1	P	0.48834	0.916	P	0.58454	0.839	D	0.88299	0.2948	10	0.41790	T	0.15	-40.7892	17.7377	0.88399	0.0:0.0:1.0:0.0	.	422	P43155	CACP_HUMAN	L	341;422	ENSP00000315013:P422L	ENSP00000315013:P422L	P	-	2	0	CRAT	130900412	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	9.657000	0.98554	2.667000	0.90743	0.561000	0.74099	CCC	.	.		0.587	CRAT-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253700.1			A	131860591	G	A	131860591	3	1	237	1	0	0	0	0	1	0	0	0	3849	1232	43	3	635	3	CRAT	9	131860591	Missense_Mutation	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	572933	131860591	9352840	112	33018										
C9orf98	158067	hgsc.bcm.edu	37	chr9	135739158	135739158	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tgttcagatgtttgcagagcCacattgcctgaagaaaggaa	11	7	1	4			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr9:135739158C>T	ENST00000298545.3	-	4	748	c.227G>A	c.(226-228)tGg>tAg	p.W76*	AK8_ENST00000477396.1_5'UTR	NM_152572.2	NP_689785.1	Q96MA6	KAD8_HUMAN	adenylate kinase 8	76	Adenylate kinase 1.				nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)			NS(1)|kidney(2)|large_intestine(4)|lung(11)|pancreas(2)|prostate(1)|urinary_tract(2)	23						TTTGCAGAGCCACATTGCCTG	0.423																																					p.W76X		Atlas-SNP	.											.	AK8	45	.	0			c.G227A						.						74	67	69					9																	135739158		2203	4300	6503	SO:0001587	stop_gained	158067	exon4			CAGAGCCACATTG	AK093446	CCDS6954.1	9q34.13	2013-04-29	2010-12-07	2010-12-07	ENSG00000165695	ENSG00000165695	2.7.4.3	"Adenylate kinases"	26526	protein-coding gene	gene with protein product		615365	"chromosome 9 open reading frame 98"	C9orf98		21080915	Standard	NM_152572		Approved	FLJ32704	uc004cbu.1	Q96MA6	OTTHUMG00000021009	ENST00000298545.3:c.227G>A	chr9.hg19:g.135739158C>T	ENSP00000298545:p.Trp76*	136.0	0.0		127.0	17.0	NM_152572	A8K821|Q8N9W9	Nonsense_Mutation	SNP	ENST00000298545.3	hg19	CCDS6954.1	.	.	.	.	.	.	.	.	.	.	C	41	9.072439	0.99057	.	.	ENSG00000165695	ENST00000298545	.	.	.	5.05	5.05	0.67936	.	0.315252	0.30565	N	0.009346	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	-16.959	12.8217	0.57696	0.1633:0.8367:0.0:0.0	.	.	.	.	X	76	.	ENSP00000298545:W76X	W	-	2	0	AK8	134728979	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	3.043000	0.49823	2.492000	0.84095	0.563000	0.77884	TGG	.	.		0.423	AK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055413.1	NM_152572		T	135739158	C	T	135739158	4	4	237	1	0	0	0	0	0	1	0	0	2511	595	21	3	1252	3	C9orf98	9	135739158	Nonsense_Mutation	SNP	C	TCGA-ED-A459-01A-11D-A25V-10	3878567	135739158	5474273	113	33019										
ITIH5	80760	hgsc.bcm.edu	37	chr10	7627889	7627889	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gtgggtgacatatggtgaatGtacactttcccatccctgat	10	9	0	3			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr10:7627889G>T	ENST00000256861.6	-	8	1161	c.1083C>A	c.(1081-1083)taC>taA	p.Y361*	ITIH5_ENST00000298441.6_Nonsense_Mutation_p.Y147*|ITIH5_ENST00000434980.1_5'UTR|ITIH5_ENST00000397145.2_Nonsense_Mutation_p.Y361*|ITIH5_ENST00000446830.2_Nonsense_Mutation_p.Y143*|ITIH5_ENST00000397146.2_Nonsense_Mutation_p.Y361*	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	361	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						TATGGTGAATGTACACTTTCC	0.383																																					p.Y361X		Atlas-SNP	.											ITIH5_ENST00000397145,NS,carcinoma,0,2	ITIH5	343	.	0			c.C1083A						.						180	144	156					10																	7627889		2203	4300	6503	SO:0001587	stop_gained	80760	exon8			GTGAATGTACACT			10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"inter-alpha (globulin) inhibitor H5"			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.1083C>A	chr10.hg19:g.7627889G>T	ENSP00000256861:p.Tyr361*	305.0	1.0		410.0	79.0	NM_001001851	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Nonsense_Mutation	SNP	ENST00000256861.6	hg19		.	.	.	.	.	.	.	.	.	.	G	36	5.846805	0.97016	.	.	ENSG00000123243	ENST00000256861;ENST00000397146;ENST00000298441;ENST00000446830;ENST00000397145	.	.	.	5.3	2.36	0.29203	.	0.054481	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-25.7311	8.7698	0.34724	0.3863:0.0:0.6137:0.0	.	.	.	.	X	361;361;147;143;361	.	ENSP00000256861:Y361X	Y	-	3	2	ITIH5	7667895	1.000000	0.71417	0.992000	0.48379	0.836000	0.47400	1.685000	0.37659	0.200000	0.20447	0.561000	0.74099	TAC	.	.		0.383	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569		T	7627889	G	T	7627889	4	4	237	1	0	0	0	0	0	1	0	0	7916	1372	48	3	1896	3	ITIH5	10	7627889	Nonsense_Mutation	SNP	G	TCGA-ED-A459-01A-11D-A25V-10		7627889	127906858	114	33020										
MYO3A	53904	hgsc.bcm.edu	37	chr10	26462749	26462749	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tggagagtaacaacagagtgTatcagactccaaaaaaaatg	9	6	1	3			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr10:26462749T>A	ENST00000265944.5	+	30	3722	c.3556T>A	c.(3556-3558)Tat>Aat	p.Y1186N	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	1186					ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						CAACAGAGTGTATCAGACTCC	0.398																																					p.Y1186N		Atlas-SNP	.											.	MYO3A	371	.	0			c.T3556A						.						69	67	68					10																	26462749		2203	4300	6503	SO:0001583	missense	53904	exon30			AGAGTGTATCAGA	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.3556T>A	chr10.hg19:g.26462749T>A	ENSP00000265944:p.Tyr1186Asn	109.0	0.0		122.0	11.0	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	hg19	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	T	4.270	0.049165	0.08243	.	.	ENSG00000095777	ENST00000265944	T	0.76448	-1.02	5.29	1.69	0.24217	.	1.446850	0.03518	N	0.220553	T	0.67069	0.2854	L	0.27053	0.805	0.19575	N	0.999961	B	0.24823	0.112	B	0.21360	0.034	T	0.51196	-0.8736	10	0.28530	T	0.3	.	8.7328	0.34510	0.0:0.2236:0.0:0.7764	.	1186	Q8NEV4	MYO3A_HUMAN	N	1186	ENSP00000265944:Y1186N	ENSP00000265944:Y1186N	Y	+	1	0	MYO3A	26502755	0.000000	0.05858	0.016000	0.15963	0.024000	0.10985	0.491000	0.22419	0.413000	0.25759	0.533000	0.62120	TAT	.	.		0.398	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		A	26462749	T	A	26462749	3	1	237	1	0	0	0	0	1	0	0	0	10085	1638	57	4	3666	4	MYO3A	10	26462749	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	18834860	26462749	109071998	115	33021										
PDSS1	23590	hgsc.bcm.edu	37	chr10	27024491	27024491	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ggttagccactggtcctgtcCtgtttgcctgtcagcaggta	12	11	1	0	rs541206852		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr10:27024491C>T	ENST00000376215.5	+	10	1062	c.1009C>T	c.(1009-1011)Ctg>Ttg	p.L337L	PDSS1_ENST00000470978.1_3'UTR|PDSS1_ENST00000376203.5_Intron	NM_014317.3	NP_055132.2	Q5T2R2	DPS1_HUMAN	prenyl (decaprenyl) diphosphate synthase, subunit 1	337					isoprenoid biosynthetic process (GO:0008299)|protein heterotetramerization (GO:0051290)|small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	mitochondrial matrix (GO:0005759)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|trans-hexaprenyltranstransferase activity (GO:0000010)|trans-octaprenyltranstransferase activity (GO:0050347)			autonomic_ganglia(1)|endometrium(1)|kidney(7)|large_intestine(6)|lung(5)|prostate(1)	21						TGGTCCTGTCCTGTTTGCCTG	0.507													C|||	1	0.000199681	0	0	5008	,	,		21830	0		0	False		,,,				2504	0.001				p.L337L		Atlas-SNP	.											.	PDSS1	36	.	0			c.C1009T						.						118	104	109					10																	27024491		2203	4300	6503	SO:0001819	synonymous_variant	23590	exon10			CCTGTCCTGTTTG	AF118395	CCDS31168.1	10p12.2	2006-04-12	2006-02-14	2006-02-14	ENSG00000148459	ENSG00000148459			17759	protein-coding gene	gene with protein product	"coenzyme Q1 homolog (yeast)"	607429	"trans-prenyltransferase"	TPRT		10972372	Standard	NM_014317		Approved	TPT, COQ1	uc001isv.3	Q5T2R2	OTTHUMG00000017844	ENST00000376215.5:c.1009C>T	chr10.hg19:g.27024491C>T		199.0	0.0		331.0	85.0	NM_014317	Q53F75|Q6P473|Q86WQ8|Q9Y2W5	Silent	SNP	ENST00000376215.5	hg19	CCDS31168.1																																																																																			.	.		0.507	PDSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047276.1			T	27024491	C	T	27024491	2	4	237	1	0	0	0	0	0	0	0	1	11702	680	24	3		3	PDSS1	10	27024491	Silent	SNP	C	TCGA-ED-A459-01A-11D-A25V-10	561742	27024491	108510256	116	33022										
OIT3	170392	hgsc.bcm.edu	37	chr10	74660156	74660156	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tttttatgacatctgcgacgAggactgccatggcagctgct	11	10	1	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr10:74660156A>T	ENST00000334011.5	+	3	676	c.458A>T	c.(457-459)gAg>gTg	p.E153V		NM_152635.1	NP_689848.1	Q8WWZ8	OIT3_HUMAN	oncoprotein induced transcript 3	153						nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)	35	Prostate(51;0.0198)					ATCTGCGACGAGGACTGCCAT	0.483																																					p.E153V	Colon(7;19 345 13446 17537)	Atlas-SNP	.											.	OIT3	62	.	0			c.A458T						.						51	49	49					10																	74660156		2203	4300	6503	SO:0001583	missense	170392	exon3			GCGACGAGGACTG		CCDS7318.1	10q22.2-q22.3	2004-04-21			ENSG00000138315	ENSG00000138315			29953	protein-coding gene	gene with protein product		609330				12975309, 12939600	Standard	NM_152635		Approved	LZP, FLJ39116	uc001jte.1	Q8WWZ8	OTTHUMG00000018444	ENST00000334011.5:c.458A>T	chr10.hg19:g.74660156A>T	ENSP00000333900:p.Glu153Val	113.0	0.0		120.0	35.0	NM_152635	A0AVP3|Q8N1M8	Missense_Mutation	SNP	ENST00000334011.5	hg19	CCDS7318.1	.	.	.	.	.	.	.	.	.	.	A	13.29	2.193942	0.38707	.	.	ENSG00000138315	ENST00000334011;ENST00000415725	T	0.40476	1.03	5.22	4.03	0.46877	.	0.542530	0.16138	N	0.227863	T	0.16214	0.0390	N	0.02539	-0.55	0.26426	N	0.976028	B	0.02656	0.0	B	0.06405	0.002	T	0.16012	-1.0417	10	0.15066	T	0.55	-17.7355	7.9603	0.30068	0.7248:0.0:0.0:0.2752	.	153	Q8WWZ8	OIT3_HUMAN	V	153	ENSP00000333900:E153V	ENSP00000333900:E153V	E	+	2	0	OIT3	74330162	1.000000	0.71417	0.999000	0.59377	0.843000	0.47879	3.809000	0.55606	2.197000	0.70478	0.528000	0.53228	GAG	.	.		0.483	OIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048596.1	NM_152635		T	74660156	A	T	74660156	3	4	237	1	0	0	0	0	1	0	0	0	10858	304	11	4	468	4	OIT3	10	74660156	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	47635665	74660156	60874591	117	33023										
ANXA7	310	hgsc.bcm.edu	37	chr10	75147463	75147463	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ataccttgccataggaggtcTtaaatgctgctttaattttt	7	7	1	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr10:75147463T>A	ENST00000372921.5	-	7	673	c.617A>T	c.(616-618)aAg>aTg	p.K206M	ANXA7_ENST00000535178.1_Missense_Mutation_p.K76M|ANXA7_ENST00000492380.1_5'UTR	NM_001156.3	NP_001147.1	P20073	ANXA7_HUMAN	annexin A7	228					autophagy (GO:0006914)|cell proliferation (GO:0008283)|cellular calcium ion homeostasis (GO:0006874)|cellular water homeostasis (GO:0009992)|epithelial cell differentiation (GO:0030855)|hemostasis (GO:0007599)|membrane fusion (GO:0061025)|negative regulation of gene expression (GO:0010629)|regulation of cell shape (GO:0008360)|response to calcium ion (GO:0051592)|response to organic cyclic compound (GO:0014070)|response to salt stress (GO:0009651)|social behavior (GO:0035176)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|integrin binding (GO:0005178)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	26	Prostate(51;0.0119)					ATAGGAGGTCTTAAATGCTGC	0.428																																					p.K228M		Atlas-SNP	.											.	ANXA7	50	.	0			c.A683T						.						217	206	210					10																	75147463		2203	4300	6503	SO:0001583	missense	310	exon8			GAGGTCTTAAATG	J04543	CCDS7325.1, CCDS7326.1	10q22.2	2005-11-09			ENSG00000138279	ENSG00000138279		"Annexins"	545	protein-coding gene	gene with protein product		186360		ANX7		7515686	Standard	NM_001156		Approved		uc001jtz.2	P20073	OTTHUMG00000018463	ENST00000372921.5:c.617A>T	chr10.hg19:g.75147463T>A	ENSP00000362012:p.Lys206Met	213.0	0.0		255.0	31.0	NM_004034	Q5F2H3|Q5T0M6|Q5T0M7	Missense_Mutation	SNP	ENST00000372921.5	hg19	CCDS7325.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.437420	0.83885	.	.	ENSG00000138279	ENST00000372921;ENST00000372919;ENST00000535178	T;T;T	0.06608	3.28;3.28;3.28	5.96	5.96	0.96718	Annexin repeat, conserved site (1);	0.146548	0.47455	D	0.000227	T	0.30166	0.0756	M	0.87097	2.86	0.58432	D	0.999994	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.83275	0.996;0.996;0.993;0.988;0.993	T	0.06734	-1.0810	10	0.87932	D	0	.	14.3967	0.67015	0.0:0.0:0.0:1.0	.	206;206;133;206;228	Q53HM8;B2R7L2;B4DWU2;P20073-2;P20073	.;.;.;.;ANXA7_HUMAN	M	206;228;76	ENSP00000362012:K206M;ENSP00000362010:K228M;ENSP00000442864:K76M	ENSP00000362010:K228M	K	-	2	0	ANXA7	74817469	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.190000	0.72057	2.284000	0.76573	0.528000	0.53228	AAG	.	.		0.428	ANXA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048646.2	NM_001156		A	75147463	T	A	75147463	3	1	237	1	0	0	0	0	1	0	0	0	723	1609	56	4	811	4	ANXA7	10	75147463	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	487307	75147463	60387284	118	33024										
MYOF	26509	hgsc.bcm.edu	37	chr10	95116494	95116494	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ttctgaaggagccatttttcTcctccagcgtctgcggcgga	11	12	3	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr10:95116494T>A	ENST00000359263.4	-	30	3231	c.3232A>T	c.(3232-3234)Aga>Tga	p.R1078*	MYOF_ENST00000371502.4_Nonsense_Mutation_p.R1078*|MYOF_ENST00000358334.5_Nonsense_Mutation_p.R1065*|MYOF_ENST00000371501.4_Nonsense_Mutation_p.R1078*	NM_013451.3	NP_038479.1	Q9NZM1	MYOF_HUMAN	myoferlin	1078	Poly-Arg.				blood circulation (GO:0008015)|cellular response to heat (GO:0034605)|muscle contraction (GO:0006936)|plasma membrane repair (GO:0001778)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)	caveola (GO:0005901)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)			NS(2)|autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(7)|large_intestine(15)|lung(14)|ovary(4)|prostate(4)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						GCCATTTTTCTCCTCCAGCGT	0.473																																					p.R1078X		Atlas-SNP	.											.	MYOF	177	.	0			c.A3232T						.						120	112	115					10																	95116494		1913	4121	6034	SO:0001587	stop_gained	26509	exon30			TTTTTCTCCTCCA	AB033033	CCDS41550.1, CCDS41551.1	10q24	2014-06-27	2008-11-26	2008-11-26	ENSG00000138119	ENSG00000138119			3656	protein-coding gene	gene with protein product	"fer-1-like family member 3"	604603	"fer-1 (C.elegans)-like 3 (myoferlin)", "fer-1-like 3, myoferlin (C. elegans)"	FER1L3		10607832, 10995573, 17702744	Standard	NM_013451		Approved	KIAA1207	uc001kin.3	Q9NZM1	OTTHUMG00000018772	ENST00000359263.4:c.3232A>T	chr10.hg19:g.95116494T>A	ENSP00000352208:p.Arg1078*	218.0	0.0		213.0	14.0	NM_013451	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	Nonsense_Mutation	SNP	ENST00000359263.4	hg19	CCDS41551.1	.	.	.	.	.	.	.	.	.	.	T	44	10.772633	0.99465	.	.	ENSG00000138119	ENST00000358334;ENST00000359263;ENST00000371501;ENST00000371502	.	.	.	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-24.1745	12.9678	0.58494	0.0:0.0:0.1436:0.8564	.	.	.	.	X	1065;1078;1078;1078	.	ENSP00000351094:R1065X	R	-	1	2	MYOF	95106484	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.224000	0.65288	2.253000	0.74438	0.454000	0.30748	AGA	.	.		0.473	MYOF-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049423.2	NM_013451		A	95116494	T	A	95116494	4	1	237	1	0	0	0	0	0	1	0	0	10098	1559	54	4	3053	4	MYOF	10	95116494	Nonsense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	19969031	95116494	40418253	119	33025										
SFXN4	119559	hgsc.bcm.edu	37	chr10	120914639	120914639	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gtccatgaccgcaatcccctTaatggattcaagacttcggg	9	12	1	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr10:120914639T>A	ENST00000355697.2	-	11	686	c.667A>T	c.(667-669)Aag>Tag	p.K223*	SFXN4_ENST00000330036.6_Nonsense_Mutation_p.K214*|SFXN4_ENST00000461438.1_5'UTR	NM_213649.1	NP_998814.1	Q6P4A7	SFXN4_HUMAN	sideroflexin 4	223					iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)			central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	11		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0261)		GCAATCCCCTTAATGGATTCA	0.468																																					p.K223X		Atlas-SNP	.											.	SFXN4	24	.	0			c.A667T						.						142	121	128					10																	120914639		2203	4300	6503	SO:0001587	stop_gained	119559	exon11			TCCCCTTAATGGA		CCDS7610.1	10q26.11	2006-03-13			ENSG00000183605	ENSG00000183605		"Sideroflexins"	16088	protein-coding gene	gene with protein product		615564				14756423	Standard	NM_213649		Approved		uc001leb.3	Q6P4A7	OTTHUMG00000019147	ENST00000355697.2:c.667A>T	chr10.hg19:g.120914639T>A	ENSP00000347924:p.Lys223*	251.0	0.0		204.0	15.0	NM_213649	Q6WSU4|Q86TD9	Nonsense_Mutation	SNP	ENST00000355697.2	hg19	CCDS7610.1	.	.	.	.	.	.	.	.	.	.	T	26.8	4.774647	0.90108	.	.	ENSG00000183605	ENST00000355697;ENST00000330036;ENST00000392875;ENST00000369131	.	.	.	4.77	2.73	0.32206	.	0.855801	0.09976	N	0.731614	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.4705	9.8113	0.40824	0.0:0.0:0.5066:0.4934	.	.	.	.	X	223;214;106;107	.	ENSP00000333200:K214X	K	-	1	0	SFXN4	120904629	0.000000	0.05858	0.106000	0.21319	0.016000	0.09150	0.511000	0.22739	1.215000	0.43411	-0.226000	0.12346	AAG	.	.		0.468	SFXN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050642.3	XM_058406		A	120914639	T	A	120914639	4	1	237	1	0	0	0	0	0	1	0	0	14212	1763	61	4	362	4	SFXN4	10	120914639	Nonsense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	25798145	120914639	14620108	120	33026										
UBQLNL	143630	hgsc.bcm.edu	37	chr11	5537570	5537570	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tggttgcctgcagtcttcacTatcactcgagtggcacttga	10	11	3	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:5537570T>A	ENST00000380184.1	-	1	365	c.102A>T	c.(100-102)atA>atT	p.I34I	HBG2_ENST00000380259.2_Intron	NM_145053.4	NP_659490.4	Q8IYU4	UBQLN_HUMAN	ubiquilin-like	34	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.									endometrium(1)|kidney(3)|large_intestine(9)|lung(13)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.136)		CAGTCTTCACTATCACTCGAG	0.488																																					p.I34I		Atlas-SNP	.											.	UBQLNL	74	.	0			c.A102T						.						124	112	116					11																	5537570		2201	4297	6498	SO:0001819	synonymous_variant	143630	exon1			CTTCACTATCACT	AK127987	CCDS31385.1	11p15.4	2014-02-12			ENSG00000175518	ENSG00000175518		"Ubiquilin family"	28294	protein-coding gene	gene with protein product							Standard	NM_145053		Approved	MGC20470, MGC26958	uc001maz.4	Q8IYU4	OTTHUMG00000066903	ENST00000380184.1:c.102A>T	chr11.hg19:g.5537570T>A		110.0	0.0		138.0	10.0	NM_145053	Q6ZRU1|Q96EK3|Q96MB0	Silent	SNP	ENST00000380184.1	hg19	CCDS31385.1																																																																																			.	.		0.488	UBQLNL-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143386.1	NM_145053		A	5537570	T	A	5537570	2	1	237	1	0	0	0	0	0	0	0	1	16915	1512	53	4		4	UBQLNL	11	5537570	Silent	SNP	T	TCGA-ED-A459-01A-11D-A25V-10		5537570	129468946	121	33027										
CCKBR	887	hgsc.bcm.edu	37	chr11	6291552	6291552	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gcatcgctggcccagtgcgcGggtccgccagacctggtgag	16	14	0	2	rs200729292		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:6291552G>A	ENST00000334619.2	+	3	831	c.638G>A	c.(637-639)cGg>cAg	p.R213Q	CCKBR_ENST00000525462.1_Missense_Mutation_p.R213Q|CCKBR_ENST00000532715.1_Missense_Mutation_p.R129Q	NM_176875.3	NP_795344.1	P32239	GASR_HUMAN	cholecystokinin B receptor	213					cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cholecystokinin signaling pathway (GO:0038188)|digestion (GO:0007586)|digestive tract development (GO:0048565)|feeding behavior (GO:0007631)|gastric acid secretion (GO:0001696)|gland development (GO:0048732)|metabolic process (GO:0008152)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|sensory perception (GO:0007600)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|cholecystokinin receptor activity (GO:0004951)|gastrin receptor activity (GO:0015054)|phosphatidylinositol phospholipase C activity (GO:0004435)|type B gastrin/cholecystokinin receptor binding (GO:0031741)			NS(2)|breast(2)|endometrium(4)|kidney(13)|large_intestine(10)|lung(22)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.139)	Pentagastrin(DB00183)	CCCAGTGCGCGGGTCCGCCAG	0.582																																					p.R213Q		Atlas-SNP	.											CCKBR_ENST00000525462,right_upper_lobe,carcinoma,0,2	CCKBR	232	.	0			c.G638A						.						86	88	88					11																	6291552		2201	4296	6497	SO:0001583	missense	887	exon3			GTGCGCGGGTCCG	D13305	CCDS7761.1	11p15.4	2012-08-10			ENSG00000110148	ENSG00000110148		"GPCR / Class A : Cholecystokinin receptors"	1571	protein-coding gene	gene with protein product		118445				1280419	Standard	NM_176875		Approved		uc001mcp.3	P32239	OTTHUMG00000133380	ENST00000334619.2:c.638G>A	chr11.hg19:g.6291552G>A	ENSP00000335544:p.Arg213Gln	113.0	0.0		97.0	48.0	NM_176875	A8K7P9|O75824|Q16144|Q92492|Q96LC6|Q9NYK7|Q9UBV1	Missense_Mutation	SNP	ENST00000334619.2	hg19	CCDS7761.1	.	.	.	.	.	.	.	.	.	.	G	10.36	1.328675	0.24167	.	.	ENSG00000110148	ENST00000334619;ENST00000532715;ENST00000525462	T;T;T	0.37752	1.18;1.18;1.18	5.09	2.01	0.26516	GPCR, rhodopsin-like superfamily (1);	0.230162	0.38164	N	0.001783	T	0.25717	0.0626	N	0.10809	0.05	0.09310	N	1	D;B;B	0.76494	0.999;0.052;0.122	P;B;B	0.60012	0.867;0.019;0.058	T	0.13818	-1.0495	10	0.13108	T	0.6	.	3.9652	0.09428	0.3551:0.172:0.473:0.0	.	213;147;213	P32239-2;P32239-3;P32239	.;.;GASR_HUMAN	Q	213;129;213	ENSP00000335544:R213Q;ENSP00000432079:R129Q;ENSP00000435534:R213Q	ENSP00000335544:R213Q	R	+	2	0	CCKBR	6248128	0.000000	0.05858	0.726000	0.30738	0.995000	0.86356	-0.202000	0.09451	0.560000	0.29169	0.655000	0.94253	CGG	.	.		0.582	CCKBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257230.2	NM_176875		A	6291552	G	A	6291552	3	1	237	1	0	0	0	0	1	0	0	0	2883	1116	39	1	648	1	CCKBR	11	6291552	Missense_Mutation	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	753982	6291552	128714964	122	33028										
DENND5A	23258	hgsc.bcm.edu	37	chr11	9182408	9182408	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tcttttccaccagcatcctcTtggtctacaaggaagcagtc	7	13	3	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:9182408T>G	ENST00000328194.3	-	12	2608	c.2288A>C	c.(2287-2289)aAg>aCg	p.K763T	DENND5A_ENST00000530044.1_Missense_Mutation_p.K763T|DENND5A_ENST00000527700.1_Missense_Mutation_p.K106T	NM_001243254.1|NM_015213.3	NP_001230183.1|NP_056028.2	Q6IQ26	DEN5A_HUMAN	DENN/MADD domain containing 5A	763					positive regulation of Rab GTPase activity (GO:0032851)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(16)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						CAGCATCCTCTTGGTCTACAA	0.517																																					p.K763T		Atlas-SNP	.											.	DENND5A	84	.	0			c.A2288C						.						146	133	137					11																	9182408		2201	4296	6497	SO:0001583	missense	23258	exon12			ATCCTCTTGGTCT	AB029014	CCDS31423.1, CCDS58119.1	11p15.3	2012-10-03	2008-08-14	2008-08-14	ENSG00000184014	ENSG00000184014		"DENN/MADD domain containing"	19344	protein-coding gene	gene with protein product			"RAB6 interacting protein 1"	RAB6IP1		10470851	Standard	NM_015213		Approved	KIAA1091, FLJ22354, FLJ33829, FLJ43455	uc001mhl.3	Q6IQ26	OTTHUMG00000165716	ENST00000328194.3:c.2288A>C	chr11.hg19:g.9182408T>G	ENSP00000328524:p.Lys763Thr	224.0	0.0		286.0	17.0	NM_015213	B4DJ15|E9PS91|Q96GN3|Q9H6U7|Q9UFV0|Q9UPR1	Missense_Mutation	SNP	ENST00000328194.3	hg19	CCDS31423.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.461535	0.84317	.	.	ENSG00000184014	ENST00000328194;ENST00000530044;ENST00000527700	T;T;T	0.16196	2.36;2.36;2.36	5.81	4.68	0.58851	.	0.000000	0.85682	D	0.000000	T	0.43897	0.1268	M	0.80422	2.495	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.992;0.999	T	0.44862	-0.9300	10	0.72032	D	0.01	.	13.2774	0.60194	0.0:0.0:0.1323:0.8677	.	763;763	E9PS91;Q6IQ26	.;DEN5A_HUMAN	T	763;763;106	ENSP00000328524:K763T;ENSP00000435866:K763T;ENSP00000432549:K106T	ENSP00000328524:K763T	K	-	2	0	DENND5A	9138984	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	8.040000	0.89188	1.019000	0.39547	0.529000	0.55759	AAG	.	.		0.517	DENND5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385910.2	NM_015213		G	9182408	T	G	9182408	3	3	237	1	0	0	0	0	1	0	0	0	4438	1609	56	5	1623	5	DENND5A	11	9182408	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	2890856	9182408	125824108	123	33029										
TPH1	7166	hgsc.bcm.edu	37	chr11	18057649	18057649	+	Nonsense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	attctgagtttcttctttttGattttcgggactcgatatgt	8	6	3	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:18057649G>C	ENST00000250018.2	-	2	720	c.158C>G	c.(157-159)tCa>tGa	p.S53*	TPH1_ENST00000341556.2_Nonsense_Mutation_p.S53*	NM_004179.2	NP_004170.1	P17752	TPH1_HUMAN	tryptophan hydroxylase 1	53	ACT. {ECO:0000255|PROSITE- ProRule:PRU01007}.				aromatic amino acid family metabolic process (GO:0009072)|bone remodeling (GO:0046849)|cellular nitrogen compound metabolic process (GO:0034641)|circadian rhythm (GO:0007623)|indolalkylamine biosynthetic process (GO:0046219)|mammary gland alveolus development (GO:0060749)|negative regulation of ossification (GO:0030279)|response to immobilization stress (GO:0035902)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|neuron projection (GO:0043005)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|tryptophan 5-monooxygenase activity (GO:0004510)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(14)|prostate(1)|stomach(1)	25					L-Tryptophan(DB00150)|Tetrahydrobiopterin(DB00360)	TCTTCTTTTTGATTTTCGGGA	0.348																																					p.S53X		Atlas-SNP	.											.	TPH1	44	.	0			c.C158G						.						115	109	111					11																	18057649		2200	4293	6493	SO:0001587	stop_gained	7166	exon2			CTTTTTGATTTTC	X52836	CCDS7829.1	11p15.3-p14	2012-10-02	2008-07-31	2003-04-04	ENSG00000129167	ENSG00000129167	1.14.16.4		12008	protein-coding gene	gene with protein product	"tryptophan 5-monooxygenase"	191060	"tryptophan hydroxylase (tryptophan 5-monooxygenase)"	TPRH, TPH		1463016	Standard	NM_004179		Approved		uc001mnp.2	P17752	OTTHUMG00000166421	ENST00000250018.2:c.158C>G	chr11.hg19:g.18057649G>C	ENSP00000250018:p.Ser53*	51.0	0.0		58.0	13.0	NM_004179	D3DQX6|O95188|O95189|Q16736|Q3KPG8	Nonsense_Mutation	SNP	ENST00000250018.2	hg19	CCDS7829.1	.	.	.	.	.	.	.	.	.	.	G	36	5.857374	0.97030	.	.	ENSG00000129167	ENST00000250018;ENST00000341556;ENST00000528338	.	.	.	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	-14.2116	19.7758	0.96391	0.0:0.0:1.0:0.0	.	.	.	.	X	53;53;63	.	ENSP00000250018:S53X	S	-	2	0	TPH1	18014225	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.768000	0.98965	2.752000	0.94435	0.655000	0.94253	TCA	.	.		0.348	TPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389696.1	NM_004179		C	18057649	G	C	18057649	4	2	237	1	0	0	0	0	0	1	0	0	16416	1294	45	4	1212	4	TPH1	11	18057649	Nonsense_Mutation	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	8875241	18057649	116948867	124	33030										
SAA1	6288	hgsc.bcm.edu	37	chr11	18291314	18291315	+	Frame_Shift_Ins	INS	-	-	A													0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ggccatggtgcggaggactcINSgctggctgatcaggctgcca					rs11545465|rs150951768		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:18291314_18291315insA	ENST00000405158.2	+	4	465_466	c.281_282insA	c.(280-285)tcgctgfs	p.L95fs	SAA1_ENST00000356524.4_Frame_Shift_Ins_p.L95fs|SAA1_ENST00000532858.1_Frame_Shift_Ins_p.L95fs	NM_000331.4	NP_000322	P0DJI8	SAA1_HUMAN	serum amyloid A1	95					acute-phase response (GO:0006953)|innate immune response (GO:0045087)|lymphocyte chemotaxis (GO:0048247)|macrophage chemotaxis (GO:0048246)|negative regulation of inflammatory response (GO:0050728)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of interleukin-1 secretion (GO:0050716)|regulation of protein secretion (GO:0050708)	endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)	G-protein coupled receptor binding (GO:0001664)|heparin binding (GO:0008201)			endometrium(1)|large_intestine(3)|lung(2)|stomach(3)	9					Human Serum Albumin(DB00062)|Serum albumin iodonated(DB00064)	GCGGAGGACTCGCTGGCTGATC	0.525																																					p.S94fs		Atlas-INDEL	.											.	SAA1	14	.	0			c.281_282insA						.																																			SO:0001589	frameshift_variant	6288	exon4			.	M10906	CCDS7835.1	11p15.1	2014-01-30			ENSG00000173432	ENSG00000173432		"Endogenous ligands"	10513	protein-coding gene	gene with protein product		104750		SAA		2595451, 9305847	Standard	NM_199161		Approved	PIG4, TP53I4	uc021qeo.1	P0DJI8	OTTHUMG00000166147	Exception_encountered	chr11.hg19:g.18291314_18291315insA	ENSP00000384906:p.Leu95fs	257.0	0.0		290.0	97.0	NM_199161	P02735|P02736|P02737|Q16730|Q16834|Q16835|Q16879|Q3KRB3|Q6FG67|Q96QN0|Q9UCK9|Q9UCL0	Frame_Shift_Ins	INS	ENST00000405158.2	hg19	CCDS7835.1																																																																																			.	.		0.525	SAA1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395864.1	NM_199161		A	18291315	-	A	18291314	7	5	237	1	0	1	1	0	0	0	0	0	13813	893	31	0	291	0	SAA1	11	18291314	Frame_Shift_Ins	INS	-	TCGA-ED-A459-01A-11D-A25V-10	233665	18291314	116715202	125	33031										
METT5D1	196074	hgsc.bcm.edu	37	chr11	28135039	28135039	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ggagcaaacagatcaaactcAagcccaggagttacacagat	9	10	2	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:28135039A>C	ENST00000407364.3	+	3	510	c.158A>C	c.(157-159)cAa>cCa	p.Q53P	METTL15_ENST00000403099.1_Missense_Mutation_p.Q53P|METTL15_ENST00000379199.2_Missense_Mutation_p.Q53P|METTL15_ENST00000342303.5_Missense_Mutation_p.Q53P|METTL15_ENST00000303459.6_Missense_Mutation_p.Q53P|METTL15_ENST00000406787.3_Missense_Mutation_p.Q53P			A6NJ78	MET15_HUMAN	methyltransferase like 15	53							methyltransferase activity (GO:0008168)			NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	14						GATCAAACTCAAGCCCAGGAG	0.383																																					p.Q53P		Atlas-SNP	.											.	METTL15	63	.	0			c.A158C						.						58	65	62					11																	28135039		2202	4299	6501	SO:0001583	missense	196074	exon3			AAACTCAAGCCCA	AL832668	CCDS31450.1, CCDS44559.1, CCDS73269.1	11p14.1	2011-03-02	2011-03-02	2011-03-02	ENSG00000169519	ENSG00000169519			26606	protein-coding gene	gene with protein product			"methyltransferase 5 domain containing 1"	METT5D1		12477932	Standard	NM_152636		Approved	FLJ33979	uc001msh.2	A6NJ78	OTTHUMG00000150448	ENST00000407364.3:c.158A>C	chr11.hg19:g.28135039A>C	ENSP00000384369:p.Gln53Pro	124.0	0.0		152.0	53.0	NM_152636	A8MRS5|B7WNU2|Q3MHD3|Q8N601|Q8NBA7	Missense_Mutation	SNP	ENST00000407364.3	hg19	CCDS44559.1	.	.	.	.	.	.	.	.	.	.	A	5.952	0.359640	0.11239	.	.	ENSG00000169519	ENST00000406787;ENST00000342303;ENST00000403099;ENST00000407364;ENST00000379199;ENST00000303459	T;T;T;T;T;T	0.45668	1.48;1.51;0.9;1.93;0.89;1.51	5.68	-3.3	0.05003	.	0.857111	0.10391	N	0.680392	T	0.24547	0.0595	N	0.22421	0.69	0.09310	N	1	B;B;P	0.38420	0.022;0.34;0.63	B;B;B	0.31495	0.019;0.093;0.131	T	0.08722	-1.0708	10	0.46703	T	0.11	.	12.8532	0.57869	0.6363:0.0:0.3637:0.0	.	53;53;53	A6NJ78;A6NJ78-2;A6NJ78-4	MET15_HUMAN;.;.	P	53	ENSP00000385507:Q53P;ENSP00000342259:Q53P;ENSP00000385860:Q53P;ENSP00000384369:Q53P;ENSP00000368497:Q53P;ENSP00000307251:Q53P	ENSP00000307251:Q53P	Q	+	2	0	METTL15	28091615	0.202000	0.23423	0.000000	0.03702	0.105000	0.19272	0.241000	0.18065	-0.559000	0.06110	-0.353000	0.07706	CAA	.	.		0.383	METTL15-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318135.2	NM_152636		C	28135039	A	C	28135039	3	2	237	1	0	0	0	0	1	0	0	0	9501	130	5	5	160	5	METT5D1	11	28135039	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	9843725	28135039	106871477	126	33032										
PATL1	219988	hgsc.bcm.edu	37	chr11	59420493	59420493	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	attgagattccgatgctgacTgaaaaacatacaccacattc	6	10	0	3			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:59420493T>A	ENST00000300146.9	-	10	1206		c.e10-2			NM_152716.2	NP_689929.2	Q86TB9	PATL1_HUMAN	protein associated with topoisomerase II homolog 1 (yeast)						cytoplasmic mRNA processing body assembly (GO:0033962)|deadenylation-dependent decapping of nuclear-transcribed mRNA (GO:0000290)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(2)|lung(5)|ovary(1)|prostate(2)	11						CGATGCTGACTGAAAAACATA	0.393																																					.		Atlas-SNP	.											.	PATL1	92	.	0			c.1122-2A>T						.						154	142	146					11																	59420493		1900	4126	6026	SO:0001630	splice_region_variant	219988	exon11			GCTGACTGAAAAA	AK094193	CCDS44613.1	11q12.1	2012-06-07	2007-10-18		ENSG00000166889	ENSG00000166889			26721	protein-coding gene	gene with protein product		614660				17936923	Standard	NM_152716		Approved	FLJ36874, Pat1b	uc001noe.4	Q86TB9	OTTHUMG00000167423	ENST00000300146.9:c.1122-2A>T	chr11.hg19:g.59420493T>A		92.0	0.0		117.0	12.0	NM_152716	B3KXT9|Q2TA86|Q6P166|Q8N9M6|Q8NI63	Splice_Site	SNP	ENST00000300146.9	hg19	CCDS44613.1	.	.	.	.	.	.	.	.	.	.	T	19.09	3.760179	0.69763	.	.	ENSG00000166889	ENST00000300146;ENST00000428532	.	.	.	5.14	5.14	0.70334	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.9127	0.70770	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	PATL1	59177069	1.000000	0.71417	0.996000	0.52242	0.954000	0.61252	4.008000	0.57103	2.073000	0.62155	0.482000	0.46254	.	.	.		0.393	PATL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394559.1	NM_152716	Intron	A	59420493	T	A	59420493	5	1	237	1	0	0	0	0	0	0	1	0	11484	1594	55	4	1232	4	PATL1	11	59420493	Splice_Site	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	31285454	59420493	75586023	127	33033										
MS4A2	2206	hgsc.bcm.edu	37	chr11	59857913	59857913	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gacattttttcatcatttaaAgcaggttatccattctgggg	8	7	3	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:59857913A>T	ENST00000278888.3	+	3	393	c.291A>T	c.(289-291)aaA>aaT	p.K97N		NM_000139.4	NP_000130.1	Q01362	FCERB_HUMAN	membrane-spanning 4-domains, subfamily A, member 2	97					activation of phospholipase C activity (GO:0007202)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of mast cell degranulation (GO:0043306)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|Fc-epsilon receptor I complex (GO:0032998)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(4)|lung(9)|ovary(1)|upper_aerodigestive_tract(2)	17		all_epithelial(135;0.245)			Omalizumab(DB00043)	CATCATTTAAAGCAGGTTATC	0.348																																					p.K97N		Atlas-SNP	.											.	MS4A2	41	.	0			c.A291T						.						173	166	169					11																	59857913		2200	4294	6494	SO:0001583	missense	2206	exon3			ATTTAAAGCAGGT	M89796	CCDS7980.1, CCDS73292.1	11q12-q13	2012-02-28	2012-02-28		ENSG00000149534	ENSG00000149534			7316	protein-coding gene	gene with protein product	"Fc fragment of IgE, high affinity I, receptor for; beta polypeptide"	147138	"IgE responsiveness (atopic)", "membrane-spanning 4-domains, subfamily A, member 2 (Fc fragment of IgE, high affinity I, receptor for; beta polypeptide)"	FCER1B, IGER, APY		1386024	Standard	NM_000139		Approved	MS4A1	uc001nop.3	Q01362	OTTHUMG00000167239	ENST00000278888.3:c.291A>T	chr11.hg19:g.59857913A>T	ENSP00000278888:p.Lys97Asn	43.0	0.0		50.0	9.0	NM_000139	Q54A81	Missense_Mutation	SNP	ENST00000278888.3	hg19	CCDS7980.1	.	.	.	.	.	.	.	.	.	.	A	15.75	2.927106	0.52759	.	.	ENSG00000149534	ENST00000278888	T	0.02446	4.29	4.68	-0.461	0.12172	.	2.377010	0.01012	N	0.003859	T	0.04137	0.0115	M	0.68317	2.08	0.09310	N	1	B;B	0.33280	0.405;0.031	B;B	0.33254	0.16;0.078	T	0.41858	-0.9485	10	0.21014	T	0.42	-7.1959	1.106	0.01693	0.4213:0.1667:0.0906:0.3214	.	27;97	Q14298;Q01362	.;FCERB_HUMAN	N	97	ENSP00000278888:K97N	ENSP00000278888:K97N	K	+	3	2	MS4A2	59614489	0.038000	0.19896	0.000000	0.03702	0.986000	0.74619	0.199000	0.17237	-0.078000	0.12730	0.528000	0.53228	AAA	.	.		0.348	MS4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393844.1			T	59857913	A	T	59857913	3	4	237	1	0	0	0	0	1	0	0	0	9869	69	3	4	301	4	MS4A2	11	59857913	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	437420	59857913	75148603	128	33034										
CD6	923	hgsc.bcm.edu	37	chr11	60777231	60777231	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gggctgccccactccttgtcCggcaggatgtactactcatg	11	14	1	0	rs150066453		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:60777231C>G	ENST00000313421.7	+	5	1155	c.969C>G	c.(967-969)tcC>tcG	p.S323S	CD6_ENST00000452451.2_Silent_p.S323S|CD6_ENST00000346437.4_Silent_p.S323S|CD6_ENST00000352009.5_Silent_p.S323S|CD6_ENST00000344028.5_Silent_p.S323S|CD6_ENST00000545105.1_Intron	NM_006725.4	NP_006716.3	P30203	CD6_HUMAN	CD6 molecule	323	SRCR 3. {ECO:0000255|PROSITE- ProRule:PRU00196}.				cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	scavenger receptor activity (GO:0005044)			endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)	18						ACTCCTTGTCCGGCAGGATGT	0.612																																					p.S323S	Pancreas(169;904 2017 4767 38890 42505)	Atlas-SNP	.											.	CD6	122	.	0			c.C969G						.						75	68	70					11																	60777231		2203	4299	6502	SO:0001819	synonymous_variant	923	exon5			CTTGTCCGGCAGG		CCDS7999.1, CCDS58137.1, CCDS58138.1	11q12.2	2006-03-28	2006-03-28		ENSG00000013725	ENSG00000013725		"CD molecules"	1691	protein-coding gene	gene with protein product		186720	"CD6 antigen"			9013954	Standard	NM_006725		Approved	Tp120	uc001nqq.3	P30203	OTTHUMG00000167823	ENST00000313421.7:c.969C>G	chr11.hg19:g.60777231C>G		120.0	0.0		127.0	39.0	NM_006725	A4KAD4|A4KAD5|Q9UMF2|Q9Y4K7|Q9Y4K8|Q9Y4K9|Q9Y4L0	Silent	SNP	ENST00000313421.7	hg19	CCDS7999.1																																																																																			.	C|1.000;T|0.000		0.612	CD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396449.1	NM_006725		G	60777231	C	G	60777231	2	3	237	1	0	0	0	0	0	0	0	1	3030	639	23	4		4	CD6	11	60777231	Silent	SNP	C	TCGA-ED-A459-01A-11D-A25V-10	919318	60777231	74229285	129	33035										
VWCE	220001	hgsc.bcm.edu	37	chr11	61026645	61026645	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tgaagcaccggcctcgagggTgatgctgtcgggggcccagg	18	11	0	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:61026645T>A	ENST00000335613.5	-	20	2756	c.2370A>T	c.(2368-2370)tcA>tcT	p.S790S	VWCE_ENST00000535710.1_Silent_p.S255S	NM_152718.2	NP_689931.2	Q96DN2	VWCE_HUMAN	von Willebrand factor C and EGF domains	790						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37						GCCTCGAGGGTGATGCTGTCG	0.562																																					p.S790S		Atlas-SNP	.											.	VWCE	84	.	0			c.A2370T						.						41	43	42					11																	61026645		2203	4299	6502	SO:0001819	synonymous_variant	220001	exon20			CGAGGGTGATGCT	AK056571	CCDS8002.1	11q12.2	2006-08-04			ENSG00000167992	ENSG00000167992			26487	protein-coding gene	gene with protein product		611115				12869306	Standard	NM_152718		Approved	URG11, FLJ32009, VWC1	uc001nra.3	Q96DN2	OTTHUMG00000168208	ENST00000335613.5:c.2370A>T	chr11.hg19:g.61026645T>A		112.0	0.0		145.0	8.0	NM_152718	A5PKV0|Q7Z7L6|Q86WK8	Silent	SNP	ENST00000335613.5	hg19	CCDS8002.1																																																																																			.	.		0.562	VWCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398811.1	NM_152718		A	61026645	T	A	61026645	2	1	237	1	0	0	0	0	0	0	0	1	17260	1683	59	4		4	VWCE	11	61026645	Silent	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	249414	61026645	73979871	130	33036										
PLCB3	5331	hgsc.bcm.edu	37	chr11	64023034	64023034	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	atcctgaagatgttctcagcAgacaagaagcgggtggagac	13	8	1	5			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:64023034A>T	ENST00000540288.1	+	7	646	c.543A>T	c.(541-543)gcA>gcT	p.A181A	PLCB3_ENST00000325234.5_Silent_p.A114A|PLCB3_ENST00000279230.6_Silent_p.A181A	NM_000932.2	NP_000923.1	Q01970	PLCB3_HUMAN	phospholipase C, beta 3 (phosphatidylinositol-specific)	181					inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|regulation of systemic arterial blood pressure (GO:0003073)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|urinary_tract(1)	33						TGTTCTCAGCAGACAAGAAGC	0.622																																					p.A181A		Atlas-SNP	.											.	PLCB3	103	.	0			c.A543T						.						108	106	107					11																	64023034		2201	4297	6498	SO:0001819	synonymous_variant	5331	exon7			CTCAGCAGACAAG	Z26649	CCDS8064.1, CCDS53654.1	11q13	2008-03-18			ENSG00000149782	ENSG00000149782	3.1.4.11		9056	protein-coding gene	gene with protein product		600230				7849701	Standard	NM_000932		Approved		uc009ypg.2	Q01970	OTTHUMG00000167816	ENST00000540288.1:c.543A>T	chr11.hg19:g.64023034A>T		134.0	0.0		136.0	7.0	NM_000932	A5PKZ6|G5E960|Q8N1A4	Silent	SNP	ENST00000540288.1	hg19	CCDS8064.1																																																																																			.	.		0.622	PLCB3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396405.1			T	64023034	A	T	64023034	2	4	237	1	0	0	0	0	0	0	0	1	12038	175	7	4		4	PLCB3	11	64023034	Silent	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	2996389	64023034	70983482	131	33037										
SLC22A12	116085	hgsc.bcm.edu	37	chr11	64366298	64366298	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	aggtcttgctttcagccatgCgggaggagctgagcatgggc	16	9	2	1	rs150255373		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:64366298C>A	ENST00000377574.1	+	6	1720	c.973C>A	c.(973-975)Cgg>Agg	p.R325R	SLC22A12_ENST00000336464.7_Silent_p.R291R|SLC22A12_ENST00000377567.2_Silent_p.R217R|SLC22A12_ENST00000377572.1_Silent_p.R217R|SLC22A12_ENST00000473690.1_Silent_p.R104R	NM_144585.2	NP_653186.2	Q96S37	S22AC_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 12	325			Missing (affects urate transport). {ECO:0000269|PubMed:15327384}.		cellular homeostasis (GO:0019725)|response to drug (GO:0042493)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|urate transmembrane transporter activity (GO:0015143)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27					Losartan(DB00678)|Probenecid(DB01032)	TTCAGCCATGCGGGAGGAGCT	0.662																																					p.R325R		Atlas-SNP	.											.	SLC22A12	68	.	0			c.C973A						.						33	32	32					11																	64366298		2201	4296	6497	SO:0001819	synonymous_variant	116085	exon6			GCCATGCGGGAGG	AB071863	CCDS8075.1, CCDS60835.1, CCDS60836.1	11q13.1	2013-05-22	2008-01-11		ENSG00000197891	ENSG00000197891		"Solute carriers"	17989	protein-coding gene	gene with protein product		607096	"solute carrier family 22 (organic anion/cation transporter), member 12"			12024214	Standard	NM_144585		Approved	OAT4L, RST, URAT1	uc009yps.2	Q96S37	OTTHUMG00000045213	ENST00000377574.1:c.973C>A	chr11.hg19:g.64366298C>A		46.0	0.0		34.0	19.0	NM_144585	B7WPG1|G3XAN7|Q19PF7|Q19PF8|Q19PF9|Q19PG0|Q6UXW3|Q96DT2	Silent	SNP	ENST00000377574.1	hg19	CCDS8075.1																																																																																			.	C|1.000;T|0.000		0.662	SLC22A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104966.2	NM_144585		A	64366298	C	A	64366298	2	1	237	1	0	0	0	0	0	0	0	1	14458	759	27	1		1	SLC22A12	11	64366298	Silent	SNP	C	TCGA-ED-A459-01A-11D-A25V-10	343264	64366298	70640218	132	33038										
FAU	740	hgsc.bcm.edu	37	chr11	64888161	64888161	+	5'Flank	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	attacaaaagacttaagagtTggcattggggcccttcttct	9	8	2	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:64888161T>A	ENST00000279242.2	+	0	0				FAU_ENST00000531743.1_Missense_Mutation_p.N132Y|MRPL49_ENST00000534078.1_5'Flank|FAU_ENST00000529639.1_Missense_Mutation_p.N132Y|FAU_ENST00000279259.3_3'UTR|FAU_ENST00000527548.1_Missense_Mutation_p.N132Y|MRPL49_ENST00000526171.1_5'Flank|ZNHIT2_ENST00000310597.4_5'Flank|MRPL49_ENST00000531705.1_5'Flank|FAU_ENST00000525297.1_Missense_Mutation_p.N97Y	NM_004927.3	NP_004918.1	Q13405	RM49_HUMAN	mitochondrial ribosomal protein L49						translation (GO:0006412)	mitochondrial ribosome (GO:0005761)	structural constituent of ribosome (GO:0003735)			endometrium(1)|ovary(1)	2						ACTTAAGAGTTGGCATTGGGG	0.478																																					p.N132Y		Atlas-SNP	.											.	FAU	17	.	0			c.A394T						.						61	68	66					11																	64888161		2201	4297	6498	SO:0001631	upstream_gene_variant	2197	exon5			AAGAGTTGGCATT		CCDS8096.1	11q13.1	2012-11-14	2001-10-16	2001-10-19	ENSG00000149792	ENSG00000149792		"Mitochondrial ribosomal proteins / large subunits"	1176	protein-coding gene	gene with protein product	"neighbor of FAU", "next to FAU"	606866	"chromosome 11 open reading frame 4"	C11orf4		8786148	Standard	NM_004927		Approved	NOF, NOF1, L49mt	uc001oda.2	Q13405	OTTHUMG00000165608		chr11.hg19:g.64888161T>A	Exception_encountered	118.0	0.0		137.0	7.0	NM_001997	B2R4G6	Missense_Mutation	SNP	ENST00000279242.2	hg19	CCDS8096.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.557611	0.86231	.	.	ENSG00000149806	ENST00000529639;ENST00000531743;ENST00000525297;ENST00000527548	T;T;T;T	0.46819	0.86;0.86;0.86;0.86	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.62514	0.2434	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.66732	-0.5849	7	0.87932	D	0	.	13.4889	0.61382	0.0:0.0:0.0:1.0	.	.	.	.	Y	132;132;97;132	ENSP00000435370:N132Y;ENSP00000431822:N132Y;ENSP00000436110:N97Y;ENSP00000434440:N132Y	ENSP00000436110:N97Y	N	-	1	0	FAU	64644737	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	7.771000	0.85420	2.090000	0.63153	0.533000	0.62120	AAC	.	.		0.478	MRPL49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385293.1	NM_004927		A	64888161	T	A	64888161	1	1	237	0	1	0	0	0	0	0	0	0	5702	1812	63	4		4	FAU	11	64888161	5'Flank	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	521863	64888161	70118355	133	33039										
SPDYC	387778	hgsc.bcm.edu	37	chr11	64939933	64939933	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	caaacgacatggaggaggacCtggagggccccaaatgtgag	15	9	0	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:64939933C>T	ENST00000377185.2	+	5	455	c.373C>T	c.(373-375)Ctg>Ttg	p.L125L	AP003068.18_ENST00000534819.1_RNA	NM_001008778.1	NP_001008778.1			speedy/RINGO cell cycle regulator family member C											breast(1)|endometrium(3)|large_intestine(2)|lung(9)|prostate(1)	16						GGAGGAGGACCTGGAGGGCCC	0.552																																					p.L125L		Atlas-SNP	.											.	SPDYC	31	.	0			c.C373T						.						116	119	118					11																	64939933		2201	4297	6498	SO:0001819	synonymous_variant	387778	exon5			GAGGACCTGGAGG	AY820305	CCDS31606.1	11q13.1	2013-05-08	2013-05-08		ENSG00000204710	ENSG00000204710		"Speedy homologs"	32681	protein-coding gene	gene with protein product		614030	"speedy homolog C (Xenopus laevis)"			15611625	Standard	NM_001008778		Approved	Ringo2	uc010rnz.2	Q5MJ68	OTTHUMG00000165611	ENST00000377185.2:c.373C>T	chr11.hg19:g.64939933C>T		206.0	0.0		263.0	17.0	NM_001008778		Silent	SNP	ENST00000377185.2	hg19	CCDS31606.1																																																																																			.	.		0.552	SPDYC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385299.1	NM_001008778		T	64939933	C	T	64939933	2	4	237	1	0	0	0	0	0	0	0	1	15043	680	24	3		3	SPDYC	11	64939933	Silent	SNP	C	TCGA-ED-A459-01A-11D-A25V-10	51772	64939933	70066583	134	33040										
TSKU	25987	hgsc.bcm.edu	37	chr11	76506948	76506950	+	In_Frame_Del	DEL	CAC	CAC	-													0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gatctcagccacaacctgctCaccagcatctcacccactgc					rs542831459		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	CAC	CAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:76506948_76506950delCAC	ENST00000527881.1	+	2	1314_1316	c.288_290delCAC	c.(286-291)ctcacc>ctc	p.T97del	TSKU_ENST00000333090.4_In_Frame_Del_p.T97del			Q8WUA8	TSK_HUMAN	tsukushi, small leucine rich proteoglycan	97					anterior commissure morphogenesis (GO:0021960)|ciliary body morphogenesis (GO:0061073)|corpus callosum morphogenesis (GO:0021540)|lateral ventricle development (GO:0021670)|negative regulation of Wnt signaling pathway (GO:0030178)|regulation of gene expression (GO:0010468)	extracellular space (GO:0005615)				NS(1)|large_intestine(4)|lung(6)|urinary_tract(1)	12	Ovarian(111;0.112)					ACAACCTGCTCACCAGCATCTCA	0.631																																					p.96_97del		Atlas-Indel,Pindel	.											.	TSKU	26	.	0			c.287_289del						.																																			SO:0001651	inframe_deletion	25987	exon2			.	AK075476	CCDS8246.1	11q13.5	2012-12-05	2012-12-05	2006-11-21	ENSG00000182704	ENSG00000182704			28850	protein-coding gene	gene with protein product		608015	"leucine rich repeat containing 54", "tsukushin", "tsukushi small leucine rich proteoglycan homolog (Xenopus laevis)"	LRRC54		11085516, 19710929, 22880013	Standard	NM_001258210		Approved	E2IG4, TSK	uc031qcw.1	Q8WUA8		ENST00000527881.1:c.288_290delCAC	chr11.hg19:g.76506948_76506950delCAC	ENSP00000434847:p.Thr97del	212.0	0.0		211.0	22.0	NM_001258210	B3KQT7|Q6UXK1|Q9UG10|Q9UJX9	In_Frame_Del	DEL	ENST00000527881.1	hg19	CCDS8246.1																																																																																			.	.		0.631	TSKU-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382871.1	NM_015516		-	76506950	CAC	-	76506948	7	5	237	1	0	1	0	1	0	0	0	0	16642	813	29	0	290	0	TSKU	11	76506948	In_Frame_Del	DEL	CAC	TCGA-ED-A459-01A-11D-A25V-10	11567015	76506948	58499568	135	33041										
TAF1D	79101	hgsc.bcm.edu	37	chr11	93471382	93471382	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tttcttcttatctattagtgAgtatataggatttctccttc	5	7	4	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:93471382A>G	ENST00000448108.2	-	3	1002	c.352T>C	c.(352-354)Tca>Cca	p.S118P	TAF1D_ENST00000546088.1_5'Flank|SNORA40_ENST00000388090.1_RNA	NM_024116.3	NP_077021.1	Q9H5J8	TAF1D_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, D, 41kDa	118					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	microtubule organizing center (GO:0005815)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			large_intestine(1)|lung(3)|prostate(1)|skin(2)	7						TCTATTAGTGAGTATATAGGA	0.368																																					p.S118P		Atlas-SNP	.											.	TAF1D	18	.	0			c.T352C						.						146	151	149					11																	93471382		2201	4298	6499	SO:0001583	missense	79101	exon3			TTAGTGAGTATAT		CCDS8293.1	11q21	2012-05-30	2008-09-30	2008-09-30	ENSG00000166012	ENSG00000166012			28759	protein-coding gene	gene with protein product		612823	"Josephin domain containing 3"	JOSD3		15520167, 17318177	Standard	NM_024116		Approved	MGC5306, TAF(I)41	uc001pec.3	Q9H5J8	OTTHUMG00000167451	ENST00000448108.2:c.352T>C	chr11.hg19:g.93471382A>G	ENSP00000410409:p.Ser118Pro	31.0	0.0		22.0	8.0	NM_024116	Q6I9Y6	Missense_Mutation	SNP	ENST00000448108.2	hg19	CCDS8293.1	.	.	.	.	.	.	.	.	.	.	A	8.461	0.855386	0.17106	.	.	ENSG00000166012	ENST00000448108	.	.	.	5.25	2.92	0.33932	.	0.431966	0.21800	N	0.068940	T	0.34890	0.0913	L	0.52364	1.645	0.09310	N	0.999999	B	0.31769	0.339	B	0.33620	0.167	T	0.33929	-0.9849	9	0.87932	D	0	-14.656	6.3122	0.21171	0.8063:0.0:0.1937:0.0	.	118	Q9H5J8	TAF1D_HUMAN	P	118	.	ENSP00000314971:S118P	S	-	1	0	TAF1D	93111030	0.675000	0.27558	0.026000	0.17262	0.002000	0.02628	2.391000	0.44424	0.938000	0.37419	0.528000	0.53228	TCA	.	.		0.368	TAF1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394662.2	NM_024116		G	93471382	A	G	93471382	3	3	237	1	0	0	0	0	1	0	0	0	15537	304	11	2	500	2	TAF1D	11	93471382	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	16964434	93471382	41535134	136	33042										
KIAA1377	57562	hgsc.bcm.edu	37	chr11	101834387	101834387	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	cctagtcactgtgataccatCactgccatcatattgttctt	5	12	4	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:101834387C>T	ENST00000263468.8	+	6	2891	c.2621C>T	c.(2620-2622)tCa>tTa	p.S874L	KIAA1377_ENST00000537689.1_Missense_Mutation_p.S675L	NM_020802.2	NP_065853.2	Q9P2H0	K1377_HUMAN	KIAA1377	874										breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(18)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	53	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)		GTGATACCATCACTGCCATCA	0.413																																					p.S874L		Atlas-SNP	.											.	KIAA1377	111	.	0			c.C2621T						.						96	84	88					11																	101834387		2203	4299	6502	SO:0001583	missense	57562	exon6			TACCATCACTGCC	AK095004	CCDS31658.1	11q22.2	2006-02-03			ENSG00000110318	ENSG00000110318			29264	protein-coding gene	gene with protein product		614634				10718198	Standard	XM_005271627		Approved		uc001pgm.3	Q9P2H0	OTTHUMG00000167319	ENST00000263468.8:c.2621C>T	chr11.hg19:g.101834387C>T	ENSP00000263468:p.Ser874Leu	127.0	0.0		183.0	55.0	NM_020802	Q4G0U6	Missense_Mutation	SNP	ENST00000263468.8	hg19	CCDS31658.1	.	.	.	.	.	.	.	.	.	.	C	8.758	0.922990	0.18056	.	.	ENSG00000110318	ENST00000263468;ENST00000537689	T;T	0.10382	2.88;2.88	5.77	3.89	0.44902	.	0.501227	0.20139	N	0.098412	T	0.13286	0.0322	M	0.64997	1.995	0.09310	N	1	B	0.27351	0.176	B	0.26202	0.067	T	0.10847	-1.0612	10	0.51188	T	0.08	-6.3323	11.2068	0.48773	0.0:0.8529:0.0:0.1471	.	874	Q9P2H0	K1377_HUMAN	L	874;675	ENSP00000263468:S874L;ENSP00000443184:S675L	ENSP00000263468:S874L	S	+	2	0	KIAA1377	101339597	0.004000	0.15560	0.017000	0.16124	0.030000	0.12068	1.924000	0.40065	1.582000	0.49881	0.655000	0.94253	TCA	.	.		0.413	KIAA1377-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394140.1	NM_020802		T	101834387	C	T	101834387	3	4	237	1	0	0	0	0	1	0	0	0	8236	838	29	3	2643	3	KIAA1377	11	101834387	Missense_Mutation	SNP	C	TCGA-ED-A459-01A-11D-A25V-10	8363005	101834387	33172129	137	33043										
IL10RA	3587	hgsc.bcm.edu	37	chr11	117869879	117869879	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ggggacacacagggtggctcGgccttgggccaccacagtcc	15	14	0	0	rs199604463	byFrequency	TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:117869879G>T	ENST00000227752.3	+	7	1380	c.1260G>T	c.(1258-1260)tcG>tcT	p.S420S	IL10RA_ENST00000533700.1_3'UTR|IL10RA_ENST00000541785.1_Silent_p.S400S|IL10RA_ENST00000545409.1_Silent_p.S271S	NM_001558.3	NP_001549.2	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha	420			S -> L (in dbSNP:rs2229114). {ECO:0000269|Ref.2}.		cytokine-mediated signaling pathway (GO:0019221)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-10 receptor activity (GO:0004920)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(2)|prostate(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.07e-05)|Epithelial(105;0.00108)		AGGGTGGCTCGGCCTTGGGCC	0.627																																					p.S420S		Atlas-SNP	.											.	IL10RA	46	.	0			c.G1260T						.						48	51	50					11																	117869879		2200	4296	6496	SO:0001819	synonymous_variant	3587	exon7			TGGCTCGGCCTTG	U00672	CCDS8388.1	11q23	2014-09-17			ENSG00000110324	ENSG00000110324		"Interleukins and interleukin receptors", "CD molecules"	5964	protein-coding gene	gene with protein product		146933		IL10R		8120391	Standard	NR_026691		Approved	HIL-10R, CDW210A, CD210a, CD210	uc001prv.3	Q13651	OTTHUMG00000166523	ENST00000227752.3:c.1260G>T	chr11.hg19:g.117869879G>T		130.0	0.0		126.0	42.0	NM_001558	A8K6I0|B0YJ27	Silent	SNP	ENST00000227752.3	hg19	CCDS8388.1																																																																																			.	G|1.000;A|0.000		0.627	IL10RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390167.1			T	117869879	G	T	117869879	2	4	237	1	0	0	0	0	0	0	0	1	7629	1103	39	1		1	IL10RA	11	117869879	Silent	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	16035492	117869879	17136637	138	33044										
ITFG2	55846	hgsc.bcm.edu	37	chr12	2927434	2927434	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	acaccaaggtcatgctgatcAgcgacatcggtgggcatgcc	12	12	2	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:2927434A>T	ENST00000228799.2	+	4	536	c.397A>T	c.(397-399)Agc>Tgc	p.S133C	ITFG2_ENST00000419778.2_Intron|ITFG2_ENST00000542548.1_5'UTR	NM_018463.3	NP_060933.3	Q969R8	ITFG2_HUMAN	integrin alpha FG-GAP repeat containing 2	133					germinal center B cell differentiation (GO:0002314)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)				central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(13)|upper_aerodigestive_tract(2)	19			OV - Ovarian serous cystadenocarcinoma(31;0.000818)			CATGCTGATCAGCGACATCGG	0.557																																					p.S133C		Atlas-SNP	.											.	ITFG2	38	.	0			c.A397T						.						155	117	130					12																	2927434		2203	4300	6503	SO:0001583	missense	55846	exon4			CTGATCAGCGACA	AF220048	CCDS8513.1	12p13.33	2006-11-29		2006-07-25	ENSG00000111203	ENSG00000111203			30879	protein-coding gene	gene with protein product						12477932	Standard	NM_018463		Approved	MDS028	uc001qlb.2	Q969R8	OTTHUMG00000130617	ENST00000228799.2:c.397A>T	chr12.hg19:g.2927434A>T	ENSP00000228799:p.Ser133Cys	142.0	0.0		144.0	54.0	NM_018463	A8K4Z5|D3DUQ2|Q6PKU5|Q96SX6	Missense_Mutation	SNP	ENST00000228799.2	hg19	CCDS8513.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.447864	0.84101	.	.	ENSG00000111203	ENST00000228799	T	0.71461	-0.57	4.69	3.55	0.40652	.	0.039659	0.85682	D	0.000000	T	0.75376	0.3841	M	0.77820	2.39	0.80722	D	1	D;D	0.56287	0.975;0.975	P;P	0.50659	0.594;0.647	T	0.76583	-0.2906	10	0.66056	D	0.02	-21.1302	9.4155	0.38519	0.9158:0.0:0.0842:0.0	.	133;133	Q969R8;Q6PKU5	ITFG2_HUMAN;.	C	133	ENSP00000228799:S133C	ENSP00000228799:S133C	S	+	1	0	ITFG2	2797695	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.080000	0.64437	0.830000	0.34757	0.533000	0.62120	AGC	.	.		0.557	ITFG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253091.1	NM_018463		T	2927434	A	T	2927434	3	4	237	1	0	0	0	0	1	0	0	0	7879	188	7	4	411	4	ITFG2	12	2927434	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10		2927434	130924461	139	33045										
PRH1	5554	hgsc.bcm.edu	37	chr12	11036772	11036772	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ccttcatttaaatcctgagcTgagctgaaggccagcagggc	11	11	1	3			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:11036772T>A	ENST00000428168.2	-	1	82	c.45A>T	c.(43-45)tcA>tcT	p.S15S	PRR4_ENST00000536668.1_5'UTR	NM_006250.3	NP_006241.2	P02810	PRPC_HUMAN	proline-rich protein HaeIII subfamily 1	15						extracellular space (GO:0005615)				endometrium(1)|kidney(1)|lung(2)|upper_aerodigestive_tract(1)	5				BRCA - Breast invasive adenocarcinoma(232;0.245)		AATCCTGAGCTGAGCTGAAGG	0.493																																					p.S15S		Atlas-SNP	.											.	PRH1	17	.	0			c.A45T						.						80	79	80					12																	11036772		2203	4300	6503	SO:0001819	synonymous_variant	5554	exon1			CTGAGCTGAGCTG			12p13.2	2013-05-10			ENSG00000231887	ENSG00000231887			9366	protein-coding gene	gene with protein product		168730				3009472	Standard	NM_001291314		Approved	Pa	uc021qvf.1	P02810		ENST00000428168.2:c.45A>T	chr12.hg19:g.11036772T>A		214.0	0.0		218.0	15.0	NM_006250	A2VCM0|A3KN66|A5D902|B2RMW2|Q4VBP2|Q53XA2|Q6P2F6	Silent	SNP	ENST00000428168.2	hg19																																																																																				.	.		0.493	PRH1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_006250		A	11036772	T	A	11036772	2	1	237	1	0	0	0	0	0	0	0	1	12494	1567	55	4		4	PRH1	12	11036772	Silent	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	8109338	11036772	122815123	140	33046										
NELL2	4753	hgsc.bcm.edu	37	chr12	44913954	44913954	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	agcactcattctctgggagaAtgctgaattcacactccaca	7	12	3	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:44913954A>T	ENST00000429094.2	-	19	2738	c.2234T>A	c.(2233-2235)aTt>aAt	p.I745N	NELL2_ENST00000452445.2_Missense_Mutation_p.I745N|NELL2_ENST00000333837.4_Missense_Mutation_p.I768N|NELL2_ENST00000549027.1_Missense_Mutation_p.I744N|NELL2_ENST00000551601.1_Missense_Mutation_p.I697N|NELL2_ENST00000395487.2_Missense_Mutation_p.I744N|NELL2_ENST00000437801.2_Missense_Mutation_p.I795N	NM_001145108.1	NP_001138580.1	Q99435	NELL2_HUMAN	NEL-like 2 (chicken)	745	VWFC 3. {ECO:0000255|PROSITE- ProRule:PRU00220}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(16)|lung(30)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	65	Lung SC(27;0.192)	Lung NSC(34;0.144)		GBM - Glioblastoma multiforme(48;0.092)		CTCTGGGAGAATGCTGAATTC	0.547																																					p.I795N		Atlas-SNP	.											.	NELL2	286	.	0			c.T2384A						.						80	67	72					12																	44913954		2203	4300	6503	SO:0001583	missense	4753	exon20			GGGAGAATGCTGA	D83018	CCDS8746.1, CCDS44863.1, CCDS44864.1, CCDS53781.1	12q12	2012-01-30	2001-11-28		ENSG00000184613	ENSG00000184613			7751	protein-coding gene	gene with protein product		602320	"nel (chicken)-like 2"			19249368	Standard	NM_006159		Approved	NRP2	uc010skz.1	Q99435	OTTHUMG00000169464	ENST00000429094.2:c.2234T>A	chr12.hg19:g.44913954A>T	ENSP00000390680:p.Ile745Asn	125.0	0.0		171.0	48.0	NM_001145107	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Missense_Mutation	SNP	ENST00000429094.2	hg19	CCDS8746.1	.	.	.	.	.	.	.	.	.	.	A	15.26	2.781160	0.49891	.	.	ENSG00000184613	ENST00000395487;ENST00000429094;ENST00000551601;ENST00000452445;ENST00000549027;ENST00000333837;ENST00000437801	T;T;T;T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21	5.07	5.07	0.68467	von Willebrand factor, type C (4);	0.136036	0.48767	D	0.000172	T	0.66426	0.2788	L	0.60455	1.87	0.30030	N	0.813516	B;B;B;B;B	0.27013	0.044;0.166;0.145;0.055;0.166	B;B;B;B;B	0.34346	0.084;0.18;0.039;0.066;0.116	T	0.66304	-0.5957	10	0.39692	T	0.17	-8.2482	14.8307	0.70146	1.0:0.0:0.0:0.0	.	768;795;697;745;744	B7Z2U7;B7Z9U3;F8VVB6;Q99435;Q96JS2	.;.;.;NELL2_HUMAN;.	N	744;745;697;745;744;768;795	ENSP00000378866:I744N;ENSP00000390680:I745N;ENSP00000449332:I697N;ENSP00000394612:I745N;ENSP00000447927:I744N;ENSP00000327988:I768N;ENSP00000416341:I795N	ENSP00000327988:I768N	I	-	2	0	NELL2	43200221	1.000000	0.71417	0.990000	0.47175	0.897000	0.52465	4.483000	0.60264	1.885000	0.54596	0.528000	0.53228	ATT	.	.		0.547	NELL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404180.1	NM_006159		T	44913954	A	T	44913954	3	4	237	1	0	0	0	0	1	0	0	0	10343	101	4	4	224	4	NELL2	12	44913954	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	33877182	44913954	88937941	141	33047										
KRT86	3892	hgsc.bcm.edu	37	chr12	52699941	52699941	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ggccgagctggagggtgcccTgcagaaggccaagcaggaca	17	11	0	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:52699941T>A	ENST00000423955.2	+	9	1302	c.1124T>A	c.(1123-1125)cTg>cAg	p.L375Q	RP11-845M18.6_ENST00000552441.1_RNA|KRT86_ENST00000544024.1_Missense_Mutation_p.L375Q|KRT86_ENST00000293525.5_Missense_Mutation_p.L375Q			O43790	KRT86_HUMAN	keratin 86	375	Coil 2.|Rod.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(1)|cervix(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(357;0.189)		GAGGGTGCCCTGCAGAAGGCC	0.637											OREG0021845	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L375Q		Atlas-SNP	.											.	KRT86	33	.	0			c.T1124A						.						63	63	63					12																	52699941		2203	4300	6503	SO:0001583	missense	3892	exon7			GTGCCCTGCAGAA	X99142	CCDS41785.1	12q13	2013-01-16	2006-07-17	2006-07-17		ENSG00000170442		"-", "Intermediate filaments type II, keratins (basic)"	6463	protein-coding gene	gene with protein product	"hard keratin type II 6"	601928	"keratin, hair, basic, 6 (monilethrix)"	KRTHB6		9241275, 16831889	Standard	NM_002284		Approved	MNX, Hb6	uc001sad.3	O43790		ENST00000423955.2:c.1124T>A	chr12.hg19:g.52699941T>A	ENSP00000444533:p.Leu375Gln	204.0	0.0	987	116.0	6.0	NM_002284	P78387	Missense_Mutation	SNP	ENST00000423955.2	hg19	CCDS41785.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.485795	0.84854	.	.	ENSG00000170442;ENSG00000170442;ENSG00000170442;ENSG00000258832	ENST00000544024;ENST00000423955;ENST00000293525;ENST00000553310	D;D;D	0.92299	-3.01;-3.01;-3.01	5.49	5.49	0.81192	Filament (1);	0.000000	0.33005	U	0.005395	D	0.97688	0.9242	H	0.98664	4.295	0.48341	D	0.999633	D	0.89917	1.0	D	0.97110	1.0	D	0.99004	1.0812	10	0.87932	D	0	.	14.1668	0.65483	0.0:0.0:0.0:1.0	.	375	O43790	KRT86_HUMAN	Q	375	ENSP00000443169:L375Q;ENSP00000444533:L375Q;ENSP00000293525:L375Q	ENSP00000293525:L375Q	L	+	2	0	AC021066.1;KRT86	50986208	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	7.947000	0.87758	2.089000	0.63090	0.454000	0.30748	CTG	.	.		0.637	KRT86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404911.1	NM_002284		A	52699941	T	A	52699941	3	1	237	1	0	0	0	0	1	0	0	0	8509	1580	55	4	1150	4	KRT86	12	52699941	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	7785987	52699941	81151954	142	33048										
ANKRD52	283373	hgsc.bcm.edu	37	chr12	56636966	56636966	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ctaacccaatggcgccgggcCgctcctggctgtaggggcag	15	14	0	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:56636966C>A	ENST00000267116.7	-	28	3312	c.3191G>T	c.(3190-3192)cGg>cTg	p.R1064L	ANKRD52_ENST00000548241.1_Intron	NM_173595.3	NP_775866.2	Q8NB46	ANR52_HUMAN	ankyrin repeat domain 52	1064										endometrium(9)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)|skin(1)	29						GGCGCCGGGCCGCTCCTGGCT	0.607																																					p.R1064L		Atlas-SNP	.											.	ANKRD52	81	.	0			c.G3191T						.						11	12	12					12																	56636966		1875	4081	5956	SO:0001583	missense	283373	exon28			CCGGGCCGCTCCT	AK091555	CCDS44920.1	12q13.3	2013-01-10			ENSG00000139645	ENSG00000139645		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits", "Ankyrin repeat domain containing"	26614	protein-coding gene	gene with protein product	"protein phosphatase 6 ankyrin repeat subunit C"						Standard	NM_173595		Approved	FLJ34236, PP6-ARS-C	uc001skm.4	Q8NB46	OTTHUMG00000170329	ENST00000267116.7:c.3191G>T	chr12.hg19:g.56636966C>A	ENSP00000267116:p.Arg1064Leu	24.0	0.0		18.0	5.0	NM_173595	A6NE79|B1Q2K2	Missense_Mutation	SNP	ENST00000267116.7	hg19	CCDS44920.1	.	.	.	.	.	.	.	.	.	.	C	14.28	2.487538	0.44249	.	.	ENSG00000139645	ENST00000267116;ENST00000417002	T	0.64803	-0.12	3.62	3.62	0.41486	.	0.077520	0.52532	D	0.000067	T	0.47911	0.1471	N	0.19112	0.55	0.58432	D	0.999999	P	0.40875	0.731	B	0.39562	0.303	T	0.54938	-0.8218	10	0.46703	T	0.11	.	14.6424	0.68734	0.0:1.0:0.0:0.0	.	1064	Q8NB46	ANR52_HUMAN	L	1064	ENSP00000267116:R1064L	ENSP00000267116:R1064L	R	-	2	0	ANKRD52	54923233	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	5.460000	0.66691	2.049000	0.60858	0.555000	0.69702	CGG	.	.		0.607	ANKRD52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408539.1	NM_173595		A	56636966	C	A	56636966	3	1	237	1	0	0	0	0	1	0	0	0	678	652	23	1	43	1	ANKRD52	12	56636966	Missense_Mutation	SNP	C	TCGA-ED-A459-01A-11D-A25V-10	3937025	56636966	77214929	143	33049										
NACA	4666	hgsc.bcm.edu	37	chr12	57114439	57114439	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ggggggtgttgggacccgcaGtcttttgagaagaggtcacc	17	8	2	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:57114439G>T	ENST00000454682.1	-	3	1156	c.875C>A	c.(874-876)aCt>aAt	p.T292N	NACA_ENST00000546392.1_Intron|NACA_ENST00000356769.3_Intron|NACA_ENST00000551793.1_Intron|NACA_ENST00000393891.4_Intron|NACA_ENST00000550952.1_Missense_Mutation_p.T292N|NACA_ENST00000548563.1_Intron|NACA_ENST00000552540.1_Intron	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	292	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						GGGACCCGCAGTCTTTTGAGA	0.498			T	BCL6	NHL																																p.T292N		Atlas-SNP	.		Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	.	NACA	131	.	0			c.C875A						.						65	64	65					12																	57114439		1568	3582	5150	SO:0001583	missense	4666	exon3			CCCGCAGTCTTTT	X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"nascent-polypeptide-associated complex alpha polypeptide"			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.875C>A	chr12.hg19:g.57114439G>T	ENSP00000403817:p.Thr292Asn	30.0	0.0		37.0	4.0	NM_001113203		Missense_Mutation	SNP	ENST00000454682.1	hg19		.	.	.	.	.	.	.	.	.	.	g	12.99	2.103170	0.37145	.	.	ENSG00000196531	ENST00000454682;ENST00000550952	T;T	0.60171	0.21;0.74	3.92	2.93	0.34026	.	.	.	.	.	T	0.36580	0.0972	N	0.08118	0	0.09310	N	1	D;P	0.59357	0.985;0.941	B;B	0.42422	0.387;0.203	T	0.16364	-1.0405	9	0.87932	D	0	.	8.9241	0.35630	0.0:0.2297:0.7703:0.0	.	292;292	E9PAV3;F8VU71	.;.	N	292	ENSP00000403817:T292N;ENSP00000448035:T292N	ENSP00000403817:T292N	T	-	2	0	NACA	55400706	0.044000	0.20184	0.079000	0.20413	0.259000	0.26198	1.666000	0.37460	1.928000	0.55862	0.282000	0.19409	ACT	.	.		0.498	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594		T	57114439	G	T	57114439	3	4	237	1	0	0	0	0	1	0	0	0	10142	1029	36	3	5389	3	NACA	12	57114439	Missense_Mutation	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	477473	57114439	76737456	144	33050										
SDR9C7	121214	hgsc.bcm.edu	37	chr12	57324233	57324233	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ttcgttgggaccactgggcaGgcccacaccagcattgttca	11	13	1	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:57324233G>A	ENST00000293502.1	-	2	480	c.337C>T	c.(337-339)Ctg>Ttg	p.L113L		NM_148897.2	NP_683695.1	Q8NEX9	DR9C7_HUMAN	short chain dehydrogenase/reductase family 9C, member 7	113					oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	retinol dehydrogenase activity (GO:0004745)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|pancreas(1)	7						CCACTGGGCAGGCCCACACCA	0.552																																					p.L113L		Atlas-SNP	.											.	SDR9C7	31	.	0			c.C337T						.						68	61	63					12																	57324233		2203	4300	6503	SO:0001819	synonymous_variant	121214	exon2			TGGGCAGGCCCAC	AY044434	CCDS8926.1	12q13.3	2014-09-04			ENSG00000170426	ENSG00000170426	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	29958	protein-coding gene	gene with protein product		609769				12234675, 19027726	Standard	NM_148897		Approved	SDR-O, RDHS	uc010sqw.2	Q8NEX9	OTTHUMG00000171004	ENST00000293502.1:c.337C>T	chr12.hg19:g.57324233G>A		141.0	0.0		196.0	11.0	NM_148897	B3KVB4	Silent	SNP	ENST00000293502.1	hg19	CCDS8926.1																																																																																			.	.		0.552	SDR9C7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411211.1	NM_148897		A	57324233	G	A	57324233	2	1	237	1	0	0	0	0	0	0	0	1	13989	991	35	3		3	SDR9C7	12	57324233	Silent	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	209794	57324233	76527662	145	33051										
SLC6A15	55117	hgsc.bcm.edu	37	chr12	85279337	85279337	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gtagagagctacaaaatagcAcacctgcaaaataaaatgat	7	7	0	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:85279337A>G	ENST00000266682.5	-	4	992	c.451T>C	c.(451-453)Tgc>Cgc	p.C151R	SLC6A15_ENST00000551388.1_Intron|SLC6A15_ENST00000450363.3_Missense_Mutation_p.C151R|SLC6A15_ENST00000552192.1_Missense_Mutation_p.C44R	NM_182767.5	NP_877499.1	Q9H2J7	S6A15_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 15	151					amino acid transport (GO:0006865)|ion transport (GO:0006811)|leucine transport (GO:0015820)|neurotransmitter transport (GO:0006836)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)|proline:sodium symporter activity (GO:0005298)			kidney(1)|large_intestine(18)|lung(15)|ovary(1)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	44						ACAAAATAGCACACCTGCAAA	0.343																																					p.C151R		Atlas-SNP	.											.	SLC6A15	159	.	0			c.T451C						.						89	86	87					12																	85279337		2203	4300	6503	SO:0001583	missense	55117	exon4			AATAGCACACCTG	AF265577	CCDS9026.1, CCDS9027.1, CCDS53816.1	12q21.31	2013-07-15	2008-09-02		ENSG00000072041	ENSG00000072041		"Solute carriers"	13621	protein-coding gene	gene with protein product	"homolog of rat orphan transporter v7-3", "sodium/chloride dependent neurotransmitter transporter Homo sapiens orphan neurotransmitter transporter NTT7"	607971	"solute carrier family 6 (neurotransmitter transporter), member 15"			10471414, 11112352, 16185194	Standard	NM_182767		Approved	hv7-3, NTT73, FLJ10316, V7-3, SBAT1	uc001szv.4	Q9H2J7	OTTHUMG00000169742	ENST00000266682.5:c.451T>C	chr12.hg19:g.85279337A>G	ENSP00000266682:p.Cys151Arg	115.0	0.0		135.0	45.0	NM_018057	A8K592|B7Z2P7|E7ESJ5|Q9H9F5	Missense_Mutation	SNP	ENST00000266682.5	hg19	CCDS9026.1	.	.	.	.	.	.	.	.	.	.	A	18.08	3.544481	0.65198	.	.	ENSG00000072041	ENST00000266682;ENST00000552192;ENST00000450363	T;T;T	0.74632	-0.86;-0.86;-0.86	5.11	3.94	0.45596	.	0.000000	0.85682	D	0.000000	D	0.85792	0.5779	M	0.85710	2.77	0.80722	D	1	P;D	0.67145	0.915;0.996	P;D	0.72075	0.821;0.976	D	0.86458	0.1777	10	0.62326	D	0.03	.	11.5065	0.50471	0.8654:0.0:0.0:0.1346	.	151;151	Q9H9F5;Q9H2J7	.;S6A15_HUMAN	R	151;44;151	ENSP00000266682:C151R;ENSP00000450145:C44R;ENSP00000390706:C151R	ENSP00000266682:C151R	C	-	1	0	SLC6A15	83803468	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.026000	0.76455	0.874000	0.35823	0.477000	0.44152	TGC	.	.		0.343	SLC6A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405678.1	NM_018057, NM_182767		G	85279337	A	G	85279337	3	3	237	1	0	0	0	0	1	0	0	0	14693	159	6	2	1891	2	SLC6A15	12	85279337	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	27955104	85279337	48572558	146	33052										
LRRIQ1	84125	hgsc.bcm.edu	37	chr12	85449747	85449747	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ttaagagaagatgcaagccaAcagctaataataagtagtgc	9	6	0	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:85449747A>T	ENST00000393217.2	+	8	1237	c.1176A>T	c.(1174-1176)caA>caT	p.Q392H		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	392										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		ATGCAAGCCAACAGCTAATAA	0.294																																					p.Q392H		Atlas-SNP	.											.	LRRIQ1	512	.	0			c.A1176T						.						51	57	55					12																	85449747		2201	4292	6493	SO:0001583	missense	84125	exon8			AAGCCAACAGCTA	AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.1176A>T	chr12.hg19:g.85449747A>T	ENSP00000376910:p.Gln392His	27.0	0.0		45.0	5.0	NM_001079910	Q567P4|Q9BS17|Q9HA36	Missense_Mutation	SNP	ENST00000393217.2	hg19	CCDS41816.1	.	.	.	.	.	.	.	.	.	.	A	13.62	2.291674	0.40594	.	.	ENSG00000133640	ENST00000256007;ENST00000378580;ENST00000393217	T	0.52983	0.64	4.95	2.49	0.30216	.	0.464479	0.20777	N	0.085877	T	0.33059	0.0850	N	0.22421	0.69	0.09310	N	1	P;P	0.51653	0.804;0.947	B;P	0.44561	0.258;0.453	T	0.13361	-1.0512	10	0.54805	T	0.06	.	7.1546	0.25630	0.6749:0.0:0.3251:0.0	.	392;367	Q96JM4;C9JI57	LRIQ1_HUMAN;.	H	392;367;392	ENSP00000376910:Q392H	ENSP00000256007:Q392H	Q	+	3	2	LRRIQ1	83973878	0.000000	0.05858	0.013000	0.15412	0.069000	0.16628	0.718000	0.25866	0.214000	0.20742	-0.856000	0.03024	CAA	.	.		0.294	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165		T	85449747	A	T	85449747	3	4	237	1	0	0	0	0	1	0	0	0	9038	40	2	4	1202	4	LRRIQ1	12	85449747	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	170410	85449747	48402148	147	33053										
NTS	4922	hgsc.bcm.edu	37	chr12	86276027	86276027	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	caggaagatattcttgatacTggaaatgacaaaaatggaaa	9	4	1	3			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:86276027T>A	ENST00000256010.6	+	4	494	c.387T>A	c.(385-387)acT>acA	p.T129T	NTS_ENST00000551529.1_Silent_p.T54T	NM_006183.4	NP_006174.1	P30990	NEUT_HUMAN	neurotensin	129					regulation of blood vessel size (GO:0050880)|signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)				large_intestine(2)|lung(6)	8						TTCTTGATACTGGAAATGACA	0.323																																					p.T129T		Atlas-SNP	.											.	NTS	25	.	0			c.T387A						.						60	65	63					12																	86276027		2203	4296	6499	SO:0001819	synonymous_variant	4922	exon4			TGATACTGGAAAT		CCDS9029.1	12q21.31	2013-02-26			ENSG00000133636	ENSG00000133636		"Endogenous ligands"	8038	protein-coding gene	gene with protein product	"neuromedin N", "pro-neurotensin/neuromedin"	162650					Standard	NM_006183		Approved		uc001tag.3	P30990	OTTHUMG00000169832	ENST00000256010.6:c.387T>A	chr12.hg19:g.86276027T>A		107.0	0.0		127.0	9.0	NM_006183		Silent	SNP	ENST00000256010.6	hg19	CCDS9029.1																																																																																			.	.		0.323	NTS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406111.2			A	86276027	T	A	86276027	2	1	237	1	0	0	0	0	0	0	0	1	10718	1567	55	4		4	NTS	12	86276027	Silent	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	826280	86276027	47575868	148	33054										
KITLG	4254	hgsc.bcm.edu	37	chr12	88900157	88900157	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	taagacttggctgtctcttcTggaaaaagaagaaagacata	9	6	2	4			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:88900157T>A	ENST00000228280.5	-	8	897		c.e8-2		KITLG_ENST00000347404.5_Splice_Site|KITLG_ENST00000357116.4_Splice_Site|KITLG_ENST00000378535.4_Splice_Site	NM_000899.4	NP_000890.1	P21583	SCF_HUMAN	KIT ligand						cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|negative regulation of mast cell apoptotic process (GO:0033026)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mast cell proliferation (GO:0070668)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of myeloid leukocyte differentiation (GO:0002763)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Ras protein signal transduction (GO:0046579)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	stem cell factor receptor binding (GO:0005173)			kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|stomach(1)	9						CTGTCTCTTCTGGAAAAAGAA	0.323									Testicular Cancer, Familial Clustering of																												.		Atlas-SNP	.											.	KITLG	26	.	0			c.715-2A>T						.						140	146	144					12																	88900157		2203	4300	6503	SO:0001630	splice_region_variant	4254	exon9	Familial Cancer Database		CTCTTCTGGAAAA	M59964	CCDS31867.1, CCDS31868.1	12q22	2010-11-23			ENSG00000049130	ENSG00000049130			6343	protein-coding gene	gene with protein product	"mast cell growth factor", "stem cell factor", "steel factor", "familial progressive hyperpigmentation 2"	184745		MGF		2208279, 1707188, 19375057	Standard	NM_003994		Approved	SCF, SF, Kitl, KL-1, FPH2	uc001tav.3	P21583	OTTHUMG00000169888	ENST00000228280.5:c.715-2A>T	chr12.hg19:g.88900157T>A		80.0	0.0		96.0	10.0	NM_000899	A0AV09|A8K2Q4|B7ZLM4|Q16487|Q68DZ2|Q7M4N8|Q9UQK7	Splice_Site	SNP	ENST00000228280.5	hg19	CCDS31868.1	.	.	.	.	.	.	.	.	.	.	T	18.21	3.572537	0.65765	.	.	ENSG00000049130	ENST00000378535;ENST00000228280;ENST00000347404	.	.	.	5.47	5.47	0.80525	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.31	0.60374	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	KITLG	87424288	1.000000	0.71417	1.000000	0.80357	0.854000	0.48673	3.640000	0.54350	2.070000	0.61991	0.477000	0.44152	.	.	.		0.323	KITLG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406424.2	NM_003994	Intron	A	88900157	T	A	88900157	5	1	237	1	0	0	0	0	0	0	1	0	8339	1594	55	4	116	4	KITLG	12	88900157	Splice_Site	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	2624130	88900157	44951738	149	33055										
STAB2	55576	hgsc.bcm.edu	37	chr12	104067722	104067722	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ggaacatgcaataacaggatAgacagcgatggggcctgcct	13	9	0	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:104067722A>T	ENST00000388887.2	+	23	2613	c.2409A>T	c.(2407-2409)atA>atT	p.I803I		NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						ATAACAGGATAGACAGCGATG	0.582																																					p.I803I		Atlas-SNP	.											.	STAB2	370	.	0			c.A2409T						.						88	76	80					12																	104067722		2203	4300	6503	SO:0001819	synonymous_variant	55576	exon23			CAGGATAGACAGC	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"hyaluronic acid receptor for endocytosis"	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.2409A>T	chr12.hg19:g.104067722A>T		150.0	0.0		141.0	13.0	NM_017564		Silent	SNP	ENST00000388887.2	hg19	CCDS31888.1																																																																																			.	.		0.582	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			T	104067722	A	T	104067722	2	4	237	1	0	0	0	0	0	0	0	1	15253	410	15	4		4	STAB2	12	104067722	Silent	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	15167565	104067722	29784173	150	33056										
ALKBH2	121642	hgsc.bcm.edu	37	chr12	109526088	109526088	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	cttctttctcacgggaagacTgtggtaccagtgcgtgttgg	13	9	2	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:109526088T>G	ENST00000429722.2	-	4	1072	c.709A>C	c.(709-711)Agt>Cgt	p.S237R	ALKBH2_ENST00000343075.3_Missense_Mutation_p.S237R|ALKBH2_ENST00000440112.2_3'UTR	NM_001145374.1	NP_001138846.1	Q6NS38	ALKB2_HUMAN	alkB, alkylation repair homolog 2 (E. coli)	237	Fe2OG dioxygenase. {ECO:0000255|PROSITE- ProRule:PRU00805}.				DNA dealkylation involved in DNA repair (GO:0006307)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|oxidative demethylation (GO:0070989)|oxidative DNA demethylation (GO:0035511)	nucleoplasm (GO:0005654)	cytosine C-5 DNA demethylase activity (GO:0051747)|DNA-N1-methyladenine dioxygenase activity (GO:0043734)|ferrous iron binding (GO:0008198)			endometrium(1)|kidney(3)|large_intestine(1)|lung(3)	8					Vitamin C(DB00126)	ACGGGAAGACTGTGGTACCAG	0.488								Direct reversal of damage																													p.S237R		Atlas-SNP	.											.	ALKBH2	16	.	0			c.A709C						.						121	122	121					12																	109526088		2203	4300	6503	SO:0001583	missense	121642	exon4			GAAGACTGTGGTA	AY754389	CCDS31897.1, CCDS55883.1	12q24.11	2008-04-24			ENSG00000189046	ENSG00000189046		"Alkylation repair homologs"	32487	protein-coding gene	gene with protein product		610602					Standard	NM_001145374		Approved	MGC90512, ABH2	uc010sxj.1	Q6NS38	OTTHUMG00000169246	ENST00000429722.2:c.709A>C	chr12.hg19:g.109526088T>G	ENSP00000398181:p.Ser237Arg	67.0	0.0		63.0	23.0	NM_001001655	A4PET2|Q5XLE3	Missense_Mutation	SNP	ENST00000429722.2	hg19	CCDS31897.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.561254	0.86335	.	.	ENSG00000189046	ENST00000429722;ENST00000343075;ENST00000435370	T;T	0.15372	2.43;2.43	5.49	5.49	0.81192	Oxoglutarate/iron-dependent oxygenase (2);	0.000000	0.85682	D	0.000000	T	0.33206	0.0855	L	0.48218	1.51	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.03077	-1.1075	10	0.20046	T	0.44	-26.5377	14.7744	0.69713	0.0:0.0:0.0:1.0	.	237	Q6NS38	ALKB2_HUMAN	R	237	ENSP00000398181:S237R;ENSP00000343021:S237R	ENSP00000343021:S237R	S	-	1	0	ALKBH2	108010471	1.000000	0.71417	0.999000	0.59377	0.791000	0.44710	7.401000	0.79962	2.074000	0.62210	0.460000	0.39030	AGT	.	.		0.488	ALKBH2-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403063.2	NM_001001655		G	109526088	T	G	109526088	3	3	237	1	0	0	0	0	1	0	0	0	527	1580	55	5	80	5	ALKBH2	12	109526088	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	5458366	109526088	24325807	151	33057										
OASL	8638	hgsc.bcm.edu	37	chr12	121458369	121458369	+	Missense_Mutation	SNP	T	T	A													0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gtctcccagagaaaactaacTggctggaaacagagcctctc							TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:121458369T>A	ENST00000257570.5	-	6	1810	c.1540A>T	c.(1540-1542)Agt>Tgt	p.S514C	OASL_ENST00000339275.5_3'UTR	NM_003733.3	NP_003724.1	Q15646	OASL_HUMAN	2'-5'-oligoadenylate synthetase-like	514					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|thyroid hormone receptor binding (GO:0046966)|transferase activity (GO:0016740)			NS(1)|endometrium(3)|large_intestine(4)|lung(4)|skin(2)	14	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					GAAAACTAACTGGCTGGAAAC	0.502																																					p.S514C	Colon(192;517 2041 31392 31913 39966)	Atlas-SNP	.											.	OASL	49	.	0			c.A1540T						.						70	72	71					12																	121458369		2203	4300	6503	SO:0001583	missense	8638	exon6			ACTAACTGGCTGG	AF063611	CCDS9211.1, CCDS9212.1, CCDS73536.1	12q24.2	2008-08-05			ENSG00000135114	ENSG00000135114			8090	protein-coding gene	gene with protein product		603281				10087211	Standard	NM_003733		Approved	TRIP14, p59OASL	uc001tzj.2	Q15646	OTTHUMG00000154981	ENST00000257570.5:c.1540A>T	chr12.hg19:g.121458369T>A	ENSP00000257570:p.Ser514Cys	72.0	0.0		58.0	8.0	NM_003733	B2RAZ2|I1YDD2|O75686|Q17R95|Q9Y6K6|Q9Y6K7	Missense_Mutation	SNP	ENST00000257570.5	hg19	CCDS9211.1	.	.	.	.	.	.	.	.	.	.	T	11.94	1.789833	0.31685	.	.	ENSG00000135114	ENST00000257570	T	0.06371	3.31	4.8	-0.206	0.13193	.	1.817350	0.03138	N	0.166123	T	0.06462	0.0166	L	0.36672	1.1	0.09310	N	1	B	0.12013	0.005	B	0.12156	0.007	T	0.42189	-0.9466	10	0.87932	D	0	-14.9306	3.2323	0.06752	0.172:0.286:0.0:0.542	.	514	Q15646	OASL_HUMAN	C	514	ENSP00000257570:S514C	ENSP00000257570:S514C	S	-	1	0	OASL	119942752	0.003000	0.15002	0.001000	0.08648	0.036000	0.12997	0.206000	0.17375	0.075000	0.16796	0.533000	0.62120	AGT	.	.		0.502	OASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337875.2	NM_003733		A	121458369	T	A	121458369	3	1	237	1	0	0	0	0	1	0	0	0	10811	1580	55	4	8	4	OASL	12	121458369	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	11932281	121458369	12393526	152	33058	172	2								
OASL	8638	hgsc.bcm.edu	37	chr12	121458371	121458371	+	Missense_Mutation	SNP	G	G	C													0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ctcccagagaaaactaactgGctggaaacagagcctctcct							TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:121458371G>C	ENST00000257570.5	-	6	1808	c.1538C>G	c.(1537-1539)gCc>gGc	p.A513G	OASL_ENST00000339275.5_3'UTR	NM_003733.3	NP_003724.1	Q15646	OASL_HUMAN	2'-5'-oligoadenylate synthetase-like	513					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|thyroid hormone receptor binding (GO:0046966)|transferase activity (GO:0016740)			NS(1)|endometrium(3)|large_intestine(4)|lung(4)|skin(2)	14	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					AAACTAACTGGCTGGAAACAG	0.507																																					p.A513G	Colon(192;517 2041 31392 31913 39966)	Atlas-SNP	.											.	OASL	49	.	0			c.C1538G						.						71	72	72					12																	121458371		2203	4300	6503	SO:0001583	missense	8638	exon6			TAACTGGCTGGAA	AF063611	CCDS9211.1, CCDS9212.1, CCDS73536.1	12q24.2	2008-08-05			ENSG00000135114	ENSG00000135114			8090	protein-coding gene	gene with protein product		603281				10087211	Standard	NM_003733		Approved	TRIP14, p59OASL	uc001tzj.2	Q15646	OTTHUMG00000154981	ENST00000257570.5:c.1538C>G	chr12.hg19:g.121458371G>C	ENSP00000257570:p.Ala513Gly	74.0	0.0		58.0	8.0	NM_003733	B2RAZ2|I1YDD2|O75686|Q17R95|Q9Y6K6|Q9Y6K7	Missense_Mutation	SNP	ENST00000257570.5	hg19	CCDS9211.1	.	.	.	.	.	.	.	.	.	.	G	6.597	0.478568	0.12521	.	.	ENSG00000135114	ENST00000257570	T	0.05855	3.38	4.8	-6.94	0.01633	.	30.692100	0.01045	N	0.004377	T	0.03783	0.0107	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33163	-0.9879	10	0.41790	T	0.15	-20.326	0.8567	0.01184	0.2006:0.2009:0.1907:0.4078	.	513	Q15646	OASL_HUMAN	G	513	ENSP00000257570:A513G	ENSP00000257570:A513G	A	-	2	0	OASL	119942754	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-0.177000	0.09796	-1.740000	0.01345	-0.140000	0.14226	GCC	.	.		0.507	OASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337875.2	NM_003733		C	121458371	G	C	121458371	3	2	237	1	0	0	0	0	1	0	0	0	10811	1203	42	4	10	4	OASL	12	121458371	Missense_Mutation	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	2	121458371	12393524	153	33059	172	2								
B3GNT4	79369	hgsc.bcm.edu	37	chr12	122691677	122691677	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	acagtgcggcgcctccaggcTatcatggaagatgctgaact	12	11	1	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:122691677T>A	ENST00000324189.4	+	3	1235	c.879T>A	c.(877-879)gcT>gcA	p.A293A	B3GNT4_ENST00000535274.1_Silent_p.A268A|B3GNT4_ENST00000546192.1_Silent_p.A268A|B3GNT4_ENST00000545141.1_Intron	NM_030765.2	NP_110392.1	Q9C0J1	B3GN4_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 4	293					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	13	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000297)|Epithelial(86;0.000497)|BRCA - Breast invasive adenocarcinoma(302;0.222)		GCCTCCAGGCTATCATGGAAG	0.567																																					p.A293A		Atlas-SNP	.											.	B3GNT4	35	.	0			c.T879A						.						119	105	110					12																	122691677		2203	4300	6503	SO:0001819	synonymous_variant	79369	exon3			CCAGGCTATCATG	AB049586	CCDS9227.1	12q24	2013-02-19						"Beta 3-glycosyltransferases"	15683	protein-coding gene	gene with protein product		605864				11042166	Standard	NM_030765		Approved	B3GN-T4, beta3Gn-T4	uc001ubx.3	Q9C0J1		ENST00000324189.4:c.879T>A	chr12.hg19:g.122691677T>A		142.0	0.0		95.0	11.0	NM_030765	Q8N5W4|Q8N934|Q8ND21|Q8WWR5|Q8WY02|Q96QH5	Silent	SNP	ENST00000324189.4	hg19	CCDS9227.1																																																																																			.	.		0.567	B3GNT4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000401595.1	NM_030765		A	122691677	T	A	122691677	2	1	237	1	0	0	0	0	0	0	0	1	1259	1509	53	4		4	B3GNT4	12	122691677	Silent	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	1233306	122691677	11160218	154	33060										
MMP17	4326	hgsc.bcm.edu	37	chr12	132334436	132334436	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gcctcccgcctggcggcatcGacgctgccttctcctgggcc	12	19	1	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:132334436G>A	ENST00000360564.1	+	9	1396	c.1294G>A	c.(1294-1296)Gac>Aac	p.D432N	MMP17_ENST00000535004.1_Intron|MMP17_ENST00000535291.1_Missense_Mutation_p.D348N	NM_016155.4	NP_057239.4	Q9ULZ9	MMP17_HUMAN	matrix metallopeptidase 17 (membrane-inserted)	432					positive regulation of catalytic activity (GO:0043085)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(1)	5	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.82e-07)|Epithelial(86;1.51e-06)|all cancers(50;2.35e-05)	Marimastat(DB00786)	TGGCGGCATCGACGCTGCCTT	0.597																																					p.D432N		Atlas-SNP	.											MMP17_ENST00000360564,NS,carcinoma,0,2	MMP17	77	.	0			c.G1294A						.						107	112	111					12																	132334436		2203	4300	6503	SO:0001583	missense	4326	exon9			GGCATCGACGCTG	X89576	CCDS31927.1	12q24.3	2005-08-08	2005-08-08		ENSG00000198598	ENSG00000198598			7163	protein-coding gene	gene with protein product		602285	"matrix metalloproteinase 17 (membrane-inserted)"			9878265	Standard	NM_016155		Approved	MT4-MMP	uc001ujc.1	Q9ULZ9	OTTHUMG00000168050	ENST00000360564.1:c.1294G>A	chr12.hg19:g.132334436G>A	ENSP00000353767:p.Asp432Asn	311.0	1.0		188.0	26.0	NM_016155	Q14850	Missense_Mutation	SNP	ENST00000360564.1	hg19	CCDS31927.1	.	.	.	.	.	.	.	.	.	.	G	19.90	3.911954	0.72983	.	.	ENSG00000198598	ENST00000360564;ENST00000535291;ENST00000534865;ENST00000542648	T;T;T;T	0.08282	3.11;3.11;3.11;3.11	4.58	4.58	0.56647	Hemopexin/matrixin (2);	0.000000	0.85682	D	0.000000	T	0.36082	0.0954	M	0.88570	2.965	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	T	0.47661	-0.9100	10	0.87932	D	0	.	17.3957	0.87444	0.0:0.0:1.0:0.0	.	432	Q9ULZ9	MMP17_HUMAN	N	432;348;273;62	ENSP00000353767:D432N;ENSP00000441106:D348N;ENSP00000442104:D273N;ENSP00000439542:D62N	ENSP00000353767:D432N	D	+	1	0	MMP17	130900389	1.000000	0.71417	0.046000	0.18839	0.181000	0.23173	9.750000	0.98875	2.112000	0.64535	0.471000	0.43371	GAC	.	.		0.597	MMP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397757.1	NM_016155		A	132334436	G	A	132334436	3	1	237	1	0	0	0	0	1	0	0	0	9665	1058	37	1	1328	1	MMP17	12	132334436	Missense_Mutation	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	9642759	132334436	1517459	155	33061										
SLITRK5	26050	hgsc.bcm.edu	37	chr13	88330413	88330414	+	Missense_Mutation	DNP	TT	TT	AA													0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	acagccccccgagtgctgtcTttgtagaacccaaccggaac							TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr13:88330413_88330414TT>AA	ENST00000325089.6	+	2	2989_2990	c.2770_2771TT>AA	c.(2770-2772)TTt>AAt	p.F924N	SLITRK5_ENST00000400028.3_Missense_Mutation_p.F683N	NM_015567.1	NP_056382.1	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5	924					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|cardiovascular system development (GO:0072358)|dendrite morphogenesis (GO:0048813)|grooming behavior (GO:0007625)|response to xenobiotic stimulus (GO:0009410)|skin development (GO:0043588)|striatum development (GO:0021756)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(14)|lung(40)|ovary(2)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(4)	81	all_neural(89;0.101)|Medulloblastoma(90;0.163)					GAGTGCTGTCTTTGTAGAACCC	0.55																																					p.F924I|p.F924Y		Atlas-SNP	.											.	SLITRK5	192	.	0			c.T2770A|c.T2771A						.																																			SO:0001583	missense	26050	exon2			GCTGTCTTTGTAG|CTGTCTTTGTAGA	AB020725	CCDS9465.1	13q31.1	2004-04-16	2004-01-08		ENSG00000165300	ENSG00000165300			20295	protein-coding gene	gene with protein product		609680	"leucine rich repeat containing 11"	LRRC11		10048485, 14557068	Standard	NM_015567		Approved	bA364G4.2, KIAA0918	uc001vln.3	O94991	OTTHUMG00000017167	Exception_encountered	chr13.hg19:g.88330413_88330414delinsAA	ENSP00000366283:p.Phe924Asn	88.0|87.0	0.0		97.0	8.0|7.0	NM_015567	B3KNB8|B4DSH5|Q5VT81	Missense_Mutation	SNP	ENST00000325089.6	hg19	CCDS9465.1																																																																																			.	.		0.55	SLITRK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045416.3			AA	88330414	TT	AA	88330413	3	1	237	1	0	0	0	0	1	0	0	0	14761	1609	56	4	2772	4	SLITRK5	13	88330413	Missense_Mutation	DNP	TT	TCGA-ED-A459-01A-11D-A25V-10		88330413	26839465	156	33062										
RALGAPA1	253959	hgsc.bcm.edu	37	chr14	36154285	36154285	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gcgcatctggttctgcttgtTtagaatatcagggaggtctt	12	7	4	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr14:36154285T>C	ENST00000389698.3	-	19	3016	c.2626A>G	c.(2626-2628)Aac>Gac	p.N876D	RALGAPA1_ENST00000307138.6_Missense_Mutation_p.N876D|RALGAPA1_ENST00000258840.6_Missense_Mutation_p.N923D|RALGAPA1_ENST00000382366.3_Missense_Mutation_p.N889D	NM_014990.1	NP_055805.1	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1 (catalytic)	876					activation of Ral GTPase activity (GO:0032859)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(7)|large_intestine(14)|lung(21)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						TTCTGCTTGTTTAGAATATCA	0.453																																					p.N876D		Atlas-SNP	.											.	RALGAPA1	289	.	0			c.A2626G						.						30	28	28					14																	36154285		2199	4294	6493	SO:0001583	missense	253959	exon19			GCTTGTTTAGAAT	AK126975	CCDS32064.1, CCDS32065.1, CCDS61439.1	14q13.2	2012-01-26	2009-09-09	2009-09-09	ENSG00000174373	ENSG00000174373			17770	protein-coding gene	gene with protein product	"tuberin-like protein 1", "GAP-related interacting protein to E12"	608884	"GTPase activating RANGAP domain-like 1", "GTPase activating Rap/RanGAP domain-like 1"	GARNL1		19520869	Standard	NM_014990		Approved	GRIPE, DKFZp667F074, KIAA0884, Tulip1, RalGAPalpha1	uc001wtj.3	Q6GYQ0	OTTHUMG00000170619	ENST00000389698.3:c.2626A>G	chr14.hg19:g.36154285T>C	ENSP00000374348:p.Asn876Asp	104.0	0.0		80.0	37.0	NM_194301	A6NMA4|B9EK38|C5NU19|O94960|Q6GYP9|Q6ZT23|Q86YF3|Q86YF5|Q8ND69	Missense_Mutation	SNP	ENST00000389698.3	hg19	CCDS32065.1	.	.	.	.	.	.	.	.	.	.	T	15.88	2.962179	0.53400	.	.	ENSG00000174373	ENST00000389698;ENST00000307138;ENST00000335518;ENST00000258840;ENST00000382366;ENST00000553892	D;D;D;D;D	0.94184	-3.33;-3.33;-3.37;-3.37;-3.37	6.07	6.07	0.98685	.	0.095237	0.64402	D	0.000001	D	0.90369	0.6986	L	0.32530	0.975	0.41780	D	0.989818	B;B;B;B;B	0.33212	0.353;0.089;0.402;0.167;0.025	B;B;B;B;B	0.39339	0.154;0.049;0.297;0.079;0.024	D	0.87928	0.2708	10	0.14252	T	0.57	-13.6835	16.6277	0.84984	0.0:0.0:0.0:1.0	.	923;889;923;876;876	Q6GYQ0-6;B9EK38;Q6GYQ0-3;Q6GYQ0-2;Q6GYQ0	.;.;.;.;RGPA1_HUMAN	D	876;876;876;923;889;923	ENSP00000374348:N876D;ENSP00000302647:N876D;ENSP00000258840:N923D;ENSP00000371803:N889D;ENSP00000451877:N923D	ENSP00000258840:N923D	N	-	1	0	RALGAPA1	35224036	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.399000	0.59703	2.330000	0.79161	0.528000	0.53228	AAC	.	.		0.453	RALGAPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409829.1	XM_210022		C	36154285	T	C	36154285	3	2	237	1	0	0	0	0	1	0	0	0	13028	1841	64	2	3725	2	RALGAPA1	14	36154285	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10		36154285	71195255	157	33063										
BTBD7	55727	hgsc.bcm.edu	37	chr14	93714872	93714872	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	accaaactctcttagcactcGaatctgaatttcatagctga	5	11	3	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr14:93714872G>A	ENST00000334746.5	-	9	2378	c.2071C>T	c.(2071-2073)Cga>Tga	p.R691*	BTBD7_ENST00000554565.1_Nonsense_Mutation_p.R340*|BTBD7_ENST00000393170.2_Nonsense_Mutation_p.R265*	NM_001002860.2	NP_001002860.2	Q9P203	BTBD7_HUMAN	BTB (POZ) domain containing 7	691					multicellular organismal development (GO:0007275)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)	nucleus (GO:0005634)		p.R691*(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|skin(8)|upper_aerodigestive_tract(1)	35		all_cancers(154;0.08)		Epithelial(152;0.196)|COAD - Colon adenocarcinoma(157;0.212)|all cancers(159;0.223)		CTTAGCACTCGAATCTGAATT	0.527																																					p.R691X		Atlas-SNP	.											BTBD7,colon,carcinoma,0,1	BTBD7	112	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C2071T						.						87	80	82					14																	93714872		2203	4300	6503	SO:0001587	stop_gained	55727	exon9			GCACTCGAATCTG	AB040958	CCDS32146.1, CCDS32147.1, CCDS73684.1	14q32.13	2013-01-08			ENSG00000011114	ENSG00000011114		"BTB/POZ domain containing"	18269	protein-coding gene	gene with protein product		610386				10819331, 11527404	Standard	NM_001289133		Approved	FLJ10648, FUP1	uc001ybo.3	Q9P203	OTTHUMG00000171269	ENST00000334746.5:c.2071C>T	chr14.hg19:g.93714872G>A	ENSP00000335615:p.Arg691*	93.0	0.0		89.0	25.0	NM_001002860	A8K5V7|Q69Z05|Q7Z308|Q86TS0|Q9HAA4|Q9NVM0	Nonsense_Mutation	SNP	ENST00000334746.5	hg19	CCDS32146.1	.	.	.	.	.	.	.	.	.	.	G	37	6.226650	0.97394	.	.	ENSG00000011114	ENST00000334746;ENST00000554565;ENST00000553975;ENST00000393170	.	.	.	5.81	4.84	0.62591	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	17.6058	0.88037	0.0:0.0:0.8683:0.1317	.	.	.	.	X	691;340;306;265	.	ENSP00000335615:R691X	R	-	1	2	BTBD7	92784625	1.000000	0.71417	0.716000	0.30569	0.977000	0.68977	6.258000	0.72487	2.753000	0.94483	0.563000	0.77884	CGA	.	.		0.527	BTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412701.1	NM_001002860		A	93714872	G	A	93714872	4	1	237	1	0	0	0	0	0	1	0	0	1548	1066	37	1	1339	1	BTBD7	14	93714872	Nonsense_Mutation	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	57560587	93714872	13634668	158	33064										
TRPM1	4308	hgsc.bcm.edu	37	chr15	31325077	31325077	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	aatggccacgagatctgtgaTgttccagtactcctgaagcc	10	11	1	3			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr15:31325077T>A	ENST00000256552.6	-	22	2914	c.2767A>T	c.(2767-2769)Atc>Ttc	p.I923F	RP11-348B17.1_ENST00000558755.1_RNA|TRPM1_ENST00000542188.1_Missense_Mutation_p.I940F|TRPM1_ENST00000397795.2_Missense_Mutation_p.I901F|RP11-348B17.1_ENST00000561299.1_RNA	NM_001252024.1	NP_001238953.1			transient receptor potential cation channel, subfamily M, member 1											NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		AGATCTGTGATGTTCCAGTAC	0.463																																					p.I940F		Atlas-SNP	.											.	TRPM1	183	.	0			c.A2818T						.						170	161	164					15																	31325077		1938	4138	6076	SO:0001583	missense	4308	exon21			CTGTGATGTTCCA	AF071787	CCDS10024.2, CCDS58345.1, CCDS58346.1, CCDS58347.1	15q13.3	2014-01-28		2002-01-18	ENSG00000134160	ENSG00000134160		"Voltage-gated ion channels / Transient receptor potential cation channels"	7146	protein-coding gene	gene with protein product		603576	"melastatin 1"	MLSN1		9806836, 9537257, 16382100	Standard	NM_001252020		Approved	LTRPC1, CSNB1C	uc021sia.1	Q7Z4N2	OTTHUMG00000129267	ENST00000256552.6:c.2767A>T	chr15.hg19:g.31325077T>A	ENSP00000256552:p.Ile923Phe	253.0	0.0		236.0	10.0	NM_001252020		Missense_Mutation	SNP	ENST00000256552.6	hg19	CCDS58346.1	.	.	.	.	.	.	.	.	.	.	T	24.5	4.535466	0.85812	.	.	ENSG00000134160	ENST00000397795;ENST00000542188;ENST00000256552;ENST00000397793	D;D;D	0.98849	-5.18;-5.18;-5.18	5.59	5.59	0.84812	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.97901	0.9310	L	0.45470	1.425	0.80722	D	1	P;P	0.41929	0.765;0.594	B;P	0.48334	0.439;0.574	D	0.99044	1.0825	10	0.87932	D	0	-29.3404	15.7614	0.78082	0.0:0.0:0.0:1.0	.	895;901	Q7Z4N2-3;Q7Z4N2	.;TRPM1_HUMAN	F	901;940;923;901	ENSP00000380897:I901F;ENSP00000437849:I940F;ENSP00000256552:I923F	ENSP00000256552:I923F	I	-	1	0	TRPM1	29112369	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.260000	0.72502	2.114000	0.64651	0.523000	0.50628	ATC	.	.		0.463	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420		A	31325077	T	A	31325077	3	1	237	1	0	0	0	0	1	0	0	0	16600	1464	51	4	2138	4	TRPM1	15	31325077	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10		31325077	71206315	159	33065										
RASGRP1	10125	hgsc.bcm.edu	37	chr15	38818572	38818572	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tggtcagcatgacttgcaacAgttggttacttcgacacagg	11	9	1	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr15:38818572A>T	ENST00000310803.5	-	3	431	c.254T>A	c.(253-255)cTg>cAg	p.L85Q	RASGRP1_ENST00000561180.1_Missense_Mutation_p.L136Q|RP11-275I4.1_ENST00000559544.1_RNA|RASGRP1_ENST00000539159.1_Missense_Mutation_p.L37Q|RASGRP1_ENST00000558164.1_Missense_Mutation_p.L85Q|RASGRP1_ENST00000450598.2_Missense_Mutation_p.L85Q|RASGRP1_ENST00000559830.1_Missense_Mutation_p.L85Q	NM_001128602.1|NM_005739.3	NP_001122074.1|NP_005730.2	O95267	GRP1_HUMAN	RAS guanyl releasing protein 1 (calcium and DAG-regulated)	85	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.|Ras exchanger motif region; required for transforming activity. {ECO:0000250}.				activation of Rho GTPase activity (GO:0032862)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response to antigenic stimulus (GO:0002437)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|platelet activation (GO:0030168)|Ras protein signal transduction (GO:0007265)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)|secretory granule localization (GO:0032252)|signal transduction (GO:0007165)|vesicle transport along microtubule (GO:0047496)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|lipid binding (GO:0008289)			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)		GACTTGCAACAGTTGGTTACT	0.458																																					p.L85Q		Atlas-SNP	.											.	RASGRP1	50	.	0			c.T254A						.						134	130	131					15																	38818572		1948	4147	6095	SO:0001583	missense	10125	exon3			TGCAACAGTTGGT	AF106071	CCDS45221.1, CCDS45222.1	15q15	2013-01-10				ENSG00000172575		"EF-hand domain containing"	9878	protein-coding gene	gene with protein product		603962				10087292, 9789079	Standard	NM_005739		Approved	CalDAG-GEFII, RASGRP	uc001zke.4	O95267		ENST00000310803.5:c.254T>A	chr15.hg19:g.38818572A>T	ENSP00000310244:p.Leu85Gln	85.0	0.0		99.0	26.0	NM_001128602	Q56CZ0|Q58G75|Q59HB1|Q5I3A8|Q6GV31|Q6NX39|Q7LDG6|Q9UI94|Q9UNN9	Missense_Mutation	SNP	ENST00000310803.5	hg19	CCDS45222.1	.	.	.	.	.	.	.	.	.	.	A	12.80	2.047458	0.36085	.	.	ENSG00000172575	ENST00000310803;ENST00000450598;ENST00000415523;ENST00000431814;ENST00000539159;ENST00000414708;ENST00000541438	T;T;T;T	0.54071	0.59;0.59;0.59;0.59	4.62	3.48	0.39840	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (3);	0.160455	0.43260	N	0.000594	T	0.50154	0.1599	L	0.60845	1.875	0.52501	D	0.99995	B;B	0.24317	0.062;0.101	B;B	0.30782	0.12;0.098	T	0.51371	-0.8714	10	0.72032	D	0.01	-3.4223	10.6141	0.45441	0.8559:0.0:0.0:0.1441	.	85;85	O95267;O95267-2	GRP1_HUMAN;.	Q	85;85;85;85;37;85;85	ENSP00000310244:L85Q;ENSP00000388540:L85Q;ENSP00000444762:L37Q;ENSP00000413105:L85Q	ENSP00000310244:L85Q	L	-	2	0	RASGRP1	36605864	1.000000	0.71417	0.810000	0.32431	0.390000	0.30446	6.019000	0.70818	0.782000	0.33613	0.379000	0.24179	CTG	.	.		0.458	RASGRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418223.1	NM_005739		T	38818572	A	T	38818572	3	4	237	1	0	0	0	0	1	0	0	0	13089	188	7	4	2199	4	RASGRP1	15	38818572	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	7493495	38818572	63712820	160	33066										
C15orf23	90417	hgsc.bcm.edu	37	chr15	40675114	40675114	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	acagagtgcgattcccacccActtccgcctagctaccggaa	8	16	0	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr15:40675114A>T	ENST00000249776.8	+	1	193	c.78A>T	c.(76-78)ccA>ccT	p.P26P	KNSTRN_ENST00000416151.2_Silent_p.P26P|KNSTRN_ENST00000608100.1_5'Flank|KNSTRN_ENST00000448395.2_Silent_p.P26P	NM_033286.3	NP_150628.3			kinetochore-localized astrin/SPAG5 binding protein																		ATTCCCACCCACTTCCGCCTA	0.562																																					p.P26P		Atlas-SNP	.											.	.	.	.	0			c.A78T						.						44	48	46					15																	40675114		1872	4108	5980	SO:0001819	synonymous_variant	90417	exon1			CCACCCACTTCCG	AK027408	CCDS42021.1, CCDS45226.1, CCDS45227.1	15q15.1	2013-01-17	2012-12-04	2012-12-04	ENSG00000128944	ENSG00000128944			30767	protein-coding gene	gene with protein product	"small kinetochore-associated protein", "kinetochore-localized astrin-binding protein", "TRAF4 associated factor 1"	614718	"chromosome 15 open reading frame 23"	C15orf23		12477932	Standard	NM_033286		Approved	FLJ14502, SKAP, kinastrin, TRAF4AF1	uc001zll.3	Q9Y448	OTTHUMG00000172454	ENST00000249776.8:c.78A>T	chr15.hg19:g.40675114A>T		108.0	0.0		122.0	9.0	NM_033286		Silent	SNP	ENST00000249776.8	hg19	CCDS42021.1																																																																																			.	.		0.562	KNSTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418636.1	NM_001142761		T	40675114	A	T	40675114	2	4	237	1	0	0	0	0	0	0	0	1	1787	146	6	4		4	C15orf23	15	40675114	Silent	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	1856542	40675114	61856278	161	33067										
CASC5	57082	hgsc.bcm.edu	37	chr15	40917526	40917526	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	aatcacttagaaactcagccGgtctctagcaaagattcagg	8	10	4	2	rs369221746		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr15:40917526G>T	ENST00000346991.5	+	11	5532	c.5142G>T	c.(5140-5142)ccG>ccT	p.P1714P	CASC5_ENST00000399668.2_Silent_p.P1688P			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	1714					acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		AAACTCAGCCGGTCTCTAGCA	0.398																																					p.P1714P		Atlas-SNP	.											.	CASC5	269	.	0			c.G5142T						.						79	76	77					15																	40917526		1828	4080	5908	SO:0001819	synonymous_variant	57082	exon11			TCAGCCGGTCTCT	AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	24054	protein-coding gene	gene with protein product	"cancer/testis antigen 29", "kinetochore null 1 homolog (C. elegans)", "blinkin, bub-linking kinetochore protein", "protein phosphatase 1, regulatory subunit 55"	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.5142G>T	chr15.hg19:g.40917526G>T		66.0	0.0		82.0	5.0	NM_170589	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Silent	SNP	ENST00000346991.5	hg19	CCDS42023.1																																																																																			.	.		0.398	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508		T	40917526	G	T	40917526	2	4	237	1	0	0	0	0	0	0	0	1	2665	1103	39	1		1	CASC5	15	40917526	Silent	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	242412	40917526	61613866	162	33068										
TGM7	116179	hgsc.bcm.edu	37	chr15	43571320	43571320	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	atgtccagacactacctcaaTagacaagtggggaggctcca	10	11	1	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr15:43571320T>C	ENST00000452443.2	-	11	1838	c.1834A>G	c.(1834-1836)Att>Gtt	p.I612V		NM_052955.2	NP_443187.1	Q96PF1	TGM7_HUMAN	transglutaminase 7	612					peptide cross-linking (GO:0018149)		metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(2)|prostate(4)|skin(1)	39		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.14e-07)	L-Glutamine(DB00130)	ACTACCTCAATAGACAAGTGG	0.572																																					p.I612V		Atlas-SNP	.											.	TGM7	86	.	0			c.A1834G						.						72	61	65					15																	43571320		2202	4299	6501	SO:0001583	missense	116179	exon11			CCTCAATAGACAA	AF363393	CCDS32213.1	15q15.2	2004-07-01				ENSG00000159495		"Transglutaminases"	30790	protein-coding gene	gene with protein product	"transglutaminase Z"	606776				11390390	Standard	NM_052955		Approved	TGMZ	uc001zrf.1	Q96PF1		ENST00000452443.2:c.1834A>G	chr15.hg19:g.43571320T>C	ENSP00000389466:p.Ile612Val	90.0	0.0		113.0	6.0	NM_052955		Missense_Mutation	SNP	ENST00000452443.2	hg19	CCDS32213.1	.	.	.	.	.	.	.	.	.	.	T	15.98	2.991898	0.54041	.	.	ENSG00000159495	ENST00000452443	T	0.71222	-0.55	5.17	5.17	0.71159	Transglutaminase, C-terminal (2);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.78426	0.4281	L	0.55990	1.75	0.28708	N	0.9037	D	0.69078	0.997	D	0.80764	0.994	T	0.71724	-0.4506	10	0.29301	T	0.29	-10.6882	11.4439	0.50112	0.0:0.0:0.0:1.0	.	612	Q96PF1	TGM7_HUMAN	V	612	ENSP00000389466:I612V	ENSP00000389466:I612V	I	-	1	0	TGM7	41358612	0.987000	0.35691	0.918000	0.36340	0.440000	0.31957	1.643000	0.37217	1.963000	0.57068	0.528000	0.53228	ATT	.	.		0.572	TGM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432489.1	NM_052955		C	43571320	T	C	43571320	3	2	237	1	0	0	0	0	1	0	0	0	15850	1406	49	2	310	2	TGM7	15	43571320	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	2653794	43571320	58960072	163	33069										
MAP1A	4130	hgsc.bcm.edu	37	chr15	43819173	43819173	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	cacatgaagaatgaacccacTactccctcatggctggctga	8	13	1	4			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr15:43819173T>A	ENST00000300231.5	+	4	5952	c.5502T>A	c.(5500-5502)acT>acA	p.T1834T	MAP1A_ENST00000382031.1_Silent_p.T2072T|MAP1A_ENST00000399453.1_Silent_p.T1834T			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	1834					microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	ATGAACCCACTACTCCCTCAT	0.617																																					p.T1834T		Atlas-SNP	.											.	MAP1A	189	.	0			c.T5502A						.						84	83	84					15																	43819173		1964	4162	6126	SO:0001819	synonymous_variant	4130	exon4			ACCCACTACTCCC	U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.5502T>A	chr15.hg19:g.43819173T>A		145.0	0.0		139.0	8.0	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Silent	SNP	ENST00000300231.5	hg19	CCDS42031.1																																																																																			.	.		0.617	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373		A	43819173	T	A	43819173	2	1	237	1	0	0	0	0	0	0	0	1	9236	1509	53	4		4	MAP1A	15	43819173	Silent	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	247853	43819173	58712219	164	33070										
USP8	9101	hgsc.bcm.edu	37	chr15	50782610	50782610	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	agattcctgctgagcgggatAgggaaccttccaaactgaag	12	9	0	3			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr15:50782610A>G	ENST00000396444.3	+	14	2460	c.2122A>G	c.(2122-2124)Agg>Ggg	p.R708G	USP8_ENST00000433963.1_Missense_Mutation_p.R708G|USP8_ENST00000425032.3_Missense_Mutation_p.R602G|USP8_ENST00000307179.4_Missense_Mutation_p.R708G	NM_001128610.1|NM_005154.3	NP_001122082.1|NP_005145.3	P40818	UBP8_HUMAN	ubiquitin specific peptidase 8	708					cell proliferation (GO:0008283)|endosome organization (GO:0007032)|mitotic cytokinesis (GO:0000281)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|Ras protein signal transduction (GO:0007265)|ubiquitin-dependent protein catabolic process (GO:0006511)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|midbody (GO:0030496)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				all cancers(107;0.000225)|GBM - Glioblastoma multiforme(94;0.000771)		TGAGCGGGATAGGGAACCTTC	0.502																																					p.R708G		Atlas-SNP	.											.	USP8	90	.	0			c.A2122G						.						119	114	116					15																	50782610		2196	4294	6490	SO:0001583	missense	9101	exon14			CGGGATAGGGAAC	D29956	CCDS10137.1, CCDS61632.1	15q21.1	2014-03-03	2005-08-08		ENSG00000138592	ENSG00000138592		"Ubiquitin-specific peptidases"	12631	protein-coding gene	gene with protein product		603158	"ubiquitin specific protease 8"			12838346, 9582025, 24482476	Standard	NM_005154		Approved	HumORF8, KIAA0055, UBPY, SPG59	uc001zyl.4	P40818	OTTHUMG00000131645	ENST00000396444.3:c.2122A>G	chr15.hg19:g.50782610A>G	ENSP00000379721:p.Arg708Gly	137.0	0.0		146.0	43.0	NM_001128610	B4DKA8|Q2TB31|Q7Z3U2|Q86VA0|Q8IWI7	Missense_Mutation	SNP	ENST00000396444.3	hg19	CCDS10137.1	.	.	.	.	.	.	.	.	.	.	A	14.01	2.407400	0.42715	.	.	ENSG00000138592	ENST00000396444;ENST00000433963;ENST00000307179;ENST00000425032	T;T;T;T	0.02446	4.29;4.29;4.29;4.29	5.6	0.0629	0.14346	.	0.213831	0.47455	D	0.000225	T	0.03178	0.0093	L	0.32530	0.975	0.32942	D	0.518504	B;B	0.33583	0.418;0.411	B;B	0.33042	0.157;0.11	T	0.13845	-1.0494	10	0.49607	T	0.09	-9.3646	16.1962	0.82025	0.4289:0.5711:0.0:0.0	.	602;708	B4DKA8;P40818	.;UBP8_HUMAN	G	708;708;708;602	ENSP00000379721:R708G;ENSP00000405537:R708G;ENSP00000302239:R708G;ENSP00000412682:R602G	ENSP00000302239:R708G	R	+	1	2	USP8	48569902	0.968000	0.33430	0.305000	0.25099	0.760000	0.43138	2.451000	0.44952	-0.164000	0.10927	0.528000	0.53228	AGG	.	.		0.502	USP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254541.1	NM_005154		G	50782610	A	G	50782610	3	3	237	1	0	0	0	0	1	0	0	0	17104	411	15	2	2172	2	USP8	15	50782610	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	6963437	50782610	51748782	165	33071										
AP4E1	23431	hgsc.bcm.edu	37	chr15	51285722	51285722	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tcaagctataactaaaaaggAtcaatctcaagttcttaccc	4	10	4	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr15:51285722A>T	ENST00000261842.5	+	17	2352	c.2246A>T	c.(2245-2247)gAt>gTt	p.D749V	AP4E1_ENST00000560508.1_Missense_Mutation_p.D674V	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	749					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	coated pit (GO:0005905)|Golgi apparatus (GO:0005794)|membrane coat (GO:0030117)				breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(5)|skin(2)	27				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		ACTAAAAAGGATCAATCTCAA	0.398																																					p.D749V		Atlas-SNP	.											.	AP4E1	78	.	0			c.A2246T						.						111	99	103					15																	51285722		2196	4294	6490	SO:0001583	missense	23431	exon17			AAAAGGATCAATC	AB030653	CCDS32240.1, CCDS58362.1	15q21.2	2014-09-17			ENSG00000081014	ENSG00000081014			573	protein-coding gene	gene with protein product		607244				10436028, 21620353	Standard	NM_007347		Approved	AP-4-EPSILON, SPG51	uc001zyx.2	Q9UPM8	OTTHUMG00000172458	ENST00000261842.5:c.2246A>T	chr15.hg19:g.51285722A>T	ENSP00000261842:p.Asp749Val	76.0	0.0		95.0	8.0	NM_007347	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	Missense_Mutation	SNP	ENST00000261842.5	hg19	CCDS32240.1	.	.	.	.	.	.	.	.	.	.	A	11.73	1.726980	0.30593	.	.	ENSG00000081014	ENST00000261842	T	0.18338	2.22	5.29	4.17	0.49024	.	0.298700	0.37178	N	0.002207	T	0.09774	0.0240	N	0.19112	0.55	0.24216	N	0.995458	B	0.20671	0.047	B	0.19148	0.024	T	0.16482	-1.0401	10	0.34782	T	0.22	-12.0798	6.545	0.22400	0.7445:0.1709:0.0845:0.0	.	749	Q9UPM8	AP4E1_HUMAN	V	749	ENSP00000261842:D749V	ENSP00000261842:D749V	D	+	2	0	AP4E1	49073014	0.971000	0.33674	0.349000	0.25694	0.973000	0.67179	2.456000	0.44997	1.988000	0.58038	0.460000	0.39030	GAT	.	.		0.398	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418656.1			T	51285722	A	T	51285722	3	4	237	1	0	0	0	0	1	0	0	0	752	333	12	4	2312	4	AP4E1	15	51285722	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	503112	51285722	51245670	166	33072										
LMAN1L	79748	hgsc.bcm.edu	37	chr15	75115899	75115899	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ttggttaccacccccggttaGggatgcagctgtccgcatgg	13	12	0	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr15:75115899G>T	ENST00000309664.5	+	12	1338		c.e12-1		CPLX3_ENST00000395018.4_5'Flank|RP11-414J4.2_ENST00000564823.1_RNA|LMAN1L_ENST00000379709.3_Splice_Site	NM_021819.2	NP_068591.2	Q9HAT1	LMA1L_HUMAN	lectin, mannose-binding, 1 like							integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(2)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						CCCCCGGTTAGGGATGCAGCT	0.552																																					.		Atlas-SNP	.											.	LMAN1L	43	.	0			c.1200-1G>T						.						79	73	75					15																	75115899		2197	4296	6493	SO:0001630	splice_region_variant	79748	exon12			CGGTTAGGGATGC	AF303398	CCDS10270.1	15q24.1	2005-08-05			ENSG00000140506	ENSG00000140506			6632	protein-coding gene	gene with protein product		609548				11255007	Standard	NM_021819		Approved	ERGL, ERGIC-53L	uc002ayt.1	Q9HAT1	OTTHUMG00000142813	ENST00000309664.5:c.1200-1G>T	chr15.hg19:g.75115899G>T		81.0	0.0		51.0	7.0	NM_021819	Q6UWN2	Splice_Site	SNP	ENST00000309664.5	hg19	CCDS10270.1	.	.	.	.	.	.	.	.	.	.	G	6.238	0.412061	0.11812	.	.	ENSG00000140506	ENST00000309664;ENST00000379709	.	.	.	5.18	3.31	0.37934	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.1271	0.31005	0.187:0.0:0.813:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	LMAN1L	72902952	0.998000	0.40836	0.406000	0.26421	0.135000	0.20990	4.701000	0.61810	0.703000	0.31848	0.561000	0.74099	.	.	.		0.552	LMAN1L-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286397.4		Intron	T	75115899	G	T	75115899	5	4	237	1	0	0	0	0	0	0	1	0	8846	1014	35	3	1245	3	LMAN1L	15	75115899	Splice_Site	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	23830177	75115899	27415493	167	33073										
LINGO1	84894	hgsc.bcm.edu	37	chr15	77907675	77907675	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	cagcgtcagctgctccaggcTgttgaggccgctgaaggcgc	15	13	1	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr15:77907675T>G	ENST00000355300.6	-	2	748	c.574A>C	c.(574-576)Agc>Cgc	p.S192R	LINGO1_ENST00000561030.1_Missense_Mutation_p.S186R	NM_032808.5	NP_116197.4	Q96FE5	LIGO1_HUMAN	leucine rich repeat and Ig domain containing 1	192					central nervous system neuron development (GO:0021954)|negative regulation of axonogenesis (GO:0050771)|negative regulation of oligodendrocyte differentiation (GO:0048715)|neuron projection development (GO:0031175)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein kinase B signaling (GO:0043491)|regulation of axonogenesis (GO:0050770)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	31						TGCTCCAGGCTGTTGAGGCCG	0.597																																					p.S192R		Atlas-SNP	.											.	LINGO1	76	.	0			c.A574C						.						119	125	123					15																	77907675		2168	4271	6439	SO:0001583	missense	84894	exon2			CCAGGCTGTTGAG	AK027500	CCDS45313.1, CCDS73766.1	15q24	2013-01-11	2007-02-01	2007-02-01		ENSG00000169783		"Immunoglobulin superfamily / I-set domain containing"	21205	protein-coding gene	gene with protein product		609791	"leucine rich repeat neuronal 6A"	LRRN6A		14686891	Standard	XM_006720723		Approved	FLJ14594, LERN1	uc002bct.1	Q96FE5		ENST00000355300.6:c.574A>C	chr15.hg19:g.77907675T>G	ENSP00000347451:p.Ser192Arg	133.0	0.0		138.0	57.0	NM_032808	D3DW80|Q6NUK3|Q6UXM3|Q6VVG0|Q6VVG1|Q6VVG2|Q8N3K5|Q96K52	Missense_Mutation	SNP	ENST00000355300.6	hg19	CCDS45313.1	.	.	.	.	.	.	.	.	.	.	T	17.13	3.312077	0.60414	.	.	ENSG00000169783	ENST00000355300	D	0.81659	-1.52	5.29	3.01	0.34805	.	0.079382	0.85682	D	0.000000	T	0.77731	0.4174	L	0.42581	1.335	0.80722	D	1	D	0.60575	0.988	P	0.51777	0.679	T	0.74343	-0.3696	10	0.37606	T	0.19	.	8.9041	0.35512	0.0:0.1513:0.0:0.8487	.	192	Q96FE5	LIGO1_HUMAN	R	192	ENSP00000347451:S192R	ENSP00000347451:S192R	S	-	1	0	LINGO1	75694730	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.256000	0.58810	0.863000	0.35553	0.459000	0.35465	AGC	.	.		0.597	LINGO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419546.1	NM_032808		G	77907675	T	G	77907675	3	3	237	1	0	0	0	0	1	0	0	0	8823	1580	55	5	1292	5	LINGO1	15	77907675	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	2791776	77907675	24623717	168	33074										
ALPK3	57538	hgsc.bcm.edu	37	chr15	85401062	85401062	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	cagagtgcacagaccctgctGctgagcccctgtacctcccg	10	17	0	3			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr15:85401062G>T	ENST00000258888.5	+	6	3866	c.3699G>T	c.(3697-3699)ctG>ctT	p.L1233L		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1233					heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			AGACCCTGCTGCTGAGCCCCT	0.682																																					p.L1233L		Atlas-SNP	.											.	ALPK3	289	.	0			c.G3699T						.						59	40	47					15																	85401062		2203	4299	6502	SO:0001819	synonymous_variant	57538	exon6			CCTGCTGCTGAGC	AY044449	CCDS10333.1	15q25.2	2013-01-29			ENSG00000136383	ENSG00000136383		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17574	protein-coding gene	gene with protein product	"myocyte induction differentiation originator", "muscle alpha-kinase"					10021370	Standard	NM_020778		Approved	MAK, KIAA1330, Midori	uc002ble.3	Q96L96	OTTHUMG00000148667	ENST00000258888.5:c.3699G>T	chr15.hg19:g.85401062G>T		32.0	0.0		24.0	7.0	NM_020778	Q9P2L6	Silent	SNP	ENST00000258888.5	hg19	CCDS10333.1																																																																																			.	.		0.682	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778		T	85401062	G	T	85401062	2	4	237	1	0	0	0	0	0	0	0	1	546	1306	46	3		3	ALPK3	15	85401062	Silent	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	7493387	85401062	17130330	169	33075										
TPSD1	23430	hgsc.bcm.edu	37	chr16	1308140	1308140	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tttgcaacgcggaatatcacAccggcctccatacgggccac	9	15	1	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr16:1308140A>T	ENST00000211076.3	+	4	749	c.601A>T	c.(601-603)Acc>Tcc	p.T201S	RP11-616M22.5_ENST00000566997.1_RNA|TPSD1_ENST00000397534.2_Missense_Mutation_p.T194S|PRSS29P_ENST00000568091.1_lincRNA	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	201	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				GGAATATCACACCGGCCTCCA	0.637																																					p.T201S		Atlas-SNP	.											.	TPSD1	47	.	0			c.A601T						.						52	51	51					16																	1308140		2194	4299	6493	SO:0001583	missense	23430	exon4			TATCACACCGGCC	AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"mMCP-7-like II", "mMCP-7-like I", "MMCP-7-LIKE-2"	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.601A>T	chr16.hg19:g.1308140A>T	ENSP00000211076:p.Thr201Ser	244.0	0.0		275.0	14.0	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Missense_Mutation	SNP	ENST00000211076.3	hg19	CCDS10432.1	.	.	.	.	.	.	.	.	.	.	N	2.623	-0.288029	0.05605	.	.	ENSG00000095917	ENST00000397534;ENST00000211076	D;D	0.88664	-2.41;-2.41	3.31	-4.99	0.03010	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	1.254980	0.05769	N	0.606319	T	0.65585	0.2705	N	0.02697	-0.525	0.09310	N	1	B;B	0.14012	0.009;0.009	B;B	0.21360	0.034;0.034	T	0.60949	-0.7161	10	0.08599	T	0.76	.	0.3843	0.00400	0.2046:0.2921:0.2158:0.2875	.	185;201	C9JJL5;Q9BZJ3	.;TRYD_HUMAN	S	194;201	ENSP00000380668:T194S;ENSP00000211076:T201S	ENSP00000211076:T201S	T	+	1	0	TPSD1	1248141	0.019000	0.18553	0.001000	0.08648	0.002000	0.02628	0.552000	0.23376	-0.557000	0.06126	-0.622000	0.04023	ACC	.	.		0.637	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2			T	1308140	A	T	1308140	3	4	237	1	0	0	0	0	1	0	0	0	16440	159	6	4	615	4	TPSD1	16	1308140	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10		1308140	89046613	170	33076										
CLCN7	1186	hgsc.bcm.edu	37	chr16	1510832	1510832	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gatactgcccttgatgacccTgtacttgaggccagccaggt	11	12	0	3			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr16:1510832T>A	ENST00000382745.4	-	5	1074	c.469A>T	c.(469-471)Agg>Tgg	p.R157W	CLCN7_ENST00000262318.8_Missense_Mutation_p.R133W|CLCN7_ENST00000448525.1_Missense_Mutation_p.R133W	NM_001287.5	NP_001278.1	P51798	CLCN7_HUMAN	chloride channel, voltage-sensitive 7	157					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|response to pH (GO:0009268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(2)|central_nervous_system(3)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|skin(2)	24		Hepatocellular(780;0.0893)				TTGATGACCCTGTACTTGAGG	0.642																																					p.R157W		Atlas-SNP	.											.	CLCN7	53	.	0			c.A469T						.						93	79	84					16																	1510832		2199	4300	6499	SO:0001583	missense	1186	exon5			TGACCCTGTACTT	Z67743	CCDS32361.1, CCDS45378.1	16p13	2012-09-26	2012-02-23		ENSG00000103249	ENSG00000103249		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ion channels / Chloride channels : Voltage-sensitive"	2025	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 63"	602727	"chloride channel 7"			8543009	Standard	NM_001114331		Approved	CLC-7, OPTA2, CLC7, ClC-7, PPP1R63	uc002clv.3	P51798	OTTHUMG00000044467	ENST00000382745.4:c.469A>T	chr16.hg19:g.1510832T>A	ENSP00000372193:p.Arg157Trp	169.0	0.0		156.0	13.0	NM_001287	A6NEJ7|A8K5T9|A8K7X1|B3KPN3|E9PDB9|Q9NYX5	Missense_Mutation	SNP	ENST00000382745.4	hg19	CCDS32361.1	.	.	.	.	.	.	.	.	.	.	T	16.30	3.084302	0.55861	.	.	ENSG00000103249	ENST00000448525;ENST00000262318;ENST00000382745;ENST00000428756	D;D	0.84873	-1.91;-1.91	4.7	-4.2	0.03823	Chloride channel, core (2);	0.650704	0.15751	N	0.246406	T	0.72724	0.3496	N	0.24115	0.695	0.30683	N	0.752097	B;P	0.36712	0.001;0.566	B;B	0.32393	0.008;0.145	T	0.64909	-0.6296	10	0.54805	T	0.06	-21.6841	17.2688	0.87095	0.0:0.0:0.7037:0.2963	.	133;157	E9PDB9;P51798	.;CLCN7_HUMAN	W	133;110;157;99	ENSP00000410907:R133W;ENSP00000372193:R157W	ENSP00000262318:R110W	R	-	1	2	CLCN7	1450833	0.016000	0.18221	0.779000	0.31741	0.948000	0.59901	-0.084000	0.11268	-0.489000	0.06716	-0.438000	0.05819	AGG	.	.		0.642	CLCN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103598.2	NM_001287		A	1510832	T	A	1510832	3	1	237	1	0	0	0	0	1	0	0	0	3470	1579	55	4	2032	4	CLCN7	16	1510832	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	202692	1510832	88843921	171	33077										
PGP	283871	hgsc.bcm.edu	37	chr16	2263817	2263817	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tagacacgcagtcactttccTgattattcttcacatcccct	4	14	3	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr16:2263817T>A	ENST00000333503.7	-	2	907	c.878A>T	c.(877-879)cAg>cTg	p.Q293L	BRICD5_ENST00000562360.1_5'Flank|RP11-304L19.8_ENST00000561544.1_lincRNA|BRICD5_ENST00000566018.1_5'Flank|BRICD5_ENST00000328540.3_5'Flank	NM_001042371.2	NP_001035830.1	A6NDG6	PGP_HUMAN	phosphoglycolate phosphatase	293					carbohydrate metabolic process (GO:0005975)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)		magnesium ion binding (GO:0000287)|nucleotide phosphatase activity, acting on free nucleotides (GO:0098519)|phosphoglycolate phosphatase activity (GO:0008967)|protein tyrosine phosphatase activity (GO:0004725)			skin(1)	1						GTCACTTTCCTGATTATTCTT	0.517																																					p.Q293L	GBM(63;906 1080 2092 17773 18795)	Atlas-SNP	.											.	PGP	6	.	0			c.A878T						.						127	129	128					16																	2263817		1975	4166	6141	SO:0001583	missense	283871	exon2			CTTTCCTGATTAT	BC035985	CCDS42104.1	16p13.3	2012-10-02				ENSG00000184207	3.1.3.18		8909	protein-coding gene	gene with protein product		172280					Standard	NM_001042371		Approved		uc002cpk.1	A6NDG6		ENST00000333503.7:c.878A>T	chr16.hg19:g.2263817T>A	ENSP00000330918:p.Gln293Leu	201.0	0.0		273.0	15.0	NM_001042371		Missense_Mutation	SNP	ENST00000333503.7	hg19	CCDS42104.1	.	.	.	.	.	.	.	.	.	.	T	11.51	1.660391	0.29515	.	.	ENSG00000184207	ENST00000333503	T	0.31769	1.48	4.76	4.76	0.60689	HAD-like domain (2);	0.186034	0.48286	D	0.000184	T	0.23886	0.0578	L	0.33093	0.98	0.80722	D	1	B	0.09022	0.002	B	0.15052	0.012	T	0.04333	-1.0959	10	0.25751	T	0.34	-24.7375	13.2447	0.60016	0.0:0.0:0.0:1.0	.	293	A6NDG6	PGP_HUMAN	L	293	ENSP00000330918:Q293L	ENSP00000330918:Q293L	Q	-	2	0	PGP	2203818	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	1.300000	0.33436	1.991000	0.58162	0.533000	0.62120	CAG	.	.		0.517	PGP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435095.1	NM_024118		A	2263817	T	A	2263817	3	1	237	1	0	0	0	0	1	0	0	0	11811	1580	55	4	91	4	PGP	16	2263817	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	752985	2263817	88090936	172	33078										
VWA3A	146177	hgsc.bcm.edu	37	chr16	22126671	22126671	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ttgttgtctcctcccagcctCcaggaacttaagctctgggt	9	13	2	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr16:22126671C>T	ENST00000389398.5	+	9	789	c.693C>T	c.(691-693)ctC>ctT	p.L231L	VWA3A_ENST00000389397.4_5'UTR	NM_173615.3	NP_775886.3	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	231						extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7				GBM - Glioblastoma multiforme(48;0.0439)		CTCCCAGCCTCCAGGAACTTA	0.443																																					p.L231L		Atlas-SNP	.											.	VWA3A	115	.	0			c.C693T						.						33	34	34					16																	22126671		1863	4111	5974	SO:0001819	synonymous_variant	146177	exon9			CAGCCTCCAGGAA	AK128606, AK098260	CCDS45441.1	16p12.1	2008-02-05				ENSG00000175267			27088	protein-coding gene	gene with protein product						12477932	Standard	XM_006721021		Approved	FLJ46765, FLJ40941	uc010vbq.2	A6NCI4		ENST00000389398.5:c.693C>T	chr16.hg19:g.22126671C>T		116.0	0.0		173.0	36.0	NM_173615	A4QMU8|A6NNC0|Q6UTX4|Q6ZQZ9|Q8IUY6|Q8N9W1	Silent	SNP	ENST00000389398.5	hg19	CCDS45441.1																																																																																			.	.		0.443	VWA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430052.1			T	22126671	C	T	22126671	2	4	237	1	0	0	0	0	0	0	0	1	17255	842	30	3		3	VWA3A	16	22126671	Silent	SNP	C	TCGA-ED-A459-01A-11D-A25V-10	19862854	22126671	68228082	173	33079										
ZNF629	23361	hgsc.bcm.edu	37	chr16	30793613	30793613	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tgccgtgggtgagctgatgcTggaggagcacagagcgatcc	17	9	0	3	rs200655215		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr16:30793613T>A	ENST00000262525.4	-	3	2243	c.2036A>T	c.(2035-2037)cAg>cTg	p.Q679L	RP11-2C24.6_ENST00000575562.1_RNA	NM_001080417.1	NP_001073886.1	Q9UEG4	ZN629_HUMAN	zinc finger protein 629	679					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(3)|urinary_tract(1)	22			Colorectal(24;0.198)			GAGCTGATGCTGGAGGAGCAC	0.592																																					p.Q679L		Atlas-SNP	.											.	ZNF629	44	.	0			c.A2036T						.						24	25	25					16																	30793613		2045	4204	6249	SO:0001583	missense	23361	exon3			TGATGCTGGAGGA	AB002324	CCDS45463.1	16p11.2	2013-01-08				ENSG00000102870		"Zinc fingers, C2H2-type"	29008	protein-coding gene	gene with protein product			"zinc finger protein 65"	ZNF65		9205841	Standard	NM_001080417		Approved	KIAA0326	uc002dzs.1	Q9UEG4		ENST00000262525.4:c.2036A>T	chr16.hg19:g.30793613T>A	ENSP00000262525:p.Gln679Leu	140.0	0.0		186.0	13.0	NM_001080417	Q15938	Missense_Mutation	SNP	ENST00000262525.4	hg19	CCDS45463.1	.	.	.	.	.	.	.	.	.	.	T	13.40	2.226046	0.39300	.	.	ENSG00000102870	ENST00000262525	T	0.51325	0.71	5.89	5.89	0.94794	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.42053	D	0.000772	T	0.38453	0.1041	N	0.19112	0.55	0.21652	N	0.999607	P	0.38922	0.651	B	0.42163	0.378	T	0.30208	-0.9986	10	0.26408	T	0.33	-24.1685	15.2948	0.73894	0.0:0.0:0.0:1.0	.	679	Q9UEG4	ZN629_HUMAN	L	679	ENSP00000262525:Q679L	ENSP00000262525:Q679L	Q	-	2	0	ZNF629	30701114	0.000000	0.05858	0.935000	0.37517	0.994000	0.84299	0.243000	0.18106	2.254000	0.74563	0.459000	0.35465	CAG	.	T|1.000;C|0.000		0.592	ZNF629-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434291.1	NM_015309		A	30793613	T	A	30793613	3	1	237	1	0	0	0	0	1	0	0	0	18068	1580	55	4	577	4	ZNF629	16	30793613	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	8666942	30793613	59561140	174	33080										
NIP7	51388	hgsc.bcm.edu	37	chr16	69375171	69375171	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tctgggtcgaatcactgaaaAtacttctcagtaccagggcg	10	10	3	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr16:69375171A>G	ENST00000254940.5	+	4	771	c.371A>G	c.(370-372)aAt>aGt	p.N124S	COG8_ENST00000306875.4_5'Flank|COG8_ENST00000562081.1_5'Flank|RP11-343C2.7_ENST00000564737.1_Intron|RP11-343C2.9_ENST00000563634.1_Intron|NIP7_ENST00000254941.6_Intron	NM_016101.4	NP_057185.1	Q9Y221	NIP7_HUMAN	NIP7, nucleolar pre-rRNA processing protein	124	C-terminal domain.|PUA. {ECO:0000255|PROSITE- ProRule:PRU00161}.				ribosome assembly (GO:0042255)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)	6		Ovarian(137;0.101)				ATCACTGAAAATACTTCTCAG	0.443																																					p.N124S		Atlas-SNP	.											.	NIP7	20	.	0			c.A371G						.						112	103	106					16																	69375171		2198	4300	6498	SO:0001583	missense	51388	exon4			CTGAAAATACTTC	AB112439	CCDS10877.1, CCDS56003.1	16q22.1	2013-03-04	2013-03-04		ENSG00000132603	ENSG00000132603			24328	protein-coding gene	gene with protein product			"nuclear import 7 homolog (S. cerevisiae)"			14660641, 22195017	Standard	NM_016101		Approved	CGI-37, FLJ10296, HSPC031, KD93	uc002exa.3	Q9Y221	OTTHUMG00000137568	ENST00000254940.5:c.371A>G	chr16.hg19:g.69375171A>G	ENSP00000254940:p.Asn124Ser	208.0	0.0		136.0	73.0	NM_016101	B2RD04|Q9NZZ0	Missense_Mutation	SNP	ENST00000254940.5	hg19	CCDS10877.1	.	.	.	.	.	.	.	.	.	.	A	13.98	2.399639	0.42512	.	.	ENSG00000132603	ENST00000254940	.	.	.	5.53	5.53	0.82687	Pseudouridine synthase/archaeosine transglycosylase (2);PUA-like domain (1);	0.000000	0.85682	D	0.000000	T	0.53061	0.1773	L	0.42245	1.32	0.80722	D	1	B	0.12013	0.005	B	0.17433	0.018	T	0.49978	-0.8881	9	0.35671	T	0.21	-23.6487	10.8189	0.46593	0.9264:0.0:0.0736:0.0	.	124	Q9Y221	NIP7_HUMAN	S	124	.	ENSP00000254940:N124S	N	+	2	0	NIP7	67932672	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.466000	0.53071	2.101000	0.63845	0.459000	0.35465	AAT	.	.		0.443	NIP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268947.2	NM_016101		G	69375171	A	G	69375171	3	3	237	1	0	0	0	0	1	0	0	0	10430	101	4	2	385	2	NIP7	16	69375171	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	38581558	69375171	20979582	175	33081										
TP53	7157	hgsc.bcm.edu	37	chr17	7578190	7578190	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	accagacctcaggcggctcaTagggcaccaccacactatgt	9	15	2	1	rs121912666		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr17:7578190T>C	ENST00000269305.4	-	6	848	c.659A>G	c.(658-660)tAt>tGt	p.Y220C	TP53_ENST00000413465.2_Missense_Mutation_p.Y220C|TP53_ENST00000420246.2_Missense_Mutation_p.Y220C|TP53_ENST00000455263.2_Missense_Mutation_p.Y220C|TP53_ENST00000445888.2_Missense_Mutation_p.Y220C|TP53_ENST00000359597.4_Missense_Mutation_p.Y220C|TP53_ENST00000574684.1_Intron	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	220	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		Y -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:7682763, ECO:0000269|PubMed:9450901}.|Y -> D (in sporadic cancers; somatic mutation).|Y -> F (in a sporadic cancer; somatic mutation).|Y -> H (in sporadic cancers; somatic mutation).|Y -> N (in sporadic cancers; somatic mutation).|Y -> S (in a brain tumor with no family history; germline mutation and in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Y220C(278)|p.Y127C(24)|p.Y220S(12)|p.?(11)|p.0?(8)|p.D208fs*1(1)|p.Y220_P223delYEPP(1)|p.V218_E224delVPYEPPE(1)|p.V218_E221delVPYE(1)|p.Y127S(1)|p.V218_Y220delVPY(1)|p.Y220fs*25(1)|p.V216_Y220delVVVPY(1)|p.Y220fs*2(1)|p.V218fs*26(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	AGGCGGCTCATAGGGCACCAC	0.557		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.Y220C	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,carcinoma,0,1	TP53	33396	.	343	Substitution - Missense(315)|Unknown(11)|Whole gene deletion(8)|Deletion - In frame(5)|Deletion - Frameshift(3)|Insertion - Frameshift(1)	ovary(55)|breast(54)|lung(37)|upper_aerodigestive_tract(35)|urinary_tract(19)|oesophagus(19)|large_intestine(17)|liver(17)|central_nervous_system(16)|stomach(15)|haematopoietic_and_lymphoid_tissue(15)|endometrium(14)|soft_tissue(8)|biliary_tract(6)|bone(5)|pancreas(4)|prostate(4)|peritoneum(2)|small_intestine(1)	c.A659G	GRCh37	CM015378|CM951227	TP53	M	rs121912666	.						102	94	97					17																	7578190		2203	4300	6503	SO:0001583	missense	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GGCTCATAGGGCA	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.659A>G	chr17.hg19:g.7578190T>C	ENSP00000269305:p.Tyr220Cys	212.0	0.0		158.0	75.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.248510	0.80024	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99840	-7.08;-7.08;-7.08;-7.08;-7.08;-7.08;-7.08;-7.08	5.28	5.28	0.74379	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99822	0.9921	M	0.89287	3.02	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;0.998;0.996;1.0;0.999;0.998;1.0	D	0.96735	0.9542	10	0.87932	D	0	-1.87	13.4753	0.61306	0.0:0.0:0.0:1.0	.	181;220;220;127;220;220;220	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	C	220;220;220;220;220;220;209;127;88;127	ENSP00000410739:Y220C;ENSP00000352610:Y220C;ENSP00000269305:Y220C;ENSP00000398846:Y220C;ENSP00000391127:Y220C;ENSP00000391478:Y220C;ENSP00000425104:Y88C;ENSP00000423862:Y127C	ENSP00000269305:Y220C	Y	-	2	0	TP53	7518915	1.000000	0.71417	0.585000	0.28666	0.993000	0.82548	6.232000	0.72313	2.128000	0.65567	0.460000	0.39030	TAT	.	.		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7578190	T	C	7578190	3	2	237	1	0	0	0	0	1	0	0	0	16396	1406	49	2	635	2	TP53	17	7578190	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10		7578190	73617020	176	33082										
MYH8	4626	hgsc.bcm.edu	37	chr17	10317595	10317595	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ggcatagtcatatgggttggTggtgatcaggagcatttctg	15	5	3	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr17:10317595T>A	ENST00000403437.2	-	11	1016	c.922A>T	c.(922-924)Acc>Tcc	p.T308S	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	308	Myosin motor.				ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)			NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						TATGGGTTGGTGGTGATCAGG	0.388									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling																												p.T308S		Atlas-SNP	.											.	MYH8	346	.	0			c.A922T						.						232	221	224					17																	10317595		2203	4300	6503	SO:0001583	missense	4626	exon11	Familial Cancer Database	Carney Complex Variant	GGTTGGTGGTGAT		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020		"Myosins / Myosin superfamily : Class II"	7578	protein-coding gene	gene with protein product		160741	"myosin, heavy polypeptide 8, skeletal muscle, perinatal"			2373371	Standard	NM_002472		Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.922A>T	chr17.hg19:g.10317595T>A	ENSP00000384330:p.Thr308Ser	332.0	0.0		257.0	26.0	NM_002472	Q14910	Missense_Mutation	SNP	ENST00000403437.2	hg19	CCDS11153.1	.	.	.	.	.	.	.	.	.	.	T	16.15	3.042154	0.55003	.	.	ENSG00000133020	ENST00000252173;ENST00000403437	T	0.70749	-0.51	4.83	4.83	0.62350	Myosin head, motor domain (2);	0.000000	0.42964	U	0.000637	T	0.61874	0.2382	L	0.35414	1.06	0.47094	D	0.999317	B	0.12013	0.005	B	0.21917	0.037	T	0.59537	-0.7436	10	0.44086	T	0.13	.	14.5571	0.68109	0.0:0.0:0.0:1.0	.	308	P13535	MYH8_HUMAN	S	308	ENSP00000384330:T308S	ENSP00000252173:T308S	T	-	1	0	MYH8	10258320	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.939000	0.63526	2.036000	0.60181	0.533000	0.62120	ACC	.	.		0.388	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472		A	10317595	T	A	10317595	3	1	237	1	0	0	0	0	1	0	0	0	10050	1696	59	4	5011	4	MYH8	17	10317595	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	2739405	10317595	70877615	177	33083										
COPS3	8533	hgsc.bcm.edu	37	chr17	17179373	17179373	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	cagcaaggacgcccaaggagTgttcttgtacatccagagcc	11	12	1	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr17:17179373T>A	ENST00000268717.5	-	2	267	c.161A>T	c.(160-162)cAc>cTc	p.H54L	COPS3_ENST00000439936.2_Missense_Mutation_p.H34L|COPS3_ENST00000539941.2_Missense_Mutation_p.H34L	NM_003653.3	NP_003644.2	Q9UNS2	CSN3_HUMAN	COP9 signalosome subunit 3	54					cullin deneddylation (GO:0010388)|in utero embryonic development (GO:0001701)|response to light stimulus (GO:0009416)|signal transduction (GO:0007165)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)				NS(1)|large_intestine(3)|lung(6)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	13						GCCCAAGGAGTGTTCTTGTAC	0.438																																					p.H54L		Atlas-SNP	.											.	COPS3	41	.	0			c.A161T						.						121	107	112					17																	17179373		2203	4300	6503	SO:0001583	missense	8533	exon2			AAGGAGTGTTCTT	AF031647	CCDS11183.1, CCDS56022.1	17p11.2	2013-03-14	2013-03-14		ENSG00000141030	ENSG00000141030			2239	protein-coding gene	gene with protein product		604665	"COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 3", "COP9 constitutive photomorphogenic homolog subunit 3 (Arabidopsis)"			9535219, 10191102	Standard	NM_003653		Approved	SGN3, CSN3	uc002grd.3	Q9UNS2	OTTHUMG00000059281	ENST00000268717.5:c.161A>T	chr17.hg19:g.17179373T>A	ENSP00000268717:p.His54Leu	164.0	0.0		126.0	14.0	NM_003653	B2R683|B4DY81|O43191|Q7LDR6	Missense_Mutation	SNP	ENST00000268717.5	hg19	CCDS11183.1	.	.	.	.	.	.	.	.	.	.	T	26.8	4.774654	0.90108	.	.	ENSG00000141030	ENST00000268717;ENST00000539941;ENST00000417352;ENST00000439936	T;T;T	0.46819	0.86;0.86;0.86	5.06	5.06	0.68205	.	0.000000	0.85682	D	0.000000	T	0.71634	0.3363	M	0.86502	2.82	0.80722	D	1	D	0.76494	0.999	D	0.72625	0.978	T	0.77466	-0.2577	10	0.66056	D	0.02	-22.038	14.2848	0.66240	0.0:0.0:0.0:1.0	.	54	Q9UNS2	CSN3_HUMAN	L	54;34;54;78	ENSP00000268717:H54L;ENSP00000437606:H34L;ENSP00000409028:H54L	ENSP00000268717:H54L	H	-	2	0	COPS3	17120098	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.801000	0.85960	2.023000	0.59567	0.454000	0.30748	CAC	.	.		0.438	COPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131603.2			A	17179373	T	A	17179373	3	1	237	1	0	0	0	0	1	0	0	0	3736	1696	59	4	1154	4	COPS3	17	17179373	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	6861778	17179373	64015837	178	33084										
SUPT6H	6830	hgsc.bcm.edu	37	chr17	27017195	27017196	+	Frame_Shift_Del	DEL	AG	AG	-													0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gcctaccgctctcccaacacAgaggagatcttcaatatgtt							TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr17:27017195_27017196delAG	ENST00000314616.6	+	26	3721_3722	c.3438_3439delAG	c.(3436-3441)acagagfs	p.E1148fs	SUPT6H_ENST00000347486.4_Frame_Shift_Del_p.E1148fs	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	1148	Interaction with KDM6A. {ECO:0000250}.				chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					CTCCCAACACAGAGGAGATCTT	0.48																																					p.1146_1146del		Atlas-Indel,Pindel	.											.	SUPT6H	165	.	0			c.3437_3438del						.																																			SO:0001589	frameshift_variant	6830	exon26			.	U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"SH2 domain containing"	11470	protein-coding gene	gene with protein product		601333	"suppressor of Ty (S.cerevisiae) 6 homolog"			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85		ENST00000314616.6:c.3438_3439delAG	chr17.hg19:g.27017197_27017198delAG	ENSP00000319104:p.Glu1148fs	267.0	0.0		277.0	80.0	NM_003170	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Frame_Shift_Del	DEL	ENST00000314616.6	hg19	CCDS32596.1																																																																																			.	.		0.48	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170		-	27017196	AG	-	27017195	7	5	237	1	0	1	0	1	0	0	0	0	15415	175	7	0	3536	0	SUPT6H	17	27017195	Frame_Shift_Del	DEL	AG	TCGA-ED-A459-01A-11D-A25V-10	9837822	27017195	54178015	179	33085										
CCR7	1236	hgsc.bcm.edu	37	chr17	38711882	38711882	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ttgagcctcttgaaatagatAtaggtcaacacgaccagccc	8	11	2	3			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr17:38711882A>G	ENST00000246657.2	-	3	311	c.249T>C	c.(247-249)taT>taC	p.Y83Y	CCR7_ENST00000579344.1_Silent_p.Y77Y	NM_001838.3	NP_001829.1	P32248	CCR7_HUMAN	chemokine (C-C motif) receptor 7	83					activation of Rho GTPase activity (GO:0032862)|cellular response to cytokine stimulus (GO:0071345)|chemokine (C-C motif) ligand 19 signaling pathway (GO:0038115)|chemokine (C-C motif) ligand 21 signaling pathway (GO:0038116)|chemokine-mediated signaling pathway (GO:0070098)|dendritic cell chemotaxis (GO:0002407)|establishment of T cell polarity (GO:0001768)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interleukin-12 secretion (GO:0072610)|lymphocyte migration into lymph node (GO:0097022)|mature dendritic cell differentiation (GO:0097029)|myeloid dendritic cell chemotaxis (GO:0002408)|negative regulation of leukocyte apoptotic process (GO:2000107)|negative thymic T cell selection (GO:0045060)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell motility (GO:2000147)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of glycoprotein biosynthetic process involved in immunological synapse formation (GO:2000526)|positive regulation of humoral immune response (GO:0002922)|positive regulation of hypersensitivity (GO:0002885)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of immunological synapse formation (GO:2000522)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of T cell costimulation (GO:2000525)|positive regulation of T cell receptor signaling pathway (GO:0050862)|regulation of dendritic cell dendrite assembly (GO:2000547)|regulation of interferon-gamma production (GO:0032649)|regulation of interleukin-1 beta secretion (GO:0050706)|release of sequestered calcium ion into cytosol (GO:0051209)|response to lipopolysaccharide (GO:0032496)|response to nitric oxide (GO:0071731)|response to prostaglandin E (GO:0034695)|ruffle organization (GO:0031529)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|C-C motif chemokine 19 receptor activity (GO:0038117)|C-C motif chemokine 21 receptor activity (GO:0038121)|chemokine (C-C motif) ligand 19 binding (GO:0035757)|chemokine (C-C motif) ligand 21 binding (GO:0035758)|G-protein coupled receptor activity (GO:0004930)			breast(1)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		Breast(137;0.000496)				TGAAATAGATATAGGTCAACA	0.522																																					p.Y83Y		Atlas-SNP	.											.	CCR7	31	.	0			c.T249C						.						103	98	99					17																	38711882		2203	4300	6503	SO:0001819	synonymous_variant	1236	exon3			ATAGATATAGGTC		CCDS11369.1	17q12-q21.2	2012-08-08			ENSG00000126353	ENSG00000126353		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1608	protein-coding gene	gene with protein product		600242		CMKBR7, EBI1		8383238	Standard	NM_001838		Approved	BLR2, CDw197, CD197	uc002huw.3	P32248	OTTHUMG00000133375	ENST00000246657.2:c.249T>C	chr17.hg19:g.38711882A>G		150.0	0.0		173.0	23.0	NM_001838		Silent	SNP	ENST00000246657.2	hg19	CCDS11369.1																																																																																			.	.		0.522	CCR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257222.1			G	38711882	A	G	38711882	2	3	237	1	0	0	0	0	0	0	0	1	2948	456	16	2		2	CCR7	17	38711882	Silent	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	11694687	38711882	42483328	180	33086										
KRT40	125115	hgsc.bcm.edu	37	chr17	39135187	39135187	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	cggatctcggccagctggttCtccaggttatcgatcagaca	11	12	3	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr17:39135187C>T	ENST00000398486.2	-	8	1225	c.1065G>A	c.(1063-1065)gaG>gaA	p.E355E	KRT40_ENST00000377755.4_Silent_p.E355E	NM_182497.3	NP_872303.2	Q6A162	K1C40_HUMAN	keratin 40	355	Coil 2.|Rod.					intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9		Breast(137;0.00043)				CCAGCTGGTTCTCCAGGTTAT	0.597																																					p.E355E		Atlas-SNP	.											.	KRT40	27	.	0			c.G1065A						.						89	98	95					17																	39135187		2202	4295	6497	SO:0001819	synonymous_variant	125115	exon8			CTGGTTCTCCAGG	AK093919	CCDS42320.1	17q21.2	2013-01-16			ENSG00000204889	ENSG00000204889		"-", "Intermediate filaments type I, keratins (acidic)"	26707	protein-coding gene	gene with protein product						16831889	Standard	NM_182497		Approved	FLJ36600, KA36	uc010cxh.1	Q6A162	OTTHUMG00000133596	ENST00000398486.2:c.1065G>A	chr17.hg19:g.39135187C>T		176.0	0.0		152.0	49.0	NM_182497	Q6IFU5	Silent	SNP	ENST00000398486.2	hg19	CCDS42320.1																																																																																			.	.		0.597	KRT40-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257701.3	NM_182497		T	39135187	C	T	39135187	2	4	237	1	0	0	0	0	0	0	0	1	8487	912	32	3		3	KRT40	17	39135187	Silent	SNP	C	TCGA-ED-A459-01A-11D-A25V-10	423305	39135187	42060023	181	33087										
STAT3	6774	hgsc.bcm.edu	37	chr17	40474482	40474482	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tgttcagctgctgctttgtgTatggttccacggactggatc	12	9	1	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr17:40474482T>A	ENST00000264657.5	-	21	2231	c.1919A>T	c.(1918-1920)tAc>tTc	p.Y640F	STAT3_ENST00000389272.3_Missense_Mutation_p.Y542F|STAT3_ENST00000588969.1_Missense_Mutation_p.Y640F|STAT3_ENST00000404395.3_Missense_Mutation_p.Y640F|STAT3_ENST00000585517.1_Missense_Mutation_p.Y640F	NM_003150.3|NM_139276.2	NP_003141.2|NP_644805.1	P40763	STAT3_HUMAN	signal transducer and activator of transcription 3 (acute-phase response factor)	640	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				acute-phase response (GO:0006953)|astrocyte differentiation (GO:0048708)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|cellular response to hormone stimulus (GO:0032870)|cytokine-mediated signaling pathway (GO:0019221)|eating behavior (GO:0042755)|eye photoreceptor cell differentiation (GO:0001754)|glucose homeostasis (GO:0042593)|growth hormone receptor signaling pathway (GO:0060396)|interleukin-6-mediated signaling pathway (GO:0070102)|intracellular receptor signaling pathway (GO:0030522)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of neuron migration (GO:2001223)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|radial glial cell differentiation (GO:0060019)|regulation of multicellular organism growth (GO:0040014)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|sexual reproduction (GO:0019953)|signal transduction (GO:0007165)|stem cell maintenance (GO:0019827)|temperature homeostasis (GO:0001659)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		all_cancers(22;1.39e-06)|all_epithelial(22;2.95e-05)|Breast(137;0.000135)		BRCA - Breast invasive adenocarcinoma(366;0.139)		CTGCTTTGTGTATGGTTCCAC	0.463									Hyperimmunoglobulin E Recurrent Infection Syndrome																												p.Y640F		Atlas-SNP	.											STAT3,NS,lymphoid_neoplasm,0,46	STAT3	268	.	0			c.A1919T						.						243	213	223					17																	40474482		2203	4300	6503	SO:0001583	missense	6774	exon21	Familial Cancer Database	HIES, Hyper IgE syndrome, autosomal dominant (Job syndrome) / recessive	TTTGTGTATGGTT	BC014482	CCDS32656.1, CCDS32657.1, CCDS59288.1	17q21	2014-09-17			ENSG00000168610	ENSG00000168610		"SH2 domain containing"	11364	protein-coding gene	gene with protein product		102582				7512451	Standard	NM_139276		Approved	APRF	uc002hzl.1	P40763	OTTHUMG00000150645	ENST00000264657.5:c.1919A>T	chr17.hg19:g.40474482T>A	ENSP00000264657:p.Tyr640Phe	343.0	0.0		390.0	22.0	NM_003150	A8K7B8|K7ENL3|O14916|Q9BW54	Missense_Mutation	SNP	ENST00000264657.5	hg19	CCDS32656.1	.	.	.	.	.	.	.	.	.	.	T	19.36	3.813449	0.70912	.	.	ENSG00000168610	ENST00000264657;ENST00000389272;ENST00000404395	D;D;D	0.89196	-2.48;-2.48;-2.48	4.64	4.64	0.57946	SH2 motif (4);	0.000000	0.85682	D	0.000000	D	0.87120	0.6098	N	0.16016	0.355	0.80722	D	1	D;D;D	0.59357	0.982;0.985;0.985	D;D;D	0.78314	0.984;0.991;0.991	T	0.82589	-0.0382	10	0.06891	T	0.86	-37.3581	14.2314	0.65895	0.0:0.0:0.0:1.0	.	640;640;640	P40763-2;P40763;B5BTZ6	.;STAT3_HUMAN;.	F	640;542;640	ENSP00000264657:Y640F;ENSP00000373923:Y542F;ENSP00000384943:Y640F	ENSP00000264657:Y640F	Y	-	2	0	STAT3	37728008	1.000000	0.71417	0.964000	0.40570	0.715000	0.41141	7.868000	0.87116	1.953000	0.56701	0.460000	0.39030	TAC	.	.		0.463	STAT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319353.3	NM_139276, NM_003150		A	40474482	T	A	40474482	3	1	237	1	0	0	0	0	1	0	0	0	15281	1638	57	4	409	4	STAT3	17	40474482	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	1339295	40474482	40720728	182	33088										
SLC25A39	51629	hgsc.bcm.edu	37	chr17	42398495	42398495	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tgagcgccagccaccctgagCcactgcagttcgaacacagg	11	15	0	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr17:42398495C>T	ENST00000377095.5	-	8	741	c.622G>A	c.(622-624)Gct>Act	p.A208T	SLC25A39_ENST00000225308.8_Missense_Mutation_p.A200T|SLC25A39_ENST00000586016.1_Missense_Mutation_p.A76T|SLC25A39_ENST00000590194.1_Missense_Mutation_p.A200T|SLC25A39_ENST00000537904.2_Missense_Mutation_p.A185T	NM_001143780.1	NP_001137252.1	Q9BZJ4	S2539_HUMAN	solute carrier family 25, member 39	208					heme biosynthetic process (GO:0006783)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)		p.A200T(1)		endometrium(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	7		Prostate(33;0.0233)		BRCA - Breast invasive adenocarcinoma(366;0.189)		CCACCCTGAGCCACTGCAGTT	0.642																																					p.A208T		Atlas-SNP	.											SLC25A39,NS,carcinoma,0,1	SLC25A39	24	.	1	Substitution - Missense(1)	lung(1)	c.G622A						.						31	28	29					17																	42398495		2202	4299	6501	SO:0001583	missense	51629	exon8			CCTGAGCCACTGC	BC096819	CCDS11482.1, CCDS45700.1	17q12	2013-05-22			ENSG00000013306	ENSG00000013306		"Solute carriers"	24279	protein-coding gene	gene with protein product		610820				16949250	Standard	NM_001143780		Approved	FLJ22407, CGI-69	uc002ign.2	Q9BZJ4	OTTHUMG00000132628	ENST00000377095.5:c.622G>A	chr17.hg19:g.42398495C>T	ENSP00000366299:p.Ala208Thr	119.0	0.0		86.0	23.0	NM_001143780	A8JZZ2|D3DX51|D3DX54|Q4V9M1|Q9P182|Q9UF66|Q9Y379	Missense_Mutation	SNP	ENST00000377095.5	hg19	CCDS45700.1	.	.	.	.	.	.	.	.	.	.	C	14.76	2.631520	0.46944	.	.	ENSG00000013306	ENST00000225308;ENST00000377095;ENST00000537904	T;T;T	0.79141	-1.24;-1.24;-1.24	5.31	1.99	0.26369	Mitochondrial carrier domain (2);	0.256023	0.38164	N	0.001790	T	0.67353	0.2884	L	0.41492	1.28	0.38462	D	0.947234	B;B;B	0.18166	0.002;0.026;0.005	B;B;B	0.29077	0.009;0.098;0.012	T	0.61865	-0.6975	10	0.36615	T	0.2	-0.5426	7.7893	0.29110	0.1909:0.6602:0.0:0.1489	.	185;208;200	B4DFG5;Q9BZJ4;Q9BZJ4-2	.;S2539_HUMAN;.	T	200;208;185	ENSP00000225308:A200T;ENSP00000366299:A208T;ENSP00000444540:A185T	ENSP00000225308:A200T	A	-	1	0	SLC25A39	39754021	0.995000	0.38212	1.000000	0.80357	0.860000	0.49131	1.445000	0.35079	0.791000	0.33826	0.655000	0.94253	GCT	.	.		0.642	SLC25A39-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457745.1	NM_016016		T	42398495	C	T	42398495	3	4	237	1	0	0	0	0	1	0	0	0	14518	739	26	3	477	3	SLC25A39	17	42398495	Missense_Mutation	SNP	C	TCGA-ED-A459-01A-11D-A25V-10	1924013	42398495	38796715	183	33089										
CACNA1G	8913	hgsc.bcm.edu	37	chr17	48668930	48668930	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ggtgctcatgaagaccatggAcaacgtggccaccttctgca	11	12	2	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr17:48668930A>G	ENST00000359106.5	+	11	2588	c.2588A>G	c.(2587-2589)gAc>gGc	p.D863G	CACNA1G_ENST00000513964.1_Missense_Mutation_p.D863G|CACNA1G_ENST00000503485.1_Missense_Mutation_p.D863G|CACNA1G_ENST00000507336.1_Missense_Mutation_p.D863G|CACNA1G_ENST00000502264.1_Missense_Mutation_p.D863G|CACNA1G_ENST00000352832.5_Missense_Mutation_p.D863G|CACNA1G_ENST00000354983.4_Missense_Mutation_p.D863G|CACNA1G_ENST00000507510.2_Missense_Mutation_p.D863G|CACNA1G_ENST00000416767.4_Missense_Mutation_p.D863G|CACNA1G_ENST00000512389.1_Missense_Mutation_p.D863G|CACNA1G_ENST00000360761.4_Missense_Mutation_p.D863G|CACNA1G_ENST00000510366.1_Missense_Mutation_p.D863G|CACNA1G_ENST00000515165.1_Missense_Mutation_p.D863G|CACNA1G_ENST00000515765.1_Missense_Mutation_p.D863G|CACNA1G_ENST00000429973.2_Missense_Mutation_p.D863G|CACNA1G_ENST00000507609.1_Missense_Mutation_p.D863G|CACNA1G_ENST00000510115.1_Missense_Mutation_p.D863G|CACNA1G_ENST00000513689.2_Missense_Mutation_p.D863G|CACNA1G_ENST00000358244.5_Missense_Mutation_p.D863G|CACNA1G_ENST00000515411.1_Missense_Mutation_p.D863G|CACNA1G_ENST00000514079.1_Missense_Mutation_p.D863G|CACNA1G_ENST00000514181.1_Missense_Mutation_p.D863G|CACNA1G_ENST00000505165.1_Missense_Mutation_p.D863G|CACNA1G_ENST00000514717.1_Missense_Mutation_p.D863G|CACNA1G_ENST00000442258.2_Missense_Mutation_p.D863G|CACNA1G_ENST00000507896.1_Missense_Mutation_p.D863G	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	863					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	AAGACCATGGACAACGTGGCC	0.632																																					p.D863G		Atlas-SNP	.											.	CACNA1G	659	.	0			c.A2588G						.						54	58	57					17																	48668930		2200	4285	6485	SO:0001583	missense	8913	exon11			CCATGGACAACGT	AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.2588A>G	chr17.hg19:g.48668930A>G	ENSP00000352011:p.Asp863Gly	128.0	0.0		99.0	32.0	NM_001256360	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Missense_Mutation	SNP	ENST00000359106.5	hg19	CCDS45730.1	.	.	.	.	.	.	.	.	.	.	a	27.4	4.825215	0.90955	.	.	ENSG00000006283	ENST00000360761;ENST00000352832;ENST00000416767;ENST00000354983;ENST00000442258;ENST00000502264;ENST00000512389;ENST00000513964;ENST00000514717;ENST00000510366;ENST00000503485;ENST00000507510;ENST00000507336;ENST00000513689;ENST00000507609;ENST00000510115;ENST00000515165;ENST00000514181;ENST00000515765;ENST00000514079;ENST00000358244;ENST00000359106;ENST00000429973;ENST00000515411;ENST00000505165;ENST00000507896	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97404	-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37	5.55	5.55	0.83447	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.96525	0.8866	N	0.25890	0.77	0.80722	D	1	D;D;D;D;D;D;D;D;D;P;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.999;1.0;0.999;0.999;1.0;0.999;0.999;1.0;0.999;0.763;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;P;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	0.996;1.0;0.999;0.998;0.999;0.999;0.998;1.0;0.998;0.852;1.0;1.0;1.0;1.0;0.998;1.0;1.0;0.999;1.0;1.0;0.999;1.0;1.0;1.0;0.999;0.999	D	0.94741	0.7919	10	0.11794	T	0.64	.	15.6931	0.77469	1.0:0.0:0.0:0.0	.	863;863;863;863;863;863;863;863;863;863;863;863;863;863;863;863;863;863;863;863;863;863;863;863;863;863	Q19QZ5;Q19QZ1;Q19QZ4;Q19R07;Q19QY8;Q19R10;Q19QZ6;Q19QZ3;Q19R06;Q19R00;Q19R04;O43497-10;Q19QZ9;Q19QZ7;Q19R08;Q19QZ8;Q19R03;O43497-4;Q19R02;Q19R12;Q19R17;Q19R11;Q2TAC4;O43497;Q19R13;O43497-11	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;CAC1G_HUMAN;.;.	G	863	ENSP00000353990:D863G;ENSP00000339302:D863G;ENSP00000392390:D863G;ENSP00000347078:D863G;ENSP00000409759:D863G;ENSP00000425522:D863G;ENSP00000426261:D863G;ENSP00000425451:D863G;ENSP00000422407:D863G;ENSP00000426814:D863G;ENSP00000427238:D863G;ENSP00000423112:D863G;ENSP00000420918:D863G;ENSP00000426172:D863G;ENSP00000423045:D863G;ENSP00000427173:D863G;ENSP00000426098:D863G;ENSP00000425698:D863G;ENSP00000426232:D863G;ENSP00000423317:D863G;ENSP00000350979:D863G;ENSP00000352011:D863G;ENSP00000414388:D863G;ENSP00000423155:D863G;ENSP00000422268:D863G;ENSP00000421518:D863G	ENSP00000339302:D863G	D	+	2	0	CACNA1G	46023929	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.334000	0.96470	2.119000	0.64992	0.379000	0.24179	GAC	.	.		0.632	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896		G	48668930	A	G	48668930	3	3	237	1	0	0	0	0	1	0	0	0	2546	275	10	2	2630	2	CACNA1G	17	48668930	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	6270435	48668930	32526280	184	33090										
STXBP4	252983	hgsc.bcm.edu	37	chr17	53077023	53077023	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gcttgggagatagcattcatAagacaaaaatccgacaacat	8	8	1	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr17:53077023A>T	ENST00000376352.2	+	6	525	c.318A>T	c.(316-318)atA>atT	p.I106I	STXBP4_ENST00000434978.2_Silent_p.I106I|STXBP4_ENST00000299341.4_Silent_p.I31I|STXBP4_ENST00000398391.2_Silent_p.I31I|STXBP4_ENST00000405898.1_Silent_p.I106I	NM_178509.5	NP_848604.3	Q6ZWJ1	STXB4_HUMAN	syntaxin binding protein 4	106					cellular response to DNA damage stimulus (GO:0006974)|glucose transport (GO:0015758)|insulin receptor signaling pathway (GO:0008286)|positive regulation of cell cycle G1/S phase transition (GO:1902808)|positive regulation of keratinocyte proliferation (GO:0010838)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(4)|ovary(1)|upper_aerodigestive_tract(2)	19						TAGCATTCATAAGACAAAAAT	0.343																																					p.I106I		Atlas-SNP	.											.	STXBP4	41	.	0			c.A318T						.						68	66	66					17																	53077023		2203	4300	6503	SO:0001819	synonymous_variant	252983	exon6			ATTCATAAGACAA	BC041485	CCDS11584.2	17q22	2008-02-05			ENSG00000166263	ENSG00000166263			19694	protein-coding gene	gene with protein product		610415				12855681	Standard	XM_005257187		Approved	Synip, MGC50337	uc002iuf.1	Q6ZWJ1	OTTHUMG00000074043	ENST00000376352.2:c.318A>T	chr17.hg19:g.53077023A>T		125.0	0.0		144.0	8.0	NM_178509	Q8IVZ5	Silent	SNP	ENST00000376352.2	hg19	CCDS11584.2																																																																																			.	.		0.343	STXBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157184.1	NM_178509		T	53077023	A	T	53077023	2	4	237	1	0	0	0	0	0	0	0	1	15370	352	13	4		4	STXBP4	17	53077023	Silent	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	4408093	53077023	28118187	185	33091										
RNF43	54894	hgsc.bcm.edu	37	chr17	56435407	56435407	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gaggaataggaggcctggacTgggggactccggtttctggg	19	7	1	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr17:56435407T>A	ENST00000584437.1	-	8	3685	c.1730A>T	c.(1729-1731)cAg>cTg	p.Q577L	RNF43_ENST00000500597.2_Missense_Mutation_p.Q536L|RNF43_ENST00000583753.1_Missense_Mutation_p.Q536L|RNF43_ENST00000407977.2_Missense_Mutation_p.Q577L|RNF43_ENST00000581868.1_Missense_Mutation_p.Q450L|RNF43_ENST00000577625.1_Missense_Mutation_p.Q450L|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000577716.1_Missense_Mutation_p.Q577L			Q68DV7	RNF43_HUMAN	ring finger protein 43	577	Pro-rich.				negative regulation of Wnt signaling pathway (GO:0030178)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|stem cell proliferation (GO:0072089)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(5)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(14)|lung(9)|ovary(2)|pancreas(10)|prostate(1)|skin(4)	60	Medulloblastoma(34;0.127)|all_neural(34;0.237)					AGGCCTGGACTGGGGGACTCC	0.622																																					p.Q577L		Atlas-SNP	.											.	RNF43	157	.	0			c.A1730T						.						65	76	73					17																	56435407		2202	4300	6502	SO:0001583	missense	54894	exon9			CTGGACTGGGGGA		CCDS11607.1	17q23.2	2013-01-09						"RING-type (C3HC4) zinc fingers"	18505	protein-coding gene	gene with protein product		612482					Standard	NM_017763		Approved	FLJ20315, DKFZp781H0392, URCC	uc002iwh.4	Q68DV7		ENST00000584437.1:c.1730A>T	chr17.hg19:g.56435407T>A	ENSP00000463069:p.Gln577Leu	125.0	0.0		121.0	14.0	NM_017763	A8K4R2|B7Z443|B7Z5D5|B7Z5J5|Q65ZA4|Q6AI04|Q9NXD0	Missense_Mutation	SNP	ENST00000584437.1	hg19	CCDS11607.1	.	.	.	.	.	.	.	.	.	.	T	4.514	0.095399	0.08681	.	.	ENSG00000108375	ENST00000407977;ENST00000500597	T;T	0.21543	2.0;2.0	5.3	0.145	0.14829	.	1.080280	0.07039	N	0.829808	T	0.12646	0.0307	N	0.24115	0.695	0.09310	N	1	B;B;B	0.09022	0.0;0.002;0.0	B;B;B	0.09377	0.002;0.004;0.0	T	0.40365	-0.9567	10	0.10377	T	0.69	-19.7098	8.0507	0.30577	0.121:0.0:0.3768:0.5021	.	536;577;577	Q68DV7-2;Q68DV7-4;Q68DV7	.;.;RNF43_HUMAN	L	577;536	ENSP00000385328:Q577L;ENSP00000441969:Q536L	ENSP00000385328:Q577L	Q	-	2	0	RNF43	53790406	0.862000	0.29867	0.058000	0.19502	0.020000	0.10135	-0.171000	0.09883	-0.666000	0.05310	-1.203000	0.01651	CAG	.	.		0.622	RNF43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444713.1	NM_017763		A	56435407	T	A	56435407	3	1	237	1	0	0	0	0	1	0	0	0	13510	1580	55	4	629	4	RNF43	17	56435407	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	3358384	56435407	24759803	186	33092										
BCAS3	54828	hgsc.bcm.edu	37	chr17	59155891	59155891	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	cttgatctcaacagtctcagGtaggaaatgagaattaggga	11	6	2	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr17:59155891G>A	ENST00000390652.5	+	22	2403		c.e22+1		BCAS3_ENST00000408905.3_Splice_Site|BCAS3_ENST00000588874.1_Splice_Site|BCAS3_ENST00000407086.3_Splice_Site|BCAS3_ENST00000589222.1_Splice_Site|BCAS3_ENST00000588462.1_Splice_Site|BCAS3_ENST00000585744.1_Splice_Site	NM_001099432.1	NP_001092902.1			breast carcinoma amplified sequence 3											NS(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(24)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)			ACAGTCTCAGGTAGGAAATGA	0.403																																					.		Atlas-SNP	.											.	BCAS3	90	.	0			c.2372+1G>A						.						65	58	60					17																	59155891		1925	4142	6067	SO:0001630	splice_region_variant	54828	exon22			TCTCAGGTAGGAA	AF361219	CCDS11626.1, CCDS45749.1	17q23.2	2013-06-25			ENSG00000141376	ENSG00000141376		"WD repeat domain containing"	14347	protein-coding gene	gene with protein product		607470				12378525	Standard	NM_017679		Approved	FLJ20128	uc002iyv.4	Q9H6U6	OTTHUMG00000180064	ENST00000390652.5:c.2372+1G>A	chr17.hg19:g.59155891G>A		138.0	0.0		154.0	44.0	NM_001099432		Splice_Site	SNP	ENST00000390652.5	hg19	CCDS45749.1	.	.	.	.	.	.	.	.	.	.	G	32	5.179424	0.94846	.	.	ENSG00000141376	ENST00000390652;ENST00000407086;ENST00000408905	.	.	.	5.31	5.31	0.75309	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.3441	0.94356	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	BCAS3	56510673	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.567000	0.98161	2.658000	0.90341	0.585000	0.79938	.	.	.		0.403	BCAS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449578.1	NM_017679	Intron	A	59155891	G	A	59155891	5	1	237	1	0	0	0	0	0	0	1	0	1352	1275	44	3	2455	3	BCAS3	17	59155891	Splice_Site	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	2720484	59155891	22039319	187	33093										
BPTF	2186	hgsc.bcm.edu	37	chr17	65920668	65920668	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ctttttttcctgcagagtggAgaaagaaaaggcacaagcag	11	7	0	3			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr17:65920668A>G	ENST00000321892.4	+	17	6153	c.6092A>G	c.(6091-6093)gAg>gGg	p.E2031G	BPTF_ENST00000424123.3_Missense_Mutation_p.E1892G|BPTF_ENST00000335221.5_Missense_Mutation_p.E2031G|BPTF_ENST00000306378.6_Missense_Mutation_p.E1905G			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	2031					anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			TGCAGAGTGGAGAAAGAAAAG	0.413																																					p.E2031G		Atlas-SNP	.											.	BPTF	415	.	0			c.A6092G						.						85	81	82					17																	65920668		2203	4300	6503	SO:0001583	missense	2186	exon17			GAGTGGAGAAAGA	AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"Zinc fingers, PHD-type"	3581	protein-coding gene	gene with protein product		601819	"fetal Alzheimer antigen"	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.6092A>G	chr17.hg19:g.65920668A>G	ENSP00000315454:p.Glu2031Gly	261.0	0.0		293.0	105.0	NM_004459	Q6NX67|Q7Z7D6|Q9UIG2	Missense_Mutation	SNP	ENST00000321892.4	hg19		.	.	.	.	.	.	.	.	.	.	A	18.60	3.658798	0.67586	.	.	ENSG00000171634	ENST00000306378;ENST00000335221;ENST00000321892	T;T;T	0.15718	2.4;2.4;2.4	5.12	5.12	0.69794	.	.	.	.	.	T	0.32882	0.0844	L	0.36672	1.1	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.83275	0.996;0.994	T	0.06427	-1.0827	9	0.87932	D	0	.	15.2325	0.73401	1.0:0.0:0.0:0.0	.	1905;2031	Q12830-2;Q12830-4	.;.	G	1905;2031;2031	ENSP00000307208:E1905G;ENSP00000334351:E2031G;ENSP00000315454:E2031G	ENSP00000307208:E1905G	E	+	2	0	BPTF	63351130	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.073000	0.93992	2.054000	0.61138	0.528000	0.53228	GAG	.	.		0.413	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459		G	65920668	A	G	65920668	3	3	237	1	0	0	0	0	1	0	0	0	1497	304	11	2	6158	2	BPTF	17	65920668	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	6764777	65920668	15274542	188	33094										
KIF19	124602	hgsc.bcm.edu	37	chr17	72349367	72349367	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	cgtgttcaaggctggtactgGggcctggcaggcaaaaagct	15	9	1	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr17:72349367G>T	ENST00000389916.4	+	16	2285	c.2147G>T	c.(2146-2148)gGg>gTg	p.G716V	AC103809.2_ENST00000599136.1_5'Flank	NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	716					ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						GCTGGTACTGGGGCCTGGCAG	0.627																																					p.G716V		Atlas-SNP	.											.	KIF19	102	.	0			c.G2147T						.						32	38	36					17																	72349367		2054	4193	6247	SO:0001583	missense	124602	exon16			GTACTGGGGCCTG	AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"Kinesins"	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.2147G>T	chr17.hg19:g.72349367G>T	ENSP00000374566:p.Gly716Val	201.0	0.0		192.0	88.0	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Missense_Mutation	SNP	ENST00000389916.4	hg19	CCDS32718.2	.	.	.	.	.	.	.	.	.	.	G	9.346	1.064263	0.20067	.	.	ENSG00000196169	ENST00000389916	T	0.69306	-0.39	5.14	4.17	0.49024	.	.	.	.	.	T	0.45397	0.1340	N	0.08118	0	0.36603	D	0.874798	B	0.21381	0.055	B	0.17722	0.019	T	0.48747	-0.9008	9	0.44086	T	0.13	.	10.8457	0.46741	0.0897:0.0:0.9103:0.0	.	716	Q2TAC6	KIF19_HUMAN	V	716	ENSP00000374566:G716V	ENSP00000374566:G716V	G	+	2	0	KIF19	69860962	0.959000	0.32827	0.253000	0.24343	0.023000	0.10783	3.731000	0.55013	1.169000	0.42739	0.456000	0.33151	GGG	.	.		0.627	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209		T	72349367	G	T	72349367	3	4	237	1	0	0	0	0	1	0	0	0	8291	1232	43	3	2209	3	KIF19	17	72349367	Missense_Mutation	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	6428699	72349367	8845843	189	33095										
LAMA1	284217	hgsc.bcm.edu	37	chr18	7013887	7013887	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ggttgcaggcgtcccccgacGtccccctcaggtcacagtca	11	17	3	0	rs377575918		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr18:7013887G>T	ENST00000389658.3	-	23	3383	c.3290C>A	c.(3289-3291)aCg>aAg	p.T1097K		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1097	Laminin EGF-like 13. {ECO:0000255|PROSITE-ProRule:PRU00460}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				GTCCCCCGACGTCCCCCTCAG	0.582																																					p.T1097K		Atlas-SNP	.											.	LAMA1	458	.	0			c.C3290A						.																																			SO:0001583	missense	284217	exon23			CCCGACGTCCCCC	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.3290C>A	chr18.hg19:g.7013887G>T	ENSP00000374309:p.Thr1097Lys	259.0	0.0		196.0	88.0	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	hg19	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.166549	0.78339	.	.	ENSG00000101680	ENST00000389658	T	0.61980	0.06	5.9	5.9	0.94986	EGF-like, laminin (3);	0.000000	0.85682	D	0.000000	D	0.84238	0.5428	M	0.93420	3.415	0.49213	D	0.999763	D	0.89917	1.0	D	0.73708	0.981	D	0.87579	0.2483	10	0.72032	D	0.01	.	16.5088	0.84279	0.0:0.1306:0.8694:0.0	.	1097	P25391	LAMA1_HUMAN	K	1097	ENSP00000374309:T1097K	ENSP00000374309:T1097K	T	-	2	0	LAMA1	7003887	1.000000	0.71417	0.957000	0.39632	0.486000	0.33341	7.048000	0.76606	2.783000	0.95769	0.637000	0.83480	ACG	.	.		0.582	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		T	7013887	G	T	7013887	3	4	237	1	0	0	0	0	1	0	0	0	8614	1145	40	1	6101	1	LAMA1	18	7013887	Missense_Mutation	SNP	G	TCGA-ED-A459-01A-11D-A25V-10		7013887	71063361	190	33096										
MATK	4145	hgsc.bcm.edu	37	chr19	3779601	3779601	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ccaggagacgcaccaggttcTcgtgttgcatcttcctgggg	13	12	2	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr19:3779601T>A	ENST00000310132.6	-	10	1255	c.857A>T	c.(856-858)gAg>gTg	p.E286V	MATK_ENST00000395040.2_Missense_Mutation_p.E245V|MATK_ENST00000585778.1_Missense_Mutation_p.E286V|MATK_ENST00000395045.2_Missense_Mutation_p.E287V	NM_139355.2	NP_647612.1	P42679	MATK_HUMAN	megakaryocyte-associated tyrosine kinase	286	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|mesoderm development (GO:0007498)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)	cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|skin(2)|stomach(2)|urinary_tract(1)	26		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)		CACCAGGTTCTCGTGTTGCAT	0.706																																					p.E287V		Atlas-SNP	.											.	MATK	108	.	0			c.A860T						.						21	21	21					19																	3779601		2201	4298	6499	SO:0001583	missense	4145	exon10			AGGTTCTCGTGTT	L18974	CCDS12113.1, CCDS12114.1, CCDS42468.1	19p13.3	2013-02-14						"SH2 domain containing"	6906	protein-coding gene	gene with protein product	"Csk-homologous kinase", "tyrosine-protein kinase CTK", "protein kinase HYL", "hematopoietic consensus tyrosine-lacking kinase", "tyrosylprotein kinase", "hydroxyaryl-protein kinase", "Csk-type protein tyrosine kinase", "HYL tyrosine kinase", "tyrosine kinase MATK", "leukocyte carboxyl-terminal src kinase related"	600038				8288563, 7530249	Standard	NM_139355		Approved	HYLTK, CTK, HYL, Lsk, CHK, HHYLTK, DKFZp434N1212, MGC1708, MGC2101	uc002lyt.3	P42679		ENST00000310132.6:c.857A>T	chr19.hg19:g.3779601T>A	ENSP00000308734:p.Glu286Val	55.0	0.0		34.0	7.0	NM_002378	B3KNZ9|Q9NST8	Missense_Mutation	SNP	ENST00000310132.6	hg19	CCDS12114.1	.	.	.	.	.	.	.	.	.	.	T	12.59	1.984240	0.35036	.	.	ENSG00000007264	ENST00000395045;ENST00000310132;ENST00000395040	T;T;T	0.62639	0.01;0.01;0.01	3.93	1.43	0.22495	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.148199	0.40222	U	0.001150	T	0.48370	0.1496	L	0.43757	1.38	0.25262	N	0.989585	B;B;B	0.12630	0.002;0.006;0.002	B;B;B	0.16289	0.015;0.004;0.015	T	0.42413	-0.9453	10	0.59425	D	0.04	-17.8713	5.9103	0.19025	0.0:0.3304:0.0:0.6696	.	286;287;286	F1T0G6;B3KNZ9;P42679	.;.;MATK_HUMAN	V	287;286;245	ENSP00000378485:E287V;ENSP00000308734:E286V;ENSP00000378481:E245V	ENSP00000308734:E286V	E	-	2	0	MATK	3730601	1.000000	0.71417	0.813000	0.32504	0.759000	0.43091	2.220000	0.42908	0.045000	0.15804	0.246000	0.17985	GAG	.	.		0.706	MATK-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453639.1	NM_139355		A	3779601	T	A	3779601	3	1	237	1	0	0	0	0	1	0	0	0	9341	1551	54	4	686	4	MATK	19	3779601	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10		3779601	55349382	191	33097										
DNMT1	1786	hgsc.bcm.edu	37	chr19	10251564	10251564	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gctcgctcggctcacaggctTgggacttgggcttgcccttc	13	14	1	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr19:10251564T>G	ENST00000340748.4	-	31	3603	c.3368A>C	c.(3367-3369)cAa>cCa	p.Q1123P	DNMT1_ENST00000359526.4_Missense_Mutation_p.Q1139P|DNMT1_ENST00000589538.1_5'UTR|DNMT1_ENST00000540357.1_Missense_Mutation_p.Q1123P			P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1	1123	Interaction with the PRC2/EED-EZH2 complex. {ECO:0000250}.				cellular response to amino acid stimulus (GO:0071230)|chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|gene silencing (GO:0016458)|maintenance of DNA methylation (GO:0010216)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|regulation of cell proliferation (GO:0042127)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|replication fork (GO:0005657)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methyl-CpG binding (GO:0008327)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(5)|endometrium(8)|kidney(5)|large_intestine(21)|lung(11)|ovary(2)|pancreas(1)|prostate(10)|skin(5)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Procainamide(DB01035)	CTCACAGGCTTGGGACTTGGG	0.597																																					p.Q1139P		Atlas-SNP	.											.	DNMT1	148	.	0			c.A3416C						.						76	69	72					19																	10251564		2203	4300	6503	SO:0001583	missense	1786	exon32			CAGGCTTGGGACT	X63692	CCDS12228.1, CCDS45958.1	19p13.2	2014-09-17				ENSG00000130816	2.1.1.37		2976	protein-coding gene	gene with protein product		126375		DNMT		1594447	Standard	NM_001379		Approved	MCMT, CXXC9	uc010xlc.2	P26358		ENST00000340748.4:c.3368A>C	chr19.hg19:g.10251564T>G	ENSP00000345739:p.Gln1123Pro	60.0	0.0		65.0	27.0	NM_001130823	A0AV63|B7ZLW6|Q9UHG5|Q9ULA2|Q9UMZ6	Missense_Mutation	SNP	ENST00000340748.4	hg19	CCDS12228.1	.	.	.	.	.	.	.	.	.	.	T	11.01	1.513982	0.27123	.	.	ENSG00000130816	ENST00000359526;ENST00000540357;ENST00000340748;ENST00000541266	T;T;T	0.24538	1.85;1.85;1.85	5.6	-2.64	0.06114	.	0.505328	0.21369	N	0.075678	T	0.18841	0.0452	L	0.44542	1.39	0.09310	N	1	B;B;B	0.15141	0.012;0.012;0.004	B;B;B	0.12156	0.007;0.007;0.003	T	0.24404	-1.0161	10	0.40728	T	0.16	.	11.6486	0.51275	0.1045:0.0:0.5741:0.3214	.	1123;1139;1123	F5GX68;P26358-2;P26358	.;.;DNMT1_HUMAN	P	1139;1123;1123;991	ENSP00000352516:Q1139P;ENSP00000440457:Q1123P;ENSP00000345739:Q1123P	ENSP00000345739:Q1123P	Q	-	2	0	DNMT1	10112564	0.000000	0.05858	0.001000	0.08648	0.018000	0.09664	-0.050000	0.11904	-0.219000	0.10003	-0.313000	0.08912	CAA	.	.		0.597	DNMT1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451166.1	NM_001379		G	10251564	T	G	10251564	3	3	237	1	0	0	0	0	1	0	0	0	4677	1812	63	5	1522	5	DNMT1	19	10251564	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	6471963	10251564	48877419	192	33098										
DNM2	1785	hgsc.bcm.edu	37	chr19	10906053	10906053	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tttgtctcttctcagatggaGtttgacgagaaggacttacg	11	7	2	3			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr19:10906053G>C	ENST00000355667.6	+	9	1214	c.1134G>C	c.(1132-1134)gaG>gaC	p.E378D	DNM2_ENST00000408974.4_Missense_Mutation_p.E378D|DNM2_ENST00000314646.5_Missense_Mutation_p.E378D|DNM2_ENST00000585892.1_Missense_Mutation_p.E378D|DNM2_ENST00000389253.4_Missense_Mutation_p.E378D|DNM2_ENST00000359692.6_Missense_Mutation_p.E378D	NM_001005360.2|NM_001190716.1	NP_001005360.1|NP_001177645.1	P50570	DYN2_HUMAN	dynamin 2	378					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|endocytosis (GO:0006897)|G2/M transition of mitotic cell cycle (GO:0000086)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|nitric oxide metabolic process (GO:0046209)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic vesicle transport (GO:0048489)|transferrin transport (GO:0033572)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	enzyme binding (GO:0019899)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|microtubule binding (GO:0008017)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	42			Epithelial(33;4.17e-05)|all cancers(31;8.48e-05)			CTCAGATGGAGTTTGACGAGA	0.562			"F, N, Splice, Mis, O"		ETP ALL																																p.E378D		Atlas-SNP	.		Rec	yes		19	19p13.2	1785	dynamin 2		L	.	DNM2	175	.	0			c.G1134C						.						172	129	143					19																	10906053		2203	4300	6503	SO:0001583	missense	1785	exon9			GATGGAGTTTGAC		CCDS32907.1, CCDS32908.1, CCDS45968.1, CCDS45969.1, CCDS59351.1	19p	2014-09-17						"Pleckstrin homology (PH) domain containing"	2974	protein-coding gene	gene with protein product	"dynamin II", "cytoskeletal protein"	602378				7590285, 9143510	Standard	NM_001190716		Approved	DYNII, DYN2, CMTDIB, CMTDI1, DI-CMTB	uc002mps.2	P50570		ENST00000355667.6:c.1134G>C	chr19.hg19:g.10906053G>C	ENSP00000347890:p.Glu378Asp	110.0	0.0		131.0	42.0	NM_001005361	A8K1B6|E7EV30|E9PEQ4|K7ESI9|Q5I0Y0|Q7Z5S3|Q9UPH4	Missense_Mutation	SNP	ENST00000355667.6	hg19	CCDS45968.1	.	.	.	.	.	.	.	.	.	.	G	11.42	1.633801	0.29068	.	.	ENSG00000079805	ENST00000389252;ENST00000408974;ENST00000355667;ENST00000359692;ENST00000389253;ENST00000314646	T;T;T;T;T	0.72725	-0.68;-0.68;-0.68;-0.68;-0.68	5.29	3.03	0.35002	Dynamin central domain (1);	0.441600	0.25938	N	0.027333	T	0.47507	0.1449	N	0.16066	0.365	0.49389	D	0.999787	B;B;B;B;P	0.39576	0.31;0.004;0.002;0.024;0.679	B;B;B;B;B	0.40066	0.248;0.029;0.012;0.033;0.318	T	0.37384	-0.9708	10	0.09590	T	0.72	-6.6102	6.9382	0.24478	0.327:0.0:0.673:0.0	.	111;378;378;378;378	B4DJ53;A8K1B6;P50570-2;P50570;E9PEQ4	.;.;.;DYN2_HUMAN;.	D	367;378;378;378;378;378	ENSP00000386192:E378D;ENSP00000347890:E378D;ENSP00000352721:E378D;ENSP00000373905:E378D;ENSP00000313164:E378D	ENSP00000313164:E378D	E	+	3	2	DNM2	10767053	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	2.032000	0.41127	1.249000	0.43950	-0.140000	0.14226	GAG	.	.		0.562	DNM2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452592.1	NM_004945		C	10906053	G	C	10906053	3	2	237	1	0	0	0	0	1	0	0	0	4674	1020	36	4	1168	4	DNM2	19	10906053	Missense_Mutation	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	654489	10906053	48222930	193	33099										
UPF1	5976	hgsc.bcm.edu	37	chr19	18967008	18967008	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	cttccagcatgcctgagctgCagaagctgcagcagctgaaa	11	12	0	3			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr19:18967008C>T	ENST00000599848.1	+	13	1965	c.1756C>T	c.(1756-1758)Cag>Tag	p.Q586*	UPF1_ENST00000262803.5_Nonsense_Mutation_p.Q575*			Q92900	RENT1_HUMAN	UPF1 regulator of nonsense transcripts homolog (yeast)	586					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|dosage compensation by inactivation of X chromosome (GO:0009048)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translational termination (GO:0006449)|RNA metabolic process (GO:0016070)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	40						GCCTGAGCTGCAGAAGCTGCA	0.602																																					p.Q575X		Atlas-SNP	.											.	UPF1	88	.	0			c.C1723T						.						50	49	49					19																	18967008		2203	4300	6503	SO:0001587	stop_gained	5976	exon13			GAGCTGCAGAAGC	AF074016	CCDS12386.1, CCDS74315.1	19p13.2-p13.11	2012-02-29	2006-02-07	2006-02-07	ENSG00000005007	ENSG00000005007			9962	protein-coding gene	gene with protein product	"UP Frameshift 1", "smg-2 homolog, nonsense mediated mRNA decay factor (C. elegans)"	601430	"regulator of nonsense transcripts 1"	RENT1		8855285, 9064659	Standard	XM_005260015		Approved	HUPF1, KIAA0221, NORF1, pNORF1, smg-2	uc002nkf.3	Q92900		ENST00000599848.1:c.1756C>T	chr19.hg19:g.18967008C>T	ENSP00000470142:p.Gln586*	120.0	0.0		130.0	8.0	NM_002911	O00239|O43343|Q86Z25|Q92842	Nonsense_Mutation	SNP	ENST00000599848.1	hg19		.	.	.	.	.	.	.	.	.	.	C	42	9.541753	0.99199	.	.	ENSG00000005007	ENST00000262803	.	.	.	4.29	4.29	0.51040	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07990	T	0.79	-34.5199	16.0865	0.81056	0.0:1.0:0.0:0.0	.	.	.	.	X	575	.	ENSP00000262803:Q575X	Q	+	1	0	UPF1	18828008	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.245000	0.78237	2.102000	0.63906	0.655000	0.94253	CAG	.	.		0.602	UPF1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000464684.1	NM_002911		T	18967008	C	T	18967008	4	4	237	1	0	0	0	0	0	1	0	0	17018	711	25	3	1773	3	UPF1	19	18967008	Nonsense_Mutation	SNP	C	TCGA-ED-A459-01A-11D-A25V-10	8060955	18967008	40161975	194	33100										
CILP2	148113	hgsc.bcm.edu	37	chr19	19656087	19656087	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gacaagtacgagtacaacgtGgtccccttccgagagggcac	12	12	0	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr19:19656087G>A	ENST00000291495.5	+	8	2818	c.2733G>A	c.(2731-2733)gtG>gtA	p.V911V	CILP2_ENST00000586018.1_Silent_p.V917V	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	911						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				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						AGTACAACGTGGTCCCCTTCC	0.667																																					p.V911V		Atlas-SNP	.											.	CILP2	84	.	0			c.G2733A						.						40	30	33					19																	19656087		2203	4300	6503	SO:0001819	synonymous_variant	148113	exon8			CAACGTGGTCCCC	AF542080	CCDS12405.1	19p13.11	2013-01-14				ENSG00000160161		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	24213	protein-coding gene	gene with protein product		612419				12477932	Standard	NM_153221		Approved	MGC45771	uc002nmv.4	Q8IUL8		ENST00000291495.5:c.2733G>A	chr19.hg19:g.19656087G>A		142.0	0.0		115.0	26.0	NM_153221	Q6NV88|Q8N4A6|Q8WV21	Silent	SNP	ENST00000291495.5	hg19	CCDS12405.1																																																																																			.	.		0.667	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221		A	19656087	G	A	19656087	2	1	237	1	0	0	0	0	0	0	0	1	3432	1335	47	3		3	CILP2	19	19656087	Silent	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	689079	19656087	39472896	195	33101										
ZNF85	7639	hgsc.bcm.edu	37	chr19	21132284	21132284	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	aatgtgaagaatgtggcaaaGcctttaagcagtcctcaaac	9	8	1	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr19:21132284G>T	ENST00000328178.8	+	4	1077	c.964G>T	c.(964-966)Gcc>Tcc	p.A322S	ZNF85_ENST00000601023.1_Missense_Mutation_p.A263S|ZNF85_ENST00000345030.6_Missense_Mutation_p.A289S	NM_001256173.1|NM_003429.4	NP_001243102.1|NP_003420.2	Q03923	ZNF85_HUMAN	zinc finger protein 85	322					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)	20						ATGTGGCAAAGCCTTTAAGCA	0.363																																					p.A352S		Atlas-SNP	.											.	ZNF85	72	.	0			c.G1054T						.						44	48	47					19																	21132284		2201	4299	6500	SO:0001583	missense	7639	exon5			GGCAAAGCCTTTA	U35376	CCDS32977.1, CCDS58657.1	19p12	2013-01-08	2006-05-12			ENSG00000105750		"Zinc fingers, C2H2-type", "-"	13160	protein-coding gene	gene with protein product		603899	"zinc finger protein 85 (HPF4, HTF1)"			2505992	Standard	NM_003429		Approved	HPF4, HTF1	uc031rjx.1	Q03923		ENST00000328178.8:c.964G>T	chr19.hg19:g.21132284G>T	ENSP00000329793:p.Ala322Ser	32.0	0.0		18.0	12.0	NM_001256171	B9ZVP4|Q6NVI0	Missense_Mutation	SNP	ENST00000328178.8	hg19	CCDS32977.1	.	.	.	.	.	.	.	.	.	.	.	11.36	1.616013	0.28801	.	.	ENSG00000105750	ENST00000328178;ENST00000345030;ENST00000421385	T;T	0.35973	1.28;1.28	1.35	-0.224	0.13115	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.27063	0.0663	N	0.01454	-0.855	0.09310	N	0.999996	D;D;P	0.69078	0.97;0.997;0.951	P;D;P	0.79108	0.779;0.992;0.899	T	0.24083	-1.0170	9	0.66056	D	0.02	.	6.601	0.22701	0.0:0.0:0.3319:0.668	.	289;263;322	Q03923-2;Q49A12;Q03923	.;.;ZNF85_HUMAN	S	322;289;197	ENSP00000329793:A322S;ENSP00000342340:A289S	ENSP00000329793:A322S	A	+	1	0	ZNF85	20924124	0.000000	0.05858	0.337000	0.25536	0.718000	0.41266	-0.776000	0.04674	-0.240000	0.09696	0.462000	0.41574	GCC	.	.		0.363	ZNF85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463430.1	NM_003429		T	21132284	G	T	21132284	3	4	237	1	0	0	0	0	1	0	0	0	18208	971	34	3	978	3	ZNF85	19	21132284	Missense_Mutation	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	1476197	21132284	37996699	196	33102										
TSHZ3	57616	hgsc.bcm.edu	37	chr19	31768845	31768845	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tccactttggcaactttctcAgtgacctttttcaccagctc	5	14	2	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr19:31768845A>T	ENST00000240587.4	-	2	2181	c.1854T>A	c.(1852-1854)acT>acA	p.T618T		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	618					in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					CAACTTTCTCAGTGACCTTTT	0.582																																					p.T618T		Atlas-SNP	.											.	TSHZ3	549	.	0			c.T1854A						.						70	77	74					19																	31768845		2203	4300	6503	SO:0001819	synonymous_variant	57616	exon2			TTTCTCAGTGACC	AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	30700	protein-coding gene	gene with protein product	"teashirt 3"	614119	"zinc finger protein 537", "teashirt family zinc finger 3"	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.1854T>A	chr19.hg19:g.31768845A>T		169.0	0.0		192.0	14.0	NM_020856	Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	hg19	CCDS12421.2																																																																																			.	.		0.582	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856		T	31768845	A	T	31768845	2	4	237	1	0	0	0	0	0	0	0	1	16640	175	7	4		4	TSHZ3	19	31768845	Silent	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	10636561	31768845	27360138	197	33103										
ZNF585B	92285	hgsc.bcm.edu	37	chr19	37677114	37677114	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	aagtaaacaatttcccacagTgaccacatttataaggtttc	5	9	0	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr19:37677114T>A	ENST00000532828.2	-	5	1576	c.1325A>T	c.(1324-1326)cAc>cTc	p.H442L	ZNF585B_ENST00000527838.1_3'UTR|ZNF585B_ENST00000312908.5_Missense_Mutation_p.H30L|ZNF585B_ENST00000531805.1_Missense_Mutation_p.H387L|CTC-454I21.3_ENST00000585860.2_Intron	NM_152279.3	NP_689492.3	Q52M93	Z585B_HUMAN	zinc finger protein 585B	442					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|endometrium(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TTTCCCACAGTGACCACATTT	0.393																																					p.H442L	Melanoma(93;882 1454 18863 28917 48427)	Atlas-SNP	.											.	ZNF585B	91	.	0			c.A1325T						.						109	109	109					19																	37677114		2203	4300	6503	SO:0001583	missense	92285	exon5			CCACAGTGACCAC	AK027834	CCDS12500.1	19q13.13	2013-01-08				ENSG00000245680		"Zinc fingers, C2H2-type", "-"	30948	protein-coding gene	gene with protein product						12477932	Standard	NM_152279		Approved	FLJ14928, SZFP41	uc002ofq.3	Q52M93		ENST00000532828.2:c.1325A>T	chr19.hg19:g.37677114T>A	ENSP00000433773:p.His442Leu	139.0	0.0		128.0	11.0	NM_152279	Q8IZD3|Q96JW6	Missense_Mutation	SNP	ENST00000532828.2	hg19	CCDS12500.1	.	.	.	.	.	.	.	.	.	.	T	7.252	0.603380	0.14002	.	.	ENSG00000245680	ENST00000531805;ENST00000532828;ENST00000312908	T;T;T	0.34667	1.35;3.4;3.4	2.35	2.35	0.29111	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.400480	0.18380	N	0.142995	T	0.18173	0.0436	N	0.05487	-0.04	0.09310	N	1	B;B	0.25441	0.03;0.126	B;B	0.24701	0.055;0.046	T	0.18366	-1.0339	10	0.66056	D	0.02	.	7.821	0.29288	0.0:0.0:0.0:1.0	.	387;442	E9PQH3;Q52M93	.;Z585B_HUMAN	L	387;442;30	ENSP00000436774:H387L;ENSP00000433773:H442L;ENSP00000442139:H30L	ENSP00000442139:H30L	H	-	2	0	ZNF585B	42368954	0.000000	0.05858	0.782000	0.31804	0.710000	0.40934	0.580000	0.23803	1.063000	0.40649	0.254000	0.18369	CAC	.	.		0.393	ZNF585B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388272.2	NM_152279		A	37677114	T	A	37677114	3	1	237	1	0	0	0	0	1	0	0	0	18033	1696	59	4	988	4	ZNF585B	19	37677114	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	5908269	37677114	21451869	198	33104										
KCNK6	9424	hgsc.bcm.edu	37	chr19	38817261	38817261	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tacacaacgccactgactgaTgcgggcaaggccttctccat	9	14	1	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr19:38817261T>A	ENST00000263372.3	+	2	458	c.351T>A	c.(349-351)gaT>gaA	p.D117E		NM_004823.1	NP_004814.1	Q9Y257	KCNK6_HUMAN	potassium channel, subfamily K, member 6	117					negative regulation of systemic arterial blood pressure (GO:0003085)|potassium ion transport (GO:0006813)|regulation of resting membrane potential (GO:0060075)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(3)	17	all_cancers(60;5.83e-07)		Lung(45;0.00047)|LUSC - Lung squamous cell carcinoma(53;0.000613)		Ibutilide(DB00308)|Quinidine(DB00908)	CACTGACTGATGCGGGCAAGG	0.577																																					p.D117E		Atlas-SNP	.											.	KCNK6	37	.	0			c.T351A						.						101	99	100					19																	38817261		2203	4299	6502	SO:0001583	missense	9424	exon2			GACTGATGCGGGC	AF117708	CCDS12513.1	19q13.1	2012-03-07				ENSG00000099337		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6281	protein-coding gene	gene with protein product		603939				10075682, 10393428, 16382106	Standard	NM_004823		Approved	K2p6.1, TWIK-2	uc002oic.3	Q9Y257		ENST00000263372.3:c.351T>A	chr19.hg19:g.38817261T>A	ENSP00000263372:p.Asp117Glu	56.0	0.0		58.0	4.0	NM_004823	Q9HB47	Missense_Mutation	SNP	ENST00000263372.3	hg19	CCDS12513.1	.	.	.	.	.	.	.	.	.	.	T	14.89	2.670890	0.47781	.	.	ENSG00000099337	ENST00000263372	T	0.24151	1.87	4.74	-6.88	0.01665	Ion transport 2 (1);	0.103141	0.64402	D	0.000006	T	0.20007	0.0481	L	0.42686	1.345	0.25253	N	0.989658	P	0.42123	0.771	P	0.47528	0.549	T	0.34054	-0.9844	10	0.07175	T	0.84	.	13.6951	0.62572	0.0:0.3003:0.0:0.6997	.	117	Q9Y257	KCNK6_HUMAN	E	117	ENSP00000263372:D117E	ENSP00000263372:D117E	D	+	3	2	KCNK6	43509101	0.000000	0.05858	0.001000	0.08648	0.553000	0.35397	-0.757000	0.04772	-1.059000	0.03193	-2.060000	0.00399	GAT	.	.		0.577	KCNK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460524.1	NM_004823		A	38817261	T	A	38817261	3	1	237	1	0	0	0	0	1	0	0	0	8079	1461	51	4	357	4	KCNK6	19	38817261	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	1140147	38817261	20311722	199	33105										
LRFN1	57622	hgsc.bcm.edu	37	chr19	39805513	39805513	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	acaggaaggcgtcaaaggccGccgactccacccggcggatc	13	15	1	0	rs201576239		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr19:39805513G>A	ENST00000248668.4	-	1	463	c.464C>T	c.(463-465)gCg>gTg	p.A155V	CTC-246B18.8_ENST00000601911.1_RNA	NM_020862.1	NP_065913.1	Q9P244	LRFN1_HUMAN	leucine rich repeat and fibronectin type III domain containing 1	155						cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				central_nervous_system(2)|cervix(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	18	all_cancers(60;1.85e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;1.96e-27)|all cancers(26;2.05e-24)|Lung(45;0.000278)|LUSC - Lung squamous cell carcinoma(53;0.000335)			GTCAAAGGCCGCCGACTCCAC	0.667																																					p.A155V		Atlas-SNP	.											LRFN1,NS,carcinoma,0,1	LRFN1	59	.	0			c.C464T						.	G	VAL/ALA	1,3979		0,1,1989	16	19	18		464	3.1	0.7	19		18	1,8303		0,1,4151	yes	missense	LRFN1	NM_020862.1	64	0,2,6140	AA,AG,GG		0.012,0.0251,0.0163	benign	155/772	39805513	2,12282	1990	4152	6142	SO:0001583	missense	57622	exon1			AAGGCCGCCGACT	BC014678	CCDS46071.1	19q13.2	2013-02-11				ENSG00000128011		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	29290	protein-coding gene	gene with protein product		612807				10819331, 16828986	Standard	NM_020862		Approved	KIAA1484, SALM2	uc002okw.2	Q9P244		ENST00000248668.4:c.464C>T	chr19.hg19:g.39805513G>A	ENSP00000248668:p.Ala155Val	87.0	0.0		72.0	5.0	NM_020862	Q8TBS9	Missense_Mutation	SNP	ENST00000248668.4	hg19	CCDS46071.1	.	.	.	.	.	.	.	.	.	.	G	11.59	1.682719	0.29872	2.51E-4	1.2E-4	ENSG00000128011	ENST00000248668	T	0.52526	0.66	4.22	3.14	0.36123	.	0.000000	0.39687	N	0.001296	T	0.36771	0.0979	L	0.58810	1.83	0.29475	N	0.856736	B	0.31351	0.32	B	0.21360	0.034	T	0.25222	-1.0138	10	0.16420	T	0.52	.	10.3862	0.44140	0.0:0.3893:0.6107:0.0	.	155	Q9P244	LRFN1_HUMAN	V	155	ENSP00000248668:A155V	ENSP00000248668:A155V	A	-	2	0	LRFN1	44497353	0.399000	0.25287	0.701000	0.30321	0.753000	0.42808	3.042000	0.49815	0.941000	0.37499	0.555000	0.69702	GCG	.	.		0.667	LRFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463835.1	NM_020862		A	39805513	G	A	39805513	3	1	237	1	0	0	0	0	1	0	0	0	8946	1087	38	1	1859	1	LRFN1	19	39805513	Missense_Mutation	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	988252	39805513	19323470	200	33106										
ZNF613	79898	hgsc.bcm.edu	37	chr19	52448896	52448896	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	agctcagacctcattaactaAcagtgcgttccaagcagaga	8	11	2	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr19:52448896A>T	ENST00000293471.6	+	6	2439	c.1760A>T	c.(1759-1761)aAc>aTc	p.N587I	ZNF613_ENST00000391794.4_Missense_Mutation_p.N551I|ZNF613_ENST00000601794.1_Intron	NM_001031721.3	NP_001026891.2	Q6PF04	ZN613_HUMAN	zinc finger protein 613	587					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	19		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.0183)		TCATTAACTAACAGTGCGTTC	0.443																																					p.N587I		Atlas-SNP	.											.	ZNF613	62	.	0			c.A1760T						.						84	71	76					19																	52448896		2203	4300	6503	SO:0001583	missense	79898	exon6			TAACTAACAGTGC	AK027565	CCDS12844.1, CCDS33089.1	19q13.41	2013-01-08						"Zinc fingers, C2H2-type", "-"	25827	protein-coding gene	gene with protein product						12477932	Standard	NM_001031721		Approved	FLJ13590	uc002pxz.2	Q6PF04		ENST00000293471.6:c.1760A>T	chr19.hg19:g.52448896A>T	ENSP00000293471:p.Asn587Ile	165.0	0.0		226.0	80.0	NM_001031721	Q96SS9	Missense_Mutation	SNP	ENST00000293471.6	hg19	CCDS33089.1	.	.	.	.	.	.	.	.	.	.	A	4.035	0.004091	0.07866	.	.	ENSG00000176024	ENST00000293471;ENST00000391794;ENST00000535279	T;T	0.05513	3.52;3.43	2.93	-0.467	0.12150	.	.	.	.	.	T	0.02888	0.0086	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43065	-0.9414	9	0.45353	T	0.12	.	3.1906	0.06615	0.2797:0.0:0.3769:0.3434	.	587	Q6PF04	ZN613_HUMAN	I	587;551;261	ENSP00000293471:N587I;ENSP00000375671:N551I	ENSP00000293471:N587I	N	+	2	0	ZNF613	57140708	0.000000	0.05858	0.000000	0.03702	0.052000	0.14988	-1.597000	0.02089	-0.182000	0.10602	0.482000	0.46254	AAC	.	.		0.443	ZNF613-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461104.2	NM_024840		T	52448896	A	T	52448896	3	4	237	1	0	0	0	0	1	0	0	0	18053	43	2	4	1774	4	ZNF613	19	52448896	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	12643383	52448896	6680087	201	33107										
LENG8	114823	hgsc.bcm.edu	37	chr19	54962528	54962528	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	accccaaggtccagatggcgGccaacgtgggtgatcaacgt	13	12	1	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr19:54962528G>A	ENST00000326764.5	+	2	486	c.7G>A	c.(7-9)Gcc>Acc	p.A3T	LENG8-AS1_ENST00000416022.1_RNA|LENG8_ENST00000376514.2_Missense_Mutation_p.A3T|LENG8-AS1_ENST00000429922.1_RNA|LENG8-AS1_ENST00000448978.1_RNA	NM_052925.2	NP_443157.1	Q96PV6	LENG8_HUMAN	leukocyte receptor cluster (LRC) member 8	0										breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.139)		CCAGATGGCGGCCAACGTGGG	0.552																																					p.A3T		Atlas-SNP	.											.	LENG8	73	.	0			c.G7A						.						97	85	89					19																	54962528		2203	4300	6503	SO:0001583	missense	114823	exon2			ATGGCGGCCAACG	AF211975	CCDS12894.1	19q13.4	2008-02-05			ENSG00000167615	ENSG00000167615			15500	protein-coding gene	gene with protein product						10941842	Standard	XM_005278248		Approved	KIAA1932, MGC40108, pp13842	uc002qfw.2	Q96PV6	OTTHUMG00000065548	ENST00000326764.5:c.7G>A	chr19.hg19:g.54962528G>A	ENSP00000318374:p.Ala3Thr	179.0	0.0		188.0	65.0	NM_052925	B0VJY9|Q8IZ27|Q8NCX6	Missense_Mutation	SNP	ENST00000326764.5	hg19	CCDS12894.1	.	.	.	.	.	.	.	.	.	.	G	17.35	3.366444	0.61513	.	.	ENSG00000167615	ENST00000326764;ENST00000301196;ENST00000439657;ENST00000376514;ENST00000376526;ENST00000443957;ENST00000431846	T;T;T;T	0.52526	1.28;0.66;1.06;1.14	4.92	3.88	0.44766	.	0.134765	0.49305	N	0.000158	T	0.38214	0.1032	L	0.43152	1.355	0.34148	D	0.66717	B;B	0.26602	0.154;0.015	B;B	0.23716	0.048;0.019	T	0.52011	-0.8632	10	0.51188	T	0.08	-24.64	9.9603	0.41693	0.0964:0.0:0.9036:0.0	.	3;3	Q96PV6-2;F8W9Q9	.;.	T	3	ENSP00000318374:A3T;ENSP00000399507:A3T;ENSP00000365709:A3T;ENSP00000388053:A3T	ENSP00000301196:A3T	A	+	1	0	LENG8	59654340	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.603000	0.61105	1.386000	0.46466	0.462000	0.41574	GCC	.	.		0.552	LENG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140523.2	NM_052925		A	54962528	G	A	54962528	3	1	237	1	0	0	0	0	1	0	0	0	8733	1203	42	3	9	3	LENG8	19	54962528	Missense_Mutation	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	2513632	54962528	4166455	202	33108										
ZNF547	284306	hgsc.bcm.edu	37	chr19	57889239	57889239	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gaaaaaggtcttatggttgcAgtgaatgtgggaaattcttt	12	3	2	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr19:57889239A>T	ENST00000282282.3	+	4	1045	c.895A>T	c.(895-897)Agt>Tgt	p.S299C	AC003002.4_ENST00000597658.1_Intron	NM_173631.2	NP_775902.2	Q8IVP9	ZN547_HUMAN	zinc finger protein 547	299					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	12		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TTATGGTTGCAGTGAATGTGG	0.408																																					p.S299C		Atlas-SNP	.											.	ZNF547	45	.	0			c.A895T						.						119	118	118					19																	57889239		2203	4300	6503	SO:0001583	missense	284306	exon4			GGTTGCAGTGAAT	AK055662	CCDS33131.1	19q13.43	2013-01-08				ENSG00000152433		"Zinc fingers, C2H2-type", "-"	26432	protein-coding gene	gene with protein product							Standard	NM_173631		Approved	FLJ31100	uc002qol.3	Q8IVP9		ENST00000282282.3:c.895A>T	chr19.hg19:g.57889239A>T	ENSP00000282282:p.Ser299Cys	117.0	0.0		130.0	9.0	NM_173631	A8K5Z9|Q96NC4	Missense_Mutation	SNP	ENST00000282282.3	hg19	CCDS33131.1	.	.	.	.	.	.	.	.	.	.	A	16.23	3.065261	0.55432	.	.	ENSG00000152433	ENST00000391704;ENST00000282282	T	0.16897	2.31	1.87	1.87	0.25490	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.35998	0.0951	M	0.77486	2.375	0.09310	N	1	D;D;D	0.76494	0.997;0.999;0.997	P;D;P	0.67900	0.753;0.954;0.907	T	0.05733	-1.0867	9	0.56958	D	0.05	.	6.3787	0.21521	0.7503:0.2496:0.0:0.0	.	299;299;299	Q8IVP9-2;C9JTQ3;Q8IVP9	.;.;ZN547_HUMAN	C	299	ENSP00000282282:S299C	ENSP00000282282:S299C	S	+	1	0	ZNF547	62581051	0.000000	0.05858	0.010000	0.14722	0.938000	0.57974	-1.061000	0.03472	1.126000	0.42016	0.402000	0.26972	AGT	.	.		0.408	ZNF547-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465787.1	NM_173631		T	57889239	A	T	57889239	3	4	237	1	0	0	0	0	1	0	0	0	17994	188	7	4	905	4	ZNF547	19	57889239	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	2926711	57889239	1239744	203	33109										
ZNF211	10520	hgsc.bcm.edu	37	chr19	58152706	58152706	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gtccacagtgaagaaaggccTtatgaatgcaatgaatgtgg	12	6	0	4			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr19:58152706T>G	ENST00000347302.3	+	3	1031	c.852T>G	c.(850-852)ccT>ccG	p.P284P	ZNF211_ENST00000544273.1_Silent_p.P296P|ZNF211_ENST00000240731.4_Silent_p.P297P|ZNF211_ENST00000541801.1_Silent_p.P275P|ZNF211_ENST00000391703.3_Silent_p.P223P|ZNF211_ENST00000420680.1_Silent_p.P288P|ZNF211_ENST00000299871.5_Silent_p.P349P|ZNF211_ENST00000254182.7_Silent_p.P275P	NM_198855.2	NP_942152.1	Q13398	ZN211_HUMAN	zinc finger protein 211	284					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		AAGAAAGGCCTTATGAATGCA	0.413																																					p.P349P		Atlas-SNP	.											.	ZNF211	78	.	0			c.T1047G						.						115	108	110					19																	58152706		2203	4300	6503	SO:0001819	synonymous_variant	10520	exon5			AAGGCCTTATGAA	U38904	CCDS12956.1, CCDS12957.1, CCDS58686.1, CCDS58687.1, CCDS58688.1, CCDS74468.1	19q13.4	2013-01-08			ENSG00000121417	ENSG00000121417		"Zinc fingers, C2H2-type", "-"	13003	protein-coding gene	gene with protein product		601856				7633419, 9096115	Standard	NM_006385		Approved	ZNF-25, CH2H2-25	uc031rng.1	Q13398	OTTHUMG00000168012	ENST00000347302.3:c.852T>G	chr19.hg19:g.58152706T>G		94.0	0.0		77.0	23.0	NM_001265597	B4DH10|B4DLC9|B4E3C9|B9ZVS7|B9ZVW1|F8WDV2|Q05BQ7|Q2TAL7|Q59EG4|Q59G36|Q5EBL6	Silent	SNP	ENST00000347302.3	hg19	CCDS12957.1	.	.	.	.	.	.	.	.	.	.	T	9.043	0.990163	0.18966	.	.	ENSG00000121417	ENST00000407202	.	.	.	3.51	3.51	0.40186	.	.	.	.	.	T	0.55273	0.1910	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52162	-0.8612	4	.	.	.	.	6.3576	0.21410	0.3538:0.0:0.0:0.6462	.	.	.	.	V	288	.	.	L	+	1	2	ZNF211	62844518	0.000000	0.05858	0.476000	0.27291	0.993000	0.82548	-1.016000	0.03633	1.605000	0.50152	0.472000	0.43445	TTA	.	.		0.413	ZNF211-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397502.1			G	58152706	T	G	58152706	2	3	237	1	0	0	0	0	0	0	0	1	17782	1596	56	5		5	ZNF211	19	58152706	Silent	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	263467	58152706	976277	204	33110										
MYH7B	57644	hgsc.bcm.edu	37	chr20	33582028	33582028	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	catggatgaagctctttttcAagatgaagccgctgctgcgc	11	10	2	3			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr20:33582028A>G	ENST00000262873.7	+	25	2742	c.2650A>G	c.(2650-2652)Aag>Gag	p.K884E		NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	842						membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			GCTCTTTTTCAAGATGAAGCC	0.647																																					p.K884E		Atlas-SNP	.											.	MYH7B	145	.	0			c.A2650G						.						92	104	100					20																	33582028		2076	4235	6311	SO:0001583	missense	57644	exon27			TTTTTCAAGATGA	AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"Myosins / Myosin superfamily : Class II"	15906	protein-coding gene	gene with protein product		609928	"myosin, heavy polypeptide 7B, cardiac muscle, beta"			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.2650A>G	chr20.hg19:g.33582028A>G	ENSP00000262873:p.Lys884Glu	285.0	0.0		320.0	116.0	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Missense_Mutation	SNP	ENST00000262873.7	hg19	CCDS42869.1	.	.	.	.	.	.	.	.	.	.	A	19.55	3.848416	0.71603	.	.	ENSG00000078814	ENST00000262873	D	0.93488	-3.23	4.33	4.33	0.51752	.	0.000000	0.39615	N	0.001304	D	0.97043	0.9034	M	0.91300	3.195	0.50632	D	0.999884	D	0.56746	0.977	D	0.71656	0.974	D	0.97755	1.0217	10	0.66056	D	0.02	.	13.9525	0.64126	1.0:0.0:0.0:0.0	.	842	A7E2Y1	MYH7B_HUMAN	E	884	ENSP00000262873:K884E	ENSP00000262873:K884E	K	+	1	0	MYH7B	33045689	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	9.135000	0.94478	1.943000	0.56356	0.459000	0.35465	AAG	.	.		0.647	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884		G	33582028	A	G	33582028	3	3	237	1	0	0	0	0	1	0	0	0	10049	131	5	2	2748	2	MYH7B	20	33582028	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10		33582028	29443492	205	33111										
AURKA	6790	hgsc.bcm.edu	37	chr20	54961584	54961584	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tttggacctccaactggagcTgtagcctagaatggaagaga	12	8	0	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr20:54961584T>A	ENST00000347343.2	-	3	315	c.48A>T	c.(46-48)acA>acT	p.T16T	AURKA_ENST00000395913.3_Silent_p.T16T|AURKA_ENST00000395909.4_Silent_p.T16T|AURKA_ENST00000395911.1_Silent_p.T16T|AURKA_ENST00000312783.6_Silent_p.T16T|AURKA_ENST00000371356.2_Silent_p.T16T|AURKA_ENST00000395914.1_Silent_p.T16T|AURKA_ENST00000395907.1_Silent_p.T16T|AURKA_ENST00000395915.3_Silent_p.T16T	NM_003600.2	NP_003591.2	O14965	AURKA_HUMAN	aurora kinase A	16					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|anterior/posterior axis specification (GO:0009948)|centrosome localization (GO:0051642)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic centrosome separation (GO:0007100)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein binding (GO:0032091)|negative regulation of spindle checkpoint (GO:0090233)|neuron projection extension (GO:1990138)|positive regulation of mitosis (GO:0045840)|positive regulation of oocyte maturation (GO:1900195)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein autophosphorylation (GO:0046777)|protein localization to centrosome (GO:0071539)|protein phosphorylation (GO:0006468)|regulation of centrosome cycle (GO:0046605)|regulation of protein stability (GO:0031647)|spindle assembly involved in female meiosis I (GO:0007057)|spindle stabilization (GO:0043146)	axon hillock (GO:0043203)|centrosome (GO:0005813)|cytosol (GO:0005829)|germinal vesicle (GO:0042585)|meiotic spindle (GO:0072687)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole centrosome (GO:0031616)	ATP binding (GO:0005524)|histone serine kinase activity (GO:0035174)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			breast(2)|cervix(1)|endometrium(1)|large_intestine(4)|lung(9)|ovary(2)|prostate(1)|skin(2)	22			Colorectal(105;0.202)			CAACTGGAGCTGTAGCCTAGA	0.403																																					p.T16T	Melanoma(34;439 1292 51416 52695)|GBM(144;1525 2517 48902 51835)|Esophageal Squamous(191;569 2880 14195 30540)	Atlas-SNP	.											.	AURKA	42	.	0			c.A48T						.						54	54	54					20																	54961584		2203	4300	6503	SO:0001819	synonymous_variant	6790	exon3			TGGAGCTGTAGCC	BC001280	CCDS13451.1	20q13	2012-07-23	2003-07-21	2003-07-23	ENSG00000087586	ENSG00000087586		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	11393	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 47", "Aurora-A kinase"	603072	"serine/threonine kinase 15", " serine/threonine kinase 6"	STK15, STK6		9174055, 9771714	Standard	NM_003600		Approved	BTAK, AurA, STK7, ARK1, PPP1R47, AIK	uc002xxi.1	O14965	OTTHUMG00000032796	ENST00000347343.2:c.48A>T	chr20.hg19:g.54961584T>A		99.0	0.0		126.0	7.0	NM_198437	E1P5F9|O60445|O75873|Q9BQD6|Q9UPG5	Silent	SNP	ENST00000347343.2	hg19	CCDS13451.1																																																																																			.	.		0.403	AURKA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079804.3	NM_003600		A	54961584	T	A	54961584	2	1	237	1	0	0	0	0	0	0	0	1	1221	1567	55	4		4	AURKA	20	54961584	Silent	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	21379556	54961584	8063936	206	33112										
DNAJC5	80331	hgsc.bcm.edu	37	chr20	62562355	62562355	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ccccgaggatctggaggcacAgctgcagtctgacgagaggg	16	11	2	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr20:62562355A>T	ENST00000360864.4	+	4	626	c.473A>T	c.(472-474)cAg>cTg	p.Q158L	DNAJC5_ENST00000369911.2_Missense_Mutation_p.Q158L	NM_025219.2	NP_079495.1	Q9H3Z4	DNJC5_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 5	158					cell death (GO:0008219)|exocytosis (GO:0006887)|negative regulation of neuron apoptotic process (GO:0043524)|neurotransmitter secretion (GO:0007269)|regulated secretory pathway (GO:0045055)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)	clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)				cervix(1)|endometrium(1)|lung(1)|pancreas(1)|upper_aerodigestive_tract(1)	5	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					CTGGAGGCACAGCTGCAGTCT	0.627																																					p.Q158L		Atlas-SNP	.											.	DNAJC5	16	.	0			c.A473T						.						101	80	87					20																	62562355		2203	4300	6503	SO:0001583	missense	80331	exon4			AGGCACAGCTGCA		CCDS13546.1	20q13.33	2014-09-17			ENSG00000101152	ENSG00000101152		"Heat shock proteins / DNAJ (HSP40)"	16235	protein-coding gene	gene with protein product		611203	"ceroid-lipofuscinosis, neuronal 4 (Kufs disease)"	CLN4			Standard	NM_025219		Approved	FLJ00118, FLJ13070, DNAJC5A	uc002yhf.3	Q9H3Z4	OTTHUMG00000033007	ENST00000360864.4:c.473A>T	chr20.hg19:g.62562355A>T	ENSP00000354111:p.Gln158Leu	155.0	0.0		143.0	10.0	NM_025219	A8K0M0|B3KY68|E1P5G8|Q9H3Z5|Q9H7H2	Missense_Mutation	SNP	ENST00000360864.4	hg19	CCDS13546.1	.	.	.	.	.	.	.	.	.	.	A	32	5.154334	0.94686	.	.	ENSG00000101152	ENST00000369911;ENST00000360864	T;T	0.71579	-0.55;-0.58	5.91	5.91	0.95273	.	0.064025	0.64402	D	0.000004	T	0.81931	0.4927	M	0.86953	2.85	0.80722	D	1	P;P	0.42735	0.734;0.788	P;B	0.50490	0.642;0.218	T	0.82744	-0.0306	10	0.40728	T	0.16	.	16.3512	0.83208	1.0:0.0:0.0:0.0	.	158;158	Q9H3Z4-2;Q9H3Z4	.;DNJC5_HUMAN	L	158	ENSP00000358927:Q158L;ENSP00000354111:Q158L	ENSP00000354111:Q158L	Q	+	2	0	DNAJC5	62032799	1.000000	0.71417	0.998000	0.56505	0.877000	0.50540	8.520000	0.90566	2.266000	0.75297	0.533000	0.62120	CAG	.	.		0.627	DNAJC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080244.1	NM_025219		T	62562355	A	T	62562355	3	4	237	1	0	0	0	0	1	0	0	0	4652	188	7	4	483	4	DNAJC5	20	62562355	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	7600771	62562355	463165	207	33113										
DSCAM	1826	hgsc.bcm.edu	37	chr21	41384983	41384984	+	Missense_Mutation	DNP	GC	GC	AG													0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ataccagggtgtaagattttGcgtaaggattgtttcctttc					rs200591095		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr21:41384983_41384984GC>AG	ENST00000400454.1	-	33	6493_6494	c.6016_6017GC>CT	c.(6016-6018)GCa>CTa	p.A2006L		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	2006				HRPGDLIHLPPYLRMDFLLNRGGPGTSRDLSLGQACLEPQK SRTLKRPTVLEPIPMEAASSASSTREGQSWQPGAVATLPQR EGAELGQAAKMSSSQESLLDSRGHLKGNNPYAKSYTLV -> IGQVTSYICLHTLEWTFC (in Ref. 1; AAC17966). {ECO:0000305}.	cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				GTAAGATTTTGCGTAAGGATTG	0.46																																					p.A2006V|p.A2006P	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.|DSCAM,colon,carcinoma,0,1	DSCAM	347	.	0			c.C6017T|c.G6016C						.																																			SO:0001583	missense	1826	exon33			GATTTTGCGTAAG|ATTTTGCGTAAGG	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.6016_6017delinsAG	chr21.hg19:g.41384983_41384984delinsAG	ENSP00000383303:p.Ala2006Leu	172.0|173.0	0.0		134.0|136.0	26.0	NM_001389	O60468	Missense_Mutation	SNP	ENST00000400454.1	hg19	CCDS42929.1																																																																																			.	G|1.000;C|0.000|.		0.46	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		AG	41384984	GC	AG	41384983	3	1	237	1	0	0	0	0	1	0	0	0	4770	1319	46	3	25	3	DSCAM	21	41384983	Missense_Mutation	DNP	GC	TCGA-ED-A459-01A-11D-A25V-10		41384983	6744912	208	33114										
NEFH	4744	hgsc.bcm.edu	37	chr22	29885288	29885292	+	Frame_Shift_Del	DEL	AGCAA	AGCAA	-													0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	cctgagaaggccaagtctccAgcaaaggaagaggcaaagtc					rs544011483|rs575224034	byFrequency	TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	AGCAA	AGCAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr22:29885288_29885292delAGCAA	ENST00000310624.6	+	4	1692_1696	c.1659_1663delAGCAA	c.(1657-1665)ccagcaaagfs	p.AK554fs		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	554	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.A554A(1)		cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						CCAAGTCTCCAGCAAAGGAAGAGGC	0.571																																					p.553_554del		Atlas-Indel,Pindel	.											.	NEFH	178	.	1	Substitution - coding silent(1)	skin(1)	c.1658_1662del						.																																			SO:0001589	frameshift_variant	4744	exon4			.		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1659_1663delAGCAA	chr22.hg19:g.29885288_29885292delAGCAA	ENSP00000311997:p.Ala554fs	325.0	0.0		220.0	66.0	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Frame_Shift_Del	DEL	ENST00000310624.6	hg19	CCDS13858.1																																																																																			.	.		0.571	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		-	29885292	AGCAA	-	29885288	7	5	237	1	0	1	0	1	0	0	0	0	10323	175	7	0	1673	0	NEFH	22	29885288	Frame_Shift_Del	DEL	AGCAA	TCGA-ED-A459-01A-11D-A25V-10		29885288	21419278	209	33115										
HMOX1	3162	hgsc.bcm.edu	37	chr22	35789564	35789564	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ctcagctttctggtggcgacAgttgctgtagggctttatgc	13	9	2	0	rs140740892	byFrequency	TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr22:35789564A>T	ENST00000216117.8	+	5	1179	c.840A>T	c.(838-840)acA>acT	p.T280T		NM_002133.2	NP_002124.1	P09601	HMOX1_HUMAN	heme oxygenase (decycling) 1	280					angiogenesis (GO:0001525)|cell death (GO:0008219)|cellular iron ion homeostasis (GO:0006879)|cellular response to arsenic-containing substance (GO:0071243)|cellular response to cadmium ion (GO:0071276)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient (GO:0031670)|endothelial cell proliferation (GO:0001935)|erythrocyte homeostasis (GO:0034101)|excretion (GO:0007588)|heme catabolic process (GO:0042167)|heme oxidation (GO:0006788)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|iron ion homeostasis (GO:0055072)|low-density lipoprotein particle clearance (GO:0034383)|negative regulation of DNA binding (GO:0043392)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of mast cell cytokine production (GO:0032764)|negative regulation of mast cell degranulation (GO:0043305)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smooth muscle cell proliferation (GO:0048662)|porphyrin-containing compound metabolic process (GO:0006778)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of vasodilation (GO:0045909)|protein homooligomerization (GO:0051260)|regulation of angiogenesis (GO:0045765)|regulation of blood pressure (GO:0008217)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to estrogen (GO:0043627)|response to hydrogen peroxide (GO:0042542)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|smooth muscle hyperplasia (GO:0014806)|transmembrane transport (GO:0055085)|wound healing involved in inflammatory response (GO:0002246)	caveola (GO:0005901)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|heme binding (GO:0020037)|heme oxygenase (decyclizing) activity (GO:0004392)|metal ion binding (GO:0046872)|phospholipase D activity (GO:0004630)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	16					Vitamin E(DB00163)	TGGTGGCGACAGTTGCTGTAG	0.587																																					p.T280T		Atlas-SNP	.											.	HMOX1	32	.	0			c.A840T						.						142	135	137					22																	35789564		2203	4300	6503	SO:0001819	synonymous_variant	3162	exon5			GGCGACAGTTGCT		CCDS13914.1	22q12	2003-10-13			ENSG00000100292	ENSG00000100292	1.14.99.3		5013	protein-coding gene	gene with protein product		141250				10591208	Standard	NM_002133		Approved	bK286B10, HO-1	uc003ant.2	P09601	OTTHUMG00000150960	ENST00000216117.8:c.840A>T	chr22.hg19:g.35789564A>T		179.0	0.0		141.0	8.0	NM_002133		Silent	SNP	ENST00000216117.8	hg19	CCDS13914.1																																																																																			.	A|0.997;G|0.003		0.587	HMOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320657.1			T	35789564	A	T	35789564	2	4	237	1	0	0	0	0	0	0	0	1	7252	175	7	4		4	HMOX1	22	35789564	Silent	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	5904276	35789564	15515002	210	33116										
EIF3D	8664	hgsc.bcm.edu	37	chr22	36919311	36919311	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	attgtttctggaactttttcTgcagtcgaatgcgttctctg	9	8	3	0			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr22:36919311T>A	ENST00000216190.8	-	6	780	c.410A>T	c.(409-411)cAg>cTg	p.Q137L	EIF3D_ENST00000541106.1_Missense_Mutation_p.Q88L|EIF3D_ENST00000405442.1_Missense_Mutation_p.Q137L	NM_003753.3	NP_003744.1			eukaryotic translation initiation factor 3, subunit D											cervix(1)|endometrium(2)|large_intestine(6)|lung(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	15						GAACTTTTTCTGCAGTCGAAT	0.423																																					p.Q137L		Atlas-SNP	.											.	EIF3D	37	.	0			c.A410T						.						176	176	176					22																	36919311		2203	4300	6503	SO:0001583	missense	8664	exon6			TTTTTCTGCAGTC	U54558	CCDS13930.1	22q13.1	2007-07-27	2007-07-27	2007-07-27	ENSG00000100353	ENSG00000100353			3278	protein-coding gene	gene with protein product		603915	"eukaryotic translation initiation factor 3, subunit 7 zeta, 66/67kDa"	EIF3S7		9341143	Standard	NM_003753		Approved	eIF3-p66, eIF3-zeta, eIF3d	uc003apr.3	O15371	OTTHUMG00000150599	ENST00000216190.8:c.410A>T	chr22.hg19:g.36919311T>A	ENSP00000216190:p.Gln137Leu	102.0	0.0		115.0	9.0	NM_003753		Missense_Mutation	SNP	ENST00000216190.8	hg19	CCDS13930.1	.	.	.	.	.	.	.	.	.	.	T	16.16	3.043136	0.55003	.	.	ENSG00000100353	ENST00000216190;ENST00000397177;ENST00000541106;ENST00000405442;ENST00000455547;ENST00000457241;ENST00000432675	.	.	.	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.54515	0.1863	L	0.39898	1.24	0.80722	D	1	P;P	0.41947	0.766;0.475	B;B	0.44044	0.277;0.439	T	0.51092	-0.8749	9	0.28530	T	0.3	-11.3341	16.0098	0.80391	0.0:0.0:0.0:1.0	.	88;137	B4DVY1;O15371	.;EIF3D_HUMAN	L	137;137;88;137;137;137;137	.	ENSP00000216190:Q137L	Q	-	2	0	EIF3D	35249257	1.000000	0.71417	1.000000	0.80357	0.845000	0.48019	7.132000	0.77251	2.254000	0.74563	0.533000	0.62120	CAG	.	.		0.423	EIF3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319026.1			A	36919311	T	A	36919311	3	1	237	1	0	0	0	0	1	0	0	0	5016	1580	55	4	1276	4	EIF3D	22	36919311	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	1129747	36919311	14385255	211	33117										
ACO2	50	hgsc.bcm.edu	37	chr22	41911430	41911430	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tgttcttctgattggcactgActcccacacccccaatggtg	8	14	2	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr22:41911430A>T	ENST00000216254.4	+	5	597	c.575A>T	c.(574-576)gAc>gTc	p.D192V	ACO2_ENST00000396512.3_Missense_Mutation_p.D192V	NM_001098.2	NP_001089.1	Q99798	ACON_HUMAN	aconitase 2, mitochondrial	192	Substrate binding. {ECO:0000250}.				cell death (GO:0008219)|cellular metabolic process (GO:0044237)|citrate metabolic process (GO:0006101)|generation of precursor metabolites and energy (GO:0006091)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	3 iron, 4 sulfur cluster binding (GO:0051538)|4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron ion binding (GO:0005506)			breast(3)|endometrium(5)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	23						ATTGGCACTGACTCCCACACC	0.517																																					p.D192V		Atlas-SNP	.											.	ACO2	58	.	0			c.A575T						.						85	87	86					22																	41911430		2203	4300	6503	SO:0001583	missense	50	exon5			GCACTGACTCCCA	AH006514	CCDS14017.1	22q13.2	2013-05-21			ENSG00000100412	ENSG00000100412	4.2.1.3		118	protein-coding gene	gene with protein product	"aconitate hydratase, mitochondrial"	100850				10591208	Standard	NM_001098		Approved	ACONM	uc003bac.3	Q99798	OTTHUMG00000030544	ENST00000216254.4:c.575A>T	chr22.hg19:g.41911430A>T	ENSP00000216254:p.Asp192Val	133.0	0.0		158.0	16.0	NM_001098	O75809|Q5JZ41|Q6FHX0|Q8TAQ6	Missense_Mutation	SNP	ENST00000216254.4	hg19	CCDS14017.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.698931	0.88830	.	.	ENSG00000100412	ENST00000544234;ENST00000216254;ENST00000396512	D;D	0.97232	-4.3;-4.3	5.46	5.46	0.80206	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 1/3 (1);Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha (3);	0.000000	0.85682	D	0.000000	D	0.99360	0.9775	H	0.99959	5.06	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97903	1.0304	10	0.87932	D	0	.	15.5309	0.75960	1.0:0.0:0.0:0.0	.	192;192	A2A274;Q99798	.;ACON_HUMAN	V	173;192;192	ENSP00000216254:D192V;ENSP00000379769:D192V	ENSP00000216254:D192V	D	+	2	0	ACO2	40241376	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.962000	0.93254	2.063000	0.61619	0.533000	0.62120	GAC	.	.		0.517	ACO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259151.1	NM_001098		T	41911430	A	T	41911430	3	4	237	1	0	0	0	0	1	0	0	0	147	275	10	4	593	4	ACO2	22	41911430	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	4992119	41911430	9393136	212	33118										
MEI1	150365	hgsc.bcm.edu	37	chr22	42099396	42099396	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	ccttgtgaggcatacctcccTggtcacgcaactggtgtctc	10	14	2	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr22:42099396T>A	ENST00000401548.3	+	2	276	c.236T>A	c.(235-237)cTg>cAg	p.L79Q	MEI1_ENST00000540833.1_5'UTR|MEI1_ENST00000400107.1_5'UTR|MEI1_ENST00000300398.4_5'UTR	NM_152513.3	NP_689726.3			meiosis inhibitor 1											breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						CATACCTCCCTGGTCACGCAA	0.428																																					p.L79Q		Atlas-SNP	.											.	MEI1	87	.	0			c.T236A						.						77	73	74					22																	42099396		1963	4142	6105	SO:0001583	missense	150365	exon2			CCTCCCTGGTCAC	AK092934	CCDS46718.1	22q13.2	2013-10-11			ENSG00000167077	ENSG00000167077			28613	protein-coding gene	gene with protein product	"spermatogenesis associated 38"	608797				16683055	Standard	XM_006724154		Approved	MGC40042, SPATA38	uc003baz.1	Q5TIA1	OTTHUMG00000030083	ENST00000401548.3:c.236T>A	chr22.hg19:g.42099396T>A	ENSP00000384115:p.Leu79Gln	123.0	0.0		106.0	7.0	NM_152513		Missense_Mutation	SNP	ENST00000401548.3	hg19	CCDS46718.1	.	.	.	.	.	.	.	.	.	.	T	11.32	1.605379	0.28623	.	.	ENSG00000167077	ENST00000401548	T	0.20069	2.1	5.22	1.28	0.21552	.	0.979204	0.08343	N	0.960514	T	0.17066	0.0410	L	0.47716	1.5	0.09310	N	0.999998	P;P	0.46220	0.874;0.571	B;B	0.41088	0.347;0.252	T	0.20338	-1.0278	10	0.36615	T	0.2	-5.5299	3.4015	0.07325	0.1705:0.2671:0.0:0.5624	.	79;79	Q5TIA1;Q5TIA1-4	MEI1_HUMAN;.	Q	79	ENSP00000384115:L79Q	ENSP00000384115:L79Q	L	+	2	0	MEI1	40429342	0.081000	0.21417	0.900000	0.35374	0.495000	0.33615	0.721000	0.25911	0.846000	0.35142	0.397000	0.26171	CTG	.	.		0.428	MEI1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000074937.3	NM_152513		A	42099396	T	A	42099396	3	1	237	1	0	0	0	0	1	0	0	0	9474	1580	55	4	242	4	MEI1	22	42099396	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	187966	42099396	9205170	213	33119										
ZBED4	9889	hgsc.bcm.edu	37	chr22	50278080	50278104	+	Frame_Shift_Del	DEL	ACCTCCCTGCTCTCCATTACGATGA	ACCTCCCTGCTCTCCATTACGATGA	-													0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	cctggtggggtcgtctccccAcctccctgctctccattacg							TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	ACCTCCCTGCTCTCCATTACGATGA	ACCTCCCTGCTCTCCATTACGATGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr22:50278080_50278104delACCTCCCTGCTCTCCATTACGATGA	ENST00000216268.5	+	2	1247_1271	c.770_794delACCTCCCTGCTCTCCATTACGATGA	c.(769-795)cacctccctgctctccattacgatgaafs	p.HLPALHYDE257fs		NM_014838.2	NP_055653.2	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	257						cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	44		all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)|BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		TCGTCTCCCCACCTCCCTGCTCTCCATTACGATGAACCTGCAGAG	0.547																																					p.257_265del		Atlas-Indel,Pindel	.											.	ZBED4	102	.	0			c.769_793del						.																																			SO:0001589	frameshift_variant	9889	exon2			.	AB014537	CCDS33677.1	22q13.33	2013-05-03			ENSG00000100426	ENSG00000100426		"Zinc fingers, BED-type"	20721	protein-coding gene	gene with protein product		612552				23533661	Standard	NM_014838		Approved	KIAA0637	uc003bix.2	O75132	OTTHUMG00000150291	ENST00000216268.5:c.770_794delACCTCCCTGCTCTCCATTACGATGA	chr22.hg19:g.50278080_50278104delACCTCCCTGCTCTCCATTACGATGA	ENSP00000216268:p.His257fs	164.0	0.0		136.0	25.0	NM_014838	B2RZH1|Q1ECU0|Q9UGG8	Frame_Shift_Del	DEL	ENST00000216268.5	hg19	CCDS33677.1																																																																																			.	.		0.547	ZBED4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317408.2	NM_014838		-	50278104	ACCTCCCTGCTCTCCATTACGATGA	-	50278080	7	5	237	1	0	1	0	1	0	0	0	0	17535	159	6	0	772	0	ZBED4	22	50278080	Frame_Shift_Del	DEL	ACCTCCCTGCTCTCCATTACGATGA	TCGA-ED-A459-01A-11D-A25V-10	8178684	50278080	1026486	214	33120										
NLGN4X	57502	hgsc.bcm.edu	37	chrX	6069270	6069270	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	cctctctccagtggggggtgAggcataggggacccctaagt	15	11	1	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chrX:6069270A>T	ENST00000381095.3	-	2	865	c.238T>A	c.(238-240)Tca>Aca	p.S80T	NLGN4X_ENST00000381093.2_Missense_Mutation_p.S80T|NLGN4X_ENST00000381092.1_Missense_Mutation_p.S80T|NLGN4X_ENST00000469740.1_5'UTR|NLGN4X_ENST00000275857.6_Missense_Mutation_p.S80T|NLGN4X_ENST00000538097.1_Missense_Mutation_p.S80T	NM_001282145.1|NM_001282146.1|NM_181332.1	NP_001269074.1|NP_001269075.1|NP_851849.1	Q8N0W4	NLGNX_HUMAN	neuroligin 4, X-linked	80					adult behavior (GO:0030534)|brainstem development (GO:0003360)|cell-cell junction organization (GO:0045216)|cerebellum development (GO:0021549)|learning (GO:0007612)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|neuron cell-cell adhesion (GO:0007158)|neuron differentiation (GO:0030182)|organ growth (GO:0035265)|presynaptic membrane assembly (GO:0097105)|social behavior (GO:0035176)|synapse organization (GO:0050808)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|chloride ion binding (GO:0031404)|neurexin family protein binding (GO:0042043)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)			breast(1)|cervix(2)|endometrium(4)|large_intestine(21)|lung(39)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	81						GTGGGGGGTGAGGCATAGGGG	0.557																																					p.S80T		Atlas-SNP	.											.	NLGN4X	191	.	0			c.T238A						.						75	69	71					X																	6069270		2203	4300	6503	SO:0001583	missense	57502	exon2			GGGGTGAGGCATA	AB033086	CCDS14126.1	Xp22.33	2008-02-05	2004-05-21	2004-05-26	ENSG00000146938	ENSG00000146938			14287	protein-coding gene	gene with protein product		300427	"neuroligin 4"	NLGN4		10574462	Standard	XM_005274564		Approved	KIAA1260, NLGN, HLNX	uc004crr.3	Q8N0W4	OTTHUMG00000021093	ENST00000381095.3:c.238T>A	chrX.hg19:g.6069270A>T	ENSP00000370485:p.Ser80Thr	156.0	0.0		368.0	26.0	NM_181332	Q6UX10|Q9ULG0	Missense_Mutation	SNP	ENST00000381095.3	hg19	CCDS14126.1	.	.	.	.	.	.	.	.	.	.	A	8.100	0.776351	0.16051	.	.	ENSG00000146938	ENST00000381095;ENST00000381093;ENST00000275857;ENST00000381092;ENST00000538097	T;T;T;T;T	0.58060	0.36;0.36;0.36;0.36;0.36	4.2	4.2	0.49525	Carboxylesterase, type B (1);	.	.	.	.	T	0.25457	0.0619	N	0.02334	-0.595	0.25812	N	0.984382	B;B;B	0.11235	0.004;0.0;0.002	B;B;B	0.14023	0.01;0.002;0.004	T	0.09930	-1.0652	9	0.08837	T	0.75	.	11.9007	0.52682	1.0:0.0:0.0:0.0	.	80;80;80	A6NMU8;Q8N0W4;Q8N0W4-2	.;NLGNX_HUMAN;.	T	80	ENSP00000370485:S80T;ENSP00000370483:S80T;ENSP00000275857:S80T;ENSP00000370482:S80T;ENSP00000439203:S80T	ENSP00000275857:S80T	S	-	1	0	NLGN4X	6079270	1.000000	0.71417	0.996000	0.52242	0.954000	0.61252	1.890000	0.39728	1.388000	0.46506	0.486000	0.48141	TCA	.	.		0.557	NLGN4X-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055673.1	NM_020742		T	6069270	A	T	6069270	3	4	237	1	0	0	0	0	1	0	0	0	10473	304	11	4	2232	4	NLGN4X	23	6069270	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10		6069270	149201290	215	33121										
ZNF41	7592	hgsc.bcm.edu	37	chrX	47307358	47307358	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	caggacaaacgtacggtttcTctcctgtatggattctctga	9	10	2	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chrX:47307358T>C	ENST00000377065.4	-	5	2450	c.1811A>G	c.(1810-1812)gAg>gGg	p.E604G	ZNF41_ENST00000465311.1_5'Flank|ZNF41_ENST00000313116.7_Missense_Mutation_p.E604G|ZNF41_ENST00000397050.2_Missense_Mutation_p.E614G	NM_153380.2	NP_700359.1	P51814	ZNF41_HUMAN	zinc finger protein 41	646					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|upper_aerodigestive_tract(2)	24		all_lung(315;0.000129)				GTACGGTTTCTCTCCTGTATG	0.448																																					p.E604G		Atlas-SNP	.											.	ZNF41	71	.	0			c.A1811G						.						90	71	77					X																	47307358		2203	4300	6503	SO:0001583	missense	7592	exon5			GGTTTCTCTCCTG	X60155	CCDS14279.1	Xp11.23	2013-01-08			ENSG00000147124	ENSG00000147124		"Zinc fingers, C2H2-type", "-"	13107	protein-coding gene	gene with protein product		314995				2037297	Standard	NM_007130		Approved	MGC8941, MRX89	uc004dhy.4	P51814	OTTHUMG00000021448	ENST00000377065.4:c.1811A>G	chrX.hg19:g.47307358T>C	ENSP00000366265:p.Glu604Gly	103.0	0.0		236.0	202.0	NM_007130	A8K1V6|B4DH01|Q96LE8|Q9UMC4|Q9UMV5|Q9UMV6|Q9UMV7|Q9UMV8|Q9UMV9|Q9UMW0|Q9UMW1	Missense_Mutation	SNP	ENST00000377065.4	hg19	CCDS14279.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.969907	0.74246	.	.	ENSG00000147124	ENST00000313116;ENST00000377065;ENST00000397050	T;T;T	0.27557	1.66;1.66;1.66	3.98	3.98	0.46160	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.35677	N	0.003051	T	0.49508	0.1561	M	0.64404	1.975	0.35516	D	0.801006	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.998;0.999;0.999	T	0.62627	-0.6814	10	0.87932	D	0	.	10.3222	0.43773	0.0:0.0:0.0:1.0	.	604;606;614;638;646	P51814-6;P51814-2;P51814-3;P51814-5;P51814	.;.;.;.;ZNF41_HUMAN	G	604;604;614	ENSP00000315173:E604G;ENSP00000366265:E604G;ENSP00000380243:E614G	ENSP00000315173:E604G	E	-	2	0	ZNF41	47192302	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.227000	0.65305	1.798000	0.52647	0.486000	0.48141	GAG	.	.		0.448	ZNF41-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056429.1	NM_153380		C	47307358	T	C	47307358	3	2	237	1	0	0	0	0	1	0	0	0	17904	1551	54	2	532	2	ZNF41	23	47307358	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	41238088	47307358	107963202	216	33122										
HUWE1	10075	hgsc.bcm.edu	37	chrX	53672381	53672381	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	tgaggactgccagcaccactTgcatatcagaggaagccaat	10	11	1	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chrX:53672381T>A	ENST00000342160.3	-	6	843	c.386A>T	c.(385-387)cAa>cTa	p.Q129L	HUWE1_ENST00000262854.6_Missense_Mutation_p.Q129L|HUWE1_ENST00000218328.8_Missense_Mutation_p.Q129L			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	129					base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						CAGCACCACTTGCATATCAGA	0.438																																					p.Q129L		Atlas-SNP	.											.	HUWE1	724	.	0			c.A386T						.						81	64	70					X																	53672381		2203	4300	6503	SO:0001583	missense	10075	exon7			ACCACTTGCATAT	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"HECT, UBA and WWE domain containing 1"			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.386A>T	chrX.hg19:g.53672381T>A	ENSP00000340648:p.Gln129Leu	53.0	0.0		127.0	7.0	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	hg19	CCDS35301.1	.	.	.	.	.	.	.	.	.	.	T	16.20	3.055444	0.55325	.	.	ENSG00000086758	ENST00000342160;ENST00000262854;ENST00000218328;ENST00000432528	T;T;T	0.66815	-0.08;-0.08;-0.23	5.47	5.47	0.80525	Armadillo-like helical (1);E3 ubiquitin ligase, domain of unknown function DUF908 (1);Armadillo-type fold (1);	0.079709	0.51477	D	0.000089	T	0.51500	0.1678	N	0.19112	0.55	0.58432	D	0.999995	B	0.27013	0.166	B	0.26310	0.068	T	0.49103	-0.8974	10	0.30078	T	0.28	.	13.4813	0.61336	0.0:0.0:0.0:1.0	.	129	Q7Z6Z7	HUWE1_HUMAN	L	129	ENSP00000340648:Q129L;ENSP00000262854:Q129L;ENSP00000218328:Q129L	ENSP00000218328:Q129L	Q	-	2	0	HUWE1	53689106	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.040000	0.76551	1.826000	0.53198	0.486000	0.48141	CAA	.	.		0.438	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		A	53672381	T	A	53672381	3	1	237	1	0	0	0	0	1	0	0	0	7470	1812	63	4	13050	4	HUWE1	23	53672381	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	6365023	53672381	101598179	217	33123										
HNRNPH2	3188	hgsc.bcm.edu	37	chrX	100667970	100667970	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gcagagttaccggtgaggcaGatgttgaatttgctactcat	12	7	1	4			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chrX:100667970G>T	ENST00000316594.5	+	2	1072	c.994G>T	c.(994-996)Gat>Tat	p.D332Y		NM_001032393.2|NM_001199973.1|NM_001199974.1|NM_019597.4	NP_001027565.1|NP_001186902.1|NP_001186903.1|NP_062543.1	P55795	HNRH2_HUMAN	heterogeneous nuclear ribonucleoprotein H2 (H')	332	2 X 16 AA Gly-rich approximate repeats.|RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|large_intestine(2)|lung(6)|skin(1)	12						CGGTGAGGCAGATGTTGAATT	0.408																																					p.D332Y		Atlas-SNP	.											.	HNRNPH2	50	.	0			c.G994T						.						119	104	109					X																	100667970		2203	4300	6503	SO:0001583	missense	3188	exon2			GAGGCAGATGTTG	U01923	CCDS14485.1	Xq22	2013-02-12		2008-04-18	ENSG00000126945	ENSG00000126945		"RNA binding motif (RRM) containing"	5042	protein-coding gene	gene with protein product		300610		HNRPH2		7499401	Standard	NM_019597		Approved	hnRNPH', FTP3, HNRPH'	uc004ehn.3	P55795	OTTHUMG00000022029	ENST00000316594.5:c.994G>T	chrX.hg19:g.100667970G>T	ENSP00000361927:p.Asp332Tyr	140.0	0.0		265.0	197.0	NM_001032393	A1L400|Q9HHA7	Missense_Mutation	SNP	ENST00000316594.5	hg19	CCDS14485.1	.	.	.	.	.	.	.	.	.	.	G	15.82	2.945270	0.53079	.	.	ENSG00000126945	ENST00000457902;ENST00000316594	T	0.06142	3.34	4.62	4.62	0.57501	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.13884	0.0336	N	0.24115	0.695	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.04165	-1.0972	10	0.72032	D	0.01	-21.913	14.0571	0.64776	0.0:0.0:1.0:0.0	.	332	P55795	HNRH2_HUMAN	Y	287;332	ENSP00000361927:D332Y	ENSP00000361927:D332Y	D	+	1	0	HNRNPH2	100554626	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.562000	0.98145	2.281000	0.76405	0.513000	0.50165	GAT	.	.		0.408	HNRNPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057556.1	NM_019597		T	100667970	G	T	100667970	3	4	237	1	0	0	0	0	1	0	0	0	7276	942	33	3	996	3	HNRNPH2	23	100667970	Missense_Mutation	SNP	G	TCGA-ED-A459-01A-11D-A25V-10	46995589	100667970	54602590	218	33124										
IRS4	8471	hgsc.bcm.edu	37	chrX	107977707	107977707	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gtggtggcatttgctgttgcTtgctttgagttaatttgcca	12	6	0	1			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chrX:107977707T>A	ENST00000372129.2	-	1	1944	c.1868A>T	c.(1867-1869)aAg>aTg	p.K623M	RP6-24A23.6_ENST00000563887.1_5'Flank|RP6-24A23.3_ENST00000608811.1_RNA|RP6-24A23.3_ENST00000436013.1_RNA	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	623					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						TTGCTGTTGCTTGCTTTGAGT	0.502																																					p.K623M		Atlas-SNP	.											.	IRS4	253	.	0			c.A1868T						.						215	213	214					X																	107977707		2203	4300	6503	SO:0001583	missense	8471	exon1			TGTTGCTTGCTTT	AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.1868A>T	chrX.hg19:g.107977707T>A	ENSP00000361202:p.Lys623Met	32.0	0.0		79.0	4.0	NM_003604		Missense_Mutation	SNP	ENST00000372129.2	hg19	CCDS14544.1	.	.	.	.	.	.	.	.	.	.	T	14.10	2.434515	0.43224	.	.	ENSG00000133124	ENST00000372129	T	0.38722	1.12	4.9	2.47	0.30058	.	3.127220	0.00678	N	0.000660	T	0.41903	0.1179	L	0.54323	1.7	0.26051	N	0.981479	B	0.26081	0.141	B	0.29942	0.109	T	0.38457	-0.9660	10	0.52906	T	0.07	-8.8109	4.4981	0.11851	0.4376:0.0:0.1407:0.4217	.	623	O14654	IRS4_HUMAN	M	623	ENSP00000361202:K623M	ENSP00000361202:K623M	K	-	2	0	IRS4	107864363	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	1.366000	0.34193	1.807000	0.52817	0.486000	0.48141	AAG	.	.		0.502	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604		A	107977707	T	A	107977707	3	1	237	1	0	0	0	0	1	0	0	0	7851	1609	56	4	1909	4	IRS4	23	107977707	Missense_Mutation	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	7309737	107977707	47292853	219	33125										
TKTL1	8277	hgsc.bcm.edu	37	chrX	153558006	153558006	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	gaattagtgccagacatatcAtagtggccgtgaaatgcatg	11	7	1	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chrX:153558006A>T	ENST00000369915.3	+	13	1948	c.1759A>T	c.(1759-1761)Ata>Tta	p.I587L	TKTL1_ENST00000369912.2_Missense_Mutation_p.I531L|TKTL1_ENST00000217905.7_Missense_Mutation_p.I327L	NM_001145933.1|NM_012253.3	NP_001139405.1|NP_036385.3	P51854	TKTL1_HUMAN	transketolase-like 1	587					glucose catabolic process (GO:0006007)|thiamine metabolic process (GO:0006772)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|transketolase activity (GO:0004802)			NS(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(5)|prostate(1)|skin(1)|urinary_tract(2)	34	all_cancers(53;5.05e-16)|all_epithelial(53;1.82e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CAGACATATCATAGTGGCCGT	0.448																																					p.I587L		Atlas-SNP	.											.	TKTL1	61	.	0			c.A1759T						.						226	202	210					X																	153558006		2203	4300	6503	SO:0001583	missense	8277	exon13			CATATCATAGTGG	X91817	CCDS35448.1, CCDS55541.1	Xq28	2008-02-05			ENSG00000007350	ENSG00000007350			11835	protein-coding gene	gene with protein product		300044				8838793	Standard	NM_012253		Approved	TKR, TKT2	uc004fkg.3	P51854	OTTHUMG00000022707	ENST00000369915.3:c.1759A>T	chrX.hg19:g.153558006A>T	ENSP00000358931:p.Ile587Leu	97.0	0.0		222.0	16.0	NM_012253	A8K896|Q5TYJ8|Q5TYJ9|Q8TC75	Missense_Mutation	SNP	ENST00000369915.3	hg19	CCDS35448.1	.	.	.	.	.	.	.	.	.	.	A	13.88	2.368715	0.42003	.	.	ENSG00000007350	ENST00000369915;ENST00000441970;ENST00000217905;ENST00000369912	T;T;T	0.75589	-0.95;-0.95;-0.95	5.53	-4.18	0.03846	Transketolase, C-terminal/Pyruvate-ferredoxin oxidoreductase, domain II (1);Transketolase-like, C-terminal (1);	0.780183	0.12326	N	0.478801	T	0.72961	0.3526	M	0.81341	2.54	0.09310	N	1	B;B;B	0.21821	0.0;0.061;0.061	B;B;B	0.22601	0.002;0.04;0.04	T	0.62353	-0.6872	10	0.49607	T	0.09	-0.2941	14.6864	0.69052	0.4062:0.0:0.5938:0.0	.	327;581;587	B7Z7M4;B7Z7I0;P51854	.;.;TKTL1_HUMAN	L	587;548;327;531	ENSP00000358931:I587L;ENSP00000217905:I327L;ENSP00000358928:I531L	ENSP00000217905:I327L	I	+	1	0	TKTL1	153211200	0.001000	0.12720	0.000000	0.03702	0.046000	0.14306	0.006000	0.13152	-0.996000	0.03455	-0.662000	0.03851	ATA	.	.		0.448	TKTL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058923.1	NM_012253		T	153558006	A	T	153558006	3	4	237	1	0	0	0	0	1	0	0	0	15950	217	8	4	1809	4	TKTL1	23	153558006	Missense_Mutation	SNP	A	TCGA-ED-A459-01A-11D-A25V-10	45580299	153558006	1712554	220	33126										
F8	2157	hgsc.bcm.edu	37	chrX	154158501	154158501	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0227272727272727	5	1	0.995778437557988	2.70851735015773	0.700478625040792	1	1	0	agaaataggtttctgctgctTggaaaaaccatctctttgag	9	7	2	2			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chrX:154158501T>A	ENST00000360256.4	-	14	3764	c.3564A>T	c.(3562-3564)ccA>ccT	p.P1188P		NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	1188	B.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	copper ion binding (GO:0005507)|oxidoreductase activity (GO:0016491)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(27)|liver(1)|lung(47)|ovary(5)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(5)|urinary_tract(2)	120	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	TTCTGCTGCTTGGAAAAACCA	0.328																																					p.P1188P		Atlas-SNP	.											.	F8	646	.	0			c.A3564T						.						48	49	48					X																	154158501		2203	4297	6500	SO:0001819	synonymous_variant	2157	exon14			GCTGCTTGGAAAA	M90707	CCDS35457.1, CCDS44026.1	Xq28	2014-09-17	2008-07-29		ENSG00000185010	ENSG00000185010			3546	protein-coding gene	gene with protein product	"Factor VIIIF8B", "hemophilia A"	300841		F8C		6438528, 3935400	Standard	NM_000132		Approved	FVIII, DXS1253E, HEMA	uc004fmt.3	P00451	OTTHUMG00000022688	ENST00000360256.4:c.3564A>T	chrX.hg19:g.154158501T>A		68.0	0.0		134.0	7.0	NM_000132	Q14286|Q5HY69	Silent	SNP	ENST00000360256.4	hg19	CCDS35457.1																																																																																			.	.		0.328	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4			A	154158501	T	A	154158501	2	1	237	1	0	0	0	0	0	0	0	1	5352	1799	63	4		4	F8	23	154158501	Silent	SNP	T	TCGA-ED-A459-01A-11D-A25V-10	600495	154158501	1112059	221	33127										
ZMYND12	84217	hgsc.bcm.edu	37	chr1	42921631	42921631	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	acacctcacagcagagtctgCgccccttggggactgccagt	11	15	2	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:42921631C>T	ENST00000372565.3	-	1	307	c.38G>A	c.(37-39)cGc>cAc	p.R13H	PPCS_ENST00000372560.3_5'Flank|ZMYND12_ENST00000433602.2_5'UTR|PPCS_ENST00000455780.1_5'Flank|PPCS_ENST00000372562.1_5'Flank|PPCS_ENST00000372561.3_5'Flank|PPCS_ENST00000372556.3_5'Flank	NM_032257.4	NP_115633.3	Q9H0C1	ZMY12_HUMAN	zinc finger, MYND-type containing 12	13						intracellular (GO:0005622)	metal ion binding (GO:0046872)			NS(1)|endometrium(2)|large_intestine(3)|lung(5)|ovary(2)|prostate(2)|skin(2)	17	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				GCAGAGTCTGCGCCCCTTGGG	0.627																																					p.R13H		Atlas-SNP	.											.	ZMYND12	35	.	0			c.G38A						.						54	48	50					1																	42921631		2203	4300	6503	SO:0001583	missense	84217	exon1			AGTCTGCGCCCCT	AK057384	CCDS467.1	1p34.1	2008-02-05			ENSG00000066185	ENSG00000066185		"Zinc fingers, MYND-type"	21192	protein-coding gene	gene with protein product						11230166	Standard	NM_032257		Approved	DKFZp434N2435	uc001chj.3	Q9H0C1	OTTHUMG00000007333	ENST00000372565.3:c.38G>A	chr1.hg19:g.42921631C>T	ENSP00000361646:p.Arg13His	52.0	0.0		56.0	10.0	NM_032257	Q5VUS6|Q8TC87|Q96M51	Missense_Mutation	SNP	ENST00000372565.3	hg19	CCDS467.1	.	.	.	.	.	.	.	.	.	.	C	19.18	3.778003	0.70107	.	.	ENSG00000066185	ENST00000372565	T	0.46451	0.87	5.04	5.04	0.67666	.	0.207898	0.41823	D	0.000808	T	0.57095	0.2030	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	D	0.71184	0.972	T	0.57329	-0.7830	10	0.56958	D	0.05	-12.7733	10.8881	0.46978	0.1875:0.8125:0.0:0.0	.	13	Q9H0C1	ZMY12_HUMAN	H	13	ENSP00000361646:R13H	ENSP00000361646:R13H	R	-	2	0	ZMYND12	42694218	1.000000	0.71417	1.000000	0.80357	0.522000	0.34438	2.641000	0.46587	2.612000	0.88384	0.563000	0.77884	CGC	.	.		0.627	ZMYND12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019170.1	NM_032257		T	42921631	C	T	42921631	3	4	238	1	0	0	0	0	1	0	0	0	17722	768	27	1	1091	1	ZMYND12	1	42921631	Missense_Mutation	SNP	C	TCGA-ED-A4XI-01A-11D-A25V-10		42921631	206328990	1	33128										
MIER1	57708	hgsc.bcm.edu	37	chr1	67436525	67436525	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	gatcagctcctgtgggacccTgagtacttaccagaagataa	10	10	1	3			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:67436525T>C	ENST00000355356.3	+	8	797	c.648T>C	c.(646-648)ccT>ccC	p.P216P	MIER1_ENST00000401042.3_Silent_p.P216P|MIER1_ENST00000355977.6_Silent_p.P153P|MIER1_ENST00000371014.1_Silent_p.P269P|MIER1_ENST00000401041.1_Silent_p.P269P|MIER1_ENST00000371018.3_Silent_p.P233P|MIER1_ENST00000357692.2_Silent_p.P233P|MIER1_ENST00000371016.1_Silent_p.P233P	NM_001077701.2|NM_001077704.2	NP_001071169.1|NP_001071172.1	Q8N108	MIER1_HUMAN	mesoderm induction early response 1, transcriptional regulator	216	ELM2. {ECO:0000255|PROSITE- ProRule:PRU00512}.|Interaction with HDAC1.				positive regulation of chromatin silencing (GO:0031937)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(3)	15						TGTGGGACCCTGAGTACTTAC	0.328																																					p.P269P		Atlas-SNP	.											.	MIER1	86	.	0			c.T807C						.						82	77	79					1																	67436525		1828	4092	5920	SO:0001819	synonymous_variant	57708	exon9			GGACCCTGAGTAC		CCDS41347.1, CCDS41348.1, CCDS53325.1, CCDS53326.1, CCDS53327.1, CCDS53328.1, CCDS53329.1, CCDS53330.1, CCDS60163.1	1p31.2	2013-07-23	2013-07-23		ENSG00000198160	ENSG00000198160			29657	protein-coding gene	gene with protein product			"mesoderm induction early response 1 homolog (Xenopus laevis)"			12242014, 12482978	Standard	NM_020948		Approved	hMI-ER1, MI-ER1, KIAA1610	uc001dde.2	Q8N108	OTTHUMG00000009194	ENST00000355356.3:c.648T>C	chr1.hg19:g.67436525T>C		118.0	0.0		126.0	11.0	NM_001077700	C9JFD4|Q08AE0|Q32NC4|Q5T104|Q5TAD1|Q5TAD2|Q5TAD4|Q5TAD5|Q6AHY8|Q86TB4|Q8N156|Q8N161|Q8NC37|Q8NES4|Q8NES5|Q8NES6|Q8WWG2|Q9HCG2	Silent	SNP	ENST00000355356.3	hg19	CCDS41348.1																																																																																			.	.		0.328	MIER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025491.2	NM_020948		C	67436525	T	C	67436525	2	2	238	1	0	0	0	0	0	0	0	1	9589	1567	55	2		2	MIER1	1	67436525	Silent	SNP	T	TCGA-ED-A4XI-01A-11D-A25V-10	24514894	67436525	181814096	2	33129										
GBP2	2634	hgsc.bcm.edu	37	chr1	89578243	89578243	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	ggtaacctcctggtttagaaAatgttccctgcttgacatct	8	10	1	2			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:89578243A>T	ENST00000370466.3	-	8	1542	c.1274T>A	c.(1273-1275)tTt>tAt	p.F425Y	GBP2_ENST00000463660.1_5'UTR	NM_004120.3	NP_004111.2	P32456	GBP2_HUMAN	guanylate binding protein 2, interferon-inducible	425					cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(1)	20		Lung NSC(277;0.0908)		all cancers(265;0.0151)|Epithelial(280;0.0284)		TGGTTTAGAAAATGTTCCCTG	0.428																																					p.F425Y		Atlas-SNP	.											.	GBP2	58	.	0			c.T1274A						.						175	166	169					1																	89578243		2203	4300	6503	SO:0001583	missense	2634	exon8			TTAGAAAATGTTC	BC073163	CCDS719.1	1p22.2	2008-02-05			ENSG00000162645	ENSG00000162645			4183	protein-coding gene	gene with protein product		600412				1715024	Standard	NM_004120		Approved		uc001dmz.1	P32456	OTTHUMG00000010662	ENST00000370466.3:c.1274T>A	chr1.hg19:g.89578243A>T	ENSP00000359497:p.Phe425Tyr	233.0	0.0		193.0	25.0	NM_004120	Q6GPH0|Q6IAU2|Q86TB0	Missense_Mutation	SNP	ENST00000370466.3	hg19	CCDS719.1	.	.	.	.	.	.	.	.	.	.	A	6.621	0.482934	0.12581	.	.	ENSG00000162645	ENST00000370466	T	0.02085	4.46	3.56	-2.84	0.05751	Guanylate-binding protein, C-terminal (3);	0.094194	0.42682	U	0.000679	T	0.00412	0.0013	N	0.11756	0.17	0.09310	N	1	B	0.12630	0.006	B	0.20184	0.028	T	0.38394	-0.9663	10	0.17832	T	0.49	-8.5448	8.7717	0.34735	0.3966:0.0:0.0:0.6034	.	425	P32456	GBP2_HUMAN	Y	425	ENSP00000359497:F425Y	ENSP00000359497:F425Y	F	-	2	0	GBP2	89350831	0.001000	0.12720	0.004000	0.12327	0.011000	0.07611	-0.264000	0.08658	-0.714000	0.04975	-0.490000	0.04691	TTT	.	.		0.428	GBP2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029406.2	NM_004120		T	89578243	A	T	89578243	3	4	238	1	0	0	0	0	1	0	0	0	6282	14	1	4	517	4	GBP2	1	89578243	Missense_Mutation	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	22141718	89578243	159672378	3	33130										
HFM1	164045	hgsc.bcm.edu	37	chr1	91784929	91784929	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	tcttgtatgggaatgcatccTagttgagcctgaataagact	10	7	1	3			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:91784929T>C	ENST00000370425.3	-	24	2699	c.2601A>G	c.(2599-2601)ctA>ctG	p.L867L	HFM1_ENST00000294696.5_Silent_p.L99L|HFM1_ENST00000462405.1_5'UTR|HFM1_ENST00000370424.3_Silent_p.L546L	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	867	SEC63.				resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		GAATGCATCCTAGTTGAGCCT	0.383																																					p.L867L		Atlas-SNP	.											.	HFM1	188	.	0			c.A2601G						.						100	96	97					1																	91784929		2203	4300	6503	SO:0001819	synonymous_variant	164045	exon24			GCATCCTAGTTGA	AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"SEC63 domain containing 1"	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.2601A>G	chr1.hg19:g.91784929T>C		111.0	0.0		88.0	14.0	NM_001017975	B1B0B6|Q8N9Q0	Silent	SNP	ENST00000370425.3	hg19	CCDS30769.2	.	.	.	.	.	.	.	.	.	.	T	8.633	0.894213	0.17613	.	.	ENSG00000162669	ENST00000430465	.	.	.	5.0	3.79	0.43588	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.8832	0.18866	0.2429:0.0756:0.0:0.6815	.	.	.	.	W	123	.	.	X	-	2	0	HFM1	91557517	0.862000	0.29867	1.000000	0.80357	0.984000	0.73092	-0.066000	0.11598	1.996000	0.58369	0.528000	0.53228	TAG	.	.		0.383	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975		C	91784929	T	C	91784929	2	2	238	1	0	0	0	0	0	0	0	1	7092	1509	53	2		2	HFM1	1	91784929	Silent	SNP	T	TCGA-ED-A4XI-01A-11D-A25V-10	2206686	91784929	157465692	4	33131										
C1orf146	388649	hgsc.bcm.edu	37	chr1	92711222	92711222	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	ctgaatagtgattcagttaaCccaaattagagtaccaactt	6	8	1	3			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:92711222C>A	ENST00000370375.3	+	6	682	c.534C>A	c.(532-534)aaC>aaA	p.N178K	C1orf146_ENST00000370373.2_Missense_Mutation_p.N119K	NM_001012425.1	NP_001012425.1	Q5VVC0	CA146_HUMAN	chromosome 1 open reading frame 146	178										breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	8		all_lung(203;0.00528)|Lung NSC(277;0.0193)		all cancers(265;0.00846)|Epithelial(280;0.0952)		ATTCAGTTAACCCAAATTAGA	0.284																																					p.N178K		Atlas-SNP	.											.	C1orf146	21	.	0			c.C534A						.						55	59	58					1																	92711222		2203	4297	6500	SO:0001583	missense	388649	exon6			AGTTAACCCAAAT		CCDS30772.1	1p22.1	2008-02-05			ENSG00000203910	ENSG00000203910			24032	protein-coding gene	gene with protein product						15496913	Standard	NM_001012425		Approved		uc001doq.3	Q5VVC0	OTTHUMG00000010285	ENST00000370375.3:c.534C>A	chr1.hg19:g.92711222C>A	ENSP00000359401:p.Asn178Lys	176.0	0.0		153.0	28.0	NM_001012425	Q5VVC4	Missense_Mutation	SNP	ENST00000370375.3	hg19	CCDS30772.1	.	.	.	.	.	.	.	.	.	.	C	12.00	1.807788	0.31961	.	.	ENSG00000203910	ENST00000370375;ENST00000370373	.	.	.	4.86	-2.77	0.05877	.	0.737577	0.11935	N	0.515324	T	0.11495	0.0280	L	0.27053	0.805	0.09310	N	1	B	0.25609	0.13	B	0.21917	0.037	T	0.30297	-0.9983	9	0.52906	T	0.07	-11.9764	10.2976	0.43633	0.0:0.4187:0.0:0.5813	.	178	Q5VVC0	CA146_HUMAN	K	178;157	.	ENSP00000359399:N157K	N	+	3	2	C1orf146	92483810	0.000000	0.05858	0.001000	0.08648	0.113000	0.19764	-0.721000	0.04963	-0.455000	0.07054	0.655000	0.94253	AAC	.	.		0.284	C1orf146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028364.1	NM_001012425		A	92711222	C	A	92711222	3	1	238	1	0	0	0	0	1	0	0	0	2005	506	18	3	552	3	C1orf146	1	92711222	Missense_Mutation	SNP	C	TCGA-ED-A4XI-01A-11D-A25V-10	926293	92711222	156539399	5	33132										
PALMD	54873	hgsc.bcm.edu	37	chr1	100154912	100154912	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	acaaagatgcaccctctccaAagccaaggctgagccccaga	8	15	1	3			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:100154912A>C	ENST00000263174.4	+	7	1471	c.1096A>C	c.(1096-1098)Aag>Cag	p.K366Q	PALMD_ENST00000605497.1_Missense_Mutation_p.K366Q	NM_017734.4	NP_060204.1	Q9NP74	PALMD_HUMAN	palmdelphin	366					regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|membrane (GO:0016020)				central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(8)|ovary(6)|pancreas(1)|prostate(2)	31		all_epithelial(167;0.000813)|all_lung(203;0.0214)|Lung NSC(277;0.0216)		Epithelial(280;0.067)|all cancers(265;0.117)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)		ACCCTCTCCAAAGCCAAGGCT	0.458																																					p.K366Q		Atlas-SNP	.											.	PALMD	64	.	0			c.A1096C						.						52	48	49					1																	100154912		2203	4300	6503	SO:0001583	missense	54873	exon7			TCTCCAAAGCCAA	AJ312214	CCDS758.1	1p22-p21	2008-07-18			ENSG00000099260	ENSG00000099260			15846	protein-coding gene	gene with protein product		610182		C1orf11		11478809	Standard	NM_017734		Approved	FLJ20271, PALML	uc001dsg.3	Q9NP74	OTTHUMG00000010764	ENST00000263174.4:c.1096A>C	chr1.hg19:g.100154912A>C	ENSP00000263174:p.Lys366Gln	159.0	0.0		126.0	13.0	NM_017734	Q9H7E6|Q9NPM5|Q9NPM6|Q9NPS0	Missense_Mutation	SNP	ENST00000263174.4	hg19	CCDS758.1	.	.	.	.	.	.	.	.	.	.	A	5.985	0.365684	0.11352	.	.	ENSG00000099260	ENST00000263174	T	0.18338	2.22	5.93	3.62	0.41486	.	0.561503	0.20364	N	0.093794	T	0.04272	0.0118	L	0.44542	1.39	0.21325	N	0.999729	B;P	0.34724	0.045;0.465	B;B	0.31101	0.023;0.124	T	0.35674	-0.9779	10	0.31617	T	0.26	-8.0102	6.2561	0.20874	0.729:0.1344:0.1366:0.0	.	366;286	Q9NP74;Q9NP74-2	PALMD_HUMAN;.	Q	366	ENSP00000263174:K366Q	ENSP00000263174:K366Q	K	+	1	0	PALMD	99927500	0.006000	0.16342	0.409000	0.26459	0.134000	0.20937	0.468000	0.22051	0.496000	0.27904	0.460000	0.39030	AAG	.	.		0.458	PALMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029672.1	NM_017734		C	100154912	A	C	100154912	3	2	238	1	0	0	0	0	1	0	0	0	11420	15	1	5	1122	5	PALMD	1	100154912	Missense_Mutation	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	7443690	100154912	149095709	6	33133										
SPAG17	200162	hgsc.bcm.edu	37	chr1	118548101	118548101	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	ctgaagtatgcctcatgatgTacctgccagctcgcagctgc	10	13	1	2			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:118548101T>A	ENST00000336338.5	-	32	4777	c.4712A>T	c.(4711-4713)tAc>tTc	p.Y1571F		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1571						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		CCTCATGATGTACCTGCCAGC	0.448																																					p.Y1571F		Atlas-SNP	.											.	SPAG17	263	.	0			c.A4712T						.						141	136	138					1																	118548101		2203	4300	6503	SO:0001583	missense	200162	exon32			ATGATGTACCTGC		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.4712A>T	chr1.hg19:g.118548101T>A	ENSP00000337804:p.Tyr1571Phe	104.0	0.0		103.0	8.0	NM_206996	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	hg19	CCDS899.1	.	.	.	.	.	.	.	.	.	.	T	16.87	3.241748	0.58995	.	.	ENSG00000155761	ENST00000336338;ENST00000437255	T	0.68903	-0.36	5.72	5.72	0.89469	.	0.056586	0.64402	D	0.000001	T	0.76343	0.3974	M	0.73962	2.25	0.39965	D	0.974715	D	0.89917	1.0	D	0.66847	0.947	T	0.80777	-0.1231	10	0.87932	D	0	.	14.9829	0.71324	0.0:0.0:0.0:1.0	.	1571	Q6Q759	SPG17_HUMAN	F	1571;51	ENSP00000337804:Y1571F	ENSP00000337804:Y1571F	Y	-	2	0	SPAG17	118349624	1.000000	0.71417	0.998000	0.56505	0.121000	0.20230	5.486000	0.66856	2.177000	0.69029	0.533000	0.62120	TAC	.	.		0.448	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		A	118548101	T	A	118548101	3	1	238	1	0	0	0	0	1	0	0	0	14994	1638	57	4	2027	4	SPAG17	1	118548101	Missense_Mutation	SNP	T	TCGA-ED-A4XI-01A-11D-A25V-10	18393189	118548101	130702520	7	33134										
FLG	2312	hgsc.bcm.edu	37	chr1	152281931	152281931	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	tgggtgtccacgaatggtgtCctgaccctcttgggacgctg	14	11	1	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:152281931C>A	ENST00000368799.1	-	3	5466	c.5431G>T	c.(5431-5433)Gac>Tac	p.D1811Y	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1811	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CGAATGGTGTCCTGACCCTCT	0.597									Ichthyosis																												p.D1811Y		Atlas-SNP	.											FLG,left_upper_lobe,carcinoma,0,1	FLG	900	.	0			c.G5431T						.						344	352	349					1																	152281931		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGGTGTCCTGACC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.5431G>T	chr1.hg19:g.152281931C>A	ENSP00000357789:p.Asp1811Tyr	384.0	1.0		466.0	65.0	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	hg19	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	C	9.802	1.180789	0.21787	.	.	ENSG00000143631	ENST00000368799;ENST00000271820	T	0.01705	4.68	3.72	1.79	0.24919	.	.	.	.	.	T	0.03477	0.0100	M	0.80028	2.48	0.09310	N	1	D	0.76494	0.999	D	0.80764	0.994	T	0.33624	-0.9861	9	0.62326	D	0.03	.	6.2456	0.20815	0.0:0.7607:0.0:0.2393	.	1811	P20930	FILA_HUMAN	Y	1811;46	ENSP00000357789:D1811Y	ENSP00000271820:D46Y	D	-	1	0	FLG	150548555	0.000000	0.05858	0.029000	0.17559	0.111000	0.19643	-1.742000	0.01835	0.366000	0.24427	0.447000	0.29281	GAC	.	.		0.597	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152281931	C	A	152281931	3	1	238	1	0	0	0	0	1	0	0	0	5930	855	30	3	6758	3	FLG	1	152281931	Missense_Mutation	SNP	C	TCGA-ED-A4XI-01A-11D-A25V-10	33733830	152281931	96968690	8	33135										
SPRR2B	6701	hgsc.bcm.edu	37	chr1	153043186	153043186	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	gcactgctgaggtgggcaggGctgtggacactttggtggtg	19	7	0	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:153043186G>A	ENST00000368755.2	-	1	130	c.130C>T	c.(130-132)Ccc>Tcc	p.P44S	SPRR2B_ENST00000341611.2_Missense_Mutation_p.P44S|SPRR2B_ENST00000368752.4_Missense_Mutation_p.P44S			P35325	SPR2B_HUMAN	small proline-rich protein 2B	44	3 X 9 AA tandem repeats of P-K-C-P-[EQ]- P-C-P-P.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)				endometrium(2)|large_intestine(1)|lung(2)	5	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			GGTGGGCAGGGCTGTGGACAC	0.617																																					p.P44S		Atlas-SNP	.											.	SPRR2B	15	.	0			c.C130T						.						95	88	90					1																	153043186		2203	4297	6500	SO:0001583	missense	6701	exon3			GGCAGGGCTGTGG	AF333952	CCDS30865.1	1q21-q22	2008-02-05			ENSG00000196805	ENSG00000196805			11262	protein-coding gene	gene with protein product		182268				8325635	Standard	NM_001017418		Approved		uc001fbg.3	P35325	OTTHUMG00000013863	ENST00000368755.2:c.130C>T	chr1.hg19:g.153043186G>A	ENSP00000357744:p.Pro44Ser	216.0	0.0		207.0	24.0	NM_001017418	Q5T528	Missense_Mutation	SNP	ENST00000368755.2	hg19	CCDS30865.1	.	.	.	.	.	.	.	.	.	.	G	11.06	1.527789	0.27299	.	.	ENSG00000196805	ENST00000368755;ENST00000341611;ENST00000368752	T;T;T	0.29917	1.55;1.55;1.55	3.34	1.12	0.20585	.	0.490293	0.15324	N	0.268362	T	0.09202	0.0227	.	.	.	0.09310	N	1	B	0.27700	0.186	B	0.30855	0.121	T	0.24190	-1.0167	9	0.87932	D	0	.	4.6748	0.12706	0.1334:0.0:0.6562:0.2103	.	44	P35325	SPR2B_HUMAN	S	44	ENSP00000357744:P44S;ENSP00000340703:P44S;ENSP00000357741:P44S	ENSP00000340703:P44S	P	-	1	0	SPRR2B	151309810	0.009000	0.17119	0.001000	0.08648	0.755000	0.42902	0.405000	0.21015	0.478000	0.27488	0.455000	0.32223	CCC	.	.		0.617	SPRR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038905.2			A	153043186	G	A	153043186	3	1	238	1	0	0	0	0	1	0	0	0	15113	1203	42	3	92	3	SPRR2B	1	153043186	Missense_Mutation	SNP	G	TCGA-ED-A4XI-01A-11D-A25V-10	761255	153043186	96207435	9	33136										
OR10T2	128360	hgsc.bcm.edu	37	chr1	158368778	158368778	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	tgtcacaaatgaggttggtgGccaccaaagcaataaagaaa	10	7	1	2			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:158368778G>T	ENST00000334438.1	-	1	478	c.479C>A	c.(478-480)gCc>gAc	p.A160D		NM_001004475.1	NP_001004475.1	Q8NGX3	O10T2_HUMAN	olfactory receptor, family 10, subfamily T, member 2	160						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_hematologic(112;0.0378)					GAGGTTGGTGGCCACCAAAGC	0.468																																					p.A160D		Atlas-SNP	.											.	OR10T2	76	.	0			c.C479A						.						68	66	67					1																	158368778		2203	4300	6503	SO:0001583	missense	128360	exon1			TTGGTGGCCACCA	AB065643	CCDS30895.1	1q23.1	2012-08-09			ENSG00000186306	ENSG00000186306		"GPCR / Class A : Olfactory receptors"	14816	protein-coding gene	gene with protein product							Standard	NM_001004475		Approved		uc010pih.2	Q8NGX3	OTTHUMG00000017521	ENST00000334438.1:c.479C>A	chr1.hg19:g.158368778G>T	ENSP00000334115:p.Ala160Asp	60.0	0.0		85.0	5.0	NM_001004475	Q6IF98	Missense_Mutation	SNP	ENST00000334438.1	hg19	CCDS30895.1	.	.	.	.	.	.	.	.	.	.	G	7.889	0.731896	0.15507	.	.	ENSG00000186306	ENST00000334438	T	0.00130	8.69	4.57	2.7	0.31948	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41823	D	0.000819	T	0.00039	0.0001	N	0.13003	0.285	0.09310	N	1	P	0.47191	0.891	P	0.54889	0.763	T	0.01280	-1.1397	10	0.44086	T	0.13	.	5.6799	0.17769	0.1753:0.0:0.6681:0.1565	.	160	Q8NGX3	O10T2_HUMAN	D	160	ENSP00000334115:A160D	ENSP00000334115:A160D	A	-	2	0	OR10T2	156635402	0.000000	0.05858	0.987000	0.45799	0.799000	0.45148	0.554000	0.23407	0.546000	0.28920	0.655000	0.94253	GCC	.	.		0.468	OR10T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046371.1	NM_001004475		T	158368778	G	T	158368778	3	4	238	1	0	0	0	0	1	0	0	0	10928	1203	42	3	467	3	OR10T2	1	158368778	Missense_Mutation	SNP	G	TCGA-ED-A4XI-01A-11D-A25V-10	5325592	158368778	90881843	10	33137										
HSD17B7	51478	hgsc.bcm.edu	37	chr1	162760596	162760596	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	tgtgagtgcgcgaagatgcgAaaggtggttttgatcaccgg	16	6	1	3			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:162760596A>G	ENST00000254521.3	+	1	61	c.6A>G	c.(4-6)cgA>cgG	p.R2R	HSD17B7_ENST00000367917.3_Silent_p.R2R|HSD17B7_ENST00000485405.1_3'UTR|HSD17B7_ENST00000367913.1_Silent_p.R2R|HSD17B7_ENST00000367915.1_Silent_p.R2R	NM_016371.2	NP_057455.1	P56937	DHB7_HUMAN	hydroxysteroid (17-beta) dehydrogenase 7	2					cholesterol biosynthetic process (GO:0006695)|estrogen biosynthetic process (GO:0006703)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	3-keto sterol reductase activity (GO:0000253)|estradiol 17-beta-dehydrogenase activity (GO:0004303)			endometrium(3)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	9	all_hematologic(112;0.115)					CGAAGATGCGAAAGGTGGTTT	0.607																																					p.R2R		Atlas-SNP	.											.	HSD17B7	25	.	0			c.A6G						.						59	48	51					1																	162760596		2203	4300	6503	SO:0001819	synonymous_variant	51478	exon1			GATGCGAAAGGTG	AF098786	CCDS1242.1	1q23	2011-09-14			ENSG00000132196	ENSG00000132196	1.1.1.270	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	5215	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 37C, member 1"	606756				10544267, 10419022, 19027726	Standard	NM_016371		Approved	PRAP, SDR37C1	uc001gci.3	P56937	OTTHUMG00000034420	ENST00000254521.3:c.6A>G	chr1.hg19:g.162760596A>G		547.0	0.0		671.0	86.0	NM_016371	Q5T246|Q7Z4V9|Q8WWS2|Q9UF00	Silent	SNP	ENST00000254521.3	hg19	CCDS1242.1																																																																																			.	.		0.607	HSD17B7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083207.1	NM_016371		G	162760596	A	G	162760596	2	3	238	1	0	0	0	0	0	0	0	1	7397	233	9	2		2	HSD17B7	1	162760596	Silent	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	4391818	162760596	86490025	11	33138										
POGK	57645	hgsc.bcm.edu	37	chr1	166818288	166818288	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	gcctccgtctgcctcgggatAtcacagagctgcccgagtgg	13	14	2	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:166818288A>G	ENST00000367875.1	+	5	832	c.472A>G	c.(472-474)Atc>Gtc	p.I158V	POGK_ENST00000536514.1_Missense_Mutation_p.I73V|POGK_ENST00000367876.4_Missense_Mutation_p.I158V|POGK_ENST00000537173.1_Missense_Mutation_p.I40V			Q9P215	POGK_HUMAN	pogo transposable element with KRAB domain	158					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	22						GCCTCGGGATATCACAGAGCT	0.557																																					p.I158V	GBM(76;192 1530 30153 48742)	Atlas-SNP	.											.	POGK	54	.	0			c.A472G						.						106	101	103					1																	166818288		2203	4300	6503	SO:0001583	missense	57645	exon5			CGGGATATCACAG	AB040946	CCDS1254.1	1q23.2	2013-01-08			ENSG00000143157	ENSG00000143157		"-"	18800	protein-coding gene	gene with protein product	"KRAB box domain containing 2"						Standard	NM_017542		Approved	KIAA15131, LST003, BASS2, KRBOX2	uc001gdt.1	Q9P215	OTTHUMG00000034325	ENST00000367875.1:c.472A>G	chr1.hg19:g.166818288A>G	ENSP00000356849:p.Ile158Val	304.0	0.0		340.0	63.0	NM_017542	Q5TIJ1|Q8TE07	Missense_Mutation	SNP	ENST00000367875.1	hg19	CCDS1254.1	.	.	.	.	.	.	.	.	.	.	A	9.958	1.222131	0.22457	.	.	ENSG00000143157	ENST00000537173;ENST00000536514;ENST00000449930;ENST00000367876;ENST00000367875	T;T;T;T;T	0.35605	1.33;1.3;4.79;4.71;4.71	5.39	-1.24	0.09435	.	0.634401	0.13847	N	0.358600	T	0.09335	0.0230	N	0.19112	0.55	0.23070	N	0.998344	B;B;B	0.13594	0.004;0.008;0.008	B;B;B	0.15870	0.014;0.006;0.006	T	0.20240	-1.0281	9	0.62326	D	0.03	-18.915	10.1994	0.43073	0.2428:0.6429:0.0:0.1142	.	40;73;158	G3V1P0;B4DS22;Q9P215	.;.;POGK_HUMAN	V	40;73;158;158;158	ENSP00000442763:I40V;ENSP00000441187:I73V;ENSP00000404402:I158V;ENSP00000356850:I158V;ENSP00000356849:I158V	ENSP00000356849:I158V	I	+	1	0	POGK	165084912	0.021000	0.18746	0.086000	0.20670	0.959000	0.62525	-0.176000	0.09811	-0.370000	0.08016	0.533000	0.62120	ATC	.	.		0.557	POGK-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082888.1	NM_017542		G	166818288	A	G	166818288	3	3	238	1	0	0	0	0	1	0	0	0	12194	449	16	2	486	2	POGK	1	166818288	Missense_Mutation	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	4057692	166818288	82432333	12	33139										
PTPRC	5788	hgsc.bcm.edu	37	chr1	198682109	198682109	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	agagcctcagattattttttGtagaagtgaagctgcacatc	9	7	1	4			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:198682109G>A	ENST00000367376.2	+	12	1364	c.1193G>A	c.(1192-1194)tGt>tAt	p.C398Y	PTPRC_ENST00000352140.3_Missense_Mutation_p.C350Y|PTPRC_ENST00000442510.2_Missense_Mutation_p.C400Y|PTPRC_ENST00000348564.6_Missense_Mutation_p.C239Y|PTPRC_ENST00000594404.1_Missense_Mutation_p.C237Y	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	398	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|bone marrow development (GO:0048539)|cell cycle phase transition (GO:0044770)|cell surface receptor signaling pathway (GO:0007166)|defense response to virus (GO:0051607)|dephosphorylation (GO:0016311)|hematopoietic progenitor cell differentiation (GO:0002244)|immunoglobulin biosynthetic process (GO:0002378)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of antigen receptor-mediated signaling pathway (GO:0050857)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of T cell proliferation (GO:0042102)|protein dephosphorylation (GO:0006470)|regulation of cell cycle (GO:0051726)|release of sequestered calcium ion into cytosol (GO:0051209)|stem cell development (GO:0048864)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			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						ATTATTTTTTGTAGAAGTGAA	0.323																																					p.C400Y		Atlas-SNP	.											.	PTPRC	229	.	0			c.G1199A						.						104	113	110					1																	198682109		2203	4300	6503	SO:0001583	missense	5788	exon12			TTTTTTGTAGAAG	Y00062	CCDS1397.1, CCDS1398.1, CCDS44291.1, CCDS1397.2, CCDS1398.2, CCDS44291.2	1q31-q32	2014-09-17			ENSG00000081237	ENSG00000081237		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9666	protein-coding gene	gene with protein product		151460		CD45		2169617	Standard	NM_001267798		Approved	LCA, T200, GP180	uc001gur.2	P08575	OTTHUMG00000035702	ENST00000367376.2:c.1193G>A	chr1.hg19:g.198682109G>A	ENSP00000356346:p.Cys398Tyr	110.0	0.0		140.0	9.0	NM_002838	A8K7W6|Q16614|Q9H0Y6	Missense_Mutation	SNP	ENST00000367376.2	hg19		.	.	.	.	.	.	.	.	.	.	G	12.44	1.939446	0.34189	.	.	ENSG00000081237	ENST00000367376;ENST00000367366;ENST00000352140;ENST00000535566;ENST00000530727;ENST00000442510;ENST00000367367;ENST00000348564	T	0.56941	0.43	3.86	2.91	0.33838	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.474926	0.18045	N	0.153479	T	0.66446	0.2790	M	0.65975	2.015	0.09310	N	1	D;D;D;D;D	0.76494	0.998;0.999;0.994;0.999;0.993	D;D;D;D;D	0.76071	0.969;0.987;0.949;0.949;0.93	T	0.54529	-0.8280	10	0.87932	D	0	.	8.7144	0.34403	0.0:0.0:0.7741:0.2259	.	334;334;239;350;398	F5GXZ3;B4DSZ5;B1ALS3;E9PC28;P08575	.;.;.;.;PTPRC_HUMAN	Y	400;334;350;350;284;398;332;237	ENSP00000193532:C350Y	ENSP00000306782:C237Y	C	+	2	0	PTPRC	196948732	0.043000	0.20138	0.002000	0.10522	0.002000	0.02628	1.531000	0.36018	1.158000	0.42547	0.591000	0.81541	TGT	.	.		0.323	PTPRC-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding				A	198682109	G	A	198682109	3	1	238	1	0	0	0	0	1	0	0	0	12812	1377	48	3	1246	3	PTPRC	1	198682109	Missense_Mutation	SNP	G	TCGA-ED-A4XI-01A-11D-A25V-10	31863821	198682109	50568512	13	33140										
MARK1	4139	hgsc.bcm.edu	37	chr1	220826560	220826560	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	agcactttccatggtgaacaGctccgggagcgacgcagcgt	13	12	0	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:220826560G>A	ENST00000366917.4	+	16	2120	c.1854G>A	c.(1852-1854)caG>caA	p.Q618Q	MARK1_ENST00000402574.1_Silent_p.Q483Q|MARK1_ENST00000366918.4_Silent_p.Q596Q					MAP/microtubule affinity-regulating kinase 1											central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(12)|lung(22)|ovary(4)|pancreas(1)|skin(3)|stomach(3)|urinary_tract(1)	63				GBM - Glioblastoma multiforme(131;0.0407)		ATGGTGAACAGCTCCGGGAGC	0.562																																					p.Q618Q		Atlas-SNP	.											.	MARK1	161	.	0			c.G1854A						.						95	84	87					1																	220826560		2203	4300	6503	SO:0001819	synonymous_variant	4139	exon16			TGAACAGCTCCGG	AF154845	CCDS31029.2, CCDS65789.1, CCDS73033.1, CCDS73034.1	1q41	2013-06-27			ENSG00000116141	ENSG00000116141			6896	protein-coding gene	gene with protein product		606511				9108484	Standard	NM_018650		Approved	MARK, PAR-1C	uc001hmn.4	Q9P0L2	OTTHUMG00000037351	ENST00000366917.4:c.1854G>A	chr1.hg19:g.220826560G>A		230.0	0.0		237.0	12.0	NM_018650		Silent	SNP	ENST00000366917.4	hg19	CCDS31029.2																																																																																			.	.		0.562	MARK1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090899.1			A	220826560	G	A	220826560	2	1	238	1	0	0	0	0	0	0	0	1	9321	962	34	3		3	MARK1	1	220826560	Silent	SNP	G	TCGA-ED-A4XI-01A-11D-A25V-10	22144451	220826560	28424061	14	33141										
OR2M5	127059	hgsc.bcm.edu	37	chr1	248308834	248308834	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	gctatattgccatttgccacCctctaagatacaccaatctc	4	14	2	1	rs150844237		TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:248308834C>G	ENST00000366476.1	+	1	385	c.385C>G	c.(385-387)Cct>Gct	p.P129A		NM_001004690.1	NP_001004690.1	A3KFT3	OR2M5_HUMAN	olfactory receptor, family 2, subfamily M, member 5	129						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	49	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0388)			CATTTGCCACCCTCTAAGATA	0.443																																					p.P129A		Atlas-SNP	.											.	OR2M5	117	.	0			c.C385G						.						287	286	287					1																	248308834		2203	4300	6503	SO:0001583	missense	127059	exon1			TGCCACCCTCTAA		CCDS31105.1	1q44	2012-08-09		2004-03-10	ENSG00000162727	ENSG00000162727		"GPCR / Class A : Olfactory receptors"	19576	protein-coding gene	gene with protein product				OR2M5P			Standard	NM_001004690		Approved		uc010pze.2	A3KFT3	OTTHUMG00000040447	ENST00000366476.1:c.385C>G	chr1.hg19:g.248308834C>G	ENSP00000355432:p.Pro129Ala	400.0	0.0		508.0	26.0	NM_001004690		Missense_Mutation	SNP	ENST00000366476.1	hg19	CCDS31105.1	.	.	.	.	.	.	.	.	.	.	c	13.37	2.217809	0.39201	.	.	ENSG00000162727	ENST00000366476	T	0.01838	4.61	3.28	3.28	0.37604	GPCR, rhodopsin-like superfamily (1);	0.000000	0.31949	U	0.006810	T	0.14227	0.0344	H	0.98314	4.2	0.33242	D	0.557303	D	0.54964	0.969	P	0.48770	0.589	T	0.57046	-0.7878	10	0.87932	D	0	.	14.4562	0.67418	0.0:1.0:0.0:0.0	.	129	A3KFT3	OR2M5_HUMAN	A	129	ENSP00000355432:P129A	ENSP00000355432:P129A	P	+	1	0	OR2M5	246375457	0.996000	0.38824	0.033000	0.17914	0.084000	0.17831	5.640000	0.67875	1.528000	0.49103	0.492000	0.49549	CCT	.	C|1.000;T|0.000		0.443	OR2M5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097343.1	NM_001004690		G	248308834	C	G	248308834	3	3	238	1	0	0	0	0	1	0	0	0	11022	623	22	4	387	4	OR2M5	1	248308834	Missense_Mutation	SNP	C	TCGA-ED-A4XI-01A-11D-A25V-10	27482274	248308834	941787	15	33142										
OR2T11	127077	hgsc.bcm.edu	37	chr1	248789769	248789769	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	agagggcatgcggtggatggTtaacaagatgagggagtagg	19	3	0	3			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:248789769T>C	ENST00000330803.2	-	1	722	c.661A>G	c.(661-663)Acc>Gcc	p.T221A		NM_001001964.1	NP_001001964.1	Q8NH01	O2T11_HUMAN	olfactory receptor, family 2, subfamily T, member 11 (gene/pseudogene)	221						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|large_intestine(5)|lung(20)|skin(2)	28	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CGGTGGATGGTTAACAAGATG	0.488																																					p.T221A		Atlas-SNP	.											.	OR2T11	64	.	0			c.A661G						.						67	70	69					1																	248789769		2053	4233	6286	SO:0001583	missense	127077	exon1			GGATGGTTAACAA	BK004476	CCDS31122.1	1q44	2013-10-10	2013-10-10		ENSG00000183130	ENSG00000183130		"GPCR / Class A : Olfactory receptors"	19574	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily T, member 11"				Standard	NM_001001964		Approved	OR2T11Q	uc001ier.1	Q8NH01	OTTHUMG00000040384	ENST00000330803.2:c.661A>G	chr1.hg19:g.248789769T>C	ENSP00000328934:p.Thr221Ala	198.0	0.0		224.0	18.0	NM_001001964	Q6IEY6	Missense_Mutation	SNP	ENST00000330803.2	hg19	CCDS31122.1	.	.	.	.	.	.	.	.	.	.	.	0.012	-1.652132	0.00785	.	.	ENSG00000183130	ENST00000330803	T	0.00029	8.91	4.23	0.506	0.16961	GPCR, rhodopsin-like superfamily (1);	0.000000	0.43260	D	0.000596	T	0.00073	0.0002	N	0.10945	0.07	0.09310	N	1	B	0.19706	0.038	B	0.31245	0.126	T	0.12967	-1.0527	10	0.07175	T	0.84	.	7.8476	0.29435	0.0:0.3676:0.0:0.6324	.	221	Q8NH01	O2T11_HUMAN	A	221	ENSP00000328934:T221A	ENSP00000328934:T221A	T	-	1	0	OR2T11	246856392	0.008000	0.16893	0.001000	0.08648	0.002000	0.02628	0.367000	0.20382	0.185000	0.20105	0.528000	0.53228	ACC	.	.		0.488	OR2T11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097134.1	NM_001001964		C	248789769	T	C	248789769	3	2	238	1	0	0	0	0	1	0	0	0	11027	1725	60	2	293	2	OR2T11	1	248789769	Missense_Mutation	SNP	T	TCGA-ED-A4XI-01A-11D-A25V-10	480935	248789769	460852	16	33143										
ZNF638	27332	hgsc.bcm.edu	37	chr2	71629093	71629093	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	atttgttttgaaggaaacagAagaaatgtgtgtgatgcttg	12	2	0	4			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr2:71629093A>G	ENST00000409544.1	+	16	3335	c.2705A>G	c.(2704-2706)gAa>gGa	p.E902G	ZNF638_ENST00000355812.3_Missense_Mutation_p.E902G|ZNF638_ENST00000264447.4_Missense_Mutation_p.E902G	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	902					regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						AAGGAAACAGAAGAAATGTGT	0.269																																					p.E902G		Atlas-SNP	.											.	ZNF638	179	.	0			c.A2705G						.						69	74	72					2																	71629093		2203	4297	6500	SO:0001583	missense	27332	exon16			AAACAGAAGAAAT	D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"RNA binding motif (RRM) containing"	17894	protein-coding gene	gene with protein product		614349	"zinc finger, matrin-like"	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.2705A>G	chr2.hg19:g.71629093A>G	ENSP00000386433:p.Glu902Gly	62.0	0.0		49.0	9.0	NM_014497	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Missense_Mutation	SNP	ENST00000409544.1	hg19	CCDS1917.1	.	.	.	.	.	.	.	.	.	.	A	16.34	3.094463	0.56075	.	.	ENSG00000075292	ENST00000394137;ENST00000355812;ENST00000264447;ENST00000409544	T;T;T	0.59772	0.24;1.24;1.24	5.69	5.69	0.88448	.	0.382752	0.27691	N	0.018253	T	0.54886	0.1886	M	0.61703	1.905	0.80722	D	1	P;P;P;P	0.38827	0.518;0.465;0.649;0.518	B;B;B;B	0.36666	0.115;0.085;0.23;0.115	T	0.56896	-0.7903	10	0.38643	T	0.18	-14.4221	13.8977	0.63783	1.0:0.0:0.0:0.0	.	902;902;902;902	A8K583;Q14966-4;Q14966-3;Q14966	.;.;.;ZN638_HUMAN	G	481;902;902;902	ENSP00000348066:E902G;ENSP00000264447:E902G;ENSP00000386433:E902G	ENSP00000264447:E902G	E	+	2	0	ZNF638	71482601	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	5.314000	0.65804	2.167000	0.68274	0.477000	0.44152	GAA	.	.		0.269	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497		G	71629093	A	G	71629093	3	3	238	1	0	0	0	0	1	0	0	0	18070	246	9	2	2763	2	ZNF638	2	71629093	Missense_Mutation	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10		71629093	171570280	17	33144										
DNAH6	1768	hgsc.bcm.edu	37	chr2	84921530	84921530	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	ataattatgatagttttcatGaagacctgaggaagttgtac	9	4	1	4			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr2:84921530G>A	ENST00000237449.6	+	45	7458	c.7450G>A	c.(7450-7452)Gaa>Aaa	p.E2484K	DNAH6_ENST00000398278.2_Missense_Mutation_p.E2435K|DNAH6_ENST00000602588.1_Missense_Mutation_p.E456K|DNAH6_ENST00000389394.3_Missense_Mutation_p.E2484K			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	2484	AAA 4. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						TAGTTTTCATGAAGACCTGAG	0.423																																					p.E2484K		Atlas-SNP	.											.	DNAH6	194	.	0			c.G7450A						.						161	145	150					2																	84921530		692	1591	2283	SO:0001583	missense	1768	exon46			TTTCATGAAGACC	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.7450G>A	chr2.hg19:g.84921530G>A	ENSP00000237449:p.Glu2484Lys	152.0	0.0		158.0	13.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	hg19	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	G	35	5.582390	0.96578	.	.	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.41400	1.0;1.2;1.0	5.47	5.47	0.80525	Dynein heavy chain, P-loop containing D4 domain (1);ATPase, AAA+ type, core (1);	.	.	.	.	T	0.72087	0.3417	M	0.93420	3.415	0.58432	D	0.999999	D;D	0.58970	0.966;0.984	P;P	0.61800	0.884;0.894	T	0.80155	-0.1500	9	0.72032	D	0.01	.	18.0925	0.89479	0.0:0.0:1.0:0.0	.	2484;2435	Q9C0G6;Q9C0G6-4	DYH6_HUMAN;.	K	2484;2435;2484	ENSP00000374045:E2484K;ENSP00000381326:E2435K;ENSP00000237449:E2484K	ENSP00000237449:E2484K	E	+	1	0	DNAH6	84775041	1.000000	0.71417	0.996000	0.52242	0.964000	0.63967	8.279000	0.89901	2.565000	0.86533	0.655000	0.94253	GAA	.	.		0.423	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		A	84921530	G	A	84921530	3	1	238	1	0	0	0	0	1	0	0	0	4607	1291	45	3	7628	3	DNAH6	2	84921530	Missense_Mutation	SNP	G	TCGA-ED-A4XI-01A-11D-A25V-10	13292437	84921530	158277843	18	33145										
FER1L5	0	hgsc.bcm.edu	37	chr2	97312182	97312182	+	IGR	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	tggaagggaatgatcccgtgTggaatgaggtagacaacagg	16	5	0	3			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr2:97312182T>A								KANSL3 (8067 upstream) : FER1L5 (23772 downstream)																							TGATCCCGTGTGGAATGAGGT	0.507																																					p.W44R		Atlas-SNP	.											.	FER1L5	113	.	0			c.T130A						.						176	150	158					2																	97312182		692	1591	2283	SO:0001628	intergenic_variant	90342	exon2			CCCGTGTGGAATG																													chr2.hg19:g.97312182T>A		325.0	0.0		273.0	14.0	NM_001113382		Missense_Mutation	SNP		hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.87|13.87	2.367208|2.367208	0.41902|0.41902	.|.	.|.	ENSG00000214272|ENSG00000214272	ENST00000342152|ENST00000414152;ENST00000436930	.|.	.|.	.|.	3.58|3.58	3.58|3.58	0.41010|0.41010	.|C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	1.523470|.	0.04630|.	N|.	0.403585|.	.|T	.|0.72938	.|0.3523	M|M	0.79123|0.79123	2.44|2.44	.|.	.|.	.|.	.|D	.|0.76494	.|0.999	.|D	.|0.87578	.|0.998	.|T	.|0.80469	.|-0.1369	.|7	0.02654|0.87932	T|D	1|0	.|.	8.8311|8.8311	0.35085|0.35085	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|44	.|A0AVI2	.|FR1L5_HUMAN	X|R	4|44	.|.	ENSP00000441631:C4X|ENSP00000444148:W44R	C|W	+|+	3|1	2|0	FER1L5|FER1L5	96675909|96675909	0.993000|0.993000	0.37304|0.37304	0.905000|0.905000	0.35620|0.35620	0.852000|0.852000	0.48524|0.48524	3.479000|3.479000	0.53165|0.53165	1.873000|1.873000	0.54277|0.54277	0.454000|0.454000	0.30748|0.30748	TGT|TGG	.	.	0	0.507									A	97312182	T	A	97312182	1	1	238	0	1	0	0	0	0	0	0	0	5822	1696	59	4		4	FER1L5	2	97312182	IGR	SNP	T	TCGA-ED-A4XI-01A-11D-A25V-10	12390652	97312182	145887191	19	33146										
SCN1A	6323	hgsc.bcm.edu	37	chr2	166852534	166852534	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	acttcttactcctggtcgagGtataggcttttgcggttttt	10	8	1	0	rs143088184		TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr2:166852534G>T	ENST00000303395.4	-	24	4569	c.4570C>A	c.(4570-4572)Cct>Act	p.P1524T	SCN1A_ENST00000375405.3_Missense_Mutation_p.P1513T|AC010127.3_ENST00000595647.1_RNA|AC010127.3_ENST00000597623.1_RNA|SCN1A_ENST00000409050.1_Missense_Mutation_p.P1496T|SCN1A_ENST00000423058.2_Missense_Mutation_p.P1524T			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1524					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CCTGGTCGAGGTATAGGCTTT	0.338																																					p.P1524T		Atlas-SNP	.											.	SCN1A	641	.	0			c.C4570A						.	G	THR/PRO,THR/PRO,THR/PRO,THR/PRO	1,4405	2.1+/-5.4	0,1,2202	128	123	124		4570,4486,4570,4537	5.8	1	2	dbSNP_134	124	0,8600		0,0,4300	no	missense,missense,missense,missense	SCN1A	NM_001165963.1,NM_001165964.1,NM_001202435.1,NM_006920.4	38,38,38,38	0,1,6502	TT,TG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	1524/2010,1496/1982,1524/2010,1513/1999	166852534	1,13005	2203	4300	6503	SO:0001583	missense	6323	exon24			GTCGAGGTATAGG	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10585	protein-coding gene	gene with protein product		182389	"febrile convulsions 3"	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.4570C>A	chr2.hg19:g.166852534G>T	ENSP00000303540:p.Pro1524Thr	50.0	0.0		50.0	5.0	NM_001165963	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	hg19	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.038482	0.93630	2.27E-4	0.0	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.97138	-4.26;-4.26;-4.21;-4.18	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	D	0.98912	0.9631	M	0.92367	3.3	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99342	1.0912	10	0.87932	D	0	.	20.1438	0.98071	0.0:0.0:1.0:0.0	.	1513	P35498-2	.	T	1524;1524;1513;1496	ENSP00000407030:P1524T;ENSP00000303540:P1524T;ENSP00000364554:P1513T;ENSP00000386312:P1496T	ENSP00000303540:P1524T	P	-	1	0	SCN1A	166560780	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.810000	0.99221	2.768000	0.95171	0.650000	0.86243	CCT	.	G|1.000;T|0.000		0.338	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		T	166852534	G	T	166852534	3	4	238	1	0	0	0	0	1	0	0	0	13929	1261	44	3	1471	3	SCN1A	2	166852534	Missense_Mutation	SNP	G	TCGA-ED-A4XI-01A-11D-A25V-10	69540352	166852534	76346839	20	33147										
ABCB11	8647	hgsc.bcm.edu	37	chr2	169791714	169791714	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	ctgaacacatagctgaaatgGagcccctcattggagattaa	9	9	1	3			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr2:169791714G>A	ENST00000263817.6	-	23	3160	c.3036C>T	c.(3034-3036)ctC>ctT	p.L1012L		NM_003742.2	NP_003733.2	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 11	1012	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|canalicular bile acid transport (GO:0015722)|small molecule metabolic process (GO:0044281)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|bile acid-exporting ATPase activity (GO:0015432)|canalicular bile acid transmembrane transporter activity (GO:0015126)|sodium-exporting ATPase activity, phosphorylative mechanism (GO:0008554)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(16)|lung(26)|ovary(3)|stomach(1)	57					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Chlorpromazine(DB00477)|Cimetidine(DB00501)|Clofazimine(DB00845)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Digoxin(DB00390)|Doxorubicin(DB00997)|Ethinyl Estradiol(DB00977)|Fluorescein(DB00693)|Fusidic Acid(DB02703)|Glyburide(DB01016)|Ketoconazole(DB01026)|Novobiocin(DB01051)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Ponatinib(DB08901)|Pravastatin(DB00175)|Progesterone(DB00396)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Rosuvastatin(DB01098)|Tamoxifen(DB00675)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	AGCTGAAATGGAGCCCCTCAT	0.423																																					p.L1012L		Atlas-SNP	.											.	ABCB11	136	.	0			c.C3036T						.						151	142	145					2																	169791714		1911	4118	6029	SO:0001819	synonymous_variant	8647	exon23			GAAATGGAGCCCC	AF091582	CCDS46444.1	2q24	2012-03-14			ENSG00000073734	ENSG00000073734		"ATP binding cassette transporters / subfamily B"	42	protein-coding gene	gene with protein product	"ABC member 16, MDR/TAP subfamily"	603201	"progressive familial intrahepatic cholestasis 2", "bile salt export pump"	BSEP, PFIC2		9806540	Standard	NM_003742		Approved	ABC16, SPGP, PFIC-2, PGY4	uc002ueo.1	O95342	OTTHUMG00000154039	ENST00000263817.6:c.3036C>T	chr2.hg19:g.169791714G>A		174.0	0.0		165.0	16.0	NM_003742	Q53TL2|Q9UNB2	Silent	SNP	ENST00000263817.6	hg19	CCDS46444.1																																																																																			.	.		0.423	ABCB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333616.2	NM_003742		A	169791714	G	A	169791714	2	1	238	1	0	0	0	0	0	0	0	1	42	1161	41	3		3	ABCB11	2	169791714	Silent	SNP	G	TCGA-ED-A4XI-01A-11D-A25V-10	2939180	169791714	73407659	21	33148										
ASNSD1	54529	hgsc.bcm.edu	37	chr2	190531503	190531503	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	gaagaaaatgttaatagcctGagtcaaatttcagcagactt	8	6	2	3			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr2:190531503G>T	ENST00000260952.4	+	4	1058	c.645G>T	c.(643-645)ctG>ctT	p.L215L	ASNSD1_ENST00000607062.1_Intron	NM_019048.2	NP_061921	Q9NWL6	ASND1_HUMAN	asparagine synthetase domain containing 1	215					asparagine biosynthetic process (GO:0006529)|glutamine metabolic process (GO:0006541)		asparagine synthase (glutamine-hydrolyzing) activity (GO:0004066)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(3)	25			OV - Ovarian serous cystadenocarcinoma(117;0.00318)|Epithelial(96;0.0449)|all cancers(119;0.118)			TTAATAGCCTGAGTCAAATTT	0.333																																					p.L215L		Atlas-SNP	.											.	ASNSD1	63	.	0			c.G645T						.						50	55	54					2																	190531503		2201	4299	6500	SO:0001819	synonymous_variant	54529	exon4			TAGCCTGAGTCAA	AY116969	CCDS2300.1	2q32.2	2012-09-20			ENSG00000138381	ENSG00000138381			24910	protein-coding gene	gene with protein product							Standard	NM_019048		Approved	NS3TP1, FLJ20752, NBLA00058	uc002uqt.3	Q9NWL6	OTTHUMG00000132665	ENST00000260952.4:c.645G>T	chr2.hg19:g.190531503G>T		46.0	0.0		57.0	7.0	NM_019048	D3DPH6|Q3LIC3|Q4ZG45	Silent	SNP	ENST00000260952.4	hg19	CCDS2300.1																																																																																			.	.		0.333	ASNSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255919.3	NM_019048		T	190531503	G	T	190531503	2	4	238	1	0	0	0	0	0	0	0	1	1049	1277	45	3		3	ASNSD1	2	190531503	Silent	SNP	G	TCGA-ED-A4XI-01A-11D-A25V-10	20739789	190531503	52667870	22	33149										
ZDBF2	57683	hgsc.bcm.edu	37	chr2	207175044	207175044	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	gaggcctcctaagcaaaaggGgcgtgtggcttctcaatgcc	13	11	1	0			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr2:207175044G>T	ENST00000374423.3	+	5	6178	c.5792G>T	c.(5791-5793)gGg>gTg	p.G1931V		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1931							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						AAGCAAAAGGGGCGTGTGGCT	0.433																																					p.G1931V		Atlas-SNP	.											.	ZDBF2	531	.	0			c.G5792T						.						71	71	71					2																	207175044		1958	4153	6111	SO:0001583	missense	57683	exon5			AAAAGGGGCGTGT	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"Zinc fingers, DBF-type"	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.5792G>T	chr2.hg19:g.207175044G>T	ENSP00000363545:p.Gly1931Val	217.0	0.0		251.0	31.0	NM_020923	Q6ZNP7|Q6ZSN8	Missense_Mutation	SNP	ENST00000374423.3	hg19	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	G	7.815	0.716570	0.15306	.	.	ENSG00000204186	ENST00000374423	T	0.45276	0.9	5.64	4.76	0.60689	.	.	.	.	.	T	0.31888	0.0811	N	0.19112	0.55	0.20638	N	0.999874	B	0.19583	0.037	B	0.17722	0.019	T	0.25328	-1.0135	9	0.52906	T	0.07	.	14.4819	0.67590	0.0706:0.0:0.9294:0.0	.	1931	Q9HCK1	ZDBF2_HUMAN	V	1931	ENSP00000363545:G1931V	ENSP00000363545:G1931V	G	+	2	0	ZDBF2	206883289	0.974000	0.33945	0.002000	0.10522	0.001000	0.01503	2.264000	0.43302	1.396000	0.46663	0.558000	0.71614	GGG	.	.		0.433	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		T	207175044	G	T	207175044	3	4	238	1	0	0	0	0	1	0	0	0	17614	1232	43	3	5802	3	ZDBF2	2	207175044	Missense_Mutation	SNP	G	TCGA-ED-A4XI-01A-11D-A25V-10	16643541	207175044	36024329	23	33150										
CAMP	820	hgsc.bcm.edu	37	chr3	48266103	48266103	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	tcctttccagctggtgaagcGgtgtatggggacagtgaccc	14	10	0	2	rs375338469		TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr3:48266103G>A	ENST00000576243.1	+	3	460	c.320G>A	c.(319-321)cGg>cAg	p.R107Q	CAMP_ENST00000296435.2_Missense_Mutation_p.R110Q			P49913	CAMP_HUMAN	cathelicidin antimicrobial peptide	107					antibacterial humoral response (GO:0019731)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to peptidoglycan (GO:0071224)|cellular response to tumor necrosis factor (GO:0071356)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|killing by host of symbiont cells (GO:0051873)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of growth of symbiont on or near host surface (GO:0044140)|phagosome maturation (GO:0090382)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein phosphorylation (GO:0001934)	cell projection (GO:0042995)|cell wall (GO:0005618)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|specific granule (GO:0042581)				endometrium(2)|large_intestine(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6				BRCA - Breast invasive adenocarcinoma(193;0.000614)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		CTGGTGAAGCGGTGTATGGGG	0.567																																					p.R110Q		Atlas-SNP	.											.	CAMP	12	.	0			c.G329A						.	G	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	144	135	138		320	-6.1	0	3		138	0,8600		0,0,4300	no	missense	CAMP	NM_004345.4	43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	107/171	48266103	1,13005	2203	4300	6503	SO:0001583	missense	820	exon3			TGAAGCGGTGTAT	BC055089	CCDS2762.1, CCDS2762.2	3p21.3	2014-01-30			ENSG00000164047	ENSG00000164047		"Endogenous ligands"	1472	protein-coding gene	gene with protein product		600474				7624374	Standard	NM_004345		Approved	CAP18, FALL39, FALL-39, LL37	uc003csj.3	P49913	OTTHUMG00000133526	ENST00000576243.1:c.320G>A	chr3.hg19:g.48266103G>A	ENSP00000458149:p.Arg107Gln	231.0	0.0		187.0	27.0	NM_004345	Q71SN9	Missense_Mutation	SNP	ENST00000576243.1	hg19		.	.	.	.	.	.	.	.	.	.	G	2.258	-0.369857	0.05069	2.27E-4	0.0	ENSG00000164047	ENST00000296435	.	.	.	5.49	-6.14	0.02111	.	1.302650	0.04982	N	0.465755	T	0.11067	0.0270	N	0.02334	-0.595	0.09310	N	1	B	0.12013	0.005	B	0.04013	0.001	T	0.36359	-0.9751	9	0.02654	T	1	-12.3855	7.7195	0.28723	0.3798:0.0:0.5027:0.1176	.	107	P49913	CAMP_HUMAN	Q	107	.	ENSP00000296435:R107Q	R	+	2	0	CAMP	48241107	0.000000	0.05858	0.003000	0.11579	0.754000	0.42855	-1.300000	0.02751	-0.947000	0.03673	-0.291000	0.09656	CGG	.	.		0.567	CAMP-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_004345		A	48266103	G	A	48266103	3	1	238	1	0	0	0	0	1	0	0	0	2612	1116	39	1	330	1	CAMP	3	48266103	Missense_Mutation	SNP	G	TCGA-ED-A4XI-01A-11D-A25V-10		48266103	149756327	24	33151										
APEH	327	hgsc.bcm.edu	37	chr3	49720037	49720037	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	tgcaagccatgtggcccttaTgggtggttcccatggtggct	14	10	0	0			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr3:49720037T>C	ENST00000296456.5	+	19	2151	c.1751T>C	c.(1750-1752)aTg>aCg	p.M584T	AC099668.5_ENST00000563780.1_RNA|APEH_ENST00000438011.1_Missense_Mutation_p.M584T	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase	584					beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GTGGCCCTTATGGGTGGTTCC	0.587																																					p.M584T		Atlas-SNP	.											.	APEH	45	.	0			c.T1751C						.						194	177	183					3																	49720037		2203	4300	6503	SO:0001583	missense	327	exon19			CCCTTATGGGTGG	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"acylaminoacyl-peptidase"	102645	"N-acylaminoacyl-peptide hydrolase"	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882	ENST00000296456.5:c.1751T>C	chr3.hg19:g.49720037T>C	ENSP00000296456:p.Met584Thr	223.0	0.0		193.0	35.0	NM_001640	Q9BQ33|Q9P0Y2	Missense_Mutation	SNP	ENST00000296456.5	hg19	CCDS2801.1	.	.	.	.	.	.	.	.	.	.	T	11.76	1.735959	0.30774	.	.	ENSG00000164062	ENST00000296456;ENST00000438011	T;T	0.42513	0.97;0.97	5.27	5.27	0.74061	Peptidase S9, prolyl oligopeptidase, catalytic domain (1);	0.441047	0.29280	N	0.012613	T	0.26484	0.0647	N	0.20807	0.61	0.31683	N	0.642892	B;B	0.13594	0.002;0.008	B;B	0.19946	0.027;0.027	T	0.24190	-1.0167	10	0.12103	T	0.63	-3.8282	11.2314	0.48914	0.0:0.0:0.1531:0.8469	.	584;584	C9JIF9;P13798	.;ACPH_HUMAN	T	584	ENSP00000296456:M584T;ENSP00000415862:M584T	ENSP00000296456:M584T	M	+	2	0	APEH	49695041	0.998000	0.40836	0.988000	0.46212	0.998000	0.95712	2.997000	0.49457	1.987000	0.57996	0.533000	0.62120	ATG	.	.		0.587	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2			C	49720037	T	C	49720037	3	2	238	1	0	0	0	0	1	0	0	0	768	1464	51	2	1825	2	APEH	3	49720037	Missense_Mutation	SNP	T	TCGA-ED-A4XI-01A-11D-A25V-10	1453934	49720037	148302393	25	33152										
CISH	1154	hgsc.bcm.edu	37	chr3	50645332	50645332	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	gtgcaggaggccacatagtgCtgcacaaggctgaccacatc	12	12	0	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr3:50645332C>A	ENST00000348721.3	-	3	663	c.483G>T	c.(481-483)caG>caT	p.Q161H	CISH_ENST00000443053.2_Missense_Mutation_p.Q178H	NM_145071.2	NP_659508.1	Q9NSE2	CISH_HUMAN	cytokine inducible SH2-containing protein	161	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				intracellular signal transduction (GO:0035556)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of signal transduction (GO:0009968)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein ubiquitination (GO:0016567)|regulation of cell growth (GO:0001558)	cytosol (GO:0005829)|plasma membrane (GO:0005886)				breast(2)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)		CCACATAGTGCTGCACAAGGC	0.607																																					p.Q178H		Atlas-SNP	.											.	CISH	27	.	0			c.G534T						.						55	55	55					3																	50645332		2203	4300	6503	SO:0001583	missense	1154	exon4			ATAGTGCTGCACA	Z77852	CCDS2831.1, CCDS46834.1	3p21.3	2013-02-14			ENSG00000114737	ENSG00000114737		"Suppressors of cytokine signaling", "SH2 domain containing"	1984	protein-coding gene	gene with protein product		602441				9465889, 7796808	Standard	NM_013324		Approved	CIS, G18, CIS-1, SOCS	uc003dax.3	Q9NSE2	OTTHUMG00000156853	ENST00000348721.3:c.483G>T	chr3.hg19:g.50645332C>A	ENSP00000294173:p.Gln161His	122.0	0.0		101.0	7.0	NM_013324	B2R9N1|G5E9R1|Q9NS38|Q9Y5R1	Missense_Mutation	SNP	ENST00000348721.3	hg19	CCDS2831.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.710738	0.89112	.	.	ENSG00000114737	ENST00000443053;ENST00000348721	D;D	0.89050	-2.46;-2.46	5.8	4.92	0.64577	SH2 motif (5);	0.165822	0.56097	D	0.000033	D	0.87795	0.6267	L	0.37466	1.105	0.80722	D	1	P;P	0.51240	0.929;0.943	P;P	0.53722	0.703;0.733	D	0.85983	0.1484	10	0.38643	T	0.18	-4.7135	11.2134	0.48813	0.0:0.8574:0.0:0.1426	.	178;161	G5E9R1;Q9NSE2	.;CISH_HUMAN	H	178;161	ENSP00000409346:Q178H;ENSP00000294173:Q161H	ENSP00000294173:Q161H	Q	-	3	2	CISH	50620336	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.090000	0.57693	2.730000	0.93505	0.563000	0.77884	CAG	.	.		0.607	CISH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346245.1	NM_145071		A	50645332	C	A	50645332	3	1	238	1	0	0	0	0	1	0	0	0	3439	796	28	3	297	3	CISH	3	50645332	Missense_Mutation	SNP	C	TCGA-ED-A4XI-01A-11D-A25V-10	925295	50645332	147377098	26	33153										
BAP1	8314	hgsc.bcm.edu	37	chr3	52441262	52441262	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	gataggcacatagctgacaaAgtggaacgcctccatggtcc	11	11	0	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr3:52441262A>C	ENST00000460680.1	-	7	979	c.508T>G	c.(508-510)Ttt>Gtt	p.F170V	BAP1_ENST00000296288.5_Missense_Mutation_p.F170V	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0	Interaction with HIP2.				anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.F170V(2)|p.E166fs*13(1)		NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		TAGCTGACAAAGTGGAACGCC	0.577			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.F170V	GBM(101;493 1458 7992 21037 25532)	Atlas-SNP	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	BAP1,NS,carcinoma,+1,2	BAP1	371	.	3	Substitution - Missense(2)|Deletion - Frameshift(1)	prostate(1)|eye(1)|kidney(1)	c.T508G						.						83	81	82					3																	52441262		2203	4300	6503	SO:0001583	missense	8314	exon7			TGACAAAGTGGAA	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.508T>G	chr3.hg19:g.52441262A>C	ENSP00000417132:p.Phe170Val	160.0	0.0		148.0	23.0	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Missense_Mutation	SNP	ENST00000460680.1	hg19	CCDS2853.1	.	.	.	.	.	.	.	.	.	.	A	29.8	5.040462	0.93630	.	.	ENSG00000163930	ENST00000460680;ENST00000296288;ENST00000470173	T;T;T	0.75260	-0.92;-0.92;-0.92	5.95	5.95	0.96441	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (3);	0.000000	0.85682	D	0.000000	D	0.90174	0.6929	H	0.94462	3.54	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.92742	0.6209	10	0.87932	D	0	-8.6289	16.4216	0.83760	1.0:0.0:0.0:0.0	.	170	Q92560	BAP1_HUMAN	V	170;170;91	ENSP00000417132:F170V;ENSP00000296288:F170V;ENSP00000417776:F91V	ENSP00000296288:F170V	F	-	1	0	BAP1	52416302	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.297000	0.96120	2.285000	0.76669	0.533000	0.62120	TTT	.	.		0.577	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			C	52441262	A	C	52441262	3	2	238	1	0	0	0	0	1	0	0	0	1311	72	3	5	1725	5	BAP1	3	52441262	Missense_Mutation	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	1795930	52441262	145581168	27	33154										
KBTBD12	166348	hgsc.bcm.edu	37	chr3	127642469	127642469	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	aatcagatgatcttaacataTccagagaagagagcattctg	8	7	3	4			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr3:127642469T>A	ENST00000405109.1	+	2	1032	c.565T>A	c.(565-567)Tcc>Acc	p.S189T	KBTBD12_ENST00000407609.3_Intron|KBTBD12_ENST00000405256.1_Missense_Mutation_p.S189T|KBTBD12_ENST00000343941.4_Intron			Q3ZCT8	KBTBC_HUMAN	kelch repeat and BTB (POZ) domain containing 12	189	BACK.									endometrium(1)|large_intestine(6)|lung(5)|ovary(1)	13						TCTTAACATATCCAGAGAAGA	0.363																																					p.S189T		Atlas-SNP	.											.	KBTBD12	41	.	0			c.T565A						.						55	50	52					3																	127642469		1868	4108	5976	SO:0001583	missense	166348	exon1			AACATATCCAGAG		CCDS33848.2	3q21.3	2013-01-08	2009-10-01	2009-10-01	ENSG00000187715	ENSG00000187715		"BTB/POZ domain containing"	25731	protein-coding gene	gene with protein product			"kelch domain containing 6"	KLHDC6			Standard	NM_207335		Approved	FLJ46299	uc010hsr.3	Q3ZCT8	OTTHUMG00000150508	ENST00000405109.1:c.565T>A	chr3.hg19:g.127642469T>A	ENSP00000385957:p.Ser189Thr	111.0	0.0		105.0	5.0	NM_207335	B5MCC6|Q6ZRK1	Missense_Mutation	SNP	ENST00000405109.1	hg19	CCDS33848.2	.	.	.	.	.	.	.	.	.	.	T	7.720	0.696999	0.15106	.	.	ENSG00000187715	ENST00000405109;ENST00000405256	T;T	0.68903	-0.36;-0.36	5.75	0.194	0.15143	BTB/Kelch-associated (2);	.	.	.	.	T	0.55033	0.1895	L	0.39020	1.185	0.31939	N	0.611124	B	0.11235	0.004	B	0.17098	0.017	T	0.53913	-0.8371	9	0.48119	T	0.1	.	11.4285	0.50025	0.4579:0.0:0.0:0.5421	.	189	Q3ZCT8	KBTBC_HUMAN	T	189	ENSP00000385957:S189T;ENSP00000385879:S189T	ENSP00000385957:S189T	S	+	1	0	KBTBD12	129125159	0.972000	0.33761	0.120000	0.21714	0.962000	0.63368	1.529000	0.35996	-0.183000	0.10585	-0.710000	0.03640	TCC	.	.		0.363	KBTBD12-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318682.1	NM_207335		A	127642469	T	A	127642469	3	1	238	1	0	0	0	0	1	0	0	0	8000	1435	50	4	567	4	KBTBD12	3	127642469	Missense_Mutation	SNP	T	TCGA-ED-A4XI-01A-11D-A25V-10	75201207	127642469	70379961	28	33155										
NMNAT3	349565	hgsc.bcm.edu	37	chr3	139292479	139292479	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	tgccttgccatggtctgggcCttccatctggggtggagatc	14	11	2	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr3:139292479C>T	ENST00000296202.7	-	5	718	c.337G>A	c.(337-339)Ggc>Agc	p.G113S	RP11-319G6.1_ENST00000381790.3_RNA|NMNAT3_ENST00000511444.1_Intron|NMNAT3_ENST00000339837.5_Missense_Mutation_p.G76S|NMNAT3_ENST00000512391.1_Intron|RP11-319G6.1_ENST00000515247.1_RNA|NMNAT3_ENST00000406824.1_Missense_Mutation_p.G3S|NMNAT3_ENST00000406164.1_Missense_Mutation_p.G76S|NMNAT3_ENST00000413939.2_Intron|NMNAT3_ENST00000507242.1_5'UTR			Q96T66	NMNA3_HUMAN	nicotinamide nucleotide adenylyltransferase 3	113					NAD biosynthetic process (GO:0009435)|NAD metabolic process (GO:0019674)|response to wounding (GO:0009611)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|nicotinamide-nucleotide adenylyltransferase activity (GO:0000309)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)			endometrium(2)|kidney(1)|large_intestine(2)|lung(4)	9						TGGTCTGGGCCTTCCATCTGG	0.532																																					p.G76S		Atlas-SNP	.											.	NMNAT3	29	.	0			c.G226A						.						235	189	205					3																	139292479		2203	4300	6503	SO:0001583	missense	349565	exon4			CTGGGCCTTCCAT	AF345564	CCDS3111.1, CCDS56282.1	3q23	2013-09-20			ENSG00000163864	ENSG00000163864			20989	protein-coding gene	gene with protein product		608702				12574164	Standard	NM_178177		Approved	PNAT3	uc003etk.3	Q96T66	OTTHUMG00000159951	ENST00000296202.7:c.337G>A	chr3.hg19:g.139292479C>T	ENSP00000296202:p.Gly113Ser	253.0	0.0		209.0	22.0	NM_178177	B3KVR6|D3DNF2|D3DNF3|Q8N4G1	Missense_Mutation	SNP	ENST00000296202.7	hg19		.	.	.	.	.	.	.	.	.	.	C	14.12	2.441334	0.43326	.	.	ENSG00000163864	ENST00000406164;ENST00000406824;ENST00000339837;ENST00000296202;ENST00000509291	D;D;D;D;D	0.97688	-4.26;-3.96;-4.26;-4.49;-3.07	4.28	4.28	0.50868	Cytidylyltransferase (1);Rossmann-like alpha/beta/alpha sandwich fold (1);	1.476730	0.03816	N	0.266736	D	0.93939	0.8060	N	0.08118	0	0.31342	N	0.683481	B	0.18863	0.031	B	0.22880	0.042	T	0.81185	-0.1048	10	0.16420	T	0.52	-22.9019	14.5326	0.67936	0.0:1.0:0.0:0.0	.	113	Q96T66	NMNA3_HUMAN	S	76;3;76;113;113	ENSP00000384319:G76S;ENSP00000384684:G3S;ENSP00000340523:G76S;ENSP00000296202:G113S;ENSP00000427634:G113S	ENSP00000296202:G113S	G	-	1	0	NMNAT3	140775169	0.946000	0.32159	0.688000	0.30117	0.561000	0.35649	3.298000	0.51818	2.665000	0.90641	0.563000	0.77884	GGC	.	.		0.532	NMNAT3-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000358469.1	NM_178177		T	139292479	C	T	139292479	3	4	238	1	0	0	0	0	1	0	0	0	10509	681	24	3	429	3	NMNAT3	3	139292479	Missense_Mutation	SNP	C	TCGA-ED-A4XI-01A-11D-A25V-10	11650010	139292479	58729951	29	33156										
EPHB3	2049	hgsc.bcm.edu	37	chr3	184294923	184294923	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	acggtgtctcgggcaagagcCctctgccgcctcgttatgcg	13	14	2	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr3:184294923C>A	ENST00000330394.2	+	5	1758	c.1306C>A	c.(1306-1308)Cct>Act	p.P436T	EIF2B5_ENST00000444495.1_Intron	NM_004443.3	NP_004434.2	P54753	EPHB3_HUMAN	EPH receptor B3	436	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell migration (GO:0016477)|central nervous system projection neuron axonogenesis (GO:0021952)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|digestive tract morphogenesis (GO:0048546)|ephrin receptor signaling pathway (GO:0048013)|palate development (GO:0060021)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of axonogenesis (GO:0050770)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell-cell adhesion (GO:0022407)|regulation of Rac GTPase activity (GO:0032314)|retinal ganglion cell axon guidance (GO:0031290)|substrate adhesion-dependent cell spreading (GO:0034446)|thymus development (GO:0048538)|urogenital system development (GO:0001655)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|ephrin receptor activity (GO:0005003)			breast(5)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_cancers(143;1.89e-10)|Ovarian(172;0.0339)		Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22)			GGGCAAGAGCCCTCTGCCGCC	0.637																																					p.P436T		Atlas-SNP	.											.	EPHB3	114	.	0			c.C1306A						.						40	37	38					3																	184294923		2203	4300	6503	SO:0001583	missense	2049	exon5			AAGAGCCCTCTGC	X75208	CCDS3268.1	3q27.1	2013-09-19	2004-10-28		ENSG00000182580	ENSG00000182580		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3394	protein-coding gene	gene with protein product		601839	"EphB3"	ETK2		8397371	Standard	NM_004443		Approved	Hek2, Tyro6	uc003foz.3	P54753	OTTHUMG00000156710	ENST00000330394.2:c.1306C>A	chr3.hg19:g.184294923C>A	ENSP00000332118:p.Pro436Thr	68.0	0.0		60.0	7.0	NM_004443	Q7Z740	Missense_Mutation	SNP	ENST00000330394.2	hg19	CCDS3268.1	.	.	.	.	.	.	.	.	.	.	C	18.31	3.595241	0.66219	.	.	ENSG00000182580	ENST00000330394	T	0.57273	0.41	5.3	5.3	0.74995	Fibronectin, type III (1);Immunoglobulin-like fold (1);	0.058251	0.64402	D	0.000001	T	0.62841	0.2461	M	0.75884	2.315	0.80722	D	1	P	0.44946	0.846	P	0.47118	0.538	T	0.64504	-0.6392	10	0.42905	T	0.14	.	18.305	0.90177	0.0:1.0:0.0:0.0	.	436	P54753	EPHB3_HUMAN	T	436	ENSP00000332118:P436T	ENSP00000332118:P436T	P	+	1	0	EPHB3	185777617	1.000000	0.71417	1.000000	0.80357	0.449000	0.32228	6.045000	0.71020	2.639000	0.89480	0.448000	0.29417	CCT	.	.		0.637	EPHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345413.1	NM_004443		A	184294923	C	A	184294923	3	1	238	1	0	0	0	0	1	0	0	0	5178	623	22	3	1324	3	EPHB3	3	184294923	Missense_Mutation	SNP	C	TCGA-ED-A4XI-01A-11D-A25V-10	45002444	184294923	13727507	30	33157										
CLDN1	9076	hgsc.bcm.edu	37	chr3	190030766	190030766	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	gccaacggtggccacaaagaTtgctatcactcccaggagga	11	12	1	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr3:190030766T>C	ENST00000295522.3	-	2	551	c.283A>G	c.(283-285)Atc>Gtc	p.I95V		NM_021101.4	NP_066924.1	O95832	CLD1_HUMAN	claudin 1	95					calcium-independent cell-cell adhesion (GO:0016338)|cell adhesion (GO:0007155)|cell-cell junction organization (GO:0045216)|establishment of skin barrier (GO:0061436)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			lung(9)	9	all_cancers(143;2.95e-10)|Ovarian(172;0.0512)		Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05)	GBM - Glioblastoma multiforme(93;0.015)		GCCACAAAGATTGCTATCACT	0.468																																					p.I95V		Atlas-SNP	.											.	CLDN1	23	.	0			c.A283G						.						246	225	232					3																	190030766		2203	4300	6503	SO:0001583	missense	9076	exon2			CAAAGATTGCTAT	AF101051	CCDS3295.1	3q28-q29	2008-07-18			ENSG00000163347	ENSG00000163347		"Claudins"	2032	protein-coding gene	gene with protein product	"senescence-associated epithelial membrane protein 1"	603718				10828592, 9892664	Standard	NM_021101		Approved	SEMP1, ILVASC	uc003fsh.3	O95832	OTTHUMG00000156214	ENST00000295522.3:c.283A>G	chr3.hg19:g.190030766T>C	ENSP00000295522:p.Ile95Val	195.0	0.0		191.0	17.0	NM_021101		Missense_Mutation	SNP	ENST00000295522.3	hg19	CCDS3295.1	.	.	.	.	.	.	.	.	.	.	T	8.296	0.818813	0.16607	.	.	ENSG00000163347	ENST00000295522;ENST00000545382	D	0.87966	-2.32	5.82	5.82	0.92795	.	0.177351	0.64402	D	0.000019	T	0.76751	0.4031	N	0.16790	0.44	0.35587	D	0.806767	B	0.20368	0.044	B	0.28011	0.085	T	0.74090	-0.3777	10	0.14252	T	0.57	.	10.1995	0.43075	0.0:0.0777:0.0:0.9223	.	95	O95832	CLD1_HUMAN	V	95;50	ENSP00000295522:I95V	ENSP00000295522:I95V	I	-	1	0	CLDN1	191513460	0.800000	0.28916	0.993000	0.49108	0.957000	0.61999	1.117000	0.31234	2.225000	0.72522	0.459000	0.35465	ATC	.	.		0.468	CLDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343516.2	NM_021101		C	190030766	T	C	190030766	3	2	238	1	0	0	0	0	1	0	0	0	3473	1493	52	2	364	2	CLDN1	3	190030766	Missense_Mutation	SNP	T	TCGA-ED-A4XI-01A-11D-A25V-10	5735843	190030766	7991664	31	33158										
HTT	3064	hgsc.bcm.edu	37	chr4	3240242	3240242	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	gccccagtttctagacgactTcttcccaccccaggacatca	6	17	3	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr4:3240242T>A	ENST00000355072.5	+	65	9105	c.8960T>A	c.(8959-8961)tTc>tAc	p.F2987Y		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	2987					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		CTAGACGACTTCTTCCCACCC	0.557																																					p.F2987Y		Atlas-SNP	.											.	HTT	221	.	0			c.T8960A						.						69	76	74					4																	3240242		1997	4169	6166	SO:0001583	missense	3064	exon65			ACGACTTCTTCCC	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.8960T>A	chr4.hg19:g.3240242T>A	ENSP00000347184:p.Phe2987Tyr	202.0	0.0		197.0	18.0	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	hg19	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	T	28.8	4.955624	0.92726	.	.	ENSG00000197386	ENST00000355072	T	0.67523	-0.27	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	T	0.68988	0.3061	M	0.78049	2.395	0.58432	D	0.999999	D	0.54964	0.969	B	0.43386	0.418	T	0.75861	-0.3168	10	0.72032	D	0.01	.	13.5472	0.61711	0.0:0.0:0.0:1.0	.	2987	P42858	HD_HUMAN	Y	2987	ENSP00000347184:F2987Y	ENSP00000347184:F2987Y	F	+	2	0	HTT	3210040	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.693000	0.84214	1.784000	0.52394	0.455000	0.32223	TTC	.	.		0.557	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		A	3240242	T	A	3240242	3	1	238	1	0	0	0	0	1	0	0	0	7466	1783	62	4	9218	4	HTT	4	3240242	Missense_Mutation	SNP	T	TCGA-ED-A4XI-01A-11D-A25V-10		3240242	187914034	32	33159										
UBE2K	3093	hgsc.bcm.edu	37	chr4	39780009	39780009	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	atagtggccttgtcttcaaaAtcatgggatgtagagactgc	11	7	3	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr4:39780009A>G	ENST00000261427.5	+	7	842	c.558A>G	c.(556-558)aaA>aaG	p.K186K	UBE2K_ENST00000295963.6_Silent_p.K125K|UBE2K_ENST00000438068.2_3'UTR|UBE2K_ENST00000503368.1_Silent_p.K135K|UBE2K_ENST00000445950.2_Silent_p.K143K	NM_001111112.1|NM_005339.4	NP_001104582.1|NP_005330.1	P61086	UBE2K_HUMAN	ubiquitin-conjugating enzyme E2K	186	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.				intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|protein K48-linked ubiquitination (GO:0070936)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)			large_intestine(1)|lung(1)|ovary(2)	4						TGTCTTCAAAATCATGGGATG	0.403																																					p.K186K	NSCLC(101;689 1592 16105 29682 31745)	Atlas-SNP	.											.	UBE2K	16	.	0			c.A558G						.						152	146	148					4																	39780009		2203	4300	6503	SO:0001819	synonymous_variant	3093	exon7			TTCAAAATCATGG	U58522	CCDS33976.1, CCDS47043.1, CCDS47044.1	4p14	2011-05-19	2011-05-19	2007-12-04	ENSG00000078140	ENSG00000078140		"Ubiquitin-conjugating enzymes E2"	4914	protein-coding gene	gene with protein product		602846	"huntingtin interacting protein 2", "ubiquitin-conjugating enzyme E2K (UBC1 homolog, yeast)"	HIP2		8702625, 17873885	Standard	NM_005339		Approved	HYPG, UBC1	uc003guu.4	P61086	OTTHUMG00000160543	ENST00000261427.5:c.558A>G	chr4.hg19:g.39780009A>G		63.0	0.0		86.0	6.0	NM_005339	A6NJC1|A8K5Y9|B2RDF8|C9JGP1|O54806|P27924|Q16721|Q9CVV9|Q9Y2D3	Silent	SNP	ENST00000261427.5	hg19	CCDS33976.1																																																																																			.	.		0.403	UBE2K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361061.1	NM_005339		G	39780009	A	G	39780009	2	3	238	1	0	0	0	0	0	0	0	1	16877	98	4	2		2	UBE2K	4	39780009	Silent	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	36539767	39780009	151374267	33	33160										
BMP2K	55589	hgsc.bcm.edu	37	chr4	79808426	79808426	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	cttttggttctgttcctttcAtttctcattcaggcaagtta	6	9	4	0			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr4:79808426A>G	ENST00000335016.5	+	15	2216	c.2050A>G	c.(2050-2052)Att>Gtt	p.I684V	PAQR3_ENST00000295462.3_3'UTR	NM_198892.1	NP_942595.1	Q9NSY1	BMP2K_HUMAN	BMP2 inducible kinase	684					regulation of bone mineralization (GO:0030500)	nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatase regulator activity (GO:0019208)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	13						TGTTCCTTTCATTTCTCATTC	0.393																																					p.I684V		Atlas-SNP	.											.	BMP2K	169	.	0			c.A2050G						.						107	100	103					4																	79808426		1928	4137	6065	SO:0001583	missense	55589	exon15			CCTTTCATTTCTC	AB015331	CCDS34019.1, CCDS47083.1	4q21.21	2008-05-15			ENSG00000138756	ENSG00000138756			18041	protein-coding gene	gene with protein product							Standard	NM_017593		Approved	DKFZp434K0614, BIKe	uc003hlk.3	Q9NSY1	OTTHUMG00000160900	ENST00000335016.5:c.2050A>G	chr4.hg19:g.79808426A>G	ENSP00000334836:p.Ile684Val	97.0	0.0		101.0	12.0	NM_198892	O94791|Q4W5H2|Q8IYF2|Q8N2G7|Q8NHG9|Q9NTG8	Missense_Mutation	SNP	ENST00000335016.5	hg19	CCDS47083.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.65|15.65	2.897736|2.897736	0.52227|0.52227	.|.	.|.	ENSG00000138756|ENSG00000138756	ENST00000502613|ENST00000335016	.|T	.|0.21031	.|2.03	5.79|5.79	5.79|5.79	0.91817|0.91817	.|.	.|1.203230	.|0.05992	.|N	.|0.646188	T|T	0.26810|0.26810	0.0656|0.0656	L|L	0.57536|0.57536	1.79|1.79	0.80722|0.80722	D|D	1|1	.|B	.|0.20459	.|0.045	.|B	.|0.15052	.|0.012	T|T	0.06041|0.06041	-1.0849|-1.0849	5|10	.|0.30078	.|T	.|0.28	-16.3946|-16.3946	12.051|12.051	0.53507|0.53507	0.8563:0.1437:0.0:0.0|0.8563:0.1437:0.0:0.0	.|.	.|684	.|Q9NSY1	.|BMP2K_HUMAN	R|V	376|684	.|ENSP00000334836:I684V	.|ENSP00000334836:I684V	H|I	+|+	2|1	0|0	BMP2K|BMP2K	80027450|80027450	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	1.610000|1.610000	0.36869|0.36869	2.223000|2.223000	0.72356|0.72356	0.455000|0.455000	0.32223|0.32223	CAT|ATT	.	.		0.393	BMP2K-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_017593		G	79808426	A	G	79808426	3	3	238	1	0	0	0	0	1	0	0	0	1460	217	8	2	2146	2	BMP2K	4	79808426	Missense_Mutation	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	40028417	79808426	111345850	34	33161										
SYNPO2	171024	hgsc.bcm.edu	37	chr4	119947795	119947795	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	tgtgcagaccatccagtggaAtaagtgaggctttgatatct	11	7	1	3			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr4:119947795A>G	ENST00000429713.2	+	3	453	c.271A>G	c.(271-273)Ata>Gta	p.I91V	SYNPO2_ENST00000448416.2_Intron|SYNPO2_ENST00000307142.4_Missense_Mutation_p.I91V|SYNPO2_ENST00000434046.2_Missense_Mutation_p.I91V	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	91						actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|Z disc (GO:0030018)	14-3-3 protein binding (GO:0071889)|muscle alpha-actinin binding (GO:0051371)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						ATCCAGTGGAATAAGTGAGGC	0.423																																					p.I91V		Atlas-SNP	.											.	SYNPO2	353	.	0			c.A271G						.						96	99	98					4																	119947795		2203	4300	6503	SO:0001583	missense	171024	exon3			AGTGGAATAAGTG	AJ010482	CCDS34054.1, CCDS47128.1, CCDS47129.1, CCDS75185.1, CCDS75186.1	4q26	2008-08-29			ENSG00000172403	ENSG00000172403			17732	protein-coding gene	gene with protein product						11673475, 17828378	Standard	NM_133477		Approved	MYOPODIN	uc010inb.3	Q9UMS6	OTTHUMG00000161165	ENST00000429713.2:c.271A>G	chr4.hg19:g.119947795A>G	ENSP00000395143:p.Ile91Val	95.0	0.0		87.0	9.0	NM_001128934	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Missense_Mutation	SNP	ENST00000429713.2	hg19	CCDS47129.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	4.284|4.284	0.051816|0.051816	0.08291|0.08291	.|.	.|.	ENSG00000172403|ENSG00000172403	ENST00000307142;ENST00000429713;ENST00000434046|ENST00000504178	T;T;T|.	0.07444|.	3.19;3.2;3.19|.	5.63|5.63	3.23|3.23	0.37069|0.37069	PDZ/DHR/GLGF (1);|.	0.562038|.	0.18017|.	N|.	0.154370|.	T|T	0.36908|0.36908	0.0984|0.0984	N|N	0.17474|0.17474	0.49|0.49	0.38950|0.38950	D|D	0.958333|0.958333	B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0|.	B;B;B;B|.	0.04013|.	0.0;0.001;0.001;0.001|.	T|T	0.14615|0.14615	-1.0466|-1.0466	10|5	0.11182|.	T|.	0.66|.	-2.8154|-2.8154	7.3145|7.3145	0.26493|0.26493	0.7515:0.0:0.2485:0.0|0.7515:0.0:0.2485:0.0	.|.	91;91;91;91|.	B9EG60;Q9UMS6-2;E9PEM2;Q9UMS6|.	.;.;.;SYNP2_HUMAN|.	V|S	91|42	ENSP00000306015:I91V;ENSP00000395143:I91V;ENSP00000390965:I91V|.	ENSP00000306015:I91V|.	I|N	+|+	1|2	0|0	SYNPO2|SYNPO2	120167243|120167243	0.998000|0.998000	0.40836|0.40836	0.876000|0.876000	0.34364|0.34364	0.640000|0.640000	0.38277|0.38277	1.416000|1.416000	0.34759|0.34759	0.950000|0.950000	0.37743|0.37743	0.528000|0.528000	0.53228|0.53228	ATA|AAT	.	.		0.423	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1			G	119947795	A	G	119947795	3	3	238	1	0	0	0	0	1	0	0	0	15472	101	4	2	281	2	SYNPO2	4	119947795	Missense_Mutation	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	40139369	119947795	71206481	35	33162										
NUDT6	11162	hgsc.bcm.edu	37	chr4	123814211	123814211	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	cactcacatcttaagcattcTtcctggcaaaaatttatggt	5	10	3	0			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr4:123814211T>C	ENST00000304430.5	-	5	756	c.723A>G	c.(721-723)gaA>gaG	p.E241E	NUDT6_ENST00000339154.2_Silent_p.E72E|FGF2_ENST00000608478.1_3'UTR|FGF2_ENST00000264498.3_3'UTR|NUDT6_ENST00000502270.1_Silent_p.E72E|NUDT6_ENST00000608639.1_5'Flank	NM_007083.4	NP_009014.2	P53370	NUDT6_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 6	241	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.			E -> Q (in Ref. 4; AAA67062). {ECO:0000305}.		mitochondrion (GO:0005739)|nucleus (GO:0005634)	growth factor activity (GO:0008083)|hydrolase activity (GO:0016787)			endometrium(2)|lung(1)|prostate(1)|skin(1)|stomach(1)	6						TTAAGCATTCTTCCTGGCAAA	0.448																																					p.E241E		Atlas-SNP	.											.	NUDT6	50	.	0			c.A723G						.						126	121	123					4																	123814211		2203	4300	6503	SO:0001819	synonymous_variant	11162	exon5			GCATTCTTCCTGG	AF019632	CCDS3729.1, CCDS43268.1	4q26	2011-02-21			ENSG00000170917	ENSG00000170917		"Nudix motif containing"	8053	protein-coding gene	gene with protein product		606261				7984147, 10022609	Standard	NM_198041		Approved	gfg-1, gfg, FGF2AS, FGF-AS	uc003iew.3	P53370	OTTHUMG00000039507	ENST00000304430.5:c.723A>G	chr4.hg19:g.123814211T>C		140.0	0.0		124.0	6.0	NM_007083	A8K756|O95097|Q9UQD9	Silent	SNP	ENST00000304430.5	hg19	CCDS43268.1																																																																																			.	.		0.448	NUDT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095331.3	NM_007083		C	123814211	T	C	123814211	2	2	238	1	0	0	0	0	0	0	0	1	10752	1606	56	2		2	NUDT6	4	123814211	Silent	SNP	T	TCGA-ED-A4XI-01A-11D-A25V-10	3866416	123814211	67340065	36	33163										
SPATA4	132851	hgsc.bcm.edu	37	chr4	177113883	177113883	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	gggattgcttagtaattctgAtaacctaatgttatctttaa	7	5	2	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr4:177113883A>C	ENST00000280191.2	-	4	691	c.583T>G	c.(583-585)Tca>Gca	p.S195A	SPATA4_ENST00000515234.1_Missense_Mutation_p.S22A	NM_144644.2	NP_653245.2	Q8NEY3	SPAT4_HUMAN	spermatogenesis associated 4	195						cytoplasm (GO:0005737)				NS(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)	22		Breast(14;0.0011)|Prostate(90;0.0129)|Melanoma(52;0.0133)|Renal(120;0.0376)|all_hematologic(60;0.124)		all cancers(43;2.9e-20)|Epithelial(43;1.99e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.58e-09)|GBM - Glioblastoma multiforme(59;0.000162)|STAD - Stomach adenocarcinoma(60;0.000543)|LUSC - Lung squamous cell carcinoma(193;0.096)		AGTAATTCTGATAACCTAATG	0.378																																					p.S195A		Atlas-SNP	.											.	SPATA4	44	.	0			c.T583G						.						81	82	82					4																	177113883		2203	4300	6503	SO:0001583	missense	132851	exon4			ATTCTGATAACCT	AY040204	CCDS3826.1	4q34.2	2008-02-05			ENSG00000150628	ENSG00000150628			17333	protein-coding gene	gene with protein product		609879					Standard	NM_144644		Approved	TSARG2, SPEF1B	uc003iuo.1	Q8NEY3	OTTHUMG00000160788	ENST00000280191.2:c.583T>G	chr4.hg19:g.177113883A>C	ENSP00000280191:p.Ser195Ala	100.0	0.0		83.0	9.0	NM_144644	Q8NCS5|Q8WW15	Missense_Mutation	SNP	ENST00000280191.2	hg19	CCDS3826.1	.	.	.	.	.	.	.	.	.	.	A	15.03	2.712351	0.48517	.	.	ENSG00000150628	ENST00000280191;ENST00000515234	T	0.23147	1.92	5.27	-4.24	0.03777	.	0.214168	0.37304	N	0.002141	T	0.21881	0.0527	L	0.42245	1.32	0.09310	N	0.999999	P	0.39883	0.693	B	0.43838	0.433	T	0.29088	-1.0023	10	0.42905	T	0.14	-17.5849	12.1759	0.54186	0.2333:0.0:0.0:0.7667	.	195	Q8NEY3	SPAT4_HUMAN	A	195;22	ENSP00000280191:S195A	ENSP00000280191:S195A	S	-	1	0	SPATA4	177350877	0.674000	0.27549	0.187000	0.23214	0.965000	0.64279	1.029000	0.30140	-0.248000	0.09583	-0.327000	0.08410	TCA	.	.		0.378	SPATA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362326.1	NM_144644		C	177113883	A	C	177113883	3	2	238	1	0	0	0	0	1	0	0	0	15025	333	12	5	346	5	SPATA4	4	177113883	Missense_Mutation	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	53299672	177113883	14040393	37	33164										
FAM149A	25854	hgsc.bcm.edu	37	chr4	187073131	187073131	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	gaaatgttatttgaagggaaAgtgaaccctcagacccagag	11	7	1	4			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr4:187073131A>G	ENST00000356371.5	+	4	891	c.891A>G	c.(889-891)aaA>aaG	p.K297K	FAM149A_ENST00000502970.1_Silent_p.K6K|FAM149A_ENST00000503432.1_Silent_p.K6K|FAM149A_ENST00000389354.5_Silent_p.K6K|FAM149A_ENST00000227065.4_Silent_p.K6K|FAM149A_ENST00000514153.1_Silent_p.K6K|FAM149A_ENST00000514829.1_3'UTR			A5PLN7	F149A_HUMAN	family with sequence similarity 149, member A	297										breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(2)	25		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.19e-10)|BRCA - Breast invasive adenocarcinoma(30;1.22e-05)|GBM - Glioblastoma multiforme(59;0.000122)|STAD - Stomach adenocarcinoma(60;0.000288)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.166)		TTGAAGGGAAAGTGAACCCTC	0.512																																					p.K6K		Atlas-SNP	.											.	FAM149A	52	.	0			c.A18G						.						134	117	123					4																	187073131		2203	4300	6503	SO:0001819	synonymous_variant	25854	exon3			AGGGAAAGTGAAC	AK057166	CCDS34117.1	4q35.1	2012-04-19			ENSG00000109794	ENSG00000109794			24527	protein-coding gene	gene with protein product							Standard	NM_015398		Approved	DKFZP564J102, MST119, MSTP119	uc010isl.3	A5PLN7	OTTHUMG00000160565	ENST00000356371.5:c.891A>G	chr4.hg19:g.187073131A>G		261.0	0.0		252.0	11.0	NM_001006655	B5MDB8|Q2TAN6|Q7Z2S5|Q9Y4T9	Silent	SNP	ENST00000356371.5	hg19																																																																																				.	.		0.512	FAM149A-201	KNOWN	basic	protein_coding	protein_coding		NM_001006655		G	187073131	A	G	187073131	2	3	238	1	0	0	0	0	0	0	0	1	5460	69	3	2		2	FAM149A	4	187073131	Silent	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	9959248	187073131	4081145	38	33165										
MARCH11	441061	hgsc.bcm.edu	37	chr5	16067841	16067841	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	tttaacacatcccagtgcaaAttcacagctcgccagcgctt	6	14	1	0			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr5:16067841A>C	ENST00000332432.8	-	4	1147	c.948T>G	c.(946-948)aaT>aaG	p.N316K		NM_001102562.1	NP_001096032.1	A6NNE9	MARHB_HUMAN	membrane-associated ring finger (C3HC4) 11	316					protein ubiquitination (GO:0016567)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(14)|urinary_tract(1)	20						CCCAGTGCAAATTCACAGCTC	0.428																																					p.N316K		Atlas-SNP	.											.	MARCH11	50	.	0			c.T948G						.						61	60	60					5																	16067841		1902	4137	6039	SO:0001583	missense	441061	exon4			GTGCAAATTCACA	BC150513	CCDS47192.1	5p15.1	2013-01-09			ENSG00000183654	ENSG00000183654		"RING-type (C3HC4) zinc fingers", "MARCH membrane-associated ring fingers"	33609	protein-coding gene	gene with protein product		613338				17604280	Standard	NM_001102562		Approved	MARCH-XI	uc003jfo.2	A6NNE9	OTTHUMG00000161789	ENST00000332432.8:c.948T>G	chr5.hg19:g.16067841A>C	ENSP00000333181:p.Asn316Lys	69.0	0.0		75.0	8.0	NM_001102562	A7E2S6	Missense_Mutation	SNP	ENST00000332432.8	hg19	CCDS47192.1	.	.	.	.	.	.	.	.	.	.	A	18.04	3.535515	0.64972	.	.	ENSG00000183654	ENST00000332432	T	0.35789	1.29	5.54	-2.2	0.06994	.	0.000000	0.85682	D	0.000000	T	0.51839	0.1698	M	0.64170	1.965	0.54753	D	0.99998	D	0.89917	1.0	D	0.91635	0.999	T	0.54556	-0.8276	10	0.87932	D	0	-21.0751	13.2983	0.60311	0.5631:0.0:0.4369:0.0	.	316	A6NNE9	MARHB_HUMAN	K	316	ENSP00000333181:N316K	ENSP00000333181:N316K	N	-	3	2	MARCH11	16120841	0.961000	0.32948	0.941000	0.38009	0.979000	0.70002	0.064000	0.14437	-0.359000	0.08150	-0.290000	0.09829	AAT	.	.		0.428	MARCH11-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000366096.2	NM_001102562		C	16067841	A	C	16067841	3	2	238	1	0	0	0	0	1	0	0	0	9309	98	4	5	264	5	MARCH11	5	16067841	Missense_Mutation	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10		16067841	164847419	39	33166										
ERAP2	64167	hgsc.bcm.edu	37	chr5	96215831	96215831	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	gttaccctgctcatgaacaaAttgcactgctggttccagag	9	11	1	2			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr5:96215831A>G	ENST00000437043.3	+	2	1153	c.442A>G	c.(442-444)Att>Gtt	p.I148V	ERAP2_ENST00000379904.4_Missense_Mutation_p.I148V|ERAP2_ENST00000510309.1_Missense_Mutation_p.I148V|CTD-2260A17.2_ENST00000501338.1_Intron	NM_001130140.1|NM_022350.3	NP_001123612.1|NP_071745.1	Q6P179	ERAP2_HUMAN	endoplasmic reticulum aminopeptidase 2	148					antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|regulation of blood pressure (GO:0008217)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24		all_cancers(142;0.000311)|all_epithelial(76;1.54e-06)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0596)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0703)		TCATGAACAAATTGCACTGCT	0.418																																					p.I148V		Atlas-SNP	.											.	ERAP2	77	.	0			c.A442G						.						88	80	83					5																	96215831		2203	4300	6503	SO:0001583	missense	64167	exon2			GAACAAATTGCAC	AF191545	CCDS4086.1	5q15	2007-11-21			ENSG00000164308	ENSG00000164308			29499	protein-coding gene	gene with protein product	"leukocyte-derived arginine aminopeptidase"	609497				12799365, 15908954	Standard	NM_022350		Approved	L-RAP, LRAP	uc003kmt.3	Q6P179	OTTHUMG00000128718	ENST00000437043.3:c.442A>G	chr5.hg19:g.96215831A>G	ENSP00000400376:p.Ile148Val	205.0	0.0		209.0	24.0	NM_001130140	Q7Z5K1|Q8TD32|Q8WVJ4|Q9HBX2	Missense_Mutation	SNP	ENST00000437043.3	hg19	CCDS4086.1	.	.	.	.	.	.	.	.	.	.	A	14.21	2.468388	0.43839	.	.	ENSG00000164308	ENST00000437043;ENST00000510373;ENST00000513084;ENST00000379904;ENST00000510309	T;T;T;T;T	0.04119	3.7;3.7;3.7;3.7;3.7	4.55	3.38	0.38709	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.147069	0.44285	D	0.000461	T	0.03178	0.0093	N	0.16790	0.44	0.36856	D	0.888169	B;B	0.23937	0.094;0.015	B;B	0.28139	0.051;0.086	T	0.45775	-0.9238	10	0.13470	T	0.59	.	8.8314	0.35087	0.9069:0.0:0.0931:0.0	.	148;148	Q6P179-3;Q6P179	.;ERAP2_HUMAN	V	148	ENSP00000400376:I148V;ENSP00000421175:I148V;ENSP00000421849:I148V;ENSP00000369235:I148V;ENSP00000425758:I148V	ENSP00000369235:I148V	I	+	1	0	ERAP2	96241587	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	2.226000	0.42963	1.825000	0.53177	0.383000	0.25322	ATT	.	.		0.418	ERAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250623.2	NM_022350		G	96215831	A	G	96215831	3	3	238	1	0	0	0	0	1	0	0	0	5206	101	4	2	444	2	ERAP2	5	96215831	Missense_Mutation	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	80147990	96215831	84699429	40	33167										
HSPA9	3313	hgsc.bcm.edu	37	chr5	137893621	137893621	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	tactatcccattggcatcaaTgtcaaatgtaacttcaatct	4	10	4	0			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr5:137893621T>C	ENST00000297185.3	-	13	1695	c.1570A>G	c.(1570-1572)Att>Gtt	p.I524V	SNORD63_ENST00000411005.1_RNA|HSPA9_ENST00000501917.2_Intron	NM_004134.6	NP_004125.3	P38646	GRP75_HUMAN	heat shock 70kDa protein 9 (mortalin)	524					cellular protein metabolic process (GO:0044267)|negative regulation of apoptotic process (GO:0043066)|protein export from nucleus (GO:0006611)|protein folding (GO:0006457)|protein targeting to mitochondrion (GO:0006626)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(1)|kidney(4)|large_intestine(8)|lung(12)|upper_aerodigestive_tract(1)	28			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			TTGGCATCAATGTCAAATGTA	0.433																																					p.I524V		Atlas-SNP	.											.	HSPA9	49	.	0			c.A1570G						.						96	89	91					5																	137893621		2203	4300	6503	SO:0001583	missense	3313	exon13			CATCAATGTCAAA	L11066	CCDS4208.1	5q31.1	2011-09-02	2006-10-31	2006-10-31	ENSG00000113013	ENSG00000113013		"Heat shock proteins / HSP70"	5244	protein-coding gene	gene with protein product		600548	"heat shock 70kDa protein 9B (mortalin-2)"	HSPA9B		7684501	Standard	NM_004134		Approved	GRP75, PBP74, mot-2, mthsp75	uc003ldf.3	P38646	OTTHUMG00000129206	ENST00000297185.3:c.1570A>G	chr5.hg19:g.137893621T>C	ENSP00000297185:p.Ile524Val	224.0	0.0		211.0	34.0	NM_004134	B2RCM1|P30036|P31932|Q1HB43|Q53H23|Q6GU03|Q9BWB7|Q9UC56	Missense_Mutation	SNP	ENST00000297185.3	hg19	CCDS4208.1	.	.	.	.	.	.	.	.	.	.	T	25.1	4.607813	0.87258	.	.	ENSG00000113013	ENST00000297185;ENST00000541333;ENST00000540484	T	0.01051	5.4	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	T	0.06826	0.0174	M	0.73598	2.24	0.80722	D	1	D	0.56746	0.977	D	0.87578	0.998	T	0.03587	-1.1022	10	0.66056	D	0.02	-17.9805	14.9425	0.71006	0.0:0.0:0.0:1.0	.	524	P38646	GRP75_HUMAN	V	524;477;510	ENSP00000297185:I524V	ENSP00000297185:I524V	I	-	1	0	HSPA9	137921520	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.986000	0.88173	2.086000	0.62901	0.533000	0.62120	ATT	.	.		0.433	HSPA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251285.1	NM_004134		C	137893621	T	C	137893621	3	2	238	1	0	0	0	0	1	0	0	0	7426	1464	51	2	489	2	HSPA9	5	137893621	Missense_Mutation	SNP	T	TCGA-ED-A4XI-01A-11D-A25V-10	41677790	137893621	43021639	41	33168										
PCDHA5	56143	hgsc.bcm.edu	37	chr5	140203713	140203713	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	gtcccacctctacagacaacGtgagttttctaatattaaca	5	11	2	2			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr5:140203713G>A	ENST00000529859.1	+	1	2352		c.e1+1		PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000378126.3_Missense_Mutation_p.V785M|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529619.1_Splice_Site|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5						cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(3)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TACAGACAACGTGAGTTTTCT	0.423																																					p.V785M		Atlas-SNP	.											.	PCDHA5	361	.	0			c.G2353A						.						69	67	68					5																	140203713		2203	4300	6503	SO:0001630	splice_region_variant	56143	exon1			GACAACGTGAGTT	AF152483	CCDS54917.1	5q31	2010-11-26				ENSG00000204965		"Cadherins / Protocadherins : Clustered"	8671	other	complex locus constituent	"ortholog of mouse CNR6", "KIAA0345-like 9"	606311		CNRS6		10380929, 10662547	Standard	NM_018908		Approved	CNR6, CRNR6, CNRN6, PCDH-ALPHA5		Q9Y5H7		ENST00000529859.1:c.2352+1G>A	chr5.hg19:g.140203713G>A		161.0	0.0		132.0	11.0	NM_031501	O75284|Q8N4R3	Missense_Mutation	SNP	ENST00000529859.1	hg19	CCDS54917.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.467|8.467	0.856611|0.856611	0.17106|0.17106	.|.	.|.	ENSG00000204965|ENSG00000204965	ENST00000529619;ENST00000529859|ENST00000378126	.|T	.|0.50001	.|0.76	3.61|3.61	2.72|2.72	0.32119|0.32119	.|.	.|.	.|.	.|.	.|.	.|T	.|0.26666	.|0.0652	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|P	.|0.36183	.|0.542	.|B	.|0.26770	.|0.073	.|T	.|0.05007	.|-1.0912	.|7	.|.	.|.	.|.	.|.	7.6406|7.6406	0.28292|0.28292	0.2731:0.0:0.7269:0.0|0.2731:0.0:0.7269:0.0	.|.	.|785	.|Q9Y5H7-2	.|.	.|M	-1|785	.|ENSP00000367366:V785M	.|.	.|V	+|+	.|1	.|0	PCDHA5|PCDHA5	140183897|140183897	.|.	.|.	0.671000|0.671000	0.29857|0.29857	0.036000|0.036000	0.12997|0.12997	.|.	.|.	1.961000|1.961000	0.56991|0.56991	0.491000|0.491000	0.48974|0.48974	.|GTG	.	.		0.423	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908	Intron	A	140203713	G	A	140203713	5	1	238	1	0	0	0	0	0	0	1	0	11536	1159	40	1	2355	1	PCDHA5	5	140203713	Splice_Site	SNP	G	TCGA-ED-A4XI-01A-11D-A25V-10	2310092	140203713	40711547	42	33169										
PCDHB5	26167	hgsc.bcm.edu	37	chr5	140516630	140516630	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	gccacagaccgcggctccccGgcgctgagcagcgaggcgct	15	17	0	2			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr5:140516630G>A	ENST00000231134.5	+	1	1831	c.1614G>A	c.(1612-1614)ccG>ccA	p.P538P		NM_015669.2	NP_056484.1	Q9Y5E4	PCDB5_HUMAN	protocadherin beta 5	538	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|kidney(1)|large_intestine(18)|lung(25)|ovary(3)|prostate(6)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	81			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GCGGCTCCCCGGCGCTGAGCA	0.682																																					p.P538P		Atlas-SNP	.											.	PCDHB5	184	.	0			c.G1614A						.						40	45	43					5																	140516630		2202	4299	6501	SO:0001819	synonymous_variant	26167	exon1			CTCCCCGGCGCTG	AF152498	CCDS4247.1	5q31	2010-01-26			ENSG00000113209	ENSG00000113209		"Cadherins / Protocadherins : Clustered"	8690	other	protocadherin		606331				10380929	Standard	NM_015669		Approved	DKFZp586B0217, PCDH-BETA5	uc003liq.3	Q9Y5E4	OTTHUMG00000129616	ENST00000231134.5:c.1614G>A	chr5.hg19:g.140516630G>A		15.0	0.0		17.0	6.0	NM_015669	Q549F4|Q9UFU9	Silent	SNP	ENST00000231134.5	hg19	CCDS4247.1																																																																																			.	.		0.682	PCDHB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251811.1	NM_015669		A	140516630	G	A	140516630	2	1	238	1	0	0	0	0	0	0	0	1	11554	1103	39	1		1	PCDHB5	5	140516630	Silent	SNP	G	TCGA-ED-A4XI-01A-11D-A25V-10	312917	140516630	40398630	43	33170										
KIAA0141	9812	hgsc.bcm.edu	37	chr5	141314143	141314143	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	aatatctttggcttgcagccAacaatggggtatgcgatctc	10	9	2	0			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr5:141314143A>T	ENST00000432126.2	+	10	1275	c.1141A>T	c.(1141-1143)Aac>Tac	p.N381Y	KIAA0141_ENST00000194118.4_Missense_Mutation_p.N381Y	NM_001142603.1|NM_014773.3	NP_001136075.1|NP_055588.3	Q14154	DELE_HUMAN	KIAA0141	381					extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)	mitochondrion (GO:0005739)				endometrium(3)|large_intestine(4)|lung(5)|skin(1)|urinary_tract(3)	16		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCTTGCAGCCAACAATGGGGT	0.507																																					p.N381Y		Atlas-SNP	.											.	KIAA0141	44	.	0			c.A1141T						.						116	110	112					5																	141314143		2203	4300	6503	SO:0001583	missense	9812	exon10			GCAGCCAACAATG	BC011269	CCDS4268.1	5q31	2011-05-05			ENSG00000081791	ENSG00000081791			28969	protein-coding gene	gene with protein product	"death ligand signal enhancer"	615741				20563667	Standard	XM_005268549		Approved	DELE	uc003llt.3	Q14154	OTTHUMG00000129662	ENST00000432126.2:c.1141A>T	chr5.hg19:g.141314143A>T	ENSP00000396225:p.Asn381Tyr	164.0	0.0		145.0	11.0	NM_001142603	Q969R4|Q96EU9	Missense_Mutation	SNP	ENST00000432126.2	hg19	CCDS4268.1	.	.	.	.	.	.	.	.	.	.	A	19.29	3.798993	0.70567	.	.	ENSG00000081791	ENST00000432126;ENST00000194118	T;T	0.52295	0.67;0.67	5.54	1.8	0.24995	Tetratricopeptide-like helical (1);	0.764793	0.12673	N	0.448617	T	0.52419	0.1733	L	0.55103	1.725	0.25299	N	0.98929	D	0.55385	0.971	P	0.55161	0.77	T	0.40001	-0.9586	10	0.66056	D	0.02	-3.3035	6.8394	0.23955	0.7294:0.0:0.2706:0.0	.	381	Q14154	DELE_HUMAN	Y	381	ENSP00000396225:N381Y;ENSP00000194118:N381Y	ENSP00000194118:N381Y	N	+	1	0	KIAA0141	141294327	0.993000	0.37304	0.987000	0.45799	0.961000	0.63080	2.270000	0.43355	0.358000	0.24211	0.528000	0.53228	AAC	.	.		0.507	KIAA0141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251863.2	NM_014773		T	141314143	A	T	141314143	3	4	238	1	0	0	0	0	1	0	0	0	8165	130	5	4	1179	4	KIAA0141	5	141314143	Missense_Mutation	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	797513	141314143	39601117	44	33171										
GEMIN5	25929	hgsc.bcm.edu	37	chr5	154311099	154311099	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	gcaaccttttgttactggagCttgtgctacagcattcccgt	9	11	0	0			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr5:154311099C>T	ENST00000285873.7	-	5	775	c.700G>A	c.(700-702)Gct>Act	p.A234T		NM_001252156.1|NM_015465.4	NP_001239085.1|NP_056280.2	Q8TEQ6	GEMI5_HUMAN	gem (nuclear organelle) associated protein 5	234					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|protein complex assembly (GO:0006461)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)	poly(A) RNA binding (GO:0044822)|snRNA binding (GO:0017069)			breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			GTTACTGGAGCTTGTGCTACA	0.373																																					p.A234T		Atlas-SNP	.											.	GEMIN5	120	.	0			c.G700A						.						154	135	141					5																	154311099		2203	4300	6503	SO:0001583	missense	25929	exon5			CTGGAGCTTGTGC	AK022748	CCDS4330.1	5q34	2013-01-10			ENSG00000082516	ENSG00000082516		"WD repeat domain containing"	20043	protein-coding gene	gene with protein product		607005				11714716	Standard	NM_015465		Approved		uc003lvx.3	Q8TEQ6	OTTHUMG00000130189	ENST00000285873.7:c.700G>A	chr5.hg19:g.154311099C>T	ENSP00000285873:p.Ala234Thr	119.0	0.0		140.0	27.0	NM_015465	Q14CV0|Q8WWV4|Q969W4|Q9H9K3|Q9UFI5	Missense_Mutation	SNP	ENST00000285873.7	hg19	CCDS4330.1	.	.	.	.	.	.	.	.	.	.	C	0.035	-1.310998	0.01342	.	.	ENSG00000082516	ENST00000285873	T	0.70282	-0.47	5.43	1.47	0.22746	WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.325766	0.32608	N	0.005870	T	0.37210	0.0995	N	0.11154	0.105	0.23366	N	0.997821	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.21449	-1.0245	10	0.02654	T	1	-5.5997	1.2209	0.01924	0.1481:0.1644:0.154:0.5336	.	233;234	B7ZLC9;Q8TEQ6	.;GEMI5_HUMAN	T	234	ENSP00000285873:A234T	ENSP00000285873:A234T	A	-	1	0	GEMIN5	154291292	0.035000	0.19736	0.998000	0.56505	0.111000	0.19643	0.021000	0.13489	0.352000	0.24053	-0.302000	0.09304	GCT	.	.		0.373	GEMIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252507.1			T	154311099	C	T	154311099	3	4	238	1	0	0	0	0	1	0	0	0	6339	797	28	3	3922	3	GEMIN5	5	154311099	Missense_Mutation	SNP	C	TCGA-ED-A4XI-01A-11D-A25V-10	12996956	154311099	26604161	45	33172										
RIPK1	8737	hgsc.bcm.edu	37	chr6	3106115	3106115	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	gtatcagaacaatggattatAtagctcacatggctttggaa	9	6	2	1	rs377213073		TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr6:3106115A>G	ENST00000259808.4	+	9	1704	c.1406A>G	c.(1405-1407)tAt>tGt	p.Y469C	RIPK1_ENST00000380409.2_Missense_Mutation_p.Y469C|RIPK1_ENST00000479389.1_3'UTR|RIPK1_ENST00000541791.1_Missense_Mutation_p.Y423C			Q13546	RIPK1_HUMAN	receptor (TNFRSF)-interacting serine-threonine kinase 1	469	Interaction with SQSTM1.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|amyloid fibril formation (GO:1990000)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular protein catabolic process (GO:0044257)|cellular response to growth factor stimulus (GO:0071363)|cellular response to tumor necrosis factor (GO:0071356)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|necroptotic signaling pathway (GO:0097527)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|peptidyl-serine autophosphorylation (GO:0036289)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of ATP:ADP antiporter activity (GO:0070926)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to tumor necrosis factor (GO:0034612)|ripoptosome assembly (GO:0097343)|ripoptosome assembly involved in necroptotic process (GO:1901026)|T cell apoptotic process (GO:0070231)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|death domain binding (GO:0070513)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	23	Ovarian(93;0.0386)	all_hematologic(90;0.0895)				AATGGATTATATAGCTCACAT	0.493																																					p.Y469C		Atlas-SNP	.											.	RIPK1	56	.	0			c.A1406G						.	A	CYS/TYR	1,4405	2.1+/-5.4	0,1,2202	71	60	64		1406	-1	0	6		64	0,8600		0,0,4300	no	missense	RIPK1	NM_003804.3	194	0,1,6502	GG,GA,AA		0.0,0.0227,0.0077	probably-damaging	469/672	3106115	1,13005	2203	4300	6503	SO:0001583	missense	8737	exon8			GATTATATAGCTC	U25994	CCDS4482.1	6p25.2	2008-02-05			ENSG00000137275	ENSG00000137275			10019	protein-coding gene	gene with protein product		603453				7538908, 8612133	Standard	XM_005249458		Approved	RIP	uc003mux.3	Q13546	OTTHUMG00000014134	ENST00000259808.4:c.1406A>G	chr6.hg19:g.3106115A>G	ENSP00000259808:p.Tyr469Cys	212.0	0.0		230.0	10.0	NM_003804	A0AV89|B2RAG1|B4E3F9|Q13180|Q59H33	Missense_Mutation	SNP	ENST00000259808.4	hg19	CCDS4482.1	.	.	.	.	.	.	.	.	.	.	A	12.88	2.069635	0.36470	2.27E-4	0.0	ENSG00000137275	ENST00000259808;ENST00000541791;ENST00000380409;ENST00000453483	T;T;T	0.76968	-1.06;-0.52;-1.06	4.95	-1.05	0.10036	.	1.155410	0.06093	N	0.663997	T	0.64768	0.2628	L	0.55481	1.735	0.09310	N	1	D;D	0.61697	0.99;0.985	P;P	0.56474	0.799;0.527	T	0.52616	-0.8552	10	0.38643	T	0.18	-1.8055	1.2455	0.01972	0.3372:0.2916:0.0873:0.2839	.	423;469	Q13546-2;Q13546	.;RIPK1_HUMAN	C	469;423;469;71	ENSP00000259808:Y469C;ENSP00000442294:Y423C;ENSP00000369773:Y469C	ENSP00000259808:Y469C	Y	+	2	0	RIPK1	3051114	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-0.037000	0.12164	-0.007000	0.14345	0.533000	0.62120	TAT	.	.		0.493	RIPK1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039659.2	NM_003804		G	3106115	A	G	3106115	3	3	238	1	0	0	0	0	1	0	0	0	13395	449	16	2	1436	2	RIPK1	6	3106115	Missense_Mutation	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10		3106115	168008952	46	33173										
FARS2	10667	hgsc.bcm.edu	37	chr6	5369076	5369076	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	cctctgtggctgatcaaggaGagggtgaaggagcacttcta	14	8	3	3			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr6:5369076G>A	ENST00000324331.6	+	2	609	c.273G>A	c.(271-273)gaG>gaA	p.E91E	FARS2_ENST00000274680.4_Silent_p.E91E			O95363	SYFM_HUMAN	phenylalanyl-tRNA synthetase 2, mitochondrial	91					gene expression (GO:0010467)|phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA aminoacylation for protein translation (GO:0006418)|tRNA processing (GO:0008033)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|phenylalanine-tRNA ligase activity (GO:0004826)|tRNA binding (GO:0000049)			endometrium(3)|kidney(1)|large_intestine(5)|lung(3)|prostate(1)|stomach(2)	15	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)	TGATCAAGGAGAGGGTGAAGG	0.577																																					p.E91E		Atlas-SNP	.											.	FARS2	33	.	0			c.G273A						.						71	57	62					6																	5369076		2203	4300	6503	SO:0001819	synonymous_variant	10667	exon2			CAAGGAGAGGGTG	AF097441	CCDS4494.1	6p25.1	2011-07-01	2007-02-23	2004-12-03	ENSG00000145982	ENSG00000145982	6.1.1.20	"Aminoacyl tRNA synthetases / Class II"	21062	protein-coding gene	gene with protein product	"phenylalanine tRNA ligase 2, mitochondrial"	611592	"phenylalanine-tRNA synthetase 1 (mitochondrial)"	FARS1		10329163	Standard	NM_006567		Approved	dJ236A3.1	uc003mwr.2	O95363	OTTHUMG00000014178	ENST00000324331.6:c.273G>A	chr6.hg19:g.5369076G>A		276.0	0.0		275.0	11.0	NM_006567	B2R664|Q53F66|Q5TCS3|Q6FG29|Q9NPY7|Q9P062	Silent	SNP	ENST00000324331.6	hg19	CCDS4494.1																																																																																			.	.		0.577	FARS2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467790.1	NM_006567		A	5369076	G	A	5369076	2	1	238	1	0	0	0	0	0	0	0	1	5686	933	33	3		3	FARS2	6	5369076	Silent	SNP	G	TCGA-ED-A4XI-01A-11D-A25V-10	2262961	5369076	165745991	47	33174										
KIAA1244	57221	hgsc.bcm.edu	37	chr6	138629875	138629875	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	tctataatcttcctcccttaGgaaaaggccaagctccagtg	7	12	2	0			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr6:138629875G>C	ENST00000251691.4	+	24	4139		c.e24-1			NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		TCCTCCCTTAGGAAAAGGCCA	0.448																																					.		Atlas-SNP	.											.	KIAA1244	236	.	0			c.3974-1G>C						.						137	133	134					6																	138629875		2203	4300	6503	SO:0001630	splice_region_variant	57221	exon24			CCCTTAGGAAAAG	AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	21213	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 33"		"chromosome 6 open reading frame 92"	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.3974-1G>C	chr6.hg19:g.138629875G>C		161.0	0.0		149.0	9.0	NM_020340		Splice_Site	SNP	ENST00000251691.4	hg19	CCDS5189.2	.	.	.	.	.	.	.	.	.	.	G	18.32	3.597971	0.66332	.	.	ENSG00000112379	ENST00000251691	.	.	.	5.89	5.89	0.94794	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.2617	0.98447	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	KIAA1244	138671568	1.000000	0.71417	0.999000	0.59377	0.517000	0.34286	9.869000	0.99810	2.793000	0.96121	0.655000	0.94253	.	.	.		0.448	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340	Intron	C	138629875	G	C	138629875	5	2	238	1	0	0	0	0	0	0	1	0	8226	1014	35	4	4067	4	KIAA1244	6	138629875	Splice_Site	SNP	G	TCGA-ED-A4XI-01A-11D-A25V-10	133260799	138629875	32485192	48	33175										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152638095	152638095	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	aaaattaattcaagcatttcAttgtattcttctaaatgtga	4	5	4	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr6:152638095A>G	ENST00000367255.5	-	87	17200	c.16599T>C	c.(16597-16599)aaT>aaC	p.N5533N	SYNE1_ENST00000356820.4_Silent_p.N57N|SYNE1_ENST00000423061.1_Silent_p.N5462N|SYNE1_ENST00000448038.1_Silent_p.N5462N|SYNE1_ENST00000265368.4_Silent_p.N5533N|SYNE1_ENST00000341594.5_Silent_p.N5145N	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	5533					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		CAAGCATTTCATTGTATTCTT	0.348										HNSCC(10;0.0054)																											p.N5533N		Atlas-SNP	.											.	SYNE1	3227	.	0			c.T16599C						.						103	102	102					6																	152638095		2203	4300	6503	SO:0001819	synonymous_variant	23345	exon87			CATTTCATTGTAT	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.16599T>C	chr6.hg19:g.152638095A>G		56.0	0.0		63.0	7.0	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	hg19	CCDS5236.2																																																																																			.	.		0.348	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		G	152638095	A	G	152638095	2	3	238	1	0	0	0	0	0	0	0	1	15460	214	8	2		2	SYNE1	6	152638095	Silent	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	14008220	152638095	18476972	49	33176										
TAGAP	117289	hgsc.bcm.edu	37	chr6	159457832	159457832	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	tttccaaacgagagcctaccCggggcacggggaagtcccct	12	14	0	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr6:159457832C>T	ENST00000367066.3	-	10	1554	c.1223G>A	c.(1222-1224)cGg>cAg	p.R408Q	RP1-111C20.4_ENST00000607796.1_RNA|RP1-111C20.4_ENST00000606466.1_RNA|RP1-111C20.4_ENST00000607391.1_RNA|TAGAP_ENST00000326965.6_Missense_Mutation_p.R230Q|RP1-111C20.4_ENST00000606470.1_RNA	NM_001278733.1|NM_054114.3	NP_001265662.1|NP_473455.2	Q8N103	TAGAP_HUMAN	T-cell activation RhoGTPase activating protein	408					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|autonomic_ganglia(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(2)|skin(1)	23		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.16e-16)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		AGAGCCTACCCGGGGCACGGG	0.572																																					p.R408Q		Atlas-SNP	.											.	TAGAP	75	.	0			c.G1223A						.						59	61	60					6																	159457832		2203	4300	6503	SO:0001583	missense	117289	exon10			CCTACCCGGGGCA	AF385429	CCDS5261.1, CCDS5262.1, CCDS5263.1	6q25.3	2011-09-07	2008-03-25		ENSG00000164691	ENSG00000164691		"Rho GTPase activating proteins"	15669	protein-coding gene	gene with protein product		609667	"T-cell activation GTPase activating protein"			16375659, 18311140, 18356936	Standard	NM_152133		Approved	FLJ32631, IDDM21, ARHGAP47	uc003qrz.3	Q8N103	OTTHUMG00000015923	ENST00000367066.3:c.1223G>A	chr6.hg19:g.159457832C>T	ENSP00000356033:p.Arg408Gln	157.0	0.0		146.0	17.0	NM_054114	Q2NKM8|Q8NI40|Q96KZ2|Q96QA2	Missense_Mutation	SNP	ENST00000367066.3	hg19	CCDS5261.1	.	.	.	.	.	.	.	.	.	.	C	5.985	0.365634	0.11352	.	.	ENSG00000164691	ENST00000367066;ENST00000326965;ENST00000539071	T;T	0.16457	2.34;2.63	6.05	-10.3	0.00346	.	1.110370	0.06750	N	0.779814	T	0.01387	0.0045	N	0.02011	-0.69	0.09310	N	0.999999	B	0.12630	0.006	B	0.06405	0.002	T	0.48801	-0.9003	10	0.02654	T	1	-0.7484	21.2762	0.99950	0.0:0.2287:0.0:0.7713	.	408	Q8N103	TAGAP_HUMAN	Q	408;230;73	ENSP00000356033:R408Q;ENSP00000322650:R230Q	ENSP00000322650:R230Q	R	-	2	0	TAGAP	159377820	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.398000	0.01051	-2.181000	0.00765	-0.827000	0.03088	CGG	.	.		0.572	TAGAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042890.1	NM_054114		T	159457832	C	T	159457832	3	4	238	1	0	0	0	0	1	0	0	0	15552	652	23	1	976	1	TAGAP	6	159457832	Missense_Mutation	SNP	C	TCGA-ED-A4XI-01A-11D-A25V-10	6819737	159457832	11657235	50	33177										
CCR6	1235	hgsc.bcm.edu	37	chr6	167550283	167550283	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	cttttgtcttcaaccaaaaaTacaacacccaaggcagcgat	5	12	2	0			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr6:167550283T>C	ENST00000341935.5	+	3	1117	c.565T>C	c.(565-567)Tac>Cac	p.Y189H	CCR6_ENST00000349984.4_Missense_Mutation_p.Y189H|CCR6_ENST00000400926.2_Missense_Mutation_p.Y189H|RP11-517H2.6_ENST00000609590.1_RNA	NM_031409.3	NP_113597.2	P51684	CCR6_HUMAN	chemokine (C-C motif) receptor 6	189					cellular component movement (GO:0006928)|cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|humoral immune response (GO:0006959)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)|receptor activity (GO:0004872)			endometrium(3)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)	14		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;8.21e-20)|BRCA - Breast invasive adenocarcinoma(81;4.55e-06)|GBM - Glioblastoma multiforme(31;0.00507)		CAACCAAAAATACAACACCCA	0.517																																					p.Y189H		Atlas-SNP	.											.	CCR6	36	.	0			c.T565C						.						101	95	97					6																	167550283		2203	4300	6503	SO:0001583	missense	1235	exon3			CAAAAATACAACA	U68030	CCDS5298.1	6q27	2012-08-08			ENSG00000112486	ENSG00000112486		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1607	protein-coding gene	gene with protein product		601835		STRL22		8886020	Standard	NM_031409		Approved	CKR-L3, GPR-CY4, CMKBR6, GPR29, DRY-6, DCR2, BN-1, CD196	uc010kkm.3	P51684	OTTHUMG00000016015	ENST00000341935.5:c.565T>C	chr6.hg19:g.167550283T>C	ENSP00000343952:p.Tyr189His	212.0	0.0		215.0	37.0	NM_004367	E1P5C6|P78553|Q92846	Missense_Mutation	SNP	ENST00000341935.5	hg19	CCDS5298.1	.	.	.	.	.	.	.	.	.	.	T	10.97	1.502385	0.26949	.	.	ENSG00000112486	ENST00000400926;ENST00000341935;ENST00000349984	T;T;T	0.72505	-0.66;-0.66;-0.66	4.94	4.94	0.65067	GPCR, rhodopsin-like superfamily (1);	0.985479	0.08239	U	0.976353	T	0.56001	0.1956	L	0.33710	1.025	0.80722	D	1	B	0.29552	0.248	B	0.41135	0.348	T	0.45234	-0.9275	10	0.24483	T	0.36	.	13.7779	0.63066	0.0:0.0:0.0:1.0	.	189	P51684	CCR6_HUMAN	H	189	ENSP00000383715:Y189H;ENSP00000343952:Y189H;ENSP00000339393:Y189H	ENSP00000343952:Y189H	Y	+	1	0	CCR6	167470273	1.000000	0.71417	0.155000	0.22561	0.013000	0.08279	5.417000	0.66423	1.836000	0.53414	0.533000	0.62120	TAC	.	.		0.517	CCR6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043118.1			C	167550283	T	C	167550283	3	2	238	1	0	0	0	0	1	0	0	0	2947	1406	49	2	571	2	CCR6	6	167550283	Missense_Mutation	SNP	T	TCGA-ED-A4XI-01A-11D-A25V-10	8092451	167550283	3564784	51	33178										
PDGFA	5154	hgsc.bcm.edu	37	chr7	540840	540840	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	taacctcacctggacttcttTtaattttggcttcttcctga	5	11	3	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr7:540840T>C	ENST00000354513.5	-	5	885	c.493A>G	c.(493-495)Aaa>Gaa	p.K165E	PDGFA_ENST00000402802.3_Missense_Mutation_p.K165E	NM_002607.5	NP_002598.4	P04085	PDGFA_HUMAN	platelet-derived growth factor alpha polypeptide	165					actin cytoskeleton organization (GO:0030036)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell activation (GO:0001775)|cell projection assembly (GO:0030031)|cell-cell signaling (GO:0007267)|embryo development (GO:0009790)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|lung alveolus development (GO:0048286)|negative chemotaxis (GO:0050919)|negative regulation of phosphatidylinositol biosynthetic process (GO:0010512)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of branching involved in salivary gland morphogenesis by epithelial-mesenchymal signaling (GO:0060683)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of smooth muscle cell migration (GO:0014910)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to inorganic substance (GO:0010035)|response to retinoic acid (GO:0032526)|response to wounding (GO:0009611)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi membrane (GO:0000139)|microvillus (GO:0005902)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|growth factor activity (GO:0008083)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	16		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|Epithelial(4;1.1e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.7e-17)|all cancers(6;4.89e-15)		TGGACTTCTTTTAATTTTGGC	0.557																																					p.K165E		Atlas-SNP	.											.	PDGFA	34	.	0			c.A493G						.						285	267	273					7																	540840		2203	4296	6499	SO:0001583	missense	5154	exon5			CTTCTTTTAATTT		CCDS34578.1, CCDS47524.1	7p22	2008-07-18			ENSG00000197461	ENSG00000197461			8799	protein-coding gene	gene with protein product	"PDGF A-chain", "platelet-derived growth factor alpha chain"	173430				1505216, 2536956	Standard	NM_002607		Approved	PDGF1, PDGF-A	uc003sir.3	P04085	OTTHUMG00000151412	ENST00000354513.5:c.493A>G	chr7.hg19:g.540840T>C	ENSP00000346508:p.Lys165Glu	180.0	0.0		192.0	28.0	NM_002607	B5BU73	Missense_Mutation	SNP	ENST00000354513.5	hg19	CCDS34578.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.82|14.82	2.648079|2.648079	0.47258|0.47258	.|.	.|.	ENSG00000197461|ENSG00000197461	ENST00000402802;ENST00000354513|ENST00000400761	T;T|.	0.47177|.	0.85;0.85|.	4.98|4.98	4.98|4.98	0.66077|0.66077	Platelet-derived growth factor (PDGF) (3);|.	0.149699|0.149699	0.64402|0.64402	N|D	0.000016|0.000016	T|T	0.61311|0.61311	0.2337|0.2337	L|L	0.46885|0.46885	1.475|1.475	0.49299|0.49299	D|D	0.999775|0.999775	D;D;D|.	0.71674|.	0.975;0.998;0.987|.	P;D;P|.	0.72625|.	0.72;0.978;0.895|.	T|T	0.59247|0.59247	-0.7490|-0.7490	10|6	0.18276|.	T|.	0.48|.	-14.308|-14.308	14.3501|14.3501	0.66694|0.66694	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	179;165;165|.	Q32M96;P04085-2;P04085|.	.;.;PDGFA_HUMAN|.	E|R	165|171	ENSP00000383889:K165E;ENSP00000346508:K165E|.	ENSP00000346508:K165E|.	K|K	-|-	1|2	0|0	PDGFA|PDGFA	507366|507366	1.000000|1.000000	0.71417|0.71417	0.989000|0.989000	0.46669|0.46669	0.994000|0.994000	0.84299|0.84299	3.094000|3.094000	0.50227|0.50227	1.859000|1.859000	0.53934|0.53934	0.533000|0.533000	0.62120|0.62120	AAA|AAA	.	.		0.557	PDGFA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322534.1			C	540840	T	C	540840	3	2	238	1	0	0	0	0	1	0	0	0	11666	1850	64	2	165	2	PDGFA	7	540840	Missense_Mutation	SNP	T	TCGA-ED-A4XI-01A-11D-A25V-10		540840	158597823	52	33179										
HDAC9	9734	hgsc.bcm.edu	37	chr7	18688120	18688120	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	ttacatcctcagtctcccttGgcaacaaaagagagaatttc	6	11	2	2			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr7:18688120G>A	ENST00000432645.2	+	10	1272	c.1272G>A	c.(1270-1272)ttG>ttA	p.L424L	HDAC9_ENST00000406072.1_Silent_p.L411L|HDAC9_ENST00000524023.1_Silent_p.L347L|HDAC9_ENST00000417496.2_Silent_p.L422L|HDAC9_ENST00000441542.2_Silent_p.L427L|HDAC9_ENST00000456174.2_Silent_p.L396L|HDAC9_ENST00000428307.2_Silent_p.L380L|HDAC9_ENST00000406451.4_Silent_p.L424L|HDAC9_ENST00000405010.3_Silent_p.L424L|HDAC9_ENST00000401921.1_Silent_p.L383L	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	424					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|regulation of skeletal muscle fiber development (GO:0048742)|regulation of striated muscle cell differentiation (GO:0051153)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|liver(2)|lung(37)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	82	all_lung(11;0.187)				Valproic Acid(DB00313)	AGTCTCCCTTGGCAACAAAAG	0.463																																					p.L427L		Atlas-SNP	.											.	HDAC9	560	.	0			c.G1281A						.						77	76	77					7																	18688120		1886	4117	6003	SO:0001819	synonymous_variant	9734	exon10			TCCCTTGGCAACA	AF124924	CCDS47553.1, CCDS47554.1, CCDS47555.1, CCDS47557.1, CCDS56465.1, CCDS56466.1, CCDS56467.1, CCDS56468.1, CCDS75565.1	7p21.1	2008-05-15			ENSG00000048052	ENSG00000048052			14065	protein-coding gene	gene with protein product		606543				10523670, 10487760	Standard	NM_178425		Approved	KIAA0744, HDAC, MITR, HD7, HDAC7B	uc003sui.3	Q9UKV0	OTTHUMG00000152487	ENST00000432645.2:c.1272G>A	chr7.hg19:g.18688120G>A		63.0	0.0		65.0	9.0	NM_178425	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Silent	SNP	ENST00000432645.2	hg19	CCDS47555.1																																																																																			.	.		0.463	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1			A	18688120	G	A	18688120	2	1	238	1	0	0	0	0	0	0	0	1	7023	1339	47	3		3	HDAC9	7	18688120	Silent	SNP	G	TCGA-ED-A4XI-01A-11D-A25V-10	18147280	18688120	140450543	53	33180										
CNOT4	4850	hgsc.bcm.edu	37	chr7	135122994	135122994	+	Frame_Shift_Del	DEL	A	A	-													0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	ggtagccacaggtgcaagggAaaaagttgatatcatctatc							TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr7:135122994delA	ENST00000315544.5	-	2	365	c.86delT	c.(85-87)ttcfs	p.F29fs	CNOT4_ENST00000541284.1_Frame_Shift_Del_p.F29fs|CNOT4_ENST00000356162.4_Frame_Shift_Del_p.F29fs|CNOT4_ENST00000361528.4_Frame_Shift_Del_p.F29fs|CNOT4_ENST00000414802.1_Frame_Shift_Del_p.F29fs|CNOT4_ENST00000428680.2_Frame_Shift_Del_p.F29fs|CNOT4_ENST00000451834.1_Frame_Shift_Del_p.F29fs|CNOT4_ENST00000423368.2_Frame_Shift_Del_p.F29fs	NM_001190848.1	NP_001177777.1	O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	29					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|protein autoubiquitination (GO:0051865)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)	22						GGTGCAAGGGAAAAAGTTGAT	0.453																																					p.F29fs	Ovarian(51;766 1130 5502 35047 50875)	Atlas-Indel,Pindel	.											.	CNOT4	146	.	0			c.87delC						.						85	81	82					7																	135122994		1924	4134	6058	SO:0001589	frameshift_variant	4850	exon2			.	AF180475	CCDS43650.1, CCDS47719.1, CCDS55164.1, CCDS55165.1, CCDS55166.1, CCDS55167.1	7q33	2013-09-19			ENSG00000080802	ENSG00000080802		"RNA binding motif (RRM) containing"	7880	protein-coding gene	gene with protein product		604911		NOT4		10637334	Standard	NM_013316		Approved	CLONE243, NOT4H	uc011kpy.2	O95628	OTTHUMG00000155568	ENST00000315544.5:c.86delT	chr7.hg19:g.135122994delA	ENSP00000326731:p.Phe29fs	248.0	0.0		221.0	35.0	NM_001190847	B7Z6I4|E7ET38|F8VQP3|O95339|O95627|Q8IYM7|Q8NCL0|Q9NPQ1|Q9NZN6	Frame_Shift_Del	DEL	ENST00000315544.5	hg19	CCDS55166.1																																																																																			.	.		0.453	CNOT4-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_013316		-	135122994	A	-	135122994	7	5	238	1	0	1	0	1	0	0	0	0	3623	246	9	0	1978	0	CNOT4	7	135122994	Frame_Shift_Del	DEL	A	TCGA-ED-A4XI-01A-11D-A25V-10	116434874	135122994	24015669	54	33181										
LGI3	203190	hgsc.bcm.edu	37	chr8	22006415	22006415	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	cccagtggtaaatgtaagagCcgccaaacagctgggccacg	12	12	0	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr8:22006415C>T	ENST00000306317.2	-	8	1194	c.905G>A	c.(904-906)gGc>gAc	p.G302D	LGI3_ENST00000424267.2_Missense_Mutation_p.G278D	NM_139278.2	NP_644807.1	Q8N145	LGI3_HUMAN	leucine-rich repeat LGI family, member 3	302					exocytosis (GO:0006887)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|extracellular region (GO:0005576)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	catalytic activity (GO:0003824)			endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	17				Colorectal(74;0.00189)|COAD - Colon adenocarcinoma(73;0.0612)|READ - Rectum adenocarcinoma(644;0.0999)		AATGTAAGAGCCGCCAAACAG	0.612																																					p.G302D		Atlas-SNP	.											.	LGI3	44	.	0			c.G905A						.						62	55	57					8																	22006415		2203	4300	6503	SO:0001583	missense	203190	exon8			TAAGAGCCGCCAA	AJ487518	CCDS6025.1	8p21.2	2008-07-28			ENSG00000168481	ENSG00000168481			18711	protein-coding gene	gene with protein product		608302				12023020, 18628660	Standard	NM_139278		Approved		uc003xav.3	Q8N145	OTTHUMG00000131599	ENST00000306317.2:c.905G>A	chr8.hg19:g.22006415C>T	ENSP00000302297:p.Gly302Asp	228.0	0.0		158.0	29.0	NM_139278	A5PLP2|Q86TL4|Q8N296	Missense_Mutation	SNP	ENST00000306317.2	hg19	CCDS6025.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.473992	0.84640	.	.	ENSG00000168481	ENST00000306317;ENST00000424267	T;T	0.05649	3.41;3.41	4.6	4.6	0.57074	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	T	0.21387	0.0515	L	0.57536	1.79	0.58432	D	0.999999	D;D	0.89917	0.999;1.0	D;D	0.91635	0.975;0.999	T	0.00280	-1.1852	10	0.87932	D	0	-45.5027	14.9741	0.71257	0.0:1.0:0.0:0.0	.	278;302	A5PLP2;Q8N145	.;LGI3_HUMAN	D	302;278	ENSP00000302297:G302D;ENSP00000399121:G278D	ENSP00000302297:G302D	G	-	2	0	LGI3	22062360	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.922000	0.70036	2.366000	0.80165	0.561000	0.74099	GGC	.	.		0.612	LGI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254482.1			T	22006415	C	T	22006415	3	4	238	1	0	0	0	0	1	0	0	0	8762	739	26	3	745	3	LGI3	8	22006415	Missense_Mutation	SNP	C	TCGA-ED-A4XI-01A-11D-A25V-10		22006415	124357607	55	33182										
MMP16	4325	hgsc.bcm.edu	37	chr8	89180168	89180168	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	gcgaatagctttacgagtctCagggtctcctacttttggag	11	9	2	0			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr8:89180168C>A	ENST00000286614.6	-	4	720	c.439G>T	c.(439-441)Gag>Tag	p.E147*	MMP16_ENST00000544227.1_5'UTR	NM_005941.4	NP_005932.2	P51512	MMP16_HUMAN	matrix metallopeptidase 16 (membrane-inserted)	147					chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)	Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(51)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	81					Marimastat(DB00786)	TTACGAGTCTCAGGGTCTCCT	0.373																																					p.E147X		Atlas-SNP	.											.	MMP16	176	.	0			c.G439T						.						111	101	105					8																	89180168		2203	4300	6503	SO:0001587	stop_gained	4325	exon4			GAGTCTCAGGGTC	D85511	CCDS6246.1	8q21	2009-01-09	2005-08-08		ENSG00000156103	ENSG00000156103			7162	protein-coding gene	gene with protein product		602262	"matrix metalloproteinase 16 (membrane-inserted)", "chromosome 8 open reading frame 57"	C8orf57		7559440	Standard	NM_005941		Approved	MT3-MMP, DKFZp761D112	uc003yeb.4	P51512	OTTHUMG00000163769	ENST00000286614.6:c.439G>T	chr8.hg19:g.89180168C>A	ENSP00000286614:p.Glu147*	149.0	0.0		142.0	7.0	NM_005941	B2RAN7|Q14824|Q52H48	Nonsense_Mutation	SNP	ENST00000286614.6	hg19	CCDS6246.1	.	.	.	.	.	.	.	.	.	.	C	37	6.147893	0.97324	.	.	ENSG00000156103	ENST00000286614;ENST00000522726	.	.	.	6.16	6.16	0.99307	.	0.042023	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	.	20.8598	0.99761	0.0:1.0:0.0:0.0	.	.	.	.	X	147;164	.	ENSP00000286614:E147X	E	-	1	0	MMP16	89249284	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.768000	0.62293	2.937000	0.99478	0.650000	0.86243	GAG	.	.		0.373	MMP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375304.2	NM_005941		A	89180168	C	A	89180168	4	1	238	1	0	0	0	0	0	1	0	0	9664	835	29	3	1568	3	MMP16	8	89180168	Nonsense_Mutation	SNP	C	TCGA-ED-A4XI-01A-11D-A25V-10	67173753	89180168	57183854	56	33183										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113348909	113348909	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	aatgaaatcatatattggttCtgtttgaaggacagtaaaat	8	3	2	2			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr8:113348909C>G	ENST00000297405.5	-	44	7235	c.6991G>C	c.(6991-6993)Gaa>Caa	p.E2331Q	CSMD3_ENST00000343508.3_Missense_Mutation_p.E2291Q|CSMD3_ENST00000352409.3_Missense_Mutation_p.E2261Q|CSMD3_ENST00000455883.2_Missense_Mutation_p.E2227Q	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2331	CUB 13. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TATATTGGTTCTGTTTGAAGG	0.318										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.E2331Q		Atlas-SNP	.											.	CSMD3	2325	.	0			c.G6991C						.						110	112	111					8																	113348909		2203	4300	6503	SO:0001583	missense	114788	exon44			TTGGTTCTGTTTG	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.6991G>C	chr8.hg19:g.113348909C>G	ENSP00000297405:p.Glu2331Gln	85.0	0.0		98.0	22.0	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	29.7	5.028607	0.93518	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18	5.64	5.64	0.86602	CUB (5);	0.000000	0.64402	D	0.000001	T	0.81408	0.4816	M	0.83312	2.635	0.58432	D	0.999998	D;D;D	0.89917	0.999;0.996;1.0	D;D;D	0.83275	0.996;0.996;0.991	T	0.78610	-0.2137	10	0.34782	T	0.22	.	19.8946	0.96949	0.0:1.0:0.0:0.0	.	2227;2331;2291	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	Q	2291;2331;1601;2227;2261	ENSP00000345799:E2291Q;ENSP00000297405:E2331Q;ENSP00000341558:E1601Q;ENSP00000412263:E2227Q;ENSP00000343124:E2261Q	ENSP00000297405:E2331Q	E	-	1	0	CSMD3	113418085	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.651000	0.83577	2.937000	0.99478	0.650000	0.86243	GAA	.	.		0.318	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		G	113348909	C	G	113348909	3	3	238	1	0	0	0	0	1	0	0	0	3948	922	32	4	4244	4	CSMD3	8	113348909	Missense_Mutation	SNP	C	TCGA-ED-A4XI-01A-11D-A25V-10	24168741	113348909	33015113	57	33184										
SQLE	6713	hgsc.bcm.edu	37	chr8	126030343	126030343	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	atataatatgaggcatccacTtactggtggaggaatgactg	11	6	0	2			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr8:126030343T>G	ENST00000265896.5	+	8	2145	c.1247T>G	c.(1246-1248)cTt>cGt	p.L416R	SQLE_ENST00000523430.1_Missense_Mutation_p.L321R	NM_003129.3	NP_003120.2	Q14534	ERG1_HUMAN	squalene epoxidase	416					cellular aromatic compound metabolic process (GO:0006725)|cholesterol biosynthetic process (GO:0006695)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|squalene monooxygenase activity (GO:0004506)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)	14	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)		Butenafine(DB01091)|Naftifine(DB00735)|Terbinafine(DB00857)	AGGCATCCACTTACTGGTGGA	0.368																																					p.L416R		Atlas-SNP	.											.	SQLE	29	.	0			c.T1247G						.						113	109	110					8																	126030343		1828	4073	5901	SO:0001583	missense	6713	exon8			ATCCACTTACTGG	D78130	CCDS47918.1	8q24.1	2014-06-23			ENSG00000104549	ENSG00000104549	1.14.13.132		11279	protein-coding gene	gene with protein product	"squalene monooxygenase"	602019				9286711	Standard	NM_003129		Approved		uc011liq.2	Q14534	OTTHUMG00000164990	ENST00000265896.5:c.1247T>G	chr8.hg19:g.126030343T>G	ENSP00000265896:p.Leu416Arg	40.0	0.0		49.0	7.0	NM_003129	Q9UEK6	Missense_Mutation	SNP	ENST00000265896.5	hg19	CCDS47918.1	.	.	.	.	.	.	.	.	.	.	T	17.27	3.348267	0.61183	.	.	ENSG00000104549	ENST00000523430;ENST00000265896;ENST00000541193;ENST00000518931	T;T;T	0.49139	0.79;0.79;0.79	5.38	5.38	0.77491	Aromatic-ring hydroxylase-like (1);Squalene epoxidase (1);	0.000000	0.85682	D	0.000000	T	0.78027	0.4219	H	0.95574	3.69	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85256	0.1047	10	0.87932	D	0	-20.2226	15.3909	0.74741	0.0:0.0:0.0:1.0	.	416	Q14534	ERG1_HUMAN	R	321;416;221;68	ENSP00000430331:L321R;ENSP00000265896:L416R;ENSP00000429916:L68R	ENSP00000265896:L416R	L	+	2	0	SQLE	126099525	1.000000	0.71417	1.000000	0.80357	0.143000	0.21401	7.831000	0.86748	2.037000	0.60232	0.533000	0.62120	CTT	.	.		0.368	SQLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381362.1	NM_003129		G	126030343	T	G	126030343	3	3	238	1	0	0	0	0	1	0	0	0	15143	1609	56	5	1176	5	SQLE	8	126030343	Missense_Mutation	SNP	T	TCGA-ED-A4XI-01A-11D-A25V-10	12681434	126030343	20333679	58	33185										
OR13J1	392309	hgsc.bcm.edu	37	chr9	35869767	35869767	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	aggacaggcagatgaatgccAggggtacaggcagcagcagg	17	8	0	2			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr9:35869767A>T	ENST00000377981.2	-	1	694	c.632T>A	c.(631-633)cTg>cAg	p.L211Q		NM_001004487.1	NP_001004487.1	Q8NGT2	O13J1_HUMAN	olfactory receptor, family 13, subfamily J, member 1	211						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|large_intestine(1)|lung(3)|skin(1)	6	all_epithelial(49;0.169)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00494)|STAD - Stomach adenocarcinoma(86;0.194)			GATGAATGCCAGGGGTACAGG	0.622																																					p.L211Q		Atlas-SNP	.											.	OR13J1	37	.	0			c.T632A						.						56	45	49					9																	35869767		2203	4300	6503	SO:0001583	missense	392309	exon1			AATGCCAGGGGTA		CCDS35011.1	9p13.3	2013-09-24			ENSG00000168828	ENSG00000168828		"GPCR / Class A : Olfactory receptors"	15108	protein-coding gene	gene with protein product							Standard	NM_001004487		Approved		uc011lph.2	Q8NGT2	OTTHUMG00000019879	ENST00000377981.2:c.632T>A	chr9.hg19:g.35869767A>T	ENSP00000367219:p.Leu211Gln	135.0	0.0		108.0	7.0	NM_001004487	B2RN66|Q6IF20|Q96R40	Missense_Mutation	SNP	ENST00000377981.2	hg19	CCDS35011.1	.	.	.	.	.	.	.	.	.	.	A	8.953	0.968595	0.18659	.	.	ENSG00000168828	ENST00000377981	T	0.49432	0.78	4.5	0.877	0.19145	GPCR, rhodopsin-like superfamily (1);	0.335275	0.21315	N	0.076577	T	0.67618	0.2912	M	0.91249	3.19	0.09310	N	1	D	0.89917	1.0	D	0.74348	0.983	T	0.57124	-0.7865	10	0.87932	D	0	.	4.9583	0.14054	0.6677:0.1581:0.1743:0.0	.	211	Q8NGT2	O13J1_HUMAN	Q	211	ENSP00000367219:L211Q	ENSP00000367219:L211Q	L	-	2	0	OR13J1	35859767	0.000000	0.05858	0.323000	0.25347	0.000000	0.00434	0.461000	0.21940	0.142000	0.18901	-1.133000	0.01973	CTG	.	.		0.622	OR13J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052381.1			T	35869767	A	T	35869767	3	4	238	1	0	0	0	0	1	0	0	0	10953	188	7	4	309	4	OR13J1	9	35869767	Missense_Mutation	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10		35869767	105343664	59	33186										
TMEFF1	8577	hgsc.bcm.edu	37	chr9	103271393	103271393	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	ccagaaagagataacagtaaTagcaagaggaccatgctact	9	8	0	3			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr9:103271393T>C	ENST00000374879.4	+	3	845	c.413T>C	c.(412-414)aTa>aCa	p.I138T	TMEFF1_ENST00000334943.6_Missense_Mutation_p.I99T|MSANTD3-TMEFF1_ENST00000502978.1_Silent_p.N101N	NM_003692.4	NP_003683.2	Q8IYR6	TEFF1_HUMAN	transmembrane protein with EGF-like and two follistatin-like domains 1	138	Kazal-like 1. {ECO:0000255|PROSITE- ProRule:PRU00798}.				multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|kidney(1)|large_intestine(7)|lung(9)|stomach(1)	19		Acute lymphoblastic leukemia(62;0.0452)				ATAACAGTAATAGCAAGAGGA	0.373																																					p.I212T		Atlas-SNP	.											.	.	.	.	0			c.T635C						.						100	99	99					9																	103271393		2203	4300	6503	SO:0001583	missense	100526694	exon3			CAGTAATAGCAAG	U19878	CCDS6750.1	9q31	2010-05-04			ENSG00000241697	ENSG00000241697			11866	protein-coding gene	gene with protein product	"tomoregulin-1", "cancer/testis antigen family 120, member 1"	603421		C9orf2		9730596	Standard	NM_003692		Approved	H7365, CT120.1		Q8IYR6	OTTHUMG00000020367	ENST00000374879.4:c.413T>C	chr9.hg19:g.103271393T>C	ENSP00000364013:p.Ile138Thr	55.0	0.0		63.0	15.0	NM_001198812	Q13086|Q8N3T8	Missense_Mutation	SNP	ENST00000374879.4	hg19	CCDS6750.1	.	.	.	.	.	.	.	.	.	.	T	13.72	2.321581	0.41096	.	.	ENSG00000241697	ENST00000334943;ENST00000374879	T;T	0.04156	3.69;3.69	5.58	5.58	0.84498	Proteinase inhibitor I1, Kazal (1);Protease inhibitor, Kazal-type (1);	0.066028	0.64402	D	0.000010	T	0.05777	0.0151	L	0.35542	1.07	0.20926	N	0.999828	B;B	0.11235	0.004;0.002	B;B	0.16722	0.016;0.0	T	0.26326	-1.0106	10	0.54805	T	0.06	-8.2017	13.6963	0.62582	0.0:0.0:0.0:1.0	.	138;99	Q8IYR6;Q8IYR6-2	TEFF1_HUMAN;.	T	99;138	ENSP00000334447:I99T;ENSP00000364013:I138T	ENSP00000334447:I99T	I	+	2	0	TMEFF1	102311214	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	3.674000	0.54598	2.113000	0.64589	0.528000	0.53228	ATA	.	.		0.373	TMEFF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053418.1	NM_003692		C	103271393	T	C	103271393	3	2	238	1	0	0	0	0	1	0	0	0	16028	1406	49	2	423	2	TMEFF1	9	103271393	Missense_Mutation	SNP	T	TCGA-ED-A4XI-01A-11D-A25V-10	67401626	103271393	37942038	60	33187										
ORM2	5005	hgsc.bcm.edu	37	chr9	117093116	117093116	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	cagttacctgaatgtccagcGggagaatgggaccgtctcca	12	11	1	2			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr9:117093116G>A	ENST00000431067.2	+	3	338	c.302G>A	c.(301-303)cGg>cAg	p.R101Q	ORM2_ENST00000412657.1_3'UTR	NM_000608.2	NP_000599.1	P19652	A1AG2_HUMAN	orosomucoid 2	101					acute-phase response (GO:0006953)|regulation of immune system process (GO:0002682)|transport (GO:0006810)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|large_intestine(1)|lung(1)|skin(2)|urinary_tract(1)	7		Myeloproliferative disorder(63;0.163)			Chlorpromazine(DB00477)|Oxycodone(DB00497)|Thalidomide(DB01041)	AATGTCCAGCGGGAGAATGGG	0.552																																					p.R101Q	NSCLC(65;867 1308 1814 2391 12508)	Atlas-SNP	.											.	ORM2	13	.	0			c.G302A						.						80	77	78					9																	117093116		2203	4300	6503	SO:0001583	missense	5005	exon3			TCCAGCGGGAGAA		CCDS6804.1	9q32	2013-09-19			ENSG00000228278	ENSG00000228278		"Lipocalins"	8499	protein-coding gene	gene with protein product	"alpha-1-acid glycoprotein, type 2"	138610				4711474, 2970990	Standard	NM_000608		Approved	AGP-B, AGP-B', AGP2		P19652	OTTHUMG00000021014	ENST00000431067.2:c.302G>A	chr9.hg19:g.117093116G>A	ENSP00000394936:p.Arg101Gln	143.0	0.0		167.0	21.0	NM_000608	B2R5L2|Q16571|Q5T538|Q6IB74	Missense_Mutation	SNP	ENST00000431067.2	hg19	CCDS6804.1	.	.	.	.	.	.	.	.	.	.	-	17.22	3.335318	0.60853	.	.	ENSG00000228278	ENST00000431067	T	0.13657	2.57	2.72	2.72	0.32119	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.283482	0.32736	N	0.005715	T	0.33147	0.0853	M	0.79475	2.455	0.24851	N	0.992406	D	0.89917	1.0	D	0.74674	0.984	T	0.02220	-1.1193	10	0.87932	D	0	-13.5568	9.1868	0.37176	0.0:0.0:1.0:0.0	.	101	P19652	A1AG2_HUMAN	Q	101	ENSP00000394936:R101Q	ENSP00000394936:R101Q	R	+	2	0	ORM2	116132937	0.038000	0.19896	0.013000	0.15412	0.012000	0.07955	3.528000	0.53524	1.864000	0.54056	0.500000	0.49745	CGG	.	.		0.552	ORM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055432.1	NM_000608		A	117093116	G	A	117093116	3	1	238	1	0	0	0	0	1	0	0	0	11277	1116	39	1	312	1	ORM2	9	117093116	Missense_Mutation	SNP	G	TCGA-ED-A4XI-01A-11D-A25V-10	13821723	117093116	24120315	61	33188										
CDK5RAP2	55755	hgsc.bcm.edu	37	chr9	123210343	123210343	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	cctgggtggcagggagacgaTacatatttcctaatgaccgg	13	9	0	2			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr9:123210343T>C	ENST00000349780.4	-	22	3034	c.2855A>G	c.(2854-2856)tAt>tGt	p.Y952C	CDK5RAP2_ENST00000359309.3_Missense_Mutation_p.Y952C|CDK5RAP2_ENST00000360822.3_Missense_Mutation_p.Y920C|CDK5RAP2_ENST00000360190.4_Missense_Mutation_p.Y952C	NM_018249.4	NP_060719.4	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	952	Interaction with MAPRE1.				brain development (GO:0007420)|centrosome organization (GO:0051297)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of centriole replication (GO:0046600)|negative regulation of neuron differentiation (GO:0045665)|neurogenesis (GO:0022008)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of spindle checkpoint (GO:0090231)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)			breast(6)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	58						AGGGAGACGATACATATTTCC	0.468																																					p.Y952C		Atlas-SNP	.											.	CDK5RAP2	157	.	0			c.A2855G						.						105	108	107					9																	123210343		2203	4300	6503	SO:0001583	missense	55755	exon22			AGACGATACATAT	BK005504	CCDS6823.1, CCDS43871.1, CCDS75888.1	9q33.3	2014-02-21			ENSG00000136861	ENSG00000136861			18672	protein-coding gene	gene with protein product	"centrosomin"	608201	"microcephaly, primary autosomal recessive 3"	MCPH3		10721722, 17764569, 24466316	Standard	NM_018249		Approved	C48, FLJ10867, CEP215	uc004bkf.4	Q96SN8	OTTHUMG00000021043	ENST00000349780.4:c.2855A>G	chr9.hg19:g.123210343T>C	ENSP00000343818:p.Tyr952Cys	203.0	0.0		189.0	24.0	NM_018249	Q5JV18|Q7Z3L4|Q7Z3U1|Q7Z7I6|Q9BSW0|Q9H6J6|Q9HCD9|Q9NV90|Q9UIW9	Missense_Mutation	SNP	ENST00000349780.4	hg19	CCDS6823.1	.	.	.	.	.	.	.	.	.	.	T	7.260	0.604943	0.14002	.	.	ENSG00000136861	ENST00000360822;ENST00000359309;ENST00000349780;ENST00000360190;ENST00000416449;ENST00000425647;ENST00000345313	T;T;T;T;T;T	0.38887	3.87;3.81;3.88;3.78;2.19;1.11	4.83	2.47	0.30058	.	1.242190	0.05894	N	0.628697	T	0.46347	0.1388	N	0.19112	0.55	0.09310	N	1	B;B;B;B;B;D	0.76494	0.009;0.002;0.009;0.244;0.005;0.999	B;B;B;B;B;D	0.76071	0.007;0.004;0.01;0.141;0.005;0.987	T	0.28808	-1.0032	10	0.49607	T	0.09	.	3.7924	0.08726	0.0:0.2142:0.1874:0.5984	.	3;721;920;952;952;346	Q5JTU8;Q6MZT4;Q96SN8-2;Q96SN8-4;Q96SN8;B1AMJ5	.;.;.;.;CK5P2_HUMAN;.	C	920;952;952;952;346;3;724	ENSP00000354065:Y920C;ENSP00000352258:Y952C;ENSP00000343818:Y952C;ENSP00000353317:Y952C;ENSP00000400395:Y346C;ENSP00000409941:Y3C	ENSP00000341695:Y724C	Y	-	2	0	CDK5RAP2	122250164	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	0.041000	0.13927	0.222000	0.20900	0.383000	0.25322	TAT	.	.		0.468	CDK5RAP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055535.1	NM_018249		C	123210343	T	C	123210343	3	2	238	1	0	0	0	0	1	0	0	0	3148	1406	49	2	2894	2	CDK5RAP2	9	123210343	Missense_Mutation	SNP	T	TCGA-ED-A4XI-01A-11D-A25V-10	6117227	123210343	18003088	62	33189										
C9orf98	158067	hgsc.bcm.edu	37	chr9	135698618	135698618	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	caagcctgtatttctgggccAggagggcggcctgcagactt	14	11	1	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr9:135698618A>T	ENST00000298545.3	-	9	1384	c.863T>A	c.(862-864)cTg>cAg	p.L288Q	AK8_ENST00000477396.1_5'UTR	NM_152572.2	NP_689785.1	Q96MA6	KAD8_HUMAN	adenylate kinase 8	288	Adenylate kinase 2.				nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)			NS(1)|kidney(2)|large_intestine(4)|lung(11)|pancreas(2)|prostate(1)|urinary_tract(2)	23						TTTCTGGGCCAGGAGGGCGGC	0.627																																					p.L288Q		Atlas-SNP	.											.	AK8	45	.	0			c.T863A						.						91	99	96					9																	135698618		2203	4300	6503	SO:0001583	missense	158067	exon9			TGGGCCAGGAGGG	AK093446	CCDS6954.1	9q34.13	2013-04-29	2010-12-07	2010-12-07	ENSG00000165695	ENSG00000165695	2.7.4.3	"Adenylate kinases"	26526	protein-coding gene	gene with protein product		615365	"chromosome 9 open reading frame 98"	C9orf98		21080915	Standard	NM_152572		Approved	FLJ32704	uc004cbu.1	Q96MA6	OTTHUMG00000021009	ENST00000298545.3:c.863T>A	chr9.hg19:g.135698618A>T	ENSP00000298545:p.Leu288Gln	140.0	0.0		121.0	11.0	NM_152572	A8K821|Q8N9W9	Missense_Mutation	SNP	ENST00000298545.3	hg19	CCDS6954.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.047467	0.75846	.	.	ENSG00000165695	ENST00000298545	D	0.81499	-1.5	5.61	4.47	0.54385	.	0.230691	0.36591	N	0.002503	D	0.92378	0.7581	H	0.96943	3.91	0.43385	D	0.995493	D	0.89917	1.0	D	0.91635	0.999	D	0.93217	0.6605	10	0.87932	D	0	-23.719	10.8686	0.46870	0.9267:0.0:0.0733:0.0	.	288	Q96MA6	KAD8_HUMAN	Q	288	ENSP00000298545:L288Q	ENSP00000298545:L288Q	L	-	2	0	AK8	134688439	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.998000	0.76277	1.070000	0.40811	0.533000	0.62120	CTG	.	.		0.627	AK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055413.1	NM_152572		T	135698618	A	T	135698618	3	4	238	1	0	0	0	0	1	0	0	0	2511	188	7	4	596	4	C9orf98	9	135698618	Missense_Mutation	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	12488275	135698618	5514813	63	33190										
PMPCA	23203	hgsc.bcm.edu	37	chr9	139313081	139313081	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	tccttctcggctggtgggccCggcaagggcatgttctccag	14	13	2	0	rs553050557	byFrequency	TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr9:139313081C>G	ENST00000371717.3	+	9	1074	c.1065C>G	c.(1063-1065)ccC>ccG	p.P355P	PMPCA_ENST00000399219.3_Silent_p.P224P|PMPCA_ENST00000462616.1_3'UTR	NM_001282946.1|NM_015160.1	NP_001269875.1|NP_055975.1	Q10713	MPPA_HUMAN	peptidase (mitochondrial processing) alpha	355					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			endometrium(3)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|urinary_tract(1)	14		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;9.3e-06)|Epithelial(140;1.15e-05)		CTGGTGGGCCCGGCAAGGGCA	0.597																																					p.P355P		Atlas-SNP	.											.	PMPCA	29	.	0			c.C1065G						.						82	75	77					9																	139313081		2203	4300	6503	SO:0001819	synonymous_variant	23203	exon9			TGGGCCCGGCAAG	D21064	CCDS35180.1, CCDS65192.1	9q34.3	2008-02-05	2003-06-13	2003-06-20	ENSG00000165688	ENSG00000165688			18667	protein-coding gene	gene with protein product		613036	"inositol polyphosphate-5-phosphatase, 72 kD"	INPP5E		8590280, 7788527	Standard	NM_015160		Approved	KIAA0123, Alpha-MPP	uc004chl.3	Q10713	OTTHUMG00000020926	ENST00000371717.3:c.1065C>G	chr9.hg19:g.139313081C>G		139.0	0.0		137.0	9.0	NM_015160	B4DKL3|E7ET61|Q16639|Q5SXM9|Q8N513	Silent	SNP	ENST00000371717.3	hg19	CCDS35180.1																																																																																			.	.		0.597	PMPCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055054.1	NM_015160		G	139313081	C	G	139313081	2	3	238	1	0	0	0	0	0	0	0	1	12149	639	23	4		4	PMPCA	9	139313081	Silent	SNP	C	TCGA-ED-A4XI-01A-11D-A25V-10	3614463	139313081	1900350	64	33191										
NRP1	8829	hgsc.bcm.edu	37	chr10	33515205	33515205	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	agccgtgacaaagcgcagaaGgcccaagtctacctgcaaga	11	12	1	3			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr10:33515205G>A	ENST00000265371.4	-	8	1519	c.994C>T	c.(994-996)Ctt>Ttt	p.L332F	NRP1_ENST00000374867.2_Missense_Mutation_p.L332F|NRP1_ENST00000374822.4_Missense_Mutation_p.L332F|NRP1_ENST00000374821.5_Missense_Mutation_p.L332F|NRP1_ENST00000374823.5_Missense_Mutation_p.L332F|NRP1_ENST00000374875.1_Missense_Mutation_p.L151F|NRP1_ENST00000432372.2_Missense_Mutation_p.L332F|NRP1_ENST00000374816.3_Missense_Mutation_p.L332F|NRP1_ENST00000395995.1_Missense_Mutation_p.L332F			O14786	NRP1_HUMAN	neuropilin 1	332	F5/8 type C 1. {ECO:0000255|PROSITE- ProRule:PRU00081}.				angiogenesis (GO:0001525)|angiogenesis involved in coronary vascular morphogenesis (GO:0060978)|artery morphogenesis (GO:0048844)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell signaling (GO:0007267)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|commissural neuron axon guidance (GO:0071679)|coronary artery morphogenesis (GO:0060982)|dendrite development (GO:0016358)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell chemotaxis (GO:0035767)|endothelial tip cell fate specification (GO:0097102)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|patterning of blood vessels (GO:0001569)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of cytokine activity (GO:0060301)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of retinal ganglion cell axon guidance (GO:1902336)|positive regulation of smooth muscle cell migration (GO:0014911)|protein localization to early endosome (GO:1902946)|regulation of retinal ganglion cell axon guidance (GO:0090259)|regulation of vesicle-mediated transport (GO:0060627)|renal artery morphogenesis (GO:0061441)|response to wounding (GO:0009611)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal ganglion cell axon guidance (GO:0031290)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|sympathetic ganglion development (GO:0061549)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|VEGF-activated neuropilin signaling pathway (GO:0038190)|VEGF-activated neuropilin signaling pathway involved in axon guidance (GO:1902378)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neurofilament (GO:0005883)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|semaphorin receptor complex (GO:0002116)|sorting endosome (GO:0097443)	coreceptor activity (GO:0015026)|cytokine binding (GO:0019955)|growth factor binding (GO:0019838)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)|semaphorin receptor activity (GO:0017154)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(2)	48					Palifermin(DB00039)|Pegaptanib(DB04895)	AAGCGCAGAAGGCCCAAGTCT	0.498																																					p.L332F	Melanoma(104;886 1489 44640 45944 51153)	Atlas-SNP	.											.	NRP1	126	.	0			c.C994T						.						81	69	73					10																	33515205		2203	4300	6503	SO:0001583	missense	8829	exon7			GCAGAAGGCCCAA	AF016050	CCDS7177.1, CCDS31179.1, CCDS31180.1	10p12	2006-02-23			ENSG00000099250	ENSG00000099250		"CD molecules"	8004	protein-coding gene	gene with protein product		602069				9529250, 9331348	Standard	NM_003873		Approved	NRP, VEGF165R, CD304	uc001iwx.4	O14786	OTTHUMG00000019343	ENST00000265371.4:c.994C>T	chr10.hg19:g.33515205G>A	ENSP00000265371:p.Leu332Phe	91.0	0.0		107.0	11.0	NM_001244973	B0LPG9|O60461|Q5T7F1|Q5T7F2|Q5T7F3|Q86T59|Q96I90|Q96IH5	Missense_Mutation	SNP	ENST00000265371.4	hg19	CCDS7177.1	.	.	.	.	.	.	.	.	.	.	G	0.008	-1.896663	0.00522	.	.	ENSG00000099250	ENST00000265371;ENST00000374875;ENST00000374867;ENST00000395995;ENST00000374822;ENST00000374821;ENST00000374823;ENST00000374816;ENST00000432372	D;D;D;D;D;D;D;D;D	0.98178	-4.77;-4.77;-4.77;-4.77;-4.77;-4.77;-4.77;-4.77;-4.77	5.62	1.44	0.22558	Coagulation factor 5/8 C-terminal type domain (4);Galactose-binding domain-like (1);	0.227351	0.44285	D	0.000462	D	0.88566	0.6471	N	0.01048	-1.04	0.41790	D	0.989864	B;B;B;B;P;P;B;B;B	0.43352	0.0;0.004;0.004;0.0;0.766;0.804;0.0;0.0;0.002	B;B;B;B;B;B;B;B;B	0.41917	0.003;0.02;0.009;0.007;0.364;0.37;0.003;0.004;0.003	D	0.87551	0.2465	10	0.02654	T	1	-8.9796	6.1874	0.20506	0.2331:0.1292:0.6377:0.0	.	332;332;332;332;332;332;332;151;332	A8K9V7;E7EX60;Q5T7F0;Q5T7F1;O14786-2;Q68DN3;O14786;Q5JWQ6;E9PEP6	.;.;.;.;.;.;NRP1_HUMAN;.;.	F	332;151;332;332;332;332;332;332;5	ENSP00000265371:L332F;ENSP00000364009:L151F;ENSP00000364001:L332F;ENSP00000379317:L332F;ENSP00000363955:L332F;ENSP00000363954:L332F;ENSP00000363956:L332F;ENSP00000363949:L332F;ENSP00000408911:L5F	ENSP00000265371:L332F	L	-	1	0	NRP1	33555211	0.999000	0.42202	0.928000	0.36995	0.027000	0.11550	1.755000	0.38379	0.248000	0.21435	-0.266000	0.10368	CTT	.	.		0.498	NRP1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051203.2			A	33515205	G	A	33515205	3	1	238	1	0	0	0	0	1	0	0	0	10669	1000	35	3	1832	3	NRP1	10	33515205	Missense_Mutation	SNP	G	TCGA-ED-A4XI-01A-11D-A25V-10		33515205	102019542	65	33192										
ZNF33A	7581	hgsc.bcm.edu	37	chr10	38345268	38345268	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	taaatcggaacttgctcaacAtcagagatcacatacagggg	9	9	3	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr10:38345268A>T	ENST00000458705.2	+	5	2371	c.2213A>T	c.(2212-2214)cAt>cTt	p.H738L	ZNF33A_ENST00000469037.2_Intron|ZNF33A_ENST00000374618.3_Missense_Mutation_p.H739L|ZNF33A_ENST00000307441.9_Missense_Mutation_p.H738L|ZNF33A_ENST00000432900.2_Missense_Mutation_p.H745L			Q06730	ZN33A_HUMAN	zinc finger protein 33A	738					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(2)|large_intestine(8)|liver(2)|lung(27)|ovary(2)|prostate(1)|skin(2)	46						CTTGCTCAACATCAGAGATCA	0.383																																					p.H739L		Atlas-SNP	.											.	ZNF33A	103	.	0			c.A2216T						.						106	102	103					10																	38345268		2203	4300	6503	SO:0001583	missense	7581	exon5			CTCAACATCAGAG	D31763	CCDS31182.1, CCDS60514.1, CCDS73088.1, CCDS73089.1	10p11.2	2013-01-08	2005-03-18		ENSG00000189180	ENSG00000189180		"Zinc fingers, C2H2-type", "-"	13096	protein-coding gene	gene with protein product	"zinc finger and ZAK associated protein with KRAB domain"	194521	"zinc finger protein 33a (KOX 31)", "zinc finger protein 11A"	ZNF33, ZNF11A		2014798, 8464732	Standard	NM_006974		Approved	KOX5, KOX31, KIAA0065, FLJ23404, ZZAPK	uc031pui.1	Q06730	OTTHUMG00000017983	ENST00000458705.2:c.2213A>T	chr10.hg19:g.38345268A>T	ENSP00000387713:p.His738Leu	131.0	0.0		123.0	21.0	NM_006954	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Missense_Mutation	SNP	ENST00000458705.2	hg19	CCDS31182.1	.	.	.	.	.	.	.	.	.	.	A	11.26	1.585753	0.28268	.	.	ENSG00000189180	ENST00000374618;ENST00000432900;ENST00000458705;ENST00000307441	D;D;D;D	0.86865	-2.18;-2.18;-2.18;-2.18	1.92	1.92	0.25849	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.35096	N	0.003450	D	0.93539	0.7938	H	0.95224	3.64	0.31398	N	0.677078	D;D;D	0.69078	0.964;0.971;0.997	P;P;D	0.63597	0.504;0.637;0.916	D	0.90977	0.4824	10	0.87932	D	0	.	7.4341	0.27145	1.0:0.0:0.0:0.0	.	745;738;739	F6TH33;Q06730;F8WAJ5	.;ZN33A_HUMAN;.	L	739;745;738;738	ENSP00000363747:H739L;ENSP00000402467:H745L;ENSP00000387713:H738L;ENSP00000304268:H738L	ENSP00000304268:H738L	H	+	2	0	ZNF33A	38385274	1.000000	0.71417	0.998000	0.56505	0.374000	0.29953	5.998000	0.70653	0.864000	0.35578	0.260000	0.18958	CAT	.	.		0.383	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974		T	38345268	A	T	38345268	3	4	238	1	0	0	0	0	1	0	0	0	17869	217	8	4	2230	4	ZNF33A	10	38345268	Missense_Mutation	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	4830063	38345268	97189479	66	33193										
ZNF485	220992	hgsc.bcm.edu	37	chr10	44112662	44112662	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	gtaagaaatgtgggaaagccTttcggcacagctcaggcctt	12	9	1	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr10:44112662T>C	ENST00000361807.3	+	5	1365	c.1171T>C	c.(1171-1173)Ttt>Ctt	p.F391L	ZNF485_ENST00000374435.3_Missense_Mutation_p.F391L|ZNF485_ENST00000374437.2_Missense_Mutation_p.F300L	NM_145312.3	NP_660355.2	Q8NCK3	ZN485_HUMAN	zinc finger protein 485	391					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	16						TGGGAAAGCCTTTCGGCACAG	0.443																																					p.F391L		Atlas-SNP	.											.	ZNF485	102	.	0			c.T1171C						.						59	58	58					10																	44112662		2203	4300	6503	SO:0001583	missense	220992	exon5			AAAGCCTTTCGGC	AK074679	CCDS7205.2	10q11.21	2013-01-08			ENSG00000198298	ENSG00000198298		"Zinc fingers, C2H2-type", "-"	23440	protein-coding gene	gene with protein product							Standard	NM_145312		Approved		uc010qfc.2	Q8NCK3	OTTHUMG00000018040	ENST00000361807.3:c.1171T>C	chr10.hg19:g.44112662T>C	ENSP00000354694:p.Phe391Leu	91.0	0.0		90.0	7.0	NM_145312	B4DSE6|Q96CL0	Missense_Mutation	SNP	ENST00000361807.3	hg19	CCDS7205.2	.	.	.	.	.	.	.	.	.	.	T	14.97	2.693663	0.48202	.	.	ENSG00000198298	ENST00000361807;ENST00000374437;ENST00000374435	T;T;T	0.46063	0.88;0.88;0.88	1.59	1.59	0.23543	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.63896	0.2550	M	0.87617	2.895	0.32192	N	0.578896	D	0.89917	1.0	D	0.97110	1.0	T	0.67917	-0.5546	9	0.87932	D	0	.	7.233	0.26053	0.0:0.0:0.0:1.0	.	391	Q8NCK3	ZN485_HUMAN	L	391;300;391	ENSP00000354694:F391L;ENSP00000363560:F300L;ENSP00000363558:F391L	ENSP00000354694:F391L	F	+	1	0	ZNF485	43432668	1.000000	0.71417	0.533000	0.28001	0.985000	0.73830	6.169000	0.71913	0.982000	0.38575	0.260000	0.18958	TTT	.	.		0.443	ZNF485-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047719.2	NM_145312		C	44112662	T	C	44112662	3	2	238	1	0	0	0	0	1	0	0	0	17953	1609	56	2	1185	2	ZNF485	10	44112662	Missense_Mutation	SNP	T	TCGA-ED-A4XI-01A-11D-A25V-10	5767394	44112662	91422085	67	33194										
DDX50	79009	hgsc.bcm.edu	37	chr10	70679601	70679601	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	ttcaaagcatttggccatccAgtgtcattggtctcagaggc	10	10	3	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr10:70679601A>T	ENST00000373585.3	+	8	1210	c.1103A>T	c.(1102-1104)cAg>cTg	p.Q368L		NM_024045.1	NP_076950.1	Q9BQ39	DDX50_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 50	368						membrane (GO:0016020)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	29						TTGGCCATCCAGTGTCATTGG	0.358																																					p.Q368L		Atlas-SNP	.											.	DDX50	65	.	0			c.A1103T						.						92	92	92					10																	70679601		2203	4300	6503	SO:0001583	missense	79009	exon8			CCATCCAGTGTCA	AF334103	CCDS7283.1	10q22.2	2010-09-30			ENSG00000107625	ENSG00000107625		"DEAD-boxes"	17906	protein-coding gene	gene with protein product		610373				11891046	Standard	NM_024045		Approved	GU2, MGC3199, GUB, RH-II/GuB	uc001jou.3	Q9BQ39	OTTHUMG00000018362	ENST00000373585.3:c.1103A>T	chr10.hg19:g.70679601A>T	ENSP00000362687:p.Gln368Leu	282.0	0.0		219.0	20.0	NM_024045	Q5VX37|Q8WV76|Q9BWI8	Missense_Mutation	SNP	ENST00000373585.3	hg19	CCDS7283.1	.	.	.	.	.	.	.	.	.	.	A	14.41	2.526230	0.44969	.	.	ENSG00000107625	ENST00000373585;ENST00000541832	T	0.04234	3.67	4.94	4.94	0.65067	.	0.158822	0.53938	D	0.000051	T	0.05502	0.0145	L	0.37850	1.14	0.40437	D	0.98	B	0.26445	0.149	B	0.20955	0.032	T	0.39921	-0.9590	10	0.36615	T	0.2	-5.6776	14.8851	0.70560	1.0:0.0:0.0:0.0	.	368	Q9BQ39	DDX50_HUMAN	L	368	ENSP00000362687:Q368L	ENSP00000362687:Q368L	Q	+	2	0	DDX50	70349607	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.343000	0.59348	1.970000	0.57323	0.397000	0.26171	CAG	.	.		0.358	DDX50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048363.1	NM_024045		T	70679601	A	T	70679601	3	4	238	1	0	0	0	0	1	0	0	0	4370	188	7	4	1133	4	DDX50	10	70679601	Missense_Mutation	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	26566939	70679601	64855146	68	33195										
MINPP1	9562	hgsc.bcm.edu	37	chr10	89312033	89312033	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	cctgatatttgtgctttaccActgtgaaaatgctaagactc	7	9	0	3			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr10:89312033A>G	ENST00000371996.4	+	5	1303	c.1262A>G	c.(1261-1263)cAc>cGc	p.H421R	MINPP1_ENST00000472891.1_3'UTR|MINPP1_ENST00000371994.4_3'UTR|MINPP1_ENST00000536010.1_Missense_Mutation_p.H220R	NM_004897.4	NP_004888.2	Q9UNW1	MINP1_HUMAN	multiple inositol-polyphosphate phosphatase 1	421					bone mineralization (GO:0030282)|dephosphorylation (GO:0016311)|inositol phosphate metabolic process (GO:0043647)|ossification (GO:0001503)|polyphosphate metabolic process (GO:0006797)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	acid phosphatase activity (GO:0003993)|bisphosphoglycerate 3-phosphatase activity (GO:0034417)|inositol hexakisphosphate 2-phosphatase activity (GO:0052826)|phosphohistidine phosphatase activity (GO:0008969)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|urinary_tract(2)	5		Colorectal(252;0.122)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00123)		GTGCTTTACCACTGTGAAAAT	0.383																																					p.H421R		Atlas-SNP	.											.	MINPP1	22	.	0			c.A1262G						.						133	128	130					10																	89312033		2203	4300	6503	SO:0001583	missense	9562	exon5			TTTACCACTGTGA	AF046915	CCDS7384.1, CCDS53551.1, CCDS53552.1	10q23	2010-05-04	2010-05-04		ENSG00000107789	ENSG00000107789	3.1.3.62		7102	protein-coding gene	gene with protein product		605391	"multiple inositol polyphosphate histidine phosphatase, 1"			10087200	Standard	NM_004897		Approved	MIPP	uc001keu.3	Q9UNW1	OTTHUMG00000018678	ENST00000371996.4:c.1262A>G	chr10.hg19:g.89312033A>G	ENSP00000361064:p.His421Arg	196.0	0.0		173.0	7.0	NM_004897	F5H683|O95172|O95286|Q59EJ2|Q9UGA3	Missense_Mutation	SNP	ENST00000371996.4	hg19	CCDS7384.1	.	.	.	.	.	.	.	.	.	.	A	12.26	1.885766	0.33255	.	.	ENSG00000107789	ENST00000371996;ENST00000546140;ENST00000536010	T;T	0.26660	1.72;1.72	6.08	6.08	0.98989	.	0.156143	0.64402	D	0.000016	T	0.15132	0.0365	N	0.16098	0.37	0.44168	D	0.996977	B	0.17852	0.024	B	0.24155	0.051	T	0.19257	-1.0311	10	0.17369	T	0.5	-22.4426	10.1859	0.42998	0.9267:0.0:0.0733:0.0	.	421	Q9UNW1	MINP1_HUMAN	R	421;280;220	ENSP00000361064:H421R;ENSP00000437823:H220R	ENSP00000361064:H421R	H	+	2	0	MINPP1	89302013	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	5.130000	0.64745	2.333000	0.79357	0.482000	0.46254	CAC	.	.		0.383	MINPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049221.1			G	89312033	A	G	89312033	3	3	238	1	0	0	0	0	1	0	0	0	9597	159	6	2	1318	2	MINPP1	10	89312033	Missense_Mutation	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	18632432	89312033	46222714	69	33196										
FGF8	2253	hgsc.bcm.edu	37	chr10	103534534	103534534	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	ggcgttgatgcgcttgttggCcaggacctgcacgtgcttcc	14	12	0	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr10:103534534C>T	ENST00000344255.3	-	4	258	c.259G>A	c.(259-261)Gcc>Acc	p.A87T	FGF8_ENST00000347978.2_Missense_Mutation_p.A69T|FGF8_ENST00000485728.1_5'UTR|FGF8_ENST00000346714.3_Missense_Mutation_p.A58T|FGF8_ENST00000320185.2_Missense_Mutation_p.A98T			P55075	FGF8_HUMAN	fibroblast growth factor 8 (androgen-induced)	87					anatomical structure morphogenesis (GO:0009653)|aorta morphogenesis (GO:0035909)|apoptotic process (GO:0006915)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|cell migration involved in mesendoderm migration (GO:0090134)|cell proliferation in forebrain (GO:0021846)|corticotropin hormone secreting cell differentiation (GO:0060128)|dopaminergic neuron differentiation (GO:0071542)|dorsal/ventral axon guidance (GO:0033563)|embryonic hindlimb morphogenesis (GO:0035116)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain morphogenesis (GO:0048853)|forebrain neuron development (GO:0021884)|gastrulation (GO:0007369)|gonad development (GO:0008406)|heart looping (GO:0001947)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|lung morphogenesis (GO:0060425)|male genitalia development (GO:0030539)|MAPK cascade (GO:0000165)|mesodermal cell migration (GO:0008078)|mesonephros development (GO:0001823)|metanephros development (GO:0001656)|midbrain-hindbrain boundary development (GO:0030917)|motor neuron axon guidance (GO:0008045)|negative regulation of cardiac muscle tissue development (GO:0055026)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate morphogenesis (GO:0001839)|neuroepithelial cell differentiation (GO:0060563)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|organ induction (GO:0001759)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|pallium development (GO:0021543)|patterning of blood vessels (GO:0001569)|pharyngeal system development (GO:0060037)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of mitosis (GO:0045840)|positive regulation of organ growth (GO:0046622)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|response to oxidative stress (GO:0006979)|signal transduction involved in regulation of gene expression (GO:0023019)|subpallium development (GO:0021544)|thyroid gland development (GO:0030878)|thyroid-stimulating hormone-secreting cell differentiation (GO:0060129)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|type 1 fibroblast growth factor receptor binding (GO:0005105)|type 2 fibroblast growth factor receptor binding (GO:0005111)			endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(2)	5		Colorectal(252;0.122)		Epithelial(162;3.94e-09)|all cancers(201;2.13e-07)		CGCTTGTTGGCCAGGACCTGC	0.657																																					p.A98T		Atlas-SNP	.											.	FGF8	23	.	0			c.G292A						.						87	77	80					10																	103534534		2203	4300	6503	SO:0001583	missense	2253	exon4			TGTTGGCCAGGAC	D38752	CCDS7515.1, CCDS7516.1, CCDS7517.1, CCDS7518.1, CCDS73185.1	10q25-q26	2014-01-30			ENSG00000107831	ENSG00000107831		"Endogenous ligands"	3686	protein-coding gene	gene with protein product		600483				8595889	Standard	NM_033164		Approved	AIGF	uc001ktq.2	P55075	OTTHUMG00000018940	ENST00000344255.3:c.259G>A	chr10.hg19:g.103534534C>T	ENSP00000340039:p.Ala87Thr	96.0	0.0		87.0	4.0	NM_033163	A1A514|Q14915|Q15766	Missense_Mutation	SNP	ENST00000344255.3	hg19	CCDS7517.1	.	.	.	.	.	.	.	.	.	.	C	15.60	2.882909	0.51908	.	.	ENSG00000107831	ENST00000344255;ENST00000320185;ENST00000346714;ENST00000347978	D;D;D;D	0.81579	-1.51;-1.51;-1.51;-1.51	4.52	3.62	0.41486	.	0.412269	0.23536	N	0.047134	T	0.68659	0.3025	L	0.28458	0.855	0.37131	D	0.901278	B;B;B;B	0.31625	0.199;0.093;0.332;0.013	B;B;B;B	0.21708	0.025;0.023;0.036;0.012	T	0.72824	-0.4176	10	0.62326	D	0.03	-11.971	12.8014	0.57588	0.0:0.9198:0.0:0.0802	.	58;69;98;87	P55075-2;P55075-3;P55075-4;P55075	.;.;.;FGF8_HUMAN	T	87;98;58;69	ENSP00000340039:A87T;ENSP00000321797:A98T;ENSP00000344306:A58T;ENSP00000321945:A69T	ENSP00000321797:A98T	A	-	1	0	FGF8	103524524	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.802000	0.47916	1.142000	0.42291	0.486000	0.48141	GCC	.	.		0.657	FGF8-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049999.1	NM_006119, NM_033165		T	103534534	C	T	103534534	3	4	238	1	0	0	0	0	1	0	0	0	5866	739	26	3	454	3	FGF8	10	103534534	Missense_Mutation	SNP	C	TCGA-ED-A4XI-01A-11D-A25V-10	14222501	103534534	32000213	70	33197										
CCDC147	159686	hgsc.bcm.edu	37	chr10	106166547	106166547	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	ggttgaaaaagagctgctccTccaggtagcatttttgtttt	10	7	0	2			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr10:106166547T>G	ENST00000369704.3	+	15	2386	c.2252T>G	c.(2251-2253)cTc>cGc	p.L751R		NM_001008723.1	NP_001008723.1	Q5T655	CC147_HUMAN		751						extracellular space (GO:0005615)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	52		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;7.55e-10)|all cancers(201;3.37e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0189)		GAGCTGCTCCTCCAGGTAGCA	0.453																																					p.L751R		Atlas-SNP	.											.	CCDC147	137	.	0			c.T2252G						.						109	109	109					10																	106166547		2203	4300	6503	SO:0001583	missense	159686	exon15			TGCTCCTCCAGGT																												ENST00000369704.3:c.2252T>G	chr10.hg19:g.106166547T>G	ENSP00000358718:p.Leu751Arg	89.0	0.0		121.0	15.0	NM_001008723	D3DRA6|Q8NA27	Missense_Mutation	SNP	ENST00000369704.3	hg19	CCDS31282.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.418241	0.83449	.	.	ENSG00000120051	ENST00000369704	T	0.54675	0.56	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.68357	0.2992	M	0.78637	2.42	0.80722	D	1	D	0.52996	0.957	P	0.55222	0.771	T	0.68614	-0.5362	10	0.39692	T	0.17	-7.9849	16.8061	0.85666	0.0:0.0:0.0:1.0	.	751	Q5T655	CC147_HUMAN	R	751	ENSP00000358718:L751R	ENSP00000358718:L751R	L	+	2	0	CCDC147	106156537	0.993000	0.37304	0.111000	0.21465	0.919000	0.55068	7.394000	0.79862	2.367000	0.80283	0.528000	0.53228	CTC	.	.		0.453	CCDC147-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050216.1			G	106166547	T	G	106166547	3	3	238	1	0	0	0	0	1	0	0	0	2783	1551	54	5	2310	5	CCDC147	10	106166547	Missense_Mutation	SNP	T	TCGA-ED-A4XI-01A-11D-A25V-10	2632013	106166547	29368200	71	33198										
CSRP3	8048	hgsc.bcm.edu	37	chr11	19206570	19206570	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	tcttcccacagatggcacagCggaaacaggtcttgtgccaa	10	12	2	1	rs377066670		TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr11:19206570C>T	ENST00000533783.1	-	6	677	c.437G>A	c.(436-438)cGc>cAc	p.R146H	CSRP3_ENST00000265968.3_Missense_Mutation_p.R146H	NM_003476.4	NP_003467.1	P50461	CSRP3_HUMAN	cysteine and glycine-rich protein 3 (cardiac LIM protein)	146	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue development (GO:0048738)|cardiac myofibril assembly (GO:0055003)|cellular calcium ion homeostasis (GO:0006874)|detection of muscle stretch (GO:0035995)|protein localization to organelle (GO:0033365)|regulation of the force of heart contraction (GO:0002026)|skeletal muscle tissue development (GO:0007519)	cytoskeleton (GO:0005856)|nucleus (GO:0005634)|Z disc (GO:0030018)	actinin binding (GO:0042805)|structural constituent of muscle (GO:0008307)|telethonin binding (GO:0031433)|zinc ion binding (GO:0008270)			kidney(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(2)	10						GATGGCACAGCGGAAACAGGT	0.458																																					p.R146H		Atlas-SNP	.											CSRP3,NS,malignant_melanoma,0,1	CSRP3	24	.	0			c.G437A						.	C	HIS/ARG,HIS/ARG	0,4398		0,0,2199	100	89	93		437,437	5.4	1	11		93	1,8585	1.2+/-3.3	0,1,4292	no	missense,missense	CSRP3	NM_001127656.1,NM_003476.3	29,29	0,1,6491	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	146/195,146/195	19206570	1,12983	2199	4293	6492	SO:0001583	missense	8048	exon6			GCACAGCGGAAAC	U20324	CCDS7848.1	11p15.1	2014-09-17				ENSG00000129170			2472	protein-coding gene	gene with protein product		600824				7490106	Standard	NM_003476		Approved	CLP, MLP, CMD1M	uc001mpk.3	P50461		ENST00000533783.1:c.437G>A	chr11.hg19:g.19206570C>T	ENSP00000431813:p.Arg146His	160.0	0.0		152.0	17.0	NM_003476	Q9P131	Missense_Mutation	SNP	ENST00000533783.1	hg19	CCDS7848.1	.	.	.	.	.	.	.	.	.	.	C	33	5.246411	0.95305	0.0	1.16E-4	ENSG00000129170	ENST00000265968;ENST00000533783	D;D	0.91295	-2.82;-2.82	5.41	5.41	0.78517	Zinc finger, LIM-type (5);	0.000000	0.85682	D	0.000000	D	0.95430	0.8516	M	0.83384	2.64	0.80722	D	1	D	0.62365	0.991	D	0.64506	0.926	D	0.95733	0.8776	10	0.72032	D	0.01	-7.824	18.7893	0.91966	0.0:1.0:0.0:0.0	.	146	P50461	CSRP3_HUMAN	H	146	ENSP00000265968:R146H;ENSP00000431813:R146H	ENSP00000265968:R146H	R	-	2	0	CSRP3	19163146	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.794000	0.85869	2.552000	0.86080	0.655000	0.94253	CGC	.	.		0.458	CSRP3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394484.1	NM_003476		T	19206570	C	T	19206570	3	4	238	1	0	0	0	0	1	0	0	0	3971	768	27	1	155	1	CSRP3	11	19206570	Missense_Mutation	SNP	C	TCGA-ED-A4XI-01A-11D-A25V-10		19206570	115799946	72	33199										
NELL1	4745	hgsc.bcm.edu	37	chr11	20805310	20805310	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	caagagtgaattcaccatttTggccactgtacagcagaagc	9	10	1	3			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr11:20805310T>C	ENST00000357134.5	+	3	421	c.269T>C	c.(268-270)tTg>tCg	p.L90S	NELL1_ENST00000532434.1_Missense_Mutation_p.L90S|NELL1_ENST00000325319.5_Missense_Mutation_p.L90S|NELL1_ENST00000298925.5_Missense_Mutation_p.L118S	NM_006157.3|NM_201551.1	NP_006148.2|NP_963845.1	Q92832	NELL1_HUMAN	NEL-like 1 (chicken)	90	Laminin G-like.				cell differentiation (GO:0030154)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of osteoblast proliferation (GO:0033689)|nervous system development (GO:0007399)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of gene expression (GO:0010468)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(5)|kidney(3)|large_intestine(15)|lung(36)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	70						TTCACCATTTTGGCCACTGTA	0.433																																					p.L90S		Atlas-SNP	.											.	NELL1	179	.	0			c.T269C						.						116	105	109					11																	20805310		2203	4300	6503	SO:0001583	missense	4745	exon3			CCATTTTGGCCAC	AK127805	CCDS7855.1, CCDS44555.1, CCDS73267.1, CCDS73268.1	11p15.1	2008-02-01	2001-11-28		ENSG00000165973	ENSG00000165973			7750	protein-coding gene	gene with protein product		602319	"nel (chicken)-like 1"			8975702	Standard	NM_006157		Approved	IDH3GL, FLJ45906	uc001mqe.3	Q92832	OTTHUMG00000166042	ENST00000357134.5:c.269T>C	chr11.hg19:g.20805310T>C	ENSP00000349654:p.Leu90Ser	115.0	0.0		92.0	19.0	NM_006157	B2CKC1|Q4VB90|Q4VB91|Q6NSY8|Q9Y472	Missense_Mutation	SNP	ENST00000357134.5	hg19	CCDS7855.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.403579	0.83230	.	.	ENSG00000165973	ENST00000298925;ENST00000357134;ENST00000325319;ENST00000532434	T;T;T;T	0.02085	4.46;4.46;4.46;4.46	5.9	5.9	0.94986	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);Laminin G, thrombospondin-type, N-terminal (1);	0.174039	0.38959	N	0.001506	T	0.09069	0.0224	L	0.60845	1.875	0.42578	D	0.993207	D;P;D;P	0.55800	0.973;0.954;0.958;0.883	P;P;P;B	0.59546	0.859;0.726;0.844;0.399	T	0.03068	-1.1076	10	0.49607	T	0.09	-0.7057	16.315	0.82915	0.0:0.0:0.0:1.0	.	90;118;90;90	F5H6I3;B3KXR2;Q92832-2;Q92832	.;.;.;NELL1_HUMAN	S	118;90;90;90	ENSP00000298925:L118S;ENSP00000349654:L90S;ENSP00000317837:L90S;ENSP00000437170:L90S	ENSP00000298925:L118S	L	+	2	0	NELL1	20761886	1.000000	0.71417	0.954000	0.39281	0.825000	0.46686	7.780000	0.85658	2.250000	0.74265	0.533000	0.62120	TTG	.	.		0.433	NELL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387588.1	NM_006157		C	20805310	T	C	20805310	3	2	238	1	0	0	0	0	1	0	0	0	10342	1821	63	2	279	2	NELL1	11	20805310	Missense_Mutation	SNP	T	TCGA-ED-A4XI-01A-11D-A25V-10	1598740	20805310	114201206	73	33200										
PRR5L	79899	hgsc.bcm.edu	37	chr11	36459019	36459019	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	cctgcaggcaatattttatcCagttcaggttagtctcattg	8	9	2	0			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr11:36459019C>A	ENST00000378867.3	+	7	792	c.437C>A	c.(436-438)cCa>cAa	p.P146Q	PRR5L_ENST00000389693.3_3'UTR|PRR5L_ENST00000530639.1_Missense_Mutation_p.P146Q|PRR5L_ENST00000311599.5_Missense_Mutation_p.P120Q|PRR5L_ENST00000527487.1_Missense_Mutation_p.P146Q	NM_024841.4	NP_079117.3	Q6MZQ0	PRR5L_HUMAN	proline rich 5 like	146					negative regulation of protein phosphorylation (GO:0001933)|negative regulation of signal transduction (GO:0009968)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|regulation of fibroblast migration (GO:0010762)|TORC2 signaling (GO:0038203)	mitochondrion (GO:0005739)|TORC2 complex (GO:0031932)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(7)|ovary(1)	19						ATATTTTATCCAGTTCAGGTT	0.522																																					p.P146Q		Atlas-SNP	.											.	PRR5L	35	.	0			c.C437A						.						194	166	175					11																	36459019		2202	4298	6500	SO:0001583	missense	79899	exon7			TTTATCCAGTTCA		CCDS31463.1, CCDS53617.1	11p13-p12	2009-07-09				ENSG00000135362			25878	protein-coding gene	gene with protein product	"protein observed with Rictor-2"	611728				17461779	Standard	NM_024841		Approved	FLJ14213, PROTOR-2	uc001mwp.3	Q6MZQ0		ENST00000378867.3:c.437C>A	chr11.hg19:g.36459019C>A	ENSP00000368144:p.Pro146Gln	114.0	0.0		124.0	5.0	NM_024841	A4QN22|E9PKY1|Q96H46|Q9H7V4	Missense_Mutation	SNP	ENST00000378867.3	hg19	CCDS31463.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.818956	0.90873	.	.	ENSG00000135362	ENST00000530639;ENST00000311599;ENST00000378867;ENST00000527487	T;T;T;T	0.75938	-0.87;1.68;-0.87;-0.98	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	D	0.86611	0.5974	M	0.75777	2.31	0.80722	D	1	D;D;D	0.89917	0.981;1.0;0.966	P;D;P	0.91635	0.883;0.999;0.883	D	0.87662	0.2535	10	0.87932	D	0	-29.8435	19.0681	0.93122	0.0:1.0:0.0:0.0	.	146;65;146	E9PKY1;Q6MZQ0-3;Q6MZQ0	.;.;PRR5L_HUMAN	Q	146;120;146;146	ENSP00000435050:P146Q;ENSP00000310103:P120Q;ENSP00000368144:P146Q;ENSP00000435241:P146Q	ENSP00000310103:P120Q	P	+	2	0	PRR5L	36415595	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.260000	0.72502	2.659000	0.90383	0.655000	0.94253	CCA	.	.		0.522	PRR5L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389209.1	NM_024841		A	36459019	C	A	36459019	3	1	238	1	0	0	0	0	1	0	0	0	12614	594	21	3	461	3	PRR5L	11	36459019	Missense_Mutation	SNP	C	TCGA-ED-A4XI-01A-11D-A25V-10	15653709	36459019	98547497	74	33201										
RNF169	254225	hgsc.bcm.edu	37	chr11	74546763	74546763	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	ttctgtcagccctgagagcaAtgacagcatctccgaagaac	9	12	3	3			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr11:74546763A>G	ENST00000299563.4	+	6	1128	c.1115A>G	c.(1114-1116)aAt>aGt	p.N372S		NM_001098638.1	NP_001092108.1	Q8NCN4	RN169_HUMAN	ring finger protein 169	372					cellular response to DNA damage stimulus (GO:0006974)|negative regulation of double-strand break repair (GO:2000780)|protein ubiquitination (GO:0016567)	intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|site of double-strand break (GO:0035861)	K63-linked polyubiquitin binding (GO:0070530)|ligase activity (GO:0016874)|nucleosome binding (GO:0031491)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|urinary_tract(1)	15						CCTGAGAGCAATGACAGCATC	0.527																																					p.N372S		Atlas-SNP	.											.	RNF169	36	.	0			c.A1115G						.						156	161	160					11																	74546763		2064	4204	6268	SO:0001583	missense	254225	exon6			AGAGCAATGACAG	AB082522	CCDS41691.1	11q13.4	2008-02-05			ENSG00000166439	ENSG00000166439		"RING-type (C3HC4) zinc fingers"	26961	protein-coding gene	gene with protein product						12056414	Standard	NM_001098638		Approved	KIAA1991	uc001ovl.4	Q8NCN4	OTTHUMG00000165516	ENST00000299563.4:c.1115A>G	chr11.hg19:g.74546763A>G	ENSP00000299563:p.Asn372Ser	183.0	0.0		155.0	12.0	NM_001098638	Q6N015	Missense_Mutation	SNP	ENST00000299563.4	hg19	CCDS41691.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.218294	0.79464	.	.	ENSG00000166439	ENST00000299563	T	0.52295	0.67	6.05	6.05	0.98169	.	0.000000	0.85682	D	0.000000	T	0.69369	0.3103	M	0.78637	2.42	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.73088	-0.4093	10	0.72032	D	0.01	-30.6562	14.5452	0.68024	1.0:0.0:0.0:0.0	.	372	Q8NCN4	RN169_HUMAN	S	372	ENSP00000299563:N372S	ENSP00000299563:N372S	N	+	2	0	RNF169	74224411	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.730000	0.91510	2.320000	0.78422	0.528000	0.53228	AAT	.	.		0.527	RNF169-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384741.1	XM_495886		G	74546763	A	G	74546763	3	3	238	1	0	0	0	0	1	0	0	0	13475	101	4	2	1137	2	RNF169	11	74546763	Missense_Mutation	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	38087744	74546763	60459753	75	33202										
TAF1D	79101	hgsc.bcm.edu	37	chr11	93472409	93472409	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	ttgaatccactcaccttcgaTttgcaagttccacagcatca	5	13	2	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr11:93472409T>C	ENST00000448108.2	-	2	712	c.62A>G	c.(61-63)aAt>aGt	p.N21S	C11orf54_ENST00000540113.1_5'Flank|C11orf54_ENST00000331239.4_5'Flank|C11orf54_ENST00000528099.1_5'Flank|C11orf54_ENST00000528288.1_5'Flank|C11orf54_ENST00000354421.3_5'Flank	NM_024116.3	NP_077021.1	Q9H5J8	TAF1D_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, D, 41kDa	21					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	microtubule organizing center (GO:0005815)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			large_intestine(1)|lung(3)|prostate(1)|skin(2)	7						TCACCTTCGATTTGCAAGTTC	0.318																																					p.N21S		Atlas-SNP	.											.	TAF1D	18	.	0			c.A62G						.						153	142	146					11																	93472409		2201	4298	6499	SO:0001583	missense	79101	exon2			CTTCGATTTGCAA		CCDS8293.1	11q21	2012-05-30	2008-09-30	2008-09-30	ENSG00000166012	ENSG00000166012			28759	protein-coding gene	gene with protein product		612823	"Josephin domain containing 3"	JOSD3		15520167, 17318177	Standard	NM_024116		Approved	MGC5306, TAF(I)41	uc001pec.3	Q9H5J8	OTTHUMG00000167451	ENST00000448108.2:c.62A>G	chr11.hg19:g.93472409T>C	ENSP00000410409:p.Asn21Ser	73.0	0.0		80.0	15.0	NM_024116	Q6I9Y6	Missense_Mutation	SNP	ENST00000448108.2	hg19	CCDS8293.1	.	.	.	.	.	.	.	.	.	.	T	9.351	1.065427	0.20067	.	.	ENSG00000166012	ENST00000448108	.	.	.	3.22	2.08	0.27032	.	0.308799	0.22698	N	0.056729	T	0.20700	0.0498	L	0.27053	0.805	0.21355	N	0.999713	P	0.37500	0.597	B	0.37047	0.24	T	0.08006	-1.0743	9	0.27785	T	0.31	-22.3659	5.1205	0.14858	0.0:0.1378:0.0:0.8622	.	21	Q9H5J8	TAF1D_HUMAN	S	21	.	ENSP00000314971:N21S	N	-	2	0	TAF1D	93112057	0.330000	0.24705	0.544000	0.28141	0.226000	0.24999	0.230000	0.17852	0.617000	0.30160	0.533000	0.62120	AAT	.	.		0.318	TAF1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394662.2	NM_024116		C	93472409	T	C	93472409	3	2	238	1	0	0	0	0	1	0	0	0	15537	1493	52	2	794	2	TAF1D	11	93472409	Missense_Mutation	SNP	T	TCGA-ED-A4XI-01A-11D-A25V-10	18925646	93472409	41534107	76	33203										
SIAE	54414	hgsc.bcm.edu	37	chr11	124517357	124517357	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	atgagtgcagggaatgtgcaAttgtacagatccgtgttata	12	5	0	2			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr11:124517357A>G	ENST00000263593.3	-	7	1042	c.870T>C	c.(868-870)aaT>aaC	p.N290N	SIAE_ENST00000545756.1_Silent_p.N255N			Q9HAT2	SIAE_HUMAN	sialic acid acetylesterase	290					carbohydrate metabolic process (GO:0005975)|regulation of immune system process (GO:0002682)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	sialate O-acetylesterase activity (GO:0001681)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(2)	15	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.63e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0243)		GGAATGTGCAATTGTACAGAT	0.458																																					p.N290N		Atlas-SNP	.											.	SIAE	37	.	0			c.T870C						.						139	124	129					11																	124517357		2201	4299	6500	SO:0001819	synonymous_variant	54414	exon7			TGTGCAATTGTAC	AF300796	CCDS8449.1, CCDS55795.1	11q24	2005-12-15	2005-12-15	2005-12-15		ENSG00000110013			18187	protein-coding gene	gene with protein product	"sialic acid-specific acetylesterase II"	610079	"Ysg2 homolog (mouse)"	YSG2		10464298	Standard	NM_001199922		Approved	CSE-C, MGC87009, LSE	uc001qan.3	Q9HAT2		ENST00000263593.3:c.870T>C	chr11.hg19:g.124517357A>G		100.0	0.0		116.0	17.0	NM_170601	B3KPB0|Q8IUT9|Q9HAU7|Q9NT71	Silent	SNP	ENST00000263593.3	hg19	CCDS8449.1																																																																																			.	.		0.458	SIAE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387070.1	NM_170601		G	124517357	A	G	124517357	2	3	238	1	0	0	0	0	0	0	0	1	14313	98	4	2		2	SIAE	11	124517357	Silent	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	31044948	124517357	10489159	77	33204										
IGSF9B	22997	hgsc.bcm.edu	37	chr11	133799610	133799610	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	cctccatcatagcctggttcCcaggacacgttggcagttgt	10	13	1	0			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr11:133799610C>T	ENST00000321016.8	-	12	1817	c.1587G>A	c.(1585-1587)tgG>tgA	p.W529*	IGSF9B_ENST00000533871.2_Nonsense_Mutation_p.W529*			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	529	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		AGCCTGGTTCCCAGGACACGT	0.592																																					p.W529X		Atlas-SNP	.											.	IGSF9B	290	.	0			c.G1587A						.						126	140	135					11																	133799610		2086	4200	6286	SO:0001587	stop_gained	22997	exon12			TGGTTCCCAGGAC	AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.1587G>A	chr11.hg19:g.133799610C>T	ENSP00000317980:p.Trp529*	154.0	0.0		133.0	14.0	NM_014987	G5EA26	Nonsense_Mutation	SNP	ENST00000321016.8	hg19		.	.	.	.	.	.	.	.	.	.	C	41	9.129628	0.99075	.	.	ENSG00000080854	ENST00000321016;ENST00000533871;ENST00000527648	.	.	.	5.37	5.37	0.77165	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.1228	0.93371	0.0:1.0:0.0:0.0	.	.	.	.	X	529;371;529	.	ENSP00000317980:W529X	W	-	3	0	IGSF9B	133304820	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.757000	0.85209	2.505000	0.84491	0.655000	0.94253	TGG	.	.		0.592	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502		T	133799610	C	T	133799610	4	4	238	1	0	0	0	0	0	1	0	0	7615	624	22	3	2494	3	IGSF9B	11	133799610	Nonsense_Mutation	SNP	C	TCGA-ED-A4XI-01A-11D-A25V-10	9282253	133799610	1206906	78	33205										
IQSEC3	440073	hgsc.bcm.edu	37	chr12	266301	266301	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	tcagaaggtggagcggctcaTtgaggccttcaggtaaggcc	15	9	3	2			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr12:266301T>C	ENST00000538872.1	+	6	2382	c.2264T>C	c.(2263-2265)aTt>aCt	p.I755T	IQSEC3_ENST00000326261.4_Missense_Mutation_p.I755T|IQSEC3_ENST00000382841.2_Missense_Mutation_p.I452T			Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3	755	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)		GAGCGGCTCATTGAGGCCTTC	0.637																																					p.I755T		Atlas-SNP	.											.	IQSEC3	154	.	0			c.T2264C						.						36	34	35					12																	266301		2201	4299	6500	SO:0001583	missense	440073	exon6			GGCTCATTGAGGC	AB029033	CCDS31725.1, CCDS53728.1	12p13.33	2014-03-18			ENSG00000120645	ENSG00000120645			29193	protein-coding gene	gene with protein product		612118				10470851	Standard	NM_001170738		Approved	KIAA1110, MGC30156	uc001qhw.2	Q9UPP2	OTTHUMG00000167975	ENST00000538872.1:c.2264T>C	chr12.hg19:g.266301T>C	ENSP00000437554:p.Ile755Thr	385.0	0.0		315.0	45.0	NM_001170738	A6NIF2|A6NKV9|Q8TB43	Missense_Mutation	SNP	ENST00000538872.1	hg19	CCDS53728.1	.	.	.	.	.	.	.	.	.	.	T	15.84	2.952702	0.53293	.	.	ENSG00000120645	ENST00000538872;ENST00000326261;ENST00000382841	T;T;T	0.78481	-1.18;-1.18;-1.18	3.86	3.86	0.44501	SEC7-like, alpha orthogonal bundle (1);SEC7-like (4);	0.048933	0.85682	D	0.000000	T	0.82015	0.4945	L	0.47016	1.485	0.80722	D	1	D;P	0.56521	0.976;0.928	P;P	0.61940	0.896;0.839	D	0.84001	0.0343	10	0.87932	D	0	.	12.955	0.58421	0.0:0.0:0.0:1.0	.	755;452	Q9UPP2;Q9UPP2-2	IQEC3_HUMAN;.	T	755;755;452	ENSP00000437554:I755T;ENSP00000315662:I755T;ENSP00000372292:I452T	ENSP00000315662:I755T	I	+	2	0	IQSEC3	136562	1.000000	0.71417	0.994000	0.49952	0.230000	0.25150	7.888000	0.87302	1.536000	0.49237	0.260000	0.18958	ATT	.	.		0.637	IQSEC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397382.3	XM_495902		C	266301	T	C	266301	3	2	238	1	0	0	0	0	1	0	0	0	7828	1493	52	2	2286	2	IQSEC3	12	266301	Missense_Mutation	SNP	T	TCGA-ED-A4XI-01A-11D-A25V-10		266301	133585594	79	33206										
CACNA1C	775	hgsc.bcm.edu	37	chr12	2614096	2614096	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	ttttgtacttaacttggttcTcggtgtgcttagcgggtaag	12	6	1	0			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr12:2614096T>C	ENST00000347598.4	+	8	1202	c.1202T>C	c.(1201-1203)cTc>cCc	p.L401P	CACNA1C_ENST00000480911.1_Missense_Mutation_p.L401P|CACNA1C_ENST00000399591.1_Missense_Mutation_p.L401P|CACNA1C_ENST00000399638.1_Missense_Mutation_p.L401P|CACNA1C_ENST00000399641.1_Intron|CACNA1C_ENST00000399637.1_Missense_Mutation_p.L401P|CACNA1C_ENST00000399601.1_Missense_Mutation_p.L401P|CACNA1C_ENST00000399597.1_Missense_Mutation_p.L401P|CACNA1C_ENST00000399629.1_Missense_Mutation_p.L401P|CACNA1C_ENST00000335762.5_Missense_Mutation_p.L401P|CACNA1C_ENST00000402845.3_Missense_Mutation_p.L401P|CACNA1C_ENST00000399617.1_Intron|CACNA1C_ENST00000399603.1_Intron|CACNA1C_ENST00000399634.1_Intron|CACNA1C_ENST00000327702.7_Missense_Mutation_p.L401P|CACNA1C_ENST00000399649.1_Missense_Mutation_p.L401P|CACNA1C_ENST00000399595.1_Missense_Mutation_p.L401P|CACNA1C_ENST00000399644.1_Missense_Mutation_p.L401P|CACNA1C_ENST00000399606.1_Missense_Mutation_p.L401P|CACNA1C_ENST00000344100.3_Missense_Mutation_p.L401P|CACNA1C_ENST00000399655.1_Missense_Mutation_p.L401P|CACNA1C_ENST00000491104.1_Intron|CACNA1C_ENST00000399621.1_Missense_Mutation_p.L401P|CACNA1C_ENST00000406454.3_Intron	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	401					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	AACTTGGTTCTCGGTGTGCTT	0.398																																					p.L401P		Atlas-SNP	.											.	CACNA1C	1023	.	0			c.T1202C						.						109	102	104					12																	2614096		1884	4133	6017	SO:0001583	missense	775	exon8			TGGTTCTCGGTGT	AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.1202T>C	chr12.hg19:g.2614096T>C	ENSP00000266376:p.Leu401Pro	176.0	0.0		156.0	17.0	NM_001129831	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Missense_Mutation	SNP	ENST00000347598.4	hg19	CCDS44788.1	.	.	.	.	.	.	.	.	.	.	T	19.06	3.753376	0.69648	.	.	ENSG00000151067	ENST00000335762;ENST00000399655;ENST00000480911;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399595	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.98926	-5.24;-5.24;-5.24;-5.24;-5.24;-5.24;-5.24;-5.24;-5.24;-5.24;-5.24;-5.24;-5.24;-5.24;-5.24;-5.24;-5.24;-5.24	5.27	5.27	0.74061	Ion transport (1);	.	.	.	.	D	0.99441	0.9802	H	0.96633	3.855	0.80722	D	1	D;D;D;D;D;D;D;B;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;0.987;0.999;1.0;1.0;1.0;0.3;1.0;1.0;0.999;0.994;1.0;0.994;0.999;1.0;1.0;0.999;1.0	D;D;P;D;D;D;D;P;D;D;D;P;D;P;D;D;D;D;D	0.97110	0.998;0.999;0.859;0.998;0.999;0.999;0.999;0.673;1.0;0.999;0.999;0.843;0.999;0.843;0.996;0.999;0.999;0.996;0.999	D	0.98310	1.0523	9	0.87932	D	0	.	15.3726	0.74577	0.0:0.0:0.0:1.0	.	401;398;401;401;401;401;401;401;401;401;401;401;401;401;401;401;401;401;401	Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-11;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;Q13936-12	.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	P	401	ENSP00000336982:L401P;ENSP00000382563:L401P;ENSP00000437936:L401P;ENSP00000382552:L401P;ENSP00000382547:L401P;ENSP00000382506:L401P;ENSP00000382530:L401P;ENSP00000382546:L401P;ENSP00000382500:L401P;ENSP00000266376:L401P;ENSP00000382515:L401P;ENSP00000382510:L401P;ENSP00000341092:L401P;ENSP00000382537:L401P;ENSP00000329877:L401P;ENSP00000382557:L401P;ENSP00000385724:L401P;ENSP00000382504:L401P	ENSP00000329877:L401P	L	+	2	0	CACNA1C	2484357	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.868000	0.87116	2.209000	0.71365	0.533000	0.62120	CTC	.	.		0.398	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719		C	2614096	T	C	2614096	3	2	238	1	0	0	0	0	1	0	0	0	2542	1551	54	2	1340	2	CACNA1C	12	2614096	Missense_Mutation	SNP	T	TCGA-ED-A4XI-01A-11D-A25V-10	2347795	2614096	131237799	80	33207										
AKAP3	10566	hgsc.bcm.edu	37	chr12	4737905	4737905	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	gaaccgaacatcttggaactCtgctgtactcttctccaggt	8	12	4	0			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr12:4737905C>T	ENST00000545990.2	-	5	687	c.163G>A	c.(163-165)Gag>Aag	p.E55K	AKAP3_ENST00000228850.1_Missense_Mutation_p.E55K|RP11-500M8.7_ENST00000536588.1_Intron	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	55					acrosome reaction (GO:0007340)|cellular component movement (GO:0006928)|protein localization (GO:0008104)|single fertilization (GO:0007338)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	acrosomal vesicle (GO:0001669)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	protein kinase A binding (GO:0051018)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						TCTTGGAACTCTGCTGTACTC	0.478																																					p.E55K		Atlas-SNP	.											.	AKAP3	212	.	0			c.G163A						.						69	61	64					12																	4737905		2203	4300	6503	SO:0001583	missense	10566	exon4			GGAACTCTGCTGT	U85715	CCDS8531.1	12p13.3	2009-03-12				ENSG00000111254		"A-kinase anchor proteins"	373	protein-coding gene	gene with protein product	"Fibrous Sheath Protein of 95 kDa", "cancer/testis antigen 82"	604689				10334916, 10319321	Standard	NM_001278309		Approved	FSP95, SOB1, AKAP110, CT82	uc001qnb.4	O75969		ENST00000545990.2:c.163G>A	chr12.hg19:g.4737905C>T	ENSP00000440994:p.Glu55Lys	191.0	0.0		181.0	37.0	NM_006422	O75945|Q86X01|Q9UM61	Missense_Mutation	SNP	ENST00000545990.2	hg19	CCDS8531.1	.	.	.	.	.	.	.	.	.	.	C	18.58	3.655085	0.67472	.	.	ENSG00000111254	ENST00000228850;ENST00000545990;ENST00000540967;ENST00000536414	T;T;T;T	0.30981	1.51;1.51;1.51;1.51	4.78	4.78	0.61160	.	0.430236	0.22055	N	0.065249	T	0.18882	0.0453	N	0.08118	0	0.27525	N	0.951278	B	0.30482	0.281	B	0.30029	0.11	T	0.22836	-1.0205	10	0.72032	D	0.01	-5.2182	15.174	0.72896	0.0:1.0:0.0:0.0	.	55	O75969	AKAP3_HUMAN	K	55	ENSP00000228850:E55K;ENSP00000440994:E55K;ENSP00000442376:E55K;ENSP00000439382:E55K	ENSP00000228850:E55K	E	-	1	0	AKAP3	4608166	0.900000	0.30661	0.885000	0.34714	0.893000	0.52053	2.616000	0.46376	2.631000	0.89168	0.655000	0.94253	GAG	.	.		0.478	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	NM_006422		T	4737905	C	T	4737905	3	4	238	1	0	0	0	0	1	0	0	0	452	922	32	3	2406	3	AKAP3	12	4737905	Missense_Mutation	SNP	C	TCGA-ED-A4XI-01A-11D-A25V-10	2123809	4737905	129113990	81	33208										
LEMD3	23592	hgsc.bcm.edu	37	chr12	65633985	65633985	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	accttacatgcctattccacAtgtacgcgattccttaatac	4	13	0	0			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr12:65633985A>G	ENST00000308330.2	+	8	2119	c.2093A>G	c.(2092-2094)cAt>cGt	p.H698R		NM_001167614.1|NM_014319.4	NP_001161086.1|NP_055134.2	Q9Y2U8	MAN1_HUMAN	LEM domain containing 3	698					negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of cell cycle (GO:0051726)|skeletal muscle cell differentiation (GO:0035914)	integral component of membrane (GO:0016021)|integral component of nuclear inner membrane (GO:0005639)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	36			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0104)		CCTATTCCACATGTACGCGAT	0.323																																					p.H698R		Atlas-SNP	.											.	LEMD3	68	.	0			c.A2093G						.						135	128	131					12																	65633985		2203	4300	6503	SO:0001583	missense	23592	exon8			TTCCACATGTACG	AF263918	CCDS8972.1	12q14	2008-02-05			ENSG00000174106	ENSG00000174106			28887	protein-coding gene	gene with protein product		607844				10671519, 15489854	Standard	NM_014319		Approved	MAN1	uc001ssl.2	Q9Y2U8	OTTHUMG00000168840	ENST00000308330.2:c.2093A>G	chr12.hg19:g.65633985A>G	ENSP00000308369:p.His698Arg	113.0	0.0		131.0	8.0	NM_014319	Q9NT47|Q9NYA5	Missense_Mutation	SNP	ENST00000308330.2	hg19	CCDS8972.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.117937	0.77323	.	.	ENSG00000174106	ENST00000308330	T	0.57752	0.38	5.03	5.03	0.67393	Inner nuclear membrane protein MAN1 (1);	0.000000	0.85682	D	0.000000	T	0.70386	0.3218	M	0.71581	2.175	0.80722	D	1	D	0.58268	0.982	D	0.70227	0.968	T	0.71560	-0.4556	9	.	.	.	-14.0796	15.4702	0.75434	1.0:0.0:0.0:0.0	.	698	Q9Y2U8	MAN1_HUMAN	R	698	ENSP00000308369:H698R	.	H	+	2	0	LEMD3	63920252	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	8.440000	0.90311	2.185000	0.69588	0.482000	0.46254	CAT	.	.		0.323	LEMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401312.2			G	65633985	A	G	65633985	3	3	238	1	0	0	0	0	1	0	0	0	8730	217	8	2	2123	2	LEMD3	12	65633985	Missense_Mutation	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	60896080	65633985	68217910	82	33209										
C12orf64	283310	hgsc.bcm.edu	37	chr12	80746178	80746178	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	tgtggctctgtgcaacaagtTtgatatctgtattcagtgga	11	6	3	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr12:80746178T>A	ENST00000547103.1	+	44	5312	c.5306T>A	c.(5305-5307)tTt>tAt	p.F1769Y	OTOGL_ENST00000458043.2_Missense_Mutation_p.F1781Y			Q3ZCN5	OTOGL_HUMAN	otogelin-like	1769					L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						TGCAACAAGTTTGATATCTGT	0.348																																					p.F1781Y		Atlas-SNP	.											.	OTOGL	235	.	0			c.T5342A						.						127	118	121					12																	80746178		1886	4113	5999	SO:0001583	missense	283310	exon44			ACAAGTTTGATAT	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"chromosome 12 open reading frame 64"	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.5306T>A	chr12.hg19:g.80746178T>A	ENSP00000447211:p.Phe1769Tyr	80.0	0.0		96.0	8.0	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.53|16.53	3.148777|3.148777	0.57151|0.57151	.|.	.|.	ENSG00000165899|ENSG00000165899	ENST00000547103;ENST00000458043|ENST00000298820	D;D|.	0.86030|.	-2.06;-2.06|.	6.04|6.04	4.86|4.86	0.63082|0.63082	.|.	.|.	.|.	.|.	.|.	T|T	0.39655|0.39655	0.1086|0.1086	L|L	0.41492|0.41492	1.28|1.28	0.28928|0.28928	N|N	0.891723|0.891723	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.29852|0.29852	-0.9998|-0.9998	7|5	0.02654|.	T|.	1|.	.|.	8.8769|8.8769	0.35352|0.35352	0.3644:0.0:0.0:0.6356|0.3644:0.0:0.0:0.6356	.|.	.|.	.|.	.|.	Y|M	1769;1781|224	ENSP00000447211:F1769Y;ENSP00000400895:F1781Y|.	ENSP00000400895:F1781Y|.	F|L	+|+	2|1	0|2	OTOGL|OTOGL	79270309|79270309	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.793000|0.793000	0.44817|0.44817	4.240000|4.240000	0.58701|0.58701	2.317000|2.317000	0.78254|0.78254	0.460000|0.460000	0.39030|0.39030	TTT|TTG	.	.		0.348	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591		A	80746178	T	A	80746178	3	1	238	1	0	0	0	0	1	0	0	0	1709	1841	64	4	5516	4	C12orf64	12	80746178	Missense_Mutation	SNP	T	TCGA-ED-A4XI-01A-11D-A25V-10	15112193	80746178	53105717	83	33210										
COX6A1	1337	hgsc.bcm.edu	37	chr12	120878337	120878337	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	ccaactggctacgaagatgaAtaaagagaatctggaccact	9	9	1	3			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr12:120878337A>G	ENST00000229379.2	+	3	364	c.327A>G	c.(325-327)gaA>gaG	p.E109E	AL021546.6_ENST00000551806.1_Intron	NM_004373.3	NP_004364.2	P12074	CX6A1_HUMAN	cytochrome c oxidase subunit VIa polypeptide 1	109					cellular metabolic process (GO:0044237)|generation of precursor metabolites and energy (GO:0006091)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex IV (GO:0005751)	cytochrome-c oxidase activity (GO:0004129)					all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					ACGAAGATGAATAAAGAGAAT	0.493																																					p.E109E		Atlas-SNP	.											.	COX6A1	5	.	0			c.A327G						.						50	42	45					12																	120878337		2203	4297	6500	SO:0001819	synonymous_variant	1337	exon3			AGATGAATAAAGA	X15341	CCDS9197.1	12q24	2011-07-04			ENSG00000111775	ENSG00000111775	1.9.3.1	"Mitochondrial respiratory chain complex / Complex IV"	2277	protein-coding gene	gene with protein product		602072		COX6A		9284905	Standard	NM_004373		Approved		uc001tyf.2	P12074	OTTHUMG00000047791	ENST00000229379.2:c.327A>G	chr12.hg19:g.120878337A>G		252.0	0.0		221.0	28.0	NM_004373	B2R500|O43714|Q32Q37	Silent	SNP	ENST00000229379.2	hg19	CCDS9197.1																																																																																			.	.		0.493	COX6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108984.3	NM_004373		G	120878337	A	G	120878337	2	3	238	1	0	0	0	0	0	0	0	1	3776	98	4	2		2	COX6A1	12	120878337	Silent	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	40132159	120878337	12973558	84	33211										
PCDH9	5101	hgsc.bcm.edu	37	chr13	67801110	67801110	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	ctgtggcactaatagttgttAagtataacccacgtcggttg	10	8	0	0			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr13:67801110A>T	ENST00000377865.2	-	1	1597	c.1463T>A	c.(1462-1464)tTa>tAa	p.L488*	PCDH9_ENST00000328454.5_Nonsense_Mutation_p.L488*|PCDH9_ENST00000377861.3_Nonsense_Mutation_p.L488*|PCDH9_ENST00000544246.1_Nonsense_Mutation_p.L488*|PCDH9_ENST00000456367.1_Nonsense_Mutation_p.L488*			Q9HC56	PCDH9_HUMAN	protocadherin 9	488	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				forebrain development (GO:0030900)|homophilic cell adhesion (GO:0007156)	cell-cell contact zone (GO:0044291)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(33)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	103		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		AATAGTTGTTAAGTATAACCC	0.418																																					p.L488X		Atlas-SNP	.											.	PCDH9	252	.	0			c.T1463A						.						104	105	105					13																	67801110		2203	4300	6503	SO:0001587	stop_gained	5101	exon2			GTTGTTAAGTATA	AF169692	CCDS9443.1, CCDS9444.1	13q21.32	2010-02-22			ENSG00000184226	ENSG00000184226		"Cadherins / Protocadherins : Non-clustered"	8661	protein-coding gene	gene with protein product		603581				9787079	Standard	NM_020403		Approved		uc001vik.3	Q9HC56	OTTHUMG00000017040	ENST00000377865.2:c.1463T>A	chr13.hg19:g.67801110A>T	ENSP00000367096:p.Leu488*	170.0	0.0		202.0	33.0	NM_203487	A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	Nonsense_Mutation	SNP	ENST00000377865.2	hg19	CCDS9444.1	.	.	.	.	.	.	.	.	.	.	A	35	5.468908	0.96274	.	.	ENSG00000184226	ENST00000544246;ENST00000377865;ENST00000456367;ENST00000328454;ENST00000377861	.	.	.	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.6438	0.85155	1.0:0.0:0.0:0.0	.	.	.	.	X	488	.	ENSP00000332060:L488X	L	-	2	0	PCDH9	66699111	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.333000	0.79357	0.533000	0.62120	TTA	.	.		0.418	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1	NM_203487		T	67801110	A	T	67801110	4	4	238	1	0	0	0	0	0	1	0	0	11527	372	13	4	2266	4	PCDH9	13	67801110	Nonsense_Mutation	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10		67801110	47368768	85	33212										
NALCN	259232	hgsc.bcm.edu	37	chr13	101726938	101726938	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	agcgtaacacagcagcaagaGaaacatgcctactatgataa	8	9	0	2			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr13:101726938G>C	ENST00000251127.6	-	36	4111	c.4030C>G	c.(4030-4032)Ctc>Gtc	p.L1344V		NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	1344					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					AGCAGCAAGAGAAACATGCCT	0.433																																					p.L1344V		Atlas-SNP	.											NALCN,NS,malignant_melanoma,0,1	NALCN	431	.	0			c.C4030G						.						118	116	117					13																	101726938		2203	4300	6503	SO:0001583	missense	259232	exon36			GCAAGAGAAACAT	AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"Ion channels / Sodium leak channels, non-selective"	19082	protein-coding gene	gene with protein product		611549	"voltage gated channel like 1"	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.4030C>G	chr13.hg19:g.101726938G>C	ENSP00000251127:p.Leu1344Val	38.0	0.0		43.0	7.0	NM_052867	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Missense_Mutation	SNP	ENST00000251127.6	hg19	CCDS9498.1	.	.	.	.	.	.	.	.	.	.	G	17.53	3.413265	0.62511	.	.	ENSG00000102452	ENST00000251127	D	0.98701	-5.08	5.8	3.8	0.43715	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98710	0.9567	M	0.74467	2.265	0.80722	D	1	D	0.62365	0.991	D	0.70016	0.967	D	0.99232	1.0882	10	0.87932	D	0	.	9.7274	0.40339	0.2412:0.0:0.7588:0.0	.	1344	Q8IZF0	NALCN_HUMAN	V	1344	ENSP00000251127:L1344V	ENSP00000251127:L1344V	L	-	1	0	NALCN	100524939	1.000000	0.71417	0.973000	0.42090	0.944000	0.59088	1.980000	0.40618	1.467000	0.48044	0.585000	0.79938	CTC	.	.		0.433	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867		C	101726938	G	C	101726938	3	2	238	1	0	0	0	0	1	0	0	0	10157	942	33	4	1222	4	NALCN	13	101726938	Missense_Mutation	SNP	G	TCGA-ED-A4XI-01A-11D-A25V-10	33925828	101726938	13442940	86	33213										
NALCN	259232	hgsc.bcm.edu	37	chr13	101759941	101759941	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	gtatgggtggttctctctgaGttcctcttcttgcactttcc	9	11	4	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr13:101759941G>T	ENST00000251127.6	-	22	2557	c.2476C>A	c.(2476-2478)Ctc>Atc	p.L826I		NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	826					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					TTCTCTCTGAGTTCCTCTTCT	0.493																																					p.L826I		Atlas-SNP	.											.	NALCN	431	.	0			c.C2476A						.						174	154	161					13																	101759941		2203	4300	6503	SO:0001583	missense	259232	exon22			CTCTGAGTTCCTC	AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"Ion channels / Sodium leak channels, non-selective"	19082	protein-coding gene	gene with protein product		611549	"voltage gated channel like 1"	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.2476C>A	chr13.hg19:g.101759941G>T	ENSP00000251127:p.Leu826Ile	133.0	0.0		141.0	24.0	NM_052867	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Missense_Mutation	SNP	ENST00000251127.6	hg19	CCDS9498.1	.	.	.	.	.	.	.	.	.	.	G	17.30	3.355229	0.61293	.	.	ENSG00000102452	ENST00000251127	D	0.98135	-4.74	5.52	4.49	0.54785	.	0.000000	0.64402	D	0.000001	D	0.97176	0.9077	M	0.64997	1.995	0.80722	D	1	D	0.55800	0.973	P	0.51945	0.685	D	0.96490	0.9363	10	0.54805	T	0.06	.	11.7106	0.51623	0.1515:0.0:0.8485:0.0	.	826	Q8IZF0	NALCN_HUMAN	I	826	ENSP00000251127:L826I	ENSP00000251127:L826I	L	-	1	0	NALCN	100557942	1.000000	0.71417	0.368000	0.25939	0.865000	0.49528	3.850000	0.55918	2.583000	0.87209	0.650000	0.86243	CTC	.	.		0.493	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867		T	101759941	G	T	101759941	3	4	238	1	0	0	0	0	1	0	0	0	10157	1029	36	3	2832	3	NALCN	13	101759941	Missense_Mutation	SNP	G	TCGA-ED-A4XI-01A-11D-A25V-10	33003	101759941	13409937	87	33214										
ZNF828	283489	hgsc.bcm.edu	37	chr13	115090198	115090198	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	tgaaccttggaagccgttccCtgctgtctccccagagccta	9	15	1	2			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr13:115090198C>T	ENST00000361283.1	+	3	1190	c.881C>T	c.(880-882)cCt>cTt	p.P294L		NM_001164144.1|NM_001164145.1|NM_032436.2	NP_001157616.1|NP_001157617.1|NP_115812.1	Q96JM3	CHAP1_HUMAN	chromosome alignment maintaining phosphoprotein 1	294	Mediates interaction with MAD2L2.|Pro-rich.				attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation (GO:0051315)|protein localization to kinetochore (GO:0034501)|protein localization to microtubule (GO:0035372)|sister chromatid biorientation (GO:0031134)	condensed chromosome (GO:0000793)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)										AAGCCGTTCCCTGCTGTCTCC	0.607																																					p.P294L		Atlas-SNP	.											.	.	.	.	0			c.C881T						.						50	58	55					13																	115090198		2203	4300	6503	SO:0001583	missense	283489	exon3			CGTTCCCTGCTGT	AK074894	CCDS9545.1	13q34	2013-01-07	2011-10-07	2011-10-07	ENSG00000198824	ENSG00000198824		"Zinc fingers, C2H2-type"	20311	protein-coding gene	gene with protein product	"chromosome alignment-maintaining phosphoprotein"		"chromosome 13 open reading frame 8", "zinc finger protein 828"	C13orf8, ZNF828		21063390	Standard	NM_032436		Approved	CAMP, CHAMP	uc010ahb.3	Q96JM3	OTTHUMG00000017404	ENST00000361283.1:c.881C>T	chr13.hg19:g.115090198C>T	ENSP00000354730:p.Pro294Leu	79.0	0.0		67.0	4.0	NM_001164144	B3KU06|Q6P181|Q8NC88|Q9BST0	Missense_Mutation	SNP	ENST00000361283.1	hg19	CCDS9545.1	.	.	.	.	.	.	.	.	.	.	C	14.14	2.446661	0.43429	.	.	ENSG00000198824	ENST00000361283	T	0.01438	4.89	5.92	5.92	0.95590	.	0.108147	0.41500	D	0.000868	T	0.02533	0.0077	L	0.49126	1.545	0.45183	D	0.998199	B	0.33171	0.4	B	0.30782	0.12	T	0.63883	-0.6536	9	.	.	.	-5.2128	20.3325	0.98724	0.0:1.0:0.0:0.0	.	294	Q96JM3	ZN828_HUMAN	L	294	ENSP00000354730:P294L	.	P	+	2	0	ZNF828	114108300	0.494000	0.26043	0.996000	0.52242	0.991000	0.79684	5.310000	0.65780	2.805000	0.96524	0.655000	0.94253	CCT	.	.		0.607	CHAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045977.2	NM_032436		T	115090198	C	T	115090198	3	4	238	1	0	0	0	0	1	0	0	0	18196	681	24	3	883	3	ZNF828	13	115090198	Missense_Mutation	SNP	C	TCGA-ED-A4XI-01A-11D-A25V-10	13330257	115090198	79680	88	33215										
NUBPL	80224	hgsc.bcm.edu	37	chr14	32031297	32031297	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	tctggcgccgggagtgagacCctaaaacaaagaagaacaca	11	10	1	3			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr14:32031297C>T	ENST00000281081.7	+	2	177	c.132C>T	c.(130-132)acC>acT	p.T44T	CTD-2213F21.3_ENST00000548096.1_RNA	NM_001201573.1|NM_001201574.1|NM_025152.2	NP_001188502.1|NP_001188503.1|NP_079428.2	Q8TB37	NUBPL_HUMAN	nucleotide binding protein-like	44					mitochondrial respiratory chain complex I assembly (GO:0032981)|mitochondrion morphogenesis (GO:0070584)	mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			endometrium(1)|lung(2)|prostate(1)|skin(1)	5	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.214)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0677)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0102)		GGAGTGAGACCCTAAAACAAA	0.383																																					p.T44T		Atlas-SNP	.											.	NUBPL	21	.	0			c.C132T						.						51	48	49					14																	32031297		1817	4067	5884	SO:0001819	synonymous_variant	80224	exon2			TGAGACCCTAAAA	AK022722	CCDS41940.1	14q12	2012-10-12	2005-01-07	2005-01-07	ENSG00000151413	ENSG00000151413		"Mitochondrial respiratory chain complex assembly factors"	20278	protein-coding gene	gene with protein product	"iron-sulfur protein required for NADH dehydrogenase"	613621	"chromosome 14 open reading frame 127"	C14orf127			Standard	NM_025152		Approved	FLJ12660, IND1, huInd1	uc001wrk.4	Q8TB37	OTTHUMG00000170521	ENST00000281081.7:c.132C>T	chr14.hg19:g.32031297C>T		67.0	0.0		62.0	11.0	NM_025152	B4DHZ1|Q86TZ4|Q9H9M2	Silent	SNP	ENST00000281081.7	hg19	CCDS41940.1																																																																																			.	.		0.383	NUBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409519.1	NM_025152		T	32031297	C	T	32031297	2	4	238	1	0	0	0	0	0	0	0	1	10726	610	22	3		3	NUBPL	14	32031297	Silent	SNP	C	TCGA-ED-A4XI-01A-11D-A25V-10		32031297	75318243	89	33216										
ARHGAP5	394	hgsc.bcm.edu	37	chr14	32563379	32563379	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	agtaaagccaagtcatactaTagaagaacacattcagatgc	7	8	2	3			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr14:32563379T>A	ENST00000345122.3	+	2	3819	c.3504T>A	c.(3502-3504)taT>taA	p.Y1168*	ARHGAP5_ENST00000539826.2_Nonsense_Mutation_p.Y1168*|ARHGAP5_ENST00000433497.1_Intron|ARHGAP5_ENST00000556611.1_Nonsense_Mutation_p.Y1168*|ARHGAP5_ENST00000396582.2_Intron|ARHGAP5_ENST00000432921.1_Nonsense_Mutation_p.Y1168*	NM_001030055.1	NP_001025226.1	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5	1168					cell adhesion (GO:0007155)|GTP catabolic process (GO:0006184)|mammary gland development (GO:0030879)|positive regulation of cell migration (GO:0030335)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell size (GO:0008361)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(10)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(12)|ovary(4)|skin(1)|stomach(1)|urinary_tract(4)	55	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)		AGTCATACTATAGAAGAACAC	0.368																																					p.Y1168X	NSCLC(9;77 350 3443 29227 41353)	Atlas-SNP	.											.	ARHGAP5	166	.	0			c.T3504A						.						82	86	85					14																	32563379		2203	4300	6503	SO:0001587	stop_gained	394	exon2			ATACTATAGAAGA	U17032	CCDS32062.1, CCDS45095.1	14q12	2010-02-05						"Rho GTPase activating proteins"	675	protein-coding gene	gene with protein product		602680	"growth factor independent 2"	GFI2		8537347	Standard	XM_005267635		Approved	RhoGAP5, p190-B, p190BRhoGAP	uc001wrn.3	Q13017		ENST00000345122.3:c.3504T>A	chr14.hg19:g.32563379T>A	ENSP00000371897:p.Tyr1168*	163.0	0.0		141.0	11.0	NM_001173	A1L375|A1L376|A8KAA1|D3DS89|D3DS90|Q05BE8|Q05BU8|Q59ER0|Q6DHZ3	Nonsense_Mutation	SNP	ENST00000345122.3	hg19	CCDS32062.1	.	.	.	.	.	.	.	.	.	.	T	44	10.934715	0.99491	.	.	ENSG00000100852	ENST00000556611;ENST00000539826;ENST00000345122;ENST00000432921	.	.	.	5.39	1.36	0.22044	.	0.384990	0.30043	N	0.010548	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11485	T	0.65	.	10.1991	0.43073	0.0:0.2792:0.0:0.7208	.	.	.	.	X	1168	.	ENSP00000371897:Y1168X	Y	+	3	2	ARHGAP5	31633130	0.712000	0.27916	0.999000	0.59377	0.984000	0.73092	-0.194000	0.09559	0.044000	0.15775	0.460000	0.39030	TAT	.	.		0.368	ARHGAP5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409735.1	NM_001030055		A	32563379	T	A	32563379	4	1	238	1	0	0	0	0	0	1	0	0	886	1413	49	4	3506	4	ARHGAP5	14	32563379	Nonsense_Mutation	SNP	T	TCGA-ED-A4XI-01A-11D-A25V-10	532082	32563379	74786161	90	33217										
MAGEL2	54551	hgsc.bcm.edu	37	chr15	23890789	23890789	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	gggaaaatttgccgctgctaCcgggggtccgggctgggcct	17	11	0	0			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr15:23890789C>T	ENST00000532292.1	-	1	386	c.292G>A	c.(292-294)Gta>Ata	p.V98I		NM_019066.4	NP_061939.3	Q9UJ55	MAGL2_HUMAN	MAGE-like 2	0					Arp2/3 complex-mediated actin nucleation (GO:0034314)|protein K63-linked ubiquitination (GO:0070534)|retrograde transport, endosome to Golgi (GO:0042147)	endosome (GO:0005768)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;1.84e-06)|Epithelial(43;1.2e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)		GCCGCTGCTACCGGGGGTCCG	0.632																																					p.V701I		Atlas-SNP	.											.	MAGEL2	108	.	0			c.G2101A						.						11	12	12					15																	23890789		1848	4076	5924	SO:0001583	missense	54551	exon1			CTGCTACCGGGGG	AJ243531	CCDS73700.1	15q11-q12	2008-07-18				ENSG00000254585			6814	protein-coding gene	gene with protein product		605283		NDNL1		10556298	Standard	NM_019066		Approved	nM15	uc001ywj.4	Q9UJ55		ENST00000532292.1:c.292G>A	chr15.hg19:g.23890789C>T	ENSP00000433433:p.Val98Ile	100.0	0.0		76.0	21.0	NM_019066		Missense_Mutation	SNP	ENST00000532292.1	hg19																																																																																				.	.		0.632	MAGEL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395182.2	NM_019066		T	23890789	C	T	23890789	3	4	238	1	0	0	0	0	1	0	0	0	9198	507	18	3	1652	3	MAGEL2	15	23890789	Missense_Mutation	SNP	C	TCGA-ED-A4XI-01A-11D-A25V-10		23890789	78640603	91	33218										
UBR1	197131	hgsc.bcm.edu	37	chr15	43318859	43318859	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	catggcctgatacacctggtTtcctaaatagatggaaaata	8	8	0	2			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr15:43318859T>G	ENST00000290650.4	-	23	2513	c.2435A>C	c.(2434-2436)aAa>aCa	p.K812T	UBR1_ENST00000382177.2_Missense_Mutation_p.E794D	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	812					cellular response to leucine (GO:0071233)|negative regulation of TOR signaling (GO:0032007)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|proteasome complex (GO:0000502)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		TACACCTGGTTTCCTAAATAG	0.308																																					p.K812T		Atlas-SNP	.											.	UBR1	124	.	0			c.A2435C						.						115	116	116					15																	43318859		2202	4298	6500	SO:0001583	missense	197131	exon23			CCTGGTTTCCTAA		CCDS10091.1	15q13	2008-06-23			ENSG00000159459	ENSG00000159459		"Ubiquitin protein ligase E3 component n-recognins"	16808	protein-coding gene	gene with protein product		605981				9653112	Standard	NM_174916		Approved		uc001zqq.3	Q8IWV7	OTTHUMG00000130702	ENST00000290650.4:c.2435A>C	chr15.hg19:g.43318859T>G	ENSP00000290650:p.Lys812Thr	47.0	0.0		52.0	12.0	NM_174916	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Missense_Mutation	SNP	ENST00000290650.4	hg19	CCDS10091.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.0|25.0	4.597318|4.597318	0.87055|0.87055	.|.	.|.	ENSG00000159459|ENSG00000159459	ENST00000382177|ENST00000290650;ENST00000546274	T|T	0.50001|0.59906	0.76|0.23	4.81|4.81	4.81|4.81	0.61882|0.61882	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.75817|0.75817	0.3901|0.3901	M|M	0.84082|0.84082	2.675|2.675	0.58432|0.58432	D|D	0.999999|0.999999	.|D;D	.|0.89917	.|0.999;1.0	.|D;D	.|0.85130	.|0.968;0.997	T|T	0.74965|0.74965	-0.3484|-0.3484	7|10	0.33940|0.23891	T|T	0.23|0.37	-18.0994|-18.0994	14.8176|14.8176	0.70048|0.70048	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|812;812	.|B4DYL2;Q8IWV7	.|.;UBR1_HUMAN	D|T	794|812	ENSP00000371612:E794D|ENSP00000290650:K812T	ENSP00000371612:E794D|ENSP00000290650:K812T	E|K	-|-	3|2	2|0	UBR1|UBR1	41106151|41106151	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	7.341000|7.341000	0.79300|0.79300	2.141000|2.141000	0.66446|0.66446	0.455000|0.455000	0.32223|0.32223	GAA|AAA	.	.		0.308	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916		G	43318859	T	G	43318859	3	3	238	1	0	0	0	0	1	0	0	0	16916	1841	64	5	2914	5	UBR1	15	43318859	Missense_Mutation	SNP	T	TCGA-ED-A4XI-01A-11D-A25V-10	19428070	43318859	59212533	92	33219										
DENND4A	10260	hgsc.bcm.edu	37	chr15	65994749	65994749	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	ctttcacataagctgggagaCaaataaaccacagtccataa	6	10	1	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr15:65994749C>A	ENST00000431932.2	-	17	2532	c.2324G>T	c.(2323-2325)tGt>tTt	p.C775F	DENND4A_ENST00000443035.3_Missense_Mutation_p.C775F	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	775					positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						AGCTGGGAGACAAATAAACCA	0.413																																					p.C775F		Atlas-SNP	.											.	DENND4A	217	.	0			c.G2324T						.						70	61	64					15																	65994749		1855	4102	5957	SO:0001583	missense	10260	exon17			GGGAGACAAATAA	AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27				"DENN/MADD domain containing"	24321	protein-coding gene	gene with protein product		600382	"c-myc promoter binding protein"	MYCPBP		8056341, 12906859	Standard	NM_005848		Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.2324G>T	chr15.hg19:g.65994749C>A	ENSP00000396830:p.Cys775Phe	189.0	0.0		190.0	9.0	NM_001144823	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Missense_Mutation	SNP	ENST00000431932.2	hg19	CCDS45285.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.584304	0.86748	.	.	ENSG00000174485	ENST00000443035;ENST00000431932	T;T	0.05382	3.45;3.46	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.30008	0.0751	M	0.80847	2.515	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.996	T	0.00626	-1.1638	10	0.54805	T	0.06	.	19.9918	0.97368	0.0:1.0:0.0:0.0	.	775;775	E7EPL3;Q7Z401	.;MYCPP_HUMAN	F	775	ENSP00000391167:C775F;ENSP00000396830:C775F	ENSP00000396830:C775F	C	-	2	0	DENND4A	63781803	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.728000	0.93425	0.585000	0.79938	TGT	.	.		0.413	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848		A	65994749	C	A	65994749	3	1	238	1	0	0	0	0	1	0	0	0	4435	478	17	3	3464	3	DENND4A	15	65994749	Missense_Mutation	SNP	C	TCGA-ED-A4XI-01A-11D-A25V-10	22675890	65994749	36536643	93	33220										
CT62	196993	hgsc.bcm.edu	37	chr15	71404534	71404534	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	ggaaccacaggagaaatggcTgaatgttctgtgggtgtggc	16	6	1	2			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr15:71404534T>A	ENST00000449977.2	-	3	594	c.88A>T	c.(88-90)Agc>Tgc	p.S30C	THSD4_ENST00000355327.3_Intron|CT62_ENST00000566432.1_Missense_Mutation_p.S30C	NM_001102658.1	NP_001096128.1	P0C5K7	CT62_HUMAN	cancer/testis antigen 62	30										NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(2)	6						GAGAAATGGCTGAATGTTCTG	0.522																																					p.S30C		Atlas-SNP	.											.	CT62	7	.	0			c.A88T						.						97	116	110					15																	71404534		2067	4216	6283	SO:0001583	missense	196993	exon3			AATGGCTGAATGT	BC039359, AL080151	CCDS45295.1	15q23	2011-03-09			ENSG00000225362	ENSG00000225362			27286	protein-coding gene	gene with protein product						15905330	Standard	NM_001102658		Approved		uc002ata.2	P0C5K7		ENST00000449977.2:c.88A>T	chr15.hg19:g.71404534T>A	ENSP00000399356:p.Ser30Cys	110.0	0.0		102.0	12.0	NM_001102658		Missense_Mutation	SNP	ENST00000449977.2	hg19	CCDS45295.1	.	.	.	.	.	.	.	.	.	.	T	9.590	1.125872	0.20959	.	.	ENSG00000225362	ENST00000449977	.	.	.	1.88	0.689	0.18033	.	.	.	.	.	T	0.32526	0.0832	N	0.08118	0	0.09310	N	1	D	0.71674	0.998	D	0.70716	0.97	T	0.14008	-1.0488	8	0.87932	D	0	.	4.7512	0.13061	0.0:0.0:0.3315:0.6685	.	30	P0C5K7	CT62_HUMAN	C	30	.	ENSP00000399356:S30C	S	-	1	0	CT62	69191588	0.000000	0.05858	0.001000	0.08648	0.047000	0.14425	-0.661000	0.05311	0.173000	0.19788	0.528000	0.53228	AGC	.	.		0.522	CT62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420810.1	NM_001102658		A	71404534	T	A	71404534	3	1	238	1	0	0	0	0	1	0	0	0	3992	1580	55	4	330	4	CT62	15	71404534	Missense_Mutation	SNP	T	TCGA-ED-A4XI-01A-11D-A25V-10	5409785	71404534	31126858	94	33221										
THSD4	79875	hgsc.bcm.edu	37	chr15	71548960	71548960	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	ctgctttattaggtatgtccAgaaagcagtagaagtatccg	10	7	0	2			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr15:71548960A>G	ENST00000355327.3	+	6	1055	c.921A>G	c.(919-921)ccA>ccG	p.P307P	THSD4_ENST00000261862.6_Silent_p.P307P			Q6ZMP0	THSD4_HUMAN	thrombospondin, type I, domain containing 4	307	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				elastic fiber assembly (GO:0048251)	extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)	metalloendopeptidase activity (GO:0004222)			breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(20)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						AGGTATGTCCAGAAAGCAGTA	0.408																																					p.P307P		Atlas-SNP	.											.	THSD4	75	.	0			c.A921G						.						137	138	137					15																	71548960		1852	4102	5954	SO:0001819	synonymous_variant	79875	exon5			ATGTCCAGAAAGC	AK023772	CCDS10238.2, CCDS66817.1	15q23	2009-11-09			ENSG00000187720	ENSG00000187720			25835	protein-coding gene	gene with protein product		614476				19734141	Standard	NM_001286429		Approved	FVSY9334, PRO34005, FLJ13710, ADAMTSL6	uc002atb.1	Q6ZMP0	OTTHUMG00000133389	ENST00000355327.3:c.921A>G	chr15.hg19:g.71548960A>G		115.0	0.0		106.0	11.0	NM_024817	B2RTY3|B4DR13|Q6MZI3|Q6UXZ8|Q9H8E4	Silent	SNP	ENST00000355327.3	hg19	CCDS10238.2																																																																																			.	.		0.408	THSD4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257253.2	NM_024817		G	71548960	A	G	71548960	2	3	238	1	0	0	0	0	0	0	0	1	15893	175	7	2		2	THSD4	15	71548960	Silent	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	144426	71548960	30982432	95	33222										
BLM	641	hgsc.bcm.edu	37	chr15	91354495	91354495	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	aggccccggaagaagtgccgCtgaggagctcgacgaggaaa	16	10	0	2			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr15:91354495C>A	ENST00000355112.3	+	21	4053	c.3935C>A	c.(3934-3936)gCt>gAt	p.A1312D	BLM_ENST00000560509.1_Missense_Mutation_p.A1181D|BLM_ENST00000560136.1_3'UTR	NM_000057.2	NP_000048.1	P54132	BLM_HUMAN	Bloom syndrome, RecQ helicase-like	1312					alpha-beta T cell differentiation (GO:0046632)|ATP catabolic process (GO:0006200)|cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA strand renaturation (GO:0000733)|double-strand break repair via homologous recombination (GO:0000724)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell division (GO:0051782)|negative regulation of DNA recombination (GO:0045910)|negative regulation of mitotic recombination (GO:0045950)|negative regulation of thymocyte apoptotic process (GO:0070244)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of transcription, DNA-templated (GO:0045893)|protein oligomerization (GO:0051259)|regulation of binding (GO:0051098)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to X-ray (GO:0010165)|telomere maintenance (GO:0000723)	cytoplasm (GO:0005737)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nuclear chromosome (GO:0000228)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|pronucleus (GO:0045120)|replication fork (GO:0005657)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent helicase activity (GO:0008026)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|p53 binding (GO:0002039)|single-stranded DNA binding (GO:0003697)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(11)|liver(4)|lung(9)|ovary(6)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)			AGAAGTGCCGCTGAGGAGCTC	0.498			"Mis, N, F"			"leukemia, lymphoma, skin squamous cell , other cancers"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Bloom syndrome																												p.A1312D		Atlas-SNP	.	yes	Rec		Bloom Syndrome	15	15q26.1	641	Bloom Syndrome		"L, E"	.	BLM	122	.	0			c.C3935A						.						77	78	77					15																	91354495		2198	4298	6496	SO:0001583	missense	641	exon21	Familial Cancer Database		GTGCCGCTGAGGA	U39817	CCDS10363.1, CCDS73782.1	15q26.1	2014-09-17	2009-03-19		ENSG00000197299	ENSG00000197299			1058	protein-coding gene	gene with protein product		604610	"Bloom syndrome"			9388193	Standard	NM_000057		Approved	BS, RECQL3, RECQ2	uc002bpr.3	P54132	OTTHUMG00000149834	ENST00000355112.3:c.3935C>A	chr15.hg19:g.91354495C>A	ENSP00000347232:p.Ala1312Asp	81.0	0.0		87.0	4.0	NM_000057	Q52M96	Missense_Mutation	SNP	ENST00000355112.3	hg19	CCDS10363.1	.	.	.	.	.	.	.	.	.	.	C	12.14	1.847823	0.32606	.	.	ENSG00000197299	ENST00000355112;ENST00000536925;ENST00000543977	T	0.41758	0.99	5.87	1.71	0.24356	.	1.049400	0.07467	N	0.901657	T	0.19446	0.0467	N	0.08118	0	0.09310	N	1	B;B	0.13145	0.007;0.007	B;B	0.11329	0.006;0.006	T	0.28554	-1.0040	10	0.15499	T	0.54	-4.528	3.3163	0.07034	0.3083:0.4584:0.1494:0.0839	.	1312;1312	B2RAN0;P54132	.;BLM_HUMAN	D	1312;942;499	ENSP00000347232:A1312D	ENSP00000347232:A1312D	A	+	2	0	BLM	89155499	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	0.973000	0.29422	0.934000	0.37316	-0.169000	0.13324	GCT	.	.		0.498	BLM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313495.1			A	91354495	C	A	91354495	3	1	238	1	0	0	0	0	1	0	0	0	1445	797	28	3	4013	3	BLM	15	91354495	Missense_Mutation	SNP	C	TCGA-ED-A4XI-01A-11D-A25V-10	19805535	91354495	11176897	96	33223										
JMJD5	79831	hgsc.bcm.edu	37	chr16	27232040	27232040	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	tgagcttctcggtcagcttcTggtggtcgtagccaggatag	14	9	3	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr16:27232040T>C	ENST00000286096.4	+	8	1413	c.1240T>C	c.(1240-1242)Tgg>Cgg	p.W414R	KDM8_ENST00000567785.1_3'UTR|KDM8_ENST00000441782.2_Missense_Mutation_p.W452R|KDM8_ENST00000380948.2_Missense_Mutation_p.W218R|KDM8_ENST00000568965.1_Missense_Mutation_p.W218R	NM_024773.2	NP_079049.2	Q8N371	KDM8_HUMAN	lysine (K)-specific demethylase 8	414	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				G2/M transition of mitotic cell cycle (GO:0000086)|histone H3-K36 demethylation (GO:0070544)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone demethylase activity (H3-K36 specific) (GO:0051864)|metal ion binding (GO:0046872)										GGTCAGCTTCTGGTGGTCGTA	0.512																																					p.W452R		Atlas-SNP	.											.	.	.	.	0			c.T1354C						.						99	96	97					16																	27232040		2197	4300	6497	SO:0001583	missense	79831	exon8			AGCTTCTGGTGGT	AK023860	CCDS10627.1, CCDS45448.1	16p12.1	2012-03-28	2012-03-28	2012-03-28	ENSG00000155666	ENSG00000155666		"Chromatin-modifying enzymes / K-demethylases"	25840	protein-coding gene	gene with protein product		611917	"jumonji domain containing 5"	JMJD5		20457893	Standard	NM_024773		Approved	FLJ13798	uc010vcn.1	Q8N371	OTTHUMG00000131677	ENST00000286096.4:c.1240T>C	chr16.hg19:g.27232040T>C	ENSP00000286096:p.Trp414Arg	192.0	0.0		207.0	23.0	NM_001145348	B4DLU9|Q6VAK5|Q9H8B1	Missense_Mutation	SNP	ENST00000286096.4	hg19	CCDS10627.1	.	.	.	.	.	.	.	.	.	.	T	16.75	3.209437	0.58343	.	.	ENSG00000155666	ENST00000380948;ENST00000286096;ENST00000441782	T;T;T	0.34859	1.34;1.34;1.34	5.28	5.28	0.74379	Transcription factor jumonji/aspartyl beta-hydroxylase (2);	0.167364	0.56097	D	0.000023	T	0.60235	0.2253	M	0.75264	2.295	0.51012	D	0.999909	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.65125	-0.6244	10	0.87932	D	0	-21.331	14.0533	0.64751	0.0:0.0:0.0:1.0	.	452;218;414	Q8N371-3;Q8N371-2;Q8N371	.;.;KDM8_HUMAN	R	218;414;452	ENSP00000370335:W218R;ENSP00000286096:W414R;ENSP00000398410:W452R	ENSP00000286096:W414R	W	+	1	0	JMJD5	27139541	1.000000	0.71417	1.000000	0.80357	0.188000	0.23474	7.946000	0.87746	2.000000	0.58554	0.460000	0.39030	TGG	.	.		0.512	KDM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254580.3	NM_024773		C	27232040	T	C	27232040	3	2	238	1	0	0	0	0	1	0	0	0	7961	1580	55	2	1384	2	JMJD5	16	27232040	Missense_Mutation	SNP	T	TCGA-ED-A4XI-01A-11D-A25V-10		27232040	63122713	97	33224										
ATXN2L	11273	hgsc.bcm.edu	37	chr16	28846411	28846411	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	cccatgcttcagagcaacccAcgcatgctgacgtcgggcag	11	15	1	2			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr16:28846411A>G	ENST00000336783.4	+	19	2633	c.2466A>G	c.(2464-2466)ccA>ccG	p.P822P	RP11-24N18.1_ENST00000563565.1_RNA|ATXN2L_ENST00000570200.1_Silent_p.P822P|ATXN2L_ENST00000565845.1_3'UTR|ATXN2L_ENST00000382686.4_Silent_p.P822P|ATXN2L_ENST00000325215.6_Silent_p.P822P|ATXN2L_ENST00000340394.8_Silent_p.P822P|ATXN2L_ENST00000564304.1_Silent_p.P828P|ATXN2L_ENST00000395547.2_Silent_p.P822P	NM_007245.3	NP_009176.2	Q8WWM7	ATX2L_HUMAN	ataxin 2-like	822					regulation of cytoplasmic mRNA processing body assembly (GO:0010603)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|membrane (GO:0016020)|nuclear speck (GO:0016607)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36						AGAGCAACCCACGCATGCTGA	0.627																																					p.P822P		Atlas-SNP	.											.	ATXN2L	159	.	0			c.A2466G						.						103	90	94					16																	28846411		2197	4299	6496	SO:0001819	synonymous_variant	11273	exon19			CAACCCACGCATG		CCDS10639.1, CCDS10640.1, CCDS10641.1, CCDS32423.1, CCDS45451.1, CCDS58443.1	16p11	2008-02-05			ENSG00000168488	ENSG00000168488			31326	protein-coding gene	gene with protein product		607931				11784712, 14769358	Standard	NM_007245		Approved	A2lp, A2D	uc002dqy.4	Q8WWM7	OTTHUMG00000097038	ENST00000336783.4:c.2466A>G	chr16.hg19:g.28846411A>G		200.0	0.0		168.0	22.0	NM_148414	A8K1R6|B9EGM2|E9PAR9|O95135|Q63ZY4|Q6NVJ8|Q6PJW6|Q8IU61|Q8IU95|Q8WWM3|Q8WWM4|Q8WWM5|Q8WWM6|Q99703	Silent	SNP	ENST00000336783.4	hg19	CCDS10641.1																																																																																			.	.		0.627	ATXN2L-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214139.1	NM_007245		G	28846411	A	G	28846411	2	3	238	1	0	0	0	0	0	0	0	1	1212	146	6	2		2	ATXN2L	16	28846411	Silent	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	1614371	28846411	61508342	98	33225										
ZNF646	9726	hgsc.bcm.edu	37	chr16	31088438	31088438	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	gccagagccacacgctgggcAtctacccctgtgccatctgt	10	16	2	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr16:31088438A>G	ENST00000394979.2	+	1	1216	c.793A>G	c.(793-795)Atc>Gtc	p.I265V	ZNF668_ENST00000564456.1_5'Flank|ZNF646_ENST00000300850.5_Missense_Mutation_p.I265V|ZNF668_ENST00000300849.4_5'Flank			O15015	ZN646_HUMAN	zinc finger protein 646	265					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(1)|lung(21)|ovary(1)|prostate(4)|skin(3)	49						CACGCTGGGCATCTACCCCTG	0.577																																					p.I265V		Atlas-SNP	.											.	ZNF646	133	.	0			c.A793G						.						94	85	88					16																	31088438		2197	4300	6497	SO:0001583	missense	9726	exon2			CTGGGCATCTACC	AB002294	CCDS10702.1	16p11.2	2013-01-08			ENSG00000167395	ENSG00000167395		"Zinc fingers, C2H2-type"	29004	protein-coding gene	gene with protein product							Standard	NM_014699		Approved	KIAA0296	uc002eap.3	O15015	OTTHUMG00000047355	ENST00000394979.2:c.793A>G	chr16.hg19:g.31088438A>G	ENSP00000378429:p.Ile265Val	179.0	0.0		151.0	16.0	NM_014699	Q8IVD8	Missense_Mutation	SNP	ENST00000394979.2	hg19		.	.	.	.	.	.	.	.	.	.	A	4.702	0.130532	0.08981	.	.	ENSG00000167395	ENST00000300850;ENST00000394979;ENST00000439353	T;T	0.27557	1.66;1.66	5.51	-2.02	0.07388	.	.	.	.	.	T	0.10981	0.0268	N	0.03016	-0.435	0.09310	N	1	B	0.09022	0.002	B	0.12837	0.008	T	0.35126	-0.9801	9	0.02654	T	1	-4.9644	13.236	0.59969	0.3109:0.0:0.6891:0.0	.	265	O15015-2	.	V	265;265;30	ENSP00000300850:I265V;ENSP00000378429:I265V	ENSP00000300850:I265V	I	+	1	0	ZNF646	30995939	0.000000	0.05858	0.814000	0.32528	0.760000	0.43138	-1.108000	0.03313	-0.152000	0.11156	-0.290000	0.09829	ATC	.	.		0.577	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699		G	31088438	A	G	31088438	3	3	238	1	0	0	0	0	1	0	0	0	18077	217	8	2	795	2	ZNF646	16	31088438	Missense_Mutation	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	2242027	31088438	59266315	99	33226										
NOD2	64127	hgsc.bcm.edu	37	chr16	50744637	50744637	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	ggctggacccccgcagaagaGcccagccaccctgggcctgg	14	17	0	2			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr16:50744637G>A	ENST00000300589.2	+	4	920	c.815G>A	c.(814-816)aGc>aAc	p.S272N	RP11-327F22.6_ENST00000602304.1_RNA|NOD2_ENST00000526417.2_3'UTR	NM_022162.1	NP_071445.1	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain containing 2	272					activation of MAPK activity (GO:0000187)|activation of MAPK activity involved in innate immune response (GO:0035419)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to peptidoglycan (GO:0071224)|cytokine production involved in immune response (GO:0002367)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|detection of biotic stimulus (GO:0009595)|detection of muramyl dipeptide (GO:0032498)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|innate immune response (GO:0045087)|innate immune response in mucosa (GO:0002227)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|macrophage inflammatory protein-1 alpha production (GO:0071608)|maintenance of gastrointestinal epithelium (GO:0030277)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-18 production (GO:0032701)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of macrophage apoptotic process (GO:2000110)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell mediated immunity (GO:0002710)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of tumor necrosis factor production (GO:0032720)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of B cell activation (GO:0050871)|positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria (GO:0006965)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell cytokine production (GO:0002732)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gamma-delta T cell activation (GO:0046645)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of prostaglandin-E synthase activity (GO:2000363)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type 2 immune response (GO:0002830)|protein oligomerization (GO:0051259)|regulation of inflammatory response (GO:0050727)|regulation of neutrophil chemotaxis (GO:0090022)|response to exogenous dsRNA (GO:0043330)|response to lipopolysaccharide (GO:0032496)|response to muramyl dipeptide (GO:0032495)|response to nutrient (GO:0007584)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|enzyme binding (GO:0019899)|muramyl dipeptide binding (GO:0032500)|peptidoglycan binding (GO:0042834)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(30)|ovary(3)|skin(3)	52		all_cancers(37;0.0156)				CCGCAGAAGAGCCCAGCCACC	0.622																																					p.S272N		Atlas-SNP	.											.	NOD2	118	.	0			c.G815A						.						38	39	38					16																	50744637		2198	4300	6498	SO:0001583	missense	64127	exon4			AGAAGAGCCCAGC	AF178930	CCDS10746.1	16q12	2014-09-17	2006-12-08	2006-12-08	ENSG00000167207	ENSG00000167207		"Nucleotide-binding domain and leucine rich repeat containing"	5331	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 2", "NOD-like receptor C2", "NLR family, CARD domain containing 2"	605956	"caspase recruitment domain family, member 15"	IBD1, CARD15		7809109, 8587604	Standard	XM_005256084		Approved	BLAU, CD, PSORAS1, CLR16.3, NLRC2	uc002egm.1	Q9HC29	OTTHUMG00000133171	ENST00000300589.2:c.815G>A	chr16.hg19:g.50744637G>A	ENSP00000300589:p.Ser272Asn	125.0	0.0		105.0	10.0	NM_022162	E2JEQ6|Q96RH5|Q96RH6|Q96RH8	Missense_Mutation	SNP	ENST00000300589.2	hg19	CCDS10746.1	.	.	.	.	.	.	.	.	.	.	G	7.690	0.690817	0.15039	.	.	ENSG00000167207	ENST00000526417;ENST00000300589	T	0.70399	-0.48	5.63	5.63	0.86233	.	0.078343	0.56097	D	0.000026	T	0.68054	0.2959	M	0.66939	2.045	0.22996	N	0.998451	B;B;B	0.13145	0.007;0.007;0.004	B;B;B	0.11329	0.004;0.006;0.004	T	0.54662	-0.8260	10	0.21014	T	0.42	.	15.1771	0.72920	0.0:0.0:1.0:0.0	.	56;245;272	D6CHF9;Q9HC29-2;Q9HC29	.;.;NOD2_HUMAN	N	245;272	ENSP00000300589:S272N	ENSP00000300589:S272N	S	+	2	0	NOD2	49302138	0.001000	0.12720	0.985000	0.45067	0.248000	0.25809	0.945000	0.29056	2.655000	0.90218	0.462000	0.41574	AGC	.	.		0.622	NOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256876.2	NM_022162		A	50744637	G	A	50744637	3	1	238	1	0	0	0	0	1	0	0	0	10526	971	34	3	829	3	NOD2	16	50744637	Missense_Mutation	SNP	G	TCGA-ED-A4XI-01A-11D-A25V-10	19656199	50744637	39610116	100	33227										
CDH11	1009	hgsc.bcm.edu	37	chr16	64981642	64981642	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	ctagggagctcagggacccgGccactgagcccctgccttca	12	16	2	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr16:64981642G>T	ENST00000268603.4	-	13	2870	c.2255C>A	c.(2254-2256)gCc>gAc	p.A752D	CDH11_ENST00000566827.1_Missense_Mutation_p.A626D|CDH11_ENST00000394156.3_3'UTR	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	752					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A752V(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		CAGGGACCCGGCCACTGAGCC	0.502			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)																											p.A752D		Atlas-SNP	.		Dom	yes		16	16q22.1	1009	"cadherin 11, type 2, OB-cadherin (osteoblast)"		M	CDH11,colon,carcinoma,0,1	CDH11	260	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2255A						.						78	81	80					16																	64981642		2203	4300	6503	SO:0001583	missense	1009	exon13			GACCCGGCCACTG	D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"Cadherins / Major cadherins"	1750	protein-coding gene	gene with protein product	"OB-Cadherin"	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.2255C>A	chr16.hg19:g.64981642G>T	ENSP00000268603:p.Ala752Asp	161.0	0.0		130.0	8.0	NM_001797	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Missense_Mutation	SNP	ENST00000268603.4	hg19	CCDS10803.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.243198	0.79912	.	.	ENSG00000140937	ENST00000268603;ENST00000538390	D	0.82526	-1.62	6.17	6.17	0.99709	Cadherin, cytoplasmic domain (1);	0.000000	0.85682	D	0.000000	D	0.92724	0.7687	M	0.90252	3.1	0.80722	D	1	D	0.54207	0.965	D	0.63381	0.914	D	0.93033	0.6450	10	0.87932	D	0	.	19.8676	0.96824	0.0:0.0:1.0:0.0	.	752	P55287	CAD11_HUMAN	D	752;735	ENSP00000268603:A752D	ENSP00000268603:A752D	A	-	2	0	CDH11	63539143	1.000000	0.71417	0.985000	0.45067	0.984000	0.73092	9.869000	0.99810	2.941000	0.99782	0.655000	0.94253	GCC	.	.		0.502	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664		T	64981642	G	T	64981642	3	4	238	1	0	0	0	0	1	0	0	0	3099	1203	42	3	139	3	CDH11	16	64981642	Missense_Mutation	SNP	G	TCGA-ED-A4XI-01A-11D-A25V-10	14237005	64981642	25373111	101	33228										
FBXO31	79791	hgsc.bcm.edu	37	chr16	87376481	87376503	+	Splice_Site	DEL	GCCGGCTGGTGGGCTCACCTCCT	GCCGGCTGGTGGGCTCACCTCCT	-													0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	cagggccggctggtgggctcAcctcctgcctcccgccggac					rs140641305	byFrequency	TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	GCCGGCTGGTGGGCTCACCTCCT	GCCGGCTGGTGGGCTCACCTCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr16:87376481_87376503delGCCGGCTGGTGGGCTCACCTCCT	ENST00000311635.7	-	5	724_745	c.712_733delAGGAGGTGAGCCCACCAGCCGGC	c.(712-735)aggaggtgagcccaccagccggca>ca	p.RR*AHQPA238fs		NM_001282683.1|NM_024735.3	NP_001269612.1|NP_079011.3	Q5XUX0	FBX31_HUMAN	F-box protein 31	238					cellular response to DNA damage stimulus (GO:0006974)|cyclin catabolic process (GO:0008054)|mitotic G1 DNA damage checkpoint (GO:0031571)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)	p.G68G(1)|p.G240G(1)|p.S67S(1)|p.S239S(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)	17				BRCA - Breast invasive adenocarcinoma(80;0.0272)		TGGTGGGCTCACCTCCTGCCTCCCGCCGGACATCCTGTGGTGG	0.561																																					p.243_244del		Pindel	.											.	FBXO31	82	.	4	Substitution - coding silent(4)	endometrium(4)	c.729_732del						.																																			SO:0001630	splice_region_variant	79791	exon5			.	BC002985	CCDS32501.1, CCDS73922.1	16q24	2008-12-18	2004-05-27			ENSG00000103264		"F-boxes /  "other""	16510	protein-coding gene	gene with protein product		609102	"F-box only protein 31"				Standard	NM_024735		Approved	FBX14, FBXO14, Fbx31, MGC15419	uc002fjw.3	Q5XUX0		ENST00000311635.7:c.732+1AGGAGGTGAGCCCACCAGCCGGC>-	chr16.hg19:g.87376481_87376503delGCCGGCTGGTGGGCTCACCTCCT		201.0	0.0		151.0	11.0	NM_024735	Q5K680|Q8WYV1|Q96D73|Q9UFV4	Frame_Shift_Del	DEL	ENST00000311635.7	hg19	CCDS32501.1																																																																																			.	.		0.561	FBXO31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430799.2	NM_024735	Frame_Shift_Del	-	87376503	GCCGGCTGGTGGGCTCACCTCCT	-	87376481	8	5	238	1	0	1	0	1	0	0	1	0	5749	173	6	0	905	0	FBXO31	16	87376481	Splice_Site	DEL	GCCGGCTGGTGGGCTCACCTCCT	TCGA-ED-A4XI-01A-11D-A25V-10	22394839	87376481	2978272	102	33229										
ITGAE	3682	hgsc.bcm.edu	37	chr17	3680880	3680880	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	gtgcagaagggagctgagcaCgaaaggggcacctcccttgg	16	10	0	2			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr17:3680880C>T	ENST00000263087.4	-	2	207	c.109G>A	c.(109-111)Gtg>Atg	p.V37M		NM_002208.4	NP_002199.3	P38570	ITAE_HUMAN	integrin, alpha E (antigen CD103, human mucosal lymphocyte antigen 1; alpha polypeptide)	37					cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	external side of plasma membrane (GO:0009897)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	41				UCEC - Uterine corpus endometrioid carcinoma (3;0.0813)		GAGCTGAGCACGAAAGGGGCA	0.622																																					p.V37M	NSCLC(182;635 2928 8995 38788)	Atlas-SNP	.											.	ITGAE	96	.	0			c.G109A						.						76	70	72					17																	3680880		2203	4300	6503	SO:0001583	missense	3682	exon2			TGAGCACGAAAGG	L25851	CCDS32531.1	17p13	2010-03-23				ENSG00000083457		"CD molecules", "Integrins"	6147	protein-coding gene	gene with protein product		604682				8119947	Standard	NM_002208		Approved	CD103, HUMINAE	uc002fwo.4	P38570		ENST00000263087.4:c.109G>A	chr17.hg19:g.3680880C>T	ENSP00000263087:p.Val37Met	140.0	0.0		147.0	20.0	NM_002208	Q17RS6|Q9NZU9	Missense_Mutation	SNP	ENST00000263087.4	hg19	CCDS32531.1	.	.	.	.	.	.	.	.	.	.	C	17.53	3.412563	0.62511	.	.	ENSG00000083457	ENST00000263087	D	0.95554	-3.74	4.37	4.37	0.52481	.	.	.	.	.	D	0.95778	0.8626	L	0.46157	1.445	0.32342	N	0.559569	D	0.89917	1.0	P	0.60609	0.877	D	0.95088	0.8219	9	0.56958	D	0.05	.	12.7158	0.57113	0.0:1.0:0.0:0.0	.	37	P38570	ITAE_HUMAN	M	37	ENSP00000263087:V37M	ENSP00000263087:V37M	V	-	1	0	ITGAE	3627629	0.725000	0.28048	0.963000	0.40424	0.489000	0.33432	0.967000	0.29344	2.732000	0.93576	0.609000	0.83330	GTG	.	.		0.622	ITGAE-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438169.1	NM_002208		T	3680880	C	T	3680880	3	4	238	1	0	0	0	0	1	0	0	0	7894	536	19	1	3550	1	ITGAE	17	3680880	Missense_Mutation	SNP	C	TCGA-ED-A4XI-01A-11D-A25V-10		3680880	77514330	103	33230										
CAMTA2	23125	hgsc.bcm.edu	37	chr17	4876952	4876952	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	ggtgcagaaggctcatgcccCggaaggggcttccatgggcc	16	12	1	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr17:4876952C>T	ENST00000348066.3	-	13	2252	c.2129G>A	c.(2128-2130)cGg>cAg	p.R710Q	CAMTA2_ENST00000414043.3_Missense_Mutation_p.R733Q|CAMTA2_ENST00000361571.5_Missense_Mutation_p.R709Q|RP5-1050D4.2_ENST00000430920.1_RNA|CAMTA2_ENST00000381311.5_Missense_Mutation_p.R712Q|CAMTA2_ENST00000358183.4_Missense_Mutation_p.R710Q|CAMTA2_ENST00000572543.1_Missense_Mutation_p.R715Q	NM_015099.3	NP_055914.2	O94983	CMTA2_HUMAN	calmodulin binding transcription activator 2	710					cardiac muscle hypertrophy in response to stress (GO:0014898)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	31						GCTCATGCCCCGGAAGGGGCT	0.647																																					p.R733Q		Atlas-SNP	.											.	CAMTA2	93	.	0			c.G2198A						.						51	52	51					17																	4876952		2203	4300	6503	SO:0001583	missense	23125	exon13			ATGCCCCGGAAGG	AB020716	CCDS11063.1, CCDS54071.1, CCDS54072.1, CCDS54073.1	17p13.3	2004-09-01			ENSG00000108509	ENSG00000108509			18807	protein-coding gene	gene with protein product		611508				11925432	Standard	NM_015099		Approved	KIAA0909	uc010cku.2	O94983	OTTHUMG00000099417	ENST00000348066.3:c.2129G>A	chr17.hg19:g.4876952C>T	ENSP00000321813:p.Arg710Gln	105.0	0.0		90.0	11.0	NM_001171167	B9EGL0|D3DTL5|E7EWU5|Q7Z6M8|Q8N3V0|Q8NDG4|Q96G17	Missense_Mutation	SNP	ENST00000348066.3	hg19	CCDS11063.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.542269	0.85917	.	.	ENSG00000108509	ENST00000414043;ENST00000381311;ENST00000361571;ENST00000358183;ENST00000348066	T;T;T;T;T	0.71222	-0.55;-0.55;-0.55;-0.55;-0.55	4.85	4.85	0.62838	Ankyrin repeat-containing domain (2);	0.079635	0.49305	D	0.000147	T	0.77558	0.4148	L	0.38649	1.16	0.50313	D	0.999866	P;D;D;D;D	0.89917	0.595;0.99;0.984;0.972;1.0	B;P;P;B;D	0.81914	0.082;0.604;0.455;0.267;0.995	T	0.79284	-0.1867	10	0.62326	D	0.03	-19.2077	15.5004	0.75695	0.0:1.0:0.0:0.0	.	686;733;712;710;709	B7ZM30;E7EWU5;O94983-3;O94983;O94983-4	.;.;.;CMTA2_HUMAN;.	Q	733;712;709;710;710	ENSP00000412886:R733Q;ENSP00000370712:R712Q;ENSP00000354828:R709Q;ENSP00000350910:R710Q;ENSP00000321813:R710Q	ENSP00000321813:R710Q	R	-	2	0	CAMTA2	4817676	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.596000	0.82721	2.528000	0.85240	0.655000	0.94253	CGG	.	.		0.647	CAMTA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216876.1	NM_015099		T	4876952	C	T	4876952	3	4	238	1	0	0	0	0	1	0	0	0	2616	652	23	1	1573	1	CAMTA2	17	4876952	Missense_Mutation	SNP	C	TCGA-ED-A4XI-01A-11D-A25V-10	1196072	4876952	76318258	104	33231										
NCOR1	9611	hgsc.bcm.edu	37	chr17	15942894	15942923	+	In_Frame_Del	DEL	CCTTCCTGATAATGTCTTCCAGCCCAAGAT	CCTTCCTGATAATGTCTTCCAGCCCAAGAT	-													0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	atcaaagcttcccatgagagCcttcctgataatgtcttcca					rs3205089|rs371002943		TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	CCTTCCTGATAATGTCTTCCAGCCCAAGAT	CCTTCCTGATAATGTCTTCCAGCCCAAGAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr17:15942894_15942923delCCTTCCTGATAATGTCTTCCAGCCCAAGAT	ENST00000268712.3	-	44	7036_7065	c.6779_6808delATCTTGGGCTGGAAGACATTATCAGGAAGG	c.(6778-6810)aatcttgggctggaagacattatcaggaaggct>act	p.2260_2270NLGLEDIIRKA>T	AC002553.1_ENST00000442828.1_5'Flank|NCOR1_ENST00000395851.1_In_Frame_Del_p.2157_2167NLGLEDIIRKA>T|NCOR1_ENST00000395857.3_In_Frame_Del_p.844_854NLGLEDIIRKA>T	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	2260	ID2. {ECO:0000250}.|Interaction with C1D. {ECO:0000250}.				CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		CCCATGAGAGCCTTCCTGATAATGTCTTCCAGCCCAAGATTACTGGCAGG	0.457																																					p.2260_2270del		Pindel	.											.	NCOR1	240	.	0			c.6780_6809del						.																																			SO:0001651	inframe_deletion	9611	exon44			.	AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"thyroid hormone- and retinoic acid receptor-associated corepressor 1", "protein phosphatase 1, regulatory subunit 109"	600849	"nuclear receptor co-repressor 1"			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.6779_6808delATCTTGGGCTGGAAGACATTATCAGGAAGG	chr17.hg19:g.15942894_15942923delCCTTCCTGATAATGTCTTCCAGCCCAAGAT	ENSP00000268712:p.Asn2260_Ala2270delinsThr	181.0	0.0		178.0	11.0	NM_006311	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	In_Frame_Del	DEL	ENST00000268712.3	hg19	CCDS11175.1																																																																																			.	.		0.457	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		-	15942923	CCTTCCTGATAATGTCTTCCAGCCCAAGAT	-	15942894	7	5	238	1	0	1	0	1	0	0	0	0	10244	739	26	0	526	0	NCOR1	17	15942894	In_Frame_Del	DEL	CCTTCCTGATAATGTCTTCCAGCCCAAGAT	TCGA-ED-A4XI-01A-11D-A25V-10	11065942	15942894	65252316	105	33232										
SLC5A10	125206	hgsc.bcm.edu	37	chr17	18872410	18872410	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	ttgtgcacatctgcctgggcTggaacttctacctctccacc	8	15	3	0			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr17:18872410T>G	ENST00000395645.3	+	6	517	c.499T>G	c.(499-501)Tgg>Ggg	p.W167G	SLC5A10_ENST00000395643.2_Missense_Mutation_p.W167G|SLC5A10_ENST00000395642.1_Missense_Mutation_p.W111G|SLC5A10_ENST00000317977.6_Missense_Mutation_p.W111G|SLC5A10_ENST00000417251.2_Missense_Mutation_p.W167G|FAM83G_ENST00000388995.6_3'UTR|SLC5A10_ENST00000395647.2_Missense_Mutation_p.W167G	NM_001042450.2	NP_001035915.1	A0PJK1	SC5AA_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 10	167					sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(3)|ovary(3)|prostate(3)|skin(3)	24						CTGCCTGGGCTGGAACTTCTA	0.622																																					p.W167G		Atlas-SNP	.											.	SLC5A10	55	.	0			c.T499G						.						156	118	131					17																	18872410		2203	4300	6503	SO:0001583	missense	125206	exon6			CTGGGCTGGAACT		CCDS11201.2, CCDS42275.1, CCDS59277.1, CCDS59278.1, CCDS74008.1	17p11.2	2013-07-19	2013-07-19		ENSG00000154025	ENSG00000154025		"Solute carriers"	23155	protein-coding gene	gene with protein product			"solute carrier family 5 (sodium/glucose cotransporter), member 10"				Standard	NM_152351		Approved	SGLT5	uc002gut.2	A0PJK1	OTTHUMG00000178143	ENST00000395645.3:c.499T>G	chr17.hg19:g.18872410T>G	ENSP00000379007:p.Trp167Gly	209.0	0.0		156.0	12.0	NM_001042450	A8MUC9|B4DPI0|B7WPR4|Q6P5X0|Q8IXM4|Q96LQ1	Missense_Mutation	SNP	ENST00000395645.3	hg19	CCDS42275.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.207991	0.79240	.	.	ENSG00000154025	ENST00000317977;ENST00000395647;ENST00000395642;ENST00000417251;ENST00000395645;ENST00000395643	D;D;D;D;D;D	0.92149	-2.98;-2.36;-2.98;-2.36;-2.36;-2.35	4.82	3.73	0.42828	.	0.000000	0.85682	D	0.000000	D	0.95294	0.8473	M	0.86740	2.835	0.80722	D	1	D;D;D;D;D	0.67145	0.993;0.991;0.993;0.991;0.996	P;P;P;P;P	0.61533	0.842;0.864;0.842;0.864;0.89	D	0.94685	0.7869	10	0.66056	D	0.02	.	10.3686	0.44039	0.0:0.0795:0.0:0.9205	.	167;167;167;167;111	B4DPI0;A0PJK1-2;A0PJK1;A0PJK1-4;A0PJK1-3	.;.;SC5AA_HUMAN;.;.	G	111;167;111;167;167;167	ENSP00000324346:W111G;ENSP00000379008:W167G;ENSP00000379004:W111G;ENSP00000401875:W167G;ENSP00000379007:W167G;ENSP00000379005:W167G	ENSP00000324346:W111G	W	+	1	0	SLC5A10	18813135	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.663000	0.83820	0.796000	0.33947	0.379000	0.24179	TGG	.	.		0.622	SLC5A10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132129.2	NM_152351		G	18872410	T	G	18872410	3	3	238	1	0	0	0	0	1	0	0	0	14677	1580	55	5	521	5	SLC5A10	17	18872410	Missense_Mutation	SNP	T	TCGA-ED-A4XI-01A-11D-A25V-10	2929516	18872410	62322800	106	33233										
CCL13	6357	hgsc.bcm.edu	37	chr17	32685070	32685070	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	gaaccaaactgggcaaggagAtctgtgctgacccaaaggag	13	9	1	2			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr17:32685070A>G	ENST00000225844.2	+	3	292	c.217A>G	c.(217-219)Atc>Gtc	p.I73V		NM_005408.2	NP_005399.1	Q99616	CCL13_HUMAN	chemokine (C-C motif) ligand 13	73					cell-cell signaling (GO:0007267)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|cytoskeleton organization (GO:0007010)|eosinophil chemotaxis (GO:0048245)|immune response (GO:0006955)|inflammatory response (GO:0006954)|regulation of cell shape (GO:0008360)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	chemokine activity (GO:0008009)|receptor binding (GO:0005102)			large_intestine(1)|prostate(1)	2		Ovarian(249;0.0443)|Breast(31;0.151)				GGGCAAGGAGATCTGTGCTGA	0.507																																					p.I73V		Atlas-SNP	.											.	CCL13	17	.	0			c.A217G						.						68	66	67					17																	32685070		2203	4300	6503	SO:0001583	missense	6357	exon3			AAGGAGATCTGTG	AJ001634	CCDS11281.1	17q11.2	2013-02-25	2002-08-22	2002-08-23	ENSG00000181374	ENSG00000181374		"Chemokine ligands", "Endogenous ligands"	10611	protein-coding gene	gene with protein product		601391	"small inducible cytokine subfamily A (Cys-Cys), member 13"	SCYA13		8661057	Standard	NM_005408		Approved	MCP-4, NCC-1, SCYL1, CKb10, MGC17134	uc002hic.3	Q99616	OTTHUMG00000132890	ENST00000225844.2:c.217A>G	chr17.hg19:g.32685070A>G	ENSP00000225844:p.Ile73Val	104.0	0.0		146.0	13.0	NM_005408	O95689|Q6ICQ6	Missense_Mutation	SNP	ENST00000225844.2	hg19	CCDS11281.1	.	.	.	.	.	.	.	.	.	.	A	9.344	1.063655	0.20067	.	.	ENSG00000181374	ENST00000225844	T	0.03831	3.79	4.74	-6.44	0.01920	CC chemokine, conserved site (1);Chemokine interleukin-8-like domain (3);	.	.	.	.	T	0.01558	0.0050	.	.	.	0.21802	N	0.999538	B	0.02656	0.0	B	0.26517	0.07	T	0.44081	-0.9351	8	0.05721	T	0.95	.	0.2509	0.00205	0.2607:0.2515:0.2422:0.2456	.	73	Q99616	CCL13_HUMAN	V	73	ENSP00000225844:I73V	ENSP00000225844:I73V	I	+	1	0	CCL13	29709183	0.000000	0.05858	0.190000	0.23270	0.063000	0.16089	-0.938000	0.03938	-1.973000	0.00999	-0.379000	0.06801	ATC	.	.		0.507	CCL13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256389.1	NM_005408		G	32685070	A	G	32685070	3	3	238	1	0	0	0	0	1	0	0	0	2886	333	12	2	227	2	CCL13	17	32685070	Missense_Mutation	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	13812660	32685070	48510140	107	33234										
SPAG9	9043	hgsc.bcm.edu	37	chr17	49048126	49048126	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	acaagcatagacttcaagggCgtctgactaccaggctcctg	10	12	2	2	rs112947211		TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr17:49048126C>A	ENST00000262013.7	-	29	4000	c.3792G>T	c.(3790-3792)acG>acT	p.T1264T	SPAG9_ENST00000505279.1_Silent_p.T1254T|SPAG9_ENST00000357122.4_Silent_p.T1250T|SPAG9_ENST00000510283.1_Silent_p.T1120T	NM_001130528.2	NP_001124000.1	O60271	JIP4_HUMAN	sperm associated antigen 9	1264					activation of JUN kinase activity (GO:0007257)|muscle cell differentiation (GO:0042692)|negative regulation of protein homodimerization activity (GO:0090074)|positive regulation of cell migration (GO:0030335)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron differentiation (GO:0045666)|protein homooligomerization (GO:0051260)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|striated muscle cell differentiation (GO:0051146)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)				NS(1)|breast(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			ACTTCAAGGGCGTCTGACTAC	0.517																																					p.T1264T		Atlas-SNP	.											.	SPAG9	151	.	0			c.G3792T						.						142	113	123					17																	49048126		2203	4300	6503	SO:0001819	synonymous_variant	9043	exon29			CAAGGGCGTCTGA	AB011088	CCDS11577.1, CCDS45740.1, CCDS58577.1, CCDS58578.1	17q21.33	2013-09-23			ENSG00000008294	ENSG00000008294			14524	protein-coding gene	gene with protein product	"sperm surface protein", "JNK/SAPK-associated protein", "JNK interacting protein", "sperm specific protein", "c-Jun NH2-terminal kinase-associated leucine zipper protein", "Max-binding protein", "JNK-associated leucine-zipper protein", "HLC-4 protein", "lung cancer oncogene 4", "proliferation-inducing gene 6", "cancer/testis antigen 89"	605430				9480848, 11106729	Standard	NM_003971		Approved	HSS, SYD1, KIAA0516, MGC14967, MGC74461, MGC117291, JLP, PHET, HLC4, PIG6, FLJ13450, FLJ14006, FLJ26141, FLJ34602, CT89	uc002itc.3	O60271	OTTHUMG00000162316	ENST00000262013.7:c.3792G>T	chr17.hg19:g.49048126C>A		198.0	0.0		143.0	17.0	NM_001130528	A6H8U5|A8MSX0|B4DHH2|O60905|Q3KQU8|Q3MKM7|Q86WC7|Q86WC8|Q8IZX7|Q96II0|Q9H811	Silent	SNP	ENST00000262013.7	hg19	CCDS45740.1																																																																																			.	C|0.999;T|0.001		0.517	SPAG9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368543.2	NM_003971		A	49048126	C	A	49048126	2	1	238	1	0	0	0	0	0	0	0	1	15000	755	27	1		1	SPAG9	17	49048126	Silent	SNP	C	TCGA-ED-A4XI-01A-11D-A25V-10	16363056	49048126	32147084	108	33235										
KIF2B	84643	hgsc.bcm.edu	37	chr17	51901391	51901391	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	agggcatttatgctctggtgGcacaggatgtctttctcctg	12	9	3	0			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr17:51901391G>A	ENST00000268919.4	+	1	1153	c.997G>A	c.(997-999)Gca>Aca	p.A333T		NM_032559.4	NP_115948.4	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	333	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(15)|lung(58)|ovary(5)|prostate(4)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						TGCTCTGGTGGCACAGGATGT	0.483																																					p.A333T		Atlas-SNP	.											.	KIF2B	254	.	0			c.G997A						.						107	109	108					17																	51901391		2203	4300	6503	SO:0001583	missense	84643	exon1			CTGGTGGCACAGG	AF333335	CCDS32685.1	17q22	2014-08-12			ENSG00000141200	ENSG00000141200		"Kinesins"	29443	protein-coding gene	gene with protein product		615142				11416179	Standard	NM_032559		Approved		uc002iua.2	Q8N4N8	OTTHUMG00000177756	ENST00000268919.4:c.997G>A	chr17.hg19:g.51901391G>A	ENSP00000268919:p.Ala333Thr	117.0	0.0		121.0	18.0	NM_032559	Q96MA2|Q9BXG6	Missense_Mutation	SNP	ENST00000268919.4	hg19	CCDS32685.1	.	.	.	.	.	.	.	.	.	.	G	18.37	3.608153	0.66558	.	.	ENSG00000141200	ENST00000268919;ENST00000416491	T	0.74737	-0.87	5.63	4.67	0.58626	Kinesin, motor domain (4);	0.115539	0.38326	N	0.001727	T	0.76870	0.4048	M	0.64676	1.99	0.50813	D	0.999891	P	0.46706	0.883	P	0.48089	0.566	T	0.78663	-0.2116	10	0.52906	T	0.07	.	13.7237	0.62745	0.0751:0.0:0.9249:0.0	.	333	Q8N4N8	KIF2B_HUMAN	T	333;221	ENSP00000268919:A333T	ENSP00000268919:A333T	A	+	1	0	KIF2B	49256390	1.000000	0.71417	0.303000	0.25071	0.618000	0.37518	9.680000	0.98651	1.507000	0.48752	0.655000	0.94253	GCA	.	.		0.483	KIF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438854.1	NM_032559		A	51901391	G	A	51901391	3	1	238	1	0	0	0	0	1	0	0	0	8307	1203	42	3	999	3	KIF2B	17	51901391	Missense_Mutation	SNP	G	TCGA-ED-A4XI-01A-11D-A25V-10	2853265	51901391	29293819	109	33236										
KCNH6	81033	hgsc.bcm.edu	37	chr17	61613399	61613399	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	ccaacaccaactccgagaagGtcttctccatctgcgtcatg	7	15	4	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr17:61613399G>A	ENST00000583023.1	+	6	1482	c.1471G>A	c.(1471-1473)Gtc>Atc	p.V491I	KCNH6_ENST00000581784.1_Missense_Mutation_p.V438I|KCNH6_ENST00000314672.5_Missense_Mutation_p.V491I|KCNH6_ENST00000456941.2_Missense_Mutation_p.V438I|KCNH6_ENST00000580652.1_Missense_Mutation_p.V491I	NM_030779.2	NP_110406.1	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 6	491					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(4)|large_intestine(6)|lung(20)|ovary(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	54					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	CTCCGAGAAGGTCTTCTCCAT	0.532																																					p.V491I		Atlas-SNP	.											.	KCNH6	122	.	0			c.G1471A						.						89	73	79					17																	61613399		2203	4300	6503	SO:0001583	missense	81033	exon6			GAGAAGGTCTTCT	AF311913	CCDS11638.1, CCDS11639.1, CCDS62290.1	17q23.3	2012-07-05				ENSG00000173826		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18862	protein-coding gene	gene with protein product		608168				16382104	Standard	NM_030779		Approved	Kv11.2, erg2, HERG2	uc002jay.3	Q9H252		ENST00000583023.1:c.1471G>A	chr17.hg19:g.61613399G>A	ENSP00000463533:p.Val491Ile	151.0	0.0		145.0	16.0	NM_030779	Q9BRD7	Missense_Mutation	SNP	ENST00000583023.1	hg19	CCDS11638.1	.	.	.	.	.	.	.	.	.	.	G	12.79	2.043710	0.36085	.	.	ENSG00000173826	ENST00000314672;ENST00000456941	D;D	0.97976	-4.64;-4.33	4.36	3.31	0.37934	Ion transport (1);	0.121467	0.53938	D	0.000055	D	0.89171	0.6639	N	0.04043	-0.29	0.25427	N	0.988218	B;B;B;B;B	0.15719	0.014;0.004;0.012;0.003;0.0	B;B;B;B;B	0.27076	0.076;0.023;0.007;0.015;0.003	T	0.79024	-0.1972	10	0.02654	T	1	.	3.5223	0.07747	0.3663:0.0:0.6337:0.0	.	368;491;438;491;491	B4DPJ3;B4DKC0;Q9H252-2;Q9H252;Q9H252-3	.;.;.;KCNH6_HUMAN;.	I	491;438	ENSP00000318212:V491I;ENSP00000396900:V438I	ENSP00000318212:V491I	V	+	1	0	KCNH6	58967131	1.000000	0.71417	1.000000	0.80357	0.703000	0.40648	7.478000	0.81082	2.244000	0.73946	0.313000	0.20887	GTC	.	.		0.532	KCNH6-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443853.1	NM_030779		A	61613399	G	A	61613399	3	1	238	1	0	0	0	0	1	0	0	0	8045	1261	44	3	1493	3	KCNH6	17	61613399	Missense_Mutation	SNP	G	TCGA-ED-A4XI-01A-11D-A25V-10	9712008	61613399	19581811	110	33237										
NPLOC4	55666	hgsc.bcm.edu	37	chr17	79589216	79589216	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	tttttagcaagttgagggatTtgttggaggaggctgttatc	14	3	0	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr17:79589216T>A	ENST00000331134.6	-	3	400	c.185A>T	c.(184-186)aAa>aTa	p.K62I	NPLOC4_ENST00000374747.5_Missense_Mutation_p.K62I|NPLOC4_ENST00000539314.1_5'UTR	NM_017921.2	NP_060391.2	Q8TAT6	NPL4_HUMAN	nuclear protein localization 4 homolog (S. cerevisiae)	62					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|Golgi organization (GO:0007030)|membrane fusion (GO:0061025)	endoplasmic reticulum (GO:0005783)|nuclear outer membrane-endoplasmic reticulum membrane network (GO:0042175)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11	all_neural(118;0.0878)|Melanoma(429;0.242)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			GTTGAGGGATTTGTTGGAGGA	0.468																																					p.K62I		Atlas-SNP	.											.	NPLOC4	27	.	0			c.A185T						.						116	110	112					17																	79589216		1870	4117	5987	SO:0001583	missense	55666	exon3			AGGGATTTGTTGG	AB040932	CCDS45812.1	17q25.3	2012-09-20			ENSG00000182446	ENSG00000182446			18261	protein-coding gene	gene with protein product		606590				11574150, 10811609	Standard	NM_017921		Approved	NPL4, FLJ20657, KIAA1499	uc002kas.3	Q8TAT6	OTTHUMG00000177990	ENST00000331134.6:c.185A>T	chr17.hg19:g.79589216T>A	ENSP00000331487:p.Lys62Ile	93.0	0.0		89.0	9.0	NM_017921	Q8N3J1|Q9H8V2|Q9H964|Q9NWR5|Q9P229	Missense_Mutation	SNP	ENST00000331134.6	hg19	CCDS45812.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.818320	0.90790	.	.	ENSG00000182446	ENST00000331134;ENST00000374747	.	.	.	5.21	5.21	0.72293	Nuclear pore localisation protein Npl4, ubiquitin-like domain (1);	0.000000	0.85682	D	0.000000	T	0.74351	0.3705	M	0.68952	2.095	0.80722	D	1	D;D	0.62365	0.981;0.991	P;P	0.62184	0.838;0.899	T	0.73994	-0.3807	9	0.36615	T	0.2	-22.3983	15.038	0.71764	0.0:0.0:0.0:1.0	.	62;62	Q8TAT6-2;Q8TAT6	.;NPL4_HUMAN	I	62;61	.	ENSP00000331487:K62I	K	-	2	0	NPLOC4	77199621	1.000000	0.71417	0.987000	0.45799	0.992000	0.81027	6.911000	0.75746	2.088000	0.63022	0.482000	0.46254	AAA	.	.		0.468	NPLOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440140.1			A	79589216	T	A	79589216	3	1	238	1	0	0	0	0	1	0	0	0	10595	1841	64	4	1701	4	NPLOC4	17	79589216	Missense_Mutation	SNP	T	TCGA-ED-A4XI-01A-11D-A25V-10	17975817	79589216	1605994	111	33238										
MYOM1	8736	hgsc.bcm.edu	37	chr18	3155037	3155037	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	tctttgttggcctccaagcaCttcacatccaagggagcagc	9	13	2	0			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr18:3155037C>T	ENST00000356443.4	-	11	1884	c.1551G>A	c.(1549-1551)aaG>aaA	p.K517K	MYOM1_ENST00000261606.7_Silent_p.K517K|MYOM1_ENST00000400569.3_Silent_p.K517K	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	517	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						CCTCCAAGCACTTCACATCCA	0.478																																					p.K517K		Atlas-SNP	.											.	MYOM1	192	.	0			c.G1551A						.						58	59	58					18																	3155037		1967	4163	6130	SO:0001819	synonymous_variant	8736	exon11			CAAGCACTTCACA	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7613	protein-coding gene	gene with protein product	"skelemin"	603508	"myomesin 1 (skelemin) (185kD)", "myomesin 1 (skelemin) 185kDa", "myomesin 1, 185kDa"			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.1551G>A	chr18.hg19:g.3155037C>T		78.0	0.0		72.0	9.0	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Silent	SNP	ENST00000356443.4	hg19	CCDS45824.1																																																																																			.	.		0.478	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803		T	3155037	C	T	3155037	2	4	238	1	0	0	0	0	0	0	0	1	10100	564	20	3		3	MYOM1	18	3155037	Silent	SNP	C	TCGA-ED-A4XI-01A-11D-A25V-10		3155037	74922211	112	33239										
NDUFV2	4729	hgsc.bcm.edu	37	chr18	9119504	9119504	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	attgtaaaaaactatccagaAggccataaagcagcagctgt	8	8	0	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr18:9119504A>G	ENST00000318388.6	+	4	330	c.216A>G	c.(214-216)gaA>gaG	p.E72E	NDUFV2_ENST00000400033.1_Silent_p.E75E|RP11-21J18.1_ENST00000579126.1_RNA|RP11-143J12.2_ENST00000582375.1_RNA|NDUFV2_ENST00000465096.1_3'UTR|RP11-143J12.2_ENST00000583081.1_RNA	NM_021074.4	NP_066552.2	P19404	NDUV2_HUMAN	NADH dehydrogenase (ubiquinone) flavoprotein 2, 24kDa	72					cardiac muscle tissue development (GO:0048738)|cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|nervous system development (GO:0007399)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|lung(4)|ovary(1)|stomach(1)	7						ACTATCCAGAAGGCCATAAAG	0.358																																					p.E72E		Atlas-SNP	.											.	NDUFV2	17	.	0			c.A216G						.						53	53	53					18																	9119504		2203	4299	6502	SO:0001819	synonymous_variant	4729	exon4			TCCAGAAGGCCAT	X84421	CCDS11842.1	18p11.22	2011-07-04	2002-08-29		ENSG00000178127	ENSG00000178127	1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7717	protein-coding gene	gene with protein product	"complex I 24kDa subunit", "NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial"	600532	"NADH dehydrogenase (ubiquinone) flavoprotein 2 (24kD)"			9763677, 7607668	Standard	NM_021074		Approved	CI-24k	uc002knu.3	P19404	OTTHUMG00000131593	ENST00000318388.6:c.216A>G	chr18.hg19:g.9119504A>G		118.0	0.0		113.0	11.0	NM_021074	Q9BV41	Silent	SNP	ENST00000318388.6	hg19	CCDS11842.1																																																																																			.	.		0.358	NDUFV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254475.2	NM_021074		G	9119504	A	G	9119504	2	3	238	1	0	0	0	0	0	0	0	1	10309	69	3	2		2	NDUFV2	18	9119504	Silent	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	5964467	9119504	68957744	113	33240										
MOCOS	55034	hgsc.bcm.edu	37	chr18	33778679	33778679	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	ctcacagccagaacatcagcAgcaagctcacccatgacact	6	16	3	2			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr18:33778679A>G	ENST00000261326.5	+	3	280	c.259A>G	c.(259-261)Agc>Ggc	p.S87G		NM_017947.2	NP_060417.2			molybdenum cofactor sulfurase											breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|liver(1)|lung(15)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						GAACATCAGCAGCAAGCTCAC	0.522																																					p.S87G		Atlas-SNP	.											.	MOCOS	84	.	0			c.A259G						.						157	122	134					18																	33778679		2203	4300	6503	SO:0001583	missense	55034	exon3			ATCAGCAGCAAGC	AK000740	CCDS11919.1	18q12	2003-12-18			ENSG00000075643	ENSG00000075643			18234	protein-coding gene	gene with protein product		613274				11302742	Standard	NM_017947		Approved	HMCS, FLJ20733, MOS	uc002kzq.4	Q96EN8	OTTHUMG00000132590	ENST00000261326.5:c.259A>G	chr18.hg19:g.33778679A>G	ENSP00000261326:p.Ser87Gly	222.0	0.0		237.0	12.0	NM_017947		Missense_Mutation	SNP	ENST00000261326.5	hg19	CCDS11919.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.549254	0.86127	.	.	ENSG00000075643	ENST00000261326	D	0.86432	-2.12	5.58	5.58	0.84498	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	0.000000	0.85682	D	0.000000	D	0.89818	0.6825	M	0.67625	2.065	0.40017	D	0.97536	P	0.49447	0.924	P	0.53760	0.734	D	0.90666	0.4594	10	0.56958	D	0.05	-26.102	12.1284	0.53930	1.0:0.0:0.0:0.0	.	87	Q96EN8	MOCOS_HUMAN	G	87	ENSP00000261326:S87G	ENSP00000261326:S87G	S	+	1	0	MOCOS	32032677	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.476000	0.81055	2.126000	0.65437	0.460000	0.39030	AGC	.	.		0.522	MOCOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255801.1			G	33778679	A	G	33778679	3	3	238	1	0	0	0	0	1	0	0	0	9698	188	7	2	269	2	MOCOS	18	33778679	Missense_Mutation	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	24659175	33778679	44298569	114	33241										
SERPINB3	6317	hgsc.bcm.edu	37	chr18	61325772	61325772	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	gtttgactttccacccaggaGttaatcttctttcgactttc	6	11	2	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr18:61325772G>T	ENST00000283752.5	-	5	587	c.444C>A	c.(442-444)aaC>aaA	p.N148K	SERPINB11_ENST00000489748.1_RNA|SERPINB3_ENST00000332821.8_Missense_Mutation_p.N148K	NM_006919.2	NP_008850.1	P29508	SPB3_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 3	148					negative regulation of catalytic activity (GO:0043086)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)|virus receptor activity (GO:0001618)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	36						CCACCCAGGAGTTAATCTTCT	0.418																																					p.N148K		Atlas-SNP	.											.	SERPINB3	90	.	0			c.C444A						.						109	98	102					18																	61325772		2203	4298	6501	SO:0001583	missense	6317	exon5			CCAGGAGTTAATC	U19568	CCDS11987.1	18q21.3	2014-02-18	2005-08-18		ENSG00000057149	ENSG00000057149		"Serine (or cysteine) peptidase inhibitors"	10569	protein-coding gene	gene with protein product		600517	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3"	SCC, SCCA1		7724531, 24172014	Standard	NM_006919		Approved	T4-A, HsT1196	uc002lji.3	P29508	OTTHUMG00000060403	ENST00000283752.5:c.444C>A	chr18.hg19:g.61325772G>T	ENSP00000283752:p.Asn148Lys	105.0	0.0		103.0	12.0	NM_006919	A6NDM2|B2RBT5|B3W5Y6|Q53H28|Q53YB5|Q86VF3|Q86W04|Q8IWL4|Q8IXI3|Q96J21|Q9BYF8	Missense_Mutation	SNP	ENST00000283752.5	hg19	CCDS11987.1	.	.	.	.	.	.	.	.	.	.	G	14.75	2.629054	0.46944	.	.	ENSG00000057149	ENST00000283752;ENST00000332821	D;D	0.92348	-3.02;-3.02	2.97	-0.434	0.12283	Serpin domain (3);	0.000000	0.41194	D	0.000924	D	0.97420	0.9156	H	0.99834	4.825	0.34867	D	0.743223	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.95192	0.8309	10	0.87932	D	0	.	7.7049	0.28644	0.6339:0.0:0.3661:0.0	.	148;148;148	P29508-2;P29508;Q5K684	.;SPB3_HUMAN;.	K	148	ENSP00000283752:N148K;ENSP00000329498:N148K	ENSP00000283752:N148K	N	-	3	2	SERPINB3	59476752	0.004000	0.15560	0.995000	0.50966	0.841000	0.47740	-0.228000	0.09114	-0.091000	0.12440	-0.463000	0.05309	AAC	.	.		0.418	SERPINB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133791.1	NM_006919		T	61325772	G	T	61325772	3	4	238	1	0	0	0	0	1	0	0	0	14117	1020	36	3	744	3	SERPINB3	18	61325772	Missense_Mutation	SNP	G	TCGA-ED-A4XI-01A-11D-A25V-10	27547093	61325772	16751476	115	33242										
ADNP2	22850	hgsc.bcm.edu	37	chr18	77895740	77895740	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	tcaattagatgtcgatgccaAtggcaacctgctctttcccc	7	13	2	1	rs113879497	byFrequency	TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr18:77895740A>T	ENST00000262198.4	+	4	2899	c.2444A>T	c.(2443-2445)aAt>aTt	p.N815I		NM_014913.3	NP_055728.1	Q6IQ32	ADNP2_HUMAN	ADNP homeobox 2	815					cellular response to oxidative stress (GO:0034599)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell death (GO:0060548)|neuron differentiation (GO:0030182)|positive regulation of cell growth (GO:0030307)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(9)|liver(1)|lung(15)|ovary(5)|prostate(2)	42		all_cancers(4;1.06e-15)|all_epithelial(4;2.36e-10)|all_lung(4;0.000302)|Lung NSC(4;0.000518)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0256)|all_hematologic(56;0.15)|Melanoma(33;0.2)		Epithelial(2;1.1e-11)|OV - Ovarian serous cystadenocarcinoma(15;7.54e-09)|BRCA - Breast invasive adenocarcinoma(31;0.00247)|STAD - Stomach adenocarcinoma(84;0.164)		GTCGATGCCAATGGCAACCTG	0.478																																					p.N815I		Atlas-SNP	.											.	ADNP2	102	.	0			c.A2444T						.						95	94	94					18																	77895740		2203	4300	6503	SO:0001583	missense	22850	exon4			ATGCCAATGGCAA	AB020670	CCDS32853.1	18q23	2013-01-07	2007-07-17	2007-07-17	ENSG00000101544	ENSG00000101544		"Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	23803	protein-coding gene	gene with protein product			"zinc finger protein 508"	ZNF508			Standard	NM_014913		Approved	KIAA0863	uc002lnw.3	Q6IQ32	OTTHUMG00000172535	ENST00000262198.4:c.2444A>T	chr18.hg19:g.77895740A>T	ENSP00000262198:p.Asn815Ile	91.0	0.0		94.0	16.0	NM_014913	A8K951|O94943|Q9H9P3	Missense_Mutation	SNP	ENST00000262198.4	hg19	CCDS32853.1	.	.	.	.	.	.	.	.	.	.	A	13.66	2.303087	0.40795	.	.	ENSG00000101544	ENST00000262198	.	.	.	5.18	2.77	0.32553	.	0.326264	0.28895	N	0.013794	T	0.37972	0.1023	M	0.61703	1.905	0.09310	N	1	B	0.30973	0.302	B	0.33042	0.157	T	0.21999	-1.0229	8	.	.	.	-16.8291	8.4314	0.32759	0.8287:0.0:0.1713:0.0	.	815	Q6IQ32	ADNP2_HUMAN	I	815	.	.	N	+	2	0	ADNP2	75996731	0.000000	0.05858	0.514000	0.27761	0.909000	0.53808	0.670000	0.25157	0.416000	0.25844	0.533000	0.62120	AAT	.	A|0.999;G|0.001		0.478	ADNP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418979.1	NM_014913		T	77895740	A	T	77895740	3	4	238	1	0	0	0	0	1	0	0	0	324	101	4	4	2454	4	ADNP2	18	77895740	Missense_Mutation	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	16569968	77895740	181508	116	33243										
CD70	970	hgsc.bcm.edu	37	chr19	6586092	6586092	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	tgtttcgggaaggcaaaagtGtcccagtgaggttggtgcag	16	6	0	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr19:6586092G>T	ENST00000245903.3	-	3	670	c.521C>A	c.(520-522)aCa>aAa	p.T174K	CD70_ENST00000423145.3_Intron	NM_001252.3	NP_001243.1	P32970	CD70_HUMAN	CD70 molecule	174					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|extrinsic apoptotic signaling pathway (GO:0097191)|immune response (GO:0006955)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	protease binding (GO:0002020)|receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|skin(1)	11						AGGCAAAAGTGTCCCAGTGAG	0.542																																					p.T174K	Pancreas(183;2617 2876 10173 34193)	Atlas-SNP	.											.	CD70	24	.	0			c.C521A						.						68	55	59					19																	6586092		2203	4300	6503	SO:0001583	missense	970	exon3			AAAAGTGTCCCAG	L08096	CCDS12170.1	19p13	2013-05-22	2006-10-27	2006-10-27		ENSG00000125726		"Tumor necrosis factor (ligand) superfamily", "CD molecules"	11937	protein-coding gene	gene with protein product		602840	"tumor necrosis factor (ligand) superfamily, member 7"	CD27LG, TNFSF7		8387892, 8120384	Standard	NM_001252		Approved	CD27L	uc002mfi.3	P32970		ENST00000245903.3:c.521C>A	chr19.hg19:g.6586092G>T	ENSP00000245903:p.Thr174Lys	93.0	0.0		102.0	16.0	NM_001252	B4DPR8|Q53XX4|Q96J57	Missense_Mutation	SNP	ENST00000245903.3	hg19	CCDS12170.1	.	.	.	.	.	.	.	.	.	.	G	13.69	2.312654	0.40895	.	.	ENSG00000125726	ENST00000245903	D	0.94330	-3.4	4.42	4.42	0.53409	Tumour necrosis factor (3);Tumour necrosis factor-like (2);	0.278703	0.25848	N	0.027906	D	0.86640	0.5981	N	0.14661	0.345	0.09310	N	1	P	0.37914	0.611	B	0.37015	0.239	T	0.82220	-0.0565	10	0.66056	D	0.02	.	12.8622	0.57920	0.0:0.0:1.0:0.0	.	174	P32970	CD70_HUMAN	K	174	ENSP00000245903:T174K	ENSP00000245903:T174K	T	-	2	0	CD70	6537092	0.410000	0.25376	0.017000	0.16124	0.002000	0.02628	2.532000	0.45659	2.184000	0.69523	0.556000	0.70494	ACA	.	.		0.542	CD70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457860.1			T	6586092	G	T	6586092	3	4	238	1	0	0	0	0	1	0	0	0	3035	1377	48	3	64	3	CD70	19	6586092	Missense_Mutation	SNP	G	TCGA-ED-A4XI-01A-11D-A25V-10		6586092	52542891	117	33244										
MUC16	94025	hgsc.bcm.edu	37	chr19	9059729	9059729	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	actgagtcagctaggacagaGgaaggagattcatgtgtata	13	5	2	3			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr19:9059729G>C	ENST00000397910.4	-	3	27920	c.27717C>G	c.(27715-27717)tcC>tcG	p.S9239S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9241	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTAGGACAGAGGAAGGAGATT	0.463																																					p.S9239S		Atlas-SNP	.											.	MUC16	4315	.	0			c.C27717G						.						96	96	96					19																	9059729		2069	4228	6297	SO:0001819	synonymous_variant	94025	exon3			GACAGAGGAAGGA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.27717C>G	chr19.hg19:g.9059729G>C		367.0	0.0		281.0	26.0	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.463	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	9059729	G	C	9059729	2	2	238	1	0	0	0	0	0	0	0	1	9982	987	35	4		4	MUC16	19	9059729	Silent	SNP	G	TCGA-ED-A4XI-01A-11D-A25V-10	2473637	9059729	50069254	118	33245										
KEAP1	9817	hgsc.bcm.edu	37	chr19	10600002	10600002	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	tcagctggtcctgaccatcaTagcccccagcagcatagata	8	14	2	2			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr19:10600002T>C	ENST00000171111.5	-	5	2121	c.1574A>G	c.(1573-1575)tAt>tGt	p.Y525C	CTC-429L19.3_ENST00000592671.1_RNA|KEAP1_ENST00000588024.1_5'Flank|KEAP1_ENST00000393623.2_Missense_Mutation_p.Y525C	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	525					cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)				breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	CTGACCATCATAGCCCCCAGC	0.597																																					p.Y525C		Atlas-SNP	.											.	KEAP1	182	.	0			c.A1574G						.						76	58	64					19																	10600002		2203	4300	6503	SO:0001583	missense	9817	exon5			CCATCATAGCCCC	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"Kelch-like", "BTB/POZ domain containing"	23177	protein-coding gene	gene with protein product	"kelch-like family member 19"	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.1574A>G	chr19.hg19:g.10600002T>C	ENSP00000171111:p.Tyr525Cys	197.0	0.0		152.0	9.0	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Missense_Mutation	SNP	ENST00000171111.5	hg19	CCDS12239.1	.	.	.	.	.	.	.	.	.	.	T	17.50	3.405638	0.62288	.	.	ENSG00000079999	ENST00000171111;ENST00000393623	T;T	0.77229	-1.08;-1.08	5.73	5.73	0.89815	Kelch-type beta propeller (1);	0.123265	0.56097	D	0.000026	D	0.85957	0.5818	M	0.64170	1.965	0.51012	D	0.999904	D	0.89917	1.0	D	0.97110	1.0	D	0.86649	0.1897	10	0.56958	D	0.05	.	14.01	0.64490	0.0:0.0:0.0:1.0	.	525	Q14145	KEAP1_HUMAN	C	525	ENSP00000171111:Y525C;ENSP00000377245:Y525C	ENSP00000171111:Y525C	Y	-	2	0	KEAP1	10461002	1.000000	0.71417	0.997000	0.53966	0.580000	0.36256	5.540000	0.67205	2.200000	0.70718	0.477000	0.44152	TAT	.	.		0.597	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289		C	10600002	T	C	10600002	3	2	238	1	0	0	0	0	1	0	0	0	8150	1406	49	2	308	2	KEAP1	19	10600002	Missense_Mutation	SNP	T	TCGA-ED-A4XI-01A-11D-A25V-10	1540273	10600002	48528981	119	33246										
ZNF254	9534	hgsc.bcm.edu	37	chr19	24309164	24309164	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	atatggacatgagaatttacAgttaagaaaaggctgtaaaa	9	3	0	2			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr19:24309164A>T	ENST00000357002.4	+	4	477	c.362A>T	c.(361-363)cAg>cTg	p.Q121L	ZNF254_ENST00000342944.6_Missense_Mutation_p.Q36L	NM_001278661.1|NM_001278662.1|NM_001278664.1|NM_001278677.1|NM_001278678.1|NM_203282.2	NP_001265590.1|NP_001265591.1|NP_001265593.1|NP_001265606.1|NP_001265607.1|NP_975011.3	O75437	ZN254_HUMAN	zinc finger protein 254	121					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)						all_cancers(12;0.086)|all_lung(12;0.00528)|Lung NSC(12;0.00731)|all_epithelial(12;0.0186)				GAGAATTTACAGTTAAGAAAA	0.378																																					p.Q121L		Atlas-SNP	.											.	ZNF254	88	.	0			c.A362T						.						64	67	66					19																	24309164		2203	4299	6502	SO:0001583	missense	9534	exon4			ATTTACAGTTAAG	AF054180	CCDS32983.1, CCDS62622.1, CCDS62623.1, CCDS74323.1, CCDS74324.1	19p13	2013-01-08				ENSG00000213096		"Zinc fingers, C2H2-type", "-"	13047	protein-coding gene	gene with protein product		604768	"zinc finger protein 539"	ZNF91L, ZNF539		9653160	Standard	NM_001278661		Approved	HD-ZNF1, BMZF-5	uc002nru.3	O75437		ENST00000357002.4:c.362A>T	chr19.hg19:g.24309164A>T	ENSP00000349494:p.Gln121Leu	91.0	0.0		120.0	6.0	NM_203282	A4QPC0|Q86XL7	Missense_Mutation	SNP	ENST00000357002.4	hg19	CCDS32983.1	.	.	.	.	.	.	.	.	.	.	A	11.17	1.558381	0.27827	.	.	ENSG00000213096	ENST00000342944;ENST00000357002;ENST00000392281	T;T	0.08008	3.14;3.36	1.3	1.3	0.21679	.	.	.	.	.	T	0.11665	0.0284	M	0.79258	2.445	0.09310	N	1	B	0.18610	0.029	B	0.21151	0.033	T	0.20739	-1.0266	9	0.49607	T	0.09	.	6.3276	0.21253	1.0:0.0:0.0:0.0	.	121	O75437	ZN254_HUMAN	L	36;121;121	ENSP00000445527:Q36L;ENSP00000349494:Q121L	ENSP00000445527:Q36L	Q	+	2	0	ZNF254	24101004	0.001000	0.12720	0.005000	0.12908	0.034000	0.12701	0.386000	0.20702	0.565000	0.29255	0.260000	0.18958	CAG	.	.		0.378	ZNF254-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466453.1	NM_004876		T	24309164	A	T	24309164	3	4	238	1	0	0	0	0	1	0	0	0	17813	188	7	4	376	4	ZNF254	19	24309164	Missense_Mutation	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	13709162	24309164	34819819	120	33247										
ZFP82	284406	hgsc.bcm.edu	37	chr19	36884090	36884090	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	tcaccagtatgaattctgtgAtggagaataagatgataacc	9	6	2	5			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr19:36884090A>C	ENST00000392161.3	-	5	1394	c.1152T>G	c.(1150-1152)caT>caG	p.H384Q	ZFP82_ENST00000392171.1_Missense_Mutation_p.H384Q	NM_133466.2	NP_597723.1	Q8N141	ZFP82_HUMAN	ZFP82 zinc finger protein	384					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						GAATTCTGTGATGGAGAATAA	0.378																																					p.H384Q		Atlas-SNP	.											.	ZFP82	71	.	0			c.T1152G						.						114	113	113					19																	36884090		2203	4300	6503	SO:0001583	missense	284406	exon5			TCTGTGATGGAGA	AL834267	CCDS12493.1	19q13.13	2013-01-08	2012-11-27	2008-07-01		ENSG00000181007		"Zinc fingers, C2H2-type", "-"	28682	protein-coding gene	gene with protein product			"zinc finger protein 545", "zinc finger protein 82 homolog (mouse)", "zinc finger protein 82"	ZNF545		11853319	Standard	NM_133466		Approved	MGC45380, KIAA1948	uc002ody.1	Q8N141		ENST00000392161.3:c.1152T>G	chr19.hg19:g.36884090A>C	ENSP00000431265:p.His384Gln	101.0	0.0		114.0	11.0	NM_133466	Q8NC63|Q8TF53	Missense_Mutation	SNP	ENST00000392161.3	hg19	CCDS12493.1	.	.	.	.	.	.	.	.	.	.	A	14.93	2.683835	0.47991	.	.	ENSG00000181007	ENST00000392161;ENST00000392171	D;D	0.86865	-2.18;-2.18	4.53	2.44	0.29823	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.42964	D	0.000627	D	0.94377	0.8192	H	0.96430	3.82	0.31754	N	0.634165	D	0.89917	1.0	D	0.97110	1.0	D	0.92064	0.5659	10	0.87932	D	0	.	7.1164	0.25418	0.8075:0.0:0.1925:0.0	.	384	Q8N141	ZFP82_HUMAN	Q	384	ENSP00000431265:H384Q;ENSP00000446080:H384Q	ENSP00000431265:H384Q	H	-	3	2	ZFP82	41575930	0.997000	0.39634	1.000000	0.80357	0.993000	0.82548	2.095000	0.41729	0.279000	0.22186	0.482000	0.46254	CAT	.	.		0.378	ZFP82-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109552.2	NM_133466		C	36884090	A	C	36884090	3	2	238	1	0	0	0	0	1	0	0	0	17668	330	12	5	450	5	ZFP82	19	36884090	Missense_Mutation	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	12574926	36884090	22244893	121	33248										
CIC	23152	hgsc.bcm.edu	37	chr19	42798805	42798805	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	ctagagtatgacaaggtgccAtactcctccctgcggcgcac	10	14	0	2			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr19:42798805A>G	ENST00000575354.2	+	19	4417	c.4377A>G	c.(4375-4377)ccA>ccG	p.P1459P	CIC_ENST00000160740.3_Silent_p.P1457P|CIC_ENST00000572681.2_Silent_p.P2365P	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	1459					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				ACAAGGTGCCATACTCCTCCC	0.637			"Mis, F, S"		oligodendroglioma																																p.P1459P		Atlas-SNP	.		Rec	yes		19	19q13.2	23152	capicua homolog		O	.	CIC	249	.	0			c.A4377G						.						79	72	75					19																	42798805		2203	4300	6503	SO:0001819	synonymous_variant	23152	exon19			GGTGCCATACTCC	AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"capicua (Drosophila) homolog", "capicua homolog (Drosophila)"			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.4377A>G	chr19.hg19:g.42798805A>G		148.0	0.0		114.0	18.0	NM_015125	Q7LGI1|Q9UEG5|Q9Y6T1	Silent	SNP	ENST00000575354.2	hg19	CCDS12601.1																																																																																			.	.		0.637	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			G	42798805	A	G	42798805	2	3	238	1	0	0	0	0	0	0	0	1	3426	204	8	2		2	CIC	19	42798805	Silent	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	5914715	42798805	16330178	122	33249										
SCAF1	58506	hgsc.bcm.edu	37	chr19	50156751	50156751	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	gaagaggaggaggaagaggaAgaggaggaggagcagcagcc	21	4	0	3			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr19:50156751A>G	ENST00000360565.3	+	7	3229	c.3105A>G	c.(3103-3105)gaA>gaG	p.E1035E		NM_021228.2	NP_067051.2	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	1035	Glu-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	20		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00113)|GBM - Glioblastoma multiforme(134;0.0204)		aggaagaggaagaggaggagg	0.682																																					p.E1035E		Atlas-SNP	.											.	SCAF1	78	.	0			c.A3105G						.						9	12	11					19																	50156751		2196	4287	6483	SO:0001819	synonymous_variant	58506	exon7			AGAGGAAGAGGAG	AK024444	CCDS33074.1	19q13.3-q13.4	2011-01-10			ENSG00000126461	ENSG00000126461			30403	protein-coding gene	gene with protein product						11461075	Standard	NM_021228		Approved	SR-A1, FLJ00034	uc002poq.3	Q9H7N4		ENST00000360565.3:c.3105A>G	chr19.hg19:g.50156751A>G		23.0	0.0		19.0	6.0	NM_021228	Q7Z5V7|Q8WVA1|Q9NR59	Silent	SNP	ENST00000360565.3	hg19	CCDS33074.1																																																																																			.	.		0.682	SCAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465764.1	NM_021228		G	50156751	A	G	50156751	2	3	238	1	0	0	0	0	0	0	0	1	13883	69	3	2		2	SCAF1	19	50156751	Silent	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	7357946	50156751	8972232	123	33250										
NLRP12	91662	hgsc.bcm.edu	37	chr19	54310856	54310856	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	gacagctctatcaggtttggAttggtgcacagggccgctgc	14	10	2	0			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr19:54310856A>T	ENST00000324134.6	-	4	2304	c.2136T>A	c.(2134-2136)aaT>aaA	p.N712K	NLRP12_ENST00000345770.5_Missense_Mutation_p.N713K|NLRP12_ENST00000391772.1_Missense_Mutation_p.N713K|NLRP12_ENST00000351894.4_Missense_Mutation_p.N712K|NLRP12_ENST00000354278.3_Missense_Mutation_p.N712K|NLRP12_ENST00000391773.1_Missense_Mutation_p.N713K|NLRP12_ENST00000535162.1_Missense_Mutation_p.N712K|NLRP12_ENST00000391775.3_Missense_Mutation_p.N712K	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	712					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to cytokine stimulus (GO:0071345)|dendritic cell migration (GO:0036336)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of signal transduction (GO:0009968)|negative regulation of Toll signaling pathway (GO:0045751)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of MHC class I biosynthetic process (GO:0045345)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of interleukin-18 biosynthetic process (GO:0045381)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)			NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(36)|ovary(5)|pancreas(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	80	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		TCAGGTTTGGATTGGTGCACA	0.562																																					p.L712L		Atlas-SNP	.											.	NLRP12	236	.	0			c.G2136A						.						101	88	92					19																	54310856		2203	4300	6503	SO:0001583	missense	91662	exon4			GTTTGGATTGGTG	AY095146	CCDS12864.1, CCDS62784.1, CCDS62785.1	19q13.42	2014-09-17	2006-12-08	2006-12-08	ENSG00000142405	ENSG00000142405		"Nucleotide-binding domain and leucine rich repeat containing"	22938	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 12"	609648	"NACHT, leucine rich repeat and PYD containing 12"	NALP12		12563287, 12019269	Standard	NM_001277129		Approved	RNO2, PYPAF7, Monarch1, PAN6, CLR19.3	uc002qcj.5	P59046	OTTHUMG00000060776	ENST00000324134.6:c.2136T>A	chr19.hg19:g.54310856A>T	ENSP00000319377:p.Asn712Lys	158.0	0.0		133.0	6.0	NM_144687	A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Silent	SNP	ENST00000324134.6	hg19	CCDS12864.1	.	.	.	.	.	.	.	.	.	.	A	15.26	2.780015	0.49891	.	.	ENSG00000142405	ENST00000324134;ENST00000535162;ENST00000351894;ENST00000354278;ENST00000391775;ENST00000391773;ENST00000345770;ENST00000391772	D;D;D;D;D;D;D	0.90385	-2.66;-2.66;-2.66;-2.66;-2.66;-2.33;-2.33	3.85	-4.67	0.03319	.	0.652514	0.12395	U	0.472677	D	0.92658	0.7667	M	0.80847	2.515	0.09310	N	0.999996	D;P;P;D	0.60575	0.988;0.65;0.931;0.961	P;P;P;P	0.60541	0.876;0.515;0.742;0.864	D	0.87435	0.2391	10	0.66056	D	0.02	.	9.3022	0.37853	0.5708:0.0:0.4292:0.0	.	713;712;712;712	F2Z321;A8K407;A8MTQ2;P59046	.;.;.;NAL12_HUMAN	K	712;712;712;712;712;713;713;713	ENSP00000319377:N712K;ENSP00000438030:N712K;ENSP00000340473:N712K;ENSP00000346231:N712K;ENSP00000375655:N712K;ENSP00000375653:N713K;ENSP00000375652:N713K	ENSP00000319377:N712K	N	-	3	2	NLRP12	59002668	0.000000	0.05858	0.001000	0.08648	0.024000	0.10985	-4.163000	0.00282	-0.852000	0.04141	-0.384000	0.06662	AAT	.	.		0.562	NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000134340.1	NM_144687		T	54310856	A	T	54310856	3	4	238	1	0	0	0	0	1	0	0	0	10483	330	12	4	1173	4	NLRP12	19	54310856	Missense_Mutation	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	4154105	54310856	4818127	124	33251										
CHMP2A	27243	hgsc.bcm.edu	37	chr19	59063031	59063031	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	ggcactcagtccctccgcagGttcttaagccgttcctccag	9	16	2	0			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr19:59063031G>T	ENST00000600118.1	-	5	1079	c.654C>A	c.(652-654)aaC>aaA	p.N218K	CHMP2A_ENST00000312547.2_Missense_Mutation_p.N218K|CHMP2A_ENST00000601220.1_Missense_Mutation_p.N218K			O43633	CHM2A_HUMAN	charged multivesicular body protein 2A	218	Interaction with VPS4B.|Interaction with VTA1.				endosomal transport (GO:0016197)|establishment of protein localization (GO:0045184)|membrane organization (GO:0061024)|positive regulation of viral release from host cell (GO:1902188)|protein transport (GO:0015031)|regulation of viral process (GO:0050792)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	protein domain specific binding (GO:0019904)			endometrium(1)|kidney(1)|large_intestine(3)|lung(2)	7		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)		CCCTCCGCAGGTTCTTAAGCC	0.552																																					p.N218K		Atlas-SNP	.											.	CHMP2A	25	.	0			c.C654A						.						60	65	63					19																	59063031		2203	4300	6503	SO:0001583	missense	27243	exon6			CCGCAGGTTCTTA	AF042384	CCDS12986.1	19q13.43	2014-09-04	2011-09-21		ENSG00000130724	ENSG00000130724		"Charged multivesicular body proteins"	30216	protein-coding gene	gene with protein product	"putative breast adenocarcinoma marker (32kD)", "VPS2 homolog A (S. cerevisiae)"	610893	"chromatin modifying protein 2A"			15173323, 11559748	Standard	XM_005258746		Approved	BC-2, CHMP2, VPS2, VPS2A	uc002qtk.3	O43633	OTTHUMG00000183547	ENST00000600118.1:c.654C>A	chr19.hg19:g.59063031G>T	ENSP00000469240:p.Asn218Lys	76.0	0.0		69.0	5.0	NM_198426	B2R4W6|Q3ZTT0	Missense_Mutation	SNP	ENST00000600118.1	hg19	CCDS12986.1	.	.	.	.	.	.	.	.	.	.	G	9.989	1.230373	0.22542	.	.	ENSG00000130724	ENST00000312547	T	0.77489	-1.1	4.83	2.65	0.31530	.	0.000000	0.85682	D	0.000000	T	0.50548	0.1622	N	0.08118	0	0.58432	D	0.999999	B	0.25904	0.137	B	0.12156	0.007	T	0.39165	-0.9627	10	0.07813	T	0.8	.	8.6462	0.34007	0.196:0.0:0.804:0.0	.	218	O43633	CHM2A_HUMAN	K	218	ENSP00000310440:N218K	ENSP00000310440:N218K	N	-	3	2	CHMP2A	63754843	1.000000	0.71417	0.996000	0.52242	0.372000	0.29890	3.644000	0.54381	0.710000	0.31997	0.650000	0.86243	AAC	.	.		0.552	CHMP2A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467088.1	NM_014453		T	59063031	G	T	59063031	3	4	238	1	0	0	0	0	1	0	0	0	3356	1252	44	3	18	3	CHMP2A	19	59063031	Missense_Mutation	SNP	G	TCGA-ED-A4XI-01A-11D-A25V-10	4752175	59063031	65952	125	33252										
PLK1S1	55857	hgsc.bcm.edu	37	chr20	21213370	21213370	+	RNA	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	tccatgtttacgcttatcacAggtttgaatattggcagcgg	10	8	1	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr20:21213370A>T	ENST00000457464.1	+	0	1380																											CGCTTATCACAGGTTTGAATA	0.433																																					.		Atlas-SNP	.											.	.	.	.	0			c.1384-2A>T						.						51	52	52					20																	21213370		1986	4174	6160			55857	exon9			TATCACAGGTTTG																													chr20.hg19:g.21213370A>T		113.0	0.0		132.0	7.0	NM_001163023		Splice_Site	SNP	ENST00000457464.1	hg19																																																																																				.	.		0.433	PLK1S1-003	KNOWN	not_organism_supported|sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000078262.2			T	21213370	A	T	21213370	1	4	238	0	1	0	0	0	0	0	0	0	12104	202	7	4		4	PLK1S1	20	21213370	RNA	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10		21213370	41812150	126	33253										
DIDO1	11083	hgsc.bcm.edu	37	chr20	61511821	61511821	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	cctcgtggtccaccaaggtaAgagggtgaggggcctctgct	15	11	1	2			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr20:61511821A>G	ENST00000266070.4	-	16	5812	c.5487T>C	c.(5485-5487)tcT>tcC	p.S1829S	DIDO1_ENST00000395343.1_Silent_p.S1829S	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	1829	Pro-rich.				apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					CACCAAGGTAAGAGGGTGAGG	0.602																																					p.S1829S	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											.	DIDO1	321	.	0			c.T5487C						.						66	74	72					20																	61511821		2203	4300	6503	SO:0001819	synonymous_variant	11083	exon16			AAGGTAAGAGGGT	AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"Zinc fingers, PHD-type"	2680	protein-coding gene	gene with protein product		604140	"chromosome 20 open reading frame 158", "death associated transcription factor 1"	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.5487T>C	chr20.hg19:g.61511821A>G		156.0	0.0		129.0	14.0	NM_001193369	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Silent	SNP	ENST00000266070.4	hg19	CCDS33506.1																																																																																			.	.		0.602	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796		G	61511821	A	G	61511821	2	3	238	1	0	0	0	0	0	0	0	1	4524	59	3	2		2	DIDO1	20	61511821	Silent	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	40298451	61511821	1513699	127	33254										
KRTAP13-3	337960	hgsc.bcm.edu	37	chr21	31797785	31797785	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	ttctaggtggaaaatagattGgatggcagaatctggatcta	12	4	3	2			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr21:31797785G>A	ENST00000390690.2	-	1	501	c.446C>T	c.(445-447)cCa>cTa	p.P149L		NM_181622.1	NP_853653.1	Q3SY46	KR133_HUMAN	keratin associated protein 13-3	149						intermediate filament (GO:0005882)				endometrium(1)|large_intestine(1)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	14						AAAATAGATTGGATGGCAGAA	0.428																																					p.P149L		Atlas-SNP	.											.	KRTAP13-3	47	.	0			c.C446T						.						57	55	56					21																	31797785		1925	4161	6086	SO:0001583	missense	337960	exon1			TAGATTGGATGGC	AP001708	CCDS13591.1	21q22.1	2006-03-13			ENSG00000240432	ENSG00000240432		"Keratin associated proteins"	18925	protein-coding gene	gene with protein product						12359730	Standard	NM_181622		Approved	KAP13.3	uc002yob.1	Q3SY46	OTTHUMG00000057776	ENST00000390690.2:c.446C>T	chr21.hg19:g.31797785G>A	ENSP00000375109:p.Pro149Leu	103.0	0.0		72.0	7.0	NM_181622	Q3LI78	Missense_Mutation	SNP	ENST00000390690.2	hg19	CCDS13591.1	.	.	.	.	.	.	.	.	.	.	g	15.25	2.779012	0.49891	.	.	ENSG00000240432	ENST00000390690;ENST00000448917	T	0.09445	2.98	4.03	4.03	0.46877	.	0.175309	0.26742	U	0.022739	T	0.31389	0.0795	M	0.82132	2.575	0.09310	N	1	D	0.71674	0.998	D	0.66847	0.947	T	0.03597	-1.1021	10	0.66056	D	0.02	0.0569	12.1568	0.54081	0.0:0.0:1.0:0.0	.	149	Q3SY46	KR133_HUMAN	L	149;139	ENSP00000375109:P149L	ENSP00000375109:P149L	P	-	2	0	KRTAP13-3	30719656	0.287000	0.24315	0.008000	0.14137	0.002000	0.02628	2.354000	0.44098	2.570000	0.86706	0.568000	0.79292	CCA	.	.		0.428	KRTAP13-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128228.2			A	31797785	G	A	31797785	3	1	238	1	0	0	0	0	1	0	0	0	8533	1348	47	3	76	3	KRTAP13-3	21	31797785	Missense_Mutation	SNP	G	TCGA-ED-A4XI-01A-11D-A25V-10		31797785	16332110	128	33255										
CSTB	1476	hgsc.bcm.edu	37	chr21	45194153	45194153	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	ataaggtcaagggcttgtttTcatgagggagagattggaac	14	4	2	2			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr21:45194153T>C	ENST00000291568.5	-	3	402	c.227A>G	c.(226-228)gAa>gGa	p.E76G		NM_000100.3	NP_000091.1	P04080	CYTB_HUMAN	cystatin B (stefin B)	76					adult locomotory behavior (GO:0008344)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|endopeptidase inhibitor activity (GO:0004866)|poly(A) RNA binding (GO:0044822)|protease binding (GO:0002020)			lung(1)|prostate(1)	2				STAD - Stomach adenocarcinoma(101;0.168)		GGGCTTGTTTTCATGAGGGAG	0.527																																					p.E76G	Esophageal Squamous(58;831 1093 17019 29789 35147)	Atlas-SNP	.											.	CSTB	3	.	0			c.A227G						.						246	212	224					21																	45194153		2203	4300	6503	SO:0001583	missense	1476	exon3			TTGTTTTCATGAG	L03558	CCDS13701.1	21q22.3	2014-09-17			ENSG00000160213	ENSG00000160213			2482	protein-coding gene	gene with protein product		601145		EPM1, STFB		8596935	Standard	NM_000100		Approved	CST6, PME	uc002zdr.4	P04080	OTTHUMG00000086886	ENST00000291568.5:c.227A>G	chr21.hg19:g.45194153T>C	ENSP00000291568:p.Glu76Gly	335.0	0.0		341.0	26.0	NM_000100		Missense_Mutation	SNP	ENST00000291568.5	hg19	CCDS13701.1	.	.	.	.	.	.	.	.	.	.	T	18.52	3.641191	0.67244	.	.	ENSG00000160213	ENST00000291568	T	0.77098	-1.07	5.46	5.46	0.80206	Proteinase inhibitor I25, cystatin (2);	0.237197	0.42053	D	0.000767	D	0.82462	0.5042	.	.	.	0.28066	N	0.932773	D	0.57571	0.98	P	0.57679	0.825	T	0.77351	-0.2620	9	0.40728	T	0.16	-13.3196	11.9348	0.52868	0.0:0.0:0.0:1.0	.	76	P04080	CYTB_HUMAN	G	76	ENSP00000291568:E76G	ENSP00000291568:E76G	E	-	2	0	CSTB	44018581	0.993000	0.37304	0.149000	0.22428	0.589000	0.36550	4.155000	0.58131	2.074000	0.62210	0.459000	0.35465	GAA	.	.		0.527	CSTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195689.1	NM_000100		C	45194153	T	C	45194153	3	2	238	1	0	0	0	0	1	0	0	0	3984	1783	62	2	73	2	CSTB	21	45194153	Missense_Mutation	SNP	T	TCGA-ED-A4XI-01A-11D-A25V-10	13396368	45194153	2935742	129	33256										
RASD2	23551	hgsc.bcm.edu	37	chr22	35942929	35942929	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	actcataccgcatggtggtgCtgggtgcctctcgggtgggc	16	11	2	0			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr22:35942929C>G	ENST00000216127.4	+	2	715	c.73C>G	c.(73-75)Ctg>Gtg	p.L25V		NM_014310.3	NP_055125.2	Q96D21	RHES_HUMAN	RASD family, member 2	25					locomotory behavior (GO:0007626)|negative regulation of protein ubiquitination (GO:0031397)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein sumoylation (GO:0033235)|regulation of cAMP-mediated signaling (GO:0043949)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission, dopaminergic (GO:0001963)	plasma membrane (GO:0005886)	G-protein beta-subunit binding (GO:0031681)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(2)|large_intestine(1)|lung(8)|prostate(1)|skin(1)	13						CATGGTGGTGCTGGGTGCCTC	0.577																																					p.L25V		Atlas-SNP	.											.	RASD2	34	.	0			c.C73G						.						100	75	84					22																	35942929		2203	4300	6503	SO:0001583	missense	23551	exon2			GTGGTGCTGGGTG	AF279143	CCDS13916.1	22q13.1	2014-05-09			ENSG00000100302	ENSG00000100302			18229	protein-coding gene	gene with protein product	"tumor endothelial marker 2", "Ras homolog enriched in striatum"	612842				10947988, 10467249, 14724584	Standard	NM_014310		Approved	TEM2, Rhes, MGC:4834	uc003anx.3	Q96D21	OTTHUMG00000150607	ENST00000216127.4:c.73C>G	chr22.hg19:g.35942929C>G	ENSP00000216127:p.Leu25Val	150.0	0.0		129.0	15.0	NM_014310	O95520|Q5THY8	Missense_Mutation	SNP	ENST00000216127.4	hg19	CCDS13916.1	.	.	.	.	.	.	.	.	.	.	C	18.56	3.651205	0.67472	.	.	ENSG00000100302	ENST00000216127	T	0.76448	-1.02	5.3	4.07	0.47477	Small GTP-binding protein domain (1);	0.000000	0.64402	D	0.000001	D	0.83801	0.5333	L	0.49256	1.55	0.44110	D	0.996881	D	0.76494	0.999	D	0.74674	0.984	D	0.84290	0.0499	10	0.51188	T	0.08	.	14.8621	0.70389	0.0:0.9189:0.0:0.0811	.	25	Q96D21	RHES_HUMAN	V	25	ENSP00000216127:L25V	ENSP00000216127:L25V	L	+	1	2	RASD2	34272875	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	2.019000	0.41001	2.499000	0.84300	0.558000	0.71614	CTG	.	.		0.577	RASD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319063.1	NM_014310		G	35942929	C	G	35942929	3	3	238	1	0	0	0	0	1	0	0	0	13082	796	28	4	75	4	RASD2	22	35942929	Missense_Mutation	SNP	C	TCGA-ED-A4XI-01A-11D-A25V-10		35942929	15361637	130	33257										
GRAP2	9402	hgsc.bcm.edu	37	chr22	40351828	40351828	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	ttttcttccatgtagattttAagtaaccaagaggagtggtt	9	5	1	2			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr22:40351828A>T	ENST00000344138.4	+	3	347	c.84A>T	c.(82-84)ttA>ttT	p.L28F	GRAP2_ENST00000540310.1_Intron|GRAP2_ENST00000543252.1_Missense_Mutation_p.L28F|GRAP2_ENST00000407075.3_Missense_Mutation_p.L28F|GRAP2_ENST00000399090.2_Intron|GRAP2_ENST00000478445.1_3'UTR|GRAP2_ENST00000544756.1_Intron	NM_004810.2	NP_004801.1	O75791	GRAP2_HUMAN	GRB2-related adaptor protein 2	28	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cell-cell signaling (GO:0007267)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of signal transduction (GO:0009967)|Ras protein signal transduction (GO:0007265)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|nucleus (GO:0005634)	SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	14						TGTAGATTTTAAGTAACCAAG	0.453																																					p.L28F		Atlas-SNP	.											.	GRAP2	29	.	0			c.A84T						.						77	72	73					22																	40351828		2203	4300	6503	SO:0001583	missense	9402	exon3			GATTTTAAGTAAC	AF102694	CCDS13999.1	22q13.2	2013-02-14			ENSG00000100351	ENSG00000100351		"SH2 domain containing"	4563	protein-coding gene	gene with protein product		604518				9878555, 10224278	Standard	XM_005261836		Approved	Grf40, GrbX, GRBLG, GADS, Mona	uc003ayh.2	O75791	OTTHUMG00000151097	ENST00000344138.4:c.84A>T	chr22.hg19:g.40351828A>T	ENSP00000339186:p.Leu28Phe	109.0	0.0		100.0	4.0	NM_004810	B7Z8I3|O43726|Q9NRB7	Missense_Mutation	SNP	ENST00000344138.4	hg19	CCDS13999.1	.	.	.	.	.	.	.	.	.	.	A	16.65	3.183080	0.57800	.	.	ENSG00000100351	ENST00000344138;ENST00000543252;ENST00000420971;ENST00000407075	T;T;T;T	0.58652	0.32;0.32;0.32;0.32	5.46	0.272	0.15645	Src homology-3 domain (4);	0.234859	0.34110	N	0.004247	T	0.69584	0.3127	M	0.75085	2.285	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.66756	-0.5843	10	0.87932	D	0	-10.2871	7.3065	0.26451	0.5728:0.2186:0.2086:0.0	.	28;28	Q6FI14;O75791	.;GRAP2_HUMAN	F	28	ENSP00000339186:L28F;ENSP00000446350:L28F;ENSP00000396355:L28F;ENSP00000385607:L28F	ENSP00000339186:L28F	L	+	3	2	GRAP2	38681774	0.998000	0.40836	0.993000	0.49108	0.878000	0.50629	0.618000	0.24373	-0.175000	0.10725	-1.139000	0.01908	TTA	.	.		0.453	GRAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321295.1	NM_004810		T	40351828	A	T	40351828	3	4	238	1	0	0	0	0	1	0	0	0	6763	359	13	4	90	4	GRAP2	22	40351828	Missense_Mutation	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	4408899	40351828	10952738	131	33258										
ARSA	410	hgsc.bcm.edu	37	chr22	51064685	51064685	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	agaccggagcagccgcctcgGgacatacgcatggtctcagg	14	13	1	1			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr22:51064685G>T	ENST00000547307.1	-	5	1275	c.870C>A	c.(868-870)tcC>tcA	p.S290S	ARSA_ENST00000216124.5_Silent_p.S292S|ARSA_ENST00000356098.5_Silent_p.S292S|ARSA_ENST00000453344.2_Silent_p.S206S|ARSA_ENST00000395619.3_Silent_p.S292S|ARSA_ENST00000547805.1_Silent_p.S290S|ARSA_ENST00000610191.1_5'Flank|ARSA_ENST00000395621.3_Silent_p.S292S			P15289	ARSA_HUMAN	arylsulfatase A	290				S -> P (in Ref. 5; AK098659). {ECO:0000305}.	autophagy (GO:0006914)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|central nervous system development (GO:0007417)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to methylmercury (GO:0051597)|response to nutrient (GO:0007584)|response to pH (GO:0009268)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum lumen (GO:0005788)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|cerebroside-sulfatase activity (GO:0004098)|sulfuric ester hydrolase activity (GO:0008484)			endometrium(1)|large_intestine(1)|lung(5)|pancreas(1)|skin(1)	9		all_cancers(38;8.8e-15)|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)	Micafungin(DB01141)|Suramin(DB04786)	AGCCGCCTCGGGACATACGCA	0.642																																					p.S292S		Atlas-SNP	.											.	ARSA	19	.	0			c.C876A						.						47	42	44					22																	51064685		2203	4300	6503	SO:0001819	synonymous_variant	410	exon6			GCCTCGGGACATA	X52150	CCDS14100.1, CCDS46736.1, CCDS14100.2	22q13.33	2013-09-19			ENSG00000100299	ENSG00000100299	3.1.6.8	"Arylsulfatase family"	713	protein-coding gene	gene with protein product	"metachromatic leucodystrophy"	607574				15772092	Standard	NM_000487		Approved		uc003bmz.5	P15289	OTTHUMG00000150180	ENST00000547307.1:c.870C>A	chr22.hg19:g.51064685G>T		133.0	0.0		99.0	4.0	NM_001085426	B2RCA6|B7XD04|F8WCC8|Q6ICI5|Q96CJ0	Silent	SNP	ENST00000547307.1	hg19																																																																																				.	.		0.642	ARSA-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000487		T	51064685	G	T	51064685	2	4	238	1	0	0	0	0	0	0	0	1	987	1219	43	3		3	ARSA	22	51064685	Silent	SNP	G	TCGA-ED-A4XI-01A-11D-A25V-10	10712857	51064685	239881	132	33259										
NXF3	56000	hgsc.bcm.edu	37	chrX	102334164	102334164	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	ctcaccttccttgaacacccCgttgacagaaaagcagagca	7	14	1	4			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chrX:102334164C>T	ENST00000395065.3	-	16	1464	c.1363G>A	c.(1363-1365)Ggg>Agg	p.G455R	NXF3_ENST00000425644.1_Missense_Mutation_p.G127R	NM_022052.1	NP_071335.1	Q9H4D5	NXF3_HUMAN	nuclear RNA export factor 3	455	NTF2. {ECO:0000255|PROSITE- ProRule:PRU00137}.				mRNA export from nucleus (GO:0006406)|poly(A)+ mRNA export from nucleus (GO:0016973)	cytoplasm (GO:0005737)|nuclear RNA export factor complex (GO:0042272)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)	p.G455W(1)		NS(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(15)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26						TTGAACACCCCGTTGACAGAA	0.587																																					p.G455R		Atlas-SNP	.											.	NXF3	81	.	1	Substitution - Missense(1)	lung(1)	c.G1363A						.						251	223	233					X																	102334164		2203	4300	6503	SO:0001583	missense	56000	exon16			ACACCCCGTTGAC	AJ277527	CCDS14503.1	Xq22	2008-02-05			ENSG00000147206	ENSG00000147206			8073	protein-coding gene	gene with protein product		300316				11073998	Standard	NM_022052		Approved		uc004eju.3	Q9H4D5	OTTHUMG00000022088	ENST00000395065.3:c.1363G>A	chrX.hg19:g.102334164C>T	ENSP00000378504:p.Gly455Arg	270.0	0.0		275.0	87.0	NM_022052	B4DYS7|Q5H9I1|Q9H1A9	Missense_Mutation	SNP	ENST00000395065.3	hg19	CCDS14503.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	14.37|14.37	2.514215|2.514215	0.44763|0.44763	.|.	.|.	ENSG00000147206|ENSG00000147206	ENST00000395065;ENST00000425644|ENST00000427570	T;T|.	0.63580|.	-0.05;-0.05|.	4.22|4.22	3.35|3.35	0.38373|0.38373	Nuclear transport factor 2, Eukaryote (1);Nuclear transport factor 2 (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.84665|0.84665	0.5522|0.5522	H|H	0.96239|0.96239	3.79|3.79	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.87578|.	0.975;0.998|.	D|D	0.86659|0.86659	0.1903|0.1903	10|5	0.87932|.	D|.	0|.	-4.1391|-4.1391	9.8204|9.8204	0.40878|0.40878	0.0:0.8909:0.0:0.1091|0.0:0.8909:0.0:0.1091	.|.	351;455|.	E9PEY7;Q9H4D5|.	.;NXF3_HUMAN|.	R|Q	455;127|331	ENSP00000378504:G455R;ENSP00000401026:G127R|.	ENSP00000378504:G455R|.	G|R	-|-	1|2	0|0	NXF3|NXF3	102220820|102220820	0.996000|0.996000	0.38824|0.38824	0.015000|0.015000	0.15790|0.15790	0.327000|0.327000	0.28475|0.28475	5.633000|5.633000	0.67825|0.67825	0.898000|0.898000	0.36418|0.36418	0.593000|0.593000	0.82588|0.82588	GGG|CGG	.	.		0.587	NXF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057684.1	NM_022052		T	102334164	C	T	102334164	3	4	238	1	0	0	0	0	1	0	0	0	10794	652	23	1	248	1	NXF3	23	102334164	Missense_Mutation	SNP	C	TCGA-ED-A4XI-01A-11D-A25V-10		102334164	52936396	133	33260										
TEX13A	56157	hgsc.bcm.edu	37	chrX	104464383	104464383	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	ccttctgtgcaaacccctccGgcagtggccaggcctggcca	11	17	1	0			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chrX:104464383G>T	ENST00000413579.1	-	3	606	c.495C>A	c.(493-495)gcC>gcA	p.A165A	IL1RAPL2_ENST00000344799.4_Intron|IL1RAPL2_ENST00000372582.1_Intron|TEX13A_ENST00000372578.3_Silent_p.A165A|TEX13A_ENST00000372575.1_Silent_p.A165A			Q9BXU3	TX13A_HUMAN	testis expressed 13A	165							zinc ion binding (GO:0008270)			large_intestine(5)|ovary(2)|upper_aerodigestive_tract(1)	8						AAACCCCTCCGGCAGTGGCCA	0.647																																					p.A165A		Atlas-SNP	.											.	TEX13A	55	.	0			c.C495A						.						23	27	26					X																	104464383		2079	4102	6181	SO:0001819	synonymous_variant	56157	exon3			CCCTCCGGCAGTG	AF285597	CCDS76005.1	Xq28	2012-04-20	2007-03-13		ENSG00000133149	ENSG00000268629			11735	protein-coding gene	gene with protein product		300312	"testis expressed sequence 13A"			11279525	Standard	NM_031274		Approved		uc004ema.3	Q9BXU3	OTTHUMG00000022133	ENST00000413579.1:c.495C>A	chrX.hg19:g.104464383G>T		15.0	0.0		7.0	4.0	NM_031274	B1B1G8|Q32NB6	Silent	SNP	ENST00000413579.1	hg19																																																																																				.	.		0.647	TEX13A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_031274		T	104464383	G	T	104464383	2	4	238	1	0	0	0	0	0	0	0	1	15791	1103	39	1		1	TEX13A	23	104464383	Silent	SNP	G	TCGA-ED-A4XI-01A-11D-A25V-10	2130219	104464383	50806177	134	33261										
MAGEA4	4103	hgsc.bcm.edu	37	chrX	151093077	151093077	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	5	1	0.898100172711572	2.00148038490007	0.656735751295337	1	1	0	agcagctttgttagaggaggAagagggagtctgagcatgag	17	4	1	4			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chrX:151093077A>T	ENST00000360243.2	+	3	1208	c.941A>T	c.(940-942)gAa>gTa	p.E314V	MAGEA4_ENST00000276344.2_Missense_Mutation_p.E314V|MAGEA4_ENST00000370337.4_Missense_Mutation_p.E314V|MAGEA4_ENST00000393920.1_Missense_Mutation_p.E314V|MAGEA4_ENST00000370335.1_Missense_Mutation_p.E314V|MAGEA4_ENST00000370340.3_Missense_Mutation_p.E314V|MAGEA4_ENST00000393921.1_Missense_Mutation_p.E314V	NM_001011550.1	NP_001011550.1	P43358	MAGA4_HUMAN	melanoma antigen family A, 4	314										breast(2)|central_nervous_system(4)|endometrium(1)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)	27	Acute lymphoblastic leukemia(192;6.56e-05)					TTAGAGGAGGAAGAGGGAGTC	0.572																																					p.E314V		Atlas-SNP	.											.	MAGEA4	68	.	0			c.A941T						.						67	66	67					X																	151093077		2203	4300	6503	SO:0001583	missense	4103	exon3			AGGAGGAAGAGGG		CCDS14702.1	Xq28	2009-03-13			ENSG00000147381	ENSG00000147381			6802	protein-coding gene	gene with protein product	"melanoma-associated antigen 4", "cancer/testis antigen family 1, member 4"	300175		MAGE4		8575766	Standard	XM_005274677		Approved	MAGE4A, MAGE4B, MAGE-41, MAGE-X2, MGC21336, CT1.4	uc004ffa.3	P43358	OTTHUMG00000024174	ENST00000360243.2:c.941A>T	chrX.hg19:g.151093077A>T	ENSP00000353379:p.Glu314Val	132.0	0.0		103.0	8.0	NM_001011548	Q14798	Missense_Mutation	SNP	ENST00000360243.2	hg19	CCDS14702.1	.	.	.	.	.	.	.	.	.	.	A	7.227	0.598562	0.13939	.	.	ENSG00000147381	ENST00000276344;ENST00000393921;ENST00000370337;ENST00000393920;ENST00000370340;ENST00000370335;ENST00000360243	T;T;T;T;T;T;T	0.02050	4.48;4.48;4.48;4.48;4.48;4.48;4.48	1.74	-2.88	0.05682	.	1.413460	0.04436	N	0.370110	T	0.02267	0.0070	M	0.67569	2.06	0.09310	N	1	P	0.37663	0.604	B	0.24269	0.052	T	0.38845	-0.9642	9	.	.	.	.	0.1052	0.00052	0.3372:0.2417:0.1811:0.24	.	314	P43358	MAGA4_HUMAN	V	314	ENSP00000276344:E314V;ENSP00000377498:E314V;ENSP00000359362:E314V;ENSP00000377497:E314V;ENSP00000359365:E314V;ENSP00000359360:E314V;ENSP00000353379:E314V	.	E	+	2	0	MAGEA4	150843733	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-0.830000	0.04410	-0.905000	0.03871	-0.915000	0.02750	GAA	.	.		0.572	MAGEA4-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060898.1	NM_002362		T	151093077	A	T	151093077	3	4	238	1	0	0	0	0	1	0	0	0	9177	246	9	4	943	4	MAGEA4	23	151093077	Missense_Mutation	SNP	A	TCGA-ED-A4XI-01A-11D-A25V-10	46628694	151093077	4177483	135	33262										
AGMAT	79814	hgsc.bcm.edu	37	chr1	15909713	15909713	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtcagaggaatacagccagcTgctacaattttctcataggc	9	10	2	1			TCGA-ED-A5KG-01A-11D-A27I-10	TCGA-ED-A5KG-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c986f8b-3eb9-493f-89a4-c408397dd414	f9ce62ee-6802-40bc-8021-23159fb6d4eb	g.chr1:15909713T>G	ENST00000375826.3	-	2	592	c.450A>C	c.(448-450)gcA>gcC	p.A150A	RP4-680D5.2_ENST00000428945.1_RNA|DNAJC16_ENST00000483270.1_Intron	NM_024758.4	NP_079034.3	Q9BSE5	SPEB_HUMAN	agmatine ureohydrolase (agmatinase)	150					agmatine biosynthetic process (GO:0097055)|cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|putrescine biosynthetic process from arginine (GO:0033388)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	agmatinase activity (GO:0008783)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(6)|lung(2)|skin(1)	12		Breast(348;0.000207)|Colorectal(325;0.000258)|Lung NSC(340;0.000359)|all_lung(284;0.000486)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.93e-07)|COAD - Colon adenocarcinoma(227;3.91e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000121)|KIRC - Kidney renal clear cell carcinoma(229;0.00257)|STAD - Stomach adenocarcinoma(313;0.00734)|READ - Rectum adenocarcinoma(331;0.0649)		TACAGCCAGCTGCTACAATTT	0.493																																					p.A150A	NSCLC(126;1678 1780 25805 43508 49531)	Atlas-SNP	.											.	AGMAT	25	.	0			c.A450C						.						59	60	60					1																	15909713		2203	4300	6503	SO:0001819	synonymous_variant	79814	exon2			GCCAGCTGCTACA	AY057097	CCDS160.1	1p36.13	2009-01-05			ENSG00000116771	ENSG00000116771			18407	protein-coding gene	gene with protein product						11804860, 14648699, 11914032	Standard	NM_024758		Approved	FLJ23384	uc001awv.2	Q9BSE5	OTTHUMG00000002357	ENST00000375826.3:c.450A>C	chr1.hg19:g.15909713T>G		53.0	0.0		64.0	10.0	NM_024758	Q5TDH1|Q9H5J3	Silent	SNP	ENST00000375826.3	hg19	CCDS160.1																																																																																			.	.		0.493	AGMAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006763.1	NM_024758		G	15909713	T	G	15909713	2	3	239	1	0	0	0	0	0	0	0	1	385	1567	55	5		5	AGMAT	1	15909713	Silent	SNP	T	TCGA-ED-A5KG-01A-11D-A27I-10		15909713	233340908	1	33263										
LRRIQ3	127255	hgsc.bcm.edu	37	chr1	74507289	74507289	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gcaacttgtgccatggctacAactcttactttttctttatg	6	10	2	0			TCGA-ED-A5KG-01A-11D-A27I-10	TCGA-ED-A5KG-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c986f8b-3eb9-493f-89a4-c408397dd414	f9ce62ee-6802-40bc-8021-23159fb6d4eb	g.chr1:74507289A>T	ENST00000395089.1	-	6	1325	c.1326T>A	c.(1324-1326)gtT>gtA	p.V442V	LRRIQ3_ENST00000354431.4_Silent_p.V442V			A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	442										NS(2)|breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(13)|liver(1)|lung(27)|ovary(3)|prostate(1)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(5)	73						CCATGGCTACAACTCTTACTT	0.333																																					p.V442V		Atlas-SNP	.											.	LRRIQ3	146	.	0			c.T1326A						.						208	191	197					1																	74507289		1843	4095	5938	SO:0001819	synonymous_variant	127255	exon7			GGCTACAACTCTT	BX647210	CCDS41350.1	1p31.1	2008-06-12	2008-06-12	2008-06-12	ENSG00000162620	ENSG00000162620			28318	protein-coding gene	gene with protein product			"leucine rich repeat containing 44"	LRRC44		12477932	Standard	NM_001105659		Approved	MGC22773	uc001dfy.4	A6PVS8	OTTHUMG00000009508	ENST00000395089.1:c.1326T>A	chr1.hg19:g.74507289A>T		44.0	0.0		42.0	4.0	NM_001105659	A6PVS9|Q6P5P7|Q6ZMV4|Q8WUE0	Silent	SNP	ENST00000395089.1	hg19	CCDS41350.1																																																																																			.	.		0.333	LRRIQ3-008	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316539.1	NM_145258		T	74507289	A	T	74507289	2	4	239	1	0	0	0	0	0	0	0	1	9039	117	5	4		4	LRRIQ3	1	74507289	Silent	SNP	A	TCGA-ED-A5KG-01A-11D-A27I-10	58597576	74507289	174743332	2	33264										
CNTN2	6900	hgsc.bcm.edu	37	chr1	205041630	205041630	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gctccgcggcgacctcctggCaacatctcctggactttctc	9	17	2	0			TCGA-ED-A5KG-01A-11D-A27I-10	TCGA-ED-A5KG-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c986f8b-3eb9-493f-89a4-c408397dd414	f9ce62ee-6802-40bc-8021-23159fb6d4eb	g.chr1:205041630C>A	ENST00000331830.4	+	21	3035	c.2751C>A	c.(2749-2751)ggC>ggA	p.G917G		NM_005076.3	NP_005067.1	Q02246	CNTN2_HUMAN	contactin 2 (axonal)	917	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|central nervous system myelination (GO:0022010)|cerebral cortex GABAergic interneuron migration (GO:0021853)|clustering of voltage-gated potassium channels (GO:0045163)|establishment of protein localization to juxtaparanode region of axon (GO:0071206)|learning (GO:0007612)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|positive regulation of protein processing (GO:0010954)|presynaptic membrane organization (GO:0097090)|receptor internalization (GO:0031623)|regulation of astrocyte differentiation (GO:0048710)|regulation of axon diameter (GO:0031133)|regulation of neuronal synaptic plasticity (GO:0048168)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|juxtaparanode region of axon (GO:0044224)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated potassium channel complex (GO:0008076)	carbohydrate binding (GO:0030246)|identical protein binding (GO:0042802)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(11)|lung(23)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	54	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			GACCTCCTGGCAACATCTCCT	0.552																																					p.G917G	Melanoma(183;2548 2817 37099 41192)	Atlas-SNP	.											.	CNTN2	116	.	0			c.C2751A						.						72	71	71					1																	205041630		2203	4300	6503	SO:0001819	synonymous_variant	6900	exon21			TCCTGGCAACATC	X67734	CCDS1449.1	1q32.1	2013-02-11			ENSG00000184144	ENSG00000184144		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2172	protein-coding gene	gene with protein product		190197		TAX, AXT		8307567, 8586965	Standard	NM_005076		Approved	TAG-1, TAX1	uc001hbr.3	Q02246	OTTHUMG00000037105	ENST00000331830.4:c.2751C>A	chr1.hg19:g.205041630C>A		72.0	0.0		80.0	8.0	NM_005076	P78432|Q5T054	Silent	SNP	ENST00000331830.4	hg19	CCDS1449.1																																																																																			.	.		0.552	CNTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090080.3	NM_005076		A	205041630	C	A	205041630	2	1	239	1	0	0	0	0	0	0	0	1	3643	697	25	3		3	CNTN2	1	205041630	Silent	SNP	C	TCGA-ED-A5KG-01A-11D-A27I-10	130534341	205041630	44208991	3	33265										
ADCY2	108	hgsc.bcm.edu	37	chr5	7396525	7396525	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gctctacgagtcctactactGcatgagccagcagcacccgc	9	16	1	1			TCGA-ED-A5KG-01A-11D-A27I-10	TCGA-ED-A5KG-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c986f8b-3eb9-493f-89a4-c408397dd414	f9ce62ee-6802-40bc-8021-23159fb6d4eb	g.chr5:7396525G>A	ENST00000338316.4	+	1	205	c.116G>A	c.(115-117)tGc>tAc	p.C39Y		NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	39					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						TCCTACTACTGCATGAGCCAG	0.701																																					p.C39Y		Atlas-SNP	.											.	ADCY2	337	.	0			c.G116A						.						44	36	39					5																	7396525		2203	4300	6503	SO:0001583	missense	108	exon1			ACTACTGCATGAG	AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"Adenylate cyclases"	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.116G>A	chr5.hg19:g.7396525G>A	ENSP00000342952:p.Cys39Tyr	94.0	0.0		63.0	4.0	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Missense_Mutation	SNP	ENST00000338316.4	hg19	CCDS3872.2	.	.	.	.	.	.	.	.	.	.	G	1.084	-0.665988	0.03428	.	.	ENSG00000078295	ENST00000338316	T	0.76060	-0.99	3.51	3.51	0.40186	.	0.209765	0.40064	U	0.001190	T	0.56804	0.2010	L	0.29908	0.895	0.80722	D	1	B	0.12630	0.006	B	0.09377	0.004	T	0.50996	-0.8761	10	0.05436	T	0.98	.	12.1741	0.54176	0.0:0.0:1.0:0.0	.	39	Q08462	ADCY2_HUMAN	Y	39	ENSP00000342952:C39Y	ENSP00000342952:C39Y	C	+	2	0	ADCY2	7449525	1.000000	0.71417	0.979000	0.43373	0.352000	0.29268	7.804000	0.85993	1.475000	0.48197	0.305000	0.20034	TGC	.	.		0.701	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546		A	7396525	G	A	7396525	3	1	239	1	0	0	0	0	1	0	0	0	294	1319	46	3	118	3	ADCY2	5	7396525	Missense_Mutation	SNP	G	TCGA-ED-A5KG-01A-11D-A27I-10		7396525	173518735	4	33266										
ADAMTS12	81792	hgsc.bcm.edu	37	chr5	33891885	33891885	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctggctgaggctgtctcccaTagcaaagcgccccaaagtta	10	13	1	1			TCGA-ED-A5KG-01A-11D-A27I-10	TCGA-ED-A5KG-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c986f8b-3eb9-493f-89a4-c408397dd414	f9ce62ee-6802-40bc-8021-23159fb6d4eb	g.chr5:33891885T>C	ENST00000504830.1	-	1	412	c.77A>G	c.(76-78)tAt>tGt	p.Y26C	ADAMTS12_ENST00000352040.3_Missense_Mutation_p.Y26C|ADAMTS12_ENST00000515401.1_Missense_Mutation_p.Y26C	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	26					cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						CTGTCTCCCATAGCAAAGCGC	0.512										HNSCC(64;0.19)																											p.Y26C		Atlas-SNP	.											.	ADAMTS12	464	.	0			c.A77G						.						107	115	112					5																	33891885		2203	4300	6503	SO:0001583	missense	81792	exon1			CTCCCATAGCAAA	AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"ADAM metallopeptidases with thrombospondin type 1 motif"	14605	protein-coding gene	gene with protein product		606184	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.77A>G	chr5.hg19:g.33891885T>C	ENSP00000422554:p.Tyr26Cys	353.0	0.0		361.0	22.0	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	hg19	CCDS34140.1	.	.	.	.	.	.	.	.	.	.	T	9.105	1.005063	0.19199	.	.	ENSG00000151388	ENST00000504830;ENST00000352040;ENST00000515401	T;T;T	0.58940	0.3;0.3;2.87	5.61	0.551	0.17225	.	1.661270	0.02918	N	0.137613	T	0.36082	0.0954	N	0.08118	0	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.19647	-1.0299	10	0.40728	T	0.16	.	3.8638	0.09007	0.1494:0.248:0.0:0.6026	.	26;26;26	P58397-3;D6REX0;P58397	.;.;ATS12_HUMAN	C	26	ENSP00000422554:Y26C;ENSP00000344847:Y26C;ENSP00000421638:Y26C	ENSP00000344847:Y26C	Y	-	2	0	ADAMTS12	33927642	0.021000	0.18746	0.005000	0.12908	0.703000	0.40648	0.365000	0.20348	0.077000	0.16863	0.477000	0.44152	TAT	.	.		0.512	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		C	33891885	T	C	33891885	3	2	239	1	0	0	0	0	1	0	0	0	257	1406	49	2	4803	2	ADAMTS12	5	33891885	Missense_Mutation	SNP	T	TCGA-ED-A5KG-01A-11D-A27I-10	26495360	33891885	147023375	5	33267										
OR11A1	26531	hgsc.bcm.edu	37	chr6	29395394	29395394	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	gacaaattcagtaatagtttCgtttcctgtggagacaattt	8	6	1	1			TCGA-ED-A5KG-01A-11D-A27I-10	TCGA-ED-A5KG-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c986f8b-3eb9-493f-89a4-c408397dd414	f9ce62ee-6802-40bc-8021-23159fb6d4eb	g.chr6:29395394C>T	ENST00000377149.1	-	5	497	c.25G>A	c.(25-27)Gaa>Aaa	p.E9K	OR5V1_ENST00000377154.1_Intron|OR11A1_ENST00000377147.2_Missense_Mutation_p.E9K|OR11A1_ENST00000377148.1_Missense_Mutation_p.E9K			Q9GZK7	O11A1_HUMAN	olfactory receptor, family 11, subfamily A, member 1	9						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|large_intestine(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	19						GTAATAGTTTCGTTTCCTGTG	0.393																																					p.E9K		Atlas-SNP	.											.	OR11A1	30	.	0			c.G25A						.						60	58	59					6																	29395394		1509	2709	4218	SO:0001583	missense	26531	exon1			TAGTTTCGTTTCC		CCDS34363.1	6p22.2-p21.31	2014-02-19	2002-02-28		ENSG00000204694	ENSG00000204694		"GPCR / Class A : Olfactory receptors"	8176	protein-coding gene	gene with protein product			"olfactory receptor, family 11, subfamily A, member 2"	OR11A2			Standard	XM_005249001		Approved	hs6M1-18	uc003nmg.3	Q9GZK7	OTTHUMG00000031225	ENST00000377149.1:c.25G>A	chr6.hg19:g.29395394C>T	ENSP00000366354:p.Glu9Lys	68.0	0.0		89.0	6.0	NM_013937	A2BF33|A6NFQ3|B0S7T2|Q5ST16|Q9GZK8	Missense_Mutation	SNP	ENST00000377149.1	hg19	CCDS34363.1	.	.	.	.	.	.	.	.	.	.	c	6.981	0.551005	0.13374	.	.	ENSG00000204694	ENST00000377148;ENST00000377149;ENST00000377147	T;T;T	0.00333	8.07;8.07;8.07	3.66	-0.976	0.10286	.	.	.	.	.	T	0.00039	0.0001	N	0.17248	0.465	0.09310	N	1	B	0.17038	0.02	B	0.06405	0.002	T	0.04537	-1.0944	9	0.38643	T	0.18	0.5553	10.4396	0.44457	0.0:0.5807:0.2074:0.212	.	9	Q9GZK7	O11A1_HUMAN	K	9	ENSP00000366353:E9K;ENSP00000366354:E9K;ENSP00000366352:E9K	ENSP00000366352:E9K	E	-	1	0	OR11A1	29503373	0.000000	0.05858	0.000000	0.03702	0.039000	0.13416	-0.993000	0.03720	-1.263000	0.02455	-2.938000	0.00087	GAA	.	.		0.393	OR11A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000193778.1			T	29395394	C	T	29395394	3	4	239	1	0	0	0	0	1	0	0	0	10933	893	31	1	926	1	OR11A1	6	29395394	Missense_Mutation	SNP	C	TCGA-ED-A5KG-01A-11D-A27I-10		29395394	141719673	6	33268										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152536122	152536122	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttttgatttccttatcattcAagggtaacctatatccaagc	5	9	2	1			TCGA-ED-A5KG-01A-11D-A27I-10	TCGA-ED-A5KG-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c986f8b-3eb9-493f-89a4-c408397dd414	f9ce62ee-6802-40bc-8021-23159fb6d4eb	g.chr6:152536122A>T	ENST00000367255.5	-	122	22866	c.22265T>A	c.(22264-22266)tTg>tAg	p.L7422*	SYNE1_ENST00000448038.1_Nonsense_Mutation_p.L7351*|SYNE1_ENST00000341594.5_Nonsense_Mutation_p.L7034*|SYNE1_ENST00000265368.4_Nonsense_Mutation_p.L7422*|SYNE1_ENST00000356820.4_Nonsense_Mutation_p.L1946*|SYNE1_ENST00000423061.1_Nonsense_Mutation_p.L7351*	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	7422					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		CTTATCATTCAAGGGTAACCT	0.393										HNSCC(10;0.0054)																											p.L7422X		Atlas-SNP	.											.	SYNE1	3227	.	0			c.T22265A						.						157	148	151					6																	152536122		2203	4300	6503	SO:0001587	stop_gained	23345	exon122			TCATTCAAGGGTA	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.22265T>A	chr6.hg19:g.152536122A>T	ENSP00000356224:p.Leu7422*	81.0	0.0		75.0	4.0	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Nonsense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	A	49	15.221097	0.99826	.	.	ENSG00000131018	ENST00000367255;ENST00000367257;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820;ENST00000367251	.	.	.	5.97	5.97	0.96955	.	0.000000	0.47455	D	0.000231	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.4461	0.83932	1.0:0.0:0.0:0.0	.	.	.	.	X	7422;68;7351;7422;7351;7034;1946;344	.	ENSP00000265368:L7422X	L	-	2	0	SYNE1	152577815	1.000000	0.71417	0.976000	0.42696	0.944000	0.59088	9.276000	0.95745	2.285000	0.76669	0.528000	0.53228	TTG	.	.		0.393	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152536122	A	T	152536122	4	4	239	1	0	0	0	0	0	1	0	0	15460	131	5	4	4301	4	SYNE1	6	152536122	Nonsense_Mutation	SNP	A	TCGA-ED-A5KG-01A-11D-A27I-10	123140728	152536122	18578945	7	33269										
RHBDD2	57414	hgsc.bcm.edu	37	chr7	75511359	75511359	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	caaagctgggggaagtggagGatgccagaggtttcacccca	15	9	1	1			TCGA-ED-A5KG-01A-11D-A27I-10	TCGA-ED-A5KG-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c986f8b-3eb9-493f-89a4-c408397dd414	f9ce62ee-6802-40bc-8021-23159fb6d4eb	g.chr7:75511359G>T	ENST00000006777.6	+	2	526	c.391G>T	c.(391-393)Gat>Tat	p.D131Y	RHBDD2_ENST00000428119.1_5'Flank|RHBDD2_ENST00000318622.4_5'UTR|RHBDD2_ENST00000468304.1_Intron	NM_001040456.1	NP_001035546.1	Q6NTF9	RHBD2_HUMAN	rhomboid domain containing 2	131						Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase activity (GO:0004252)			kidney(1)|lung(4)|prostate(1)	6						GGAAGTGGAGGATGCCAGAGG	0.582																																					p.D131Y		Atlas-SNP	.											.	RHBDD2	49	.	0			c.G391T						.						121	129	127					7																	75511359		2149	4253	6402	SO:0001583	missense	57414	exon2			GTGGAGGATGCCA	AF226732	CCDS43602.1, CCDS43603.1	7q11	2008-09-04	2006-02-22	2006-02-22	ENSG00000005486	ENSG00000005486			23082	protein-coding gene	gene with protein product		615203	"rhomboid, veinlet-like 7 (Drosophila)"	RHBDL7		12838346	Standard	XM_005250511		Approved	NPD007	uc003udw.1	Q6NTF9	OTTHUMG00000156435	ENST00000006777.6:c.391G>T	chr7.hg19:g.75511359G>T	ENSP00000006777:p.Asp131Tyr	225.0	0.0		258.0	21.0	NM_001040456	Q7L534|Q9H5W6|Q9HBK7|Q9UDT2	Missense_Mutation	SNP	ENST00000006777.6	hg19	CCDS43602.1	.	.	.	.	.	.	.	.	.	.	G	17.72	3.459677	0.63401	.	.	ENSG00000005486	ENST00000006777;ENST00000413229	T	0.13657	2.57	5.1	5.1	0.69264	Peptidase S54, rhomboid domain (1);	0.497273	0.21411	N	0.074974	T	0.20455	0.0492	N	0.22421	0.69	0.80722	D	1	D	0.56287	0.975	P	0.59948	0.866	T	0.00759	-1.1578	10	0.49607	T	0.09	-8.2077	13.43	0.61049	0.0:0.1572:0.8428:0.0	.	131	Q6NTF9	RHBD2_HUMAN	Y	131;176	ENSP00000006777:D131Y	ENSP00000006777:D131Y	D	+	1	0	RHBDD2	75349295	1.000000	0.71417	0.999000	0.59377	0.832000	0.47134	3.425000	0.52771	2.652000	0.90054	0.655000	0.94253	GAT	.	.		0.582	RHBDD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344176.1	NM_020684		T	75511359	G	T	75511359	3	4	239	1	0	0	0	0	1	0	0	0	13332	1174	41	3	397	3	RHBDD2	7	75511359	Missense_Mutation	SNP	G	TCGA-ED-A5KG-01A-11D-A27I-10		75511359	83627304	8	33270										
ZNF862	643641	hgsc.bcm.edu	37	chr7	149558968	149558968	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggcggctccacggcatctgcTtggacaaactggaggtagcg	15	11	1	0			TCGA-ED-A5KG-01A-11D-A27I-10	TCGA-ED-A5KG-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c986f8b-3eb9-493f-89a4-c408397dd414	f9ce62ee-6802-40bc-8021-23159fb6d4eb	g.chr7:149558968T>A	ENST00000223210.4	+	7	2964	c.2719T>A	c.(2719-2721)Ttg>Atg	p.L907M	RP4-751H13.7_ENST00000608963.1_RNA	NM_001099220.1	NP_001092690.1	O60290	ZN862_HUMAN	zinc finger protein 862	907					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(1)	34						CGGCATCTGCTTGGACAAACT	0.612																																					p.L907M		Atlas-SNP	.											.	ZNF862	97	.	0			c.T2719A						.						60	64	63					7																	149558968		2036	4204	6240	SO:0001583	missense	643641	exon7			ATCTGCTTGGACA	AB011115	CCDS47741.1	7q36.1	2013-01-11			ENSG00000106479	ENSG00000106479		"Zinc fingers, C2H2-type", "-"	34519	protein-coding gene	gene with protein product							Standard	NM_001099220		Approved		uc010lpn.3	O60290	OTTHUMG00000158093	ENST00000223210.4:c.2719T>A	chr7.hg19:g.149558968T>A	ENSP00000223210:p.Leu907Met	103.0	0.0		101.0	5.0	NM_001099220	A0AUL8	Missense_Mutation	SNP	ENST00000223210.4	hg19	CCDS47741.1	.	.	.	.	.	.	.	.	.	.	T	10.86	1.470352	0.26423	.	.	ENSG00000106479	ENST00000223210	T	0.01159	5.25	5.39	-5.56	0.02529	.	0.000000	0.42172	D	0.000754	T	0.02571	0.0078	N	0.20986	0.625	0.09310	N	1	D	0.89917	1.0	D	0.85130	0.997	T	0.00891	-1.1525	10	0.42905	T	0.14	-18.9508	19.4009	0.94629	0.0:0.8501:0.0:0.1499	.	907	O60290	ZN862_HUMAN	M	907	ENSP00000223210:L907M	ENSP00000223210:L907M	L	+	1	2	ZNF862	149189901	0.001000	0.12720	0.002000	0.10522	0.363000	0.29612	-1.068000	0.03447	-1.143000	0.02866	-0.264000	0.10439	TTG	.	.		0.612	ZNF862-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350165.1	NM_001099220		A	149558968	T	A	149558968	3	1	239	1	0	0	0	0	1	0	0	0	18210	1606	56	4	2745	4	ZNF862	7	149558968	Missense_Mutation	SNP	T	TCGA-ED-A5KG-01A-11D-A27I-10	74047609	149558968	9579695	9	33271										
CSMD1	64478	hgsc.bcm.edu	37	chr8	2949136	2949136	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttgtaaaatttgattgttcaGtatgattcccacttaagact	6	6	1	3			TCGA-ED-A5KG-01A-11D-A27I-10	TCGA-ED-A5KG-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c986f8b-3eb9-493f-89a4-c408397dd414	f9ce62ee-6802-40bc-8021-23159fb6d4eb	g.chr8:2949136G>A	ENST00000520002.1	-	49	7745	c.7190C>T	c.(7189-7191)aCt>aTt	p.T2397I	CSMD1_ENST00000602557.1_Missense_Mutation_p.T2397I|CSMD1_ENST00000537824.1_Missense_Mutation_p.T2396I|CSMD1_ENST00000602723.1_Missense_Mutation_p.T2397I|CSMD1_ENST00000400186.3_Missense_Mutation_p.T2397I|CSMD1_ENST00000542608.1_Missense_Mutation_p.T2396I			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	2397	CUB 14. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		TGATTGTTCAGTATGATTCCC	0.413																																					p.T2396I		Atlas-SNP	.											.	CSMD1	1469	.	0			c.C7187T						.						101	94	96					8																	2949136		1847	4085	5932	SO:0001583	missense	64478	exon48			TGTTCAGTATGAT			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.7190C>T	chr8.hg19:g.2949136G>A	ENSP00000430733:p.Thr2397Ile	29.0	0.0		32.0	4.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	hg19		.	.	.	.	.	.	.	.	.	.	G	11.39	1.625372	0.28889	.	.	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608	T;T;T;T	0.18502	2.21;2.21;2.21;2.21	5.8	4.91	0.64330	CUB (5);	0.073354	0.56097	D	0.000027	T	0.29256	0.0728	L	0.50919	1.6	0.80722	D	1	B;B;P	0.48911	0.317;0.14;0.917	B;B;P	0.52386	0.376;0.311;0.697	T	0.01557	-1.1325	10	0.48119	T	0.1	.	16.7039	0.85366	0.0:0.1297:0.8703:0.0	.	2397;2397;2396	E5RIG2;Q96PZ7;F5H2I8	.;CSMD1_HUMAN;.	I	2397;2397;2258;2396;2396	ENSP00000383047:T2397I;ENSP00000430733:T2397I;ENSP00000441462:T2396I;ENSP00000446243:T2396I	ENSP00000320445:T2258I	T	-	2	0	CSMD1	2936543	1.000000	0.71417	0.715000	0.30552	0.032000	0.12392	6.321000	0.72881	1.407000	0.46875	0.555000	0.69702	ACT	.	.		0.413	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		A	2949136	G	A	2949136	3	1	239	1	0	0	0	0	1	0	0	0	3946	1029	36	3	3599	3	CSMD1	8	2949136	Missense_Mutation	SNP	G	TCGA-ED-A5KG-01A-11D-A27I-10		2949136	143414886	10	33272										
ODF1	4956	hgsc.bcm.edu	37	chr8	103572783	103572783	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aacccgatcaagtcaaagttCgagtgaaggatggaaaggta	12	6	2	1			TCGA-ED-A5KG-01A-11D-A27I-10	TCGA-ED-A5KG-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c986f8b-3eb9-493f-89a4-c408397dd414	f9ce62ee-6802-40bc-8021-23159fb6d4eb	g.chr8:103572783C>A	ENST00000285402.3	+	2	580	c.424C>A	c.(424-426)Cga>Aga	p.R142R	ODF1_ENST00000518835.1_5'UTR	NM_024410.3	NP_077721.2	Q14990	ODFP1_HUMAN	outer dense fiber of sperm tails 1	142					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|outer dense fiber (GO:0001520)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(14;2.76e-05)|all_epithelial(15;4.54e-08)|Lung NSC(17;4.08e-05)|all_lung(17;9.15e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000125)|STAD - Stomach adenocarcinoma(118;0.0826)			AGTCAAAGTTCGAGTGAAGGA	0.448																																					p.R142R		Atlas-SNP	.											.	ODF1	55	.	0			c.C424A						.						170	150	157					8																	103572783		2203	4300	6503	SO:0001819	synonymous_variant	4956	exon2			AAAGTTCGAGTGA	M93131	CCDS6293.1	8q22	2011-09-05	2002-10-21		ENSG00000155087	ENSG00000155087		"Heat shock proteins / HSPB"	8113	protein-coding gene	gene with protein product	"cancer/testis antigen 133"	182878	"outer dense fibre of sperm tails 1"			8305202	Standard	NM_024410		Approved	ODFPG, ODF27, RT7, HSPB10, CT133	uc003ykt.2	Q14990	OTTHUMG00000164719	ENST00000285402.3:c.424C>A	chr8.hg19:g.103572783C>A		192.0	0.0		245.0	13.0	NM_024410	Q3SX72	Silent	SNP	ENST00000285402.3	hg19	CCDS6293.1																																																																																			.	.		0.448	ODF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379884.1			A	103572783	C	A	103572783	2	1	239	1	0	0	0	0	0	0	0	1	10835	876	31	1		1	ODF1	8	103572783	Silent	SNP	C	TCGA-ED-A5KG-01A-11D-A27I-10	100623647	103572783	42791239	11	33273										
TMOD1	7111	hgsc.bcm.edu	37	chr9	100325046	100325046	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgcacacgctcatgagtaacCagcagtactaccaggccctg	9	14	1	1			TCGA-ED-A5KG-01A-11D-A27I-10	TCGA-ED-A5KG-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c986f8b-3eb9-493f-89a4-c408397dd414	f9ce62ee-6802-40bc-8021-23159fb6d4eb	g.chr9:100325046C>T	ENST00000259365.4	+	5	643	c.430C>T	c.(430-432)Cag>Tag	p.Q144*	TMOD1_ENST00000375175.1_Nonsense_Mutation_p.Q17*|TMOD1_ENST00000395211.2_Nonsense_Mutation_p.Q144*	NM_003275.3	NP_003266.1	P28289	TMOD1_HUMAN	tropomodulin 1	144					adult locomotory behavior (GO:0008344)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)	cortical cytoskeleton (GO:0030863)|cytosol (GO:0005829)|membrane (GO:0016020)|myofibril (GO:0030016)				breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(2)|urinary_tract(1)	11		Acute lymphoblastic leukemia(62;0.154)		STAD - Stomach adenocarcinoma(157;0.105)		CATGAGTAACCAGCAGTACTA	0.592																																					p.Q144X		Atlas-SNP	.											.	TMOD1	29	.	0			c.C430T						.						164	145	152					9																	100325046		2203	4300	6503	SO:0001587	stop_gained	7111	exon5			AGTAACCAGCAGT		CCDS6726.1	9q22	2008-07-21		2003-03-21	ENSG00000136842	ENSG00000136842			11871	protein-coding gene	gene with protein product		190930		D9S57E, TMOD		1370827, 8661028	Standard	NM_003275		Approved	ETMOD	uc004axl.2	P28289	OTTHUMG00000020325	ENST00000259365.4:c.430C>T	chr9.hg19:g.100325046C>T	ENSP00000259365:p.Gln144*	106.0	0.0		113.0	6.0	NM_001166116	B2RB77|Q5T7W3|Q9BUF1	Nonsense_Mutation	SNP	ENST00000259365.4	hg19	CCDS6726.1	.	.	.	.	.	.	.	.	.	.	C	38	6.960216	0.97964	.	.	ENSG00000136842	ENST00000395211;ENST00000259365;ENST00000375175	.	.	.	4.72	4.72	0.59763	.	0.155442	0.44285	D	0.000464	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.9597	18.1729	0.89752	0.0:1.0:0.0:0.0	.	.	.	.	X	144;144;17	.	ENSP00000259365:Q144X	Q	+	1	0	TMOD1	99364867	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.293000	0.43558	2.580000	0.87095	0.655000	0.94253	CAG	.	.		0.592	TMOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053320.2	NM_003275		T	100325046	C	T	100325046	4	4	239	1	0	0	0	0	0	1	0	0	16248	595	21	3	444	3	TMOD1	9	100325046	Nonsense_Mutation	SNP	C	TCGA-ED-A5KG-01A-11D-A27I-10		100325046	40888385	12	33274										
OR51A4	401666	hgsc.bcm.edu	37	chr11	4967860	4967860	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtgaaagggaagggaagaacCaggagcatgctcttaaagga	15	5	1	2			TCGA-ED-A5KG-01A-11D-A27I-10	TCGA-ED-A5KG-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c986f8b-3eb9-493f-89a4-c408397dd414	f9ce62ee-6802-40bc-8021-23159fb6d4eb	g.chr11:4967860C>A	ENST00000380373.2	-	1	496	c.471G>T	c.(469-471)ctG>ctT	p.L157L	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001005329.1	NP_001005329.1	Q8NGJ6	O51A4_HUMAN	olfactory receptor, family 51, subfamily A, member 4	157						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L157L(1)		large_intestine(3)|lung(15)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	29		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)		AGGGAAGAACCAGGAGCATGC	0.438																																					p.L157L		Atlas-SNP	.											OR51A4,NS,carcinoma,-2,1	OR51A4	73	.	1	Substitution - coding silent(1)	lung(1)	c.G471T						.						181	176	177					11																	4967860		2191	4266	6457	SO:0001819	synonymous_variant	401666	exon1			AAGAACCAGGAGC	AB065798	CCDS31367.1	11p15.4	2012-08-09			ENSG00000205497	ENSG00000205497		"GPCR / Class A : Olfactory receptors"	14795	protein-coding gene	gene with protein product							Standard	NM_001005329		Approved		uc010qys.2	Q8NGJ6	OTTHUMG00000066614	ENST00000380373.2:c.471G>T	chr11.hg19:g.4967860C>A		206.0	0.0		237.0	13.0	NM_001005329		Silent	SNP	ENST00000380373.2	hg19	CCDS31367.1																																																																																			.	.		0.438	OR51A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142821.1	NM_001005329		A	4967860	C	A	4967860	2	1	239	1	0	0	0	0	0	0	0	1	11096	581	21	3		3	OR51A4	11	4967860	Silent	SNP	C	TCGA-ED-A5KG-01A-11D-A27I-10		4967860	130038656	13	33275										
OR8B4	283162	hgsc.bcm.edu	37	chr11	124294075	124294075	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctaaaggctttggatctgccCtctgcagaaggaatacagag	11	9	2	2			TCGA-ED-A5KG-01A-11D-A27I-10	TCGA-ED-A5KG-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c986f8b-3eb9-493f-89a4-c408397dd414	f9ce62ee-6802-40bc-8021-23159fb6d4eb	g.chr11:124294075C>T	ENST00000356130.3	-	1	714	c.693G>A	c.(691-693)gaG>gaA	p.E231E		NM_001005196.1	NP_001005196.1	Q96RC9	OR8B4_HUMAN	olfactory receptor, family 8, subfamily B, member 4	231						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(1)|urinary_tract(1)	32		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		TGGATCTGCCCTCTGCAGAAG	0.438																																					p.E231E		Atlas-SNP	.											.	OR8B4	60	.	0			c.G693A						.						76	72	74					11																	124294075		2201	4299	6500	SO:0001819	synonymous_variant	283162	exon1			TCTGCCCTCTGCA	AB065831	CCDS31710.1	11q24	2012-08-09		2001-06-29	ENSG00000198657	ENSG00000198657		"GPCR / Class A : Olfactory receptors"	8473	protein-coding gene	gene with protein product				OR8B4P			Standard	NM_001005196		Approved		uc010sak.2	Q96RC9	OTTHUMG00000165916	ENST00000356130.3:c.693G>A	chr11.hg19:g.124294075C>T		92.0	0.0		98.0	4.0	NM_001005196	B2RNF8|Q6IFQ7	Silent	SNP	ENST00000356130.3	hg19	CCDS31710.1																																																																																			.	.		0.438	OR8B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387055.1	NM_001005196		T	124294075	C	T	124294075	2	4	239	1	0	0	0	0	0	0	0	1	11238	680	24	3		3	OR8B4	11	124294075	Silent	SNP	C	TCGA-ED-A5KG-01A-11D-A27I-10	119326215	124294075	10712441	14	33276										
HEATR3	55027	hgsc.bcm.edu	37	chr16	50106573	50106573	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gaagggtgtttggagattgtGttaaagtatttaagtaggtt	14	0	0	1			TCGA-ED-A5KG-01A-11D-A27I-10	TCGA-ED-A5KG-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c986f8b-3eb9-493f-89a4-c408397dd414	f9ce62ee-6802-40bc-8021-23159fb6d4eb	g.chr16:50106573G>T	ENST00000299192.7	+	5	761	c.570G>T	c.(568-570)gtG>gtT	p.V190V	HEATR3_ENST00000285767.4_Silent_p.V104V	NM_182922.2	NP_891552.1	Q7Z4Q2	HEAT3_HUMAN	HEAT repeat containing 3	190										cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	28						TGGAGATTGTGTTAAAGTATT	0.338																																					p.V190V		Atlas-SNP	.											.	HEATR3	59	.	0			c.G570T						.						205	192	197					16																	50106573		2198	4300	6498	SO:0001819	synonymous_variant	55027	exon5			GATTGTGTTAAAG	BC018730	CCDS10739.1	16q12.1	2008-02-05			ENSG00000155393	ENSG00000155393			26087	protein-coding gene	gene with protein product		614951				12477932	Standard	XM_005256013		Approved	FLJ20718	uc002efw.3	Q7Z4Q2	OTTHUMG00000133174	ENST00000299192.7:c.570G>T	chr16.hg19:g.50106573G>T		130.0	0.0		82.0	5.0	NM_182922	A8K1N4|Q8N525|Q8WV56|Q96CC9|Q9NWN7	Silent	SNP	ENST00000299192.7	hg19	CCDS10739.1																																																																																			.	.		0.338	HEATR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256880.2	NM_182922		T	50106573	G	T	50106573	2	4	239	1	0	0	0	0	0	0	0	1	7038	1364	48	3		3	HEATR3	16	50106573	Silent	SNP	G	TCGA-ED-A5KG-01A-11D-A27I-10		50106573	40248180	15	33277										
ACCN1	40	hgsc.bcm.edu	37	chr17	32483120	32483120	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aactgcttgggtttgtagtgCttgaagttggccttctgccg	13	8	1	1			TCGA-ED-A5KG-01A-11D-A27I-10	TCGA-ED-A5KG-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c986f8b-3eb9-493f-89a4-c408397dd414	f9ce62ee-6802-40bc-8021-23159fb6d4eb	g.chr17:32483120C>T	ENST00000359872.6	-	1	1193	c.432G>A	c.(430-432)aaG>aaA	p.K144K		NM_001094.4	NP_001085.2	Q16515	ASIC2_HUMAN	acid-sensing (proton-gated) ion channel 2	144					central nervous system development (GO:0007417)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|ion transmembrane transport (GO:0034220)|monovalent inorganic cation transport (GO:0015672)|negative regulation of apoptotic process (GO:0043066)|peripheral nervous system development (GO:0007422)|phototransduction (GO:0007602)|positive regulation of synapse assembly (GO:0051965)|protein localization to synapse (GO:0035418)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of membrane potential (GO:0042391)|regulation of systemic arterial blood pressure by aortic arch baroreceptor feedback (GO:0003026)|regulation of vasoconstriction (GO:0019229)|response to acid chemical (GO:0001101)|response to acidic pH (GO:0010447)|sensory perception of sound (GO:0007605)|sensory perception of sour taste (GO:0050915)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ion gated channel activity (GO:0022839)|ligand-gated sodium channel activity (GO:0015280)|voltage-gated sodium channel activity (GO:0005248)									Amiloride(DB00594)	GTTTGTAGTGCTTGAAGTTGG	0.592																																					p.K144K		Atlas-SNP	.											.	.	.	.	0			c.G432A						.						97	105	103					17																	32483120		2136	4256	6392	SO:0001819	synonymous_variant	40	exon1			GTAGTGCTTGAAG	AL834182	CCDS11276.1, CCDS42296.1	17q11.2-q12	2012-02-23	2012-02-22	2012-02-22	ENSG00000108684	ENSG00000108684		"Ion channels / Acid-sensing (proton-gated) ion channels"	99	protein-coding gene	gene with protein product	"degenerin"	601784	"amiloride-sensitive cation channel 1, neuronal"	ACCN, ACCN1		8921408	Standard	NM_183377		Approved	ASIC2a, BNC1, BNaC1, hBNaC1, MDEG	uc002hhu.3	Q16515	OTTHUMG00000132885	ENST00000359872.6:c.432G>A	chr17.hg19:g.32483120C>T		135.0	0.0		180.0	14.0	NM_001094	E9PBX2|Q13553|Q6DJU1|Q8N3E2	Silent	SNP	ENST00000359872.6	hg19	CCDS42296.1																																																																																			.	.		0.592	ASIC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447552.1	NM_183377, NM_001094		T	32483120	C	T	32483120	2	4	239	1	0	0	0	0	0	0	0	1	128	796	28	3		3	ACCN1	17	32483120	Silent	SNP	C	TCGA-ED-A5KG-01A-11D-A27I-10		32483120	48712090	16	33278										
CA4	762	hgsc.bcm.edu	37	chr17	58235740	58235740	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctacctgggctcactcaccaCaccgacctgcgatgagaagg	10	15	2	1			TCGA-ED-A5KG-01A-11D-A27I-10	TCGA-ED-A5KG-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c986f8b-3eb9-493f-89a4-c408397dd414	f9ce62ee-6802-40bc-8021-23159fb6d4eb	g.chr17:58235740C>T	ENST00000300900.4	+	7	776	c.677C>T	c.(676-678)aCa>aTa	p.T226I		NM_000717.3	NP_000708.1	P22748	CAH4_HUMAN	carbonic anhydrase IV	226	Substrate binding. {ECO:0000305}.				bicarbonate transport (GO:0015701)|one-carbon metabolic process (GO:0006730)|organ development (GO:0048513)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|secretory granule membrane (GO:0030667)|trans-Golgi network (GO:0005802)|transport vesicle membrane (GO:0030658)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(2)|lung(5)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;3.83e-12)|all cancers(12;6.83e-11)		Acetazolamide(DB00819)|Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Brinzolamide(DB01194)|Chlorothiazide(DB00880)|Cyclothiazide(DB00606)|Diclofenamide(DB01144)|Dorzolamide(DB00869)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methazolamide(DB00703)|Methyclothiazide(DB00232)|Topiramate(DB00273)|Trichlormethiazide(DB01021)|Zonisamide(DB00909)	TCACTCACCACACCGACCTGC	0.602																																					p.T226I		Atlas-SNP	.											.	CA4	20	.	0			c.C677T						.						110	83	92					17																	58235740		2203	4300	6503	SO:0001583	missense	762	exon7			TCACCACACCGAC	L10955	CCDS11624.1	17q23.1	2012-08-21			ENSG00000167434	ENSG00000167434	4.2.1.1	"Carbonic anhydrases"	1375	protein-coding gene	gene with protein product		114760	"retinitis pigmentosa 17 (autosomal dominant)"	RP17		8325641	Standard	NM_000717		Approved	CAIV, Car4	uc002iym.4	P22748		ENST00000300900.4:c.677C>T	chr17.hg19:g.58235740C>T	ENSP00000300900:p.Thr226Ile	103.0	0.0		130.0	8.0	NM_000717	B4DQA4|Q6FHI7	Missense_Mutation	SNP	ENST00000300900.4	hg19	CCDS11624.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.996852	0.74818	.	.	ENSG00000167434	ENST00000300900	T	0.77229	-1.08	5.54	5.54	0.83059	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.000000	0.85682	D	0.000000	D	0.89570	0.6753	H	0.95679	3.705	0.80722	D	1	D	0.67145	0.996	P	0.56514	0.8	D	0.92413	0.5939	10	0.87932	D	0	.	14.9783	0.71293	0.0:1.0:0.0:0.0	.	226	P22748	CAH4_HUMAN	I	226	ENSP00000300900:T226I	ENSP00000300900:T226I	T	+	2	0	CA4	55590522	0.998000	0.40836	0.957000	0.39632	0.626000	0.37791	4.321000	0.59209	2.589000	0.87451	0.491000	0.48974	ACA	.	.		0.602	CA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449189.1	NM_000717		T	58235740	C	T	58235740	3	4	239	1	0	0	0	0	1	0	0	0	2520	478	17	3	703	3	CA4	17	58235740	Missense_Mutation	SNP	C	TCGA-ED-A5KG-01A-11D-A27I-10	25752620	58235740	22959470	17	33279										
DNAH17	8632	hgsc.bcm.edu	37	chr17	76451796	76451796	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggtatttcttggtgaagtagCccacgtaggacacgaaggca	13	8	1	1			TCGA-ED-A5KG-01A-11D-A27I-10	TCGA-ED-A5KG-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c986f8b-3eb9-493f-89a4-c408397dd414	f9ce62ee-6802-40bc-8021-23159fb6d4eb	g.chr17:76451796C>T	ENST00000585328.1	-	63	10209	c.10085G>A	c.(10084-10086)gGc>gAc	p.G3362D	DNAH17_ENST00000586052.1_Intron|DNAH17_ENST00000389840.5_Missense_Mutation_p.G3353D	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	3353					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			GGTGAAGTAGCCCACGTAGGA	0.537																																					p.G3367D		Atlas-SNP	.											.	DNAH17	347	.	0			c.G10100A						.						79	62	68					17																	76451796		2203	4299	6502	SO:0001583	missense	8632	exon63			AAGTAGCCCACGT	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"Axonemal dyneins"	2946	protein-coding gene	gene with protein product		610063	"dynein, axonemal, heavy polypeptide 17", "dynein, axonemal, heavy chain like 1", "dynein, axonemal, heavy like 1"	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.10085G>A	chr17.hg19:g.76451796C>T	ENSP00000465516:p.Gly3362Asp	198.0	0.0		187.0	8.0	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Missense_Mutation	SNP	ENST00000585328.1	hg19		.	.	.	.	.	.	.	.	.	.	C	34	5.354418	0.95830	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	D	0.83075	-1.68	5.06	5.06	0.68205	.	0.093775	0.46758	D	0.000264	D	0.95294	0.8473	H	0.99169	4.455	0.58432	D	0.999997	D	0.67145	0.996	D	0.73708	0.981	D	0.97710	1.0190	10	0.87932	D	0	.	18.4429	0.90673	0.0:1.0:0.0:0.0	.	3362	E7EUM8	.	D	3362;3353	ENSP00000374490:G3353D	ENSP00000300671:G3362D	G	-	2	0	DNAH17	73963391	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.611000	0.82962	2.334000	0.79466	0.655000	0.94253	GGC	.	.		0.537	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		T	76451796	C	T	76451796	3	4	239	1	0	0	0	0	1	0	0	0	4603	739	26	3	3364	3	DNAH17	17	76451796	Missense_Mutation	SNP	C	TCGA-ED-A5KG-01A-11D-A27I-10	18216056	76451796	4743414	18	33280										
L3MBTL4	91133	hgsc.bcm.edu	37	chr18	6243330	6243330	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tcatgtttggtcttttcacaCcatcctactggatgaatgtc	7	10	3	1			TCGA-ED-A5KG-01A-11D-A27I-10	TCGA-ED-A5KG-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c986f8b-3eb9-493f-89a4-c408397dd414	f9ce62ee-6802-40bc-8021-23159fb6d4eb	g.chr18:6243330C>T	ENST00000284898.6	-	7	623	c.423G>A	c.(421-423)tgG>tgA	p.W141*	L3MBTL4_ENST00000400105.2_Nonsense_Mutation_p.W141*|L3MBTL4_ENST00000400104.3_Nonsense_Mutation_p.W141*|L3MBTL4_ENST00000535782.1_5'Flank|L3MBTL4_ENST00000317931.7_Nonsense_Mutation_p.W141*	NM_173464.3	NP_775735.2	Q8NA19	LMBL4_HUMAN	l(3)mbt-like 4 (Drosophila)	141					chromatin modification (GO:0016568)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(17)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		Colorectal(10;0.0249)				TCTTTTCACACCATCCTACTG	0.383																																					p.W141X	Esophageal Squamous(41;748 902 17366 28959 43175)	Atlas-SNP	.											.	L3MBTL4	87	.	0			c.G423A						.						175	157	163					18																	6243330		2203	4300	6503	SO:0001587	stop_gained	91133	exon7			TTCACACCATCCT	BC039316	CCDS11839.2	18p11.31-p11.23	2013-01-10			ENSG00000154655	ENSG00000154655		"Sterile alpha motif (SAM) domain containing"	26677	protein-coding gene	gene with protein product						14702039	Standard	NM_173464		Approved	FLJ35936, HsT1031	uc010dkt.3	Q8NA19	OTTHUMG00000131573	ENST00000284898.6:c.423G>A	chr18.hg19:g.6243330C>T	ENSP00000284898:p.Trp141*	109.0	0.0		118.0	5.0	NM_173464	A8MTL8|Q8IXS3	Nonsense_Mutation	SNP	ENST00000284898.6	hg19	CCDS11839.2	.	.	.	.	.	.	.	.	.	.	C	29.9	5.046465	0.93740	.	.	ENSG00000154655	ENST00000400105;ENST00000317931;ENST00000284898;ENST00000400104	.	.	.	4.21	4.21	0.49690	.	0.000000	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.4228	0.67196	0.0:1.0:0.0:0.0	.	.	.	.	X	141	.	ENSP00000284898:W141X	W	-	3	0	L3MBTL4	6233330	1.000000	0.71417	0.999000	0.59377	0.848000	0.48234	5.015000	0.64035	2.338000	0.79540	0.491000	0.48974	TGG	.	.		0.383	L3MBTL4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254448.2	NM_173464		T	6243330	C	T	6243330	4	4	239	1	0	0	0	0	0	1	0	0	8603	508	18	3	1504	3	L3MBTL4	18	6243330	Nonsense_Mutation	SNP	C	TCGA-ED-A5KG-01A-11D-A27I-10		6243330	71833918	19	33281										
KIAA0802	23255	hgsc.bcm.edu	37	chr18	8824928	8824928	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gacaggaccgaggtggggcgGgcagggcacgaggacagcac	20	10	0	0			TCGA-ED-A5KG-01A-11D-A27I-10	TCGA-ED-A5KG-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c986f8b-3eb9-493f-89a4-c408397dd414	f9ce62ee-6802-40bc-8021-23159fb6d4eb	g.chr18:8824928G>A	ENST00000306329.11	+	13	4377	c.4377G>A	c.(4375-4377)cgG>cgA	p.R1459R	SOGA2_ENST00000518815.1_Silent_p.R465R|SOGA2_ENST00000306285.7_Silent_p.R465R|SOGA2_ENST00000400050.3_Silent_p.R1099R|SOGA2_ENST00000359865.3_Silent_p.R1140R|SOGA2_ENST00000517570.1_Silent_p.R1099R																							AGGTGGGGCGGGCAGGGCACG	0.617																																					p.R1140R		Atlas-SNP	.											.	.	.	.	0			c.G3420A						.						73	61	65					18																	8824928		2203	4300	6503	SO:0001819	synonymous_variant	23255	exon15			GGGGCGGGCAGGG																												ENST00000306329.11:c.4377G>A	chr18.hg19:g.8824928G>A		76.0	0.0		63.0	4.0	NM_015210		Silent	SNP	ENST00000306329.11	hg19																																																																																				.	.		0.617	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1			A	8824928	G	A	8824928	2	1	239	1	0	0	0	0	0	0	0	1	8203	1219	43	3		3	KIAA0802	18	8824928	Silent	SNP	G	TCGA-ED-A5KG-01A-11D-A27I-10	2581598	8824928	69252320	20	33282										
MYO5B	4645	hgsc.bcm.edu	37	chr18	47390748	47390748	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttctctgactccagctcttgCctctggaagacagcccaagg	9	14	3	2			TCGA-ED-A5KG-01A-11D-A27I-10	TCGA-ED-A5KG-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c986f8b-3eb9-493f-89a4-c408397dd414	f9ce62ee-6802-40bc-8021-23159fb6d4eb	g.chr18:47390748C>A	ENST00000285039.7	-	28	3905	c.3606G>T	c.(3604-3606)agG>agT	p.R1202S	MYO5B_ENST00000587895.1_5'UTR|MYO5B_ENST00000324581.6_Missense_Mutation_p.R343S	NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	1202					endosome localization (GO:0032439)|metabolic process (GO:0008152)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)|vesicle-mediated transport (GO:0016192)|water transport (GO:0006833)	apical cortex (GO:0045179)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|protein complex (GO:0043234)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|Rab GTPase binding (GO:0017137)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(4)	87				READ - Rectum adenocarcinoma(32;0.103)		CCAGCTCTTGCCTCTGGAAGA	0.577																																					p.R1202S		Atlas-SNP	.											.	MYO5B	178	.	0			c.G3606T						.						97	108	105					18																	47390748		1979	4148	6127	SO:0001583	missense	4645	exon28			CTCTTGCCTCTGG	AB032945	CCDS42436.1	18q	2011-09-27			ENSG00000167306	ENSG00000167306		"Myosins / Myosin superfamily : Class V"	7603	protein-coding gene	gene with protein product		606540				8884266, 17462998	Standard	NM_001080467		Approved	KIAA1119	uc002leb.2	Q9ULV0		ENST00000285039.7:c.3606G>T	chr18.hg19:g.47390748C>A	ENSP00000285039:p.Arg1202Ser	47.0	0.0		47.0	4.0	NM_001080467	B0I1R3|Q0P656|Q9H6Y6	Missense_Mutation	SNP	ENST00000285039.7	hg19	CCDS42436.1	.	.	.	.	.	.	.	.	.	.	C	17.80	3.478980	0.63849	.	.	ENSG00000167306	ENST00000285039;ENST00000324581	T;T	0.05649	3.41;3.41	5.5	1.14	0.20703	.	0.000000	0.85682	D	0.000000	T	0.19565	0.0470	M	0.80183	2.485	0.53688	D	0.999973	P;D	0.89917	0.882;1.0	P;D	0.83275	0.521;0.996	T	0.16335	-1.0406	10	0.13853	T	0.58	.	10.3118	0.43712	0.0:0.6334:0.0:0.3666	.	1202;343	Q9ULV0;Q9H6Y6	MYO5B_HUMAN;.	S	1202;343	ENSP00000285039:R1202S;ENSP00000315531:R343S	ENSP00000285039:R1202S	R	-	3	2	MYO5B	45644746	0.766000	0.28496	0.998000	0.56505	0.902000	0.53008	-0.042000	0.12063	0.294000	0.22547	-0.224000	0.12420	AGG	.	.		0.577	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2			A	47390748	C	A	47390748	3	1	239	1	0	0	0	0	1	0	0	0	10088	738	26	3	1992	3	MYO5B	18	47390748	Missense_Mutation	SNP	C	TCGA-ED-A5KG-01A-11D-A27I-10	38565820	47390748	30686500	21	33283										
IRGC	56269	hgsc.bcm.edu	37	chr19	44223141	44223141	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cctgctggtctccccccgccGctgcggggccgtcgagaccc	13	20	1	1			TCGA-ED-A5KG-01A-11D-A27I-10	TCGA-ED-A5KG-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c986f8b-3eb9-493f-89a4-c408397dd414	f9ce62ee-6802-40bc-8021-23159fb6d4eb	g.chr19:44223141G>A	ENST00000244314.5	+	2	630	c.431G>A	c.(430-432)cGc>cAc	p.R144H		NM_019612.3	NP_062558.1	Q6NXR0	IIGP5_HUMAN	immunity-related GTPase family, cinema	144	IRG-type G.					membrane (GO:0016020)	GTP binding (GO:0005525)|hydrolase activity, acting on acid anhydrides (GO:0016817)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|skin(2)	25		Prostate(69;0.0435)				TCCCCCCGCCGCTGCGGGGCC	0.652																																					p.R144H	Colon(189;350 2037 11447 13433 38914)	Atlas-SNP	.											.	IRGC	67	.	0			c.G431A						.						12	12	12					19																	44223141		2114	4167	6281	SO:0001583	missense	56269	exon2			CCCGCCGCTGCGG	BC066939	CCDS12629.1	19q13.32	2008-02-05	2005-10-31	2005-10-31	ENSG00000124449	ENSG00000124449			28835	protein-coding gene	gene with protein product			"immunity-related GTPase family, cinema 1"	IRGC1		12477932	Standard	NM_019612		Approved	Iigp5, CINEMA	uc002oxh.3	Q6NXR0	OTTHUMG00000154587	ENST00000244314.5:c.431G>A	chr19.hg19:g.44223141G>A	ENSP00000244314:p.Arg144His	42.0	0.0		18.0	9.0	NM_019612	Q05BR8	Missense_Mutation	SNP	ENST00000244314.5	hg19	CCDS12629.1	.	.	.	.	.	.	.	.	.	.	G	17.54	3.415973	0.62511	.	.	ENSG00000124449	ENST00000244314	T	0.27720	1.65	5.71	4.65	0.58169	.	0.000000	0.64402	D	0.000001	T	0.56232	0.1971	M	0.77406	2.37	0.46927	D	0.99925	D	0.89917	1.0	D	0.81914	0.995	T	0.61392	-0.7072	10	0.59425	D	0.04	.	14.4208	0.67183	0.0:0.1485:0.8515:0.0	.	144	Q6NXR0	IIGP5_HUMAN	H	144	ENSP00000244314:R144H	ENSP00000244314:R144H	R	+	2	0	IRGC	48914981	1.000000	0.71417	0.033000	0.17914	0.509000	0.34042	5.579000	0.67457	1.380000	0.46344	0.555000	0.69702	CGC	.	.		0.652	IRGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336191.1	NM_019612		A	44223141	G	A	44223141	3	1	239	1	0	0	0	0	1	0	0	0	7847	1087	38	1	433	1	IRGC	19	44223141	Missense_Mutation	SNP	G	TCGA-ED-A5KG-01A-11D-A27I-10		44223141	14905842	22	33284										
ZNF83	55769	hgsc.bcm.edu	37	chr19	53116801	53116801	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttgtaaggtttctctccagtGtggattctccagtgatttac	9	8	2	1			TCGA-ED-A5KG-01A-11D-A27I-10	TCGA-ED-A5KG-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c986f8b-3eb9-493f-89a4-c408397dd414	f9ce62ee-6802-40bc-8021-23159fb6d4eb	g.chr19:53116801G>A	ENST00000597597.1	-	2	3270	c.1017C>T	c.(1015-1017)caC>caT	p.H339H	ZNF83_ENST00000601257.1_Intron|ZNF83_ENST00000544146.1_Silent_p.H339H|ZNF83_ENST00000391789.4_Silent_p.H311H|ZNF83_ENST00000536937.1_Silent_p.H339H|ZNF83_ENST00000545872.1_Silent_p.H339H|ZNF83_ENST00000594682.2_3'UTR|ZNF83_ENST00000600714.1_Intron|ZNF83_ENST00000301096.3_Silent_p.H339H|ZNF83_ENST00000541777.2_Silent_p.H339H			P51522	ZNF83_HUMAN	zinc finger protein 83	339					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	18				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)		TCTCTCCAGTGTGGATTCTCC	0.418																																					p.H339H		Atlas-SNP	.											ZNF83,NS,carcinoma,0,2	ZNF83	73	.	0			c.C1017T						.						118	120	120					19																	53116801		2203	4300	6503	SO:0001819	synonymous_variant	55769	exon3			TCCAGTGTGGATT	M27877	CCDS12854.1	19q13.3	2013-01-08	2006-05-12			ENSG00000167766		"Zinc fingers, C2H2-type"	13158	protein-coding gene	gene with protein product		194558	"zinc finger protein 83 (HPF1)", "zinc finger protein 816B"	ZNF816B		8088807	Standard	NM_018300		Approved	FLJ11015, HPF1	uc010epy.3	P51522		ENST00000597597.1:c.1017C>T	chr19.hg19:g.53116801G>A		92.0	2.0		99.0	9.0	NM_018300	A8MT75|Q3ZCX0|Q6PI08	Silent	SNP	ENST00000597597.1	hg19	CCDS12854.1																																																																																			.	.		0.418	ZNF83-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463700.1	NM_018300		A	53116801	G	A	53116801	2	1	239	1	0	0	0	0	0	0	0	1	18198	1368	48	3		3	ZNF83	19	53116801	Silent	SNP	G	TCGA-ED-A5KG-01A-11D-A27I-10	8893660	53116801	6012182	23	33285										
SRC	6714	hgsc.bcm.edu	37	chr20	36031248	36031248	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtccttcgggatcctgctgaCtgagctcaccacaaagggac	11	13	1	2			TCGA-ED-A5KG-01A-11D-A27I-10	TCGA-ED-A5KG-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c986f8b-3eb9-493f-89a4-c408397dd414	f9ce62ee-6802-40bc-8021-23159fb6d4eb	g.chr20:36031248C>G	ENST00000373578.2	+	13	1716	c.1367C>G	c.(1366-1368)aCt>aGt	p.T456S	SRC_ENST00000373567.2_Missense_Mutation_p.T456S|SRC_ENST00000358208.4_Missense_Mutation_p.T456S|SRC_ENST00000477066.1_3'UTR|SRC_ENST00000373558.2_Missense_Mutation_p.T462S|SRC_ENST00000360723.4_Missense_Mutation_p.T462S|SRC_ENST00000445403.1_Missense_Mutation_p.T456S	NM_198291.1	NP_938033.1	P12931	SRC_HUMAN	SRC proto-oncogene, non-receptor tyrosine kinase	456	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|bone resorption (GO:0045453)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cellular response to progesterone stimulus (GO:0071393)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|membrane organization (GO:0061024)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of mitochondrial depolarization (GO:0051902)|negative regulation of protein homooligomerization (GO:0032463)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oogenesis (GO:0048477)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of integrin activation (GO:0033625)|positive regulation of podosome assembly (GO:0071803)|positive regulation of protein kinase B signaling (GO:0051897)|progesterone receptor signaling pathway (GO:0050847)|protein autophosphorylation (GO:0046777)|Ras protein signal transduction (GO:0007265)|regulation of bone resorption (GO:0045124)|regulation of caveolin-mediated endocytosis (GO:2001286)|regulation of cell-cell adhesion (GO:0022407)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of epithelial cell migration (GO:0010632)|regulation of intracellular estrogen receptor signaling pathway (GO:0033146)|regulation of protein binding (GO:0043393)|regulation of vascular permeability (GO:0043114)|response to interleukin-1 (GO:0070555)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|stress fiber assembly (GO:0043149)|T cell costimulation (GO:0031295)|transforming growth factor beta receptor signaling pathway (GO:0007179)|uterus development (GO:0060065)|viral process (GO:0016032)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|ephrin receptor binding (GO:0046875)|growth factor receptor binding (GO:0070851)|heme binding (GO:0020037)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphoprotein binding (GO:0051219)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(16)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	30		Myeloproliferative disorder(115;0.00878)			Bosutinib(DB06616)|Dasatinib(DB01254)|Ponatinib(DB08901)	ATCCTGCTGACTGAGCTCACC	0.602																																					p.T456S		Atlas-SNP	.											.	SRC	52	.	0			c.C1367G						.						111	98	102					20																	36031248		2203	4300	6503	SO:0001583	missense	6714	exon13			TGCTGACTGAGCT	AF077754	CCDS13294.1	20q12-q13	2014-06-25	2014-06-25		ENSG00000197122	ENSG00000197122		"SH2 domain containing"	11283	protein-coding gene	gene with protein product		190090	"v-src avian sarcoma (Schmidt-Ruppin A-2) viral oncogene homolog"	SRC1		2582238	Standard	NM_005417		Approved	ASV, c-src	uc002xgy.3	P12931	OTTHUMG00000032417	ENST00000373578.2:c.1367C>G	chr20.hg19:g.36031248C>G	ENSP00000362680:p.Thr456Ser	124.0	0.0		138.0	12.0	NM_005417	E1P5V4|Q76P87|Q86VB9|Q9H5A8	Missense_Mutation	SNP	ENST00000373578.2	hg19	CCDS13294.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.047008	0.75846	.	.	ENSG00000197122	ENST00000445403;ENST00000373578;ENST00000360723;ENST00000358208;ENST00000373567;ENST00000373558	D;D;D;D;D;D	0.82619	-1.63;-1.63;-1.63;-1.63;-1.63;-1.63	4.63	4.63	0.57726	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.75376	0.3841	N	0.11064	0.09	0.80722	D	1	P	0.51240	0.943	P	0.48552	0.581	T	0.80968	-0.1145	10	0.72032	D	0.01	.	15.3531	0.74405	0.0:1.0:0.0:0.0	.	456	P12931	SRC_HUMAN	S	456;456;462;456;456;462	ENSP00000408503:T456S;ENSP00000362680:T456S;ENSP00000353950:T462S;ENSP00000350941:T456S;ENSP00000362668:T456S;ENSP00000362659:T462S	ENSP00000350941:T456S	T	+	2	0	SRC	35464662	1.000000	0.71417	0.974000	0.42286	0.980000	0.70556	5.873000	0.69644	2.550000	0.86006	0.561000	0.74099	ACT	.	.		0.602	SRC-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268142.1	NM_005417		G	36031248	C	G	36031248	3	3	239	1	0	0	0	0	1	0	0	0	15149	565	20	4	1405	4	SRC	20	36031248	Missense_Mutation	SNP	C	TCGA-ED-A5KG-01A-11D-A27I-10		36031248	26994272	24	33286										
C22orf9	23313	hgsc.bcm.edu	37	chr22	45595761	45595761	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agtggggggtcacctccaccGtcgtcctcccggaagaactc	12	15	1	1			TCGA-ED-A5KG-01A-11D-A27I-10	TCGA-ED-A5KG-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c986f8b-3eb9-493f-89a4-c408397dd414	f9ce62ee-6802-40bc-8021-23159fb6d4eb	g.chr22:45595761G>A	ENST00000336156.5	-	8	1073	c.1008C>T	c.(1006-1008)gaC>gaT	p.D336D	KIAA0930_ENST00000474515.1_5'UTR|KIAA0930_ENST00000391627.2_Silent_p.D302D|KIAA0930_ENST00000251993.7_Silent_p.D341D|KIAA0930_ENST00000443310.3_Silent_p.D318D|MIR1249_ENST00000408671.1_RNA	NM_001009880.1	NP_001009880.1	Q6ICG6	K0930_HUMAN	KIAA0930	336										endometrium(1)|kidney(4)|large_intestine(2)|lung(7)|urinary_tract(1)	15						CACCTCCACCGTCGTCCTCCC	0.562																																					p.D341D		Atlas-SNP	.											.	KIAA0930	43	.	0			c.C1023T						.						98	94	96					22																	45595761		2203	4300	6503	SO:0001819	synonymous_variant	23313	exon8			TCCACCGTCGTCC	AK025608	CCDS33665.1, CCDS33666.1	22q13.31	2011-02-23	2011-02-23	2011-02-23	ENSG00000100364	ENSG00000100364			1314	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 9"	C22orf9		10231032	Standard	NM_015264		Approved	bK268H5.C22.1	uc003bfw.1	Q6ICG6	OTTHUMG00000151263	ENST00000336156.5:c.1008C>T	chr22.hg19:g.45595761G>A		69.0	0.0		74.0	4.0	NM_015264	B0QY17|B0QY19|B3KT48|Q6ZVE5|Q7Z6K9|Q8IZ76|Q9Y2E2	Silent	SNP	ENST00000336156.5	hg19	CCDS33665.1																																																																																			.	.		0.562	KIAA0930-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321975.2	NM_001009880		A	45595761	G	A	45595761	2	1	239	1	0	0	0	0	0	0	0	1	2153	1136	40	1		1	C22orf9	22	45595761	Silent	SNP	G	TCGA-ED-A5KG-01A-11D-A27I-10		45595761	5708805	25	33287										
CXorf58	254158	hgsc.bcm.edu	37	chrX	23934445	23934445	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtattaatgccgtcaagtaaGgtgacgtttcatgatgtaca	10	6	2	2			TCGA-ED-A5KG-01A-11D-A27I-10	TCGA-ED-A5KG-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c986f8b-3eb9-493f-89a4-c408397dd414	f9ce62ee-6802-40bc-8021-23159fb6d4eb	g.chrX:23934445G>A	ENST00000379211.3	+	5	972	c.423G>A	c.(421-423)aaG>aaA	p.K141K		NM_001169574.1|NM_152761.2	NP_001163045.1|NP_689974.2	Q96LI9	CX058_HUMAN	chromosome X open reading frame 58	141										breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|prostate(1)	14						CGTCAAGTAAGGTGACGTTTC	0.299																																					p.K141K		Atlas-SNP	.											.	CXorf58	53	.	0			c.G423A						.						106	93	97					X																	23934445		2202	4298	6500	SO:0001630	splice_region_variant	254158	exon5			AAGTAAGGTGACG	AK058173	CCDS14209.1	Xp22.11	2012-11-28			ENSG00000165182	ENSG00000165182			26356	protein-coding gene	gene with protein product							Standard	NM_152761		Approved	FLJ25444	uc004daz.1	Q96LI9	OTTHUMG00000021258	ENST00000379211.3:c.423+1G>A	chrX.hg19:g.23934445G>A		143.0	0.0		152.0	9.0	NM_152761		Silent	SNP	ENST00000379211.3	hg19	CCDS14209.1	.	.	.	.	.	.	.	.	.	.	g	8.504	0.864873	0.17250	.	.	ENSG00000165182	ENST00000435707	.	.	.	5.0	5.0	0.66597	.	.	.	.	.	T	0.70272	0.3205	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.69914	-0.5016	4	.	.	.	-1.6058	14.2859	0.66245	0.0:0.0:1.0:0.0	.	.	.	.	S	115	.	.	G	+	1	0	CXorf58	23844366	1.000000	0.71417	0.869000	0.34112	0.261000	0.26267	5.194000	0.65125	2.064000	0.61679	0.411000	0.27672	GGT	.	.		0.299	CXorf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056071.1	NM_152761	Silent	A	23934445	G	A	23934445	5	1	239	1	0	0	0	0	0	0	1	0	4116	1014	35	3	437	3	CXorf58	23	23934445	Splice_Site	SNP	G	TCGA-ED-A5KG-01A-11D-A27I-10		23934445	131336115	26	33288										
DMD	1756	hgsc.bcm.edu	37	chrX	31525469	31525469	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tccaaacgtctttgtaacagGactgcatcatcggaaccttc	7	12	2	0			TCGA-ED-A5KG-01A-11D-A27I-10	TCGA-ED-A5KG-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c986f8b-3eb9-493f-89a4-c408397dd414	f9ce62ee-6802-40bc-8021-23159fb6d4eb	g.chrX:31525469G>T	ENST00000357033.4	-	56	8525	c.8319C>A	c.(8317-8319)gtC>gtA	p.V2773V	DMD_ENST00000445312.1_5'UTR|DMD_ENST00000359836.1_Silent_p.V313V|DMD_ENST00000541735.1_Silent_p.V313V|DMD_ENST00000474231.1_Silent_p.V313V|DMD_ENST00000378707.3_Silent_p.V313V|DMD_ENST00000343523.2_Silent_p.V313V|DMD_ENST00000378677.2_Silent_p.V2769V	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	2773					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				TTTGTAACAGGACTGCATCAT	0.423																																					p.V2773V		Atlas-SNP	.											.	DMD	2127	.	0			c.C8319A						.						181	146	158					X																	31525469		2202	4300	6502	SO:0001819	synonymous_variant	1756	exon56			TAACAGGACTGCA	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.8319C>A	chrX.hg19:g.31525469G>T		133.0	0.0		166.0	8.0	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Silent	SNP	ENST00000357033.4	hg19	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	G	4.269	0.049096	0.08243	.	.	ENSG00000198947	ENST00000465285	.	.	.	5.68	3.89	0.44902	.	.	.	.	.	T	0.45094	0.1325	.	.	.	0.30887	N	0.730797	.	.	.	.	.	.	T	0.47812	-0.9088	4	.	.	.	.	9.5377	0.39233	0.0754:0.0:0.781:0.1437	.	.	.	.	T	502	.	.	P	-	1	0	DMD	31435390	0.440000	0.25618	0.289000	0.24876	0.988000	0.76386	0.952000	0.29149	1.131000	0.42111	0.594000	0.82650	CCT	.	.		0.423	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		T	31525469	G	T	31525469	2	4	239	1	0	0	0	0	0	0	0	1	4582	1161	41	3		3	DMD	23	31525469	Silent	SNP	G	TCGA-ED-A5KG-01A-11D-A27I-10	7591024	31525469	123745091	27	33289										
HLX	3142	hgsc.bcm.edu	37	chr1	221053601	221053602	+	In_Frame_Ins	INS	-	-	CAGCAACAGCCGCCG													0	0	1	0	NA	0	1	1	0	agcagcagcaacagccgcagINScagcaacagcctccgcctcc							TCGA-ED-A627-01A-12D-A30V-10	TCGA-ED-A627-10B-01D-A30V-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f59d69bf-3766-4425-a07e-7b5a15b05580	52ca40d4-025d-419f-acf2-feeca914604d	g.chr1:221053601_221053602insCAGCAACAGCCGCCG	ENST00000366903.6	+	1	1903_1904	c.402_403insCAGCAACAGCCGCCG	c.(403-405)cag>CAGCAACAGCCGCCGcag	p.135_135Q>QQQPPQ	HLA-AS1_ENST00000552026.1_RNA|HLX_ENST00000549319.1_5'Flank	NM_021958.3	NP_068777.1	Q14774	HLX_HUMAN	H2.0-like homeobox	135	Poly-Gln.|Pro-rich.			QQQ -> RRE (in Ref. 1; M60721). {ECO:0000305}.	cell differentiation (GO:0030154)|embryonic digestive tract morphogenesis (GO:0048557)|enteric nervous system development (GO:0048484)|liver development (GO:0001889)|multicellular organismal development (GO:0007275)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|positive regulation of cell proliferation (GO:0008284)|positive regulation of organ growth (GO:0046622)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(9)|lung(11)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	32				GBM - Glioblastoma multiforme(131;0.00914)		aacagccgcagcagcaacagcC	0.718																																					p.Q134delinsQQQQPP		Atlas-INDEL	.											.	HLX	67	.	0			c.402_403insCAGCAACAGCCGCCG						.																																			SO:0001652	inframe_insertion	3142	exon1			.	BC033808	CCDS1527.1	1q41	2011-06-20	2007-07-26	2007-07-26	ENSG00000136630	ENSG00000136630		"Homeoboxes / ANTP class : NKL subclass"	4978	protein-coding gene	gene with protein product		142995	"H2.0 (Drosophila)-like homeo box 1", "H2.0-like homeobox 1 (Drosophila)", "H2.0-like homeobox 1"	HLX1		1676597, 7806220	Standard	NM_021958		Approved	HB24	uc001hmv.4	Q14774	OTTHUMG00000037352	Exception_encountered	chr1.hg19:g.221053601_221053602insCAGCAACAGCCGCCG	Exception_encountered	85.0	0.0		86.0	14.0	NM_021958	B2R8A8|Q15988|Q59HE7|Q9NZ75	In_Frame_Ins	INS	ENST00000366903.6	hg19	CCDS1527.1																																																																																			.	.		0.718	HLX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090902.3	NM_021958		CAGCAACAGCCGCCG	221053602	-	CAGCAACAGCCGCCG	221053601	7	5	240	1	0	1	1	0	0	0	0	0	7225	962	34	0	404	0	HLX	1	221053601	In_Frame_Ins	INS	-	TCGA-ED-A627-01A-12D-A30V-10		221053601	28197020	1	33290										
PCDHGB4	8641	hgsc.bcm.edu	37	chr5	140769325	140769325	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	gctgcgcacgggcgaagtgcGcacagcgcgtgccttaggcg	17	13	0	0	rs201153580	byFrequency	TCGA-ED-A627-01A-12D-A30V-10	TCGA-ED-A627-10B-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f59d69bf-3766-4425-a07e-7b5a15b05580	52ca40d4-025d-419f-acf2-feeca914604d	g.chr5:140769325G>A	ENST00000519479.1	+	1	1874	c.1874G>A	c.(1873-1875)cGc>cAc	p.R625H	PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_003736.2|NM_018925.2|NM_032098.1	NP_003727.1|NP_061748.1|NP_115269.1	Q9UN71	PCDGG_HUMAN	protocadherin gamma subfamily B, 4	625	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(9)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(2)	37			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGCGAAGTGCGCACAGCGCGT	0.692																																					p.R625H		Atlas-SNP	.											.	PCDHGB4	125	.	0			c.G1874A						.						34	39	37					5																	140769325		2134	4244	6378	SO:0001583	missense	8641	exon1			AAGTGCGCACAGC	AF152520	CCDS54928.1, CCDS75337.1	5q31	2010-01-26				ENSG00000253953		"Cadherins / Protocadherins : Clustered"	8711	other	protocadherin	"fibroblast cadherin FIB2", "cadherin 20"	603058				10380929	Standard	NM_003736		Approved	FIB2, CDH20, PCDH-GAMMA-B4		Q9UN71		ENST00000519479.1:c.1874G>A	chr5.hg19:g.140769325G>A	ENSP00000428288:p.Arg625His	43.0	0.0		55.0	4.0	NM_032098	O15099|Q2M267|Q9UN64	Missense_Mutation	SNP	ENST00000519479.1	hg19	CCDS54928.1	.	.	.	.	.	.	.	.	.	.	.	18.92	3.725536	0.68959	.	.	ENSG00000253953	ENST00000519479	T	0.52754	0.65	5.05	4.16	0.48862	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.73783	0.3631	M	0.90425	3.115	0.28014	N	0.934786	D;D	0.89917	1.0;1.0	D;D	0.87578	0.992;0.998	T	0.68488	-0.5395	9	0.87932	D	0	.	14.0879	0.64971	0.0776:0.0:0.9224:0.0	.	625;625	Q9UN71-2;Q9UN71	.;PCDGG_HUMAN	H	625	ENSP00000428288:R625H	ENSP00000428288:R625H	R	+	2	0	PCDHGB4	140749509	1.000000	0.71417	1.000000	0.80357	0.183000	0.23260	6.406000	0.73276	2.503000	0.84419	0.563000	0.77884	CGC	.	.		0.692	PCDHGB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374745.1	NM_003736		A	140769325	G	A	140769325	3	1	240	1	0	0	0	0	1	0	0	0	11574	1087	38	1	1876	1	PCDHGB4	5	140769325	Missense_Mutation	SNP	G	TCGA-ED-A627-01A-12D-A30V-10		140769325	40145935	2	33291										
SUPT16H	11198	hgsc.bcm.edu	37	chr14	21820872	21820872	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	NA	0	1	1	0	ggggtgcagagctgtgtctgGaaccacggttagagccacgg	17	9	1	2			TCGA-ED-A627-01A-12D-A30V-10	TCGA-ED-A627-10B-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f59d69bf-3766-4425-a07e-7b5a15b05580	52ca40d4-025d-419f-acf2-feeca914604d	g.chr14:21820872G>T	ENST00000216297.2	-	26	3442	c.3104C>A	c.(3103-3105)tCc>tAc	p.S1035Y		NM_007192.3	NP_009123.1	Q9Y5B9	SP16H_HUMAN	suppressor of Ty 16 homolog (S. cerevisiae)	1035					DNA repair (GO:0006281)|DNA replication (GO:0006260)|gene expression (GO:0010467)|nucleosome disassembly (GO:0006337)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_cancers(95;0.00115)		Epithelial(56;1.62e-06)|all cancers(55;1.49e-05)	GBM - Glioblastoma multiforme(265;0.0159)		GCTGTGTCTGGAACCACGGTT	0.502																																					p.S1035Y		Atlas-SNP	.											.	SUPT16H	84	.	0			c.C3104A						.						166	152	157					14																	21820872		2203	4300	6503	SO:0001583	missense	11198	exon26			TGTCTGGAACCAC	AF152961	CCDS9569.1	14q11.1	2008-08-13	2001-11-28		ENSG00000092201	ENSG00000092201			11465	protein-coding gene	gene with protein product	"facilitates chromatin remodeling 140 kDa subunit"	605012	"suppressor of Ty (S.cerevisiae) 16 homolog"			9489704, 11239457	Standard	NM_007192		Approved	FACT, FACTP140, SPT16/CDC68, FLJ14010, FLJ10857, CDC68	uc001wao.2	Q9Y5B9	OTTHUMG00000029685	ENST00000216297.2:c.3104C>A	chr14.hg19:g.21820872G>T	ENSP00000216297:p.Ser1035Tyr	56.0	0.0		72.0	5.0	NM_007192	Q6GMT8|Q6P2F1|Q6PJM1|Q9NRX0	Missense_Mutation	SNP	ENST00000216297.2	hg19	CCDS9569.1	.	.	.	.	.	.	.	.	.	.	G	18.16	3.562925	0.65538	.	.	ENSG00000092201	ENST00000216297	.	.	.	4.99	4.99	0.66335	.	0.276731	0.30565	N	0.009359	T	0.44371	0.1290	N	0.22421	0.69	0.80722	D	1	P	0.34462	0.454	B	0.31614	0.133	T	0.50600	-0.8809	9	0.62326	D	0.03	-9.4727	15.3682	0.74541	0.0:0.0:1.0:0.0	.	1035	Q9Y5B9	SP16H_HUMAN	Y	1035	.	ENSP00000216297:S1035Y	S	-	2	0	SUPT16H	20890712	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.839000	0.69395	2.607000	0.88179	0.650000	0.86243	TCC	.	.		0.502	SUPT16H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074025.2			T	21820872	G	T	21820872	3	4	240	1	0	0	0	0	1	0	0	0	15411	1174	41	3	43	3	SUPT16H	14	21820872	Missense_Mutation	SNP	G	TCGA-ED-A627-01A-12D-A30V-10		21820872	85528668	3	33292										
PLEKHM2	23207	hgsc.bcm.edu	37	chr1	16059140	16059140	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	acagccagcagctcctcccgCcctgggtcatctacctgagc	9	18	2	1			TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr1:16059140C>T	ENST00000375799.3	+	19	3066	c.2839C>T	c.(2839-2841)Ccc>Tcc	p.P947S	RP11-288I21.1_ENST00000453804.1_RNA|PLEKHM2_ENST00000477849.1_3'UTR|PLEKHM2_ENST00000375793.2_Missense_Mutation_p.P927S	NM_015164.2	NP_055979.2	Q8IWE5	PKHM2_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 2	947					Golgi organization (GO:0007030)	cytoplasm (GO:0005737)	kinesin binding (GO:0019894)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.000259)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00057)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		GCTCCTCCCGCCCTGGGTCAT	0.622																																					p.P947S		Atlas-SNP	.											.	PLEKHM2	94	.	0			c.C2839T						.						40	46	44					1																	16059140		1981	4175	6156	SO:0001583	missense	23207	exon19			CTCCCGCCCTGGG	AB020649	CCDS44063.1	1p36.13	2013-01-10			ENSG00000116786	ENSG00000116786		"Pleckstrin homology (PH) domain containing"	29131	protein-coding gene	gene with protein product		609613				10048485	Standard	NM_015164		Approved	KIAA0842	uc010obo.2	Q8IWE5	OTTHUMG00000003062	ENST00000375799.3:c.2839C>T	chr1.hg19:g.16059140C>T	ENSP00000364956:p.Pro947Ser	28.0	0.0		28.0	10.0	NM_015164	O94928|Q5VT65|Q6NUH9|Q7L8G1|Q8IVT7|Q8N2T4|Q96AY0|Q9NTF7	Missense_Mutation	SNP	ENST00000375799.3	hg19	CCDS44063.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.107765	0.77096	.	.	ENSG00000116786	ENST00000375799;ENST00000375793	T;T	0.48522	0.82;0.81	5.29	4.38	0.52667	.	0.063735	0.64402	D	0.000006	T	0.49253	0.1546	N	0.20986	0.625	0.53688	D	0.999975	D	0.63046	0.992	P	0.57283	0.817	T	0.53136	-0.8481	10	0.59425	D	0.04	-14.9992	14.1217	0.65192	0.0:0.8398:0.1602:0.0	.	947	Q8IWE5	PKHM2_HUMAN	S	947;927	ENSP00000364956:P947S;ENSP00000364950:P927S	ENSP00000364950:P927S	P	+	1	0	PLEKHM2	15931727	0.989000	0.36119	0.822000	0.32727	0.622000	0.37654	4.311000	0.59147	1.211000	0.43351	0.655000	0.94253	CCC	.	.		0.622	PLEKHM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008463.1	NM_015164		T	16059140	C	T	16059140	3	4	241	1	0	0	0	0	1	0	0	0	12090	739	26	3	2913	3	PLEKHM2	1	16059140	Missense_Mutation	SNP	C	TCGA-ED-A66X-01A-11D-A30V-10		16059140	233191481	1	33293										
C1orf77	26097	hgsc.bcm.edu	37	chr1	153615718	153615718	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	ctaaggtcaaaacctgctccGaggtggacgagccgtagctc	12	12	1	0	rs138105302		TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr1:153615718G>A	ENST00000368694.3	+	5	731	c.419G>A	c.(418-420)cGa>cAa	p.R140Q	CHTOP_ENST00000368687.1_Missense_Mutation_p.R115Q|CHTOP_ENST00000403433.1_Intron|CHTOP_ENST00000368686.1_3'UTR|CHTOP_ENST00000495554.1_Intron|CHTOP_ENST00000368690.3_Intron	NM_001206612.1|NM_015607.3	NP_001193541.1|NP_056422.2	Q9Y3Y2	CHTOP_HUMAN	chromatin target of PRMT1	140	Arg/Gly-rich.				mRNA export from nucleus (GO:0006406)|positive regulation of ATPase activity (GO:0032781)|positive regulation of helicase activity (GO:0051096)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear speck (GO:0016607)|transcription export complex (GO:0000346)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(3)|liver(1)|lung(6)	13						AACCTGCTCCGAGGTGGACGA	0.537																																					p.R141Q		Atlas-SNP	.											.	CHTOP	34	.	0			c.G422A						.	G	GLN/ARG,GLN/ARG	0,4406		0,0,2203	126	124	124		422,419	5.4	1	1	dbSNP_134	124	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	CHTOP	NM_001206612.1,NM_015607.3	43,43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	141/250,140/249	153615718	1,13005	2203	4300	6503	SO:0001583	missense	26097	exon5			TGCTCCGAGGTGG		CCDS1048.1, CCDS72917.1, CCDS72918.1	1q21.3	2011-03-24	2011-03-24	2011-03-24	ENSG00000160679	ENSG00000160679			24511	protein-coding gene	gene with protein product	"small protein rich in arginine and glycine", "Friend of Prmt1"	614206	"chromosome 1 open reading frame 77"	C1orf77		19254951	Standard	NM_015607		Approved	DKFZP547E1010, SRAG, FOP	uc001fcn.2	Q9Y3Y2	OTTHUMG00000037052	ENST00000368694.3:c.419G>A	chr1.hg19:g.153615718G>A	ENSP00000357683:p.Arg140Gln	83.0	0.0		145.0	13.0	NM_001206612	D3DV55|Q0VAQ8|Q2VPI9|Q5T7Y8|Q5T7Y9|Q5T7Z0|Q6NSM4|Q6PB28|Q8WYT9|Q9BUC5|Q9H034|Q9H2L0	Missense_Mutation	SNP	ENST00000368694.3	hg19	CCDS1048.1	.	.	.	.	.	.	.	.	.	.	G	16.38	3.107452	0.56291	0.0	1.16E-4	ENSG00000160679	ENST00000368694;ENST00000368687	D;D	0.87966	-2.32;-2.32	5.44	5.44	0.79542	.	0.298829	0.31257	N	0.007967	D	0.83229	0.5209	L	0.29908	0.895	0.80722	D	1	D;D	0.61697	0.99;0.983	P;P	0.55455	0.776;0.602	T	0.80621	-0.1301	10	0.25106	T	0.35	.	16.8052	0.85625	0.0:0.0:1.0:0.0	.	141;140	Q9Y3Y2-3;Q9Y3Y2	.;CHTOP_HUMAN	Q	140;115	ENSP00000357683:R140Q;ENSP00000357676:R115Q	ENSP00000357676:R115Q	R	+	2	0	CHTOP	151882342	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.532000	0.73825	2.832000	0.97577	0.655000	0.94253	CGA	.	G|1.000;A|0.000		0.537	CHTOP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000089967.1	NM_015607		A	153615718	G	A	153615718	3	1	241	1	0	0	0	0	1	0	0	0	2061	1058	37	1	433	1	C1orf77	1	153615718	Missense_Mutation	SNP	G	TCGA-ED-A66X-01A-11D-A30V-10	137556578	153615718	95634903	2	33294										
PYHIN1	149628	hgsc.bcm.edu	37	chr1	158908870	158908870	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	gaaaaataaactacttgtagAaaagaaaaaaaccatctgaa	5	5	1	3			TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr1:158908870A>C	ENST00000368140.1	+	4	657	c.412A>C	c.(412-414)Aaa>Caa	p.K138Q	PYHIN1_ENST00000368135.4_Splice_Site_p.K138Q|PYHIN1_ENST00000392254.2_Splice_Site_p.K138Q|PYHIN1_ENST00000368138.3_Splice_Site_p.K129Q|PYHIN1_ENST00000392252.3_Splice_Site_p.K129Q	NM_152501.4|NM_198928.4|NM_198929.4	NP_689714.2|NP_945146.1|NP_945147.1	Q6K0P9	IFIX_HUMAN	pyrin and HIN domain family, member 1	138					cell cycle (GO:0007049)	nucleus (GO:0005634)				breast(2)|endometrium(3)|large_intestine(10)|lung(32)|ovary(3)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_hematologic(112;0.0378)					CTACTTGTAGAAAAGAAAAAA	0.363																																					p.K138Q		Atlas-SNP	.											.	PYHIN1	208	.	0			c.A412C						.						36	38	37					1																	158908870		2203	4300	6503	SO:0001630	splice_region_variant	149628	exon4			TTGTAGAAAAGAA	AY185344	CCDS1178.1, CCDS1179.1, CCDS30907.1, CCDS30908.1	1q23.1	2008-02-05			ENSG00000163564	ENSG00000163564			28894	protein-coding gene	gene with protein product		612677				15122330	Standard	NM_152501		Approved	IFIX, MGC23885	uc001ftb.3	Q6K0P9	OTTHUMG00000037109	ENST00000368140.1:c.412-1A>C	chr1.hg19:g.158908870A>C		105.0	0.0		176.0	17.0	NM_152501	Q5T3W6|Q6K0P6|Q6K0P7|Q6K0P8|Q8WW65	Missense_Mutation	SNP	ENST00000368140.1	hg19	CCDS1178.1	.	.	.	.	.	.	.	.	.	.	A	11.98	1.800300	0.31869	.	.	ENSG00000163564	ENST00000458222;ENST00000368140;ENST00000368138;ENST00000392254;ENST00000392252;ENST00000368135	T;T;T;T;T;T	0.37915	1.17;3.3;3.32;3.32;3.33;1.29	2.27	1.12	0.20585	.	.	.	.	.	T	0.37972	0.1023	M	0.74881	2.28	0.09310	N	1	D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;0.99	D;D;D;D;P	0.83275	0.994;0.982;0.996;0.991;0.844	T	0.09271	-1.0682	8	.	.	.	.	4.027	0.09692	0.8189:0.0:0.1811:0.0	.	129;138;129;138;138	Q6K0P9-4;Q6K0P9-3;Q6K0P9-2;Q6K0P9;Q6K0P9-5	.;.;.;IFIX_HUMAN;.	Q	138;138;129;138;129;138	ENSP00000407616:K138Q;ENSP00000357122:K138Q;ENSP00000357120:K129Q;ENSP00000376083:K138Q;ENSP00000376082:K129Q;ENSP00000357117:K138Q	.	K	+	1	0	PYHIN1	157175494	0.999000	0.42202	0.071000	0.20095	0.008000	0.06430	0.994000	0.29693	0.305000	0.22832	0.455000	0.32223	AAA	.	.		0.363	PYHIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090110.1	NM_152501	Missense_Mutation	C	158908870	A	C	158908870	5	2	241	1	0	0	0	0	0	0	1	0	12880	260	9	5	422	5	PYHIN1	1	158908870	Splice_Site	SNP	A	TCGA-ED-A66X-01A-11D-A30V-10	5293152	158908870	90341751	3	33295										
KIAA1614	57710	hgsc.bcm.edu	37	chr1	180907742	180907742	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	tgttgccaccatcaactccaCgggcatcaccctctccctgt	6	18	3	0	rs372082964	byFrequency	TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr1:180907742C>T	ENST00000367588.4	+	6	2868	c.2813C>T	c.(2812-2814)aCg>aTg	p.T938M	KIAA1614_ENST00000367587.1_Missense_Mutation_p.T559M	NM_020950.1	NP_066001.1	Q5VZ46	K1614_HUMAN	KIAA1614	938										NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	33						ATCAACTCCACGGGCATCACC	0.582													C|||	5	0.000998403	0	0	5008	,	,		22787	0.005		0	False		,,,				2504	0				p.T938M		Atlas-SNP	.											.	KIAA1614	75	.	0			c.C2813T						.	C	MET/THR	2,4336		0,2,2167	75	80	78		2813	-0.3	0	1		78	0,8564		0,0,4282	no	missense	KIAA1614	NM_020950.1	81	0,2,6449	TT,TC,CC		0.0,0.0461,0.0155	benign	938/1191	180907742	2,12900	2169	4282	6451	SO:0001583	missense	57710	exon6			ACTCCACGGGCAT	AB046834	CCDS41442.1	1q25.3	2008-02-05			ENSG00000135835	ENSG00000135835			29327	protein-coding gene	gene with protein product							Standard	NM_020950		Approved		uc001gok.2	Q5VZ46	OTTHUMG00000035183	ENST00000367588.4:c.2813C>T	chr1.hg19:g.180907742C>T	ENSP00000356560:p.Thr938Met	97.0	0.0		161.0	29.0	NM_020950	Q5VZ45|Q9HCF8	Missense_Mutation	SNP	ENST00000367588.4	hg19	CCDS41442.1	.	.	.	.	.	.	.	.	.	.	C	2.837	-0.241378	0.05906	4.61E-4	0.0	ENSG00000135835	ENST00000367588;ENST00000367587	T;T	0.24151	2.44;1.87	3.97	-0.342	0.12635	.	0.765722	0.11519	N	0.555895	T	0.11707	0.0285	N	0.19112	0.55	0.33091	D	0.537893	B;B	0.28584	0.216;0.065	B;B	0.15870	0.009;0.014	T	0.19289	-1.0310	9	0.44086	T	0.13	-0.0074	2.461	0.04541	0.4086:0.325:0.0:0.2663	.	559;938	Q5VZ46-2;Q5VZ46	.;K1614_HUMAN	M	938;559	ENSP00000356560:T938M;ENSP00000356559:T559M	ENSP00000356559:T559M	T	+	2	0	KIAA1614	179174365	0.000000	0.05858	0.003000	0.11579	0.410000	0.31052	-0.690000	0.05138	-0.160000	0.11002	-0.226000	0.12346	ACG	.	.		0.582	KIAA1614-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085151.1	XM_046531		T	180907742	C	T	180907742	3	4	241	1	0	0	0	0	1	0	0	0	8257	536	19	1	2835	1	KIAA1614	1	180907742	Missense_Mutation	SNP	C	TCGA-ED-A66X-01A-11D-A30V-10	21998872	180907742	68342879	4	33296										
TRIM67	440730	hgsc.bcm.edu	37	chr1	231349708	231349708	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	ttcatgccagccctcagcctCaaccgcaacgtgcaggtaca	8	16	3	0			TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr1:231349708C>G	ENST00000366653.5	+	9	2271	c.2271C>G	c.(2269-2271)ctC>ctG	p.L757L	TRIM67_ENST00000366652.2_Intron|TRIM67_ENST00000449018.3_Silent_p.L695L|TRIM67_ENST00000444294.3_Silent_p.L755L			Q6ZTA4	TRI67_HUMAN	tripartite motif containing 67	757	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Breast(184;0.0871)	all_cancers(173;0.189)|Prostate(94;0.167)				CCCTCAGCCTCAACCGCAACG	0.622																																					p.L757L		Atlas-SNP	.											.	TRIM67	160	.	0			c.C2271G						.						48	54	52					1																	231349708		2123	4222	6345	SO:0001819	synonymous_variant	440730	exon9			CAGCCTCAACCGC	AK126782	CCDS44333.1, CCDS73048.1	1q42.2	2014-02-17	2011-01-25		ENSG00000119283	ENSG00000119283		"Tripartite motif containing / Tripartite motif containing", "Fibronectin type III domain containing", "RING-type (C3HC4) zinc fingers"	31859	protein-coding gene	gene with protein product		610584	"tripartite motif-containing 67"				Standard	NM_001004342		Approved	TNL	uc009xfn.1	Q6ZTA4	OTTHUMG00000037958	ENST00000366653.5:c.2271C>G	chr1.hg19:g.231349708C>G		133.0	0.0		171.0	23.0	NM_001004342	Q5TER7|Q5TER8|Q7Z4K7	Silent	SNP	ENST00000366653.5	hg19	CCDS44333.1																																																																																			.	.		0.622	TRIM67-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092649.3	NM_001004342		G	231349708	C	G	231349708	2	3	241	1	0	0	0	0	0	0	0	1	16555	813	29	4		4	TRIM67	1	231349708	Silent	SNP	C	TCGA-ED-A66X-01A-11D-A30V-10	50441966	231349708	17900913	5	33297										
KIF26B	55083	hgsc.bcm.edu	37	chr1	245530501	245530501	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	cttggggtcagcaatggggcGgaaaagaagagcgggtcccc	17	9	1	2	rs537827807		TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr1:245530501G>A	ENST00000407071.2	+	3	1271	c.831G>A	c.(829-831)gcG>gcA	p.A277A	KIF26B_ENST00000479506.1_3'UTR	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	277					establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			GCAATGGGGCGGAAAAGAAGA	0.617													G|||	1	0.000199681	0	0.0014	5008	,	,		18670	0		0	False		,,,				2504	0				p.A277A		Atlas-SNP	.											.	KIF26B	343	.	0			c.G831A						.						30	41	38					1																	245530501		2008	4168	6176	SO:0001819	synonymous_variant	55083	exon3			TGGGGCGGAAAAG	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"Kinesins"	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.831G>A	chr1.hg19:g.245530501G>A		152.0	0.0		260.0	23.0	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Silent	SNP	ENST00000407071.2	hg19	CCDS44342.1																																																																																			.	.		0.617	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354		A	245530501	G	A	245530501	2	1	241	1	0	0	0	0	0	0	0	1	8304	1103	39	1		1	KIF26B	1	245530501	Silent	SNP	G	TCGA-ED-A66X-01A-11D-A30V-10	14180793	245530501	3720120	6	33298										
OR2T6	254879	hgsc.bcm.edu	37	chr1	248551768	248551768	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	tcctcacacccttattaaacCctctcatctacagtctgagg	4	15	4	1			TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr1:248551768C>T	ENST00000355728.2	+	1	859	c.859C>T	c.(859-861)Cct>Tct	p.P287S		NM_001005471.1	NP_001005471.1	Q8NHC8	OR2T6_HUMAN	olfactory receptor, family 2, subfamily T, member 6	287						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(5)|lung(38)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CTTATTAAACCCTCTCATCTA	0.463																																					p.P287S		Atlas-SNP	.											.	OR2T6	101	.	0			c.C859T						.						89	87	88					1																	248551768		2203	4300	6503	SO:0001583	missense	254879	exon1			TTAAACCCTCTCA	AF399481	CCDS31114.1	1q44	2012-08-09		2004-03-10	ENSG00000198104	ENSG00000198104		"GPCR / Class A : Olfactory receptors"	15018	protein-coding gene	gene with protein product				OR2T6P, OR2T9			Standard	NM_001005471		Approved	OST703	uc001iei.1	Q8NHC8	OTTHUMG00000040448	ENST00000355728.2:c.859C>T	chr1.hg19:g.248551768C>T	ENSP00000347965:p.Pro287Ser	101.0	0.0		152.0	34.0	NM_001005471	A6NE36	Missense_Mutation	SNP	ENST00000355728.2	hg19	CCDS31114.1	.	.	.	.	.	.	.	.	.	.	C	17.81	3.480690	0.63849	.	.	ENSG00000198104	ENST00000355728	T	0.63417	-0.04	4.2	4.2	0.49525	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44902	D	0.000408	D	0.87075	0.6087	H	0.98754	4.32	0.36589	D	0.873971	D	0.76494	0.999	D	0.68621	0.959	D	0.94373	0.7597	10	0.87932	D	0	.	16.6996	0.85345	0.0:1.0:0.0:0.0	.	287	Q8NHC8	OR2T6_HUMAN	S	287	ENSP00000347965:P287S	ENSP00000347965:P287S	P	+	1	0	OR2T6	246618391	1.000000	0.71417	0.999000	0.59377	0.969000	0.65631	3.748000	0.55142	2.330000	0.79161	0.643000	0.83706	CCT	.	.		0.463	OR2T6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097344.1	NM_001005471		T	248551768	C	T	248551768	3	4	241	1	0	0	0	0	1	0	0	0	11038	623	22	3	861	3	OR2T6	1	248551768	Missense_Mutation	SNP	C	TCGA-ED-A66X-01A-11D-A30V-10	3021267	248551768	698853	7	33299										
ACADL	33	hgsc.bcm.edu	37	chr2	211069378	211069379	+	Frame_Shift_Ins	INS	-	-	T													0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	ggcactagctggcaaccgtaINStatcttcaaagaatagttct							TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr2:211069378_211069379insT	ENST00000233710.3	-	7	1023_1024	c.796_797insA	c.(796-798)atafs	p.I266fs	AC006994.2_ENST00000412065.1_RNA	NM_001608.3	NP_001599.1	P28330	ACADL_HUMAN	acyl-CoA dehydrogenase, long chain	266					carnitine catabolic process (GO:0042413)|carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid catabolic process (GO:0044242)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|long-chain fatty acid catabolic process (GO:0042758)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of fatty acid oxidation (GO:0046322)|oxidation-reduction process (GO:0055114)|protein homotetramerization (GO:0051289)|regulation of cholesterol metabolic process (GO:0090181)|small molecule metabolic process (GO:0044281)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)|palmitoyl-CoA oxidase activity (GO:0016401)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	14		Renal(323;0.202)		Epithelial(149;0.00631)|Lung(261;0.0438)|LUSC - Lung squamous cell carcinoma(261;0.0466)|all cancers(144;0.0621)		TGGCAACCGTATATCTTCAAAG	0.376																																					p.I266fs		Atlas-Indel,Pindel	.											.	ACADL	38	.	0			c.797_798insA						.																																			SO:0001589	frameshift_variant	33	exon7			.	M74096	CCDS2389.1	2q34	2012-07-13	2010-04-30		ENSG00000115361	ENSG00000115361	1.3.99.13		88	protein-coding gene	gene with protein product		609576	"acyl-Coenzyme A dehydrogenase, long chain"			1774065	Standard	NM_001608		Approved	LCAD, ACAD4	uc002vdz.4	P28330	OTTHUMG00000132989	ENST00000233710.3:c.797dupA	chr2.hg19:g.211069379_211069379dupT	ENSP00000233710:p.Ile266fs	63.0	0.0		68.0	12.0	NM_001608	B2R8T3|Q8IUN8	Frame_Shift_Ins	INS	ENST00000233710.3	hg19	CCDS2389.1																																																																																			.	.		0.376	ACADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256561.2	NM_001608		T	211069379	-	T	211069378	7	5	241	1	0	1	1	0	0	0	0	0	112	449	16	0	515	0	ACADL	2	211069378	Frame_Shift_Ins	INS	-	TCGA-ED-A66X-01A-11D-A30V-10		211069378	32129995	8	33300										
SLC15A2	6565	hgsc.bcm.edu	37	chr3	121630500	121630500	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	ccttaccaatactgggaggaCaagtggtacacacgtgagta	11	9	0	1			TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr3:121630500C>A	ENST00000489711.1	+	4	803	c.415C>A	c.(415-417)Caa>Aaa	p.Q139K	SLC15A2_ENST00000295605.2_Intron	NM_021082.3	NP_066568.3	Q16348	S15A2_HUMAN	solute carrier family 15 (oligopeptide transporter), member 2	139					drug transport (GO:0015893)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antibiotic transporter activity (GO:0042895)|dipeptide transporter activity (GO:0042936)|high-affinity oligopeptide transporter activity (GO:0015334)|peptide:proton symporter activity (GO:0015333)			NS(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(17)|skin(6)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(114;0.0967)	Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Fosinopril(DB00492)|Glyburide(DB01016)|Moexipril(DB00691)|Nateglinide(DB00731)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Tranexamic Acid(DB00302)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	ACTGGGAGGACAAGTGGTACA	0.398																																					p.Q139K		Atlas-SNP	.											.	SLC15A2	92	.	0			c.C415A						.						184	147	160					3																	121630500		2203	4300	6503	SO:0001583	missense	6565	exon4			GGAGGACAAGTGG	BC044572	CCDS3007.1, CCDS54631.1	3q21.1	2013-07-18	2013-07-18		ENSG00000163406	ENSG00000163406		"Solute carriers"	10921	protein-coding gene	gene with protein product		602339	"solute carrier family 15 (H+/peptide transporter), member 2"			7756356	Standard	NM_021082		Approved	PEPT2	uc003eep.2	Q16348	OTTHUMG00000159423	ENST00000489711.1:c.415C>A	chr3.hg19:g.121630500C>A	ENSP00000417085:p.Gln139Lys	72.0	0.0		86.0	18.0	NM_021082	A8K1A5|B4E2A7	Missense_Mutation	SNP	ENST00000489711.1	hg19	CCDS3007.1	.	.	.	.	.	.	.	.	.	.	C	0	-2.593473	0.00126	.	.	ENSG00000163406	ENST00000489711;ENST00000469013	T;T	0.58060	0.36;0.36	5.31	3.38	0.38709	Major facilitator superfamily domain, general substrate transporter (1);	1.306830	0.04625	N	0.402676	T	0.37489	0.1005	N	0.20574	0.59	0.09310	N	0.999999	B	0.02656	0.0	B	0.06405	0.002	T	0.14671	-1.0464	10	0.05620	T	0.96	2.9286	11.4056	0.49896	0.6409:0.359:0.0:0.0	.	139	Q16348	S15A2_HUMAN	K	139;77	ENSP00000417085:Q139K;ENSP00000418704:Q77K	ENSP00000418704:Q77K	Q	+	1	0	SLC15A2	123113190	0.997000	0.39634	0.147000	0.22382	0.056000	0.15407	2.674000	0.46867	0.686000	0.31488	-0.169000	0.13324	CAA	.	.		0.398	SLC15A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355239.1	NM_021082		A	121630500	C	A	121630500	3	1	241	1	0	0	0	0	1	0	0	0	14414	479	17	3	429	3	SLC15A2	3	121630500	Missense_Mutation	SNP	C	TCGA-ED-A66X-01A-11D-A30V-10		121630500	76391930	9	33301										
COL6A5	256076	hgsc.bcm.edu	37	chr3	130107781	130107781	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	ctcatcacagatggagtagcGcaggatgatgtgagagatcc	13	8	2	4			TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr3:130107781G>A	ENST00000432398.2	+	6	2714	c.2220G>A	c.(2218-2220)gcG>gcA	p.A740A	COL6A5_ENST00000265379.6_Silent_p.A740A	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	740	Nonhelical region.|VWFA 4. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						ATGGAGTAGCGCAGGATGATG	0.463																																					p.A740A		Atlas-SNP	.											.	COL6A5	205	.	0			c.G2220A						.						61	52	55					3																	130107781		692	1591	2283	SO:0001819	synonymous_variant	256076	exon6			AGTAGCGCAGGAT	AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"Collagens"	26674	protein-coding gene	gene with protein product	"von Willebrand factor A domain containing 4"	611916	"collagen, type XXIX, alpha 1"	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.2220G>A	chr3.hg19:g.130107781G>A		110.0	0.0		120.0	44.0	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Silent	SNP	ENST00000432398.2	hg19																																																																																				.	.		0.463	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264		A	130107781	G	A	130107781	2	1	241	1	0	0	0	0	0	0	0	1	3704	1074	38	1		1	COL6A5	3	130107781	Silent	SNP	G	TCGA-ED-A66X-01A-11D-A30V-10	8477281	130107781	67914649	10	33302										
EPHB1	2047	hgsc.bcm.edu	37	chr3	134670256	134670256	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	tgaaaacctgaacaccatccGcacctaccaggtgtgcaatg	8	13	0	2			TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr3:134670256G>A	ENST00000398015.3	+	3	537	c.167G>A	c.(166-168)cGc>cAc	p.R56H	EPHB1_ENST00000488154.1_3'UTR	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	56	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|camera-type eye morphogenesis (GO:0048593)|cell chemotaxis (GO:0060326)|cell-substrate adhesion (GO:0031589)|central nervous system projection neuron axonogenesis (GO:0021952)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|neural precursor cell proliferation (GO:0061351)|neurogenesis (GO:0022008)|optic nerve morphogenesis (GO:0021631)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of JNK cascade (GO:0046328)|retinal ganglion cell axon guidance (GO:0031290)	axon (GO:0030424)|early endosome membrane (GO:0031901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|transmembrane-ephrin receptor activity (GO:0005005)	p.R56L(2)|p.R56P(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(63)|ovary(8)|pancreas(2)|prostate(8)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	130						AACACCATCCGCACCTACCAG	0.517																																					p.R56H		Atlas-SNP	.											EPHB1_ENST00000398015,rectum,carcinoma,0,5	EPHB1	519	.	3	Substitution - Missense(3)	lung(3)	c.G167A						.						38	43	41					3																	134670256		2155	4278	6433	SO:0001583	missense	2047	exon3			CCATCCGCACCTA	L40636	CCDS46921.1	3q21-q23	2013-02-11	2004-10-28			ENSG00000154928		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3392	protein-coding gene	gene with protein product		600600	"EphB1"	EPHT2		8666391	Standard	NM_004441		Approved	Hek6	uc003eqt.3	P54762		ENST00000398015.3:c.167G>A	chr3.hg19:g.134670256G>A	ENSP00000381097:p.Arg56His	64.0	0.0		74.0	10.0	NM_004441	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Missense_Mutation	SNP	ENST00000398015.3	hg19	CCDS46921.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.469822	0.84533	.	.	ENSG00000154928	ENST00000460895;ENST00000398015;ENST00000497173;ENST00000473867;ENST00000474732	T;T;T;T;T	0.04360	3.64;3.64;3.64;3.64;3.64	5.64	5.64	0.86602	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	T	0.19366	0.0465	L	0.57130	1.785	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.00563	-1.1669	10	0.29301	T	0.29	.	19.7209	0.96143	0.0:0.0:1.0:0.0	.	56;56	B5A969;P54762	.;EPHB1_HUMAN	H	34;56;34;34;34	ENSP00000417435:R34H;ENSP00000381097:R56H;ENSP00000419688:R34H;ENSP00000417216:R34H;ENSP00000418352:R34H	ENSP00000381097:R56H	R	+	2	0	EPHB1	136152946	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.651000	0.90000	0.650000	0.86243	CGC	.	.		0.517	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357671.1	NM_004441		A	134670256	G	A	134670256	3	1	241	1	0	0	0	0	1	0	0	0	5176	1087	38	1	177	1	EPHB1	3	134670256	Missense_Mutation	SNP	G	TCGA-ED-A66X-01A-11D-A30V-10	4562475	134670256	63352174	11	33303										
MUC4	4585	hgsc.bcm.edu	37	chr3	195487851	195487851	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	cagggtgtcatagatgcatgAgctatctccgtcacagttgg	12	9	3	2			TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr3:195487851A>T	ENST00000346145.4	-	15	2083	c.2044T>A	c.(2044-2046)Tca>Aca	p.S682T	MUC4_ENST00000475231.1_Missense_Mutation_p.S4866T|MUC4_ENST00000463781.3_Missense_Mutation_p.S4918T|MUC4_ENST00000349607.4_Missense_Mutation_p.S631T	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	1675					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TAGATGCATGAGCTATCTCCG	0.512																																					p.S4918T		Atlas-SNP	.											.	MUC4	1505	.	0			c.T14752A						.						145	125	132					3																	195487851		2203	4300	6503	SO:0001583	missense	4585	exon16			TGCATGAGCTATC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"Mucins"	7514	protein-coding gene	gene with protein product		158372	"mucin 4, tracheobronchial"			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000346145.4:c.2044T>A	chr3.hg19:g.195487851A>T	ENSP00000304207:p.Ser682Thr	82.0	0.0		131.0	15.0	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000346145.4	hg19	CCDS3310.1	.	.	.	.	.	.	.	.	.	.	.	8.711	0.912074	0.17907	.	.	ENSG00000145113	ENST00000349607;ENST00000346145;ENST00000463781;ENST00000475231;ENST00000392409	T;T;T;T	0.38077	1.16;1.52;1.5;1.5	4.98	0.731	0.18277	.	0.983616	0.08275	N	0.970793	T	0.23492	0.0568	N	0.22421	0.69	0.09310	N	1	P;B;B;B;B;P	0.36660	0.549;0.306;0.306;0.167;0.167;0.564	B;B;B;B;B;B	0.39562	0.163;0.142;0.142;0.045;0.045;0.303	T	0.22906	-1.0203	10	0.27785	T	0.31	-0.0725	4.0156	0.09642	0.0941:0.4189:0.3461:0.141	.	4790;631;682;4918;4866;1623	E7ESK3;Q99102-12;Q99102-13;E9PDY6;E7ENC5;Q99102-10	.;.;.;.;.;.	T	631;682;4918;4866;1418	ENSP00000338109:S631T;ENSP00000304207:S682T;ENSP00000417498:S4918T;ENSP00000420243:S4866T	ENSP00000304207:S682T	S	-	1	0	MUC4	196973522	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.143000	0.16115	0.122000	0.18314	-0.373000	0.07131	TCA	.	.		0.512	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406		T	195487851	A	T	195487851	3	4	241	1	0	0	0	0	1	0	0	0	9987	304	11	4	1526	4	MUC4	3	195487851	Missense_Mutation	SNP	A	TCGA-ED-A66X-01A-11D-A30V-10	60817595	195487851	2534579	12	33304										
GABRA4	2557	hgsc.bcm.edu	37	chr4	46976276	46976276	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	tgatttgatggtttcacttgAtacggtttgcccaatcaaat	8	7	2	3			TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr4:46976276A>G	ENST00000264318.3	-	6	1676	c.694T>C	c.(694-696)Tca>Cca	p.S232P		NM_000809.3|NM_001204266.1|NM_001204267.1	NP_000800.2|NP_001191195.1|NP_001191196.1	P48169	GBRA4_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 4	232					central nervous system development (GO:0007417)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|regulation of response to drug (GO:2001023)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45					Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	GTTTCACTTGATACGGTTTGC	0.383																																					p.S232P	Ovarian(6;283 369 8234 12290 33402)	Atlas-SNP	.											.	GABRA4	129	.	0			c.T694C						.						122	113	116					4																	46976276		2203	4300	6503	SO:0001583	missense	2557	exon6			CACTTGATACGGT		CCDS3473.1	4p12	2012-06-22			ENSG00000109158	ENSG00000109158		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4078	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 4"	137141				7607683	Standard	NM_000809		Approved		uc021xnz.1	P48169	OTTHUMG00000099431	ENST00000264318.3:c.694T>C	chr4.hg19:g.46976276A>G	ENSP00000264318:p.Ser232Pro	80.0	0.0		84.0	12.0	NM_000809	Q8IYR7	Missense_Mutation	SNP	ENST00000264318.3	hg19	CCDS3473.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.456681	0.84317	.	.	ENSG00000109158	ENST00000264318	T	0.79554	-1.28	5.1	5.1	0.69264	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	D	0.88665	0.6498	M	0.75615	2.305	0.58432	D	0.999998	D	0.89917	1.0	D	0.87578	0.998	D	0.88899	0.3351	10	0.48119	T	0.1	.	14.2289	0.65877	1.0:0.0:0.0:0.0	.	232	P48169	GBRA4_HUMAN	P	232	ENSP00000264318:S232P	ENSP00000264318:S232P	S	-	1	0	GABRA4	46671033	1.000000	0.71417	0.760000	0.31359	0.737000	0.42083	7.179000	0.77665	2.147000	0.66899	0.528000	0.53228	TCA	.	.		0.383	GABRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216893.1			G	46976276	A	G	46976276	3	3	241	1	0	0	0	0	1	0	0	0	6171	333	12	2	986	2	GABRA4	4	46976276	Missense_Mutation	SNP	A	TCGA-ED-A66X-01A-11D-A30V-10		46976276	144178000	13	33305										
ANKH	56172	hgsc.bcm.edu	37	chr5	14749332	14749332	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	cgggaaacaaagaggttgacAataggccgactgattctctg	12	8	1	3			TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr5:14749332A>C	ENST00000284268.6	-	6	1101	c.771T>G	c.(769-771)atT>atG	p.I257M	ANKH_ENST00000535119.1_Missense_Mutation_p.I59M|ANKH_ENST00000503939.1_5'UTR	NM_054027.4	NP_473368.1	Q9HCJ1	ANKH_HUMAN	ANKH inorganic pyrophosphate transport regulator	257					locomotory behavior (GO:0007626)|regulation of bone mineralization (GO:0030500)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|outer membrane (GO:0019867)|plasma membrane (GO:0005886)	inorganic diphosphate transmembrane transporter activity (GO:0030504)|inorganic phosphate transmembrane transporter activity (GO:0005315)|phosphate ion transmembrane transporter activity (GO:0015114)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(13)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	29						AGAGGTTGACAATAGGCCGAC	0.517																																					p.I257M		Atlas-SNP	.											.	ANKH	64	.	0			c.T771G						.						108	109	109					5																	14749332		2203	4300	6503	SO:0001583	missense	56172	exon6			GTTGACAATAGGC	AF274753	CCDS3885.1	5p15.2	2013-06-19	2013-06-19		ENSG00000154122	ENSG00000154122			15492	protein-coding gene	gene with protein product		605145	"ankylosis, progressive (mouse) homolog", "craniometaphyseal dysplasia, Jackson type (dominant)", "ankylosis, progressive homolog (mouse)"	CCAL2, CMDJ		10894769, 12297989, 11326338	Standard	NM_054027		Approved	HANK, ANK, CPPDD	uc003jfm.4	Q9HCJ1	OTTHUMG00000090539	ENST00000284268.6:c.771T>G	chr5.hg19:g.14749332A>C	ENSP00000284268:p.Ile257Met	59.0	0.0		63.0	10.0	NM_054027	B2RCA7|B3KMG4|D3DTD4|Q9NQW2	Missense_Mutation	SNP	ENST00000284268.6	hg19	CCDS3885.1	.	.	.	.	.	.	.	.	.	.	A	18.67	3.673655	0.67928	.	.	ENSG00000154122	ENST00000535119;ENST00000284268	D;D	0.95853	-3.83;-3.83	5.91	-7.87	0.01183	.	0.000000	0.85682	D	0.000000	D	0.95341	0.8488	L	0.54323	1.7	0.49389	D	0.999783	D	0.69078	0.997	D	0.83275	0.996	D	0.94319	0.7552	10	0.72032	D	0.01	-50.9292	12.974	0.58527	0.653:0.0:0.266:0.0809	.	257	Q9HCJ1	ANKH_HUMAN	M	59;257	ENSP00000442524:I59M;ENSP00000284268:I257M	ENSP00000284268:I257M	I	-	3	3	ANKH	14802332	0.009000	0.17119	0.249000	0.24280	0.847000	0.48162	-0.981000	0.03766	-1.417000	0.02017	-0.899000	0.02877	ATT	.	.		0.517	ANKH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207063.1	NM_054027		C	14749332	A	C	14749332	3	2	241	1	0	0	0	0	1	0	0	0	627	126	5	5	735	5	ANKH	5	14749332	Missense_Mutation	SNP	A	TCGA-ED-A66X-01A-11D-A30V-10		14749332	166165928	14	33306										
NFKBIL1	534	hgsc.bcm.edu	37	chr6	31515977	31515977	+	5'Flank	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	ctccacttcccgccgccaacGccgagaacgtcgctttcgtc	8	19	0	1			TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr6:31515977G>A	ENST00000303892.5	-	0	0				ATP6V1G2-DDX39B_ENST00000475917.1_5'Flank|NFKBIL1_ENST00000376145.4_Missense_Mutation_p.R32H|ATP6V1G2_ENST00000376151.4_5'Flank|ATP6V1G2-DDX39B_ENST00000376185.1_5'Flank|ATP6V1G2_ENST00000483251.1_5'Flank|ATP6V1G2_ENST00000483170.1_5'Flank|NFKBIL1_ENST00000376148.4_Missense_Mutation_p.R32H	NM_130463.3|NM_138282.2	NP_569730.1|NP_612139.1	O95670	VATG2_HUMAN	ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G2						cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances (GO:0016820)			breast(1)|large_intestine(2)|lung(1)|prostate(1)	5						CGCCGCCAACGCCGAGAACGT	0.622																																					p.R32H		Atlas-SNP	.											.	NFKBIL1	17	.	0			c.G95A						.						78	57	64					6																	31515977		1510	2709	4219	SO:0001631	upstream_gene_variant	4795	exon2			GCCAACGCCGAGA	Y14768	CCDS4698.1, CCDS4699.1, CCDS56413.1	6p21.3	2011-03-29	2006-01-13	2002-05-10	ENSG00000213760	ENSG00000213760		"ATPases / V-type"	862	protein-coding gene	gene with protein product		606853	"ATPase, H+ transporting, lysosomal (vacuolar proton pump)", "ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G isoform 2"	ATP6G, ATP6G2		10202016	Standard	NM_138282		Approved	Vma10, NG38, Em:AC004181.3	uc003nua.3	O95670	OTTHUMG00000166618		chr6.hg19:g.31515977G>A	Exception_encountered	58.0	0.0		61.0	7.0	NM_005007	B5MEF0|Q2L6F8|Q5HYU8|Q5RJ63	Missense_Mutation	SNP	ENST00000303892.5	hg19	CCDS4698.1	.	.	.	.	.	.	.	.	.	.	g	21.5	4.155963	0.78114	.	.	ENSG00000204498	ENST00000376146;ENST00000542852;ENST00000376148;ENST00000376145	T;T;T	0.35973	1.6;1.28;1.66	5.03	4.15	0.48705	.	0.236672	0.41500	D	0.000877	T	0.22781	0.0550	N	0.08118	0	0.80722	D	1	D;B;D	0.71674	0.998;0.244;0.998	D;B;D	0.69479	0.964;0.022;0.964	T	0.06373	-1.0830	10	0.34782	T	0.22	-9.3574	9.7473	0.40455	0.0993:0.0:0.9007:0.0	.	9;32;32	Q5STV6;Q5STV4;Q9UBC1	.;.;IKBL1_HUMAN	H	9;9;32;32	ENSP00000365316:R9H;ENSP00000365318:R32H;ENSP00000365315:R32H	ENSP00000365315:R32H	R	+	2	0	NFKBIL1	31623956	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.543000	0.45752	2.340000	0.79590	0.651000	0.88453	CGC	.	.		0.622	ATP6V1G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076399.3	NM_130463		A	31515977	G	A	31515977	1	1	241	0	1	0	0	0	0	0	0	0	10390	1087	38	1		1	NFKBIL1	6	31515977	5'Flank	SNP	G	TCGA-ED-A66X-01A-11D-A30V-10		31515977	139599090	15	33307										
TMEM200A	114801	hgsc.bcm.edu	37	chr6	130761733	130761733	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	tggttgttcgtggcaaaatcCggctttattccccatctggt	10	10	1	0			TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr6:130761733C>T	ENST00000296978.3	+	3	1037	c.166C>T	c.(166-168)Cgg>Tgg	p.R56W	TMEM200A_ENST00000545622.1_Missense_Mutation_p.R56W|TMEM200A_ENST00000392429.1_Missense_Mutation_p.R56W	NM_001258276.1|NM_001258277.1|NM_001258278.1	NP_001245205.1|NP_001245206.1|NP_001245207.1	Q86VY9	T200A_HUMAN	transmembrane protein 200A	56						integral component of membrane (GO:0016021)				NS(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(30)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52				GBM - Glioblastoma multiforme(226;0.0139)|OV - Ovarian serous cystadenocarcinoma(155;0.12)		TGGCAAAATCCGGCTTTATTC	0.498																																					p.R56W		Atlas-SNP	.											.	TMEM200A	108	.	0			c.C166T						.						134	133	133					6																	130761733		2203	4300	6503	SO:0001583	missense	114801	exon3			AAAATCCGGCTTT	AB067500	CCDS5140.1	6q23.1	2009-09-04	2007-12-18	2007-12-18	ENSG00000164484	ENSG00000164484			21075	protein-coding gene	gene with protein product			"KIAA1913"	KIAA1913		15722956	Standard	NM_001258276		Approved	TTMC	uc010kfh.4	Q86VY9	OTTHUMG00000015557	ENST00000296978.3:c.166C>T	chr6.hg19:g.130761733C>T	ENSP00000296978:p.Arg56Trp	108.0	0.0		142.0	12.0	NM_001258277	Q96PX5	Missense_Mutation	SNP	ENST00000296978.3	hg19	CCDS5140.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.169103	0.78339	.	.	ENSG00000164484	ENST00000296978;ENST00000545622;ENST00000392429	.	.	.	5.45	4.57	0.56435	.	0.000000	0.85682	D	0.000000	T	0.69663	0.3136	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75233	-0.3390	9	0.87932	D	0	.	15.4391	0.75168	0.1402:0.8598:0.0:0.0	.	56	Q86VY9	T200A_HUMAN	W	56	.	ENSP00000296978:R56W	R	+	1	2	TMEM200A	130803426	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.923000	0.56469	1.250000	0.43966	0.650000	0.86243	CGG	.	.		0.498	TMEM200A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042201.1	NM_052913		T	130761733	C	T	130761733	3	4	241	1	0	0	0	0	1	0	0	0	16138	643	23	1	168	1	TMEM200A	6	130761733	Missense_Mutation	SNP	C	TCGA-ED-A66X-01A-11D-A30V-10	99245756	130761733	40353334	16	33308										
ARID1B	57492	hgsc.bcm.edu	37	chr6	157099362	157099362	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	ccaccaccatgcccaccaccTccaccaccaccacgcactac	2	25	0	0			TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr6:157099362T>A	ENST00000350026.5	+	1	300	c.299T>A	c.(298-300)cTc>cAc	p.L100H	ARID1B_ENST00000275248.4_Missense_Mutation_p.L42H|RP11-230C9.3_ENST00000604792.1_RNA|ARID1B_ENST00000367148.1_Missense_Mutation_p.L100H|MIR4466_ENST00000606121.1_RNA|RP11-230C9.2_ENST00000603191.1_lincRNA|ARID1B_ENST00000346085.5_Missense_Mutation_p.L100H	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	100	His-rich.				chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		gcccaccacctccaccaccac	0.637																																					p.L100H		Atlas-SNP	.											.	ARID1B	320	.	0			c.T299A						.						10	17	15					6																	157099362		1859	3596	5455	SO:0001583	missense	57492	exon1			ACCACCTCCACCA	AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"-"	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.299T>A	chr6.hg19:g.157099362T>A	ENSP00000055163:p.Leu100His	28.0	0.0		36.0	8.0	NM_017519	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Missense_Mutation	SNP	ENST00000350026.5	hg19	CCDS5251.2	.	.	.	.	.	.	.	.	.	.	t	7.657	0.684140	0.14907	.	.	ENSG00000049618	ENST00000346085;ENST00000350026;ENST00000367148;ENST00000275248	T;T;T;T	0.75821	1.18;1.18;1.18;-0.97	2.48	0.998	0.19857	.	.	.	.	.	T	0.26557	0.0649	N	0.17082	0.46	0.23421	N	0.997716	P;P;P	0.43352	0.704;0.804;0.688	B;B;B	0.29440	0.047;0.102;0.102	T	0.28996	-1.0026	9	0.87932	D	0	.	0.197	0.00141	0.2086:0.2495:0.2129:0.329	.	100;100;42	Q8NFD5;Q8NFD5-2;G3XAA0	ARI1B_HUMAN;.;.	H	100;100;100;42	ENSP00000344546:L100H;ENSP00000055163:L100H;ENSP00000356116:L100H;ENSP00000275248:L42H	ENSP00000275248:L42H	L	+	2	0	ARID1B	157141054	0.981000	0.34729	0.995000	0.50966	0.981000	0.71138	0.013000	0.13310	0.890000	0.36211	0.312000	0.20444	CTC	.	.		0.637	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732		A	157099362	T	A	157099362	3	1	241	1	0	0	0	0	1	0	0	0	914	1551	54	4	301	4	ARID1B	6	157099362	Missense_Mutation	SNP	T	TCGA-ED-A66X-01A-11D-A30V-10	26337629	157099362	14015705	17	33309										
RPS6KA2	6196	hgsc.bcm.edu	37	chr6	166912106	166912106	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	gaaggagtacgctctcttgtCgtggtcaatggcctccttac	11	11	2	0			TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr6:166912106C>T	ENST00000265678.4	-	8	860	c.637G>A	c.(637-639)Gac>Aac	p.D213N	RPS6KA2_ENST00000405189.3_Missense_Mutation_p.D124N|RPS6KA2_ENST00000366863.2_Missense_Mutation_p.D59N|RPS6KA2_ENST00000481261.2_Missense_Mutation_p.D124N|RPS6KA2_ENST00000510118.1_Missense_Mutation_p.D238N|RPS6KA2_ENST00000503859.1_Missense_Mutation_p.D221N	NM_021135.4	NP_066958.2	Q15349	KS6A2_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 2	213	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|brain renin-angiotensin system (GO:0002035)|cardiac muscle cell apoptotic process (GO:0010659)|cellular response to carbohydrate stimulus (GO:0071322)|heart contraction (GO:0060047)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of meiosis (GO:0045835)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oocyte maturation (GO:0001556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of gene expression (GO:0010628)|regulation of protein processing (GO:0070613)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|ribosomal protein S6 kinase activity (GO:0004711)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	45		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)		GCTCTCTTGTCGTGGTCAATG	0.602																																					p.D221N		Atlas-SNP	.											.	RPS6KA2	212	.	0			c.G661A						.						208	144	165					6																	166912106		2203	4300	6503	SO:0001583	missense	6196	exon9			TCTTGTCGTGGTC	L07598	CCDS5294.1, CCDS34570.1	6q27	2011-04-05	2002-08-29		ENSG00000071242	ENSG00000071242			10431	protein-coding gene	gene with protein product		601685	"ribosomal protein S6 kinase, 90kD, polypeptide 2"			8141249	Standard	NM_001006932		Approved	RSK, RSK3, HU-2	uc003qvc.1	Q15349	OTTHUMG00000016007	ENST00000265678.4:c.637G>A	chr6.hg19:g.166912106C>T	ENSP00000265678:p.Asp213Asn	51.0	0.0		62.0	6.0	NM_001006932	B3KTK9|Q15419|Q59GJ3|Q5TI68|Q96J38|Q9UJN5	Missense_Mutation	SNP	ENST00000265678.4	hg19	CCDS5294.1	.	.	.	.	.	.	.	.	.	.	C	32	5.127325	0.94473	.	.	ENSG00000071242	ENST00000265678;ENST00000510118;ENST00000503859;ENST00000481261;ENST00000405189;ENST00000366863;ENST00000507350	T;T;T;T;T;T;T	0.71934	-0.13;-0.13;-0.13;-0.13;-0.13;-0.13;-0.61	4.99	4.99	0.66335	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.61578	0.2358	N	0.11818	0.18	0.80722	D	1	B;B;D	0.89917	0.175;0.012;1.0	B;B;D	0.85130	0.025;0.005;0.997	T	0.60662	-0.7219	10	0.13853	T	0.58	.	17.6519	0.88167	0.0:1.0:0.0:0.0	.	238;221;213	F2Z2J1;Q15349-3;Q15349	.;.;KS6A2_HUMAN	N	213;238;221;124;124;59;124	ENSP00000265678:D213N;ENSP00000422435:D238N;ENSP00000427015:D221N;ENSP00000422484:D124N;ENSP00000386050:D124N;ENSP00000355828:D59N;ENSP00000422197:D124N	ENSP00000265678:D213N	D	-	1	0	RPS6KA2	166832096	1.000000	0.71417	0.988000	0.46212	0.996000	0.88848	7.193000	0.77780	2.461000	0.83175	0.655000	0.94253	GAC	.	.		0.602	RPS6KA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043075.3	NM_021135		T	166912106	C	T	166912106	3	4	241	1	0	0	0	0	1	0	0	0	13666	884	31	1	1620	1	RPS6KA2	6	166912106	Missense_Mutation	SNP	C	TCGA-ED-A66X-01A-11D-A30V-10	9812744	166912106	4202961	18	33310										
BAZ1B	9031	hgsc.bcm.edu	37	chr7	72891607	72891607	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	gaggtctccagcttttctagGaactcatcttgtacctcatt	7	11	5	0			TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr7:72891607G>A	ENST00000339594.4	-	7	2522	c.2184C>T	c.(2182-2184)ttC>ttT	p.F728F	BAZ1B_ENST00000404251.1_Silent_p.F728F	NM_032408.3	NP_115784.1	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	728					cellular response to DNA damage stimulus (GO:0006974)|chromatin assembly or disassembly (GO:0006333)|chromatin-mediated maintenance of transcription (GO:0048096)|double-strand break repair (GO:0006302)|heart morphogenesis (GO:0003007)|histone phosphorylation (GO:0016572)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone kinase activity (GO:0035173)|lysine-acetylated histone binding (GO:0070577)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|vitamin D receptor activator activity (GO:0071884)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(5)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Lung NSC(55;0.0659)|all_lung(88;0.152)				GCTTTTCTAGGAACTCATCTT	0.468																																					p.F728F	Esophageal Squamous(112;1167 1561 21085 43672 48228)	Atlas-SNP	.											.	BAZ1B	147	.	0			c.C2184T						.						88	83	84					7																	72891607		2203	4300	6503	SO:0001819	synonymous_variant	9031	exon7			TTCTAGGAACTCA	AF084479	CCDS5549.1	7q11.23	2013-01-28			ENSG00000009954	ENSG00000009954		"Zinc fingers, PHD-type"	961	protein-coding gene	gene with protein product	"Williams-Beuren syndrome chromosome region 9", "Williams-Beuren syndrome chromosome region 10", "transcription factor WSTF"	605681		WBSCR9, WBSCR10		9858827, 9828126	Standard	NM_032408		Approved	WSTF	uc003tyc.3	Q9UIG0	OTTHUMG00000023847	ENST00000339594.4:c.2184C>T	chr7.hg19:g.72891607G>A		74.0	0.0		79.0	21.0	NM_032408	B9EGK3|D3DXE9|O95039|O95247|O95277|Q6P1K4|Q86UJ6	Silent	SNP	ENST00000339594.4	hg19	CCDS5549.1																																																																																			.	.		0.468	BAZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252123.4	NM_032408		A	72891607	G	A	72891607	2	1	241	1	0	0	0	0	0	0	0	1	1330	1165	41	3		3	BAZ1B	7	72891607	Silent	SNP	G	TCGA-ED-A66X-01A-11D-A30V-10		72891607	86247056	19	33311										
VPS13B	157680	hgsc.bcm.edu	37	chr8	100711796	100711796	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	aagcctttgaaagcaaacctGagtttcaccaaactggatca	7	10	2	2			TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr8:100711796G>T	ENST00000358544.2	+	36	6276	c.6165G>T	c.(6163-6165)ctG>ctT	p.L2055L	VPS13B_ENST00000357162.2_Silent_p.L2030L|VPS13B_ENST00000395996.1_3'UTR	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	2055					protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			AAGCAAACCTGAGTTTCACCA	0.348																																					p.L2055L	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											.	VPS13B	811	.	0			c.G6165T						.						51	55	54					8																	100711796		2202	4299	6501	SO:0001819	synonymous_variant	157680	exon36			AAACCTGAGTTTC	AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.6165G>T	chr8.hg19:g.100711796G>T		77.0	0.0		133.0	6.0	NM_017890	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Silent	SNP	ENST00000358544.2	hg19	CCDS6280.1																																																																																			.	.		0.348	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		T	100711796	G	T	100711796	2	4	241	1	0	0	0	0	0	0	0	1	17205	1277	45	3		3	VPS13B	8	100711796	Silent	SNP	G	TCGA-ED-A66X-01A-11D-A30V-10		100711796	45652226	20	33312										
EIF3E	3646	hgsc.bcm.edu	37	chr8	109240530	109240530	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	gaagaggtcaataatattatCgcgacctttggggtgattga	12	5	1	3			TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr8:109240530C>G	ENST00000220849.5	-	7	750	c.688G>C	c.(688-690)Gat>Cat	p.D230H	RP11-35G22.1_ENST00000520037.1_RNA|EIF3E_ENST00000519030.1_Missense_Mutation_p.D137H|EIF3E_ENST00000519517.1_5'UTR	NM_001568.2	NP_001559.1			eukaryotic translation initiation factor 3, subunit E										EIF3E/RSPO2(6)	NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(57;6.84e-10)			ATAATATTATCGCGACCTTTG	0.368																																					p.D230H	GBM(15;360 410 8460 34179 52246)	Atlas-SNP	.											EIF3E,NS,carcinoma,0,1	EIF3E	73	.	0			c.G688C						.						104	107	106					8																	109240530		2203	4300	6503	SO:0001583	missense	3646	exon7			TATTATCGCGACC	U94175	CCDS6308.1	8q22-q23	2010-03-10	2007-07-27	2007-07-27	ENSG00000104408	ENSG00000104408			3277	protein-coding gene	gene with protein product		602210	"eukaryotic translation initiation factor 3, subunit 6 48kDa"	INT6, EIF3S6		9403073, 9295280	Standard	NM_001568		Approved	eIF3-p48, eIF3e	uc003ymu.3	P60228	OTTHUMG00000164858	ENST00000220849.5:c.688G>C	chr8.hg19:g.109240530C>G	ENSP00000220849:p.Asp230His	251.0	1.0		460.0	50.0	NM_001568		Missense_Mutation	SNP	ENST00000220849.5	hg19	CCDS6308.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.4|21.4	4.150273|4.150273	0.78001|0.78001	.|.	.|.	ENSG00000104408|ENSG00000104408	ENST00000220849;ENST00000519030;ENST00000519627|ENST00000522352	T;T;T|T	0.47528|0.50813	0.84;0.84;0.84|0.73	5.36|5.36	5.36|5.36	0.76844|0.76844	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.69540|0.69540	0.3122|0.3122	M|M	0.81497|0.81497	2.545|2.545	0.80722|0.80722	D|D	1|1	D;P|.	0.89917|.	1.0;0.888|.	D;B|.	0.72625|.	0.978;0.364|.	T|T	0.71052|0.71052	-0.4704|-0.4704	10|7	0.62326|0.49607	D|T	0.03|0.09	-24.3332|-24.3332	19.4524|19.4524	0.94873|0.94873	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	230;230|.	B2R806;P60228|.	.;EIF3E_HUMAN|.	H|P	230;137;103|53	ENSP00000220849:D230H;ENSP00000428796:D137H;ENSP00000430839:D103H|ENSP00000428170:R53P	ENSP00000220849:D230H|ENSP00000428170:R53P	D|R	-|-	1|2	0|0	EIF3E|EIF3E	109309706|109309706	1.000000|1.000000	0.71417|0.71417	0.985000|0.985000	0.45067|0.45067	0.989000|0.989000	0.77384|0.77384	7.776000|7.776000	0.85560|0.85560	2.661000|2.661000	0.90470|0.90470	0.585000|0.585000	0.79938|0.79938	GAT|CGA	.	.		0.368	EIF3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380612.2	NM_001568		G	109240530	C	G	109240530	3	3	241	1	0	0	0	0	1	0	0	0	5017	884	31	4	677	4	EIF3E	8	109240530	Missense_Mutation	SNP	C	TCGA-ED-A66X-01A-11D-A30V-10	8528734	109240530	37123492	21	33313										
LRRTM3	347731	hgsc.bcm.edu	37	chr10	68686790	68686790	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	aggatgccctaagggctgtaGgtgtgaaggcaaaatggtat	15	5	0	1			TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr10:68686790G>T	ENST00000361320.4	+	2	694	c.116G>T	c.(115-117)aGg>aTg	p.R39M	CTNNA3_ENST00000433211.2_Intron|CTNNA3_ENST00000373744.4_Intron	NM_178011.3	NP_821079.3	Q86VH5	LRRT3_HUMAN	leucine rich repeat transmembrane neuronal 3	39	LRRNT.				positive regulation of beta-amyloid formation (GO:1902004)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)		p.R39K(2)		breast(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	41						AAGGGCTGTAGGTGTGAAGGC	0.463																																					p.R39M		Atlas-SNP	.											LRRTM3_ENST00000361320,NS,carcinoma,0,2	LRRTM3	241	.	2	Substitution - Missense(2)	lung(2)	c.G116T						.						118	115	116					10																	68686790		2203	4300	6503	SO:0001583	missense	347731	exon2			GCTGTAGGTGTGA	BX640611	CCDS7270.1	10q22.1	2007-01-22				ENSG00000198739			19410	protein-coding gene	gene with protein product		610869				12676565	Standard	XR_247527		Approved		uc001jmz.1	Q86VH5		ENST00000361320.4:c.116G>T	chr10.hg19:g.68686790G>T	ENSP00000355187:p.Arg39Met	92.0	0.0		97.0	8.0	NM_178011	A8K2A3|Q2NKX7|Q6N0A3	Missense_Mutation	SNP	ENST00000361320.4	hg19	CCDS7270.1	.	.	.	.	.	.	.	.	.	.	G	14.75	2.628246	0.46944	.	.	ENSG00000198739	ENST00000361320;ENST00000373722	D	0.96427	-4.01	5.23	5.23	0.72850	Leucine-rich repeat-containing N-terminal (2);	0.000000	0.85682	D	0.000000	D	0.98099	0.9373	M	0.80422	2.495	0.53688	D	0.999979	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	D	0.98945	1.0792	10	0.87932	D	0	.	17.9434	0.89032	0.0:0.0:1.0:0.0	.	39;39	Q86VH5;Q86VH5-2	LRRT3_HUMAN;.	M	39	ENSP00000355187:R39M	ENSP00000355187:R39M	R	+	2	0	LRRTM3	68356796	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.009000	0.88606	2.613000	0.88420	0.655000	0.94253	AGG	.	.		0.463	LRRTM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048277.2	NM_178011		T	68686790	G	T	68686790	3	4	241	1	0	0	0	0	1	0	0	0	9050	1000	35	3	122	3	LRRTM3	10	68686790	Missense_Mutation	SNP	G	TCGA-ED-A66X-01A-11D-A30V-10		68686790	66847957	22	33314										
MKI67	4288	hgsc.bcm.edu	37	chr10	129913861	129913861	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	agcactttctttctctgttgCgtaatcagtttgtaatccag	7	9	3	0	rs201650569		TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr10:129913861C>T	ENST00000368654.3	-	7	1186	c.811G>A	c.(811-813)Gca>Aca	p.A271T	MKI67_ENST00000368653.3_Intron	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	271					cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)	p.A271T(1)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TTCTCTGTTGCGTAATCAGTT	0.433																																					p.A271T		Atlas-SNP	.											MKI67,NS,carcinoma,0,1	MKI67	363	.	1	Substitution - Missense(1)	endometrium(1)	c.G811A						.	T	,THR/ALA	0,4406		0,0,2203	84	88	87		,811	-7.2	0	10		87	1,8599	818.9+/-406.8	0,1,4299	yes	intron,missense	MKI67	NM_001145966.1,NM_002417.4	,58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,benign	,271/3257	129913861	1,13005	2203	4300	6503	SO:0001583	missense	4288	exon7			CTGTTGCGTAATC	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 105"	176741	"antigen identified by monoclonal antibody Ki-67"			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.811G>A	chr10.hg19:g.129913861C>T	ENSP00000357643:p.Ala271Thr	46.0	0.0		81.0	18.0	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	hg19	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	T	0.017	-1.511489	0.00984	0.0	1.16E-4	ENSG00000148773	ENST00000368654;ENST00000537609	T	0.21031	2.03	3.59	-7.17	0.01511	.	1.919400	0.02775	N	0.120183	T	0.10766	0.0263	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34502	-0.9826	10	0.87932	D	0	.	7.5658	0.27879	0.0942:0.5353:0.2549:0.1155	.	271	P46013	KI67_HUMAN	T	271	ENSP00000357643:A271T	ENSP00000357643:A271T	A	-	1	0	MKI67	129803851	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-4.644000	0.00204	-3.899000	0.00093	-1.061000	0.02294	GCA	.	.		0.433	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		T	129913861	C	T	129913861	3	4	241	1	0	0	0	0	1	0	0	0	9607	768	27	1	8995	1	MKI67	10	129913861	Missense_Mutation	SNP	C	TCGA-ED-A66X-01A-11D-A30V-10	61227071	129913861	5620886	23	33315										
MUC2	4583	hgsc.bcm.edu	37	chr11	1083119	1083119	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	ttcctgtacaacctgaccacCtgccagcagacctgccgctc	7	18	0	2	rs567072224		TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr11:1083119C>T	ENST00000441003.2	+	16	2046	c.2019C>T	c.(2017-2019)acC>acT	p.T673T	MUC2_ENST00000359061.5_Silent_p.T673T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	673					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ACCTGACCACCTGCCAGCAGA	0.657													C|||	1	0.000199681	0	0	5008	,	,		13018	0.001		0	False		,,,				2504	0				p.T673T		Atlas-SNP	.											.	MUC2	614	.	0			c.C2019T						.						18	22	21					11																	1083119		2041	4182	6223	SO:0001819	synonymous_variant	4583	exon16			GACCACCTGCCAG	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.2019C>T	chr11.hg19:g.1083119C>T		7.0	0.0		15.0	8.0	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	hg19																																																																																				.	.		0.657	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1083119	C	T	1083119	2	4	241	1	0	0	0	0	0	0	0	1	9984	668	24	3		3	MUC2	11	1083119	Silent	SNP	C	TCGA-ED-A66X-01A-11D-A30V-10		1083119	133923397	24	33316										
SLCO2B1	11309	hgsc.bcm.edu	37	chr11	74880711	74880711	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	actcaggctttgtgttgtagGgatcctgtttgcagtgacca	12	8	1	1			TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr11:74880711G>A	ENST00000289575.5	+	6	1078	c.683G>A	c.(682-684)gGg>gAg	p.G228E	SLCO2B1_ENST00000454962.2_Intron|SLCO2B1_ENST00000531756.1_Intron|SLCO2B1_ENST00000532236.1_Splice_Site_p.G112E|SLCO2B1_ENST00000526660.1_Intron|SLCO2B1_ENST00000428359.2_Splice_Site_p.G206E|SLCO2B1_ENST00000341411.4_Intron|SLCO2B1_ENST00000525650.1_Splice_Site_p.G84E	NM_007256.4	NP_009187	O94956	SO2B1_HUMAN	solute carrier organic anion transporter family, member 2B1	228					liver development (GO:0001889)|sodium-independent icosanoid transport (GO:0071718)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bile acid transmembrane transporter activity (GO:0015125)|organic anion transmembrane transporter activity (GO:0008514)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(2)|endometrium(1)|large_intestine(7)|lung(20)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	39					Acetic acid(DB03166)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Digoxin(DB00390)|Dinoprostone(DB00917)|Ergoloid mesylate(DB01049)|Estradiol(DB00783)|Estrone(DB00655)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Glyburide(DB01016)|Ibuprofen(DB01050)|Iloprost(DB01088)|Latanoprost(DB00654)|Montelukast(DB00471)|Niacin(DB00627)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rosuvastatin(DB01098)|Salicylic acid(DB00936)|Tolbutamide(DB01124)	TGTGTTGTAGGGATCCTGTTT	0.567																																					p.G228E		Atlas-SNP	.											.	SLCO2B1	84	.	0			c.G683A						.						118	119	119					11																	74880711		2200	4293	6493	SO:0001630	splice_region_variant	11309	exon6			TTGTAGGGATCCT	AB026256	CCDS8235.1, CCDS44683.1, CCDS53679.1	11q13	2013-05-22	2003-11-25	2003-11-26				"Solute carriers"	10962	protein-coding gene	gene with protein product		604988	"solute carrier family 21 (organic anion transporter), member 9"	SLC21A9			Standard	NM_007256		Approved	OATP-B, OATP2B1	uc001owb.3	O94956		ENST00000289575.5:c.683-1G>A	chr11.hg19:g.74880711G>A		47.0	0.0		79.0	8.0	NM_007256	A8K2G9|B4DGA9|B4DTB0|E7ERN5|E9PPU8|Q9H2Z0|Q9UFU1	Missense_Mutation	SNP	ENST00000289575.5	hg19	CCDS8235.1	.	.	.	.	.	.	.	.	.	.	G	17.31	3.358214	0.61403	.	.	ENSG00000137491	ENST00000289575;ENST00000532236;ENST00000525650;ENST00000428359;ENST00000526839	T;T;T;T;T	0.52526	0.66;0.66;0.66;0.66;0.66	4.9	4.9	0.64082	Major facilitator superfamily domain, general substrate transporter (1);	0.062800	0.64402	D	0.000005	T	0.77046	0.4073	H	0.94462	3.54	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.996;0.999	D	0.83944	0.0313	9	.	.	.	.	15.6121	0.76733	0.0:0.0:1.0:0.0	.	84;228	E9PPU8;O94956	.;SO2B1_HUMAN	E	228;112;84;206;104	ENSP00000289575:G228E;ENSP00000434112:G112E;ENSP00000436324:G84E;ENSP00000388912:G206E;ENSP00000434742:G104E	.	G	+	2	0	SLCO2B1	74558359	1.000000	0.71417	0.992000	0.48379	0.651000	0.38670	5.782000	0.68973	2.521000	0.84997	0.650000	0.86243	GGG	.	.		0.567	SLCO2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383933.1	NM_007256	Missense_Mutation	A	74880711	G	A	74880711	5	1	241	1	0	0	0	0	0	0	1	0	14742	1246	43	3	705	3	SLCO2B1	11	74880711	Splice_Site	SNP	G	TCGA-ED-A66X-01A-11D-A30V-10	73797592	74880711	60125805	25	33317										
AKAP3	10566	hgsc.bcm.edu	37	chr12	4724998	4724998	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	tccttctcatagcgcagcacCgactgcagaacctcgcccac	7	18	1	1			TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr12:4724998C>T	ENST00000545990.2	-	6	2993	c.2469G>A	c.(2467-2469)tcG>tcA	p.S823S	RP11-500M8.7_ENST00000536588.1_Intron|AKAP3_ENST00000228850.1_Silent_p.S823S	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	823					acrosome reaction (GO:0007340)|cellular component movement (GO:0006928)|protein localization (GO:0008104)|single fertilization (GO:0007338)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	acrosomal vesicle (GO:0001669)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	protein kinase A binding (GO:0051018)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						AGCGCAGCACCGACTGCAGAA	0.567																																					p.S823S		Atlas-SNP	.											.	AKAP3	212	.	0			c.G2469A						.						137	111	120					12																	4724998		2203	4300	6503	SO:0001819	synonymous_variant	10566	exon5			CAGCACCGACTGC	U85715	CCDS8531.1	12p13.3	2009-03-12				ENSG00000111254		"A-kinase anchor proteins"	373	protein-coding gene	gene with protein product	"Fibrous Sheath Protein of 95 kDa", "cancer/testis antigen 82"	604689				10334916, 10319321	Standard	NM_001278309		Approved	FSP95, SOB1, AKAP110, CT82	uc001qnb.4	O75969		ENST00000545990.2:c.2469G>A	chr12.hg19:g.4724998C>T		96.0	0.0		134.0	21.0	NM_006422	O75945|Q86X01|Q9UM61	Silent	SNP	ENST00000545990.2	hg19	CCDS8531.1																																																																																			.	.		0.567	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	NM_006422		T	4724998	C	T	4724998	2	4	241	1	0	0	0	0	0	0	0	1	452	639	23	1		1	AKAP3	12	4724998	Silent	SNP	C	TCGA-ED-A66X-01A-11D-A30V-10		4724998	129126897	26	33318										
DPY19L2	283417	hgsc.bcm.edu	37	chr12	64057564	64057564	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	agtgcgaaaagtcatctcccGttccaaagatgagaggtgag	12	8	2	3			TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr12:64057564G>A	ENST00000324472.4	-	3	607	c.424C>T	c.(424-426)Cgg>Tgg	p.R142W	RP11-415I12.3_ENST00000509615.2_RNA	NM_173812.4	NP_776173.3	Q6NUT2	D19L2_HUMAN	dpy-19-like 2 (C. elegans)	142					multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|nuclear inner membrane (GO:0005637)|nucleus (GO:0005634)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	45			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		GTCATCTCCCGTTCCAAAGAT	0.328																																					p.R142W		Atlas-SNP	.											DPY19L2,NS,carcinoma,0,1	DPY19L2	97	.	0			c.C424T						.						62	59	60					12																	64057564		2203	4297	6500	SO:0001583	missense	283417	exon3			TCTCCCGTTCCAA		CCDS31851.1	12q14.2	2012-11-14			ENSG00000177990	ENSG00000177990			19414	protein-coding gene	gene with protein product	"spermatogenesis associated 34"	613893				12975309	Standard	XM_006719348		Approved	FLJ32949, SPATA34	uc001srp.1	Q6NUT2	OTTHUMG00000168712	ENST00000324472.4:c.424C>T	chr12.hg19:g.64057564G>A	ENSP00000315988:p.Arg142Trp	509.0	0.0		392.0	47.0	NM_173812	A4FVC1|B4E191|Q3ZCX2|Q6UWG8|Q96LZ9	Missense_Mutation	SNP	ENST00000324472.4	hg19	CCDS31851.1	.	.	.	.	.	.	.	.	.	.	G	13.20	2.166839	0.38217	.	.	ENSG00000177990	ENST00000324472	T	0.62941	-0.01	2.5	0.161	0.14977	.	0.067668	0.56097	U	0.000027	T	0.75213	0.3819	M	0.84585	2.705	0.80722	D	1	D	0.89917	1.0	D	0.72338	0.977	T	0.73477	-0.3970	9	.	.	.	.	7.3823	0.26862	0.0:0.0:0.3847:0.6153	.	142	Q6NUT2	D19L2_HUMAN	W	142	ENSP00000315988:R142W	.	R	-	1	2	DPY19L2	62343831	1.000000	0.71417	1.000000	0.80357	0.864000	0.49448	4.915000	0.63355	0.347000	0.23924	0.184000	0.17185	CGG	.	.		0.328	DPY19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400689.2	NM_173812		A	64057564	G	A	64057564	3	1	241	1	0	0	0	0	1	0	0	0	4743	1144	40	1	1932	1	DPY19L2	12	64057564	Missense_Mutation	SNP	G	TCGA-ED-A66X-01A-11D-A30V-10	59332566	64057564	69794331	27	33319										
EEA1	8411	hgsc.bcm.edu	37	chr12	93170633	93170633	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	tatttacccgtctcactgttActgaaaagcctttcccacag	5	13	1	1			TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr12:93170633A>G	ENST00000322349.8	-	28	4364	c.4100T>C	c.(4099-4101)gTa>gCa	p.V1367A		NM_003566.3	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1	1367					early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|synaptic vesicle to endosome fusion (GO:0016189)|vesicle fusion (GO:0006906)	axonal spine (GO:0044308)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|recycling endosome (GO:0055037)|serine-pyruvate aminotransferase complex (GO:0005969)	1-phosphatidylinositol binding (GO:0005545)|calmodulin binding (GO:0005516)|GTP-dependent protein binding (GO:0030742)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(5)|large_intestine(11)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	36						TCTCACTGTTACTGAAAAGCC	0.338																																					p.V1367A		Atlas-SNP	.											.	EEA1	104	.	0			c.T4100C						.						206	195	199					12																	93170633		2203	4300	6503	SO:0001583	missense	8411	exon28			ACTGTTACTGAAA	L40157	CCDS31874.1	12q22	2007-02-23	2007-02-23			ENSG00000102189		"Zinc fingers, FYVE domain containing"	3185	protein-coding gene	gene with protein product		605070	"early endosome antigen 1, 162kD"			7768953, 9697774	Standard	NM_003566		Approved	ZFYVE2	uc001tck.3	Q15075	OTTHUMG00000170110	ENST00000322349.8:c.4100T>C	chr12.hg19:g.93170633A>G	ENSP00000317955:p.Val1367Ala	78.0	0.0		83.0	14.0	NM_003566	Q14221	Missense_Mutation	SNP	ENST00000322349.8	hg19	CCDS31874.1	.	.	.	.	.	.	.	.	.	.	A	16.73	3.203372	0.58234	.	.	ENSG00000102189	ENST00000322349	T	0.71934	-0.61	5.48	5.48	0.80851	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, FYVE-type (2);Zinc finger, FYVE-related (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.47852	D	0.000204	T	0.77025	0.4070	L	0.35593	1.075	0.80722	D	1	P	0.50710	0.938	D	0.66716	0.946	T	0.79388	-0.1824	10	0.66056	D	0.02	.	15.5639	0.76273	1.0:0.0:0.0:0.0	.	1367	Q15075	EEA1_HUMAN	A	1367	ENSP00000317955:V1367A	ENSP00000317955:V1367A	V	-	2	0	EEA1	91694764	1.000000	0.71417	0.969000	0.41365	0.122000	0.20287	9.300000	0.96151	2.070000	0.61991	0.528000	0.53228	GTA	.	.		0.338	EEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407304.1	NM_003566		G	93170633	A	G	93170633	3	3	241	1	0	0	0	0	1	0	0	0	4923	391	14	2	143	2	EEA1	12	93170633	Missense_Mutation	SNP	A	TCGA-ED-A66X-01A-11D-A30V-10	29113069	93170633	40681262	28	33320										
PABPC3	5042	hgsc.bcm.edu	37	chr13	25671806	25671806	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	gtgggtccacgtcctgcagcTgctgctgctgctgcagctac	13	14	0	0	rs537105482|rs150143049|rs558565724	byFrequency	TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr13:25671806T>A	ENST00000281589.3	+	1	1507	c.1470T>A	c.(1468-1470)gcT>gcA	p.A490A		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	490					mRNA metabolic process (GO:0016071)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		GTCctgcagctgctgctgctg	0.537													t|||	1	0.000199681	0	0	5008	,	,		21148	0		0.001	False		,,,				2504	0				p.A490A		Atlas-SNP	.											PABPC3,colon,carcinoma,0,1	PABPC3	129	.	0			c.T1470A						.						49	46	47					13																	25671806		2203	4300	6503	SO:0001819	synonymous_variant	5042	exon1			TGCAGCTGCTGCT	AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"RNA binding motif (RRM) containing"	8556	protein-coding gene	gene with protein product	"testis PABP"	604680	"poly(A)-binding protein, cytoplasmic 3"	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	ENST00000281589.3:c.1470T>A	chr13.hg19:g.25671806T>A		41.0	0.0		55.0	3.0	NM_030979	Q8NHV0|Q9H086	Silent	SNP	ENST00000281589.3	hg19	CCDS9311.1																																																																																			.	.		0.537	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979		A	25671806	T	A	25671806	2	1	241	1	0	0	0	0	0	0	0	1	11374	1567	55	4		4	PABPC3	13	25671806	Silent	SNP	T	TCGA-ED-A66X-01A-11D-A30V-10		25671806	89498072	29	33321										
YY1	7528	hgsc.bcm.edu	37	chr14	100705845	100705845	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	cccatgatcgctctgcagccGctggtcaccgacgacccgac	10	18	2	1			TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr14:100705845G>T	ENST00000262238.4	+	1	524	c.264G>T	c.(262-264)ccG>ccT	p.P88P	RP11-638I2.4_ENST00000554537.1_RNA	NM_003403.3	NP_003394.1	P25490	TYY1_HUMAN	YY1 transcription factor	88	Interaction with the SMAD1/SMAD4 complex.				anterior/posterior pattern specification (GO:0009952)|camera-type eye morphogenesis (GO:0048593)|cell differentiation (GO:0030154)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|chromosome organization (GO:0051276)|double-strand break repair via homologous recombination (GO:0000724)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to prostaglandin F (GO:0034696)|response to UV-C (GO:0010225)|RNA localization (GO:0006403)|spermatogenesis (GO:0007283)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|four-way junction DNA binding (GO:0000400)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|large_intestine(1)|liver(2)|lung(1)|prostate(4)|skin(1)	11		Melanoma(154;0.152)				CTCTGCAGCCGCTGGTCACCG	0.736																																					p.P88P		Atlas-SNP	.											.	YY1	20	.	0			c.G264T						.						24	19	21					14																	100705845		2182	4273	6455	SO:0001819	synonymous_variant	7528	exon1			GCAGCCGCTGGTC	BC020324	CCDS9957.1	14q	2013-01-08			ENSG00000100811	ENSG00000100811		"INO80 complex subunits", "Zinc fingers, C2H2-type"	12856	protein-coding gene	gene with protein product	"INO80 complex subunit S", "Yin and Yang 1 protein"	600013				1655281, 7912122	Standard	NM_003403		Approved	NF-E1, DELTA, UCRBP, YIN-YANG-1, INO80S	uc001ygy.2	P25490	OTTHUMG00000150479	ENST00000262238.4:c.264G>T	chr14.hg19:g.100705845G>T		30.0	0.0		47.0	7.0	NM_003403	Q14935	Silent	SNP	ENST00000262238.4	hg19	CCDS9957.1																																																																																			.	.		0.736	YY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318277.1	NM_003403		T	100705845	G	T	100705845	2	4	241	1	0	0	0	0	0	0	0	1	17522	1074	38	1		1	YY1	14	100705845	Silent	SNP	G	TCGA-ED-A66X-01A-11D-A30V-10		100705845	6643695	30	33322										
TJP1	7082	hgsc.bcm.edu	37	chr15	30010303	30010303	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	tgatgggagcacctgaaggtTtagatgctacttctggaggc	14	7	1	3			TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr15:30010303T>C	ENST00000346128.6	-	22	4370	c.3896A>G	c.(3895-3897)aAa>aGa	p.K1299R	TJP1_ENST00000400011.2_Missense_Mutation_p.K1223R|TJP1_ENST00000356107.6_Missense_Mutation_p.K1299R|TJP1_ENST00000545208.2_Missense_Mutation_p.K1219R	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	1299					apoptotic process (GO:0006915)|blastocyst formation (GO:0001825)|cell-cell junction assembly (GO:0007043)|cell-cell signaling involved in cell-cell junction organization (GO:1901350)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to glucose stimulus (GO:0071333)|hippo signaling (GO:0035329)|membrane organization (GO:0061024)|negative regulation of vascular permeability (GO:0043116)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to magnetism (GO:0071000)|sensory perception of sound (GO:0007605)	apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gap junction (GO:0005921)|intercalated disc (GO:0014704)|intercellular canaliculus (GO:0046581)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(4)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(1)	68		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)		ACCTGAAGGTTTAGATGCTAC	0.368																																					p.K1299R	Melanoma(77;681 1843 6309 6570)	Atlas-SNP	.											TJP1,NS,carcinoma,0,1	TJP1	140	.	0			c.A3896G						.						201	188	192					15																	30010303		1837	4078	5915	SO:0001583	missense	7082	exon22			GAAGGTTTAGATG		CCDS42007.1, CCDS45199.1, CCDS73702.1	15q13	2012-07-12	2012-07-12		ENSG00000104067	ENSG00000104067			11827	protein-coding gene	gene with protein product	"zona occludens 1", "tight junction protein ZO-1"	601009				8825647	Standard	XM_005254616		Approved	ZO-1, MGC133289, DKFZp686M05161	uc001zcr.3	Q07157	OTTHUMG00000137397	ENST00000346128.6:c.3896A>G	chr15.hg19:g.30010303T>C	ENSP00000281537:p.Lys1299Arg	105.0	1.0		134.0	30.0	NM_003257	B4E3K1|Q2NKP3|Q4ZGJ6	Missense_Mutation	SNP	ENST00000346128.6	hg19	CCDS42007.1	.	.	.	.	.	.	.	.	.	.	T	14.44	2.536996	0.45176	.	.	ENSG00000104067	ENST00000346128;ENST00000400011;ENST00000545208;ENST00000400007;ENST00000356107	T;T	0.12361	2.69;2.71	5.79	3.51	0.40186	.	0.342545	0.35067	N	0.003472	T	0.11324	0.0276	L	0.38838	1.175	0.80722	D	1	B;B;B;B	0.22746	0.074;0.056;0.004;0.069	B;B;B;B	0.23018	0.037;0.027;0.004;0.043	T	0.07829	-1.0752	10	0.48119	T	0.1	.	9.4824	0.38908	0.0:0.1412:0.0:0.8588	.	1292;1219;1299;1223	A9CQZ8;Q07157-2;Q07157;G5E9E7	.;.;ZO1_HUMAN;.	R	1299;1223;1299;1219;1219	ENSP00000281537:K1299R;ENSP00000382890:K1223R	ENSP00000281537:K1299R	K	-	2	0	TJP1	27797595	1.000000	0.71417	0.906000	0.35671	0.968000	0.65278	3.977000	0.56874	1.034000	0.39945	0.533000	0.62120	AAA	.	.		0.368	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257		C	30010303	T	C	30010303	3	2	241	1	0	0	0	0	1	0	0	0	15944	1841	64	2	1378	2	TJP1	15	30010303	Missense_Mutation	SNP	T	TCGA-ED-A66X-01A-11D-A30V-10		30010303	72521089	31	33323										
DNAJA4	55466	hgsc.bcm.edu	37	chr15	78562999	78562999	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	gttctttggtggtggtggacGgatggctagagagagaagag	19	3	1	3			TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr15:78562999G>A	ENST00000394852.3	+	2	483	c.293G>A	c.(292-294)cGg>cAg	p.R98Q	DNAJA4_ENST00000343789.3_Missense_Mutation_p.R98Q|DNAJA4_ENST00000394855.3_Missense_Mutation_p.R127Q|DNAJA4_ENST00000446172.2_Missense_Mutation_p.R71Q	NM_001130182.1	NP_001123654.1	Q8WW22	DNJA4_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 4	98					negative regulation of inclusion body assembly (GO:0090084)|protein refolding (GO:0042026)|response to heat (GO:0009408)	cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|unfolded protein binding (GO:0051082)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	8						GGTGGTGGACGGATGGCTAGA	0.448																																					p.R127Q		Atlas-SNP	.											.	DNAJA4	63	.	0			c.G380A						.						127	123	124					15																	78562999		2196	4293	6489	SO:0001583	missense	55466	exon3			GTGGACGGATGGC	AF116663	CCDS10299.2, CCDS45316.1, CCDS45317.1	15q24.1	2011-09-02			ENSG00000140403	ENSG00000140403		"Heat shock proteins / DNAJ (HSP40)"	14885	protein-coding gene	gene with protein product						11147971	Standard	NM_018602		Approved	PRO1472	uc002bdi.3	Q8WW22	OTTHUMG00000143733	ENST00000394852.3:c.293G>A	chr15.hg19:g.78562999G>A	ENSP00000378321:p.Arg98Gln	83.0	0.0		111.0	22.0	NM_018602	E9PDM9|Q6AW87|Q8N5Z4|Q8N7P2	Missense_Mutation	SNP	ENST00000394852.3	hg19	CCDS45316.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.597407	0.87055	.	.	ENSG00000140403	ENST00000394855;ENST00000343789;ENST00000394852;ENST00000446172	T;T;T;T	0.72835	-0.69;-0.69;-0.69;-0.69	5.63	5.63	0.86233	Heat shock protein DnaJ, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.82513	0.5053	M	0.76574	2.34	0.80722	D	1	D;D;D;D	0.89917	0.997;0.998;0.997;1.0	P;D;P;D	0.72075	0.749;0.928;0.834;0.976	T	0.77736	-0.2476	10	0.13853	T	0.58	-4.1385	18.2734	0.90076	0.0:0.0:1.0:0.0	.	13;71;98;127	Q9P1H1;E9PDM9;Q8WW22;Q8WW22-2	.;.;DNJA4_HUMAN;.	Q	127;98;98;71	ENSP00000378324:R127Q;ENSP00000339581:R98Q;ENSP00000378321:R98Q;ENSP00000413499:R71Q	ENSP00000339581:R98Q	R	+	2	0	DNAJA4	76350054	1.000000	0.71417	0.996000	0.52242	0.858000	0.48976	7.752000	0.85141	2.652000	0.90054	0.655000	0.94253	CGG	.	.		0.448	DNAJA4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289801.1	NM_018602		A	78562999	G	A	78562999	3	1	241	1	0	0	0	0	1	0	0	0	4616	1116	39	1	445	1	DNAJA4	15	78562999	Missense_Mutation	SNP	G	TCGA-ED-A66X-01A-11D-A30V-10	48552696	78562999	23968393	32	33324										
PFAS	5198	hgsc.bcm.edu	37	chr17	8170947	8170947	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	gtggcgtggccttcgtgggcGgcttcagctatgcagatgtc	16	10	1	1			TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr17:8170947G>A	ENST00000314666.6	+	26	3479	c.3346G>A	c.(3346-3348)Ggc>Agc	p.G1116S	PFAS_ENST00000545834.1_Missense_Mutation_p.G692S	NM_012393.2	NP_036525.1	O15067	PUR4_HUMAN	phosphoribosylformylglycinamidine synthase	1116	Glutamine amidotransferase type-1.				'de novo' IMP biosynthetic process (GO:0006189)|glutamine metabolic process (GO:0006541)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|phosphoribosylformylglycinamidine synthase activity (GO:0004642)			central_nervous_system(3)|endometrium(8)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	35					L-Glutamine(DB00130)	CTTCGTGGGCGGCTTCAGCTA	0.617																																					p.G1116S		Atlas-SNP	.											.	PFAS	91	.	0			c.G3346A						.						132	118	123					17																	8170947		2203	4300	6503	SO:0001583	missense	5198	exon26			GTGGGCGGCTTCA	AB002359	CCDS11136.1	17p13.1	2008-07-31	2008-07-31		ENSG00000178921	ENSG00000178921	6.3.5.3		8863	protein-coding gene	gene with protein product	"FGAR amidotransferase"	602133				8110788	Standard	NM_012393		Approved	PURL, FGARAT, KIAA0361	uc002gkr.3	O15067	OTTHUMG00000108188	ENST00000314666.6:c.3346G>A	chr17.hg19:g.8170947G>A	ENSP00000313490:p.Gly1116Ser	54.0	0.0		77.0	9.0	NM_012393	A6H8V8	Missense_Mutation	SNP	ENST00000314666.6	hg19	CCDS11136.1	.	.	.	.	.	.	.	.	.	.	G	19.71	3.878432	0.72294	.	.	ENSG00000178921	ENST00000545834;ENST00000314666;ENST00000546020	T;T	0.68181	-0.31;0.44	5.68	4.72	0.59763	Glutamine amidotransferase type 1 (1);	0.058138	0.64402	N	0.000002	D	0.86932	0.6052	H	0.97186	3.955	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.90273	0.4309	10	0.87932	D	0	-22.0096	12.2022	0.54333	0.0826:0.0:0.9174:0.0	.	1116;1116	A8K8N7;O15067	.;PUR4_HUMAN	S	692;1116;525	ENSP00000441706:G692S;ENSP00000313490:G1116S	ENSP00000313490:G1116S	G	+	1	0	PFAS	8111672	1.000000	0.71417	0.902000	0.35471	0.192000	0.23643	8.817000	0.91985	1.412000	0.46977	0.563000	0.77884	GGC	.	.		0.617	PFAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226994.2			A	8170947	G	A	8170947	3	1	241	1	0	0	0	0	1	0	0	0	11763	1116	39	1	3444	1	PFAS	17	8170947	Missense_Mutation	SNP	G	TCGA-ED-A66X-01A-11D-A30V-10		8170947	73024263	33	33325										
TADA2A	6871	hgsc.bcm.edu	37	chr17	35804825	35804825	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	acaattatgcagaatgggacTtgagagacattgattttgtt	10	4	0	4			TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr17:35804825T>C	ENST00000394395.2	+	8	732	c.559T>C	c.(559-561)Ttg>Ctg	p.L187L	TADA2A_ENST00000225396.6_Silent_p.L187L|TADA2A_ENST00000417170.1_Silent_p.L187L|TADA2A_ENST00000586023.1_Silent_p.L187L|TADA2A_ENST00000591992.1_3'UTR	NM_001166105.1	NP_001159577.1	O75478	TAD2A_HUMAN	transcriptional adaptor 2A	187					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|nucleus (GO:0005634)|PCAF complex (GO:0000125)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|zinc ion binding (GO:0008270)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|lung(3)|prostate(1)|skin(1)	13						AGAATGGGACTTGAGAGACAT	0.403																																					p.L187L		Atlas-SNP	.											.	TADA2A	91	.	0			c.T559C						.						235	224	228					17																	35804825		2203	4300	6503	SO:0001819	synonymous_variant	6871	exon8			TGGGACTTGAGAG	AK022767	CCDS11319.1, CCDS45656.1	17q12-q21	2014-04-10	2009-10-02	2009-10-02	ENSG00000108264	ENSG00000276234			11531	protein-coding gene	gene with protein product		602276	"transcriptional adaptor 2 (ADA2 homolog, yeast)-like"	TADA2L		8552087	Standard	XM_006722043		Approved	ADA2, hADA2, ADA2A	uc002hnt.3	O75478	OTTHUMG00000188469	ENST00000394395.2:c.559T>C	chr17.hg19:g.35804825T>C		139.0	0.0		163.0	21.0	NM_001488	A8MVD0|B3KMU9|Q9BVJ0|Q9UCW2|Q9UP49	Silent	SNP	ENST00000394395.2	hg19	CCDS11319.1																																																																																			.	.		0.403	TADA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256677.3	NM_001488		C	35804825	T	C	35804825	2	2	241	1	0	0	0	0	0	0	0	1	15525	1606	56	2		2	TADA2A	17	35804825	Silent	SNP	T	TCGA-ED-A66X-01A-11D-A30V-10	27633878	35804825	45390385	34	33326										
BRIP1	83990	hgsc.bcm.edu	37	chr17	59821818	59821818	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	tctcctttgtatttgattgcGtcatagtacacctgcagtaa	7	9	2	1	rs374362388		TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr17:59821818G>A	ENST00000259008.2	-	15	2499	c.2232C>T	c.(2230-2232)gaC>gaT	p.D744D	BRIP1_ENST00000577598.1_Silent_p.D744D	NM_032043.2	NP_114432.2	Q9BX63	FANCJ_HUMAN	BRCA1 interacting protein C-terminal helicase 1	744					DNA damage checkpoint (GO:0000077)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(9)|kidney(5)|large_intestine(9)|liver(2)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	55						ATTTGATTGCGTCATAGTACA	0.328			"F, N, Mis"			"AML, leukemia, breast"		Involved in tolerance or repair of DNA crosslinks																													p.D744D		Atlas-SNP	.	yes	Rec		"Fanconi anaemia J, breast cancer susceptiblity"	17	17q22	83990	BRCA1 interacting protein C-terminal helicase 1		"L, E"	BRIP1_ENST00000259008,colon,carcinoma,0,2	BRIP1	237	.	0			c.C2232T						.	G		0,4406		0,0,2203	169	169	169		2232	0.8	1	17		169	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	BRIP1	NM_032043.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		744/1250	59821818	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	83990	exon15			GATTGCGTCATAG	AF360549	CCDS11631.1	17q22.2	2014-09-17				ENSG00000136492		"Fanconi anemia, complementation groups"	20473	protein-coding gene	gene with protein product	"BRCA1/BRCA2-associated helicase 1"	605882				11595410, 11301010	Standard	NM_032043		Approved	OF, BACH1, FANCJ	uc002izk.2	Q9BX63		ENST00000259008.2:c.2232C>T	chr17.hg19:g.59821818G>A		214.0	2.0		223.0	37.0	NM_032043	Q3MJE2|Q8NCI5	Silent	SNP	ENST00000259008.2	hg19	CCDS11631.1																																																																																			.	.		0.328	BRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445362.1	NM_032043		A	59821818	G	A	59821818	2	1	241	1	0	0	0	0	0	0	0	1	1516	1136	40	1		1	BRIP1	17	59821818	Silent	SNP	G	TCGA-ED-A66X-01A-11D-A30V-10	24016993	59821818	21373392	35	33327										
FASN	2194	hgsc.bcm.edu	37	chr17	80049392	80049392	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	gggcctcaggatgatgtgcaCgttggagcccccgaagccaa	14	12	1	1			TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr17:80049392C>T	ENST00000306749.2	-	9	1416	c.1198G>A	c.(1198-1200)Gtg>Atg	p.V400M		NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	400	Beta-ketoacyl synthase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	ATGATGTGCACGTTGGAGCCC	0.716																																					p.V400M	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.G1198A						.						31	32	32					17																	80049392		2173	4289	6462	SO:0001583	missense	2194	exon9			TGTGCACGTTGGA	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.1198G>A	chr17.hg19:g.80049392C>T	ENSP00000304592:p.Val400Met	127.0	0.0		159.0	18.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	hg19	CCDS11801.1	.	.	.	.	.	.	.	.	.	.	C	17.04	3.288358	0.59976	.	.	ENSG00000169710	ENST00000306749	T	0.27402	1.67	5.1	4.13	0.48395	Thiolase-like, subgroup (1);Thiolase-like (1);	0.293303	0.31427	N	0.007679	T	0.59074	0.2167	M	0.90082	3.085	0.54753	D	0.999984	D	0.89917	1.0	D	0.66196	0.942	T	0.67597	-0.5630	10	0.62326	D	0.03	-34.0693	12.9511	0.58401	0.0:0.921:0.0:0.079	.	400	P49327	FAS_HUMAN	M	400	ENSP00000304592:V400M	ENSP00000304592:V400M	V	-	1	0	FASN	77642681	1.000000	0.71417	0.557000	0.28306	0.150000	0.21749	7.317000	0.79018	2.381000	0.81170	0.484000	0.47621	GTG	.	.		0.716	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		T	80049392	C	T	80049392	3	4	241	1	0	0	0	0	1	0	0	0	5691	536	19	1	6477	1	FASN	17	80049392	Missense_Mutation	SNP	C	TCGA-ED-A66X-01A-11D-A30V-10	20227574	80049392	1145818	36	33328										
TUBB4	10382	hgsc.bcm.edu	37	chr19	6495427	6495427	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	atgaaggtcgcggccatcttCaggccgcggggcgggatgtc	17	11	2	1	rs531220948		TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr19:6495427C>T	ENST00000264071.2	-	4	1454	c.1083G>A	c.(1081-1083)ctG>ctA	p.L361L	CTD-2396E7.10_ENST00000596027.1_RNA|TUBB4A_ENST00000540257.1_Silent_p.L361L|CTD-2396E7.9_ENST00000599292.1_RNA			P04350	TBB4A_HUMAN	tubulin, beta 4A class IVa	361					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|internode region of axon (GO:0033269)|microtubule (GO:0005874)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)										CGGCCATCTTCAGGCCGCGGG	0.617																																					p.L361L		Atlas-SNP	.											.	.	.	.	0			c.G1083A						.						172	151	158					19																	6495427		2203	4300	6503	SO:0001819	synonymous_variant	10382	exon4			CATCTTCAGGCCG	AK075307	CCDS12168.1	19p13.3	2014-02-05	2011-10-11	2011-10-10	ENSG00000104833	ENSG00000104833		"Tubulins"	20774	protein-coding gene	gene with protein product	"class IVa beta-tubulin"	602662	"tubulin, beta 4", "tubulin, beta 4 class IVa", "dystonia 4, torsion (autosomal dominant)"	TUBB4, DYT4		6865944, 6462917, 23595291	Standard	NM_001289123		Approved	beta-5	uc002mfg.1	P04350		ENST00000264071.2:c.1083G>A	chr19.hg19:g.6495427C>T		41.0	0.0		48.0	10.0	NM_006087	B3KQP4|Q969E5	Silent	SNP	ENST00000264071.2	hg19	CCDS12168.1																																																																																			.	.		0.617	TUBB4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457841.1	NM_006087		T	6495427	C	T	6495427	2	4	241	1	0	0	0	0	0	0	0	1	16773	813	29	3		3	TUBB4	19	6495427	Silent	SNP	C	TCGA-ED-A66X-01A-11D-A30V-10		6495427	52633556	37	33329										
RYR1	6261	hgsc.bcm.edu	37	chr19	38993172	38993172	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	tttcagcaccaccgagatggCgctggcgctgaaccgctacc	11	15	1	2			TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr19:38993172C>T	ENST00000359596.3	+	48	7640	c.7640C>T	c.(7639-7641)gCg>gTg	p.A2547V	RYR1_ENST00000360985.3_Missense_Mutation_p.A2547V|RYR1_ENST00000355481.4_Missense_Mutation_p.A2547V			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	2547	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	ACCGAGATGGCGCTGGCGCTG	0.657																																					p.A2547V		Atlas-SNP	.											RYR1,NS,carcinoma,0,1	RYR1	708	.	0			c.C7640T						.						39	32	34					19																	38993172		2203	4299	6502	SO:0001583	missense	6261	exon48			AGATGGCGCTGGC	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.7640C>T	chr19.hg19:g.38993172C>T	ENSP00000352608:p.Ala2547Val	29.0	0.0		37.0	5.0	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	C	15.55	2.867444	0.51588	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.91068	-2.78;-2.78;-2.78	3.97	3.97	0.46021	.	0.000000	0.64402	U	0.000003	D	0.95188	0.8440	M	0.82823	2.61	0.52501	D	0.999957	D;D	0.76494	0.999;0.999	D;D	0.78314	0.991;0.98	D	0.95903	0.8917	10	0.87932	D	0	.	15.3225	0.74132	0.0:1.0:0.0:0.0	.	2547;2547	P21817-2;P21817	.;RYR1_HUMAN	V	2547	ENSP00000352608:A2547V;ENSP00000347667:A2547V;ENSP00000354254:A2547V	ENSP00000347667:A2547V	A	+	2	0	RYR1	43685012	1.000000	0.71417	0.997000	0.53966	0.743000	0.42351	7.534000	0.82004	2.216000	0.71823	0.313000	0.20887	GCG	.	.		0.657	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			T	38993172	C	T	38993172	3	4	241	1	0	0	0	0	1	0	0	0	13783	768	27	1	7830	1	RYR1	19	38993172	Missense_Mutation	SNP	C	TCGA-ED-A66X-01A-11D-A30V-10	32497745	38993172	20135811	38	33330										
SIGLEC8	27181	hgsc.bcm.edu	37	chr19	51961351	51961351	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	ctccaaatgtccccaaggagTtggaatcggccctgggtctc	11	13	1	0			TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr19:51961351T>C	ENST00000321424.3	-	1	357	c.291A>G	c.(289-291)caA>caG	p.Q97Q	SIGLEC8_ENST00000430817.1_Silent_p.Q97Q|SIGLEC8_ENST00000597352.1_5'Flank|SIGLEC8_ENST00000340550.5_Silent_p.Q97Q	NM_014442.2	NP_055257.2	Q9NYZ4	SIGL8_HUMAN	sialic acid binding Ig-like lectin 8	97	Ig-like V-type.				cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(11)|liver(3)|lung(15)|ovary(2)|skin(4)|stomach(3)|urinary_tract(2)	50		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000627)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		CCCCAAGGAGTTGGAATCGGC	0.557																																					p.Q97Q		Atlas-SNP	.											.	SIGLEC8	130	.	0			c.A291G						.						187	167	174					19																	51961351		2203	4300	6503	SO:0001819	synonymous_variant	27181	exon1			AAGGAGTTGGAAT	AF195092	CCDS33086.1	19q13.33-q13.41	2013-01-29			ENSG00000105366	ENSG00000105366		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10877	protein-coding gene	gene with protein product		605639				10625619	Standard	XR_243922		Approved	SIGLEC-8, SAF2, SIGLEC8L, MGC59785	uc002pwt.3	Q9NYZ4		ENST00000321424.3:c.291A>G	chr19.hg19:g.51961351T>C		168.0	0.0		147.0	24.0	NM_014442	Q7Z728	Silent	SNP	ENST00000321424.3	hg19	CCDS33086.1																																																																																			.	.		0.557	SIGLEC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463648.2	NM_014442		C	51961351	T	C	51961351	2	2	241	1	0	0	0	0	0	0	0	1	14329	1722	60	2		2	SIGLEC8	19	51961351	Silent	SNP	T	TCGA-ED-A66X-01A-11D-A30V-10	12968179	51961351	7167632	39	33331										
CNOT3	4849	hgsc.bcm.edu	37	chr19	54652191	54652191	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	cctagcggaggcggaggcggCggcagcggaggtggagggag	24	8	0	0			TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr19:54652191C>A	ENST00000406403.1	+	10	2806	c.1203C>A	c.(1201-1203)ggC>ggA	p.G401G	CNOT3_ENST00000221232.5_Silent_p.G401G|CNOT3_ENST00000358389.3_Silent_p.G220G			O75175	CNOT3_HUMAN	CCR4-NOT transcription complex, subunit 3	401	Gly/Ser-rich.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|nucleus (GO:0005634)				endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(7)|urinary_tract(3)	28	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					gcggaggcggcggcagcggag	0.716																																					p.G401G		Atlas-SNP	.											.	CNOT3	133	.	0			c.C1203A						.																																			SO:0001819	synonymous_variant	4849	exon11			AGGCGGCGGCAGC	AF180474	CCDS12880.1	19q13.4	2011-02-14			ENSG00000088038	ENSG00000088038			7879	protein-coding gene	gene with protein product	"NOT3 (negative regulator of transcription 3, yeast) homolog"	604910		NOT3		10637334, 9734811	Standard	NM_014516		Approved	NOT3H, KIAA0691, LENG2	uc002qdj.2	O75175	OTTHUMG00000066468	ENST00000406403.1:c.1203C>A	chr19.hg19:g.54652191C>A		47.0	0.0		85.0	7.0	NM_014516	Q9NZN7|Q9UF76	Silent	SNP	ENST00000406403.1	hg19	CCDS12880.1	.	.	.	.	.	.	.	.	.	.	c	0.017	-1.498541	0.01001	.	.	ENSG00000088038	ENST00000440571	.	.	.	2.62	-5.24	0.02789	.	.	.	.	.	T	0.15739	0.0379	.	.	.	0.09310	N	0.999997	.	.	.	.	.	.	T	0.22695	-1.0209	4	.	.	.	-3.8349	0.5641	0.00684	0.4184:0.2186:0.1553:0.2077	.	.	.	.	E	323	.	.	A	+	2	0	CNOT3	59344003	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-4.613000	0.00208	-1.406000	0.02045	-1.506000	0.00953	GCG	.	.		0.716	CNOT3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142130.3	NM_014516		A	54652191	C	A	54652191	2	1	241	1	0	0	0	0	0	0	0	1	3622	755	27	1		1	CNOT3	19	54652191	Silent	SNP	C	TCGA-ED-A66X-01A-11D-A30V-10	2690840	54652191	4476792	40	33332										
ISM1	140862	hgsc.bcm.edu	37	chr20	13279761	13279761	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	aaggacttccgctggaaggaCgccagcgggcccaaggagaa	15	11	0	1	rs572363345		TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr20:13279761C>T	ENST00000262487.4	+	6	1056	c.1050C>T	c.(1048-1050)gaC>gaT	p.D350D	TASP1_ENST00000539805.1_Intron	NM_080826.1	NP_543016.1	B1AKI9	ISM1_HUMAN	isthmin 1, angiogenesis inhibitor	350	AMOP. {ECO:0000255|PROSITE- ProRule:PRU00347}.					extracellular region (GO:0005576)				NS(1)|autonomic_ganglia(1)|endometrium(1)|large_intestine(8)|lung(5)|urinary_tract(1)	17						GCTGGAAGGACGCCAGCGGGC	0.647													C|||	1	0.000199681	8e-04	0	5008	,	,		18261	0		0	False		,,,				2504	0				p.D350D		Atlas-SNP	.											.	ISM1	41	.	0			c.C1050T						.						41	47	45					20																	13279761		2144	4237	6381	SO:0001819	synonymous_variant	140862	exon6			GAAGGACGCCAGC	AL133463	CCDS46579.1	20p12.1	2013-05-15	2013-05-15	2008-12-23	ENSG00000101230	ENSG00000101230			16213	protein-coding gene	gene with protein product		615793	"chromosome 20 open reading frame 82", "isthmin 1 homolog (zebrafish)"	C20orf82			Standard	NM_080826		Approved	bA149I18.1	uc010gce.1	B1AKI9		ENST00000262487.4:c.1050C>T	chr20.hg19:g.13279761C>T		64.0	0.0		64.0	6.0	NM_080826	Q8WVH9	Silent	SNP	ENST00000262487.4	hg19	CCDS46579.1																																																																																			.	.		0.647	ISM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078039.2			T	13279761	C	T	13279761	2	4	241	1	0	0	0	0	0	0	0	1	7869	535	19	1		1	ISM1	20	13279761	Silent	SNP	C	TCGA-ED-A66X-01A-11D-A30V-10		13279761	49745759	41	33333										
DHX35	60625	hgsc.bcm.edu	37	chr20	37630379	37630379	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	2	1	0.605173587474472	3.93362831858407	0.327802359882006	1	1	0	ttttttctttttagaaattcCgggatttctttaatcaaaat	4	5	3	1	rs539104890	byFrequency	TCGA-ED-A66X-01A-11D-A30V-10	TCGA-ED-A66X-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	eb66e2cc-2bbc-465c-8778-a7920ea2c3bc	7b7ee2a3-d880-4f02-a19a-1c79c4b15239	g.chr20:37630379C>T	ENST00000252011.3	+	9	682	c.649C>T	c.(649-651)Cgg>Tgg	p.R217W	DHX35_ENST00000373323.4_Missense_Mutation_p.R186W|DHX35_ENST00000373325.2_Missense_Mutation_p.R217W	NM_021931.3	NP_068750.2	Q9H5Z1	DHX35_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 35	217	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(13)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	40		Myeloproliferative disorder(115;0.00878)				TTAGAAATTCCGGGATTTCTT	0.328													C|||	2	0.000399361	0	0.0014	5008	,	,		17282	0		0.001	False		,,,				2504	0				p.R217W		Atlas-SNP	.											.	DHX35	82	.	0			c.C649T						.						85	93	90					20																	37630379		2203	4300	6503	SO:0001583	missense	60625	exon9			AAATTCCGGGATT	AK026412	CCDS13310.1, CCDS54463.1	20q11.22-q12	2003-06-13	2003-06-13	2003-06-13	ENSG00000101452	ENSG00000101452		"DEAH-boxes"	15861	protein-coding gene	gene with protein product			"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 35"	C20orf15, DDX35			Standard	NM_001190809		Approved	FLJ22759, KAIA0875	uc002xjh.3	Q9H5Z1	OTTHUMG00000032463	ENST00000252011.3:c.649C>T	chr20.hg19:g.37630379C>T	ENSP00000252011:p.Arg217Trp	45.0	0.0		53.0	7.0	NM_021931	A2RTX3|B4E0J0|F5GXM6|Q5THR0|Q9H4H7|Q9H6T6	Missense_Mutation	SNP	ENST00000252011.3	hg19	CCDS13310.1	.	.	.	.	.	.	.	.	.	.	C	17.13	3.309937	0.60414	.	.	ENSG00000101452	ENST00000373325;ENST00000252011;ENST00000373323;ENST00000441485	T;T;T;T	0.07908	3.15;3.15;3.15;3.15	5.64	3.59	0.41128	DEAD-like helicase (2);	0.152772	0.64402	D	0.000018	T	0.17874	0.0429	M	0.72894	2.215	0.44289	D	0.997154	D;D	0.59357	0.985;0.973	P;B	0.54815	0.761;0.38	T	0.00599	-1.1651	10	0.87932	D	0	.	7.7121	0.28684	0.2941:0.6236:0.0:0.0823	.	186;217	F5GXM6;Q9H5Z1	.;DHX35_HUMAN	W	217;217;186;182	ENSP00000362422:R217W;ENSP00000252011:R217W;ENSP00000362420:R186W;ENSP00000414630:R182W	ENSP00000252011:R217W	R	+	1	2	DHX35	37063793	1.000000	0.71417	1.000000	0.80357	0.854000	0.48673	3.050000	0.49877	1.523000	0.49018	0.561000	0.74099	CGG	.	.		0.328	DHX35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079212.2	NM_021931		T	37630379	C	T	37630379	3	4	241	1	0	0	0	0	1	0	0	0	4510	643	23	1	683	1	DHX35	20	37630379	Missense_Mutation	SNP	C	TCGA-ED-A66X-01A-11D-A30V-10	24350618	37630379	25395141	42	33334										
KIAA0562	9731	hgsc.bcm.edu	37	chr1	3753156	3753156	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	acatgcctcccctccgagcaTcgctgatgtctgcattactc	7	16	1	1			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr1:3753156T>C	ENST00000378230.3	-	10	1544	c.1220A>G	c.(1219-1221)gAt>gGt	p.D407G	CEP104_ENST00000460038.1_Intron	NM_014704.3	NP_055519.1	O60308	CE104_HUMAN	centrosomal protein 104kDa	407						centriole (GO:0005814)	glutamate binding (GO:0016595)|glycine binding (GO:0016594)|thienylcyclohexylpiperidine binding (GO:0016596)			breast(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(14)|lung(8)|prostate(1)|skin(3)	39						CCTCCGAGCATCGCTGATGTC	0.562																																					p.D407G		Atlas-SNP	.											.	CEP104	79	.	0			c.A1220G						.						122	103	109					1																	3753156		2203	4300	6503	SO:0001583	missense	9731	exon10			CGAGCATCGCTGA	AB011134	CCDS30571.1	1p36.32	2014-02-20	2011-05-06	2011-05-06	ENSG00000116198	ENSG00000116198			24866	protein-coding gene	gene with protein product	"glycine, glutamate, thienylcyclohexylpiperidine binding protein"		"KIAA0562"	KIAA0562		7488117, 21399614	Standard	NM_014704		Approved	GlyBP, RP1-286D6.4	uc001aky.2	O60308	OTTHUMG00000003507	ENST00000378230.3:c.1220A>G	chr1.hg19:g.3753156T>C	ENSP00000367476:p.Asp407Gly	39.0	0.0		37.0	10.0	NM_014704	Q5JSQ3|Q5SR24|Q5SR25|Q6PKF5|Q86W32|Q86X14	Missense_Mutation	SNP	ENST00000378230.3	hg19	CCDS30571.1	.	.	.	.	.	.	.	.	.	.	T	9.716	1.158297	0.21454	.	.	ENSG00000116198	ENST00000378230;ENST00000443466	T;T	0.44881	1.43;0.91	5.36	-1.83	0.07833	.	1.209250	0.05472	N	0.553328	T	0.31071	0.0785	L	0.46157	1.445	0.09310	N	1	B;B	0.11235	0.004;0.001	B;B	0.11329	0.006;0.002	T	0.21861	-1.0233	10	0.30854	T	0.27	.	2.3825	0.04357	0.1118:0.1328:0.2315:0.5238	.	407;407	O60308-3;O60308	.;CE104_HUMAN	G	407;101	ENSP00000367476:D407G;ENSP00000411927:D101G	ENSP00000367476:D407G	D	-	2	0	CEP104	3743016	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.327000	0.19663	-0.148000	0.11234	-0.280000	0.10049	GAT	.	.		0.562	CEP104-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009747.3	NM_014704		C	3753156	T	C	3753156	3	2	242	1	0	0	0	0	1	0	0	0	8193	1435	50	2	1609	2	KIAA0562	1	3753156	Missense_Mutation	SNP	T	TCGA-ED-A66Y-01A-11D-A30V-10		3753156	245497465	1	33335										
GUCA2B	2981	hgsc.bcm.edu	37	chr1	42620502	42620502	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	ggaccttcagcctgtctgcgCctcgcaggaggcttccagca	12	15	2	0			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr1:42620502C>T	ENST00000372581.1	+	2	272	c.242C>T	c.(241-243)gCc>gTc	p.A81V		NM_007102.2	NP_009033.1	Q16661	GUC2B_HUMAN	guanylate cyclase activator 2B (uroguanylin)	81					body fluid secretion (GO:0007589)|cGMP biosynthetic process (GO:0006182)|excretion (GO:0007588)|negative regulation of blood pressure (GO:0045776)|positive regulation of guanylate cyclase activity (GO:0031284)	extracellular vesicular exosome (GO:0070062)	calcium sensitive guanylate cyclase activator activity (GO:0008048)			breast(1)|large_intestine(2)	3	Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				CCTGTCTGCGCCTCGCAGGAG	0.682																																					p.A81V		Atlas-SNP	.											.	GUCA2B	9	.	0			c.C242T						.						53	52	52					1																	42620502		2203	4300	6503	SO:0001583	missense	2981	exon2			TCTGCGCCTCGCA	BC069301	CCDS464.1	1p34-p33	2014-01-30			ENSG00000044012	ENSG00000044012		"Endogenous ligands"	4683	protein-coding gene	gene with protein product	"prepro-uroguanylin"	601271				8605041, 9268639	Standard	NM_007102		Approved		uc001chc.1	Q16661	OTTHUMG00000007024	ENST00000372581.1:c.242C>T	chr1.hg19:g.42620502C>T	ENSP00000361662:p.Ala81Val	112.0	0.0		123.0	85.0	NM_007102	Q52LV0	Missense_Mutation	SNP	ENST00000372581.1	hg19	CCDS464.1	.	.	.	.	.	.	.	.	.	.	C	11.75	1.732299	0.30684	.	.	ENSG00000044012	ENST00000372581	T	0.45668	0.89	4.83	3.84	0.44239	.	0.954188	0.08731	N	0.902024	T	0.37999	0.1024	L	0.47716	1.5	0.09310	N	1	B	0.34181	0.44	B	0.35114	0.196	T	0.24512	-1.0158	10	0.45353	T	0.12	-3.245	8.7125	0.34393	0.289:0.711:0.0:0.0	.	81	Q16661	GUC2B_HUMAN	V	81	ENSP00000361662:A81V	ENSP00000361662:A81V	A	+	2	0	GUCA2B	42393089	0.000000	0.05858	0.007000	0.13788	0.465000	0.32709	0.383000	0.20651	2.221000	0.72209	0.609000	0.83330	GCC	.	.		0.682	GUCA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000018307.1	NM_007102		T	42620502	C	T	42620502	3	4	242	1	0	0	0	0	1	0	0	0	6901	739	26	3	248	3	GUCA2B	1	42620502	Missense_Mutation	SNP	C	TCGA-ED-A66Y-01A-11D-A30V-10	38867346	42620502	206630119	2	33336										
TOR1AIP2	163590	hgsc.bcm.edu	37	chr1	179815558	179815558	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	ccttctggccattctcaaacCcatagctcagctccaggtca	6	16	4	0			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr1:179815558C>T	ENST00000367612.3	-	6	1448	c.1061G>A	c.(1060-1062)gGg>gAg	p.G354E	TOR1AIP2_ENST00000609928.1_Missense_Mutation_p.G354E	NM_145034.4	NP_659471.1	Q9H496	IFG15_HUMAN	torsin A interacting protein 2	0										cervix(1)|endometrium(3)|large_intestine(1)|lung(10)|ovary(1)|skin(2)	18						ATTCTCAAACCCATAGCTCAG	0.507																																					p.G354E		Atlas-SNP	.											.	TOR1AIP2	38	.	0			c.G1061A						.						89	87	88					1																	179815558		2203	4300	6503	SO:0001583	missense	163590	exon7			TCAAACCCATAGC		CCDS1334.1	1q25.2	2012-02-09			ENSG00000169905	ENSG00000169905			24055	protein-coding gene	gene with protein product		614513				15767459	Standard	NM_145034		Approved	LULL1, NET9, IFRG15	uc001gnk.3	Q8NFQ8	OTTHUMG00000035265	ENST00000367612.3:c.1061G>A	chr1.hg19:g.179815558C>T	ENSP00000356584:p.Gly354Glu	51.0	0.0		80.0	32.0	NM_001199260	Q05BU2	Missense_Mutation	SNP	ENST00000367612.3	hg19	CCDS1334.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.126128	0.77549	.	.	ENSG00000169905	ENST00000367612	T	0.46819	0.86	5.63	5.63	0.86233	.	0.062803	0.64402	D	0.000008	T	0.71584	0.3357	M	0.82630	2.6	0.42341	D	0.992334	D	0.71674	0.998	D	0.85130	0.997	T	0.75972	-0.3129	10	0.87932	D	0	-20.1791	15.9248	0.79609	0.0:0.8649:0.1351:0.0	.	354	Q8NFQ8	TOIP2_HUMAN	E	354	ENSP00000356584:G354E	ENSP00000356584:G354E	G	-	2	0	TOR1AIP2	178082181	0.998000	0.40836	0.941000	0.38009	0.969000	0.65631	3.418000	0.52721	2.652000	0.90054	0.655000	0.94253	GGG	.	.		0.507	TOR1AIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085304.1	NM_145034		T	179815558	C	T	179815558	3	4	242	1	0	0	0	0	1	0	0	0	16388	623	22	3	355	3	TOR1AIP2	1	179815558	Missense_Mutation	SNP	C	TCGA-ED-A66Y-01A-11D-A30V-10	137195056	179815558	69435063	3	33337										
KCNT2	343450	hgsc.bcm.edu	37	chr1	196274416	196274416	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	agtctttggctctgaattgcAtgaatctcatgttggcgggg	13	7	3	2			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr1:196274416A>C	ENST00000294725.9	-	22	3458	c.2543T>G	c.(2542-2544)aTg>aGg	p.M848R	KCNT2_ENST00000367433.5_Missense_Mutation_p.M824R|KCNT2_ENST00000367431.4_Missense_Mutation_p.M774R|KCNT2_ENST00000451324.2_Intron|KCNT2_ENST00000498426.1_5'UTR|KCNT2_ENST00000609185.1_Missense_Mutation_p.M774R			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	848					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(16)|lung(43)|ovary(5)|pancreas(1)|prostate(1)|skin(11)|stomach(2)|upper_aerodigestive_tract(1)	97						TCTGAATTGCATGAATCTCAT	0.363																																					p.M848R		Atlas-SNP	.											.	KCNT2	243	.	0			c.T2543G						.						135	125	128					1																	196274416		2203	4300	6503	SO:0001583	missense	343450	exon22			AATTGCATGAATC	BX647852, AY359444, AK127807	CCDS1384.1, CCDS72994.1, CCDS72995.1	1q31.3	2012-07-05			ENSG00000162687	ENSG00000162687		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18866	protein-coding gene	gene with protein product	"sodium and chloride activated ATP sensitive potassium channel"	610044				16382103	Standard	NM_198503		Approved	KCa4.2, SLICK, SLO2.1	uc001gtd.1	Q6UVM3	OTTHUMG00000035611	ENST00000294725.9:c.2543T>G	chr1.hg19:g.196274416A>C	ENSP00000294725:p.Met848Arg	113.0	0.0		167.0	58.0	NM_198503	Q3SY59|Q5VTN1|Q6ZMT3	Missense_Mutation	SNP	ENST00000294725.9	hg19	CCDS1384.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.975969	0.74360	.	.	ENSG00000162687	ENST00000367433;ENST00000367431;ENST00000294725	T;T;T	0.78707	-1.2;-1.2;-1.2	4.56	4.56	0.56223	.	0.000000	0.64402	D	0.000001	D	0.88142	0.6357	M	0.83953	2.67	0.80722	D	1	D;D;D;D;D	0.89917	0.999;1.0;1.0;0.999;0.999	D;D;D;D;D	0.78314	0.979;0.991;0.991;0.986;0.979	D	0.90114	0.4194	10	0.87932	D	0	-23.6099	14.3678	0.66817	1.0:0.0:0.0:0.0	.	848;806;824;774;848	A9LNM6;Q6UVM3-4;Q6UVM3-2;Q6UVM3-3;Q6UVM3	.;.;.;.;KCNT2_HUMAN	R	824;774;848	ENSP00000356403:M824R;ENSP00000356401:M774R;ENSP00000294725:M848R	ENSP00000294725:M848R	M	-	2	0	KCNT2	194541039	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.087000	0.94110	2.042000	0.60477	0.528000	0.53228	ATG	.	.		0.363	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503		C	196274416	A	C	196274416	3	2	242	1	0	0	0	0	1	0	0	0	8101	217	8	5	892	5	KCNT2	1	196274416	Missense_Mutation	SNP	A	TCGA-ED-A66Y-01A-11D-A30V-10	16458858	196274416	52976205	4	33338										
APOB	338	hgsc.bcm.edu	37	chr2	21249795	21249795	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	aatccttgcttcccaaaaagAgcttccaatgttggctcaaa	6	11	1	1			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr2:21249795A>G	ENST00000233242.1	-	15	2236	c.2109T>C	c.(2107-2109)gcT>gcC	p.A703A	APOB_ENST00000399256.4_Silent_p.A703A	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	703					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCCCAAAAAGAGCTTCCAATG	0.428																																					p.A703A		Atlas-SNP	.											.	APOB	761	.	0			c.T2109C						.						91	91	91					2																	21249795		2203	4300	6503	SO:0001819	synonymous_variant	338	exon15			AAAAAGAGCTTCC	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.2109T>C	chr2.hg19:g.21249795A>G		212.0	0.0		150.0	78.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Silent	SNP	ENST00000233242.1	hg19	CCDS1703.1																																																																																			.	.		0.428	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			G	21249795	A	G	21249795	2	3	242	1	0	0	0	0	0	0	0	1	785	291	11	2		2	APOB	2	21249795	Silent	SNP	A	TCGA-ED-A66Y-01A-11D-A30V-10		21249795	221949578	5	33339										
USP34	9736	hgsc.bcm.edu	37	chr2	61430400	61430400	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	cataaacgtcatctttgcccTgaaggttaaagatgataaaa	7	7	2	3			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr2:61430400T>G	ENST00000398571.2	-	75	9461		c.e75-2		RP11-493E12.2_ENST00000609422.1_RNA	NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34						positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			ATCTTTGCCCTGAAGGTTAAA	0.308																																					.		Atlas-SNP	.											.	USP34	334	.	0			c.9385-2A>C						.						91	82	84					2																	61430400		1837	4085	5922	SO:0001630	splice_region_variant	9736	exon76			TTGCCCTGAAGGT	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"Ubiquitin-specific peptidases"	20066	protein-coding gene	gene with protein product		615295	"ubiquitin specific protease 34"			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.9385-2A>C	chr2.hg19:g.61430400T>G		57.0	0.0		55.0	35.0	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Splice_Site	SNP	ENST00000398571.2	hg19	CCDS42686.1	.	.	.	.	.	.	.	.	.	.	T	16.32	3.090177	0.55968	.	.	ENSG00000115464	ENST00000263989;ENST00000398569;ENST00000398571	.	.	.	5.27	5.27	0.74061	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1912	0.73047	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	USP34	61283904	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.040000	0.89188	1.981000	0.57761	0.377000	0.23210	.	.	.		0.308	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4		Intron	G	61430400	T	G	61430400	5	3	242	1	0	0	0	0	0	0	1	0	17080	1594	55	5	1281	5	USP34	2	61430400	Splice_Site	SNP	T	TCGA-ED-A66Y-01A-11D-A30V-10	40180605	61430400	181768973	6	33340										
MPHOSPH10	10199	hgsc.bcm.edu	37	chr2	71360572	71360572	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	tcaaactctctgaaatggagGcctatttagaaaacatagaa	7	7	2	3			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr2:71360572G>T	ENST00000244230.2	+	2	986	c.634G>T	c.(634-636)Gcc>Tcc	p.A212S	MPHOSPH10_ENST00000498451.2_Missense_Mutation_p.A212S	NM_005791.2	NP_005782.1	O00566	MPP10_HUMAN	M-phase phosphoprotein 10 (U3 small nucleolar ribonucleoprotein)	212					negative regulation of phosphatase activity (GO:0010923)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|rRNA processing (GO:0006364)	chromosome (GO:0005694)|nucleolus (GO:0005730)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|pancreas(2)|skin(2)|stomach(1)	26						TGAAATGGAGGCCTATTTAGA	0.348																																					p.A212S		Atlas-SNP	.											.	MPHOSPH10	81	.	0			c.G634T						.						66	73	71					2																	71360572		2201	4300	6501	SO:0001583	missense	10199	exon2			ATGGAGGCCTATT	X98494	CCDS1916.1	2p13.3	2014-06-12			ENSG00000124383	ENSG00000124383			7213	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 106"	605503				8885239, 9450966	Standard	NM_005791		Approved	MPP10, MPP10P, CT90, PPP1R106	uc002sht.2	O00566	OTTHUMG00000129715	ENST00000244230.2:c.634G>T	chr2.hg19:g.71360572G>T	ENSP00000244230:p.Ala212Ser	278.0	0.0		161.0	91.0	NM_005791	A0AVJ8	Missense_Mutation	SNP	ENST00000244230.2	hg19	CCDS1916.1	.	.	.	.	.	.	.	.	.	.	G	9.315	1.056662	0.19907	.	.	ENSG00000124383	ENST00000244230;ENST00000425650	T;T	0.09723	2.95;2.95	5.04	-2.54	0.06307	.	0.633297	0.17067	N	0.188303	T	0.05960	0.0155	L	0.27053	0.805	0.30308	N	0.788775	B;B	0.15719	0.014;0.014	B;B	0.17979	0.016;0.02	T	0.28586	-1.0039	10	0.27785	T	0.31	.	6.6831	0.23131	0.2764:0.0:0.5691:0.1544	.	212;212	B3KPV5;O00566	.;MPP10_HUMAN	S	212;72	ENSP00000244230:A212S;ENSP00000393034:A72S	ENSP00000244230:A212S	A	+	1	0	MPHOSPH10	71214080	1.000000	0.71417	0.964000	0.40570	0.864000	0.49448	1.189000	0.32114	-0.026000	0.13895	0.484000	0.47621	GCC	.	.		0.348	MPHOSPH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251924.2	NM_005791		T	71360572	G	T	71360572	3	4	242	1	0	0	0	0	1	0	0	0	9734	1203	42	3	640	3	MPHOSPH10	2	71360572	Missense_Mutation	SNP	G	TCGA-ED-A66Y-01A-11D-A30V-10	9930172	71360572	171838801	7	33341										
SCN9A	6335	hgsc.bcm.edu	37	chr2	167149749	167149749	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	cttggtactcacctgttggtAaaggttttcccagtaatctt	8	9	2	0	rs200457046		TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr2:167149749A>T	ENST00000409435.1	-	8	1098	c.1099T>A	c.(1099-1101)Tac>Aac	p.Y367N	AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Missense_Mutation_p.Y368N|SCN9A_ENST00000375387.4_Missense_Mutation_p.Y368N|SCN9A_ENST00000409672.1_Missense_Mutation_p.Y367N			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	367					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	ACCTGTTGGTAAAGGTTTTCC	0.403																																					p.Y367N		Atlas-SNP	.											.	SCN9A	296	.	0			c.T1099A						.						35	36	36					2																	167149749		1938	4159	6097	SO:0001583	missense	6335	exon9			GTTGGTAAAGGTT	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10597	protein-coding gene	gene with protein product		603415	"sodium channel, voltage-gated, type IX, alpha polypeptide"			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.1099T>A	chr2.hg19:g.167149749A>T	ENSP00000386330:p.Tyr367Asn	96.0	0.0		85.0	30.0	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Missense_Mutation	SNP	ENST00000409435.1	hg19	CCDS46441.1	.	.	.	.	.	.	.	.	.	.	A	26.4	4.738741	0.89573	.	.	ENSG00000169432	ENST00000409672;ENST00000375387;ENST00000303354;ENST00000409435;ENST00000454569;ENST00000452182	D;D;D;D;D;D	0.98633	-5.04;-5.04;-5.04;-5.04;-5.04;-5.04	5.88	5.88	0.94601	Ion transport (1);	0.312551	0.27871	N	0.017511	D	0.99513	0.9826	H	0.97896	4.1	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.98045	1.0384	10	0.87932	D	0	.	16.275	0.82640	1.0:0.0:0.0:0.0	.	367;367;368	E7EUN6;Q15858;E9PF08	.;SCN9A_HUMAN;.	N	367;368;368;367;232;232	ENSP00000386306:Y367N;ENSP00000364536:Y368N;ENSP00000304748:Y368N;ENSP00000386330:Y367N;ENSP00000413212:Y232N;ENSP00000393141:Y232N	ENSP00000304748:Y368N	Y	-	1	0	SCN9A	166857995	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	9.331000	0.96430	2.248000	0.74166	0.477000	0.44152	TAC	.	.		0.403	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977		T	167149749	A	T	167149749	3	4	242	1	0	0	0	0	1	0	0	0	13940	362	13	4	4910	4	SCN9A	2	167149749	Missense_Mutation	SNP	A	TCGA-ED-A66Y-01A-11D-A30V-10	95789177	167149749	76049624	8	33342										
ARPC2	10109	hgsc.bcm.edu	37	chr2	219114171	219114171	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	ccgggactacctgcactaccAcatcaagtgctctaaggtga	9	13	2	1			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr2:219114171A>G	ENST00000295685.10	+	8	1022	c.761A>G	c.(760-762)cAc>cGc	p.H254R	ARPC2_ENST00000477992.1_3'UTR|ARPC2_ENST00000315717.5_Missense_Mutation_p.H254R	NM_005731.2	NP_005722.1	O15144	ARPC2_HUMAN	actin related protein 2/3 complex, subunit 2, 34kDa	254					Arp2/3 complex-mediated actin nucleation (GO:0034314)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural constituent of cytoskeleton (GO:0005200)			cervix(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)	6		Renal(207;0.0474)		Epithelial(149;1.21e-06)|all cancers(144;0.000212)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0103)		CTGCACTACCACATCAAGTGC	0.532																																					p.H254R		Atlas-SNP	.											.	ARPC2	25	.	0			c.A761G						.						141	105	118					2																	219114171		2203	4300	6503	SO:0001583	missense	10109	exon8			ACTACCACATCAA	AF006085	CCDS2410.1	2q36.1	2011-07-06	2002-08-29		ENSG00000163466	ENSG00000163466		"Actin related protein 2/3 complex subunits"	705	protein-coding gene	gene with protein product		604224	"actin related protein 2/3 complex, subunit 2 (34 kD)"			9359840, 9230079	Standard	NM_005731		Approved	p34-Arc, ARC34	uc002vhd.4	O15144	OTTHUMG00000133618	ENST00000295685.10:c.761A>G	chr2.hg19:g.219114171A>G	ENSP00000295685:p.His254Arg	55.0	0.0		45.0	18.0	NM_005731	Q92801|Q9P1D4	Missense_Mutation	SNP	ENST00000295685.10	hg19	CCDS2410.1	.	.	.	.	.	.	.	.	.	.	A	27.9	4.875975	0.91664	.	.	ENSG00000163466	ENST00000315717;ENST00000295685;ENST00000456575	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.87589	0.6215	H	0.95679	3.705	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91020	0.4856	9	0.87932	D	0	.	16.8222	0.85835	1.0:0.0:0.0:0.0	.	254	O15144	ARPC2_HUMAN	R	254;254;69	.	ENSP00000295685:H254R	H	+	2	0	ARPC2	218822416	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.297000	0.96120	2.371000	0.80710	0.533000	0.62120	CAC	.	.		0.532	ARPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256777.2	NM_005731		G	219114171	A	G	219114171	3	3	242	1	0	0	0	0	1	0	0	0	971	159	6	2	791	2	ARPC2	2	219114171	Missense_Mutation	SNP	A	TCGA-ED-A66Y-01A-11D-A30V-10	51964422	219114171	24085202	9	33343										
TRIP12	9320	hgsc.bcm.edu	37	chr2	230657707	230657707	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	acctctaactacaaggtatcTctcgatggcttgtaccaaag	7	11	2	0			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr2:230657707T>A	ENST00000283943.5	-	26	4076	c.3898A>T	c.(3898-3900)Aga>Tga	p.R1300*	TRIP12_ENST00000389045.3_Nonsense_Mutation_p.R1030*|TRIP12_ENST00000389044.4_Nonsense_Mutation_p.R1348*	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	1300					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		ACAAGGTATCTCTCGATGGCT	0.383																																					p.R1300X		Atlas-SNP	.											.	TRIP12	207	.	0			c.A3898T						.						106	100	102					2																	230657707		2203	4300	6503	SO:0001587	stop_gained	9320	exon26			GGTATCTCTCGAT	L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.3898A>T	chr2.hg19:g.230657707T>A	ENSP00000283943:p.Arg1300*	90.0	0.0		68.0	40.0	NM_004238	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Nonsense_Mutation	SNP	ENST00000283943.5	hg19	CCDS33391.1	.	.	.	.	.	.	.	.	.	.	T	45	11.751387	0.99599	.	.	ENSG00000153827	ENST00000283943;ENST00000389045;ENST00000389044	.	.	.	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.4378	0.50078	0.0:0.0:0.2765:0.7235	.	.	.	.	X	1300;1030;1348	.	ENSP00000283943:R1300X	R	-	1	2	TRIP12	230365951	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.039000	0.49791	2.157000	0.67596	0.528000	0.53228	AGA	.	.		0.383	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238		A	230657707	T	A	230657707	4	1	242	1	0	0	0	0	0	1	0	0	16571	1559	54	4	2144	4	TRIP12	2	230657707	Nonsense_Mutation	SNP	T	TCGA-ED-A66Y-01A-11D-A30V-10	11543536	230657707	12541666	10	33344										
TOP2B	7155	hgsc.bcm.edu	37	chr3	25654029	25654029	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	cttcttcttcagcaacttttTgctggcatctgccttcatag	6	12	5	0			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr3:25654029T>C	ENST00000264331.4	-	28	3762	c.3763A>G	c.(3763-3765)Aaa>Gaa	p.K1255E	TOP2B_ENST00000542520.1_Missense_Mutation_p.K107E|TOP2B_ENST00000540199.1_Missense_Mutation_p.K107E|TOP2B_ENST00000435706.2_Missense_Mutation_p.K1250E|TOP2B_ENST00000475717.1_5'Flank	NM_001068.2	NP_001059.2	Q02880	TOP2B_HUMAN	topoisomerase (DNA) II beta 180kDa	1255					ATP catabolic process (GO:0006200)|axonogenesis (GO:0007409)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|forebrain development (GO:0030900)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|neuron migration (GO:0001764)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein kinase C binding (GO:0005080)			breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|skin(2)|stomach(1)	36					Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Etoposide(DB00773)	AGCAACTTTTTGCTGGCATCT	0.348																																					p.K1250E		Atlas-SNP	.											.	TOP2B	98	.	0			c.A3748G						.						137	135	136					3																	25654029		1852	4086	5938	SO:0001583	missense	7155	exon28			ACTTTTTGCTGGC	X68060	CCDS46776.1	3p24.2	2012-08-30	2002-08-29		ENSG00000077097	ENSG00000077097	5.99.1.3		11990	protein-coding gene	gene with protein product		126431	"topoisomerase (DNA) II beta (180kD)"			1309226, 1333583	Standard	NM_001068		Approved		uc003cdj.3	Q02880	OTTHUMG00000155596	ENST00000264331.4:c.3763A>G	chr3.hg19:g.25654029T>C	ENSP00000264331:p.Lys1255Glu	43.0	0.0		48.0	28.0	NM_001068	Q13600|Q9UMG8|Q9UQP8	Missense_Mutation	SNP	ENST00000264331.4	hg19		.	.	.	.	.	.	.	.	.	.	T	16.75	3.210851	0.58343	.	.	ENSG00000077097	ENST00000542520;ENST00000435706;ENST00000264331;ENST00000540199	T;T;T;T	0.54675	0.56;0.86;0.85;0.56	6.16	6.16	0.99307	.	0.081183	0.85682	D	0.000000	T	0.51736	0.1692	M	0.66297	2.02	0.52099	D	0.99994	B;B	0.32918	0.27;0.39	B;B	0.36504	0.113;0.226	T	0.51260	-0.8728	10	0.05620	T	0.96	-15.984	16.8061	0.85666	0.0:0.0:0.0:1.0	.	1255;1250	Q02880;Q02880-2	TOP2B_HUMAN;.	E	107;1250;1255;107	ENSP00000446023:K107E;ENSP00000396704:K1250E;ENSP00000264331:K1255E;ENSP00000437352:K107E	ENSP00000264331:K1255E	K	-	1	0	TOP2B	25629033	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.576000	0.82467	2.367000	0.80283	0.528000	0.53228	AAA	.	.		0.348	TOP2B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding				C	25654029	T	C	25654029	3	2	242	1	0	0	0	0	1	0	0	0	16381	1821	63	2	1153	2	TOP2B	3	25654029	Missense_Mutation	SNP	T	TCGA-ED-A66Y-01A-11D-A30V-10		25654029	172368401	11	33345										
HEMK1	51409	hgsc.bcm.edu	37	chr3	50609148	50609148	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	tctgtggggacagtttcagaGcctgaggccggcactttgga	15	9	2	2			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr3:50609148G>A	ENST00000232854.4	+	3	788	c.236G>A	c.(235-237)aGc>aAc	p.S79N	HEMK1_ENST00000434410.1_Missense_Mutation_p.S79N|C3orf18_ENST00000449241.1_5'Flank|HEMK1_ENST00000455834.1_Missense_Mutation_p.S79N	NM_016173.3	NP_057257.1	Q9Y5R4	HEMK1_HUMAN	HemK methyltransferase family member 1	79					DNA methylation (GO:0006306)	mitochondrion (GO:0005739)	DNA binding (GO:0003677)|N-methyltransferase activity (GO:0008170)|protein methyltransferase activity (GO:0008276)			lung(3)	3				BRCA - Breast invasive adenocarcinoma(193;0.000283)|KIRC - Kidney renal clear cell carcinoma(197;0.0179)|Kidney(197;0.0212)		CAGTTTCAGAGCCTGAGGCCG	0.577											OREG0015589	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S79N		Atlas-SNP	.											.	HEMK1	17	.	0			c.G236A						.						114	124	121					3																	50609148		2203	4300	6503	SO:0001583	missense	51409	exon3			TTCAGAGCCTGAG	AF172244	CCDS2830.1	3p21	2008-02-05			ENSG00000114735	ENSG00000114735			24923	protein-coding gene	gene with protein product						10690633	Standard	XM_005265218		Approved	MTQ1	uc003dav.3	Q9Y5R4	OTTHUMG00000156849	ENST00000232854.4:c.236G>A	chr3.hg19:g.50609148G>A	ENSP00000232854:p.Ser79Asn	77.0	0.0	971	56.0	33.0	NM_016173		Missense_Mutation	SNP	ENST00000232854.4	hg19	CCDS2830.1	.	.	.	.	.	.	.	.	.	.	g	16.07	3.019096	0.54576	.	.	ENSG00000114735	ENST00000434410;ENST00000232854;ENST00000455834	T;T;T	0.13778	2.56;2.56;2.56	5.53	4.66	0.58398	.	0.112508	0.56097	N	0.000022	T	0.13286	0.0322	L	0.51422	1.61	0.35938	D	0.833036	P	0.39044	0.656	B	0.37387	0.248	T	0.21177	-1.0253	10	0.27785	T	0.31	-10.0777	10.6039	0.45384	0.0887:0.0:0.9113:0.0	.	79	Q9Y5R4	HEMK1_HUMAN	N	79	ENSP00000404843:S79N;ENSP00000232854:S79N;ENSP00000404334:S79N	ENSP00000232854:S79N	S	+	2	0	HEMK1	50584152	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.316000	0.51960	1.493000	0.48517	0.651000	0.88453	AGC	.	.		0.577	HEMK1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346231.1	NM_016173		A	50609148	G	A	50609148	3	1	242	1	0	0	0	0	1	0	0	0	7060	971	34	3	242	3	HEMK1	3	50609148	Missense_Mutation	SNP	G	TCGA-ED-A66Y-01A-11D-A30V-10	24955119	50609148	147413282	12	33346										
DNAH1	25981	hgsc.bcm.edu	37	chr3	52415808	52415809	+	Missense_Mutation	DNP	GG	GG	TC													0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	aatgcactcctgctgggcgtGggtggcagcggccgcagctc							TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr3:52415808_52415809GG>TC	ENST00000420323.2	+	49	8022_8023	c.7761_7762GG>TC	c.(7759-7764)gtGGgt>gtTCgt	p.G2588R		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	2588	AAA 4. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		TGCTGGGCGTGGGTGGCAGCGG	0.678																																					p.V2587V|p.G2588R		Atlas-SNP	.											.	DNAH1	534	.	0			c.G7761T|c.G7762C						.																																			SO:0001583	missense	25981	exon49			GGGCGTGGGTGGC|GGCGTGGGTGGCA	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	Exception_encountered	chr3.hg19:g.52415808_52415809delinsTC	ENSP00000401514:p.Gly2588Arg	112.0|110.0	0.0		78.0	23.0|24.0	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Silent|Missense_Mutation	SNP	ENST00000420323.2	hg19	CCDS46842.1																																																																																			.	.		0.678	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		TC	52415809	GG	TC	52415808	3	4	242	1	0	0	0	0	1	0	0	0	4599	1335	47	3	7951	3	DNAH1	3	52415808	Missense_Mutation	DNP	GG	TCGA-ED-A66Y-01A-11D-A30V-10	1806660	52415808	145606622	13	33347										
PHF7	51533	hgsc.bcm.edu	37	chr3	52448577	52448577	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	gggaatttcttcagaaagacAatatcagcgtgcattatttc	8	7	3	2			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr3:52448577A>G	ENST00000327906.3	+	4	820	c.160A>G	c.(160-162)Aat>Gat	p.N54D	PHF7_ENST00000482327.1_3'UTR|PHF7_ENST00000347025.2_Missense_Mutation_p.N54D	NM_016483.4	NP_057567.3	Q9BWX1	PHF7_HUMAN	PHD finger protein 7	54						Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			breast(2)|large_intestine(4)|lung(3)	9				BRCA - Breast invasive adenocarcinoma(193;1.71e-05)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)|OV - Ovarian serous cystadenocarcinoma(275;0.0275)		TCAGAAAGACAATATCAGCGT	0.428																																					p.N54D		Atlas-SNP	.											.	PHF7	29	.	0			c.A160G						.						129	129	129					3																	52448577		2203	4300	6503	SO:0001583	missense	51533	exon4			AAAGACAATATCA	AY014283	CCDS2854.1, CCDS2855.1	3p21.31	2013-01-28			ENSG00000010318	ENSG00000010318		"Zinc fingers, PHD-type"	18458	protein-coding gene	gene with protein product						11042152, 11829468	Standard	NM_016483		Approved	NYD-SP6, HSPC226	uc003ddy.3	Q9BWX1	OTTHUMG00000158495	ENST00000327906.3:c.160A>G	chr3.hg19:g.52448577A>G	ENSP00000333024:p.Asn54Asp	105.0	0.0		85.0	45.0	NM_016483	K4DI82	Missense_Mutation	SNP	ENST00000327906.3	hg19	CCDS2854.1	.	.	.	.	.	.	.	.	.	.	A	13.16	2.154905	0.38021	.	.	ENSG00000010318	ENST00000478707;ENST00000327906;ENST00000347025;ENST00000454052	D;D;D	0.92699	-2.11;-2.11;-3.09	5.45	1.58	0.23477	.	0.464026	0.25159	N	0.032681	D	0.85856	0.5794	L	0.43152	1.355	0.31581	N	0.655053	B;B	0.11235	0.004;0.004	B;B	0.06405	0.002;0.002	T	0.77253	-0.2656	10	0.34782	T	0.22	-12.5926	6.9802	0.24698	0.6934:0.0:0.3066:0.0	.	54;54	A8K856;Q9BWX1	.;PHF7_HUMAN	D	54;54;54;19	ENSP00000419316:N54D;ENSP00000333024:N54D;ENSP00000246282:N54D	ENSP00000333024:N54D	N	+	1	0	PHF7	52423617	0.905000	0.30787	0.992000	0.48379	0.922000	0.55478	0.501000	0.22578	0.025000	0.15241	0.460000	0.39030	AAT	.	.		0.428	PHF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351155.1	NM_016483		G	52448577	A	G	52448577	3	3	242	1	0	0	0	0	1	0	0	0	11848	130	5	2	170	2	PHF7	3	52448577	Missense_Mutation	SNP	A	TCGA-ED-A66Y-01A-11D-A30V-10	32769	52448577	145573853	14	33348										
FAM55C	91775	hgsc.bcm.edu	37	chr3	101520122	101520122	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	agccactttcatcgacagcaGtggacagtttgtttcctccc	8	13	1	0			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr3:101520122G>A	ENST00000491511.2	+	5	1093	c.137G>A	c.(136-138)aGt>aAt	p.S46N	NXPE3_ENST00000273347.5_Missense_Mutation_p.S46N|NXPE3_ENST00000422132.1_Missense_Mutation_p.S46N|NXPE3_ENST00000477909.1_Missense_Mutation_p.S46N	NM_001134456.1	NP_001127928.1	Q969Y0	NXPE3_HUMAN	neurexophilin and PC-esterase domain family, member 3	46						extracellular region (GO:0005576)											ATCGACAGCAGTGGACAGTTT	0.473																																					p.S46N		Atlas-SNP	.											.	.	.	.	0			c.G137A						.						137	134	135					3																	101520122		2203	4300	6503	SO:0001583	missense	91775	exon5			ACAGCAGTGGACA	AK054664	CCDS2945.1	3q12.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000144815	ENSG00000144815			28238	protein-coding gene	gene with protein product			"family with sequence similarity 55, member C"	FAM55C		12975309	Standard	NM_001134456		Approved	MGC15606	uc003dvn.3	Q969Y0	OTTHUMG00000159179	ENST00000491511.2:c.137G>A	chr3.hg19:g.101520122G>A	ENSP00000417485:p.Ser46Asn	229.0	0.0		180.0	51.0	NM_145037	A8K0X4|D3DN53|Q7Z2S8	Missense_Mutation	SNP	ENST00000491511.2	hg19	CCDS2945.1	.	.	.	.	.	.	.	.	.	.	G	11.94	1.789467	0.31685	.	.	ENSG00000144815	ENST00000273347;ENST00000474165;ENST00000491511;ENST00000477909;ENST00000422132	T;T;T;T	0.12255	2.7;2.7;2.7;2.7	5.82	4.94	0.65067	.	0.268626	0.43747	D	0.000540	T	0.07503	0.0189	N	0.14661	0.345	0.24627	N	0.993647	B	0.02656	0.0	B	0.04013	0.001	T	0.28964	-1.0027	10	0.28530	T	0.3	-6.0747	7.1937	0.25841	0.1042:0.3735:0.5223:0.0	.	46	Q969Y0	FA55C_HUMAN	N	46	ENSP00000273347:S46N;ENSP00000417485:S46N;ENSP00000418369:S46N;ENSP00000396421:S46N	ENSP00000273347:S46N	S	+	2	0	FAM55C	103002812	1.000000	0.71417	0.968000	0.41197	0.973000	0.67179	2.491000	0.45303	1.427000	0.47276	0.655000	0.94253	AGT	.	.		0.473	NXPE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353711.2	NM_145037		A	101520122	G	A	101520122	3	1	242	1	0	0	0	0	1	0	0	0	5594	1029	36	3	143	3	FAM55C	3	101520122	Missense_Mutation	SNP	G	TCGA-ED-A66Y-01A-11D-A30V-10	49071545	101520122	96502308	15	33349										
ARHGAP31	57514	hgsc.bcm.edu	37	chr3	119134792	119134792	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	ttctaagcctttccacaggtCaaggccaggaagacctcaga	9	12	3	2			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr3:119134792C>A	ENST00000264245.4	+	12	4548	c.4016C>A	c.(4015-4017)tCa>tAa	p.S1339*		NM_020754.2	NP_065805.2	Q2M1Z3	RHG31_HUMAN	Rho GTPase activating protein 31	1339					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(3)|large_intestine(11)|lung(29)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	67						TTCCACAGGTCAAGGCCAGGA	0.512																																					p.S1339X	Pancreas(7;176 297 5394 51128 51241)	Atlas-SNP	.											.	ARHGAP31	175	.	0			c.C4016A						.						106	110	109					3																	119134792		1931	4119	6050	SO:0001587	stop_gained	57514	exon12			ACAGGTCAAGGCC		CCDS43135.1	3q13.33	2011-06-29			ENSG00000031081	ENSG00000031081		"Rho GTPase activating proteins"	29216	protein-coding gene	gene with protein product		610911				9786927, 12819203, 16519628	Standard	NM_020754		Approved	CDGAP	uc003ecj.4	Q2M1Z3	OTTHUMG00000159362	ENST00000264245.4:c.4016C>A	chr3.hg19:g.119134792C>A	ENSP00000264245:p.Ser1339*	98.0	0.0		85.0	31.0	NM_020754	Q9ULL6	Nonsense_Mutation	SNP	ENST00000264245.4	hg19	CCDS43135.1	.	.	.	.	.	.	.	.	.	.	C	46	12.182408	0.99644	.	.	ENSG00000031081	ENST00000264245	.	.	.	5.74	5.74	0.90152	.	0.684343	0.13377	N	0.392473	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.2859	0.94069	0.0:1.0:0.0:0.0	.	.	.	.	X	1339	.	ENSP00000264245:S1339X	S	+	2	0	ARHGAP31	120617482	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	5.824000	0.69279	2.873000	0.98535	0.563000	0.77884	TCA	.	.		0.512	ARHGAP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354942.2			A	119134792	C	A	119134792	4	1	242	1	0	0	0	0	0	1	0	0	880	838	29	3	4062	3	ARHGAP31	3	119134792	Nonsense_Mutation	SNP	C	TCGA-ED-A66Y-01A-11D-A30V-10	17614670	119134792	78887638	16	33350										
MME	4311	hgsc.bcm.edu	37	chr3	154860094	154860094	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	cagcctcagccgaacctacaAggagtccagaaatgctttcc	8	14	1	1			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr3:154860094A>T	ENST00000460393.1	+	12	1283	c.1163A>T	c.(1162-1164)aAg>aTg	p.K388M	MME_ENST00000492661.1_Missense_Mutation_p.K388M|MME_ENST00000462745.1_Missense_Mutation_p.K388M|MME_ENST00000360490.2_Missense_Mutation_p.K388M|MME_ENST00000493237.1_Missense_Mutation_p.K388M	NM_000902.3|NM_007287.2	NP_000893.2|NP_009218.2	P08473	NEP_HUMAN	membrane metallo-endopeptidase	388					angiotensin maturation (GO:0002003)|beta-amyloid metabolic process (GO:0050435)|cellular protein metabolic process (GO:0044267)|cellular response to cytokine stimulus (GO:0071345)|cellular response to UV-A (GO:0071492)|cellular response to UV-B (GO:0071493)|creatinine metabolic process (GO:0046449)|kidney development (GO:0001822)|peptide metabolic process (GO:0006518)|proteolysis (GO:0006508)|replicative senescence (GO:0090399)|sensory perception of pain (GO:0019233)	axon (GO:0030424)|brush border (GO:0005903)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(31)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)|Liraglutide(DB06655)	CGAACCTACAAGGAGTCCAGA	0.388																																					p.K388M		Atlas-SNP	.											.	MME	133	.	0			c.A1163T						.						73	77	75					3																	154860094		2203	4300	6503	SO:0001583	missense	4311	exon12			CCTACAAGGAGTC		CCDS3172.1	3q25.2	2012-01-31	2007-02-21		ENSG00000196549	ENSG00000196549	3.4.24.11	"CD molecules"	7154	protein-coding gene	gene with protein product	"neutral endopeptidase", "enkephalinase", "neprilysin"	120520					Standard	NM_007287		Approved	CALLA, CD10, NEP	uc003fad.1	P08473	OTTHUMG00000158455	ENST00000460393.1:c.1163A>T	chr3.hg19:g.154860094A>T	ENSP00000418525:p.Lys388Met	129.0	0.0		96.0	26.0	NM_007287	A8K6U6|D3DNJ9|Q3MIX4	Missense_Mutation	SNP	ENST00000460393.1	hg19	CCDS3172.1	.	.	.	.	.	.	.	.	.	.	A	17.14	3.314176	0.60414	.	.	ENSG00000196549	ENST00000492661;ENST00000460393;ENST00000462745;ENST00000493237;ENST00000360490	T;T;T;T;T	0.75589	-0.95;-0.95;-0.95;-0.95;-0.95	5.93	4.74	0.60224	Peptidase M13 (1);Metallopeptidase, catalytic domain (1);	0.144335	0.64402	D	0.000007	D	0.84110	0.5400	M	0.68317	2.08	0.50467	D	0.99987	D	0.89917	1.0	D	0.91635	0.999	D	0.85170	0.0997	10	0.87932	D	0	-25.7891	13.1247	0.59346	0.8663:0.1337:0.0:0.0	.	388	P08473	NEP_HUMAN	M	388	ENSP00000420389:K388M;ENSP00000418525:K388M;ENSP00000419653:K388M;ENSP00000417079:K388M;ENSP00000353679:K388M	ENSP00000353679:K388M	K	+	2	0	MME	156342788	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.974000	0.63771	1.013000	0.39391	0.477000	0.44152	AAG	.	.		0.388	MME-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351076.1	NM_000902		T	154860094	A	T	154860094	3	4	242	1	0	0	0	0	1	0	0	0	9654	72	3	4	1205	4	MME	3	154860094	Missense_Mutation	SNP	A	TCGA-ED-A66Y-01A-11D-A30V-10	35725302	154860094	43162336	17	33351										
PAK2	5062	hgsc.bcm.edu	37	chr3	196509562	196509562	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	gataagcctccagcacctccTgtgcgaatgagcagcaccat	9	14	0	1			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr3:196509562T>C	ENST00000327134.3	+	2	367	c.45T>C	c.(43-45)ccT>ccC	p.P15P	RNU6-42P_ENST00000384165.1_RNA	NM_002577.4	NP_002568.2	Q13177	PAK2_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 2	15					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis (GO:2001271)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of defense response to virus by virus (GO:0050690)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activator activity (GO:0030296)			breast(1)|cervix(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)	12	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.07e-23)|all cancers(36;6.38e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00405)		CAGCACCTCCTGTGCGAATGA	0.428																																					p.P15P		Atlas-SNP	.											.	PAK2	113	.	0			c.T45C						.						114	119	118					3																	196509562		2203	4300	6503	SO:0001819	synonymous_variant	5062	exon2			ACCTCCTGTGCGA	U24153	CCDS3321.1	3q29	2008-06-17	2008-06-17			ENSG00000180370	2.7.11.1		8591	protein-coding gene	gene with protein product	"S6/H4 kinase"	605022	"p21 (CDKN1A)-activated kinase 2"			7744004, 7618083	Standard	NM_002577		Approved	PAK65, PAKgamma	uc003fwy.4	Q13177		ENST00000327134.3:c.45T>C	chr3.hg19:g.196509562T>C		212.0	0.0		200.0	9.0	NM_002577	Q13154|Q6ISC3	Silent	SNP	ENST00000327134.3	hg19	CCDS3321.1																																																																																			.	.		0.428	PAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340548.1	NM_002577		C	196509562	T	C	196509562	2	2	242	1	0	0	0	0	0	0	0	1	11410	1567	55	2		2	PAK2	3	196509562	Silent	SNP	T	TCGA-ED-A66Y-01A-11D-A30V-10	41649468	196509562	1512868	18	33352										
COPS4	51138	hgsc.bcm.edu	37	chr4	83984336	83984336	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	atctagataggatcatcagaGgaaatcaacttcaagaattt	7	6	5	3			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr4:83984336G>A	ENST00000264389.2	+	7	958	c.823G>A	c.(823-825)Gga>Aga	p.G275R	COPS4_ENST00000503682.1_Missense_Mutation_p.G275R|COPS4_ENST00000511653.1_Missense_Mutation_p.G275R|COPS4_ENST00000509093.1_Missense_Mutation_p.G275R	NM_016129.2	NP_057213.2	Q9BT78	CSN4_HUMAN	COP9 signalosome subunit 4	275	PCI.				cullin deneddylation (GO:0010388)|protein deneddylation (GO:0000338)	cell junction (GO:0030054)|COP9 signalosome (GO:0008180)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)				endometrium(2)|kidney(2)|large_intestine(3)|lung(4)|urinary_tract(2)	13		Hepatocellular(203;0.114)				GATCATCAGAGGAAATCAACT	0.423																																					p.G275R		Atlas-SNP	.											.	COPS4	31	.	0			c.G823A						.						90	87	88					4																	83984336		2203	4300	6503	SO:0001583	missense	51138	exon7			ATCAGAGGAAATC	AF100757	CCDS3600.1, CCDS58909.1	4q21.22	2013-03-14	2013-03-14		ENSG00000138663	ENSG00000138663			16702	protein-coding gene	gene with protein product			"COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 4", "COP9 constitutive photomorphogenic homolog subunit 4 (Arabidopsis)"			9707402	Standard	NM_016129		Approved	CSN4	uc003hoa.3	Q9BT78	OTTHUMG00000130298	ENST00000264389.2:c.823G>A	chr4.hg19:g.83984336G>A	ENSP00000264389:p.Gly275Arg	130.0	0.0		99.0	53.0	NM_016129	B3KN88|B3KST5|Q561W7|Q9NW31|Q9Y677	Missense_Mutation	SNP	ENST00000264389.2	hg19	CCDS3600.1	.	.	.	.	.	.	.	.	.	.	G	10.94	1.493629	0.26774	.	.	ENSG00000138663	ENST00000509093;ENST00000264389;ENST00000509317;ENST00000503682;ENST00000511653	T;T;T;T;T	0.26957	1.7;1.7;1.7;1.7;1.7	5.67	5.67	0.87782	Proteasome component (PCI) domain (1);	0.000000	0.85682	D	0.000000	T	0.06462	0.0166	N	0.00061	-2.33	0.80722	D	1	B;B;B;B	0.13145	0.007;0.004;0.002;0.0	B;B;B;B	0.12156	0.007;0.007;0.003;0.003	T	0.46205	-0.9208	10	0.13108	T	0.6	-21.6451	19.7712	0.96366	0.0:0.0:1.0:0.0	.	275;275;275;275	B3KST5;D6RFN0;D6RAX7;Q9BT78	.;.;.;CSN4_HUMAN	R	275;275;163;275;275	ENSP00000425976:G275R;ENSP00000264389:G275R;ENSP00000425486:G163R;ENSP00000424791:G275R;ENSP00000424655:G275R	ENSP00000264389:G275R	G	+	1	0	COPS4	84203360	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.733000	0.84916	2.677000	0.91161	0.585000	0.79938	GGA	.	.		0.423	COPS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252643.1			A	83984336	G	A	83984336	3	1	242	1	0	0	0	0	1	0	0	0	3737	1001	35	3	849	3	COPS4	4	83984336	Missense_Mutation	SNP	G	TCGA-ED-A66Y-01A-11D-A30V-10		83984336	107169940	19	33353										
KLHL2	11275	hgsc.bcm.edu	37	chr4	166238988	166238988	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	ttttttaaaggagtttgtgcAgttaatggtctgttatatgt	10	2	1	0			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr4:166238988A>G	ENST00000226725.6	+	14	1879	c.1620A>G	c.(1618-1620)gcA>gcG	p.A540A	KLHL2_ENST00000509028.1_3'UTR|KLHL2_ENST00000538127.1_Silent_p.A452A|KLHL2_ENST00000421009.2_Silent_p.A443A|KLHL2_ENST00000514860.1_Silent_p.A544A|KLHL2_ENST00000506761.1_Silent_p.A374A	NM_007246.3	NP_009177.3	O95198	KLHL2_HUMAN	kelch-like family member 2	540					protein ubiquitination (GO:0016567)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)	actin binding (GO:0003779)			endometrium(3)|large_intestine(5)|lung(4)|prostate(1)|urinary_tract(1)	14	all_hematologic(180;0.221)			GBM - Glioblastoma multiforme(119;2.94e-27)|COAD - Colon adenocarcinoma(41;1.4e-05)|Kidney(143;4.95e-05)|KIRC - Kidney renal clear cell carcinoma(143;0.000927)		GAGTTTGTGCAGTTAATGGTC	0.348																																					p.A544A		Atlas-SNP	.											.	KLHL2	42	.	0			c.A1632G						.						138	135	136					4																	166238988		2203	4300	6503	SO:0001819	synonymous_variant	11275	exon14			TTGTGCAGTTAAT	AF059569	CCDS34094.1, CCDS54815.1, CCDS54816.1	4q21.2	2013-01-30	2013-01-30		ENSG00000109466	ENSG00000109466		"Kelch-like", "BTB/POZ domain containing"	6353	protein-coding gene	gene with protein product	"mayven"	605774	"kelch (Drosophila)-like 2 (Mayven)", "kelch-like 2, Mayven (Drosophila)"			10397770, 16035103	Standard	NM_007246		Approved	MAV	uc011cjm.2	O95198	OTTHUMG00000161294	ENST00000226725.6:c.1620A>G	chr4.hg19:g.166238988A>G		134.0	0.0		95.0	33.0	NM_001161521	A6NCM7|B2RD18|B4DFH7|F5H6M3|Q8N484|Q8TBH5	Silent	SNP	ENST00000226725.6	hg19	CCDS34094.1																																																																																			.	.		0.348	KLHL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364439.1			G	166238988	A	G	166238988	2	3	242	1	0	0	0	0	0	0	0	1	8383	175	7	2		2	KLHL2	4	166238988	Silent	SNP	A	TCGA-ED-A66Y-01A-11D-A30V-10	82254652	166238988	24915288	20	33354										
TRIO	7204	hgsc.bcm.edu	37	chr5	14270940	14270940	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	cttctgtatttcagggtttcGaaaaaacgatgaaatgaaag	9	5	2	2			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr5:14270940G>A	ENST00000344204.4	+	2	188	c.164G>A	c.(163-165)cGa>cAa	p.R55Q	TRIO_ENST00000537187.1_Missense_Mutation_p.R55Q|TRIO_ENST00000509967.2_Missense_Mutation_p.R6Q	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	55					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118	Lung NSC(4;0.000742)					TCAGGGTTTCGAAAAAACGAT	0.353																																					p.R55Q		Atlas-SNP	.											.	TRIO	305	.	0			c.G164A						.						71	75	74					5																	14270940		2203	4300	6503	SO:0001583	missense	7204	exon2			GGTTTCGAAAAAA	AF091395	CCDS3883.1	5p14-p15.1	2013-01-11	2012-07-12		ENSG00000038382	ENSG00000038382		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing"	12303	protein-coding gene	gene with protein product		601893	"triple functional domain (PTPRF interacting)"			8643598	Standard	NM_007118		Approved	ARHGEF23	uc003jff.3	O75962	OTTHUMG00000131057	ENST00000344204.4:c.164G>A	chr5.hg19:g.14270940G>A	ENSP00000339299:p.Arg55Gln	85.0	0.0		70.0	43.0	NM_007118	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Missense_Mutation	SNP	ENST00000344204.4	hg19	CCDS3883.1	.	.	.	.	.	.	.	.	.	.	G	17.39	3.376758	0.61735	.	.	ENSG00000038382	ENST00000344204;ENST00000537187;ENST00000509967	T;T;T	0.64085	-0.08;-0.08;0.55	5.18	5.18	0.71444	.	0.000000	0.46758	D	0.000277	T	0.43433	0.1247	N	0.19112	0.55	0.41943	D	0.990624	P;P	0.43352	0.479;0.804	B;B	0.33392	0.07;0.163	T	0.43766	-0.9371	10	0.26408	T	0.33	.	15.9884	0.80179	0.0:0.0:1.0:0.0	.	6;55	F5H228;O75962	.;TRIO_HUMAN	Q	55;55;6	ENSP00000339299:R55Q;ENSP00000446348:R55Q;ENSP00000445592:R6Q	ENSP00000339299:R55Q	R	+	2	0	TRIO	14323940	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.456000	0.53000	2.576000	0.86940	0.655000	0.94253	CGA	.	.		0.353	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118		A	14270940	G	A	14270940	3	1	242	1	0	0	0	0	1	0	0	0	16567	1058	37	1	170	1	TRIO	5	14270940	Missense_Mutation	SNP	G	TCGA-ED-A66Y-01A-11D-A30V-10		14270940	166644320	21	33355										
MAP1B	4131	hgsc.bcm.edu	37	chr5	71493321	71493321	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	aagggcttcagtaagccccaTggatgagcccgtgcctgact	12	12	1	2			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr5:71493321T>A	ENST00000296755.7	+	5	4437	c.4139T>A	c.(4138-4140)aTg>aAg	p.M1380K		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1380					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		GTAAGCCCCATGGATGAGCCC	0.463																																					p.M1380K	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.T4139A						.						70	72	71					5																	71493321		2203	4300	6503	SO:0001583	missense	4131	exon5			GCCCCATGGATGA	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.4139T>A	chr5.hg19:g.71493321T>A	ENSP00000296755:p.Met1380Lys	108.0	0.0		134.0	50.0	NM_005909	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	hg19	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	T	10.96	1.497796	0.26861	.	.	ENSG00000131711	ENST00000296755	T	0.03330	3.97	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.09291	0.0229	N	0.24115	0.695	0.49299	D	0.999771	D;D	0.60160	0.987;0.987	D;D	0.66196	0.942;0.942	T	0.38929	-0.9638	10	0.41790	T	0.15	-24.5744	15.9994	0.80280	0.0:0.0:0.0:1.0	.	1254;1380	A2BDK6;P46821	.;MAP1B_HUMAN	K	1380	ENSP00000296755:M1380K	ENSP00000296755:M1380K	M	+	2	0	MAP1B	71529077	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	3.742000	0.55097	2.187000	0.69744	0.459000	0.35465	ATG	.	.		0.463	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		A	71493321	T	A	71493321	3	1	242	1	0	0	0	0	1	0	0	0	9237	1464	51	4	4157	4	MAP1B	5	71493321	Missense_Mutation	SNP	T	TCGA-ED-A66Y-01A-11D-A30V-10	57222381	71493321	109421939	22	33356										
ADAMTS19	171019	hgsc.bcm.edu	37	chr5	128887587	128887587	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	tgtgtgcacaaagatgaaccAtgtgatactgttggtaagtg	12	5	0	3			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr5:128887587A>C	ENST00000274487.4	+	7	1486	c.1341A>C	c.(1339-1341)ccA>ccC	p.P447P	CTC-575N7.1_ENST00000503616.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	447	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		AAGATGAACCATGTGATACTG	0.313																																					p.P447P		Atlas-SNP	.											.	ADAMTS19	216	.	0			c.A1341C						.						60	61	60					5																	128887587		2202	4291	6493	SO:0001819	synonymous_variant	171019	exon7			TGAACCATGTGAT	AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"ADAM metallopeptidases with thrombospondin type 1 motif"	17111	protein-coding gene	gene with protein product		607513	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.1341A>C	chr5.hg19:g.128887587A>C		76.0	0.0		105.0	36.0	NM_133638		Silent	SNP	ENST00000274487.4	hg19	CCDS4146.1																																																																																			.	.		0.313	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638		C	128887587	A	C	128887587	2	2	242	1	0	0	0	0	0	0	0	1	264	204	8	5		5	ADAMTS19	5	128887587	Silent	SNP	A	TCGA-ED-A66Y-01A-11D-A30V-10	57394266	128887587	52027673	23	33357										
IL4	3565	hgsc.bcm.edu	37	chr5	132009824	132009824	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	ttgtccacggacacaagtgcGatatcaccttacaggagatc	9	11	1	1			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr5:132009824G>C	ENST00000231449.2	+	1	147	c.82G>C	c.(82-84)Gat>Cat	p.D28H	IL4_ENST00000350025.2_Missense_Mutation_p.D28H	NM_000589.3	NP_000580.1	P05112	IL4_HUMAN	interleukin 4	28					B cell costimulation (GO:0031296)|B cell differentiation (GO:0030183)|cellular defense response (GO:0006968)|cellular response to mercury ion (GO:0071288)|chemotaxis (GO:0006935)|cholesterol metabolic process (GO:0008203)|connective tissue growth factor biosynthetic process (GO:0045189)|defense response to protozoan (GO:0042832)|dendritic cell differentiation (GO:0097028)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|female pregnancy (GO:0007565)|immune response (GO:0006955)|innate immune response in mucosa (GO:0002227)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of apoptotic process (GO:0043066)|negative regulation of chronic inflammatory response (GO:0002677)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of macrophage activation (GO:0043031)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of T-helper 17 cell differentiation (GO:2000320)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of isotype switching to IgE isotypes (GO:0048295)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|regulation of immune response (GO:0050776)|regulation of isotype switching (GO:0045191)|regulation of phosphorylation (GO:0042325)|regulation of proton transport (GO:0010155)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to nutrient (GO:0007584)|response to organic cyclic compound (GO:0014070)|T-helper 1 cell lineage commitment (GO:0002296)|T-helper 2 cell cytokine production (GO:0035745)|T-helper 2 cell differentiation (GO:0045064)|type 2 immune response (GO:0042092)	external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)|interleukin-4 receptor binding (GO:0005136)			NS(1)|large_intestine(3)|lung(3)|prostate(1)	8		all_cancers(142;2.81e-05)|all_lung(232;1.47e-05)|Lung NSC(810;2.31e-05)|all_neural(839;0.0459)|Ovarian(839;0.0481)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	GBM - Glioblastoma multiforme(465;0.00245)		ACACAAGTGCGATATCACCTT	0.498																																					p.D28H		Atlas-SNP	.											.	IL4	14	.	0			c.G82C						.						210	191	197					5																	132009824		2203	4300	6503	SO:0001583	missense	3565	exon1			AAGTGCGATATCA	M23442	CCDS4158.1, CCDS4159.1	5q23-q31	2011-07-14			ENSG00000113520	ENSG00000113520		"Interleukins and interleukin receptors"	6014	protein-coding gene	gene with protein product	"B_cell stimulatory factor 1", "lymphocyte stimulatory factor 1", "B cell growth factor 1"	147780				3016727	Standard	NM_000589		Approved	BSF1, IL-4, BCGF1, BCGF-1, MGC79402	uc003kxk.2	P05112	OTTHUMG00000059724	ENST00000231449.2:c.82G>C	chr5.hg19:g.132009824G>C	ENSP00000231449:p.Asp28His	63.0	0.0		66.0	30.0	NM_172348	Q14630|Q6NZ77	Missense_Mutation	SNP	ENST00000231449.2	hg19	CCDS4158.1	.	.	.	.	.	.	.	.	.	.	G	10.60	1.394897	0.25205	.	.	ENSG00000113520	ENST00000231449;ENST00000350025	T;T	0.51574	0.7;0.7	5.78	-6.56	0.01848	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	1.515320	0.03939	N	0.286609	T	0.36991	0.0987	L	0.42744	1.35	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.12156	0.007;0.007	T	0.29458	-1.0011	10	0.41790	T	0.15	0.0921	8.51	0.33211	0.3256:0.2684:0.406:0.0	.	28;28	Q5FC01;P05112	.;IL4_HUMAN	H	28	ENSP00000231449:D28H;ENSP00000325190:D28H	ENSP00000231449:D28H	D	+	1	0	IL4	132037723	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.029000	0.01430	-1.530000	0.01751	-0.795000	0.03280	GAT	.	.		0.498	IL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132786.1	NM_000589		C	132009824	G	C	132009824	3	2	242	1	0	0	0	0	1	0	0	0	7705	1058	37	4	84	4	IL4	5	132009824	Missense_Mutation	SNP	G	TCGA-ED-A66Y-01A-11D-A30V-10	3122237	132009824	48905436	24	33358										
PCDHA13	56136	hgsc.bcm.edu	37	chr5	140262349	140262349	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	atgcagatattggagtaaacTcggcattgacctaccgactg	10	9	0	2			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr5:140262349T>A	ENST00000289272.2	+	1	496	c.496T>A	c.(496-498)Tcg>Acg	p.S166T	PCDHA12_ENST00000398631.2_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA13_ENST00000409494.1_Missense_Mutation_p.S166T|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000527624.1_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	166	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|biliary_tract(2)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(18)|liver(3)|lung(23)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGAGTAAACTCGGCATTGAC	0.428																																					p.S166T	Melanoma(147;1739 1852 5500 27947 37288)	Atlas-SNP	.											.	PCDHA13	213	.	0			c.T496A						.						98	94	95					5																	140262349		2203	4300	6503	SO:0001583	missense	56136	exon1			GTAAACTCGGCAT	AF152478	CCDS4240.1	5q31	2010-11-26			ENSG00000239389	ENSG00000239389		"Cadherins / Protocadherins : Clustered"	8667	other	complex locus constituent	"KIAA0345-like 1", "ortholog of mouse CNR5"	606319		CNRS5		10380929, 10662547	Standard	NM_018904		Approved	CNR5, CRNR5, CNRN5, PCDH-ALPHA13		Q9Y5I0	OTTHUMG00000129614	ENST00000289272.2:c.496T>A	chr5.hg19:g.140262349T>A	ENSP00000289272:p.Ser166Thr	144.0	0.0		139.0	70.0	NM_031865	O75277	Missense_Mutation	SNP	ENST00000289272.2	hg19	CCDS4240.1	.	.	.	.	.	.	.	.	.	.	T	12.96	2.094321	0.36952	.	.	ENSG00000239389	ENST00000409494;ENST00000289272	T;T	0.39997	1.05;1.05	5.49	-5.76	0.02376	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.51873	0.1700	M	0.67397	2.05	0.09310	N	0.999999	B;B;P	0.35411	0.251;0.029;0.5	P;B;P	0.46076	0.486;0.202;0.503	T	0.61397	-0.7071	9	0.56958	D	0.05	.	19.8719	0.96853	0.0:0.0:0.6175:0.3825	.	166;166;166	Q9Y5I0;C9JA99;Q9Y5I0-2	PCDAD_HUMAN;.;.	T	166	ENSP00000386821:S166T;ENSP00000289272:S166T	ENSP00000289272:S166T	S	+	1	0	PCDHA13	140242533	0.000000	0.05858	0.002000	0.10522	0.915000	0.54546	-0.130000	0.10498	-0.589000	0.05874	0.402000	0.26972	TCG	.	.		0.428	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904		A	140262349	T	A	140262349	3	1	242	1	0	0	0	0	1	0	0	0	11532	1551	54	4	498	4	PCDHA13	5	140262349	Missense_Mutation	SNP	T	TCGA-ED-A66Y-01A-11D-A30V-10	8252525	140262349	40652911	25	33359										
PCDHGA10	56106	hgsc.bcm.edu	37	chr5	140794859	140794859	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	agcggtggccgcggtctcctGcgtcttcctggccttcgtca	13	15	3	0			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr5:140794859G>T	ENST00000398610.2	+	1	2117	c.2117G>T	c.(2116-2118)tGc>tTc	p.C706F	PCDHGA4_ENST00000571252.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB7_ENST00000398594.2_5'Flank|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA8_ENST00000398604.2_Intron	NM_018913.2|NM_032090.1	NP_061736.1|NP_114479.1	Q9Y5H3	PCDGA_HUMAN	protocadherin gamma subfamily A, 10	706					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGGTCTCCTGCGTCTTCCTG	0.642																																					p.C706F		Atlas-SNP	.											.	PCDHGA10	114	.	0			c.G2117T						.						70	81	77					5																	140794859		2203	4296	6499	SO:0001583	missense	56106	exon1			TCTCCTGCGTCTT		CCDS47292.1, CCDS75343.1	5q31	2010-01-26			ENSG00000253846	ENSG00000253846		"Cadherins / Protocadherins : Clustered"	8697	other	protocadherin		606297				10380929	Standard	NM_018913		Approved	PCDH-GAMMA-A10		Q9Y5H3	OTTHUMG00000163688	ENST00000398610.2:c.2117G>T	chr5.hg19:g.140794859G>T	ENSP00000381611:p.Cys706Phe	113.0	0.0		113.0	57.0	NM_032090	Q9Y5E0	Missense_Mutation	SNP	ENST00000398610.2	hg19	CCDS47292.1	.	.	.	.	.	.	.	.	.	.	g	2.026	-0.423484	0.04734	.	.	ENSG00000253846	ENST00000398610	T	0.09350	2.99	5.57	3.68	0.42216	.	.	.	.	.	T	0.12220	0.0297	L	0.58101	1.795	0.09310	N	1	P;B	0.38863	0.65;0.162	B;B	0.40636	0.335;0.066	T	0.12967	-1.0527	9	0.13470	T	0.59	.	8.6572	0.34071	0.0908:0.1666:0.7426:0.0	.	706;706	Q9Y5H3-2;Q9Y5H3	.;PCDGA_HUMAN	F	706	ENSP00000381611:C706F	ENSP00000381611:C706F	C	+	2	0	PCDHGA10	140775043	0.000000	0.05858	0.177000	0.23020	0.001000	0.01503	0.367000	0.20382	1.363000	0.46019	-0.136000	0.14681	TGC	.	.		0.642	PCDHGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374747.1	NM_018913		T	140794859	G	T	140794859	3	4	242	1	0	0	0	0	1	0	0	0	11560	1319	46	3	2119	3	PCDHGA10	5	140794859	Missense_Mutation	SNP	G	TCGA-ED-A66Y-01A-11D-A30V-10	532510	140794859	40120401	26	33360										
DBN1	1627	hgsc.bcm.edu	37	chr5	176899177	176899177	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	tccaggcctggctgctggccAgtgctgcagtaccatgccat	12	14	0	0			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr5:176899177A>G	ENST00000309007.5	-	1	306				DBN1_ENST00000393565.1_Intron|DBN1_ENST00000292385.5_Missense_Mutation_p.L12P	NM_004395.3	NP_004386	Q16643	DREB_HUMAN	drebrin 1						actin filament organization (GO:0007015)|cell communication by chemical coupling (GO:0010643)|cell communication by electrical coupling (GO:0010644)|maintenance of protein location in cell (GO:0032507)|neural precursor cell proliferation (GO:0061351)|regulation of dendrite development (GO:0050773)|regulation of neuronal synaptic plasticity (GO:0048168)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|gap junction (GO:0005921)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|profilin binding (GO:0005522)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(12)|ovary(1)|skin(2)	25	all_cancers(89;2.17e-05)|Renal(175;0.000269)|Lung NSC(126;0.0014)|all_lung(126;0.0025)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCTGCTGGCCAGTGCTGCAGT	0.657																																					p.L12P		Atlas-SNP	.											.	DBN1	122	.	0			c.T35C						.						58	54	55					5																	176899177		2203	4300	6503	SO:0001627	intron_variant	1627	exon2			CTGGCCAGTGCTG		CCDS4420.1, CCDS4421.1	5q35.3	2008-02-05			ENSG00000113758	ENSG00000113758			2695	protein-coding gene	gene with protein product		126660		D0S117E		8216329	Standard	NM_004395		Approved		uc003mgy.2	Q16643	OTTHUMG00000130856	ENST00000309007.5:c.86+1259T>C	chr5.hg19:g.176899177A>G		112.0	0.0		103.0	48.0	NM_080881	A8MV58|B2RBG0|Q9UFZ5	Missense_Mutation	SNP	ENST00000309007.5	hg19	CCDS4420.1	.	.	.	.	.	.	.	.	.	.	A	14.88	2.666158	0.47677	.	.	ENSG00000113758	ENST00000292385	T	0.34472	1.36	3.16	3.16	0.36331	.	.	.	.	.	T	0.50154	0.1599	.	.	.	0.80722	D	1	D	0.69078	0.997	D	0.78314	0.991	T	0.42464	-0.9450	8	0.29301	T	0.29	.	8.0882	0.30784	1.0:0.0:0.0:0.0	.	12	Q16643-2	.	P	12	ENSP00000292385:L12P	ENSP00000292385:L12P	L	-	2	0	DBN1	176831783	0.977000	0.34250	1.000000	0.80357	0.785000	0.44390	1.462000	0.35266	1.696000	0.51158	0.317000	0.21355	CTG	.	.		0.657	DBN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253429.2	NM_080881		G	176899177	A	G	176899177	1	3	242	0	1	0	0	0	0	0	0	0	4254	188	7	2		2	DBN1	5	176899177	Intron	SNP	A	TCGA-ED-A66Y-01A-11D-A30V-10	36104318	176899177	4016083	27	33361										
DNAH8	1769	hgsc.bcm.edu	37	chr6	38838323	38838323	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	attaaccatccaccctggaaCctgaaactcgtgcaggtaaa	7	12	0	1			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr6:38838323C>A	ENST00000359357.3	+	47	6578	c.6324C>A	c.(6322-6324)aaC>aaA	p.N2108K	DNAH8_ENST00000441566.1_Missense_Mutation_p.N2072K|DNAH8_ENST00000449981.2_Missense_Mutation_p.N2325K			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	2108	AAA 2. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						CACCCTGGAACCTGAAACTCG	0.378																																					p.N2325K		Atlas-SNP	.											.	DNAH8	1239	.	0			c.C6975A						.						54	52	53					6																	38838323		2203	4300	6503	SO:0001583	missense	1769	exon49			CTGGAACCTGAAA	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.6324C>A	chr6.hg19:g.38838323C>A	ENSP00000352312:p.Asn2108Lys	48.0	0.0		56.0	36.0	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	hg19		.	.	.	.	.	.	.	.	.	.	C	12.07	1.827304	0.32329	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.23754	1.93;1.92;1.89	5.87	-1.78	0.07957	.	0.100929	0.64402	D	0.000004	T	0.06234	0.0161	L	0.28400	0.85	0.41476	D	0.988135	B	0.13145	0.007	B	0.12156	0.007	T	0.20042	-1.0287	10	0.35671	T	0.21	.	8.8054	0.34934	0.0:0.4647:0.1061:0.4292	.	2108	Q96JB1	DYH8_HUMAN	K	2313;2313;2108;2072	ENSP00000333363:N2313K;ENSP00000352312:N2108K;ENSP00000402294:N2072K	ENSP00000333363:N2313K	N	+	3	2	DNAH8	38946301	0.878000	0.30173	0.993000	0.49108	0.988000	0.76386	-0.087000	0.11215	-0.281000	0.09141	0.655000	0.94253	AAC	.	.		0.378	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		A	38838323	C	A	38838323	3	1	242	1	0	0	0	0	1	0	0	0	4609	506	18	3	6502	3	DNAH8	6	38838323	Missense_Mutation	SNP	C	TCGA-ED-A66Y-01A-11D-A30V-10		38838323	132276744	28	33362										
KIAA1586	57691	hgsc.bcm.edu	37	chr6	56918222	56918222	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	agatatttaagaatattataGaagagaatgccaaaatctgt	7	3	1	4			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr6:56918222G>A	ENST00000370733.4	+	4	1132	c.925G>A	c.(925-927)Gaa>Aaa	p.E309K	KIAA1586_ENST00000545356.1_Missense_Mutation_p.E282K	NM_020931.2	NP_065982.1	Q9HCI6	K1586_HUMAN	KIAA1586	309							nucleic acid binding (GO:0003676)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|skin(1)	18	Lung NSC(77;0.0969)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			GAATATTATAGAAGAGAATGC	0.333																																					p.E309K		Atlas-SNP	.											.	KIAA1586	59	.	0			c.G925A						.						47	51	49					6																	56918222		2203	4296	6499	SO:0001583	missense	57691	exon4			ATTATAGAAGAGA	AB046806	CCDS34480.1, CCDS69138.1	6p12.1	2014-03-27			ENSG00000168116	ENSG00000168116			21360	protein-coding gene	gene with protein product						10997877	Standard	NM_001286274		Approved		uc003pdj.3	Q9HCI6	OTTHUMG00000014915	ENST00000370733.4:c.925G>A	chr6.hg19:g.56918222G>A	ENSP00000359768:p.Glu309Lys	127.0	0.0		78.0	44.0	NM_020931	A8K4M3|Q8IW25	Missense_Mutation	SNP	ENST00000370733.4	hg19	CCDS34480.1	.	.	.	.	.	.	.	.	.	.	g	12.31	1.900405	0.33535	.	.	ENSG00000168116	ENST00000370733;ENST00000545356	T;T	0.19250	2.16;2.16	3.41	3.41	0.39046	Ribonuclease H-like (1);	.	.	.	.	T	0.09949	0.0244	N	0.08118	0	0.25415	N	0.988322	D;D	0.67145	0.996;0.996	D;D	0.75484	0.986;0.986	T	0.12604	-1.0541	9	0.10902	T	0.67	-17.0673	10.5148	0.44883	0.0:0.0:1.0:0.0	.	282;309	F5H2N6;Q9HCI6	.;K1586_HUMAN	K	309;282	ENSP00000359768:E309K;ENSP00000445507:E282K	ENSP00000359768:E309K	E	+	1	0	KIAA1586	57026181	0.275000	0.24201	0.995000	0.50966	0.988000	0.76386	1.201000	0.32259	1.898000	0.54952	0.467000	0.42956	GAA	.	.		0.333	KIAA1586-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041033.1	NM_020931		A	56918222	G	A	56918222	3	1	242	1	0	0	0	0	1	0	0	0	8254	943	33	3	939	3	KIAA1586	6	56918222	Missense_Mutation	SNP	G	TCGA-ED-A66Y-01A-11D-A30V-10	18079899	56918222	114196845	29	33363										
EYS	346007	hgsc.bcm.edu	37	chr6	65767551	65767551	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	agaagtaattaccaggttggTcaatgcaggtggctccattt	11	7	1	1			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr6:65767551T>C	ENST00000370621.3	-	13	2619	c.2093A>G	c.(2092-2094)gAc>gGc	p.D698G	EYS_ENST00000503581.1_Missense_Mutation_p.D698G|EYS_ENST00000370616.2_Missense_Mutation_p.D698G			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	698	EGF-like 8; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						ACCAGGTTGGTCAATGCAGGT	0.368																																					p.D698G		Atlas-SNP	.											.	EYS	527	.	0			c.A2093G						.						219	176	189					6																	65767551		692	1591	2283	SO:0001583	missense	346007	exon13			GGTTGGTCAATGC		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.2093A>G	chr6.hg19:g.65767551T>C	ENSP00000359655:p.Asp698Gly	257.0	0.0		241.0	150.0	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	hg19		.	.	.	.	.	.	.	.	.	.	T	18.81	3.704042	0.68615	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	D;D;D	0.95554	-3.74;-3.74;-3.74	5.37	4.18	0.49190	.	.	.	.	.	D	0.97114	0.9057	M	0.88310	2.945	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.97095	0.9793	9	0.72032	D	0.01	.	10.2552	0.43392	0.1475:0.0:0.0:0.8525	.	698	Q5T1H1-1	.	G	698	ENSP00000424243:D698G;ENSP00000359655:D698G;ENSP00000359650:D698G	ENSP00000359650:D698G	D	-	2	0	EYS	65824272	1.000000	0.71417	0.858000	0.33744	0.700000	0.40528	4.392000	0.59659	0.838000	0.34948	0.482000	0.46254	GAC	.	.		0.368	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		C	65767551	T	C	65767551	3	2	242	1	0	0	0	0	1	0	0	0	5334	1667	58	2	7310	2	EYS	6	65767551	Missense_Mutation	SNP	T	TCGA-ED-A66Y-01A-11D-A30V-10	8849329	65767551	105347516	30	33364										
POPDC3	64208	hgsc.bcm.edu	37	chr6	105606476	105606476	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	tctttttcctatatatacccTgtcattcaaggcatagagtt	5	9	3	1			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr6:105606476T>C	ENST00000254765.3	-	4	1023	c.745A>G	c.(745-747)Agg>Ggg	p.R249G	BVES-AS1_ENST00000369120.2_RNA|BVES-AS1_ENST00000369122.3_RNA|BVES-AS1_ENST00000580854.1_RNA|BVES-AS1_ENST00000580511.1_RNA|POPDC3_ENST00000474760.1_5'UTR	NM_022361.4	NP_071756.2	Q9HBV1	POPD3_HUMAN	popeye domain containing 3	249					regulation of membrane potential (GO:0042391)	integral component of membrane (GO:0016021)				NS(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|skin(3)|urinary_tract(1)	26		all_cancers(87;4.87e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0157)|Colorectal(196;0.202)|Lung NSC(302;0.238)				ATATATACCCTGTCATTCAAG	0.398																																					p.R249G		Atlas-SNP	.											.	POPDC3	47	.	0			c.A745G						.						161	160	161					6																	105606476		2203	4300	6503	SO:0001583	missense	64208	exon4			ATACCCTGTCATT	BC022323	CCDS5052.1	6q21	2003-06-12			ENSG00000132429	ENSG00000132429			17649	protein-coding gene	gene with protein product		605824				10882522	Standard	NM_022361		Approved	POP3, MGC22671, bA355M14.1	uc003prb.3	Q9HBV1	OTTHUMG00000015293	ENST00000254765.3:c.745A>G	chr6.hg19:g.105606476T>C	ENSP00000254765:p.Arg249Gly	156.0	0.0		138.0	83.0	NM_022361	B2RA98|Q5T3Y8|Q8TBW6	Missense_Mutation	SNP	ENST00000254765.3	hg19	CCDS5052.1	.	.	.	.	.	.	.	.	.	.	T	17.51	3.407862	0.62399	.	.	ENSG00000132429	ENST00000254765;ENST00000429112	T;T	0.31510	1.49;1.49	5.99	5.99	0.97316	Cyclic nucleotide-binding-like (1);	0.047737	0.85682	D	0.000000	T	0.23846	0.0577	L	0.34521	1.04	0.45056	D	0.998073	P	0.48089	0.905	P	0.48598	0.583	T	0.02424	-1.1161	10	0.72032	D	0.01	-27.2323	16.4719	0.84113	0.0:0.0:0.0:1.0	.	249	Q9HBV1	POPD3_HUMAN	G	249;95	ENSP00000254765:R249G;ENSP00000414409:R95G	ENSP00000254765:R249G	R	-	1	2	POPDC3	105713169	1.000000	0.71417	0.989000	0.46669	0.623000	0.37688	3.882000	0.56160	2.292000	0.77174	0.482000	0.46254	AGG	.	.		0.398	POPDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041651.1	NM_022361		C	105606476	T	C	105606476	3	2	242	1	0	0	0	0	1	0	0	0	12265	1579	55	2	134	2	POPDC3	6	105606476	Missense_Mutation	SNP	T	TCGA-ED-A66Y-01A-11D-A30V-10	39838925	105606476	65508591	31	33365										
L3MBTL3	84456	hgsc.bcm.edu	37	chr6	130381199	130381199	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	agcatcaatcctttccatatAacaaaaatggattcaaagtt	4	8	2	0			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr6:130381199A>T	ENST00000529410.1	+	12	1257	c.778A>T	c.(778-780)Aac>Tac	p.N260Y	L3MBTL3_ENST00000361794.2_Missense_Mutation_p.N260Y|L3MBTL3_ENST00000526019.1_Missense_Mutation_p.N235Y|L3MBTL3_ENST00000368139.2_Missense_Mutation_p.N235Y|L3MBTL3_ENST00000368136.2_Missense_Mutation_p.N260Y|L3MBTL3_ENST00000533560.1_Missense_Mutation_p.N235Y			Q96JM7	LMBL3_HUMAN	l(3)mbt-like 3 (Drosophila)	260					chromatin modification (GO:0016568)|erythrocyte maturation (GO:0043249)|granulocyte differentiation (GO:0030851)|macrophage differentiation (GO:0030225)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				cervix(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|skin(4)|stomach(1)|urinary_tract(1)	43				GBM - Glioblastoma multiforme(226;0.0266)|OV - Ovarian serous cystadenocarcinoma(155;0.154)		CTTTCCATATAACAAAAATGG	0.388																																					p.N260Y		Atlas-SNP	.											.	L3MBTL3	99	.	0			c.A778T						.						111	101	104					6																	130381199		2203	4300	6503	SO:0001583	missense	84456	exon10			CCATATAACAAAA	AB058701	CCDS34537.1, CCDS34538.1	6q23	2013-01-10			ENSG00000198945	ENSG00000198945		"Sterile alpha motif (SAM) domain containing"	23035	protein-coding gene	gene with protein product							Standard	NM_032438		Approved	KIAA1798	uc003qbt.3	Q96JM7	OTTHUMG00000015554	ENST00000529410.1:c.778A>T	chr6.hg19:g.130381199A>T	ENSP00000431962:p.Asn260Tyr	135.0	0.0		96.0	24.0	NM_032438	Q4VXE1|Q5VUM9|Q6P9B5	Missense_Mutation	SNP	ENST00000529410.1	hg19	CCDS34537.1	.	.	.	.	.	.	.	.	.	.	A	11.23	1.578220	0.28180	.	.	ENSG00000198945	ENST00000529410;ENST00000533560;ENST00000361794;ENST00000368139;ENST00000526019;ENST00000368136	D;D;D;D;D;D	0.85258	-1.96;-1.96;-1.96;-1.96;-1.96;-1.96	5.27	5.27	0.74061	.	0.148216	0.64402	D	0.000011	T	0.77942	0.4206	L	0.43923	1.385	0.45307	D	0.998302	D;B	0.69078	0.997;0.128	P;B	0.60609	0.877;0.029	T	0.78780	-0.2070	10	0.02654	T	1	.	10.6949	0.45892	0.8575:0.0:0.0:0.1425	.	235;260	Q96JM7-2;Q96JM7	.;LMBL3_HUMAN	Y	260;235;260;235;235;260	ENSP00000431962:N260Y;ENSP00000437185:N235Y;ENSP00000354526:N260Y;ENSP00000357121:N235Y;ENSP00000436706:N235Y;ENSP00000357118:N260Y	ENSP00000354526:N260Y	N	+	1	0	L3MBTL3	130422892	0.997000	0.39634	1.000000	0.80357	0.719000	0.41307	2.669000	0.46825	2.121000	0.65114	0.374000	0.22700	AAC	.	.		0.388	L3MBTL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042195.2	XM_027074		T	130381199	A	T	130381199	3	4	242	1	0	0	0	0	1	0	0	0	8602	362	13	4	808	4	L3MBTL3	6	130381199	Missense_Mutation	SNP	A	TCGA-ED-A66Y-01A-11D-A30V-10	24774723	130381199	40733868	32	33366										
ABCB5	340273	hgsc.bcm.edu	37	chr7	20785063	20785063	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	tattgaaggtctccctgaggTaagaaaatttctgaaatctt	8	6	3	4	rs373651350		TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr7:20785063T>A	ENST00000404938.2	+	26	4081		c.e26+2		ABCB5_ENST00000258738.6_Splice_Site	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5						antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (GO:0002485)|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO:0002489)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|cell differentiation (GO:0030154)|compound eye corneal lens development (GO:0048058)|positive regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002591)|regulation of membrane potential (GO:0042391)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|efflux transmembrane transporter activity (GO:0015562)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(1)|pancreas(1)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)	77						CTCCCTGAGGTAAGAAAATTT	0.393																																					.		Atlas-SNP	.											.	ABCB5	357	.	0			c.3429+2T>A						.						41	39	39					7																	20785063		2203	4300	6503	SO:0001630	splice_region_variant	340273	exon26			CTGAGGTAAGAAA	U66692	CCDS5371.1, CCDS55090.1, CCDS55091.1, CCDS55092.1	7p14	2012-03-14			ENSG00000004846	ENSG00000004846		"ATP binding cassette transporters / subfamily B"	46	protein-coding gene	gene with protein product	"P-glycoprotein ABCB5", "ATP-binding cassette protein"	611785				8894702, 12960149	Standard	NM_001163942		Approved	EST422562, ABCB5beta, ABCB5alpha	uc010kuh.3	Q2M3G0	OTTHUMG00000094789	ENST00000404938.2:c.3429+2T>A	chr7.hg19:g.20785063T>A		64.0	0.0		72.0	37.0	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Splice_Site	SNP	ENST00000404938.2	hg19	CCDS55090.1	.	.	.	.	.	.	.	.	.	.	T	19.46	3.832276	0.71258	.	.	ENSG00000004846	ENST00000404938;ENST00000258738	.	.	.	5.08	3.85	0.44370	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.8378	0.46698	0.1411:0.0:0.0:0.8589	.	.	.	.	.	-1	.	.	.	+	.	.	ABCB5	20751588	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.108000	0.71522	2.024000	0.59613	0.533000	0.62120	.	.	.		0.393	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559	Intron	A	20785063	T	A	20785063	5	1	242	1	0	0	0	0	0	0	1	0	44	1652	57	4	3570	4	ABCB5	7	20785063	Splice_Site	SNP	T	TCGA-ED-A66Y-01A-11D-A30V-10		20785063	138353600	33	33367										
HNRNPA2B1	3181	hgsc.bcm.edu	37	chr7	26233251	26233251	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	caccctggttgccatatccaGgtcctccaccaccatatcct	5	18	0	0			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr7:26233251G>T	ENST00000354667.4	-	9	989	c.821C>A	c.(820-822)cCt>cAt	p.P274H	HNRNPA2B1_ENST00000356674.7_Missense_Mutation_p.P262H|HNRNPA2B1_ENST00000476233.1_5'Flank	NM_031243.2	NP_112533.1	P22626	ROA2_HUMAN	heterogeneous nuclear ribonucleoprotein A2/B1	274	Gly-rich.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|RNA splicing (GO:0008380)|RNA transport (GO:0050658)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA intronic binding (GO:0097157)|RNA binding (GO:0003723)|single-stranded telomeric DNA binding (GO:0043047)		HNRNPA2B1/ETV1(8)	breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	22						GCCATATCCAGGTCCTCCACC	0.438			T	ETV1	prostate																																p.P274H		Atlas-SNP	.		Dom	yes		7	7p15	3181	heterogeneous nuclear ribonucleoprotein A2/B1		E	.	HNRNPA2B1	70	.	0			c.C821A						.						105	103	104					7																	26233251		2203	4300	6503	SO:0001583	missense	3181	exon9			TATCCAGGTCCTC	D28877	CCDS5397.1, CCDS43557.1	7p15	2013-02-12		2007-08-16	ENSG00000122566	ENSG00000122566		"RNA binding motif (RRM) containing"	5033	protein-coding gene	gene with protein product		600124		HNRPA2B1		8029005	Standard	NM_002137		Approved		uc003sxr.4	P22626	OTTHUMG00000023471	ENST00000354667.4:c.821C>A	chr7.hg19:g.26233251G>T	ENSP00000346694:p.Pro274His	78.0	0.0		82.0	5.0	NM_031243	A8K064|P22627|Q9UC98|Q9UDJ2	Missense_Mutation	SNP	ENST00000354667.4	hg19	CCDS43557.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.44|11.44	1.639486|1.639486	0.29157|0.29157	.|.	.|.	ENSG00000122566|ENSG00000122566	ENST00000409814|ENST00000354667;ENST00000356674	.|D;D	.|0.85556	.|-2.0;-2.0	5.94|5.94	5.94|5.94	0.96194|0.96194	.|.	.|0.000000	.|0.64402	.|D	.|0.000002	T|T	0.80670|0.80670	0.4667|0.4667	L|L	0.34521|0.34521	1.04|1.04	0.38441|0.38441	D|D	0.9467|0.9467	.|B;B	.|0.13594	.|0.008;0.005	.|B;B	.|0.13407	.|0.004;0.009	T|T	0.74210|0.74210	-0.3739|-0.3739	6|10	0.45353|0.30078	T|T	0.12|0.28	.|.	19.9542|19.9542	0.97213|0.97213	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|262;274	.|P22626-2;P22626	.|.;ROA2_HUMAN	M|H	208|274;262	.|ENSP00000346694:P274H;ENSP00000349101:P262H	ENSP00000386735:L208M|ENSP00000346694:P274H	L|P	-|-	1|2	2|0	HNRNPA2B1|HNRNPA2B1	26199776|26199776	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.786000|0.786000	0.44442|0.44442	5.168000|5.168000	0.64978|0.64978	2.816000|2.816000	0.96949|0.96949	0.561000|0.561000	0.74099|0.74099	CTG|CCT	.	.		0.438	HNRNPA2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214109.1	NM_002137		T	26233251	G	T	26233251	3	4	242	1	0	0	0	0	1	0	0	0	7268	1000	35	3	252	3	HNRNPA2B1	7	26233251	Missense_Mutation	SNP	G	TCGA-ED-A66Y-01A-11D-A30V-10	5448188	26233251	132905412	34	33368										
PDE1C	5137	hgsc.bcm.edu	37	chr7	31918700	31918700	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	gagcatcatccccatctgccGcgtgaaggtggaggccagcc	13	14	2	1			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr7:31918700G>A	ENST00000396191.1	-	4	789	c.334C>T	c.(334-336)Cgg>Tgg	p.R112W	PDE1C_ENST00000396182.2_Missense_Mutation_p.R112W|PDE1C_ENST00000321453.7_Missense_Mutation_p.R112W|PDE1C_ENST00000396184.3_Missense_Mutation_p.R112W|PDE1C_ENST00000396193.1_Missense_Mutation_p.R172W	NM_001191057.1	NP_001177986.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	112					activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)	cytosol (GO:0005829)	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	81			GBM - Glioblastoma multiforme(11;0.216)		Caffeine(DB00201)	CCCATCTGCCGCGTGAAGGTG	0.557																																					p.R172W		Atlas-SNP	.											PDE1C_ENST00000396193,NS,carcinoma,0,3	PDE1C	465	.	0			c.C514T						.						103	92	96					7																	31918700		2203	4300	6503	SO:0001583	missense	5137	exon5			TCTGCCGCGTGAA	U40371	CCDS5437.1, CCDS55099.1, CCDS55100.1	7p15.1-p14.3	2008-05-15	2002-08-29		ENSG00000154678	ENSG00000154678	3.1.4.17	"Phosphodiesterases"	8776	protein-coding gene	gene with protein product		602987	"phosphodiesterase 1C, calmodulin-dependent (70kD)"			8557689	Standard	XM_005249769		Approved	Hcam3	uc003tco.2	Q14123	OTTHUMG00000023836	ENST00000396191.1:c.334C>T	chr7.hg19:g.31918700G>A	ENSP00000379494:p.Arg112Trp	42.0	0.0		50.0	23.0	NM_001191058	B3KPC6|E9PE92|Q14124|Q8NB10	Missense_Mutation	SNP	ENST00000396191.1	hg19	CCDS55099.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.060875	0.76074	.	.	ENSG00000154678	ENST00000396193;ENST00000396191;ENST00000321453;ENST00000396184;ENST00000396182	T;T;T;T;T	0.76316	-0.99;-1.01;-1.01;-0.96;-0.96	5.72	1.46	0.22682	-cyclic nucleotide phosphodiesterase N-terminal (1);5&apos (1);3&apos (1);	0.063961	0.64402	D	0.000006	D	0.87366	0.6159	M	0.82056	2.57	0.58432	D	0.999997	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.996	D	0.88426	0.3032	10	0.87932	D	0	.	15.0182	0.71605	0.0:0.0:0.4909:0.5091	.	112;172;112	Q14123-2;E9PE92;Q14123	.;.;PDE1C_HUMAN	W	172;112;112;112;112	ENSP00000379496:R172W;ENSP00000379494:R112W;ENSP00000318105:R112W;ENSP00000379487:R112W;ENSP00000379485:R112W	ENSP00000318105:R112W	R	-	1	2	PDE1C	31885225	0.728000	0.28080	0.367000	0.25926	0.870000	0.49936	0.908000	0.28545	0.260000	0.21731	0.655000	0.94253	CGG	.	.		0.557	PDE1C-006	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328458.1			A	31918700	G	A	31918700	3	1	242	1	0	0	0	0	1	0	0	0	11644	1086	38	1	1626	1	PDE1C	7	31918700	Missense_Mutation	SNP	G	TCGA-ED-A66Y-01A-11D-A30V-10	5685449	31918700	127219963	35	33369										
CDHR3	222256	hgsc.bcm.edu	37	chr7	105662822	105662822	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	aagaaagcggaggctcttgtTgagacaggaacagtgacact	13	7	1	3			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr7:105662822T>C	ENST00000317716.9	+	14	2084	c.2004T>C	c.(2002-2004)gtT>gtC	p.V668V	CDHR3_ENST00000542731.1_Silent_p.V668V|CDHR3_ENST00000478080.1_Silent_p.V580V|CDHR3_ENST00000343407.5_Intron|CDHR3_ENST00000470188.1_Intron	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	668	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						AGGCTCTTGTTGAGACAGGAA	0.483																																					p.V668V		Atlas-SNP	.											.	CDHR3	153	.	0			c.T2004C						.						206	196	200					7																	105662822		1994	4174	6168	SO:0001819	synonymous_variant	222256	exon14			TCTTGTTGAGACA	AK126338	CCDS47684.1, CCDS75651.1	7q22.2	2011-07-01			ENSG00000128536	ENSG00000128536		"Cadherins / Cadherin-related"	26308	protein-coding gene	gene with protein product		615610					Standard	NM_152750		Approved	FLJ44366, FLJ23834, CDH28	uc003vdl.4	Q6ZTQ4	OTTHUMG00000157520	ENST00000317716.9:c.2004T>C	chr7.hg19:g.105662822T>C		203.0	0.0		189.0	87.0	NM_152750	Q8TCI7	Silent	SNP	ENST00000317716.9	hg19	CCDS47684.1	.	.	.	.	.	.	.	.	.	.	T	6.894	0.534379	0.13188	.	.	ENSG00000128536	ENST00000468477	.	.	.	5.39	1.27	0.21489	.	.	.	.	.	T	0.66015	0.2747	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63111	-0.6710	4	.	.	.	-7.3726	12.8312	0.57746	0.0:0.0:0.3901:0.6099	.	.	.	.	S	137	.	.	L	+	2	0	CDHR3	105450058	0.993000	0.37304	1.000000	0.80357	0.575000	0.36095	0.363000	0.20301	0.393000	0.25203	0.533000	0.62120	TTG	.	.		0.483	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	NM_152750		C	105662822	T	C	105662822	2	2	242	1	0	0	0	0	0	0	0	1	3122	1799	63	2		2	CDHR3	7	105662822	Silent	SNP	T	TCGA-ED-A66Y-01A-11D-A30V-10	73744122	105662822	53475841	36	33370										
ASAH1	427	hgsc.bcm.edu	37	chr8	17921966	17921967	+	Splice_Site	INS	-	-	T													0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	tccctcagcgcacaattaccINSttttttgtcttctgctacta					rs200455852		TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr8:17921966_17921967insT	ENST00000262097.6	-	6	767_768	c.456_457insA	c.(454-459)aaaggt>aaaAggt	p.G153fs	ASAH1_ENST00000314146.10_Splice_Site_p.G147fs|ASAH1_ENST00000520781.1_Intron|ASAH1_ENST00000417108.2_Intron|ASAH1_ENST00000381733.4_Splice_Site_p.G169fs	NM_177924.3	NP_808592.2	Q13510	ASAH1_HUMAN	N-acylsphingosine amidohydrolase (acid ceramidase) 1	153					cell death (GO:0008219)|ceramide metabolic process (GO:0006672)|glycosphingolipid metabolic process (GO:0006687)|lung development (GO:0030324)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	catalytic activity (GO:0003824)|ceramidase activity (GO:0017040)			breast(1)|endometrium(2)|large_intestine(4)|lung(2)	9				Colorectal(111;0.0646)|COAD - Colon adenocarcinoma(73;0.228)		GCACAATTACCTTTTTTGTCTT	0.312																																					p.G169fs		Atlas-Indel,Pindel	.											.	ASAH1	71	.	0			c.505_506insA						.																																			SO:0001630	splice_region_variant	427	exon6			.	U70063	CCDS6005.1, CCDS6006.1, CCDS47813.1	8p22	2007-03-27	2002-09-11	2002-09-13	ENSG00000104763	ENSG00000104763			735	protein-coding gene	gene with protein product		613468	"N-acylsphingosine amidohydrolase (acid ceramidase)"	ASAH		8955159, 10610716	Standard	NM_004315		Approved	AC, PHP32, FLJ21558	uc003wyn.2	Q13510	OTTHUMG00000096997	ENST00000262097.6:c.457+1->A	chr8.hg19:g.17921972_17921972dupT		68.0	0.0		45.0	18.0	NM_004315	E9PDS0|Q6W898|Q96AS2	Frame_Shift_Ins	INS	ENST00000262097.6	hg19	CCDS6006.1																																																																																			.	.		0.312	ASAH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214077.2	NM_004315	Frame_Shift_Ins	T	17921967	-	T	17921966	8	5	242	1	0	1	1	0	0	0	1	0	1006	695	24	0	766	0	ASAH1	8	17921966	Splice_Site	INS	-	TCGA-ED-A66Y-01A-11D-A30V-10		17921966	128442056	37	33371										
KCNU1	157855	hgsc.bcm.edu	37	chr8	36788612	36788612	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	ctcttgtctggaagaaaccgGtgtaagctggggcttctgtc	13	9	3	1			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr8:36788612G>T	ENST00000399881.3	+	25	2917	c.2880G>T	c.(2878-2880)cgG>cgT	p.R960R	KCNU1_ENST00000518904.1_3'UTR	NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	960					multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		GAAGAAACCGGTGTAAGCTGG	0.433																																					p.R960R		Atlas-SNP	.											.	KCNU1	359	.	0			c.G2880T						.						139	134	136					8																	36788612		1901	4119	6020	SO:0001819	synonymous_variant	157855	exon25			AAACCGGTGTAAG	BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.2880G>T	chr8.hg19:g.36788612G>T		146.0	0.0		149.0	63.0	NM_001031836		Silent	SNP	ENST00000399881.3	hg19	CCDS55220.1																																																																																			.	.		0.433	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836		T	36788612	G	T	36788612	2	4	242	1	0	0	0	0	0	0	0	1	8102	1248	44	3		3	KCNU1	8	36788612	Silent	SNP	G	TCGA-ED-A66Y-01A-11D-A30V-10	18866646	36788612	109575410	38	33372										
KIAA2026	158358	hgsc.bcm.edu	37	chr9	5968170	5968170	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	tctttcaatttcttttttttCtttttcttcttttttgccct	1	9	6	0			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr9:5968170C>A	ENST00000399933.3	-	3	2060	c.2061G>T	c.(2059-2061)aaG>aaT	p.K687N	KIAA2026_ENST00000381461.2_Missense_Mutation_p.K687N	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	687	Lys-rich.									breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		TCTTTTTTTTCTTTTTCTTCT	0.343																																					p.K687N		Atlas-SNP	.											.	KIAA2026	231	.	0			c.G2061T						.						48	44	45					9																	5968170		1811	4073	5884	SO:0001583	missense	158358	exon3			TTTTTTCTTTTTC	AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.2061G>T	chr9.hg19:g.5968170C>A	ENSP00000382815:p.Lys687Asn	89.0	0.0		76.0	37.0	NM_001017969	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Missense_Mutation	SNP	ENST00000399933.3	hg19		.	.	.	.	.	.	.	.	.	.	C	14.22	2.469582	0.43839	.	.	ENSG00000183354	ENST00000399933;ENST00000381461	.	.	.	5.88	4.05	0.47172	.	0.000000	0.51477	U	0.000095	T	0.49847	0.1581	L	0.32530	0.975	0.27743	N	0.944402	D	0.89917	1.0	D	0.74348	0.983	T	0.42932	-0.9422	9	0.87932	D	0	.	9.8146	0.40844	0.0:0.7915:0.0:0.2085	.	687	Q5HYC2	K2026_HUMAN	N	687	.	ENSP00000370870:K687N	K	-	3	2	KIAA2026	5958170	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.967000	0.40491	0.839000	0.34971	0.491000	0.48974	AAG	.	.		0.343	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969		A	5968170	C	A	5968170	3	1	242	1	0	0	0	0	1	0	0	0	8279	912	32	3	4274	3	KIAA2026	9	5968170	Missense_Mutation	SNP	C	TCGA-ED-A66Y-01A-11D-A30V-10		5968170	135245261	39	33373										
RG9MTD3	158234	hgsc.bcm.edu	37	chr9	37762014	37762014	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	catcctagaggagacaggtgAagatggacttcctgaaggct	13	8	0	5			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr9:37762014A>C	ENST00000297994.3	+	2	151	c.86A>C	c.(85-87)gAa>gCa	p.E29A	TRMT10B_ENST00000537911.1_Missense_Mutation_p.E29A|TRMT10B_ENST00000377753.2_Missense_Mutation_p.E29A|TRMT10B_ENST00000377754.2_5'UTR|RP11-613M10.9_ENST00000540557.1_Intron	NM_144964.2	NP_659401.2	Q6PF06	TM10B_HUMAN	tRNA methyltransferase 10 homolog B (S. cerevisiae)	29							methyltransferase activity (GO:0008168)										GAGACAGGTGAAGATGGACTT	0.557																																					p.E29A		Atlas-SNP	.											.	.	.	.	0			c.A86C						.						61	65	64					9																	37762014		2046	4190	6236	SO:0001583	missense	158234	exon2			CAGGTGAAGATGG	BC057774	CCDS43804.1, CCDS69598.1, CCDS69600.1, CCDS69601.1	9p13.1	2012-06-28	2012-06-28	2012-06-28	ENSG00000165275	ENSG00000165275			26454	protein-coding gene	gene with protein product			"RNA (guanine-9-) methyltransferase domain containing 3"	RG9MTD3		14702039	Standard	XM_005251373		Approved	FLJ31455, bA3J10.9	uc004aai.3	Q6PF06	OTTHUMG00000019933	ENST00000297994.3:c.86A>C	chr9.hg19:g.37762014A>C	ENSP00000297994:p.Glu29Ala	145.0	0.0		139.0	62.0	NM_144964	B7Z216|B7Z3D3|Q05DJ4|Q5QP83|Q8NAG2|Q96N36	Missense_Mutation	SNP	ENST00000297994.3	hg19	CCDS43804.1	.	.	.	.	.	.	.	.	.	.	A	13.02	2.110977	0.37242	.	.	ENSG00000165275	ENST00000377753;ENST00000537911;ENST00000297994	T;T;T	0.36878	1.42;1.23;1.77	5.52	-1.2	0.09554	.	0.781997	0.11921	N	0.516711	T	0.19287	0.0463	L	0.27053	0.805	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.002;0.002;0.001	T	0.24012	-1.0172	10	0.20519	T	0.43	-1.3102	4.7347	0.12982	0.4656:0.289:0.2455:0.0	.	29;29;29	B7Z216;B7Z3D3;Q6PF06	.;.;RG9D3_HUMAN	A	29	ENSP00000366982:E29A;ENSP00000444997:E29A;ENSP00000297994:E29A	ENSP00000297994:E29A	E	+	2	0	RG9MTD3	37752014	0.855000	0.29742	0.025000	0.17156	0.125000	0.20455	0.445000	0.21677	-0.164000	0.10927	-0.313000	0.08912	GAA	.	.		0.557	TRMT10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052482.1	NM_144964		C	37762014	A	C	37762014	3	2	242	1	0	0	0	0	1	0	0	0	13288	246	9	5	88	5	RG9MTD3	9	37762014	Missense_Mutation	SNP	A	TCGA-ED-A66Y-01A-11D-A30V-10	31793844	37762014	103451417	40	33374										
RORB	6096	hgsc.bcm.edu	37	chr9	77286750	77286752	+	In_Frame_Del	DEL	AAA	AAA	-													0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	gaaagtccagaagcttcaggAaaaaatttattttgcacttc							TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	AAA	AAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr9:77286750_77286752delAAA	ENST00000396204.2	+	9	1190_1192	c.1190_1192delAAA	c.(1189-1194)gaaaaa>gaa	p.K398del	RORB_ENST00000376896.3_In_Frame_Del_p.K387del			Q92753	RORB_HUMAN	RAR-related orphan receptor B	398	Ligand-binding. {ECO:0000255}.				amacrine cell differentiation (GO:0035881)|cellular response to retinoic acid (GO:0071300)|eye photoreceptor cell development (GO:0042462)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|rhythmic process (GO:0048511)|transcription initiation from RNA polymerase II promoter (GO:0006367)|visual perception (GO:0007601)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(2)|large_intestine(4)|lung(1)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	12					Melatonin(DB01065)	AAGCTTCAGGAAAAAATTTATTT	0.438																																					p.386_386del		Atlas-Indel,Pindel	.											.	RORB	89	.	0			c.1156_1158del						.																																			SO:0001651	inframe_deletion	6096	exon9			.	Y08639	CCDS6646.1	9q22	2013-01-16			ENSG00000198963	ENSG00000198963		"Nuclear hormone receptors"	10259	protein-coding gene	gene with protein product		601972				7926749	Standard	NM_006914		Approved	RZRB, NR1F2, ROR-BETA	uc004ajh.3	Q92753	OTTHUMG00000020026	ENST00000396204.2:c.1190_1192delAAA	chr9.hg19:g.77286753_77286755delAAA	ENSP00000379507:p.Lys398del	247.0	0.0		288.0	120.0	NM_006914	Q8WX73	In_Frame_Del	DEL	ENST00000396204.2	hg19																																																																																				.	.		0.438	RORB-201	KNOWN	basic	protein_coding	protein_coding				-	77286752	AAA	-	77286750	7	5	242	1	0	1	0	1	0	0	0	0	13544	246	9	0	1191	0	RORB	9	77286750	In_Frame_Del	DEL	AAA	TCGA-ED-A66Y-01A-11D-A30V-10	39524736	77286750	63926681	41	33375										
ACTL7A	10881	hgsc.bcm.edu	37	chr9	111625276	111625276	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	ggtgggccatggcgtgtcctAcgtggtccccatctacgagg	15	12	1	0	rs112558776		TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr9:111625276A>G	ENST00000333999.3	+	1	674	c.674A>G	c.(673-675)tAc>tGc	p.Y225C		NM_006687.2	NP_006678.1	Q9Y615	ACL7A_HUMAN	actin-like 7A	225						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|male germ cell nucleus (GO:0001673)|motile cilium (GO:0031514)|nucleus (GO:0005634)|protein complex (GO:0043234)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(2)|large_intestine(4)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						GGCGTGTCCTACGTGGTCCCC	0.617																																					p.Y225C	Esophageal Squamous(177;1480 3591 17554)	Atlas-SNP	.											.	ACTL7A	34	.	0			c.A674G						.						73	70	71					9																	111625276		2203	4300	6503	SO:0001583	missense	10881	exon1			TGTCCTACGTGGT	BC014610	CCDS6772.1	9q31	2008-02-05			ENSG00000187003	ENSG00000187003			161	protein-coding gene	gene with protein product		604303				10373328	Standard	NM_006687		Approved		uc004bdj.1	Q9Y615	OTTHUMG00000020461	ENST00000333999.3:c.674A>G	chr9.hg19:g.111625276A>G	ENSP00000334300:p.Tyr225Cys	44.0	0.0		47.0	18.0	NM_006687	B2RC83|Q5JSV0	Missense_Mutation	SNP	ENST00000333999.3	hg19	CCDS6772.1	.	.	.	.	.	.	.	.	.	.	A	15.00	2.703545	0.48412	.	.	ENSG00000187003	ENST00000333999	T	0.30182	1.54	5.68	5.68	0.88126	.	0.000000	0.42172	D	0.000753	T	0.25791	0.0628	L	0.31664	0.95	0.51482	D	0.999923	B	0.15473	0.013	B	0.12837	0.008	T	0.03728	-1.1009	10	0.87932	D	0	.	14.1785	0.65559	1.0:0.0:0.0:0.0	.	225	Q9Y615	ACL7A_HUMAN	C	225	ENSP00000334300:Y225C	ENSP00000334300:Y225C	Y	+	2	0	ACTL7A	110665097	1.000000	0.71417	0.968000	0.41197	0.885000	0.51271	9.261000	0.95576	2.288000	0.76882	0.528000	0.53228	TAC	.	A|0.500;C|0.500		0.617	ACTL7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053570.1	NM_006687		G	111625276	A	G	111625276	3	3	242	1	0	0	0	0	1	0	0	0	200	391	14	2	676	2	ACTL7A	9	111625276	Missense_Mutation	SNP	A	TCGA-ED-A66Y-01A-11D-A30V-10	34338526	111625276	29588155	42	33376										
SVIL	6840	hgsc.bcm.edu	37	chr10	29812533	29812533	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	gtgggtgatgggagggttcgCccgttccaggcttcctcttc	15	11	1	1	rs374116755		TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr10:29812533C>T	ENST00000355867.4	-	15	3762	c.3010G>A	c.(3010-3012)Gcg>Acg	p.A1004T	SVIL_ENST00000535393.1_5'Flank|SVIL_ENST00000375398.2_Missense_Mutation_p.A1004T|SVIL_ENST00000375400.3_Missense_Mutation_p.A578T	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1004					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				GGAGGGTTCGCCCGTTCCAGG	0.527																																					p.A1004T		Atlas-SNP	.											.	SVIL	226	.	0			c.G3010A						.	C	THR/ALA,THR/ALA	0,4406		0,0,2203	99	92	95		1732,3010	0.8	0	10		95	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	SVIL	NM_003174.3,NM_021738.2	58,58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	578/1789,1004/2215	29812533	1,13005	2203	4300	6503	SO:0001583	missense	6840	exon15			GGTTCGCCCGTTC	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"archvillin"	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.3010G>A	chr10.hg19:g.29812533C>T	ENSP00000348128:p.Ala1004Thr	109.0	0.0		98.0	52.0	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	hg19	CCDS7164.1	.	.	.	.	.	.	.	.	.	.	C	5.567	0.289514	0.10567	0.0	1.16E-4	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867	T;T;T	0.11385	2.78;2.84;2.84	5.01	0.769	0.18492	.	1.300130	0.04940	N	0.458396	T	0.09069	0.0224	L	0.41236	1.265	0.09310	N	1	B;B	0.21071	0.051;0.0	B;B	0.13407	0.009;0.002	T	0.37686	-0.9695	9	.	.	.	-0.3226	3.6715	0.08276	0.1367:0.5773:0.1327:0.1533	.	578;1004	O95425-2;O95425	.;SVIL_HUMAN	T	578;1004;1004	ENSP00000364549:A578T;ENSP00000364547:A1004T;ENSP00000348128:A1004T	.	A	-	1	0	SVIL	29852539	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.173000	0.16724	0.622000	0.30249	0.557000	0.71058	GCG	.	.		0.527	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1			T	29812533	C	T	29812533	3	4	242	1	0	0	0	0	1	0	0	0	15436	739	26	3	3730	3	SVIL	10	29812533	Missense_Mutation	SNP	C	TCGA-ED-A66Y-01A-11D-A30V-10		29812533	105722214	43	33377										
FGFR2	2263	hgsc.bcm.edu	37	chr10	123276885	123276885	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	gatatcccaatagaattaccCgccaagcacgtatattcccc	5	14	0	1	rs121918491		TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr10:123276885C>T	ENST00000358487.5	-	8	1304	c.1032G>A	c.(1030-1032)gcG>gcA	p.A344A	FGFR2_ENST00000360144.3_Intron|FGFR2_ENST00000478859.1_Silent_p.A116A|FGFR2_ENST00000357555.5_Silent_p.A255A|FGFR2_ENST00000490349.1_5'UTR|FGFR2_ENST00000369060.4_Intron|FGFR2_ENST00000457416.2_Intron|FGFR2_ENST00000351936.6_Silent_p.A344A|FGFR2_ENST00000356226.4_Silent_p.A229A|FGFR2_ENST00000369056.1_Intron|FGFR2_ENST00000346997.2_Silent_p.A344A|FGFR2_ENST00000369061.4_Intron|FGFR2_ENST00000369059.1_Intron	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2	344	Ig-like C2-type 3.		A -> G (in CS and JWS). {ECO:0000269|PubMed:7581378, ECO:0000269|PubMed:7874170}.|A -> P (in CS and PS). {ECO:0000269|PubMed:8644708}.		angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)			breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	TAGAATTACCCGCCAAGCACG	0.438		5	Mis		"gastric. NSCLC, endometrial"		"Crouzon, Pfeiffer, and Apert syndromes"		Saethre-Chotzen syndrome;Apert syndrome																												p.A344A		Atlas-SNP	.		Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	.	FGFR2	758	.	0			c.G1032A	GRCh37	CS941488	FGFR2	S	rs121918491	.						128	114	119					10																	123276885		2203	4300	6503	SO:0001819	synonymous_variant	2263	exon8	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	ATTACCCGCCAAG	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3689	protein-coding gene	gene with protein product	"Crouzon syndrome", "Pfeiffer syndrome"	176943	"bacteria-expressed kinase", "keratinocyte growth factor receptor", "craniofacial dysostosis 1", "Jackson-Weiss syndrome"	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.1032G>A	chr10.hg19:g.123276885C>T		78.0	0.0		46.0	41.0	NM_000141	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	Silent	SNP	ENST00000358487.5	hg19	CCDS31298.1																																																																																			.	.		0.438	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141		T	123276885	C	T	123276885	2	4	242	1	0	0	0	0	0	0	0	1	5874	639	23	1		1	FGFR2	10	123276885	Silent	SNP	C	TCGA-ED-A66Y-01A-11D-A30V-10	93464352	123276885	12257862	44	33378										
CD6	923	hgsc.bcm.edu	37	chr11	60774061	60774061	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	ttcaggtcatccatctccagCcccacctgaccagctcaaca	5	18	4	1			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr11:60774061C>T	ENST00000313421.7	+	2	251	c.65C>T	c.(64-66)gCc>gTc	p.A22V	CD6_ENST00000452451.2_Missense_Mutation_p.A22V|CD6_ENST00000344028.5_Missense_Mutation_p.A22V|CD6_ENST00000346437.4_Missense_Mutation_p.A22V|CD6_ENST00000352009.5_Missense_Mutation_p.A22V|CD6_ENST00000545105.1_3'UTR	NM_006725.4	NP_006716.3	P30203	CD6_HUMAN	CD6 molecule	22					cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	scavenger receptor activity (GO:0005044)			endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)	18						CCATCTCCAGCCCCACCTGAC	0.577																																					p.A22V	Pancreas(169;904 2017 4767 38890 42505)	Atlas-SNP	.											.	CD6	122	.	0			c.C65T						.						87	77	80					11																	60774061		2203	4299	6502	SO:0001583	missense	923	exon2			CTCCAGCCCCACC		CCDS7999.1, CCDS58137.1, CCDS58138.1	11q12.2	2006-03-28	2006-03-28		ENSG00000013725	ENSG00000013725		"CD molecules"	1691	protein-coding gene	gene with protein product		186720	"CD6 antigen"			9013954	Standard	NM_006725		Approved	Tp120	uc001nqq.3	P30203	OTTHUMG00000167823	ENST00000313421.7:c.65C>T	chr11.hg19:g.60774061C>T	ENSP00000323280:p.Ala22Val	45.0	0.0		36.0	13.0	NM_006725	A4KAD4|A4KAD5|Q9UMF2|Q9Y4K7|Q9Y4K8|Q9Y4K9|Q9Y4L0	Missense_Mutation	SNP	ENST00000313421.7	hg19	CCDS7999.1	.	.	.	.	.	.	.	.	.	.	C	15.83	2.948374	0.53186	.	.	ENSG00000013725	ENST00000344028;ENST00000346437;ENST00000313421;ENST00000542157;ENST00000433107;ENST00000452451;ENST00000352009	T;T;T;T;T;T;T	0.01495	4.88;4.89;4.83;4.86;5.0;4.87;4.87	3.94	3.02	0.34903	.	1.862780	0.03623	N	0.236678	T	0.03136	0.0092	L	0.27053	0.805	0.09310	N	1	D;P;P;P;P	0.53151	0.958;0.86;0.775;0.666;0.78	P;P;B;B;B	0.47528	0.549;0.453;0.306;0.194;0.265	T	0.52238	-0.8602	10	0.38643	T	0.18	.	11.4748	0.50291	0.0:0.8166:0.1834:0.0	.	22;22;22;22;22	E7ER04;P30203-5;P30203-4;P30203;Q8N4Q7	.;.;.;CD6_HUMAN;.	V	22	ENSP00000344108:A22V;ENSP00000345566:A22V;ENSP00000323280:A22V;ENSP00000440055:A22V;ENSP00000410638:A22V;ENSP00000390676:A22V;ENSP00000340628:A22V	ENSP00000323280:A22V	A	+	2	0	CD6	60530637	0.001000	0.12720	0.002000	0.10522	0.014000	0.08584	1.059000	0.30517	1.232000	0.43678	0.561000	0.74099	GCC	.	.		0.577	CD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396449.1	NM_006725		T	60774061	C	T	60774061	3	4	242	1	0	0	0	0	1	0	0	0	3030	739	26	3	71	3	CD6	11	60774061	Missense_Mutation	SNP	C	TCGA-ED-A66Y-01A-11D-A30V-10		60774061	74232455	45	33379										
SCGB2A2	4250	hgsc.bcm.edu	37	chr11	62038372	62038372	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	ggctctggctgccccttattGgagaatgtgatttccaagac	11	10	1	3			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr11:62038372G>A	ENST00000227918.2	+	2	137	c.75G>A	c.(73-75)ttG>ttA	p.L25L	SCGB2A2_ENST00000525380.1_Silent_p.L25L	NM_002411.2	NP_002402.1	Q13296	SG2A2_HUMAN	secretoglobin, family 2A, member 2	25										large_intestine(1)|lung(4)|ovary(1)|prostate(1)	7						GCCCCTTATTGGAGAATGTGA	0.443																																					p.L25L		Atlas-SNP	.											.	SCGB2A2	13	.	0			c.G75A						.						72	66	68					11																	62038372		2202	4299	6501	SO:0001819	synonymous_variant	4250	exon2			CTTATTGGAGAAT	AF015224	CCDS8018.1	11q13	2011-12-14	2002-03-22	2002-03-22	ENSG00000110484	ENSG00000110484		"Secretoglobins"	7050	protein-coding gene	gene with protein product	"mammaglobin A"	605562	"mammaglobin 1"	MGB1		9488047, 8631025, 22155607	Standard	XM_005274005		Approved	UGB2, MGC71974	uc001ntc.3	Q13296	OTTHUMG00000167509	ENST00000227918.2:c.75G>A	chr11.hg19:g.62038372G>A		62.0	0.0		90.0	38.0	NM_002411	A1A522|Q86WH8	Silent	SNP	ENST00000227918.2	hg19	CCDS8018.1																																																																																			.	.		0.443	SCGB2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394860.1	NM_002411		A	62038372	G	A	62038372	2	1	242	1	0	0	0	0	0	0	0	1	13915	1339	47	3		3	SCGB2A2	11	62038372	Silent	SNP	G	TCGA-ED-A66Y-01A-11D-A30V-10	1264311	62038372	72968144	46	33380										
LRTM2	654429	hgsc.bcm.edu	37	chr12	1943454	1943454	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	gggacgcttggaccagcttgCctgcaccctgcccaaggagc	13	15	0	0			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr12:1943454C>T	ENST00000543818.1	+	5	1522	c.680C>T	c.(679-681)gCc>gTc	p.A227V	CACNA2D4_ENST00000587995.1_Intron|LRTM2_ENST00000535041.1_Missense_Mutation_p.A227V|LRTM2_ENST00000299194.1_Missense_Mutation_p.A227V|CACNA2D4_ENST00000585732.1_Intron|LRTM2_ENST00000543730.1_3'UTR|CACNA2D4_ENST00000382722.5_Intron|CACNA2D4_ENST00000586184.1_Intron|CACNA2D4_ENST00000588077.1_Intron|CACNA2D4_ENST00000585708.1_Intron	NM_001039029.2|NM_001163925.1|NM_001163926.1	NP_001034118.1|NP_001157397.1|NP_001157398.1	Q8N967	LRTM2_HUMAN	leucine-rich repeats and transmembrane domains 2	227	LRRCT.					integral component of membrane (GO:0016021)				NS(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	20	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.000834)			GACCAGCTTGCCTGCACCCTG	0.582																																					p.A227V		Atlas-SNP	.											.	LRTM2	43	.	0			c.C680T						.						50	46	47					12																	1943454		2203	4300	6503	SO:0001583	missense	654429	exon5			AGCTTGCCTGCAC	AK095610	CCDS31726.1	12p13.33	2008-02-05				ENSG00000166159			32443	protein-coding gene	gene with protein product							Standard	NM_001039029		Approved		uc010sdx.1	Q8N967		ENST00000543818.1:c.680C>T	chr12.hg19:g.1943454C>T	ENSP00000446278:p.Ala227Val	27.0	0.0		31.0	16.0	NM_001039029	A7E2U6	Missense_Mutation	SNP	ENST00000543818.1	hg19	CCDS31726.1	.	.	.	.	.	.	.	.	.	.	C	13.84	2.357335	0.41801	.	.	ENSG00000166159	ENST00000543818;ENST00000299194;ENST00000535041	T;T;T	0.51325	0.71;0.71;0.71	5.35	5.35	0.76521	Cysteine-rich flanking region, C-terminal (1);	0.225081	0.45126	D	0.000399	T	0.31670	0.0804	N	0.13098	0.295	0.42351	D	0.992373	B	0.10296	0.003	B	0.12156	0.007	T	0.09684	-1.0663	10	0.29301	T	0.29	.	13.9656	0.64207	0.1516:0.8483:0.0:0.0	.	227	Q8N967	LRTM2_HUMAN	V	227	ENSP00000446278:A227V;ENSP00000299194:A227V;ENSP00000444737:A227V	ENSP00000299194:A227V	A	+	2	0	LRTM2	1813715	0.837000	0.29446	0.985000	0.45067	0.997000	0.91878	3.835000	0.55805	2.497000	0.84241	0.563000	0.77884	GCC	.	.		0.582	LRTM2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398055.1			T	1943454	C	T	1943454	3	4	242	1	0	0	0	0	1	0	0	0	9054	739	26	3	690	3	LRTM2	12	1943454	Missense_Mutation	SNP	C	TCGA-ED-A66Y-01A-11D-A30V-10		1943454	131908441	47	33381										
PLEKHA5	54477	hgsc.bcm.edu	37	chr12	19436617	19436617	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	gaacttacagatcggaagtgTcttcaccaattcagagagga	10	8	3	2			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr12:19436617T>C	ENST00000299275.6	+	11	1705	c.1699T>C	c.(1699-1701)Tct>Cct	p.S567P	PLEKHA5_ENST00000309364.4_Missense_Mutation_p.S567P|PLEKHA5_ENST00000355397.3_Missense_Mutation_p.S567P|PLEKHA5_ENST00000539256.1_Missense_Mutation_p.S325P|PLEKHA5_ENST00000359180.3_Missense_Mutation_p.S567P|PLEKHA5_ENST00000538714.1_Missense_Mutation_p.S567P|PLEKHA5_ENST00000317589.4_Missense_Mutation_p.S567P|PLEKHA5_ENST00000543806.1_Missense_Mutation_p.S459P|PLEKHA5_ENST00000510738.2_3'UTR|PLEKHA5_ENST00000424268.1_Missense_Mutation_p.S459P|PLEKHA5_ENST00000429027.2_Missense_Mutation_p.S573P	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5	567					reproductive system development (GO:0061458)	cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					ATCGGAAGTGTCTTCACCAAT	0.468																																					p.S573P	Pancreas(196;329 2193 11246 14234 19524)	Atlas-SNP	.											.	PLEKHA5	198	.	0			c.T1717C						.						56	56	56					12																	19436617		2203	4300	6503	SO:0001583	missense	54477	exon12			GAAGTGTCTTCAC	AF302150	CCDS8682.1, CCDS44840.1, CCDS44840.2, CCDS55809.1, CCDS58213.1, CCDS58214.1	12p12	2013-01-10			ENSG00000052126	ENSG00000052126		"Pleckstrin homology (PH) domain containing"	30036	protein-coding gene	gene with protein product		607770				11214970, 11001876	Standard	NM_001143821		Approved	PEPP2, KIAA1686, FLJ10667	uc031qgo.1	Q9HAU0	OTTHUMG00000167921	ENST00000299275.6:c.1699T>C	chr12.hg19:g.19436617T>C	ENSP00000299275:p.Ser567Pro	73.0	0.0		78.0	33.0	NM_001256470	A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	Missense_Mutation	SNP	ENST00000299275.6	hg19	CCDS8682.1	.	.	.	.	.	.	.	.	.	.	T	13.56	2.274787	0.40194	.	.	ENSG00000052126	ENST00000317589;ENST00000355397;ENST00000359180;ENST00000542828;ENST00000309364;ENST00000429027;ENST00000299275;ENST00000539256;ENST00000538714;ENST00000424268;ENST00000543806;ENST00000536974	T;T;T;T;T;T;T;T;T;T;T	0.14893	2.47;2.47;2.47;2.47;2.47;2.47;2.47;2.47;2.47;2.47;2.47	3.86	-2.34	0.06704	.	0.176958	0.51477	D	0.000087	T	0.30696	0.0773	M	0.74258	2.255	0.29973	N	0.818423	D;D;P;P;D;D;D	0.63046	0.988;0.959;0.93;0.84;0.96;0.992;0.987	P;P;P;B;P;P;D	0.63703	0.759;0.882;0.766;0.432;0.634;0.894;0.917	T	0.17776	-1.0358	10	0.27785	T	0.31	-5.3793	10.0627	0.42284	0.5132:0.0:0.0:0.4868	.	567;459;459;573;573;567;567	Q9HAU0-4;F5H0I0;E7EME8;B4DHK5;E9PHQ3;Q9HAU0;Q9HAU0-2	.;.;.;.;.;PKHA5_HUMAN;.	P	567;567;567;574;567;573;567;325;567;459;459;459	ENSP00000325155:S567P;ENSP00000347560:S567P;ENSP00000352104:S567P;ENSP00000311239:S567P;ENSP00000404296:S573P;ENSP00000299275:S567P;ENSP00000440611:S325P;ENSP00000439673:S567P;ENSP00000400411:S459P;ENSP00000439837:S459P;ENSP00000440371:S459P	ENSP00000299275:S567P	S	+	1	0	PLEKHA5	19327884	0.999000	0.42202	0.488000	0.27440	0.427000	0.31564	1.263000	0.33004	-0.541000	0.06257	-0.490000	0.04691	TCT	.	.		0.468	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	NM_019012		C	19436617	T	C	19436617	3	2	242	1	0	0	0	0	1	0	0	0	12068	1667	58	2	1741	2	PLEKHA5	12	19436617	Missense_Mutation	SNP	T	TCGA-ED-A66Y-01A-11D-A30V-10	17493163	19436617	114415278	48	33382										
SUOX	6821	hgsc.bcm.edu	37	chr12	56397423	56397423	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	ctgctcaggagtcaacacacAtatacactaaggaggaagtg	10	9	2	0			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr12:56397423A>G	ENST00000394109.3	+	3	974	c.250A>G	c.(250-252)Ata>Gta	p.I84V	SUOX_ENST00000394115.2_Missense_Mutation_p.I84V|SUOX_ENST00000356124.4_Missense_Mutation_p.I84V|SUOX_ENST00000266971.3_Missense_Mutation_p.I84V|SUOX_ENST00000548274.1_Missense_Mutation_p.I84V|SUOX_ENST00000551841.2_Missense_Mutation_p.I84V|SUOX_ENST00000550478.1_3'UTR			P51687	SUOX_HUMAN	sulfite oxidase	84	Cytochrome b5 heme-binding. {ECO:0000255|PROSITE-ProRule:PRU00279}.				cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)	mitochondrial matrix (GO:0005759)	electron carrier activity (GO:0009055)|heme binding (GO:0020037)|molybdenum ion binding (GO:0030151)|molybdopterin cofactor binding (GO:0043546)|sulfite oxidase activity (GO:0008482)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(6)	15			UCEC - Uterine corpus endometrioid carcinoma (6;0.0471)|OV - Ovarian serous cystadenocarcinoma(18;0.119)			GTCAACACACATATACACTAA	0.488																																					p.I84V		Atlas-SNP	.											.	SUOX	33	.	0			c.A250G						.						75	74	75					12																	56397423		2203	4300	6503	SO:0001583	missense	6821	exon6			ACACACATATACA	BC065193	CCDS8901.2	12q13.13	2011-02-10			ENSG00000139531	ENSG00000139531	1.8.3.1		11460	protein-coding gene	gene with protein product		606887				7599189	Standard	XM_005269112		Approved		uc001siz.3	P51687	OTTHUMG00000128503	ENST00000394109.3:c.250A>G	chr12.hg19:g.56397423A>G	ENSP00000377668:p.Ile84Val	97.0	0.0		71.0	25.0	NM_000456		Missense_Mutation	SNP	ENST00000394109.3	hg19	CCDS8901.2	.	.	.	.	.	.	.	.	.	.	A	0.018	-1.486477	0.01018	.	.	ENSG00000139531	ENST00000356124;ENST00000266971;ENST00000394115;ENST00000552258;ENST00000548274;ENST00000546833;ENST00000551841;ENST00000394109	D;D;D;T;D;T;D	0.91464	-2.85;-2.85;-2.85;-1.16;-2.85;-1.16;-2.85	4.91	-3.56	0.04626	Cytochrome b5 (3);	1.070900	0.07135	N	0.846331	T	0.76421	0.3985	N	0.17872	0.535	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.61729	-0.7003	10	0.12766	T	0.61	-4.0698	0.4729	0.00535	0.3668:0.2453:0.1492:0.2387	.	84	P51687	SUOX_HUMAN	V	84	ENSP00000348440:I84V;ENSP00000266971:I84V;ENSP00000377674:I84V;ENSP00000450049:I84V;ENSP00000450245:I84V;ENSP00000449872:I84V;ENSP00000377668:I84V	ENSP00000266971:I84V	I	+	1	0	SUOX	54683690	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-0.466000	0.06672	-0.445000	0.07159	-0.353000	0.07706	ATA	.	.		0.488	SUOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250309.1	NM_000456		G	56397423	A	G	56397423	3	3	242	1	0	0	0	0	1	0	0	0	15410	217	8	2	260	2	SUOX	12	56397423	Missense_Mutation	SNP	A	TCGA-ED-A66Y-01A-11D-A30V-10	36960806	56397423	77454472	49	33383										
LRRIQ1	84125	hgsc.bcm.edu	37	chr12	85521764	85521764	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	agaaaggaaaaagagaaaatAttgtgaatatccgaaaacag	9	3	0	3			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr12:85521764A>G	ENST00000393217.2	+	18	4223	c.4162A>G	c.(4162-4164)Att>Gtt	p.I1388V		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	1388										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		AAGAGAAAATATTGTGAATAT	0.343																																					p.I1388V		Atlas-SNP	.											.	LRRIQ1	512	.	0			c.A4162G						.						121	122	122					12																	85521764		1829	4092	5921	SO:0001583	missense	84125	exon18			GAAAATATTGTGA	AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.4162A>G	chr12.hg19:g.85521764A>G	ENSP00000376910:p.Ile1388Val	249.0	0.0		285.0	137.0	NM_001079910	Q567P4|Q9BS17|Q9HA36	Missense_Mutation	SNP	ENST00000393217.2	hg19	CCDS41816.1	.	.	.	.	.	.	.	.	.	.	A	3.049	-0.195710	0.06259	.	.	ENSG00000133640	ENST00000393217	T	0.51071	0.72	4.68	2.31	0.28768	.	.	.	.	.	T	0.21590	0.0520	N	0.08118	0	0.09310	N	1	B	0.14805	0.011	B	0.13407	0.009	T	0.17715	-1.0360	9	0.23302	T	0.38	.	1.6159	0.02703	0.5628:0.1315:0.1622:0.1435	.	1388	Q96JM4	LRIQ1_HUMAN	V	1388	ENSP00000376910:I1388V	ENSP00000376910:I1388V	I	+	1	0	LRRIQ1	84045895	0.000000	0.05858	0.001000	0.08648	0.512000	0.34134	0.700000	0.25601	0.391000	0.25143	-0.326000	0.08463	ATT	.	.		0.343	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165		G	85521764	A	G	85521764	3	3	242	1	0	0	0	0	1	0	0	0	9038	449	16	2	4232	2	LRRIQ1	12	85521764	Missense_Mutation	SNP	A	TCGA-ED-A66Y-01A-11D-A30V-10	29124341	85521764	48330131	50	33384										
HSPH1	10808	hgsc.bcm.edu	37	chr13	31715296	31715296	+	Nonsense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	tgttaagaaggtctttccctAactgccagaccaagttggct	9	10	1	2			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr13:31715296A>C	ENST00000320027.5	-	13	2161	c.1817T>G	c.(1816-1818)tTa>tGa	p.L606*	HSPH1_ENST00000445273.2_Nonsense_Mutation_p.L608*|HSPH1_ENST00000429785.2_Nonsense_Mutation_p.L425*|HSPH1_ENST00000380405.4_Nonsense_Mutation_p.L562*|HSPH1_ENST00000380406.5_Nonsense_Mutation_p.L565*	NM_006644.2	NP_006635.2	Q92598	HS105_HUMAN	heat shock 105kDa/110kDa protein 1	606					chaperone mediated protein folding requiring cofactor (GO:0051085)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of NK T cell activation (GO:0051135)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	27		Lung SC(185;0.0257)		all cancers(112;0.00385)|Epithelial(112;0.0328)|OV - Ovarian serous cystadenocarcinoma(117;0.0375)|GBM - Glioblastoma multiforme(144;0.125)		GTCTTTCCCTAACTGCCAGAC	0.358																																					p.L606X		Atlas-SNP	.											.	HSPH1	65	.	0			c.T1817G						.						132	124	127					13																	31715296		2203	4299	6502	SO:0001587	stop_gained	10808	exon13			TTCCCTAACTGCC	AB003333	CCDS9340.1, CCDS66525.1, CCDS73559.1	13q12.2-q13.3	2011-09-02			ENSG00000120694	ENSG00000120694		"Heat shock proteins / HSP70"	16969	protein-coding gene	gene with protein product		610703				9610721, 9931472	Standard	XM_005266236		Approved	HSP105B, KIAA0201, HSP105A, NY-CO-25	uc001utj.3	Q92598	OTTHUMG00000016685	ENST00000320027.5:c.1817T>G	chr13.hg19:g.31715296A>C	ENSP00000318687:p.Leu606*	96.0	0.0		106.0	52.0	NM_006644	B4DYH1|O95739|Q5TBM6|Q5TBM7|Q5TBM8|Q9UPC4	Nonsense_Mutation	SNP	ENST00000320027.5	hg19	CCDS9340.1	.	.	.	.	.	.	.	.	.	.	A	40	8.315047	0.98757	.	.	ENSG00000120694	ENST00000320027;ENST00000380405;ENST00000380406;ENST00000445273;ENST00000429785	.	.	.	6.05	6.05	0.98169	.	0.000000	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.4936	16.5932	0.84781	1.0:0.0:0.0:0.0	.	.	.	.	X	606;562;565;608;425	.	ENSP00000318687:L606X	L	-	2	0	HSPH1	30613296	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.917000	0.92751	2.320000	0.78422	0.528000	0.53228	TTA	.	.		0.358	HSPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044384.1			C	31715296	A	C	31715296	4	2	242	1	0	0	0	0	0	1	0	0	7440	372	13	5	783	5	HSPH1	13	31715296	Nonsense_Mutation	SNP	A	TCGA-ED-A66Y-01A-11D-A30V-10		31715296	83454582	51	33385										
NBEA	26960	hgsc.bcm.edu	37	chr13	35806707	35806707	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	tttgtagactttgccccattCctatctcgtacacttcttgg	6	12	2	1			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr13:35806707C>T	ENST00000400445.3	+	34	6261	c.5727C>T	c.(5725-5727)ttC>ttT	p.F1909F	NBEA_ENST00000310336.4_Silent_p.F1909F|NBEA_ENST00000540320.1_Silent_p.F1909F|NBEA_ENST00000379939.2_Silent_p.F1906F	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	1909					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		TTGCCCCATTCCTATCTCGTA	0.328																																					p.F1909F		Atlas-SNP	.											.	NBEA	340	.	0			c.C5727T						.						50	47	48					13																	35806707		1814	4069	5883	SO:0001819	synonymous_variant	26960	exon34			CCCATTCCTATCT	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.5727C>T	chr13.hg19:g.35806707C>T		123.0	0.0		145.0	67.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Silent	SNP	ENST00000400445.3	hg19	CCDS45026.1																																																																																			.	.		0.328	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		T	35806707	C	T	35806707	2	4	242	1	0	0	0	0	0	0	0	1	10196	854	30	3		3	NBEA	13	35806707	Silent	SNP	C	TCGA-ED-A66Y-01A-11D-A30V-10	4091411	35806707	79363171	52	33386										
RB1	5925	hgsc.bcm.edu	37	chr13	48951053	48951053	+	Splice_Site	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	ttctgtttttacctcctaaaGaactgcacagtgaatccaaa	5	10	1	2	rs587778831		TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr13:48951053G>A	ENST00000267163.4	+	13	1353		c.e13-1			NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1						androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(11)		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(DB00071)|Insulin Regular(DB00030)"	ACCTCCTAAAGAACTGCACAG	0.318		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)																											.		Atlas-SNP	.	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	RB1,NS,carcinoma,0,1	RB1	1068	.	26	Whole gene deletion(15)|Unknown(11)	bone(11)|breast(5)|central_nervous_system(2)|lung(2)|adrenal_gland(1)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)|ovary(1)	c.1216-1G>A	GRCh37	CS971888	RB1	S		.						83	90	88					13																	48951053		2203	4300	6503	SO:0001630	splice_region_variant	5925	exon13	Familial Cancer Database		CCTAAAGAACTGC	M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1216-1G>A	chr13.hg19:g.48951053G>A		105.0	0.0		62.0	54.0	NM_000321	A8K5E3|P78499|Q5VW46|Q8IZL4	Splice_Site	SNP	ENST00000267163.4	hg19	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.063103	0.76187	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	.	.	.	5.93	5.93	0.95920	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.3495	0.98807	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	RB1	47849054	1.000000	0.71417	1.000000	0.80357	0.727000	0.41649	8.600000	0.90860	2.814000	0.96858	0.591000	0.81541	.	.	.		0.318	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1		Intron	A	48951053	G	A	48951053	5	1	242	1	0	0	0	0	0	0	1	0	13113	956	33	3	1265	3	RB1	13	48951053	Splice_Site	SNP	G	TCGA-ED-A66Y-01A-11D-A30V-10	13144346	48951053	66218825	53	33387										
SLITRK6	84189	hgsc.bcm.edu	37	chr13	86370519	86370519	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	cacaatttattagcattgtgCcatctttttcctcacaattg	4	10	2	0			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr13:86370519C>G	ENST00000400286.2	-	2	723	c.125G>C	c.(124-126)gGc>gCc	p.G42A		NM_032229.2	NP_115605.2	Q9H5Y7	SLIK6_HUMAN	SLIT and NTRK-like family, member 6	42	LRRNT 1.				adult locomotory behavior (GO:0008344)|auditory behavior (GO:0031223)|auditory receptor cell morphogenesis (GO:0002093)|axonogenesis (GO:0007409)|cochlea development (GO:0090102)|innervation (GO:0060384)|lens development in camera-type eye (GO:0002088)|linear vestibuloocular reflex (GO:0060007)|multicellular organism growth (GO:0035264)|sensory perception of sound (GO:0007605)|startle response (GO:0001964)|synapse assembly (GO:0007416)|vestibulocochlear nerve development (GO:0021562)|visual perception (GO:0007601)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)				breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(18)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_neural(89;0.117)|Medulloblastoma(90;0.163)			GBM - Glioblastoma multiforme(99;0.0456)		TAGCATTGTGCCATCTTTTTC	0.398																																					p.G42A		Atlas-SNP	.											.	SLITRK6	150	.	0			c.G125C						.						97	91	93					13																	86370519		1894	4113	6007	SO:0001583	missense	84189	exon2			ATTGTGCCATCTT	AK026427	CCDS41903.1	13q31.1	2006-04-12			ENSG00000184564	ENSG00000184564			23503	protein-coding gene	gene with protein product		609681				14557068	Standard	NM_032229		Approved	FLJ22774	uc001vll.1	Q9H5Y7	OTTHUMG00000017157	ENST00000400286.2:c.125G>C	chr13.hg19:g.86370519C>G	ENSP00000383143:p.Gly42Ala	131.0	0.0		74.0	61.0	NM_032229	A8K9S8|Q495Q0|Q6AW93|Q9HAA8|Q9NT60	Missense_Mutation	SNP	ENST00000400286.2	hg19	CCDS41903.1	.	.	.	.	.	.	.	.	.	.	C	16.84	3.232781	0.58777	.	.	ENSG00000184564	ENST00000400286	T	0.59502	0.26	6.17	6.17	0.99709	.	0.053590	0.85682	D	0.000000	T	0.64360	0.2591	M	0.62723	1.935	0.47341	D	0.999397	D	0.61697	0.99	P	0.50659	0.647	T	0.67031	-0.5773	10	0.72032	D	0.01	-6.7433	13.6567	0.62341	0.0:0.9262:0.0:0.0738	.	42	Q9H5Y7	SLIK6_HUMAN	A	42	ENSP00000383143:G42A	ENSP00000383143:G42A	G	-	2	0	SLITRK6	85268520	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.984000	0.56923	2.941000	0.99782	0.655000	0.94253	GGC	.	.		0.398	SLITRK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045404.2	NM_032229		G	86370519	C	G	86370519	3	3	242	1	0	0	0	0	1	0	0	0	14762	739	26	4	2404	4	SLITRK6	13	86370519	Missense_Mutation	SNP	C	TCGA-ED-A66Y-01A-11D-A30V-10	37419466	86370519	28799359	54	33388										
RNASE1	6035	hgsc.bcm.edu	37	chr14	21270068	21270068	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	gcgcctcatcatttggttacAgtaggtggagctgctgctgg	14	9	2	0			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr14:21270068A>G	ENST00000397967.4	-	2	666	c.160T>C	c.(160-162)Tgt>Cgt	p.C54R	RNASE1_ENST00000412779.2_Missense_Mutation_p.C54R|RNASE1_ENST00000340900.3_Missense_Mutation_p.C54R|RNASE1_ENST00000397970.4_Missense_Mutation_p.C54R|RNASE1_ENST00000555698.1_Missense_Mutation_p.C14R	NM_002933.4	NP_002924.1	P07998	RNAS1_HUMAN	ribonuclease, RNase A family, 1 (pancreatic)	54					RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	extracellular vesicular exosome (GO:0070062)	nucleic acid binding (GO:0003676)|pancreatic ribonuclease activity (GO:0004522)			central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	5	all_cancers(95;0.00671)	all_lung(585;0.235)	Epithelial(56;9.21e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0126)	Guanidine(DB00536)|L-Aspartic Acid(DB00128)	ATTTGGTTACAGTAGGTGGAG	0.567																																					p.C54R		Atlas-SNP	.											.	RNASE1	14	.	0			c.T160C						.						95	88	90					14																	21270068		2203	4300	6503	SO:0001583	missense	6035	exon3			GGTTACAGTAGGT	BC005324	CCDS9559.1	14q11.2	2014-03-13			ENSG00000129538	ENSG00000129538	3.1.27.5	"Ribonucleases, RNase A"	10044	protein-coding gene	gene with protein product		180440		RNS1		8588814	Standard	NM_002933		Approved		uc001vyi.3	P07998	OTTHUMG00000029603	ENST00000397967.4:c.160T>C	chr14.hg19:g.21270068A>G	ENSP00000381057:p.Cys54Arg	49.0	0.0		52.0	22.0	NM_198235	B2R589|D3DS06|Q16830|Q16869|Q1KHR2|Q6ICS5|Q9UCB4|Q9UCB5	Missense_Mutation	SNP	ENST00000397967.4	hg19	CCDS9559.1	.	.	.	.	.	.	.	.	.	.	A	15.00	2.703007	0.48412	.	.	ENSG00000129538	ENST00000397967;ENST00000340900;ENST00000412779;ENST00000555698;ENST00000397970	D;D;D;D;D	0.96802	-4.13;-4.13;-4.13;-4.13;-4.13	5.02	5.02	0.67125	Ribonuclease A, domain (4);	0.000000	0.85682	D	0.000000	D	0.98934	0.9638	H	0.99487	4.59	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.98640	1.0675	10	0.72032	D	0.01	-43.7209	11.0542	0.47909	1.0:0.0:0.0:0.0	.	54	P07998	RNAS1_HUMAN	R	54;54;54;14;54	ENSP00000381057:C54R;ENSP00000344193:C54R;ENSP00000399493:C54R;ENSP00000451058:C14R;ENSP00000381060:C54R	ENSP00000344193:C54R	C	-	1	0	RNASE1	20339908	1.000000	0.71417	0.998000	0.56505	0.116000	0.19942	2.562000	0.45914	2.117000	0.64856	0.459000	0.35465	TGT	.	.		0.567	RNASE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073791.3			G	21270068	A	G	21270068	3	3	242	1	0	0	0	0	1	0	0	0	13414	188	7	2	314	2	RNASE1	14	21270068	Missense_Mutation	SNP	A	TCGA-ED-A66Y-01A-11D-A30V-10		21270068	86079472	55	33389										
SUPT16H	11198	hgsc.bcm.edu	37	chr14	21828639	21828644	+	In_Frame_Del	DEL	TATTAT	TATTAT	-													0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	ctggaacaaagcatgcttaaTattattgtacaaaatatcca							TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	TATTAT	TATTAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr14:21828639_21828644delTATTAT	ENST00000216297.2	-	18	2443_2448	c.2105_2110delATAATA	c.(2104-2112)aataatatt>att	p.NN702del		NM_007192.3	NP_009123.1	Q9Y5B9	SP16H_HUMAN	suppressor of Ty 16 homolog (S. cerevisiae)	702					DNA repair (GO:0006281)|DNA replication (GO:0006260)|gene expression (GO:0010467)|nucleosome disassembly (GO:0006337)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_cancers(95;0.00115)		Epithelial(56;1.62e-06)|all cancers(55;1.49e-05)	GBM - Glioblastoma multiforme(265;0.0159)		GCATGCTTAATATTATTGTACAAAAT	0.388																																					p.702_704del		Pindel	.											.	SUPT16H	84	.	0			c.2106_2111del						.																																			SO:0001651	inframe_deletion	11198	exon18			.	AF152961	CCDS9569.1	14q11.1	2008-08-13	2001-11-28		ENSG00000092201	ENSG00000092201			11465	protein-coding gene	gene with protein product	"facilitates chromatin remodeling 140 kDa subunit"	605012	"suppressor of Ty (S.cerevisiae) 16 homolog"			9489704, 11239457	Standard	NM_007192		Approved	FACT, FACTP140, SPT16/CDC68, FLJ14010, FLJ10857, CDC68	uc001wao.2	Q9Y5B9	OTTHUMG00000029685	ENST00000216297.2:c.2105_2110delATAATA	chr14.hg19:g.21828639_21828644delTATTAT	ENSP00000216297:p.Asn702_Asn703del	230.0	0.0		230.0	48.0	NM_007192	Q6GMT8|Q6P2F1|Q6PJM1|Q9NRX0	In_Frame_Del	DEL	ENST00000216297.2	hg19	CCDS9569.1																																																																																			.	.		0.388	SUPT16H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074025.2			-	21828644	TATTAT	-	21828639	7	5	242	1	0	1	0	1	0	0	0	0	15411	1406	49	0	1069	0	SUPT16H	14	21828639	In_Frame_Del	DEL	TATTAT	TCGA-ED-A66Y-01A-11D-A30V-10	558571	21828639	85520901	56	33390										
GPHN	10243	hgsc.bcm.edu	37	chr14	67147861	67147861	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	caggaatcttgcagaagaccGcagtgggataaatctcaaag	11	8	2	2	rs530173903		TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr14:67147861G>A	ENST00000315266.5	+	2	1222	c.101G>A	c.(100-102)cGc>cAc	p.R34H	GPHN_ENST00000459628.1_Missense_Mutation_p.R34H|GPHN_ENST00000543237.1_Missense_Mutation_p.R34H|GPHN_ENST00000478722.1_Missense_Mutation_p.R34H|GPHN_ENST00000305960.9_Missense_Mutation_p.R34H	NM_001024218.1	NP_001019389.1	Q9NQX3	GEPH_HUMAN	gephyrin	34	MPT Mo-transferase.				establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycine receptor clustering (GO:0072579)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|molybdopterin adenylyltransferase activity (GO:0061598)|molybdopterin molybdotransferase activity (GO:0061599)|transferase activity (GO:0016740)	p.R34H(1)		large_intestine(8)|liver(1)|ovary(2)|stomach(1)	12		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		GCAGAAGACCGCAGTGGGATA	0.308			T	MLL	AL								G|||	1	0.000199681	8e-04	0	5008	,	,		15274	0		0	False		,,,				2504	0				p.R34H		Atlas-SNP	.		Dom	yes		14	14q24	10243	gephyrin (GPH)		L	GPHN_ENST00000478722,colon,carcinoma,0,1	GPHN	79	.	1	Substitution - Missense(1)	large_intestine(1)	c.G101A						.						85	89	88					14																	67147861		2203	4300	6503	SO:0001583	missense	10243	exon2			AAGACCGCAGTGG	AB037806	CCDS9777.1, CCDS32103.1	14q23.3	2008-04-22			ENSG00000171723	ENSG00000171723			15465	protein-coding gene	gene with protein product		603930				1319186, 10325225, 18403029	Standard	XM_005267250		Approved	KIAA1385	uc001xix.3	Q9NQX3	OTTHUMG00000029785	ENST00000315266.5:c.101G>A	chr14.hg19:g.67147861G>A	ENSP00000312771:p.Arg34His	93.0	0.0		92.0	47.0	NM_001024218	Q9H4E9|Q9P2G2	Missense_Mutation	SNP	ENST00000315266.5	hg19	CCDS32103.1	.	.	.	.	.	.	.	.	.	.	G	18.53	3.643659	0.67244	.	.	ENSG00000171723	ENST00000315266;ENST00000478722;ENST00000459628;ENST00000543237;ENST00000305960	T;T;T;T;T	0.77489	-1.1;-1.1;-1.1;-1.1;-1.1	5.11	5.11	0.69529	Molybdenum cofactor synthesis (1);Molybdopterin binding (4);	0.000000	0.85682	D	0.000000	D	0.84723	0.5535	L	0.49455	1.56	0.54753	D	0.99998	P;D;P;D;D	0.89917	0.69;1.0;0.507;0.999;0.998	B;D;B;D;P	0.72338	0.182;0.977;0.052;0.951;0.752	D	0.86042	0.1520	10	0.66056	D	0.02	-3.3065	16.0118	0.80409	0.0:0.0:1.0:0.0	.	34;34;34;34;34	F8W7D6;F5H039;Q9NQX3;Q9NQX3-2;G3V582	.;.;GEPH_HUMAN;.;.	H	34	ENSP00000312771:R34H;ENSP00000417901:R34H;ENSP00000452220:R34H;ENSP00000438404:R34H;ENSP00000303019:R34H	ENSP00000303019:R34H	R	+	2	0	GPHN	66217614	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.659000	0.91116	2.374000	0.81015	0.579000	0.79373	CGC	.	.		0.308	GPHN-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000074299.2	NM_020806		A	67147861	G	A	67147861	3	1	242	1	0	0	0	0	1	0	0	0	6618	1087	38	1	107	1	GPHN	14	67147861	Missense_Mutation	SNP	G	TCGA-ED-A66Y-01A-11D-A30V-10	45319222	67147861	40201679	57	33391										
MGA	23269	hgsc.bcm.edu	37	chr15	42052603	42052603	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	agaagcgtttgcttattatcGccggacacacactgccaatg	9	11	0	1			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr15:42052603G>A	ENST00000570161.1	+	19	7274	c.7274G>A	c.(7273-7275)cGc>cAc	p.R2425H	MGA_ENST00000389936.4_Missense_Mutation_p.R2386H|MGA_ENST00000545763.1_Missense_Mutation_p.R2216H|MGA_ENST00000219905.7_Missense_Mutation_p.R2425H|MGA_ENST00000566586.1_Missense_Mutation_p.R2216H			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	GCTTATTATCGCCGGACACAC	0.453																																					p.R2425H		Atlas-SNP	.											.	MGA	264	.	0			c.G7274A						.						119	119	119					15																	42052603		1907	4120	6027	SO:0001583	missense	23269	exon20			ATTATCGCCGGAC	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.7274G>A	chr15.hg19:g.42052603G>A	ENSP00000457035:p.Arg2425His	129.0	0.0		121.0	77.0	NM_001164273	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	hg19	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.992781	0.93167	.	.	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	D;D;D	0.99158	-5.5;-5.5;-5.5	5.53	5.53	0.82687	.	0.000000	0.52532	D	0.000066	D	0.99336	0.9767	M	0.82630	2.6	0.36413	D	0.863838	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.991	D	0.99955	1.1615	10	0.87932	D	0	.	19.4485	0.94857	0.0:0.0:1.0:0.0	.	1041;2216;2425	B4DVS1;F5H7K2;E7ENI0	.;.;.	H	2425;2386;2216	ENSP00000219905:R2425H;ENSP00000374586:R2386H;ENSP00000442467:R2216H	ENSP00000219905:R2425H	R	+	2	0	MGA	39839895	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.778000	0.75043	2.583000	0.87209	0.655000	0.94253	CGC	.	.		0.453	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		A	42052603	G	A	42052603	3	1	242	1	0	0	0	0	1	0	0	0	9549	1087	38	1	7348	1	MGA	15	42052603	Missense_Mutation	SNP	G	TCGA-ED-A66Y-01A-11D-A30V-10		42052603	60478789	58	33392										
MMP15	4324	hgsc.bcm.edu	37	chr16	58074513	58074513	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	ggagcactccagcaaccccaAtgccatcatggcgccgttct	9	16	2	0	rs147717123		TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr16:58074513A>G	ENST00000219271.3	+	5	1606	c.821A>G	c.(820-822)aAt>aGt	p.N274S		NM_002428.2	NP_002419.1	P51511	MMP15_HUMAN	matrix metallopeptidase 15 (membrane-inserted)	274					cellular protein modification process (GO:0006464)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)|response to estradiol (GO:0032355)	extracellular matrix (GO:0031012)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	18					Marimastat(DB00786)	AGCAACCCCAATGCCATCATG	0.607													A|||	1	0.000199681	8e-04	0	5008	,	,		21006	0		0	False		,,,				2504	0				p.N274S		Atlas-SNP	.											.	MMP15	58	.	0			c.A821G						.	A	SER/ASN	4,4392	8.1+/-20.4	0,4,2194	102	85	91		821	0.5	1	16	dbSNP_134	91	0,8600		0,0,4300	yes	missense	MMP15	NM_002428.2	46	0,4,6494	GG,GA,AA		0.0,0.091,0.0308	benign	274/670	58074513	4,12992	2198	4300	6498	SO:0001583	missense	4324	exon5			ACCCCAATGCCAT	Z48482	CCDS10792.1	16q13	2008-05-14	2005-08-08		ENSG00000102996	ENSG00000102996			7161	protein-coding gene	gene with protein product		602261	"matrix metalloproteinase 15 (membrane-inserted)"			9070935, 9119382	Standard	NM_002428		Approved	MT2-MMP, MTMMP2, SMCP-2	uc002ena.3	P51511	OTTHUMG00000133466	ENST00000219271.3:c.821A>G	chr16.hg19:g.58074513A>G	ENSP00000219271:p.Asn274Ser	71.0	0.0		32.0	24.0	NM_002428	A0A2U6|Q14111	Missense_Mutation	SNP	ENST00000219271.3	hg19	CCDS10792.1	.	.	.	.	.	.	.	.	.	.	A	1.918	-0.449009	0.04572	9.1E-4	0.0	ENSG00000102996	ENST00000219271	T	0.21361	2.01	5.17	0.52	0.17040	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.402298	0.29987	N	0.010697	T	0.04137	0.0115	N	0.00690	-1.25	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.43686	-0.9376	10	0.02654	T	1	.	7.4918	0.27466	0.1477:0.3817:0.4706:0.0	.	274	P51511	MMP15_HUMAN	S	274	ENSP00000219271:N274S	ENSP00000219271:N274S	N	+	2	0	MMP15	56632014	0.033000	0.19621	0.954000	0.39281	0.950000	0.60333	0.463000	0.21972	0.195000	0.20347	-0.313000	0.08912	AAT	.	A|1.000;G|0.000		0.607	MMP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257342.1	NM_002428		G	58074513	A	G	58074513	3	3	242	1	0	0	0	0	1	0	0	0	9663	101	4	2	839	2	MMP15	16	58074513	Missense_Mutation	SNP	A	TCGA-ED-A66Y-01A-11D-A30V-10		58074513	32280240	59	33393										
CHD3	1107	hgsc.bcm.edu	37	chr17	7798720	7798720	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	ggtggggggagccacctgtaGcagtgccagcccctcaacag	15	13	1	0			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr17:7798720G>A	ENST00000330494.7	+	10	1717	c.1567G>A	c.(1567-1569)Gca>Aca	p.A523T	CHD3_ENST00000380358.4_Missense_Mutation_p.A582T|CHD3_ENST00000358181.4_Missense_Mutation_p.A523T	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	523	Chromo 1. {ECO:0000255|PROSITE- ProRule:PRU00053}.				centrosome organization (GO:0051297)|chromatin assembly or disassembly (GO:0006333)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|spindle organization (GO:0007051)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(11)|kidney(6)|large_intestine(13)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	65		Prostate(122;0.202)				GCCACCTGTAGCAGTGCCAGC	0.572																																					p.A582T		Atlas-SNP	.											.	CHD3	169	.	0			c.G1744A						.						99	85	90					17																	7798720		2203	4300	6503	SO:0001583	missense	1107	exon10			CCTGTAGCAGTGC	U08379	CCDS32553.2, CCDS32554.1, CCDS32555.1	17p13	2013-01-28			ENSG00000170004	ENSG00000170004		"Zinc fingers, PHD-type"	1918	protein-coding gene	gene with protein product		602120				9326634, 7560064	Standard	NM_001005271		Approved	Mi-2a, ZFH, Mi2-ALPHA	uc002gjd.2	Q12873	OTTHUMG00000150427	ENST00000330494.7:c.1567G>A	chr17.hg19:g.7798720G>A	ENSP00000332628:p.Ala523Thr	88.0	0.0		61.0	32.0	NM_001005271	D3DTQ9|E9PG89|Q9Y4I0	Missense_Mutation	SNP	ENST00000330494.7	hg19	CCDS32554.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.350|8.350	0.830587|0.830587	0.16820|0.16820	.|.	.|.	ENSG00000170004|ENSG00000170004	ENST00000380358;ENST00000358181;ENST00000330494|ENST00000452447	D;D;D|.	0.90133|.	-2.62;-2.56;-2.56|.	5.4|5.4	1.08|1.08	0.20341|0.20341	Chromo domain-like (1);Chromo domain/shadow (1);|.	0.308380|.	0.23250|.	N|.	0.050241|.	T|T	0.28333|0.28333	0.0700|0.0700	N|N	0.20685|0.20685	0.6|0.6	0.21064|0.21064	N|N	0.999799|0.999799	B;B;B|.	0.06786|.	0.001;0.0;0.001|.	B;B;B|.	0.08055|.	0.003;0.001;0.003|.	T|T	0.25152|0.25152	-1.0140|-1.0140	10|5	0.38643|.	T|.	0.18|.	-0.9048|-0.9048	9.4055|9.4055	0.38460|0.38460	0.0648:0.0:0.5507:0.3845|0.0648:0.0:0.5507:0.3845	.|.	523;523;582|.	Q12873-2;Q12873;E9PG89|.	.;CHD3_HUMAN;.|.	T|N	582;523;523|393	ENSP00000369716:A582T;ENSP00000350907:A523T;ENSP00000332628:A523T|.	ENSP00000332628:A523T|.	A|S	+|+	1|2	0|0	CHD3|CHD3	7739445|7739445	0.005000|0.005000	0.15991|0.15991	0.801000|0.801000	0.32222|0.32222	0.197000|0.197000	0.23852|0.23852	0.926000|0.926000	0.28804|0.28804	0.088000|0.088000	0.17205|0.17205	-0.314000|-0.314000	0.08810|0.08810	GCA|AGC	.	.		0.572	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1	NM_001005273		A	7798720	G	A	7798720	3	1	242	1	0	0	0	0	1	0	0	0	3328	971	34	3	1886	3	CHD3	17	7798720	Missense_Mutation	SNP	G	TCGA-ED-A66Y-01A-11D-A30V-10		7798720	73396490	60	33394										
KRT38	8687	hgsc.bcm.edu	37	chr17	39595474	39595474	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	cctgctcgtggttgctcttgAgggagagctgctcctccttc	12	13	1	2			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr17:39595474A>T	ENST00000246646.3	-	3	712	c.713T>A	c.(712-714)cTc>cAc	p.L238H		NM_006771.3	NP_006762.3	O76015	KRT38_HUMAN	keratin 38	238	Coil 1B.|Rod.					extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	29		Breast(137;0.000496)				GTTGCTCTTGAGGGAGAGCTG	0.652																																					p.L238H		Atlas-SNP	.											.	KRT38	63	.	0			c.T713A						.						52	48	49					17																	39595474		2203	4300	6503	SO:0001583	missense	8687	exon3			CTCTTGAGGGAGA	Y16794	CCDS11392.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000171360	ENSG00000171360		"-", "Intermediate filaments type I, keratins (acidic)"	6456	protein-coding gene	gene with protein product		604542	"keratin, hair, acidic, 8"	KRTHA8		9756910, 16831889	Standard	NM_006771		Approved		uc002hwq.1	O76015	OTTHUMG00000133439	ENST00000246646.3:c.713T>A	chr17.hg19:g.39595474A>T	ENSP00000246646:p.Leu238His	55.0	0.0		28.0	12.0	NM_006771	A2RRM5|Q6A164	Missense_Mutation	SNP	ENST00000246646.3	hg19	CCDS11392.1	.	.	.	.	.	.	.	.	.	.	A	17.41	3.382271	0.61845	.	.	ENSG00000171360	ENST00000246646	D	0.91011	-2.77	4.31	4.31	0.51392	Filament (1);	0.000000	0.41500	D	0.000877	D	0.97139	0.9065	H	0.98738	4.315	0.37050	D	0.897551	D	0.89917	1.0	D	0.77557	0.99	D	0.99924	1.1274	10	0.87932	D	0	.	12.7835	0.57491	1.0:0.0:0.0:0.0	.	238	O76015	KRT38_HUMAN	H	238	ENSP00000246646:L238H	ENSP00000246646:L238H	L	-	2	0	KRT38	36849000	1.000000	0.71417	0.988000	0.46212	0.522000	0.34438	7.004000	0.76317	1.812000	0.52913	0.397000	0.26171	CTC	.	.		0.652	KRT38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257307.2	NM_006771		T	39595474	A	T	39595474	3	4	242	1	0	0	0	0	1	0	0	0	8484	304	11	4	677	4	KRT38	17	39595474	Missense_Mutation	SNP	A	TCGA-ED-A66Y-01A-11D-A30V-10	31796754	39595474	41599736	61	33395										
ZFP161	7541	hgsc.bcm.edu	37	chr18	5290910	5290910	+	Frame_Shift_Del	DEL	C	C	-													0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	tgcttccgcagccatcgctgCcgcctgcaactgttctgtct							TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr18:5290910delC	ENST00000357006.4	-	4	1635	c.1297delG	c.(1297-1299)gcafs	p.A434fs	ZBTB14_ENST00000400143.3_Frame_Shift_Del_p.A434fs	NM_001143823.2|NM_001243704.1	NP_001137295.1|NP_001230633.1	O43829	ZBT14_HUMAN	zinc finger and BTB domain containing 14	434					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)										GCCATCGCTGCCGCCTGCAAC	0.552																																					p.A433fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.1298delC						.						118	95	102					18																	5290910		2203	4300	6503	SO:0001589	frameshift_variant	7541	exon4			.	D89859	CCDS11837.1	18p11.31	2013-09-19	2013-01-08	2013-01-08	ENSG00000198081	ENSG00000198081		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	12860	protein-coding gene	gene with protein product		602126	"zinc finger protein 161 homolog (mouse)", "zinc finger protein 161", "ZFP161 zinc finger protein"	ZFP161		9244432	Standard	NM_001243702		Approved	ZNF478	uc010dkp.3	O43829	OTTHUMG00000131563	ENST00000357006.4:c.1297delG	chr18.hg19:g.5290910delC	ENSP00000349503:p.Ala434fs	74.0	0.0		48.0	23.0	NM_001243702	O00403|Q2TB80	Frame_Shift_Del	DEL	ENST00000357006.4	hg19	CCDS11837.1																																																																																			.	.		0.552	ZBTB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254425.1	NM_003409		-	5290910	C	-	5290910	7	5	242	1	0	1	0	1	0	0	0	0	17655	739	26	0	56	0	ZFP161	18	5290910	Frame_Shift_Del	DEL	C	TCGA-ED-A66Y-01A-11D-A30V-10		5290910	72786338	62	33396										
EPB41L3	23136	hgsc.bcm.edu	37	chr18	5419718	5419718	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	tgggagctatacctttccctCgtgccggatggccgagatgg	14	11	0	1			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr18:5419718C>A	ENST00000341928.2	-	12	1838	c.1498G>T	c.(1498-1500)Gag>Tag	p.E500*	EPB41L3_ENST00000427684.2_5'UTR|EPB41L3_ENST00000540638.2_Nonsense_Mutation_p.E518*|EPB41L3_ENST00000544123.1_Nonsense_Mutation_p.E518*|EPB41L3_ENST00000342933.3_Nonsense_Mutation_p.E500*|EPB41L3_ENST00000542146.1_5'UTR|EPB41L3_ENST00000400111.3_Nonsense_Mutation_p.E518*|EPB41L3_ENST00000542652.2_5'UTR	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	500	Hydrophilic.				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						ACCTTTCCCTCGTGCCGGATG	0.542																																					p.E500X		Atlas-SNP	.											EPB41L3,lower_third,carcinoma,0,1	EPB41L3	222	.	0			c.G1498T						.						168	122	137					18																	5419718		2203	4300	6503	SO:0001587	stop_gained	23136	exon12			TTCCCTCGTGCCG	AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.1498G>T	chr18.hg19:g.5419718C>A	ENSP00000343158:p.Glu500*	42.0	0.0		39.0	23.0	NM_012307	B7Z4I5|F5GX05|O95713|Q9BRP5	Nonsense_Mutation	SNP	ENST00000341928.2	hg19	CCDS11838.1	.	.	.	.	.	.	.	.	.	.	C	42	9.250942	0.99115	.	.	ENSG00000082397	ENST00000341928;ENST00000540638;ENST00000544123;ENST00000545076;ENST00000342933;ENST00000400111	.	.	.	5.61	5.61	0.85477	.	1.720280	0.02468	N	0.087254	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	.	18.9964	0.92815	0.0:1.0:0.0:0.0	.	.	.	.	X	500;409;518;409;500;518	.	ENSP00000343158:E500X	E	-	1	0	EPB41L3	5409718	1.000000	0.71417	0.984000	0.44739	0.995000	0.86356	5.481000	0.66826	2.808000	0.96608	0.655000	0.94253	GAG	.	.		0.542	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307		A	5419718	C	A	5419718	4	1	242	1	0	0	0	0	0	1	0	0	5156	893	31	1	1809	1	EPB41L3	18	5419718	Nonsense_Mutation	SNP	C	TCGA-ED-A66Y-01A-11D-A30V-10	128808	5419718	72657530	63	33397										
CDC37	11140	hgsc.bcm.edu	37	chr19	10506763	10506763	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	tctgccttgccgccctcggcCacctccagctccttcagttt	7	19	2	0			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr19:10506763C>T	ENST00000222005.2	-	2	272	c.219G>A	c.(217-219)gtG>gtA	p.V73V		NM_007065.3	NP_008996.1	Q16543	CDC37_HUMAN	cell division cycle 37	73					protein targeting (GO:0006605)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	heat shock protein binding (GO:0031072)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	16			OV - Ovarian serous cystadenocarcinoma(20;4.65e-10)|Epithelial(33;6.48e-07)|all cancers(31;2.31e-06)	GBM - Glioblastoma multiforme(1328;0.0318)		CGCCCTCGGCCACCTCCAGCT	0.657																																					p.V73V		Atlas-SNP	.											.	CDC37	32	.	0			c.G219A						.						90	91	91					19																	10506763		2203	4300	6503	SO:0001819	synonymous_variant	11140	exon2			CTCGGCCACCTCC	U63131	CCDS12237.1	19p13.2	2013-01-17	2013-01-17		ENSG00000105401	ENSG00000105401			1735	protein-coding gene	gene with protein product	"CDC37 cell division cycle 37 homolog", "Hsp90 co-chaperone Cdc37", "CDC37 (cell division cycle 37, S. cerevisiae, homolog)"	605065	"CDC37 (cell division cycle 37, S. cerevisiae, homolog)", "CDC37 cell division cycle 37 homolog (S. cerevisiae)", "cell division cycle 37 homolog (S. cerevisiae)"			8703009, 8666233	Standard	NM_007065		Approved	P50CDC37	uc002mof.1	Q16543		ENST00000222005.2:c.219G>A	chr19.hg19:g.10506763C>T		87.0	0.0		95.0	31.0	NM_007065	Q53YA2	Silent	SNP	ENST00000222005.2	hg19	CCDS12237.1																																																																																			.	.		0.657	CDC37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451987.1	NM_007065		T	10506763	C	T	10506763	2	4	242	1	0	0	0	0	0	0	0	1	3070	581	21	3		3	CDC37	19	10506763	Silent	SNP	C	TCGA-ED-A66Y-01A-11D-A30V-10		10506763	48622220	64	33398										
SMARCA4	6597	hgsc.bcm.edu	37	chr19	11132515	11132515	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	cccgccgcctgctgctgacgGgcacaccgctgcagaacaag	12	17	0	2			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr19:11132515G>A	ENST00000429416.3	+	20	3012	c.2731G>A	c.(2731-2733)Ggc>Agc	p.G911S	SMARCA4_ENST00000450717.3_Missense_Mutation_p.G911S|SMARCA4_ENST00000541122.2_Missense_Mutation_p.G911S|SMARCA4_ENST00000589677.1_Missense_Mutation_p.G911S|SMARCA4_ENST00000444061.3_Missense_Mutation_p.G911S|SMARCA4_ENST00000358026.2_Missense_Mutation_p.G911S|SMARCA4_ENST00000590574.1_Missense_Mutation_p.G911S|SMARCA4_ENST00000413806.3_Missense_Mutation_p.G911S|SMARCA4_ENST00000344626.4_Missense_Mutation_p.G911S	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	911	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				GCTGCTGACGGGCACACCGCT	0.592			"F, N, Mis"		NSCLC																																p.G911S		Atlas-SNP	.		Rec	yes		19	19p13.2	6597	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"		E	.	SMARCA4	502	.	1	Unknown(1)	lung(1)	c.G2731A						.						91	69	76					19																	11132515		2203	4300	6503	SO:0001583	missense	6597	exon19			CTGACGGGCACAC	D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"SNF2-like 4", "global transcription activator homologous sequence", "sucrose nonfermenting-like 4", "mitotic growth and transcription activator", "BRM/SWI2-related gene 1", "homeotic gene regulator", "nuclear protein GRB1", "brahma protein-like 1", "ATP-dependent helicase SMARCA4"	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.2731G>A	chr19.hg19:g.11132515G>A	ENSP00000395654:p.Gly911Ser	51.0	0.0		58.0	20.0	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	hg19	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	G	19.03	3.747479	0.69533	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	D;D;D;D;D;D;D	0.95821	-3.82;-3.82;-3.82;-3.82;-3.82;-3.82;-3.82	4.51	4.51	0.55191	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.85682	D	0.000000	D	0.98798	0.9595	H	0.99197	4.465	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.997;0.999;0.999;0.999	D	0.99278	1.0895	10	0.87932	D	0	-36.4224	16.1519	0.81629	0.0:0.0:1.0:0.0	.	911;911;911;911;911;131;911;911	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;A7E2E1;P51532	.;.;.;.;.;.;.;SMCA4_HUMAN	S	911;911;975;911;911;911;911;911	ENSP00000395654:G911S;ENSP00000350720:G911S;ENSP00000343896:G911S;ENSP00000445036:G911S;ENSP00000392837:G911S;ENSP00000397783:G911S;ENSP00000414727:G911S	ENSP00000343896:G911S	G	+	1	0	SMARCA4	10993515	1.000000	0.71417	0.988000	0.46212	0.003000	0.03518	9.657000	0.98554	2.348000	0.79779	0.655000	0.94253	GGC	.	.		0.592	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		A	11132515	G	A	11132515	3	1	242	1	0	0	0	0	1	0	0	0	14785	1232	43	3	2801	3	SMARCA4	19	11132515	Missense_Mutation	SNP	G	TCGA-ED-A66Y-01A-11D-A30V-10	625752	11132515	47996468	65	33399										
ELAVL3	1995	hgsc.bcm.edu	37	chr19	11577461	11577461	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	ccaacttgcaggactcgatgTcgccaatgctgccgaagaga	11	12	0	1			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr19:11577461T>C	ENST00000359227.3	-	2	615	c.191A>G	c.(190-192)gAc>gGc	p.D64G	RN7SL669P_ENST00000581926.1_RNA|CTC-398G3.6_ENST00000585656.1_3'UTR|ELAVL3_ENST00000438662.2_Missense_Mutation_p.D64G	NM_001420.3|NM_032281.2	NP_001411.2|NP_115657.2	Q14576	ELAV3_HUMAN	ELAV like neuron-specific RNA binding protein 3	64	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)		AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)			breast(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	15						GGACTCGATGTCGCCAATGCT	0.542																																					p.D64G		Atlas-SNP	.											.	ELAVL3	58	.	0			c.A191G						.						162	142	149					19																	11577461		2203	4300	6503	SO:0001583	missense	1995	exon2			TCGATGTCGCCAA		CCDS32912.1, CCDS45978.1	19p13.2	2013-10-03	2013-10-03			ENSG00000196361		"RNA binding motif (RRM) containing"	3314	protein-coding gene	gene with protein product	"Hu antigen C", "paraneoplastic limbic encephalitis antigen 21", "paraneoplastic cerebellar degeneration-associated antigen", "ELAV-like protein 3"	603458	"ELAV (embryonic lethal, abnormal vision, Drosophila)-like 3 (Hu antigen C)"			9799595	Standard	NM_001420		Approved	HUC, PLE21, DKFZp547J036, HUCL, MGC20653	uc002mry.1	Q14576		ENST00000359227.3:c.191A>G	chr19.hg19:g.11577461T>C	ENSP00000352162:p.Asp64Gly	67.0	0.0		87.0	44.0	NM_032281	Q16135|Q96CL8|Q96QS9	Missense_Mutation	SNP	ENST00000359227.3	hg19	CCDS32912.1	.	.	.	.	.	.	.	.	.	.	T	18.40	3.614948	0.66672	.	.	ENSG00000196361	ENST00000359227;ENST00000438662	T;T	0.74842	-0.88;2.38	4.83	4.83	0.62350	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.055425	0.64402	D	0.000001	T	0.70815	0.3267	L	0.37466	1.105	0.58432	D	0.999992	B;B	0.27286	0.005;0.174	B;B	0.37989	0.061;0.262	T	0.72697	-0.4215	10	0.87932	D	0	.	13.5217	0.61572	0.0:0.0:0.0:1.0	.	64;64	Q14576;Q14576-2	ELAV3_HUMAN;.	G	64	ENSP00000352162:D64G;ENSP00000390878:D64G	ENSP00000352162:D64G	D	-	2	0	ELAVL3	11438461	1.000000	0.71417	0.991000	0.47740	0.970000	0.65996	7.705000	0.84606	2.040000	0.60383	0.523000	0.50628	GAC	.	.		0.542	ELAVL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458827.2	NM_001420		C	11577461	T	C	11577461	3	2	242	1	0	0	0	0	1	0	0	0	5053	1667	58	2	936	2	ELAVL3	19	11577461	Missense_Mutation	SNP	T	TCGA-ED-A66Y-01A-11D-A30V-10	444946	11577461	47551522	66	33400										
OR10H4	126541	hgsc.bcm.edu	37	chr19	16059854	16059854	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	atagcatcatatctgaatttAacctctttggcttctcagcc	5	11	4	1			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr19:16059854A>T	ENST00000322107.1	+	1	37	c.37A>T	c.(37-39)Aac>Tac	p.N13Y		NM_001004465.1	NP_001004465.1	Q8NGA5	O10H4_HUMAN	olfactory receptor, family 10, subfamily H, member 4	13						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	17						ATCTGAATTTAACCTCTTTGG	0.438																																					p.N13Y		Atlas-SNP	.											.	OR10H4	48	.	0			c.A37T						.						249	217	228					19																	16059854		2203	4300	6503	SO:0001583	missense	126541	exon1			GAATTTAACCTCT	AC011517	CCDS32941.1	19p13.12	2013-09-24			ENSG00000176231	ENSG00000176231		"GPCR / Class A : Olfactory receptors"	15388	protein-coding gene	gene with protein product							Standard	NM_001004465		Approved		uc010xov.2	Q8NGA5	OTTHUMG00000182268	ENST00000322107.1:c.37A>T	chr19.hg19:g.16059854A>T	ENSP00000318834:p.Asn13Tyr	73.0	0.0		82.0	38.0	NM_001004465	Q6IFJ2|Q96R57	Missense_Mutation	SNP	ENST00000322107.1	hg19	CCDS32941.1	.	.	.	.	.	.	.	.	.	.	a	6.992	0.553063	0.13374	.	.	ENSG00000176231	ENST00000322107	T	0.02974	4.09	1.53	0.142	0.14816	.	0.169496	0.27482	U	0.019179	T	0.00906	0.0030	N	0.00436	-1.5	0.09310	N	1	B	0.20887	0.049	B	0.25987	0.065	T	0.47812	-0.9088	10	0.72032	D	0.01	.	5.1888	0.15199	0.4575:0.5425:0.0:0.0	.	13	Q8NGA5	O10H4_HUMAN	Y	13	ENSP00000318834:N13Y	ENSP00000318834:N13Y	N	+	1	0	OR10H4	15920854	0.951000	0.32395	0.013000	0.15412	0.013000	0.08279	0.601000	0.24119	0.691000	0.31592	0.386000	0.25728	AAC	.	.		0.438	OR10H4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460311.1			T	16059854	A	T	16059854	3	4	242	1	0	0	0	0	1	0	0	0	10917	362	13	4	39	4	OR10H4	19	16059854	Missense_Mutation	SNP	A	TCGA-ED-A66Y-01A-11D-A30V-10	4482393	16059854	43069129	67	33401										
CPAMD8	27151	hgsc.bcm.edu	37	chr19	17091417	17091417	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	ggcccgatagcacaatattgCcccgtgcagccacctcgtag	10	15	0	0			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr19:17091417C>T	ENST00000443236.1	-	14	1647	c.1616G>A	c.(1615-1617)gGc>gAc	p.G539D	CPAMD8_ENST00000388925.4_Intron	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	492			D -> E (in dbSNP:rs3745335).			extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						CACAATATTGCCCCGTGCAGC	0.562																																					p.G539D		Atlas-SNP	.											CPAMD8,right_lower_lobe,carcinoma,0,1	CPAMD8	192	.	0			c.G1616A						.						71	77	75					19																	17091417		2004	4170	6174	SO:0001583	missense	27151	exon14			ATATTGCCCCGTG	AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.1616G>A	chr19.hg19:g.17091417C>T	ENSP00000402505:p.Gly539Asp	89.0	0.0		89.0	40.0	NM_015692	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	hg19	CCDS42519.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.89|15.89	2.965350|2.965350	0.53507|0.53507	.|.	.|.	ENSG00000160111|ENSG00000160111	ENST00000443236|ENST00000291440	.|.	.|.	.|.	2.9|2.9	2.9|2.9	0.33743|0.33743	.|Alpha-2-macroglobulin, N-terminal 2 (1);	.|0.000000	.|0.64402	.|U	.|0.000004	D|D	0.84566|0.84566	0.5500|0.5500	M|M	0.92784|0.92784	3.345|3.345	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.91635	.|0.999	D|D	0.88464|0.88464	0.3057|0.3057	5|9	.|0.87932	.|D	.|0	.|.	13.7238|13.7238	0.62745|0.62745	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|492	.|Q8IZJ3	.|CPMD8_HUMAN	T|D	550|539	.|.	.|ENSP00000291440:G539D	A|G	-|-	1|2	0|0	CPAMD8|CPAMD8	16952417|16952417	1.000000|1.000000	0.71417|0.71417	0.922000|0.922000	0.36590|0.36590	0.155000|0.155000	0.21991|0.21991	4.624000|4.624000	0.61254|0.61254	1.184000|1.184000	0.42957|0.42957	0.467000|0.467000	0.42956|0.42956	GCA|GGC	.	.		0.562	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692		T	17091417	C	T	17091417	3	4	242	1	0	0	0	0	1	0	0	0	3797	739	26	3	4298	3	CPAMD8	19	17091417	Missense_Mutation	SNP	C	TCGA-ED-A66Y-01A-11D-A30V-10	1031563	17091417	42037566	68	33402										
ZNF30	90075	hgsc.bcm.edu	37	chr19	35435350	35435350	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	aggaatgtggaaagacttttAgtcgagcctcgtaccttgta	11	7	0	1			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr19:35435350A>G	ENST00000601142.1	+	5	1717	c.1480A>G	c.(1480-1482)Agt>Ggt	p.S494G	ZNF30_ENST00000426813.2_Missense_Mutation_p.S413G|ZNF30_ENST00000439785.1_Missense_Mutation_p.S495G|ZNF30_ENST00000303586.7_Missense_Mutation_p.S495G|ZNF30_ENST00000601957.1_3'UTR			P17039	ZNF30_HUMAN	zinc finger protein 30	494					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)	16	all_lung(56;8.38e-08)|Lung NSC(56;1.31e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)	GBM - Glioblastoma multiforme(1328;0.0265)		AAAGACTTTTAGTCGAGCCTC	0.453																																					p.S495G		Atlas-SNP	.											.	ZNF30	44	.	0			c.A1483G						.						84	91	89					19																	35435350		2199	4299	6498	SO:0001583	missense	90075	exon5			ACTTTTAGTCGAG	X52359	CCDS46044.1, CCDS46045.1	19q13.13	2013-01-08	2006-05-10			ENSG00000168661		"Zinc fingers, C2H2-type", "-"	13090	protein-coding gene	gene with protein product			"zinc finger protein 30 (KOX 28)"				Standard	NM_001099437		Approved	KOX28, DKFZp686N19164, FLJ20562	uc010edq.1	P17039		ENST00000601142.1:c.1480A>G	chr19.hg19:g.35435350A>G	ENSP00000469954:p.Ser494Gly	79.0	0.0		64.0	31.0	NM_001099438	A5PLP1|A8K320|B4DIC0|Q6N068	Missense_Mutation	SNP	ENST00000601142.1	hg19	CCDS46045.1	.	.	.	.	.	.	.	.	.	.	a	9.150	1.016152	0.19355	.	.	ENSG00000168661	ENST00000439785;ENST00000303586;ENST00000426813;ENST00000342559	T;T	0.07567	3.18;3.18	2.42	1.2	0.21068	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05777	0.0151	L	0.34521	1.04	0.09310	N	1	B;B	0.30281	0.236;0.275	B;B	0.20577	0.028;0.03	T	0.33189	-0.9878	9	0.49607	T	0.09	.	5.7624	0.18207	0.7624:0.0:0.0:0.2376	.	495;494	P17039-2;P17039	.;ZNF30_HUMAN	G	495;494;413;203	ENSP00000403441:S495G;ENSP00000416457:S413G	ENSP00000303889:S494G	S	+	1	0	ZNF30	40127190	0.000000	0.05858	0.001000	0.08648	0.053000	0.15095	0.316000	0.19469	1.111000	0.41721	0.416000	0.27883	AGT	.	.		0.453	ZNF30-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464432.1	NM_194325		G	35435350	A	G	35435350	3	3	242	1	0	0	0	0	1	0	0	0	17845	420	15	2	1497	2	ZNF30	19	35435350	Missense_Mutation	SNP	A	TCGA-ED-A66Y-01A-11D-A30V-10	18343933	35435350	23693633	69	33403										
NLRP9	338321	hgsc.bcm.edu	37	chr19	56223263	56223263	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	ccagtcgaggttcaggctccTcagtgttttgcaggcgatga	13	10	2	1			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr19:56223263T>A	ENST00000332836.2	-	8	2773	c.2746A>T	c.(2746-2748)Agg>Tgg	p.R916W	CTD-2611O12.7_ENST00000597680.1_RNA|CTD-2611O12.8_ENST00000596293.1_RNA	NM_176820.2	NP_789790.2	Q7RTR0	NALP9_HUMAN	NLR family, pyrin domain containing 9	916						cytoplasm (GO:0005737)	ATP binding (GO:0005524)			NS(2)|breast(5)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(15)|lung(21)|ovary(2)|prostate(3)|skin(7)|urinary_tract(3)	74		Colorectal(82;0.000133)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.123)		TTCAGGCTCCTCAGTGTTTTG	0.587																																					p.R916W		Atlas-SNP	.											.	NLRP9	163	.	0			c.A2746T						.						103	83	90					19																	56223263		2202	4299	6501	SO:0001583	missense	338321	exon8			GGCTCCTCAGTGT	AY154464	CCDS12934.1	19q13.43	2006-12-08	2006-12-08	2006-12-08				"Nucleotide-binding domain and leucine rich repeat containing"	22941	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 9"	609663	"NACHT, leucine rich repeat and PYD containing 9"	NALP9		12563287	Standard	NM_176820		Approved	NOD6, PAN12, CLR19.1	uc002qly.3	Q7RTR0		ENST00000332836.2:c.2746A>T	chr19.hg19:g.56223263T>A	ENSP00000331857:p.Arg916Trp	69.0	0.0		80.0	47.0	NM_176820	B2RN12|Q86W27	Missense_Mutation	SNP	ENST00000332836.2	hg19	CCDS12934.1	.	.	.	.	.	.	.	.	.	.	T	14.26	2.481527	0.44147	.	.	ENSG00000185792	ENST00000332836;ENST00000333452	T	0.52754	0.65	3.09	-0.674	0.11369	.	.	.	.	.	T	0.42040	0.1185	M	0.64997	1.995	0.09310	N	1	B	0.19935	0.04	B	0.15870	0.014	T	0.38672	-0.9650	9	0.51188	T	0.08	.	8.9279	0.35652	0.0:0.0:0.6137:0.3863	.	916	Q7RTR0	NALP9_HUMAN	W	916	ENSP00000331857:R916W	ENSP00000331857:R916W	R	-	1	2	NLRP9	60915075	0.016000	0.18221	0.002000	0.10522	0.035000	0.12851	0.104000	0.15313	-0.197000	0.10350	0.529000	0.55759	AGG	.	.		0.587	NLRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453653.1	NM_176820		A	56223263	T	A	56223263	3	1	242	1	0	0	0	0	1	0	0	0	10493	1550	54	4	237	4	NLRP9	19	56223263	Missense_Mutation	SNP	T	TCGA-ED-A66Y-01A-11D-A30V-10	20787913	56223263	2905720	70	33404										
CTNNBL1	56259	hgsc.bcm.edu	37	chr20	36431330	36431330	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	accatgccatgattggccccGaaggcacagacaactgccat	9	14	0	2			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr20:36431330G>T	ENST00000361383.6	+	11	1210	c.1093G>T	c.(1093-1095)Gaa>Taa	p.E365*	CTNNBL1_ENST00000473857.1_3'UTR|CTNNBL1_ENST00000405275.2_Nonsense_Mutation_p.E338*|CTNNBL1_ENST00000373473.1_Nonsense_Mutation_p.E178*|CTNNBL1_ENST00000373469.1_Nonsense_Mutation_p.E113*	NM_030877.3	NP_110517.2	Q8WYA6	CTBL1_HUMAN	catenin, beta like 1	365					apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|positive regulation of apoptotic process (GO:0043065)|RNA splicing (GO:0008380)|somatic diversification of immunoglobulins (GO:0016445)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|Prp19 complex (GO:0000974)|spliceosomal complex (GO:0005681)	enzyme binding (GO:0019899)			autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(6)|lung(6)|ovary(3)|urinary_tract(1)	28		Myeloproliferative disorder(115;0.00878)				GATTGGCCCCGAAGGCACAGA	0.468																																					p.E365X	Ovarian(184;582 2038 3273 4106 42608)	Atlas-SNP	.											.	CTNNBL1	78	.	0			c.G1093T						.						131	121	124					20																	36431330		2203	4300	6503	SO:0001587	stop_gained	56259	exon11			GGCCCCGAAGGCA	AL023804	CCDS13298.1	20q11.23-q12	2011-06-03	2002-05-27	2002-05-31	ENSG00000132792	ENSG00000132792			15879	protein-coding gene	gene with protein product	"nuclear associated protein"	611537	"chromosome 20 open reading frame 33"	C20orf33		12659813, 21385873	Standard	NM_030877		Approved	FLJ21108, P14L, P14, NAP, NYD-SP19	uc021wdj.1	Q8WYA6	OTTHUMG00000032428	ENST00000361383.6:c.1093G>T	chr20.hg19:g.36431330G>T	ENSP00000355050:p.Glu365*	154.0	0.0		150.0	68.0	NM_030877	B4DE16|Q0VAL9|Q0VAM0|Q53HI8|Q5JWZ2|Q5JWZ3|Q5JWZ7|Q5JWZ8|Q8N454|Q8NCL2|Q8TBD6|Q96KD2|Q9H7A5|Q9NQF9|Q9NTX0|Q9Y3M7	Nonsense_Mutation	SNP	ENST00000361383.6	hg19	CCDS13298.1	.	.	.	.	.	.	.	.	.	.	G	40	7.969218	0.98588	.	.	ENSG00000132792	ENST00000361383;ENST00000405275;ENST00000373473;ENST00000373469	.	.	.	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.16896	T	0.51	-25.273	18.4237	0.90602	0.0:0.0:1.0:0.0	.	.	.	.	X	365;338;178;113	.	ENSP00000355050:E365X	E	+	1	0	CTNNBL1	35864744	1.000000	0.71417	0.972000	0.41901	0.822000	0.46500	9.750000	0.98875	2.593000	0.87608	0.462000	0.41574	GAA	.	.		0.468	CTNNBL1-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079125.1	NM_030877		T	36431330	G	T	36431330	4	4	242	1	0	0	0	0	0	1	0	0	4020	1059	37	1	1135	1	CTNNBL1	20	36431330	Nonsense_Mutation	SNP	G	TCGA-ED-A66Y-01A-11D-A30V-10		36431330	26594190	71	33405										
DONSON	29980	hgsc.bcm.edu	37	chr21	34958454	34958454	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	ctcagtactttttgaggacgGaatatcaggctcggagaatg	12	7	2	2			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr21:34958454G>T	ENST00000303071.5	-	3	502	c.436C>A	c.(436-438)Ccg>Acg	p.P146T	DONSON_ENST00000303113.6_Missense_Mutation_p.P146T|DONSON_ENST00000453626.1_Missense_Mutation_p.P146T|AP000304.12_ENST00000429238.1_Missense_Mutation_p.S107Y|DONSON_ENST00000432378.1_Missense_Mutation_p.P146T	NM_017613.3	NP_060083.1	Q9NYP3	DONS_HUMAN	downstream neighbor of SON	146					multicellular organismal development (GO:0007275)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(1)|ovary(1)	11						TTTGAGGACGGAATATCAGGC	0.383											OREG0003565	type=REGULATORY REGION|Gene=DONSON|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.P146T		Atlas-SNP	.											.	DONSON	34	.	0			c.C436A						.						65	58	60					21																	34958454		2203	4300	6503	SO:0001583	missense	29980	exon3			AGGACGGAATATC	AF000002	CCDS13632.1	21q22.1	2008-07-31			ENSG00000159147	ENSG00000159147			2993	protein-coding gene	gene with protein product		611428		C21orf60		10773462, 10950926	Standard	NM_017613		Approved	B17, C2TA, DKFZP434M035	uc002ysk.4	Q9NYP3	OTTHUMG00000065904	ENST00000303071.5:c.436C>A	chr21.hg19:g.34958454G>T	ENSP00000307143:p.Pro146Thr	208.0	0.0	851	126.0	40.0	NM_017613	Q8NC53|Q9NSR9|Q9NVZ5|Q9NYP1|Q9NYP2	Missense_Mutation	SNP	ENST00000303071.5	hg19	CCDS13632.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	8.677|8.677|8.677	0.904206|0.904206|0.904206	0.17760|0.17760|0.17760	.|.|.	.|.|.	ENSG00000159147|ENSG00000159147|ENSG00000159147;ENSG00000249209	ENST00000437395|ENST00000303113;ENST00000453626;ENST00000303071;ENST00000432378|ENST00000440810;ENST00000429238	.|.|.	.|.|.	.|.|.	5.56|5.56|5.56	0.616|0.616|0.616	0.17613|0.17613|0.17613	.|.|.	.|0.492213|.	.|0.22952|.	.|N|.	.|0.053650|.	T|T|T	0.45856|0.45856|0.45856	0.1363|0.1363|0.1363	M|M|M	0.76002|0.76002|0.76002	2.32|2.32|2.32	0.09310|0.09310|0.09310	N|N|N	1|1|1	.|B;B;B|.	.|0.12630|.	.|0.006;0.001;0.0|.	.|B;B;B|.	.|0.10450|.	.|0.004;0.005;0.001|.	T|T|T	0.40001|0.40001|0.40001	-0.9586|-0.9586|-0.9586	5|9|5	.|0.24483|.	.|T|.	.|0.36|.	-0.21|-0.21|-0.21	4.6922|4.6922|4.6922	0.12786|0.12786|0.12786	0.3018:0.0:0.5583:0.1399|0.3018:0.0:0.5583:0.1399|0.3018:0.0:0.5583:0.1399	.|.|.	.|146;146;146|.	.|F8W8A5;C9J4K5;Q9NYP3|.	.|.;.;DONS_HUMAN|.	L|T|Y	116|146|4;107	.|.|.	.|ENSP00000307143:P146T|.	F|P|S	-|-|-	3|1|2	2|0|0	DONSON|DONSON|DONSON;AP000304.12	33880324|33880324|33880324	0.002000|0.002000|0.002000	0.14202|0.14202|0.14202	0.000000|0.000000|0.000000	0.03702|0.03702|0.03702	0.010000|0.010000|0.010000	0.07245|0.07245|0.07245	0.558000|0.558000|0.558000	0.23469|0.23469|0.23469	0.035000|0.035000|0.035000	0.15519|0.15519|0.15519	-0.244000|-0.244000|-0.244000	0.11960|0.11960|0.11960	TTC|CCG|TCC	.	.		0.383	DONSON-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141184.1	NM_017613		T	34958454	G	T	34958454	3	4	242	1	0	0	0	0	1	0	0	0	4708	1174	41	3	1296	3	DONSON	21	34958454	Missense_Mutation	SNP	G	TCGA-ED-A66Y-01A-11D-A30V-10		34958454	13171441	72	33406										
MORC2	22880	hgsc.bcm.edu	37	chr22	31332568	31332568	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	gtttctgcttctcttcctgcGtcttcatgtcctttctgaat	6	12	5	1			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr22:31332568G>T	ENST00000397641.3	-	17	2075	c.1667C>A	c.(1666-1668)aCg>aAg	p.T556K	MORC2_ENST00000469915.1_5'UTR|MORC2_ENST00000215862.4_Missense_Mutation_p.T494K			Q9Y6X9	MORC2_HUMAN	MORC family CW-type zinc finger 2	556						cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	21						CTCTTCCTGCGTCTTCATGTC	0.517																																					p.T494K		Atlas-SNP	.											MORC2,NS,neuroblastoma,0,1	MORC2	78	.	0			c.C1481A						.						187	164	171					22																	31332568		2203	4300	6503	SO:0001583	missense	22880	exon18			TCCTGCGTCTTCA	AB020659	CCDS33636.1	22q12.2	2005-06-15	2005-06-15	2005-06-15	ENSG00000133422	ENSG00000133422			23573	protein-coding gene	gene with protein product			"zinc finger, CW-type with coiled-coil domain 1", "zinc finger, CW type with coiled-coil domain 1"	ZCWCC1		14607086	Standard	XM_005261391		Approved	ZCW3, KIAA0852, AC004542.C22.1	uc003aje.1	Q9Y6X9	OTTHUMG00000151193	ENST00000397641.3:c.1667C>A	chr22.hg19:g.31332568G>T	ENSP00000380763:p.Thr556Lys	60.0	0.0		51.0	3.0	NM_014941	B2RNB1|Q9UF28|Q9Y6V2	Missense_Mutation	SNP	ENST00000397641.3	hg19		.	.	.	.	.	.	.	.	.	.	G	24.7	4.562281	0.86335	.	.	ENSG00000133422	ENST00000397641;ENST00000215862	T;T	0.11821	2.74;2.74	6.06	5.01	0.66863	.	0.231431	0.45126	D	0.000390	T	0.14313	0.0346	L	0.43152	1.355	0.80722	D	1	B	0.32573	0.376	B	0.35550	0.205	T	0.06698	-1.0812	10	0.13470	T	0.59	.	17.0806	0.86597	0.0:0.1265:0.8735:0.0	.	556	Q9Y6X9	MORC2_HUMAN	K	556;494	ENSP00000380763:T556K;ENSP00000215862:T494K	ENSP00000215862:T494K	T	-	2	0	MORC2	29662568	1.000000	0.71417	0.998000	0.56505	0.954000	0.61252	4.717000	0.61923	2.871000	0.98454	0.655000	0.94253	ACG	.	.		0.517	MORC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000321710.2	NM_014941		T	31332568	G	T	31332568	3	4	242	1	0	0	0	0	1	0	0	0	9711	1145	40	1	1471	1	MORC2	22	31332568	Missense_Mutation	SNP	G	TCGA-ED-A66Y-01A-11D-A30V-10		31332568	19971998	73	33407										
GRAMD4	23151	hgsc.bcm.edu	37	chr22	47033858	47033858	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	attggaaaaacatttcttacGtgagtaccagaaagcgcttg	9	7	1	2			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chr22:47033858G>C	ENST00000406902.1	+	3	496		c.e3+1		GRAMD4_ENST00000361034.3_Splice_Site			Q6IC98	GRAM4_HUMAN	GRAM domain containing 4						apoptotic process (GO:0006915)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)	12		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|BRCA - Breast invasive adenocarcinoma(115;0.166)		CATTTCTTACGTGAGTACCAG	0.522																																					.		Atlas-SNP	.											.	GRAMD4	53	.	0			c.283+1G>C						.						105	107	106					22																	47033858		2203	4300	6503	SO:0001630	splice_region_variant	23151	exon2			TCTTACGTGAGTA		CCDS33672.1	22q13.31	2008-03-03			ENSG00000075240	ENSG00000075240			29113	protein-coding gene	gene with protein product	"death-inducing-protein"	613691				15565177	Standard	NM_015124		Approved	KIAA0767, DIP	uc003bhx.3	Q6IC98	OTTHUMG00000150402	ENST00000406902.1:c.283+1G>C	chr22.hg19:g.47033858G>C		114.0	0.0		81.0	7.0	NM_015124	A9IN51|A9IN57|Q68EN0|Q9UGE6|Q9Y4B9	Splice_Site	SNP	ENST00000406902.1	hg19	CCDS33672.1	.	.	.	.	.	.	.	.	.	.	G	18.64	3.666786	0.67814	.	.	ENSG00000075240	ENST00000406902;ENST00000361034	.	.	.	4.12	4.12	0.48240	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3847	0.74687	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GRAMD4	45412522	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	8.935000	0.92923	2.046000	0.60703	0.306000	0.20318	.	.	.		0.522	GRAMD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317969.1	NM_015124	Intron	C	47033858	G	C	47033858	5	2	242	1	0	0	0	0	0	0	1	0	6761	1159	40	4	290	4	GRAMD4	22	47033858	Splice_Site	SNP	G	TCGA-ED-A66Y-01A-11D-A30V-10	15701290	47033858	4270708	74	33408										
RPS6KA3	6197	hgsc.bcm.edu	37	chrX	20181160	20181160	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	agccttgtctttttaaaaccTagaaaaagtgcaaaattagt	6	6	1	1			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chrX:20181160T>A	ENST00000379565.3	-	19	1972		c.e19-2		RPS6KA3_ENST00000479809.1_Splice_Site|RPS6KA3_ENST00000544447.1_Splice_Site|RPS6KA3_ENST00000379548.4_Splice_Site|RPS6KA3_ENST00000540702.1_Splice_Site	NM_004586.2	NP_004577.1	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 3						axon guidance (GO:0007411)|cell cycle (GO:0007049)|central nervous system development (GO:0007417)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(14)|lung(7)|ovary(1)|stomach(1)	41					Acetylsalicylic acid(DB00945)	TTTTAAAACCTAGAAAAAGTG	0.328																																					.		Atlas-SNP	.											.	RPS6KA3	110	.	0			c.1765-2A>T						.						123	107	113					X																	20181160		2203	4300	6503	SO:0001630	splice_region_variant	6197	exon20			AAAACCTAGAAAA	U08316	CCDS14197.1	Xp22.2-p22.1	2013-06-03	2002-08-29		ENSG00000177189	ENSG00000177189			10432	protein-coding gene	gene with protein product		300075	"ribosomal protein S6 kinase, 90kD, polypeptide 3", "mental retardation, X-linked 19", "Coffin-Lowry syndrome"	MRX19, CLS		8141249, 11896450, 16879200	Standard	XM_005274573		Approved	RSK, RSK2, HU-3	uc004czu.3	P51812	OTTHUMG00000021231	ENST00000379565.3:c.1765-2A>T	chrX.hg19:g.20181160T>A		208.0	0.0		213.0	108.0	NM_004586	B2R9V4|Q4VAP3|Q59H26|Q5JPK8|Q7Z3Z7	Splice_Site	SNP	ENST00000379565.3	hg19	CCDS14197.1	.	.	.	.	.	.	.	.	.	.	T	18.69	3.677847	0.68042	.	.	ENSG00000177189	ENST00000379565;ENST00000544447;ENST00000379548;ENST00000540702	.	.	.	5.04	5.04	0.67666	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.9516	0.64121	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	RPS6KA3	20091081	1.000000	0.71417	0.996000	0.52242	0.837000	0.47467	8.018000	0.88722	1.670000	0.50864	0.339000	0.21740	.	.	.		0.328	RPS6KA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056011.3	NM_004586	Intron	A	20181160	T	A	20181160	5	1	242	1	0	0	0	0	0	0	1	0	13667	1536	53	4	475	4	RPS6KA3	23	20181160	Splice_Site	SNP	T	TCGA-ED-A66Y-01A-11D-A30V-10		20181160	135089400	75	33409										
TFE3	7030	hgsc.bcm.edu	37	chrX	48888982	48888982	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	ggctctccaggtctttggagCgctgctgctccttctgcagc	12	14	3	0			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chrX:48888982C>T	ENST00000315869.7	-	9	1473	c.1214G>A	c.(1213-1215)cGc>cAc	p.R405H	TFE3_ENST00000487451.1_5'UTR	NM_006521.4	NP_006512.2	P19532	TFE3_HUMAN	transcription factor binding to IGHM enhancer 3	405					humoral immune response (GO:0006959)|positive regulation of cell adhesion (GO:0045785)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of osteoclast differentiation (GO:0045670)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)		NONO/TFE3(2)|PRCC/TFE3(25)|SFPQ/TFE3(6)|CLTC/TFE3(2)|ASPSCR1/TFE3(167)	central_nervous_system(1)	1						GTCTTTGGAGCGCTGCTGCTC	0.602			T	"SFPQ, ASPSCR1, PRCC, NONO, CLTC"	"papillary renal, alveolar soft part sarcoma, renal"																																p.R405H		Atlas-SNP	.		Dom	yes		X	Xp11.22	7030	transcription factor binding to IGHM enhancer 3		E	.	TFE3	93	.	0			c.G1214A						.						34	31	32					X																	48888982		2202	4296	6498	SO:0001583	missense	7030	exon9			TTGGAGCGCTGCT	X96717	CCDS14315.3	Xp11.22	2013-05-21			ENSG00000068323	ENSG00000068323		"Basic helix-loop-helix proteins"	11752	protein-coding gene	gene with protein product	transcription factor E family, member A	314310				1672758, 1685140	Standard	NM_006521		Approved	TFEA, bHLHe33	uc004dmb.3	P19532	OTTHUMG00000022690	ENST00000315869.7:c.1214G>A	chrX.hg19:g.48888982C>T	ENSP00000314129:p.Arg405His	80.0	0.0		75.0	41.0	NM_006521	A8MZL6|Q5JU74|Q92757|Q92758|Q99964	Missense_Mutation	SNP	ENST00000315869.7	hg19	CCDS14315.3	.	.	.	.	.	.	.	.	.	.	c	24.7	4.562467	0.86335	.	.	ENSG00000068323	ENST00000315869	D	0.97642	-4.47	5.64	3.88	0.44766	Helix-loop-helix DNA-binding (2);	0.000000	0.85682	D	0.000000	D	0.94430	0.8208	L	0.49455	1.56	0.58432	D	0.999996	B	0.24317	0.101	B	0.17722	0.019	D	0.90485	0.4463	10	0.56958	D	0.05	-7.8538	10.5431	0.45045	0.0:0.8379:0.0:0.1621	.	405	P19532	TFE3_HUMAN	H	405	ENSP00000314129:R405H	ENSP00000314129:R405H	R	-	2	0	TFE3	48775926	1.000000	0.71417	0.962000	0.40283	0.983000	0.72400	7.721000	0.84768	0.549000	0.28973	0.462000	0.41574	CGC	.	.		0.602	TFE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058872.2	NM_006521		T	48888982	C	T	48888982	3	4	242	1	0	0	0	0	1	0	0	0	15815	768	27	1	521	1	TFE3	23	48888982	Missense_Mutation	SNP	C	TCGA-ED-A66Y-01A-11D-A30V-10	28707822	48888982	106381578	76	33410										
NOX1	27035	hgsc.bcm.edu	37	chrX	100104411	100104411	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	ccctgcagatccagtagaaaTagatctgaaatcagcaagag	9	9	2	5			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chrX:100104411T>C	ENST00000372966.3	-	11	1506	c.1301A>G	c.(1300-1302)tAt>tGt	p.Y434C	NOX1_ENST00000372964.1_Intron|NOX1_ENST00000372960.4_Missense_Mutation_p.Y397C|NOX1_ENST00000217885.5_Intron	NM_007052.4|NM_013955.2	NP_008983.2|NP_039249.1	Q9Y5S8	NOX1_HUMAN	NADPH oxidase 1	434	Interaction with NOXO1.				angiogenesis (GO:0001525)|cell migration (GO:0016477)|cellular response to hyperoxia (GO:0071455)|cellular stress response to acidic pH (GO:1990451)|extracellular matrix organization (GO:0030198)|hydrogen peroxide metabolic process (GO:0042743)|inflammatory response (GO:0006954)|intracellular pH elevation (GO:0051454)|NADP metabolic process (GO:0006739)|oxidation-reduction process (GO:0055114)|oxygen metabolic process (GO:0072592)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of JNK cascade (GO:0046330)|positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902177)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation vascular endothelial growth factor production (GO:0010575)|proton transport (GO:0015992)|regulation of blood pressure (GO:0008217)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|respiratory burst (GO:0045730)|signal transduction (GO:0007165)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|early endosome (GO:0005769)|integral component of membrane (GO:0016021)|invadopodium membrane (GO:0071438)|NADPH oxidase complex (GO:0043020)	metal ion binding (GO:0046872)|NADP binding (GO:0050661)|Rac GTPase binding (GO:0048365)|superoxide-generating NADPH oxidase activity (GO:0016175)|voltage-gated proton channel activity (GO:0030171)			cervix(1)|lung(3)|ovary(1)|skin(2)	7						CCAGTAGAAATAGATCTGAAA	0.438																																					p.Y434C		Atlas-SNP	.											.	NOX1	79	.	0			c.A1301G						.						66	52	57					X																	100104411		2203	4300	6503	SO:0001583	missense	27035	exon11			TAGAAATAGATCT	AF127763	CCDS14474.1, CCDS14475.1, CCDS65298.1	Xq22	2008-08-01			ENSG00000007952	ENSG00000007952			7889	protein-coding gene	gene with protein product	"mitogenic oxidase (pyridine nucleotide-dependent superoxide-generating)", "NADPH oxidase homolog-1", "NADPH oxidase 1 variant NOH-1L"	300225				10485709, 10615049	Standard	NM_007052		Approved	NOH1, NOH-1, MOX1, GP91-2	uc004egj.3	Q9Y5S8	OTTHUMG00000022007	ENST00000372966.3:c.1301A>G	chrX.hg19:g.100104411T>C	ENSP00000362057:p.Tyr434Cys	129.0	0.0		130.0	57.0	NM_007052	A8K836|O95691|Q2PP02	Missense_Mutation	SNP	ENST00000372966.3	hg19	CCDS14474.1	.	.	.	.	.	.	.	.	.	.	T	15.61	2.884711	0.51908	.	.	ENSG00000007952	ENST00000372966;ENST00000372960;ENST00000372957	D;D	0.95238	-3.65;-3.65	4.38	3.15	0.36227	Ferric reductase, NAD binding (1);	0.145948	0.47455	D	0.000228	D	0.97663	0.9234	H	0.95187	3.635	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.993;0.999	D	0.96837	0.9615	10	0.87932	D	0	-7.0052	9.3262	0.37995	0.0:0.0:0.1789:0.8211	.	397;434	A6NGA6;Q9Y5S8	.;NOX1_HUMAN	C	434;397;123	ENSP00000362057:Y434C;ENSP00000362051:Y397C	ENSP00000362048:Y123C	Y	-	2	0	NOX1	99991067	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.094000	0.57721	0.510000	0.28216	0.441000	0.28932	TAT	.	.		0.438	NOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057495.1	NM_007052		C	100104411	T	C	100104411	3	2	242	1	0	0	0	0	1	0	0	0	10565	1406	49	2	405	2	NOX1	23	100104411	Missense_Mutation	SNP	T	TCGA-ED-A66Y-01A-11D-A30V-10	51215429	100104411	55166149	77	33411										
RAB33A	9363	hgsc.bcm.edu	37	chrX	129306277	129306277	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0256410256410256	2	1	0.535779816513761	0	0.60884070058382	0.428571428571429	1	0	gggagaagaccgtggaaatcGagggcgagaagatcaaggtg	18	5	1	4			TCGA-ED-A66Y-01A-11D-A30V-10	TCGA-ED-A66Y-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	934fcec3-38d8-46e9-b760-15fc041e8284	88b29a81-2646-4944-88a9-6dc6dd70aaa7	g.chrX:129306277G>T	ENST00000257017.4	+	1	655	c.241G>T	c.(241-243)Gag>Tag	p.E81*		NM_004794.2	NP_004785.1	Q14088	RB33A_HUMAN	RAB33A, member RAS oncogene family	81					antigen processing and presentation (GO:0019882)|GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(5)	11						CGTGGAAATCGAGGGCGAGAA	0.627																																					p.E81X		Atlas-SNP	.											.	RAB33A	24	.	0			c.G241T						.						73	62	66					X																	129306277		2203	4300	6503	SO:0001587	stop_gained	9363	exon1			GAAATCGAGGGCG	D14889	CCDS14621.1	Xq26	2008-02-05			ENSG00000134594	ENSG00000134594		"RAB, member RAS oncogene"	9773	protein-coding gene	gene with protein product		300333				7688322, 9512502	Standard	NM_004794		Approved	RabS10	uc004evl.3	Q14088	OTTHUMG00000022391	ENST00000257017.4:c.241G>T	chrX.hg19:g.129306277G>T	ENSP00000257017:p.Glu81*	61.0	0.0		48.0	17.0	NM_004794	Q5JUZ6|Q92465	Nonsense_Mutation	SNP	ENST00000257017.4	hg19	CCDS14621.1	.	.	.	.	.	.	.	.	.	.	G	41	9.051778	0.99050	.	.	ENSG00000134594	ENST00000257017	.	.	.	4.69	4.69	0.59074	.	0.102867	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-20.474	13.5967	0.61994	0.0:0.1522:0.8478:0.0	.	.	.	.	X	81	.	ENSP00000257017:E81X	E	+	1	0	RAB33A	129133958	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.196000	0.72094	2.314000	0.78098	0.600000	0.82982	GAG	.	.		0.627	RAB33A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058246.1	NM_004794		T	129306277	G	T	129306277	4	4	242	1	0	0	0	0	0	1	0	0	12937	1059	37	1	243	1	RAB33A	23	129306277	Nonsense_Mutation	SNP	G	TCGA-ED-A66Y-01A-11D-A30V-10	29201866	129306277	25964283	78	33412										
CREG2	200407	hgsc.bcm.edu	37	chr2	101971822	101971823	+	Frame_Shift_Ins	INS	-	-	T													0.107142857142857	3	1	1.78681318681319	0	1.93571428571429	0.1	0.617038875103394	0	gatcttccggatcaacgatgINSttttttctgcatgtgaaaaa							TCGA-ED-A7PX-01A-51D-A34Z-10	TCGA-ED-A7PX-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	282d9c17-9d34-43d9-952e-bf14edf7bc65	4fd69f63-3ae5-4678-8647-a7e5eabd7486	g.chr2:101971822_101971823insT	ENST00000324768.5	-	3	754_755	c.617_618insA	c.(616-618)aacfs	p.N206fs		NM_153836.3	NP_722578.1	Q8IUH2	CREG2_HUMAN	cellular repressor of E1A-stimulated genes 2	206						endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)	FMN binding (GO:0010181)|oxidoreductase activity (GO:0016491)			endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	10						GATCAACGATGTTTTTTCTGCA	0.396																																					p.N206fs		Atlas-Indel,Pindel	.											.	CREG2	21	.	0			c.618_619insA						.																																			SO:0001589	frameshift_variant	200407	exon3			.	AB046109	CCDS2052.1	2q12.1	2007-08-01			ENSG00000175874	ENSG00000175874			14272	protein-coding gene	gene with protein product						12408961	Standard	NM_153836		Approved		uc002tba.2	Q8IUH2	OTTHUMG00000130692	ENST00000324768.5:c.618dupA	chr2.hg19:g.101971828_101971828dupT	ENSP00000315203:p.Asn206fs	117.0	0.0		186.0	64.0	NM_153836	Q86X03|Q8N540|Q8N9E3	Frame_Shift_Ins	INS	ENST00000324768.5	hg19	CCDS2052.1																																																																																			.	.		0.396	CREG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253188.2	NM_153836		T	101971823	-	T	101971822	7	5	243	1	0	1	1	0	0	0	0	0	3867	1368	48	0	262	0	CREG2	2	101971822	Frame_Shift_Ins	INS	-	TCGA-ED-A7PX-01A-51D-A34Z-10		101971822	141227551	1	33413										
SP110	3431	hgsc.bcm.edu	37	chr2	231067440	231067440	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.107142857142857	3	1	1.78681318681319	0	1.93571428571429	0.1	0.617038875103394	0	attccgtgtctagatgaggcTgtccctggaccaaataatga	10	9	1	3			TCGA-ED-A7PX-01A-51D-A34Z-10	TCGA-ED-A7PX-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	282d9c17-9d34-43d9-952e-bf14edf7bc65	4fd69f63-3ae5-4678-8647-a7e5eabd7486	g.chr2:231067440T>G	ENST00000358662.4	-	9	981	c.903A>C	c.(901-903)acA>acC	p.T301T	SP110_ENST00000392048.3_Splice_Site|SP110_ENST00000338556.3_Intron|SP110_ENST00000258381.6_Silent_p.T301T|SP110_ENST00000258382.5_Silent_p.T301T|SP110_ENST00000486146.2_5'Flank|SP110_ENST00000540870.1_Silent_p.T307T	NM_004509.3	NP_004500	Q9HB58	SP110_HUMAN	SP110 nuclear body protein	301					regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			breast(4)|endometrium(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Renal(207;0.0112)|all_lung(227;0.0223)|Lung NSC(271;0.0983)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.169)		Epithelial(121;2.61e-12)|all cancers(144;6.39e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.0097)		TAGATGAGGCTGTCCCTGGAC	0.453																																					p.T307T		Atlas-SNP	.											.	SP110	105	.	0			c.A921C						.						166	159	161					2																	231067440		2203	4300	6503	SO:0001819	synonymous_variant	3431	exon10			TGAGGCTGTCCCT	L22343	CCDS2474.1, CCDS2475.1, CCDS2476.1, CCDS54435.1	2q37.1	2014-09-17	2001-12-19	2001-12-20	ENSG00000135899	ENSG00000135899			5401	protein-coding gene	gene with protein product		604457	"interferon-induced protein 41, 30kD"	IFI41, IFI75		7693701, 10388521	Standard	NM_080424		Approved		uc002vqg.3	Q9HB58	OTTHUMG00000133204	ENST00000358662.4:c.903A>C	chr2.hg19:g.231067440T>G		142.0	0.0		157.0	20.0	NM_001185015	B4DVI4|F5H1M1|Q14976|Q14977|Q53TG2|Q8WUZ6|Q9HCT8	Silent	SNP	ENST00000358662.4	hg19	CCDS2474.1	.	.	.	.	.	.	.	.	.	.	T	4.191	0.034178	0.08101	.	.	ENSG00000135899	ENST00000392048	.	.	.	3.72	1.29	0.21616	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999995	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.501	0.07673	0.0:0.1279:0.2335:0.6387	.	.	.	.	.	-1	.	.	.	-	.	.	SP110	230775684	0.000000	0.05858	0.005000	0.12908	0.007000	0.05969	-0.292000	0.08332	0.275000	0.22094	0.460000	0.39030	.	.	.		0.453	SP110-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000332414.1	NM_080424		G	231067440	T	G	231067440	2	3	243	1	0	0	0	0	0	0	0	1	14976	1567	55	5		5	SP110	2	231067440	Silent	SNP	T	TCGA-ED-A7PX-01A-51D-A34Z-10	129095618	231067440	12131933	2	33414										
BAP1	8314	hgsc.bcm.edu	37	chr3	52436639	52436640	+	Frame_Shift_Ins	INS	-	-	A													0.107142857142857	3	1	1.78681318681319	0	1.93571428571429	0.1	0.617038875103394	0	tcctgagccagcatggagatINSaaaggtgcagatgaactcat							TCGA-ED-A7PX-01A-51D-A34Z-10	TCGA-ED-A7PX-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	282d9c17-9d34-43d9-952e-bf14edf7bc65	4fd69f63-3ae5-4678-8647-a7e5eabd7486	g.chr3:52436639_52436640insA	ENST00000460680.1	-	16	2505_2506	c.2034_2035insT	c.(2032-2037)tttatcfs	p.I679fs	BAP1_ENST00000296288.5_Frame_Shift_Ins_p.I661fs	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.C676fs*10(1)		NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		AGCATGGAGATAAAGGTGCAGA	0.554			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.I679fs	GBM(101;493 1458 7992 21037 25532)	Atlas-Indel,Pindel	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.,1	BAP1	371	.	1	Deletion - Frameshift(1)	kidney(1)	c.2035_2036insT						.																																			SO:0001589	frameshift_variant	8314	exon16			.	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.2035dupT	chr3.hg19:g.52436642_52436642dupA	ENSP00000417132:p.Ile679fs	84.0	0.0		67.0	35.0	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Frame_Shift_Ins	INS	ENST00000460680.1	hg19	CCDS2853.1																																																																																			.	.		0.554	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			A	52436640	-	A	52436639	7	5	243	1	0	1	1	0	0	0	0	0	1311	1406	49	0	162	0	BAP1	3	52436639	Frame_Shift_Ins	INS	-	TCGA-ED-A7PX-01A-51D-A34Z-10		52436639	145585791	3	33415										
HTRA3	94031	hgsc.bcm.edu	37	chr4	8304197	8304197	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.107142857142857	3	1	1.78681318681319	0	1.93571428571429	0.1	0.617038875103394	0	gtttcatttccagactggaaGaagcgcttcatcggcatacg	10	10	2	2			TCGA-ED-A7PX-01A-51D-A34Z-10	TCGA-ED-A7PX-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	282d9c17-9d34-43d9-952e-bf14edf7bc65	4fd69f63-3ae5-4678-8647-a7e5eabd7486	g.chr4:8304197G>A	ENST00000307358.2	+	7	1263	c.1059G>A	c.(1057-1059)aaG>aaA	p.K353K		NM_053044.3	NP_444272.1	P83110	HTRA3_HUMAN	HtrA serine peptidase 3	353					negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|ovary(2)|prostate(1)|urinary_tract(1)	18						CAGACTGGAAGAAGCGCTTCA	0.582																																					p.K353K		Atlas-SNP	.											.	HTRA3	39	.	0			c.G1059A						.						163	143	150					4																	8304197		2203	4300	6503	SO:0001819	synonymous_variant	94031	exon7			CTGGAAGAAGCGC	AY040094	CCDS3400.1, CCDS75105.1	4p16.1	2008-02-05			ENSG00000170801	ENSG00000170801			30406	protein-coding gene	gene with protein product	"pregnancy-related serine protease"	608785				12513693, 14500695	Standard	XM_005248040		Approved	Tasp, Prsp	uc003gla.3	P83110	OTTHUMG00000090561	ENST00000307358.2:c.1059G>A	chr4.hg19:g.8304197G>A		46.0	0.0		76.0	28.0	NM_053044	Q7Z7A2	Silent	SNP	ENST00000307358.2	hg19	CCDS3400.1																																																																																			.	.		0.582	HTRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092669.1	NM_053044		A	8304197	G	A	8304197	2	1	243	1	0	0	0	0	0	0	0	1	7464	933	33	3		3	HTRA3	4	8304197	Silent	SNP	G	TCGA-ED-A7PX-01A-51D-A34Z-10		8304197	182850079	4	33416										
TBC1D9	23158	hgsc.bcm.edu	37	chr4	141543809	141543809	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.107142857142857	3	1	1.78681318681319	0	1.93571428571429	0.1	0.617038875103394	0	tgtcgggggccaggctggccGgcaggggctcaacagactcc	17	13	1	1	rs199802386		TCGA-ED-A7PX-01A-51D-A34Z-10	TCGA-ED-A7PX-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	282d9c17-9d34-43d9-952e-bf14edf7bc65	4fd69f63-3ae5-4678-8647-a7e5eabd7486	g.chr4:141543809G>A	ENST00000442267.2	-	21	3415	c.3341C>T	c.(3340-3342)cCg>cTg	p.P1114L		NM_015130.2	NP_055945.2	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)	1114							calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	31	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				CAGGCTGGCCGGCAGGGGCTC	0.672													G|||	1	0.000199681	0	0	5008	,	,		17744	0		0	False		,,,				2504	0.001				p.P1114L		Atlas-SNP	.											TBC1D9_ENST00000442267,NS,carcinoma,0,2	TBC1D9	198	.	0			c.C3341T						.						32	39	37					4																	141543809		1983	4152	6135	SO:0001583	missense	23158	exon21			CTGGCCGGCAGGG	AB020689	CCDS47136.1	4q31.1	2013-01-10	2006-07-12		ENSG00000109436	ENSG00000109436		"EF-hand domain containing"	21710	protein-coding gene	gene with protein product			"TBC1 domain family, member 9"			12970790	Standard	NM_015130		Approved	KIAA0882, MDR1	uc010ioj.3	Q6ZT07	OTTHUMG00000161405	ENST00000442267.2:c.3341C>T	chr4.hg19:g.141543809G>A	ENSP00000411197:p.Pro1114Leu	34.0	0.0		49.0	21.0	NM_015130	A6H8U8|D3DNZ1|O94958	Missense_Mutation	SNP	ENST00000442267.2	hg19	CCDS47136.1	.	.	.	.	.	.	.	.	.	.	G	8.488	0.861436	0.17178	.	.	ENSG00000109436	ENST00000442267	T	0.45276	0.9	4.94	4.94	0.65067	.	.	.	.	.	T	0.32496	0.0831	L	0.36672	1.1	0.09310	N	0.999996	B	0.20780	0.048	B	0.17433	0.018	T	0.10917	-1.0609	9	0.28530	T	0.3	.	9.9724	0.41763	0.0:0.1291:0.6568:0.2141	.	1114	Q6ZT07	TBCD9_HUMAN	L	1114	ENSP00000411197:P1114L	ENSP00000411197:P1114L	P	-	2	0	TBC1D9	141763259	0.258000	0.24033	0.035000	0.18076	0.518000	0.34316	2.855000	0.48333	2.273000	0.75805	0.655000	0.94253	CCG	.	G|0.998;A|0.002		0.672	TBC1D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364806.1	NM_015130		A	141543809	G	A	141543809	3	1	243	1	0	0	0	0	1	0	0	0	15642	1116	39	1	463	1	TBC1D9	4	141543809	Missense_Mutation	SNP	G	TCGA-ED-A7PX-01A-51D-A34Z-10	133239612	141543809	49610467	5	33417										
FNIP2	57600	hgsc.bcm.edu	37	chr4	159790466	159790466	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.107142857142857	3	1	1.78681318681319	0	1.93571428571429	0.1	0.617038875103394	0	cattccccgaaatgaaagctCagatagcgccctgggagaca	10	12	1	3			TCGA-ED-A7PX-01A-51D-A34Z-10	TCGA-ED-A7PX-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	282d9c17-9d34-43d9-952e-bf14edf7bc65	4fd69f63-3ae5-4678-8647-a7e5eabd7486	g.chr4:159790466C>T	ENST00000264433.6	+	13	2753	c.2678C>T	c.(2677-2679)tCa>tTa	p.S893L	FNIP2_ENST00000379346.3_Missense_Mutation_p.S916L	NM_020840.1	NP_065891.1	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2	893	Interaction with PRKAA1.				intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein phosphorylation (GO:0006468)|regulation of protein phosphorylation (GO:0001932)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)	9	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.00936)		AATGAAAGCTCAGATAGCGCC	0.587																																					p.S893L		Atlas-SNP	.											.	FNIP2	90	.	0			c.C2678T						.						25	27	26					4																	159790466		2071	4219	6290	SO:0001583	missense	57600	exon13			AAAGCTCAGATAG	AB040883	CCDS47155.1	4q32.1	2012-10-31			ENSG00000052795	ENSG00000052795			29280	protein-coding gene	gene with protein product	"O6-methylguanine-induced apoptosis 1"	612768				18403135	Standard	NM_020840		Approved	KIAA1450, FNIPL, MAPO1	uc003iqe.4	Q9P278	OTTHUMG00000161983	ENST00000264433.6:c.2678C>T	chr4.hg19:g.159790466C>T	ENSP00000264433:p.Ser893Leu	35.0	0.0		51.0	22.0	NM_020840	Q05DC3|Q96I31|Q9H994	Missense_Mutation	SNP	ENST00000264433.6	hg19	CCDS47155.1	.	.	.	.	.	.	.	.	.	.	C	10.33	1.319261	0.23994	.	.	ENSG00000052795	ENST00000264433;ENST00000379346	T;T	0.35048	1.34;1.33	5.57	2.89	0.33648	.	0.362778	0.29165	N	0.012956	T	0.25827	0.0629	L	0.42487	1.325	0.30400	N	0.780137	B	0.14012	0.009	B	0.13407	0.009	T	0.17715	-1.0360	9	.	.	.	.	6.2858	0.21033	0.0:0.6498:0.1322:0.2179	.	893	Q9P278	FNIP2_HUMAN	L	893;916	ENSP00000264433:S893L;ENSP00000368651:S916L	.	S	+	2	0	FNIP2	160009916	1.000000	0.71417	0.343000	0.25615	0.081000	0.17604	3.298000	0.51818	0.385000	0.24970	0.655000	0.94253	TCA	.	.		0.587	FNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366602.1	NM_020840		T	159790466	C	T	159790466	3	4	243	1	0	0	0	0	1	0	0	0	5984	838	29	3	2728	3	FNIP2	4	159790466	Missense_Mutation	SNP	C	TCGA-ED-A7PX-01A-51D-A34Z-10	18246657	159790466	31363810	6	33418										
ZNF366	167465	hgsc.bcm.edu	37	chr5	71757293	71757293	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.107142857142857	3	1	1.78681318681319	0	1.93571428571429	0.1	0.617038875103394	0	caagtcgaaatgcacatcctCgtctttgatcatcttcattt	5	11	4	1			TCGA-ED-A7PX-01A-51D-A34Z-10	TCGA-ED-A7PX-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	282d9c17-9d34-43d9-952e-bf14edf7bc65	4fd69f63-3ae5-4678-8647-a7e5eabd7486	g.chr5:71757293C>T	ENST00000318442.5	-	2	521	c.31G>A	c.(31-33)Gag>Aag	p.E11K		NM_152625.1	NP_689838.1	Q8N895	ZN366_HUMAN	zinc finger protein 366	11					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|estrogen receptor binding (GO:0030331)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	35		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)		TGCACATCCTCGTCTTTGATC	0.453																																					p.E11K		Atlas-SNP	.											.	ZNF366	108	.	0			c.G31A						.						75	71	72					5																	71757293		2200	4298	6498	SO:0001583	missense	167465	exon2			CATCCTCGTCTTT	AK097115	CCDS4015.1	5q13.1	2013-01-08			ENSG00000178175	ENSG00000178175		"Zinc fingers, C2H2-type"	18316	protein-coding gene	gene with protein product		610159					Standard	NM_152625		Approved	FLJ39796	uc003kce.1	Q8N895	OTTHUMG00000100965	ENST00000318442.5:c.31G>A	chr5.hg19:g.71757293C>T	ENSP00000313158:p.Glu11Lys	58.0	0.0		75.0	27.0	NM_152625	Q5HYI9|Q7RTV4	Missense_Mutation	SNP	ENST00000318442.5	hg19	CCDS4015.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.502522	0.85176	.	.	ENSG00000178175	ENST00000318442;ENST00000414109	T;T	0.36699	1.24;1.24	5.85	5.85	0.93711	.	0.000000	0.64402	D	0.000002	T	0.51719	0.1691	L	0.36672	1.1	0.48830	D	0.999715	D	0.89917	1.0	D	0.63793	0.918	T	0.50474	-0.8824	10	0.87932	D	0	-52.8482	20.1775	0.98187	0.0:1.0:0.0:0.0	.	11	Q8N895	ZN366_HUMAN	K	11	ENSP00000313158:E11K;ENSP00000391333:E11K	ENSP00000313158:E11K	E	-	1	0	ZNF366	71793049	1.000000	0.71417	0.426000	0.26672	0.921000	0.55340	5.766000	0.68843	2.771000	0.95319	0.561000	0.74099	GAG	.	.		0.453	ZNF366-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218574.3			T	71757293	C	T	71757293	3	4	243	1	0	0	0	0	1	0	0	0	17885	893	31	1	2219	1	ZNF366	5	71757293	Missense_Mutation	SNP	C	TCGA-ED-A7PX-01A-51D-A34Z-10		71757293	109157967	7	33419										
PCDHB16	57717	hgsc.bcm.edu	37	chr5	140563725	140563725	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.107142857142857	3	1	1.78681318681319	0	1.93571428571429	0.1	0.617038875103394	0	tgcgggagttcgagttccgcGtgagcgccacagaccgcggc	16	13	0	2			TCGA-ED-A7PX-01A-51D-A34Z-10	TCGA-ED-A7PX-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	282d9c17-9d34-43d9-952e-bf14edf7bc65	4fd69f63-3ae5-4678-8647-a7e5eabd7486	g.chr5:140563725G>A	ENST00000361016.2	+	1	2746	c.1591G>A	c.(1591-1593)Gtg>Atg	p.V531M		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	531	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGAGTTCCGCGTGAGCGCCAC	0.682																																					p.V531M		Atlas-SNP	.											.	PCDHB16	159	.	0			c.G1591A						.						36	39	38					5																	140563725		1853	3453	5306	SO:0001583	missense	57717	exon1			TTCCGCGTGAGCG	AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"Cadherins / Protocadherins : Clustered"	14546	other	protocadherin	"cadherin ME1", "protocadherin-3x", "PCDHbeta 16"	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325	ENST00000361016.2:c.1591G>A	chr5.hg19:g.140563725G>A	ENSP00000354293:p.Val531Met	27.0	0.0		35.0	5.0	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	hg19	CCDS4251.1	.	.	.	.	.	.	.	.	.	.	g	21.8	4.198465	0.79015	.	.	ENSG00000196963	ENST00000361016	T	0.71698	-0.59	4.26	4.26	0.50523	Cadherin (5);Cadherin-like (1);	0.000000	0.31404	N	0.007710	D	0.87732	0.6251	H	0.96889	3.9	0.46521	D	0.999081	D	0.65815	0.995	P	0.59012	0.85	D	0.92460	0.5977	10	0.72032	D	0.01	.	16.3541	0.83228	0.0:0.0:1.0:0.0	.	531	Q9NRJ7	PCDBG_HUMAN	M	531	ENSP00000354293:V531M	ENSP00000354293:V531M	V	+	1	0	PCDHB16	140543909	1.000000	0.71417	0.998000	0.56505	0.376000	0.30014	6.189000	0.72051	1.931000	0.55961	0.580000	0.79431	GTG	.	.		0.682	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957		A	140563725	G	A	140563725	3	1	243	1	0	0	0	0	1	0	0	0	11550	1145	40	1	1593	1	PCDHB16	5	140563725	Missense_Mutation	SNP	G	TCGA-ED-A7PX-01A-51D-A34Z-10	68806432	140563725	40351535	8	33420										
RNF14	9604	hgsc.bcm.edu	37	chr5	141358344	141358344	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.107142857142857	3	1	1.78681318681319	0	1.93571428571429	0.1	0.617038875103394	0	atcagagatggccaggttcaAtgcctcaactgcccagaacc	9	13	3	2			TCGA-ED-A7PX-01A-51D-A34Z-10	TCGA-ED-A7PX-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	282d9c17-9d34-43d9-952e-bf14edf7bc65	4fd69f63-3ae5-4678-8647-a7e5eabd7486	g.chr5:141358344A>G	ENST00000394520.2	+	5	1092	c.783A>G	c.(781-783)caA>caG	p.Q261Q	RNF14_ENST00000394515.3_Intron|RNF14_ENST00000540015.1_Intron|RNF14_ENST00000394519.1_Silent_p.Q261Q|RNF14_ENST00000347642.3_Silent_p.Q261Q|AC005740.5_ENST00000520882.1_RNA|RNF14_ENST00000394514.2_Silent_p.Q135Q|RNF14_ENST00000356143.1_Silent_p.Q261Q	NM_001201365.1|NM_004290.4	NP_001188294.1|NP_004281.1	Q9UBS8	RNF14_HUMAN	ring finger protein 14	261					androgen receptor signaling pathway (GO:0030521)|positive regulation of transcription, DNA-templated (GO:0045893)|protein ubiquitination (GO:0016567)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|small conjugating protein ligase activity (GO:0019787)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15		all_hematologic(541;0.0536)|Ovarian(839;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.0407)		GCCAGGTTCAATGCCTCAACT	0.488																																					p.Q261Q		Atlas-SNP	.											.	RNF14	30	.	0			c.A783G						.						124	127	126					5																	141358344		2203	4300	6503	SO:0001819	synonymous_variant	9604	exon5			GGTTCAATGCCTC	AF060544	CCDS4270.1, CCDS4271.1	5q23.3-q31.1	2008-02-05			ENSG00000013561	ENSG00000013561		"RING-type (C3HC4) zinc fingers"	10058	protein-coding gene	gene with protein product		605675				10085091, 10320776	Standard	NM_183399		Approved	ARA54, HFB30, TRIAD2	uc003lmc.3	Q9UBS8	OTTHUMG00000129660	ENST00000394520.2:c.783A>G	chr5.hg19:g.141358344A>G		33.0	0.0		49.0	8.0	NM_001201365	A0AV26|A6NMR2|A8MTW5|B3KN72|B7ZLV2|D3DQE4|O94793|Q6IBV0	Silent	SNP	ENST00000394520.2	hg19	CCDS4270.1																																																																																			.	.		0.488	RNF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251860.2	NM_004290		G	141358344	A	G	141358344	2	3	243	1	0	0	0	0	0	0	0	1	13458	98	4	2		2	RNF14	5	141358344	Silent	SNP	A	TCGA-ED-A7PX-01A-51D-A34Z-10	794619	141358344	39556916	9	33421										
GRIA1	2890	hgsc.bcm.edu	37	chr5	153149816	153149816	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.107142857142857	3	1	1.78681318681319	0	1.93571428571429	0.1	0.617038875103394	0	gcggaccacagaggaggggaTgattcgagtgaggaaatcca	16	7	0	3			TCGA-ED-A7PX-01A-51D-A34Z-10	TCGA-ED-A7PX-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	282d9c17-9d34-43d9-952e-bf14edf7bc65	4fd69f63-3ae5-4678-8647-a7e5eabd7486	g.chr5:153149816T>C	ENST00000285900.5	+	13	2454	c.2111T>C	c.(2110-2112)aTg>aCg	p.M704T	GRIA1_ENST00000340592.5_Missense_Mutation_p.M704T|GRIA1_ENST00000518142.1_Missense_Mutation_p.M624T|GRIA1_ENST00000521843.2_Missense_Mutation_p.M635T|GRIA1_ENST00000448073.4_Missense_Mutation_p.M714T|GRIA1_ENST00000518783.1_Missense_Mutation_p.M714T	NM_000827.3|NM_001258019.1	NP_000818.2|NP_001244948.1	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1	704					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|axonal spine (GO:0044308)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|neuron spine (GO:0044309)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|PDZ domain binding (GO:0030165)			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)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Perampanel(DB08883)|Sevoflurane(DB01236)	GAGGAGGGGATGATTCGAGTG	0.483																																					p.M714T		Atlas-SNP	.											.	GRIA1	321	.	0			c.T2141C						.						141	127	132					5																	153149816		2203	4300	6503	SO:0001583	missense	2890	exon13			AGGGGATGATTCG		CCDS4322.1, CCDS47318.1, CCDS58986.1, CCDS58987.1, CCDS58988.1, CCDS58989.1	5q33	2012-08-29			ENSG00000155511	ENSG00000155511		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4571	protein-coding gene	gene with protein product		138248		GLUR1		1652753, 1319477	Standard	NM_000827		Approved	GluA1, GLURA	uc011dcy.2	P42261	OTTHUMG00000130148	ENST00000285900.5:c.2111T>C	chr5.hg19:g.153149816T>C	ENSP00000285900:p.Met704Thr	68.0	0.0		104.0	39.0	NM_001258021	B7Z2S0|B7Z2W8|B7Z3F6|B7Z9G9|D3DQI4|E7ESV8|Q2NKM6	Missense_Mutation	SNP	ENST00000285900.5	hg19	CCDS4322.1	.	.	.	.	.	.	.	.	.	.	T	15.09	2.731460	0.48939	.	.	ENSG00000155511	ENST00000285900;ENST00000544403;ENST00000518142;ENST00000537037;ENST00000340592;ENST00000521843;ENST00000544794;ENST00000518783;ENST00000448073	T;T;T;T;T;T;T	0.38401	1.67;1.67;1.14;1.67;1.67;1.67;1.14	5.41	5.41	0.78517	Ionotropic glutamate receptor (2);	0.039962	0.85682	D	0.000000	T	0.27832	0.0685	N	0.17474	0.49	0.58432	D	0.999991	P;P;B;B;B	0.35124	0.485;0.485;0.002;0.43;0.122	B;B;B;B;B	0.36922	0.236;0.236;0.029;0.152;0.138	T	0.17198	-1.0377	10	0.87932	D	0	.	14.6134	0.68531	0.0:0.0:0.0:1.0	.	714;714;624;704;704	E7ESV8;B7Z9G9;B7Z3F6;P42261-2;P42261	.;.;.;.;GRIA1_HUMAN	T	704;704;624;658;704;637;635;714;714	ENSP00000285900:M704T;ENSP00000427920:M624T;ENSP00000339343:M704T;ENSP00000427864:M637T;ENSP00000442108:M635T;ENSP00000428994:M714T;ENSP00000415569:M714T	ENSP00000285900:M704T	M	+	2	0	GRIA1	153130009	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.859000	0.86982	2.042000	0.60477	0.533000	0.62120	ATG	.	.		0.483	GRIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252456.3			C	153149816	T	C	153149816	3	2	243	1	0	0	0	0	1	0	0	0	6776	1464	51	2	2161	2	GRIA1	5	153149816	Missense_Mutation	SNP	T	TCGA-ED-A7PX-01A-51D-A34Z-10	11791472	153149816	27765444	10	33422										
CUL9	23113	hgsc.bcm.edu	37	chr6	43172740	43172740	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.107142857142857	3	1	1.78681318681319	0	1.93571428571429	0.1	0.617038875103394	0	gttactgtaaactctatgagCacttgcagagagcaggctcc	10	10	1	2			TCGA-ED-A7PX-01A-51D-A34Z-10	TCGA-ED-A7PX-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	282d9c17-9d34-43d9-952e-bf14edf7bc65	4fd69f63-3ae5-4678-8647-a7e5eabd7486	g.chr6:43172740C>G	ENST00000252050.4	+	23	4603	c.4519C>G	c.(4519-4521)Cac>Gac	p.H1507D	CUL9_ENST00000372647.2_Missense_Mutation_p.H1507D|CUL9_ENST00000354495.3_Missense_Mutation_p.H1397D	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	1507					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						ACTCTATGAGCACTTGCAGAG	0.562																																					p.H1507D		Atlas-SNP	.											.	CUL9	248	.	0			c.C4519G						.						95	100	98					6																	43172740		2203	4300	6503	SO:0001583	missense	23113	exon23			TATGAGCACTTGC	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"parkin-like cytoplasmic p53 binding protein", "p53-associated parkin-like cytoplasmic protein"	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.4519C>G	chr6.hg19:g.43172740C>G	ENSP00000252050:p.His1507Asp	36.0	0.0		51.0	19.0	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Missense_Mutation	SNP	ENST00000252050.4	hg19	CCDS4890.1	.	.	.	.	.	.	.	.	.	.	C	15.56	2.869784	0.51588	.	.	ENSG00000112659	ENST00000252050;ENST00000354495;ENST00000372647	T;T;T	0.73363	-0.74;-0.74;-0.74	5.07	4.2	0.49525	Cullin, N-terminal (1);	0.764287	0.12753	N	0.442018	T	0.40145	0.1105	N	0.08118	0	0.27551	N	0.950508	B;B;B	0.24920	0.114;0.042;0.042	B;B;B	0.34346	0.122;0.18;0.18	T	0.42616	-0.9441	10	0.62326	D	0.03	-5.5672	8.3214	0.32132	0.1546:0.7667:0.0:0.0787	.	1397;1507;1507	Q8IWT3-3;E9PEZ1;Q8IWT3	.;.;CUL9_HUMAN	D	1507;1397;1507	ENSP00000252050:H1507D;ENSP00000346490:H1397D;ENSP00000361730:H1507D	ENSP00000252050:H1507D	H	+	1	0	CUL9	43280718	0.046000	0.20272	0.545000	0.28153	0.988000	0.76386	2.129000	0.42055	1.141000	0.42275	0.462000	0.41574	CAC	.	.		0.562	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		G	43172740	C	G	43172740	3	3	243	1	0	0	0	0	1	0	0	0	4063	710	25	4	4605	4	CUL9	6	43172740	Missense_Mutation	SNP	C	TCGA-ED-A7PX-01A-51D-A34Z-10		43172740	127942327	11	33423										
RADIL	55698	hgsc.bcm.edu	37	chr7	4917455	4917455	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.107142857142857	3	1	1.78681318681319	0	1.93571428571429	0.1	0.617038875103394	0	cagcacgtactggccggcctGcctggggtccagggcgtacc	15	15	0	0			TCGA-ED-A7PX-01A-51D-A34Z-10	TCGA-ED-A7PX-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	282d9c17-9d34-43d9-952e-bf14edf7bc65	4fd69f63-3ae5-4678-8647-a7e5eabd7486	g.chr7:4917455G>T	ENST00000399583.3	-	2	503	c.316C>A	c.(316-318)Cag>Aag	p.Q106K	RADIL_ENST00000536091.1_Missense_Mutation_p.Q106K	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	106	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		TGGCCGGCCTGCCTGGGGTCC	0.682																																					p.Q106K		Atlas-SNP	.											.	RADIL	110	.	0			c.C316A						.						32	38	36					7																	4917455		2039	4159	6198	SO:0001583	missense	55698	exon2			CGGCCTGCCTGGG	AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.316C>A	chr7.hg19:g.4917455G>T	ENSP00000382492:p.Gln106Lys	23.0	0.0		37.0	9.0	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	hg19	CCDS43544.1	.	.	.	.	.	.	.	.	.	.	G	0.037	-1.300779	0.01364	.	.	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000536091;ENST00000457174	T;T;T	0.16597	2.33;2.33;2.33	5.84	-6.1	0.02138	Ras-association (3);	0.987507	0.08283	N	0.969709	T	0.05181	0.0138	N	0.08118	0	0.09310	N	1	B	0.12630	0.006	B	0.06405	0.002	T	0.38972	-0.9636	10	0.10902	T	0.67	-0.2306	2.2366	0.04010	0.1814:0.1949:0.3937:0.23	.	106	Q96JH8	RADIL_HUMAN	K	106;80;106;106	ENSP00000382492:Q106K;ENSP00000442533:Q106K;ENSP00000398057:Q106K	ENSP00000320946:Q80K	Q	-	1	0	RADIL	4883981	0.000000	0.05858	0.000000	0.03702	0.052000	0.14988	-0.496000	0.06436	-1.453000	0.01928	0.561000	0.74099	CAG	.	.		0.682	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059		T	4917455	G	T	4917455	3	4	243	1	0	0	0	0	1	0	0	0	13012	1328	46	3	2967	3	RADIL	7	4917455	Missense_Mutation	SNP	G	TCGA-ED-A7PX-01A-51D-A34Z-10		4917455	154221208	12	33424										
KCNS2	3788	hgsc.bcm.edu	37	chr8	99440423	99440423	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.107142857142857	3	1	1.78681318681319	0	1.93571428571429	0.1	0.617038875103394	0	cagcgggagttctacttcgaCcgcaaccctgagctcttccc	9	16	2	1			TCGA-ED-A7PX-01A-51D-A34Z-10	TCGA-ED-A7PX-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	282d9c17-9d34-43d9-952e-bf14edf7bc65	4fd69f63-3ae5-4678-8647-a7e5eabd7486	g.chr8:99440423C>A	ENST00000287042.4	+	2	566	c.216C>A	c.(214-216)gaC>gaA	p.D72E	KCNS2_ENST00000521839.1_Missense_Mutation_p.D72E	NM_020697.2	NP_065748.1	Q9ULS6	KCNS2_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 2	72					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			autonomic_ganglia(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	31	Breast(36;2.4e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.0448)			TCTACTTCGACCGCAACCCTG	0.602																																					p.D72E	Pancreas(138;844 2489 9202 24627)	Atlas-SNP	.											.	KCNS2	93	.	0			c.C216A						.						131	101	111					8																	99440423		2203	4300	6503	SO:0001583	missense	3788	exon2			CTTCGACCGCAAC	AB032970	CCDS6279.1	8q22	2011-07-05			ENSG00000156486	ENSG00000156486		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6301	protein-coding gene	gene with protein product		602906				9305895, 16382104	Standard	NM_020697		Approved	Kv9.2	uc003yin.3	Q9ULS6	OTTHUMG00000044337	ENST00000287042.4:c.216C>A	chr8.hg19:g.99440423C>A	ENSP00000287042:p.Asp72Glu	38.0	0.0		48.0	15.0	NM_020697	A8KAN1	Missense_Mutation	SNP	ENST00000287042.4	hg19	CCDS6279.1	.	.	.	.	.	.	.	.	.	.	c	20.2	3.949719	0.73787	.	.	ENSG00000156486	ENST00000287042;ENST00000521839	T;T	0.64085	-0.08;-0.08	5.4	4.33	0.51752	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.000000	0.85682	D	0.000000	T	0.80417	0.4619	M	0.85373	2.75	0.42774	D	0.993847	D	0.76494	0.999	D	0.81914	0.995	D	0.84243	0.0473	10	0.87932	D	0	.	15.0064	0.71516	0.0:0.9196:0.0:0.0804	.	72	Q9ULS6	KCNS2_HUMAN	E	72	ENSP00000287042:D72E;ENSP00000430712:D72E	ENSP00000287042:D72E	D	+	3	2	KCNS2	99509599	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.362000	0.52314	2.523000	0.85059	0.558000	0.71614	GAC	.	.		0.602	KCNS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103134.1	NM_020697		A	99440423	C	A	99440423	3	1	243	1	0	0	0	0	1	0	0	0	8098	506	18	3	218	3	KCNS2	8	99440423	Missense_Mutation	SNP	C	TCGA-ED-A7PX-01A-51D-A34Z-10		99440423	46923599	13	33425										
APBA1	320	hgsc.bcm.edu	37	chr9	72071267	72071267	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.107142857142857	3	1	1.78681318681319	0	1.93571428571429	0.1	0.617038875103394	0	ggagttggagcgaggcatccGccggcgggccatcagcacaa	16	12	1	0			TCGA-ED-A7PX-01A-51D-A34Z-10	TCGA-ED-A7PX-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	282d9c17-9d34-43d9-952e-bf14edf7bc65	4fd69f63-3ae5-4678-8647-a7e5eabd7486	g.chr9:72071267G>A	ENST00000265381.4	-	8	1906	c.1684C>T	c.(1684-1686)Cgg>Tgg	p.R562W	APBA1_ENST00000470082.1_5'UTR	NM_001163.3	NP_001154.2	Q02410	APBA1_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 1	562	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				axon cargo transport (GO:0008088)|cell adhesion (GO:0007155)|gamma-aminobutyric acid secretion (GO:0014051)|glutamate secretion (GO:0014047)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein complex assembly (GO:0006461)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synaptic vesicle (GO:0008021)	beta-amyloid binding (GO:0001540)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(4)|kidney(2)|large_intestine(12)|lung(13)|prostate(3)|skin(3)	37						CGAGGCATCCGCCGGCGGGCC	0.572																																					p.R562W		Atlas-SNP	.											.	APBA1	96	.	0			c.C1684T						.						241	229	233					9																	72071267		2203	4300	6503	SO:0001583	missense	320	exon8			GCATCCGCCGGCG	AF029106	CCDS6630.1	9q13-q21	2008-07-18	2008-07-18		ENSG00000107282	ENSG00000107282			578	protein-coding gene	gene with protein product		602414		MINT1		7678331, 7719031	Standard	NM_001163		Approved	D9S411E, X11	uc004ahh.2	Q02410	OTTHUMG00000019984	ENST00000265381.4:c.1684C>T	chr9.hg19:g.72071267G>A	ENSP00000265381:p.Arg562Trp	47.0	0.0		63.0	21.0	NM_001163	O14914|O60570|Q5VYR8	Missense_Mutation	SNP	ENST00000265381.4	hg19	CCDS6630.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.149517	0.78001	.	.	ENSG00000107282	ENST00000265381	T	0.21031	2.03	6.06	-0.61	0.11604	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.052490	0.64402	D	0.000001	T	0.45716	0.1356	M	0.75615	2.305	0.58432	D	0.999998	D	0.89917	1.0	D	0.70935	0.971	T	0.55848	-0.8076	10	0.87932	D	0	-15.6655	19.3569	0.94418	0.0:0.0:0.3196:0.6804	.	562	Q02410	APBA1_HUMAN	W	562	ENSP00000265381:R562W	ENSP00000265381:R562W	R	-	1	2	APBA1	71261087	1.000000	0.71417	0.976000	0.42696	0.976000	0.68499	2.556000	0.45862	-0.381000	0.07882	-0.169000	0.13324	CGG	.	.		0.572	APBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052589.2	NM_001163		A	72071267	G	A	72071267	3	1	243	1	0	0	0	0	1	0	0	0	756	1086	38	1	853	1	APBA1	9	72071267	Missense_Mutation	SNP	G	TCGA-ED-A7PX-01A-51D-A34Z-10		72071267	69142164	14	33426										
TSC1	7248	hgsc.bcm.edu	37	chr9	135797282	135797282	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.107142857142857	3	1	1.78681318681319	0	1.93571428571429	0.1	0.617038875103394	0	aaaaggagacgaagttgcaaGggtacattccataaaggcga	12	6	0	1			TCGA-ED-A7PX-01A-51D-A34Z-10	TCGA-ED-A7PX-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	282d9c17-9d34-43d9-952e-bf14edf7bc65	4fd69f63-3ae5-4678-8647-a7e5eabd7486	g.chr9:135797282G>A	ENST00000298552.3	-	7	808	c.587C>T	c.(586-588)cCt>cTt	p.P196L	TSC1_ENST00000545250.1_Missense_Mutation_p.P145L|TSC1_ENST00000403810.1_Missense_Mutation_p.P196L|TSC1_ENST00000475903.1_5'UTR|TSC1_ENST00000440111.2_Missense_Mutation_p.P196L	NM_000368.4|NM_001162426.1|NM_001162427.1	NP_000359.1|NP_001155898.1|NP_001155899.1	Q92574	TSC1_HUMAN	tuberous sclerosis 1	196					activation of Rho GTPase activity (GO:0032862)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|insulin receptor signaling pathway (GO:0008286)|kidney development (GO:0001822)|myelination (GO:0042552)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of TOR signaling (GO:0032007)|negative regulation of translation (GO:0017148)|neural tube closure (GO:0001843)|positive regulation of focal adhesion assembly (GO:0051894)|potassium ion transport (GO:0006813)|protein heterooligomerization (GO:0051291)|protein stabilization (GO:0050821)|regulation of cell cycle (GO:0051726)|regulation of cell-matrix adhesion (GO:0001952)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of protein kinase activity (GO:0045859)|regulation of stress fiber assembly (GO:0051492)|regulation of translation (GO:0006417)|response to insulin (GO:0032868)|rRNA export from nucleus (GO:0006407)|synapse organization (GO:0050808)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|lamellipodium (GO:0030027)|membrane (GO:0016020)|protein complex (GO:0043234)|TSC1-TSC2 complex (GO:0033596)	chaperone binding (GO:0051087)|GTPase regulator activity (GO:0030695)|protein N-terminus binding (GO:0047485)	p.?(1)		NS(1)|bone(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(9)|lung(20)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	65				OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06)		GAAGTTGCAAGGGTACATTCC	0.443			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.P196L		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 1	9	9q34	7248	tuberous sclerosis 1 gene		"E, O"	.	TSC1	167	.	1	Unknown(1)	bone(1)	c.C587T						.						138	132	134					9																	135797282		2203	4300	6503	SO:0001583	missense	7248	exon7	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	TTGCAAGGGTACA	AF013168	CCDS6956.1, CCDS55350.1	9q34	2014-09-17			ENSG00000165699	ENSG00000165699			12362	protein-coding gene	gene with protein product		605284		TSC		9242607, 10806479	Standard	NM_000368		Approved	KIAA0243, LAM, hamartin	uc004cca.2	Q92574	OTTHUMG00000020844	ENST00000298552.3:c.587C>T	chr9.hg19:g.135797282G>A	ENSP00000298552:p.Pro196Leu	60.0	0.0		46.0	30.0	NM_000368	B7Z897|Q5VVN5	Missense_Mutation	SNP	ENST00000298552.3	hg19	CCDS6956.1	.	.	.	.	.	.	.	.	.	.	G	36	5.673373	0.96754	.	.	ENSG00000165699	ENST00000298552;ENST00000440111;ENST00000545250;ENST00000537172;ENST00000424271;ENST00000403810	D;D;D;D;D	0.96459	-4.02;-4.02;-4.02;-4.02;-4.02	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	D	0.98432	0.9478	M	0.87269	2.87	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0	D	0.98844	1.0756	10	0.87932	D	0	-16.8015	19.6603	0.95864	0.0:0.0:1.0:0.0	.	75;145;196;196;196;196	B7Z604;B7Z897;Q86WV8;Q59IT9;Q32NF0;Q92574	.;.;.;.;.;TSC1_HUMAN	L	196;196;145;75;75;196	ENSP00000298552:P196L;ENSP00000394524:P196L;ENSP00000444017:P145L;ENSP00000438099:P75L;ENSP00000386093:P196L	ENSP00000298552:P196L	P	-	2	0	TSC1	134787103	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.894000	0.99253	0.591000	0.81541	CCT	.	.		0.443	TSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054799.1			A	135797282	G	A	135797282	3	1	243	1	0	0	0	0	1	0	0	0	16620	1000	35	3	2975	3	TSC1	9	135797282	Missense_Mutation	SNP	G	TCGA-ED-A7PX-01A-51D-A34Z-10	63726015	135797282	5416149	15	33427										
OR51V1	283111	hgsc.bcm.edu	37	chr11	5221116	5221116	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.107142857142857	3	1	1.78681318681319	0	1.93571428571429	0.1	0.617038875103394	0	gggaaaggtgcttgccaaaaCggtgcaccattgtgaggcta	14	8	0	1			TCGA-ED-A7PX-01A-51D-A34Z-10	TCGA-ED-A7PX-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	282d9c17-9d34-43d9-952e-bf14edf7bc65	4fd69f63-3ae5-4678-8647-a7e5eabd7486	g.chr11:5221116C>T	ENST00000321255.1	-	1	814	c.815G>A	c.(814-816)cGt>cAt	p.R272H		NM_001004760.2	NP_001004760.2	Q9H2C8	O51V1_HUMAN	olfactory receptor, family 51, subfamily V, member 1	272					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(13)|lung(19)|skin(2)|upper_aerodigestive_tract(2)	39		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.83e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CTTGCCAAAACGGTGCACCAT	0.473																																					p.R272H		Atlas-SNP	.											.	OR51V1	77	.	0			c.G815A						.						129	113	118					11																	5221116		2201	4298	6499	SO:0001583	missense	283111	exon1			CCAAAACGGTGCA	BK004432	CCDS31375.1	11p15.4	2012-08-09			ENSG00000176742	ENSG00000176742		"GPCR / Class A : Olfactory receptors"	19597	protein-coding gene	gene with protein product				OR51A12			Standard	NM_001004760		Approved		uc010qyz.2	Q9H2C8	OTTHUMG00000066671	ENST00000321255.1:c.815G>A	chr11.hg19:g.5221116C>T	ENSP00000321729:p.Arg272His	34.0	0.0		76.0	31.0	NM_001004760		Missense_Mutation	SNP	ENST00000321255.1	hg19	CCDS31375.1	.	.	.	.	.	.	.	.	.	.	C	10.85	1.466749	0.26335	.	.	ENSG00000176742	ENST00000321255	T	0.37235	1.21	5.27	4.35	0.52113	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	D	0.000096	T	0.46502	0.1396	M	0.85542	2.76	0.27457	N	0.953251	P	0.39940	0.696	B	0.40940	0.344	T	0.53500	-0.8430	10	0.72032	D	0.01	.	13.0188	0.58773	0.0:0.9208:0.0:0.0792	.	272	Q9H2C8	O51V1_HUMAN	H	272	ENSP00000321729:R272H	ENSP00000321729:R272H	R	-	2	0	OR51V1	5177692	0.008000	0.16893	0.707000	0.30419	0.090000	0.18270	0.602000	0.24134	1.431000	0.47355	0.655000	0.94253	CGT	.	.		0.473	OR51V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142965.1	NM_001004760		T	5221116	C	T	5221116	3	4	243	1	0	0	0	0	1	0	0	0	11116	536	19	1	153	1	OR51V1	11	5221116	Missense_Mutation	SNP	C	TCGA-ED-A7PX-01A-51D-A34Z-10		5221116	129785400	16	33428										
DRAP1	10589	hgsc.bcm.edu	37	chr11	65687843	65687843	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.107142857142857	3	1	1.78681318681319	0	1.93571428571429	0.1	0.617038875103394	0	catcgagctggagcagcagtTtgacttcttgaaggacctgg	13	9	1	2			TCGA-ED-A7PX-01A-51D-A34Z-10	TCGA-ED-A7PX-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	282d9c17-9d34-43d9-952e-bf14edf7bc65	4fd69f63-3ae5-4678-8647-a7e5eabd7486	g.chr11:65687843T>G	ENST00000312515.2	+	4	484	c.239T>G	c.(238-240)tTt>tGt	p.F80C	C11orf68_ENST00000438576.2_5'Flank|DRAP1_ENST00000532933.1_Missense_Mutation_p.F60C|C11orf68_ENST00000530188.1_5'Flank|DRAP1_ENST00000376991.2_Missense_Mutation_p.F80C|C11orf68_ENST00000449692.3_5'Flank|DRAP1_ENST00000527119.1_Missense_Mutation_p.F36C	NM_006442.3	NP_006433.2	Q14919	NC2A_HUMAN	DR1-associated protein 1 (negative cofactor 2 alpha)	80					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(1)	5				READ - Rectum adenocarcinoma(159;0.166)		GAGCAGCAGTTTGACTTCTTG	0.627																																					p.F80C		Atlas-SNP	.											.	DRAP1	18	.	0			c.T239G						.						76	78	77					11																	65687843		2201	4296	6497	SO:0001583	missense	10589	exon4			AGCAGTTTGACTT	U41843	CCDS8123.1	11q13	2010-09-29			ENSG00000175550	ENSG00000175550			3019	protein-coding gene	gene with protein product	"negative cofactor 2 alpha", "DR1-associated corepressor"	602289				8608938	Standard	NM_006442		Approved	NC2-alpha	uc001ogj.2	Q14919	OTTHUMG00000166723	ENST00000312515.2:c.239T>G	chr11.hg19:g.65687843T>G	ENSP00000307850:p.Phe80Cys	35.0	0.0		42.0	9.0	NM_006442	Q13448	Missense_Mutation	SNP	ENST00000312515.2	hg19	CCDS8123.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.575947	0.86645	.	.	ENSG00000175550	ENST00000312515;ENST00000376991;ENST00000527119;ENST00000532933	T;T	0.50813	0.73;0.73	4.33	4.33	0.51752	Histone-fold (1);	0.000000	0.85682	D	0.000000	T	0.61527	0.2354	L	0.58101	1.795	0.80722	D	1	D	0.89917	1.0	D	0.67725	0.953	T	0.65261	-0.6211	10	0.87932	D	0	-7.0965	11.7748	0.51979	0.0:0.0:0.0:1.0	.	80	Q14919	NC2A_HUMAN	C	80;80;36;60	ENSP00000437287:F36C;ENSP00000432445:F60C	ENSP00000307850:F80C	F	+	2	0	DRAP1	65444419	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.132000	0.77251	1.744000	0.51775	0.533000	0.62120	TTT	.	.		0.627	DRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391197.2	NM_006442		G	65687843	T	G	65687843	3	3	243	1	0	0	0	0	1	0	0	0	4757	1841	64	5	253	5	DRAP1	11	65687843	Missense_Mutation	SNP	T	TCGA-ED-A7PX-01A-51D-A34Z-10	60466727	65687843	69318673	17	33429										
ERBB3	2065	hgsc.bcm.edu	37	chr12	56495713	56495713	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.107142857142857	3	1	1.78681318681319	0	1.93571428571429	0.1	0.617038875103394	0	tttcaggggcctggacatcaGgccccccatgtccattatgc	10	14	2	0			TCGA-ED-A7PX-01A-51D-A34Z-10	TCGA-ED-A7PX-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	282d9c17-9d34-43d9-952e-bf14edf7bc65	4fd69f63-3ae5-4678-8647-a7e5eabd7486	g.chr12:56495713G>T	ENST00000267101.3	+	28	4343	c.3903G>T	c.(3901-3903)caG>caT	p.Q1301H	ERBB3_ENST00000549832.1_Missense_Mutation_p.Q421H|ERBB3_ENST00000553131.1_Missense_Mutation_p.Q542H|ERBB3_ENST00000415288.2_Missense_Mutation_p.Q1242H|PA2G4_ENST00000552766.1_5'Flank|ERBB3_ENST00000450146.2_Missense_Mutation_p.Q658H|RP11-603J24.9_ENST00000548861.1_Intron|PA2G4_ENST00000303305.6_5'Flank|RP11-603J24.17_ENST00000548595.1_RNA	NM_001982.3	NP_001973.2	P21860	ERBB3_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3	1301					cranial nerve development (GO:0021545)|endocardial cushion development (GO:0003197)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of cell adhesion (GO:0007162)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of secretion (GO:0051048)|negative regulation of signal transduction (GO:0009968)|neuron apoptotic process (GO:0051402)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell proliferation (GO:0042127)|Schwann cell differentiation (GO:0014037)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein tyrosine kinase activator activity (GO:0030296)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			CTGGACATCAGGCCCCCCATG	0.537																																					p.Q1301H		Atlas-SNP	.											.	ERBB3	350	.	0			c.G3903T						.						107	117	114					12																	56495713		2203	4300	6503	SO:0001583	missense	2065	exon28			ACATCAGGCCCCC	M34309	CCDS31833.1, CCDS44918.1	12q13	2013-07-09	2013-07-09			ENSG00000065361			3431	protein-coding gene	gene with protein product		190151	"lethal congenital contracture syndrome 2"	LCCS2			Standard	NM_001982		Approved	HER3	uc001sjh.3	P21860	OTTHUMG00000170140	ENST00000267101.3:c.3903G>T	chr12.hg19:g.56495713G>T	ENSP00000267101:p.Gln1301His	39.0	0.0		55.0	25.0	NM_001982	A8K6L6|B4DIK7|B4DV32|E9PDT8|Q9BUD7	Missense_Mutation	SNP	ENST00000267101.3	hg19	CCDS31833.1	.	.	.	.	.	.	.	.	.	.	G	3.395	-0.123576	0.06795	.	.	ENSG00000065361	ENST00000267101;ENST00000450146;ENST00000415288;ENST00000550070;ENST00000553131;ENST00000549832	T;T;T;T;T	0.78707	-1.06;-0.97;-1.05;-1.2;-0.93	5.39	-2.98	0.05513	.	0.563354	0.17890	N	0.158548	T	0.44138	0.1279	N	0.04508	-0.205	0.29846	N	0.828808	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.25152	-1.0140	10	0.19147	T	0.46	.	1.1483	0.01780	0.3152:0.1409:0.3421:0.2018	.	1242;421;1301	P21860-4;B3KWG5;P21860	.;.;ERBB3_HUMAN	H	1301;658;1242;424;542;421	ENSP00000267101:Q1301H;ENSP00000399178:Q658H;ENSP00000408340:Q1242H;ENSP00000449129:Q542H;ENSP00000448729:Q421H	ENSP00000267101:Q1301H	Q	+	3	2	ERBB3	54781980	0.002000	0.14202	0.773000	0.31616	0.337000	0.28794	-0.178000	0.09782	-0.700000	0.05070	-0.262000	0.10625	CAG	.	.		0.537	ERBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407619.3			T	56495713	G	T	56495713	3	4	243	1	0	0	0	0	1	0	0	0	5210	991	35	3	4144	3	ERBB3	12	56495713	Missense_Mutation	SNP	G	TCGA-ED-A7PX-01A-51D-A34Z-10		56495713	77356182	18	33430										
SRGAP1	57522	hgsc.bcm.edu	37	chr12	64437335	64437335	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.107142857142857	3	1	1.78681318681319	0	1.93571428571429	0.1	0.617038875103394	0	ttttcaagtactatattcatGatctttctgatttaattgat	4	5	4	3			TCGA-ED-A7PX-01A-51D-A34Z-10	TCGA-ED-A7PX-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	282d9c17-9d34-43d9-952e-bf14edf7bc65	4fd69f63-3ae5-4678-8647-a7e5eabd7486	g.chr12:64437335G>A	ENST00000355086.3	+	6	1305	c.781G>A	c.(781-783)Gat>Aat	p.D261N	RP11-196H14.2_ENST00000535594.1_RNA|SRGAP1_ENST00000357825.3_Missense_Mutation_p.D261N|SRGAP1_ENST00000543397.1_Missense_Mutation_p.D221N	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	261	F-BAR domain.				axon guidance (GO:0007411)|cell migration (GO:0016477)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	65			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		CTATATTCATGATCTTTCTGA	0.294																																					p.D261N		Atlas-SNP	.											.	SRGAP1	146	.	0			c.G781A						.						91	76	81					12																	64437335		2203	4300	6503	SO:0001583	missense	57522	exon6			ATTCATGATCTTT	AB037725	CCDS8967.1	12q13.13	2011-07-04			ENSG00000196935	ENSG00000196935		"Rho GTPase activating proteins"	17382	protein-coding gene	gene with protein product		606523				11672528	Standard	NM_020762		Approved	KIAA1304, ARHGAP13	uc010ssp.1	Q7Z6B7	OTTHUMG00000168750	ENST00000355086.3:c.781G>A	chr12.hg19:g.64437335G>A	ENSP00000347198:p.Asp261Asn	106.0	0.0		223.0	44.0	NM_020762	Q9H8A3|Q9P2P2	Missense_Mutation	SNP	ENST00000355086.3	hg19	CCDS8967.1	.	.	.	.	.	.	.	.	.	.	G	35	5.510171	0.96386	.	.	ENSG00000196935	ENST00000355086;ENST00000357825;ENST00000543397	T;T;T	0.49139	0.79;0.79;2.36	5.56	5.56	0.83823	.	0.000000	0.35739	U	0.003007	T	0.70535	0.3235	M	0.89601	3.045	0.80722	D	1	P;P;P	0.49185	0.884;0.847;0.92	P;P;P	0.53593	0.636;0.73;0.73	T	0.75091	-0.3440	9	.	.	.	.	19.9239	0.97097	0.0:0.0:1.0:0.0	.	261;221;261	Q7Z6B7;G5EA48;Q7Z6B7-2	SRGP1_HUMAN;.;.	N	261;261;221	ENSP00000347198:D261N;ENSP00000350480:D261N;ENSP00000437948:D221N	.	D	+	1	0	SRGAP1	62723602	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	9.787000	0.99055	2.797000	0.96272	0.563000	0.77884	GAT	.	.		0.294	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400896.1			A	64437335	G	A	64437335	3	1	243	1	0	0	0	0	1	0	0	0	15160	1290	45	3	803	3	SRGAP1	12	64437335	Missense_Mutation	SNP	G	TCGA-ED-A7PX-01A-51D-A34Z-10	7941622	64437335	69414560	19	33431										
FAM48A	55578	hgsc.bcm.edu	37	chr13	37583904	37583904	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.107142857142857	3	1	1.78681318681319	0	1.93571428571429	0.1	0.617038875103394	0	tagctgagctgtttgtgctgCtgctgctgccatagccattt	11	10	0	1			TCGA-ED-A7PX-01A-51D-A34Z-10	TCGA-ED-A7PX-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	282d9c17-9d34-43d9-952e-bf14edf7bc65	4fd69f63-3ae5-4678-8647-a7e5eabd7486	g.chr13:37583904C>T	ENST00000350612.6	-	26	2465	c.2245G>A	c.(2245-2247)Gca>Aca	p.A749T	SUPT20H_ENST00000464744.1_Missense_Mutation_p.S715N|SUPT20H_ENST00000356185.3_Missense_Mutation_p.S715N|SUPT20H_ENST00000360252.4_Missense_Mutation_p.S715N|SUPT20H_ENST00000475892.1_Missense_Mutation_p.S793N	NM_001014286.2	NP_001014308.2	Q8NEM7	SP20H_HUMAN	suppressor of Ty 20 homolog (S. cerevisiae)	749	Gln-rich.				autophagy (GO:0006914)|chromatin organization (GO:0006325)|gastrulation (GO:0007369)	SAGA complex (GO:0000124)|SAGA-type complex (GO:0070461)	transcription cofactor activity (GO:0003712)										GTTTGTGCTGCTGCTGCTGCC	0.453																																					p.A749T		Atlas-SNP	.											.	.	.	.	0			c.G2245A						.						116	106	110					13																	37583904		2203	4300	6503	SO:0001583	missense	55578	exon26			GTGCTGCTGCTGC	AF093250	CCDS9362.1, CCDS31959.1, CCDS61311.1	13q13	2012-11-29	2012-11-29	2012-11-29	ENSG00000102710	ENSG00000102710			20596	protein-coding gene	gene with protein product	"p38 interacting protein", "transcription factor (p38 interacting protein)"	613417	"chromosome 13 open reading frame 19", "family with sequence similarity 48, member A"	C13orf19, FAM48A		12070015 , 16685401	Standard	NM_001278480		Approved	SPT20, bA421P11.4, P38IP	uc001uwg.3	Q8NEM7	OTTHUMG00000016747	ENST00000350612.6:c.2245G>A	chr13.hg19:g.37583904C>T	ENSP00000218894:p.Ala749Thr	201.0	0.0		233.0	10.0	NM_001014286	E7ER46|Q71RF3|Q9Y6A6	Missense_Mutation	SNP	ENST00000350612.6	hg19	CCDS31959.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.87|10.87	1.472182|1.472182	0.26423|0.26423	.|.	.|.	ENSG00000102710|ENSG00000102710	ENST00000350612|ENST00000360252;ENST00000475892;ENST00000356185;ENST00000536874;ENST00000464744	T|T;T;T;T	0.35236|0.50548	1.32|0.74;0.75;0.74;0.74	5.52|5.52	4.68|4.68	0.58851|0.58851	.|.	0.256846|.	0.27936|.	N|.	0.017255|.	T|T	0.39759|0.39759	0.1090|0.1090	L|L	0.48642|0.48642	1.525|1.525	0.80722|0.80722	D|D	1|1	B|B;B;B	0.06786|0.02656	0.001|0.0;0.0;0.0	B|B;B;B	0.06405|0.04013	0.002|0.0;0.0;0.001	T|T	0.22034|0.22034	-1.0228|-1.0228	10|9	0.48119|0.39692	T|T	0.1|0.17	-11.2654|-11.2654	9.8977|9.8977	0.41329|0.41329	0.0:0.844:0.0:0.156|0.0:0.844:0.0:0.156	.|.	749|793;715;715	Q8NEM7|E7ER46;A8K8L1;Q8NEM7-2	FA48A_HUMAN|.;.;.	T|N	749|715;793;715;714;715	ENSP00000218894:A749T|ENSP00000353388:S715N;ENSP00000417510:S793N;ENSP00000348512:S715N;ENSP00000419754:S715N	ENSP00000218894:A749T|ENSP00000348512:S715N	A|S	-|-	1|2	0|0	FAM48A|FAM48A	36481904|36481904	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	2.697000|2.697000	0.47060|0.47060	1.350000|1.350000	0.45770|0.45770	0.467000|0.467000	0.42956|0.42956	GCA|AGC	.	.		0.453	SUPT20H-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354766.1	NM_017569		T	37583904	C	T	37583904	3	4	243	1	0	0	0	0	1	0	0	0	5580	797	28	3	98	3	FAM48A	13	37583904	Missense_Mutation	SNP	C	TCGA-ED-A7PX-01A-51D-A34Z-10		37583904	77585974	20	33432										
NIN	51199	hgsc.bcm.edu	37	chr14	51196346	51196346	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.107142857142857	3	1	1.78681318681319	0	1.93571428571429	0.1	0.617038875103394	0	tgaagctgcagaaactgctcCctgggcaccatcggacaggc	12	13	0	2			TCGA-ED-A7PX-01A-51D-A34Z-10	TCGA-ED-A7PX-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	282d9c17-9d34-43d9-952e-bf14edf7bc65	4fd69f63-3ae5-4678-8647-a7e5eabd7486	g.chr14:51196346C>A	ENST00000382041.3	-	29	6163	c.5973G>T	c.(5971-5973)agG>agT	p.R1991S	NIN_ENST00000245441.5_Missense_Mutation_p.R1991S|NIN_ENST00000382043.4_Missense_Mutation_p.R1278S|NIN_ENST00000453196.1_Missense_Mutation_p.R1991S|NIN_ENST00000324330.9_3'UTR|NIN_ENST00000389868.3_3'UTR|NIN_ENST00000530997.2_Missense_Mutation_p.R1991S	NM_016350.4|NM_182946.1	NP_057434.4|NP_891991	Q8N4C6	NIN_HUMAN	ninein (GSK3B interacting protein)	1991					centrosome localization (GO:0051642)|centrosome-templated microtubule nucleation (GO:0090222)|microtubule anchoring at centrosome (GO:0034454)	centriole (GO:0005814)|centrosome (GO:0005813)|microtubule (GO:0005874)|nucleolus (GO:0005730)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(13)|lung(16)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	71	all_epithelial(31;0.00244)|Breast(41;0.127)					GAAACTGCTCCCTGGGCACCA	0.577			T	PDGFRB	MPD																																p.R1991S		Atlas-SNP	.		Dom	yes		14	14q24	51199	ninein (GSK3B interacting protein)		L	.	NIN	475	.	0			c.G5973T						.						116	105	108					14																	51196346		2203	4300	6503	SO:0001583	missense	51199	exon29			CTGCTCCCTGGGC	AF212162	CCDS32078.1, CCDS32079.1, CCDS32078.2	14q21-q22	2013-01-10			ENSG00000100503	ENSG00000100503		"EF-hand domain containing"	14906	protein-coding gene	gene with protein product		608684				11004522, 11162463	Standard	NM_020921		Approved		uc001wyi.3	Q8N4C6	OTTHUMG00000029569	ENST00000382041.3:c.5973G>T	chr14.hg19:g.51196346C>A	ENSP00000371472:p.Arg1991Ser	115.0	0.0		105.0	56.0	NM_020921	A6NDB8|B7WPA3|C9JSB6|C9JSG2|C9JXL2|Q5BKU3|Q6P0P6|Q9BWU6|Q9C012|Q9C013|Q9C014|Q9H5I6|Q9HAT7|Q9HBY5|Q9HCK7|Q9UH61	Missense_Mutation	SNP	ENST00000382041.3	hg19	CCDS32079.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.0|22.0	4.224096|4.224096	0.79576|0.79576	.|.	.|.	ENSG00000100503|ENSG00000100503	ENST00000530997;ENST00000389869;ENST00000530853|ENST00000245441;ENST00000311149;ENST00000382043;ENST00000324292;ENST00000382041;ENST00000453196	.|T;T;T;T	.|0.12255	.|3.38;2.7;3.19;3.14	5.23|5.23	4.32|4.32	0.51571|0.51571	.|.	.|0.476626	.|0.22821	.|N	.|0.055235	.|T	.|0.33030	.|0.0849	M|M	0.64997|0.64997	1.995|1.995	0.80722|0.80722	D|D	1|1	.|D;D;D;P;D	.|0.89917	.|0.993;1.0;0.996;0.94;0.996	.|D;D;D;P;D	.|0.87578	.|0.963;0.998;0.99;0.678;0.99	.|T	.|0.00855	.|-1.1539	.|10	.|0.40728	.|T	.|0.16	-15.8915|-15.8915	13.9493|13.9493	0.64106|0.64106	0.0:0.9224:0.0:0.0776|0.0:0.9224:0.0:0.0776	.|.	.|1997;1991;1991;1278;1991	.|Q8N4C6-5;C9J066;Q8N4C6;Q5BKU3;Q8N4C6-7	.|.;.;NIN_HUMAN;.;.	X|S	1482|1991;1974;1278;1997;1991;1991	.|ENSP00000245441:R1991S;ENSP00000371474:R1278S;ENSP00000371472:R1991S;ENSP00000412391:R1991S	.|ENSP00000245441:R1991S	G|R	-|-	1|3	0|2	NIN|NIN	50266096|50266096	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.895000|0.895000	0.52256|0.52256	1.921000|1.921000	0.40035|0.40035	2.624000|2.624000	0.88883|0.88883	0.650000|0.650000	0.86243|0.86243	GGA|AGG	.	.		0.577	NIN-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395207.2	NM_182946		A	51196346	C	A	51196346	3	1	243	1	0	0	0	0	1	0	0	0	10426	622	22	3	588	3	NIN	14	51196346	Missense_Mutation	SNP	C	TCGA-ED-A7PX-01A-51D-A34Z-10		51196346	56153194	21	33433										
PRIMA1	145270	hgsc.bcm.edu	37	chr14	94245606	94245606	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.107142857142857	3	1	1.78681318681319	0	1.93571428571429	0.1	0.617038875103394	0	ccggcactggcagacgtgtcGgcagctgtcagtcactttgg	14	12	2	1			TCGA-ED-A7PX-01A-51D-A34Z-10	TCGA-ED-A7PX-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	282d9c17-9d34-43d9-952e-bf14edf7bc65	4fd69f63-3ae5-4678-8647-a7e5eabd7486	g.chr14:94245606G>A	ENST00000393140.1	-	3	247	c.145C>T	c.(145-147)Cga>Tga	p.R49*	PRIMA1_ENST00000316227.3_Nonsense_Mutation_p.R49*|PRIMA1_ENST00000393143.1_Nonsense_Mutation_p.R49*	NM_178013.3	NP_821092.1	Q86XR5	PRIMA_HUMAN	proline rich membrane anchor 1	49					establishment of localization in cell (GO:0051649)|neurotransmitter catabolic process (GO:0042135)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|synapse (GO:0045202)				endometrium(1)|large_intestine(2)|lung(3)|skin(1)	7		all_cancers(154;0.127)		Epithelial(152;0.138)|COAD - Colon adenocarcinoma(157;0.229)		CAGACGTGTCGGCAGCTGTCA	0.647																																					p.R49X		Atlas-SNP	.											.	PRIMA1	21	.	0			c.C145T						.						33	28	29					14																	94245606		2201	4299	6500	SO:0001587	stop_gained	145270	exon3			CGTGTCGGCAGCT		CCDS9912.1	14q32.13	2008-08-29			ENSG00000175785	ENSG00000175785			18319	protein-coding gene	gene with protein product	"membrane anchor of acetylcholinesterase"	613851				11804574	Standard	NM_178013		Approved	PRIMA	uc001ybw.1	Q86XR5	OTTHUMG00000141313	ENST00000393140.1:c.145C>T	chr14.hg19:g.94245606G>A	ENSP00000376848:p.Arg49*	22.0	0.0		28.0	16.0	NM_178013	Q86XR6	Nonsense_Mutation	SNP	ENST00000393140.1	hg19	CCDS9912.1	.	.	.	.	.	.	.	.	.	.	G	37	6.039999	0.97226	.	.	ENSG00000175785	ENST00000393140;ENST00000393143;ENST00000316227	.	.	.	4.86	4.86	0.63082	.	0.163970	0.40554	N	0.001072	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	-0.6267	13.5121	0.61519	0.0:0.0:1.0:0.0	.	.	.	.	X	49	.	ENSP00000320948:R49X	R	-	1	2	PRIMA1	93315359	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.650000	0.61440	2.254000	0.74563	0.549000	0.68633	CGA	.	.		0.647	PRIMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280658.1	NM_178013		A	94245606	G	A	94245606	4	1	243	1	0	0	0	0	0	1	0	0	12504	1124	39	1	328	1	PRIMA1	14	94245606	Nonsense_Mutation	SNP	G	TCGA-ED-A7PX-01A-51D-A34Z-10	43049260	94245606	13103934	22	33434										
JAG2	3714	hgsc.bcm.edu	37	chr14	105612177	105612177	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.107142857142857	3	1	1.78681318681319	0	1.93571428571429	0.1	0.617038875103394	0	gtggctcttctgcgccgcacTccccccaggcctcacagggt	11	18	3	0			TCGA-ED-A7PX-01A-51D-A34Z-10	TCGA-ED-A7PX-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	282d9c17-9d34-43d9-952e-bf14edf7bc65	4fd69f63-3ae5-4678-8647-a7e5eabd7486	g.chr14:105612177T>C	ENST00000331782.3	-	23	3246	c.2843A>G	c.(2842-2844)gAg>gGg	p.E948G	JAG2_ENST00000347004.2_Missense_Mutation_p.E910G	NM_002226.4	NP_002217.3	Q9Y219	JAG2_HUMAN	jagged 2	948					auditory receptor cell fate commitment (GO:0009912)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|epithelial cell apoptotic process involved in palatal shelf morphogenesis (GO:1990134)|gamma-delta T cell differentiation (GO:0042492)|in utero embryonic development (GO:0001701)|morphogenesis of embryonic epithelium (GO:0016331)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|respiratory system process (GO:0003016)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|T cell differentiation (GO:0030217)|thymic T cell selection (GO:0045061)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)			breast(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(7)|prostate(2)|skin(5)	22		all_cancers(154;0.0336)|all_epithelial(191;0.0729)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00989)|all cancers(16;0.0114)|Epithelial(46;0.0272)	Epithelial(152;0.047)|OV - Ovarian serous cystadenocarcinoma(161;0.148)|all cancers(159;0.208)		TGCGCCGCACTCCCCCCAGGC	0.687																																					p.E948G		Atlas-SNP	.											.	JAG2	69	.	0			c.A2843G						.						27	21	23					14																	105612177		2144	4260	6404	SO:0001583	missense	3714	exon23			CCGCACTCCCCCC	AF020201	CCDS9998.1, CCDS9999.1	14q32	2008-08-01			ENSG00000184916	ENSG00000184916			6189	protein-coding gene	gene with protein product		602570				9315665, 10662552	Standard	NM_002226		Approved		uc001yqg.4	Q9Y219	OTTHUMG00000140172	ENST00000331782.3:c.2843A>G	chr14.hg19:g.105612177T>C	ENSP00000328169:p.Glu948Gly	115.0	0.0		119.0	5.0	NM_002226	Q9UE17|Q9UE99|Q9UNK8|Q9Y6P9|Q9Y6Q0	Missense_Mutation	SNP	ENST00000331782.3	hg19	CCDS9998.1	.	.	.	.	.	.	.	.	.	.	T	13.63	2.294824	0.40594	.	.	ENSG00000184916	ENST00000331782;ENST00000347004	D;D	0.87334	-2.23;-2.24	3.6	2.39	0.29439	.	0.356734	0.25762	U	0.028466	D	0.82724	0.5099	L	0.52573	1.65	0.38453	D	0.947009	B;B	0.29646	0.253;0.164	B;B	0.32980	0.156;0.075	T	0.78130	-0.2324	10	0.56958	D	0.05	.	8.9426	0.35740	0.0:0.0:0.1887:0.8113	.	910;948	Q9Y219-2;Q9Y219	.;JAG2_HUMAN	G	948;910	ENSP00000328169:E948G;ENSP00000328566:E910G	ENSP00000328169:E948G	E	-	2	0	JAG2	104683222	0.885000	0.30320	0.990000	0.47175	0.797000	0.45037	1.450000	0.35134	0.254000	0.21573	0.358000	0.22013	GAG	.	.		0.687	JAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276506.2			C	105612177	T	C	105612177	3	2	243	1	0	0	0	0	1	0	0	0	7944	1551	54	2	889	2	JAG2	14	105612177	Missense_Mutation	SNP	T	TCGA-ED-A7PX-01A-51D-A34Z-10	11366571	105612177	1737363	23	33435										
AKAP13	11214	hgsc.bcm.edu	37	chr15	86124170	86124171	+	Nonsense_Mutation	DNP	AC	AC	TT													0.107142857142857	3	1	1.78681318681319	0	1.93571428571429	0.1	0.617038875103394	0	cagagaacaccacctcctggAcaagatactcaacaatttca							TCGA-ED-A7PX-01A-51D-A34Z-10	TCGA-ED-A7PX-10A-01D-A34Z-10	A|C	A|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	282d9c17-9d34-43d9-952e-bf14edf7bc65	4fd69f63-3ae5-4678-8647-a7e5eabd7486	g.chr15:86124170_86124171AC>TT	ENST00000394518.2	+	7	2966_2967	c.2871_2872AC>TT	c.(2869-2874)ggACaa>ggTTaa	p.Q958*	AKAP13_ENST00000361243.2_Nonsense_Mutation_p.Q958*|RP11-815J21.2_ENST00000561409.1_RNA	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	958					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						CACCTCCTGGACAAGATACTCA	0.441																																					p.G957G|p.Q958X	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.A2871T|c.C2872T						.																																			SO:0001587	stop_gained	11214	exon7			TCCTGGACAAGAT|CCTGGACAAGATA	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"A-kinase anchor proteins", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	371	protein-coding gene	gene with protein product		604686	"lymphoid blast crisis oncogene"	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		Exception_encountered	chr15.hg19:g.86124170_86124171delinsTT	ENSP00000378026:p.Gln958*	59.0|61.0	0.0		56.0	17.0|16.0	NM_007200	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Silent|Nonsense_Mutation	SNP	ENST00000394518.2	hg19	CCDS32319.1																																																																																			.	.		0.441	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200		TT	86124171	AC	TT	86124170	4	4	243	1	0	0	0	0	0	1	0	0	449	262	10	4	2893	4	AKAP13	15	86124170	Nonsense_Mutation	DNP	AC	TCGA-ED-A7PX-01A-51D-A34Z-10		86124170	16407222	24	33436										
FAM92B	339145	hgsc.bcm.edu	37	chr16	85133752	85133752	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.107142857142857	3	1	1.78681318681319	0	1.93571428571429	0.1	0.617038875103394	0	cccacacgctcacctggctgGcgagagactgaagaacagat	11	13	1	4			TCGA-ED-A7PX-01A-51D-A34Z-10	TCGA-ED-A7PX-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	282d9c17-9d34-43d9-952e-bf14edf7bc65	4fd69f63-3ae5-4678-8647-a7e5eabd7486	g.chr16:85133752G>A	ENST00000539556.1	-	8	901	c.746C>T	c.(745-747)gCc>gTc	p.A249V		NM_198491.1	NP_940893.1	Q6ZTR7	FA92B_HUMAN	family with sequence similarity 92, member B	249										breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	16						CACCTGGCTGGCGAGAGACTG	0.572																																					p.A249V		Atlas-SNP	.											.	FAM92B	29	.	0			c.C746T						.						68	55	59					16																	85133752		2198	4300	6498	SO:0001583	missense	339145	exon7			TGGCTGGCGAGAG		CCDS32500.1	16q24.1	2005-09-22				ENSG00000153789			24781	protein-coding gene	gene with protein product						12477932	Standard	NM_198491		Approved	FLJ44299	uc021tlz.1	Q6ZTR7		ENST00000539556.1:c.746C>T	chr16.hg19:g.85133752G>A	ENSP00000443411:p.Ala249Val	28.0	0.0		37.0	11.0	NM_198491		Missense_Mutation	SNP	ENST00000539556.1	hg19	CCDS32500.1	.	.	.	.	.	.	.	.	.	.	G	12.98	2.101252	0.37048	.	.	ENSG00000153789	ENST00000393246;ENST00000539556	T	0.34667	1.35	4.82	1.75	0.24633	.	1.048890	0.07502	N	0.907383	T	0.30166	0.0756	L	0.43923	1.385	0.09310	N	1	B	0.14012	0.009	B	0.19148	0.024	T	0.29427	-1.0012	10	0.40728	T	0.16	-2.212	6.2424	0.20797	0.3156:0.0:0.6844:0.0	.	249	Q6ZTR7	FA92B_HUMAN	V	249	ENSP00000443411:A249V	ENSP00000376937:A249V	A	-	2	0	FAM92B	83691253	0.000000	0.05858	0.007000	0.13788	0.083000	0.17756	-0.212000	0.09319	0.446000	0.26666	0.462000	0.41574	GCC	.	.		0.572	FAM92B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_198491		A	85133752	G	A	85133752	3	1	243	1	0	0	0	0	1	0	0	0	5661	1203	42	3	176	3	FAM92B	16	85133752	Missense_Mutation	SNP	G	TCGA-ED-A7PX-01A-51D-A34Z-10		85133752	5221001	25	33437										
P2RX1	5023	hgsc.bcm.edu	37	chr17	3806509	3806509	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.107142857142857	3	1	1.78681318681319	0	1.93571428571429	0.1	0.617038875103394	0	tccataccttctcagccaggGtgctgaagttctggcctgac	10	13	2	2			TCGA-ED-A7PX-01A-51D-A34Z-10	TCGA-ED-A7PX-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	282d9c17-9d34-43d9-952e-bf14edf7bc65	4fd69f63-3ae5-4678-8647-a7e5eabd7486	g.chr17:3806509G>T	ENST00000225538.3	-	7	1008	c.734C>A	c.(733-735)aCc>aAc	p.T245N		NM_002558.2	NP_002549.1	P51575	P2RX1_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 1	245					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ceramide biosynthetic process (GO:0046513)|insemination (GO:0007320)|ion transport (GO:0006811)|neuronal action potential (GO:0019228)|platelet activation (GO:0030168)|positive regulation of ion transport (GO:0043270)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of vascular smooth muscle contraction (GO:0003056)|response to ATP (GO:0033198)|serotonin secretion by platelet (GO:0002554)|signal transduction (GO:0007165)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|vasoconstriction (GO:0042310)	external side of cell outer membrane (GO:0031240)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|drug binding (GO:0008144)|extracellular ATP-gated cation channel activity (GO:0004931)|purinergic nucleotide receptor activity (GO:0001614)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)	13				LUAD - Lung adenocarcinoma(2;1.9e-05)|Lung(3;0.0173)		CTCAGCCAGGGTGCTGAAGTT	0.582																																					p.T245N		Atlas-SNP	.											.	P2RX1	38	.	0			c.C734A						.						80	74	76					17																	3806509		2203	4300	6503	SO:0001583	missense	5023	exon7			GCCAGGGTGCTGA	X83688	CCDS11040.1	17p13.3	2012-01-17				ENSG00000108405		"Purinergic receptors", "Ligand-gated ion channels / Purinergic receptors, ionotropic"	8533	protein-coding gene	gene with protein product		600845				8834001	Standard	NM_002558		Approved	P2X1	uc002fww.3	P51575		ENST00000225538.3:c.734C>A	chr17.hg19:g.3806509G>T	ENSP00000225538:p.Thr245Asn	36.0	0.0		25.0	12.0	NM_002558	Q9UK84	Missense_Mutation	SNP	ENST00000225538.3	hg19	CCDS11040.1	.	.	.	.	.	.	.	.	.	.	G	8.596	0.885606	0.17540	.	.	ENSG00000108405	ENST00000225538	T	0.04083	3.71	5.43	2.12	0.27331	.	0.609805	0.18718	N	0.133118	T	0.04724	0.0128	L	0.28115	0.83	0.09310	N	1	B	0.25169	0.119	B	0.36418	0.224	T	0.40001	-0.9586	10	0.49607	T	0.09	-14.7021	5.6267	0.17487	0.0825:0.4055:0.3961:0.1158	.	245	P51575	P2RX1_HUMAN	N	245	ENSP00000225538:T245N	ENSP00000225538:T245N	T	-	2	0	P2RX1	3753258	0.001000	0.12720	0.318000	0.25279	0.287000	0.27160	0.357000	0.20199	0.174000	0.19809	-0.217000	0.12591	ACC	.	.		0.582	P2RX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438391.1	NM_002558		T	3806509	G	T	3806509	3	4	243	1	0	0	0	0	1	0	0	0	11348	1261	44	3	489	3	P2RX1	17	3806509	Missense_Mutation	SNP	G	TCGA-ED-A7PX-01A-51D-A34Z-10		3806509	77388701	26	33438										
KIAA0427	9811	hgsc.bcm.edu	37	chr18	46163025	46163026	+	Nonsense_Mutation	DNP	CC	CC	GA													0.107142857142857	3	1	1.78681318681319	0	1.93571428571429	0.1	0.617038875103394	0	accgctggacagcagctgttCcttctcccgagggcgagccc					rs141933283		TCGA-ED-A7PX-01A-51D-A34Z-10	TCGA-ED-A7PX-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	282d9c17-9d34-43d9-952e-bf14edf7bc65	4fd69f63-3ae5-4678-8647-a7e5eabd7486	g.chr18:46163025_46163026CC>GA	ENST00000256413.3	+	3	516_517	c.221_222CC>GA	c.(220-222)tCC>tGA	p.S74*	CTIF_ENST00000382998.4_Nonsense_Mutation_p.S74*	NM_014772.2	NP_055587.1	O43310	CTIF_HUMAN	CBP80/20-dependent translation initiation factor	74	Interaction with NCBP1/CBP80.				nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translational initiation (GO:0006446)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(14)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	31						AGCAGCTGTTCCTTCTCCCGAG	0.644																																					p.S74C|p.S74S		Atlas-SNP	.											.	CTIF	102	.	0			c.C221G|c.C222A						.																																			SO:0001587	stop_gained	9811	exon3			GCTGTTCCTTCTC|CTGTTCCTTCTCC	AB007887	CCDS11935.1, CCDS45864.1	18q21.1	2011-01-20	2011-01-20	2011-01-20	ENSG00000134030	ENSG00000134030			23925	protein-coding gene	gene with protein product		613178	"KIAA0427"	KIAA0427		9455477, 19648179	Standard	NM_014772		Approved		uc002ldd.3	O43310	OTTHUMG00000132656	Exception_encountered	chr18.hg19:g.46163025_46163026delinsGA	ENSP00000256413:p.Ser74*	88.0|86.0	0.0		85.0	35.0	NM_014772	B3KTR8|Q8IVD5	Missense_Mutation|Silent	SNP	ENST00000256413.3	hg19	CCDS11935.1																																																																																			.	C|1.000;T|0.000|.		0.644	CTIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255907.1	NM_014772		GA	46163026	CC	GA	46163025	4	3	243	1	0	0	0	0	0	1	0	0	8185	855	30	4	227	4	KIAA0427	18	46163025	Nonsense_Mutation	DNP	CC	TCGA-ED-A7PX-01A-51D-A34Z-10		46163025	31914223	27	33439										
MCM8	84515	hgsc.bcm.edu	37	chr20	5935894	5935894	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.107142857142857	3	1	1.78681318681319	0	1.93571428571429	0.1	0.617038875103394	0	tgcatgggtttggcaatacaTcaggtaactatttgtcttat	9	6	2	0			TCGA-ED-A7PX-01A-51D-A34Z-10	TCGA-ED-A7PX-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	282d9c17-9d34-43d9-952e-bf14edf7bc65	4fd69f63-3ae5-4678-8647-a7e5eabd7486	g.chr20:5935894T>A	ENST00000378896.3	+	5	860	c.483T>A	c.(481-483)caT>caA	p.H161Q	MCM8_ENST00000378883.1_Missense_Mutation_p.H161Q|MCM8_ENST00000378886.2_Missense_Mutation_p.H161Q|MCM8_ENST00000265187.4_Missense_Mutation_p.H161Q	NM_001281520.1|NM_032485.4|NM_182802.1	NP_001268449.1|NP_115874.3|NP_877954.1	Q9UJA3	MCM8_HUMAN	minichromosome maintenance complex component 8	161					cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)|G1/S transition of mitotic cell cycle (GO:0000082)|male gamete generation (GO:0048232)|mitotic cell cycle (GO:0000278)	MCM8-MCM9 complex (GO:0097362)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	23						TGGCAATACATCAGGTAACTA	0.368																																					p.H161Q		Atlas-SNP	.											.	MCM8	125	.	0			c.T483A						.						173	161	165					20																	5935894		2203	4300	6503	SO:0001583	missense	84515	exon5			AATACATCAGGTA	AJ439063	CCDS13094.1, CCDS13095.1, CCDS63226.1, CCDS63227.1	20p12.3	2007-04-04	2007-04-04	2003-07-09	ENSG00000125885	ENSG00000125885			16147	protein-coding gene	gene with protein product	"REC homolog (Drosophila)"	608187	"chromosome 20 open reading frame 154"	C20orf154		12527764	Standard	NM_032485		Approved	MGC4816, MGC12866, MGC119522, MGC119523, dJ967N21.5, REC	uc002wmi.3	Q9UJA3	OTTHUMG00000031822	ENST00000378896.3:c.483T>A	chr20.hg19:g.5935894T>A	ENSP00000368174:p.His161Gln	77.0	0.0		50.0	39.0	NM_032485	B2RBG7|D3DW08|E7EQU7|Q495R4|Q495R6|Q495R7|Q86US4|Q969I5	Missense_Mutation	SNP	ENST00000378896.3	hg19	CCDS13094.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.789269	0.90367	.	.	ENSG00000125885	ENST00000378896;ENST00000378883;ENST00000399350;ENST00000378886;ENST00000265187	T;T;T;T	0.10668	2.85;2.85;2.85;2.85	5.76	5.76	0.90799	Nucleic acid-binding, OB-fold-like (1);	0.000000	0.85682	D	0.000000	T	0.32675	0.0837	M	0.77616	2.38	0.80722	D	1	D;D;P;P	0.69078	0.991;0.997;0.937;0.949	P;D;P;P	0.66847	0.885;0.947;0.661;0.642	T	0.03025	-1.1081	10	0.27785	T	0.31	-18.5568	16.3786	0.83431	0.0:0.0:0.0:1.0	.	161;161;161;161	Q9UJA3-2;E7EQU7;Q9UJA3-3;Q9UJA3	.;.;.;MCM8_HUMAN	Q	161	ENSP00000368174:H161Q;ENSP00000368161:H161Q;ENSP00000368164:H161Q;ENSP00000265187:H161Q	ENSP00000265187:H161Q	H	+	3	2	MCM8	5883894	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	2.521000	0.45563	2.323000	0.78572	0.528000	0.53228	CAT	.	.		0.368	MCM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077900.1	NM_032485		A	5935894	T	A	5935894	3	1	243	1	0	0	0	0	1	0	0	0	9402	1432	50	4	497	4	MCM8	20	5935894	Missense_Mutation	SNP	T	TCGA-ED-A7PX-01A-51D-A34Z-10		5935894	57089626	28	33440										
HMCN1	83872	hgsc.bcm.edu	37	chr1	185897698	185897698	+	Nonsense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	1	1	0.557692307692308	0	0.608391608391608	1	1	0	agaatctgccagtgtgaactTagatattgcaaaggtcactt	9	7	2	3			TCGA-ED-A7PY-01A-11D-A33Q-10	TCGA-ED-A7PY-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e067207-764e-452a-9e8b-5cf53b052abc	f017e474-7862-4fff-8064-742a7c3c8e52	g.chr1:185897698T>G	ENST00000271588.4	+	10	1680	c.1451T>G	c.(1450-1452)tTa>tGa	p.L484*	HMCN1_ENST00000367492.2_Nonsense_Mutation_p.L484*	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	484	Ig-like C2-type 1.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						AGTGTGAACTTAGATATTGCA	0.373																																					p.L484X		Atlas-SNP	.											.	HMCN1	797	.	0			c.T1451G						.						147	138	141					1																	185897698		2203	4300	6503	SO:0001587	stop_gained	83872	exon10			TGAACTTAGATAT	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.1451T>G	chr1.hg19:g.185897698T>G	ENSP00000271588:p.Leu484*	49.0	0.0		81.0	8.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Nonsense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	T	38	7.259555	0.98171	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	.	.	.	5.35	4.43	0.53597	.	0.057434	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.146	0.72653	0.0:0.0:0.8523:0.1477	.	.	.	.	X	484	.	ENSP00000271588:L484X	L	+	2	0	HMCN1	184164321	1.000000	0.71417	0.972000	0.41901	0.419000	0.31324	4.847000	0.62867	1.221000	0.43506	-0.219000	0.12488	TTA	.	.		0.373	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		G	185897698	T	G	185897698	4	3	244	1	0	0	0	0	0	1	0	0	7229	1764	61	5	1489	5	HMCN1	1	185897698	Nonsense_Mutation	SNP	T	TCGA-ED-A7PY-01A-11D-A33Q-10		185897698	63352923	1	33441										
FMN2	56776	hgsc.bcm.edu	37	chr1	240286619	240286619	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	1	1	0.557692307692308	0	0.608391608391608	1	1	0	gggaaccgtgtaatcagaatGcccagacgaatgcagcttcg	12	10	1	2			TCGA-ED-A7PY-01A-11D-A33Q-10	TCGA-ED-A7PY-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e067207-764e-452a-9e8b-5cf53b052abc	f017e474-7862-4fff-8064-742a7c3c8e52	g.chr1:240286619G>A	ENST00000319653.9	+	2	1986	c.1756G>A	c.(1756-1758)Gcc>Acc	p.A586T		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	586					cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			TAATCAGAATGCCCAGACGAA	0.488																																					p.A586T		Atlas-SNP	.											.	FMN2	451	.	0			c.G1756A						.						131	116	121					1																	240286619		2203	4300	6503	SO:0001583	missense	56776	exon2			CAGAATGCCCAGA	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.1756G>A	chr1.hg19:g.240286619G>A	ENSP00000318884:p.Ala586Thr	43.0	0.0		95.0	82.0	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	hg19	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	G	10.53	1.377302	0.24944	.	.	ENSG00000155816	ENST00000447095;ENST00000319653	T;T	0.80214	-1.35;-1.35	5.69	4.78	0.61160	DEP domain (1);	0.359229	0.25951	N	0.027243	D	0.82912	0.5140	L	0.59436	1.845	0.80722	D	1	D	0.59767	0.986	P	0.50970	0.655	D	0.84909	0.0847	10	0.66056	D	0.02	.	14.7369	0.69422	0.0694:0.0:0.9306:0.0	.	586	Q9NZ56	FMN2_HUMAN	T	19;586	ENSP00000409308:A19T;ENSP00000318884:A586T	ENSP00000318884:A586T	A	+	1	0	FMN2	238353242	0.128000	0.22383	0.099000	0.21106	0.197000	0.23852	1.416000	0.34759	1.549000	0.49425	0.655000	0.94253	GCC	.	.		0.488	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		A	240286619	G	A	240286619	3	1	244	1	0	0	0	0	1	0	0	0	5958	1319	46	3	1762	3	FMN2	1	240286619	Missense_Mutation	SNP	G	TCGA-ED-A7PY-01A-11D-A33Q-10	54388921	240286619	8964002	2	33442										
BIRC6	57448	hgsc.bcm.edu	37	chr2	32641025	32641025	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	1	1	0.557692307692308	0	0.608391608391608	1	1	0	gttaacctcaaagaatggttTtgagagagaaaaaacgtctg	10	5	2	3			TCGA-ED-A7PY-01A-11D-A33Q-10	TCGA-ED-A7PY-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e067207-764e-452a-9e8b-5cf53b052abc	f017e474-7862-4fff-8064-742a7c3c8e52	g.chr2:32641025T>C	ENST00000421745.2	+	10	2800	c.2666T>C	c.(2665-2667)tTt>tCt	p.F889S		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	889					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					AAGAATGGTTTTGAGAGAGAA	0.383																																					p.F889S	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.T2666C						.						70	70	70					2																	32641025		2203	4300	6503	SO:0001583	missense	57448	exon10			ATGGTTTTGAGAG	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.2666T>C	chr2.hg19:g.32641025T>C	ENSP00000393596:p.Phe889Ser	144.0	0.0		184.0	40.0	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	hg19	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	T	0.094	-1.162749	0.01673	.	.	ENSG00000115760	ENST00000421745	T	0.61742	0.08	5.65	-1.31	0.09230	.	0.874234	0.10158	N	0.708707	T	0.24275	0.0588	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.17868	-1.0355	10	0.15499	T	0.54	.	1.9279	0.03321	0.3148:0.0788:0.3589:0.2475	.	889	Q9NR09	BIRC6_HUMAN	S	889	ENSP00000393596:F889S	ENSP00000393596:F889S	F	+	2	0	BIRC6	32494529	0.043000	0.20138	0.714000	0.30535	0.691000	0.40173	-0.028000	0.12350	0.084000	0.17077	-0.313000	0.08912	TTT	.	.		0.383	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		C	32641025	T	C	32641025	3	2	244	1	0	0	0	0	1	0	0	0	1438	1841	64	2	2704	2	BIRC6	2	32641025	Missense_Mutation	SNP	T	TCGA-ED-A7PY-01A-11D-A33Q-10		32641025	210558348	3	33443										
NRXN1	9378	hgsc.bcm.edu	37	chr2	51255367	51255367	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	1	1	0.557692307692308	0	0.608391608391608	1	1	0	cccaggagcagcagcgagagGcacagaagaaaacagccccc	12	14	0	3			TCGA-ED-A7PY-01A-11D-A33Q-10	TCGA-ED-A7PY-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e067207-764e-452a-9e8b-5cf53b052abc	f017e474-7862-4fff-8064-742a7c3c8e52	g.chr2:51255367G>T	ENST00000406316.2	-	2	1521	c.45C>A	c.(43-45)tgC>tgA	p.C15*	NRXN1_ENST00000406859.3_Nonsense_Mutation_p.C15*|NRXN1_ENST00000401669.2_Nonsense_Mutation_p.C15*|NRXN1_ENST00000405581.1_Nonsense_Mutation_p.C15*|NRXN1_ENST00000402717.3_Nonsense_Mutation_p.C15*|NRXN1_ENST00000404971.1_Nonsense_Mutation_p.C15*|NRXN1_ENST00000405472.3_Nonsense_Mutation_p.C15*	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	15					adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			GCAGCGAGAGGCACAGAAGAA	0.716																																					p.C15X		Atlas-SNP	.											.	NRXN1	1118	.	0			c.C45A						.						4	5	5					2																	51255367		1825	3976	5801	SO:0001587	stop_gained	9378	exon2			CGAGAGGCACAGA	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.45C>A	chr2.hg19:g.51255367G>T	ENSP00000384311:p.Cys15*	16.0	0.0		17.0	9.0	NM_004801	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Nonsense_Mutation	SNP	ENST00000406316.2	hg19	CCDS54360.1	.	.	.	.	.	.	.	.	.	.	G	47	13.174682	0.99725	.	.	ENSG00000179915	ENST00000404971;ENST00000406316;ENST00000405472;ENST00000401669;ENST00000536085;ENST00000402717;ENST00000406859;ENST00000405581	.	.	.	5.05	4.17	0.49024	.	227.466000	0.01991	U	0.045489	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05436	T	0.98	.	7.6862	0.28542	0.0927:0.2201:0.6873:0.0	.	.	.	.	X	15	.	ENSP00000385017:C15X	C	-	3	2	NRXN1	51108871	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.285000	0.43487	1.121000	0.41925	0.514000	0.50259	TGC	.	.		0.716	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			T	51255367	G	T	51255367	4	4	244	1	0	0	0	0	0	1	0	0	10674	1195	42	3	4953	3	NRXN1	2	51255367	Nonsense_Mutation	SNP	G	TCGA-ED-A7PY-01A-11D-A33Q-10	18614342	51255367	191944006	4	33444										
HECW2	57520	hgsc.bcm.edu	37	chr2	197184307	197184307	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	1	1	0.557692307692308	0	0.608391608391608	1	1	0	cacccatggacctctcagagCaggtcgctgtccccggcctg	11	17	1	1			TCGA-ED-A7PY-01A-11D-A33Q-10	TCGA-ED-A7PY-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e067207-764e-452a-9e8b-5cf53b052abc	f017e474-7862-4fff-8064-742a7c3c8e52	g.chr2:197184307C>T	ENST00000260983.3	-	9	1489	c.1307G>A	c.(1306-1308)tGc>tAc	p.C436Y	HECW2_ENST00000409111.1_Missense_Mutation_p.C80Y	NM_020760.1	NP_065811.1	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	436					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(24)|lung(45)|ovary(5)|pancreas(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	113						CCTCTCAGAGCAGGTCGCTGT	0.498																																					p.C436Y		Atlas-SNP	.											.	HECW2	239	.	0			c.G1307A						.						55	56	56					2																	197184307		2203	4300	6503	SO:0001583	missense	57520	exon9			TCAGAGCAGGTCG	AL390186	CCDS33354.1	2q32.3	2004-12-13			ENSG00000138411	ENSG00000138411			29853	protein-coding gene	gene with protein product						10718198, 12890487	Standard	NM_020760		Approved	KIAA1301, NEDL2	uc002utm.1	Q9P2P5	OTTHUMG00000154435	ENST00000260983.3:c.1307G>A	chr2.hg19:g.197184307C>T	ENSP00000260983:p.Cys436Tyr	87.0	0.0		85.0	29.0	NM_020760	B8ZZB4|Q17RT5|Q68DF8|Q9NPS9	Missense_Mutation	SNP	ENST00000260983.3	hg19	CCDS33354.1	.	.	.	.	.	.	.	.	.	.	C	1.486	-0.555945	0.03967	.	.	ENSG00000138411	ENST00000409111;ENST00000260983	T;T	0.30981	1.51;1.53	5.64	3.84	0.44239	.	1.089900	0.06720	N	0.774739	T	0.23289	0.0563	N	0.19112	0.55	0.23802	N	0.996804	P	0.34462	0.454	B	0.28784	0.094	T	0.29088	-1.0023	10	0.40728	T	0.16	.	14.3605	0.66768	0.0:0.6543:0.3457:0.0	.	436	Q9P2P5	HECW2_HUMAN	Y	80;436	ENSP00000386775:C80Y;ENSP00000260983:C436Y	ENSP00000260983:C436Y	C	-	2	0	HECW2	196892552	0.032000	0.19561	0.023000	0.16930	0.004000	0.04260	0.190000	0.17057	0.926000	0.37118	-0.181000	0.13052	TGC	.	.		0.498	HECW2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335199.3	NM_020760		T	197184307	C	T	197184307	3	4	244	1	0	0	0	0	1	0	0	0	7052	710	25	3	3495	3	HECW2	2	197184307	Missense_Mutation	SNP	C	TCGA-ED-A7PY-01A-11D-A33Q-10	145928940	197184307	46015066	5	33445										
IL17RD	54756	hgsc.bcm.edu	37	chr3	57130461	57130461	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	1	1	0.557692307692308	0	0.608391608391608	1	1	0	ggagttcatcagtgtagctgCggcaaccaagatctgctttg	12	9	3	1	rs146776354		TCGA-ED-A7PY-01A-11D-A33Q-10	TCGA-ED-A7PY-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e067207-764e-452a-9e8b-5cf53b052abc	f017e474-7862-4fff-8064-742a7c3c8e52	g.chr3:57130461C>T	ENST00000296318.7	-	13	2268	c.2180G>A	c.(2179-2181)cGc>cAc	p.R727H	IL17RD_ENST00000463523.1_Missense_Mutation_p.R583H|IL17RD_ENST00000427856.2_Missense_Mutation_p.R703H|IL17RD_ENST00000320057.5_Missense_Mutation_p.R583H	NM_017563.3	NP_060033.3	Q8NFM7	I17RD_HUMAN	interleukin 17 receptor D	727					signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)	16				KIRC - Kidney renal clear cell carcinoma(284;0.0173)|Kidney(284;0.0204)		AGTGTAGCTGCGGCAACCAAG	0.527																																					p.R727H		Atlas-SNP	.											.	IL17RD	93	.	0			c.G2180A						.	C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	183	169	174		2180	-6.5	0.5	3	dbSNP_134	174	0,8600		0,0,4300	no	missense	IL17RD	NM_017563.3	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	727/740	57130461	1,13005	2203	4300	6503	SO:0001583	missense	54756	exon13			TAGCTGCGGCAAC	AF494208	CCDS2880.2	3p21.1	2008-02-05			ENSG00000144730	ENSG00000144730		"Interleukins and interleukin receptors"	17616	protein-coding gene	gene with protein product		606807				11802164, 12604616	Standard	NM_017563		Approved	SEF, IL17RLM, FLJ35755, IL-17RD	uc003dil.3	Q8NFM7	OTTHUMG00000150171	ENST00000296318.7:c.2180G>A	chr3.hg19:g.57130461C>T	ENSP00000296318:p.Arg727His	118.0	0.0		120.0	29.0	NM_017563	Q2NKP7|Q58EZ7|Q6RVF4|Q6UWI5|Q8N113|Q8NFS0|Q9UFA0	Missense_Mutation	SNP	ENST00000296318.7	hg19	CCDS2880.2	.	.	.	.	.	.	.	.	.	.	C	12.62	1.993148	0.35131	2.27E-4	0.0	ENSG00000144730	ENST00000296318;ENST00000320057;ENST00000427856;ENST00000463523	T;T;T;T	0.08896	3.06;3.05;3.04;3.05	5.78	-6.46	0.01908	.	0.734007	0.13495	N	0.383729	T	0.02342	0.0072	N	0.01576	-0.805	0.21290	N	0.99974	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45877	-0.9231	10	0.17832	T	0.49	-0.6985	12.3348	0.55060	0.0:0.0903:0.0891:0.8207	.	727;703	Q8NFM7;Q8NFM7-3	I17RD_HUMAN;.	H	727;583;703;583	ENSP00000296318:R727H;ENSP00000322250:R583H;ENSP00000399209:R703H;ENSP00000417516:R583H	ENSP00000296318:R727H	R	-	2	0	IL17RD	57105501	0.998000	0.40836	0.505000	0.27651	0.636000	0.38137	0.249000	0.18216	-1.236000	0.02542	-0.142000	0.14014	CGC	.	C|1.000;T|0.000		0.527	IL17RD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316680.1	NM_017563		T	57130461	C	T	57130461	3	4	244	1	0	0	0	0	1	0	0	0	7651	768	27	1	43	1	IL17RD	3	57130461	Missense_Mutation	SNP	C	TCGA-ED-A7PY-01A-11D-A33Q-10		57130461	140891969	6	33446										
COL6A6	131873	hgsc.bcm.edu	37	chr3	130293202	130293202	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	1	1	0.557692307692308	0	0.608391608391608	1	1	0	ggccgcggaagccctgagacAcagaggtatcgacatctact	12	12	1	2			TCGA-ED-A7PY-01A-11D-A33Q-10	TCGA-ED-A7PY-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e067207-764e-452a-9e8b-5cf53b052abc	f017e474-7862-4fff-8064-742a7c3c8e52	g.chr3:130293202A>G	ENST00000358511.6	+	7	3411	c.3380A>G	c.(3379-3381)cAc>cGc	p.H1127R	COL6A6_ENST00000453409.2_Missense_Mutation_p.H1127R	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	1127	Nonhelical region.|VWFA 6. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						GCCCTGAGACACAGAGGTATC	0.562																																					p.H1127R		Atlas-SNP	.											.	COL6A6	497	.	0			c.A3380G						.						78	88	85					3																	130293202		2022	4179	6201	SO:0001583	missense	131873	exon7			TGAGACACAGAGG	AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.3380A>G	chr3.hg19:g.130293202A>G	ENSP00000351310:p.His1127Arg	171.0	0.0		183.0	74.0	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	hg19	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	A	0.021	-1.429275	0.01117	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	T;T	0.76448	-1.02;-1.02	5.28	-4.49	0.03504	von Willebrand factor, type A (3);	0.824174	0.10883	N	0.623530	T	0.44685	0.1305	N	0.00778	-1.195	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.42413	-0.9453	10	0.11182	T	0.66	.	15.5559	0.76192	0.4941:0.0:0.5059:0.0	.	1127	A6NMZ7	CO6A6_HUMAN	R	1127	ENSP00000351310:H1127R;ENSP00000399236:H1127R	ENSP00000351310:H1127R	H	+	2	0	COL6A6	131775892	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.769000	0.04710	-1.147000	0.02851	-1.139000	0.01908	CAC	.	.		0.562	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		G	130293202	A	G	130293202	3	3	244	1	0	0	0	0	1	0	0	0	3705	159	6	2	3406	2	COL6A6	3	130293202	Missense_Mutation	SNP	A	TCGA-ED-A7PY-01A-11D-A33Q-10	73162741	130293202	67729228	7	33447										
IRF2	3660	hgsc.bcm.edu	37	chr4	185339323	185339323	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	1	1	0.557692307692308	0	0.608391608391608	1	1	0	tgaatcacccaagattacctTgatgtgcttaactttgtctt	6	9	2	3			TCGA-ED-A7PY-01A-11D-A33Q-10	TCGA-ED-A7PY-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e067207-764e-452a-9e8b-5cf53b052abc	f017e474-7862-4fff-8064-742a7c3c8e52	g.chr4:185339323T>A	ENST00000393593.3	-	5	616	c.409A>T	c.(409-411)Aag>Tag	p.K137*	IRF2_ENST00000512020.1_5'UTR	NM_002199.3	NP_002190.2	P14316	IRF2_HUMAN	interferon regulatory factor 2	137					blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K137Q(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(2)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	22		all_lung(41;7.86e-14)|Lung NSC(41;1.87e-13)|Colorectal(36;0.00146)|Hepatocellular(41;0.00826)|Renal(120;0.00992)|Prostate(90;0.0115)|all_neural(102;0.0573)|all_hematologic(60;0.0592)		all cancers(43;3.94e-27)|Epithelial(43;5.3e-24)|OV - Ovarian serous cystadenocarcinoma(60;1.06e-10)|Colorectal(24;7.98e-07)|STAD - Stomach adenocarcinoma(60;3.95e-05)|GBM - Glioblastoma multiforme(59;8.3e-05)|COAD - Colon adenocarcinoma(29;0.000106)|BRCA - Breast invasive adenocarcinoma(30;0.000311)|LUSC - Lung squamous cell carcinoma(40;0.0128)|READ - Rectum adenocarcinoma(43;0.0419)		AAGATTACCTTGATGTGCTTA	0.403																																					p.K137X		Atlas-SNP	.											IRF2,NS,carcinoma,0,1	IRF2	53	.	1	Substitution - Missense(1)	liver(1)	c.A409T						.						316	259	279					4																	185339323		2203	4300	6503	SO:0001587	stop_gained	3660	exon5			TTACCTTGATGTG		CCDS3835.1	4q34.1-q35.1	2008-07-29				ENSG00000168310			6117	protein-coding gene	gene with protein product		147576				2475256	Standard	NM_002199		Approved		uc003iwf.4	P14316		ENST00000393593.3:c.409A>T	chr4.hg19:g.185339323T>A	ENSP00000377218:p.Lys137*	183.0	0.0		94.0	65.0	NM_002199	D6RCK5|H0Y8S3|Q6IAS7|Q96B99	Nonsense_Mutation	SNP	ENST00000393593.3	hg19	CCDS3835.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	26.1|26.1	4.703939|4.703939	0.88924|0.88924	.|.	.|.	ENSG00000168310|ENSG00000168310	ENST00000393593;ENST00000507523;ENST00000510814;ENST00000506230;ENST00000505316|ENST00000505067	.|.	.|.	.|.	6.17|6.17	6.17|6.17	0.99709|0.99709	.|.	0.770201|.	0.13187|.	N|.	0.407046|.	.|T	.|0.64594	.|0.2612	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.71148	.|-0.4677	.|3	0.02654|.	T|.	1|.	-2.7951|-2.7951	12.6398|12.6398	0.56702|0.56702	0.0:0.0:0.1377:0.8623|0.0:0.0:0.1377:0.8623	.|.	.|.	.|.	.|.	X|L	137|35	.|.	ENSP00000377218:K137X|.	K|Q	-|-	1|2	0|0	IRF2|IRF2	185576317|185576317	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.977000|0.977000	0.68977|0.68977	2.991000|2.991000	0.49409|0.49409	2.371000|2.371000	0.80710|0.80710	0.533000|0.533000	0.62120|0.62120	AAG|CAA	.	.		0.403	IRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361393.1			A	185339323	T	A	185339323	4	1	244	1	0	0	0	0	0	1	0	0	7837	1821	63	4	660	4	IRF2	4	185339323	Nonsense_Mutation	SNP	T	TCGA-ED-A7PY-01A-11D-A33Q-10		185339323	5814953	8	33448										
SNX14	57231	hgsc.bcm.edu	37	chr6	86223594	86223594	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	1	1	0.557692307692308	0	0.608391608391608	1	1	0	tggagagagcgaggttcagtGttttcacagaatatagcatc	12	6	2	2			TCGA-ED-A7PY-01A-11D-A33Q-10	TCGA-ED-A7PY-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e067207-764e-452a-9e8b-5cf53b052abc	f017e474-7862-4fff-8064-742a7c3c8e52	g.chr6:86223594G>A	ENST00000314673.3	-	26	2753	c.2577C>T	c.(2575-2577)aaC>aaT	p.N859N	SNX14_ENST00000369627.2_Silent_p.N850N|SNX14_ENST00000513865.1_Silent_p.N578N|SNX14_ENST00000505648.1_Silent_p.N807N|SNX14_ENST00000346348.3_Silent_p.N806N|SNX14_ENST00000508980.1_5'UTR	NM_153816.3	NP_722523.1	Q9Y5W7	SNX14_HUMAN	sorting nexin 14	859					protein transport (GO:0015031)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	integral component of membrane (GO:0016021)	phosphatidylinositol binding (GO:0035091)			NS(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(11)|skin(1)	22		all_cancers(76;4.83e-07)|Acute lymphoblastic leukemia(125;3.3e-08)|Prostate(29;2.55e-07)|all_hematologic(105;3.66e-05)|all_epithelial(107;0.000695)|Lung NSC(302;0.197)|all_lung(197;0.24)		BRCA - Breast invasive adenocarcinoma(108;0.0423)		GAGGTTCAGTGTTTTCACAGA	0.294																																					p.N859N		Atlas-SNP	.											.	SNX14	58	.	0			c.C2577T						.						76	78	77					6																	86223594		2203	4296	6499	SO:0001819	synonymous_variant	57231	exon26			TTCAGTGTTTTCA	AF121863	CCDS5003.1, CCDS5004.1, CCDS75490.1	6q15	2008-10-22			ENSG00000135317	ENSG00000135317		"Sorting nexins"	14977	protein-coding gene	gene with protein product						11485546, 11736640	Standard	XM_005248738		Approved	RGS-PX2	uc003pkr.3	Q9Y5W7	OTTHUMG00000015140	ENST00000314673.3:c.2577C>T	chr6.hg19:g.86223594G>A		48.0	0.0		39.0	5.0	NM_153816	B4DI55|Q4VBR3|Q5TCF9|Q5TCG0|Q6NUI7|Q6PI37|Q9BSD1	Silent	SNP	ENST00000314673.3	hg19	CCDS5004.1	.	.	.	.	.	.	.	.	.	.	G	6.149	0.395673	0.11638	.	.	ENSG00000135317	ENST00000508658	.	.	.	5.41	1.71	0.24356	.	.	.	.	.	T	0.42585	0.1209	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.28933	-1.0028	4	.	.	.	-15.0848	8.9203	0.35607	0.4363:0.0:0.5637:0.0	.	.	.	.	I	98	.	.	T	-	2	0	SNX14	86280313	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	1.496000	0.35638	-0.009000	0.14296	0.555000	0.69702	ACA	.	.		0.294	SNX14-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041393.2	NM_153816		A	86223594	G	A	86223594	2	1	244	1	0	0	0	0	0	0	0	1	14900	1368	48	3		3	SNX14	6	86223594	Silent	SNP	G	TCGA-ED-A7PY-01A-11D-A33Q-10		86223594	84891473	9	33449										
CLDN20	49861	hgsc.bcm.edu	37	chr6	155597357	155597357	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333333333333333	1	1	0.557692307692308	0	0.608391608391608	1	1	0	ggagctatctatatcggattCatttctgcaatgctgttgtt	9	7	3	0			TCGA-ED-A7PY-01A-11D-A33Q-10	TCGA-ED-A7PY-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e067207-764e-452a-9e8b-5cf53b052abc	f017e474-7862-4fff-8064-742a7c3c8e52	g.chr6:155597357C>A	ENST00000367165.3	+	2	884	c.504C>A	c.(502-504)ttC>ttA	p.F168L	TFB1M_ENST00000367166.4_Intron	NM_001001346.3	NP_001001346.1	P56880	CLD20_HUMAN	claudin 20	168					calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			endometrium(1)|lung(2)	3				OV - Ovarian serous cystadenocarcinoma(155;7.82e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0114)		ATATCGGATTCATTTCTGCAA	0.443																																					p.F168L		Atlas-SNP	.											.	CLDN20	10	.	0			c.C504A						.						86	79	81					6																	155597357		2203	4300	6503	SO:0001583	missense	49861	exon2			CGGATTCATTTCT	BC020838	CCDS5249.1	6q25	2008-08-01			ENSG00000171217	ENSG00000171217		"Claudins"	2042	protein-coding gene	gene with protein product						16836752	Standard	NM_001001346		Approved		uc003qql.2	P56880	OTTHUMG00000015882	ENST00000367165.3:c.504C>A	chr6.hg19:g.155597357C>A	ENSP00000356133:p.Phe168Leu	147.0	0.0		141.0	51.0	NM_001001346		Missense_Mutation	SNP	ENST00000367165.3	hg19	CCDS5249.1	.	.	.	.	.	.	.	.	.	.	C	14.32	2.500608	0.44455	.	.	ENSG00000171217	ENST00000367165	D	0.88354	-2.37	5.71	2.54	0.30619	.	0.053027	0.85682	D	0.000000	D	0.82788	0.5113	M	0.66439	2.03	0.44175	D	0.996981	P	0.52692	0.955	P	0.45167	0.472	T	0.82602	-0.0376	10	0.66056	D	0.02	.	9.2758	0.37698	0.0:0.6574:0.0:0.3426	.	168	P56880	CLD20_HUMAN	L	168	ENSP00000356133:F168L	ENSP00000356133:F168L	F	+	3	2	CLDN20	155639049	0.998000	0.40836	0.644000	0.29465	0.344000	0.29017	0.542000	0.23222	0.751000	0.32900	-0.251000	0.11542	TTC	.	.		0.443	CLDN20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042818.1	NM_001001346		A	155597357	C	A	155597357	3	1	244	1	0	0	0	0	1	0	0	0	3484	825	29	3	506	3	CLDN20	6	155597357	Missense_Mutation	SNP	C	TCGA-ED-A7PY-01A-11D-A33Q-10	69373763	155597357	15517710	10	33450										
KIF20B	9585	hgsc.bcm.edu	37	chr10	91498042	91498042	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	1	1	0.557692307692308	0	0.608391608391608	1	1	0	gtagttgaaggaaagagagcGctttcagaacttacacaagg	12	6	1	3			TCGA-ED-A7PY-01A-11D-A33Q-10	TCGA-ED-A7PY-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e067207-764e-452a-9e8b-5cf53b052abc	f017e474-7862-4fff-8064-742a7c3c8e52	g.chr10:91498042G>A	ENST00000371728.3	+	20	3509	c.3444G>A	c.(3442-3444)gcG>gcA	p.A1148A	KIF20B_ENST00000416354.1_Silent_p.A1178A|KIF20B_ENST00000478929.1_3'UTR|KIF20B_ENST00000394289.2_Silent_p.A1148A|KIF20B_ENST00000260753.4_Silent_p.A1108A	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	1148					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|neural tube closure (GO:0001843)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization (GO:0070201)|regulation of mitosis (GO:0007088)|regulation of neuron migration (GO:2001222)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|WW domain binding (GO:0050699)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	58						GAAAGAGAGCGCTTTCAGAAC	0.338																																					p.A1108A		Atlas-SNP	.											.	KIF20B	191	.	0			c.G3324A						.						71	80	77					10																	91498042		2203	4297	6500	SO:0001819	synonymous_variant	9585	exon20			GAGAGCGCTTTCA	L16782	CCDS7407.1, CCDS60590.1	10q23.31	2009-08-06	2008-07-31	2008-07-31	ENSG00000138182	ENSG00000138182			7212	protein-coding gene	gene with protein product	"cancer/testis antigen 90"	605498	"M-phase phosphoprotein 1"	MPHOSPH1		8885239, 8290587, 11470801	Standard	NM_016195		Approved	MPP1, KRMP1, CT90	uc001kgr.1	Q96Q89	OTTHUMG00000018725	ENST00000371728.3:c.3444G>A	chr10.hg19:g.91498042G>A		102.0	0.0		95.0	36.0	NM_016195	A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Silent	SNP	ENST00000371728.3	hg19																																																																																				.	.		0.338	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195		A	91498042	G	A	91498042	2	1	244	1	0	0	0	0	0	0	0	1	8296	1074	38	1		1	KIF20B	10	91498042	Silent	SNP	G	TCGA-ED-A7PY-01A-11D-A33Q-10		91498042	44036705	11	33451										
DCLRE1A	9937	hgsc.bcm.edu	37	chr10	115602174	115602174	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	1	1	0.557692307692308	0	0.608391608391608	1	1	0	atgtgggtttagagttacagCctcaaaggcagtgttgatgg	14	5	1	2			TCGA-ED-A7PY-01A-11D-A33Q-10	TCGA-ED-A7PY-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e067207-764e-452a-9e8b-5cf53b052abc	f017e474-7862-4fff-8064-742a7c3c8e52	g.chr10:115602174C>A	ENST00000361384.2	-	6	3510	c.2593G>T	c.(2593-2595)Gct>Tct	p.A865S	DCLRE1A_ENST00000369305.1_Missense_Mutation_p.A865S	NM_014881.3	NP_055696.3	Q6PJP8	DCR1A_HUMAN	DNA cross-link repair 1A	865					mitotic nuclear division (GO:0007067)|nucleotide-excision repair (GO:0006289)	nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|skin(2)|urinary_tract(1)	31				Epithelial(162;0.0157)|all cancers(201;0.0171)		AGAGTTACAGCCTCAAAGGCA	0.418								Other identified genes with known or suspected DNA repair function																													p.A865S		Atlas-SNP	.											.	DCLRE1A	80	.	0			c.G2593T						.						236	214	222					10																	115602174		2203	4300	6503	SO:0001583	missense	9937	exon6			TTACAGCCTCAAA		CCDS7584.1	10q25.1	2010-06-24	2010-06-24		ENSG00000198924	ENSG00000198924			17660	protein-coding gene	gene with protein product	"PSO2 homolog (S. cerevisiae)"	609682	"DNA cross-link repair 1A (PSO2 homolog, S. cerevisiae)"			9806498, 17804464	Standard	NM_014881		Approved	SNM1, PSO2, KIAA0086, hSNM1	uc031pxf.1	Q6PJP8	OTTHUMG00000019077	ENST00000361384.2:c.2593G>T	chr10.hg19:g.115602174C>A	ENSP00000355185:p.Ala865Ser	92.0	0.0		98.0	38.0	NM_014881	D3DRC1|Q14701|Q6P5Y3|Q6PKL4	Missense_Mutation	SNP	ENST00000361384.2	hg19	CCDS7584.1	.	.	.	.	.	.	.	.	.	.	C	11.71	1.719324	0.30503	.	.	ENSG00000198924	ENST00000361384;ENST00000369305	T;T	0.75477	-0.94;-0.94	5.96	-1.81	0.07882	Beta-lactamase-like (1);	0.836577	0.11199	N	0.588989	T	0.51517	0.1679	N	0.19112	0.55	0.19945	N	0.999946	B	0.15719	0.014	B	0.22152	0.038	T	0.34004	-0.9846	10	0.15952	T	0.53	-4.1529	4.6068	0.12382	0.2502:0.2104:0.0:0.5394	.	865	Q6PJP8	DCR1A_HUMAN	S	865	ENSP00000355185:A865S;ENSP00000358311:A865S	ENSP00000355185:A865S	A	-	1	0	DCLRE1A	115592164	0.917000	0.31117	0.998000	0.56505	0.954000	0.61252	0.244000	0.18124	0.118000	0.18165	-0.136000	0.14681	GCT	.	.		0.418	DCLRE1A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050444.1	NM_014881		A	115602174	C	A	115602174	3	1	244	1	0	0	0	0	1	0	0	0	4296	739	26	3	545	3	DCLRE1A	10	115602174	Missense_Mutation	SNP	C	TCGA-ED-A7PY-01A-11D-A33Q-10	24104132	115602174	19932573	12	33452										
OR51S1	119692	hgsc.bcm.edu	37	chr11	4869943	4869943	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	1	1	0.557692307692308	0	0.608391608391608	1	1	0	ggccagcaggaatggcagggGcagatggagacccaggcatc	17	10	0	2			TCGA-ED-A7PY-01A-11D-A33Q-10	TCGA-ED-A7PY-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e067207-764e-452a-9e8b-5cf53b052abc	f017e474-7862-4fff-8064-742a7c3c8e52	g.chr11:4869943G>A	ENST00000322101.2	-	1	571	c.496C>T	c.(496-498)Ccc>Tcc	p.P166S	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001004758.1	NP_001004758.1	Q8NGJ8	O51S1_HUMAN	olfactory receptor, family 51, subfamily S, member 1	166						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(15)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		AATGGCAGGGGCAGATGGAGA	0.557																																					p.P166S		Atlas-SNP	.											.	OR51S1	83	.	0			c.C496T						.						105	106	106					11																	4869943		2201	4298	6499	SO:0001583	missense	119692	exon1			GCAGGGGCAGATG	AB065796	CCDS31362.1	11p15.4	2012-08-09			ENSG00000176922	ENSG00000176922		"GPCR / Class A : Olfactory receptors"	15204	protein-coding gene	gene with protein product							Standard	NM_001004758		Approved		uc010qyo.2	Q8NGJ8	OTTHUMG00000066506	ENST00000322101.2:c.496C>T	chr11.hg19:g.4869943G>A	ENSP00000322754:p.Pro166Ser	82.0	0.0		93.0	46.0	NM_001004758	B9EGZ1|Q6IFI2	Missense_Mutation	SNP	ENST00000322101.2	hg19	CCDS31362.1	.	.	.	.	.	.	.	.	.	.	G	18.78	3.695891	0.68386	.	.	ENSG00000176922	ENST00000322101	T	0.50001	0.76	5.25	5.25	0.73442	GPCR, rhodopsin-like superfamily (1);	0.156809	0.30302	N	0.009931	T	0.61135	0.2323	M	0.82193	2.58	0.37096	D	0.899678	P	0.43024	0.798	P	0.46049	0.502	T	0.72786	-0.4188	10	0.87932	D	0	-22.3842	17.5702	0.87933	0.0:0.0:1.0:0.0	.	166	Q8NGJ8	O51S1_HUMAN	S	166	ENSP00000322754:P166S	ENSP00000322754:P166S	P	-	1	0	OR51S1	4826519	1.000000	0.71417	0.998000	0.56505	0.878000	0.50629	3.964000	0.56780	2.729000	0.93468	0.655000	0.94253	CCC	.	.		0.557	OR51S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142179.1	NM_001004758		A	4869943	G	A	4869943	3	1	244	1	0	0	0	0	1	0	0	0	11114	1203	42	3	478	3	OR51S1	11	4869943	Missense_Mutation	SNP	G	TCGA-ED-A7PY-01A-11D-A33Q-10		4869943	130136573	13	33453										
OR4C15	81309	hgsc.bcm.edu	37	chr11	55322154	55322154	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	1	1	0.557692307692308	0	0.608391608391608	1	1	0	ttcctgtccttcctggatgcGtgcttctcatctgtcatcac	7	14	4	0			TCGA-ED-A7PY-01A-11D-A33Q-10	TCGA-ED-A7PY-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e067207-764e-452a-9e8b-5cf53b052abc	f017e474-7862-4fff-8064-742a7c3c8e52	g.chr11:55322154G>C	ENST00000314644.2	+	1	372	c.372G>C	c.(370-372)gcG>gcC	p.A124A		NM_001001920.1	NP_001001920.1	Q8NGM1	OR4CF_HUMAN	olfactory receptor, family 4, subfamily C, member 15	70						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(31)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(5)	56						TCCTGGATGCGTGCTTCTCAT	0.473										HNSCC(20;0.049)																											p.A124A		Atlas-SNP	.											OR4C15,NS,neuroblastoma,0,1	OR4C15	145	.	0			c.G372C						.						191	156	168					11																	55322154		2201	4296	6497	SO:0001819	synonymous_variant	81309	exon1			GGATGCGTGCTTC	BK004319	CCDS31501.1	11q11	2012-08-09			ENSG00000181939	ENSG00000181939		"GPCR / Class A : Olfactory receptors"	15171	protein-coding gene	gene with protein product							Standard	NM_001001920		Approved		uc010rig.2	Q8NGM1	OTTHUMG00000166714	ENST00000314644.2:c.372G>C	chr11.hg19:g.55322154G>C		41.0	0.0		62.0	5.0	NM_001001920	Q6IFE2	Silent	SNP	ENST00000314644.2	hg19	CCDS31501.1																																																																																			.	.		0.473	OR4C15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391164.1	NM_001001920		C	55322154	G	C	55322154	2	2	244	1	0	0	0	0	0	0	0	1	11057	1132	40	4		4	OR4C15	11	55322154	Silent	SNP	G	TCGA-ED-A7PY-01A-11D-A33Q-10	50452211	55322154	79684362	14	33454										
OR9G1	390174	hgsc.bcm.edu	37	chr11	56468353	56468353	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	1	1	0.557692307692308	0	0.608391608391608	1	1	0	tcatcaccaagaaaacgtttTcctttaacttctgccgtgaa	5	11	3	2			TCGA-ED-A7PY-01A-11D-A33Q-10	TCGA-ED-A7PY-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e067207-764e-452a-9e8b-5cf53b052abc	f017e474-7862-4fff-8064-742a7c3c8e52	g.chr11:56468353T>A	ENST00000312153.1	+	1	490	c.490T>A	c.(490-492)Tcc>Acc	p.S164T		NM_001005213.1	NP_001005213.1	Q8NH87	OR9G1_HUMAN	olfactory receptor, family 9, subfamily G, member 1	164						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|kidney(1)|lung(25)|stomach(2)|upper_aerodigestive_tract(1)	31						GAAAACGTTTTCCTTTAACTT	0.433																																					p.S164T		Atlas-SNP	.											.	.	.	.	0			c.T490A						.						164	158	160					11																	56468353		2201	4296	6497	SO:0001583	missense	504191	exon1			ACGTTTTCCTTTA	AB065500	CCDS31536.1	11q11	2012-08-09			ENSG00000174914	ENSG00000174914		"GPCR / Class A : Olfactory receptors"	15319	protein-coding gene	gene with protein product				OR9G5			Standard	NM_001005213		Approved			Q8NH87	OTTHUMG00000167112	ENST00000312153.1:c.490T>A	chr11.hg19:g.56468353T>A	ENSP00000309012:p.Ser164Thr	156.0	0.0		138.0	37.0	NM_001013358	Q6IEU9|Q8NGQ0	Missense_Mutation	SNP	ENST00000312153.1	hg19	CCDS31536.1	.	.	.	.	.	.	.	.	.	.	T	2.727	-0.265243	0.05754	.	.	ENSG00000174914	ENST00000312153	T	0.00216	8.53	4.52	-6.13	0.02118	GPCR, rhodopsin-like superfamily (1);	1.486790	0.03858	N	0.273426	T	0.00109	0.0003	N	0.16016	0.355	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.25187	-1.0139	10	0.48119	T	0.1	-2.8801	4.6664	0.12668	0.6557:0.1128:0.1207:0.1108	.	164	Q8NH87	OR9G1_HUMAN	T	164	ENSP00000309012:S164T	ENSP00000309012:S164T	S	+	1	0	OR9G1	56224929	0.000000	0.05858	0.001000	0.08648	0.226000	0.24999	-1.685000	0.01930	-0.722000	0.04922	0.467000	0.42956	TCC	.	.		0.433	OR9G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393253.1	NM_001005213		A	56468353	T	A	56468353	3	1	244	1	0	0	0	0	1	0	0	0	11259	1783	62	4	492	4	OR9G1	11	56468353	Missense_Mutation	SNP	T	TCGA-ED-A7PY-01A-11D-A33Q-10	1146199	56468353	78538163	15	33455										
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	103029663	103029663	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	1	1	0.557692307692308	0	0.608391608391608	1	1	0	aacgctcagcattcccaagaTtttattttattggtgatgat	7	7	1	3			TCGA-ED-A7PY-01A-11D-A33Q-10	TCGA-ED-A7PY-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e067207-764e-452a-9e8b-5cf53b052abc	f017e474-7862-4fff-8064-742a7c3c8e52	g.chr11:103029663T>A	ENST00000375735.2	+	28	4429	c.4285T>A	c.(4285-4287)Ttt>Att	p.F1429I	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.F1429I|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	1429	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		ATTCCCAAGATTTTATTTTAT	0.308																																					p.F1429I		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.T4285A						.						42	39	40					11																	103029663		1792	4059	5851	SO:0001583	missense	79659	exon28			CCAAGATTTTATT	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.4285T>A	chr11.hg19:g.103029663T>A	ENSP00000364887:p.Phe1429Ile	214.0	0.0		167.0	60.0	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	hg19	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	T	29.1	4.978285	0.92982	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.80123	-1.34;-1.34	5.36	5.36	0.76844	Dynein heavy chain, domain-2 (1);	0.000000	0.56097	U	0.000040	D	0.93844	0.8031	H	0.98446	4.235	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	D	0.96197	0.9142	10	0.87932	D	0	.	15.658	0.77158	0.0:0.0:0.0:1.0	.	1429;1429	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	I	1429	ENSP00000364887:F1429I;ENSP00000381167:F1429I	ENSP00000364887:F1429I	F	+	1	0	DYNC2H1	102534873	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.996000	0.70639	2.158000	0.67659	0.460000	0.39030	TTT	.	.		0.308	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		A	103029663	T	A	103029663	3	1	244	1	0	0	0	0	1	0	0	0	4848	1493	52	4	4395	4	DYNC2H1	11	103029663	Missense_Mutation	SNP	T	TCGA-ED-A7PY-01A-11D-A33Q-10	46561310	103029663	31976853	16	33456										
SORL1	6653	hgsc.bcm.edu	37	chr11	121476237	121476237	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	1	1	0.557692307692308	0	0.608391608391608	1	1	0	gttcagtgtctcagcaaggcAcacaacaccaatgactttgt	8	11	2	1			TCGA-ED-A7PY-01A-11D-A33Q-10	TCGA-ED-A7PY-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e067207-764e-452a-9e8b-5cf53b052abc	f017e474-7862-4fff-8064-742a7c3c8e52	g.chr11:121476237A>G	ENST00000260197.7	+	35	5034	c.4905A>G	c.(4903-4905)gcA>gcG	p.A1635A	SORL1_ENST00000532694.1_Silent_p.A481A|SORL1_ENST00000525532.1_Silent_p.A579A|SORL1_ENST00000534286.1_Silent_p.A545A|SORL1_ENST00000527934.1_Silent_p.A250A	NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	1635	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell death (GO:0008219)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902960)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of neurofibrillary tangle assembly (GO:1902997)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of tau-protein kinase activity (GO:1902948)|positive regulation of choline O-acetyltransferase activity (GO:1902771)|positive regulation of early endosome to recycling endosome transport (GO:1902955)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|positive regulation of protein localization to early endosome (GO:1902966)|post-Golgi vesicle-mediated transport (GO:0006892)|protein maturation (GO:0051604)|protein retention in Golgi apparatus (GO:0045053)|protein targeting (GO:0006605)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|receptor-mediated endocytosis (GO:0006898)|regulation of smooth muscle cell migration (GO:0014910)|signal transduction (GO:0007165)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|nuclear envelope lumen (GO:0005641)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)|beta-amyloid binding (GO:0001540)|low-density lipoprotein particle binding (GO:0030169)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(2)|lung(34)|ovary(5)|pancreas(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(2)	91		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		TCAGCAAGGCACACAACACCA	0.448																																					p.A1635A		Atlas-SNP	.											.	SORL1	218	.	0			c.A4905G						.						209	194	199					11																	121476237		2203	4299	6502	SO:0001819	synonymous_variant	6653	exon35			CAAGGCACACAAC	Y08110	CCDS8436.1	11q23.2-q24.4	2014-06-05	2011-01-25		ENSG00000137642	ENSG00000137642		"Fibronectin type III domain containing"	11185	protein-coding gene	gene with protein product	"LDLR relative with 11 ligand-binding repeats"	602005	"chromosome 11 open reading frame 32", "sortilin-related receptor, L(DLR class) A repeats-containing"	C11orf32		9157966, 8940146	Standard	NM_003105		Approved	gp250, LR11, LRP9, SorLA, SorLA-1	uc001pxx.3	Q92673	OTTHUMG00000166057	ENST00000260197.7:c.4905A>G	chr11.hg19:g.121476237A>G		136.0	0.0		138.0	70.0	NM_003105	B2RNX7|Q92856	Silent	SNP	ENST00000260197.7	hg19	CCDS8436.1																																																																																			.	.		0.448	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2	NM_003105		G	121476237	A	G	121476237	2	3	244	1	0	0	0	0	0	0	0	1	14949	146	6	2		2	SORL1	11	121476237	Silent	SNP	A	TCGA-ED-A7PY-01A-11D-A33Q-10	18446574	121476237	13530279	17	33457										
MLL2	8085	hgsc.bcm.edu	37	chr12	49443599	49443599	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	1	1	0.557692307692308	0	0.608391608391608	1	1	0	cagtgagtcagtacagagccGtagggagccctcatctcggg	14	11	3	2			TCGA-ED-A7PY-01A-11D-A33Q-10	TCGA-ED-A7PY-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e067207-764e-452a-9e8b-5cf53b052abc	f017e474-7862-4fff-8064-742a7c3c8e52	g.chr12:49443599G>A	ENST00000301067.7	-	11	3771	c.3772C>T	c.(3772-3774)Cgg>Tgg	p.R1258W		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	1258					chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										GTACAGAGCCGTAGGGAGCCC	0.627																																					p.R1258W		Atlas-SNP	.											MLL2_ENST00000301067,caecum,carcinoma,+2,2	MLL2	1173	.	0			c.C3772T						.						90	94	93					12																	49443599		1966	4157	6123	SO:0001583	missense	8085	exon11			AGAGCCGTAGGGA	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.3772C>T	chr12.hg19:g.49443599G>A	ENSP00000301067:p.Arg1258Trp	193.0	0.0		146.0	62.0	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	hg19	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	G	11.59	1.685483	0.29872	.	.	ENSG00000167548	ENST00000301067	D	0.82803	-1.65	5.81	3.92	0.45320	.	0.000000	0.35349	N	0.003276	D	0.82852	0.5127	N	0.14661	0.345	0.31778	N	0.631284	D	0.89917	1.0	D	0.77557	0.99	D	0.84859	0.0818	10	0.87932	D	0	.	12.9492	0.58389	0.0:0.0:0.705:0.295	.	1258	O14686	MLL2_HUMAN	W	1258	ENSP00000301067:R1258W	ENSP00000301067:R1258W	R	-	1	2	MLL2	47729866	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	2.732000	0.47352	0.728000	0.32382	0.655000	0.94253	CGG	.	.		0.627	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			A	49443599	G	A	49443599	3	1	244	1	0	0	0	0	1	0	0	0	9630	1144	40	1	13017	1	MLL2	12	49443599	Missense_Mutation	SNP	G	TCGA-ED-A7PY-01A-11D-A33Q-10		49443599	84408296	18	33458										
MLL2	8085	hgsc.bcm.edu	37	chr12	49448415	49448415	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	1	1	0.557692307692308	0	0.608391608391608	1	1	0	tgggccctgggctccccccaGgggacaccactggacaccgg	14	17	0	0			TCGA-ED-A7PY-01A-11D-A33Q-10	TCGA-ED-A7PY-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e067207-764e-452a-9e8b-5cf53b052abc	f017e474-7862-4fff-8064-742a7c3c8e52	g.chr12:49448415G>T	ENST00000301067.7	-	3	295	c.296C>A	c.(295-297)cCt>cAt	p.P99H		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	99					chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										GCTCCCCCCAGGGGACACCAC	0.617																																					p.P99H		Atlas-SNP	.											.	MLL2	1173	.	0			c.C296A						.						24	27	26					12																	49448415		1930	4123	6053	SO:0001583	missense	8085	exon3			CCCCCAGGGGACA	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.296C>A	chr12.hg19:g.49448415G>T	ENSP00000301067:p.Pro99His	142.0	0.0		118.0	5.0	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	hg19	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	G	12.50	1.955884	0.34471	.	.	ENSG00000167548	ENST00000301067;ENST00000547610	T	0.79033	-1.23	4.9	4.9	0.64082	.	.	.	.	.	T	0.66066	0.2752	N	0.14661	0.345	0.21861	N	0.999502	B	0.06786	0.001	B	0.06405	0.002	T	0.61028	-0.7145	9	0.87932	D	0	.	15.6037	0.76646	0.0:0.0:1.0:0.0	.	99	O14686	MLL2_HUMAN	H	99	ENSP00000301067:P99H	ENSP00000301067:P99H	P	-	2	0	MLL2	47734682	1.000000	0.71417	0.999000	0.59377	0.917000	0.54804	6.498000	0.73679	2.247000	0.74100	0.557000	0.71058	CCT	.	.		0.617	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			T	49448415	G	T	49448415	3	4	244	1	0	0	0	0	1	0	0	0	9630	1000	35	3	16525	3	MLL2	12	49448415	Missense_Mutation	SNP	G	TCGA-ED-A7PY-01A-11D-A33Q-10	4816	49448415	84403480	19	33459										
PCDH17	27253	hgsc.bcm.edu	37	chr13	58299287	58299287	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333333333333333	1	1	0.557692307692308	0	0.608391608391608	1	1	0	gccagccgggattccagtgaGatgggtgctgttcttgagca	15	9	1	2	rs540534018		TCGA-ED-A7PY-01A-11D-A33Q-10	TCGA-ED-A7PY-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e067207-764e-452a-9e8b-5cf53b052abc	f017e474-7862-4fff-8064-742a7c3c8e52	g.chr13:58299287G>A	ENST00000377918.3	+	4	3365	c.3339G>A	c.(3337-3339)gaG>gaA	p.E1113E		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	1113					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(30)|liver(2)|lung(54)|ovary(4)|pancreas(2)|prostate(5)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		ATTCCAGTGAGATGGGTGCTG	0.522																																					p.E1113E	Melanoma(72;952 1291 1619 12849 33676)	Atlas-SNP	.											.	PCDH17	304	.	0			c.G3339A						.						164	168	167					13																	58299287		2203	4300	6503	SO:0001819	synonymous_variant	27253	exon4			CAGTGAGATGGGT	AF029343	CCDS31986.1	13q21.1	2010-01-26			ENSG00000118946	ENSG00000118946		"Cadherins / Protocadherins : Non-clustered"	14267	protein-coding gene	gene with protein product		611760				10835267	Standard	NM_001040429		Approved	PCDH68, PCH68	uc001vhq.1	O14917	OTTHUMG00000016992	ENST00000377918.3:c.3339G>A	chr13.hg19:g.58299287G>A		107.0	0.0		141.0	56.0	NM_001040429	A8K1R5|Q5VVW9|Q5VVX0	Silent	SNP	ENST00000377918.3	hg19	CCDS31986.1																																																																																			.	.		0.522	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429		A	58299287	G	A	58299287	2	1	244	1	0	0	0	0	0	0	0	1	11521	933	33	3		3	PCDH17	13	58299287	Silent	SNP	G	TCGA-ED-A7PY-01A-11D-A33Q-10		58299287	56870591	20	33460										
RTL1	388015	hgsc.bcm.edu	37	chr14	101350343	101350343	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	1	1	0.557692307692308	0	0.608391608391608	1	1	0	gggaagtctccgatcaggggGctgttttcctgcagtagagc	15	9	2	1			TCGA-ED-A7PY-01A-11D-A33Q-10	TCGA-ED-A7PY-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e067207-764e-452a-9e8b-5cf53b052abc	f017e474-7862-4fff-8064-742a7c3c8e52	g.chr14:101350343G>T	ENST00000534062.1	-	1	841	c.783C>A	c.(781-783)agC>agA	p.S261R	MIR432_ENST00000606207.1_RNA|MIR127_ENST00000384876.1_RNA|MIR431_ENST00000385266.1_RNA|MIR433_ENST00000384837.1_RNA|MIR136_ENST00000385207.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	261					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)				breast(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(5)|pancreas(1)|prostate(2)|skin(2)	21						CGATCAGGGGGCTGTTTTCCT	0.532																																					p.S261R		Atlas-SNP	.											.	RTL1	120	.	0			c.C783A						.						92	80	84					14																	101350343		692	1591	2283	SO:0001583	missense	388015	exon1			CAGGGGGCTGTTT		CCDS53910.1	14q32.2	2012-04-18			ENSG00000254656	ENSG00000254656			14665	protein-coding gene	gene with protein product		611896				16155747, 15854907, 12796779	Standard	NM_001134888		Approved	PEG11, MART1, Mar1	uc010txj.1	A6NKG5	OTTHUMG00000167573	ENST00000534062.1:c.783C>A	chr14.hg19:g.101350343G>T	ENSP00000435342:p.Ser261Arg	67.0	0.0		52.0	27.0	NM_001134888	E9PKS8	Missense_Mutation	SNP	ENST00000534062.1	hg19	CCDS53910.1	.	.	.	.	.	.	.	.	.	.	G	11.96	1.794023	0.31777	.	.	ENSG00000254656	ENST00000534062	T	0.24723	1.84	3.42	0.538	0.17150	.	.	.	.	.	T	0.44329	0.1288	M	0.70595	2.14	0.22213	N	0.999287	D	0.76494	0.999	D	0.75020	0.985	T	0.19844	-1.0293	9	0.72032	D	0.01	.	7.3034	0.26434	0.3245:0.0:0.6755:0.0	.	261	E9PKS8	.	R	261	ENSP00000435342:S261R	ENSP00000435342:S261R	S	-	3	2	RTL1	100420096	0.998000	0.40836	0.356000	0.25785	0.249000	0.25844	1.159000	0.31749	0.108000	0.17862	-0.258000	0.10820	AGC	.	.		0.532	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888		T	101350343	G	T	101350343	3	4	244	1	0	0	0	0	1	0	0	0	13739	1194	42	3	3297	3	RTL1	14	101350343	Missense_Mutation	SNP	G	TCGA-ED-A7PY-01A-11D-A33Q-10		101350343	5999197	21	33461										
HAUS2	55142	hgsc.bcm.edu	37	chr15	42858992	42858992	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	1	1	0.557692307692308	0	0.608391608391608	1	1	0	ttttacttctaaagttcatgTccaaactattaatgccaagt	4	8	2	0			TCGA-ED-A7PY-01A-11D-A33Q-10	TCGA-ED-A7PY-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e067207-764e-452a-9e8b-5cf53b052abc	f017e474-7862-4fff-8064-742a7c3c8e52	g.chr15:42858992T>C	ENST00000260372.3	+	6	749	c.686T>C	c.(685-687)gTc>gCc	p.V229A	RP11-265N6.2_ENST00000567089.1_RNA|HAUS2_ENST00000568876.1_Missense_Mutation_p.V198A|RP11-265N6.2_ENST00000561902.1_RNA	NM_018097.2	NP_060567.1	Q9NVX0	HAUS2_HUMAN	HAUS augmin-like complex, subunit 2	229					centrosome organization (GO:0051297)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|HAUS complex (GO:0070652)|microtubule (GO:0005874)|nucleus (GO:0005634)				endometrium(1)|large_intestine(1)|lung(1)	3						AAAGTTCATGTCCAAACTATT	0.294																																					p.V229A		Atlas-SNP	.											.	HAUS2	12	.	0			c.T686C						.						52	51	51					15																	42858992		2203	4298	6501	SO:0001583	missense	55142	exon6			TTCATGTCCAAAC	AK001322	CCDS10090.1, CCDS45247.1	15q15.1	2014-02-20	2009-04-20	2009-04-20	ENSG00000137814	ENSG00000137814		"HAUS augmin-like complex subunits"	25530	protein-coding gene	gene with protein product		613429	"chromosome 15 open reading frame 25", "centrosomal protein 27kDa"	C15orf25, CEP27		14702039, 14654843, 19427217	Standard	NM_018097		Approved	FLJ10460, HsT17025	uc001zqe.3	Q9NVX0	OTTHUMG00000130678	ENST00000260372.3:c.686T>C	chr15.hg19:g.42858992T>C	ENSP00000260372:p.Val229Ala	110.0	0.0		97.0	4.0	NM_018097	C9JH36|Q9H9B3	Missense_Mutation	SNP	ENST00000260372.3	hg19	CCDS10090.1	.	.	.	.	.	.	.	.	.	.	T	7.950	0.744615	0.15710	.	.	ENSG00000137814	ENST00000260372;ENST00000391623	T	0.48836	0.8	6.17	-2.29	0.06805	.	1.592470	0.03642	N	0.239712	T	0.41236	0.1150	L	0.54323	1.7	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.36311	-0.9753	10	0.48119	T	0.1	-6.1854	5.5836	0.17262	0.0:0.3481:0.2977:0.3541	.	198;229	Q9NVX0-3;Q9NVX0	.;HAUS2_HUMAN	A	229;198	ENSP00000260372:V229A	ENSP00000260372:V229A	V	+	2	0	HAUS2	40646284	0.000000	0.05858	0.000000	0.03702	0.233000	0.25261	0.086000	0.14935	-0.058000	0.13177	-0.256000	0.11100	GTC	.	.		0.294	HAUS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253173.1	NM_018097		C	42858992	T	C	42858992	3	2	244	1	0	0	0	0	1	0	0	0	6975	1667	58	2	708	2	HAUS2	15	42858992	Missense_Mutation	SNP	T	TCGA-ED-A7PY-01A-11D-A33Q-10		42858992	59672400	22	33462										
CDAN1	146059	hgsc.bcm.edu	37	chr15	43027807	43027807	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	1	1	0.557692307692308	0	0.608391608391608	1	1	0	atctgtgaggcttcctgtccGgctggggaggggcgacccca	16	12	1	1	rs371090455		TCGA-ED-A7PY-01A-11D-A33Q-10	TCGA-ED-A7PY-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e067207-764e-452a-9e8b-5cf53b052abc	f017e474-7862-4fff-8064-742a7c3c8e52	g.chr15:43027807G>A	ENST00000356231.3	-	4	867	c.844C>T	c.(844-846)Cgg>Tgg	p.R282W		NM_138477.2	NP_612486.2	Q8IWY9	CDAN1_HUMAN	codanin 1	282					chromatin assembly (GO:0031497)|chromatin organization (GO:0006325)|negative regulation of DNA replication (GO:0008156)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	24		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;2.49e-07)		CTTCCTGTCCGGCTGGGGAGG	0.577																																					p.R282W		Atlas-SNP	.											.	CDAN1	70	.	0			c.C844T						.	G	TRP/ARG	1,4401		0,1,2200	41	44	43		844	1.6	0.1	15		43	0,8576		0,0,4288	no	missense	CDAN1	NM_138477.2	101	0,1,6488	AA,AG,GG		0.0,0.0227,0.0077	benign	282/1228	43027807	1,12977	2201	4288	6489	SO:0001583	missense	146059	exon4			CTGTCCGGCTGGG	AF525398	CCDS32209.1	15q15.2	2012-04-25	2012-04-25			ENSG00000140326			1713	protein-coding gene	gene with protein product		607465	"congenital dyserythropoietic anemia, type I"			8634422, 12434312	Standard	XM_005254177		Approved	CDA-I, CDAI	uc001zql.3	Q8IWY9		ENST00000356231.3:c.844C>T	chr15.hg19:g.43027807G>A	ENSP00000348564:p.Arg282Trp	122.0	0.0		95.0	23.0	NM_138477	Q6NYD0|Q7Z7L5|Q969N3	Missense_Mutation	SNP	ENST00000356231.3	hg19	CCDS32209.1	.	.	.	.	.	.	.	.	.	.	G	8.051	0.765986	0.15983	2.27E-4	0.0	ENSG00000140326	ENST00000356231;ENST00000267892	D	0.88124	-2.34	5.68	1.64	0.23874	.	0.482595	0.23365	N	0.048974	T	0.73845	0.3639	L	0.33485	1.01	0.21256	N	0.999742	B	0.34255	0.445	B	0.25140	0.058	T	0.64635	-0.6361	10	0.52906	T	0.07	-13.3476	3.943	0.09336	0.2631:0.0:0.5654:0.1716	.	282	Q8IWY9	CDAN1_HUMAN	W	282;280	ENSP00000348564:R282W	ENSP00000267892:R280W	R	-	1	2	CDAN1	40815099	0.025000	0.19082	0.149000	0.22428	0.007000	0.05969	0.810000	0.27183	0.306000	0.22856	-0.254000	0.11334	CGG	.	.		0.577	CDAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431103.1	XM_085300		A	43027807	G	A	43027807	3	1	244	1	0	0	0	0	1	0	0	0	3056	1115	39	1	2939	1	CDAN1	15	43027807	Missense_Mutation	SNP	G	TCGA-ED-A7PY-01A-11D-A33Q-10	168815	43027807	59503585	23	33463										
AP2B1	163	hgsc.bcm.edu	37	chr17	33932839	33932839	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	1	1	0.557692307692308	0	0.608391608391608	1	1	0	agccagacatggccatcatgGctgtaaacagctttgtgaag	11	9	1	2			TCGA-ED-A7PY-01A-11D-A33Q-10	TCGA-ED-A7PY-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e067207-764e-452a-9e8b-5cf53b052abc	f017e474-7862-4fff-8064-742a7c3c8e52	g.chr17:33932839G>T	ENST00000262325.7	+	4	812	c.259G>T	c.(259-261)Gct>Tct	p.A87S	AP2B1_ENST00000312678.8_Missense_Mutation_p.A87S|AP2B1_ENST00000592545.1_Missense_Mutation_p.A87S|AP2B1_ENST00000538556.1_Missense_Mutation_p.A30S|AP2B1_ENST00000589344.1_Missense_Mutation_p.A87S|AP2B1_ENST00000537622.2_Missense_Mutation_p.A87S	NM_001282.2	NP_001273.1	P63010	AP2B1_HUMAN	adaptor-related protein complex 2, beta 1 subunit	87					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	clathrin binding (GO:0030276)|protein transporter activity (GO:0008565)			NS(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)		GGCCATCATGGCTGTAAACAG	0.428																																					p.A87S		Atlas-SNP	.											.	AP2B1	70	.	0			c.G259T						.						101	94	96					17																	33932839		2203	4300	6503	SO:0001583	missense	163	exon4			ATCATGGCTGTAA	M34175	CCDS32621.1, CCDS32622.1	17q11.2-q12	2010-06-18			ENSG00000006125	ENSG00000006125			563	protein-coding gene	gene with protein product		601025		ADTB2, CLAPB1		8262066, 8595912	Standard	XM_005257937		Approved		uc002hjq.3	P63010		ENST00000262325.7:c.259G>T	chr17.hg19:g.33932839G>T	ENSP00000262325:p.Ala87Ser	79.0	0.0		90.0	34.0	NM_001282	A6NJP3|P21851|Q7Z451|Q96J19	Missense_Mutation	SNP	ENST00000262325.7	hg19	CCDS32622.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.863089	0.91511	.	.	ENSG00000006125	ENST00000262325;ENST00000312678;ENST00000538556;ENST00000537622	T;T;T;T	0.26067	1.76;1.76;1.76;1.76	5.54	5.54	0.83059	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.49915	0.1585	L	0.58428	1.81	0.80722	D	1	P;P;B	0.48911	0.859;0.917;0.252	P;D;P	0.69824	0.888;0.966;0.523	T	0.43925	-0.9361	10	0.66056	D	0.02	-23.47	18.487	0.90833	0.0:0.0:1.0:0.0	.	87;87;87	B4DWG4;P63010;P63010-2	.;AP2B1_HUMAN;.	S	87;87;30;87	ENSP00000262325:A87S;ENSP00000314414:A87S;ENSP00000440563:A30S;ENSP00000437413:A87S	ENSP00000262325:A87S	A	+	1	0	AP2B1	30956952	1.000000	0.71417	1.000000	0.80357	0.657000	0.38888	8.011000	0.88624	2.603000	0.88011	0.467000	0.42956	GCT	.	.		0.428	AP2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448969.1			T	33932839	G	T	33932839	3	4	244	1	0	0	0	0	1	0	0	0	741	1203	42	3	269	3	AP2B1	17	33932839	Missense_Mutation	SNP	G	TCGA-ED-A7PY-01A-11D-A33Q-10		33932839	47262371	24	33464										
ONECUT2	9480	hgsc.bcm.edu	37	chr18	55103728	55103728	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	1	1	0.557692307692308	0	0.608391608391608	1	1	0	cacgacaaaatgctcagcccCaacttcgacgcgcaccacac	6	18	1	0			TCGA-ED-A7PY-01A-11D-A33Q-10	TCGA-ED-A7PY-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e067207-764e-452a-9e8b-5cf53b052abc	f017e474-7862-4fff-8064-742a7c3c8e52	g.chr18:55103728C>T	ENST00000491143.2	+	1	812	c.780C>T	c.(778-780)ccC>ccT	p.P260P	AC090340.1_ENST00000581316.1_RNA	NM_004852.2	NP_004843.2	O95948	ONEC2_HUMAN	one cut homeobox 2	260					cell fate commitment (GO:0045165)|cilium assembly (GO:0042384)|endocrine pancreas development (GO:0031018)|epithelial cell development (GO:0002064)|liver development (GO:0001889)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ morphogenesis (GO:0009887)|peripheral nervous system neuron development (GO:0048935)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell-matrix adhesion (GO:0001952)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|lung(4)|ovary(2)|skin(1)	15		Colorectal(73;0.234)		READ - Rectum adenocarcinoma(59;0.227)|Colorectal(16;0.245)		TGCTCAGCCCCAACTTCGACG	0.687																																					p.P260P		Atlas-SNP	.											.	ONECUT2	42	.	0			c.C780T						.						52	62	58					18																	55103728		2188	4278	6466	SO:0001819	synonymous_variant	9480	exon1			CAGCCCCAACTTC	Y18198	CCDS42440.1	18q21.31	2012-03-09	2007-07-16		ENSG00000119547	ENSG00000119547		"Homeoboxes / CUT class"	8139	protein-coding gene	gene with protein product		604894	"one cut domain, family member 2"			9915796	Standard	NM_004852		Approved	OC-2	uc002lgo.3	O95948	OTTHUMG00000159776	ENST00000491143.2:c.780C>T	chr18.hg19:g.55103728C>T		61.0	0.0		68.0	29.0	NM_004852		Silent	SNP	ENST00000491143.2	hg19	CCDS42440.1																																																																																			.	.		0.687	ONECUT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357264.3			T	55103728	C	T	55103728	2	4	244	1	0	0	0	0	0	0	0	1	10878	581	21	3		3	ONECUT2	18	55103728	Silent	SNP	C	TCGA-ED-A7PY-01A-11D-A33Q-10		55103728	22973520	25	33465										
ZNF69	7620	hgsc.bcm.edu	37	chr19	12015547	12015547	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	1	1	0.557692307692308	0	0.608391608391608	1	1	0	ccaggttccagatgacaggcTgaacttccaggagaagaaag	12	9	0	5			TCGA-ED-A7PY-01A-11D-A33Q-10	TCGA-ED-A7PY-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e067207-764e-452a-9e8b-5cf53b052abc	f017e474-7862-4fff-8064-742a7c3c8e52	g.chr19:12015547T>C	ENST00000429654.2	+	4	475	c.335T>C	c.(334-336)cTg>cCg	p.L112P	ZNF69_ENST00000340180.5_Missense_Mutation_p.L98P			Q9UC07	ZNF69_HUMAN	zinc finger protein 69	112					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|skin(2)	4				Lung(535;0.011)		GATGACAGGCTGAACTTCCAG	0.383																																					p.L98P		Atlas-SNP	.											.	ZNF69	27	.	0			c.T293C						.						119	124	123					19																	12015547		2203	4300	6503	SO:0001583	missense	7620	exon4			ACAGGCTGAACTT	X60076	CCDS32914.1	19p13.2	2013-01-08	2006-05-12		ENSG00000198429	ENSG00000198429		"Zinc fingers, C2H2-type", "-"	13138	protein-coding gene	gene with protein product		194543	"zinc finger protein 69 (Cos5)"			1639391	Standard	NM_021915		Approved	Cos5	uc002mst.4	Q9UC07	OTTHUMG00000156526	ENST00000429654.2:c.335T>C	chr19.hg19:g.12015547T>C	ENSP00000402985:p.Leu112Pro	149.0	0.0		121.0	11.0	NM_021915	Q86VA7	Missense_Mutation	SNP	ENST00000429654.2	hg19		.	.	.	.	.	.	.	.	.	.	t	9.329	1.060060	0.19987	.	.	ENSG00000198429	ENST00000429654;ENST00000445911;ENST00000340180	T;T;T	0.09163	3.01;4.09;4.16	0.118	0.118	0.14667	.	.	.	.	.	T	0.20577	0.0495	L	0.49571	1.57	0.09310	N	1	D	0.89917	1.0	D	0.79784	0.993	T	0.10847	-1.0612	9	0.54805	T	0.06	.	4.4137	0.11445	0.0:1.0E-4:0.0:0.9999	.	98	C9JR48	.	P	112;98;98	ENSP00000402985:L112P;ENSP00000388784:L98P;ENSP00000345333:L98P	ENSP00000345333:L98P	L	+	2	0	ZNF69	11876547	0.004000	0.15560	0.006000	0.13384	0.069000	0.16628	-0.834000	0.04391	0.165000	0.19558	0.163000	0.16589	CTG	.	.		0.383	ZNF69-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000344082.1	NM_021915		C	12015547	T	C	12015547	3	2	244	1	0	0	0	0	1	0	0	0	18110	1580	55	2	307	2	ZNF69	19	12015547	Missense_Mutation	SNP	T	TCGA-ED-A7PY-01A-11D-A33Q-10		12015547	47113436	26	33466										
ZNF676	163223	hgsc.bcm.edu	37	chr19	22362861	22362861	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333333333333333	1	1	0.557692307692308	0	0.608391608391608	1	1	0	gtttctctccagtatgaattCtcttgtgtctagtaaggctt	8	8	3	1	rs201300029	byFrequency	TCGA-ED-A7PY-01A-11D-A33Q-10	TCGA-ED-A7PY-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e067207-764e-452a-9e8b-5cf53b052abc	f017e474-7862-4fff-8064-742a7c3c8e52	g.chr19:22362861C>A	ENST00000397121.2	-	3	1975	c.1658G>T	c.(1657-1659)aGa>aTa	p.R553I		NM_001001411.2	NP_001001411.2	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	553					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R553I(1)		NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(49)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	67		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				AGTATGAATTCTCTTGTGTCT	0.378													C|||	2	0.000399361	8e-04	0	5008	,	,		21155	0.001		0	False		,,,				2504	0				p.R553I		Atlas-SNP	.											ZNF676,NS,carcinoma,0,3	ZNF676	146	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1658T						.	C	ILE/ARG	11,4231		0,11,2110	64	67	66		1658	-1.6	0	19		66	0,8508		0,0,4254	yes	missense	ZNF676	NM_001001411.2	97	0,11,6364	AA,AC,CC		0.0,0.2593,0.0863	benign	553/589	22362861	11,12739	2121	4254	6375	SO:0001583	missense	163223	exon3			TGAATTCTCTTGT	AK097798	CCDS42539.1	19p12	2013-01-08				ENSG00000196109		"Zinc fingers, C2H2-type"	20429	protein-coding gene	gene with protein product							Standard	NM_001001411		Approved		uc002nqs.1	Q8N7Q3		ENST00000397121.2:c.1658G>T	chr19.hg19:g.22362861C>A	ENSP00000380310:p.Arg553Ile	73.0	0.0		50.0	7.0	NM_001001411	A8MVX5	Missense_Mutation	SNP	ENST00000397121.2	hg19	CCDS42539.1	.	.	.	.	.	.	.	.	.	.	.	1.558	-0.537453	0.04082	0.002593	0.0	ENSG00000196109	ENST00000397121	T	0.24908	1.83	0.819	-1.64	0.08318	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13543	0.0328	L	0.31476	0.935	0.36586	D	0.873843	B	0.33494	0.414	B	0.23018	0.043	T	0.30736	-0.9968	9	0.35671	T	0.21	.	7.768	0.28991	0.3982:0.6018:0.0:0.0	.	553	Q8N7Q3	ZN676_HUMAN	I	553	ENSP00000380310:R553I	ENSP00000380310:R553I	R	-	2	0	ZNF676	22154701	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.989000	0.03736	-2.950000	0.00293	-2.994000	0.00078	AGA	.	.		0.378	ZNF676-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464392.1	NM_001001411		A	22362861	C	A	22362861	3	1	244	1	0	0	0	0	1	0	0	0	18098	913	32	3	112	3	ZNF676	19	22362861	Missense_Mutation	SNP	C	TCGA-ED-A7PY-01A-11D-A33Q-10	10347314	22362861	36766122	27	33467										
SCRT2	85508	hgsc.bcm.edu	37	chr20	644968	644968	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	1	1	0.557692307692308	0	0.608391608391608	1	1	0	tcggaagtagcgcgccgacaGgctcgactgcgggctttcgg	16	12	0	0			TCGA-ED-A7PY-01A-11D-A33Q-10	TCGA-ED-A7PY-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e067207-764e-452a-9e8b-5cf53b052abc	f017e474-7862-4fff-8064-742a7c3c8e52	g.chr20:644968G>A	ENST00000246104.6	-	2	848	c.271C>T	c.(271-273)Ctg>Ttg	p.L91L	RP5-850E9.3_ENST00000488788.2_Intron	NM_033129.3	NP_149120.1	Q9NQ03	SCRT2_HUMAN	scratch family zinc finger 2	91					negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of neuron migration (GO:2001222)	nuclear chromatin (GO:0000790)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			kidney(1)|liver(1)|ovary(1)	3						CGCGCCGACAGGCTCGACTGC	0.746																																					p.L91L		Atlas-SNP	.											.	SCRT2	16	.	0			c.C271T						.						7	7	7					20																	644968		1630	3722	5352	SO:0001819	synonymous_variant	85508	exon2			CCGACAGGCTCGA		CCDS13006.1	20p13	2013-10-09	2013-10-09		ENSG00000215397	ENSG00000215397		"Zinc fingers, C2H2-type"	15952	protein-coding gene	gene with protein product			"scratch (drosophila homolog) 2, zinc finger protein", "scratch homolog 2, zinc finger protein (Drosophila)"			11274425	Standard	NM_033129		Approved	ZNF898B	uc002wec.3	Q9NQ03	OTTHUMG00000130829	ENST00000246104.6:c.271C>T	chr20.hg19:g.644968G>A		39.0	0.0		30.0	16.0	NM_033129		Silent	SNP	ENST00000246104.6	hg19	CCDS13006.1																																																																																			.	.		0.746	SCRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253383.2	NM_033129		A	644968	G	A	644968	2	1	244	1	0	0	0	0	0	0	0	1	13957	991	35	3		3	SCRT2	20	644968	Silent	SNP	G	TCGA-ED-A7PY-01A-11D-A33Q-10		644968	62380552	28	33468										
MED14	9282	hgsc.bcm.edu	37	chrX	40511063	40511063	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0333333333333333	1	1	0.557692307692308	0	0.608391608391608	1	1	0	taaaaacaatagtgtctatgGacgcccaccagggggcagtg	12	9	1	0			TCGA-ED-A7PY-01A-11D-A33Q-10	TCGA-ED-A7PY-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e067207-764e-452a-9e8b-5cf53b052abc	f017e474-7862-4fff-8064-742a7c3c8e52	g.chrX:40511063G>T	ENST00000324817.1	-	31	4478	c.4360C>A	c.(4360-4362)Cca>Aca	p.P1454T		NM_004229.3	NP_004220.2	O60244	MED14_HUMAN	mediator complex subunit 14	1454					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(2)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						AGTGTCTATGGACGCCCACCA	0.383																																					p.P1454T		Atlas-SNP	.											.	MED14	108	.	0			c.C4360A						.						45	39	41					X																	40511063		2203	4299	6502	SO:0001583	missense	9282	exon31			TCTATGGACGCCC	AB006651	CCDS14254.1	Xp11.4	2008-05-14	2007-07-30	2007-07-30	ENSG00000180182	ENSG00000180182			2370	protein-coding gene	gene with protein product		300182	"cofactor required for Sp1 transcriptional activation, subunit 2, 150kDa"	CXorf4, CRSP2		9989412, 9598311	Standard	NM_004229		Approved	EXLM1, CRSP150, TRAP170, RGR1, CSRP	uc004dex.4	O60244	OTTHUMG00000024107	ENST00000324817.1:c.4360C>A	chrX.hg19:g.40511063G>T	ENSP00000323720:p.Pro1454Thr	505.0	1.0		409.0	131.0	NM_004229	Q4KMR7|Q9UNB3	Missense_Mutation	SNP	ENST00000324817.1	hg19	CCDS14254.1	.	.	.	.	.	.	.	.	.	.	G	16.24	3.067812	0.55539	.	.	ENSG00000180182	ENST00000324817	.	.	.	5.88	5.88	0.94601	.	0.157371	0.56097	D	0.000024	T	0.47340	0.1440	N	0.22421	0.69	0.51233	D	0.999919	B	0.33694	0.421	B	0.29785	0.107	T	0.51180	-0.8738	9	0.87932	D	0	.	19.1532	0.93499	0.0:0.0:1.0:0.0	.	1454	O60244	MED14_HUMAN	T	1454	.	ENSP00000323720:P1454T	P	-	1	0	MED14	40396007	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	6.186000	0.72026	2.474000	0.83562	0.600000	0.82982	CCA	.	.		0.383	MED14-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060692.1	NM_004229		T	40511063	G	T	40511063	3	4	244	1	0	0	0	0	1	0	0	0	9441	1174	41	3	8	3	MED14	23	40511063	Missense_Mutation	SNP	G	TCGA-ED-A7PY-01A-11D-A33Q-10		40511063	114759497	29	33469										
PPP1R3F	89801	hgsc.bcm.edu	37	chrX	49138482	49138483	+	Frame_Shift_Ins	INS	-	-	TAGCCCCCACCTGA													0.0333333333333333	1	1	0.557692307692308	0	0.608391608391608	1	1	0	ggagtcagtgggtccactggINStagcccccacccctctccgt							TCGA-ED-A7PY-01A-11D-A33Q-10	TCGA-ED-A7PY-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e067207-764e-452a-9e8b-5cf53b052abc	f017e474-7862-4fff-8064-742a7c3c8e52	g.chrX:49138482_49138483insTAGCCCCCACCTGA	ENST00000055335.6	+	3	1115_1116	c.1099_1100insTAGCCCCCACCTGA	c.(1099-1101)gtafs	p.-367fs	PPP1R3F_ENST00000495799.1_Frame_Shift_Ins_p.-21fs|PPP1R3F_ENST00000466508.1_Frame_Shift_Ins_p.-21fs|PPP1R3F_ENST00000438316.1_Frame_Shift_Ins_p.-38fs|PPP1R3F_ENST00000376188.1_Frame_Shift_Ins_p.-21fs	NM_033215.4	NP_149992.3	Q6ZSY5	PPR3F_HUMAN	protein phosphatase 1, regulatory subunit 3F						regulation of glycogen (starch) synthase activity (GO:2000465)|regulation of glycogen biosynthetic process (GO:0005979)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycogen binding (GO:2001069)|protein phosphatase binding (GO:0019903)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(4)	27	Ovarian(276;0.236)					GGGTCCACTGGTAGCCCCCACC	0.545																																					p.V367_A368delinsVAPTX		Atlas-Indel,Pindel	.											.	PPP1R3F	56	.	0			c.1099_1100insTAGCCCCCACCTGA						.																																			SO:0001589	frameshift_variant	89801	exon3			.		CCDS35254.1, CCDS55415.1	Xp11.23	2012-04-17	2011-10-04		ENSG00000049769	ENSG00000049769		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14944	protein-coding gene	gene with protein product			"protein phosphatase 1, regulatory (inhibitor) subunit 3F"			11948623	Standard	NM_033215		Approved	Hb2E	uc004dnh.2	Q6ZSY5	OTTHUMG00000024139	Exception_encountered	chrX.hg19:g.49138482_49138483insTAGCCCCCACCTGA	ENSP00000055335:p.Val367fs	179.0	0.0		124.0	10.0	NM_033215	A2VDJ8|B3KPW2|E9PCM3	Frame_Shift_Ins	INS	ENST00000055335.6	hg19	CCDS35254.1																																																																																			.	.		0.545	PPP1R3F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060819.2	NM_033215		TAGCCCCCACCTGA	49138483	-	TAGCCCCCACCTGA	49138482	7	5	244	1	0	1	1	0	0	0	0	0	12387	1261	44	0	1109	0	PPP1R3F	23	49138482	Frame_Shift_Ins	INS	-	TCGA-ED-A7PY-01A-11D-A33Q-10	8627419	49138482	106132078	30	33470										
MIB2	142678	hgsc.bcm.edu	37	chr1	1561031	1561031	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tccaccccggggcgctcaccAaggtgccgggggggctgggc	18	15	1	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr1:1561031A>T	ENST00000357210.4	+	8	1360	c.1144A>T	c.(1144-1146)Aag>Tag	p.K382*	MIB2_ENST00000520777.1_Nonsense_Mutation_p.K435*|MIB2_ENST00000355826.5_Nonsense_Mutation_p.K425*|MIB2_ENST00000505820.2_Nonsense_Mutation_p.K439*|MIB2_ENST00000378712.1_Nonsense_Mutation_p.K259*|MIB2_ENST00000504599.1_Nonsense_Mutation_p.K338*|MIB2_ENST00000360522.4_Nonsense_Mutation_p.K382*|MIB2_ENST00000378710.3_Intron|MIB2_ENST00000518681.1_Nonsense_Mutation_p.K374*|MIB2_ENST00000378708.1_Intron	NM_080875.2	NP_543151.2	Q96AX9	MIB2_HUMAN	mindbomb E3 ubiquitin protein ligase 2	382					Notch signaling pathway (GO:0007219)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)	early endosome (GO:0005769)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|lung(7)|prostate(4)|upper_aerodigestive_tract(1)	18	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;5.26e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.54e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|BRCA - Breast invasive adenocarcinoma(365;0.00786)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		GGCGCTCACCAAGGTGCCGGG	0.682																																					p.K439X		Atlas-SNP	.											.	MIB2	62	.	0			c.A1315T						.						10	12	11					1																	1561031		1913	4062	5975	SO:0001587	stop_gained	142678	exon8			CTCACCAAGGTGC	AK097106	CCDS41224.1, CCDS41224.2, CCDS53261.1, CCDS53262.1, CCDS53263.1, CCDS53264.1	1p36.33	2013-01-10	2012-02-23	2005-04-01	ENSG00000197530	ENSG00000197530		"Zinc fingers, ZZ-type", "Ankyrin repeat domain containing"	30577	protein-coding gene	gene with protein product		611141	"zinc finger, ZZ type with ankyrin repeat domain 1", "mindbomb homolog 2 (Drosophila)"	ZZANK1		12761501	Standard	NM_080875		Approved	skeletrophin, ZZZ5, FLJ39787	uc001agg.3	Q96AX9	OTTHUMG00000074647	ENST00000357210.4:c.1144A>T	chr1.hg19:g.1561031A>T	ENSP00000349741:p.Lys382*	71.0	0.0		76.0	41.0	NM_080875	A2AGM5|A2AGM6|B3KV93|B3KVF4|B3KXY1|B4DZ57|E9PGU1|E9PHQ1|F8WA73|J3KNZ7|Q7Z437|Q8IY62|Q8N786|Q8N897|Q8N8R2|Q8N911|Q8NB36|Q8NCY1|Q8NG59|Q8NG60|Q8NG61|Q8NI59|Q8WYN1	Nonsense_Mutation	SNP	ENST00000357210.4	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	27.1|27.1	4.799871|4.799871	0.90538|0.90538	.|.	.|.	ENSG00000197530|ENSG00000197530	ENST00000520777;ENST00000357210;ENST00000360522;ENST00000355826;ENST00000518681;ENST00000505820;ENST00000378712;ENST00000504599|ENST00000514234	.|.	.|.	.|.	4.41|4.41	3.17|3.17	0.36434|0.36434	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.59115	.|0.2170	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.56559	.|-0.7959	.|4	0.02654|.	T|.	1|.	-15.7819|-15.7819	9.3025|9.3025	0.37853|0.37853	0.8394:0.0:0.0:0.1606|0.8394:0.0:0.0:0.1606	.|.	.|.	.|.	.|.	X|L	435;382;382;425;374;439;259;338|232	.|.	ENSP00000348081:K425X|.	K|Q	+|+	1|2	0|0	MIB2|MIB2	1550894|1550894	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.931000|0.931000	0.56810|0.56810	6.626000|6.626000	0.74253|0.74253	1.764000|1.764000	0.52075|0.52075	0.379000|0.379000	0.24179|0.24179	AAG|CAA	.	.		0.682	MIB2-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_080875		T	1561031	A	T	1561031	4	4	245	1	0	0	0	0	0	1	0	0	9576	131	5	4	1345	4	MIB2	1	1561031	Nonsense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10		1561031	247689590	1	33471										
USP48	84196	hgsc.bcm.edu	37	chr1	22083087	22083087	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	catgtagtcactacaagtgcTtggacataagtagagtgcct	10	8	1	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr1:22083087T>A	ENST00000308271.9	-	3	1012	c.364A>T	c.(364-366)Agc>Tgc	p.S122C	USP48_ENST00000421625.2_Missense_Mutation_p.S122C|USP48_ENST00000400301.1_Missense_Mutation_p.S122C|USP48_ENST00000529637.1_Missense_Mutation_p.S122C	NM_032236.5	NP_115612.4	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 48	122	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			NS(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(14)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)		CTACAAGTGCTTGGACATAAG	0.473																																					p.S122C		Atlas-SNP	.											.	USP48	91	.	0			c.A364T						.						141	141	141					1																	22083087		2203	4300	6503	SO:0001583	missense	84196	exon3			AAGTGCTTGGACA	AF502942	CCDS30623.1, CCDS44084.1	1p36.12	2008-02-05	2005-08-08	2004-04-07	ENSG00000090686	ENSG00000090686		"Ubiquitin-specific peptidases"	18533	protein-coding gene	gene with protein product			"ubiquitin specific protease 31", "ubiquitin specific protease 48"	USP31		12838346	Standard	XM_005246009		Approved	FLJ23277, FLJ11328, FLJ20103, FLJ23054, MGC14879	uc001bfb.3	Q86UV5	OTTHUMG00000007798	ENST00000308271.9:c.364A>T	chr1.hg19:g.22083087T>A	ENSP00000309262:p.Ser122Cys	299.0	0.0		314.0	153.0	NM_001032730	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Missense_Mutation	SNP	ENST00000308271.9	hg19	CCDS30623.1	.	.	.	.	.	.	.	.	.	.	T	18.28	3.590189	0.66105	.	.	ENSG00000090686	ENST00000400301;ENST00000308271;ENST00000529637;ENST00000421625	T;T;T;T	0.05649	3.41;3.41;3.41;3.41	5.55	5.55	0.83447	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.090377	0.85682	D	0.000000	T	0.14056	0.0340	L	0.28400	0.85	0.50171	D	0.999855	D;D;P;D;D;D	0.71674	0.997;0.993;0.804;0.969;0.969;0.998	D;P;P;P;P;P	0.63113	0.911;0.87;0.694;0.517;0.613;0.855	T	0.01834	-1.1264	10	0.56958	D	0.05	.	14.8709	0.70456	0.0:0.0:0.0:1.0	.	122;122;122;122;122;122	B7ZKS7;B7ZKS3;Q86UV5-7;Q86UV5-3;Q86UV5-2;Q86UV5	.;.;.;.;.;UBP48_HUMAN	C	122	ENSP00000383157:S122C;ENSP00000309262:S122C;ENSP00000431949:S122C;ENSP00000406256:S122C	ENSP00000309262:S122C	S	-	1	0	USP48	21955674	1.000000	0.71417	1.000000	0.80357	0.166000	0.22503	4.869000	0.63028	2.099000	0.63709	0.533000	0.62120	AGC	.	.		0.473	USP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021372.1	NM_032236		A	22083087	T	A	22083087	3	1	245	1	0	0	0	0	1	0	0	0	17094	1609	56	4	2851	4	USP48	1	22083087	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	20522056	22083087	227167534	2	33472										
C1orf63	57035	hgsc.bcm.edu	37	chr1	25571745	25571745	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gtcaatgttggttgttcctaGagctttcgctgcattggttt	11	7	1	1	rs147790749		TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr1:25571745G>A	ENST00000243189.7	-	3	844	c.568C>T	c.(568-570)Cta>Tta	p.L190L	RP3-465N24.6_ENST00000607698.1_lincRNA|C1orf63_ENST00000431849.2_Silent_p.L190L|C1orf63_ENST00000417642.2_Silent_p.L183L	NM_020317.3	NP_064713.3	Q9BUV0	RSRP1_HUMAN		190										breast(1)|large_intestine(1)|lung(4)|pancreas(1)	7		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;7.9e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;6.43e-07)|STAD - Stomach adenocarcinoma(196;0.000333)|BRCA - Breast invasive adenocarcinoma(304;0.000443)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.000932)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GTTGTTCCTAGAGCTTTCGCT	0.383																																					p.L190L		Atlas-SNP	.											.	C1orf63	17	.	0			c.C568T						.	A		1,4405	825.8+/-416.5	0,1,2202	153	136	142		568	3.3	0.1	1	dbSNP_134	142	0,8600		0,0,4300	no	coding-synonymous	C1orf63	NM_020317.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		190/291	25571745	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	57035	exon3			TTCCTAGAGCTTT																												ENST00000243189.7:c.568C>T	chr1.hg19:g.25571745G>A		75.0	0.0		65.0	20.0	NM_020317	A8K917|Q49AA4|Q5TH71|Q9GZP6	Silent	SNP	ENST00000243189.7	hg19	CCDS260.1																																																																																			.	G|1.000;A|0.000		0.383	C1orf63-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000101966.2			A	25571745	G	A	25571745	2	1	245	1	0	0	0	0	0	0	0	1	2055	933	33	3		3	C1orf63	1	25571745	Silent	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	3488658	25571745	223678876	3	33473										
TMEM57	55219	hgsc.bcm.edu	37	chr1	25810611	25810611	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tttctcattctcctaggctgGaacaagacattaaaaagtta	6	8	2	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr1:25810611G>A	ENST00000374343.4	+	7	1338	c.1159G>A	c.(1159-1161)Gaa>Aaa	p.E387K	TMEM57_ENST00000399763.3_Missense_Mutation_p.E29K|TMEM57_ENST00000399766.3_Missense_Mutation_p.E160K	NM_018202.4	NP_060672.2	Q8N5G2	MACOI_HUMAN	transmembrane protein 57	387					brain development (GO:0007420)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuron projection terminus (GO:0044306)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|synapse (GO:0045202)				breast(3)|endometrium(2)|kidney(2)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	27		Colorectal(325;0.000147)|Renal(390;0.00211)|Lung NSC(340;0.00715)|all_lung(284;0.00989)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0675)|all_neural(195;0.201)		UCEC - Uterine corpus endometrioid carcinoma (279;0.042)|OV - Ovarian serous cystadenocarcinoma(117;1.85e-26)|Colorectal(126;2.99e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|STAD - Stomach adenocarcinoma(196;0.000766)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|GBM - Glioblastoma multiforme(114;0.0191)|READ - Rectum adenocarcinoma(331;0.0649)		TCCTAGGCTGGAACAAGACAT	0.547																																					p.E387K		Atlas-SNP	.											.	TMEM57	72	.	0			c.G1159A						.						58	62	60					1																	25810611		2203	4300	6503	SO:0001583	missense	55219	exon7			AGGCTGGAACAAG	AK001609	CCDS30638.1, CCDS60034.1	1p36.11	2008-02-05			ENSG00000204178	ENSG00000204178			25572	protein-coding gene	gene with protein product		610301				12459264, 15255972	Standard	XM_005245931		Approved	FLJ10747	uc001bkk.3	Q8N5G2	OTTHUMG00000003473	ENST00000374343.4:c.1159G>A	chr1.hg19:g.25810611G>A	ENSP00000363463:p.Glu387Lys	265.0	1.0		267.0	110.0	NM_018202	B1AK00|Q2TLX5|Q2TLX6|Q9NVG6	Missense_Mutation	SNP	ENST00000374343.4	hg19	CCDS30638.1	.	.	.	.	.	.	.	.	.	.	G	36	5.684625	0.96784	.	.	ENSG00000204178	ENST00000399766;ENST00000399763;ENST00000374343	T;D;T	0.86627	1.62;-2.15;2.6	6.01	6.01	0.97437	.	0.000000	0.85682	D	0.000000	D	0.94414	0.8203	M	0.84683	2.71	0.80722	D	1	D;D;D	0.89917	0.998;1.0;1.0	D;D;D	0.91635	0.994;0.999;0.998	D	0.93903	0.7190	10	0.54805	T	0.06	-18.9469	19.5093	0.95135	0.0:0.0:1.0:0.0	.	29;160;387	Q8N5G2-2;Q8N5G2-3;Q8N5G2	.;.;MACOI_HUMAN	K	160;29;387	ENSP00000382668:E160K;ENSP00000382666:E29K;ENSP00000363463:E387K	ENSP00000363463:E387K	E	+	1	0	TMEM57	25683198	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.447000	0.97595	2.861000	0.98227	0.650000	0.86243	GAA	.	.		0.547	TMEM57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009659.2	NM_018202		A	25810611	G	A	25810611	3	1	245	1	0	0	0	0	1	0	0	0	16199	1175	41	3	1185	3	TMEM57	1	25810611	Missense_Mutation	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	238866	25810611	223440010	4	33474										
SLC30A2	7780	hgsc.bcm.edu	37	chr1	26365755	26365755	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gaacttcccttggaggcggcTgctggctgtcttcagcacag	13	12	2	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr1:26365755T>A	ENST00000374278.3	-	7	1084	c.868A>T	c.(868-870)Agc>Tgc	p.S290C	SLC30A2_ENST00000374276.3_Missense_Mutation_p.S339C	NM_032513.3	NP_115902.1	Q9BRI3	ZNT2_HUMAN	solute carrier family 30 (zinc transporter), member 2	290					positive regulation of sequestering of zinc ion (GO:0061090)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)	cation transmembrane transporter activity (GO:0008324)			cervix(1)|endometrium(2)|kidney(1)|lung(8)|stomach(1)	13		Colorectal(325;3.46e-05)|Lung NSC(340;6.18e-05)|all_lung(284;9.43e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;7.09e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000728)|BRCA - Breast invasive adenocarcinoma(304;0.000969)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00614)|READ - Rectum adenocarcinoma(331;0.0649)		TGGAGGCGGCTGCTGGCTGTC	0.597																																					p.S339C		Atlas-SNP	.											.	SLC30A2	29	.	0			c.A1015T						.						68	62	64					1																	26365755		2203	4300	6503	SO:0001583	missense	7780	exon8			GGCGGCTGCTGGC	AK023491	CCDS272.1, CCDS30644.1	1p35.3	2013-05-22			ENSG00000158014	ENSG00000158014		"Solute carriers"	11013	protein-coding gene	gene with protein product		609617		ZNT2			Standard	NM_001004434		Approved		uc001blg.1	Q9BRI3	OTTHUMG00000007508	ENST00000374278.3:c.868A>T	chr1.hg19:g.26365755T>A	ENSP00000363396:p.Ser290Cys	74.0	0.0		78.0	41.0	NM_001004434	Q71RC8	Missense_Mutation	SNP	ENST00000374278.3	hg19	CCDS272.1	.	.	.	.	.	.	.	.	.	.	T	13.18	2.159612	0.38119	.	.	ENSG00000158014	ENST00000374278;ENST00000374276	T;T	0.64991	-0.13;-0.13	5.63	-11.1	0.00147	.	1.156630	0.06172	N	0.677951	T	0.48295	0.1492	L	0.42744	1.35	0.09310	N	1	B;B	0.10296	0.002;0.003	B;B	0.18263	0.021;0.012	T	0.48293	-0.9048	10	0.56958	D	0.05	-0.4516	11.5943	0.50964	0.2604:0.6304:0.0:0.1092	.	290;339	Q9BRI3;Q9BRI3-2	ZNT2_HUMAN;.	C	290;339	ENSP00000363396:S290C;ENSP00000363394:S339C	ENSP00000363394:S339C	S	-	1	0	SLC30A2	26238342	0.000000	0.05858	0.000000	0.03702	0.317000	0.28152	-2.347000	0.01095	-1.583000	0.01638	0.379000	0.24179	AGC	.	.		0.597	SLC30A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019742.1	NM_032513		A	26365755	T	A	26365755	3	1	245	1	0	0	0	0	1	0	0	0	14570	1580	55	4	107	4	SLC30A2	1	26365755	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	555144	26365755	222884866	5	33475										
COL16A1	1307	hgsc.bcm.edu	37	chr1	32157244	32157244	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	cagatctctcctggccggccCtgtggggggataagggggag	18	10	1	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr1:32157244C>A	ENST00000373672.3	-	18	1774		c.e18-1		COL16A1_ENST00000373668.3_Splice_Site|COL16A1_ENST00000271069.6_Splice_Site	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1						cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female pregnancy (GO:0007565)|integrin-mediated signaling pathway (GO:0007229)	collagen type XVI trimer (GO:0005597)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(15)|ovary(8)|prostate(4)	48		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		CTGGCCGGCCCTGTGGGGGGA	0.652																																					.	Colon(143;498 1786 21362 25193 36625)	Atlas-SNP	.											.	COL16A1	137	.	0			c.1258-1G>T						.						105	112	109					1																	32157244		1921	4121	6042	SO:0001630	splice_region_variant	1307	exon19			CCGGCCCTGTGGG	M92642	CCDS41297.1	1p35-p34	2013-01-16			ENSG00000084636	ENSG00000084636		"Collagens"	2193	protein-coding gene	gene with protein product		120326				1631157	Standard	NM_001856		Approved		uc001btk.1	Q07092	OTTHUMG00000003883	ENST00000373672.3:c.1258-1G>T	chr1.hg19:g.32157244C>A		227.0	1.0		193.0	87.0	NM_001856	Q16593|Q59F89|Q71RG9	Splice_Site	SNP	ENST00000373672.3	hg19	CCDS41297.1	.	.	.	.	.	.	.	.	.	.	C	15.44	2.833443	0.50951	.	.	ENSG00000084636	ENST00000373672;ENST00000271069;ENST00000373668;ENST00000373667	.	.	.	4.79	4.79	0.61399	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1384	0.72590	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	COL16A1	31929831	1.000000	0.71417	1.000000	0.80357	0.613000	0.37349	6.052000	0.71080	2.391000	0.81399	0.462000	0.41574	.	.	.		0.652	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856	Intron	A	32157244	C	A	32157244	5	1	245	1	0	0	0	0	0	0	1	0	3675	695	24	3	3773	3	COL16A1	1	32157244	Splice_Site	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	5791489	32157244	217093377	6	33476										
OSCP1	127700	hgsc.bcm.edu	37	chr1	36904373	36904373	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tcaccttatccatgctggccTggttcagtttcataatggag	9	10	3	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr1:36904373T>A	ENST00000356637.5	-	3	344	c.281A>T	c.(280-282)cAg>cTg	p.Q94L	OSCP1_ENST00000315643.9_Missense_Mutation_p.Q94L|OSCP1_ENST00000235532.5_Missense_Mutation_p.Q84L|OSCP1_ENST00000433045.2_Missense_Mutation_p.Q39L|OSCP1_ENST00000354267.3_Missense_Mutation_p.Q84L			Q8WVF1	OSCP1_HUMAN	organic solute carrier partner 1	94					transport (GO:0006810)	plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	22						CATGCTGGCCTGGTTCAGTTT	0.468																																					p.Q84L		Atlas-SNP	.											.	OSCP1	48	.	0			c.A251T						.						101	90	94					1																	36904373		2203	4300	6503	SO:0001583	missense	127700	exon2			CTGGCCTGGTTCA		CCDS409.1, CCDS410.1, CCDS409.2	1p34.3	2009-07-06	2009-07-06	2009-07-06	ENSG00000116885	ENSG00000116885			29971	protein-coding gene	gene with protein product	"oxidored nitro domain containing protein"	608854	"chromosome 1 open reading frame 102"	C1orf102		12477932	Standard	NM_145047		Approved	NOR1	uc001caq.3	Q8WVF1	OTTHUMG00000008139	ENST00000356637.5:c.281A>T	chr1.hg19:g.36904373T>A	ENSP00000349052:p.Gln94Leu	39.0	0.0		40.0	12.0	NM_145047	A6NHM5|A6NHS9|A6NIN9|Q4AEJ0|Q8N7G2|Q8TDF1	Missense_Mutation	SNP	ENST00000356637.5	hg19		.	.	.	.	.	.	.	.	.	.	T	16.64	3.179923	0.57800	.	.	ENSG00000116885	ENST00000235532;ENST00000356637;ENST00000433045;ENST00000445843;ENST00000315643;ENST00000354267	T;T;T;T;T;T	0.31510	1.49;1.49;1.49;1.49;1.49;1.49	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	T	0.32194	0.0821	L	0.56769	1.78	0.80722	D	1	P;B;B	0.37352	0.591;0.228;0.27	B;B;B	0.36186	0.219;0.138;0.216	T	0.05784	-1.0864	10	0.28530	T	0.3	.	15.4635	0.75381	0.0:0.0:0.0:1.0	.	84;84;94	Q8WVF1-4;Q8WVF1-3;Q8WVF1	.;.;OSCP1_HUMAN	L	84;94;39;54;94;84	ENSP00000235532:Q84L;ENSP00000349052:Q94L;ENSP00000390820:Q39L;ENSP00000396417:Q54L;ENSP00000314541:Q94L;ENSP00000346216:Q84L	ENSP00000235532:Q84L	Q	-	2	0	OSCP1	36676960	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.927000	0.56499	2.250000	0.74265	0.533000	0.62120	CAG	.	.		0.468	OSCP1-010	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000389759.1	NM_145047		A	36904373	T	A	36904373	3	1	245	1	0	0	0	0	1	0	0	0	11295	1580	55	4	1084	4	OSCP1	1	36904373	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	4747129	36904373	212346248	7	33477										
EPHA10	284656	hgsc.bcm.edu	37	chr1	38230698	38230698	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gacagagctgcatccggcagAggaagaggcgcagcgggtgt	18	9	0	3			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr1:38230698A>T	ENST00000373048.4	-	1	40	c.41T>A	c.(40-42)cTc>cAc	p.L14H	EPHA10_ENST00000319637.6_Missense_Mutation_p.L14H|EPHA10_ENST00000427468.2_Missense_Mutation_p.L14H	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	14					ephrin receptor signaling pathway (GO:0048013)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane-ephrin receptor activity (GO:0005005)			NS(2)|breast(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(13)|prostate(3)|skin(8)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				CATCCGGCAGAGGAAGAGGCG	0.692																																					p.L14H		Atlas-SNP	.											.	EPHA10	120	.	0			c.T41A						.						12	15	14					1																	38230698		2200	4295	6495	SO:0001583	missense	284656	exon1			CGGCAGAGGAAGA	AK090974	CCDS425.1, CCDS41305.1	1p34.3	2013-02-11			ENSG00000183317	ENSG00000183317		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	19987	protein-coding gene	gene with protein product		611123				12477932	Standard	NM_001099439		Approved	FLJ16103, FLJ33655	uc009vvi.3	Q5JZY3	OTTHUMG00000004325	ENST00000373048.4:c.41T>A	chr1.hg19:g.38230698A>T	ENSP00000362139:p.Leu14His	47.0	0.0		40.0	24.0	NM_001099439	A4FU89|J3KPB5|Q6NW42	Missense_Mutation	SNP	ENST00000373048.4	hg19	CCDS41305.1	.	.	.	.	.	.	.	.	.	.	A	12.36	1.915646	0.33815	.	.	ENSG00000183317	ENST00000427468;ENST00000373048;ENST00000319637	T;T;T	0.78003	-1.14;-1.13;4.31	5.19	-1.18	0.09617	.	1.399080	0.05203	N	0.505331	T	0.63189	0.2490	N	0.14661	0.345	0.38080	D	0.936641	B;B	0.30542	0.187;0.284	B;B	0.36244	0.156;0.22	T	0.48811	-0.9002	10	0.44086	T	0.13	.	4.98	0.14160	0.4937:0.1605:0.3458:0.0	.	14;14	Q5JZY3;Q5JZY3-2	EPHAA_HUMAN;.	H	14	ENSP00000397746:L14H;ENSP00000362139:L14H;ENSP00000316395:L14H	ENSP00000316395:L14H	L	-	2	0	EPHA10	38003285	0.033000	0.19621	0.030000	0.17652	0.802000	0.45316	0.081000	0.14823	-0.382000	0.07870	0.519000	0.50382	CTC	.	.		0.692	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000012497.2	NM_173641		T	38230698	A	T	38230698	3	4	245	1	0	0	0	0	1	0	0	0	5168	304	11	4	3091	4	EPHA10	1	38230698	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	1326325	38230698	211019923	8	33478										
YBX1	4904	hgsc.bcm.edu	37	chr1	43162928	43162928	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	cggggatatagaccacgattCcgcaggtatggtccacgtaa	12	10	0	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr1:43162928C>T	ENST00000321358.7	+	6	874	c.735C>T	c.(733-735)ttC>ttT	p.F245F		NM_004559.3	NP_004550.2	P67809	YBOX1_HUMAN	Y box binding protein 1	245					CRD-mediated mRNA stabilization (GO:0070934)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell division (GO:0051781)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|extracellular vesicular exosome (GO:0070062)|histone pre-mRNA 3'end processing complex (GO:0071204)|intracellular membrane-bounded organelle (GO:0043231)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|U12-type spliceosomal complex (GO:0005689)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)			large_intestine(2)|lung(4)|ovary(4)|prostate(4)|upper_aerodigestive_tract(2)	16	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GACCACGATTCCGCAGGTATG	0.438																																					p.F245F		Atlas-SNP	.											.	YBX1	49	.	0			c.C735T						.						104	86	92					1																	43162928		2203	4300	6503	SO:0001819	synonymous_variant	4904	exon6			ACGATTCCGCAGG	BC013838	CCDS470.1	1p34	2008-02-05	2005-08-11	2005-08-11	ENSG00000065978	ENSG00000065978			8014	protein-coding gene	gene with protein product		154030	"nuclease sensitive element binding protein 1"	NSEP1		1891370, 3174636	Standard	NM_004559		Approved	YB-1, YB1, DBPB, NSEP-1, MDR-NF1, BP-8, CSDB, CSDA2	uc001chs.3	P67809	OTTHUMG00000007523	ENST00000321358.7:c.735C>T	chr1.hg19:g.43162928C>T		220.0	0.0		179.0	57.0	NM_004559	P16990|P16991|Q14972|Q15325|Q5FVF0	Silent	SNP	ENST00000321358.7	hg19	CCDS470.1	.	.	.	.	.	.	.	.	.	.	C	9.695	1.152938	0.21371	.	.	ENSG00000065978	ENST00000318612;ENST00000436427	.	.	.	5.6	3.68	0.42216	.	.	.	.	.	T	0.51466	0.1676	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37197	-0.9716	5	0.24483	T	0.36	-2.5623	6.7295	0.23375	0.0:0.6894:0.0:0.3106	.	.	.	.	F	236;295	.	ENSP00000361621:S236F	S	+	2	0	YBX1	42935515	0.978000	0.34361	1.000000	0.80357	0.975000	0.68041	0.034000	0.13776	0.643000	0.30638	0.563000	0.77884	TCC	.	.		0.438	YBX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019786.2	NM_004559		T	43162928	C	T	43162928	2	4	245	1	0	0	0	0	0	0	0	1	17484	854	30	3		3	YBX1	1	43162928	Silent	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	4932230	43162928	206087693	9	33479										
FAM73A	374986	hgsc.bcm.edu	37	chr1	78325806	78325806	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	cagctttaattgtgaaagcaCgaaaggtaaacttgttctgt	9	6	1	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr1:78325806C>T	ENST00000370791.3	+	11	1302	c.1270C>T	c.(1270-1272)Cga>Tga	p.R424*	FAM73A_ENST00000443751.2_Nonsense_Mutation_p.R386*	NM_001270384.1|NM_198549.3	NP_001257313.1|NP_940951.1	Q8NAN2	FA73A_HUMAN	family with sequence similarity 73, member A	424						integral component of membrane (GO:0016021)				breast(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	19				Colorectal(170;0.226)		TGTGAAAGCACGAAAGGTAAA	0.323																																					p.R424X		Atlas-SNP	.											.	FAM73A	56	.	0			c.C1270T						.						45	46	46					1																	78325806		2203	4300	6503	SO:0001587	stop_gained	374986	exon11			AAAGCACGAAAGG		CCDS681.1, CCDS72809.1	1p31.1	2008-02-05			ENSG00000180488	ENSG00000180488			24741	protein-coding gene	gene with protein product							Standard	NM_001270384		Approved	FLJ35093	uc010ork.3	Q8NAN2	OTTHUMG00000009766	ENST00000370791.3:c.1270C>T	chr1.hg19:g.78325806C>T	ENSP00000359827:p.Arg424*	120.0	0.0		99.0	35.0	NM_198549	Q6MZG0	Nonsense_Mutation	SNP	ENST00000370791.3	hg19	CCDS681.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.750257	0.89753	.	.	ENSG00000180488	ENST00000370791;ENST00000443751	.	.	.	5.48	3.41	0.39046	.	0.069985	0.56097	D	0.000032	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	-9.9574	8.484	0.33061	0.2587:0.6544:0.0:0.0869	.	.	.	.	X	424;386	.	ENSP00000359827:R424X	R	+	1	2	FAM73A	78098394	0.987000	0.35691	1.000000	0.80357	0.909000	0.53808	1.308000	0.33528	1.313000	0.45069	0.563000	0.77884	CGA	.	.		0.323	FAM73A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000026931.1	NM_198549		T	78325806	C	T	78325806	4	4	245	1	0	0	0	0	0	1	0	0	5625	528	19	1	1312	1	FAM73A	1	78325806	Nonsense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	35162878	78325806	170924815	10	33480										
MCOLN2	255231	hgsc.bcm.edu	37	chr1	85403666	85403666	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ccggtgccgcatccttacatTatatgcctggaaataaccca	7	13	0	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr1:85403666T>A	ENST00000370608.3	-	10	1277	c.1210A>T	c.(1210-1212)Aat>Tat	p.N404Y	MCOLN2_ENST00000531325.1_5'UTR|MCOLN2_ENST00000284027.5_Missense_Mutation_p.N376Y	NM_153259.2	NP_694991.2	Q8IZK6	MCLN2_HUMAN	mucolipin 2	404					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)	18				all cancers(265;0.0111)|Epithelial(280;0.0263)|OV - Ovarian serous cystadenocarcinoma(397;0.217)		ATCCTTACATTATATGCCTGG	0.418																																					p.N404Y		Atlas-SNP	.											.	MCOLN2	60	.	0			c.A1210T						.						69	71	70					1																	85403666		2203	4300	6503	SO:0001583	missense	255231	exon10			TTACATTATATGC	AK094010	CCDS30762.1	1p22	2011-12-16			ENSG00000153898	ENSG00000153898		"Voltage-gated ion channels / Transient receptor potential cation channels"	13357	protein-coding gene	gene with protein product		607399				16382100	Standard	XM_005270719		Approved	TRPML2, FLJ36691, TRP-ML2	uc001dkm.3	Q8IZK6	OTTHUMG00000009954	ENST00000370608.3:c.1210A>T	chr1.hg19:g.85403666T>A	ENSP00000359640:p.Asn404Tyr	377.0	0.0		369.0	152.0	NM_153259	A6NI99|Q2M3I6|Q5TAG5|Q8N9R3	Missense_Mutation	SNP	ENST00000370608.3	hg19	CCDS30762.1	.	.	.	.	.	.	.	.	.	.	T	17.00	3.276951	0.59758	.	.	ENSG00000153898	ENST00000370608;ENST00000284027	T;T	0.69685	-0.42;-0.42	6.07	6.07	0.98685	Polycystin cation channel, PKD1/PKD2 (1);	0.040162	0.85682	D	0.000000	T	0.67850	0.2937	L	0.45581	1.43	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.64245	-0.6453	10	0.13108	T	0.6	-35.197	16.6277	0.84984	0.0:0.0:0.0:1.0	.	404	Q8IZK6	MCLN2_HUMAN	Y	404;376	ENSP00000359640:N404Y;ENSP00000284027:N376Y	ENSP00000284027:N376Y	N	-	1	0	MCOLN2	85176254	1.000000	0.71417	0.820000	0.32676	0.083000	0.17756	7.698000	0.84413	2.330000	0.79161	0.528000	0.53228	AAT	.	.		0.418	MCOLN2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027567.2	NM_153259		A	85403666	T	A	85403666	3	1	245	1	0	0	0	0	1	0	0	0	9405	1754	61	4	510	4	MCOLN2	1	85403666	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	7077860	85403666	163846955	11	33481										
ABCA4	24	hgsc.bcm.edu	37	chr1	94548999	94548999	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tgtctaggagtgtgggaagcTgtaattgacagtaaaacaat	12	4	1	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr1:94548999T>A	ENST00000370225.3	-	7	855		c.e7-2		ABCA4_ENST00000535735.1_Splice_Site	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4						phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			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)		TGTGGGAAGCTGTAATTGACA	0.383																																					.		Atlas-SNP	.											.	ABCA4	275	.	0			c.769-2A>T						.						139	153	149					1																	94548999		2203	4300	6503	SO:0001630	splice_region_variant	24	exon8			GGAAGCTGTAATT	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.769-2A>T	chr1.hg19:g.94548999T>A		35.0	0.0		55.0	6.0	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Splice_Site	SNP	ENST00000370225.3	hg19	CCDS747.1	.	.	.	.	.	.	.	.	.	.	T	19.97	3.925846	0.73213	.	.	ENSG00000198691	ENST00000370225;ENST00000535735	.	.	.	5.59	5.59	0.84812	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0668	0.80887	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	ABCA4	94321587	1.000000	0.71417	0.999000	0.59377	0.794000	0.44872	6.891000	0.75639	2.246000	0.74042	0.533000	0.62120	.	.	.		0.383	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350	Intron	A	94548999	T	A	94548999	5	1	245	1	0	0	0	0	0	0	1	0	34	1594	55	4	6230	4	ABCA4	1	94548999	Splice_Site	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	9145333	94548999	154701622	12	33482										
LPPR5	163404	hgsc.bcm.edu	37	chr1	99418684	99418684	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ctttggatggaaaggtttttCgggctctcatgatgagatct	12	6	2	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr1:99418684C>A	ENST00000263177.4	-	3	784	c.563G>T	c.(562-564)cGa>cTa	p.R188L	LPPR5_ENST00000370188.3_Missense_Mutation_p.R188L	NM_001037317.1	NP_001032394.1	Q32ZL2	LPPR5_HUMAN		188						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)										AAAGGTTTTTCGGGCTCTCAT	0.418																																					p.R188L		Atlas-SNP	.											.	.	.	.	0			c.G563T						.						126	113	117					1																	99418684		2203	4300	6503	SO:0001583	missense	0	exon3			GTTTTTCGGGCTC																												ENST00000263177.4:c.563G>T	chr1.hg19:g.99418684C>A	ENSP00000263177:p.Arg188Leu	90.0	0.0		90.0	40.0	NM_001010861	A8MPX4|B7UCH3|Q32ZD0|Q3ZCU7	Missense_Mutation	SNP	ENST00000263177.4	hg19	CCDS30778.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.975196	0.74360	.	.	ENSG00000117598	ENST00000370188;ENST00000263177	T;T	0.75477	-0.94;-0.94	5.16	5.16	0.70880	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.85261	0.5656	M	0.79693	2.465	0.53688	D	0.999972	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.87028	0.2133	10	0.87932	D	0	.	17.9943	0.89178	0.0:1.0:0.0:0.0	.	188;188	Q32ZL2-2;Q32ZL2	.;LPPR5_HUMAN	L	188	ENSP00000359207:R188L;ENSP00000263177:R188L	ENSP00000263177:R188L	R	-	2	0	AL161744.1	99191272	1.000000	0.71417	0.721000	0.30653	0.314000	0.28054	7.445000	0.80570	2.563000	0.86464	0.655000	0.94253	CGA	.	.		0.418	LPPR5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393221.1			A	99418684	C	A	99418684	3	1	245	1	0	0	0	0	1	0	0	0	8937	884	31	1	418	1	LPPR5	1	99418684	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	4869685	99418684	149831937	13	33483										
OLFM3	118427	hgsc.bcm.edu	37	chr1	102270187	102270187	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ccgatttcatcagccattagGtcgatgtcagagaatccacc	8	12	3	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr1:102270187G>T	ENST00000338858.5	-	6	1043	c.1044C>A	c.(1042-1044)gaC>gaA	p.D348E	OLFM3_ENST00000536598.1_3'UTR|OLFM3_ENST00000462354.1_5'UTR|OLFM3_ENST00000370103.4_Missense_Mutation_p.D328E			Q96PB7	NOE3_HUMAN	olfactomedin 3	348	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				eye photoreceptor cell development (GO:0042462)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)				breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(24)|ovary(3)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	43		all_epithelial(167;1.87e-06)|all_lung(203;8.12e-05)|Lung NSC(277;0.000189)		all cancers(265;0.0843)|Epithelial(280;0.0921)|COAD - Colon adenocarcinoma(174;0.145)		CAGCCATTAGGTCGATGTCAG	0.473																																					p.D328E		Atlas-SNP	.											.	OLFM3	178	.	0			c.C984A						.						88	75	80					1																	102270187		2203	4300	6503	SO:0001583	missense	118427	exon6			CATTAGGTCGATG	AF397392	CCDS30781.1, CCDS72832.1	1p22	2008-05-23			ENSG00000118733	ENSG00000118733			17990	protein-coding gene	gene with protein product	"optimedin"	607567				12019210, 16115881	Standard	NM_001288821		Approved	NOE3	uc001dug.2	Q96PB7	OTTHUMG00000010941	ENST00000338858.5:c.1044C>A	chr1.hg19:g.102270187G>T	ENSP00000345192:p.Asp348Glu	133.0	0.0		178.0	89.0	NM_058170	Q5T3V6|Q6IMI7|Q6IMI8|Q6IMI9|Q6IMJ1|Q8TBG1|Q96PB2|Q96PB3|Q96PB4|Q96PB5|Q96PB6	Missense_Mutation	SNP	ENST00000338858.5	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.64|16.64	3.180330|3.180330	0.57800|0.57800	.|.	.|.	ENSG00000118733|ENSG00000118733	ENST00000370103;ENST00000338858|ENST00000424771	D;D|.	0.94000|.	-3.33;-3.33|.	5.77|5.77	2.56|2.56	0.30785|0.30785	Olfactomedin-like (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.67439|0.67439	0.2893|0.2893	M|M	0.86953|0.86953	2.85|2.85	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;0.992|.	D;D|.	0.97110|.	1.0;0.987|.	T|T	0.71781|0.71781	-0.4489|-0.4489	10|6	0.87932|0.87932	D|D	0|0	.|.	8.7937|8.7937	0.34866|0.34866	0.3525:0.0:0.6475:0.0|0.3525:0.0:0.6475:0.0	.|.	328;348|.	Q5T3V6;Q96PB7|.	.;NOE3_HUMAN|.	E|N	328;348|199	ENSP00000359121:D328E;ENSP00000345192:D348E|.	ENSP00000345192:D348E|ENSP00000407686:T199N	D|T	-|-	3|2	2|0	OLFM3|OLFM3	102042775|102042775	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.995000|0.995000	0.86356|0.86356	2.438000|2.438000	0.44837|0.44837	0.799000|0.799000	0.34018|0.34018	0.650000|0.650000	0.86243|0.86243	GAC|ACC	.	.		0.473	OLFM3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000030142.1			T	102270187	G	T	102270187	3	4	245	1	0	0	0	0	1	0	0	0	10863	1252	44	3	396	3	OLFM3	1	102270187	Missense_Mutation	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	2851503	102270187	146980434	14	33484										
NOTCH2	4853	hgsc.bcm.edu	37	chr1	120462971	120462971	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ggtgctgctgtgtccatggcCgtcgatcaatggggtcatct	14	10	3	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr1:120462971C>T	ENST00000256646.2	-	30	5579	c.5360G>A	c.(5359-5361)cGg>cAg	p.R1787Q	NOTCH2_ENST00000493703.1_5'Flank	NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	1787					apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		TGTCCATGGCCGTCGATCAAT	0.532			"N, F, Mis"		"marginal zone lymphoma, DLBCL"				Alagille Syndrome																												p.R1787Q		Atlas-SNP	.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	.	NOTCH2	348	.	0			c.G5360A						.						177	137	151					1																	120462971		2203	4300	6503	SO:0001583	missense	4853	exon30	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	CATGGCCGTCGAT	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"Ankyrin repeat domain containing"	7882	protein-coding gene	gene with protein product		600275	"Notch (Drosophila) homolog 2", "Notch homolog 2 (Drosophila)"			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.5360G>A	chr1.hg19:g.120462971C>T	ENSP00000256646:p.Arg1787Gln	130.0	0.0		114.0	7.0	NM_024408	Q5T3X7|Q99734|Q9H240	Missense_Mutation	SNP	ENST00000256646.2	hg19	CCDS908.1	.	.	.	.	.	.	.	.	.	.	C	36	5.739306	0.96873	.	.	ENSG00000134250	ENST00000256646	D	0.85702	-2.02	5.82	5.82	0.92795	.	0.000000	0.36815	U	0.002381	D	0.90497	0.7023	M	0.62088	1.915	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.90405	0.4405	10	0.66056	D	0.02	.	19.0775	0.93168	0.0:1.0:0.0:0.0	.	1787	Q04721	NOTC2_HUMAN	Q	1787	ENSP00000256646:R1787Q	ENSP00000256646:R1787Q	R	-	2	0	NOTCH2	120264494	1.000000	0.71417	0.967000	0.41034	0.867000	0.49689	7.755000	0.85180	2.761000	0.94854	0.655000	0.94253	CGG	.	.		0.532	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408		T	120462971	C	T	120462971	3	4	245	1	0	0	0	0	1	0	0	0	10557	652	23	1	2075	1	NOTCH2	1	120462971	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	18192784	120462971	128787650	15	33485										
GJA5	2702	hgsc.bcm.edu	37	chr1	147230478	147230478	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ccaggttgtctgtgttttgtTgggaggccatattattgctg	13	6	1	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr1:147230478T>C	ENST00000271348.2	-	2	1030	c.869A>G	c.(868-870)cAa>cGa	p.Q290R	GJA5_ENST00000369237.1_Missense_Mutation_p.Q290R|RP11-433J22.2_ENST00000428911.1_RNA	NM_005266.5	NP_005257.2	P36382	CXA5_HUMAN	gap junction protein, alpha 5, 40kDa	290					angiogenesis (GO:0001525)|artery morphogenesis (GO:0048844)|atrial cardiac muscle cell action potential (GO:0086014)|atrial septum development (GO:0003283)|AV node cell to bundle of His cell communication by electrical coupling (GO:0086053)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|gap junction assembly (GO:0016264)|mitral valve development (GO:0003174)|outflow tract morphogenesis (GO:0003151)|pulmonary valve formation (GO:0003193)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|transmembrane transport (GO:0055085)|ventricular septum development (GO:0003281)	connexon complex (GO:0005922)|gap junction (GO:0005921)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)	gap junction channel activity involved in AV node cell-bundle of His cell electrical coupling (GO:0086077)|gap junction channel activity involved in cardiac conduction electrical coupling (GO:0086075)|gap junction hemi-channel activity (GO:0055077)			breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	20	all_hematologic(923;0.0276)		LUSC - Lung squamous cell carcinoma(543;0.202)			TGTGTTTTGTTGGGAGGCCAT	0.527																																					p.Q290R		Atlas-SNP	.											.	GJA5	64	.	0			c.A869G						.						152	148	150					1																	147230478		2203	4300	6503	SO:0001583	missense	2702	exon2			TTTTGTTGGGAGG		CCDS929.1	1q21.1	2008-02-05	2007-01-16		ENSG00000143140	ENSG00000265107		"Ion channels / Gap junction proteins (connexins)"	4279	protein-coding gene	gene with protein product	"connexin 40"	121013	"gap junction protein, alpha 5, 40kD (connexin 40)", "gap junction protein, alpha 5, 40kDa (connexin 40)"				Standard	NM_005266		Approved	CX40	uc001eps.1	P36382	OTTHUMG00000014020	ENST00000271348.2:c.869A>G	chr1.hg19:g.147230478T>C	ENSP00000271348:p.Gln290Arg	110.0	0.0		192.0	27.0	NM_005266	Q5T3B6|Q5U0N6	Missense_Mutation	SNP	ENST00000271348.2	hg19	CCDS929.1	.	.	.	.	.	.	.	.	.	.	T	10.25	1.299225	0.23650	.	.	ENSG00000143140	ENST00000271348;ENST00000369237	D;D	0.81739	-1.53;-1.53	5.07	0.79	0.18613	.	0.559513	0.18427	N	0.141554	T	0.45175	0.1329	N	0.16903	0.455	0.41508	D	0.988324	B	0.13145	0.007	B	0.09377	0.004	T	0.33189	-0.9878	10	0.46703	T	0.11	.	6.0386	0.19722	0.0:0.2054:0.1364:0.6582	.	290	P36382	CXA5_HUMAN	R	290	ENSP00000271348:Q290R;ENSP00000358240:Q290R	ENSP00000271348:Q290R	Q	-	2	0	GJA5	145697102	1.000000	0.71417	0.991000	0.47740	0.536000	0.34869	4.770000	0.62309	0.243000	0.21327	0.460000	0.39030	CAA	.	.		0.527	GJA5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039422.2	NM_181703		C	147230478	T	C	147230478	3	2	245	1	0	0	0	0	1	0	0	0	6412	1812	63	2	211	2	GJA5	1	147230478	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	26767507	147230478	102020143	16	33486										
VPS45	11311	hgsc.bcm.edu	37	chr1	150054960	150054960	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tcaaaatgaccattctagtgCtctccaggtcagtccaattt	6	11	4	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr1:150054960C>T	ENST00000369130.3	+	10	1643	c.1097C>T	c.(1096-1098)gCt>gTt	p.A366V	VPS45_ENST00000535106.1_Missense_Mutation_p.A297V|VPS45_ENST00000369128.5_Missense_Mutation_p.A261V	NM_001279354.1|NM_007259.3	NP_001266283.1|NP_009190.2	Q9NRW7	VPS45_HUMAN	vacuolar protein sorting 45 homolog (S. cerevisiae)	366					blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|vesicle docking involved in exocytosis (GO:0006904)	endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	21	Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			CATTCTAGTGCTCTCCAGGTC	0.463																																					p.A366V		Atlas-SNP	.											.	VPS45	47	.	0			c.C1097T						.						78	76	77					1																	150054960		2203	4300	6503	SO:0001583	missense	11311	exon10			CTAGTGCTCTCCA	U35246	CCDS944.1, CCDS60244.1, CCDS72904.1	1q21.2	2008-02-05	2006-12-19	2006-12-19	ENSG00000136631	ENSG00000136631			14579	protein-coding gene	gene with protein product		610035	"vacuolar protein sorting 45A (yeast homolog)", "vacuolar protein sorting 45A (yeast)"	VPS45B, VPS45A		8996080	Standard	NM_007259		Approved	h-vps45, H1	uc001etp.3	Q9NRW7	OTTHUMG00000012511	ENST00000369130.3:c.1097C>T	chr1.hg19:g.150054960C>T	ENSP00000358126:p.Ala366Val	115.0	0.0		178.0	121.0	NM_007259	D3DUZ9|F5H8K1|Q15715|Q53FR8|Q5T4P6|Q9Y4Z6	Missense_Mutation	SNP	ENST00000369130.3	hg19	CCDS944.1	.	.	.	.	.	.	.	.	.	.	C	19.79	3.893249	0.72524	.	.	ENSG00000136631	ENST00000369130;ENST00000369128;ENST00000543996;ENST00000535106;ENST00000419023	T;T;T;T	0.76968	-1.06;-1.06;-1.06;-1.06	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	T	0.59280	0.2182	L	0.45470	1.425	0.80722	D	1	B;B;B;B	0.28971	0.229;0.041;0.08;0.089	B;B;B;B	0.32090	0.112;0.091;0.063;0.14	T	0.62770	-0.6784	10	0.05525	T	0.97	.	19.2671	0.93993	0.0:1.0:0.0:0.0	.	261;366;186;366	F5H8K1;Q53FR8;A0AR27;Q9NRW7	.;.;.;VPS45_HUMAN	V	366;261;241;297;297	ENSP00000358126:A366V;ENSP00000358124:A261V;ENSP00000440690:A297V;ENSP00000400143:A297V	ENSP00000358124:A261V	A	+	2	0	VPS45	148321584	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.622000	0.83099	2.788000	0.95919	0.650000	0.86243	GCT	.	.		0.463	VPS45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034964.1	NM_007259		T	150054960	C	T	150054960	3	4	245	1	0	0	0	0	1	0	0	0	17226	797	28	3	1135	3	VPS45	1	150054960	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	2824482	150054960	99195661	17	33487										
CRTC2	200186	hgsc.bcm.edu	37	chr1	153924016	153924016	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gtacatggcgggccaaggagGaggcaggcagagaggggtgg	22	6	0	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr1:153924016G>T	ENST00000368633.1	-	11	1251	c.1124C>A	c.(1123-1125)tCc>tAc	p.S375Y	CRTC2_ENST00000476883.1_5'Flank|CRTC2_ENST00000368630.3_Missense_Mutation_p.S55Y	NM_181715.2	NP_859066.1	Q53ET0	CRTC2_HUMAN	CREB regulated transcription coactivator 2	375	Ser-rich.				gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|histone H3-K9 acetylation (GO:0043970)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	cAMP response element binding protein binding (GO:0008140)	p.S375F(1)		NS(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	27	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			GGCCAAGGAGGAGGCAGGCAG	0.642																																					p.S375Y		Atlas-SNP	.											CRTC2,extremity,malignant_melanoma,0,1	CRTC2	58	.	1	Substitution - Missense(1)	skin(1)	c.C1124A						.						54	59	58					1																	153924016		2202	4300	6502	SO:0001583	missense	200186	exon11			AAGGAGGAGGCAG	AY360172	CCDS30875.1	1q21.3	2008-02-05			ENSG00000160741	ENSG00000160741			27301	protein-coding gene	gene with protein product		608972				14506290, 14536081	Standard	NM_181715		Approved	TORC2	uc021pab.1	Q53ET0	OTTHUMG00000037156	ENST00000368633.1:c.1124C>A	chr1.hg19:g.153924016G>T	ENSP00000357622:p.Ser375Tyr	27.0	0.0		55.0	37.0	NM_181715	Q6UUV8|Q7Z3X7|Q8N332	Missense_Mutation	SNP	ENST00000368633.1	hg19	CCDS30875.1	.	.	.	.	.	.	.	.	.	.	G	17.70	3.454705	0.63290	.	.	ENSG00000160741	ENST00000368630;ENST00000368633	T;T	0.48201	0.82;2.59	4.63	4.63	0.57726	.	0.538685	0.19321	N	0.117131	T	0.55226	0.1907	L	0.57536	1.79	0.41428	D	0.987841	D	0.69078	0.997	D	0.65573	0.936	T	0.56577	-0.7956	10	0.52906	T	0.07	-14.715	15.0183	0.71605	0.0:0.0:1.0:0.0	.	375	Q53ET0	CRTC2_HUMAN	Y	55;375	ENSP00000357619:S55Y;ENSP00000357622:S375Y	ENSP00000357619:S55Y	S	-	2	0	CRTC2	152190640	1.000000	0.71417	0.998000	0.56505	0.722000	0.41435	5.617000	0.67716	2.396000	0.81511	0.557000	0.71058	TCC	.	.		0.642	CRTC2-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090272.3	NM_181715		T	153924016	G	T	153924016	3	4	245	1	0	0	0	0	1	0	0	0	3902	1174	41	3	973	3	CRTC2	1	153924016	Missense_Mutation	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	3869056	153924016	95326605	18	33488										
UBE2Q1	55585	hgsc.bcm.edu	37	chr1	154527989	154527989	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tacacaggtcggagatgatcCtcttcagatgctgcaatagc	10	10	2	3			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr1:154527989C>T	ENST00000292211.4	-	3	531	c.452G>A	c.(451-453)aGg>aAg	p.R151K	UBE2Q1-AS1_ENST00000441613.1_RNA|UBE2Q1_ENST00000497453.1_5'UTR	NM_017582.6	NP_060052.3	Q7Z7E8	UB2Q1_HUMAN	ubiquitin-conjugating enzyme E2Q family member 1	151					embryo implantation (GO:0007566)|fertilization (GO:0009566)|mating behavior (GO:0007617)|prolactin secretion (GO:0070459)|protein ubiquitination (GO:0016567)|reproductive system development (GO:0061458)|suckling behavior (GO:0001967)		acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)			endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(6)|upper_aerodigestive_tract(1)	16	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			GGAGATGATCCTCTTCAGATG	0.512																																					p.R151K		Atlas-SNP	.											.	UBE2Q1	35	.	0			c.G452A						.						135	127	130					1																	154527989		2203	4300	6503	SO:0001583	missense	55585	exon3			ATGATCCTCTTCA	AJ243666	CCDS1069.1	1q22	2008-05-02	2008-05-02	2005-08-05	ENSG00000160714	ENSG00000160714		"Ubiquitin-conjugating enzymes E2"	15698	protein-coding gene	gene with protein product			"ubiquitin-conjugating enzyme E2Q (putative)"	UBE2Q			Standard	NM_017582		Approved	PRO3094, NICE-5	uc001fff.1	Q7Z7E8	OTTHUMG00000037265	ENST00000292211.4:c.452G>A	chr1.hg19:g.154527989C>T	ENSP00000292211:p.Arg151Lys	70.0	0.0		99.0	21.0	NM_017582	B4DF92|Q3B841|Q5I0X2|Q6IS04|Q6P7P2|Q96MV4|Q9BVX5|Q9UGL6	Missense_Mutation	SNP	ENST00000292211.4	hg19	CCDS1069.1	.	.	.	.	.	.	.	.	.	.	C	14.41	2.526163	0.44969	.	.	ENSG00000160714	ENST00000292211	T	0.42513	0.97	4.52	3.6	0.41247	.	0.060403	0.64402	D	0.000003	T	0.15435	0.0372	L	0.32530	0.975	0.33822	D	0.629146	B	0.14438	0.01	B	0.10450	0.005	T	0.06391	-1.0829	10	0.29301	T	0.29	-16.7599	11.8151	0.52204	0.0:0.913:0.0:0.087	.	151	Q7Z7E8	UB2Q1_HUMAN	K	151	ENSP00000292211:R151K	ENSP00000292211:R151K	R	-	2	0	UBE2Q1	152794613	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.407000	0.59754	1.265000	0.44215	0.455000	0.32223	AGG	.	.		0.512	UBE2Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090704.1	NM_017582		T	154527989	C	T	154527989	3	4	245	1	0	0	0	0	1	0	0	0	16884	681	24	3	860	3	UBE2Q1	1	154527989	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	603973	154527989	94722632	19	33489										
DCST1	149095	hgsc.bcm.edu	37	chr1	155023119	155023119	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ccgctggcggatatcctgcaCcgcggctgcccgctcctgcg	13	18	0	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr1:155023119C>A	ENST00000295542.1	+	17	1992	c.1896C>A	c.(1894-1896)caC>caA	p.H632Q	ADAM15_ENST00000447332.3_5'Flank|ADAM15_ENST00000355956.2_5'Flank|ADAM15_ENST00000368412.3_5'Flank|DCST1_ENST00000423025.2_Missense_Mutation_p.H607Q|ADAM15_ENST00000356955.2_5'Flank|ADAM15_ENST00000449910.2_5'Flank|ADAM15_ENST00000271836.6_5'Flank|ADAM15_ENST00000368410.2_5'Flank|ADAM15_ENST00000360674.4_5'Flank|ADAM15_ENST00000531455.1_5'Flank|ADAM15_ENST00000368413.1_5'Flank|ADAM15_ENST00000359280.4_5'Flank	NM_152494.3	NP_689707.2	Q5T197	DCST1_HUMAN	DC-STAMP domain containing 1	632						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	27	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)			ATATCCTGCACCGCGGCTGCC	0.711											OREG0013846	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.H632Q		Atlas-SNP	.											.	DCST1	69	.	0			c.C1896A						.						7	9	8					1																	155023119		2062	4078	6140	SO:0001583	missense	149095	exon17			CCTGCACCGCGGC	AK057347	CCDS1083.1, CCDS44235.1	1q22	2008-02-05			ENSG00000163357	ENSG00000163357			26539	protein-coding gene	gene with protein product							Standard	NM_152494		Approved	FLJ32785	uc001fgn.2	Q5T197	OTTHUMG00000041314	ENST00000295542.1:c.1896C>A	chr1.hg19:g.155023119C>A	ENSP00000295542:p.His632Gln	19.0	0.0	1767	27.0	10.0	NM_152494	B4DXA0|E9PHV3|Q5T198|Q6P1W6|Q71S70|Q96M70	Missense_Mutation	SNP	ENST00000295542.1	hg19	CCDS1083.1	.	.	.	.	.	.	.	.	.	.	C	14.18	2.457415	0.43634	.	.	ENSG00000163357	ENST00000295542;ENST00000423025	T;T	0.21734	1.99;2.0	5.02	1.98	0.26296	.	1.256760	0.06619	U	0.757118	T	0.05364	0.0142	L	0.29908	0.895	0.80722	D	1	B;B	0.20459	0.045;0.045	B;B	0.16722	0.016;0.016	T	0.34079	-0.9843	10	0.29301	T	0.29	-17.4989	4.6556	0.12615	0.0:0.5704:0.1606:0.269	.	607;632	E9PHV3;Q5T197	.;DCST1_HUMAN	Q	632;607	ENSP00000295542:H632Q;ENSP00000387369:H607Q	ENSP00000295542:H632Q	H	+	3	2	DCST1	153289743	0.995000	0.38212	0.998000	0.56505	0.609000	0.37215	0.326000	0.19646	0.122000	0.18314	0.655000	0.94253	CAC	.	.		0.711	DCST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099006.1	NM_152494		A	155023119	C	A	155023119	3	1	245	1	0	0	0	0	1	0	0	0	4304	506	18	3	1958	3	DCST1	1	155023119	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	495130	155023119	94227502	20	33490										
AIM2	9447	hgsc.bcm.edu	37	chr1	159043068	159043068	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	agacgttttgccaaaagcatAtaattcaacttctgaaaaat	5	7	2	2	rs145394745		TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr1:159043068A>G	ENST00000368130.4	-	2	510	c.222T>C	c.(220-222)taT>taC	p.Y74Y	AIM2_ENST00000411768.1_5'UTR	NM_004833.1	NP_004824.1	O14862	AIM2_HUMAN	absent in melanoma 2	74	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.				activation of innate immune response (GO:0002218)|apoptotic process (GO:0006915)|cellular response to drug (GO:0035690)|cellular response to interferon-beta (GO:0035458)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta secretion (GO:0050702)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein oligomerization (GO:0032461)|pyroptosis (GO:0070269)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	AIM2 inflammasome complex (GO:0097169)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)			breast(1)|large_intestine(1)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(1)	16	all_hematologic(112;0.0429)					CCAAAAGCATATAATTCAACT	0.453																																					p.Y74Y		Atlas-SNP	.											.	AIM2	70	.	0			c.T222C						.	A		0,4406		0,0,2203	83	85	84		222	-3.9	0	1	dbSNP_134	84	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	AIM2	NM_004833.1		0,1,6502	GG,GA,AA		0.0116,0.0,0.0077		74/344	159043068	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9447	exon2			AAGCATATAATTC	AF024714	CCDS1181.1	1q22	2008-07-18			ENSG00000163568	ENSG00000163568			357	protein-coding gene	gene with protein product		604578				9242382	Standard	NM_004833		Approved	PYHIN4	uc001ftj.1	O14862	OTTHUMG00000037183	ENST00000368130.4:c.222T>C	chr1.hg19:g.159043068A>G		168.0	0.0		228.0	82.0	NM_004833	A8K7M7|Q5T3V9|Q96FG9	Silent	SNP	ENST00000368130.4	hg19	CCDS1181.1																																																																																			.	A|1.000;G|0.000		0.453	AIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090341.1	NM_004833		G	159043068	A	G	159043068	2	3	245	1	0	0	0	0	0	0	0	1	432	456	16	2		2	AIM2	1	159043068	Silent	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	4019949	159043068	90207553	21	33491										
NCSTN	23385	hgsc.bcm.edu	37	chr1	160323960	160323960	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tggtgctggtgtccctgctgTcatcctcaggaggccaaatc	12	12	2	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr1:160323960T>G	ENST00000294785.5	+	11	1357	c.1232T>G	c.(1231-1233)gTc>gGc	p.V411G	NCSTN_ENST00000535857.1_Missense_Mutation_p.V273G|NCSTN_ENST00000368063.1_Missense_Mutation_p.V391G|NCSTN_ENST00000368065.4_Missense_Mutation_p.V153G|NCSTN_ENST00000392212.4_Missense_Mutation_p.V391G|NCSTN_ENST00000459963.1_3'UTR	NM_015331.2	NP_056146.1	Q92542	NICA_HUMAN	nicastrin	411					amyloid precursor protein catabolic process (GO:0042987)|apoptotic signaling pathway (GO:0097190)|beta-amyloid metabolic process (GO:0050435)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|myeloid cell homeostasis (GO:0002262)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|protein processing (GO:0016485)|proteolysis (GO:0006508)|T cell proliferation (GO:0042098)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	endopeptidase activity (GO:0004175)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(2)	34	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GTCCCTGCTGTCATCCTCAGG	0.577																																					p.V411G		Atlas-SNP	.											.	NCSTN	64	.	0			c.T1232G						.						155	122	133					1																	160323960		2203	4300	6503	SO:0001583	missense	23385	exon11			CTGCTGTCATCCT	AF240468	CCDS1203.1	1q22-q23	2014-09-17			ENSG00000162736	ENSG00000162736			17091	protein-coding gene	gene with protein product		605254				9039502, 10993067	Standard	XM_005245053		Approved	KIAA0253, APH2	uc001fvx.3	Q92542	OTTHUMG00000033110	ENST00000294785.5:c.1232T>G	chr1.hg19:g.160323960T>G	ENSP00000294785:p.Val411Gly	131.0	0.0		145.0	39.0	NM_015331	Q5T207|Q5T208|Q86VV5	Missense_Mutation	SNP	ENST00000294785.5	hg19	CCDS1203.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	22.1|22.1	4.244750|4.244750	0.79912|0.79912	.|.	.|.	ENSG00000162736|ENSG00000162736	ENST00000424645;ENST00000435149|ENST00000294785;ENST00000368063;ENST00000535857;ENST00000368067;ENST00000392212;ENST00000368065;ENST00000424754	.|T;T;T;T;T;T	.|0.71579	.|-0.58;-0.58;-0.58;-0.58;-0.58;-0.58	5.3|5.3	5.3|5.3	0.74995|0.74995	.|.	.|0.122362	.|0.56097	.|D	.|0.000035	T|T	0.74465|0.74465	0.3720|0.3720	M|M	0.66939|0.66939	2.045|2.045	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.76494	.|0.999;0.998;0.998	.|D;D;D	.|0.69824	.|0.933;0.929;0.966	T|T	0.72616|0.72616	-0.4239|-0.4239	5|10	.|0.20519	.|T	.|0.43	-21.6824|-21.6824	14.0769|14.0769	0.64895|0.64895	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|273;391;411	.|F6Y097;Q92542-2;Q92542	.|.;.;NICA_HUMAN	A|G	247;88|411;391;273;118;391;153;155	.|ENSP00000294785:V411G;ENSP00000357042:V391G;ENSP00000442605:V273G;ENSP00000376047:V391G;ENSP00000357044:V153G;ENSP00000410124:V155G	.|ENSP00000294785:V411G	S|V	+|+	1|2	0|0	NCSTN|NCSTN	158590584|158590584	0.982000|0.982000	0.34865|0.34865	0.045000|0.045000	0.18777|0.18777	0.996000|0.996000	0.88848|0.88848	4.813000|4.813000	0.62620|0.62620	2.022000|2.022000	0.59522|0.59522	0.533000|0.533000	0.62120|0.62120	TCA|GTC	.	.		0.577	NCSTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080622.1	NM_015331		G	160323960	T	G	160323960	3	3	245	1	0	0	0	0	1	0	0	0	10250	1667	58	5	1274	5	NCSTN	1	160323960	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	1280892	160323960	88926661	22	33492										
ATF6	22926	hgsc.bcm.edu	37	chr1	161832997	161832997	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tcttactttagcaggaactcAgggagtgagctacaagtgta	11	7	2	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr1:161832997A>T	ENST00000367942.3	+	14	1681	c.1614A>T	c.(1612-1614)tcA>tcT	p.S538S		NM_007348.3	NP_031374.2	P18850	ATF6A_HUMAN	activating transcription factor 6	538	Interaction with THBS4.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response (GO:0006990)|protein folding (GO:0006457)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to stress (GO:0006950)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(14)|ovary(3)|skin(1)|stomach(1)	34	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.00953)		Pseudoephedrine(DB00852)	GCAGGAACTCAGGGAGTGAGC	0.358																																					p.S538S		Atlas-SNP	.											.	ATF6	84	.	0			c.A1614T						.						103	100	101					1																	161832997		2203	4300	6503	SO:0001819	synonymous_variant	22926	exon14			GAACTCAGGGAGT	AB015856	CCDS1235.1	1q22-q23	2013-01-10			ENSG00000118217	ENSG00000118217		"basic leucine zipper proteins"	791	protein-coding gene	gene with protein product	"activating transcription factor 6 alpha"	605537				9837962, 9271374, 11256944	Standard	NM_007348		Approved	ATF6A	uc001gbs.3	P18850	OTTHUMG00000023961	ENST00000367942.3:c.1614A>T	chr1.hg19:g.161832997A>T		172.0	0.0		225.0	65.0	NM_007348	O15139|Q5VW62|Q6IPB5|Q9UEC9	Silent	SNP	ENST00000367942.3	hg19	CCDS1235.1																																																																																			.	.		0.358	ATF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060304.2	NM_007348		T	161832997	A	T	161832997	2	4	245	1	0	0	0	0	0	0	0	1	1084	175	7	4		4	ATF6	1	161832997	Silent	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	1509037	161832997	87417624	23	33493										
ASTN1	460	hgsc.bcm.edu	37	chr1	176915125	176915125	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	aatggttgttgtaaccaaagAacatctccccaaagagggtc	9	9	1	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr1:176915125A>G	ENST00000367654.3	-	13	2421	c.2210T>C	c.(2209-2211)tTc>tCc	p.F737S	ASTN1_ENST00000367657.3_Missense_Mutation_p.F729S|ASTN1_ENST00000361833.2_Missense_Mutation_p.F729S|ASTN1_ENST00000281881.3_5'UTR|ASTN1_ENST00000424564.2_Missense_Mutation_p.F729S	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	737					locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						GTAACCAAAGAACATCTCCCC	0.498																																					p.F729S		Atlas-SNP	.											.	ASTN1	314	.	0			c.T2186C						.						122	122	122					1																	176915125		2203	4300	6503	SO:0001583	missense	460	exon13			CCAAAGAACATCT	AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"astrotactin"	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.2210T>C	chr1.hg19:g.176915125A>G	ENSP00000356626:p.Phe737Ser	116.0	0.0		144.0	39.0	NM_004319	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Missense_Mutation	SNP	ENST00000367654.3	hg19		.	.	.	.	.	.	.	.	.	.	A	24.9	4.579551	0.86645	.	.	ENSG00000152092	ENST00000367657;ENST00000361833;ENST00000367654;ENST00000424564;ENST00000541808	T;T;T;T	0.15718	2.4;2.82;2.82;2.41	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.27697	0.0681	N	0.19112	0.55	0.80722	D	1	D;D;D	0.69078	0.997;0.981;0.981	D;D;D	0.78314	0.991;0.972;0.972	T	0.08868	-1.0701	10	0.72032	D	0.01	-33.8887	14.8389	0.70209	1.0:0.0:0.0:0.0	.	737;729;729	O14525;O14525-2;B1AJS1	ASTN1_HUMAN;.;.	S	729;729;737;729;729	ENSP00000356629:F729S;ENSP00000354536:F729S;ENSP00000356626:F737S;ENSP00000395041:F729S	ENSP00000354536:F729S	F	-	2	0	ASTN1	175181748	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.647000	0.91057	1.997000	0.58415	0.533000	0.62120	TTC	.	.		0.498	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319		G	176915125	A	G	176915125	3	3	245	1	0	0	0	0	1	0	0	0	1064	246	9	2	1746	2	ASTN1	1	176915125	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	15082128	176915125	72335496	24	33494										
RGS16	6004	hgsc.bcm.edu	37	chr1	182569551	182569551	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ggtaggagtccttctccatcAgggtacgtgtcttcccctga	11	12	3	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr1:182569551A>T	ENST00000367558.5	-	5	633	c.485T>A	c.(484-486)cTg>cAg	p.L162Q		NM_002928.3	NP_002919.3	O15492	RGS16_HUMAN	regulator of G-protein signaling 16	162	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)			NS(1)|endometrium(3)|large_intestine(2)|lung(4)|ovary(1)	11						CTTCTCCATCAGGGTACGTGT	0.602																																					p.L162Q		Atlas-SNP	.											.	RGS16	25	.	0			c.T485A						.						163	130	141					1																	182569551		2203	4300	6503	SO:0001583	missense	6004	exon5			TCCATCAGGGTAC	U70426	CCDS1348.1	1q25-q31	2008-02-05	2007-08-14		ENSG00000143333	ENSG00000143333		"Regulators of G-protein signaling"	9997	protein-coding gene	gene with protein product		602514	"regulator of G-protein signalling 16"			9469939	Standard	NM_002928		Approved	A28-RGS14, RGS-r	uc001gpl.4	O15492	OTTHUMG00000035212	ENST00000367558.5:c.485T>A	chr1.hg19:g.182569551A>T	ENSP00000356529:p.Leu162Gln	75.0	0.0		73.0	21.0	NM_002928	B2R4M4|Q5VYN9|Q99701	Missense_Mutation	SNP	ENST00000367558.5	hg19	CCDS1348.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.542476	0.85917	.	.	ENSG00000143333	ENST00000367558	T	0.38722	1.12	5.38	5.38	0.77491	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);	0.000000	0.85682	D	0.000000	T	0.76870	0.4048	H	0.97365	3.99	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85663	0.1290	10	0.87932	D	0	.	15.0472	0.71835	1.0:0.0:0.0:0.0	.	162	O15492	RGS16_HUMAN	Q	162	ENSP00000356529:L162Q	ENSP00000356529:L162Q	L	-	2	0	RGS16	180836174	1.000000	0.71417	0.893000	0.35052	0.663000	0.39108	9.004000	0.93583	2.042000	0.60477	0.454000	0.30748	CTG	.	.		0.602	RGS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085188.1	NM_002928		T	182569551	A	T	182569551	3	4	245	1	0	0	0	0	1	0	0	0	13313	188	7	4	127	4	RGS16	1	182569551	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	5654426	182569551	66681070	25	33495										
KCNK2	3776	hgsc.bcm.edu	37	chr1	215345508	215345508	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tcactctaacaactattggaTttggtgactacgttgcaggt	9	8	2	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr1:215345508T>A	ENST00000444842.2	+	5	955	c.805T>A	c.(805-807)Ttt>Att	p.F269I	KCNK2_ENST00000391895.2_Missense_Mutation_p.F265I|KCNK2_ENST00000391894.2_Missense_Mutation_p.F254I	NM_001017425.2|NM_014217.3	NP_001017425.2|NP_055032.1	O95069	KCNK2_HUMAN	potassium channel, subfamily K, member 2	269					G-protein coupled receptor signaling pathway (GO:0007186)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	outward rectifier potassium channel activity (GO:0015271)|potassium channel inhibitor activity (GO:0019870)|potassium ion leak channel activity (GO:0022841)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|upper_aerodigestive_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(81;0.0399)|all cancers(67;0.0556)|GBM - Glioblastoma multiforme(131;0.068)	Dofetilide(DB00204)|Dronedarone(DB04855)	AACTATTGGATTTGGTGACTA	0.408																																					p.F269I		Atlas-SNP	.											.	KCNK2	135	.	0			c.T805A						.						152	127	136					1																	215345508		2203	4300	6503	SO:0001583	missense	3776	exon5			ATTGGATTTGGTG	AF004711	CCDS31024.1, CCDS41466.1, CCDS41467.1	1q41	2012-03-07			ENSG00000082482	ENSG00000082482		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6277	protein-coding gene	gene with protein product		603219				9721223, 16382106	Standard	NM_001017424		Approved	K2p2.1, TREK-1	uc001hkr.4	O95069	OTTHUMG00000037017	ENST00000444842.2:c.805T>A	chr1.hg19:g.215345508T>A	ENSP00000394033:p.Phe269Ile	107.0	0.0		158.0	22.0	NM_001017425	A1Z1V3|A8K618|B2RCS4|B7ZL56|D3DTA5|Q5DP47|Q5DP48|Q9NRT2|Q9UNE3	Missense_Mutation	SNP	ENST00000444842.2	hg19	CCDS41467.1	.	.	.	.	.	.	.	.	.	.	T	26.5	4.743789	0.89663	.	.	ENSG00000082482	ENST00000391895;ENST00000391894;ENST00000444842	T;T;T	0.29655	1.56;1.56;1.56	5.5	5.5	0.81552	Ion transport 2 (1);	0.000000	0.85682	D	0.000000	T	0.57184	0.2036	M	0.82132	2.575	0.80722	D	1	D;D;P	0.63880	0.957;0.993;0.46	P;D;B	0.67382	0.781;0.951;0.327	T	0.61987	-0.6949	10	0.56958	D	0.05	.	15.6222	0.76816	0.0:0.0:0.0:1.0	.	254;269;265	O95069-2;O95069;O95069-3	.;KCNK2_HUMAN;.	I	265;254;269	ENSP00000375765:F265I;ENSP00000375764:F254I;ENSP00000394033:F269I	ENSP00000375764:F254I	F	+	1	0	KCNK2	213412131	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.040000	0.89188	2.087000	0.62958	0.460000	0.39030	TTT	.	.		0.408	KCNK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089856.2	NM_014217		A	215345508	T	A	215345508	3	1	245	1	0	0	0	0	1	0	0	0	8075	1493	52	4	866	4	KCNK2	1	215345508	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	32775957	215345508	33905113	26	33496										
C1orf35	79169	hgsc.bcm.edu	37	chr1	228290668	228290668	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tcctcctcgcggctcgggccCgcgcatggcgcccggccctt	13	20	0	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr1:228290668C>A	ENST00000272139.4	-	2	411	c.177G>T	c.(175-177)gcG>gcT	p.A59A	C1orf35_ENST00000472617.1_5'UTR	NM_024319.2	NP_077295.1	Q9BU76	MMTA2_HUMAN	chromosome 1 open reading frame 35	59							poly(A) RNA binding (GO:0044822)			large_intestine(1)|lung(1)|skin(1)	3		Prostate(94;0.0488)				GGCTCGGGCCCGCGCATGGCG	0.751																																					p.A59A		Atlas-SNP	.											.	C1orf35	17	.	0			c.G177T						.						2	3	2					1																	228290668		1419	3164	4583	SO:0001819	synonymous_variant	79169	exon2			CGGGCCCGCGCAT	AY137773	CCDS1566.1	1q42.13	2012-06-25			ENSG00000143793	ENSG00000143793			19032	protein-coding gene	gene with protein product	"multiple myeloma tumor-associated protein 2"					12545221	Standard	NM_024319		Approved	MGC4174, MMTAG2	uc001hrx.3	Q9BU76	OTTHUMG00000037793	ENST00000272139.4:c.177G>T	chr1.hg19:g.228290668C>A		14.0	0.0		27.0	18.0	NM_024319	Q6P5Y0|Q6ZTZ6|Q6ZWA6|Q8IZH3	Silent	SNP	ENST00000272139.4	hg19	CCDS1566.1																																																																																			.	.		0.751	C1orf35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092245.1	NM_024319		A	228290668	C	A	228290668	2	1	245	1	0	0	0	0	0	0	0	1	2040	639	23	1		1	C1orf35	1	228290668	Silent	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	12945160	228290668	20959953	27	33497										
DISC1	27185	hgsc.bcm.edu	37	chr1	232144628	232144628	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tccaggaagccaggggaagcCtgtctgtagaagatgagagg	16	7	1	3			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr1:232144628C>A	ENST00000439617.2	+	11	2193	c.2140C>A	c.(2140-2142)Ctg>Atg	p.L714M	DISC1_ENST00000537876.1_3'UTR|DISC1_ENST00000366637.3_Missense_Mutation_p.L46M|DISC1_ENST00000427560.1_3'UTR|DISC1_ENST00000535983.1_Silent_p.A693A	NM_001164537.1|NM_001164540.1|NM_018662.2	NP_001158009.1|NP_001158012.1|NP_061132.2	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1	714	Interaction with ATF4 and ATF5.|Necessary and sufficient for interaction with PCNT and localization at the centrosome.				canonical Wnt signaling pathway (GO:0060070)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cerebral cortex radially oriented cell migration (GO:0021799)|microtubule cytoskeleton organization (GO:0000226)|mitochondrial calcium ion homeostasis (GO:0051560)|neuron migration (GO:0001764)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neuron projection development (GO:0010975)|regulation of synapse maturation (GO:0090128)|TOR signaling (GO:0031929)	cell junction (GO:0030054)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|postsynaptic membrane (GO:0045211)				breast(1)|cervix(1)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	15		all_cancers(173;0.0208)|Prostate(94;0.0975)				CAGGGGAAGCCTGTCTGTAGA	0.537																																					p.L746M		Atlas-SNP	.											.	DISC1	207	.	0			c.C2236A						.						63	65	64					1																	232144628		1963	4150	6113	SO:0001583	missense	27185	exon12			GGAAGCCTGTCTG	AF222980	CCDS31055.1, CCDS31056.1, CCDS53482.1, CCDS53483.1, CCDS53484.1, CCDS59205.1, CCDS59206.1, CCDS59207.1	1q42.1	2008-02-05			ENSG00000162946	ENSG00000162946			2888	protein-coding gene	gene with protein product		605210				10814723	Standard	NM_001164550		Approved		uc010pxh.2	Q9NRI5	OTTHUMG00000037835	ENST00000439617.2:c.2140C>A	chr1.hg19:g.232144628C>A	ENSP00000403888:p.Leu714Met	102.0	0.0		145.0	22.0	NM_001164537	A6NLH2|C4P091|C4P095|C4P0A1|C4P0A3|C4P0B3|C4P0B6|C4P0C1|C9J6D0|O75045|Q5VT44|Q5VT45|Q8IXJ0|Q8IXJ1|Q9BX19|Q9NRI3|Q9NRI4	Missense_Mutation	SNP	ENST00000439617.2	hg19		.	.	.	.	.	.	.	.	.	.	C	17.73	3.461168	0.63513	.	.	ENSG00000162946	ENST00000439617;ENST00000366637;ENST00000366638;ENST00000532576;ENST00000427560	T	0.09163	3.01	4.5	1.23	0.21249	.	0.821609	0.10223	N	0.700707	T	0.21718	0.0523	.	.	.	0.09310	N	1	D;D;D;D;D;D;D	0.71674	0.994;0.997;0.998;0.994;0.994;0.994;0.994	P;D;P;P;P;P;P	0.65010	0.864;0.931;0.904;0.864;0.878;0.878;0.878	T	0.12400	-1.0549	9	0.46703	T	0.11	-0.3675	4.5187	0.11949	0.0:0.5046:0.2565:0.239	.	746;592;746;714;592;714;714	C4P096;C4P094;E2QRA4;C4P098;F5H1F1;Q9NRI5-2;Q9NRI5	.;.;.;.;.;.;DISC1_HUMAN	M	714;714;746;592;46	ENSP00000403888:L714M	ENSP00000355597:L714M	L	+	1	2	DISC1	230211251	0.003000	0.15002	0.004000	0.12327	0.683000	0.39861	0.433000	0.21477	0.456000	0.26937	0.650000	0.86243	CTG	.	.		0.537	DISC1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000092351.2	NM_018662		A	232144628	C	A	232144628	3	1	245	1	0	0	0	0	1	0	0	0	4540	680	24	3	2918	3	DISC1	1	232144628	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	3853960	232144628	17105993	28	33498										
MTR	4548	hgsc.bcm.edu	37	chr1	237025590	237025590	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ttggccaccttatccctttcAtggaaaaagaaagagaagaa	8	8	1	3			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr1:237025590A>T	ENST00000366577.5	+	21	2645	c.2251A>T	c.(2251-2253)Atg>Ttg	p.M751L	MTR_ENST00000535889.1_Missense_Mutation_p.M700L	NM_000254.2	NP_000245.2	Q99707	METH_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase	751	B12-binding N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00666}.				cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|methylation (GO:0032259)|nervous system development (GO:0007399)|pteridine-containing compound metabolic process (GO:0042558)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	cobalamin binding (GO:0031419)|methionine synthase activity (GO:0008705)|S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	67	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)	TATCCCTTTCATGGAAAAAGA	0.448																																					p.M751L		Atlas-SNP	.											.	MTR	127	.	0			c.A2251T						.						156	158	158					1																	237025590		2203	4300	6503	SO:0001583	missense	4548	exon21			CCTTTCATGGAAA	U73338	CCDS1614.1, CCDS73054.1	1q43	2011-05-12			ENSG00000116984	ENSG00000116984	2.1.1.13		7468	protein-coding gene	gene with protein product		156570				8968735	Standard	NM_000254		Approved	cblG	uc001hyi.4	Q99707	OTTHUMG00000040060	ENST00000366577.5:c.2251A>T	chr1.hg19:g.237025590A>T	ENSP00000355536:p.Met751Leu	87.0	0.0		98.0	25.0	NM_000254	A1L4N8|A9Z1W4|B9EGF7|Q99713|Q99723	Missense_Mutation	SNP	ENST00000366577.5	hg19	CCDS1614.1	.	.	.	.	.	.	.	.	.	.	A	17.86	3.492167	0.64074	.	.	ENSG00000116984	ENST00000417743;ENST00000366577;ENST00000535889;ENST00000366576	T;T;D	0.81996	-0.21;-0.35;-1.56	5.23	5.23	0.72850	Methionine synthase, cobalamin (vitamin B12)-binding module, cap (4);	0.000000	0.85682	D	0.000000	T	0.77068	0.4076	L	0.35341	1.055	0.48696	D	0.999692	B;B;B	0.21071	0.051;0.051;0.051	B;B;B	0.24006	0.05;0.05;0.05	T	0.74019	-0.3799	10	0.51188	T	0.08	-30.9363	15.2972	0.73919	1.0:0.0:0.0:0.0	.	751;700;751	B7ZLW8;B7ZLW7;Q99707	.;.;METH_HUMAN	L	605;751;700;305	ENSP00000355536:M751L;ENSP00000441845:M700L;ENSP00000355535:M305L	ENSP00000355535:M305L	M	+	1	0	MTR	235092213	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	8.722000	0.91452	2.195000	0.70347	0.528000	0.53228	ATG	.	.		0.448	MTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096632.2	NM_000254		T	237025590	A	T	237025590	3	4	245	1	0	0	0	0	1	0	0	0	9967	217	8	4	2333	4	MTR	1	237025590	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	4880962	237025590	12225031	29	33499										
KIF26B	55083	hgsc.bcm.edu	37	chr1	245851297	245851297	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	cagaagcaactcgctgggcaGggcgacagtcagccactacg	13	13	1	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr1:245851297G>T	ENST00000407071.2	+	12	5452	c.5012G>T	c.(5011-5013)aGg>aTg	p.R1671M	KIF26B_ENST00000366518.4_Missense_Mutation_p.R1290M	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	1671	Ser-rich.				establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			TCGCTGGGCAGGGCGACAGTC	0.667																																					p.R1671M		Atlas-SNP	.											.	KIF26B	343	.	0			c.G5012T						.						6	9	8					1																	245851297		1994	4075	6069	SO:0001583	missense	55083	exon12			TGGGCAGGGCGAC	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"Kinesins"	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.5012G>T	chr1.hg19:g.245851297G>T	ENSP00000385545:p.Arg1671Met	64.0	0.0		73.0	38.0	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Missense_Mutation	SNP	ENST00000407071.2	hg19	CCDS44342.1	.	.	.	.	.	.	.	.	.	.	G	13.26	2.184440	0.38609	.	.	ENSG00000162849	ENST00000407071;ENST00000366518;ENST00000413001	T;T	0.80033	-1.33;-1.33	5.28	5.28	0.74379	.	.	.	.	.	D	0.89466	0.6723	M	0.75447	2.3	0.58432	D	0.999992	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.90593	0.4538	9	0.87932	D	0	.	17.0795	0.86594	0.0:0.0:1.0:0.0	.	1290;1671	B7WPD9;Q2KJY2	.;KI26B_HUMAN	M	1671;1290;1287	ENSP00000385545:R1671M;ENSP00000355475:R1290M	ENSP00000355475:R1290M	R	+	2	0	KIF26B	243917920	1.000000	0.71417	0.853000	0.33588	0.135000	0.20990	7.833000	0.86765	2.478000	0.83669	0.561000	0.74099	AGG	.	.		0.667	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354		T	245851297	G	T	245851297	3	4	245	1	0	0	0	0	1	0	0	0	8304	1000	35	3	5058	3	KIF26B	1	245851297	Missense_Mutation	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	8825707	245851297	3399324	30	33500										
AHCTF1	25909	hgsc.bcm.edu	37	chr1	247013752	247013752	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ttagtagtttcttcaactgcTggttccaacagctgagatga	9	8	2	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr1:247013752T>A	ENST00000391829.2	-	33	5679	c.5556A>T	c.(5554-5556)ccA>ccT	p.P1852P	AHCTF1_ENST00000366508.1_Silent_p.P1887P|AHCTF1_ENST00000326225.3_Silent_p.P1861P|AHCTF1_ENST00000470300.1_5'UTR			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	1852	Disordered. {ECO:0000250}.|Necessary for nuclear localization. {ECO:0000250}.				cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(6)|cervix(3)|endometrium(8)|kidney(6)|large_intestine(12)|liver(2)|lung(21)|ovary(5)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	74	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			CTTCAACTGCTGGTTCCAACA	0.348																																					p.P1861P	Colon(145;197 1800 4745 15099 26333)	Atlas-SNP	.											.	AHCTF1	187	.	0			c.A5583T						.						16	17	17					1																	247013752		2088	4227	6315	SO:0001819	synonymous_variant	25909	exon33			AACTGCTGGTTCC		CCDS1629.1, CCDS1629.2	1q44	2008-09-09			ENSG00000153207	ENSG00000153207			24618	protein-coding gene	gene with protein product	"ELYS transcription factor like protein TMBS62"	610853				11952839	Standard	NM_015446		Approved	ELYS	uc001ibv.2	Q8WYP5	OTTHUMG00000040706	ENST00000391829.2:c.5556A>T	chr1.hg19:g.247013752T>A		214.0	0.0		317.0	175.0	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Silent	SNP	ENST00000391829.2	hg19																																																																																				.	.		0.348	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446		A	247013752	T	A	247013752	2	1	245	1	0	0	0	0	0	0	0	1	408	1567	55	4		4	AHCTF1	1	247013752	Silent	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	1162455	247013752	2236869	31	33501										
OR2L3	391192	hgsc.bcm.edu	37	chr1	248224411	248224411	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	caaaagaatgtgtgtgctgaTgataacagggtcttggatca	12	5	2	3			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr1:248224411T>C	ENST00000359959.3	+	1	428	c.428T>C	c.(427-429)aTg>aCg	p.M143T	OR2L13_ENST00000366478.2_Intron	NM_001004687.1	NP_001004687.1	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L, member 3	143						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|large_intestine(7)|lung(28)|prostate(1)|skin(1)|urinary_tract(1)	41	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)			TGTGTGCTGATGATAACAGGG	0.428																																					p.M143T		Atlas-SNP	.											.	OR2L3	97	.	0			c.T428C						.						230	245	240					1																	248224411		2203	4300	6503	SO:0001583	missense	391192	exon1			TGCTGATGATAAC	AB065950	CCDS31104.1	1q44	2012-08-09			ENSG00000198128	ENSG00000198128		"GPCR / Class A : Olfactory receptors"	15009	protein-coding gene	gene with protein product							Standard	NM_001004687		Approved		uc001idx.1	Q8NG85	OTTHUMG00000040195	ENST00000359959.3:c.428T>C	chr1.hg19:g.248224411T>C	ENSP00000353044:p.Met143Thr	67.0	0.0		117.0	29.0	NM_001004687	B9EH44	Missense_Mutation	SNP	ENST00000359959.3	hg19	CCDS31104.1	.	.	.	.	.	.	.	.	.	.	.	8.564	0.878541	0.17395	.	.	ENSG00000198128	ENST00000359959	T	0.38240	1.15	1.91	1.91	0.25777	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38272	U	0.001749	T	0.48484	0.1502	M	0.79693	2.465	0.09310	N	1	P	0.38148	0.62	P	0.50378	0.639	T	0.41251	-0.9519	10	0.72032	D	0.01	.	6.0993	0.20039	0.0:0.1477:0.0:0.8523	.	143	Q8NG85	OR2L3_HUMAN	T	143	ENSP00000353044:M143T	ENSP00000353044:M143T	M	+	2	0	OR2L3	246291034	0.061000	0.20836	0.857000	0.33713	0.130000	0.20726	2.938000	0.48987	0.853000	0.35312	0.379000	0.24179	ATG	.	.		0.428	OR2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096852.1	NM_001004687		C	248224411	T	C	248224411	3	2	245	1	0	0	0	0	1	0	0	0	11017	1464	51	2	430	2	OR2L3	1	248224411	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	1210659	248224411	1026210	32	33502										
SNTG2	54221	hgsc.bcm.edu	37	chr2	1094065	1094065	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tctgagcacaacgtccctgtCgtcatatcaaaaatattcga	6	11	3	1	rs369324271		TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr2:1094065C>T	ENST00000308624.5	+	4	423	c.294C>T	c.(292-294)gtC>gtT	p.V98V	SNTG2_ENST00000407292.1_Intron	NM_018968.3	NP_061841.2	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2	98	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|syntrophin complex (GO:0016013)	PDZ domain binding (GO:0030165)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		ACGTCCCTGTCGTCATATCAA	0.383																																					p.V98V		Atlas-SNP	.											.	SNTG2	125	.	0			c.C294T						.	C		0,3768		0,0,1884	117	111	113		294	1.6	1	2		113	2,8210		0,2,4104	no	coding-synonymous	SNTG2	NM_018968.3		0,2,5988	TT,TC,CC		0.0244,0.0,0.0167		98/540	1094065	2,11978	1884	4106	5990	SO:0001819	synonymous_variant	54221	exon4			CCCTGTCGTCATA	AJ003029	CCDS46220.1	2p25	2008-05-23			ENSG00000172554	ENSG00000172554			13741	protein-coding gene	gene with protein product		608715				10747910	Standard	NM_018968		Approved	SYN5, G2SYN	uc002qwq.3	Q9NY99	OTTHUMG00000151370	ENST00000308624.5:c.294C>T	chr2.hg19:g.1094065C>T		180.0	0.0		156.0	36.0	NM_018968	Q05AH5	Silent	SNP	ENST00000308624.5	hg19	CCDS46220.1																																																																																			.	.		0.383	SNTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322454.1	NM_018968		T	1094065	C	T	1094065	2	4	245	1	0	0	0	0	0	0	0	1	14890	871	31	1		1	SNTG2	2	1094065	Silent	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10		1094065	242105308	33	33503										
MYT1L	23040	hgsc.bcm.edu	37	chr2	1926446	1926446	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ggcgtccttccggggaagtcCtcttctggccggacatgctg	14	13	2	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr2:1926446C>T	ENST00000399161.2	-	10	1842	c.1095G>A	c.(1093-1095)gaG>gaA	p.E365E	MYT1L_ENST00000428368.2_Silent_p.E365E	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	365					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		CGGGGAAGTCCTCTTCTGGCC	0.592																																					p.E365E		Atlas-SNP	.											.	MYT1L	241	.	0			c.G1095A						.						38	41	40					2																	1926446		2080	4214	6294	SO:0001819	synonymous_variant	23040	exon10			GAAGTCCTCTTCT	AF036943	CCDS46222.1	2p25.3	2013-01-10			ENSG00000186487	ENSG00000186487		"Zinc fingers, C2HC-type containing"	7623	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 1"	613084				9373037	Standard	XM_006711862		Approved	KIAA1106, NZF1, ZC2HC4B	uc002qxd.3	Q9UL68	OTTHUMG00000151407	ENST00000399161.2:c.1095G>A	chr2.hg19:g.1926446C>T		96.0	0.0		69.0	17.0	NM_015025	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Silent	SNP	ENST00000399161.2	hg19																																																																																				.	.		0.592	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025		T	1926446	C	T	1926446	2	4	245	1	0	0	0	0	0	0	0	1	10116	680	24	3		3	MYT1L	2	1926446	Silent	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	832381	1926446	241272927	34	33504										
SMC6	79677	hgsc.bcm.edu	37	chr2	17896176	17896176	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gaaactcagaaactattatcGgtggccgtgaggtccctggt	12	9	1	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr2:17896176G>A	ENST00000448223.2	-	16	1951	c.1682C>T	c.(1681-1683)cCg>cTg	p.P561L	SMC6_ENST00000351948.4_Missense_Mutation_p.P561L|SMC6_ENST00000402989.1_Missense_Mutation_p.P561L|SMC6_ENST00000381272.4_Missense_Mutation_p.P587L	NM_001142286.1	NP_001135758.1	Q96SB8	SMC6_HUMAN	structural maintenance of chromosomes 6	561	Flexible hinge.				cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|intracellular (GO:0005622)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			NS(1)|biliary_tract(1)|breast(6)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					AACTATTATCGGTGGCCGTGA	0.408																																					p.P561L		Atlas-SNP	.											.	SMC6	102	.	0			c.C1682T						.						109	106	107					2																	17896176		2203	4300	6503	SO:0001583	missense	79677	exon16			ATTATCGGTGGCC	AJ310551	CCDS1690.1	2p24.3	2008-02-05	2006-07-06	2006-07-06	ENSG00000163029	ENSG00000163029		"Structural maintenance of chromosomes proteins"	20466	protein-coding gene	gene with protein product		609387	"SMC6 structural maintenance of chromosomes 6-like 1 (yeast)"	SMC6L1		11230166	Standard	NM_024624		Approved	FLJ22116	uc002rcn.3	Q96SB8	OTTHUMG00000090675	ENST00000448223.2:c.1682C>T	chr2.hg19:g.17896176G>A	ENSP00000404092:p.Pro561Leu	100.0	0.0		106.0	9.0	NM_001142286	A8K8Q6|D6W518|Q05BV4|Q9H0X3|Q9H6M0	Missense_Mutation	SNP	ENST00000448223.2	hg19	CCDS1690.1	.	.	.	.	.	.	.	.	.	.	G	14.95	2.688544	0.48097	.	.	ENSG00000163029	ENST00000448223;ENST00000351948;ENST00000381272;ENST00000402989;ENST00000446852	T;T;T;T;T	0.33438	2.62;2.62;2.13;2.62;1.41	6.16	5.01	0.66863	RecF/RecN/SMC (1);	0.490255	0.24776	N	0.035700	T	0.15609	0.0376	N	0.08118	0	0.33300	D	0.564735	B;B;B	0.19817	0.039;0.005;0.014	B;B;B	0.20955	0.013;0.002;0.032	T	0.15665	-1.0429	10	0.08179	T	0.78	.	13.4742	0.61299	0.0:0.0:0.2466:0.7534	.	587;587;561	C9JMN1;Q96SB8-2;Q96SB8	.;.;SMC6_HUMAN	L	561;561;587;561;587	ENSP00000404092:P561L;ENSP00000323439:P561L;ENSP00000370672:P587L;ENSP00000384539:P561L;ENSP00000408644:P587L	ENSP00000323439:P561L	P	-	2	0	SMC6	17759657	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.559000	0.45888	1.152000	0.42452	-0.265000	0.10407	CCG	.	.		0.408	SMC6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207359.1	NM_024624		A	17896176	G	A	17896176	3	1	245	1	0	0	0	0	1	0	0	0	14802	1116	39	1	1645	1	SMC6	2	17896176	Missense_Mutation	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	15969730	17896176	225303197	35	33505										
SLC30A3	7781	hgsc.bcm.edu	37	chr2	27480785	27480785	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ggacgtacaacaggttggcaCagactgcgatgctggcggtc	15	10	0	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr2:27480785C>A	ENST00000233535.4	-	4	918	c.566G>T	c.(565-567)tGt>tTt	p.C189F	SLC30A3_ENST00000447008.2_Missense_Mutation_p.C184F	NM_003459.4	NP_003450.2	Q99726	ZNT3_HUMAN	solute carrier family 30 (zinc transporter), member 3	189					positive regulation of transport (GO:0051050)|regulation of sequestering of zinc ion (GO:0061088)|transmembrane transport (GO:0055085)|transport (GO:0006810)|zinc ion transmembrane transport (GO:0071577)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	zinc transporting ATPase activity (GO:0015633)			NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(11)|pancreas(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CAGGTTGGCACAGACTGCGAT	0.642																																					p.C189F		Atlas-SNP	.											.	SLC30A3	39	.	0			c.G566T						.						47	46	46					2																	27480785		2203	4300	6503	SO:0001583	missense	7781	exon4			TTGGCACAGACTG	U76010	CCDS1743.1	2p23.3	2013-05-22			ENSG00000115194	ENSG00000115194		"Solute carriers"	11014	protein-coding gene	gene with protein product		602878		ZNT3		8962159	Standard	NM_003459		Approved		uc002rjj.3	Q99726	OTTHUMG00000128409	ENST00000233535.4:c.566G>T	chr2.hg19:g.27480785C>A	ENSP00000233535:p.Cys189Phe	137.0	0.0		127.0	33.0	NM_003459	Q8TC03	Missense_Mutation	SNP	ENST00000233535.4	hg19	CCDS1743.1	.	.	.	.	.	.	.	.	.	.	C	13.00	2.107511	0.37145	.	.	ENSG00000115194	ENST00000233535;ENST00000447008;ENST00000432351;ENST00000426924;ENST00000424577	T;T;T;T;T	0.62498	0.02;0.02;0.02;0.02;0.02	5.34	5.34	0.76211	.	0.226724	0.45606	D	0.000359	T	0.43100	0.1232	N	0.04132	-0.27	0.38463	D	0.947264	B;B	0.15141	0.003;0.012	B;B	0.20577	0.018;0.03	T	0.39121	-0.9629	10	0.37606	T	0.19	-10.1632	16.9199	0.86161	0.0:1.0:0.0:0.0	.	184;189	F5H3B7;Q99726	.;ZNT3_HUMAN	F	189;184;140;176;167	ENSP00000233535:C189F;ENSP00000415226:C184F;ENSP00000414320:C140F;ENSP00000393545:C176F;ENSP00000403959:C167F	ENSP00000233535:C189F	C	-	2	0	SLC30A3	27334289	0.859000	0.29813	1.000000	0.80357	0.996000	0.88848	1.252000	0.32874	2.666000	0.90696	0.561000	0.74099	TGT	.	.		0.642	SLC30A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250189.2			A	27480785	C	A	27480785	3	1	245	1	0	0	0	0	1	0	0	0	14571	478	17	3	620	3	SLC30A3	2	27480785	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	9584609	27480785	215718588	36	33506										
SPAST	6683	hgsc.bcm.edu	37	chr2	32341205	32341205	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tagtggaacagctgttaaatTtgatgatatagctggtcaag	11	4	1	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr2:32341205T>A	ENST00000315285.3	+	7	1147	c.1022T>A	c.(1021-1023)tTt>tAt	p.F341Y	SPAST_ENST00000345662.1_Missense_Mutation_p.F309Y	NM_014946.3	NP_055761.2			spastin											breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(8)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					GCTGTTAAATTTGATGATATA	0.368																																					p.F341Y		Atlas-SNP	.											.	SPAST	61	.	0			c.T1022A						.						136	135	135					2																	32341205		2203	4300	6503	SO:0001583	missense	6683	exon7			TTAAATTTGATGA	AJ246001	CCDS1778.1, CCDS1779.1	2p24-p21	2014-09-17	2005-03-15	2005-03-17	ENSG00000021574	ENSG00000021574		"ATPases / AAA-type"	11233	protein-coding gene	gene with protein product		604277	"spastic paraplegia 4 (autosomal dominant; spastin)"	SPG4		10493830, 10610178	Standard	NM_014946		Approved	FSP2, ADPSP, KIAA1083	uc002roc.3	Q9UBP0	OTTHUMG00000128455	ENST00000315285.3:c.1022T>A	chr2.hg19:g.32341205T>A	ENSP00000320885:p.Phe341Tyr	95.0	0.0		80.0	29.0	NM_014946		Missense_Mutation	SNP	ENST00000315285.3	hg19	CCDS1778.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.845844	0.91277	.	.	ENSG00000021574	ENST00000345662;ENST00000315285	D;D	0.95307	-3.67;-3.67	5.58	5.58	0.84498	.	0.048853	0.85682	D	0.000000	D	0.94434	0.8209	L	0.33710	1.025	0.80722	D	1	D;P	0.59357	0.985;0.952	P;P	0.58172	0.834;0.761	D	0.95167	0.8286	10	0.72032	D	0.01	-44.0228	15.4125	0.74937	0.0:0.0:0.0:1.0	.	309;341	E5KRP6;Q9UBP0	.;SPAST_HUMAN	Y	309;341	ENSP00000340817:F309Y;ENSP00000320885:F341Y	ENSP00000320885:F341Y	F	+	2	0	SPAST	32194709	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	6.307000	0.72815	2.120000	0.65058	0.377000	0.23210	TTT	.	.		0.368	SPAST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250253.1	NM_199436		A	32341205	T	A	32341205	3	1	245	1	0	0	0	0	1	0	0	0	15012	1841	64	4	1048	4	SPAST	2	32341205	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	4860420	32341205	210858168	37	33507										
GTF2A1L	11036	hgsc.bcm.edu	37	chr2	48848041	48848041	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	taattgaaggagttcggaatCtatttgctgaagaaggtata	11	3	1	3			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr2:48848041C>G	ENST00000403751.3	+	2	110	c.73C>G	c.(73-75)Cta>Gta	p.L25V	GTF2A1L_ENST00000430487.2_Intron|STON1-GTF2A1L_ENST00000394754.1_Missense_Mutation_p.L729V|STON1-GTF2A1L_ENST00000309827.2_Missense_Mutation_p.L729V|STON1-GTF2A1L_ENST00000402114.2_Missense_Mutation_p.L729V|STON1-GTF2A1L_ENST00000394751.3_Missense_Mutation_p.L729V|GTF2A1L_ENST00000468326.1_3'UTR|STON1-GTF2A1L_ENST00000405008.1_Missense_Mutation_p.L729V	NM_006872.3	NP_006863.2	Q9UNN4	TF2AY_HUMAN	general transcription factor IIA, 1-like	25					cognition (GO:0050890)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|transcription factor TFIIA complex (GO:0005672)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			lung(7)	7		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AGTTCGGAATCTATTTGCTGA	0.299																																					p.L729V		Atlas-SNP	.											.	STON1-GTF2A1L	180	.	0			c.C2185G						.						60	60	60					2																	48848041		2203	4298	6501	SO:0001583	missense	286749	exon3			CGGAATCTATTTG	AF106857	CCDS46281.1, CCDS54359.1	2p16.3	2007-08-02			ENSG00000242441	ENSG00000242441			30727	protein-coding gene	gene with protein product	"TFIIA alpha/beta like factor"	605358				10364255, 11889132, 16525715	Standard	NM_006872		Approved	ALF		Q9UNN4	OTTHUMG00000152038	ENST00000403751.3:c.73C>G	chr2.hg19:g.48848041C>G	ENSP00000384597:p.Leu25Val	85.0	0.0		52.0	22.0	NM_001198594	B4DY14|Q53FD9|Q5D050	Missense_Mutation	SNP	ENST00000403751.3	hg19	CCDS46281.1	.	.	.	.	.	.	.	.	.	.	C	15.17	2.754370	0.49362	.	.	ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000242441;ENSG00000242441	ENST00000405008;ENST00000402114;ENST00000394754;ENST00000309827;ENST00000394751;ENST00000394749;ENST00000437125;ENST00000403751	T;T;T;T;T;T;T	0.45668	0.89;0.89;0.89;0.89;0.89;0.89;0.89	4.7	3.81	0.43845	Transcription factor IIA, alpha subunit, N-terminal (1);Transcription factor IIA, helical (1);	0.000000	0.64402	D	0.000005	T	0.58623	0.2135	L	0.58969	1.84	0.80722	D	1	B;D;D;D	0.76494	0.264;0.999;0.992;0.999	B;D;P;D	0.87578	0.03;0.998;0.883;0.997	T	0.61879	-0.6972	10	0.72032	D	0.01	.	12.2031	0.54337	0.0:0.9167:0.0:0.0833	.	729;729;25;729	A8MXJ1;B5MCF5;Q9UNN4;Q53S48	.;.;TF2AY_HUMAN;.	V	729;729;729;729;729;24;25;25	ENSP00000385499:L729V;ENSP00000385701:L729V;ENSP00000378236:L729V;ENSP00000311493:L729V;ENSP00000378234:L729V;ENSP00000396702:L25V;ENSP00000384597:L25V	ENSP00000384597:L25V	L	+	1	2	STON1-GTF2A1L;GTF2A1L	48701545	0.987000	0.35691	0.667000	0.29798	0.597000	0.36814	2.797000	0.47877	1.334000	0.45468	0.561000	0.74099	CTA	.	.		0.299	GTF2A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323852.4	NM_006872		G	48848041	C	G	48848041	3	3	245	1	0	0	0	0	1	0	0	0	6862	912	32	4	79	4	GTF2A1L	2	48848041	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	16506836	48848041	194351332	38	33508										
CNRIP1	25927	hgsc.bcm.edu	37	chr2	68544310	68544310	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ggcatggtgatctggatgggTtgccgttctccactcttcgt	13	10	3	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr2:68544310T>A	ENST00000263655.3	-	2	914	c.309A>T	c.(307-309)caA>caT	p.Q103H	CNRIP1_ENST00000409559.3_Missense_Mutation_p.Q103H|CNRIP1_ENST00000409862.1_Missense_Mutation_p.Q103H|CNRIP1_ENST00000481714.1_5'UTR	NM_015463.2	NP_056278.1	Q96F85	CNRP1_HUMAN	cannabinoid receptor interacting protein 1	103										kidney(1)|large_intestine(5)|liver(1)|lung(1)|skin(1)	9						TCTGGATGGGTTGCCGTTCTC	0.478																																					p.Q103H		Atlas-SNP	.											.	CNRIP1	45	.	0			c.A309T						.						189	163	172					2																	68544310		2203	4300	6503	SO:0001583	missense	25927	exon2			GATGGGTTGCCGT	AL110235	CCDS1886.1, CCDS46311.1	2p13	2008-02-05	2007-11-29	2007-11-29	ENSG00000119865	ENSG00000119865			24546	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 32"	C2orf32		12477932	Standard	NM_015463		Approved	DKFZP566K1924, CRIP1, CRIP1a, CRIP1b	uc002sek.4	Q96F85	OTTHUMG00000129565	ENST00000263655.3:c.309A>T	chr2.hg19:g.68544310T>A	ENSP00000263655:p.Gln103His	188.0	0.0		111.0	66.0	NM_001111101	B2R4D0|Q49AN4|Q9UFZ0	Missense_Mutation	SNP	ENST00000263655.3	hg19	CCDS1886.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.006418	0.74932	.	.	ENSG00000119865	ENST00000409559;ENST00000263655;ENST00000409862	.	.	.	5.16	-1.52	0.08637	.	0.000000	0.85682	D	0.000000	T	0.67202	0.2868	L	0.55990	1.75	0.53005	D	0.999962	D;D;D	0.89917	1.0;0.997;0.999	D;D;D	0.87578	0.998;0.958;0.997	T	0.67114	-0.5752	9	0.87932	D	0	-0.8663	12.7446	0.57273	0.0:0.6951:0.0:0.3049	.	103;103;103	B8ZZB8;Q96F85;Q96F85-2	.;CNRP1_HUMAN;.	H	103	.	ENSP00000263655:Q103H	Q	-	3	2	CNRIP1	68397814	0.999000	0.42202	0.992000	0.48379	0.998000	0.95712	0.466000	0.22019	-0.364000	0.08088	0.454000	0.30748	CAA	.	.		0.478	CNRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251758.1	NM_015463		A	68544310	T	A	68544310	3	1	245	1	0	0	0	0	1	0	0	0	3635	1722	60	4	254	4	CNRIP1	2	68544310	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	19696269	68544310	174655063	39	33509										
ZC3H6	376940	hgsc.bcm.edu	37	chr2	113067546	113067546	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gtaaagaatatgatgagtacAgcacctacagtgatgacaac	9	7	0	5			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr2:113067546A>T	ENST00000409871.1	+	4	822	c.421A>T	c.(421-423)Agc>Tgc	p.S141C	ZC3H6_ENST00000343936.4_Missense_Mutation_p.S141C	NM_198581.2	NP_940983.2	P61129	ZC3H6_HUMAN	zinc finger CCCH-type containing 6	141							metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(4)|prostate(2)	35						TGATGAGTACAGCACCTACAG	0.368																																					p.S141C		Atlas-SNP	.											.	ZC3H6	93	.	0			c.A421T						.						63	57	59					2																	113067546		1867	4098	5965	SO:0001583	missense	376940	exon4			GAGTACAGCACCT	AK123404	CCDS46393.1	2q13	2012-07-05	2005-06-02	2005-06-02	ENSG00000188177	ENSG00000188177		"Zinc fingers, CCCH-type domain containing"	24762	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 6"	ZC3HDC6			Standard	NM_198581		Approved	FLJ41410, FLJ45877, KIAA2035	uc002thq.1	P61129	OTTHUMG00000153286	ENST00000409871.1:c.421A>T	chr2.hg19:g.113067546A>T	ENSP00000386764:p.Ser141Cys	278.0	0.0		252.0	83.0	NM_198581	A9JR71|Q6ZW96	Missense_Mutation	SNP	ENST00000409871.1	hg19	CCDS46393.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.703558	0.88924	.	.	ENSG00000188177	ENST00000409871;ENST00000343936;ENST00000542974	T;T	0.18338	2.22;2.22	5.86	5.86	0.93980	.	0.101889	0.64402	D	0.000005	T	0.43722	0.1260	M	0.75264	2.295	0.58432	D	0.999992	D	0.89917	1.0	D	0.83275	0.996	T	0.39742	-0.9599	10	0.87932	D	0	-16.894	15.4305	0.75092	1.0:0.0:0.0:0.0	.	141	P61129	ZC3H6_HUMAN	C	141;141;118	ENSP00000386764:S141C;ENSP00000340298:S141C	ENSP00000340298:S141C	S	+	1	0	ZC3H6	112784017	1.000000	0.71417	0.998000	0.56505	0.947000	0.59692	4.494000	0.60347	2.233000	0.73108	0.459000	0.35465	AGC	.	.		0.368	ZC3H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330551.1	NM_198581		T	113067546	A	T	113067546	3	4	245	1	0	0	0	0	1	0	0	0	17586	188	7	4	435	4	ZC3H6	2	113067546	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	44523236	113067546	130131827	40	33510										
CSRNP3	80034	hgsc.bcm.edu	37	chr2	166535809	166535809	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ttatgccaactcttcaactcTgtattaccaaatagatagcc	4	11	3	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr2:166535809T>A	ENST00000342316.4	+	5	1576	c.1304T>A	c.(1303-1305)cTg>cAg	p.L435Q	CSRNP3_ENST00000409420.1_Missense_Mutation_p.L467Q|CSRNP3_ENST00000314499.7_Missense_Mutation_p.L435Q	NM_024969.3	NP_079245.2	Q8WYN3	CSRN3_HUMAN	cysteine-serine-rich nuclear protein 3	435					apoptotic process (GO:0006915)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|cervix(1)|endometrium(1)|large_intestine(9)|lung(15)|ovary(3)|skin(2)	33						TCTTCAACTCTGTATTACCAA	0.423																																					p.L435Q		Atlas-SNP	.											.	CSRNP3	73	.	0			c.T1304A						.						117	121	120					2																	166535809		2203	4300	6503	SO:0001583	missense	80034	exon7			CAACTCTGTATTA	AB063300	CCDS2225.1	2q24.3	2012-04-17	2009-01-07	2009-01-07	ENSG00000178662	ENSG00000178662		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	30729	protein-coding gene	gene with protein product	"TGF beta induced apotosis protein 2", "protein phosphatase 1, regulatory subunit 73"		"family with sequence similarity 130, member A2"	FAM130A2		17726538	Standard	NM_024969		Approved	FLJ32093, TAIP-2, PPP1R73	uc002udg.3	Q8WYN3	OTTHUMG00000132145	ENST00000342316.4:c.1304T>A	chr2.hg19:g.166535809T>A	ENSP00000344042:p.Leu435Gln	103.0	0.0		56.0	32.0	NM_001172173	B3KPR4|Q53SG0|Q6ZTX3|Q9HAF9	Missense_Mutation	SNP	ENST00000342316.4	hg19	CCDS2225.1	.	.	.	.	.	.	.	.	.	.	T	14.55	2.569117	0.45798	.	.	ENSG00000178662	ENST00000421875;ENST00000431452;ENST00000314499;ENST00000342316;ENST00000409420	T;T;T;T	0.58210	0.35;0.35;0.35;0.35	5.88	5.88	0.94601	.	0.217184	0.40908	D	0.000991	T	0.48519	0.1504	L	0.29908	0.895	0.39894	D	0.973807	P	0.46512	0.879	P	0.45377	0.478	T	0.52457	-0.8573	10	0.49607	T	0.09	-11.0577	16.3009	0.82811	0.0:0.0:0.0:1.0	.	435	Q8WYN3	CSRN3_HUMAN	Q	435;442;435;435;467	ENSP00000412081:L435Q;ENSP00000318258:L435Q;ENSP00000344042:L435Q;ENSP00000387195:L467Q	ENSP00000318258:L435Q	L	+	2	0	CSRNP3	166244055	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.574000	0.60900	2.246000	0.74042	0.533000	0.62120	CTG	.	.		0.423	CSRNP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255191.2	NM_024969		A	166535809	T	A	166535809	3	1	245	1	0	0	0	0	1	0	0	0	3967	1580	55	4	1318	4	CSRNP3	2	166535809	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	53468263	166535809	76663564	41	33511										
SLC25A12	8604	hgsc.bcm.edu	37	chr2	172666177	172666177	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	catctcttctggtaaatttgTcccgaacaaaatcattaacc	4	11	3	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr2:172666177T>A	ENST00000422440.2	-	13	1281	c.1244A>T	c.(1243-1245)gAc>gTc	p.D415V	SLC25A12_ENST00000392592.4_Missense_Mutation_p.D308V	NM_003705.4	NP_003696.2	O75746	CMC1_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 12	415					aspartate transport (GO:0015810)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|upper_aerodigestive_tract(1)	23			OV - Ovarian serous cystadenocarcinoma(117;0.216)		L-Aspartic Acid(DB00128)	GGTAAATTTGTCCCGAACAAA	0.398																																					p.D415V		Atlas-SNP	.											.	SLC25A12	59	.	0			c.A1244T						.						107	110	109					2																	172666177		2203	4300	6503	SO:0001583	missense	8604	exon13			AATTTGTCCCGAA	Y14494	CCDS33327.1	2q24	2013-05-22	2012-03-29		ENSG00000115840	ENSG00000115840		"Solute carriers", "EF-hand domain containing"	10982	protein-coding gene	gene with protein product		603667	"solute carrier family 25 (mitochondrial carrier, Aralar), member 12"			9722566, 10702666, 11566871	Standard	NM_003705		Approved	Aralar	uc002uhh.3	O75746	OTTHUMG00000134290	ENST00000422440.2:c.1244A>T	chr2.hg19:g.172666177T>A	ENSP00000388658:p.Asp415Val	213.0	0.0		165.0	33.0	NM_003705	B3KR64|Q96AM8	Missense_Mutation	SNP	ENST00000422440.2	hg19	CCDS33327.1	.	.	.	.	.	.	.	.	.	.	t	27.2	4.811540	0.90707	.	.	ENSG00000115840	ENST00000422440;ENST00000392592	T;T	0.79454	-1.27;-1.27	5.47	5.47	0.80525	Mitochondrial carrier domain (2);	0.085034	0.85682	D	0.000000	D	0.83737	0.5319	L	0.43701	1.375	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.74674	0.984;0.984	D	0.84899	0.0841	10	0.56958	D	0.05	-17.6289	15.5355	0.75998	0.0:0.0:0.0:1.0	.	308;415	B3KR64;O75746	.;CMC1_HUMAN	V	415;308	ENSP00000388658:D415V;ENSP00000376371:D308V	ENSP00000376371:D308V	D	-	2	0	SLC25A12	172374423	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.838000	0.86804	2.065000	0.61736	0.528000	0.53228	GAC	.	.		0.398	SLC25A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259010.2	NM_003705		A	172666177	T	A	172666177	3	1	245	1	0	0	0	0	1	0	0	0	14489	1667	58	4	816	4	SLC25A12	2	172666177	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	6130368	172666177	70533196	42	33512										
TTN	7273	hgsc.bcm.edu	37	chr2	179407911	179407911	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ccttcatttaaggaagtaacAgtgtgctctaggactgtggg	12	7	2	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr2:179407911A>T	ENST00000591111.1	-	297	92090	c.91866T>A	c.(91864-91866)acT>acA	p.T30622T	TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342992.6_Silent_p.T29695T|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Silent_p.T23390T|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000590807.1_RNA|RP11-65L3.4_ENST00000604692.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000589042.1_Silent_p.T32263T|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Silent_p.T23323T|TTN_ENST00000460472.2_Silent_p.T23198T|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000590040.1_RNA			Q8WZ42	TITIN_HUMAN	titin	30622	Fibronectin type-III 123. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGGAAGTAACAGTGTGCTCTA	0.458																																					p.T32263T		Atlas-SNP	.											.	TTN	18412	.	0			c.T96789A						.						231	221	225					2																	179407911		1927	4146	6073	SO:0001819	synonymous_variant	7273	exon347			AGTAACAGTGTGC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.91866T>A	chr2.hg19:g.179407911A>T		76.0	0.0		73.0	41.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.458	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179407911	A	T	179407911	2	4	245	1	0	0	0	0	0	0	0	1	16750	175	7	4		4	TTN	2	179407911	Silent	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	6741734	179407911	63791462	43	33513										
TTN	7273	hgsc.bcm.edu	37	chr2	179594820	179594820	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	aggagatgtagagaccagacCttttacaaagagagtggctt	12	6	0	4			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr2:179594820C>T	ENST00000591111.1	-	60	17580	c.17356G>A	c.(17356-17358)Gaa>Aaa	p.E5786K	TTN_ENST00000342992.6_Splice_Site_p.E4859K|TTN-AS1_ENST00000582847.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Splice_Site_p.E6103K|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron			Q8WZ42	TITIN_HUMAN	titin	12587					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GAGACCAGACCTTTTACAAAG	0.502																																					p.E6103K		Atlas-SNP	.											.	TTN	18412	.	0			c.G18307A						.						51	47	48					2																	179594820		1910	4121	6031	SO:0001630	splice_region_variant	7273	exon62			CCAGACCTTTTAC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.17356+1G>A	chr2.hg19:g.179594820C>T		50.0	0.0		34.0	12.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	15.99	2.994324	0.54041	.	.	ENSG00000155657	ENST00000342992	T	0.46819	0.86	5.69	5.69	0.88448	Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.62011	0.2393	L	0.41710	1.295	0.80722	D	1	D	0.69078	0.997	D	0.75020	0.985	T	0.55270	-0.8167	8	.	.	.	.	20.181	0.98201	0.0:1.0:0.0:0.0	.	5786	Q8WZ42	TITIN_HUMAN	K	4859	ENSP00000343764:E4859K	.	E	-	1	0	TTN	179303065	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.776000	0.85560	2.840000	0.97914	0.655000	0.94253	GAA	.	.		0.502	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	Missense_Mutation	T	179594820	C	T	179594820	5	4	245	1	0	0	0	0	0	0	1	0	16750	695	24	3	86426	3	TTN	2	179594820	Splice_Site	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	186909	179594820	63604553	44	33514										
TTN	7273	hgsc.bcm.edu	37	chr2	179611653	179611653	+	Intron	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tcggaacgccatatttcataAgctgaacccctctcttctgt	6	13	3	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr2:179611653A>C	ENST00000591111.1	-	46	10585				TTN_ENST00000360870.5_Silent_p.A5158A|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000589042.1_Intron|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000578746.1_RNA			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATATTTCATAAGCTGAACCCC	0.403																																					p.A5158A		Atlas-SNP	.											.	TTN	18412	.	0			c.T15474G						.						126	124	125					2																	179611653		2203	4299	6502	SO:0001627	intron_variant	7273	exon46			TTCATAAGCTGAA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10361-5005T>G	chr2.hg19:g.179611653A>C		80.0	0.0		78.0	26.0	NM_133379	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179611653	A	C	179611653	1	2	245	0	1	0	0	0	0	0	0	0	16750	59	3	5		5	TTN	2	179611653	Intron	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	16833	179611653	63587720	45	33515										
COL3A1	1281	hgsc.bcm.edu	37	chr2	189861938	189861938	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ggtggccctggaggacctggCcctcaggtacgtagctttcc	14	13	1	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr2:189861938C>A	ENST00000304636.3	+	25	1979	c.1809C>A	c.(1807-1809)ggC>ggA	p.G603G	COL3A1_ENST00000317840.5_Silent_p.G603G	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	603	Triple-helical region.				aging (GO:0007568)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell-matrix adhesion (GO:0007160)|cellular response to amino acid stimulus (GO:0071230)|cerebral cortex development (GO:0021987)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|digestive tract development (GO:0048565)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of immune response (GO:0050777)|negative regulation of neuron migration (GO:2001223)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|positive regulation of Rho protein signal transduction (GO:0035025)|response to cytokine (GO:0034097)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	collagen type III trimer (GO:0005586)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)	GAGGACCTGGCCCTCAGGTAC	0.433																																					p.G603G		Atlas-SNP	.											.	COL3A1	292	.	0			c.C1809A						.						144	146	146					2																	189861938		2203	4300	6503	SO:0001819	synonymous_variant	1281	exon25			ACCTGGCCCTCAG	X15332	CCDS2297.1	2q32.2	2014-09-17	2008-06-23		ENSG00000168542	ENSG00000168542		"Collagens"	2201	protein-coding gene	gene with protein product		120180	"Ehlers-Danlos syndrome type IV, autosomal dominant"	EDS4A		2780304, 2834369	Standard	NM_000090		Approved		uc002uqj.1	P02461	OTTHUMG00000132648	ENST00000304636.3:c.1809C>A	chr2.hg19:g.189861938C>A		121.0	0.0		84.0	39.0	NM_000090	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Silent	SNP	ENST00000304636.3	hg19	CCDS2297.1																																																																																			.	.		0.433	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090		A	189861938	C	A	189861938	2	1	245	1	0	0	0	0	0	0	0	1	3690	726	26	3		3	COL3A1	2	189861938	Silent	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	10250285	189861938	53337435	46	33516										
BMPR2	659	hgsc.bcm.edu	37	chr2	203379609	203379609	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	aacctgtttcctgttcttatAggagaccgtaaacaaggtct	8	9	2	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr2:203379609A>T	ENST00000374580.4	+	5	1068		c.e5-1		BMPR2_ENST00000374574.2_Splice_Site	NM_001204.6	NP_001195.2	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor, type II (serine/threonine kinase)						activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|brain development (GO:0007420)|cellular response to starvation (GO:0009267)|chondrocyte development (GO:0002063)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm formation (GO:0001707)|negative regulation of cell growth (GO:0030308)|negative regulation of chondrocyte proliferation (GO:1902731)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of vasoconstriction (GO:0045906)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of bone mineralization (GO:0030501)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|regulation of cell proliferation (GO:0042127)|regulation of lung blood pressure (GO:0014916)|retina vasculature development in camera-type eye (GO:0061298)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|venous blood vessel development (GO:0060841)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|fully spanning plasma membrane (GO:0044214)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	activin receptor activity, type II (GO:0016362)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(11)|lung(7)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	42						CTGTTCTTATAGGAGACCGTA	0.348																																					.		Atlas-SNP	.											.	BMPR2	142	.	0			c.530-2A>T						.						107	99	102					2																	203379609		2203	4300	6503	SO:0001630	splice_region_variant	659	exon5			TCTTATAGGAGAC	Z48923	CCDS33361.1	2q33-q34	2014-09-17			ENSG00000204217	ENSG00000204217			1078	protein-coding gene	gene with protein product		600799	"primary pulmonary hypertension 1"	PPH1		7791754	Standard	NM_001204		Approved	BRK-3, T-ALK, BMPR3, BMPR-II	uc002uzf.4	Q13873	OTTHUMG00000133617	ENST00000374580.4:c.530-1A>T	chr2.hg19:g.203379609A>T		59.0	0.0		60.0	19.0	NM_001204	Q13161|Q16569|Q4ZG08|Q53SA5|Q585T8	Splice_Site	SNP	ENST00000374580.4	hg19	CCDS33361.1	.	.	.	.	.	.	.	.	.	.	A	19.30	3.801825	0.70682	.	.	ENSG00000204217	ENST00000374580;ENST00000374574	.	.	.	5.92	5.92	0.95590	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3678	0.83341	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	BMPR2	203087854	1.000000	0.71417	0.934000	0.37439	0.597000	0.36814	8.630000	0.90987	2.254000	0.74563	0.528000	0.53228	.	.	.		0.348	BMPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257743.1	NM_001204	Intron	T	203379609	A	T	203379609	5	4	245	1	0	0	0	0	0	0	1	0	1471	434	15	4	546	4	BMPR2	2	203379609	Splice_Site	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	13517671	203379609	39819764	47	33517										
ADAM23	8745	hgsc.bcm.edu	37	chr2	207429764	207429764	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	aatgtgactgcacagaatccTggggtggctgcatcatggag	14	8	1	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr2:207429764T>A	ENST00000264377.3	+	14	1694	c.1366T>A	c.(1366-1368)Tgg>Agg	p.W456R	ADAM23_ENST00000374415.3_Missense_Mutation_p.W456R|ADAM23_ENST00000374416.1_Missense_Mutation_p.W456R	NM_003812.2	NP_003803.1	O75077	ADA23_HUMAN	ADAM metallopeptidase domain 23	456	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell adhesion (GO:0007155)|central nervous system development (GO:0007417)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|endometrium(6)|kidney(3)|large_intestine(5)|liver(2)|lung(22)|ovary(2)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	51				LUSC - Lung squamous cell carcinoma(261;0.0961)|Lung(261;0.182)|Epithelial(149;0.205)		CACAGAATCCTGGGGTGGCTG	0.363																																					p.W456R	Melanoma(194;1127 2130 19620 24042 27855)	Atlas-SNP	.											.	ADAM23	239	.	0			c.T1366A						.						182	179	180					2																	207429764		2203	4300	6503	SO:0001583	missense	8745	exon14			GAATCCTGGGGTG	AB009672	CCDS2369.1	2q33	2008-06-12	2005-08-18		ENSG00000114948	ENSG00000114948		"ADAM metallopeptidase domain containing"	202	protein-coding gene	gene with protein product		603710	"a disintegrin and metalloproteinase domain 23"			9693107	Standard	NM_003812		Approved	MDC3	uc002vbq.4	O75077	OTTHUMG00000132919	ENST00000264377.3:c.1366T>A	chr2.hg19:g.207429764T>A	ENSP00000264377:p.Trp456Arg	73.0	0.0		49.0	23.0	NM_003812	A2RU59	Missense_Mutation	SNP	ENST00000264377.3	hg19	CCDS2369.1	.	.	.	.	.	.	.	.	.	.	T	18.18	3.566111	0.65651	.	.	ENSG00000114948	ENST00000264377;ENST00000374416;ENST00000431817;ENST00000374415	T;T;T	0.08282	3.11;3.11;3.11	5.28	4.11	0.48088	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.52532	D	0.000077	T	0.16171	0.0389	L	0.55213	1.73	0.58432	D	0.999998	D	0.56521	0.976	P	0.58013	0.831	T	0.07693	-1.0759	10	0.16420	T	0.52	.	10.8285	0.46647	0.0:0.0747:0.0:0.9253	.	456	O75077	ADA23_HUMAN	R	456;456;350;456	ENSP00000264377:W456R;ENSP00000363537:W456R;ENSP00000363536:W456R	ENSP00000264377:W456R	W	+	1	0	ADAM23	207138009	1.000000	0.71417	1.000000	0.80357	0.833000	0.47200	6.005000	0.70716	0.825000	0.34637	0.460000	0.39030	TGG	.	.		0.363	ADAM23-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256431.2	NM_003812		A	207429764	T	A	207429764	3	1	245	1	0	0	0	0	1	0	0	0	245	1580	55	4	1420	4	ADAM23	2	207429764	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	4050155	207429764	35769609	48	33518										
STK36	27148	hgsc.bcm.edu	37	chr2	219553490	219553490	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ggtcctgagcagtcttctctCcagctgcagtgattctgttg	11	11	3	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr2:219553490C>T	ENST00000295709.3	+	12	1730	c.1451C>T	c.(1450-1452)tCc>tTc	p.S484F	STK36_ENST00000440309.1_Missense_Mutation_p.S484F|STK36_ENST00000392105.3_Missense_Mutation_p.S484F|STK36_ENST00000392106.2_Missense_Mutation_p.S484F	NM_015690.4	NP_056505.2			serine/threonine kinase 36											biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(20)|ovary(4)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	52		Renal(207;0.0915)		Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984)		AGTCTTCTCTCCAGCTGCAGT	0.567																																					p.S484F		Atlas-SNP	.											.	STK36	111	.	0			c.C1451T						.						177	159	165					2																	219553490		2203	4300	6503	SO:0001583	missense	27148	exon12			TTCTCTCCAGCTG	AB033104	CCDS2421.1, CCDS58750.1	2q35	2010-06-25	2010-06-25		ENSG00000163482	ENSG00000163482			17209	protein-coding gene	gene with protein product	"fused homolog (Drosophila)"	607652	"serine/threonine kinase 36 (fused homolog, Drosophila)"			10806483	Standard	NM_001243313		Approved	KIAA1278, FU	uc002viu.3	Q9NRP7	OTTHUMG00000133079	ENST00000295709.3:c.1451C>T	chr2.hg19:g.219553490C>T	ENSP00000295709:p.Ser484Phe	134.0	0.0		126.0	40.0	NM_015690		Missense_Mutation	SNP	ENST00000295709.3	hg19	CCDS2421.1	.	.	.	.	.	.	.	.	.	.	C	15.02	2.710289	0.48517	.	.	ENSG00000163482	ENST00000295709;ENST00000392106;ENST00000392105;ENST00000440309	T;T;T;T	0.69435	-0.4;-0.4;0.72;-0.4	5.38	4.5	0.54988	Armadillo-like helical (1);	0.516425	0.16439	N	0.214399	T	0.51244	0.1663	N	0.19112	0.55	0.30533	N	0.767276	P;P	0.37636	0.603;0.468	B;B	0.33042	0.157;0.075	T	0.58999	-0.7536	10	0.87932	D	0	-5.8795	13.6629	0.62378	0.0:0.6794:0.3206:0.0	.	484;484	Q9NRP7-2;Q9NRP7	.;STK36_HUMAN	F	484	ENSP00000295709:S484F;ENSP00000375955:S484F;ENSP00000375954:S484F;ENSP00000394095:S484F	ENSP00000295709:S484F	S	+	2	0	STK36	219261734	0.207000	0.23482	1.000000	0.80357	0.988000	0.76386	1.110000	0.31147	1.480000	0.48289	-0.211000	0.12701	TCC	.	.		0.567	STK36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256723.2			T	219553490	C	T	219553490	3	4	245	1	0	0	0	0	1	0	0	0	15317	855	30	3	1493	3	STK36	2	219553490	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	12123726	219553490	23645883	49	33519										
SPEG	10290	hgsc.bcm.edu	37	chr2	220341676	220341676	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tgcggtggtggtcgagggaaAaccactgccggacatcatgt	15	9	1	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr2:220341676A>T	ENST00000312358.7	+	19	4664	c.4532A>T	c.(4531-4533)aAa>aTa	p.K1511I	SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	1511	Ig-like 8.				cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		GTCGAGGGAAAACCACTGCCG	0.632																																					p.K1511I		Atlas-SNP	.											.	SPEG	272	.	0			c.A4532T						.						69	75	73					2																	220341676		2079	4210	6289	SO:0001583	missense	10290	exon19			AGGGAAAACCACT	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"Immunoglobulin superfamily / I-set domain containing"	16901	protein-coding gene	gene with protein product		615950	"aortic preferentially expressed gene 1"	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.4532A>T	chr2.hg19:g.220341676A>T	ENSP00000311684:p.Lys1511Ile	70.0	0.0		38.0	10.0	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	hg19	CCDS42824.1	.	.	.	.	.	.	.	.	.	.	a	19.66	3.869107	0.72065	.	.	ENSG00000072195	ENST00000312358;ENST00000265327	T	0.68331	-0.32	5.19	4.05	0.47172	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.37348	U	0.002129	T	0.63792	0.2541	L	0.35593	1.075	0.80722	D	1	P	0.47253	0.892	P	0.51487	0.671	T	0.67252	-0.5717	10	0.72032	D	0.01	.	10.3472	0.43913	0.9225:0.0:0.0775:0.0	.	1511	Q15772	SPEG_HUMAN	I	1511	ENSP00000311684:K1511I	ENSP00000265327:K1511I	K	+	2	0	SPEG	220049920	1.000000	0.71417	0.903000	0.35520	0.924000	0.55760	4.281000	0.58965	1.954000	0.56735	0.478000	0.44815	AAA	.	.		0.632	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		T	220341676	A	T	220341676	3	4	245	1	0	0	0	0	1	0	0	0	15051	14	1	4	4618	4	SPEG	2	220341676	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	788186	220341676	22857697	50	33520										
INHA	3623	hgsc.bcm.edu	37	chr2	220439764	220439764	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ctgtcccctctgtacctgctCagcccggcctgaggccacgc	10	19	2	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr2:220439764C>A	ENST00000243786.2	+	2	797	c.617C>A	c.(616-618)tCa>tAa	p.S206*	INHA_ENST00000489456.1_3'UTR	NM_002191.3	NP_002182.1	P05111	INHA_HUMAN	inhibin, alpha	206					cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|erythrocyte differentiation (GO:0030218)|hemoglobin biosynthetic process (GO:0042541)|male gonad development (GO:0008584)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell cycle (GO:0045786)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of phosphorylation (GO:0042326)|nervous system development (GO:0007399)|ovarian follicle development (GO:0001541)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|regulation of cell cycle (GO:0051726)|regulation of cell proliferation (GO:0042127)|response to external stimulus (GO:0009605)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|inhibin A complex (GO:0043512)|inhibin-betaglycan-ActRII complex (GO:0034673)|neuronal cell body (GO:0043025)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|hormone activity (GO:0005179)|receptor binding (GO:0005102)			large_intestine(2)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	10		Renal(207;0.0183)		Epithelial(149;4.58e-07)|all cancers(144;4.31e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		TGTACCTGCTCAGCCCGGCCT	0.687																																					p.S206X		Atlas-SNP	.											.	INHA	30	.	0			c.C617A						.						59	58	58					2																	220439764		2203	4300	6503	SO:0001587	stop_gained	3623	exon2			CCTGCTCAGCCCG		CCDS2444.1	2q35	2013-09-19			ENSG00000123999	ENSG00000123999			6065	protein-coding gene	gene with protein product		147380				3345731	Standard	NM_002191		Approved		uc002vmk.2	P05111	OTTHUMG00000059237	ENST00000243786.2:c.617C>A	chr2.hg19:g.220439764C>A	ENSP00000243786:p.Ser206*	66.0	0.0		38.0	14.0	NM_002191	A8K8H5	Nonsense_Mutation	SNP	ENST00000243786.2	hg19	CCDS2444.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.211943	0.79240	.	.	ENSG00000123999	ENST00000243786	.	.	.	5.48	4.41	0.53225	.	0.629214	0.15987	N	0.235029	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.17832	T	0.49	-10.6525	8.3908	0.32526	0.0:0.7167:0.1635:0.1198	.	.	.	.	X	206	.	ENSP00000243786:S206X	S	+	2	0	INHA	220148008	0.091000	0.21658	0.962000	0.40283	0.888000	0.51559	1.067000	0.30616	2.564000	0.86499	0.561000	0.74099	TCA	.	.		0.687	INHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131425.1			A	220439764	C	A	220439764	4	1	245	1	0	0	0	0	0	1	0	0	7749	838	29	3	623	3	INHA	2	220439764	Nonsense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	98088	220439764	22759609	51	33521										
DOCK10	55619	hgsc.bcm.edu	37	chr2	225702538	225702538	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	atggcacttggccacaatgtCggtcagaaccctgcaaaagc	10	12	1	1	rs369073678		TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr2:225702538C>G	ENST00000258390.7	-	25	2858	c.2791G>C	c.(2791-2793)Gac>Cac	p.D931H	DOCK10_ENST00000409592.3_Missense_Mutation_p.D925H	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	931					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		GCCACAATGTCGGTCAGAACC	0.458																																					p.D931H		Atlas-SNP	.											.	DOCK10	308	.	0			c.G2791C						.						74	72	73					2																	225702538		1939	4142	6081	SO:0001583	missense	55619	exon25			CAATGTCGGTCAG	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"Pleckstrin homology (PH) domain containing"	23479	protein-coding gene	gene with protein product	"zizimin3"	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.2791G>C	chr2.hg19:g.225702538C>G	ENSP00000258390:p.Asp931His	57.0	0.0		58.0	22.0	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Missense_Mutation	SNP	ENST00000258390.7	hg19	CCDS46528.1	.	.	.	.	.	.	.	.	.	.	C	0.107	-1.144478	0.01728	.	.	ENSG00000135905	ENST00000409592;ENST00000258390	T;T	0.67345	3.78;-0.26	5.82	4.9	0.64082	.	0.204155	0.51477	D	0.000084	T	0.33030	0.0849	N	0.02158	-0.66	0.41256	D	0.986748	B;B	0.09022	0.002;0.001	B;B	0.10450	0.005;0.005	T	0.41088	-0.9528	10	0.02654	T	1	.	9.586	0.39517	0.1444:0.777:0.0:0.0786	.	931;925	Q96BY6;B3FL70	DOC10_HUMAN;.	H	925;931	ENSP00000386694:D925H;ENSP00000258390:D931H	ENSP00000258390:D931H	D	-	1	0	DOCK10	225410782	0.994000	0.37717	0.975000	0.42487	0.256000	0.26092	2.684000	0.46951	2.756000	0.94617	0.563000	0.77884	GAC	.	.		0.458	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1			G	225702538	C	G	225702538	3	3	245	1	0	0	0	0	1	0	0	0	4687	884	31	4	3897	4	DOCK10	2	225702538	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	5262774	225702538	17496835	52	33522										
B3GNT7	93010	hgsc.bcm.edu	37	chr2	232263636	232263636	+	Nonstop_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	cgcaagctccaggtgctctgAccccagccgggctactagga	12	15	1	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr2:232263636A>T	ENST00000287590.5	+	2	1467	c.1206A>T	c.(1204-1206)tgA>tgT	p.*402C		NM_145236.2	NP_660279.1	Q8NFL0	B3GN7_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7	0					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)			endometrium(2)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(1)	17		Renal(207;0.025)|all_hematologic(139;0.094)|Acute lymphoblastic leukemia(138;0.164)|Medulloblastoma(418;0.232)		Epithelial(121;3.22e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0139)		AGGTGCTCTGACCCCAGCCGG	0.652																																					p.X402C		Atlas-SNP	.											.	B3GNT7	38	.	0			c.A1206T						.						8	9	8					2																	232263636		2017	4180	6197	SO:0001578	stop_lost	93010	exon2			GCTCTGACCCCAG	AK000770	CCDS46540.1	2q36.1	2013-02-21			ENSG00000156966	ENSG00000156966		"Beta 3-glycosyltransferases"	18811	protein-coding gene	gene with protein product		615313				12061784	Standard	NM_145236		Approved	beta3GnT7	uc002vrs.3	Q8NFL0	OTTHUMG00000153880	ENST00000287590.5:c.1206A>T	chr2.hg19:g.232263636A>T	ENSP00000287590:p.*402Cysext*6	11.0	0.0		8.0	6.0	NM_145236	B3KWY4|B7WNP0	Missense_Mutation	SNP	ENST00000287590.5	hg19	CCDS46540.1	.	.	.	.	.	.	.	.	.	.	a	12.52	1.963017	0.34659	.	.	ENSG00000156966	ENST00000287590	.	.	.	5.05	3.91	0.45181	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.5012	0.07673	0.7611:0.0:0.2389:0.0	.	.	.	.	C	402	.	.	X	+	3	0	B3GNT7	231971880	.	.	0.916000	0.36221	0.905000	0.53344	.	.	1.905000	0.55150	0.454000	0.30748	TGA	.	.		0.652	B3GNT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332827.1	NM_145236		T	232263636	A	T	232263636	4	4	245	1	0	0	0	0	0	0	0	0	1262	288	10	4	1212	4	B3GNT7	2	232263636	Nonstop_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	6561098	232263636	10935737	53	33523										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266098	41266098	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gcagcaacagtcttacctggActctggaatccattctggtg	10	11	3	0	rs121913396|rs121913416		TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr3:41266098A>G	ENST00000349496.5	+	3	375	c.95A>G	c.(94-96)gAc>gGc	p.D32G	CTNNB1_ENST00000396183.3_Missense_Mutation_p.D32G|CTNNB1_ENST00000405570.1_Missense_Mutation_p.D32G|CTNNB1_ENST00000453024.1_Missense_Mutation_p.D25G|CTNNB1_ENST00000396185.3_Missense_Mutation_p.D32G	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	32			D -> A (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|D -> G (in PTR and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629}.|D -> Y (in PTR, hepatoblastoma and hepatocellular carcinoma; dbSNP:rs28931588). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:11703283, ECO:0000269|PubMed:9927029}.|Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.D32G(65)|p.A5_A80del(53)|p.D32V(33)|p.D32A(16)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.WQQQSYLD25?(5)|p.W25_D32del(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.S29_H36del(1)|p.D32del(1)|p.M14_S45del(1)|p.Q28_D32>H(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.D32fs*9(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TCTTACCTGGACTCTGGAATC	0.483	D32V(HEC265_ENDOMETRIUM)|D32V(HEC6_ENDOMETRIUM)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.D32G	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,+1,128	CTNNB1	4904	.	260	Deletion - In frame(120)|Substitution - Missense(114)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(154)|large_intestine(24)|pancreas(19)|central_nervous_system(16)|stomach(14)|endometrium(7)|skin(7)|ovary(4)|prostate(3)|pituitary(3)|small_intestine(2)|NS(2)|adrenal_gland(1)|soft_tissue(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)	c.A95G						.						92	77	82					3																	41266098		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	ACCTGGACTCTGG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.95A>G	chr3.hg19:g.41266098A>G	ENSP00000344456:p.Asp32Gly	182.0	0.0		114.0	106.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.308122	0.81247	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.50001	0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.69788	0.3150	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.74137	-0.3762	10	0.87932	D	0	0.3843	16.0676	0.80897	1.0:0.0:0.0:0.0	.	32	P35222	CTNB1_HUMAN	G	25;32;32;32;32;25;32;32;32	ENSP00000400508:D25G;ENSP00000385604:D32G;ENSP00000412219:D32G;ENSP00000379486:D32G;ENSP00000344456:D32G;ENSP00000411226:D25G;ENSP00000379488:D32G;ENSP00000409302:D32G;ENSP00000401599:D32G	ENSP00000344456:D32G	D	+	2	0	CTNNB1	41241102	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.201000	0.70794	0.533000	0.62120	GAC	.	.		0.483	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266098	A	G	41266098	3	3	245	1	0	0	0	0	1	0	0	0	4018	275	10	2	101	2	CTNNB1	3	41266098	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10		41266098	156756332	54	33524										
CACNA2D2	9254	hgsc.bcm.edu	37	chr3	50418547	50418547	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gtccagttgagctcattgagGatgacagtggctggggggaa	17	6	1	3	rs56287038	byFrequency	TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr3:50418547G>A	ENST00000479441.1	-	7	662	c.663C>T	c.(661-663)atC>atT	p.I221I	CACNA2D2_ENST00000424201.2_Silent_p.I221I|CACNA2D2_ENST00000360963.3_Silent_p.I152I|CACNA2D2_ENST00000395083.1_Silent_p.I221I|CACNA2D2_ENST00000423994.2_Silent_p.I221I|CACNA2D2_ENST00000435965.1_Silent_p.I221I|CACNA2D2_ENST00000429770.1_Silent_p.I221I|CACNA2D2_ENST00000266039.3_Silent_p.I221I			Q9NY47	CA2D2_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 2	221					energy reserve metabolic process (GO:0006112)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|positive regulation of organ growth (GO:0046622)|regulation of insulin secretion (GO:0050796)|regulation of multicellular organism growth (GO:0040014)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|cervix(1)|endometrium(4)|large_intestine(4)|lung(8)|ovary(2)|prostate(4)|skin(4)|urinary_tract(1)	31				BRCA - Breast invasive adenocarcinoma(193;0.000365)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)	Amiodarone(DB01118)|Bepridil(DB01244)|Felodipine(DB01023)|Gabapentin(DB00996)|Isradipine(DB00270)|Nitrendipine(DB01054)|Spironolactone(DB00421)	GCTCATTGAGGATGACAGTGG	0.612																																					p.I221I		Atlas-SNP	.											.	CACNA2D2	82	.	0			c.C663T						.						123	128	126					3																	50418547		2203	4300	6503	SO:0001819	synonymous_variant	9254	exon7			ATTGAGGATGACA	AF040709	CCDS33763.1, CCDS54588.1, CCDS63647.1	3p21.3	2004-02-27			ENSG00000007402	ENSG00000007402		"Calcium channel subunits"	1400	protein-coding gene	gene with protein product	"gene 26"	607082					Standard	XM_005265581		Approved	KIAA0558	uc003daq.3	Q9NY47	OTTHUMG00000156887	ENST00000479441.1:c.663C>T	chr3.hg19:g.50418547G>A		81.0	0.0		56.0	18.0	NM_001174051	A7MD15|Q9NY48|Q9UEW0|Q9Y268	Silent	SNP	ENST00000479441.1	hg19	CCDS54588.1																																																																																			.	G|0.887;T|0.113		0.612	CACNA2D2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346457.1	NM_006030		A	50418547	G	A	50418547	2	1	245	1	0	0	0	0	0	0	0	1	2551	1164	41	3		3	CACNA2D2	3	50418547	Silent	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	9152449	50418547	147603883	55	33525										
OR5H14	403273	hgsc.bcm.edu	37	chr3	97868527	97868527	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ctctctctgaatgcaagataCagttgttttcgtttgcaatc	7	9	2	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr3:97868527C>A	ENST00000437310.1	+	1	358	c.298C>A	c.(298-300)Cag>Aag	p.Q100K	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005514.1	NP_001005514.1	A6NHG9	O5H14_HUMAN	olfactory receptor, family 5, subfamily H, member 14	100						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Q100K(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	31						ATGCAAGATACAGTTGTTTTC	0.393																																					p.Q100K		Atlas-SNP	.											OR5H14,NS,carcinoma,0,1	OR5H14	56	.	1	Substitution - Missense(1)	lung(1)	c.C298A						.						202	209	207					3																	97868527		2203	4299	6502	SO:0001583	missense	403273	exon1			AAGATACAGTTGT		CCDS33798.1	3q11.2	2013-09-23			ENSG00000236032	ENSG00000236032		"GPCR / Class A : Olfactory receptors"	31286	protein-coding gene	gene with protein product							Standard	NM_001005514		Approved		uc003dsg.1	A6NHG9	OTTHUMG00000160079	ENST00000437310.1:c.298C>A	chr3.hg19:g.97868527C>A	ENSP00000401706:p.Gln100Lys	165.0	0.0		182.0	26.0	NM_001005514	B9EH15	Missense_Mutation	SNP	ENST00000437310.1	hg19	CCDS33798.1	.	.	.	.	.	.	.	.	.	.	C	16.85	3.237609	0.58886	.	.	ENSG00000236032	ENST00000437310	T	0.00462	7.26	2.49	2.49	0.30216	GPCR, rhodopsin-like superfamily (1);	0.000000	0.45361	D	0.000379	T	0.01421	0.0046	H	0.97491	4.015	0.19300	N	0.999972	P	0.48089	0.905	P	0.49451	0.611	T	0.13926	-1.0491	10	0.72032	D	0.01	.	10.6214	0.45483	0.0:1.0:0.0:0.0	.	100	A6NHG9	O5H14_HUMAN	K	100	ENSP00000401706:Q100K	ENSP00000401706:Q100K	Q	+	1	0	OR5H14	99351217	1.000000	0.71417	0.006000	0.13384	0.041000	0.13682	6.590000	0.74085	1.380000	0.46344	0.195000	0.17529	CAG	.	.		0.393	OR5H14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359112.1			A	97868527	C	A	97868527	3	1	245	1	0	0	0	0	1	0	0	0	11169	479	17	3	300	3	OR5H14	3	97868527	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	47449980	97868527	100153903	56	33526										
MORC1	27136	hgsc.bcm.edu	37	chr3	108698446	108698446	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	aagaagcaactttacaactgCcactcacagaaactctggct	6	12	2	2	rs201675482		TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr3:108698446C>A	ENST00000483760.1	-	23	2373	c.2330G>T	c.(2329-2331)gGc>gTc	p.G777V	MORC1_ENST00000232603.5_Missense_Mutation_p.G798V					MORC family CW-type zinc finger 1											breast(7)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(47)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	105						TTTACAACTGCCACTCACAGA	0.413																																					p.G798V		Atlas-SNP	.											.	MORC1	211	.	0			c.G2393T						.						118	112	114					3																	108698446		2203	4300	6503	SO:0001583	missense	27136	exon24			CAACTGCCACTCA	AF084946	CCDS2955.1	3q13	2011-10-26	2005-06-15	2005-06-15	ENSG00000114487	ENSG00000114487			7198	protein-coding gene	gene with protein product	"cancer/testis antigen 33"	603205	"microrchidia (mouse) homolog", "microrchidia homolog (mouse)"	MORC		10369865	Standard	NM_014429		Approved	ZCW6, CT33	uc003dxl.3	Q86VD1	OTTHUMG00000159209	ENST00000483760.1:c.2330G>T	chr3.hg19:g.108698446C>A	ENSP00000417282:p.Gly777Val	124.0	0.0		102.0	24.0	NM_014429		Missense_Mutation	SNP	ENST00000483760.1	hg19		.	.	.	.	.	.	.	.	.	.	C	14.11	2.437450	0.43224	.	.	ENSG00000114487	ENST00000232603;ENST00000483760	T;T	0.06449	3.33;3.3	5.25	-0.433	0.12287	.	1.786500	0.02702	N	0.111811	T	0.05593	0.0147	L	0.32530	0.975	0.09310	N	1	B;B	0.21381	0.055;0.055	B;B	0.17433	0.018;0.018	T	0.38067	-0.9678	10	0.27785	T	0.31	0.026	3.5674	0.07905	0.1775:0.3688:0.0:0.4537	.	777;798	E7ERX1;Q86VD1	.;MORC1_HUMAN	V	798;777	ENSP00000232603:G798V;ENSP00000417282:G777V	ENSP00000232603:G798V	G	-	2	0	MORC1	110181136	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.058000	0.11750	0.016000	0.14998	0.655000	0.94253	GGC	.	C|1.000;T|0.000		0.413	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1			A	108698446	C	A	108698446	3	1	245	1	0	0	0	0	1	0	0	0	9710	739	26	3	581	3	MORC1	3	108698446	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	10829919	108698446	89323984	57	33527										
CD96	10225	hgsc.bcm.edu	37	chr3	111342600	111342600	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ggaattttattttcaaaataGgatatccagctacatcttca	5	7	3	0	rs77738677	byFrequency	TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr3:111342600G>T	ENST00000283285.5	+	10	1359		c.e10-1		CD96_ENST00000352690.4_Splice_Site	NM_198196.2	NP_937839.1	P40200	TACT_HUMAN	CD96 molecule						cell adhesion (GO:0007155)|immune response (GO:0006955)|regulation of immune response (GO:0050776)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(4)|liver(2)|lung(14)|skin(5)	35						TTTCAAAATAGGATATCCAGC	0.368									Opitz Trigonocephaly syndrome																												.		Atlas-SNP	.											.	CD96	75	.	0			c.1181-1G>T						.						80	77	78					3																	111342600		2203	4299	6502	SO:0001630	splice_region_variant	10225	exon9	Familial Cancer Database	C syndrome, Trigonocephaly syndrome	AAAATAGGATATC	M88282	CCDS2958.1, CCDS2959.1	3p13-q13.2	2013-01-11	2006-03-28		ENSG00000153283	ENSG00000153283		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	16892	protein-coding gene	gene with protein product		606037	"CD96 antigen"			1313846	Standard	XR_241462		Approved	TACTILE	uc003dxx.3	P40200	OTTHUMG00000159275	ENST00000283285.5:c.1229-1G>T	chr3.hg19:g.111342600G>T		284.0	0.0		304.0	108.0	NM_005816	Q5JPB3	Splice_Site	SNP	ENST00000283285.5	hg19	CCDS2959.1	.	.	.	.	.	.	.	.	.	.	G	15.06	2.719710	0.48728	.	.	ENSG00000153283	ENST00000352690;ENST00000283285	.	.	.	4.02	4.02	0.46733	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.9321	0.52853	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CD96	112825290	0.980000	0.34600	0.885000	0.34714	0.295000	0.27426	2.142000	0.42177	2.537000	0.85549	0.655000	0.94253	.	.	G|0.995;A|0.005		0.368	CD96-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354312.2		Intron	T	111342600	G	T	111342600	5	4	245	1	0	0	0	0	0	0	1	0	3050	1014	35	3	1266	3	CD96	3	111342600	Splice_Site	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	2644154	111342600	86679830	58	33528										
ZBTB20	26137	hgsc.bcm.edu	37	chr3	114058003	114058003	+	Frame_Shift_Del	DEL	G	G	-													0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	cacctgggggtgtgcctgcaGggggggtcccattgctggca							TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr3:114058003delG	ENST00000474710.1	-	5	2253	c.2075delC	c.(2074-2076)cctfs	p.P692fs	ZBTB20_ENST00000357258.3_Frame_Shift_Del_p.P619fs|ZBTB20_ENST00000464560.1_Frame_Shift_Del_p.P619fs|ZBTB20_ENST00000462705.1_Frame_Shift_Del_p.P619fs|ZBTB20_ENST00000471418.1_Frame_Shift_Del_p.P619fs|ZBTB20_ENST00000393785.2_Frame_Shift_Del_p.P619fs|ZBTB20_ENST00000481632.1_Frame_Shift_Del_p.P619fs	NM_001164342.1	NP_001157814.1	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20	692						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)	p.P619fs*43(1)		breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(8)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	48				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)		TGTGCCTGCAGGGGGGGTCCC	0.632																																					p.P692fs	NSCLC(69;748 1344 9802 11203 30933)	Atlas-Indel,Pindel	.											.	ZBTB20	157	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2076delT						.						56	55	55					3																	114058003		2203	4300	6503	SO:0001589	frameshift_variant	26137	exon5			.	AF139460	CCDS2981.1, CCDS54626.1	3q13.2	2013-01-08	2004-07-16	2004-07-16	ENSG00000181722	ENSG00000181722		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	13503	protein-coding gene	gene with protein product		606025	"zinc finger protein 288"	ZNF288		10965110, 11352661	Standard	XM_005247339		Approved	ODA-8S, DKFZp566F123, DPZF	uc003ebi.3	Q9HC78	OTTHUMG00000159366	ENST00000474710.1:c.2075delC	chr3.hg19:g.114058003delG	ENSP00000419153:p.Pro692fs	70.0	0.0		70.0	22.0	NM_001164342	Q63HP6|Q8N6R5|Q9Y410	Frame_Shift_Del	DEL	ENST00000474710.1	hg19	CCDS54626.1																																																																																			.	.		0.632	ZBTB20-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354951.1	NM_015642		-	114058003	G	-	114058003	7	5	245	1	0	1	0	1	0	0	0	0	17544	1000	35	0	154	0	ZBTB20	3	114058003	Frame_Shift_Del	DEL	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	2715403	114058003	83964427	59	33529										
KALRN	8997	hgsc.bcm.edu	37	chr3	124437851	124437851	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ggaggatgctgtccagatctCgggtcacttccacattcacc	10	13	3	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr3:124437851C>T	ENST00000291478.5	+	27	3567	c.3404C>T	c.(3403-3405)tCg>tTg	p.S1135L	KALRN_ENST00000360013.3_Missense_Mutation_p.S2832L|KALRN_ENST00000428018.2_Missense_Mutation_p.S1103L	NM_007064.3	NP_008995.2	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	2831					apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						GTCCAGATCTCGGGTCACTTC	0.552																																					p.S2832L		Atlas-SNP	.											.	KALRN	556	.	0			c.C8495T						.						89	87	88					3																	124437851		2203	4300	6503	SO:0001583	missense	8997	exon60			AGATCTCGGGTCA	U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	4814	protein-coding gene	gene with protein product	"serine/threonine kinase with Dbl and pleckstrin homology domains"	604605	"huntingtin-associated protein interacting protein (duo)"	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000291478.5:c.3404C>T	chr3.hg19:g.124437851C>T	ENSP00000291478:p.Ser1135Leu	102.0	0.0		116.0	18.0	NM_001024660	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Missense_Mutation	SNP	ENST00000291478.5	hg19	CCDS3028.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.6|25.6	4.650666|4.650666	0.87958|0.87958	.|.	.|.	ENSG00000160145|ENSG00000160145	ENST00000354186|ENST00000360013;ENST00000291478;ENST00000428018	.|T;T;T	.|0.65364	.|-0.15;-0.15;-0.15	5.41|5.41	5.41|5.41	0.78517|0.78517	.|Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.|0.079259	.|0.52532	.|D	.|0.000067	T|T	0.51958|0.51958	0.1705|0.1705	L|L	0.33093|0.33093	0.98|0.98	0.41765|0.41765	D|D	0.989733|0.989733	.|P;B	.|0.41159	.|0.74;0.344	.|B;B	.|0.34489	.|0.184;0.06	T|T	0.56098|0.56098	-0.8035|-0.8035	5|10	.|0.44086	.|T	.|0.13	.|.	19.3942|19.3942	0.94598|0.94598	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1135;2831	.|C9JQ37;O60229	.|.;KALRN_HUMAN	W|L	2801|2832;1135;1103	.|ENSP00000353109:S2832L;ENSP00000291478:S1135L;ENSP00000402419:S1103L	.|ENSP00000291478:S1135L	R|S	+|+	1|2	2|0	KALRN|KALRN	125920541|125920541	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.965000|0.965000	0.64279|0.64279	3.901000|3.901000	0.56303|0.56303	2.816000|2.816000	0.96949|0.96949	0.563000|0.563000	0.77884|0.77884	CGG|TCG	.	.		0.552	KALRN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000246891.5	NM_003947		T	124437851	C	T	124437851	3	4	245	1	0	0	0	0	1	0	0	0	7984	893	31	1	8889	1	KALRN	3	124437851	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	10379848	124437851	73584579	60	33530										
KALRN	8997	hgsc.bcm.edu	37	chr3	124437876	124437876	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	cacttccacattcaccacctGctggggaaccctgagtttgc	8	15	1	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr3:124437876G>A	ENST00000291478.5	+	27	3592	c.3429G>A	c.(3427-3429)ctG>ctA	p.L1143L	KALRN_ENST00000360013.3_Silent_p.L2840L|KALRN_ENST00000428018.2_Silent_p.L1111L	NM_007064.3	NP_008995.2	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	2839					apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						TTCACCACCTGCTGGGGAACC	0.542																																					p.L2840L		Atlas-SNP	.											.	KALRN	556	.	0			c.G8520A						.						82	79	80					3																	124437876		2203	4300	6503	SO:0001819	synonymous_variant	8997	exon60			CCACCTGCTGGGG	U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	4814	protein-coding gene	gene with protein product	"serine/threonine kinase with Dbl and pleckstrin homology domains"	604605	"huntingtin-associated protein interacting protein (duo)"	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000291478.5:c.3429G>A	chr3.hg19:g.124437876G>A		97.0	0.0		119.0	20.0	NM_001024660	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000291478.5	hg19	CCDS3028.1	.	.	.	.	.	.	.	.	.	.	G	5.073	0.199194	0.09652	.	.	ENSG00000160145	ENST00000354186	.	.	.	5.41	1.58	0.23477	.	.	.	.	.	T	0.51109	0.1655	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35076	-0.9803	4	.	.	.	.	4.6724	0.12696	0.0715:0.2775:0.4246:0.2265	.	.	.	.	Y	2809	.	.	C	+	2	0	KALRN	125920566	1.000000	0.71417	0.998000	0.56505	0.972000	0.66771	0.637000	0.24659	0.107000	0.17824	-0.253000	0.11424	TGC	.	.		0.542	KALRN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000246891.5	NM_003947		A	124437876	G	A	124437876	2	1	245	1	0	0	0	0	0	0	0	1	7984	1306	46	3		3	KALRN	3	124437876	Silent	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	25	124437876	73584554	61	33531										
SLC12A8	84561	hgsc.bcm.edu	37	chr3	124909320	124909320	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	aaacagcacaggctcccacaTgaacagctgggtcttccacc	8	15	1	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr3:124909320T>A	ENST00000393469.4	-	2	146	c.97A>T	c.(97-99)Atg>Ttg	p.M33L	SLC12A8_ENST00000314584.7_5'UTR|SLC12A8_ENST00000469902.1_Missense_Mutation_p.M33L|SLC12A8_ENST00000423114.2_Missense_Mutation_p.M62L	NM_001195483.1	NP_001182412	A0AV02	S12A8_HUMAN	solute carrier family 12, member 8	33					potassium ion transport (GO:0006813)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)	p.M33L(1)		endometrium(2)|kidney(2)|lung(12)	16						GGCTCCCACATGAACAGCTGG	0.582																																					p.M33L		Atlas-SNP	.											SLC12A8_ENST00000393469,NS,carcinoma,0,1	SLC12A8	81	.	1	Substitution - Missense(1)	ovary(1)	c.A97T						.						132	142	139					3																	124909320		2040	4197	6237	SO:0001583	missense	84561	exon3			CCCACATGAACAG		CCDS43143.1	3q21.2	2013-07-18	2013-07-18		ENSG00000221955	ENSG00000221955		"Solute carriers"	15595	protein-coding gene	gene with protein product	"solute carrier family 12 (sodium/potassium/chloride transporters), member 8", "cation-chloride cotransporter 9"	611316				11863360	Standard	NM_024628		Approved	CCC9	uc003ehv.4	A0AV02	OTTHUMG00000159483	ENST00000393469.4:c.97A>T	chr3.hg19:g.124909320T>A	ENSP00000377112:p.Met33Leu	304.0	0.0		334.0	60.0	NM_024628	C9JJJ2|Q68D04|Q6I9Z2|Q6P4C0|Q7Z3A6|Q86WK0|Q8NFX9|Q8WUI3|Q96RF9|Q9H5P9	Missense_Mutation	SNP	ENST00000393469.4	hg19	CCDS43143.1	.	.	.	.	.	.	.	.	.	.	C	13.14	2.148037	0.37923	.	.	ENSG00000221955	ENST00000393469;ENST00000423114;ENST00000469902;ENST00000462437	D;D;D;D	0.95272	-2.21;-2.21;-2.21;-3.66	5.03	1.25	0.21368	.	.	.	.	.	D	0.87341	0.6153	N	0.22421	0.69	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.74551	-0.3628	9	0.25106	T	0.35	.	8.5487	0.33438	0.0:0.6188:0.0:0.3812	.	62;33	A0AV02-2;A0AV02	.;S12A8_HUMAN	L	33;62;33;1	ENSP00000377112:M33L;ENSP00000404243:M62L;ENSP00000418783:M33L;ENSP00000418636:M1L	ENSP00000377112:M33L	M	-	1	0	SLC12A8	126392010	0.374000	0.25081	0.602000	0.28890	0.667000	0.39255	0.405000	0.21015	-0.160000	0.11002	-0.735000	0.03563	ATG	.	.		0.582	SLC12A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355711.4	NM_024628		A	124909320	T	A	124909320	3	1	245	1	0	0	0	0	1	0	0	0	14404	1464	51	4	2095	4	SLC12A8	3	124909320	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	471444	124909320	73113110	62	33532										
NEK11	79858	hgsc.bcm.edu	37	chr3	130884346	130884346	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ctcggaactttcagcagctgAgtgttgatgtactccatgta	10	9	1	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr3:130884346A>T	ENST00000510769.1	+	8	1097	c.844A>T	c.(844-846)Agt>Tgt	p.S282C	NEK11_ENST00000508196.1_Missense_Mutation_p.S387C|NEK11_ENST00000429253.2_Missense_Mutation_p.S387C|NEK11_ENST00000383366.4_Missense_Mutation_p.S387C|NEK11_ENST00000356918.4_Missense_Mutation_p.S387C|NEK11_ENST00000511262.1_Missense_Mutation_p.S387C|NEK11_ENST00000507910.1_Missense_Mutation_p.S387C|NEK11_ENST00000510688.1_Missense_Mutation_p.S387C|NEK11_ENST00000412440.2_Missense_Mutation_p.S239C					NIMA-related kinase 11											breast(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(14)|stomach(1)|urinary_tract(2)	33						TCAGCAGCTGAGTGTTGATGT	0.328																																					p.S387C		Atlas-SNP	.											.	NEK11	76	.	0			c.A1159T						.						87	90	89					3																	130884346		2203	4300	6503	SO:0001583	missense	79858	exon12			CAGCTGAGTGTTG	AK027148	CCDS3069.1, CCDS46915.1, CCDS54639.1	3q22.1	2012-11-15	2012-11-15		ENSG00000114670	ENSG00000114670			18593	protein-coding gene	gene with protein product		609779	"NIMA (never in mitosis gene a)- related kinase 11"				Standard	NM_024800		Approved	FLJ23495	uc003eny.3	Q8NG66	OTTHUMG00000159654	ENST00000510769.1:c.844A>T	chr3.hg19:g.130884346A>T	ENSP00000421549:p.Ser282Cys	171.0	0.0		186.0	98.0	NM_024800		Missense_Mutation	SNP	ENST00000510769.1	hg19		.	.	.	.	.	.	.	.	.	.	A	22.3	4.265998	0.80358	.	.	ENSG00000114670	ENST00000510769;ENST00000429253;ENST00000356918;ENST00000510688;ENST00000511262;ENST00000383366;ENST00000412440;ENST00000507910;ENST00000508196	T;T;T;T;T;T;T;T;T	0.72725	-0.62;-0.41;-0.55;-0.44;-0.54;-0.41;-0.68;-0.55;-0.41	5.65	3.24	0.37175	.	0.759465	0.11815	N	0.526839	T	0.70833	0.3269	L	0.43923	1.385	0.09310	N	1	D;D;D;D;D;P	0.60575	0.988;0.973;0.983;0.978;0.963;0.921	P;P;P;P;P;P	0.53593	0.73;0.639;0.613;0.711;0.518;0.518	T	0.58713	-0.7588	10	0.62326	D	0.03	.	8.0131	0.30365	0.7909:0.1367:0.0723:0.0	.	387;282;239;387;387;387	Q8NG66-3;E9PHI8;B4DDN2;Q8NG66-4;Q8NG66;Q8NG66-2	.;.;.;.;NEK11_HUMAN;.	C	282;387;387;387;387;387;239;387;387	ENSP00000421549:S282C;ENSP00000397180:S387C;ENSP00000349389:S387C;ENSP00000423458:S387C;ENSP00000425114:S387C;ENSP00000372857:S387C;ENSP00000411888:S239C;ENSP00000426662:S387C;ENSP00000421851:S387C	ENSP00000349389:S387C	S	+	1	0	NEK11	132367036	0.003000	0.15002	0.000000	0.03702	0.864000	0.49448	1.867000	0.39499	0.485000	0.27652	0.528000	0.53228	AGT	.	.		0.328	NEK11-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000356757.1	NM_024800		T	130884346	A	T	130884346	3	4	245	1	0	0	0	0	1	0	0	0	10332	304	11	4	1197	4	NEK11	3	130884346	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	5975026	130884346	67138084	63	33533										
PLSCR4	57088	hgsc.bcm.edu	37	chr3	145924525	145924525	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tcctgggtagccagtaggtgGagggacagctgttccagggg	18	8	0	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr3:145924525G>A	ENST00000354952.2	-	4	382	c.142C>T	c.(142-144)Cca>Tca	p.P48S	PLSCR4_ENST00000383083.2_Missense_Mutation_p.P48S|PLSCR4_ENST00000446574.2_Missense_Mutation_p.P48S|PLSCR4_ENST00000493382.1_Missense_Mutation_p.P48S|PLSCR4_ENST00000433593.2_Missense_Mutation_p.P33S	NM_020353.2	NP_065086.2	Q9NRQ2	PLS4_HUMAN	phospholipid scramblase 4	48	Proline-rich domain (PRD). {ECO:0000250}.				cellular response to lipopolysaccharide (GO:0071222)|phospholipid scrambling (GO:0017121)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|CD4 receptor binding (GO:0042609)|enzyme binding (GO:0019899)|phospholipid scramblase activity (GO:0017128)			kidney(1)|large_intestine(6)|lung(9)|urinary_tract(1)	17						CCAGTAGGTGGAGGGACAGCT	0.448																																					p.P48S		Atlas-SNP	.											.	PLSCR4	44	.	0			c.C142T						.						32	33	33					3																	145924525		2203	4300	6503	SO:0001583	missense	57088	exon4			TAGGTGGAGGGAC	AF199023	CCDS3133.1, CCDS54651.1	3q24	2008-07-18			ENSG00000114698	ENSG00000114698			16497	protein-coding gene	gene with protein product		607612				10930526	Standard	NM_020353		Approved		uc003evt.4	Q9NRQ2	OTTHUMG00000159415	ENST00000354952.2:c.142C>T	chr3.hg19:g.145924525G>A	ENSP00000347038:p.Pro48Ser	108.0	0.0		124.0	17.0	NM_020353	A8K2E9|Q2TTR3|Q658L3|Q6ZR73|Q7Z505	Missense_Mutation	SNP	ENST00000354952.2	hg19	CCDS3133.1	.	.	.	.	.	.	.	.	.	.	G	15.50	2.853010	0.51270	.	.	ENSG00000114698	ENST00000354952;ENST00000383083;ENST00000433593;ENST00000446574;ENST00000493382;ENST00000460350;ENST00000460885;ENST00000476202;ENST00000481701;ENST00000498625	T;T;T;T;T;T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.82	4.0	3.12	0.35913	.	0.524004	0.17648	N	0.166778	T	0.43612	0.1255	L	0.60845	1.875	0.09310	N	1	B;B	0.30793	0.295;0.099	B;B	0.31614	0.133;0.037	T	0.43734	-0.9373	10	0.72032	D	0.01	.	9.8013	0.40766	0.0:0.2095:0.7905:0.0	.	48;48	E9PHR9;Q9NRQ2	.;PLS4_HUMAN	S	48;48;33;48;48;48;48;48;48;48	ENSP00000347038:P48S;ENSP00000372561:P48S;ENSP00000415605:P33S;ENSP00000399315:P48S;ENSP00000419040:P48S;ENSP00000417896:P48S;ENSP00000420385:P48S;ENSP00000418173:P48S;ENSP00000418419:P48S;ENSP00000417248:P48S	ENSP00000347038:P48S	P	-	1	0	PLSCR4	147407215	0.002000	0.14202	0.273000	0.24645	0.962000	0.63368	0.705000	0.25675	1.012000	0.39366	0.650000	0.86243	CCA	.	.		0.448	PLSCR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355172.1	NM_020353		A	145924525	G	A	145924525	3	1	245	1	0	0	0	0	1	0	0	0	12121	1174	41	3	871	3	PLSCR4	3	145924525	Missense_Mutation	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	15040179	145924525	52097905	64	33534										
SGEF	26084	hgsc.bcm.edu	37	chr3	153842229	153842229	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tgaaaggacaaggaacatttGatggggaaggtaagcattta	13	3	0	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr3:153842229G>C	ENST00000356448.4	+	3	1398	c.1114G>C	c.(1114-1116)Gat>Cat	p.D372H	ARHGEF26_ENST00000465093.1_Missense_Mutation_p.D372H|ARHGEF26_ENST00000465817.1_Missense_Mutation_p.D372H	NM_001251962.1	NP_001238891.1	Q96DR7	ARHGQ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 26	372					endothelial cell morphogenesis (GO:0001886)|ruffle assembly (GO:0097178)	cell projection (GO:0042995)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	23						AGGAACATTTGATGGGGAAGG	0.289																																					p.D372H	GBM(163;191 2003 24758 29593 48540)|Ovarian(152;631 1885 20165 22910 51013)	Atlas-SNP	.											SGEF,colon,carcinoma,0,3	ARHGEF26	158	.	0			c.G1114C						.						78	77	77					3																	153842229		1798	4058	5856	SO:0001583	missense	26084	exon3			ACATTTGATGGGG	BC016628	CCDS46938.1, CCDS58858.1	3q25.2	2013-01-10			ENSG00000114790	ENSG00000114790		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	24490	protein-coding gene	gene with protein product	"Src homology 3 domain-containing guanine nucleotide exchange factor"					15133129, 12697679	Standard	NM_015595		Approved	DKFZP434D146, SGEF	uc021xgc.1	Q96DR7	OTTHUMG00000159098	ENST00000356448.4:c.1114G>C	chr3.hg19:g.153842229G>C	ENSP00000348828:p.Asp372His	48.0	0.0		50.0	28.0	NM_001251962	B3KVP8|E9PBD0|Q68CL1|Q6AZ96|Q6Q8Q8|Q96AW8|Q96DR6|Q9H9D7|Q9H9R2|Q9UFW5	Missense_Mutation	SNP	ENST00000356448.4	hg19	CCDS46938.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.094882	0.76870	.	.	ENSG00000114790	ENST00000356448;ENST00000465093;ENST00000465817	T;T;T	0.60548	0.18;0.18;1.94	5.76	5.76	0.90799	.	0.048978	0.85682	D	0.000000	T	0.70613	0.3244	L	0.44542	1.39	0.53005	D	0.999967	D;D	0.89917	1.0;1.0	D;D	0.67231	0.95;0.915	T	0.70626	-0.4820	10	0.59425	D	0.04	-22.8259	19.9857	0.97347	0.0:0.0:1.0:0.0	.	372;372	E9PBD0;Q96DR7	.;ARHGQ_HUMAN	H	372	ENSP00000348828:D372H;ENSP00000423418:D372H;ENSP00000423295:D372H	ENSP00000348828:D372H	D	+	1	0	ARHGEF26	155324919	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.405000	0.80007	2.706000	0.92434	0.655000	0.94253	GAT	.	.		0.289	ARHGEF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353287.3	NM_015595		C	153842229	G	C	153842229	3	2	245	1	0	0	0	0	1	0	0	0	14220	1290	45	4	1120	4	SGEF	3	153842229	Missense_Mutation	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	7917704	153842229	44180201	65	33535										
TTC14	151613	hgsc.bcm.edu	37	chr3	180322340	180322340	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gctcttctcttccaccacacCtatctggtattaaattaggt	5	12	3	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr3:180322340C>A	ENST00000296015.4	+	5	778	c.646C>A	c.(646-648)Cta>Ata	p.L216I	RP11-496B10.3_ENST00000472596.1_lincRNA|TTC14_ENST00000382584.4_Missense_Mutation_p.L216I|TTC14_ENST00000412756.2_Missense_Mutation_p.L216I	NM_133462.3	NP_597719.1	Q96N46	TTC14_HUMAN	tetratricopeptide repeat domain 14	216							RNA binding (GO:0003723)			endometrium(3)|kidney(5)|large_intestine(9)|lung(24)|ovary(2)|pancreas(1)|skin(1)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			TCCACCACACCTATCTGGTAT	0.333																																					p.L216I		Atlas-SNP	.											.	TTC14	112	.	0			c.C646A						.						66	65	65					3																	180322340		2203	4295	6498	SO:0001583	missense	151613	exon5			CCACACCTATCTG	AB075860	CCDS3237.1, CCDS46963.1, CCDS75055.1	3q27.2	2013-01-10			ENSG00000163728	ENSG00000163728		"Tetratricopeptide (TTC) repeat domain containing"	24697	protein-coding gene	gene with protein product						11853319	Standard	NM_001042601		Approved	FLJ00166, KIAA1980	uc003fkk.3	Q96N46	OTTHUMG00000157859	ENST00000296015.4:c.646C>A	chr3.hg19:g.180322340C>A	ENSP00000296015:p.Leu216Ile	153.0	0.0		167.0	41.0	NM_001042601	G5E9X0|Q6UWJ7|Q8TF22	Missense_Mutation	SNP	ENST00000296015.4	hg19	CCDS3237.1	.	.	.	.	.	.	.	.	.	.	C	14.62	2.590530	0.46214	.	.	ENSG00000163728	ENST00000296015;ENST00000412756;ENST00000382584;ENST00000492617;ENST00000495660	T;T	0.50001	0.76;0.76	5.71	2.82	0.32997	.	0.284900	0.34386	N	0.004002	T	0.37652	0.1011	L	0.46157	1.445	0.80722	D	1	P;B;B	0.45283	0.855;0.063;0.376	B;B;B	0.40702	0.338;0.04;0.09	T	0.09509	-1.0671	10	0.35671	T	0.21	-4.525	8.4286	0.32744	0.1229:0.7405:0.0:0.1365	.	216;216;216	Q96N46-2;G5E9X0;Q96N46	.;.;TTC14_HUMAN	I	216;216;216;116;116	ENSP00000296015:L216I;ENSP00000372027:L216I	ENSP00000296015:L216I	L	+	1	2	TTC14	181805034	0.015000	0.18098	0.982000	0.44146	0.971000	0.66376	0.296000	0.19083	0.705000	0.31890	0.650000	0.86243	CTA	.	.		0.333	TTC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349786.1	NM_133462		A	180322340	C	A	180322340	3	1	245	1	0	0	0	0	1	0	0	0	16696	680	24	3	664	3	TTC14	3	180322340	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	26480111	180322340	17700090	66	33536										
POLN	353497	hgsc.bcm.edu	37	chr4	2209958	2209958	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	aattattatatgtaatatgtTttcttttaagattaatgctt	4	2	1	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr4:2209958T>G	ENST00000511885.2	-	5	823	c.470A>C	c.(469-471)aAa>aCa	p.K157T	POLN_ENST00000382865.1_Missense_Mutation_p.K157T|POLN_ENST00000515357.1_5'UTR			Q7Z5Q5	DPOLN_HUMAN	polymerase (DNA directed) nu	157					double-strand break repair via homologous recombination (GO:0000724)|interstrand cross-link repair (GO:0036297)|translesion synthesis (GO:0019985)	nucleus (GO:0005634)	cyclin binding (GO:0030332)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)			kidney(6)|large_intestine(5)|liver(1)|lung(8)|ovary(2)|skin(4)|urinary_tract(2)	28			OV - Ovarian serous cystadenocarcinoma(23;0.0955)			TGTAATATGTTTTCTTTTAAG	0.323								DNA polymerases (catalytic subunits)																													p.K157T		Atlas-SNP	.											.	POLN	82	.	0			c.A470C						.						56	58	57					4																	2209958		2203	4299	6502	SO:0001583	missense	353497	exon3			ATATGTTTTCTTT	AF044578	CCDS3360.1	4p16.3	2012-05-18			ENSG00000130997	ENSG00000130997		"DNA polymerases"	18870	protein-coding gene	gene with protein product		610887				12794064	Standard	NM_181808		Approved		uc003ger.2	Q7Z5Q5	OTTHUMG00000090081	ENST00000511885.2:c.470A>C	chr4.hg19:g.2209958T>G	ENSP00000435506:p.Lys157Thr	82.0	0.0		143.0	21.0	NM_181808	A2A336|B4E158|Q4TTW4|Q6ZNF4	Missense_Mutation	SNP	ENST00000511885.2	hg19	CCDS3360.1	.	.	.	.	.	.	.	.	.	.	T	14.04	2.416734	0.42918	.	.	ENSG00000130997	ENST00000511885;ENST00000382865	T;T	0.50548	0.74;0.74	5.27	5.27	0.74061	.	0.376324	0.26915	N	0.021848	T	0.45577	0.1349	L	0.29908	0.895	0.30641	N	0.756507	D;P	0.65815	0.995;0.877	P;B	0.51582	0.674;0.417	T	0.52457	-0.8573	10	0.56958	D	0.05	-12.1722	11.5991	0.50993	0.0:0.0:0.0:1.0	.	157;157	E7ERY2;Q7Z5Q5	.;DPOLN_HUMAN	T	157	ENSP00000435506:K157T;ENSP00000372316:K157T	ENSP00000372316:K157T	K	-	2	0	POLN	2179756	0.835000	0.29415	0.929000	0.37066	0.103000	0.19146	0.913000	0.28611	1.987000	0.57996	0.459000	0.35465	AAA	.	.		0.323	POLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000205684.2	NM_181808		G	2209958	T	G	2209958	3	3	245	1	0	0	0	0	1	0	0	0	12216	1841	64	5	2320	5	POLN	4	2209958	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10		2209958	188944318	67	33537										
RGS12	6002	hgsc.bcm.edu	37	chr4	3427240	3427240	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	cgcccctatatcgagtctggAcggacagcgggttgtcttgg	14	11	2	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr4:3427240A>G	ENST00000344733.5	+	14	4188	c.3284A>G	c.(3283-3285)gAc>gGc	p.D1095G	RGS12_ENST00000508158.1_3'UTR|RGS12_ENST00000336727.3_Missense_Mutation_p.D1095G|RGS12_ENST00000306648.7_Missense_Mutation_p.D493G|RGS12_ENST00000382788.3_Missense_Mutation_p.D1095G|RGS12_ENST00000338806.4_Missense_Mutation_p.D447G|RGS12_ENST00000538395.1_Missense_Mutation_p.D437G	NM_198229.2	NP_937872.1	O14924	RGS12_HUMAN	regulator of G-protein signaling 12	1095	RBD 2. {ECO:0000255|PROSITE- ProRule:PRU00262}.				positive regulation of GTPase activity (GO:0043547)|regulation of catalytic activity (GO:0050790)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|GTPase regulator activity (GO:0030695)|receptor signaling protein activity (GO:0005057)			autonomic_ganglia(1)|breast(4)|endometrium(3)|kidney(2)|large_intestine(9)|lung(16)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		TCGAGTCTGGACGGACAGCGG	0.577																																					p.D1095G		Atlas-SNP	.											.	RGS12	128	.	0			c.A3284G						.						130	138	135					4																	3427240		2203	4300	6503	SO:0001583	missense	6002	exon14			GTCTGGACGGACA	AF035152	CCDS3366.1, CCDS3367.1, CCDS3368.1	4p16.3	2008-02-05	2007-08-14		ENSG00000159788	ENSG00000159788		"Regulators of G-protein signaling"	9994	protein-coding gene	gene with protein product		602512	"regulator of G-protein signalling 12"			9651375	Standard	NM_198229		Approved		uc003ggw.3	O14924	OTTHUMG00000090277	ENST00000344733.5:c.3284A>G	chr4.hg19:g.3427240A>G	ENSP00000339381:p.Asp1095Gly	131.0	0.0		148.0	35.0	NM_002926	B1AQ30|B1AQ31|B1AQ32|B7Z764|E7EMN9|O14922|O14923|O43510|O75338|Q147X0|Q8WX95	Missense_Mutation	SNP	ENST00000344733.5	hg19	CCDS3366.1	.	.	.	.	.	.	.	.	.	.	A	16.97	3.269248	0.59540	.	.	ENSG00000159788	ENST00000344733;ENST00000336727;ENST00000382788;ENST00000306648;ENST00000338806;ENST00000538395	T;T;T;T;T;T	0.41758	1.28;1.29;1.29;1.02;0.99;1.04	4.76	4.76	0.60689	Raf-like Ras-binding (3);	0.000000	0.85682	D	0.000000	T	0.59729	0.2215	L	0.58101	1.795	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.984;1.0;1.0;1.0	D;D;D;D;P;D;D;D	0.97110	1.0;1.0;1.0;1.0;0.885;1.0;1.0;1.0	T	0.61544	-0.7041	10	0.52906	T	0.07	-29.3243	13.7417	0.62852	1.0:0.0:0.0:0.0	.	437;294;294;437;447;493;1095;1095	B7Z764;B3KVS7;A8K440;O14924-2;O14924-3;Q8WX95;O14924;O14924-4	.;.;.;.;.;.;RGS12_HUMAN;.	G	1095;1095;1095;493;447;437	ENSP00000339381:D1095G;ENSP00000338509:D1095G;ENSP00000372238:D1095G;ENSP00000304459:D493G;ENSP00000342133:D447G;ENSP00000438888:D437G	ENSP00000304459:D493G	D	+	2	0	RGS12	3397038	1.000000	0.71417	0.961000	0.40146	0.498000	0.33706	8.418000	0.90250	1.903000	0.55091	0.529000	0.55759	GAC	.	.		0.577	RGS12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206602.1	NM_002926		G	3427240	A	G	3427240	3	3	245	1	0	0	0	0	1	0	0	0	13310	275	10	2	3392	2	RGS12	4	3427240	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	1217282	3427240	187727036	68	33538										
LCORL	254251	hgsc.bcm.edu	37	chr4	18023321	18023322	+	In_Frame_Ins	INS	-	-	GCGGCGGCAGCA													0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ggcactgagcggcggcggcgINSgcggcggcagcagcggcggc							TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr4:18023321_18023322insGCGGCGGCAGCA	ENST00000382226.5	-	1	161_162	c.53_54insTGCTGCCGCCGC	c.(52-54)gcc>gcTGCTGCCGCCGCc	p.18_18A>AAAAA	LCORL_ENST00000512376.2_5'UTR|LCORL_ENST00000326877.4_In_Frame_Ins_p.18_18A>AAAAA|LCORL_ENST00000539056.1_5'UTR|LCORL_ENST00000382224.1_5'Flank	NM_001166139.1	NP_001159611.1	Q8N3X6	LCORL_HUMAN	ligand dependent nuclear receptor corepressor-like	18	Ala-rich.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)			kidney(1)|large_intestine(1)|lung(1)|prostate(1)	4						cggcggcggcggcggcggcagc	0.688																																					p.A18delinsAAAAA		Atlas-INDEL	.											.	LCORL	60	.	0			c.54_55insTGCTGCCGCCGC						.																																			SO:0001652	inframe_insertion	254251	exon1			.		CCDS3425.1, CCDS54749.1	4p15.32	2006-06-14			ENSG00000178177	ENSG00000178177			30776	protein-coding gene	gene with protein product		611799				12560079	Standard	NM_153686		Approved	MLR1, FLJ30696	uc021xmr.1	Q8N3X6	OTTHUMG00000128538	ENST00000382226.5:c.42_53dupTGCTGCCGCCGC	chr4.hg19:g.18023321_18023322insGCGGCGGCAGCA	ENSP00000371661:p.AlaAlaAlaAla22dup	47.0	0.0		72.0	15.0	NM_001166139	Q96NK1	In_Frame_Ins	INS	ENST00000382226.5	hg19	CCDS54749.1																																																																																			.	.		0.688	LCORL-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_153686		GCGGCGGCAGCA	18023322	-	GCGGCGGCAGCA	18023321	7	5	245	1	0	1	1	0	0	0	0	0	8699	1103	39	0	1967	0	LCORL	4	18023321	In_Frame_Ins	INS	-	TCGA-ED-A7PZ-01A-11D-A33Q-10	14596081	18023321	173130955	69	33539										
UCHL1	7345	hgsc.bcm.edu	37	chr4	41266155	41266155	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ttccggtgaaccatggcgccAgttcagaggacaccctgctg	12	13	1	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr4:41266155A>T	ENST00000284440.4	+	8	706	c.562A>T	c.(562-564)Agt>Tgt	p.S188C	UCHL1_ENST00000512788.1_Missense_Mutation_p.S188C|UCHL1_ENST00000503431.1_Missense_Mutation_p.S188C|UCHL1_ENST00000508768.1_Missense_Mutation_p.S172C	NM_004181.4	NP_004172.2	P09936	UCHL1_HUMAN	ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase)	188					adult walking behavior (GO:0007628)|axon target recognition (GO:0007412)|axon transport of mitochondrion (GO:0019896)|cell death (GO:0008219)|cell proliferation (GO:0008283)|eating behavior (GO:0042755)|muscle fiber development (GO:0048747)|negative regulation of MAP kinase activity (GO:0043407)|neuromuscular process (GO:0050905)|protein deubiquitination (GO:0016579)|response to ischemia (GO:0002931)|sensory perception of pain (GO:0019233)|ubiquitin-dependent protein catabolic process (GO:0006511)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	alpha-2A adrenergic receptor binding (GO:0031694)|cysteine-type endopeptidase activity (GO:0004197)|ligase activity (GO:0016874)|omega peptidase activity (GO:0008242)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|skin(2)	8						CCATGGCGCCAGTTCAGAGGA	0.443																																					p.S188C		Atlas-SNP	.											.	UCHL1	19	.	0			c.A562T						.						166	156	159					4																	41266155		2203	4300	6503	SO:0001583	missense	7345	exon8			GGCGCCAGTTCAG	BC000332	CCDS3462.1	4p13	2011-07-21			ENSG00000154277	ENSG00000154277	3.4.19.12	"Parkinson disease"	12513	protein-coding gene	gene with protein product		191342		PARK5		1840236	Standard	NM_004181		Approved	PGP9.5, Uch-L1	uc003gvo.3	P09936	OTTHUMG00000099377	ENST00000284440.4:c.562A>T	chr4.hg19:g.41266155A>T	ENSP00000284440:p.Ser188Cys	69.0	0.0		97.0	53.0	NM_004181	Q4W5K6|Q71UM0	Missense_Mutation	SNP	ENST00000284440.4	hg19	CCDS3462.1	.	.	.	.	.	.	.	.	.	.	A	16.63	3.175699	0.57692	.	.	ENSG00000154277	ENST00000503431;ENST00000284440;ENST00000508768;ENST00000512788	T;T;T;T	0.63255	0.59;0.59;-0.03;0.59	5.5	5.5	0.81552	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (3);	0.207764	0.48286	D	0.000200	T	0.61464	0.2349	L	0.38733	1.17	0.45342	D	0.998331	D	0.65815	0.995	P	0.53689	0.732	T	0.56019	-0.8048	10	0.15952	T	0.53	-22.6167	14.3367	0.66595	1.0:0.0:0.0:0.0	.	188	P09936	UCHL1_HUMAN	C	188;188;172;188	ENSP00000422542:S188C;ENSP00000284440:S188C;ENSP00000426895:S172C;ENSP00000423623:S188C	ENSP00000284440:S188C	S	+	1	0	UCHL1	40960912	1.000000	0.71417	0.990000	0.47175	0.814000	0.46013	7.028000	0.76470	2.308000	0.77769	0.533000	0.62120	AGT	.	.		0.443	UCHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216827.1	NM_004181		T	41266155	A	T	41266155	3	4	245	1	0	0	0	0	1	0	0	0	16935	188	7	4	592	4	UCHL1	4	41266155	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	23242834	41266155	149888121	70	33540										
POLR2B	5431	hgsc.bcm.edu	37	chr4	57873096	57873096	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	cggatcatatctgatggcctAaaatactctttagctactgg	8	9	3	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr4:57873096A>T	ENST00000381227.1	+	11	1745	c.1332A>T	c.(1330-1332)ctA>ctT	p.L444L	POLR2B_ENST00000314595.5_Silent_p.L444L|POLR2B_ENST00000441246.2_Silent_p.L437L|POLR2B_ENST00000431623.2_Silent_p.L369L			P30876	RPB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide B, 140kDa	444					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonucleoside binding (GO:0032549)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(10)|large_intestine(9)|lung(17)|ovary(2)|prostate(4)|skin(1)	52	Glioma(25;0.08)|all_neural(26;0.181)					CTGATGGCCTAAAATACTCTT	0.408																																					p.L444L		Atlas-SNP	.											.	POLR2B	108	.	0			c.A1332T						.						84	90	88					4																	57873096		2203	4300	6503	SO:0001819	synonymous_variant	5431	exon10			TGGCCTAAAATAC		CCDS3511.1	4q12	2013-01-21	2002-08-29		ENSG00000047315	ENSG00000047315		"RNA polymerase subunits"	9188	protein-coding gene	gene with protein product		180661	"polymerase (RNA) II (DNA directed) polypeptide B (140kD)"			1518060, 8034326	Standard	NM_000938		Approved	RPB2	uc003hcl.1	P30876	OTTHUMG00000128771	ENST00000381227.1:c.1332A>T	chr4.hg19:g.57873096A>T		263.0	0.0		461.0	111.0	NM_000938	A8K1A8|Q8IZ61	Silent	SNP	ENST00000381227.1	hg19	CCDS3511.1																																																																																			.	.		0.408	POLR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250692.1	NM_000938		T	57873096	A	T	57873096	2	4	245	1	0	0	0	0	0	0	0	1	12224	349	13	4		4	POLR2B	4	57873096	Silent	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	16606941	57873096	133281180	71	33541										
LPHN3	23284	hgsc.bcm.edu	37	chr4	62862048	62862048	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	acctacttcatttggagtttTataggaccagcaactttgat	7	8	1	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr4:62862048T>C	ENST00000514591.1	+	19	3401	c.3072T>C	c.(3070-3072)ttT>ttC	p.F1024F	LPHN3_ENST00000504896.1_Silent_p.F1024F|LPHN3_ENST00000545650.1_Silent_p.F1024F|LPHN3_ENST00000508946.1_Silent_p.F1024F|LPHN3_ENST00000506700.1_Silent_p.F1024F|LPHN3_ENST00000506746.1_Silent_p.F1092F|LPHN3_ENST00000511324.1_Silent_p.F1092F|LPHN3_ENST00000508693.1_Silent_p.F1092F|LPHN3_ENST00000514996.1_Silent_p.F1024F|LPHN3_ENST00000512091.2_Silent_p.F1024F|LPHN3_ENST00000509896.1_Silent_p.F1092F|LPHN3_ENST00000507164.1_Silent_p.F1092F|LPHN3_ENST00000514157.1_Silent_p.F1024F|LPHN3_ENST00000506720.1_Silent_p.F1092F|LPHN3_ENST00000507625.1_Silent_p.F1092F			Q9HAR2	LPHN3_HUMAN	latrophilin 3	1011					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						TTTGGAGTTTTATAGGACCAG	0.393																																					p.F1024F		Atlas-SNP	.											.	LPHN3	800	.	0			c.T3072C						.						190	183	185					4																	62862048		1891	4122	6013	SO:0001819	synonymous_variant	23284	exon17			GAGTTTTATAGGA	AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"-", "GPCR / Class B : Orphans"	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.3072T>C	chr4.hg19:g.62862048T>C		132.0	0.0		65.0	50.0	NM_015236	E9PE04|O94867|Q9NWK5	Silent	SNP	ENST00000514591.1	hg19	CCDS54768.1	.	.	.	.	.	.	.	.	.	.	T	6.319	0.426890	0.11987	.	.	ENSG00000150471	ENST00000502815	.	.	.	4.85	4.85	0.62838	.	.	.	.	.	T	0.70325	0.3211	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.70156	-0.4949	4	.	.	.	.	14.4383	0.67298	0.0:0.0:0.0:1.0	.	.	.	.	H	482	.	.	Y	+	1	0	LPHN3	62544643	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.233000	0.51311	1.818000	0.53035	0.460000	0.39030	TAT	.	.		0.393	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1			C	62862048	T	C	62862048	2	2	245	1	0	0	0	0	0	0	0	1	8926	1751	61	2		2	LPHN3	4	62862048	Silent	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	4988952	62862048	128292228	72	33542										
PTPN13	5783	hgsc.bcm.edu	37	chr4	87692580	87692580	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tcagactctaagcaacatggTatcacaggcacagagtcatc	8	11	4	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr4:87692580T>A	ENST00000411767.2	+	31	5123	c.5060T>A	c.(5059-5061)gTa>gAa	p.V1687E	PTPN13_ENST00000427191.2_Missense_Mutation_p.V1668E|PTPN13_ENST00000316707.6_Missense_Mutation_p.V1496E|PTPN13_ENST00000436978.1_Missense_Mutation_p.V1692E|PTPN13_ENST00000511467.1_Missense_Mutation_p.V1692E			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	1687					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		AGCAACATGGTATCACAGGCA	0.428																																					p.V1692E		Atlas-SNP	.											.	PTPN13	203	.	0			c.T5075A						.						92	92	92					4																	87692580		2070	4221	6291	SO:0001583	missense	5783	exon31			ACATGGTATCACA		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.5060T>A	chr4.hg19:g.87692580T>A	ENSP00000407249:p.Val1687Glu	223.0	0.0		100.0	82.0	NM_080685	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	hg19	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	T	10.55	1.382560	0.25031	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T;T	0.53857	0.6;0.62;0.69;0.6;0.62	4.92	2.27	0.28462	.	1.043520	0.07682	N	0.937336	T	0.39118	0.1066	L	0.34521	1.04	0.09310	N	1	B;B;P;B	0.39717	0.001;0.321;0.684;0.321	B;B;B;B	0.40602	0.003;0.334;0.265;0.334	T	0.28870	-1.0030	10	0.30854	T	0.27	.	2.1852	0.03885	0.1275:0.1492:0.132:0.5912	.	1496;1668;1687;1692	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	E	1668;1692;1496;1687;1692;1636	ENSP00000408368:V1668E;ENSP00000394794:V1692E;ENSP00000322675:V1496E;ENSP00000407249:V1687E;ENSP00000426626:V1692E	ENSP00000322675:V1496E	V	+	2	0	PTPN13	87911604	0.000000	0.05858	0.001000	0.08648	0.563000	0.35712	0.055000	0.14229	0.838000	0.34948	-0.263000	0.10527	GTA	.	.		0.428	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			A	87692580	T	A	87692580	3	1	245	1	0	0	0	0	1	0	0	0	12795	1638	57	4	5193	4	PTPN13	4	87692580	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	24830532	87692580	103461696	73	33543										
INTU	27152	hgsc.bcm.edu	37	chr4	128628111	128628111	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tgatggtttagaagaaagtgGgaccttgcttaaggtgtgtg	15	3	0	3			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr4:128628111G>A	ENST00000335251.6	+	12	2361	c.2258G>A	c.(2257-2259)gGg>gAg	p.G753E		NM_015693.3	NP_056508.2	Q9ULD6	INTU_HUMAN	inturned planar cell polarity protein	753					cilium assembly (GO:0042384)|hair follicle morphogenesis (GO:0031069)|keratinocyte differentiation (GO:0030216)|limb development (GO:0060173)|negative regulation of cell division (GO:0051782)|negative regulation of keratinocyte proliferation (GO:0010839)|nervous system development (GO:0007399)|positive regulation of smoothened signaling pathway (GO:0045880)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord dorsal/ventral patterning (GO:0021513)	cytoplasm (GO:0005737)				breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	43						GAAGAAAGTGGGACCTTGCTT	0.438																																					p.G753E		Atlas-SNP	.											.	INTU	92	.	0			c.G2258A						.						188	190	189					4																	128628111		2203	4300	6503	SO:0001583	missense	27152	exon12			AAAGTGGGACCTT	BC051698	CCDS34061.1	4q28.2	2013-03-05	2013-03-05	2006-10-24	ENSG00000164066	ENSG00000164066			29239	protein-coding gene	gene with protein product		610621	"PDZ domain containing 6", "inturned planar cell polarity effector homolog (Drosophila)"	PDZK6, PDZD6		10574462, 21761479	Standard	NM_015693		Approved	KIAA1284	uc003ifk.2	Q9ULD6	OTTHUMG00000161202	ENST00000335251.6:c.2258G>A	chr4.hg19:g.128628111G>A	ENSP00000334003:p.Gly753Glu	77.0	0.0		39.0	31.0	NM_015693	A1L4N5|D6RAE6|D6RBT4|Q4W5I8|Q86V55	Missense_Mutation	SNP	ENST00000335251.6	hg19	CCDS34061.1	.	.	.	.	.	.	.	.	.	.	G	4.171	0.030270	0.08101	.	.	ENSG00000164066	ENST00000335251	.	.	.	4.36	2.57	0.30868	.	0.313071	0.33670	N	0.004678	T	0.34803	0.0910	L	0.47716	1.5	0.80722	D	1	P	0.38504	0.634	B	0.36186	0.219	T	0.13602	-1.0503	9	0.09338	T	0.73	-2.0343	3.9214	0.09245	0.1529:0.1265:0.5827:0.1378	.	753	Q9ULD6	PDZD6_HUMAN	E	753	.	ENSP00000334003:G753E	G	+	2	0	INTU	128847561	0.988000	0.35896	0.339000	0.25562	0.013000	0.08279	2.472000	0.45136	0.730000	0.32425	0.650000	0.86243	GGG	.	.		0.438	INTU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364147.2	XM_371707		A	128628111	G	A	128628111	3	1	245	1	0	0	0	0	1	0	0	0	7795	1232	43	3	2304	3	INTU	4	128628111	Missense_Mutation	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	40935531	128628111	62526165	74	33544										
SH3D19	152503	hgsc.bcm.edu	37	chr4	152080413	152080413	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	aagtttctagttctctcaacAttactgagctttccagatac	5	10	3	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr4:152080413A>T	ENST00000409252.2	-	8	1601	c.894T>A	c.(892-894)aaT>aaA	p.N298K	SH3D19_ENST00000424281.1_Missense_Mutation_p.N262K|SH3D19_ENST00000427414.2_Missense_Mutation_p.N262K|SH3D19_ENST00000409598.4_Missense_Mutation_p.N298K|SH3D19_ENST00000514152.1_Missense_Mutation_p.N298K|SH3D19_ENST00000455740.1_Missense_Mutation_p.N298K|SH3D19_ENST00000304527.4_Missense_Mutation_p.N298K			Q5HYK7	SH319_HUMAN	SH3 domain containing 19	298	Pro-rich.				cytoskeleton organization (GO:0007010)|membrane organization (GO:0061024)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of cell morphogenesis (GO:0022604)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)			autonomic_ganglia(1)|endometrium(1)|large_intestine(3)|lung(10)|ovary(1)|skin(3)|urinary_tract(1)	20	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)				TTCTCTCAACATTACTGAGCT	0.363																																					p.N298K		Atlas-SNP	.											.	SH3D19	54	.	0			c.T894A						.						124	117	120					4																	152080413		2203	4300	6503	SO:0001583	missense	152503	exon9			CTCAACATTACTG	BX647422	CCDS34077.2, CCDS47143.1, CCDS47144.1	4q31.3	2009-03-05	2009-03-05	2009-03-05	ENSG00000109686	ENSG00000109686			30418	protein-coding gene	gene with protein product	"EEN binding protein"	608674				12477932	Standard	NM_001009555		Approved	DKFZp434D0215, EVE1, EBP, Kryn, SH3P19	uc010ipl.1	Q5HYK7	OTTHUMG00000154051	ENST00000409252.2:c.894T>A	chr4.hg19:g.152080413A>T	ENSP00000386848:p.Asn298Lys	96.0	0.0		68.0	21.0	NM_001128923	B7Z296|Q08EK1|Q32N10|Q5U3B8|Q86XB3|Q8N5E7|Q9UFC8	Missense_Mutation	SNP	ENST00000409252.2	hg19	CCDS34077.2	.	.	.	.	.	.	.	.	.	.	A	11.22	1.573240	0.28092	.	.	ENSG00000109686	ENST00000409598;ENST00000304527;ENST00000455740;ENST00000424281;ENST00000427414;ENST00000409252;ENST00000514152	T;T;T;T;T;T;T	0.69561	-0.41;0.25;-0.41;-0.39;-0.39;0.25;-0.41	5.52	0.48	0.16804	.	0.587217	0.16016	N	0.233521	T	0.55545	0.1927	L	0.54323	1.7	0.09310	N	1	P;P;P;P	0.40834	0.611;0.73;0.73;0.611	B;B;B;B	0.42771	0.159;0.302;0.397;0.159	T	0.42464	-0.9450	10	0.16896	T	0.51	-8.0147	4.1815	0.10378	0.5186:0.0:0.3285:0.1529	.	298;298;262;76	Q5HYK7;Q5HYK7-2;Q5HYK7-3;B3KY23	SH319_HUMAN;.;.;.	K	298;298;298;262;262;298;298	ENSP00000387030:N298K;ENSP00000302913:N298K;ENSP00000416708:N298K;ENSP00000404542:N262K;ENSP00000415694:N262K;ENSP00000386848:N298K;ENSP00000423449:N298K	ENSP00000302913:N298K	N	-	3	2	SH3D19	152299863	0.012000	0.17670	0.541000	0.28102	0.326000	0.28443	0.162000	0.16501	0.178000	0.19917	0.460000	0.39030	AAT	.	.		0.363	SH3D19-002	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335132.3	NM_001009555		T	152080413	A	T	152080413	3	4	245	1	0	0	0	0	1	0	0	0	14264	214	8	4	1530	4	SH3D19	4	152080413	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	23452302	152080413	39073863	75	33545										
IRX4	50805	hgsc.bcm.edu	37	chr5	1882077	1882077	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gctctcgtagaccgggcagtAgaccggcgcctgggccgagg	17	13	1	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr5:1882077A>T	ENST00000505790.1	-	3	598	c.142T>A	c.(142-144)Tac>Aac	p.Y48N	IRX4_ENST00000505938.1_5'Flank|IRX4_ENST00000513692.1_Missense_Mutation_p.Y48N|IRX4_ENST00000231357.2_Missense_Mutation_p.Y48N|CTD-2194D22.3_ENST00000506335.1_RNA	NM_001278634.1	NP_001265563.1	P78413	IRX4_HUMAN	iroquois homeobox 4	48					establishment of organ orientation (GO:0048561)|heart development (GO:0007507)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|lung(7)|ovary(1)|prostate(1)	10				GBM - Glioblastoma multiforme(108;0.242)		ACCGGGCAGTAGACCGGCGCC	0.726																																					p.Y48N		Atlas-SNP	.											.	IRX4	45	.	0			c.T142A						.						3	4	4					5																	1882077		1796	3742	5538	SO:0001583	missense	50805	exon2			GGCAGTAGACCGG	AF124733	CCDS3867.1, CCDS75225.1	5p15.33	2011-06-20	2007-07-13		ENSG00000113430	ENSG00000113430		"Homeoboxes / TALE class"	6129	protein-coding gene	gene with protein product		606199	"iroquois homeobox protein 4"			10625552	Standard	NM_016358		Approved		uc003jcz.2	P78413	OTTHUMG00000090411	ENST00000505790.1:c.142T>A	chr5.hg19:g.1882077A>T	ENSP00000423161:p.Tyr48Asn	76.0	0.0		87.0	59.0	NM_016358	B2RMW5|D3DTC5|H1AFL0|H1AFL1|Q2NL64|Q9UHR2	Missense_Mutation	SNP	ENST00000505790.1	hg19	CCDS3867.1	.	.	.	.	.	.	.	.	.	.	a	19.62	3.861304	0.71949	.	.	ENSG00000113430	ENST00000231357;ENST00000505790;ENST00000513692;ENST00000511126	T;T;T;D	0.83075	-0.11;-0.11;-0.11;-1.68	3.9	3.9	0.45041	.	0.000000	0.64402	U	0.000001	D	0.86606	0.5973	L	0.43923	1.385	0.58432	D	0.999999	D	0.71674	0.998	D	0.80764	0.994	D	0.86851	0.2023	10	0.52906	T	0.07	-16.9238	12.6999	0.57026	1.0:0.0:0.0:0.0	.	48	P78413	IRX4_HUMAN	N	48	ENSP00000231357:Y48N;ENSP00000423161:Y48N;ENSP00000424235:Y48N;ENSP00000421772:Y48N	ENSP00000231357:Y48N	Y	-	1	0	IRX4	1935077	1.000000	0.71417	1.000000	0.80357	0.805000	0.45488	7.924000	0.87555	1.544000	0.49359	0.378000	0.23410	TAC	.	.		0.726	IRX4-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365500.1	NM_016358		T	1882077	A	T	1882077	3	4	245	1	0	0	0	0	1	0	0	0	7855	420	15	4	1433	4	IRX4	5	1882077	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10		1882077	179033183	76	33546										
ERBB2IP	55914	hgsc.bcm.edu	37	chr5	65322213	65322213	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gaggaaatgggtgatatgcaAaaattaaaagtcattaattt	9	2	1	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr5:65322213A>C	ENST00000284037.5	+	13	1493	c.1104A>C	c.(1102-1104)caA>caC	p.Q368H	ERBB2IP_ENST00000380936.1_Missense_Mutation_p.Q368H|ERBB2IP_ENST00000508515.1_Missense_Mutation_p.Q368H|ERBB2IP_ENST00000416865.2_Missense_Mutation_p.Q368H|ERBB2IP_ENST00000380939.2_Missense_Mutation_p.Q368H|ERBB2IP_ENST00000506030.1_Missense_Mutation_p.Q368H|ERBB2IP_ENST00000511297.1_Missense_Mutation_p.Q368H|ERBB2IP_ENST00000380943.2_Missense_Mutation_p.Q368H|ERBB2IP_ENST00000380938.2_Missense_Mutation_p.Q368H|ERBB2IP_ENST00000380935.1_Missense_Mutation_p.Q368H	NM_001253697.1	NP_001240626.1	Q96RT1	LAP2_HUMAN	erbb2 interacting protein	368					basal protein localization (GO:0045175)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell growth (GO:0016049)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|signal transduction (GO:0007165)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|hemidesmosome (GO:0030056)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ErbB-2 class receptor binding (GO:0005176)|integrin binding (GO:0005178)|structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|skin(2)	36		Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191)		GTGATATGCAAAAATTAAAAG	0.303																																					p.Q368H		Atlas-SNP	.											.	ERBB2IP	120	.	0			c.A1104C						.						59	65	63					5																	65322213		2203	4290	6493	SO:0001583	missense	55914	exon13			TATGCAAAAATTA		CCDS3990.1, CCDS34172.1, CCDS58951.1, CCDS58952.1, CCDS58953.1, CCDS58954.1	5p14.3-q12.3	2008-07-18	2001-11-29		ENSG00000112851	ENSG00000112851			15842	protein-coding gene	gene with protein product	"densin-180-like protein", "ERBB2-interacting protein"	606944	"erbb2-interacting protein"			10574462, 10878805	Standard	NM_001253697		Approved	ERBIN, LAP2	uc011cqx.2	Q96RT1	OTTHUMG00000097808	ENST00000284037.5:c.1104A>C	chr5.hg19:g.65322213A>C	ENSP00000284037:p.Gln368His	82.0	0.0		88.0	18.0	NM_001253701	A0AVR1|B4E3F1|B7ZLV9|E7EQW9|E9PCR8|Q1RMD0|Q86W38|Q9NR18|Q9NW48|Q9ULJ5	Missense_Mutation	SNP	ENST00000284037.5	hg19	CCDS58953.1	.	.	.	.	.	.	.	.	.	.	A	18.62	3.663090	0.67700	.	.	ENSG00000112851	ENST00000284037;ENST00000380943;ENST00000416865;ENST00000380939;ENST00000380936;ENST00000380935;ENST00000380938;ENST00000511297;ENST00000506030;ENST00000508515	T;T;T;T;T;T;T;T;T;T	0.56776	0.44;0.44;2.31;0.44;0.44;0.44;0.44;0.44;0.44;0.44	4.93	-3.27	0.05048	.	0.000000	0.85682	D	0.000000	T	0.54046	0.1834	L	0.28014	0.82	0.54753	D	0.999988	D;D;D;D;D;D;D;D	0.76494	0.995;0.999;0.995;0.999;0.999;0.999;0.993;0.998	D;D;D;D;D;D;D;D	0.91635	0.95;0.986;0.95;0.999;0.987;0.998;0.946;0.968	T	0.54951	-0.8216	10	0.72032	D	0.01	.	12.7342	0.57214	0.4041:0.0:0.5959:0.0	.	368;368;368;368;368;368;368;368	B4DIP2;Q96RT1-4;E9PCR8;B7ZLV9;E7EQW9;Q96RT1;Q96RT1-7;Q96RT1-2	.;.;.;.;.;LAP2_HUMAN;.;.	H	368	ENSP00000284037:Q368H;ENSP00000370330:Q368H;ENSP00000397833:Q368H;ENSP00000370326:Q368H;ENSP00000370323:Q368H;ENSP00000370322:Q368H;ENSP00000370325:Q368H;ENSP00000422766:Q368H;ENSP00000426632:Q368H;ENSP00000422015:Q368H	ENSP00000284037:Q368H	Q	+	3	2	ERBB2IP	65357969	1.000000	0.71417	0.987000	0.45799	0.985000	0.73830	0.647000	0.24812	-0.542000	0.06249	-0.899000	0.02877	CAA	.	.		0.303	ERBB2IP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215070.1	NM_018695		C	65322213	A	C	65322213	3	2	245	1	0	0	0	0	1	0	0	0	5209	11	1	5	1146	5	ERBB2IP	5	65322213	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	63440136	65322213	115593047	77	33547										
GPR98	84059	hgsc.bcm.edu	37	chr5	90070014	90070014	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tggatgtagactgagtcccaGaagaccattgtgttgcacac	11	9	0	4			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr5:90070014G>A	ENST00000405460.2	+	60	12393	c.12297G>A	c.(12295-12297)caG>caA	p.Q4099Q		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	4099	Calx-beta 27. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		CTGAGTCCCAGAAGACCATTG	0.418																																					p.Q4099Q		Atlas-SNP	.											.	GPR98	605	.	0			c.G12297A						.						86	83	84					5																	90070014		1974	4146	6120	SO:0001819	synonymous_variant	84059	exon60			GTCCCAGAAGACC	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.12297G>A	chr5.hg19:g.90070014G>A		65.0	0.0		51.0	11.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	hg19	CCDS47246.1																																																																																			.	.		0.418	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		A	90070014	G	A	90070014	2	1	245	1	0	0	0	0	0	0	0	1	6730	933	33	3		3	GPR98	5	90070014	Silent	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	24747801	90070014	90845246	78	33548										
ADAMTS19	171019	hgsc.bcm.edu	37	chr5	128977564	128977564	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gttttcagcatgttatttgcAcaggattatggtgcaaggta	11	5	1	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr5:128977564A>T	ENST00000274487.4	+	11	1910	c.1765A>T	c.(1765-1767)Aca>Tca	p.T589S	CTC-575N7.1_ENST00000503616.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	589	Disintegrin.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		TGTTATTTGCACAGGATTATG	0.378																																					p.T589S		Atlas-SNP	.											.	ADAMTS19	216	.	0			c.A1765T						.						191	163	173					5																	128977564		2203	4300	6503	SO:0001583	missense	171019	exon11			ATTTGCACAGGAT	AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"ADAM metallopeptidases with thrombospondin type 1 motif"	17111	protein-coding gene	gene with protein product		607513	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.1765A>T	chr5.hg19:g.128977564A>T	ENSP00000274487:p.Thr589Ser	86.0	0.0		79.0	20.0	NM_133638		Missense_Mutation	SNP	ENST00000274487.4	hg19	CCDS4146.1	.	.	.	.	.	.	.	.	.	.	A	12.22	1.871418	0.33069	.	.	ENSG00000145808	ENST00000274487	T	0.64260	-0.09	3.85	2.68	0.31781	.	0.087960	0.44902	D	0.000403	T	0.45716	0.1356	N	0.21142	0.635	0.35230	D	0.776866	P	0.46220	0.874	B	0.42555	0.391	T	0.53165	-0.8477	9	.	.	.	.	9.8019	0.40770	0.9158:0.0:0.0842:0.0	.	589	Q8TE59	ATS19_HUMAN	S	589	ENSP00000274487:T589S	.	T	+	1	0	ADAMTS19	129005463	0.999000	0.42202	0.848000	0.33437	0.980000	0.70556	2.334000	0.43920	0.819000	0.34492	0.482000	0.46254	ACA	.	.		0.378	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638		T	128977564	A	T	128977564	3	4	245	1	0	0	0	0	1	0	0	0	264	159	6	4	1807	4	ADAMTS19	5	128977564	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	38907550	128977564	51937696	79	33549										
CXXC5	51523	hgsc.bcm.edu	37	chr5	139060694	139060694	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gcctgcctgacatggaggctGtggcaggtgccgaagccctc	15	13	0	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr5:139060694G>A	ENST00000302517.3	+	2	1300	c.586G>A	c.(586-588)Gtg>Atg	p.V196M	CXXC5_ENST00000511048.1_Missense_Mutation_p.V196M|CXXC5_ENST00000515038.1_3'UTR	NM_016463.7	NP_057547.5	Q7LFL8	CXXC5_HUMAN	CXXC finger protein 5	196					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(1)	12			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CATGGAGGCTGTGGCAGGTGC	0.627																																					p.V196M		Atlas-SNP	.											.	CXXC5	27	.	0			c.G586A						.						26	33	31					5																	139060694		2129	4242	6371	SO:0001583	missense	51523	exon2			GAGGCTGTGGCAG	AK024338	CCDS43370.1	5q31.3	2014-02-18	2011-12-01						26943	protein-coding gene	gene with protein product	"retinoid-inducible nuclear factor", "WT1-induced Inhibitor of Dishevelled"	612752				11042152, 19001364, 19182210, 20220130	Standard	NM_016463		Approved	HSPC195, RINF, WID	uc010jfg.1	Q7LFL8		ENST00000302517.3:c.586G>A	chr5.hg19:g.139060694G>A	ENSP00000302543:p.Val196Met	72.0	0.0		55.0	13.0	NM_016463	B3KND0|C8CBA8|Q8TB79|Q9NV51|Q9P0S8	Missense_Mutation	SNP	ENST00000302517.3	hg19	CCDS43370.1	.	.	.	.	.	.	.	.	.	.	G	17.25	3.341980	0.61073	.	.	ENSG00000171604	ENST00000302517;ENST00000511048;ENST00000511457	T;T;T	0.47869	0.83;0.83;0.83	5.68	5.68	0.88126	.	0.128526	0.53938	D	0.000048	T	0.50701	0.1631	N	0.24115	0.695	0.40705	D	0.982513	D	0.67145	0.996	P	0.57548	0.823	T	0.45877	-0.9231	10	0.33141	T	0.24	-27.0177	17.9548	0.89065	0.0:0.0:1.0:0.0	.	196	Q7LFL8	CXXC5_HUMAN	M	196	ENSP00000302543:V196M;ENSP00000427379:V196M;ENSP00000430949:V196M	ENSP00000302543:V196M	V	+	1	0	CXXC5	139040878	1.000000	0.71417	0.967000	0.41034	0.607000	0.37147	6.803000	0.75180	2.681000	0.91329	0.561000	0.74099	GTG	.	.		0.627	CXXC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372744.1	NM_016463		A	139060694	G	A	139060694	3	1	245	1	0	0	0	0	1	0	0	0	4101	1377	48	3	588	3	CXXC5	5	139060694	Missense_Mutation	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	10083130	139060694	41854566	80	33550										
PCDHB13	56123	hgsc.bcm.edu	37	chr5	140595369	140595369	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ctggacgccaacgacaactcGcccttcgtgctgtacccgct	9	17	0	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr5:140595369G>A	ENST00000341948.4	+	1	1861	c.1674G>A	c.(1672-1674)tcG>tcA	p.S558S		NM_018933.2	NP_061756.1	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13	558	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(4)|lung(24)|ovary(5)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	66			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACGACAACTCGCCCTTCGTGC	0.721																																					p.S558S		Atlas-SNP	.											PCDHB13,colon,carcinoma,0,2	PCDHB13	142	.	0			c.G1674A						.						23	26	25					5																	140595369		2202	4291	6493	SO:0001819	synonymous_variant	56123	exon1			CAACTCGCCCTTC	AF152492	CCDS4255.1	5q31	2010-01-26			ENSG00000187372	ENSG00000187372		"Cadherins / Protocadherins : Clustered"	8684	other	protocadherin		606339				10380929	Standard	NM_018933		Approved	PCDH-BETA13	uc003lja.1	Q9Y5F0	OTTHUMG00000129615	ENST00000341948.4:c.1674G>A	chr5.hg19:g.140595369G>A		25.0	0.0		30.0	17.0	NM_018933	A8K9V6	Silent	SNP	ENST00000341948.4	hg19	CCDS4255.1																																																																																			.	.		0.721	PCDHB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251810.1	NM_018933		A	140595369	G	A	140595369	2	1	245	1	0	0	0	0	0	0	0	1	11547	1074	38	1		1	PCDHB13	5	140595369	Silent	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	1534675	140595369	40319891	81	33551										
GRIA1	2890	hgsc.bcm.edu	37	chr5	153035418	153035418	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	atggcatcggctaccactacAttcttgcaaatctggtgagt	9	10	2	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr5:153035418A>T	ENST00000285900.5	+	5	1028	c.685A>T	c.(685-687)Att>Ttt	p.I229F	GRIA1_ENST00000521843.2_Missense_Mutation_p.I160F|GRIA1_ENST00000448073.4_Missense_Mutation_p.I239F|GRIA1_ENST00000518142.1_Missense_Mutation_p.I149F|GRIA1_ENST00000340592.5_Missense_Mutation_p.I229F|GRIA1_ENST00000518783.1_Missense_Mutation_p.I239F	NM_000827.3|NM_001258019.1	NP_000818.2|NP_001244948.1	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1	229					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|axonal spine (GO:0044308)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|neuron spine (GO:0044309)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|PDZ domain binding (GO:0030165)			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)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Perampanel(DB08883)|Sevoflurane(DB01236)	CTACCACTACATTCTTGCAAA	0.443																																					p.I239F		Atlas-SNP	.											.	GRIA1	321	.	0			c.A715T						.						122	112	115					5																	153035418		2203	4300	6503	SO:0001583	missense	2890	exon5			CACTACATTCTTG		CCDS4322.1, CCDS47318.1, CCDS58986.1, CCDS58987.1, CCDS58988.1, CCDS58989.1	5q33	2012-08-29			ENSG00000155511	ENSG00000155511		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4571	protein-coding gene	gene with protein product		138248		GLUR1		1652753, 1319477	Standard	NM_000827		Approved	GluA1, GLURA	uc011dcy.2	P42261	OTTHUMG00000130148	ENST00000285900.5:c.685A>T	chr5.hg19:g.153035418A>T	ENSP00000285900:p.Ile229Phe	66.0	0.0		75.0	22.0	NM_001258021	B7Z2S0|B7Z2W8|B7Z3F6|B7Z9G9|D3DQI4|E7ESV8|Q2NKM6	Missense_Mutation	SNP	ENST00000285900.5	hg19	CCDS4322.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.562863	0.86335	.	.	ENSG00000155511	ENST00000285900;ENST00000544403;ENST00000518142;ENST00000537037;ENST00000340592;ENST00000521843;ENST00000544794;ENST00000518783;ENST00000448073	T;T;T;T;T;T;T	0.28666	1.6;1.6;1.6;1.6;1.6;1.6;1.6	4.84	4.84	0.62591	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	T	0.49184	0.1542	L	0.54323	1.7	0.80722	D	1	D;D;P;D;D;P	0.89917	1.0;1.0;0.941;1.0;1.0;0.813	D;D;P;D;D;P	0.91635	0.999;0.999;0.587;0.999;0.999;0.518	T	0.41360	-0.9513	10	0.36615	T	0.2	.	13.8871	0.63714	1.0:0.0:0.0:0.0	.	239;239;149;239;229;229	E7ESV8;B7Z9G9;B7Z3F6;B7Z2W8;P42261-2;P42261	.;.;.;.;.;GRIA1_HUMAN	F	229;229;149;183;229;160;160;239;239	ENSP00000285900:I229F;ENSP00000427920:I149F;ENSP00000339343:I229F;ENSP00000427864:I160F;ENSP00000442108:I160F;ENSP00000428994:I239F;ENSP00000415569:I239F	ENSP00000285900:I229F	I	+	1	0	GRIA1	153015611	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.578000	0.90777	1.934000	0.56057	0.450000	0.29827	ATT	.	.		0.443	GRIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252456.3			T	153035418	A	T	153035418	3	4	245	1	0	0	0	0	1	0	0	0	6776	217	8	4	703	4	GRIA1	5	153035418	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	12440049	153035418	27879842	82	33552										
TIMD4	91937	hgsc.bcm.edu	37	chr5	156381475	156381475	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tttacatcgttgaaccagccAggcacttctatgcggcagca	9	12	1	1	rs371298031		TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr5:156381475A>T	ENST00000274532.2	-	2	407	c.351T>A	c.(349-351)ccT>ccA	p.P117P	TIMD4_ENST00000407087.3_Silent_p.P117P	NM_138379.2	NP_612388.2	Q96H15	TIMD4_HUMAN	T-cell immunoglobulin and mucin domain containing 4	117	Ig-like V-type.					integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(23)|ovary(2)|skin(2)	37	Renal(175;0.00488)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TGAACCAGCCAGGCACTTCTA	0.507																																					p.P117P		Atlas-SNP	.											.	TIMD4	94	.	0			c.T351A						.						85	78	81					5																	156381475		2203	4300	6503	SO:0001819	synonymous_variant	91937	exon2			CCAGCCAGGCACT	BC008988	CCDS4332.1, CCDS54943.1	5q33.3	2013-01-11			ENSG00000145850	ENSG00000145850		"Immunoglobulin superfamily / V-set domain containing"	25132	protein-coding gene	gene with protein product		610096				12477932	Standard	NM_001146726		Approved		uc003lwh.2	Q96H15	OTTHUMG00000130244	ENST00000274532.2:c.351T>A	chr5.hg19:g.156381475A>T		72.0	0.0		68.0	45.0	NM_138379	B5MCL9	Silent	SNP	ENST00000274532.2	hg19	CCDS4332.1																																																																																			.	.		0.507	TIMD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252568.1	NM_138379		T	156381475	A	T	156381475	2	4	245	1	0	0	0	0	0	0	0	1	15918	175	7	4		4	TIMD4	5	156381475	Silent	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	3346057	156381475	24533785	83	33553										
NIPAL4	348938	hgsc.bcm.edu	37	chr5	156899882	156899882	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ccactgttattagactggaaGacaagaacgtccttgtggac	10	9	0	3			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr5:156899882G>A	ENST00000311946.7	+	6	1431	c.1315G>A	c.(1315-1317)Gac>Aac	p.D439N	ADAM19_ENST00000430702.2_Intron|NIPAL4_ENST00000435489.2_Missense_Mutation_p.D420N	NM_001099287.1	NP_001092757.1	Q0D2K0	NIPA4_HUMAN	NIPA-like domain containing 4	439						integral component of membrane (GO:0016021)	magnesium ion transmembrane transporter activity (GO:0015095)			breast(3)|endometrium(3)|kidney(1)|large_intestine(1)|lung(12)|prostate(1)|skin(1)	22						TAGACTGGAAGACAAGAACGT	0.483																																					p.D439N		Atlas-SNP	.											.	NIPAL4	48	.	0			c.G1315A						.						44	43	43					5																	156899882		1900	4124	6024	SO:0001583	missense	348938	exon6			CTGGAAGACAAGA	AK026158	CCDS47328.1, CCDS54944.1	5q33.3	2009-03-24	2009-03-24		ENSG00000172548	ENSG00000172548			28018	protein-coding gene	gene with protein product	"ichthyin"	609383	"NIPA-like 4"			8619474, 9110174, 15317751	Standard	NM_001099287		Approved	ICHYN	uc003lwx.4	Q0D2K0	OTTHUMG00000163497	ENST00000311946.7:c.1315G>A	chr5.hg19:g.156899882G>A	ENSP00000311687:p.Asp439Asn	74.0	0.0		64.0	43.0	NM_001099287	A8S6F1|A8S6F5|A8S6F8|B4DLF3|Q0D2J8|Q0D2J9	Missense_Mutation	SNP	ENST00000311946.7	hg19	CCDS47328.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.277479	0.80580	.	.	ENSG00000172548	ENST00000435489;ENST00000311946	D;D	0.92348	-2.83;-3.02	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	D	0.94311	0.8172	L	0.36672	1.1	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	D	0.93554	0.6889	10	0.45353	T	0.12	-30.539	20.3437	0.98782	0.0:0.0:1.0:0.0	.	420;439	Q0D2K0-2;Q0D2K0	.;NIPA4_HUMAN	N	420;439	ENSP00000406456:D420N;ENSP00000311687:D439N	ENSP00000311687:D439N	D	+	1	0	NIPAL4	156832460	1.000000	0.71417	1.000000	0.80357	0.510000	0.34073	8.141000	0.89618	2.815000	0.96918	0.561000	0.74099	GAC	.	.		0.483	NIPAL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373789.1	NM_001099287		A	156899882	G	A	156899882	3	1	245	1	0	0	0	0	1	0	0	0	10436	942	33	3	1337	3	NIPAL4	5	156899882	Missense_Mutation	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	518407	156899882	24015378	84	33554										
C5orf54	63920	hgsc.bcm.edu	37	chr5	159821530	159821530	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	cagtatggaaaaggaggacaCtatattctatgccaatttct	8	7	2	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr5:159821530C>G	ENST00000408953.3	-	2	1475	c.968G>C	c.(967-969)aGt>aCt	p.S323T	C5orf54_ENST00000523213.1_Missense_Mutation_p.S323T	NM_022090.3	NP_071373.2														breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	12						aaggaggacactatattctat	0.383																																					p.S323T		Atlas-SNP	.											.	C5orf54	46	.	0			c.G968C						.						48	49	49					5																	159821530		2203	4299	6502	SO:0001583	missense	63920	exon2			AGGACACTATATT																												ENST00000408953.3:c.968G>C	chr5.hg19:g.159821530C>G	ENSP00000386184:p.Ser323Thr	88.0	0.0		81.0	18.0	NM_022090		Missense_Mutation	SNP	ENST00000408953.3	hg19	CCDS34283.1	.	.	.	.	.	.	.	.	.	.	C	0.802	-0.755028	0.03019	.	.	ENSG00000221886	ENST00000408953;ENST00000523213	D;D	0.84146	-1.81;-1.81	2.78	0.73	0.18271	.	.	.	.	.	T	0.63604	0.2525	N	0.05230	-0.09	0.21579	N	0.99964	B	0.06786	0.001	B	0.06405	0.002	T	0.49051	-0.8979	9	0.13470	T	0.59	.	4.523	0.11968	0.0:0.6256:0.0:0.3744	.	323	Q8IZ13	CE054_HUMAN	T	323	ENSP00000386184:S323T;ENSP00000428831:S323T	ENSP00000386184:S323T	S	-	2	0	C5orf54	159754108	0.996000	0.38824	0.999000	0.59377	0.997000	0.91878	0.140000	0.16056	0.160000	0.19432	0.655000	0.94253	AGT	.	.		0.383	C5orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374143.1			G	159821530	C	G	159821530	3	3	245	1	0	0	0	0	1	0	0	0	2312	565	20	4	820	4	C5orf54	5	159821530	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	2921648	159821530	21093730	85	33555										
FGFR4	2264	hgsc.bcm.edu	37	chr5	176520211	176520211	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	catcctgtacgcgtcgggctCcctggccttggctgtgctcc	12	16	0	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr5:176520211C>T	ENST00000292408.4	+	9	1375	c.1130C>T	c.(1129-1131)tCc>tTc	p.S377F	FGFR4_ENST00000292410.3_Intron|FGFR4_ENST00000393637.1_Intron|FGFR4_ENST00000502906.1_Missense_Mutation_p.S377F|FGFR4_ENST00000393648.2_Intron	NM_002011.3|NM_213647.1	NP_002002.3|NP_998812.1	P22455	FGFR4_HUMAN	fibroblast growth factor receptor 4	377					alveolar secondary septum development (GO:0061144)|cell migration (GO:0016477)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphate ion homeostasis (GO:0055062)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of proteolysis (GO:0045862)|protein autophosphorylation (GO:0046777)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cholesterol homeostasis (GO:2000188)|regulation of extracellular matrix disassembly (GO:0010715)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	34	all_cancers(89;5.93e-05)|Renal(175;0.000269)|Lung NSC(126;0.0088)|all_lung(126;0.0142)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Palifermin(DB00039)|Ponatinib(DB08901)	GCGTCGGGCTCCCTGGCCTTG	0.692										TSP Lung(9;0.080)																											p.S377F		Atlas-SNP	.											.	FGFR4	174	.	0			c.C1130T						.						42	35	37					5																	176520211		2203	4298	6501	SO:0001583	missense	2264	exon9			CGGGCTCCCTGGC	AF202063	CCDS4410.1, CCDS4411.1	5q35.2	2013-09-19			ENSG00000160867	ENSG00000160867		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3691	protein-coding gene	gene with protein product		134935					Standard	XM_005265837		Approved	JTK2, CD334	uc003mfm.3	P22455	OTTHUMG00000151523	ENST00000292408.4:c.1130C>T	chr5.hg19:g.176520211C>T	ENSP00000292408:p.Ser377Phe	109.0	0.0		85.0	25.0	NM_002011	G3JVM2|G3JVM5|G3JVM7|G3JVM9|O43785|Q14309|Q71TW8|Q8TDA0|Q96KE5	Missense_Mutation	SNP	ENST00000292408.4	hg19	CCDS4410.1	.	.	.	.	.	.	.	.	.	.	C	3.574	-0.086980	0.07097	.	.	ENSG00000160867	ENST00000292408;ENST00000502906;ENST00000377207	T;T	0.80994	-1.44;-1.44	4.98	4.98	0.66077	.	0.411878	0.28996	N	0.013475	T	0.59838	0.2223	N	0.11818	0.18	0.80722	D	1	B	0.13145	0.007	B	0.12156	0.007	T	0.54820	-0.8236	10	0.08837	T	0.75	.	8.1914	0.31370	0.0:0.7557:0.1599:0.0844	.	377	P22455	FGFR4_HUMAN	F	377;377;605	ENSP00000292408:S377F;ENSP00000424960:S377F	ENSP00000292408:S377F	S	+	2	0	FGFR4	176452817	0.997000	0.39634	0.983000	0.44433	0.827000	0.46813	2.519000	0.45546	2.317000	0.78254	0.561000	0.74099	TCC	.	.		0.692	FGFR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253410.1			T	176520211	C	T	176520211	3	4	245	1	0	0	0	0	1	0	0	0	5876	855	30	3	1160	3	FGFR4	5	176520211	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	16698681	176520211	4395049	86	33556										
ZNF454	285676	hgsc.bcm.edu	37	chr5	178392529	178392529	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ctcttcccttactgaacatcAgagaattcatactggagaga	7	10	3	3			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr5:178392529A>T	ENST00000320129.3	+	5	1427	c.1124A>T	c.(1123-1125)cAg>cTg	p.Q375L	ZNF454_ENST00000519564.1_Missense_Mutation_p.Q375L	NM_001178090.1|NM_182594.2	NP_001171561.1|NP_872400.2	Q8N9F8	ZN454_HUMAN	zinc finger protein 454	375					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(11)|lung(18)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	46	all_cancers(89;0.000904)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.225)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.234)		ACTGAACATCAGAGAATTCAT	0.408																																					p.Q375L		Atlas-SNP	.											.	ZNF454	99	.	0			c.A1124T						.						40	43	42					5																	178392529		2203	4300	6503	SO:0001583	missense	285676	exon5			AACATCAGAGAAT	AK094763	CCDS4441.1	5q35.3	2013-01-08			ENSG00000178187	ENSG00000178187		"Zinc fingers, C2H2-type", "-"	21200	protein-coding gene	gene with protein product							Standard	NM_182594		Approved	FLJ37444	uc021yjc.1	Q8N9F8	OTTHUMG00000130891	ENST00000320129.3:c.1124A>T	chr5.hg19:g.178392529A>T	ENSP00000326249:p.Gln375Leu	101.0	0.0		98.0	34.0	NM_001178089	Q2M1P2|Q2M323	Missense_Mutation	SNP	ENST00000320129.3	hg19	CCDS4441.1	.	.	.	.	.	.	.	.	.	.	A	14.43	2.533295	0.45073	.	.	ENSG00000178187	ENST00000320129;ENST00000519564	T;T	0.05580	3.42;3.42	4.07	4.07	0.47477	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.38837	N	0.001558	T	0.03520	0.0101	N	0.04655	-0.195	0.31085	N	0.711441	B	0.17667	0.023	B	0.13407	0.009	T	0.09185	-1.0686	10	0.51188	T	0.08	-12.8824	11.3069	0.49340	1.0:0.0:0.0:0.0	.	375	Q8N9F8	ZN454_HUMAN	L	375	ENSP00000326249:Q375L;ENSP00000430354:Q375L	ENSP00000326249:Q375L	Q	+	2	0	ZNF454	178325135	0.004000	0.15560	1.000000	0.80357	0.997000	0.91878	1.527000	0.35975	1.845000	0.53610	0.454000	0.30748	CAG	.	.		0.408	ZNF454-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253476.2	XM_209718		T	178392529	A	T	178392529	3	4	245	1	0	0	0	0	1	0	0	0	17938	188	7	4	1138	4	ZNF454	5	178392529	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	1872318	178392529	2522731	87	33557										
HIVEP1	3096	hgsc.bcm.edu	37	chr6	12124094	12124094	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ctggcttgaatactctgaatGttcctggatgtcaccgggaa	11	9	2	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr6:12124094G>T	ENST00000379388.2	+	4	4398	c.4066G>T	c.(4066-4068)Gtt>Ttt	p.V1356F	HIVEP1_ENST00000541134.1_5'Flank	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	1356					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				TACTCTGAATGTTCCTGGATG	0.433																																					p.V1356F		Atlas-SNP	.											.	HIVEP1	242	.	0			c.G4066T						.						77	72	74					6																	12124094		1911	4150	6061	SO:0001583	missense	3096	exon4			CTGAATGTTCCTG	J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"Zinc fingers, C2H2-type"	4920	protein-coding gene	gene with protein product		194540	"human immunodeficiency virus type I enhancer-binding protein 1", "zinc finger protein 40"	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.4066G>T	chr6.hg19:g.12124094G>T	ENSP00000368698:p.Val1356Phe	86.0	0.0		158.0	24.0	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Missense_Mutation	SNP	ENST00000379388.2	hg19	CCDS43426.1	.	.	.	.	.	.	.	.	.	.	G	18.95	3.732437	0.69189	.	.	ENSG00000095951	ENST00000379388	T	0.20881	2.04	5.79	4.03	0.46877	.	0.250947	0.20930	N	0.083115	T	0.36026	0.0952	M	0.86740	2.835	0.80722	D	1	D	0.71674	0.998	P	0.61874	0.895	T	0.38415	-0.9662	9	.	.	.	-12.0308	12.3092	0.54920	0.136:0.0:0.864:0.0	.	1356	P15822	ZEP1_HUMAN	F	1356	ENSP00000368698:V1356F	.	V	+	1	0	HIVEP1	12232080	1.000000	0.71417	0.252000	0.24328	0.940000	0.58332	4.622000	0.61240	0.802000	0.34089	0.655000	0.94253	GTT	.	.		0.433	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114		T	12124094	G	T	12124094	3	4	245	1	0	0	0	0	1	0	0	0	7195	1377	48	3	4076	3	HIVEP1	6	12124094	Missense_Mutation	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10		12124094	158990973	88	33558										
OR12D3	81797	hgsc.bcm.edu	37	chr6	29342331	29342331	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	catagaaaagacataccaccAtaaaatgggaggcacaagtg	9	8	0	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr6:29342331A>G	ENST00000396806.3	-	1	737	c.734T>C	c.(733-735)aTg>aCg	p.M245T	OR5V1_ENST00000377154.1_Intron	NM_030959.2	NP_112221.1	Q9UGF7	O12D3_HUMAN	olfactory receptor, family 12, subfamily D, member 3	245						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)	23						ACATACCACCATAAAATGGGA	0.463																																					p.M245T		Atlas-SNP	.											.	OR12D3	55	.	0			c.T734C						.						66	64	65					6																	29342331		1511	2708	4219	SO:0001583	missense	81797	exon1			ACCACCATAAAAT		CCDS4658.1	6p22.1	2013-09-24			ENSG00000112462	ENSG00000112462		"GPCR / Class A : Olfactory receptors"	13963	protein-coding gene	gene with protein product							Standard	NM_030959		Approved	hs6M1-27	uc003nme.3	Q9UGF7	OTTHUMG00000031051	ENST00000396806.3:c.734T>C	chr6.hg19:g.29342331A>G	ENSP00000380023:p.Met245Thr	137.0	0.0		173.0	16.0	NM_030959	A2BDZ1|Q5SQI8|Q6IF23	Missense_Mutation	SNP	ENST00000396806.3	hg19	CCDS4658.1	.	.	.	.	.	.	.	.	.	.	A	0.025	-1.378804	0.01204	.	.	ENSG00000112462	ENST00000377143;ENST00000396806	T	0.35236	1.32	4.19	0.423	0.16463	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.03095	0.0091	N	0.02202	-0.64	0.09310	N	1	B	0.02656	0.0	B	0.13407	0.009	T	0.46952	-0.9154	9	0.02654	T	1	-2.9467	8.616	0.33831	0.4425:0.0:0.5575:0.0	.	245	Q9UGF7	O12D3_HUMAN	T	245	ENSP00000380023:M245T	ENSP00000366348:M245T	M	-	2	0	OR12D3	29450310	0.000000	0.05858	0.011000	0.14972	0.666000	0.39218	-0.256000	0.08757	-0.074000	0.12820	0.172000	0.16884	ATG	.	.		0.463	OR12D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076056.3			G	29342331	A	G	29342331	3	3	245	1	0	0	0	0	1	0	0	0	10941	217	8	2	220	2	OR12D3	6	29342331	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	17218237	29342331	141772736	89	33559										
RNF39	80352	hgsc.bcm.edu	37	chr6	30039406	30039406	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tggtggggccagttgtacgcTgcggcggtcggcggagatga	20	8	0	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr6:30039406T>G	ENST00000244360.6	-	4	842	c.745A>C	c.(745-747)Agc>Cgc	p.S249R	RNF39_ENST00000376751.3_Missense_Mutation_p.S249R	NM_025236.3	NP_079512.2	Q9H2S5	RNF39_HUMAN	ring finger protein 39	249	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)										AGTTGTACGCTGCGGCGGTCG	0.721																																					p.S249R	NSCLC(8;188 360 1520 20207 31481)	Atlas-SNP	.											.	RNF39	27	.	0			c.A745C						.						2	2	2					6																	30039406		1146	2075	3221	SO:0001583	missense	80352	exon4			GTACGCTGCGGCG	AF238315	CCDS4673.1, CCDS4674.1	6p21.3	2013-01-09			ENSG00000204618	ENSG00000204618		"RING-type (C3HC4) zinc fingers"	18064	protein-coding gene	gene with protein product		607524				11130983, 11716498	Standard	NM_170769		Approved	HZFw1, LIRF	uc003npe.3	Q9H2S5	OTTHUMG00000031288	ENST00000244360.6:c.745A>C	chr6.hg19:g.30039406T>G	ENSP00000244360:p.Ser249Arg	2.0	0.0		20.0	8.0	NM_025236	A2BEK3|A6NCD6|B0S858|Q5SPM8|Q5SPM9|Q5SPN0|Q5SRJ9|Q5SRK1|Q5SS29|Q9H2S3|Q9H2S4	Missense_Mutation	SNP	ENST00000244360.6	hg19	CCDS4673.1	.	.	.	.	.	.	.	.	.	.	t	14.36	2.511611	0.44660	.	.	ENSG00000204618	ENST00000376751;ENST00000244360	T;T	0.11495	2.77;2.77	4.7	0.99	0.19807	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	0.119810	0.36665	N	0.002478	T	0.02767	0.0083	L	0.33668	1.02	0.27010	N	0.964703	B;B	0.21071	0.051;0.009	B;B	0.29077	0.098;0.022	T	0.40739	-0.9547	10	0.48119	T	0.1	-18.9153	7.3644	0.26764	0.0:0.2778:0.0:0.7222	.	249;249	Q9H2S5;Q9H2S5-2	RNF39_HUMAN;.	R	249	ENSP00000365942:S249R;ENSP00000244360:S249R	ENSP00000244360:S249R	S	-	1	0	RNF39	30147385	0.000000	0.05858	0.984000	0.44739	0.246000	0.25737	0.219000	0.17641	0.006000	0.14734	0.381000	0.24937	AGC	.	.		0.721	RNF39-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076625.3	NM_170769		G	30039406	T	G	30039406	3	3	245	1	0	0	0	0	1	0	0	0	13506	1580	55	5	521	5	RNF39	6	30039406	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	697075	30039406	141075661	90	33560										
DHX16	8449	hgsc.bcm.edu	37	chr6	30621047	30621048	+	Frame_Shift_Ins	INS	-	-	T													0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ctcttctcgtgttttgcctaINStttttttgggcattttctta					rs200009023		TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr6:30621047_30621048insT	ENST00000376442.3	-	20	3292_3293	c.3097_3098insA	c.(3097-3099)atafs	p.I1033fs	DHX16_ENST00000376437.5_Frame_Shift_Ins_p.I552fs	NM_001164239.1|NM_003587.4	NP_001157711.1|NP_003578.2	O60231	DHX16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 16	1033					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)	p.I1033fs*>10(1)		kidney(2)|ovary(2)	4						TGTTTTGCCTATTTTTTTGGGC	0.416																																					p.I1033fs		Atlas-Indel,Pindel	.											.,1	DHX16	119	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.3098_3099insA						.																																			SO:0001589	frameshift_variant	8449	exon20			.	AB001601	CCDS4685.1	6p21.3	2010-02-17	2003-06-13	2003-06-20	ENSG00000204560	ENSG00000204560		"DEAH-boxes"	2739	protein-coding gene	gene with protein product		603405	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 16"	DDX16		9547260	Standard	NM_003587		Approved	DBP2, Prp2, PRPF2	uc003nqz.3	O60231	OTTHUMG00000031060	ENST00000376442.3:c.3098dupA	chr6.hg19:g.30621054_30621054dupT	ENSP00000365625:p.Ile1033fs	100.0	0.0		165.0	82.0	NM_003587	O60322|Q5JP45|Q969X7|Q96QC1	Frame_Shift_Ins	INS	ENST00000376442.3	hg19	CCDS4685.1																																																																																			.	.		0.416	DHX16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076076.2	NM_003587		T	30621048	-	T	30621047	7	5	245	1	0	1	1	0	0	0	0	0	4504	449	16	0	31	0	DHX16	6	30621047	Frame_Shift_Ins	INS	-	TCGA-ED-A7PZ-01A-11D-A33Q-10	581641	30621047	140494020	91	33561										
DPCR1	135656	hgsc.bcm.edu	37	chr6	30918786	30918786	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	cagaaaatagagaaagcacaGccaatgagaagaccacacca	8	10	0	4			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr6:30918786G>T	ENST00000462446.1	+	2	2573	c.2545G>T	c.(2545-2547)Gcc>Tcc	p.A849S	DPCR1_ENST00000304311.2_5'UTR|HCG21_ENST00000419481.1_RNA			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	293						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						AGAAAGCACAGCCAATGAGAA	0.478																																					p.A849S		Atlas-SNP	.											.	DPCR1	99	.	0			c.G2545T						.						79	73	75					6																	30918786		692	1591	2283	SO:0001583	missense	135656	exon2			AGCACAGCCAATG	AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.2545G>T	chr6.hg19:g.30918786G>T	ENSP00000417182:p.Ala849Ser	45.0	0.0		94.0	45.0	NM_080870	C9IZC0|Q658M7|Q8WYN2	Missense_Mutation	SNP	ENST00000462446.1	hg19	CCDS4692.2	.	.	.	.	.	.	.	.	.	.	g	0.721	-0.783597	0.02907	.	.	ENSG00000168631	ENST00000462446	T	0.49432	0.78	0.645	-1.29	0.09288	.	.	.	.	.	T	0.11707	0.0285	L	0.47716	1.5	0.09310	N	0.999998	D	0.55172	0.97	B	0.39152	0.292	T	0.25012	-1.0144	8	0.08381	T	0.77	.	.	.	.	.	849	E9PEI6	.	S	849	ENSP00000417182:A849S	ENSP00000417182:A849S	A	+	1	0	DPCR1	31026765	0.000000	0.05858	0.011000	0.14972	0.010000	0.07245	-0.572000	0.05881	-0.330000	0.08514	0.154000	0.16183	GCC	.	.		0.478	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870		T	30918786	G	T	30918786	3	4	245	1	0	0	0	0	1	0	0	0	4714	971	34	3	2551	3	DPCR1	6	30918786	Missense_Mutation	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	297739	30918786	140196281	92	33562										
TNXB	7148	hgsc.bcm.edu	37	chr6	32015532	32015532	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tgtggtgctgtcagcagagaTggggcccagtcgtttcctgc	15	10	1	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr6:32015532T>A	ENST00000375244.3	-	30	10504	c.10303A>T	c.(10303-10305)Atc>Ttc	p.I3435F	TNXB_ENST00000375247.2_Missense_Mutation_p.I3433F|TNXB_ENST00000451343.1_5'Flank			P22105	TENX_HUMAN	tenascin XB	3480	Fibronectin type-III 26. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						TCAGCAGAGATGGGGCCCAGT	0.622																																					p.I3433F		Atlas-SNP	.											.	TNXB	553	.	0			c.A10297T						.						31	38	36					6																	32015532		1342	2577	3919	SO:0001583	missense	7148	exon30			CAGAGATGGGGCC	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.10303A>T	chr6.hg19:g.32015532T>A	ENSP00000364393:p.Ile3435Phe	45.0	0.0		76.0	22.0	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	hg19		.	.	.	.	.	.	.	.	.	.	T	9.330	1.060266	0.19987	.	.	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.04654	3.58;3.58	4.76	-5.29	0.02747	.	1.287300	0.05452	N	0.549714	T	0.02342	0.0072	M	0.74258	2.255	0.09310	N	1	B	0.21821	0.061	B	0.28305	0.088	T	0.45411	-0.9263	10	0.35671	T	0.21	.	7.6649	0.28426	0.0:0.5218:0.1037:0.3744	.	3433	P22105-3	.	F	3435;3433	ENSP00000364393:I3435F;ENSP00000364396:I3433F	ENSP00000364393:I3435F	I	-	1	0	TNXB	32123510	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-2.767000	0.00782	-0.846000	0.04174	-1.039000	0.02377	ATC	.	.		0.622	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		A	32015532	T	A	32015532	3	1	245	1	0	0	0	0	1	0	0	0	16361	1464	51	4	4476	4	TNXB	6	32015532	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	1096746	32015532	139099535	93	33563										
LRFN2	57497	hgsc.bcm.edu	37	chr6	40400714	40400714	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ccgccggtcaatatcaggggGtacaaagagcagccccttgg	13	12	2	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr6:40400714G>T	ENST00000338305.6	-	2	681	c.139C>A	c.(139-141)Ccc>Acc	p.P47T		NM_020737.1	NP_065788.1	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III domain containing 2	47	LRRNT.					cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	58	Ovarian(28;0.0418)|Colorectal(47;0.196)					ATATCAGGGGGTACAAAGAGC	0.617																																					p.P47T		Atlas-SNP	.											.	LRFN2	133	.	0			c.C139A						.						46	52	50					6																	40400714		2203	4300	6503	SO:0001583	missense	57497	exon2			CAGGGGGTACAAA	AB033072	CCDS34443.1	6p21.2-p21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000156564	ENSG00000156564		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	21226	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 2"	612808	"KIAA1246"	KIAA1246, SALM1		16495444, 16828986	Standard	NM_020737		Approved	FIGLER2	uc003oph.1	Q9ULH4	OTTHUMG00000014662	ENST00000338305.6:c.139C>A	chr6.hg19:g.40400714G>T	ENSP00000345985:p.Pro47Thr	91.0	0.0		146.0	63.0	NM_020737	A5PKU3|Q5SYP9	Missense_Mutation	SNP	ENST00000338305.6	hg19	CCDS34443.1	.	.	.	.	.	.	.	.	.	.	G	19.48	3.835636	0.71373	.	.	ENSG00000156564	ENST00000338305	T	0.04360	3.64	5.52	5.52	0.82312	Leucine-rich repeat-containing N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.14700	0.0355	M	0.69358	2.11	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.00354	-1.1794	10	0.87932	D	0	.	17.9922	0.89172	0.0:0.0:1.0:0.0	.	47	Q9ULH4	LRFN2_HUMAN	T	47	ENSP00000345985:P47T	ENSP00000345985:P47T	P	-	1	0	LRFN2	40508692	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	9.869000	0.99810	2.620000	0.88729	0.655000	0.94253	CCC	.	.		0.617	LRFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040488.1	XM_166372		T	40400714	G	T	40400714	3	4	245	1	0	0	0	0	1	0	0	0	8947	1261	44	3	2238	3	LRFN2	6	40400714	Missense_Mutation	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	8385182	40400714	130714353	94	33564										
TREML1	340205	hgsc.bcm.edu	37	chr6	41121500	41121500	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gcctaggataactcacctggGggcagtatgttcagagagac	13	9	2	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr6:41121500G>A	ENST00000426005.2	-	2	415	c.372C>T	c.(370-372)ccC>ccT	p.P124P	TREML1_ENST00000373127.4_Silent_p.P124P|TREML1_ENST00000437044.2_Intron	NM_178174.2	NP_835468.1	Q86YW5	TRML1_HUMAN	triggering receptor expressed on myeloid cells-like 1	124					calcium-mediated signaling (GO:0019722)|innate immune response (GO:0045087)|platelet activation (GO:0030168)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)				breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)	13	Ovarian(28;0.0418)|Colorectal(47;0.196)					ACTCACCTGGGGGCAGTATGT	0.607																																					p.P124P		Atlas-SNP	.											.	TREML1	20	.	0			c.C372T						.						46	51	49					6																	41121500		2203	4300	6503	SO:0001819	synonymous_variant	340205	exon2			ACCTGGGGGCAGT	AF534822	CCDS4851.1, CCDS64420.1, CCDS64421.1	6p21.1	2013-01-11			ENSG00000161911	ENSG00000161911		"Immunoglobulin superfamily / V-set domain containing"	20434	protein-coding gene	gene with protein product	"TREM-like transcript 1"	609714				12393607, 12645956	Standard	NM_178174		Approved	TLT1, dJ238O23.3	uc011duc.3	Q86YW5	OTTHUMG00000016231	ENST00000426005.2:c.372C>T	chr6.hg19:g.41121500G>A		85.0	0.0		150.0	20.0	NM_178174	Q496B3|Q8IWY1|Q8IWY2	Silent	SNP	ENST00000426005.2	hg19	CCDS4851.1																																																																																			.	.		0.607	TREML1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043538.2	NM_178174		A	41121500	G	A	41121500	2	1	245	1	0	0	0	0	0	0	0	1	16487	1219	43	3		3	TREML1	6	41121500	Silent	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	720786	41121500	129993567	95	33565										
CAPN11	11131	hgsc.bcm.edu	37	chr6	44149032	44149032	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gcttctagagttcaagatccTgtggaaaaaactcaagaaat	8	7	3	3			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr6:44149032T>A	ENST00000398776.1	+	19	1951	c.1913T>A	c.(1912-1914)cTg>cAg	p.L638Q	CAPN11_ENST00000542245.1_Missense_Mutation_p.L638Q	NM_007058.3	NP_008989.2	Q9UMQ6	CAN11_HUMAN	calpain 11	638	Domain IV.|EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				proteolysis (GO:0006508)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|peptidase activity (GO:0008233)			breast(3)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)	36	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			TTCAAGATCCTGTGGAAAAAA	0.512																																					p.L638Q		Atlas-SNP	.											.	CAPN11	66	.	0			c.T1913A						.						65	66	66					6																	44149032		1874	4104	5978	SO:0001583	missense	11131	exon19			AGATCCTGTGGAA	AJ242832	CCDS47436.1	6p12	2013-01-10			ENSG00000137225	ENSG00000137225		"EF-hand domain containing"	1478	protein-coding gene	gene with protein product		604822				10409436	Standard	NM_007058		Approved		uc003owt.1	Q9UMQ6	OTTHUMG00000014758	ENST00000398776.1:c.1913T>A	chr6.hg19:g.44149032T>A	ENSP00000381758:p.Leu638Gln	63.0	0.0		95.0	52.0	NM_007058	B2RA64|Q5T3G1|Q8N4R5	Missense_Mutation	SNP	ENST00000398776.1	hg19	CCDS47436.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.594535	0.86953	.	.	ENSG00000137225	ENST00000398776;ENST00000542245	D;D	0.81579	-1.51;-1.51	4.93	4.93	0.64822	EF-hand-like domain (1);	0.000000	0.36066	N	0.002819	D	0.93058	0.7790	H	0.98901	4.365	0.49687	D	0.999811	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95466	0.8547	10	0.87932	D	0	.	13.907	0.63843	0.0:0.0:0.0:1.0	.	292;638	B4DT90;Q9UMQ6	.;CAN11_HUMAN	Q	638	ENSP00000381758:L638Q;ENSP00000441078:L638Q	ENSP00000381758:L638Q	L	+	2	0	CAPN11	44257010	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.856000	0.86956	2.066000	0.61787	0.448000	0.29417	CTG	.	.		0.512	CAPN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040714.3			A	44149032	T	A	44149032	3	1	245	1	0	0	0	0	1	0	0	0	2626	1580	55	4	1987	4	CAPN11	6	44149032	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	3027532	44149032	126966035	96	33566										
GSTA4	2941	hgsc.bcm.edu	37	chr6	52849299	52849299	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	agtatctaattatagccttcTgggccatgttaaccacttcc	6	11	2	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr6:52849299T>A	ENST00000370959.1	-	5	494	c.377A>T	c.(376-378)cAg>cTg	p.Q126L	GSTA4_ENST00000486559.1_5'UTR|GSTA4_ENST00000541324.1_Missense_Mutation_p.Q33L|GSTA4_ENST00000370960.1_Missense_Mutation_p.Q33L			O15217	GSTA4_HUMAN	glutathione S-transferase alpha 4	126	GST C-terminal.				glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	glutathione transferase activity (GO:0004364)|protein homodimerization activity (GO:0042803)			endometrium(1)|lung(3)|skin(2)|urinary_tract(1)	7	Lung NSC(77;0.103)				Glutathione(DB00143)	TATAGCCTTCTGGGCCATGTT	0.448																																					p.Q126L		Atlas-SNP	.											.	GSTA4	20	.	0			c.A377T						.						127	111	116					6																	52849299		2203	4300	6503	SO:0001583	missense	2941	exon5			GCCTTCTGGGCCA	AF020918	CCDS4948.1	6p12.2	2012-06-21	2008-11-26		ENSG00000170899	ENSG00000170899	2.5.1.18	"Glutathione S-transferases / Soluble"	4629	protein-coding gene	gene with protein product		605450	"glutathione S-transferase A4"			9480897	Standard	NM_001512		Approved		uc003pbf.3	O15217	OTTHUMG00000014868	ENST00000370959.1:c.377A>T	chr6.hg19:g.52849299T>A	ENSP00000359998:p.Gln126Leu	70.0	0.0		156.0	65.0	NM_001512	B2RD15|Q5T7Q8|Q6P4G1|Q9BX18|Q9H414	Missense_Mutation	SNP	ENST00000370959.1	hg19	CCDS4948.1	.	.	.	.	.	.	.	.	.	.	T	16.25	3.070658	0.55539	.	.	ENSG00000170899	ENST00000370963;ENST00000541324;ENST00000370960;ENST00000370959;ENST00000457564	T;T;T;T;T	0.01838	4.61;4.61;4.61;4.61;4.61	5.0	5.0	0.66597	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);Glutathione S-transferase, C-terminal (1);	0.873402	0.10333	N	0.687322	T	0.01489	0.0048	L	0.43923	1.385	0.33135	D	0.543598	B	0.23058	0.079	B	0.22386	0.039	T	0.39354	-0.9618	10	0.72032	D	0.01	-2.9179	14.6648	0.68899	0.0:0.0:0.0:1.0	.	126	O15217	GSTA4_HUMAN	L	126;33;33;126;33	ENSP00000360002:Q126L;ENSP00000439439:Q33L;ENSP00000359999:Q33L;ENSP00000359998:Q126L;ENSP00000394228:Q33L	ENSP00000359998:Q126L	Q	-	2	0	GSTA4	52957258	0.391000	0.25221	1.000000	0.80357	0.889000	0.51656	3.562000	0.53777	1.996000	0.58369	0.455000	0.32223	CAG	.	.		0.448	GSTA4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040946.1	NM_001512		A	52849299	T	A	52849299	3	1	245	1	0	0	0	0	1	0	0	0	6842	1580	55	4	303	4	GSTA4	6	52849299	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	8700267	52849299	118265768	97	33567										
KHDRBS2	202559	hgsc.bcm.edu	37	chr6	62407112	62407112	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ggtcttaccgtagctgtcatAggcatcctcacttactccat	7	13	3	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr6:62407112A>T	ENST00000281156.4	-	8	1218	c.940T>A	c.(940-942)Tat>Aat	p.Y314N		NM_152688.2	NP_689901.2	Q5VWX1	KHDR2_HUMAN	KH domain containing, RNA binding, signal transduction associated 2	314					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) binding (GO:0008143)|poly(U) RNA binding (GO:0008266)			NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|liver(1)|lung(13)|ovary(3)|prostate(3)|skin(12)|upper_aerodigestive_tract(2)|urinary_tract(1)	49				BRCA - Breast invasive adenocarcinoma(397;0.149)		TAGCTGTCATAGGCATCCTCA	0.393																																					p.Y314N		Atlas-SNP	.											.	KHDRBS2	103	.	0			c.T940A						.						132	108	116					6																	62407112		2203	4300	6503	SO:0001583	missense	202559	exon8			TGTCATAGGCATC	BC034043	CCDS4963.1	6q11.1	2013-09-20			ENSG00000112232	ENSG00000112232			18114	protein-coding gene	gene with protein product	"Sam68-like mammalian protein 1"	610487					Standard	NM_152688		Approved	SLM1, SLM-1, MGC26664	uc003peg.2	Q5VWX1	OTTHUMG00000014936	ENST00000281156.4:c.940T>A	chr6.hg19:g.62407112A>T	ENSP00000281156:p.Tyr314Asn	53.0	0.0		94.0	43.0	NM_152688	A8K7M8|Q8N4I4|Q8TCZ4	Missense_Mutation	SNP	ENST00000281156.4	hg19	CCDS4963.1	.	.	.	.	.	.	.	.	.	.	A	19.50	3.839534	0.71488	.	.	ENSG00000112232	ENST00000281156	T	0.61040	0.14	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.70771	0.3262	M	0.77103	2.36	0.54753	D	0.999984	D	0.89917	1.0	D	0.87578	0.998	T	0.75825	-0.3181	10	0.72032	D	0.01	-1.8458	14.2277	0.65871	1.0:0.0:0.0:0.0	.	314	Q5VWX1	KHDR2_HUMAN	N	314	ENSP00000281156:Y314N	ENSP00000281156:Y314N	Y	-	1	0	KHDRBS2	62465071	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.303000	0.72794	2.161000	0.67846	0.528000	0.53228	TAT	.	.		0.393	KHDRBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041066.2	NM_152688		T	62407112	A	T	62407112	3	4	245	1	0	0	0	0	1	0	0	0	8156	420	15	4	117	4	KHDRBS2	6	62407112	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	9557813	62407112	108707955	98	33568										
DDX43	55510	hgsc.bcm.edu	37	chr6	74118988	74118988	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	caggttttagatgaagcagaCaagatgttggacatgggatt	13	4	0	4			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr6:74118988C>A	ENST00000370336.4	+	10	1355	c.1197C>A	c.(1195-1197)gaC>gaA	p.D399E	DDX43_ENST00000479773.1_3'UTR	NM_018665.2	NP_061135.2	Q9NXZ2	DDX43_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 43	399	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)			NS(1)|breast(2)|central_nervous_system(1)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	24						ATGAAGCAGACAAGATGTTGG	0.373																																					p.D399E		Atlas-SNP	.											.	DDX43	69	.	0			c.C1197A						.						195	184	188					6																	74118988		2203	4300	6503	SO:0001583	missense	55510	exon10			AGCAGACAAGATG		CCDS4977.1	6q13	2014-01-21			ENSG00000080007	ENSG00000080007		"DEAD-boxes"	18677	protein-coding gene	gene with protein product	"cancer/testis antigen 13"	606286				10919659	Standard	NM_018665		Approved	HAGE, DKFZp434H2114, CT13	uc003pgw.3	Q9NXZ2	OTTHUMG00000015033	ENST00000370336.4:c.1197C>A	chr6.hg19:g.74118988C>A	ENSP00000359361:p.Asp399Glu	90.0	0.0		77.0	17.0	NM_018665	B4E0C8|Q6NXR1	Missense_Mutation	SNP	ENST00000370336.4	hg19	CCDS4977.1	.	.	.	.	.	.	.	.	.	.	C	14.73	2.623597	0.46840	.	.	ENSG00000080007	ENST00000370336	T	0.07444	3.19	4.82	2.89	0.33648	RNA helicase, ATP-dependent, DEAD-box, conserved site (1);DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.31857	0.0810	H	0.98178	4.165	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.50355	-0.8838	10	0.87932	D	0	.	10.4945	0.44770	0.0:0.8172:0.0:0.1828	.	399	Q9NXZ2	DDX43_HUMAN	E	399	ENSP00000359361:D399E	ENSP00000359361:D399E	D	+	3	2	DDX43	74175709	1.000000	0.71417	1.000000	0.80357	0.217000	0.24651	1.702000	0.37836	1.066000	0.40716	0.455000	0.32223	GAC	.	.		0.373	DDX43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041219.3	NM_018665		A	74118988	C	A	74118988	3	1	245	1	0	0	0	0	1	0	0	0	4365	477	17	3	1235	3	DDX43	6	74118988	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	11711876	74118988	96996079	99	33569										
COL12A1	1303	hgsc.bcm.edu	37	chr6	75887629	75887629	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gtagtctcatctgtcaccttTaggtttcgaggtgctccttt	9	10	3	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr6:75887629T>A	ENST00000322507.8	-	12	2496	c.2187A>T	c.(2185-2187)ctA>ctT	p.L729L	COL12A1_ENST00000416123.2_Silent_p.L729L|COL12A1_ENST00000483888.2_Silent_p.L729L|COL12A1_ENST00000345356.6_Intron	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	729	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						CTGTCACCTTTAGGTTTCGAG	0.313																																					p.L729L		Atlas-SNP	.											.	COL12A1	385	.	0			c.A2187T						.						92	88	89					6																	75887629		1813	4083	5896	SO:0001819	synonymous_variant	1303	exon12			CACCTTTAGGTTT	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.2187A>T	chr6.hg19:g.75887629T>A		38.0	0.0		36.0	33.0	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Silent	SNP	ENST00000322507.8	hg19	CCDS43482.1																																																																																			.	.		0.313	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		A	75887629	T	A	75887629	2	1	245	1	0	0	0	0	0	0	0	1	3671	1741	61	4		4	COL12A1	6	75887629	Silent	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	1768641	75887629	95227438	100	33570										
SNAP91	9892	hgsc.bcm.edu	37	chr6	84417640	84417640	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ccgatccgtgagcgtttggcCcgacatcttctgtggtcgcg	13	13	2	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr6:84417640C>A	ENST00000439399.2	-	2	323	c.7G>T	c.(7-9)Ggc>Tgc	p.G3C	SNAP91_ENST00000437520.1_Missense_Mutation_p.G3C|SNAP91_ENST00000520302.1_Missense_Mutation_p.G3C|SNAP91_ENST00000521743.1_Missense_Mutation_p.G3C|SNAP91_ENST00000195649.6_Missense_Mutation_p.G3C|SNAP91_ENST00000521485.1_Missense_Mutation_p.G3C|SNAP91_ENST00000369694.2_Missense_Mutation_p.G3C|SNAP91_ENST00000520213.1_Missense_Mutation_p.G3C|SNAP91_ENST00000428679.2_Missense_Mutation_p.G3C	NM_014841.2	NP_055656.1	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa	3					clathrin coat assembly (GO:0048268)|protein transport (GO:0015031)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|protein kinase binding (GO:0019901)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(22)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		AGCGTTTGGCCCGACATCTTC	0.587																																					p.G3C		Atlas-SNP	.											SNAP91_ENST00000439399,right_lower_lobe,carcinoma,0,2	SNAP91	199	.	0			c.G7T						.						55	60	58					6																	84417640		1985	4168	6153	SO:0001583	missense	9892	exon2			TTTGGCCCGACAT	AB014556	CCDS47455.1, CCDS56437.1, CCDS56438.1	6q15	2012-12-07	2012-12-07		ENSG00000065609	ENSG00000065609			14986	protein-coding gene	gene with protein product		607923	"synaptosomal-associated protein, 91 kDa (mouse) homolog", "synaptosomal-associated protein, 91kDa homolog (mouse)"			9734811, 12493563, 10436022	Standard	NM_014841		Approved	KIAA0656, AP180, CALM	uc003pka.3	O60641	OTTHUMG00000015114	ENST00000439399.2:c.7G>T	chr6.hg19:g.84417640C>A	ENSP00000400459:p.Gly3Cys	25.0	0.0		42.0	41.0	NM_001242794	A8K0L7|E5RI02|Q5JX13|Q68DL9|Q6P9D3|Q9NTY7	Missense_Mutation	SNP	ENST00000439399.2	hg19	CCDS47455.1	.	.	.	.	.	.	.	.	.	.	C	33	5.234605	0.95207	.	.	ENSG00000065609	ENST00000521485;ENST00000369694;ENST00000439399;ENST00000195649;ENST00000428679;ENST00000437520;ENST00000520302;ENST00000521743;ENST00000520213;ENST00000521931;ENST00000519779;ENST00000518309;ENST00000369690;ENST00000523484;ENST00000519825	T;T;T;T;T;T;T;T;T;T	0.56444	0.98;0.96;0.96;0.98;0.99;1.34;0.98;0.96;1.34;0.46	5.36	5.36	0.76844	.	0.092984	0.85682	D	0.000000	T	0.71384	0.3333	M	0.80847	2.515	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.75625	-0.3253	10	0.87932	D	0	-7.6719	19.0968	0.93255	0.0:1.0:0.0:0.0	.	3;3;3	O60641-3;E5RI02;E1P549	.;.;.	C	3	ENSP00000429776:G3C;ENSP00000358708:G3C;ENSP00000400459:G3C;ENSP00000195649:G3C;ENSP00000412492:G3C;ENSP00000413277:G3C;ENSP00000428511:G3C;ENSP00000428215:G3C;ENSP00000428026:G3C;ENSP00000430071:G3C	ENSP00000195649:G3C	G	-	1	0	SNAP91	84474359	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.811000	0.86092	2.516000	0.84829	0.462000	0.41574	GGC	.	.		0.587	SNAP91-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375296.1			A	84417640	C	A	84417640	3	1	245	1	0	0	0	0	1	0	0	0	14848	623	22	3	2824	3	SNAP91	6	84417640	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	8530011	84417640	86697427	101	33571										
CNR1	1268	hgsc.bcm.edu	37	chr6	88854869	88854869	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ggaatttctgtgggaagtacCctaatttggatgccatgtca	11	7	2	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr6:88854869C>T	ENST00000537554.1	-	2	3687	c.125G>A	c.(124-126)gGg>gAg	p.G42E	CNR1_ENST00000549890.1_Missense_Mutation_p.G42E|CNR1_ENST00000549716.1_Intron|CNR1_ENST00000369499.2_Missense_Mutation_p.G42E|CNR1_ENST00000535130.1_Missense_Mutation_p.G42E|CNR1_ENST00000369501.2_Missense_Mutation_p.G42E|CNR1_ENST00000428600.2_Missense_Mutation_p.G42E|CNR1_ENST00000362094.5_Intron|CNR1_ENST00000468898.1_Intron	NM_001160226.1|NM_001160258.1	NP_001153698.1|NP_001153730.1	P21554	CNR1_HUMAN	cannabinoid receptor 1 (brain)	42					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|aging (GO:0007568)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose homeostasis (GO:0042593)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|negative regulation of action potential (GO:0045759)|negative regulation of blood pressure (GO:0045776)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of mast cell activation (GO:0033004)|negative regulation of nitric-oxide synthase activity (GO:0051001)|positive regulation of acute inflammatory response to antigenic stimulus (GO:0002866)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood pressure (GO:0045777)|positive regulation of fever generation (GO:0031622)|positive regulation of neuron projection development (GO:0010976)|regulation of feeding behavior (GO:0060259)|regulation of insulin secretion (GO:0050796)|regulation of penile erection (GO:0060405)|regulation of synaptic transmission, GABAergic (GO:0032228)|regulation of synaptic transmission, glutamatergic (GO:0051966)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to morphine (GO:0043278)|response to nicotine (GO:0035094)|response to nutrient (GO:0007584)|sensory perception of pain (GO:0019233)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)|drug binding (GO:0008144)			breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|prostate(1)|skin(10)|urinary_tract(1)	37		all_cancers(76;8.24e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;4.11e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.00011)		BRCA - Breast invasive adenocarcinoma(108;0.15)	Dronabinol(DB00470)|Nabilone(DB00486)|Rimonabant(DB06155)	TGGGAAGTACCCTAATTTGGA	0.507																																					p.G42E		Atlas-SNP	.											.	CNR1	91	.	0			c.G125A						.						126	116	119					6																	88854869		2203	4300	6503	SO:0001583	missense	1268	exon4			AAGTACCCTAATT	AF107262	CCDS5015.1, CCDS5016.1, CCDS5016.2	6q14-q15	2012-08-08			ENSG00000118432	ENSG00000118432		"GPCR / Class A : Cannabinoid receptors"	2159	protein-coding gene	gene with protein product		114610		CNR			Standard	NM_016083		Approved	CB1K5, CB-R, CB1, CANN6, CB1A	uc003pmq.4	P21554	OTTHUMG00000015184	ENST00000537554.1:c.125G>A	chr6.hg19:g.88854869C>T	ENSP00000441046:p.Gly42Glu	87.0	0.0		102.0	90.0	NM_001160258	B2R9T4|E1P512|Q13949|Q495Z0|Q4PLI4|Q4VBM6|Q5JVL5|Q5UB37|Q9UNN0	Missense_Mutation	SNP	ENST00000537554.1	hg19	CCDS5015.1	.	.	.	.	.	.	.	.	.	.	C	8.676	0.904070	0.17760	.	.	ENSG00000118432	ENST00000369501;ENST00000535130;ENST00000537554;ENST00000369499;ENST00000549890;ENST00000428600;ENST00000551417	T;T;T;T;T;T	0.75367	-0.93;-0.93;-0.93;-0.93;-0.93;-0.93	5.77	5.77	0.91146	.	0.319833	0.38111	N	0.001818	T	0.56891	0.2016	L	0.43152	1.355	0.80722	D	1	B	0.17038	0.02	B	0.15052	0.012	T	0.60551	-0.7241	10	0.87932	D	0	.	13.2318	0.59947	0.0:0.9276:0.0:0.0724	.	42	P21554	CNR1_HUMAN	E	42	ENSP00000358513:G42E;ENSP00000442689:G42E;ENSP00000441046:G42E;ENSP00000358511:G42E;ENSP00000446819:G42E;ENSP00000412192:G42E	ENSP00000358511:G42E	G	-	2	0	CNR1	88911588	0.998000	0.40836	0.979000	0.43373	0.112000	0.19704	3.768000	0.55295	2.732000	0.93576	0.563000	0.77884	GGG	.	.		0.507	CNR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354204.2			T	88854869	C	T	88854869	3	4	245	1	0	0	0	0	1	0	0	0	3633	623	22	3	1297	3	CNR1	6	88854869	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	4437229	88854869	82260198	102	33572										
TCF21	6943	hgsc.bcm.edu	37	chr6	134210900	134210900	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ctccaagctggacacgctcaGgctggcgtccagctacatcg	11	15	1	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr6:134210900G>A	ENST00000367882.4	+	1	625	c.365G>A	c.(364-366)aGg>aAg	p.R122K	RP3-323P13.2_ENST00000607573.1_RNA|RP3-323P13.2_ENST00000607641.1_RNA|RP3-323P13.2_ENST00000606544.1_RNA|TCF21_ENST00000237316.3_Missense_Mutation_p.R122K|RP3-323P13.2_ENST00000607033.1_RNA	NM_003206.3	NP_003197.2	O43680	TCF21_HUMAN	transcription factor 21	122	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				branching involved in ureteric bud morphogenesis (GO:0001658)|branchiomeric skeletal muscle development (GO:0014707)|bronchiole development (GO:0060435)|diaphragm development (GO:0060539)|embryonic digestive tract morphogenesis (GO:0048557)|epithelial cell differentiation (GO:0030855)|gland development (GO:0048732)|glomerulus development (GO:0032835)|kidney development (GO:0001822)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|lung vasculature development (GO:0060426)|metanephric glomerular capillary formation (GO:0072277)|metanephric mesenchymal cell differentiation (GO:0072162)|morphogenesis of a branching structure (GO:0001763)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|reproductive structure development (GO:0048608)|respiratory system development (GO:0060541)|Sertoli cell differentiation (GO:0060008)|sex determination (GO:0007530)|spleen development (GO:0048536)|ureteric bud development (GO:0001657)|vasculature development (GO:0001944)	nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|protein dimerization activity (GO:0046983)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			cervix(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	13	Colorectal(23;0.221)|Breast(56;0.247)			GBM - Glioblastoma multiforme(68;0.00518)|OV - Ovarian serous cystadenocarcinoma(155;0.00783)		GACACGCTCAGGCTGGCGTCC	0.627																																					p.R122K		Atlas-SNP	.											.	TCF21	30	.	0			c.G365A						.						89	88	89					6																	134210900		2199	4299	6498	SO:0001583	missense	6943	exon1			CGCTCAGGCTGGC	AF047419	CCDS5167.1	6q23.2	2014-09-17			ENSG00000118526	ENSG00000118526		"Basic helix-loop-helix proteins"	11632	protein-coding gene	gene with protein product		603306				9507058	Standard	NM_198392		Approved	POD1, bHLHa23	uc003qei.4	O43680	OTTHUMG00000015608	ENST00000367882.4:c.365G>A	chr6.hg19:g.134210900G>A	ENSP00000356857:p.Arg122Lys	221.0	0.0		155.0	36.0	NM_003206	E1P581|O43545|Q6ICV0|Q9BZ14	Missense_Mutation	SNP	ENST00000367882.4	hg19	CCDS5167.1	.	.	.	.	.	.	.	.	.	.	G	33	5.231283	0.95207	.	.	ENSG00000118526	ENST00000367882;ENST00000237316	D;D	0.98105	-4.72;-4.72	4.17	4.17	0.49024	Helix-loop-helix DNA-binding (5);	0.000000	0.85682	D	0.000000	D	0.97108	0.9055	L	0.33339	1.005	0.80722	D	1	P	0.52061	0.95	D	0.66716	0.946	D	0.97789	1.0237	10	0.51188	T	0.08	-26.9552	16.86	0.86014	0.0:0.0:1.0:0.0	.	122	O43680	TCF21_HUMAN	K	122	ENSP00000356857:R122K;ENSP00000237316:R122K	ENSP00000237316:R122K	R	+	2	0	TCF21	134252593	1.000000	0.71417	0.985000	0.45067	0.997000	0.91878	9.813000	0.99286	2.033000	0.60031	0.462000	0.41574	AGG	.	.		0.627	TCF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042292.1	NM_198392		A	134210900	G	A	134210900	3	1	245	1	0	0	0	0	1	0	0	0	15706	1000	35	3	367	3	TCF21	6	134210900	Missense_Mutation	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	45356031	134210900	36904167	103	33573										
BCLAF1	9774	hgsc.bcm.edu	37	chr6	136597179	136597179	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	actttacctgctcaggtgacTgagtttctttctttactgtt	7	9	3	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr6:136597179T>A	ENST00000531224.1	-	5	1736	c.1484A>T	c.(1483-1485)cAg>cTg	p.Q495L	BCLAF1_ENST00000527759.1_Missense_Mutation_p.Q493L|BCLAF1_ENST00000530767.1_Intron|BCLAF1_ENST00000527536.1_Missense_Mutation_p.Q495L|BCLAF1_ENST00000392348.2_Missense_Mutation_p.Q493L|BCLAF1_ENST00000353331.4_Missense_Mutation_p.Q493L	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1	495					apoptotic process (GO:0006915)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA-templated transcription, initiation (GO:2000144)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of response to DNA damage stimulus (GO:2001022)|regulation of DNA-templated transcription in response to stress (GO:0043620)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			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)		CTCAGGTGACTGAGTTTCTTT	0.393																																					p.Q495L	Colon(142;1534 1789 5427 7063 28491)	Atlas-SNP	.											.	BCLAF1	203	.	0			c.A1484T						.						189	198	195					6																	136597179		2203	4300	6503	SO:0001583	missense	9774	exon5			GGTGACTGAGTTT	AF249273	CCDS5177.1, CCDS47485.1, CCDS47486.1, CCDS75525.1	6q22-q23	2007-03-02			ENSG00000029363	ENSG00000029363			16863	protein-coding gene	gene with protein product		612588				8724849, 10330179	Standard	NM_001077440		Approved	KIAA0164, BTF	uc003qgx.1	Q9NYF8	OTTHUMG00000033323	ENST00000531224.1:c.1484A>T	chr6.hg19:g.136597179T>A	ENSP00000435210:p.Gln495Leu	113.0	0.0		132.0	42.0	NM_014739	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Missense_Mutation	SNP	ENST00000531224.1	hg19	CCDS5177.1	.	.	.	.	.	.	.	.	.	.	T	14.80	2.644507	0.47258	.	.	ENSG00000029363	ENST00000531224;ENST00000353331;ENST00000527536;ENST00000527759;ENST00000392348;ENST00000529826	T;T;T;T;T;T	0.14640	2.49;2.49;2.49;2.49;2.49;2.49	5.22	5.22	0.72569	.	0.000000	0.56097	D	0.000022	T	0.06781	0.0173	N	0.08118	0	0.80722	D	1	D;B;D	0.56968	0.978;0.106;0.978	P;B;P	0.61328	0.887;0.019;0.887	T	0.42361	-0.9456	10	0.15952	T	0.53	-7.0642	10.6694	0.45749	0.1428:0.0:0.0:0.8572	.	493;493;495	Q9NYF8-2;Q9NYF8-3;Q9NYF8	.;.;BCLF1_HUMAN	L	495;493;495;493;493;495	ENSP00000435210:Q495L;ENSP00000229446:Q493L;ENSP00000435441:Q495L;ENSP00000434826:Q493L;ENSP00000376159:Q493L;ENSP00000431734:Q495L	ENSP00000229446:Q493L	Q	-	2	0	BCLAF1	136638872	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.966000	0.49208	2.124000	0.65301	0.373000	0.22412	CAG	.	.		0.393	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739		A	136597179	T	A	136597179	3	1	245	1	0	0	0	0	1	0	0	0	1383	1580	55	4	1314	4	BCLAF1	6	136597179	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	2386279	136597179	34517888	104	33574										
PLEKHG1	57480	hgsc.bcm.edu	37	chr6	151151983	151151983	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ctctaccagactatgtgaagAtagcacttctagtcgccctt	7	12	2	3			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr6:151151983A>G	ENST00000358517.2	+	15	1947	c.1736A>G	c.(1735-1737)gAt>gGt	p.D579G	PLEKHG1_ENST00000367328.1_Missense_Mutation_p.D579G			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	579							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(19)|ovary(5)|prostate(4)|stomach(1)|urinary_tract(3)	53			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		CTATGTGAAGATAGCACTTCT	0.527																																					p.D579G		Atlas-SNP	.											.	PLEKHG1	97	.	0			c.A1736G						.						137	123	128					6																	151151983		2203	4300	6503	SO:0001583	missense	57480	exon16			GTGAAGATAGCAC	AB033035	CCDS34552.1	6q25.1	2013-01-11			ENSG00000120278	ENSG00000120278		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	20884	protein-coding gene	gene with protein product						10574462	Standard	XM_005267064		Approved	KIAA1209, ARHGEF41	uc003qny.1	Q9ULL1	OTTHUMG00000015824	ENST00000358517.2:c.1736A>G	chr6.hg19:g.151151983A>G	ENSP00000351318:p.Asp579Gly	101.0	0.0		60.0	50.0	NM_001029884	Q5T1F2	Missense_Mutation	SNP	ENST00000358517.2	hg19	CCDS34552.1	.	.	.	.	.	.	.	.	.	.	A	10.28	1.307249	0.23821	.	.	ENSG00000120278	ENST00000367328;ENST00000535018;ENST00000358517	T;T	0.59083	0.29;0.29	5.55	5.55	0.83447	.	0.474690	0.25009	N	0.033850	T	0.37972	0.1023	L	0.54323	1.7	0.26701	N	0.971156	B;B;B	0.32245	0.116;0.361;0.361	B;B;B	0.29077	0.098;0.081;0.081	T	0.36962	-0.9726	10	0.46703	T	0.11	.	15.7008	0.77541	1.0:0.0:0.0:0.0	.	386;579;579	Q5EBL9;Q5JYA6;Q9ULL1	.;.;PKHG1_HUMAN	G	579	ENSP00000356297:D579G;ENSP00000351318:D579G	ENSP00000351318:D579G	D	+	2	0	PLEKHG1	151193676	1.000000	0.71417	0.861000	0.33841	0.124000	0.20399	5.439000	0.66556	2.114000	0.64651	0.459000	0.35465	GAT	.	.		0.527	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042691.1			G	151151983	A	G	151151983	3	3	245	1	0	0	0	0	1	0	0	0	12077	333	12	2	1790	2	PLEKHG1	6	151151983	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	14554804	151151983	19963084	105	33575										
TTLL2	83887	hgsc.bcm.edu	37	chr6	167754699	167754699	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	acacatggaaattccaacatCgacgctgcaaaaagtgacag	8	10	0	1	rs201555411		TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr6:167754699C>A	ENST00000239587.5	+	3	1399	c.1311C>A	c.(1309-1311)atC>atA	p.I437I		NM_031949.4	NP_114155.4	Q9BWV7	TTLL2_HUMAN	tubulin tyrosine ligase-like family, member 2	437					cellular protein modification process (GO:0006464)		ligase activity (GO:0016874)			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(66;7.8e-06)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		ATTCCAACATCGACGCTGCAA	0.423																																					p.I437I		Atlas-SNP	.											TTLL2,NS,carcinoma,0,1	TTLL2	82	.	0			c.C1311A						.						99	94	96					6																	167754699		2203	4300	6503	SO:0001819	synonymous_variant	83887	exon3			CAACATCGACGCT	AK093039	CCDS5301.1	6q27	2013-02-14		2004-01-14	ENSG00000120440	ENSG00000120440		"Tubulin tyrosine ligase-like family"	21211	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 104"	C6orf104		11054573	Standard	XM_006715572		Approved	NYD-TSPG, dJ366N23.3	uc003qvs.1	Q9BWV7	OTTHUMG00000016023	ENST00000239587.5:c.1311C>A	chr6.hg19:g.167754699C>A		66.0	0.0		56.0	54.0	NM_031949	B2RB11|B3KS77|Q7Z6R8|Q86X22	Silent	SNP	ENST00000239587.5	hg19	CCDS5301.1																																																																																			.	C|1.000;T|0.000		0.423	TTLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043127.3	NM_031949		A	167754699	C	A	167754699	2	1	245	1	0	0	0	0	0	0	0	1	16742	874	31	1		1	TTLL2	6	167754699	Silent	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	16602716	167754699	3360368	106	33576										
PHF10	55274	hgsc.bcm.edu	37	chr6	170112536	170112536	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	cgaccatcttcgccatcatcTgaatcaccatcactgtctag	5	15	6	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr6:170112536T>A	ENST00000339209.4	-	8	1026	c.903A>T	c.(901-903)tcA>tcT	p.S301S	PHF10_ENST00000366780.4_Silent_p.S299S	NM_018288.3|NM_133325.2	NP_060758.2|NP_579866.2	Q8WUB8	PHF10_HUMAN	PHD finger protein 10	301	Essential to induce neural progenitor proliferation. {ECO:0000250}.				nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	npBAF complex (GO:0071564)	zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|liver(3)|lung(4)|prostate(2)|urinary_tract(1)	14		Breast(66;5.08e-05)|Ovarian(120;0.208)		OV - Ovarian serous cystadenocarcinoma(33;1.4e-21)|BRCA - Breast invasive adenocarcinoma(81;1.4e-07)|GBM - Glioblastoma multiforme(31;0.00176)		CGCCATCATCTGAATCACCAT	0.478																																					p.S301S		Atlas-SNP	.											.	PHF10	76	.	0			c.A903T						.						161	158	159					6																	170112536		2203	4300	6503	SO:0001819	synonymous_variant	55274	exon8			ATCATCTGAATCA	AF338735	CCDS5308.2, CCDS5309.2	6q27	2014-05-13			ENSG00000130024	ENSG00000130024		"Zinc fingers, PHD-type"	18250	protein-coding gene	gene with protein product		613069				11827455	Standard	NM_018288		Approved	FLJ10975, XAP135, BAF45a	uc011egy.2	Q8WUB8	OTTHUMG00000016058	ENST00000339209.4:c.903A>T	chr6.hg19:g.170112536T>A		258.0	0.0		171.0	147.0	NM_018288	Q2YDA3|Q53HG8|Q9BXD2|Q9NV26	Silent	SNP	ENST00000339209.4	hg19	CCDS5308.2																																																																																			.	.		0.478	PHF10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346732.1	NM_018288		A	170112536	T	A	170112536	2	1	245	1	0	0	0	0	0	0	0	1	11830	1567	55	4		4	PHF10	6	170112536	Silent	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	2357837	170112536	1002531	107	33577										
FTSJ2	29960	hgsc.bcm.edu	37	chr7	2279075	2279075	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gtgcctgcggcgttgaccttCtgcaccgccacctgactcca	10	17	1	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr7:2279075C>G	ENST00000242257.8	-	2	304	c.276G>C	c.(274-276)caG>caC	p.Q92H	NUDT1_ENST00000397048.1_5'Flank|FTSJ2_ENST00000486040.1_5'UTR|NUDT1_ENST00000397046.1_5'Flank|NUDT1_ENST00000397049.1_5'Flank|NUDT1_ENST00000356714.1_5'Flank|FTSJ2_ENST00000440306.2_Missense_Mutation_p.Q92H|FTSJ2_ENST00000407040.1_5'Flank	NM_013393.1	NP_037525.1			FtsJ RNA methyltransferase homolog 2 (E. coli)											endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	12		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0822)|OV - Ovarian serous cystadenocarcinoma(56;2.7e-14)		CGTTGACCTTCTGCACCGCCA	0.652																																					p.Q92H		Atlas-SNP	.											.	FTSJ2	22	.	0			c.G276C						.						25	25	25					7																	2279075		2202	4300	6502	SO:0001583	missense	29960	exon2			GACCTTCTGCACC	AF093415	CCDS5328.1	7p22	2012-06-12	2012-06-12		ENSG00000122687	ENSG00000122687			16352	protein-coding gene	gene with protein product	"rRNA (uridine-2'-O-)-methyltransferase", "MRM2 RNA methyltransferase homolog (S. cerevisiae)"	606906				11827451	Standard	NM_013393		Approved	FJH1, MRM2	uc003slm.3	Q9UI43	OTTHUMG00000023866	ENST00000242257.8:c.276G>C	chr7.hg19:g.2279075C>G	ENSP00000242257:p.Gln92His	38.0	0.0		38.0	20.0	NM_013393		Missense_Mutation	SNP	ENST00000242257.8	hg19	CCDS5328.1	.	.	.	.	.	.	.	.	.	.	C	11.58	1.679829	0.29783	.	.	ENSG00000122687	ENST00000242257;ENST00000440306	T;T	0.34472	1.36;1.36	6.03	3.17	0.36434	Ribosomal RNA methyltransferase RrmJ/FtsJ (1);	0.456425	0.23404	N	0.048554	T	0.32224	0.0822	L	0.53780	1.695	0.45161	D	0.998179	B	0.13594	0.008	B	0.20577	0.03	T	0.15350	-1.0440	10	0.62326	D	0.03	.	8.0968	0.30833	0.0:0.628:0.2439:0.1281	.	92	Q9UI43	RRMJ2_HUMAN	H	92	ENSP00000242257:Q92H;ENSP00000392343:Q92H	ENSP00000242257:Q92H	Q	-	3	2	FTSJ2	2245601	0.860000	0.29831	0.616000	0.29078	0.179000	0.23085	0.570000	0.23653	0.828000	0.34709	0.655000	0.94253	CAG	.	.		0.652	FTSJ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060187.1	NM_013393		G	2279075	C	G	2279075	3	3	245	1	0	0	0	0	1	0	0	0	6096	912	32	4	472	4	FTSJ2	7	2279075	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10		2279075	156859588	108	33578										
USP42	84132	hgsc.bcm.edu	37	chr7	6189834	6189834	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gcagacagcgacagtgacccGaaagaaaacggcctagcgcc	12	13	0	3			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr7:6189834G>A	ENST00000306177.5	+	13	2165	c.2007G>A	c.(2005-2007)ccG>ccA	p.P669P		NM_032172.2	NP_115548.1	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42	669					cell differentiation (GO:0030154)|protein deubiquitination (GO:0016579)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(2)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	35		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)		ACAGTGACCCGAAAGAAAACG	0.572																																					p.P669P		Atlas-SNP	.											.	USP42	138	.	0			c.G2007A						.						35	39	37					7																	6189834		2048	4199	6247	SO:0001819	synonymous_variant	84132	exon13			TGACCCGAAAGAA	AK022759	CCDS47535.1	7p22.2	2005-08-08	2005-08-08		ENSG00000106346	ENSG00000106346		"Ubiquitin-specific peptidases"	20068	protein-coding gene	gene with protein product			"ubiquitin specific protease 42"			12838346	Standard	NM_032172		Approved	FLJ12697	uc011jwp.2	Q9H9J4	OTTHUMG00000151888	ENST00000306177.5:c.2007G>A	chr7.hg19:g.6189834G>A		48.0	0.0		50.0	31.0	NM_032172	A2RUE3|B5MDA5|Q0VIN8|Q3C166|Q6P9B4	Silent	SNP	ENST00000306177.5	hg19	CCDS47535.1																																																																																			.	.		0.572	USP42-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324262.3	XM_166526		A	6189834	G	A	6189834	2	1	245	1	0	0	0	0	0	0	0	1	17088	1045	37	1		1	USP42	7	6189834	Silent	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	3910759	6189834	152948829	109	33579										
PHF14	9678	hgsc.bcm.edu	37	chr7	11030469	11030469	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	caattgtggcattacagtccAtgaaggtaatgttgctttct	9	7	1	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr7:11030469A>G	ENST00000403050.3	+	4	1492	c.1040A>G	c.(1039-1041)cAt>cGt	p.H347R	PHF14_ENST00000445996.2_Missense_Mutation_p.H62R	NM_014660.3	NP_055475.2	O94880	PHF14_HUMAN	PHD finger protein 14	347					lung alveolus development (GO:0048286)|negative regulation of mesenchymal cell proliferation involved in lung development (GO:2000791)|negative regulation of platelet-derived growth factor receptor-alpha signaling pathway (GO:2000584)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(2)|breast(1)|endometrium(4)|kidney(5)|large_intestine(5)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	35				UCEC - Uterine corpus endometrioid carcinoma (126;0.205)		ATTACAGTCCATGAAGGTAAT	0.368																																					p.H347R		Atlas-SNP	.											.	PHF14	90	.	0			c.A1040G						.						120	108	112					7																	11030469		1892	4129	6021	SO:0001583	missense	9678	exon4			CAGTCCATGAAGG	AB018326	CCDS47542.1	7p21.3	2013-01-28			ENSG00000106443	ENSG00000106443		"Zinc fingers, PHD-type"	22203	protein-coding gene	gene with protein product						9872452	Standard	NM_014660		Approved	KIAA0783	uc003sry.2	O94880	OTTHUMG00000150463	ENST00000403050.3:c.1040A>G	chr7.hg19:g.11030469A>G	ENSP00000385795:p.His347Arg	99.0	0.0		122.0	50.0	NM_014660	A7MCZ3|B4DI82	Missense_Mutation	SNP	ENST00000403050.3	hg19	CCDS47542.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.522455	0.85600	.	.	ENSG00000106443	ENST00000403050;ENST00000445996	D;D	0.99005	-5.32;-5.32	5.08	5.08	0.68730	Zinc finger, PHD-finger (2);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.049587	0.85682	D	0.000000	D	0.99489	0.9818	H	0.95402	3.665	0.80722	D	1	D;D;D;D	0.89917	0.96;0.968;0.991;1.0	D;D;D;D	0.80764	0.923;0.954;0.991;0.994	D	0.98202	1.0468	10	0.87932	D	0	.	15.1637	0.72803	1.0:0.0:0.0:0.0	.	62;62;347;347	O94880-2;B4DG57;A8MSQ1;O94880	.;.;.;PHF14_HUMAN	R	347;62	ENSP00000385795:H347R;ENSP00000403907:H62R	ENSP00000385795:H347R	H	+	2	0	PHF14	10996994	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.270000	0.95690	2.045000	0.60652	0.477000	0.44152	CAT	.	.		0.368	PHF14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318212.1	NM_014660		G	11030469	A	G	11030469	3	3	245	1	0	0	0	0	1	0	0	0	11834	217	8	2	1054	2	PHF14	7	11030469	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	4840635	11030469	148108194	110	33580										
IGF2BP3	10643	hgsc.bcm.edu	37	chr7	23391021	23391021	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	aaccagcaggcgcagaggcaAatcacatggtttctgcttgg	12	10	2	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr7:23391021A>T	ENST00000258729.3	-	6	942	c.586T>A	c.(586-588)Ttg>Atg	p.L196M	IGF2BP3_ENST00000491719.1_5'UTR	NM_006547.2	NP_006538.2	O00425	IF2B3_HUMAN	insulin-like growth factor 2 mRNA binding protein 3	196	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.				anatomical structure morphogenesis (GO:0009653)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation regulator activity (GO:0045182)			breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(14)|ovary(2)|prostate(2)|skin(4)|stomach(1)	34						CGCAGAGGCAAATCACATGGT	0.572																																					p.L196M		Atlas-SNP	.											.	IGF2BP3	71	.	0			c.T586A						.						94	86	88					7																	23391021		2203	4300	6503	SO:0001583	missense	10643	exon6			GAGGCAAATCACA	AF117108	CCDS5382.1	7p15.3	2014-02-19			ENSG00000136231	ENSG00000136231		"RNA binding motif (RRM) containing"	28868	protein-coding gene	gene with protein product	"IGF II mRNA binding protein 3", "cancer/testis antigen 98"	608259				9891060, 9178771	Standard	NM_006547		Approved	IMP-3, CT98, IMP3	uc003swg.3	O00425	OTTHUMG00000128445	ENST00000258729.3:c.586T>A	chr7.hg19:g.23391021A>T	ENSP00000258729:p.Leu196Met	67.0	0.0		69.0	35.0	NM_006547	A0A4Z5|Q63HM0|Q6MZZ2|Q86VB1	Missense_Mutation	SNP	ENST00000258729.3	hg19	CCDS5382.1	.	.	.	.	.	.	.	.	.	.	A	19.13	3.767709	0.69878	.	.	ENSG00000136231	ENST00000258729	T	0.45668	0.89	5.88	-2.67	0.06059	K Homology (1);K Homology, type 1 (1);	0.116863	0.56097	D	0.000024	T	0.31389	0.0795	L	0.35487	1.065	0.33660	D	0.609529	P	0.37158	0.585	P	0.47206	0.541	T	0.32161	-0.9917	10	0.38643	T	0.18	-8.5335	3.3418	0.07122	0.2347:0.2999:0.3682:0.0972	.	196	O00425	IF2B3_HUMAN	M	196	ENSP00000258729:L196M	ENSP00000258729:L196M	L	-	1	2	IGF2BP3	23357546	0.944000	0.32072	0.997000	0.53966	0.948000	0.59901	0.141000	0.16076	-0.062000	0.13088	0.459000	0.35465	TTG	.	.		0.572	IGF2BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250243.2	NM_006547		T	23391021	A	T	23391021	3	4	245	1	0	0	0	0	1	0	0	0	7584	11	1	4	1193	4	IGF2BP3	7	23391021	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	12360552	23391021	135747642	111	33581										
AVL9	23080	hgsc.bcm.edu	37	chr7	32599056	32599056	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	aagaggatcagtatggcatgCccctggccatcttcacaaag	10	11	3	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr7:32599056C>A	ENST00000318709.4	+	10	1416	c.1195C>A	c.(1195-1197)Ccc>Acc	p.P399T	AVL9_ENST00000409301.1_Missense_Mutation_p.P399T|AVL9_ENST00000404479.1_Missense_Mutation_p.P399T	NM_015060.1	NP_055875.1	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	399					cell migration (GO:0016477)	integral component of membrane (GO:0016021)|recycling endosome (GO:0055037)				endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						GTATGGCATGCCCCTGGCCAT	0.393																																					p.P399T		Atlas-SNP	.											.	AVL9	66	.	0			c.C1195A						.						52	53	53					7																	32599056		2119	4034	6153	SO:0001583	missense	23080	exon10			GGCATGCCCCTGG	D87682	CCDS34613.1	7p14.3	2013-05-01	2008-10-03	2008-10-03	ENSG00000105778	ENSG00000105778			28994	protein-coding gene	gene with protein product		612927	"KIAA0241"	KIAA0241		17229886, 22595670	Standard	XM_005249668		Approved		uc003tcv.1	Q8NBF6	OTTHUMG00000152929	ENST00000318709.4:c.1195C>A	chr7.hg19:g.32599056C>A	ENSP00000315568:p.Pro399Thr	126.0	0.0		128.0	32.0	NM_015060	Q92573	Missense_Mutation	SNP	ENST00000318709.4	hg19	CCDS34613.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.829534	0.90955	.	.	ENSG00000105778	ENST00000318709;ENST00000409301;ENST00000329714;ENST00000404479;ENST00000446718	T;T;T;T	0.74421	-0.84;-0.84;-0.84;-0.84	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	D	0.89294	0.6674	M	0.89840	3.065	0.80722	D	1	D;D;D	0.89917	1.0;0.975;1.0	D;P;D	0.91635	0.999;0.796;0.999	D	0.90751	0.4657	10	0.87932	D	0	-12.1445	19.3887	0.94570	0.0:1.0:0.0:0.0	.	399;399;399	Q8N6Z3;Q8NBF6-2;Q8NBF6	.;.;AVL9_HUMAN	T	399;399;399;399;330	ENSP00000315568:P399T;ENSP00000387011:P399T;ENSP00000385242:P399T;ENSP00000395134:P330T	ENSP00000315568:P399T	P	+	1	0	AVL9	32565581	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.458000	0.80787	2.826000	0.97356	0.655000	0.94253	CCC	.	.		0.393	AVL9-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328643.1	NM_015060		A	32599056	C	A	32599056	3	1	245	1	0	0	0	0	1	0	0	0	1228	739	26	3	1233	3	AVL9	7	32599056	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	9208035	32599056	126539607	112	33582										
GLI3	2737	hgsc.bcm.edu	37	chr7	42007259	42007259	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tggggttcagtcgcggaaacAttccattcacttgttttagc	10	9	2	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr7:42007259A>T	ENST00000395925.3	-	14	2450	c.2366T>A	c.(2365-2367)aTg>aAg	p.M789K	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	789					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						TCGCGGAAACATTCCATTCAC	0.512									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																												p.M789K		Atlas-SNP	.											.	GLI3	312	.	0			c.T2366A						.						288	281	283					7																	42007259		2203	4300	6503	SO:0001583	missense	2737	exon14	Familial Cancer Database	;	GGAAACATTCCAT		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"Zinc fingers, C2H2-type"	4319	protein-coding gene	gene with protein product	"zinc finger protein GLI3", "oncogene GLI3", "DNA-binding protein"	165240	"Greig cephalopolysyndactyly syndrome", "GLI-Kruppel family member GLI3", "glioma-associated oncogene family zinc finger 3"	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.2366T>A	chr7.hg19:g.42007259A>T	ENSP00000379258:p.Met789Lys	139.0	0.0		144.0	65.0	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Missense_Mutation	SNP	ENST00000395925.3	hg19	CCDS5465.1	.	.	.	.	.	.	.	.	.	.	A	12.26	1.883752	0.33255	.	.	ENSG00000106571	ENST00000395925	T	0.12879	2.64	5.58	3.23	0.37069	.	0.347019	0.41194	D	0.000939	T	0.13927	0.0337	L	0.57536	1.79	0.80722	D	1	B	0.16396	0.017	B	0.17098	0.017	T	0.04930	-1.0917	10	0.34782	T	0.22	.	8.8253	0.35052	0.7879:0.0:0.2121:0.0	.	789	P10071	GLI3_HUMAN	K	789	ENSP00000379258:M789K	ENSP00000379258:M789K	M	-	2	0	GLI3	41973784	1.000000	0.71417	0.997000	0.53966	0.964000	0.63967	3.692000	0.54727	0.428000	0.26173	0.533000	0.62120	ATG	.	.		0.512	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168		T	42007259	A	T	42007259	3	4	245	1	0	0	0	0	1	0	0	0	6447	217	8	4	2384	4	GLI3	7	42007259	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	9408203	42007259	117131404	113	33583										
HECW1	23072	hgsc.bcm.edu	37	chr7	43484963	43484963	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	cgccaagatctccgagagcaCggtcttctcctcgcaagacg	10	15	3	3			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr7:43484963C>A	ENST00000395891.2	+	11	2797	c.2192C>A	c.(2191-2193)aCg>aAg	p.T731K	HECW1_ENST00000453890.1_Missense_Mutation_p.T731K	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	731					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						TCCGAGAGCACGGTCTTCTCC	0.632																																					p.T731K		Atlas-SNP	.											.	HECW1	540	.	0			c.C2192A						.						70	76	74					7																	43484963		2134	4233	6367	SO:0001583	missense	23072	exon11			AGAGCACGGTCTT	AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.2192C>A	chr7.hg19:g.43484963C>A	ENSP00000379228:p.Thr731Lys	93.0	0.0		65.0	29.0	NM_015052	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Missense_Mutation	SNP	ENST00000395891.2	hg19	CCDS5469.2	.	.	.	.	.	.	.	.	.	.	C	25.5	4.641062	0.87859	.	.	ENSG00000002746	ENST00000395891;ENST00000453890;ENST00000265522	T;T	0.45276	1.38;0.9	4.62	4.62	0.57501	.	0.419197	0.26812	N	0.022366	T	0.53562	0.1804	L	0.36672	1.1	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.85130	0.997;0.975	T	0.45498	-0.9257	10	0.19590	T	0.45	.	17.4549	0.87604	0.0:1.0:0.0:0.0	.	731;731	B4DH42;Q76N89	.;HECW1_HUMAN	K	731	ENSP00000379228:T731K;ENSP00000407774:T731K	ENSP00000265522:T731K	T	+	2	0	HECW1	43451488	1.000000	0.71417	0.995000	0.50966	0.965000	0.64279	7.567000	0.82357	2.106000	0.64143	0.591000	0.81541	ACG	.	.		0.632	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052		A	43484963	C	A	43484963	3	1	245	1	0	0	0	0	1	0	0	0	7051	536	19	1	2226	1	HECW1	7	43484963	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	1477704	43484963	115653700	114	33584										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48278844	48278844	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	catattgttgtcagattcccAcagacacttccttggagaag	8	10	1	3			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr7:48278844A>T	ENST00000435803.1	+	9	928	c.904A>T	c.(904-906)Aca>Tca	p.T302S		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	302					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						TCAGATTCCCACAGACACTTC	0.433																																					p.T302S		Atlas-SNP	.											.	ABCA13	1192	.	0			c.A904T						.						68	66	66					7																	48278844		1916	4130	6046	SO:0001583	missense	154664	exon9			ATTCCCACAGACA	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.904A>T	chr7.hg19:g.48278844A>T	ENSP00000411096:p.Thr302Ser	53.0	0.0		50.0	21.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	A	2.938	-0.219609	0.06061	.	.	ENSG00000179869	ENST00000435803	D	0.89343	-2.5	4.87	2.46	0.29980	.	0.606251	0.14683	N	0.304644	T	0.79082	0.4386	N	0.19112	0.55	0.09310	N	0.999999	B	0.10296	0.003	B	0.11329	0.006	T	0.69643	-0.5090	10	0.72032	D	0.01	.	6.3152	0.21186	0.7983:0.0:0.2017:0.0	.	302	Q86UQ4	ABCAD_HUMAN	S	302	ENSP00000411096:T302S	ENSP00000411096:T302S	T	+	1	0	ABCA13	48249390	0.467000	0.25831	0.046000	0.18839	0.043000	0.13939	0.894000	0.28350	0.886000	0.36113	0.533000	0.62120	ACA	.	.		0.433	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		T	48278844	A	T	48278844	3	4	245	1	0	0	0	0	1	0	0	0	31	159	6	4	767	4	ABCA13	7	48278844	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	4793881	48278844	110859819	115	33585										
MUC17	140453	hgsc.bcm.edu	37	chr7	100676441	100676441	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tgcctgtcagcaccaggctgGtggtcagttctgaggctagc	14	11	3	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr7:100676441G>A	ENST00000306151.4	+	3	1808	c.1744G>A	c.(1744-1746)Gtg>Atg	p.V582M		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	582	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					CACCAGGCTGGTGGTCAGTTC	0.473																																					p.V582M		Atlas-SNP	.											.	MUC17	804	.	0			c.G1744A						.						263	269	267					7																	100676441		2203	4300	6503	SO:0001583	missense	140453	exon3			AGGCTGGTGGTCA	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.1744G>A	chr7.hg19:g.100676441G>A	ENSP00000302716:p.Val582Met	77.0	0.0		69.0	38.0	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	g	2.045	-0.419012	0.04766	.	.	ENSG00000169876	ENST00000306151	T	0.02763	4.17	0.647	-0.467	0.12150	.	.	.	.	.	T	0.01800	0.0057	N	0.14661	0.345	0.09310	N	1	B	0.23806	0.091	B	0.17979	0.02	T	0.46062	-0.9218	9	0.46703	T	0.11	.	4.6401	0.12545	0.2876:0.0:0.7124:0.0	.	582	Q685J3	MUC17_HUMAN	M	582	ENSP00000302716:V582M	ENSP00000302716:V582M	V	+	1	0	MUC17	100463161	0.007000	0.16637	0.000000	0.03702	0.001000	0.01503	0.635000	0.24629	-0.175000	0.10725	0.395000	0.25975	GTG	.	.		0.473	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		A	100676441	G	A	100676441	3	1	245	1	0	0	0	0	1	0	0	0	9983	1261	44	3	1754	3	MUC17	7	100676441	Missense_Mutation	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	52397597	100676441	58462222	116	33586										
MUC17	140453	hgsc.bcm.edu	37	chr7	100684989	100684989	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ggactccaacactctggtgaCcacttctactgaagccagtt	8	13	2	2	rs190089107		TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr7:100684989C>T	ENST00000306151.4	+	3	10356	c.10292C>T	c.(10291-10293)aCc>aTc	p.T3431I		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	3431	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					ACTCTGGTGACCACTTCTACT	0.488																																					p.T3431I		Atlas-SNP	.											.	MUC17	804	.	0			c.C10292T						.						231	239	236					7																	100684989		2203	4300	6503	SO:0001583	missense	140453	exon3			TGGTGACCACTTC	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.10292C>T	chr7.hg19:g.100684989C>T	ENSP00000302716:p.Thr3431Ile	97.0	0.0		99.0	47.0	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	8.430	0.848466	0.17034	.	.	ENSG00000169876	ENST00000306151	T	0.01933	4.55	1.52	-0.968	0.10313	.	.	.	.	.	T	0.02767	0.0083	N	0.19112	0.55	0.09310	N	1	P	0.51449	0.945	P	0.53062	0.717	T	0.47142	-0.9140	9	0.39692	T	0.17	.	6.214	0.20646	0.0:0.7206:0.0:0.2794	.	3431	Q685J3	MUC17_HUMAN	I	3431	ENSP00000302716:T3431I	ENSP00000302716:T3431I	T	+	2	0	MUC17	100471709	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	1.155000	0.31700	-0.582000	0.05929	0.186000	0.17326	ACC	.	C|1.000;G|0.000		0.488	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		T	100684989	C	T	100684989	3	4	245	1	0	0	0	0	1	0	0	0	9983	507	18	3	10302	3	MUC17	7	100684989	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	8548	100684989	58453674	117	33587										
RBM28	55131	hgsc.bcm.edu	37	chr7	127978350	127978350	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ttgagagctttacctgcttcTaggaggtttttgaactgaac	10	7	1	3			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr7:127978350T>G	ENST00000223073.2	-	5	609	c.495A>C	c.(493-495)ctA>ctC	p.L165L	RBM28_ENST00000415472.2_Intron	NM_018077.2	NP_060547.2	Q9NW13	RBM28_HUMAN	RNA binding motif protein 28	165	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleolus (GO:0005730)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|kidney(7)|large_intestine(3)|lung(8)|ovary(2)	21						TACCTGCTTCTAGGAGGTTTT	0.418																																					p.L165L		Atlas-SNP	.											.	RBM28	71	.	0			c.A495C						.						122	112	116					7																	127978350		2203	4300	6503	SO:0001819	synonymous_variant	55131	exon5			TGCTTCTAGGAGG	AK001239	CCDS5801.1, CCDS55159.1	7q32.2	2013-02-12			ENSG00000106344	ENSG00000106344		"RNA binding motif (RRM) containing"	21863	protein-coding gene	gene with protein product		612074					Standard	NM_018077		Approved	FLJ10377	uc003vmp.2	Q9NW13	OTTHUMG00000157711	ENST00000223073.2:c.495A>C	chr7.hg19:g.127978350T>G		106.0	0.0		103.0	43.0	NM_018077	A4D100|B4DU52|E9PDD9|Q53H65|Q96CV3	Silent	SNP	ENST00000223073.2	hg19	CCDS5801.1																																																																																			.	.		0.418	RBM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349442.2	NM_018077		G	127978350	T	G	127978350	2	3	245	1	0	0	0	0	0	0	0	1	13143	1509	53	5		5	RBM28	7	127978350	Silent	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	27293361	127978350	31160313	118	33588										
CPA4	51200	hgsc.bcm.edu	37	chr7	129951962	129951962	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gtcccacctgcaccactgtcTgtaagtactcgcttatttat	6	13	1	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr7:129951962T>A	ENST00000222482.4	+	10	1106	c.1078T>A	c.(1078-1080)Tat>Aat	p.Y360N	CPA4_ENST00000445470.2_Splice_Site_p.Y327N|CPA4_ENST00000493259.1_Splice_Site_p.Y256N	NM_016352.3	NP_057436.2	Q9UI42	CBPA4_HUMAN	carboxypeptidase A4	360					histone acetylation (GO:0016573)	extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Melanoma(18;0.0435)					CACCACTGTCTGTAAGTACTC	0.502																																					p.Y360N		Atlas-SNP	.											.	CPA4	47	.	0			c.T1078A						.						76	71	73					7																	129951962		2203	4300	6503	SO:0001630	splice_region_variant	51200	exon10			ACTGTCTGTAAGT	AF095719	CCDS5818.1, CCDS55163.1	7q32	2008-07-18			ENSG00000128510	ENSG00000128510			15740	protein-coding gene	gene with protein product	"carboxypeptidase A3"	607635				10383164, 10860668	Standard	NM_016352		Approved	CPA3	uc003vpr.3	Q9UI42	OTTHUMG00000157825	ENST00000222482.4:c.1078+1T>A	chr7.hg19:g.129951962T>A		57.0	0.0		51.0	25.0	NM_016352	B7Z576|Q86UY9	Missense_Mutation	SNP	ENST00000222482.4	hg19	CCDS5818.1	.	.	.	.	.	.	.	.	.	.	T	25.4	4.637109	0.87760	.	.	ENSG00000128510	ENST00000445470;ENST00000222482;ENST00000538687;ENST00000493259	T;T;T	0.05786	3.39;3.39;3.39	5.88	5.88	0.94601	Peptidase M14, carboxypeptidase A (2);	0.129240	0.53938	D	0.000045	T	0.32466	0.0830	M	0.90309	3.105	0.80722	D	1	D;D	0.89917	1.0;0.995	D;D	0.85130	0.997;0.962	T	0.24190	-1.0167	10	0.87932	D	0	.	15.1337	0.72545	0.0:0.0:0.0:1.0	.	327;360	B7Z576;Q9UI42	.;CBPA4_HUMAN	N	327;360;165;256	ENSP00000412947:Y327N;ENSP00000222482:Y360N;ENSP00000419660:Y256N	ENSP00000222482:Y360N	Y	+	1	0	CPA4	129739198	1.000000	0.71417	1.000000	0.80357	0.708000	0.40852	6.796000	0.75145	2.257000	0.74773	0.459000	0.35465	TAT	.	.		0.502	CPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349725.1	NM_016352	Missense_Mutation	A	129951962	T	A	129951962	5	1	245	1	0	0	0	0	0	0	1	0	3794	1594	55	4	1116	4	CPA4	7	129951962	Splice_Site	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	1973612	129951962	29186701	119	33589										
HIPK2	28996	hgsc.bcm.edu	37	chr7	139416674	139416675	+	Missense_Mutation	DNP	TC	TC	AA													0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	cgacagggggatgttcttgcTctggctatacactttgctgt							TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr7:139416674_139416675TC>AA	ENST00000406875.3	-	2	253_254	c.159_160GA>TT	c.(157-162)caGAgc>caTTgc	p.53_54QS>HC	HIPK2_ENST00000428878.2_Missense_Mutation_p.53_54QS>HC|HIPK2_ENST00000342645.6_Missense_Mutation_p.53_54QS>HC	NM_022740.4	NP_073577.3	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2	53					adult walking behavior (GO:0007628)|anterior/posterior pattern specification (GO:0009952)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|erythrocyte differentiation (GO:0030218)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|retina layer formation (GO:0010842)|SMAD protein signal transduction (GO:0060395)|smoothened signaling pathway (GO:0007224)|transforming growth factor beta receptor signaling pathway (GO:0007179)|voluntary musculoskeletal movement (GO:0050882)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|virion binding (GO:0046790)			breast(4)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Melanoma(164;0.205)					ATGTTCTTGCTCTGGCTATACA	0.54																																					p.S54C|p.Q53H		Atlas-SNP	.											.	HIPK2	192	.	0			c.A160T|c.G159T						.																																			SO:0001583	missense	28996	exon2			TCTTGCTCTGGCT|CTTGCTCTGGCTA	AF208291	CCDS75666.1, CCDS75667.1	7q32-q34	2004-01-29	2001-11-29		ENSG00000064393	ENSG00000064393			14402	protein-coding gene	gene with protein product		606868	"homeodomain-interacting protein kinase 2"			11120354	Standard	NM_001113239		Approved		uc003vvf.4	Q9H2X6	OTTHUMG00000157704	ENST00000406875.3:c.159_160delinsAA	chr7.hg19:g.139416674_139416675delinsAA	ENSP00000385571:p.Q53_S54delinsHC	135.0	0.0		122.0|124.0	66.0|67.0	NM_022740	Q75MR7|Q8WWI4|Q9H2Y1	Missense_Mutation	SNP	ENST00000406875.3	hg19																																																																																				.	.		0.54	HIPK2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000349430.3	NM_022740		AA	139416675	TC	AA	139416674	3	1	245	1	0	0	0	0	1	0	0	0	7126	1551	54	4	3492	4	HIPK2	7	139416674	Missense_Mutation	DNP	TC	TCGA-ED-A7PZ-01A-11D-A33Q-10	9464712	139416674	19721989	120	33590										
MRPS33	51650	hgsc.bcm.edu	37	chr7	140710338	140710338	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tcactaaacagtttcaccacTttcatagacttggaattagt	5	9	3	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr7:140710338T>C	ENST00000393008.3	-	2	251	c.96A>G	c.(94-96)aaA>aaG	p.K32K	MRPS33_ENST00000472343.1_5'Flank|MRPS33_ENST00000496958.1_Silent_p.K32K|MRPS33_ENST00000324787.5_Silent_p.K32K|MRPS33_ENST00000467334.1_Silent_p.K22K|MRPS33_ENST00000469351.1_Silent_p.K32K	NM_016071.3	NP_057155.1	Q9Y291	RT33_HUMAN	mitochondrial ribosomal protein S33	32					translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)	structural constituent of ribosome (GO:0003735)			breast(2)|endometrium(1)|kidney(1)	4	Melanoma(164;0.00956)					GTTTCACCACTTTCATAGACT	0.468																																					p.K32K		Atlas-SNP	.											.	MRPS33	8	.	0			c.A96G						.						163	146	151					7																	140710338		2203	4300	6503	SO:0001819	synonymous_variant	51650	exon2			CACCACTTTCATA	AF078858	CCDS5864.1	7q34	2012-09-13			ENSG00000090263	ENSG00000090263		"Mitochondrial ribosomal proteins / small subunits"	16634	protein-coding gene	gene with protein product		611993				11279123, 10810093	Standard	NM_016071		Approved	CGI-139	uc003vwe.4	Q9Y291	OTTHUMG00000157456	ENST00000393008.3:c.96A>G	chr7.hg19:g.140710338T>C		161.0	0.0		156.0	57.0	NM_016071		Silent	SNP	ENST00000393008.3	hg19	CCDS5864.1																																																																																			.	.		0.468	MRPS33-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348878.1	NM_053035		C	140710338	T	C	140710338	2	2	245	1	0	0	0	0	0	0	0	1	9851	1606	56	2		2	MRPS33	7	140710338	Silent	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	1293664	140710338	18428325	121	33591										
CNPY1	285888	hgsc.bcm.edu	37	chr7	155301641	155301641	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	aaaaatacaattttttaaatTcttggtatattttgtctcct	3	5	2	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr7:155301641T>A	ENST00000321736.5	-	2	254	c.92A>T	c.(91-93)gAa>gTa	p.E31V	CNPY1_ENST00000406197.1_Missense_Mutation_p.E31V|AC008060.5_ENST00000415333.1_RNA	NM_001103176.1	NP_001096646.1	Q3B7I2	CNPY1_HUMAN	canopy FGF signaling regulator 1	31										breast(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)	8	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.171)		TTTTTTAAATTCTTGGTATAT	0.388																																					p.E31V		Atlas-SNP	.											.	CNPY1	20	.	0			c.A92T						.						69	68	68					7																	155301641		1794	4061	5855	SO:0001583	missense	285888	exon2			TTAAATTCTTGGT		CCDS43684.1	7q36.3	2014-02-12	2013-07-23		ENSG00000146910	ENSG00000146910			27786	protein-coding gene	gene with protein product		612493	"canopy 1 homolog (zebrafish)"			16488878	Standard	NM_001103176		Approved		uc003wmc.1	Q3B7I2	OTTHUMG00000151353	ENST00000321736.5:c.92A>T	chr7.hg19:g.155301641T>A	ENSP00000317439:p.Glu31Val	124.0	0.0		107.0	42.0	NM_001103176	A6NGX3	Missense_Mutation	SNP	ENST00000321736.5	hg19	CCDS43684.1	.	.	.	.	.	.	.	.	.	.	T	14.51	2.556167	0.45487	.	.	ENSG00000146910	ENST00000406197;ENST00000321736	T;T	0.32272	1.46;1.46	4.85	3.69	0.42338	.	0.113150	0.64402	D	0.000020	T	0.20659	0.0497	.	.	.	0.30935	N	0.726513	B	0.25351	0.124	B	0.21917	0.037	T	0.18335	-1.0340	9	0.87932	D	0	-17.5333	3.6404	0.08165	0.1304:0.0756:0.1355:0.6585	.	31	Q3B7I2	CNPY1_HUMAN	V	31	ENSP00000384514:E31V;ENSP00000317439:E31V	ENSP00000317439:E31V	E	-	2	0	CNPY1	154994402	1.000000	0.71417	0.520000	0.27837	0.443000	0.32047	2.600000	0.46240	0.709000	0.31976	0.455000	0.32223	GAA	.	.		0.388	CNPY1-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322335.1	XM_001129537		A	155301641	T	A	155301641	3	1	245	1	0	0	0	0	1	0	0	0	3629	1783	62	4	198	4	CNPY1	7	155301641	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	14591303	155301641	3837022	122	33592										
MNX1	3110	hgsc.bcm.edu	37	chr7	156802352	156802352	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	acgggggccgcagggtactcAcagttgaagtcgggcatctt	15	10	2	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr7:156802352A>T	ENST00000252971.6	-	1	992		c.e1+1		MNX1-AS2_ENST00000429228.1_RNA|MNX1_ENST00000469500.1_5'Flank|MNX1_ENST00000543409.1_5'Flank|MNX1-AS1_ENST00000480284.1_RNA	NM_005515.3	NP_005506.3	P50219	MNX1_HUMAN	motor neuron and pancreas homeobox 1						anatomical structure morphogenesis (GO:0009653)|diaphragm development (GO:0060539)|dorsal/ventral neural tube patterning (GO:0021904)|endocrine pancreas development (GO:0031018)|humoral immune response (GO:0006959)|motor neuron axon guidance (GO:0008045)|nerve development (GO:0021675)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spinal cord motor neuron cell fate specification (GO:0021520)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(1)|lung(4)|skin(1)	7	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CAGGGTACTCACAGTTGAAGT	0.711																																					.		Atlas-SNP	.											.	MNX1	17	.	0			c.691+2T>A						.						11	11	11					7																	156802352		2133	4174	6307	SO:0001630	splice_region_variant	3110	exon2			GTACTCACAGTTG	AF107457	CCDS34788.1, CCDS55187.1	7q36	2012-03-09	2007-08-09	2007-08-09	ENSG00000130675	ENSG00000130675		"Homeoboxes / ANTP class : HOXL subclass"	4979	protein-coding gene	gene with protein product		142994	"homeo box HB9", "homeobox HB9"	HLXB9		9843207	Standard	NM_001165255		Approved	HB9, HOXHB9, SCRA1	uc003wmz.4	P50219	OTTHUMG00000157181	ENST00000252971.6:c.691+1T>A	chr7.hg19:g.156802352A>T		69.0	0.0		55.0	24.0	NM_005515	F5H401|Q9Y648	Splice_Site	SNP	ENST00000252971.6	hg19	CCDS34788.1	.	.	.	.	.	.	.	.	.	.	A	18.54	3.646622	0.67358	.	.	ENSG00000130675	ENST00000252971;ENST00000542972	.	.	.	3.12	3.12	0.35913	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.7819	0.46382	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MNX1	156495113	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.846000	0.86887	1.331000	0.45412	0.449000	0.29647	.	.	.		0.711	MNX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347796.3		Intron	T	156802352	A	T	156802352	5	4	245	1	0	0	0	0	0	0	1	0	9688	173	6	4	583	4	MNX1	7	156802352	Splice_Site	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	1500711	156802352	2336311	123	33593										
MSR1	4481	hgsc.bcm.edu	37	chr8	16035438	16035438	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gagcgagcatcaaatttcacAgattcggagcagctatcagt	10	9	3	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr8:16035438A>T	ENST00000262101.5	-	2	181	c.60T>A	c.(58-60)tcT>tcA	p.S20S	MSR1_ENST00000355282.2_Silent_p.S20S|MSR1_ENST00000445506.2_Silent_p.S38S|MSR1_ENST00000536385.1_5'UTR|MSR1_ENST00000381998.4_Silent_p.S20S|MSR1_ENST00000350896.3_Silent_p.S20S			P21757	MSRE_HUMAN	macrophage scavenger receptor 1	20					cholesterol transport (GO:0030301)|lipoprotein transport (GO:0042953)|plasma lipoprotein particle clearance (GO:0034381)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|receptor-mediated endocytosis (GO:0006898)	collagen trimer (GO:0005581)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|plasma membrane (GO:0005886)	low-density lipoprotein particle binding (GO:0030169)|scavenger receptor activity (GO:0005044)			haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(7)|lung(14)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	37				Colorectal(111;0.00475)|COAD - Colon adenocarcinoma(73;0.0164)		CAAATTTCACAGATTCGGAGC	0.418																																					p.S20S		Atlas-SNP	.											.	MSR1	140	.	0			c.T60A						.						87	80	82					8																	16035438		2203	4300	6503	SO:0001819	synonymous_variant	4481	exon2			TTTCACAGATTCG	D13263	CCDS5995.1, CCDS5996.1, CCDS5997.1	8p22	2006-02-22			ENSG00000038945	ENSG00000038945		"CD molecules"	7376	protein-coding gene	gene with protein product		153622				2251254	Standard	NM_138715		Approved	SCARA1, CD204	uc003wwz.3	P21757	OTTHUMG00000094809	ENST00000262101.5:c.60T>A	chr8.hg19:g.16035438A>T		77.0	0.0		41.0	36.0	NM_138715	D3DSP3|O60505|P21759|Q45F10	Silent	SNP	ENST00000262101.5	hg19	CCDS5995.1																																																																																			.	.		0.418	MSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211627.2			T	16035438	A	T	16035438	2	4	245	1	0	0	0	0	0	0	0	1	9895	175	7	4		4	MSR1	8	16035438	Silent	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10		16035438	130328584	124	33594										
TEX15	56154	hgsc.bcm.edu	37	chr8	30705371	30705371	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	acatttctttggcctggggtAtgtcttttggtttcgggaaa	12	6	2	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr8:30705371A>G	ENST00000256246.2	-	1	1237	c.1163T>C	c.(1162-1164)aTa>aCa	p.I388T	TEX15_ENST00000523186.1_5'Flank	NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	388					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)					NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		GGCCTGGGGTATGTCTTTTGG	0.338																																					p.I388T		Atlas-SNP	.											.	TEX15	350	.	0			c.T1163C						.						110	109	109					8																	30705371		2203	4299	6502	SO:0001583	missense	56154	exon1			TGGGGTATGTCTT	AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"cancer/testis antigen 42"	605795	"testis expressed sequence 15"			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.1163T>C	chr8.hg19:g.30705371A>G	ENSP00000256246:p.Ile388Thr	124.0	0.0		60.0	51.0	NM_031271		Missense_Mutation	SNP	ENST00000256246.2	hg19	CCDS6080.1	.	.	.	.	.	.	.	.	.	.	A	8.274	0.814017	0.16537	.	.	ENSG00000133863	ENST00000256246	T	0.12039	2.72	5.61	0.49	0.16861	.	0.199081	0.35320	N	0.003300	T	0.06781	0.0173	N	0.17082	0.46	0.09310	N	1	B	0.21821	0.061	B	0.19391	0.025	T	0.25779	-1.0122	10	0.87932	D	0	.	3.6348	0.08145	0.5706:0.0:0.153:0.2763	.	388	Q9BXT5	TEX15_HUMAN	T	388	ENSP00000256246:I388T	ENSP00000256246:I388T	I	-	2	0	TEX15	30824913	0.549000	0.26481	0.005000	0.12908	0.001000	0.01503	1.452000	0.35156	0.132000	0.18615	-0.256000	0.11100	ATA	.	.		0.338	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			G	30705371	A	G	30705371	3	3	245	1	0	0	0	0	1	0	0	0	15794	449	16	2	7222	2	TEX15	8	30705371	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	14669933	30705371	115658651	125	33595										
RGS20	8601	hgsc.bcm.edu	37	chr8	54792132	54792132	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gccaagcccagggaagaagaCgccaccgctgggcagagctc	14	14	0	3			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr8:54792132C>T	ENST00000297313.3	+	2	572	c.480C>T	c.(478-480)gaC>gaT	p.D160D	RGS20_ENST00000276500.4_5'Flank|RGS20_ENST00000344277.6_Intron|RGS20_ENST00000522225.1_5'Flank|RP11-1070A24.2_ENST00000606037.1_RNA	NM_170587.2	NP_733466.1	O76081	RGS20_HUMAN	regulator of G-protein signaling 20	160					positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			breast(2)|endometrium(1)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(7;1.37e-06)|Epithelial(17;0.000126)|all cancers(17;0.0009)			GGGAAGAAGACGCCACCGCTG	0.706																																					p.D160D		Atlas-SNP	.											.	RGS20	51	.	0			c.C480T						.						11	9	10					8																	54792132		2045	4035	6080	SO:0001819	synonymous_variant	8601	exon2			AGAAGACGCCACC	AF074979	CCDS6155.1, CCDS6156.1, CCDS69482.1	8q11.23	2008-07-25	2007-08-14		ENSG00000147509	ENSG00000147509		"Regulators of G-protein signaling"	14600	protein-coding gene	gene with protein product		607193	"regulator of G-protein signalling 20"			9748279, 9748280	Standard	NM_003702		Approved	RGSZ1, ZGAP1	uc003xrp.3	O76081	OTTHUMG00000164750	ENST00000297313.3:c.480C>T	chr8.hg19:g.54792132C>T		90.0	0.0		95.0	20.0	NM_170587	Q96BG9	Silent	SNP	ENST00000297313.3	hg19	CCDS6155.1																																																																																			.	.		0.706	RGS20-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000380058.1			T	54792132	C	T	54792132	2	4	245	1	0	0	0	0	0	0	0	1	13318	535	19	1		1	RGS20	8	54792132	Silent	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	24086761	54792132	91571890	126	33596										
PREX2	80243	hgsc.bcm.edu	37	chr8	69143582	69143582	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ttctaggctgtacaagctgtGcgagccacctcccccagctg	10	15	1	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr8:69143582G>T	ENST00000288368.4	+	40	5067	c.4790G>T	c.(4789-4791)tGc>tTc	p.C1597F		NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	1597					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						TACAAGCTGTGCGAGCCACCT	0.448																																					p.C1597F		Atlas-SNP	.											.	PREX2	614	.	0			c.G4790T						.						67	58	61					8																	69143582		2203	4300	6503	SO:0001583	missense	80243	exon40			AGCTGTGCGAGCC	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.4790G>T	chr8.hg19:g.69143582G>T	ENSP00000288368:p.Cys1597Phe	70.0	0.0		92.0	34.0	NM_024870	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	hg19	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	G	19.87	3.907386	0.72868	.	.	ENSG00000046889	ENST00000288368	T	0.61040	0.14	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.67822	0.2934	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.70263	-0.4920	10	0.87932	D	0	.	16.5942	0.84791	0.0:0.0:1.0:0.0	.	1597	Q70Z35	PREX2_HUMAN	F	1597	ENSP00000288368:C1597F	ENSP00000288368:C1597F	C	+	2	0	PREX2	69306136	1.000000	0.71417	0.993000	0.49108	0.904000	0.53231	6.408000	0.73285	2.655000	0.90218	0.551000	0.68910	TGC	.	.		0.448	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		T	69143582	G	T	69143582	3	4	245	1	0	0	0	0	1	0	0	0	12489	1319	46	3	5177	3	PREX2	8	69143582	Missense_Mutation	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	14351450	69143582	77220440	127	33597										
TERF1	7013	hgsc.bcm.edu	37	chr8	73932979	73932979	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	atcagccctgatgatttgggGttcaattgaaaaggaacatg	11	6	2	3			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr8:73932979G>C	ENST00000276603.5	+	3	499	c.476G>C	c.(475-477)gGt>gCt	p.G159A	TERF1_ENST00000276602.6_Missense_Mutation_p.G159A|RNU6-285P_ENST00000410556.1_RNA	NM_017489.2	NP_059523.2	P54274	TERF1_HUMAN	telomeric repeat binding factor (NIMA-interacting) 1	159	TRFH dimerization.				age-dependent telomere shortening (GO:0001309)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of DNA replication (GO:0008156)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via semi-conservative replication (GO:0032214)|negative regulation of telomere maintenance via telomerase (GO:0032211)|positive regulation of apoptotic process (GO:0043065)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of mitosis (GO:0045840)|positive regulation of mitotic cell cycle (GO:0045931)|protein homooligomerization (GO:0051260)|response to drug (GO:0042493)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)|telomere maintenance via telomere shortening (GO:0010834)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nuclear telomere cap complex (GO:0000783)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|double-stranded telomeric DNA binding (GO:0003691)|microtubule binding (GO:0008017)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|telomeric DNA binding (GO:0042162)			central_nervous_system(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	9	Breast(64;0.218)		Epithelial(68;0.0984)			ATGATTTGGGGTTCAATTGAA	0.289																																					p.G159A		Atlas-SNP	.											.	TERF1	48	.	0			c.G476C						.						42	40	40					8																	73932979		2202	4293	6495	SO:0001583	missense	7013	exon3			TTTGGGGTTCAAT	U74382	CCDS6210.1, CCDS6211.1	8q21.11	2011-05-24			ENSG00000147601	ENSG00000147601			11728	protein-coding gene	gene with protein product		600951		TRBF1		9391075	Standard	NM_003218		Approved	PIN2, TRF1, TRF	uc003xzd.2	P54274	OTTHUMG00000164522	ENST00000276603.5:c.476G>C	chr8.hg19:g.73932979G>C	ENSP00000276603:p.Gly159Ala	266.0	0.0		356.0	135.0	NM_017489	A7XP29|Q15553|Q8NHT6|Q93029	Missense_Mutation	SNP	ENST00000276603.5	hg19	CCDS6211.1	.	.	.	.	.	.	.	.	.	.	G	3.503	-0.101319	0.06967	.	.	ENSG00000147601	ENST00000276603;ENST00000276602;ENST00000518874;ENST00000517390	.	.	.	4.82	-1.45	0.08828	Telomere repeat-binding factor, dimerisation domain (4);	1.369990	0.04350	N	0.355562	T	0.12944	0.0314	N	0.00926	-1.1	0.21782	N	0.999542	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.21621	-1.0240	9	0.18276	T	0.48	.	8.8466	0.35174	0.544:0.3273:0.1288:0.0	.	159;159	P54274-2;P54274	.;TERF1_HUMAN	A	159;159;127;55	.	ENSP00000276602:G159A	G	+	2	0	TERF1	74095533	0.090000	0.21635	0.978000	0.43139	0.991000	0.79684	-0.285000	0.08410	-0.148000	0.11234	0.467000	0.42956	GGT	.	.		0.289	TERF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379093.1	NM_017489		C	73932979	G	C	73932979	3	2	245	1	0	0	0	0	1	0	0	0	15776	1261	44	4	486	4	TERF1	8	73932979	Missense_Mutation	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	4789397	73932979	72431043	128	33598										
ZFAND1	79752	hgsc.bcm.edu	37	chr8	82615054	82615054	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tccaggtttccaaagtatgaTccaagggtaaggcttctcct	9	10	1	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr8:82615054T>C	ENST00000220669.5	-	8	701	c.683A>G	c.(682-684)gAt>gGt	p.D228G	ZFAND1_ENST00000519338.1_5'UTR|ZFAND1_ENST00000521895.1_Silent_p.G118G|ZFAND1_ENST00000523096.1_Missense_Mutation_p.D221G|ZFAND1_ENST00000521287.1_Missense_Mutation_p.D121G|ZFAND1_ENST00000522520.1_Missense_Mutation_p.D121G	NM_024699.2	NP_078975.2	Q8TCF1	ZFAN1_HUMAN	zinc finger, AN1-type domain 1	228							zinc ion binding (GO:0008270)			kidney(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13						CAAAGTATGATCCAAGGGTAA	0.353																																					p.D228G		Atlas-SNP	.											.	ZFAND1	29	.	0			c.A683G						.						128	139	135					8																	82615054		2203	4300	6503	SO:0001583	missense	79752	exon8			GTATGATCCAAGG		CCDS6232.1, CCDS55250.1, CCDS55251.1	8q21.13	2006-07-07						"Zinc fingers, AN1-type domain containing"	25858	protein-coding gene	gene with protein product						12477932	Standard	NM_024699		Approved	FLJ14007	uc003ycj.2	Q8TCF1		ENST00000220669.5:c.683A>G	chr8.hg19:g.82615054T>C	ENSP00000220669:p.Asp228Gly	182.0	0.0		202.0	25.0	NM_024699	E5RIG0|E5RJ99|Q658R7|Q6IA32|Q6PGQ6|Q9H810	Missense_Mutation	SNP	ENST00000220669.5	hg19	CCDS6232.1	.	.	.	.	.	.	.	.	.	.	T	19.63	3.863645	0.71949	.	.	ENSG00000104231	ENST00000523096;ENST00000220669;ENST00000522520;ENST00000521287	.	.	.	5.61	5.61	0.85477	.	0.143872	0.64402	D	0.000011	T	0.65407	0.2688	M	0.65975	2.015	0.80722	D	1	P;P	0.47762	0.9;0.9	P;P	0.49012	0.598;0.493	T	0.67650	-0.5616	9	0.48119	T	0.1	.	15.794	0.78394	0.0:0.0:0.0:1.0	.	221;228	E5RIG0;Q8TCF1	.;ZFAN1_HUMAN	G	221;228;121;121	.	ENSP00000220669:D228G	D	-	2	0	ZFAND1	82777609	1.000000	0.71417	0.975000	0.42487	0.982000	0.71751	7.198000	0.77823	2.137000	0.66172	0.477000	0.44152	GAT	.	.		0.353	ZFAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379739.1	NM_024699		C	82615054	T	C	82615054	3	2	245	1	0	0	0	0	1	0	0	0	17641	1435	50	2	127	2	ZFAND1	8	82615054	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	8682075	82615054	63748968	129	33599										
TP53INP1	94241	hgsc.bcm.edu	37	chr8	95952315	95952315	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gactcaaactggagaaagcaGgaatcacttgtatcagccaa	9	9	3	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr8:95952315G>T	ENST00000342697.4	-	3	653	c.246C>A	c.(244-246)tcC>tcA	p.S82S	NDUFAF6_ENST00000396113.1_Intron|TP53INP1_ENST00000448464.2_Silent_p.S82S|TP53INP1_ENST00000378776.4_Silent_p.S82S	NM_033285.3	NP_150601.1	Q96A56	T53I1_HUMAN	tumor protein p53 inducible nuclear protein 1	82					apoptotic process (GO:0006915)|autophagic cell death (GO:0048102)|autophagy (GO:0006914)|cell cycle arrest (GO:0007050)|cellular response to ethanol (GO:0071361)|cellular response to hydroperoxide (GO:0071447)|cellular response to methyl methanesulfonate (GO:0072703)|cellular response to UV (GO:0034644)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of autophagy (GO:0010508)|positive regulation of transcription, DNA-templated (GO:0045893)|response to heat (GO:0009408)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)	antioxidant activity (GO:0016209)			kidney(2)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	9	Breast(36;8.75e-07)					GGAGAAAGCAGGAATCACTTG	0.473																																					p.S82S		Atlas-SNP	.											.	TP53INP1	22	.	0			c.C246A						.						118	117	118					8																	95952315		2203	4300	6503	SO:0001819	synonymous_variant	94241	exon3			AAAGCAGGAATCA	AF409115	CCDS6265.1, CCDS47899.1	8q22	2004-03-11				ENSG00000164938			18022	protein-coding gene	gene with protein product		606185				11511362, 12438758	Standard	NM_033285		Approved	DKFZp434M1317, FLJ22139, P53DINP1, SIP, TP53INP1A, TP53INP1B, Teap	uc003yhg.3	Q96A56		ENST00000342697.4:c.246C>A	chr8.hg19:g.95952315G>T		161.0	0.0		165.0	23.0	NM_001135733	B2RCE5|Q969R9	Silent	SNP	ENST00000342697.4	hg19	CCDS6265.1																																																																																			.	.		0.473	TP53INP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379818.1			T	95952315	G	T	95952315	2	4	245	1	0	0	0	0	0	0	0	1	16403	987	35	3		3	TP53INP1	8	95952315	Silent	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	13337261	95952315	50411707	130	33600										
OSR2	116039	hgsc.bcm.edu	37	chr8	99963924	99963924	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ctcacaccccgcggcaggacTtctagagaagcccaggatct	10	15	3	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr8:99963924T>G	ENST00000297565.4	+	4	1430	c.934T>G	c.(934-936)Ttc>Gtc	p.F312V	OSR2_ENST00000457907.2_Missense_Mutation_p.F433V|OSR2_ENST00000435298.2_3'UTR|OSR2_ENST00000522510.1_Missense_Mutation_p.F312V	NM_001142462.1	NP_001135934.1	Q8N2R0	OSR2_HUMAN	odd-skipped related transciption factor 2	312					bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|chondrocyte differentiation (GO:0002062)|embryo development (GO:0009790)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal joint development (GO:0072498)|embryonic skeletal joint morphogenesis (GO:0060272)|embryonic skeletal limb joint morphogenesis (GO:0036023)|embryonic skeletal system morphogenesis (GO:0048704)|eyelid development in camera-type eye (GO:0061029)|head development (GO:0060322)|mesonephros development (GO:0001823)|metanephros development (GO:0001656)|middle ear morphogenesis (GO:0042474)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis (GO:0042476)|osteoblast proliferation (GO:0033687)|palate development (GO:0060021)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gastrulation (GO:2000543)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Breast(36;4.14e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.0136)			GCGGCAGGACTTCTAGAGAAG	0.627																																					p.F312V		Atlas-SNP	.											.	OSR2	56	.	0			c.T934G						.						27	30	30					8																	99963924		1976	4135	6111	SO:0001583	missense	116039	exon4			CAGGACTTCTAGA	AY038072	CCDS47901.1, CCDS47902.1, CCDS69520.1	8q22.2	2013-10-17	2013-10-17			ENSG00000164920		"Zinc fingers, C2H2-type"	15830	protein-coding gene	gene with protein product		611297	"odd-skipped related 2 (Drosophila)"				Standard	XM_005250779		Approved	FLJ90037	uc003yir.3	Q8N2R0		ENST00000297565.4:c.934T>G	chr8.hg19:g.99963924T>G	ENSP00000297565:p.Phe312Val	49.0	0.0		69.0	29.0	NM_001142462	A8K626|B4E3B7|Q96AM6|Q96LB6|Q96LB7	Missense_Mutation	SNP	ENST00000297565.4	hg19	CCDS47901.1	.	.	.	.	.	.	.	.	.	.	T	16.70	3.196137	0.58126	.	.	ENSG00000164920	ENST00000297565;ENST00000522510;ENST00000457907	T;T;T	0.12361	2.98;2.98;2.69	5.32	5.32	0.75619	.	0.089158	0.47093	D	0.000246	T	0.19167	0.0460	M	0.86097	2.795	0.46458	D	0.99905	P;B	0.43094	0.799;0.043	B;B	0.30401	0.115;0.011	T	0.12915	-1.0529	9	.	.	.	.	15.4552	0.75308	0.0:0.0:0.0:1.0	.	433;312	B4E3B7;Q8N2R0	.;OSR2_HUMAN	V	312;312;433	ENSP00000297565:F312V;ENSP00000430780:F312V;ENSP00000414657:F433V	.	F	+	1	0	OSR2	100033100	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.449000	0.80643	2.222000	0.72286	0.533000	0.62120	TTC	.	.		0.627	OSR2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000379505.1	NM_053001		G	99963924	T	G	99963924	3	3	245	1	0	0	0	0	1	0	0	0	11303	1609	56	5	944	5	OSR2	8	99963924	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	4011609	99963924	46400098	131	33601										
DENND3	22898	hgsc.bcm.edu	37	chr8	142151309	142151309	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gcttttcatgtaggatgagtActgtttctacaatggcaaaa	9	6	2	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr8:142151309A>G	ENST00000262585.2	+	4	547	c.269A>G	c.(268-270)tAc>tGc	p.Y90C	DENND3_ENST00000518347.1_Missense_Mutation_p.Y170C|DENND3_ENST00000519811.1_Missense_Mutation_p.Y170C|DENND3_ENST00000424248.1_Missense_Mutation_p.Y90C	NM_014957.2	NP_055772.2	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	90					cellular protein catabolic process (GO:0044257)|endosome to lysosome transport (GO:0008333)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(4)|stomach(2)|urinary_tract(1)	55	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)			TAGGATGAGTACTGTTTCTAC	0.527																																					p.Y90C		Atlas-SNP	.											.	DENND3	127	.	0			c.A269G						.						165	122	137					8																	142151309		2203	4300	6503	SO:0001583	missense	22898	exon4			ATGAGTACTGTTT	AB020677	CCDS34947.1	8q24.3	2013-01-10				ENSG00000105339		"DENN/MADD domain containing", "WD repeat domain containing"	29134	protein-coding gene	gene with protein product						10048485	Standard	NM_014957		Approved	KIAA0870	uc003yvy.3	A2RUS2		ENST00000262585.2:c.269A>G	chr8.hg19:g.142151309A>G	ENSP00000262585:p.Tyr90Cys	61.0	0.0		78.0	23.0	NM_014957	B7ZM28|O94947|Q2TAM7|Q6ZMS6|Q96DK3	Missense_Mutation	SNP	ENST00000262585.2	hg19	CCDS34947.1	.	.	.	.	.	.	.	.	.	.	A	3.007	-0.204700	0.06180	.	.	ENSG00000105339	ENST00000519291;ENST00000518347;ENST00000262585;ENST00000424248;ENST00000519811;ENST00000523058;ENST00000518249	T;T;T;T	0.45668	2.92;2.51;2.92;0.89	5.14	-0.135	0.13477	.	0.959493	0.08722	N	0.903310	T	0.25195	0.0612	N	0.16478	0.41	0.09310	N	1	B;B;B	0.12630	0.004;0.002;0.006	B;B;B	0.08055	0.002;0.002;0.003	T	0.21280	-1.0250	10	0.38643	T	0.18	-21.0611	7.603	0.28087	0.3016:0.4882:0.2102:0.0	.	170;90;170	E9PF32;A2RUS2;E5RIR7	.;DEND3_HUMAN;.	C	103;170;90;90;170;170;3	ENSP00000262585:Y90C;ENSP00000410594:Y90C;ENSP00000428714:Y170C;ENSP00000430786:Y170C	ENSP00000262585:Y90C	Y	+	2	0	DENND3	142220491	0.000000	0.05858	0.018000	0.16275	0.151000	0.21798	0.014000	0.13333	-0.270000	0.09285	0.533000	0.62120	TAC	.	.		0.527	DENND3-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_014957		G	142151309	A	G	142151309	3	3	245	1	0	0	0	0	1	0	0	0	4434	391	14	2	279	2	DENND3	8	142151309	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	42187385	142151309	4212713	132	33602										
ZNF16	7564	hgsc.bcm.edu	37	chr8	146157778	146157778	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ctggtgtgaagtccccctccTgggagagggactgtggcagc	16	11	0	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr8:146157778T>A	ENST00000276816.4	-	4	581	c.395A>T	c.(394-396)cAg>cTg	p.Q132L	ZNF16_ENST00000394909.2_Missense_Mutation_p.Q132L	NM_001029976.2	NP_001025147.2	P17020	ZNF16_HUMAN	zinc finger protein 16	132	Necessary for transcription activation.				cell cycle (GO:0007049)|cell division (GO:0051301)|cellular response to sodium dodecyl sulfate (GO:0072707)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell cycle phase transition (GO:1901989)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of kinase activity (GO:0033674)|positive regulation of megakaryocyte differentiation (GO:0045654)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|kidney(4)|large_intestine(5)|lung(9)|ovary(5)|prostate(1)|skin(1)|urinary_tract(1)	29	all_cancers(97;8.72e-12)|all_epithelial(106;1.07e-10)|Lung NSC(106;7.18e-05)|all_lung(105;0.00021)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;0.136)	Epithelial(56;3.45e-38)|all cancers(56;3.04e-33)|BRCA - Breast invasive adenocarcinoma(115;0.0424)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.02)|KIRC - Kidney renal clear cell carcinoma(644;0.0486)		GTCCCCCTCCTGGGAGAGGGA	0.567																																					p.Q132L		Atlas-SNP	.											.	ZNF16	80	.	0			c.A395T						.						71	77	75					8																	146157778		2203	4300	6503	SO:0001583	missense	7564	exon3			CCCTCCTGGGAGA	X52340	CCDS6437.1	8q24	2013-01-08	2006-05-10		ENSG00000170631	ENSG00000170631		"Zinc fingers, C2H2-type"	12947	protein-coding gene	gene with protein product		601262	"zinc finger protein 16 (KOX 9)"				Standard	NM_006958		Approved	KOX9	uc003zeu.3	P17020	OTTHUMG00000165253	ENST00000276816.4:c.395A>T	chr8.hg19:g.146157778T>A	ENSP00000276816:p.Gln132Leu	68.0	0.0		91.0	46.0	NM_006958	B3KXM4|D3DWP2|Q45SH7|Q96FG0|Q9NRA4	Missense_Mutation	SNP	ENST00000276816.4	hg19	CCDS6437.1	.	.	.	.	.	.	.	.	.	.	T	8.998	0.979507	0.18812	.	.	ENSG00000170631	ENST00000276816;ENST00000394909;ENST00000532351	T;T;T	0.10005	2.92;2.92;4.54	3.85	-3.33	0.04958	.	.	.	.	.	T	0.04318	0.0119	N	0.08118	0	0.09310	N	1	B	0.26400	0.148	B	0.19391	0.025	T	0.43605	-0.9381	9	0.24483	T	0.36	.	7.4432	0.27196	0.0:0.5521:0.161:0.2869	.	132	P17020	ZNF16_HUMAN	L	132	ENSP00000276816:Q132L;ENSP00000378369:Q132L;ENSP00000434321:Q132L	ENSP00000276816:Q132L	Q	-	2	0	ZNF16	146128582	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-2.768000	0.00781	-0.757000	0.04697	0.460000	0.39030	CAG	.	.		0.567	ZNF16-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000382978.1	NM_006958		A	146157778	T	A	146157778	3	1	245	1	0	0	0	0	1	0	0	0	17753	1580	55	4	1657	4	ZNF16	8	146157778	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	4006469	146157778	206244	133	33603										
VLDLR	7436	hgsc.bcm.edu	37	chr9	2641451	2641451	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gtatcccagtgtcctggagaTgtgatggtgaaaatgattgt	13	5	0	4			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr9:2641451T>A	ENST00000382100.3	+	4	756	c.400T>A	c.(400-402)Tgt>Agt	p.C134S	VLDLR_ENST00000382099.2_Missense_Mutation_p.C134S|RP11-125B21.2_ENST00000599229.1_RNA	NM_003383.3	NP_003374.3	P98155	VLDLR_HUMAN	very low density lipoprotein receptor	134	LDL-receptor class A 3. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cholesterol metabolic process (GO:0008203)|glycoprotein transport (GO:0034436)|lipid transport (GO:0006869)|memory (GO:0007613)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|positive regulation of dendrite development (GO:1900006)|positive regulation of protein kinase activity (GO:0045860)|receptor-mediated endocytosis (GO:0006898)|reelin-mediated signaling pathway (GO:0038026)|signal transduction (GO:0007165)|ventral spinal cord development (GO:0021517)|very-low-density lipoprotein particle clearance (GO:0034447)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|very-low-density lipoprotein particle (GO:0034361)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|glycoprotein binding (GO:0001948)|glycoprotein transporter activity (GO:0034437)|low-density lipoprotein receptor activity (GO:0005041)|reelin receptor activity (GO:0038025)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	24				GBM - Glioblastoma multiforme(50;0.0668)|Lung(218;0.123)		GTCCTGGAGATGTGATGGTGA	0.428																																					p.C134S		Atlas-SNP	.											.	VLDLR	68	.	0			c.T400A						.						244	220	228					9																	2641451		2203	4300	6503	SO:0001583	missense	7436	exon4			TGGAGATGTGATG		CCDS6446.1, CCDS34979.1	9p24	2014-01-24			ENSG00000147852	ENSG00000147852		"Low density lipoprotein receptors"	12698	protein-coding gene	gene with protein product		192977				8294473	Standard	XM_006716864		Approved	CARMQ1, CHRMQ1, VLDLRCH	uc003zhk.1	P98155	OTTHUMG00000019447	ENST00000382100.3:c.400T>A	chr9.hg19:g.2641451T>A	ENSP00000371532:p.Cys134Ser	127.0	0.0		60.0	50.0	NM_003383	B2RMZ7|D3DRH6|Q5VVF6	Missense_Mutation	SNP	ENST00000382100.3	hg19	CCDS6446.1	.	.	.	.	.	.	.	.	.	.	T	32	5.135462	0.94517	.	.	ENSG00000147852	ENST00000382100;ENST00000382099	D;D	0.99751	-6.63;-6.63	6.07	6.07	0.98685	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.64402	D	0.000018	D	0.99904	0.9954	H	0.99705	4.715	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.96006	0.8997	10	0.87932	D	0	.	16.6288	0.85011	0.0:0.0:0.0:1.0	.	134;134	Q5VVF5;P98155	.;VLDLR_HUMAN	S	134	ENSP00000371532:C134S;ENSP00000371531:C134S	ENSP00000371531:C134S	C	+	1	0	VLDLR	2631451	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.698000	0.84413	2.326000	0.78906	0.533000	0.62120	TGT	.	.		0.428	VLDLR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051519.2	NM_003383		A	2641451	T	A	2641451	3	1	245	1	0	0	0	0	1	0	0	0	17189	1464	51	4	414	4	VLDLR	9	2641451	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10		2641451	138571980	134	33604										
GABBR2	9568	hgsc.bcm.edu	37	chr9	101068512	101068512	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gggtcaggaaggagacagcgGccccgatgatgcacatgatc	15	10	1	3			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr9:101068512G>A	ENST00000259455.2	-	15	2579	c.2120C>T	c.(2119-2121)gCc>gTc	p.A707V		NM_005458.7	NP_005449.5	O75899	GABR2_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 2	707					G-protein coupled receptor signaling pathway (GO:0007186)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled GABA receptor activity (GO:0004965)		NOTCH1_ENST00000277541/GABBR2(2)	breast(4)|endometrium(4)|large_intestine(12)|lung(21)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	49		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	GGAGACAGCGGCCCCGATGAT	0.572																																					p.A707V		Atlas-SNP	.											.	GABBR2	126	.	0			c.C2120T						.						147	100	116					9																	101068512		2203	4300	6503	SO:0001583	missense	9568	exon15			ACAGCGGCCCCGA	AF069755	CCDS6736.1	9q22.1-q22.3	2012-08-29	2006-02-16	2006-02-16	ENSG00000136928	ENSG00000136928		"GABA receptors", "GPCR / Class C : GABA(B) receptors"	4507	protein-coding gene	gene with protein product		607340	"G protein-coupled receptor 51"	GPR51		10087195	Standard	NM_005458		Approved	HG20, GABABR2, GPRC3B	uc004ays.3	O75899	OTTHUMG00000020345	ENST00000259455.2:c.2120C>T	chr9.hg19:g.101068512G>A	ENSP00000259455:p.Ala707Val	186.0	0.0		77.0	69.0	NM_005458	O75974|O75975|Q5VXZ2|Q8WX04|Q9P1R2|Q9UNR1|Q9UNS9	Missense_Mutation	SNP	ENST00000259455.2	hg19	CCDS6736.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.904030	0.92035	.	.	ENSG00000136928	ENST00000259455	D	0.86694	-2.16	5.0	5.0	0.66597	GPCR, family 3, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.87330	0.6150	N	0.13327	0.33	0.80722	D	1	D	0.69078	0.997	D	0.77004	0.989	D	0.87769	0.2604	10	0.38643	T	0.18	.	15.8197	0.78631	0.0:0.0:1.0:0.0	.	707	O75899	GABR2_HUMAN	V	707	ENSP00000259455:A707V	ENSP00000259455:A707V	A	-	2	0	GABBR2	100108333	1.000000	0.71417	0.998000	0.56505	0.983000	0.72400	9.641000	0.98458	2.328000	0.79073	0.561000	0.74099	GCC	.	.		0.572	GABBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053373.1			A	101068512	G	A	101068512	3	1	245	1	0	0	0	0	1	0	0	0	6164	1203	42	3	725	3	GABBR2	9	101068512	Missense_Mutation	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	98427061	101068512	40144919	135	33605										
AKNA	80709	hgsc.bcm.edu	37	chr9	117139221	117139221	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tgtgttccttgggctgagggCagaagaatctggtcgtttct	14	7	2	3			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr9:117139221C>T	ENST00000307564.4	-	3	1027	c.866G>A	c.(865-867)tGc>tAc	p.C289Y	AKNA_ENST00000374075.5_Missense_Mutation_p.C208Y|AKNA_ENST00000312033.3_Missense_Mutation_p.C289Y|AKNA_ENST00000223791.3_5'UTR|AKNA_ENST00000374088.3_Missense_Mutation_p.C289Y	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	289					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						GGGCTGAGGGCAGAAGAATCT	0.582																																					p.C289Y		Atlas-SNP	.											.	AKNA	119	.	0			c.G866A						.						119	106	110					9																	117139221		2203	4300	6503	SO:0001583	missense	80709	exon3			TGAGGGCAGAAGA	AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.866G>A	chr9.hg19:g.117139221C>T	ENSP00000303769:p.Cys289Tyr	91.0	0.0		30.0	26.0	NM_030767	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Missense_Mutation	SNP	ENST00000307564.4	hg19	CCDS6805.1	.	.	.	.	.	.	.	.	.	.	C	10.88	1.475252	0.26511	.	.	ENSG00000106948	ENST00000307564;ENST00000394582;ENST00000374088;ENST00000374075;ENST00000312033;ENST00000394574	T;T;T;T	0.35973	2.49;2.49;2.49;1.28	4.62	-0.0976	0.13632	.	0.998707	0.08102	N	0.997607	T	0.18257	0.0438	N	0.24115	0.695	0.09310	N	1	P;P;P	0.39157	0.483;0.531;0.662	B;B;B	0.31191	0.092;0.059;0.125	T	0.19516	-1.0303	10	0.62326	D	0.03	-2.6896	2.5187	0.04675	0.3038:0.4387:0.1499:0.1076	.	289;289;208	Q7Z591-6;Q7Z591;Q7Z591-2	.;AKNA_HUMAN;.	Y	289;130;289;208;289;289	ENSP00000303769:C289Y;ENSP00000363201:C289Y;ENSP00000363188:C208Y;ENSP00000309222:C289Y	ENSP00000303769:C289Y	C	-	2	0	AKNA	116179042	0.135000	0.22499	0.130000	0.21974	0.138000	0.21146	0.473000	0.22132	0.281000	0.22233	0.561000	0.74099	TGC	.	.		0.582	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767		T	117139221	C	T	117139221	3	4	245	1	0	0	0	0	1	0	0	0	463	710	25	3	3533	3	AKNA	9	117139221	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	16070709	117139221	24074210	136	33606										
URM1	81605	hgsc.bcm.edu	37	chr9	131133678	131133678	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	acatggctgcgcccttgtcaGtggaggtggagttcgggtga	17	8	1	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr9:131133678G>C	ENST00000372853.4	+	1	81	c.19G>C	c.(19-21)Gtg>Ctg	p.V7L	URM1_ENST00000452446.1_Missense_Mutation_p.V7L|URM1_ENST00000372850.1_Missense_Mutation_p.V7L|URM1_ENST00000372847.1_Missense_Mutation_p.V7L	NM_001265582.1|NM_030914.3	NP_001252511.1|NP_112176.1			ubiquitin related modifier 1											cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)	5						GCCCTTGTCAGTGGAGGTGGA	0.642																																					p.V7L		Atlas-SNP	.											.	URM1	19	.	0			c.G19C						.						42	44	43					9																	131133678		2203	4300	6503	SO:0001583	missense	81605	exon1			TTGTCAGTGGAGG	AK097029	CCDS6900.1, CCDS48035.1, CCDS59148.1	9q34.13	2010-06-24	2010-06-24	2006-11-28	ENSG00000167118	ENSG00000167118			28378	protein-coding gene	gene with protein product		612693	"chromosome 9 open reading frame 74", "ubiquitin related modifier 1 homolog (S. cerevisiae)"	C9orf74		16046629, 16864801	Standard	NM_030914		Approved	MGC2668	uc011may.2	Q9BTM9	OTTHUMG00000020742	ENST00000372853.4:c.19G>C	chr9.hg19:g.131133678G>C	ENSP00000361944:p.Val7Leu	90.0	0.0		40.0	33.0	NM_001265582		Missense_Mutation	SNP	ENST00000372853.4	hg19	CCDS6900.1	.	.	.	.	.	.	.	.	.	.	G	14.84	2.656387	0.47467	.	.	ENSG00000167118	ENST00000372853;ENST00000452446;ENST00000372850;ENST00000372847	.	.	.	5.28	5.28	0.74379	Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp (1);Beta-grasp fold, ferredoxin-type (1);	0.237244	0.36482	N	0.002579	T	0.33760	0.0874	N	0.04508	-0.205	0.40356	D	0.979184	B;B	0.32781	0.384;0.001	B;B	0.36666	0.23;0.006	T	0.41466	-0.9507	9	0.87932	D	0	-9.8629	12.0435	0.53466	0.0:0.1731:0.8269:0.0	.	7;7	Q9BTM9-2;Q9BTM9	.;URM1_HUMAN	L	7	.	ENSP00000361938:V7L	V	+	1	0	URM1	130173499	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.043000	0.49823	2.746000	0.94184	0.655000	0.94253	GTG	.	.		0.642	URM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054422.1	NM_030914		C	131133678	G	C	131133678	3	2	245	1	0	0	0	0	1	0	0	0	17042	1029	36	4	21	4	URM1	9	131133678	Missense_Mutation	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	13994457	131133678	10079753	137	33607										
NTNG2	84628	hgsc.bcm.edu	37	chr9	135116364	135116364	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	accggcttctgcgagtgccgCgagggcgcggcgggccccaa	17	15	1	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr9:135116364C>A	ENST00000393229.3	+	7	2066	c.1290C>A	c.(1288-1290)cgC>cgA	p.R430R	NTNG2_ENST00000490694.1_3'UTR|NTNG2_ENST00000393228.4_Silent_p.R422R|NTNG2_ENST00000360670.3_Silent_p.R436R	NM_032536.2	NP_115925.2	Q96CW9	NTNG2_HUMAN	netrin G2	430	Laminin EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axonogenesis (GO:0007409)	anchored component of plasma membrane (GO:0046658)|axon (GO:0030424)				central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	29				OV - Ovarian serous cystadenocarcinoma(145;1.23e-05)|Epithelial(140;0.000173)		GCGAGTGCCGCGAGGGCGCGG	0.721																																					p.R430R		Atlas-SNP	.											.	NTNG2	66	.	0			c.C1290A						.						27	26	27					9																	135116364		2200	4298	6498	SO:0001819	synonymous_variant	84628	exon7			GTGCCGCGAGGGC	AB058760	CCDS6946.1	9q34	2013-03-01	2003-12-02	2003-12-03	ENSG00000196358	ENSG00000196358		"Netrins"	14288	protein-coding gene	gene with protein product	"Netrin-G2"		"netrin G1"	NTNG1			Standard	NM_032536		Approved	KIAA1857, Lmnt2	uc004cbh.2	Q96CW9	OTTHUMG00000020835	ENST00000393229.3:c.1290C>A	chr9.hg19:g.135116364C>A		47.0	0.0		23.0	22.0	NM_032536	Q5JUJ2|Q6UXY0|Q96JH0	Silent	SNP	ENST00000393229.3	hg19	CCDS6946.1																																																																																			.	.		0.721	NTNG2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054779.1	NM_032536		A	135116364	C	A	135116364	2	1	245	1	0	0	0	0	0	0	0	1	10714	755	27	1		1	NTNG2	9	135116364	Silent	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	3982686	135116364	6097067	138	33608										
DHTKD1	55526	hgsc.bcm.edu	37	chr10	12126675	12126675	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	aaagactggtttgccaagcgGtttgaggaactgcaaaagga	13	6	0	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr10:12126675G>T	ENST00000263035.4	+	3	509	c.447G>T	c.(445-447)cgG>cgT	p.R149R	DHTKD1_ENST00000465617.1_Intron	NM_018706.5	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain containing 1	149					cell death (GO:0008219)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hematopoietic progenitor cell differentiation (GO:0002244)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(1)	44		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)			TTGCCAAGCGGTTTGAGGAAC	0.453																																					p.R149R		Atlas-SNP	.											.	DHTKD1	104	.	0			c.G447T						.						162	164	163					10																	12126675		2203	4300	6503	SO:0001819	synonymous_variant	55526	exon3			CAAGCGGTTTGAG	BC002477	CCDS7087.1	10p14	2003-11-24			ENSG00000181192	ENSG00000181192			23537	protein-coding gene	gene with protein product		614984				10997877	Standard	NM_018706		Approved	KIAA1630, MGC3090, DKFZP762M115	uc001ild.5	Q96HY7	OTTHUMG00000017677	ENST00000263035.4:c.447G>T	chr10.hg19:g.12126675G>T		139.0	0.0		132.0	63.0	NM_018706	Q68CU5|Q9BUM8|Q9HCE2	Silent	SNP	ENST00000263035.4	hg19	CCDS7087.1																																																																																			.	.		0.453	DHTKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046777.1	NM_018706		T	12126675	G	T	12126675	2	4	245	1	0	0	0	0	0	0	0	1	4502	1248	44	3		3	DHTKD1	10	12126675	Silent	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10		12126675	123408072	139	33609										
MKX	283078	hgsc.bcm.edu	37	chr10	28023482	28023482	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	aaagatcccgagtggtttctTtgccttgtttttcccatcat	7	10	2	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr10:28023482T>A	ENST00000375790.5	-	5	1173	c.741A>T	c.(739-741)caA>caT	p.Q247H	MKX_ENST00000419761.1_Missense_Mutation_p.Q247H			Q8IYA7	MKX_HUMAN	mohawk homeobox	247					collagen fibril organization (GO:0030199)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|positive regulation of collagen biosynthetic process (GO:0032967)|tendon cell differentiation (GO:0035990)|tendon sheath development (GO:0002932)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(2)|skin(2)	16						AGTGGTTTCTTTGCCTTGTTT	0.438																																					p.Q247H		Atlas-SNP	.											.	MKX	43	.	0			c.A741T						.						206	194	198					10																	28023482		2203	4300	6503	SO:0001583	missense	283078	exon5			GTTTCTTTGCCTT	BC036207	CCDS7156.1	10p12.1	2011-06-20	2006-03-31	2006-03-31	ENSG00000150051	ENSG00000150051		"Homeoboxes / TALE class"	23729	protein-coding gene	gene with protein product		601332	"chromosome 10 open reading frame 48", "iroquois homeobox protein-like 1"	C10orf48, IRXL1		16408284	Standard	NM_173576		Approved	MGC39616	uc001itx.4	Q8IYA7	OTTHUMG00000017862	ENST00000375790.5:c.741A>T	chr10.hg19:g.28023482T>A	ENSP00000364946:p.Gln247His	142.0	0.0		119.0	63.0	NM_001242702	B3KWM5	Missense_Mutation	SNP	ENST00000375790.5	hg19	CCDS7156.1	.	.	.	.	.	.	.	.	.	.	T	16.20	3.056995	0.55325	.	.	ENSG00000150051	ENST00000375790;ENST00000419761	T;T	0.17528	2.27;2.27	5.99	0.568	0.17333	.	0.207528	0.51477	D	0.000093	T	0.15696	0.0378	L	0.44542	1.39	0.30965	N	0.723181	P	0.34837	0.472	B	0.37888	0.26	T	0.11397	-1.0589	10	0.66056	D	0.02	-8.1533	10.5158	0.44889	0.0:0.3744:0.0:0.6256	.	247	Q8IYA7	MKX_HUMAN	H	247	ENSP00000364946:Q247H;ENSP00000400896:Q247H	ENSP00000364946:Q247H	Q	-	3	2	MKX	28063488	1.000000	0.71417	0.984000	0.44739	0.981000	0.71138	1.114000	0.31196	0.168000	0.19655	0.529000	0.55759	CAA	.	.		0.438	MKX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047332.3	NM_173576		A	28023482	T	A	28023482	3	1	245	1	0	0	0	0	1	0	0	0	9619	1838	64	4	329	4	MKX	10	28023482	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	15896807	28023482	107511265	140	33610										
EPC1	80314	hgsc.bcm.edu	37	chr10	32560684	32560684	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	cccaatcagaacctgagttgTtgcagaattggcagcagtta	10	9	1	3			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr10:32560684T>A	ENST00000263062.8	-	14	2505	c.2236A>T	c.(2236-2238)Aca>Tca	p.T746S	RP11-166N17.1_ENST00000415731.2_RNA|EPC1_ENST00000319778.6_Missense_Mutation_p.T723S|EPC1_ENST00000375110.2_Missense_Mutation_p.T673S	NM_025209.2	NP_079485.1	Q9H2F5	EPC1_HUMAN	enhancer of polycomb homolog 1 (Drosophila)	746					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(5)|urinary_tract(1)	24		Prostate(175;0.0199)				ACCTGAGTTGTTGCAGAATTG	0.423																																					p.T746S		Atlas-SNP	.											.	EPC1	74	.	0			c.A2236T						.						206	193	197					10																	32560684		2203	4300	6503	SO:0001583	missense	80314	exon14			GAGTTGTTGCAGA	AF277374	CCDS7172.1, CCDS60511.1, CCDS73083.1	10p11	2005-12-12			ENSG00000120616	ENSG00000120616			19876	protein-coding gene	gene with protein product		610999				10976108	Standard	NM_025209		Approved	Epl1	uc001iwg.2	Q9H2F5	OTTHUMG00000017925	ENST00000263062.8:c.2236A>T	chr10.hg19:g.32560684T>A	ENSP00000263062:p.Thr746Ser	147.0	0.0		139.0	71.0	NM_025209	B4DSC3|D3DRX7|Q5VW54|Q5VW56|Q5VW58|Q8NAQ4|Q8NE21|Q96LF4|Q96RR6|Q9H7T7	Missense_Mutation	SNP	ENST00000263062.8	hg19	CCDS7172.1	.	.	.	.	.	.	.	.	.	.	T	5.504	0.277946	0.10403	.	.	ENSG00000120616	ENST00000375110;ENST00000319778;ENST00000263062	.	.	.	5.37	4.23	0.50019	.	0.093976	0.64402	D	0.000001	T	0.33440	0.0863	N	0.19112	0.55	0.36500	D	0.868942	B;B;B	0.24721	0.11;0.046;0.002	B;B;B	0.24006	0.05;0.02;0.015	T	0.22173	-1.0224	9	0.06891	T	0.86	-4.7732	12.5282	0.56098	0.0:0.0:0.1396:0.8604	.	673;723;746	Q9H2F5-3;Q9H2F5-2;Q9H2F5	.;.;EPC1_HUMAN	S	673;723;746	.	ENSP00000263062:T746S	T	-	1	0	EPC1	32600690	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.484000	0.60271	0.859000	0.35456	0.378000	0.23410	ACA	.	.		0.423	EPC1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047484.1			A	32560684	T	A	32560684	3	1	245	1	0	0	0	0	1	0	0	0	5162	1725	60	4	282	4	EPC1	10	32560684	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	4537202	32560684	102974063	141	33611										
FRMPD2	143162	hgsc.bcm.edu	37	chr10	49392912	49392912	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ggcctgaatactctccctcaTtaatgacaaaccctgtaatc	5	13	2	2	rs529008159		TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr10:49392912T>A	ENST00000374201.3	-	19	2674	c.2372A>T	c.(2371-2373)aAt>aTt	p.N791I	FRMPD2_ENST00000305531.3_Missense_Mutation_p.N766I|FRMPD2_ENST00000407470.4_Missense_Mutation_p.N759I	NM_001018071.3|NM_001042512.2	NP_001018081|NP_001035977.2	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2	791	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				tight junction assembly (GO:0070830)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)	1-phosphatidylinositol binding (GO:0005545)			NS(2)|autonomic_ganglia(2)|breast(5)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(15)|lung(24)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	66				Kidney(211;0.201)		CTCTCCCTCATTAATGACAAA	0.393																																					p.N791I		Atlas-SNP	.											.	FRMPD2	157	.	0			c.A2372T						.						77	72	74					10																	49392912		2203	4300	6503	SO:0001583	missense	143162	exon19			CCCTCATTAATGA	AK123038	CCDS31195.1	10q11	2010-10-13			ENSG00000170324	ENSG00000170324			28572	protein-coding gene	gene with protein product		613323	"PDZ domain containing 5C"	PDZD5C, PDZK5C			Standard	NM_001018071		Approved	MGC35285	uc001jdv.3	Q68DX3	OTTHUMG00000018171	ENST00000374201.3:c.2372A>T	chr10.hg19:g.49392912T>A	ENSP00000363317:p.Asn791Ile	86.0	0.0		78.0	28.0	NM_001018071	B7WNW0|B7ZML5|Q2VY07|Q6GMQ9|Q6ZN38|Q6ZWI2|Q8N5T9	Missense_Mutation	SNP	ENST00000374201.3	hg19	CCDS31195.1	.	.	.	.	.	.	.	.	.	.	T	6.881	0.531961	0.13127	.	.	ENSG00000170324	ENST00000374201;ENST00000305531;ENST00000407470	T;T;T	0.27402	1.67;1.67;1.67	5.15	1.42	0.22433	PDZ/DHR/GLGF (4);	.	.	.	.	T	0.07593	0.0191	N	0.00670	-1.27	0.25495	N	0.987608	B;B;B	0.22800	0.019;0.075;0.019	B;B;B	0.18263	0.013;0.021;0.013	T	0.23619	-1.0183	9	0.33940	T	0.23	.	1.1533	0.01790	0.2456:0.0984:0.1509:0.5052	.	766;791;759	Q68DX3-2;Q68DX3;F8WCT2	.;FRPD2_HUMAN;.	I	791;766;759	ENSP00000363317:N791I;ENSP00000307079:N766I;ENSP00000384339:N759I	ENSP00000307079:N766I	N	-	2	0	FRMPD2	49062918	1.000000	0.71417	0.954000	0.39281	0.943000	0.58893	2.627000	0.46469	0.923000	0.37045	0.482000	0.46254	AAT	.	.		0.393	FRMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047923.3	NM_152428		A	49392912	T	A	49392912	3	1	245	1	0	0	0	0	1	0	0	0	6066	1493	52	4	1601	4	FRMPD2	10	49392912	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	16832228	49392912	86141835	142	33612										
C10orf72	196740	hgsc.bcm.edu	37	chr10	50256624	50256624	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tcacgctagtgacagtctccCctgagctgtagaagaaaaag	10	10	2	4			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr10:50256624C>A	ENST00000332853.4	-	6	697	c.674G>T	c.(673-675)gGg>gTg	p.G225V		NM_001031746.3	NP_001026916.2	Q8IW00	VSTM4_HUMAN	V-set and transmembrane domain containing 4	225						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(14)|skin(2)	31						GACAGTCTCCCCTGAGCTGTA	0.478																																					p.G225V		Atlas-SNP	.											.	VSTM4	83	.	0			c.G674T						.						62	56	58					10																	50256624		2203	4300	6503	SO:0001583	missense	196740	exon6			GTCTCCCCTGAGC	BC041414	CCDS7228.1, CCDS31198.1	10q11.23	2013-01-11	2011-07-01	2011-07-01	ENSG00000165633	ENSG00000165633		"Immunoglobulin superfamily / V-set domain containing"	26470	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 72"	C10orf72			Standard	XR_246075		Approved	FLJ31737	uc001jhf.2	Q8IW00	OTTHUMG00000018184	ENST00000332853.4:c.674G>T	chr10.hg19:g.50256624C>A	ENSP00000331062:p.Gly225Val	72.0	0.0		79.0	12.0	NM_001031746	B4DNI6|Q96MX7	Missense_Mutation	SNP	ENST00000332853.4	hg19	CCDS31198.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.059076	0.76074	.	.	ENSG00000165633	ENST00000332853	T	0.13778	2.56	6.06	6.06	0.98353	.	0.053530	0.85682	D	0.000000	T	0.24160	0.0585	L	0.34521	1.04	0.80722	D	1	D	0.63880	0.993	P	0.58660	0.843	T	0.00086	-1.2094	10	0.66056	D	0.02	-40.5081	16.1283	0.81408	0.0:1.0:0.0:0.0	.	225	Q8IW00	VSTM4_HUMAN	V	225	ENSP00000331062:G225V	ENSP00000331062:G225V	G	-	2	0	VSTM4	49926630	1.000000	0.71417	0.996000	0.52242	0.976000	0.68499	4.436000	0.59948	2.871000	0.98454	0.655000	0.94253	GGG	.	.		0.478	VSTM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047966.2	NM_144984		A	50256624	C	A	50256624	3	1	245	1	0	0	0	0	1	0	0	0	1617	623	22	3	300	3	C10orf72	10	50256624	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	863712	50256624	85278123	143	33613										
CLRN3	119467	hgsc.bcm.edu	37	chr10	129681969	129681969	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gggccactcaccaccgagccCgttccaggtgtacacccccg	10	19	1	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr10:129681969C>A	ENST00000368671.3	-	2	562	c.400G>T	c.(400-402)Ggg>Tgg	p.G134W		NM_152311.3	NP_689524.1	Q8NCR9	CLRN3_HUMAN	clarin 3	134						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				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)				CCACCGAGCCCGTTCCAGGTG	0.562																																					p.G134W		Atlas-SNP	.											.	CLRN3	27	.	0			c.G400T						.						71	69	70					10																	129681969		2203	4300	6503	SO:0001583	missense	119467	exon2			CGAGCCCGTTCCA	BC029478	CCDS7656.1	10q26.2	2006-11-24	2006-11-23	2006-11-23	ENSG00000180745	ENSG00000180745			20795	protein-coding gene	gene with protein product			"transmembrane protein 12"	TMEM12		12145752, 12080385	Standard	NM_152311		Approved	MGC32871, USH3AL1	uc001lka.1	Q8NCR9	OTTHUMG00000019253	ENST00000368671.3:c.400G>T	chr10.hg19:g.129681969C>A	ENSP00000357660:p.Gly134Trp	120.0	0.0		89.0	43.0	NM_152311	Q6MZX8	Missense_Mutation	SNP	ENST00000368671.3	hg19	CCDS7656.1	.	.	.	.	.	.	.	.	.	.	C	16.93	3.258323	0.59321	.	.	ENSG00000180745	ENST00000368671	T	0.77229	-1.08	5.21	5.21	0.72293	.	0.229367	0.37261	N	0.002172	D	0.84575	0.5502	L	0.60455	1.87	0.24579	N	0.993883	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.77117	-0.2706	10	0.59425	D	0.04	-7.3572	11.5595	0.50768	0.2262:0.7738:0.0:0.0	.	134;66	Q8NCR9;Q8NCR9-2	CLRN3_HUMAN;.	W	134	ENSP00000357660:G134W	ENSP00000357660:G134W	G	-	1	0	CLRN3	129571959	0.703000	0.27826	0.286000	0.24833	0.979000	0.70002	3.070000	0.50033	2.426000	0.82243	0.655000	0.94253	GGG	.	.		0.562	CLRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050987.1	NM_152311		A	129681969	C	A	129681969	3	1	245	1	0	0	0	0	1	0	0	0	3561	652	23	1	288	1	CLRN3	10	129681969	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	79425345	129681969	5852778	144	33614										
GPR123	84435	hgsc.bcm.edu	37	chr10	134942775	134942775	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ggcgaccccttccccatggtCacccagcccgagggcagtga	12	17	1	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr10:134942775C>T	ENST00000392607.3	+	7	1879	c.1443C>T	c.(1441-1443)gtC>gtT	p.V481V	GPR123_ENST00000392606.2_Silent_p.V384V|GPR123_ENST00000607359.1_Silent_p.V1200V	NM_001083909.1	NP_001077378.1	Q86SQ6	GP123_HUMAN	G protein-coupled receptor 123	481					G-protein coupled receptor signaling pathway (GO:0007186)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(3)	14		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)		TCCCCATGGTCACCCAGCCCG	0.731																																					p.V481V		Atlas-SNP	.											.	GPR123	118	.	0			c.C1443T						.						9	10	10					10																	134942775		2049	4009	6058	SO:0001819	synonymous_variant	84435	exon7			CATGGTCACCCAG	AB058731	CCDS41580.1	10q26	2014-08-08			ENSG00000197177	ENSG00000197177		"-", "GPCR / Class B : Orphans"	13838	protein-coding gene	gene with protein product		612302				12565841	Standard	XM_005252695		Approved	KIAA1828	uc001llw.3	Q86SQ6	OTTHUMG00000019304	ENST00000392607.3:c.1443C>T	chr10.hg19:g.134942775C>T		58.0	0.0		49.0	22.0	NM_001083909	A5HL16|A6NG50|Q5T234|Q86SN7|Q96JJ9	Silent	SNP	ENST00000392607.3	hg19	CCDS41580.1																																																																																			.	.		0.731	GPR123-003	NOVEL	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051113.2			T	134942775	C	T	134942775	2	4	245	1	0	0	0	0	0	0	0	1	6645	813	29	3		3	GPR123	10	134942775	Silent	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	5260806	134942775	591972	145	33615										
HBE1	3046	hgsc.bcm.edu	37	chr11	5291051	5291051	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gcccaaggcttcacctccagCctcttccacattcatcttgc	5	18	4	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr11:5291051C>A	ENST00000380237.1	-	3	414	c.70G>T	c.(70-72)Gct>Tct	p.A24S	HBG2_ENST00000380259.2_Intron|HBE1_ENST00000292896.2_Missense_Mutation_p.A24S|HBG2_ENST00000380252.1_Intron			P02100	HBE_HUMAN	hemoglobin, epsilon 1	24					blood coagulation (GO:0007596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein heterooligomerization (GO:0051291)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|hemoglobin complex (GO:0005833)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|oxygen transporter activity (GO:0005344)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|skin(1)	20		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.34e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCACCTCCAGCCTCTTCCACA	0.493																																					p.A24S		Atlas-SNP	.											.	HBE1	42	.	0			c.G70T						.						116	104	108					11																	5291051		2201	4297	6498	SO:0001583	missense	3046	exon1			CTCCAGCCTCTTC	BC015537	CCDS7756.1	11p15.5	2012-10-02			ENSG00000213931	ENSG00000213931			4830	protein-coding gene	gene with protein product		142100				2649166	Standard	NM_005330		Approved	HBE	uc001mal.1	P02100	OTTHUMG00000066675	ENST00000380237.1:c.70G>T	chr11.hg19:g.5291051C>A	ENSP00000369586:p.Ala24Ser	91.0	0.0		61.0	11.0	NM_005330	Q6FH44	Missense_Mutation	SNP	ENST00000380237.1	hg19	CCDS7756.1	.	.	.	.	.	.	.	.	.	.	C	12.90	2.076211	0.36662	.	.	ENSG00000213931	ENST00000380237;ENST00000292896;ENST00000396895	D;D;D	0.89123	-2.47;-2.47;-2.47	5.81	-4.13	0.03904	Globin-like (1);Globin, structural domain (1);	1.765680	0.03665	U	0.243169	D	0.86707	0.5997	L	0.43152	1.355	0.09310	N	1	B	0.23806	0.091	B	0.39771	0.309	T	0.76375	-0.2982	10	0.87932	D	0	-1.4852	5.0442	0.14475	0.0894:0.3965:0.0888:0.4253	.	24	P02100	HBE_HUMAN	S	24	ENSP00000369586:A24S;ENSP00000292896:A24S;ENSP00000380104:A24S	ENSP00000292896:A24S	A	-	1	0	HBE1	5247627	0.000000	0.05858	0.879000	0.34478	0.384000	0.30261	-0.113000	0.10774	-0.591000	0.05859	-1.128000	0.01989	GCT	.	.		0.493	HBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142973.2	NM_005330		A	5291051	C	A	5291051	3	1	245	1	0	0	0	0	1	0	0	0	6989	739	26	3	385	3	HBE1	11	5291051	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10		5291051	129715465	146	33616										
SWAP70	23075	hgsc.bcm.edu	37	chr11	9750888	9750888	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ctaattttgctttctgttttAgtccttgcctgacaaagatg	7	8	1	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr11:9750888A>T	ENST00000318950.6	+	6	892		c.e6-1		SWAP70_ENST00000447399.2_Splice_Site	NM_015055.2	NP_055870.2	Q9UH65	SWP70_HUMAN	SWAP switching B-cell complex 70kDa subunit						isotype switching (GO:0045190)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|DNA binding (GO:0003677)			NS(1)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(2)|pancreas(1)	11				all cancers(16;1.21e-10)|Epithelial(150;2.81e-09)|BRCA - Breast invasive adenocarcinoma(625;0.00649)		TTTCTGTTTTAGTCCTTGCCT	0.279																																					.		Atlas-SNP	.											.	SWAP70	40	.	0			c.790-2A>T						.						62	67	65					11																	9750888		2201	4294	6495	SO:0001630	splice_region_variant	23075	exon6			TGTTTTAGTCCTT	AB014540	CCDS31426.1, CCDS73257.1	11p15	2013-01-10			ENSG00000133789	ENSG00000133789		"Pleckstrin homology (PH) domain containing", "EF-hand domain containing"	17070	protein-coding gene	gene with protein product		604762				9734811, 10681448	Standard	XM_005252829		Approved	KIAA0640, SWAP-70	uc001mhw.3	Q9UH65	OTTHUMG00000165865	ENST00000318950.6:c.790-1A>T	chr11.hg19:g.9750888A>T		145.0	0.0		115.0	36.0	NM_015055	D3DQV1|O75135|Q7LCY6|Q9P061|Q9P0Z8	Splice_Site	SNP	ENST00000318950.6	hg19	CCDS31426.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.211506	0.79240	.	.	ENSG00000133789	ENST00000447399;ENST00000318950;ENST00000534662	.	.	.	5.52	5.52	0.82312	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.6436	0.77029	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SWAP70	9707464	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	8.962000	0.93254	2.100000	0.63781	0.533000	0.62120	.	.	.		0.279	SWAP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386766.2	NM_015055	Intron	T	9750888	A	T	9750888	5	4	245	1	0	0	0	0	0	0	1	0	15440	434	15	4	810	4	SWAP70	11	9750888	Splice_Site	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	4459837	9750888	125255628	147	33617										
SBF2	81846	hgsc.bcm.edu	37	chr11	9853870	9853870	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	accacttcttgagttcttccAacatacaacaggcaggcgat	7	12	2	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr11:9853870A>G	ENST00000256190.8	-	27	3690	c.3553T>C	c.(3553-3555)Tgg>Cgg	p.W1185R		NM_030962.3	NP_112224.1	Q86WG5	MTMRD_HUMAN	SET binding factor 2	1185	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				cell death (GO:0008219)|myelination (GO:0042552)|positive regulation of Rab GTPase activity (GO:0032851)|protein tetramerization (GO:0051262)	membrane (GO:0016020)|vacuolar membrane (GO:0005774)	phosphatase activity (GO:0016791)|phosphatase regulator activity (GO:0019208)|phosphatidylinositol binding (GO:0035091)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(4)|endometrium(8)|kidney(2)|large_intestine(8)|lung(16)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)		GAGTTCTTCCAACATACAACA	0.502																																					p.W1185R		Atlas-SNP	.											.	SBF2	146	.	0			c.T3553C						.						122	108	113					11																	9853870		2201	4294	6495	SO:0001583	missense	81846	exon27			TCTTCCAACATAC	AB051553	CCDS31427.1	11p15.3	2014-09-17	2004-11-12	2004-11-12	ENSG00000133812	ENSG00000133812		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins", "DENN/MADD domain containing", "Pleckstrin homology (PH) domain containing"	2135	protein-coding gene	gene with protein product	"myotubularin related 13"	607697	"Charcot-Marie-Tooth neuropathy 4B2 (autosomal recessive, with myelin outfolding)", "DENN/MADD domain containing 7B"	CMT4B2		10644431	Standard	NM_030962		Approved	KIAA1766, MTMR13, DENND7B	uc001mib.2	Q86WG5	OTTHUMG00000165890	ENST00000256190.8:c.3553T>C	chr11.hg19:g.9853870A>G	ENSP00000256190:p.Trp1185Arg	120.0	0.0		98.0	24.0	NM_030962	Q3MJF0|Q68DQ3|Q6P459|Q6PJD1|Q7Z325|Q7Z621|Q86VE2|Q96FE2|Q9C097	Missense_Mutation	SNP	ENST00000256190.8	hg19	CCDS31427.1	.	.	.	.	.	.	.	.	.	.	A	27.6	4.847013	0.91277	.	.	ENSG00000133812	ENST00000256190	D	0.93189	-3.18	5.53	5.53	0.82687	Myotubularin phosphatase domain (1);Myotubularin-related (1);	0.000000	0.85682	D	0.000000	D	0.97620	0.9220	H	0.94925	3.6	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	D	0.98786	1.0734	10	0.87932	D	0	.	15.9464	0.79796	1.0:0.0:0.0:0.0	.	1185	Q86WG5	MTMRD_HUMAN	R	1185	ENSP00000256190:W1185R	ENSP00000256190:W1185R	W	-	1	0	SBF2	9810446	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.272000	0.95707	2.232000	0.73038	0.402000	0.26972	TGG	.	.		0.502	SBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386911.2	NM_030962		G	9853870	A	G	9853870	3	3	245	1	0	0	0	0	1	0	0	0	13874	130	5	2	2052	2	SBF2	11	9853870	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	102982	9853870	125152646	148	33618										
CD44	960	hgsc.bcm.edu	37	chr11	35236397	35236397	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ccttcctgattgctcattacAggagaccaagacacattcca	6	13	1	3	rs200427375		TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr11:35236397A>T	ENST00000428726.2	+	15	1933		c.e15-1		CD44_ENST00000360158.4_Splice_Site|CD44_ENST00000526669.2_Intron|CD44_ENST00000263398.6_Splice_Site|CD44_ENST00000278386.6_Intron|CD44_ENST00000352818.4_Intron|CD44_ENST00000434472.2_Splice_Site|RP1-68D18.2_ENST00000510619.2_RNA|CD44_ENST00000449691.2_Splice_Site|RP1-68D18.4_ENST00000528869.1_RNA|CD44_ENST00000433892.2_Splice_Site|CD44_ENST00000415148.2_Splice_Site|CD44_ENST00000437706.2_Splice_Site|CD44_ENST00000433354.2_Splice_Site	NM_000610.3	NP_000601.3	P16070	CD44_HUMAN	CD44 molecule (Indian blood group)						blood coagulation (GO:0007596)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in ureteric bud morphogenesis (GO:0001658)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cell-matrix adhesion (GO:0007160)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|monocyte aggregation (GO:0070487)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of monocyte aggregation (GO:1900625)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|Wnt signaling pathway (GO:0016055)|wound healing involved in inflammatory response (GO:0002246)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|pancreas(1)|skin(1)	23	all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.00731)		Hyaluronan(DB08818)	TGCTCATTACAGGAGACCAAG	0.418																																					.		Atlas-SNP	.											.	CD44	48	.	0			c.1811-2A>T						.						108	96	100					11																	35236397		2202	4298	6500	SO:0001630	splice_region_variant	960	exon15			CATTACAGGAGAC	M59040	CCDS7897.1, CCDS31455.1, CCDS31456.1, CCDS31457.1, CCDS31458.1, CCDS55754.1, CCDS55755.1	11p13	2014-07-18	2006-03-28		ENSG00000026508	ENSG00000026508		"CD molecules", "Blood group antigens", "Proteoglycans / Cell surface : Other"	1681	protein-coding gene	gene with protein product	"hematopoietic cell E- and L-selectin ligand", "chondroitin sulfate proteoglycan 8"	107269	"CD44 antigen (homing function and Indian blood group system)"	MIC4, MDU2, MDU3		2454887	Standard	NM_001202555		Approved	IN, MC56, Pgp1, CD44R, HCELL, CSPG8	uc001mvu.3	P16070	OTTHUMG00000044388	ENST00000428726.2:c.1811-1A>T	chr11.hg19:g.35236397A>T		92.0	0.0		57.0	36.0	NM_000610	A5YRN9|B6EAT9|D3DR12|D3DR13|O95370|P22511|Q04858|Q13419|Q13957|Q13958|Q13959|Q13960|Q13961|Q13967|Q13968|Q13980|Q15861|Q16064|Q16065|Q16066|Q16208|Q16522|Q86T72|Q86Z27|Q8N694|Q92493|Q96J24|Q9H5A5|Q9UC28|Q9UC29|Q9UC30|Q9UCB0|Q9UJ36	Splice_Site	SNP	ENST00000428726.2	hg19	CCDS7897.1	.	.	.	.	.	.	.	.	.	.	A	13.33	2.205698	0.39003	.	.	ENSG00000026508	ENST00000263398;ENST00000415148;ENST00000433354;ENST00000449691;ENST00000437706;ENST00000360158;ENST00000428726;ENST00000433892;ENST00000434472;ENST00000442151;ENST00000526000;ENST00000279452;ENST00000525688;ENST00000278385	.	.	.	4.46	4.46	0.54185	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.4259	0.44378	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CD44	35192973	0.997000	0.39634	0.963000	0.40424	0.123000	0.20343	3.508000	0.53378	2.228000	0.72767	0.533000	0.62120	.	.	.		0.418	CD44-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388927.1	NM_000610	Intron	T	35236397	A	T	35236397	5	4	245	1	0	0	0	0	0	0	1	0	3019	202	7	4	1867	4	CD44	11	35236397	Splice_Site	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	25382527	35236397	99770119	149	33619										
OR8H2	390151	hgsc.bcm.edu	37	chr11	55873254	55873254	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ctacttgcgtctctcatctcTtgggagtcaccatcttttat	6	12	5	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr11:55873254T>G	ENST00000313503.1	+	1	736	c.736T>G	c.(736-738)Ttg>Gtg	p.L246V		NM_001005200.1	NP_001005200.1	Q8N162	OR8H2_HUMAN	olfactory receptor, family 8, subfamily H, member 2	246						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(38)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	61	Esophageal squamous(21;0.00693)					CTCTCATCTCTTGGGAGTCAC	0.363										HNSCC(53;0.14)																											p.L246V		Atlas-SNP	.											.	OR8H2	117	.	0			c.T736G						.						97	96	97					11																	55873254		2201	4296	6497	SO:0001583	missense	390151	exon1			CATCTCTTGGGAG	AB065657	CCDS31518.1	11q11	2012-08-09			ENSG00000181767	ENSG00000181767		"GPCR / Class A : Olfactory receptors"	15308	protein-coding gene	gene with protein product							Standard	NM_001005200		Approved		uc010riy.2	Q8N162	OTTHUMG00000166832	ENST00000313503.1:c.736T>G	chr11.hg19:g.55873254T>G	ENSP00000323982:p.Leu246Val	113.0	0.0		85.0	24.0	NM_001005200	Q6IFC1	Missense_Mutation	SNP	ENST00000313503.1	hg19	CCDS31518.1	.	.	.	.	.	.	.	.	.	.	t	3.019	-0.202212	0.06219	.	.	ENSG00000181767	ENST00000313503	T	0.38077	1.16	3.58	0.192	0.15134	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41605	D	0.000848	T	0.24967	0.0606	N	0.20401	0.57	0.09310	N	1	P	0.35944	0.529	P	0.48524	0.58	T	0.09185	-1.0686	10	0.30078	T	0.28	.	0.6683	0.00854	0.3831:0.2695:0.126:0.2214	.	246	Q8N162	OR8H2_HUMAN	V	246	ENSP00000323982:L246V	ENSP00000323982:L246V	L	+	1	2	OR8H2	55629830	0.000000	0.05858	0.045000	0.18777	0.207000	0.24258	-1.518000	0.02246	0.271000	0.22005	-0.503000	0.04515	TTG	.	.		0.363	OR8H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391540.1	NM_001005200		G	55873254	T	G	55873254	3	3	245	1	0	0	0	0	1	0	0	0	11247	1606	56	5	738	5	OR8H2	11	55873254	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	20636857	55873254	79133262	150	33620										
OR8H1	219469	hgsc.bcm.edu	37	chr11	56058142	56058142	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	cagccttttggacataataaCtgggtaacgtagaggactgc	11	8	0	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr11:56058142C>T	ENST00000313022.2	-	1	424	c.397G>A	c.(397-399)Gtt>Att	p.V133I		NM_001005199.1	NP_001005199.1	Q8NGG4	OR8H1_HUMAN	olfactory receptor, family 8, subfamily H, member 1	133						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Esophageal squamous(21;0.00448)					GACATAATAACTGGGTAACGT	0.443																																					p.V133I		Atlas-SNP	.											.	OR8H1	89	.	0			c.G397A						.						102	98	100					11																	56058142		2201	4296	6497	SO:0001583	missense	219469	exon1			TAATAACTGGGTA	AB065836	CCDS31526.1	11q11	2012-08-09			ENSG00000181693	ENSG00000181693		"GPCR / Class A : Olfactory receptors"	14824	protein-coding gene	gene with protein product							Standard	NM_001005199		Approved		uc010rje.2	Q8NGG4	OTTHUMG00000162671	ENST00000313022.2:c.397G>A	chr11.hg19:g.56058142C>T	ENSP00000323595:p.Val133Ile	124.0	0.0		86.0	21.0	NM_001005199	B2RNI7|Q6IFC5	Missense_Mutation	SNP	ENST00000313022.2	hg19	CCDS31526.1	.	.	.	.	.	.	.	.	.	.	C	9.831	1.188492	0.21954	.	.	ENSG00000181693	ENST00000313022;ENST00000395186	T	0.01335	5.0	3.94	0.528	0.17089	GPCR, rhodopsin-like superfamily (1);	0.620606	0.14356	N	0.324791	T	0.01124	0.0037	L	0.31845	0.965	0.09310	N	1	B	0.15141	0.012	B	0.17433	0.018	T	0.48692	-0.9013	10	0.35671	T	0.21	.	0.2847	0.00249	0.3323:0.2689:0.1627:0.2361	.	133	Q8NGG4	OR8H1_HUMAN	I	133;129	ENSP00000323595:V133I	ENSP00000323595:V133I	V	-	1	0	OR8H1	55814718	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-1.991000	0.01478	0.367000	0.24454	0.544000	0.68410	GTT	.	.		0.443	OR8H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370019.1	NM_001005199		T	56058142	C	T	56058142	3	4	245	1	0	0	0	0	1	0	0	0	11246	565	20	3	540	3	OR8H1	11	56058142	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	184888	56058142	78948374	151	33621										
CLP1	10978	hgsc.bcm.edu	37	chr11	57427466	57427466	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ctacatcgagcggcctgcagAtgtcgaagagggtttctcta	12	10	1	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr11:57427466A>T	ENST00000533682.1	+	2	1243	c.518A>T	c.(517-519)gAt>gTt	p.D173V	CLP1_ENST00000302731.4_Intron|CLP1_ENST00000525602.1_Missense_Mutation_p.D173V|CLP1_ENST00000529430.1_Missense_Mutation_p.D184V			Q5KU26	COL12_HUMAN	cleavage and polyadenylation factor I subunit 1	0					carbohydrate mediated signaling (GO:0009756)|defense response (GO:0006952)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)|phagocytosis, recognition (GO:0006910)|protein homooligomerization (GO:0051260)|receptor-mediated endocytosis (GO:0006898)	collagen trimer (GO:0005581)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galactose binding (GO:0005534)|low-density lipoprotein particle binding (GO:0030169)|metal ion binding (GO:0046872)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|stomach(1)	15						CGGCCTGCAGATGTCGAAGAG	0.552																																					p.D173V		Atlas-SNP	.											.	CLP1	40	.	0			c.A518T						.						48	42	44					11																	57427466		2201	4296	6497	SO:0001583	missense	10978	exon2			CTGCAGATGTCGA	BC000446	CCDS7964.1, CCDS44600.1	11q12.1	2012-10-02	2012-10-02		ENSG00000172409	ENSG00000172409	2.7.1.78		16999	protein-coding gene	gene with protein product	"ATP/GTPbinding protein", "polyribonucleotide 5'-hydroxyl-kinase"	608757	"CLP1, cleavage and polyadenylation factor I subunit, homolog (S. cerevisiae)"			8896421, 11060040	Standard	NM_006831		Approved	HEAB, hClp1	uc001nkw.3	Q92989	OTTHUMG00000167146	ENST00000533682.1:c.518A>T	chr11.hg19:g.57427466A>T	ENSP00000434995:p.Asp173Val	87.0	0.0		56.0	30.0	NM_006831	Q6P9F2|Q8TCR2|Q8WZA4|Q9BY85|Q9BYH7	Missense_Mutation	SNP	ENST00000533682.1	hg19	CCDS7964.1	.	.	.	.	.	.	.	.	.	.	a	25.3	4.620264	0.87460	.	.	ENSG00000172409	ENST00000529430;ENST00000533682;ENST00000525602	T;T;T	0.25912	1.77;1.77;1.77	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.44912	0.1316	L	0.50847	1.595	0.80722	D	1	D	0.63046	0.992	D	0.71184	0.972	T	0.21280	-1.0250	10	0.40728	T	0.16	-9.864	15.6143	0.76753	1.0:0.0:0.0:0.0	.	173	Q92989	CLP1_HUMAN	V	184;173;173	ENSP00000433406:D184V;ENSP00000434995:D173V;ENSP00000436066:D173V	ENSP00000436066:D173V	D	+	2	0	CLP1	57184042	1.000000	0.71417	0.779000	0.31741	0.789000	0.44602	9.212000	0.95126	2.169000	0.68431	0.468000	0.43344	GAT	.	.		0.552	CLP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393462.3	NM_006831		T	57427466	A	T	57427466	3	4	245	1	0	0	0	0	1	0	0	0	3552	333	12	4	520	4	CLP1	11	57427466	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	1369324	57427466	77579050	152	33622										
TMX2	51075	hgsc.bcm.edu	37	chr11	57505430	57505441	+	In_Frame_Del	DEL	TGGCCAACACAA	TGGCCAACACAA	-													0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	cattttcatgtttagtaaagTggccaacacaattcttttct							TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	TGGCCAACACAA	TGGCCAACACAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr11:57505430_57505441delTGGCCAACACAA	ENST00000278422.4	+	3	308_319	c.296_307delTGGCCAACACAA	c.(295-309)gtggccaacacaatt>gtt	p.ANTI100del	TMX2-CTNND1_ENST00000528395.1_Intron|TMX2_ENST00000378312.4_Intron	NM_015959.3	NP_057043.1	Q9Y320	TMX2_HUMAN	thioredoxin-related transmembrane protein 2	100					cell redox homeostasis (GO:0045454)	integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|urinary_tract(2)	12						TTTAGTAAAGTGGCCAACACAATTCTTTTCTT	0.42																																					p.99_102del		Atlas-Indel,Pindel	.											.	TMX2	29	.	0			c.295_306del						.																																			SO:0001651	inframe_deletion	51075	exon3			.	AF132965	CCDS7967.1, CCDS44601.1	11q12.1	2012-09-20	2009-02-23	2009-02-23	ENSG00000213593	ENSG00000213593		"Protein disulfide isomerases"	30739	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 12"		"thioredoxin domain containing 14"	TXNDC14		12670024	Standard	NM_015959		Approved	PDIA12	uc001nlc.2	Q9Y320	OTTHUMG00000167200	ENST00000278422.4:c.296_307delTGGCCAACACAA	chr11.hg19:g.57505430_57505441delTGGCCAACACAA	ENSP00000278422:p.Ala100_Ile103del	160.0	0.0		82.0	22.0	NM_015959	B7Z4R4|Q53G73|Q561W0|Q5J7Q7|Q8NBP9|Q9H3L1	In_Frame_Del	DEL	ENST00000278422.4	hg19	CCDS7967.1																																																																																			.	.		0.42	TMX2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393708.1	NM_015959		-	57505441	TGGCCAACACAA	-	57505430	7	5	245	1	0	1	0	1	0	0	0	0	16282	1696	59	0	306	0	TMX2	11	57505430	In_Frame_Del	DEL	TGGCCAACACAA	TCGA-ED-A7PZ-01A-11D-A33Q-10	77964	57505430	77501086	153	33623										
SLC22A9	114571	hgsc.bcm.edu	37	chr11	63176219	63176219	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ggctcccctcatgatgatccTaagtgtgtattctccacccc	7	15	2	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr11:63176219T>C	ENST00000279178.3	+	9	1718	c.1469T>C	c.(1468-1470)cTa>cCa	p.L490P	SLC22A9_ENST00000310969.4_3'UTR	NM_080866.2	NP_543142.2	Q8IVM8	S22A9_HUMAN	solute carrier family 22 (organic anion transporter), member 9	490					hormone transport (GO:0009914)|short-chain fatty acid import (GO:0015913)|sodium-independent organic anion transport (GO:0043252)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	anion:anion antiporter activity (GO:0015301)|short-chain fatty acid uptake transporter activity (GO:0015636)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)	18						ATGATGATCCTAAGTGTGTAT	0.488																																					p.L490P		Atlas-SNP	.											.	SLC22A9	77	.	0			c.T1469C						.						143	127	132					11																	63176219		2201	4298	6499	SO:0001583	missense	114571	exon9			TGATCCTAAGTGT	AP001880	CCDS8043.1	11q12.3	2014-05-20	2008-01-11		ENSG00000149742	ENSG00000149742		"Solute carriers"	16261	protein-coding gene	gene with protein product		607579				11327718, 17393504	Standard	NM_080866		Approved	OAT4, FLJ23666, UST3, OAT7	uc001nww.3	Q8IVM8	OTTHUMG00000167805	ENST00000279178.3:c.1469T>C	chr11.hg19:g.63176219T>C	ENSP00000279178:p.Leu490Pro	102.0	0.0		87.0	29.0	NM_080866	A0AVB7|A4PB24|Q8TCC8|Q8TEC0|Q8WYN7	Missense_Mutation	SNP	ENST00000279178.3	hg19	CCDS8043.1	.	.	.	.	.	.	.	.	.	.	T	12.71	2.019672	0.35606	.	.	ENSG00000149742	ENST00000279178	T	0.61510	0.1	2.63	2.63	0.31362	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.561525	0.18066	N	0.152763	T	0.81640	0.4865	H	0.97682	4.055	0.26267	N	0.97848	D	0.89917	1.0	D	0.79108	0.992	T	0.72225	-0.4355	10	0.87932	D	0	.	8.7198	0.34434	0.0:0.0:0.0:1.0	.	490	Q8IVM8	S22A9_HUMAN	P	490	ENSP00000279178:L490P	ENSP00000279178:L490P	L	+	2	0	SLC22A9	62932795	0.006000	0.16342	0.006000	0.13384	0.042000	0.13812	1.609000	0.36858	1.224000	0.43551	0.172000	0.16884	CTA	.	.		0.488	SLC22A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396371.1	NM_080866		C	63176219	T	C	63176219	3	2	245	1	0	0	0	0	1	0	0	0	14476	1522	53	2	1503	2	SLC22A9	11	63176219	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	5670789	63176219	71830297	154	33624										
SLC22A9	114571	hgsc.bcm.edu	37	chr11	63177289	63177289	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tctaggagaaaagaccccagAgaaccaaagcaagaggatcc	10	10	1	4			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr11:63177289A>T	ENST00000279178.3	+	10	1866	c.1617A>T	c.(1615-1617)agA>agT	p.R539S	SLC22A9_ENST00000310969.4_3'UTR	NM_080866.2	NP_543142.2	Q8IVM8	S22A9_HUMAN	solute carrier family 22 (organic anion transporter), member 9	539					hormone transport (GO:0009914)|short-chain fatty acid import (GO:0015913)|sodium-independent organic anion transport (GO:0043252)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	anion:anion antiporter activity (GO:0015301)|short-chain fatty acid uptake transporter activity (GO:0015636)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)	18						AAGACCCCAGAGAACCAAAGC	0.418																																					p.R539S		Atlas-SNP	.											.	SLC22A9	77	.	0			c.A1617T						.						68	72	71					11																	63177289		2201	4298	6499	SO:0001583	missense	114571	exon10			CCCCAGAGAACCA	AP001880	CCDS8043.1	11q12.3	2014-05-20	2008-01-11		ENSG00000149742	ENSG00000149742		"Solute carriers"	16261	protein-coding gene	gene with protein product		607579				11327718, 17393504	Standard	NM_080866		Approved	OAT4, FLJ23666, UST3, OAT7	uc001nww.3	Q8IVM8	OTTHUMG00000167805	ENST00000279178.3:c.1617A>T	chr11.hg19:g.63177289A>T	ENSP00000279178:p.Arg539Ser	72.0	0.0		61.0	41.0	NM_080866	A0AVB7|A4PB24|Q8TCC8|Q8TEC0|Q8WYN7	Missense_Mutation	SNP	ENST00000279178.3	hg19	CCDS8043.1	.	.	.	.	.	.	.	.	.	.	A	8.781	0.928174	0.18131	.	.	ENSG00000149742	ENST00000279178	T	0.64618	-0.11	2.9	0.449	0.16619	.	1.787490	0.02935	N	0.139719	T	0.59622	0.2207	M	0.69523	2.12	0.09310	N	1	B	0.29552	0.248	B	0.29598	0.104	T	0.25187	-1.0139	10	0.30078	T	0.28	.	4.7987	0.13284	0.7029:0.0:0.2971:0.0	.	539	Q8IVM8	S22A9_HUMAN	S	539	ENSP00000279178:R539S	ENSP00000279178:R539S	R	+	3	2	SLC22A9	62933865	0.484000	0.25964	0.001000	0.08648	0.003000	0.03518	1.770000	0.38532	-0.024000	0.13941	0.332000	0.21555	AGA	.	.		0.418	SLC22A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396371.1	NM_080866		T	63177289	A	T	63177289	3	4	245	1	0	0	0	0	1	0	0	0	14476	301	11	4	1655	4	SLC22A9	11	63177289	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	1070	63177289	71829227	155	33625										
C11orf84	144097	hgsc.bcm.edu	37	chr11	63585819	63585819	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ggagccggcccaggggactcCgccccctcgagcttcctggt	14	17	0	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr11:63585819C>T	ENST00000294244.4	+	3	888	c.589C>T	c.(589-591)Cgc>Tgc	p.R197C		NM_138471.1	NP_612480.1	Q9BUA3	CK084_HUMAN	chromosome 11 open reading frame 84	197	Pro-rich.									endometrium(3)|kidney(1)|lung(3)|skin(1)	8						CAGGGGACTCCGCCCCCTCGA	0.612																																					p.R197C		Atlas-SNP	.											.	C11orf84	33	.	0			c.C589T						.						42	52	49					11																	63585819		2201	4298	6499	SO:0001583	missense	144097	exon3			GGACTCCGCCCCC	BC007540	CCDS31594.1	11q13.1	2014-02-10			ENSG00000168005	ENSG00000168005			25115	protein-coding gene	gene with protein product						12477932	Standard	NM_138471		Approved		uc001nxt.3	Q9BUA3	OTTHUMG00000167746	ENST00000294244.4:c.589C>T	chr11.hg19:g.63585819C>T	ENSP00000294244:p.Arg197Cys	52.0	0.0		31.0	19.0	NM_138471	Q68CV7|Q6PHS2|Q96IH0	Missense_Mutation	SNP	ENST00000294244.4	hg19	CCDS31594.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.069228	0.76301	.	.	ENSG00000168005	ENST00000294244	T	0.62105	0.05	5.54	5.54	0.83059	.	0.441048	0.25291	N	0.031737	T	0.76054	0.3934	L	0.56769	1.78	0.50467	D	0.999879	D	0.89917	1.0	D	0.87578	0.998	T	0.77611	-0.2523	10	0.87932	D	0	-27.3467	14.987	0.71356	0.0:1.0:0.0:0.0	.	197	Q9BUA3	CK084_HUMAN	C	197	ENSP00000294244:R197C	ENSP00000294244:R197C	R	+	1	0	C11orf84	63342395	0.996000	0.38824	0.993000	0.49108	0.776000	0.43924	3.729000	0.54999	2.610000	0.88304	0.561000	0.74099	CGC	.	.		0.612	C11orf84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396084.1	NM_138471		T	63585819	C	T	63585819	3	4	245	1	0	0	0	0	1	0	0	0	1669	652	23	1	599	1	C11orf84	11	63585819	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	408530	63585819	71420697	156	33626										
FAT3	120114	hgsc.bcm.edu	37	chr11	92534161	92534161	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tcctgacaatggctggatggTcacaaagggtaattttaacc	10	8	1	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr11:92534161T>C	ENST00000298047.6	+	9	7999	c.7982T>C	c.(7981-7983)gTc>gCc	p.V2661A	FAT3_ENST00000409404.2_Missense_Mutation_p.V2661A|FAT3_ENST00000525166.1_Missense_Mutation_p.V2511A			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	2661	Cadherin 24. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				GGCTGGATGGTCACAAAGGGT	0.463										TCGA Ovarian(4;0.039)																											p.V2661A		Atlas-SNP	.											.	FAT3	1822	.	0			c.T7982C						.						36	34	35					11																	92534161		1880	4110	5990	SO:0001583	missense	120114	exon9			GGATGGTCACAAA	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.7982T>C	chr11.hg19:g.92534161T>C	ENSP00000298047:p.Val2661Ala	121.0	0.0		83.0	51.0	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	hg19		.	.	.	.	.	.	.	.	.	.	T	16.85	3.236298	0.58886	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.50001	0.76;0.76;0.76	6.17	6.17	0.99709	.	.	.	.	.	T	0.61739	0.2371	M	0.67569	2.06	0.80722	D	1	D	0.61080	0.989	P	0.58520	0.84	T	0.56938	-0.7896	9	0.18276	T	0.48	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	2661	Q8TDW7-3	.	A	2661;2661;2511	ENSP00000298047:V2661A;ENSP00000387040:V2661A;ENSP00000432586:V2511A	ENSP00000298047:V2661A	V	+	2	0	FAT3	92173809	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.975000	0.88055	2.371000	0.80710	0.533000	0.62120	GTC	.	.		0.463	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		C	92534161	T	C	92534161	3	2	245	1	0	0	0	0	1	0	0	0	5699	1667	58	2	8016	2	FAT3	11	92534161	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	28948342	92534161	42472355	157	33627										
MMP7	4316	hgsc.bcm.edu	37	chr11	102398359	102398359	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ttaaagcctttgacactaatCgatccactgtaatatgcggt	7	9	0	1	rs138303399		TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr11:102398359C>A	ENST00000260227.4	-	3	432	c.380G>T	c.(379-381)cGa>cTa	p.R127L		NM_002423.3	NP_002414.1	P09237	MMP7_HUMAN	matrix metallopeptidase 7 (matrilysin, uterine)	127					antibacterial peptide secretion (GO:0002779)|collagen catabolic process (GO:0030574)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|regulation of cell proliferation (GO:0042127)|response to drug (GO:0042493)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			large_intestine(6)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12	all_cancers(8;2.04e-05)|all_epithelial(12;0.00053)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0105)|all cancers(10;0.0496)|Lung(13;0.109)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0147)	Marimastat(DB00786)	TGACACTAATCGATCCACTGT	0.423																																					p.R127L		Atlas-SNP	.											.	MMP7	27	.	0			c.G380T						.						127	122	124					11																	102398359		2203	4299	6502	SO:0001583	missense	4316	exon3			ACTAATCGATCCA	Z11887	CCDS8317.1	11q21-q22	2008-02-05	2005-08-08		ENSG00000137673	ENSG00000137673	3.4.24.23		7174	protein-coding gene	gene with protein product		178990	"matrix metalloproteinase 7 (matrilysin, uterine)"	MPSL1		8978768	Standard	NM_002423		Approved	PUMP-1	uc001phb.3	P09237	OTTHUMG00000048193	ENST00000260227.4:c.380G>T	chr11.hg19:g.102398359C>A	ENSP00000260227:p.Arg127Leu	93.0	0.0		68.0	20.0	NM_002423	Q9BTK9	Missense_Mutation	SNP	ENST00000260227.4	hg19	CCDS8317.1	.	.	.	.	.	.	.	.	.	.	C	10.37	1.332448	0.24167	.	.	ENSG00000137673	ENST00000260227	T	0.53640	0.61	4.85	-2.09	0.07232	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	1.285220	0.05639	N	0.583068	T	0.34803	0.0910	L	0.48260	1.515	0.09310	N	1	B;B;B	0.29232	0.238;0.097;0.097	B;B;B	0.31946	0.138;0.078;0.054	T	0.22243	-1.0222	10	0.27785	T	0.31	-22.2589	0.1779	0.00120	0.2343:0.1986:0.2399:0.3271	.	127;127;127	B4DDW4;Q53GF1;P09237	.;.;MMP7_HUMAN	L	127	ENSP00000260227:R127L	ENSP00000260227:R127L	R	-	2	0	MMP7	101903569	0.000000	0.05858	0.071000	0.20095	0.325000	0.28411	0.262000	0.18460	-0.318000	0.08665	-0.251000	0.11542	CGA	.	C|1.000;T|0.000		0.423	MMP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109633.2			A	102398359	C	A	102398359	3	1	245	1	0	0	0	0	1	0	0	0	9676	884	31	1	439	1	MMP7	11	102398359	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	9864198	102398359	32608157	158	33628										
GUCY1A2	2977	hgsc.bcm.edu	37	chr11	106810255	106810255	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	aacggggtagacagtcgcagCaggaccctttcaaaggtggc	14	10	1	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr11:106810255C>T	ENST00000526355.2	-	4	1605	c.1137G>A	c.(1135-1137)ctG>ctA	p.L379L	GUCY1A2_ENST00000282249.2_Silent_p.L379L|GUCY1A2_ENST00000347596.2_Silent_p.L379L	NM_000855.2	NP_000846.1	P33402	GCYA2_HUMAN	guanylate cyclase 1, soluble, alpha 2	379					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|positive regulation of cGMP biosynthetic process (GO:0030828)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)			breast(5)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(18)|liver(1)|lung(32)|ovary(1)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	74		all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068)		BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476)	Isosorbide Mononitrate(DB01020)|Nitric Oxide(DB00435)	ACAGTCGCAGCAGGACCCTTT	0.468																																					p.L379L		Atlas-SNP	.											.	GUCY1A2	180	.	0			c.G1137A						.						91	92	92					11																	106810255		2201	4298	6499	SO:0001819	synonymous_variant	2977	exon4			TCGCAGCAGGACC	X63282	CCDS8335.1, CCDS58170.1	11q21-q22	2008-03-18			ENSG00000152402	ENSG00000152402	4.6.1.2		4684	protein-coding gene	gene with protein product		601244		GUC1A2		1683630	Standard	NM_000855		Approved	GC-SA2	uc001pjg.2	P33402	OTTHUMG00000166296	ENST00000526355.2:c.1137G>A	chr11.hg19:g.106810255C>T		189.0	0.0		123.0	35.0	NM_000855	A1L4C4|B7ZLT5	Silent	SNP	ENST00000526355.2	hg19	CCDS8335.1																																																																																			.	.		0.468	GUCY1A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389003.2			T	106810255	C	T	106810255	2	4	245	1	0	0	0	0	0	0	0	1	6902	697	25	3		3	GUCY1A2	11	106810255	Silent	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	4411896	106810255	28196261	159	33629										
DRD2	1813	hgsc.bcm.edu	37	chr11	113281601	113281601	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gtcacagtgtatgttcaggaTgtgtgtgatgaagaagggca	15	4	2	3			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr11:113281601T>C	ENST00000362072.3	-	8	1524	c.1180A>G	c.(1180-1182)Atc>Gtc	p.I394V	DRD2_ENST00000538967.1_Missense_Mutation_p.I396V|DRD2_ENST00000355319.2_Missense_Mutation_p.I396V|DRD2_ENST00000346454.3_Missense_Mutation_p.I365V|DRD2_ENST00000544518.1_Missense_Mutation_p.I393V|DRD2_ENST00000542968.1_Missense_Mutation_p.I394V|RP11-159N11.3_ENST00000546284.1_RNA	NM_000795.3	NP_000786.1	P14416	DRD2_HUMAN	dopamine receptor D2	394	Agonist binding. {ECO:0000250}.				activation of protein kinase activity (GO:0032147)|adenohypophysis development (GO:0021984)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adult walking behavior (GO:0007628)|arachidonic acid secretion (GO:0050482)|associative learning (GO:0008306)|auditory behavior (GO:0031223)|axonogenesis (GO:0007409)|behavioral response to cocaine (GO:0048148)|behavioral response to ethanol (GO:0048149)|branching morphogenesis of a nerve (GO:0048755)|cellular calcium ion homeostasis (GO:0006874)|cerebral cortex GABAergic interneuron migration (GO:0021853)|circadian regulation of gene expression (GO:0032922)|dopamine metabolic process (GO:0042417)|feeding behavior (GO:0007631)|G-protein coupled receptor internalization (GO:0002031)|grooming behavior (GO:0007625)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|long-term memory (GO:0007616)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of circadian sleep/wake cycle, sleep (GO:0042321)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of dopamine receptor signaling pathway (GO:0060160)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of insulin secretion (GO:0046676)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein secretion (GO:0050709)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|neurological system process involved in regulation of systemic arterial blood pressure (GO:0001976)|neuron-neuron synaptic transmission (GO:0007270)|orbitofrontal cortex development (GO:0021769)|peristalsis (GO:0030432)|phosphatidylinositol metabolic process (GO:0046488)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|pigmentation (GO:0043473)|positive regulation of cytokinesis (GO:0032467)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of dopamine uptake involved in synaptic transmission (GO:0051586)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of receptor internalization (GO:0002092)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of urine volume (GO:0035810)|prepulse inhibition (GO:0060134)|protein localization (GO:0008104)|regulation of cAMP metabolic process (GO:0030814)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of heart rate (GO:0002027)|regulation of locomotion involved in locomotory behavior (GO:0090325)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of potassium ion transport (GO:0043266)|regulation of sodium ion transport (GO:0002028)|regulation of synapse structural plasticity (GO:0051823)|regulation of synaptic transmission, GABAergic (GO:0032228)|release of sequestered calcium ion into cytosol (GO:0051209)|response to amphetamine (GO:0001975)|response to axon injury (GO:0048678)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to histamine (GO:0034776)|response to hypoxia (GO:0001666)|response to inactivity (GO:0014854)|response to iron ion (GO:0010039)|response to light stimulus (GO:0009416)|response to morphine (GO:0043278)|response to nicotine (GO:0035094)|response to toxic substance (GO:0009636)|sensory perception of smell (GO:0007608)|striatum development (GO:0021756)|synapse assembly (GO:0007416)|synaptic transmission, dopaminergic (GO:0001963)|temperature homeostasis (GO:0001659)|visual learning (GO:0008542)|Wnt signaling pathway (GO:0016055)	acrosomal vesicle (GO:0001669)|axon (GO:0030424)|axon terminus (GO:0043679)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endocytic vesicle (GO:0030139)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|sperm flagellum (GO:0036126)|synaptic vesicle membrane (GO:0030672)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity, coupled via Gi/Go (GO:0001591)|drug binding (GO:0008144)|identical protein binding (GO:0042802)|potassium channel regulator activity (GO:0015459)			endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(18)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	39		all_cancers(61;3.91e-16)|all_epithelial(67;2.95e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000977)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0494)		BRCA - Breast invasive adenocarcinoma(274;5.77e-06)|Epithelial(105;6.66e-05)|all cancers(92;0.000307)|OV - Ovarian serous cystadenocarcinoma(223;0.216)	Acepromazine(DB01614)|Acetophenazine(DB01063)|Alizapride(DB01425)|Amantadine(DB00915)|Amisulpride(DB06288)|Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Desipramine(DB01151)|Domperidone(DB01184)|Dopamine(DB00988)|Doxepin(DB01142)|Droperidol(DB00450)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Memantine(DB01043)|Mesoridazine(DB00933)|Methotrimeprazine(DB01403)|Metoclopramide(DB01233)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Molindone(DB01618)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Perphenazine(DB00850)|Pimozide(DB01100)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sertindole(DB06144)|Sulpiride(DB00391)|Tetrabenazine(DB04844)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Thiothixene(DB01623)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)	ATGTTCAGGATGTGTGTGATG	0.597																																					p.I394V		Atlas-SNP	.											.	DRD2	98	.	0			c.A1180G						.						198	144	162					11																	113281601		2201	4296	6497	SO:0001583	missense	1813	exon8			TCAGGATGTGTGT	M29066	CCDS8361.1, CCDS8362.1	11q22-q23	2012-08-08						"GPCR / Class A : Dopamine receptors"	3023	protein-coding gene	gene with protein product		126450					Standard	NM_000795		Approved		uc001poa.4	P14416		ENST00000362072.3:c.1180A>G	chr11.hg19:g.113281601T>C	ENSP00000354859:p.Ile394Val	149.0	0.0		104.0	65.0	NM_000795	Q9NZR3|Q9UPA9	Missense_Mutation	SNP	ENST00000362072.3	hg19	CCDS8361.1	.	.	.	.	.	.	.	.	.	.	T	13.99	2.402652	0.42613	.	.	ENSG00000149295	ENST00000355319;ENST00000346454;ENST00000362072;ENST00000544518;ENST00000542968;ENST00000538967	T;T;T;T;T;T	0.38887	1.11;1.11;1.11;1.11;1.11;1.11	5.86	5.86	0.93980	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.44393	0.1291	L	0.31294	0.92	0.80722	D	1	B;B;P	0.34934	0.254;0.296;0.476	B;B;P	0.47786	0.283;0.124;0.557	T	0.25572	-1.0128	10	0.18710	T	0.47	.	16.2436	0.82429	0.0:0.0:0.0:1.0	.	393;365;394	F8VUV1;P14416-2;P14416	.;.;DRD2_HUMAN	V	396;365;394;393;394;396	ENSP00000347474:I396V;ENSP00000278597:I365V;ENSP00000354859:I394V;ENSP00000441068:I393V;ENSP00000442172:I394V;ENSP00000438215:I396V	ENSP00000278597:I365V	I	-	1	0	DRD2	112786811	1.000000	0.71417	1.000000	0.80357	0.659000	0.38960	8.025000	0.88777	2.232000	0.73038	0.533000	0.62120	ATC	.	.		0.597	DRD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395834.1	NM_000795		C	113281601	T	C	113281601	3	2	245	1	0	0	0	0	1	0	0	0	4759	1464	51	2	155	2	DRD2	11	113281601	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	6471346	113281601	21724915	160	33630										
OR8D1	283159	hgsc.bcm.edu	37	chr11	124180322	124180322	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	catatgccatggcagtcaggAggtaaccctcagccaccaca	9	14	2	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr11:124180322A>T	ENST00000357821.2	-	1	411	c.341T>A	c.(340-342)cTc>cAc	p.L114H		NM_001002917.1	NP_001002917.1	Q8WZ84	OR8D1_HUMAN	olfactory receptor, family 8, subfamily D, member 1	114						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(1)|lung(7)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0528)		GGCAGTCAGGAGGTAACCCTC	0.478																																					p.L114H		Atlas-SNP	.											.	OR8D1	53	.	0			c.T341A						.						78	72	74					11																	124180322		2201	4299	6500	SO:0001583	missense	283159	exon1			GTCAGGAGGTAAC	AF238489	CCDS31706.1	11q25	2012-08-09			ENSG00000196341	ENSG00000196341		"GPCR / Class A : Olfactory receptors"	8481	protein-coding gene	gene with protein product				OR8D3			Standard	NM_001002917		Approved	OST004	uc010sag.2	Q8WZ84	OTTHUMG00000165977	ENST00000357821.2:c.341T>A	chr11.hg19:g.124180322A>T	ENSP00000350474:p.Leu114His	117.0	0.0		118.0	83.0	NM_001002917	B2RNL4|Q6IEW1|Q8NGH0	Missense_Mutation	SNP	ENST00000357821.2	hg19	CCDS31706.1	.	.	.	.	.	.	.	.	.	.	a	17.39	3.376924	0.61735	.	.	ENSG00000196341	ENST00000357821	T	0.03717	3.83	4.29	4.29	0.51040	GPCR, rhodopsin-like superfamily (1);	0.311359	0.18016	U	0.154411	T	0.22975	0.0555	H	0.94847	3.59	0.09310	N	1	D	0.67145	0.996	P	0.60886	0.88	T	0.20472	-1.0274	10	0.87932	D	0	.	13.302	0.60330	1.0:0.0:0.0:0.0	.	114	Q8WZ84	OR8D1_HUMAN	H	114	ENSP00000350474:L114H	ENSP00000350474:L114H	L	-	2	0	OR8D1	123685532	0.290000	0.24343	0.003000	0.11579	0.014000	0.08584	4.269000	0.58890	1.813000	0.52934	0.416000	0.27883	CTC	.	.		0.478	OR8D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387285.1	NM_001002917		T	124180322	A	T	124180322	3	4	245	1	0	0	0	0	1	0	0	0	11240	304	11	4	588	4	OR8D1	11	124180322	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	10898721	124180322	10826194	161	33631										
CACNA1C	775	hgsc.bcm.edu	37	chr12	2717739	2717739	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ccccatctacaactaccgtgTggagatctccatcttcttca	5	15	5	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr12:2717739T>A	ENST00000347598.4	+	28	3479	c.3479T>A	c.(3478-3480)gTg>gAg	p.V1160E	CACNA1C_ENST00000399649.1_Missense_Mutation_p.V1140E|CACNA1C_ENST00000399655.1_Missense_Mutation_p.V1140E|CACNA1C_ENST00000399591.1_Missense_Mutation_p.V1140E|CACNA1C-AS3_ENST00000543559.1_RNA|CACNA1C_ENST00000399634.1_Missense_Mutation_p.V1140E|CACNA1C_ENST00000399595.1_Missense_Mutation_p.V1140E|CACNA1C_ENST00000344100.3_Missense_Mutation_p.V1140E|CACNA1C_ENST00000399638.1_Missense_Mutation_p.V1140E|CACNA1C_ENST00000399601.1_Missense_Mutation_p.V1140E|CACNA1C_ENST00000399603.1_Missense_Mutation_p.V1140E|CACNA1C_ENST00000399637.1_Missense_Mutation_p.V1140E|CACNA1C_ENST00000399606.1_Missense_Mutation_p.V1160E|CACNA1C_ENST00000399641.1_Missense_Mutation_p.V1140E|CACNA1C_ENST00000399629.1_Missense_Mutation_p.V1140E|CACNA1C_ENST00000327702.7_Missense_Mutation_p.V1140E|CACNA1C_ENST00000480911.1_Missense_Mutation_p.V1140E|CACNA1C_ENST00000399597.1_Missense_Mutation_p.V1140E|CACNA1C_ENST00000399617.1_Missense_Mutation_p.V1140E|CACNA1C_ENST00000406454.3_Missense_Mutation_p.V1140E|CACNA1C_ENST00000402845.3_Missense_Mutation_p.V1140E|CACNA1C_ENST00000399644.1_Missense_Mutation_p.V1140E|CACNA1C_ENST00000399621.1_Missense_Mutation_p.V1140E|CACNA1C_ENST00000335762.5_Missense_Mutation_p.V1165E	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	1160	Dihydropyridine binding. {ECO:0000250}.				adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	AACTACCGTGTGGAGatctcc	0.537																																					p.V1160E		Atlas-SNP	.											.	CACNA1C	1023	.	0			c.T3479A						.						106	94	98					12																	2717739		2203	4300	6503	SO:0001583	missense	775	exon28			ACCGTGTGGAGAT	AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.3479T>A	chr12.hg19:g.2717739T>A	ENSP00000266376:p.Val1160Glu	92.0	0.0		115.0	18.0	NM_199460	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Missense_Mutation	SNP	ENST00000347598.4	hg19	CCDS44788.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.651912	0.88056	.	.	ENSG00000151067	ENST00000335762;ENST00000399655;ENST00000480911;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595;ENST00000322367	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.98474	-4.95;-4.95;-4.95;-4.95;-4.95;-4.95;-4.95;-4.95;-4.95;-4.95;-4.95;-4.95;-4.95;-4.95;-4.95;-4.95;-4.95;-4.95;-4.95;-4.95;-4.95;-4.95;-4.95	4.74	4.74	0.60224	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98397	0.9467	L	0.52905	1.665	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;P;D;D;D;D;D;D;P;D;D;D;D;D;D	0.89917	0.999;1.0;0.999;0.999;1.0;1.0;0.999;0.999;0.961;1.0;1.0;0.564;0.999;1.0;1.0;0.998;0.993;1.0;0.749;0.998;1.0;1.0;0.999;0.994;1.0	D;D;D;D;D;D;D;D;P;D;D;B;D;D;D;D;P;D;B;D;D;D;D;D;D	0.91635	0.996;0.997;0.99;0.996;0.998;0.997;0.999;0.953;0.786;0.998;0.996;0.312;0.999;0.998;0.999;0.991;0.786;0.998;0.288;0.991;0.998;0.998;0.995;0.986;0.997	D	0.99612	1.0981	10	0.72032	D	0.01	.	14.6917	0.69091	0.0:0.0:0.0:1.0	.	1140;1137;1160;1140;1140;1140;1140;1140;1140;1160;1140;1111;1160;1140;1140;1140;1140;1140;1140;1140;1140;1140;1140;1140;1140	Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-23;Q13936-28;Q13936-11;E9PDJ1;E9PDJ0;F5GY28;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;F5H638;Q13936-12	.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	E	1165;1140;1140;1140;1140;1140;1140;1140;1140;1140;1160;1160;1140;1140;1140;1140;1140;1140;1140;1140;1140;1140;1140;981	ENSP00000336982:V1165E;ENSP00000382563:V1140E;ENSP00000437936:V1140E;ENSP00000382552:V1140E;ENSP00000382547:V1140E;ENSP00000382506:V1140E;ENSP00000382530:V1140E;ENSP00000382546:V1140E;ENSP00000382500:V1140E;ENSP00000382549:V1140E;ENSP00000266376:V1160E;ENSP00000382515:V1160E;ENSP00000382510:V1140E;ENSP00000341092:V1140E;ENSP00000382537:V1140E;ENSP00000329877:V1140E;ENSP00000382557:V1140E;ENSP00000385724:V1140E;ENSP00000382512:V1140E;ENSP00000382542:V1140E;ENSP00000382526:V1140E;ENSP00000385896:V1140E;ENSP00000382504:V1140E	ENSP00000323129:V981E	V	+	2	0	CACNA1C	2588000	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.525000	0.81892	2.116000	0.64780	0.533000	0.62120	GTG	.	.		0.537	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719		A	2717739	T	A	2717739	3	1	245	1	0	0	0	0	1	0	0	0	2542	1696	59	4	3697	4	CACNA1C	12	2717739	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10		2717739	131134156	162	33632										
TULP3	7289	hgsc.bcm.edu	37	chr12	3047308	3047308	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	cagtttgctctcaaggtggcAgaacagaactatggaaaatc	10	8	1	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr12:3047308A>T	ENST00000448120.2	+	10	1103	c.1052A>T	c.(1051-1053)cAg>cTg	p.Q351L	TULP3_ENST00000397132.2_Missense_Mutation_p.Q351L	NM_003324.4	NP_003315.2	O75386	TULP3_HUMAN	tubby like protein 3	351					anterior/posterior pattern specification (GO:0009952)|bone development (GO:0060348)|brain development (GO:0007420)|bronchus morphogenesis (GO:0060434)|central nervous system neuron differentiation (GO:0021953)|embryonic camera-type eye development (GO:0031076)|embryonic digit morphogenesis (GO:0042733)|embryonic neurocranium morphogenesis (GO:0048702)|G-protein coupled receptor signaling pathway (GO:0007186)|ganglion development (GO:0061548)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of transcription, DNA-templated (GO:0006355)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cilium (GO:0005929)|extracellular region (GO:0005576)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	enzyme binding (GO:0019899)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein complex binding (GO:0032403)			endometrium(1)|large_intestine(4)|lung(13)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22			OV - Ovarian serous cystadenocarcinoma(31;0.000818)			TCAAGGTGGCAGAACAGAACT	0.483																																					p.Q351L		Atlas-SNP	.											.	TULP3	45	.	0			c.A1052T						.						112	102	106					12																	3047308		2203	4300	6503	SO:0001583	missense	7289	exon10			GGTGGCAGAACAG	AF045583	CCDS8519.1, CCDS53737.1	12p13	2014-02-21			ENSG00000078246	ENSG00000078246		"Intraflagellar transport homologs"	12425	protein-coding gene	gene with protein product		604730				9828123	Standard	NM_003324		Approved	TUBL3	uc001qlj.2	O75386	OTTHUMG00000168152	ENST00000448120.2:c.1052A>T	chr12.hg19:g.3047308A>T	ENSP00000410051:p.Gln351Leu	104.0	0.0		124.0	93.0	NM_003324	B3KNB7|B7Z6A2|D3DUQ4|F8WBZ9|Q8N5B0	Missense_Mutation	SNP	ENST00000448120.2	hg19	CCDS8519.1	.	.	.	.	.	.	.	.	.	.	a	10.27	1.304855	0.23736	.	.	ENSG00000078246	ENST00000228245;ENST00000544943;ENST00000542730;ENST00000448120;ENST00000397132	D;D;D	0.96491	-4.03;-4.03;-4.03	5.2	5.2	0.72013	Tubby, C-terminal (3);	0.231550	0.45361	D	0.000373	D	0.95825	0.8641	L	0.36672	1.1	0.48511	D	0.999661	B;B;D	0.71674	0.028;0.024;0.998	B;B;D	0.62955	0.056;0.032;0.909	D	0.95450	0.8533	10	0.66056	D	0.02	-20.4892	8.8747	0.35339	0.9167:0.0:0.0833:0.0	.	175;351;351	B7Z1E7;O75386;F8WBZ9	.;TULP3_HUMAN;.	L	351;78;175;351;351	ENSP00000442631:Q78L;ENSP00000410051:Q351L;ENSP00000380321:Q351L	ENSP00000228245:Q351L	Q	+	2	0	TULP3	2917569	1.000000	0.71417	0.963000	0.40424	0.068000	0.16541	6.368000	0.73104	1.955000	0.56771	0.529000	0.55759	CAG	.	.		0.483	TULP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398468.1	NM_003324		T	3047308	A	T	3047308	3	4	245	1	0	0	0	0	1	0	0	0	16790	188	7	4	1090	4	TULP3	12	3047308	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	329569	3047308	130804587	163	33633										
KCNA5	3741	hgsc.bcm.edu	37	chr12	5153590	5153590	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	cacggcctcgacggccgcctCccgaggacgaggaggaagaa	15	14	0	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr12:5153590C>T	ENST00000252321.3	+	1	506	c.277C>T	c.(277-279)Ccc>Tcc	p.P93S		NM_002234.3	NP_002225.2	P22460	KCNA5_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 5	93					atrial cardiac muscle cell action potential (GO:0086014)|membrane hyperpolarization (GO:0060081)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of potassium ion transport (GO:0043267)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of myoblast proliferation (GO:2000288)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transport (GO:0043266)|regulation of vasoconstriction (GO:0019229)|response to hypoxia (GO:0001666)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|intracellular canaliculus (GO:0046691)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|potassium channel inhibitor activity (GO:0019870)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization (GO:0086089)			NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(21)|ovary(5)|prostate(2)|upper_aerodigestive_tract(2)	52					Dalfampridine(DB06637)	ACGGCCGCCTCCCGAGGACGA	0.726																																					p.P93S		Atlas-SNP	.											.	KCNA5	138	.	0			c.C277T						.						10	12	11					12																	5153590		2173	4249	6422	SO:0001583	missense	3741	exon1			CCGCCTCCCGAGG	M83254	CCDS8536.1	12p13	2012-07-05				ENSG00000130037		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6224	protein-coding gene	gene with protein product		176267				16382104	Standard	NM_002234		Approved	Kv1.5, HK2, HPCN1	uc001qni.4	P22460		ENST00000252321.3:c.277C>T	chr12.hg19:g.5153590C>T	ENSP00000252321:p.Pro93Ser	31.0	0.0		30.0	22.0	NM_002234	Q4KKT8|Q4VAJ1|Q4VAJ2|Q9UDA4	Missense_Mutation	SNP	ENST00000252321.3	hg19	CCDS8536.1	.	.	.	.	.	.	.	.	.	.	C	13.63	2.293620	0.40594	.	.	ENSG00000130037	ENST00000252321	D	0.97303	-4.33	4.49	-2.52	0.06346	.	7739.210000	0.00166	N	0.000000	D	0.92459	0.7606	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	D	0.85588	0.1244	10	0.27785	T	0.31	.	7.5544	0.27817	0.1078:0.2767:0.5351:0.0804	.	93	P22460	KCNA5_HUMAN	S	93	ENSP00000252321:P93S	ENSP00000252321:P93S	P	+	1	0	KCNA5	5023851	0.000000	0.05858	0.000000	0.03702	0.510000	0.34073	-1.555000	0.02170	-0.772000	0.04602	-0.295000	0.09555	CCC	.	.		0.726	KCNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398925.2	NM_002234		T	5153590	C	T	5153590	3	4	245	1	0	0	0	0	1	0	0	0	8015	855	30	3	279	3	KCNA5	12	5153590	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	2106282	5153590	128698305	164	33634										
CLEC2B	9976	hgsc.bcm.edu	37	chr12	10005943	10005943	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ccattttctttcggtgtaacAtctagctgttgctgcaccat	7	11	2	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr12:10005943A>G	ENST00000228438.2	-	5	1339	c.406T>C	c.(406-408)Tgt>Cgt	p.C136R	CLEC2B_ENST00000538152.1_Missense_Mutation_p.C67R	NM_005127.2	NP_005118.2	Q92478	CLC2B_HUMAN	C-type lectin domain family 2, member B	136	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.			ATARCY -> TTAQIQ (in Ref. 6). {ECO:0000305}.		integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			endometrium(1)|large_intestine(3)|lung(1)	5						TCGGTGTAACATCTAGCTGTT	0.383																																					p.C136R		Atlas-SNP	.											.	CLEC2B	19	.	0			c.T406C						.						190	158	169					12																	10005943		2203	4300	6503	SO:0001583	missense	9976	exon5			TGTAACATCTAGC	X96719	CCDS8605.1	12p13-p12	2005-02-09	2005-02-09	2005-02-09		ENSG00000110852		"C-type lectin domain containing"	2053	protein-coding gene	gene with protein product		603242	"C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 2 (activation-induced)"	CLECSF2		9038101	Standard	NM_005127		Approved	AICL, HP10085	uc001qwn.3	Q92478		ENST00000228438.2:c.406T>C	chr12.hg19:g.10005943A>G	ENSP00000228438:p.Cys136Arg	77.0	0.0		79.0	60.0	NM_005127	B2R9U1|Q8IZE9|Q9BS74|Q9UQB4	Missense_Mutation	SNP	ENST00000228438.2	hg19	CCDS8605.1	.	.	.	.	.	.	.	.	.	.	A	0.139	-1.104296	0.01828	.	.	ENSG00000110852	ENST00000228438;ENST00000538152	T;T	0.60672	0.17;0.17	2.94	2.94	0.34122	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.000000	0.47093	D	0.000254	T	0.61299	0.2336	M	0.90369	3.11	0.58432	D	0.999995	B	0.22414	0.069	B	0.30401	0.115	T	0.58901	-0.7554	10	0.24483	T	0.36	.	7.7084	0.28663	1.0:0.0:0.0:0.0	.	136	Q92478	CLC2B_HUMAN	R	136;67	ENSP00000228438:C136R;ENSP00000437946:C67R	ENSP00000228438:C136R	C	-	1	0	CLEC2B	9897210	0.016000	0.18221	0.948000	0.38648	0.059000	0.15707	0.871000	0.28023	1.604000	0.50143	0.528000	0.53228	TGT	.	.		0.383	CLEC2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399881.1	NM_005127		G	10005943	A	G	10005943	3	3	245	1	0	0	0	0	1	0	0	0	3509	217	8	2	47	2	CLEC2B	12	10005943	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	4852353	10005943	123845952	165	33635										
TAS2R9	50835	hgsc.bcm.edu	37	chr12	10962090	10962091	+	Frame_Shift_Ins	INS	-	-	A													0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gtaacaagaaaaatgagatcINSaggcaaaggataaagggaac							TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr12:10962090_10962091insA	ENST00000240691.2	-	1	676_677	c.584_585insT	c.(583-585)ctgfs	p.L195fs	TAS2R8_ENST00000240615.2_5'Flank	NM_023917.2	NP_076406.1	Q9NYW1	TA2R9_HUMAN	taste receptor, type 2, member 9	195					detection of chemical stimulus involved in sensory perception of taste (GO:0050912)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	taste receptor activity (GO:0008527)			endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						AAAATGAGATCAGGCAAAGGAT	0.431																																					p.L195fs		Atlas-Indel,Pindel	.											.	TAS2R9	39	.	0			c.585_586insT						.																																			SO:0001589	frameshift_variant	50835	exon1			.	AF227135	CCDS8633.1	12p13	2012-08-22			ENSG00000121381	ENSG00000121381		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14917	protein-coding gene	gene with protein product		604795				10761934, 10766242	Standard	NM_023917		Approved	T2R9, TRB6	uc001qyx.3	Q9NYW1	OTTHUMG00000168507	ENST00000240691.2:c.585dupT	chr12.hg19:g.10962091_10962091dupA	ENSP00000240691:p.Leu195fs	132.0	0.0		168.0	27.0	NM_023917	Q502V7|Q50KT0|Q50KT1|Q645W9	Frame_Shift_Ins	INS	ENST00000240691.2	hg19	CCDS8633.1																																																																																			.	.		0.431	TAS2R9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399933.1			A	10962091	-	A	10962090	7	5	245	1	0	1	1	0	0	0	0	0	15603	813	29	0	357	0	TAS2R9	12	10962090	Frame_Shift_Ins	INS	-	TCGA-ED-A7PZ-01A-11D-A33Q-10	956147	10962090	122889805	166	33636										
ADAMTS20	80070	hgsc.bcm.edu	37	chr12	43826449	43826449	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	cttgtgaagacacagttaccAtggcatagttcttgggtagg	12	7	1	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr12:43826449A>G	ENST00000389420.3	-	20	2885	c.2886T>C	c.(2884-2886)caT>caC	p.H962H	ADAMTS20_ENST00000395541.2_Silent_p.H116H|ADAMTS20_ENST00000553158.1_Silent_p.H962H	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	962					extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		CACAGTTACCATGGCATAGTT	0.388																																					p.H962H		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.T2886C						.						144	126	132					12																	43826449		2203	4300	6503	SO:0001819	synonymous_variant	80070	exon20			GTTACCATGGCAT	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.2886T>C	chr12.hg19:g.43826449A>G		120.0	0.0		141.0	94.0	NM_025003	A6NNC9|J3QT00	Silent	SNP	ENST00000389420.3	hg19	CCDS31778.2																																																																																			.	.		0.388	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		G	43826449	A	G	43826449	2	3	245	1	0	0	0	0	0	0	0	1	266	214	8	2		2	ADAMTS20	12	43826449	Silent	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	32864359	43826449	90025446	167	33637										
HDAC7	51564	hgsc.bcm.edu	37	chr12	48191236	48191236	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	aacaggaggcaaaaagctgcTgagcatggagcgggtggctc	16	8	0	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr12:48191236T>G	ENST00000427332.2	-	6	547	c.391A>C	c.(391-393)Agc>Cgc	p.S131R	HDAC7_ENST00000080059.7_Missense_Mutation_p.S170R|HDAC7_ENST00000380610.4_Missense_Mutation_p.S187R|HDAC7_ENST00000552960.1_Missense_Mutation_p.S153R|HDAC7_ENST00000354334.3_Missense_Mutation_p.S170R			Q8WUI4	HDAC7_HUMAN	histone deacetylase 7	131	Interaction with MEF2A. {ECO:0000250}.|Transcription repression 1. {ECO:0000250}.				cell-cell junction assembly (GO:0007043)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25				GBM - Glioblastoma multiforme(48;0.137)		AAAAAGCTGCTGAGCATGGAG	0.617																																					p.S170R		Atlas-SNP	.											.	HDAC7	71	.	0			c.A508C						.						115	108	110					12																	48191236		2203	4300	6503	SO:0001583	missense	51564	exon6			AGCTGCTGAGCAT	AF239243	CCDS8756.2, CCDS41776.1	12q13.1	2008-02-25	2008-02-25	2008-02-25	ENSG00000061273	ENSG00000061273			14067	protein-coding gene	gene with protein product		606542	"histone deacetylase 7A"	HDAC7A		10922406, 10640276	Standard	NM_015401		Approved	DKFZP586J0917	uc010slo.2	Q8WUI4	OTTHUMG00000152968	ENST00000427332.2:c.391A>C	chr12.hg19:g.48191236T>G	ENSP00000404394:p.Ser131Arg	68.0	0.0		72.0	54.0	NM_001098416	B3KY08|B4DWI0|B4E0Q5|Q6P1W9|Q6W9G7|Q7Z4K2|Q7Z5I1|Q96K01|Q9BR73|Q9H7L0|Q9NW41|Q9NWA9|Q9NYK9|Q9UFU7	Missense_Mutation	SNP	ENST00000427332.2	hg19		.	.	.	.	.	.	.	.	.	.	T	16.59	3.164491	0.57476	.	.	ENSG00000061273	ENST00000080059;ENST00000354334;ENST00000552960;ENST00000380610;ENST00000427332;ENST00000447463;ENST00000434070;ENST00000421231	T;T;T;T;T;T;T;T	0.25250	1.81;1.81;1.81;1.81;1.81;1.81;1.81;1.81	4.84	2.5	0.30297	.	0.391229	0.28700	N	0.014427	T	0.20373	0.0490	L	0.38175	1.15	0.28826	N	0.897409	P;P;P	0.45474	0.688;0.859;0.634	B;B;B	0.43274	0.28;0.414;0.219	T	0.06215	-1.0839	10	0.51188	T	0.08	.	7.9829	0.30194	0.0:0.1704:0.0:0.8296	.	170;153;170	Q8WUI4-5;Q8WUI4-6;Q8WUI4-7	.;.;.	R	170;170;153;187;131;131;131;131	ENSP00000080059:S170R;ENSP00000351326:S170R;ENSP00000448532:S153R;ENSP00000369984:S187R;ENSP00000404394:S131R;ENSP00000389501:S131R;ENSP00000388561:S131R;ENSP00000412155:S131R	ENSP00000080059:S170R	S	-	1	0	HDAC7	46477503	0.995000	0.38212	0.998000	0.56505	0.996000	0.88848	0.801000	0.27055	0.456000	0.26937	0.533000	0.62120	AGC	.	.		0.617	HDAC7-013	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000328804.2			G	48191236	T	G	48191236	3	3	245	1	0	0	0	0	1	0	0	0	7021	1580	55	5	2551	5	HDAC7	12	48191236	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	4364787	48191236	85660659	168	33638										
LARP4	113251	hgsc.bcm.edu	37	chr12	50869368	50869368	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ccccctaaagagccatcttcAgttcttgtgcagccactacg	7	15	3	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr12:50869368A>T	ENST00000398473.2	+	16	2008	c.1896A>T	c.(1894-1896)tcA>tcT	p.S632S	LARP4_ENST00000429001.3_Silent_p.S638S|LARP4_ENST00000347328.5_Silent_p.S561S|LARP4_ENST00000518444.1_Silent_p.S631S|LARP4_ENST00000293618.8_Silent_p.S561S	NM_052879.4|NM_199188.2	NP_443111.4|NP_954658.2	Q71RC2	LARP4_HUMAN	La ribonucleoprotein domain family, member 4	632					cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(1)|skin(2)|urinary_tract(1)	23						AGCCATCTTCAGTTCTTGTGC	0.443																																					p.S632S		Atlas-SNP	.											.	LARP4	58	.	0			c.A1896T						.						157	159	158					12																	50869368		1832	4095	5927	SO:0001819	synonymous_variant	113251	exon16			ATCTTCAGTTCTT	AY004310	CCDS41782.1, CCDS44879.1, CCDS44880.1, CCDS44879.2, CCDS53789.1, CCDS53790.1	12q13.12	2005-08-09			ENSG00000161813	ENSG00000161813		"La ribonucleoprotein domain containing"	24320	protein-coding gene	gene with protein product						12477932	Standard	NM_052879		Approved	PP13296	uc001rwp.2	Q71RC2	OTTHUMG00000163724	ENST00000398473.2:c.1896A>T	chr12.hg19:g.50869368A>T		152.0	0.0		175.0	45.0	NM_052879	A8K6T1|E9PDG5|G3XAA8|G5E976|Q5CZ97|Q6ZV14|Q96NF9	Silent	SNP	ENST00000398473.2	hg19	CCDS41782.1																																																																																			.	.		0.443	LARP4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374981.1	NM_052879		T	50869368	A	T	50869368	2	4	245	1	0	0	0	0	0	0	0	1	8639	175	7	4		4	LARP4	12	50869368	Silent	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	2678132	50869368	82982527	169	33639										
STAT6	6778	hgsc.bcm.edu	37	chr12	57498539	57498539	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	aacagggcagagcagcagttCccaggaatgctgttctccaa	11	11	1	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr12:57498539C>G	ENST00000300134.3	-	10	1384	c.1059G>C	c.(1057-1059)ggG>ggC	p.G353G	STAT6_ENST00000454075.3_Silent_p.G353G|STAT6_ENST00000537215.2_Silent_p.G243G|STAT6_ENST00000556155.1_Silent_p.G353G|STAT6_ENST00000543873.2_Silent_p.G353G|STAT6_ENST00000538913.2_Silent_p.G243G	NM_001178078.1|NM_003153.4	NP_001171549.1|NP_003144.3	P42226	STAT6_HUMAN	signal transducer and activator of transcription 6, interleukin-4 induced	353					cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|mammary gland epithelial cell proliferation (GO:0033598)|mammary gland morphogenesis (GO:0060443)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of isotype switching to IgE isotypes (GO:0048295)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|T-helper 1 cell lineage commitment (GO:0002296)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane raft (GO:0045121)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein phosphatase binding (GO:0019903)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(2)|lung(8)|ovary(4)|skin(1)	28						AGCAGCAGTTCCCAGGAATGC	0.557																																					p.G353G		Atlas-SNP	.											.	STAT6	69	.	0			c.G1059C						.						130	105	114					12																	57498539		2203	4300	6503	SO:0001819	synonymous_variant	6778	exon10			GCAGTTCCCAGGA	BC005823, BQ028928	CCDS8931.1, CCDS53804.1	12q13	2013-02-14				ENSG00000166888		"SH2 domain containing"	11368	protein-coding gene	gene with protein product		601512				9605853, 8085155	Standard	NM_003153		Approved	D12S1644, IL-4-STAT	uc001sna.3	P42226		ENST00000300134.3:c.1059G>C	chr12.hg19:g.57498539C>G		69.0	0.0		71.0	19.0	NM_001178079	A8K316|B7ZA27|F5GXI9|Q5FBW5|Q71UP4	Silent	SNP	ENST00000300134.3	hg19	CCDS8931.1	.	.	.	.	.	.	.	.	.	.	C	9.796	1.179159	0.21787	.	.	ENSG00000166888	ENST00000553533	.	.	.	4.79	0.643	0.17770	.	.	.	.	.	T	0.56877	0.2015	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48747	-0.9008	4	.	.	.	-14.7093	9.1917	0.37204	0.2581:0.2814:0.4605:0.0	.	.	.	.	Q	54	.	.	E	-	1	0	STAT6	55784806	0.072000	0.21174	0.996000	0.52242	0.995000	0.86356	0.054000	0.14205	-0.065000	0.13021	-0.127000	0.14921	GAA	.	.		0.557	STAT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412248.3	NM_003153		G	57498539	C	G	57498539	2	3	245	1	0	0	0	0	0	0	0	1	15285	842	30	4		4	STAT6	12	57498539	Silent	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	6629171	57498539	76353356	170	33640										
C12orf56	115749	hgsc.bcm.edu	37	chr12	64724758	64724758	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	acctgagaggagattctttcAgacttctggactctttgctt	9	9	4	3			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr12:64724758A>T	ENST00000543942.2	-	3	1096	c.470T>A	c.(469-471)cTg>cAg	p.L157Q	RPS11P6_ENST00000535684.1_RNA|C12orf56_ENST00000333722.5_Missense_Mutation_p.L157Q	NM_001170633.1	NP_001164104.1	Q8IXR9	CL056_HUMAN	chromosome 12 open reading frame 56	157										NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)	15			GBM - Glioblastoma multiforme(3;0.000582)	GBM - Glioblastoma multiforme(28;0.0259)		AGATTCTTTCAGACTTCTGGA	0.299																																					p.L157Q		Atlas-SNP	.											.	C12orf56	42	.	0			c.T470A						.						46	44	44					12																	64724758		1804	4054	5858	SO:0001583	missense	115749	exon3			TCTTTCAGACTTC		CCDS44935.1, CCDS61182.1	12q14.2	2012-08-15			ENSG00000185306	ENSG00000185306			26967	protein-coding gene	gene with protein product							Standard	NM_001099676		Approved		uc021qzu.1	Q8IXR9	OTTHUMG00000168782	ENST00000543942.2:c.470T>A	chr12.hg19:g.64724758A>T	ENSP00000446101:p.Leu157Gln	65.0	0.0		70.0	57.0	NM_001170633		Missense_Mutation	SNP	ENST00000543942.2	hg19		.	.	.	.	.	.	.	.	.	.	A	1.143	-0.648932	0.03506	.	.	ENSG00000185306	ENST00000333722;ENST00000543942;ENST00000433716;ENST00000543259	.	.	.	3.63	1.19	0.21007	.	1.003290	0.08032	N	0.993706	T	0.30103	0.0754	L	0.41027	1.25	0.09310	N	1	B	0.28713	0.22	B	0.29176	0.099	T	0.28713	-1.0035	8	.	.	.	-0.1005	3.0377	0.06128	0.671:0.0:0.1186:0.2104	.	157	Q8IXR9-2	.	Q	157;157;157;144	.	.	L	-	2	0	C12orf56	63011025	0.000000	0.05858	0.057000	0.19452	0.010000	0.07245	0.286000	0.18902	0.238000	0.21222	0.402000	0.26972	CTG	.	.		0.299	C12orf56-008	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000401058.2	NM_001099676		T	64724758	A	T	64724758	3	4	245	1	0	0	0	0	1	0	0	0	1702	188	7	4	1442	4	C12orf56	12	64724758	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	7226219	64724758	69127137	171	33641										
UTP20	27340	hgsc.bcm.edu	37	chr12	101693811	101693811	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ttcatagaggcactcttcatGactgttgacaaaggaagctt	9	8	3	3			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr12:101693811G>T	ENST00000261637.4	+	14	1821	c.1647G>T	c.(1645-1647)atG>atT	p.M549I		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	549					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						CACTCTTCATGACTGTTGACA	0.438																																					p.M549I		Atlas-SNP	.											.	UTP20	222	.	0			c.G1647T						.						182	171	175					12																	101693811		2203	4300	6503	SO:0001583	missense	27340	exon14			CTTCATGACTGTT	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"down regulated in metastasis"	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.1647G>T	chr12.hg19:g.101693811G>T	ENSP00000261637:p.Met549Ile	286.0	1.0		198.0	180.0	NM_014503	Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	hg19	CCDS9081.1	.	.	.	.	.	.	.	.	.	.	G	1.788	-0.480141	0.04383	.	.	ENSG00000120800	ENST00000261637	T	0.64438	-0.1	5.39	1.35	0.21983	Armadillo-type fold (1);	1.509520	0.02968	N	0.143982	T	0.44685	0.1305	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.09377	0.004	T	0.24368	-1.0162	10	0.33940	T	0.23	1.6205	5.1172	0.14840	0.2409:0.2885:0.4706:0.0	.	549	O75691	UTP20_HUMAN	I	549	ENSP00000261637:M549I	ENSP00000261637:M549I	M	+	3	0	UTP20	100217942	0.131000	0.22433	0.002000	0.10522	0.075000	0.17131	0.373000	0.20484	0.235000	0.21160	-0.181000	0.13052	ATG	.	.		0.438	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		T	101693811	G	T	101693811	3	4	245	1	0	0	0	0	1	0	0	0	17114	1290	45	3	1701	3	UTP20	12	101693811	Missense_Mutation	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	36969053	101693811	32158084	172	33642										
VSIG10	54621	hgsc.bcm.edu	37	chr12	118533474	118533474	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	agagagaagcgaggctcagcTggccggaggctagagttgga	18	7	1	3			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr12:118533474T>A	ENST00000359236.5	-	2	501	c.225A>T	c.(223-225)ccA>ccT	p.P75P	VSIG10_ENST00000536905.1_5'UTR	NM_019086.5	NP_061959.2	Q8N0Z9	VSI10_HUMAN	V-set and immunoglobulin domain containing 10	75	Ig-like C2-type 1.					integral component of membrane (GO:0016021)				endometrium(5)|large_intestine(3)|lung(6)|skin(1)|stomach(1)|urinary_tract(1)	17						GAGGCTCAGCTGGCCGGAGGC	0.582																																					p.P75P		Atlas-SNP	.											.	VSIG10	41	.	0			c.A225T						.						68	79	76					12																	118533474		2139	4259	6398	SO:0001819	synonymous_variant	54621	exon2			CTCAGCTGGCCGG		CCDS44992.1	12q24.23	2013-01-29			ENSG00000176834	ENSG00000176834		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	26078	protein-coding gene	gene with protein product						12477932	Standard	NM_019086		Approved		uc001tws.3	Q8N0Z9		ENST00000359236.5:c.225A>T	chr12.hg19:g.118533474T>A		137.0	0.0		139.0	132.0	NM_019086	Q9NWQ7	Silent	SNP	ENST00000359236.5	hg19	CCDS44992.1																																																																																			.	.		0.582	VSIG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401273.2	NM_019086		A	118533474	T	A	118533474	2	1	245	1	0	0	0	0	0	0	0	1	17238	1567	55	4		4	VSIG10	12	118533474	Silent	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	16839663	118533474	15318421	173	33643										
WASF3	10810	hgsc.bcm.edu	37	chr13	27239184	27239184	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ggcaaacatgctgaagacatAtttggtgagttgtttaatga	11	4	0	4			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr13:27239184A>G	ENST00000335327.5	+	4	331	c.153A>G	c.(151-153)atA>atG	p.I51M	WASF3_ENST00000496788.1_3'UTR|WASF3_ENST00000361042.4_Missense_Mutation_p.I51M	NM_006646.5	NP_006637.2	Q9UPY6	WASF3_HUMAN	WAS protein family, member 3	51					actin filament polymerization (GO:0030041)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|oligodendrocyte development (GO:0014003)|positive regulation of myelination (GO:0031643)|protein complex assembly (GO:0006461)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)				breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|pancreas(1)|prostate(2)|skin(2)	22	Colorectal(5;0.000247)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0114)|Epithelial(112;0.046)|OV - Ovarian serous cystadenocarcinoma(117;0.0547)|Lung(94;0.105)|LUSC - Lung squamous cell carcinoma(192;0.155)		CTGAAGACATATTTGGTGAGT	0.433																																					p.I51M		Atlas-SNP	.											.	WASF3	68	.	0			c.A153G						.						108	101	103					13																	27239184		2203	4300	6503	SO:0001583	missense	10810	exon4			AGACATATTTGGT	AB020707	CCDS9318.1	13q12	2008-06-23			ENSG00000132970	ENSG00000132970			12734	protein-coding gene	gene with protein product		605068				10381382	Standard	NM_006646		Approved	WAVE3, SCAR3, KIAA0900	uc001uqv.3	Q9UPY6	OTTHUMG00000016621	ENST00000335327.5:c.153A>G	chr13.hg19:g.27239184A>G	ENSP00000335055:p.Ile51Met	71.0	0.0		41.0	15.0	NM_006646	O94974|Q86VQ2	Missense_Mutation	SNP	ENST00000335327.5	hg19	CCDS9318.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.190623	0.78789	.	.	ENSG00000132970	ENST00000361042;ENST00000335327	T;T	0.68765	-0.35;-0.35	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.73636	0.3612	M	0.69358	2.11	0.58432	D	0.999998	P;P	0.48589	0.706;0.912	B;P	0.50934	0.425;0.654	T	0.74734	-0.3565	10	0.44086	T	0.13	-25.4541	15.8529	0.78947	1.0:0.0:0.0:0.0	.	51;51	Q86VQ2;Q9UPY6	.;WASF3_HUMAN	M	51	ENSP00000354325:I51M;ENSP00000335055:I51M	ENSP00000335055:I51M	I	+	3	3	WASF3	26137184	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.127000	0.50484	2.147000	0.66899	0.528000	0.53228	ATA	.	.		0.433	WASF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044258.1			G	27239184	A	G	27239184	3	3	245	1	0	0	0	0	1	0	0	0	17269	439	16	2	159	2	WASF3	13	27239184	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10		27239184	87930694	174	33644										
FLT1	2321	hgsc.bcm.edu	37	chr13	29001941	29001941	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	aacacatttgactgttttatGctcagcaagattgtataatt	6	6	1	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr13:29001941G>A	ENST00000282397.4	-	9	1475	c.1224C>T	c.(1222-1224)agC>agT	p.S408S	FLT1_ENST00000539099.1_Silent_p.S408S|FLT1_ENST00000541932.1_Silent_p.S408S	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	408	Ig-like C2-type 4.				blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	ACTGTTTTATGCTCAGCAAGA	0.398																																					p.S408S		Atlas-SNP	.											.	FLT1	393	.	0			c.C1224T						.						160	142	148					13																	29001941		2203	4300	6503	SO:0001819	synonymous_variant	2321	exon9			TTTTATGCTCAGC	AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3763	protein-coding gene	gene with protein product	"vascular endothelial growth factor receptor 1", "vascular permeability factor receptor"	165070	"fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.1224C>T	chr13.hg19:g.29001941G>A		83.0	0.0		38.0	19.0	NM_002019	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Silent	SNP	ENST00000282397.4	hg19	CCDS9330.1																																																																																			.	.		0.398	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1			A	29001941	G	A	29001941	2	1	245	1	0	0	0	0	0	0	0	1	5949	1310	46	3		3	FLT1	13	29001941	Silent	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	1762757	29001941	86167937	175	33645										
EPSTI1	94240	hgsc.bcm.edu	37	chr13	43469145	43469146	+	Splice_Site	DNP	CC	CC	AA													0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	agagaaaagaaaaaactcacCcagctgttaccgctattcat							TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr13:43469145_43469146CC>AA	ENST00000398762.3	-	11	946_947	c.947_948GG>TT	c.(946-948)tGG>tTT	p.W316F	EPSTI1_ENST00000313624.7_Splice_Site_p.W305F|EPSTI1_ENST00000313640.7_Splice_Site_p.W316F			Q96J88	ESIP1_HUMAN	epithelial stromal interaction 1 (breast)	316										endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|skin(1)	17		Lung NSC(96;3.6e-06)|Breast(139;0.00869)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		GBM - Glioblastoma multiforme(144;0.000528)|BRCA - Breast invasive adenocarcinoma(63;0.0858)		AAAAACTCACCCAGCTGTTACC	0.386																																					p.W316C|p.W316L		Atlas-SNP	.											.	EPSTI1	47	.	0			c.G948T|c.G947T						.																																			SO:0001630	splice_region_variant	94240	exon11			ACTCACCCAGCTG|CTCACCCAGCTGT	AF396928	CCDS9387.1, CCDS31964.1	13q13.3	2011-06-27			ENSG00000133106	ENSG00000133106			16465	protein-coding gene	gene with protein product	"epithelial stromal interaction protein 1"	607441				11991720	Standard	NM_033255		Approved	BRESI1, MGC29634	uc001uyw.2	Q96J88	OTTHUMG00000016814	ENST00000398762.3:c.947_948delinsAA	chr13.hg19:g.43469145_43469146delinsAA		83.0|82.0	0.0		21.0	13.0	NM_001002264	Q8IVC7|Q8NDQ7	Missense_Mutation	SNP	ENST00000398762.3	hg19	CCDS9387.1																																																																																			.	.		0.386	EPSTI1-010	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400321.1	NM_001002264	Missense_Mutation	AA	43469146	CC	AA	43469145	5	1	245	1	0	0	0	0	0	0	1	0	5200	637	22	3	296	3	EPSTI1	13	43469145	Splice_Site	DNP	CC	TCGA-ED-A7PZ-01A-11D-A33Q-10	14467204	43469145	71700733	176	33646										
RB1	5925	hgsc.bcm.edu	37	chr13	49027173	49027173	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	aaacaatcaaaggaccgagaAggaccaactgatcaccttga	8	10	2	3			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr13:49027173A>C	ENST00000267163.4	+	18	1878	c.1740A>C	c.(1738-1740)gaA>gaC	p.E580D		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	580	Pocket; binds T and E1A.|Spacer.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(10)|p.R579fs*29(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(DB00071)|Insulin Regular(DB00030)"	AGGACCGAGAAGGACCAACTG	0.343		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)																											p.E580D		Atlas-SNP	.	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	.	RB1	1068	.	26	Whole gene deletion(15)|Unknown(10)|Deletion - Frameshift(1)	bone(10)|haematopoietic_and_lymphoid_tissue(4)|breast(4)|eye(2)|adrenal_gland(1)|soft_tissue(1)|endometrium(1)|urinary_tract(1)|lung(1)|liver(1)	c.A1740C						.						122	115	117					13																	49027173		2203	4300	6503	SO:0001583	missense	5925	exon18	Familial Cancer Database		CCGAGAAGGACCA	M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1740A>C	chr13.hg19:g.49027173A>C	ENSP00000267163:p.Glu580Asp	46.0	0.0		32.0	11.0	NM_000321	A8K5E3|P78499|Q5VW46|Q8IZL4	Missense_Mutation	SNP	ENST00000267163.4	hg19	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	A	10.07	1.250301	0.22880	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	D	0.92348	-3.02	5.75	0.379	0.16213	.	0.125321	0.56097	D	0.000033	D	0.87160	0.6108	M	0.62723	1.935	0.47341	D	0.999392	B	0.02656	0.0	B	0.04013	0.001	T	0.76274	-0.3019	10	0.32370	T	0.25	.	5.8904	0.18909	0.5421:0.0:0.3405:0.1174	.	580	P06400	RB_HUMAN	D	559;580	ENSP00000267163:E580D	ENSP00000267163:E580D	E	+	3	2	RB1	47925174	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	1.067000	0.30616	0.099000	0.17552	0.533000	0.62120	GAA	.	.		0.343	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			C	49027173	A	C	49027173	3	2	245	1	0	0	0	0	1	0	0	0	13113	69	3	5	1810	5	RB1	13	49027173	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	5558028	49027173	66142705	177	33647										
ABCC4	10257	hgsc.bcm.edu	37	chr13	95816633	95816633	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	aacaaatgtcattatttaccTgagctgcagtgtttaggaga	9	6	1	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr13:95816633T>A	ENST00000376887.4	-	16	2288	c.2174A>T	c.(2173-2175)cAg>cTg	p.Q725L	ABCC4_ENST00000412704.1_Intron|ABCC4_ENST00000536256.1_Splice_Site_p.Q650L|ABCC4_ENST00000431522.1_Splice_Site_p.Q725L	NM_005845.3	NP_005836.2	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	725	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				blood coagulation (GO:0007596)|oxidation-reduction process (GO:0055114)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of smooth muscle cell proliferation (GO:0048661)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)	15-hydroxyprostaglandin dehydrogenase (NAD+) activity (GO:0016404)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(1)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cefazolin(DB01327)|Celecoxib(DB00482)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Flurbiprofen(DB00712)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Lamivudine(DB00709)|Leucovorin(DB00650)|Meloxicam(DB00814)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Probenecid(DB01032)|Rosuvastatin(DB01098)|Sildenafil(DB00203)|Sorafenib(DB00398)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tenofovir(DB00300)|Tioguanine(DB00352)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Zidovudine(DB00495)	ATTATTTACCTGAGCTGCAGT	0.383																																					p.Q725L		Atlas-SNP	.											.	ABCC4	248	.	0			c.A2174T						.						92	88	89					13																	95816633		2203	4300	6503	SO:0001630	splice_region_variant	10257	exon16			TTTACCTGAGCTG	U66682	CCDS9474.1	13q31	2012-03-14			ENSG00000125257	ENSG00000125257		"ATP binding cassette transporters / subfamily C"	55	protein-coding gene	gene with protein product	"canalicular multispecific organic anion transporter (ABC superfamily)", "bA464I2.1 (ATP-binding cassette, sub-family C (CFTR/MRP), member 4)", "multidrug resistance-associated protein 4", "multispecific organic anion transporter B"	605250				8894702, 9661885	Standard	NM_005845		Approved	MRP4, EST170205, MOAT-B, MOATB	uc001vmd.4	O15439	OTTHUMG00000017216	ENST00000376887.4:c.2175+1A>T	chr13.hg19:g.95816633T>A		100.0	0.0		60.0	15.0	NM_005845	A9Z1Z7|Q8IVZ4|Q8IZN6|Q8NEW8|Q9Y6J2	Missense_Mutation	SNP	ENST00000376887.4	hg19	CCDS9474.1	.	.	.	.	.	.	.	.	.	.	T	15.13	2.743117	0.49151	.	.	ENSG00000125257	ENST00000376887;ENST00000536256;ENST00000431522	D;D;D	0.94184	-3.37;-2.84;-2.84	5.39	3.97	0.46021	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.225800	0.47093	D	0.000250	D	0.95277	0.8468	M	0.92219	3.285	0.80722	D	1	B;B;B	0.28971	0.209;0.229;0.105	B;B;B	0.38954	0.286;0.25;0.169	D	0.93939	0.7221	10	0.87932	D	0	.	11.1043	0.48193	0.1687:0.0:0.0:0.8313	.	650;725;725	B7Z3Q7;Q8IVZ4;O15439	.;.;MRP4_HUMAN	L	725;650;725	ENSP00000366084:Q725L;ENSP00000442024:Q650L;ENSP00000398562:Q725L	ENSP00000366084:Q725L	Q	-	2	0	ABCC4	94614634	1.000000	0.71417	0.966000	0.40874	0.727000	0.41649	3.120000	0.50430	0.811000	0.34303	0.528000	0.53228	CAG	.	.		0.383	ABCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045478.2	NM_005845	Missense_Mutation	A	95816633	T	A	95816633	5	1	245	1	0	0	0	0	0	0	1	0	55	1594	55	4	1916	4	ABCC4	13	95816633	Splice_Site	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	46789460	95816633	19353245	178	33648										
RNASE1	6035	hgsc.bcm.edu	37	chr14	21270099	21270099	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ctgctgctgggggaactgtcTgagtccatatgctgccgctg	14	11	1	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr14:21270099T>A	ENST00000397967.4	-	2	635	c.129A>T	c.(127-129)tcA>tcT	p.S43S	RNASE1_ENST00000555698.1_Silent_p.S3S|RNASE1_ENST00000340900.3_Silent_p.S43S|RNASE1_ENST00000412779.2_Silent_p.S43S|RNASE1_ENST00000397970.4_Silent_p.S43S	NM_002933.4	NP_002924.1	P07998	RNAS1_HUMAN	ribonuclease, RNase A family, 1 (pancreatic)	43					RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	extracellular vesicular exosome (GO:0070062)	nucleic acid binding (GO:0003676)|pancreatic ribonuclease activity (GO:0004522)			central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	5	all_cancers(95;0.00671)	all_lung(585;0.235)	Epithelial(56;9.21e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0126)	Guanidine(DB00536)|L-Aspartic Acid(DB00128)	GGGAACTGTCTGAGTCCATAT	0.572																																					p.S43S		Atlas-SNP	.											.	RNASE1	14	.	0			c.A129T						.						69	65	66					14																	21270099		2203	4300	6503	SO:0001819	synonymous_variant	6035	exon3			ACTGTCTGAGTCC	BC005324	CCDS9559.1	14q11.2	2014-03-13			ENSG00000129538	ENSG00000129538	3.1.27.5	"Ribonucleases, RNase A"	10044	protein-coding gene	gene with protein product		180440		RNS1		8588814	Standard	NM_002933		Approved		uc001vyi.3	P07998	OTTHUMG00000029603	ENST00000397967.4:c.129A>T	chr14.hg19:g.21270099T>A		41.0	0.0		43.0	8.0	NM_198235	B2R589|D3DS06|Q16830|Q16869|Q1KHR2|Q6ICS5|Q9UCB4|Q9UCB5	Silent	SNP	ENST00000397967.4	hg19	CCDS9559.1																																																																																			.	.		0.572	RNASE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073791.3			A	21270099	T	A	21270099	2	1	245	1	0	0	0	0	0	0	0	1	13414	1567	55	4		4	RNASE1	14	21270099	Silent	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10		21270099	86079441	179	33649										
DACT1	51339	hgsc.bcm.edu	37	chr14	59112597	59112597	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	attctccccaccgaagcagtGgtcgaaagaatcaaaggccg	10	12	2	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr14:59112597G>T	ENST00000335867.4	+	4	1280	c.1256G>T	c.(1255-1257)tGg>tTg	p.W419L	DACT1_ENST00000556859.1_Missense_Mutation_p.W138L|DACT1_ENST00000395153.3_Missense_Mutation_p.W382L|DACT1_ENST00000541264.2_Missense_Mutation_p.W138L			Q9NYF0	DACT1_HUMAN	dishevelled-binding antagonist of beta-catenin 1	419					dendrite morphogenesis (GO:0048813)|embryonic hindgut morphogenesis (GO:0048619)|gastrulation with mouth forming second (GO:0001702)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of catenin import into nucleus (GO:0035412)|regulation of protein stability (GO:0031647)|regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000095)|synapse organization (GO:0050808)|Wnt signaling pathway (GO:0016055)	beta-catenin destruction complex (GO:0030877)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|protein kinase A binding (GO:0051018)|protein kinase C binding (GO:0005080)			endometrium(7)|kidney(3)|large_intestine(11)|lung(27)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	53						CCGAAGCAGTGGTCGAAAGAA	0.572																																					p.W419L		Atlas-SNP	.											.	DACT1	119	.	0			c.G1256T						.						58	62	61					14																	59112597		2203	4300	6503	SO:0001583	missense	51339	exon4			AGCAGTGGTCGAA	AF251079	CCDS9736.1, CCDS41961.1	14q22.3	2013-05-15	2013-05-15		ENSG00000165617	ENSG00000165617			17748	protein-coding gene	gene with protein product		607861	"dapper homolog 1, antagonist of beta-catenin (xenopus)", "dapper, antagonist of beta-catenin, homolog 1 (Xenopus laevis)"			11970895	Standard	NM_001079520		Approved	DAPPER1, THYEX3, HDPR1, DAPPER, FRODO	uc001xdw.3	Q9NYF0	OTTHUMG00000140324	ENST00000335867.4:c.1256G>T	chr14.hg19:g.59112597G>T	ENSP00000337439:p.Trp419Leu	59.0	0.0		38.0	19.0	NM_016651	A8MYJ2|Q86TY0	Missense_Mutation	SNP	ENST00000335867.4	hg19	CCDS9736.1	.	.	.	.	.	.	.	.	.	.	G	2.967	-0.213384	0.06140	.	.	ENSG00000165617	ENST00000556859;ENST00000395151;ENST00000395153;ENST00000335867;ENST00000541264	T;T;T;T;T	0.41400	1.0;1.0;1.0;1.0;1.0	5.35	4.46	0.54185	.	0.442842	0.27567	N	0.018793	T	0.34832	0.0911	L	0.56769	1.78	0.33000	D	0.526163	P;B	0.35348	0.496;0.288	B;B	0.33521	0.165;0.086	T	0.42224	-0.9464	10	0.10636	T	0.68	-4.7606	10.9689	0.47428	0.1503:0.0:0.8497:0.0	.	382;419	A8MYJ2;Q9NYF0	.;DACT1_HUMAN	L	138;138;382;419;138	ENSP00000451598:W138L;ENSP00000378581:W138L;ENSP00000378582:W382L;ENSP00000337439:W419L;ENSP00000442850:W138L	ENSP00000337439:W419L	W	+	2	0	DACT1	58182350	1.000000	0.71417	0.996000	0.52242	0.046000	0.14306	3.059000	0.49947	1.271000	0.44313	0.563000	0.77884	TGG	.	.		0.572	DACT1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325515.1	NM_016651		T	59112597	G	T	59112597	3	4	245	1	0	0	0	0	1	0	0	0	4224	1357	47	3	1270	3	DACT1	14	59112597	Missense_Mutation	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	37842498	59112597	48236943	180	33650										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64522760	64522760	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ctcgaagccatcattataccCtacagagtagatgttggtaa	8	9	1	2	rs373355920		TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr14:64522760C>G	ENST00000344113.4	+	49	10055	c.9843C>G	c.(9841-9843)ccC>ccG	p.P3281P	SYNE2_ENST00000358025.3_Silent_p.P3281P|SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000554584.1_Silent_p.P3314P	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	3281					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)	p.P3281P(1)		NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		TCATTATACCCTACAGAGTAG	0.433																																					p.P3281P		Atlas-SNP	.											SYNE2,caecum,carcinoma,0,1	SYNE2	577	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C9843G						.						78	72	74					14																	64522760		1942	4136	6078	SO:0001819	synonymous_variant	23224	exon49			TATACCCTACAGA	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.9843C>G	chr14.hg19:g.64522760C>G		227.0	0.0		176.0	58.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	hg19	CCDS41963.1																																																																																			.	.		0.433	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		G	64522760	C	G	64522760	2	3	245	1	0	0	0	0	0	0	0	1	15461	668	24	4		4	SYNE2	14	64522760	Silent	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	5410163	64522760	42826780	181	33651										
SLC10A1	6554	hgsc.bcm.edu	37	chr14	70263762	70263764	+	In_Frame_Del	DEL	GAA	GAA	-													0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	cagcccagcgagagcatgatGaagaacaacatgaacaccag					rs200032457	byFrequency	TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr14:70263762_70263764delGAA	ENST00000216540.4	-	1	242_244	c.109_111delTTC	c.(109-111)ttcdel	p.F37del		NM_003049.3	NP_003040.1	Q14973	NTCP_HUMAN	solute carrier family 10 (sodium/bile acid cotransporter), member 1	37					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bile acid:sodium symporter activity (GO:0008508)			NS(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)	14				all cancers(60;0.00228)|BRCA - Breast invasive adenocarcinoma(234;0.0137)|OV - Ovarian serous cystadenocarcinoma(108;0.0226)	Bumetanide(DB00887)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Ethinyl Estradiol(DB00977)|Indomethacin(DB00328)|Liothyronine(DB00279)|Liotrix(DB01583)|Pitavastatin(DB08860)|Probenecid(DB01032)|Progesterone(DB00396)|Testosterone(DB00624)|Ursodeoxycholic acid(DB01586)	AGAGCATGATGAAGAACAACATG	0.567																																					p.37_38del		Atlas-Indel,Pindel	.											.	SLC10A1	32	.	0			c.110_112del						.																																			SO:0001651	inframe_deletion	6554	exon1			.	L21893	CCDS9797.1	14q24.2	2013-07-18	2013-07-18		ENSG00000100652	ENSG00000100652		"Solute carriers"	10905	protein-coding gene	gene with protein product		182396				8132774	Standard	NM_003049		Approved	NTCP	uc001xlr.2	Q14973	OTTHUMG00000171236	ENST00000216540.4:c.109_111delTTC	chr14.hg19:g.70263765_70263767delGAA	ENSP00000216540:p.Phe37del	114.0	0.0		88.0	43.0	NM_003049	B9EGB6|Q2TU29	In_Frame_Del	DEL	ENST00000216540.4	hg19	CCDS9797.1																																																																																			.	.		0.567	SLC10A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412464.1			-	70263764	GAA	-	70263762	7	5	245	1	0	1	0	1	0	0	0	0	14388	1281	45	0	958	0	SLC10A1	14	70263762	In_Frame_Del	DEL	GAA	TCGA-ED-A7PZ-01A-11D-A33Q-10	5741002	70263762	37085778	182	33652										
MLH3	27030	hgsc.bcm.edu	37	chr14	75505088	75505088	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	agtgctcatcaaacaggcaaTaaacttgttatctacttgct	6	9	3	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr14:75505088T>C	ENST00000556740.1	-	5	3633	c.3598A>G	c.(3598-3600)Att>Gtt	p.I1200V	MLH3_ENST00000544985.1_Missense_Mutation_p.I160V|MLH3_ENST00000556257.1_Intron|MLH3_ENST00000355774.2_Missense_Mutation_p.I1200V|MLH3_ENST00000238662.7_Missense_Mutation_p.I1200V|MLH3_ENST00000380968.2_Missense_Mutation_p.I146V|MLH3_ENST00000555671.1_5'Flank			Q9UHC1	MLH3_HUMAN	mutL homolog 3	1200					ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44				BRCA - Breast invasive adenocarcinoma(234;0.00688)		AAACAGGCAATAAACTTGTTA	0.368								Mismatch excision repair (MMR)																													p.I1200V		Atlas-SNP	.											.	MLH3	200	.	0			c.A3598G						.						134	122	126					14																	75505088		2203	4300	6503	SO:0001583	missense	27030	exon6			AGGCAATAAACTT	AF195657	CCDS9837.1, CCDS32123.1	14q24.3	2014-09-17	2013-09-12			ENSG00000119684			7128	protein-coding gene	gene with protein product		604395	"mutL (E. coli) homolog 3", "mutL homolog 3 (E. coli)"			10615123	Standard	XR_245681		Approved		uc001xrd.1	Q9UHC1		ENST00000556740.1:c.3598A>G	chr14.hg19:g.75505088T>C	ENSP00000452316:p.Ile1200Val	77.0	0.0		57.0	21.0	NM_014381	P49751|Q56DK9|Q9P292|Q9UHC0	Missense_Mutation	SNP	ENST00000556740.1	hg19	CCDS32123.1	.	.	.	.	.	.	.	.	.	.	T	19.12	3.766194	0.69878	.	.	ENSG00000119684	ENST00000355774;ENST00000380968;ENST00000238662;ENST00000556740;ENST00000544985	T;T;D;T;T	0.86230	-1.21;-1.21;-2.09;-1.21;0.24	5.58	5.58	0.84498	MutL, C-terminal, dimerisation (1);	0.053490	0.85682	D	0.000000	D	0.92919	0.7747	M	0.78285	2.405	0.32419	N	0.549637	D;D	0.71674	0.998;0.984	D;D	0.66716	0.938;0.946	D	0.94788	0.7959	10	0.66056	D	0.02	-18.7395	15.7499	0.77976	0.0:0.0:0.0:1.0	.	1200;1200	Q9UHC1-2;Q9UHC1	.;MLH3_HUMAN	V	1200;146;1200;1200;160	ENSP00000348020:I1200V;ENSP00000370355:I146V;ENSP00000238662:I1200V;ENSP00000452316:I1200V;ENSP00000441371:I160V	ENSP00000238662:I1200V	I	-	1	0	MLH3	74574841	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	5.300000	0.65721	2.134000	0.65973	0.459000	0.35465	ATT	.	.		0.368	MLH3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415006.1	NM_014381		C	75505088	T	C	75505088	3	2	245	1	0	0	0	0	1	0	0	0	9627	1406	49	2	795	2	MLH3	14	75505088	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	5241326	75505088	31844452	183	33653										
SERPINA3	12	hgsc.bcm.edu	37	chr14	95088801	95088801	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gctgacctgtcagggatcacAggggccaggaacctagcagt	14	11	2	1	rs1802958	byFrequency	TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr14:95088801A>T	ENST00000467132.1	+	4	2189	c.1041A>T	c.(1039-1041)acA>acT	p.T347T	SERPINA3_ENST00000482740.1_Silent_p.T129T|SERPINA3_ENST00000393078.3_Silent_p.T347T|RP11-986E7.7_ENST00000553947.1_3'UTR|SERPINA3_ENST00000393080.4_Silent_p.T347T			P01011	AACT_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3	347					acute-phase response (GO:0006953)|inflammatory response (GO:0006954)|maintenance of gastrointestinal epithelium (GO:0030277)|negative regulation of endopeptidase activity (GO:0010951)|regulation of lipid metabolic process (GO:0019216)|regulation of proteolysis (GO:0030162)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	DNA binding (GO:0003677)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(17)|ovary(2)|pancreas(1)|skin(3)|stomach(1)	40		all_cancers(154;0.0525)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.212)|Epithelial(152;0.228)		CAGGGATCACAGGGGCCAGGA	0.498																																					p.T347T		Atlas-SNP	.											.	SERPINA3	78	.	0			c.A1041T						.						74	69	71					14																	95088801		2203	4300	6503	SO:0001819	synonymous_variant	12	exon4			GATCACAGGGGCC	K01500	CCDS32150.1	14q32.1	2014-06-03	2005-08-18		ENSG00000196136	ENSG00000196136		"Serine (or cysteine) peptidase inhibitors"	16	protein-coding gene	gene with protein product		107280	"alpha-1-antichymotrypsin", "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3"	AACT		3260956, 24172014	Standard	NM_001085		Approved	ACT, alpha-1-antichymotrypsin	uc001ydp.3	P01011	OTTHUMG00000029851	ENST00000467132.1:c.1041A>T	chr14.hg19:g.95088801A>T		124.0	0.0		76.0	21.0	NM_001085	B3KVQ7|Q13703|Q2TU87|Q2TU88|Q59GP9|Q6LBY8|Q6LDT7|Q6NSC9|Q8N177|Q96DW8|Q9UC47|Q9UNU9	Silent	SNP	ENST00000467132.1	hg19	CCDS32150.1																																																																																			.	A|0.990;G|0.010		0.498	SERPINA3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268080.3	NM_001085		T	95088801	A	T	95088801	2	4	245	1	0	0	0	0	0	0	0	1	14105	175	7	4		4	SERPINA3	14	95088801	Silent	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	19583713	95088801	12260739	184	33654										
HERC2	8924	hgsc.bcm.edu	37	chr15	28460799	28460799	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	cgaggtggcagtgaagggtgCgtgcccttccacgaccttca	14	12	1	1	rs558450056		TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr15:28460799C>G	ENST00000261609.7	-	39	6286	c.6178G>C	c.(6178-6180)Gca>Cca	p.A2060P		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2									p.A2060P(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		GTGAAGGGTGCGTGCCCTTCC	0.617																																					p.A2060P		Atlas-SNP	.											HERC2,NS,carcinoma,0,1	HERC2	501	.	1	Substitution - Missense(1)	lung(1)	c.G6178C						.						17	14	15					15																	28460799		2201	4292	6493	SO:0001583	missense	8924	exon39			AGGGTGCGTGCCC	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.6178G>C	chr15.hg19:g.28460799C>G	ENSP00000261609:p.Ala2060Pro	123.0	0.0		101.0	65.0	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	hg19	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	C	11.01	1.513389	0.27123	.	.	ENSG00000128731	ENST00000261609	T	0.39787	1.06	4.28	2.38	0.29361	.	0.220211	0.37136	N	0.002237	T	0.24547	0.0595	N	0.19112	0.55	0.34906	D	0.746953	B	0.26975	0.165	B	0.19148	0.024	T	0.19976	-1.0289	10	0.48119	T	0.1	.	8.8827	0.35384	0.1481:0.7732:0.0:0.0788	.	2060	O95714	HERC2_HUMAN	P	2060	ENSP00000261609:A2060P	ENSP00000261609:A2060P	A	-	1	0	HERC2	26134394	1.000000	0.71417	0.041000	0.18516	0.553000	0.35397	2.487000	0.45268	0.448000	0.26722	-0.347000	0.07816	GCA	.	.		0.617	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		G	28460799	C	G	28460799	3	3	245	1	0	0	0	0	1	0	0	0	7067	768	27	4	8546	4	HERC2	15	28460799	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10		28460799	74070593	185	33655										
JMJD7-PLA2G4B	100137049	hgsc.bcm.edu	37	chr15	42137485	42137485	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tctactgtgccctcaacaccAaagggcagagcctgaccact	8	15	2	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr15:42137485A>G	ENST00000452633.1	+	15	1676	c.1324A>G	c.(1324-1326)Aaa>Gaa	p.K442E	PLA2G4B_ENST00000542534.2_Missense_Mutation_p.K673E|JMJD7-PLA2G4B_ENST00000382448.4_Missense_Mutation_p.K673E|JMJD7-PLA2G4B_ENST00000342159.4_Missense_Mutation_p.K673E|PLA2G4B_ENST00000458483.1_Missense_Mutation_p.K442E			P0C869	PA24B_HUMAN	phospholipase A2, group IVB (cytosolic)	442	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|arachidonic acid metabolic process (GO:0019369)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|parturition (GO:0007567)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular region (GO:0005576)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|calcium-dependent phospholipid binding (GO:0005544)|lysophospholipase activity (GO:0004622)						all_cancers(109;1.84e-13)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		all cancers(2;1.08e-30)|Epithelial(2;1.43e-22)|OV - Ovarian serous cystadenocarcinoma(18;1.13e-17)|GBM - Glioblastoma multiforme(94;9.77e-07)|Colorectal(2;0.0129)|COAD - Colon adenocarcinoma(120;0.0371)		CCTCAACACCAAAGGGCAGAG	0.562																																					p.K673E		Atlas-SNP	.											.	JMJD7-PLA2G4B	90	.	0			c.A2017G						.						65	61	62					15																	42137485		2203	4300	6503	SO:0001583	missense	8681	exon19			AACACCAAAGGGC	AF065215	CCDS45241.1	15q11.2-q21.3	2010-08-17			ENSG00000243708	ENSG00000243708	3.1.1.4		9036	protein-coding gene	gene with protein product		606088				9705332	Standard	NM_001114633		Approved	cPLA2-beta, HsT16992		P0C869	OTTHUMG00000156809	ENST00000452633.1:c.1324A>G	chr15.hg19:g.42137485A>G	ENSP00000396045:p.Lys442Glu	85.0	0.0		48.0	8.0	NM_005090	B4DRT9|O95712|Q19KD5|Q19KD6|Q59GF9|Q8TB10|Q9UKV7	Missense_Mutation	SNP	ENST00000452633.1	hg19	CCDS45241.1	.	.	.	.	.	.	.	.	.	.	.	26.4	4.738644	0.89573	.	.	ENSG00000168970;ENSG00000168970;ENSG00000168970;ENSG00000243708	ENST00000382448;ENST00000342159;ENST00000458483;ENST00000452633	T;T;T;T	0.04502	3.61;3.61;3.61;3.61	5.31	5.31	0.75309	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	0.000000	0.64402	D	0.000002	T	0.21962	0.0529	M	0.79258	2.445	0.47009	D	0.999281	D;D;D;D	0.89917	1.0;0.999;1.0;0.998	D;D;D;D	0.97110	1.0;0.996;1.0;0.994	T	0.00360	-1.1790	10	0.59425	D	0.04	-1.8065	14.5476	0.68044	1.0:0.0:0.0:0.0	.	442;673;143;673	P0C869;P0C869-7;P0C869-4;P0C869-6	PA24B_HUMAN;.;.;.	E	673;673;442;442	ENSP00000371886:K673E;ENSP00000342785:K673E;ENSP00000416610:K442E;ENSP00000396045:K442E	ENSP00000342785:K673E	K	+	1	0	JMJD7-PLA2G4B;PLA2G4B	39924777	1.000000	0.71417	0.999000	0.59377	0.918000	0.54935	7.148000	0.77389	2.146000	0.66826	0.459000	0.35465	AAA	.	.		0.562	PLA2G4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000345969.1	NM_001114633		G	42137485	A	G	42137485	3	3	245	1	0	0	0	0	1	0	0	0	7964	131	5	2	2091	2	JMJD7-PLA2G4B	15	42137485	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	13676686	42137485	60393907	186	33656										
TP53BP1	7158	hgsc.bcm.edu	37	chr15	43700285	43700285	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gaaaggattttcacggggttGcctatgaaggagacaggaaa	14	5	1	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr15:43700285G>T	ENST00000263801.3	-	27	5839	c.5587C>A	c.(5587-5589)Caa>Aaa	p.Q1863K	TP53BP1_ENST00000450115.2_Splice_Site_p.Q1866K|TP53BP1_ENST00000382039.3_Splice_Site_p.Q1818K|TP53BP1_ENST00000382044.4_Splice_Site_p.Q1868K	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	1863					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)			breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		TCACGGGGTTGCCTATGAAGG	0.448								Other conserved DNA damage response genes																													p.Q1868K		Atlas-SNP	.											.	TP53BP1	157	.	0			c.C5602A						.						65	64	64					15																	43700285		2201	4298	6499	SO:0001630	splice_region_variant	7158	exon27			GGGGTTGCCTATG	U09477	CCDS10096.1, CCDS45250.1, CCDS45251.1	15q15-q21	2007-08-02	2007-08-02		ENSG00000067369	ENSG00000067369			11999	protein-coding gene	gene with protein product		605230	"tumor protein p53-binding protein, 1"			8016121, 9748285	Standard	NM_005657		Approved	53BP1, p202	uc001zrr.4	Q12888	OTTHUMG00000059757	ENST00000263801.3:c.5586-1C>A	chr15.hg19:g.43700285G>T		71.0	0.0		35.0	5.0	NM_001141980	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Missense_Mutation	SNP	ENST00000263801.3	hg19	CCDS10096.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.330941	0.81690	.	.	ENSG00000067369	ENST00000263801;ENST00000382044;ENST00000382039;ENST00000450115	D;D;D;D	0.86297	-2.1;-2.1;-2.1;-2.1	5.36	5.36	0.76844	BRCT (1);	0.195493	0.46442	D	0.000296	D	0.85115	0.5623	L	0.50333	1.59	0.42923	D	0.994298	B;B;B	0.33549	0.417;0.246;0.355	B;B;B	0.35470	0.108;0.189;0.203	T	0.82898	-0.0229	10	0.29301	T	0.29	-10.7917	18.4214	0.90591	0.0:0.0:1.0:0.0	.	1863;1868;1866	Q12888;Q12888-2;F8VY86	TP53B_HUMAN;.;.	K	1863;1868;1818;1866	ENSP00000263801:Q1863K;ENSP00000371475:Q1868K;ENSP00000371470:Q1818K;ENSP00000393497:Q1866K	ENSP00000263801:Q1863K	Q	-	1	0	TP53BP1	41487577	1.000000	0.71417	1.000000	0.80357	0.777000	0.43975	7.589000	0.82641	2.663000	0.90544	0.591000	0.81541	CAA	.	.		0.448	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3		Missense_Mutation	T	43700285	G	T	43700285	5	4	245	1	0	0	0	0	0	0	1	0	16398	1333	46	3	339	3	TP53BP1	15	43700285	Splice_Site	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	1562800	43700285	58831107	187	33657										
SLC12A1	6557	hgsc.bcm.edu	37	chr15	48577419	48577419	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ttaaaaaagctggcaagttgAacattactaagacaacgcct	7	8	0	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr15:48577419A>T	ENST00000558405.1	+	20	2616	c.2602A>T	c.(2602-2604)Aac>Tac	p.N868Y	SLC12A1_ENST00000396577.3_Missense_Mutation_p.N868Y|SLC12A1_ENST00000380993.3_Missense_Mutation_p.N868Y			Q13621	S12A1_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 1	868					cell death (GO:0008219)|chemical homeostasis (GO:0048878)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|kidney development (GO:0001822)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:potassium:chloride symporter activity (GO:0008511)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|prostate(2)|skin(1)	59		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Potassium Chloride(DB00761)|Quinethazone(DB01325)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	TGGCAAGTTGAACATTACTAA	0.373																																					p.N868Y		Atlas-SNP	.											.	SLC12A1	243	.	0			c.A2602T						.						106	113	111					15																	48577419		2198	4297	6495	SO:0001583	missense	6557	exon21			AAGTTGAACATTA		CCDS10129.2, CCDS53940.1	15q15-q21	2013-07-18	2013-07-18		ENSG00000074803	ENSG00000074803		"Solute carriers"	10910	protein-coding gene	gene with protein product		600839				8640224	Standard	NM_000338		Approved	NKCC2	uc010bem.3	Q13621	OTTHUMG00000131495	ENST00000558405.1:c.2602A>T	chr15.hg19:g.48577419A>T	ENSP00000453409:p.Asn868Tyr	223.0	1.0		156.0	90.0	NM_001184832	A8JYA2|E9PDW4	Missense_Mutation	SNP	ENST00000558405.1	hg19	CCDS10129.2	.	.	.	.	.	.	.	.	.	.	A	9.497	1.102260	0.20632	.	.	ENSG00000074803	ENST00000380993;ENST00000396577	D;D	0.85339	-1.97;-1.97	5.52	1.61	0.23674	.	0.245554	0.46758	D	0.000277	T	0.76543	0.4002	L	0.34521	1.04	0.35231	D	0.776947	B;B	0.22541	0.017;0.071	B;B	0.28385	0.028;0.089	T	0.74262	-0.3722	10	0.62326	D	0.03	.	8.3507	0.32301	0.5657:0.3659:0.0684:0.0	.	868;868	E9PDW4;Q13621	.;S12A1_HUMAN	Y	868	ENSP00000370381:N868Y;ENSP00000379822:N868Y	ENSP00000370381:N868Y	N	+	1	0	SLC12A1	46364711	1.000000	0.71417	0.998000	0.56505	0.133000	0.20885	2.108000	0.41854	0.446000	0.26666	0.533000	0.62120	AAC	.	.		0.373	SLC12A1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417131.1			T	48577419	A	T	48577419	3	4	245	1	0	0	0	0	1	0	0	0	14397	246	9	4	2780	4	SLC12A1	15	48577419	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	4877134	48577419	53953973	188	33658										
PRTG	283659	hgsc.bcm.edu	37	chr15	55931838	55931838	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	accattaacaggagctacatAcgtttgaaggtacagaacca	8	9	0	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr15:55931838A>T	ENST00000389286.4	-	13	2372		c.e13+1			NM_173814.4	NP_776175.2			protogenin											breast(1)|endometrium(6)|kidney(4)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)		GGAGCTACATACGTTTGAAGG	0.493																																					.		Atlas-SNP	.											.	PRTG	110	.	0			c.2324+2T>A						.						115	118	117					15																	55931838		2003	4172	6175	SO:0001630	splice_region_variant	283659	exon14			CTACATACGTTTG	AK098622	CCDS42040.1	15q21.3	2013-02-11	2010-06-24		ENSG00000166450	ENSG00000166450		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	26373	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 5"	613261	"protogenin homolog (Gallus gallus)"				Standard	NM_173814		Approved	FLJ25756, IGDCC5	uc002adg.3	Q2VWP7		ENST00000389286.4:c.2324+1T>A	chr15.hg19:g.55931838A>T		102.0	0.0		91.0	31.0	NM_173814		Splice_Site	SNP	ENST00000389286.4	hg19	CCDS42040.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.727835	0.89390	.	.	ENSG00000166450	ENST00000389286	.	.	.	5.81	5.81	0.92471	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3502	0.74376	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PRTG	53719130	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.625000	0.90965	2.213000	0.71641	0.533000	0.62120	.	.	.		0.493	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814	Intron	T	55931838	A	T	55931838	5	4	245	1	0	0	0	0	0	0	1	0	12650	405	14	4	1158	4	PRTG	15	55931838	Splice_Site	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	7354419	55931838	46599554	189	33659										
RFX7	64864	hgsc.bcm.edu	37	chr15	56388218	56388218	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gtctgtattacttttctgccCcaaaagggcactaggtgtct	9	10	3	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr15:56388218C>T	ENST00000559447.2	-	9	1688	c.1417G>A	c.(1417-1419)Ggg>Agg	p.G473R	RFX7_ENST00000317318.6_Missense_Mutation_p.G570R|RFX7_ENST00000423270.1_Missense_Mutation_p.G570R|RFX7_ENST00000422057.1_Missense_Mutation_p.G473R			Q2KHR2	RFX7_HUMAN	regulatory factor X, 7	473					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						CTTTTCTGCCCCAAAAGGGCA	0.453																																					p.G570R		Atlas-SNP	.											.	RFX7	170	.	0			c.G1708A						.						65	59	61					15																	56388218		1888	4098	5986	SO:0001583	missense	64864	exon9			TCTGCCCCAAAAG			15q21.3	2008-08-04	2008-08-04	2008-08-04		ENSG00000181827			25777	protein-coding gene	gene with protein product		612660	"regulatory factor X domain containing 2"	RFXDC2			Standard	NM_022841		Approved	FLJ12994	uc010bfn.3	Q2KHR2		ENST00000559447.2:c.1417G>A	chr15.hg19:g.56388218C>T	ENSP00000453281:p.Gly473Arg	64.0	0.0		29.0	7.0	NM_022841	Q6ZRR1|Q6ZTY6|Q8N3J0|Q9H7A9|Q9H956	Missense_Mutation	SNP	ENST00000559447.2	hg19		.	.	.	.	.	.	.	.	.	.	C	13.90	2.375275	0.42105	.	.	ENSG00000181827	ENST00000422057;ENST00000317318;ENST00000423270	T;T;T	0.54071	0.6;0.59;0.6	5.09	5.09	0.68999	.	0.000000	0.56097	D	0.000025	T	0.34164	0.0888	N	0.19112	0.55	0.45791	D	0.998677	P;P	0.46706	0.745;0.883	B;B	0.36719	0.169;0.231	T	0.33059	-0.9883	10	0.62326	D	0.03	-2.5911	11.0249	0.47739	0.0:0.9147:0.0:0.0853	.	473;473	Q2KHR2;C9JU50	RFX7_HUMAN;.	R	473;570;570	ENSP00000387504:G473R;ENSP00000313299:G570R;ENSP00000397644:G570R	ENSP00000313299:G570R	G	-	1	0	RFX7	54175510	0.352000	0.24895	0.868000	0.34077	0.973000	0.67179	4.349000	0.59385	2.336000	0.79503	0.655000	0.94253	GGG	.	.		0.453	RFX7-001	KNOWN	non_canonical_U12|basic	protein_coding	protein_coding	OTTHUMT00000418841.3	NM_022841		T	56388218	C	T	56388218	3	4	245	1	0	0	0	0	1	0	0	0	13283	623	22	3	2678	3	RFX7	15	56388218	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	456380	56388218	46143174	190	33660										
RLBP1	6017	hgsc.bcm.edu	37	chr15	89754011	89754011	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	catggctggtggatgaagtgGatggctttgaaccgggctgg	18	6	0	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr15:89754011G>T	ENST00000268125.5	-	8	1153	c.714C>A	c.(712-714)atC>atA	p.I238I		NM_000326.4	NP_000317.1	P12271	RLBP1_HUMAN	retinaldehyde binding protein 1	238	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	cell body (GO:0044297)|cytosol (GO:0005829)	11-cis retinal binding (GO:0005502)|retinol binding (GO:0019841)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(1)|prostate(1)|skin(1)	18	Lung NSC(78;0.0472)|all_lung(78;0.089)				Vitamin A(DB00162)	GGATGAAGTGGATGGCTTTGA	0.582																																					p.I238I		Atlas-SNP	.											.	RLBP1	34	.	0			c.C714A						.						155	118	131					15																	89754011		2200	4299	6499	SO:0001819	synonymous_variant	6017	exon8			GAAGTGGATGGCT	BC004199	CCDS32324.1	15q26.1	2007-07-16	2001-11-28			ENSG00000140522			10024	protein-coding gene	gene with protein product		180090	"retinaldehyde-binding protein 1"			1733864, 9326942	Standard	NM_000326		Approved	CRALBP	uc002bnl.3	P12271		ENST00000268125.5:c.714C>A	chr15.hg19:g.89754011G>T		202.0	0.0		211.0	87.0	NM_000326	B2R667	Silent	SNP	ENST00000268125.5	hg19	CCDS32324.1																																																																																			.	.		0.582	RLBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421135.1	NM_000326		T	89754011	G	T	89754011	2	4	245	1	0	0	0	0	0	0	0	1	13403	1164	41	3		3	RLBP1	15	89754011	Silent	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	33365793	89754011	12777381	191	33661										
FLYWCH1	84256	hgsc.bcm.edu	37	chr16	2980531	2980531	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ggtgtactggaagtgccgccAacatgctgagctgggctgcc	15	11	0	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr16:2980531A>G	ENST00000253928.9	+	4	851	c.446A>G	c.(445-447)cAa>cGa	p.Q149R	FLYWCH1_ENST00000399667.2_Missense_Mutation_p.Q149R|FLYWCH1_ENST00000416288.2_Missense_Mutation_p.Q148R			Q4VC44	FWCH1_HUMAN	FLYWCH-type zinc finger 1	149						cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(1)|lung(3)	4						AAGTGCCGCCAACATGCTGAG	0.672																																					p.Q148R		Atlas-SNP	.											.	FLYWCH1	27	.	0			c.A443G						.						11	12	12					16																	2980531		1973	4130	6103	SO:0001583	missense	84256	exon4			GCCGCCAACATGC	AL136585	CCDS45390.1	16p13.3	2013-01-10	2007-06-21	2007-06-21	ENSG00000059122	ENSG00000059122		"Zinc fingers"	25404	protein-coding gene	gene with protein product						11230166, 10997877	Standard	XM_006720959		Approved	DKFZp761A132	uc002csc.3	Q4VC44		ENST00000253928.9:c.446A>G	chr16.hg19:g.2980531A>G	ENSP00000253928:p.Gln149Arg	50.0	0.0		69.0	27.0	NM_020912	D3DUA1|Q6ZSQ1|Q8WV62|Q9BQG6|Q9BUS5|Q9HCM0	Missense_Mutation	SNP	ENST00000253928.9	hg19		.	.	.	.	.	.	.	.	.	.	A	8.605	0.887820	0.17540	.	.	ENSG00000059122	ENST00000399667;ENST00000253928;ENST00000416288	.	.	.	3.42	1.16	0.20824	Zinc finger, FLYWCH-type (1);	.	.	.	.	T	0.27765	0.0683	L	0.31664	0.95	0.09310	N	1	B;B	0.25904	0.033;0.137	B;B	0.25140	0.018;0.058	T	0.22695	-1.0209	8	0.52906	T	0.07	.	5.022	0.14365	0.7451:0.0:0.2549:0.0	.	149;148	Q4VC44;Q4VC44-2	FWCH1_HUMAN;.	R	149;149;148	.	ENSP00000253928:Q149R	Q	+	2	0	FLYWCH1	2920532	0.009000	0.17119	0.013000	0.15412	0.329000	0.28539	2.019000	0.41001	0.218000	0.20820	0.533000	0.62120	CAA	.	.		0.672	FLYWCH1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000436479.1	NM_032296		G	2980531	A	G	2980531	3	3	245	1	0	0	0	0	1	0	0	0	5955	130	5	2	449	2	FLYWCH1	16	2980531	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10		2980531	87374222	192	33662										
CCDC64B	146439	hgsc.bcm.edu	37	chr16	3085406	3085406	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ggaatgagtcccgccgctccAgcacaaaggggaagaagccc	13	13	0	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr16:3085406A>T	ENST00000572449.1	-	2	154	c.92T>A	c.(91-93)cTg>cAg	p.L31Q	RP11-473M20.5_ENST00000382225.3_RNA|CCDC64B_ENST00000573514.1_5'Flank|CCDC64B_ENST00000389347.4_Missense_Mutation_p.L31Q			A1A5D9	BICR2_HUMAN	coiled-coil domain containing 64B	31										breast(1)|endometrium(2)|large_intestine(1)	4						CCGCCGCTCCAGCACAAAGGG	0.677																																					p.L31Q		Atlas-SNP	.											.	CCDC64B	19	.	0			c.T92A						.						13	16	15					16																	3085406		1871	4084	5955	SO:0001583	missense	146439	exon1			CGCTCCAGCACAA	BC128602	CCDS45393.1	16p13.3	2008-07-04				ENSG00000162069			33584	protein-coding gene	gene with protein product							Standard	NM_001103175		Approved		uc002ctf.4	A1A5D9		ENST00000572449.1:c.92T>A	chr16.hg19:g.3085406A>T	ENSP00000459043:p.Leu31Gln	59.0	0.0		66.0	39.0	NM_001103175	Q658L9	Missense_Mutation	SNP	ENST00000572449.1	hg19	CCDS45393.1	.	.	.	.	.	.	.	.	.	.	a	17.24	3.340349	0.60963	.	.	ENSG00000162069	ENST00000389347	T	0.31510	1.49	5.08	5.08	0.68730	.	0.135593	0.31976	N	0.006764	T	0.47563	0.1452	L	0.50333	1.59	0.41676	D	0.989269	D	0.71674	0.998	D	0.69142	0.962	T	0.48210	-0.9055	10	0.62326	D	0.03	-16.8351	12.8084	0.57626	1.0:0.0:0.0:0.0	.	31	A1A5D9	BICR2_HUMAN	Q	31	ENSP00000373998:L31Q	ENSP00000373998:L31Q	L	-	2	0	CCDC64B	3025407	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	2.470000	0.45119	1.913000	0.55393	0.375000	0.23000	CTG	.	.		0.677	CCDC64B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436991.1			T	3085406	A	T	3085406	3	4	245	1	0	0	0	0	1	0	0	0	2838	188	7	4	1470	4	CCDC64B	16	3085406	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	104875	3085406	87269347	193	33663										
A2BP1	54715	hgsc.bcm.edu	37	chr16	7629893	7629893	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ccaatatccccttcaggttcCgggatccggacctcagacaa	8	15	2	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr16:7629893C>T	ENST00000550418.1	+	6	1373	c.385C>T	c.(385-387)Cgg>Tgg	p.R129W	RBFOX1_ENST00000535565.2_Intron|RBFOX1_ENST00000340209.4_Missense_Mutation_p.R134W|RBFOX1_ENST00000355637.4_Missense_Mutation_p.R149W|RBFOX1_ENST00000547372.1_Missense_Mutation_p.R172W|RBFOX1_ENST00000311745.5_Missense_Mutation_p.R149W|RBFOX1_ENST00000553186.1_Missense_Mutation_p.R129W|RBFOX1_ENST00000547338.1_Missense_Mutation_p.R129W|RBFOX1_ENST00000436368.2_Missense_Mutation_p.R149W|RBFOX1_ENST00000422070.4_Missense_Mutation_p.R172W|RBFOX1_ENST00000552089.1_Missense_Mutation_p.R164W	NM_018723.3	NP_061193.2	Q9NWB1	RFOX1_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 1	129	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|neuromuscular process controlling balance (GO:0050885)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|RNA transport (GO:0050658)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	nucleotide binding (GO:0000166)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|lung(17)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)	55						CTTCAGGTTCCGGGATCCGGA	0.542																																					p.R149W	Ovarian(157;934 2567 15163 39509)	Atlas-SNP	.											RBFOX1_ENST00000550418,NS,adenoma,0,6	RBFOX1	341	.	0			c.C445T						.						99	91	93					16																	7629893		2197	4300	6497	SO:0001583	missense	54715	exon3			AGGTTCCGGGATC	AF107203	CCDS10531.1, CCDS10532.1, CCDS45405.1, CCDS55983.1, CCDS55984.1	16p13.3	2013-02-12			ENSG00000078328	ENSG00000078328		"RNA binding motif (RRM) containing"	18222	protein-coding gene	gene with protein product	"ataxin 2-binding protein 1", "hexaribonucleotide binding protein 1"	605104				10814712, 16260614	Standard	NM_018723		Approved	A2BP1, FOX-1, HRNBP1	uc002cyy.2	Q9NWB1	OTTHUMG00000129551	ENST00000550418.1:c.385C>T	chr16.hg19:g.7629893C>T	ENSP00000450031:p.Arg129Trp	165.0	0.0		214.0	103.0	NM_145891	Q7Z7I7|Q8TAE3|Q8TAF2|Q8WYB2|Q9NS20	Missense_Mutation	SNP	ENST00000550418.1	hg19	CCDS55983.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.555076	0.86231	.	.	ENSG00000078328	ENST00000547605;ENST00000550418;ENST00000553186;ENST00000547372;ENST00000422070;ENST00000552089;ENST00000551752;ENST00000547338;ENST00000436368;ENST00000311745;ENST00000355637;ENST00000352951;ENST00000340209	T;T;T;T;T;T;T;T;T;T;T;T	0.36340	2.33;2.33;2.33;2.33;2.33;1.26;2.33;2.33;2.33;2.33;2.33;2.33	5.39	5.39	0.77823	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.57125	0.2032	M	0.64170	1.965	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	0.999;0.999;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.91635	0.99;0.996;0.999;0.996;0.996;0.996;0.999;0.996	T	0.59332	-0.7474	10	0.87932	D	0	-7.8681	14.0697	0.64852	0.1505:0.8495:0.0:0.0	.	149;172;149;149;149;129;129;172	F8WAC5;B7Z1U7;Q9NWB1-2;Q9NWB1-4;Q9NWB1-5;Q9NWB1-3;Q9NWB1;F8VZG9	.;.;.;.;.;.;RFOX1_HUMAN;.	W	128;129;129;172;172;164;129;129;149;149;149;149;134	ENSP00000450402:R128W;ENSP00000450031:R129W;ENSP00000447753:R129W;ENSP00000446842:R172W;ENSP00000391269:R172W;ENSP00000448496:R164W;ENSP00000447281:R129W;ENSP00000447717:R129W;ENSP00000402745:R149W;ENSP00000309117:R149W;ENSP00000347855:R149W;ENSP00000344196:R134W	ENSP00000309117:R149W	R	+	1	2	RBFOX1	7569894	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.713000	0.47194	2.537000	0.85549	0.655000	0.94253	CGG	.	.		0.542	RBFOX1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409492.2	NM_145891		T	7629893	C	T	7629893	3	4	245	1	0	0	0	0	1	0	0	0	3	643	23	1	486	1	A2BP1	16	7629893	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	4544487	7629893	82724860	194	33664										
KIAA0430	9665	hgsc.bcm.edu	37	chr16	15727694	15727694	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gtccagctactgcaacttctGgtgacccttaagaaatgtta	8	10	1	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr16:15727694G>T	ENST00000396368.3	-	5	1219	c.1013C>A	c.(1012-1014)cCa>cAa	p.P338Q	KIAA0430_ENST00000548025.1_Intron|KIAA0430_ENST00000344181.3_Missense_Mutation_p.P160Q|KIAA0430_ENST00000540441.2_Missense_Mutation_p.P338Q|KIAA0430_ENST00000551742.1_Missense_Mutation_p.P338Q|KIAA0430_ENST00000602337.1_Intron	NM_001184998.1|NM_001184999.1|NM_014647.3	NP_001171927.1|NP_001171928.1|NP_055462.2	Q9Y4F3	MARF1_HUMAN	KIAA0430	338					double-strand break repair (GO:0006302)|female meiotic division (GO:0007143)|negative regulation of phosphatase activity (GO:0010923)|oogenesis (GO:0048477)|regulation of gene expression (GO:0010468)	membrane (GO:0016020)|peroxisome (GO:0005777)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(4)|endometrium(8)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(5)|skin(1)	40						TGCAACTTCTGGTGACCCTTA	0.398																																					p.P338Q		Atlas-SNP	.											.	KIAA0430	154	.	0			c.C1013A						.						55	52	53					16																	15727694		1813	4082	5895	SO:0001583	missense	9665	exon5			ACTTCTGGTGACC	AB007890	CCDS10562.2, CCDS53990.1, CCDS55991.1	16p13.11	2013-01-11			ENSG00000166783	ENSG00000166783		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	29562	protein-coding gene	gene with protein product	"limkain b1", "protein phosphatase 1, regulatory subunit 34", "meiosis arrest female 1"	614593				9455477, 10493829, 15932519, 22442484, 23090997	Standard	NM_014647		Approved	LKAP, PPP1R34, Marf1	uc010uzw.2	Q9Y4F3	OTTHUMG00000129884	ENST00000396368.3:c.1013C>A	chr16.hg19:g.15727694G>T	ENSP00000379654:p.Pro338Gln	110.0	0.0		133.0	51.0	NM_014647	A8MSK2|B2RNX2|B4DYY9|B7ZMG1|B7ZMG2|F8VV09|Q6P1R6|Q8WYR2|Q9Y4J9	Missense_Mutation	SNP	ENST00000396368.3	hg19	CCDS10562.2	.	.	.	.	.	.	.	.	.	.	G	28.5	4.927974	0.92389	.	.	ENSG00000166783	ENST00000396368;ENST00000540441;ENST00000321370;ENST00000344181;ENST00000551742;ENST00000551298	.	.	.	5.78	5.78	0.91487	.	0.098545	0.64402	D	0.000001	T	0.74107	0.3673	L	0.56769	1.78	0.37147	D	0.901981	P;P	0.45827	0.867;0.79	P;P	0.54815	0.761;0.581	T	0.76963	-0.2764	9	0.66056	D	0.02	.	20.3754	0.98918	0.0:0.0:1.0:0.0	.	337;337	Q9Y4F3-5;Q9Y4F3	.;LKAP_HUMAN	Q	338;338;337;160;338;338	.	ENSP00000315718:P337Q	P	-	2	0	KIAA0430	15635195	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.221000	0.89774	2.894000	0.99253	0.591000	0.81541	CCA	.	.		0.398	KIAA0430-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252131.2	NM_014647		T	15727694	G	T	15727694	3	4	245	1	0	0	0	0	1	0	0	0	8186	1348	47	3	4310	3	KIAA0430	16	15727694	Missense_Mutation	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	8097801	15727694	74627059	195	33665										
MYH11	4629	hgsc.bcm.edu	37	chr16	15853461	15853461	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tctcaaatccagctatatccAggatccccaggaaggaagcc	8	13	1	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr16:15853461A>T	ENST00000300036.5	-	12	1482	c.1373T>A	c.(1372-1374)cTg>cAg	p.L458Q	MYH11_ENST00000452625.2_Missense_Mutation_p.L465Q|MYH11_ENST00000396324.3_Missense_Mutation_p.L465Q|MYH11_ENST00000576790.2_Missense_Mutation_p.L458Q	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	458	Myosin motor.				axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						AGCTATATCCAGGATCCCCAG	0.532			T	CBFB	AML																																p.L465Q		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"myosin, heavy polypeptide 11, smooth muscle"		L	.	MYH11	520	.	0			c.T1394A						.						144	135	138					16																	15853461		2197	4300	6497	SO:0001583	missense	4629	exon13			ATATCCAGGATCC	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"Myosins / Myosin superfamily : Class II"	7569	protein-coding gene	gene with protein product		160745	"myosin, heavy polypeptide 11, smooth muscle"			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.1373T>A	chr16.hg19:g.15853461A>T	ENSP00000300036:p.Leu458Gln	122.0	0.0		125.0	63.0	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Missense_Mutation	SNP	ENST00000300036.5	hg19	CCDS10565.1	.	.	.	.	.	.	.	.	.	.	A	28.9	4.961010	0.92791	.	.	ENSG00000133392	ENST00000300036;ENST00000338282;ENST00000396320;ENST00000396324;ENST00000452625	D;D;D;D	0.84146	-1.81;-1.81;-1.81;-1.81	5.75	5.75	0.90469	Myosin head, motor domain (3);	0.000000	0.64402	D	0.000004	D	0.96188	0.8757	H	0.99609	4.655	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.999;0.999	D	0.98104	1.0416	10	0.87932	D	0	.	15.2367	0.73436	1.0:0.0:0.0:0.0	.	465;458;458;465;458;465	B1PS43;D2JYH7;P35749;Q3MNF1;Q3MIV8;Q3MNF0	.;.;MYH11_HUMAN;.;.;.	Q	458;458;465;465;465	ENSP00000300036:L458Q;ENSP00000345136:L458Q;ENSP00000379616:L465Q;ENSP00000407821:L465Q	ENSP00000300036:L458Q	L	-	2	0	MYH11	15760962	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.339000	0.96797	2.185000	0.69588	0.459000	0.35465	CTG	.	.		0.532	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113		T	15853461	A	T	15853461	3	4	245	1	0	0	0	0	1	0	0	0	10040	188	7	4	4700	4	MYH11	16	15853461	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	125767	15853461	74501292	196	33666										
CHD9	80205	hgsc.bcm.edu	37	chr16	53341643	53341643	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	atttgtcaaacagttctgaaAggaaagtggccttcagctag	10	7	3	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr16:53341643A>C	ENST00000398510.3	+	32	6918	c.6831A>C	c.(6829-6831)aaA>aaC	p.K2277N	CHD9_ENST00000447540.1_Missense_Mutation_p.K2278N|CHD9_ENST00000564845.1_Missense_Mutation_p.K2277N|CHD9_ENST00000566029.1_Missense_Mutation_p.K2277N			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	2277					cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				CAGTTCTGAAAGGAAAGTGGC	0.403																																					p.K2277N		Atlas-SNP	.											.	CHD9	203	.	0			c.A6831C						.						58	58	58					16																	53341643		1915	4125	6040	SO:0001583	missense	80205	exon33			TCTGAAAGGAAAG	AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.6831A>C	chr16.hg19:g.53341643A>C	ENSP00000381522:p.Lys2277Asn	165.0	0.0		183.0	31.0	NM_025134	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Missense_Mutation	SNP	ENST00000398510.3	hg19		.	.	.	.	.	.	.	.	.	.	A	15.32	2.800049	0.50208	.	.	ENSG00000177200	ENST00000447540;ENST00000398510;ENST00000450543	D;D	0.88431	-2.33;-2.38	5.71	4.62	0.57501	.	0.000000	0.64402	D	0.000008	D	0.91616	0.7351	L	0.55481	1.735	0.53005	D	0.999963	D;D;D;D;D	0.89917	0.999;0.999;1.0;0.999;1.0	D;D;D;D;D	0.85130	0.994;0.991;0.997;0.994;0.996	D	0.89847	0.4007	10	0.38643	T	0.18	-22.8772	9.6337	0.39795	0.8479:0.0:0.1521:0.0	.	343;2277;2278;2277;2277	C9JR69;B7ZML1;Q3L8U1-3;Q3L8U1;Q3L8U1-2	.;.;.;CHD9_HUMAN;.	N	2278;2277;343	ENSP00000396345:K2278N;ENSP00000381522:K2277N	ENSP00000381522:K2277N	K	+	3	2	CHD9	51899144	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.335000	0.43929	1.095000	0.41419	0.528000	0.53228	AAA	.	.		0.403	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134		C	53341643	A	C	53341643	3	2	245	1	0	0	0	0	1	0	0	0	3334	69	3	5	6957	5	CHD9	16	53341643	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	37488182	53341643	37013110	197	33667										
GPR114	221188	hgsc.bcm.edu	37	chr16	57608882	57608882	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	aagtgtcagggcctgccatgAcactgtcactgtgctgggcc	13	12	2	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr16:57608882A>G	ENST00000340339.4	+	11	1887	c.1364A>G	c.(1363-1365)gAc>gGc	p.D455G	GPR114_ENST00000394361.4_3'UTR|GPR114_ENST00000349457.3_Missense_Mutation_p.D455G	NM_153837.1	NP_722579.1	Q8IZF4	GP114_HUMAN	G protein-coupled receptor 114	455					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(5)|ovary(2)|stomach(1)|urinary_tract(1)	23						GCCTGCCATGACACTGTCACT	0.642																																					p.D455G		Atlas-SNP	.											.	GPR114	52	.	0			c.A1364G						.						86	66	73					16																	57608882		2198	4300	6498	SO:0001583	missense	221188	exon11			GCCATGACACTGT	AY140956	CCDS10785.1	16q13	2014-08-08			ENSG00000159618	ENSG00000159618		"-", "GPCR / Class B : Orphans"	19010	protein-coding gene	gene with protein product						12435584	Standard	NM_153837		Approved	PGR27	uc002ely.3	Q8IZF4	OTTHUMG00000133461	ENST00000340339.4:c.1364A>G	chr16.hg19:g.57608882A>G	ENSP00000342981:p.Asp455Gly	36.0	0.0		36.0	6.0	NM_153837	B3KXZ5|Q6ZMH7|Q6ZML4|Q86SL8|Q8IZ14	Missense_Mutation	SNP	ENST00000340339.4	hg19	CCDS10785.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.95|13.95	2.390974|2.390974	0.42410|0.42410	.|.	.|.	ENSG00000159618|ENSG00000159618	ENST00000340339;ENST00000349457|ENST00000394361	T;T|.	0.44083|.	0.93;0.93|.	5.56|5.56	5.56|5.56	0.83823|0.83823	GPCR, family 2-like (1);|.	0.100786|.	0.43579|.	D|.	0.000551|.	T|T	0.52964|0.52964	0.1767|0.1767	L|L	0.55017|0.55017	1.72|1.72	0.38398|0.38398	D|D	0.945598|0.945598	D|B	0.89917|0.28605	1.0|0.217	D|B	0.97110|0.24701	1.0|0.055	T|T	0.58578|0.58578	-0.7612|-0.7612	10|8	0.19147|0.62326	T|D	0.46|0.03	.|.	13.0786|13.0786	0.59100|0.59100	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	455|416	Q8IZF4|B4E148	GP114_HUMAN|.	G|A	455|416	ENSP00000342981:D455G;ENSP00000290823:D455G|.	ENSP00000342981:D455G|ENSP00000377888:T416A	D|T	+|+	2|1	0|0	GPR114|GPR114	56166383|56166383	0.997000|0.997000	0.39634|0.39634	0.454000|0.454000	0.27019|0.27019	0.326000|0.326000	0.28443|0.28443	3.773000|3.773000	0.55333|0.55333	2.116000|2.116000	0.64780|0.64780	0.402000|0.402000	0.26972|0.26972	GAC|ACA	.	.		0.642	GPR114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257336.3	NM_153837		G	57608882	A	G	57608882	3	3	245	1	0	0	0	0	1	0	0	0	6639	275	10	2	1402	2	GPR114	16	57608882	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	4267239	57608882	32745871	198	33668										
CCDC135	84229	hgsc.bcm.edu	37	chr16	57731872	57731872	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	acgctccagaatggaggtccTgagggagaaggtggaggagg	19	6	0	3			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr16:57731872T>A	ENST00000360716.3	+	3	232	c.11T>A	c.(10-12)cTg>cAg	p.L4Q	RP11-405F3.4_ENST00000563062.1_RNA|CCDC135_ENST00000336825.8_Missense_Mutation_p.L4Q|CCDC135_ENST00000394337.4_Missense_Mutation_p.L4Q			Q8IY82	CC135_HUMAN		4					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30						ATGGAGGTCCTGAGggagaag	0.607																																					p.L4Q		Atlas-SNP	.											.	CCDC135	97	.	0			c.T11A						.						70	71	71					16																	57731872		2198	4300	6498	SO:0001583	missense	84229	exon2			AGGTCCTGAGGGA																												ENST00000360716.3:c.11T>A	chr16.hg19:g.57731872T>A	ENSP00000353942:p.Leu4Gln	52.0	0.0		39.0	8.0	NM_032269	A8K943|Q8NAA0|Q9H080	Missense_Mutation	SNP	ENST00000360716.3	hg19	CCDS10787.1	.	.	.	.	.	.	.	.	.	.	T	16.15	3.042265	0.55003	.	.	ENSG00000159625	ENST00000394337;ENST00000336825;ENST00000360716	T;T;T	0.19250	2.6;2.16;2.6	4.3	4.3	0.51218	.	0.000000	0.47455	D	0.000228	T	0.41627	0.1167	M	0.66939	2.045	0.31928	N	0.612499	D;D	0.76494	0.999;0.999	D;D	0.87578	0.998;0.998	T	0.52011	-0.8632	10	0.87932	D	0	-11.9756	10.1444	0.42755	0.0:0.0:0.0:1.0	.	4;4	Q8IY82-2;Q8IY82	.;CC135_HUMAN	Q	4	ENSP00000377869:L4Q;ENSP00000338938:L4Q;ENSP00000353942:L4Q	ENSP00000338938:L4Q	L	+	2	0	CCDC135	56289373	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	3.418000	0.52721	2.165000	0.68154	0.448000	0.29417	CTG	.	.		0.607	CCDC135-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433323.2			A	57731872	T	A	57731872	3	1	245	1	0	0	0	0	1	0	0	0	2771	1580	55	4	13	4	CCDC135	16	57731872	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	122990	57731872	32622881	199	33669										
CTCF	10664	hgsc.bcm.edu	37	chr16	67662374	67662374	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	cagaagcagcttctcgacatGcacttcaagcgctatcacga	8	13	3	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr16:67662374G>A	ENST00000264010.4	+	9	2064	c.1620G>A	c.(1618-1620)atG>atA	p.M540I	CTCF_ENST00000401394.1_Missense_Mutation_p.M212I	NM_006565.3	NP_006556.1	P49711	CTCF_HUMAN	CCCTC-binding factor (zinc finger protein)	540					chromatin modification (GO:0016568)|chromosome segregation (GO:0007059)|DNA methylation (GO:0006306)|maintenance of DNA methylation (GO:0010216)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome positioning (GO:0016584)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone acetylation (GO:0035065)|regulation of histone methylation (GO:0031060)|regulation of molecular function, epigenetic (GO:0040030)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin insulator sequence binding (GO:0043035)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(6)|central_nervous_system(2)|cervix(1)|endometrium(34)|haematopoietic_and_lymphoid_tissue(7)|kidney(3)|large_intestine(9)|liver(1)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	79		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0166)|Epithelial(162;0.0577)		TTCTCGACATGCACTTCAAGC	0.542																																					p.M540I	Colon(175;1200 1966 6945 23069 27405)	Atlas-SNP	.											.	CTCF	193	.	0			c.G1620A						.						213	177	189					16																	67662374		2198	4300	6498	SO:0001583	missense	10664	exon9			CGACATGCACTTC	U25435	CCDS10841.1, CCDS54029.1	16q21-q22.3	2013-01-08			ENSG00000102974	ENSG00000102974		"Zinc fingers, C2H2-type"	13723	protein-coding gene	gene with protein product	"11 zinc finger transcriptional repressor"	604167				8649389, 18550811	Standard	NM_006565		Approved		uc002etl.3	P49711	OTTHUMG00000137539	ENST00000264010.4:c.1620G>A	chr16.hg19:g.67662374G>A	ENSP00000264010:p.Met540Ile	168.0	0.0		178.0	113.0	NM_006565	B5MC38|Q53XI7|Q59EL8	Missense_Mutation	SNP	ENST00000264010.4	hg19	CCDS10841.1	.	.	.	.	.	.	.	.	.	.	G	18.45	3.626207	0.66901	.	.	ENSG00000102974	ENST00000264010;ENST00000401394	T;T	0.59502	0.26;0.26	5.72	5.72	0.89469	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.42040	0.1185	N	0.12663	0.25	0.80722	D	1	B;B	0.29627	0.023;0.252	B;B	0.25884	0.011;0.064	T	0.26224	-1.0109	10	0.29301	T	0.29	-3.2266	19.488	0.95037	0.0:0.0:1.0:0.0	.	212;540	B5MC38;P49711	.;CTCF_HUMAN	I	540;212	ENSP00000264010:M540I;ENSP00000384707:M212I	ENSP00000264010:M540I	M	+	3	0	CTCF	66219875	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.845000	0.86875	2.702000	0.92279	0.462000	0.41574	ATG	.	.		0.542	CTCF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268870.2	NM_006565		A	67662374	G	A	67662374	3	1	245	1	0	0	0	0	1	0	0	0	4002	1319	46	3	1646	3	CTCF	16	67662374	Missense_Mutation	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	9930502	67662374	22692379	200	33670										
SLC12A4	6560	hgsc.bcm.edu	37	chr16	67985728	67985728	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	acgggagggaggacccacccTggagcacaccagcagctgcc	14	15	0	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr16:67985728T>A	ENST00000316341.3	-	8	1270	c.1130A>T	c.(1129-1131)cAg>cTg	p.Q377L	SLC12A4_ENST00000422611.2_Missense_Mutation_p.Q379L|SLC12A4_ENST00000338335.3_Missense_Mutation_p.Q377L|SLC12A4_ENST00000576616.1_Missense_Mutation_p.Q377L|SLC12A4_ENST00000537830.2_Missense_Mutation_p.Q371L|SLC12A4_ENST00000541864.2_Missense_Mutation_p.Q346L|SLC12A4_ENST00000572037.1_Missense_Mutation_p.Q329L|SLC12A4_ENST00000572010.1_5'Flank	NM_001145961.1|NM_005072.4	NP_001139433.1|NP_005063.1	Q9UP95	S12A4_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 4	377					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(2)|ovary(2)|prostate(4)|skin(2)|urinary_tract(3)	29		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)	Bumetanide(DB00887)|Potassium Chloride(DB00761)	GGACCCACCCTGGAGCACACC	0.632																																					p.Q379L		Atlas-SNP	.											.	SLC12A4	81	.	0			c.A1136T						.						47	34	38					16																	67985728		2198	4300	6498	SO:0001583	missense	6560	exon7			CCACCCTGGAGCA		CCDS10855.1, CCDS54030.1, CCDS54031.1, CCDS54032.1	16q22.1	2013-07-18	2013-07-18		ENSG00000124067	ENSG00000124067		"Solute carriers"	10913	protein-coding gene	gene with protein product		604119				8663127	Standard	NM_005072		Approved	KCC1	uc010ceu.2	Q9UP95	OTTHUMG00000137535	ENST00000316341.3:c.1130A>T	chr16.hg19:g.67985728T>A	ENSP00000318557:p.Gln377Leu	55.0	0.0		72.0	44.0	NM_001145962	B4DF69|B4DR04|B4DZ82|B7ZAV0|F5H066|F5H0S9|F5H3C0|O60632|O75893|Q13953|Q96LD5	Missense_Mutation	SNP	ENST00000316341.3	hg19	CCDS10855.1	.	.	.	.	.	.	.	.	.	.	T	5.354	0.250690	0.10130	.	.	ENSG00000124067	ENST00000422611;ENST00000541864;ENST00000537830;ENST00000338335;ENST00000316341	T;T;T;T;T	0.61980	0.06;0.06;0.06;0.06;0.06	4.33	4.33	0.51752	.	0.148508	0.64402	D	0.000014	T	0.21962	0.0529	N	0.00112	-2.095	0.37516	D	0.917357	B;B;B;B;B;B	0.10296	0.0;0.0;0.003;0.0;0.0;0.0	B;B;B;B;B;B	0.13407	0.0;0.0;0.009;0.0;0.0;0.0	T	0.32693	-0.9897	10	0.11182	T	0.66	.	13.6063	0.62050	0.0:0.0:0.0:1.0	.	379;377;346;371;377;377	F5H3C0;B4DF30;F5H066;F5H0S9;Q9UP95-2;Q9UP95	.;.;.;.;.;S12A4_HUMAN	L	379;346;371;377;377	ENSP00000395983:Q379L;ENSP00000438334:Q346L;ENSP00000445962:Q371L;ENSP00000343374:Q377L;ENSP00000318557:Q377L	ENSP00000318557:Q377L	Q	-	2	0	SLC12A4	66543229	0.776000	0.28616	1.000000	0.80357	0.941000	0.58515	0.775000	0.26689	1.958000	0.56883	0.383000	0.25322	CAG	.	.		0.632	SLC12A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268864.4	NM_005072		A	67985728	T	A	67985728	3	1	245	1	0	0	0	0	1	0	0	0	14400	1580	55	4	2195	4	SLC12A4	16	67985728	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	323354	67985728	22369025	201	33671										
HYDIN	54768	hgsc.bcm.edu	37	chr16	70852337	70852337	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	caccgagtagggcagagggtTctccaacttgatggaggctg	15	9	1	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr16:70852337T>A	ENST00000393567.2	-	84	14716	c.14566A>T	c.(14566-14568)Aac>Tac	p.N4856Y		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	4856					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				GGCAGAGGGTTCTCCAACTTG	0.582																																					p.N4856Y		Atlas-SNP	.											.	HYDIN	788	.	0			c.A14566T						.						37	35	36					16																	70852337		1960	4156	6116	SO:0001583	missense	54768	exon84			GAGGGTTCTCCAA	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.14566A>T	chr16.hg19:g.70852337T>A	ENSP00000377197:p.Asn4856Tyr	69.0	0.0		77.0	16.0	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	hg19	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.825014	0.90955	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.10192	2.9	5.84	5.84	0.93424	.	0.000000	0.35615	U	0.003090	T	0.42040	0.1185	M	0.90252	3.1	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.51180	-0.8738	10	0.87932	D	0	.	15.8872	0.79261	0.0:0.0:0.0:1.0	.	4855	F8WD23	.	Y	4856;4855	ENSP00000377197:N4856Y	ENSP00000313052:N4855Y	N	-	1	0	HYDIN	69409838	1.000000	0.71417	1.000000	0.80357	0.871000	0.50021	7.384000	0.79751	2.227000	0.72691	0.496000	0.49642	AAC	.	.		0.582	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			A	70852337	T	A	70852337	3	1	245	1	0	0	0	0	1	0	0	0	7476	1783	62	4	811	4	HYDIN	16	70852337	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	2866609	70852337	19502416	202	33672										
CDH15	1013	hgsc.bcm.edu	37	chr16	89256721	89256721	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gaatgaggccccgctgcaggCggctgcccttagggctgagc	16	13	0	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr16:89256721C>A	ENST00000289746.2	+	8	1114	c.1049C>A	c.(1048-1050)gCg>gAg	p.A350E		NM_004933.2	NP_004924.1	P55291	CAD15_HUMAN	cadherin 15, type 1, M-cadherin (myotubule)	350	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)	caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(80;0.0261)		CCGCTGCAGGCGGCTGCCCTT	0.637																																					p.A350E		Atlas-SNP	.											.	CDH15	54	.	0			c.C1049A						.						26	26	26					16																	89256721		2195	4297	6492	SO:0001583	missense	1013	exon8			TGCAGGCGGCTGC	D83542	CCDS10976.1	16q24.3	2010-01-26	2008-10-30		ENSG00000129910	ENSG00000129910		"Cadherins / Major cadherins"	1754	protein-coding gene	gene with protein product		114019	"cadherin 15, M-cadherin (myotubule)"	CDH3, CDH14		1427864	Standard	NM_004933		Approved		uc002fmt.3	P55291	OTTHUMG00000138045	ENST00000289746.2:c.1049C>A	chr16.hg19:g.89256721C>A	ENSP00000289746:p.Ala350Glu	161.0	0.0		111.0	22.0	NM_004933		Missense_Mutation	SNP	ENST00000289746.2	hg19	CCDS10976.1	.	.	.	.	.	.	.	.	.	.	C	0.344	-0.948778	0.02304	.	.	ENSG00000129910	ENST00000289746	T	0.61627	0.09	4.37	2.29	0.28610	Cadherin (4);Cadherin-like (1);	0.469026	0.16700	U	0.203181	T	0.48390	0.1497	L	0.53249	1.67	0.09310	N	1	P	0.42993	0.797	B	0.41088	0.347	T	0.33624	-0.9861	10	0.36615	T	0.2	.	6.0759	0.19915	0.0:0.6608:0.1571:0.1821	.	350	P55291	CAD15_HUMAN	E	350	ENSP00000289746:A350E	ENSP00000289746:A350E	A	+	2	0	CDH15	87784222	0.026000	0.19158	0.565000	0.28409	0.023000	0.10783	0.300000	0.19156	0.839000	0.34971	-0.266000	0.10368	GCG	.	.		0.637	CDH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269920.1	NM_004933		A	89256721	C	A	89256721	3	1	245	1	0	0	0	0	1	0	0	0	3102	768	27	1	1079	1	CDH15	16	89256721	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	18404384	89256721	1098032	203	33673										
ACAP1	9744	hgsc.bcm.edu	37	chr17	7251303	7251303	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tgactcatgggagccagaacTagtgaaggtaacttagcgta	12	7	1	3			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr17:7251303T>A	ENST00000158762.3	+	15	1612	c.1406T>A	c.(1405-1407)cTa>cAa	p.L469Q	ACAP1_ENST00000570504.1_5'Flank|ACAP1_ENST00000574499.1_5'Flank|ACAP1_ENST00000575415.1_5'Flank|ACAP1_ENST00000571471.1_5'Flank	NM_014716.3	NP_055531.1	Q15027	ACAP1_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 1	469	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.|Required for interaction with GULP1.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)	endosome (GO:0005768)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(3)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|prostate(3)|skin(1)|urinary_tract(1)	33						GAGCCAGAACTAGTGAAGGTA	0.587																																					p.L469Q		Atlas-SNP	.											.	ACAP1	66	.	0			c.T1406A						.						86	79	82					17																	7251303		2203	4300	6503	SO:0001583	missense	9744	exon15			CAGAACTAGTGAA	D30758	CCDS11101.1	17p13.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000072818	ENSG00000072818		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16467	protein-coding gene	gene with protein product		607763	"centaurin, beta 1"	CENTB1		11050434, 11062263	Standard	NM_014716		Approved	KIAA0050	uc002ggd.2	Q15027	OTTHUMG00000102199	ENST00000158762.3:c.1406T>A	chr17.hg19:g.7251303T>A	ENSP00000158762:p.Leu469Gln	38.0	0.0		25.0	17.0	NM_014716	Q53XN9	Missense_Mutation	SNP	ENST00000158762.3	hg19	CCDS11101.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.342215	0.81911	.	.	ENSG00000072818	ENST00000158762	T	0.38401	1.14	5.01	5.01	0.66863	.	0.148584	0.45606	D	0.000348	T	0.43033	0.1229	N	0.25201	0.72	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.20306	-1.0279	10	0.23891	T	0.37	.	12.713	0.57100	0.0:0.0:0.0:1.0	.	469	Q15027	ACAP1_HUMAN	Q	469	ENSP00000158762:L469Q	ENSP00000158762:L469Q	L	+	2	0	ACAP1	7192027	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.552000	0.82192	2.106000	0.64143	0.459000	0.35465	CTA	.	.		0.587	ACAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220049.4	NM_014716		A	7251303	T	A	7251303	3	1	245	1	0	0	0	0	1	0	0	0	118	1522	53	4	1464	4	ACAP1	17	7251303	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10		7251303	73943907	204	33674										
TP53	7157	hgsc.bcm.edu	37	chr17	7577531	7577538	+	Frame_Shift_Del	DEL	GGGCCTCC	GGGCCTCC	-													0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	agtgtgatgatggtgaggatGggcctccggttcatgccgcc					rs11540652|rs28934571|rs587782329|rs587782082		TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	GGGCCTCC	GGGCCTCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr17:7577531_7577538delGGGCCTCC	ENST00000269305.4	-	7	932_939	c.743_750delGGAGGCCC	c.(742-750)cggaggcccfs	p.RRP248fs	TP53_ENST00000413465.2_Frame_Shift_Del_p.RRP248fs|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000445888.2_Frame_Shift_Del_p.RRP248fs|TP53_ENST00000455263.2_Frame_Shift_Del_p.RRP248fs|TP53_ENST00000420246.2_Frame_Shift_Del_p.RRP248fs|TP53_ENST00000359597.4_Frame_Shift_Del_p.RRP248fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	248	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.		NR -> IP (in a sporadic cancer; somatic mutation).|NR -> KW (in sporadic cancers; somatic mutation).|R -> C (in a sporadic cancer; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:7682763}.|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs11540652). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:2263646, ECO:0000269|PubMed:7682763, ECO:0000269|PubMed:7887414}.|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:8829627}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R248Q(580)|p.R249S(348)|p.R248L(75)|p.P250L(45)|p.R249M(38)|p.R249W(37)|p.R249G(30)|p.R249K(20)|p.R248P(19)|p.R155Q(18)|p.R249T(16)|p.P250S(12)|p.R248R(8)|p.0?(8)|p.R249fs*96(6)|p.R249R(6)|p.?(5)|p.I251fs*94(5)|p.P250H(4)|p.P250P(4)|p.P250F(3)|p.R155L(3)|p.P250N(2)|p.R155P(2)|p.P250A(2)|p.M246_P250delMNRRP(2)|p.R249fs*14(2)|p.P250Q(2)|p.R248fs*16(2)|p.N247_R248delNR(2)|p.P250_L252delPIL(2)|p.P250_I251insXXXXXX(1)|p.N247_P250delNRRP(1)|p.unknown(1)|p.R248fs*>39(1)|p.R249fs*15(1)|p.P250T(1)|p.P250_T253delPILT(1)|p.R249_P250insR(1)|p.R249_I251delRPI(1)|p.R248_P250delRRP(1)|p.I251fs*13(1)|p.N247_R249delNRR(1)|p.P250_I251insXXXXXXX(1)|p.R248C(1)|p.I251fs*96(1)|p.R249_T256delRPILTIIT(1)|p.N247_R248>IP(1)|p.R249_P250>SS(1)|p.R249_P250delRP(1)|p.P250_I251insX(1)|p.P250fs*14(1)|p.G245fs*14(1)|p.R249fs*19(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TGGTGAGGATGGGCCTCCGGTTCATGCC	0.577	R248Q(BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(HCC1143_BREAST)|R248Q(HCC70_BREAST)|R248Q(HEC1A_ENDOMETRIUM)|R248Q(HS683_CENTRAL_NERVOUS_SYSTEM)|R248Q(HSC4_UPPER_AERODIGESTIVE_TRACT)|R248Q(KASUMI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KYSE150_OESOPHAGUS)|R248Q(MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NAMALWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NCIH211_LUNG)|R248Q(NCIN87_STOMACH)|R248Q(NIHOVCAR3_OVARY)|R248Q(NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(P12ICHIKAWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(PANC0203_PANCREAS)|R248Q(PC14_LUNG)|R248Q(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(RT112_URINARY_TRACT)|R248Q(SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SF295_CENTRAL_NERVOUS_SYSTEM)|R248Q(SKUT1_SOFT_TISSUE)|R248Q(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SW1463_LARGE_INTESTINE)|R248Q(WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.248_251del	Pancreas(47;798 1329 9957 10801)	Atlas-Indel,Pindel	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,NS,malignant_melanoma,+1,4	TP53	33396	.	1331	Substitution - Missense(1258)|Substitution - coding silent(18)|Deletion - Frameshift(14)|Deletion - In frame(13)|Insertion - Frameshift(8)|Whole gene deletion(8)|Unknown(6)|Insertion - In frame(4)|Complex - compound substitution(2)	liver(260)|lung(173)|large_intestine(168)|breast(120)|upper_aerodigestive_tract(107)|haematopoietic_and_lymphoid_tissue(90)|central_nervous_system(56)|oesophagus(54)|stomach(53)|urinary_tract(53)|ovary(50)|skin(35)|endometrium(29)|prostate(18)|pancreas(12)|bone(10)|biliary_tract(9)|cervix(8)|kidney(4)|soft_tissue(4)|vulva(3)|thyroid(3)|adrenal_gland(3)|peritoneum(2)|small_intestine(2)|eye(1)|genital_tract(1)|pituitary(1)|salivary_gland(1)|thymus(1)	c.744_751del	GRCh37	CM920675|CM973401	TP53	M	rs11540652	.																																			SO:0001589	frameshift_variant	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	.	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.743_750delGGAGGCCC	chr17.hg19:g.7577531_7577538delGGGCCTCC	ENSP00000269305:p.Arg248fs	77.0	0.0		24.0	18.0	NM_001126112	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Del	DEL	ENST00000269305.4	hg19	CCDS11118.1																																																																																			.	.		0.577	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		-	7577538	GGGCCTCC	-	7577531	7	5	245	1	0	1	0	1	0	0	0	0	16396	1335	47	0	540	0	TP53	17	7577531	Frame_Shift_Del	DEL	GGGCCTCC	TCGA-ED-A7PZ-01A-11D-A33Q-10	326228	7577531	73617679	205	33675										
SHMT1	6470	hgsc.bcm.edu	37	chr17	18250860	18250860	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	cgtggcagagattttcttctTgtctgtcatgaacccatggg	11	9	4	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr17:18250860T>A	ENST00000316694.3	-	5	603	c.469A>T	c.(469-471)Aag>Tag	p.K157*	SHMT1_ENST00000539052.1_Nonsense_Mutation_p.K19*|SHMT1_ENST00000354098.3_Nonsense_Mutation_p.K157*|SHMT1_ENST00000352886.6_Nonsense_Mutation_p.K157*	NM_004169.3	NP_004160.3	P34896	GLYC_HUMAN	serine hydroxymethyltransferase 1 (soluble)	157					carnitine biosynthetic process (GO:0045329)|cellular nitrogen compound metabolic process (GO:0034641)|folic acid metabolic process (GO:0046655)|glycine biosynthetic process from serine (GO:0019264)|L-serine catabolic process (GO:0006565)|protein homotetramerization (GO:0051289)|protein tetramerization (GO:0051262)|purine nucleobase biosynthetic process (GO:0009113)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	amino acid binding (GO:0016597)|glycine hydroxymethyltransferase activity (GO:0004372)|L-allo-threonine aldolase activity (GO:0008732)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)	13					Glycine(DB00145)|Mimosine(DB01055)|Tetrahydrofolic acid(DB00116)	ATTTTCTTCTTGTCTGTCATG	0.502																																					p.K157X		Atlas-SNP	.											.	SHMT1	36	.	0			c.A469T						.						136	135	135					17																	18250860		2203	4300	6503	SO:0001587	stop_gained	6470	exon5			TCTTCTTGTCTGT		CCDS11196.1, CCDS11197.1, CCDS62112.1	17p11.2	2010-04-23			ENSG00000176974	ENSG00000176974	2.1.2.1		10850	protein-coding gene	gene with protein product	"cytoplasmic serine hydroxymethyltransferase", "14 kDa protein"	182144				8505317	Standard	NM_004169		Approved	CSHMT, SHMT, MGC15229, MGC24556	uc002gta.3	P34896	OTTHUMG00000059094	ENST00000316694.3:c.469A>T	chr17.hg19:g.18250860T>A	ENSP00000318868:p.Lys157*	86.0	0.0		137.0	43.0	NM_148918	B4DPM9|D3DXD0|Q96HY0|Q9UMD1|Q9UMD2	Nonsense_Mutation	SNP	ENST00000316694.3	hg19	CCDS11196.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.847223	0.91277	.	.	ENSG00000176974	ENST00000316694;ENST00000352886;ENST00000539052;ENST00000354098;ENST00000395685	.	.	.	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	-37.6832	15.4913	0.75607	0.0:0.0:0.0:1.0	.	.	.	.	X	157;157;19;157;157	.	ENSP00000318868:K157X	K	-	1	0	SHMT1	18191585	1.000000	0.71417	0.994000	0.49952	0.994000	0.84299	7.858000	0.86971	2.114000	0.64651	0.379000	0.24179	AAG	.	.		0.502	SHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130831.2	NM_004169		A	18250860	T	A	18250860	4	1	245	1	0	0	0	0	0	1	0	0	14300	1821	63	4	1014	4	SHMT1	17	18250860	Nonsense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	10673329	18250860	62944350	206	33676										
RDM1	201299	hgsc.bcm.edu	37	chr17	34257110	34257110	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gatttctgaaaaagctgcttCcggtcgcatgccttttgggc	11	10	1	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr17:34257110C>A	ENST00000293273.6	-	2	291	c.246G>T	c.(244-246)cgG>cgT	p.R82R	RDM1_ENST00000431884.2_Silent_p.R82R|RDM1_ENST00000425909.3_Silent_p.R82R|RDM1_ENST00000394528.3_Silent_p.R82R|RDM1_ENST00000394529.3_Silent_p.R59R|RDM1_ENST00000591402.1_Silent_p.R59R|RDM1_ENST00000430160.2_Silent_p.R59R|RDM1_ENST00000394527.1_Silent_p.R59R|RDM1_ENST00000419453.2_Silent_p.R59R	NM_145654.3	NP_663629.1	Q8NG50	RDM1_HUMAN	RAD52 motif containing 1	82	Necessary for nuclear localization and for nucleolar accumulation in response to heat shock.|RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				DNA recombination (GO:0006310)|DNA repair (GO:0006281)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|kidney(3)|large_intestine(2)|ovary(1)|skin(1)|stomach(1)	9		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		AAAGCTGCTTCCGGTCGCATG	0.473								Other identified genes with known or suspected DNA repair function																													p.R82R		Atlas-SNP	.											.	RDM1	46	.	0			c.G246T						.						107	118	114					17																	34257110		2203	4300	6503	SO:0001819	synonymous_variant	201299	exon2			CTGCTTCCGGTCG	AB080728	CCDS11301.1, CCDS42299.1, CCDS54111.1, CCDS54108.1, CCDS54109.1, CCDS54110.1, CCDS59280.1, CCDS59281.1	17q11.2	2014-04-10	2014-04-10	2005-10-20	ENSG00000187456	ENSG00000278023		"RNA binding motif (RRM) containing"	19950	protein-coding gene	gene with protein product		612896	"RAD52 homolog B (S. cerevisiae)", "RAD52 motif 1"	RAD52B		15611051	Standard	NM_001163120		Approved	MGC33977	uc002hkh.3	Q8NG50	OTTHUMG00000188399	ENST00000293273.6:c.246G>T	chr17.hg19:g.34257110C>A		104.0	0.0		158.0	31.0	NM_001034836	A0JP55|A8MV46|A8MY68|A8MZ92|A8RCS5|A8RCT0|A8RCT5|A8RCT8|A8RCU3|A8RCU8|A8RCW0|A8RCW5	Silent	SNP	ENST00000293273.6	hg19	CCDS11301.1																																																																																			.	.		0.473	RDM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256588.2	NM_145654		A	34257110	C	A	34257110	2	1	245	1	0	0	0	0	0	0	0	1	13212	842	30	3		3	RDM1	17	34257110	Silent	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	16006250	34257110	46938100	207	33677										
KRT40	125115	hgsc.bcm.edu	37	chr17	39140202	39140202	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gcgttggtctcctccaggctGcgcaccttctccagatagct	10	15	2	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr17:39140202G>T	ENST00000398486.2	-	3	484	c.324C>A	c.(322-324)cgC>cgA	p.R108R	KRT40_ENST00000377755.4_Silent_p.R108R	NM_182497.3	NP_872303.2	Q6A162	K1C40_HUMAN	keratin 40	108	Coil 1A.|Rod.					intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9		Breast(137;0.00043)				CCTCCAGGCTGCGCACCTTCT	0.522																																					p.R108R		Atlas-SNP	.											.	KRT40	27	.	0			c.C324A						.						186	186	186					17																	39140202		2203	4295	6498	SO:0001819	synonymous_variant	125115	exon3			CAGGCTGCGCACC	AK093919	CCDS42320.1	17q21.2	2013-01-16			ENSG00000204889	ENSG00000204889		"-", "Intermediate filaments type I, keratins (acidic)"	26707	protein-coding gene	gene with protein product						16831889	Standard	NM_182497		Approved	FLJ36600, KA36	uc010cxh.1	Q6A162	OTTHUMG00000133596	ENST00000398486.2:c.324C>A	chr17.hg19:g.39140202G>T		93.0	0.0		120.0	46.0	NM_182497	Q6IFU5	Silent	SNP	ENST00000398486.2	hg19	CCDS42320.1																																																																																			.	.		0.522	KRT40-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257701.3	NM_182497		T	39140202	G	T	39140202	2	4	245	1	0	0	0	0	0	0	0	1	8487	1306	46	3		3	KRT40	17	39140202	Silent	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	4883092	39140202	42055008	208	33678										
KRT37	8688	hgsc.bcm.edu	37	chr17	39579146	39579146	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	cttctgcgtcccgcacttgtCcgcctccaccagctggtgaa	9	17	1	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr17:39579146C>T	ENST00000225550.3	-	3	615	c.616G>A	c.(616-618)Gac>Aac	p.D206N	AC003958.2_ENST00000432258.1_RNA	NM_003770.4	NP_003761.3	O76014	KRT37_HUMAN	keratin 37	206	Coil 1B.|Rod.					extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	25		Breast(137;0.000496)				CCGCACTTGTCCGCCTCCACC	0.637																																					p.D206N		Atlas-SNP	.											.	KRT37	61	.	0			c.G616A						.						76	68	71					17																	39579146		2203	4300	6503	SO:0001583	missense	8688	exon3			ACTTGTCCGCCTC	Y16793	CCDS32653.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000108417	ENSG00000108417		"-", "Intermediate filaments type I, keratins (acidic)"	6455	protein-coding gene	gene with protein product		604541	"keratin, hair, acidic, 7"	KRTHA7		9756910, 16831889	Standard	NM_003770		Approved		uc002hwp.1	O76014	OTTHUMG00000133606	ENST00000225550.3:c.616G>A	chr17.hg19:g.39579146C>T	ENSP00000225550:p.Asp206Asn	50.0	0.0		49.0	25.0	NM_003770		Missense_Mutation	SNP	ENST00000225550.3	hg19	CCDS32653.1	.	.	.	.	.	.	.	.	.	.	.	20.5	4.007700	0.75046	.	.	ENSG00000108417	ENST00000225550	D	0.89485	-2.52	4.78	4.78	0.61160	Filament (1);	0.000000	0.48767	D	0.000161	D	0.94830	0.8330	M	0.85710	2.77	0.48830	D	0.99971	D	0.89917	1.0	D	0.77557	0.99	D	0.95718	0.8764	10	0.87932	D	0	.	16.7565	0.85501	0.0:1.0:0.0:0.0	.	206	O76014	KRT37_HUMAN	N	206	ENSP00000225550:D206N	ENSP00000225550:D206N	D	-	1	0	KRT37	36832672	1.000000	0.71417	0.975000	0.42487	0.177000	0.22998	5.961000	0.70356	2.202000	0.70862	0.655000	0.94253	GAC	.	.		0.637	KRT37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257714.2	NM_003770		T	39579146	C	T	39579146	3	4	245	1	0	0	0	0	1	0	0	0	8483	855	30	3	753	3	KRT37	17	39579146	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	438944	39579146	41616064	209	33679										
KRT35	3886	hgsc.bcm.edu	37	chr17	39637038	39637038	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tagccggccaggcggtcgttCagggattgcatggtctcctt	14	11	2	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr17:39637038C>G	ENST00000393989.1	-	1	354	c.312G>C	c.(310-312)ctG>ctC	p.L104L	KRT35_ENST00000246639.2_Silent_p.L74L	NM_002280.4	NP_002271.3	Q92764	KRT35_HUMAN	keratin 35	104	Coil 1A.|Rod.				anatomical structure morphogenesis (GO:0009653)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	29		Breast(137;0.000286)				GGCGGTCGTTCAGGGATTGCA	0.642																																					p.L104L		Atlas-SNP	.											.	KRT35	58	.	0			c.G312C						.						64	69	67					17																	39637038		2203	4300	6503	SO:0001819	synonymous_variant	3886	exon1			GTCGTTCAGGGAT	X90762	CCDS11394.2	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000197079	ENSG00000197079		"-", "Intermediate filaments type I, keratins (acidic)"	6453	protein-coding gene	gene with protein product	"hard keratin type I 5"	602764	"keratin, hair, acidic, 5"	KRTHA5		8823373, 16831889	Standard	NM_002280		Approved	Ha-5	uc002hws.3	Q92764	OTTHUMG00000133425	ENST00000393989.1:c.312G>C	chr17.hg19:g.39637038C>G		96.0	0.0		103.0	57.0	NM_002280	O76012|Q92651	Silent	SNP	ENST00000393989.1	hg19	CCDS11394.2																																																																																			.	.		0.642	KRT35-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_002280		G	39637038	C	G	39637038	2	3	245	1	0	0	0	0	0	0	0	1	8481	813	29	4		4	KRT35	17	39637038	Silent	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	57892	39637038	41558172	210	33680										
AOC2	314	hgsc.bcm.edu	37	chr17	41001329	41001329	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	taccgaatccagatccacagCccccttggcatacacatacc	5	17	0	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr17:41001329C>G	ENST00000253799.3	+	2	1842	c.1815C>G	c.(1813-1815)agC>agG	p.S605R	AOC2_ENST00000452774.2_Intron|AOC3_ENST00000308423.2_5'Flank	NM_009590.2	NP_033720.2	O75106	AOC2_HUMAN	amine oxidase, copper containing 2 (retina-specific)	605					amine metabolic process (GO:0009308)|catecholamine metabolic process (GO:0006584)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	aliphatic-amine oxidase activity (GO:0052595)|aminoacetone:oxygen oxidoreductase(deaminating) activity (GO:0052594)|copper ion binding (GO:0005507)|electron carrier activity (GO:0009055)|phenethylamine:oxygen oxidoreductase (deaminating) activity (GO:0052596)|primary amine oxidase activity (GO:0008131)|quinone binding (GO:0048038)|tryptamine:oxygen oxidoreductase (deaminating) activity (GO:0052593)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(14)|ovary(4)|skin(2)	30		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)		AGATCCACAGCCCCCTTGGCA	0.622																																					p.S605R		Atlas-SNP	.											.	AOC2	61	.	0			c.C1815G						.						93	100	98					17																	41001329		2203	4300	6503	SO:0001583	missense	314	exon2			CCACAGCCCCCTT	AF081363	CCDS11443.1, CCDS45690.1	17q21	2012-07-13				ENSG00000131480	1.4.3.21		549	protein-coding gene	gene with protein product		602268				9119395, 9722954	Standard	NM_001158		Approved	RAO, DAO2	uc002ibu.3	O75106		ENST00000253799.3:c.1815C>G	chr17.hg19:g.41001329C>G	ENSP00000253799:p.Ser605Arg	99.0	0.0		117.0	23.0	NM_009590	A5PKW2|O00120|O75105|Q4TTW5|Q9UNY0	Missense_Mutation	SNP	ENST00000253799.3	hg19	CCDS11443.1	.	.	.	.	.	.	.	.	.	.	C	12.78	2.040090	0.35989	.	.	ENSG00000131480	ENST00000253799	T	0.03951	3.75	5.02	1.79	0.24919	Copper amine oxidase, C-terminal (3);	0.081242	0.85682	D	0.000000	T	0.17704	0.0425	M	0.81239	2.535	0.80722	D	1	D	0.67145	0.996	D	0.69824	0.966	T	0.00601	-1.1650	10	0.56958	D	0.05	-8.6457	9.2367	0.37470	0.0:0.6829:0.0:0.3171	.	605	O75106	AOC2_HUMAN	R	605	ENSP00000253799:S605R	ENSP00000253799:S605R	S	+	3	2	AOC2	38254855	1.000000	0.71417	0.980000	0.43619	0.216000	0.24613	0.945000	0.29056	0.707000	0.31934	-0.254000	0.11334	AGC	.	.		0.622	AOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452442.1	NM_009590, NM_001158		G	41001329	C	G	41001329	3	3	245	1	0	0	0	0	1	0	0	0	727	738	26	4	1821	4	AOC2	17	41001329	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	1364291	41001329	40193881	211	33681										
OSBPL7	114881	hgsc.bcm.edu	37	chr17	45897358	45897358	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ttgtgccagcccttcagaggCcacttcctcttcttgagcag	9	14	3	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr17:45897358C>A	ENST00000007414.3	-	3	371	c.180G>T	c.(178-180)tgG>tgT	p.W60C	OSBPL7_ENST00000392507.3_Missense_Mutation_p.W60C	NM_145798.2	NP_665741.1	Q9BZF2	OSBL7_HUMAN	oxysterol binding protein-like 7	60	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cellular response to cholesterol (GO:0071397)|lipid transport (GO:0006869)|positive regulation of proteasomal protein catabolic process (GO:1901800)	autophagic vacuole (GO:0005776)|cytosol (GO:0005829)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)	p.W60*(1)		autonomic_ganglia(1)|endometrium(6)|kidney(2)|large_intestine(5)|liver(2)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32						CCTTCAGAGGCCACTTCCTCT	0.647																																					p.W60C		Atlas-SNP	.											OSBPL7,NS,carcinoma,0,1	OSBPL7	65	.	1	Substitution - Nonsense(1)	endometrium(1)	c.G180T						.						33	30	31					17																	45897358		2203	4300	6503	SO:0001583	missense	114881	exon3			CAGAGGCCACTTC	AF392446	CCDS11515.1	17q21	2013-01-10				ENSG00000006025		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16387	protein-coding gene	gene with protein product		606735				14593528, 11735225	Standard	NM_145798		Approved	ORP7, MGC71150	uc002ilx.1	Q9BZF2		ENST00000007414.3:c.180G>T	chr17.hg19:g.45897358C>A	ENSP00000007414:p.Trp60Cys	30.0	0.0		38.0	20.0	NM_145798	D3DTT6|Q6PIV6	Missense_Mutation	SNP	ENST00000007414.3	hg19	CCDS11515.1	.	.	.	.	.	.	.	.	.	.	C	12.19	1.863586	0.32884	.	.	ENSG00000006025	ENST00000007414;ENST00000392507	T;T	0.20598	2.06;2.06	4.86	3.9	0.45041	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.207171	0.45126	D	0.000397	T	0.49064	0.1535	M	0.88181	2.935	0.80722	D	1	D	0.89917	1.0	D	0.74348	0.983	T	0.54801	-0.8239	10	0.72032	D	0.01	-16.9164	10.1261	0.42649	0.0:0.905:0.0:0.095	.	60	Q9BZF2	OSBL7_HUMAN	C	60	ENSP00000007414:W60C;ENSP00000376295:W60C	ENSP00000007414:W60C	W	-	3	0	OSBPL7	43252357	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.603000	0.67619	1.037000	0.40024	0.561000	0.74099	TGG	.	.		0.647	OSBPL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441367.1	NM_017731		A	45897358	C	A	45897358	3	1	245	1	0	0	0	0	1	0	0	0	11291	740	26	3	2432	3	OSBPL7	17	45897358	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	4896029	45897358	35297852	212	33682										
DLX4	1748	hgsc.bcm.edu	37	chr17	48050405	48050405	+	Intron	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ctaccccctcgctccctcctCgccccctacaccgtgttgtg	6	22	0	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr17:48050405C>A	ENST00000240306.3	+	2	578				DLX4_ENST00000411890.2_Silent_p.L12L|DLX4_ENST00000503410.1_Intron	NM_138281.2	NP_612138.1	Q92988	DLX4_HUMAN	distal-less homeobox 4						multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(3)	10						GCTCCCTCCTCGCCCCCTACA	0.627																																					p.L12L		Atlas-SNP	.											.	DLX4	25	.	0			c.C36A						.						51	61	58					17																	48050405		2203	4300	6503	SO:0001627	intron_variant	1748	exon1			CCTCCTCGCCCCC		CCDS11555.1, CCDS45728.1	17q21.33	2011-06-20			ENSG00000108813	ENSG00000108813		"Homeoboxes / ANTP class : NKL subclass"	2917	protein-coding gene	gene with protein product		601911		DLX7, DLX9			Standard	NM_138281		Approved	DLX8, BP1	uc002ipv.3	Q92988	OTTHUMG00000161839	ENST00000240306.3:c.284-32C>A	chr17.hg19:g.48050405C>A		283.0	0.0		292.0	113.0	NM_001934	D3DTX2|D3DTX3|O60480|Q13265|Q6PJK0|Q9HBE0	Silent	SNP	ENST00000240306.3	hg19	CCDS11555.1																																																																																			.	.		0.627	DLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366214.1			A	48050405	C	A	48050405	1	1	245	0	1	0	0	0	0	0	0	0	4575	871	31	1		1	DLX4	17	48050405	Intron	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	2153047	48050405	33144805	213	33683										
PPM1E	4591	hgsc.bcm.edu	37	chr17	57057829	57057829	+	IGR	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	acgtgctggaagacccaggcTacctagatctcacacaaata	8	12	1	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr17:57057829T>A	ENST00000393066.3	-	0	3622				PPM1E_ENST00000308249.2_Missense_Mutation_p.Y569N	NM_001005207.2	NP_001005207.1	O94972	TRI37_HUMAN	tripartite motif containing 37						aggresome assembly (GO:0070842)|negative regulation of centriole replication (GO:0046600)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autoubiquitination (GO:0051865)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|peroxisome (GO:0005777)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(13)|ovary(1)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					AGACCCAGGCTACCTAGATCT	0.498									Mulibrey Nanism																												p.Y569N		Atlas-SNP	.											.	PPM1E	97	.	0			c.T1705A						.						92	83	86					17																	57057829		2203	4300	6503	SO:0001628	intergenic_variant	22843	exon7	Familial Cancer Database	Perheentupa syndrome	CCAGGCTACCTAG	AB020705	CCDS32694.1, CCDS45746.1	17q	2014-02-17	2011-01-25	2001-11-30		ENSG00000108395		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	7523	protein-coding gene	gene with protein product	"RING-B-box-coiled-coil protein"	605073	"tripartite motif-containing 37"	MUL		9106536, 10888877	Standard	NM_015294		Approved	KIAA0898, POB1, TEF3	uc002iwy.4	O94972			chr17.hg19:g.57057829T>A		133.0	0.0		119.0	47.0	NM_014906	Q7Z3E6|Q8IYF7|Q8WYF7	Missense_Mutation	SNP	ENST00000393066.3	hg19	CCDS45746.1	.	.	.	.	.	.	.	.	.	.	T	16.64	3.180128	0.57800	.	.	ENSG00000175175	ENST00000308249;ENST00000443121	T	0.24350	1.86	5.74	5.74	0.90152	.	0.167698	0.53938	D	0.000058	T	0.33990	0.0882	L	0.29908	0.895	0.41422	D	0.987805	D;D	0.59357	0.958;0.985	P;P	0.55391	0.587;0.775	T	0.08106	-1.0738	10	0.59425	D	0.04	-3.7716	16.0334	0.80603	0.0:0.0:0.0:1.0	.	578;569	Q8WY54-3;Q8WY54-2	.;.	N	569;420	ENSP00000312411:Y569N	ENSP00000312411:Y569N	Y	+	1	0	PPM1E	54412611	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.517000	0.53443	2.197000	0.70478	0.402000	0.26972	TAC	.	.		0.498	TRIM37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445928.1	NM_015294		A	57057829	T	A	57057829	1	1	245	0	1	0	0	0	0	0	0	0	12350	1522	53	4		4	PPM1E	17	57057829	IGR	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	9007424	57057829	24137381	214	33684										
ABCA5	23461	hgsc.bcm.edu	37	chr17	67283767	67283767	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	atctcacctgcaagaatgtcAgcttcatccatgaaatgagt	7	10	3	3			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr17:67283767A>T	ENST00000392676.3	-	15	2092	c.2028T>A	c.(2026-2028)gcT>gcA	p.A676A	ABCA5_ENST00000392677.2_Silent_p.A676A|ABCA5_ENST00000588877.1_Silent_p.A676A			Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 5	676	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cholesterol efflux (GO:0033344)|high-density lipoprotein particle remodeling (GO:0034375)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|reverse cholesterol transport (GO:0043691)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(18)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	54	Breast(10;3.72e-11)				Tacrolimus(DB00864)	CAAGAATGTCAGCTTCATCCA	0.388																																					p.A676A		Atlas-SNP	.											.	ABCA5	162	.	0			c.T2028A						.						157	155	156					17																	67283767		2203	4300	6503	SO:0001819	synonymous_variant	23461	exon14			AATGTCAGCTTCA	U66672	CCDS11685.1	17q24.3	2012-03-14			ENSG00000154265	ENSG00000154265		"ATP binding cassette transporters / subfamily A"	35	protein-coding gene	gene with protein product		612503				8894702	Standard	NM_172232		Approved	EST90625	uc002jig.2	Q8WWZ7		ENST00000392676.3:c.2028T>A	chr17.hg19:g.67283767A>T		87.0	0.0		106.0	19.0	NM_018672	Q8IVJ2|Q96LJ1|Q96MS4|Q96PZ9|Q9NY14	Silent	SNP	ENST00000392676.3	hg19	CCDS11685.1																																																																																			.	.		0.388	ABCA5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450654.1	NM_018672		T	67283767	A	T	67283767	2	4	245	1	0	0	0	0	0	0	0	1	35	175	7	4		4	ABCA5	17	67283767	Silent	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	10225938	67283767	13911443	215	33685										
AZI1	22994	hgsc.bcm.edu	37	chr17	79193699	79193699	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ccagcaccttcctcttctgcTcgctgcctgtgaccacggag	9	17	2	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr17:79193699T>A	ENST00000269392.4	-	2	405	c.158A>T	c.(157-159)gAg>gTg	p.E53V	AZI1_ENST00000450824.2_Missense_Mutation_p.E53V|AZI1_ENST00000575907.1_Missense_Mutation_p.E53V|AZI1_ENST00000374782.3_Missense_Mutation_p.E53V	NM_014984.2	NP_055799.2	Q9UPN4	CP131_HUMAN		53					cell differentiation (GO:0030154)|G2/M transition of mitotic cell cycle (GO:0000086)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular protein transport (GO:0090316)|regulation of centrosome duplication (GO:0010824)|spermatogenesis (GO:0007283)	BBSome (GO:0034464)|cell projection (GO:0042995)|centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(1)|lung(12)|ovary(2)|prostate(3)|urinary_tract(5)	36	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			CCTCTTCTGCTCGCTGCCTGT	0.652																																					p.E53V		Atlas-SNP	.											.	AZI1	145	.	0			c.A158T						.						135	115	122					17																	79193699		2203	4300	6503	SO:0001583	missense	22994	exon2			TTCTGCTCGCTGC																												ENST00000269392.4:c.158A>T	chr17.hg19:g.79193699T>A	ENSP00000269392:p.Glu53Val	93.0	0.0		92.0	18.0	NM_014984	A6NHI8|B2RN11|Q96F50	Missense_Mutation	SNP	ENST00000269392.4	hg19		.	.	.	.	.	.	.	.	.	.	T	12.56	1.975780	0.34848	.	.	ENSG00000141577	ENST00000450824;ENST00000374782;ENST00000269392	T;T;T	0.25749	1.78;1.78;1.78	3.72	1.38	0.22167	.	0.298284	0.30464	N	0.009574	T	0.38665	0.1049	L	0.57536	1.79	0.09310	N	1	D;D;D;D	0.76494	0.996;0.996;0.994;0.999	P;P;P;D	0.85130	0.9;0.9;0.869;0.997	T	0.09292	-1.0681	10	0.72032	D	0.01	-12.4528	4.2967	0.10904	0.0:0.1136:0.207:0.6794	.	53;53;53;53	B2RN10;Q9UPN4;Q9UPN4-3;Q9UPN4-2	.;AZI1_HUMAN;.;.	V	53	ENSP00000393583:E53V;ENSP00000363914:E53V;ENSP00000269392:E53V	ENSP00000269392:E53V	E	-	2	0	AZI1	76808294	0.049000	0.20398	0.056000	0.19401	0.586000	0.36452	0.816000	0.27267	0.413000	0.25759	0.379000	0.24179	GAG	.	.		0.652	AZI1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000256070.1			A	79193699	T	A	79193699	3	1	245	1	0	0	0	0	1	0	0	0	1240	1551	54	4	3184	4	AZI1	17	79193699	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	11909932	79193699	2001511	216	33686										
SMCHD1	23347	hgsc.bcm.edu	37	chr18	2732311	2732311	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	agactattaagttgcttcccAgtagccatgttgcaagacta	8	9	0	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr18:2732311A>T	ENST00000320876.6	+	25	3435	c.3097A>T	c.(3097-3099)Agt>Tgt	p.S1033C	RP11-703M24.5_ENST00000583546.1_RNA|SMCHD1_ENST00000261598.8_Missense_Mutation_p.S1033C	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	1033					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						GTTGCTTCCCAGTAGCCATGT	0.373																																					p.S1033C		Atlas-SNP	.											.	SMCHD1	88	.	0			c.A3097T						.						150	136	140					18																	2732311		1865	4107	5972	SO:0001583	missense	23347	exon25			CTTCCCAGTAGCC	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.3097A>T	chr18.hg19:g.2732311A>T	ENSP00000326603:p.Ser1033Cys	194.0	0.0		176.0	80.0	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Missense_Mutation	SNP	ENST00000320876.6	hg19	CCDS45822.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.219684	0.79464	.	.	ENSG00000101596	ENST00000320876;ENST00000261598	T;T	0.47177	0.85;0.87	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.66336	0.2779	M	0.63843	1.955	0.43334	D	0.995379	D	0.89917	1.0	D	0.83275	0.996	T	0.70063	-0.4975	10	0.87932	D	0	-17.0425	15.1893	0.73032	1.0:0.0:0.0:0.0	.	1033	A6NHR9	SMHD1_HUMAN	C	1033	ENSP00000326603:S1033C;ENSP00000261598:S1033C	ENSP00000261598:S1033C	S	+	1	0	SMCHD1	2722311	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.165000	0.77544	1.974000	0.57490	0.533000	0.62120	AGT	.	.		0.373	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			T	2732311	A	T	2732311	3	4	245	1	0	0	0	0	1	0	0	0	14803	188	7	4	3195	4	SMCHD1	18	2732311	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10		2732311	75344937	217	33687										
PTPRM	5797	hgsc.bcm.edu	37	chr18	7949192	7949192	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gatacagggcattgatgtgcGagatgctcctctgaaggaaa	13	7	1	3			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr18:7949192G>A	ENST00000332175.8	+	6	1714	c.677G>A	c.(676-678)cGa>cAa	p.R226Q	PTPRM_ENST00000400060.4_Missense_Mutation_p.R226Q|PTPRM_ENST00000580170.1_Missense_Mutation_p.R226Q|PTPRM_ENST00000400053.4_Missense_Mutation_p.R164Q|PTPRM_ENST00000444013.1_Missense_Mutation_p.R13Q	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	226	Ig-like C2-type.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.R226L(1)		breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				ATTGATGTGCGAGATGCTCCT	0.458																																					p.R226Q		Atlas-SNP	.											PTPRM,NS,carcinoma,0,1	PTPRM	185	.	1	Substitution - Missense(1)	lung(1)	c.G677A						.						121	108	113					18																	7949192		2203	4300	6503	SO:0001583	missense	5797	exon6			ATGTGCGAGATGC	X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.677G>A	chr18.hg19:g.7949192G>A	ENSP00000331418:p.Arg226Gln	72.0	0.0		54.0	11.0	NM_001105244	A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	ENST00000332175.8	hg19	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	G	10.29	1.308618	0.23821	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053;ENST00000444013	T;T;T;T	0.50548	1.99;1.99;1.99;0.74	5.86	2.0	0.26442	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.174053	0.48286	N	0.000184	T	0.32585	0.0834	L	0.47716	1.5	0.09310	N	1	P;B;B	0.52463	0.953;0.006;0.006	B;B;B	0.41374	0.355;0.002;0.002	T	0.22103	-1.0226	10	0.16420	T	0.52	.	5.4981	0.16813	0.1254:0.1146:0.641:0.119	.	13;226;226	E7EVX9;A7MBN1;P28827	.;.;PTPRM_HUMAN	Q	226;226;164;13	ENSP00000331418:R226Q;ENSP00000382933:R226Q;ENSP00000382927:R164Q;ENSP00000387608:R13Q	ENSP00000331418:R226Q	R	+	2	0	PTPRM	7939192	0.995000	0.38212	0.003000	0.11579	0.732000	0.41865	4.642000	0.61383	0.150000	0.19136	0.650000	0.86243	CGA	.	.		0.458	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			A	7949192	G	A	7949192	3	1	245	1	0	0	0	0	1	0	0	0	12821	1058	37	1	699	1	PTPRM	18	7949192	Missense_Mutation	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	5216881	7949192	70128056	218	33688										
IMPA2	3613	hgsc.bcm.edu	37	chr18	12028869	12028869	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tgattggaagctccacattgGcactctgccacctggcctca	9	14	2	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr18:12028869G>T	ENST00000269159.3	+	7	870	c.628G>T	c.(628-630)Gca>Tca	p.A210S	RP11-703I16.1_ENST00000587619.1_RNA|IMPA2_ENST00000589238.1_Missense_Mutation_p.A21S|IMPA2_ENST00000588927.1_Missense_Mutation_p.A21S	NM_014214.2	NP_055029.1	O14732	IMPA2_HUMAN	inositol(myo)-1(or 4)-monophosphatase 2	210					inositol biosynthetic process (GO:0006021)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol phosphorylation (GO:0046854)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	inositol monophosphate 1-phosphatase activity (GO:0008934)|inositol monophosphate 3-phosphatase activity (GO:0052832)|inositol monophosphate 4-phosphatase activity (GO:0052833)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(1)|skin(2)|stomach(2)|urinary_tract(1)	12					Lithium(DB01356)	CTCCACATTGGCACTCTGCCA	0.607																																					p.A210S		Atlas-SNP	.											.	IMPA2	27	.	0			c.G628T						.						97	94	95					18																	12028869		2203	4300	6503	SO:0001583	missense	3613	exon7			ACATTGGCACTCT	AF014398	CCDS11855.1	18p11.2	2008-03-18			ENSG00000141401	ENSG00000141401	3.1.3.25		6051	protein-coding gene	gene with protein product		605922				9322233	Standard	NM_014214		Approved		uc002kqp.2	O14732	OTTHUMG00000131693	ENST00000269159.3:c.628G>T	chr18.hg19:g.12028869G>T	ENSP00000269159:p.Ala210Ser	61.0	0.0		58.0	23.0	NM_014214	B0YJ29|Q9UJT3	Missense_Mutation	SNP	ENST00000269159.3	hg19	CCDS11855.1	.	.	.	.	.	.	.	.	.	.	G	16.77	3.216138	0.58452	.	.	ENSG00000141401	ENST00000269159	T	0.40476	1.03	5.75	5.75	0.90469	.	0.061316	0.64402	D	0.000004	T	0.35740	0.0942	N	0.25144	0.715	0.50813	D	0.999891	B;B	0.12013	0.005;0.003	B;B	0.17433	0.012;0.018	T	0.09574	-1.0668	10	0.56958	D	0.05	-27.4388	19.9417	0.97165	0.0:0.0:1.0:0.0	.	183;210	O14732-2;O14732	.;IMPA2_HUMAN	S	210	ENSP00000269159:A210S	ENSP00000269159:A210S	A	+	1	0	IMPA2	12018869	1.000000	0.71417	0.982000	0.44146	0.920000	0.55202	4.597000	0.61062	2.720000	0.93068	0.655000	0.94253	GCA	.	.		0.607	IMPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254601.1			T	12028869	G	T	12028869	3	4	245	1	0	0	0	0	1	0	0	0	7732	1203	42	3	654	3	IMPA2	18	12028869	Missense_Mutation	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	4079677	12028869	66048379	219	33689										
B4GALT6	9331	hgsc.bcm.edu	37	chr18	29264373	29264373	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gattggaaacccgcatcatcCgcctgagcacagacatcttc	8	14	2	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr18:29264373C>T	ENST00000306851.5	-	1	313	c.17G>A	c.(16-18)cGg>cAg	p.R6Q	B4GALT6_ENST00000237019.7_Missense_Mutation_p.R6Q|RP11-549B18.1_ENST00000565978.1_RNA|B4GALT6_ENST00000383131.3_Missense_Mutation_p.R6Q	NM_004775.3	NP_004766.2	Q9UBX8	B4GT6_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 6	6					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(6)|pancreas(1)	20			OV - Ovarian serous cystadenocarcinoma(10;0.00791)			CCGCATCATCCGCCTGAGCAC	0.572																																					p.R6Q		Atlas-SNP	.											.	B4GALT6	44	.	0			c.G17A						.						178	148	158					18																	29264373		2203	4300	6503	SO:0001583	missense	9331	exon1			ATCATCCGCCTGA	AF038664	CCDS11900.1	18q11	2013-02-19			ENSG00000118276	ENSG00000118276		"Beta 4-glycosyltransferases"	929	protein-coding gene	gene with protein product	"UDP-Gal:glucosylceramide beta-1,4-galactosyltransferase"	604017				9597550, 12180132	Standard	NM_004775		Approved	beta4GalT-VI	uc002kwz.4	Q9UBX8	OTTHUMG00000131980	ENST00000306851.5:c.17G>A	chr18.hg19:g.29264373C>T	ENSP00000306459:p.Arg6Gln	72.0	0.0		58.0	11.0	NM_004775	O60514|Q6NT09	Missense_Mutation	SNP	ENST00000306851.5	hg19	CCDS11900.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.234781	0.79800	.	.	ENSG00000118276	ENST00000306851;ENST00000237019;ENST00000383131	T;T;T	0.52057	1.09;0.85;0.68	5.22	4.35	0.52113	.	0.644914	0.13949	N	0.351648	T	0.40247	0.1109	L	0.54323	1.7	0.37105	D	0.900095	P;B;B	0.38745	0.645;0.005;0.384	B;B;B	0.30495	0.116;0.003;0.078	T	0.45425	-0.9262	10	0.44086	T	0.13	-8.0387	11.5759	0.50860	0.0:0.9126:0.0:0.0874	.	6;6;6	Q6NT09;G3XA83;Q9UBX8	.;.;B4GT6_HUMAN	Q	6	ENSP00000306459:R6Q;ENSP00000237019:R6Q;ENSP00000372613:R6Q	ENSP00000237019:R6Q	R	-	2	0	B4GALT6	27518371	1.000000	0.71417	0.992000	0.48379	0.994000	0.84299	1.653000	0.37323	1.185000	0.42971	0.561000	0.74099	CGG	.	.		0.572	B4GALT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254942.2	NM_004775		T	29264373	C	T	29264373	3	4	245	1	0	0	0	0	1	0	0	0	1275	652	23	1	1167	1	B4GALT6	18	29264373	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	17235504	29264373	48812875	220	33690										
PIAS2	9063	hgsc.bcm.edu	37	chr18	44408008	44408008	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tcttcgtcagaagagctttcTattgtaagatcaataacatc	6	8	4	3	rs373537803		TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr18:44408008T>G	ENST00000585916.1	-	11	1421	c.1422A>C	c.(1420-1422)atA>atC	p.I474I	PIAS2_ENST00000545673.1_Silent_p.I184I|PIAS2_ENST00000324794.7_Silent_p.I474I	NM_004671.3	NP_004662.2	O75928	PIAS2_HUMAN	protein inhibitor of activated STAT, 2	474					androgen receptor signaling pathway (GO:0030521)|negative regulation of androgen receptor signaling pathway (GO:0060766)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein sumoylation (GO:0016925)|regulation of osteoblast differentiation (GO:0045667)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|SUMO ligase activity (GO:0019789)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	22						AAGAGCTTTCTATTGTAAGAT	0.413																																					p.I474I		Atlas-SNP	.											.	PIAS2	85	.	0			c.A1422C						.						137	122	127					18																	44408008		2203	4300	6503	SO:0001819	synonymous_variant	9063	exon11			GCTTTCTATTGTA	AF077953	CCDS32824.1, CCDS32825.1	18q12.1-q12.3	2011-10-11				ENSG00000078043		"Zinc fingers, MIZ-type"	17311	protein-coding gene	gene with protein product	"zinc finger, MIZ-type containing 4"	603567				9724754, 9256341	Standard	NM_004671		Approved	PIASX-BETA, miz, PIASX-ALPHA, ZMIZ4	uc002lck.3	O75928		ENST00000585916.1:c.1422A>C	chr18.hg19:g.44408008T>G		97.0	0.0		71.0	33.0	NM_173206	O75927|Q96BT5|Q96KE3	Silent	SNP	ENST00000585916.1	hg19	CCDS32824.1																																																																																			.	.		0.413	PIAS2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445656.2	NM_004671		G	44408008	T	G	44408008	2	3	245	1	0	0	0	0	0	0	0	1	11885	1512	53	5		5	PIAS2	18	44408008	Silent	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	15143635	44408008	33669240	221	33691										
CDH20	28316	hgsc.bcm.edu	37	chr18	59158023	59158023	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	actgggaccgaccctttgtaTgtcggcaaggtaagaaatgc	12	9	0	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr18:59158023T>C	ENST00000262717.4	+	2	635	c.237T>C	c.(235-237)taT>taC	p.Y79Y	CDH20_ENST00000536675.2_Silent_p.Y79Y|CDH20_ENST00000538374.1_Silent_p.Y79Y			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2	79	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|skin(3)	61		Colorectal(73;0.186)				ACCCTTTGTATGTCGGCAAGG	0.448																																					p.Y79Y		Atlas-SNP	.											.	CDH20	117	.	0			c.T237C						.						113	114	114					18																	59158023		2203	4300	6503	SO:0001819	synonymous_variant	28316	exon1			TTTGTATGTCGGC	AF217289	CCDS11977.1	18q21.33	2010-01-26			ENSG00000101542	ENSG00000101542		"Cadherins / Major cadherins"	1760	protein-coding gene	gene with protein product		605807				10995570	Standard	NM_031891		Approved	CDH7L3, Cdh7	uc010dps.1	Q9HBT6	OTTHUMG00000132768	ENST00000262717.4:c.237T>C	chr18.hg19:g.59158023T>C		131.0	0.0		112.0	47.0	NM_031891	Q495S3	Silent	SNP	ENST00000262717.4	hg19	CCDS11977.1																																																																																			.	.		0.448	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256141.2	NM_031891		C	59158023	T	C	59158023	2	2	245	1	0	0	0	0	0	0	0	1	3108	1471	51	2		2	CDH20	18	59158023	Silent	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	14750015	59158023	18919225	222	33692										
SERPINB3	6317	hgsc.bcm.edu	37	chr18	61325773	61325773	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tttgactttccacccaggagTtaatcttctttcgactttct	5	11	3	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr18:61325773T>C	ENST00000283752.5	-	5	586	c.443A>G	c.(442-444)aAc>aGc	p.N148S	SERPINB11_ENST00000489748.1_RNA|SERPINB3_ENST00000332821.8_Missense_Mutation_p.N148S	NM_006919.2	NP_008850.1	P29508	SPB3_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 3	148					negative regulation of catalytic activity (GO:0043086)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)|virus receptor activity (GO:0001618)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	36						CACCCAGGAGTTAATCTTCTT	0.413																																					p.N148S		Atlas-SNP	.											.	SERPINB3	90	.	0			c.A443G						.						110	99	103					18																	61325773		2203	4298	6501	SO:0001583	missense	6317	exon5			CAGGAGTTAATCT	U19568	CCDS11987.1	18q21.3	2014-02-18	2005-08-18		ENSG00000057149	ENSG00000057149		"Serine (or cysteine) peptidase inhibitors"	10569	protein-coding gene	gene with protein product		600517	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3"	SCC, SCCA1		7724531, 24172014	Standard	NM_006919		Approved	T4-A, HsT1196	uc002lji.3	P29508	OTTHUMG00000060403	ENST00000283752.5:c.443A>G	chr18.hg19:g.61325773T>C	ENSP00000283752:p.Asn148Ser	106.0	0.0		113.0	22.0	NM_006919	A6NDM2|B2RBT5|B3W5Y6|Q53H28|Q53YB5|Q86VF3|Q86W04|Q8IWL4|Q8IXI3|Q96J21|Q9BYF8	Missense_Mutation	SNP	ENST00000283752.5	hg19	CCDS11987.1	.	.	.	.	.	.	.	.	.	.	T	17.51	3.407977	0.62399	.	.	ENSG00000057149	ENST00000283752;ENST00000332821	D;D	0.92048	-2.96;-2.96	2.97	2.97	0.34412	Serpin domain (3);	0.000000	0.41194	D	0.000924	D	0.96895	0.8986	H	0.96208	3.785	0.39652	D	0.970482	D;D;D	0.89917	1.0;0.998;0.998	D;P;P	0.91635	0.999;0.876;0.876	D	0.97533	1.0081	10	0.87932	D	0	.	11.271	0.49138	0.0:0.0:0.0:1.0	.	148;148;148	P29508-2;P29508;Q5K684	.;SPB3_HUMAN;.	S	148	ENSP00000283752:N148S;ENSP00000329498:N148S	ENSP00000283752:N148S	N	-	2	0	SERPINB3	59476753	1.000000	0.71417	0.999000	0.59377	0.843000	0.47879	6.271000	0.72569	1.615000	0.50252	0.374000	0.22700	AAC	.	.		0.413	SERPINB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133791.1	NM_006919		C	61325773	T	C	61325773	3	2	245	1	0	0	0	0	1	0	0	0	14117	1725	60	2	745	2	SERPINB3	18	61325773	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	2167750	61325773	16751475	223	33693										
GRIN3B	116444	hgsc.bcm.edu	37	chr19	1005395	1005395	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	catcctcttcagacgcaccgTgtccagcaagacgcccaagt	8	16	2	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr19:1005395T>A	ENST00000234389.3	+	3	1914	c.1895T>A	c.(1894-1896)gTg>gAg	p.V632E	AC004528.4_ENST00000588380.1_RNA	NM_138690.1	NP_619635.1	O60391	NMD3B_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3B	632					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|protein insertion into membrane (GO:0051205)|regulation of calcium ion transport (GO:0051924)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|neurotransmitter receptor activity (GO:0030594)			breast(1)|kidney(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000226)|all_lung(49;0.000353)|Breast(49;0.00066)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Secobarbital(DB00418)	AGACGCACCGTGTCCAGCAAG	0.647																																					p.V632E		Atlas-SNP	.											.	GRIN3B	46	.	0			c.T1895A						.						120	112	114					19																	1005395		2203	4300	6503	SO:0001583	missense	116444	exon3			GCACCGTGTCCAG		CCDS32861.1	19p13.3	2014-05-06			ENSG00000116032	ENSG00000116032		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	16768	protein-coding gene	gene with protein product		606651					Standard	XM_003403700		Approved	GluN3B	uc002lqo.1	O60391	OTTHUMG00000181904	ENST00000234389.3:c.1895T>A	chr19.hg19:g.1005395T>A	ENSP00000234389:p.Val632Glu	128.0	0.0		97.0	70.0	NM_138690	Q5EAK7|Q7RTW9	Missense_Mutation	SNP	ENST00000234389.3	hg19	CCDS32861.1	.	.	.	.	.	.	.	.	.	.	T	16.66	3.184765	0.57909	.	.	ENSG00000116032	ENST00000234389	T	0.25414	1.8	4.36	2.07	0.26955	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.418400	0.24957	N	0.034250	T	0.49541	0.1563	M	0.84948	2.725	0.51767	D	0.999932	D	0.69078	0.997	D	0.68039	0.955	T	0.49082	-0.8976	10	0.87932	D	0	.	9.7544	0.40494	0.0:0.0:0.3349:0.6651	.	632	O60391	NMD3B_HUMAN	E	632	ENSP00000234389:V632E	ENSP00000234389:V632E	V	+	2	0	GRIN3B	956395	0.911000	0.30947	0.097000	0.21041	0.885000	0.51271	1.385000	0.34408	0.064000	0.16427	0.254000	0.18369	GTG	.	.		0.647	GRIN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103923.2			A	1005395	T	A	1005395	3	1	245	1	0	0	0	0	1	0	0	0	6793	1696	59	4	1905	4	GRIN3B	19	1005395	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10		1005395	58123588	224	33694										
C19orf6	91304	hgsc.bcm.edu	37	chr19	1014293	1014293	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	acggccaggcccgggaagctCccgcggccgccgctgtcaca	14	18	1	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr19:1014293C>G	ENST00000356663.3	-	2	526	c.405G>C	c.(403-405)ggG>ggC	p.G135G	TMEM259_ENST00000333175.5_Silent_p.G135G	NM_001033026.1	NP_001028198.1	Q4ZIN3	MBRL_HUMAN	transmembrane protein 259	135						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)											CCGGGAAGCTCCCGCGGCCGC	0.632																																					p.G135G		Atlas-SNP	.											.	.	.	.	0			c.G405C						.						36	39	38					19																	1014293		2202	4300	6502	SO:0001819	synonymous_variant	91304	exon2			GAAGCTCCCGCGG	BC008957	CCDS12052.1, CCDS32862.1	19p13.3	2013-02-06	2013-02-06	2013-02-06	ENSG00000182087	ENSG00000182087			17039	protein-coding gene	gene with protein product	"membralin", "aspecific BCL2 ARE-binding protein 1"	611011	"chromosome 19 open reading frame 6"	C19orf6		12638133, 16084606	Standard	XM_005259675		Approved	MGC4022, ASBABP1, MBRL	uc002lqr.1	Q4ZIN3		ENST00000356663.3:c.405G>C	chr19.hg19:g.1014293C>G		132.0	0.0		100.0	33.0	NM_033420	O60392|Q8NF79|Q96H30	Silent	SNP	ENST00000356663.3	hg19	CCDS32862.1																																																																																			.	.		0.632	TMEM259-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458236.1	NM_033420		G	1014293	C	G	1014293	2	3	245	1	0	0	0	0	0	0	0	1	1943	842	30	4		4	C19orf6	19	1014293	Silent	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	8898	1014293	58114690	225	33695										
ATP8B3	148229	hgsc.bcm.edu	37	chr19	1796124	1796124	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gttgaagtccattatggccaGgacctggtagacccgttcct	11	11	0	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr19:1796124G>T	ENST00000310127.6	-	17	2132	c.1894C>A	c.(1894-1896)Ctg>Atg	p.L632M	ATP8B3_ENST00000539485.1_Missense_Mutation_p.L632M|ATP8B3_ENST00000525591.1_Missense_Mutation_p.L585M	NM_138813.3	NP_620168.1	O60423	AT8B3_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 3	632					binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ATTATGGCCAGGACCTGGTAG	0.667											OREG0025127	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L632M		Atlas-SNP	.											.	ATP8B3	108	.	0			c.C1894A						.						63	68	66					19																	1796124		2025	4171	6196	SO:0001583	missense	148229	exon17			TGGCCAGGACCTG	AA827939	CCDS45901.1, CCDS54196.1	19p13.3	2010-04-28	2010-04-28		ENSG00000130270	ENSG00000130270		"ATPases / P-type"	13535	protein-coding gene	gene with protein product	"aminophospholipid translocase ATP8B3", "potential phospholipid-transporting ATPase IK"	605866	"ATPase, Class I, type 8B, member 3", "ATPase, class I, type 8B, member 3"			11015572	Standard	NM_138813		Approved	ATPIK	uc002ltw.4	O60423	OTTHUMG00000166189	ENST00000310127.6:c.1894C>A	chr19.hg19:g.1796124G>T	ENSP00000311336:p.Leu632Met	94.0	0.0	598	75.0	36.0	NM_138813	Q7Z485|Q8IVB8|Q8N4Y8|Q96M22	Missense_Mutation	SNP	ENST00000310127.6	hg19	CCDS45901.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.092795	0.76756	.	.	ENSG00000130270	ENST00000310127;ENST00000539485;ENST00000525591	T;T;T	0.72282	-0.64;-0.64;-0.64	4.8	4.8	0.61643	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.64402	D	0.000003	D	0.86581	0.5967	M	0.93328	3.405	0.37288	D	0.908141	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.90425	0.4420	10	0.66056	D	0.02	.	10.8197	0.46597	0.0881:0.0:0.9119:0.0	.	632;585	O60423;Q7Z485	AT8B3_HUMAN;.	M	632;632;585	ENSP00000311336:L632M;ENSP00000443574:L632M;ENSP00000437115:L585M	ENSP00000311336:L632M	L	-	1	2	ATP8B3	1747124	1.000000	0.71417	0.924000	0.36721	0.746000	0.42486	4.013000	0.57138	2.384000	0.81235	0.561000	0.74099	CTG	.	.		0.667	ATP8B3-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388279.1	NM_138813		T	1796124	G	T	1796124	3	4	245	1	0	0	0	0	1	0	0	0	1196	991	35	3	2090	3	ATP8B3	19	1796124	Missense_Mutation	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	781831	1796124	57332859	226	33696										
MUC16	94025	hgsc.bcm.edu	37	chr19	9071656	9071656	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ggtgatcgtcatttctgcagAttttgtcttaatagaggagg	12	5	3	3			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr19:9071656A>C	ENST00000397910.4	-	3	15993	c.15790T>G	c.(15790-15792)Tct>Gct	p.S5264A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5266	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						ATTTCTGCAGATTTTGTCTTA	0.512																																					p.S5264A		Atlas-SNP	.											.	MUC16	4315	.	0			c.T15790G						.						177	173	174					19																	9071656		2050	4188	6238	SO:0001583	missense	94025	exon3			CTGCAGATTTTGT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.15790T>G	chr19.hg19:g.9071656A>C	ENSP00000381008:p.Ser5264Ala	95.0	0.0		50.0	22.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	a	3.924	-0.017585	0.07681	.	.	ENSG00000181143	ENST00000397910	T	0.02395	4.31	1.94	-0.305	0.12784	.	.	.	.	.	T	0.02267	0.0070	L	0.29908	0.895	.	.	.	P	0.49961	0.93	B	0.40444	0.329	T	0.43940	-0.9360	8	0.87932	D	0	.	4.3269	0.11045	0.6175:0.0:0.3825:0.0	.	5264	B5ME49	.	A	5264	ENSP00000381008:S5264A	ENSP00000381008:S5264A	S	-	1	0	MUC16	8932656	0.005000	0.15991	0.000000	0.03702	0.003000	0.03518	0.323000	0.19593	-0.147000	0.11254	0.369000	0.22263	TCT	.	.		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	9071656	A	C	9071656	3	2	245	1	0	0	0	0	1	0	0	0	9982	333	12	5	28061	5	MUC16	19	9071656	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	7275532	9071656	50057327	227	33697										
S1PR5	53637	hgsc.bcm.edu	37	chr19	10624601	10624601	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ctggggcgatgagcgctccgAgccgctgaagctcccatcaa	13	14	1	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr19:10624601A>T	ENST00000439028.3	-	2	1212	c.1087T>A	c.(1087-1089)Tcg>Acg	p.S363T	S1PR5_ENST00000333430.4_Missense_Mutation_p.S363T	NM_001166215.1	NP_001159687.1	Q9H228	S1PR5_HUMAN	sphingosine-1-phosphate receptor 5	363					regulation of neuron differentiation (GO:0045664)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sphingosine-1-phosphate receptor activity (GO:0038036)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	12					Fingolimod(DB08868)	GAGCGCTCCGAGCCGCTGAAG	0.736																																					p.S363T		Atlas-SNP	.											.	S1PR5	33	.	0			c.T1087A						.						9	13	11					19																	10624601		2114	4130	6244	SO:0001583	missense	53637	exon2			GCTCCGAGCCGCT	AK074661	CCDS12240.1	19p13.2	2012-08-08	2008-04-30	2008-04-30		ENSG00000180739		"GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"	14299	protein-coding gene	gene with protein product		605146	"endothelial differentiation, sphingolipid G-protein-coupled receptor, 8"	EDG8		10799507	Standard	NM_030760		Approved	Edg-8	uc002mou.2	Q9H228		ENST00000439028.3:c.1087T>A	chr19.hg19:g.10624601A>T	ENSP00000416915:p.Ser363Thr	46.0	0.0		18.0	15.0	NM_030760	Q6NW11	Missense_Mutation	SNP	ENST00000439028.3	hg19	CCDS12240.1	.	.	.	.	.	.	.	.	.	.	A	8.508	0.865793	0.17250	.	.	ENSG00000180739	ENST00000439028;ENST00000333430	D;D	0.81908	-1.55;-1.55	4.27	3.23	0.37069	.	16.274900	0.00166	U	0.000003	T	0.78648	0.4316	L	0.32530	0.975	0.09310	N	1	B	0.11235	0.004	B	0.09377	0.004	T	0.62525	-0.6836	10	0.72032	D	0.01	.	9.1471	0.36939	0.8363:0.0:0.0:0.1636	.	363	Q9H228	S1PR5_HUMAN	T	363	ENSP00000416915:S363T;ENSP00000328472:S363T	ENSP00000328472:S363T	S	-	1	0	S1PR5	10485601	0.035000	0.19736	0.004000	0.12327	0.034000	0.12701	0.426000	0.21363	0.665000	0.31066	0.260000	0.18958	TCG	.	.		0.736	S1PR5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452015.1	NM_030760		T	10624601	A	T	10624601	3	4	245	1	0	0	0	0	1	0	0	0	13812	304	11	4	113	4	S1PR5	19	10624601	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	1552945	10624601	48504382	228	33698										
RTBDN	83546	hgsc.bcm.edu	37	chr19	12936625	12936625	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ggagcttcccggccccgtcgTcctggtctgggacgaggtac	15	14	1	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr19:12936625T>A	ENST00000458671.2	-	6	737	c.585A>T	c.(583-585)ggA>ggT	p.G195G	RTBDN_ENST00000322912.5_Silent_p.G227G|CTD-2265O21.3_ENST00000588469.1_RNA|RTBDN_ENST00000592204.1_Silent_p.G205G|RTBDN_ENST00000589272.1_3'UTR|RTBDN_ENST00000393233.2_3'UTR	NM_001080997.2	NP_001074466.1	Q9BSG5	RTBDN_HUMAN	retbindin	195						extracellular region (GO:0005576)				kidney(1)|large_intestine(5)|liver(1)|lung(4)|prostate(1)	12						GGCCCCGTCGTCCTGGTCTGG	0.701											OREG0025275	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G227G		Atlas-SNP	.											.	RTBDN	26	.	0			c.A681T						.						26	24	24					19																	12936625		2202	4299	6501	SO:0001819	synonymous_variant	83546	exon7			CCGTCGTCCTGGT	AY028917	CCDS12283.1, CCDS45994.1, CCDS59355.1, CCDS59356.1	19p13	2006-03-22				ENSG00000132026			30310	protein-coding gene	gene with protein product		609553				12107411	Standard	NM_001080997		Approved	FLJ36353	uc002mvj.4	Q9BSG5		ENST00000458671.2:c.585A>T	chr19.hg19:g.12936625T>A		156.0	0.0	683	105.0	89.0	NM_031429	F1T0I8|Q9BWT5	Silent	SNP	ENST00000458671.2	hg19	CCDS45994.1																																																																																			.	.		0.701	RTBDN-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000451513.1	NM_031429		A	12936625	T	A	12936625	2	1	245	1	0	0	0	0	0	0	0	1	13732	1654	58	4		4	RTBDN	19	12936625	Silent	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	2312024	12936625	46192358	229	33699										
OR7C2	26658	hgsc.bcm.edu	37	chr19	15052983	15052983	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tttctcctccgtcctaagagTatctgccagaggccagcaca	8	14	2	2	rs78307433|rs3044711|rs397816267	byFrequency	TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr19:15052983T>C	ENST00000248072.3	+	1	683	c.683T>C	c.(682-684)gTa>gCa	p.V228A		NM_012377.1	NP_036509.1	O60412	OR7C2_HUMAN	olfactory receptor, family 7, subfamily C, member 2	228						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(3)|lung(8)|ovary(2)|skin(2)	15	Ovarian(108;0.203)					GTCCTAAGAGTATCTGCCAGA	0.468																																					p.V228A		Atlas-SNP	.											.	OR7C2	50	.	0			c.T683C						.						168	156	160					19																	15052983		2203	4300	6503	SO:0001583	missense	26658	exon1			TAAGAGTATCTGC	U86255	CCDS12320.1	19p13.1	2012-08-09				ENSG00000127529		"GPCR / Class A : Olfactory receptors"	8374	protein-coding gene	gene with protein product				OR7C3			Standard	NM_012377		Approved	OR19-18	uc010xoc.2	O60412		ENST00000248072.3:c.683T>C	chr19.hg19:g.15052983T>C	ENSP00000248072:p.Val228Ala	101.0	0.0		1064.0	44.0	NM_012377	O43881|Q6IFP9	Missense_Mutation	SNP	ENST00000248072.3	hg19	CCDS12320.1	.	.	.	.	.	.	.	.	.	.	t	12.45	1.940332	0.34283	.	.	ENSG00000127529	ENST00000248072	T	0.00115	8.71	3.89	3.89	0.44902	GPCR, rhodopsin-like superfamily (1);	0.356137	0.19827	U	0.105170	T	0.00210	0.0006	L	0.56396	1.775	0.09310	N	1	B	0.25272	0.122	B	0.32980	0.156	T	0.22730	-1.0208	10	0.87932	D	0	.	10.9678	0.47422	0.0:0.0:0.0:1.0	.	228	O60412	OR7C2_HUMAN	A	228	ENSP00000248072:V228A	ENSP00000248072:V228A	V	+	2	0	OR7C2	14913983	0.075000	0.21258	0.003000	0.11579	0.004000	0.04260	1.824000	0.39072	1.770000	0.52166	0.421000	0.28195	GTA	.	.		0.468	OR7C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466281.1			C	15052983	T	C	15052983	3	2	245	1	0	0	0	0	1	0	0	0	11227	1638	57	2	685	2	OR7C2	19	15052983	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	2116358	15052983	44076000	230	33700										
FCHO1	23149	hgsc.bcm.edu	37	chr19	17886926	17886926	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ccgaggcagcagcggcacagCtcagggccaccgcgggcagc	16	16	1	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr19:17886926C>A	ENST00000596536.1	+	16	1421	c.1138C>A	c.(1138-1140)Ctc>Atc	p.L380I	FCHO1_ENST00000596951.1_Missense_Mutation_p.L380I|FCHO1_ENST00000539407.1_Missense_Mutation_p.L380I|FCHO1_ENST00000389133.4_Missense_Mutation_p.L380I|FCHO1_ENST00000595033.1_Missense_Mutation_p.L330I|FCHO1_ENST00000252771.7_Missense_Mutation_p.L380I|FCHO1_ENST00000600676.1_Missense_Mutation_p.L380I|FCHO1_ENST00000597512.1_Missense_Mutation_p.L387I|FCHO1_ENST00000594202.1_Missense_Mutation_p.L380I	NM_015122.2	NP_055937.1	O14526	FCHO1_HUMAN	FCH domain only 1	380	Mediates interaction with the adaptor protein complex AP-2.				clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)	coated pit (GO:0005905)|plasma membrane (GO:0005886)	AP-2 adaptor complex binding (GO:0035612)			NS(2)|breast(1)|large_intestine(6)|liver(1)|lung(12)	22						AGCGGCACAGCTCAGGGCCAC	0.677																																					p.L380I		Atlas-SNP	.											.	FCHO1	69	.	0			c.C1138A						.						68	61	63					19																	17886926		2203	4300	6503	SO:0001583	missense	23149	exon15			GCACAGCTCAGGG	AB006628	CCDS32955.1, CCDS59365.1, CCDS59366.1	19p13.12	2008-02-05				ENSG00000130475			29002	protein-coding gene	gene with protein product		613437				12477932	Standard	NM_001161357		Approved	KIAA0290	uc002nhg.3	O14526		ENST00000596536.1:c.1138C>A	chr19.hg19:g.17886926C>A	ENSP00000470731:p.Leu380Ile	45.0	0.0		34.0	32.0	NM_001161358	A6NHE6|A8K5U5|B4E120|Q05C93|Q8IW22	Missense_Mutation	SNP	ENST00000596536.1	hg19	CCDS32955.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.116144	0.77323	.	.	ENSG00000130475	ENST00000252771;ENST00000389133;ENST00000539407	T;T;T	0.51325	0.71;0.71;0.71	4.65	4.65	0.58169	.	0.000000	0.64402	D	0.000001	T	0.67869	0.2939	M	0.78916	2.43	0.51233	D	0.999911	D;D	0.89917	0.999;1.0	D;D	0.83275	0.991;0.996	T	0.71659	-0.4526	10	0.59425	D	0.04	-25.0572	13.0187	0.58773	0.0:1.0:0.0:0.0	.	380;380	O14526;O14526-2	FCHO1_HUMAN;.	I	380	ENSP00000252771:L380I;ENSP00000373785:L380I;ENSP00000437978:L380I	ENSP00000252771:L380I	L	+	1	0	FCHO1	17747926	1.000000	0.71417	0.997000	0.53966	0.630000	0.37929	6.454000	0.73493	2.115000	0.64714	0.491000	0.48974	CTC	.	.		0.677	FCHO1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466946.2	NM_015122		A	17886926	C	A	17886926	3	1	245	1	0	0	0	0	1	0	0	0	5795	797	28	3	1188	3	FCHO1	19	17886926	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	2833943	17886926	41242057	231	33701										
ZNF486	90649	hgsc.bcm.edu	37	chr19	20308783	20308783	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	atactacatcctcaaatctaActgaacataagacaactcat	2	11	3	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr19:20308783A>G	ENST00000335117.8	+	4	1321	c.1264A>G	c.(1264-1266)Act>Gct	p.T422A	CTC-260E6.6_ENST00000586657.1_RNA|CTC-260E6.6_ENST00000585498.1_RNA|CTC-260E6.6_ENST00000593655.1_RNA	NM_052852.3	NP_443084.2	Q96H40	ZN486_HUMAN	zinc finger protein 486	422					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	11						CTCAAATCTAACTGAACATAA	0.383																																					p.T422A		Atlas-SNP	.											.	ZNF486	74	.	0			c.A1264G						.						29	32	31					19																	20308783		2195	4291	6486	SO:0001583	missense	90649	exon4			AATCTAACTGAAC	BC008936	CCDS46029.1	19p12	2014-02-13	2003-12-16	2003-12-17	ENSG00000256229	ENSG00000256229		"Zinc fingers, C2H2-type", "-"	20807	protein-coding gene	gene with protein product			"KRAB domain only 2"	KRBO2			Standard	NM_052852		Approved	MGC2396	uc002nou.3	Q96H40	OTTHUMG00000179731	ENST00000335117.8:c.1264A>G	chr19.hg19:g.20308783A>G	ENSP00000335042:p.Thr422Ala	113.0	0.0		71.0	28.0	NM_052852	Q0VG00	Missense_Mutation	SNP	ENST00000335117.8	hg19	CCDS46029.1	.	.	.	.	.	.	.	.	.	.	-	4.646	0.120118	0.08881	.	.	ENSG00000256229	ENST00000545779;ENST00000335117	T	0.35605	1.3	0.85	0.85	0.18980	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.30324	0.0761	N	0.17723	0.515	0.09310	N	1	P	0.52316	0.952	P	0.54664	0.758	T	0.10847	-1.0612	9	0.51188	T	0.08	.	2.9159	0.05752	0.6536:0.0:0.3464:0.0	.	422	Q96H40	ZN486_HUMAN	A	461;422	ENSP00000335042:T422A	ENSP00000335042:T422A	T	+	1	0	ZNF486	20169783	0.000000	0.05858	0.248000	0.24265	0.247000	0.25773	-0.760000	0.04756	0.166000	0.19597	0.164000	0.16699	ACT	.	.		0.383	ZNF486-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447843.2	NM_052852		G	20308783	A	G	20308783	3	3	245	1	0	0	0	0	1	0	0	0	17954	43	2	2	1278	2	ZNF486	19	20308783	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	2421857	20308783	38820200	232	33702										
MLL4	9757	hgsc.bcm.edu	37	chr19	36214899	36214899	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ctcctcggcgtcggacccccCgagaaaatggtgcgaactgc	12	15	0	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr19:36214899C>T	ENST00000222270.7	+	8	3325	c.3325C>T	c.(3325-3327)Cga>Tga	p.R1109*	KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000420124.1_Nonsense_Mutation_p.R1109*	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	1109					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										TCGGACCCCCCGAGAAAATGG	0.567																																					p.R1109X		Atlas-SNP	.											.	MLL4	229	.	0			c.C3325T						.						16	19	18					19																	36214899		1733	3896	5629	SO:0001587	stop_gained	8085	exon8			ACCCCCCGAGAAA	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"Chromatin-modifying enzymes / K-methyltransferases"	15840	protein-coding gene	gene with protein product	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.3325C>T	chr19.hg19:g.36214899C>T	ENSP00000222270:p.Arg1109*	72.0	0.0		137.0	21.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Nonsense_Mutation	SNP	ENST00000222270.7	hg19	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	C	41	8.982603	0.99025	.	.	ENSG00000105663	ENST00000222270;ENST00000420124	.	.	.	5.97	4.94	0.65067	.	0.000000	0.37761	N	0.001951	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.14	0.65313	0.1791:0.8209:0.0:0.0	.	.	.	.	X	1109	.	ENSP00000222270:R1109X	R	+	1	2	AD000671.1	40906739	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.193000	0.42658	1.435000	0.47434	0.655000	0.94253	CGA	.	.		0.567	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727		T	36214899	C	T	36214899	4	4	245	1	0	0	0	0	0	1	0	0	9632	644	23	1	3355	1	MLL4	19	36214899	Nonsense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	15906116	36214899	22914084	233	33703										
SIPA1L3	23094	hgsc.bcm.edu	37	chr19	38572737	38572737	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gcagcgagatcaccctcagcGagtgtgacgcggaggacgcg	16	12	2	2	rs377070862		TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr19:38572737G>A	ENST00000222345.6	+	3	1041	c.532G>A	c.(532-534)Gag>Aag	p.E178K		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	178					hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CACCCTCAGCGAGTGTGACGC	0.721																																					p.E178K		Atlas-SNP	.											.	SIPA1L3	150	.	0			c.G532A						.	G	LYS/GLU	1,4395		0,1,2197	27	33	31		532	5.2	1	19		31	0,8592		0,0,4296	no	missense	SIPA1L3	NM_015073.1	56	0,1,6493	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	178/1782	38572737	1,12987	2198	4296	6494	SO:0001583	missense	23094	exon3			CTCAGCGAGTGTG	AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738			23801	protein-coding gene	gene with protein product							Standard	XM_005258671		Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.532G>A	chr19.hg19:g.38572737G>A	ENSP00000222345:p.Glu178Lys	37.0	0.0		58.0	11.0	NM_015073	Q2TV87	Missense_Mutation	SNP	ENST00000222345.6	hg19	CCDS33007.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.752569	0.89753	2.27E-4	0.0	ENSG00000105738	ENST00000222345	T	0.81415	-1.49	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	D	0.85256	0.5655	L	0.32530	0.975	0.58432	D	0.999997	D	0.89917	1.0	D	0.87578	0.998	D	0.86958	0.2090	10	0.72032	D	0.01	-36.8277	17.5458	0.87861	0.0:0.0:1.0:0.0	.	178	O60292	SI1L3_HUMAN	K	178	ENSP00000222345:E178K	ENSP00000222345:E178K	E	+	1	0	SIPA1L3	43264577	1.000000	0.71417	1.000000	0.80357	0.534000	0.34807	9.657000	0.98554	2.434000	0.82447	0.563000	0.77884	GAG	.	.		0.721	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278		A	38572737	G	A	38572737	3	1	245	1	0	0	0	0	1	0	0	0	14346	1059	37	1	534	1	SIPA1L3	19	38572737	Missense_Mutation	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	2357838	38572737	20556246	234	33704										
ACTN4	81	hgsc.bcm.edu	37	chr19	39207845	39207845	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	taccggcgtgtgcacaagccGcccaaggtgcaggagaagtg	15	11	0	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr19:39207845G>A	ENST00000252699.2	+	10	1108	c.1032G>A	c.(1030-1032)ccG>ccA	p.P344P	ACTN4_ENST00000390009.3_Silent_p.P125P|ACTN4_ENST00000424234.2_Intron	NM_004924.4	NP_004915.2	O43707	ACTN4_HUMAN	actinin, alpha 4	344					actin filament bundle assembly (GO:0051017)|blood coagulation (GO:0007596)|negative regulation of cellular component movement (GO:0051271)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cellular component movement (GO:0051272)|positive regulation of pinocytosis (GO:0048549)|positive regulation of sodium:proton antiporter activity (GO:0032417)|protein localization to tight junction (GO:1902396)|protein transport (GO:0015031)|regulation of apoptotic process (GO:0042981)|response to hypoxia (GO:0001666)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule lumen (GO:0031093)|protein complex (GO:0043234)|pseudopodium (GO:0031143)|ribonucleoprotein complex (GO:0030529)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|nucleoside binding (GO:0001882)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|urinary_tract(3)	30	all_cancers(60;1.57e-05)|Ovarian(47;0.103)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			TGCACAAGCCGCCCAAGGTGC	0.627																																					p.P344P	Colon(168;199 1940 10254 46213 46384)	Atlas-SNP	.											.	ACTN4	69	.	0			c.G1032A						.						110	84	93					19																	39207845		2203	4300	6503	SO:0001819	synonymous_variant	81	exon10			CAAGCCGCCCAAG	D89980	CCDS12518.1	19q13	2013-01-10			ENSG00000130402	ENSG00000130402		"EF-hand domain containing"	166	protein-coding gene	gene with protein product		604638	"focal segmental glomerulosclerosis 1"	FSGS1		9461087, 10700177	Standard	NM_004924		Approved		uc002oja.2	O43707	OTTHUMG00000137382	ENST00000252699.2:c.1032G>A	chr19.hg19:g.39207845G>A		101.0	0.0		176.0	14.0	NM_004924	A4K467|D6PXK4|O76048	Silent	SNP	ENST00000252699.2	hg19	CCDS12518.1																																																																																			.	.		0.627	ACTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268091.1			A	39207845	G	A	39207845	2	1	245	1	0	0	0	0	0	0	0	1	207	1074	38	1		1	ACTN4	19	39207845	Silent	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	635108	39207845	19921138	235	33705										
CEACAM7	1087	hgsc.bcm.edu	37	chr19	42187899	42187899	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tacccaccacaggtaggttgTgttctgagtctcaggttgac	11	10	2	2	rs201378485		TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr19:42187899T>A	ENST00000006724.3	-	3	724	c.523A>T	c.(523-525)Aca>Tca	p.T175S	CEACAM7_ENST00000338196.4_Intron|CEACAM7_ENST00000599715.1_5'Flank|CEACAM7_ENST00000602225.1_Intron|CEACAM7_ENST00000401731.1_Missense_Mutation_p.T175S	NM_006890.3	NP_008821.1	Q14002	CEAM7_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 7	175	Ig-like C2-type.					anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	18				OV - Ovarian serous cystadenocarcinoma(3;0.0027)|all cancers(3;0.00979)|Epithelial(262;0.0366)		AGGTAGGTTGTGTTCTGAGTC	0.527																																					p.T175S		Atlas-SNP	.											.	CEACAM7	33	.	0			c.A523T						.						169	160	163					19																	42187899		2203	4300	6503	SO:0001583	missense	1087	exon3			AGGTTGTGTTCTG	X98311	CCDS12583.1	19q13.2	2013-01-29			ENSG00000007306	ENSG00000007306		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1819	protein-coding gene	gene with protein product	"carcinoembryonic antigen gene family member 2"			CGM2		7806520, 9135022	Standard	XM_005278379		Approved	CEA	uc002ori.1	Q14002	OTTHUMG00000151063	ENST00000006724.3:c.523A>T	chr19.hg19:g.42187899T>A	ENSP00000006724:p.Thr175Ser	91.0	0.0		130.0	86.0	NM_006890	A8K848|O15148|O15149|Q0VAC1|Q13983|Q9UPJ2	Missense_Mutation	SNP	ENST00000006724.3	hg19	CCDS12583.1	.	.	.	.	.	.	.	.	.	.	T	14.68	2.608016	0.46527	.	.	ENSG00000007306	ENST00000006724;ENST00000412062;ENST00000401731	T;T	0.12774	2.65;2.65	2.83	1.74	0.24563	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.23649	0.0572	L	0.50847	1.595	0.09310	N	1	B	0.31519	0.327	P	0.51055	0.657	T	0.39522	-0.9610	9	0.72032	D	0.01	.	5.0416	0.14462	0.0:0.1706:0.0:0.8294	.	175	Q14002	CEAM7_HUMAN	S	175;154;175	ENSP00000006724:T175S;ENSP00000385932:T175S	ENSP00000006724:T175S	T	-	1	0	CEACAM7	46879739	0.001000	0.12720	0.051000	0.19133	0.240000	0.25518	0.139000	0.16036	1.060000	0.40578	0.260000	0.18958	ACA	.	T|1.000;C|0.000		0.527	CEACAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321145.1	NM_006890		A	42187899	T	A	42187899	3	1	245	1	0	0	0	0	1	0	0	0	3199	1696	59	4	282	4	CEACAM7	19	42187899	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	2980054	42187899	16941084	236	33706										
KCNN4	3783	hgsc.bcm.edu	37	chr19	44271859	44271859	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gtcatacaggatcatgtgcaTctgggtgggaggagaggatc	16	6	3	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr19:44271859T>C	ENST00000262888.3	-	8	1515	c.1120A>G	c.(1120-1122)Atg>Gtg	p.M374V		NM_002250.2	NP_002241.1	O15554	KCNN4_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4	374					calcium ion transport (GO:0006816)|cell volume homeostasis (GO:0006884)|defense response (GO:0006952)|immune system process (GO:0002376)|phospholipid translocation (GO:0045332)|positive regulation of protein secretion (GO:0050714)|positive regulation of T cell receptor signaling pathway (GO:0050862)|potassium ion export (GO:0071435)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|saliva secretion (GO:0046541)|stabilization of membrane potential (GO:0030322)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|Intermediate conductance calcium-activated potassium channel activity (GO:0022894)|protein phosphatase binding (GO:0019903)			biliary_tract(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	15		Prostate(69;0.0352)			Clotrimazole(DB00257)|Enflurane(DB00228)|Halothane(DB01159)|Miconazole(DB01110)|Procaine(DB00721)|Quinine(DB00468)	ATCATGTGCATCTGGGTGGGA	0.572																																					p.M374V		Atlas-SNP	.											.	KCNN4	37	.	0			c.A1120G						.						104	104	104					19																	44271859		2203	4300	6503	SO:0001630	splice_region_variant	3783	exon8			TGTGCATCTGGGT	AF022797	CCDS12630.1	19q13.2	2012-07-05				ENSG00000104783		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6293	protein-coding gene	gene with protein product		602754				9380751, 9407042, 16382103	Standard	NM_002250		Approved	KCa3.1, hSK4, hKCa4, hIKCa1	uc002oxl.3	O15554		ENST00000262888.3:c.1120-1A>G	chr19.hg19:g.44271859T>C		69.0	0.0		82.0	49.0	NM_002250	Q53XR4	Missense_Mutation	SNP	ENST00000262888.3	hg19	CCDS12630.1	.	.	.	.	.	.	.	.	.	.	T	13.70	2.314385	0.40996	.	.	ENSG00000104783	ENST00000262888;ENST00000407385	D	0.99854	-7.19	3.87	3.87	0.44632	Calmodulin-binding domain (2);	0.042709	0.85682	D	0.000000	D	0.98960	0.9646	L	0.27053	0.805	0.52501	D	0.999958	B;B	0.33171	0.116;0.4	B;B	0.34873	0.026;0.191	D	0.99981	1.2604	10	0.29301	T	0.29	-42.0596	11.2923	0.49258	0.0:0.0:0.0:1.0	.	268;374	D1MQ10;O15554	.;KCNN4_HUMAN	V	374;242	ENSP00000262888:M374V	ENSP00000262888:M374V	M	-	1	0	KCNN4	48963699	1.000000	0.71417	1.000000	0.80357	0.822000	0.46500	3.808000	0.55598	1.989000	0.58080	0.528000	0.53228	ATG	.	.		0.572	KCNN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463598.1	NM_002250	Missense_Mutation	C	44271859	T	C	44271859	5	2	245	1	0	0	0	0	0	0	1	0	8090	1449	50	2	167	2	KCNN4	19	44271859	Splice_Site	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	2083960	44271859	14857124	237	33707										
PTGIR	5739	hgsc.bcm.edu	37	chr19	47127137	47127137	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gctcagcgccaggcagcgctCcacggccatggcaaagagga	14	14	1	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr19:47127137C>T	ENST00000291294.2	-	2	479	c.346G>A	c.(346-348)Gag>Aag	p.E116K	PTGIR_ENST00000594275.1_Intron|PTGIR_ENST00000598865.1_Intron|PTGIR_ENST00000597185.1_Intron|PTGIR_ENST00000596260.1_Missense_Mutation_p.E116K	NM_000960.3	NP_000951.1	P43119	PI2R_HUMAN	prostaglandin I2 (prostacyclin) receptor (IP)	116					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of GTPase activity (GO:0043547)|response to lipopolysaccharide (GO:0032496)	cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	13		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000327)|all cancers(93;0.000641)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0331)	Dinoprost Tromethamine(DB01160)|Epoprostenol(DB01240)|Iloprost(DB01088)|Treprostinil(DB00374)	AGGCAGCGCTCCACGGCCATG	0.711																																					p.E116K		Atlas-SNP	.											.	PTGIR	31	.	0			c.G346A						.						15	14	15					19																	47127137		2185	4272	6457	SO:0001583	missense	5739	exon2			AGCGCTCCACGGC		CCDS12686.1	19q13.3	2012-08-08				ENSG00000160013		"GPCR / Class A : Prostanoid receptors"	9602	protein-coding gene	gene with protein product		600022				7759114	Standard	NM_000960		Approved	IP	uc002pex.3	P43119		ENST00000291294.2:c.346G>A	chr19.hg19:g.47127137C>T	ENSP00000291294:p.Glu116Lys	57.0	0.0		98.0	20.0	NM_000960		Missense_Mutation	SNP	ENST00000291294.2	hg19	CCDS12686.1	.	.	.	.	.	.	.	.	.	.	C	29.4	5.002773	0.93287	.	.	ENSG00000160013	ENST00000291294	T	0.74632	-0.86	4.85	3.81	0.43845	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.87549	0.6205	M	0.91300	3.195	0.47547	D	0.999453	D	0.89917	1.0	D	0.91635	0.999	D	0.89142	0.3517	10	0.87932	D	0	-11.5675	10.9984	0.47591	0.0:0.9092:0.0:0.0908	.	116	P43119	PI2R_HUMAN	K	116	ENSP00000291294:E116K	ENSP00000291294:E116K	E	-	1	0	PTGIR	51818977	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.612000	0.82975	1.264000	0.44198	0.563000	0.77884	GAG	.	.		0.711	PTGIR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466581.1			T	47127137	C	T	47127137	3	4	245	1	0	0	0	0	1	0	0	0	12764	864	30	3	822	3	PTGIR	19	47127137	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	2855278	47127137	12001846	238	33708										
PRR12	57479	hgsc.bcm.edu	37	chr19	50102990	50102992	+	In_Frame_Del	DEL	CTC	CTC	-													0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ctcgagacgctgccctccttCtcctcggatgaggaagactc							TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr19:50102990_50102992delCTC	ENST00000418929.2	+	5	4152_4154	c.4140_4142delCTC	c.(4138-4143)ttctcc>ttc	p.S1382del		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	0							DNA binding (GO:0003677)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)|prostate(2)	11		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		TGCCCTCCTTCTCCTCGGATGAG	0.616																																					p.1380_1381del		Atlas-Indel,Pindel	.											.	PRR12	157	.	0			c.4139_4141del						.																																			SO:0001651	inframe_deletion	57479	exon5			.	AB033031	CCDS46143.1	19q13.33	2008-07-02	2006-02-06	2006-02-06		ENSG00000126464			29217	protein-coding gene	gene with protein product			"KIAA1205"	KIAA1205		10574462	Standard	NM_020719		Approved		uc002poo.4	Q9ULL5		ENST00000418929.2:c.4140_4142delCTC	chr19.hg19:g.50102993_50102995delCTC	ENSP00000394510:p.Ser1382del	86.0	0.0		126.0	23.0	NM_020719	E9PB06|Q8N4J6	In_Frame_Del	DEL	ENST00000418929.2	hg19	CCDS46143.1																																																																																			.	.		0.616	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719		-	50102992	CTC	-	50102990	7	5	245	1	0	1	0	1	0	0	0	0	12596	912	32	0	4158	0	PRR12	19	50102990	In_Frame_Del	DEL	CTC	TCGA-ED-A7PZ-01A-11D-A33Q-10	2975853	50102990	9025993	239	33709										
ZNF808	388558	hgsc.bcm.edu	37	chr19	53056843	53056843	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	cccacaaaaacaggaagtacAcatgagagaaaaatctttcc	6	10	1	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr19:53056843A>T	ENST00000359798.4	+	5	854	c.674A>T	c.(673-675)cAc>cTc	p.H225L		NM_001039886.3	NP_001034975.2	Q8N4W9	ZN808_HUMAN	zinc finger protein 808	225					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(8)|kidney(3)|lung(12)|urinary_tract(1)	24				OV - Ovarian serous cystadenocarcinoma(262;0.00501)|GBM - Glioblastoma multiforme(134;0.0213)		CAGGAAGTACACATGAGAGAA	0.383																																					p.H225L		Atlas-SNP	.											.	ZNF808	81	.	0			c.A674T						.						131	138	136					19																	53056843		2203	4300	6503	SO:0001583	missense	388558	exon5			AAGTACACATGAG	CR749856	CCDS46167.1	19q13.41	2013-01-08			ENSG00000198482	ENSG00000198482		"Zinc fingers, C2H2-type", "-"	33230	protein-coding gene	gene with protein product							Standard	NM_001039886		Approved		uc010epq.1	Q8N4W9	OTTHUMG00000158230	ENST00000359798.4:c.674A>T	chr19.hg19:g.53056843A>T	ENSP00000352846:p.His225Leu	70.0	0.0		153.0	98.0	NM_001039886	Q68CN7	Missense_Mutation	SNP	ENST00000359798.4	hg19	CCDS46167.1	.	.	.	.	.	.	.	.	.	.	.	8.272	0.813496	0.16537	.	.	ENSG00000198482	ENST00000359798	T	0.25912	1.77	1.01	1.01	0.19927	.	.	.	.	.	T	0.35508	0.0934	H	0.96748	3.875	0.09310	N	1	P	0.49783	0.928	B	0.37047	0.24	T	0.49244	-0.8960	9	0.66056	D	0.02	.	3.8502	0.08951	0.6045:0.3954:0.0:0.0	.	225	Q8N4W9	ZN808_HUMAN	L	225	ENSP00000352846:H225L	ENSP00000352846:H225L	H	+	2	0	ZNF808	57748655	0.000000	0.05858	0.002000	0.10522	0.036000	0.12997	0.950000	0.29122	0.701000	0.31803	0.254000	0.18369	CAC	.	.		0.383	ZNF808-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350447.3	NM_001039886		T	53056843	A	T	53056843	3	4	245	1	0	0	0	0	1	0	0	0	18188	159	6	4	684	4	ZNF808	19	53056843	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	2953853	53056843	6072140	240	33710										
BIRC8	112401	hgsc.bcm.edu	37	chr19	53793422	53793422	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	catgtcccttctcttctagcAgatatttgcaacctggatac	6	12	2	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr19:53793422A>T	ENST00000426466.1	-	1	1453	c.206T>A	c.(205-207)cTg>cAg	p.L69Q		NM_033341.4	NP_203127.3	Q96P09	BIRC8_HUMAN	baculoviral IAP repeat containing 8	69					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(10)|urinary_tract(1)	19				GBM - Glioblastoma multiforme(134;0.00304)		CTCTTCTAGCAGATATTTGCA	0.433																																					p.L69Q		Atlas-SNP	.											.	BIRC8	54	.	0			c.T206A						.						130	125	126					19																	53793422		2203	4300	6503	SO:0001583	missense	112401	exon1			TCTAGCAGATATT	AF164682	CCDS12863.1	19q13.3-q13.4	2011-01-25	2011-01-25			ENSG00000163098		"Baculoviral IAP repeat containing"	14878	protein-coding gene	gene with protein product	"IAP-like protein 2", "inhibitor of apoptosis-like protein 2"		"baculoviral IAP repeat-containing 8"			11390657	Standard	NM_033341		Approved	ILP-2, hILP2	uc002qbk.3	Q96P09		ENST00000426466.1:c.206T>A	chr19.hg19:g.53793422A>T	ENSP00000412957:p.Leu69Gln	132.0	0.0		196.0	124.0	NM_033341	Q6IPY1|Q96RW5	Missense_Mutation	SNP	ENST00000426466.1	hg19	CCDS12863.1	.	.	.	.	.	.	.	.	.	.	A	11.38	1.622332	0.28889	.	.	ENSG00000163098	ENST00000426466	T	0.73897	-0.79	0.502	0.502	0.16932	Baculoviral inhibition of apoptosis protein repeat (5);	.	.	.	.	D	0.87378	0.6162	H	0.96269	3.795	0.41402	D	0.987682	D	0.89917	1.0	D	0.81914	0.995	D	0.84814	0.0792	9	0.87932	D	0	-5.0376	5.4107	0.16346	0.9999:0.0:1.0E-4:0.0	.	69	Q96P09	BIRC8_HUMAN	Q	69	ENSP00000412957:L69Q	ENSP00000412957:L69Q	L	-	2	0	BIRC8	58485234	0.894000	0.30519	0.011000	0.14972	0.004000	0.04260	2.000000	0.40816	0.486000	0.27676	0.344000	0.21773	CTG	.	.		0.433	BIRC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464357.1	NM_033341		T	53793422	A	T	53793422	3	4	245	1	0	0	0	0	1	0	0	0	1440	188	7	4	508	4	BIRC8	19	53793422	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	736579	53793422	5335561	241	33711										
NLRP2	55655	hgsc.bcm.edu	37	chr19	55493848	55493848	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	cccgtgcagttttgcagagcTggtcttcagggactggcctg	14	11	2	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr19:55493848T>A	ENST00000543010.1	+	6	925	c.782T>A	c.(781-783)cTg>cAg	p.L261Q	NLRP2_ENST00000537859.1_Missense_Mutation_p.L239Q|NLRP2_ENST00000448584.2_Missense_Mutation_p.L261Q|NLRP2_ENST00000427260.2_Missense_Mutation_p.L238Q|NLRP2_ENST00000263437.6_Missense_Mutation_p.L258Q|NLRP2_ENST00000538819.1_Missense_Mutation_p.L237Q|NLRP2_ENST00000391721.4_Missense_Mutation_p.L237Q|NLRP2_ENST00000339757.7_Missense_Mutation_p.L239Q	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	261	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|Pyrin domain binding (GO:0032090)			large_intestine(4)|liver(1)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	11			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		TTTGCAGAGCTGGTCTTCAGG	0.532																																					p.L261Q		Atlas-SNP	.											.	NLRP2	161	.	0			c.T782A						.						56	54	55					19																	55493848		2203	4300	6503	SO:0001583	missense	55655	exon6			CAGAGCTGGTCTT	AK000517	CCDS12913.1, CCDS54318.1, CCDS54319.1	19q13.42	2008-02-05	2006-12-08	2006-12-08	ENSG00000022556	ENSG00000022556		"Nucleotide-binding domain and leucine rich repeat containing"	22948	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2"	609364	"NACHT, leucine rich repeat and PYD containing 2"	NALP2		12563287, 11270363	Standard	NM_001174081		Approved	FLJ20510, PYPAF2, NBS1, PAN1, CLR19.9	uc021vbq.1	Q9NX02	OTTHUMG00000167763	ENST00000543010.1:c.782T>A	chr19.hg19:g.55493848T>A	ENSP00000445135:p.Leu261Gln	123.0	0.0		177.0	48.0	NM_017852	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Missense_Mutation	SNP	ENST00000543010.1	hg19	CCDS12913.1	.	.	.	.	.	.	.	.	.	.	T	14.42	2.531553	0.45073	.	.	ENSG00000022556	ENST00000543010;ENST00000391721;ENST00000339757;ENST00000448584;ENST00000537859;ENST00000427260;ENST00000538819;ENST00000263437	D;D;D;D;D;D;D;D	0.82255	-1.59;-1.59;-1.59;-1.59;-1.59;-1.59;-1.59;-1.59	1.55	1.55	0.23275	NACHT nucleoside triphosphatase (1);	.	.	.	.	D	0.91908	0.7438	H	0.94964	3.605	0.09310	N	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.77004	0.989;0.962;0.986;0.976;0.986	T	0.80879	-0.1185	9	0.87932	D	0	.	7.2028	0.25891	0.0:0.0:0.0:1.0	.	238;239;258;237;261	B4DZL7;Q9NX02-2;A8K9G6;Q9NX02-4;Q9NX02	.;.;.;.;NALP2_HUMAN	Q	261;237;239;261;239;238;237;258	ENSP00000445135:L261Q;ENSP00000375601:L237Q;ENSP00000344074:L239Q;ENSP00000409370:L261Q;ENSP00000440601:L239Q;ENSP00000402474:L238Q;ENSP00000441133:L237Q;ENSP00000263437:L258Q	ENSP00000263437:L258Q	L	+	2	0	NLRP2	60185660	0.084000	0.21492	0.004000	0.12327	0.015000	0.08874	3.079000	0.50104	0.987000	0.38709	0.397000	0.26171	CTG	.	.		0.532	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852		A	55493848	T	A	55493848	3	1	245	1	0	0	0	0	1	0	0	0	10486	1580	55	4	800	4	NLRP2	19	55493848	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	1700426	55493848	3635135	242	33712										
ZNF256	10172	hgsc.bcm.edu	37	chr19	58453484	58453484	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	atctttccctaatgaggtctCcctggtgctgaacacgtaca	8	12	2	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr19:58453484C>G	ENST00000282308.3	-	3	888	c.692G>C	c.(691-693)gGa>gCa	p.G231A	ZNF256_ENST00000598928.1_3'UTR	NM_005773.2	NP_005764.2	Q9Y2P7	ZN256_HUMAN	zinc finger protein 256	231					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0155)		AATGAGGTCTCCCTGGTGCTG	0.428																																					p.G231A	NSCLC(55;1313 1552 8040 11996)	Atlas-SNP	.											.	ZNF256	117	.	0			c.G692C						.						195	174	181					19																	58453484		2203	4300	6503	SO:0001583	missense	10172	exon3			AGGTCTCCCTGGT	AF067165	CCDS12966.1	19q13	2013-01-08				ENSG00000152454		"Zinc fingers, C2H2-type", "-"	13049	protein-coding gene	gene with protein product		606956					Standard	NM_005773		Approved	BMZF-3	uc002qqu.3	Q9Y2P7		ENST00000282308.3:c.692G>C	chr19.hg19:g.58453484C>G	ENSP00000282308:p.Gly231Ala	106.0	0.0		201.0	25.0	NM_005773	B2RA92|Q53Y85|Q9BV71	Missense_Mutation	SNP	ENST00000282308.3	hg19	CCDS12966.1	.	.	.	.	.	.	.	.	.	.	.	8.561	0.877749	0.17395	.	.	ENSG00000152454	ENST00000282308	T	0.27104	1.69	3.04	-2.04	0.07343	.	.	.	.	.	T	0.14743	0.0356	N	0.25332	0.735	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.28004	-1.0057	9	0.59425	D	0.04	.	4.6251	0.12474	0.0:0.3883:0.1644:0.4474	.	231	Q9Y2P7	ZN256_HUMAN	A	231	ENSP00000282308:G231A	ENSP00000282308:G231A	G	-	2	0	ZNF256	63145296	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-2.132000	0.01309	-0.186000	0.10533	-0.384000	0.06662	GGA	.	.		0.428	ZNF256-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466702.1			G	58453484	C	G	58453484	3	3	245	1	0	0	0	0	1	0	0	0	17814	855	30	4	1195	4	ZNF256	19	58453484	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	2959636	58453484	675499	243	33713										
TASP1	55617	hgsc.bcm.edu	37	chr20	13550171	13550171	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	cacttgtggtcatgatgttaGgagggcaagagggtattcca	14	6	1	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr20:13550171G>T	ENST00000337743.4	-	7	671	c.551C>A	c.(550-552)cCt>cAt	p.P184H	TASP1_ENST00000480436.1_5'UTR|TASP1_ENST00000539805.1_Intron	NM_017714.2	NP_060184.2	Q9H6P5	TASP1_HUMAN	taspase, threonine aspartase, 1	184					positive regulation of transcription, DNA-templated (GO:0045893)		threonine-type endopeptidase activity (GO:0004298)			NS(1)|breast(1)|endometrium(2)|large_intestine(11)|liver(1)|lung(11)|stomach(2)|urinary_tract(2)	31						CATGATGTTAGGAGGGCAAGA	0.338																																					p.P184H		Atlas-SNP	.											.	TASP1	52	.	0			c.C551A						.						89	92	91					20																	13550171		2203	4300	6503	SO:0001583	missense	55617	exon7			ATGTTAGGAGGGC	AK000219	CCDS13116.1	20p12	2005-10-15	2005-10-15	2005-10-15	ENSG00000089123	ENSG00000089123	3.4.25.-		15859	protein-coding gene	gene with protein product		608270	"chromosome 20 open reading frame 13"	C20orf13		14636557	Standard	XR_430268		Approved	FLJ20212, dJ585I14.2	uc002woi.3	Q9H6P5	OTTHUMG00000031904	ENST00000337743.4:c.551C>A	chr20.hg19:g.13550171G>T	ENSP00000338624:p.Pro184His	43.0	0.0		44.0	30.0	NM_017714	B7Z690|B7Z963|Q5TDU9|Q9BQN0|Q9NQ08|Q9NTS6|Q9NXJ2	Missense_Mutation	SNP	ENST00000337743.4	hg19	CCDS13116.1	.	.	.	.	.	.	.	.	.	.	G	17.86	3.492158	0.64074	.	.	ENSG00000089123	ENST00000378157;ENST00000337743;ENST00000455532	D;D	0.87650	-2.28;-2.28	5.88	5.88	0.94601	.	0.217137	0.49916	D	0.000128	D	0.90700	0.7082	L	0.53249	1.67	0.80722	D	1	D;D	0.54207	0.965;0.959	P;P	0.60789	0.879;0.806	D	0.90948	0.4803	10	0.72032	D	0.01	-13.3836	14.6531	0.68811	0.0:0.0:0.8545:0.1455	.	184;161	Q9H6P5;Q5JWM4	TASP1_HUMAN;.	H	161;184;161	ENSP00000338624:P184H;ENSP00000400580:P161H	ENSP00000338624:P184H	P	-	2	0	TASP1	13498171	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.289000	0.65656	2.779000	0.95612	0.650000	0.86243	CCT	.	.		0.338	TASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078041.2	NM_017714		T	13550171	G	T	13550171	3	4	245	1	0	0	0	0	1	0	0	0	15604	1000	35	3	743	3	TASP1	20	13550171	Missense_Mutation	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10		13550171	49475349	244	33714										
GZF1	64412	hgsc.bcm.edu	37	chr20	23350846	23350846	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gtatgtgtcatccaagctttCggataaattgctgtcttttg	9	7	2	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr20:23350846C>T	ENST00000338121.5	+	6	1981	c.1904C>T	c.(1903-1905)tCg>tTg	p.S635L	GZF1_ENST00000544236.1_Missense_Mutation_p.S159L|GZF1_ENST00000377051.2_Missense_Mutation_p.S635L|GZF1_ENST00000542987.1_Missense_Mutation_p.S144L			Q9H116	GZF1_HUMAN	GDNF-inducible zinc finger protein 1	635					branching involved in ureteric bud morphogenesis (GO:0001658)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)|sequence-specific DNA binding (GO:0043565)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|urinary_tract(2)	24	Lung NSC(19;0.0605)|Colorectal(13;0.0993)|all_lung(19;0.135)					TCCAAGCTTTCGGATAAATTG	0.478																																					p.S635L		Atlas-SNP	.											.	GZF1	61	.	0			c.C1904T						.						107	86	93					20																	23350846		2203	4300	6503	SO:0001583	missense	64412	exon5			AGCTTTCGGATAA	AK025447	CCDS13151.1	20p11.21	2013-01-09	2006-09-19	2006-09-19	ENSG00000125812	ENSG00000125812		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	15808	protein-coding gene	gene with protein product		613842	"zinc finger protein 336"	ZNF336		14522971, 16049025	Standard	NM_022482		Approved	dJ322G13.2, ZBTB23	uc002wsz.3	Q9H116	OTTHUMG00000032069	ENST00000338121.5:c.1904C>T	chr20.hg19:g.23350846C>T	ENSP00000338290:p.Ser635Leu	177.0	0.0		119.0	13.0	NM_022482	A8K199|B2RBC3|B3KPL4|B4DF58|D3DW39|Q54A22|Q96N08|Q9BQK9|Q9H117|Q9H6W6	Missense_Mutation	SNP	ENST00000338121.5	hg19	CCDS13151.1	.	.	.	.	.	.	.	.	.	.	C	12.04	1.818664	0.32145	.	.	ENSG00000125812	ENST00000544236;ENST00000338121;ENST00000542987;ENST00000377051	T;T;T;T	0.10668	3.02;2.85;3.31;2.85	5.77	4.83	0.62350	.	0.489251	0.17196	N	0.183330	T	0.07863	0.0197	L	0.32530	0.975	0.20638	N	0.999874	P	0.48640	0.913	B	0.31191	0.125	T	0.17501	-1.0367	10	0.56958	D	0.05	.	13.8745	0.63645	0.0:0.9271:0.0:0.0729	.	635	Q9H116	GZF1_HUMAN	L	159;635;144;635	ENSP00000445458:S159L;ENSP00000338290:S635L;ENSP00000445118:S144L;ENSP00000366250:S635L	ENSP00000338290:S635L	S	+	2	0	GZF1	23298846	0.186000	0.23225	0.104000	0.21259	0.024000	0.10985	3.577000	0.53885	1.453000	0.47775	-0.136000	0.14681	TCG	.	.		0.478	GZF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078333.1	NM_022482		T	23350846	C	T	23350846	3	4	245	1	0	0	0	0	1	0	0	0	6923	893	31	1	1922	1	GZF1	20	23350846	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	9800675	23350846	39674674	245	33715										
C20orf112	140688	hgsc.bcm.edu	37	chr20	31043960	31043960	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ccgtatttgacgcggctccgCagcccgtcggcaccgcagcc	12	18	0	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr20:31043960C>T	ENST00000359676.5	-	3	490	c.348G>A	c.(346-348)ctG>ctA	p.L116L	C20orf112_ENST00000475781.1_5'UTR|RP5-1184F4.5_ENST00000442179.1_RNA	NM_001256798.1|NM_080616.4	NP_001243727.1|NP_542183.2	Q96MY1	NOL4L_HUMAN		116						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(3)|kidney(2)|large_intestine(5)|lung(5)	15						CGCGGCTCCGCAGCCCGTCGG	0.652																																					p.L360L		Atlas-SNP	.											.	C20orf112	39	.	0			c.G1080A						.						63	68	66					20																	31043960		2203	4299	6502	SO:0001819	synonymous_variant	140688	exon6			GCTCCGCAGCCCG																												ENST00000359676.5:c.348G>A	chr20.hg19:g.31043960C>T		56.0	0.0		48.0	12.0	NM_001256798	Q5JYB7|Q6P0Y4|Q9BR34|Q9NQF6	Silent	SNP	ENST00000359676.5	hg19	CCDS13202.1																																																																																			.	.		0.652	C20orf112-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078628.2			T	31043960	C	T	31043960	2	4	245	1	0	0	0	0	0	0	0	1	2083	697	25	3		3	C20orf112	20	31043960	Silent	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	7693114	31043960	31981560	246	33716										
RBPJL	11317	hgsc.bcm.edu	37	chr20	43942173	43942173	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gctctcagacggtctccacaCgctacctctctgtggaggat	10	14	3	1	rs370206478		TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr20:43942173C>T	ENST00000343694.3	+	7	757	c.685C>T	c.(685-687)Cgc>Tgc	p.R229C	RBPJL_ENST00000372741.3_Missense_Mutation_p.R229C|RBPJL_ENST00000372743.1_Missense_Mutation_p.R229C	NM_001281448.1|NM_001281449.1|NM_014276.2	NP_001268377.1|NP_001268378.1|NP_055091.2	Q9UBG7	RBPJL_HUMAN	recombination signal binding protein for immunoglobulin kappa J region-like	229					positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Myeloproliferative disorder(115;0.0122)				GGTCTCCACACGCTACCTCTC	0.612																																					p.R229C		Atlas-SNP	.											.	RBPJL	67	.	0			c.C685T						.	C	CYS/ARG	0,4406		0,0,2203	97	77	84		685	4.1	1	20		84	1,8599	1.2+/-3.3	0,1,4299	no	missense	RBPJL	NM_014276.2	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	229/518	43942173	1,13005	2203	4300	6503	SO:0001583	missense	11317	exon7			TCCACACGCTACC	AB024964	CCDS13349.1, CCDS63283.1, CCDS63284.1	20q13.12	2013-10-18	2007-02-26	2007-02-26	ENSG00000124232	ENSG00000124232			13761	protein-coding gene	gene with protein product			"recombining binding protein suppressor of hairless (Drosophila)-like"	RBPSUHL		9929984	Standard	NM_014276		Approved	RBP-L, SUH, SUHL	uc002xns.3	Q9UBG7	OTTHUMG00000033055	ENST00000343694.3:c.685C>T	chr20.hg19:g.43942173C>T	ENSP00000341243:p.Arg229Cys	59.0	0.0		65.0	47.0	NM_014276	O95723|Q5QPU9|Q5QPV0|Q9ULV9	Missense_Mutation	SNP	ENST00000343694.3	hg19	CCDS13349.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.135960	0.77662	0.0	1.16E-4	ENSG00000124232	ENST00000372743;ENST00000372741;ENST00000343694	T;T;T	0.38077	1.16;1.16;1.16	5.06	4.11	0.48088	Beta-trefoil (2);	0.000000	0.64402	D	0.000001	T	0.58380	0.2118	M	0.73598	2.24	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.63120	-0.6708	10	0.87932	D	0	-31.8817	12.0946	0.53747	0.3117:0.6883:0.0:0.0	.	229;229	Q5QPV1;Q9UBG7	.;RBPJL_HUMAN	C	229	ENSP00000361828:R229C;ENSP00000361826:R229C;ENSP00000341243:R229C	ENSP00000341243:R229C	R	+	1	0	RBPJL	43375587	0.996000	0.38824	0.955000	0.39395	0.961000	0.63080	3.414000	0.52693	1.339000	0.45563	0.557000	0.71058	CGC	.	.		0.612	RBPJL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080391.1	NM_014276		T	43942173	C	T	43942173	3	4	245	1	0	0	0	0	1	0	0	0	13177	536	19	1	711	1	RBPJL	20	43942173	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	12898213	43942173	19083347	247	33717										
PREX1	57580	hgsc.bcm.edu	37	chr20	47273608	47273608	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tcgtggccaccaggaggcgcAgagggcggcgggagcagaag	20	10	0	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr20:47273608A>T	ENST00000371941.3	-	18	2115	c.2093T>A	c.(2092-2094)cTg>cAg	p.L698Q	PREX1_ENST00000396220.1_Missense_Mutation_p.L698Q	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	698	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			CAGGAGGCGCAGAGGGCGGCG	0.642																																					p.L698Q		Atlas-SNP	.											.	PREX1	441	.	0			c.T2093A						.						64	50	54					20																	47273608		2203	4300	6503	SO:0001583	missense	57580	exon18			AGGCGCAGAGGGC	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.2093T>A	chr20.hg19:g.47273608A>T	ENSP00000361009:p.Leu698Gln	36.0	0.0		45.0	13.0	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	hg19	CCDS13410.1	.	.	.	.	.	.	.	.	.	.	A	27.7	4.857728	0.91433	.	.	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.54675	0.56;0.56	5.12	5.12	0.69794	PDZ/DHR/GLGF (2);	0.150693	0.29868	U	0.010993	T	0.60051	0.2239	L	0.29908	0.895	0.58432	D	0.999997	D	0.89917	1.0	D	0.64877	0.93	T	0.64791	-0.6324	10	0.87932	D	0	.	14.9361	0.70957	1.0:0.0:0.0:0.0	.	698	Q8TCU6	PREX1_HUMAN	Q	698	ENSP00000361009:L698Q;ENSP00000379522:L698Q	ENSP00000361009:L698Q	L	-	2	0	PREX1	46707015	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	9.333000	0.96459	1.926000	0.55796	0.459000	0.35465	CTG	.	.		0.642	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		T	47273608	A	T	47273608	3	4	245	1	0	0	0	0	1	0	0	0	12488	188	7	4	2978	4	PREX1	20	47273608	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	3331435	47273608	15751912	248	33718										
PREX1	57580	hgsc.bcm.edu	37	chr20	47444283	47444283	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gcgctcggactcccgggcggCcgcgcacgggccggggccgg	20	17	0	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr20:47444283C>T	ENST00000371941.3	-	1	137	c.115G>A	c.(115-117)Gcc>Acc	p.A39T	PREX1_ENST00000396220.1_Missense_Mutation_p.A39T	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	39					actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			Tcccgggcggccgcgcacggg	0.786																																					p.A39T		Atlas-SNP	.											.	PREX1	441	.	0			c.G115A						.						4	4	4					20																	47444283		1839	3824	5663	SO:0001583	missense	57580	exon1			GGGCGGCCGCGCA	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.115G>A	chr20.hg19:g.47444283C>T	ENSP00000361009:p.Ala39Thr	70.0	0.0		62.0	16.0	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	hg19	CCDS13410.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.054883	0.75960	.	.	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.61627	0.11;0.09	3.09	3.09	0.35607	Dbl homology (DH) domain (1);	.	.	.	.	T	0.54743	0.1877	N	0.08118	0	0.30375	N	0.78254	D	0.63880	0.993	D	0.72338	0.977	T	0.55431	-0.8142	9	0.48119	T	0.1	.	10.948	0.47312	0.0:1.0:0.0:0.0	.	39	Q8TCU6	PREX1_HUMAN	T	39	ENSP00000361009:A39T;ENSP00000379522:A39T	ENSP00000361009:A39T	A	-	1	0	PREX1	46877690	0.868000	0.29978	1.000000	0.80357	0.503000	0.33858	-0.052000	0.11865	1.579000	0.49836	0.195000	0.17529	GCC	.	.		0.786	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		T	47444283	C	T	47444283	3	4	245	1	0	0	0	0	1	0	0	0	12488	739	26	3	5024	3	PREX1	20	47444283	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	170675	47444283	15581237	249	33719										
ZFP64	55734	hgsc.bcm.edu	37	chr20	50782528	50782528	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tttccgtgggcaggtaagttTgatagccatgttcaaaaaca	10	7	1	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr20:50782528T>A	ENST00000216923.4	-	3	672	c.323A>T	c.(322-324)cAa>cTa	p.Q108L	ZFP64_ENST00000477786.1_5'UTR|ZFP64_ENST00000371515.4_Missense_Mutation_p.Q106L|ZFP64_ENST00000346617.4_Intron|ZFP64_ENST00000371518.2_Missense_Mutation_p.Q108L|ZFP64_ENST00000361387.2_Missense_Mutation_p.Q108L	NM_018197.2|NM_199426.1	NP_060667.2|NP_955458.1	Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	108					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						CAGGTAAGTTTGATAGCCATG	0.428																																					p.Q108L		Atlas-SNP	.											.	ZFP64	240	.	0			c.A323T						.						156	138	144					20																	50782528		2203	4300	6503	SO:0001583	missense	55734	exon3			TAAGTTTGATAGC	AK001596	CCDS13439.1, CCDS13440.1, CCDS13441.1, CCDS13442.1	20q13.11-q13.13	2013-01-08	2012-11-27		ENSG00000020256	ENSG00000020256		"Zinc fingers, C2H2-type"	15940	protein-coding gene	gene with protein product			"zinc finger protein 338", "zinc finger protein 64 homolog (mouse)", "zinc finger protein 64"	ZNF338		9034307	Standard	NM_199427		Approved	FLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1	uc002xwl.3	Q9NPA5	OTTHUMG00000032756	ENST00000216923.4:c.323A>T	chr20.hg19:g.50782528T>A	ENSP00000216923:p.Gln108Leu	107.0	0.0		94.0	66.0	NM_018197	Q9NTS7|Q9NVH4	Missense_Mutation	SNP	ENST00000216923.4	hg19	CCDS13440.1	.	.	.	.	.	.	.	.	.	.	T	19.38	3.816946	0.70912	.	.	ENSG00000020256	ENST00000371518;ENST00000361387;ENST00000216923;ENST00000371515;ENST00000371516	T;T;T;T	0.08807	3.14;3.14;3.07;3.05	5.76	5.76	0.90799	.	0.000000	0.56097	D	0.000031	T	0.24236	0.0587	L	0.56769	1.78	0.50632	D	0.999885	D;D;D	0.64830	0.994;0.994;0.993	D;D;D	0.74348	0.983;0.983;0.977	T	0.00563	-1.1669	10	0.33141	T	0.24	-13.2416	14.6387	0.68708	0.0:0.0:0.0:1.0	.	106;108;108	Q5JWM1;Q9NPA5;Q9NTW7	.;ZF64A_HUMAN;ZF64B_HUMAN	L	108;108;108;106;108	ENSP00000360573:Q108L;ENSP00000355179:Q108L;ENSP00000216923:Q108L;ENSP00000360570:Q106L	ENSP00000216923:Q108L	Q	-	2	0	ZFP64	50215935	1.000000	0.71417	0.998000	0.56505	0.470000	0.32858	5.576000	0.67437	2.201000	0.70794	0.533000	0.62120	CAA	.	.		0.428	ZFP64-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079744.1	NM_018197		A	50782528	T	A	50782528	3	1	245	1	0	0	0	0	1	0	0	0	17667	1812	63	4	2929	4	ZFP64	20	50782528	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	3338245	50782528	12242992	250	33720										
PHACTR3	116154	hgsc.bcm.edu	37	chr20	58318246	58318246	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tgtgaggaggaacagcaaacTggccaccctgggcaggatct	14	10	1	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr20:58318246T>A	ENST00000371015.1	+	2	670	c.203T>A	c.(202-204)cTg>cAg	p.L68Q	PHACTR3_ENST00000395636.2_Missense_Mutation_p.L27Q|PHACTR3_ENST00000361300.4_Missense_Mutation_p.L27Q|PHACTR3_ENST00000541461.1_Missense_Mutation_p.L27Q|PHACTR3_ENST00000355648.4_Missense_Mutation_p.L27Q|PHACTR3_ENST00000359926.3_Missense_Mutation_p.L65Q|PHACTR3_ENST00000395639.4_Missense_Mutation_p.L27Q	NM_001281507.1|NM_080672.3	NP_001268436.1|NP_542403.1	Q96KR7	PHAR3_HUMAN	phosphatase and actin regulator 3	68						nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|liver(2)|lung(32)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	59	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)			AACAGCAAACTGGCCACCCTG	0.537																																					p.L68Q		Atlas-SNP	.											.	PHACTR3	104	.	0			c.T203A						.						78	80	79					20																	58318246		2203	4300	6503	SO:0001583	missense	116154	exon2			GCAAACTGGCCAC	AJ311122	CCDS13480.1, CCDS13481.1, CCDS42895.1, CCDS56202.1	20q13.32-q13.33	2014-06-13	2004-05-20	2004-05-20	ENSG00000087495	ENSG00000087495		"Phosphatase and actin regulators"	15833	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 123"	608725	"chromosome 20 open reading frame 101"	C20orf101		15107502	Standard	NM_001199505		Approved	PPP1R123	uc002yau.3	Q96KR7	OTTHUMG00000032869	ENST00000371015.1:c.203T>A	chr20.hg19:g.58318246T>A	ENSP00000360054:p.Leu68Gln	194.0	0.0		154.0	107.0	NM_080672	B1AKX0|B1AN68|B1AN69|B2RB46|Q32P33|Q707P6|Q9H4T4	Missense_Mutation	SNP	ENST00000371015.1	hg19	CCDS13480.1	.	.	.	.	.	.	.	.	.	.	T	26.5	4.745995	0.89663	.	.	ENSG00000087495	ENST00000359926;ENST00000371015;ENST00000395639;ENST00000541461;ENST00000355648;ENST00000395636;ENST00000361300	T;T;T;T;T;T;T	0.39787	1.43;1.46;1.06;1.44;1.44;1.44;1.06	4.41	4.41	0.53225	.	0.000000	0.64402	D	0.000002	T	0.58104	0.2099	L	0.54323	1.7	0.80722	D	1	D;D;D	0.71674	0.998;0.998;0.996	D;P;P	0.76071	0.987;0.898;0.871	T	0.61888	-0.6970	10	0.87932	D	0	-2.44	12.8102	0.57635	0.0:0.0:0.0:1.0	.	27;68;65	Q96KR7-3;Q96KR7;B1AKX0	.;PHAR3_HUMAN;.	Q	65;68;27;27;27;27;27	ENSP00000353002:L65Q;ENSP00000360054:L68Q;ENSP00000379001:L27Q;ENSP00000442483:L27Q;ENSP00000347866:L27Q;ENSP00000378998:L27Q;ENSP00000354555:L27Q	ENSP00000347866:L27Q	L	+	2	0	PHACTR3	57751641	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.822000	0.86651	1.621000	0.50320	0.379000	0.24179	CTG	.	.		0.537	PHACTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079923.3	NM_080672		A	58318246	T	A	58318246	3	1	245	1	0	0	0	0	1	0	0	0	11820	1580	55	4	209	4	PHACTR3	20	58318246	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	7535718	58318246	4707274	251	33721										
PSMA7	5688	hgsc.bcm.edu	37	chr20	60713291	60713291	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tttcaatggcttcgtcagtaTagttcttctccaggaactcg	8	10	4	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr20:60713291T>C	ENST00000370873.4	-	5	653	c.527A>G	c.(526-528)tAt>tGt	p.Y176C	PSMA7_ENST00000484488.1_5'UTR|PSMA7_ENST00000370861.1_Missense_Mutation_p.Y106C	NM_002792.3	NP_002783.1	O14818	PSA7_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 7	176					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|proteasome core complex, alpha-subunit complex (GO:0019773)	identical protein binding (GO:0042802)|threonine-type endopeptidase activity (GO:0004298)			large_intestine(1)|lung(2)	3	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.28e-07)			TTCGTCAGTATAGTTCTTCTC	0.488																																					p.Y176C		Atlas-SNP	.											.	PSMA7	13	.	0			c.A527G						.						200	131	154					20																	60713291		2203	4300	6503	SO:0001583	missense	5688	exon5			TCAGTATAGTTCT	AF022815	CCDS13489.1	20q13.33	2008-07-02			ENSG00000101182	ENSG00000101182		"Proteasome (prosome, macropain) subunits"	9536	protein-coding gene	gene with protein product	"proteasome subunit XAPC7", "proteasome subunit RC6-1"	606607				8764072	Standard	NM_002792		Approved	XAPC7, C6, HSPC, RC6-1	uc002ybx.2	O14818	OTTHUMG00000032895	ENST00000370873.4:c.527A>G	chr20.hg19:g.60713291T>C	ENSP00000359910:p.Tyr176Cys	143.0	0.0		138.0	95.0	NM_002792	B2R515|Q5JXJ2|Q9BR53|Q9H4K5|Q9UEU8	Missense_Mutation	SNP	ENST00000370873.4	hg19	CCDS13489.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	16.38|16.38	3.106349|3.106349	0.56291|0.56291	.|.	.|.	ENSG00000101182|ENSG00000101182	ENST00000442551|ENST00000370873;ENST00000370861	.|T;T	.|0.29142	.|1.58;1.58	5.12|5.12	4.02|4.02	0.46733|0.46733	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.72028|0.72028	0.3410|0.3410	H|H	0.99764|0.99764	4.76|4.76	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.77557	.|0.99	T|T	0.80712|0.80712	-0.1260|-0.1260	5|10	.|0.87932	.|D	.|0	.|.	10.76|10.76	0.46259|0.46259	0.0:0.075:0.0:0.925|0.0:0.075:0.0:0.925	.|.	.|176	.|O14818	.|PSA7_HUMAN	V|C	102|176;106	.|ENSP00000359910:Y176C;ENSP00000359898:Y106C	.|ENSP00000359898:Y106C	I|Y	-|-	1|2	0|0	PSMA7|PSMA7	60146686|60146686	1.000000|1.000000	0.71417|0.71417	0.741000|0.741000	0.31004|0.31004	0.493000|0.493000	0.33554|0.33554	7.690000|7.690000	0.84178|0.84178	0.811000|0.811000	0.34303|0.34303	0.460000|0.460000	0.39030|0.39030	ATA|TAT	.	.		0.488	PSMA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079975.1	NM_002792		C	60713291	T	C	60713291	3	2	245	1	0	0	0	0	1	0	0	0	12684	1406	49	2	231	2	PSMA7	20	60713291	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	2395045	60713291	2312229	252	33722										
GATA5	140628	hgsc.bcm.edu	37	chr20	61040413	61040413	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tacctggggggccatgctggGcccagggcacactggggacg	18	12	0	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr20:61040413G>T	ENST00000252997.2	-	6	1082	c.1021C>A	c.(1021-1023)Ccc>Acc	p.P341T		NM_080473.4	NP_536721.1	Q9BWX5	GATA5_HUMAN	GATA binding protein 5	341					blood coagulation (GO:0007596)|cellular response to BMP stimulus (GO:0071773)|intestinal epithelial cell differentiation (GO:0060575)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enhancer sequence-specific DNA binding (GO:0001158)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			kidney(1)|lung(3)|ovary(1)|stomach(1)	6	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;3.08e-06)			GCCATGCTGGGCCCAGGGCAC	0.677																																					p.P341T		Atlas-SNP	.											.	GATA5	22	.	0			c.C1021A						.						21	21	21					20																	61040413		2199	4299	6498	SO:0001583	missense	140628	exon6			TGCTGGGCCCAGG	BC047790, BC117356	CCDS13499.1	20q13.33	2013-07-17	2001-11-28		ENSG00000130700	ENSG00000130700		"GATA zinc finger domain containing"	15802	protein-coding gene	gene with protein product		611496	"GATA-binding protein 5"			9566909	Standard	NM_080473		Approved	bB379O24.1, GATAS	uc002ycx.1	Q9BWX5	OTTHUMG00000032919	ENST00000252997.2:c.1021C>A	chr20.hg19:g.61040413G>T	ENSP00000252997:p.Pro341Thr	8.0	0.0		13.0	8.0	NM_080473	D9ZGF7|Q17RE2|Q86VU4	Missense_Mutation	SNP	ENST00000252997.2	hg19	CCDS13499.1	.	.	.	.	.	.	.	.	.	.	G	0.057	-1.233072	0.01505	.	.	ENSG00000130700	ENST00000370545;ENST00000540404;ENST00000252997	D	0.98400	-4.91	4.87	2.87	0.33458	.	0.556031	0.18783	N	0.131286	D	0.94748	0.8305	L	0.47716	1.5	0.09310	N	1	B	0.30406	0.278	B	0.22386	0.039	D	0.85861	0.1410	10	0.09843	T	0.71	-3.955	9.6717	0.40017	0.1789:0.0:0.8211:0.0	.	341	Q9BWX5	GATA5_HUMAN	T	341;361;341	ENSP00000252997:P341T	ENSP00000252997:P341T	P	-	1	0	GATA5	60473808	0.006000	0.16342	0.033000	0.17914	0.019000	0.09904	1.132000	0.31418	0.612000	0.30071	-0.464000	0.05259	CCC	.	.		0.677	GATA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080038.2	NM_080473		T	61040413	G	T	61040413	3	4	245	1	0	0	0	0	1	0	0	0	6265	1203	42	3	180	3	GATA5	20	61040413	Missense_Mutation	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	327122	61040413	1985107	253	33723										
ITGB2	3689	hgsc.bcm.edu	37	chr21	46308698	46308698	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gcagccctctgagtccctctCcttgcaggtcctgcccttca	8	18	3	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr21:46308698C>G	ENST00000397850.2	-	15	2442	c.1990G>C	c.(1990-1992)Gag>Cag	p.E664Q	ITGB2_ENST00000355153.4_Missense_Mutation_p.E664Q|ITGB2_ENST00000302347.5_Missense_Mutation_p.E664Q|ITGB2_ENST00000397852.1_Missense_Mutation_p.E664Q|ITGB2_ENST00000397854.3_Missense_Mutation_p.E607Q|ITGB2_ENST00000397857.1_Missense_Mutation_p.E664Q			P05107	ITB2_HUMAN	integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)	664					apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|neutrophil chemotaxis (GO:0030593)|receptor clustering (GO:0043113)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|vesicle (GO:0031982)	cell adhesion molecule binding (GO:0050839)|glycoprotein binding (GO:0001948)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(4)|skin(3)	35				Colorectal(79;0.0669)	Simvastatin(DB00641)	GAGTCCCTCTCCTTGCAGGTC	0.637																																					p.E664Q		Atlas-SNP	.											.	ITGB2	107	.	0			c.G1990C						.						78	70	73					21																	46308698		2203	4300	6503	SO:0001583	missense	3689	exon14			CCCTCTCCTTGCA	AK222505	CCDS13716.1	21q22.3	2014-09-17	2006-03-02		ENSG00000160255	ENSG00000160255		"CD molecules", "Complement system", "Integrins"	6155	protein-coding gene	gene with protein product		600065	"integrin, beta 2 (antigen CD18 (p95), lymphocyte function-associated antigen 1; macrophage antigen 1 (mac-1) beta subunit)"	CD18, MFI7			Standard	NM_000211		Approved	LFA-1, MAC-1	uc002zgf.3	P05107	OTTHUMG00000090257	ENST00000397850.2:c.1990G>C	chr21.hg19:g.46308698C>G	ENSP00000380948:p.Glu664Gln	37.0	0.0		34.0	23.0	NM_000211	B3KTS8|D3DSM1|Q16418|Q53HS5|Q9UD72	Missense_Mutation	SNP	ENST00000397850.2	hg19	CCDS13716.1	.	.	.	.	.	.	.	.	.	.	C	18.89	3.719643	0.68844	.	.	ENSG00000160255	ENST00000397852;ENST00000397857;ENST00000397854;ENST00000355153;ENST00000397850;ENST00000302347	D;D;D;D;D;D	0.83075	-1.68;-1.68;-1.68;-1.68;-1.68;-1.68	4.86	3.91	0.45181	Integrin beta subunit, tail (2);	.	.	.	.	D	0.87755	0.6257	M	0.80028	2.48	0.46927	D	0.99925	P;D	0.57899	0.943;0.981	P;P	0.54759	0.733;0.76	D	0.88448	0.3047	9	0.51188	T	0.08	.	12.2769	0.54741	0.0:0.8274:0.1726:0.0	.	607;664	A8MYE6;P05107	.;ITB2_HUMAN	Q	664;664;607;664;664;664	ENSP00000380950:E664Q;ENSP00000380955:E664Q;ENSP00000380952:E607Q;ENSP00000347279:E664Q;ENSP00000380948:E664Q;ENSP00000303242:E664Q	ENSP00000303242:E664Q	E	-	1	0	ITGB2	45133126	1.000000	0.71417	0.984000	0.44739	0.552000	0.35366	3.436000	0.52856	2.221000	0.72209	0.650000	0.86243	GAG	.	.		0.637	ITGB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206566.2	NM_000211		G	46308698	C	G	46308698	3	3	245	1	0	0	0	0	1	0	0	0	7903	864	30	4	331	4	ITGB2	21	46308698	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10		46308698	1821197	254	33724										
PCBP3	54039	hgsc.bcm.edu	37	chr21	47333904	47333904	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ccattccctaccgcccaaagCccgcctccacccctgtcatt	4	22	1	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr21:47333904C>T	ENST00000400314.1	+	10	978	c.640C>T	c.(640-642)Ccc>Tcc	p.P214S	PCBP3_ENST00000400309.1_Missense_Mutation_p.P214S|PCBP3_ENST00000449640.1_Missense_Mutation_p.P214S|PCBP3_ENST00000400304.1_Missense_Mutation_p.P182S|PCBP3_ENST00000400310.1_Missense_Mutation_p.P214S|PCBP3_ENST00000400308.1_Intron			P57721	PCBP3_HUMAN	poly(rC) binding protein 3	214					mRNA metabolic process (GO:0016071)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			biliary_tract(1)|endometrium(3)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17	all_hematologic(128;0.24)			Colorectal(79;0.0411)|READ - Rectum adenocarcinoma(84;0.0649)		CCGCCCAAAGCCCGCCTCCAC	0.612																																					p.P214S		Atlas-SNP	.											.	PCBP3	82	.	0			c.C640T						.						71	82	78					21																	47333904		1997	4173	6170	SO:0001583	missense	54039	exon8			CCAAAGCCCGCCT	AF176329	CCDS42974.2, CCDS46652.1	21q22.3	2013-07-16	2001-11-28		ENSG00000183570	ENSG00000183570			8651	protein-coding gene	gene with protein product		608502	"poly(rC)-binding protein 3"			10936052	Standard	NM_020528		Approved		uc002zhq.2	P57721	OTTHUMG00000090399	ENST00000400314.1:c.640C>T	chr21.hg19:g.47333904C>T	ENSP00000383168:p.Pro214Ser	33.0	0.0		26.0	11.0	NM_020528	A8MPS2|A8MQ26|B7WNN9|B7WPC1|Q8N9K6|Q96EP6	Missense_Mutation	SNP	ENST00000400314.1	hg19	CCDS42974.2	.	.	.	.	.	.	.	.	.	.	C	26.1	4.704342	0.88924	.	.	ENSG00000183570	ENST00000400314;ENST00000400310;ENST00000400309;ENST00000449640;ENST00000346743;ENST00000400304	T;T;T;T;T	0.41400	1.0;1.0;1.0;1.0;1.0	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.49372	0.1553	M	0.82193	2.58	0.80722	D	1	P;B;P;B	0.47677	0.63;0.149;0.899;0.136	B;B;B;B	0.39185	0.293;0.26;0.293;0.105	T	0.61412	-0.7068	10	0.49607	T	0.09	-29.1813	18.6084	0.91275	0.0:1.0:0.0:0.0	.	182;214;214;214	E9PFP8;P57721-4;P57721;P57721-5	.;.;PCBP3_HUMAN;.	S	214;214;214;214;214;182	ENSP00000383168:P214S;ENSP00000383165:P214S;ENSP00000383164:P214S;ENSP00000401198:P214S;ENSP00000383159:P182S	ENSP00000330225:P214S	P	+	1	0	PCBP3	46158332	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.368000	0.79567	2.385000	0.81259	0.563000	0.77884	CCC	.	.		0.612	PCBP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206808.2			T	47333904	C	T	47333904	3	4	245	1	0	0	0	0	1	0	0	0	11511	739	26	3	670	3	PCBP3	21	47333904	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	1025206	47333904	795991	255	33725										
P2RX6	9127	hgsc.bcm.edu	37	chr22	21377002	21377002	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ggctaactgctgggtcgacgAggactgccccgaaggggagg	18	10	0	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr22:21377002A>T	ENST00000413302.2	+	4	573	c.425A>T	c.(424-426)gAg>gTg	p.E142V	P2RX6_ENST00000336296.2_Missense_Mutation_p.E132V|P2RX6_ENST00000401443.1_Missense_Mutation_p.E116V|P2RX6_ENST00000443995.3_Missense_Mutation_p.E89V|P2RX6_ENST00000402329.3_Intron			O15547	P2RX6_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 6	142					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|muscle contraction (GO:0006936)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|channel activity (GO:0015267)|extracellular ATP-gated cation channel activity (GO:0004931)|identical protein binding (GO:0042802)|purinergic nucleotide receptor activity (GO:0001614)|transmembrane signaling receptor activity (GO:0004888)										TGGGTCGACGAGGACTGCCCC	0.667																																					p.E142V		Atlas-SNP	.											.	.	.	.	0			c.A425T						.						42	35	37					22																	21377002		2203	4299	6502	SO:0001583	missense	9127	exon4			TCGACGAGGACTG		CCDS13788.2, CCDS54504.1	22q11.21	2012-01-17	2008-03-28	2008-03-28	ENSG00000099957	ENSG00000099957		"Purinergic receptors", "Ligand-gated ion channels / Purinergic receptors, ionotropic"	8538	protein-coding gene	gene with protein product		608077	"purinergic receptor P2X-like 1, orphan receptor"	P2RXL1		9242461, 10591208, 8786426	Standard	NM_005446		Approved	P2XM, MGC129625, P2X6	uc010gsu.1	O15547	OTTHUMG00000150689	ENST00000413302.2:c.425A>T	chr22.hg19:g.21377002A>T	ENSP00000416193:p.Glu142Val	80.0	0.0		98.0	30.0	NM_005446	F6V3D7|Q32MB6|Q58F04|Q6IC33|Q9UL50	Missense_Mutation	SNP	ENST00000413302.2	hg19	CCDS13788.2	.	.	.	.	.	.	.	.	.	.	A	13.39	2.221988	0.39300	.	.	ENSG00000099957	ENST00000413302;ENST00000336296;ENST00000401443;ENST00000443995	T;T;T;T	0.04758	3.56;3.56;3.56;3.56	5.06	3.99	0.46301	.	0.648718	0.14434	N	0.319879	T	0.07369	0.0186	M	0.62723	1.935	0.33432	D	0.581202	B;B	0.17667	0.023;0.019	B;B	0.18561	0.022;0.013	T	0.02398	-1.1165	10	0.48119	T	0.1	-11.5456	8.9488	0.35776	0.8122:0.1878:0.0:0.0	.	142;116	O15547;F6V3D7	P2RX6_HUMAN;.	V	142;132;116;89	ENSP00000416193:E142V;ENSP00000338797:E132V;ENSP00000385309:E116V;ENSP00000408088:E89V	ENSP00000338797:E132V	E	+	2	0	P2RX6	19707002	0.899000	0.30636	0.880000	0.34516	0.954000	0.61252	1.034000	0.30204	0.839000	0.34971	0.397000	0.26171	GAG	.	.		0.667	P2RX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319625.2	NM_005446		T	21377002	A	T	21377002	3	4	245	1	0	0	0	0	1	0	0	0	11353	304	11	4	439	4	P2RX6	22	21377002	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10		21377002	29927564	256	33726										
C22orf30	253143	hgsc.bcm.edu	37	chr22	32108298	32108298	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ctgcatggtaggcatgtggcTggagaagctccgtttttttg	14	7	0	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr22:32108298T>A	ENST00000327423.6	-	4	5716	c.5527A>T	c.(5527-5529)Agc>Tgc	p.S1843C	PRR14L_ENST00000397493.2_Missense_Mutation_p.S1843C|PRR14L_ENST00000434485.1_Missense_Mutation_p.S1843C	NM_173566.2	NP_775837.2	Q5THK1	PR14L_HUMAN	proline rich 14-like	1843										endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(5)|skin(1)|urinary_tract(2)	14						GGCATGTGGCTGGAGAAGCTC	0.522																																					p.S1843C		Atlas-SNP	.											.	PRR14L	198	.	0			c.A5527T						.						79	82	81					22																	32108298		2203	4300	6503	SO:0001583	missense	253143	exon4			TGTGGCTGGAGAA	BC040859	CCDS13900.2	22q12.2	2011-01-25	2011-01-25	2011-01-25	ENSG00000183530	ENSG00000183530			28738	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 30"	C22orf30		12477932	Standard	NM_173566		Approved	MGC50372	uc003alp.4	Q5THK1	OTTHUMG00000030139	ENST00000327423.6:c.5527A>T	chr22.hg19:g.32108298T>A	ENSP00000331845:p.Ser1843Cys	142.0	0.0		158.0	78.0	NM_173566	Q5THK4|Q6ZNN1|Q6ZWH0|Q8IW74|Q9H5T4	Missense_Mutation	SNP	ENST00000327423.6	hg19	CCDS13900.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	21.2|21.2	4.111749|4.111749	0.77210|0.77210	.|.	.|.	ENSG00000183530|ENSG00000183530	ENST00000330495|ENST00000397493;ENST00000327423;ENST00000434485	.|T;T;T	.|0.39406	.|1.08;1.08;1.08	5.66|5.66	5.66|5.66	0.87406|0.87406	.|.	.|0.113966	.|0.64402	.|D	.|0.000010	T|T	0.62159|0.62159	0.2405|0.2405	M|M	0.63843|0.63843	1.955|1.955	0.36269|0.36269	D|D	0.855075|0.855075	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.77557	.|0.99;0.983;0.99	T|T	0.71699|0.71699	-0.4514|-0.4514	5|10	.|0.87932	.|D	.|0	-3.216|-3.216	15.0747|15.0747	0.72069|0.72069	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|1843;1843;1843	.|Q5THK1-2;Q5THK1;Q5THK1-4	.|.;PR14L_HUMAN;.	L|C	145|1843	.|ENSP00000380630:S1843C;ENSP00000331845:S1843C;ENSP00000388314:S1843C	.|ENSP00000331845:S1843C	Q|S	-|-	2|1	0|0	PRR14L|PRR14L	30438298|30438298	1.000000|1.000000	0.71417|0.71417	0.992000|0.992000	0.48379|0.48379	0.989000|0.989000	0.77384|0.77384	2.730000|2.730000	0.47335|0.47335	2.155000|2.155000	0.67459|0.67459	0.533000|0.533000	0.62120|0.62120	CAG|AGC	.	.		0.522	PRR14L-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074993.2	NM_173566		A	32108298	T	A	32108298	3	1	245	1	0	0	0	0	1	0	0	0	2144	1580	55	4	952	4	C22orf30	22	32108298	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	10731296	32108298	19196268	257	33727										
KCNJ4	3761	hgsc.bcm.edu	37	chr22	38823554	38823554	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ggcagagcttgccgtcgcgcAccgaaatgaccgcgtggtgg	16	12	0	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr22:38823554A>T	ENST00000303592.3	-	2	842	c.584T>A	c.(583-585)gTg>gAg	p.V195E	RP3-434P1.6_ENST00000433230.1_RNA	NM_004981.1|NM_152868.2	NP_004972.1|NP_690607.1	P48050	KCNJ4_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 4	195					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)|PDZ domain binding (GO:0030165)			endometrium(7)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	23	Melanoma(58;0.0286)					GCCGTCGCGCACCGAAATGAC	0.627																																					p.V195E		Atlas-SNP	.											.	KCNJ4	74	.	0			c.T584A						.						47	46	46					22																	38823554		2203	4300	6503	SO:0001583	missense	3761	exon2			TCGCGCACCGAAA	U07364	CCDS13971.1	22q13.1	2011-07-05			ENSG00000168135	ENSG00000168135		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6265	protein-coding gene	gene with protein product		600504				8016146, 16382105	Standard	NM_152868		Approved	Kir2.3, HIR, HRK1, hIRK2, IRK3	uc003avs.1	P48050	OTTHUMG00000151131	ENST00000303592.3:c.584T>A	chr22.hg19:g.38823554A>T	ENSP00000306497:p.Val195Glu	44.0	0.0		55.0	31.0	NM_004981	Q14D44	Missense_Mutation	SNP	ENST00000303592.3	hg19	CCDS13971.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.116740	0.77323	.	.	ENSG00000168135	ENST00000303592	D	0.94184	-3.37	4.94	4.94	0.65067	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.077579	0.52532	D	0.000063	D	0.91646	0.7360	N	0.22421	0.69	0.45899	D	0.998742	P	0.41643	0.758	P	0.50162	0.633	D	0.92831	0.6280	10	0.66056	D	0.02	.	14.9516	0.71080	1.0:0.0:0.0:0.0	.	195	P48050	IRK4_HUMAN	E	195	ENSP00000306497:V195E	ENSP00000306497:V195E	V	-	2	0	KCNJ4	37153500	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	9.292000	0.96076	2.001000	0.58596	0.454000	0.30748	GTG	.	.		0.627	KCNJ4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321447.1	NM_004981		T	38823554	A	T	38823554	3	4	245	1	0	0	0	0	1	0	0	0	8062	159	6	4	757	4	KCNJ4	22	38823554	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	6715256	38823554	12481012	258	33728										
PNPLA3	80339	hgsc.bcm.edu	37	chr22	44332942	44332942	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ccttcacaggcatctgcaacAggccccagccaggcctgaag	10	16	2	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr22:44332942A>T	ENST00000216180.3	+	6	942	c.769A>T	c.(769-771)Agg>Tgg	p.R257W	PNPLA3_ENST00000423180.2_Missense_Mutation_p.R253W	NM_025225.2	NP_079501.2	Q9NST1	PLPL3_HUMAN	patatin-like phospholipase domain containing 3	257					acylglycerol acyl-chain remodeling (GO:0036155)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride catabolic process (GO:0019433)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	diolein transacylation activity (GO:0051265)|mono-olein transacylation activity (GO:0051264)|phospholipase A2 activity (GO:0004623)|triglyceride lipase activity (GO:0004806)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(3)|prostate(1)|skin(1)|stomach(2)	19		Ovarian(80;0.024)|all_neural(38;0.0416)				CATCTGCAACAGGCCCCAGCC	0.602																																					p.R257W		Atlas-SNP	.											.	PNPLA3	53	.	0			c.A769T						.						56	50	52					22																	44332942		2203	4300	6503	SO:0001583	missense	80339	exon6			TGCAACAGGCCCC		CCDS14054.1	22q13.31	2014-03-14	2006-05-26	2006-05-26	ENSG00000100344	ENSG00000100344	3.1.1.3	"Patatin-like phospholipase domain containing"	18590	protein-coding gene	gene with protein product		609567	"chromosome 22 open reading frame 20", "adiponutrin"	C22orf20, ADPN		16799181, 19029121	Standard	NM_025225		Approved	dJ796I17.1, FLJ22012, adiponutrin, iPLA2epsilon	uc003bei.1	Q9NST1	OTTHUMG00000150555	ENST00000216180.3:c.769A>T	chr22.hg19:g.44332942A>T	ENSP00000216180:p.Arg257Trp	49.0	0.0		50.0	17.0	NM_025225	B0QYI0|B2RCL3|B3KW00|Q6P1A1|Q96CB4	Missense_Mutation	SNP	ENST00000216180.3	hg19	CCDS14054.1	.	.	.	.	.	.	.	.	.	.	A	16.97	3.267463	0.59540	.	.	ENSG00000100344	ENST00000216180;ENST00000423180	T;T	0.78003	-1.14;-1.14	5.34	-6.67	0.01783	Acyl transferase/acyl hydrolase/lysophospholipase (1);	0.976138	0.08355	N	0.958683	T	0.63616	0.2526	L	0.48642	1.525	0.09310	N	1	P	0.39831	0.69	B	0.38327	0.271	T	0.57860	-0.7738	10	0.46703	T	0.11	-7.3393	4.6593	0.12634	0.1532:0.2429:0.4842:0.1197	.	257	Q9NST1	PLPL3_HUMAN	W	257;253	ENSP00000216180:R257W;ENSP00000397987:R253W	ENSP00000216180:R257W	R	+	1	2	PNPLA3	42664275	0.000000	0.05858	0.007000	0.13788	0.040000	0.13550	-0.994000	0.03716	-0.817000	0.04335	0.379000	0.24179	AGG	.	.		0.602	PNPLA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318891.1	NM_025225		T	44332942	A	T	44332942	3	4	245	1	0	0	0	0	1	0	0	0	12175	179	7	4	791	4	PNPLA3	22	44332942	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	5509388	44332942	6971624	259	33729										
ARHGAP8	23779	hgsc.bcm.edu	37	chr22	45210622	45210622	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tcaaggtcctgtggaacatcTtgaagcccctcatcaggtat	9	11	4	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chr22:45210622T>G	ENST00000389774.2	+	6	604	c.463T>G	c.(463-465)Ttg>Gtg	p.L155V	ARHGAP8_ENST00000356099.6_Missense_Mutation_p.L124V|PRR5-ARHGAP8_ENST00000352766.7_Missense_Mutation_p.L334V|ARHGAP8_ENST00000336963.4_Missense_Mutation_p.L124V|PRR5-ARHGAP8_ENST00000361473.5_Missense_Mutation_p.L255V|ARHGAP8_ENST00000517296.3_Missense_Mutation_p.L334V|ARHGAP8_ENST00000389773.5_Missense_Mutation_p.L246V	NM_001017526.1	NP_001017526.1	P85298	RHG08_HUMAN	Rho GTPase activating protein 8	155	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(9)|prostate(1)|skin(7)	29		all_neural(38;0.00409)|Ovarian(80;0.00976)|Glioma(61;0.0649)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0204)		GTGGAACATCTTGAAGCCCCT	0.582																																					p.L246V		Atlas-SNP	.											.	PRR5-ARHGAP8	53	.	0			c.T736G						.						143	115	125					22																	45210622		2203	4300	6503	SO:0001583	missense	553158	exon8			AACATCTTGAAGC	AF177331	CCDS14060.2, CCDS33664.1, CCDS56233.1	22q13.3	2010-05-11			ENSG00000241484	ENSG00000241484		"Rho GTPase activating proteins"	677	protein-coding gene	gene with protein product		609405				10591208	Standard	NM_001198726		Approved	FLJ20185, BPGAP1		P85298	OTTHUMG00000030234	ENST00000389774.2:c.463T>G	chr22.hg19:g.45210622T>G	ENSP00000374424:p.Leu155Val	79.0	0.0		88.0	21.0	NM_181334	A6ZJ79|A6ZJ80|O75983|O95695|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Missense_Mutation	SNP	ENST00000389774.2	hg19	CCDS33664.1	.	.	.	.	.	.	.	.	.	.	T	12.99	2.104867	0.37145	.	.	ENSG00000248405;ENSG00000248405;ENSG00000241484;ENSG00000241484;ENSG00000241484;ENSG00000241484;ENSG00000241484	ENST00000361473;ENST00000352766;ENST00000517296;ENST00000389773;ENST00000389774;ENST00000336963;ENST00000356099	T;T;T;T;T;T;T	0.23147	1.92;1.92;1.92;1.92;1.92;1.92;1.92	4.04	3.0	0.34707	Cellular retinaldehyde-binding/triple function, C-terminal (5);	.	.	.	.	T	0.15696	0.0378	N	0.20445	0.575	0.24311	N	0.995082	B;B;P;B;B;B;B	0.36683	0.033;0.013;0.565;0.033;0.033;0.027;0.1	B;B;B;B;B;B;B	0.33846	0.043;0.016;0.171;0.063;0.026;0.082;0.098	T	0.11108	-1.0601	9	0.49607	T	0.09	.	8.8767	0.35350	0.0:0.0914:0.0:0.9086	.	160;124;160;155;165;334;255	B7ZMA4;A6ZJ79;A2RU51;P85298;Q6PCC7;B1AHC4;B1AHC3	.;.;.;RHG08_HUMAN;.;.;.	V	255;334;334;246;155;124;124	ENSP00000354732:L255V;ENSP00000262731:L334V;ENSP00000429240:L334V;ENSP00000374423:L246V;ENSP00000374424:L155V;ENSP00000337287:L124V;ENSP00000348407:L124V	ENSP00000337287:L124V	L	+	1	2	PRR5-ARHGAP8;ARHGAP8	43589286	1.000000	0.71417	0.581000	0.28614	0.727000	0.41649	3.562000	0.53777	0.616000	0.30141	0.529000	0.55759	TTG	.	.		0.582	ARHGAP8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000075088.4	NM_017701		G	45210622	T	G	45210622	3	3	245	1	0	0	0	0	1	0	0	0	888	1606	56	5	481	5	ARHGAP8	22	45210622	Missense_Mutation	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	877680	45210622	6093944	260	33730										
MBTPS2	51360	hgsc.bcm.edu	37	chrX	21887622	21887622	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	accctcttcccaaggactctCctgccattggacccagaggc	8	17	2	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chrX:21887622C>T	ENST00000379484.5	+	7	895	c.796C>T	c.(796-798)Cct>Tct	p.P266S	MBTPS2_ENST00000365779.2_Missense_Mutation_p.P266S	NM_015884.3	NP_056968.1	O43462	MBTP2_HUMAN	membrane-bound transcription factor peptidase, site 2	266					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cholesterol metabolic process (GO:0008203)|endoplasmic reticulum unfolded protein response (GO:0030968)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|endometrium(3)|large_intestine(3)|lung(13)|ovary(1)|skin(2)	24						CAAGGACTCTCCTGCCATTGG	0.393																																					p.P266S		Atlas-SNP	.											.	MBTPS2	52	.	0			c.C796T						.						119	105	110					X																	21887622		2203	4300	6503	SO:0001583	missense	51360	exon7			GACTCTCCTGCCA	AF019612	CCDS14201.1	Xp22.12-p22.11	2014-02-03	2005-08-17		ENSG00000012174	ENSG00000012174			15455	protein-coding gene	gene with protein product		300294	"membrane-bound transcription factor protease, site 2", "keratosis follicularis spinulosa decalvans"	KFSD		9847074, 9659902, 20672378	Standard	NM_015884		Approved	S2P	uc004dae.3	O43462	OTTHUMG00000021237	ENST00000379484.5:c.796C>T	chrX.hg19:g.21887622C>T	ENSP00000368798:p.Pro266Ser	60.0	0.0		69.0	64.0	NM_015884	Q9UM70|Q9UMD3	Missense_Mutation	SNP	ENST00000379484.5	hg19	CCDS14201.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.153233	0.78114	.	.	ENSG00000012174	ENST00000379484;ENST00000365779	D;D	0.95821	-3.82;-2.68	4.84	4.84	0.62591	Peptidase M50 (1);	0.052899	0.85682	D	0.000000	D	0.96087	0.8725	M	0.74881	2.28	0.80722	D	1	P;P	0.47762	0.9;0.817	P;B	0.49799	0.622;0.401	D	0.95522	0.8595	10	0.37606	T	0.19	-16.8949	17.4296	0.87536	0.0:1.0:0.0:0.0	.	266;266	O43462;B9ZVQ3	MBTP2_HUMAN;.	S	266	ENSP00000368798:P266S;ENSP00000368796:P266S	ENSP00000368796:P266S	P	+	1	0	MBTPS2	21797543	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	5.769000	0.68865	2.386000	0.81285	0.600000	0.82982	CCT	.	.		0.393	MBTPS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056026.1			T	21887622	C	T	21887622	3	4	245	1	0	0	0	0	1	0	0	0	9371	855	30	3	822	3	MBTPS2	23	21887622	Missense_Mutation	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10		21887622	133382938	261	33731										
DMD	1756	hgsc.bcm.edu	37	chrX	32429921	32429921	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ccttgtctgcaatataagctGccaactgcttgtcaatgaat	7	10	2	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chrX:32429921G>T	ENST00000357033.4	-	30	4387	c.4181C>A	c.(4180-4182)gCa>gAa	p.A1394E	DMD_ENST00000378677.2_Missense_Mutation_p.A1390E	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	1394					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				AATATAAGCTGCCAACTGCTT	0.453																																					p.A1394E		Atlas-SNP	.											.	DMD	2127	.	0			c.C4181A						.						125	93	104					X																	32429921		2202	4300	6502	SO:0001583	missense	1756	exon30			TAAGCTGCCAACT	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.4181C>A	chrX.hg19:g.32429921G>T	ENSP00000354923:p.Ala1394Glu	54.0	0.0		60.0	60.0	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	hg19	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	G	15.74	2.922775	0.52653	.	.	ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280	T;T	0.16457	2.34;2.34	5.68	5.68	0.88126	.	0.701259	0.11231	U	0.585641	T	0.12902	0.0313	N	0.22421	0.69	0.80722	D	1	B;P;B;B;B	0.40144	0.275;0.704;0.18;0.18;0.18	B;B;B;B;B	0.35182	0.128;0.197;0.06;0.037;0.037	T	0.21724	-1.0237	10	0.07813	T	0.8	.	18.7838	0.91946	0.0:0.0:1.0:0.0	.	1386;1394;1390;53;50	P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6	.;DMD_HUMAN;.;.;.	E	1386;53;50;1390;1394;1394;1271	ENSP00000367948:A1390E;ENSP00000354923:A1394E	ENSP00000354923:A1394E	A	-	2	0	DMD	32339842	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	4.916000	0.63362	2.381000	0.81170	0.506000	0.49869	GCA	.	.		0.453	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		T	32429921	G	T	32429921	3	4	245	1	0	0	0	0	1	0	0	0	4582	1319	46	3	7224	3	DMD	23	32429921	Missense_Mutation	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	10542299	32429921	122840639	262	33732										
BCOR	54880	hgsc.bcm.edu	37	chrX	39932115	39932115	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gcgctctggccaacactctcTgctgcaaagctgggtttgga	12	12	2	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chrX:39932115T>A	ENST00000378444.4	-	4	2712	c.2484A>T	c.(2482-2484)gcA>gcT	p.A828A	BCOR_ENST00000397354.3_Silent_p.A828A|BCOR_ENST00000378455.4_Silent_p.A828A|BCOR_ENST00000342274.4_Silent_p.A828A	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	828					heart development (GO:0007507)|histone H2A monoubiquitination (GO:0035518)|negative regulation of bone mineralization (GO:0030502)|negative regulation of histone H3-K36 methylation (GO:0000415)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|palate development (GO:0060021)|specification of axis polarity (GO:0065001)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	heat shock protein binding (GO:0031072)|histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			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						CAACACTCTCTGCTGCAAAGC	0.557			"F, N, S, T"	RARA	"retinoblastoma, AML, APL(translocation)"		oculo-facio-cardio-dental genetic																														p.A828A		Atlas-SNP	.		Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	BCOR	351	.	0			c.A2484T						.						63	60	61					X																	39932115		2202	4300	6502	SO:0001819	synonymous_variant	54880	exon4			ACTCTCTGCTGCA	AF317391	CCDS14250.1, CCDS48092.1, CCDS48093.1	Xp11.4	2014-09-17	2010-06-10		ENSG00000183337	ENSG00000183337		"Ankyrin repeat domain containing"	20893	protein-coding gene	gene with protein product		300485	"BCL6 co-repressor"			10898795	Standard	NM_017745		Approved	FLJ20285, KIAA1575	uc004den.4	Q6W2J9	OTTHUMG00000024100	ENST00000378444.4:c.2484A>T	chrX.hg19:g.39932115T>A		63.0	0.0		44.0	39.0	NM_001123385	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Silent	SNP	ENST00000378444.4	hg19	CCDS48093.1																																																																																			.	.		0.557	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745		A	39932115	T	A	39932115	2	1	245	1	0	0	0	0	0	0	0	1	1386	1567	55	4		4	BCOR	23	39932115	Silent	SNP	T	TCGA-ED-A7PZ-01A-11D-A33Q-10	7502194	39932115	115338445	263	33733										
MAOA	4128	hgsc.bcm.edu	37	chrX	43603116	43603116	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	aagtggagcggctacatggaAggggcagttgaggctggaga	19	5	0	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chrX:43603116A>T	ENST00000338702.3	+	13	1461	c.1338A>T	c.(1336-1338)gaA>gaT	p.E446D	MAOA_ENST00000542639.1_Missense_Mutation_p.E313D	NM_000240.3	NP_000231.1	P21397	AOFA_HUMAN	monoamine oxidase A	446					cellular biogenic amine metabolic process (GO:0006576)|dopamine catabolic process (GO:0042420)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter catabolic process (GO:0042135)|neurotransmitter secretion (GO:0007269)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|xenobiotic metabolic process (GO:0006805)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	primary amine oxidase activity (GO:0008131)			NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	18					Almotriptan(DB00918)|Dopamine(DB00988)|Ephedra(DB01363)|Flavin adenine dinucleotide(DB03147)|Furazolidone(DB00614)|Isocarboxazid(DB01247)|Linezolid(DB00601)|Methamphetamine(DB01577)|Minaprine(DB00805)|Moclobemide(DB01171)|Nandrolone decanoate(DB08804)|Naratriptan(DB00952)|Nicotine(DB00184)|Pargyline(DB01626)|Phenelzine(DB00780)|Phentermine(DB00191)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Procaine(DB00721)|Pseudoephedrine(DB00852)|Riboflavin(DB00140)|Rizatriptan(DB00953)|Selegiline(DB01037)|Sertraline(DB01104)|Sumatriptan(DB00669)|Testosterone(DB00624)|Tranylcypromine(DB00752)|Zolmitriptan(DB00315)|Zonisamide(DB00909)	GCTACATGGAAGGGGCAGTTG	0.562																																					p.E446D		Atlas-SNP	.											.	MAOA	48	.	0			c.A1338T						.						62	41	48					X																	43603116		2175	4250	6425	SO:0001583	missense	4128	exon13			CATGGAAGGGGCA		CCDS14260.1, CCDS59163.1	Xp11.4-p11.3	2008-02-05			ENSG00000189221	ENSG00000189221	1.4.3.4		6833	protein-coding gene	gene with protein product		309850					Standard	NM_000240		Approved		uc004dfy.4	P21397	OTTHUMG00000021387	ENST00000338702.3:c.1338A>T	chrX.hg19:g.43603116A>T	ENSP00000340684:p.Glu446Asp	43.0	0.0		34.0	31.0	NM_000240	B4DF46|Q16426	Missense_Mutation	SNP	ENST00000338702.3	hg19	CCDS14260.1	.	.	.	.	.	.	.	.	.	.	A	14.49	2.552321	0.45487	.	.	ENSG00000189221	ENST00000338702;ENST00000542639	D;D	0.92965	-3.14;-3.14	5.93	-1.63	0.08345	Amine oxidase (1);	0.000000	0.85682	D	0.000000	D	0.84723	0.5535	L	0.28192	0.835	0.54753	D	0.999987	B	0.25850	0.136	B	0.35114	0.196	T	0.69124	-0.5228	10	0.14252	T	0.57	.	11.2426	0.48979	0.5702:0.0:0.4298:0.0	.	446	P21397	AOFA_HUMAN	D	446;313	ENSP00000340684:E446D;ENSP00000440846:E313D	ENSP00000340684:E446D	E	+	3	2	MAOA	43488060	1.000000	0.71417	0.994000	0.49952	0.639000	0.38242	1.039000	0.30266	-0.177000	0.10690	-0.314000	0.08810	GAA	.	.		0.562	MAOA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056300.1	NM_000240		T	43603116	A	T	43603116	3	4	245	1	0	0	0	0	1	0	0	0	9234	69	3	4	1388	4	MAOA	23	43603116	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	3671001	43603116	111667444	264	33734										
PRAF2	11230	hgsc.bcm.edu	37	chrX	48931536	48931536	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tagtagaggaggttgttgatGacgcggtggcaccatcgctg	16	7	0	3			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chrX:48931536G>T	ENST00000376390.4	-	1	194	c.111C>A	c.(109-111)gtC>gtA	p.V37V	PRAF2_ENST00000491199.1_5'Flank|WDR45_ENST00000553851.1_Intron|PRAF2_ENST00000376386.3_Silent_p.V37V|AF196779.12_ENST00000376358.3_Intron	NM_007213.1	NP_009144.1	O60831	PRAF2_HUMAN	PRA1 domain family, member 2	37					L-glutamate transport (GO:0015813)|protein transport (GO:0015031)	endosome (GO:0005768)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	8						GGTTGTTGATGACGCGGTGGC	0.667																																					p.V37V		Atlas-SNP	.											.	PRAF2	14	.	0			c.C111A						.						94	77	83					X																	48931536		2203	4300	6503	SO:0001819	synonymous_variant	11230	exon1			GTTGATGACGCGG	BC021213	CCDS14317.1	Xp11.23	2008-02-05	2004-11-15		ENSG00000243279	ENSG00000243279			28911	protein-coding gene	gene with protein product		300840	"PRA1 domain family 2"			16481131	Standard	NM_007213		Approved	JM4		O60831	OTTHUMG00000034499	ENST00000376390.4:c.111C>A	chrX.hg19:g.48931536G>T		25.0	0.0		41.0	34.0	NM_007213	B2RD20	Silent	SNP	ENST00000376390.4	hg19	CCDS14317.1																																																																																			.	.		0.667	PRAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083415.2	NM_007213		T	48931536	G	T	48931536	2	4	245	1	0	0	0	0	0	0	0	1	12434	1277	45	3		3	PRAF2	23	48931536	Silent	SNP	G	TCGA-ED-A7PZ-01A-11D-A33Q-10	5328420	48931536	106339024	265	33735										
OPHN1	4983	hgsc.bcm.edu	37	chrX	67293091	67293091	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	tgccttcttgctgtcacccgAggcggaggcactggcggtgc	15	13	2	0			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chrX:67293091A>T	ENST00000355520.5	-	20	2378	c.1737T>A	c.(1735-1737)ccT>ccA	p.P579P	OPHN1_ENST00000484842.1_5'UTR|OPHN1_ENST00000540071.1_Silent_p.P579P	NM_002547.2	NP_002538.1	O60890	OPHN1_HUMAN	oligophrenin 1	579					actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|negative regulation of proteasomal protein catabolic process (GO:1901799)|nervous system development (GO:0007399)|regulation of endocytosis (GO:0030100)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of synaptic transmission, glutamatergic (GO:0051966)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|substrate-dependent cell migration, cell extension (GO:0006930)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|terminal bouton (GO:0043195)	phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(3)|skin(2)	31						CTGTCACCCGAGGCGGAGGCA	0.473																																					p.P579P		Atlas-SNP	.											.	OPHN1	75	.	0			c.T1737A						.						104	78	87					X																	67293091		2203	4300	6503	SO:0001819	synonymous_variant	4983	exon20			CACCCGAGGCGGA	AJ001189	CCDS14388.1	Xq12	2011-07-04			ENSG00000079482	ENSG00000079482		"Rho GTPase activating proteins"	8148	protein-coding gene	gene with protein product		300127	"mental retardation, X-linked 60"	MRX60		9195162, 9582072	Standard	NM_002547		Approved	OPN1, ARHGAP41	uc004dww.4	O60890	OTTHUMG00000021744	ENST00000355520.5:c.1737T>A	chrX.hg19:g.67293091A>T		97.0	0.0		98.0	91.0	NM_002547	B9EIP8|Q5JQ81|Q6PCC1|Q8WX47	Silent	SNP	ENST00000355520.5	hg19	CCDS14388.1																																																																																			.	.		0.473	OPHN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057011.1	NM_002547		T	67293091	A	T	67293091	2	4	245	1	0	0	0	0	0	0	0	1	10884	291	11	4		4	OPHN1	23	67293091	Silent	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	18361555	67293091	87977469	266	33736										
IL13RA2	3598	hgsc.bcm.edu	37	chrX	114249118	114249118	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	caaacccatctttgtaatgtAgattcttagtaatgatggtc	7	7	2	2			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chrX:114249118A>T	ENST00000371936.1	-	5	515	c.266T>A	c.(265-267)cTa>cAa	p.L89Q	IL13RA2_ENST00000243213.1_Missense_Mutation_p.L89Q|IL13RA2_ENST00000468224.1_5'UTR			Q14627	I13R2_HUMAN	interleukin 13 receptor, alpha 2	89	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	cytokine receptor activity (GO:0004896)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(6)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	23						TTTGTAATGTAGATTCTTAGT	0.358																																					p.L89Q		Atlas-SNP	.											.	IL13RA2	66	.	0			c.T266A						.						95	75	82					X																	114249118		2203	4300	6503	SO:0001583	missense	3598	exon4			TAATGTAGATTCT	X95302	CCDS14565.1	Xq23	2014-01-21			ENSG00000123496	ENSG00000123496		"Interleukins and interleukin receptors", "CD molecules"	5975	protein-coding gene	gene with protein product	"cancer/testis antigen 19"	300130				8663118, 9083087	Standard	NM_000640		Approved	IL-13R, IL13BP, CD213a2, CT19	uc004epx.3	Q14627	OTTHUMG00000022229	ENST00000371936.1:c.266T>A	chrX.hg19:g.114249118A>T	ENSP00000361004:p.Leu89Gln	54.0	0.0		43.0	40.0	NM_000640	A8K7E2|O00667	Missense_Mutation	SNP	ENST00000371936.1	hg19	CCDS14565.1	.	.	.	.	.	.	.	.	.	.	A	18.23	3.578881	0.65878	.	.	ENSG00000123496	ENST00000371936;ENST00000243213	T;T	0.40225	1.04;1.04	5.18	5.18	0.71444	Fibronectin, type III (1);Immunoglobulin-like fold (1);	0.332186	0.29002	N	0.013449	T	0.60663	0.2286	M	0.70275	2.135	0.48288	D	0.999629	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.946	T	0.61973	-0.6952	10	0.48119	T	0.1	-12.0276	10.1104	0.42559	1.0:0.0:0.0:0.0	.	89;89	D0EFR8;Q14627	.;I13R2_HUMAN	Q	89	ENSP00000361004:L89Q;ENSP00000243213:L89Q	ENSP00000243213:L89Q	L	-	2	0	IL13RA2	114155374	0.976000	0.34144	0.864000	0.33941	0.948000	0.59901	5.374000	0.66167	1.912000	0.55364	0.437000	0.28790	CTA	.	.		0.358	IL13RA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057966.1	NM_000640		T	114249118	A	T	114249118	3	4	245	1	0	0	0	0	1	0	0	0	7639	420	15	4	904	4	IL13RA2	23	114249118	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	46956027	114249118	41021442	267	33737										
KIAA1210	57481	hgsc.bcm.edu	37	chrX	118223434	118223434	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	gttgtccttctctaaggacaAgtgcgagaaagggacattcc	11	9	1	1			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chrX:118223434A>T	ENST00000402510.2	-	11	1758	c.1759T>A	c.(1759-1761)Ttg>Atg	p.L587M		NM_020721.1	NP_065772.1	Q9ULL0	K1210_HUMAN	KIAA1210	587										breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(31)|ovary(4)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	64						TCTAAGGACAAGTGCGAGAAA	0.493																																					p.L587M		Atlas-SNP	.											.	KIAA1210	171	.	0			c.T1759A						.						114	103	107					X																	118223434		1970	4153	6123	SO:0001583	missense	57481	exon11			AGGACAAGTGCGA	AB033036	CCDS48156.1	Xq24	2012-10-04			ENSG00000250423	ENSG00000250423			29218	protein-coding gene	gene with protein product						10574462	Standard	NM_020721		Approved		uc004era.4	Q9ULL0	OTTHUMG00000162980	ENST00000402510.2:c.1759T>A	chrX.hg19:g.118223434A>T	ENSP00000384670:p.Leu587Met	42.0	0.0		42.0	40.0	NM_020721	B7ZCI8|Q5JPN4	Missense_Mutation	SNP	ENST00000402510.2	hg19	CCDS48156.1	.	.	.	.	.	.	.	.	.	.	A	14.14	2.446212	0.43429	.	.	ENSG00000250423	ENST00000402510	T	0.15603	2.41	5.21	-2.44	0.06502	.	.	.	.	.	T	0.13543	0.0328	N	0.19112	0.55	0.09310	N	1	P	0.50156	0.932	P	0.50659	0.647	T	0.15983	-1.0418	9	0.45353	T	0.12	.	5.8306	0.18579	0.5243:0.0:0.3428:0.1329	.	587	Q9ULL0	K1210_HUMAN	M	587	ENSP00000384670:L587M	ENSP00000384670:L587M	L	-	1	2	RP13-347D8.6	118107462	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.300000	0.08243	-0.905000	0.03871	-0.404000	0.06349	TTG	.	.		0.493	KIAA1210-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371251.2	NM_020721		T	118223434	A	T	118223434	3	4	245	1	0	0	0	0	1	0	0	0	8223	69	3	4	3386	4	KIAA1210	23	118223434	Missense_Mutation	SNP	A	TCGA-ED-A7PZ-01A-11D-A33Q-10	3974316	118223434	37047126	268	33738										
MAGEC1	9947	hgsc.bcm.edu	37	chrX	140994576	140994576	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0297397769516729	8	1	0.858278145695364	1.94543046357616	0.550593527427215	1	1	0	ttgagtcttttccagagttcCcctgagagaactcacagtac	8	11	2	4			TCGA-ED-A7PZ-01A-11D-A33Q-10	TCGA-ED-A7PZ-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9271fe2-2c4b-4513-8eac-853a1acc9568	84111421-4619-45db-918a-9570d676c285	g.chrX:140994576C>A	ENST00000285879.4	+	4	1672	c.1386C>A	c.(1384-1386)tcC>tcA	p.S462S	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	462										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					TCCAGAGTTCCCCTGAGAGAA	0.483										HNSCC(15;0.026)																											p.S462S		Atlas-SNP	.											.	MAGEC1	317	.	0			c.C1386A						.						99	109	105					X																	140994576		2203	4299	6502	SO:0001819	synonymous_variant	9947	exon4			GAGTTCCCCTGAG	AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"cancer/testis antigen family 7, member 1"	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.1386C>A	chrX.hg19:g.140994576C>A		123.0	0.0		121.0	12.0	NM_005462	A0PK03|O75451|Q8TCV4	Silent	SNP	ENST00000285879.4	hg19	CCDS35417.1																																																																																			.	.		0.483	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462		A	140994576	C	A	140994576	2	1	245	1	0	0	0	0	0	0	0	1	9189	610	22	3		3	MAGEC1	23	140994576	Silent	SNP	C	TCGA-ED-A7PZ-01A-11D-A33Q-10	22771142	140994576	14275984	269	33739										
TAS1R3	83756	hgsc.bcm.edu	37	chr1	1266874	1266874	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	gggcgaggccgaggaggctgGcctccgcagccggacacggc	19	14	0	0			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr1:1266874G>A	ENST00000339381.5	+	1	181	c.149G>A	c.(148-150)gGc>gAc	p.G50D		NM_152228.1	NP_689414	Q7RTX0	TS1R3_HUMAN	taste receptor, type 1, member 3	50					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			kidney(2)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.88e-21)|Colorectal(212;0.000157)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00251)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.146)		GAGGAGGCTGGCCTCCGCAGC	0.697																																					p.G50D		Atlas-SNP	.											.	TAS1R3	39	.	0			c.G149A						.						8	9	9					1																	1266874		2153	4233	6386	SO:0001583	missense	83756	exon1			AGGCTGGCCTCCG	AC026283	CCDS30556.1	1p36	2012-08-22			ENSG00000169962	ENSG00000169962		"Taste receptors / Type 1", "GPCR / Unclassified : Taste receptors"	15661	protein-coding gene	gene with protein product		605865				11319557	Standard	XM_006710939		Approved	T1R3	uc010nyk.2	Q7RTX0	OTTHUMG00000003071	ENST00000339381.5:c.149G>A	chr1.hg19:g.1266874G>A	ENSP00000344411:p.Gly50Asp	31.0	0.0		40.0	6.0	NM_152228	Q5TA49|Q8NGW9	Missense_Mutation	SNP	ENST00000339381.5	hg19	CCDS30556.1	.	.	.	.	.	.	.	.	.	.	G	2.293	-0.362003	0.05103	.	.	ENSG00000169962	ENST00000339381	D	0.86030	-2.06	4.11	-6.03	0.02185	.	1.914590	0.02568	N	0.097455	T	0.62853	0.2462	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.58086	-0.7698	10	0.10111	T	0.7	.	2.2584	0.04060	0.3662:0.3453:0.1774:0.1111	.	50	Q7RTX0	TS1R3_HUMAN	D	50	ENSP00000344411:G50D	ENSP00000344411:G50D	G	+	2	0	TAS1R3	1256737	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-1.572000	0.02136	-0.703000	0.05049	-0.802000	0.03209	GGC	.	.		0.697	TAS1R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008493.1			A	1266874	G	A	1266874	3	1	246	1	0	0	0	0	1	0	0	0	15579	1203	42	3	151	3	TAS1R3	1	1266874	Missense_Mutation	SNP	G	TCGA-ED-A7XO-01A-11D-A34Z-10		1266874	247983747	1	33740										
UBR4	23352	hgsc.bcm.edu	37	chr1	19408022	19408022	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	cacttctccttgggctgttcCagaaagccttggaggttctt	10	11	2	1			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr1:19408022C>A	ENST00000375254.3	-	103	15081	c.15054G>T	c.(15052-15054)ctG>ctT	p.L5018L	UBR4_ENST00000375226.2_Silent_p.L4994L|UBR4_ENST00000375217.2_Silent_p.L5011L|UBR4_ENST00000375267.2_Silent_p.L5018L|UBR4_ENST00000429347.2_Silent_p.L541L|UBR4_ENST00000375224.1_Silent_p.L725L|UBR4_ENST00000375225.3_Silent_p.L93L|AL137127.1_ENST00000582644.1_RNA|UBR4_ENST00000543981.1_Silent_p.L682L	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	5018					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.L5018L(1)		breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		TGGGCTGTTCCAGAAAGCCTT	0.537																																					p.L5018L		Atlas-SNP	.											UBR4,colon,carcinoma,0,1	UBR4	415	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G15054T						.						159	164	162					1																	19408022		2203	4300	6503	SO:0001819	synonymous_variant	23352	exon103			CTGTTCCAGAAAG	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.15054G>T	chr1.hg19:g.19408022C>A		56.0	1.0		91.0	24.0	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Silent	SNP	ENST00000375254.3	hg19	CCDS189.1																																																																																			.	.		0.537	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		A	19408022	C	A	19408022	2	1	246	1	0	0	0	0	0	0	0	1	16919	581	21	3		3	UBR4	1	19408022	Silent	SNP	C	TCGA-ED-A7XO-01A-11D-A34Z-10	18141148	19408022	229842599	2	33741										
FAF1	11124	hgsc.bcm.edu	37	chr1	51323604	51323604	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	aagaaaaaagtacttaccacTaagtcccaattattttgttc	4	8	0	1			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr1:51323604T>A	ENST00000396153.2	-	2	562	c.111A>T	c.(109-111)ttA>ttT	p.L37F	FAF1_ENST00000371778.4_Missense_Mutation_p.L37F	NM_007051.2	NP_008982.1	Q9UNN5	FAF1_HUMAN	Fas (TNFRSF6) associated factor 1	37	UBA.				apoptotic process (GO:0006915)|cell death (GO:0008219)|cytoplasmic sequestering of NF-kappaB (GO:0007253)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of protein complex assembly (GO:0031334)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of cell adhesion (GO:0030155)|regulation of protein catabolic process (GO:0042176)|regulation of protein kinase activity (GO:0045859)	CD95 death-inducing signaling complex (GO:0031265)|Cdc48p-Npl4p-Ufd1p AAA ATPase complex (GO:0034098)|cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	heat shock protein binding (GO:0031072)|NF-kappaB binding (GO:0051059)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)	p.0?(5)		breast(2)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|pancreas(2)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)		TACTTACCACTAAGTCCCAAT	0.294																																					p.L37F		Atlas-SNP	.											.	FAF1	64	.	5	Whole gene deletion(5)	central_nervous_system(3)|thyroid(1)|haematopoietic_and_lymphoid_tissue(1)	c.A111T						.						84	84	84					1																	51323604		2202	4287	6489	SO:0001583	missense	11124	exon2			TACCACTAAGTCC	AF132938	CCDS554.1	1p32.3	2012-09-20			ENSG00000185104	ENSG00000185104		"UBX domain containing"	3578	protein-coding gene	gene with protein product	"TNFRSF6-associated factor 1", "UBX domain protein 3A"	604460				10462485	Standard	NM_007051		Approved	CGI-03, hFAF1, HFAF1s, UBXD12, UBXN3A	uc001cse.1	Q9UNN5	OTTHUMG00000007930	ENST00000396153.2:c.111A>T	chr1.hg19:g.51323604T>A	ENSP00000379457:p.Leu37Phe	223.0	0.0		260.0	42.0	NM_007051	Q549F0|Q9UF34|Q9UNT3|Q9Y2Z3	Missense_Mutation	SNP	ENST00000396153.2	hg19	CCDS554.1	.	.	.	.	.	.	.	.	.	.	T	16.96	3.266682	0.59540	.	.	ENSG00000185104	ENST00000396153;ENST00000371778;ENST00000371780;ENST00000543607	.	.	.	5.4	0.405	0.16361	.	0.267967	0.31636	N	0.007302	T	0.68952	0.3057	M	0.68317	2.08	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.67833	-0.5568	9	0.87932	D	0	-19.6609	9.2373	0.37475	0.0:0.4175:0.0:0.5825	.	37	Q9UNN5	FAF1_HUMAN	F	37;37;29;37	.	ENSP00000360843:L37F	L	-	3	2	FAF1	51096192	1.000000	0.71417	0.999000	0.59377	0.781000	0.44180	0.902000	0.28459	0.070000	0.16634	-0.467000	0.05162	TTA	.	.		0.294	FAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021807.1	NM_007051		A	51323604	T	A	51323604	3	1	246	1	0	0	0	0	1	0	0	0	5374	1519	53	4	1913	4	FAF1	1	51323604	Missense_Mutation	SNP	T	TCGA-ED-A7XO-01A-11D-A34Z-10	31915582	51323604	197927017	3	33742										
PDE4B	5142	hgsc.bcm.edu	37	chr1	66713174	66713174	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	aaaatggcccttccccaggtCggagtccactggatccccag	10	15	0	0	rs367809652		TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr1:66713174C>G	ENST00000329654.4	+	4	500	c.313C>G	c.(313-315)Cgg>Ggg	p.R105G	PDE4B_ENST00000371049.3_Missense_Mutation_p.R105G|PDE4B_ENST00000423207.2_Missense_Mutation_p.R90G	NM_001037341.1	NP_001032418.1	Q07343	PDE4B_HUMAN	phosphodiesterase 4B, cAMP-specific	105					cAMP catabolic process (GO:0006198)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to lipopolysaccharide (GO:0071222)|leukocyte migration (GO:0050900)|negative regulation of relaxation of cardiac muscle (GO:1901898)|neutrophil chemotaxis (GO:0030593)|neutrophil homeostasis (GO:0001780)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of high voltage-gated calcium channel activity (GO:1901841)|T cell receptor signaling pathway (GO:0050852)	cell periphery (GO:0071944)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	37					Adenosine monophosphate(DB00131)|Amrinone(DB01427)|Caffeine(DB00201)|Dyphylline(DB00651)|Enprofylline(DB00824)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Papaverine(DB01113)|Pentoxifylline(DB00806)|Roflumilast(DB01656)|Theobromine(DB01412)|Theophylline(DB00277)	TTCCCCAGGTCGGAGTCCACT	0.527																																					p.R105G		Atlas-SNP	.											.	PDE4B	231	.	0			c.C313G						.						168	181	177					1																	66713174		2203	4300	6503	SO:0001583	missense	5142	exon4			CCAGGTCGGAGTC	L20971	CCDS632.1, CCDS30742.1, CCDS30743.1, CCDS72802.1	1p31	2010-06-24	2010-06-24		ENSG00000184588	ENSG00000184588		"Phosphodiesterases"	8781	protein-coding gene	gene with protein product	"phosphodiesterase E4 dunce homolog (Drosophila)"	600127	"phosphodiesterase 4B, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E4)", "phosphodiesterase 4B, cAMP-specific (phosphodiesterase E4 dunce homolog, Drosophila)"	DPDE4			Standard	XM_005270925		Approved		uc001dco.3	Q07343	OTTHUMG00000009088	ENST00000329654.4:c.313C>G	chr1.hg19:g.66713174C>G	ENSP00000332116:p.Arg105Gly	99.0	0.0		91.0	26.0	NM_001037341	A5YW33|O15443|Q13945|Q5TEK4|Q5TEK5|Q5TEK6	Missense_Mutation	SNP	ENST00000329654.4	hg19	CCDS632.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.126219	0.77549	.	.	ENSG00000184588	ENST00000329654;ENST00000341517;ENST00000371049;ENST00000423207;ENST00000412480	T;T;T;T;D	0.82167	-0.58;-0.58;-0.58;-0.61;-1.58	5.95	4.98	0.66077	.	0.151906	0.64402	D	0.000010	T	0.78407	0.4278	L	0.43923	1.385	0.58432	D	0.99999	P;P;P	0.46327	0.876;0.803;0.802	P;B;B	0.48840	0.592;0.388;0.388	T	0.78802	-0.2061	10	0.45353	T	0.12	.	15.9685	0.79995	0.1354:0.8646:0.0:0.0	.	90;95;105	Q07343-3;Q59GM8;Q07343	.;.;PDE4B_HUMAN	G	105;105;105;90;13	ENSP00000332116:R105G;ENSP00000342637:R105G;ENSP00000360088:R105G;ENSP00000392947:R90G;ENSP00000397548:R13G	ENSP00000332116:R105G	R	+	1	2	PDE4B	66485762	0.813000	0.29090	1.000000	0.80357	0.985000	0.73830	1.613000	0.36900	2.817000	0.96982	0.563000	0.77884	CGG	.	.		0.527	PDE4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025188.3	NM_002600		G	66713174	C	G	66713174	3	3	246	1	0	0	0	0	1	0	0	0	11649	875	31	4	563	4	PDE4B	1	66713174	Missense_Mutation	SNP	C	TCGA-ED-A7XO-01A-11D-A34Z-10	15389570	66713174	182537447	4	33743										
FLG	2312	hgsc.bcm.edu	37	chr1	152281994	152281994	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	ctgctcgtggcgggatctttGtcttcctccagtgctgggcc	13	13	2	0	rs200622741		TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr1:152281994G>T	ENST00000368799.1	-	3	5403	c.5368C>A	c.(5368-5370)Caa>Aaa	p.Q1790K	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1790	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CGGGATCTTTGTCTTCCTCCA	0.602									Ichthyosis																												p.Q1790K		Atlas-SNP	.											.	FLG	900	.	0			c.C5368A						.						227	234	232					1																	152281994		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	ATCTTTGTCTTCC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.5368C>A	chr1.hg19:g.152281994G>T	ENSP00000357789:p.Gln1790Lys	125.0	0.0		122.0	31.0	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	hg19	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	G	9.568	1.120337	0.20877	.	.	ENSG00000143631	ENST00000368799;ENST00000271820	T	0.03330	3.97	4.33	4.33	0.51752	.	.	.	.	.	T	0.08891	0.0220	M	0.82923	2.615	0.09310	N	1	P	0.40332	0.713	P	0.54815	0.761	T	0.01583	-1.1319	9	0.62326	D	0.03	-0.7334	12.5761	0.56365	0.0:0.0:1.0:0.0	.	1790	P20930	FILA_HUMAN	K	1790;25	ENSP00000357789:Q1790K	ENSP00000271820:Q25K	Q	-	1	0	FLG	150548618	0.000000	0.05858	0.015000	0.15790	0.014000	0.08584	0.027000	0.13621	2.411000	0.81874	0.558000	0.71614	CAA	.	.		0.602	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		T	152281994	G	T	152281994	3	4	246	1	0	0	0	0	1	0	0	0	5930	1386	48	3	6821	3	FLG	1	152281994	Missense_Mutation	SNP	G	TCGA-ED-A7XO-01A-11D-A34Z-10	85568820	152281994	96968627	5	33744										
HMCN1	83872	hgsc.bcm.edu	37	chr1	185902929	185902929	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	ctagtgaaggtggatcatcaGccgcttcagttttcctcaca	9	11	4	1			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr1:185902929G>A	ENST00000271588.4	+	11	2030	c.1801G>A	c.(1801-1803)Gcc>Acc	p.A601T	HMCN1_ENST00000367492.2_Missense_Mutation_p.A601T	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	601	Ig-like C2-type 2.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TGGATCATCAGCCGCTTCAGT	0.398																																					p.A601T		Atlas-SNP	.											.	HMCN1	797	.	0			c.G1801A						.						149	147	147					1																	185902929		2203	4300	6503	SO:0001583	missense	83872	exon11			TCATCAGCCGCTT	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.1801G>A	chr1.hg19:g.185902929G>A	ENSP00000271588:p.Ala601Thr	55.0	0.0		68.0	10.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	G	1.786	-0.480608	0.04383	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.63580	-0.05;-0.05	5.67	0.0917	0.14469	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.484771	0.23805	N	0.044397	T	0.28466	0.0704	N	0.04636	-0.2	0.09310	N	1	B	0.09022	0.002	B	0.11329	0.006	T	0.16012	-1.0417	10	0.09590	T	0.72	.	4.2845	0.10848	0.3279:0.0:0.427:0.2451	.	601	Q96RW7	HMCN1_HUMAN	T	601	ENSP00000271588:A601T;ENSP00000356462:A601T	ENSP00000271588:A601T	A	+	1	0	HMCN1	184169552	0.000000	0.05858	0.075000	0.20258	0.215000	0.24574	-0.182000	0.09726	0.318000	0.23185	0.655000	0.94253	GCC	.	.		0.398	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		A	185902929	G	A	185902929	3	1	246	1	0	0	0	0	1	0	0	0	7229	971	34	3	1843	3	HMCN1	1	185902929	Missense_Mutation	SNP	G	TCGA-ED-A7XO-01A-11D-A34Z-10	33620935	185902929	63347692	6	33745										
KIF14	9928	hgsc.bcm.edu	37	chr1	200562884	200562884	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	aatactcactgtcccaccaaAatttttgatagtactgttaa	4	9	1	1			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr1:200562884A>C	ENST00000367350.4	-	15	3001	c.2563T>G	c.(2563-2565)Ttt>Gtt	p.F855V		NM_014875.2	NP_055690.1	Q15058	KIF14_HUMAN	kinesin family member 14	855	FHA.				ATP catabolic process (GO:0006200)|cytoskeleton-dependent intracellular transport (GO:0030705)|establishment of protein localization (GO:0045184)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of integrin activation (GO:0033624)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of Rap protein signal transduction (GO:0032487)|substrate adhesion-dependent cell spreading (GO:0034446)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|PDZ domain binding (GO:0030165)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(8)|kidney(8)|large_intestine(15)|lung(13)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	61						GTCCCACCAAAATTTTTGATA	0.333																																					p.F855V		Atlas-SNP	.											.	KIF14	156	.	0			c.T2563G						.						135	126	129					1																	200562884		2203	4300	6503	SO:0001583	missense	9928	exon15			CACCAAAATTTTT	D26361	CCDS30963.1	1q32.1	2008-03-03			ENSG00000118193	ENSG00000118193		"Kinesins"	19181	protein-coding gene	gene with protein product		611279				7584044	Standard	NM_014875		Approved	KIAA0042	uc010ppk.1	Q15058	OTTHUMG00000035723	ENST00000367350.4:c.2563T>G	chr1.hg19:g.200562884A>C	ENSP00000356319:p.Phe855Val	73.0	0.0		79.0	14.0	NM_014875	Q14CI8|Q4G0A5|Q5T1W3	Missense_Mutation	SNP	ENST00000367350.4	hg19	CCDS30963.1	.	.	.	.	.	.	.	.	.	.	A	5.104	0.204786	0.09704	.	.	ENSG00000118193	ENST00000367350	D	0.86366	-2.11	5.15	4.01	0.46588	Forkhead-associated (FHA) domain (3);SMAD/FHA domain (1);	0.323428	0.29924	N	0.010856	T	0.68357	0.2992	N	0.04768	-0.165	0.22728	N	0.998803	B	0.02656	0.0	B	0.09377	0.004	T	0.52845	-0.8521	10	0.14656	T	0.56	.	5.6288	0.17497	0.4903:0.258:0.0:0.2518	.	855	Q15058	KIF14_HUMAN	V	855	ENSP00000356319:F855V	ENSP00000356319:F855V	F	-	1	0	KIF14	198829507	0.016000	0.18221	0.072000	0.20136	0.694000	0.40290	0.195000	0.17155	0.770000	0.33336	0.460000	0.39030	TTT	.	.		0.333	KIF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086878.1	NM_014875		C	200562884	A	C	200562884	3	2	246	1	0	0	0	0	1	0	0	0	8285	14	1	5	2447	5	KIF14	1	200562884	Missense_Mutation	SNP	A	TCGA-ED-A7XO-01A-11D-A34Z-10	14659955	200562884	48687737	7	33746										
IGFN1	91156	hgsc.bcm.edu	37	chr1	201196308	201196308	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	gagaacacgctgggccaggcAgtcagcactgccaccctcat	11	15	2	1			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr1:201196308A>T	ENST00000335211.4	+	23	11215	c.11085A>T	c.(11083-11085)gcA>gcT	p.A3695A	IGFN1_ENST00000295591.8_3'UTR	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	1238						nucleus (GO:0005634)|Z disc (GO:0030018)				autonomic_ganglia(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						TGGGCCAGGCAGTCAGCACTG	0.637																																					p.A3695A		Atlas-SNP	.											.	IGFN1	220	.	0			c.A11085T						.						35	22	26					1																	201196308		2201	4299	6500	SO:0001819	synonymous_variant	91156	exon23			CCAGGCAGTCAGC	AY245430	CCDS53455.1	1q32.1	2013-02-11			ENSG00000163395	ENSG00000163395		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	24607	protein-coding gene	gene with protein product							Standard	NM_001164586		Approved	DKFZp434B1231, EEF1A2BP1	uc001gwc.3	Q86VF2	OTTHUMG00000035728	ENST00000335211.4:c.11085A>T	chr1.hg19:g.201196308A>T		29.0	0.0		45.0	17.0	NM_001164586	F8WAI1|Q9NT72	Silent	SNP	ENST00000335211.4	hg19	CCDS53455.1	.	.	.	.	.	.	.	.	.	.	A	0.379	-0.929845	0.02359	.	.	ENSG00000163395	ENST00000412892	.	.	.	5.19	-10.4	0.00318	.	.	.	.	.	T	0.33265	0.0857	.	.	.	0.58432	D	0.999995	.	.	.	.	.	.	T	0.39961	-0.9588	4	.	.	.	.	2.2452	0.04030	0.1875:0.4022:0.1592:0.2512	.	.	.	.	C	1113	.	.	S	+	1	0	IGFN1	199462931	0.000000	0.05858	0.047000	0.18901	0.028000	0.11728	-7.115000	0.00044	-2.294000	0.00663	-1.392000	0.01152	AGT	.	.		0.637	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275		T	201196308	A	T	201196308	2	4	246	1	0	0	0	0	0	0	0	1	7599	175	7	4		4	IGFN1	1	201196308	Silent	SNP	A	TCGA-ED-A7XO-01A-11D-A34Z-10	633424	201196308	48054313	8	33747										
HEATR5B	54497	hgsc.bcm.edu	37	chr2	37295937	37295937	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	ttaggataaaggaaacacatCgtctggagtacacagcctcc	9	10	1	0			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr2:37295937C>T	ENST00000233099.5	-	8	1159	c.1064G>A	c.(1063-1065)cGa>cAa	p.R355Q	HEATR5B_ENST00000354531.2_Missense_Mutation_p.R355Q	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	355						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				GGAAACACATCGTCTGGAGTA	0.488																																					p.R355Q		Atlas-SNP	.											.	HEATR5B	185	.	0			c.G1064A						.						86	76	79					2																	37295937		2203	4300	6503	SO:0001583	missense	54497	exon8			ACACATCGTCTGG	AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.1064G>A	chr2.hg19:g.37295937C>T	ENSP00000233099:p.Arg355Gln	53.0	0.0		65.0	13.0	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Missense_Mutation	SNP	ENST00000233099.5	hg19	CCDS33181.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.143512	0.77888	.	.	ENSG00000008869	ENST00000233099;ENST00000354531;ENST00000424416	T;T	0.08193	3.12;3.12	5.81	4.93	0.64822	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.09992	0.0245	L	0.49350	1.555	0.58432	D	0.999999	P	0.51057	0.941	B	0.38327	0.271	T	0.10497	-1.0627	10	0.37606	T	0.19	-11.206	16.8801	0.86060	0.0:0.8717:0.1283:0.0	.	355	Q9P2D3	HTR5B_HUMAN	Q	355	ENSP00000233099:R355Q;ENSP00000346531:R355Q	ENSP00000233099:R355Q	R	-	2	0	HEATR5B	37149441	1.000000	0.71417	0.996000	0.52242	0.961000	0.63080	4.899000	0.63245	1.445000	0.47624	0.655000	0.94253	CGA	.	.		0.488	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024		T	37295937	C	T	37295937	3	4	246	1	0	0	0	0	1	0	0	0	7041	884	31	1	5267	1	HEATR5B	2	37295937	Missense_Mutation	SNP	C	TCGA-ED-A7XO-01A-11D-A34Z-10		37295937	205903436	9	33748										
NAGK	55577	hgsc.bcm.edu	37	chr2	71304745	71304745	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	gcgtgggctctgtgtggaagAgctgggagctgctgaaggaa	19	6	1	2			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr2:71304745A>T	ENST00000244204.6	+	9	885	c.823A>T	c.(823-825)Agc>Tgc	p.S275C	NAGK_ENST00000443872.2_Missense_Mutation_p.S127C|NAGK_ENST00000455662.2_Missense_Mutation_p.S321C|NAGK_ENST00000418807.3_Missense_Mutation_p.S224C|NAGK_ENST00000443938.2_Missense_Mutation_p.S271C			Q9UJ70	NAGK_HUMAN	N-acetylglucosamine kinase	275					carbohydrate phosphorylation (GO:0046835)|N-acetylglucosamine metabolic process (GO:0006044)|N-acetylmannosamine metabolic process (GO:0006051)|N-acetylneuraminate catabolic process (GO:0019262)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|N-acetylglucosamine kinase activity (GO:0045127)			breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|urinary_tract(1)	18					N-Acetyl-D-glucosamine(DB00141)	TGTGTGGAAGAGCTGGGAGCT	0.612																																					p.S321C		Atlas-SNP	.											.	NAGK	34	.	0			c.A961T						.						52	46	48					2																	71304745		2203	4300	6503	SO:0001583	missense	55577	exon9			TGGAAGAGCTGGG	AJ242910	CCDS33220.1, CCDS33220.2	2p24.3-p24.1	2008-02-05			ENSG00000124357	ENSG00000124357	2.7.1.59		17174	protein-coding gene	gene with protein product		606828				10824116	Standard	NM_017567		Approved	GNK	uc002shp.4	Q9UJ70	OTTHUMG00000153239	ENST00000244204.6:c.823A>T	chr2.hg19:g.71304745A>T	ENSP00000244204:p.Ser275Cys	47.0	0.0		61.0	10.0	NM_017567	B4DLZ5|Q53HD5|Q6IA84|Q9BS29|Q9BVP0|Q9NV37	Missense_Mutation	SNP	ENST00000244204.6	hg19		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	A|A|A	29.2|29.2|29.2	4.988801|4.988801|4.988801	0.93106|0.93106|0.93106	.|.|.	.|.|.	ENSG00000124357|ENSG00000124357|ENSG00000124357	ENST00000524537|ENST00000443938|ENST00000244204;ENST00000455662;ENST00000418807	.|.|T;T;T	.|.|0.32272	.|.|1.46;1.46;1.46	5.63|5.63|5.63	5.63|5.63|5.63	0.86233|0.86233|0.86233	.|.|ATPase, BadF/BadG/BcrA/BcrD type (1);	.|.|0.000000	.|.|0.85682	.|.|D	.|.|0.000000	T|T|T	0.60392|0.60392|0.60392	0.2265|0.2265|0.2265	M|M|M	0.86651|0.86651|0.86651	2.83|2.83|2.83	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|.|D	.|.|0.89917	.|.|1.0	.|.|D	.|.|0.79784	.|.|0.993	T|T|T	0.67277|0.67277|0.67277	-0.5711|-0.5711|-0.5711	5|5|10	.|.|0.66056	.|.|D	.|.|0.02	-6.7711|-6.7711|-6.7711	13.794|13.794|13.794	0.63160|0.63160|0.63160	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.|.	.|.|275	.|.|Q9UJ70	.|.|NAGK_HUMAN	V|S|C	39|292|275;321;224	.|.|ENSP00000244204:S275C;ENSP00000389087:S321C;ENSP00000396070:S224C	.|.|ENSP00000244204:S275C	E|R|S	+|+|+	2|3|1	0|2|0	NAGK|NAGK|NAGK	71158253|71158253|71158253	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.982000|0.982000|0.982000	0.71751|0.71751|0.71751	7.966000|7.966000|7.966000	0.87956|0.87956|0.87956	2.137000|2.137000|2.137000	0.66172|0.66172|0.66172	0.533000|0.533000|0.533000	0.62120|0.62120|0.62120	GAG|AGA|AGC	.	.		0.612	NAGK-032	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471889.1			T	71304745	A	T	71304745	3	4	246	1	0	0	0	0	1	0	0	0	10151	304	11	4	995	4	NAGK	2	71304745	Missense_Mutation	SNP	A	TCGA-ED-A7XO-01A-11D-A34Z-10	34008808	71304745	171894628	10	33749										
HECW2	57520	hgsc.bcm.edu	37	chr2	197081786	197081786	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	ctttccactgcagcccagaaCcaccgaattacaatatgatt	5	13	0	2			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr2:197081786C>A	ENST00000260983.3	-	27	4622	c.4440G>T	c.(4438-4440)tgG>tgT	p.W1480C	HECW2_ENST00000409111.1_Missense_Mutation_p.W1124C|snoU13_ENST00000459047.1_RNA	NM_020760.1	NP_065811.1	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	1480	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(24)|lung(45)|ovary(5)|pancreas(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	113						CAGCCCAGAACCACCGAATTA	0.348																																					p.W1480C		Atlas-SNP	.											.	HECW2	239	.	0			c.G4440T						.						175	163	167					2																	197081786		2203	4300	6503	SO:0001583	missense	57520	exon27			CCAGAACCACCGA	AL390186	CCDS33354.1	2q32.3	2004-12-13			ENSG00000138411	ENSG00000138411			29853	protein-coding gene	gene with protein product						10718198, 12890487	Standard	NM_020760		Approved	KIAA1301, NEDL2	uc002utm.1	Q9P2P5	OTTHUMG00000154435	ENST00000260983.3:c.4440G>T	chr2.hg19:g.197081786C>A	ENSP00000260983:p.Trp1480Cys	88.0	0.0		93.0	18.0	NM_020760	B8ZZB4|Q17RT5|Q68DF8|Q9NPS9	Missense_Mutation	SNP	ENST00000260983.3	hg19	CCDS33354.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.335301	0.81801	.	.	ENSG00000138411	ENST00000409111;ENST00000260983	T;T	0.49432	0.78;0.78	4.85	4.85	0.62838	HECT (4);	0.060243	0.64402	D	0.000001	T	0.76133	0.3945	M	0.90922	3.16	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.82176	-0.0587	10	0.87932	D	0	.	18.535	0.91008	0.0:1.0:0.0:0.0	.	1480	Q9P2P5	HECW2_HUMAN	C	1124;1480	ENSP00000386775:W1124C;ENSP00000260983:W1480C	ENSP00000260983:W1480C	W	-	3	0	HECW2	196790031	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.272000	0.78516	2.674000	0.91012	0.655000	0.94253	TGG	.	.		0.348	HECW2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335199.3	NM_020760		A	197081786	C	A	197081786	3	1	246	1	0	0	0	0	1	0	0	0	7052	508	18	3	290	3	HECW2	2	197081786	Missense_Mutation	SNP	C	TCGA-ED-A7XO-01A-11D-A34Z-10	125777041	197081786	46117587	11	33750										
PLXNB1	5364	hgsc.bcm.edu	37	chr3	48451118	48451118	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	aatcacctggaacaggtcatCcacgaacttctgcagggtgc	10	12	3	0			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr3:48451118C>A	ENST00000358536.4	-	33	6069	c.5800G>T	c.(5800-5802)Gat>Tat	p.D1934Y	PLXNB1_ENST00000358459.4_Missense_Mutation_p.D1751Y|PLXNB1_ENST00000448774.2_Missense_Mutation_p.D545Y|PLXNB1_ENST00000456774.1_Missense_Mutation_p.D1751Y|PLXNB1_ENST00000296440.6_Missense_Mutation_p.D1934Y	NM_002673.4	NP_002664.2	O43157	PLXB1_HUMAN	plexin B1	1934					axon guidance (GO:0007411)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast proliferation (GO:0033689)|neuron projection morphogenesis (GO:0048812)|ossification involved in bone maturation (GO:0043931)|positive regulation of axonogenesis (GO:0050772)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	GTPase activating protein binding (GO:0032794)|receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		AACAGGTCATCCACGAACTTC	0.617																																					p.D1934Y		Atlas-SNP	.											.	PLXNB1	150	.	0			c.G5800T						.						54	52	53					3																	48451118		2203	4300	6503	SO:0001583	missense	5364	exon33			GGTCATCCACGAA	X87904	CCDS2765.1	3p21.31	2008-07-18			ENSG00000164050	ENSG00000164050		"Plexins"	9103	protein-coding gene	gene with protein product		601053		PLXN5		8570614, 11035813	Standard	XM_005265234		Approved	SEP, KIAA0407	uc003csw.2	O43157	OTTHUMG00000133527	ENST00000358536.4:c.5800G>T	chr3.hg19:g.48451118C>A	ENSP00000351338:p.Asp1934Tyr	74.0	0.0		93.0	10.0	NM_001130082	A6H8Y2|Q6NY20|Q9UIV7|Q9UJ92|Q9UJ93	Missense_Mutation	SNP	ENST00000358536.4	hg19	CCDS2765.1	.	.	.	.	.	.	.	.	.	.	c	15.15	2.748711	0.49257	.	.	ENSG00000164050	ENST00000296440;ENST00000358459;ENST00000358536;ENST00000448774;ENST00000456774	T;T;T;T;T	0.18016	2.24;2.24;2.24;2.24;2.24	4.16	4.16	0.48862	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);Ras GTPase-activating protein (1);	0.000000	0.85682	D	0.000000	T	0.52370	0.1730	M	0.93420	3.415	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.68224	-0.5465	10	0.87932	D	0	.	15.4419	0.75190	0.0:1.0:0.0:0.0	.	1934;1751	O43157;O43157-2	PLXB1_HUMAN;.	Y	1934;1751;1934;545;1751	ENSP00000296440:D1934Y;ENSP00000351242:D1751Y;ENSP00000351338:D1934Y;ENSP00000389320:D545Y;ENSP00000414199:D1751Y	ENSP00000296440:D1934Y	D	-	1	0	PLXNB1	48426122	1.000000	0.71417	0.998000	0.56505	0.022000	0.10575	7.683000	0.84093	1.868000	0.54150	0.306000	0.20318	GAT	.	.		0.617	PLXNB1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344454.1	NM_002673		A	48451118	C	A	48451118	3	1	246	1	0	0	0	0	1	0	0	0	12132	855	30	3	631	3	PLXNB1	3	48451118	Missense_Mutation	SNP	C	TCGA-ED-A7XO-01A-11D-A34Z-10		48451118	149571312	12	33751										
KIAA1524	57650	hgsc.bcm.edu	37	chr3	108281998	108281998	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	agcaggaaaatctggcagtgGagcagcctccaataatattc	10	9	1	0			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr3:108281998G>C	ENST00000295746.8	-	13	1685	c.1609C>G	c.(1609-1611)Cca>Gca	p.P537A	KIAA1524_ENST00000487834.1_5'UTR|KIAA1524_ENST00000491772.1_Missense_Mutation_p.P378A	NM_020890.2	NP_065941.2	Q8TCG1	CIP2A_HUMAN	KIAA1524	537					positive regulation of neural precursor cell proliferation (GO:2000179)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.P537S(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(21)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						TCTGGCAGTGGAGCAGCCTCC	0.403																																					p.P537A		Atlas-SNP	.											KIAA1524,NS,carcinoma,0,1	KIAA1524	82	.	1	Substitution - Missense(1)	kidney(1)	c.C1609G						.						148	151	150					3																	108281998		2203	4300	6503	SO:0001583	missense	57650	exon13			GCAGTGGAGCAGC	AB040957	CCDS33812.1	3q13.13	2014-01-14			ENSG00000163507	ENSG00000163507			29302	protein-coding gene	gene with protein product	"cancerous inhibitor of protein phosphatase 2A"	610643				10819331, 24214971	Standard	NM_020890		Approved	CIP2A	uc003dxb.4	Q8TCG1	OTTHUMG00000159233	ENST00000295746.8:c.1609C>G	chr3.hg19:g.108281998G>C	ENSP00000295746:p.Pro537Ala	174.0	1.0		200.0	34.0	NM_020890	A1L4J7|B9EGC3|Q6P4G6|Q8WVP8|Q96PI2|Q9H9C6|Q9P204	Missense_Mutation	SNP	ENST00000295746.8	hg19	CCDS33812.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.558597	0.86231	.	.	ENSG00000163507	ENST00000491772;ENST00000295746	T;T	0.70282	-0.47;-0.47	5.62	5.62	0.85841	.	0.048819	0.85682	D	0.000000	D	0.82926	0.5143	M	0.64997	1.995	0.80722	D	1	D	0.71674	0.998	D	0.71184	0.972	D	0.83423	0.0034	10	0.62326	D	0.03	-11.6132	19.6484	0.95791	0.0:0.0:1.0:0.0	.	537	Q8TCG1	CIP2A_HUMAN	A	378;537	ENSP00000419487:P378A;ENSP00000295746:P537A	ENSP00000295746:P537A	P	-	1	0	KIAA1524	109764688	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.852000	0.75430	2.646000	0.89796	0.557000	0.71058	CCA	.	.		0.403	KIAA1524-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353975.2	NM_020890		C	108281998	G	C	108281998	3	2	246	1	0	0	0	0	1	0	0	0	8248	1174	41	4	1144	4	KIAA1524	3	108281998	Missense_Mutation	SNP	G	TCGA-ED-A7XO-01A-11D-A34Z-10	59830880	108281998	89740432	13	33752										
ZIC4	84107	hgsc.bcm.edu	37	chr3	147113833	147113833	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	tgtggttggcctgttccgggCcgccgacgtgctccacggtg	16	13	0	0			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr3:147113833C>G	ENST00000383075.3	-	3	1006	c.494G>C	c.(493-495)gGc>gCc	p.G165A	ZIC4_ENST00000425731.3_Missense_Mutation_p.G203A|ZIC4_ENST00000473123.1_Missense_Mutation_p.G165A|ZIC4_ENST00000484399.1_Missense_Mutation_p.G165A|ZIC4_ENST00000491672.1_Intron|ZIC4_ENST00000525172.2_Missense_Mutation_p.G215A	NM_032153.5	NP_115529.2	Q8N9L1	ZIC4_HUMAN	Zic family member 4	165						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(34)|upper_aerodigestive_tract(4)	57						CTGTTCCGGGCCGCCGACGTG	0.612																																					p.G215A		Atlas-SNP	.											.	ZIC4	174	.	0			c.G644C						.						97	108	104					3																	147113833		2203	4300	6503	SO:0001583	missense	84107	exon3			TCCGGGCCGCCGA	AF332509	CCDS43160.1, CCDS54652.1, CCDS54653.1, CCDS58857.1	3q24	2013-01-08	2003-02-21		ENSG00000174963	ENSG00000174963		"Zinc fingers, C2H2-type"	20393	protein-coding gene	gene with protein product		608948	"zinc finger protein of the cerebellum 4"				Standard	NM_001168378		Approved		uc011bno.2	Q8N9L1	OTTHUMG00000037281	ENST00000383075.3:c.494G>C	chr3.hg19:g.147113833C>G	ENSP00000372553:p.Gly165Ala	65.0	0.0		61.0	8.0	NM_001168378	A0AVA2|B2RMQ8|B4DF89|B7Z2L2|C9J7D5|J3KQG1|Q4G157|Q9BZ94	Missense_Mutation	SNP	ENST00000383075.3	hg19	CCDS43160.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.833095	0.91036	.	.	ENSG00000174963	ENST00000383075;ENST00000425731;ENST00000525172;ENST00000484399;ENST00000473123;ENST00000462748	D;D;D;D;D;D	0.90900	-2.75;-2.75;-2.75;-2.75;-2.75;-2.75	5.2	5.2	0.72013	.	0.000000	0.47093	D	0.000256	D	0.91348	0.7271	N	0.13327	0.33	0.80722	D	1	P;D	0.89917	0.84;1.0	B;D	0.91635	0.399;0.999	D	0.93223	0.6610	10	0.66056	D	0.02	.	18.7355	0.91753	0.0:1.0:0.0:0.0	.	215;165	B7Z2L2;Q8N9L1	.;ZIC4_HUMAN	A	165;203;215;165;165;165	ENSP00000372553:G165A;ENSP00000397695:G203A;ENSP00000435509:G215A;ENSP00000417855:G165A;ENSP00000420775:G165A;ENSP00000420627:G165A	ENSP00000372553:G165A	G	-	2	0	ZIC4	148596523	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.487000	0.81328	2.425000	0.82216	0.511000	0.50034	GGC	.	.		0.612	ZIC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355504.1			G	147113833	C	G	147113833	3	3	246	1	0	0	0	0	1	0	0	0	17696	739	26	4	522	4	ZIC4	3	147113833	Missense_Mutation	SNP	C	TCGA-ED-A7XO-01A-11D-A34Z-10	38831835	147113833	50908597	14	33753										
HTR3C	170572	hgsc.bcm.edu	37	chr3	183772621	183772621	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	ttccgtccattcaccaactaCagcatccctacccgtgtcaa	4	17	2	0	rs180785188	byFrequency	TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr3:183772621C>A	ENST00000318351.1	+	2	214	c.180C>A	c.(178-180)taC>taA	p.Y60*		NM_130770.2	NP_570126.2	Q8WXA8	5HT3C_HUMAN	5-hydroxytryptamine (serotonin) receptor 3C, ionotropic	60					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(2)	32	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)		Ergoloid mesylate(DB01049)	TCACCAACTACAGCATCCCTA	0.502																																					p.Y60X		Atlas-SNP	.											.	HTR3C	65	.	0			c.C180A						.						150	123	132					3																	183772621		2203	4300	6503	SO:0001587	stop_gained	170572	exon2			CAACTACAGCATC	AF459285	CCDS3250.1	3q27	2012-05-22	2012-02-03		ENSG00000178084	ENSG00000178084		"5-HT (serotonin) receptors", "Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"	24003	protein-coding gene	gene with protein product		610121	"5-hydroxytryptamine (serotonin) receptor 3, family member C"			12801637, 15157181	Standard	NM_130770		Approved		uc003fmk.3	Q8WXA8	OTTHUMG00000156862	ENST00000318351.1:c.180C>A	chr3.hg19:g.183772621C>A	ENSP00000322617:p.Tyr60*	56.0	0.0		81.0	16.0	NM_130770	A2RRR5	Nonsense_Mutation	SNP	ENST00000318351.1	hg19	CCDS3250.1	.	.	.	.	.	.	.	.	.	.	.	19.11	3.763495	0.69763	.	.	ENSG00000178084	ENST00000318351	.	.	.	4.43	3.53	0.40419	.	1.328610	0.04740	N	0.422591	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.3392	10.8101	0.46543	0.0:0.6269:0.3731:0.0	.	.	.	.	X	60	.	ENSP00000322617:Y60X	Y	+	3	2	HTR3C	185255315	0.201000	0.23410	0.058000	0.19502	0.777000	0.43975	0.731000	0.26058	1.041000	0.40125	0.561000	0.74099	TAC	.	C|0.999;T|0.001		0.502	HTR3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346296.1	NM_130770		A	183772621	C	A	183772621	4	1	246	1	0	0	0	0	0	1	0	0	7455	489	17	3	186	3	HTR3C	3	183772621	Nonsense_Mutation	SNP	C	TCGA-ED-A7XO-01A-11D-A34Z-10	36658788	183772621	14249809	15	33754										
KIAA1211	57482	hgsc.bcm.edu	37	chr4	57180856	57180856	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	ggggagggccggcggggcgcGgaggaggaggatctggggga	27	6	1	0			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr4:57180856G>A	ENST00000504228.1	+	6	1293	c.1188G>A	c.(1186-1188)gcG>gcA	p.A396A	KIAA1211_ENST00000541073.1_Silent_p.A389A|KIAA1211_ENST00000264229.6_Silent_p.A396A			Q6ZU35	K1211_HUMAN	KIAA1211	396	Glu-rich.									endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					ggcggggcgcggaggaggagg	0.687																																					p.A396A		Atlas-SNP	.											.	KIAA1211	178	.	0			c.G1188A						.						9	11	10					4																	57180856		1922	4039	5961	SO:0001819	synonymous_variant	57482	exon8			GGGCGCGGAGGAG	AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.1188G>A	chr4.hg19:g.57180856G>A		26.0	0.0		41.0	15.0	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Silent	SNP	ENST00000504228.1	hg19	CCDS43230.1																																																																																			.	.		0.687	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722		A	57180856	G	A	57180856	2	1	246	1	0	0	0	0	0	0	0	1	8224	1103	39	1		1	KIAA1211	4	57180856	Silent	SNP	G	TCGA-ED-A7XO-01A-11D-A34Z-10		57180856	133973420	16	33755										
TKTL2	84076	hgsc.bcm.edu	37	chr4	164393739	164393739	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	caaaagcaatggttcgaccaCgtgtagcacagcctagtgcc	10	12	0	0			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr4:164393739C>A	ENST00000280605.3	-	1	1308	c.1148G>T	c.(1147-1149)cGt>cTt	p.R383L		NM_032136.4	NP_115512.3	Q9H0I9	TKTL2_HUMAN	transketolase-like 2	383						cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|transketolase activity (GO:0004802)			breast(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(42)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	70	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				GGTTCGACCACGTGTAGCACA	0.438																																					p.R383L		Atlas-SNP	.											.	TKTL2	130	.	0			c.G1148T						.						87	87	87					4																	164393739		2203	4300	6503	SO:0001583	missense	84076	exon1			CGACCACGTGTAG	BC028707	CCDS3805.1	4q32.2	2009-10-06			ENSG00000151005	ENSG00000151005			25313	protein-coding gene	gene with protein product	"similar to transketolase"					11230166	Standard	NM_032136		Approved	FLJ32975, DKFZP434L1717	uc003iqp.4	Q9H0I9	OTTHUMG00000161527	ENST00000280605.3:c.1148G>T	chr4.hg19:g.164393739C>A	ENSP00000280605:p.Arg383Leu	72.0	0.0		61.0	11.0	NM_032136	A4FVB4|Q8NCT0|Q96M82	Missense_Mutation	SNP	ENST00000280605.3	hg19	CCDS3805.1	.	.	.	.	.	.	.	.	.	.	C	18.99	3.738952	0.69304	.	.	ENSG00000151005	ENST00000280605	T	0.44083	0.93	4.29	3.42	0.39159	Transketolase-like, pyrimidine-binding domain (2);	0.064498	0.64402	D	0.000012	T	0.62490	0.2432	M	0.78637	2.42	0.80722	D	1	D	0.76494	0.999	D	0.72625	0.978	T	0.66968	-0.5789	10	0.59425	D	0.04	-6.503	12.3612	0.55205	0.0:0.8283:0.1717:0.0	.	383	Q9H0I9	TKTL2_HUMAN	L	383	ENSP00000280605:R383L	ENSP00000280605:R383L	R	-	2	0	TKTL2	164613189	0.948000	0.32251	0.060000	0.19600	0.995000	0.86356	3.072000	0.50049	1.351000	0.45789	0.655000	0.94253	CGT	.	.		0.438	TKTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365207.1	NM_032136		A	164393739	C	A	164393739	3	1	246	1	0	0	0	0	1	0	0	0	15951	536	19	1	736	1	TKTL2	4	164393739	Missense_Mutation	SNP	C	TCGA-ED-A7XO-01A-11D-A34Z-10	107212883	164393739	26760537	17	33756										
WDR17	116966	hgsc.bcm.edu	37	chr4	177041041	177041041	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	tccctgcttctcttagttggTgctggaatgcagaggatgtg	13	8	1	1			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr4:177041041T>C	ENST00000280190.4	+	5	559	c.403T>C	c.(403-405)Tgc>Cgc	p.C135R	WDR17_ENST00000508596.1_Missense_Mutation_p.C111R|WDR17_ENST00000507824.2_Missense_Mutation_p.C135R|WDR17_ENST00000393643.2_Missense_Mutation_p.C111R			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	135										breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(18)|lung(46)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	92		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)		TCTTAGTTGGTGCTGGAATGC	0.408																																					p.C135R		Atlas-SNP	.											.	WDR17	198	.	0			c.T403C						.						164	156	158					4																	177041041		2203	4300	6503	SO:0001583	missense	116966	exon5			AGTTGGTGCTGGA	AF492460	CCDS3825.1, CCDS43284.1, CCDS43284.2	4q34	2013-01-09			ENSG00000150627	ENSG00000150627		"WD repeat domain containing"	16661	protein-coding gene	gene with protein product		609005				12401215	Standard	NM_170710		Approved		uc003iuj.3	Q8IZU2	OTTHUMG00000160791	ENST00000280190.4:c.403T>C	chr4.hg19:g.177041041T>C	ENSP00000280190:p.Cys135Arg	181.0	0.0		179.0	20.0	NM_170710	E7EQX0|Q0QD35	Missense_Mutation	SNP	ENST00000280190.4	hg19	CCDS3825.1	.	.	.	.	.	.	.	.	.	.	T	12.05	1.821275	0.32237	.	.	ENSG00000150627	ENST00000508596;ENST00000393643;ENST00000280190;ENST00000507824	T;T;T	0.64438	-0.1;-0.1;-0.1	5.18	3.99	0.46301	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.76140	0.3946	M	0.73962	2.25	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.83275	0.996;0.996	T	0.74633	-0.3600	10	0.39692	T	0.17	-9.5264	11.4386	0.50083	0.1352:0.0:0.0:0.8648	.	111;135	E7EQX0;Q8IZU2	.;WDR17_HUMAN	R	111;111;135;135	ENSP00000422763:C111R;ENSP00000377258:C111R;ENSP00000280190:C135R	ENSP00000280190:C135R	C	+	1	0	WDR17	177278035	1.000000	0.71417	1.000000	0.80357	0.351000	0.29236	5.758000	0.68776	0.792000	0.33850	-0.301000	0.09380	TGC	.	.		0.408	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2			C	177041041	T	C	177041041	3	2	246	1	0	0	0	0	1	0	0	0	17292	1696	59	2	417	2	WDR17	4	177041041	Missense_Mutation	SNP	T	TCGA-ED-A7XO-01A-11D-A34Z-10	12647302	177041041	14113235	18	33757										
CWC27	10283	hgsc.bcm.edu	37	chr5	64079679	64079679	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	tcaggatgaatttcattcacGgttgcgttttaatcggagag	11	6	3	2			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr5:64079679G>T	ENST00000381070.3	+	4	486	c.269G>T	c.(268-270)cGg>cTg	p.R90L	CWC27_ENST00000508024.1_Missense_Mutation_p.R90L	NM_005869.2	NP_005860.2	Q6UX04	CWC27_HUMAN	CWC27 spliceosome-associated protein homolog (S. cerevisiae)	90	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)	p.R90Q(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(5)|prostate(1)	21						TTTCATTCACGGTTGCGTTTT	0.418																																					p.R90L		Atlas-SNP	.											CWC27,colon,carcinoma,0,1	CWC27	47	.	1	Substitution - Missense(1)	large_intestine(1)	c.G269T						.						193	187	189					5																	64079679		2203	4300	6503	SO:0001583	missense	10283	exon4			ATTCACGGTTGCG	AF039692	CCDS3982.2, CCDS75252.1	5q12.3	2010-01-26	2010-01-26	2010-01-26	ENSG00000153015	ENSG00000153015			10664	protein-coding gene	gene with protein product			"serologically defined colon cancer antigen 10"	SDCCAG10		9610721, 19941820	Standard	XM_005248399		Approved	NY-CO-10	uc003jtn.1	Q6UX04	OTTHUMG00000074069	ENST00000381070.3:c.269G>T	chr5.hg19:g.64079679G>T	ENSP00000370460:p.Arg90Leu	69.0	0.0		77.0	18.0	NM_005869	O60529|O60530|Q96EM3	Missense_Mutation	SNP	ENST00000381070.3	hg19	CCDS3982.2	.	.	.	.	.	.	.	.	.	.	G	23.4	4.409288	0.83340	.	.	ENSG00000153015	ENST00000381070;ENST00000508024;ENST00000538793	T;T	0.22743	1.94;1.94	5.45	3.68	0.42216	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (3);Cyclophilin-like (1);	0.000000	0.85682	D	0.000000	T	0.45875	0.1364	M	0.78456	2.415	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.997;0.996;0.998	T	0.47471	-0.9115	10	0.87932	D	0	.	11.9914	0.53178	0.1377:0.0:0.8623:0.0	.	90;90;90;90	Q6UX04-2;Q6UX04;F5H636;D6REK3	.;CWC27_HUMAN;.;.	L	90	ENSP00000370460:R90L;ENSP00000426802:R90L	ENSP00000370460:R90L	R	+	2	0	CWC27	64115435	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.195000	0.94971	0.868000	0.35678	0.585000	0.79938	CGG	.	.		0.418	CWC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157247.4	NM_005869		T	64079679	G	T	64079679	3	4	246	1	0	0	0	0	1	0	0	0	4072	1116	39	1	283	1	CWC27	5	64079679	Missense_Mutation	SNP	G	TCGA-ED-A7XO-01A-11D-A34Z-10		64079679	116835581	19	33758										
VCAN	1462	hgsc.bcm.edu	37	chr5	82836639	82836639	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	agaggtaccatcagaaccacAtgacagtaatgatgaaagta	9	7	1	5			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr5:82836639A>G	ENST00000265077.3	+	8	8382	c.7817A>G	c.(7816-7818)cAt>cGt	p.H2606R	VCAN_ENST00000502527.2_Intron|VCAN_ENST00000342785.4_Intron|VCAN-AS1_ENST00000512090.1_RNA|VCAN-AS1_ENST00000513899.1_RNA|VCAN_ENST00000343200.5_Missense_Mutation_p.H1619R|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000512590.2_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	2606	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	TCAGAACCACATGACAGTAAT	0.363																																					p.H2606R		Atlas-SNP	.											.	VCAN	498	.	0			c.A7817G						.						90	91	90					5																	82836639		2203	4300	6503	SO:0001583	missense	1462	exon8			AACCACATGACAG	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.7817A>G	chr5.hg19:g.82836639A>G	ENSP00000265077:p.His2606Arg	74.0	0.0		74.0	21.0	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	hg19	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	A	2.180	-0.387810	0.04932	.	.	ENSG00000038427	ENST00000265077;ENST00000343200	T;T	0.30981	1.51;1.51	5.68	1.98	0.26296	.	0.737333	0.13013	N	0.420682	T	0.24661	0.0598	L	0.59436	1.845	0.09310	N	0.999997	B;B	0.18013	0.01;0.025	B;B	0.14023	0.01;0.008	T	0.34279	-0.9835	10	0.14656	T	0.56	.	5.8658	0.18775	0.7039:0.1491:0.1471:0.0	.	1619;2606	P13611-2;P13611	.;CSPG2_HUMAN	R	2606;1619	ENSP00000265077:H2606R;ENSP00000340062:H1619R	ENSP00000265077:H2606R	H	+	2	0	VCAN	82872395	0.028000	0.19301	0.002000	0.10522	0.147000	0.21601	1.508000	0.35769	0.102000	0.17638	0.379000	0.24179	CAT	.	.		0.363	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		G	82836639	A	G	82836639	3	3	246	1	0	0	0	0	1	0	0	0	17153	217	8	2	7843	2	VCAN	5	82836639	Missense_Mutation	SNP	A	TCGA-ED-A7XO-01A-11D-A34Z-10	18756960	82836639	98078621	20	33759										
SLCO4C1	353189	hgsc.bcm.edu	37	chr5	101592902	101592902	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	aaactcagcgtaagtgcaacTccagatgtgaacagtgcaaa	9	9	1	2			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr5:101592902T>C	ENST00000310954.6	-	8	1672	c.1386A>G	c.(1384-1386)ggA>ggG	p.G462G		NM_180991.4	NP_851322.3			solute carrier organic anion transporter family, member 4C1											breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	50		all_cancers(142;1.86e-08)|all_epithelial(76;5.24e-12)|Prostate(80;0.00124)|Colorectal(57;0.00332)|Ovarian(225;0.024)|Lung NSC(167;0.0402)|all_lung(232;0.0486)		Epithelial(69;4.07e-14)|COAD - Colon adenocarcinoma(37;0.00986)		TAAGTGCAACTCCAGATGTGA	0.373																																					p.G462G		Atlas-SNP	.											.	SLCO4C1	113	.	0			c.A1386G						.						109	107	108					5																	101592902		2203	4300	6503	SO:0001819	synonymous_variant	353189	exon8			TGCAACTCCAGAT	AY273896	CCDS34205.1	5q21	2013-05-22	2003-11-25		ENSG00000173930	ENSG00000173930		"Solute carriers"	23612	protein-coding gene	gene with protein product		609013					Standard	NM_180991		Approved	SLC21A20, OATP4C1, OATPX, OATP-H	uc003knm.3	Q6ZQN7	OTTHUMG00000162757	ENST00000310954.6:c.1386A>G	chr5.hg19:g.101592902T>C		272.0	0.0		353.0	73.0	NM_180991		Silent	SNP	ENST00000310954.6	hg19	CCDS34205.1																																																																																			.	.		0.373	SLCO4C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370332.1	NM_180991		C	101592902	T	C	101592902	2	2	246	1	0	0	0	0	0	0	0	1	14745	1538	54	2		2	SLCO4C1	5	101592902	Silent	SNP	T	TCGA-ED-A7XO-01A-11D-A34Z-10	18756263	101592902	79322358	21	33760										
ABCC10	89845	hgsc.bcm.edu	37	chr6	43401071	43401071	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	atggccagcaaccaggaaatGctacagcacaaggatgcgcg	12	11	0	0	rs367899886		TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr6:43401071G>A	ENST00000372530.4	+	3	1568	c.1353G>A	c.(1351-1353)atG>atA	p.M451I	ABCC10_ENST00000443426.2_3'UTR|ABCC10_ENST00000244533.3_Missense_Mutation_p.M408I	NM_001198934.1	NP_001185863.1	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	451	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(8)|lung(21)|ovary(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)		Cyclosporine(DB00091)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Estradiol(DB00783)|Etoposide(DB00773)|Gemcitabine(DB00441)|Methotrexate(DB00563)|Paclitaxel(DB01229)|Sildenafil(DB00203)|Tenofovir(DB00300)|Verapamil(DB00661)|Vincristine(DB00541)	ACCAGGAAATGCTACAGCACA	0.597																																					p.M451I		Atlas-SNP	.											.	ABCC10	118	.	0			c.G1353A						.	G	ILE/MET,ILE/MET	0,4406		0,0,2203	68	58	61		1353,1224	5.5	1	6		61	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ABCC10	NM_001198934.1,NM_033450.2	10,10	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	451/1493,408/1465	43401071	1,13005	2203	4300	6503	SO:0001583	missense	89845	exon3			GGAAATGCTACAG	U66684	CCDS4896.1, CCDS56430.1	6p12.3	2012-03-14			ENSG00000124574	ENSG00000124574		"ATP binding cassette transporters / subfamily C"	52	protein-coding gene	gene with protein product		612509				8894702	Standard	NM_033450		Approved	EST182763, MRP7, SIMRP7	uc003ouy.1	Q5T3U5	OTTHUMG00000014733	ENST00000372530.4:c.1353G>A	chr6.hg19:g.43401071G>A	ENSP00000361608:p.Met451Ile	49.0	0.0		63.0	8.0	NM_001198934	Q8NHX7|Q9H7N2|Q9NXY3|Q9UF48	Missense_Mutation	SNP	ENST00000372530.4	hg19	CCDS56430.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.202212	0.79127	0.0	1.16E-4	ENSG00000124574	ENST00000372515;ENST00000372530;ENST00000244533	D;D;D	0.89552	-2.53;-2.53;-2.53	5.5	5.5	0.81552	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.88592	0.6478	L	0.56199	1.76	0.80722	D	1	P;P	0.50617	0.937;0.81	P;B	0.54312	0.748;0.433	D	0.85384	0.1121	10	0.18276	T	0.48	-42.0023	19.3941	0.94598	0.0:0.0:1.0:0.0	.	408;451	Q5T3U5-2;Q5T3U5	.;MRP7_HUMAN	I	7;451;408	ENSP00000361593:M7I;ENSP00000361608:M451I;ENSP00000244533:M408I	ENSP00000244533:M408I	M	+	3	0	ABCC10	43509049	1.000000	0.71417	1.000000	0.80357	0.782000	0.44232	9.869000	0.99810	2.593000	0.87608	0.650000	0.86243	ATG	.	.		0.597	ABCC10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040603.2	NM_033450		A	43401071	G	A	43401071	3	1	246	1	0	0	0	0	1	0	0	0	50	1319	46	3	1226	3	ABCC10	6	43401071	Missense_Mutation	SNP	G	TCGA-ED-A7XO-01A-11D-A34Z-10		43401071	127713996	22	33761										
COL12A1	1303	hgsc.bcm.edu	37	chr6	75887438	75887438	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	gtcctgagaaatattcaggaAttacagatacttcatatttc	6	7	2	2			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr6:75887438A>G	ENST00000322507.8	-	12	2687	c.2378T>C	c.(2377-2379)aTt>aCt	p.I793T	COL12A1_ENST00000416123.2_Missense_Mutation_p.I793T|COL12A1_ENST00000345356.6_Intron|COL12A1_ENST00000483888.2_Missense_Mutation_p.I793T	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	793	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						ATATTCAGGAATTACAGATAC	0.438																																					p.I793T		Atlas-SNP	.											.	COL12A1	385	.	0			c.T2378C						.						238	232	234					6																	75887438		1871	4093	5964	SO:0001583	missense	1303	exon12			TCAGGAATTACAG	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.2378T>C	chr6.hg19:g.75887438A>G	ENSP00000325146:p.Ile793Thr	140.0	0.0		139.0	25.0	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	hg19	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	A	0.097	-1.157645	0.01686	.	.	ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000416123;ENST00000483888	T;T;T	0.52754	0.65;0.65;0.65	5.73	4.57	0.56435	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.157403	0.43260	N	0.000594	T	0.09423	0.0232	N	0.12746	0.255	0.09310	N	0.999997	B;B	0.11235	0.004;0.004	B;B	0.10450	0.005;0.005	T	0.30966	-0.9960	10	0.08599	T	0.76	.	9.5865	0.39519	0.859:0.0:0.141:0.0	.	793;793	D6RGG3;Q99715	.;COCA1_HUMAN	T	793	ENSP00000325146:I793T;ENSP00000412864:I793T;ENSP00000421216:I793T	ENSP00000325146:I793T	I	-	2	0	COL12A1	75944158	1.000000	0.71417	0.987000	0.45799	0.035000	0.12851	2.691000	0.47010	0.991000	0.38814	-0.263000	0.10527	ATT	.	.		0.438	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		G	75887438	A	G	75887438	3	3	246	1	0	0	0	0	1	0	0	0	3671	101	4	2	7033	2	COL12A1	6	75887438	Missense_Mutation	SNP	A	TCGA-ED-A7XO-01A-11D-A34Z-10	32486367	75887438	95227629	23	33762										
LCA5	167691	hgsc.bcm.edu	37	chr6	80197406	80197406	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	ctctgtcaatttcattcagtTtagcaagtagcatttctctc	5	10	5	0			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr6:80197406T>C	ENST00000392959.1	-	9	2020	c.1409A>G	c.(1408-1410)aAa>aGa	p.K470R	LCA5_ENST00000369846.4_Missense_Mutation_p.K470R	NM_181714.3	NP_859065.2	Q86VQ0	LCA5_HUMAN	Leber congenital amaurosis 5	470					intraciliary transport (GO:0042073)|photoreceptor cell maintenance (GO:0045494)|protein transport (GO:0015031)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein complex binding (GO:0032403)			haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	32		all_cancers(76;3.32e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0176)		BRCA - Breast invasive adenocarcinoma(397;0.0657)		TTCATTCAGTTTAGCAAGTAG	0.373																																					p.K470R		Atlas-SNP	.											.	LCA5	71	.	0			c.A1409G						.						140	140	140					6																	80197406		2203	4300	6503	SO:0001583	missense	167691	exon8			TTCAGTTTAGCAA		CCDS4990.1	6q14	2014-01-28			ENSG00000135338	ENSG00000135338			31923	protein-coding gene	gene with protein product	"lebercilin"	611408	"chromosome 6 open reading frame 152"	C6orf152		10631161, 17546029	Standard	NM_181714		Approved		uc003pix.3	Q86VQ0	OTTHUMG00000015080	ENST00000392959.1:c.1409A>G	chr6.hg19:g.80197406T>C	ENSP00000376686:p.Lys470Arg	242.0	0.0		231.0	49.0	NM_001122769	E1P542|Q9BWX7	Missense_Mutation	SNP	ENST00000392959.1	hg19	CCDS4990.1	.	.	.	.	.	.	.	.	.	.	T	16.75	3.208625	0.58343	.	.	ENSG00000135338	ENST00000369846;ENST00000392959	T;T	0.51325	0.71;0.71	5.94	5.94	0.96194	.	0.053073	0.64402	D	0.000001	T	0.60792	0.2296	M	0.66939	2.045	0.42502	D	0.99293	D	0.89917	1.0	D	0.87578	0.998	T	0.65311	-0.6199	10	0.66056	D	0.02	-28.0041	15.5756	0.76380	0.0:0.0:0.0:1.0	.	470	Q86VQ0	LCA5_HUMAN	R	470	ENSP00000358861:K470R;ENSP00000376686:K470R	ENSP00000358861:K470R	K	-	2	0	LCA5	80254125	1.000000	0.71417	1.000000	0.80357	0.209000	0.24338	3.191000	0.50981	2.265000	0.75225	0.482000	0.46254	AAA	.	.		0.373	LCA5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259269.1	NM_181714		C	80197406	T	C	80197406	3	2	246	1	0	0	0	0	1	0	0	0	8665	1841	64	2	688	2	LCA5	6	80197406	Missense_Mutation	SNP	T	TCGA-ED-A7XO-01A-11D-A34Z-10	4309968	80197406	90917661	24	33763										
MYB	4602	hgsc.bcm.edu	37	chr6	135515497	135515497	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	ttactttgtaatttcagagaCactataatgatgaagaccct	6	7	1	4			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr6:135515497C>A	ENST00000367814.4	+	8	1033	c.847C>A	c.(847-849)Cac>Aac	p.H283N	MYB_ENST00000531845.1_3'UTR|MYB_ENST00000442647.2_Missense_Mutation_p.H283N|MYB_ENST00000528774.1_Missense_Mutation_p.H283N|MYB_ENST00000525369.1_Missense_Mutation_p.H283N|MYB_ENST00000533624.1_Intron|MYB_ENST00000534044.1_Missense_Mutation_p.H283N|MYB_ENST00000534121.1_Missense_Mutation_p.H283N|MYB_ENST00000341911.5_Missense_Mutation_p.H283N|MYB-AS1_ENST00000455534.1_RNA|MYB_ENST00000420123.2_Missense_Mutation_p.H259N|MYB_ENST00000316528.8_Missense_Mutation_p.H283N|MYB_ENST00000527615.1_Missense_Mutation_p.H283N	NM_001161659.1|NM_005375.2	NP_001155131.1|NP_005366.2	P10242	MYB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog	283	Transcription activation domain (PubMed:2189102). {ECO:0000269|PubMed:2189102}.				B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|chromatin remodeling (GO:0006338)|embryonic digestive tract development (GO:0048566)|G1/S transition of mitotic cell cycle (GO:0000082)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 methylation (GO:0051574)|positive regulation of T-helper cell differentiation (GO:0045624)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|thymus development (GO:0048538)	nuclear matrix (GO:0016363)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(4)|endometrium(1)|kidney(2)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	all_epithelial(2;0.109)|Breast(56;0.158)|Colorectal(23;0.221)	Lung NSC(302;3.08e-05)|Ovarian(999;0.208)		OV - Ovarian serous cystadenocarcinoma(155;0.0079)|GBM - Glioblastoma multiforme(68;0.0117)		ATTTCAGAGACACTATAATGA	0.423			T	NFIB	adenoid cystic carcinoma																																p.H283N		Atlas-SNP	.		Dom	yes		6	6q22-23	4602	v-myb myeloblastosis viral oncogene homolog		E	.	MYB	137	.	0			c.C847A						.						75	75	75					6																	135515497		2203	4300	6503	SO:0001583	missense	4602	exon8			CAGAGACACTATA		CCDS5174.1, CCDS47481.1, CCDS47482.1, CCDS55058.1, CCDS55059.1, CCDS55060.1, CCDS55061.1, CCDS55062.1	6q22-q23	2013-07-09	2013-07-09		ENSG00000118513	ENSG00000118513			7545	protein-coding gene	gene with protein product		189990				17599807	Standard	NM_001130172		Approved	c-myb	uc003qfh.3	P10242	OTTHUMG00000015629	ENST00000367814.4:c.847C>A	chr6.hg19:g.135515497C>A	ENSP00000356788:p.His283Asn	61.0	0.0		62.0	9.0	NM_001161656	E9PI07|E9PLZ5|E9PNA4|E9PNL6|E9PRS2|P78391|P78392|P78525|P78526|Q14023|Q14024|Q708E4|Q708E7|Q9UE83	Missense_Mutation	SNP	ENST00000367814.4	hg19	CCDS5174.1	.	.	.	.	.	.	.	.	.	.	C	14.81	2.645697	0.47258	.	.	ENSG00000118513	ENST00000341911;ENST00000442647;ENST00000316528;ENST00000237302;ENST00000367814;ENST00000527615;ENST00000420123;ENST00000525369;ENST00000528774;ENST00000534121;ENST00000534044;ENST00000430686	T;T;T;T;T;T;T;T;T	0.31769	2.73;2.25;2.23;2.25;1.48;2.01;2.73;2.72;1.9	5.46	5.46	0.80206	Transcription regulator Wos2-domain (1);	0.000000	0.85682	D	0.000000	T	0.35711	0.0941	L	0.46157	1.445	0.58432	D	0.999999	D;D;D;D;D;D;D;D;D	0.76494	0.997;0.999;0.997;0.999;0.971;0.996;0.998;0.971;0.997	D;D;D;D;P;D;D;P;D	0.87578	0.992;0.996;0.99;0.998;0.9;0.955;0.993;0.9;0.994	T	0.05354	-1.0890	10	0.08381	T	0.77	-10.4564	19.3016	0.94146	0.0:1.0:0.0:0.0	.	283;259;283;283;283;283;283;283;283	E9PLZ5;E9PMQ0;P10242-2;E9PNL6;E9PRS2;E9PNA4;P10242-4;P10242;Q708E1	.;.;.;.;.;.;.;MYB_HUMAN;.	N	283;283;283;283;283;283;259;283;283;283;283;237	ENSP00000339992:H283N;ENSP00000410825:H283N;ENSP00000326328:H283N;ENSP00000356788:H283N;ENSP00000433227:H283N;ENSP00000435938:H283N;ENSP00000434723:H283N;ENSP00000432851:H283N;ENSP00000435055:H283N	ENSP00000237302:H283N	H	+	1	0	MYB	135557190	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.089000	0.71384	2.552000	0.86080	0.561000	0.74099	CAC	.	.		0.423	MYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042347.4			A	135515497	C	A	135515497	3	1	246	1	0	0	0	0	1	0	0	0	10016	478	17	3	877	3	MYB	6	135515497	Missense_Mutation	SNP	C	TCGA-ED-A7XO-01A-11D-A34Z-10	55318091	135515497	35599570	25	33764										
KIAA1549	57670	hgsc.bcm.edu	37	chr7	138603314	138603314	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	gagaatgtgtcctgctgaatGcaagggctgcgtgcgatgca	15	8	0	2			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr7:138603314G>A	ENST00000422774.1	-	2	1106	c.1058C>T	c.(1057-1059)gCa>gTa	p.A353V	KIAA1549_ENST00000440172.1_Missense_Mutation_p.A353V|KIAA1549_ENST00000242365.4_Missense_Mutation_p.A303V			Q9HCM3	K1549_HUMAN	KIAA1549	353						integral component of membrane (GO:0016021)			KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						CCTGCTGAATGCAAGGGCTGC	0.488			O	BRAF	pilocytic astrocytoma																																p.A353V	NSCLC(119;1534 1718 44213 46230 50068)	Atlas-SNP	.		Dom	yes		7	7q34	57670	KIAA1549		O	.	KIAA1549	314	.	0			c.C1058T						.						193	203	200					7																	138603314		2164	4259	6423	SO:0001583	missense	57670	exon2			CTGAATGCAAGGG		CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.1058C>T	chr7.hg19:g.138603314G>A	ENSP00000416040:p.Ala353Val	32.0	0.0		55.0	9.0	NM_020910	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Missense_Mutation	SNP	ENST00000422774.1	hg19	CCDS56513.1	.	.	.	.	.	.	.	.	.	.	G	9.553	1.116425	0.20795	.	.	ENSG00000122778	ENST00000440172;ENST00000242365;ENST00000422774	T;T;T	0.26518	1.73;1.74;1.74	4.56	1.7	0.24286	.	0.463200	0.18261	N	0.146605	T	0.15825	0.0381	L	0.27053	0.805	0.09310	N	1	B;B	0.12630	0.006;0.002	B;B	0.15052	0.005;0.012	T	0.18398	-1.0338	10	0.51188	T	0.08	.	6.4708	0.22007	0.0777:0.1288:0.659:0.1345	.	353;353	Q9HCM3;Q9HCM3-2	K1549_HUMAN;.	V	353;303;353	ENSP00000406661:A353V;ENSP00000242365:A303V;ENSP00000416040:A353V	ENSP00000242365:A303V	A	-	2	0	KIAA1549	138253854	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.055000	0.11807	-0.059000	0.13154	-1.471000	0.01009	GCA	.	.		0.488	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1			A	138603314	G	A	138603314	3	1	246	1	0	0	0	0	1	0	0	0	8253	1319	46	3	4870	3	KIAA1549	7	138603314	Missense_Mutation	SNP	G	TCGA-ED-A7XO-01A-11D-A34Z-10		138603314	20535349	26	33765										
PLAG1	5324	hgsc.bcm.edu	37	chr8	57080762	57080762	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	tttggtttcaccacgcttacGtttccctgaagggactttct	8	11	2	1	rs144724863		TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr8:57080762G>A	ENST00000316981.3	-	4	546	c.67C>T	c.(67-69)Cgt>Tgt	p.R23C	PLAG1_ENST00000429357.2_Missense_Mutation_p.R23C|PLAG1_ENST00000423799.2_Intron	NM_001114634.1|NM_002655.2	NP_001108106.1|NP_002646.2	Q6DJT9	PLAG1_HUMAN	pleiomorphic adenoma gene 1	23	Interacts with KPNA2.				gland morphogenesis (GO:0022612)|multicellular organism growth (GO:0035264)|negative regulation of gene expression (GO:0010629)|organ growth (GO:0035265)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland growth (GO:0060736)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R23C(1)	CTNNB1/PLAG1(60)|LIFR_ENST00000263409/PLAG1(10)|HAS2/PLAG1(10)|FGFR1_ENST00000447712/PLAG1(28)|COL1A2/PLAG1(3)|CHCHD7/PLAG1(12)|TCEA1_ENST00000521604/PLAG1(3)	breast(3)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(7)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28		all_lung(136;0.0548)|Lung NSC(129;0.0718)|all_epithelial(80;0.125)	Epithelial(17;0.00179)|all cancers(17;0.0125)			CCACGCTTACGTTTCCCTGAA	0.448			T	"TCEA1, LIFR, CTNNB1, CHCHD7"	salivary adenoma																																p.R23C		Atlas-SNP	.		Dom	yes		8	8q12	5324	pleiomorphic adenoma gene 1		E	PLAG1_ENST00000316981,colon,carcinoma,+1,1	PLAG1	123	.	1	Substitution - Missense(1)	large_intestine(1)	c.C67T						.	G	CYS/ARG,,CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	115	104	108		67,,67	5.5	1	8	dbSNP_134	108	0,8600		0,0,4300	no	missense,intron,missense	PLAG1	NM_001114634.1,NM_001114635.1,NM_002655.2	180,,180	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,,probably-damaging	23/501,,23/501	57080762	1,13005	2203	4300	6503	SO:0001583	missense	5324	exon3			GCTTACGTTTCCC	U65002	CCDS6165.1, CCDS47860.1	8q12	2010-07-30				ENSG00000181690		"Zinc fingers, C2H2-type"	9045	protein-coding gene	gene with protein product		603026				9268638	Standard	NM_002655		Approved	ZNF912	uc010lyi.3	Q6DJT9		ENST00000316981.3:c.67C>T	chr8.hg19:g.57080762G>A	ENSP00000325546:p.Arg23Cys	110.0	0.0		98.0	8.0	NM_001114634	B4DLC2|Q59GH8|Q9Y4L2	Missense_Mutation	SNP	ENST00000316981.3	hg19	CCDS6165.1	.	.	.	.	.	.	.	.	.	.	G	17.93	3.509050	0.64410	2.27E-4	0.0	ENSG00000181690	ENST00000316981;ENST00000429357	T;T	0.13901	2.55;2.55	5.46	5.46	0.80206	.	0.052285	0.85682	D	0.000000	T	0.20820	0.0501	N	0.14661	0.345	0.80722	D	1	D	0.89917	1.0	P	0.58928	0.848	T	0.05852	-1.0860	10	0.87932	D	0	-17.9986	19.6662	0.95894	0.0:0.0:1.0:0.0	.	23	Q6DJT9	PLAG1_HUMAN	C	23	ENSP00000325546:R23C;ENSP00000416537:R23C	ENSP00000325546:R23C	R	-	1	0	PLAG1	57243316	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.650000	0.83521	2.695000	0.91970	0.563000	0.77884	CGT	.	G|1.000;A|0.000		0.448	PLAG1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378212.1	NM_002655		A	57080762	G	A	57080762	3	1	246	1	0	0	0	0	1	0	0	0	12027	1145	40	1	1443	1	PLAG1	8	57080762	Missense_Mutation	SNP	G	TCGA-ED-A7XO-01A-11D-A34Z-10		57080762	89283260	27	33766										
PREX2	80243	hgsc.bcm.edu	37	chr8	68864764	68864764	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	gtgggcacgctggagttcctGgtgtcggtgagtgtccccgg	18	10	0	1			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr8:68864764G>T	ENST00000288368.4	+	1	412	c.135G>T	c.(133-135)ctG>ctT	p.L45L	PREX2_ENST00000529398.1_3'UTR	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	45	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						TGGAGTTCCTGGTGTCGGTGA	0.701																																					p.L45L		Atlas-SNP	.											.	PREX2	614	.	0			c.G135T						.						27	27	27					8																	68864764		2202	4297	6499	SO:0001819	synonymous_variant	80243	exon1			GTTCCTGGTGTCG	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.135G>T	chr8.hg19:g.68864764G>T		101.0	0.0		113.0	14.0	NM_025170	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Silent	SNP	ENST00000288368.4	hg19	CCDS6201.1																																																																																			.	.		0.701	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		T	68864764	G	T	68864764	2	4	246	1	0	0	0	0	0	0	0	1	12489	1335	47	3		3	PREX2	8	68864764	Silent	SNP	G	TCGA-ED-A7XO-01A-11D-A34Z-10	11784002	68864764	77499258	28	33767										
ANGPT1	284	hgsc.bcm.edu	37	chr8	108348431	108348431	+	5'UTR	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	gtctgttgaagaagttgcttCtctagcttgtaggtggataa	12	5	2	2			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr8:108348431C>G	ENST00000520734.1	-	0	207				ANGPT1_ENST00000520052.1_5'UTR			Q15389	ANGP1_HUMAN	angiopoietin 1						activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell-substrate adhesion (GO:0031589)|glomerulus vasculature development (GO:0072012)|hemopoiesis (GO:0030097)|heparin biosynthetic process (GO:0030210)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of vascular permeability (GO:0043116)|positive chemotaxis (GO:0050918)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of receptor internalization (GO:0002092)|protein localization to cell surface (GO:0034394)|regulation of satellite cell proliferation (GO:0014842)|sprouting angiogenesis (GO:0002040)|Tie signaling pathway (GO:0048014)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(13)|ovary(4)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	43	Breast(1;5.06e-08)		OV - Ovarian serous cystadenocarcinoma(57;5.53e-09)			GAAGTTGCTTCTCTAGCTTGT	0.323																																					p.E174D		Atlas-SNP	.											.	ANGPT1	111	.	0			c.G522C						.						123	114	117					8																	108348431		2203	4300	6503	SO:0001623	5_prime_UTR_variant	284	exon3			TTGCTTCTCTAGC	D13628	CCDS6306.1, CCDS56551.1	8q23.1	2013-02-06			ENSG00000154188	ENSG00000154188		"Fibrinogen C domain containing"	484	protein-coding gene	gene with protein product		601667				9545648	Standard	NM_001146		Approved	KIAA0003, Ang1	uc003ymn.3	Q15389	OTTHUMG00000164812	ENST00000520734.1:c.-79G>C	chr8.hg19:g.108348431C>G		133.0	0.0		157.0	32.0	NM_001199859	Q5HYA0	Missense_Mutation	SNP	ENST00000520734.1	hg19		.	.	.	.	.	.	.	.	.	.	C	20.6	4.022044	0.75275	.	.	ENSG00000154188	ENST00000517746;ENST00000297450	T;T	0.51071	0.72;0.72	5.74	2.97	0.34412	.	0.000000	0.85682	D	0.000000	T	0.64349	0.2590	M	0.78049	2.395	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.69142	0.962;0.962	T	0.65721	-0.6099	10	0.66056	D	0.02	.	9.3822	0.38320	0.0:0.6544:0.0:0.3456	.	174;174	Q5HYA0;Q15389	.;ANGP1_HUMAN	D	174	ENSP00000428340:E174D;ENSP00000297450:E174D	ENSP00000297450:E174D	E	-	3	2	ANGPT1	108417607	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	2.519000	0.45546	0.789000	0.33779	-0.136000	0.14681	GAG	.	.		0.323	ANGPT1-002	PUTATIVE	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000380428.2	NM_001146, NM_139290		G	108348431	C	G	108348431	1	3	246	0	1	0	0	0	0	0	0	0	610	912	32	4		4	ANGPT1	8	108348431	5'UTR	SNP	C	TCGA-ED-A7XO-01A-11D-A34Z-10	39483667	108348431	38015591	29	33768										
DOCK8	81704	hgsc.bcm.edu	37	chr9	371468	371468	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	aagtgaaaattaagctccccGctaagctcacagtaaatcac	6	11	2	1			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr9:371468G>T	ENST00000453981.1	+	17	2021	c.1909G>T	c.(1909-1911)Gct>Tct	p.A637S	DOCK8_ENST00000382331.1_Intron|DOCK8_ENST00000382329.1_Missense_Mutation_p.A104S|DOCK8_ENST00000432829.2_Missense_Mutation_p.A569S|DOCK8_ENST00000469391.1_Missense_Mutation_p.A569S			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	637	DHR-1.				blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		TAAGCTCCCCGCTAAGCTCAC	0.418																																					p.A637S		Atlas-SNP	.											.	DOCK8	401	.	0			c.G1909T						.						109	101	104					9																	371468		2203	4300	6503	SO:0001583	missense	81704	exon17			CTCCCCGCTAAGC	AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.1909G>T	chr9.hg19:g.371468G>T	ENSP00000408464:p.Ala637Ser	109.0	0.0		117.0	20.0	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Missense_Mutation	SNP	ENST00000453981.1	hg19	CCDS6440.2	.	.	.	.	.	.	.	.	.	.	G	33	5.221864	0.95139	.	.	ENSG00000107099	ENST00000453981;ENST00000287364;ENST00000432829;ENST00000469391;ENST00000382329	T;T;T;T	0.14516	2.5;2.5;2.5;2.5	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.34745	0.0908	L	0.56769	1.78	0.80722	D	1	D;P;D	0.61697	0.99;0.903;0.973	D;P;P	0.65874	0.939;0.787;0.906	T	0.00180	-1.1948	10	0.33141	T	0.24	.	20.3409	0.98764	0.0:0.0:1.0:0.0	.	569;104;637	E9PH09;A2A369;Q8NF50	.;.;DOCK8_HUMAN	S	637;637;569;569;104	ENSP00000408464:A637S;ENSP00000394888:A569S;ENSP00000419438:A569S;ENSP00000371766:A104S	ENSP00000287364:A637S	A	+	1	0	DOCK8	361468	1.000000	0.71417	0.572000	0.28498	0.971000	0.66376	9.756000	0.98918	2.814000	0.96858	0.655000	0.94253	GCT	.	.		0.418	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307		T	371468	G	T	371468	3	4	246	1	0	0	0	0	1	0	0	0	4695	1087	38	1	1975	1	DOCK8	9	371468	Missense_Mutation	SNP	G	TCGA-ED-A7XO-01A-11D-A34Z-10		371468	140841963	30	33769										
DDX58	23586	hgsc.bcm.edu	37	chr9	32489378	32489378	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	tattgtgttttttcctttcaTagcaggcaaagcaagctcta	7	8	2	0			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr9:32489378T>C	ENST00000379883.2	-	6	920	c.763A>G	c.(763-765)Atg>Gtg	p.M255V	DDX58_ENST00000545044.1_Missense_Mutation_p.M52V|DDX58_ENST00000379882.1_Missense_Mutation_p.M210V|DDX58_ENST00000542096.1_Missense_Mutation_p.M184V|DDX58_ENST00000379868.1_Missense_Mutation_p.M52V	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	255	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.|Interaction with ZC3HAV1.				cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell migration (GO:0030334)|regulation of type III interferon production (GO:0034344)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RIG-I signaling pathway (GO:0039529)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|identical protein binding (GO:0042802)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		TTTCCTTTCATAGCAGGCAAA	0.338																																					p.M255V		Atlas-SNP	.											.	DDX58	82	.	0			c.A763G						.						141	125	130					9																	32489378		2203	4300	6503	SO:0001583	missense	23586	exon6			CTTTCATAGCAGG	AF038963	CCDS6526.1	9p12	2011-08-05			ENSG00000107201	ENSG00000107201		"DEAD-boxes"	19102	protein-coding gene	gene with protein product	"RNA helicase RIG-I", "retinoic acid inducible gene I"	609631				21690088	Standard	NM_014314		Approved	RIG-I, FLJ13599, DKFZp434J1111	uc003zra.3	O95786	OTTHUMG00000019746	ENST00000379883.2:c.763A>G	chr9.hg19:g.32489378T>C	ENSP00000369213:p.Met255Val	130.0	0.0		190.0	25.0	NM_014314	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Missense_Mutation	SNP	ENST00000379883.2	hg19	CCDS6526.1	.	.	.	.	.	.	.	.	.	.	T	9.566	1.119783	0.20877	.	.	ENSG00000107201	ENST00000379882;ENST00000379883;ENST00000379868;ENST00000542096;ENST00000545044	T;T;T;T;T	0.14144	2.53;2.53;2.53;2.53;2.53	4.99	-1.29	0.09288	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	1.278900	0.05219	N	0.508173	T	0.07279	0.0184	N	0.08118	0	0.09310	N	1	B;B;B;B	0.10296	0.001;0.003;0.002;0.001	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.39921	-0.9590	10	0.62326	D	0.03	-0.0574	5.7646	0.18219	0.3167:0.0:0.4129:0.2705	.	52;210;184;255	F5H5W6;O95786-2;B3KWW1;O95786	.;.;.;DDX58_HUMAN	V	210;255;52;184;52	ENSP00000369212:M210V;ENSP00000369213:M255V;ENSP00000369197:M52V;ENSP00000442160:M184V;ENSP00000443055:M52V	ENSP00000369197:M52V	M	-	1	0	DDX58	32479378	0.001000	0.12720	0.018000	0.16275	0.976000	0.68499	-0.619000	0.05572	0.022000	0.15160	0.533000	0.62120	ATG	.	.		0.338	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314		C	32489378	T	C	32489378	3	2	246	1	0	0	0	0	1	0	0	0	4377	1406	49	2	2066	2	DDX58	9	32489378	Missense_Mutation	SNP	T	TCGA-ED-A7XO-01A-11D-A34Z-10	32117910	32489378	108724053	31	33770										
S1PR3	1903	hgsc.bcm.edu	37	chr9	91616133	91616133	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	gtgatggcaactgccctcccGccgcgtctccagccggtgcg	13	17	1	1			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr9:91616133G>A	ENST00000375846.3	+	1	4713	c.18G>A	c.(16-18)ccG>ccA	p.P6P	S1PR3_ENST00000358157.2_Silent_p.P6P			Q99500	S1PR3_HUMAN	sphingosine-1-phosphate receptor 3	6					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|anatomical structure morphogenesis (GO:0009653)|cytokine production (GO:0001816)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of establishment of endothelial barrier (GO:1903141)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of interleukin-1 beta production (GO:0032651)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|integrin binding (GO:0005178)|lipid binding (GO:0008289)|sphingosine-1-phosphate receptor activity (GO:0038036)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|skin(1)	34						CTGCCCTCCCGCCGCGTCTCC	0.622											OREG0019291	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P6P		Atlas-SNP	.											.	S1PR3	49	.	0			c.G18A						.						54	63	60					9																	91616133		2203	4299	6502	SO:0001819	synonymous_variant	1903	exon2			CCTCCCGCCGCGT	AF022139	CCDS6680.1	9q22.1-q22.2	2012-08-08	2008-04-30	2008-04-30	ENSG00000213694	ENSG00000213694		"GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"	3167	protein-coding gene	gene with protein product	"sphingosine-1-phosphate receptor 3"	601965	"endothelial differentiation, sphingolipid G-protein-coupled receptor, 3"	EDG3		8878560, 9409733	Standard	NM_005226		Approved	EDG-3	uc004aqe.4	Q99500	OTTHUMG00000020173	ENST00000375846.3:c.18G>A	chr9.hg19:g.91616133G>A		43.0	0.0	1283	48.0	10.0	NM_005226	Q5SQD8|Q7Z5I2	Silent	SNP	ENST00000375846.3	hg19	CCDS6680.1																																																																																			.	.		0.622	S1PR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052979.2	NM_005226		A	91616133	G	A	91616133	2	1	246	1	0	0	0	0	0	0	0	1	13810	1074	38	1		1	S1PR3	9	91616133	Silent	SNP	G	TCGA-ED-A7XO-01A-11D-A34Z-10	59126755	91616133	49597298	32	33771										
CDH23	64072	hgsc.bcm.edu	37	chr10	73330627	73330627	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	gtccaggacatggaccccatCttcatcaacctgccttacag	7	15	3	0			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr10:73330627C>A	ENST00000224721.6	+	7	725	c.720C>A	c.(718-720)atC>atA	p.I240I	CDH23_ENST00000398809.4_Silent_p.I235I|CDH23_ENST00000398842.3_Silent_p.I235I|CDH23_ENST00000461841.3_Silent_p.I280I|CDH23_ENST00000299366.7_Silent_p.I280I	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	235	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.		P -> L (in DFNB12; dbSNP:rs121908354). {ECO:0000269|PubMed:17850630, ECO:0000269|PubMed:22899989, ECO:0000269|PubMed:24767429}.		calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						TGGACCCCATCTTCATCAACC	0.532											OREG0020254	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I235I		Atlas-SNP	.											.	CDH23	365	.	0			c.C705A						.						176	174	175					10																	73330627		2131	4252	6383	SO:0001819	synonymous_variant	64072	exon8			CCCCATCTTCATC	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"Cadherins / Cadherin-related"	13733	protein-coding gene	gene with protein product	"cadherin-related family member 23"	605516	"cadherin related 23", "cadherin-like 23"	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.720C>A	chr10.hg19:g.73330627C>A		105.0	0.0	1144	83.0	13.0	NM_052836	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	hg19																																																																																				.	.		0.532	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836		A	73330627	C	A	73330627	2	1	246	1	0	0	0	0	0	0	0	1	3110	903	32	3		3	CDH23	10	73330627	Silent	SNP	C	TCGA-ED-A7XO-01A-11D-A34Z-10		73330627	62204120	33	33772										
AP2A2	161	hgsc.bcm.edu	37	chr11	985500	985500	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	tgaacaaagcccaagaaccgCccaagtcgaagaaggtccag	10	12	0	3			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr11:985500C>T	ENST00000448903.2	+	8	1021	c.880C>T	c.(880-882)Ccc>Tcc	p.P294S	AP2A2_ENST00000534328.1_Missense_Mutation_p.P294S|AP2A2_ENST00000332231.5_Missense_Mutation_p.P295S	NM_001242837.1|NM_012305.3	NP_001229766.1|NP_036437.1	O94973	AP2A2_HUMAN	adaptor-related protein complex 2, alpha 2 subunit	294					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(2)	21		all_cancers(49;9.46e-06)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.75e-24)|BRCA - Breast invasive adenocarcinoma(625;5.73e-05)|Lung(200;0.0696)|LUSC - Lung squamous cell carcinoma(625;0.082)		CCAAGAACCGCCCAAGTCGAA	0.577																																					p.P295S		Atlas-SNP	.											.	AP2A2	50	.	0			c.C883T						.						102	109	106					11																	985500		2111	4232	6343	SO:0001583	missense	161	exon8			GAACCGCCCAAGT	AB020706	CCDS44512.1, CCDS73234.1	11p15.5	2008-07-18			ENSG00000183020	ENSG00000183020			562	protein-coding gene	gene with protein product	"alpha-adaptin C; Huntingtin interacting protein J", "adaptin, alpha B", "clathrin-associated/assembly/adaptor protein, large, alpha 2"	607242		CLAPA2, ADTAB		9700202, 2564002	Standard	NM_012305		Approved	DKFZP564D1864, HYPJ, KIAA0899, HIP9	uc001lst.2	O94973	OTTHUMG00000165627	ENST00000448903.2:c.880C>T	chr11.hg19:g.985500C>T	ENSP00000413234:p.Pro294Ser	27.0	0.0		46.0	8.0	NM_001242837	O75403|Q53ET1|Q96SI8	Missense_Mutation	SNP	ENST00000448903.2	hg19	CCDS44512.1	.	.	.	.	.	.	.	.	.	.	C	16.35	3.098902	0.56183	.	.	ENSG00000183020	ENST00000534328;ENST00000417081;ENST00000448903;ENST00000332231;ENST00000448757;ENST00000329626	T;T;T	0.37915	1.17;1.17;1.17	3.89	3.89	0.44902	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.52517	0.1739	L	0.42008	1.315	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	T	0.58736	-0.7584	10	0.87932	D	0	-26.413	16.2713	0.82622	0.0:1.0:0.0:0.0	.	295;294	O94973-2;O94973	.;AP2A2_HUMAN	S	294;294;294;295;295;167	ENSP00000436059:P294S;ENSP00000413234:P294S;ENSP00000327694:P295S	ENSP00000328024:P167S	P	+	1	0	AP2A2	975500	1.000000	0.71417	0.725000	0.30721	0.012000	0.07955	7.646000	0.83445	1.903000	0.55091	0.655000	0.94253	CCC	.	.		0.577	AP2A2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385431.2	NM_012305		T	985500	C	T	985500	3	4	246	1	0	0	0	0	1	0	0	0	740	739	26	3	910	3	AP2A2	11	985500	Missense_Mutation	SNP	C	TCGA-ED-A7XO-01A-11D-A34Z-10		985500	134021016	34	33773										
SPTBN2	6712	hgsc.bcm.edu	37	chr11	66460755	66460755	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	ctgctgggctcgcagggcatCctccagtcgcttccctcgaa	11	16	0	0			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr11:66460755C>A	ENST00000533211.1	-	24	5087	c.4756G>T	c.(4756-4758)Gat>Tat	p.D1586Y	SPTBN2_ENST00000529997.1_Missense_Mutation_p.D1586Y|SPTBN2_ENST00000309996.2_Missense_Mutation_p.D1586Y			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	1586					actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						CGCAGGGCATCCTCCAGTCGC	0.627																																					p.D1586Y		Atlas-SNP	.											.	SPTBN2	188	.	0			c.G4756T						.						69	71	70					11																	66460755		2200	4295	6495	SO:0001583	missense	6712	exon23			GGGCATCCTCCAG	AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"Pleckstrin homology (PH) domain containing"	11276	protein-coding gene	gene with protein product		604985	"spinocerebellar ataxia 5"	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.4756G>T	chr11.hg19:g.66460755C>A	ENSP00000432568:p.Asp1586Tyr	52.0	0.0		41.0	15.0	NM_006946	O14872|O14873	Missense_Mutation	SNP	ENST00000533211.1	hg19	CCDS8150.1	.	.	.	.	.	.	.	.	.	.	C	15.39	2.818476	0.50633	.	.	ENSG00000173898	ENST00000533211;ENST00000309996;ENST00000529997	T;T;T	0.53423	0.62;0.62;0.62	4.38	4.38	0.52667	.	0.199359	0.42420	D	0.000713	T	0.62245	0.2412	M	0.66560	2.04	0.21675	N	0.999591	P	0.39376	0.67	P	0.55455	0.776	T	0.57063	-0.7875	10	0.87932	D	0	.	12.3561	0.55176	0.0:0.8284:0.1716:0.0	.	1586	O15020	SPTN2_HUMAN	Y	1586	ENSP00000432568:D1586Y;ENSP00000311489:D1586Y;ENSP00000433593:D1586Y	ENSP00000311489:D1586Y	D	-	1	0	SPTBN2	66217331	0.847000	0.29606	0.989000	0.46669	0.710000	0.40934	3.765000	0.55272	2.268000	0.75426	0.462000	0.41574	GAT	.	.		0.627	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946		A	66460755	C	A	66460755	3	1	246	1	0	0	0	0	1	0	0	0	15135	855	30	3	2476	3	SPTBN2	11	66460755	Missense_Mutation	SNP	C	TCGA-ED-A7XO-01A-11D-A34Z-10	65475255	66460755	68545761	35	33774										
KLHL35	283212	hgsc.bcm.edu	37	chr11	75134789	75134789	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	cacatctgtgcctggatcatAggtgaagattttgctcatga	10	8	3	3			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr11:75134789A>T	ENST00000539798.1	-	5	1509	c.1510T>A	c.(1510-1512)Tat>Aat	p.Y504N	KLHL35_ENST00000376292.4_Missense_Mutation_p.Y284N	NM_001039548.2	NP_001034637.2	Q6PF15	KLH35_HUMAN	kelch-like family member 35	504										lung(2)|stomach(1)	3						CCTGGATCATAGGTGAAGATT	0.587																																					p.Y504N	Colon(77;683 1691 18820 23811)	Atlas-SNP	.											.	KLHL35	15	.	0			c.T1510A						.						125	132	130					11																	75134789		1988	4161	6149	SO:0001583	missense	283212	exon5			GATCATAGGTGAA		CCDS44685.1, CCDS44685.2	11q13.4	2013-02-22	2013-02-22		ENSG00000149243	ENSG00000149243		"Kelch-like", "BTB/POZ domain containing"	26597	protein-coding gene	gene with protein product			"kelch-like 35 (Drosophila)"				Standard	NM_001039548		Approved	FLJ33790	uc001owm.2	Q6PF15	OTTHUMG00000133573	ENST00000539798.1:c.1510T>A	chr11.hg19:g.75134789A>T	ENSP00000438526:p.Tyr504Asn	35.0	0.0		32.0	9.0	NM_001039548	A2RU06|F5H412|Q86XM7|Q8NBB1	Missense_Mutation	SNP	ENST00000539798.1	hg19	CCDS44685.2	.	.	.	.	.	.	.	.	.	.	A	24.2	4.503140	0.85176	.	.	ENSG00000149243	ENST00000376292;ENST00000539798	T;T	0.74106	-0.81;-0.81	5.12	5.12	0.69794	Kelch-type beta propeller (1);	0.082416	0.50627	D	0.000118	D	0.89199	0.6647	H	0.94345	3.525	0.58432	D	0.999997	D	0.76494	0.999	D	0.76071	0.987	D	0.91799	0.5450	10	0.87932	D	0	.	12.9174	0.58213	1.0:0.0:0.0:0.0	.	284	Q6PF15	KLH35_HUMAN	N	284;504	ENSP00000365469:Y284N;ENSP00000438526:Y504N	ENSP00000365469:Y284N	Y	-	1	0	KLHL35	74812437	1.000000	0.71417	0.993000	0.49108	0.982000	0.71751	7.159000	0.77483	2.152000	0.67230	0.528000	0.53228	TAT	.	.		0.587	KLHL35-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_173583		T	75134789	A	T	75134789	3	4	246	1	0	0	0	0	1	0	0	0	8397	420	15	4	249	4	KLHL35	11	75134789	Missense_Mutation	SNP	A	TCGA-ED-A7XO-01A-11D-A34Z-10	8674034	75134789	59871727	36	33775										
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	103006470	103006470	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	cagggacgattacaattcagGcccccttttgaagaaatccg	9	11	1	2			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr11:103006470G>C	ENST00000375735.2	+	17	2511	c.2367G>C	c.(2365-2367)agG>agC	p.R789S	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Missense_Mutation_p.R789S	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	789	Stem. {ECO:0000250}.		R -> K (in dbSNP:rs7358374).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		TACAATTCAGGCCCCCTTTTG	0.333																																					p.R789S		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.G2367C						.						37	34	35					11																	103006470		1788	4056	5844	SO:0001583	missense	79659	exon17			ATTCAGGCCCCCT	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.2367G>C	chr11.hg19:g.103006470G>C	ENSP00000364887:p.Arg789Ser	144.0	0.0		140.0	32.0	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	hg19	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	G	11.86	1.763448	0.31228	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.28895	1.59;1.59	5.3	-0.564	0.11774	.	0.739342	0.11903	U	0.518428	T	0.24470	0.0593	L	0.60067	1.865	0.47476	D	0.999437	B;B	0.17667	0.023;0.019	B;B	0.17722	0.011;0.019	T	0.21655	-1.0239	10	0.07990	T	0.79	.	9.4185	0.38536	0.6089:0.0:0.3911:0.0	.	789;789	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	S	789	ENSP00000364887:R789S;ENSP00000381167:R789S	ENSP00000364887:R789S	R	+	3	2	DYNC2H1	102511680	0.968000	0.33430	0.997000	0.53966	0.987000	0.75469	0.155000	0.16362	-0.002000	0.14469	0.563000	0.77884	AGG	.	.		0.333	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		C	103006470	G	C	103006470	3	2	246	1	0	0	0	0	1	0	0	0	4848	1194	42	4	2433	4	DYNC2H1	11	103006470	Missense_Mutation	SNP	G	TCGA-ED-A7XO-01A-11D-A34Z-10	27871681	103006470	32000046	37	33776										
PDE3A	5139	hgsc.bcm.edu	37	chr12	20769305	20769305	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	ccagcatcaaactgcaggaaGcaccttcatccaggtggcat	9	13	2	0			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr12:20769305G>A	ENST00000359062.3	+	4	1451	c.1411G>A	c.(1411-1413)Gca>Aca	p.A471T	PDE3A_ENST00000544307.1_3'UTR	NM_000921.4|NM_001244683.1	NP_000912.3|NP_001231612.1	Q14432	PDE3A_HUMAN	phosphodiesterase 3A, cGMP-inhibited	471					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP-mediated signaling (GO:0019934)|diterpenoid metabolic process (GO:0016101)|lipid metabolic process (GO:0006629)|negative regulation of apoptotic process (GO:0043066)|negative regulation of vascular permeability (GO:0043116)|oocyte maturation (GO:0001556)|positive regulation of oocyte development (GO:0060282)|positive regulation of vascular permeability (GO:0043117)|regulation of meiosis (GO:0040020)|response to cAMP (GO:0051591)|response to drug (GO:0042493)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(7)|lung(29)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	58	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Caffeine(DB00201)|Cilostazol(DB01166)|Enoximone(DB04880)|Ibudilast(DB05266)|Levosimendan(DB00922)|Milrinone(DB00235)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Tofisopam(DB08811)	ACTGCAGGAAGCACCTTCATC	0.507																																					p.A471T		Atlas-SNP	.											.	PDE3A	184	.	0			c.G1411A						.						106	91	96					12																	20769305		2203	4300	6503	SO:0001583	missense	5139	exon4			CAGGAAGCACCTT		CCDS31754.1	12p12.2	2011-04-15			ENSG00000172572	ENSG00000172572	3.1.4.17	"Phosphodiesterases"	8778	protein-coding gene	gene with protein product		123805				1315035, 10679291	Standard	NM_000921		Approved	CGI-PDE	uc001reh.2	Q14432	OTTHUMG00000168962	ENST00000359062.3:c.1411G>A	chr12.hg19:g.20769305G>A	ENSP00000351957:p.Ala471Thr	47.0	0.0		40.0	9.0	NM_000921	O60865|Q13348|Q17RD1	Missense_Mutation	SNP	ENST00000359062.3	hg19	CCDS31754.1	.	.	.	.	.	.	.	.	.	.	G	2.253	-0.371105	0.05034	.	.	ENSG00000172572	ENST00000359062	T	0.52983	0.64	5.26	4.34	0.51931	.	14.108600	0.00166	N	0.000000	T	0.44286	0.1286	L	0.48642	1.525	0.09310	N	1	B	0.19583	0.037	B	0.18263	0.021	T	0.24764	-1.0151	10	0.22109	T	0.4	.	7.3806	0.26854	0.0785:0.0:0.4891:0.4325	.	471	Q14432	PDE3A_HUMAN	T	471	ENSP00000351957:A471T	ENSP00000351957:A471T	A	+	1	0	PDE3A	20660572	0.044000	0.20184	0.985000	0.45067	0.053000	0.15095	0.556000	0.23438	1.304000	0.44892	0.655000	0.94253	GCA	.	.		0.507	PDE3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401756.2			A	20769305	G	A	20769305	3	1	246	1	0	0	0	0	1	0	0	0	11646	971	34	3	1425	3	PDE3A	12	20769305	Missense_Mutation	SNP	G	TCGA-ED-A7XO-01A-11D-A34Z-10		20769305	113082590	38	33777										
CUX2	23316	hgsc.bcm.edu	37	chr12	111655734	111655734	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	tcctgtattaaaaagcttccAagccgaggtaagacccaggg	10	10	0	1			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr12:111655734A>T	ENST00000261726.6	+	3	369	c.215A>T	c.(214-216)cAa>cTa	p.Q72L	CUX2_ENST00000551604.2_3'UTR	NM_015267.3	NP_056082.2	O14529	CUX2_HUMAN	cut-like homeobox 2	72					cellular response to organic substance (GO:0071310)|cognition (GO:0050890)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of synapse assembly (GO:0051965)|short-term memory (GO:0007614)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(24)|ovary(5)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	55						AAAAGCTTCCAAGCCGAGGTA	0.577																																					p.Q72L		Atlas-SNP	.											.	CUX2	145	.	0			c.A215T						.						76	82	80					12																	111655734		1879	4099	5978	SO:0001583	missense	23316	exon3			GCTTCCAAGCCGA	AB006631	CCDS41837.1	12q24.12	2011-06-20	2007-11-07	2007-11-07	ENSG00000111249	ENSG00000111249		"Homeoboxes / CUT class"	19347	protein-coding gene	gene with protein product		610648	"cut-like 2 (Drosophila)"	CUTL2			Standard	NM_015267		Approved	KIAA0293, CDP2	uc001tsa.2	O14529	OTTHUMG00000169546	ENST00000261726.6:c.215A>T	chr12.hg19:g.111655734A>T	ENSP00000261726:p.Gln72Leu	36.0	0.0		53.0	11.0	NM_015267	A7E2Y4	Missense_Mutation	SNP	ENST00000261726.6	hg19	CCDS41837.1	.	.	.	.	.	.	.	.	.	.	A	19.12	3.764998	0.69878	.	.	ENSG00000111249	ENST00000261726;ENST00000397643;ENST00000552889	T	0.50001	0.76	5.3	5.3	0.74995	.	0.515830	0.19381	N	0.115664	T	0.66346	0.2780	M	0.61703	1.905	0.53005	D	0.999967	D;D	0.89917	1.0;0.993	D;D	0.83275	0.996;0.977	T	0.68849	-0.5300	10	0.87932	D	0	-9.279	14.5312	0.67926	1.0:0.0:0.0:0.0	.	132;72	F5GWR6;O14529	.;CUX2_HUMAN	L	72;132;10	ENSP00000261726:Q72L	ENSP00000261726:Q72L	Q	+	2	0	CUX2	110140117	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.843000	0.86859	2.131000	0.65755	0.533000	0.62120	CAA	.	.		0.577	CUX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404765.1	NM_015267		T	111655734	A	T	111655734	3	4	246	1	0	0	0	0	1	0	0	0	4067	130	5	4	225	4	CUX2	12	111655734	Missense_Mutation	SNP	A	TCGA-ED-A7XO-01A-11D-A34Z-10	90886429	111655734	22196161	39	33778										
CLIP1	6249	hgsc.bcm.edu	37	chr12	122845703	122845703	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	gtggacaggagcgaacaagcCatatttgggttgacactgaa	13	7	0	2			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr12:122845703C>T	ENST00000540338.1	-	4	849	c.808G>A	c.(808-810)Ggc>Agc	p.G270S	CLIP1_ENST00000545889.1_5'UTR|CLIP1_ENST00000537178.1_Missense_Mutation_p.G270S|CLIP1_ENST00000302528.7_Missense_Mutation_p.G270S|CLIP1_ENST00000361654.4_Missense_Mutation_p.G270S|CLIP1_ENST00000358808.2_Missense_Mutation_p.G270S			P30622	CLIP1_HUMAN	CAP-GLY domain containing linker protein 1	270	CAP-Gly 2. {ECO:0000255|PROSITE- ProRule:PRU00045}.				microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|positive regulation of microtubule polymerization (GO:0031116)|transport (GO:0006810)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|intermediate filament (GO:0005882)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	metal ion binding (GO:0046872)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|nucleic acid binding (GO:0003676)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|endometrium(4)|kidney(5)|large_intestine(16)|liver(1)|lung(21)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)		GCGAACAAGCCATATTTGGGT	0.418																																					p.G270S		Atlas-SNP	.											.	CLIP1	126	.	0			c.G808A						.						84	90	88					12																	122845703		2203	4300	6503	SO:0001583	missense	6249	exon5			ACAAGCCATATTT		CCDS9232.1, CCDS9233.1, CCDS58285.1	12q24.3	2013-01-17	2007-01-05	2007-01-05	ENSG00000130779	ENSG00000130779			10461	protein-coding gene	gene with protein product	"restin"	179838	"restin (Reed-Steinberg cell-expressed intermediate filament-associated protein)"	RSN		8222754	Standard	NM_001247997		Approved	CYLN1, CLIP170, CLIP, CLIP-170	uc001ucg.2	P30622	OTTHUMG00000168922	ENST00000540338.1:c.808G>A	chr12.hg19:g.122845703C>T	ENSP00000439093:p.Gly270Ser	50.0	0.0		62.0	15.0	NM_002956	A0AVD3|Q17RS4|Q29RG0	Missense_Mutation	SNP	ENST00000540338.1	hg19	CCDS58285.1	.	.	.	.	.	.	.	.	.	.	C	34	5.364610	0.95877	.	.	ENSG00000130779	ENST00000302528;ENST00000358808;ENST00000542885;ENST00000537178;ENST00000540338;ENST00000540304;ENST00000537004	D;D;D;D;D;D	0.88975	-2.45;-2.45;-2.45;-2.45;-2.45;-2.45	5.32	5.32	0.75619	Cytoskeleton-associated protein, Gly-rich domain (4);	0.000000	0.85682	D	0.000000	D	0.97167	0.9074	H	0.98754	4.32	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.98903	1.0777	10	0.87932	D	0	-14.504	18.9994	0.92828	0.0:1.0:0.0:0.0	.	270;270;270;270	F6VGP8;P30622-2;P30622-1;P30622	.;.;.;CLIP1_HUMAN	S	270;270;115;270;270;270;270	ENSP00000303585:G270S;ENSP00000351665:G270S;ENSP00000445531:G270S;ENSP00000439093:G270S;ENSP00000437786:G270S;ENSP00000441409:G270S	ENSP00000303585:G270S	G	-	1	0	CLIP1	121411656	1.000000	0.71417	0.997000	0.53966	0.960000	0.62799	7.818000	0.86416	2.486000	0.83907	0.561000	0.74099	GGC	.	.		0.418	CLIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401625.1	NM_002956		T	122845703	C	T	122845703	3	4	246	1	0	0	0	0	1	0	0	0	3534	594	21	3	3559	3	CLIP1	12	122845703	Missense_Mutation	SNP	C	TCGA-ED-A7XO-01A-11D-A34Z-10	11189969	122845703	11006192	40	33779										
C14orf37	145407	hgsc.bcm.edu	37	chr14	58478850	58478850	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	ttcttaccttgtcttttaatTtttccatccagcttctcact	2	12	3	0			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr14:58478850T>C	ENST00000267485.7	-	6	2302	c.2108A>G	c.(2107-2109)aAa>aGa	p.K703R		NM_001001872.2	NP_001001872.2	Q86TY3	CN037_HUMAN	chromosome 14 open reading frame 37	703						integral component of membrane (GO:0016021)				breast(7)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|skin(1)	33						GTCTTTTAATTTTTCCATCCA	0.279																																					p.K703R		Atlas-SNP	.											.	C14orf37	87	.	0			c.A2108G						.						24	27	26					14																	58478850		2190	4286	6476	SO:0001583	missense	145407	exon6			TTTAATTTTTCCA		CCDS32089.1	14q23.1	2012-09-03			ENSG00000139971	ENSG00000139971			19846	protein-coding gene	gene with protein product							Standard	NM_001001872		Approved		uc001xdc.3	Q86TY3	OTTHUMG00000171173	ENST00000267485.7:c.2108A>G	chr14.hg19:g.58478850T>C	ENSP00000267485:p.Lys703Arg	446.0	0.0		573.0	89.0	NM_001001872	A8K8Z8|Q6P5Q1|Q86TY1	Missense_Mutation	SNP	ENST00000267485.7	hg19	CCDS32089.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.171830	0.78452	.	.	ENSG00000139971	ENST00000267485;ENST00000438670	T	0.35048	1.33	5.38	5.38	0.77491	.	0.154140	0.46758	D	0.000277	T	0.56804	0.2010	L	0.58101	1.795	0.39110	D	0.961454	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.999	T	0.62595	-0.6821	10	0.87932	D	0	-22.2224	14.9326	0.70929	0.0:0.0:0.0:1.0	.	741;703;703	B4DMS4;A8K990;Q86TY3	.;.;CN037_HUMAN	R	703;741	ENSP00000267485:K703R	ENSP00000267485:K703R	K	-	2	0	C14orf37	57548603	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.086000	0.64474	2.173000	0.68751	0.529000	0.55759	AAA	.	.		0.279	C14orf37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412059.1	NM_001001872		C	58478850	T	C	58478850	3	2	246	1	0	0	0	0	1	0	0	0	1773	1841	64	2	228	2	C14orf37	14	58478850	Missense_Mutation	SNP	T	TCGA-ED-A7XO-01A-11D-A34Z-10		58478850	48870690	41	33780										
KCNH5	27133	hgsc.bcm.edu	37	chr14	63468076	63468076	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	tgaatcatcctctattggctGtttgaacaacgtaatatcct	6	9	2	2	rs527943803		TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr14:63468076G>T	ENST00000322893.7	-	4	674	c.406C>A	c.(406-408)Cag>Aag	p.Q136K	KCNH5_ENST00000394964.2_Missense_Mutation_p.Q78K|KCNH5_ENST00000420622.2_Missense_Mutation_p.Q136K|KCNH5_ENST00000394968.1_Missense_Mutation_p.Q78K	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	136	PAC. {ECO:0000255|PROSITE- ProRule:PRU00141}.				potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		TCTATTGGCTGTTTGAACAAC	0.338																																					p.Q136K		Atlas-SNP	.											.	KCNH5	320	.	0			c.C406A						.						110	99	103					14																	63468076		2203	4300	6503	SO:0001583	missense	27133	exon4			TTGGCTGTTTGAA	U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.406C>A	chr14.hg19:g.63468076G>T	ENSP00000321427:p.Gln136Lys	68.0	0.0		94.0	16.0	NM_172375	C9JP98	Missense_Mutation	SNP	ENST00000322893.7	hg19	CCDS9756.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.322019	0.81580	.	.	ENSG00000140015	ENST00000322893;ENST00000420622;ENST00000394968;ENST00000394964	D;D;D;D	0.98947	-5.26;-5.06;-5.03;-5.04	5.64	5.64	0.86602	PAS-associated, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98686	0.9559	M	0.74881	2.28	0.80722	D	1	B;P;P;D	0.56035	0.188;0.739;0.739;0.974	B;B;B;P	0.55615	0.074;0.259;0.259;0.78	D	0.98760	1.0724	10	0.25106	T	0.35	.	19.7059	0.96071	0.0:0.0:1.0:0.0	.	78;78;136;136	Q86XI1;Q8NCM2-3;Q8NCM2-2;Q8NCM2	.;.;.;KCNH5_HUMAN	K	136;136;78;78	ENSP00000321427:Q136K;ENSP00000395439:Q136K;ENSP00000378419:Q78K;ENSP00000378415:Q78K	ENSP00000321427:Q136K	Q	-	1	0	KCNH5	62537829	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.673000	0.90976	0.591000	0.81541	CAG	.	.		0.338	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318		T	63468076	G	T	63468076	3	4	246	1	0	0	0	0	1	0	0	0	8044	1386	48	3	2626	3	KCNH5	14	63468076	Missense_Mutation	SNP	G	TCGA-ED-A7XO-01A-11D-A34Z-10	4989226	63468076	43881464	42	33781										
AHSA1	10598	hgsc.bcm.edu	37	chr14	77931884	77931884	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	tcactgccaccttcacaggcTaagcctgctccttcaaaaac	5	16	3	0			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr14:77931884T>G	ENST00000216479.3	+	6	724	c.564T>G	c.(562-564)gcT>gcG	p.A188A	AHSA1_ENST00000535854.2_Silent_p.A188A|SNORA46_ENST00000391069.1_RNA|AHSA1_ENST00000555457.1_Intron	NM_012111.2	NP_036243.1	O95433	AHSA1_HUMAN	AHA1, activator of heat shock 90kDa protein ATPase homolog 1 (yeast)	188					positive regulation of ATPase activity (GO:0032781)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	ATPase activator activity (GO:0001671)|chaperone binding (GO:0051087)			endometrium(1)|kidney(3)|large_intestine(1)|prostate(1)|skin(1)|stomach(1)	8			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)		CTTCACAGGCTAAGCCTGCTC	0.443																																					p.A188A		Atlas-SNP	.											.	AHSA1	24	.	0			c.T564G						.						99	90	93					14																	77931884		2203	4300	6503	SO:0001819	synonymous_variant	10598	exon6			ACAGGCTAAGCCT	AJ243310	CCDS9863.1	14q	2008-02-05	2003-04-04	2003-04-11		ENSG00000100591			1189	protein-coding gene	gene with protein product		608466	"chromosome 14 open reading frame 3"	C14orf3			Standard	NM_012111		Approved	p38	uc001xtw.3	O95433		ENST00000216479.3:c.564T>G	chr14.hg19:g.77931884T>G		31.0	0.0		36.0	7.0	NM_012111	B2R9L2|B4DUR9|Q96IL6|Q9P060	Silent	SNP	ENST00000216479.3	hg19	CCDS9863.1	.	.	.	.	.	.	.	.	.	.	T	5.905	0.350993	0.11182	.	.	ENSG00000100591	ENST00000553374	.	.	.	6.07	-3.06	0.05379	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-5.2836	3.3522	0.07156	0.1594:0.4833:0.1465:0.2107	.	.	.	.	E	134	.	.	X	+	1	0	AHSA1	77001637	0.019000	0.18553	0.209000	0.23619	0.287000	0.27160	-0.340000	0.07821	-0.420000	0.07427	-0.256000	0.11100	TAA	.	.		0.443	AHSA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414017.1	NM_012111		G	77931884	T	G	77931884	2	3	246	1	0	0	0	0	0	0	0	1	418	1509	53	5		5	AHSA1	14	77931884	Silent	SNP	T	TCGA-ED-A7XO-01A-11D-A34Z-10	14463808	77931884	29417656	43	33782										
ALDH1A2	8854	hgsc.bcm.edu	37	chr15	58254254	58254254	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	atcagtgacgttggaaaacaCtgtgggctcaatgaaaaacc	10	8	2	2			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr15:58254254C>A	ENST00000249750.4	-	10	1974	c.1207G>T	c.(1207-1209)Gtg>Ttg	p.V403L	ALDH1A2_ENST00000537372.1_Missense_Mutation_p.V382L|ALDH1A2_ENST00000347587.3_Missense_Mutation_p.V365L|ALDH1A2_ENST00000558231.1_Missense_Mutation_p.V374L|ALDH1A2_ENST00000559517.1_Missense_Mutation_p.V307L	NM_003888.3	NP_003879.2	O94788	AL1A2_HUMAN	aldehyde dehydrogenase 1 family, member A2	403					9-cis-retinoic acid biosynthetic process (GO:0042904)|anterior/posterior pattern specification (GO:0009952)|blood vessel development (GO:0001568)|cardiac muscle tissue development (GO:0048738)|cellular response to retinoic acid (GO:0071300)|determination of bilateral symmetry (GO:0009855)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract development (GO:0048566)|embryonic forelimb morphogenesis (GO:0035115)|face development (GO:0060324)|heart morphogenesis (GO:0003007)|hindbrain development (GO:0030902)|kidney development (GO:0001822)|liver development (GO:0001889)|lung development (GO:0030324)|midgut development (GO:0007494)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of cell proliferation (GO:0008285)|neural crest cell development (GO:0014032)|neural tube development (GO:0021915)|neuron differentiation (GO:0030182)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|proximal/distal pattern formation (GO:0009954)|regulation of endothelial cell proliferation (GO:0001936)|response to cytokine (GO:0034097)|response to estradiol (GO:0032355)|response to vitamin A (GO:0033189)|retinal metabolic process (GO:0042574)|retinoic acid metabolic process (GO:0042573)|retinoic acid receptor signaling pathway (GO:0048384)|retinol metabolic process (GO:0042572)|ureter maturation (GO:0035799)|vitamin A metabolic process (GO:0006776)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)	3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|retinal binding (GO:0016918)|retinal dehydrogenase activity (GO:0001758)			NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(15)|prostate(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(80;0.152)|all cancers(107;0.18)	Tretinoin(DB00755)|Vitamin A(DB00162)	TTGGAAAACACTGTGGGCTCA	0.483																																					p.V403L		Atlas-SNP	.											.	ALDH1A2	69	.	0			c.G1207T						.						118	113	115					15																	58254254		2192	4292	6484	SO:0001583	missense	8854	exon10			AAAACACTGTGGG	AB015228	CCDS10163.1, CCDS10164.1, CCDS45266.1, CCDS55968.1	15q21.2	2011-02-18			ENSG00000128918	ENSG00000128918		"Aldehyde dehydrogenases"	15472	protein-coding gene	gene with protein product	"retinaldehyde dehydrogenase 2"	603687				9819382	Standard	NM_003888		Approved	RALDH2	uc002aex.3	O94788	OTTHUMG00000132624	ENST00000249750.4:c.1207G>T	chr15.hg19:g.58254254C>A	ENSP00000249750:p.Val403Leu	148.0	0.0		158.0	25.0	NM_003888	B3KY52|B4DZR2|F5H2Y9|H0YM00|Q2PJS6|Q8NHQ4|Q9UBR8|Q9UFY0	Missense_Mutation	SNP	ENST00000249750.4	hg19	CCDS10163.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.977836	0.92982	.	.	ENSG00000128918	ENST00000249750;ENST00000430119;ENST00000543386;ENST00000347587;ENST00000537372	T;T;T	0.80304	-1.36;-1.36;-1.36	5.87	5.87	0.94306	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.000000	0.85682	D	0.000000	D	0.85120	0.5624	L	0.45470	1.425	0.80722	D	1	P;P;D;P	0.60160	0.657;0.605;0.987;0.81	B;B;P;P	0.55391	0.246;0.159;0.775;0.511	D	0.85486	0.1182	10	0.87932	D	0	.	20.5827	0.99408	0.0:1.0:0.0:0.0	.	374;382;365;403	B4DH89;F5H2Y9;O94788-2;O94788	.;.;.;AL1A2_HUMAN	L	403;307;374;365;382	ENSP00000249750:V403L;ENSP00000309623:V365L;ENSP00000438296:V382L	ENSP00000249750:V403L	V	-	1	0	ALDH1A2	56041546	1.000000	0.71417	0.973000	0.42090	0.635000	0.38103	7.818000	0.86416	2.941000	0.99782	0.655000	0.94253	GTG	.	.		0.483	ALDH1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255869.1			A	58254254	C	A	58254254	3	1	246	1	0	0	0	0	1	0	0	0	491	565	20	3	365	3	ALDH1A2	15	58254254	Missense_Mutation	SNP	C	TCGA-ED-A7XO-01A-11D-A34Z-10		58254254	44277138	44	33783										
SGK269	79834	hgsc.bcm.edu	37	chr15	77407661	77407661	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	tttagctttgctcttacagaTctgaaagataataaaacaat	5	6	2	3			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr15:77407661T>A	ENST00000560626.2	-	7	4553	c.4078A>T	c.(4078-4080)Atc>Ttc	p.I1360F	PEAK1_ENST00000312493.4_Splice_Site_p.I1360F			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	1360	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										CTCTTACAGATCTGAAAGATA	0.413																																					p.I1360F		Atlas-SNP	.											.	.	.	.	0			c.A4078T						.						44	39	41					15																	77407661		1874	4108	5982	SO:0001630	splice_region_variant	0	exon8			TACAGATCTGAAA		CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.4078-1A>T	chr15.hg19:g.77407661T>A		41.0	0.0		47.0	8.0	NM_024776	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Missense_Mutation	SNP	ENST00000560626.2	hg19	CCDS42062.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.391983	0.83011	.	.	ENSG00000173517	ENST00000312493	T	0.75154	-0.91	5.35	5.35	0.76521	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.84795	0.5551	M	0.66939	2.045	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.86626	0.1882	10	0.87932	D	0	-7.2398	15.328	0.74182	0.0:0.0:0.0:1.0	.	1360	Q9H792	PEAK1_HUMAN	F	1360	ENSP00000309230:I1360F	ENSP00000309230:I1360F	I	-	1	0	AC087465.1	75194716	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.040000	0.89188	2.044000	0.60594	0.459000	0.35465	ATC	.	.		0.413	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3		Missense_Mutation	A	77407661	T	A	77407661	5	1	246	1	0	0	0	0	0	0	1	0	14226	1449	50	4	1166	4	SGK269	15	77407661	Splice_Site	SNP	T	TCGA-ED-A7XO-01A-11D-A34Z-10	19153407	77407661	25123731	45	33784										
TNRC6A	27327	hgsc.bcm.edu	37	chr16	24831569	24831569	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	cctaaaaacatcactgctccGtcccgcccacctccgggact	6	19	1	0	rs552703108		TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr16:24831569G>A	ENST00000395799.3	+	22	5319	c.5190G>A	c.(5188-5190)ccG>ccA	p.P1730P	CTD-2515A14.1_ENST00000568895.1_RNA|TNRC6A_ENST00000432286.2_Silent_p.P208P|TNRC6A_ENST00000315183.7_Silent_p.P1681P	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	1730	Sufficient for interaction with AGO2.				cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		TCACTGCTCCGTCCCGCCCAC	0.527													G|||	1	0.000199681	0	0	5008	,	,		18949	0.001		0	False		,,,				2504	0				p.P1730P		Atlas-SNP	.											.	TNRC6A	171	.	0			c.G5190A						.						131	124	126					16																	24831569		2197	4300	6497	SO:0001819	synonymous_variant	27327	exon22			TGCTCCGTCCCGC	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"Trinucleotide (CAG) repeat containing"	11969	protein-coding gene	gene with protein product		610739	"trinucleotide repeat containing 6"	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.5190G>A	chr16.hg19:g.24831569G>A		100.0	0.0		121.0	28.0	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Silent	SNP	ENST00000395799.3	hg19	CCDS10624.2	.	.	.	.	.	.	.	.	.	.	G	10.32	1.317944	0.23994	.	.	ENSG00000090905	ENST00000450465	.	.	.	5.79	2.8	0.32819	.	.	.	.	.	T	0.55257	0.1909	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48779	-0.9005	4	.	.	.	-6.5693	7.0156	0.24887	0.2073:0.1262:0.6665:0.0	.	.	.	.	I	621	.	.	V	+	1	0	TNRC6A	24739070	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.533000	0.36040	0.797000	0.33971	0.655000	0.94253	GTC	.	.		0.527	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		A	24831569	G	A	24831569	2	1	246	1	0	0	0	0	0	0	0	1	16355	1132	40	1		1	TNRC6A	16	24831569	Silent	SNP	G	TCGA-ED-A7XO-01A-11D-A34Z-10		24831569	65523184	46	33785										
TP53	7157	hgsc.bcm.edu	37	chr17	7577511	7577511	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	ctcctgacctggagtcttccAgtgtgatgatggtgaggatg	14	8	1	4	rs28934577		TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr17:7577511A>G	ENST00000269305.4	-	7	959	c.770T>C	c.(769-771)cTg>cCg	p.L257P	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.L257P|TP53_ENST00000445888.2_Missense_Mutation_p.L257P|TP53_ENST00000359597.4_Missense_Mutation_p.L257P|TP53_ENST00000420246.2_Missense_Mutation_p.L257P|TP53_ENST00000413465.2_Missense_Mutation_p.L257P	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	257	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		L -> P (in sporadic cancers; somatic mutation).|L -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs28934577).|L -> R (in sporadic cancers; somatic mutation).|L -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.L257Q(8)|p.L257P(8)|p.L257fs*6(2)|p.?(1)|p.T256fs*87(1)|p.L257R(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGAGTCTTCCAGTGTGATGAT	0.582		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.L257P	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000413465,colon,carcinoma,+1,27	TP53	33396	.	29	Substitution - Missense(17)|Whole gene deletion(8)|Deletion - Frameshift(3)|Unknown(1)	large_intestine(4)|oesophagus(4)|bone(4)|haematopoietic_and_lymphoid_tissue(3)|ovary(3)|central_nervous_system(2)|liver(2)|upper_aerodigestive_tract(1)|stomach(1)|biliary_tract(1)|kidney(1)|breast(1)|skin(1)|pancreas(1)	c.T770C	GRCh37	CD941800|CM941332	TP53	D|M	rs28934577	.						139	99	113					17																	7577511		2203	4300	6503	SO:0001583	missense	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	TCTTCCAGTGTGA	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.770T>C	chr17.hg19:g.7577511A>G	ENSP00000269305:p.Leu257Pro	80.0	0.0		64.0	17.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	A	15.36	2.810004	0.50421	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D;D	0.99905	-7.7;-7.7;-7.7;-7.7;-7.7;-7.7;-7.7	4.62	3.53	0.40419	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.64402	D	0.000001	D	0.99904	0.9954	M	0.92507	3.315	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;1.0;1.0;1.0;1.0	D	0.96890	0.9652	10	0.87932	D	0	-7.3975	9.0966	0.36642	0.8362:0.0:0.0:0.1638	.	257;257;257;257;257	P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;P53_HUMAN;.;.	P	257;257;257;257;257;257;246;125	ENSP00000410739:L257P;ENSP00000352610:L257P;ENSP00000269305:L257P;ENSP00000398846:L257P;ENSP00000391127:L257P;ENSP00000391478:L257P;ENSP00000425104:L125P	ENSP00000269305:L257P	L	-	2	0	TP53	7518236	1.000000	0.71417	0.981000	0.43875	0.405000	0.30901	9.087000	0.94110	0.889000	0.36185	0.379000	0.24179	CTG	.	.		0.582	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		G	7577511	A	G	7577511	3	3	246	1	0	0	0	0	1	0	0	0	16396	188	7	2	520	2	TP53	17	7577511	Missense_Mutation	SNP	A	TCGA-ED-A7XO-01A-11D-A34Z-10		7577511	73617699	47	33786										
EMR3	84658	hgsc.bcm.edu	37	chr19	14748990	14748990	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	cacagcgggaacgccatagcCgactgggaacatgatccact	11	13	0	1	rs553930762		TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr19:14748990C>T	ENST00000253673.5	-	11	1511	c.1411G>A	c.(1411-1413)Ggc>Agc	p.G471S	EMR3_ENST00000344373.4_Missense_Mutation_p.G419S|EMR3_ENST00000443157.2_Missense_Mutation_p.G345S|EMR3_ENST00000599900.1_Missense_Mutation_p.G256S	NM_032571.3	NP_115960.2	Q9BY15	EMR3_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 3	471					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(14)|ovary(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	50						ACGCCATAGCCGACTGGGAAC	0.537													C|||	1	0.000199681	8e-04	0	5008	,	,		21358	0		0	False		,,,				2504	0				p.G471S		Atlas-SNP	.											.	EMR3	99	.	0			c.G1411A						.						184	143	157					19																	14748990		2203	4300	6503	SO:0001583	missense	84658	exon11			CATAGCCGACTGG	AF239764	CCDS12315.1, CCDS74296.1, CCDS74297.1	19p13.1	2014-08-08				ENSG00000131355		"-", "GPCR / Class B : Orphans"	23647	protein-coding gene	gene with protein product		606101				11279179, 12975309	Standard	XM_005260118		Approved		uc002mzi.4	Q9BY15		ENST00000253673.5:c.1411G>A	chr19.hg19:g.14748990C>T	ENSP00000253673:p.Gly471Ser	52.0	0.0		88.0	18.0	NM_032571		Missense_Mutation	SNP	ENST00000253673.5	hg19	CCDS12315.1	.	.	.	.	.	.	.	.	.	.	C	17.17	3.320316	0.60634	.	.	ENSG00000131355	ENST00000443157;ENST00000253673;ENST00000344373	D;D;D	0.84516	-1.86;-1.86;-1.86	4.34	4.34	0.51931	GPCR, family 2-like (1);	.	.	.	.	D	0.92993	0.7770	M	0.89287	3.02	0.38781	D	0.95476	D;D;D	0.89917	0.998;1.0;1.0	D;D;D	0.83275	0.954;0.975;0.996	D	0.94908	0.8062	9	0.72032	D	0.01	.	14.4024	0.67056	0.0:1.0:0.0:0.0	.	345;419;471	E7EW83;Q9BY15-2;Q9BY15	.;.;EMR3_HUMAN	S	345;471;419	ENSP00000396208:G345S;ENSP00000253673:G471S;ENSP00000340758:G419S	ENSP00000253673:G471S	G	-	1	0	EMR3	14609990	1.000000	0.71417	0.959000	0.39883	0.064000	0.16182	6.088000	0.71371	2.245000	0.73994	0.650000	0.86243	GGC	.	.		0.537	EMR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466488.1	NM_032571		T	14748990	C	T	14748990	3	4	246	1	0	0	0	0	1	0	0	0	5108	652	23	1	571	1	EMR3	19	14748990	Missense_Mutation	SNP	C	TCGA-ED-A7XO-01A-11D-A34Z-10		14748990	44379993	48	33787										
ENTPD6	955	hgsc.bcm.edu	37	chr20	25203506	25203506	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	acgagctgtgtgctgccagaGtgtcagaggtccttcaaaac	12	10	2	2			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr20:25203506G>T	ENST00000376652.4	+	12	1241	c.1078G>T	c.(1078-1080)Gtg>Ttg	p.V360L	ENTPD6_ENST00000433259.2_Missense_Mutation_p.V326L|ENTPD6_ENST00000354989.5_Missense_Mutation_p.V343L|ENTPD6_ENST00000485936.1_3'UTR|ENTPD6_ENST00000360031.2_Missense_Mutation_p.V359L			O75354	ENTP6_HUMAN	ectonucleoside triphosphate diphosphohydrolase 6 (putative)	360					response to calcium ion (GO:0051592)|response to magnesium ion (GO:0032026)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	guanosine-5'-triphosphate,3'-diphosphate diphosphatase activity (GO:0008894)|nucleoside-triphosphatase activity (GO:0017111)|uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|prostate(1)|skin(1)	27						TGCTGCCAGAGTGTCAGAGGT	0.587																																					p.V360L		Atlas-SNP	.											.	ENTPD6	57	.	0			c.G1078T						.						159	131	141					20																	25203506		2203	4300	6503	SO:0001583	missense	955	exon12			GCCAGAGTGTCAG	AF039916	CCDS13170.1, CCDS46586.1	20p11.21	2010-06-24	2010-06-24		ENSG00000197586	ENSG00000197586			3368	protein-coding gene	gene with protein product		603160	"interleukin 6 signal transducer-2"	CD39L2, IL6ST2		9676430	Standard	NM_001247		Approved	NTPDase-6, dJ738P15.3	uc002wuj.2	O75354	OTTHUMG00000032116	ENST00000376652.4:c.1078G>T	chr20.hg19:g.25203506G>T	ENSP00000365840:p.Val360Leu	39.0	0.0		55.0	12.0	NM_001247	A6NCX6|D3DW49|Q5QPJ2|Q5QPJ5|Q7Z5B5|Q8N3H3|Q8TAS7|Q9UJD1	Missense_Mutation	SNP	ENST00000376652.4	hg19	CCDS13170.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	12.41|12.41|12.41	1.929468|1.929468|1.929468	0.34096|0.34096|0.34096	.|.|.	.|.|.	ENSG00000197586|ENSG00000197586|ENSG00000197586	ENST00000433417;ENST00000447877|ENST00000376666|ENST00000354989;ENST00000360031;ENST00000525986;ENST00000376641;ENST00000376652;ENST00000433259	.|.|T;T;T;T	.|.|0.19806	.|.|2.68;2.68;2.68;2.12	5.67|5.67|5.67	3.73|3.73|3.73	0.42828|0.42828|0.42828	.|.|.	.|.|0.059782	.|.|0.64402	.|.|D	.|.|0.000002	T|T|T	0.33789|0.33789|0.33789	0.0875|0.0875|0.0875	M|M|M	0.84433|0.84433|0.84433	2.695|2.695|2.695	0.52501|0.52501|0.52501	D|D|D	0.99995|0.99995|0.99995	.|.|B;P;P;P;B;B;P;P	.|.|0.45474	.|.|0.093;0.859;0.553;0.488;0.337;0.29;0.46;0.46	.|.|B;P;B;B;B;B;B;B	.|.|0.46275	.|.|0.036;0.51;0.302;0.277;0.249;0.305;0.147;0.147	T|T|T	0.15206|0.15206|0.15206	-1.0445|-1.0445|-1.0445	5|5|10	.|.|0.36615	.|.|T	.|.|0.2	-17.3432|-17.3432|-17.3432	11.2278|11.2278|11.2278	0.48895|0.48895|0.48895	0.1499:0.0:0.8501:0.0|0.1499:0.0:0.8501:0.0|0.1499:0.0:0.8501:0.0	.|.|.	.|.|108;342;360;326;343;359;359;360	.|.|B4DHS2;B4DDM7;B4DNK6;Q5QPI9;O75354-2;D3DW49;Q5QPJ2;O75354	.|.|.;.;.;.;.;.;.;ENTP6_HUMAN	D|I|L	280;218|183|343;359;280;256;360;326	.|.|ENSP00000347084:V343L;ENSP00000353131:V359L;ENSP00000365840:V360L;ENSP00000401895:V326L	.|.|ENSP00000347084:V343L	E|S|V	+|+|+	3|2|1	2|0|0	ENTPD6|ENTPD6|ENTPD6	25151506|25151506|25151506	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.711000|0.711000|0.711000	0.30485|0.30485|0.30485	0.031000|0.031000|0.031000	0.12232|0.12232|0.12232	6.486000|6.486000|6.486000	0.73629|0.73629|0.73629	0.762000|0.762000|0.762000	0.33152|0.33152|0.33152	0.462000|0.462000|0.462000	0.41574|0.41574|0.41574	GAG|AGT|GTG	.	.		0.587	ENTPD6-020	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078414.2			T	25203506	G	T	25203506	3	4	246	1	0	0	0	0	1	0	0	0	5145	1029	36	3	1127	3	ENTPD6	20	25203506	Missense_Mutation	SNP	G	TCGA-ED-A7XO-01A-11D-A34Z-10		25203506	37822014	49	33788										
CTNNBL1	56259	hgsc.bcm.edu	37	chr20	36470822	36470822	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	agattgaaggggaaaaacacGtatgtatccctgcctcactt	9	9	1	2			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr20:36470822G>A	ENST00000361383.6	+	13	1509		c.e13+1		CTNNBL1_ENST00000473857.1_Splice_Site|CTNNBL1_ENST00000405275.2_Splice_Site|CTNNBL1_ENST00000373469.1_Splice_Site|CTNNBL1_ENST00000373473.1_Splice_Site	NM_030877.3	NP_110517.2	Q8WYA6	CTBL1_HUMAN	catenin, beta like 1						apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|positive regulation of apoptotic process (GO:0043065)|RNA splicing (GO:0008380)|somatic diversification of immunoglobulins (GO:0016445)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|Prp19 complex (GO:0000974)|spliceosomal complex (GO:0005681)	enzyme binding (GO:0019899)			autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(6)|lung(6)|ovary(3)|urinary_tract(1)	28		Myeloproliferative disorder(115;0.00878)				GGAAAAACACGTATGTATCCC	0.483																																					.	Ovarian(184;582 2038 3273 4106 42608)	Atlas-SNP	.											.	CTNNBL1	78	.	0			c.1392+1G>A						.						189	139	156					20																	36470822		2203	4300	6503	SO:0001630	splice_region_variant	56259	exon13			AAACACGTATGTA	AL023804	CCDS13298.1	20q11.23-q12	2011-06-03	2002-05-27	2002-05-31	ENSG00000132792	ENSG00000132792			15879	protein-coding gene	gene with protein product	"nuclear associated protein"	611537	"chromosome 20 open reading frame 33"	C20orf33		12659813, 21385873	Standard	NM_030877		Approved	FLJ21108, P14L, P14, NAP, NYD-SP19	uc021wdj.1	Q8WYA6	OTTHUMG00000032428	ENST00000361383.6:c.1392+1G>A	chr20.hg19:g.36470822G>A		78.0	0.0		89.0	17.0	NM_030877	B4DE16|Q0VAL9|Q0VAM0|Q53HI8|Q5JWZ2|Q5JWZ3|Q5JWZ7|Q5JWZ8|Q8N454|Q8NCL2|Q8TBD6|Q96KD2|Q9H7A5|Q9NQF9|Q9NTX0|Q9Y3M7	Splice_Site	SNP	ENST00000361383.6	hg19	CCDS13298.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.126312	0.77549	.	.	ENSG00000132792	ENST00000361383;ENST00000405275;ENST00000373473;ENST00000373469	.	.	.	5.25	5.25	0.73442	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.8358	0.88696	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CTNNBL1	35904236	1.000000	0.71417	0.984000	0.44739	0.956000	0.61745	9.090000	0.94144	2.462000	0.83206	0.650000	0.86243	.	.	.		0.483	CTNNBL1-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079125.1	NM_030877	Intron	A	36470822	G	A	36470822	5	1	246	1	0	0	0	0	0	0	1	0	4020	1159	40	1	1443	1	CTNNBL1	20	36470822	Splice_Site	SNP	G	TCGA-ED-A7XO-01A-11D-A34Z-10	11267316	36470822	26554698	50	33789										
EWSR1	2130	hgsc.bcm.edu	37	chr22	29695604	29695604	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	cttaggtggtgatcgtggcaGaggtggccctggtggcatgc	18	8	0	2			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chr22:29695604G>T	ENST00000397938.2	+	16	2013	c.1694G>T	c.(1693-1695)aGa>aTa	p.R565I	EWSR1_ENST00000332035.6_Missense_Mutation_p.R509I|EWSR1_ENST00000331029.7_Missense_Mutation_p.R527I|EWSR1_ENST00000332050.6_Missense_Mutation_p.R492I|EWSR1_ENST00000406548.1_Missense_Mutation_p.R564I|EWSR1_ENST00000414183.2_Missense_Mutation_p.R570I	NM_001163285.1|NM_001163286.1|NM_005243.3|NM_013986.3	NP_001156757.1|NP_001156758.1|NP_005234.1|NP_053733.2	Q01844	EWS_HUMAN	EWS RNA-binding protein 1	565	Arg/Gly/Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		EWSR1/ATF1(347)|EWSR1/POU5F1(10)|EWSR1/PBX1(3)|EWSR1/DDIT3(45)|EWSR1/FEV(11)|EWSR1/CREB1(44)|EWSR1/SMARCA5(2)|EWSR1/ETV4(6)|EWSR1/ERG(178)|EWSR1/ZNF384(4)|EWSR1/ETV1(7)|EWSR1/FLI1(2569)|EWSR1/NR4A3(146)|EWSR1/SP3(3)|EWSR1/PATZ1(2)|EWSR1/WT1(234)|EWSR1/NFATC2(9)	breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|liver(1)|lung(6)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						GATCGTGGCAGAGGTGGCCCT	0.617			T	"FLI1, ERG, ZNF278, NR4A3, FEV, ATF1, ETV1, ETV4, WT1, ZNF384, CREB1, POU5F1,  PBX1"	"Ewing sarcoma,  desmoplastic small round cell tumor , ALL, clear cell sarcoma, sarcoma, myoepithelioma"																																p.R570I		Atlas-SNP	.		Dom	yes		22	22q12	2130	Ewing sarcoma breakpoint region 1 (EWS)		"L, M"	.	EWSR1	104	.	0			c.G1709T						.						89	73	78					22																	29695604		2203	4300	6503	SO:0001583	missense	2130	exon17			GTGGCAGAGGTGG		CCDS13851.1, CCDS13852.1, CCDS13852.2, CCDS54512.1, CCDS54513.1, CCDS54514.1	22q12.2	2013-05-24	2013-05-24		ENSG00000182944	ENSG00000182944		"RNA binding motif (RRM) containing"	3508	protein-coding gene	gene with protein product		133450	"Ewing sarcoma breakpoint region 1"			1522903	Standard	NM_005243		Approved	EWS	uc003aev.3	Q01844	OTTHUMG00000151107	ENST00000397938.2:c.1694G>T	chr22.hg19:g.29695604G>T	ENSP00000381031:p.Arg565Ile	107.0	0.0		116.0	21.0	NM_013986	B0QYK1|Q5THL0|Q92635|Q96FE8|Q96MN4|Q96MX4|Q9BWA2	Missense_Mutation	SNP	ENST00000397938.2	hg19	CCDS13851.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.91|15.91	2.971664|2.971664	0.53614|0.53614	.|.	.|.	ENSG00000182944|ENSG00000182944	ENST00000360091|ENST00000332050;ENST00000397938;ENST00000406548;ENST00000331029;ENST00000414183;ENST00000332035	.|D;D;D;D;D;D	.|0.97161	.|-4.19;-3.65;-3.78;-4.27;-3.79;-3.67	5.19|5.19	5.19|5.19	0.71726|0.71726	.|.	.|0.000000	.|0.85682	.|U	.|0.000000	D|D	0.94879|0.94879	0.8345|0.8345	L|L	0.50333|0.50333	1.59|1.59	0.58432|0.58432	D|D	0.999998|0.999998	.|B;B;B;B;B	.|0.30068	.|0.267;0.267;0.267;0.267;0.267	.|B;B;B;B;B	.|0.24541	.|0.054;0.054;0.054;0.037;0.037	D|D	0.94055|0.94055	0.7321|0.7321	5|10	.|0.66056	.|D	.|0.02	.|.	15.1429|15.1429	0.72623|0.72623	0.0:0.0:0.8583:0.1417|0.0:0.0:0.8583:0.1417	.|.	.|509;564;509;570;565	.|Q96MN4;Q96FE8;B0QYK1;Q96MX4;Q01844	.|.;.;.;.;EWS_HUMAN	H|I	216|492;565;564;527;570;509	.|ENSP00000330896:R492I;ENSP00000381031:R565I;ENSP00000385726:R564I;ENSP00000330516:R527I;ENSP00000400142:R570I;ENSP00000331699:R509I	.|ENSP00000330516:R527I	Q|R	+|+	3|2	2|0	EWSR1|EWSR1	28025604|28025604	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.890000|0.890000	0.51754|0.51754	4.766000|4.766000	0.62279|0.62279	2.423000|2.423000	0.82170|0.82170	0.313000|0.313000	0.20887|0.20887	CAG|AGA	.	.		0.617	EWSR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321345.1	NM_005243		T	29695604	G	T	29695604	3	4	246	1	0	0	0	0	1	0	0	0	5298	942	33	3	1873	3	EWSR1	22	29695604	Missense_Mutation	SNP	G	TCGA-ED-A7XO-01A-11D-A34Z-10		29695604	21608962	51	33790										
RAI2	10742	hgsc.bcm.edu	37	chrX	17819379	17819379	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	attcagaactctgaggcatcGggatggggatgggaataggg	17	5	2	2			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chrX:17819379G>A	ENST00000545871.1	-	3	1212	c.752C>T	c.(751-753)cCg>cTg	p.P251L	RAI2_ENST00000451717.1_Missense_Mutation_p.P251L|RAI2_ENST00000415486.3_Missense_Mutation_p.P201L|RAI2_ENST00000360011.1_Missense_Mutation_p.P251L|RAI2_ENST00000331511.1_Missense_Mutation_p.P251L	NM_001172739.1|NM_001172743.1	NP_001166210|NP_001166214	Q9Y5P3	RAI2_HUMAN	retinoic acid induced 2	251	Pro-rich.				embryo development (GO:0009790)					breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|prostate(1)	22	Hepatocellular(33;0.183)					CTGAGGCATCGGGATGGGGAT	0.592																																					p.P251L		Atlas-SNP	.											.	RAI2	66	.	0			c.C752T						.						85	83	84					X																	17819379		2203	4300	6503	SO:0001583	missense	10742	exon3			GGCATCGGGATGG	Z93242	CCDS14183.1, CCDS55374.1	Xp22	2008-02-05			ENSG00000131831	ENSG00000131831			9835	protein-coding gene	gene with protein product		300217				10049581, 10394933	Standard	NR_033348		Approved		uc010nfa.3	Q9Y5P3	OTTHUMG00000021209	ENST00000545871.1:c.752C>T	chrX.hg19:g.17819379G>A	ENSP00000444210:p.Pro251Leu	53.0	0.0		63.0	19.0	NM_001172739	B1B1K2|B4DQM9|E7EMN4|Q8N6X7	Missense_Mutation	SNP	ENST00000545871.1	hg19	CCDS14183.1	.	.	.	.	.	.	.	.	.	.	g	13.05	2.122722	0.37436	.	.	ENSG00000131831	ENST00000331511;ENST00000360011;ENST00000545871;ENST00000451717;ENST00000415486	T;T;T;T;T	0.69040	-0.37;-0.37;-0.37;-0.37;0.06	5.29	4.43	0.53597	.	0.000000	0.85682	D	0.000000	T	0.74733	0.3755	L	0.61218	1.895	0.58432	D	0.999998	D;D	0.69078	0.997;0.997	P;P	0.57324	0.726;0.818	T	0.77480	-0.2572	10	0.72032	D	0.01	-9.9766	12.9581	0.58442	0.0806:0.0:0.9194:0.0	.	201;251	E7EMN4;Q9Y5P3	.;RAI2_HUMAN	L	251;251;251;251;201	ENSP00000333456:P251L;ENSP00000353106:P251L;ENSP00000444210:P251L;ENSP00000401323:P251L;ENSP00000392578:P201L	ENSP00000333456:P251L	P	-	2	0	RAI2	17729300	1.000000	0.71417	0.822000	0.32727	0.918000	0.54935	8.691000	0.91279	1.218000	0.43458	0.597000	0.82753	CCG	.	.		0.592	RAI2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055937.1	NM_021785		A	17819379	G	A	17819379	3	1	246	1	0	0	0	0	1	0	0	0	13024	1116	39	1	844	1	RAI2	23	17819379	Missense_Mutation	SNP	G	TCGA-ED-A7XO-01A-11D-A34Z-10		17819379	137451181	52	33791										
PTCHD1	139411	hgsc.bcm.edu	37	chrX	23398175	23398175	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	gtatcagaacgttacctggtCaccagcctgattctggtggt	11	10	3	2			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chrX:23398175C>A	ENST00000379361.4	+	2	1679	c.819C>A	c.(817-819)gtC>gtA	p.V273V		NM_173495.2	NP_775766.2	Q96NR3	PTHD1_HUMAN	patched domain containing 1	273	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				cognition (GO:0050890)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(4)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(4)|skin(2)|urinary_tract(2)	42						GTTACCTGGTCACCAGCCTGA	0.527																																					p.V273V		Atlas-SNP	.											.	PTCHD1	213	.	0			c.C819A						.						161	137	145					X																	23398175		2203	4300	6503	SO:0001819	synonymous_variant	139411	exon2			CCTGGTCACCAGC	AK054858	CCDS35215.2	Xp22.13	2008-02-05			ENSG00000165186	ENSG00000165186			26392	protein-coding gene	gene with protein product		300828					Standard	NM_173495		Approved	FLJ30296	uc004dal.4	Q96NR3	OTTHUMG00000021251	ENST00000379361.4:c.819C>A	chrX.hg19:g.23398175C>A		48.0	0.0		59.0	21.0	NM_173495	B4DQH0|Q0IJ60|Q6P6B8	Silent	SNP	ENST00000379361.4	hg19	CCDS35215.2																																																																																			.	.		0.527	PTCHD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056047.2	NM_173495		A	23398175	C	A	23398175	2	1	246	1	0	0	0	0	0	0	0	1	12744	813	29	3		3	PTCHD1	23	23398175	Silent	SNP	C	TCGA-ED-A7XO-01A-11D-A34Z-10	5578796	23398175	131872385	53	33792										
GPR112	139378	hgsc.bcm.edu	37	chrX	135441570	135441570	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0185185185185185	1	1	0.386111111111111	1.54444444444444	0	1	1	0	aaacttcacacaagatcaatTgacgttattagtaaactgtg	6	7	2	2			TCGA-ED-A7XO-01A-11D-A34Z-10	TCGA-ED-A7XO-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a3d6c15a-8dd7-4b2c-b41a-33c2d4412d80	a83a44f3-45ec-4725-bef7-e1656fef6932	g.chrX:135441570T>C	ENST00000394143.1	+	11	7391	c.7100T>C	c.(7099-7101)tTg>tCg	p.L2367S	GPR112_ENST00000412101.1_Missense_Mutation_p.L2162S|GPR112_ENST00000287534.4_Intron|GPR112_ENST00000394141.1_Missense_Mutation_p.L2162S|GPR112_ENST00000370652.1_Missense_Mutation_p.L2367S	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	2367					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					CAAGATCAATTGACGTTATTA	0.338																																					p.L2367S		Atlas-SNP	.											.	GPR112	459	.	0			c.T7100C						.						134	114	121					X																	135441570		2203	4300	6503	SO:0001583	missense	139378	exon11			ATCAATTGACGTT	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"-", "GPCR / Class B : Orphans"	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.7100T>C	chrX.hg19:g.135441570T>C	ENSP00000377699:p.Leu2367Ser	111.0	0.0		167.0	63.0	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	hg19	CCDS35409.1	.	.	.	.	.	.	.	.	.	.	T	10.29	1.308371	0.23821	.	.	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000394141	T;T;T;T	0.44482	0.96;0.96;0.92;0.92	6.08	3.38	0.38709	.	.	.	.	.	T	0.39226	0.1070	N	0.08118	0	0.09310	N	1	D;D	0.71674	0.998;0.997	D;D	0.68943	0.961;0.957	T	0.13899	-1.0492	9	0.66056	D	0.02	.	6.8344	0.23927	0.0:0.2132:0.0:0.7867	.	2162;2367	Q8IZF6-3;Q8IZF6	.;GP112_HUMAN	S	2367;2367;2162;2162	ENSP00000377699:L2367S;ENSP00000359686:L2367S;ENSP00000416526:L2162S;ENSP00000377697:L2162S	ENSP00000359686:L2367S	L	+	2	0	GPR112	135269236	0.139000	0.22563	0.006000	0.13384	0.015000	0.08874	1.294000	0.33365	0.889000	0.36185	0.486000	0.48141	TTG	.	.		0.338	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1			C	135441570	T	C	135441570	3	2	246	1	0	0	0	0	1	0	0	0	6637	1821	63	2	7130	2	GPR112	23	135441570	Missense_Mutation	SNP	T	TCGA-ED-A7XO-01A-11D-A34Z-10	112043395	135441570	19828990	54	33793										
NDUFS5	4725	hgsc.bcm.edu	37	chr1	39494585	39494585	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	aagatagaatatgatgatttCgtagagtgtttgcttcggca	11	4	0	5	rs372457176		TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr1:39494585C>T	ENST00000372969.3	+	2	276	c.189C>T	c.(187-189)ttC>ttT	p.F63F	NDUFS5_ENST00000372967.3_Silent_p.F63F	NM_004552.2	NP_004543.1	O43920	NDUS5_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 5, 15kDa (NADH-coenzyme Q reductase)	63					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|mitochondrial respiratory chain complex I assembly (GO:0032981)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			endometrium(1)|kidney(1)|large_intestine(2)|upper_aerodigestive_tract(1)	5	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;1.93e-18)			ATGATGATTTCGTAGAGTGTT	0.393																																					p.F63F		Atlas-SNP	.											NDUFS5,colon,carcinoma,0,2	NDUFS5	13	.	0			c.C189T						.	C	,	1,4405	2.1+/-5.4	0,1,2202	114	108	110		189,189	-11.4	0	1		110	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	NDUFS5	NM_001184979.1,NM_004552.2	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	63/107,63/107	39494585	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	4725	exon2			TGATTTCGTAGAG	AF047434	CCDS434.1	1p34.2-p33	2011-07-04	2002-08-29		ENSG00000168653	ENSG00000168653		"Mitochondrial respiratory chain complex / Complex I"	7712	protein-coding gene	gene with protein product	"complex I 51kDa subunit", "NADH dehydrogenase [ubiquinone] iron-sulfur protein 5"	603847	"NADH dehydrogenase (ubiquinone) Fe-S protein 5 (15kD) (NADH-coenzyme Q reductase)"			9763677, 9653160	Standard	NM_004552		Approved	CI-15k	uc001ccy.3	O43920	OTTHUMG00000007497	ENST00000372969.3:c.189C>T	chr1.hg19:g.39494585C>T		89.0	0.0		86.0	31.0	NM_001184979		Silent	SNP	ENST00000372969.3	hg19	CCDS434.1																																																																																			.	.		0.393	NDUFS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019688.1	NM_004552		T	39494585	C	T	39494585	2	4	247	1	0	0	0	0	0	0	0	1	10304	883	31	1		1	NDUFS5	1	39494585	Silent	SNP	C	TCGA-ED-A7XP-01A-11D-A34Z-10		39494585	209756036	1	33794										
JAK1	3716	hgsc.bcm.edu	37	chr1	65306964	65306964	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	atcctctttaggaagcgcttTtcaaaatgtgtggggtccac	10	9	2	0			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr1:65306964T>G	ENST00000342505.4	-	19	2861	c.2613A>C	c.(2611-2613)gaA>gaC	p.E871D	JAK1_ENST00000465376.1_5'Flank	NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	871					cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	GGAAGCGCTTTTCAAAATGTG	0.478			Mis		ALL																																p.E871D		Atlas-SNP	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	.	JAK1	209	.	0			c.A2613C						.						101	101	101					1																	65306964		1915	4126	6041	SO:0001583	missense	3716	exon19			GCGCTTTTCAAAA	M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.2613A>C	chr1.hg19:g.65306964T>G	ENSP00000343204:p.Glu871Asp	145.0	0.0		129.0	45.0	NM_002227	Q59GQ2|Q9UD26	Missense_Mutation	SNP	ENST00000342505.4	hg19	CCDS41346.1	.	.	.	.	.	.	.	.	.	.	T	13.49	2.251769	0.39797	.	.	ENSG00000162434	ENST00000342505	T	0.77489	-1.1	4.74	1.13	0.20643	Protein kinase-like domain (1);	.	.	.	.	T	0.71204	0.3312	M	0.72894	2.215	0.42632	D	0.993388	D	0.55172	0.97	P	0.51229	0.663	T	0.69468	-0.5137	9	0.40728	T	0.16	-7.1745	10.8454	0.46741	0.0:0.349:0.0:0.651	.	871	P23458	JAK1_HUMAN	D	871	ENSP00000343204:E871D	ENSP00000343204:E871D	E	-	3	2	JAK1	65079552	0.997000	0.39634	0.997000	0.53966	0.752000	0.42762	0.314000	0.19432	-0.136000	0.11475	-1.481000	0.00988	GAA	.	.		0.478	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227		G	65306964	T	G	65306964	3	3	247	1	0	0	0	0	1	0	0	0	7946	1838	64	5	879	5	JAK1	1	65306964	Missense_Mutation	SNP	T	TCGA-ED-A7XP-01A-11D-A34Z-10	25812379	65306964	183943657	2	33795										
ST7L	54879	hgsc.bcm.edu	37	chr1	113098573	113098573	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	gaaagaaagcataggcaattGcttcactatcaccccgtttc	7	11	2	1			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr1:113098573G>A	ENST00000358039.4	-	12	1617	c.1313C>T	c.(1312-1314)gCa>gTa	p.A438V	ST7L_ENST00000369668.2_Missense_Mutation_p.A438V|ST7L_ENST00000369666.1_Missense_Mutation_p.A421V|ST7L_ENST00000538187.1_Missense_Mutation_p.A382V|ST7L_ENST00000490067.1_Missense_Mutation_p.A421V|ST7L_ENST00000463235.1_5'UTR|ST7L_ENST00000360743.4_Missense_Mutation_p.A438V|ST7L_ENST00000369669.1_Missense_Mutation_p.A255V|ST7L_ENST00000343210.7_Missense_Mutation_p.A438V|ST7L_ENST00000544629.1_Missense_Mutation_p.A373V|ST7L_ENST00000543570.1_Intron	NM_017744.4|NM_138727.3	NP_060214.2|NP_620055.1	Q8TDW4	ST7L_HUMAN	suppression of tumorigenicity 7 like	438					negative regulation of cell growth (GO:0030308)	integral component of membrane (GO:0016021)				endometrium(1)|kidney(4)|large_intestine(3)|lung(1)|prostate(2)|stomach(1)|urinary_tract(3)	15	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		ATAGGCAATTGCTTCACTATC	0.373																																					p.A438V		Atlas-SNP	.											.	ST7L	31	.	0			c.C1313T						.						126	116	119					1																	113098573		2203	4300	6503	SO:0001583	missense	54879	exon12			GCAATTGCTTCAC	AB081317	CCDS848.1, CCDS849.1, CCDS850.1, CCDS852.1	1p13.1	2008-06-06			ENSG00000007341	ENSG00000007341			18441	protein-coding gene	gene with protein product						12012006	Standard	NM_138729		Approved	FLJ20284, STLR, ST7R, FAM4B	uc001ecd.3	Q8TDW4	OTTHUMG00000011753	ENST00000358039.4:c.1313C>T	chr1.hg19:g.113098573G>A	ENSP00000350734:p.Ala438Val	55.0	0.0		63.0	20.0	NM_138729	A8K4S7|Q49AH6|Q5TEI4|Q5U5K6|Q6N067|Q7Z2Z0|Q7Z3C2|Q8N7P8|Q8TDW1|Q8TDW2|Q8TDW3|Q9NXF3	Missense_Mutation	SNP	ENST00000358039.4	hg19	CCDS848.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	34|34	5.390251|5.390251	0.95988|0.95988	.|.	.|.	ENSG00000007341|ENSG00000007341	ENST00000358039;ENST00000360743;ENST00000369673;ENST00000544629;ENST00000369669;ENST00000490067;ENST00000369668;ENST00000343210;ENST00000369666;ENST00000538187|ENST00000418497	T;T;T;T;T;T;T;T;T|.	0.27104|.	1.69;1.69;1.69;1.69;1.69;1.69;1.69;1.69;1.69|.	5.59|5.59	5.59|5.59	0.84812|0.84812	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.79499|.	0.4456|.	M|M	0.83953|0.83953	2.67|2.67	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D;D;D;D|.	0.97110|.	0.998;0.998;0.999;1.0;1.0;1.0;1.0;1.0|.	T|.	0.80018|.	-0.1558|.	10|.	0.87932|.	D|.	0|.	-14.6353|-14.6353	19.1881|19.1881	0.93653|0.93653	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	382;373;373;438;421;421;438;438|.	B7Z7D4;B7Z3J2;F5H2P3;Q8TDW4-5;Q8TDW4-6;Q8TDW4-3;Q8TDW4-2;Q8TDW4|.	.;.;.;.;.;.;.;ST7L_HUMAN|.	V|X	438;438;219;373;255;421;438;438;421;382|213	ENSP00000350734:A438V;ENSP00000353972:A438V;ENSP00000445499:A373V;ENSP00000358683:A255V;ENSP00000417140:A421V;ENSP00000358682:A438V;ENSP00000345312:A438V;ENSP00000358680:A421V;ENSP00000444021:A382V|.	ENSP00000345312:A438V|.	A|Q	-|-	2|1	0|0	ST7L|ST7L	112900096|112900096	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.983000|0.983000	0.72400|0.72400	9.864000|9.864000	0.99589|0.99589	2.625000|2.625000	0.88918|0.88918	0.585000|0.585000	0.79938|0.79938	GCA|CAA	.	.		0.373	ST7L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032504.3			A	113098573	G	A	113098573	3	1	247	1	0	0	0	0	1	0	0	0	15245	1319	46	3	469	3	ST7L	1	113098573	Missense_Mutation	SNP	G	TCGA-ED-A7XP-01A-11D-A34Z-10	47791609	113098573	136152048	3	33796										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181701775	181701775	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	ttcgaggaggagcgcatcagCcgtggggggtccctcaaggg	18	10	2	0			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr1:181701775C>A	ENST00000367573.2	+	20	2553	c.2553C>A	c.(2551-2553)agC>agA	p.S851R	CACNA1E_ENST00000357570.5_Missense_Mutation_p.S802R|CACNA1E_ENST00000526775.1_Missense_Mutation_p.S832R|CACNA1E_ENST00000360108.3_Missense_Mutation_p.S832R|CACNA1E_ENST00000358338.5_Missense_Mutation_p.S783R|CACNA1E_ENST00000367567.4_Missense_Mutation_p.S458R|CACNA1E_ENST00000367570.1_Missense_Mutation_p.S851R	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	851					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						AGCGCATCAGCCGTGGGGGGT	0.682																																					p.S851R		Atlas-SNP	.											.	CACNA1E	778	.	0			c.C2553A						.						12	15	14					1																	181701775		1884	4072	5956	SO:0001583	missense	777	exon20			CATCAGCCGTGGG	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.2553C>A	chr1.hg19:g.181701775C>A	ENSP00000356545:p.Ser851Arg	61.0	0.0		98.0	18.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	C	9.422	1.083395	0.20309	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.96104	-3.85;-3.85;-3.85;-3.85;-3.91;-3.85;-3.85	4.14	3.21	0.36854	.	2.396100	0.01164	N	0.006715	D	0.89033	0.6600	N	0.08118	0	0.36238	D	0.853065	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.77958	-0.2392	10	0.18710	T	0.47	.	6.7396	0.23428	0.0:0.6747:0.2256:0.0997	.	832;851;851	Q15878-2;Q15878;Q15878-3	.;CAC1E_HUMAN;.	R	851;832;802;783;458;832;851	ENSP00000356542:S851R;ENSP00000434814:S832R;ENSP00000350183:S802R;ENSP00000351101:S783R;ENSP00000356539:S458R;ENSP00000353222:S832R;ENSP00000356545:S851R	ENSP00000350183:S802R	S	+	3	2	CACNA1E	179968398	0.079000	0.21365	0.999000	0.59377	0.943000	0.58893	0.077000	0.14738	1.302000	0.44855	0.561000	0.74099	AGC	.	.		0.682	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		A	181701775	C	A	181701775	3	1	247	1	0	0	0	0	1	0	0	0	2544	738	26	3	2631	3	CACNA1E	1	181701775	Missense_Mutation	SNP	C	TCGA-ED-A7XP-01A-11D-A34Z-10	68603202	181701775	67548846	4	33797										
HMCN1	83872	hgsc.bcm.edu	37	chr1	185976272	185976272	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	ttttctaggcctttatttttGggcgatcctaatgttgaact	8	7	1	1			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr1:185976272G>A	ENST00000271588.4	+	30	4717	c.4488G>A	c.(4486-4488)ttG>ttA	p.L1496L	HMCN1_ENST00000367492.2_Silent_p.L1496L	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	1496	Ig-like C2-type 12.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						CTTTATTTTTGGGCGATCCTA	0.348																																					p.L1496L		Atlas-SNP	.											.	HMCN1	797	.	0			c.G4488A						.						72	78	76					1																	185976272		2203	4300	6503	SO:0001819	synonymous_variant	83872	exon30			ATTTTTGGGCGAT	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.4488G>A	chr1.hg19:g.185976272G>A		119.0	0.0		172.0	139.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	hg19	CCDS30956.1																																																																																			.	.		0.348	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		A	185976272	G	A	185976272	2	1	247	1	0	0	0	0	0	0	0	1	7229	1339	47	3		3	HMCN1	1	185976272	Silent	SNP	G	TCGA-ED-A7XP-01A-11D-A34Z-10	4274497	185976272	63274349	5	33798										
KCNH1	3756	hgsc.bcm.edu	37	chr1	210856666	210856666	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	tctctgattctggggactgtGgcctcgatatttcaaacaac	9	10	3	1			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr1:210856666G>T	ENST00000271751.4	-	11	2954	c.2927C>A	c.(2926-2928)cCa>cAa	p.P976Q	KCNH1_ENST00000367007.4_Missense_Mutation_p.P949Q			O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 1	976					myoblast fusion (GO:0007520)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|phosphorelay sensor kinase activity (GO:0000155)	p.P976Q(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|lung(35)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)		TGGGGACTGTGGCCTCGATAT	0.438																																					p.P976Q		Atlas-SNP	.											KCNH1,NS,carcinoma,0,1	KCNH1	199	.	1	Substitution - Missense(1)	lung(1)	c.C2927A						.						95	105	102					1																	210856666		2203	4300	6503	SO:0001583	missense	3756	exon11			GACTGTGGCCTCG	AJ001366	CCDS1496.1, CCDS31015.1	1q32.2	2012-07-05			ENSG00000143473	ENSG00000143473		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6250	protein-coding gene	gene with protein product		603305				9738473, 16382104	Standard	NM_172362		Approved	Kv10.1, eag, h-eag, eag1	uc001hib.2	O95259	OTTHUMG00000036309	ENST00000271751.4:c.2927C>A	chr1.hg19:g.210856666G>T	ENSP00000271751:p.Pro976Gln	85.0	0.0		130.0	15.0	NM_172362	B1AQ26|O76035|Q14CL3	Missense_Mutation	SNP	ENST00000271751.4	hg19	CCDS1496.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.663640	0.88251	.	.	ENSG00000143473	ENST00000271751;ENST00000367007	D;D	0.99388	-5.81;-5.79	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	D	0.99096	0.9689	L	0.55481	1.735	0.80722	D	1	D;D	0.65815	0.987;0.995	P;D	0.64042	0.878;0.921	D	0.99855	1.1076	10	0.54805	T	0.06	.	18.462	0.90741	0.0:0.0:1.0:0.0	.	949;976	Q14CL3;O95259	.;KCNH1_HUMAN	Q	976;949	ENSP00000271751:P976Q;ENSP00000355974:P949Q	ENSP00000271751:P976Q	P	-	2	0	KCNH1	208923289	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.507000	0.97996	2.360000	0.80028	0.655000	0.94253	CCA	.	.		0.438	KCNH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088332.1	NM_002238		T	210856666	G	T	210856666	3	4	247	1	0	0	0	0	1	0	0	0	8040	1348	47	3	46	3	KCNH1	1	210856666	Missense_Mutation	SNP	G	TCGA-ED-A7XP-01A-11D-A34Z-10	24880394	210856666	38393955	6	33799										
SLC30A1	7779	hgsc.bcm.edu	37	chr1	211749034	211749047	+	Frame_Shift_Del	DEL	AAAACGTCTTTAAT	AAAACGTCTTTAAT	-													0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	cgtgaattccgtgattatgaAaaacgtctttaatggtttta					rs41283138		TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	AAAACGTCTTTAAT	AAAACGTCTTTAAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr1:211749034_211749047delAAAACGTCTTTAAT	ENST00000367001.4	-	2	1336_1349	c.1207_1220delATTAAAGACGTTTT	c.(1207-1221)attaaagacgtttttfs	p.IKDVF403fs		NM_021194.2	NP_067017.2	Q9Y6M5	ZNT1_HUMAN	solute carrier family 30 (zinc transporter), member 1	403					cadmium ion transmembrane transport (GO:0070574)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|cellular zinc ion homeostasis (GO:0006882)|detoxification of cadmium ion (GO:0071585)|in utero embryonic development (GO:0001701)|negative regulation of calcium ion import (GO:0090281)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of zinc ion transmembrane import (GO:0071584)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)	calcium channel inhibitor activity (GO:0019855)|zinc ion transmembrane transporter activity (GO:0005385)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(1)|ovary(3)|prostate(1)	11				OV - Ovarian serous cystadenocarcinoma(81;0.00535)|GBM - Glioblastoma multiforme(131;0.051)|all cancers(67;0.0604)|Epithelial(68;0.0978)		GTGATTATGAAAAACGTCTTTAATGGTTTTAGCC	0.416																																					p.403_407del		Atlas-Indel,Pindel	.											.	SLC30A1	27	.	0			c.1208_1221del						.																																			SO:0001589	frameshift_variant	7779	exon2			.	AF323590	CCDS1499.1	1q32.3	2013-05-22			ENSG00000170385	ENSG00000170385		"Solute carriers"	11012	protein-coding gene	gene with protein product		609521		ZNT1			Standard	NM_021194		Approved	ZRC1	uc001hio.1	Q9Y6M5	OTTHUMG00000036995	ENST00000367001.4:c.1207_1220delATTAAAGACGTTTT	chr1.hg19:g.211749034_211749047delAAAACGTCTTTAAT	ENSP00000355968:p.Ile403fs	75.0	0.0		80.0	65.0	NM_021194	Q0VAK9|Q9BZF6	Frame_Shift_Del	DEL	ENST00000367001.4	hg19	CCDS1499.1																																																																																			.	.		0.416	SLC30A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104738.2			-	211749047	AAAACGTCTTTAAT	-	211749034	7	5	247	1	0	1	0	1	0	0	0	0	14568	14	1	0	307	0	SLC30A1	1	211749034	Frame_Shift_Del	DEL	AAAACGTCTTTAAT	TCGA-ED-A7XP-01A-11D-A34Z-10	892368	211749034	37501587	7	33800										
PARP1	142	hgsc.bcm.edu	37	chr1	226590006	226590006	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	tccacctcaacgtcagggtgCcggatggagtggcccacctt	12	14	2	0			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr1:226590006C>T	ENST00000366794.5	-	2	338	c.195G>A	c.(193-195)cgG>cgA	p.R65R	PARP1_ENST00000366792.1_Silent_p.R65R|PARP1_ENST00000366790.3_Silent_p.R65R|PARP1_ENST00000366791.5_Silent_p.R65R	NM_001618.3	NP_001609.2	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase 1	65					base-excision repair (GO:0006284)|cellular response to insulin stimulus (GO:0032869)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|gene expression (GO:0010467)|macrophage differentiation (GO:0030225)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|protein ADP-ribosylation (GO:0006471)|protein autoprocessing (GO:0016540)|protein poly-ADP-ribosylation (GO:0070212)|regulation of growth rate (GO:0040009)|signal transduction involved in regulation of gene expression (GO:0023019)|telomere maintenance (GO:0000723)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NAD binding (GO:0051287)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(4)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	44	Breast(184;0.133)			GBM - Glioblastoma multiforme(131;0.0531)		CGTCAGGGTGCCGGATGGAGT	0.542								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA																													p.R65R		Atlas-SNP	.											.	PARP1	100	.	0			c.G195A						.						87	77	81					1																	226590006		2203	4300	6503	SO:0001819	synonymous_variant	142	exon2			AGGGTGCCGGATG	BC037545	CCDS1554.1	1q41-q42	2010-02-16	2008-07-28	2004-08-26	ENSG00000143799	ENSG00000143799	2.4.2.30	"Poly (ADP-ribose) polymerases"	270	protein-coding gene	gene with protein product		173870	"ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)", "poly (ADP-ribose) polymerase family, member 1"	PPOL, ADPRT		10964595	Standard	NM_001618		Approved	PARP	uc001hqd.4	P09874	OTTHUMG00000037556	ENST00000366794.5:c.195G>A	chr1.hg19:g.226590006C>T		26.0	0.0		40.0	31.0	NM_001618	B1ANJ4|Q8IUZ9	Silent	SNP	ENST00000366794.5	hg19	CCDS1554.1																																																																																			.	.		0.542	PARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091519.1	NM_001618		T	226590006	C	T	226590006	2	4	247	1	0	0	0	0	0	0	0	1	11463	726	26	3		3	PARP1	1	226590006	Silent	SNP	C	TCGA-ED-A7XP-01A-11D-A34Z-10	14840972	226590006	22660615	8	33801										
APOB	338	hgsc.bcm.edu	37	chr2	21233705	21233705	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	gagttaggtcagccagagttCgtccagtaagctccacgcca	11	12	1	1			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr2:21233705C>T	ENST00000233242.1	-	26	6162	c.6035G>A	c.(6034-6036)cGa>cAa	p.R2012Q		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	2012					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGCCAGAGTTCGTCCAGTAAG	0.433																																					p.R2012Q		Atlas-SNP	.											APOB,NS,malignant_melanoma,0,1	APOB	761	.	0			c.G6035A						.						173	159	164					2																	21233705		2203	4300	6503	SO:0001583	missense	338	exon26			AGAGTTCGTCCAG	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.6035G>A	chr2.hg19:g.21233705C>T	ENSP00000233242:p.Arg2012Gln	217.0	0.0		194.0	57.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	C	0.863	-0.734763	0.03111	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.00705	5.81	5.46	2.69	0.31865	.	0.834050	0.10100	N	0.716077	T	0.00845	0.0028	L	0.38838	1.175	0.09310	N	0.999998	B	0.18166	0.026	B	0.10450	0.005	T	0.48151	-0.9060	10	0.18710	T	0.47	.	8.486	0.33071	0.0:0.6244:0.0:0.3756	.	2012	P04114	APOB_HUMAN	Q	2012	ENSP00000233242:R2012Q	ENSP00000233242:R2012Q	R	-	2	0	APOB	21087210	0.000000	0.05858	0.076000	0.20297	0.117000	0.20001	-0.405000	0.07196	0.275000	0.22094	-0.300000	0.09419	CGA	.	.		0.433	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			T	21233705	C	T	21233705	3	4	247	1	0	0	0	0	1	0	0	0	785	884	31	1	7672	1	APOB	2	21233705	Missense_Mutation	SNP	C	TCGA-ED-A7XP-01A-11D-A34Z-10		21233705	221965668	9	33802										
ST6GAL2	84620	hgsc.bcm.edu	37	chr2	107460245	107460245	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	ggggagggctcatgtgcggcGcccatgatggcccgctgctt	17	12	1	1			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr2:107460245G>T	ENST00000409382.3	-	2	799	c.189C>A	c.(187-189)ggC>ggA	p.G63G	ST6GAL2_ENST00000409087.3_Silent_p.G63G|AC016994.2_ENST00000425419.1_RNA|ST6GAL2_ENST00000361686.4_Silent_p.G63G	NM_001142351.1	NP_001135823.1	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 2	63					growth (GO:0040007)|multicellular organismal development (GO:0007275)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	beta-galactoside alpha-2,6-sialyltransferase activity (GO:0003835)	p.G63G(1)		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						CATGTGCGGCGCCCATGATGG	0.716																																					p.G63G		Atlas-SNP	.											ST6GAL2,NS,carcinoma,0,1	ST6GAL2	159	.	1	Substitution - coding silent(1)	endometrium(1)	c.C189A						.						14	17	16					2																	107460245		2181	4274	6455	SO:0001819	synonymous_variant	84620	exon2			TGCGGCGCCCATG	AB059555	CCDS2073.1, CCDS46380.1	2q11-q12	2008-02-05	2005-02-07	2005-02-07	ENSG00000144057	ENSG00000144057	2.4.99.2		10861	protein-coding gene	gene with protein product		608472	"sialyltransferase 2 (monosialoganglioside sialyltransferase)"	SIAT2			Standard	NM_032528		Approved	KIAA1877, St6gal2, St6GalII	uc002tdr.3	Q96JF0	OTTHUMG00000130923	ENST00000409382.3:c.189C>A	chr2.hg19:g.107460245G>T		32.0	0.0		40.0	16.0	NM_032528	D3DVK3|Q53QP4|Q86Y44|Q8IUG7|Q96HE4	Silent	SNP	ENST00000409382.3	hg19	CCDS2073.1																																																																																			.	.		0.716	ST6GAL2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330065.1	NM_032528		T	107460245	G	T	107460245	2	4	247	1	0	0	0	0	0	0	0	1	15237	1074	38	1		1	ST6GAL2	2	107460245	Silent	SNP	G	TCGA-ED-A7XP-01A-11D-A34Z-10	86226540	107460245	135739128	10	33803										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196891574	196891574	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	gaagactttcagatgttgtgGaactaaatccagtacgtgtt	10	6	1	2			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr2:196891574G>T	ENST00000312428.6	-	7	677	c.577C>A	c.(577-579)Cca>Aca	p.P193T	DNAH7_ENST00000410072.1_Missense_Mutation_p.P193T	NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	193	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						AGATGTTGTGGAACTAAATCC	0.358																																					p.P193T		Atlas-SNP	.											.	DNAH7	512	.	0			c.C577A						.						138	131	133					2																	196891574		1873	4096	5969	SO:0001583	missense	56171	exon7			GTTGTGGAACTAA	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.577C>A	chr2.hg19:g.196891574G>T	ENSP00000311273:p.Pro193Thr	105.0	0.0		89.0	26.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	hg19	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.208443	0.79240	.	.	ENSG00000118997	ENST00000312428;ENST00000410072;ENST00000312446	T;T	0.25250	1.81;2.43	5.92	5.92	0.95590	.	0.066917	0.64402	D	0.000012	T	0.31765	0.0807	L	0.57536	1.79	0.58432	D	0.999999	B	0.21225	0.053	B	0.21917	0.037	T	0.02885	-1.1098	10	0.37606	T	0.19	.	19.9123	0.97029	0.0:0.0:1.0:0.0	.	193	Q8WXX0	DYH7_HUMAN	T	193	ENSP00000311273:P193T;ENSP00000386260:P193T	ENSP00000311273:P193T	P	-	1	0	DNAH7	196599819	1.000000	0.71417	0.966000	0.40874	0.835000	0.47333	6.390000	0.73204	2.801000	0.96364	0.650000	0.86243	CCA	.	.		0.358	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		T	196891574	G	T	196891574	3	4	247	1	0	0	0	0	1	0	0	0	4608	1174	41	3	11733	3	DNAH7	2	196891574	Missense_Mutation	SNP	G	TCGA-ED-A7XP-01A-11D-A34Z-10	89431329	196891574	46307799	11	33804										
MAP2	4133	hgsc.bcm.edu	37	chr2	210561763	210561763	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	ctcatctctcctgtgttaagCggaaaaccacaggtgactgt	9	11	2	1	rs369892280		TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr2:210561763C>T	ENST00000360351.4	+	9	5016	c.4510C>T	c.(4510-4512)Cgg>Tgg	p.R1504W	MAP2_ENST00000361559.4_Intron|MAP2_ENST00000199940.6_Intron|MAP2_ENST00000475600.1_Intron|MAP2_ENST00000392194.1_Intron|MAP2_ENST00000447185.1_Missense_Mutation_p.R1500W	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	1504					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	CTGTGTTAAGCGGAAAACCAC	0.373																																					p.R1504W	Pancreas(27;423 979 28787 29963)	Atlas-SNP	.											.	MAP2	372	.	0			c.C4510T						.						84	90	88					2																	210561763		2203	4300	6503	SO:0001583	missense	4133	exon9			GTTAAGCGGAAAA		CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"A-kinase anchor proteins"	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.4510C>T	chr2.hg19:g.210561763C>T	ENSP00000353508:p.Arg1504Trp	99.0	0.0		81.0	29.0	NM_002374	Q17S04|Q8IUX2|Q99975|Q99976	Missense_Mutation	SNP	ENST00000360351.4	hg19	CCDS2384.1	.	.	.	.	.	.	.	.	.	.	C	16.09	3.023133	0.54683	.	.	ENSG00000078018	ENST00000360351;ENST00000447185	T;T	0.27104	1.69;1.69	5.56	5.56	0.83823	MAP2/Tau projection (1);	0.000000	0.53938	D	0.000043	T	0.48241	0.1489	M	0.61703	1.905	0.54753	D	0.99998	D;D	0.89917	1.0;1.0	D;D	0.81914	0.987;0.995	T	0.45145	-0.9281	10	0.87932	D	0	-9.1904	14.385	0.66938	0.1477:0.8523:0.0:0.0	.	1500;1504	P11137-3;P11137	.;MAP2_HUMAN	W	1504;1500	ENSP00000353508:R1504W;ENSP00000392164:R1500W	ENSP00000353508:R1504W	R	+	1	2	MAP2	210270008	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.715000	0.47210	2.626000	0.88956	0.650000	0.86243	CGG	.	.		0.373	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538		T	210561763	C	T	210561763	3	4	247	1	0	0	0	0	1	0	0	0	9244	759	27	1	4532	1	MAP2	2	210561763	Missense_Mutation	SNP	C	TCGA-ED-A7XP-01A-11D-A34Z-10	13670189	210561763	32637610	12	33805										
INHA	3623	hgsc.bcm.edu	37	chr2	220439974	220439974	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	ctccttccaggagctgggctGggaacggtggatcgtgtacc	15	11	0	0			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr2:220439974G>T	ENST00000243786.2	+	2	1007	c.827G>T	c.(826-828)tGg>tTg	p.W276L		NM_002191.3	NP_002182.1	P05111	INHA_HUMAN	inhibin, alpha	276					cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|erythrocyte differentiation (GO:0030218)|hemoglobin biosynthetic process (GO:0042541)|male gonad development (GO:0008584)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell cycle (GO:0045786)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of phosphorylation (GO:0042326)|nervous system development (GO:0007399)|ovarian follicle development (GO:0001541)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|regulation of cell cycle (GO:0051726)|regulation of cell proliferation (GO:0042127)|response to external stimulus (GO:0009605)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|inhibin A complex (GO:0043512)|inhibin-betaglycan-ActRII complex (GO:0034673)|neuronal cell body (GO:0043025)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|hormone activity (GO:0005179)|receptor binding (GO:0005102)			large_intestine(2)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	10		Renal(207;0.0183)		Epithelial(149;4.58e-07)|all cancers(144;4.31e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		GAGCTGGGCTGGGAACGGTGG	0.607																																					p.W276L		Atlas-SNP	.											.	INHA	30	.	0			c.G827T						.						141	140	140					2																	220439974		2203	4300	6503	SO:0001583	missense	3623	exon2			TGGGCTGGGAACG		CCDS2444.1	2q35	2013-09-19			ENSG00000123999	ENSG00000123999			6065	protein-coding gene	gene with protein product		147380				3345731	Standard	NM_002191		Approved		uc002vmk.2	P05111	OTTHUMG00000059237	ENST00000243786.2:c.827G>T	chr2.hg19:g.220439974G>T	ENSP00000243786:p.Trp276Leu	89.0	0.0		102.0	37.0	NM_002191	A8K8H5	Missense_Mutation	SNP	ENST00000243786.2	hg19	CCDS2444.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.681252	0.88542	.	.	ENSG00000123999	ENST00000243786	D	0.89746	-2.56	5.48	5.48	0.80851	Transforming growth factor-beta, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.96346	0.8808	H	0.94620	3.56	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97199	0.9863	9	.	.	.	-17.1134	19.3612	0.94438	0.0:0.0:1.0:0.0	.	276	P05111	INHA_HUMAN	L	276	ENSP00000243786:W276L	.	W	+	2	0	INHA	220148218	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.772000	0.91757	2.564000	0.86499	0.561000	0.74099	TGG	.	.		0.607	INHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131425.1			T	220439974	G	T	220439974	3	4	247	1	0	0	0	0	1	0	0	0	7749	1357	47	3	833	3	INHA	2	220439974	Missense_Mutation	SNP	G	TCGA-ED-A7XP-01A-11D-A34Z-10	9878211	220439974	22759399	13	33806										
CUL3	8452	hgsc.bcm.edu	37	chr2	225376243	225376243	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	tcttcattaattctagcttcTactttctttatatatactga	2	8	5	1			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr2:225376243T>C	ENST00000264414.4	-	6	1049	c.711A>G	c.(709-711)gtA>gtG	p.V237V	CUL3_ENST00000344951.4_Silent_p.V171V|CUL3_ENST00000409096.1_Silent_p.V213V|CUL3_ENST00000432260.2_5'Flank|CUL3_ENST00000409777.1_Silent_p.V213V	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3	237					cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|COPII vesicle coating (GO:0048208)|cyclin catabolic process (GO:0008054)|embryonic cleavage (GO:0040016)|ER to Golgi vesicle-mediated transport (GO:0006888)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation (GO:0007369)|integrin-mediated signaling pathway (GO:0007229)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic metaphase plate congression (GO:0007080)|negative regulation of Rho protein signal transduction (GO:0035024)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|stem cell division (GO:0017145)|stress fiber assembly (GO:0043149)|trophectodermal cellular morphogenesis (GO:0001831)|Wnt signaling pathway (GO:0016055)	Cul3-RING ubiquitin ligase complex (GO:0031463)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|nucleus (GO:0005634)|polar microtubule (GO:0005827)	POZ domain binding (GO:0031208)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	46		all_lung(227;0.00877)|Lung NSC(271;0.011)|Renal(207;0.0112)|all_hematologic(139;0.138)		Epithelial(121;1.58e-11)|all cancers(144;1.43e-08)|Lung(261;0.00863)|LUSC - Lung squamous cell carcinoma(224;0.00902)		TTCTAGCTTCTACTTTCTTTA	0.313																																					p.V243V		Atlas-SNP	.											.	CUL3	96	.	0			c.A729G						.						138	138	138					2																	225376243		2203	4299	6502	SO:0001819	synonymous_variant	8452	exon6			AGCTTCTACTTTC	U58089	CCDS2462.1, CCDS58751.1	2q36.2	2011-05-24			ENSG00000036257	ENSG00000036257			2553	protein-coding gene	gene with protein product		603136				8681378, 17192413	Standard	NM_003590		Approved		uc002vny.3	Q13618	OTTHUMG00000133167	ENST00000264414.4:c.711A>G	chr2.hg19:g.225376243T>C		202.0	0.0		154.0	47.0	NM_001257198	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	Silent	SNP	ENST00000264414.4	hg19	CCDS2462.1																																																																																			.	.		0.313	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256871.2			C	225376243	T	C	225376243	2	2	247	1	0	0	0	0	0	0	0	1	4058	1509	53	2		2	CUL3	2	225376243	Silent	SNP	T	TCGA-ED-A7XP-01A-11D-A34Z-10	4936269	225376243	17823130	14	33807										
KAT2B	8850	hgsc.bcm.edu	37	chr3	20181810	20181810	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	gggatgtgagctaaatccacGgatcccgtacacagaatttt	10	9	0	2			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr3:20181810G>T	ENST00000263754.4	+	13	2413	c.1958G>T	c.(1957-1959)cGg>cTg	p.R653L	MIR3135A_ENST00000578460.1_RNA	NM_003884.4	NP_003875.3	Q92831	KAT2B_HUMAN	K(lysine) acetyltransferase 2B	653					cell cycle arrest (GO:0007050)|cellular response to insulin stimulus (GO:0032869)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|histone H3-K9 acetylation (GO:0043970)|internal peptidyl-lysine acetylation (GO:0018393)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|Notch signaling pathway (GO:0007219)|peptidyl-lysine acetylation (GO:0018394)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein acetylation (GO:0006473)|regulation of protein ADP-ribosylation (GO:0010835)|rhythmic process (GO:0048511)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	A band (GO:0031672)|actomyosin (GO:0042641)|Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|I band (GO:0031674)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)	acetyltransferase activity (GO:0016407)|cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|histone acetyltransferase activity (GO:0004402)|histone deacetylase binding (GO:0042826)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	40						CTAAATCCACGGATCCCGTAC	0.418																																					p.R653L		Atlas-SNP	.											.	KAT2B	73	.	0			c.G1958T						.						83	83	83					3																	20181810		2203	4300	6503	SO:0001583	missense	8850	exon13			ATCCACGGATCCC	U57316	CCDS2634.1	3p24	2011-07-01	2008-07-04	2008-07-04	ENSG00000114166	ENSG00000114166		"Chromatin-modifying enzymes / K-acetyltransferases"	8638	protein-coding gene	gene with protein product		602303	"p300/CBP-associated factor"	PCAF		8684459, 9722949	Standard	NM_003884		Approved	P/CAF, GCN5, GCN5L	uc003cbq.3	Q92831	OTTHUMG00000130481	ENST00000263754.4:c.1958G>T	chr3.hg19:g.20181810G>T	ENSP00000263754:p.Arg653Leu	71.0	0.0		95.0	4.0	NM_003884	Q6NSK1	Missense_Mutation	SNP	ENST00000263754.4	hg19	CCDS2634.1	.	.	.	.	.	.	.	.	.	.	G	14.87	2.664209	0.47572	.	.	ENSG00000114166	ENST00000263754	T	0.22539	1.95	5.41	0.467	0.16721	Acyl-CoA N-acyltransferase (2);	0.381500	0.34460	N	0.003954	T	0.23171	0.0560	M	0.80847	2.515	0.34711	D	0.727731	B	0.26845	0.161	B	0.17979	0.02	T	0.15037	-1.0451	10	0.59425	D	0.04	-1.2702	9.042	0.36322	0.4368:0.0:0.5632:0.0	.	653	Q92831	KAT2B_HUMAN	L	653	ENSP00000263754:R653L	ENSP00000263754:R653L	R	+	2	0	KAT2B	20156814	1.000000	0.71417	0.930000	0.37139	0.720000	0.41350	1.635000	0.37134	-0.127000	0.11661	0.655000	0.94253	CGG	.	.		0.418	KAT2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252880.1	NM_003884		T	20181810	G	T	20181810	3	4	247	1	0	0	0	0	1	0	0	0	7991	1116	39	1	2008	1	KAT2B	3	20181810	Missense_Mutation	SNP	G	TCGA-ED-A7XP-01A-11D-A34Z-10		20181810	177840620	15	33808										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266101	41266101	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	gcaacagtcttacctggactCtggaatccattctggtgcca	9	12	3	0	rs121913416|rs121913400		TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr3:41266101C>G	ENST00000349496.5	+	3	378	c.98C>G	c.(97-99)tCt>tGt	p.S33C	CTNNB1_ENST00000405570.1_Missense_Mutation_p.S33C|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S33C|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S26C|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S33C	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	33			Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> F (in PTR, MDB and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10666372}.|S -> L (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> Y (in colorectal cancer and PTR; enhances transactivation of target genes). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:9065402}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S33C(168)|p.S33F(97)|p.S33Y(60)|p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.S33L(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S33N(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.D32fs*9(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.S29_H36del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.D32_H36>D(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TACCTGGACTCTGGAATCCAT	0.488	S33C(SKMEL1_SKIN)|S33F(SW1573_LUNG)|S33Y(SW48_LARGE_INTESTINE)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S33C	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,0,359	CTNNB1	4904	.	468	Substitution - Missense(331)|Deletion - In frame(111)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(165)|central_nervous_system(82)|large_intestine(40)|endometrium(37)|stomach(32)|skin(21)|ovary(20)|pituitary(19)|pancreas(12)|lung(7)|biliary_tract(6)|soft_tissue(4)|bone(4)|breast(3)|prostate(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|parathyroid(2)|small_intestine(2)|thyroid(1)|NS(1)|urinary_tract(1)|adrenal_gland(1)	c.C98G						.						92	77	82					3																	41266101		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	TGGACTCTGGAAT	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.98C>G	chr3.hg19:g.41266101C>G	ENSP00000344456:p.Ser33Cys	215.0	1.0		149.0	16.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.381716	0.82792	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.51071	0.72;0.72;0.72;0.72;0.72;0.72;0.72;0.72;0.72	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.72053	0.3413	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74188	-0.3746	10	0.87932	D	0	-10.7796	19.9596	0.97236	0.0:1.0:0.0:0.0	.	33	P35222	CTNB1_HUMAN	C	26;33;33;33;33;26;33;33;33	ENSP00000400508:S26C;ENSP00000385604:S33C;ENSP00000412219:S33C;ENSP00000379486:S33C;ENSP00000344456:S33C;ENSP00000411226:S26C;ENSP00000379488:S33C;ENSP00000409302:S33C;ENSP00000401599:S33C	ENSP00000344456:S33C	S	+	2	0	CTNNB1	41241105	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.726000	0.93360	0.655000	0.94253	TCT	.	.		0.488	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266101	C	G	41266101	3	3	247	1	0	0	0	0	1	0	0	0	4018	913	32	4	104	4	CTNNB1	3	41266101	Missense_Mutation	SNP	C	TCGA-ED-A7XP-01A-11D-A34Z-10	21084291	41266101	156756329	16	33809										
SLC9A10	285335	hgsc.bcm.edu	37	chr3	111981884	111981884	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	gaccattatgaatatccagcGccaactgaactcatgaccaa	6	12	1	3			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr3:111981884G>A	ENST00000305815.5	-	10	1336	c.1084C>T	c.(1084-1086)Cgc>Tgc	p.R362C	SLC9C1_ENST00000487372.1_Missense_Mutation_p.R314C	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	362					cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										AATATCCAGCGCCAACTGAAC	0.368																																					p.R362C		Atlas-SNP	.											.	.	.	.	0			c.C1084T						.						105	102	103					3																	111981884		2203	4300	6503	SO:0001583	missense	285335	exon10			TCCAGCGCCAACT	AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"Solute carriers"	31401	protein-coding gene	gene with protein product	"sperm-NHE"	612738	"solute carrier family 9, isoform 10", "solute carrier family 9, member 10"	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.1084C>T	chr3.hg19:g.111981884G>A	ENSP00000306627:p.Arg362Cys	206.0	0.0		198.0	69.0	NM_183061	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	hg19	CCDS33817.1	.	.	.	.	.	.	.	.	.	.	G	17.51	3.408688	0.62399	.	.	ENSG00000172139	ENST00000305815;ENST00000487372	T;T	0.20598	2.06;2.39	5.78	4.89	0.63831	Cation/H+ exchanger (1);	0.000000	0.64402	D	0.000013	T	0.42630	0.1211	L	0.61218	1.895	0.46954	D	0.999267	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.34104	-0.9842	10	0.72032	D	0.01	-16.5632	12.1441	0.54014	0.0:0.0:0.8287:0.1713	.	314;362	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	C	362;314	ENSP00000306627:R362C;ENSP00000420688:R314C	ENSP00000306627:R362C	R	-	1	0	SLC9A10	113464574	1.000000	0.71417	1.000000	0.80357	0.622000	0.37654	4.968000	0.63728	1.409000	0.46915	0.543000	0.68304	CGC	.	.		0.368	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061		A	111981884	G	A	111981884	3	1	247	1	0	0	0	0	1	0	0	0	14725	1087	38	1	2529	1	SLC9A10	3	111981884	Missense_Mutation	SNP	G	TCGA-ED-A7XP-01A-11D-A34Z-10	70715783	111981884	86040546	17	33810										
ARHGAP31	57514	hgsc.bcm.edu	37	chr3	119133178	119133178	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	aactccagtcctgctttcaaAgggcggcccggaaagagaag	12	11	1	1			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr3:119133178A>C	ENST00000264245.4	+	12	2934	c.2402A>C	c.(2401-2403)aAg>aCg	p.K801T		NM_020754.2	NP_065805.2	Q2M1Z3	RHG31_HUMAN	Rho GTPase activating protein 31	801					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(3)|large_intestine(11)|lung(29)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	67						CTGCTTTCAAAGGGCGGCCCG	0.552																																					p.K801T	Pancreas(7;176 297 5394 51128 51241)	Atlas-SNP	.											.	ARHGAP31	175	.	0			c.A2402C						.						55	57	56					3																	119133178		1892	4104	5996	SO:0001583	missense	57514	exon12			TTTCAAAGGGCGG		CCDS43135.1	3q13.33	2011-06-29			ENSG00000031081	ENSG00000031081		"Rho GTPase activating proteins"	29216	protein-coding gene	gene with protein product		610911				9786927, 12819203, 16519628	Standard	NM_020754		Approved	CDGAP	uc003ecj.4	Q2M1Z3	OTTHUMG00000159362	ENST00000264245.4:c.2402A>C	chr3.hg19:g.119133178A>C	ENSP00000264245:p.Lys801Thr	46.0	0.0		35.0	12.0	NM_020754	Q9ULL6	Missense_Mutation	SNP	ENST00000264245.4	hg19	CCDS43135.1	.	.	.	.	.	.	.	.	.	.	A	10.45	1.354238	0.24512	.	.	ENSG00000031081	ENST00000264245;ENST00000543280	T	0.07567	3.18	5.0	1.21	0.21127	.	0.975022	0.08426	N	0.947581	T	0.04543	0.0124	N	0.19112	0.55	0.09310	N	1	B	0.28128	0.201	B	0.24155	0.051	T	0.46652	-0.9176	10	0.17369	T	0.5	.	3.1138	0.06367	0.5034:0.0:0.172:0.3246	.	801	Q2M1Z3	RHG31_HUMAN	T	801	ENSP00000264245:K801T	ENSP00000264245:K801T	K	+	2	0	ARHGAP31	120615868	0.000000	0.05858	0.001000	0.08648	0.048000	0.14542	0.098000	0.15189	0.116000	0.18110	0.533000	0.62120	AAG	.	.		0.552	ARHGAP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354942.2			C	119133178	A	C	119133178	3	2	247	1	0	0	0	0	1	0	0	0	880	72	3	5	2448	5	ARHGAP31	3	119133178	Missense_Mutation	SNP	A	TCGA-ED-A7XP-01A-11D-A34Z-10	7151294	119133178	78889252	18	33811										
SEC22A	26984	hgsc.bcm.edu	37	chr3	122978413	122978413	+	Frame_Shift_Del	DEL	G	G	-													0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	acatcattgcatttttccttGgaacagcagcctgcctttac							TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr3:122978413delG	ENST00000309934.4	+	5	1596	c.700delG	c.(700-702)ggafs	p.G234fs	SEC22A_ENST00000492595.1_Frame_Shift_Del_p.G234fs|SEC22A_ENST00000481965.2_Frame_Shift_Del_p.L75fs	NM_012430.4	NP_036562.2	Q96IW7	SC22A_HUMAN	SEC22 vesicle trafficking protein homolog A (S. cerevisiae)	234					ER to Golgi vesicle-mediated transport (GO:0006888)|protein transport (GO:0015031)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			NS(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)	10				GBM - Glioblastoma multiforme(114;0.0548)		ATTTTTCCTTGGAACAGCAGC	0.358																																					p.L233fs		Atlas-Indel,Pindel	.											.	SEC22A	29	.	0			c.699delT						.						89	88	88					3																	122978413		2203	4298	6501	SO:0001589	frameshift_variant	26984	exon6			.	AF100749	CCDS3021.1	3q21.1	2006-04-25	2006-04-25	2006-04-25	ENSG00000121542	ENSG00000121542			20260	protein-coding gene	gene with protein product		612442	"SEC22 vesicle trafficking protein-like 2 (S. cerevisiae)"	SEC22L2		9094723, 9501016	Standard	NM_012430		Approved		uc003ege.3	Q96IW7	OTTHUMG00000159495	ENST00000309934.4:c.700delG	chr3.hg19:g.122978413delG	ENSP00000310521:p.Gly234fs	370.0	0.0		335.0	113.0	NM_012430	B2RE26|Q9Y682	Frame_Shift_Del	DEL	ENST00000309934.4	hg19	CCDS3021.1																																																																																			.	.		0.358	SEC22A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355770.2	NM_012430		-	122978413	G	-	122978413	7	5	247	1	0	1	0	1	0	0	0	0	14003	1349	47	0	718	0	SEC22A	3	122978413	Frame_Shift_Del	DEL	G	TCGA-ED-A7XP-01A-11D-A34Z-10	3845235	122978413	75044017	19	33812										
TMEM44	93109	hgsc.bcm.edu	37	chr3	194336377	194336377	+	Frame_Shift_Del	DEL	C	C	-													0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	ctctggcttccttggcaaatCctaaggcctgtctcatcttg							TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr3:194336377delC	ENST00000392432.2	-	8	1179	c.974delG	c.(973-975)ggafs	p.G325fs	TMEM44_ENST00000347147.4_Frame_Shift_Del_p.G278fs|TMEM44_ENST00000273580.7_Frame_Shift_Del_p.G278fs|TMEM44_ENST00000473092.1_Frame_Shift_Del_p.G278fs|TMEM44_ENST00000381975.3_Frame_Shift_Del_p.G278fs	NM_001166305.1	NP_001159777.1	Q2T9K0	TMM44_HUMAN	transmembrane protein 44	325						integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|urinary_tract(1)	8	all_cancers(143;1.41e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;4.34e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;9.06e-06)		CTTGGCAAATCCTAAGGCCTG	0.488																																					p.G325fs		Atlas-Indel,Pindel	.											.	TMEM44	42	.	0			c.975delA						.						233	219	224					3																	194336377		2203	4300	6503	SO:0001589	frameshift_variant	93109	exon8			.	AL833026	CCDS3308.1, CCDS33921.1, CCDS3308.2, CCDS54698.1, CCDS54699.1	3q29	2005-08-16			ENSG00000145014	ENSG00000145014			25120	protein-coding gene	gene with protein product							Standard	NM_138399		Approved	DKFZp686O18124	uc010hzn.3	Q2T9K0	OTTHUMG00000156023	ENST00000392432.2:c.974delG	chr3.hg19:g.194336377delC	ENSP00000376227:p.Gly325fs	166.0	0.0		118.0	45.0	NM_001166305	A1L3V7|B7ZLZ5|B7ZLZ6|C9JJ62|E9PGA9|Q0P6F7|Q6ZT47|Q8IXR1|Q8N4G3	Frame_Shift_Del	DEL	ENST00000392432.2	hg19	CCDS54699.1																																																																																			.	.		0.488	TMEM44-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000342750.1	NM_138399		-	194336377	C	-	194336377	7	5	247	1	0	1	0	1	0	0	0	0	16183	855	30	0	503	0	TMEM44	3	194336377	Frame_Shift_Del	DEL	C	TCGA-ED-A7XP-01A-11D-A34Z-10	71357964	194336377	3686053	20	33813										
PTPN13	5783	hgsc.bcm.edu	37	chr4	87683886	87683886	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	attttgacttttagtgccttCtactcctgtgcatctcacca	5	12	2	1			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr4:87683886C>A	ENST00000411767.2	+	24	3623	c.3560C>A	c.(3559-3561)tCt>tAt	p.S1187Y	PTPN13_ENST00000316707.6_Missense_Mutation_p.S996Y|PTPN13_ENST00000427191.2_Missense_Mutation_p.S1168Y|PTPN13_ENST00000511467.1_Missense_Mutation_p.S1187Y|PTPN13_ENST00000436978.1_Missense_Mutation_p.S1187Y			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	1187					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		TTAGTGCCTTCTACTCCTGTG	0.383																																					p.S1187Y		Atlas-SNP	.											.	PTPN13	203	.	0			c.C3560A						.						72	72	72					4																	87683886		1920	4130	6050	SO:0001583	missense	5783	exon24			TGCCTTCTACTCC		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.3560C>A	chr4.hg19:g.87683886C>A	ENSP00000407249:p.Ser1187Tyr	82.0	0.0		48.0	24.0	NM_080683	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	hg19	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	C	18.21	3.574332	0.65878	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T;T	0.56275	0.5;0.52;0.61;0.47;0.52	5.26	5.26	0.73747	.	0.134034	0.34628	N	0.003809	T	0.61236	0.2331	M	0.61703	1.905	0.34315	D	0.685872	D;D;D;D	0.71674	0.998;0.98;0.966;0.98	D;P;P;P	0.79108	0.992;0.648;0.73;0.731	T	0.63501	-0.6623	10	0.02654	T	1	.	9.5356	0.39220	0.0:0.7808:0.1434:0.0758	.	996;1168;1187;1187	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	Y	1168;1187;996;1187;1187;1136	ENSP00000408368:S1168Y;ENSP00000394794:S1187Y;ENSP00000322675:S996Y;ENSP00000407249:S1187Y;ENSP00000426626:S1187Y	ENSP00000322675:S996Y	S	+	2	0	PTPN13	87902910	0.999000	0.42202	1.000000	0.80357	0.918000	0.54935	1.487000	0.35540	2.439000	0.82584	0.650000	0.86243	TCT	.	.		0.383	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			A	87683886	C	A	87683886	3	1	247	1	0	0	0	0	1	0	0	0	12795	913	32	3	3650	3	PTPN13	4	87683886	Missense_Mutation	SNP	C	TCGA-ED-A7XP-01A-11D-A34Z-10		87683886	103470390	21	33814										
SEC24B	10427	hgsc.bcm.edu	37	chr4	110384263	110384263	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	tgaaccagcaaccaggagcaCagcagttgtacagcaggggt	13	10	0	1			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr4:110384263C>T	ENST00000265175.5	+	2	395	c.340C>T	c.(340-342)Cag>Tag	p.Q114*	SEC24B_ENST00000399100.2_Nonsense_Mutation_p.Q114*|SEC24B_ENST00000504968.2_Nonsense_Mutation_p.Q145*	NM_006323.2	NP_006314.2	O95487	SC24B_HUMAN	SEC24 family member B	114					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|aorta morphogenesis (GO:0035909)|auditory receptor cell stereocilium organization (GO:0060088)|cellular protein metabolic process (GO:0044267)|cochlear nucleus development (GO:0021747)|COPII vesicle coating (GO:0048208)|coronary artery morphogenesis (GO:0060982)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|lung lobe morphogenesis (GO:0060463)|membrane organization (GO:0061024)|neural tube closure (GO:0001843)|outflow tract morphogenesis (GO:0003151)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|pulmonary artery morphogenesis (GO:0061156)|regulation of cargo loading into COPII-coated vesicle (GO:1901301)|regulation of establishment of planar polarity involved in neural tube closure (GO:0090178)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|membrane (GO:0016020)	transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)		ACCAGGAGCACAGCAGTTGTA	0.493																																					p.Q114X		Atlas-SNP	.											.	SEC24B	186	.	0			c.C340T						.						117	119	119					4																	110384263		2033	4195	6228	SO:0001587	stop_gained	10427	exon2			GGAGCACAGCAGT	AJ131245	CCDS43260.1, CCDS47124.1, CCDS75179.1	4q25	2013-10-21	2013-10-21		ENSG00000138802	ENSG00000138802			10704	protein-coding gene	gene with protein product		607184	"SEC24 (S. cerevisiae) related gene family, member B", "SEC24 family, member B (S. cerevisiae)"			10075675, 10329445	Standard	XM_005262688		Approved		uc003hzk.3	O95487	OTTHUMG00000161372	ENST00000265175.5:c.340C>T	chr4.hg19:g.110384263C>T	ENSP00000265175:p.Gln114*	88.0	0.0		37.0	21.0	NM_006323	B7ZKM8|B7ZKN4|Q0VG08	Nonsense_Mutation	SNP	ENST00000265175.5	hg19	CCDS47124.1	.	.	.	.	.	.	.	.	.	.	C	33	5.209344	0.95069	.	.	ENSG00000138802	ENST00000504968;ENST00000399100;ENST00000265175	.	.	.	5.26	5.26	0.73747	.	1.205850	0.05841	N	0.619316	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.24483	T	0.36	-1.3669	17.0668	0.86561	0.0:1.0:0.0:0.0	.	.	.	.	X	145;114;114	.	ENSP00000265175:Q114X	Q	+	1	0	SEC24B	110603712	1.000000	0.71417	1.000000	0.80357	0.795000	0.44927	3.403000	0.52615	2.464000	0.83262	0.467000	0.42956	CAG	.	.		0.493	SEC24B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364693.2			T	110384263	C	T	110384263	4	4	247	1	0	0	0	0	0	1	0	0	14010	479	17	3	346	3	SEC24B	4	110384263	Nonsense_Mutation	SNP	C	TCGA-ED-A7XP-01A-11D-A34Z-10	22700377	110384263	80770013	22	33815										
IRX1	79192	hgsc.bcm.edu	37	chr5	3599650	3599650	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	aaggtgacatggggagcgcgCagcaaggaccaggaagatgg	18	7	0	2			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr5:3599650C>A	ENST00000302006.3	+	2	640	c.588C>A	c.(586-588)cgC>cgA	p.R196R	CTD-2012M11.3_ENST00000559410.1_RNA	NM_024337.3	NP_077313.3	P78414	IRX1_HUMAN	iroquois homeobox 1	196					proximal/distal pattern formation involved in metanephric nephron development (GO:0072272)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			biliary_tract(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(18)|ovary(2)|pancreas(1)|prostate(5)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						GGGGAGCGCGCAGCAAGGACC	0.632																																					p.R196R		Atlas-SNP	.											.	IRX1	106	.	0			c.C588A						.						85	73	77					5																	3599650		2203	4300	6503	SO:0001819	synonymous_variant	79192	exon2			AGCGCGCAGCAAG	U90307	CCDS34132.1	5p15.33	2011-12-16	2007-07-13		ENSG00000170549	ENSG00000170549		"Homeoboxes / TALE class"	14358	protein-coding gene	gene with protein product		606197					Standard	NM_024337		Approved	IRX-5	uc003jde.3	P78414	OTTHUMG00000161632	ENST00000302006.3:c.588C>A	chr5.hg19:g.3599650C>A		60.0	0.0		68.0	31.0	NM_024337	Q7Z2F8|Q8N312	Silent	SNP	ENST00000302006.3	hg19	CCDS34132.1																																																																																			.	.		0.632	IRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365546.1	NM_024337		A	3599650	C	A	3599650	2	1	247	1	0	0	0	0	0	0	0	1	7852	697	25	3		3	IRX1	5	3599650	Silent	SNP	C	TCGA-ED-A7XP-01A-11D-A34Z-10		3599650	177315610	23	33816										
COL9A1	1297	hgsc.bcm.edu	37	chr6	71003965	71003965	+	Frame_Shift_Del	DEL	T	T	-													0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	ctttataggtaaagattcaaTcctgttgcagtcaacaaaaa					rs534004614		TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr6:71003965delT	ENST00000357250.6	-	5	759	c.601delA	c.(601-603)attfs	p.I201fs	COL9A1_ENST00000370496.3_Frame_Shift_Del_p.I201fs	NM_001851.4	NP_001842.3	P20849	CO9A1_HUMAN	collagen, type IX, alpha 1	201	Laminin G-like.|Nonhelical region (NC4).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|organ morphogenesis (GO:0009887)|tissue homeostasis (GO:0001894)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(44)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)	80						AAAGATTCAATCCTGTTGCAG	0.428																																					p.I201fs		Atlas-Indel,Pindel	.											.	COL9A1	228	.	0			c.602delT						.						124	121	122					6																	71003965		2203	4300	6503	SO:0001589	frameshift_variant	1297	exon5			.		CCDS4971.1, CCDS47447.1	6q13	2013-05-07			ENSG00000112280	ENSG00000112280		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2217	protein-coding gene	gene with protein product		120210				1429648	Standard	NM_001851		Approved		uc003pfg.4	P20849	OTTHUMG00000014988	ENST00000357250.6:c.601delA	chr6.hg19:g.71003965delT	ENSP00000349790:p.Ile201fs	120.0	0.0		113.0	45.0	NM_001851	Q13699|Q13700|Q5TF52|Q6P467|Q96BM8|Q99225|Q9H151|Q9H152|Q9Y6P2|Q9Y6P3	Frame_Shift_Del	DEL	ENST00000357250.6	hg19	CCDS4971.1																																																																																			.	.		0.428	COL9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041131.2			-	71003965	T	-	71003965	7	5	247	1	0	1	0	1	0	0	0	0	3709	1435	50	0	2376	0	COL9A1	6	71003965	Frame_Shift_Del	DEL	T	TCGA-ED-A7XP-01A-11D-A34Z-10		71003965	100111102	24	33817										
MDN1	23195	hgsc.bcm.edu	37	chr6	90484380	90484380	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	actttgtttccgtagaagccGcactcgacccacttgcaaat	7	13	0	1			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr6:90484380G>A	ENST00000369393.3	-	13	2009	c.1894C>T	c.(1894-1896)Cgg>Tgg	p.R632W	MDN1_ENST00000428876.1_Missense_Mutation_p.R632W			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	632					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		CGTAGAAGCCGCACTCGACCC	0.433																																					p.R632W		Atlas-SNP	.											MDN1,caecum,carcinoma,0,1	MDN1	478	.	0			c.C1894T						.						161	146	151					6																	90484380		2203	4300	6503	SO:0001583	missense	23195	exon13			GAAGCCGCACTCG	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.1894C>T	chr6.hg19:g.90484380G>A	ENSP00000358400:p.Arg632Trp	163.0	0.0		148.0	10.0	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	hg19	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	G	14.28	2.487838	0.44249	.	.	ENSG00000112159	ENST00000369393;ENST00000428876;ENST00000439638	T;T;T	0.18810	3.93;3.93;2.19	5.32	4.43	0.53597	ATPase, AAA+ type, core (1);	0.473273	0.22025	N	0.065668	T	0.14700	0.0355	L	0.51422	1.61	0.09310	N	0.999998	D;P	0.56968	0.978;0.955	P;P	0.51657	0.586;0.676	T	0.04386	-1.0955	10	0.51188	T	0.08	.	9.3334	0.38036	0.0:0.1402:0.5705:0.2893	.	559;632	Q5T795;Q9NU22	.;MDN1_HUMAN	W	632;632;559	ENSP00000358400:R632W;ENSP00000413970:R632W;ENSP00000409664:R559W	ENSP00000358400:R632W	R	-	1	2	MDN1	90541101	0.015000	0.18098	0.985000	0.45067	0.962000	0.63368	1.251000	0.32862	1.204000	0.43247	0.655000	0.94253	CGG	.	.		0.433	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			A	90484380	G	A	90484380	3	1	247	1	0	0	0	0	1	0	0	0	9424	1086	38	1	15256	1	MDN1	6	90484380	Missense_Mutation	SNP	G	TCGA-ED-A7XP-01A-11D-A34Z-10	19480415	90484380	80630687	25	33818										
WISP3	8838	hgsc.bcm.edu	37	chr6	112375575	112375575	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	agcgacatgcaggggctcctCttctccactcttctgcttgc	9	15	4	0			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr6:112375575C>A	ENST00000368666.2	+	1	301	c.15C>A	c.(13-15)ctC>ctA	p.L5L	WISP3_ENST00000483439.1_3'UTR|WISP3_ENST00000230529.5_Silent_p.L5L|WISP3_ENST00000604763.1_Silent_p.L5L|WISP3_ENST00000361714.1_Silent_p.L23L	NM_198239.1	NP_937882.1	O95389	WISP3_HUMAN	WNT1 inducible signaling pathway protein 3	5					cell-cell signaling (GO:0007267)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	extracellular space (GO:0005615)				breast(1)|central_nervous_system(1)|large_intestine(3)|lung(7)|prostate(1)	13		all_cancers(87;0.000196)|Acute lymphoblastic leukemia(125;1.18e-05)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0283)|OV - Ovarian serous cystadenocarcinoma(136;0.0613)|Epithelial(106;0.0827)|GBM - Glioblastoma multiforme(226;0.0972)|BRCA - Breast invasive adenocarcinoma(108;0.246)		AGGGGCTCCTCTTCTCCACTC	0.592																																					p.L23L		Atlas-SNP	.											.	WISP3	33	.	0			c.C69A						.						167	150	155					6																	112375575		2203	4300	6503	SO:0001819	synonymous_variant	8838	exon1			GCTCCTCTTCTCC	AF100781	CCDS5097.1, CCDS5098.1	6q21	2014-05-06			ENSG00000112761	ENSG00000112761			12771	protein-coding gene	gene with protein product		603400				9843955	Standard	NM_003880		Approved	CCN6	uc003pvo.3	O95389	OTTHUMG00000185101	ENST00000368666.2:c.15C>A	chr6.hg19:g.112375575C>A		62.0	0.0		75.0	13.0	NM_198239	Q3KR29|Q5H8W4|Q6UXH6	Silent	SNP	ENST00000368666.2	hg19	CCDS5098.1																																																																																			.	.		0.592	WISP3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041873.2	NM_003880		A	112375575	C	A	112375575	2	1	247	1	0	0	0	0	0	0	0	1	17389	900	32	3		3	WISP3	6	112375575	Silent	SNP	C	TCGA-ED-A7XP-01A-11D-A34Z-10	21891195	112375575	58739492	26	33819										
PIK3CG	5294	hgsc.bcm.edu	37	chr7	106545719	106545719	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	aaaatgaggaggatgctaaaAagtattttcttgatcagatc	9	4	2	3			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr7:106545719A>T	ENST00000359195.3	+	11	3506	c.3196A>T	c.(3196-3198)Aag>Tag	p.K1066*	PIK3CG_ENST00000496166.1_Nonsense_Mutation_p.K1066*|PIK3CG_ENST00000440650.2_Nonsense_Mutation_p.K1066*	NM_001282427.1|NM_002649.2	NP_001269356.1|NP_002640.2	P48736	PK3CG_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	1066	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cytokine production (GO:0001816)|dendritic cell chemotaxis (GO:0002407)|endocytosis (GO:0006897)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte apoptotic process (GO:0097284)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|natural killer cell chemotaxis (GO:0035747)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of triglyceride catabolic process (GO:0010897)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion mediated by integrin (GO:0033628)|respiratory burst involved in defense response (GO:0002679)|secretory granule localization (GO:0032252)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell proliferation (GO:0042098)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(9)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(16)|liver(4)|lung(59)|ovary(4)|pancreas(4)|prostate(3)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	132						GGATGCTAAAAAGTATTTTCT	0.413																																					p.K1066X		Atlas-SNP	.											.	PIK3CG	279	.	0			c.A3196T						.						138	136	137					7																	106545719		2203	4300	6503	SO:0001587	stop_gained	5294	exon11			GCTAAAAAGTATT		CCDS5739.1	7q22	2012-07-13	2012-07-13		ENSG00000105851	ENSG00000105851	2.7.1.153		8978	protein-coding gene	gene with protein product		601232	"phosphoinositide-3-kinase, catalytic, gamma polypeptide"				Standard	XM_005250443		Approved		uc003vdw.3	P48736	OTTHUMG00000157641	ENST00000359195.3:c.3196A>T	chr7.hg19:g.106545719A>T	ENSP00000352121:p.Lys1066*	160.0	0.0		123.0	37.0	NM_002649	A4D0Q6|Q8IV23|Q9BZC8	Nonsense_Mutation	SNP	ENST00000359195.3	hg19	CCDS5739.1	.	.	.	.	.	.	.	.	.	.	A	41	8.754976	0.98941	.	.	ENSG00000105851	ENST00000440650;ENST00000496166;ENST00000359195	.	.	.	5.94	5.94	0.96194	.	0.138048	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-26.1533	16.4075	0.83691	1.0:0.0:0.0:0.0	.	.	.	.	X	1066	.	ENSP00000352121:K1066X	K	+	1	0	PIK3CG	106332955	1.000000	0.71417	0.997000	0.53966	0.990000	0.78478	3.996000	0.57009	2.275000	0.75901	0.528000	0.53228	AAG	.	.		0.413	PIK3CG-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349294.1			T	106545719	A	T	106545719	4	4	247	1	0	0	0	0	0	1	0	0	11925	15	1	4	3234	4	PIK3CG	7	106545719	Nonsense_Mutation	SNP	A	TCGA-ED-A7XP-01A-11D-A34Z-10		106545719	52592944	27	33820										
INSIG1	3638	hgsc.bcm.edu	37	chr7	155094008	155094008	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	ctgtccttgactttagcagcCctatctttgggcctttggtg	10	11	1	1			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr7:155094008C>T	ENST00000340368.4	+	4	796	c.585C>T	c.(583-585)gcC>gcT	p.A195A	INSIG1_ENST00000342407.5_Intron|INSIG1_ENST00000344756.4_Silent_p.A43A	NM_005542.4	NP_005533.2	O15503	INSI1_HUMAN	insulin induced gene 1	195					cell proliferation (GO:0008283)|cholesterol biosynthetic process (GO:0006695)|cranial suture morphogenesis (GO:0060363)|inner ear morphogenesis (GO:0042472)|metabolic process (GO:0008152)|middle ear morphogenesis (GO:0042474)|negative regulation of cargo loading into COPII-coated vesicle (GO:1901303)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of steroid biosynthetic process (GO:0010894)|palate development (GO:0060021)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)|triglyceride metabolic process (GO:0006641)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|SREBP-SCAP-Insig complex (GO:0032937)				endometrium(2)|kidney(2)|large_intestine(1)|lung(11)|prostate(1)|upper_aerodigestive_tract(2)	19	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CTTTAGCAGCCCTATCTTTGG	0.423																																					p.A195A		Atlas-SNP	.											.	INSIG1	20	.	0			c.C585T						.						108	103	104					7																	155094008		2203	4300	6503	SO:0001819	synonymous_variant	3638	exon4			AGCAGCCCTATCT		CCDS5938.1, CCDS5939.1	7q36	2008-07-18			ENSG00000186480	ENSG00000186480			6083	protein-coding gene	gene with protein product	"INSIG-1 membrane protein"	602055				9268630	Standard	NM_005542		Approved	CL-6, MGC1405	uc003wly.3	O15503	OTTHUMG00000151330	ENST00000340368.4:c.585C>T	chr7.hg19:g.155094008C>T		239.0	0.0		221.0	67.0	NM_005542	A4D2N1|A8K6L0|Q53XW8|Q9BUV5	Silent	SNP	ENST00000340368.4	hg19	CCDS5938.1	.	.	.	.	.	.	.	.	.	.	C	10.30	1.311724	0.23821	.	.	ENSG00000186480	ENST00000476756	.	.	.	5.73	-1.21	0.09524	.	.	.	.	.	T	0.43366	0.1244	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.29671	-1.0004	4	.	.	.	.	3.963	0.09418	0.1993:0.3996:0.2927:0.1084	.	.	.	.	S	104	.	.	P	+	1	0	INSIG1	154724943	0.012000	0.17670	0.994000	0.49952	0.750000	0.42670	-0.697000	0.05098	0.017000	0.15025	0.650000	0.86243	CCT	.	.		0.423	INSIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322244.3	NM_198336		T	155094008	C	T	155094008	2	4	247	1	0	0	0	0	0	0	0	1	7774	610	22	3		3	INSIG1	7	155094008	Silent	SNP	C	TCGA-ED-A7XP-01A-11D-A34Z-10	48548289	155094008	4044655	28	33821										
SPAG1	6674	hgsc.bcm.edu	37	chr8	101237520	101237520	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	tccggcaaaagagatgatctCaaaacaagcaggagactcca	9	10	1	3			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr8:101237520C>T	ENST00000388798.2	+	14	1999	c.1808C>T	c.(1807-1809)tCa>tTa	p.S603L	SPAG1_ENST00000251809.3_Missense_Mutation_p.S603L|SPAG1_ENST00000523302.1_3'UTR	NM_003114.4	NP_003105.2	Q07617	SPAG1_HUMAN	sperm associated antigen 1	603					axonemal dynein complex assembly (GO:0070286)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	all_cancers(14;2.35e-05)|all_epithelial(15;5.2e-08)|Lung NSC(17;0.000283)|all_lung(17;0.000823)	Breast(495;0.195)	Epithelial(11;1.12e-09)|all cancers(13;1.26e-07)|OV - Ovarian serous cystadenocarcinoma(57;4.37e-05)|STAD - Stomach adenocarcinoma(118;0.0525)	KIRC - Kidney renal clear cell carcinoma(542;0.00178)|READ - Rectum adenocarcinoma(644;0.236)		GAGATGATCTCAAAACAAGCA	0.537																																					p.S603L		Atlas-SNP	.											.	SPAG1	80	.	0			c.C1808T						.						51	48	49					8																	101237520		2203	4300	6503	SO:0001583	missense	6674	exon14			TGATCTCAAAACA	AF311312	CCDS34930.1	8q22	2014-01-21			ENSG00000104450	ENSG00000104450		"Tetratricopeptide (TTC) repeat domain containing"	11212	protein-coding gene	gene with protein product		603395				16368546	Standard	NM_172218		Approved	SP75, FLJ32920, HSD-3.8, TPIS, CT140	uc003yjh.2	Q07617	OTTHUMG00000164706	ENST00000388798.2:c.1808C>T	chr8.hg19:g.101237520C>T	ENSP00000373450:p.Ser603Leu	66.0	0.0		65.0	12.0	NM_003114	A6NP70|B3KQ58|G3XAM3|Q7Z5G1	Missense_Mutation	SNP	ENST00000388798.2	hg19	CCDS34930.1	.	.	.	.	.	.	.	.	.	.	C	12.18	1.860563	0.32884	.	.	ENSG00000104450	ENST00000251809;ENST00000388798	T;T	0.62105	0.05;0.05	5.17	3.38	0.38709	.	1.524830	0.03627	N	0.237311	T	0.55000	0.1893	L	0.38175	1.15	0.09310	N	1	B	0.13145	0.007	B	0.09377	0.004	T	0.37337	-0.9710	10	0.32370	T	0.25	-0.0032	9.5565	0.39341	0.0:0.8314:0.0:0.1686	.	603	Q07617	SPAG1_HUMAN	L	603	ENSP00000251809:S603L;ENSP00000373450:S603L	ENSP00000251809:S603L	S	+	2	0	SPAG1	101306696	0.025000	0.19082	0.001000	0.08648	0.006000	0.05464	1.305000	0.33493	0.846000	0.35142	0.650000	0.86243	TCA	.	.		0.537	SPAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379853.2	NM_172218		T	101237520	C	T	101237520	3	4	247	1	0	0	0	0	1	0	0	0	14990	838	29	3	1858	3	SPAG1	8	101237520	Missense_Mutation	SNP	C	TCGA-ED-A7XP-01A-11D-A34Z-10		101237520	45126502	29	33822										
ADAMTSL1	92949	hgsc.bcm.edu	37	chr9	18777646	18777646	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	gcctcataaacacgtgtctgGcttcagcagctccctgcgga	10	14	3	0			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr9:18777646G>A	ENST00000380548.4	+	19	3758	c.3419G>A	c.(3418-3420)gGc>gAc	p.G1140D		NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	1140						proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(2)|lung(17)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(50;1.29e-17)		CACGTGTCTGGCTTCAGCAGC	0.657																																					p.G1140D		Atlas-SNP	.											.	ADAMTSL1	306	.	0			c.G3419A						.						32	36	35					9																	18777646		2064	4198	6262	SO:0001583	missense	92949	exon19			TGTCTGGCTTCAG	AF176313	CCDS6485.1, CCDS47954.1	9p21.3	2013-01-11			ENSG00000178031	ENSG00000178031		"Immunoglobulin superfamily / I-set domain containing"	14632	protein-coding gene	gene with protein product	"punctin"	609198	"chromosome 9 open reading frame 94"	C9orf94		9628581, 11805097	Standard	NM_001040272		Approved	ADAMTSR1, FLJ35283	uc003zne.4	Q8N6G6	OTTHUMG00000019604	ENST00000380548.4:c.3419G>A	chr9.hg19:g.18777646G>A	ENSP00000369921:p.Gly1140Asp	39.0	0.0		28.0	14.0	NM_001040272	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Missense_Mutation	SNP	ENST00000380548.4	hg19	CCDS47954.1	.	.	.	.	.	.	.	.	.	.	G	14.51	2.557837	0.45590	.	.	ENSG00000178031	ENST00000380548	T	0.63255	-0.03	6.03	6.03	0.97812	.	0.063246	0.08080	U	1.000000	T	0.52853	0.1760	N	0.19112	0.55	0.80722	D	1	B	0.14012	0.009	B	0.10450	0.005	T	0.21724	-1.0237	10	0.49607	T	0.09	.	14.6915	0.69091	0.0687:0.0:0.9313:0.0	.	1140	Q8N6G6	ATL1_HUMAN	D	1140	ENSP00000369921:G1140D	ENSP00000369921:G1140D	G	+	2	0	ADAMTSL1	18767646	1.000000	0.71417	0.973000	0.42090	0.783000	0.44284	4.274000	0.58921	2.868000	0.98415	0.557000	0.71058	GGC	.	.		0.657	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1			A	18777646	G	A	18777646	3	1	247	1	0	0	0	0	1	0	0	0	274	1203	42	3	3497	3	ADAMTSL1	9	18777646	Missense_Mutation	SNP	G	TCGA-ED-A7XP-01A-11D-A34Z-10		18777646	122435785	30	33823										
IFNA13	3447	hgsc.bcm.edu	37	chr9	21367937	21367937	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	gtgggtctcagggagatcacAgcccagagagcagcttgact	14	10	2	3			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr9:21367937A>C	ENST00000449498.1	-	1	138	c.73T>G	c.(73-75)Tgt>Ggt	p.C25G		NM_006900.3	NP_008831.3	P01562	IFNA1_HUMAN	interferon, alpha 13	24					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			breast(2)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)|skin(1)	9				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.0173)		GGGAGATCACAGCCCAGAGAG	0.537																																					p.C25G		Atlas-SNP	.											.	IFNA13	19	.	0			c.T73G						.						64	71	69					9																	21367937		2203	4297	6500	SO:0001583	missense	3447	exon1			GATCACAGCCCAG		CCDS6505.2	9p22	2010-12-10			ENSG00000233816	ENSG00000233816		"Interferons"	5419	protein-coding gene	gene with protein product		147578				1385305	Standard	NM_006900		Approved		uc003zpa.2	P01562	OTTHUMG00000019675	ENST00000449498.1:c.73T>G	chr9.hg19:g.21367937A>C	ENSP00000394494:p.Cys25Gly	120.0	0.0		86.0	11.0	NM_006900	D4Q9M8|Q14605|Q2M1L8|Q52LB8|Q5VYQ2|Q7M4Q1|Q8WZ68|Q9UMJ3	Missense_Mutation	SNP	ENST00000449498.1	hg19	CCDS6505.2	.	.	.	.	.	.	.	.	.	.	A	12.97	2.096066	0.36952	.	.	ENSG00000233816	ENST00000449498	T	0.05786	3.39	2.56	2.56	0.30785	.	0.000000	0.85682	D	0.000000	T	0.23611	0.0571	M	0.85630	2.765	0.09310	N	1	D	0.89917	1.0	D	0.85130	0.997	T	0.01583	-1.1319	10	0.87932	D	0	.	8.2194	0.31532	1.0:0.0:0.0:0.0	.	25	E9PB07	.	G	25	ENSP00000394494:C25G	ENSP00000394494:C25G	C	-	1	0	IFNA13	21357937	0.511000	0.26179	0.005000	0.12908	0.010000	0.07245	4.285000	0.58989	1.167000	0.42706	0.260000	0.18958	TGT	.	.		0.537	IFNA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051904.2	NM_006900		C	21367937	A	C	21367937	3	2	247	1	0	0	0	0	1	0	0	0	7542	188	7	5	503	5	IFNA13	9	21367937	Missense_Mutation	SNP	A	TCGA-ED-A7XP-01A-11D-A34Z-10	2590291	21367937	119845494	31	33824										
CDKN2A	1029	hgsc.bcm.edu	37	chr9	21971111	21971111	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	gccctcccgggcagcgtcgtGcacgggtcgggtgagagtgg	19	12	0	1	rs121913385		TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr9:21971111G>C	ENST00000304494.5	-	2	517	c.247C>G	c.(247-249)Cac>Gac	p.H83D	RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000530628.2_Missense_Mutation_p.A97G|CDKN2A_ENST00000446177.1_Missense_Mutation_p.H83D|CDKN2A_ENST00000498124.1_Missense_Mutation_p.H83D|CDKN2A_ENST00000579122.1_Missense_Mutation_p.H83D|CDKN2A_ENST00000361570.3_Missense_Mutation_p.A138G|CDKN2A_ENST00000494262.1_Missense_Mutation_p.H32D|CDKN2A_ENST00000578845.2_Missense_Mutation_p.H32D|CDKN2A_ENST00000479692.2_Missense_Mutation_p.H32D|CDKN2A_ENST00000579755.1_Missense_Mutation_p.A97G|CDKN2A_ENST00000498628.2_Missense_Mutation_p.H32D|CDKN2A_ENST00000497750.1_Missense_Mutation_p.H32D	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	83			H -> N (in a lung tumor).|H -> Q (in dbSNP:rs34968276).|H -> Y (in a pancreas and a head and neck tumor).		cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular senescence (GO:2000774)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|Ras protein signal transduction (GO:0007265)|replicative senescence (GO:0090399)|senescence-associated heterochromatin focus assembly (GO:0035986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|senescence-associated heterochromatin focus (GO:0035985)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.0?(1315)|p.?(44)|p.H83Y(30)|p.A138V(2)|p.H83fs*2(2)|p.H83N(1)|p.V82fs*62(1)|p.0(1)|p.V82_G89>G(1)|p.E61_L94del(1)|p.R137fs*48(1)|p.A68fs*3(1)|p.P81_A85del(1)|p.R80fs*34(1)|p.V82_E88del(1)		NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		GCAGCGTCGTGCACGGGTCGG	0.741	H83Y(CALU3_LUNG)|H83Y(HS944T_SKIN)|H83Y(JHH2_LIVER)|H83Y(OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|H83Y(SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)																											p.A97G		Atlas-SNP	.											CDKN2A_ENST00000498124,NS,carcinoma,0,37	CDKN2A	4810	.	1403	Whole gene deletion(1316)|Unknown(44)|Substitution - Missense(33)|Deletion - Frameshift(6)|Deletion - In frame(3)|Complex - deletion inframe(1)	haematopoietic_and_lymphoid_tissue(284)|skin(175)|central_nervous_system(171)|lung(154)|urinary_tract(93)|bone(74)|oesophagus(59)|soft_tissue(58)|upper_aerodigestive_tract(56)|pleura(51)|ovary(36)|pancreas(34)|breast(33)|kidney(32)|thyroid(13)|NS(12)|biliary_tract(12)|stomach(12)|autonomic_ganglia(9)|liver(7)|meninges(7)|large_intestine(6)|salivary_gland(5)|thymus(4)|vulva(2)|endometrium(2)|prostate(2)	c.C290G	GRCh37	CM053801|CM056557	CDKN2A	M	rs121913385	.						12	15	14					9																	21971111		2176	4259	6435	SO:0001583	missense	1029	exon2			CGTCGTGCACGGG	L27211	CCDS6510.1, CCDS6511.1, CCDS6511.2, CCDS56565.1	9p21	2014-09-17	2012-03-08		ENSG00000147889	ENSG00000147889			1787	protein-coding gene	gene with protein product		600160	"cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)"	CDKN2, MLM		8152487, 7606716	Standard	NM_058195		Approved	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf	uc003zpk.3	P42771	OTTHUMG00000019686	ENST00000304494.5:c.247C>G	chr9.hg19:g.21971111G>C	ENSP00000307101:p.His83Asp	71.0	0.0		35.0	17.0	NM_058195	A5X2G7|D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	Missense_Mutation	SNP	ENST00000304494.5	hg19	CCDS6510.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.6|22.6	4.311283|4.311283	0.81358|0.81358	.|.	.|.	ENSG00000147889|ENSG00000147889	ENST00000361570;ENST00000530628|ENST00000304494;ENST00000446177	T;T|T;T	0.80393|0.71341	-1.37;-1.3|-0.56;-0.56	5.93|5.93	5.93|5.93	0.95920|0.95920	.|Ankyrin repeat-containing domain (4);	0.000000|.	0.37261|.	N|.	0.002164|.	T|T	0.77370|0.77370	0.4120|0.4120	L|L	0.27053|0.27053	0.805|0.805	0.45962|0.45962	D|D	0.998784|0.998784	P|D	0.36144|0.71674	0.539|0.998	B|D	0.37480|0.79784	0.251|0.993	T|T	0.77773|0.77773	-0.2462|-0.2462	10|9	0.54805|0.52906	T|T	0.06|0.07	-15.192|-15.192	19.1026|19.1026	0.93279|0.93279	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	138|83	Q8N726|P42771	CD2A2_HUMAN|CD2A1_HUMAN	G|D	138;97|83	ENSP00000355153:A138G;ENSP00000432664:A97G|ENSP00000307101:H83D;ENSP00000394932:H83D	ENSP00000355153:A138G|ENSP00000307101:H83D	A|H	-|-	2|1	0|0	CDKN2A|CDKN2A	21961111|21961111	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.915000|0.915000	0.54546|0.54546	8.665000|8.665000	0.91144|0.91144	2.803000|2.803000	0.96430|0.96430	0.650000|0.650000	0.86243|0.86243	GCA|CAC	.	.		0.741	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	NM_000077		C	21971111	G	C	21971111	3	2	247	1	0	0	0	0	1	0	0	0	3163	1319	46	4	231	4	CDKN2A	9	21971111	Missense_Mutation	SNP	G	TCGA-ED-A7XP-01A-11D-A34Z-10	603174	21971111	119242320	32	33825										
C9orf135	138255	hgsc.bcm.edu	37	chr9	72459518	72459518	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	tgtgtaattcaacatatcggCgactgggaaccgatgaatcc	10	9	1	1	rs372154813		TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr9:72459518C>T	ENST00000377197.3	+	2	325	c.238C>T	c.(238-240)Cga>Tga	p.R80*	C9orf135_ENST00000527647.1_Nonsense_Mutation_p.R80*|C9orf135_ENST00000466872.2_Intron	NM_001010940.1	NP_001010940.1	Q5VTT2	CI135_HUMAN	chromosome 9 open reading frame 135	80						integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	7						AACATATCGGCGACTGGGAAC	0.383																																					p.R80X		Atlas-SNP	.											.	C9orf135	25	.	0			c.C238T						.	C	stop/ARG	0,4406		0,0,2203	81	84	83		238	1.9	0.6	9		83	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained	C9orf135	NM_001010940.1		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		80/230	72459518	1,13005	2203	4300	6503	SO:0001587	stop_gained	138255	exon2			TATCGGCGACTGG		CCDS35041.1	9q21.11	2013-06-07	2013-06-07	2013-06-07	ENSG00000204711	ENSG00000204711			31422	protein-coding gene	gene with protein product							Standard	XM_005251705		Approved		uc004ahl.3	Q5VTT2	OTTHUMG00000019985	ENST00000377197.3:c.238C>T	chr9.hg19:g.72459518C>T	ENSP00000366402:p.Arg80*	76.0	0.0		43.0	13.0	NM_001010940	A7E2U4|B2RN61	Nonsense_Mutation	SNP	ENST00000377197.3	hg19	CCDS35041.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.44|16.44	3.124574|3.124574	0.56613|0.56613	0.0|0.0	1.16E-4|1.16E-4	ENSG00000204711|ENSG00000204711	ENST00000480564|ENST00000377197;ENST00000527647	.|.	.|.	.|.	5.35|5.35	1.93|1.93	0.25924|0.25924	.|.	.|0.141488	.|0.32015	.|N	.|0.006707	T|.	0.24509|.	0.0594|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.35425|.	-0.9789|.	3|.	.|0.02654	.|T	.|1	-11.4236|-11.4236	11.3758|11.3758	0.49726|0.49726	0.6508:0.3492:0.0:0.0|0.6508:0.3492:0.0:0.0	.|.	.|.	.|.	.|.	V|X	53|80	.|.	.|ENSP00000366402:R80X	A|R	+|+	2|1	0|2	C9orf135|C9orf135	71649338|71649338	0.194000|0.194000	0.23325|0.23325	0.616000|0.616000	0.29078|0.29078	0.341000|0.341000	0.28922|0.28922	0.333000|0.333000	0.19768|0.19768	0.615000|0.615000	0.30124|0.30124	0.655000|0.655000	0.94253|0.94253	GCG|CGA	.	.		0.383	C9orf135-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000052591.1	NM_001010940		T	72459518	C	T	72459518	4	4	247	1	0	0	0	0	0	1	0	0	2460	760	27	1	244	1	C9orf135	9	72459518	Nonsense_Mutation	SNP	C	TCGA-ED-A7XP-01A-11D-A34Z-10	50488407	72459518	68753913	33	33826										
GPR120	338557	hgsc.bcm.edu	37	chr10	95326941	95326941	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	gggtcctgggcggcgggcgcGggcagtgctgctggcgctca	21	12	1	0	rs567274570	byFrequency	TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr10:95326941G>T	ENST00000371483.4	+	1	520	c.464G>T	c.(463-465)cGg>cTg	p.R155L	FFAR4_ENST00000371481.4_Missense_Mutation_p.R155L|FFAR4_ENST00000604414.1_Missense_Mutation_p.R155L	NM_181745.3	NP_859529.2	Q5NUL3	FFAR4_HUMAN	free fatty acid receptor 4	155					hormone secretion (GO:0046879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of inflammatory response (GO:0050728)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of glucose transport (GO:0010827)	endocytic vesicle (GO:0030139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fatty acid binding (GO:0005504)|taste receptor activity (GO:0008527)										CGGCGGGCGCGGGCAGTGCTG	0.726																																					p.R155L		Atlas-SNP	.											.	.	.	.	0			c.G464T						.						11	13	12					10																	95326941		2178	4225	6403	SO:0001583	missense	338557	exon1			GGGCGCGGGCAGT		CCDS31248.1, CCDS55720.1	10q23.33	2012-11-16	2012-11-16	2012-11-16	ENSG00000186188	ENSG00000186188		"GPCR / Class A : Fatty acid receptors"	19061	protein-coding gene	gene with protein product		609044	"G protein-coupled receptor 129", "G protein-coupled receptor 120", "omega-3 fatty acid receptor 1"	GPR129, GPR120, O3FAR1		20471368, 19723586, 15619630, 20813258	Standard	NM_181745		Approved	PGR4	uc010qnt.2	Q5NUL3	OTTHUMG00000034409	ENST00000371483.4:c.464G>T	chr10.hg19:g.95326941G>T	ENSP00000360538:p.Arg155Leu	58.0	0.0		48.0	17.0	NM_001195755	Q495H1|Q5VY25|Q5VY26|Q7Z605|Q86SM7	Missense_Mutation	SNP	ENST00000371483.4	hg19	CCDS31248.1	.	.	.	.	.	.	.	.	.	.	G	0.237	-1.016727	0.02078	.	.	ENSG00000186188	ENST00000371481;ENST00000371483	T;T	0.35973	1.28;1.28	5.22	3.29	0.37713	GPCR, rhodopsin-like superfamily (1);	0.308893	0.27622	N	0.018559	T	0.24928	0.0605	L	0.35644	1.08	0.23773	N	0.996882	B;B	0.10296	0.001;0.003	B;B	0.11329	0.001;0.006	T	0.20405	-1.0276	10	0.56958	D	0.05	-20.9351	4.555	0.12133	0.2115:0.0:0.5726:0.2159	.	155;155	Q5NUL3-2;Q5NUL3	.;O3FA1_HUMAN	L	155	ENSP00000360536:R155L;ENSP00000360538:R155L	ENSP00000360536:R155L	R	+	2	0	O3FAR1	95316931	0.217000	0.23597	0.768000	0.31515	0.034000	0.12701	0.328000	0.19681	0.675000	0.31264	-0.254000	0.11334	CGG	.	.		0.726	FFAR4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000083179.1	NM_181745		T	95326941	G	T	95326941	3	4	247	1	0	0	0	0	1	0	0	0	6644	1116	39	1	466	1	GPR120	10	95326941	Missense_Mutation	SNP	G	TCGA-ED-A7XP-01A-11D-A34Z-10		95326941	40207806	34	33827										
ZNF195	7748	hgsc.bcm.edu	37	chr11	3380429	3380429	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	ttttcacacttgtagggtttCtctccagtatgaattctctt	6	9	3	1			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr11:3380429C>A	ENST00000399602.4	-	6	1935	c.1809G>T	c.(1807-1809)gaG>gaT	p.E603D	ZNF195_ENST00000005082.9_Missense_Mutation_p.E580D|ZNF195_ENST00000354599.6_Missense_Mutation_p.E531D|ZNF195_ENST00000343338.7_Missense_Mutation_p.E535D|ZNF195_ENST00000526601.1_Missense_Mutation_p.E584D|ZNF195_ENST00000528796.1_Intron|ZNF195_ENST00000429541.2_Missense_Mutation_p.E535D	NM_001130520.2	NP_001123992.1	O14628	ZN195_HUMAN	zinc finger protein 195	603					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)	17		Medulloblastoma(188;0.00106)|Breast(177;0.00328)|all_neural(188;0.00681)|Ovarian(85;0.00965)		BRCA - Breast invasive adenocarcinoma(625;0.0361)|LUSC - Lung squamous cell carcinoma(625;0.2)		TGTAGGGTTTCTCTCCAGTAT	0.378																																					p.E603D		Atlas-SNP	.											ZNF195_ENST00000399602,NS,carcinoma,0,2	ZNF195	77	.	0			c.G1809T						.						65	68	67					11																	3380429		2064	4227	6291	SO:0001583	missense	7748	exon6			GGGTTTCTCTCCA		CCDS41604.1, CCDS44521.1, CCDS44522.1, CCDS55736.1, CCDS55737.1, CCDS58111.1	11p15.5	2013-01-08			ENSG00000005801	ENSG00000005801		"Zinc fingers, C2H2-type", "-"	12986	protein-coding gene	gene with protein product		602187				9344677	Standard	NM_001130520		Approved		uc001lxt.3	O14628	OTTHUMG00000011694	ENST00000399602.4:c.1809G>T	chr11.hg19:g.3380429C>A	ENSP00000382511:p.Glu603Asp	100.0	1.0		83.0	35.0	NM_001130520	A8K234|B3KTK2|B4DEL0|C9JLY9|L7MNK2|Q0VAJ6|Q658N8|Q6ZNA9	Missense_Mutation	SNP	ENST00000399602.4	hg19	CCDS44522.1	.	.	.	.	.	.	.	.	.	.	c	13.24	2.178400	0.38511	.	.	ENSG00000005801	ENST00000354599;ENST00000399602;ENST00000343338;ENST00000429541;ENST00000005082;ENST00000526601	T;T;T;T;T;T	0.26810	1.71;1.71;1.71;1.71;1.71;1.71	1.27	1.27	0.21489	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.34978	0.0916	L	0.49256	1.55	0.23913	N	0.996487	B;P;P;P;P;P	0.45902	0.02;0.868;0.552;0.84;0.606;0.84	B;B;P;B;P;B	0.55087	0.232;0.319;0.656;0.213;0.768;0.213	T	0.12630	-1.0540	9	0.72032	D	0.01	.	7.9805	0.30181	0.0:1.0:0.0:0.0	.	584;462;580;535;603;531	O14628-6;Q59EZ7;O14628-5;O14628-7;O14628;O14628-4	.;.;.;.;ZN195_HUMAN;.	D	531;603;535;535;580;584	ENSP00000346613:E531D;ENSP00000382511:E603D;ENSP00000344483:E535D;ENSP00000387998:E535D;ENSP00000005082:E580D;ENSP00000435828:E584D	ENSP00000005082:E580D	E	-	3	2	ZNF195	3337005	1.000000	0.71417	0.032000	0.17829	0.341000	0.28922	1.484000	0.35508	0.638000	0.30545	0.305000	0.20034	GAG	.	.		0.378	ZNF195-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000032321.2			A	3380429	C	A	3380429	3	1	247	1	0	0	0	0	1	0	0	0	17773	912	32	3	84	3	ZNF195	11	3380429	Missense_Mutation	SNP	C	TCGA-ED-A7XP-01A-11D-A34Z-10		3380429	131626087	35	33828										
CFL1	1072	hgsc.bcm.edu	37	chr11	65623665	65623665	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	tgaagacttacgcaccttcaTgtcgttgaacaccttgatga	8	10	1	5			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr11:65623665T>A	ENST00000525451.2	-	3	767	c.52A>T	c.(52-54)Atg>Ttg	p.M18L	CFL1_ENST00000531413.1_Start_Codon_SNP_p.M1L|CFL1_ENST00000527344.1_Start_Codon_SNP_p.M1L|CFL1_ENST00000534769.1_Missense_Mutation_p.M56L|CFL1_ENST00000524553.1_Start_Codon_SNP_p.M1L|CFL1_ENST00000531407.1_Start_Codon_SNP_p.M1L|CFL1_ENST00000308162.5_Missense_Mutation_p.M18L			P23528	COF1_HUMAN	cofilin 1 (non-muscle)	18	ADF-H. {ECO:0000255|PROSITE- ProRule:PRU00599}.				actin cytoskeleton organization (GO:0030036)|actin filament depolymerization (GO:0030042)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytoskeleton organization (GO:0007010)|establishment of cell polarity (GO:0030010)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|mitotic cytokinesis (GO:0000281)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell size (GO:0045792)|neural crest cell migration (GO:0001755)|neural fold formation (GO:0001842)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of actin filament depolymerization (GO:0030836)|protein import into nucleus (GO:0006606)|protein phosphorylation (GO:0006468)|regulation of cell morphogenesis (GO:0022604)|response to amino acid (GO:0043200)|response to virus (GO:0009615)|Rho protein signal transduction (GO:0007266)	cell-cell junction (GO:0005911)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				breast(1)|kidney(1)|large_intestine(2)|lung(2)	6				READ - Rectum adenocarcinoma(159;0.169)		CGCACCTTCATGTCGTTGAAC	0.527																																					p.M18L	Esophageal Squamous(90;820 1366 3932 32351 42291)	Atlas-SNP	.											.	CFL1	15	.	0			c.A52T						.						91	82	85					11																	65623665		2201	4297	6498	SO:0001583	missense	1072	exon2			CCTTCATGTCGTT	X95404	CCDS8114.1	11q13.1	2010-12-03			ENSG00000172757	ENSG00000172757			1874	protein-coding gene	gene with protein product		601442		CFL		8800436	Standard	NM_005507		Approved		uc001ofs.3	P23528		ENST00000525451.2:c.52A>T	chr11.hg19:g.65623665T>A	ENSP00000432660:p.Met18Leu	79.0	0.0		62.0	23.0	NM_005507	B3KUQ1|Q53Y87|Q9UCA2	Missense_Mutation	SNP	ENST00000525451.2	hg19	CCDS8114.1	.	.	.	.	.	.	.	.	.	.	T	16.74	3.205823	0.58234	.	.	ENSG00000172757	ENST00000525451;ENST00000308162;ENST00000527344;ENST00000531407;ENST00000524553;ENST00000534769;ENST00000531413;ENST00000532134;ENST00000530413;ENST00000534784;ENST00000526975	D;D;T;T;T;D;T;D;T;T;D	0.82526	-1.62;-1.62;-1.36;-1.36;-1.36;-1.62;-1.36;-1.62;-1.36;-1.36;-1.62	4.13	2.98	0.34508	Actin-binding, cofilin/tropomyosin type (1);	0.000000	0.85682	D	0.000000	T	0.62097	0.2400	N	0.03917	-0.325	0.80722	D	1	B	0.23316	0.083	B	0.35931	0.214	T	0.55062	-0.8199	10	0.02654	T	1	.	8.5544	0.33471	0.1726:0.0:0.0:0.8273	.	18	P23528	COF1_HUMAN	L	18;18;1;1;1;56;1;18;1;1;18	ENSP00000432660:M18L;ENSP00000309629:M18L;ENSP00000432155:M1L;ENSP00000433910:M1L;ENSP00000432226:M1L;ENSP00000431696:M56L;ENSP00000433131:M1L;ENSP00000436431:M18L;ENSP00000436899:M1L;ENSP00000433308:M1L;ENSP00000432153:M18L	ENSP00000309629:M18L	M	-	1	0	CFL1	65380241	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.938000	0.70170	0.892000	0.36259	0.533000	0.62120	ATG	.	.		0.527	CFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390701.3	NM_005507		A	65623665	T	A	65623665	3	1	247	1	0	0	0	0	1	0	0	0	3292	1464	51	4	460	4	CFL1	11	65623665	Missense_Mutation	SNP	T	TCGA-ED-A7XP-01A-11D-A34Z-10	62243236	65623665	69382851	36	33829										
C11orf54	28970	hgsc.bcm.edu	37	chr11	93494680	93494680	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	attgtttgtctgttatcttaGgggtttgatttgcgactgga	12	4	2	1			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr11:93494680G>A	ENST00000331239.4	+	9	953		c.e9-1		C11orf54_ENST00000540113.1_Splice_Site|C11orf54_ENST00000354421.3_Splice_Site|C11orf54_ENST00000528099.1_Splice_Site|C11orf54_ENST00000528288.1_Splice_Site			Q9H0W9	CK054_HUMAN	chromosome 11 open reading frame 54						metabolic process (GO:0008152)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|large_intestine(1)|lung(5)	8		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				TGTTATCTTAGGGGTTTGATT	0.343																																					.		Atlas-SNP	.											.	C11orf54	23	.	0			c.625-1G>A						.						136	134	134					11																	93494680		2201	4298	6499	SO:0001630	splice_region_variant	28970	exon8			ATCTTAGGGGTTT	AF092133	CCDS8294.1, CCDS66204.1, CCDS73365.1, CCDS73366.1	11q21	2012-08-09			ENSG00000182919	ENSG00000182919			30204	protein-coding gene	gene with protein product		615810				16522806	Standard	NM_014039		Approved	PTD012	uc001pef.3	Q9H0W9	OTTHUMG00000167452	ENST00000331239.4:c.775-1G>A	chr11.hg19:g.93494680G>A		129.0	0.0		140.0	40.0	NM_014039	A8K850|Q6FI88|Q6XYB0|Q96EI3|Q96IX1|Q9Y6B4	Splice_Site	SNP	ENST00000331239.4	hg19		.	.	.	.	.	.	.	.	.	.	G	20.3	3.959116	0.74016	.	.	ENSG00000182919	ENST00000528288;ENST00000331239;ENST00000528099;ENST00000354421;ENST00000540113;ENST00000524485;ENST00000533154	.	.	.	5.17	5.17	0.71159	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.6695	0.91506	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	C11orf54	93134328	1.000000	0.71417	1.000000	0.80357	0.804000	0.45430	9.308000	0.96247	2.407000	0.81776	0.561000	0.74099	.	.	.		0.343	C11orf54-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394671.1	NM_014039	Intron	A	93494680	G	A	93494680	5	1	247	1	0	0	0	0	0	0	1	0	1651	1014	35	3	650	3	C11orf54	11	93494680	Splice_Site	SNP	G	TCGA-ED-A7XP-01A-11D-A34Z-10	27871015	93494680	41511836	37	33830										
CASP4	837	hgsc.bcm.edu	37	chr11	104819259	104819259	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	ctgccactgaaagatacataCgtggcgttgaagagcagaaa	11	8	0	5	rs144482787		TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr11:104819259C>A	ENST00000444739.2	-	6	1836		c.e6+1		CASP4_ENST00000531333.1_5'Flank|CASP4_ENST00000393150.3_Splice_Site	NM_001225.3	NP_001216.1	P49662	CASP4_HUMAN	caspase 4, apoptosis-related cysteine peptidase						apoptotic process (GO:0006915)|execution phase of apoptosis (GO:0097194)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of inflammatory response (GO:0050727)	AIM2 inflammasome complex (GO:0097169)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|IPAF inflammasome complex (GO:0072557)|membrane (GO:0016020)|mitochondrion (GO:0005739)|NLRP3 inflammasome complex (GO:0072559)	cysteine-type endopeptidase activity (GO:0004197)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(1)|skin(1)|urinary_tract(2)	23		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000854)|Epithelial(105;0.00879)|all cancers(92;0.0357)		AAGATACATACGTGGCGTTGA	0.438																																					.		Atlas-SNP	.											.	CASP4	57	.	0			c.757+1G>T						.						124	91	102					11																	104819259		2202	4299	6501	SO:0001630	splice_region_variant	837	exon7			TACATACGTGGCG	U25804	CCDS8327.1, CCDS41704.1	11q22.2-q22.3	2006-02-17	2005-08-17		ENSG00000196954	ENSG00000196954		"Caspases"	1505	protein-coding gene	gene with protein product		602664	"caspase 4, apoptosis-related cysteine protease"			7797510, 9250871	Standard	NM_001225		Approved	ICE(rel)II, ICH-2, TX	uc001pid.1	P49662	OTTHUMG00000166078	ENST00000444739.2:c.925+1G>T	chr11.hg19:g.104819259C>A		70.0	0.0		46.0	15.0	NM_033306	A2NHL8|A2NHM0	Splice_Site	SNP	ENST00000444739.2	hg19	CCDS8327.1	.	.	.	.	.	.	.	.	.	.	C	11.86	1.763490	0.31228	.	.	ENSG00000196954	ENST00000444739;ENST00000393150;ENST00000355546	.	.	.	5.08	5.08	0.68730	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9508	0.79835	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CASP4	104324469	1.000000	0.71417	1.000000	0.80357	0.288000	0.27193	5.233000	0.65337	2.351000	0.79841	0.484000	0.47621	.	.	C|1.000;T|0.000		0.438	CASP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387751.1	NM_001225	Intron	A	104819259	C	A	104819259	5	1	247	1	0	0	0	0	0	0	1	0	2675	550	19	1	219	1	CASP4	11	104819259	Splice_Site	SNP	C	TCGA-ED-A7XP-01A-11D-A34Z-10	11324579	104819259	30187257	38	33831										
ARCN1	372	hgsc.bcm.edu	37	chr11	118452209	118452209	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	gaagatttggagaccctaagGctcttctcaagagtggtaag	12	7	2	3			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr11:118452209G>A	ENST00000264028.4	+	2	347	c.252G>A	c.(250-252)agG>agA	p.R84R	ARCN1_ENST00000534182.2_Intron|ARCN1_ENST00000359415.4_Silent_p.R125R|ARCN1_ENST00000392859.3_Intron	NM_001655.4	NP_001646.2	P48444	COPD_HUMAN	archain 1	84					adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer maturation (GO:0021691)|COPI coating of Golgi vesicle (GO:0048205)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|pigmentation (GO:0043473)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	clathrin adaptor complex (GO:0030131)|COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(3)|lung(4)|ovary(2)|urinary_tract(1)	13	all_hematologic(175;0.0349)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)		AGACCCTAAGGCTCTTCTCAA	0.383																																					p.R84R		Atlas-SNP	.											.	ARCN1	33	.	0			c.G252A						.						73	74	74					11																	118452209		2200	4295	6495	SO:0001819	synonymous_variant	372	exon2			CCTAAGGCTCTTC	X81197	CCDS8400.1, CCDS44749.1	11q23.3	2010-04-21	2003-01-29		ENSG00000095139	ENSG00000095139			649	protein-coding gene	gene with protein product		600820	"coatomer protein complex, subunit delta"	COPD		7782067, 8854871	Standard	NM_001655		Approved		uc001ptq.3	P48444	OTTHUMG00000166340	ENST00000264028.4:c.252G>A	chr11.hg19:g.118452209G>A		70.0	0.0		56.0	25.0	NM_001655	B4E1X2|E9PEU4|Q52M80	Silent	SNP	ENST00000264028.4	hg19	CCDS8400.1																																																																																			.	.		0.383	ARCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389278.1			A	118452209	G	A	118452209	2	1	247	1	0	0	0	0	0	0	0	1	842	1194	42	3		3	ARCN1	11	118452209	Silent	SNP	G	TCGA-ED-A7XP-01A-11D-A34Z-10	13632950	118452209	16554307	39	33832										
KDM5A	5927	hgsc.bcm.edu	37	chr12	443421	443421	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	acataccagtgcaagtagttGatggaataactccagtgatc	9	8	0	2			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr12:443421G>C	ENST00000399788.2	-	11	1838	c.1476C>G	c.(1474-1476)atC>atG	p.I492M	KDM5A_ENST00000382815.4_Missense_Mutation_p.I492M	NM_001042603.1	NP_001036068.1	P29375	KDM5A_HUMAN	lysine (K)-specific demethylase 5A	492	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|multicellular organismal development (GO:0007275)|negative regulation of histone deacetylase activity (GO:1901726)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			NS(2)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(29)|ovary(1)|prostate(5)|skin(6)|stomach(1)|urinary_tract(2)	77						GCAAGTAGTTGATGGAATAAC	0.393			T	NUP98	AML																																p.I492M		Atlas-SNP	.		Dom	yes		12	12p11	5927	"lysine (K)-specific demethylase 5A, JARID1A"		L	.	KDM5A	307	.	0			c.C1476G						.						131	124	126					12																	443421		2096	4248	6344	SO:0001583	missense	5927	exon11			GTAGTTGATGGAA		CCDS41736.1	12p13.33	2013-01-28	2009-04-06	2009-04-06	ENSG00000073614	ENSG00000073614		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	9886	protein-coding gene	gene with protein product		180202	"retinoblastoma-binding protein 2", "Jumonji, AT rich interactive domain 1A (RBBP2-like)", "jumonji, AT rich interactive domain 1A"	RBBP2, JARID1A		1857421	Standard	NM_001042603		Approved		uc001qif.1	P29375	OTTHUMG00000168055	ENST00000399788.2:c.1476C>G	chr12.hg19:g.443421G>C	ENSP00000382688:p.Ile492Met	148.0	0.0		86.0	39.0	NM_001042603	A8MV76|Q4LE72|Q86XZ1	Missense_Mutation	SNP	ENST00000399788.2	hg19	CCDS41736.1	.	.	.	.	.	.	.	.	.	.	G	18.49	3.635627	0.67130	.	.	ENSG00000073614	ENST00000261253;ENST00000399787;ENST00000399788;ENST00000382815;ENST00000544760	T;T;T	0.72615	-0.67;-0.67;-0.67	5.44	3.52	0.40303	Transcription factor jumonji/aspartyl beta-hydroxylase (2);Transcription factor jumonji (1);	0.000000	0.85682	D	0.000000	D	0.84142	0.5407	M	0.88181	2.935	0.54753	D	0.999981	D;D;D;D	0.89917	0.999;0.999;0.99;1.0	D;D;D;D	0.97110	0.998;0.989;0.965;1.0	D	0.83954	0.0318	10	0.87932	D	0	-12.2809	8.7855	0.34818	0.1926:0.0:0.8074:0.0	.	111;492;492;492	B4DVX3;F5H1F7;P29375;P29375-2	.;.;KDM5A_HUMAN;.	M	111;451;492;492;111	ENSP00000382688:I492M;ENSP00000372265:I492M;ENSP00000440622:I111M	ENSP00000261253:I111M	I	-	3	3	KDM5A	313682	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.998000	0.49465	0.580000	0.29522	0.655000	0.94253	ATC	.	.		0.393	KDM5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397812.1	NM_005056		C	443421	G	C	443421	3	2	247	1	0	0	0	0	1	0	0	0	8142	1280	45	4	3668	4	KDM5A	12	443421	Missense_Mutation	SNP	G	TCGA-ED-A7XP-01A-11D-A34Z-10		443421	133408474	40	33833										
LARP4	113251	hgsc.bcm.edu	37	chr12	50869602	50869602	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	atacctcagggagtgactcgAcgtaatggcaaagagcaata	11	8	1	2			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr12:50869602A>G	ENST00000398473.2	+	16	2242	c.2130A>G	c.(2128-2130)cgA>cgG	p.R710R	LARP4_ENST00000293618.8_Silent_p.R639R|LARP4_ENST00000518444.1_Silent_p.R709R|LARP4_ENST00000429001.3_Silent_p.R716R|LARP4_ENST00000347328.5_Silent_p.R639R	NM_052879.4|NM_199188.2	NP_443111.4|NP_954658.2	Q71RC2	LARP4_HUMAN	La ribonucleoprotein domain family, member 4	710					cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(1)|skin(2)|urinary_tract(1)	23						GAGTGACTCGACGTAATGGCA	0.453																																					p.R710R		Atlas-SNP	.											.	LARP4	58	.	0			c.A2130G						.						72	73	73					12																	50869602		1914	4133	6047	SO:0001819	synonymous_variant	113251	exon16			GACTCGACGTAAT	AY004310	CCDS41782.1, CCDS44879.1, CCDS44880.1, CCDS44879.2, CCDS53789.1, CCDS53790.1	12q13.12	2005-08-09			ENSG00000161813	ENSG00000161813		"La ribonucleoprotein domain containing"	24320	protein-coding gene	gene with protein product						12477932	Standard	NM_052879		Approved	PP13296	uc001rwp.2	Q71RC2	OTTHUMG00000163724	ENST00000398473.2:c.2130A>G	chr12.hg19:g.50869602A>G		141.0	0.0		91.0	20.0	NM_052879	A8K6T1|E9PDG5|G3XAA8|G5E976|Q5CZ97|Q6ZV14|Q96NF9	Silent	SNP	ENST00000398473.2	hg19	CCDS41782.1																																																																																			.	.		0.453	LARP4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374981.1	NM_052879		G	50869602	A	G	50869602	2	3	247	1	0	0	0	0	0	0	0	1	8639	262	10	2		2	LARP4	12	50869602	Silent	SNP	A	TCGA-ED-A7XP-01A-11D-A34Z-10	50426181	50869602	82982293	41	33834										
MYF5	4617	hgsc.bcm.edu	37	chr12	81112792	81112792	+	Frame_Shift_Del	DEL	G	G	-													0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	attcacagcctgcaactccaGgggcttctagttccaggctt							TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr12:81112792delG	ENST00000228644.3	+	3	882	c.730delG	c.(730-732)gggfs	p.G244fs		NM_005593.2	NP_005584.2	P13349	MYF5_HUMAN	myogenic factor 5	244					camera-type eye development (GO:0043010)|cartilage condensation (GO:0001502)|embryonic skeletal system morphogenesis (GO:0048704)|extracellular matrix organization (GO:0030198)|muscle cell differentiation (GO:0042692)|muscle cell fate commitment (GO:0042693)|muscle organ development (GO:0007517)|muscle tissue morphogenesis (GO:0060415)|ossification (GO:0001503)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell-matrix adhesion (GO:0001952)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal muscle cell differentiation (GO:0035914)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)	protein heterodimerization activity (GO:0046982)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(8)|lung(15)|ovary(2)|pancreas(1)	30						TGCAACTCCAGGGGCTTCTAG	0.507																																					p.P243fs		Atlas-Indel,Pindel	.											.	MYF5	78	.	0			c.729delA						.						81	81	81					12																	81112792		2203	4300	6503	SO:0001589	frameshift_variant	4617	exon3			.		CCDS9020.1	12q21	2013-05-21			ENSG00000111049	ENSG00000111049		"Basic helix-loop-helix proteins"	7565	protein-coding gene	gene with protein product		159990				8978788, 12105204	Standard	NM_005593		Approved	bHLHc2	uc001szg.2	P13349	OTTHUMG00000170166	ENST00000228644.3:c.730delG	chr12.hg19:g.81112792delG	ENSP00000228644:p.Gly244fs	76.0	0.0		75.0	22.0	NM_005593	Q6ISR9	Frame_Shift_Del	DEL	ENST00000228644.3	hg19	CCDS9020.1																																																																																			.	.		0.507	MYF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407757.1	NM_005593		-	81112792	G	-	81112792	7	5	247	1	0	1	0	1	0	0	0	0	10036	1000	35	0	740	0	MYF5	12	81112792	Frame_Shift_Del	DEL	G	TCGA-ED-A7XP-01A-11D-A34Z-10	30243190	81112792	52739103	42	33835										
COL4A2	1284	hgsc.bcm.edu	37	chr13	111141810	111141810	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	agggtgacaaaggtgccccaGggagagcaggcctgtatggc	17	9	0	2			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr13:111141810G>C	ENST00000360467.5	+	35	3532	c.3226G>C	c.(3226-3228)Ggg>Cgg	p.G1076R		NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	1076	Triple-helical region.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	extracellular matrix structural constituent (GO:0005201)			NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	80	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			AGGTGCCCCAGGGAGAGCAGG	0.493																																					p.G1076R		Atlas-SNP	.											.	COL4A2	178	.	0			c.G3226C						.						115	120	119					13																	111141810		2041	4187	6228	SO:0001583	missense	1284	exon35			GCCCCAGGGAGAG	AK025912	CCDS41907.1	13q34	2013-09-05			ENSG00000134871	ENSG00000134871		"Collagens"	2203	protein-coding gene	gene with protein product	"canstatin", "collagen type IV alpha 2"	120090				2439508, 3025878	Standard	NM_001846		Approved	FLJ22259, DKFZp686I14213	uc001vqx.3	P08572	OTTHUMG00000017344	ENST00000360467.5:c.3226G>C	chr13.hg19:g.111141810G>C	ENSP00000353654:p.Gly1076Arg	107.0	0.0		66.0	15.0	NM_001846	Q14052|Q548C3|Q5VZA9|Q66K23	Missense_Mutation	SNP	ENST00000360467.5	hg19	CCDS41907.1	.	.	.	.	.	.	.	.	.	.	G	18.78	3.695909	0.68386	.	.	ENSG00000134871	ENST00000360467;ENST00000257309	D	0.99637	-6.29	5.52	5.52	0.82312	.	0.000000	0.56097	D	0.000034	D	0.99792	0.9912	H	0.97465	4.01	0.48087	D	0.999583	D	0.89917	1.0	D	0.97110	1.0	D	0.97059	0.9769	10	0.72032	D	0.01	.	16.3909	0.83537	0.0:0.0:1.0:0.0	.	1076	P08572	CO4A2_HUMAN	R	1076	ENSP00000353654:G1076R	ENSP00000257309:G1076R	G	+	1	0	COL4A2	109939811	0.998000	0.40836	0.045000	0.18777	0.005000	0.04900	4.984000	0.63838	2.595000	0.87683	0.655000	0.94253	GGG	.	.		0.493	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846		C	111141810	G	C	111141810	3	2	247	1	0	0	0	0	1	0	0	0	3692	1000	35	4	3360	4	COL4A2	13	111141810	Missense_Mutation	SNP	G	TCGA-ED-A7XP-01A-11D-A34Z-10		111141810	4028068	43	33836										
SLC7A7	9056	hgsc.bcm.edu	37	chr14	23242904	23242904	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	caactgacatacacaggaccTggaggtaccttgtggcagac	11	11	0	2			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr14:23242904T>G	ENST00000397532.3	-	10	1976	c.1451A>C	c.(1450-1452)cAg>cCg	p.Q484P	SLC7A7_ENST00000555702.1_Missense_Mutation_p.Q484P|SLC7A7_ENST00000554517.1_Missense_Mutation_p.Q218P|SLC7A7_ENST00000397528.4_Missense_Mutation_p.Q484P|SLC7A7_ENST00000397529.2_Missense_Mutation_p.Q484P|SLC7A7_ENST00000285850.7_Missense_Mutation_p.Q484P|SLC7A7_ENST00000554061.1_5'UTR			Q9UM01	YLAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, y+L system), member 7	484					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|protein complex assembly (GO:0006461)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)			breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(2)	20	all_cancers(95;8.44e-05)			GBM - Glioblastoma multiforme(265;0.00741)		ACACAGGACCTGGAGGTACCT	0.473																																					p.Q484P		Atlas-SNP	.											.	SLC7A7	36	.	0			c.A1451C						.						112	98	103					14																	23242904		2203	4300	6503	SO:0001583	missense	9056	exon11			AGGACCTGGAGGT	AF092032	CCDS9574.1	14q11.2	2014-09-17	2011-07-12		ENSG00000155465	ENSG00000155465		"Solute carriers"	11065	protein-coding gene	gene with protein product		603593		LPI		9829974	Standard	NM_001126106		Approved	y+LAT-1	uc001wgs.4	Q9UM01	OTTHUMG00000028692	ENST00000397532.3:c.1451A>C	chr14.hg19:g.23242904T>G	ENSP00000380666:p.Gln484Pro	78.0	0.0		52.0	17.0	NM_001126105	B2RAU0|D3DS26|O95984|Q53XC1|Q86U07|Q9P2V5	Missense_Mutation	SNP	ENST00000397532.3	hg19	CCDS9574.1	.	.	.	.	.	.	.	.	.	.	T	19.70	3.876801	0.72180	.	.	ENSG00000155465	ENST00000285850;ENST00000555702;ENST00000397532;ENST00000404278;ENST00000397529;ENST00000397528;ENST00000554517	D;D;D;D;D;D	0.93366	-2.85;-2.85;-2.85;-2.85;-2.85;-3.21	5.52	5.52	0.82312	.	0.054265	0.85682	D	0.000000	D	0.96210	0.8764	M	0.76328	2.33	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.96618	0.9457	10	0.87932	D	0	.	13.6011	0.62020	0.0:0.0:0.0:1.0	.	484	Q9UM01	YLAT1_HUMAN	P	484;484;484;457;484;484;218	ENSP00000285850:Q484P;ENSP00000451881:Q484P;ENSP00000380666:Q484P;ENSP00000380663:Q484P;ENSP00000380662:Q484P;ENSP00000452083:Q218P	ENSP00000285850:Q484P	Q	-	2	0	SLC7A7	22312744	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	4.542000	0.60677	2.097000	0.63578	0.460000	0.39030	CAG	.	.		0.473	SLC7A7-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071636.3			G	23242904	T	G	23242904	3	3	247	1	0	0	0	0	1	0	0	0	14718	1580	55	5	88	5	SLC7A7	14	23242904	Missense_Mutation	SNP	T	TCGA-ED-A7XP-01A-11D-A34Z-10		23242904	84106636	44	33837										
RALGAPA1	253959	hgsc.bcm.edu	37	chr14	36008806	36008806	+	3'UTR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	tcatggacatgcggcttttgCtagttcgaggagacattgga	13	7	1	1			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr14:36008806C>T	ENST00000389698.3	-	0	6615				RALGAPA1_ENST00000307138.6_Missense_Mutation_p.S2065N|RALGAPA1_ENST00000258840.6_3'UTR	NM_014990.1	NP_055805.1	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1 (catalytic)						activation of Ral GTPase activity (GO:0032859)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(7)|large_intestine(14)|lung(21)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						GCGGCTTTTGCTAGTTCGAGG	0.537																																					p.S2065N		Atlas-SNP	.											.	RALGAPA1	289	.	0			c.G6194A						.						88	83	85					14																	36008806		2203	4297	6500	SO:0001624	3_prime_UTR_variant	253959	exon40			CTTTTGCTAGTTC	AK126975	CCDS32064.1, CCDS32065.1, CCDS61439.1	14q13.2	2012-01-26	2009-09-09	2009-09-09	ENSG00000174373	ENSG00000174373			17770	protein-coding gene	gene with protein product	"tuberin-like protein 1", "GAP-related interacting protein to E12"	608884	"GTPase activating RANGAP domain-like 1", "GTPase activating Rap/RanGAP domain-like 1"	GARNL1		19520869	Standard	NM_014990		Approved	GRIPE, DKFZp667F074, KIAA0884, Tulip1, RalGAPalpha1	uc001wtj.3	Q6GYQ0	OTTHUMG00000170619	ENST00000389698.3:c.*114G>A	chr14.hg19:g.36008806C>T		65.0	0.0		64.0	18.0	NM_194301	A6NMA4|B9EK38|C5NU19|O94960|Q6GYP9|Q6ZT23|Q86YF3|Q86YF5|Q8ND69	Missense_Mutation	SNP	ENST00000389698.3	hg19	CCDS32065.1	.	.	.	.	.	.	.	.	.	.	C	18.10	3.547936	0.65311	.	.	ENSG00000174373	ENST00000307138;ENST00000554259	D;D	0.97114	-3.51;-4.25	5.53	5.53	0.82687	.	0.190858	0.38111	N	0.001815	D	0.95462	0.8526	N	0.22421	0.69	0.80722	D	1	P	0.46784	0.884	P	0.47864	0.559	D	0.95613	0.8674	10	0.54805	T	0.06	-7.7228	19.8246	0.96612	0.0:1.0:0.0:0.0	.	2065	Q6GYQ0-2	.	N	2065;704	ENSP00000302647:S2065N;ENSP00000451133:S704N	ENSP00000302647:S2065N	S	-	2	0	RALGAPA1	35078557	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.654000	0.67974	2.751000	0.94390	0.561000	0.74099	AGC	.	.		0.537	RALGAPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409829.1	XM_210022		T	36008806	C	T	36008806	1	4	247	0	1	0	0	0	0	0	0	0	13028	797	28	3		3	RALGAPA1	14	36008806	3'UTR	SNP	C	TCGA-ED-A7XP-01A-11D-A34Z-10	12765902	36008806	71340734	45	33838										
FLRT2	23768	hgsc.bcm.edu	37	chr14	86089754	86089754	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	cccatttacaccccaaatggGggcattaattacacagactg	7	12	0	1			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr14:86089754G>A	ENST00000330753.4	+	2	2663	c.1896G>A	c.(1894-1896)ggG>ggA	p.G632G	FLRT2_ENST00000554746.1_Silent_p.G632G	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	632					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		CCCCAAATGGGGGCATTAATT	0.493																																					p.G632G		Atlas-SNP	.											.	FLRT2	168	.	0			c.G1896A						.						201	210	207					14																	86089754		2203	4296	6499	SO:0001819	synonymous_variant	23768	exon2			AAATGGGGGCATT	AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070		"Fibronectin type III domain containing"	3761	protein-coding gene	gene with protein product		604807				10644439, 16872596	Standard	XM_005267490		Approved		uc001xvr.3	O43155		ENST00000330753.4:c.1896G>A	chr14.hg19:g.86089754G>A		81.0	0.0		55.0	26.0	NM_013231	A0AV84|B7ZLP3	Silent	SNP	ENST00000330753.4	hg19	CCDS9877.1																																																																																			.	.		0.493	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1			A	86089754	G	A	86089754	2	1	247	1	0	0	0	0	0	0	0	1	5947	1219	43	3		3	FLRT2	14	86089754	Silent	SNP	G	TCGA-ED-A7XP-01A-11D-A34Z-10	50080948	86089754	21259786	46	33839										
C16orf70	80262	hgsc.bcm.edu	37	chr16	67159932	67159932	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	actaatgtttgatgctttcaAtcagagacttaaggtaacta	7	6	2	2	rs528433156		TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr16:67159932A>G	ENST00000219139.3	+	3	406	c.218A>G	c.(217-219)aAt>aGt	p.N73S	C16orf70_ENST00000569683.1_3'UTR|C16orf70_ENST00000569600.1_Missense_Mutation_p.N73S	NM_025187.3	NP_079463.2	Q9BSU1	CP070_HUMAN	chromosome 16 open reading frame 70	73										cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(3)|skin(1)	17		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0017)|Epithelial(162;0.00655)|all cancers(182;0.0579)		GATGCTTTCAATCAGAGACTT	0.373													A|||	1	0.000199681	0	0	5008	,	,		22231	0		0	False		,,,				2504	0.001				p.N73S		Atlas-SNP	.											.	C16orf70	38	.	0			c.A218G						.						137	136	137					16																	67159932		2200	4300	6500	SO:0001583	missense	80262	exon3			CTTTCAATCAGAG	AK022138	CCDS10828.1	16q22.1	2011-01-25	2006-04-12	2006-04-12	ENSG00000125149	ENSG00000125149			29564	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 6"	C16orf6, LIN10		12477932	Standard	NM_025187		Approved	lin-10, FLJ12076	uc002erd.3	Q9BSU1	OTTHUMG00000137510	ENST00000219139.3:c.218A>G	chr16.hg19:g.67159932A>G	ENSP00000219139:p.Asn73Ser	36.0	0.0		30.0	9.0	NM_025187	Q9HA86	Missense_Mutation	SNP	ENST00000219139.3	hg19	CCDS10828.1	.	.	.	.	.	.	.	.	.	.	A	12.72	2.022540	0.35701	.	.	ENSG00000125149	ENST00000219139	.	.	.	6.17	3.93	0.45458	.	0.000000	0.85682	D	0.000000	T	0.17066	0.0410	N	0.02674	-0.535	0.52501	D	0.999953	B;B	0.24092	0.026;0.097	B;B	0.24269	0.02;0.052	T	0.17471	-1.0368	9	0.02654	T	1	-16.5417	6.8364	0.23939	0.7923:0.0:0.0731:0.1346	.	51;73	Q9BSU1-2;Q9BSU1	.;CP070_HUMAN	S	73	.	ENSP00000219139:N73S	N	+	2	0	C16orf70	65717433	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.883000	0.69721	0.556000	0.29098	0.533000	0.62120	AAT	.	.		0.373	C16orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268829.2	NM_025187		G	67159932	A	G	67159932	3	3	247	1	0	0	0	0	1	0	0	0	1831	101	4	2	228	2	C16orf70	16	67159932	Missense_Mutation	SNP	A	TCGA-ED-A7XP-01A-11D-A34Z-10		67159932	23194821	47	33840										
PSMB10	5699	hgsc.bcm.edu	37	chr16	67968561	67968561	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	tgtggttccaggcacaaagtGgtagcggccagacctgggag	16	9	0	1			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr16:67968561G>A	ENST00000358514.4	-	8	1061	c.724C>T	c.(724-726)Cac>Tac	p.H242Y	CTRL_ENST00000576408.1_5'Flank|CTC-479C5.12_ENST00000573493.1_3'UTR|CTRL_ENST00000574481.1_5'Flank	NM_002801.3	NP_002792.1	P40306	PSB10_HUMAN	proteasome (prosome, macropain) subunit, beta type, 10	242					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cell morphogenesis (GO:0000902)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|humoral immune response (GO:0006959)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|T cell proliferation (GO:0042098)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|spermatoproteasome complex (GO:1990111)	threonine-type endopeptidase activity (GO:0004298)			NS(2)|endometrium(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00415)|Epithelial(162;0.0182)|all cancers(182;0.119)	Carfilzomib(DB08889)	GGCACAAAGTGGTAGCGGCCA	0.587																																					p.H242Y		Atlas-SNP	.											.	PSMB10	19	.	0			c.C724T						.						124	120	121					16																	67968561		2198	4300	6498	SO:0001583	missense	5699	exon8			CAAAGTGGTAGCG	Y13640	CCDS10853.1	16q22.1	2008-02-05			ENSG00000205220	ENSG00000205220		"Proteasome (prosome, macropain) subunits"	9538	protein-coding gene	gene with protein product		176847		MECL1		8268911	Standard	NM_002801		Approved	LMP10, MGC1665, beta2i	uc002eux.2	P40306	OTTHUMG00000137553	ENST00000358514.4:c.724C>T	chr16.hg19:g.67968561G>A	ENSP00000351314:p.His242Tyr	62.0	0.0		53.0	22.0	NM_002801	B2R5J4|Q5U098	Missense_Mutation	SNP	ENST00000358514.4	hg19	CCDS10853.1	.	.	.	.	.	.	.	.	.	.	G	16.38	3.106125	0.56291	.	.	ENSG00000205220	ENST00000358514	T	0.29655	1.56	5.78	-0.444	0.12245	Proteasome beta subunit, C-terminal (1);	0.780910	0.12241	N	0.486502	T	0.19565	0.0470	L	0.36672	1.1	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.21484	-1.0244	10	0.51188	T	0.08	-10.3564	3.8928	0.09127	0.0787:0.1311:0.3873:0.4029	.	242	P40306	PSB10_HUMAN	Y	242	ENSP00000351314:H242Y	ENSP00000351314:H242Y	H	-	1	0	PSMB10	66526062	0.288000	0.24324	0.103000	0.21229	0.785000	0.44390	0.484000	0.22308	0.316000	0.23135	0.555000	0.69702	CAC	.	.		0.587	PSMB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268887.1	NM_002801		A	67968561	G	A	67968561	3	1	247	1	0	0	0	0	1	0	0	0	12687	1348	47	3	101	3	PSMB10	16	67968561	Missense_Mutation	SNP	G	TCGA-ED-A7XP-01A-11D-A34Z-10	808629	67968561	22386192	48	33841										
TP53	7157	hgsc.bcm.edu	37	chr17	7577534	7577534	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	gtgatgatggtgaggatgggCctccggttcatgccgcccat	15	10	1	3	rs28934571		TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr17:7577534C>A	ENST00000269305.4	-	7	936	c.747G>T	c.(745-747)agG>agT	p.R249S	TP53_ENST00000445888.2_Missense_Mutation_p.R249S|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.R249S|TP53_ENST00000455263.2_Missense_Mutation_p.R249S|TP53_ENST00000413465.2_Missense_Mutation_p.R249S|TP53_ENST00000420246.2_Missense_Mutation_p.R249S	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	249	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> G (in sporadic cancers; somatic mutation).|R -> I (in a sporadic cancer; somatic mutation).|R -> K (in sporadic cancers; somatic mutation).|R -> M (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:17224074}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> S (in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; dbSNP:rs28934571). {ECO:0000269|PubMed:1694291, ECO:0000269|PubMed:16959974}.|R -> T (in sporadic cancers; somatic mutation).|R -> W (in sporadic cancers; somatic mutation).|RP -> SA (in a sporadic cancer; somatic mutation).|RP -> SS (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R249S(348)|p.0?(8)|p.R249R(5)|p.?(5)|p.M246_P250delMNRRP(2)|p.R248_P250delRRP(1)|p.R249_P250delRP(1)|p.R249_P250insR(1)|p.R249_P250>SS(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*14(1)|p.R249_T256delRPILTIIT(1)|p.P250fs*14(1)|p.R249_I251delRPI(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TGAGGATGGGCCTCCGGTTCA	0.572		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.R249S	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,right_lower_lobe,carcinoma,-2,1	TP53	33396	.	378	Substitution - Missense(348)|Deletion - In frame(8)|Whole gene deletion(8)|Unknown(5)|Substitution - coding silent(5)|Insertion - Frameshift(1)|Insertion - In frame(1)|Deletion - Frameshift(1)|Complex - compound substitution(1)	liver(240)|lung(44)|upper_aerodigestive_tract(12)|breast(12)|central_nervous_system(10)|stomach(7)|ovary(6)|prostate(6)|cervix(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(5)|biliary_tract(5)|urinary_tract(5)|bone(4)|endometrium(3)|oesophagus(3)|skin(2)|peritoneum(1)|kidney(1)|salivary_gland(1)|pancreas(1)	c.G747T						.						155	113	127					17																	7577534		2203	4300	6503	SO:0001583	missense	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GATGGGCCTCCGG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.747G>T	chr17.hg19:g.7577534C>A	ENSP00000269305:p.Arg249Ser	94.0	0.0		48.0	27.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.344264	0.61073	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D;D	0.99865	-7.29;-7.29;-7.29;-7.29;-7.29;-7.29;-7.29	4.62	-0.0929	0.13654	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99792	0.9912	M	0.92367	3.3	0.50039	D	0.999848	D;D;D;D;D	0.89917	0.996;0.996;0.997;0.99;1.0	D;D;D;D;D	0.79108	0.968;0.966;0.981;0.955;0.992	D	0.98720	1.0708	10	0.72032	D	0.01	-3.0658	3.2479	0.06803	0.1392:0.5551:0.1362:0.1695	rs28934571	249;249;249;249;249	P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;P53_HUMAN;.;.	S	249;249;249;249;249;249;238;117	ENSP00000410739:R249S;ENSP00000352610:R249S;ENSP00000269305:R249S;ENSP00000398846:R249S;ENSP00000391127:R249S;ENSP00000391478:R249S;ENSP00000425104:R117S	ENSP00000269305:R249S	R	-	3	2	TP53	7518259	0.011000	0.17503	0.998000	0.56505	0.783000	0.44284	-1.379000	0.02554	0.253000	0.21552	0.462000	0.41574	AGG	.	.		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577534	C	A	7577534	3	1	247	1	0	0	0	0	1	0	0	0	16396	738	26	3	543	3	TP53	17	7577534	Missense_Mutation	SNP	C	TCGA-ED-A7XP-01A-11D-A34Z-10		7577534	73617676	49	33842										
RNF43	54894	hgsc.bcm.edu	37	chr17	56435197	56435197	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	tctgtgggtgtcgggcagagAggctggatttttgcaagttg	17	5	1	1	rs552361417		TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr17:56435197A>T	ENST00000584437.1	-	8	3895	c.1940T>A	c.(1939-1941)cTc>cAc	p.L647H	RNF43_ENST00000581868.1_Missense_Mutation_p.L520H|RNF43_ENST00000583753.1_Missense_Mutation_p.L606H|RNF43_ENST00000500597.2_Missense_Mutation_p.L606H|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000577625.1_Missense_Mutation_p.L520H|RNF43_ENST00000577716.1_Missense_Mutation_p.L647H|RNF43_ENST00000407977.2_Missense_Mutation_p.L647H			Q68DV7	RNF43_HUMAN	ring finger protein 43	647	Pro-rich.				negative regulation of Wnt signaling pathway (GO:0030178)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|stem cell proliferation (GO:0072089)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(5)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(14)|lung(9)|ovary(2)|pancreas(10)|prostate(1)|skin(4)	60	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TCGGGCAGAGAGGCTGGATTT	0.647																																					p.L647H		Atlas-SNP	.											.	RNF43	157	.	0			c.T1940A						.						70	80	77					17																	56435197		2200	4295	6495	SO:0001583	missense	54894	exon9			GCAGAGAGGCTGG		CCDS11607.1	17q23.2	2013-01-09						"RING-type (C3HC4) zinc fingers"	18505	protein-coding gene	gene with protein product		612482					Standard	NM_017763		Approved	FLJ20315, DKFZp781H0392, URCC	uc002iwh.4	Q68DV7		ENST00000584437.1:c.1940T>A	chr17.hg19:g.56435197A>T	ENSP00000463069:p.Leu647His	89.0	0.0		82.0	7.0	NM_017763	A8K4R2|B7Z443|B7Z5D5|B7Z5J5|Q65ZA4|Q6AI04|Q9NXD0	Missense_Mutation	SNP	ENST00000584437.1	hg19	CCDS11607.1	.	.	.	.	.	.	.	.	.	.	A	5.076	0.199650	0.09652	.	.	ENSG00000108375	ENST00000407977;ENST00000500597	T;T	0.22134	1.97;1.97	4.66	3.53	0.40419	.	0.906266	0.09229	N	0.830816	T	0.16896	0.0406	L	0.29908	0.895	0.09310	N	1	B;B;B	0.09022	0.001;0.002;0.001	B;B;B	0.12156	0.004;0.007;0.001	T	0.26052	-1.0114	10	0.87932	D	0	-18.1991	7.4488	0.27227	0.7895:0.0:0.0:0.2105	.	606;647;647	Q68DV7-2;Q68DV7-4;Q68DV7	.;.;RNF43_HUMAN	H	647;606	ENSP00000385328:L647H;ENSP00000441969:L606H	ENSP00000385328:L647H	L	-	2	0	RNF43	53790196	0.992000	0.36948	0.408000	0.26446	0.302000	0.27658	1.577000	0.36515	0.737000	0.32582	0.172000	0.16884	CTC	.	.		0.647	RNF43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444713.1	NM_017763		T	56435197	A	T	56435197	3	4	247	1	0	0	0	0	1	0	0	0	13510	304	11	4	419	4	RNF43	17	56435197	Missense_Mutation	SNP	A	TCGA-ED-A7XP-01A-11D-A34Z-10	48857663	56435197	24760013	50	33843										
C17orf47	284083	hgsc.bcm.edu	37	chr17	56620718	56620718	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	caccatcagaatctttaaggAcagagagtttgagcaatgag	10	7	2	4			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr17:56620718A>G	ENST00000321691.3	-	1	1011	c.830T>C	c.(829-831)gTc>gCc	p.V277A	RP11-112H10.4_ENST00000578022.1_RNA|SEPT4_ENST00000412945.3_5'Flank|SEPT4_ENST00000457347.2_5'Flank|RP11-112H10.4_ENST00000580589.1_RNA|RP11-112H10.4_ENST00000580769.1_RNA	NM_001038704.2	NP_001033793	Q8NEP4	CQ047_HUMAN	chromosome 17 open reading frame 47	277										NS(1)|breast(2)|endometrium(1)|kidney(4)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	24	Medulloblastoma(34;0.127)|all_neural(34;0.237)					ATCTTTAAGGACAGAGAGTTT	0.453																																					p.V277A		Atlas-SNP	.											.	C17orf47	59	.	0			c.T830C						.						98	95	96					17																	56620718		2203	4300	6503	SO:0001583	missense	284083	exon1			TTAAGGACAGAGA		CCDS32691.1	17q23.2	2012-10-11			ENSG00000181013	ENSG00000181013			26844	protein-coding gene	gene with protein product							Standard	NM_001038704		Approved	FLJ40121	uc002iwq.2	Q8NEP4	OTTHUMG00000179244	ENST00000321691.3:c.830T>C	chr17.hg19:g.56620718A>G	ENSP00000354874:p.Val277Ala	107.0	0.0		130.0	50.0	NM_001038704	Q8N821	Missense_Mutation	SNP	ENST00000321691.3	hg19	CCDS32691.1	.	.	.	.	.	.	.	.	.	.	A	16.43	3.120417	0.56613	.	.	ENSG00000181013	ENST00000321691	T	0.37058	1.22	5.46	2.08	0.27032	.	0.976288	0.08395	N	0.952368	T	0.24624	0.0597	N	0.24115	0.695	0.09310	N	1	B	0.23891	0.093	B	0.19666	0.026	T	0.26950	-1.0088	10	0.59425	D	0.04	0.2948	6.5089	0.22210	0.7201:0.0:0.2799:0.0	.	277	Q8NEP4	CQ047_HUMAN	A	277	ENSP00000354874:V277A	ENSP00000354874:V277A	V	-	2	0	C17orf47	53975717	0.904000	0.30761	0.044000	0.18714	0.075000	0.17131	1.330000	0.33781	0.380000	0.24823	-0.376000	0.06991	GTC	.	.		0.453	C17orf47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445443.1	NM_001038704		G	56620718	A	G	56620718	3	3	247	1	0	0	0	0	1	0	0	0	1860	275	10	2	890	2	C17orf47	17	56620718	Missense_Mutation	SNP	A	TCGA-ED-A7XP-01A-11D-A34Z-10	185521	56620718	24574492	51	33844										
SLC26A11	6448	hgsc.bcm.edu	37	chr17	78196581	78196581	+	5'Flank	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	ctacaccttccatgagcccgCctacgctgtgctgctggcct	9	17	0	1			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr17:78196581C>T	ENST00000326317.6	-	0	0				SLC26A11_ENST00000361193.3_Missense_Mutation_p.A121V|SLC26A11_ENST00000571602.1_3'UTR|SGSH_ENST00000572208.1_5'Flank|SLC26A11_ENST00000411502.3_Missense_Mutation_p.A121V|SGSH_ENST00000570923.1_5'Flank|SLC26A11_ENST00000546047.2_Missense_Mutation_p.A121V|SLC26A11_ENST00000572725.1_Missense_Mutation_p.A121V|SGSH_ENST00000534910.1_5'Flank	NM_000199.3	NP_000190.1	P51688	SPHM_HUMAN	N-sulfoglucosamine sulfohydrolase						carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|proteoglycan metabolic process (GO:0006029)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	catalytic activity (GO:0003824)|metal ion binding (GO:0046872)|N-sulfoglucosamine sulfohydrolase activity (GO:0016250)|sulfuric ester hydrolase activity (GO:0008484)			central_nervous_system(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			CATGAGCCCGCCTACGCTGTG	0.617																																					p.A121V		Atlas-SNP	.											.	SLC26A11	60	.	0			c.C362T						.						176	150	159					17																	78196581		2203	4300	6503	SO:0001631	upstream_gene_variant	284129	exon4			AGCCCGCCTACGC	BC047318	CCDS11770.1	17q25.3	2011-11-08	2008-07-31			ENSG00000181523	3.10.1.1		10818	protein-coding gene	gene with protein product	"sulfamidase", "mucopolysaccharidosis type IIIA"	605270				7493035	Standard	NM_000199		Approved	HSS, MPS3A, SFMD	uc002jxz.4	P51688			chr17.hg19:g.78196581C>T	Exception_encountered	86.0	0.0		93.0	47.0	NM_173626	A8K5E2	Missense_Mutation	SNP	ENST00000326317.6	hg19	CCDS11770.1	.	.	.	.	.	.	.	.	.	.	c	10.67	1.416625	0.25552	.	.	ENSG00000181045	ENST00000411502;ENST00000546047;ENST00000361193	D;D;D	0.94330	-3.4;-3.4;-3.4	4.69	4.69	0.59074	.	0.508626	0.21916	N	0.067228	D	0.87470	0.6185	N	0.25890	0.77	0.09310	N	1	B	0.13145	0.007	B	0.14023	0.01	T	0.75263	-0.3379	10	0.26408	T	0.33	-24.8582	12.2081	0.54363	0.0:0.9145:0.0:0.0855	.	121	Q86WA9	S2611_HUMAN	V	121	ENSP00000403998:A121V;ENSP00000440724:A121V;ENSP00000355384:A121V	ENSP00000355384:A121V	A	+	2	0	SLC26A11	75811176	0.558000	0.26554	0.188000	0.23233	0.937000	0.57800	0.467000	0.22035	2.183000	0.69458	0.455000	0.32223	GCC	.	.		0.617	SGSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437695.1	NM_000199		T	78196581	C	T	78196581	1	4	247	0	1	0	0	0	0	0	0	0	14531	739	26	3		3	SLC26A11	17	78196581	5'Flank	SNP	C	TCGA-ED-A7XP-01A-11D-A34Z-10	21575863	78196581	2998629	52	33845										
AMH	268	hgsc.bcm.edu	37	chr19	2249687	2249687	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	gccctctctacggcggctggGggcctggctgcgggaccctg	17	15	1	0			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr19:2249687G>T	ENST00000221496.4	+	1	378	c.356G>T	c.(355-357)gGg>gTg	p.G119V	MIR4321_ENST00000592276.1_RNA	NM_000479.3	NP_000470	P03971	MIS_HUMAN	anti-Mullerian hormone	119					aging (GO:0007568)|cell-cell signaling (GO:0007267)|gonadal mesoderm development (GO:0007506)|Mullerian duct regression (GO:0001880)|positive regulation of gene expression (GO:0010628)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|preantral ovarian follicle growth (GO:0001546)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|sex determination (GO:0007530)|sex differentiation (GO:0007548)|urogenital system development (GO:0001655)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone activity (GO:0005179)|receptor binding (GO:0005102)			lung(2)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CGGCGGCTGGGGGCCTGGCTG	0.716									Persistant Mullerian Duct Syndrome (type I and II)																												p.G119V		Atlas-SNP	.											.	AMH	12	.	0			c.G356T						.						4	5	5					19																	2249687		1704	3520	5224	SO:0001583	missense	268	exon1	Familial Cancer Database	PMDS, Persistent Oviduct Syndrome	GGCTGGGGGCCTG	K03474	CCDS12085.1	19p13.3	2014-01-30				ENSG00000104899		"Endogenous ligands"	464	protein-coding gene	gene with protein product		600957				3754790, 18784351	Standard	NM_000479		Approved	MIS	uc002lvh.2	P03971		ENST00000221496.4:c.356G>T	chr19.hg19:g.2249687G>T	ENSP00000221496:p.Gly119Val	32.0	0.0		41.0	16.0	NM_000479	O75246|Q6GTN3	Missense_Mutation	SNP	ENST00000221496.4	hg19	CCDS12085.1	.	.	.	.	.	.	.	.	.	.	G	13.73	2.325721	0.41197	.	.	ENSG00000104899	ENST00000221496	D	0.81579	-1.51	3.91	1.72	0.24424	Anti-Mullerian hormone, N-terminal (1);	1.022220	0.07832	U	0.961496	T	0.75064	0.3799	L	0.46157	1.445	0.09310	N	1	P	0.36412	0.552	B	0.39339	0.297	T	0.60702	-0.7211	10	0.40728	T	0.16	-2.3679	6.2185	0.20667	0.1206:0.0:0.6967:0.1827	.	119	P03971	MIS_HUMAN	V	119	ENSP00000221496:G119V	ENSP00000221496:G119V	G	+	2	0	AMH	2200687	0.000000	0.05858	0.001000	0.08648	0.604000	0.37047	0.395000	0.20850	0.105000	0.17753	0.456000	0.33151	GGG	.	.		0.716	AMH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451276.3	NM_000479		T	2249687	G	T	2249687	3	4	247	1	0	0	0	0	1	0	0	0	572	1232	43	3	358	3	AMH	19	2249687	Missense_Mutation	SNP	G	TCGA-ED-A7XP-01A-11D-A34Z-10		2249687	56879296	53	33846										
IFI30	10437	hgsc.bcm.edu	37	chr19	18284657	18284657	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	tttgcccctgctgcgatgacCctgtcgccacttctgctgtt	9	15	1	1			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr19:18284657C>T	ENST00000407280.3	+	1	181	c.6C>T	c.(4-6)acC>acT	p.T2T	PIK3R2_ENST00000593731.1_3'UTR	NM_006332.3	NP_006323.2	P13284	GILT_HUMAN	interferon, gamma-inducible protein 30	2					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of fibroblast proliferation (GO:0048147)|protein stabilization (GO:0050821)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	oxidoreductase activity, acting on a sulfur group of donors (GO:0016667)			endometrium(1)|kidney(2)|large_intestine(1)|stomach(1)	5						CTGCGATGACCCTGTCGCCAC	0.667																																					p.T2T		Atlas-SNP	.											IFI30,NS,carcinoma,0,1	IFI30	12	.	0			c.C6T						.						18	20	19					19																	18284657		2035	3901	5936	SO:0001819	synonymous_variant	10437	exon1			GATGACCCTGTCG	J03909	CCDS46015.1	19p13.1	2008-07-16				ENSG00000216490			5398	protein-coding gene	gene with protein product	"gamma-interferon-inducible lysosomal thiol reductase", "interferon gamma-inducible protein 30 preproprotein"	604664				3136170, 10639150	Standard	NM_006332		Approved	IFI-30, GILT, IP30, MGC32056	uc002nic.1	P13284		ENST00000407280.3:c.6C>T	chr19.hg19:g.18284657C>T		24.0	0.0		15.0	4.0	NM_006332	Q76MF9|Q8NEI4|Q8WU77|Q9UL08	Silent	SNP	ENST00000407280.3	hg19	CCDS46015.1																																																																																			.	.		0.667	IFI30-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466396.3	NM_006332		T	18284657	C	T	18284657	2	4	247	1	0	0	0	0	0	0	0	1	7524	610	22	3		3	IFI30	19	18284657	Silent	SNP	C	TCGA-ED-A7XP-01A-11D-A34Z-10	16034970	18284657	40844326	54	33847										
LILRA2	11027	hgsc.bcm.edu	37	chr19	55086255	55086255	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	ccctgtggtgaccttaggagGgaacgtgaccctccagtgtg	14	11	0	2			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr19:55086255G>T	ENST00000251377.3	+	5	543	c.410G>T	c.(409-411)gGg>gTg	p.G137V	LILRA2_ENST00000495786.1_3'UTR|LILRA2_ENST00000251376.3_Missense_Mutation_p.G137V|LILRB1_ENST00000396321.2_Intron|LILRB1_ENST00000448689.1_Intron|LILRB1_ENST00000418536.2_Intron|LILRA2_ENST00000391737.1_Missense_Mutation_p.G125V|LILRA2_ENST00000391738.3_Missense_Mutation_p.G137V			Q8N149	LIRA2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 2	137	Ig-like C2-type 2.				defense response (GO:0006952)|immune system process (GO:0002376)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(33)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	50				GBM - Glioblastoma multiforme(193;0.0963)		ACCTTAGGAGGGAACGTGACC	0.557																																					p.G137V		Atlas-SNP	.											.	LILRA2	99	.	0			c.G410T						.						159	145	150					19																	55086255		2203	4300	6503	SO:0001583	missense	11027	exon4			TAGGAGGGAACGT	U82275	CCDS12900.1, CCDS46179.1, CCDS74453.1	19q13.4	2013-01-11			ENSG00000239998	ENSG00000239998		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6603	protein-coding gene	gene with protein product		604812				9079806, 9548455	Standard	XM_005258452		Approved	LIR-7, ILT1, CD85h, LIR7		Q8N149	OTTHUMG00000065703	ENST00000251377.3:c.410G>T	chr19.hg19:g.55086255G>T	ENSP00000251377:p.Gly137Val	53.0	0.0		66.0	18.0	NM_001130917	O75020	Missense_Mutation	SNP	ENST00000251377.3	hg19	CCDS46179.1	.	.	.	.	.	.	.	.	.	.	G	11.68	1.710724	0.30322	.	.	ENSG00000239998	ENST00000439534;ENST00000251377;ENST00000391738;ENST00000251376;ENST00000391737	T;T;T;T;T	0.00808	5.67;5.67;5.67;5.67;5.67	2.93	-0.556	0.11803	Immunoglobulin-like fold (1);	0.540376	0.16737	N	0.201585	T	0.03348	0.0097	M	0.80616	2.505	0.09310	N	1	P;D;P;D;D	0.89917	0.929;0.965;0.92;0.98;1.0	P;P;P;P;D	0.75020	0.526;0.815;0.825;0.867;0.985	T	0.34750	-0.9816	10	0.54805	T	0.06	.	3.0008	0.06012	0.2877:0.2383:0.474:0.0	.	137;137;125;137;137	Q99702;E9PDF4;A8MZH0;Q8N149;Q8N149-2	.;.;.;LIRA2_HUMAN;.	V	137;137;137;137;125	ENSP00000388131:G137V;ENSP00000251377:G137V;ENSP00000375618:G137V;ENSP00000251376:G137V;ENSP00000375617:G125V	ENSP00000251376:G137V	G	+	2	0	LILRA2	59778067	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	0.194000	0.17135	0.109000	0.17891	-0.358000	0.07595	GGG	.	.		0.557	LILRA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140813.2			T	55086255	G	T	55086255	3	4	247	1	0	0	0	0	1	0	0	0	8794	1232	43	3	424	3	LILRA2	19	55086255	Missense_Mutation	SNP	G	TCGA-ED-A7XP-01A-11D-A34Z-10	36801598	55086255	4042728	55	33848										
ZNF329	79673	hgsc.bcm.edu	37	chr19	58639664	58639664	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	gatgaaagtcttgccacattCtttacattcatagggtttct	7	8	4	1			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr19:58639664C>T	ENST00000598312.1	-	4	1440	c.1207G>A	c.(1207-1209)Gaa>Aaa	p.E403K	ZNF329_ENST00000358067.4_Missense_Mutation_p.E403K	NM_024620.3	NP_078896.3	Q86UD4	ZN329_HUMAN	zinc finger protein 329	403					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|large_intestine(10)|lung(5)|skin(3)|urinary_tract(1)	20		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.029)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.017)|Lung(386;0.216)		TTGCCACATTCTTTACATTCA	0.468																																					p.E403K		Atlas-SNP	.											.	ZNF329	70	.	0			c.G1207A						.						79	71	73					19																	58639664		2203	4300	6503	SO:0001583	missense	79673	exon4			CACATTCTTTACA	AK022648	CCDS12972.1	19q13.43	2013-01-08				ENSG00000181894		"Zinc fingers, C2H2-type"	14209	protein-coding gene	gene with protein product							Standard	XM_006723381		Approved	FLJ12586	uc002qrn.3	Q86UD4		ENST00000598312.1:c.1207G>A	chr19.hg19:g.58639664C>T	ENSP00000470008:p.Glu403Lys	111.0	0.0		112.0	17.0	NM_024620	B3KR32|Q9H9R7	Missense_Mutation	SNP	ENST00000598312.1	hg19	CCDS12972.1	.	.	.	.	.	.	.	.	.	.	C	14.90	2.672738	0.47781	.	.	ENSG00000181894	ENST00000358067;ENST00000500161	T;T	0.07327	3.2;3.2	4.31	4.31	0.51392	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.39341	N	0.001388	T	0.16085	0.0387	L	0.43598	1.365	0.33806	D	0.627229	D	0.57571	0.98	P	0.53490	0.727	T	0.03957	-1.0989	10	0.56958	D	0.05	-17.1643	16.7502	0.85483	0.0:1.0:0.0:0.0	.	403	Q86UD4	ZN329_HUMAN	K	403	ENSP00000350773:E403K;ENSP00000439527:E403K	ENSP00000350773:E403K	E	-	1	0	ZNF329	63331476	0.000000	0.05858	0.970000	0.41538	0.862000	0.49288	0.485000	0.22324	2.691000	0.91804	0.655000	0.94253	GAA	.	.		0.468	ZNF329-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466724.1	NM_024620		T	58639664	C	T	58639664	3	4	247	1	0	0	0	0	1	0	0	0	17862	922	32	3	422	3	ZNF329	19	58639664	Missense_Mutation	SNP	C	TCGA-ED-A7XP-01A-11D-A34Z-10	3553409	58639664	489319	56	33849										
SGK2	10110	hgsc.bcm.edu	37	chr20	42195738	42195738	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	ccaatgggaacatcaacctgGggccttcagccaacccaaag	9	14	2	0			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr20:42195738G>C	ENST00000341458.4	+	2	466	c.247G>C	c.(247-249)Ggg>Cgg	p.G83R	SGK2_ENST00000426287.1_Missense_Mutation_p.G49R|SGK2_ENST00000373100.1_Missense_Mutation_p.G23R|SGK2_ENST00000373077.1_Missense_Mutation_p.G23R|SGK2_ENST00000373092.3_Missense_Mutation_p.G23R|SGK2_ENST00000423407.3_Missense_Mutation_p.G23R	NM_016276.3	NP_057360.2	Q9HBY8	SGK2_HUMAN	serum/glucocorticoid regulated kinase 2	83					intracellular signal transduction (GO:0035556)|ion transmembrane transport (GO:0034220)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|response to oxidative stress (GO:0006979)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|sodium channel regulator activity (GO:0017080)	p.G83W(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(11)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			CATCAACCTGGGGCCTTCAGC	0.532																																					p.G83R		Atlas-SNP	.											SGK2,NS,carcinoma,0,1	SGK2	50	.	1	Substitution - Missense(1)	lung(1)	c.G247C						.						106	106	106					20																	42195738		2203	4300	6503	SO:0001583	missense	10110	exon2			AACCTGGGGCCTT	AF169034	CCDS13320.1, CCDS13321.1	20q13.2	2008-07-04			ENSG00000101049	ENSG00000101049			13900	protein-coding gene	gene with protein product		607589				10548550	Standard	NM_016276		Approved		uc002xkv.3	Q9HBY8	OTTHUMG00000033054	ENST00000341458.4:c.247G>C	chr20.hg19:g.42195738G>C	ENSP00000340608:p.Gly83Arg	56.0	0.0		68.0	20.0	NM_016276	Q52PK5|Q5H8Y6|Q5H8Z1|Q5TZR3|Q9UKG6	Missense_Mutation	SNP	ENST00000341458.4	hg19	CCDS13320.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.604612	0.87157	.	.	ENSG00000101049	ENST00000373100;ENST00000373092;ENST00000373077;ENST00000412111;ENST00000423407;ENST00000341458;ENST00000426287	T;T;T;T;T;T;T	0.71579	-0.54;-0.54;-0.53;0.05;-0.54;-0.58;-0.54	4.59	4.59	0.56863	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.75228	0.3821	L	0.27053	0.805	0.80722	D	1	D;D;D	0.76494	0.999;0.981;0.981	D;P;D	0.76071	0.987;0.878;0.921	T	0.77509	-0.2561	10	0.54805	T	0.06	.	15.697	0.77509	0.0:0.0:1.0:0.0	.	49;83;23	Q9HBY8-3;Q9HBY8;Q9HBY8-2	.;SGK2_HUMAN;.	R	23;23;23;23;23;83;49	ENSP00000362192:G23R;ENSP00000362184:G23R;ENSP00000362168:G23R;ENSP00000396222:G23R;ENSP00000392795:G23R;ENSP00000340608:G83R;ENSP00000412214:G49R	ENSP00000340608:G83R	G	+	1	0	SGK2	41629152	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.044000	0.93805	2.474000	0.83562	0.609000	0.83330	GGG	.	.		0.532	SGK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080383.1			C	42195738	G	C	42195738	3	2	247	1	0	0	0	0	1	0	0	0	14224	1232	43	4	253	4	SGK2	20	42195738	Missense_Mutation	SNP	G	TCGA-ED-A7XP-01A-11D-A34Z-10		42195738	20829782	57	33850										
AURKA	6790	hgsc.bcm.edu	37	chr20	54961384	54961384	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	tggagacaggatgaggtacaCtggttgcctgcaattgcttc	13	8	0	2			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chr20:54961384C>T	ENST00000347343.2	-	3	515	c.248G>A	c.(247-249)aGt>aAt	p.S83N	AURKA_ENST00000395911.1_Missense_Mutation_p.S83N|AURKA_ENST00000395913.3_Missense_Mutation_p.S83N|AURKA_ENST00000395914.1_Missense_Mutation_p.S83N|AURKA_ENST00000395907.1_Missense_Mutation_p.S83N|AURKA_ENST00000395915.3_Missense_Mutation_p.S83N|AURKA_ENST00000371356.2_Missense_Mutation_p.S83N|AURKA_ENST00000312783.6_Missense_Mutation_p.S83N|AURKA_ENST00000395909.4_Missense_Mutation_p.S83N	NM_003600.2	NP_003591.2	O14965	AURKA_HUMAN	aurora kinase A	83					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|anterior/posterior axis specification (GO:0009948)|centrosome localization (GO:0051642)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic centrosome separation (GO:0007100)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein binding (GO:0032091)|negative regulation of spindle checkpoint (GO:0090233)|neuron projection extension (GO:1990138)|positive regulation of mitosis (GO:0045840)|positive regulation of oocyte maturation (GO:1900195)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein autophosphorylation (GO:0046777)|protein localization to centrosome (GO:0071539)|protein phosphorylation (GO:0006468)|regulation of centrosome cycle (GO:0046605)|regulation of protein stability (GO:0031647)|spindle assembly involved in female meiosis I (GO:0007057)|spindle stabilization (GO:0043146)	axon hillock (GO:0043203)|centrosome (GO:0005813)|cytosol (GO:0005829)|germinal vesicle (GO:0042585)|meiotic spindle (GO:0072687)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole centrosome (GO:0031616)	ATP binding (GO:0005524)|histone serine kinase activity (GO:0035174)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			breast(2)|cervix(1)|endometrium(1)|large_intestine(4)|lung(9)|ovary(2)|prostate(1)|skin(2)	22			Colorectal(105;0.202)			ATGAGGTACACTGGTTGCCTG	0.493																																					p.S83N	Melanoma(34;439 1292 51416 52695)|GBM(144;1525 2517 48902 51835)|Esophageal Squamous(191;569 2880 14195 30540)	Atlas-SNP	.											.	AURKA	42	.	0			c.G248A						.						179	156	164					20																	54961384		2203	4300	6503	SO:0001583	missense	6790	exon3			GGTACACTGGTTG	BC001280	CCDS13451.1	20q13	2012-07-23	2003-07-21	2003-07-23	ENSG00000087586	ENSG00000087586		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	11393	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 47", "Aurora-A kinase"	603072	"serine/threonine kinase 15", " serine/threonine kinase 6"	STK15, STK6		9174055, 9771714	Standard	NM_003600		Approved	BTAK, AurA, STK7, ARK1, PPP1R47, AIK	uc002xxi.1	O14965	OTTHUMG00000032796	ENST00000347343.2:c.248G>A	chr20.hg19:g.54961384C>T	ENSP00000216911:p.Ser83Asn	227.0	0.0		200.0	77.0	NM_198437	E1P5F9|O60445|O75873|Q9BQD6|Q9UPG5	Missense_Mutation	SNP	ENST00000347343.2	hg19	CCDS13451.1	.	.	.	.	.	.	.	.	.	.	C	10.33	1.321452	0.23994	.	.	ENSG00000087586	ENST00000395909;ENST00000395914;ENST00000347343;ENST00000395915;ENST00000312783;ENST00000371356;ENST00000395913;ENST00000395911;ENST00000395907;ENST00000441357;ENST00000420474;ENST00000422322;ENST00000456249	T;T;T;T;T;T;T;T;T;T;T;T;T	0.70399	-0.22;-0.22;-0.22;-0.22;-0.22;-0.22;-0.22;-0.22;-0.48;-0.06;2.72;2.5;2.43	4.15	-0.229	0.13094	.	1.261820	0.05133	N	0.492845	T	0.54303	0.1850	L	0.38175	1.15	0.09310	N	1	B;B;B;B;B;B;B	0.34015	0.0;0.435;0.003;0.001;0.002;0.215;0.0	B;B;B;B;B;B;B	0.30572	0.0;0.117;0.004;0.002;0.004;0.07;0.001	T	0.38714	-0.9648	10	0.31617	T	0.26	-29.8103	1.7637	0.02998	0.3297:0.3575:0.204:0.1088	.	83;83;83;83;83;83;83	Q5QPD1;Q5QPD2;A3KFJ1;Q5QPD4;A3KFJ0;B2R6Z3;O14965	.;.;.;.;.;.;AURKA_HUMAN	N	83	ENSP00000379245:S83N;ENSP00000379250:S83N;ENSP00000216911:S83N;ENSP00000379251:S83N;ENSP00000321591:S83N;ENSP00000360407:S83N;ENSP00000379249:S83N;ENSP00000379247:S83N;ENSP00000379243:S83N;ENSP00000393452:S83N;ENSP00000388073:S83N;ENSP00000405042:S83N;ENSP00000405170:S83N	ENSP00000321591:S83N	S	-	2	0	AURKA	54394791	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-0.022000	0.12480	0.006000	0.14734	0.655000	0.94253	AGT	.	.		0.493	AURKA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079804.3	NM_003600		T	54961384	C	T	54961384	3	4	247	1	0	0	0	0	1	0	0	0	1221	565	20	3	991	3	AURKA	20	54961384	Missense_Mutation	SNP	C	TCGA-ED-A7XP-01A-11D-A34Z-10	12765646	54961384	8064136	58	33851										
DMD	1756	hgsc.bcm.edu	37	chrX	31496267	31496267	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	gagagagtcaatgaggagatCgcccacgggctgccaggatc	15	10	1	3	rs398124077		TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chrX:31496267C>A	ENST00000357033.4	-	59	9099	c.8893G>T	c.(8893-8895)Gat>Tat	p.D2965Y	DMD_ENST00000378677.2_Missense_Mutation_p.D2961Y|DMD_ENST00000359836.1_Missense_Mutation_p.D505Y|DMD_ENST00000541735.1_Missense_Mutation_p.D505Y|DMD_ENST00000445312.1_5'Flank|DMD_ENST00000378707.3_Missense_Mutation_p.D505Y|DMD_ENST00000474231.1_Missense_Mutation_p.D505Y|DMD_ENST00000343523.2_Missense_Mutation_p.D505Y	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	2965					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.D505Y(1)|p.D1624Y(1)|p.D2961Y(1)|p.D2960Y(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				ATGAGGAGATCGCCCACGGGC	0.532																																					p.D2965Y		Atlas-SNP	.											.	DMD	2127	.	4	Substitution - Missense(4)	lung(4)	c.G8893T						.						57	47	50					X																	31496267		2202	4300	6502	SO:0001583	missense	1756	exon59			GGAGATCGCCCAC	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.8893G>T	chrX.hg19:g.31496267C>A	ENSP00000354923:p.Asp2965Tyr	111.0	0.0		104.0	30.0	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	hg19	CCDS14233.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.69|17.69	3.452010|3.452010	0.63290|0.63290	.|.	.|.	ENSG00000198947|ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000358062;ENST00000378677;ENST00000357033;ENST00000359836;ENST00000343523;ENST00000542849;ENST00000535280;ENST00000378707;ENST00000541735;ENST00000474231|ENST00000465285	T;T;T;T;T;T;T;T|.	0.50277|.	0.75;0.75;0.75;0.75;0.75;0.75;0.75;0.75|.	5.4|5.4	5.4|5.4	0.78164|0.78164	.|.	0.000000|.	0.38164|.	U|.	0.001785|.	T|T	0.77558|0.77558	0.4148|0.4148	M|M	0.76838|0.76838	2.35|2.35	0.58432|0.58432	D|D	0.999995|0.999995	D;D;D;D;D;D;D;D;D;D;D|.	0.89917|.	0.999;1.0;1.0;1.0;1.0;0.999;1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D;D;D;D;D;D;D|.	0.87578|.	0.997;0.994;0.996;0.994;0.994;0.988;0.998;0.998;0.989;0.98;0.998|.	T|T	0.77846|0.77846	-0.2436|-0.2436	10|5	0.87932|.	D|.	0|.	.|.	18.4984|18.4984	0.90873|0.90873	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	2957;2965;2961;1624;1621;505;505;505;505;505;2842|.	P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6;F8VX32;E7ESB2;E7EQS5;E7EQR9;F5GZY3;F5GZT3|.	.;DMD_HUMAN;.;.;.;.;.;.;.;.;.|.	Y|L	2957;1624;1621;661;2961;2965;505;505;2965;2842;505;505;505|693	ENSP00000350765:D661Y;ENSP00000367948:D2961Y;ENSP00000354923:D2965Y;ENSP00000352894:D505Y;ENSP00000340057:D505Y;ENSP00000367979:D505Y;ENSP00000444119:D505Y;ENSP00000417123:D505Y|.	ENSP00000340057:D505Y|.	D|R	-|-	1|2	0|0	DMD|DMD	31406188|31406188	1.000000|1.000000	0.71417|0.71417	0.916000|0.916000	0.36221|0.36221	0.422000|0.422000	0.31414|0.31414	7.445000|7.445000	0.80570|0.80570	2.397000|2.397000	0.81536|0.81536	0.529000|0.529000	0.55759|0.55759	GAT|CGA	.	.		0.532	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		A	31496267	C	A	31496267	3	1	247	1	0	0	0	0	1	0	0	0	4582	884	31	1	2362	1	DMD	23	31496267	Missense_Mutation	SNP	C	TCGA-ED-A7XP-01A-11D-A34Z-10		31496267	123774293	59	33852										
PRRG1	5638	hgsc.bcm.edu	37	chrX	37285115	37285115	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	ttcctcacgggagaaaaagcCaattccatattaaaacgcta	6	10	1	1			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chrX:37285115C>A	ENST00000542554.1	+	4	305	c.33C>A	c.(31-33)gcC>gcA	p.A11A	PRRG1_ENST00000449135.2_Silent_p.A11A|PRRG1_ENST00000378628.4_Silent_p.A11A|TM4SF2_ENST00000465127.1_Silent_p.A11A|PRRG1_ENST00000543642.1_Silent_p.A11A|PRRG1_ENST00000463135.1_Silent_p.A11A|PRRG1_ENST00000491253.1_Intron	NM_001173489.1	NP_001166960.1	O14668	TMG1_HUMAN	proline rich Gla (G-carboxyglutamic acid) 1	11						extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	15						GAGAAAAAGCCAATTCCATAT	0.353																																					p.A11A		Atlas-SNP	.											.	PRRG1	42	.	0			c.C33A						.						47	46	46					X																	37285115		2202	4300	6502	SO:0001819	synonymous_variant	5638	exon3			AAAAGCCAATTCC	AF009242	CCDS14239.1, CCDS55397.1	Xp21.1	2010-08-13	2004-05-27		ENSG00000130962	ENSG00000130962			9469	protein-coding gene	gene with protein product		604428	"proline-rich Gla (G-carboxyglutamic acid) polypeptide 1"			9256434	Standard	NM_000950		Approved	PRGP1	uc004ddo.3	O14668	OTTHUMG00000021360	ENST00000542554.1:c.33C>A	chrX.hg19:g.37285115C>A		566.0	1.0		354.0	130.0	NM_001173490	B2R7A3|C9JXL7|D3DWA9|Q5JT66	Silent	SNP	ENST00000542554.1	hg19	CCDS14239.1																																																																																			.	.		0.353	PRRG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056228.2	NM_000950		A	37285115	C	A	37285115	2	1	247	1	0	0	0	0	0	0	0	1	12617	581	21	3		3	PRRG1	23	37285115	Silent	SNP	C	TCGA-ED-A7XP-01A-11D-A34Z-10	5788848	37285115	117985445	60	33853										
FAM123B	139285	hgsc.bcm.edu	37	chrX	63412194	63412194	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	4	1	1.0938737479618	2.95345911949686	0.671240708976558	1	1	0	tatgtcaccacaacctgtcaAtgaatcaaagcttttcaggg	7	10	4	1			TCGA-ED-A7XP-01A-11D-A34Z-10	TCGA-ED-A7XP-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1041e66f-f2c8-4391-a397-b067e8d51acd	dcbe4804-a5e8-4a45-bccb-c61bca357514	g.chrX:63412194A>G	ENST00000330258.3	-	2	1245	c.973T>C	c.(973-975)Ttg>Ctg	p.L325L	AMER1_ENST00000374869.3_Silent_p.L325L|AMER1_ENST00000403336.1_Silent_p.L325L	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	325					adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)									CAACCTGTCAATGAATCAAAG	0.532																																					p.L325L		Atlas-SNP	.											.	.	.	.	67	Whole gene deletion(67)	kidney(65)|ovary(1)|large_intestine(1)	c.T973C						.						148	127	134					X																	63412194		2203	4300	6503	SO:0001819	synonymous_variant	139285	exon2			CTGTCAATGAATC	AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"-"	26837	protein-coding gene	gene with protein product	"Wilms Tumor on the X", "adenomatous polyposis coli membrane recruitment 1"	300647	"family with sequence similarity 123B"	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.973T>C	chrX.hg19:g.63412194A>G		97.0	0.0		87.0	9.0	NM_152424	A2IB86|Q8N885	Silent	SNP	ENST00000330258.3	hg19	CCDS14377.2																																																																																			.	.		0.532	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		G	63412194	A	G	63412194	2	3	247	1	0	0	0	0	0	0	0	1	5428	98	4	2		2	FAM123B	23	63412194	Silent	SNP	A	TCGA-ED-A7XP-01A-11D-A34Z-10	26127079	63412194	91858366	61	33854										
KCNN3	3782	hgsc.bcm.edu	37	chr1	154842230	154842231	+	In_Frame_Ins	INS	-	-	CTGCTGCTGCTG													0.103448275862069	3	1	1.79166666666667	0	2.015625	0.142857142857143	0.729941291585128	0	tgctgctgctgctgctgctgINSctgctgctgctgaagctgcg							TCGA-ED-A82E-01A-11D-A34Z-10	TCGA-ED-A82E-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	64aa69e5-4ab1-45b5-aca6-c2584ac511a3	6a4d2501-89d2-42d5-9182-f5eb7a368506	g.chr1:154842230_154842231insCTGCTGCTGCTG	ENST00000271915.4	-	1	525_526	c.210_211insCAGCAGCAGCAG	c.(208-213)cagcag>cagCAGCAGCAGCAGcag	p.70_71QQ>QQQQQQ	KCNN3_ENST00000358505.2_5'Flank	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	70	Gln-rich.				potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	tgctgctgctgctgctgctgct	0.698																																					p.Q71delinsQQQQQ		Atlas-INDEL	.											.	KCNN3	141	.	0			c.211_212insCAGCAGCAGCAG						.																																			SO:0001652	inframe_insertion	3782	exon1			.	AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.199_210dupCAGCAGCAGCAG	chr1.hg19:g.154842230_154842231insCTGCTGCTGCTG	ENSP00000271915:p.Gln78_Gln79dup	78.0	0.0		66.0	18.0	NM_001204087	B1ANX0|O43517|Q86VF9|Q8WXG7	In_Frame_Ins	INS	ENST00000271915.4	hg19	CCDS30880.1																																																																																			.	.		0.698	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249		CTGCTGCTGCTG	154842231	-	CTGCTGCTGCTG	154842230	7	5	248	1	0	1	1	0	0	0	0	0	8089	1328	46	0	2038	0	KCNN3	1	154842230	In_Frame_Ins	INS	-	TCGA-ED-A82E-01A-11D-A34Z-10		154842230	94408391	1	33855										
TNN	63923	hgsc.bcm.edu	37	chr1	175048581	175048581	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.103448275862069	3	1	1.79166666666667	0	2.015625	0.142857142857143	0.729941291585128	0	cggctggcctgccccggggcGtgcagcggccacgggcgttg	19	15	0	0	rs374925420		TCGA-ED-A82E-01A-11D-A34Z-10	TCGA-ED-A82E-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	64aa69e5-4ab1-45b5-aca6-c2584ac511a3	6a4d2501-89d2-42d5-9182-f5eb7a368506	g.chr1:175048581G>A	ENST00000239462.4	+	3	635	c.522G>A	c.(520-522)gcG>gcA	p.A174A		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	174	EGF-like 1.				axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		GCCCCGGGGCGTGCAGCGGCC	0.736																																					p.A174A		Atlas-SNP	.											.	TNN	297	.	0			c.G522A						.	G		0,4160		0,0,2080	5	7	6		522	-8.9	0.4	1		6	1,8017		0,1,4008	no	coding-synonymous	TNN	NM_022093.1		0,1,6088	AA,AG,GG		0.0125,0.0,0.0082		174/1300	175048581	1,12177	2080	4009	6089	SO:0001819	synonymous_variant	63923	exon3			CGGGGCGTGCAGC	AK127044	CCDS30943.1	1q23-q24	2013-02-11			ENSG00000120332	ENSG00000120332		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	22942	protein-coding gene	gene with protein product							Standard	NM_022093		Approved		uc001gkl.1	Q9UQP3	OTTHUMG00000034882	ENST00000239462.4:c.522G>A	chr1.hg19:g.175048581G>A		38.0	0.0		44.0	18.0	NM_022093	B9EGP3|Q5R360	Silent	SNP	ENST00000239462.4	hg19	CCDS30943.1																																																																																			.	.		0.736	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527		A	175048581	G	A	175048581	2	1	248	1	0	0	0	0	0	0	0	1	16338	1132	40	1		1	TNN	1	175048581	Silent	SNP	G	TCGA-ED-A82E-01A-11D-A34Z-10	20206351	175048581	74202040	2	33856										
SPTBN1	6711	hgsc.bcm.edu	37	chr2	54857137	54857137	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.103448275862069	3	1	1.79166666666667	0	2.015625	0.142857142857143	0.729941291585128	0	cacccaagtgagaaggaaatCaaagcccagcaggacaaact	9	11	1	1			TCGA-ED-A82E-01A-11D-A34Z-10	TCGA-ED-A82E-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	64aa69e5-4ab1-45b5-aca6-c2584ac511a3	6a4d2501-89d2-42d5-9182-f5eb7a368506	g.chr2:54857137C>T	ENST00000356805.4	+	15	3059	c.2778C>T	c.(2776-2778)atC>atT	p.I926I	SPTBN1_ENST00000333896.5_Silent_p.I913I	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	926					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			AGAAGGAAATCAAAGCCCAGC	0.582																																					p.I926I		Atlas-SNP	.											.	SPTBN1	378	.	0			c.C2778T						.						67	62	64					2																	54857137		2203	4300	6503	SO:0001819	synonymous_variant	6711	exon15			GGAAATCAAAGCC		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"Pleckstrin homology (PH) domain containing"	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.2778C>T	chr2.hg19:g.54857137C>T		25.0	0.0		25.0	15.0	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Silent	SNP	ENST00000356805.4	hg19	CCDS33198.1																																																																																			.	.		0.582	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			T	54857137	C	T	54857137	2	4	248	1	0	0	0	0	0	0	0	1	15134	816	29	3		3	SPTBN1	2	54857137	Silent	SNP	C	TCGA-ED-A82E-01A-11D-A34Z-10		54857137	188342236	3	33857										
STXBP5L	9515	hgsc.bcm.edu	37	chr3	120941851	120941851	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.103448275862069	3	1	1.79166666666667	0	2.015625	0.142857142857143	0.729941291585128	0	catgttttttcctatgtagcGaaccattcataatattctct	4	9	2	0			TCGA-ED-A82E-01A-11D-A34Z-10	TCGA-ED-A82E-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	64aa69e5-4ab1-45b5-aca6-c2584ac511a3	6a4d2501-89d2-42d5-9182-f5eb7a368506	g.chr3:120941851G>A	ENST00000273666.6	+	11	1229	c.958G>A	c.(958-960)Gaa>Aaa	p.E320K	STXBP5L_ENST00000471454.1_Splice_Site_p.E320K|STXBP5L_ENST00000492541.1_Splice_Site_p.E320K|STXBP5L_ENST00000472879.1_Splice_Site_p.E320K|STXBP5L_ENST00000497029.1_Splice_Site_p.E320K	NM_014980.2	NP_055795.1	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	320					exocytosis (GO:0006887)|glucose homeostasis (GO:0042593)|negative regulation of insulin secretion (GO:0046676)|positive regulation of protein secretion (GO:0050714)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(12)|lung(28)|ovary(7)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				GBM - Glioblastoma multiforme(114;0.0694)		CCTATGTAGCGAACCATTCAT	0.368																																					p.E320K		Atlas-SNP	.											.	STXBP5L	159	.	0			c.G958A						.						140	129	132					3																	120941851		1860	4096	5956	SO:0001630	splice_region_variant	9515	exon11			TGTAGCGAACCAT	AB023223	CCDS43137.1	3q13.33-q21.1	2013-01-10			ENSG00000145087	ENSG00000145087		"WD repeat domain containing"	30757	protein-coding gene	gene with protein product		609381				10231032, 14767561	Standard	NM_014980		Approved	KIAA1006, LLGL4	uc003eec.4	Q9Y2K9	OTTHUMG00000159426	ENST00000273666.6:c.957-1G>A	chr3.hg19:g.120941851G>A		141.0	0.0		131.0	53.0	NM_014980	Q4G1B4|Q6PIC3	Missense_Mutation	SNP	ENST00000273666.6	hg19	CCDS43137.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.268878	0.80469	.	.	ENSG00000145087	ENST00000273666;ENST00000471454;ENST00000472879;ENST00000497029;ENST00000492541;ENST00000471262	T;T;T;T;T;T	0.38560	1.83;1.84;1.64;1.13;1.63;1.83	4.65	4.65	0.58169	WD40 repeat-like-containing domain (1);Lethal giant larvae homologue 2 (1);	0.321837	0.36815	N	0.002385	T	0.61413	0.2345	M	0.64997	1.995	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.995	T	0.58470	-0.7631	10	0.31617	T	0.26	-6.7613	17.7198	0.88348	0.0:0.0:1.0:0.0	.	320;320	E9PFI2;Q9Y2K9	.;STB5L_HUMAN	K	320	ENSP00000273666:E320K;ENSP00000420019:E320K;ENSP00000419627:E320K;ENSP00000420287:E320K;ENSP00000420666:E320K;ENSP00000420167:E320K	ENSP00000273666:E320K	E	+	1	0	STXBP5L	122424541	1.000000	0.71417	1.000000	0.80357	0.735000	0.41995	9.657000	0.98554	2.397000	0.81536	0.462000	0.41574	GAA	.	.		0.368	STXBP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355256.3		Missense_Mutation	A	120941851	G	A	120941851	5	1	248	1	0	0	0	0	0	0	1	0	15372	1072	37	1	996	1	STXBP5L	3	120941851	Splice_Site	SNP	G	TCGA-ED-A82E-01A-11D-A34Z-10		120941851	77080579	4	33858										
ZBBX	79740	hgsc.bcm.edu	37	chr3	166960379	166960379	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.103448275862069	3	1	1.79166666666667	0	2.015625	0.142857142857143	0.729941291585128	0	cttatattcagtgattggctGctgaaatctgggaactcttc	9	8	3	2			TCGA-ED-A82E-01A-11D-A34Z-10	TCGA-ED-A82E-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	64aa69e5-4ab1-45b5-aca6-c2584ac511a3	6a4d2501-89d2-42d5-9182-f5eb7a368506	g.chr3:166960379G>A	ENST00000392766.2	-	20	2530	c.2190C>T	c.(2188-2190)agC>agT	p.S730S	ZBBX_ENST00000455345.2_Silent_p.S769S|ZBBX_ENST00000307529.5_Silent_p.S769S|ZBBX_ENST00000392764.1_Silent_p.S701S|ZBBX_ENST00000392767.2_Silent_p.S730S	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	730						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(9)|liver(1)|lung(38)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	70						GTGATTGGCTGCTGAAATCTG	0.378																																					p.S769S		Atlas-SNP	.											.	ZBBX	299	.	0			c.C2307T						.						95	92	93					3																	166960379		1823	4079	5902	SO:0001819	synonymous_variant	79740	exon21			TTGGCTGCTGAAA	AK026702	CCDS3199.2, CCDS56295.1, CCDS56296.1	3q26.1	2010-03-23			ENSG00000169064	ENSG00000169064			26245	protein-coding gene	gene with protein product						12477932	Standard	NM_024687		Approved	FLJ23049	uc011bpc.2	A8MT70	OTTHUMG00000133560	ENST00000392766.2:c.2190C>T	chr3.hg19:g.166960379G>A		86.0	0.0		76.0	32.0	NM_001199201	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Silent	SNP	ENST00000392766.2	hg19	CCDS3199.2																																																																																			.	.		0.378	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687		A	166960379	G	A	166960379	2	1	248	1	0	0	0	0	0	0	0	1	17531	1310	46	3		3	ZBBX	3	166960379	Silent	SNP	G	TCGA-ED-A82E-01A-11D-A34Z-10	46018528	166960379	31062051	5	33859										
PCDH12	51294	hgsc.bcm.edu	37	chr5	141336991	141336991	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.103448275862069	3	1	1.79166666666667	0	2.015625	0.142857142857143	0.729941291585128	0	gaggcgctctcagagatttcCagctcctgctcgcctttggg	12	13	1	1			TCGA-ED-A82E-01A-11D-A34Z-10	TCGA-ED-A82E-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	64aa69e5-4ab1-45b5-aca6-c2584ac511a3	6a4d2501-89d2-42d5-9182-f5eb7a368506	g.chr5:141336991C>A	ENST00000231484.3	-	1	1636	c.426G>T	c.(424-426)ctG>ctT	p.L142L	PCDH12_ENST00000512221.1_5'Flank	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	142	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGAGATTTCCAGCTCCTGCT	0.572																																					p.L142L		Atlas-SNP	.											.	PCDH12	133	.	0			c.G426T						.						108	124	119					5																	141336991		2203	4300	6503	SO:0001819	synonymous_variant	51294	exon1			GATTTCCAGCTCC	AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"Cadherins / Protocadherins : Non-clustered"	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.426G>T	chr5.hg19:g.141336991C>A		128.0	0.0		86.0	46.0	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Silent	SNP	ENST00000231484.3	hg19	CCDS4269.1																																																																																			.	.		0.572	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580		A	141336991	C	A	141336991	2	1	248	1	0	0	0	0	0	0	0	1	11519	581	21	3		3	PCDH12	5	141336991	Silent	SNP	C	TCGA-ED-A82E-01A-11D-A34Z-10		141336991	39578269	6	33860										
ZNF311	282890	hgsc.bcm.edu	37	chr6	28963999	28963999	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.103448275862069	3	1	1.79166666666667	0	2.015625	0.142857142857143	0.729941291585128	0	tgctcatggagaattagatcTgagtgccaactgaagttttt	10	6	2	4			TCGA-ED-A82E-01A-11D-A34Z-10	TCGA-ED-A82E-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	64aa69e5-4ab1-45b5-aca6-c2584ac511a3	6a4d2501-89d2-42d5-9182-f5eb7a368506	g.chr6:28963999T>G	ENST00000377179.3	-	7	1292	c.780A>C	c.(778-780)tcA>tcC	p.S260S	ZNF311_ENST00000483450.1_5'UTR	NM_001010877.2	NP_001010877.2	Q5JNZ3	ZN311_HUMAN	zinc finger protein 311	260					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|skin(3)|upper_aerodigestive_tract(2)	28						GAATTAGATCTGAGTGCCAAC	0.398																																					p.S260S		Atlas-SNP	.											.	ZNF311	59	.	0			c.A780C						.						65	76	72					6																	28963999		1509	2708	4217	SO:0001819	synonymous_variant	282890	exon7			TAGATCTGAGTGC	AL833166	CCDS34357.1	6p21.33	2013-01-08			ENSG00000197935	ENSG00000197935		"Zinc fingers, C2H2-type", "-"	13847	protein-coding gene	gene with protein product							Standard	XM_006715067		Approved		uc003nlu.2	Q5JNZ3	OTTHUMG00000031292	ENST00000377179.3:c.780A>C	chr6.hg19:g.28963999T>G		129.0	0.0		158.0	48.0	NM_001010877	A2BFK5|B0S7Y4|Q92971	Silent	SNP	ENST00000377179.3	hg19	CCDS34357.1																																																																																			.	.		0.398	ZNF311-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076631.3	XM_212581		G	28963999	T	G	28963999	2	3	248	1	0	0	0	0	0	0	0	1	17849	1567	55	5		5	ZNF311	6	28963999	Silent	SNP	T	TCGA-ED-A82E-01A-11D-A34Z-10		28963999	142151068	7	33861										
FOXP2	93986	hgsc.bcm.edu	37	chr7	114269944	114269944	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.103448275862069	3	1	1.79166666666667	0	2.015625	0.142857142857143	0.729941291585128	0	agcagcaacagcagcagcagCaacaacagcagcaacaacag	9	13	0	0			TCGA-ED-A82E-01A-11D-A34Z-10	TCGA-ED-A82E-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	64aa69e5-4ab1-45b5-aca6-c2584ac511a3	6a4d2501-89d2-42d5-9182-f5eb7a368506	g.chr7:114269944C>A	ENST00000393494.2	+	5	760	c.481C>A	c.(481-483)Caa>Aaa	p.Q161K	FOXP2_ENST00000390668.3_Missense_Mutation_p.Q185K|FOXP2_ENST00000393498.2_Missense_Mutation_p.Q141K|AC020606.1_ENST00000580664.1_RNA|FOXP2_ENST00000403559.4_Missense_Mutation_p.Q178K|FOXP2_ENST00000408937.3_Missense_Mutation_p.Q186K|FOXP2_ENST00000393489.3_Missense_Mutation_p.Q69K|FOXP2_ENST00000360232.4_Missense_Mutation_p.Q161K|FOXP2_ENST00000350908.4_Missense_Mutation_p.Q161K|FOXP2_ENST00000378237.3_Missense_Mutation_p.Q161K|FOXP2_ENST00000393491.3_Missense_Mutation_p.Q69K|FOXP2_ENST00000393500.3_Missense_Mutation_p.Q86K			O15409	FOXP2_HUMAN	forkhead box P2	161	Gln-rich.				camera-type eye development (GO:0043010)|caudate nucleus development (GO:0021757)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|growth (GO:0040007)|lung alveolus development (GO:0048286)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of mesenchymal cell proliferation (GO:0002053)|post-embryonic development (GO:0009791)|putamen development (GO:0021758)|righting reflex (GO:0060013)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|vocal learning (GO:0042297)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	52						gcagcagcagcaacaacagca	0.478																																					p.Q186K		Atlas-SNP	.											.	FOXP2	133	.	0			c.C556A						.						37	37	37					7																	114269944		2202	4298	6500	SO:0001583	missense	93986	exon5			CAGCAGCAACAAC	U80741	CCDS5760.1, CCDS5761.1, CCDS43635.1, CCDS5761.2, CCDS55154.1	7q31	2008-07-18			ENSG00000128573	ENSG00000128573		"Forkhead boxes"	13875	protein-coding gene	gene with protein product	"trinucleotide repeat containing 10", "forkhead/winged-helix transcription factor", "speech and language disorder 1", "CAG repeat protein 44"	605317		TNRC10, SPCH1		11586359, 9225980	Standard	NM_014491		Approved	CAGH44	uc003vgz.3	O15409	OTTHUMG00000023131	ENST00000393494.2:c.481C>A	chr7.hg19:g.114269944C>A	ENSP00000377132:p.Gln161Lys	36.0	0.0		23.0	5.0	NM_001172767	A0AUV6|A4D0U8|A6NNW4|B4DLD9|Q6ZND1|Q75MJ3|Q8IZE0|Q8N0W2|Q8N6B7|Q8N6B8|Q8NFQ1|Q8NFQ2|Q8NFQ3|Q8NFQ4|Q8TD74	Missense_Mutation	SNP	ENST00000393494.2	hg19	CCDS5760.1	.	.	.	.	.	.	.	.	.	.	C	12.07	1.828116	0.32329	.	.	ENSG00000128573	ENST00000393500;ENST00000324462;ENST00000393494;ENST00000408937;ENST00000403559;ENST00000350908;ENST00000393498;ENST00000378237;ENST00000393489;ENST00000360232;ENST00000452963;ENST00000390668;ENST00000393491	T;T;T;T;T;T;T;T;T;T	0.36520	1.57;1.25;1.6;1.57;1.25;1.25;1.6;1.25;1.6;1.6	5.96	5.96	0.96718	.	0.339974	0.26026	N	0.026793	T	0.32194	0.0821	N	0.03608	-0.345	0.53688	D	0.999974	P;P;P;P;P;P;P	0.43578	0.713;0.713;0.713;0.811;0.811;0.713;0.811	P;P;P;P;P;P;P	0.57846	0.678;0.678;0.678;0.828;0.828;0.678;0.828	T	0.06752	-1.0809	10	0.02654	T	1	.	20.0296	0.97533	0.0:1.0:0.0:0.0	.	161;178;69;161;185;161;186	B7ZLK5;B4DLD9;Q0PRL4;O15409-6;Q8N6B5;O15409;O15409-4	.;.;.;.;.;FOXP2_HUMAN;.	K	86;161;161;186;178;161;139;161;69;161;167;185;69	ENSP00000377137:Q86K;ENSP00000377132:Q161K;ENSP00000386200:Q186K;ENSP00000385069:Q178K;ENSP00000265436:Q161K;ENSP00000367482:Q161K;ENSP00000377129:Q69K;ENSP00000353367:Q161K;ENSP00000375084:Q185K;ENSP00000377130:Q69K	ENSP00000319424:Q161K	Q	+	1	0	FOXP2	114057180	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	3.922000	0.56462	2.831000	0.97527	0.650000	0.86243	CAA	.	.		0.478	FOXP2-014	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317366.1	NM_014491		A	114269944	C	A	114269944	3	1	248	1	0	0	0	0	1	0	0	0	6035	711	25	3	629	3	FOXP2	7	114269944	Missense_Mutation	SNP	C	TCGA-ED-A82E-01A-11D-A34Z-10		114269944	44868719	8	33862										
PTPRN2	5799	hgsc.bcm.edu	37	chr7	157931034	157931034	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.103448275862069	3	1	1.79166666666667	0	2.015625	0.142857142857143	0.729941291585128	0	cttggggccatccgcctgttCtccagactctcccagggccg	11	17	2	1			TCGA-ED-A82E-01A-11D-A34Z-10	TCGA-ED-A82E-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	64aa69e5-4ab1-45b5-aca6-c2584ac511a3	6a4d2501-89d2-42d5-9182-f5eb7a368506	g.chr7:157931034C>T	ENST00000389418.4	-	7	1093	c.1084G>A	c.(1084-1086)Gaa>Aaa	p.E362K	PTPRN2_ENST00000389416.4_Missense_Mutation_p.E345K|PTPRN2_ENST00000389413.3_Missense_Mutation_p.E362K|PTPRN2_ENST00000404321.2_Missense_Mutation_p.E385K|PTPRN2_ENST00000409483.1_Missense_Mutation_p.E324K	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	362					negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		TCCGCCTGTTCTCCAGACTCT	0.677																																					p.E362K		Atlas-SNP	.											.	PTPRN2	243	.	0			c.G1084A						.						44	48	47					7																	157931034		2203	4300	6503	SO:0001583	missense	5799	exon7			CCTGTTCTCCAGA	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9677	protein-coding gene	gene with protein product	"IAR PTPRP"	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.1084G>A	chr7.hg19:g.157931034C>T	ENSP00000374069:p.Glu362Lys	67.0	0.0		59.0	25.0	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Missense_Mutation	SNP	ENST00000389418.4	hg19	CCDS5947.1	.	.	.	.	.	.	.	.	.	.	C	13.34	2.209221	0.39003	.	.	ENSG00000155093	ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321	T;T;T;T;T	0.04119	3.71;3.9;3.92;3.7;3.91	4.24	3.35	0.38373	.	.	.	.	.	T	0.04003	0.0112	N	0.19112	0.55	0.09310	N	1	P;P;P;P;P	0.50156	0.932;0.888;0.932;0.888;0.888	B;B;P;B;B	0.45428	0.395;0.287;0.48;0.287;0.221	T	0.23440	-1.0188	9	0.07990	T	0.79	.	10.3514	0.43939	0.0:0.7999:0.2001:0.0	.	385;324;362;345;362	Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932	.;.;.;.;PTPR2_HUMAN	K	324;362;345;362;385	ENSP00000387114:E324K;ENSP00000374064:E362K;ENSP00000374067:E345K;ENSP00000374069:E362K;ENSP00000385464:E385K	ENSP00000374064:E362K	E	-	1	0	PTPRN2	157623795	0.005000	0.15991	0.001000	0.08648	0.038000	0.13279	0.968000	0.29357	0.859000	0.35456	0.655000	0.94253	GAA	.	.		0.677	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1			T	157931034	C	T	157931034	3	4	248	1	0	0	0	0	1	0	0	0	12823	922	32	3	2031	3	PTPRN2	7	157931034	Missense_Mutation	SNP	C	TCGA-ED-A82E-01A-11D-A34Z-10	43661090	157931034	1207629	9	33863										
PAPPA	5069	hgsc.bcm.edu	37	chr9	119109470	119109470	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.103448275862069	3	1	1.79166666666667	0	2.015625	0.142857142857143	0.729941291585128	0	aatgttccttccagtgccgtCaccctgcacaattgaaaggt	8	12	1	1			TCGA-ED-A82E-01A-11D-A34Z-10	TCGA-ED-A82E-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	64aa69e5-4ab1-45b5-aca6-c2584ac511a3	6a4d2501-89d2-42d5-9182-f5eb7a368506	g.chr9:119109470C>T	ENST00000328252.3	+	15	4315	c.3946C>T	c.(3946-3948)Cac>Tac	p.H1316Y	PAPPA_ENST00000534838.1_Missense_Mutation_p.H354Y	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	1316	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|female pregnancy (GO:0007565)|response to follicle-stimulating hormone (GO:0032354)|response to glucocorticoid (GO:0051384)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(9)|kidney(2)|large_intestine(23)|lung(33)|ovary(4)|pancreas(2)|prostate(5)|skin(7)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	98						CCAGTGCCGTCACCCTGCACA	0.542																																					p.H1316Y		Atlas-SNP	.											.	PAPPA	243	.	0			c.C3946T						.						145	106	119					9																	119109470		2203	4300	6503	SO:0001583	missense	5069	exon15			TGCCGTCACCCTG		CCDS6813.1	9q33.1	2014-03-05			ENSG00000182752	ENSG00000182752			8602	protein-coding gene	gene with protein product	"insulin-like growth factor-dependent IGF binding protein-4 protease", "aspecific BCL2 ARE-binding protein 2", "differentially placenta 1 expressed protein"	176385				7679961	Standard	NM_002581		Approved	PAPP-A, PAPPA1, IGFBP-4ase, PAPA, ASBABP2, DIPLA1	uc004bjn.3	Q13219	OTTHUMG00000021045	ENST00000328252.3:c.3946C>T	chr9.hg19:g.119109470C>T	ENSP00000330658:p.His1316Tyr	113.0	0.0		130.0	53.0	NM_002581	B1AMF9|Q08371|Q68G52|Q9UDK7	Missense_Mutation	SNP	ENST00000328252.3	hg19	CCDS6813.1	.	.	.	.	.	.	.	.	.	.	C	11.63	1.695810	0.30052	.	.	ENSG00000182752	ENST00000328252;ENST00000534838	T;T	0.64085	-0.08;-0.08	5.86	4.97	0.65823	Complement control module (2);Sushi/SCR/CCP (3);	0.199744	0.52532	D	0.000063	T	0.46678	0.1405	N	0.19112	0.55	0.34019	D	0.652428	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.51896	-0.8647	10	0.18710	T	0.47	-27.0103	15.2045	0.73169	0.0:0.9326:0.0:0.0674	.	354;1316	F5GZ19;Q13219	.;PAPP1_HUMAN	Y	1316;354	ENSP00000330658:H1316Y;ENSP00000441461:H354Y	ENSP00000330658:H1316Y	H	+	1	0	PAPPA	118149291	1.000000	0.71417	0.995000	0.50966	0.797000	0.45037	3.898000	0.56281	1.490000	0.48466	-0.137000	0.14449	CAC	.	.		0.542	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581		T	119109470	C	T	119109470	3	4	248	1	0	0	0	0	1	0	0	0	11441	826	29	3	4004	3	PAPPA	9	119109470	Missense_Mutation	SNP	C	TCGA-ED-A82E-01A-11D-A34Z-10		119109470	22103961	10	33864										
MORN5	254956	hgsc.bcm.edu	37	chr9	124936889	124936889	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.103448275862069	3	1	1.79166666666667	0	2.015625	0.142857142857143	0.729941291585128	0	agtcaaggactataggaaccGctttctaagaaacgcaggta	10	8	2	1			TCGA-ED-A82E-01A-11D-A34Z-10	TCGA-ED-A82E-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	64aa69e5-4ab1-45b5-aca6-c2584ac511a3	6a4d2501-89d2-42d5-9182-f5eb7a368506	g.chr9:124936889G>A	ENST00000373764.3	+	4	484	c.422G>A	c.(421-423)cGc>cAc	p.R141H	MORN5_ENST00000486801.1_3'UTR|MORN5_ENST00000536616.1_Missense_Mutation_p.R141H	NM_198469.2	NP_940871.2	Q5VZ52	MORN5_HUMAN	MORN repeat containing 5	141								p.R141H(1)		endometrium(3)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	9						TATAGGAACCGCTTTCTAAGA	0.458																																					p.R141H		Atlas-SNP	.											MORN5,NS,carcinoma,0,1	MORN5	19	.	1	Substitution - Missense(1)	kidney(1)	c.G422A						.						102	94	97					9																	124936889		2203	4300	6503	SO:0001583	missense	254956	exon4			GGAACCGCTTTCT	AK128877	CCDS6836.1, CCDS75894.1	9q34.11	2008-06-23	2008-06-23	2008-06-23	ENSG00000185681	ENSG00000185681			17841	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 113", "chromosome 9 open reading frame 18"	C9orf113, C9orf18			Standard	XM_005251878		Approved	FLJ46909	uc004blw.2	Q5VZ52	OTTHUMG00000020599	ENST00000373764.3:c.422G>A	chr9.hg19:g.124936889G>A	ENSP00000362869:p.Arg141His	76.0	0.0		70.0	15.0	NM_198469	B7Z7I5|Q6ZQN1	Missense_Mutation	SNP	ENST00000373764.3	hg19	CCDS6836.1	.	.	.	.	.	.	.	.	.	.	G	5.420	0.262613	0.10294	.	.	ENSG00000185681	ENST00000373764;ENST00000536616	T;T	0.25414	1.93;1.8	5.12	2.33	0.28932	.	0.506126	0.23241	N	0.050350	T	0.24547	0.0595	M	0.75447	2.3	0.09310	N	1	B;B	0.27416	0.178;0.028	B;B	0.17098	0.017;0.003	T	0.16541	-1.0399	10	0.40728	T	0.16	-20.8112	6.8063	0.23779	0.3606:0.0:0.6394:0.0	.	141;141	B7Z7I5;Q5VZ52	.;MORN5_HUMAN	H	141	ENSP00000362869:R141H;ENSP00000437483:R141H	ENSP00000362869:R141H	R	+	2	0	MORN5	123976710	0.005000	0.15991	0.206000	0.23566	0.063000	0.16089	1.192000	0.32150	0.350000	0.24002	0.650000	0.86243	CGC	.	.		0.458	MORN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053910.2	NM_198469		A	124936889	G	A	124936889	3	1	248	1	0	0	0	0	1	0	0	0	9720	1087	38	1	436	1	MORN5	9	124936889	Missense_Mutation	SNP	G	TCGA-ED-A82E-01A-11D-A34Z-10	5827419	124936889	16276542	11	33865										
CD81	975	hgsc.bcm.edu	37	chr11	2416714	2416715	+	Frame_Shift_Ins	INS	-	-	AA													0.103448275862069	3	1	1.79166666666667	0	2.015625	0.142857142857143	0.729941291585128	0	tggtggatgatgacgccaacINSaacgccaaggctgtggtgaa							TCGA-ED-A82E-01A-11D-A34Z-10	TCGA-ED-A82E-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	64aa69e5-4ab1-45b5-aca6-c2584ac511a3	6a4d2501-89d2-42d5-9182-f5eb7a368506	g.chr11:2416714_2416715insAA	ENST00000263645.5	+	5	679_680	c.423_424insAA	c.(424-426)aacfs	p.N142fs	CD81_ENST00000492627.1_Frame_Shift_Ins_p.N71fs|CD81_ENST00000481687.1_Frame_Shift_Ins_p.N148fs|CD81_ENST00000524805.1_3'UTR|CD81_ENST00000381036.3_Frame_Shift_Ins_p.N180fs|CD81_ENST00000526072.1_Frame_Shift_Ins_p.N71fs	NM_004356.3	NP_004347.1	P60033	CD81_HUMAN	CD81 molecule	142					activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of 1-phosphatidylinositol 4-kinase activity (GO:0043128)|positive regulation of cell proliferation (GO:0008284)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein localization (GO:0008104)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of immune response (GO:0050776)|viral entry into host cell (GO:0046718)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	MHC class II protein complex binding (GO:0023026)			endometrium(1)|lung(3)|skin(1)	5		all_epithelial(84;0.000161)|Breast(177;0.000962)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|all_neural(188;0.0137)|Lung NSC(207;0.209)		BRCA - Breast invasive adenocarcinoma(625;0.000338)|LUSC - Lung squamous cell carcinoma(625;0.191)		ATGACGCCAACAACGCCAAGGC	0.678																																					p.N141fs		Atlas-Indel,Pindel	.											.	CD81	11	.	0			c.423_424insAA						.																																			SO:0001589	frameshift_variant	975	exon5			.		CCDS7734.1, CCDS73240.1	11p15.5	2014-09-17	2006-03-28		ENSG00000110651	ENSG00000110651		"CD molecules", "Tetraspanins"	1701	protein-coding gene	gene with protein product		186845	"CD81 antigen (target of antiproliferative antibody 1)"	TAPA1		1650385	Standard	XM_005253260		Approved	TAPA-1, TSPAN28	uc001lwf.1	P60033	OTTHUMG00000009892	ENST00000263645.5:c.424_425dupAA	chr11.hg19:g.2416715_2416716dupAA	ENSP00000263645:p.Asn142fs	82.0	0.0		57.0	30.0	NM_004356	P18582|Q5U0J6	Frame_Shift_Ins	INS	ENST00000263645.5	hg19	CCDS7734.1																																																																																			.	.		0.678	CD81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027357.4	NM_004356		AA	2416715	-	AA	2416714	7	5	248	1	0	1	1	0	0	0	0	0	3041	477	17	0	441	0	CD81	11	2416714	Frame_Shift_Ins	INS	-	TCGA-ED-A82E-01A-11D-A34Z-10		2416714	132589802	12	33866										
INCENP	3619	hgsc.bcm.edu	37	chr11	61906404	61906404	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.103448275862069	3	1	1.79166666666667	0	2.015625	0.142857142857143	0.729941291585128	0	tcgtggccccacaatgacacGgagattgccaacagcacacc	9	15	0	2			TCGA-ED-A82E-01A-11D-A34Z-10	TCGA-ED-A82E-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	64aa69e5-4ab1-45b5-aca6-c2584ac511a3	6a4d2501-89d2-42d5-9182-f5eb7a368506	g.chr11:61906404G>T	ENST00000394818.3	+	7	1420	c.1218G>T	c.(1216-1218)acG>acT	p.T406T	INCENP_ENST00000278849.4_Silent_p.T406T	NM_001040694.1	NP_001035784.1	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	406					chromosome segregation (GO:0007059)|cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	central element (GO:0000801)|chromocenter (GO:0010369)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lateral element (GO:0000800)|microtubule (GO:0005874)|midbody (GO:0030496)|pericentric heterochromatin (GO:0005721)|protein complex (GO:0043234)|spindle (GO:0005819)		p.T406T(2)		breast(1)|endometrium(1)|kidney(6)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						ACAATGACACGGAGATTGCCA	0.582																																					p.T406T		Atlas-SNP	.											INCENP_ENST00000394818,colon,carcinoma,0,2	INCENP	122	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G1218T						.						134	122	126					11																	61906404		2202	4299	6501	SO:0001819	synonymous_variant	3619	exon7			TGACACGGAGATT	AF282265	CCDS31582.1, CCDS44624.1	11q12.3	2013-01-17	2002-08-29		ENSG00000149503	ENSG00000149503			6058	protein-coding gene	gene with protein product		604411	"inner centromere protein antigens (135kD, 155kD)"			1860899, 11453556	Standard	NM_001040694		Approved	FLJ31633	uc001nsw.1	Q9NQS7	OTTHUMG00000167470	ENST00000394818.3:c.1218G>T	chr11.hg19:g.61906404G>T		44.0	0.0		45.0	3.0	NM_001040694	A8MQD2|Q5Y192	Silent	SNP	ENST00000394818.3	hg19	CCDS44624.1																																																																																			.	.		0.582	INCENP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394723.2	NM_020238		T	61906404	G	T	61906404	2	4	248	1	0	0	0	0	0	0	0	1	7742	1103	39	1		1	INCENP	11	61906404	Silent	SNP	G	TCGA-ED-A82E-01A-11D-A34Z-10	59489690	61906404	73100112	13	33867										
SART1	9092	hgsc.bcm.edu	37	chr11	65743929	65743929	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.103448275862069	3	1	1.79166666666667	0	2.015625	0.142857142857143	0.729941291585128	0	gggaggaggatgaggatcccGagcggaagggggccatcgtg	21	7	0	1			TCGA-ED-A82E-01A-11D-A34Z-10	TCGA-ED-A82E-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	64aa69e5-4ab1-45b5-aca6-c2584ac511a3	6a4d2501-89d2-42d5-9182-f5eb7a368506	g.chr11:65743929G>A	ENST00000312397.5	+	13	1728	c.1636G>A	c.(1636-1638)Gag>Aag	p.E546K		NM_005146.4	NP_005137.1	O43290	SNUT1_HUMAN	squamous cell carcinoma antigen recognized by T cells	546					cell cycle arrest (GO:0007050)|intrinsic apoptotic signaling pathway (GO:0097193)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of cytotoxic T cell differentiation (GO:0045585)|spliceosomal snRNP assembly (GO:0000387)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						TGAGGATCCCGAGCGGAAGGG	0.652																																					p.E546K		Atlas-SNP	.											.	SART1	41	.	0			c.G1636A						.						34	37	36					11																	65743929		2201	4296	6497	SO:0001583	missense	9092	exon13			GATCCCGAGCGGA	AB006198	CCDS31611.1	11q13.1	2009-01-06	2006-12-07		ENSG00000175467	ENSG00000175467			10538	protein-coding gene	gene with protein product	"small nuclear ribonucleoprotein 110kDa (U4/U6.U5)"	605941	"squamous cell carcinoma antigen recognised by T cells"			9449708	Standard	NM_005146		Approved	Ara1, Snu66, SNRNP110	uc001ogl.3	O43290	OTTHUMG00000166771	ENST00000312397.5:c.1636G>A	chr11.hg19:g.65743929G>A	ENSP00000310448:p.Glu546Lys	35.0	0.0		23.0	13.0	NM_005146	A6NDN1|Q53GB5	Missense_Mutation	SNP	ENST00000312397.5	hg19	CCDS31611.1	.	.	.	.	.	.	.	.	.	.	G	14.76	2.632773	0.47049	.	.	ENSG00000175467	ENST00000312397;ENST00000542816	T	0.22134	1.97	5.1	4.19	0.49359	.	0.126858	0.51477	D	0.000087	T	0.16385	0.0394	L	0.44542	1.39	0.42425	D	0.992656	P	0.35348	0.496	B	0.25614	0.062	T	0.05305	-1.0893	10	0.87932	D	0	-32.6416	11.3252	0.49444	0.0885:0.0:0.9115:0.0	.	546	O43290	SNUT1_HUMAN	K	546;388	ENSP00000310448:E546K	ENSP00000310448:E546K	E	+	1	0	SART1	65500505	1.000000	0.71417	0.829000	0.32907	0.858000	0.48976	6.651000	0.74372	1.389000	0.46526	0.491000	0.48974	GAG	.	.		0.652	SART1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391409.1			A	65743929	G	A	65743929	3	1	248	1	0	0	0	0	1	0	0	0	13861	1059	37	1	1686	1	SART1	11	65743929	Missense_Mutation	SNP	G	TCGA-ED-A82E-01A-11D-A34Z-10	3837525	65743929	69262587	14	33868										
ADIPOR2	79602	hgsc.bcm.edu	37	chr12	1893123	1893123	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.103448275862069	3	1	1.79166666666667	0	2.015625	0.142857142857143	0.729941291585128	0	cggaggggttccttaaggccGccaccatagggcagataggc	15	11	0	1			TCGA-ED-A82E-01A-11D-A34Z-10	TCGA-ED-A82E-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	64aa69e5-4ab1-45b5-aca6-c2584ac511a3	6a4d2501-89d2-42d5-9182-f5eb7a368506	g.chr12:1893123G>A	ENST00000357103.4	+	7	1167	c.916G>A	c.(916-918)Gcc>Acc	p.A306T		NM_024551.2	NP_078827.2	Q86V24	ADR2_HUMAN	adiponectin receptor 2	306					adiponectin-activated signaling pathway (GO:0033211)|fatty acid oxidation (GO:0019395)|female pregnancy (GO:0007565)|heart development (GO:0007507)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of cell growth (GO:0030308)|positive regulation of glucose import (GO:0046326)|response to nutrient (GO:0007584)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hormone binding (GO:0042562)|receptor activity (GO:0004872)			endometrium(1)|large_intestine(3)|lung(7)|stomach(1)	12	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.000382)			CCTTAAGGCCGCCACCATAGG	0.547																																					p.A306T		Atlas-SNP	.											ADIPOR2,colon,carcinoma,0,1	ADIPOR2	30	.	0			c.G916A						.						87	82	84					12																	1893123		2203	4300	6503	SO:0001583	missense	79602	exon7			AAGGCCGCCACCA	AY424280	CCDS8511.1	12p13	2012-08-22			ENSG00000006831	ENSG00000006831		"GPCR / Unclassified : Adiponectin receptors"	24041	protein-coding gene	gene with protein product		607946				12802337	Standard	NM_024551		Approved	PAQR2, ACDCR2	uc001qjm.3	Q86V24	OTTHUMG00000130139	ENST00000357103.4:c.916G>A	chr12.hg19:g.1893123G>A	ENSP00000349616:p.Ala306Thr	147.0	0.0		110.0	67.0	NM_024551	Q53YY5|Q9H737	Missense_Mutation	SNP	ENST00000357103.4	hg19	CCDS8511.1	.	.	.	.	.	.	.	.	.	.	G	12.59	1.983434	0.35036	.	.	ENSG00000006831	ENST00000357103	T	0.31510	1.49	5.67	5.67	0.87782	.	0.046236	0.85682	D	0.000000	T	0.17365	0.0417	N	0.03608	-0.345	0.58432	D	0.99999	B	0.16396	0.017	B	0.14023	0.01	T	0.11446	-1.0587	10	0.21540	T	0.41	-10.6523	19.7848	0.96432	0.0:0.0:1.0:0.0	.	306	Q86V24	ADR2_HUMAN	T	306	ENSP00000349616:A306T	ENSP00000349616:A306T	A	+	1	0	ADIPOR2	1763384	1.000000	0.71417	0.996000	0.52242	0.971000	0.66376	6.556000	0.73932	2.673000	0.90976	0.655000	0.94253	GCC	.	.		0.547	ADIPOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252447.2	NM_024551		A	1893123	G	A	1893123	3	1	248	1	0	0	0	0	1	0	0	0	319	1087	38	1	938	1	ADIPOR2	12	1893123	Missense_Mutation	SNP	G	TCGA-ED-A82E-01A-11D-A34Z-10		1893123	131958772	15	33869										
ATF7	11016	hgsc.bcm.edu	37	chr12	53928285	53928285	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.103448275862069	3	1	1.79166666666667	0	2.015625	0.142857142857143	0.729941291585128	0	ctccctgctctctgtacttaCcccatttgcctgttggatgg	8	14	1	0			TCGA-ED-A82E-01A-11D-A34Z-10	TCGA-ED-A82E-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	64aa69e5-4ab1-45b5-aca6-c2584ac511a3	6a4d2501-89d2-42d5-9182-f5eb7a368506	g.chr12:53928285C>G	ENST00000548446.2	-	6	706		c.e6+1		ATF7_ENST00000420353.2_Splice_Site|ATF7_ENST00000456903.4_Splice_Site|ATF7_ENST00000328463.7_Splice_Site|RP11-793H13.10_ENST00000591834.1_Splice_Site|ATF7_ENST00000415113.1_Splice_Site			P17544	ATF7_HUMAN	activating transcription factor 7						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear periphery (GO:0034399)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|mitogen-activated protein kinase binding (GO:0051019)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)|urinary_tract(1)	9					Pseudoephedrine(DB00852)	TCTGTACTTACCCCATTTGCC	0.478																																					.		Atlas-SNP	.											.	ATF7	51	.	0			c.560+1G>C						.						201	195	197					12																	53928285		1968	4161	6129	SO:0001630	splice_region_variant	11016	exon7			TACTTACCCCATT	X52943	CCDS44906.1, CCDS58238.1	12q13	2013-01-10				ENSG00000170653		"basic leucine zipper proteins"	792	protein-coding gene	gene with protein product		606371				1694576, 11278933	Standard	NM_006856		Approved	ATFA	uc001sdz.3	P17544	OTTHUMG00000169776	ENST00000548446.2:c.593+1G>C	chr12.hg19:g.53928285C>G		106.0	0.0		111.0	6.0	NM_006856	A5D6Y4|B2RMP1|B4DQL4|Q13814|Q8IVR8|Q9UD83	Splice_Site	SNP	ENST00000548446.2	hg19		.	.	.	.	.	.	.	.	.	.	C	22.3	4.274719	0.80580	.	.	ENSG00000170653	ENST00000548446;ENST00000328463;ENST00000415113;ENST00000420353;ENST00000456903	.	.	.	4.23	4.23	0.50019	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9044	0.79412	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ATF7	52214552	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.187000	0.77730	2.350000	0.79820	0.561000	0.74099	.	.	.		0.478	ATF7-007	KNOWN	NMD_exception|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000406302.2	NM_001130059	Intron	G	53928285	C	G	53928285	5	3	248	1	0	0	0	0	0	0	1	0	1086	521	18	4	918	4	ATF7	12	53928285	Splice_Site	SNP	C	TCGA-ED-A82E-01A-11D-A34Z-10	52035162	53928285	79923610	16	33870										
SLITRK5	26050	hgsc.bcm.edu	37	chr13	88329198	88329198	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.103448275862069	3	1	1.79166666666667	0	2.015625	0.142857142857143	0.729941291585128	0	tgaataacaacctcctgcagGccatgccctcaggcgtcttc	8	15	2	1	rs372673658		TCGA-ED-A82E-01A-11D-A34Z-10	TCGA-ED-A82E-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	64aa69e5-4ab1-45b5-aca6-c2584ac511a3	6a4d2501-89d2-42d5-9182-f5eb7a368506	g.chr13:88329198G>A	ENST00000325089.6	+	2	1774	c.1555G>A	c.(1555-1557)Gcc>Acc	p.A519T	SLITRK5_ENST00000400028.3_Missense_Mutation_p.A278T	NM_015567.1	NP_056382.1	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5	519					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|cardiovascular system development (GO:0072358)|dendrite morphogenesis (GO:0048813)|grooming behavior (GO:0007625)|response to xenobiotic stimulus (GO:0009410)|skin development (GO:0043588)|striatum development (GO:0021756)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(14)|lung(40)|ovary(2)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(4)	81	all_neural(89;0.101)|Medulloblastoma(90;0.163)					CCTCCTGCAGGCCATGCCCTC	0.527																																					p.A519T		Atlas-SNP	.											.	SLITRK5	192	.	0			c.G1555A						.	G	THR/ALA	0,4406		0,0,2203	67	70	69		1555	0.9	1	13		69	1,8599		0,1,4299	no	missense	SLITRK5	NM_015567.1	58	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	519/959	88329198	1,13005	2203	4300	6503	SO:0001583	missense	26050	exon2			CTGCAGGCCATGC	AB020725	CCDS9465.1	13q31.1	2004-04-16	2004-01-08		ENSG00000165300	ENSG00000165300			20295	protein-coding gene	gene with protein product		609680	"leucine rich repeat containing 11"	LRRC11		10048485, 14557068	Standard	NM_015567		Approved	bA364G4.2, KIAA0918	uc001vln.3	O94991	OTTHUMG00000017167	ENST00000325089.6:c.1555G>A	chr13.hg19:g.88329198G>A	ENSP00000366283:p.Ala519Thr	89.0	0.0		48.0	33.0	NM_015567	B3KNB8|B4DSH5|Q5VT81	Missense_Mutation	SNP	ENST00000325089.6	hg19	CCDS9465.1	.	.	.	.	.	.	.	.	.	.	G	2.279	-0.365156	0.05103	0.0	1.16E-4	ENSG00000165300	ENST00000325089;ENST00000400028	T;T	0.56776	0.44;0.44	5.23	0.903	0.19296	.	0.587641	0.17737	N	0.163719	T	0.23611	0.0571	N	0.05574	-0.02	0.29587	N	0.848702	B;B	0.02656	0.0;0.0	B;B	0.15052	0.012;0.006	T	0.10567	-1.0624	9	.	.	.	-5.743	2.4147	0.04433	0.2036:0.1425:0.5095:0.1445	.	278;519	B4DSH5;O94991	.;SLIK5_HUMAN	T	519;278	ENSP00000366283:A519T;ENSP00000442244:A278T	.	A	+	1	0	SLITRK5	87127199	0.977000	0.34250	0.999000	0.59377	0.998000	0.95712	0.237000	0.17985	0.109000	0.17891	0.561000	0.74099	GCC	.	.		0.527	SLITRK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045416.3			A	88329198	G	A	88329198	3	1	248	1	0	0	0	0	1	0	0	0	14761	1203	42	3	1557	3	SLITRK5	13	88329198	Missense_Mutation	SNP	G	TCGA-ED-A82E-01A-11D-A34Z-10		88329198	26840680	17	33871										
METT11D1	64745	hgsc.bcm.edu	37	chr14	21464877	21464877	+	Intron	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.103448275862069	3	1	1.79166666666667	0	2.015625	0.142857142857143	0.729941291585128	0	cgccggcacggcaggtatggGgggtgtgaccaaaatcagtg	17	9	1	1			TCGA-ED-A82E-01A-11D-A34Z-10	TCGA-ED-A82E-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	64aa69e5-4ab1-45b5-aca6-c2584ac511a3	6a4d2501-89d2-42d5-9182-f5eb7a368506	g.chr14:21464877G>T	ENST00000339374.6	+	13	1498				METTL17_ENST00000556670.2_Intron|RP11-84C10.4_ENST00000557335.1_RNA|SLC39A2_ENST00000298681.4_5'Flank|METTL17_ENST00000382985.4_Silent_p.G424G|SLC39A2_ENST00000554422.1_5'Flank	NM_001029991.1|NM_022734.2	NP_001025162.1|NP_073571.1	Q9H7H0	MET17_HUMAN	methyltransferase like 17						translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	copper ion binding (GO:0005507)|methyltransferase activity (GO:0008168)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|skin(2)	20						GCAGGTATGGGGGGTGTGACC	0.587																																					p.G424G		Atlas-SNP	.											.	METTL17	46	.	0			c.G1272T						.						93	93	93					14																	21464877		2203	4300	6503	SO:0001627	intron_variant	64745	exon13			GTATGGGGGGTGT	AK024512	CCDS9562.1, CCDS41913.1	14q11.2	2011-03-03	2011-03-02	2011-03-02	ENSG00000165792	ENSG00000165792			19280	protein-coding gene	gene with protein product			"methyltransferase 11 domain containing 1"	METT11D1		11278769	Standard	XM_006720235		Approved	FLJ20859	uc001vyn.3	Q9H7H0	OTTHUMG00000029610	ENST00000339374.6:c.1265+7G>T	chr14.hg19:g.21464877G>T		65.0	0.0		48.0	13.0	NM_001029991	Q9BSH1|Q9BZH2|Q9BZH3	Silent	SNP	ENST00000339374.6	hg19	CCDS9562.1																																																																																			.	.		0.587	METTL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073804.4	NM_022734		T	21464877	G	T	21464877	1	4	248	0	1	0	0	0	0	0	0	0	9500	1219	43	3		3	METT11D1	14	21464877	Intron	SNP	G	TCGA-ED-A82E-01A-11D-A34Z-10		21464877	85884663	18	33872										
SPPL2A	84888	hgsc.bcm.edu	37	chr15	51039809	51039809	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.103448275862069	3	1	1.79166666666667	0	2.015625	0.142857142857143	0.729941291585128	0	gagaatacattttcacagtaAtgttatctcctagagtctga	7	7	3	3			TCGA-ED-A82E-01A-11D-A34Z-10	TCGA-ED-A82E-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	64aa69e5-4ab1-45b5-aca6-c2584ac511a3	6a4d2501-89d2-42d5-9182-f5eb7a368506	g.chr15:51039809A>C	ENST00000261854.5	-	5	741	c.467T>G	c.(466-468)aTt>aGt	p.I156S	RP11-507J18.2_ENST00000558317.1_RNA	NM_032802.3	NP_116191.2	Q8TCT8	SPP2A_HUMAN	signal peptide peptidase like 2A	156					membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|regulation of immune response (GO:0050776)	extracellular vesicular exosome (GO:0070062)|Golgi-associated vesicle membrane (GO:0030660)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	15				all cancers(107;0.000712)|GBM - Glioblastoma multiforme(94;0.00314)		TTTCACAGTAATGTTATCTCC	0.363																																					p.I156S	Melanoma(50;790 1209 4069 22965 33125)	Atlas-SNP	.											.	SPPL2A	26	.	0			c.T467G						.						92	89	90					15																	51039809		2196	4293	6489	SO:0001583	missense	84888	exon5			ACAGTAATGTTAT		CCDS10138.1	15q21.2	2012-02-21			ENSG00000138600	ENSG00000138600			30227	protein-coding gene	gene with protein product	"intramembrane protease 3", "presenilin-like protein 2"	608238				12077416, 12139484	Standard	NM_032802		Approved	IMP3, PSL2	uc001zyv.3	Q8TCT8	OTTHUMG00000131647	ENST00000261854.5:c.467T>G	chr15.hg19:g.51039809A>C	ENSP00000261854:p.Ile156Ser	207.0	0.0		162.0	94.0	NM_032802	B2RDS0|Q8TAW1|Q96SZ8	Missense_Mutation	SNP	ENST00000261854.5	hg19	CCDS10138.1	.	.	.	.	.	.	.	.	.	.	A	9.143	1.014404	0.19277	.	.	ENSG00000138600	ENST00000261854	T	0.07800	3.16	5.73	4.58	0.56647	.	0.097598	0.64402	D	0.000001	T	0.10680	0.0261	L	0.42245	1.32	0.09310	N	1	P	0.36599	0.56	B	0.39876	0.312	T	0.08700	-1.0709	10	0.87932	D	0	-10.3558	12.0718	0.53620	0.8709:0.0:0.0:0.1291	.	156	Q8TCT8	PSL2_HUMAN	S	156	ENSP00000261854:I156S	ENSP00000261854:I156S	I	-	2	0	AC012100.1	48827101	1.000000	0.71417	0.135000	0.22099	0.159000	0.22180	6.640000	0.74319	0.955000	0.37878	0.533000	0.62120	ATT	.	.		0.363	SPPL2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254543.3	NM_032802		C	51039809	A	C	51039809	3	2	248	1	0	0	0	0	1	0	0	0	15103	101	4	5	1139	5	SPPL2A	15	51039809	Missense_Mutation	SNP	A	TCGA-ED-A82E-01A-11D-A34Z-10		51039809	51491583	19	33873										
IDH2	3418	hgsc.bcm.edu	37	chr15	90631838	90631838	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.103448275862069	3	1	1.79166666666667	0	2.015625	0.142857142857143	0.729941291585128	0	cctggtcgccatgggcgtgcCtgccaatggtgatgggcttg	16	11	0	1	rs121913503		TCGA-ED-A82E-01A-11D-A34Z-10	TCGA-ED-A82E-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	64aa69e5-4ab1-45b5-aca6-c2584ac511a3	6a4d2501-89d2-42d5-9182-f5eb7a368506	g.chr15:90631838C>T	ENST00000330062.3	-	4	628	c.515G>A	c.(514-516)aGg>aAg	p.R172K	IDH2_ENST00000539790.1_Missense_Mutation_p.R42K|IDH2_ENST00000540499.2_Missense_Mutation_p.R120K|IDH2_ENST00000559482.1_Intron	NM_002168.2	NP_002159.2	P48735	IDHP_HUMAN	isocitrate dehydrogenase 2 (NADP+), mitochondrial	172					2-oxoglutarate metabolic process (GO:0006103)|carbohydrate metabolic process (GO:0005975)|cellular metabolic process (GO:0044237)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)	p.R172K(116)|p.R172M(21)|p.R172N(1)		biliary_tract(11)|bone(19)|central_nervous_system(107)|endometrium(1)|haematopoietic_and_lymphoid_tissue(953)|large_intestine(8)|lung(5)|skin(5)	1109	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.106)			ATGGGCGTGCCTGCCAATGGT	0.632			M		GBM																																p.R172K		Atlas-SNP	.		Dom	yes		15	15q26.1	3418	"socitrate dehydrogenase 2 (NADP+), mitochondrial "		M	IDH2,NS,haematopoietic_neoplasm,0,179	IDH2	1372	.	138	Substitution - Missense(138)	haematopoietic_and_lymphoid_tissue(67)|central_nervous_system(65)|biliary_tract(6)	c.G515A						.						85	81	82					15																	90631838		2200	4298	6498	SO:0001583	missense	3418	exon4			GCGTGCCTGCCAA		CCDS10359.1	15q26.1	2014-09-17			ENSG00000182054	ENSG00000182054	1.1.1.42		5383	protein-coding gene	gene with protein product		147650					Standard	NM_001289910		Approved		uc002box.3	P48735	OTTHUMG00000149815	ENST00000330062.3:c.515G>A	chr15.hg19:g.90631838C>T	ENSP00000331897:p.Arg172Lys	151.0	0.0		100.0	49.0	NM_002168	B2R6L6|B4DFL2|Q96GT3	Missense_Mutation	SNP	ENST00000330062.3	hg19	CCDS10359.1	.	.	.	.	.	.	.	.	.	.	C	15.86	2.957149	0.53293	.	.	ENSG00000182054	ENST00000330062;ENST00000539790;ENST00000540499	D;D;D	0.86432	-2.12;-2.12;-2.12	5.93	4.07	0.47477	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.95217	0.8449	H	0.96889	3.9	0.49687	D	0.999812	D	0.89917	1.0	D	0.91635	0.999	D	0.95096	0.8226	10	0.87932	D	0	.	10.781	0.46377	0.0:0.8464:0.0:0.1536	.	172	P48735	IDHP_HUMAN	K	172;42;120	ENSP00000331897:R172K;ENSP00000438457:R42K;ENSP00000446147:R120K	ENSP00000331897:R172K	R	-	2	0	IDH2	88432842	1.000000	0.71417	0.025000	0.17156	0.001000	0.01503	7.797000	0.85911	0.862000	0.35528	-0.258000	0.10820	AGG	.	.		0.632	IDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313426.1			T	90631838	C	T	90631838	3	4	248	1	0	0	0	0	1	0	0	0	7504	681	24	3	875	3	IDH2	15	90631838	Missense_Mutation	SNP	C	TCGA-ED-A82E-01A-11D-A34Z-10	39592029	90631838	11899554	20	33874										
XYLT1	64131	hgsc.bcm.edu	37	chr16	17353089	17353089	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.103448275862069	3	1	1.79166666666667	0	2.015625	0.142857142857143	0.729941291585128	0	ccgtggctgctgttggctgcGgctctgtccccgggaggcag	17	13	1	0			TCGA-ED-A82E-01A-11D-A34Z-10	TCGA-ED-A82E-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	64aa69e5-4ab1-45b5-aca6-c2584ac511a3	6a4d2501-89d2-42d5-9182-f5eb7a368506	g.chr16:17353089G>A	ENST00000261381.6	-	3	753	c.669C>T	c.(667-669)gcC>gcT	p.A223A		NM_022166.3	NP_071449.1	Q86Y38	XYLT1_HUMAN	xylosyltransferase I	223					cellular response to heat (GO:0034605)|chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)	p.A223A(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						TGTTGGCTGCGGCTCTGTCCC	0.592																																					p.A223A		Atlas-SNP	.											XYLT1,NS,carcinoma,0,1	XYLT1	147	.	1	Substitution - coding silent(1)	lung(1)	c.C669T						.						106	117	113					16																	17353089		2197	4300	6497	SO:0001819	synonymous_variant	64131	exon3			GGCTGCGGCTCTG	AJ277441	CCDS10569.1	16p12	2013-02-25			ENSG00000103489	ENSG00000103489	2.4.2.26	"Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	15516	protein-coding gene	gene with protein product	"protein xylosyltransferase 1"	608124				11099377	Standard	NM_022166		Approved	XT-I, PXYLT1	uc002dfa.3	Q86Y38	OTTHUMG00000129975	ENST00000261381.6:c.669C>T	chr16.hg19:g.17353089G>A		148.0	0.0		153.0	69.0	NM_022166	Q9H1B6	Silent	SNP	ENST00000261381.6	hg19	CCDS10569.1																																																																																			.	.		0.592	XYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252241.2	NM_022166		A	17353089	G	A	17353089	2	1	248	1	0	0	0	0	0	0	0	1	17478	1103	39	1		1	XYLT1	16	17353089	Silent	SNP	G	TCGA-ED-A82E-01A-11D-A34Z-10		17353089	73001664	21	33875										
TBC1D26	353149	hgsc.bcm.edu	37	chr17	15644532	15644532	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.103448275862069	3	1	1.79166666666667	0	2.015625	0.142857142857143	0.729941291585128	0	gggcgcttacccagttgctcGctggtgagaggcactccctg	14	13	0	1			TCGA-ED-A82E-01A-11D-A34Z-10	TCGA-ED-A82E-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	64aa69e5-4ab1-45b5-aca6-c2584ac511a3	6a4d2501-89d2-42d5-9182-f5eb7a368506	g.chr17:15644532G>A	ENST00000437605.2	+	10	893	c.643G>A	c.(643-645)Gct>Act	p.A215T	AC005324.6_ENST00000580194.1_RNA|AC005324.6_ENST00000434017.1_RNA|AC005324.6_ENST00000433873.1_RNA|ZNF286A_ENST00000413242.2_3'UTR	NM_178571.4	NP_848666	Q86UD7	TBC26_HUMAN	TBC1 domain family, member 26	215	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						Rab GTPase activator activity (GO:0005097)			endometrium(1)|large_intestine(1)|lung(4)|skin(1)	7				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.078)		CCAGTTGCTCGCTGGTGAGAG	0.647																																					p.A215T		Atlas-SNP	.											.	TBC1D26	16	.	0			c.G643A						.						88	93	91					17																	15644532		2175	4275	6450	SO:0001583	missense	353149	exon10			TTGCTCGCTGGTG		CCDS42265.1	17p11.2	2008-11-04			ENSG00000214946	ENSG00000214946			28745	protein-coding gene	gene with protein product						11347906	Standard	NM_178571		Approved	MGC51025	uc010cov.3	Q86UD7	OTTHUMG00000059071	ENST00000437605.2:c.643G>A	chr17.hg19:g.15644532G>A	ENSP00000410111:p.Ala215Thr	37.0	0.0		22.0	14.0	NM_178571	A8K929|Q4G172	Missense_Mutation	SNP	ENST00000437605.2	hg19	CCDS42265.1																																																																																			.	.		0.647	TBC1D26-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178571		A	15644532	G	A	15644532	3	1	248	1	0	0	0	0	1	0	0	0	15631	1087	38	1	673	1	TBC1D26	17	15644532	Missense_Mutation	SNP	G	TCGA-ED-A82E-01A-11D-A34Z-10		15644532	65550678	22	33876										
MED29	55588	hgsc.bcm.edu	37	chr19	39883132	39883133	+	Frame_Shift_Ins	INS	-	-	GATTCAGAAC													0.103448275862069	3	1	1.79166666666667	0	2.015625	0.142857142857143	0.729941291585128	0	aaggttgcggcccaaaacttINSgattcagaacactaacatcg							TCGA-ED-A82E-01A-11D-A34Z-10	TCGA-ED-A82E-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	64aa69e5-4ab1-45b5-aca6-c2584ac511a3	6a4d2501-89d2-42d5-9182-f5eb7a368506	g.chr19:39883132_39883133insGATTCAGAAC	ENST00000599213.2	+	2	272_273	c.245_246insGATTCAGAAC	c.(244-249)ttgattfs	p.-83fs	PAF1_ENST00000595564.1_5'Flank|MED29_ENST00000594368.1_Frame_Shift_Ins_p.-83fs|PAF1_ENST00000221265.3_5'Flank|PAF1_ENST00000221266.7_5'Flank|MED29_ENST00000315588.5_Frame_Shift_Ins_p.-104fs			Q9NX70	MED29_HUMAN	mediator complex subunit 29						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	mediator complex (GO:0016592)|nucleus (GO:0005634)				lung(2)|ovary(1)|pancreas(1)	4	all_cancers(60;7.82e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;1.88e-06)|Ovarian(47;0.0512)		Epithelial(26;1.04e-26)|all cancers(26;7.68e-24)|Lung(45;0.000168)|LUSC - Lung squamous cell carcinoma(53;0.000199)			GCCCAAAACTTGATTCAGAACA	0.426																																					p.L103fs		Pindel	.											.	MED29	13	.	0			c.308_309insGATTCAGAAC						.																																			SO:0001589	frameshift_variant	55588	exon2			.	AL137304, AY729650	CCDS33021.1	19q13.2	2007-07-30	2007-07-30	2007-07-30		ENSG00000063322			23074	protein-coding gene	gene with protein product		612914	"intersex-like (Drosophila)"	IXL		15555573	Standard	NM_017592		Approved	DKFZp434H247	uc010xux.3	Q9NX70		ENST00000599213.2:c.246_255dupGATTCAGAAC	chr19.hg19:g.39883133_39883142dupGATTCAGAAC	ENSP00000471802:p.Ile83fs	86.0	0.0		52.0	13.0	NM_017592	B4DNQ6|M0R2E4|Q5XX09|Q9NTF4	Frame_Shift_Ins	INS	ENST00000599213.2	hg19																																																																																				.	.		0.426	MED29-011	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000470870.1	XM_290829		GATTCAGAAC	39883133	-	GATTCAGAAC	39883132	7	5	248	1	0	1	1	0	0	0	0	0	9456	1821	63	0	314	0	MED29	19	39883132	Frame_Shift_Ins	INS	-	TCGA-ED-A82E-01A-11D-A34Z-10		39883132	19245851	23	33877										
RCN3	57333	hgsc.bcm.edu	37	chr19	50031779	50031779	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.103448275862069	3	1	1.79166666666667	0	2.015625	0.142857142857143	0.729941291585128	0	tctgttgctactgaggcacgGggcccaggggaagccatccc	14	13	1	1			TCGA-ED-A82E-01A-11D-A34Z-10	TCGA-ED-A82E-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	64aa69e5-4ab1-45b5-aca6-c2584ac511a3	6a4d2501-89d2-42d5-9182-f5eb7a368506	g.chr19:50031779G>A	ENST00000270645.3	+	2	497	c.50G>A	c.(49-51)gGg>gAg	p.G17E		NM_020650.2	NP_065701.2	Q96D15	RCN3_HUMAN	reticulocalbin 3, EF-hand calcium binding domain	17						endoplasmic reticulum (GO:0005783)	calcium ion binding (GO:0005509)			endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	12		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.0966)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00295)|GBM - Glioblastoma multiforme(134;0.0159)		CTGAGGCACGGGGCCCAGGGG	0.682																																					p.G17E		Atlas-SNP	.											.	RCN3	28	.	0			c.G50A						.						119	127	124					19																	50031779		2203	4300	6503	SO:0001583	missense	57333	exon2			GGCACGGGGCCCA	AY195859	CCDS12771.1	19q13.33	2013-01-10				ENSG00000142552		"EF-hand domain containing"	21145	protein-coding gene	gene with protein product							Standard	NM_020650		Approved	RLP49	uc002poj.3	Q96D15		ENST00000270645.3:c.50G>A	chr19.hg19:g.50031779G>A	ENSP00000270645:p.Gly17Glu	82.0	0.0		78.0	28.0	NM_020650	Q9HBZ8	Missense_Mutation	SNP	ENST00000270645.3	hg19	CCDS12771.1	.	.	.	.	.	.	.	.	.	.	G	10.37	1.331666	0.24167	.	.	ENSG00000142552	ENST00000270645	T	0.09538	2.97	4.22	3.19	0.36642	.	0.185850	0.26421	N	0.024478	T	0.06280	0.0162	N	0.19112	0.55	0.09310	N	0.999995	B	0.02656	0.0	B	0.01281	0.0	T	0.27297	-1.0078	10	0.30854	T	0.27	-34.4868	7.5145	0.27593	0.0971:0.1729:0.73:0.0	.	17	Q96D15	RCN3_HUMAN	E	17	ENSP00000270645:G17E	ENSP00000270645:G17E	G	+	2	0	RCN3	54723591	0.260000	0.24053	0.890000	0.34922	0.361000	0.29550	1.160000	0.31761	2.389000	0.81357	0.456000	0.33151	GGG	.	.		0.682	RCN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465261.1	NM_020650		A	50031779	G	A	50031779	3	1	248	1	0	0	0	0	1	0	0	0	13196	1232	43	3	52	3	RCN3	19	50031779	Missense_Mutation	SNP	G	TCGA-ED-A82E-01A-11D-A34Z-10	10148647	50031779	9097204	24	33878										
POLD1	5424	hgsc.bcm.edu	37	chr19	50917028	50917028	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.103448275862069	3	1	1.79166666666667	0	2.015625	0.142857142857143	0.729941291585128	0	ggtgacactgactccgtcatGtgccgattcggcgtgtcctc	12	13	1	2			TCGA-ED-A82E-01A-11D-A34Z-10	TCGA-ED-A82E-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	64aa69e5-4ab1-45b5-aca6-c2584ac511a3	6a4d2501-89d2-42d5-9182-f5eb7a368506	g.chr19:50917028G>T	ENST00000440232.2	+	19	2333	c.2280G>T	c.(2278-2280)atG>atT	p.M760I	POLD1_ENST00000595904.1_Missense_Mutation_p.M786I|POLD1_ENST00000599857.1_Missense_Mutation_p.M760I|CTD-2545M3.6_ENST00000599632.1_5'Flank	NM_001256849.1|NM_002691.3	NP_001243778.1|NP_002682.2	P28340	DPOD1_HUMAN	polymerase (DNA directed), delta 1, catalytic subunit	760					base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|fatty acid homeostasis (GO:0055089)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)|response to UV (GO:0009411)|small molecule metabolic process (GO:0044281)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|delta DNA polymerase complex (GO:0043625)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		ACTCCGTCATGTGCCGATTCG	0.652								DNA polymerases (catalytic subunits)																													p.M760I		Atlas-SNP	.											.	POLD1	174	.	0			c.G2280T						.						86	72	77					19																	50917028		2203	4300	6503	SO:0001583	missense	5424	exon19			CGTCATGTGCCGA		CCDS12795.1	19q13.3	2014-09-17	2012-05-18		ENSG00000062822	ENSG00000062822		"DNA polymerases"	9175	protein-coding gene	gene with protein product	"CDC2 homolog (S. cerevisiae)"	174761	"polymerase (DNA directed), delta 1, catalytic subunit (125kD)"	POLD		1722322	Standard	NM_001256849		Approved	CDC2	uc002psc.5	P28340		ENST00000440232.2:c.2280G>T	chr19.hg19:g.50917028G>T	ENSP00000406046:p.Met760Ile	51.0	0.0		56.0	7.0	NM_002691	Q8NER3|Q96H98	Missense_Mutation	SNP	ENST00000440232.2	hg19	CCDS12795.1	.	.	.	.	.	.	.	.	.	.	G	31	5.058356	0.93846	.	.	ENSG00000062822	ENST00000440232;ENST00000376930	T	0.21191	2.02	4.87	4.87	0.63330	DNA polymerase, palm domain (1);DNA-directed DNA polymerase, family B, conserved site (1);DNA-directed DNA polymerase, family B, multifunctional domain (1);	0.000000	0.85682	D	0.000000	T	0.68320	0.2988	H	0.99712	4.72	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.84442	0.0583	10	0.87932	D	0	-59.8404	17.161	0.86803	0.0:0.0:1.0:0.0	.	786;760	E7EVW0;P28340	.;DPOD1_HUMAN	I	760;761	ENSP00000406046:M760I	ENSP00000366129:M761I	M	+	3	0	POLD1	55608840	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	8.774000	0.91767	2.432000	0.82394	0.556000	0.70494	ATG	.	.		0.652	POLD1-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464732.1			T	50917028	G	T	50917028	3	4	248	1	0	0	0	0	1	0	0	0	12199	1377	48	3	2350	3	POLD1	19	50917028	Missense_Mutation	SNP	G	TCGA-ED-A82E-01A-11D-A34Z-10	885249	50917028	8211955	25	33879										
FPR1	2357	hgsc.bcm.edu	37	chr19	52249927	52249927	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.103448275862069	3	1	1.79166666666667	0	2.015625	0.142857142857143	0.729941291585128	0	aagacacttccgaacaagttGatgtccactatggtaaagac	8	9	0	3			TCGA-ED-A82E-01A-11D-A34Z-10	TCGA-ED-A82E-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	64aa69e5-4ab1-45b5-aca6-c2584ac511a3	6a4d2501-89d2-42d5-9182-f5eb7a368506	g.chr19:52249927G>T	ENST00000595042.1	-	3	462	c.321C>A	c.(319-321)atC>atA	p.I107I	FPR1_ENST00000304748.4_Silent_p.I107I	NM_001193306.1	NP_001180235.1	P21462	FPR1_HUMAN	formyl peptide receptor 1	107					activation of MAPK activity (GO:0000187)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|nitric oxide mediated signal transduction (GO:0007263)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	N-formyl peptide receptor activity (GO:0004982)|receptor activity (GO:0004872)			endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(3)	20		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00106)|OV - Ovarian serous cystadenocarcinoma(262;0.018)	Nedocromil(DB00716)	CGAACAAGTTGATGTCCACTA	0.542																																					p.I107I		Atlas-SNP	.											FPR1,NS,carcinoma,0,1	FPR1	64	.	0			c.C321A						.						130	99	110					19																	52249927		2203	4300	6503	SO:0001819	synonymous_variant	2357	exon3			CAAGTTGATGTCC	M60627	CCDS12839.1	19q13.41	2014-09-17				ENSG00000171051		"GPCR / Class A : Formyl peptide receptors"	3826	protein-coding gene	gene with protein product		136537				2161213, 12595898	Standard	NM_001193306		Approved	FPR, FMLP	uc002pxq.3	P21462		ENST00000595042.1:c.321C>A	chr19.hg19:g.52249927G>T		75.0	0.0		102.0	40.0	NM_001193306	Q14939|Q7Z6A4|Q86U52|Q9NS48	Silent	SNP	ENST00000595042.1	hg19	CCDS12839.1																																																																																			.	.		0.542	FPR1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466905.1	NM_002029		T	52249927	G	T	52249927	2	4	248	1	0	0	0	0	0	0	0	1	6046	1280	45	3		3	FPR1	19	52249927	Silent	SNP	G	TCGA-ED-A82E-01A-11D-A34Z-10	1332899	52249927	6879056	26	33880										
ADRM1	11047	hgsc.bcm.edu	37	chr20	60882773	60882773	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.103448275862069	3	1	1.79166666666667	0	2.015625	0.142857142857143	0.729941291585128	0	cgagccccgcgcccagttccGggaatggagccagcacagca	13	16	0	0			TCGA-ED-A82E-01A-11D-A34Z-10	TCGA-ED-A82E-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	64aa69e5-4ab1-45b5-aca6-c2584ac511a3	6a4d2501-89d2-42d5-9182-f5eb7a368506	g.chr20:60882773G>C	ENST00000253003.2	+	7	791	c.745G>C	c.(745-747)Ggg>Cgg	p.G249R	RP11-157P1.4_ENST00000414042.1_RNA|LAMA5_ENST00000492698.1_5'Flank	NM_007002.2|NM_175573.1	NP_008933.2|NP_783163.1	Q16186	ADRM1_HUMAN	adhesion regulating molecule 1	249	Ser-rich.				positive regulation of endopeptidase activity (GO:0010950)|proteasome assembly (GO:0043248)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteasome complex (GO:0000502)	endopeptidase activator activity (GO:0061133)|protease binding (GO:0002020)|proteasome binding (GO:0070628)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|urinary_tract(1)	5	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;2.51e-06)			GCCCAGTTCCGGGAATGGAGC	0.682																																					p.G249R		Atlas-SNP	.											.	ADRM1	28	.	0			c.G745C						.						24	28	27					20																	60882773		2191	4294	6485	SO:0001583	missense	11047	exon7			AGTTCCGGGAATG	D64154	CCDS13496.1, CCDS74747.1	20q13.33	2008-05-22			ENSG00000130706	ENSG00000130706			15759	protein-coding gene	gene with protein product		610650				8033103	Standard	NM_007002		Approved	GP110, Rpn13, ARM1	uc002yco.3	Q16186	OTTHUMG00000032904	ENST00000253003.2:c.745G>C	chr20.hg19:g.60882773G>C	ENSP00000253003:p.Gly249Arg	51.0	0.0		69.0	27.0	NM_175573	A0PKB1|Q96FJ7|Q9H1P2	Missense_Mutation	SNP	ENST00000253003.2	hg19	CCDS13496.1	.	.	.	.	.	.	.	.	.	.	G	15.75	2.925897	0.52759	.	.	ENSG00000130706	ENST00000370744;ENST00000253003	.	.	.	5.14	5.14	0.70334	.	0.371360	0.32836	N	0.005582	T	0.67813	0.2933	L	0.43152	1.355	0.58432	D	0.999999	D	0.67145	0.996	D	0.64776	0.929	T	0.68750	-0.5326	9	0.51188	T	0.08	-15.6201	16.3736	0.83374	0.0:0.0:1.0:0.0	.	249	Q16186	ADRM1_HUMAN	R	228;249	.	ENSP00000253003:G249R	G	+	1	0	ADRM1	60316168	1.000000	0.71417	0.797000	0.32132	0.485000	0.33311	4.446000	0.60014	2.391000	0.81399	0.561000	0.74099	GGG	.	.		0.682	ADRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080007.1			C	60882773	G	C	60882773	3	2	248	1	0	0	0	0	1	0	0	0	345	1116	39	4	767	4	ADRM1	20	60882773	Missense_Mutation	SNP	G	TCGA-ED-A82E-01A-11D-A34Z-10		60882773	2142747	27	33881										
ITGB2	3689	hgsc.bcm.edu	37	chr21	46309959	46309959	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.103448275862069	3	1	1.79166666666667	0	2.015625	0.142857142857143	0.729941291585128	0	gtcacactcgcagtactgccCgtatatcagcttgccgggga	11	13	2	0			TCGA-ED-A82E-01A-11D-A34Z-10	TCGA-ED-A82E-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	64aa69e5-4ab1-45b5-aca6-c2584ac511a3	6a4d2501-89d2-42d5-9182-f5eb7a368506	g.chr21:46309959C>T	ENST00000397850.2	-	13	2043	c.1591G>A	c.(1591-1593)Ggg>Agg	p.G531R	ITGB2_ENST00000355153.4_Missense_Mutation_p.G531R|ITGB2_ENST00000397852.1_Missense_Mutation_p.G531R|ITGB2_ENST00000397854.3_Missense_Mutation_p.G474R|ITGB2_ENST00000397857.1_Missense_Mutation_p.G531R|ITGB2_ENST00000302347.5_Missense_Mutation_p.G531R			P05107	ITB2_HUMAN	integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)	531	Cysteine-rich tandem repeats.				apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|neutrophil chemotaxis (GO:0030593)|receptor clustering (GO:0043113)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|vesicle (GO:0031982)	cell adhesion molecule binding (GO:0050839)|glycoprotein binding (GO:0001948)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(4)|skin(3)	35				Colorectal(79;0.0669)	Simvastatin(DB00641)	CAGTACTGCCCGTATATCAGC	0.647																																					p.G531R		Atlas-SNP	.											.	ITGB2	107	.	0			c.G1591A						.						98	81	87					21																	46309959		2202	4300	6502	SO:0001583	missense	3689	exon12			ACTGCCCGTATAT	AK222505	CCDS13716.1	21q22.3	2014-09-17	2006-03-02		ENSG00000160255	ENSG00000160255		"CD molecules", "Complement system", "Integrins"	6155	protein-coding gene	gene with protein product		600065	"integrin, beta 2 (antigen CD18 (p95), lymphocyte function-associated antigen 1; macrophage antigen 1 (mac-1) beta subunit)"	CD18, MFI7			Standard	NM_000211		Approved	LFA-1, MAC-1	uc002zgf.3	P05107	OTTHUMG00000090257	ENST00000397850.2:c.1591G>A	chr21.hg19:g.46309959C>T	ENSP00000380948:p.Gly531Arg	99.0	0.0		82.0	38.0	NM_000211	B3KTS8|D3DSM1|Q16418|Q53HS5|Q9UD72	Missense_Mutation	SNP	ENST00000397850.2	hg19	CCDS13716.1	.	.	.	.	.	.	.	.	.	.	C	17.58	3.424904	0.62733	.	.	ENSG00000160255	ENST00000397852;ENST00000397857;ENST00000397854;ENST00000355153;ENST00000397850;ENST00000302347	D;D;D;D;D;D	0.98732	-5.1;-5.1;-5.1;-5.1;-5.1;-5.1	4.77	4.77	0.60923	.	.	.	.	.	D	0.99498	0.9821	H	0.98388	4.22	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.97903	1.0304	9	0.87932	D	0	.	15.3224	0.74132	0.0:1.0:0.0:0.0	.	474;531	A8MYE6;P05107	.;ITB2_HUMAN	R	531;531;474;531;531;531	ENSP00000380950:G531R;ENSP00000380955:G531R;ENSP00000380952:G474R;ENSP00000347279:G531R;ENSP00000380948:G531R;ENSP00000303242:G531R	ENSP00000303242:G531R	G	-	1	0	ITGB2	45134387	1.000000	0.71417	0.728000	0.30774	0.021000	0.10359	7.135000	0.77276	2.470000	0.83445	0.655000	0.94253	GGG	.	.		0.647	ITGB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206566.2	NM_000211		T	46309959	C	T	46309959	3	4	248	1	0	0	0	0	1	0	0	0	7903	652	23	1	738	1	ITGB2	21	46309959	Missense_Mutation	SNP	C	TCGA-ED-A82E-01A-11D-A34Z-10		46309959	1819936	28	33882										
PMM1	5372	hgsc.bcm.edu	37	chr22	41980580	41980580	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.103448275862069	3	1	1.79166666666667	0	2.015625	0.142857142857143	0.729941291585128	0	actgcaccgtcccgttctcgGcaaacacataatcaaacttc	5	15	2	0			TCGA-ED-A82E-01A-11D-A34Z-10	TCGA-ED-A82E-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	64aa69e5-4ab1-45b5-aca6-c2584ac511a3	6a4d2501-89d2-42d5-9182-f5eb7a368506	g.chr22:41980580G>A	ENST00000216259.7	-	3	317	c.233C>T	c.(232-234)gCc>gTc	p.A78V	PMM1_ENST00000466645.1_5'UTR	NM_002676.2	NP_002667.2	Q92871	PMM1_HUMAN	phosphomannomutase 1	78					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|mannose biosynthetic process (GO:0019307)|mannose metabolic process (GO:0006013)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)	metal ion binding (GO:0046872)|phosphomannomutase activity (GO:0004615)			NS(1)|large_intestine(4)|lung(3)|ovary(1)|urinary_tract(2)	11						CCCGTTCTCGGCAAACACATA	0.537																																					p.A78V		Atlas-SNP	.											.	PMM1	21	.	0			c.C233T						.						92	87	89					22																	41980580		2203	4300	6503	SO:0001583	missense	5372	exon3			TTCTCGGCAAACA		CCDS14020.1	22q13	2008-12-01			ENSG00000100417	ENSG00000100417	5.4.2.8		9114	protein-coding gene	gene with protein product	"brain glucose-1,6-bisphosphatase"	601786				9070917, 9271215	Standard	NM_002676		Approved	Sec53	uc003bal.2	Q92871	OTTHUMG00000150972	ENST00000216259.7:c.233C>T	chr22.hg19:g.41980580G>A	ENSP00000216259:p.Ala78Val	58.0	0.0		35.0	4.0	NM_002676	A8K003|Q92586	Missense_Mutation	SNP	ENST00000216259.7	hg19	CCDS14020.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.035684	0.75617	.	.	ENSG00000100417	ENST00000216259	D	0.98455	-4.94	4.76	4.76	0.60689	HAD-like domain (2);	0.000000	0.85682	D	0.000000	D	0.97813	0.9282	M	0.87827	2.91	0.80722	D	1	B	0.18863	0.031	B	0.15484	0.013	D	0.97398	0.9994	10	0.46703	T	0.11	-32.235	17.7702	0.88489	0.0:0.0:1.0:0.0	.	78	Q92871	PMM1_HUMAN	V	78	ENSP00000216259:A78V	ENSP00000216259:A78V	A	-	2	0	PMM1	40310526	1.000000	0.71417	0.947000	0.38551	0.644000	0.38419	9.631000	0.98424	2.191000	0.70037	0.557000	0.71058	GCC	.	.		0.537	PMM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320711.3	NM_002676		A	41980580	G	A	41980580	3	1	248	1	0	0	0	0	1	0	0	0	12145	1203	42	3	579	3	PMM1	22	41980580	Missense_Mutation	SNP	G	TCGA-ED-A82E-01A-11D-A34Z-10		41980580	9323986	29	33883										
HSPG2	3339	hgsc.bcm.edu	37	chr1	22180823	22180823	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	agacctgggggagccgcagaCgggagccgtgcacctgggcc	18	13	0	2	rs369444110	byFrequency	TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr1:22180823C>T	ENST00000374695.3	-	50	6381	c.6302G>A	c.(6301-6303)cGt>cAt	p.R2101H	HSPG2_ENST00000430507.1_Missense_Mutation_p.R51H	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2101	Ig-like C2-type 6.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GAGCCGCAGACGGGAGCCGTG	0.597													C|||	2	0.000399361	0	0.0014	5008	,	,		18063	0		0	False		,,,				2504	0.001				p.R2101H		Atlas-SNP	.											.	HSPG2	311	.	0			c.G6302A						.	C	HIS/ARG	0,4382		0,0,2191	16	14	15		6302	4.6	1	1		15	1,8567		0,1,4283	no	missense	HSPG2	NM_005529.5	29	0,1,6474	TT,TC,CC		0.0117,0.0,0.0077	probably-damaging	2101/4392	22180823	1,12949	2191	4284	6475	SO:0001583	missense	3339	exon50			CGCAGACGGGAGC	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"Proteoglycans / Extracellular Matrix : Other", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5273	protein-coding gene	gene with protein product	"perlecan proteoglycan"	142461	"Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.6302G>A	chr1.hg19:g.22180823C>T	ENSP00000363827:p.Arg2101His	113.0	0.0		40.0	31.0	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	hg19	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	C	15.90	2.968677	0.53614	0.0	1.17E-4	ENSG00000142798	ENST00000374695;ENST00000430507	T;T	0.67865	-0.29;-0.29	5.56	4.64	0.57946	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.35096	N	0.003443	T	0.69922	0.3165	L	0.37507	1.11	0.40471	D	0.980346	D;D	0.89917	0.999;1.0	D;D	0.74348	0.97;0.983	T	0.67511	-0.5652	10	0.34782	T	0.22	.	9.099	0.36656	0.0:0.8332:0.0:0.1668	.	41;2101	Q59EG0;P98160	.;PGBM_HUMAN	H	2101;51	ENSP00000363827:R2101H;ENSP00000416385:R51H	ENSP00000363827:R2101H	R	-	2	0	HSPG2	22053410	0.700000	0.27796	1.000000	0.80357	0.885000	0.51271	0.698000	0.25571	2.629000	0.89072	0.655000	0.94253	CGT	.	.		0.597	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		T	22180823	C	T	22180823	3	4	249	1	0	0	0	0	1	0	0	0	7439	536	19	1	7065	1	HSPG2	1	22180823	Missense_Mutation	SNP	C	TCGA-ED-A8O5-01A-11D-A35Z-10		22180823	227069798	1	33884										
CCDC21	64793	hgsc.bcm.edu	37	chr1	26601548	26601548	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	cagccctgcagcagctgcgcAcagccgtgaaggaggtgagc	15	13	0	2			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr1:26601548A>G	ENST00000252992.4	+	12	2019	c.1888A>G	c.(1888-1890)Aca>Gca	p.T630A	CEP85_ENST00000451429.2_Missense_Mutation_p.T579A|CEP85_ENST00000469609.1_3'UTR	NM_001281517.1|NM_022778.2	NP_001268446.1|NP_073615.2	Q6P2H3	CEP85_HUMAN	centrosomal protein 85kDa	630						centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|spindle pole (GO:0000922)				breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(11)|skin(2)	25						GCAGCTGCGCACAGCCGTGAA	0.547																																					p.T630A		Atlas-SNP	.											.	CEP85	61	.	0			c.A1888G						.						47	43	44					1																	26601548		2195	4282	6477	SO:0001583	missense	64793	exon12			CTGCGCACAGCCG	AK024038	CCDS277.1, CCDS60038.1	1p36.11	2014-02-20	2011-05-06	2011-05-06	ENSG00000130695	ENSG00000130695			25309	protein-coding gene	gene with protein product			"coiled-coil domain containing 21"	CCDC21		12477932	Standard	NM_022778		Approved	DKFZP434L0117	uc001bls.1	Q6P2H3	OTTHUMG00000003380	ENST00000252992.4:c.1888A>G	chr1.hg19:g.26601548A>G	ENSP00000252992:p.Thr630Ala	132.0	0.0		59.0	39.0	NM_022778	B4DRL1|D3DPK4|F8W7K4|Q5VY68|Q5VY70|Q9H6Q1|Q9H828|Q9UF52	Missense_Mutation	SNP	ENST00000252992.4	hg19	CCDS277.1	.	.	.	.	.	.	.	.	.	.	A	11.29	1.593707	0.28445	.	.	ENSG00000130695	ENST00000451429;ENST00000252992	T;T	0.11930	2.73;2.73	5.57	2.94	0.34122	.	0.533866	0.22326	N	0.061523	T	0.08447	0.0210	L	0.35723	1.085	0.23735	N	0.996984	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.10450	0.004;0.005;0.002	T	0.38436	-0.9661	10	0.09843	T	0.71	-3.029	5.2166	0.15346	0.6046:0.0:0.2597:0.1357	.	579;630;630	F8W7K4;Q6P2H3;Q6P2H3-2	.;CEP85_HUMAN;.	A	579;630	ENSP00000417002:T579A;ENSP00000252992:T630A	ENSP00000252992:T630A	T	+	1	0	CEP85	26474135	0.980000	0.34600	1.000000	0.80357	0.978000	0.69477	0.935000	0.28924	0.933000	0.37291	0.459000	0.35465	ACA	.	.		0.547	CEP85-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009492.2	NM_022778		G	26601548	A	G	26601548	3	3	249	1	0	0	0	0	1	0	0	0	2798	159	6	2	1930	2	CCDC21	1	26601548	Missense_Mutation	SNP	A	TCGA-ED-A8O5-01A-11D-A35Z-10	4420725	26601548	222649073	2	33885										
OSBPL9	114883	hgsc.bcm.edu	37	chr1	52238325	52238325	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	tgatgatgcggaggcagggtCtgtggaggagcacaagagcg	19	6	1	3			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr1:52238325C>T	ENST00000428468.1	+	14	1102	c.1100C>T	c.(1099-1101)tCt>tTt	p.S367F	OSBPL9_ENST00000435686.2_Missense_Mutation_p.S202F|OSBPL9_ENST00000361556.5_Missense_Mutation_p.S257F|OSBPL9_ENST00000453295.1_Missense_Mutation_p.S350F|OSBPL9_ENST00000371710.3_Missense_Mutation_p.S385F|OSBPL9_ENST00000337809.4_Missense_Mutation_p.S372F|OSBPL9_ENST00000371714.1_Missense_Mutation_p.S354F|OSBPL9_ENST00000462759.1_Missense_Mutation_p.S189F|OSBPL9_ENST00000530544.1_Missense_Mutation_p.S286F|OSBPL9_ENST00000486942.1_Missense_Mutation_p.S189F|OSBPL9_ENST00000447887.1_Missense_Mutation_p.S377F|OSBPL9_ENST00000531828.1_Missense_Mutation_p.S202F			Q96SU4	OSBL9_HUMAN	oxysterol binding protein-like 9	367					lipid transport (GO:0006869)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(3)|pancreas(1)|prostate(3)|skin(1)	18						GAGGCAGGGTCTGTGGAGGAG	0.433																																					p.S377F		Atlas-SNP	.											.	OSBPL9	192	.	0			c.C1130T						.						245	216	226					1																	52238325		2203	4300	6503	SO:0001583	missense	114883	exon14			CAGGGTCTGTGGA	AF392445	CCDS558.1, CCDS41332.1, CCDS41333.1, CCDS41334.1, CCDS41332.2, CCDS41332.3, CCDS41333.2, CCDS44145.1, CCDS55598.1	1p32.3	2013-01-10			ENSG00000117859	ENSG00000117859		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16386	protein-coding gene	gene with protein product		606737					Standard	NM_148904		Approved		uc001csu.3	Q96SU4	OTTHUMG00000008234	ENST00000428468.1:c.1100C>T	chr1.hg19:g.52238325C>T	ENSP00000407168:p.Ser367Phe	97.0	0.0		39.0	27.0	NM_148909	B1AKJ8|B3KPQ4|D3DQ31|Q5TFC0|Q6IA67|Q86YQ3|Q8NB17|Q8TAS8|Q96SK4|Q9H9X2	Missense_Mutation	SNP	ENST00000428468.1	hg19	CCDS41332.3	.	.	.	.	.	.	.	.	.	.	C	18.42	3.620945	0.66787	.	.	ENSG00000117859	ENST00000371714;ENST00000371710;ENST00000337809;ENST00000447887;ENST00000435686;ENST00000428468;ENST00000453295;ENST00000530544;ENST00000531828;ENST00000361556;ENST00000462759;ENST00000486942	T;T;T;T;T	0.16196	2.39;2.6;2.6;2.36;2.4	4.92	4.92	0.64577	.	0.000000	0.85682	D	0.000000	T	0.44414	0.1292	M	0.76838	2.35	0.80722	D	1	D;D;D;D;D	0.76494	0.996;0.999;0.999;0.998;0.998	P;D;D;D;D	0.69654	0.862;0.965;0.949;0.923;0.923	T	0.45833	-0.9234	10	0.72032	D	0.01	-5.4603	18.3308	0.90268	0.0:1.0:0.0:0.0	.	350;257;383;367;372	Q86YQ3;Q96SU4-3;B1AKJ7;Q96SU4;B1AKJ6	.;.;.;OSBL9_HUMAN;.	F	354;385;372;377;202;367;350;286;202;257;189;189	ENSP00000360779:S354F;ENSP00000360775:S385F;ENSP00000337265:S372F;ENSP00000412733:S377F;ENSP00000407168:S367F	ENSP00000337265:S372F	S	+	2	0	OSBPL9	52010913	1.000000	0.71417	0.810000	0.32431	0.276000	0.26787	7.288000	0.78691	2.563000	0.86464	0.650000	0.86243	TCT	.	.		0.433	OSBPL9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000022584.4			T	52238325	C	T	52238325	3	4	249	1	0	0	0	0	1	0	0	0	11293	913	32	3	1258	3	OSBPL9	1	52238325	Missense_Mutation	SNP	C	TCGA-ED-A8O5-01A-11D-A35Z-10	25636777	52238325	197012296	3	33886										
NOTCH2	4853	hgsc.bcm.edu	37	chr1	120462183	120462183	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	tgcatcttcatcttcatcacTcaaatctgagctgcctcctc	4	15	7	1			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr1:120462183T>G	ENST00000256646.2	-	31	5752	c.5533A>C	c.(5533-5535)Agt>Cgt	p.S1845R	NOTCH2_ENST00000493703.1_5'Flank	NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	1845					apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		TCTTCATCACTCAAATCTGAG	0.502			"N, F, Mis"		"marginal zone lymphoma, DLBCL"				Alagille Syndrome																												p.S1845R		Atlas-SNP	.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	.	NOTCH2	348	.	0			c.A5533C						.						54	46	49					1																	120462183		2203	4300	6503	SO:0001583	missense	4853	exon31	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	CATCACTCAAATC	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"Ankyrin repeat domain containing"	7882	protein-coding gene	gene with protein product		600275	"Notch (Drosophila) homolog 2", "Notch homolog 2 (Drosophila)"			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.5533A>C	chr1.hg19:g.120462183T>G	ENSP00000256646:p.Ser1845Arg	140.0	0.0		164.0	49.0	NM_024408	Q5T3X7|Q99734|Q9H240	Missense_Mutation	SNP	ENST00000256646.2	hg19	CCDS908.1	.	.	.	.	.	.	.	.	.	.	T	15.51	2.856220	0.51376	.	.	ENSG00000134250	ENST00000256646	D	0.82167	-1.58	5.84	5.84	0.93424	Ankyrin repeat-containing domain (3);	0.000000	0.44285	U	0.000479	T	0.65228	0.2671	L	0.51422	1.61	0.37247	D	0.906371	P	0.51933	0.949	B	0.36666	0.23	T	0.71813	-0.4479	10	0.42905	T	0.14	.	9.8179	0.40865	0.0:0.0758:0.0:0.9242	.	1845	Q04721	NOTC2_HUMAN	R	1845	ENSP00000256646:S1845R	ENSP00000256646:S1845R	S	-	1	0	NOTCH2	120263706	0.002000	0.14202	0.997000	0.53966	0.910000	0.53928	1.521000	0.35910	2.243000	0.73865	0.533000	0.62120	AGT	.	.		0.502	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408		G	120462183	T	G	120462183	3	3	249	1	0	0	0	0	1	0	0	0	10557	1551	54	5	1898	5	NOTCH2	1	120462183	Missense_Mutation	SNP	T	TCGA-ED-A8O5-01A-11D-A35Z-10	68223858	120462183	128788438	4	33887										
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144886225	144886225	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	ctcaggtggagcatttcttcCtgaagacacctgttactgtc	9	11	2	2			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr1:144886225C>T	ENST00000369354.3	-	23	3198	c.3009G>A	c.(3007-3009)caG>caA	p.Q1003Q	PDE4DIP_ENST00000313382.9_Silent_p.Q1069Q|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000369359.4_Silent_p.Q1140Q|PDE4DIP_ENST00000530740.1_Silent_p.Q1140Q|PDE4DIP_ENST00000369356.4_Silent_p.Q1003Q			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1003					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		GCATTTCTTCCTGAAGACACC	0.507			T	PDGFRB	MPD																																p.Q1069Q		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.G3207A						.						215	215	215					1																	144886225		2203	4296	6499	SO:0001819	synonymous_variant	9659	exon26			TTCTTCCTGAAGA	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"myomegalin"	608117	"cardiomyopathy associated 2"	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.3009G>A	chr1.hg19:g.144886225C>T		198.0	0.0		241.0	29.0	NM_001198832	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Silent	SNP	ENST00000369354.3	hg19	CCDS30824.1																																																																																			.	.		0.507	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		T	144886225	C	T	144886225	2	4	249	1	0	0	0	0	0	0	0	1	11652	680	24	3		3	PDE4DIP	1	144886225	Silent	SNP	C	TCGA-ED-A8O5-01A-11D-A35Z-10	24424042	144886225	104364396	5	33888										
FLG	2312	hgsc.bcm.edu	37	chr1	152286383	152286384	+	Nonsense_Mutation	DNP	CC	CC	AT													0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	ggagccatctcttgactgctCccacgcagatccatgatggt					rs369816027		TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr1:152286383_152286384CC>AT	ENST00000368799.1	-	3	1013_1014	c.978_979GG>AT	c.(976-981)tgGGag>tgATag	p.326_327WE>**	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	326	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTTGACTGCTCCCACGCAGATC	0.569									Ichthyosis																												p.E327X|p.W326X		Atlas-SNP	.											.	FLG	900	.	0			c.G979T|c.G978A						.																																			SO:0001587	stop_gained	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	ACTGCTCCCACGC|CTGCTCCCACGCA	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.978_979delinsAT	chr1.hg19:g.152286383_152286384delinsAT	ENSP00000357789:p.W326_E327delins**	178.0|177.0	0.0		205.0|203.0	69.0	NM_002016	Q01720|Q5T583|Q9UC71	Nonsense_Mutation	SNP	ENST00000368799.1	hg19	CCDS30860.1																																																																																			.	.		0.569	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		AT	152286384	CC	AT	152286383	4	1	249	1	0	0	0	0	0	1	0	0	5930	864	30	3	11210	3	FLG	1	152286383	Nonsense_Mutation	DNP	CC	TCGA-ED-A8O5-01A-11D-A35Z-10	7400158	152286383	96964238	6	33889										
LOR	4014	hgsc.bcm.edu	37	chr1	153234342	153234342	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	ccagacccagcagaagcaggCgcctacctggccgtccaaat	10	16	0	2			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr1:153234342C>T	ENST00000368742.3	+	2	974	c.917C>T	c.(916-918)gCg>gTg	p.A306V		NM_000427.2	NP_000418.2	P23490	LORI_HUMAN	loricrin	306					keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein binding, bridging (GO:0030674)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			lung(2)	2	all_lung(78;3.35e-32)|Lung NSC(65;1.22e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CAGAAGCAGGCGCCTACCTGG	0.657																																					p.A306V		Atlas-SNP	.											.	LOR	19	.	0			c.C917T						.						8	9	9					1																	153234342		1757	3712	5469	SO:0001583	missense	4014	exon2			AGCAGGCGCCTAC	M61120	CCDS30870.1	1q21	2008-02-05			ENSG00000203782	ENSG00000203782			6663	protein-coding gene	gene with protein product		152445				2007607, 1355480	Standard	NM_000427		Approved		uc001fbm.3	P23490	OTTHUMG00000013938	ENST00000368742.3:c.917C>T	chr1.hg19:g.153234342C>T	ENSP00000357731:p.Ala306Val	178.0	0.0		214.0	51.0	NM_000427	Q5T869|Q5XKF8	Missense_Mutation	SNP	ENST00000368742.3	hg19	CCDS30870.1	.	.	.	.	.	.	.	.	.	.	C	12.91	2.080607	0.36758	.	.	ENSG00000203782	ENST00000368742	T	0.39406	1.08	4.56	2.59	0.31030	.	0.000000	0.32785	N	0.005650	T	0.07593	0.0191	N	0.14661	0.345	0.23063	N	0.998357	P	0.46952	0.887	B	0.32211	0.142	T	0.12344	-1.0551	10	0.87932	D	0	-4.9869	5.5387	0.17026	0.1946:0.7019:0.0:0.1035	.	306	P23490	LORI_HUMAN	V	306	ENSP00000357731:A306V	ENSP00000357731:A306V	A	+	2	0	LOR	151500966	0.993000	0.37304	0.999000	0.59377	0.972000	0.66771	0.806000	0.27126	1.133000	0.42147	0.563000	0.77884	GCG	.	.		0.657	LOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039107.1	NM_000427		T	153234342	C	T	153234342	3	4	249	1	0	0	0	0	1	0	0	0	8906	768	27	1	919	1	LOR	1	153234342	Missense_Mutation	SNP	C	TCGA-ED-A8O5-01A-11D-A35Z-10	947959	153234342	96016279	7	33890										
CCT3	7203	hgsc.bcm.edu	37	chr1	156287032	156287032	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	cccgcataaggtagtgctgaGctaaatctacaaatccaaga	8	10	1	2			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr1:156287032G>T	ENST00000295688.3	-	10	1179	c.899C>A	c.(898-900)gCt>gAt	p.A300D	CCT3_ENST00000368259.2_Missense_Mutation_p.A262D|CCT3_ENST00000472765.2_Missense_Mutation_p.A255D|CCT3_ENST00000368261.3_Missense_Mutation_p.A255D	NM_005998.4	NP_005989.3	P49368	TCPG_HUMAN	chaperonin containing TCP1, subunit 3 (gamma)	300					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			endometrium(4)|large_intestine(1)|liver(1)|lung(11)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	22	Hepatocellular(266;0.158)					GTAGTGCTGAGCTAAATCTAC	0.443																																					p.A300D		Atlas-SNP	.											.	CCT3	61	.	0			c.C899A						.						150	144	146					1																	156287032		2203	4300	6503	SO:0001583	missense	7203	exon10			TGCTGAGCTAAAT	BC008019	CCDS1140.2, CCDS30888.1	1q23	2011-09-02			ENSG00000163468	ENSG00000163468		"Heat Shock Proteins / Chaperonins"	1616	protein-coding gene	gene with protein product		600114		TRIC5		8110840	Standard	NM_005998		Approved	Cctg	uc001fol.2	P49368	OTTHUMG00000024061	ENST00000295688.3:c.899C>A	chr1.hg19:g.156287032G>T	ENSP00000295688:p.Ala300Asp	203.0	0.0		240.0	71.0	NM_005998	A6NE14|Q5SZY1|Q9BR64	Missense_Mutation	SNP	ENST00000295688.3	hg19	CCDS1140.2	.	.	.	.	.	.	.	.	.	.	G	34	5.385318	0.95967	.	.	ENSG00000163468	ENST00000295688;ENST00000368259;ENST00000368261;ENST00000472765	D;D;D;D	0.82711	-1.64;-1.64;-1.64;-1.64	6.14	6.14	0.99180	.	0.051911	0.85682	D	0.000000	D	0.95516	0.8543	H	0.99498	4.595	0.80722	D	1	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.83275	0.991;0.991;0.996	D	0.96895	0.9656	10	0.87932	D	0	-9.2883	18.3129	0.90207	0.0:0.0:1.0:0.0	.	262;299;300	P49368-2;E9PAQ6;P49368	.;.;TCPG_HUMAN	D	300;262;255;255	ENSP00000295688:A300D;ENSP00000357242:A262D;ENSP00000357244:A255D;ENSP00000431543:A255D	ENSP00000295688:A300D	A	-	2	0	CCT3	154553656	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.577000	0.98196	2.927000	0.99377	0.637000	0.83480	GCT	.	.		0.443	CCT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060602.3	NM_005998		T	156287032	G	T	156287032	3	4	249	1	0	0	0	0	1	0	0	0	2956	971	34	3	758	3	CCT3	1	156287032	Missense_Mutation	SNP	G	TCGA-ED-A8O5-01A-11D-A35Z-10	3052690	156287032	92963589	8	33891										
POU2F1	5451	hgsc.bcm.edu	37	chr1	167343488	167343488	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	atctccgcctctgctgccacGcccatgacgcagatccccct	7	20	2	2	rs532966862	byFrequency	TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr1:167343488G>A	ENST00000541643.3	+	7	639	c.477G>A	c.(475-477)acG>acA	p.T159T	POU2F1_ENST00000420254.3_Silent_p.T159T|POU2F1_ENST00000429375.2_Intron|POU2F1_ENST00000367862.5_Silent_p.T171T|POU2F1_ENST00000367865.1_3'UTR|POU2F1_ENST00000367866.2_Silent_p.T182T|POU2F1_ENST00000452019.1_Silent_p.T159T			P14859	PO2F1_HUMAN	POU class 2 homeobox 1	159					gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(3)|liver(2)|lung(7)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	30						CTGCTGCCACGCCCATGACGC	0.612													G|||	2	0.000399361	0	0	5008	,	,		17355	0.001		0	False		,,,				2504	0.001				p.T182T		Atlas-SNP	.											.	POU2F1	120	.	0			c.G546A						.						26	26	26					1																	167343488		2203	4299	6502	SO:0001819	synonymous_variant	5451	exon6			TGCCACGCCCATG	BC001664	CCDS1259.1, CCDS1259.2, CCDS55655.1, CCDS55656.1	1q24.2	2011-06-20	2007-07-13		ENSG00000143190	ENSG00000143190		"Homeoboxes / POU class"	9212	protein-coding gene	gene with protein product		164175	"POU domain class 2, transcription factor 1"	OTF1		1887216	Standard	NM_002697		Approved	OCT1	uc001gee.3	P14859	OTTHUMG00000034436	ENST00000541643.3:c.477G>A	chr1.hg19:g.167343488G>A		322.0	0.0		367.0	112.0	NM_002697	B1AL91|B1AL93|B4E029|J3KP77|Q5TBT7|Q6PK46|Q8NEU9|Q9BPV1	Silent	SNP	ENST00000541643.3	hg19																																																																																				.	.		0.612	POU2F1-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_002697		A	167343488	G	A	167343488	2	1	249	1	0	0	0	0	0	0	0	1	12280	1074	38	1		1	POU2F1	1	167343488	Silent	SNP	G	TCGA-ED-A8O5-01A-11D-A35Z-10	11056456	167343488	81907133	9	33892										
BAT2L2	23215	hgsc.bcm.edu	37	chr1	171511282	171511282	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	cgtcagaatcgacgtggcaaCaatggtccacccaaatcagg	10	12	2	1			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr1:171511282C>T	ENST00000338920.4	+	16	4908	c.4671C>T	c.(4669-4671)aaC>aaT	p.N1557N	PRRC2C_ENST00000367742.3_Silent_p.N1559N|PRRC2C_ENST00000426496.2_Silent_p.N1557N|PRRC2C_ENST00000392078.3_Silent_p.N1559N	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	1557					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										GACGTGGCAACAATGGTCCAC	0.438																																					p.N1557N		Atlas-SNP	.											.	.	.	.	0			c.C4671T						.						45	45	45					1																	171511282		2203	4300	6503	SO:0001819	synonymous_variant	23215	exon16			TGGCAACAATGGT	AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"BAT2 domain containing 1", "HLA-B associated transcript 2-like 2"	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.4671C>T	chr1.hg19:g.171511282C>T		233.0	0.0		323.0	110.0	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Silent	SNP	ENST00000338920.4	hg19	CCDS1296.2	.	.	.	.	.	.	.	.	.	.	C	4.247	0.044749	0.08196	.	.	ENSG00000117523	ENST00000495585	.	.	.	5.87	4.96	0.65561	.	.	.	.	.	T	0.47820	0.1466	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50709	-0.8796	4	.	.	.	.	9.4353	0.38635	0.0:0.7889:0.0:0.2111	.	.	.	.	I	105	.	.	T	+	2	0	PRRC2C	169777906	1.000000	0.71417	0.978000	0.43139	0.998000	0.95712	1.987000	0.40687	1.494000	0.48533	0.650000	0.86243	ACA	.	.		0.438	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172		T	171511282	C	T	171511282	2	4	249	1	0	0	0	0	0	0	0	1	1321	477	17	3		3	BAT2L2	1	171511282	Silent	SNP	C	TCGA-ED-A8O5-01A-11D-A35Z-10	4167794	171511282	77739339	10	33893										
MYOC	4653	hgsc.bcm.edu	37	chr1	171621369	171621369	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	tttgggtttccagctggtccCgctcccgcctcagggtgccc	12	16	1	0			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr1:171621369C>T	ENST00000037502.6	-	1	454	c.383G>A	c.(382-384)cGg>cAg	p.R128Q		NM_000261.1	NP_000252.1	Q99972	MYOC_HUMAN	myocilin, trabecular meshwork inducible glucocorticoid response	128					bone development (GO:0060348)|clustering of voltage-gated sodium channels (GO:0045162)|ERBB2-ERBB3 signaling pathway (GO:0038133)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neuron projection development (GO:0031175)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|osteoblast differentiation (GO:0001649)|positive regulation of cell migration (GO:0030335)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of MAPK cascade (GO:0043408)|skeletal muscle hypertrophy (GO:0014734)	cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|node of Ranvier (GO:0033268)|proteinaceous extracellular matrix (GO:0005578)	fibronectin binding (GO:0001968)|frizzled binding (GO:0005109)|myosin light chain binding (GO:0032027)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|prostate(1)|urinary_tract(2)	28	all_cancers(6;5.47e-10)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					CAGCTGGTCCCGCTCCCGCCT	0.612																																					p.R128Q		Atlas-SNP	.											.	MYOC	69	.	0			c.G383A						.						69	75	73					1																	171621369		2203	4300	6503	SO:0001583	missense	4653	exon1			TGGTCCCGCTCCC	BC029261	CCDS1297.1	1q23-q24	2008-02-05			ENSG00000034971	ENSG00000034971			7610	protein-coding gene	gene with protein product		601652		GLC1A		9169133, 9005853	Standard	NM_000261		Approved	TIGR, JOAG1	uc001ghu.3	Q99972	OTTHUMG00000034789	ENST00000037502.6:c.383G>A	chr1.hg19:g.171621369C>T	ENSP00000037502:p.Arg128Gln	130.0	0.0		133.0	37.0	NM_000261	B2RD84|O00620|Q7Z6Q9	Missense_Mutation	SNP	ENST00000037502.6	hg19	CCDS1297.1	.	.	.	.	.	.	.	.	.	.	C	13.45	2.242089	0.39598	.	.	ENSG00000034971	ENST00000037502;ENST00000536591;ENST00000537133	T	0.58506	0.33	5.4	2.19	0.27852	.	0.498628	0.19991	N	0.101572	T	0.26304	0.0642	M	0.68317	2.08	0.24858	N	0.992366	B	0.31837	0.342	B	0.11329	0.006	T	0.06661	-1.0814	10	0.32370	T	0.25	.	5.8767	0.18832	0.0:0.6517:0.0:0.3483	.	128	Q99972	MYOC_HUMAN	Q	128;61;128	ENSP00000037502:R128Q	ENSP00000037502:R128Q	R	-	2	0	MYOC	169887992	0.002000	0.14202	0.965000	0.40720	0.568000	0.35870	0.413000	0.21148	0.763000	0.33175	0.655000	0.94253	CGG	.	.		0.612	MYOC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084178.2	NM_000261		T	171621369	C	T	171621369	3	4	249	1	0	0	0	0	1	0	0	0	10095	652	23	1	1143	1	MYOC	1	171621369	Missense_Mutation	SNP	C	TCGA-ED-A8O5-01A-11D-A35Z-10	110087	171621369	77629252	11	33894										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181765841	181765841	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	caccgctcagggggcagggaGcggggacgatcaaaagagcg	18	10	2	1			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr1:181765841G>A	ENST00000367573.2	+	47	6246	c.6246G>A	c.(6244-6246)gaG>gaA	p.E2082E	CACNA1E_ENST00000367570.1_Silent_p.E2039E|CACNA1E_ENST00000360108.3_Silent_p.E2063E|CACNA1E_ENST00000526775.1_Silent_p.E2020E|CACNA1E_ENST00000358338.5_Silent_p.E1971E|CACNA1E_ENST00000357570.5_Silent_p.E2033E|CACNA1E_ENST00000367567.4_Silent_p.E1646E	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	2082					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						GGGGCAGGGAGCGGGGACGAT	0.552																																					p.E2082E		Atlas-SNP	.											.	CACNA1E	778	.	0			c.G6246A						.						49	51	50					1																	181765841		1969	4161	6130	SO:0001819	synonymous_variant	777	exon47			CAGGGAGCGGGGA	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.6246G>A	chr1.hg19:g.181765841G>A		153.0	0.0		162.0	51.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Silent	SNP	ENST00000367573.2	hg19	CCDS55664.1																																																																																			.	.		0.552	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		A	181765841	G	A	181765841	2	1	249	1	0	0	0	0	0	0	0	1	2544	962	34	3		3	CACNA1E	1	181765841	Silent	SNP	G	TCGA-ED-A8O5-01A-11D-A35Z-10	10144472	181765841	67484780	12	33895										
FAM5C	339479	hgsc.bcm.edu	37	chr1	190423953	190423953	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	aaacccagcaatgaagactcAgtgctatccactcccataga	6	13	1	3			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr1:190423953A>T	ENST00000367462.3	-	2	299	c.68T>A	c.(67-69)cTg>cAg	p.L23Q	BRINP3_ENST00000534846.1_5'UTR	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	23					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)											ATGAAGACTCAGTGCTATCCA	0.517																																					p.L23Q		Atlas-SNP	.											.	FAM5C	343	.	0			c.T68A						.						82	80	81					1																	190423953		2203	4300	6503	SO:0001583	missense	339479	exon2			AGACTCAGTGCTA	AB111893	CCDS1373.1	1q31.1	2013-09-18	2013-09-18	2013-09-18	ENSG00000162670	ENSG00000162670			22393	protein-coding gene	gene with protein product			"family with sequence similarity 5, member C"	FAM5C		16018821, 15193423	Standard	NM_199051		Approved	DBCCR1L, DBCCR1L1	uc001gse.1	Q76B58	OTTHUMG00000035533	ENST00000367462.3:c.68T>A	chr1.hg19:g.190423953A>T	ENSP00000356432:p.Leu23Gln	167.0	0.0		227.0	74.0	NM_199051	B3KVP1|B7Z260|O95726|Q2M330	Missense_Mutation	SNP	ENST00000367462.3	hg19	CCDS1373.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.316959	0.81469	.	.	ENSG00000162670	ENST00000367462;ENST00000445957	T;T	0.56941	2.22;0.43	5.57	5.57	0.84162	.	0.084811	0.49916	D	0.000131	T	0.67335	0.2882	L	0.55481	1.735	0.80722	D	1	D	0.65815	0.995	D	0.72982	0.979	T	0.70274	-0.4917	10	0.87932	D	0	.	13.6909	0.62544	1.0:0.0:0.0:0.0	.	23	Q76B58	FAM5C_HUMAN	Q	23	ENSP00000356432:L23Q;ENSP00000393441:L23Q	ENSP00000356432:L23Q	L	-	2	0	FAM5C	188690576	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.932000	0.92897	2.119000	0.64992	0.533000	0.62120	CTG	.	.		0.517	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086278.1	NM_199051		T	190423953	A	T	190423953	3	4	249	1	0	0	0	0	1	0	0	0	5602	188	7	4	2260	4	FAM5C	1	190423953	Missense_Mutation	SNP	A	TCGA-ED-A8O5-01A-11D-A35Z-10	8658112	190423953	58826668	13	33896										
DENND1B	163486	hgsc.bcm.edu	37	chr1	197509163	197509163	+	IGR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	ttgtaaactggtgtatattgTacagaactagaacaggtccc	9	7	0	2			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr1:197509163T>C								CRB1 (61578 upstream) : DENND1B (12221 downstream)																							GTGTATATTGTACAGAACTAG	0.343																																					p.V482V		Atlas-SNP	.											.	DENND1B	108	.	0			c.A1446G						.						161	153	155					1																	197509163		2201	4300	6501	SO:0001628	intergenic_variant	163486	exon20			ATATTGTACAGAA																													chr1.hg19:g.197509163T>C		126.0	0.0		157.0	43.0	NM_001195215		Silent	SNP		hg19																																																																																				.	.	0	0.343									C	197509163	T	C	197509163	1	2	249	0	1	0	0	0	0	0	0	0	4429	1625	57	2		2	DENND1B	1	197509163	IGR	SNP	T	TCGA-ED-A8O5-01A-11D-A35Z-10	7085210	197509163	51741458	14	33897										
DEGS1	8560	hgsc.bcm.edu	37	chr1	224380171	224380171	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	caccaaaaaggagagatggtGctggagtaaatatcattagt	11	5	1	1			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr1:224380171G>A	ENST00000323699.4	+	3	1129	c.963G>A	c.(961-963)gtG>gtA	p.V321V	DEGS1_ENST00000391877.3_Silent_p.V321V	NM_003676.3	NP_003667.1	O15121	DEGS1_HUMAN	delta(4)-desaturase, sphingolipid 1	321					small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|unsaturated fatty acid biosynthetic process (GO:0006636)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)			breast(1)|kidney(3)|large_intestine(2)|lung(4)	10	Breast(184;0.193)			GBM - Glioblastoma multiforme(131;0.00643)		GAGAGATGGTGCTGGAGTAAA	0.363																																					p.V321V		Atlas-SNP	.											.	DEGS1	24	.	0			c.G963A						.						56	52	53					1																	224380171		2203	4300	6503	SO:0001819	synonymous_variant	8560	exon3			GATGGTGCTGGAG	AF002668	CCDS1540.1	1q42.11	2013-09-02	2011-12-09	2004-12-14	ENSG00000143753	ENSG00000143753		"Fatty acid desaturases"	13709	protein-coding gene	gene with protein product	"sphingolipid delta(4)-desaturase 1", "dihydroceramide desaturase 1"	615843	"degenerative spermatocyte homolog 1, lipid desaturase (Drosophila)"			9188692, 20105137	Standard	NM_003676		Approved	MLD, Des-1, DES1, FADS7, DEGS-1	uc001hoj.3	O15121	OTTHUMG00000037496	ENST00000323699.4:c.963G>A	chr1.hg19:g.224380171G>A		127.0	0.0		148.0	35.0	NM_003676		Silent	SNP	ENST00000323699.4	hg19	CCDS1540.1																																																																																			.	.		0.363	DEGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091285.2			A	224380171	G	A	224380171	2	1	249	1	0	0	0	0	0	0	0	1	4424	1306	46	3		3	DEGS1	1	224380171	Silent	SNP	G	TCGA-ED-A8O5-01A-11D-A35Z-10	26871008	224380171	24870450	15	33898										
OR11L1	391189	hgsc.bcm.edu	37	chr1	248004283	248004283	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	tagaataccacatttccttcTcatgacctttctaacagctt	3	12	2	2			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr1:248004283T>A	ENST00000355784.2	-	1	971	c.916A>T	c.(916-918)Aga>Tga	p.R306*		NM_001001959.1	NP_001001959.1	Q8NGX0	O11L1_HUMAN	olfactory receptor, family 11, subfamily L, member 1	306						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(4)|kidney(5)|large_intestine(5)|lung(35)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	57	all_cancers(71;8.78e-05)|all_epithelial(71;9.15e-06)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.0786)|Lung NSC(105;0.0858)		OV - Ovarian serous cystadenocarcinoma(106;0.0319)			CATTTCCTTCTCATGACCTTT	0.383																																					p.R306X		Atlas-SNP	.											.	OR11L1	108	.	0			c.A916T						.						90	86	88					1																	248004283		2203	4300	6503	SO:0001587	stop_gained	391189	exon1			TCCTTCTCATGAC	AB065646	CCDS31098.1	1q44	2013-09-24			ENSG00000197591	ENSG00000197591		"GPCR / Class A : Olfactory receptors"	14998	protein-coding gene	gene with protein product							Standard	NM_001001959		Approved		uc001idn.1	Q8NGX0	OTTHUMG00000040193	ENST00000355784.2:c.916A>T	chr1.hg19:g.248004283T>A	ENSP00000348033:p.Arg306*	209.0	0.0		210.0	54.0	NM_001001959		Nonsense_Mutation	SNP	ENST00000355784.2	hg19	CCDS31098.1	.	.	.	.	.	.	.	.	.	.	T	16.55	3.154155	0.57259	.	.	ENSG00000197591	ENST00000355784	.	.	.	3.78	0.107	0.14544	.	0.882556	0.09169	U	0.839093	.	.	.	.	.	.	0.33847	D	0.632136	.	.	.	.	.	.	.	.	.	.	0.05351	T	0.99	.	4.6121	0.12408	0.0:0.2885:0.1604:0.5511	.	.	.	.	X	306	.	ENSP00000348033:R306X	R	-	1	2	OR11L1	246070906	0.000000	0.05858	0.000000	0.03702	0.661000	0.39034	0.420000	0.21263	-0.074000	0.12820	0.438000	0.28831	AGA	.	.		0.383	OR11L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096850.1	NM_001001959		A	248004283	T	A	248004283	4	1	249	1	0	0	0	0	0	1	0	0	10939	1559	54	4	56	4	OR11L1	1	248004283	Nonsense_Mutation	SNP	T	TCGA-ED-A8O5-01A-11D-A35Z-10	23624112	248004283	1246338	16	33899										
DNMT3A	1788	hgsc.bcm.edu	37	chr2	25466768	25466768	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	ttgggcctgcacccctcaccTgtagcgattccatcaaagag	9	14	2	1			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr2:25466768T>A	ENST00000264709.3	-	16	2272	c.1935A>T	c.(1933-1935)acA>acT	p.T645T	DNMT3A_ENST00000380746.4_Splice_Site_p.T456T|DNMT3A_ENST00000402667.1_Splice_Site_p.T422T|DNMT3A_ENST00000474887.1_5'UTR|DNMT3A_ENST00000321117.5_Splice_Site_p.T645T	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	645	S-adenosyl-L-methionine binding. {ECO:0000305}.|SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ACCCCTCACCTGTAGCGATTC	0.572			"Mis, F, N, S"		AML																																p.T645T		Atlas-SNP	.		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	.	DNMT3A	1807	.	0			c.A1935T						.						47	42	44					2																	25466768		2079	4055	6134	SO:0001630	splice_region_variant	1788	exon16			CTCACCTGTAGCG		CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.1936+1A>T	chr2.hg19:g.25466768T>A		81.0	0.0		43.0	15.0	NM_175629	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Silent	SNP	ENST00000264709.3	hg19	CCDS33157.1																																																																																			.	.		0.572	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	NM_022552	Silent	A	25466768	T	A	25466768	5	1	249	1	0	0	0	0	0	0	1	0	4678	1594	55	4	835	4	DNMT3A	2	25466768	Splice_Site	SNP	T	TCGA-ED-A8O5-01A-11D-A35Z-10		25466768	217732605	17	33900										
FAM179A	165186	hgsc.bcm.edu	37	chr2	29268229	29268229	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	agcgcttgctgggcgagtgcGtttcctgagtggccgtgcgg	18	10	0	1	rs371609539		TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr2:29268229G>A	ENST00000379558.4	+	19	3026	c.2675G>A	c.(2674-2676)cGt>cAt	p.R892H	FAM179A_ENST00000403861.2_Missense_Mutation_p.R837H|FAM179A_ENST00000465300.1_3'UTR	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	892										breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						GGGCGAGTGCGTTTCCTGAGT	0.612																																					p.R892H		Atlas-SNP	.											.	FAM179A	106	.	0			c.G2675A						.	G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	107	106	106		2675	4.4	1	2		106	0,8600		0,0,4300	no	missense	FAM179A	NM_199280.2	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	892/1020	29268229	1,13005	2203	4300	6503	SO:0001583	missense	165186	exon19			GAGTGCGTTTCCT	AK125239, AK125744	CCDS1769.2	2p23.2	2008-10-30			ENSG00000189350	ENSG00000189350			33715	protein-coding gene	gene with protein product						16344560	Standard	NM_199280		Approved	FLJ43249, LOC165186	uc010ezl.3	Q6ZUX3	OTTHUMG00000128432	ENST00000379558.4:c.2675G>A	chr2.hg19:g.29268229G>A	ENSP00000368876:p.Arg892His	41.0	0.0		37.0	18.0	NM_199280	Q6ZUF5	Missense_Mutation	SNP	ENST00000379558.4	hg19	CCDS1769.2	.	.	.	.	.	.	.	.	.	.	G	19.88	3.908492	0.72868	2.27E-4	0.0	ENSG00000189350	ENST00000379558;ENST00000403861	T;T	0.14144	2.53;2.53	5.33	4.45	0.53987	Armadillo-type fold (1);	0.087928	0.49916	D	0.000123	T	0.31949	0.0813	M	0.64997	1.995	0.34235	D	0.67698	D;D;D	0.89917	0.999;0.997;1.0	P;P;D	0.66196	0.8;0.745;0.942	T	0.48163	-0.9059	10	0.51188	T	0.08	.	13.8719	0.63624	0.0737:0.0:0.9263:0.0	.	837;892;190	F8W8E4;Q6ZUX3;Q6ZUX3-3	.;F179A_HUMAN;.	H	892;837	ENSP00000368876:R892H;ENSP00000384699:R837H	ENSP00000368876:R892H	R	+	2	0	FAM179A	29121733	0.995000	0.38212	0.989000	0.46669	0.542000	0.35054	2.214000	0.42853	1.479000	0.48272	0.561000	0.74099	CGT	.	.		0.612	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280		A	29268229	G	A	29268229	3	1	249	1	0	0	0	0	1	0	0	0	5510	1145	40	1	2745	1	FAM179A	2	29268229	Missense_Mutation	SNP	G	TCGA-ED-A8O5-01A-11D-A35Z-10	3801461	29268229	213931144	18	33901										
XIRP2	129446	hgsc.bcm.edu	37	chr2	167992505	167992505	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	gattctgtgaaagattcagaCaagaaaggcaaggaaacatc	10	6	2	4			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr2:167992505C>A	ENST00000409728.1	+	3	584	c.495C>A	c.(493-495)gaC>gaA	p.D165E	XIRP2_ENST00000409043.1_Missense_Mutation_p.D165E|XIRP2_ENST00000295237.9_Missense_Mutation_p.D165E|XIRP2_ENST00000409756.2_Missense_Mutation_p.D165E|XIRP2_ENST00000420519.1_Missense_Mutation_p.D165E|XIRP2-AS1_ENST00000525330.1_RNA|XIRP2_ENST00000409195.1_Missense_Mutation_p.D165E	NM_001199143.1	NP_001186072.1	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	0					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AAGATTCAGACAAGAAAGGCA	0.433																																					p.D165E		Atlas-SNP	.											.	XIRP2	914	.	0			c.C495A						.						96	96	96					2																	167992505		1904	4128	6032	SO:0001583	missense	129446	exon3			TTCAGACAAGAAA	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409728.1:c.495C>A	chr2.hg19:g.167992505C>A	ENSP00000386619:p.Asp165Glu	96.0	0.0		74.0	33.0	NM_001199143	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409728.1	hg19	CCDS56143.1	.	.	.	.	.	.	.	.	.	.	C	12.32	1.903459	0.33628	.	.	ENSG00000163092	ENST00000409043;ENST00000409728;ENST00000409195;ENST00000409756;ENST00000420519;ENST00000295237	D;D;T;D;D;T	0.85339	-1.53;-1.97;3.85;-1.53;-1.97;3.85	5.51	3.67	0.42095	.	.	.	.	.	T	0.74688	0.3749	.	.	.	0.20307	N	0.999914	B;B	0.14438	0.01;0.01	B;B	0.15484	0.013;0.013	T	0.60622	-0.7227	8	0.33940	T	0.23	-7.4776	5.804	0.18430	0.2713:0.5813:0.0:0.1474	.	165;165	A4UGR9-4;A4UGR9-6	.;.	E	165	ENSP00000386454:D165E;ENSP00000386619:D165E;ENSP00000386840:D165E;ENSP00000386724:D165E;ENSP00000415541:D165E;ENSP00000295237:D165E	ENSP00000295237:D165E	D	+	3	2	XIRP2	167700751	0.511000	0.26179	0.995000	0.50966	0.752000	0.42762	0.015000	0.13355	0.656000	0.30886	-0.216000	0.12614	GAC	.	.		0.433	XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333552.1	NM_152381		A	167992505	C	A	167992505	3	1	249	1	0	0	0	0	1	0	0	0	17445	477	17	3	501	3	XIRP2	2	167992505	Missense_Mutation	SNP	C	TCGA-ED-A8O5-01A-11D-A35Z-10	138724276	167992505	75206868	19	33902										
KBTBD10	10324	hgsc.bcm.edu	37	chr2	170377511	170377511	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	acccactgaagtcaatgacaTatggaagtaagttctcatca	7	9	3	2			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr2:170377511T>C	ENST00000284669.1	+	5	1780	c.1703T>C	c.(1702-1704)aTa>aCa	p.I568T	RP11-724O16.1_ENST00000513963.1_Missense_Mutation_p.I506T|KLHL41_ENST00000463400.1_3'UTR|BBS5_ENST00000554017.1_Missense_Mutation_p.I506T	NM_006063.2	NP_006054.2	O60662	KLH41_HUMAN	kelch-like family member 41	568					myofibril assembly (GO:0030239)|protein ubiquitination (GO:0016567)|regulation of lateral pseudopodium assembly (GO:0031275)|regulation of myoblast differentiation (GO:0045661)|regulation of myoblast proliferation (GO:2000291)|regulation of skeletal muscle cell differentiation (GO:2001014)|skeletal muscle cell differentiation (GO:0035914)|striated muscle contraction (GO:0006941)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|M band (GO:0031430)|pseudopodium (GO:0031143)											GTCAATGACATATGGAAGTAA	0.363																																					p.I568T		Atlas-SNP	.											.	.	.	.	0			c.T1703C						.						136	123	127					2																	170377511		2203	4300	6503	SO:0001583	missense	10324	exon5			ATGACATATGGAA	AF056929	CCDS2234.1	2q31.1	2013-02-22	2013-02-22	2013-01-08	ENSG00000239474	ENSG00000239474		"Kelch-like", "BTB/POZ domain containing"	16905	protein-coding gene	gene with protein product	"sarcomeric muscle protein"	607701	"kelch repeat and BTB (POZ) domain containing 10", "kelch-like 41 (Drosophila)"	KBTBD10		9655184	Standard	NM_006063		Approved	SARCOSIN, Krp1	uc002ueu.1	O60662	OTTHUMG00000132205	ENST00000284669.1:c.1703T>C	chr2.hg19:g.170377511T>C	ENSP00000284669:p.Ile568Thr	120.0	0.0		93.0	25.0	NM_006063	Q53R42	Missense_Mutation	SNP	ENST00000284669.1	hg19	CCDS2234.1	.	.	.	.	.	.	.	.	.	.	T	24.5	4.543127	0.86022	.	.	ENSG00000163093;ENSG00000251569;ENSG00000239474	ENST00000554017;ENST00000513963;ENST00000284669	T;T;T	0.68903	-0.36;-0.36;-0.36	5.29	5.29	0.74685	Kelch-type beta propeller (1);	0.096814	0.64402	D	0.000001	T	0.77651	0.4162	L	0.52011	1.625	0.53688	D	0.99997	P;D	0.57571	0.776;0.98	P;D	0.74348	0.729;0.983	T	0.79992	-0.1569	10	0.87932	D	0	.	15.5036	0.75719	0.0:0.0:0.0:1.0	.	506;568	E9PBE3;O60662	.;KBTBA_HUMAN	T	506;506;568	ENSP00000452313:I506T;ENSP00000424363:I506T;ENSP00000284669:I568T	ENSP00000284669:I568T	I	+	2	0	BBS5;RP11-724O16.1;KBTBD10	170085757	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.623000	0.83113	2.128000	0.65567	0.482000	0.46254	ATA	.	.		0.363	KLHL41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255263.1	NM_006063		C	170377511	T	C	170377511	3	2	249	1	0	0	0	0	1	0	0	0	7999	1406	49	2	1721	2	KBTBD10	2	170377511	Missense_Mutation	SNP	T	TCGA-ED-A8O5-01A-11D-A35Z-10	2385006	170377511	72821862	20	33903										
MYO3B	140469	hgsc.bcm.edu	37	chr2	171323102	171323102	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	cccaatgatgaccgagaggcCctgcagttctctcgagagag	12	12	1	4			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr2:171323102C>A	ENST00000408978.4	+	25	3038	c.2895C>A	c.(2893-2895)gcC>gcA	p.A965A	MYO3B_ENST00000409044.3_Silent_p.A965A|MYO3B_ENST00000602629.1_Intron|MYO3B_ENST00000334231.6_Silent_p.A974A	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	965	Myosin motor.				peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						ACCGAGAGGCCCTGCAGTTCT	0.567																																					p.A965A		Atlas-SNP	.											.	MYO3B	320	.	0			c.C2895A						.						91	94	93					2																	171323102		1938	4138	6076	SO:0001819	synonymous_variant	140469	exon25			AGAGGCCCTGCAG		CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"Myosins / Myosin superfamily : Class III"	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.2895C>A	chr2.hg19:g.171323102C>A		104.0	0.0		85.0	29.0	NM_001083615	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Silent	SNP	ENST00000408978.4	hg19	CCDS42773.1																																																																																			.	.		0.567	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1			A	171323102	C	A	171323102	2	1	249	1	0	0	0	0	0	0	0	1	10086	610	22	3		3	MYO3B	2	171323102	Silent	SNP	C	TCGA-ED-A8O5-01A-11D-A35Z-10	945591	171323102	71876271	21	33904										
TTN	7273	hgsc.bcm.edu	37	chr2	179639715	179639715	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	agtacacagctgtaatcttcAgcatcagacgtatcaatggt	8	9	4	1			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr2:179639715A>T	ENST00000591111.1	-	29	6947	c.6723T>A	c.(6721-6723)gcT>gcA	p.A2241A	TTN_ENST00000342992.6_Silent_p.A2241A|TTN_ENST00000589042.1_Silent_p.A2241A|TTN_ENST00000359218.5_Silent_p.A2195A|TTN_ENST00000460472.2_Silent_p.A2195A|TTN-AS1_ENST00000584485.1_RNA|TTN_ENST00000360870.5_Silent_p.A2241A|TTN_ENST00000342175.6_Silent_p.A2195A|RP11-88L24.4_ENST00000582038.2_RNA|TTN-AS1_ENST00000610005.1_RNA|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12565	Ig-like 11.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGTAATCTTCAGCATCAGACG	0.388																																					p.A2241A		Atlas-SNP	.											.	TTN	18412	.	0			c.T6723A						.						157	145	149					2																	179639715		2203	4300	6503	SO:0001819	synonymous_variant	7273	exon29			ATCTTCAGCATCA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.6723T>A	chr2.hg19:g.179639715A>T		126.0	0.0		125.0	65.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179639715	A	T	179639715	2	4	249	1	0	0	0	0	0	0	0	1	16750	175	7	4		4	TTN	2	179639715	Silent	SNP	A	TCGA-ED-A8O5-01A-11D-A35Z-10	8316613	179639715	63559658	22	33905										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196822068	196822068	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	ctcaggcatttgagacataaTgtctggagagctgaaaatgg	12	6	2	3			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr2:196822068T>C	ENST00000312428.6	-	19	3095	c.2995A>G	c.(2995-2997)Att>Gtt	p.I999V		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	999	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						TGAGACATAATGTCTGGAGAG	0.468																																					p.I999V		Atlas-SNP	.											.	DNAH7	512	.	0			c.A2995G						.						93	86	88					2																	196822068		1886	4116	6002	SO:0001583	missense	56171	exon19			ACATAATGTCTGG	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.2995A>G	chr2.hg19:g.196822068T>C	ENSP00000311273:p.Ile999Val	386.0	1.0		315.0	130.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	hg19	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	T	19.13	3.767322	0.69878	.	.	ENSG00000118997	ENST00000312428	T	0.68903	-0.36	5.57	5.57	0.84162	Dynein heavy chain, domain-2 (1);	0.000000	0.85682	D	0.000000	D	0.86727	0.6002	H	0.94423	3.535	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.90440	0.4431	10	0.87932	D	0	.	15.6854	0.77405	0.0:0.0:0.0:1.0	.	999	Q8WXX0	DYH7_HUMAN	V	999	ENSP00000311273:I999V	ENSP00000311273:I999V	I	-	1	0	DNAH7	196530313	1.000000	0.71417	0.998000	0.56505	0.372000	0.29890	7.950000	0.87804	2.248000	0.74166	0.533000	0.62120	ATT	.	.		0.468	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		C	196822068	T	C	196822068	3	2	249	1	0	0	0	0	1	0	0	0	4608	1464	51	2	9267	2	DNAH7	2	196822068	Missense_Mutation	SNP	T	TCGA-ED-A8O5-01A-11D-A35Z-10	17182353	196822068	46377305	23	33906										
EPHA4	2043	hgsc.bcm.edu	37	chr2	222301170	222301170	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	tcaagcactcgggacatgccAaaatcagacactttgcagac	8	12	2	2			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr2:222301170A>T	ENST00000281821.2	-	13	2336	c.2295T>A	c.(2293-2295)ttT>ttA	p.F765L	EPHA4_ENST00000392071.4_Missense_Mutation_p.F714L|EPHA4_ENST00000409854.1_Missense_Mutation_p.F765L|EPHA4_ENST00000409938.1_Missense_Mutation_p.F765L	NM_004438.3	NP_004429.1	P54764	EPHA4_HUMAN	EPH receptor A4	765	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adult walking behavior (GO:0007628)|cell adhesion (GO:0007155)|corticospinal tract morphogenesis (GO:0021957)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|glial cell migration (GO:0008347)|motor neuron axon guidance (GO:0008045)|negative regulation of axon regeneration (GO:0048681)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001108)|protein autophosphorylation (GO:0046777)|regulation of astrocyte differentiation (GO:0048710)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rap GTPase activity (GO:0032317)	axon (GO:0030424)|axon terminus (GO:0043679)|axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|DH domain binding (GO:0097161)|GPI-linked ephrin receptor activity (GO:0005004)|PH domain binding (GO:0042731)|protein kinase activity (GO:0004672)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		GGGACATGCCAAAATCAGACA	0.493																																					p.F765L		Atlas-SNP	.											.	EPHA4	263	.	0			c.T2295A						.						110	92	98					2																	222301170		2203	4300	6503	SO:0001583	missense	2043	exon13			CATGCCAAAATCA	L36645	CCDS2447.1	2q36.3	2013-02-11	2004-10-28		ENSG00000116106	ENSG00000116106	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3388	protein-coding gene	gene with protein product		602188	"EphA4"	TYRO1		9267020	Standard	NM_004438		Approved	Hek8	uc002vmq.3	P54764	OTTHUMG00000133142	ENST00000281821.2:c.2295T>A	chr2.hg19:g.222301170A>T	ENSP00000281821:p.Phe765Leu	91.0	0.0		78.0	33.0	NM_004438	A8K2P1|B2R601|B7Z6Q8|Q2M380	Missense_Mutation	SNP	ENST00000281821.2	hg19	CCDS2447.1	.	.	.	.	.	.	.	.	.	.	A	17.24	3.338764	0.60963	.	.	ENSG00000116106	ENST00000281821;ENST00000409854;ENST00000409938;ENST00000392071	T;T;T;T	0.81247	-1.47;-1.47;-1.47;-1.47	6.04	-3.94	0.04130	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.80534	0.4641	M	0.86573	2.825	0.58432	D	0.999999	B	0.22683	0.073	B	0.22386	0.039	T	0.69191	-0.5210	10	0.87932	D	0	.	15.0631	0.71970	0.4713:0.0:0.5287:0.0	.	765	P54764	EPHA4_HUMAN	L	765;765;765;714	ENSP00000281821:F765L;ENSP00000386276:F765L;ENSP00000386829:F765L;ENSP00000375923:F714L	ENSP00000281821:F765L	F	-	3	2	EPHA4	222009414	0.176000	0.23096	0.924000	0.36721	0.997000	0.91878	-0.240000	0.08952	-0.989000	0.03485	0.460000	0.39030	TTT	.	.		0.493	EPHA4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256836.3			T	222301170	A	T	222301170	3	4	249	1	0	0	0	0	1	0	0	0	5171	127	5	4	685	4	EPHA4	2	222301170	Missense_Mutation	SNP	A	TCGA-ED-A8O5-01A-11D-A35Z-10	25479102	222301170	20898203	24	33907										
ANKMY1	51281	hgsc.bcm.edu	37	chr2	241463346	241463346	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	cgcatggtccctttgtcgaaGctgctggtgcacggtgaggg	16	10	0	1			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr2:241463346G>T	ENST00000272972.3	-	7	1735	c.1521C>A	c.(1519-1521)agC>agA	p.S507R	ANKMY1_ENST00000405002.1_Missense_Mutation_p.S277R|ANKMY1_ENST00000403283.1_Missense_Mutation_p.S445R|ANKMY1_ENST00000462004.1_5'Flank|ANKMY1_ENST00000401804.1_Missense_Mutation_p.S596R|ANKMY1_ENST00000406958.1_Missense_Mutation_p.S268R|ANKMY1_ENST00000391987.1_Missense_Mutation_p.S507R|ANKMY1_ENST00000373320.4_Missense_Mutation_p.S277R|ANKMY1_ENST00000405523.3_Missense_Mutation_p.S366R|ANKMY1_ENST00000536462.1_Missense_Mutation_p.S319R|ANKMY1_ENST00000361678.4_Missense_Mutation_p.S366R|ANKMY1_ENST00000373318.2_Missense_Mutation_p.S366R	NM_016552.2	NP_057636.2	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1	507							metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	30		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.03e-30)|all cancers(36;4.78e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.45e-14)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.8e-06)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.01)|Colorectal(34;0.0101)|COAD - Colon adenocarcinoma(134;0.0476)		CTTTGTCGAAGCTGCTGGTGC	0.622																																					p.S507R		Atlas-SNP	.											.	ANKMY1	112	.	0			c.C1521A						.						64	61	62					2																	241463346		2203	4300	6503	SO:0001583	missense	51281	exon7			GTCGAAGCTGCTG	AB034636	CCDS2535.1, CCDS2536.1, CCDS63184.1, CCDS63185.1, CCDS74681.1	2q37.3	2013-01-10			ENSG00000144504	ENSG00000144504		"Zinc fingers, MYND-type", "Ankyrin repeat domain containing"	20987	protein-coding gene	gene with protein product							Standard	XM_005247020		Approved	FLJ20499, ZMYND13	uc002vyz.1	Q9P2S6	OTTHUMG00000133355	ENST00000272972.3:c.1521C>A	chr2.hg19:g.241463346G>T	ENSP00000272972:p.Ser507Arg	56.0	0.0		49.0	24.0	NM_016552	B2RB78|Q4ZFV3|Q8IYX5|Q8NDK5|Q9H0V8|Q9NX10	Missense_Mutation	SNP	ENST00000272972.3	hg19	CCDS2536.1	.	.	.	.	.	.	.	.	.	.	G	12.87	2.067578	0.36470	.	.	ENSG00000144504	ENST00000373318;ENST00000406958;ENST00000272972;ENST00000361678;ENST00000391987;ENST00000373320;ENST00000403283;ENST00000401804;ENST00000536462;ENST00000405523;ENST00000405002	T;T;T;T;T;T;T;T;T;T;T	0.56776	2.87;3.6;0.46;2.19;0.46;4.33;2.43;0.44;2.19;2.16;2.47	4.06	3.17	0.36434	Ankyrin repeat-containing domain (1);	2.870430	0.01215	N	0.007942	T	0.49115	0.1538	N	0.24115	0.695	0.09310	N	1	B;D;P;P;B;D;B	0.59767	0.196;0.972;0.753;0.952;0.233;0.986;0.196	B;P;B;B;B;P;B	0.50754	0.024;0.6;0.173;0.396;0.024;0.649;0.024	T	0.43491	-0.9388	10	0.18710	T	0.47	-49.9723	8.2266	0.31572	0.1193:0.0:0.8807:0.0	.	507;319;277;366;268;366;507	Q4ZFV3;F5H558;Q9P2S6-4;Q6GPI0;B5MBY4;Q9P2S6-2;Q9P2S6	.;.;.;.;.;.;ANKY1_HUMAN	R	366;268;507;366;507;277;445;596;319;366;277	ENSP00000362415:S366R;ENSP00000384555:S268R;ENSP00000272972:S507R;ENSP00000355097:S366R;ENSP00000375847:S507R;ENSP00000362417:S277R;ENSP00000383968:S445R;ENSP00000385887:S596R;ENSP00000444707:S319R;ENSP00000385635:S366R;ENSP00000385145:S277R	ENSP00000272972:S507R	S	-	3	2	ANKMY1	241112019	0.000000	0.05858	0.002000	0.10522	0.034000	0.12701	0.393000	0.20817	0.994000	0.38892	0.491000	0.48974	AGC	.	.		0.622	ANKMY1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257187.2	NM_017844		T	241463346	G	T	241463346	3	4	249	1	0	0	0	0	1	0	0	0	634	962	34	3	1348	3	ANKMY1	2	241463346	Missense_Mutation	SNP	G	TCGA-ED-A8O5-01A-11D-A35Z-10	19162176	241463346	1736027	25	33908										
SLC6A1	6529	hgsc.bcm.edu	37	chr3	11064071	11064089	+	Frame_Shift_Del	DEL	CGCTGGCCACTGGCCATCA	CGCTGGCCACTGGCCATCA	-													0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	tggataagccaggtcagatcCgctggccactggccatcacg							TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	CGCTGGCCACTGGCCATCA	CGCTGGCCACTGGCCATCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr3:11064071_11064089delCGCTGGCCACTGGCCATCA	ENST00000287766.4	+	7	1052_1070	c.631_649delCGCTGGCCACTGGCCATCA	c.(631-651)cgctggccactggccatcacgfs	p.RWPLAIT211fs	SLC6A1_ENST00000536032.1_Frame_Shift_Del_p.RWPLAIT33fs	NM_003042.3	NP_003033.3	P30531	SC6A1_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 1	211					gamma-aminobutyric acid import (GO:0051939)|learning (GO:0007612)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neurotransmitter secretion (GO:0007269)|positive regulation of gamma-aminobutyric acid secretion (GO:0014054)|protein homooligomerization (GO:0051260)|response to calcium ion (GO:0051592)|response to cocaine (GO:0042220)|response to estradiol (GO:0032355)|response to lead ion (GO:0010288)|response to purine-containing compound (GO:0014074)|response to sucrose (GO:0009744)|response to toxic substance (GO:0009636)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	26		Ovarian(110;0.0392)		OV - Ovarian serous cystadenocarcinoma(96;0.00099)	Clobazam(DB00349)|Tiagabine(DB00906)	AGGTCAGATCCGCTGGCCACTGGCCATCACGCTGGCCAT	0.566																																					p.210_216del		Atlas-INDEL	.											.	SLC6A1	88	.	0			c.630_648del						.																																			SO:0001589	frameshift_variant	6529	exon7			.		CCDS2603.1	3p25.3	2013-07-19	2013-07-19		ENSG00000157103	ENSG00000157103		"Solute carriers"	11042	protein-coding gene	gene with protein product	"GABA transporter 1"	137165	"solute carrier family 6 (neurotransmitter transporter, GABA), member 1"			8530094	Standard	NM_003042		Approved	GAT1, GABATR, GABATHG	uc010hdq.3	P30531	OTTHUMG00000044208	ENST00000287766.4:c.631_649delCGCTGGCCACTGGCCATCA	chr3.hg19:g.11064071_11064089delCGCTGGCCACTGGCCATCA	ENSP00000287766:p.Arg211fs	130.0	0.0		86.0	22.0	NM_003042	Q8N4K8	Frame_Shift_Del	DEL	ENST00000287766.4	hg19	CCDS2603.1																																																																																			.	.		0.566	SLC6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102767.2	NM_003042		-	11064089	CGCTGGCCACTGGCCATCA	-	11064071	7	5	249	1	0	1	0	1	0	0	0	0	14688	652	23	0	649	0	SLC6A1	3	11064071	Frame_Shift_Del	DEL	CGCTGGCCACTGGCCATCA	TCGA-ED-A8O5-01A-11D-A35Z-10		11064071	186958359	26	33909										
COL6A6	131873	hgsc.bcm.edu	37	chr3	130290002	130290002	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	aacaagggggtcccccaagtCctcattgtgatcaccgatgg	11	12	2	1			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr3:130290002C>T	ENST00000358511.6	+	6	2773	c.2742C>T	c.(2740-2742)gtC>gtT	p.V914V	COL6A6_ENST00000453409.2_Silent_p.V914V	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	914	Nonhelical region.|VWFA 5. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						TCCCCCAAGTCCTCATTGTGA	0.567																																					p.V914V		Atlas-SNP	.											.	COL6A6	497	.	0			c.C2742T						.						50	51	51					3																	130290002		1904	4115	6019	SO:0001819	synonymous_variant	131873	exon6			CCAAGTCCTCATT	AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.2742C>T	chr3.hg19:g.130290002C>T		128.0	0.0		98.0	52.0	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Silent	SNP	ENST00000358511.6	hg19	CCDS46911.1																																																																																			.	.		0.567	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		T	130290002	C	T	130290002	2	4	249	1	0	0	0	0	0	0	0	1	3705	842	30	3		3	COL6A6	3	130290002	Silent	SNP	C	TCGA-ED-A8O5-01A-11D-A35Z-10	119225931	130290002	67732428	27	33910										
CPA3	1359	hgsc.bcm.edu	37	chr3	148596536	148596536	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	atccactatatgttctgaagGtaaaaataactcaagaacca	5	8	2	2			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr3:148596536G>A	ENST00000296046.3	+	5	526		c.e5+1		RP11-680B3.2_ENST00000488190.1_RNA	NM_001870.2	NP_001861.2	P15088	CBPA3_HUMAN	carboxypeptidase A3 (mast cell)						angiotensin maturation (GO:0002003)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|secretory granule (GO:0030141)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.?(1)		NS(1)|breast(3)|endometrium(1)|large_intestine(3)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	35			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)			TGTTCTGAAGGTAAAAATAAC	0.308																																					.		Atlas-SNP	.											CPA3,NS,carcinoma,0,1	CPA3	75	.	1	Unknown(1)	lung(1)	c.474+1G>A						.						48	55	52					3																	148596536		2199	4292	6491	SO:0001630	splice_region_variant	1359	exon5			CTGAAGGTAAAAA		CCDS3138.1	3q24	2012-02-10			ENSG00000163751	ENSG00000163751	3.4.17.1		2298	protein-coding gene	gene with protein product	"mast cell carboxypeptidase A", "tissue carboxypeptidase A"	114851					Standard	NM_001870		Approved		uc003ewm.3	P15088	OTTHUMG00000159526	ENST00000296046.3:c.474+1G>A	chr3.hg19:g.148596536G>A		142.0	0.0		121.0	58.0	NM_001870	Q96E94	Splice_Site	SNP	ENST00000296046.3	hg19	CCDS3138.1	.	.	.	.	.	.	.	.	.	.	G	13.63	2.294177	0.40594	.	.	ENSG00000163751	ENST00000296046	.	.	.	5.19	5.19	0.71726	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.0074	0.89213	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CPA3	150079226	1.000000	0.71417	1.000000	0.80357	0.338000	0.28826	7.163000	0.77524	2.857000	0.98124	0.650000	0.86243	.	.	.		0.308	CPA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355974.1	NM_001870	Intron	A	148596536	G	A	148596536	5	1	249	1	0	0	0	0	0	0	1	0	3793	1275	44	3	493	3	CPA3	3	148596536	Splice_Site	SNP	G	TCGA-ED-A8O5-01A-11D-A35Z-10	18306534	148596536	49425894	28	33911										
PROM1	8842	hgsc.bcm.edu	37	chr4	16077499	16077499	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	ggagttcccgcacagccccaGcagcaacagggagccgagta	13	14	0	0			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr4:16077499G>A	ENST00000510224.1	-	2	279	c.31C>T	c.(31-33)Ctg>Ttg	p.L11L	PROM1_ENST00000505450.1_Silent_p.L11L|PROM1_ENST00000508167.1_Silent_p.L11L|PROM1_ENST00000539194.1_Silent_p.L11L|PROM1_ENST00000540805.1_Silent_p.L11L|PROM1_ENST00000447510.2_Silent_p.L11L|PROM1_ENST00000543373.1_Silent_p.L11L			O43490	PROM1_HUMAN	prominin 1	11					camera-type eye photoreceptor cell differentiation (GO:0060219)|glomerular parietal epithelial cell differentiation (GO:0072139)|glomerular visceral epithelial cell differentiation (GO:0072112)|photoreceptor cell maintenance (GO:0045494)|positive regulation of nephron tubule epithelial cell differentiation (GO:2000768)|retina layer formation (GO:0010842)|retina morphogenesis in camera-type eye (GO:0060042)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actinin binding (GO:0042805)|cadherin binding (GO:0045296)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|liver(1)|lung(11)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(2)	35						CACAGCCCCAGCAGCAACAGG	0.532																																					p.L11L		Atlas-SNP	.											.	PROM1	91	.	0			c.C31T						.						34	35	35					4																	16077499		2034	4193	6227	SO:0001819	synonymous_variant	8842	exon2			GCCCCAGCAGCAA	AF027208	CCDS47029.1, CCDS54746.1, CCDS54747.1, CCDS54748.1	4p15	2013-06-06	2001-11-28	2003-03-28	ENSG00000007062	ENSG00000007062		"CD molecules"	9454	protein-coding gene	gene with protein product		604365	"prominin (mouse)-like 1", "macular dystrophy, retinal 2", "Stargardt disease 4 (autosomal dominant)"	PROML1, MCDR2, STGD4		11467842	Standard	NM_006017		Approved	AC133, CD133, RP41, CORD12	uc003goo.2	O43490	OTTHUMG00000160180	ENST00000510224.1:c.31C>T	chr4.hg19:g.16077499G>A		136.0	0.0		149.0	55.0	NM_001145847	Q6SV49|Q6SV50|Q6SV51|Q6SV52|Q6SV53|Q96EN6	Silent	SNP	ENST00000510224.1	hg19	CCDS47029.1																																																																																			.	.		0.532	PROM1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359595.2	NM_006017		A	16077499	G	A	16077499	2	1	249	1	0	0	0	0	0	0	0	1	12567	962	34	3		3	PROM1	4	16077499	Silent	SNP	G	TCGA-ED-A8O5-01A-11D-A35Z-10		16077499	175076777	29	33912										
PPARGC1A	10891	hgsc.bcm.edu	37	chr4	23803848	23803848	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	taatcttgaagattctcaccCatcatcccgcagatttactg	5	12	3	3			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr4:23803848C>A	ENST00000264867.2	-	11	2259	c.2140G>T	c.(2140-2142)Gga>Tga	p.G714*	PPARGC1A_ENST00000509702.1_5'UTR	NM_013261.3	NP_037393.1	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 alpha	714	Mediates interaction with RNF34. {ECO:0000269|PubMed:22064484}.|RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				androgen metabolic process (GO:0008209)|androgen receptor signaling pathway (GO:0030521)|brown fat cell differentiation (GO:0050873)|cellular glucose homeostasis (GO:0001678)|cellular respiration (GO:0045333)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|cellular response to nitrite (GO:0071250)|cellular response to oxidative stress (GO:0034599)|cellular response to thyroid hormone stimulus (GO:0097067)|cellular response to tumor necrosis factor (GO:0071356)|circadian regulation of gene expression (GO:0032922)|digestion (GO:0007586)|fatty acid oxidation (GO:0019395)|flavone metabolic process (GO:0051552)|galactose metabolic process (GO:0006012)|gluconeogenesis (GO:0006094)|mitochondrion organization (GO:0007005)|mRNA processing (GO:0006397)|negative regulation of glycolytic process (GO:0045820)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of receptor activity (GO:2000272)|positive regulation of ATP biosynthetic process (GO:2001171)|positive regulation of cellular respiration (GO:1901857)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of histone acetylation (GO:0035066)|positive regulation of mitochondrial DNA metabolic process (GO:1901860)|positive regulation of mitochondrion organization (GO:0010822)|positive regulation of muscle tissue development (GO:1901863)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|regulation of circadian rhythm (GO:0042752)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|response to cold (GO:0009409)|response to epinephrine (GO:0071871)|response to leucine (GO:0043201)|response to muscle activity (GO:0014850)|response to norepinephrine (GO:0071873)|response to starvation (GO:0042594)|response to statin (GO:0036273)|RNA splicing (GO:0008380)|temperature homeostasis (GO:0001659)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytosol (GO:0005829)|DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|liver(1)|lung(24)|ovary(3)|skin(5)	51		Breast(46;0.0503)				GATTCTCACCCATCATCCCGC	0.408																																					p.G714X	Esophageal Squamous(29;694 744 13796 34866 44181)	Atlas-SNP	.											.	PPARGC1A	129	.	0			c.G2140T						.						132	122	126					4																	23803848		2203	4300	6503	SO:0001630	splice_region_variant	10891	exon11			CTCACCCATCATC	AF106698	CCDS3429.1	4p15.1	2013-02-12	2006-10-17	2004-02-04	ENSG00000109819	ENSG00000109819		"RNA binding motif (RRM) containing"	9237	protein-coding gene	gene with protein product		604517	"peroxisome proliferative activated receptor, gamma, coactivator 1", "peroxisome proliferative activated receptor, gamma, coactivator 1, alpha"	PPARGC1		10585775	Standard	NM_013261		Approved	PGC1, PGC1A	uc003gqs.3	Q9UBK2	OTTHUMG00000097747	ENST00000264867.2:c.2141+1G>T	chr4.hg19:g.23803848C>A		133.0	0.0		160.0	39.0	NM_013261	B7Z406|G8DM16|I3RTT5|I3RTT6|I3RTT7|I3RTT8|I3RTT9|Q3LIG1|Q4W5M7|Q9UN32	Nonsense_Mutation	SNP	ENST00000264867.2	hg19	CCDS3429.1	.	.	.	.	.	.	.	.	.	.	c	39	7.767552	0.98477	.	.	ENSG00000109819	ENST00000264867	.	.	.	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	-7.0564	19.547	0.95302	0.0:1.0:0.0:0.0	.	.	.	.	X	714	.	ENSP00000264867:G714X	G	-	1	0	PPARGC1A	23412946	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.443000	0.80521	2.697000	0.92050	0.457000	0.33378	GGA	.	.		0.408	PPARGC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214976.1	NM_013261	Nonsense_Mutation	A	23803848	C	A	23803848	5	1	249	1	0	0	0	0	0	0	1	0	12309	608	21	3	268	3	PPARGC1A	4	23803848	Splice_Site	SNP	C	TCGA-ED-A8O5-01A-11D-A35Z-10	7726349	23803848	167350428	30	33913										
CWH43	80157	hgsc.bcm.edu	37	chr4	48990664	48990664	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	acaagaagtggatgctaaccCtgctgaggataatcactatt	9	8	1	2			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr4:48990664C>A	ENST00000226432.4	+	2	397	c.214C>A	c.(214-216)Ctg>Atg	p.L72M	CWH43_ENST00000513409.1_Missense_Mutation_p.L45M	NM_025087.2	NP_079363.2	Q9H720	PG2IP_HUMAN	cell wall biogenesis 43 C-terminal homolog (S. cerevisiae)	72					GPI anchor biosynthetic process (GO:0006506)	integral component of membrane (GO:0016021)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(26)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43						GATGCTAACCCTGCTGAGGAT	0.318																																					p.L72M		Atlas-SNP	.											.	CWH43	101	.	0			c.C214A						.						62	59	60					4																	48990664		2203	4300	6503	SO:0001583	missense	80157	exon2			CTAACCCTGCTGA		CCDS3486.1, CCDS68697.1	4p12-p11	2010-09-21			ENSG00000109182	ENSG00000109182			26133	protein-coding gene	gene with protein product						17714445, 17761529	Standard	NM_025087		Approved	FLJ21511, CWH43-C	uc003gyv.3	Q9H720	OTTHUMG00000128627	ENST00000226432.4:c.214C>A	chr4.hg19:g.48990664C>A	ENSP00000226432:p.Leu72Met	144.0	0.0		146.0	39.0	NM_025087	B2RPD7	Missense_Mutation	SNP	ENST00000226432.4	hg19	CCDS3486.1	.	.	.	.	.	.	.	.	.	.	C	10.06	1.247710	0.22880	.	.	ENSG00000109182	ENST00000226432;ENST00000513409	T;T	0.49720	1.35;0.77	5.04	0.904	0.19302	.	0.000000	0.46145	D	0.000320	T	0.53578	0.1805	M	0.65975	2.015	0.21355	N	0.999719	D	0.57571	0.98	P	0.54312	0.748	T	0.48703	-0.9012	9	.	.	.	.	9.4725	0.38851	0.0:0.4969:0.0:0.5031	.	72	Q9H720	PG2IP_HUMAN	M	72;45	ENSP00000226432:L72M;ENSP00000422802:L45M	.	L	+	1	2	CWH43	48685421	0.085000	0.21516	0.044000	0.18714	0.147000	0.21601	0.258000	0.18387	0.013000	0.14918	0.563000	0.77884	CTG	.	.		0.318	CWH43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250496.2	NM_025087		A	48990664	C	A	48990664	3	1	249	1	0	0	0	0	1	0	0	0	4075	680	24	3	220	3	CWH43	4	48990664	Missense_Mutation	SNP	C	TCGA-ED-A8O5-01A-11D-A35Z-10	25186816	48990664	142163612	31	33914										
DMP1	1758	hgsc.bcm.edu	37	chr4	88583327	88583327	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	gacaagaaggaggaaactccAgactgggaagtgatgaggac	15	6	0	4			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr4:88583327A>T	ENST00000339673.6	+	6	496	c.397A>T	c.(397-399)Aga>Tga	p.R133*	DMP1_ENST00000282479.7_Nonsense_Mutation_p.R117*|RP11-742B18.1_ENST00000507894.1_RNA|RP11-742B18.1_ENST00000506814.1_RNA|RP11-742B18.1_ENST00000506480.1_RNA	NM_004407.3	NP_004398.1	Q13316	DMP1_HUMAN	dentin matrix acidic phosphoprotein 1	133					biomineral tissue development (GO:0031214)|extracellular matrix organization (GO:0030198)|ossification (GO:0001503)|positive regulation of cell-substrate adhesion (GO:0010811)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)|integrin binding (GO:0005178)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(1)|stomach(1)	32		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.227)		OV - Ovarian serous cystadenocarcinoma(123;0.000516)		AGGAAACTCCAGACTGGGAAG	0.512																																					p.R133X		Atlas-SNP	.											.	DMP1	72	.	0			c.A397T						.						89	81	83					4																	88583327		2203	4300	6503	SO:0001587	stop_gained	1758	exon6			AACTCCAGACTGG	U34037	CCDS3623.1, CCDS43249.1	4q21	2008-08-29	2008-08-29		ENSG00000152592	ENSG00000152592			2932	protein-coding gene	gene with protein product		600980	"dentin matrix acidic phosphoprotein"			8586437, 9177774	Standard	NM_001079911		Approved		uc003hqv.3	Q13316	OTTHUMG00000130598	ENST00000339673.6:c.397A>T	chr4.hg19:g.88583327A>T	ENSP00000340935:p.Arg133*	171.0	0.0		96.0	70.0	NM_004407	A1L4L3|O43265	Nonsense_Mutation	SNP	ENST00000339673.6	hg19	CCDS3623.1	.	.	.	.	.	.	.	.	.	.	A	13.21	2.170122	0.38315	.	.	ENSG00000152592	ENST00000339673;ENST00000282479	.	.	.	5.37	1.35	0.21983	.	1.159810	0.06226	N	0.687666	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.516	5.9697	0.19344	0.669:0.1509:0.1801:0.0	.	.	.	.	X	133;117	.	ENSP00000282479:R117X	R	+	1	2	DMP1	88802351	0.000000	0.05858	0.001000	0.08648	0.013000	0.08279	0.523000	0.22925	0.365000	0.24400	0.454000	0.30748	AGA	.	.		0.512	DMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253047.1			T	88583327	A	T	88583327	4	4	249	1	0	0	0	0	0	1	0	0	4585	180	7	4	415	4	DMP1	4	88583327	Nonsense_Mutation	SNP	A	TCGA-ED-A8O5-01A-11D-A35Z-10	39592663	88583327	102570949	32	33915										
INTS12	57117	hgsc.bcm.edu	37	chr4	106614468	106614468	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	caacttacctacaaacaacgCaggccaatcccatctccatg	4	16	1	0			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr4:106614468C>T	ENST00000451321.2	-	4	964	c.485G>A	c.(484-486)tGc>tAc	p.C162Y	INTS12_ENST00000394735.1_Missense_Mutation_p.C162Y|INTS12_ENST00000340139.5_Missense_Mutation_p.C162Y	NM_001142471.1	NP_001135943.1	Q96CB8	INT12_HUMAN	integrator complex subunit 12	162					snRNA processing (GO:0016180)	integrator complex (GO:0032039)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(123;5.12e-07)		ACAAACAACGCAGGCCAATCC	0.428																																					p.C162Y		Atlas-SNP	.											.	INTS12	35	.	0			c.G485A						.						139	131	134					4																	106614468		2203	4300	6503	SO:0001583	missense	57117	exon5			ACAACGCAGGCCA		CCDS3671.1	4q24	2013-01-28	2006-03-15	2006-03-15	ENSG00000138785	ENSG00000138785		"Zinc fingers, PHD-type"	25067	protein-coding gene	gene with protein product	"hypothetical nuclear factor SBBI22"	611355	"PHD finger protein 22"	PHF22		16239144	Standard	NM_020395		Approved	SBBI22, INT12	uc010ilr.3	Q96CB8	OTTHUMG00000131215	ENST00000451321.2:c.485G>A	chr4.hg19:g.106614468C>T	ENSP00000415433:p.Cys162Tyr	210.0	0.0		75.0	55.0	NM_020395	B2RC48|Q3B6Z3|Q9HD71	Missense_Mutation	SNP	ENST00000451321.2	hg19	CCDS3671.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.838145	0.91117	.	.	ENSG00000138785	ENST00000394735;ENST00000340139;ENST00000451321	D;D;D	0.99252	-5.63;-5.63;-5.63	5.71	5.71	0.89125	Zinc finger, PHD-finger (2);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.99548	0.9838	M	0.90198	3.095	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98483	1.0606	10	0.87932	D	0	-10.2296	19.8633	0.96793	0.0:1.0:0.0:0.0	.	162	Q96CB8	INT12_HUMAN	Y	162	ENSP00000378221:C162Y;ENSP00000340737:C162Y;ENSP00000415433:C162Y	ENSP00000340737:C162Y	C	-	2	0	INTS12	106833917	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.340000	0.79292	2.697000	0.92050	0.591000	0.81541	TGC	.	.		0.428	INTS12-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318624.1	NM_020395		T	106614468	C	T	106614468	3	4	249	1	0	0	0	0	1	0	0	0	7786	710	25	3	919	3	INTS12	4	106614468	Missense_Mutation	SNP	C	TCGA-ED-A8O5-01A-11D-A35Z-10	18031141	106614468	84539808	33	33916										
EGF	1950	hgsc.bcm.edu	37	chr4	110885652	110885652	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	ctctgctcagccagcagatgGgaatggtttatgccctagat	11	10	2	2	rs529423872		TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr4:110885652G>A	ENST00000265171.5	+	10	1979	c.1534G>A	c.(1534-1536)Gga>Aga	p.G512R	EGF_ENST00000503392.1_Missense_Mutation_p.G512R|EGF_ENST00000509793.1_Missense_Mutation_p.G470R	NM_001178130.1|NM_001963.4	NP_001171601.1|NP_001954.2	P01133	EGF_HUMAN	epidermal growth factor	512					activation of MAPKK activity (GO:0000186)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|branching morphogenesis of an epithelial tube (GO:0048754)|DNA replication (GO:0006260)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mammary gland alveolus development (GO:0060749)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of secretion (GO:0051048)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)|positive regulation of DNA binding (GO:0043388)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of calcium ion import (GO:0090279)|regulation of protein localization to cell surface (GO:2000008)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(1)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sucralfate(DB00364)	CCAGCAGATGGGAATGGTTTA	0.413													G|||	1	0.000199681	8e-04	0	5008	,	,		22473	0		0	False		,,,				2504	0				p.G512R		Atlas-SNP	.											.	EGF	113	.	0			c.G1534A						.						274	256	262					4																	110885652		2203	4300	6503	SO:0001583	missense	1950	exon10			CAGATGGGAATGG	X04571	CCDS3689.1, CCDS54794.1, CCDS54795.1	4q25	2012-10-02	2010-05-11		ENSG00000138798	ENSG00000138798			3229	protein-coding gene	gene with protein product		131530	"epidermal growth factor (beta-urogastrone)"				Standard	NM_001963		Approved		uc003hzy.4	P01133	OTTHUMG00000132044	ENST00000265171.5:c.1534G>A	chr4.hg19:g.110885652G>A	ENSP00000265171:p.Gly512Arg	229.0	0.0		104.0	80.0	NM_001963	B4DRK7|E7EVD2|E9PBF0|Q52LZ6	Missense_Mutation	SNP	ENST00000265171.5	hg19	CCDS3689.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.358316	0.82243	.	.	ENSG00000138798	ENST00000509793;ENST00000265171;ENST00000503392	D;D;D	0.91631	-2.88;-2.88;-2.88	5.05	5.05	0.67936	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	D	0.92701	0.7680	N	0.24115	0.695	0.80722	D	1	D;P;D	0.89917	0.997;0.941;1.0	D;P;D	0.97110	0.973;0.891;1.0	D	0.91325	0.5085	10	0.24483	T	0.36	.	18.434	0.90638	0.0:0.0:1.0:0.0	.	512;470;512	E7EVD2;P01133-2;P01133	.;.;EGF_HUMAN	R	470;512;512	ENSP00000424316:G470R;ENSP00000265171:G512R;ENSP00000421384:G512R	ENSP00000265171:G512R	G	+	1	0	EGF	111105101	1.000000	0.71417	0.996000	0.52242	0.992000	0.81027	8.427000	0.90275	2.328000	0.79073	0.561000	0.74099	GGA	.	.		0.413	EGF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255065.1			A	110885652	G	A	110885652	3	1	249	1	0	0	0	0	1	0	0	0	4964	1233	43	3	1572	3	EGF	4	110885652	Missense_Mutation	SNP	G	TCGA-ED-A8O5-01A-11D-A35Z-10	4271184	110885652	80268624	34	33917										
ALPK1	80216	hgsc.bcm.edu	37	chr4	113332992	113332992	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	tgttcctccaggcgtccctgAgggcctccatcctcgctcgg	11	17	0	1			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr4:113332992A>T	ENST00000458497.1	+	5	565	c.286A>T	c.(286-288)Agg>Tgg	p.R96W	ALPK1_ENST00000505912.1_3'UTR|ALPK1_ENST00000504176.2_Missense_Mutation_p.R18W|ALPK1_ENST00000177648.9_Missense_Mutation_p.R96W	NM_001102406.1|NM_025144.3	NP_001095876.1|NP_079420.3	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	96							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(20)|ovary(6)|prostate(2)|urinary_tract(1)	53		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		GGCGTCCCTGAGGGCCTCCAT	0.597																																					p.R96W		Atlas-SNP	.											.	ALPK1	125	.	0			c.A286T						.						37	35	35					4																	113332992		2203	4300	6503	SO:0001583	missense	80216	exon5			TCCCTGAGGGCCT	AY044164	CCDS3697.1, CCDS58923.1	4q26	2008-02-05			ENSG00000073331	ENSG00000073331			20917	protein-coding gene	gene with protein product	"lymphocyte alpha-kinase"	607347				10021370, 10819331	Standard	NM_025144		Approved	Lak, FLJ22670, KIAA1527	uc003ian.4	Q96QP1	OTTHUMG00000132911	ENST00000458497.1:c.286A>T	chr4.hg19:g.113332992A>T	ENSP00000398048:p.Arg96Trp	72.0	0.0		45.0	33.0	NM_001102406	B4E3G1|F5H138|Q68CI9|Q6P9F9|Q6ZNK4|Q9P201	Missense_Mutation	SNP	ENST00000458497.1	hg19	CCDS3697.1	.	.	.	.	.	.	.	.	.	.	A	8.734	0.917257	0.17982	.	.	ENSG00000073331	ENST00000458497;ENST00000177648;ENST00000309610;ENST00000504176	T;T;T	0.23348	1.91;1.91;1.91	5.48	3.31	0.37934	.	0.163853	0.52532	D	0.000078	T	0.38825	0.1055	L	0.40543	1.245	0.41177	D	0.986205	D;D;D;D	0.67145	0.996;0.996;0.988;0.991	P;D;P;P	0.64687	0.898;0.928;0.898;0.777	T	0.18053	-1.0349	10	0.87932	D	0	-6.3369	13.3895	0.60816	0.8163:0.1837:0.0:0.0	.	18;71;71;96	F5H138;Q9H623;E7EX13;Q96QP1	.;.;.;ALPK1_HUMAN	W	96;96;71;18	ENSP00000398048:R96W;ENSP00000177648:R96W;ENSP00000426044:R18W	ENSP00000177648:R96W	R	+	1	2	ALPK1	113552441	1.000000	0.71417	0.649000	0.29536	0.212000	0.24457	3.401000	0.52601	0.493000	0.27837	-0.445000	0.05633	AGG	.	.		0.597	ALPK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256421.2	NM_025144		T	113332992	A	T	113332992	3	4	249	1	0	0	0	0	1	0	0	0	544	295	11	4	296	4	ALPK1	4	113332992	Missense_Mutation	SNP	A	TCGA-ED-A8O5-01A-11D-A35Z-10	2447340	113332992	77821284	35	33918										
CDH18	1016	hgsc.bcm.edu	37	chr5	19473795	19473796	+	Missense_Mutation	DNP	CG	CG	AA													0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	tcaagggctcttttttgctgCgcctcagggtgataaaaagt					rs565236156		TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C|G	C|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr5:19473795_19473796CG>AA	ENST00000507958.1	-	15	2902_2903	c.1912_1913CG>TT	c.(1912-1914)CGc>TTc	p.R638F	CDH18_ENST00000510297.1_5'UTR|CDH18_ENST00000274170.4_Missense_Mutation_p.R638F|CDH18_ENST00000502796.1_3'UTR|CDH18_ENST00000382275.1_Missense_Mutation_p.R638F|CDH18_ENST00000506372.1_3'UTR			Q13634	CAD18_HUMAN	cadherin 18, type 2	638					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R638H(2)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					TTTTTTGCTGCGCCTCAGGGTG	0.431																																					p.R638L|p.R638C		Atlas-SNP	.											CDH18_ENST00000507958,NS,adenocarcinoma,-1,2|CDH18_ENST00000507958,NS,adenocarcinoma,0,4	CDH18	561	.	2	Substitution - Missense(2)	endometrium(2)	c.G1913T|c.C1912T						.																																			SO:0001583	missense	1016	exon13			TTGCTGCGCCTCA|TGCTGCGCCTCAG	U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"Cadherins / Major cadherins"	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.1912_1913delinsAA	chr5.hg19:g.19473795_19473796delinsAA	ENSP00000425093:p.Arg638Phe	38.0	0.0		33.0	10.0	NM_004934	A8K0I2|B4DHG6|Q8N5Z2	Missense_Mutation	SNP	ENST00000507958.1	hg19	CCDS3889.1																																																																																			.	.		0.431	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934		AA	19473796	CG	AA	19473795	3	1	249	1	0	0	0	0	1	0	0	0	3105	768	27	1	463	1	CDH18	5	19473795	Missense_Mutation	DNP	CG	TCGA-ED-A8O5-01A-11D-A35Z-10		19473795	161441465	36	33919										
CDH9	1007	hgsc.bcm.edu	37	chr5	26902662	26902662	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	ccctcctttacatcttcatcTacttctatcaagtaagagac	3	13	5	1			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr5:26902662T>A	ENST00000231021.4	-	7	1348	c.1176A>T	c.(1174-1176)gtA>gtT	p.V392V		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	392	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						CATCTTCATCTACTTCTATCA	0.378																																					p.V392V	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											.	CDH9	305	.	0			c.A1176T						.						129	122	124					5																	26902662		2203	4300	6503	SO:0001819	synonymous_variant	1007	exon7			TTCATCTACTTCT	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"Cadherins / Major cadherins"	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.1176A>T	chr5.hg19:g.26902662T>A		66.0	0.0		71.0	35.0	NM_016279	Q3B7I5	Silent	SNP	ENST00000231021.4	hg19	CCDS3893.1																																																																																			.	.		0.378	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		A	26902662	T	A	26902662	2	1	249	1	0	0	0	0	0	0	0	1	3119	1509	53	4		4	CDH9	5	26902662	Silent	SNP	T	TCGA-ED-A8O5-01A-11D-A35Z-10	7428867	26902662	154012598	37	33920										
CAST	831	hgsc.bcm.edu	37	chr5	96031603	96031603	+	5'UTR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	atgctggtggaacagcctcgGccaccaaggtcagtgatttc	12	11	1	1			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr5:96031603G>A	ENST00000341926.3	+	0	115				CAST_ENST00000395813.1_Missense_Mutation_p.A68T|CAST_ENST00000508608.1_Missense_Mutation_p.A53T|AC020900.2_ENST00000580431.1_RNA|CAST_ENST00000338252.3_5'UTR|CAST_ENST00000325674.7_Missense_Mutation_p.A68T|CAST_ENST00000395812.2_Missense_Mutation_p.A68T|CAST_ENST00000508830.1_Missense_Mutation_p.A68T|CAST_ENST00000359176.4_Missense_Mutation_p.A68T|CAST_ENST00000510756.1_Missense_Mutation_p.A68T			P20810	ICAL_HUMAN	calpastatin						negative regulation of endopeptidase activity (GO:0010951)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|endopeptidase inhibitor activity (GO:0004866)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(5)|ovary(1)|skin(2)	22		all_cancers(142;5.27e-07)|all_epithelial(76;8.21e-10)|all_lung(232;0.000396)|Lung NSC(167;0.000539)|Ovarian(225;0.024)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;6.85e-15)		AACAGCCTCGGCCACCAAGGT	0.468																																					p.A68T		Atlas-SNP	.											.	CAST	58	.	0			c.G202A						.						36	34	35					5																	96031603		1869	4096	5965	SO:0001623	5_prime_UTR_variant	831	exon3			GCCTCGGCCACCA	AF327443	CCDS4082.1, CCDS54882.1, CCDS54883.1, CCDS75279.1	5q15	2012-09-20			ENSG00000153113	ENSG00000153113			1515	protein-coding gene	gene with protein product		114090				8340353, 14685690, 15820218	Standard	NM_173060		Approved		uc003klx.3	P20810	OTTHUMG00000128413	ENST00000341926.3:c.-48G>A	chr5.hg19:g.96031603G>A		419.0	0.0		326.0	148.0	NM_001042440	B7Z468|G5E946|G5E9D3|O95360|Q05DE8|Q7Z4K0|Q96D08|Q9H1Z5	Missense_Mutation	SNP	ENST00000341926.3	hg19		.	.	.	.	.	.	.	.	.	.	G	7.871	0.728048	0.15507	.	.	ENSG00000153113	ENST00000505143;ENST00000508830;ENST00000511097;ENST00000395813;ENST00000359176;ENST00000325674;ENST00000395812;ENST00000421689;ENST00000510756;ENST00000514845;ENST00000506811;ENST00000514055;ENST00000508608	T;T;T;T;T;T;T;T;T;T	0.56611	0.45;1.87;4.25;1.87;2.11;1.99;2.08;0.5;2.17;2.18	4.65	0.712	0.18167	.	.	.	.	.	T	0.35941	0.0949	L	0.43152	1.355	0.09310	N	1	B;P;B;P;B;B	0.41848	0.001;0.728;0.004;0.763;0.004;0.041	B;B;B;B;B;B	0.33960	0.001;0.168;0.005;0.173;0.005;0.022	T	0.27606	-1.0069	9	0.87932	D	0	2.5497	3.7993	0.08751	0.2616:0.0:0.5645:0.1739	.	53;68;68;68;68;68	B7Z468;P20810-5;G5E9D3;P20810-7;E7ESM9;P20810-6	.;.;.;.;.;.	T	63;68;68;68;68;68;68;68;68;53;53;53;53	ENSP00000422957:A63T;ENSP00000425721:A68T;ENSP00000422951:A68T;ENSP00000379158:A68T;ENSP00000352098:A68T;ENSP00000320319:A68T;ENSP00000379157:A68T;ENSP00000396558:A68T;ENSP00000422176:A68T;ENSP00000422677:A53T	ENSP00000320319:A68T	A	+	1	0	CAST	96057359	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.018000	0.12568	0.113000	0.18004	-0.258000	0.10820	GCC	.	.		0.468	CAST-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000250199.2	NM_173062		A	96031603	G	A	96031603	1	1	249	0	1	0	0	0	0	0	0	0	2686	1203	42	3		3	CAST	5	96031603	5'UTR	SNP	G	TCGA-ED-A8O5-01A-11D-A35Z-10	69128941	96031603	84883657	38	33921										
ST8SIA4	7903	hgsc.bcm.edu	37	chr5	100222044	100222044	+	Intron	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	tcaaaaagcagaagaaagctCaccttattacaaaattgtga	6	7	2	3			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr5:100222044C>A	ENST00000231461.5	-	3	814				ST8SIA4_ENST00000507360.2_5'Flank|ST8SIA4_ENST00000451528.2_Nonstop_Mutation_p.*169L	NM_005668.4	NP_005659.1	Q92187	SIA8D_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4						axon guidance (GO:0007411)|cellular protein modification process (GO:0006464)|ganglioside biosynthetic process (GO:0001574)|N-glycan processing (GO:0006491)|nervous system development (GO:0007399)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(11)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)	25		all_cancers(142;1.5e-07)|all_epithelial(76;1.43e-10)|Prostate(80;0.000644)|Lung NSC(167;0.0059)|all_lung(232;0.00914)|Ovarian(225;0.024)|Colorectal(57;0.09)|Breast(839;0.203)		COAD - Colon adenocarcinoma(37;0.00402)		GAAGAAAGCTCACCTTATTAC	0.343																																					p.X169L		Atlas-SNP	.											.	ST8SIA4	77	.	0			c.G506T						.						55	58	57					5																	100222044		2203	4300	6503	SO:0001627	intron_variant	7903	exon3			AAAGCTCACCTTA	L41680	CCDS4091.1, CCDS47252.1	5q21	2013-03-01	2003-01-14	2005-02-07	ENSG00000113532	ENSG00000113532		"Sialyltransferases"	10871	protein-coding gene	gene with protein product	"ST8Sia IV"	602547	"sialyltransferase 8 (alpha-2, 8-polysialytransferase) D"	SIAT8D		7624364	Standard	NM_005668		Approved	PST, PST1	uc003knk.3	Q92187	OTTHUMG00000128727	ENST00000231461.5:c.503+2G>T	chr5.hg19:g.100222044C>A		150.0	0.0		114.0	47.0	NM_175052	A8KA07|G3V104|Q8N1F4|Q92693	Missense_Mutation	SNP	ENST00000231461.5	hg19	CCDS4091.1	.	.	.	.	.	.	.	.	.	.	C	14.23	2.472384	0.43942	.	.	ENSG00000113532	ENST00000451528	.	.	.	5.82	2.77	0.32553	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.6635	0.34108	0.0:0.581:0.0:0.419	.	.	.	.	L	169	.	.	X	-	2	2	ST8SIA4	100249943	1.000000	0.71417	0.994000	0.49952	0.734000	0.41952	0.775000	0.26689	0.243000	0.21327	0.557000	0.71058	TGA	.	.		0.343	ST8SIA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250632.3	NM_005668		A	100222044	C	A	100222044	1	1	249	0	1	0	0	0	0	0	0	0	15249	837	29	3		3	ST8SIA4	5	100222044	Intron	SNP	C	TCGA-ED-A8O5-01A-11D-A35Z-10	4190441	100222044	80693216	39	33922										
APC	324	hgsc.bcm.edu	37	chr5	112179352	112179352	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	ccggtgattgacagtgtttcAgaaaaggcaaatccaaacat	9	8	1	3			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr5:112179352A>T	ENST00000457016.1	+	16	8441	c.8061A>T	c.(8059-8061)tcA>tcT	p.S2687S	APC_ENST00000257430.4_Silent_p.S2687S|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Silent_p.S2687S			P25054	APC_HUMAN	adenomatous polyposis coli	2687	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		ACAGTGTTTCAGAAAAGGCAA	0.428		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											p.S2687S	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-SNP	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	.	APC	4158	.	1	Unknown(1)	skin(1)	c.A8061T						.						85	88	87					5																	112179352		2202	4300	6502	SO:0001819	synonymous_variant	324	exon17	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	TGTTTCAGAAAAG	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.8061A>T	chr5.hg19:g.112179352A>T		164.0	0.0		125.0	63.0	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	hg19	CCDS4107.1																																																																																			.	.		0.428	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112179352	A	T	112179352	2	4	249	1	0	0	0	0	0	0	0	1	763	175	7	4		4	APC	5	112179352	Silent	SNP	A	TCGA-ED-A8O5-01A-11D-A35Z-10	11957308	112179352	68735908	40	33923										
GM2A	2760	hgsc.bcm.edu	37	chr5	150646346	150646346	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	tctggatcaagatcccatgcAcagactacattggcagctgt	9	11	2	2			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr5:150646346A>G	ENST00000357164.3	+	3	623	c.298A>G	c.(298-300)Aca>Gca	p.T100A		NM_000405.4|NM_001167607.1	NP_000396.2|NP_001161079.1	P17900	SAP3_HUMAN	GM2 ganglioside activator	100					ganglioside catabolic process (GO:0006689)|glycosphingolipid metabolic process (GO:0006687)|learning or memory (GO:0007611)|lipid storage (GO:0019915)|neuromuscular process controlling balance (GO:0050885)|oligosaccharide catabolic process (GO:0009313)|positive regulation of hydrolase activity (GO:0051345)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	apical cortex (GO:0045179)|cytoplasmic side of plasma membrane (GO:0009898)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|mitochondrion (GO:0005739)	beta-N-acetylhexosaminidase activity (GO:0004563)|lipid transporter activity (GO:0005319)|phospholipase activator activity (GO:0016004)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|pancreas(1)|upper_aerodigestive_tract(2)	8		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GATCCCATGCACAGACTACAT	0.453																																					p.T100A		Atlas-SNP	.											.	GM2A	24	.	0			c.A298G						.						100	96	98					5																	150646346		2203	4300	6503	SO:0001583	missense	2760	exon3			CCATGCACAGACT		CCDS4313.1	5q33.1	2010-03-17	2004-05-20		ENSG00000196743	ENSG00000196743			4367	protein-coding gene	gene with protein product	"cerebroside sulfate activator protein", "sphingolipid activator protein 3"	613109	"GM2 ganglioside activator protein"			115863, 1915857	Standard	NM_000405		Approved	SAP-3	uc003ltr.4	P17900	OTTHUMG00000130124	ENST00000357164.3:c.298A>G	chr5.hg19:g.150646346A>G	ENSP00000349687:p.Thr100Ala	65.0	0.0		47.0	16.0	NM_001167607	B2R699|D3DQH6|Q14426|Q14428|Q6LBL5	Missense_Mutation	SNP	ENST00000357164.3	hg19	CCDS4313.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	5.719|5.719	0.317077|0.317077	0.10845|0.10845	.|.	.|.	ENSG00000196743|ENSG00000196743	ENST00000523004|ENST00000523466;ENST00000357164	.|T;T	.|0.68181	.|-0.31;-0.31	5.17|5.17	0.0696|0.0696	0.14375|0.14375	.|MD-2-related lipid-recognition (1);	.|0.638868	.|0.16196	.|N	.|0.225157	T|T	0.40473|0.40473	0.1118|0.1118	N|N	0.14661|0.14661	0.345|0.345	0.18873|0.18873	N|N	0.999986|0.999986	.|B;B;B	.|0.13145	.|0.007;0.001;0.003	.|B;B;B	.|0.14023	.|0.01;0.001;0.002	T|T	0.21793|0.21793	-1.0235|-1.0235	5|10	.|0.52906	.|T	.|0.07	-24.5435|-24.5435	1.2428|1.2428	0.01967|0.01967	0.2393:0.1217:0.4016:0.2374|0.2393:0.1217:0.4016:0.2374	.|.	.|100;58;100	.|B4DQM5;Q14427;P17900	.|.;.;SAP3_HUMAN	R|A	58|115;100	.|ENSP00000429100:T115A;ENSP00000349687:T100A	.|ENSP00000349687:T100A	H|T	+|+	2|1	0|0	GM2A|GM2A	150626539|150626539	0.001000|0.001000	0.12720|0.12720	0.196000|0.196000	0.23383|0.23383	0.047000|0.047000	0.14425|0.14425	-1.067000|-1.067000	0.03451|0.03451	0.328000|0.328000	0.23435|0.23435	-0.242000|-0.242000	0.12053|0.12053	CAC|ACA	.	.		0.453	GM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252432.1	NM_000405		G	150646346	A	G	150646346	3	3	249	1	0	0	0	0	1	0	0	0	6492	159	6	2	308	2	GM2A	5	150646346	Missense_Mutation	SNP	A	TCGA-ED-A8O5-01A-11D-A35Z-10	38466994	150646346	30268914	41	33924										
SYCP2L	221711	hgsc.bcm.edu	37	chr6	10924796	10924796	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	attatcagctacaaagaagtCatgaaaatagaaatccattt	5	6	2	3			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr6:10924796C>A	ENST00000283141.6	+	15	1436	c.1140C>A	c.(1138-1140)gtC>gtA	p.V380V	SYCP2L_ENST00000543878.1_Silent_p.V221V|RP11-637O19.3_ENST00000480294.1_3'UTR	NM_001040274.2	NP_001035364.2	Q5T4T6	SYC2L_HUMAN	synaptonemal complex protein 2-like	380						nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	36	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)	Epithelial(50;0.239)			ACAAAGAAGTCATGAAAATAG	0.338																																					p.V380V		Atlas-SNP	.											.	SYCP2L	101	.	0			c.C1140A						.						87	81	83					6																	10924796		1822	4081	5903	SO:0001819	synonymous_variant	221711	exon15			AGAAGTCATGAAA	AK128130	CCDS43423.1	6p24.2	2008-11-06	2007-07-02	2007-07-02	ENSG00000153157	ENSG00000153157			21537	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 177"	C6orf177			Standard	NM_001040274		Approved	dJ62D2.1, NO145	uc003mzo.3	Q5T4T6	OTTHUMG00000014250	ENST00000283141.6:c.1140C>A	chr6.hg19:g.10924796C>A		85.0	0.0		147.0	28.0	NM_001040274	A6NDS5|Q08GK5|Q6ZRM2|Q96EJ2	Silent	SNP	ENST00000283141.6	hg19	CCDS43423.1																																																																																			.	.		0.338	SYCP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039845.3	NM_194299		A	10924796	C	A	10924796	2	1	249	1	0	0	0	0	0	0	0	1	15448	813	29	3		3	SYCP2L	6	10924796	Silent	SNP	C	TCGA-ED-A8O5-01A-11D-A35Z-10		10924796	160190271	42	33925										
MLN	4295	hgsc.bcm.edu	37	chr6	33766966	33766966	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	gacctctgccatacactcagGgatttcttttgccctttatt	6	12	3	0	rs188344611		TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr6:33766966G>T	ENST00000430124.2	-	3	215	c.150C>A	c.(148-150)tcC>tcA	p.S50S	MLN_ENST00000507738.1_Silent_p.S50S|MLN_ENST00000266003.5_Silent_p.S50S	NM_001040109.1|NM_001184698.1|NM_002418.2	NP_001035198.1|NP_001171627.1|NP_002409.1	P12872	MOTI_HUMAN	motilin	50					cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)	extracellular region (GO:0005576)	receptor binding (GO:0005102)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|skin(1)	6						ATACACTCAGGGATTTCTTTT	0.527																																					p.S50S		Atlas-SNP	.											.	MLN	16	.	0			c.C150A						.						169	141	150					6																	33766966		2203	4300	6503	SO:0001819	synonymous_variant	4295	exon3			ACTCAGGGATTTC		CCDS4786.1, CCDS47412.1, CCDS54993.1	6p21.31	2014-01-30			ENSG00000096395	ENSG00000096395		"Endogenous ligands"	7141	protein-coding gene	gene with protein product	"prepromotilin"	158270					Standard	NM_001184698		Approved		uc003off.1	P12872	OTTHUMG00000014536	ENST00000430124.2:c.150C>A	chr6.hg19:g.33766966G>T		127.0	0.0		190.0	40.0	NM_002418	B7ZLR7|E9PDN2|J3KN51|Q2M1L2|Q5T975|Q6NSY7	Silent	SNP	ENST00000430124.2	hg19	CCDS4786.1																																																																																			.	G|1.000;A|0.000		0.527	MLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040211.4			T	33766966	G	T	33766966	2	4	249	1	0	0	0	0	0	0	0	1	9640	1219	43	3		3	MLN	6	33766966	Silent	SNP	G	TCGA-ED-A8O5-01A-11D-A35Z-10	22842170	33766966	137348101	43	33926										
STK38	11329	hgsc.bcm.edu	37	chr6	36485547	36485547	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	ttagcttatcctgaaaactaTagaacattttcacaacccac	3	11	1	2			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr6:36485547T>C	ENST00000229812.7	-	6	746	c.461A>G	c.(460-462)tAt>tGt	p.Y154C		NM_007271.2	NP_009202.1			serine/threonine kinase 38											NS(1)|endometrium(4)|large_intestine(2)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CTGAAAACTATAGAACATTTT	0.413																																					p.Y154C	Colon(180;997 3561 16158)	Atlas-SNP	.											.	STK38	54	.	0			c.A461G						.						124	114	117					6																	36485547		2203	4300	6503	SO:0001583	missense	11329	exon6			AAACTATAGAACA		CCDS4822.1	6p21	2006-10-06			ENSG00000112079	ENSG00000112079			17847	protein-coding gene	gene with protein product		606964				7761441	Standard	NM_007271		Approved	NDR	uc003omh.3	Q15208	OTTHUMG00000014598	ENST00000229812.7:c.461A>G	chr6.hg19:g.36485547T>C	ENSP00000229812:p.Tyr154Cys	103.0	0.0		212.0	50.0	NM_007271		Missense_Mutation	SNP	ENST00000229812.7	hg19	CCDS4822.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.940122	0.73557	.	.	ENSG00000112079	ENST00000229812	T	0.39592	1.07	5.86	5.86	0.93980	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.45013	0.1321	L	0.33792	1.035	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.40251	-0.9573	10	0.40728	T	0.16	.	16.2669	0.82588	0.0:0.0:0.0:1.0	.	154	Q15208	STK38_HUMAN	C	154	ENSP00000229812:Y154C	ENSP00000229812:Y154C	Y	-	2	0	STK38	36593525	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.240000	0.73641	0.533000	0.62120	TAT	.	.		0.413	STK38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040346.1	NM_007271		C	36485547	T	C	36485547	3	2	249	1	0	0	0	0	1	0	0	0	15318	1406	49	2	972	2	STK38	6	36485547	Missense_Mutation	SNP	T	TCGA-ED-A8O5-01A-11D-A35Z-10	2718581	36485547	134629520	44	33927										
TREML4	285852	hgsc.bcm.edu	37	chr6	41196780	41196780	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	tatcagcctggtggtgtctcCaggtgagctcttttcttgag	12	9	4	2			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr6:41196780C>A	ENST00000341495.2	+	2	496	c.392C>A	c.(391-393)cCa>cAa	p.P131Q	TREML4_ENST00000448827.2_Missense_Mutation_p.P131Q	NM_198153.2	NP_937796.1	Q6UXN2	TRML4_HUMAN	triggering receptor expressed on myeloid cells-like 4	131						extracellular region (GO:0005576)				breast(1)|endometrium(1)|large_intestine(1)|lung(4)|skin(1)	8	Ovarian(28;0.0327)|Colorectal(47;0.196)					GTGGTGTCTCCAGGTGAGCTC	0.507																																					p.P131Q		Atlas-SNP	.											.	TREML4	25	.	0			c.C392A						.						53	54	54					6																	41196780		2203	4300	6503	SO:0001583	missense	285852	exon2			TGTCTCCAGGTGA	AF534826	CCDS34446.1	6p21.1	2013-01-11			ENSG00000188056	ENSG00000188056		"Immunoglobulin superfamily / V-set domain containing"	30807	protein-coding gene	gene with protein product	"TREM like transcript 4"	614664				12645956	Standard	NM_198153		Approved	TLT4	uc003oqc.3	Q6UXN2	OTTHUMG00000016408	ENST00000341495.2:c.392C>A	chr6.hg19:g.41196780C>A	ENSP00000342570:p.Pro131Gln	53.0	0.0		120.0	16.0	NM_198153	B7ZL92	Missense_Mutation	SNP	ENST00000341495.2	hg19	CCDS34446.1	.	.	.	.	.	.	.	.	.	.	.	16.15	3.041096	0.55003	.	.	ENSG00000188056	ENST00000341495;ENST00000445267;ENST00000448827	T;T	0.04551	3.6;3.6	4.39	2.53	0.30540	Immunoglobulin-like fold (1);	.	.	.	.	T	0.03651	0.0104	L	0.27053	0.805	0.09310	N	1	D	0.89917	1.0	D	0.74348	0.983	T	0.38714	-0.9648	9	0.54805	T	0.06	-2.7064	5.1176	0.14843	0.2034:0.6884:0.0:0.1082	.	131	Q6UXN2	TRML4_HUMAN	Q	131	ENSP00000342570:P131Q;ENSP00000418078:P131Q	ENSP00000342570:P131Q	P	+	2	0	TREML4	41304758	0.369000	0.25039	0.050000	0.19076	0.332000	0.28634	0.981000	0.29526	0.431000	0.26258	0.591000	0.81541	CCA	.	.		0.507	TREML4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043873.2			A	41196780	C	A	41196780	3	1	249	1	0	0	0	0	1	0	0	0	16489	594	21	3	398	3	TREML4	6	41196780	Missense_Mutation	SNP	C	TCGA-ED-A8O5-01A-11D-A35Z-10	4711233	41196780	129918287	45	33928										
ABCC10	89845	hgsc.bcm.edu	37	chr6	43417802	43417802	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	ctgcagagcagccagcagggAgtccctgcctcactcggagg	14	14	1	1			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr6:43417802A>C	ENST00000372530.4	+	22	4667	c.4452A>C	c.(4450-4452)ggA>ggC	p.G1484G	ABCC10_ENST00000244533.3_Silent_p.G1456G	NM_001198934.1	NP_001185863.1	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	1484					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(8)|lung(21)|ovary(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)		Cyclosporine(DB00091)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Estradiol(DB00783)|Etoposide(DB00773)|Gemcitabine(DB00441)|Methotrexate(DB00563)|Paclitaxel(DB01229)|Sildenafil(DB00203)|Tenofovir(DB00300)|Verapamil(DB00661)|Vincristine(DB00541)	GCCAGCAGGGAGTCCCTGCCT	0.652																																					p.G1484G		Atlas-SNP	.											.	ABCC10	118	.	0			c.A4452C						.						56	63	61					6																	43417802		2203	4300	6503	SO:0001819	synonymous_variant	89845	exon22			GCAGGGAGTCCCT	U66684	CCDS4896.1, CCDS56430.1	6p12.3	2012-03-14			ENSG00000124574	ENSG00000124574		"ATP binding cassette transporters / subfamily C"	52	protein-coding gene	gene with protein product		612509				8894702	Standard	NM_033450		Approved	EST182763, MRP7, SIMRP7	uc003ouy.1	Q5T3U5	OTTHUMG00000014733	ENST00000372530.4:c.4452A>C	chr6.hg19:g.43417802A>C		185.0	0.0		288.0	58.0	NM_001198934	Q8NHX7|Q9H7N2|Q9NXY3|Q9UF48	Silent	SNP	ENST00000372530.4	hg19	CCDS56430.1																																																																																			.	.		0.652	ABCC10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040603.2	NM_033450		C	43417802	A	C	43417802	2	2	249	1	0	0	0	0	0	0	0	1	50	291	11	5		5	ABCC10	6	43417802	Silent	SNP	A	TCGA-ED-A8O5-01A-11D-A35Z-10	2221022	43417802	127697265	46	33929										
AMPH	273	hgsc.bcm.edu	37	chr7	38505102	38505102	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	atggtgaaggccttgtcggcGtgctggtcacccagttttgt	14	9	1	1	rs146457438	byFrequency	TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr7:38505102G>C	ENST00000356264.2	-	9	929	c.714C>G	c.(712-714)caC>caG	p.H238Q	AMPH_ENST00000325590.5_Missense_Mutation_p.H238Q|AMPH_ENST00000428293.2_Missense_Mutation_p.H238Q	NM_001635.3	NP_001626.1	P49418	AMPH_HUMAN	amphiphysin	238	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				endocytosis (GO:0006897)|learning (GO:0007612)|synaptic transmission (GO:0007268)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|leading edge membrane (GO:0031256)|synaptic vesicle (GO:0008021)	phospholipid binding (GO:0005543)	p.H238H(1)|p.H238Q(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(12)|liver(3)|lung(27)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)	62						CCTTGTCGGCGTGCTGGTCAC	0.502																																					p.H238Q		Atlas-SNP	.											AMPH,colon,carcinoma,0,2	AMPH	157	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	c.C714G						.						75	59	64					7																	38505102		2203	4298	6501	SO:0001583	missense	273	exon9			GTCGGCGTGCTGG		CCDS5456.1, CCDS47574.1	7p14-p13	2007-06-19	2007-06-19		ENSG00000078053	ENSG00000078053			471	protein-coding gene	gene with protein product		600418	"amphiphysin (Stiff-Mann syndrome with breast cancer 128kD autoantigen)", "amphiphysin (Stiff-Man syndrome with breast cancer 128kDa autoantigen)"			8245793	Standard	NM_139316		Approved		uc003tgu.3	P49418	OTTHUMG00000023725	ENST00000356264.2:c.714C>G	chr7.hg19:g.38505102G>C	ENSP00000348602:p.His238Gln	124.0	0.0		100.0	48.0	NM_139316	A4D1X8|A4D1X9|O43538|Q75MJ8|Q75MK5|Q75MM3|Q8N4G0	Missense_Mutation	SNP	ENST00000356264.2	hg19	CCDS5456.1	.	.	.	.	.	.	.	.	.	.	G	14.29	2.490918	0.44249	.	.	ENSG00000078053	ENST00000325590;ENST00000356264;ENST00000428293;ENST00000353242;ENST00000544070	T;T;T	0.41065	1.01;1.01;1.01	5.87	-11.7	0.00046	BAR (1);	0.107286	0.64402	D	0.000002	T	0.44829	0.1312	L	0.38531	1.155	0.30126	N	0.805235	D;D	0.71674	0.998;0.998	D;P	0.64877	0.93;0.899	T	0.79482	-0.1785	10	0.49607	T	0.09	-26.1083	20.1993	0.98256	0.4304:0.0:0.5696:0.0	.	238;238	P49418-2;P49418	.;AMPH_HUMAN	Q	238;238;238;8;238	ENSP00000317441:H238Q;ENSP00000348602:H238Q;ENSP00000390734:H238Q	ENSP00000317441:H238Q	H	-	3	2	AMPH	38471627	0.001000	0.12720	0.045000	0.18777	0.933000	0.57130	-1.559000	0.02162	-3.327000	0.00186	-2.154000	0.00331	CAC	.	G|0.999;A|0.001		0.502	AMPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226953.2	NM_001635		C	38505102	G	C	38505102	3	2	249	1	0	0	0	0	1	0	0	0	588	1136	40	4	1425	4	AMPH	7	38505102	Missense_Mutation	SNP	G	TCGA-ED-A8O5-01A-11D-A35Z-10		38505102	120633561	47	33930										
RFC2	5982	hgsc.bcm.edu	37	chr7	73657534	73657534	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	cgagtggttttagagtagatTtccatggttctcctcaaggc	11	8	2	2			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr7:73657534T>G	ENST00000055077.3	-	6	537	c.477A>C	c.(475-477)gaA>gaC	p.E159D	RFC2_ENST00000352131.3_Missense_Mutation_p.E125D	NM_181471.1	NP_852136.1	P35250	RFC2_HUMAN	replication factor C (activator 1) 2, 40kDa	159					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor C complex (GO:0005663)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(3)	8						TAGAGTAGATTTCCATGGTTC	0.522																																					p.E159D		Atlas-SNP	.											.	RFC2	27	.	0			c.A477C						.						216	182	193					7																	73657534		2203	4300	6503	SO:0001583	missense	5982	exon6			GTAGATTTCCATG		CCDS5567.1, CCDS5568.1, CCDS75618.1	7q11.23	2010-04-21	2002-08-29		ENSG00000049541	ENSG00000049541		"ATPases / AAA-type"	9970	protein-coding gene	gene with protein product	"activator 1"	600404	"replication factor C (activator 1) 2 (40kD)"			1313560, 7774928	Standard	NM_181471		Approved	A1, RFC40	uc003uaj.3	P35250	OTTHUMG00000023239	ENST00000055077.3:c.477A>C	chr7.hg19:g.73657534T>G	ENSP00000055077:p.Glu159Asp	107.0	0.0		86.0	43.0	NM_181471	B5BU07|D3DXG3|P32846|Q9BU93	Missense_Mutation	SNP	ENST00000055077.3	hg19	CCDS5568.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.169854	0.78452	.	.	ENSG00000049541	ENST00000352131;ENST00000055077	T;D	0.91577	0.79;-2.87	4.99	-1.63	0.08345	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.93216	0.7839	M	0.76002	2.32	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.90836	0.4720	10	0.87932	D	0	.	9.7016	0.40189	0.0:0.3544:0.0:0.6456	.	125;125;159	P35250-2;Q75MT5;P35250	.;.;RFC2_HUMAN	D	125;159	ENSP00000275627:E125D;ENSP00000055077:E159D	ENSP00000055077:E159D	E	-	3	2	RFC2	73295470	0.938000	0.31826	0.989000	0.46669	0.936000	0.57629	0.036000	0.13819	-0.471000	0.06891	-0.263000	0.10527	GAA	.	.		0.522	RFC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252459.2	NM_181471		G	73657534	T	G	73657534	3	3	249	1	0	0	0	0	1	0	0	0	13260	1838	64	5	611	5	RFC2	7	73657534	Missense_Mutation	SNP	T	TCGA-ED-A8O5-01A-11D-A35Z-10	35152432	73657534	85481129	48	33931										
SEMA3E	9723	hgsc.bcm.edu	37	chr7	82996922	82996922	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	tcaggagtccagcgtgtgccTgggcaggcggtaatgctcag	16	10	2	0	rs368305214		TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr7:82996922T>A	ENST00000307792.3	-	17	2775	c.2308A>T	c.(2308-2310)Agg>Tgg	p.R770W	SEMA3E_ENST00000427262.1_Missense_Mutation_p.R710W	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	770	Arg/Lys-rich (basic).				axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell-matrix adhesion (GO:0001953)|patterning of blood vessels (GO:0001569)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell shape (GO:0008360)|semaphorin-plexin signaling pathway (GO:0071526)|sprouting angiogenesis (GO:0002040)|synapse organization (GO:0050808)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(19)|ovary(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	51		Medulloblastoma(109;0.109)				AGCGTGTGCCTGGGCAGGCGG	0.413																																					p.R770W		Atlas-SNP	.											.	SEMA3E	125	.	0			c.A2308T						.						167	167	167					7																	82996922		2203	4300	6503	SO:0001583	missense	9723	exon17			TGTGCCTGGGCAG	AB002329	CCDS34674.1, CCDS55121.1	7q21.11	2013-01-11			ENSG00000170381	ENSG00000170381		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10727	protein-coding gene	gene with protein product	"M-sema H"	608166		SEMAH		9205841, 9515811	Standard	NM_012431		Approved	M-SemaK, KIAA0331, coll-5	uc003uhy.2	O15041	OTTHUMG00000154693	ENST00000307792.3:c.2308A>T	chr7.hg19:g.82996922T>A	ENSP00000303212:p.Arg770Trp	267.0	0.0		189.0	69.0	NM_012431	B4E1P1|Q75M94|Q75M97	Missense_Mutation	SNP	ENST00000307792.3	hg19	CCDS34674.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.289631	0.80914	.	.	ENSG00000170381	ENST00000307792;ENST00000427262;ENST00000541514	T;T	0.37915	1.2;1.17	5.64	4.47	0.54385	.	0.049694	0.85682	D	0.000000	T	0.61311	0.2337	M	0.81802	2.56	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.65829	-0.6073	10	0.87932	D	0	.	12.9892	0.58608	0.0:0.0:0.1347:0.8653	.	770	O15041	SEM3E_HUMAN	W	770;710;761	ENSP00000303212:R770W;ENSP00000405052:R710W	ENSP00000303212:R770W	R	-	1	2	SEMA3E	82834858	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	2.069000	0.41481	0.933000	0.37291	0.477000	0.44152	AGG	.	.		0.413	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431		A	82996922	T	A	82996922	3	1	249	1	0	0	0	0	1	0	0	0	14043	1579	55	4	23	4	SEMA3E	7	82996922	Missense_Mutation	SNP	T	TCGA-ED-A8O5-01A-11D-A35Z-10	9339388	82996922	76141741	49	33932										
RELN	5649	hgsc.bcm.edu	37	chr7	103191647	103191647	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	gctgctgctgtggtagcagaGgggcagcagaaggtgccagg	19	8	0	2			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr7:103191647G>T	ENST00000428762.1	-	41	6328	c.6169C>A	c.(6169-6171)Ctc>Atc	p.L2057I	RELN_ENST00000424685.2_Missense_Mutation_p.L2057I|RELN_ENST00000343529.5_Missense_Mutation_p.L2057I	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	2057					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		TGGTAGCAGAGGGGCAGCAGA	0.587																																					p.L2057I	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.C6169A						.						71	54	60					7																	103191647		2203	4300	6503	SO:0001583	missense	5649	exon41			AGCAGAGGGGCAG		CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.6169C>A	chr7.hg19:g.103191647G>T	ENSP00000392423:p.Leu2057Ile	68.0	0.0		55.0	24.0	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	hg19	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	G	18.10	3.547620	0.65311	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.21361	2.01;2.01;2.01	5.7	3.54	0.40534	Neuraminidase (1);	0.066024	0.64402	D	0.000011	T	0.32285	0.0824	L	0.50333	1.59	0.40919	D	0.984298	D;D	0.56968	0.977;0.978	D;D	0.70935	0.971;0.95	T	0.09574	-1.0668	10	0.42905	T	0.14	.	4.6682	0.12676	0.2076:0.217:0.5754:0.0	.	2057;2057	P78509-2;P78509	.;RELN_HUMAN	I	2057	ENSP00000392423:L2057I;ENSP00000345694:L2057I;ENSP00000388446:L2057I	ENSP00000345694:L2057I	L	-	1	0	RELN	102978883	0.997000	0.39634	1.000000	0.80357	0.998000	0.95712	1.901000	0.39838	1.384000	0.46424	0.650000	0.86243	CTC	.	.		0.587	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		T	103191647	G	T	103191647	3	4	249	1	0	0	0	0	1	0	0	0	13235	1000	35	3	4313	3	RELN	7	103191647	Missense_Mutation	SNP	G	TCGA-ED-A8O5-01A-11D-A35Z-10	20194725	103191647	55947016	50	33933										
PRKAR2B	5577	hgsc.bcm.edu	37	chr7	106781380	106781380	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	tcaaggtgacgatggtgacaActtttatgtaattgataggt	11	4	1	3			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr7:106781380A>G	ENST00000265717.4	+	5	828	c.569A>G	c.(568-570)aAc>aGc	p.N190S	PRKAR2B_ENST00000393613.2_3'UTR	NM_002736.2	NP_002727.2	P31323	KAP3_HUMAN	protein kinase, cAMP-dependent, regulatory, type II, beta	190					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fatty acid metabolic process (GO:0006631)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|mitotic cell cycle (GO:0000278)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	14						GATGGTGACAACTTTTATGTA	0.348																																					p.N190S		Atlas-SNP	.											.	PRKAR2B	34	.	0			c.A569G						.						161	155	157					7																	106781380		2203	4300	6503	SO:0001583	missense	5577	exon5			GTGACAACTTTTA		CCDS5740.1	7q22.3	2010-04-22			ENSG00000005249	ENSG00000005249	2.7.11.1		9392	protein-coding gene	gene with protein product		176912		PRKAR2		1358799	Standard	NM_002736		Approved		uc003vdx.3	P31323	OTTHUMG00000137418	ENST00000265717.4:c.569A>G	chr7.hg19:g.106781380A>G	ENSP00000265717:p.Asn190Ser	193.0	0.0		144.0	54.0	NM_002736	A4D0R9	Missense_Mutation	SNP	ENST00000265717.4	hg19	CCDS5740.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.574225	0.86542	.	.	ENSG00000005249	ENST00000265717;ENST00000543645;ENST00000539794	D	0.91577	-2.87	5.25	5.25	0.73442	Cyclic nucleotide-binding, conserved site (1);Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.000000	0.85682	D	0.000000	D	0.93858	0.8035	L	0.52905	1.665	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94458	0.7673	10	0.72032	D	0.01	-5.7271	15.4527	0.75285	1.0:0.0:0.0:0.0	.	190	P31323	KAP3_HUMAN	S	190;190;177	ENSP00000265717:N190S	ENSP00000265717:N190S	N	+	2	0	PRKAR2B	106568616	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.259000	0.95561	2.121000	0.65114	0.460000	0.39030	AAC	.	.		0.348	PRKAR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268386.1			G	106781380	A	G	106781380	3	3	249	1	0	0	0	0	1	0	0	0	12518	43	2	2	587	2	PRKAR2B	7	106781380	Missense_Mutation	SNP	A	TCGA-ED-A8O5-01A-11D-A35Z-10	3589733	106781380	52357283	51	33934										
GRM8	2918	hgsc.bcm.edu	37	chr7	126542720	126542720	+	Nonsense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	gcaagagttcggcttctaaaGtatcgatcaaatcctatttc	7	9	2	1			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr7:126542720G>C	ENST00000339582.2	-	6	1840	c.1032C>G	c.(1030-1032)taC>taG	p.Y344*	GRM8_ENST00000444921.2_Nonsense_Mutation_p.Y344*|GRM8_ENST00000480995.1_5'UTR|GRM8_ENST00000405249.1_Nonsense_Mutation_p.Y344*|GRM8_ENST00000358373.3_Nonsense_Mutation_p.Y344*			O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8	344					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of cAMP biosynthetic process (GO:0030818)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(16)|lung(62)|ovary(5)|pancreas(1)|prostate(1)|skin(14)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(4)	125		Prostate(267;0.186)				GGCTTCTAAAGTATCGATCAA	0.343										HNSCC(24;0.065)																											p.Y344X		Atlas-SNP	.											.	GRM8	377	.	0			c.C1032G						.						67	67	67					7																	126542720		2202	4300	6502	SO:0001587	stop_gained	2918	exon5			TCTAAAGTATCGA		CCDS5794.1, CCDS47696.1	7q31.3-q32.1	2012-08-29			ENSG00000179603	ENSG00000179603		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4600	protein-coding gene	gene with protein product		601116				8824806	Standard	NM_000845		Approved	GLUR8, GPRC1H, mGlu8, MGLUR8	uc003vlr.2	O00222	OTTHUMG00000022888	ENST00000339582.2:c.1032C>G	chr7.hg19:g.126542720G>C	ENSP00000344173:p.Tyr344*	103.0	0.0		95.0	50.0	NM_000845	A4D0Y3|B0FZ74|B0M0L0|O15493|O95945|O95946|Q3MIV9|Q52M02|Q6J165	Nonsense_Mutation	SNP	ENST00000339582.2	hg19	CCDS5794.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.943803	0.92593	.	.	ENSG00000179603	ENST00000339582;ENST00000444921;ENST00000358373;ENST00000405249	.	.	.	4.88	-1.71	0.08133	.	0.068522	0.64402	D	0.000011	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.4321	0.44413	0.6443:0.0:0.3557:0.0	.	.	.	.	X	344	.	ENSP00000344173:Y344X	Y	-	3	2	GRM8	126329956	0.997000	0.39634	0.995000	0.50966	0.962000	0.63368	0.523000	0.22925	-0.251000	0.09542	-0.350000	0.07774	TAC	.	.		0.343	GRM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059209.4			C	126542720	G	C	126542720	4	2	249	1	0	0	0	0	0	1	0	0	6812	1024	36	4	1768	4	GRM8	7	126542720	Nonsense_Mutation	SNP	G	TCGA-ED-A8O5-01A-11D-A35Z-10	19761340	126542720	32595943	52	33935										
CHMP7	91782	hgsc.bcm.edu	37	chr8	23104313	23104313	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	gagcgcatgtccttcctgttCtccgctttcaagaggagtcg	11	12	2	1			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr8:23104313C>G	ENST00000397677.1	+	2	753	c.105C>G	c.(103-105)ttC>ttG	p.F35L	CHMP7_ENST00000313219.7_Missense_Mutation_p.F35L	NM_152272.3	NP_689485.1	Q8WUX9	CHMP7_HUMAN	charged multivesicular body protein 7	35					endosomal transport (GO:0016197)|late endosome to vacuole transport (GO:0045324)|membrane organization (GO:0061024)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|ESCRT III complex (GO:0000815)	protein transporter activity (GO:0008565)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|urinary_tract(1)	11		Prostate(55;0.0513)		Colorectal(74;0.0155)|COAD - Colon adenocarcinoma(73;0.0632)		CCTTCCTGTTCTCCGCTTTCA	0.706											OREG0018633	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F35L		Atlas-SNP	.											.	CHMP7	34	.	0			c.C105G						.						15	14	14					8																	23104313		2202	4298	6500	SO:0001583	missense	91782	exon2			CCTGTTCTCCGCT	BC019110	CCDS6040.1	8p21.2	2011-09-21	2011-09-21		ENSG00000147457	ENSG00000147457		"Charged multivesicular body proteins"	28439	protein-coding gene	gene with protein product		611130	"CHMP family, member 7"			16856878	Standard	NM_152272		Approved	MGC29816	uc003xdc.2	Q8WUX9	OTTHUMG00000131785	ENST00000397677.1:c.105C>G	chr8.hg19:g.23104313C>G	ENSP00000380794:p.Phe35Leu	172.0	0.0	761	168.0	62.0	NM_152272	B2RDT3|B4DKJ6|D3DSS1|Q8NDM1|Q9BT50	Missense_Mutation	SNP	ENST00000397677.1	hg19	CCDS6040.1	.	.	.	.	.	.	.	.	.	.	C	14.36	2.512875	0.44660	.	.	ENSG00000147457	ENST00000397677;ENST00000313219;ENST00000519984	T;T	0.62498	0.02;0.02	5.8	2.97	0.34412	.	0.000000	0.85682	D	0.000000	T	0.70605	0.3243	M	0.77313	2.365	0.46317	D	0.998982	D	0.58620	0.983	P	0.56278	0.795	T	0.69476	-0.5135	10	0.72032	D	0.01	-13.7121	6.9878	0.24737	0.0:0.6275:0.0:0.3725	.	35	Q8WUX9	CHMP7_HUMAN	L	35	ENSP00000380794:F35L;ENSP00000324491:F35L	ENSP00000324491:F35L	F	+	3	2	CHMP7	23160258	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.590000	0.36654	0.331000	0.23511	0.655000	0.94253	TTC	.	.		0.706	CHMP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254717.1	NM_152272		G	23104313	C	G	23104313	3	3	249	1	0	0	0	0	1	0	0	0	3363	912	32	4	107	4	CHMP7	8	23104313	Missense_Mutation	SNP	C	TCGA-ED-A8O5-01A-11D-A35Z-10		23104313	123259709	53	33936										
FOXD4	2298	hgsc.bcm.edu	37	chr9	116958	116958	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	cgccgacgcggccgacaggtGcccgcccagcaccgcgccct	13	21	0	0			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr9:116958G>A	ENST00000382500.2	-	1	1459	c.1162C>T	c.(1162-1164)Cac>Tac	p.H388Y		NM_207305.4	NP_997188.2	Q12950	FOXD4_HUMAN	forkhead box D4	388					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(5)|large_intestine(2)|lung(3)|prostate(1)|skin(3)	14	all_lung(41;0.218)	all_cancers(5;0.0395)|Acute lymphoblastic leukemia(5;1.91e-07)|all_hematologic(5;1.95e-06)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)		GCCGACAGGTGCCCGCCCAGC	0.697																																					p.H388Y		Atlas-SNP	.											.	FOXD4	75	.	0			c.C1162T						.						18	27	24					9																	116958		2108	4192	6300	SO:0001583	missense	2298	exon1			ACAGGTGCCCGCC	U13223	CCDS34975.1	9p24.3	2014-09-17			ENSG00000170122	ENSG00000170122		"Forkhead boxes"	3805	protein-coding gene	gene with protein product		601092		FKHL9		7957066, 8825632, 12234674	Standard	NM_207305		Approved	FREAC5, FOXD4a	uc003zfz.4	Q12950	OTTHUMG00000021015	ENST00000382500.2:c.1162C>T	chr9.hg19:g.116958G>A	ENSP00000371940:p.His388Tyr	543.0	1.0		487.0	109.0	NM_207305	B2RN05|B9EGL7|Q5VVK1|Q8WXT6	Missense_Mutation	SNP	ENST00000382500.2	hg19	CCDS34975.1	.	.	.	.	.	.	.	.	.	.	.	4.485	0.090001	0.08632	.	.	ENSG00000170122	ENST00000382500	D	0.98012	-4.66	2.41	1.47	0.22746	.	0.891956	0.08992	U	0.864260	D	0.92632	0.7659	N	0.19112	0.55	0.09310	N	0.99999	B	0.26400	0.148	B	0.22152	0.038	D	0.86277	0.1665	10	0.48119	T	0.1	.	3.1137	0.06367	0.153:0.0:0.5801:0.2669	.	388	Q12950	FOXD4_HUMAN	Y	388	ENSP00000371940:H388Y	ENSP00000371940:H388Y	H	-	1	0	FOXD4	106958	0.841000	0.29509	0.235000	0.24058	0.009000	0.06853	1.705000	0.37867	0.333000	0.23563	-0.513000	0.04457	CAC	.	.		0.697	FOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055433.1	NM_207305		A	116958	G	A	116958	3	1	249	1	0	0	0	0	1	0	0	0	6007	1319	46	3	161	3	FOXD4	9	116958	Missense_Mutation	SNP	G	TCGA-ED-A8O5-01A-11D-A35Z-10		116958	141096473	54	33937										
INSL4	3641	hgsc.bcm.edu	37	chr9	5233727	5233727	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	gaattcattcctaatttgtcAccagagctgaagaaaccact	6	10	2	3			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr9:5233727A>G	ENST00000239316.4	+	2	375	c.270A>G	c.(268-270)tcA>tcG	p.S90S		NM_002195.1	NP_002186.1	Q14641	INSL4_HUMAN	insulin-like 4 (placenta)	90					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|female pregnancy (GO:0007565)|multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	insulin-like growth factor receptor binding (GO:0005159)|receptor binding (GO:0005102)			endometrium(2)|lung(2)|skin(1)|urinary_tract(1)	6	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0201)|Lung(218;0.14)		CTAATTTGTCACCAGAGCTGA	0.408																																					p.S90S		Atlas-SNP	.											.	INSL4	20	.	0			c.A270G						.						81	74	76					9																	5233727		2203	4300	6503	SO:0001819	synonymous_variant	3641	exon2			TTTGTCACCAGAG		CCDS6459.1	9p24	2008-02-05			ENSG00000120211	ENSG00000120211			6087	protein-coding gene	gene with protein product		600910				8666396, 9730618	Standard	NM_002195		Approved	EPIL	uc003ziy.3	Q14641	OTTHUMG00000019494	ENST00000239316.4:c.270A>G	chr9.hg19:g.5233727A>G		115.0	0.0		87.0	41.0	NM_002195	A8K678|Q5W127	Silent	SNP	ENST00000239316.4	hg19	CCDS6459.1																																																																																			.	.		0.408	INSL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051616.2	NM_002195		G	5233727	A	G	5233727	2	3	249	1	0	0	0	0	0	0	0	1	7777	146	6	2		2	INSL4	9	5233727	Silent	SNP	A	TCGA-ED-A8O5-01A-11D-A35Z-10	5116769	5233727	135979704	55	33938										
TTC16	158248	hgsc.bcm.edu	37	chr9	130485486	130485486	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	gctgctccagaagatggtggCccaggcccagcaggcgcgcc	15	15	0	2			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr9:130485486C>T	ENST00000373289.3	+	7	826	c.746C>T	c.(745-747)gCc>gTc	p.A249V	TTC16_ENST00000489226.1_3'UTR|TTC16_ENST00000393748.4_Missense_Mutation_p.A73V|PTRH1_ENST00000429848.1_Intron|PTRH1_ENST00000419060.1_Intron	NM_144965.1	NP_659402.1	Q8NEE8	TTC16_HUMAN	tetratricopeptide repeat domain 16	249										central_nervous_system(2)|endometrium(3)|lung(7)|ovary(3)|pancreas(2)|prostate(4)|skin(1)	22						AAGATGGTGGCCCAGGCCCAG	0.657																																					p.A249V		Atlas-SNP	.											.	TTC16	55	.	0			c.C746T						.						55	55	55					9																	130485486		2203	4300	6503	SO:0001583	missense	158248	exon7			TGGTGGCCCAGGC	AK057342	CCDS6875.1	9q34.13	2013-01-10			ENSG00000167094	ENSG00000167094		"Tetratricopeptide (TTC) repeat domain containing"	26536	protein-coding gene	gene with protein product						12477932	Standard	NM_144965		Approved	FLJ32780	uc004brq.1	Q8NEE8	OTTHUMG00000020711	ENST00000373289.3:c.746C>T	chr9.hg19:g.130485486C>T	ENSP00000362386:p.Ala249Val	68.0	0.0		56.0	29.0	NM_144965	B4DYG4|B5ME24|Q5JU66|Q96M72	Missense_Mutation	SNP	ENST00000373289.3	hg19	CCDS6875.1	.	.	.	.	.	.	.	.	.	.	C	8.413	0.844582	0.16963	.	.	ENSG00000167094	ENST00000373289;ENST00000393748;ENST00000316259	T	0.52526	0.66	5.08	-0.278	0.12894	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	1.774740	0.02217	N	0.063662	T	0.30355	0.0762	L	0.29908	0.895	0.09310	N	1	P;B;P	0.35656	0.514;0.185;0.514	B;B;B	0.32090	0.14;0.048;0.14	T	0.10636	-1.0621	10	0.29301	T	0.29	-7.9487	0.4353	0.00478	0.4256:0.1806:0.2135:0.1803	.	236;201;249	B4DZ42;B4DH05;Q8NEE8	.;.;TTC16_HUMAN	V	249;73;194	ENSP00000362386:A249V	ENSP00000319048:A194V	A	+	2	0	TTC16	129525307	0.014000	0.17966	0.635000	0.29338	0.237000	0.25408	0.600000	0.24104	0.107000	0.17824	-0.538000	0.04264	GCC	.	.		0.657	TTC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054224.1	NM_144965		T	130485486	C	T	130485486	3	4	249	1	0	0	0	0	1	0	0	0	16698	739	26	3	772	3	TTC16	9	130485486	Missense_Mutation	SNP	C	TCGA-ED-A8O5-01A-11D-A35Z-10	125251759	130485486	10727945	56	33939										
NOTCH1	4851	hgsc.bcm.edu	37	chr9	139390565	139390565	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	cgggcgatctgggactgcatGctggtgggagggctggagac	20	8	1	1			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr9:139390565G>C	ENST00000277541.6	-	34	7701	c.7626C>G	c.(7624-7626)agC>agG	p.S2542R		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	2542					anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		GGGACTGCATGCTGGTGGGAG	0.667			"T, Mis, O"	TRB@	T-ALL					HNSCC(8;0.001)																											p.S2542R		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"Notch homolog 1, translocation-associated (Drosophila) (TAN1)"		L	.	NOTCH1	1980	.	0			c.C7626G						.						17	23	21					9																	139390565		1985	4146	6131	SO:0001583	missense	4851	exon34			CTGCATGCTGGTG	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"Ankyrin repeat domain containing"	7881	protein-coding gene	gene with protein product		190198	"Notch (Drosophila) homolog 1 (translocation-associated)", "Notch homolog 1, translocation-associated (Drosophila)"	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.7626C>G	chr9.hg19:g.139390565G>C	ENSP00000277541:p.Ser2542Arg	100.0	0.0		61.0	20.0	NM_017617	Q59ED8|Q5SXM3	Missense_Mutation	SNP	ENST00000277541.6	hg19	CCDS43905.1	.	.	.	.	.	.	.	.	.	.	G	17.19	3.325899	0.60743	.	.	ENSG00000148400	ENST00000277541	D	0.81908	-1.55	4.98	1.53	0.23141	.	0.042024	0.85682	D	0.000000	T	0.80696	0.4672	L	0.47716	1.5	0.44771	D	0.997777	P	0.43938	0.822	P	0.51866	0.682	T	0.73972	-0.3814	10	0.26408	T	0.33	.	7.697	0.28600	0.4564:0.0:0.5435:0.0	.	2542	P46531	NOTC1_HUMAN	R	2542	ENSP00000277541:S2542R	ENSP00000277541:S2542R	S	-	3	2	NOTCH1	138510386	1.000000	0.71417	0.996000	0.52242	0.988000	0.76386	2.051000	0.41307	0.604000	0.29930	0.462000	0.41574	AGC	.	.		0.667	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		C	139390565	G	C	139390565	3	2	249	1	0	0	0	0	1	0	0	0	10556	1310	46	4	45	4	NOTCH1	9	139390565	Missense_Mutation	SNP	G	TCGA-ED-A8O5-01A-11D-A35Z-10	8905079	139390565	1822866	57	33940										
ZNF33A	7581	hgsc.bcm.edu	37	chr10	38344303	38344306	+	Frame_Shift_Del	DEL	GTGT	GTGT	-													0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	aaaccctatcaatgtaatgcGtgtgggaaaactttttgcca					rs138763916	byFrequency	TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	GTGT	GTGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr10:38344303_38344306delGTGT	ENST00000458705.2	+	5	1406_1409	c.1248_1251delGTGT	c.(1246-1251)gcgtgtfs	p.AC416fs	ZNF33A_ENST00000432900.2_Frame_Shift_Del_p.AC423fs|ZNF33A_ENST00000374618.3_Frame_Shift_Del_p.AC417fs|ZNF33A_ENST00000307441.9_Frame_Shift_Del_p.AC416fs|ZNF33A_ENST00000469037.2_Intron			Q06730	ZN33A_HUMAN	zinc finger protein 33A	416					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(2)|large_intestine(8)|liver(2)|lung(27)|ovary(2)|prostate(1)|skin(2)	46						AATGTAATGCGTGTGGGAAAACTT	0.426																																					p.417_418del		Atlas-INDEL	.											.	ZNF33A	103	.	0			c.1250_1253del						.																																			SO:0001589	frameshift_variant	7581	exon5			.	D31763	CCDS31182.1, CCDS60514.1, CCDS73088.1, CCDS73089.1	10p11.2	2013-01-08	2005-03-18		ENSG00000189180	ENSG00000189180		"Zinc fingers, C2H2-type", "-"	13096	protein-coding gene	gene with protein product	"zinc finger and ZAK associated protein with KRAB domain"	194521	"zinc finger protein 33a (KOX 31)", "zinc finger protein 11A"	ZNF33, ZNF11A		2014798, 8464732	Standard	NM_006974		Approved	KOX5, KOX31, KIAA0065, FLJ23404, ZZAPK	uc031pui.1	Q06730	OTTHUMG00000017983	ENST00000458705.2:c.1248_1251delGTGT	chr10.hg19:g.38344303_38344306delGTGT	ENSP00000387713:p.Ala416fs	108.0	0.0		105.0	45.0	NM_006954	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Frame_Shift_Del	DEL	ENST00000458705.2	hg19	CCDS31182.1																																																																																			.	.		0.426	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974		-	38344306	GTGT	-	38344303	7	5	249	1	0	1	0	1	0	0	0	0	17869	1132	40	0	1265	0	ZNF33A	10	38344303	Frame_Shift_Del	DEL	GTGT	TCGA-ED-A8O5-01A-11D-A35Z-10		38344303	97190444	58	33941										
OR51E2	81285	hgsc.bcm.edu	37	chr11	4703440	4703440	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	cgagaggacattggagtggcAgaaggccagccgcttgatca	15	9	1	3			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr11:4703440A>C	ENST00000396950.3	-	2	741	c.502T>G	c.(502-504)Tgc>Ggc	p.C168G		NM_030774.3	NP_110401.1	Q9H255	O51E2_HUMAN	olfactory receptor, family 51, subfamily E, member 2	168					cellular response to fatty acid (GO:0071398)|detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|positive regulation of blood pressure (GO:0045777)|positive regulation of renin secretion into blood stream (GO:1900135)|steroid hormone mediated signaling pathway (GO:0043401)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)|signaling receptor activity (GO:0038023)|steroid hormone receptor activity (GO:0003707)			NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(3)	23		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;3e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00476)|LUSC - Lung squamous cell carcinoma(625;0.2)		TTGGAGTGGCAGAAGGCCAGC	0.517																																					p.C168G		Atlas-SNP	.											.	OR51E2	77	.	0			c.T502G						.						82	80	80					11																	4703440		2201	4298	6499	SO:0001583	missense	81285	exon2			AGTGGCAGAAGGC	AY033942	CCDS7751.1	11p15	2012-08-09			ENSG00000167332	ENSG00000167332		"GPCR / Class A : Olfactory receptors"	15195	protein-coding gene	gene with protein product		611268				11118034	Standard	NM_030774		Approved	PSGR	uc001lzk.2	Q9H255	OTTHUMG00000133362	ENST00000396950.3:c.502T>G	chr11.hg19:g.4703440A>C	ENSP00000380153:p.Cys168Gly	94.0	0.0		90.0	39.0	NM_030774	B2RA63|Q6IF94	Missense_Mutation	SNP	ENST00000396950.3	hg19	CCDS7751.1	.	.	.	.	.	.	.	.	.	.	A	16.21	3.059137	0.55325	.	.	ENSG00000167332	ENST00000396950	T	0.00224	8.51	5.0	5.0	0.66597	GPCR, rhodopsin-like superfamily (1);	0.000000	0.50627	D	0.000107	T	0.00906	0.0030	H	0.96175	3.78	0.38000	D	0.934181	D	0.89917	1.0	D	0.97110	1.0	T	0.46693	-0.9173	10	0.87932	D	0	.	13.681	0.62484	1.0:0.0:0.0:0.0	.	168	Q9H255	O51E2_HUMAN	G	168	ENSP00000380153:C168G	ENSP00000380153:C168G	C	-	1	0	OR51E2	4660016	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.834000	0.75339	2.112000	0.64535	0.533000	0.62120	TGC	.	.		0.517	OR51E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257198.1	NM_030774		C	4703440	A	C	4703440	3	2	249	1	0	0	0	0	1	0	0	0	11104	188	7	5	464	5	OR51E2	11	4703440	Missense_Mutation	SNP	A	TCGA-ED-A8O5-01A-11D-A35Z-10		4703440	130303076	59	33942										
E2F8	79733	hgsc.bcm.edu	37	chr11	19256370	19256370	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	ccagtgtttgatttgatgatAtgatcctctatactgtaact	7	7	1	4			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr11:19256370A>T	ENST00000527884.1	-	5	919	c.687T>A	c.(685-687)caT>caA	p.H229Q	RP11-428C19.4_ENST00000527978.1_RNA|E2F8_ENST00000250024.4_Missense_Mutation_p.H229Q	NM_001256371.1|NM_001256372.1	NP_001243300.1|NP_001243301.1	A0AVK6	E2F8_HUMAN	E2F transcription factor 8	229					cell cycle comprising mitosis without cytokinesis (GO:0033301)|chorionic trophoblast cell differentiation (GO:0060718)|hepatocyte differentiation (GO:0070365)|negative regulation of cytokinesis (GO:0032466)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						ATTTGATGATATGATCCTCTA	0.418																																					p.H229Q		Atlas-SNP	.											.	E2F8	84	.	0			c.T687A						.						109	98	102					11																	19256370		2199	4293	6492	SO:0001583	missense	79733	exon5			GATGATATGATCC		CCDS7849.1	11p15	2008-02-05			ENSG00000129173	ENSG00000129173			24727	protein-coding gene	gene with protein product		612047				15722552	Standard	NM_024680		Approved	FLJ23311	uc001mpo.2	A0AVK6	OTTHUMG00000166102	ENST00000527884.1:c.687T>A	chr11.hg19:g.19256370A>T	ENSP00000434199:p.His229Gln	130.0	0.0		111.0	39.0	NM_001256372	A8K9H3|Q2VPJ3|Q3C1U6|Q5BKY4|Q8N340|Q9H5M0	Missense_Mutation	SNP	ENST00000527884.1	hg19	CCDS7849.1	.	.	.	.	.	.	.	.	.	.	A	7.449	0.642210	0.14451	.	.	ENSG00000129173	ENST00000527884;ENST00000531809;ENST00000396159;ENST00000250024	T;T	0.17054	2.3;2.3	5.52	-4.44	0.03557	.	0.696518	0.14005	N	0.347869	T	0.08447	0.0210	L	0.36672	1.1	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.39375	-0.9617	10	0.12766	T	0.61	-7.3611	3.8628	0.09004	0.2694:0.2235:0.4079:0.0992	.	229	A0AVK6	E2F8_HUMAN	Q	229	ENSP00000434199:H229Q;ENSP00000250024:H229Q	ENSP00000250024:H229Q	H	-	3	2	E2F8	19212946	0.003000	0.15002	0.808000	0.32385	0.996000	0.88848	-0.997000	0.03705	-0.807000	0.04393	0.533000	0.62120	CAT	.	.		0.418	E2F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387830.1	NM_024680		T	19256370	A	T	19256370	3	4	249	1	0	0	0	0	1	0	0	0	4875	446	16	4	1952	4	E2F8	11	19256370	Missense_Mutation	SNP	A	TCGA-ED-A8O5-01A-11D-A35Z-10	14552930	19256370	115750146	60	33943										
HRASLS2	54979	hgsc.bcm.edu	37	chr11	63325963	63325963	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	tcctgccccaccaactcctcTgcccgcttgacgattttgtt	6	17	1	1			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr11:63325963T>G	ENST00000255695.1	-	3	346	c.288A>C	c.(286-288)gcA>gcC	p.A96A		NM_017878.1	NP_060348.1	Q9NWW9	HRSL2_HUMAN	HRAS-like suppressor 2	96					lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)|transferase activity, transferring acyl groups (GO:0016746)			breast(1)|endometrium(1)|large_intestine(1)|lung(2)|prostate(1)	6						CCAACTCCTCTGCCCGCTTGA	0.552																																					p.A96A		Atlas-SNP	.											.	HRASLS2	14	.	0			c.A288C						.						263	191	216					11																	63325963		2201	4298	6499	SO:0001819	synonymous_variant	54979	exon3			CTCCTCTGCCCGC		CCDS8046.1	11q12.2	2008-07-18			ENSG00000133328	ENSG00000133328			17824	protein-coding gene	gene with protein product		613866					Standard	NM_017878		Approved	FLJ20556	uc001nxg.1	Q9NWW9	OTTHUMG00000167851	ENST00000255695.1:c.288A>C	chr11.hg19:g.63325963T>G		138.0	0.0		124.0	68.0	NM_017878	B9A7L8	Silent	SNP	ENST00000255695.1	hg19	CCDS8046.1																																																																																			.	.		0.552	HRASLS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396631.1	NM_017878		G	63325963	T	G	63325963	2	3	249	1	0	0	0	0	0	0	0	1	7359	1567	55	5		5	HRASLS2	11	63325963	Silent	SNP	T	TCGA-ED-A8O5-01A-11D-A35Z-10	44069593	63325963	71680553	61	33944										
FGF3	2248	hgsc.bcm.edu	37	chr11	69625279	69625279	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	gaacagggaggacttctgtgTgcggcgggtcttgaagcccc	16	10	2	1			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr11:69625279T>C	ENST00000334134.2	-	3	604	c.514A>G	c.(514-516)Aca>Gca	p.T172A		NM_005247.2	NP_005238.1	P11487	FGF3_HUMAN	fibroblast growth factor 3	172					anatomical structure morphogenesis (GO:0009653)|cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of cardiac muscle tissue development (GO:0055026)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|otic vesicle formation (GO:0030916)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|post-anal tail morphogenesis (GO:0036342)|semicircular canal morphogenesis (GO:0048752)|signal transduction (GO:0007165)|thymus development (GO:0048538)	extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)	growth factor activity (GO:0008083)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|urinary_tract(1)	13			LUSC - Lung squamous cell carcinoma(11;5.05e-15)|STAD - Stomach adenocarcinoma(18;0.0278)			GACTTCTGTGTGCGGCGGGTC	0.687																																					p.T172A		Atlas-SNP	.											.	FGF3	27	.	0			c.A514G						.						21	24	23					11																	69625279		2194	4266	6460	SO:0001583	missense	2248	exon3			TCTGTGTGCGGCG		CCDS8195.1	11q13	2010-06-25	2010-06-25		ENSG00000186895	ENSG00000186895			3681	protein-coding gene	gene with protein product	"INT-2 proto-oncogene protein", "oncogene INT2", "V-INT2 murine mammary tumor virus integration site oncogene homolog", "murine mammary tumor virus integration site 2, mouse"	164950	"fibroblast growth factor 3 (murine mammary tumor virus integration site (v-int-2) oncogene homolog)"	INT2			Standard	NM_005247		Approved	HBGF-3	uc001oph.3	P11487	OTTHUMG00000167888	ENST00000334134.2:c.514A>G	chr11.hg19:g.69625279T>C	ENSP00000334122:p.Thr172Ala	188.0	0.0		197.0	88.0	NM_005247	Q0VG69	Missense_Mutation	SNP	ENST00000334134.2	hg19	CCDS8195.1	.	.	.	.	.	.	.	.	.	.	T	18.26	3.584636	0.65992	.	.	ENSG00000186895	ENST00000334134	T	0.66995	-0.24	4.01	4.01	0.46588	.	0.051289	0.85682	D	0.000000	T	0.74749	0.3757	L	0.46157	1.445	0.54753	D	0.999989	D	0.76494	0.999	D	0.85130	0.997	T	0.73742	-0.3887	9	.	.	.	.	12.9501	0.58394	0.0:0.0:0.0:1.0	.	172	P11487	FGF3_HUMAN	A	172	ENSP00000334122:T172A	.	T	-	1	0	FGF3	69334460	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	5.594000	0.67557	1.440000	0.47531	0.379000	0.24179	ACA	.	.		0.687	FGF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396835.1	NM_005247		C	69625279	T	C	69625279	3	2	249	1	0	0	0	0	1	0	0	0	5861	1696	59	2	209	2	FGF3	11	69625279	Missense_Mutation	SNP	T	TCGA-ED-A8O5-01A-11D-A35Z-10	6299316	69625279	65381237	62	33945										
LRRC32	2615	hgsc.bcm.edu	37	chr11	76376969	76376969	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	gccaggcctagggtcagcagGgccaggagcagcaggatctg	17	11	2	0	rs533407564		TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr11:76376969G>A	ENST00000407242.2	-	2	272	c.30C>T	c.(28-30)gcC>gcT	p.A10A	LRRC32_ENST00000404995.1_Silent_p.A10A|AP001189.4_ENST00000447519.1_RNA|LRRC32_ENST00000260061.5_Silent_p.A10A|LRRC32_ENST00000464145.1_5'UTR	NM_005512.2	NP_005503.1	Q14392	LRC32_HUMAN	leucine rich repeat containing 32	10					negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of cytokine secretion (GO:0050710)|positive regulation of gene expression (GO:0010628)	integral component of plasma membrane (GO:0005887)				endometrium(1)|large_intestine(3)|lung(26)|upper_aerodigestive_tract(1)	31						GGGTCAGCAGGGCCAGGAGCA	0.607													G|||	1	0.000199681	8e-04	0	5008	,	,		18819	0		0	False		,,,				2504	0				p.A10A		Atlas-SNP	.											.	LRRC32	74	.	0			c.C30T						.						168	146	153					11																	76376969		2200	4292	6492	SO:0001819	synonymous_variant	2615	exon2			CAGCAGGGCCAGG	Z24680	CCDS8245.1	11q13.5-q14	2008-02-05	2005-02-25	2005-02-25	ENSG00000137507	ENSG00000137507			4161	protein-coding gene	gene with protein product		137207	"glycoprotein A repetitions predominant"	D11S833E, GARP		8180135, 1543912	Standard	NM_005512		Approved		uc001oxq.4	Q14392	OTTHUMG00000133687	ENST00000407242.2:c.30C>T	chr11.hg19:g.76376969G>A		64.0	0.0		60.0	15.0	NM_005512	Q86V06	Silent	SNP	ENST00000407242.2	hg19	CCDS8245.1																																																																																			.	.		0.607	LRRC32-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257926.2	NM_005512		A	76376969	G	A	76376969	2	1	249	1	0	0	0	0	0	0	0	1	8996	1219	43	3		3	LRRC32	11	76376969	Silent	SNP	G	TCGA-ED-A8O5-01A-11D-A35Z-10	6751690	76376969	58629547	63	33946										
ODZ4	26011	hgsc.bcm.edu	37	chr11	78419516	78419516	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	atcgatgcgtctgatcatggTgccatccacgaagtagatca	10	10	3	2			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr11:78419516T>C	ENST00000278550.7	-	27	4561	c.4099A>G	c.(4099-4101)Acc>Gcc	p.T1367A		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	1367					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										CTGATCATGGTGCCATCCACG	0.522																																					p.T1367A		Atlas-SNP	.											.	.	.	.	0			c.A4099G						.						108	102	104					11																	78419516		2068	4215	6283	SO:0001583	missense	26011	exon27			TCATGGTGCCATC	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"odz, odd Oz/ten-m homolog 4 (Drosophila)"	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.4099A>G	chr11.hg19:g.78419516T>C	ENSP00000278550:p.Thr1367Ala	107.0	0.0		89.0	40.0	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Missense_Mutation	SNP	ENST00000278550.7	hg19	CCDS44688.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.140591	0.77775	.	.	ENSG00000149256	ENST00000278550	D	0.89939	-2.59	5.52	4.4	0.53042	Six-bladed beta-propeller, TolB-like (1);	0.050063	0.85682	N	0.000000	D	0.92034	0.7476	L	0.59436	1.845	0.58432	D	0.999991	D	0.64830	0.994	D	0.70716	0.97	D	0.90929	0.4789	9	.	.	.	.	11.6913	0.51516	0.0:0.0687:0.0:0.9313	.	1367	Q6N022	TEN4_HUMAN	A	1367	ENSP00000278550:T1367A	.	T	-	1	0	ODZ4	78097164	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.884000	0.63135	1.110000	0.41699	-0.274000	0.10170	ACC	.	.		0.522	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			C	78419516	T	C	78419516	3	2	249	1	0	0	0	0	1	0	0	0	10846	1696	59	2	4242	2	ODZ4	11	78419516	Missense_Mutation	SNP	T	TCGA-ED-A8O5-01A-11D-A35Z-10	2042547	78419516	56587000	64	33947										
C11orf82	220042	hgsc.bcm.edu	37	chr11	82643852	82643852	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	aatagtcaaagcaaactgtaGcaaagatgacttccttttca	6	8	2	2			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr11:82643852G>A	ENST00000533655.1	+	6	1684	c.1472G>A	c.(1471-1473)aGc>aAc	p.S491N	C11orf82_ENST00000528759.1_3'UTR|C11orf82_ENST00000525361.1_Intron|C11orf82_ENST00000430323.2_Missense_Mutation_p.S491N|C11orf82_ENST00000329143.3_Missense_Mutation_p.S190N	NM_145018.3	NP_659455.3	Q8IXT1	DDIAS_HUMAN		491					apoptotic process (GO:0006915)|cellular response to cytokine stimulus (GO:0071345)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to hydroperoxide (GO:0071447)|cellular response to UV (GO:0034644)|hemopoiesis (GO:0030097)|mitotic cell cycle arrest (GO:0071850)|negative regulation of fibroblast apoptotic process (GO:2000270)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(17)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	33						GCAAACTGTAGCAAAGATGAC	0.408																																					p.S491N		Atlas-SNP	.											.	C11orf82	71	.	0			c.G1472A						.						43	42	42					11																	82643852		2203	4300	6503	SO:0001583	missense	220042	exon6			ACTGTAGCAAAGA																												ENST00000533655.1:c.1472G>A	chr11.hg19:g.82643852G>A	ENSP00000435421:p.Ser491Asn	61.0	0.0		58.0	27.0	NM_145018	Q96LK6|Q9H856	Missense_Mutation	SNP	ENST00000533655.1	hg19	CCDS8263.1	.	.	.	.	.	.	.	.	.	.	G	1.717	-0.497592	0.04291	.	.	ENSG00000165490	ENST00000430323;ENST00000533655;ENST00000329143	T;T;T	0.18810	2.46;2.46;2.19	6.17	3.26	0.37387	.	0.808315	0.11926	N	0.516199	T	0.19127	0.0459	L	0.51422	1.61	0.09310	N	1	B	0.32245	0.361	B	0.33042	0.157	T	0.21621	-1.0240	9	.	.	.	.	6.5349	0.22348	0.1583:0.1484:0.6933:0.0	.	491	Q8IXT1	NOXIN_HUMAN	N	491;491;190	ENSP00000414687:S491N;ENSP00000435421:S491N;ENSP00000329930:S190N	.	S	+	2	0	C11orf82	82321500	0.926000	0.31397	0.005000	0.12908	0.012000	0.07955	1.074000	0.30703	0.458000	0.26988	0.655000	0.94253	AGC	.	.		0.408	C11orf82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391936.1			A	82643852	G	A	82643852	3	1	249	1	0	0	0	0	1	0	0	0	1667	971	34	3	1486	3	C11orf82	11	82643852	Missense_Mutation	SNP	G	TCGA-ED-A8O5-01A-11D-A35Z-10	4224336	82643852	52362664	65	33948										
FAT3	120114	hgsc.bcm.edu	37	chr11	92577113	92577113	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	gttttaggcaaaggattcagGcaaaccccagcaagtttctc	9	10	2	0			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr11:92577113G>A	ENST00000298047.6	+	18	10597	c.10580G>A	c.(10579-10581)gGc>gAc	p.G3527D	FAT3_ENST00000525166.1_Missense_Mutation_p.G3377D|FAT3_ENST00000409404.2_Missense_Mutation_p.G3527D|FAT3_ENST00000533797.1_5'Flank			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	3527	Cadherin 32. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				AAGGATTCAGGCAAACCCCAG	0.443										TCGA Ovarian(4;0.039)																											p.G3527D		Atlas-SNP	.											.	FAT3	1822	.	0			c.G10580A						.						161	156	158					11																	92577113		1907	4134	6041	SO:0001583	missense	120114	exon18			ATTCAGGCAAACC	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.10580G>A	chr11.hg19:g.92577113G>A	ENSP00000298047:p.Gly3527Asp	123.0	0.0		108.0	54.0	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	hg19		.	.	.	.	.	.	.	.	.	.	G	24.4	4.528660	0.85706	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.08546	3.08;3.08;3.08	5.62	5.62	0.85841	.	.	.	.	.	T	0.41581	0.1165	M	0.92122	3.275	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.52764	-0.8532	9	0.87932	D	0	.	19.6523	0.95822	0.0:0.0:1.0:0.0	.	3527	Q8TDW7-3	.	D	3527;3527;3377	ENSP00000298047:G3527D;ENSP00000387040:G3527D;ENSP00000432586:G3377D	ENSP00000298047:G3527D	G	+	2	0	FAT3	92216761	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	9.787000	0.99055	2.650000	0.89964	0.561000	0.74099	GGC	.	.		0.443	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		A	92577113	G	A	92577113	3	1	249	1	0	0	0	0	1	0	0	0	5699	1203	42	3	10650	3	FAT3	11	92577113	Missense_Mutation	SNP	G	TCGA-ED-A8O5-01A-11D-A35Z-10	9933261	92577113	42429403	66	33949										
C11orf65	160140	hgsc.bcm.edu	37	chr11	108264021	108264021	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	atccccccatcttcaaaagcTctaatcagcccctttgttgc	4	16	4	0			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr11:108264021T>C	ENST00000529391.1	-	6	654	c.645A>G	c.(643-645)agA>agG	p.R215R	C11orf65_ENST00000393084.1_Silent_p.R215R|C11orf65_ENST00000526725.1_5'UTR|C11orf65_ENST00000525729.1_Silent_p.R166R			Q8NCR3	CK065_HUMAN	chromosome 11 open reading frame 65	215										endometrium(1)|large_intestine(3)|lung(4)|ovary(2)	10		all_cancers(61;1.38e-11)|all_epithelial(67;3.16e-07)|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;8.21e-06)|BRCA - Breast invasive adenocarcinoma(274;1.01e-05)|all cancers(92;0.000189)|Colorectal(284;0.114)|OV - Ovarian serous cystadenocarcinoma(223;0.144)		CTTCAAAAGCTCTAATCAGCC	0.423																																					p.R215R		Atlas-SNP	.											.	C11orf65	29	.	0			c.A645G						.						258	227	238					11																	108264021		2201	4298	6499	SO:0001819	synonymous_variant	160140	exon7			AAAAGCTCTAATC	BC059411	CCDS8340.1	11q22.3	2012-05-30			ENSG00000166323	ENSG00000166323			28519	protein-coding gene	gene with protein product						12477932	Standard	NM_152587		Approved	MGC33948	uc001pkh.3	Q8NCR3	OTTHUMG00000166489	ENST00000529391.1:c.645A>G	chr11.hg19:g.108264021T>C		183.0	0.0		161.0	64.0	NM_152587	B4DZU4|Q6PCA8	Silent	SNP	ENST00000529391.1	hg19	CCDS8340.1	.	.	.	.	.	.	.	.	.	.	T	0.150	-1.092298	0.01858	.	.	ENSG00000166323	ENST00000524755	.	.	.	5.54	4.42	0.53409	.	.	.	.	.	T	0.34483	0.0899	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.21965	-1.0230	4	.	.	.	-5.2084	6.4841	0.22079	0.0:0.0847:0.1575:0.7578	.	.	.	.	G	47	.	.	E	-	2	0	C11orf65	107769231	0.000000	0.05858	0.001000	0.08648	0.100000	0.18952	0.610000	0.24253	0.952000	0.37798	0.460000	0.39030	GAG	.	.		0.423	C11orf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390010.3	NM_152587		C	108264021	T	C	108264021	2	2	249	1	0	0	0	0	0	0	0	1	1657	1548	54	2		2	C11orf65	11	108264021	Silent	SNP	T	TCGA-ED-A8O5-01A-11D-A35Z-10	15686908	108264021	26742495	67	33950										
KCNA5	3741	hgsc.bcm.edu	37	chr12	5154614	5154614	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	gcaggcctccatgagggagcTggggctgctcatcttcttcc	13	13	3	1			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr12:5154614T>A	ENST00000252321.3	+	1	1530	c.1301T>A	c.(1300-1302)cTg>cAg	p.L434Q		NM_002234.3	NP_002225.2	P22460	KCNA5_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 5	434					atrial cardiac muscle cell action potential (GO:0086014)|membrane hyperpolarization (GO:0060081)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of potassium ion transport (GO:0043267)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of myoblast proliferation (GO:2000288)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transport (GO:0043266)|regulation of vasoconstriction (GO:0019229)|response to hypoxia (GO:0001666)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|intracellular canaliculus (GO:0046691)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|potassium channel inhibitor activity (GO:0019870)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization (GO:0086089)			NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(21)|ovary(5)|prostate(2)|upper_aerodigestive_tract(2)	52					Dalfampridine(DB06637)	ATGAGGGAGCTGGGGCTGCTC	0.592																																					p.L434Q		Atlas-SNP	.											KCNA5,NS,carcinoma,0,1	KCNA5	138	.	0			c.T1301A						.						48	46	47					12																	5154614		2203	4287	6490	SO:0001583	missense	3741	exon1			GGGAGCTGGGGCT	M83254	CCDS8536.1	12p13	2012-07-05				ENSG00000130037		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6224	protein-coding gene	gene with protein product		176267				16382104	Standard	NM_002234		Approved	Kv1.5, HK2, HPCN1	uc001qni.4	P22460		ENST00000252321.3:c.1301T>A	chr12.hg19:g.5154614T>A	ENSP00000252321:p.Leu434Gln	119.0	0.0		111.0	35.0	NM_002234	Q4KKT8|Q4VAJ1|Q4VAJ2|Q9UDA4	Missense_Mutation	SNP	ENST00000252321.3	hg19	CCDS8536.1	.	.	.	.	.	.	.	.	.	.	T	18.11	3.550909	0.65311	.	.	ENSG00000130037	ENST00000252321	D	0.98822	-5.16	4.87	4.87	0.63330	Ion transport (1);	0.000000	0.64402	D	0.000016	D	0.99462	0.9809	H	0.97806	4.08	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98150	1.0441	10	0.87932	D	0	.	13.8335	0.63395	0.0:0.0:0.0:1.0	.	434	P22460	KCNA5_HUMAN	Q	434	ENSP00000252321:L434Q	ENSP00000252321:L434Q	L	+	2	0	KCNA5	5024875	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.786000	0.85741	2.052000	0.61016	0.459000	0.35465	CTG	.	.		0.592	KCNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398925.2	NM_002234		A	5154614	T	A	5154614	3	1	249	1	0	0	0	0	1	0	0	0	8015	1580	55	4	1303	4	KCNA5	12	5154614	Missense_Mutation	SNP	T	TCGA-ED-A8O5-01A-11D-A35Z-10		5154614	128697281	68	33951										
C12orf12	196477	hgsc.bcm.edu	37	chr12	91347318	91347318	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	tctaacagttaaagtcctgtGccatgaacagggattcctgt	9	9	1	1			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr12:91347318G>A	ENST00000358859.2	-	1	1635	c.1202C>T	c.(1201-1203)gCa>gTa	p.A401V	CCER1_ENST00000548187.1_Intron	NM_152638.2	NP_689851.1	Q8TC90	CCER1_HUMAN	coiled-coil glutamate-rich protein 1	401																	AAAGTCCTGTGCCATGAACAG	0.378																																					p.A401V		Atlas-SNP	.											.	.	.	.	0			c.C1202T						.						77	82	80					12																	91347318		2203	4300	6503	SO:0001583	missense	196477	exon1			TCCTGTGCCATGA	BC024183	CCDS9036.1	12q21.33	2012-05-30	2012-05-30	2012-05-30	ENSG00000197651	ENSG00000197651			28373	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 12"	C12orf12		17967063	Standard	NM_152638		Approved	MGC26598	uc001tbj.3	Q8TC90	OTTHUMG00000170070	ENST00000358859.2:c.1202C>T	chr12.hg19:g.91347318G>A	ENSP00000351727:p.Ala401Val	101.0	0.0		84.0	32.0	NM_152638	Q8TC47	Missense_Mutation	SNP	ENST00000358859.2	hg19	CCDS9036.1	.	.	.	.	.	.	.	.	.	.	G	0.007	-2.001704	0.00431	.	.	ENSG00000197651	ENST00000358859	T	0.21031	2.03	5.17	4.04	0.47022	.	1.784620	0.03889	N	0.278315	T	0.09774	0.0240	N	0.04508	-0.205	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.30880	-0.9963	10	0.02654	T	1	-0.2725	7.0131	0.24873	0.8965:0.0:0.1035:0.0	.	401	Q8TC90	CL012_HUMAN	V	401	ENSP00000351727:A401V	ENSP00000351727:A401V	A	-	2	0	C12orf12	89871449	0.011000	0.17503	0.044000	0.18714	0.064000	0.16182	1.713000	0.37951	1.001000	0.39076	-0.469000	0.05056	GCA	.	.		0.378	CCER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407142.2	NM_152638		A	91347318	G	A	91347318	3	1	249	1	0	0	0	0	1	0	0	0	1678	1319	46	3	22	3	C12orf12	12	91347318	Missense_Mutation	SNP	G	TCGA-ED-A8O5-01A-11D-A35Z-10	86192704	91347318	42504577	69	33952										
BTBD11	121551	hgsc.bcm.edu	37	chr12	108029088	108029088	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	gtgatcagccagcagctgtgCgtcatcttcacacactgcta	9	13	4	1			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr12:108029088C>T	ENST00000280758.5	+	12	3186	c.2658C>T	c.(2656-2658)tgC>tgT	p.C886C	BTBD11_ENST00000357167.4_Silent_p.C423C|BTBD11_ENST00000490090.2_Silent_p.C886C|BTBD11_ENST00000494235.2_5'UTR|BTBD11_ENST00000420571.2_Silent_p.C767C	NM_001018072.1	NP_001018082.1	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11	886						integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(18)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						AGCAGCTGTGCGTCATCTTCA	0.567																																					p.C886C		Atlas-SNP	.											.	BTBD11	122	.	0			c.C2658T						.						152	136	141					12																	108029088		2203	4300	6503	SO:0001819	synonymous_variant	121551	exon12			GCTGTGCGTCATC	AK091276	CCDS31893.1, CCDS41827.1	12q24.11	2013-10-02			ENSG00000151136	ENSG00000151136		"BTB/POZ domain containing", "Ankyrin repeat domain containing"	23844	protein-coding gene	gene with protein product							Standard	XM_005268645		Approved	FLJ33957, ABTB2B	uc001tmk.1	A6QL63	OTTHUMG00000150413	ENST00000280758.5:c.2658C>T	chr12.hg19:g.108029088C>T		70.0	0.0		56.0	25.0	NM_001018072	A4FU41|B3KXG3|C9J019|C9JK80|E9PHS4|Q3ZTQ4|Q52M89|Q6ZV99|Q8N245	Silent	SNP	ENST00000280758.5	hg19	CCDS31893.1																																																																																			.	.		0.567	BTBD11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318003.1	NM_152322		T	108029088	C	T	108029088	2	4	249	1	0	0	0	0	0	0	0	1	1541	776	27	1		1	BTBD11	12	108029088	Silent	SNP	C	TCGA-ED-A8O5-01A-11D-A35Z-10	16681770	108029088	25822807	70	33953										
LRRC43	254050	hgsc.bcm.edu	37	chr12	122677397	122677397	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	aagaggttactgaagaggtcGaagggtctctggagtctgag	16	5	2	4			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr12:122677397G>A	ENST00000339777.4	+	7	1223	c.1195G>A	c.(1195-1197)Gaa>Aaa	p.E399K	LRRC43_ENST00000425921.1_Missense_Mutation_p.E214K	NM_152759.4	NP_689972.3	Q8N309	LRC43_HUMAN	leucine rich repeat containing 43	399	Glu-rich.									NS(1)|endometrium(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(2)	19	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000312)|Epithelial(86;0.000539)|BRCA - Breast invasive adenocarcinoma(302;0.225)		TGAAGAGGTCGAAGGGTCTCT	0.532																																					p.E399K		Atlas-SNP	.											.	LRRC43	105	.	0			c.G1195A						.						97	105	103					12																	122677397		2090	4234	6324	SO:0001583	missense	254050	exon7			GAGGTCGAAGGGT	AK124107	CCDS45001.1	12q24.31	2014-09-11			ENSG00000158113	ENSG00000158113			28562	protein-coding gene	gene with protein product						12477932	Standard	NM_152759		Approved	MGC35140	uc009zxm.3	Q8N309	OTTHUMG00000168915	ENST00000339777.4:c.1195G>A	chr12.hg19:g.122677397G>A	ENSP00000344233:p.Glu399Lys	263.0	0.0		188.0	85.0	NM_001098519	Q6ZVT9	Missense_Mutation	SNP	ENST00000339777.4	hg19	CCDS45001.1	.	.	.	.	.	.	.	.	.	.	G	7.653	0.683229	0.14907	.	.	ENSG00000158113	ENST00000339777;ENST00000289014;ENST00000425921	T;T	0.56444	0.46;0.89	3.73	0.829	0.18847	.	1.397600	0.04333	N	0.352750	T	0.40619	0.1124	L	0.41824	1.3	0.09310	N	1	B	0.23490	0.086	B	0.13407	0.009	T	0.16837	-1.0389	10	0.33940	T	0.23	-7.0232	3.2774	0.06903	0.2239:0.0:0.5718:0.2044	.	399	Q8N309	LRC43_HUMAN	K	399;270;214	ENSP00000344233:E399K;ENSP00000416628:E214K	ENSP00000289014:E270K	E	+	1	0	LRRC43	121243350	0.186000	0.23225	0.000000	0.03702	0.001000	0.01503	2.244000	0.43124	0.171000	0.19730	-0.150000	0.13652	GAA	.	.		0.532	LRRC43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401589.1	NM_152759		A	122677397	G	A	122677397	3	1	249	1	0	0	0	0	1	0	0	0	9010	1059	37	1	1221	1	LRRC43	12	122677397	Missense_Mutation	SNP	G	TCGA-ED-A8O5-01A-11D-A35Z-10	14648309	122677397	11174498	71	33954										
HMGB1	3146	hgsc.bcm.edu	37	chr13	31035627	31035627	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	cagccttgacaactccctttTttgctgcatcaggctttcct	6	14	1	1			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr13:31035627T>G	ENST00000405805.1	-	5	1455	c.515A>C	c.(514-516)aAa>aCa	p.K172T	HMGB1_ENST00000468384.1_5'Flank|HMGB1_ENST00000339872.4_Missense_Mutation_p.K172T|HMGB1_ENST00000399489.1_3'UTR|HMGB1_ENST00000341423.5_Missense_Mutation_p.K172T|HMGB1_ENST00000399494.1_Missense_Mutation_p.K172T			P09429	HMGB1_HUMAN	high mobility group box 1	172					apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|base-excision repair, DNA ligation (GO:0006288)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|dendritic cell chemotaxis (GO:0002407)|DNA ligation involved in DNA repair (GO:0051103)|DNA recombination (GO:0006310)|DNA topological change (GO:0006265)|inflammatory response to antigenic stimulus (GO:0002437)|innate immune response (GO:0045087)|myeloid dendritic cell activation (GO:0001773)|negative regulation of apoptotic cell clearance (GO:2000426)|negative regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0017055)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron projection development (GO:0031175)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|V(D)J recombination (GO:0033151)	cell surface (GO:0009986)|condensed chromosome (GO:0000793)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chemoattractant activity (GO:0042056)|cytokine activity (GO:0005125)|damaged DNA binding (GO:0003684)|DNA binding, bending (GO:0008301)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|RAGE receptor binding (GO:0050786)|repressing transcription factor binding (GO:0070491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription factor binding (GO:0008134)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(1)|ovary(1)	8		Lung SC(185;0.0257)		all cancers(112;0.072)|OV - Ovarian serous cystadenocarcinoma(117;0.177)|Lung(94;0.216)|GBM - Glioblastoma multiforme(144;0.232)		AACTCCCTTTTTTGCTGCATC	0.408																																					p.K172T		Atlas-SNP	.											.	HMGB1	21	.	0			c.A515C						.						28	28	28					13																	31035627		2112	4148	6260	SO:0001583	missense	3146	exon5			CCCTTTTTTGCTG	D63874	CCDS9335.1	13q12	2011-07-01	2011-04-05	2002-08-16	ENSG00000189403	ENSG00000189403		"High-mobility group / Canonical"	4983	protein-coding gene	gene with protein product	"high mobility group box 1", "Sulfoglucuronyl carbohydrate binding protein", "Amphoterin", "high mobility group protein 1"	163905	"high-mobility group (nonhistone chromosomal) protein 1", "high-mobility group box 1"	HMG1		8661151, 11279268	Standard	NM_002128		Approved	HMG3, SBP-1, DKFZp686A04236	uc001usx.3	P09429	OTTHUMG00000016670	ENST00000405805.1:c.515A>C	chr13.hg19:g.31035627T>G	ENSP00000384678:p.Lys172Thr	170.0	0.0		144.0	69.0	NM_002128	A5D8W9|Q14321|Q5T7C3|Q6IBE1	Missense_Mutation	SNP	ENST00000405805.1	hg19	CCDS9335.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.95|13.95	2.388477|2.388477	0.42308|0.42308	.|.	.|.	ENSG00000189403|ENSG00000189403	ENST00000426225|ENST00000405805;ENST00000339872;ENST00000341423;ENST00000399494	.|T;T;T;T	.|0.70631	.|-0.5;-0.5;-0.5;-0.5	5.72|5.72	5.72|5.72	0.89469|0.89469	.|.	0.211018|0.211018	0.32503|0.32503	N|N	0.006019|0.006019	T|T	0.66257|0.66257	0.2771|0.2771	L|L	0.55990|0.55990	1.75|1.75	0.80722|0.80722	D|D	1|1	.|B;B	.|0.30914	.|0.3;0.131	.|B;B	.|0.23275	.|0.045;0.026	T|T	0.67658|0.67658	-0.5614|-0.5614	7|10	0.27785|0.66056	T|D	0.31|0.02	.|.	15.9816|15.9816	0.80114|0.80114	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|133;172	.|B3KQ05;P09429	.|.;HMGB1_HUMAN	Q|T	161|172	.|ENSP00000384678:K172T;ENSP00000343040:K172T;ENSP00000345347:K172T;ENSP00000382417:K172T	ENSP00000411269:K161Q|ENSP00000343040:K172T	K|K	-|-	1|2	0|0	HMGB1|HMGB1	29933627|29933627	1.000000|1.000000	0.71417|0.71417	0.992000|0.992000	0.48379|0.48379	0.923000|0.923000	0.55619|0.55619	5.907000|5.907000	0.69908|0.69908	2.180000|2.180000	0.69256|0.69256	0.519000|0.519000	0.50382|0.50382	AAA|AAA	.	.		0.408	HMGB1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303998.2	NM_002128		G	31035627	T	G	31035627	3	3	249	1	0	0	0	0	1	0	0	0	7234	1841	64	5	136	5	HMGB1	13	31035627	Missense_Mutation	SNP	T	TCGA-ED-A8O5-01A-11D-A35Z-10		31035627	84134251	72	33955										
MAB21L1	4081	hgsc.bcm.edu	37	chr13	36049542	36049542	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	agaggcacttctttctgcagCcccccatctgcagtctgttc	8	15	4	1	rs574005569		TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr13:36049542C>T	ENST00000379919.4	-	1	1290	c.734G>A	c.(733-735)gGc>gAc	p.G245D	NBEA_ENST00000310336.4_Intron|NBEA_ENST00000537702.1_5'Flank|NBEA_ENST00000540320.1_Intron|NBEA_ENST00000400445.3_Intron|NBEA_ENST00000379939.2_Intron	NM_005584.4	NP_005575.1	Q13394	MB211_HUMAN	mab-21-like 1 (C. elegans)	245					anatomical structure morphogenesis (GO:0009653)|camera-type eye development (GO:0043010)|positive regulation of cell proliferation (GO:0008284)	nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	20		Breast(139;0.014)|Lung SC(185;0.051)|Prostate(109;0.202)		all cancers(112;9.63e-08)|Epithelial(112;1.37e-06)|BRCA - Breast invasive adenocarcinoma(63;0.000659)|OV - Ovarian serous cystadenocarcinoma(117;0.00372)|GBM - Glioblastoma multiforme(144;0.115)		CTTTCTGCAGCCCCCCATCTG	0.577													C|||	1	0.000199681	0	0	5008	,	,		17315	0		0	False		,,,				2504	0.001				p.G245D		Atlas-SNP	.											.	MAB21L1	52	.	0			c.G734A						.						70	76	74					13																	36049542		2203	4300	6503	SO:0001583	missense	4081	exon1			CTGCAGCCCCCCA	BC028170	CCDS9353.1	13q13.3	2008-02-05	2001-11-28		ENSG00000180660	ENSG00000180660			6757	protein-coding gene	gene with protein product		601280	"mab-21 (C. elegans)-like 1"			8733127	Standard	NM_005584		Approved	CAGR1		Q13394	OTTHUMG00000016723	ENST00000379919.4:c.734G>A	chr13.hg19:g.36049542C>T	ENSP00000369251:p.Gly245Asp	70.0	0.0		61.0	29.0	NM_005584	Q6I9T5	Missense_Mutation	SNP	ENST00000379919.4	hg19	CCDS9353.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.220493	0.79464	.	.	ENSG00000180660	ENST00000379919	T	0.09255	3.0	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.38453	0.1041	M	0.82323	2.585	0.80722	D	1	D	0.67145	0.996	D	0.74674	0.984	T	0.04840	-1.0923	10	0.37606	T	0.19	-21.6831	19.9576	0.97228	0.0:1.0:0.0:0.0	.	245	Q13394	MB211_HUMAN	D	245	ENSP00000369251:G245D	ENSP00000369251:G245D	G	-	2	0	MAB21L1	34947542	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.818000	0.86416	2.736000	0.93811	0.655000	0.94253	GGC	.	.		0.577	MAB21L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044459.3	NM_005584		T	36049542	C	T	36049542	3	4	249	1	0	0	0	0	1	0	0	0	9150	739	26	3	349	3	MAB21L1	13	36049542	Missense_Mutation	SNP	C	TCGA-ED-A8O5-01A-11D-A35Z-10	5013915	36049542	79120336	73	33956										
PRKD1	5587	hgsc.bcm.edu	37	chr14	30047494	30047494	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	tgtttacctgtagccaagggTggctcaaggtcttatccaca	10	10	2	0			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr14:30047494T>A	ENST00000331968.5	-	17	2736	c.2507A>T	c.(2506-2508)cAc>cTc	p.H836L	PRKD1_ENST00000415220.2_Missense_Mutation_p.H844L	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	836	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to oxidative stress (GO:0034599)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|negative regulation of cell death (GO:0060548)|negative regulation of endocytosis (GO:0045806)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein autophosphorylation (GO:0046777)|regulation of integrin-mediated signaling pathway (GO:2001044)|regulation of keratinocyte proliferation (GO:0010837)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|lung(32)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	78	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		TAGCCAAGGGTGGCTCAAGGT	0.313																																					p.H836L		Atlas-SNP	.											.	PRKD1	316	.	0			c.A2507T						.						86	86	86					14																	30047494		2203	4300	6503	SO:0001583	missense	5587	exon17			CAAGGGTGGCTCA		CCDS9637.1	14q11	2013-01-10	2004-10-28	2004-10-30	ENSG00000184304	ENSG00000184304	2.7.11.1	"Pleckstrin homology (PH) domain containing"	9407	protein-coding gene	gene with protein product		605435	"protein kinase C, mu"	PRKCM		8119958, 10965134	Standard	NM_002742		Approved	PKCM, PKD, PKC-mu	uc001wqh.3	Q15139	OTTHUMG00000140203	ENST00000331968.5:c.2507A>T	chr14.hg19:g.30047494T>A	ENSP00000333568:p.His836Leu	65.0	0.0		54.0	20.0	NM_002742	A6NL64|B2RAF6	Missense_Mutation	SNP	ENST00000331968.5	hg19	CCDS9637.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.765927	0.90020	.	.	ENSG00000184304	ENST00000331968;ENST00000415220	D;D	0.86366	-2.11;-2.11	5.7	5.7	0.88788	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.95033	0.8392	M	0.92459	3.31	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.96085	0.9057	10	0.87932	D	0	-26.9263	15.9589	0.79910	0.0:0.0:0.0:1.0	.	836	Q15139	KPCD1_HUMAN	L	836;844	ENSP00000333568:H836L;ENSP00000390535:H844L	ENSP00000333568:H836L	H	-	2	0	PRKD1	29117245	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.040000	0.89188	2.178000	0.69098	0.477000	0.44152	CAC	.	.		0.313	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2	NM_002742		A	30047494	T	A	30047494	3	1	249	1	0	0	0	0	1	0	0	0	12530	1696	59	4	239	4	PRKD1	14	30047494	Missense_Mutation	SNP	T	TCGA-ED-A8O5-01A-11D-A35Z-10		30047494	77302046	74	33957										
CDC42BPB	9578	hgsc.bcm.edu	37	chr14	103410434	103410434	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	ggtttagaggctgcccgtccCcctggatgctcagcaggcag	14	13	1	1			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr14:103410434C>T	ENST00000361246.2	-	30	4490	c.4202G>A	c.(4201-4203)gGg>gAg	p.G1401E		NM_006035.3	NP_006026.3			CDC42 binding protein kinase beta (DMPK-like)											NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(11)|liver(1)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1)	49		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)		CTGCCCGTCCCCCTGGATGCT	0.587																																					p.G1401E		Atlas-SNP	.											.	CDC42BPB	123	.	0			c.G4202A						.						93	89	90					14																	103410434		2203	4300	6503	SO:0001583	missense	9578	exon30			CCGTCCCCCTGGA	AF128625	CCDS9978.1	14q32.32	2010-05-12	2001-11-28		ENSG00000198752	ENSG00000198752			1738	protein-coding gene	gene with protein product		614062	"CDC42-binding protein kinase beta (DMPK-like)"			10198171	Standard	NM_006035		Approved	MRCKB, KIAA1124	uc001ymi.1	Q9Y5S2		ENST00000361246.2:c.4202G>A	chr14.hg19:g.103410434C>T	ENSP00000355237:p.Gly1401Glu	104.0	0.0		81.0	35.0	NM_006035		Missense_Mutation	SNP	ENST00000361246.2	hg19	CCDS9978.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.916676	0.92249	.	.	ENSG00000198752	ENST00000361246;ENST00000541396	T	0.65178	-0.14	5.46	5.46	0.80206	Citron-like (3);	0.000000	0.85682	D	0.000000	D	0.82453	0.5040	M	0.84683	2.71	0.80722	D	1	D;D	0.89917	1.0;0.992	D;D	0.83275	0.996;0.972	D	0.84676	0.0714	10	0.87932	D	0	.	19.6739	0.95923	0.0:1.0:0.0:0.0	.	1401;1401	A9JR72;Q9Y5S2	.;MRCKB_HUMAN	E	1401;512	ENSP00000355237:G1401E	ENSP00000355237:G1401E	G	-	2	0	CDC42BPB	102480187	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	7.776000	0.85560	2.728000	0.93425	0.655000	0.94253	GGG	.	.		0.587	CDC42BPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415711.1	NM_006035		T	103410434	C	T	103410434	3	4	249	1	0	0	0	0	1	0	0	0	3075	623	22	3	965	3	CDC42BPB	14	103410434	Missense_Mutation	SNP	C	TCGA-ED-A8O5-01A-11D-A35Z-10	73362940	103410434	3939106	75	33958										
MGA	23269	hgsc.bcm.edu	37	chr15	42034793	42034793	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	acacagtttgtgatgagtaaAgttggagccttgcagcagaa	12	6	0	3			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr15:42034793A>G	ENST00000570161.1	+	14	4635	c.4635A>G	c.(4633-4635)aaA>aaG	p.K1545K	MGA_ENST00000219905.7_Silent_p.K1545K|MGA_ENST00000545763.1_Intron|MGA_ENST00000389936.4_Silent_p.K1545K|MGA_ENST00000566586.1_Intron			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	Glucoamylase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TGATGAGTAAAGTTGGAGCCT	0.473																																					p.K1545K		Atlas-SNP	.											.	MGA	264	.	0			c.A4635G						.						66	66	66					15																	42034793		1956	4159	6115	SO:0001819	synonymous_variant	23269	exon15			GAGTAAAGTTGGA	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.4635A>G	chr15.hg19:g.42034793A>G		79.0	0.0		73.0	41.0	NM_001164273	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000570161.1	hg19	CCDS55959.1																																																																																			.	.		0.473	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		G	42034793	A	G	42034793	2	3	249	1	0	0	0	0	0	0	0	1	9549	69	3	2		2	MGA	15	42034793	Silent	SNP	A	TCGA-ED-A8O5-01A-11D-A35Z-10		42034793	60496599	76	33959										
MAP1A	4130	hgsc.bcm.edu	37	chr15	43821446	43821446	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	cagctcagagtctgggagagTagagaggctacgggagaagg	18	6	2	4			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr15:43821446T>A	ENST00000300231.5	+	4	8225	c.7775T>A	c.(7774-7776)gTa>gAa	p.V2592E	MAP1A_ENST00000399453.1_Missense_Mutation_p.V2592E|MAP1A_ENST00000382031.1_Missense_Mutation_p.V2830E			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	2592					microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	TCTGGGAGAGTAGAGAGGCTA	0.672																																					p.V2592E		Atlas-SNP	.											.	MAP1A	189	.	0			c.T7775A						.						34	39	38					15																	43821446		1892	4098	5990	SO:0001583	missense	4130	exon4			GGAGAGTAGAGAG	U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.7775T>A	chr15.hg19:g.43821446T>A	ENSP00000300231:p.Val2592Glu	126.0	0.0		102.0	48.0	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	ENST00000300231.5	hg19	CCDS42031.1	.	.	.	.	.	.	.	.	.	.	T	11.33	1.606111	0.28623	.	.	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231	T;T;T	0.01359	4.98;4.98;4.98	4.95	1.35	0.21983	.	.	.	.	.	T	0.00815	0.0027	N	0.08118	0	0.29001	N	0.887487	B	0.33238	0.403	B	0.33196	0.159	T	0.46048	-0.9219	9	0.20046	T	0.44	-5.8035	3.981	0.09495	0.0:0.4114:0.2171:0.3714	.	2592	P78559	MAP1A_HUMAN	E	2830;2592;2592	ENSP00000371462:V2830E;ENSP00000382380:V2592E;ENSP00000300231:V2592E	ENSP00000300231:V2592E	V	+	2	0	MAP1A	41608738	0.036000	0.19791	0.998000	0.56505	0.979000	0.70002	0.425000	0.21346	0.381000	0.24851	0.379000	0.24179	GTA	.	.		0.672	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373		A	43821446	T	A	43821446	3	1	249	1	0	0	0	0	1	0	0	0	9236	1638	57	4	7777	4	MAP1A	15	43821446	Missense_Mutation	SNP	T	TCGA-ED-A8O5-01A-11D-A35Z-10	1786653	43821446	58709946	77	33960										
FRMD5	84978	hgsc.bcm.edu	37	chr15	44487159	44487159	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	cgcggcgctgacctggatggTgcaggtgtactcgctgtcgt	16	11	0	1			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr15:44487159T>C	ENST00000417257.1	-	1	270	c.94A>G	c.(94-96)Acc>Gcc	p.T32A	FRMD5_ENST00000402883.1_Missense_Mutation_p.T32A|FRMD5_ENST00000484674.1_5'Flank	NM_032892.3	NP_116281.2	Q7Z6J6	FRMD5_HUMAN	FERM domain containing 5	32	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(2)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	14		all_cancers(109;2.29e-15)|all_epithelial(112;9.98e-13)|Lung NSC(122;4.89e-08)|all_lung(180;5.08e-07)|Melanoma(134;0.0275)		all cancers(107;8.63e-20)|GBM - Glioblastoma multiforme(94;3.63e-06)		ACCTGGATGGTGCAGGTGTAC	0.721																																					p.T32A		Atlas-SNP	.											.	FRMD5	45	.	0			c.A94G						.						7	8	8					15																	44487159		2059	4057	6116	SO:0001583	missense	84978	exon1			GGATGGTGCAGGT	BC007796	CCDS10107.2, CCDS73715.1, CCDS73716.1	15q15.3	2005-08-09			ENSG00000171877	ENSG00000171877			28214	protein-coding gene	gene with protein product							Standard	XM_005254729		Approved	MGC14161	uc001ztl.3	Q7Z6J6	OTTHUMG00000060475	ENST00000417257.1:c.94A>G	chr15.hg19:g.44487159T>C	ENSP00000403067:p.Thr32Ala	42.0	0.0		43.0	15.0	NM_032892	Q8NBG4	Missense_Mutation	SNP	ENST00000417257.1	hg19	CCDS10107.2	.	.	.	.	.	.	.	.	.	.	T	13.04	2.118347	0.37339	.	.	ENSG00000171877	ENST00000417257;ENST00000402883	T;T	0.77229	-1.08;-1.08	4.39	3.23	0.37069	FERM, N-terminal (1);Band 4.1 domain (1);FERM domain (1);	0.378404	0.24497	N	0.038009	T	0.57636	0.2067	N	0.04805	-0.155	0.80722	D	1	B	0.33807	0.426	B	0.36567	0.228	T	0.56111	-0.8033	10	0.56958	D	0.05	.	7.8785	0.29608	0.1842:0.0:0.0:0.8158	.	32	Q7Z6J6	FRMD5_HUMAN	A	32	ENSP00000403067:T32A;ENSP00000384142:T32A	ENSP00000384142:T32A	T	-	1	0	FRMD5	42274451	1.000000	0.71417	1.000000	0.80357	0.868000	0.49771	4.699000	0.61796	0.522000	0.28464	0.402000	0.26972	ACC	.	.		0.721	FRMD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133879.1	NM_032892		C	44487159	T	C	44487159	3	2	249	1	0	0	0	0	1	0	0	0	6061	1696	59	2	1674	2	FRMD5	15	44487159	Missense_Mutation	SNP	T	TCGA-ED-A8O5-01A-11D-A35Z-10	665713	44487159	58044233	78	33961										
SEMA6D	80031	hgsc.bcm.edu	37	chr15	48056061	48056061	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	gggcaggctgtgtattcccgCgtggcccgcatatgtaaaaa	13	10	0	0	rs374731818		TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr15:48056061C>A	ENST00000316364.5	+	10	1201	c.762C>A	c.(760-762)cgC>cgA	p.R254R	SEMA6D_ENST00000558014.1_Silent_p.R254R|SEMA6D_ENST00000389432.2_Silent_p.R254R|SEMA6D_ENST00000389425.3_Silent_p.R254R|SEMA6D_ENST00000355997.3_Silent_p.R254R|SEMA6D_ENST00000536845.2_Silent_p.R254R|SEMA6D_ENST00000354744.4_Silent_p.R254R|SEMA6D_ENST00000558816.1_Silent_p.R254R|SEMA6D_ENST00000358066.4_Silent_p.R254R|SEMA6D_ENST00000537942.1_Silent_p.R254R|SEMA6D_ENST00000389428.3_Silent_p.R254R|SEMA6D_ENST00000389433.2_Silent_p.R254R	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	254	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		TGTATTCCCGCGTGGCCCGCA	0.493																																					p.R254R		Atlas-SNP	.											.	SEMA6D	322	.	0			c.C762A						.						136	133	134					15																	48056061		2198	4297	6495	SO:0001819	synonymous_variant	80031	exon10			TTCCCGCGTGGCC	AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"Semaphorins"	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.762C>A	chr15.hg19:g.48056061C>A		156.0	0.0		127.0	54.0	NM_153617	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Silent	SNP	ENST00000316364.5	hg19	CCDS32225.1																																																																																			.	.		0.493	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966		A	48056061	C	A	48056061	2	1	249	1	0	0	0	0	0	0	0	1	14057	755	27	1		1	SEMA6D	15	48056061	Silent	SNP	C	TCGA-ED-A8O5-01A-11D-A35Z-10	3568902	48056061	54475331	79	33962										
FBN1	2200	hgsc.bcm.edu	37	chr15	48704920	48704920	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	ctgggtttcctcggcccatgCccattccagaaacacagtgc	9	15	0	1			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr15:48704920C>T	ENST00000316623.5	-	65	8527	c.8072G>A	c.(8071-8073)gGc>gAc	p.G2691D	FBN1_ENST00000561429.1_5'UTR	NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	2691					extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		TCGGCCCATGCCCATTCCAGA	0.502																																					p.G2691D		Atlas-SNP	.											.	FBN1	310	.	0			c.G8072A						.						157	151	153					15																	48704920		2198	4296	6494	SO:0001583	missense	2200	exon65			CCCATGCCCATTC	X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.8072G>A	chr15.hg19:g.48704920C>T	ENSP00000325527:p.Gly2691Asp	120.0	0.0		85.0	27.0	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	hg19	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.647484	0.87958	.	.	ENSG00000166147	ENST00000316623	D	0.81821	-1.54	5.38	5.38	0.77491	Growth factor, receptor (1);	0.000000	0.85682	D	0.000000	D	0.88599	0.6480	M	0.73598	2.24	0.80722	D	1	D	0.69078	0.997	D	0.66196	0.942	D	0.85789	0.1366	10	0.27785	T	0.31	.	18.926	0.92544	0.0:1.0:0.0:0.0	.	2691	P35555	FBN1_HUMAN	D	2691	ENSP00000325527:G2691D	ENSP00000325527:G2691D	G	-	2	0	FBN1	46492212	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.651000	0.83577	2.793000	0.96121	0.655000	0.94253	GGC	.	.		0.502	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			T	48704920	C	T	48704920	3	4	249	1	0	0	0	0	1	0	0	0	5710	739	26	3	551	3	FBN1	15	48704920	Missense_Mutation	SNP	C	TCGA-ED-A8O5-01A-11D-A35Z-10	648859	48704920	53826472	80	33963										
MYO5C	55930	hgsc.bcm.edu	37	chr15	52497232	52497232	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	tagctcagctgttgcaggacGgaggtcatggtgtagccgtc	15	9	2	0			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr15:52497232G>A	ENST00000261839.7	-	38	4811	c.4650C>T	c.(4648-4650)tcC>tcT	p.S1550S	RP11-430B1.2_ENST00000560518.1_lincRNA	NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	1550	Dilute. {ECO:0000255|PROSITE- ProRule:PRU00503}.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(7)|large_intestine(15)|lung(12)|ovary(7)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66				all cancers(107;0.0137)		GTTGCAGGACGGAGGTCATGG	0.587																																					p.S1550S		Atlas-SNP	.											.	MYO5C	162	.	0			c.C4650T						.						86	93	91					15																	52497232		2053	4181	6234	SO:0001819	synonymous_variant	55930	exon38			CAGGACGGAGGTC	AF272390	CCDS42036.1	15q21	2011-09-27				ENSG00000128833		"Myosins / Myosin superfamily : Class V"	7604	protein-coding gene	gene with protein product	"myosin 5C"	610022				11870218	Standard	NM_018728		Approved	MGC74969	uc010bff.3	Q9NQX4		ENST00000261839.7:c.4650C>T	chr15.hg19:g.52497232G>A		78.0	0.0		97.0	42.0	NM_018728	Q6P1W8	Silent	SNP	ENST00000261839.7	hg19	CCDS42036.1																																																																																			.	.		0.587	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728		A	52497232	G	A	52497232	2	1	249	1	0	0	0	0	0	0	0	1	10089	1103	39	1		1	MYO5C	15	52497232	Silent	SNP	G	TCGA-ED-A8O5-01A-11D-A35Z-10	3792312	52497232	50034160	81	33964										
STRA6	64220	hgsc.bcm.edu	37	chr15	74494511	74494511	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	cttacccctctggctggagcTcctcgcccccctggggctca	10	19	2	0			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr15:74494511T>C	ENST00000323940.5	-	2	343	c.98A>G	c.(97-99)gAg>gGg	p.E33G	STRA6_ENST00000416286.3_Missense_Mutation_p.E33G|STRA6_ENST00000535552.1_Missense_Mutation_p.E70G|STRA6_ENST00000423167.2_Missense_Mutation_p.E33G|STRA6_ENST00000563965.1_Missense_Mutation_p.E72G|STRA6_ENST00000574278.1_Missense_Mutation_p.E48G|RP11-60L3.1_ENST00000558645.1_RNA|STRA6_ENST00000395105.4_Missense_Mutation_p.E33G|STRA6_ENST00000574439.1_5'UTR|RP11-60L3.1_ENST00000560148.1_RNA|STRA6_ENST00000449139.2_Missense_Mutation_p.E33G|RP11-60L3.1_ENST00000561332.1_RNA|STRA6_ENST00000432245.2_Missense_Mutation_p.E33G	NM_001142617.1|NM_001142618.1|NM_001142619.1	NP_001136089.1|NP_001136090.1|NP_001136091.1	Q9BX79	STRA6_HUMAN	stimulated by retinoic acid 6	33					adrenal gland development (GO:0030325)|alveolar primary septum development (GO:0061143)|artery morphogenesis (GO:0048844)|blood vessel development (GO:0001568)|cognition (GO:0050890)|developmental growth (GO:0048589)|diaphragm development (GO:0060539)|digestive tract morphogenesis (GO:0048546)|ductus arteriosus closure (GO:0097070)|ear development (GO:0043583)|embryonic camera-type eye formation (GO:0060900)|embryonic digestive tract development (GO:0048566)|eyelid development in camera-type eye (GO:0061029)|face morphogenesis (GO:0060325)|feeding behavior (GO:0007631)|female genitalia development (GO:0030540)|head development (GO:0060322)|head morphogenesis (GO:0060323)|heart development (GO:0007507)|kidney development (GO:0001822)|learning (GO:0007612)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung vasculature development (GO:0060426)|neuromuscular process (GO:0050905)|nose morphogenesis (GO:0043585)|paramesonephric duct development (GO:0061205)|phototransduction, visible light (GO:0007603)|positive regulation of behavior (GO:0048520)|positive regulation of JAK-STAT cascade (GO:0046427)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|retinoic acid metabolic process (GO:0042573)|retinoid metabolic process (GO:0001523)|retinol transport (GO:0034633)|smooth muscle tissue development (GO:0048745)|uterus morphogenesis (GO:0061038)|ventricular septum development (GO:0003281)|vitamin A import (GO:0071939)|vocal learning (GO:0042297)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	receptor activity (GO:0004872)|vitamin transporter activity (GO:0051183)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(5)|skin(1)|stomach(2)	26						TGGCTGGAGCTCCTCGCCCCC	0.627																																					p.E72G		Atlas-SNP	.											.	STRA6	66	.	0			c.A215G						.						44	44	44					15																	74494511		2198	4297	6495	SO:0001583	missense	64220	exon2			TGGAGCTCCTCGC	AF352728	CCDS10261.1, CCDS45301.1, CCDS45302.1, CCDS55973.1, CCDS55974.1, CCDS58387.1	15q24.1	2014-07-14	2012-12-07		ENSG00000137868	ENSG00000137868			30650	protein-coding gene	gene with protein product	"retinol binding protein 4 receptor"	610745	"stimulated by retinoic acid gene 6 homolog (mouse)", "stimulated by retinoic acid 6 homolog (mouse)"			17255476, 17273977	Standard	NM_022369		Approved	FLJ12541	uc002axj.3	Q9BX79	OTTHUMG00000138998	ENST00000323940.5:c.98A>G	chr15.hg19:g.74494511T>C	ENSP00000326085:p.Glu33Gly	74.0	0.0		43.0	19.0	NM_001199042	A8K7F1|B7Z5M9|B7Z862|D3DW54|F5GYI8|I3L1G8|Q6PJF8|Q71RB9|Q7L9G1|Q7Z3U9|Q8TB21|Q9BX78|Q9H9U8	Missense_Mutation	SNP	ENST00000323940.5	hg19	CCDS10261.1	.	.	.	.	.	.	.	.	.	.	T	14.40	2.522948	0.44866	.	.	ENSG00000137868	ENST00000395105;ENST00000323940;ENST00000449139;ENST00000423167;ENST00000535552;ENST00000432245	D;D;D;D;T	0.82081	-1.55;-1.55;-1.56;-1.57;-1.26	4.51	-0.00192	0.14032	.	0.795454	0.10844	N	0.627861	D	0.84511	0.5488	M	0.67953	2.075	0.09310	N	1	P;P;D;P;P;P	0.57571	0.775;0.775;0.98;0.775;0.775;0.775	B;B;P;B;B;B	0.51453	0.306;0.306;0.67;0.306;0.306;0.306	T	0.74993	-0.3474	10	0.54805	T	0.06	-2.2681	10.9218	0.47169	0.0:0.0:0.672:0.328	.	70;71;33;33;33;72	F5GYI8;B7Z5G7;Q9BX79-2;Q9BX79-3;Q9BX79;Q9BX79-4	.;.;.;.;STRA6_HUMAN;.	G	33;33;72;33;70;33	ENSP00000378537:E33G;ENSP00000326085:E33G;ENSP00000413012:E33G;ENSP00000440238:E70G;ENSP00000407176:E33G	ENSP00000326085:E33G	E	-	2	0	STRA6	72281564	0.001000	0.12720	0.003000	0.11579	0.286000	0.27126	0.103000	0.15292	0.181000	0.19994	0.379000	0.24179	GAG	.	.		0.627	STRA6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272891.1			C	74494511	T	C	74494511	3	2	249	1	0	0	0	0	1	0	0	0	15337	1551	54	2	2027	2	STRA6	15	74494511	Missense_Mutation	SNP	T	TCGA-ED-A8O5-01A-11D-A35Z-10	21997279	74494511	28036881	82	33965										
IREB2	3658	hgsc.bcm.edu	37	chr15	78768702	78768703	+	Splice_Site	INS	-	-	T													0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	aaacatttagaacatacaggINStaagaagataaaagatcact							TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr15:78768702_78768703insT	ENST00000258886.8	+	9	1344		c.e9+1		IREB2_ENST00000560440.1_3'UTR	NM_004136.2	NP_004127	P48200	IREB2_HUMAN	iron-responsive element binding protein 2						aging (GO:0007568)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|erythrocyte homeostasis (GO:0034101)|intestinal absorption (GO:0050892)|iron ion transport (GO:0006826)|osteoclast differentiation (GO:0030316)|post-embryonic development (GO:0009791)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to iron(II) ion (GO:0010040)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|translation repressor activity (GO:0030371)			central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	41				UCEC - Uterine corpus endometrioid carcinoma (272;0.232)		GAACATACAGGTAAGAAGATAA	0.307																																					.	NSCLC(200;764 2208 35157 49871 50830)	Atlas-INDEL	.											.	IREB2	106	.	0			c.1195+1->T						.																																			SO:0001630	splice_region_variant	3658	exon9			.	M58511	CCDS10302.1	15q25.1	2013-09-20			ENSG00000136381	ENSG00000136381			6115	protein-coding gene	gene with protein product		147582				2172968	Standard	NM_004136		Approved	IRP2	uc002bdr.2	P48200	OTTHUMG00000143861	ENST00000258886.8:c.1195+1->T	chr15.hg19:g.78768703_78768703dupT		106.0	0.0		84.0	33.0	NM_004136	A8KAC7|E1CJT9|H0YKU0|Q13095|Q1HE21|Q59FQ7|Q8WVK6|Q9UF17	Splice_Site	INS	ENST00000258886.8	hg19	CCDS10302.1																																																																																			.	.		0.307	IREB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290109.3	NM_004136	Intron	T	78768703	-	T	78768702	8	5	249	1	0	1	1	0	0	0	1	0	7835	1275	44	0	1230	0	IREB2	15	78768702	Splice_Site	INS	-	TCGA-ED-A8O5-01A-11D-A35Z-10	4274191	78768702	23762690	83	33966										
AXIN1	8312	hgsc.bcm.edu	37	chr16	348175	348175	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	agcggggcgggaagtggtgcCaagcgggggcgggaggcagc	24	8	0	0			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr16:348175C>T	ENST00000262320.3	-	6	1702	c.1331G>A	c.(1330-1332)tGg>tAg	p.W444*	AXIN1_ENST00000481769.1_5'UTR|AXIN1_ENST00000354866.3_Nonsense_Mutation_p.W444*	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	444	Interaction with CTNNB1. {ECO:0000250}.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				GAAGTGGTGCCAAGCGGGGGC	0.667											OREG0003699	type=REGULATORY REGION|Gene=AXIN1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.W444X		Atlas-SNP	.											.	AXIN1	290	.	0			c.G1331A						.						9	6	7					16																	348175		2100	4145	6245	SO:0001587	stop_gained	8312	exon6			TGGTGCCAAGCGG	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.1331G>A	chr16.hg19:g.348175C>T	ENSP00000262320:p.Trp444*	63.0	0.0	587	34.0	29.0	NM_181050	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Nonsense_Mutation	SNP	ENST00000262320.3	hg19	CCDS10405.1	.	.	.	.	.	.	.	.	.	.	C	29.7	5.028316	0.93518	.	.	ENSG00000103126	ENST00000262320;ENST00000354866	.	.	.	4.48	3.45	0.39498	.	0.377447	0.27486	N	0.019155	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	-18.9049	9.5891	0.39534	0.3761:0.6239:0.0:0.0	.	.	.	.	X	444	.	ENSP00000262320:W444X	W	-	2	0	AXIN1	288176	1.000000	0.71417	1.000000	0.80357	0.068000	0.16541	3.090000	0.50191	2.324000	0.78689	0.478000	0.44815	TGG	.	.		0.667	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3			T	348175	C	T	348175	4	4	249	1	0	0	0	0	0	1	0	0	1236	595	21	3	1281	3	AXIN1	16	348175	Nonsense_Mutation	SNP	C	TCGA-ED-A8O5-01A-11D-A35Z-10		348175	90006578	84	33967										
MEFV	4210	hgsc.bcm.edu	37	chr16	3304270	3304270	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	gagtccagattcgcagctgtCttttcctctagagtcaggag	11	10	3	2			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr16:3304270C>T	ENST00000219596.1	-	2	837	c.798G>A	c.(796-798)aaG>aaA	p.K266K	MEFV_ENST00000541159.1_Intron|MEFV_ENST00000536379.1_Intron|MEFV_ENST00000339854.4_Intron	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	266	Interaction with RELA.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						TCGCAGCTGTCTTTTCCTCTA	0.572																																					p.K266K		Atlas-SNP	.											.	MEFV	170	.	0			c.G798A						.						121	137	131					16																	3304270		2197	4300	6497	SO:0001819	synonymous_variant	4210	exon2			AGCTGTCTTTTCC	AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"Tripartite motif containing / Tripartite motif containing"	6998	protein-coding gene	gene with protein product	"pyrin"	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.798G>A	chr16.hg19:g.3304270C>T		76.0	0.0		52.0	46.0	NM_000243	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Silent	SNP	ENST00000219596.1	hg19	CCDS10498.1																																																																																			.	.		0.572	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243		T	3304270	C	T	3304270	2	4	249	1	0	0	0	0	0	0	0	1	9468	912	32	3		3	MEFV	16	3304270	Silent	SNP	C	TCGA-ED-A8O5-01A-11D-A35Z-10	2956095	3304270	87050483	85	33968										
XYLT1	64131	hgsc.bcm.edu	37	chr16	17228387	17228387	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	cggcccgtcgaagacccaggCgggcaaaggagtggtacaag	16	11	0	1			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr16:17228387C>A	ENST00000261381.6	-	9	2054	c.1970G>T	c.(1969-1971)cGc>cTc	p.R657L	CTD-2576D5.4_ENST00000567344.1_RNA	NM_022166.3	NP_071449.1	Q86Y38	XYLT1_HUMAN	xylosyltransferase I	657					cellular response to heat (GO:0034605)|chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						AAGACCCAGGCGGGCAAAGGA	0.622																																					p.R657L		Atlas-SNP	.											.	XYLT1	147	.	0			c.G1970T						.						92	78	82					16																	17228387		2197	4300	6497	SO:0001583	missense	64131	exon9			CCCAGGCGGGCAA	AJ277441	CCDS10569.1	16p12	2013-02-25			ENSG00000103489	ENSG00000103489	2.4.2.26	"Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	15516	protein-coding gene	gene with protein product	"protein xylosyltransferase 1"	608124				11099377	Standard	NM_022166		Approved	XT-I, PXYLT1	uc002dfa.3	Q86Y38	OTTHUMG00000129975	ENST00000261381.6:c.1970G>T	chr16.hg19:g.17228387C>A	ENSP00000261381:p.Arg657Leu	64.0	0.0		24.0	19.0	NM_022166	Q9H1B6	Missense_Mutation	SNP	ENST00000261381.6	hg19	CCDS10569.1	.	.	.	.	.	.	.	.	.	.	C	31	5.100144	0.94197	.	.	ENSG00000103489	ENST00000261381	T	0.55760	0.5	5.33	5.33	0.75918	.	0.103350	0.64402	D	0.000001	T	0.70962	0.3284	M	0.82323	2.585	0.80722	D	1	D	0.64830	0.994	D	0.63597	0.916	T	0.75379	-0.3338	10	0.87932	D	0	-34.3226	11.4711	0.50268	0.0:0.9182:0.0:0.0817	.	657	Q86Y38	XYLT1_HUMAN	L	657	ENSP00000261381:R657L	ENSP00000261381:R657L	R	-	2	0	XYLT1	17135888	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	6.061000	0.71148	2.489000	0.83994	0.561000	0.74099	CGC	.	.		0.622	XYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252241.2	NM_022166		A	17228387	C	A	17228387	3	1	249	1	0	0	0	0	1	0	0	0	17478	768	27	1	925	1	XYLT1	16	17228387	Missense_Mutation	SNP	C	TCGA-ED-A8O5-01A-11D-A35Z-10	13924117	17228387	73126366	86	33969										
BRD7	29117	hgsc.bcm.edu	37	chr16	50357561	50357582	+	Frame_Shift_Del	DEL	TGCCATGACATACGGATAATCT	TGCCATGACATACGGATAATCT	-													0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	aaaacatccagtaaactatcTgccatgacatacggataatc					rs115202576|rs78557784|rs139109763|rs569809930	byFrequency	TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	TGCCATGACATACGGATAATCT	TGCCATGACATACGGATAATCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr16:50357561_50357582delTGCCATGACATACGGATAATCT	ENST00000394688.3	-	12	1518_1539	c.1359_1380delAGATTATCCGTATGTCATGGCA	c.(1357-1380)caagattatccgtatgtcatggcafs	p.QDYPYVMA453fs	BRD7_ENST00000394689.2_Frame_Shift_Del_p.QDYPYVMA453fs			Q9NPI1	BRD7_HUMAN	bromodomain containing 7	453					cell cycle (GO:0007049)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|prostate(2)|urinary_tract(2)	22		all_cancers(37;0.0127)				GTAAACTATCTGCCATGACATACGGATAATCTTGGCACGTGG	0.428																																					p.454_461del		Atlas-INDEL	.											BRD7,NS,carcinoma,0,2	BRD7	61	.	0			c.1360_1381del						.																																			SO:0001589	frameshift_variant	29117	exon12			.	AF213969	CCDS10742.1, CCDS54007.1	16q12.1	2008-11-18	2002-01-14		ENSG00000166164	ENSG00000166164			14310	protein-coding gene	gene with protein product			"bromodomain-containing 7"			10526152, 18809673	Standard	NM_013263		Approved	CELTIX1, BP75	uc002ege.2	Q9NPI1	OTTHUMG00000133170	ENST00000394688.3:c.1359_1380delAGATTATCCGTATGTCATGGCA	chr16.hg19:g.50357561_50357582delTGCCATGACATACGGATAATCT	ENSP00000378180:p.Gln453fs	96.0	0.0		34.0	22.0	NM_013263	Q4VC09|Q8N2L9|Q96KA4|Q9BV48|Q9UH59	Frame_Shift_Del	DEL	ENST00000394688.3	hg19	CCDS10742.1																																																																																			.	.		0.428	BRD7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256874.3	NM_013263		-	50357582	TGCCATGACATACGGATAATCT	-	50357561	7	5	249	1	0	1	0	1	0	0	0	0	1507	1567	55	0	602	0	BRD7	16	50357561	Frame_Shift_Del	DEL	TGCCATGACATACGGATAATCT	TCGA-ED-A8O5-01A-11D-A35Z-10	33129174	50357561	39997192	87	33970										
EVPLL	645027	hgsc.bcm.edu	37	chr17	18284693	18284693	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	gcccacaggaccggctgaacAgtgagcagagccaggccctg	14	14	0	3			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr17:18284693A>T	ENST00000399134.4	+	3	434	c.76A>T	c.(76-78)Agt>Tgt	p.S26C	RP1-37N7.1_ENST00000579352.1_RNA	NM_001145127.1	NP_001138599.1	A8MZ36	EVPLL_HUMAN	envoplakin-like	26										NS(1)|endometrium(1)|large_intestine(1)|lung(2)	5						CCGGCTGAACAGTGAGCAGAG	0.662																																					p.S26C		Atlas-SNP	.											.	EVPLL	10	.	0			c.A76T						.						29	35	33					17																	18284693		692	1591	2283	SO:0001583	missense	645027	exon3			CTGAACAGTGAGC		CCDS45626.1	17p11.2	2009-08-25			ENSG00000214860	ENSG00000214860			35236	protein-coding gene	gene with protein product							Standard	NM_001145127		Approved		uc002gte.3	A8MZ36	OTTHUMG00000059095	ENST00000399134.4:c.76A>T	chr17.hg19:g.18284693A>T	ENSP00000382086:p.Ser26Cys	93.0	0.0		60.0	25.0	NM_001145127	B4DPD4	Missense_Mutation	SNP	ENST00000399134.4	hg19	CCDS45626.1	.	.	.	.	.	.	.	.	.	.	.	9.321	1.058101	0.19987	.	.	ENSG00000214860	ENST00000399134	T	0.19669	2.13	.	.	.	.	.	.	.	.	T	0.15652	0.0377	N	0.24115	0.695	0.09310	N	1	D	0.61080	0.989	P	0.49637	0.617	T	0.15037	-1.0451	7	0.38643	T	0.18	.	.	.	.	.	26	A8MZ36	EVPLL_HUMAN	C	26	ENSP00000382086:S26C	ENSP00000382086:S26C	S	+	1	0	EVPLL	18225418	0.485000	0.25972	0.688000	0.30117	0.325000	0.28411	3.638000	0.54332	-0.508000	0.06540	0.063000	0.15292	AGT	.	.		0.662	EVPLL-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130836.2	NM_001145127		T	18284693	A	T	18284693	3	4	249	1	0	0	0	0	1	0	0	0	5295	188	7	4	82	4	EVPLL	17	18284693	Missense_Mutation	SNP	A	TCGA-ED-A8O5-01A-11D-A35Z-10		18284693	62910517	88	33971										
C17orf75	64149	hgsc.bcm.edu	37	chr17	30665304	30665304	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	cgttcagagtctatcgttacTgtttcaggaagcagtttttc	9	8	3	1			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr17:30665304T>G	ENST00000577809.1	-	4	463	c.414A>C	c.(412-414)acA>acC	p.T138T	C17orf75_ENST00000225805.4_Silent_p.T138T|RP11-227G15.3_ENST00000581915.1_RNA	NM_022344.3	NP_071739.2	Q9HAS0	NJMU_HUMAN	chromosome 17 open reading frame 75	138										ovary(1)	1		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)			CTATCGTTACTGTTTCAGGAA	0.353																																					p.T138T		Atlas-SNP	.											.	C17orf75	23	.	0			c.A414C						.						117	112	113					17																	30665304		1837	4099	5936	SO:0001819	synonymous_variant	64149	exon4			CGTTACTGTTTCA	AB062437	CCDS58537.1	17q11.2	2013-01-21			ENSG00000108666	ENSG00000108666			30173	protein-coding gene	gene with protein product							Standard	NM_022344		Approved	NJMU-R1	uc002hhg.3	Q9HAS0		ENST00000577809.1:c.414A>C	chr17.hg19:g.30665304T>G		282.0	0.0		231.0	93.0	NM_022344	Q7Z2H4	Silent	SNP	ENST00000577809.1	hg19	CCDS58537.1																																																																																			.	.		0.353	C17orf75-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447204.1	NM_022344		G	30665304	T	G	30665304	2	3	249	1	0	0	0	0	0	0	0	1	1882	1567	55	5		5	C17orf75	17	30665304	Silent	SNP	T	TCGA-ED-A8O5-01A-11D-A35Z-10	12380611	30665304	50529906	89	33972										
KRT36	8689	hgsc.bcm.edu	37	chr17	39644652	39644652	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	gagacagctctgtctcatacCtgcacacacagaaccctgcc	7	16	2	2			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr17:39644652C>T	ENST00000328119.6	-	3	542		c.e3-1		KRT36_ENST00000393986.2_Splice_Site	NM_003771.4	NP_003762.1	O76013	KRT36_HUMAN	keratin 36						regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural constituent of epidermis (GO:0030280)			breast(2)|cervix(1)|kidney(2)|large_intestine(3)|lung(8)|skin(1)	17		Breast(137;0.000286)				TGTCTCATACCTGCACACACA	0.602																																					.		Atlas-SNP	.											.	KRT36	52	.	0			c.543-1G>A						.						60	52	55					17																	39644652		2203	4300	6503	SO:0001630	splice_region_variant	8689	exon4			TCATACCTGCACA	Y16792	CCDS11395.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000126337	ENSG00000126337		"-", "Intermediate filaments type I, keratins (acidic)"	6454	protein-coding gene	gene with protein product		604540	"keratin, hair, acidic, 6"	KRTHA6		9756910, 16831889	Standard	XM_005257762		Approved		uc002hwt.3	O76013	OTTHUMG00000133431	ENST00000328119.6:c.543-1G>A	chr17.hg19:g.39644652C>T		52.0	0.0		53.0	25.0	NM_003771	Q86XG4	Splice_Site	SNP	ENST00000328119.6	hg19	CCDS11395.1	.	.	.	.	.	.	.	.	.	.	C	19.45	3.830211	0.71258	.	.	ENSG00000126337	ENST00000393986;ENST00000328119	.	.	.	5.84	5.84	0.93424	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.1316	0.93410	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	KRT36	36898178	1.000000	0.71417	1.000000	0.80357	0.615000	0.37417	7.487000	0.81328	2.769000	0.95229	0.563000	0.77884	.	.	.		0.602	KRT36-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259508.1	NM_003771	Intron	T	39644652	C	T	39644652	5	4	249	1	0	0	0	0	0	0	1	0	8482	695	24	3	881	3	KRT36	17	39644652	Splice_Site	SNP	C	TCGA-ED-A8O5-01A-11D-A35Z-10	8979348	39644652	41550558	90	33973										
AXIN2	8313	hgsc.bcm.edu	37	chr17	63534461	63534461	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	cttgggcaggcggtgggttcTctacaggacgtggaaaggaa	17	7	1	0			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr17:63534461T>A	ENST00000375702.5	-	4	1168	c.1060A>T	c.(1060-1062)Aga>Tga	p.R354*	CTD-2535L24.2_ENST00000577662.1_3'UTR|AXIN2_ENST00000307078.5_Splice_Site_p.R354*			Q9Y2T1	AXIN2_HUMAN	axin 2	354	Interaction with GSK3B. {ECO:0000250}.				bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to organic cyclic compound (GO:0071407)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|dorsal/ventral axis specification (GO:0009950)|intramembranous ossification (GO:0001957)|maintenance of DNA repeat elements (GO:0043570)|mRNA stabilization (GO:0048255)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell proliferation (GO:0008285)|negative regulation of osteoblast differentiation (GO:0045668)|odontogenesis (GO:0042476)|positive regulation of cell death (GO:0010942)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein phosphorylation (GO:0001934)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of chondrocyte development (GO:0061181)|regulation of mismatch repair (GO:0032423)|secondary heart field specification (GO:0003139)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)			NS(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	34						CGGTGGGTTCTCTACAGGACG	0.627									Oligodontia, Ectodermal Dysplasia and Colorectal Polyp syndrome																												p.R354X		Atlas-SNP	.											.	AXIN2	92	.	0			c.A1060T						.						47	46	46					17																	63534461		2203	4300	6503	SO:0001630	splice_region_variant	8313	exon5	Familial Cancer Database	Oligodontia-Colorectal Cancer syndrome, Tooth Agenesis-Colorectal Cancer Syndrome	GGGTTCTCTACAG	AF078165	CCDS11662.1	17q24.1	2014-09-17	2008-08-01		ENSG00000168646				904	protein-coding gene	gene with protein product	"conductin", "axil"	604025				10049590	Standard	NM_004655		Approved	MGC126582, DKFZp781B0869	uc002jfi.3	Q9Y2T1	OTTHUMG00000179353	ENST00000375702.5:c.1060-1A>T	chr17.hg19:g.63534461T>A		104.0	0.0		91.0	44.0	NM_004655	Q3MJ88|Q9H3M6|Q9UH84	Nonsense_Mutation	SNP	ENST00000375702.5	hg19		.	.	.	.	.	.	.	.	.	.	T	36	5.868443	0.97043	.	.	ENSG00000168646	ENST00000307078;ENST00000375702	.	.	.	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.4338	15.243	0.73485	0.0:0.0:0.0:1.0	.	.	.	.	X	354	.	ENSP00000302625:R354X	R	-	1	2	AXIN2	60964923	1.000000	0.71417	0.998000	0.56505	0.755000	0.42902	3.927000	0.56499	2.008000	0.58898	0.454000	0.30748	AGA	.	.		0.627	AXIN2-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000445901.1	NM_004655	Nonsense_Mutation	A	63534461	T	A	63534461	5	1	249	1	0	0	0	0	0	0	1	0	1237	1565	54	4	1499	4	AXIN2	17	63534461	Splice_Site	SNP	T	TCGA-ED-A8O5-01A-11D-A35Z-10	23889809	63534461	17660749	91	33974										
SDK2	54549	hgsc.bcm.edu	37	chr17	71361525	71361525	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	tgaacttgaccgagctgggaGcgctgggggctgcgggagac	19	9	0	3			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr17:71361525G>A	ENST00000392650.3	-	38	5177	c.5177C>T	c.(5176-5178)gCt>gTt	p.A1726V	SDK2_ENST00000410094.1_5'UTR|SDK2_ENST00000388726.3_Missense_Mutation_p.A1707V	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	1726	Fibronectin type-III 12. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(15)|lung(31)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	86						CGAGCTGGGAGCGCTGGGGGC	0.577																																					p.A1726V		Atlas-SNP	.											.	SDK2	219	.	0			c.C5177T						.						29	26	27					17																	71361525		2203	4300	6503	SO:0001583	missense	54549	exon38			CTGGGAGCGCTGG	AB040947	CCDS45769.1	17q21.31	2013-02-11	2011-12-09		ENSG00000069188	ENSG00000069188		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19308	protein-coding gene	gene with protein product		607217	"sidekick homolog 2 (chicken)"			12230981, 15213259	Standard	NM_001144952		Approved	FLJ10832, KIAA1514	uc010dfm.3	Q58EX2	OTTHUMG00000152726	ENST00000392650.3:c.5177C>T	chr17.hg19:g.71361525G>A	ENSP00000376421:p.Ala1726Val	119.0	0.0		70.0	15.0	NM_001144952	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Missense_Mutation	SNP	ENST00000392650.3	hg19	CCDS45769.1	.	.	.	.	.	.	.	.	.	.	G	16.57	3.160046	0.57368	.	.	ENSG00000069188	ENST00000409227;ENST00000392650;ENST00000388726;ENST00000424778;ENST00000316893;ENST00000410094	T;T;T	0.61742	0.08;0.08;0.08	4.95	4.95	0.65309	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.058384	0.64402	D	0.000002	T	0.64659	0.2618	M	0.73962	2.25	0.54753	D	0.999983	B;B;B	0.21147	0.052;0.007;0.005	B;B;B	0.31869	0.137;0.049;0.044	T	0.66101	-0.6007	10	0.59425	D	0.04	.	18.205	0.89852	0.0:0.0:1.0:0.0	.	1726;1726;1707	Q58EX2-2;Q58EX2;Q58EX2-3	.;SDK2_HUMAN;.	V	1350;1726;1707;883;1726;67	ENSP00000376421:A1726V;ENSP00000373378:A1707V;ENSP00000407098:A883V	ENSP00000324967:A1726V	A	-	2	0	SDK2	68873120	1.000000	0.71417	0.504000	0.27639	0.855000	0.48748	6.262000	0.72514	2.279000	0.76181	0.655000	0.94253	GCT	.	.		0.577	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064		A	71361525	G	A	71361525	3	1	249	1	0	0	0	0	1	0	0	0	13984	971	34	3	1373	3	SDK2	17	71361525	Missense_Mutation	SNP	G	TCGA-ED-A8O5-01A-11D-A35Z-10	7827064	71361525	9833685	92	33975										
DNAH17	8632	hgsc.bcm.edu	37	chr17	76497424	76497424	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	gtgaaggcctgagaactctcCacctgcaggatgagccggag	14	11	1	3			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr17:76497424C>A	ENST00000585328.1	-	35	5434	c.5310G>T	c.(5308-5310)gtG>gtT	p.V1770V	DNAH17_ENST00000389840.5_Silent_p.V1761V|DNAH17-AS1_ENST00000598378.1_3'UTR|RP11-559N14.5_ENST00000591373.1_RNA	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	1761	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			GAGAACTCTCCACCTGCAGGA	0.607																																					p.V1775V		Atlas-SNP	.											.	DNAH17	347	.	0			c.G5325T						.						49	52	51					17																	76497424		2068	4217	6285	SO:0001819	synonymous_variant	8632	exon35			ACTCTCCACCTGC	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"Axonemal dyneins"	2946	protein-coding gene	gene with protein product		610063	"dynein, axonemal, heavy polypeptide 17", "dynein, axonemal, heavy chain like 1", "dynein, axonemal, heavy like 1"	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.5310G>T	chr17.hg19:g.76497424C>A		44.0	0.0		37.0	18.0	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	hg19																																																																																				.	.		0.607	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		A	76497424	C	A	76497424	2	1	249	1	0	0	0	0	0	0	0	1	4603	581	21	3		3	DNAH17	17	76497424	Silent	SNP	C	TCGA-ED-A8O5-01A-11D-A35Z-10	5135899	76497424	4697786	93	33976										
DSC1	1823	hgsc.bcm.edu	37	chr18	28720171	28720171	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	gacagttgtagtgcacattgTaggagtttgtgagctcgctg	14	6	0	1			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr18:28720171T>C	ENST00000257198.5	-	10	1615	c.1354A>G	c.(1354-1356)Aca>Gca	p.T452A	DSC1_ENST00000257197.3_Missense_Mutation_p.T452A|RP11-408H20.2_ENST00000581836.1_RNA	NM_024421.2	NP_077739.1	Q08554	DSC1_HUMAN	desmocollin 1	452	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			OV - Ovarian serous cystadenocarcinoma(10;0.00778)			GTGCACATTGTAGGAGTTTGT	0.433																																					p.T452A		Atlas-SNP	.											.	DSC1	240	.	0			c.A1354G						.						103	96	98					18																	28720171		2203	4300	6503	SO:0001583	missense	1823	exon10			ACATTGTAGGAGT	AF293358	CCDS11894.1, CCDS11895.1	18q12.1	2010-01-26			ENSG00000134765	ENSG00000134765		"Cadherins / Major cadherins"	3035	protein-coding gene	gene with protein product		125643				8486729	Standard	NM_024421		Approved	CDHF1	uc002kwn.3	Q08554	OTTHUMG00000131982	ENST00000257198.5:c.1354A>G	chr18.hg19:g.28720171T>C	ENSP00000257198:p.Thr452Ala	163.0	0.0		107.0	43.0	NM_004948	Q9HB01	Missense_Mutation	SNP	ENST00000257198.5	hg19	CCDS11894.1	.	.	.	.	.	.	.	.	.	.	T	1.259	-0.616498	0.03663	.	.	ENSG00000134765	ENST00000257197;ENST00000257198	T;T	0.50813	0.73;0.73	5.83	-1.36	0.09085	Cadherin (4);Cadherin-like (1);	0.379741	0.22022	N	0.065704	T	0.26484	0.0647	N	0.20685	0.6	0.09310	N	1	B;B	0.31125	0.309;0.309	B;B	0.37550	0.253;0.197	T	0.26189	-1.0110	10	0.13853	T	0.58	.	5.1495	0.15002	0.4987:0.1388:0.0:0.3626	.	452;452	Q08554;Q9HB00	DSC1_HUMAN;.	A	452	ENSP00000257197:T452A;ENSP00000257198:T452A	ENSP00000257197:T452A	T	-	1	0	DSC1	26974169	0.001000	0.12720	0.003000	0.11579	0.467000	0.32768	-0.567000	0.05916	-0.115000	0.11915	-0.263000	0.10527	ACA	.	.		0.433	DSC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254946.1	NM_004948, NM_024421		C	28720171	T	C	28720171	3	2	249	1	0	0	0	0	1	0	0	0	4767	1638	57	2	1398	2	DSC1	18	28720171	Missense_Mutation	SNP	T	TCGA-ED-A8O5-01A-11D-A35Z-10		28720171	49357077	94	33977										
ATP8B3	148229	hgsc.bcm.edu	37	chr19	1784853	1784853	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	cttgagggctgggaagatgaCtcggagggccaggacaggga	19	7	0	3			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr19:1784853C>G	ENST00000310127.6	-	28	3863	c.3625G>C	c.(3625-3627)Gtc>Ctc	p.V1209L	ATP8B3_ENST00000525591.1_Missense_Mutation_p.V1172L|ATP8B3_ENST00000539485.1_Missense_Mutation_p.V1219L	NM_138813.3	NP_620168.1	O60423	AT8B3_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 3	1209					binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGGAAGATGACTCGGAGGGCC	0.622																																					p.V1209L		Atlas-SNP	.											.	ATP8B3	108	.	0			c.G3625C						.						57	60	59					19																	1784853		2140	4253	6393	SO:0001583	missense	148229	exon28			AGATGACTCGGAG	AA827939	CCDS45901.1, CCDS54196.1	19p13.3	2010-04-28	2010-04-28		ENSG00000130270	ENSG00000130270		"ATPases / P-type"	13535	protein-coding gene	gene with protein product	"aminophospholipid translocase ATP8B3", "potential phospholipid-transporting ATPase IK"	605866	"ATPase, Class I, type 8B, member 3", "ATPase, class I, type 8B, member 3"			11015572	Standard	NM_138813		Approved	ATPIK	uc002ltw.4	O60423	OTTHUMG00000166189	ENST00000310127.6:c.3625G>C	chr19.hg19:g.1784853C>G	ENSP00000311336:p.Val1209Leu	107.0	0.0		96.0	47.0	NM_138813	Q7Z485|Q8IVB8|Q8N4Y8|Q96M22	Missense_Mutation	SNP	ENST00000310127.6	hg19	CCDS45901.1	.	.	.	.	.	.	.	.	.	.	C	4.590	0.109613	0.08780	.	.	ENSG00000130270	ENST00000310127;ENST00000539485;ENST00000525591	T;T;T	0.39787	1.06;1.06;1.06	3.33	-4.36	0.03645	.	1.071130	0.07246	N	0.865097	T	0.21718	0.0523	N	0.19112	0.55	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.18209	-1.0344	10	0.37606	T	0.19	.	3.0243	0.06085	0.1282:0.4515:0.1296:0.2907	.	1209;1172	O60423;Q7Z485	AT8B3_HUMAN;.	L	1209;1219;1172	ENSP00000311336:V1209L;ENSP00000443574:V1219L;ENSP00000437115:V1172L	ENSP00000311336:V1209L	V	-	1	0	ATP8B3	1735853	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.810000	0.00755	-0.758000	0.04690	-0.459000	0.05422	GTC	.	.		0.622	ATP8B3-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388279.1	NM_138813		G	1784853	C	G	1784853	3	3	249	1	0	0	0	0	1	0	0	0	1196	565	20	4	285	4	ATP8B3	19	1784853	Missense_Mutation	SNP	C	TCGA-ED-A8O5-01A-11D-A35Z-10		1784853	57344130	95	33978										
CD70	970	hgsc.bcm.edu	37	chr19	6586380	6586380	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	aggagcggcccagtgctgggCccccctgccagtatagcctg	14	15	0	0			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr19:6586380C>A	ENST00000245903.3	-	3	382	c.233G>T	c.(232-234)gGc>gTc	p.G78V	CD70_ENST00000423145.3_Missense_Mutation_p.G78V	NM_001252.3	NP_001243.1	P32970	CD70_HUMAN	CD70 molecule	78					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|extrinsic apoptotic signaling pathway (GO:0097191)|immune response (GO:0006955)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	protease binding (GO:0002020)|receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|skin(1)	11						CAGTGCTGGGCCCCCCTGCCA	0.607																																					p.G78V	Pancreas(183;2617 2876 10173 34193)	Atlas-SNP	.											.	CD70	24	.	0			c.G233T						.						33	29	30					19																	6586380		2203	4300	6503	SO:0001583	missense	970	exon3			GCTGGGCCCCCCT	L08096	CCDS12170.1	19p13	2013-05-22	2006-10-27	2006-10-27		ENSG00000125726		"Tumor necrosis factor (ligand) superfamily", "CD molecules"	11937	protein-coding gene	gene with protein product		602840	"tumor necrosis factor (ligand) superfamily, member 7"	CD27LG, TNFSF7		8387892, 8120384	Standard	NM_001252		Approved	CD27L	uc002mfi.3	P32970		ENST00000245903.3:c.233G>T	chr19.hg19:g.6586380C>A	ENSP00000245903:p.Gly78Val	44.0	0.0		40.0	22.0	NM_001252	B4DPR8|Q53XX4|Q96J57	Missense_Mutation	SNP	ENST00000245903.3	hg19	CCDS12170.1	.	.	.	.	.	.	.	.	.	.	C	15.20	2.763199	0.49574	.	.	ENSG00000125726	ENST00000423145;ENST00000245903	D;T	0.94613	-3.47;-0.16	4.32	-0.377	0.12501	Tumour necrosis factor (3);Tumour necrosis factor-like (2);	0.834321	0.10499	N	0.667475	D	0.92756	0.7697	N	0.19112	0.55	0.21445	N	0.999687	D;D	0.63880	0.993;0.983	D;P	0.64776	0.929;0.874	D	0.84641	0.0695	10	0.72032	D	0.01	-18.934	7.3189	0.26515	0.0:0.576:0.0:0.424	.	78;78	B4DPR8;P32970	.;CD70_HUMAN	V	78	ENSP00000395294:G78V;ENSP00000245903:G78V	ENSP00000245903:G78V	G	-	2	0	CD70	6537380	0.005000	0.15991	0.091000	0.20842	0.118000	0.20060	-0.332000	0.07904	0.077000	0.16863	-0.261000	0.10672	GGC	.	.		0.607	CD70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457860.1			A	6586380	C	A	6586380	3	1	249	1	0	0	0	0	1	0	0	0	3035	739	26	3	352	3	CD70	19	6586380	Missense_Mutation	SNP	C	TCGA-ED-A8O5-01A-11D-A35Z-10	4801527	6586380	52542603	96	33979										
OR7G1	125962	hgsc.bcm.edu	37	chr19	9225702	9225702	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	ccatagaacaaggaaaaaacAgagaggtgacagccacaggt	11	8	0	3	rs146317150		TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr19:9225702A>T	ENST00000541538.1	-	1	737	c.738T>A	c.(736-738)tcT>tcA	p.S246S	OR7G1_ENST00000293614.1_Silent_p.S246S	NM_001005192.2	NP_001005192.2	Q8NGA0	OR7G1_HUMAN	olfactory receptor, family 7, subfamily G, member 1	246						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|skin(2)	20						AGGAAAAAACAGAGAGGTGAC	0.428																																					p.S246S		Atlas-SNP	.											.	OR7G1	53	.	0			c.T738A						.						96	95	95					19																	9225702		2203	4300	6503	SO:0001819	synonymous_variant	125962	exon1			AAAAACAGAGAGG		CCDS32898.1, CCDS32898.2	19p13.2	2013-09-24			ENSG00000161807	ENSG00000161807		"GPCR / Class A : Olfactory receptors"	8465	protein-coding gene	gene with protein product				OR7G1P			Standard	NM_001005192		Approved	OR19-15	uc021uoi.1	Q8NGA0	OTTHUMG00000168067	ENST00000541538.1:c.738T>A	chr19.hg19:g.9225702A>T		186.0	0.0		136.0	50.0	NM_001005192	Q6IFJ5|Q96RA1	Silent	SNP	ENST00000541538.1	hg19	CCDS32898.2																																																																																			.	.		0.428	OR7G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397912.1			T	9225702	A	T	9225702	2	4	249	1	0	0	0	0	0	0	0	1	11231	175	7	4		4	OR7G1	19	9225702	Silent	SNP	A	TCGA-ED-A8O5-01A-11D-A35Z-10	2639322	9225702	49903281	97	33980										
IL27RA	9466	hgsc.bcm.edu	37	chr19	14157256	14157256	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	ctccagattcagcctctgccCcccgtagcgtggcagtcagc	10	17	3	1			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr19:14157256C>T	ENST00000263379.2	+	8	1092	c.967C>T	c.(967-969)Ccc>Tcc	p.P323S		NM_004843.3	NP_004834.1	Q6UWB1	I27RA_HUMAN	interleukin 27 receptor, alpha	323	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T-helper 1 type immune response (GO:0002827)|regulation of isotype switching to IgG isotypes (GO:0048302)	integral component of plasma membrane (GO:0005887)	interleukin-27 receptor activity (GO:0045509)|transmembrane signaling receptor activity (GO:0004888)			breast(3)|endometrium(3)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	26						AGCCTCTGCCCCCCGTAGCGT	0.637																																					p.P323S	Colon(164;1849 1896 4443 37792 47834)	Atlas-SNP	.											.	IL27RA	56	.	0			c.C967T						.						70	74	73					19																	14157256		2203	4300	6503	SO:0001583	missense	9466	exon8			TCTGCCCCCCGTA	AF053004	CCDS12303.1	19p13.11	2013-02-11				ENSG00000104998		"Interleukins and interleukin receptors", "Fibronectin type III domain containing"	17290	protein-coding gene	gene with protein product	"T-cell cytokine receptor type 1"	605350				9600072, 11057672	Standard	NM_004843		Approved	WSX-1, TCCR, CRL1, WSX1, zcytor1, IL-27R	uc002mxx.4	Q6UWB1		ENST00000263379.2:c.967C>T	chr19.hg19:g.14157256C>T	ENSP00000263379:p.Pro323Ser	88.0	0.0		63.0	36.0	NM_004843	A0N0L1|O60624	Missense_Mutation	SNP	ENST00000263379.2	hg19	CCDS12303.1	.	.	.	.	.	.	.	.	.	.	C	18.61	3.662112	0.67700	.	.	ENSG00000104998	ENST00000263379	T	0.79749	-1.3	4.68	4.68	0.58851	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.40818	N	0.001019	D	0.88862	0.6552	M	0.80183	2.485	0.18873	N	0.999987	D	0.89917	1.0	D	0.97110	1.0	T	0.81276	-0.1006	10	0.45353	T	0.12	.	12.9653	0.58481	0.0:1.0:0.0:0.0	.	323	Q6UWB1	I27RA_HUMAN	S	323	ENSP00000263379:P323S	ENSP00000263379:P323S	P	+	1	0	IL27RA	14018256	0.553000	0.26513	0.386000	0.26170	0.183000	0.23260	3.576000	0.53878	2.433000	0.82419	0.650000	0.86243	CCC	.	.		0.637	IL27RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458539.1	NM_004843		T	14157256	C	T	14157256	3	4	249	1	0	0	0	0	1	0	0	0	7690	623	22	3	997	3	IL27RA	19	14157256	Missense_Mutation	SNP	C	TCGA-ED-A8O5-01A-11D-A35Z-10	4931554	14157256	44971727	98	33981										
EMR2	30817	hgsc.bcm.edu	37	chr19	14863218	14863218	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	gagcgagagctgcagatgcaGtgaggtgctggtgttctgga	18	6	1	3			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr19:14863218G>A	ENST00000315576.3	-	15	2162	c.1711C>T	c.(1711-1713)Ctg>Ttg	p.L571L	EMR2_ENST00000601345.1_Silent_p.L560L|EMR2_ENST00000353876.1_Silent_p.L478L|EMR2_ENST00000594076.1_Silent_p.L478L|EMR2_ENST00000596991.2_Silent_p.L560L|EMR2_ENST00000595839.1_Silent_p.L429L|EMR2_ENST00000594294.1_Silent_p.L522L|EMR2_ENST00000346057.1_Silent_p.L522L|EMR2_ENST00000392967.2_Silent_p.L560L|EMR2_ENST00000353005.1_Silent_p.L429L|EMR2_ENST00000392965.3_Silent_p.L513L|EMR2_ENST00000392964.3_3'UTR	NM_013447.3	NP_038475.2	Q9UHX3	EMR2_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 2	571					cell adhesion (GO:0007155)|cell migration (GO:0016477)|G-protein coupled receptor signaling pathway (GO:0007186)|granulocyte chemotaxis (GO:0071621)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	48						TGCAGATGCAGTGAGGTGCTG	0.567																																					p.L571L		Atlas-SNP	.											.	EMR2	99	.	0			c.C1711T						.						135	116	122					19																	14863218		2203	4300	6503	SO:0001819	synonymous_variant	30817	exon15			GATGCAGTGAGGT	AF114491	CCDS32935.1, CCDS59361.1	19p13.1	2014-08-08	2003-11-26			ENSG00000127507		"CD molecules", "-", "GPCR / Class B : Orphans"	3337	protein-coding gene	gene with protein product		606100	"egf-like module containing, mucin-like, hormone receptor-like sequence 2"				Standard	NM_013447		Approved	CD312	uc002mzp.2	Q9UHX3		ENST00000315576.3:c.1711C>T	chr19.hg19:g.14863218G>A		172.0	0.0		152.0	61.0	NM_013447	B4DQ96|E7ESD7|E9PBR1|E9PEL6|E9PFQ5|E9PG91|Q8NG96|Q9Y4B1	Silent	SNP	ENST00000315576.3	hg19	CCDS32935.1																																																																																			.	.		0.567	EMR2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466502.2			A	14863218	G	A	14863218	2	1	249	1	0	0	0	0	0	0	0	1	5107	1020	36	3		3	EMR2	19	14863218	Silent	SNP	G	TCGA-ED-A8O5-01A-11D-A35Z-10	705962	14863218	44265765	99	33982										
OR7C1	26664	hgsc.bcm.edu	37	chr19	14910799	14910799	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	gtgtggaggtgggagtctgaGcatatggccaggatgatgag	19	4	1	3			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr19:14910799G>A	ENST00000248073.2	-	1	224	c.150C>T	c.(148-150)tgC>tgT	p.C50C	OR7A5_ENST00000601611.1_Intron	NM_198944.1	NP_945182.1	O76099	OR7C1_HUMAN	olfactory receptor, family 7, subfamily C, member 1	50					spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(2)|ovary(2)|prostate(1)	18						GGGAGTCTGAGCATATGGCCA	0.493																																					p.C50C		Atlas-SNP	.											.	OR7C1	58	.	0			c.C150T						.						88	78	81					19																	14910799		2203	4300	6503	SO:0001819	synonymous_variant	26664	exon1			GTCTGAGCATATG	X89676	CCDS12317.1	19p13.1	2012-08-09						"GPCR / Class A : Olfactory receptors"	8373	protein-coding gene	gene with protein product				OR7C4			Standard	NM_198944		Approved	OR19-5	uc010xnz.2	O76099		ENST00000248073.2:c.150C>T	chr19.hg19:g.14910799G>A		248.0	0.0		199.0	93.0	NM_198944	Q15621|Q6IFP2|Q96R94	Silent	SNP	ENST00000248073.2	hg19	CCDS12317.1																																																																																			.	.		0.493	OR7C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466519.1			A	14910799	G	A	14910799	2	1	249	1	0	0	0	0	0	0	0	1	11226	963	34	3		3	OR7C1	19	14910799	Silent	SNP	G	TCGA-ED-A8O5-01A-11D-A35Z-10	47581	14910799	44218184	100	33983										
ZNF257	113835	hgsc.bcm.edu	37	chr19	22256300	22256300	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	tctctaagccagacctgatcAcctgtctggagcaaggaaaa	9	11	3	2			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr19:22256300A>G	ENST00000594947.1	+	3	304	c.160A>G	c.(160-162)Acc>Gcc	p.T54A	ZNF257_ENST00000600162.1_Missense_Mutation_p.T54A	NM_033468.2	NP_258429.2	Q9Y2Q1	ZN257_HUMAN	zinc finger protein 257	54	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|lung(4)	6		all_lung(12;0.0961)|Lung NSC(12;0.103)				AGACCTGATCACCTGTCTGGA	0.423																																					p.T54A		Atlas-SNP	.											.	ZNF257	156	.	0			c.A160G						.						135	149	144					19																	22256300		2203	4300	6503	SO:0001583	missense	113835	exon3			CTGATCACCTGTC	AF070651	CCDS46030.1	19p12	2014-02-14			ENSG00000197134	ENSG00000197134		"Zinc fingers, C2H2-type", "-"	13498	protein-coding gene	gene with protein product		606957				10585455	Standard	NM_033468		Approved	BMZF-4	uc010ecx.3	Q9Y2Q1	OTTHUMG00000182927	ENST00000594947.1:c.160A>G	chr19.hg19:g.22256300A>G	ENSP00000470209:p.Thr54Ala	79.0	0.0		89.0	44.0	NM_033468	B3KPS4|E9PG34|Q8NE34	Missense_Mutation	SNP	ENST00000594947.1	hg19	CCDS46030.1	.	.	.	.	.	.	.	.	.	.	A	7.556	0.663667	0.14710	.	.	ENSG00000197134	ENST00000435820;ENST00000397123	.	.	.	0.86	-1.53	0.08611	Krueppel-associated box (3);	.	.	.	.	T	0.27731	0.0682	L	0.37561	1.115	0.09310	N	1	B	0.29805	0.257	B	0.30572	0.117	T	0.33214	-0.9877	8	0.62326	D	0.03	.	3.0291	0.06101	0.5239:0.4761:0.0:0.0	.	54	Q9Y2Q1	ZN257_HUMAN	A	54	.	ENSP00000380312:T54A	T	+	1	0	ZNF257	22048140	0.001000	0.12720	0.144000	0.22314	0.145000	0.21501	-0.133000	0.10451	0.257000	0.21650	0.254000	0.18369	ACC	.	.		0.423	ZNF257-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464382.1			G	22256300	A	G	22256300	3	3	249	1	0	0	0	0	1	0	0	0	17815	159	6	2	170	2	ZNF257	19	22256300	Missense_Mutation	SNP	A	TCGA-ED-A8O5-01A-11D-A35Z-10	7345501	22256300	36872683	101	33984										
PSG6	5675	hgsc.bcm.edu	37	chr19	43414998	43414998	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	tgctgctggagatggagggcTtgggagtctccgctgtgcag	18	8	1	1			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr19:43414998T>A	ENST00000292125.2	-	3	484	c.440A>T	c.(439-441)aAg>aTg	p.K147M	PSG6_ENST00000187910.2_Missense_Mutation_p.K147M|PSG6_ENST00000402603.4_Missense_Mutation_p.K147M	NM_002782.4	NP_002773.1	Q00889	PSG6_HUMAN	pregnancy specific beta-1-glycoprotein 6	147					female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(19)|ovary(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	44		Prostate(69;0.00899)				GATGGAGGGCTTGGGAGTCTC	0.517																																					p.K147M		Atlas-SNP	.											.	PSG6	89	.	0			c.A440T						.						140	140	140					19																	43414998		2201	4299	6500	SO:0001583	missense	5675	exon3			GAGGGCTTGGGAG		CCDS12613.1, CCDS33038.1	19q13.2	2013-01-29			ENSG00000170848	ENSG00000170848		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9523	protein-coding gene	gene with protein product		176395				1690992	Standard	NM_002782		Approved			Q00889	OTTHUMG00000151127	ENST00000292125.2:c.440A>T	chr19.hg19:g.43414998T>A	ENSP00000292125:p.Lys147Met	93.0	0.0		65.0	36.0	NM_001031850	O75244|Q15224|Q15235|Q549K1	Missense_Mutation	SNP	ENST00000292125.2	hg19	CCDS12613.1	.	.	.	.	.	.	.	.	.	.	N	11.14	1.551896	0.27739	.	.	ENSG00000170848	ENST00000187910;ENST00000402603;ENST00000292125;ENST00000402456	T;T;T	0.01059	5.39;5.39;5.39	1.64	-3.0	0.05480	.	.	.	.	.	T	0.04363	0.0120	M	0.83603	2.65	0.09310	N	1	P;P;P	0.49559	0.743;0.716;0.925	P;P;P	0.60117	0.869;0.726;0.768	T	0.04693	-1.0933	9	0.72032	D	0.01	.	5.8099	0.18460	0.0:0.0:0.5498:0.4502	.	147;147;147	Q00889;Q00889-2;B5MCE1	PSG6_HUMAN;.;.	M	147	ENSP00000187910:K147M;ENSP00000385736:K147M;ENSP00000292125:K147M	ENSP00000187910:K147M	K	-	2	0	PSG6	48106838	0.169000	0.23002	0.000000	0.03702	0.004000	0.04260	-1.274000	0.02820	-0.960000	0.03613	0.163000	0.16589	AAG	.	.		0.517	PSG6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321436.1	NM_002782		A	43414998	T	A	43414998	3	1	249	1	0	0	0	0	1	0	0	0	12671	1609	56	4	922	4	PSG6	19	43414998	Missense_Mutation	SNP	T	TCGA-ED-A8O5-01A-11D-A35Z-10	21158698	43414998	15713985	102	33985										
DMPK	1760	hgsc.bcm.edu	37	chr19	46282568	46282568	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	agtgcagctgcgtgatccacCgccggtccccattcaccaac	9	17	1	1	rs540031135		TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr19:46282568C>T	ENST00000291270.4	-	4	511	c.386G>A	c.(385-387)cGg>cAg	p.R129Q	DMPK_ENST00000600757.1_Missense_Mutation_p.R139Q|DMPK_ENST00000343373.4_Missense_Mutation_p.R139Q|DMPK_ENST00000354227.5_Missense_Mutation_p.R129Q|DMPK_ENST00000595361.1_5'Flank|DMPK_ENST00000447742.2_Missense_Mutation_p.R129Q|DMPK_ENST00000458663.2_Missense_Mutation_p.R129Q	NM_004409.3	NP_004400.4	Q09013	DMPK_HUMAN	dystrophia myotonica-protein kinase	129	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular calcium ion homeostasis (GO:0006874)|muscle cell apoptotic process (GO:0010657)|nuclear envelope organization (GO:0006998)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|regulation of excitatory postsynaptic membrane potential involved in skeletal muscle contraction (GO:0014853)|regulation of heart contraction (GO:0008016)|regulation of myotube differentiation (GO:0010830)|regulation of skeletal muscle contraction by calcium ion signaling (GO:0014722)|regulation of sodium ion transport (GO:0002028)|regulation of synapse structural plasticity (GO:0051823)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of mitochondrial outer membrane (GO:0031307)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|myosin phosphatase regulator activity (GO:0017020)|protein serine/threonine kinase activity (GO:0004674)			endometrium(5)|kidney(1)|large_intestine(1)|lung(6)|stomach(1)|urinary_tract(2)	16		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00616)|GBM - Glioblastoma multiforme(486;0.0825)|Epithelial(262;0.24)		CGTGATCCACCGCCGGTCCCC	0.647													C|||	1	0.000199681	0	0	5008	,	,		13798	0		0	False		,,,				2504	0.001				p.R139Q	Esophageal Squamous(35;307 869 9153 24033 28903)	Atlas-SNP	.											.	DMPK	74	.	0			c.G416A						.						121	123	122					19																	46282568		2203	4300	6503	SO:0001583	missense	1760	exon3			ATCCACCGCCGGT	L19268	CCDS12674.1, CCDS46117.1, CCDS46118.1, CCDS46119.1, CCDS74400.1	19q13.3	2014-02-05					2.7.11.1		2933	protein-coding gene	gene with protein product	"dystrophia myotonica 1", "DM protein kinase", "myotonin protein kinase A", "myotonic dystrophy associated protein kinase", "thymopoietin homolog"	605377	"dystrophia myotonica 1 (includes dystrophia myotonia protein kinase)"	DM1, DM		1546325, 1546326	Standard	NM_001288765		Approved	DMK, DM1PK, MDPK, MT-PK	uc002pdf.1	Q09013		ENST00000291270.4:c.386G>A	chr19.hg19:g.46282568C>T	ENSP00000291270:p.Arg129Gln	119.0	0.0		66.0	32.0	NM_001081563	E5KR08|Q16205|Q6P5Z6	Missense_Mutation	SNP	ENST00000291270.4	hg19	CCDS12674.1	.	.	.	.	.	.	.	.	.	.	c	20.7	4.027869	0.75390	.	.	ENSG00000104936	ENST00000458663;ENST00000342805;ENST00000291270;ENST00000447742;ENST00000377750;ENST00000343373;ENST00000348168;ENST00000354227	T;T;T;T;T	0.40225	1.04;1.04;1.04;1.04;1.04	4.55	4.55	0.56014	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.43579	D	0.000559	T	0.43144	0.1234	N	0.20807	0.61	0.80722	D	1	P;P;D;D;D;D;D;D;D	0.89917	0.883;0.74;1.0;1.0;1.0;1.0;1.0;1.0;1.0	P;B;D;D;D;D;D;D;D	0.91635	0.475;0.163;0.983;0.985;0.999;0.998;0.991;0.999;0.994	T	0.18967	-1.0320	10	0.21540	T	0.41	.	8.4354	0.32784	0.0:0.8949:0.0:0.1051	.	139;129;129;155;129;129;129;176;139	B7Z9B5;Q09013-12;Q09013-16;G5E982;E5KR07;E5KR05;Q09013;Q59FU6;E5KR08	.;.;.;.;.;.;DMPK_HUMAN;.;.	Q	129;155;129;129;129;139;139;129	ENSP00000401753:R129Q;ENSP00000291270:R129Q;ENSP00000413417:R129Q;ENSP00000345997:R139Q;ENSP00000346168:R129Q	ENSP00000291270:R129Q	R	-	2	0	DMPK	50974408	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	1.676000	0.37565	2.366000	0.80165	0.561000	0.74099	CGG	.	.		0.647	DMPK-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460572.1	NM_004409		T	46282568	C	T	46282568	3	4	249	1	0	0	0	0	1	0	0	0	4586	652	23	1	1558	1	DMPK	19	46282568	Missense_Mutation	SNP	C	TCGA-ED-A8O5-01A-11D-A35Z-10	2867570	46282568	12846415	103	33986										
GLTSCR1	29998	hgsc.bcm.edu	37	chr19	48201917	48201917	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	ggagcatttgcacaaacaccAgggctccgtcctgcaccccg	10	16	0	0			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr19:48201917A>T	ENST00000396720.3	+	12	3469	c.3275A>T	c.(3274-3276)cAg>cTg	p.Q1092L	CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_015711.3	NP_056526.3	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1	1092										breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|pancreas(3)|prostate(4)|skin(2)	20		all_cancers(25;1.8e-07)|all_lung(116;5.73e-06)|Lung NSC(112;9.69e-06)|all_epithelial(76;2.42e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000358)|OV - Ovarian serous cystadenocarcinoma(262;0.000576)|Epithelial(262;0.0212)|GBM - Glioblastoma multiforme(486;0.0355)		CACAAACACCAGGGCTCCGTC	0.662											OREG0025594	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q1092L		Atlas-SNP	.											.	GLTSCR1	79	.	0			c.A3275T						.						79	82	81					19																	48201917		2013	4156	6169	SO:0001583	missense	29998	exon12			AACACCAGGGCTC	AF182077	CCDS46134.1	19q13.3	2012-11-29			ENSG00000063169	ENSG00000063169			4332	protein-coding gene	gene with protein product		605690				10708517	Standard	NM_015711		Approved		uc002phh.4	Q9NZM4		ENST00000396720.3:c.3275A>T	chr19.hg19:g.48201917A>T	ENSP00000379946:p.Gln1092Leu	92.0	0.0	952	73.0	31.0	NM_015711	A8MW01	Missense_Mutation	SNP	ENST00000396720.3	hg19	CCDS46134.1	.	.	.	.	.	.	.	.	.	.	A	18.90	3.720598	0.68959	.	.	ENSG00000063169	ENST00000396720	T	0.49432	0.78	4.28	4.28	0.50868	.	.	.	.	.	T	0.63988	0.2558	M	0.64997	1.995	0.53005	D	0.999964	D	0.67145	0.996	D	0.77557	0.99	T	0.67887	-0.5554	9	0.87932	D	0	.	12.5169	0.56038	1.0:0.0:0.0:0.0	.	1092	Q9NZM4	GSCR1_HUMAN	L	1092	ENSP00000379946:Q1092L	ENSP00000379946:Q1092L	Q	+	2	0	GLTSCR1	52893729	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.995000	0.76257	1.805000	0.52779	0.459000	0.35465	CAG	.	.		0.662	GLTSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465846.1	NM_015711		T	48201917	A	T	48201917	3	4	249	1	0	0	0	0	1	0	0	0	6482	188	7	4	3313	4	GLTSCR1	19	48201917	Missense_Mutation	SNP	A	TCGA-ED-A8O5-01A-11D-A35Z-10	1919349	48201917	10927066	104	33987										
BIRC8	112401	hgsc.bcm.edu	37	chr19	53793038	53793038	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	aaggaataaaaacaacagcgAtatgtctgtccatgcagatt	8	7	1	1			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr19:53793038A>C	ENST00000426466.1	-	1	1837	c.590T>G	c.(589-591)aTc>aGc	p.I197S		NM_033341.4	NP_203127.3	Q96P09	BIRC8_HUMAN	baculoviral IAP repeat containing 8	197					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(10)|urinary_tract(1)	19				GBM - Glioblastoma multiforme(134;0.00304)		AACAACAGCGATATGTCTGTC	0.443																																					p.I197S		Atlas-SNP	.											.	BIRC8	54	.	0			c.T590G						.						113	112	112					19																	53793038		2203	4300	6503	SO:0001583	missense	112401	exon1			ACAGCGATATGTC	AF164682	CCDS12863.1	19q13.3-q13.4	2011-01-25	2011-01-25			ENSG00000163098		"Baculoviral IAP repeat containing"	14878	protein-coding gene	gene with protein product	"IAP-like protein 2", "inhibitor of apoptosis-like protein 2"		"baculoviral IAP repeat-containing 8"			11390657	Standard	NM_033341		Approved	ILP-2, hILP2	uc002qbk.3	Q96P09		ENST00000426466.1:c.590T>G	chr19.hg19:g.53793038A>C	ENSP00000412957:p.Ile197Ser	139.0	0.0		134.0	46.0	NM_033341	Q6IPY1|Q96RW5	Missense_Mutation	SNP	ENST00000426466.1	hg19	CCDS12863.1	.	.	.	.	.	.	.	.	.	.	A	10.57	1.387200	0.25031	.	.	ENSG00000163098	ENST00000426466	T	0.78003	-1.14	0.502	-1.0	0.10196	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);	.	.	.	.	T	0.81418	0.4818	L	0.58354	1.805	0.09310	N	1	D	0.69078	0.997	D	0.72075	0.976	T	0.68780	-0.5318	9	0.87932	D	0	-7.3458	4.2707	0.10785	0.7447:0.0:0.2553:0.0	.	197	Q96P09	BIRC8_HUMAN	S	197	ENSP00000412957:I197S	ENSP00000412957:I197S	I	-	2	0	BIRC8	58484850	0.070000	0.21116	0.108000	0.21378	0.010000	0.07245	3.094000	0.50227	-0.475000	0.06852	-1.102000	0.02115	ATC	.	.		0.443	BIRC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464357.1	NM_033341		C	53793038	A	C	53793038	3	2	249	1	0	0	0	0	1	0	0	0	1440	333	12	5	124	5	BIRC8	19	53793038	Missense_Mutation	SNP	A	TCGA-ED-A8O5-01A-11D-A35Z-10	5591121	53793038	5335945	105	33988										
NLRP12	91662	hgsc.bcm.edu	37	chr19	54327156	54327156	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	ttacccctcaccaggtcctcTctctgtcctctctcccacag	4	20	4	0			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr19:54327156T>A	ENST00000324134.6	-	1	441	c.273A>T	c.(271-273)agA>agT	p.R91S	NLRP12_ENST00000351894.4_Missense_Mutation_p.R91S|NLRP12_ENST00000354278.3_Missense_Mutation_p.R91S|NLRP12_ENST00000391775.3_Missense_Mutation_p.R91S|NLRP12_ENST00000391773.1_Missense_Mutation_p.R91S|NLRP12_ENST00000535162.1_Missense_Mutation_p.R91S|NLRP12_ENST00000345770.5_Missense_Mutation_p.R91S|NLRP12_ENST00000391772.1_Missense_Mutation_p.R91S	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	91	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to cytokine stimulus (GO:0071345)|dendritic cell migration (GO:0036336)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of signal transduction (GO:0009968)|negative regulation of Toll signaling pathway (GO:0045751)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of MHC class I biosynthetic process (GO:0045345)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of interleukin-18 biosynthetic process (GO:0045381)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)			NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(36)|ovary(5)|pancreas(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	80	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		CCAGGTCCTCTCTCTGTCCTC	0.587																																					p.L91L		Atlas-SNP	.											.	NLRP12	236	.	0			c.G273T						.						104	100	102					19																	54327156		2202	4295	6497	SO:0001583	missense	91662	exon1			GTCCTCTCTCTGT	AY095146	CCDS12864.1, CCDS62784.1, CCDS62785.1	19q13.42	2014-09-17	2006-12-08	2006-12-08	ENSG00000142405	ENSG00000142405		"Nucleotide-binding domain and leucine rich repeat containing"	22938	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 12"	609648	"NACHT, leucine rich repeat and PYD containing 12"	NALP12		12563287, 12019269	Standard	NM_001277129		Approved	RNO2, PYPAF7, Monarch1, PAN6, CLR19.3	uc002qcj.5	P59046	OTTHUMG00000060776	ENST00000324134.6:c.273A>T	chr19.hg19:g.54327156T>A	ENSP00000319377:p.Arg91Ser	89.0	0.0		84.0	35.0	NM_144687	A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Silent	SNP	ENST00000324134.6	hg19	CCDS12864.1	.	.	.	.	.	.	.	.	.	.	T	10.11	1.259674	0.23051	.	.	ENSG00000142405	ENST00000324134;ENST00000535162;ENST00000351894;ENST00000354278;ENST00000391775;ENST00000391773;ENST00000345770;ENST00000391772	T;T;T;T;T;T;T	0.51071	0.72;0.72;0.72;0.72;0.72;0.72;0.72	4.87	0.253	0.15551	Pyrin (2);DEATH-like (2);	0.613015	0.13947	N	0.351800	T	0.42177	0.1191	M	0.77103	2.36	0.09310	N	0.999999	P;P;P;P	0.38280	0.625;0.625;0.625;0.625	B;B;B;B	0.34931	0.192;0.192;0.192;0.192	T	0.37033	-0.9723	10	0.66056	D	0.02	.	4.3222	0.11022	0.0:0.277:0.1667:0.5564	.	91;91;91;91	F2Z321;A8K407;A8MTQ2;P59046	.;.;.;NAL12_HUMAN	S	91	ENSP00000319377:R91S;ENSP00000438030:R91S;ENSP00000340473:R91S;ENSP00000346231:R91S;ENSP00000375655:R91S;ENSP00000375653:R91S;ENSP00000375652:R91S	ENSP00000319377:R91S	R	-	3	2	NLRP12	59018968	0.007000	0.16637	0.574000	0.28523	0.390000	0.30446	-0.208000	0.09371	-0.240000	0.09696	-0.425000	0.05940	AGA	.	.		0.587	NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000134340.1	NM_144687		A	54327156	T	A	54327156	3	1	249	1	0	0	0	0	1	0	0	0	10483	1548	54	4	3048	4	NLRP12	19	54327156	Missense_Mutation	SNP	T	TCGA-ED-A8O5-01A-11D-A35Z-10	534118	54327156	4801827	106	33989										
BFSP1	631	hgsc.bcm.edu	37	chr20	17489605	17489605	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	gccctcctccagctgactccGcagggcggccacctcccgct	10	21	0	1	rs141217196		TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr20:17489605G>T	ENST00000377873.3	-	5	703	c.664C>A	c.(664-666)Cgg>Agg	p.R222R	BFSP1_ENST00000536626.1_Silent_p.R83R|BFSP1_ENST00000544874.1_Silent_p.R83R|BFSP1_ENST00000377868.2_Silent_p.R97R	NM_001195.3	NP_001186.1	Q12934	BFSP1_HUMAN	beaded filament structural protein 1, filensin	222	Coil 2.|Rod.				cell maturation (GO:0048469)|lens fiber cell development (GO:0070307)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(7)|prostate(2)|skin(1)|stomach(1)	18						AGCTGACTCCGCAGGGCGGCC	0.642																																					p.R222R		Atlas-SNP	.											.	BFSP1	55	.	0			c.C664A						.						19	18	18					20																	17489605		2201	4295	6496	SO:0001819	synonymous_variant	631	exon5			GACTCCGCAGGGC	Y16717	CCDS13126.1, CCDS54448.1, CCDS63229.1	20p12.1	2014-06-05			ENSG00000125864	ENSG00000125864		"Intermediate filaments type VI, eye lens intermediate filaments"	1040	protein-coding gene	gene with protein product		603307				9787085	Standard	NM_001161705		Approved	CP94, CP115, LIFL-H, filensin	uc002wpo.3	Q12934	OTTHUMG00000031940	ENST00000377873.3:c.664C>A	chr20.hg19:g.17489605G>T		109.0	0.0		141.0	94.0	NM_001195	F5H0G1|O43595|O76034|O95676|Q8IVZ6|Q9HBX4	Silent	SNP	ENST00000377873.3	hg19	CCDS13126.1																																																																																			.	G|1.000;A|0.000		0.642	BFSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078119.6	NM_001195		T	17489605	G	T	17489605	2	4	249	1	0	0	0	0	0	0	0	1	1415	1086	38	1		1	BFSP1	20	17489605	Silent	SNP	G	TCGA-ED-A8O5-01A-11D-A35Z-10		17489605	45535915	107	33990										
C20orf12	55184	hgsc.bcm.edu	37	chr20	18433306	18433306	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	acctgatcctccaccataagCtgggatttccaatggactct	7	13	1	1			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr20:18433306C>T	ENST00000358866.6	-	5	518	c.496G>A	c.(496-498)Gct>Act	p.A166T	DZANK1_ENST00000357236.4_Silent_p.Q15Q|DZANK1_ENST00000487128.1_5'UTR|DZANK1_ENST00000262547.5_Missense_Mutation_p.A166T|DZANK1_ENST00000329494.5_Missense_Mutation_p.A168T			Q9NVP4	DZAN1_HUMAN	double zinc ribbon and ankyrin repeat domains 1	166							zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(10)	19						CCACCATAAGCTGGGATTTCC	0.398																																					p.A166T		Atlas-SNP	.											.	DZANK1	65	.	0			c.G496A						.						61	59	60					20																	18433306		1840	4076	5916	SO:0001583	missense	55184	exon6			CATAAGCTGGGAT	AK001462	CCDS46582.1	20p11.23	2013-01-11	2011-10-03	2011-10-03	ENSG00000089091	ENSG00000089091		"Ankyrin repeat domain containing"	15858	protein-coding gene	gene with protein product	"ankyrin repeat domain 64"		"chromosome 20 open reading frame 12"	C20orf84, C20orf12			Standard	NM_001099407		Approved	FLJ10600, dJ568F9.2, FLJ30892, bA189K21.8, ANKRD64	uc002wqq.4	Q9NVP4	OTTHUMG00000031968	ENST00000358866.6:c.496G>A	chr20.hg19:g.18433306C>T	ENSP00000351734:p.Ala166Thr	176.0	0.0		207.0	56.0	NM_001099407	B7ZLZ4|Q4F7X1|Q5QPD9|Q5QPE0|Q68DN8|Q6ZMX9|Q96NF0|Q9H1E0|Q9H442	Missense_Mutation	SNP	ENST00000358866.6	hg19	CCDS46582.1	.	.	.	.	.	.	.	.	.	.	C	8.111	0.778708	0.16120	.	.	ENSG00000089091	ENST00000262547;ENST00000329494	T;T	0.64085	-0.08;0.55	5.21	-1.55	0.08558	.	2.545780	0.01390	N	0.013202	T	0.46386	0.1390	L	0.29908	0.895	0.09310	N	0.999998	B;B	0.27380	0.177;0.082	B;B	0.26693	0.072;0.055	T	0.16129	-1.0413	10	0.12430	T	0.62	-0.2656	6.2396	0.20783	0.1215:0.4793:0.3222:0.077	.	185;166	B7Z631;Q9NVP4	.;DZAN1_HUMAN	T	166;168	ENSP00000262547:A166T;ENSP00000328866:A168T	ENSP00000262547:A166T	A	-	1	0	C20orf12	18381306	0.007000	0.16637	0.040000	0.18447	0.231000	0.25187	-0.317000	0.08060	-0.060000	0.13132	0.455000	0.32223	GCT	.	.		0.398	DZANK1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471926.1	NM_001099407		T	18433306	C	T	18433306	3	4	249	1	0	0	0	0	1	0	0	0	2087	797	28	3	1826	3	C20orf12	20	18433306	Missense_Mutation	SNP	C	TCGA-ED-A8O5-01A-11D-A35Z-10	943701	18433306	44592214	108	33991										
CEP250	11190	hgsc.bcm.edu	37	chr20	34067158	34067158	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	gggcagtccaggagaaggagGccctagtacgagagaaagcg	17	8	0	2	rs376769176		TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr20:34067158G>A	ENST00000397527.1	+	18	2917	c.2197G>A	c.(2197-2199)Gcc>Acc	p.A733T	RP3-477O4.14_ENST00000444933.1_RNA|RP3-477O4.14_ENST00000453914.1_RNA|RP3-477O4.14_ENST00000416260.1_RNA|CEP250_ENST00000342580.4_Missense_Mutation_p.A733T	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	733	Gln/Glu-rich.				centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of centriole-centriole cohesion (GO:0030997)	centriole (GO:0005814)|centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)|spindle pole centrosome (GO:0031616)	protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			GGAGAAGGAGGCCCTAGTACG	0.627																																					p.A733T		Atlas-SNP	.											.	CEP250	141	.	0			c.G2197A						.	G	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	127	113	118		2197	2.1	1	20		118	0,8600		0,0,4300	no	missense	CEP250	NM_007186.3	58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	733/2443	34067158	1,13005	2203	4300	6503	SO:0001583	missense	11190	exon18			AAGGAGGCCCTAG	AF022655	CCDS13255.1	20q11.22	2014-02-20	2006-01-11	2006-01-11	ENSG00000126001	ENSG00000126001			1859	protein-coding gene	gene with protein product		609689	"centrosomal protein 2"	CEP2		9506584, 9647649	Standard	NM_007186		Approved	C-NAP1	uc021wco.1	Q9BV73	OTTHUMG00000032343	ENST00000397527.1:c.2197G>A	chr20.hg19:g.34067158G>A	ENSP00000380661:p.Ala733Thr	161.0	0.0		226.0	69.0	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Missense_Mutation	SNP	ENST00000397527.1	hg19	CCDS13255.1	.	.	.	.	.	.	.	.	.	.	G	9.983	1.228648	0.22542	2.27E-4	0.0	ENSG00000126001	ENST00000397527;ENST00000342580	T;T	0.10288	2.89;2.9	5.15	2.07	0.26955	.	0.461084	0.20623	N	0.088726	T	0.09291	0.0229	M	0.71296	2.17	0.09310	N	1	B	0.15930	0.015	B	0.16289	0.015	T	0.34650	-0.9820	10	0.14252	T	0.57	.	0.9234	0.01320	0.2189:0.1323:0.3767:0.2721	.	733	Q9BV73	CP250_HUMAN	T	733	ENSP00000380661:A733T;ENSP00000341541:A733T	ENSP00000341541:A733T	A	+	1	0	CEP250	33530572	0.172000	0.23043	0.992000	0.48379	0.986000	0.74619	0.154000	0.16343	0.753000	0.32945	0.655000	0.94253	GCC	.	.		0.627	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186		A	34067158	G	A	34067158	3	1	249	1	0	0	0	0	1	0	0	0	3254	1203	42	3	2255	3	CEP250	20	34067158	Missense_Mutation	SNP	G	TCGA-ED-A8O5-01A-11D-A35Z-10	15633852	34067158	28958362	109	33992										
ZBTB46	140685	hgsc.bcm.edu	37	chr20	62421227	62421227	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	tcggcaggaaggacggcaccGgggagctggcccggctgtca	18	12	1	0			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr20:62421227G>T	ENST00000245663.4	-	2	1034	c.884C>A	c.(883-885)cCg>cAg	p.P295Q	ZBTB46_ENST00000302995.2_Missense_Mutation_p.P295Q|ZBTB46_ENST00000480766.1_5'Flank|ZBTB46_ENST00000395104.1_Missense_Mutation_p.P295Q	NM_025224.3	NP_079500.2	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46	295					negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of dendritic cell differentiation (GO:2001200)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)					GGACGGCACCGGGGAGCTGGC	0.627																																					p.P295Q		Atlas-SNP	.											.	ZBTB46	72	.	0			c.C884A						.						82	88	86					20																	62421227		2203	4300	6503	SO:0001583	missense	140685	exon2			GGCACCGGGGAGC	AK131482	CCDS13538.1	20q13.33	2013-01-08	2006-09-19	2006-09-19	ENSG00000130584	ENSG00000130584		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	16094	protein-coding gene	gene with protein product	"BTB-ZF protein expressed in effector lymphocytes"	614639	"BTB (POZ) domain containing 4"	ZNF340, BTBD4			Standard	NM_025224		Approved	FLJ13502, RINZF, BZEL	uc002ygv.2	Q86UZ6	OTTHUMG00000033001	ENST00000245663.4:c.884C>A	chr20.hg19:g.62421227G>T	ENSP00000245663:p.Pro295Gln	39.0	0.0		56.0	18.0	NM_025224	E1P5K9|Q5JWJ3|Q6GMV4|Q9BQK3|Q9H3Z8|Q9H3Z9	Missense_Mutation	SNP	ENST00000245663.4	hg19	CCDS13538.1	.	.	.	.	.	.	.	.	.	.	G	17.90	3.501888	0.64298	.	.	ENSG00000130584	ENST00000245663;ENST00000302995;ENST00000395104	T;T;T	0.10763	2.84;2.84;2.84	5.8	5.8	0.92144	.	0.119030	0.56097	D	0.000026	T	0.28366	0.0701	M	0.61703	1.905	0.58432	D	0.999993	D	0.71674	0.998	D	0.62955	0.909	T	0.00742	-1.1585	10	0.19590	T	0.45	.	19.0349	0.92972	0.0:0.0:1.0:0.0	.	295	Q86UZ6	ZBT46_HUMAN	Q	295	ENSP00000245663:P295Q;ENSP00000303102:P295Q;ENSP00000378536:P295Q	ENSP00000245663:P295Q	P	-	2	0	ZBTB46	61891671	1.000000	0.71417	0.987000	0.45799	0.473000	0.32948	7.415000	0.80131	2.749000	0.94314	0.655000	0.94253	CCG	.	.		0.627	ZBTB46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080232.2	NM_025224		T	62421227	G	T	62421227	3	4	249	1	0	0	0	0	1	0	0	0	17562	1116	39	1	901	1	ZBTB46	20	62421227	Missense_Mutation	SNP	G	TCGA-ED-A8O5-01A-11D-A35Z-10	28354069	62421227	604293	110	33993										
DSCAM	1826	hgsc.bcm.edu	37	chr21	41725592	41725592	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	ggtgcccgagcgctttgcaaGgcagctccacacgctgccca	12	16	0	0			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr21:41725592G>C	ENST00000400454.1	-	5	1211	c.734C>G	c.(733-735)cCt>cGt	p.P245R		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	245	Ig-like C2-type 3.				cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				CGCTTTGCAAGGCAGCTCCAC	0.567																																					p.P245R	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.	DSCAM	347	.	0			c.C734G						.						32	32	32					21																	41725592		1923	4133	6056	SO:0001583	missense	1826	exon5			TTGCAAGGCAGCT	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.734C>G	chr21.hg19:g.41725592G>C	ENSP00000383303:p.Pro245Arg	74.0	0.0		51.0	19.0	NM_001271534	O60468	Missense_Mutation	SNP	ENST00000400454.1	hg19	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.935967	0.73442	.	.	ENSG00000171587	ENST00000400454	T	0.65916	-0.18	5.31	4.42	0.53409	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.70666	0.3250	L	0.39326	1.205	0.58432	D	0.999995	D	0.76494	0.999	D	0.83275	0.996	T	0.70364	-0.4892	10	0.41790	T	0.15	.	13.9805	0.64301	0.0736:0.0:0.9264:0.0	.	245	O60469	DSCAM_HUMAN	R	245	ENSP00000383303:P245R	ENSP00000383303:P245R	P	-	2	0	DSCAM	40647462	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	9.302000	0.96175	1.352000	0.45808	0.650000	0.86243	CCT	.	.		0.567	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		C	41725592	G	C	41725592	3	2	249	1	0	0	0	0	1	0	0	0	4770	1000	35	4	5420	4	DSCAM	21	41725592	Missense_Mutation	SNP	G	TCGA-ED-A8O5-01A-11D-A35Z-10		41725592	6404303	111	33994										
LZTR1	8216	hgsc.bcm.edu	37	chr22	21348307	21348307	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	ggcgcgggagaggctggcccAggtgaggtgcctaaccgccc	18	13	0	2			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr22:21348307A>T	ENST00000215739.8	+	13	1807	c.1448A>T	c.(1447-1449)cAg>cTg	p.Q483L	LZTR1_ENST00000479606.1_3'UTR|LZTR1_ENST00000389355.3_Splice_Site_p.Q464L	NM_006767.3	NP_006758.2	Q8N653	LZTR1_HUMAN	leucine-zipper-like transcription regulator 1	483	BTB 1. {ECO:0000255|PROSITE- ProRule:PRU00037}.				anatomical structure morphogenesis (GO:0009653)|regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(13)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)	42	all_cancers(11;1.83e-25)|all_epithelial(7;9.19e-23)|Lung NSC(8;3.06e-15)|all_lung(8;5.05e-14)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)			AGGCTGGCCCAGGTGAGGTGC	0.662																																					p.Q483L		Atlas-SNP	.											.	LZTR1	99	.	0			c.A1448T						.						23	26	25					22																	21348307		2196	4298	6494	SO:0001630	splice_region_variant	8216	exon13			TGGCCCAGGTGAG	D38496	CCDS33606.1	22q11.21	2013-01-09	2004-12-10		ENSG00000099949	ENSG00000099949		"BTB/POZ domain containing"	6742	protein-coding gene	gene with protein product		600574	"leucine-zipper-like transcriptional regulator 1"			7633402, 16356934	Standard	NM_006767		Approved	LZTR-1, BTBD29	uc002zto.3	Q8N653	OTTHUMG00000150878	ENST00000215739.8:c.1449+1A>T	chr22.hg19:g.21348307A>T		129.0	0.0		99.0	37.0	NM_006767	Q14776|Q20WK0	Missense_Mutation	SNP	ENST00000215739.8	hg19	CCDS33606.1	.	.	.	.	.	.	.	.	.	.	A	14.74	2.625912	0.46840	.	.	ENSG00000099949	ENST00000539817;ENST00000215739;ENST00000389355	T;T	0.59083	0.7;0.29	5.57	4.52	0.55395	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.054362	0.85682	D	0.000000	T	0.66944	0.2841	L	0.47716	1.5	0.80722	D	1	P;B;P;D	0.63046	0.681;0.006;0.906;0.992	B;B;P;D	0.72982	0.437;0.016;0.6;0.979	T	0.66188	-0.5986	10	0.52906	T	0.07	-33.0173	10.1899	0.43019	0.8509:0.0:0.0:0.1491	.	464;442;483;442	B7Z3T9;Q6ZSY0;Q8N653;F5GXU8	.;.;LZTR1_HUMAN;.	L	442;483;464	ENSP00000215739:Q483L;ENSP00000374006:Q464L	ENSP00000215739:Q483L	Q	+	2	0	LZTR1	19678307	1.000000	0.71417	0.995000	0.50966	0.317000	0.28152	5.657000	0.67996	0.919000	0.36945	0.455000	0.32223	CAG	.	.		0.662	LZTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320387.1	NM_006767	Missense_Mutation	T	21348307	A	T	21348307	5	4	249	1	0	0	0	0	0	0	1	0	9146	202	7	4	1498	4	LZTR1	22	21348307	Splice_Site	SNP	A	TCGA-ED-A8O5-01A-11D-A35Z-10		21348307	29956259	112	33995										
EIF4ENIF1	56478	hgsc.bcm.edu	37	chr22	31851912	31851912	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	ttcctgatctgctcgggttaGagaaccacctactgaaccga	9	12	1	3			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chr22:31851912G>A	ENST00000397525.1	-	8	1248	c.1025C>T	c.(1024-1026)tCt>tTt	p.S342F	EIF4ENIF1_ENST00000344710.5_Missense_Mutation_p.S179F|EIF4ENIF1_ENST00000330125.5_Missense_Mutation_p.S342F|EIF4ENIF1_ENST00000382180.2_Missense_Mutation_p.S21F|RP11-247I13.11_ENST00000464523.1_RNA|EIF4ENIF1_ENST00000397523.1_Missense_Mutation_p.S342F	NM_001164501.1	NP_001157973.1	Q9NRA8	4ET_HUMAN	eukaryotic translation initiation factor 4E nuclear import factor 1	342						cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						GCTCGGGTTAGAGAACCACCT	0.448											OREG0003517	type=REGULATORY REGION|Gene=LOC486366|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.S342F		Atlas-SNP	.											.	EIF4ENIF1	80	.	0			c.C1025T						.						100	92	95					22																	31851912		2203	4300	6503	SO:0001583	missense	56478	exon8			GGGTTAGAGAACC	AF240775	CCDS13898.1, CCDS54520.1	22q11.2	2007-01-16			ENSG00000184708	ENSG00000184708			16687	protein-coding gene	gene with protein product		607445				10856257	Standard	NM_019843		Approved	4E-T, FLJ21601, Clast4, 2610509L04Rik	uc003akz.2	Q9NRA8	OTTHUMG00000030793	ENST00000397525.1:c.1025C>T	chr22.hg19:g.31851912G>A	ENSP00000380659:p.Ser342Phe	148.0	0.0	828	140.0	55.0	NM_019843	B1AKL2|B1AKL3|B2RBF1|Q8NCF2|Q9H708	Missense_Mutation	SNP	ENST00000397525.1	hg19	CCDS13898.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.962855	0.92791	.	.	ENSG00000184708	ENST00000344710;ENST00000397525;ENST00000330125;ENST00000397523;ENST00000382180;ENST00000420671	.	.	.	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.76630	0.4014	L	0.55481	1.735	0.80722	D	1	D;D;D;D	0.76494	0.998;0.999;0.999;0.999	D;D;D;D	0.87578	0.972;0.998;0.974;0.998	T	0.76386	-0.2978	9	0.66056	D	0.02	-15.3639	17.8153	0.88630	0.0:0.0:1.0:0.0	.	179;342;179;342	B1AKL3;Q9NRA8;Q9NRA8-2;B1AKL4	.;4ET_HUMAN;.;.	F	179;342;342;342;21;342	.	ENSP00000328103:S342F	S	-	2	0	EIF4ENIF1	30181912	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.291000	0.78721	2.885000	0.99019	0.655000	0.94253	TCT	.	.		0.448	EIF4ENIF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127926.1	NM_019843		A	31851912	G	A	31851912	3	1	249	1	0	0	0	0	1	0	0	0	5037	942	33	3	1983	3	EIF4ENIF1	22	31851912	Missense_Mutation	SNP	G	TCGA-ED-A8O5-01A-11D-A35Z-10	10503605	31851912	19452654	113	33996										
KAL1	3730	hgsc.bcm.edu	37	chrX	8667788	8667788	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	aaaccagggaaccattgttcTgcaaaaagaaaaaggaaaaa	8	6	1	1			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chrX:8667788T>C	ENST00000262648.3	-	2	357		c.e2-2			NM_000216.2	NP_000207.2	P23352	KALM_HUMAN	Kallmann syndrome 1 sequence						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|liver(1)|lung(6)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(1)	32						ACCATTGTTCTGCAAAAAGAA	0.294																																					.		Atlas-SNP	.											.	KAL1	78	.	0			c.208-2A>G						.						47	40	42					X																	8667788		2203	4300	6503	SO:0001630	splice_region_variant	3730	exon3			TTGTTCTGCAAAA		CCDS14130.1	Xp22.32	2013-02-11			ENSG00000011201	ENSG00000011201		"WAP four-disulfide core domain containing", "Fibronectin type III domain containing"	6211	protein-coding gene	gene with protein product	"anosmin-1", "WAP four-disulfide core domain 19"	300836		KAL, ADMLX		11463336	Standard	NM_000216		Approved	KALIG-1, WFDC19	uc004csf.3	P23352	OTTHUMG00000021107	ENST00000262648.3:c.208-2A>G	chrX.hg19:g.8667788T>C		866.0	0.0		683.0	242.0	NM_000216	B2RPF8	Splice_Site	SNP	ENST00000262648.3	hg19	CCDS14130.1	.	.	.	.	.	.	.	.	.	.	T	13.44	2.236625	0.39498	.	.	ENSG00000011201	ENST00000262648	.	.	.	4.56	4.56	0.56223	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.5529	0.45099	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	KAL1	8627788	1.000000	0.71417	0.981000	0.43875	0.682000	0.39822	4.227000	0.58612	1.498000	0.48600	0.417000	0.27973	.	.	.		0.294	KAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055692.1	NM_000216	Intron	C	8667788	T	C	8667788	5	2	249	1	0	0	0	0	0	0	1	0	7983	1594	55	2	1888	2	KAL1	23	8667788	Splice_Site	SNP	T	TCGA-ED-A8O5-01A-11D-A35Z-10		8667788	146602772	114	33997										
SCML2	10389	hgsc.bcm.edu	37	chrX	18276345	18276345	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	agatgagggccaaagtttccAtgtttgtttacatagacaca	9	7	0	3			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chrX:18276345A>G	ENST00000251900.4	-	10	1251	c.1092T>C	c.(1090-1092)caT>caC	p.H364H	SCML2_ENST00000398048.3_Silent_p.H100H	NM_006089.2	NP_006080.1	Q9UQR0	SCML2_HUMAN	sex comb on midleg-like 2 (Drosophila)	364					anatomical structure morphogenesis (GO:0009653)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|PcG protein complex (GO:0031519)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	36	Hepatocellular(33;0.183)					CAAAGTTTCCATGTTTGTTTA	0.443																																					p.H364H	Esophageal Squamous(100;1252 1965 19021 35517)	Atlas-SNP	.											.	SCML2	81	.	0			c.T1092C						.						84	82	82					X																	18276345		2203	4300	6503	SO:0001819	synonymous_variant	10389	exon10			GTTTCCATGTTTG	Y18004	CCDS14185.1	Xp22	2013-01-10	2001-11-28		ENSG00000102098	ENSG00000102098		"Sterile alpha motif (SAM) domain containing"	10581	protein-coding gene	gene with protein product		300208	"sex comb on midleg (Drosophila)-like 2"			10331946	Standard	NM_006089		Approved		uc004cyl.2	Q9UQR0	OTTHUMG00000021212	ENST00000251900.4:c.1092T>C	chrX.hg19:g.18276345A>G		413.0	0.0		314.0	135.0	NM_006089	Q5JXE6|Q86U98|Q8IWD0|Q8NDP2|Q9UGC5	Silent	SNP	ENST00000251900.4	hg19	CCDS14185.1																																																																																			.	.		0.443	SCML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055941.1	NM_006089		G	18276345	A	G	18276345	2	3	249	1	0	0	0	0	0	0	0	1	13925	214	8	2		2	SCML2	23	18276345	Silent	SNP	A	TCGA-ED-A8O5-01A-11D-A35Z-10	9608557	18276345	136994215	115	33998										
RPS6KA3	6197	hgsc.bcm.edu	37	chrX	20183141	20183141	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	gattaccagattcatccacaTaaagaatgttgctaggtttc	7	8	1	2			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chrX:20183141T>C	ENST00000379565.3	-	18	1847	c.1640A>G	c.(1639-1641)tAt>tGt	p.Y547C	RPS6KA3_ENST00000540702.1_Missense_Mutation_p.Y518C|RPS6KA3_ENST00000479809.1_Intron|RPS6KA3_ENST00000379548.4_Missense_Mutation_p.Y517C|RPS6KA3_ENST00000544447.1_Missense_Mutation_p.Y519C	NM_004586.2	NP_004577.1	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 3	547	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|central nervous system development (GO:0007417)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(14)|lung(7)|ovary(1)|stomach(1)	41					Acetylsalicylic acid(DB00945)	TTCATCCACATAAAGAATGTT	0.338																																					p.Y547C		Atlas-SNP	.											.	RPS6KA3	110	.	0			c.A1640G						.						92	85	88					X																	20183141		2203	4300	6503	SO:0001583	missense	6197	exon18			TCCACATAAAGAA	U08316	CCDS14197.1	Xp22.2-p22.1	2013-06-03	2002-08-29		ENSG00000177189	ENSG00000177189			10432	protein-coding gene	gene with protein product		300075	"ribosomal protein S6 kinase, 90kD, polypeptide 3", "mental retardation, X-linked 19", "Coffin-Lowry syndrome"	MRX19, CLS		8141249, 11896450, 16879200	Standard	XM_005274573		Approved	RSK, RSK2, HU-3	uc004czu.3	P51812	OTTHUMG00000021231	ENST00000379565.3:c.1640A>G	chrX.hg19:g.20183141T>C	ENSP00000368884:p.Tyr547Cys	456.0	0.0		348.0	145.0	NM_004586	B2R9V4|Q4VAP3|Q59H26|Q5JPK8|Q7Z3Z7	Missense_Mutation	SNP	ENST00000379565.3	hg19	CCDS14197.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.125108	0.77436	.	.	ENSG00000177189	ENST00000379565;ENST00000544447;ENST00000379548;ENST00000540702	T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14	5.57	5.57	0.84162	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.60261	0.2255	N	0.03224	-0.385	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.997;0.995;1.0;0.998	T	0.72510	-0.4271	10	0.87932	D	0	.	14.7398	0.69445	0.0:0.0:0.0:1.0	.	518;517;519;547	B4DG22;F5GYC4;B7ZB17;P51812	.;.;.;KS6A3_HUMAN	C	547;519;517;518	ENSP00000368884:Y547C;ENSP00000440220:Y519C;ENSP00000368865:Y517C;ENSP00000444837:Y518C	ENSP00000368865:Y517C	Y	-	2	0	RPS6KA3	20093062	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	1.862000	0.54008	0.486000	0.48141	TAT	.	.		0.338	RPS6KA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056011.3	NM_004586		C	20183141	T	C	20183141	3	2	249	1	0	0	0	0	1	0	0	0	13667	1406	49	2	602	2	RPS6KA3	23	20183141	Missense_Mutation	SNP	T	TCGA-ED-A8O5-01A-11D-A35Z-10	1906796	20183141	135087419	116	33999										
RPS6KA3	6197	hgsc.bcm.edu	37	chrX	20213230	20213230	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	gattaacctctaccaagataTcacgttccatttttgtccga	5	11	2	1			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chrX:20213230T>C	ENST00000379565.3	-	5	566	c.359A>G	c.(358-360)gAt>gGt	p.D120G	RPS6KA3_ENST00000540702.1_Missense_Mutation_p.D92G|RPS6KA3_ENST00000379548.4_Missense_Mutation_p.D91G|RPS6KA3_ENST00000544447.1_Missense_Mutation_p.D92G	NM_004586.2	NP_004577.1	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 3	120	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|central nervous system development (GO:0007417)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(14)|lung(7)|ovary(1)|stomach(1)	41					Acetylsalicylic acid(DB00945)	TACCAAGATATCACGTTCCAT	0.363																																					p.D120G		Atlas-SNP	.											.	RPS6KA3	110	.	0			c.A359G						.						182	141	155					X																	20213230		2203	4300	6503	SO:0001583	missense	6197	exon5			AAGATATCACGTT	U08316	CCDS14197.1	Xp22.2-p22.1	2013-06-03	2002-08-29		ENSG00000177189	ENSG00000177189			10432	protein-coding gene	gene with protein product		300075	"ribosomal protein S6 kinase, 90kD, polypeptide 3", "mental retardation, X-linked 19", "Coffin-Lowry syndrome"	MRX19, CLS		8141249, 11896450, 16879200	Standard	XM_005274573		Approved	RSK, RSK2, HU-3	uc004czu.3	P51812	OTTHUMG00000021231	ENST00000379565.3:c.359A>G	chrX.hg19:g.20213230T>C	ENSP00000368884:p.Asp120Gly	201.0	0.0		167.0	61.0	NM_004586	B2R9V4|Q4VAP3|Q59H26|Q5JPK8|Q7Z3Z7	Missense_Mutation	SNP	ENST00000379565.3	hg19	CCDS14197.1	.	.	.	.	.	.	.	.	.	.	T	18.51	3.639795	0.67244	.	.	ENSG00000177189	ENST00000379565;ENST00000544447;ENST00000379548;ENST00000540702;ENST00000457145;ENST00000438357	T;T;T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15;-0.15;-0.15	6.08	6.08	0.98989	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.69513	0.3119	L	0.27975	0.815	0.80722	D	1	B;B;D;B	0.89917	0.02;0.024;1.0;0.115	B;B;D;B	0.97110	0.033;0.095;1.0;0.211	T	0.72465	-0.4285	10	0.56958	D	0.05	.	15.4992	0.75684	0.0:0.0:0.0:1.0	.	92;91;92;120	B4DG22;F5GYC4;B7ZB17;P51812	.;.;.;KS6A3_HUMAN	G	120;92;91;92;91;92	ENSP00000368884:D120G;ENSP00000440220:D92G;ENSP00000368865:D91G;ENSP00000444837:D92G;ENSP00000407655:D91G;ENSP00000388512:D92G	ENSP00000368865:D91G	D	-	2	0	RPS6KA3	20123151	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	2.044000	0.60594	0.486000	0.48141	GAT	.	.		0.363	RPS6KA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056011.3	NM_004586		C	20213230	T	C	20213230	3	2	249	1	0	0	0	0	1	0	0	0	13667	1435	50	2	1935	2	RPS6KA3	23	20213230	Missense_Mutation	SNP	T	TCGA-ED-A8O5-01A-11D-A35Z-10	30089	20213230	135057330	117	34000										
DMD	1756	hgsc.bcm.edu	37	chrX	32663083	32663083	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	attaacgttttagtttacctCatgagtatgaaactggtctt	7	6	2	2			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chrX:32663083C>T	ENST00000357033.4	-	10	1353	c.1147G>A	c.(1147-1149)Gag>Aag	p.E383K	DMD_ENST00000378677.2_Missense_Mutation_p.E379K|DMD_ENST00000288447.4_Missense_Mutation_p.E375K	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	383					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.E378*(1)|p.E383*(1)|p.E379*(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				TAGTTTACCTCATGAGTATGA	0.353																																					p.E383K		Atlas-SNP	.											.	DMD	2127	.	3	Substitution - Nonsense(3)	lung(3)	c.G1147A						.						190	160	170					X																	32663083		2202	4300	6502	SO:0001583	missense	1756	exon10			TTACCTCATGAGT	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.1147G>A	chrX.hg19:g.32663083C>T	ENSP00000354923:p.Glu383Lys	164.0	0.0		134.0	62.0	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	hg19	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.166875	0.78339	.	.	ENSG00000198947	ENST00000534884;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280;ENST00000288447	T;T;T	0.47869	0.83;0.83;0.83	5.52	5.52	0.82312	.	0.000000	0.37437	U	0.002099	T	0.71324	0.3326	M	0.86953	2.85	0.80722	D	1	D;D;P;D;P	0.76494	0.96;0.999;0.944;0.996;0.955	D;D;P;D;P	0.83275	0.942;0.996;0.572;0.996;0.698	T	0.76361	-0.2987	10	0.87932	D	0	.	12.1871	0.54245	0.0:0.9198:0.0:0.0802	.	379;375;375;383;379	B1AK23;Q4G0X0;P11532-4;P11532;E9PDN5	.;.;.;DMD_HUMAN;.	K	375;379;383;383;260;375	ENSP00000367948:E379K;ENSP00000354923:E383K;ENSP00000288447:E375K	ENSP00000288447:E375K	E	-	1	0	DMD	32573004	1.000000	0.71417	1.000000	0.80357	0.516000	0.34256	7.670000	0.83925	2.458000	0.83093	0.600000	0.82982	GAG	.	.		0.353	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		T	32663083	C	T	32663083	3	4	249	1	0	0	0	0	1	0	0	0	4582	835	29	3	10433	3	DMD	23	32663083	Missense_Mutation	SNP	C	TCGA-ED-A8O5-01A-11D-A35Z-10	12449853	32663083	122607477	118	34001										
HUWE1	10075	hgsc.bcm.edu	37	chrX	53579727	53579727	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	tcagaactgccagctgctgaAgtgtcacccacagcctcctc	8	16	2	2			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chrX:53579727A>T	ENST00000342160.3	-	61	9079	c.8622T>A	c.(8620-8622)acT>acA	p.T2874T	HUWE1_ENST00000262854.6_Silent_p.T2874T			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	2874					base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						CAGCTGCTGAAGTGTCACCCA	0.587																																					p.T2874T		Atlas-SNP	.											.	HUWE1	724	.	0			c.T8622A						.						48	43	45					X																	53579727		2203	4300	6503	SO:0001819	synonymous_variant	10075	exon62			TGCTGAAGTGTCA	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"HECT, UBA and WWE domain containing 1"			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.8622T>A	chrX.hg19:g.53579727A>T		259.0	0.0		206.0	10.0	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Silent	SNP	ENST00000342160.3	hg19	CCDS35301.1	.	.	.	.	.	.	.	.	.	.	A	0.151	-1.091425	0.01858	.	.	ENSG00000086758	ENST00000427052	.	.	.	5.58	-1.93	0.07594	.	.	.	.	.	T	0.21022	0.0506	.	.	.	0.09310	N	0.999997	.	.	.	.	.	.	T	0.26815	-1.0092	4	.	.	.	.	3.4561	0.07516	0.4893:0.1069:0.2937:0.1101	.	.	.	.	I	1908	.	.	F	-	1	0	HUWE1	53596452	0.061000	0.20836	0.491000	0.27477	0.089000	0.18198	-0.345000	0.07770	-0.499000	0.06623	-1.028000	0.02416	TTC	.	.		0.587	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		T	53579727	A	T	53579727	2	4	249	1	0	0	0	0	0	0	0	1	7470	59	3	4		4	HUWE1	23	53579727	Silent	SNP	A	TCGA-ED-A8O5-01A-11D-A35Z-10	20916644	53579727	101690833	119	34002										
CXorf56	63932	hgsc.bcm.edu	37	chrX	118675326	118675326	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0416666666666667	5	1	0.774504980937154	1.21339113680154	0.710277738615536	0.265734265734266	0.917767417767419	0	cctcttgctcatgcctttgcGctccagctgtttttcaatca	6	14	4	0			TCGA-ED-A8O5-01A-11D-A35Z-10	TCGA-ED-A8O5-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a476994e-8feb-4689-b1fd-649179e672d6	c1d18b80-545a-4fe7-9486-6b7e8f52c426	g.chrX:118675326G>A	ENST00000371594.4	-	6	649	c.571C>T	c.(571-573)Cgc>Tgc	p.R191C	CXorf56_ENST00000320339.4_Missense_Mutation_p.R142C|CXorf56_ENST00000469448.1_5'UTR|CXorf56_ENST00000536133.1_Missense_Mutation_p.R177C	NM_022101.3	NP_071384.1	Q9H5V9	CX056_HUMAN	chromosome X open reading frame 56	191								p.R191G(1)		cervix(1)|endometrium(2)|lung(7)	10						ATGCCTTTGCGCTCCAGCTGT	0.493																																					p.R191C		Atlas-SNP	.											.	CXorf56	26	.	1	Substitution - Missense(1)	lung(1)	c.C571T						.						158	131	140					X																	118675326		2203	4300	6503	SO:0001583	missense	63932	exon6			CTTTGCGCTCCAG	AK026618	CCDS55484.1, CCDS55485.1	Xq24	2008-02-05			ENSG00000018610	ENSG00000018610			26239	protein-coding gene	gene with protein product						12477932	Standard	NM_022101		Approved	FLJ22965	uc004erk.2	Q9H5V9	OTTHUMG00000022276	ENST00000371594.4:c.571C>T	chrX.hg19:g.118675326G>A	ENSP00000360652:p.Arg191Cys	37.0	0.0		38.0	11.0	NM_022101	A8MPX7|B4DQN2|D3DWH9|F5GWL7|O43351	Missense_Mutation	SNP	ENST00000371594.4	hg19	CCDS14579.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.427213	0.83667	.	.	ENSG00000018610	ENST00000486230;ENST00000320339;ENST00000371594;ENST00000536133;ENST00000476164	T;T;T;T;T	0.27402	1.67;1.67;1.67;1.67;1.67	5.59	5.59	0.84812	.	0.045927	0.85682	N	0.000000	T	0.52092	0.1713	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.74348	0.983;0.983	T	0.54761	-0.8245	10	0.87932	D	0	-13.1368	12.233	0.54499	0.0:0.0:0.8302:0.1698	.	177;191	F5GWL7;Q9H5V9	.;CX056_HUMAN	C	191;142;191;177;191	ENSP00000420787:R191C;ENSP00000320345:R142C;ENSP00000360652:R191C;ENSP00000441786:R177C;ENSP00000420635:R191C	ENSP00000320345:R142C	R	-	1	0	CXorf56	118559354	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.285000	0.65633	2.352000	0.79861	0.597000	0.82753	CGC	.	.		0.493	CXorf56-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_022101		A	118675326	G	A	118675326	3	1	249	1	0	0	0	0	1	0	0	0	4114	1087	38	1	105	1	CXorf56	23	118675326	Missense_Mutation	SNP	G	TCGA-ED-A8O5-01A-11D-A35Z-10	65095599	118675326	36595234	120	34003										
ERRFI1	54206	hgsc.bcm.edu	37	chr1	8073831	8073831	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	acctcaggtttgtcttcatcGgagttaggagaagctctgtg	12	8	4	1			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr1:8073831G>A	ENST00000377482.5	-	4	1051	c.828C>T	c.(826-828)tcC>tcT	p.S276S	ERRFI1_ENST00000474874.1_Intron|ERRFI1_ENST00000467067.1_3'UTR|ERRFI1_ENST00000469499.1_3'UTR	NM_018948.3	NP_061821.1	Q9UJM3	ERRFI_HUMAN	ERBB receptor feedback inhibitor 1	276					lung alveolus development (GO:0048286)|lung epithelium development (GO:0060428)|lung vasculature development (GO:0060426)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of protein autophosphorylation (GO:0031953)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of keratinocyte differentiation (GO:0045616)|response to stress (GO:0006950)|skin morphogenesis (GO:0043589)	cytoplasm (GO:0005737)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|Rho GTPase activator activity (GO:0005100)			breast(1)|endometrium(2)|large_intestine(3)|liver(3)|lung(3)|ovary(1)|prostate(1)|skin(2)	16	Ovarian(185;0.06)|all_lung(157;0.151)	all_epithelial(116;1.76e-16)|all_lung(118;3.66e-05)|Lung NSC(185;0.000163)|Renal(390;0.000469)|Colorectal(325;0.0033)|Breast(348;0.0044)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.11)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;2.33e-70)|GBM - Glioblastoma multiforme(8;8.05e-37)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;6.9e-06)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.000985)|READ - Rectum adenocarcinoma(331;0.0642)		TGTCTTCATCGGAGTTAGGAG	0.473																																					p.S276S		Atlas-SNP	.											.	ERRFI1	42	.	0			c.C828T						.						98	101	100					1																	8073831		2203	4300	6503	SO:0001819	synonymous_variant	54206	exon4			TTCATCGGAGTTA	BC025337	CCDS94.1	1p36.23	2008-02-05			ENSG00000116285	ENSG00000116285			18185	protein-coding gene	gene with protein product		608069				10749885, 2780291, 12226756, 11003669	Standard	NM_018948		Approved	MIG-6, GENE-33, RALT	uc001aoz.3	Q9UJM3	OTTHUMG00000001221	ENST00000377482.5:c.828C>T	chr1.hg19:g.8073831G>A		161.0	0.0		68.0	44.0	NM_018948	B2RDX9|Q9NTG9|Q9UD05	Silent	SNP	ENST00000377482.5	hg19	CCDS94.1																																																																																			.	.		0.473	ERRFI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003617.1	NM_018948		A	8073831	G	A	8073831	2	1	250	1	0	0	0	0	0	0	0	1	5246	1103	39	1		1	ERRFI1	1	8073831	Silent	SNP	G	TCGA-ED-A8O6-01A-11D-A35Z-10		8073831	241176790	1	34004										
CDC42	998	hgsc.bcm.edu	37	chr1	22405002	22405002	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	ttaagtgtgttgttgtgggcGatggtgctgttggtaaaaca	15	3	0	0			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr1:22405002G>A	ENST00000344548.3	+	3	282	c.31G>A	c.(31-33)Gat>Aat	p.D11N	CDC42_ENST00000421089.2_De_novo_Start_OutOfFrame|CDC42_ENST00000400259.1_Missense_Mutation_p.D11N|CDC42_ENST00000498236.1_3'UTR|CDC42_ENST00000315554.8_Missense_Mutation_p.D11N	NM_001039802.1	NP_001034891.1	P60953	CDC42_HUMAN	cell division cycle 42	11					actin cytoskeleton organization (GO:0030036)|actin filament branching (GO:0090135)|actin filament bundle assembly (GO:0051017)|adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|canonical Wnt signaling pathway (GO:0060070)|cardiac conduction system development (GO:0003161)|cellular protein localization (GO:0034613)|dendritic cell migration (GO:0036336)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell-cell adhesion (GO:0090136)|epithelial-mesenchymal cell signaling (GO:0060684)|establishment of Golgi localization (GO:0051683)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|establishment or maintenance of cell polarity (GO:0007163)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|filopodium assembly (GO:0046847)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|heart contraction (GO:0060047)|innate immune response (GO:0045087)|keratinization (GO:0031424)|keratinocyte development (GO:0003334)|macrophage differentiation (GO:0030225)|multicellular organism growth (GO:0035264)|muscle cell differentiation (GO:0042692)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of gene expression (GO:0010629)|negative regulation of protein complex assembly (GO:0031333)|neuron fate determination (GO:0048664)|nuclear migration (GO:0007097)|nucleus localization (GO:0051647)|organelle transport along microtubule (GO:0072384)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of gene expression (GO:0010628)|positive regulation of hair follicle cell proliferation (GO:0071338)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of JNK cascade (GO:0046330)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of synapse structural plasticity (GO:0051835)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of filopodium assembly (GO:0051489)|regulation of mitosis (GO:0007088)|regulation of protein catabolic process (GO:0042176)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein kinase activity (GO:0045859)|regulation of protein stability (GO:0031647)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|sprouting angiogenesis (GO:0002040)|submandibular salivary gland formation (GO:0060661)|substantia nigra development (GO:0021762)|T cell costimulation (GO:0031295)	apical part of cell (GO:0045177)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|leading edge membrane (GO:0031256)|membrane (GO:0016020)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|spindle midzone (GO:0051233)	apolipoprotein A-I receptor binding (GO:0034191)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|protein kinase binding (GO:0019901)|thioesterase binding (GO:0031996)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(4)	12		Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;6.55e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)|Prostate(1639;0.0792)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0452)|OV - Ovarian serous cystadenocarcinoma(117;7.32e-26)|Colorectal(126;1.35e-07)|COAD - Colon adenocarcinoma(152;7.73e-06)|GBM - Glioblastoma multiforme(114;8.62e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000649)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00767)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.207)		TGTTGTGGGCGATGGTGCTGT	0.358																																					p.D11N		Atlas-SNP	.											.	CDC42	26	.	0			c.G31A						.						111	102	105					1																	22405002		2203	4300	6503	SO:0001583	missense	998	exon3			GTGGGCGATGGTG	BC018266	CCDS221.1, CCDS222.1	1p36.1	2013-01-17	2013-01-17		ENSG00000070831	ENSG00000070831			1736	protein-coding gene	gene with protein product	"GTP binding protein, 25kDa"	116952	"cell division cycle 42 (GTP-binding protein, 25kD)", "cell division cycle 42 (GTP binding protein, 25kDa)"			2124704, 2122236	Standard	NM_001039802		Approved	G25K, CDC42Hs	uc001bfr.3	P60953	OTTHUMG00000002753	ENST00000344548.3:c.31G>A	chr1.hg19:g.22405002G>A	ENSP00000341072:p.Asp11Asn	103.0	0.0		42.0	27.0	NM_001039802	P21181|P25763|Q7L8R5|Q9UDI2	Missense_Mutation	SNP	ENST00000344548.3	hg19	CCDS221.1	.	.	.	.	.	.	.	.	.	.	g	32	5.190950	0.94923	.	.	ENSG00000070831	ENST00000400259;ENST00000344548;ENST00000315554;ENST00000411827	T;T;T;T	0.80123	-1.34;-1.34;-1.34;-1.34	4.91	4.91	0.64330	Small GTP-binding protein domain (1);	0.123452	0.64402	D	0.000019	D	0.92580	0.7643	H	0.95712	3.71	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.75020	0.969;0.985;0.917	D	0.94755	0.7931	10	0.72032	D	0.01	.	16.6589	0.85236	0.0:0.0:1.0:0.0	.	11;11;11	B4E1U9;P60953;P60953-1	.;CDC42_HUMAN;.	N	11	ENSP00000383118:D11N;ENSP00000341072:D11N;ENSP00000314458:D11N;ENSP00000398327:D11N	ENSP00000314458:D11N	D	+	1	0	CDC42	22277589	1.000000	0.71417	0.998000	0.56505	0.975000	0.68041	9.123000	0.94387	2.287000	0.76781	0.650000	0.86243	GAT	.	.		0.358	CDC42-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000007787.1	NM_001791		A	22405002	G	A	22405002	3	1	250	1	0	0	0	0	1	0	0	0	3073	1058	37	1	33	1	CDC42	1	22405002	Missense_Mutation	SNP	G	TCGA-ED-A8O6-01A-11D-A35Z-10	14331171	22405002	226845619	2	34005										
SNIP1	79753	hgsc.bcm.edu	37	chr1	38006245	38006245	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	agacgttctcctttggtgggAatggccccggtgtctgtccc	13	12	2	1			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr1:38006245A>C	ENST00000296215.6	-	3	511	c.439T>G	c.(439-441)Tcc>Gcc	p.S147A	SNIP1_ENST00000468040.1_5'UTR	NM_024700.3	NP_078976.2	Q8TAD8	SNIP1_HUMAN	Smad nuclear interacting protein 1	147	Arg-rich.				I-kappaB kinase/NF-kappaB signaling (GO:0007249)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(2)|endometrium(1)|large_intestine(3)|lung(15)|ovary(1)|upper_aerodigestive_tract(1)	25		Myeloproliferative disorder(586;0.0393)				CTTTGGTGGGAATGGCCCCGG	0.607																																					p.S147A		Atlas-SNP	.											.	SNIP1	44	.	0			c.T439G						.						129	132	131					1																	38006245		2203	4300	6503	SO:0001583	missense	79753	exon3			GGTGGGAATGGCC		CCDS419.1	1p34.3	2010-07-06			ENSG00000163877	ENSG00000163877			30587	protein-coding gene	gene with protein product		608241				10887155, 15378006	Standard	NM_024700		Approved		uc001cbi.4	Q8TAD8	OTTHUMG00000004225	ENST00000296215.6:c.439T>G	chr1.hg19:g.38006245A>C	ENSP00000296215:p.Ser147Ala	83.0	0.0		48.0	20.0	NM_024700	Q96SP9|Q9H9T7	Missense_Mutation	SNP	ENST00000296215.6	hg19	CCDS419.1	.	.	.	.	.	.	.	.	.	.	A	8.391	0.839715	0.16891	.	.	ENSG00000163877	ENST00000296215;ENST00000436196	T	0.13778	2.56	5.25	0.0644	0.14353	.	0.440058	0.25055	N	0.033490	T	0.05410	0.0143	N	0.14661	0.345	0.09310	N	0.999995	B	0.02656	0.0	B	0.04013	0.001	T	0.35151	-0.9800	10	0.19590	T	0.45	-7.4856	2.5092	0.04652	0.5316:0.2299:0.1279:0.1107	.	147	Q8TAD8	SNIP1_HUMAN	A	147;131	ENSP00000296215:S147A	ENSP00000296215:S147A	S	-	1	0	SNIP1	37778832	0.877000	0.30153	0.911000	0.35937	0.461000	0.32589	0.347000	0.20014	-0.147000	0.11254	-0.290000	0.09829	TCC	.	.		0.607	SNIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012169.2	NM_024700		C	38006245	A	C	38006245	3	2	250	1	0	0	0	0	1	0	0	0	14863	246	9	5	759	5	SNIP1	1	38006245	Missense_Mutation	SNP	A	TCGA-ED-A8O6-01A-11D-A35Z-10	15601243	38006245	211244376	3	34006										
MACF1	23499	hgsc.bcm.edu	37	chr1	39789908	39789908	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	agaacatgtggagaaggttaAagaacttttgggctgggtgt	15	3	0	3			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr1:39789908A>G	ENST00000372915.3	+	33	4382	c.4295A>G	c.(4294-4296)aAa>aGa	p.K1432R	MACF1_ENST00000539005.1_Missense_Mutation_p.K1432R|MACF1_ENST00000545844.1_Missense_Mutation_p.K1432R|MACF1_ENST00000567887.1_Missense_Mutation_p.K1464R|MACF1_ENST00000361689.2_Missense_Mutation_p.K1432R|MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000317713.7_Missense_Mutation_p.K1432R|MACF1_ENST00000564288.1_Missense_Mutation_p.K1427R			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	1432					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			GAGAAGGTTAAAGAACTTTTG	0.398																																					p.K1432R		Atlas-SNP	.											.	MACF1	909	.	0			c.A4295G						.						96	91	93					1																	39789908		2203	4300	6503	SO:0001583	missense	23499	exon35			AGGTTAAAGAACT	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.4295A>G	chr1.hg19:g.39789908A>G	ENSP00000362006:p.Lys1432Arg	331.0	0.0		200.0	31.0	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	hg19		.	.	.	.	.	.	.	.	.	.	A	20.9	4.063129	0.76187	.	.	ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000530262	T;T;T;T;T;T	0.63580	0.0;-0.05;0.0;-0.03;0.16;1.96	6.16	6.16	0.99307	.	.	.	.	.	T	0.71126	0.3303	M	0.61703	1.905	0.80722	D	1	D;D;B	0.56521	0.976;0.959;0.016	P;P;B	0.59115	0.852;0.488;0.022	T	0.71297	-0.4635	9	0.40728	T	0.16	.	10.762	0.46270	0.9293:0.0:0.0707:0.0	.	1432;1432;1397	F8W8Q1;Q9UPN3-2;Q9UPN3-3	.;.;.	R	1432;1432;1432;1432;1432;1581	ENSP00000439537:K1432R;ENSP00000362006:K1432R;ENSP00000354573:K1432R;ENSP00000313438:K1432R;ENSP00000444364:K1432R;ENSP00000437059:K1581R	ENSP00000313438:K1432R	K	+	2	0	MACF1	39562495	1.000000	0.71417	1.000000	0.80357	0.837000	0.47467	5.626000	0.67777	2.367000	0.80283	0.528000	0.53228	AAA	.	.		0.398	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		G	39789908	A	G	39789908	3	3	250	1	0	0	0	0	1	0	0	0	9153	14	1	2	4425	2	MACF1	1	39789908	Missense_Mutation	SNP	A	TCGA-ED-A8O6-01A-11D-A35Z-10	1783663	39789908	209460713	4	34007										
CTH	1491	hgsc.bcm.edu	37	chr1	70899550	70899550	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	gcatgagttggtgaagcgtcAgtgtacaggttgtacaggga	16	5	1	2			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr1:70899550A>T	ENST00000370938.3	+	9	1061	c.917A>T	c.(916-918)cAg>cTg	p.Q306L	CTH_ENST00000346806.2_Missense_Mutation_p.Q262L|CTH_ENST00000411986.2_Missense_Mutation_p.Q274L	NM_001902.5	NP_001893.2	Q96IQ7	VSIG2_HUMAN	cystathionine gamma-lyase	0						integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						GTGAAGCGTCAGTGTACAGGT	0.408																																					p.Q306L		Atlas-SNP	.											.	CTH	48	.	0			c.A917T						.						122	107	112					1																	70899550		2203	4300	6503	SO:0001583	missense	1491	exon9			AGCGTCAGTGTAC	BC015807	CCDS650.1, CCDS651.1, CCDS53333.1	1p31.1	2014-06-24	2014-06-24		ENSG00000116761	ENSG00000116761	4.4.1.1		2501	protein-coding gene	gene with protein product		607657	"cystathionase (cystathionine gamma-lyase)"			1339280	Standard	NM_001902		Approved		uc001dfd.3	P32929	OTTHUMG00000009352	ENST00000370938.3:c.917A>T	chr1.hg19:g.70899550A>T	ENSP00000359976:p.Gln306Leu	82.0	0.0		50.0	8.0	NM_001902	O95791|Q9NX42	Missense_Mutation	SNP	ENST00000370938.3	hg19	CCDS650.1	.	.	.	.	.	.	.	.	.	.	A	26.5	4.740552	0.89573	.	.	ENSG00000116761	ENST00000411986;ENST00000370938;ENST00000346806	D;D;D	0.82255	-1.59;-1.59;-1.59	5.01	5.01	0.66863	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.139623	0.53938	D	0.000042	D	0.88444	0.6438	M	0.80422	2.495	0.80722	D	1	P;P;D	0.63046	0.932;0.917;0.992	P;P;D	0.62955	0.708;0.657;0.909	D	0.90431	0.4424	10	0.87932	D	0	-14.7489	14.7337	0.69402	1.0:0.0:0.0:0.0	.	274;262;306	E9PDV0;P32929-2;P32929	.;.;CGL_HUMAN	L	274;306;262	ENSP00000413407:Q274L;ENSP00000359976:Q306L;ENSP00000311554:Q262L	ENSP00000311554:Q262L	Q	+	2	0	CTH	70672138	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	9.117000	0.94347	2.033000	0.60031	0.529000	0.55759	CAG	.	.		0.408	CTH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025918.1	NM_001902		T	70899550	A	T	70899550	3	4	250	1	0	0	0	0	1	0	0	0	4011	188	7	4	951	4	CTH	1	70899550	Missense_Mutation	SNP	A	TCGA-ED-A8O6-01A-11D-A35Z-10	31109642	70899550	178351071	5	34008										
CLCA2	9635	hgsc.bcm.edu	37	chr1	86916392	86916392	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	ttccagggagtcatgctatgTatgtaccaggttacacagca	10	9	1	0			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr1:86916392T>A	ENST00000370565.4	+	12	2293	c.2131T>A	c.(2131-2133)Tat>Aat	p.Y711N	CLCA2_ENST00000498802.1_3'UTR	NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	711					cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)			NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		TCATGCTATGTATGTACCAGG	0.438																																					p.Y711N	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											.	CLCA2	102	.	0			c.T2131A						.						151	137	142					1																	86916392		2203	4300	6503	SO:0001583	missense	9635	exon12			GCTATGTATGTAC		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"chloride channel, calcium activated, family member 2", "chloride channel regulator 2"				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.2131T>A	chr1.hg19:g.86916392T>A	ENSP00000359596:p.Tyr711Asn	99.0	0.0		67.0	40.0	NM_006536	A8K2T3|Q9Y6N2	Missense_Mutation	SNP	ENST00000370565.4	hg19	CCDS708.1	.	.	.	.	.	.	.	.	.	.	T	19.55	3.848725	0.71603	.	.	ENSG00000137975	ENST00000370565	T	0.03212	4.01	5.36	4.24	0.50183	.	0.076637	0.53938	D	0.000050	T	0.12817	0.0311	M	0.89968	3.075	0.46542	D	0.999091	D	0.89917	1.0	D	0.87578	0.998	T	0.00855	-1.1539	10	0.66056	D	0.02	-10.3746	10.6832	0.45826	0.0:0.0757:0.0:0.9243	.	711	Q9UQC9	CLCA2_HUMAN	N	711	ENSP00000359596:Y711N	ENSP00000359596:Y711N	Y	+	1	0	CLCA2	86688980	1.000000	0.71417	0.983000	0.44433	0.989000	0.77384	3.442000	0.52900	0.898000	0.36418	0.528000	0.53228	TAT	.	.		0.438	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536		A	86916392	T	A	86916392	3	1	250	1	0	0	0	0	1	0	0	0	3460	1638	57	4	2177	4	CLCA2	1	86916392	Missense_Mutation	SNP	T	TCGA-ED-A8O6-01A-11D-A35Z-10	16016842	86916392	162334229	6	34009										
DENND2C	163259	hgsc.bcm.edu	37	chr1	115144131	115144131	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	agctcattctccactcacctTtgaaaaaagattgaagcagc	6	11	3	3			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr1:115144131T>A	ENST00000393274.1	-	13	2438	c.1813A>T	c.(1813-1815)Aag>Tag	p.K605*	DENND2C_ENST00000393276.3_Nonsense_Mutation_p.K548*|DENND2C_ENST00000481894.1_5'UTR|DENND2C_ENST00000393277.1_Nonsense_Mutation_p.K605*	NM_001256404.1	NP_001243333.1	Q68D51	DEN2C_HUMAN	DENN/MADD domain containing 2C	605	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|breast(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|skin(3)	37	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		CCACTCACCTTTGAAAAAAGA	0.393																																					p.K605X		Atlas-SNP	.											.	DENND2C	105	.	0			c.A1813T						.						216	231	226					1																	115144131		2203	4300	6503	SO:0001587	stop_gained	163259	exon13			TCACCTTTGAAAA		CCDS875.1, CCDS58018.1	1p13.2-p13.1	2012-10-03			ENSG00000175984	ENSG00000175984		"DENN/MADD domain containing"	24748	protein-coding gene	gene with protein product							Standard	NM_198459		Approved	FLJ37099, DKFZp686G0351, DKFZp779P1149, dJ1156J9.1, RP5-1156J9.1	uc001efd.1	Q68D51	OTTHUMG00000011893	ENST00000393274.1:c.1813A>T	chr1.hg19:g.115144131T>A	ENSP00000376955:p.Lys605*	451.0	0.0		263.0	121.0	NM_001256404	B1AL26|Q5TCX6|Q6P3R3	Nonsense_Mutation	SNP	ENST00000393274.1	hg19	CCDS58018.1	.	.	.	.	.	.	.	.	.	.	T	45	11.909491	0.99616	.	.	ENSG00000175984	ENST00000393276;ENST00000393274;ENST00000369540;ENST00000393277	.	.	.	5.54	5.54	0.83059	.	0.046307	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.73	0.77794	0.0:0.0:0.0:1.0	.	.	.	.	X	548;605;605;605	.	ENSP00000358553:K605X	K	-	1	0	DENND2C	114945654	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.403000	0.79983	2.129000	0.65627	0.477000	0.44152	AAG	.	.		0.393	DENND2C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000314822.1	NM_198459		A	115144131	T	A	115144131	4	1	250	1	0	0	0	0	0	1	0	0	4432	1850	64	4	1009	4	DENND2C	1	115144131	Nonsense_Mutation	SNP	T	TCGA-ED-A8O6-01A-11D-A35Z-10	28227739	115144131	134106490	7	34010										
KCNN3	3782	hgsc.bcm.edu	37	chr1	154842253	154842253	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	gctgctgctgaagctgcggaGgctgaggctgcagcgagggt	19	9	0	2			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr1:154842253G>T	ENST00000271915.4	-	1	503	c.188C>A	c.(187-189)cCt>cAt	p.P63H	KCNN3_ENST00000358505.2_5'Flank	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	63	Gln-rich.|Pro-rich.				potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	aagctgcggaggctgaggctg	0.697																																					p.P63H		Atlas-SNP	.											.	KCNN3	141	.	0			c.C188A						.						6	4	5					1																	154842253		1984	3925	5909	SO:0001583	missense	3782	exon1			TGCGGAGGCTGAG	AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.188C>A	chr1.hg19:g.154842253G>T	ENSP00000271915:p.Pro63His	57.0	0.0		75.0	7.0	NM_001204087	B1ANX0|O43517|Q86VF9|Q8WXG7	Missense_Mutation	SNP	ENST00000271915.4	hg19	CCDS30880.1	.	.	.	.	.	.	.	.	.	.	g	11.14	1.552427	0.27739	.	.	ENSG00000143603	ENST00000271915;ENST00000539103	T	0.56275	0.47	5.07	3.18	0.36537	.	1.727610	0.03258	N	0.182822	T	0.18551	0.0445	N	0.08118	0	0.80722	D	1	.	.	.	.	.	.	T	0.11372	-1.0590	8	0.33141	T	0.24	-4.1487	6.4327	0.21807	0.0918:0.0:0.7284:0.1798	.	.	.	.	H	63;158	ENSP00000271915:P63H	ENSP00000271915:P63H	P	-	2	0	KCNN3	153108877	0.863000	0.29885	1.000000	0.80357	0.998000	0.95712	1.873000	0.39558	0.823000	0.34589	0.563000	0.77884	CCT	.	.		0.697	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249		T	154842253	G	T	154842253	3	4	250	1	0	0	0	0	1	0	0	0	8089	1000	35	3	2061	3	KCNN3	1	154842253	Missense_Mutation	SNP	G	TCGA-ED-A8O6-01A-11D-A35Z-10	39698122	154842253	94408368	8	34011										
BCAN	63827	hgsc.bcm.edu	37	chr1	156616637	156616637	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	tcgcgggcgacgcgccactgCagggcgtgctcggcggcgcc	18	16	0	0			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr1:156616637C>A	ENST00000329117.5	+	3	472	c.136C>A	c.(136-138)Cag>Aag	p.Q46K	RP11-284F21.10_ENST00000605886.1_RNA|BCAN_ENST00000361588.5_Missense_Mutation_p.Q46K|RP11-284F21.7_ENST00000448869.1_RNA	NM_021948.4	NP_068767.3	Q96GW7	PGCB_HUMAN	brevican	46	Ig-like V-type.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hippocampus development (GO:0021766)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	55	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CGCGCCACTGCAGGGCGTGCT	0.706																																					p.Q46K		Atlas-SNP	.											.	BCAN	174	.	0			c.C136A						.						15	18	17					1																	156616637		2176	4242	6418	SO:0001583	missense	63827	exon3			CCACTGCAGGGCG	BC027971	CCDS1149.1, CCDS1150.1	1q31	2013-05-07			ENSG00000132692	ENSG00000132692		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	23059	protein-coding gene	gene with protein product	"chondroitin sulfate proteoglycan 7", "brevican proteoglycan"	600347				11054543, 11873941	Standard	NM_021948		Approved	BEHAB, MGC13038, CSPG7	uc001fpp.3	Q96GW7	OTTHUMG00000033322	ENST00000329117.5:c.136C>A	chr1.hg19:g.156616637C>A	ENSP00000331210:p.Gln46Lys	156.0	0.0		159.0	107.0	NM_198427	D3DVC2|Q5SZ10|Q5T3I5|Q8TBB9|Q9HBK1|Q9HBK4	Missense_Mutation	SNP	ENST00000329117.5	hg19	CCDS1149.1	.	.	.	.	.	.	.	.	.	.	C	6.116	0.389604	0.11581	.	.	ENSG00000132692	ENST00000441358;ENST00000255029;ENST00000329117;ENST00000457777;ENST00000361588	T;T;T;T	0.64803	-0.12;-0.12;-0.12;-0.12	4.41	4.41	0.53225	Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	0.691681	0.13058	N	0.417098	T	0.17789	0.0427	N	0.05230	-0.09	0.09310	N	1	B;B	0.20261	0.043;0.002	B;B	0.20577	0.03;0.012	T	0.11397	-1.0589	10	0.11485	T	0.65	-0.9574	9.7176	0.40284	0.2067:0.7932:0.0:0.0	.	46;46	Q96GW7;Q96GW7-2	PGCB_HUMAN;.	K	46	ENSP00000392731:Q46K;ENSP00000331210:Q46K;ENSP00000389898:Q46K;ENSP00000354925:Q46K	ENSP00000255029:Q46K	Q	+	1	0	BCAN	154883261	0.899000	0.30636	0.950000	0.38849	0.034000	0.12701	1.857000	0.39399	2.272000	0.75746	0.462000	0.41574	CAG	.	.		0.706	BCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081844.2	NM_021948		A	156616637	C	A	156616637	3	1	250	1	0	0	0	0	1	0	0	0	1345	711	25	3	142	3	BCAN	1	156616637	Missense_Mutation	SNP	C	TCGA-ED-A8O6-01A-11D-A35Z-10	1774384	156616637	92633984	9	34012										
HMCN1	83872	hgsc.bcm.edu	37	chr1	185972870	185972870	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	ttccacccaccataataggtAccaacttcccaaatgaagtc	4	14	0	1			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr1:185972870A>G	ENST00000271588.4	+	29	4598	c.4369A>G	c.(4369-4371)Acc>Gcc	p.T1457A	HMCN1_ENST00000367492.2_Missense_Mutation_p.T1457A	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	1457	Ig-like C2-type 12.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						CATAATAGGTACCAACTTCCC	0.438																																					p.T1457A		Atlas-SNP	.											.	HMCN1	797	.	0			c.A4369G						.						168	149	155					1																	185972870		2203	4300	6503	SO:0001583	missense	83872	exon29			ATAGGTACCAACT	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.4369A>G	chr1.hg19:g.185972870A>G	ENSP00000271588:p.Thr1457Ala	137.0	0.0		104.0	38.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	A	0.139	-1.104657	0.01828	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.64438	-0.1;-0.09	5.86	2.99	0.34606	Immunoglobulin-like (1);	0.270150	0.42964	N	0.000631	T	0.28896	0.0717	N	0.02296	-0.605	0.32626	N	0.522626	B	0.02656	0.0	B	0.04013	0.001	T	0.36089	-0.9762	10	0.05525	T	0.97	.	9.3547	0.38159	0.2239:0.0:0.7761:0.0	.	1457	Q96RW7	HMCN1_HUMAN	A	1457	ENSP00000271588:T1457A;ENSP00000356462:T1457A	ENSP00000271588:T1457A	T	+	1	0	HMCN1	184239493	1.000000	0.71417	0.840000	0.33206	0.336000	0.28762	2.370000	0.44240	0.388000	0.25054	-0.248000	0.11899	ACC	.	.		0.438	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		G	185972870	A	G	185972870	3	3	250	1	0	0	0	0	1	0	0	0	7229	391	14	2	4483	2	HMCN1	1	185972870	Missense_Mutation	SNP	A	TCGA-ED-A8O6-01A-11D-A35Z-10	29356233	185972870	63277751	10	34013										
HMCN1	83872	hgsc.bcm.edu	37	chr1	185988695	185988695	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	cctccaacaatcaagtcctcAggcctttctgagagagttgt	8	12	3	2			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr1:185988695A>G	ENST00000271588.4	+	35	5722	c.5493A>G	c.(5491-5493)tcA>tcG	p.S1831S	HMCN1_ENST00000367492.2_Silent_p.S1831S	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	1831	Ig-like C2-type 16.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TCAAGTCCTCAGGCCTTTCTG	0.423																																					p.S1831S		Atlas-SNP	.											.	HMCN1	797	.	0			c.A5493G						.						101	102	101					1																	185988695		2203	4299	6502	SO:0001819	synonymous_variant	83872	exon35			GTCCTCAGGCCTT	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.5493A>G	chr1.hg19:g.185988695A>G		107.0	0.0		92.0	23.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	hg19	CCDS30956.1																																																																																			.	.		0.423	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		G	185988695	A	G	185988695	2	3	250	1	0	0	0	0	0	0	0	1	7229	175	7	2		2	HMCN1	1	185988695	Silent	SNP	A	TCGA-ED-A8O6-01A-11D-A35Z-10	15825	185988695	63261926	11	34014										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186157140	186157140	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	accaacgggatcctgtttcaGggtatgtcttgccttctcat	9	11	3	0			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr1:186157140G>C	ENST00000271588.4	+	106	16769	c.16540G>C	c.(16540-16542)Ggg>Cgg	p.G5514R	HMCN1_ENST00000367492.2_Splice_Site_p.G5397R	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	5514					response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TCCTGTTTCAGGGTATGTCTT	0.478																																					p.G5514R		Atlas-SNP	.											.	HMCN1	797	.	0			c.G16540C						.						303	227	253					1																	186157140		2203	4300	6503	SO:0001630	splice_region_variant	83872	exon106			GTTTCAGGGTATG	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.16541+1G>C	chr1.hg19:g.186157140G>C		99.0	0.0		99.0	17.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	G	32	5.160114	0.94727	.	.	ENSG00000143341	ENST00000271588;ENST00000367492;ENST00000414277	D;D;D	0.87412	-2.25;-2.25;-2.25	5.71	5.71	0.89125	Growth factor, receptor (1);Epidermal growth factor-like (1);	0.000000	0.85682	D	0.000000	D	0.90501	0.7024	L	0.50333	1.59	0.49798	D	0.999824	D	0.69078	0.997	P	0.57057	0.812	D	0.90424	0.4419	10	0.56958	D	0.05	.	19.8772	0.96880	0.0:0.0:1.0:0.0	.	5514	Q96RW7	HMCN1_HUMAN	R	5514;5397;189	ENSP00000271588:G5514R;ENSP00000356462:G5397R;ENSP00000406205:G189R	ENSP00000271588:G5514R	G	+	1	0	HMCN1	184423763	1.000000	0.71417	0.964000	0.40570	0.835000	0.47333	8.000000	0.88501	2.686000	0.91538	0.650000	0.86243	GGG	.	.		0.478	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	Missense_Mutation	C	186157140	G	C	186157140	5	2	250	1	0	0	0	0	0	0	1	0	7229	1014	35	4	16962	4	HMCN1	1	186157140	Splice_Site	SNP	G	TCGA-ED-A8O6-01A-11D-A35Z-10	168445	186157140	63093481	12	34015										
LAMB3	3914	hgsc.bcm.edu	37	chr1	209796353	209796353	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	cctggtccgctggagctgggCattgaagccccgcagctgct	14	14	0	1			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr1:209796353C>T	ENST00000356082.4	-	17	2664	c.2530G>A	c.(2530-2532)Gcc>Acc	p.A844T	LAMB3_ENST00000367030.3_Missense_Mutation_p.A844T|LAMB3_ENST00000391911.1_Missense_Mutation_p.A844T|MIR4260_ENST00000583107.1_RNA	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	844	Domain I.				brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	extracellular region (GO:0005576)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		TGGAGCTGGGCATTGAAGCCC	0.672																																					p.A844T		Atlas-SNP	.											.	LAMB3	136	.	0			c.G2530A						.						65	77	73					1																	209796353		2203	4299	6502	SO:0001583	missense	3914	exon17			GCTGGGCATTGAA	D37766	CCDS1487.1	1q32	2013-03-01	2002-08-29		ENSG00000196878	ENSG00000196878		"Laminins"	6490	protein-coding gene	gene with protein product		150310	"laminin, beta 3 (nicein (125kD), kalinin (140kD), BM600 (125kD))"	LAMNB1		8088808, 7774918	Standard	NM_001127641		Approved	nicein-125kDa, kalinin-140kDa, BM600-125kDa	uc001hhh.3	Q13751	OTTHUMG00000036360	ENST00000356082.4:c.2530G>A	chr1.hg19:g.209796353C>T	ENSP00000348384:p.Ala844Thr	137.0	0.0		131.0	46.0	NM_000228	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Missense_Mutation	SNP	ENST00000356082.4	hg19	CCDS1487.1	.	.	.	.	.	.	.	.	.	.	C	7.810	0.715425	0.15306	.	.	ENSG00000196878	ENST00000391911;ENST00000356082;ENST00000367030	T;T;T	0.21361	2.01;2.01;2.01	5.21	-6.23	0.02052	.	0.891913	0.09984	N	0.730574	T	0.08088	0.0202	N	0.20685	0.6	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.35674	-0.9779	10	0.14252	T	0.57	.	2.0835	0.03640	0.24:0.1972:0.0966:0.4662	.	844	Q13751	LAMB3_HUMAN	T	844	ENSP00000375778:A844T;ENSP00000348384:A844T;ENSP00000355997:A844T	ENSP00000348384:A844T	A	-	1	0	LAMB3	207862976	0.000000	0.05858	0.001000	0.08648	0.600000	0.36913	-1.075000	0.03423	-1.857000	0.01159	0.456000	0.33151	GCC	.	.		0.672	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228		T	209796353	C	T	209796353	3	4	250	1	0	0	0	0	1	0	0	0	8621	710	25	3	1016	3	LAMB3	1	209796353	Missense_Mutation	SNP	C	TCGA-ED-A8O6-01A-11D-A35Z-10	23639213	209796353	39454268	13	34016										
SIX3	6496	hgsc.bcm.edu	37	chr2	45171797	45171797	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	tcggcagagtcgccgtccacGgcggccagcccgaccaccag	13	18	0	1			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr2:45171797G>A	ENST00000260653.3	+	2	1239	c.897G>A	c.(895-897)acG>acA	p.T299T	SIX3-AS1_ENST00000419364.1_RNA	NM_005413.3	NP_005404.1	O95343	SIX3_HUMAN	SIX homeobox 3	299					brain development (GO:0007420)|circadian behavior (GO:0048512)|diencephalon development (GO:0021536)|eye development (GO:0001654)|forebrain anterior/posterior pattern specification (GO:0021797)|forebrain dorsal/ventral pattern formation (GO:0021798)|lens induction in camera-type eye (GO:0060235)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|protein import into nucleus (GO:0006606)|telencephalon development (GO:0021537)|visual perception (GO:0007601)	nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|transcription corepressor binding (GO:0001222)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|skin(1)	11		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				CGCCGTCCACGGCGGCCAGCC	0.697																																					p.T299T		Atlas-SNP	.											.	SIX3	24	.	0			c.G897A						.						9	11	10					2																	45171797		1976	3947	5923	SO:0001819	synonymous_variant	6496	exon2			GTCCACGGCGGCC	AF092047	CCDS1821.1	2p21	2011-06-20	2007-07-13		ENSG00000138083	ENSG00000138083		"Homeoboxes / SINE class"	10889	protein-coding gene	gene with protein product		603714	"holoprosencephaly 2, alobar or semilobar", "sine oculis homeobox homolog 3 (Drosophila)"	HPE2		9889003, 10369266	Standard	NM_005413		Approved		uc002run.2	O95343	OTTHUMG00000152424	ENST00000260653.3:c.897G>A	chr2.hg19:g.45171797G>A		322.0	0.0		205.0	43.0	NM_005413	D6W5A5|Q53T42	Silent	SNP	ENST00000260653.3	hg19	CCDS1821.1																																																																																			.	.		0.697	SIX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326192.1	NM_005413		A	45171797	G	A	45171797	2	1	250	1	0	0	0	0	0	0	0	1	14363	1103	39	1		1	SIX3	2	45171797	Silent	SNP	G	TCGA-ED-A8O6-01A-11D-A35Z-10		45171797	198027576	14	34017										
SNRNP200	23020	hgsc.bcm.edu	37	chr2	96943407	96943412	+	In_Frame_Del	DEL	CCATTG	CCATTG	-													0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	ccagagcagggctgagccacCcattgctggaaaggacatcc							TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	CCATTG	CCATTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr2:96943407_96943412delCCATTG	ENST00000323853.5	-	41	5873_5878	c.5796_5801delCAATGG	c.(5794-5802)agcaatggg>agg	p.1932_1934SNG>R	SNRNP200_ENST00000349783.5_Intron	NM_014014.4	NP_054733.2	O75643	U520_HUMAN	small nuclear ribonucleoprotein 200kDa (U5)	1932	SEC63 2.				ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|lung(37)|ovary(7)|prostate(4)|skin(5)|stomach(1)|urinary_tract(1)	90						GCTGAGCCACCCATTGCTGGAAAGGA	0.558																																					p.1933_1934del		Atlas-INDEL	.											.	SNRNP200	195	.	0			c.5797_5802del						.																																			SO:0001651	inframe_deletion	23020	exon41			.	AL831994	CCDS2020.1	2q11.2	2013-05-13	2008-10-29	2008-10-29	ENSG00000144028	ENSG00000144028			30859	protein-coding gene	gene with protein product	"U5 snRNP specific protein, 200 KD"	601664	"activating signal cointegrator 1 complex subunit 3-like 1", "retinitis pigmentosa 33 (autosomal dominant)"	ASCC3L1, RP33		9872452, 8670905, 9774689, 9539711, 16612614, 19878916	Standard	NM_014014		Approved	U5-200KD, HELIC2, KIAA0788, BRR2	uc002svu.3	O75643	OTTHUMG00000130455	ENST00000323853.5:c.5796_5801delCAATGG	chr2.hg19:g.96943407_96943412delCCATTG	ENSP00000317123:p.Ser1932_Gly1934delinsArg	44.0	0.0		33.0	11.0	NM_014014	O94884|Q6NZY0|Q6PX59|Q8NBE6|Q96IF2|Q9H7S0	In_Frame_Del	DEL	ENST00000323853.5	hg19	CCDS2020.1																																																																																			.	.		0.558	SNRNP200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252846.2	NM_014014		-	96943412	CCATTG	-	96943407	7	5	250	1	0	1	0	1	0	0	0	0	14867	623	22	0	629	0	SNRNP200	2	96943407	In_Frame_Del	DEL	CCATTG	TCGA-ED-A8O6-01A-11D-A35Z-10	51771610	96943407	146255966	15	34018										
FN1	2335	hgsc.bcm.edu	37	chr2	216273051	216273051	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	tgaagtagacaggatcaaacTctgctccccatcctcagata	7	12	3	3			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr2:216273051T>C	ENST00000359671.1	-	16	2663	c.2398A>G	c.(2398-2400)Agt>Ggt	p.S800G	FN1_ENST00000323926.6_Missense_Mutation_p.S800G|FN1_ENST00000432072.2_Missense_Mutation_p.S800G|FN1_ENST00000336916.4_Missense_Mutation_p.S800G|FN1_ENST00000346544.3_Missense_Mutation_p.S800G|FN1_ENST00000357009.2_Missense_Mutation_p.S800G|FN1_ENST00000421182.1_Missense_Mutation_p.S800G|FN1_ENST00000345488.5_Missense_Mutation_p.S800G|FN1_ENST00000357867.4_Missense_Mutation_p.S800G|FN1_ENST00000446046.1_Missense_Mutation_p.S800G|FN1_ENST00000443816.1_Missense_Mutation_p.S800G|FN1_ENST00000356005.4_Missense_Mutation_p.S800G|FN1_ENST00000354785.4_Missense_Mutation_p.S800G			P02751	FINC_HUMAN	fibronectin 1	800	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316, ECO:0000255|PROSITE-ProRule:PRU00478, ECO:0000255|PROSITE-ProRule:PRU00479}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	AGGATCAAACTCTGCTCCCCA	0.428																																					p.S800G		Atlas-SNP	.											.	FN1	521	.	0			c.A2398G						.						119	117	117					2																	216273051		2203	4300	6503	SO:0001583	missense	2335	exon16			TCAAACTCTGCTC		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"Fibronectin type III domain containing", "Endogenous ligands"	3778	protein-coding gene	gene with protein product	"migration-stimulating factor", "cold-insoluble globulin"	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.2398A>G	chr2.hg19:g.216273051T>C	ENSP00000352696:p.Ser800Gly	270.0	0.0		197.0	72.0	NM_212476	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Missense_Mutation	SNP	ENST00000359671.1	hg19		.	.	.	.	.	.	.	.	.	.	T	14.82	2.650492	0.47362	.	.	ENSG00000115414	ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000265313;ENST00000359671;ENST00000346544;ENST00000345488;ENST00000357009;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005	T;T;T;T;T;T;T;T;T;T;T;T;T	0.54479	0.57;0.57;0.57;0.57;0.57;0.57;0.57;0.57;0.57;0.57;0.57;0.57;0.57	5.93	5.93	0.95920	.	0.277250	0.35838	N	0.002943	T	0.45736	0.1357	N	0.14661	0.345	0.40349	D	0.979118	D;B;P;B;P;B;B;B;B;P	0.56287	0.975;0.18;0.901;0.03;0.507;0.036;0.108;0.03;0.03;0.774	P;B;B;B;B;B;B;B;B;B	0.54174	0.744;0.082;0.323;0.018;0.138;0.035;0.134;0.018;0.018;0.129	T	0.41662	-0.9496	10	0.23891	T	0.37	.	11.4213	0.49982	0.0:0.0698:0.0:0.9302	.	800;800;800;800;800;800;800;800;800;800	P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;E7ERA1;P02751-9;P02751-14;P02751-15	.;.;.;.;.;.;.;.;.;.	G	800	ENSP00000394423:S800G;ENSP00000323534:S800G;ENSP00000338200:S800G;ENSP00000350534:S800G;ENSP00000346839:S800G;ENSP00000352696:S800G;ENSP00000265312:S800G;ENSP00000273049:S800G;ENSP00000349509:S800G;ENSP00000410422:S800G;ENSP00000415018:S800G;ENSP00000399538:S800G;ENSP00000348285:S800G	ENSP00000265313:S800G	S	-	1	0	FN1	215981296	1.000000	0.71417	1.000000	0.80357	0.798000	0.45092	3.967000	0.56802	2.271000	0.75665	0.533000	0.62120	AGT	.	.		0.428	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		C	216273051	T	C	216273051	3	2	250	1	0	0	0	0	1	0	0	0	5970	1551	54	2	5159	2	FN1	2	216273051	Missense_Mutation	SNP	T	TCGA-ED-A8O6-01A-11D-A35Z-10	119329644	216273051	26926322	16	34019										
ANKMY1	51281	hgsc.bcm.edu	37	chr2	241463326	241463326	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	tcatggacagcgccatcctcCgcatggtccctttgtcgaag	10	14	1	0	rs373595407		TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr2:241463326C>T	ENST00000272972.3	-	7	1755	c.1541G>A	c.(1540-1542)cGg>cAg	p.R514Q	ANKMY1_ENST00000373318.2_Missense_Mutation_p.R373Q|ANKMY1_ENST00000405523.3_Missense_Mutation_p.R373Q|ANKMY1_ENST00000405002.1_Missense_Mutation_p.R284Q|ANKMY1_ENST00000403283.1_Missense_Mutation_p.R452Q|ANKMY1_ENST00000406958.1_Missense_Mutation_p.R275Q|ANKMY1_ENST00000401804.1_Missense_Mutation_p.R603Q|ANKMY1_ENST00000462004.1_5'Flank|ANKMY1_ENST00000391987.1_Missense_Mutation_p.R514Q|ANKMY1_ENST00000536462.1_Missense_Mutation_p.R326Q|ANKMY1_ENST00000373320.4_Missense_Mutation_p.R284Q|ANKMY1_ENST00000361678.4_Missense_Mutation_p.R373Q	NM_016552.2	NP_057636.2	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1	514							metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	30		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.03e-30)|all cancers(36;4.78e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.45e-14)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.8e-06)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.01)|Colorectal(34;0.0101)|COAD - Colon adenocarcinoma(134;0.0476)		CGCCATCCTCCGCATGGTCCC	0.627																																					p.R514Q		Atlas-SNP	.											.	ANKMY1	112	.	0			c.G1541A						.	C	GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	51	50	50		1541,1118	2.2	0	2		50	0,8600		0,0,4300	no	missense,missense	ANKMY1	NM_016552.2,NM_017844.2	43,43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	514/942,373/718	241463326	1,13005	2203	4300	6503	SO:0001583	missense	51281	exon7			ATCCTCCGCATGG	AB034636	CCDS2535.1, CCDS2536.1, CCDS63184.1, CCDS63185.1, CCDS74681.1	2q37.3	2013-01-10			ENSG00000144504	ENSG00000144504		"Zinc fingers, MYND-type", "Ankyrin repeat domain containing"	20987	protein-coding gene	gene with protein product							Standard	XM_005247020		Approved	FLJ20499, ZMYND13	uc002vyz.1	Q9P2S6	OTTHUMG00000133355	ENST00000272972.3:c.1541G>A	chr2.hg19:g.241463326C>T	ENSP00000272972:p.Arg514Gln	52.0	0.0		41.0	19.0	NM_016552	B2RB78|Q4ZFV3|Q8IYX5|Q8NDK5|Q9H0V8|Q9NX10	Missense_Mutation	SNP	ENST00000272972.3	hg19	CCDS2536.1	.	.	.	.	.	.	.	.	.	.	C	12.62	1.993217	0.35131	2.27E-4	0.0	ENSG00000144504	ENST00000373318;ENST00000406958;ENST00000272972;ENST00000361678;ENST00000391987;ENST00000373320;ENST00000403283;ENST00000401804;ENST00000536462;ENST00000405523;ENST00000405002	T;T;T;T;T;T;T;T;T;T;T	0.67698	-0.28;-0.28;0.32;-0.28;0.32;-0.28;2.24;0.29;0.23;1.76;0.74	4.06	2.21	0.28008	Ankyrin repeat-containing domain (1);	0.161766	0.37623	N	0.002018	T	0.69006	0.3063	L	0.36672	1.1	0.09310	N	1	D;D;D;D;D;D;D	0.89917	1.0;0.989;1.0;0.957;1.0;1.0;1.0	D;P;D;B;D;D;D	0.87578	0.998;0.578;0.988;0.178;0.967;0.995;0.998	T	0.57142	-0.7862	10	0.44086	T	0.13	-19.3592	7.2496	0.26142	0.0:0.7962:0.0:0.2038	.	514;326;284;373;275;373;514	Q4ZFV3;F5H558;Q9P2S6-4;Q6GPI0;B5MBY4;Q9P2S6-2;Q9P2S6	.;.;.;.;.;.;ANKY1_HUMAN	Q	373;275;514;373;514;284;452;603;326;373;284	ENSP00000362415:R373Q;ENSP00000384555:R275Q;ENSP00000272972:R514Q;ENSP00000355097:R373Q;ENSP00000375847:R514Q;ENSP00000362417:R284Q;ENSP00000383968:R452Q;ENSP00000385887:R603Q;ENSP00000444707:R326Q;ENSP00000385635:R373Q;ENSP00000385145:R284Q	ENSP00000272972:R514Q	R	-	2	0	ANKMY1	241111999	0.140000	0.22579	0.005000	0.12908	0.021000	0.10359	2.010000	0.40913	0.439000	0.26476	0.491000	0.48974	CGG	.	.		0.627	ANKMY1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257187.2	NM_017844		T	241463326	C	T	241463326	3	4	250	1	0	0	0	0	1	0	0	0	634	652	23	1	1328	1	ANKMY1	2	241463326	Missense_Mutation	SNP	C	TCGA-ED-A8O6-01A-11D-A35Z-10	25190275	241463326	1736047	17	34020										
C2orf85	285093	hgsc.bcm.edu	37	chr2	242815105	242815105	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	aatgccgagggccccatcacGgttagtgagggctgcatcac	13	12	2	1			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr2:242815105G>A	ENST00000343216.3	+	2	1426	c.1398G>A	c.(1396-1398)acG>acA	p.T466T		NM_173821.2	NP_776182.2																					GCCCCATCACGGTTAGTGAGG	0.612																																					p.T466T		Atlas-SNP	.											C2orf85,NS,carcinoma,0,1	.	.	.	0			c.G1398A						.						59	67	65					2																	242815105		2047	4184	6231	SO:0001819	synonymous_variant	285093	exon2			CATCACGGTTAGT																												ENST00000343216.3:c.1398G>A	chr2.hg19:g.242815105G>A		82.0	0.0		53.0	19.0	NM_173821		Silent	SNP	ENST00000343216.3	hg19	CCDS42843.1																																																																																			.	.		0.612	CXXC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322310.1			A	242815105	G	A	242815105	2	1	250	1	0	0	0	0	0	0	0	1	2202	1103	39	1		1	C2orf85	2	242815105	Silent	SNP	G	TCGA-ED-A8O6-01A-11D-A35Z-10	1351779	242815105	384268	18	34021										
FYCO1	79443	hgsc.bcm.edu	37	chr3	45977942	45977942	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	gcagcagttgccacttacatCagttctccagacttcagcag	8	13	3	1			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr3:45977942C>A	ENST00000296137.2	-	15	4243	c.4038G>T	c.(4036-4038)ctG>ctT	p.L1346L	FYCO1_ENST00000535325.1_Silent_p.L1366L|FYCO1_ENST00000438446.1_Silent_p.L17L	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	1346	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.				plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)			NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		CCACTTACATCAGTTCTCCAG	0.597																																					p.L1346L		Atlas-SNP	.											.	FYCO1	115	.	0			c.G4038T						.						113	107	109					3																	45977942		2203	4300	6503	SO:0001819	synonymous_variant	79443	exon15			TTACATCAGTTCT	AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"Zinc fingers, FYVE domain containing"	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.4038G>T	chr3.hg19:g.45977942C>A		99.0	0.0		58.0	32.0	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Silent	SNP	ENST00000296137.2	hg19	CCDS2734.1	.	.	.	.	.	.	.	.	.	.	C	8.724	0.915126	0.17907	.	.	ENSG00000163820	ENST00000433878	.	.	.	5.54	0.693	0.18056	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-26.5402	4.5323	0.12011	0.1004:0.4478:0.2966:0.1552	.	.	.	.	L	135	.	.	X	-	2	2	FYCO1	45952946	0.998000	0.40836	0.939000	0.37840	0.786000	0.44442	0.470000	0.22084	-0.323000	0.08602	-2.462000	0.00205	TGA	.	.		0.597	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513		A	45977942	C	A	45977942	2	1	250	1	0	0	0	0	0	0	0	1	6133	813	29	3		3	FYCO1	3	45977942	Silent	SNP	C	TCGA-ED-A8O6-01A-11D-A35Z-10		45977942	152044488	19	34022										
HGD	3081	hgsc.bcm.edu	37	chr3	120369681	120369681	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	caagcccattgttagactttAtgtctccagctccacacaag	6	13	1	1			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr3:120369681A>T	ENST00000283871.5	-	6	833	c.374T>A	c.(373-375)aTa>aAa	p.I125K	HGD_ENST00000488183.1_5'Flank	NM_000187.3	NP_000178.2	Q93099	HGD_HUMAN	homogentisate 1,2-dioxygenase	125					cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	homogentisate 1,2-dioxygenase activity (GO:0004411)|metal ion binding (GO:0046872)			cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(2)	25				GBM - Glioblastoma multiforme(114;0.158)		GTTAGACTTTATGTCTCCAGC	0.512																																					p.I125K		Atlas-SNP	.											.	HGD	65	.	0			c.T374A						.						180	161	167					3																	120369681		2203	4296	6499	SO:0001583	missense	3081	exon6			GACTTTATGTCTC		CCDS3000.1	3q	2010-04-27	2010-04-27		ENSG00000113924	ENSG00000113924	1.13.11.5		4892	protein-coding gene	gene with protein product	"homogentisate oxidase"	607474	"homogentisate 1,2-dioxygenase (homogentisate oxidase)"	AKU		8188241	Standard	NM_000187		Approved	HGO	uc003edw.3	Q93099	OTTHUMG00000159441	ENST00000283871.5:c.374T>A	chr3.hg19:g.120369681A>T	ENSP00000283871:p.Ile125Lys	114.0	0.0		84.0	21.0	NM_000187	A8K417|B2R8Z0	Missense_Mutation	SNP	ENST00000283871.5	hg19	CCDS3000.1	.	.	.	.	.	.	.	.	.	.	A	17.73	3.461726	0.63513	.	.	ENSG00000113924	ENST00000283871;ENST00000476082	D;D	0.98901	-5.22;-5.22	6.06	4.9	0.64082	Cupin, RmlC-type (1);	0.300334	0.35739	N	0.003014	D	0.96210	0.8764	L	0.29908	0.895	0.49483	D	0.999799	B	0.10296	0.003	B	0.30855	0.121	D	0.93226	0.6613	10	0.66056	D	0.02	-33.6709	8.1307	0.31024	0.8459:0.0:0.1541:0.0	.	125	Q93099	HGD_HUMAN	K	125;84	ENSP00000283871:I125K;ENSP00000419560:I84K	ENSP00000283871:I125K	I	-	2	0	HGD	121852371	1.000000	0.71417	0.984000	0.44739	0.978000	0.69477	4.540000	0.60664	2.323000	0.78572	0.528000	0.53228	ATA	.	.		0.512	HGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355410.1			T	120369681	A	T	120369681	3	4	250	1	0	0	0	0	1	0	0	0	7093	449	16	4	999	4	HGD	3	120369681	Missense_Mutation	SNP	A	TCGA-ED-A8O6-01A-11D-A35Z-10	74391739	120369681	77652749	20	34023										
CCDC37	348807	hgsc.bcm.edu	37	chr3	126153141	126153141	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	atcattgagcaccagctggaTgagctgctagagaacctgga	12	9	1	3			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr3:126153141T>G	ENST00000352312.1	+	15	1644	c.1545T>G	c.(1543-1545)gaT>gaG	p.D515E	CCDC37_ENST00000393425.1_Missense_Mutation_p.D516E|CCDC37_ENST00000506204.1_3'UTR|CCDC37_ENST00000505024.1_Missense_Mutation_p.D516E	NM_182628.2	NP_872434.2	Q494V2	CCD37_HUMAN	coiled-coil domain containing 37	515										NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|skin(3)	23				GBM - Glioblastoma multiforme(114;0.166)		ACCAGCTGGATGAGCTGCTAG	0.617																																					p.D515E		Atlas-SNP	.											.	CCDC37	69	.	0			c.T1545G						.						69	64	66					3																	126153141		2203	4300	6503	SO:0001583	missense	348807	exon15			GCTGGATGAGCTG	AK097402	CCDS3037.1	3q21.2	2014-07-31			ENSG00000163885	ENSG00000163885			26842	protein-coding gene	gene with protein product						23569216	Standard	NM_182628		Approved	FLJ40083, MIA1	uc003eiu.1	Q494V2	OTTHUMG00000162691	ENST00000352312.1:c.1545T>G	chr3.hg19:g.126153141T>G	ENSP00000344749:p.Asp515Glu	278.0	0.0		178.0	53.0	NM_182628	D3DNA8|Q494V1|Q494V4|Q8N838	Missense_Mutation	SNP	ENST00000352312.1	hg19	CCDS3037.1	.	.	.	.	.	.	.	.	.	.	T	12.41	1.930957	0.34096	.	.	ENSG00000163885	ENST00000352312;ENST00000393425;ENST00000505024	T;T;T	0.20598	2.06;2.07;2.07	5.08	-7.49	0.01355	.	0.971544	0.08538	N	0.930996	T	0.16257	0.0391	N	0.20483	0.58	0.18873	N	0.999983	D;D	0.71674	0.998;0.996	D;P	0.63381	0.914;0.822	T	0.08597	-1.0714	10	0.02654	T	1	-10.463	6.7391	0.23424	0.1002:0.1239:0.0997:0.6762	.	516;515	Q494V2-2;Q494V2	.;CCD37_HUMAN	E	515;516;516	ENSP00000344749:D515E;ENSP00000377076:D516E;ENSP00000423046:D516E	ENSP00000344749:D515E	D	+	3	2	CCDC37	127635831	0.000000	0.05858	0.230000	0.23976	0.875000	0.50365	-2.459000	0.01000	-1.592000	0.01619	-0.353000	0.07706	GAT	.	.		0.617	CCDC37-001	KNOWN	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000370099.4	NM_182628		G	126153141	T	G	126153141	3	3	250	1	0	0	0	0	1	0	0	0	2811	1461	51	5	1599	5	CCDC37	3	126153141	Missense_Mutation	SNP	T	TCGA-ED-A8O6-01A-11D-A35Z-10	5783460	126153141	71869289	21	34024										
MCF2L2	23101	hgsc.bcm.edu	37	chr3	183017980	183017980	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	gcagctgggccttttccaggGgctcctgcaaagtgaacacc	12	13	0	1			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr3:183017980G>C	ENST00000328913.3	-	11	1415	c.1118C>G	c.(1117-1119)cCc>cGc	p.P373R	MCF2L2_ENST00000447025.2_Missense_Mutation_p.P373R|MCF2L2_ENST00000473233.1_Missense_Mutation_p.P373R|MCF2L2_ENST00000414362.2_Missense_Mutation_p.P373R	NM_015078.2	NP_055893	Q86YR7	MF2L2_HUMAN	MCF.2 cell line derived transforming sequence-like 2	373				P -> S (in Ref. 4; AAO19651 and 5; BAA74884). {ECO:0000305}.			Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(25)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			CTTTTCCAGGGGCTCCTGCAA	0.602																																					p.P373R		Atlas-SNP	.											.	MCF2L2	164	.	0			c.C1118G						.						35	35	35					3																	183017980		2203	4300	6503	SO:0001583	missense	23101	exon11			TCCAGGGGCTCCT	AB020668	CCDS3243.1	3q27	2012-07-24			ENSG00000053524	ENSG00000053524		"Rho guanine nucleotide exchange factors"	30319	protein-coding gene	gene with protein product							Standard	NM_015078		Approved	KIAA0861, ARHGEF22	uc003fli.1	Q86YR7	OTTHUMG00000158388	ENST00000328913.3:c.1118C>G	chr3.hg19:g.183017980G>C	ENSP00000328118:p.Pro373Arg	50.0	0.0		42.0	13.0	NM_015078	O94942|Q6P2B8|Q6ZVJ5|Q8N318	Missense_Mutation	SNP	ENST00000328913.3	hg19	CCDS3243.1	.	.	.	.	.	.	.	.	.	.	G	2.327	-0.354383	0.05173	.	.	ENSG00000053524	ENST00000328913;ENST00000473233;ENST00000447025;ENST00000414362	T;T;T;T	0.26518	1.73;1.73;1.73;1.73	4.59	4.59	0.56863	.	0.646275	0.15244	N	0.272701	T	0.25827	0.0629	L	0.57536	1.79	0.09310	N	1	P;P	0.44877	0.568;0.845	B;B	0.41988	0.242;0.372	T	0.10314	-1.0635	10	0.16896	T	0.51	.	11.1317	0.48351	0.0846:0.0:0.9154:0.0	.	373;373	Q86YR7-2;Q86YR7	.;MF2L2_HUMAN	R	373	ENSP00000328118:P373R;ENSP00000420070:P373R;ENSP00000388190:P373R;ENSP00000414131:P373R	ENSP00000328118:P373R	P	-	2	0	MCF2L2	184500674	0.660000	0.27420	0.486000	0.27416	0.239000	0.25481	2.971000	0.49248	2.369000	0.80426	0.655000	0.94253	CCC	.	.		0.602	MCF2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350868.1	NM_015078		C	183017980	G	C	183017980	3	2	250	1	0	0	0	0	1	0	0	0	9389	1232	43	4	2306	4	MCF2L2	3	183017980	Missense_Mutation	SNP	G	TCGA-ED-A8O6-01A-11D-A35Z-10	56864839	183017980	15004450	22	34025										
UGT2B7	7364	hgsc.bcm.edu	37	chr4	69962520	69962521	+	Frame_Shift_Del	DEL	TA	TA	-													0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	aatttcatcatgcaacagatTaagagatggtcagaccttcc							TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	TA	TA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr4:69962520_69962521delTA	ENST00000508661.1	+	1	309_310	c.282_283delTA	c.(280-285)attaagfs	p.K95fs	UGT2B7_ENST00000509763.1_Intron|UGT2B7_ENST00000305231.7_Frame_Shift_Del_p.K95fs			P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B7	95					androgen metabolic process (GO:0008209)|cellular glucuronidation (GO:0052695)|lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)			autonomic_ganglia(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38					Atorvastatin(DB01076)|Carbamazepine(DB00564)|Chenodeoxycholic acid(DB06777)|Codeine(DB00318)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Diclofenac(DB00586)|Epirubicin(DB00445)|Etodolac(DB00749)|Ezetimibe(DB00973)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naproxen(DB00788)|Oxazepam(DB00842)|Pitavastatin(DB08860)|Silodosin(DB06207)|Simvastatin(DB00641)|Suprofen(DB00870)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zidovudine(DB00495)	TGCAACAGATTAAGAGATGGTC	0.327																																					p.94_94del		Atlas-INDEL	.											.	UGT2B7	79	.	0			c.281_282del						.																																			SO:0001589	frameshift_variant	7364	exon1			.	BC030974	CCDS3526.1	4q13	2008-02-05	2005-07-20		ENSG00000171234	ENSG00000171234		"UDP glucuronosyltransferases"	12554	protein-coding gene	gene with protein product		600068	"UDP glycosyltransferase 2 family, polypeptide B7"			2159463, 7835904	Standard	NM_001074		Approved	UGT2B9	uc003heg.4	P16662	OTTHUMG00000129404	ENST00000508661.1:c.282_283delTA	chr4.hg19:g.69962520_69962521delTA	ENSP00000427659:p.Lys95fs	181.0	0.0		128.0	46.0	NM_001074	B2R810|Q6GTW0	Frame_Shift_Del	DEL	ENST00000508661.1	hg19																																																																																				.	.		0.327	UGT2B7-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000362103.1	NM_001074		-	69962521	TA	-	69962520	7	5	250	1	0	1	0	1	0	0	0	0	16977	1742	61	0	284	0	UGT2B7	4	69962520	Frame_Shift_Del	DEL	TA	TCGA-ED-A8O6-01A-11D-A35Z-10		69962520	121191756	23	34026										
DDX46	9879	hgsc.bcm.edu	37	chr5	134147507	134147507	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	agcagctcttggtctacaagAttcagatgatgaggatgctg	12	7	3	4			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr5:134147507A>G	ENST00000354283.4	+	18	2543	c.2408A>G	c.(2407-2409)gAt>gGt	p.D803G	DDX46_ENST00000452510.2_Missense_Mutation_p.D803G			Q7L014	DDX46_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	803					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GGTCTACAAGATTCAGATGAT	0.378																																					p.D803G	Colon(13;391 453 4901 21675 24897)	Atlas-SNP	.											.	DDX46	77	.	0			c.A2408G						.						127	129	129					5																	134147507		2203	4300	6503	SO:0001583	missense	9879	exon18			TACAAGATTCAGA		CCDS34240.1, CCDS75306.1	5q31.1	2010-01-25			ENSG00000145833	ENSG00000145833		"DEAD-boxes"	18681	protein-coding gene	gene with protein product							Standard	XM_005272142		Approved	KIAA0801, FLJ25329, PRPF5, Prp5	uc003kzw.3	Q7L014	OTTHUMG00000163072	ENST00000354283.4:c.2408A>G	chr5.hg19:g.134147507A>G	ENSP00000346236:p.Asp803Gly	179.0	0.0		86.0	20.0	NM_014829	O94894|Q96EI0|Q9Y658	Missense_Mutation	SNP	ENST00000354283.4	hg19	CCDS34240.1	.	.	.	.	.	.	.	.	.	.	A	16.82	3.228526	0.58777	.	.	ENSG00000145833	ENST00000452510;ENST00000354283	T;T	0.27890	1.64;1.65	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	T	0.32010	0.0815	L	0.54965	1.715	0.80722	D	1	B	0.18461	0.028	B	0.19148	0.024	T	0.08006	-1.0743	10	0.46703	T	0.11	-24.9048	15.1303	0.72517	1.0:0.0:0.0:0.0	.	803	Q7L014	DDX46_HUMAN	G	803	ENSP00000416534:D803G;ENSP00000346236:D803G	ENSP00000346236:D803G	D	+	2	0	DDX46	134175406	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.287000	0.95975	2.031000	0.59945	0.402000	0.26972	GAT	.	.		0.378	DDX46-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371584.1	NM_014829		G	134147507	A	G	134147507	3	3	250	1	0	0	0	0	1	0	0	0	4366	333	12	2	2478	2	DDX46	5	134147507	Missense_Mutation	SNP	A	TCGA-ED-A8O6-01A-11D-A35Z-10		134147507	46767753	24	34027										
PCDHGB1	56104	hgsc.bcm.edu	37	chr5	140730929	140730929	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	taatagccctcataaaagtgCgagacaaggattctgggcaa	10	8	2	1			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr5:140730929C>T	ENST00000523390.1	+	1	1102	c.1102C>T	c.(1102-1104)Cga>Tga	p.R368*	PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018922.2|NM_032095.1	NP_061745.1|NP_115266.1	Q9Y5G3	PCDGD_HUMAN	protocadherin gamma subfamily B, 1	368	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R368*(4)		central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CATAAAAGTGCGAGACAAGGA	0.433																																					p.R368X		Atlas-SNP	.											PCDHGB1_ENST00000523390,NS,carcinoma,-1,4	PCDHGB1	198	.	4	Substitution - Nonsense(4)	large_intestine(4)	c.C1102T						.						43	42	42					5																	140730929		1908	4124	6032	SO:0001587	stop_gained	56104	exon1			AAAGTGCGAGACA	AF152517	CCDS54923.1, CCDS75330.1	5q31	2010-01-26				ENSG00000254221		"Cadherins / Protocadherins : Clustered"	8708	other	protocadherin	"protocadherin gamma subfamily B, 1, isoform 2"	606299				10380929	Standard	NM_018922		Approved	PCDH-GAMMA-B1		Q9Y5G3		ENST00000523390.1:c.1102C>T	chr5.hg19:g.140730929C>T	ENSP00000429273:p.Arg368*	81.0	0.0		48.0	28.0	NM_018922	Q3SY75|Q9Y5C8	Nonsense_Mutation	SNP	ENST00000523390.1	hg19	CCDS54923.1	.	.	.	.	.	.	.	.	.	.	.	23.2	4.385450	0.82792	.	.	ENSG00000254221	ENST00000523390	.	.	.	5.49	-1.73	0.08081	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	.	11.1443	0.48422	0.6713:0.2645:0.0:0.0642	.	.	.	.	X	368	.	ENSP00000429273:R368X	R	+	1	2	PCDHGB1	140711113	0.000000	0.05858	0.001000	0.08648	0.996000	0.88848	-3.032000	0.00637	-0.205000	0.10219	0.563000	0.77884	CGA	.	.		0.433	PCDHGB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374740.1	NM_018922		T	140730929	C	T	140730929	4	4	250	1	0	0	0	0	0	1	0	0	11571	760	27	1	1104	1	PCDHGB1	5	140730929	Nonsense_Mutation	SNP	C	TCGA-ED-A8O6-01A-11D-A35Z-10	6583422	140730929	40184331	25	34028										
DOCK2	1794	hgsc.bcm.edu	37	chr5	169412861	169412861	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	atggagaccttcatcatgttCaaggacctcattggaaagaa	9	8	4	2			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr5:169412861C>A	ENST00000256935.8	+	29	3008	c.2928C>A	c.(2926-2928)ttC>ttA	p.F976L	DOCK2_ENST00000520908.1_Missense_Mutation_p.F468L|DOCK2_ENST00000523351.1_3'UTR|DOCK2_ENST00000540750.1_Missense_Mutation_p.F37L	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	976	Interaction with CRKL.				actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TCATCATGTTCAAGGACCTCA	0.468																																					p.F976L		Atlas-SNP	.											.	DOCK2	389	.	0			c.C2928A						.						257	239	245					5																	169412861		2203	4300	6503	SO:0001583	missense	1794	exon29			CATGTTCAAGGAC	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.2928C>A	chr5.hg19:g.169412861C>A	ENSP00000256935:p.Phe976Leu	93.0	0.0		54.0	11.0	NM_004946	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	hg19	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.312575	0.81358	.	.	ENSG00000134516	ENST00000256935;ENST00000520908;ENST00000540750	T;T;T	0.25085	1.82;1.82;1.82	5.19	3.38	0.38709	.	0.000000	0.85682	D	0.000000	T	0.45256	0.1333	M	0.76328	2.33	0.44611	D	0.997581	D;D	0.67145	0.996;0.982	D;D	0.70227	0.968;0.952	T	0.27872	-1.0061	10	0.33940	T	0.23	.	10.4257	0.44375	0.0:0.8124:0.0:0.1876	.	468;976	E7ERW7;Q92608	.;DOCK2_HUMAN	L	976;468;37	ENSP00000256935:F976L;ENSP00000429283:F468L;ENSP00000438827:F37L	ENSP00000256935:F976L	F	+	3	2	DOCK2	169345439	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	0.925000	0.28791	2.426000	0.82243	0.561000	0.74099	TTC	.	.		0.468	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		A	169412861	C	A	169412861	3	1	250	1	0	0	0	0	1	0	0	0	4689	825	29	3	3042	3	DOCK2	5	169412861	Missense_Mutation	SNP	C	TCGA-ED-A8O6-01A-11D-A35Z-10	28681932	169412861	11502399	26	34029										
SLC44A4	80736	hgsc.bcm.edu	37	chr6	31842544	31842544	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	aaaagttcctgttttttgtaTagaagacttccccaacagtc	6	9	0	2			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr6:31842544T>C	ENST00000229729.6	-	6	442	c.422A>G	c.(421-423)tAt>tGt	p.Y141C	SLC44A4_ENST00000544672.1_Missense_Mutation_p.Y65C|SLC44A4_ENST00000375562.4_Intron|SLC44A4_ENST00000465707.1_5'UTR	NM_025257.2	NP_079533.2	Q53GD3	CTL4_HUMAN	solute carrier family 44, member 4	141					acetylcholine biosynthetic process (GO:0008292)|acetylcholine secretion (GO:0061526)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of cell growth (GO:0030307)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(1)|urinary_tract(2)	35					Choline(DB00122)	GTTTTTTGTATAGAAGACTTC	0.527																																					p.Y141C		Atlas-SNP	.											.	SLC44A4	67	.	0			c.A422G						.						72	70	71					6																	31842544		2203	4300	6503	SO:0001583	missense	80736	exon6			TTTGTATAGAAGA	AF134726	CCDS4724.2, CCDS54989.1, CCDS54990.1	6p21.3	2014-02-17	2005-09-06	2005-09-06	ENSG00000204385	ENSG00000204385		"Solute carriers"	13941	protein-coding gene	gene with protein product		606107	"chromosome 6 open reading frame 29"	C6orf29		10677542, 15715662, 24379411	Standard	NM_025257		Approved	NG22, CTL4, FLJ14491, TPPT	uc010jti.3	Q53GD3	OTTHUMG00000031133	ENST00000229729.6:c.422A>G	chr6.hg19:g.31842544T>C	ENSP00000229729:p.Tyr141Cys	157.0	0.0		104.0	53.0	NM_025257	A2BED3|B0UXX8|B0UZY8|B4DU94|B4DWM2|E9PEK7|Q5JP84|Q5JQ93|Q658S8|Q6UX89|Q8TEW4|Q96C58|Q96K59|Q9Y332	Missense_Mutation	SNP	ENST00000229729.6	hg19	CCDS4724.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.98|15.98	2.991913|2.991913	0.54041|0.54041	.|.	.|.	ENSG00000204385|ENSG00000204385	ENST00000414427|ENST00000229729;ENST00000544672	.|T;T	.|0.56776	.|0.44;0.44	4.63|4.63	2.09|2.09	0.27110|0.27110	.|.	.|0.148255	.|0.29814	.|N	.|0.011136	T|T	0.35740|0.35740	0.0942|0.0942	L|L	0.61036|0.61036	1.89|1.89	0.35590|0.35590	D|D	0.806972|0.806972	.|P	.|0.36010	.|0.532	.|B	.|0.42087	.|0.375	T|T	0.15435|0.15435	-1.0437|-1.0437	5|10	.|0.39692	.|T	.|0.17	-26.2564|-26.2564	8.8061|8.8061	0.34938|0.34938	0.0:0.0:0.3674:0.6326|0.0:0.0:0.3674:0.6326	.|.	.|141	.|Q53GD3	.|CTL4_HUMAN	V|C	137|141;65	.|ENSP00000229729:Y141C;ENSP00000444109:Y65C	.|ENSP00000229729:Y141C	I|Y	-|-	1|2	0|0	SLC44A4|SLC44A4	31950523|31950523	0.847000|0.847000	0.29606|0.29606	0.351000|0.351000	0.25721|0.25721	0.773000|0.773000	0.43773|0.43773	1.253000|1.253000	0.32886|0.32886	0.329000|0.329000	0.23460|0.23460	0.533000|0.533000	0.62120|0.62120	ATA|TAT	.	.		0.527	SLC44A4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076234.3			C	31842544	T	C	31842544	3	2	250	1	0	0	0	0	1	0	0	0	14653	1406	49	2	1774	2	SLC44A4	6	31842544	Missense_Mutation	SNP	T	TCGA-ED-A8O6-01A-11D-A35Z-10		31842544	139272523	27	34030										
BMP5	653	hgsc.bcm.edu	37	chr6	55623820	55623820	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	taccagagtctgaactatagCgtggttggtggcattcatat	11	7	2	2			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr6:55623820C>T	ENST00000370830.3	-	6	1896	c.1198G>A	c.(1198-1200)Gct>Act	p.A400T	BMP5_ENST00000446683.2_Intron	NM_021073.2	NP_066551.1	P22003	BMP5_HUMAN	bone morphogenetic protein 5	400					cartilage development (GO:0051216)|growth (GO:0040007)|male genitalia development (GO:0030539)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of steroid biosynthetic process (GO:0010894)|ossification (GO:0001503)|pattern specification process (GO:0007389)|positive regulation of dendrite development (GO:1900006)|positive regulation of DNA-dependent DNA replication (GO:2000105)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system development (GO:0001501)|type B pancreatic cell development (GO:0003323)	extracellular space (GO:0005615)|membrane-bounded vesicle (GO:0031988)	BMP receptor binding (GO:0070700)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	45	Lung NSC(77;0.0462)		LUSC - Lung squamous cell carcinoma(124;0.181)			TGAACTATAGCGTGGTTGGTG	0.378																																					p.A400T		Atlas-SNP	.											.	BMP5	94	.	0			c.G1198A						.						160	151	154					6																	55623820		2203	4300	6503	SO:0001583	missense	653	exon6			CTATAGCGTGGTT		CCDS4958.1	6p12.1	2014-01-30			ENSG00000112175	ENSG00000112175		"Bone morphogenetic proteins", "Endogenous ligands"	1072	protein-coding gene	gene with protein product		112265				1427904, 11580864	Standard	NM_021073		Approved		uc003pcq.3	P22003	OTTHUMG00000014903	ENST00000370830.3:c.1198G>A	chr6.hg19:g.55623820C>T	ENSP00000359866:p.Ala400Thr	108.0	0.0		85.0	40.0	NM_021073	B4E0Y4|Q9H547|Q9NTM5	Missense_Mutation	SNP	ENST00000370830.3	hg19	CCDS4958.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.576608	0.86645	.	.	ENSG00000112175	ENST00000370830	D	0.86497	-2.13	5.67	5.67	0.87782	Transforming growth factor-beta, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.94315	0.8173	M	0.87328	2.875	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94278	0.7517	10	0.87932	D	0	.	20.1272	0.97986	0.0:1.0:0.0:0.0	.	400	P22003	BMP5_HUMAN	T	400	ENSP00000359866:A400T	ENSP00000359866:A400T	A	-	1	0	BMP5	55731779	1.000000	0.71417	1.000000	0.80357	0.310000	0.27922	7.776000	0.85560	2.828000	0.97474	0.655000	0.94253	GCT	.	.		0.378	BMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041000.1			T	55623820	C	T	55623820	3	4	250	1	0	0	0	0	1	0	0	0	1463	768	27	1	174	1	BMP5	6	55623820	Missense_Mutation	SNP	C	TCGA-ED-A8O6-01A-11D-A35Z-10	23781276	55623820	115491247	28	34031										
HTR1E	3354	hgsc.bcm.edu	37	chr6	87725376	87725376	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	gacatgacctgctgcacctgCtccatcctccacctctgtgt	7	17	1	1			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr6:87725376C>A	ENST00000305344.5	+	2	1027	c.324C>A	c.(322-324)tgC>tgA	p.C108*		NM_000865.2	NP_000856.1	P28566	5HT1E_HUMAN	5-hydroxytryptamine (serotonin) receptor 1E, G protein-coupled	108					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP metabolic process (GO:0030815)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			breast(3)|endometrium(2)|kidney(3)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(3)	41		all_cancers(76;7.11e-06)|Acute lymphoblastic leukemia(125;1.2e-09)|Prostate(29;3.51e-09)|all_hematologic(105;7.43e-06)|all_epithelial(107;0.00819)		BRCA - Breast invasive adenocarcinoma(108;0.055)	Aripiprazole(DB01238)|Clozapine(DB00363)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ketamine(DB01221)|Loxapine(DB00408)|Methysergide(DB00247)|Olanzapine(DB00334)|Quetiapine(DB01224)|Ziprasidone(DB00246)	GCTGCACCTGCTCCATCCTCC	0.562																																					p.C108X		Atlas-SNP	.											.	HTR1E	89	.	0			c.C324A						.						126	101	109					6																	87725376		2203	4300	6503	SO:0001587	stop_gained	3354	exon2			CACCTGCTCCATC		CCDS5006.1	6q14-q15	2013-06-19	2012-02-03		ENSG00000168830	ENSG00000168830		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5291	protein-coding gene	gene with protein product		182132	"5-hydroxytryptamine (serotonin) receptor 1E"			1608964	Standard	NM_000865		Approved	5-HT1E	uc003pli.3	P28566	OTTHUMG00000015154	ENST00000305344.5:c.324C>A	chr6.hg19:g.87725376C>A	ENSP00000307766:p.Cys108*	119.0	0.0		67.0	22.0	NM_000865	E1P503|Q9P1Y1	Nonsense_Mutation	SNP	ENST00000305344.5	hg19	CCDS5006.1	.	.	.	.	.	.	.	.	.	.	C	38	6.914581	0.97932	.	.	ENSG00000168830	ENST00000305344;ENST00000369584	.	.	.	4.57	1.19	0.21007	.	0.000000	0.64402	U	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.36615	T	0.2	.	5.8317	0.18584	0.0:0.3137:0.0:0.6863	.	.	.	.	X	108	.	ENSP00000307766:C108X	C	+	3	2	HTR1E	87782095	0.994000	0.37717	1.000000	0.80357	0.989000	0.77384	0.328000	0.19681	0.360000	0.24265	0.404000	0.27445	TGC	.	.		0.562	HTR1E-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472488.2	NM_000865		A	87725376	C	A	87725376	4	1	250	1	0	0	0	0	0	1	0	0	7448	805	28	3	326	3	HTR1E	6	87725376	Nonsense_Mutation	SNP	C	TCGA-ED-A8O6-01A-11D-A35Z-10	32101556	87725376	83389691	29	34032										
NR2E1	7101	hgsc.bcm.edu	37	chr6	108492696	108492696	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	atcccctgcaaagtgtgtggCgaccgcagctcggggaagca	14	12	0	0			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr6:108492696C>T	ENST00000368986.4	+	2	768	c.60C>T	c.(58-60)ggC>ggT	p.G20G	NR2E1_ENST00000368983.3_Silent_p.G57G	NM_003269.3	NP_003260.1	Q9Y466	NR2E1_HUMAN	nuclear receptor subfamily 2, group E, member 1	20					aggressive behavior (GO:0002118)|amygdala development (GO:0021764)|anterior commissure morphogenesis (GO:0021960)|behavioral fear response (GO:0001662)|cell fate commitment (GO:0045165)|cerebral cortex neuron differentiation (GO:0021895)|dentate gyrus development (GO:0021542)|extracellular matrix organization (GO:0030198)|forebrain generation of neurons (GO:0021872)|gene expression (GO:0010467)|glial cell migration (GO:0008347)|layer formation in cerebral cortex (GO:0021819)|long-term synaptic potentiation (GO:0060291)|negative regulation of apoptotic process (GO:0043066)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron differentiation (GO:0045665)|nervous system development (GO:0007399)|olfactory bulb development (GO:0021772)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle (GO:0045787)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of stem cell proliferation (GO:2000648)|regulation of cell migration involved in sprouting angiogenesis (GO:0090049)|regulation of dendrite morphogenesis (GO:0048814)|regulation of timing of neuron differentiation (GO:0060164)|retina development in camera-type eye (GO:0060041)|social behavior (GO:0035176)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|visual perception (GO:0007601)	nucleoplasm (GO:0005654)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(4)|liver(1)|lung(16)|prostate(1)|skin(3)	30		all_cancers(87;8.13e-05)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00866)|Colorectal(196;0.0637)		BRCA - Breast invasive adenocarcinoma(108;0.013)|Epithelial(106;0.0521)|all cancers(137;0.068)|OV - Ovarian serous cystadenocarcinoma(136;0.0689)		AAGTGTGTGGCGACCGCAGCT	0.577																																					p.G20G		Atlas-SNP	.											.	NR2E1	57	.	0			c.C60T						.						126	135	132					6																	108492696		2203	4300	6503	SO:0001819	synonymous_variant	7101	exon2			GTGTGGCGACCGC	Y13276	CCDS5063.1, CCDS69165.1	6q21	2013-01-16			ENSG00000112333	ENSG00000112333		"Nuclear hormone receptors"	7973	protein-coding gene	gene with protein product		603849		TLX		9628820	Standard	NM_003269		Approved	TLL, XTLL	uc003psg.3	Q9Y466	OTTHUMG00000015319	ENST00000368986.4:c.60C>T	chr6.hg19:g.108492696C>T		101.0	0.0		54.0	17.0	NM_003269	Q6ZMP8	Silent	SNP	ENST00000368986.4	hg19	CCDS5063.1																																																																																			.	.		0.577	NR2E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041712.2			T	108492696	C	T	108492696	2	4	250	1	0	0	0	0	0	0	0	1	10634	755	27	1		1	NR2E1	6	108492696	Silent	SNP	C	TCGA-ED-A8O6-01A-11D-A35Z-10	20767320	108492696	62622371	30	34033										
TTLL2	83887	hgsc.bcm.edu	37	chr6	167754181	167754181	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	tctatgtttgtgttactggcTttaagcctttgaccatttat	7	7	1	1			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr6:167754181T>A	ENST00000239587.5	+	3	881	c.793T>A	c.(793-795)Ttt>Att	p.F265I		NM_031949.4	NP_114155.4	Q9BWV7	TTLL2_HUMAN	tubulin tyrosine ligase-like family, member 2	265	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)		ligase activity (GO:0016874)			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(66;7.8e-06)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		TGTTACTGGCTTTAAGCCTTT	0.368																																					p.F265I		Atlas-SNP	.											.	TTLL2	82	.	0			c.T793A						.						174	177	176					6																	167754181		2203	4300	6503	SO:0001583	missense	83887	exon3			ACTGGCTTTAAGC	AK093039	CCDS5301.1	6q27	2013-02-14		2004-01-14	ENSG00000120440	ENSG00000120440		"Tubulin tyrosine ligase-like family"	21211	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 104"	C6orf104		11054573	Standard	XM_006715572		Approved	NYD-TSPG, dJ366N23.3	uc003qvs.1	Q9BWV7	OTTHUMG00000016023	ENST00000239587.5:c.793T>A	chr6.hg19:g.167754181T>A	ENSP00000239587:p.Phe265Ile	91.0	0.0		40.0	10.0	NM_031949	B2RB11|B3KS77|Q7Z6R8|Q86X22	Missense_Mutation	SNP	ENST00000239587.5	hg19	CCDS5301.1	.	.	.	.	.	.	.	.	.	.	T	11.65	1.702901	0.30232	.	.	ENSG00000120440	ENST00000239587;ENST00000540954	T	0.05580	3.42	3.4	0.819	0.18785	.	0.082324	0.47852	D	0.000214	T	0.07548	0.0190	L	0.53671	1.685	0.35763	D	0.820335	D	0.76494	0.999	D	0.76071	0.987	T	0.13150	-1.0520	10	0.72032	D	0.01	.	5.1452	0.14981	0.0:0.1031:0.1817:0.7152	.	265	Q9BWV7	TTLL2_HUMAN	I	265;192	ENSP00000239587:F265I	ENSP00000239587:F265I	F	+	1	0	TTLL2	167674171	1.000000	0.71417	0.027000	0.17364	0.003000	0.03518	3.952000	0.56691	0.054000	0.16065	-0.425000	0.05940	TTT	.	.		0.368	TTLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043127.3	NM_031949		A	167754181	T	A	167754181	3	1	250	1	0	0	0	0	1	0	0	0	16742	1609	56	4	803	4	TTLL2	6	167754181	Missense_Mutation	SNP	T	TCGA-ED-A8O6-01A-11D-A35Z-10	59261485	167754181	3360886	31	34034										
MLLT4	4301	hgsc.bcm.edu	37	chr6	168352526	168352526	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	agcagcagccccgcacgatcGagcgcagagacttgcagtac	12	14	0	1	rs371470293		TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr6:168352526G>T	ENST00000447894.2	+	29	4471	c.4471G>T	c.(4471-4473)Gag>Tag	p.E1491*	MLLT4_ENST00000392112.1_Nonsense_Mutation_p.E1474*|MLLT4_ENST00000351017.4_Nonsense_Mutation_p.E1498*|MLLT4_ENST00000400822.3_Nonsense_Mutation_p.E1490*|MLLT4_ENST00000344191.4_Nonsense_Mutation_p.E1491*|MLLT4_ENST00000392108.3_Nonsense_Mutation_p.E1491*|MLLT4_ENST00000366806.2_Nonsense_Mutation_p.E1491*			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	1491					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(13)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		CCGCACGATCGAGCGCAGAGA	0.602			T	MLL	AL																																p.E1491X		Atlas-SNP	.		Dom	yes		6	6q27	4301	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"		L	.	MLLT4	351	.	0			c.G4471T						.						52	57	55					6																	168352526		2203	4300	6503	SO:0001587	stop_gained	4301	exon29			ACGATCGAGCGCA	AB011399	CCDS47517.1, CCDS75553.1	6q27	2008-02-05	2001-11-28		ENSG00000130396	ENSG00000130396			7137	protein-coding gene	gene with protein product		159559	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 4"			8242616	Standard	NM_001040000		Approved	AF-6, AF6	uc021zij.1	P55196	OTTHUMG00000016031	ENST00000447894.2:c.4471G>T	chr6.hg19:g.168352526G>T	ENSP00000404595:p.Glu1491*	292.0	1.0		175.0	117.0	NM_001040000	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Nonsense_Mutation	SNP	ENST00000447894.2	hg19		.	.	.	.	.	.	.	.	.	.	G	47	12.971183	0.99710	.	.	ENSG00000130396	ENST00000344191;ENST00000351017;ENST00000392108;ENST00000366806;ENST00000392112;ENST00000341575;ENST00000400822;ENST00000447894	.	.	.	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-41.4019	18.7722	0.91896	0.0:0.0:1.0:0.0	.	.	.	.	X	1491;1498;1491;1491;1474;1491;1490;1491	.	ENSP00000345834:E1491X	E	+	1	0	MLLT4	168095375	1.000000	0.71417	0.968000	0.41197	0.989000	0.77384	9.180000	0.94867	2.423000	0.82170	0.561000	0.74099	GAG	.	.		0.602	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	NM_005936		T	168352526	G	T	168352526	4	4	250	1	0	0	0	0	0	1	0	0	9638	1059	37	1	4585	1	MLLT4	6	168352526	Nonsense_Mutation	SNP	G	TCGA-ED-A8O6-01A-11D-A35Z-10	598345	168352526	2762541	32	34035										
WBSCR17	64409	hgsc.bcm.edu	37	chr7	71175897	71175897	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	caagagcagcctgtacaagcGctggaacttcatccaggtga	11	11	1	2	rs370276097		TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr7:71175897G>A	ENST00000333538.5	+	10	2286	c.1652G>A	c.(1651-1653)cGc>cAc	p.R551H	WBSCR17_ENST00000498380.2_3'UTR	NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17	551	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(5)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(7)|large_intestine(22)|lung(45)|ovary(2)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	100		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				CTGTACAAGCGCTGGAACTTC	0.607																																					p.R551H		Atlas-SNP	.											.	WBSCR17	208	.	0			c.G1652A						.	G	HIS/ARG	0,4406		0,0,2203	47	42	44		1652	5.3	1	7		44	1,8599	1.2+/-3.3	0,1,4299	no	missense	WBSCR17	NM_022479.1	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	551/599	71175897	1,13005	2203	4300	6503	SO:0001583	missense	64409	exon10			ACAAGCGCTGGAA	AF410457	CCDS5540.1	7q11.23	2014-03-13			ENSG00000185274	ENSG00000185274		"Glycosyltransferase family 2 domain containing"	16347	protein-coding gene	gene with protein product	"polypeptide N-acetylgalactosaminyltransferase-like 3", "polypeptide GalNAc transferase 3"	615137				12073013, 15744064, 22787146	Standard	NM_022479		Approved	GALNTL3, GalNAc-T5L	uc003tvy.4	Q6IS24	OTTHUMG00000129783	ENST00000333538.5:c.1652G>A	chr7.hg19:g.71175897G>A	ENSP00000329654:p.Arg551His	58.0	0.0		40.0	6.0	NM_022479	Q8NFV9|Q9NTA8	Missense_Mutation	SNP	ENST00000333538.5	hg19	CCDS5540.1	.	.	.	.	.	.	.	.	.	.	G	17.26	3.344400	0.61073	0.0	1.16E-4	ENSG00000185274	ENST00000333538	T	0.32272	1.46	5.28	5.28	0.74379	Ricin B-related lectin (1);Ricin B lectin (3);	0.085119	0.64402	D	0.000013	T	0.36386	0.0965	L	0.29908	0.895	0.47819	D	0.999523	D	0.65815	0.995	P	0.56648	0.803	T	0.01940	-1.1243	10	0.15066	T	0.55	.	17.6589	0.88185	0.0:0.0:1.0:0.0	.	551	Q6IS24	GLTL3_HUMAN	H	551	ENSP00000329654:R551H	ENSP00000329654:R551H	R	+	2	0	WBSCR17	70813833	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.846000	0.48262	2.746000	0.94184	0.655000	0.94253	CGC	.	.		0.607	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252006.1	NM_022479		A	71175897	G	A	71175897	3	1	250	1	0	0	0	0	1	0	0	0	17279	1087	38	1	1690	1	WBSCR17	7	71175897	Missense_Mutation	SNP	G	TCGA-ED-A8O6-01A-11D-A35Z-10		71175897	87962766	33	34036										
MRPL15	29088	hgsc.bcm.edu	37	chr8	55047918	55047918	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	ctgccgcgtgtgagcctggcCaacttaaagccgaatcccgg	12	14	0	1			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr8:55047918C>T	ENST00000260102.4	+	1	149	c.75C>T	c.(73-75)gcC>gcT	p.A25A		NM_014175.3	NP_054894.1	Q9P015	RM15_HUMAN	mitochondrial ribosomal protein L15	25					translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)|skin(3)	10		Lung NSC(129;0.109)|all_epithelial(80;0.134)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;4.3e-07)|Epithelial(17;5.79e-05)|all cancers(17;0.000458)			TGAGCCTGGCCAACTTAAAGC	0.662																																					p.A25A		Atlas-SNP	.											.	MRPL15	26	.	0			c.C75T						.						12	14	14					8																	55047918		2077	4072	6149	SO:0001819	synonymous_variant	29088	exon1			CCTGGCCAACTTA	AB051619	CCDS6158.1	8q11.2-q13	2012-09-13			ENSG00000137547	ENSG00000137547		"Mitochondrial ribosomal proteins / large subunits"	14054	protein-coding gene	gene with protein product		611828				11543634	Standard	NM_014175		Approved	RPML7, MRP-L7, HSPC145, L15mt, MRP-L15	uc003xsa.2	Q9P015	OTTHUMG00000164315	ENST00000260102.4:c.75C>T	chr8.hg19:g.55047918C>T		508.0	0.0		435.0	126.0	NM_014175	Q96Q54|Q9H0Y1	Silent	SNP	ENST00000260102.4	hg19	CCDS6158.1																																																																																			.	.		0.662	MRPL15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378254.1	NM_014175		T	55047918	C	T	55047918	2	4	250	1	0	0	0	0	0	0	0	1	9789	581	21	3		3	MRPL15	8	55047918	Silent	SNP	C	TCGA-ED-A8O6-01A-11D-A35Z-10		55047918	91316104	34	34037										
NCOA2	10499	hgsc.bcm.edu	37	chr8	71128948	71128948	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	tttcttgtctctgccctggaGgggtcagaggtattttctcc	11	10	4	1			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr8:71128948G>A	ENST00000452400.2	-	3	214	c.33C>T	c.(31-33)ccC>ccT	p.P11P		NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	11					cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucose metabolic process (GO:0010906)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|signal transducer activity (GO:0004871)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)		PAX3/NCOA2(4)|HEY1/NCOA2(10)	NS(1)|breast(4)|endometrium(7)|kidney(4)|large_intestine(10)|lung(25)|ovary(1)|pancreas(2)|prostate(2)|skin(4)	60	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			CTGCCCTGGAGGGGTCAGAGG	0.433			T	"RUNXBP2, HEY1"	"AML, Chondrosarcoma"																																p.P11P		Atlas-SNP	.		Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	.	NCOA2	147	.	0			c.C33T						.						175	166	169					8																	71128948		1862	4116	5978	SO:0001819	synonymous_variant	10499	exon3			CCTGGAGGGGTCA	X97674	CCDS47872.1	8q13.3	2011-07-01			ENSG00000140396	ENSG00000140396		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7669	protein-coding gene	gene with protein product		601993				9111344, 8670870	Standard	XM_005251128		Approved	TIF2, GRIP1, NCoA-2, KAT13C, bHLHe75	uc003xyn.1	Q15596	OTTHUMG00000164671	ENST00000452400.2:c.33C>T	chr8.hg19:g.71128948G>A		117.0	0.0		197.0	29.0	NM_006540	Q14CD2	Silent	SNP	ENST00000452400.2	hg19	CCDS47872.1																																																																																			.	.		0.433	NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379696.1			A	71128948	G	A	71128948	2	1	250	1	0	0	0	0	0	0	0	1	10238	987	35	3		3	NCOA2	8	71128948	Silent	SNP	G	TCGA-ED-A8O6-01A-11D-A35Z-10	16081030	71128948	75235074	35	34038										
MMP16	4325	hgsc.bcm.edu	37	chr8	89209504	89209504	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	ctgacattctggggtcagtcGgtggaaggtagccgtacttt	14	8	2	1			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr8:89209504G>A	ENST00000286614.6	-	2	445	c.164C>T	c.(163-165)cCg>cTg	p.P55L	MMP16_ENST00000544227.1_5'UTR	NM_005941.4	NP_005932.2	P51512	MMP16_HUMAN	matrix metallopeptidase 16 (membrane-inserted)	55					chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)	Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(51)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	81					Marimastat(DB00786)	GGGGTCAGTCGGTGGAAGGTA	0.418																																					p.P55L		Atlas-SNP	.											.	MMP16	176	.	0			c.C164T						.						83	74	77					8																	89209504		2203	4300	6503	SO:0001583	missense	4325	exon2			TCAGTCGGTGGAA	D85511	CCDS6246.1	8q21	2009-01-09	2005-08-08		ENSG00000156103	ENSG00000156103			7162	protein-coding gene	gene with protein product		602262	"matrix metalloproteinase 16 (membrane-inserted)", "chromosome 8 open reading frame 57"	C8orf57		7559440	Standard	NM_005941		Approved	MT3-MMP, DKFZp761D112	uc003yeb.4	P51512	OTTHUMG00000163769	ENST00000286614.6:c.164C>T	chr8.hg19:g.89209504G>A	ENSP00000286614:p.Pro55Leu	147.0	0.0		210.0	29.0	NM_005941	B2RAN7|Q14824|Q52H48	Missense_Mutation	SNP	ENST00000286614.6	hg19	CCDS6246.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.283010	0.80692	.	.	ENSG00000156103	ENST00000286614;ENST00000522726	T;T	0.37752	1.18;1.18	6.07	6.07	0.98685	Peptidoglycan binding-like (2);Metallopeptidase, catalytic domain (1);	0.147359	0.64402	D	0.000009	T	0.65291	0.2677	M	0.87328	2.875	0.80722	D	1	D;D	0.62365	0.991;0.985	P;P	0.60173	0.794;0.87	T	0.68534	-0.5383	10	0.66056	D	0.02	.	20.6525	0.99598	0.0:0.0:1.0:0.0	.	55;55	P51512-2;P51512	.;MMP16_HUMAN	L	55;72	ENSP00000286614:P55L;ENSP00000429147:P72L	ENSP00000286614:P55L	P	-	2	0	MMP16	89278620	1.000000	0.71417	0.991000	0.47740	0.995000	0.86356	3.042000	0.49815	2.890000	0.99128	0.585000	0.79938	CCG	.	.		0.418	MMP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375304.2	NM_005941		A	89209504	G	A	89209504	3	1	250	1	0	0	0	0	1	0	0	0	9664	1116	39	1	1851	1	MMP16	8	89209504	Missense_Mutation	SNP	G	TCGA-ED-A8O6-01A-11D-A35Z-10	18080556	89209504	57154518	36	34039										
VPS13B	157680	hgsc.bcm.edu	37	chr8	100443809	100443809	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	ttaaagccatgttgaatataTctgaaagctgtagaagtcct	8	6	1	3			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr8:100443809T>C	ENST00000358544.2	+	22	3238	c.3127T>C	c.(3127-3129)Tct>Cct	p.S1043P	VPS13B_ENST00000357162.2_Missense_Mutation_p.S1043P|VPS13B_ENST00000395996.1_Missense_Mutation_p.S1043P	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	1043					protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			GTTGAATATATCTGAAAGCTG	0.338																																					p.S1043P	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											.	VPS13B	811	.	0			c.T3127C						.						80	88	85					8																	100443809		2202	4298	6500	SO:0001583	missense	157680	exon22			AATATATCTGAAA	AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.3127T>C	chr8.hg19:g.100443809T>C	ENSP00000351346:p.Ser1043Pro	117.0	0.0		172.0	8.0	NM_152564	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	hg19	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	T	11.88	1.770651	0.31320	.	.	ENSG00000132549	ENST00000357162;ENST00000358544;ENST00000395996	T;T;T	0.37411	1.2;1.2;1.2	4.59	-1.39	0.08997	.	1.411450	0.04107	N	0.313987	T	0.21307	0.0513	N	0.24115	0.695	0.09310	N	0.999996	B;B;B;B	0.32693	0.256;0.256;0.38;0.168	B;B;B;B	0.29440	0.064;0.099;0.102;0.064	T	0.14699	-1.0463	10	0.32370	T	0.25	.	3.9247	0.09259	0.372:0.1526:0.0:0.4754	.	1042;1043;1043;1043	Q7Z7G8-6;Q7Z7G8-2;Q7Z7G8;Q7Z7G8-3	.;.;VP13B_HUMAN;.	P	1043	ENSP00000349685:S1043P;ENSP00000351346:S1043P;ENSP00000379318:S1043P	ENSP00000349685:S1043P	S	+	1	0	VPS13B	100512985	0.090000	0.21635	0.071000	0.20095	0.808000	0.45660	0.389000	0.20751	-0.067000	0.12976	0.454000	0.30748	TCT	.	.		0.338	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		C	100443809	T	C	100443809	3	2	250	1	0	0	0	0	1	0	0	0	17205	1435	50	2	3332	2	VPS13B	8	100443809	Missense_Mutation	SNP	T	TCGA-ED-A8O6-01A-11D-A35Z-10	11234305	100443809	45920213	37	34040										
ANGPT1	284	hgsc.bcm.edu	37	chr8	108297043	108297043	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	ggcaaaaataaactcattccCcagccaatattcaccggagg	7	12	2	0			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr8:108297043C>A	ENST00000520734.1	-	6	757	c.472G>T	c.(472-474)Ggg>Tgg	p.G158W	ANGPT1_ENST00000518386.1_Intron|ANGPT1_ENST00000520052.1_Missense_Mutation_p.G157W			Q15389	ANGP1_HUMAN	angiopoietin 1	358					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell-substrate adhesion (GO:0031589)|glomerulus vasculature development (GO:0072012)|hemopoiesis (GO:0030097)|heparin biosynthetic process (GO:0030210)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of vascular permeability (GO:0043116)|positive chemotaxis (GO:0050918)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of receptor internalization (GO:0002092)|protein localization to cell surface (GO:0034394)|regulation of satellite cell proliferation (GO:0014842)|sprouting angiogenesis (GO:0002040)|Tie signaling pathway (GO:0048014)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(13)|ovary(4)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	43	Breast(1;5.06e-08)		OV - Ovarian serous cystadenocarcinoma(57;5.53e-09)			AACTCATTCCCCAGCCAATAT	0.413																																					p.G358W		Atlas-SNP	.											.	ANGPT1	111	.	0			c.G1072T						.						74	68	70					8																	108297043		2203	4300	6503	SO:0001583	missense	284	exon7			CATTCCCCAGCCA	D13628	CCDS6306.1, CCDS56551.1	8q23.1	2013-02-06			ENSG00000154188	ENSG00000154188		"Fibrinogen C domain containing"	484	protein-coding gene	gene with protein product		601667				9545648	Standard	NM_001146		Approved	KIAA0003, Ang1	uc003ymn.3	Q15389	OTTHUMG00000164812	ENST00000520734.1:c.472G>T	chr8.hg19:g.108297043C>A	ENSP00000430750:p.Gly158Trp	165.0	0.0		237.0	41.0	NM_001146	Q5HYA0	Missense_Mutation	SNP	ENST00000520734.1	hg19		.	.	.	.	.	.	.	.	.	.	C	28.5	4.928310	0.92389	.	.	ENSG00000154188	ENST00000517746;ENST00000297450;ENST00000520734;ENST00000520052	D;D;D;D	0.82526	-1.62;-1.62;-1.62;-1.62	5.73	5.73	0.89815	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.000000	0.85682	D	0.000000	D	0.95924	0.8673	H	0.99659	4.685	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.97718	1.0195	10	0.87932	D	0	.	19.8897	0.96925	0.0:1.0:0.0:0.0	.	157;358;358	E7ERK4;Q5HYA0;Q15389	.;.;ANGP1_HUMAN	W	358;357;158;157	ENSP00000428340:G358W;ENSP00000297450:G357W;ENSP00000430750:G158W;ENSP00000429349:G157W	ENSP00000297450:G357W	G	-	1	0	ANGPT1	108366219	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.709000	0.92574	0.650000	0.86243	GGG	.	.		0.413	ANGPT1-002	PUTATIVE	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000380428.2	NM_001146, NM_139290		A	108297043	C	A	108297043	3	1	250	1	0	0	0	0	1	0	0	0	610	623	22	3	436	3	ANGPT1	8	108297043	Missense_Mutation	SNP	C	TCGA-ED-A8O6-01A-11D-A35Z-10	7853234	108297043	38066979	38	34041										
PLEC	5339	hgsc.bcm.edu	37	chr8	144994165	144994165	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	ccacggtgaccttgcccgtgCggaactgacgcaacagctcc	11	16	0	2			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr8:144994165C>T	ENST00000322810.4	-	32	10404	c.10235G>A	c.(10234-10236)cGc>cAc	p.R3412H	PLEC_ENST00000345136.3_Missense_Mutation_p.R3275H|PLEC_ENST00000356346.3_Missense_Mutation_p.R3261H|PLEC_ENST00000398774.2_Missense_Mutation_p.R3243H|PLEC_ENST00000357649.2_Missense_Mutation_p.R3279H|PLEC_ENST00000354958.2_Missense_Mutation_p.R3253H|PLEC_ENST00000354589.3_Missense_Mutation_p.R3275H|PLEC_ENST00000436759.2_Missense_Mutation_p.R3302H|PLEC_ENST00000527096.1_Missense_Mutation_p.R3298H	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	3412	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						CTTGCCCGTGCGGAACTGACG	0.617																																					p.R3412H		Atlas-SNP	.											.	PLEC	1144	.	0			c.G10235A						.						62	72	69					8																	144994165		2184	4274	6458	SO:0001583	missense	5339	exon32			CCCGTGCGGAACT	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"plectin 1, intermediate filament binding protein, 500kD", "epidermolysis bullosa simplex 1 (Ogna)", "plectin 1, intermediate filament binding protein 500kDa"	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.10235G>A	chr8.hg19:g.144994165C>T	ENSP00000323856:p.Arg3412His	70.0	0.0		147.0	12.0	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	hg19	CCDS43772.1	.	.	.	.	.	.	.	.	.	.	C	6.557	0.471058	0.12461	.	.	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	T;T;T;T;T;T;T;T;T	0.78481	-1.15;-1.15;-1.18;-1.18;-1.17;-1.15;-1.15;-1.15;-1.15	4.91	3.06	0.35304	.	0.000000	0.64402	U	0.000008	T	0.70701	0.3254	M	0.64404	1.975	0.44073	D	0.996823	B;B;B;B;B;B;B;B	0.22211	0.066;0.038;0.038;0.039;0.038;0.038;0.066;0.066	B;B;B;B;B;B;B;B	0.17098	0.017;0.017;0.017;0.007;0.017;0.017;0.017;0.017	T	0.69687	-0.5078	10	0.72032	D	0.01	.	6.4724	0.22015	0.0:0.6151:0.0:0.3849	.	3302;3261;3253;3412;3243;3275;3279;3275	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	H	3275;3279;3275;3243;3412;3253;3261;3302;3298	ENSP00000344848:R3275H;ENSP00000350277:R3279H;ENSP00000346602:R3275H;ENSP00000381756:R3243H;ENSP00000323856:R3412H;ENSP00000347044:R3253H;ENSP00000348702:R3261H;ENSP00000388180:R3302H;ENSP00000434583:R3298H	ENSP00000323856:R3412H	R	-	2	0	PLEC	145066153	1.000000	0.71417	0.999000	0.59377	0.210000	0.24377	2.825000	0.48096	1.173000	0.42796	0.448000	0.29417	CGC	.	.		0.617	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		T	144994165	C	T	144994165	3	4	250	1	0	0	0	0	1	0	0	0	12061	768	27	1	3823	1	PLEC	8	144994165	Missense_Mutation	SNP	C	TCGA-ED-A8O6-01A-11D-A35Z-10	36697122	144994165	1369857	39	34042										
ZNF483	158399	hgsc.bcm.edu	37	chr9	114304927	114304927	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	atccctttccaaacatcagaGaattcatactggagagaaac	6	10	2	2			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr9:114304927G>C	ENST00000309235.5	+	6	1870	c.1712G>C	c.(1711-1713)aGa>aCa	p.R571T	ZNF483_ENST00000358151.4_Intron	NM_133464.2	NP_597721.2	Q8TF39	ZN483_HUMAN	zinc finger protein 483	571					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(11)|ovary(1)|skin(5)	31						AAACATCAGAGAATTCATACT	0.408																																					p.R571T		Atlas-SNP	.											.	ZNF483	78	.	0			c.G1712C						.						57	64	62					9																	114304927		2203	4300	6503	SO:0001583	missense	158399	exon6			ATCAGAGAATTCA	AB075842	CCDS35105.1, CCDS35106.1	9q32	2013-01-09			ENSG00000173258	ENSG00000173258		"Zinc fingers, C2H2-type", "-", "-", "-"	23384	protein-coding gene	gene with protein product							Standard	NM_001007169		Approved	ZKSCAN16, KIAA1962, ZSCAN48	uc004bff.2	Q8TF39	OTTHUMG00000020490	ENST00000309235.5:c.1712G>C	chr9.hg19:g.114304927G>C	ENSP00000311679:p.Arg571Thr	110.0	0.0		80.0	40.0	NM_133464	Q5VZN2|Q8NAE1	Missense_Mutation	SNP	ENST00000309235.5	hg19	CCDS35106.1	.	.	.	.	.	.	.	.	.	.	G	15.25	2.777428	0.49786	.	.	ENSG00000173258	ENST00000309235	T	0.02421	4.3	3.84	3.84	0.44239	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.49305	D	0.000160	T	0.09468	0.0233	L	0.45228	1.405	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.17715	-1.0360	10	0.40728	T	0.16	-27.2936	14.0547	0.64761	0.0:0.0:1.0:0.0	.	571	Q8TF39	ZN483_HUMAN	T	571	ENSP00000311679:R571T	ENSP00000311679:R571T	R	+	2	0	ZNF483	113344748	0.797000	0.28877	0.997000	0.53966	0.863000	0.49368	2.136000	0.42121	2.436000	0.82500	0.655000	0.94253	AGA	.	.		0.408	ZNF483-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053641.1	XM_088567		C	114304927	G	C	114304927	3	2	250	1	0	0	0	0	1	0	0	0	17951	942	33	4	1730	4	ZNF483	9	114304927	Missense_Mutation	SNP	G	TCGA-ED-A8O6-01A-11D-A35Z-10		114304927	26908504	40	34043										
RASSF4	83937	hgsc.bcm.edu	37	chr10	45486499	45486499	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	ctgatggaagctgacttgggCgtggaagtcccccatgaagt	14	9	0	3			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr10:45486499C>T	ENST00000340258.5	+	9	902	c.789C>T	c.(787-789)ggC>ggT	p.G263G	RASSF4_ENST00000374417.2_3'UTR|RASSF4_ENST00000334940.6_Silent_p.G272G|RASSF4_ENST00000472561.1_3'UTR	NM_032023.3	NP_114412.2	Q8WYP3	RIN2_HUMAN	Ras association (RalGDS/AF-6) domain family member 4	0					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of catalytic activity (GO:0050790)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|small GTPase regulator activity (GO:0005083)			NS(1)|endometrium(2)|large_intestine(6)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16						CTGACTTGGGCGTGGAAGTCC	0.582																																					p.G263G		Atlas-SNP	.											.	RASSF4	33	.	0			c.C789T						.						47	52	50					10																	45486499		2203	4300	6503	SO:0001819	synonymous_variant	83937	exon9			CTTGGGCGTGGAA	BC032593	CCDS7208.1	10q11.1	2008-02-22	2008-02-22		ENSG00000107551	ENSG00000107551			20793	protein-coding gene	gene with protein product		610559					Standard	NM_032023		Approved	AD037, MGC44914	uc001jbo.3	Q9H2L5	OTTHUMG00000018060	ENST00000340258.5:c.789C>T	chr10.hg19:g.45486499C>T		40.0	0.0		22.0	12.0	NM_032023	Q00425|Q5TFT8|Q9BQL3|Q9H071	Silent	SNP	ENST00000340258.5	hg19	CCDS7208.1																																																																																			.	.		0.582	RASSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047745.2	NM_032023		T	45486499	C	T	45486499	2	4	250	1	0	0	0	0	0	0	0	1	13103	755	27	1		1	RASSF4	10	45486499	Silent	SNP	C	TCGA-ED-A8O6-01A-11D-A35Z-10		45486499	90048248	41	34044										
NCOA4	8031	hgsc.bcm.edu	37	chr10	51584844	51584844	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	cccaggaatcccataagctgCggaagcctgagaatggcagt	12	11	0	1	rs148951318		TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr10:51584844C>T	ENST00000443446.1	+	8	1172	c.943C>T	c.(943-945)Cgg>Tgg	p.R315W	NCOA4_ENST00000438493.1_Missense_Mutation_p.R331W|NCOA4_ENST00000344348.6_Missense_Mutation_p.R315W|NCOA4_ENST00000414907.2_Missense_Mutation_p.R149W|NCOA4_ENST00000452682.1_Missense_Mutation_p.R331W|NCOA4_ENST00000374082.1_Missense_Mutation_p.R315W|NCOA4_ENST00000430396.2_Missense_Mutation_p.R215W|NCOA4_ENST00000374087.4_Missense_Mutation_p.R315W	NM_001145262.1	NP_001138734.1	Q13772	NCOA4_HUMAN	nuclear receptor coactivator 4	315					androgen receptor signaling pathway (GO:0030521)|male gonad development (GO:0008584)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|skin(1)	5						CCATAAGCTGCGGAAGCCTGA	0.453			T	RET	papillary thyroid																																p.R331W		Atlas-SNP	.		Dom	yes		10	10q11.2	8031	nuclear receptor coactivator 4 - PTC3 (ELE1)		E	.	NCOA4	58	.	0			c.C991T						.	C	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	80	81	81		991,991,943,943,943	1.7	0.3	10	dbSNP_134	81	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense,missense,missense,missense	NCOA4	NM_001145260.1,NM_001145261.1,NM_001145262.1,NM_001145263.1,NM_005437.3	101,101,101,101,101	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign,benign,benign,benign,benign	331/651,331/631,315/615,315/615,315/615	51584844	2,13004	2203	4300	6503	SO:0001583	missense	8031	exon9			AAGCTGCGGAAGC	L49399	CCDS73092.1, CCDS73093.1, CCDS73094.1	10q11.2	2014-04-10			ENSG00000138293	ENSG00000266412			7671	protein-coding gene	gene with protein product	"RET-activating gene ELE1"	601984				8290261, 8643607, 24695223	Standard	NM_001145260		Approved	ARA70, RFG, ELE1, PTC3, DKFZp762E1112	uc009xon.3	Q13772	OTTHUMG00000188314	ENST00000443446.1:c.943C>T	chr10.hg19:g.51584844C>T	ENSP00000390713:p.Arg315Trp	52.0	0.0		37.0	20.0	NM_001145261	A8K8W5|B4E260|E9PAV7|J3KQN8|Q14239	Missense_Mutation	SNP	ENST00000443446.1	hg19	CCDS7237.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	3.369|3.369	-0.128802|-0.128802	0.06753|0.06753	0.0|0.0	2.33E-4|2.33E-4	ENSG00000138293|ENSG00000138293	ENST00000431200|ENST00000438493;ENST00000452682;ENST00000430396;ENST00000374087;ENST00000414907;ENST00000344348;ENST00000374082;ENST00000443446	.|T;T;T;T;T;T;T;T	.|0.31510	.|1.49;1.49;1.49;1.49;1.49;1.49;1.49;1.49	4.64|4.64	1.74|1.74	0.24563|0.24563	.|.	.|0.474612	.|0.20926	.|N	.|0.083197	T|T	0.13157|0.13157	0.0319|0.0319	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B;B;B;B	.|0.11235	.|0.002;0.004;0.004;0.001	.|B;B;B;B	.|0.09377	.|0.003;0.003;0.003;0.004	T|T	0.28202|0.28202	-1.0051|-1.0051	5|9	.|.	.|.	.|.	-3.2217|-3.2217	8.2501|8.2501	0.31712|0.31712	0.0:0.3743:0.467:0.1587|0.0:0.3743:0.467:0.1587	.|.	.|215;331;331;315	.|B4DF87;B4E260;E9PAV7;Q13772	.|.;.;.;NCOA4_HUMAN	V|W	230|331;331;215;315;149;315;315;315	.|ENSP00000405146:R331W;ENSP00000395465:R331W;ENSP00000393053:R215W;ENSP00000363200:R315W;ENSP00000411018:R149W;ENSP00000344552:R315W;ENSP00000363195:R315W;ENSP00000390713:R315W	.|.	A|R	+|+	2|1	0|2	NCOA4|NCOA4	51254850|51254850	0.459000|0.459000	0.25768|0.25768	0.302000|0.302000	0.25058|0.25058	0.064000|0.064000	0.16182|0.16182	0.997000|0.997000	0.29731|0.29731	0.428000|0.428000	0.26173|0.26173	-0.795000|-0.795000	0.03280|0.03280	GCG|CGG	.	C|1.000;T|0.000		0.453	NCOA4-204	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048052.1	NM_005437		T	51584844	C	T	51584844	3	4	250	1	0	0	0	0	1	0	0	0	10240	759	27	1	1021	1	NCOA4	10	51584844	Missense_Mutation	SNP	C	TCGA-ED-A8O6-01A-11D-A35Z-10	6098345	51584844	83949903	42	34045										
ANXA11	311	hgsc.bcm.edu	37	chr10	81926706	81926706	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	cgctgcttgttggagcgactCcccaggcagtcaatgatggc	13	12	1	1	rs561842051		TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr10:81926706C>G	ENST00000438331.1	-	8	1166	c.684G>C	c.(682-684)ggG>ggC	p.G228G	ANXA11_ENST00000360615.4_Silent_p.G228G|ANXA11_ENST00000265447.4_Silent_p.G228G|ANXA11_ENST00000372231.3_Silent_p.G228G|ANXA11_ENST00000537102.1_Silent_p.G195G|ANXA11_ENST00000422982.3_Silent_p.G228G|ANXA11_ENST00000535999.1_Silent_p.G228G	NM_145869.1	NP_665876.1	P50995	ANX11_HUMAN	annexin A11	228					cytokinesis, completion of separation (GO:0007109)|phagocytosis (GO:0006909)|response to calcium ion (GO:0051592)	azurophil granule (GO:0042582)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|specific granule (GO:0042581)|spindle (GO:0005819)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|MHC class II protein complex binding (GO:0023026)|phosphatidylethanolamine binding (GO:0008429)|poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)			endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|urinary_tract(1)	17	Prostate(51;0.00985)|all_epithelial(25;0.0951)		Colorectal(32;0.109)			TGGAGCGACTCCCCAGGCAGT	0.632																																					p.G228G		Atlas-SNP	.											.	ANXA11	32	.	0			c.G684C						.						57	48	51					10																	81926706		2203	4300	6503	SO:0001819	synonymous_variant	311	exon7			GCGACTCCCCAGG	L19605	CCDS7364.1, CCDS60576.1	10q22.3	2005-11-09			ENSG00000122359	ENSG00000122359		"Annexins"	535	protein-coding gene	gene with protein product		602572		ANX11		7508441, 9503022	Standard	NM_001157		Approved		uc001kbt.1	P50995	OTTHUMG00000018604	ENST00000438331.1:c.684G>C	chr10.hg19:g.81926706C>G		41.0	0.0		21.0	9.0	NM_145868	B4DVE7	Silent	SNP	ENST00000438331.1	hg19	CCDS7364.1																																																																																			.	.		0.632	ANXA11-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049044.1	NM_145869		G	81926706	C	G	81926706	2	3	250	1	0	0	0	0	0	0	0	1	716	842	30	4		4	ANXA11	10	81926706	Silent	SNP	C	TCGA-ED-A8O6-01A-11D-A35Z-10	30341862	81926706	53608041	43	34046										
TIAL1	7073	hgsc.bcm.edu	37	chr10	121338278	121338278	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	gcaggtggtttacgagtggcCcaattggttcggatttgacg	15	7	0	1			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr10:121338278C>T	ENST00000436547.2	-	7	560	c.516G>A	c.(514-516)tgG>tgA	p.W172*	TIAL1_ENST00000463089.2_5'Flank|TIAL1_ENST00000369093.2_Nonsense_Mutation_p.W189*|TIAL1_ENST00000369092.4_Nonsense_Mutation_p.W49*	NM_003252.3	NP_003243.1	Q01085	TIAR_HUMAN	TIA1 cytotoxic granule-associated RNA binding protein-like 1	172	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				apoptotic process (GO:0006915)|defense response (GO:0006952)|germ cell development (GO:0007281)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell division (GO:0017145)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(3)|ovary(1)	13		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.00239)|BRCA - Breast invasive adenocarcinoma(275;0.0932)		TACGAGTGGCCCAATTGGTTC	0.398																																					p.W189X		Atlas-SNP	.											.	TIAL1	47	.	0			c.G567A						.						160	141	147					10																	121338278		2203	4300	6503	SO:0001587	stop_gained	7073	exon7			AGTGGCCCAATTG	AL833106	CCDS7613.1, CCDS31295.1	10q	2013-02-12	2001-11-28		ENSG00000151923	ENSG00000151923		"RNA binding motif (RRM) containing"	11804	protein-coding gene	gene with protein product		603413	"TIA1 cytotoxic granule-associated RNA-binding protein-like 1"			1326761	Standard	XM_005270108		Approved	TIAR	uc001lej.1	Q01085	OTTHUMG00000019156	ENST00000436547.2:c.516G>A	chr10.hg19:g.121338278C>T	ENSP00000394902:p.Trp172*	162.0	0.0		103.0	20.0	NM_001033925	A8K3T0|A8K4L9	Nonsense_Mutation	SNP	ENST00000436547.2	hg19	CCDS7613.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.708191	0.89018	.	.	ENSG00000151923	ENST00000369093;ENST00000369092;ENST00000436547	.	.	.	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.9553	19.646	0.95777	0.0:1.0:0.0:0.0	.	.	.	.	X	189;49;172	.	ENSP00000358088:W49X	W	-	3	0	TIAL1	121328268	1.000000	0.71417	1.000000	0.80357	0.888000	0.51559	7.644000	0.83416	2.645000	0.89757	0.591000	0.81541	TGG	.	.		0.398	TIAL1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050672.2	NM_022333, NM_003252		T	121338278	C	T	121338278	4	4	250	1	0	0	0	0	0	1	0	0	15904	624	22	3	635	3	TIAL1	10	121338278	Nonsense_Mutation	SNP	C	TCGA-ED-A8O6-01A-11D-A35Z-10	39411572	121338278	14196469	44	34047										
C10orf137	26098	hgsc.bcm.edu	37	chr10	127412384	127412385	+	Frame_Shift_Ins	INS	-	-	A													0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	tcttaattttttaagaacatINSaaaaaaactcctgaaaattc							TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr10:127412384_127412385insA	ENST00000356792.4	+	4	621_622	c.389_390insA	c.(388-393)ataaaafs	p.IK130fs	C10orf137_ENST00000337623.3_Frame_Shift_Ins_p.IK130fs	NM_001202438.1	NP_001189367.1	Q3B7T1	EDRF1_HUMAN		130					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(20)|ovary(8)|pancreas(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	61		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)				TTTAAGAACATAAAAAAACTCC	0.322																																					p.I130fs		Atlas-INDEL	.											.	C10orf137	153	.	0			c.389_390insA						.																																			SO:0001589	frameshift_variant	26098	exon4			.																												ENST00000356792.4:c.396dupA	chr10.hg19:g.127412391_127412391dupA	ENSP00000349244:p.Ile130fs	450.0	0.0		264.0	120.0	NM_015608	B2RC65|Q3KR40|Q4G190|Q5VZQ4|Q8IZ74|Q9Y3W4	Frame_Shift_Ins	INS	ENST00000356792.4	hg19	CCDS55733.1																																																																																			.	.		0.322	C10orf137-007	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388539.1			A	127412385	-	A	127412384	7	5	250	1	0	1	1	0	0	0	0	0	1596	1406	49	0	403	0	C10orf137	10	127412384	Frame_Shift_Ins	INS	-	TCGA-ED-A8O6-01A-11D-A35Z-10	6074106	127412384	8122363	45	34048										
C10orf90	118611	hgsc.bcm.edu	37	chr10	128147623	128147623	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	gcttaccactcagaggatggGgaatcgtgaactgcttcttg	12	9	2	2			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr10:128147623G>T	ENST00000284694.7	-	6	2003	c.1883C>A	c.(1882-1884)cCc>cAc	p.P628H	C10orf90_ENST00000544758.1_Missense_Mutation_p.P725H|C10orf90_ENST00000480379.1_Missense_Mutation_p.P32H|C10orf90_ENST00000356858.3_Missense_Mutation_p.P581H|C10orf90_ENST00000454341.1_Missense_Mutation_p.P531H	NM_001004298.2	NP_001004298.2	Q96M02	CJ090_HUMAN	chromosome 10 open reading frame 90	628	ALMS motif. {ECO:0000250}.				mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell growth (GO:0030308)|protein stabilization (GO:0050821)|response to ionizing radiation (GO:0010212)|response to UV (GO:0009411)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)				NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(19)|liver(1)|lung(29)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	65		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)		CAGAGGATGGGGAATCGTGAA	0.587																																					p.P628H		Atlas-SNP	.											.	C10orf90	121	.	0			c.C1883A						.						132	100	111					10																	128147623		2203	4300	6503	SO:0001583	missense	118611	exon6			GGATGGGGAATCG	BC034828	CCDS31310.1	10q26.2	2012-05-31			ENSG00000154493	ENSG00000154493			26563	protein-coding gene	gene with protein product	"fragile-site associated tumor suppressor"					20843368, 20154723	Standard	NM_001004298		Approved	FLJ32938, bA422P15.2, FATS	uc001ljq.3	Q96M02	OTTHUMG00000019245	ENST00000284694.7:c.1883C>A	chr10.hg19:g.128147623G>T	ENSP00000284694:p.Pro628His	64.0	0.0		42.0	25.0	NM_001004298	B9EIQ9|Q5JRP6|Q5T023|Q8NCV5|Q8WU75	Missense_Mutation	SNP	ENST00000284694.7	hg19	CCDS31310.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.94|15.94	2.981425|2.981425	0.53827|0.53827	.|.	.|.	ENSG00000154493|ENSG00000154493	ENST00000356858;ENST00000284694;ENST00000454341;ENST00000544758;ENST00000432642|ENST00000424927	T;T;T;T|T	0.22945|0.49432	2.01;2.07;2.04;1.93|0.78	5.01|5.01	5.01|5.01	0.66863|0.66863	.|.	0.000000|0.000000	0.43110|0.43110	D|D	0.000618|0.000618	T|T	0.62171|0.62171	0.2406|0.2406	M|M	0.65498|0.65498	2.005|2.005	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	1.0;1.0;0.999|.	T|T	0.65274|0.65274	-0.6208|-0.6208	10|8	0.87932|0.72032	D|D	0|0.01	-23.1691|-23.1691	15.1753|15.1753	0.72907|0.72907	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	725;628;531|.	F5GZL2;Q96M02;Q96M02-2|.	.;CJ090_HUMAN;.|.	H|T	581;628;531;725;628|171	ENSP00000284694:P628H;ENSP00000398786:P531H;ENSP00000444369:P725H;ENSP00000405995:P628H|ENSP00000411609:P171T	ENSP00000284694:P628H|ENSP00000411609:P171T	P|P	-|-	2|1	0|0	C10orf90|C10orf90	128137613|128137613	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.490000|0.490000	0.33462|0.33462	6.020000|6.020000	0.70826|0.70826	2.595000|2.595000	0.87683|0.87683	0.655000|0.655000	0.94253|0.94253	CCC|CCC	.	.		0.587	C10orf90-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004298		T	128147623	G	T	128147623	3	4	250	1	0	0	0	0	1	0	0	0	1625	1232	43	3	232	3	C10orf90	10	128147623	Missense_Mutation	SNP	G	TCGA-ED-A8O6-01A-11D-A35Z-10	735239	128147623	7387124	46	34049										
MRGPRD	116512	hgsc.bcm.edu	37	chr11	68747517	68747517	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	cccatctcattggtgcccacGgtgggcgtctccccaccttc	9	18	2	0			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr11:68747517G>A	ENST00000309106.3	-	1	938	c.939C>T	c.(937-939)acC>acT	p.T313T		NM_198923.2	NP_944605.2	Q8TDS7	MRGRD_HUMAN	MAS-related GPR, member D	313						extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(7)|pancreas(1)|prostate(2)	22			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			TGGTGCCCACGGTGGGCGTCT	0.687																																					p.T313T		Atlas-SNP	.											.	MRGPRD	53	.	0			c.C939T						.																																			SO:0001819	synonymous_variant	116512	exon1			GCCCACGGTGGGC	AB083627	CCDS31625.1	11q13.3	2012-08-21			ENSG00000172938	ENSG00000172938		"GPCR / Class A : Orphans"	29626	protein-coding gene	gene with protein product		607231				11551509, 12909716	Standard	NM_198923		Approved	mrgD	uc010rqf.2	Q8TDS7	OTTHUMG00000167896	ENST00000309106.3:c.939C>T	chr11.hg19:g.68747517G>A		65.0	0.0		38.0	31.0	NM_198923	Q8NGK7	Silent	SNP	ENST00000309106.3	hg19	CCDS31625.1																																																																																			.	.		0.687	MRGPRD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396874.1	NM_198923		A	68747517	G	A	68747517	2	1	250	1	0	0	0	0	0	0	0	1	9772	1103	39	1		1	MRGPRD	11	68747517	Silent	SNP	G	TCGA-ED-A8O6-01A-11D-A35Z-10		68747517	66258999	47	34050										
DDX47	51202	hgsc.bcm.edu	37	chr12	12974235	12974235	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	actgctggagaccccgcagcGtttgtttgccctagttctta	10	12	1	1			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr12:12974235G>A	ENST00000358007.3	+	3	297	c.275G>A	c.(274-276)cGt>cAt	p.R92H	DDX47_ENST00000392155.2_3'UTR|DDX47_ENST00000352940.4_Missense_Mutation_p.R92H	NM_016355.3	NP_057439.2	Q9H0S4	DDX47_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 47	92	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16		Prostate(47;0.0526)		BRCA - Breast invasive adenocarcinoma(232;0.0354)		ACCCCGCAGCGTTTGTTTGCC	0.532																																					p.R92H		Atlas-SNP	.											.	DDX47	37	.	0			c.G275A						.						144	142	142					12																	12974235		2203	4300	6503	SO:0001583	missense	51202	exon3			CGCAGCGTTTGTT	AK127712	CCDS8655.1, CCDS8656.1	12p13.2	2010-07-06			ENSG00000213782	ENSG00000213782		"DEAD-boxes"	18682	protein-coding gene	gene with protein product		615428					Standard	NM_016355		Approved	DKFZp564O176, FLJ30012, HQ0256, RRP3	uc001rax.3	Q9H0S4	OTTHUMG00000168709	ENST00000358007.3:c.275G>A	chr12.hg19:g.12974235G>A	ENSP00000350698:p.Arg92His	135.0	0.0		86.0	31.0	NM_201224	B3KXP4|G5E955|Q96GM0|Q96NV8|Q9UI98	Missense_Mutation	SNP	ENST00000358007.3	hg19	CCDS8655.1	.	.	.	.	.	.	.	.	.	.	G	17.87	3.494810	0.64186	.	.	ENSG00000213782	ENST00000352940;ENST00000358007	T;T	0.42900	0.96;2.43	5.6	4.71	0.59529	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.30696	0.0773	N	0.25094	0.71	0.58432	D	0.999999	B;B;B;B	0.26120	0.038;0.044;0.036;0.142	B;B;B;B	0.22152	0.038;0.014;0.008;0.022	T	0.06075	-1.0847	10	0.40728	T	0.16	-5.7876	14.6773	0.68989	0.0699:0.0:0.93:0.0	.	92;92;92;92	B4DYP6;Q9H4E3;G5E955;Q9H0S4	.;.;.;DDX47_HUMAN	H	92	ENSP00000319578:R92H;ENSP00000350698:R92H	ENSP00000319578:R92H	R	+	2	0	DDX47	12865502	1.000000	0.71417	0.860000	0.33809	0.824000	0.46624	9.201000	0.95017	1.370000	0.46153	0.555000	0.69702	CGT	.	.		0.532	DDX47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400674.1	NM_016355		A	12974235	G	A	12974235	3	1	250	1	0	0	0	0	1	0	0	0	4367	1145	40	1	285	1	DDX47	12	12974235	Missense_Mutation	SNP	G	TCGA-ED-A8O6-01A-11D-A35Z-10		12974235	120877660	48	34051										
OR6C74	254783	hgsc.bcm.edu	37	chr12	55641389	55641389	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	tttttcactattctcttgggGgcaactgaattttttcttct	6	8	4	1			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr12:55641389G>T	ENST00000343870.4	+	1	408	c.318G>T	c.(316-318)ggG>ggT	p.G106G		NM_001005490.1	NP_001005490.1	A6NCV1	O6C74_HUMAN	olfactory receptor, family 6, subfamily C, member 74	106						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|large_intestine(3)|lung(7)|prostate(1)	12						TTCTCTTGGGGGCAACTGAAT	0.448																																					p.G106G		Atlas-SNP	.											.	OR6C74	52	.	0			c.G318T						.						163	169	167					12																	55641389		2203	4300	6503	SO:0001819	synonymous_variant	254783	exon1			CTTGGGGGCAACT		CCDS31816.1	12q13.13	2012-08-09			ENSG00000197706	ENSG00000197706		"GPCR / Class A : Olfactory receptors"	31303	protein-coding gene	gene with protein product							Standard	NM_001005490		Approved		uc010spg.2	A6NCV1	OTTHUMG00000165162	ENST00000343870.4:c.318G>T	chr12.hg19:g.55641389G>T		80.0	0.0		57.0	22.0	NM_001005490		Silent	SNP	ENST00000343870.4	hg19	CCDS31816.1																																																																																			.	.		0.448	OR6C74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382312.1			T	55641389	G	T	55641389	2	4	250	1	0	0	0	0	0	0	0	1	11207	1219	43	3		3	OR6C74	12	55641389	Silent	SNP	G	TCGA-ED-A8O6-01A-11D-A35Z-10	42667154	55641389	78210506	49	34052										
TSFM	10102	hgsc.bcm.edu	37	chr12	58186770	58186770	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	gttttcttcgtgcacttaggGtttcttgaattcctctgagc	9	9	3	2			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr12:58186770G>T	ENST00000550559.1	+	5	500	c.485G>T	c.(484-486)gGt>gTt	p.G162V	TSFM_ENST00000350762.5_Splice_Site_p.G122V|TSFM_ENST00000543727.1_Splice_Site_p.G162V|TSFM_ENST00000497617.1_3'UTR|TSFM_ENST00000323833.8_Splice_Site_p.G183V|TSFM_ENST00000454289.3_Splice_Site_p.G162V|TSFM_ENST00000548851.1_Splice_Site_p.G162V|TSFM_ENST00000540550.1_Intron					Ts translation elongation factor, mitochondrial											endometrium(1)|kidney(1)|large_intestine(5)|prostate(1)	8	all_cancers(7;6.31e-80)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)					TGCACTTAGGGTTTCTTGAAT	0.388																																					p.G183V		Atlas-SNP	.											.	TSFM	26	.	0			c.G548T						.						124	113	117					12																	58186770		2203	4300	6503	SO:0001630	splice_region_variant	10102	exon6			CTTAGGGTTTCTT	L37936	CCDS8958.2, CCDS53809.1, CCDS53810.1, CCDS53811.1	12q14.1	2006-06-10			ENSG00000123297	ENSG00000123297			12367	protein-coding gene	gene with protein product		604723				7615523	Standard	NM_005726		Approved	EF-Tsmt, EF-TS	uc001sqh.3	P43897	OTTHUMG00000153042	ENST00000550559.1:c.484-1G>T	chr12.hg19:g.58186770G>T		109.0	0.0		64.0	21.0	NM_001172696		Missense_Mutation	SNP	ENST00000550559.1	hg19		.	.	.	.	.	.	.	.	.	.	G	9.110	1.006363	0.19199	.	.	ENSG00000123297	ENST00000454289;ENST00000543727;ENST00000323833;ENST00000350762;ENST00000550559;ENST00000548851;ENST00000434359;ENST00000457189	T;T;T	0.76578	-1.03;-1.03;-1.03	5.07	5.07	0.68467	Translation elongation factor EFTs/EF1B, dimerisation (2);	0.153055	0.64402	D	0.000015	T	0.73241	0.3562	L	0.42245	1.32	0.80722	D	1	B;B;B	0.17667	0.023;0.016;0.01	B;B;B	0.25140	0.05;0.058;0.01	T	0.71115	-0.4686	10	0.62326	D	0.03	.	15.4596	0.75342	0.0:0.0:1.0:0.0	.	122;162;183	F8W6R3;P43897;P43897-2	.;EFTS_HUMAN;.	V	162;162;183;122;162;162;112;112	ENSP00000388330:G162V;ENSP00000242983:G122V;ENSP00000389162:G112V	ENSP00000313877:G183V	G	+	2	0	TSFM	56473037	1.000000	0.71417	1.000000	0.80357	0.209000	0.24338	1.596000	0.36718	2.631000	0.89168	0.655000	0.94253	GGT	.	.		0.388	TSFM-008	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000409343.1	NM_005726	Missense_Mutation	T	58186770	G	T	58186770	5	4	250	1	0	0	0	0	0	0	1	0	16630	1275	44	3	570	3	TSFM	12	58186770	Splice_Site	SNP	G	TCGA-ED-A8O6-01A-11D-A35Z-10	2545381	58186770	75665125	50	34053										
BBS10	79738	hgsc.bcm.edu	37	chr12	76741192	76741192	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	aagtagtcacacatcaactgTgaaataaatttatgattatt	5	5	2	2			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr12:76741192T>G	ENST00000393262.3	-	2	656	c.573A>C	c.(571-573)tcA>tcC	p.S191S		NM_024685.3	NP_078961.3	Q8TAM1	BBS10_HUMAN	Bardet-Biedl syndrome 10	191					cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|regulation of protein complex assembly (GO:0043254)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	cell projection (GO:0042995)	ATP binding (GO:0005524)|RNA polymerase II repressing transcription factor binding (GO:0001103)			endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)	19						ACATCAACTGTGAAATAAATT	0.363									Bardet-Biedl syndrome																												p.S191S		Atlas-SNP	.											.	BBS10	46	.	0			c.A573C						.						88	81	83					12																	76741192		2203	4300	6503	SO:0001819	synonymous_variant	79738	exon2	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	CAACTGTGAAATA	BC026355	CCDS9014.2	12q21.2	2014-06-17	2006-04-28	2006-04-28	ENSG00000179941	ENSG00000179941		"Heat Shock Proteins / Chaperonins"	26291	protein-coding gene	gene with protein product		610148	"chromosome 12 open reading frame 58"	C12orf58		16582908	Standard	NM_024685		Approved	FLJ23560	uc001syd.1	Q8TAM1	OTTHUMG00000147352	ENST00000393262.3:c.573A>C	chr12.hg19:g.76741192T>G		182.0	0.0		109.0	33.0	NM_024685	Q96CW2|Q9H5D2	Silent	SNP	ENST00000393262.3	hg19	CCDS9014.2																																																																																			.	.		0.363	BBS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303983.2	NM_024685		G	76741192	T	G	76741192	2	3	250	1	0	0	0	0	0	0	0	1	1336	1683	59	5		5	BBS10	12	76741192	Silent	SNP	T	TCGA-ED-A8O6-01A-11D-A35Z-10	18554422	76741192	57110703	51	34054										
PRDM4	11108	hgsc.bcm.edu	37	chr12	108136024	108136024	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	gttgagcataatctcggctaTaataaaaaagcagttcattt	7	6	2	1			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr12:108136024T>C	ENST00000228437.5	-	9	2042	c.1583A>G	c.(1582-1584)tAt>tGt	p.Y528C	RP11-864J10.4_ENST00000546714.1_RNA	NM_012406.3	NP_036538.3	Q9UKN5	PRDM4_HUMAN	PR domain containing 4	528	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				cell proliferation (GO:0008283)|negative regulation of cell cycle (GO:0045786)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|methyltransferase activity (GO:0008168)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(2)|skin(2)|urinary_tract(1)	20						ATCTCGGCTATAATAAAAAAG	0.353																																					p.Y528C		Atlas-SNP	.											.	PRDM4	64	.	0			c.A1583G						.						81	78	79					12																	108136024		2203	4300	6503	SO:0001583	missense	11108	exon9			CGGCTATAATAAA	AF144757	CCDS9115.1	12q23-q24.1	2013-01-08				ENSG00000110851		"Zinc fingers, C2H2-type"	9348	protein-coding gene	gene with protein product		605780				10552934	Standard	NM_012406		Approved	PFM1	uc001tmp.3	Q9UKN5	OTTHUMG00000169914	ENST00000228437.5:c.1583A>G	chr12.hg19:g.108136024T>C	ENSP00000228437:p.Tyr528Cys	119.0	0.0		69.0	24.0	NM_012406	Q9UFA6	Missense_Mutation	SNP	ENST00000228437.5	hg19	CCDS9115.1	.	.	.	.	.	.	.	.	.	.	T	19.88	3.909270	0.72868	.	.	ENSG00000110851	ENST00000228437	T	0.81415	-1.49	5.76	5.76	0.90799	SET domain (2);	0.117422	0.64402	N	0.000012	D	0.89054	0.6606	M	0.89353	3.025	0.80722	D	1	D	0.89917	1.0	D	0.67725	0.953	D	0.87769	0.2604	10	0.05959	T	0.93	.	16.0843	0.81031	0.0:0.0:0.0:1.0	.	528	Q9UKN5	PRDM4_HUMAN	C	528	ENSP00000228437:Y528C	ENSP00000228437:Y528C	Y	-	2	0	PRDM4	106660154	1.000000	0.71417	0.956000	0.39512	0.966000	0.64601	5.656000	0.67988	2.191000	0.70037	0.533000	0.62120	TAT	.	.		0.353	PRDM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406546.1	NM_012406		C	108136024	T	C	108136024	3	2	250	1	0	0	0	0	1	0	0	0	12471	1406	49	2	838	2	PRDM4	12	108136024	Missense_Mutation	SNP	T	TCGA-ED-A8O6-01A-11D-A35Z-10	31394832	108136024	25715871	52	34055										
SDSL	113675	hgsc.bcm.edu	37	chr12	113874658	113874658	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	gtggaggacaccgaggctgtGagcgctgtgcagcagctcct	16	11	0	1			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr12:113874658G>C	ENST00000403593.4	+	7	1036	c.774G>C	c.(772-774)gtG>gtC	p.V258V	SDSL_ENST00000345635.4_Silent_p.V258V			Q96GA7	SDSL_HUMAN	serine dehydratase-like	258					cellular amino acid metabolic process (GO:0006520)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	L-serine ammonia-lyase activity (GO:0003941)|L-threonine ammonia-lyase activity (GO:0004794)|pyridoxal phosphate binding (GO:0030170)			endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)	15						CCGAGGCTGTGAGCGCTGTGC	0.612																																					p.V258V		Atlas-SNP	.											SDSL,NS,carcinoma,0,1	SDSL	36	.	0			c.G774C						.						105	77	86					12																	113874658		2203	4300	6503	SO:0001819	synonymous_variant	113675	exon8			GGCTGTGAGCGCT	AF134473	CCDS9170.1	12q24.21	2014-06-24				ENSG00000139410			30404	protein-coding gene	gene with protein product						16580895	Standard	NM_138432		Approved	SDS-RS1, cSDH	uc001tvi.3	Q96GA7		ENST00000403593.4:c.774G>C	chr12.hg19:g.113874658G>C		47.0	0.0		17.0	7.0	NM_138432		Silent	SNP	ENST00000403593.4	hg19	CCDS9170.1	.	.	.	.	.	.	.	.	.	.	G	0.224	-1.026305	0.02045	.	.	ENSG00000139410	ENST00000546672	.	.	.	3.71	0.668	0.17912	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-24.3854	8.7232	0.34454	0.0885:0.2984:0.6131:0.0	.	.	.	.	S	154	.	.	X	+	2	2	SDSL	112359041	0.986000	0.35501	0.037000	0.18230	0.039000	0.13416	1.883000	0.39658	0.311000	0.23014	0.462000	0.41574	TGA	.	.		0.612	SDSL-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404782.1	NM_138432		C	113874658	G	C	113874658	2	2	250	1	0	0	0	0	0	0	0	1	13991	1277	45	4		4	SDSL	12	113874658	Silent	SNP	G	TCGA-ED-A8O6-01A-11D-A35Z-10	5738634	113874658	19977237	53	34056										
PDS5B	23047	hgsc.bcm.edu	37	chr13	33232401	33232401	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	atttatgtttataacaagacAgttgaaggggctagaggata	11	3	0	3			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr13:33232401A>T	ENST00000315596.10	+	4	524	c.338A>T	c.(337-339)cAg>cTg	p.Q113L		NM_015032.3	NP_055847.1	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae)	113					cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of cell proliferation (GO:0008285)|regulation of cell proliferation (GO:0042127)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|lung(14)|ovary(5)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	62		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)		ATAACAAGACAGTTGAAGGGG	0.299																																					p.Q113L		Atlas-SNP	.											.	PDS5B	141	.	0			c.A338T						.						51	47	49					13																	33232401		1789	4056	5845	SO:0001583	missense	23047	exon4			CAAGACAGTTGAA	AB023196	CCDS41878.1	13q12.3	2008-02-05	2007-07-18	2007-07-18	ENSG00000083642	ENSG00000083642			20418	protein-coding gene	gene with protein product		605333	"androgen-induced proliferation inhibitor"	APRIN		8812419, 10215036	Standard	NM_015032		Approved	AS3, KIAA0979, FLJ23236, CG008	uc010abf.3	Q9NTI5	OTTHUMG00000016704	ENST00000315596.10:c.338A>T	chr13.hg19:g.33232401A>T	ENSP00000313851:p.Gln113Leu	363.0	0.0		240.0	108.0	NM_015032	Q5R3S3|Q5W0K8|Q6NSC3|Q8IXT6|Q9H5N8|Q9Y2I5|Q9Y451	Missense_Mutation	SNP	ENST00000315596.10	hg19	CCDS41878.1	.	.	.	.	.	.	.	.	.	.	A	28.4	4.916995	0.92249	.	.	ENSG00000083642	ENST00000315596;ENST00000421084	T	0.62788	-0.0	5.4	5.4	0.78164	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.76183	0.3952	M	0.78456	2.415	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.87578	0.998;0.995	T	0.74269	-0.3720	10	0.07175	T	0.84	-20.387	15.4314	0.75102	1.0:0.0:0.0:0.0	.	113;113	Q9NTI5;Q9NTI5-3	PDS5B_HUMAN;.	L	113	ENSP00000313851:Q113L	ENSP00000313851:Q113L	Q	+	2	0	PDS5B	32130401	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	7.343000	0.79319	2.038000	0.60285	0.533000	0.62120	CAG	.	.		0.299	PDS5B-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044428.3	NM_015032		T	33232401	A	T	33232401	3	4	250	1	0	0	0	0	1	0	0	0	11701	188	7	4	348	4	PDS5B	13	33232401	Missense_Mutation	SNP	A	TCGA-ED-A8O6-01A-11D-A35Z-10		33232401	81937477	54	34057										
NPAS3	64067	hgsc.bcm.edu	37	chr14	34029335	34029335	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	tttttcctgcagtccctggaTggctttgtatttgcactaaa	8	9	0	0			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr14:34029335T>A	ENST00000356141.4	+	5	477	c.477T>A	c.(475-477)gaT>gaA	p.D159E	NPAS3_ENST00000357798.5_Missense_Mutation_p.D146E|NPAS3_ENST00000551008.1_Missense_Mutation_p.D57E|NPAS3_ENST00000547068.1_Missense_Mutation_p.D55E|NPAS3_ENST00000346562.2_Missense_Mutation_p.D127E|NPAS3_ENST00000548645.1_Missense_Mutation_p.D129E|NPAS3_ENST00000341321.4_Missense_Mutation_p.D159E|NPAS3_ENST00000551492.1_Missense_Mutation_p.D164E			Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3	159	PAS 1. {ECO:0000255|PROSITE- ProRule:PRU00140}.				locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|positive regulation of transcription, DNA-templated (GO:0045893)|startle response (GO:0001964)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(4)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	40	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)		AGTCCCTGGATGGCTTTGTAT	0.323																																					p.D159E		Atlas-SNP	.											.	NPAS3	266	.	0			c.T477A						.						75	73	73					14																	34029335		2203	4300	6503	SO:0001583	missense	64067	exon5			CCTGGATGGCTTT	AF164438	CCDS9645.1, CCDS53891.1, CCDS53892.1, CCDS55912.1	14q13.1	2013-08-23			ENSG00000151322	ENSG00000151322		"Basic helix-loop-helix proteins"	19311	protein-coding gene	gene with protein product		609430					Standard	NM_022123		Approved	MOP6, PASD6, bHLHe12	uc001wru.3	Q8IXF0	OTTHUMG00000140215	ENST00000356141.4:c.477T>A	chr14.hg19:g.34029335T>A	ENSP00000348460:p.Asp159Glu	262.0	0.0		175.0	33.0	NM_001164749	Q86US6|Q86US7|Q8IXF2|Q9BY81|Q9H323|Q9Y4L8	Missense_Mutation	SNP	ENST00000356141.4	hg19	CCDS53891.1	.	.	.	.	.	.	.	.	.	.	T	19.13	3.766933	0.69878	.	.	ENSG00000151322	ENST00000551634;ENST00000551492;ENST00000346562;ENST00000341321;ENST00000548645;ENST00000356141;ENST00000357798;ENST00000547068;ENST00000551008;ENST00000546849	T;T;T;T;T;T;T;T;T;T	0.18338	2.22;2.22;2.22;2.22;2.22;2.22;2.22;2.22;2.22;2.22	5.81	3.41	0.39046	PAS (2);PAS fold (1);	0.000000	0.85682	D	0.000000	T	0.32675	0.0837	L	0.60455	1.87	0.58432	D	0.999999	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.991;0.999;0.999;1.0;1.0	T	0.02020	-1.1228	10	0.35671	T	0.21	.	8.7798	0.34785	0.0:0.2082:0.0:0.7918	.	57;129;159;127;146	F8W0C2;Q8IXF0-2;Q8IXF0;Q8IXF0-4;Q8IXF0-3	.;.;NPAS3_HUMAN;.;.	E	136;164;127;159;129;159;146;55;57;69	ENSP00000448373:D136E;ENSP00000450392:D164E;ENSP00000319610:D127E;ENSP00000344158:D159E;ENSP00000448916:D129E;ENSP00000348460:D159E;ENSP00000350446:D146E;ENSP00000449542:D55E;ENSP00000447213:D57E;ENSP00000446700:D69E	ENSP00000344158:D159E	D	+	3	2	NPAS3	33099086	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.619000	0.36965	1.022000	0.39626	0.377000	0.23210	GAT	.	.		0.323	NPAS3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276645.1			A	34029335	T	A	34029335	3	1	250	1	0	0	0	0	1	0	0	0	10573	1461	51	4	550	4	NPAS3	14	34029335	Missense_Mutation	SNP	T	TCGA-ED-A8O6-01A-11D-A35Z-10		34029335	73320205	55	34058										
OTX2	5015	hgsc.bcm.edu	37	chr14	57270981	57270981	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	atgtctgggtaccgggtcttGgcaaacagtgcttccagcac	12	11	2	0			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr14:57270981G>T	ENST00000555006.1	-	3	582	c.174C>A	c.(172-174)gcC>gcA	p.A58A	OTX2_ENST00000408990.3_Silent_p.A58A|OTX2_ENST00000554559.1_Intron|OTX2_ENST00000554788.1_Intron|OTX2_ENST00000339475.5_Silent_p.A66A			P32243	OTX2_HUMAN	orthodenticle homeobox 2	58					axon guidance (GO:0007411)|cell fate specification (GO:0001708)|diencephalon morphogenesis (GO:0048852)|dorsal/ventral pattern formation (GO:0009953)|endoderm development (GO:0007492)|eye photoreceptor cell fate commitment (GO:0042706)|forebrain development (GO:0030900)|inner ear morphogenesis (GO:0042472)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|neuron fate determination (GO:0048664)|positive regulation of embryonic development (GO:0040019)|positive regulation of gastrulation (GO:2000543)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|primitive streak formation (GO:0090009)|protein complex assembly (GO:0006461)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of smoothened signaling pathway (GO:0008589)|somite rostral/caudal axis specification (GO:0032525)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|nucleus (GO:0005634)|protein complex (GO:0043234)	eukaryotic initiation factor 4E binding (GO:0008190)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	19	Medulloblastoma(1;0.00184)|all_neural(1;0.00414)					ACCGGGTCTTGGCAAACAGTG	0.612																																					p.A66A		Atlas-SNP	.											.	OTX2	47	.	0			c.C198A						.						88	73	78					14																	57270981		2203	4300	6503	SO:0001819	synonymous_variant	5015	exon2			GGTCTTGGCAAAC	AF298117	CCDS9728.1, CCDS41960.1	14q22.3	2014-09-17	2007-02-15		ENSG00000165588	ENSG00000165588		"Homeoboxes / PRD class"	8522	protein-coding gene	gene with protein product		600037	"orthodenticle homolog 2 (Drosophila)"			7959790	Standard	NM_021728		Approved		uc031qor.1	P32243	OTTHUMG00000152338	ENST00000555006.1:c.174C>A	chr14.hg19:g.57270981G>T		126.0	0.0		62.0	16.0	NM_001270525	B2RAN5|Q6GTV3|Q9HAW3|Q9P2R1	Silent	SNP	ENST00000555006.1	hg19	CCDS41960.1																																																																																			.	.		0.612	OTX2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411522.1	NM_021728.		T	57270981	G	T	57270981	2	4	250	1	0	0	0	0	0	0	0	1	11330	1335	47	3		3	OTX2	14	57270981	Silent	SNP	G	TCGA-ED-A8O6-01A-11D-A35Z-10	23241646	57270981	50078559	56	34059										
TRIP11	9321	hgsc.bcm.edu	37	chr14	92472196	92472197	+	Frame_Shift_Ins	INS	-	-	T													0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	ttagagtctccacaatagtgINStttttttccagagaaagctg					rs570814392	byFrequency	TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr14:92472196_92472197insT	ENST00000267622.4	-	11	2496_2497	c.2123_2124insA	c.(2122-2124)aacfs	p.N708fs		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	708					protein targeting to Golgi (GO:0000042)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular septum development (GO:0003281)	acrosomal membrane (GO:0002080)|cis-Golgi network (GO:0005801)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(2)|endometrium(1)|kidney(8)|large_intestine(12)|lung(17)|ovary(7)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	58				COAD - Colon adenocarcinoma(157;0.223)		CCACAATAGTGTTTTTTTCCAG	0.366			T	PDGFRB	AML																																p.N708fs	Ovarian(84;609 1888 9852 42686)	Atlas-INDEL	.		Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	.,1	TRIP11	184	.	0			c.2124_2125insA						.																																			SO:0001589	frameshift_variant	9321	exon11			.	L40380	CCDS9899.1	14q31-q32	2008-05-02				ENSG00000100815			12305	protein-coding gene	gene with protein product		604505				7776974, 9373237	Standard	NM_004239		Approved	CEV14, Trip230, GMAP-210	uc001xzy.3	Q15643		ENST00000267622.4:c.2124dupA	chr14.hg19:g.92472203_92472203dupT	ENSP00000267622:p.Asn708fs	117.0	0.0		60.0	30.0	NM_004239	B2RUT2|O14689|O15154|O95949	Frame_Shift_Ins	INS	ENST00000267622.4	hg19	CCDS9899.1																																																																																			.	.		0.366	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1			T	92472197	-	T	92472196	7	5	250	1	0	1	1	0	0	0	0	0	16570	1368	48	0	3859	0	TRIP11	14	92472196	Frame_Shift_Ins	INS	-	TCGA-ED-A8O6-01A-11D-A35Z-10	35201215	92472196	14877344	57	34060										
ITPK1	3705	hgsc.bcm.edu	37	chr14	93407963	93407963	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	caatgctgctggaagctgggCgacacgccggcgttgcagcc	15	13	0	0			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr14:93407963C>G	ENST00000267615.6	-	11	1361	c.1188G>C	c.(1186-1188)tcG>tcC	p.S396S	ITPK1_ENST00000555495.1_Silent_p.S277S|ITPK1_ENST00000354313.3_Intron|ITPK1_ENST00000556603.2_Silent_p.S396S			Q13572	ITPK1_HUMAN	inositol-tetrakisphosphate 1-kinase	396					blood coagulation (GO:0007596)|dephosphorylation (GO:0016311)|inositol phosphate metabolic process (GO:0043647)|inositol trisphosphate metabolic process (GO:0032957)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|inositol tetrakisphosphate 1-kinase activity (GO:0047325)|inositol-1,3,4,5,6-pentakisphosphate 1-phosphatase activity (GO:0052825)|inositol-1,3,4,6-tetrakisphosphate 1-phosphatase activity (GO:0052831)|inositol-1,3,4,6-tetrakisphosphate 6-phosphatase activity (GO:0052830)|inositol-1,3,4-trisphosphate 5-kinase activity (GO:0052726)|inositol-1,3,4-trisphosphate 6-kinase activity (GO:0052725)|inositol-3,4,6-trisphosphate 1-kinase activity (GO:0052835)|isomerase activity (GO:0016853)|magnesium ion binding (GO:0000287)			endometrium(1)|large_intestine(3)|lung(6)|ovary(1)	11		all_cancers(154;0.077)|all_epithelial(191;0.247)		Epithelial(152;0.124)|all cancers(159;0.169)		GGAAGCTGGGCGACACGCCGG	0.716																																					p.S396S		Atlas-SNP	.											.	ITPK1	53	.	0			c.G1188C						.						3	2	2					14																	93407963		1528	3078	4606	SO:0001819	synonymous_variant	3705	exon11			GCTGGGCGACACG	U51336	CCDS9907.1, CCDS45157.1	14q32.12	2012-08-16	2011-04-28		ENSG00000100605	ENSG00000100605	2.7.1.134		6177	protein-coding gene	gene with protein product		601838	"inositol 1,3,4-triphosphate 5/6 kinase"			8662638, 11042108	Standard	NM_014216		Approved		uc001ybh.3	Q13572	OTTHUMG00000171226	ENST00000267615.6:c.1188G>C	chr14.hg19:g.93407963C>G		59.0	0.0		42.0	22.0	NM_001142593	Q9BTL6|Q9H2E7	Silent	SNP	ENST00000267615.6	hg19	CCDS9907.1																																																																																			.	.		0.716	ITPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412421.2	NM_014216		G	93407963	C	G	93407963	2	3	250	1	0	0	0	0	0	0	0	1	7925	755	27	4		4	ITPK1	14	93407963	Silent	SNP	C	TCGA-ED-A8O6-01A-11D-A35Z-10	935767	93407963	13941577	58	34061										
USP50	373509	hgsc.bcm.edu	37	chr15	50822035	50822035	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	tttaggatatttccggaaaaTtgagcaaatataaggagtga	10	3	0	2			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr15:50822035T>C	ENST00000532404.1	-	6	1068	c.895A>G	c.(895-897)Att>Gtt	p.I299V	USP50_ENST00000530218.1_5'UTR	NM_203494.4	NP_987090.2	Q70EL3	UBP50_HUMAN	ubiquitin specific peptidase 50	304	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|kidney(2)|large_intestine(4)|liver(1)|lung(5)	13				all cancers(107;0.000519)|GBM - Glioblastoma multiforme(94;0.00288)		TTCCGGAAAATTGAGCAAATA	0.368																																					p.I299V		Atlas-SNP	.											.	USP50	24	.	0			c.A895G						.						153	139	144					15																	50822035		1846	4081	5927	SO:0001583	missense	373509	exon6			GGAAAATTGAGCA	AI990110	CCDS53944.1	15q21.1	2008-02-05	2005-08-08			ENSG00000170236		"Ubiquitin-specific peptidases"	20079	protein-coding gene	gene with protein product			"ubiquitin specific protease 50"			12838346	Standard	NM_203494		Approved		uc021sky.1	Q70EL3		ENST00000532404.1:c.895A>G	chr15.hg19:g.50822035T>C	ENSP00000434676:p.Ile299Val	181.0	0.0		100.0	34.0	NM_203494	E9PP86	Missense_Mutation	SNP	ENST00000532404.1	hg19	CCDS53944.1	.	.	.	.	.	.	.	.	.	.	T	8.160	0.789334	0.16258	.	.	ENSG00000170236	ENST00000532404	T	0.29917	1.55	5.67	-8.07	0.01098	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	1.024370	0.07824	N	0.960209	T	0.12774	0.0310	N	0.05230	-0.09	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.38001	-0.9681	10	0.21014	T	0.42	-5.4284	13.4312	0.61057	0.0:0.7007:0.1326:0.1667	.	304	Q70EL3	UBP50_HUMAN	V	299	ENSP00000434676:I299V	ENSP00000434676:I299V	I	-	1	0	USP50	48609327	0.019000	0.18553	0.482000	0.27366	0.542000	0.35054	-0.637000	0.05459	-1.272000	0.02427	0.533000	0.62120	ATT	.	.		0.368	USP50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395249.1			C	50822035	T	C	50822035	3	2	250	1	0	0	0	0	1	0	0	0	17097	1493	52	2	117	2	USP50	15	50822035	Missense_Mutation	SNP	T	TCGA-ED-A8O6-01A-11D-A35Z-10		50822035	51709357	59	34062										
CCDC102A	92922	hgsc.bcm.edu	37	chr16	57555012	57555012	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	ctcctgcttggtcttgctcaGctcctcatacttgatcttcc	6	15	4	1			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr16:57555012G>T	ENST00000258214.2	-	4	1135	c.889C>A	c.(889-891)Ctg>Atg	p.L297M		NM_033212.3	NP_149989.2	Q96A19	C102A_HUMAN	coiled-coil domain containing 102A	297										endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)	8						GTCTTGCTCAGCTCCTCATAC	0.552																																					p.L297M		Atlas-SNP	.											.	CCDC102A	22	.	0			c.C889A						.						169	143	152					16																	57555012		2198	4300	6498	SO:0001583	missense	92922	exon4			TGCTCAGCTCCTC	BC008285	CCDS10784.1	16q13	2008-02-05			ENSG00000135736	ENSG00000135736			28097	protein-coding gene	gene with protein product						12477932	Standard	NM_033212		Approved	MGC10992	uc002elw.3	Q96A19	OTTHUMG00000133472	ENST00000258214.2:c.889C>A	chr16.hg19:g.57555012G>T	ENSP00000258214:p.Leu297Met	38.0	0.0		22.0	16.0	NM_033212	Q9BT74	Missense_Mutation	SNP	ENST00000258214.2	hg19	CCDS10784.1	.	.	.	.	.	.	.	.	.	.	G	18.88	3.718379	0.68844	.	.	ENSG00000135736	ENST00000258214	T	0.55052	0.54	4.86	3.89	0.44902	.	0.086169	0.48767	D	0.000173	T	0.65790	0.2725	L	0.60067	1.865	0.53005	D	0.999961	D	0.89917	1.0	D	0.78314	0.991	T	0.64905	-0.6297	10	0.42905	T	0.14	-22.4329	11.6568	0.51324	0.0875:0.0:0.9125:0.0	.	297	Q96A19	C102A_HUMAN	M	297	ENSP00000258214:L297M	ENSP00000258214:L297M	L	-	1	2	CCDC102A	56112513	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.162000	0.77515	1.155000	0.42497	0.555000	0.69702	CTG	.	.		0.552	CCDC102A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257348.1	NM_033212		T	57555012	G	T	57555012	3	4	250	1	0	0	0	0	1	0	0	0	2738	962	34	3	787	3	CCDC102A	16	57555012	Missense_Mutation	SNP	G	TCGA-ED-A8O6-01A-11D-A35Z-10		57555012	32799741	60	34063										
NTN1	9423	hgsc.bcm.edu	37	chr17	8926432	8926432	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	gggtcacggccacagacatcCgcgtggccttcagccgcctg	13	16	2	1			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr17:8926432C>T	ENST00000173229.2	+	2	849	c.742C>T	c.(742-744)Cgc>Tgc	p.R248C	NTN1_ENST00000546090.1_Missense_Mutation_p.R248C|NTN1_ENST00000538852.1_Missense_Mutation_p.R248C	NM_004822.2	NP_004813.2	O95631	NET1_HUMAN	netrin 1	248	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|establishment of nucleus localization (GO:0040023)|inner ear morphogenesis (GO:0042472)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of axon extension (GO:0030517)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of cell proliferation (GO:0008284)|regulation of cell migration (GO:0030334)|single organismal cell-cell adhesion (GO:0016337)	basement membrane (GO:0005604)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)			NTN1/ACLY(2)	central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(5)|lung(5)	13						CACAGACATCCGCGTGGCCTT	0.687																																					p.R248C		Atlas-SNP	.											.	NTN1	31	.	0			c.C742T						.						12	12	12					17																	8926432		2146	4234	6380	SO:0001583	missense	9423	exon2			GACATCCGCGTGG	U75586	CCDS11148.1	17p13-p12	2013-03-01			ENSG00000065320	ENSG00000065320		"Netrins"	8029	protein-coding gene	gene with protein product	"Netrin-1"	601614				9950216	Standard	NM_004822		Approved	NTN1L	uc002glw.4	O95631	OTTHUMG00000130257	ENST00000173229.2:c.742C>T	chr17.hg19:g.8926432C>T	ENSP00000173229:p.Arg248Cys	81.0	0.0		48.0	34.0	NM_004822	E9KL51	Missense_Mutation	SNP	ENST00000173229.2	hg19	CCDS11148.1	.	.	.	.	.	.	.	.	.	.	C	17.62	3.435631	0.62955	.	.	ENSG00000065320	ENST00000173229;ENST00000538852;ENST00000546090	D;D;D	0.84944	-1.92;-1.92;-1.92	4.72	4.72	0.59763	Laminin, N-terminal (3);	0.062767	0.64402	D	0.000006	D	0.93200	0.7834	M	0.93594	3.435	0.45366	D	0.998357	D	0.76494	0.999	D	0.67900	0.954	D	0.94223	0.7469	10	0.87932	D	0	.	11.3219	0.49428	0.3085:0.6915:0.0:0.0	.	248	O95631	NET1_HUMAN	C	248	ENSP00000173229:R248C;ENSP00000443259:R248C;ENSP00000441611:R248C	ENSP00000173229:R248C	R	+	1	0	NTN1	8867157	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	2.809000	0.47971	2.325000	0.78763	0.655000	0.94253	CGC	.	.		0.687	NTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252583.1			T	8926432	C	T	8926432	3	4	250	1	0	0	0	0	1	0	0	0	10709	652	23	1	744	1	NTN1	17	8926432	Missense_Mutation	SNP	C	TCGA-ED-A8O6-01A-11D-A35Z-10		8926432	72268778	61	34064										
HAP1	9001	hgsc.bcm.edu	37	chr17	39888530	39888530	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	tccagcttgctgttctcctcCatcaaaacactgttctgttt	5	13	3	0			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr17:39888530C>T	ENST00000310778.5	-	3	675	c.666G>A	c.(664-666)atG>atA	p.M222I	HAP1_ENST00000347901.4_Missense_Mutation_p.M222I|HAP1_ENST00000393939.2_Missense_Mutation_p.M222I|HAP1_ENST00000341193.5_Missense_Mutation_p.M230I|JUP_ENST00000540235.1_Intron|RN7SL399P_ENST00000471648.2_RNA			P54257	HAP1_HUMAN	huntingtin-associated protein 1	222	HAP1 N-terminal.				anterograde axon cargo transport (GO:0008089)|autophagy (GO:0006914)|brain development (GO:0007420)|cell projection organization (GO:0030030)|exocytosis (GO:0006887)|negative regulation of beta-amyloid formation (GO:1902430)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|positive regulation of neurotrophin production (GO:0032901)|positive regulation of nonmotile primary cilium assembly (GO:1902857)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|protein localization (GO:0008104)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|regulation of organelle transport along microtubule (GO:1902513)|retrograde axon cargo transport (GO:0008090)|synaptic transmission (GO:0007268)|vesicle transport along microtubule (GO:0047496)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|inclusion body (GO:0016234)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|synapse (GO:0045202)	brain-derived neurotrophic factor binding (GO:0048403)|ion channel binding (GO:0044325)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(4)|skin(1)	21		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.0677)			TGTTCTCCTCCATCAAAACAC	0.587																																					p.M230I		Atlas-SNP	.											.	HAP1	48	.	0			c.G690A						.						76	69	71					17																	39888530		2203	4300	6503	SO:0001583	missense	9001	exon3			CTCCTCCATCAAA	AF040723	CCDS11406.1, CCDS42338.1, CCDS42339.1	17q21.2-q21.3	2008-04-23	2008-04-23		ENSG00000173805	ENSG00000173805			4812	protein-coding gene	gene with protein product	"neuroan 1"	600947		HAP2		7477378, 9668110	Standard	NM_177977		Approved	HLP, hHLP1, HIP5	uc002hxn.1	P54257	OTTHUMG00000133498	ENST00000310778.5:c.666G>A	chr17.hg19:g.39888530C>T	ENSP00000309392:p.Met222Ile	123.0	0.0		79.0	20.0	NM_001079870	A8MQB5|O75358|Q59GK4|Q9H4G3|Q9HA98|Q9NY90	Missense_Mutation	SNP	ENST00000310778.5	hg19		.	.	.	.	.	.	.	.	.	.	C	12.56	1.975737	0.34848	.	.	ENSG00000173805	ENST00000393939;ENST00000310778;ENST00000347901;ENST00000341193	T;T;T;T	0.18502	2.21;2.21;2.21;2.21	3.79	1.6	0.23607	.	0.131889	0.35378	N	0.003255	T	0.11965	0.0291	L	0.47716	1.5	0.23515	N	0.99752	P;P;B;B	0.38370	0.628;0.628;0.223;0.112	B;B;B;B	0.37601	0.254;0.254;0.085;0.084	T	0.12167	-1.0558	10	0.24483	T	0.36	-9.9294	4.6835	0.12747	0.0:0.6496:0.2259:0.1245	.	222;230;222;222	P54257-3;P54257-4;P54257-2;P54257	.;.;.;HAP1_HUMAN	I	222;222;222;230	ENSP00000377513:M222I;ENSP00000309392:M222I;ENSP00000334002:M222I;ENSP00000343170:M230I	ENSP00000309392:M222I	M	-	3	0	HAP1	37142056	0.943000	0.32029	0.993000	0.49108	0.982000	0.71751	-0.195000	0.09546	0.937000	0.37394	0.561000	0.74099	ATG	.	.		0.587	HAP1-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000389619.1	NM_003949		T	39888530	C	T	39888530	3	4	250	1	0	0	0	0	1	0	0	0	6962	594	21	3	1229	3	HAP1	17	39888530	Missense_Mutation	SNP	C	TCGA-ED-A8O6-01A-11D-A35Z-10	30962098	39888530	41306680	62	34065										
GHDC	84514	hgsc.bcm.edu	37	chr17	40344403	40344403	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	gagccgaagggccagtccccGtggcccctgctctagggcct	14	16	1	0			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr17:40344403G>A	ENST00000301671.8	-	4	1186	c.745C>T	c.(745-747)Cgg>Tgg	p.R249W	GHDC_ENST00000587427.1_Missense_Mutation_p.R249W|GHDC_ENST00000593209.1_Missense_Mutation_p.R249W|GHDC_ENST00000590520.1_5'Flank|GHDC_ENST00000428494.2_Missense_Mutation_p.R210W|GHDC_ENST00000436923.2_Missense_Mutation_p.R249W|GHDC_ENST00000414034.3_Missense_Mutation_p.R249W			Q8N2G8	GHDC_HUMAN	GH3 domain containing	249						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		all_cancers(22;0.000229)|Breast(137;0.00104)|all_epithelial(22;0.00304)		BRCA - Breast invasive adenocarcinoma(366;0.124)		GCCAGTCCCCGTGGCCCCTGC	0.682																																					p.R249W		Atlas-SNP	.											.	GHDC	63	.	0			c.C745T						.						44	52	49					17																	40344403		2201	4297	6498	SO:0001583	missense	84514	exon5			GTCCCCGTGGCCC	AF316997, BC011056	CCDS11422.1, CCDS45682.1	17q21.2	2006-08-02				ENSG00000167925			24438	protein-coding gene	gene with protein product		608587				11161808, 11735219	Standard	NR_024573		Approved	LGP1	uc002hzf.4	Q8N2G8		ENST00000301671.8:c.745C>T	chr17.hg19:g.40344403G>A	ENSP00000301671:p.Arg249Trp	74.0	0.0		39.0	9.0	NM_001142623	B4DQS4|E9PDB5|Q9BXM6	Missense_Mutation	SNP	ENST00000301671.8	hg19	CCDS11422.1	.	.	.	.	.	.	.	.	.	.	G	16.44	3.123182	0.56613	.	.	ENSG00000167925	ENST00000393854;ENST00000428494;ENST00000414034;ENST00000301671;ENST00000436923	.	.	.	4.21	3.24	0.37175	.	0.513584	0.16912	N	0.194459	T	0.55273	0.1910	M	0.64997	1.995	0.09310	N	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.72338	0.962;0.977;0.977	T	0.41466	-0.9507	9	0.72032	D	0.01	-3.9091	5.6388	0.17552	0.2491:0.0:0.7509:0.0	.	210;249;249	E9PDB5;Q8N2G8-2;Q8N2G8	.;.;GHDC_HUMAN	W	193;210;249;249;249	.	ENSP00000301671:R249W	R	-	1	2	GHDC	37597929	1.000000	0.71417	0.871000	0.34182	0.902000	0.53008	2.369000	0.44231	0.986000	0.38683	0.561000	0.74099	CGG	.	.		0.682	GHDC-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449794.1	NM_032484		A	40344403	G	A	40344403	3	1	250	1	0	0	0	0	1	0	0	0	6377	1144	40	1	960	1	GHDC	17	40344403	Missense_Mutation	SNP	G	TCGA-ED-A8O6-01A-11D-A35Z-10	455873	40344403	40850807	63	34066										
CHAF1A	10036	hgsc.bcm.edu	37	chr19	4433231	4433231	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	cccccacccccagcgaggatGccgccatcccctctaagtcc	7	22	1	0			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr19:4433231G>T	ENST00000301280.5	+	13	2469	c.2368G>T	c.(2368-2370)Gcc>Tcc	p.A790S	CTB-50L17.5_ENST00000590159.1_RNA|CHAF1A_ENST00000587368.1_3'UTR	NM_005483.2	NP_005474	Q13111	CAF1A_HUMAN	chromatin assembly factor 1, subunit A (p150)	790	Binds to p60.				cell cycle (GO:0007049)|chromatin assembly (GO:0031497)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|protein complex assembly (GO:0006461)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	CAF-1 complex (GO:0033186)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|identical protein binding (GO:0042802)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	27		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGCGAGGATGCCGCCATCCC	0.652								Chromatin Structure																													p.A790S		Atlas-SNP	.											.	CHAF1A	69	.	0			c.G2368T						.						71	72	71					19																	4433231		2203	4300	6503	SO:0001583	missense	10036	exon13			GAGGATGCCGCCA	U20979	CCDS32875.1	19p13.3	2008-07-16				ENSG00000167670			1910	protein-coding gene	gene with protein product	"chromatin assembly factor I (150 kDa)"	601246				7600578	Standard	NM_005483		Approved	CAF1P150, CAF1B, CAF-1, CAF1, P150, MGC71229	uc002mal.3	Q13111		ENST00000301280.5:c.2368G>T	chr19.hg19:g.4433231G>T	ENSP00000301280:p.Ala790Ser	114.0	0.0		48.0	12.0	NM_005483	Q6NXG5|Q7Z7K3|Q9UJY8	Missense_Mutation	SNP	ENST00000301280.5	hg19	CCDS32875.1	.	.	.	.	.	.	.	.	.	.	G	0.023	-1.398176	0.01175	.	.	ENSG00000167670	ENST00000301280	T	0.25749	1.78	5.65	-6.08	0.02151	.	.	.	.	.	T	0.07503	0.0189	N	0.02011	-0.69	0.09310	N	1	B	0.21381	0.055	B	0.20384	0.029	T	0.42103	-0.9471	8	.	.	.	-0.3293	8.5728	0.33581	0.6025:0.0:0.2903:0.1072	.	790	Q13111	CAF1A_HUMAN	S	790	ENSP00000301280:A790S	.	A	+	1	0	CHAF1A	4384231	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.035000	0.03564	-0.999000	0.03442	-0.345000	0.07892	GCC	.	.		0.652	CHAF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458310.2	NM_005483		T	4433231	G	T	4433231	3	4	250	1	0	0	0	0	1	0	0	0	3313	1319	46	3	2418	3	CHAF1A	19	4433231	Missense_Mutation	SNP	G	TCGA-ED-A8O6-01A-11D-A35Z-10		4433231	54695752	64	34067										
UNC13A	23025	hgsc.bcm.edu	37	chr19	17752293	17752293	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	atcgtagtaaaccttccaggCatcgtcacccttggcatctg	8	13	2	0			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr19:17752293C>A	ENST00000519716.2	-	21	2544	c.2545G>T	c.(2545-2547)Gcc>Tcc	p.A849S	UNC13A_ENST00000552293.1_Missense_Mutation_p.A849S|UNC13A_ENST00000551649.1_Missense_Mutation_p.A849S|UNC13A_ENST00000428389.2_Missense_Mutation_p.A937S|UNC13A_ENST00000252773.7_Missense_Mutation_p.A849S|UNC13A_ENST00000550896.1_Missense_Mutation_p.A847S	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	849					beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						ACCTTCCAGGCATCGTCACCC	0.547																																					p.A849S		Atlas-SNP	.											.	UNC13A	299	.	0			c.G2545T						.						115	119	118					19																	17752293		2178	4285	6463	SO:0001583	missense	23025	exon20			TCCAGGCATCGTC	AB028955	CCDS46013.1, CCDS46013.2	19p13.12	2008-02-05				ENSG00000130477			23150	protein-coding gene	gene with protein product		609894					Standard	NM_001080421		Approved	KIAA1032, Munc13-1	uc031rjv.1	Q9UPW8		ENST00000519716.2:c.2545G>T	chr19.hg19:g.17752293C>A	ENSP00000429562:p.Ala849Ser	135.0	0.0		74.0	14.0	NM_001080421	E5RHY9	Missense_Mutation	SNP	ENST00000519716.2	hg19	CCDS46013.2	.	.	.	.	.	.	.	.	.	.	c	11.97	1.796618	0.31777	.	.	ENSG00000130477	ENST00000519716;ENST00000428389;ENST00000252773;ENST00000551649;ENST00000552293;ENST00000550896	T;T;T;T;T;T	0.81163	-1.45;-1.46;-1.45;-1.31;-1.31;-1.44	3.0	3.0	0.34707	.	0.145258	0.44902	U	0.000415	T	0.63141	0.2486	N	0.16066	0.365	0.41098	D	0.985643	B	0.33299	0.407	B	0.32393	0.145	T	0.61569	-0.7036	10	0.23302	T	0.38	-11.5082	11.8562	0.52439	0.0:1.0:0.0:0.0	.	849	Q9UPW8	UN13A_HUMAN	S	849;937;849;849;849;847	ENSP00000429562:A849S;ENSP00000400409:A937S;ENSP00000252773:A849S;ENSP00000447236:A849S;ENSP00000447572:A849S;ENSP00000446831:A847S	ENSP00000252773:A849S	A	-	1	0	UNC13A	17613293	1.000000	0.71417	0.948000	0.38648	0.467000	0.32768	7.467000	0.80930	1.706000	0.51276	0.299000	0.19835	GCC	.	.		0.547	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604		A	17752293	C	A	17752293	3	1	250	1	0	0	0	0	1	0	0	0	16999	710	25	3	2658	3	UNC13A	19	17752293	Missense_Mutation	SNP	C	TCGA-ED-A8O6-01A-11D-A35Z-10	13319062	17752293	41376690	65	34068										
GDF15	9518	hgsc.bcm.edu	37	chr19	18499391	18499391	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	cggccgcaagccgccaggggGcgccgcagagcgcgtgcgcg	19	16	0	1			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr19:18499391G>A	ENST00000252809.3	+	2	605	c.573G>A	c.(571-573)ggG>ggA	p.G191G	MIR3189_ENST00000578735.1_RNA	NM_004864.2	NP_004855.2	Q99988	GDF15_HUMAN	growth differentiation factor 15	191					cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)			kidney(2)|large_intestine(1)|liver(1)|lung(5)|prostate(2)|skin(1)	12						CCGCCAGGGGGCGCCGCAGAG	0.726											OREG0025363	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G191G		Atlas-SNP	.											.	GDF15	31	.	0			c.G573A						.						6	8	7					19																	18499391		1894	3896	5790	SO:0001819	synonymous_variant	9518	exon2			CAGGGGGCGCCGC	BC008962	CCDS12376.1	19p13.11	2008-05-14				ENSG00000130513			30142	protein-coding gene	gene with protein product	"prostate differentiation factor"	605312				11895857, 9593718	Standard	NM_004864		Approved	PLAB, MIC-1, PDF, MIC1, NAG-1, PTGFB	uc002niv.2	Q99988		ENST00000252809.3:c.573G>A	chr19.hg19:g.18499391G>A		84.0	0.0	726	51.0	11.0	NM_004864	O14629|P78360|Q9BWA0|Q9NRT0	Silent	SNP	ENST00000252809.3	hg19	CCDS12376.1																																																																																			.	.		0.726	GDF15-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466340.2	NM_004864		A	18499391	G	A	18499391	2	1	250	1	0	0	0	0	0	0	0	1	6321	1190	42	3		3	GDF15	19	18499391	Silent	SNP	G	TCGA-ED-A8O6-01A-11D-A35Z-10	747098	18499391	40629592	66	34069										
SHANK1	50944	hgsc.bcm.edu	37	chr19	51171702	51171702	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	cctcggtgctgctgccctggCtgctgcggccgctgctactg	14	16	0	0			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr19:51171702C>A	ENST00000293441.1	-	22	3533	c.3515G>T	c.(3514-3516)aGc>aTc	p.S1172I	SHANK1_ENST00000391814.1_Missense_Mutation_p.S1180I|SYT3_ENST00000544769.1_5'Flank|SHANK1_ENST00000359082.3_Missense_Mutation_p.S1163I|SHANK1_ENST00000391813.1_Missense_Mutation_p.S559I	NM_016148.2	NP_057232.2	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	1172					adult behavior (GO:0030534)|associative learning (GO:0008306)|cytoskeletal anchoring at plasma membrane (GO:0007016)|dendritic spine morphogenesis (GO:0060997)|determination of affect (GO:0050894)|habituation (GO:0046959)|long-term memory (GO:0007616)|negative regulation of actin filament bundle assembly (GO:0032232)|neuromuscular process controlling balance (GO:0050885)|olfactory behavior (GO:0042048)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|protein complex assembly (GO:0006461)|protein localization to synapse (GO:0035418)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|righting reflex (GO:0060013)|social behavior (GO:0035176)|synapse maturation (GO:0060074)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|excitatory synapse (GO:0060076)|intracellular (GO:0005622)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ankyrin repeat binding (GO:0071532)|GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|somatostatin receptor binding (GO:0031877)			breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	64		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)		GCTGCCCTGGCTGCTGCGGCC	0.761																																					p.S1172I		Atlas-SNP	.											.	SHANK1	210	.	0			c.G3515T						.						18	19	19					19																	51171702		1537	3343	4880	SO:0001583	missense	50944	exon22			CCCTGGCTGCTGC	AF163302	CCDS12799.1	19q13.3	2013-01-10			ENSG00000161681	ENSG00000161681		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	15474	protein-coding gene	gene with protein product	"somatostatin receptor-interacting protein"	604999				10551867	Standard	NM_016148		Approved	SSTRIP, SPANK-1, synamon	uc002psx.1	Q9Y566	OTTHUMG00000137380	ENST00000293441.1:c.3515G>T	chr19.hg19:g.51171702C>A	ENSP00000293441:p.Ser1172Ile	51.0	0.0		24.0	13.0	NM_016148	A8MXP5|B7WNY6|Q9NYW9	Missense_Mutation	SNP	ENST00000293441.1	hg19	CCDS12799.1	.	.	.	.	.	.	.	.	.	.	c	6.535	0.467034	0.12402	.	.	ENSG00000161681	ENST00000293441;ENST00000391813;ENST00000359082;ENST00000391814	T;T;T;T	0.65364	0.01;0.43;-0.04;-0.15	1.38	1.38	0.22167	.	0.000000	0.52532	U	0.000061	T	0.72326	0.3446	M	0.67397	2.05	0.44807	D	0.997816	D;D	0.69078	0.994;0.997	D;D	0.71184	0.937;0.972	T	0.72988	-0.4124	10	0.66056	D	0.02	.	9.7025	0.40196	0.0:1.0:0.0:0.0	.	1172;559	Q9Y566;Q9Y566-2	SHAN1_HUMAN;.	I	1172;559;1163;1180	ENSP00000293441:S1172I;ENSP00000375689:S559I;ENSP00000351984:S1163I;ENSP00000375690:S1180I	ENSP00000293441:S1172I	S	-	2	0	SHANK1	55863514	1.000000	0.71417	0.997000	0.53966	0.789000	0.44602	2.325000	0.43840	0.743000	0.32719	0.165000	0.16767	AGC	.	.		0.761	SHANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268071.1	NM_016148		A	51171702	C	A	51171702	3	1	250	1	0	0	0	0	1	0	0	0	14279	797	28	3	2978	3	SHANK1	19	51171702	Missense_Mutation	SNP	C	TCGA-ED-A8O6-01A-11D-A35Z-10	32672311	51171702	7957281	67	34070										
NRSN2	80023	hgsc.bcm.edu	37	chr20	330326	330326	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	cgttcctgcagctgcagccgCggccccagcgtggaggatgg	16	14	0	0	rs368963058		TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr20:330326C>T	ENST00000382291.3	+	3	279	c.39C>T	c.(37-39)cgC>cgT	p.R13R	NRSN2_ENST00000492242.1_Intron|NRSN2_ENST00000608736.1_Silent_p.R13R|RP5-1103G7.4_ENST00000442637.1_RNA|NRSN2_ENST00000382285.2_Silent_p.R13R	NM_024958.2	NP_079234.1	Q9GZP1	NRSN2_HUMAN	neurensin 2	13						integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)				endometrium(1)|large_intestine(2)|lung(4)|urinary_tract(1)	8		all_cancers(10;0.0834)				GCTGCAGCCGCGGCCCCAGCG	0.627																																					p.R13R		Atlas-SNP	.											.	NRSN2	20	.	0			c.C39T						.	C		1,4405	2.1+/-5.4	0,1,2202	47	44	45		39	-4.7	0	20		45	0,8600		0,0,4300	no	coding-synonymous	NRSN2	NM_024958.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		13/205	330326	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	80023	exon3			CAGCCGCGGCCCC	AL136915	CCDS12996.1	20p13	2008-02-04	2006-07-04	2006-07-04	ENSG00000125841	ENSG00000125841			16229	protein-coding gene	gene with protein product		610666	"chromosome 20 open reading frame 98"	C20orf98		16527258	Standard	NM_024958		Approved	dJ1103G7.6	uc002wdi.4	Q9GZP1	OTTHUMG00000031628	ENST00000382291.3:c.39C>T	chr20.hg19:g.330326C>T		32.0	0.0		59.0	14.0	NM_024958	A8K3B2|Q6FII5|Q9NUD3	Silent	SNP	ENST00000382291.3	hg19	CCDS12996.1																																																																																			.	.		0.627	NRSN2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077446.1	NM_024958		T	330326	C	T	330326	2	4	250	1	0	0	0	0	0	0	0	1	10672	755	27	1		1	NRSN2	20	330326	Silent	SNP	C	TCGA-ED-A8O6-01A-11D-A35Z-10		330326	62695194	68	34071										
ANKRD5	63926	hgsc.bcm.edu	37	chr20	10035112	10035112	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	ttttgttcttgtttccaggaActgctgtcatcaatttatgg	8	7	3	0			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr20:10035112A>C	ENST00000378380.3	+	9	2366	c.2037A>C	c.(2035-2037)gaA>gaC	p.E679D	SNAP25-AS1_ENST00000421143.2_RNA|AL109754.1_ENST00000408554.2_RNA|SNAP25-AS1_ENST00000603542.1_RNA|ANKEF1_ENST00000488991.1_3'UTR|ANKEF1_ENST00000378392.1_Missense_Mutation_p.E679D	NM_198798.1	NP_942093.1	Q9NU02	ANKE1_HUMAN	ankyrin repeat and EF-hand domain containing 1	679							calcium ion binding (GO:0005509)										GTTTCCAGGAACTGCTGTCAT	0.323																																					p.E679D		Atlas-SNP	.											.	.	.	.	0			c.A2037C						.						74	67	69					20																	10035112		2203	4300	6503	SO:0001583	missense	63926	exon9			CCAGGAACTGCTG	AK025322	CCDS13108.1	20p12.2	2013-01-11	2013-01-11	2013-01-11	ENSG00000132623	ENSG00000132623		"EF-hand domain containing", "Ankyrin repeat domain containing"	15803	protein-coding gene	gene with protein product			"ankyrin repeat domain 5"	ANKRD5		17142250	Standard	NM_022096		Approved	FLJ21669, dJ839B4.6	uc002wnp.3	Q9NU02	OTTHUMG00000031860	ENST00000378380.3:c.2037A>C	chr20.hg19:g.10035112A>C	ENSP00000367631:p.Glu679Asp	271.0	1.0		253.0	148.0	NM_198798	B3KUQ0|Q9H6Y9	Missense_Mutation	SNP	ENST00000378380.3	hg19	CCDS13108.1	.	.	.	.	.	.	.	.	.	.	A	8.550	0.875343	0.17395	.	.	ENSG00000132623	ENST00000378392;ENST00000378380	T;T	0.67345	-0.26;-0.26	5.08	-0.00848	0.14005	.	0.832250	0.11081	N	0.601856	T	0.54046	0.1834	L	0.53249	1.67	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.39742	-0.9599	10	0.29301	T	0.29	-1.3069	3.9688	0.09444	0.5817:0.0:0.2672:0.1511	.	679	Q9NU02	ANKR5_HUMAN	D	679	ENSP00000367644:E679D;ENSP00000367631:E679D	ENSP00000367631:E679D	E	+	3	2	ANKRD5	9983112	0.472000	0.25870	0.034000	0.17996	0.005000	0.04900	0.965000	0.29319	0.015000	0.14971	0.533000	0.62120	GAA	.	.		0.323	ANKEF1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077968.2	NM_022096		C	10035112	A	C	10035112	3	2	250	1	0	0	0	0	1	0	0	0	676	40	2	5	2067	5	ANKRD5	20	10035112	Missense_Mutation	SNP	A	TCGA-ED-A8O6-01A-11D-A35Z-10	9704786	10035112	52990408	69	34072										
HUNK	30811	hgsc.bcm.edu	37	chr21	33368209	33368209	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	atgacacagattcagaacacCaaagccctcctgaaggaccg	8	13	1	4			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr21:33368209C>T	ENST00000270112.2	+	10	1794	c.1434C>T	c.(1432-1434)acC>acT	p.T478T	HUNK_ENST00000465574.1_3'UTR	NM_014586.1	NP_055401.1	P57058	HUNK_HUMAN	hormonally up-regulated Neu-associated kinase	478					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|skin(2)|stomach(1)	30						TTCAGAACACCAAAGCCCTCC	0.557																																					p.T478T		Atlas-SNP	.											.	HUNK	74	.	0			c.C1434T						.						53	49	50					21																	33368209		2203	4300	6503	SO:0001819	synonymous_variant	30811	exon10			GAACACCAAAGCC	AJ271722	CCDS13610.1	21q22.1	2008-06-05	2008-06-05		ENSG00000142149	ENSG00000142149			13326	protein-coding gene	gene with protein product		606532	"hormonally upregulated Neu-associated kinase"			10662544, 10830953	Standard	NM_014586		Approved		uc002yph.3	P57058	OTTHUMG00000085019	ENST00000270112.2:c.1434C>T	chr21.hg19:g.33368209C>T		295.0	0.0		212.0	39.0	NM_014586		Silent	SNP	ENST00000270112.2	hg19	CCDS13610.1																																																																																			.	.		0.557	HUNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192782.1	NM_014586		T	33368209	C	T	33368209	2	4	250	1	0	0	0	0	0	0	0	1	7467	581	21	3		3	HUNK	21	33368209	Silent	SNP	C	TCGA-ED-A8O6-01A-11D-A35Z-10		33368209	14761686	70	34073										
C22orf42	150297	hgsc.bcm.edu	37	chr22	32555161	32555161	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	ctgcagcagtcacagttgagGcccccgctggggcccaggca	14	15	1	1			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr22:32555161G>C	ENST00000382097.3	-	1	114	c.42C>G	c.(40-42)ggC>ggG	p.G14G	RP1-90G24.8_ENST00000426354.1_lincRNA	NM_001010859.1	NP_001010859.1	Q6IC83	CV042_HUMAN	chromosome 22 open reading frame 42	14										NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(2)	24						CACAGTTGAGGCCCCCGCTGG	0.572																																					p.G14G		Atlas-SNP	.											.	C22orf42	37	.	0			c.C42G						.						59	58	58					22																	32555161		2203	4300	6503	SO:0001819	synonymous_variant	150297	exon1			GTTGAGGCCCCCG	BC040263	CCDS33639.1	22q12.3	2009-03-05			ENSG00000205856	ENSG00000205856			27160	protein-coding gene	gene with protein product						12477932	Standard	XM_005261369		Approved		uc003amd.3	Q6IC83	OTTHUMG00000030380	ENST00000382097.3:c.42C>G	chr22.hg19:g.32555161G>C		68.0	0.0		28.0	12.0	NM_001010859	A4QPH5	Silent	SNP	ENST00000382097.3	hg19	CCDS33639.1																																																																																			.	.		0.572	C22orf42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075268.2	NM_001010859		C	32555161	G	C	32555161	2	2	250	1	0	0	0	0	0	0	0	1	2151	1190	42	4		4	C22orf42	22	32555161	Silent	SNP	G	TCGA-ED-A8O6-01A-11D-A35Z-10		32555161	18749405	71	34074										
SBF1	6305	hgsc.bcm.edu	37	chr22	50903443	50903443	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	ggtgcacctcatcgaacaggTccgtagggcggtatgggacc	15	11	1	0			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chr22:50903443T>C	ENST00000390679.3	-	12	1503	c.1319A>G	c.(1318-1320)gAc>gGc	p.D440G	SBF1_ENST00000348911.6_Missense_Mutation_p.D441G|SBF1_ENST00000380817.3_Missense_Mutation_p.D440G			O95248	MTMR5_HUMAN	SET binding factor 1	440					cell death (GO:0008219)|positive regulation of Rab GTPase activity (GO:0032851)|protein dephosphorylation (GO:0006470)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(8)|large_intestine(3)|lung(18)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	43		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)		ATCGAACAGGTCCGTAGGGCG	0.632																																					p.D440G		Atlas-SNP	.											.	SBF1	211	.	0			c.A1319G						.						73	80	78					22																	50903443		2165	4243	6408	SO:0001583	missense	6305	exon12			AACAGGTCCGTAG	U93181	CCDS14091.1, CCDS14091.2	22q13.33	2013-01-10			ENSG00000100241	ENSG00000100241		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins", "DENN/MADD domain containing", "Pleckstrin homology (PH) domain containing"	10542	protein-coding gene	gene with protein product	"myotubularin related 5", "DENN/MADD domain containing 7A"	603560				9537414, 9736772	Standard	NM_002972		Approved	MTMR5, DENND7A	uc003blh.3	O95248	OTTHUMG00000150204	ENST00000390679.3:c.1319A>G	chr22.hg19:g.50903443T>C	ENSP00000375097:p.Asp440Gly	106.0	0.0		67.0	20.0	NM_002972	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Missense_Mutation	SNP	ENST00000390679.3	hg19		.	.	.	.	.	.	.	.	.	.	T	16.54	3.152443	0.57259	.	.	ENSG00000100241	ENST00000380817;ENST00000348911;ENST00000356279;ENST00000337034;ENST00000390679	D;D;D	0.88664	-2.41;-2.41;-2.41	3.93	3.93	0.45458	.	0.000000	0.85682	D	0.000000	D	0.93268	0.7855	M	0.75615	2.305	0.80722	D	1	D;D;D	0.89917	1.0;0.986;0.993	D;P;P	0.72338	0.977;0.795;0.879	D	0.93877	0.7167	10	0.87932	D	0	.	12.6118	0.56556	0.0:0.0:0.0:1.0	.	440;441;440	O95248;G5E933;O95248-4	MTMR5_HUMAN;.;.	G	440;441;451;450;440	ENSP00000370196:D440G;ENSP00000252027:D441G;ENSP00000375097:D440G	ENSP00000336522:D450G	D	-	2	0	SBF1	49250309	1.000000	0.71417	0.986000	0.45419	0.251000	0.25915	5.941000	0.70195	1.650000	0.50662	0.533000	0.62120	GAC	.	.		0.632	SBF1-201	KNOWN	basic	protein_coding	protein_coding				C	50903443	T	C	50903443	3	2	250	1	0	0	0	0	1	0	0	0	13873	1667	58	2	4482	2	SBF1	22	50903443	Missense_Mutation	SNP	T	TCGA-ED-A8O6-01A-11D-A35Z-10	18348282	50903443	401123	72	34075										
CYLC1	1538	hgsc.bcm.edu	37	chrX	83128066	83128066	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0273972602739726	2	1	0.532670454545455	2.43506493506493	0	0.428571428571429	1	0	taaaaaagcagaatataaaaAgtccaaagatgaaaaaggag	8	3	0	3			TCGA-ED-A8O6-01A-11D-A35Z-10	TCGA-ED-A8O6-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	221a49cd-a340-42e9-bd68-d2d4ccbc5de7	e2037316-e8bd-4188-93cb-eb040674c788	g.chrX:83128066A>G	ENST00000329312.4	+	4	387	c.350A>G	c.(349-351)aAg>aGg	p.K117R		NM_021118.1	NP_066941.1	P35663	CYLC1_HUMAN	cylicin, basic protein of sperm head cytoskeleton 1	117					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	acrosomal matrix (GO:0043159)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	58						GAATATAAAAAGTCCAAAGAT	0.373																																					p.K117R		Atlas-SNP	.											.	CYLC1	272	.	0			c.A350G						.						31	29	30					X																	83128066		2199	4290	6489	SO:0001583	missense	1538	exon4			ATAAAAAGTCCAA	Z22780	CCDS35341.1, CCDS75998.1	Xq21.1	2008-07-31			ENSG00000183035	ENSG00000183035			2582	protein-coding gene	gene with protein product	"cylicin 1"	300768				7737358, 8354692	Standard	NM_021118		Approved		uc004eei.2	P35663	OTTHUMG00000021922	ENST00000329312.4:c.350A>G	chrX.hg19:g.83128066A>G	ENSP00000331556:p.Lys117Arg	649.0	0.0		274.0	84.0	NM_021118	A0AVQ8|Q5JQQ9	Missense_Mutation	SNP	ENST00000329312.4	hg19	CCDS35341.1	.	.	.	.	.	.	.	.	.	.	a	11.87	1.768219	0.31320	.	.	ENSG00000183035	ENST00000329312;ENST00000544771	T	0.59502	0.26	4.53	-1.26	0.09376	.	.	.	.	.	T	0.42404	0.1201	L	0.34521	1.04	0.09310	N	1	B;B	0.25609	0.13;0.13	B;B	0.30029	0.11;0.11	T	0.39313	-0.9620	9	0.62326	D	0.03	0.0379	4.5435	0.12069	0.3438:0.3304:0.0:0.3258	.	117;117	P35663;F5H4V5	CYLC1_HUMAN;.	R	117	ENSP00000331556:K117R	ENSP00000331556:K117R	K	+	2	0	CYLC1	83014722	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.212000	0.17497	-0.431000	0.07307	-1.227000	0.01581	AAG	.	.		0.373	CYLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057371.1	NM_021118		G	83128066	A	G	83128066	3	3	250	1	0	0	0	0	1	0	0	0	4143	72	3	2	364	2	CYLC1	23	83128066	Missense_Mutation	SNP	A	TCGA-ED-A8O6-01A-11D-A35Z-10		83128066	72142494	73	34076										
DIRAS3	9077	hgsc.bcm.edu	37	chr1	68512917	68512917	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	ggcgcggaggataagcagggCgggcagaagccgcaaccgct	18	11	0	1			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr1:68512917C>T	ENST00000370981.1	-	4	700	c.64G>A	c.(64-66)Gcc>Acc	p.A22T	GNG12-AS1_ENST00000420587.1_RNA|GNG12-AS1_ENST00000413628.1_RNA|DIRAS3_ENST00000395201.1_Missense_Mutation_p.A22T			O95661	DIRA3_HUMAN	DIRAS family, GTP-binding RAS-like 3	22					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of gene expression by genetic imprinting (GO:0006349)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|cervix(1)|endometrium(2)|large_intestine(1)|lung(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						ATAAGCAGGGCGGGCAGAAGC	0.587																																					p.A22T		Atlas-SNP	.											.	DIRAS3	31	.	0			c.G64A						.						28	33	31					1																	68512917		2199	4292	6491	SO:0001583	missense	9077	exon2			GCAGGGCGGGCAG	U96750	CCDS641.1	1p31	2014-05-09		2005-01-27	ENSG00000162595	ENSG00000162595			687	protein-coding gene	gene with protein product		605193	"ras homolog gene family, member I"	ARHI		9874798	Standard	XM_006711027		Approved	NOEY2	uc001ded.3	O95661	OTTHUMG00000009544	ENST00000370981.1:c.64G>A	chr1.hg19:g.68512917C>T	ENSP00000360020:p.Ala22Thr	62.0	0.0		139.0	11.0	NM_004675	B3KMP3	Missense_Mutation	SNP	ENST00000370981.1	hg19	CCDS641.1	.	.	.	.	.	.	.	.	.	.	C	3.511	-0.099836	0.07010	.	.	ENSG00000162595	ENST00000370981;ENST00000395201	T;T	0.72725	-0.68;-0.68	4.15	-3.65	0.04502	.	.	.	.	.	T	0.15522	0.0374	N	0.12182	0.205	0.09310	N	1	B	0.17268	0.021	B	0.08055	0.003	T	0.14364	-1.0475	9	0.06365	T	0.9	.	1.4828	0.02441	0.1424:0.3543:0.1663:0.337	.	22	O95661	DIRA3_HUMAN	T	22	ENSP00000360020:A22T;ENSP00000378627:A22T	ENSP00000360020:A22T	A	-	1	0	DIRAS3	68285505	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-2.624000	0.00876	-0.273000	0.09246	0.467000	0.42956	GCC	.	.		0.587	DIRAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026354.2	NM_004675		T	68512917	C	T	68512917	3	4	251	1	0	0	0	0	1	0	0	0	4534	768	27	1	629	1	DIRAS3	1	68512917	Missense_Mutation	SNP	C	TCGA-ED-A97K-01A-21D-A382-10		68512917	180737704	1	34077										
LCE3D	84648	hgsc.bcm.edu	37	chr1	152552238	152552238	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	gcgccggcatcggtggtggcGcctgtggtggttcaggaagc	19	10	1	0	rs199832759		TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr1:152552238G>A	ENST00000368787.3	-	2	231	c.175C>T	c.(175-177)Cgc>Tgc	p.R59C		NM_032563.1	NP_115952.1	Q9BYE3	LCE3D_HUMAN	late cornified envelope 3D	59					keratinization (GO:0031424)					breast(1)|endometrium(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)|stomach(2)	15	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)	UCEC - Uterine corpus endometrioid carcinoma (5;0.153)|KIRC - Kidney renal clear cell carcinoma(4;0.0323)|Kidney(5;0.0378)		CGGTGGTGGCGCCTGTGGTGG	0.687																																					p.R59C		Atlas-SNP	.											.	LCE3D	28	.	0			c.C175T						.						44	54	51					1																	152552238		2203	4300	6503	SO:0001583	missense	84648	exon2			GGTGGCGCCTGTG	BI670519	CCDS1014.1	1q21	2008-02-05	2004-05-21	2004-10-15	ENSG00000163202	ENSG00000163202		"Late cornified envelopes"	16615	protein-coding gene	gene with protein product		612616	"small proline rich-like (epidermal differentiation complex) 6B"	SPRL6B, SPRL6A		11698679	Standard	NM_032563		Approved	LEP16	uc001fab.3	Q9BYE3	OTTHUMG00000012384	ENST00000368787.3:c.175C>T	chr1.hg19:g.152552238G>A	ENSP00000357776:p.Arg59Cys	159.0	0.0		248.0	63.0	NM_032563	Q3MIL1	Missense_Mutation	SNP	ENST00000368787.3	hg19	CCDS1014.1	.	.	.	.	.	.	.	.	.	.	G	6.013	0.370885	0.11409	.	.	ENSG00000163202	ENST00000368787	T	0.05447	3.44	3.8	2.88	0.33553	.	.	.	.	.	T	0.01905	0.0060	.	.	.	0.29920	N	0.822835	B	0.13145	0.007	B	0.08055	0.003	T	0.40021	-0.9585	8	0.87932	D	0	.	7.2783	0.26297	0.1248:0.0:0.8752:0.0	.	59	Q9BYE3	LCE3D_HUMAN	C	59	ENSP00000357776:R59C	ENSP00000357776:R59C	R	-	1	0	LCE3D	150818862	0.018000	0.18449	0.789000	0.31954	0.326000	0.28443	0.335000	0.19806	0.932000	0.37266	0.655000	0.94253	CGC	.	G|0.999;A|0.001		0.687	LCE3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034504.1	NM_032563		A	152552238	G	A	152552238	3	1	251	1	0	0	0	0	1	0	0	0	8681	1087	38	1	107	1	LCE3D	1	152552238	Missense_Mutation	SNP	G	TCGA-ED-A97K-01A-21D-A382-10	84039321	152552238	96698383	2	34078										
PMVK	10654	hgsc.bcm.edu	37	chr1	154898884	154898884	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	ctgctccaacgctacaacgcGgaccgtctgcgtcacggccc	10	18	2	0	rs150445298	byFrequency	TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr1:154898884G>A	ENST00000368467.3	-	4	693	c.388C>T	c.(388-390)Cgc>Tgc	p.R130C		NM_006556.3	NP_006547.1	Q15126	PMVK_HUMAN	phosphomevalonate kinase	130					cholesterol biosynthetic process (GO:0006695)|isopentenyl diphosphate biosynthetic process, mevalonate pathway (GO:0019287)|response to cholesterol (GO:0070723)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|phosphomevalonate kinase activity (GO:0004631)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)	6	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.142)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			GCTACAACGCGGACCGTCTGC	0.622													G|||	35	0.00698882	0	0	5008	,	,		21146	0		0	False		,,,				2504	0.0358				p.R130C		Atlas-SNP	.											PMVK,NS,carcinoma,0,1	PMVK	17	.	0			c.C388T						.	G	CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	81	62	68		388	4.6	0.9	1	dbSNP_134	68	0,8600		0,0,4300	no	missense	PMVK	NM_006556.3	180	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	probably-damaging	130/193	154898884	2,13004	2203	4300	6503	SO:0001583	missense	10654	exon4			CAACGCGGACCGT	L77213	CCDS1073.1	1q21.3	2012-09-20			ENSG00000163344	ENSG00000163344	2.7.4.2		9141	protein-coding gene	gene with protein product		607622				8663599, 10191291	Standard	NM_006556		Approved	PMK, PMKA, HUMPMKI	uc001ffq.3	Q15126	OTTHUMG00000037415	ENST00000368467.3:c.388C>T	chr1.hg19:g.154898884G>A	ENSP00000357452:p.Arg130Cys	52.0	1.0		70.0	22.0	NM_006556	Q5TZW9	Missense_Mutation	SNP	ENST00000368467.3	hg19	CCDS1073.1	.	.	.	.	.	.	.	.	.	.	G	16.42	3.117110	0.56505	4.54E-4	0.0	ENSG00000163344	ENST00000368467	T	0.41400	1.0	4.59	4.59	0.56863	.	0.000000	0.85682	D	0.000000	T	0.63827	0.2544	M	0.89904	3.07	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.72276	-0.4341	10	0.87932	D	0	-9.823	13.2686	0.60148	0.0:0.0:1.0:0.0	.	130	Q15126	PMVK_HUMAN	C	130	ENSP00000357452:R130C	ENSP00000357452:R130C	R	-	1	0	PMVK	153165508	1.000000	0.71417	0.892000	0.35008	0.053000	0.15095	4.037000	0.57311	2.266000	0.75297	0.561000	0.74099	CGC	.	G|1.000;A|0.000		0.622	PMVK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091088.1	NM_006556		A	154898884	G	A	154898884	3	1	251	1	0	0	0	0	1	0	0	0	12153	1116	39	1	198	1	PMVK	1	154898884	Missense_Mutation	SNP	G	TCGA-ED-A97K-01A-21D-A382-10	2346646	154898884	94351737	3	34079										
FAM5B	57795	hgsc.bcm.edu	37	chr1	177250365	177250365	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	tgaaaattaacaccttgcagGtctttggctacagcctgccc	8	12	1	1			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr1:177250365G>T	ENST00000361539.4	+	8	2365	c.2053G>T	c.(2053-2055)Gtc>Ttc	p.V685F	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	685					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	extracellular region (GO:0005576)											CACCTTGCAGGTCTTTGGCTA	0.478																																					p.V685F		Atlas-SNP	.											FAM5B,NS,carcinoma,0,1	FAM5B	191	.	0			c.G2053T						.						96	96	96					1																	177250365		2203	4300	6503	SO:0001583	missense	57795	exon8			TTGCAGGTCTTTG		CCDS1320.1	1q24	2013-08-06	2013-08-06	2013-07-31	ENSG00000198797	ENSG00000198797			13746	protein-coding gene	gene with protein product			"family with sequence similarity 5, member B"	FAM5B		15193423	Standard	NM_021165		Approved	DBCCR1L2	uc001glf.3	Q9C0B6	OTTHUMG00000034953	ENST00000361539.4:c.2053G>T	chr1.hg19:g.177250365G>T	ENSP00000354481:p.Val685Phe	94.0	1.0		56.0	19.0	NM_021165	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Missense_Mutation	SNP	ENST00000361539.4	hg19	CCDS1320.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.088059	0.76642	.	.	ENSG00000198797	ENST00000536589;ENST00000361539	T	0.20463	2.07	5.15	5.15	0.70609	.	0.062567	0.64402	D	0.000006	T	0.47266	0.1436	M	0.65498	2.005	0.80722	D	1	D;D	0.89917	1.0;0.997	D;P	0.91635	0.999;0.879	T	0.48433	-0.9036	10	0.87932	D	0	-29.1056	18.2044	0.89850	0.0:0.0:1.0:0.0	.	580;685	Q9C0B6-2;Q9C0B6	.;FAM5B_HUMAN	F	438;685	ENSP00000354481:V685F	ENSP00000354481:V685F	V	+	1	0	FAM5B	175516988	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.393000	0.73217	2.386000	0.81285	0.305000	0.20034	GTC	.	.		0.478	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1	NM_021165		T	177250365	G	T	177250365	3	4	251	1	0	0	0	0	1	0	0	0	5601	1261	44	3	2079	3	FAM5B	1	177250365	Missense_Mutation	SNP	G	TCGA-ED-A97K-01A-21D-A382-10	22351481	177250365	72000256	4	34080										
TRAF3IP3	80342	hgsc.bcm.edu	37	chr1	209953899	209953899	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	gaaggagaaagactgggatcTcagagaccagctgcaaaaga	13	7	1	4			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr1:209953899T>G	ENST00000367024.1	+	15	1913	c.1397T>G	c.(1396-1398)cTc>cGc	p.L466R	TRAF3IP3_ENST00000477431.1_Intron|TRAF3IP3_ENST00000010338.4_Missense_Mutation_p.L446R|TRAF3IP3_ENST00000367025.3_Missense_Mutation_p.L466R|TRAF3IP3_ENST00000367026.3_Missense_Mutation_p.L446R			Q9Y228	T3JAM_HUMAN	TRAF3 interacting protein 3	466						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32				OV - Ovarian serous cystadenocarcinoma(81;0.045)		GACTGGGATCTCAGAGACCAG	0.517																																					p.L466R		Atlas-SNP	.											.	TRAF3IP3	68	.	0			c.T1397G						.						92	92	92					1																	209953899		2203	4300	6503	SO:0001583	missense	80342	exon15			GGGATCTCAGAGA		CCDS1490.1, CCDS1490.2, CCDS73023.1	1q32.3-q41	2008-02-05			ENSG00000009790	ENSG00000009790			30766	protein-coding gene	gene with protein product	"TRAF3 interacting Jun N terminal kinase (JNK) activating modulator"	608255				14572659	Standard	XR_247044		Approved	T3JAM	uc001hho.3	Q9Y228	OTTHUMG00000036480	ENST00000367024.1:c.1397T>G	chr1.hg19:g.209953899T>G	ENSP00000355991:p.Leu466Arg	105.0	0.0		164.0	17.0	NM_025228	A1L464|A6NIU9|Q2YDB5|Q4VY06|Q7Z706	Missense_Mutation	SNP	ENST00000367024.1	hg19	CCDS1490.2	.	.	.	.	.	.	.	.	.	.	T	15.88	2.962599	0.53400	.	.	ENSG00000009790	ENST00000367025;ENST00000367026;ENST00000367024;ENST00000010338	D;D;D;D	0.83075	-1.68;-1.68;-1.68;-1.68	5.24	4.11	0.48088	.	0.247494	0.28754	N	0.014253	T	0.78310	0.4263	L	0.34521	1.04	0.40786	D	0.983217	P;P	0.44429	0.835;0.835	P;P	0.46917	0.531;0.531	T	0.78409	-0.2215	10	0.87932	D	0	-0.0283	8.9403	0.35725	0.0:0.0841:0.0:0.9159	.	466;446	Q9Y228;Q9Y228-2	T3JAM_HUMAN;.	R	466;446;466;446	ENSP00000355992:L466R;ENSP00000355993:L446R;ENSP00000355991:L466R;ENSP00000010338:L446R	ENSP00000010338:L446R	L	+	2	0	TRAF3IP3	208020522	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.021000	0.49651	0.826000	0.34661	0.533000	0.62120	CTC	.	.		0.517	TRAF3IP3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088734.2			G	209953899	T	G	209953899	3	3	251	1	0	0	0	0	1	0	0	0	16457	1551	54	5	1447	5	TRAF3IP3	1	209953899	Missense_Mutation	SNP	T	TCGA-ED-A97K-01A-21D-A382-10	32703534	209953899	39296722	5	34081										
NRXN1	9378	hgsc.bcm.edu	37	chr2	51254752	51254752	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	accccgccctcgccctcctcGcccgcctcgcacgggcttcc	8	25	0	0	rs546508545		TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr2:51254752G>A	ENST00000406316.2	-	2	2136	c.660C>T	c.(658-660)ggC>ggT	p.G220G	NRXN1_ENST00000404971.1_Silent_p.G220G|NRXN1_ENST00000405581.1_Silent_p.G220G|NRXN1_ENST00000406859.3_Silent_p.G220G|NRXN1_ENST00000401669.2_Silent_p.G220G|NRXN1_ENST00000402717.3_Silent_p.G220G|NRXN1_ENST00000405472.3_Silent_p.G220G	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	220	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			CGCCCTCCTCGCCCGCCTCGC	0.711																																					p.G220G		Atlas-SNP	.											NRXN1_ENST00000536085,colon,carcinoma,0,3	NRXN1	1118	.	0			c.C660T						.						11	16	14					2																	51254752		2079	4162	6241	SO:0001819	synonymous_variant	9378	exon2			CTCCTCGCCCGCC	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.660C>T	chr2.hg19:g.51254752G>A		118.0	0.0		136.0	23.0	NM_004801	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Silent	SNP	ENST00000406316.2	hg19	CCDS54360.1																																																																																			.	.		0.711	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			A	51254752	G	A	51254752	2	1	251	1	0	0	0	0	0	0	0	1	10674	1074	38	1		1	NRXN1	2	51254752	Silent	SNP	G	TCGA-ED-A97K-01A-21D-A382-10		51254752	191944621	6	34082										
DNAH6	1768	hgsc.bcm.edu	37	chr2	84861695	84861695	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	ctgctttgatgaatttaatcGaattgacatagaagttctgt	8	5	1	4	rs267599477		TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr2:84861695G>T	ENST00000237449.6	+	29	4591	c.4583G>T	c.(4582-4584)cGa>cTa	p.R1528L	DNAH6_ENST00000398278.2_Missense_Mutation_p.R1528L|DNAH6_ENST00000389394.3_Missense_Mutation_p.R1528L			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	1528	AAA 1. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						GAATTTAATCGAATTGACATA	0.463																																					p.R1528L		Atlas-SNP	.											.	DNAH6	194	.	0			c.G4583T						.						97	82	86					2																	84861695		692	1591	2283	SO:0001583	missense	1768	exon30			TTAATCGAATTGA	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.4583G>T	chr2.hg19:g.84861695G>T	ENSP00000237449:p.Arg1528Leu	92.0	0.0		100.0	4.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	hg19	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	G	35	5.471545	0.96274	.	.	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.14640	2.49;2.49;2.49	5.78	5.78	0.91487	ATPase, AAA+ type, core (1);	.	.	.	.	T	0.51907	0.1702	H	0.94385	3.53	0.49687	D	0.999819	D	0.89917	1.0	D	0.97110	1.0	T	0.64719	-0.6341	9	0.87932	D	0	.	18.7696	0.91885	0.0:0.0:1.0:0.0	.	1528	Q9C0G6	DYH6_HUMAN	L	1528	ENSP00000374045:R1528L;ENSP00000381326:R1528L;ENSP00000237449:R1528L	ENSP00000237449:R1528L	R	+	2	0	DNAH6	84715206	1.000000	0.71417	0.933000	0.37362	0.937000	0.57800	7.784000	0.85713	2.733000	0.93635	0.561000	0.74099	CGA	.	.		0.463	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		T	84861695	G	T	84861695	3	4	251	1	0	0	0	0	1	0	0	0	4607	1058	37	1	4697	1	DNAH6	2	84861695	Missense_Mutation	SNP	G	TCGA-ED-A97K-01A-21D-A382-10	33606943	84861695	158337678	7	34083										
INSIG2	51141	hgsc.bcm.edu	37	chr2	118865873	118865873	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	gcagtacgaatgtaaagttaTcgcagaaaaatctcatcagg	9	7	2	1			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr2:118865873T>A	ENST00000245787.4	+	6	859	c.653T>A	c.(652-654)aTc>aAc	p.I218N	INSIG2_ENST00000485520.1_3'UTR	NM_016133.2	NP_057217.2	Q9Y5U4	INSI2_HUMAN	insulin induced gene 2	218					cholesterol biosynthetic process (GO:0006695)|cranial suture morphogenesis (GO:0060363)|inner ear morphogenesis (GO:0042472)|middle ear morphogenesis (GO:0042474)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of steroid biosynthetic process (GO:0010894)|palate development (GO:0060021)|response to fatty acid (GO:0070542)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)|triglyceride metabolic process (GO:0006641)	endoplasmic reticulum membrane (GO:0005789)|SREBP-SCAP-Insig complex (GO:0032937)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(5)|ovary(1)	13						TGTAAAGTTATCGCAGAAAAA	0.299																																					p.I218N		Atlas-SNP	.											.	INSIG2	30	.	0			c.T653A						.						80	84	83					2																	118865873		2203	4300	6503	SO:0001583	missense	51141	exon6			AAGTTATCGCAGA	AF527632	CCDS2122.1	2q14.1	2008-02-05			ENSG00000125629	ENSG00000125629			20452	protein-coding gene	gene with protein product		608660				12242332	Standard	NM_016133		Approved		uc002tlk.3	Q9Y5U4	OTTHUMG00000058518	ENST00000245787.4:c.653T>A	chr2.hg19:g.118865873T>A	ENSP00000245787:p.Ile218Asn	401.0	0.0		571.0	91.0	NM_016133	A8K5W8|Q8TBI8	Missense_Mutation	SNP	ENST00000245787.4	hg19	CCDS2122.1	.	.	.	.	.	.	.	.	.	.	T	10.64	1.406081	0.25378	.	.	ENSG00000125629	ENST00000245787	.	.	.	5.18	2.78	0.32641	.	0.509373	0.21668	N	0.070914	T	0.30386	0.0763	N	0.19112	0.55	0.31013	N	0.71898	B	0.14438	0.01	B	0.09377	0.004	T	0.27606	-1.0069	9	0.54805	T	0.06	.	8.9186	0.35596	0.0:0.2217:0.0:0.7783	.	218	Q9Y5U4	INSI2_HUMAN	N	218	.	ENSP00000245787:I218N	I	+	2	0	INSIG2	118582343	0.911000	0.30947	0.878000	0.34440	0.975000	0.68041	1.421000	0.34815	0.990000	0.38787	0.533000	0.62120	ATC	.	.		0.299	INSIG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129624.1	NM_016133		A	118865873	T	A	118865873	3	1	251	1	0	0	0	0	1	0	0	0	7775	1435	50	4	671	4	INSIG2	2	118865873	Missense_Mutation	SNP	T	TCGA-ED-A97K-01A-21D-A382-10	34004178	118865873	124333500	8	34084										
PTPN4	5775	hgsc.bcm.edu	37	chr2	120712792	120712792	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	cagatttccagtatattcctGagaaagccccactagatagt	7	10	0	3			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr2:120712792G>T	ENST00000263708.2	+	20	2644	c.1873G>T	c.(1873-1875)Gag>Tag	p.E625*	PTPN4_ENST00000544261.1_Nonsense_Mutation_p.E258*	NM_002830.3	NP_002821.1	P29074	PTN4_HUMAN	protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte)	625					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)			endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|urinary_tract(1)	30					Alendronate(DB00630)	GTATATTCCTGAGAAAGCCCC	0.428																																					p.E625X		Atlas-SNP	.											.	PTPN4	89	.	0			c.G1873T						.						76	77	76					2																	120712792		2203	4300	6503	SO:0001587	stop_gained	5775	exon20			ATTCCTGAGAAAG		CCDS2129.1	2q14.2	2011-06-09			ENSG00000088179	ENSG00000088179		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9656	protein-coding gene	gene with protein product		176878				1648233	Standard	NM_002830		Approved	PTPMEG	uc002tmf.2	P29074	OTTHUMG00000131436	ENST00000263708.2:c.1873G>T	chr2.hg19:g.120712792G>T	ENSP00000263708:p.Glu625*	45.0	0.0		68.0	15.0	NM_002830	B2RBV8|Q9UDA7	Nonsense_Mutation	SNP	ENST00000263708.2	hg19	CCDS2129.1	.	.	.	.	.	.	.	.	.	.	G	37	6.525630	0.97637	.	.	ENSG00000088179	ENST00000263708;ENST00000544261	.	.	.	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	19.6657	0.95891	0.0:0.0:1.0:0.0	.	.	.	.	X	625;258	.	ENSP00000263708:E625X	E	+	1	0	PTPN4	120429262	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	9.756000	0.98918	2.642000	0.89623	0.555000	0.69702	GAG	.	.		0.428	PTPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254233.2			T	120712792	G	T	120712792	4	4	251	1	0	0	0	0	0	1	0	0	12805	1291	45	3	1947	3	PTPN4	2	120712792	Nonsense_Mutation	SNP	G	TCGA-ED-A97K-01A-21D-A382-10	1846919	120712792	122486581	9	34085										
NCKAP5	344148	hgsc.bcm.edu	37	chr2	133541516	133541516	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	tcactggggaccctggtttcGgacttggtggatgaaggtgc	16	8	1	1			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr2:133541516G>A	ENST00000409261.1	-	14	3241	c.2868C>T	c.(2866-2868)tcC>tcT	p.S956S	NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000317721.6_Silent_p.S956S|NCKAP5_ENST00000473859.1_5'Flank	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	956										NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						CCCTGGTTTCGGACTTGGTGG	0.572																																					p.S956S		Atlas-SNP	.											.	NCKAP5	322	.	0			c.C2868T						.						19	20	20					2																	133541516		1897	4071	5968	SO:0001819	synonymous_variant	344148	exon14			GGTTTCGGACTTG	AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"Nck associated protein 5", "peripheral clock protein"	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.2868C>T	chr2.hg19:g.133541516G>A		127.0	0.0		128.0	23.0	NM_207363	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Silent	SNP	ENST00000409261.1	hg19	CCDS46418.1																																																																																			.	.		0.572	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481		A	133541516	G	A	133541516	2	1	251	1	0	0	0	0	0	0	0	1	10232	1103	39	1		1	NCKAP5	2	133541516	Silent	SNP	G	TCGA-ED-A97K-01A-21D-A382-10	12828724	133541516	109657857	10	34086										
CPS1	1373	hgsc.bcm.edu	37	chr2	211473186	211473186	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	atcagcctgttttgaacctaGcctggattacatggtcacca	8	11	2	1			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr2:211473186G>A	ENST00000233072.5	+	19	2490	c.2294G>A	c.(2293-2295)aGc>aAc	p.S765N	CPS1_ENST00000430249.2_Missense_Mutation_p.S771N|CPS1_ENST00000451903.2_Missense_Mutation_p.S314N	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	765					anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	TTTGAACCTAGCCTGGATTAC	0.468																																					p.S771N		Atlas-SNP	.											.	CPS1	485	.	0			c.G2312A						.						142	134	137					2																	211473186		2203	4300	6503	SO:0001583	missense	1373	exon20			AACCTAGCCTGGA	AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"carbamoyl-phosphate synthetase 1, mitochondrial"				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.2294G>A	chr2.hg19:g.211473186G>A	ENSP00000233072:p.Ser765Asn	104.0	0.0		163.0	39.0	NM_001122633	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Missense_Mutation	SNP	ENST00000233072.5	hg19	CCDS2393.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.361828	0.82353	.	.	ENSG00000021826	ENST00000430249;ENST00000539150;ENST00000233072;ENST00000451903	D;D;D	0.92397	-3.03;-3.03;-3.03	6.16	6.16	0.99307	ATP-grasp fold, subdomain 2 (1);	0.000000	0.85682	D	0.000000	D	0.94062	0.8097	M	0.90483	3.12	0.80722	D	1	B;B	0.24092	0.097;0.097	B;B	0.18871	0.023;0.023	D	0.91010	0.4849	10	0.87932	D	0	-9.1252	20.8598	0.99761	0.0:0.0:1.0:0.0	.	775;765	Q59HF8;P31327	.;CPSM_HUMAN	N	771;773;765;314	ENSP00000402608:S771N;ENSP00000233072:S765N;ENSP00000406136:S314N	ENSP00000233072:S765N	S	+	2	0	CPS1	211181431	1.000000	0.71417	0.939000	0.37840	0.966000	0.64601	9.476000	0.97823	2.937000	0.99478	0.650000	0.86243	AGC	.	.		0.468	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5			A	211473186	G	A	211473186	3	1	251	1	0	0	0	0	1	0	0	0	3825	971	34	3	2390	3	CPS1	2	211473186	Missense_Mutation	SNP	G	TCGA-ED-A97K-01A-21D-A382-10	77931670	211473186	31726187	11	34087										
UGT1A8	54658	hgsc.bcm.edu	37	chr2	234526724	234526724	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	taacttatttttttcgcattGcaggagtttgtttaatgacc	7	6	0	1			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr2:234526724G>T	ENST00000373450.4	+	1	434	c.371G>T	c.(370-372)tGc>tTc	p.C124F		NM_019076.4	NP_061949.3	P22309	UD11_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A1	127					acute-phase response (GO:0006953)|bilirubin conjugation (GO:0006789)|biphenyl catabolic process (GO:0070980)|cellular glucuronidation (GO:0052695)|cellular response to ethanol (GO:0071361)|cellular response to glucocorticoid stimulus (GO:0071385)|digestion (GO:0007586)|drug metabolic process (GO:0017144)|estrogen metabolic process (GO:0008210)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|heme catabolic process (GO:0042167)|heterocycle metabolic process (GO:0046483)|liver development (GO:0001889)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of steroid metabolic process (GO:0045939)|organ regeneration (GO:0031100)|porphyrin-containing compound metabolic process (GO:0006778)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|retinoic acid metabolic process (GO:0042573)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic glucuronidation (GO:0052697)|xenobiotic metabolic process (GO:0006805)	cytochrome complex (GO:0070069)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|steroid binding (GO:0005496)			breast(1)|central_nervous_system(2)|endometrium(7)|large_intestine(5)|lung(9)|skin(4)|urinary_tract(2)	30		Breast(86;0.000766)|all_lung(227;0.00271)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0461)|Lung SC(224;0.128)		Epithelial(121;4.1e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000435)|Lung(119;0.00211)|LUSC - Lung squamous cell carcinoma(224;0.0054)	Abacavir(DB01048)|Acetaminophen(DB00316)|Adenine(DB00173)|Atorvastatin(DB01076)|Axitinib(DB06626)|Diclofenac(DB00586)|Dolutegravir(DB08930)|Eltrombopag(DB06210)|Erlotinib(DB00530)|Estradiol(DB00783)|Etoposide(DB00773)|Ezetimibe(DB00973)|Ezogabine(DB04953)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indacaterol(DB05039)|Indomethacin(DB00328)|Irinotecan(DB00762)|Losartan(DB00678)|Lovastatin(DB00227)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naltrexone(DB00704)|Naproxen(DB00788)|Nilotinib(DB04868)|Pazopanib(DB06589)|Propofol(DB00818)|Raltegravir(DB06817)|Regorafenib(DB08896)|Rifampicin(DB01045)|Simvastatin(DB00641)|Sorafenib(DB00398)|Suprofen(DB00870)|Testosterone Propionate(DB01420)	TTTTCGCATTGCAGGAGTTTG	0.353																																					p.C124F		Atlas-SNP	.											.	UGT1A8	69	.	0			c.G371T						.						119	127	124					2																	234526724		2203	4300	6503	SO:0001583	missense	54576	exon1			CGCATTGCAGGAG	M57899	CCDS2510.1	2q37.1	2014-09-17	2005-07-20		ENSG00000242366	ENSG00000242366	2.4.1.17	"UDP glucuronosyltransferases"	12530	other	complex locus constituent		191740	"UDP glycosyltransferase 1 family, polypeptide A1"	UGT1, GNT1		9295054, 9535849	Standard	NM_000463		Approved	UGT1A		P22309	OTTHUMG00000059117	ENST00000373450.4:c.371G>T	chr2.hg19:g.234526724G>T	ENSP00000362549:p.Cys124Phe	123.0	0.0		161.0	28.0	NM_019076	A6NJC3|B8K286	Missense_Mutation	SNP	ENST00000373450.4	hg19	CCDS33402.1	.	.	.	.	.	.	.	.	.	.	G	11.72	1.721590	0.30503	.	.	ENSG00000242366	ENST00000373450	T	0.79247	-1.25	3.78	3.78	0.43462	.	.	.	.	.	D	0.89227	0.6655	M	0.90019	3.08	0.42975	D	0.994448	D;D	0.61697	0.99;0.99	D;D	0.66602	0.945;0.945	D	0.92302	0.5850	9	0.87932	D	0	.	16.2097	0.82148	0.0:0.0:1.0:0.0	.	124;124	Q5DSZ6;Q9HAW9	.;UD18_HUMAN	F	124	ENSP00000362549:C124F	ENSP00000362549:C124F	C	+	2	0	UGT1A8	234191463	1.000000	0.71417	0.131000	0.22000	0.252000	0.25951	6.854000	0.75440	2.122000	0.65172	0.505000	0.49811	TGC	.	.		0.353	UGT1A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000130994.1			T	234526724	G	T	234526724	3	4	251	1	0	0	0	0	1	0	0	0	16966	1319	46	3	373	3	UGT1A8	2	234526724	Missense_Mutation	SNP	G	TCGA-ED-A97K-01A-21D-A382-10	23053538	234526724	8672649	12	34088										
TGFBR2	7048	hgsc.bcm.edu	37	chr3	30713509	30713509	+	Frame_Shift_Del	DEL	C	C	-													0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	gagacagtggcagtcaagatCtttccctatgaggagtatgc							TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr3:30713509delC	ENST00000295754.5	+	4	1216	c.834delC	c.(832-834)atcfs	p.I278fs	TGFBR2_ENST00000359013.4_Frame_Shift_Del_p.I303fs	NM_003242.5	NP_003233.4	P37173	TGFR2_HUMAN	transforming growth factor, beta receptor II (70/80kDa)	278	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|aging (GO:0007568)|apoptotic process (GO:0006915)|blood vessel development (GO:0001568)|brain development (GO:0007420)|bronchus morphogenesis (GO:0060434)|cartilage development (GO:0051216)|common-partner SMAD protein phosphorylation (GO:0007182)|digestive tract development (GO:0048565)|embryo implantation (GO:0007566)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic hemopoiesis (GO:0035162)|gastrulation (GO:0007369)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|lens development in camera-type eye (GO:0002088)|lens fiber cell apoptotic process (GO:1990086)|lung lobe morphogenesis (GO:0060463)|mammary gland morphogenesis (GO:0060443)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ regeneration (GO:0031100)|palate development (GO:0060021)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of angiogenesis (GO:0045766)|positive regulation of B cell tolerance induction (GO:0002663)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of skeletal muscle tissue regeneration (GO:0043415)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of T cell tolerance induction (GO:0002666)|positive regulation of tolerance induction to self antigen (GO:0002651)|protein phosphorylation (GO:0006468)|receptor-mediated endocytosis (GO:0006898)|regulation of cell proliferation (GO:0042127)|response to cholesterol (GO:0070723)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|smoothened signaling pathway (GO:0007224)|trachea formation (GO:0060440)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)|wound healing (GO:0042060)	caveola (GO:0005901)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|transforming growth factor beta receptor homodimeric complex (GO:0070022)	ATP binding (GO:0005524)|glycosaminoglycan binding (GO:0005539)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type II (GO:0005026)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)|type I transforming growth factor beta receptor binding (GO:0034713)|type III transforming growth factor beta receptor binding (GO:0034714)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(15)|lung(10)|ovary(3)|pancreas(12)|skin(1)|stomach(5)|upper_aerodigestive_tract(2)	53						CAGTCAAGATCTTTCCCTATG	0.498																																					p.I303fs		Atlas-INDEL	.											.	TGFBR2	139	.	0			c.908delT						.						145	137	140					3																	30713509		2203	4300	6503	SO:0001589	frameshift_variant	7048	exon5			.		CCDS2648.1, CCDS33727.1	3p22	2014-09-17	2002-08-29		ENSG00000163513	ENSG00000163513			11773	protein-coding gene	gene with protein product		190182	"transforming growth factor, beta receptor II (70-80kD)"	MFS2		1319842, 15235604	Standard	NM_001024847		Approved		uc003cen.3	P37173	OTTHUMG00000130569	ENST00000295754.5:c.834delC	chr3.hg19:g.30713509delC	ENSP00000295754:p.Ile278fs	124.0	0.0		159.0	66.0	NM_001024847	B4DTV5|Q15580|Q6DKT6|Q99474	Frame_Shift_Del	DEL	ENST00000295754.5	hg19	CCDS2648.1																																																																																			.	.		0.498	TGFBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252994.2			-	30713509	C	-	30713509	7	5	251	1	0	1	0	1	0	0	0	0	15837	903	32	0	927	0	TGFBR2	3	30713509	Frame_Shift_Del	DEL	C	TCGA-ED-A97K-01A-21D-A382-10		30713509	167308921	13	34089										
CACNA1D	776	hgsc.bcm.edu	37	chr3	53804516	53804516	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	ttccgagtgatgcgattggtGaagcttctcagcagggggga	16	7	1	2			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr3:53804516G>A	ENST00000350061.5	+	32	4492	c.3981G>A	c.(3979-3981)gtG>gtA	p.V1327V	CACNA1D_ENST00000288139.4_Silent_p.V1347V|CACNA1D_ENST00000540742.1_Silent_p.V219V|CACNA1D_ENST00000422281.2_Silent_p.V1312V	NM_001128840.1	NP_001122312.1	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type, alpha 1D subunit	1327					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|energy reserve metabolic process (GO:0006112)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during SA node cell action potential (GO:0086052)|positive regulation of calcium ion transport (GO:0051928)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|ankyrin binding (GO:0030506)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)|voltage-gated calcium channel activity involved in cardiac muscle cell action potential (GO:0086007)|voltage-gated calcium channel activity involved SA node cell action potential (GO:0086059)			breast(3)|central_nervous_system(9)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(13)|liver(1)|lung(29)|ovary(6)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	90				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TGCGATTGGTGAAGCTTCTCA	0.468																																					p.V1347V		Atlas-SNP	.											.	CACNA1D	324	.	0			c.G4041A						.						103	104	104					3																	53804516		2203	4300	6503	SO:0001819	synonymous_variant	776	exon33			ATTGGTGAAGCTT	AB209171	CCDS2872.1, CCDS46848.1, CCDS46849.1	3p14.3	2012-03-07			ENSG00000157388	ENSG00000157388		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1391	protein-coding gene	gene with protein product		114206		CCHL1A2, CACNL1A2		1664412	Standard	NM_000720		Approved	Cav1.3, CACH3, CACN4	uc003dgu.5	Q01668	OTTHUMG00000158278	ENST00000350061.5:c.3981G>A	chr3.hg19:g.53804516G>A		67.0	0.0		74.0	27.0	NM_000720	B0FYA3|Q13916|Q13931|Q71UT1|Q9UDC3	Silent	SNP	ENST00000350061.5	hg19	CCDS46848.1																																																																																			.	.		0.468	CACNA1D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350557.1	NM_000720		A	53804516	G	A	53804516	2	1	251	1	0	0	0	0	0	0	0	1	2543	1277	45	3		3	CACNA1D	3	53804516	Silent	SNP	G	TCGA-ED-A97K-01A-21D-A382-10	23091007	53804516	144217914	14	34090										
FOXP1	27086	hgsc.bcm.edu	37	chr3	71064720	71064720	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	tttagaaatgattggaaatcTtcgcacactgcttcacagcc	7	10	2	2			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr3:71064720T>A	ENST00000318789.4	-	12	1479	c.954A>T	c.(952-954)gaA>gaT	p.E318D	FOXP1_ENST00000498215.1_Missense_Mutation_p.E318D|FOXP1_ENST00000484350.1_Missense_Mutation_p.E242D|FOXP1_ENST00000493089.1_Missense_Mutation_p.E318D|FOXP1_ENST00000475937.1_Missense_Mutation_p.E318D|FOXP1_ENST00000468577.1_Missense_Mutation_p.E318D|FOXP1_ENST00000491238.1_Missense_Mutation_p.E320D	NM_001244810.1|NM_001244813.1|NM_032682.5	NP_001231739.1|NP_001231742.1|NP_116071.2	Q9H334	FOXP1_HUMAN	forkhead box P1	318					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	31		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)		ATTGGAAATCTTCGCACACTG	0.423			T	PAX5	ALL																																p.E320D		Atlas-SNP	.		Dom	yes		3	3p14.1	27086	forkhead box P1		L	.	FOXP1	104	.	0			c.A960T						.						71	68	69					3																	71064720		2203	4300	6503	SO:0001583	missense	27086	exon7			GAAATCTTCGCAC	AF146696	CCDS2914.1, CCDS33785.1, CCDS58837.1, CCDS58838.1, CCDS58839.1, CCDS74963.1, CCDS74964.1	3p14.1	2008-07-18			ENSG00000114861	ENSG00000114861		"Forkhead boxes"	3823	protein-coding gene	gene with protein product	"fork head-related protein like B", "glutamine-rich factor 1", "PAX5/FOXP1 fusion protein"	605515				8265594, 11751404	Standard	NM_032682		Approved	QRF1, 12CC4, HSPC215, hFKH1B	uc003doj.3	Q9H334	OTTHUMG00000158803	ENST00000318789.4:c.954A>T	chr3.hg19:g.71064720T>A	ENSP00000318902:p.Glu318Asp	146.0	0.0		166.0	24.0	NM_001244815	A3QVP8|B3KV70|G5E9V8|Q8NAN6|Q9BSG9|Q9H332|Q9H333|Q9P0R1	Missense_Mutation	SNP	ENST00000318789.4	hg19	CCDS2914.1	.	.	.	.	.	.	.	.	.	.	T	15.76	2.928556	0.52759	.	.	ENSG00000114861	ENST00000318789;ENST00000358280;ENST00000318796;ENST00000475937;ENST00000339693;ENST00000497355;ENST00000491238;ENST00000493089;ENST00000498215;ENST00000484350;ENST00000468577;ENST00000485326	T;T;T;T;T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8	6.07	4.9	0.64082	Zinc finger, C2H2-like (1);	0.089636	0.85682	N	0.000000	T	0.39172	0.1068	L	0.33093	0.98	0.80722	D	1	B;B;B;B;B	0.21309	0.054;0.043;0.002;0.053;0.011	B;B;B;B;B	0.24848	0.028;0.021;0.005;0.056;0.02	T	0.13710	-1.0499	10	0.39692	T	0.17	.	13.2741	0.60178	0.0:0.0:0.1368:0.8632	.	318;317;318;242;318	B3KV70;A3KMG1;G5E9V8;Q8NAN6;Q9H334	.;.;.;.;FOXP1_HUMAN	D	318;130;218;318;318;214;320;318;318;242;318;218	ENSP00000318902:E318D;ENSP00000419393:E318D;ENSP00000418225:E214D;ENSP00000420736:E320D;ENSP00000418524:E318D;ENSP00000418102:E318D;ENSP00000417857:E242D;ENSP00000418883:E318D;ENSP00000417941:E218D	ENSP00000318902:E318D	E	-	3	2	FOXP1	71147410	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.852000	0.39348	1.099000	0.41499	0.528000	0.53228	GAA	.	.		0.423	FOXP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352250.1	NM_032682		A	71064720	T	A	71064720	3	1	251	1	0	0	0	0	1	0	0	0	6034	1606	56	4	1119	4	FOXP1	3	71064720	Missense_Mutation	SNP	T	TCGA-ED-A97K-01A-21D-A382-10	17260204	71064720	126957710	15	34091										
AFAP1	60312	hgsc.bcm.edu	37	chr4	7844908	7844908	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	acgcagagcaacttggtccaCtggccgaaccgcttcttccg	10	15	1	1			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr4:7844908C>A	ENST00000360265.4	-	4	738	c.504G>T	c.(502-504)caG>caT	p.Q168H	AFAP1_ENST00000358461.2_Missense_Mutation_p.Q168H|AFAP1_ENST00000382543.3_Missense_Mutation_p.Q168H|AFAP1_ENST00000420658.1_Missense_Mutation_p.Q168H			Q8N556	AFAP1_HUMAN	actin filament associated protein 1	168	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|skin(4)|stomach(2)	32						ACTTGGTCCACTGGCCGAACC	0.542																																					p.Q168H		Atlas-SNP	.											.	AFAP1	93	.	0			c.G504T						.						102	92	95					4																	7844908		2203	4300	6503	SO:0001583	missense	60312	exon5			GGTCCACTGGCCG	AB209676	CCDS3397.1, CCDS47010.1	4p16	2014-02-12	2007-02-07		ENSG00000196526	ENSG00000196526		"Pleckstrin homology (PH) domain containing"	24017	protein-coding gene	gene with protein product		608252				14755689, 11641786, 11607843	Standard	NM_198595		Approved	AFAP-110, AFAP	uc011bwk.1	Q8N556	OTTHUMG00000125515	ENST00000360265.4:c.504G>T	chr4.hg19:g.7844908C>A	ENSP00000353402:p.Gln168His	63.0	0.0		112.0	39.0	NM_001134647	A8K442|B4DMU2|E9PDT7|Q59EY5|Q9HBY1	Missense_Mutation	SNP	ENST00000360265.4	hg19	CCDS3397.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.131945	0.77662	.	.	ENSG00000196526	ENST00000360265;ENST00000420658;ENST00000358461;ENST00000382543	T;T;T;T	0.76060	-0.99;-0.99;-0.99;-0.99	4.38	4.38	0.52667	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	D	0.84151	0.5409	M	0.76170	2.325	0.58432	D	0.999998	D;P	0.89917	1.0;0.868	D;P	0.91635	0.999;0.755	D	0.85799	0.1372	10	0.87932	D	0	-34.9815	11.1318	0.48351	0.0:0.9004:0.0:0.0996	.	168;168	E9PDT7;Q8N556	.;AFAP1_HUMAN	H	168	ENSP00000353402:Q168H;ENSP00000410689:Q168H;ENSP00000351245:Q168H;ENSP00000371983:Q168H	ENSP00000351245:Q168H	Q	-	3	2	AFAP1	7895808	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	2.765000	0.47621	2.027000	0.59764	0.485000	0.47835	CAG	.	.		0.542	AFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246842.2	NM_021638		A	7844908	C	A	7844908	3	1	251	1	0	0	0	0	1	0	0	0	353	564	20	3	1996	3	AFAP1	4	7844908	Missense_Mutation	SNP	C	TCGA-ED-A97K-01A-21D-A382-10		7844908	183309368	16	34092										
FAT4	79633	hgsc.bcm.edu	37	chr4	126370127	126370127	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	ttccctcctttctcctcttaCgagaaacttgatataacagt	4	12	2	2	rs546465658		TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr4:126370127C>T	ENST00000394329.3	+	9	7969	c.7956C>T	c.(7954-7956)taC>taT	p.Y2652Y	FAT4_ENST00000335110.5_Silent_p.Y950Y	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	2652	Cadherin 25. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						tctCCTCTTACGAGAAACTTG	0.378																																					p.Y2652Y		Atlas-SNP	.											.	FAT4	1752	.	0			c.C7956T						.						54	57	56					4																	126370127		2203	4300	6503	SO:0001819	synonymous_variant	79633	exon9			CTCTTACGAGAAA	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.7956C>T	chr4.hg19:g.126370127C>T		96.0	0.0		107.0	36.0	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	hg19	CCDS3732.3																																																																																			.	.		0.378	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		T	126370127	C	T	126370127	2	4	251	1	0	0	0	0	0	0	0	1	5700	547	19	1		1	FAT4	4	126370127	Silent	SNP	C	TCGA-ED-A97K-01A-21D-A382-10	118525219	126370127	64784149	17	34093										
NKD2	85409	hgsc.bcm.edu	37	chr5	1038444	1038444	+	Missense_Mutation	SNP	G	G	C													0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	acgagcaccaccaccaccacGagcaccaccaccaccaccac					rs538650344	byFrequency	TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr5:1038444G>C	ENST00000296849.5	+	10	1541	c.1312G>C	c.(1312-1314)Gag>Cag	p.E438Q	NKD2_ENST00000274150.4_3'UTR|NKD2_ENST00000382730.2_Missense_Mutation_p.R77P	NM_033120.3	NP_149111.1	Q969F2	NKD2_HUMAN	naked cuticle homolog 2 (Drosophila)	438	His-rich.				exocytosis (GO:0006887)|Golgi vesicle fusion to target membrane (GO:0048210)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein processing (GO:0010954)|protein targeting to plasma membrane (GO:0072661)|Wnt signaling pathway (GO:0016055)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cytoplasmic vesicle (GO:0031410)	calcium ion binding (GO:0005509)|growth factor binding (GO:0019838)|ubiquitin protein ligase binding (GO:0031625)	p.E438delE(1)		breast(1)|central_nervous_system(3)|large_intestine(1)|lung(8)|pancreas(1)	14	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09)		Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165)			ccaccaccacgagcaccacca	0.687																																					p.E438Q		Atlas-SNP	.											.,1	NKD2	39	.	1	Deletion - In frame(1)	central_nervous_system(1)	c.G1312C						.						5	4	4					5																	1038444		1925	3790	5715	SO:0001583	missense	85409	exon10			CACCACGAGCACC	AF358137	CCDS3859.1, CCDS59486.1	5p15.3	2013-01-10			ENSG00000145506	ENSG00000145506		"EF-hand domain containing"	17046	protein-coding gene	gene with protein product	"naked cuticle-2", "Dvl-binding protein NKD2"	607852				11356022, 11604995	Standard	NM_033120		Approved	Naked2	uc003jbt.2	Q969F2	OTTHUMG00000090348	ENST00000296849.5:c.1312G>C	chr5.hg19:g.1038444G>C	ENSP00000296849:p.Glu438Gln	11.0	0.0		27.0	8.0	NM_033120	Q96EK8|Q9BSN0	Missense_Mutation	SNP	ENST00000296849.5	hg19	CCDS3859.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.31|12.31	1.899877|1.899877	0.33535|0.33535	.|.	.|.	ENSG00000145506|ENSG00000145506	ENST00000296849|ENST00000382730	T|T	0.57595|0.39229	0.39|1.09	3.7|3.7	2.81|2.81	0.32909|0.32909	.|.	0.000000|.	0.49305|.	U|.	0.000155|.	T|T	0.26593|0.26593	0.0650|0.0650	N|N	0.08118|0.08118	0|0	0.20489|0.20489	N|N	0.999897|0.999897	D|.	0.67145|.	0.996|.	P|.	0.61003|.	0.882|.	T|T	0.22626|0.22626	-1.0211|-1.0211	10|7	0.87932|0.87932	D|D	0|0	-20.2951|-20.2951	9.0625|9.0625	0.36442|0.36442	0.0:0.2264:0.7736:0.0|0.0:0.2264:0.7736:0.0	.|.	438|.	Q969F2|.	NKD2_HUMAN|.	Q|P	438|77	ENSP00000296849:E438Q|ENSP00000372177:R77P	ENSP00000296849:E438Q|ENSP00000372177:R77P	E|R	+|+	1|2	0|0	NKD2|NKD2	1091444|1091444	1.000000|1.000000	0.71417|0.71417	0.975000|0.975000	0.42487|0.42487	0.967000|0.967000	0.64934|0.64934	2.791000|2.791000	0.47829|0.47829	0.530000|0.530000	0.28619|0.28619	0.561000|0.561000	0.74099|0.74099	GAG|CGA	.	.		0.687	NKD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206720.2	NM_033120		C	1038444	G	C	1038444	3	2	251	1	0	0	0	0	1	0	0	0	10451	1059	37	4	1350	4	NKD2	5	1038444	Missense_Mutation	SNP	G	TCGA-ED-A97K-01A-21D-A382-10		1038444	179876816	18	34094	173	2								
NKD2	85409	hgsc.bcm.edu	37	chr5	1038446	1038446	+	Missense_Mutation	SNP	G	G	C													0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	gagcaccaccaccaccacgaGcaccaccaccaccaccacca					rs3840989		TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr5:1038446G>C	ENST00000296849.5	+	10	1543	c.1314G>C	c.(1312-1314)gaG>gaC	p.E438D	NKD2_ENST00000274150.4_3'UTR|NKD2_ENST00000382730.2_Missense_Mutation_p.A78P	NM_033120.3	NP_149111.1	Q969F2	NKD2_HUMAN	naked cuticle homolog 2 (Drosophila)	438	His-rich.				exocytosis (GO:0006887)|Golgi vesicle fusion to target membrane (GO:0048210)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein processing (GO:0010954)|protein targeting to plasma membrane (GO:0072661)|Wnt signaling pathway (GO:0016055)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cytoplasmic vesicle (GO:0031410)	calcium ion binding (GO:0005509)|growth factor binding (GO:0019838)|ubiquitin protein ligase binding (GO:0031625)	p.E438delE(1)		breast(1)|central_nervous_system(3)|large_intestine(1)|lung(8)|pancreas(1)	14	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09)		Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165)			accaccacgagcaccaccacc	0.692																																					p.E438D		Atlas-SNP	.											.	NKD2	39	.	1	Deletion - In frame(1)	central_nervous_system(1)	c.G1314C						.						5	4	4					5																	1038446		1924	3775	5699	SO:0001583	missense	85409	exon10			CCACGAGCACCAC	AF358137	CCDS3859.1, CCDS59486.1	5p15.3	2013-01-10			ENSG00000145506	ENSG00000145506		"EF-hand domain containing"	17046	protein-coding gene	gene with protein product	"naked cuticle-2", "Dvl-binding protein NKD2"	607852				11356022, 11604995	Standard	NM_033120		Approved	Naked2	uc003jbt.2	Q969F2	OTTHUMG00000090348	ENST00000296849.5:c.1314G>C	chr5.hg19:g.1038446G>C	ENSP00000296849:p.Glu438Asp	11.0	0.0		24.0	5.0	NM_033120	Q96EK8|Q9BSN0	Missense_Mutation	SNP	ENST00000296849.5	hg19	CCDS3859.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.11|10.11	1.260604|1.260604	0.23051|0.23051	.|.	.|.	ENSG00000145506|ENSG00000145506	ENST00000382730|ENST00000296849	T|T	0.38401|0.56776	1.14|0.44	3.7|3.7	-3.46|-3.46	0.04767|0.04767	.|.	.|0.000000	.|0.49305	.|U	.|0.000155	T|T	0.23926|0.23926	0.0579|0.0579	N|N	0.08118|0.08118	0|0	0.22199|0.22199	N|N	0.999295|0.999295	.|B	.|0.20052	.|0.041	.|B	.|0.17722	.|0.019	T|T	0.07731|0.07731	-1.0757|-1.0757	7|10	0.87932|0.87932	D|D	0|0	-20.2951|-20.2951	4.7821|4.7821	0.13208|0.13208	0.5785:0.1801:0.2414:0.0|0.5785:0.1801:0.2414:0.0	.|.	.|438	.|Q969F2	.|NKD2_HUMAN	P|D	78|438	ENSP00000372177:A78P|ENSP00000296849:E438D	ENSP00000372177:A78P|ENSP00000296849:E438D	A|E	+|+	1|3	0|2	NKD2|NKD2	1091446|1091446	0.727000|0.727000	0.28069|0.28069	0.928000|0.928000	0.36995|0.36995	0.965000|0.965000	0.64279|0.64279	-0.123000|-0.123000	0.10611|0.10611	-0.615000|-0.615000	0.05679|0.05679	-0.258000|-0.258000	0.10820|0.10820	GCA|GAG	.	.		0.692	NKD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206720.2	NM_033120		C	1038446	G	C	1038446	3	2	251	1	0	0	0	0	1	0	0	0	10451	962	34	4	1352	4	NKD2	5	1038446	Missense_Mutation	SNP	G	TCGA-ED-A97K-01A-21D-A382-10	2	1038446	179876814	19	34095	173	2								
ARSK	153642	hgsc.bcm.edu	37	chr5	94922268	94922268	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	tttttctcccctttttaggtGtctcatgatgccatcaaaat	5	10	3	1			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr5:94922268G>T	ENST00000380009.4	+	5	907	c.702G>T	c.(700-702)gtG>gtT	p.V234V		NM_198150.2	NP_937793.1	Q6UWY0	ARSK_HUMAN	arylsulfatase family, member K	234					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|pancreas(1)|skin(1)	16		all_cancers(142;3.38e-06)|all_epithelial(76;6.57e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.00473)		all cancers(79;6.5e-16)		CTTTTTAGGTGTCTCATGATG	0.333																																					p.V234V		Atlas-SNP	.											.	ARSK	29	.	0			c.G702T						.						78	78	78					5																	94922268		2203	4300	6503	SO:0001819	synonymous_variant	153642	exon5			TTAGGTGTCTCAT		CCDS4073.1	5q15	2013-02-14	2006-03-07		ENSG00000164291	ENSG00000164291		"Arylsulfatase family"	25239	protein-coding gene	gene with protein product		610011	"arylsulfatase K"			12975309, 16174644	Standard	NM_198150		Approved	DKFZp313G1735, TSULF	uc003kld.3	Q6UWY0	OTTHUMG00000121166	ENST00000380009.4:c.702G>T	chr5.hg19:g.94922268G>T		288.0	0.0		355.0	57.0	NM_198150	A2BDE3|B4E1I4|Q3ZCW3|Q8N3Q8	Silent	SNP	ENST00000380009.4	hg19	CCDS4073.1																																																																																			.	.		0.333	ARSK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241652.2	NM_198150		T	94922268	G	T	94922268	2	4	251	1	0	0	0	0	0	0	0	1	996	1364	48	3		3	ARSK	5	94922268	Silent	SNP	G	TCGA-ED-A97K-01A-21D-A382-10	93883822	94922268	85992992	20	34096										
KCNN2	3781	hgsc.bcm.edu	37	chr5	113740180	113740180	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	atgactggagaatagccatgActtatgagcgtattttcttc	9	7	1	4			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr5:113740180A>T	ENST00000512097.3	+	4	1646	c.628A>T	c.(628-630)Act>Tct	p.T210S	KCNN2_ENST00000264773.3_Missense_Mutation_p.T210S|KCNN2_ENST00000507750.1_Intron			Q9H2S1	KCNN2_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	210					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transport (GO:1901379)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|protein homodimerization activity (GO:0042803)|small conductance calcium-activated potassium channel activity (GO:0016286)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(21)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(142;2.86e-05)|all_epithelial(76;9.33e-06)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Breast(839;0.159)|Lung NSC(810;0.174)|all_lung(232;0.206)		OV - Ovarian serous cystadenocarcinoma(64;1.89e-08)|Epithelial(69;2.04e-08)|all cancers(49;3.74e-06)|COAD - Colon adenocarcinoma(37;0.142)|Colorectal(14;0.195)	Miconazole(DB01110)|Procaine(DB00721)	AATAGCCATGACTTATGAGCG	0.428																																					p.T210S		Atlas-SNP	.											.	KCNN2	144	.	0			c.A628T						.						195	184	188					5																	113740180		2202	4300	6502	SO:0001583	missense	3781	exon3			GCCATGACTTATG	AF239613	CCDS4114.1, CCDS43352.1	5q22.3	2012-07-05			ENSG00000080709	ENSG00000080709		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6291	protein-coding gene	gene with protein product		605879				16382103	Standard	NM_001278204		Approved	KCa2.2, hSK2	uc003kqo.3	Q9H2S1	OTTHUMG00000128836	ENST00000512097.3:c.628A>T	chr5.hg19:g.113740180A>T	ENSP00000427120:p.Thr210Ser	54.0	0.0		48.0	7.0	NM_021614	A6NF94|Q0VFZ4|Q6PJI0|Q6X2Y2	Missense_Mutation	SNP	ENST00000512097.3	hg19	CCDS4114.1	.	.	.	.	.	.	.	.	.	.	A	19.99	3.928914	0.73327	.	.	ENSG00000080709	ENST00000512097;ENST00000264773	D;D	0.98822	-5.16;-5.16	5.29	5.29	0.74685	Potassium channel, calcium-activated, SK, conserved region (1);	0.000000	0.85682	D	0.000000	D	0.98128	0.9382	L	0.58302	1.8	0.80722	D	1	P	0.41475	0.751	P	0.50049	0.629	D	0.98126	1.0428	10	0.32370	T	0.25	.	14.8849	0.70560	1.0:0.0:0.0:0.0	.	210	Q9H2S1	KCNN2_HUMAN	S	210	ENSP00000427120:T210S;ENSP00000264773:T210S	ENSP00000264773:T210S	T	+	1	0	KCNN2	113768079	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.149000	0.94659	1.995000	0.58328	0.379000	0.24179	ACT	.	.		0.428	KCNN2-001	KNOWN	not_organism_supported|upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250775.2	NM_021614		T	113740180	A	T	113740180	3	4	251	1	0	0	0	0	1	0	0	0	8088	275	10	4	638	4	KCNN2	5	113740180	Missense_Mutation	SNP	A	TCGA-ED-A97K-01A-21D-A382-10	18817912	113740180	67175080	21	34097										
PCDHGB2	56103	hgsc.bcm.edu	37	chr5	140740865	140740865	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	agtttactgccaagtgttggGaaatgccaagtttattttga	10	5	0	1			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr5:140740865G>A	ENST00000522605.1	+	1	1163	c.1163G>A	c.(1162-1164)gGa>gAa	p.G388E	PCDHGA2_ENST00000394576.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018923.2|NM_032096.1	NP_061746.1|NP_115267.1	Q9Y5G2	PCDGE_HUMAN	protocadherin gamma subfamily B, 2	388	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAAGTGTTGGGAAATGCCAAG	0.468																																					p.G388E		Atlas-SNP	.											.	PCDHGB2	196	.	0			c.G1163A						.						65	71	69					5																	140740865		2019	4184	6203	SO:0001583	missense	56103	exon1			TGTTGGGAAATGC	AF152331	CCDS54924.1, CCDS75332.1	5q31	2010-01-26				ENSG00000253910		"Cadherins / Protocadherins : Clustered"	8709	other	protocadherin		606300				10380929	Standard	NM_018923		Approved	PCDH-GAMMA-B2		Q9Y5G2		ENST00000522605.1:c.1163G>A	chr5.hg19:g.140740865G>A	ENSP00000429018:p.Gly388Glu	166.0	0.0		178.0	46.0	NM_018923	Q3MIJ3|Q9UN65	Missense_Mutation	SNP	ENST00000522605.1	hg19	CCDS54924.1	.	.	.	.	.	.	.	.	.	.	.	0.001	-3.415317	0.00013	.	.	ENSG00000253910	ENST00000522605	T	0.01572	4.76	5.3	0.451	0.16629	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.01421	0.0046	N	0.25380	0.74	0.09310	N	1	B;B	0.13594	0.004;0.008	B;B	0.20384	0.012;0.029	T	0.47959	-0.9076	9	0.07030	T	0.85	.	9.4943	0.38978	0.3565:0.0:0.6435:0.0	.	388;388	Q9Y5G2-2;Q9Y5G2	.;PCDGE_HUMAN	E	388	ENSP00000429018:G388E	ENSP00000429018:G388E	G	+	2	0	PCDHGB2	140721049	0.000000	0.05858	0.010000	0.14722	0.001000	0.01503	0.437000	0.21543	0.066000	0.16515	-0.768000	0.03414	GGA	.	.		0.468	PCDHGB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374741.1	NM_018923		A	140740865	G	A	140740865	3	1	251	1	0	0	0	0	1	0	0	0	11572	1174	41	3	1165	3	PCDHGB2	5	140740865	Missense_Mutation	SNP	G	TCGA-ED-A97K-01A-21D-A382-10	27000685	140740865	40174395	22	34098										
SLC36A3	285641	hgsc.bcm.edu	37	chr5	150660677	150660677	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	gatgatgatctcagctgggaCgtggaactggagggcatagg	17	6	1	2			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr5:150660677C>T	ENST00000335230.3	-	9	1453	c.1042G>A	c.(1042-1044)Gtc>Atc	p.V348I	SLC36A3_ENST00000377713.3_Missense_Mutation_p.V389I	NM_181774.3	NP_861439.3	Q495N2	S36A3_HUMAN	solute carrier family 36, member 3	348						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(1)|stomach(2)|urinary_tract(2)	21		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCAGCTGGGACGTGGAACTGG	0.507																																					p.V389I		Atlas-SNP	.											.	SLC36A3	54	.	0			c.G1165A						.						223	172	189					5																	150660677		2203	4300	6503	SO:0001583	missense	285641	exon10			CTGGGACGTGGAA	AY162215	CCDS4314.1, CCDS47316.1	5q33.1	2013-07-17	2013-07-17		ENSG00000186334	ENSG00000186334		"Solute carriers"	19659	protein-coding gene	gene with protein product		608332				12809675	Standard	NM_181774		Approved	PAT3, TRAMD2, tramdorin2	uc003ltw.2	Q495N2	OTTHUMG00000130128	ENST00000335230.3:c.1042G>A	chr5.hg19:g.150660677C>T	ENSP00000334750:p.Val348Ile	89.0	0.0		119.0	13.0	NM_001145017	Q495N3|Q6ZMU7|Q6ZRU4|Q7Z6B4	Missense_Mutation	SNP	ENST00000335230.3	hg19	CCDS4314.1	.	.	.	.	.	.	.	.	.	.	C	19.58	3.853527	0.71719	.	.	ENSG00000186334	ENST00000335230;ENST00000377713	T;T	0.02552	4.25;4.25	3.82	2.95	0.34219	.	0.197168	0.42682	N	0.000670	T	0.14917	0.0360	M	0.88031	2.925	0.58432	D	0.999999	D;D;D	0.63046	0.992;0.987;0.984	P;D;P	0.64321	0.811;0.924;0.875	T	0.01036	-1.1473	10	0.59425	D	0.04	.	11.4437	0.50110	0.0:0.9115:0.0:0.0885	.	389;348;333	Q495N2-3;Q495N2;Q495N2-2	.;S36A3_HUMAN;.	I	348;389	ENSP00000334750:V348I;ENSP00000366942:V389I	ENSP00000334750:V348I	V	-	1	0	SLC36A3	150640870	0.991000	0.36638	0.998000	0.56505	0.717000	0.41224	2.886000	0.48578	0.954000	0.37851	0.561000	0.74099	GTC	.	.		0.507	SLC36A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252436.1	NM_181774		T	150660677	C	T	150660677	3	4	251	1	0	0	0	0	1	0	0	0	14610	536	19	1	378	1	SLC36A3	5	150660677	Missense_Mutation	SNP	C	TCGA-ED-A97K-01A-21D-A382-10	9919812	150660677	30254583	23	34099										
ZFP2	80108	hgsc.bcm.edu	37	chr5	178359427	178359427	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	ggacgatcatcccttaccgtGcatcaggtcattcacactgg	9	13	4	0			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr5:178359427G>T	ENST00000361362.2	+	5	1643	c.1113G>T	c.(1111-1113)gtG>gtT	p.V371V	ZFP2_ENST00000523286.1_Silent_p.V371V|ZFP2_ENST00000520301.1_Silent_p.V371V|ZFP2_ENST00000503510.2_Silent_p.V371V	NM_030613.2	NP_085116.2	Q6ZN57	ZFP2_HUMAN	ZFP2 zinc finger protein	371					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	20	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.00655)|GBM - Glioblastoma multiforme(465;0.0302)|OV - Ovarian serous cystadenocarcinoma(192;0.0615)|Epithelial(171;0.111)		CCCTTACCGTGCATCAGGTCA	0.413																																					p.V371V		Atlas-SNP	.											.	ZFP2	70	.	0			c.G1113T						.						92	84	86					5																	178359427		2203	4300	6503	SO:0001819	synonymous_variant	80108	exon5			TACCGTGCATCAG	AK025281	CCDS4440.1	5q35.3	2013-01-08	2012-11-27		ENSG00000198939	ENSG00000198939		"Zinc fingers, C2H2-type"	26138	protein-coding gene	gene with protein product			"zinc finger protein 2 homolog (mouse)"				Standard	NM_030613		Approved	FLJ21628, ZNF751	uc003mjn.1	Q6ZN57	OTTHUMG00000130885	ENST00000361362.2:c.1113G>T	chr5.hg19:g.178359427G>T		64.0	0.0		81.0	28.0	NM_030613	A5PLN5|B7ZM23|Q9H6Z6	Silent	SNP	ENST00000361362.2	hg19	CCDS4440.1																																																																																			.	.		0.413	ZFP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253470.2	NM_030613		T	178359427	G	T	178359427	2	4	251	1	0	0	0	0	0	0	0	1	17656	1306	46	3		3	ZFP2	5	178359427	Silent	SNP	G	TCGA-ED-A97K-01A-21D-A382-10	27698750	178359427	2555833	24	34100										
ZFP57	4340	hgsc.bcm.edu	37	chr6	29641328	29641328	+	IGR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	ggtggctatagaggtaggagCgcctgctgaaacatttgcca	14	8	0	2			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr6:29641328C>T	ENST00000376917.3	+	0	2160				ZFP57_ENST00000376883.1_Missense_Mutation_p.R167H|ZFP57_ENST00000488757.1_Missense_Mutation_p.R187H|ZFP57_ENST00000376881.3_Missense_Mutation_p.R167H	NM_002433.4|NM_206809.3	NP_002424.3|NP_996532.2	Q16653	MOG_HUMAN	myelin oligodendrocyte glycoprotein						cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|positive regulation of MyD88-dependent toll-like receptor signaling pathway (GO:0034126)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)|skin(2)	19						GAGGTAGGAGCGCCTGCTGAA	0.547																																					p.R187H		Atlas-SNP	.											.	ZFP57	80	.	0			c.G560A						.						79	90	86					6																	29641328		1253	2543	3796	SO:0001628	intergenic_variant	346171	exon4			TAGGAGCGCCTGC		CCDS4667.1, CCDS34366.1, CCDS34367.1, CCDS34368.1, CCDS34369.1, CCDS34370.1, CCDS47394.1, CCDS47395.1, CCDS47395.2, CCDS54977.1	6p22.1	2014-01-16			ENSG00000204655	ENSG00000204655		"Immunoglobulin superfamily / V-set domain containing", "Butyrophilins"	7197	protein-coding gene	gene with protein product		159465					Standard	NM_002433		Approved	BTN6, BTNL11	uc003nne.3	Q16653	OTTHUMG00000031099		chr6.hg19:g.29641328C>T		117.0	0.0		161.0	41.0	NM_001109809	A6NDR4|A6NNJ9|A8MY31|B0UZR9|E9PGF0|F8W9D5|O00713|O00714|O00715|Q13054|Q13055|Q14855|Q29ZN8|Q56UY0|Q5JNX7|Q5JNY1|Q5JNY2|Q5JNY4|Q5SSB5|Q5SSB6|Q5STL9|Q5STM0|Q5STM1|Q5STM2|Q5STM5|Q5SUK5|Q5SUK7|Q5SUK8|Q5SUK9|Q5SUL0|Q5SUL1|Q8IYG5|Q92891|Q92892|Q92893|Q92894|Q92895|Q93053|Q96KU9|Q96KV0|Q96KV1|Q99605	Missense_Mutation	SNP	ENST00000376917.3	hg19	CCDS34370.1	.	.	.	.	.	.	.	.	.	.	C	3.774	-0.047003	0.07407	.	.	ENSG00000204644	ENST00000488757;ENST00000376881;ENST00000376883	T;T;T	0.53206	0.63;0.63;0.63	3.73	1.9	0.25705	.	0.665558	0.13121	N	0.412196	T	0.17195	0.0413	L	0.42245	1.32	0.09310	N	1	B;B	0.25609	0.13;0.13	B;B	0.24394	0.053;0.031	T	0.19095	-1.0316	10	0.30078	T	0.28	-7.5558	7.5513	0.27798	0.0:0.7725:0.0:0.2275	.	187;167	Q9NU63-3;Q9NU63-2	.;.	H	187;167;167	ENSP00000418259:R187H;ENSP00000366078:R167H;ENSP00000366080:R167H	ENSP00000366078:R167H	R	-	2	0	ZFP57	29749307	0.000000	0.05858	0.018000	0.16275	0.030000	0.12068	-0.905000	0.04075	0.538000	0.28769	0.655000	0.94253	CGC	.	.		0.547	MOG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076160.3	NM_002433		T	29641328	C	T	29641328	1	4	251	0	1	0	0	0	0	0	0	0	17666	768	27	1		1	ZFP57	6	29641328	IGR	SNP	C	TCGA-ED-A97K-01A-21D-A382-10		29641328	141473739	25	34101										
FTSJD2	23070	hgsc.bcm.edu	37	chr6	37403498	37403498	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	ctgagcctcagctccacgtcCgatgatgaacctccctcctc	7	18	1	3			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr6:37403498C>T	ENST00000373451.4	+	2	257	c.93C>T	c.(91-93)tcC>tcT	p.S31S		NM_015050.2	NP_055865.1	Q8N1G2	CMTR1_HUMAN	cap methyltransferase 1	31					7-methylguanosine mRNA capping (GO:0006370)|cap1 mRNA methylation (GO:0097309)|mRNA methylation (GO:0080009)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)|nucleic acid binding (GO:0003676)										GCTCCACGTCCGATGATGAAC	0.507																																					p.S31S		Atlas-SNP	.											.	FTSJD2	64	.	0			c.C93T						.						158	115	130					6																	37403498		2203	4300	6503	SO:0001819	synonymous_variant	23070	exon2			CACGTCCGATGAT	BC031890	CCDS4835.1	6p21.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000137200	ENSG00000137200	2.1.1.57	"G patch domain containing"	21077	protein-coding gene	gene with protein product			"KIAA0082", "FtsJ methyltransferase domain containing 2"	KIAA0082, FTSJD2		20713356	Standard	NM_015050		Approved	MTr1, ISG95	uc003ons.3	Q8N1G2	OTTHUMG00000014624	ENST00000373451.4:c.93C>T	chr6.hg19:g.37403498C>T		117.0	0.0		182.0	41.0	NM_015050	A8K949|Q14670|Q96FJ9	Silent	SNP	ENST00000373451.4	hg19	CCDS4835.1																																																																																			.	.		0.507	CMTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040408.1	NM_015050		T	37403498	C	T	37403498	2	4	251	1	0	0	0	0	0	0	0	1	6099	639	23	1		1	FTSJD2	6	37403498	Silent	SNP	C	TCGA-ED-A97K-01A-21D-A382-10	7762170	37403498	133711569	26	34102										
ZPBP	11055	hgsc.bcm.edu	37	chr7	50097728	50097728	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	tggatgttatttgtgcagtgCggttttctactaaaggaata	11	4	1	0	rs201273041	byFrequency	TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr7:50097728C>T	ENST00000046087.2	-	4	413	c.344G>A	c.(343-345)cGc>cAc	p.R115H	ZPBP_ENST00000419417.1_Missense_Mutation_p.R114H|ZPBP_ENST00000491129.1_5'Flank	NM_001159878.1|NM_007009.2	NP_001153350.1|NP_008940.2	Q9BS86	ZPBP1_HUMAN	zona pellucida binding protein	115					acrosome assembly (GO:0001675)|binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|extracellular region (GO:0005576)|nucleus (GO:0005634)|zona pellucida receptor complex (GO:0002199)				NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(3)	29	Glioma(55;0.08)|all_neural(89;0.245)					TTGTGCAGTGCGGTTTTCTAC	0.343													C|||	2	0.000399361	8e-04	0	5008	,	,		18748	0		0	False		,,,				2504	0.001				p.R115H		Atlas-SNP	.											ZPBP,NS,carcinoma,0,1	ZPBP	65	.	0			c.G344A						.	C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	99	100	100		341,344	0.3	0.9	7		100	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	ZPBP	NM_001159878.1,NM_007009.2	29,29	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	benign,benign	114/351,115/352	50097728	3,13003	2203	4300	6503	SO:0001583	missense	11055	exon4			GCAGTGCGGTTTT	D17570	CCDS5509.1, CCDS55110.1	7p14.3	2013-01-11			ENSG00000042813	ENSG00000042813		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15662	protein-coding gene	gene with protein product		608498				9378618	Standard	NM_007009		Approved	SP38, ZPBP1	uc003tou.3	Q9BS86	OTTHUMG00000023528	ENST00000046087.2:c.344G>A	chr7.hg19:g.50097728C>T	ENSP00000046087:p.Arg115His	111.0	0.0		144.0	18.0	NM_007009	A4D253|C9JPU1|Q15941|Q75KX9|Q75MI3	Missense_Mutation	SNP	ENST00000046087.2	hg19	CCDS5509.1	.	.	.	.	.	.	.	.	.	.	C	12.73	2.025357	0.35701	0.0	3.49E-4	ENSG00000042813	ENST00000046087;ENST00000419417	T;T	0.77229	-1.08;-1.08	5.66	0.302	0.15786	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.608760	0.16866	N	0.196303	T	0.49338	0.1551	N	0.08118	0	0.09310	N	1	B;B	0.27823	0.19;0.19	B;B	0.13407	0.009;0.009	T	0.31833	-0.9929	9	.	.	.	-4.0572	5.5251	0.16953	0.0:0.3303:0.395:0.2747	.	114;115	C9JPU1;Q9BS86	.;ZPBP1_HUMAN	H	115;114	ENSP00000046087:R115H;ENSP00000402071:R114H	.	R	-	2	0	ZPBP	50068274	0.586000	0.26782	0.870000	0.34147	0.987000	0.75469	-0.386000	0.07370	0.299000	0.22661	0.591000	0.81541	CGC	.	.		0.343	ZPBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251374.1	NM_007009		T	50097728	C	T	50097728	3	4	251	1	0	0	0	0	1	0	0	0	18234	768	27	1	731	1	ZPBP	7	50097728	Missense_Mutation	SNP	C	TCGA-ED-A97K-01A-21D-A382-10		50097728	109040935	27	34103										
DYNC1I1	1780	hgsc.bcm.edu	37	chr7	95442633	95442633	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	gaagccaagactcaggcgatCtggggccattaacaaggtaa	12	9	2	1			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr7:95442633C>A	ENST00000324972.6	+	4	542	c.349C>A	c.(349-351)Ctg>Atg	p.L117M	DYNC1I1_ENST00000437599.1_Missense_Mutation_p.L117M|DYNC1I1_ENST00000447467.2_Missense_Mutation_p.L100M|DYNC1I1_ENST00000537881.1_Missense_Mutation_p.L100M|DYNC1I1_ENST00000413338.1_Missense_Mutation_p.L100M|DYNC1I1_ENST00000359388.4_Missense_Mutation_p.L100M|DYNC1I1_ENST00000457059.1_Missense_Mutation_p.L100M	NM_004411.4	NP_004402.1	O14576	DC1I1_HUMAN	dynein, cytoplasmic 1, intermediate chain 1	117	Interaction with DCTN1. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|metabolic process (GO:0008152)|vesicle transport along microtubule (GO:0047496)	cytoplasmic dynein complex (GO:0005868)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|kinetochore (GO:0000776)|microtubule (GO:0005874)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)|vesicle (GO:0031982)	microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)|spectrin binding (GO:0030507)			NS(2)|autonomic_ganglia(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(27)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	54	all_cancers(62;9.39e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.165)|all_lung(186;0.191)		STAD - Stomach adenocarcinoma(171;0.0957)			CTCAGGCGATCTGGGGCCATT	0.423																																					p.L117M		Atlas-SNP	.											.	DYNC1I1	111	.	0			c.C349A						.						68	66	67					7																	95442633		2203	4300	6503	SO:0001583	missense	1780	exon4			GGCGATCTGGGGC	AF063228	CCDS5644.1, CCDS47645.1, CCDS47646.1, CCDS64718.1	7q21.3-q22.1	2013-01-18	2005-11-24	2005-11-24	ENSG00000158560	ENSG00000158560		"Cytoplasmic dyneins", "WD repeat domain containing"	2963	protein-coding gene	gene with protein product		603772	"dynein, cytoplasmic, intermediate polypeptide 1"	DNCI1		10049579, 16260502	Standard	NM_004411		Approved	DNCIC1	uc003uoc.4	O14576	OTTHUMG00000153983	ENST00000324972.6:c.349C>A	chr7.hg19:g.95442633C>A	ENSP00000320130:p.Leu117Met	95.0	0.0		149.0	47.0	NM_004411	B4DME3|F5H050|G5E9K1|Q8TBF7|Q9Y2X1	Missense_Mutation	SNP	ENST00000324972.6	hg19	CCDS5644.1	.	.	.	.	.	.	.	.	.	.	C	12.81	2.049075	0.36181	.	.	ENSG00000158560	ENST00000447467;ENST00000324972;ENST00000537881;ENST00000437599;ENST00000359388;ENST00000413338;ENST00000518089;ENST00000457059	T;T;T;T;T;T	0.74737	-0.65;-0.61;-0.87;-0.65;-0.65;-0.65	4.64	2.75	0.32379	.	0.255117	0.31897	N	0.006889	T	0.57344	0.2047	N	0.08118	0	0.33724	D	0.617323	P;P;P;P;P	0.47604	0.667;0.898;0.775;0.897;0.855	B;P;P;B;P	0.49140	0.285;0.601;0.477;0.375;0.579	T	0.64748	-0.6334	10	0.45353	T	0.12	-15.669	5.4198	0.16394	0.0:0.602:0.1456:0.2523	.	100;117;100;117;100	Q7Z6M0;G5E9K1;O14576-2;O14576;O14576-3	.;.;.;DC1I1_HUMAN;.	M	100;117;100;117;100;100;100;100	ENSP00000392337:L100M;ENSP00000320130:L117M;ENSP00000438377:L100M;ENSP00000398118:L117M;ENSP00000352348:L100M;ENSP00000412444:L100M	ENSP00000320130:L117M	L	+	1	2	DYNC1I1	95280569	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	2.241000	0.43097	0.816000	0.34421	-0.345000	0.07892	CTG	.	.		0.423	DYNC1I1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333432.1	NM_004411		A	95442633	C	A	95442633	3	1	251	1	0	0	0	0	1	0	0	0	4844	912	32	3	359	3	DYNC1I1	7	95442633	Missense_Mutation	SNP	C	TCGA-ED-A97K-01A-21D-A382-10	45344905	95442633	63696030	28	34104										
KEL	3792	hgsc.bcm.edu	37	chr7	142641785	142641785	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	tccagggaaggtttctgaggCgagtgatgagggcatcccgg	17	8	1	3			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr7:142641785C>T	ENST00000355265.2	-	12	1832	c.1358G>A	c.(1357-1359)cGc>cAc	p.R453H	KEL_ENST00000479768.2_5'Flank	NM_000420.2	NP_000411.1	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase	453					vasoconstriction (GO:0042310)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(34)|ovary(3)|prostate(2)|skin(1)	60	Melanoma(164;0.059)					GTTTCTGAGGCGAGTGATGAG	0.602																																					p.R453H		Atlas-SNP	.											.	KEL	128	.	0			c.G1358A						.						79	69	72					7																	142641785		2203	4300	6503	SO:0001583	missense	3792	exon12			CTGAGGCGAGTGA	BC003135	CCDS34766.1	7q33	2014-07-19	2006-10-10		ENSG00000197993	ENSG00000197993		"CD molecules", "Blood group antigens"	6308	protein-coding gene	gene with protein product		613883	"Kell blood group", "Kell blood group, metalloendopeptidase"			1712490, 7683930	Standard	NM_000420		Approved	ECE3, CD238	uc003wcb.3	P23276	OTTHUMG00000157159	ENST00000355265.2:c.1358G>A	chr7.hg19:g.142641785C>T	ENSP00000347409:p.Arg453His	73.0	0.0		84.0	21.0	NM_000420	B2RBV4|Q96RS8|Q99885	Missense_Mutation	SNP	ENST00000355265.2	hg19	CCDS34766.1	.	.	.	.	.	.	.	.	.	.	C	2.913	-0.225022	0.06022	.	.	ENSG00000197993	ENST00000355265	T	0.75477	-0.94	4.87	-1.61	0.08399	Peptidase M13 (1);	0.635593	0.14786	N	0.298483	T	0.53094	0.1775	N	0.22421	0.69	0.09310	N	1	B	0.15473	0.013	B	0.10450	0.005	T	0.35076	-0.9803	10	0.14656	T	0.56	-0.0341	8.6076	0.33782	0.0:0.3935:0.0:0.6065	.	453	P23276	KELL_HUMAN	H	453	ENSP00000347409:R453H	ENSP00000347409:R453H	R	-	2	0	KEL	142351907	0.103000	0.21917	0.001000	0.08648	0.052000	0.14988	-0.542000	0.06091	-0.187000	0.10516	-0.444000	0.05651	CGC	.	.		0.602	KEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347671.2	NM_000420		T	142641785	C	T	142641785	3	4	251	1	0	0	0	0	1	0	0	0	8151	768	27	1	872	1	KEL	7	142641785	Missense_Mutation	SNP	C	TCGA-ED-A97K-01A-21D-A382-10	47199152	142641785	16496878	29	34105										
CSMD1	64478	hgsc.bcm.edu	37	chr8	3015485	3015485	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	catacaggaaatgtgggaacGgccctgtttaaaagaaaaca	10	7	0	1			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr8:3015485G>A	ENST00000520002.1	-	40	6406	c.5851C>T	c.(5851-5853)Cgt>Tgt	p.R1951C	CSMD1_ENST00000523387.1_5'UTR|CSMD1_ENST00000602557.1_Missense_Mutation_p.R1951C|CSMD1_ENST00000542608.1_Missense_Mutation_p.R1950C|CSMD1_ENST00000400186.3_Missense_Mutation_p.R1951C|CSMD1_ENST00000539096.1_Missense_Mutation_p.R1950C|CSMD1_ENST00000602723.1_Missense_Mutation_p.R1951C|CSMD1_ENST00000537824.1_Missense_Mutation_p.R1950C			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1951	Sushi 11. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		ATGTGGGAACGGCCCTGTTTA	0.403																																					p.R1950C		Atlas-SNP	.											.	CSMD1	1469	.	0			c.C5848T						.						36	34	35					8																	3015485		1867	4036	5903	SO:0001583	missense	64478	exon39			GGGAACGGCCCTG			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.5851C>T	chr8.hg19:g.3015485G>A	ENSP00000430733:p.Arg1951Cys	273.0	0.0		317.0	88.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.8|24.8	4.573582|4.573582	0.86542|0.86542	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000335551|ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096	.|T;T;T;T;T	.|0.66995	.|-0.24;-0.24;-0.24;-0.24;-0.24	5.45|5.45	5.45|5.45	0.79879|0.79879	.|Complement control module (2);Sushi/SCR/CCP (3);	.|0.068629	.|0.64402	.|D	.|0.000014	T|T	0.73923|0.73923	0.3649|0.3649	L|L	0.38175|0.38175	1.15|1.15	0.58432|0.58432	D|D	0.999999|0.999999	.|D;D;D;D	.|0.89917	.|1.0;0.991;0.998;0.987	.|D;P;P;P	.|0.63192	.|0.912;0.806;0.888;0.764	T|T	0.73266|0.73266	-0.4037|-0.4037	5|10	.|0.42905	.|T	.|0.14	.|.	18.8861|18.8861	0.92378|0.92378	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1951;1951;1950;1951	.|E5RIG2;Q96PZ7;F5H2I8;Q96PZ7-4	.|.;CSMD1_HUMAN;.;.	L|C	1430|1951;1951;1812;1950;1950;1950	.|ENSP00000383047:R1951C;ENSP00000430733:R1951C;ENSP00000441462:R1950C;ENSP00000446243:R1950C;ENSP00000441675:R1950C	.|ENSP00000320445:R1812C	P|R	-|-	2|1	0|0	CSMD1|CSMD1	3002892|3002892	1.000000|1.000000	0.71417|0.71417	0.963000|0.963000	0.40424|0.40424	0.959000|0.959000	0.62525|0.62525	5.780000|5.780000	0.68956|0.68956	2.538000|2.538000	0.85594|0.85594	0.655000|0.655000	0.94253|0.94253	CCG|CGT	.	.		0.403	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		A	3015485	G	A	3015485	3	1	251	1	0	0	0	0	1	0	0	0	3946	1116	39	1	4974	1	CSMD1	8	3015485	Missense_Mutation	SNP	G	TCGA-ED-A97K-01A-21D-A382-10		3015485	143348537	30	34106										
CSMD1	64478	hgsc.bcm.edu	37	chr8	3216751	3216751	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	gcttggtggcaccttctaaaCgatatcccaggaagcaggaa	11	10	1	0			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr8:3216751C>T	ENST00000520002.1	-	22	3785	c.3230G>A	c.(3229-3231)cGt>cAt	p.R1077H	CSMD1_ENST00000602557.1_Missense_Mutation_p.R1077H|CSMD1_ENST00000542608.1_Missense_Mutation_p.R1076H|CSMD1_ENST00000400186.3_Missense_Mutation_p.R1077H|CSMD1_ENST00000539096.1_Missense_Mutation_p.R1076H|CSMD1_ENST00000602723.1_Missense_Mutation_p.R1077H|CSMD1_ENST00000537824.1_Missense_Mutation_p.R1076H			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1077	Sushi 6. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)		p.R1076H(1)		breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		ACCTTCTAAACGATATCCCAG	0.552																																					p.R1076H		Atlas-SNP	.											CSMD1_ENST00000537824,NS,carcinoma,-1,3	CSMD1	1469	.	1	Substitution - Missense(1)	kidney(1)	c.G3227A						.						72	78	76					8																	3216751		2203	4300	6503	SO:0001583	missense	64478	exon21			TCTAAACGATATC			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.3230G>A	chr8.hg19:g.3216751C>T	ENSP00000430733:p.Arg1077His	92.0	0.0		141.0	37.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	hg19		.	.	.	.	.	.	.	.	.	.	c	20.6	4.020740	0.75275	.	.	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096	T;T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19;-0.19	5.24	5.24	0.73138	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.64402	D	0.000001	T	0.78240	0.4252	M	0.66506	2.035	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;1.0;1.0	T	0.77180	-0.2682	10	0.40728	T	0.16	.	18.8469	0.92210	0.0:1.0:0.0:0.0	.	1077;1077;1077	E5RIG2;Q96PZ7;Q96PZ7-4	.;CSMD1_HUMAN;.	H	1077;1077;939;1076;1076;1076	ENSP00000383047:R1077H;ENSP00000430733:R1077H;ENSP00000441462:R1076H;ENSP00000446243:R1076H;ENSP00000441675:R1076H	ENSP00000320445:R939H	R	-	2	0	CSMD1	3204158	1.000000	0.71417	0.925000	0.36789	0.217000	0.24651	7.612000	0.82975	2.432000	0.82394	0.550000	0.68814	CGT	.	.		0.552	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		T	3216751	C	T	3216751	3	4	251	1	0	0	0	0	1	0	0	0	3946	536	19	1	7667	1	CSMD1	8	3216751	Missense_Mutation	SNP	C	TCGA-ED-A97K-01A-21D-A382-10	201266	3216751	143147271	31	34107										
LONRF1	91694	hgsc.bcm.edu	37	chr8	12580687	12580687	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	tcaaagacttcattgacaaaAccgacagctggtatcgtggg	10	9	2	2			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr8:12580687A>G	ENST00000398246.3	-	12	2309	c.2240T>C	c.(2239-2241)gTt>gCt	p.V747A	LONRF1_ENST00000525024.1_Missense_Mutation_p.V173A|LONRF1_ENST00000533751.1_Missense_Mutation_p.V390A	NM_152271.3	NP_689484.3	Q17RB8	LONF1_HUMAN	LON peptidase N-terminal domain and ring finger 1	747	Lon.						ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)|upper_aerodigestive_tract(2)	19				READ - Rectum adenocarcinoma(644;0.236)		CATTGACAAAACCGACAGCTG	0.433																																					p.V747A		Atlas-SNP	.											.	LONRF1	45	.	0			c.T2240C						.						138	143	141					8																	12580687		1930	4119	6049	SO:0001583	missense	91694	exon12			GACAAAACCGACA	AK074329	CCDS5987.2	8p23.1	2013-01-09			ENSG00000154359	ENSG00000154359		"RING-type (C3HC4) zinc fingers"	26302	protein-coding gene	gene with protein product						18253036	Standard	XM_005273685		Approved	FLJ23749, RNF191	uc003wwd.1	Q17RB8	OTTHUMG00000165475	ENST00000398246.3:c.2240T>C	chr8.hg19:g.12580687A>G	ENSP00000381298:p.Val747Ala	102.0	0.0		147.0	33.0	NM_152271	B4DM29|B4DU84|Q8TEA0|Q9BSV1	Missense_Mutation	SNP	ENST00000398246.3	hg19	CCDS5987.2	.	.	.	.	.	.	.	.	.	.	A	20.5	4.003583	0.74932	.	.	ENSG00000154359	ENST00000398246;ENST00000525024;ENST00000533751;ENST00000524526	T;T;T;T	0.50001	0.76;0.76;0.76;0.76	5.06	5.06	0.68205	Peptidase S16, lon N-terminal (1);PUA-like domain (1);	0.000000	0.85682	D	0.000000	T	0.62514	0.2434	M	0.63428	1.95	0.80722	D	1	P;D	0.55800	0.841;0.973	P;P	0.59288	0.774;0.855	T	0.66881	-0.5811	10	0.87932	D	0	-15.7019	15.5236	0.75885	1.0:0.0:0.0:0.0	.	736;747	Q17RB8-2;Q17RB8	.;LONF1_HUMAN	A	747;173;390;350	ENSP00000381298:V747A;ENSP00000436770:V173A;ENSP00000432130:V390A;ENSP00000433327:V350A	ENSP00000381298:V747A	V	-	2	0	LONRF1	12625058	1.000000	0.71417	0.847000	0.33407	0.993000	0.82548	8.831000	0.92068	2.194000	0.70268	0.533000	0.62120	GTT	.	.		0.433	LONRF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251693.2	NM_152271		G	12580687	A	G	12580687	3	3	251	1	0	0	0	0	1	0	0	0	8903	43	2	2	85	2	LONRF1	8	12580687	Missense_Mutation	SNP	A	TCGA-ED-A97K-01A-21D-A382-10	9363936	12580687	133783335	32	34108										
FOXE1	2304	hgsc.bcm.edu	37	chr9	100616728	100616728	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	ccgccgccgccgccgccgccGccgccatcttcccaggcgcg	12	24	1	0			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr9:100616728G>A	ENST00000375123.3	+	1	1193	c.532G>A	c.(532-534)Gcc>Acc	p.A178T		NM_004473.3	NP_004464.2	O00358	FOXE1_HUMAN	forkhead box E1 (thyroid transcription factor 2)	178	Ala-rich.				anatomical structure morphogenesis (GO:0009653)|cell migration (GO:0016477)|embryonic organ morphogenesis (GO:0048562)|hair follicle morphogenesis (GO:0031069)|hard palate development (GO:0060022)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pharynx development (GO:0060465)|positive regulation of transcription, DNA-templated (GO:0045893)|soft palate development (GO:0060023)|thymus development (GO:0048538)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|lung(2)|upper_aerodigestive_tract(1)	5		Acute lymphoblastic leukemia(62;0.158)				cgccgccgccgccgccATCTT	0.791																																					p.A178T		Atlas-SNP	.											.	FOXE1	19	.	0			c.G532A						.						2	2	2					9																	100616728		529	1359	1888	SO:0001583	missense	2304	exon1			GCCGCCGCCGCCA	U89995	CCDS35078.1	9q22	2008-09-05			ENSG00000178919	ENSG00000178919		"Forkhead boxes"	3806	protein-coding gene	gene with protein product		602617	"forkhead box E2"	FKHL15, TITF2, FOXE2		9169137, 9697705	Standard	NM_004473		Approved	TTF-2, HFKH4	uc004axu.3	O00358	OTTHUMG00000020333	ENST00000375123.3:c.532G>A	chr9.hg19:g.100616728G>A	ENSP00000364265:p.Ala178Thr	204.0	0.0		240.0	14.0	NM_004473	O75765|Q5T109|Q99526	Missense_Mutation	SNP	ENST00000375123.3	hg19	CCDS35078.1	.	.	.	.	.	.	.	.	.	.	G	15.77	2.930555	0.52866	.	.	ENSG00000178919	ENST00000375123	D	0.93953	-3.32	3.94	3.02	0.34903	.	0.612880	0.14474	U	0.317365	D	0.83087	0.5178	L	0.34521	1.04	0.22571	N	0.998979	P	0.47253	0.892	B	0.30251	0.113	T	0.72969	-0.4130	10	0.13108	T	0.6	.	6.9037	0.24297	0.0993:0.1791:0.7216:0.0	.	178	O00358	FOXE1_HUMAN	T	178	ENSP00000364265:A178T	ENSP00000364265:A178T	A	+	1	0	FOXE1	99656549	0.087000	0.21565	0.898000	0.35279	0.822000	0.46500	0.422000	0.21296	0.758000	0.33059	0.557000	0.71058	GCC	.	.		0.791	FOXE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053341.1			A	100616728	G	A	100616728	3	1	251	1	0	0	0	0	1	0	0	0	6011	1087	38	1	534	1	FOXE1	9	100616728	Missense_Mutation	SNP	G	TCGA-ED-A97K-01A-21D-A382-10		100616728	40596703	33	34109										
COL13A1	1305	hgsc.bcm.edu	37	chr10	71665571	71665571	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	agggatccagggctaccacgGccggaaggtaagatggaggg	18	8	0	1			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr10:71665571G>A	ENST00000398978.3	+	17	1436	c.944G>A	c.(943-945)gGc>gAc	p.G315D	COL13A1_ENST00000398974.3_Missense_Mutation_p.G303D|COL13A1_ENST00000522165.1_Missense_Mutation_p.G296D|COL13A1_ENST00000520267.1_Missense_Mutation_p.G258D|COL13A1_ENST00000357811.3_Missense_Mutation_p.G293D|COL13A1_ENST00000398973.3_Missense_Mutation_p.G315D|COL13A1_ENST00000517713.1_Missense_Mutation_p.G293D|COL13A1_ENST00000398971.3_Missense_Mutation_p.G315D|COL13A1_ENST00000520133.1_Missense_Mutation_p.G264D|COL13A1_ENST00000398968.3_Missense_Mutation_p.G296D|COL13A1_ENST00000354547.3_Missense_Mutation_p.G293D|COL13A1_ENST00000356340.3_Missense_Mutation_p.G315D|COL13A1_ENST00000398972.3_Missense_Mutation_p.G315D|COL13A1_ENST00000398966.3_Missense_Mutation_p.G293D|COL13A1_ENST00000398964.3_Missense_Mutation_p.G286D|COL13A1_ENST00000398969.3_Missense_Mutation_p.G258D	NM_001130103.1	NP_001123575.1			collagen, type XIII, alpha 1											endometrium(5)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	28						GGCTACCACGGCCGGAAGGTA	0.552																																					p.G315D		Atlas-SNP	.											.	COL13A1	133	.	0			c.G944A						.						64	66	65					10																	71665571		1917	4109	6026	SO:0001583	missense	1305	exon17			ACCACGGCCGGAA	AJ293624	CCDS44419.1, CCDS44423.1, CCDS44424.1, CCDS44425.1, CCDS44427.1, CCDS44428.1, CCDS44423.2, CCDS44424.2, CCDS44425.2, CCDS44427.2, CCDS44428.2	10q22	2013-01-16			ENSG00000197467	ENSG00000197467		"Collagens"	2190	protein-coding gene	gene with protein product		120350					Standard	NM_001130103		Approved		uc001jql.3	Q5TAT6	OTTHUMG00000018394	ENST00000398978.3:c.944G>A	chr10.hg19:g.71665571G>A	ENSP00000381949:p.Gly315Asp	164.0	0.0		148.0	56.0	NM_001130103		Missense_Mutation	SNP	ENST00000398978.3	hg19	CCDS44419.1	.	.	.	.	.	.	.	.	.	.	G	16.36	3.100056	0.56183	.	.	ENSG00000197467	ENST00000398974;ENST00000398971;ENST00000398968;ENST00000398966;ENST00000398964;ENST00000398969;ENST00000356340;ENST00000398972;ENST00000398973;ENST00000398978;ENST00000354547;ENST00000357811;ENST00000520267;ENST00000517713;ENST00000522165;ENST00000520133	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.99619	-6.28;-6.28;-6.28;-6.28;-6.28;-6.28;-6.28;-6.28;-6.28;-6.28;-6.28;-6.28;-6.28;-6.28;-6.28;-6.28	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	D	0.99816	0.9919	H	0.98629	4.285	0.53688	D	0.999974	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	1.0;1.0;0.999;0.999;1.0;0.998;1.0;1.0;1.0;1.0;1.0;0.999;0.998;1.0;1.0;0.998;0.999;1.0;1.0	D	0.96819	0.9602	10	0.87932	D	0	-5.7723	16.6793	0.85288	0.0:0.0:1.0:0.0	.	258;315;315;315;315;293;296;315;303;315;264;293;293;324;315;296;293;286;315	B9EGD2;Q5TAT6;Q5TAT6-5;Q5TAT6-6;E9PEG9;E7ES55;E7ES51;E7ES47;E7ES46;E7ES49;E7EWL8;Q5TAT6-3;Q5TAT6-4;E7EX21;Q5TAT6-7;Q5TAT6-8;Q5TAT6-2;E7ES56;G5E987	.;CODA1_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	D	303;315;296;293;286;258;315;315;315;315;293;293;258;293;296;264	ENSP00000381946:G303D;ENSP00000381943:G315D;ENSP00000381940:G296D;ENSP00000381938:G293D;ENSP00000381936:G286D;ENSP00000381941:G258D;ENSP00000348695:G315D;ENSP00000381944:G315D;ENSP00000381945:G315D;ENSP00000381949:G315D;ENSP00000346553:G293D;ENSP00000350463:G293D;ENSP00000428057:G258D;ENSP00000430061:G293D;ENSP00000428342:G296D;ENSP00000430173:G264D	ENSP00000346553:G293D	G	+	2	0	COL13A1	71335577	1.000000	0.71417	0.996000	0.52242	0.846000	0.48090	5.579000	0.67457	2.688000	0.91661	0.563000	0.77884	GGC	.	.		0.552	COL13A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048468.1	NM_005203		A	71665571	G	A	71665571	3	1	251	1	0	0	0	0	1	0	0	0	3672	1203	42	3	1010	3	COL13A1	10	71665571	Missense_Mutation	SNP	G	TCGA-ED-A97K-01A-21D-A382-10		71665571	63869176	34	34110										
SLIT1	6585	hgsc.bcm.edu	37	chr10	98766408	98766408	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	tccacacagttggccccattCtggcactcagtcccctcaca	6	18	3	0			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr10:98766408C>A	ENST00000266058.4	-	32	3656	c.3411G>T	c.(3409-3411)caG>caT	p.Q1137H	SLIT1_ENST00000371070.4_Missense_Mutation_p.Q1137H|ARHGAP19-SLIT1_ENST00000453547.2_3'UTR	NM_003061.2	NP_003052.2	O75093	SLIT1_HUMAN	slit homolog 1 (Drosophila)	1137	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|dorsal/ventral axon guidance (GO:0033563)|establishment of nucleus localization (GO:0040023)|forebrain morphogenesis (GO:0048853)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of synapse assembly (GO:0051964)|retinal ganglion cell axon guidance (GO:0031290)|spinal cord development (GO:0021510)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(37)|ovary(5)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	78		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		TGGCCCCATTCTGGCACTCAG	0.597																																					p.Q1137H		Atlas-SNP	.											.	SLIT1	154	.	0			c.G3411T						.						42	37	39					10																	98766408		2203	4300	6503	SO:0001583	missense	6585	exon32			CCCATTCTGGCAC	AB011537	CCDS7453.1	10q23.3-q24	2008-08-01	2001-11-28		ENSG00000187122	ENSG00000187122			11085	protein-coding gene	gene with protein product		603742	"slit (Drosophila) homolog 1"	SLIL1		9693030, 9813312	Standard	NM_003061		Approved	slit1, MEGF4, Slit-1, SLIT3	uc001kmw.2	O75093	OTTHUMG00000018843	ENST00000266058.4:c.3411G>T	chr10.hg19:g.98766408C>A	ENSP00000266058:p.Gln1137His	153.0	0.0		143.0	55.0	NM_003061	Q5T0V1|Q8WWZ2|Q9UIL7	Missense_Mutation	SNP	ENST00000266058.4	hg19	CCDS7453.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.873831	0.91664	.	.	ENSG00000187122	ENST00000266058;ENST00000371070	D;D	0.90788	-2.73;-2.73	5.19	5.19	0.71726	Follistatin-like, N-terminal (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.92967	0.7762	L	0.48986	1.54	0.80722	D	1	D	0.69078	0.997	P	0.58721	0.844	D	0.93532	0.6870	10	0.87932	D	0	.	18.9192	0.92518	0.0:1.0:0.0:0.0	.	1137	O75093	SLIT1_HUMAN	H	1137	ENSP00000266058:Q1137H;ENSP00000360109:Q1137H	ENSP00000266058:Q1137H	Q	-	3	2	SLIT1	98756398	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.869000	0.69613	2.698000	0.92095	0.655000	0.94253	CAG	.	.		0.597	SLIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049636.1	NM_003061		A	98766408	C	A	98766408	3	1	251	1	0	0	0	0	1	0	0	0	14754	912	32	3	1217	3	SLIT1	10	98766408	Missense_Mutation	SNP	C	TCGA-ED-A97K-01A-21D-A382-10	27100837	98766408	36768339	35	34111										
THRSP	7069	hgsc.bcm.edu	37	chr11	77775039	77775039	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	tgatgatccccagccttctgCgggacgtgcagctgagtggg	15	11	1	3	rs147579530		TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr11:77775039C>T	ENST00000281030.2	+	1	133	c.112C>T	c.(112-114)Cgg>Tgg	p.R38W	NDUFC2-KCTD14_ENST00000530054.1_Intron|NDUFC2-KCTD14_ENST00000528251.1_Intron	NM_003251.3	NP_003242.1	Q92748	THRSP_HUMAN	thyroid hormone responsive	38					lipid metabolic process (GO:0006629)|regulation of lipid biosynthetic process (GO:0046890)|regulation of transcription, DNA-templated (GO:0006355)|regulation of triglyceride biosynthetic process (GO:0010866)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)		p.R38W(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	7	all_cancers(14;2.23e-19)|all_epithelial(13;7.49e-22)|Breast(9;6.38e-17)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;2.15e-25)			CAGCCTTCTGCGGGACGTGCA	0.607																																					p.R38W		Atlas-SNP	.											THRSP,NS,carcinoma,0,2	THRSP	18	.	1	Substitution - Missense(1)	lung(1)	c.C112T						.	C	,,,TRP/ARG	3,4397	6.2+/-15.9	0,3,2197	88	84	86		,,,112	-0.9	0.4	11	dbSNP_134	86	0,8584		0,0,4292	no	intron,intron,intron,missense	THRSP,NDUFC2-KCTD14	NM_001203260.1,NM_001203261.1,NM_001203262.1,NM_003251.3	,,,101	0,3,6489	TT,TC,CC		0.0,0.0682,0.0231	,,,probably-damaging	,,,38/147	77775039	3,12981	2200	4292	6492	SO:0001583	missense	7069	exon1			CTTCTGCGGGACG	Y08409	CCDS8256.1	11q14.1	2012-06-19	2010-06-25		ENSG00000151365	ENSG00000151365			11800	protein-coding gene	gene with protein product	"SPOT14 homolog (rat)"	601926	"thyroid hormone responsive SPOT14 (rat) homolog", "lipogenic protein 1"	LPGP1		9003802	Standard	NM_003251		Approved	SPOT14, Lpgp, S14, THRP	uc001oyx.3	Q92748	OTTHUMG00000166632	ENST00000281030.2:c.112C>T	chr11.hg19:g.77775039C>T	ENSP00000281030:p.Arg38Trp	69.0	0.0		90.0	9.0	NM_003251	B2R4W7	Missense_Mutation	SNP	ENST00000281030.2	hg19	CCDS8256.1	.	.	.	.	.	.	.	.	.	.	C	16.22	3.060281	0.55432	6.82E-4	0.0	ENSG00000151365	ENST00000281030	.	.	.	5.11	-0.846	0.10734	.	0.377447	0.25156	N	0.032720	T	0.39306	0.1073	.	.	.	0.40290	D	0.978496	P	0.37276	0.589	B	0.32980	0.156	T	0.35151	-0.9800	8	0.87932	D	0	-9.5659	9.5983	0.39587	0.468:0.4592:0.0:0.0728	.	38	Q92748	THRSP_HUMAN	W	38	.	ENSP00000281030:R38W	R	+	1	2	THRSP	77452687	0.999000	0.42202	0.424000	0.26647	0.463000	0.32649	0.630000	0.24553	0.025000	0.15241	-0.314000	0.08810	CGG	.	C|1.000;T|0.000		0.607	THRSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390939.1	NM_003251		T	77775039	C	T	77775039	3	4	251	1	0	0	0	0	1	0	0	0	15891	759	27	1	114	1	THRSP	11	77775039	Missense_Mutation	SNP	C	TCGA-ED-A97K-01A-21D-A382-10		77775039	57231477	36	34112										
KRAS	3845	hgsc.bcm.edu	37	chr12	25362794	25362794	+	3'UTR	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	accatctttgctcatcttttCtttatgttttcgaatttctc	3	10	5	0			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr12:25362794C>T	ENST00000256078.4	-	0	689				KRAS_ENST00000311936.3_Missense_Mutation_p.E168K|KRAS_ENST00000557334.1_Missense_Mutation_p.E55K	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog						actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)		UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			CTCATCTTTTCTTTATGTTTT	0.284		119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											p.E168K	Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	Atlas-SNP	.		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	.	KRAS	30930	.	0			c.G502A						.						62	60	61					12																	25362794		2201	4290	6491	SO:0001624	3_prime_UTR_variant	3845	exon5	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	TCTTTTCTTTATG	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.*56G>A	chr12.hg19:g.25362794C>T		104.0	0.0		140.0	48.0	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	hg19	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	15.48	2.847553	0.51164	.	.	ENSG00000133703	ENST00000311936;ENST00000557334	T;D	0.96136	-1.26;-3.92	5.79	5.79	0.91817	.	.	.	.	.	D	0.93501	0.7926	.	.	.	0.80722	D	1	P	0.37398	0.593	P	0.45577	0.486	D	0.90614	0.4554	8	0.06891	T	0.86	.	19.0037	0.92842	0.0:1.0:0.0:0.0	.	168	P01116-2	.	K	168;55	ENSP00000308495:E168K;ENSP00000452512:E55K	ENSP00000308495:E168K	E	-	1	0	KRAS	25254061	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.443000	0.80521	2.742000	0.94016	0.591000	0.81541	GAA	.	.		0.284	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25362794	C	T	25362794	1	4	251	0	1	0	0	0	0	0	0	0	8447	922	32	3		3	KRAS	12	25362794	3'UTR	SNP	C	TCGA-ED-A97K-01A-21D-A382-10		25362794	108489101	37	34113										
PRICKLE1	144165	hgsc.bcm.edu	37	chr12	42858348	42858348	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	tccagttccaattcctgaagCcttctactgcttgcagggcc	8	14	1	1			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr12:42858348C>T	ENST00000455697.1	-	7	1773	c.1488G>A	c.(1486-1488)agG>agA	p.R496R	RP11-328C8.4_ENST00000547824.1_RNA|PRICKLE1_ENST00000345127.3_Silent_p.R496R|PRICKLE1_ENST00000445766.2_Silent_p.R496R|PRICKLE1_ENST00000552240.1_Silent_p.R496R|PRICKLE1_ENST00000548696.1_Silent_p.R496R	NM_001144882.1|NM_001144883.1	NP_001138354.1|NP_001138355.1	Q96MT3	PRIC1_HUMAN	prickle homolog 1 (Drosophila)	496					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell myoblast differentiation (GO:2000691)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(13)|ovary(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	47	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)		ATTCCTGAAGCCTTCTACTGC	0.488																																					p.R496R		Atlas-SNP	.											.	PRICKLE1	105	.	0			c.G1488A						.						65	62	63					12																	42858348		2203	4300	6503	SO:0001819	synonymous_variant	144165	exon7			CTGAAGCCTTCTA	AK056499	CCDS8742.1	12p11-q12	2010-08-13	2006-09-12			ENSG00000139174			17019	protein-coding gene	gene with protein product		608500	"prickle-like 1 (Drosophila)"			12525887, 18976727	Standard	NM_153026		Approved	FLJ31937, EPM1B	uc010skv.2	Q96MT3		ENST00000455697.1:c.1488G>A	chr12.hg19:g.42858348C>T		123.0	0.0		108.0	26.0	NM_001144882	Q14C83|Q71QF8|Q96N00	Silent	SNP	ENST00000455697.1	hg19	CCDS8742.1																																																																																			.	.		0.488	PRICKLE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404069.1			T	42858348	C	T	42858348	2	4	251	1	0	0	0	0	0	0	0	1	12498	738	26	3		3	PRICKLE1	12	42858348	Silent	SNP	C	TCGA-ED-A97K-01A-21D-A382-10	17495554	42858348	90993547	38	34114										
KRT3	3850	hgsc.bcm.edu	37	chr12	53185086	53185086	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	cctggtagtcacgtagcagcCgcgccaggtcatccttcgcc	11	16	2	0			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr12:53185086C>A	ENST00000417996.2	-	7	1513	c.1439G>T	c.(1438-1440)cGg>cTg	p.R480L	KRT3_ENST00000309505.3_Missense_Mutation_p.R480L	NM_057088.2	NP_476429.2	P12035	K2C3_HUMAN	keratin 3	480	Coil 2.|Rod.				epithelial cell differentiation (GO:0030855)|intermediate filament cytoskeleton organization (GO:0045104)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.R480Q(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|skin(1)	23						ACGTAGCAGCCGCGCCAGGTC	0.617																																					p.R480L		Atlas-SNP	.											KRT3,colon,carcinoma,0,2	KRT3	65	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1439T						.						97	91	93					12																	53185086		2203	4300	6503	SO:0001583	missense	3850	exon7			AGCAGCCGCGCCA		CCDS44895.1	12q13.13	2013-01-16			ENSG00000186442	ENSG00000186442		"-", "Intermediate filaments type II, keratins (basic)"	6440	protein-coding gene	gene with protein product	"keratin, type II cytoskeletal 3", "cytokeratin 3"	148043				7510223, 16831889	Standard	NM_057088		Approved	CK3, K3	uc001say.3	P12035	OTTHUMG00000169799	ENST00000417996.2:c.1439G>T	chr12.hg19:g.53185086C>A	ENSP00000413479:p.Arg480Leu	59.0	0.0		69.0	3.0	NM_057088	A6NIS2|Q701L8	Missense_Mutation	SNP	ENST00000417996.2	hg19	CCDS44895.1	.	.	.	.	.	.	.	.	.	.	C	18.10	3.548780	0.65311	.	.	ENSG00000186442	ENST00000417996;ENST00000309505	T;T	0.76060	-0.99;-0.99	4.71	4.71	0.59529	Filament (1);	0.000000	0.41396	D	0.000899	D	0.87569	0.6210	M	0.88031	2.925	0.38699	D	0.952947	D	0.59767	0.986	P	0.62740	0.906	D	0.90995	0.4838	10	0.87932	D	0	.	18.2151	0.89882	0.0:1.0:0.0:0.0	.	480	P12035	K2C3_HUMAN	L	480	ENSP00000413479:R480L;ENSP00000312206:R480L	ENSP00000312206:R480L	R	-	2	0	KRT3	51471353	0.023000	0.18921	1.000000	0.80357	0.295000	0.27426	0.826000	0.27407	2.619000	0.88677	0.561000	0.74099	CGG	.	.		0.617	KRT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405930.1	NM_057088		A	53185086	C	A	53185086	3	1	251	1	0	0	0	0	1	0	0	0	8475	652	23	1	459	1	KRT3	12	53185086	Missense_Mutation	SNP	C	TCGA-ED-A97K-01A-21D-A382-10	10326738	53185086	80666809	39	34115										
ATP2B1	490	hgsc.bcm.edu	37	chr12	90015489	90015489	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	ttgtcaaagttcctgttttaTctgaacaaatagctgtagca	7	7	2	1			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr12:90015489T>G	ENST00000428670.3	-	10	1880	c.1424A>C	c.(1423-1425)gAt>gCt	p.D475A	ATP2B1_ENST00000359142.3_Missense_Mutation_p.D475A|ATP2B1_ENST00000348959.3_Missense_Mutation_p.D475A|ATP2B1_ENST00000393164.2_Missense_Mutation_p.D218A|ATP2B1_ENST00000261173.2_Missense_Mutation_p.D475A			P20020	AT2B1_HUMAN	ATPase, Ca++ transporting, plasma membrane 1	475					blood coagulation (GO:0007596)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	45						TCCTGTTTTATCTGAACAAAT	0.338																																					p.D475A		Atlas-SNP	.											.	ATP2B1	191	.	0			c.A1424C						.						113	111	112					12																	90015489		2203	4298	6501	SO:0001583	missense	490	exon9			GTTTTATCTGAAC	J04027	CCDS9035.1, CCDS41817.1	12q21.33	2010-04-20			ENSG00000070961	ENSG00000070961	3.6.3.8	"ATPases / P-type"	814	protein-coding gene	gene with protein product	"plasma membrane calcium-transporting ATPase 1"	108731				1674727	Standard	NM_001682		Approved	PMCA1	uc001tbh.3	P20020		ENST00000428670.3:c.1424A>C	chr12.hg19:g.90015489T>G	ENSP00000392043:p.Asp475Ala	60.0	0.0		62.0	26.0	NM_001001323	Q12992|Q12993|Q13819|Q13820|Q13821|Q16504|Q93082	Missense_Mutation	SNP	ENST00000428670.3	hg19	CCDS9035.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.658453	0.88154	.	.	ENSG00000070961	ENST00000261173;ENST00000348959;ENST00000359142;ENST00000428670;ENST00000393164	D;D;D;D;D	0.99960	-9.1;-9.1;-9.1;-9.1;-9.1	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	D	0.99975	0.9992	H	0.99825	4.815	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.85130	0.997;0.984;0.961	D	0.97470	1.0040	9	.	.	.	-28.7159	16.0337	0.80603	0.0:0.0:0.0:1.0	.	475;475;475	P20020-3;P20020-2;P20020-6	.;.;.	A	475;475;475;475;218	ENSP00000261173:D475A;ENSP00000343599:D475A;ENSP00000352054:D475A;ENSP00000392043:D475A;ENSP00000376869:D218A	.	D	-	2	0	ATP2B1	88539620	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.040000	0.89188	2.188000	0.69820	0.460000	0.39030	GAT	.	.		0.338	ATP2B1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406653.1	NM_001682		G	90015489	T	G	90015489	3	3	251	1	0	0	0	0	1	0	0	0	1139	1435	50	5	2444	5	ATP2B1	12	90015489	Missense_Mutation	SNP	T	TCGA-ED-A97K-01A-21D-A382-10	36830403	90015489	43836406	40	34116										
KLF5	688	hgsc.bcm.edu	37	chr13	73649897	73649901	+	Frame_Shift_Del	DEL	GATCG	GATCG	-													0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	ctgcgactggaggttcgcgcGatcggatgagctgacccgcc					rs151120175		TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	GATCG	GATCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr13:73649897_73649901delGATCG	ENST00000377687.4	+	4	1783_1787	c.1247_1251delGATCG	c.(1246-1251)cgatcgfs	p.RS416fs	KLF5_ENST00000539231.1_Frame_Shift_Del_p.RS325fs	NM_001730.3	NP_001721.2	Q13887	KLF5_HUMAN	Kruppel-like factor 5 (intestinal)	416					angiogenesis (GO:0001525)|cellular response to organic cyclic compound (GO:0071407)|cellular response to peptide (GO:1901653)|intestinal epithelial cell development (GO:0060576)|microvillus assembly (GO:0030033)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of microvillus assembly (GO:0032534)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Prostate(6;0.00187)|Breast(118;0.0735)		GBM - Glioblastoma multiforme(99;0.0011)		AGGTTCGCGCGATCGGATGAGCTGA	0.595																																					p.416_417del		Atlas-INDEL	.											.	KLF5	59	.	0			c.1246_1250del						.																																			SO:0001589	frameshift_variant	688	exon4			.	D14520	CCDS9448.1, CCDS66562.1	13q21.3	2013-01-08			ENSG00000102554	ENSG00000102554		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	6349	protein-coding gene	gene with protein product		602903		BTEB2		8479902, 9973612	Standard	NM_001730		Approved	IKLF, CKLF	uc001vje.3	Q13887	OTTHUMG00000017074	ENST00000377687.4:c.1247_1251delGATCG	chr13.hg19:g.73649897_73649901delGATCG	ENSP00000366915:p.Arg416fs	71.0	0.0		92.0	11.0	NM_001730	L0R3U5|L0R4T9|Q9UHP8	Frame_Shift_Del	DEL	ENST00000377687.4	hg19	CCDS9448.1																																																																																			.	.		0.595	KLF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045263.1			-	73649901	GATCG	-	73649897	7	5	251	1	0	1	0	1	0	0	0	0	8358	1058	37	0	1261	0	KLF5	13	73649897	Frame_Shift_Del	DEL	GATCG	TCGA-ED-A97K-01A-21D-A382-10		73649897	41519981	41	34117										
FANCM	57697	hgsc.bcm.edu	37	chr14	45605599	45605599	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	gggaaagacctttattgccgCcgtggtcatgtacaatttct	10	9	2	1			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr14:45605599C>T	ENST00000267430.5	+	1	450	c.365C>T	c.(364-366)gCc>gTc	p.A122V	FKBP3_ENST00000216330.3_5'Flank|FANCM_ENST00000556036.1_Missense_Mutation_p.A122V|FKBP3_ENST00000396062.3_5'Flank|FANCM_ENST00000542564.2_Missense_Mutation_p.A122V	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	122	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						TTTATTGCCGCCGTGGTCATG	0.552								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.A122V		Atlas-SNP	.											.	FANCM	225	.	0			c.C365T						.						76	80	78					14																	45605599		2203	4300	6503	SO:0001583	missense	57697	exon1	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TTGCCGCCGTGGT	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"Fanconi anemia, complementation groups"	23168	protein-coding gene	gene with protein product		609644	"KIAA1596"	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.365C>T	chr14.hg19:g.45605599C>T	ENSP00000267430:p.Ala122Val	114.0	0.0		158.0	38.0	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	hg19	CCDS32070.1	.	.	.	.	.	.	.	.	.	.	C	36	5.607087	0.96626	.	.	ENSG00000187790	ENST00000556036;ENST00000267430;ENST00000542564	T;T;T	0.14391	2.51;2.51;2.51	5.65	5.65	0.86999	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.190452	0.45606	D	0.000347	T	0.30572	0.0769	L	0.58354	1.805	0.50632	D	0.999888	P;P;B	0.48407	0.815;0.91;0.369	P;P;B	0.56088	0.698;0.791;0.389	T	0.00436	-1.1740	10	0.87932	D	0	.	17.2295	0.86981	0.0:1.0:0.0:0.0	.	122;122;122	B2RTQ9;Q8IYD8;Q8IYD8-2	.;FANCM_HUMAN;.	V	122	ENSP00000450596:A122V;ENSP00000267430:A122V;ENSP00000442493:A122V	ENSP00000267430:A122V	A	+	2	0	FANCM	44675349	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.360000	0.79487	2.662000	0.90505	0.563000	0.77884	GCC	.	.		0.552	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		T	45605599	C	T	45605599	3	4	251	1	0	0	0	0	1	0	0	0	5679	739	26	3	367	3	FANCM	14	45605599	Missense_Mutation	SNP	C	TCGA-ED-A97K-01A-21D-A382-10		45605599	61743941	42	34118										
C14orf39	317761	hgsc.bcm.edu	37	chr14	60950469	60950469	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	aatgatcaatttcctcatctGttgcatttatagtttcgtgt	6	7	3	1			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr14:60950469G>A	ENST00000321731.3	-	4	332	c.173C>T	c.(172-174)aCa>aTa	p.T58I		NM_174978.2	NP_777638	Q8N1H7	S6OS1_HUMAN	chromosome 14 open reading frame 39	58					multicellular organismal development (GO:0007275)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)					breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(108;0.0448)		TTCCTCATCTGTTGCATTTAT	0.284																																					p.T58I		Atlas-SNP	.											.	C14orf39	79	.	0			c.C173T						.						146	125	132					14																	60950469		2201	4297	6498	SO:0001583	missense	317761	exon4			TCATCTGTTGCAT	AK098187	CCDS9746.1	14q23.1	2012-11-05	2012-11-05	2012-11-05	ENSG00000179008	ENSG00000179008			19849	protein-coding gene	gene with protein product							Standard	NM_174978		Approved	SIX6OS1	uc001xez.4	Q8N1H7	OTTHUMG00000140332	ENST00000321731.3:c.173C>T	chr14.hg19:g.60950469G>A	ENSP00000324920:p.Thr58Ile	99.0	0.0		127.0	10.0	NM_174978	Q08AQ4	Missense_Mutation	SNP	ENST00000321731.3	hg19	CCDS9746.1	.	.	.	.	.	.	.	.	.	.	G	7.964	0.747563	0.15710	.	.	ENSG00000179008	ENST00000321731;ENST00000555476;ENST00000556799	T;T	0.41065	2.03;1.01	5.18	1.99	0.26369	.	0.424839	0.21808	N	0.068806	T	0.26122	0.0637	L	0.36672	1.1	0.22754	N	0.99877	B	0.09022	0.002	B	0.09377	0.004	T	0.11641	-1.0579	10	0.23302	T	0.38	-4.6557	4.5141	0.11926	0.2139:0.2382:0.5479:0.0	.	58	Q8N1H7	S6OS1_HUMAN	I	58;29;58	ENSP00000324920:T58I;ENSP00000451665:T29I	ENSP00000324920:T58I	T	-	2	0	C14orf39	60020222	1.000000	0.71417	0.997000	0.53966	0.835000	0.47333	0.936000	0.28938	0.659000	0.30945	-0.119000	0.15052	ACA	.	.		0.284	C14orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276948.1	NM_174978		A	60950469	G	A	60950469	3	1	251	1	0	0	0	0	1	0	0	0	1774	1377	48	3	1650	3	C14orf39	14	60950469	Missense_Mutation	SNP	G	TCGA-ED-A97K-01A-21D-A382-10	15344870	60950469	46399071	43	34119										
PPP1R13B	23368	hgsc.bcm.edu	37	chr14	104216135	104216136	+	Frame_Shift_Ins	INS	-	-	T													0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	aactttttcacatgcctgaaINStttttttcccatagagacgt							TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr14:104216135_104216136insT	ENST00000202556.9	-	8	1246_1247	c.964_965insA	c.(964-966)attfs	p.I322fs		NM_015316.2	NP_056131.2	Q96KQ4	ASPP1_HUMAN	protein phosphatase 1, regulatory subunit 13B	322					intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell cycle (GO:0045786)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(6)|kidney(2)|large_intestine(7)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.173)|all_epithelial(191;0.131)|Melanoma(154;0.155)				ACATGCCTGAATTTTTTTCCCA	0.426																																					p.I322fs		Atlas-INDEL	.											.	PPP1R13B	72	.	0			c.965_966insA						.																																			SO:0001589	frameshift_variant	23368	exon8			.	AB018314	CCDS41997.1	14q32.33	2013-01-10	2011-10-04		ENSG00000088808	ENSG00000088808		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	14950	protein-coding gene	gene with protein product		606455	"protein phosphatase 1, regulatory (inhibitor) subunit 13B"			9872452	Standard	NM_015316		Approved	p53BP2-like, KIAA0771, p85, ASPP1	uc001yof.1	Q96KQ4	OTTHUMG00000171647	ENST00000202556.9:c.965dupA	chr14.hg19:g.104216142_104216142dupT	ENSP00000202556:p.Ile322fs	79.0	0.0		78.0	25.0	NM_015316	B2RMX5|O94870	Frame_Shift_Ins	INS	ENST00000202556.9	hg19	CCDS41997.1																																																																																			.	.		0.426	PPP1R13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414591.1	NM_015316		T	104216136	-	T	104216135	7	5	251	1	0	1	1	0	0	0	0	0	12369	101	4	0	2347	0	PPP1R13B	14	104216135	Frame_Shift_Ins	INS	-	TCGA-ED-A97K-01A-21D-A382-10	43265666	104216135	3133405	44	34120										
DAPK2	23604	hgsc.bcm.edu	37	chr15	64275864	64275864	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	ggctcacaccgcgccggctcGcccggctctgccgcttcttg	12	19	3	0	rs193279006	byFrequency	TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr15:64275864G>T	ENST00000457488.1	-	3	212	c.182C>A	c.(181-183)gCg>gAg	p.A61E	DAPK2_ENST00000558069.1_Missense_Mutation_p.A61E|DAPK2_ENST00000558482.1_5'UTR|DAPK2_ENST00000261891.3_Missense_Mutation_p.A61E	NM_014326.3	NP_055141.2	Q9UIK4	DAPK2_HUMAN	death-associated protein kinase 2	61	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				anoikis (GO:0043276)|apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|skin(1)|stomach(1)	11				LUAD - Lung adenocarcinoma(2;0.215)		GCGCCGGCTCGCCCGGCTCTG	0.622																																					p.A61E		Atlas-SNP	.											.	DAPK2	31	.	0			c.C182A						.						39	38	38					15																	64275864		2203	4300	6503	SO:0001583	missense	23604	exon3			CGGCTCGCCCGGC	AB018001	CCDS10188.1	15q22.1	2008-07-18			ENSG00000035664	ENSG00000035664			2675	protein-coding gene	gene with protein product						10376525	Standard	XM_005254265		Approved	DRP-1, MGC119312	uc002amr.3	Q9UIK4	OTTHUMG00000132947	ENST00000457488.1:c.182C>A	chr15.hg19:g.64275864G>T	ENSP00000408277:p.Ala61Glu	50.0	0.0		60.0	28.0	NM_014326	E9JGM7|O75892|Q24JS1	Missense_Mutation	SNP	ENST00000457488.1	hg19	CCDS10188.1	.	.	.	.	.	.	.	.	.	.	G	19.55	3.849082	0.71603	.	.	ENSG00000035664	ENST00000261891;ENST00000457488	T;T	0.63417	-0.04;-0.04	5.35	4.43	0.53597	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.073847	0.52532	D	0.000078	T	0.62392	0.2424	N	0.12182	0.205	0.80722	D	1	D;D	0.67145	0.986;0.996	D;P	0.63703	0.917;0.89	T	0.70193	-0.4939	10	0.87932	D	0	.	15.2366	0.73436	0.0:0.1408:0.8592:0.0	.	61;61	E9JGM7;Q9UIK4	.;DAPK2_HUMAN	E	61	ENSP00000261891:A61E;ENSP00000408277:A61E	ENSP00000261891:A61E	A	-	2	0	DAPK2	62062917	1.000000	0.71417	0.987000	0.45799	0.121000	0.20230	7.952000	0.87827	1.244000	0.43870	0.555000	0.69702	GCG	.	G|1.000;A|0.000		0.622	DAPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256479.1	NM_014326		T	64275864	G	T	64275864	3	4	251	1	0	0	0	0	1	0	0	0	4238	1087	38	1	970	1	DAPK2	15	64275864	Missense_Mutation	SNP	G	TCGA-ED-A97K-01A-21D-A382-10		64275864	38255528	45	34121										
IGDCC4	57722	hgsc.bcm.edu	37	chr15	65681239	65681240	+	Frame_Shift_Ins	INS	-	-	G													0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	atctccccgttgggctctgtINSgggggggcaccagtgcagcc					rs142796011		TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr15:65681239_65681240insG	ENST00000352385.2	-	15	2822_2823	c.2613_2614insC	c.(2611-2616)cccacafs	p.T872fs		NM_020962.1	NP_066013.1	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member 4	872	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	44						TTGGGCTCTGTGGGGGGGCACC	0.663																																					p.T872fs		Atlas-INDEL	.											.,1	IGDCC4	95	.	0			c.2614_2615insC						.																																			SO:0001589	frameshift_variant	57722	exon15			.		CCDS10206.1	15q22.31	2013-02-11			ENSG00000103742	ENSG00000103742		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	13770	protein-coding gene	gene with protein product	"likely ortholog of mouse neighbor of Punc E11"						Standard	NM_020962		Approved	NOPE, LOC57722	uc002aou.1	Q8TDY8	OTTHUMG00000133136	ENST00000352385.2:c.2614dupC	chr15.hg19:g.65681246_65681246dupG	ENSP00000319623:p.Thr872fs	82.0	0.0		81.0	18.0	NM_020962	Q9HCE4	Frame_Shift_Ins	INS	ENST00000352385.2	hg19	CCDS10206.1																																																																																			.	.		0.663	IGDCC4-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256825.2	NM_020962		G	65681240	-	G	65681239	7	5	251	1	0	1	1	0	0	0	0	0	7578	1696	59	0	1162	0	IGDCC4	15	65681239	Frame_Shift_Ins	INS	-	TCGA-ED-A97K-01A-21D-A382-10	1405375	65681239	36850153	46	34122										
DNAH3	55567	hgsc.bcm.edu	37	chr16	21123354	21123354	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	catgattttctttcaggaacGcagcgatgttttgctctgcc	9	10	3	1			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr16:21123354G>A	ENST00000261383.3	-	13	1879	c.1880C>T	c.(1879-1881)gCg>gTg	p.A627V	DNAH3_ENST00000415178.1_Missense_Mutation_p.A627V	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	627	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			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)		TTTCAGGAACGCAGCGATGTT	0.373																																					p.A627V		Atlas-SNP	.											.	DNAH3	1142	.	0			c.C1880T						.						111	92	98					16																	21123354		2201	4299	6500	SO:0001583	missense	55567	exon13			AGGAACGCAGCGA	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"Axonemal dyneins"	2949	protein-coding gene	gene with protein product		603334	"dynein, axonemal, heavy polypeptide 3"			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.1880C>T	chr16.hg19:g.21123354G>A	ENSP00000261383:p.Ala627Val	56.0	0.0		73.0	16.0	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	hg19	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	G	4.561	0.104102	0.08731	.	.	ENSG00000158486	ENST00000261383;ENST00000415178;ENST00000396036	T;T	0.22945	1.93;2.09	5.72	-1.56	0.08532	.	1.142170	0.06471	N	0.731175	T	0.13586	0.0329	N	0.12746	0.255	0.09310	N	1	B;B	0.21606	0.005;0.058	B;B	0.15870	0.001;0.014	T	0.31503	-0.9941	10	0.37606	T	0.19	.	7.6628	0.28413	0.1288:0.0:0.336:0.5352	.	627;567	Q8TD57;Q8TD57-2	DYH3_HUMAN;.	V	627;627;567	ENSP00000261383:A627V;ENSP00000394245:A627V	ENSP00000261383:A627V	A	-	2	0	DNAH3	21030855	0.000000	0.05858	0.041000	0.18516	0.024000	0.10985	0.018000	0.13422	-0.202000	0.10268	-0.905000	0.02835	GCG	.	.		0.373	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		A	21123354	G	A	21123354	3	1	251	1	0	0	0	0	1	0	0	0	4605	1087	38	1	10669	1	DNAH3	16	21123354	Missense_Mutation	SNP	G	TCGA-ED-A97K-01A-21D-A382-10		21123354	69231399	47	34123										
C16orf53	79447	hgsc.bcm.edu	37	chr16	29828159	29828159	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	tgcctgcggatgggcagcccTggatgcccccgccctccgaa	13	17	0	0			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr16:29828159T>A	ENST00000320330.6	+	1	875	c.313T>A	c.(313-315)Tgg>Agg	p.W105R	AC009133.12_ENST00000564980.1_RNA|AC009133.12_ENST00000569809.1_RNA|PAGR1_ENST00000609618.1_Missense_Mutation_p.W105R|AC009133.20_ENST00000569039.1_RNA			Q9BTK6	PAGR1_HUMAN	PAXIP1 associated glutamate-rich protein 1	105	Glu-rich.					histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)											TGGGCAGCCCTGGATGCCCCC	0.697											OREG0023722	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.W105R		Atlas-SNP	.											.	.	.	.	0			c.T313A						.						8	8	8					16																	29828159		2164	4237	6401	SO:0001583	missense	79447	exon1			CAGCCCTGGATGC	BC003640	CCDS10655.1	16p11.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000185928	ENSG00000185928			28707	protein-coding gene	gene with protein product	"glutamate-rich coactivator interacting with SRC1/NCOA1", "PTIP-associated 1 protein", "glutamate-rich coactivator associated with SRC1"	612033	"chromosome 16 open reading frame 53"	C16orf53		17500065, 19039327	Standard	NM_024516		Approved	MGC4606, GAS, PA1	uc002dug.4	Q9BTK6	OTTHUMG00000132117	ENST00000320330.6:c.313T>A	chr16.hg19:g.29828159T>A	ENSP00000326519:p.Trp105Arg	85.0	0.0	812	95.0	15.0	NM_024516	A2ICR6	Missense_Mutation	SNP	ENST00000320330.6	hg19	CCDS10655.1	.	.	.	.	.	.	.	.	.	.	T	28.0	4.878795	0.91740	.	.	ENSG00000185928	ENST00000320330	.	.	.	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.77253	0.4103	M	0.69823	2.125	0.53688	D	0.99997	D	0.89917	1.0	D	0.91635	0.999	T	0.80072	-0.1535	9	0.87932	D	0	-7.1584	13.2408	0.59995	0.0:0.0:0.0:1.0	.	105	Q9BTK6	PA1_HUMAN	R	105	.	ENSP00000326519:W105R	W	+	1	0	C16orf53	29735660	1.000000	0.71417	1.000000	0.80357	0.845000	0.48019	5.308000	0.65768	2.088000	0.63022	0.533000	0.62120	TGG	.	.		0.697	PAGR1-002	PUTATIVE	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000473165.1	NM_024516		A	29828159	T	A	29828159	3	1	251	1	0	0	0	0	1	0	0	0	1820	1580	55	4	315	4	C16orf53	16	29828159	Missense_Mutation	SNP	T	TCGA-ED-A97K-01A-21D-A382-10	8704805	29828159	60526594	48	34124										
NF1	4763	hgsc.bcm.edu	37	chr17	29587388	29587388	+	Splice_Site	DEL	T	T	-													0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	tgactttgcatttttgaaggTttttccttgatatagcatct							TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr17:29587388delT	ENST00000358273.4	+	34	4815	c.4432delT	c.(4432-4434)ttt>tt	p.F1479fs	NF1_ENST00000356175.3_Splice_Site_p.F1458fs	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	1479					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TTTTTGAAGGTTTTTCCTTGA	0.333			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																											p.R1477fs		Atlas-INDEL	.	yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	.	NF1	1586	.	12	Whole gene deletion(8)|Unknown(4)	soft_tissue(7)|autonomic_ganglia(2)|central_nervous_system(2)|lung(1)	c.4431delG						.						103	98	100					17																	29587388		2203	4300	6503	SO:0001630	splice_region_variant	4763	exon34	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	.		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.4431-1T>-	chr17.hg19:g.29587388delT		49.0	0.0		45.0	13.0	NM_001042492	O00662|Q14284|Q14930|Q14931|Q9UMK3	Frame_Shift_Del	DEL	ENST00000358273.4	hg19	CCDS42292.1																																																																																			.	.		0.333	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267	Frame_Shift_Del	-	29587388	T	-	29587388	8	5	251	1	0	1	0	1	0	0	1	0	10365	1739	60	0	4627	0	NF1	17	29587388	Splice_Site	DEL	T	TCGA-ED-A97K-01A-21D-A382-10		29587388	51607822	49	34125										
GAS2L2	246176	hgsc.bcm.edu	37	chr17	34072620	34072620	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	ctggggatgtagaccccactGcgagggatgaccccagacct	13	13	0	3			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr17:34072620G>T	ENST00000254466.6	-	6	1923	c.1896C>A	c.(1894-1896)cgC>cgA	p.R632R	GAS2L2_ENST00000587565.1_Silent_p.R616R	NM_139285.3	NP_644814.1	Q8NHY3	GA2L2_HUMAN	growth arrest-specific 2 like 2	632					cell cycle arrest (GO:0007050)|microtubule bundle formation (GO:0001578)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	actin filament binding (GO:0051015)|cytoskeletal adaptor activity (GO:0008093)|microtubule binding (GO:0008017)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		AGACCCCACTGCGAGGGATGA	0.592																																					p.R632R		Atlas-SNP	.											.	GAS2L2	94	.	0			c.C1896A						.						102	109	106					17																	34072620		2203	4300	6503	SO:0001819	synonymous_variant	246176	exon6			CCCACTGCGAGGG	AF508784	CCDS11298.1	17q21	2014-05-06			ENSG00000132139	ENSG00000270765			24846	protein-coding gene	gene with protein product		611398				12584248	Standard	NM_139285		Approved	GAR17	uc002hjv.2	Q8NHY3	OTTHUMG00000188386	ENST00000254466.6:c.1896C>A	chr17.hg19:g.34072620G>T		72.0	0.0		96.0	4.0	NM_139285	Q8NHY4	Silent	SNP	ENST00000254466.6	hg19	CCDS11298.1																																																																																			.	.		0.592	GAS2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256497.1	NM_139285		T	34072620	G	T	34072620	2	4	251	1	0	0	0	0	0	0	0	1	6255	1306	46	3		3	GAS2L2	17	34072620	Silent	SNP	G	TCGA-ED-A97K-01A-21D-A382-10	4485232	34072620	47122590	50	34126										
KRT10	3858	hgsc.bcm.edu	37	chr17	38975315	38975315	+	Missense_Mutation	SNP	T	T	G													0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	cgccgccggaactgccgccgTggccgccgccgtggccgccg							TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr17:38975315T>G	ENST00000269576.5	-	7	1481	c.1472A>C	c.(1471-1473)cAc>cCc	p.H491P	TMEM99_ENST00000301665.3_5'Flank	NM_000421.3	NP_000412	P13645	K1C10_HUMAN	keratin 10	491	Gly-rich.|Ser-rich.|Tail.			Missing (in Ref. 1; AAA60544). {ECO:0000305}.	cellular response to calcium ion (GO:0071277)|keratinocyte differentiation (GO:0030216)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of epidermis (GO:0030280)			NS(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	11		Breast(137;0.000301)				actgccgccgtggccgccgcc	0.806																																					p.H491P		Atlas-SNP	.											.	KRT10	56	.	0			c.A1472C						.						1	1	1					17																	38975315		210	489	699	SO:0001583	missense	3858	exon7			CCGCCGTGGCCGC	J04029	CCDS11377.1	17q21.2	2013-06-20	2008-08-01		ENSG00000186395	ENSG00000186395		"-", "Intermediate filaments type I, keratins (acidic)"	6413	protein-coding gene	gene with protein product	"cytokeratin 10", "epidermolytic hyperkeratosis"	148080	"keratosis palmaris et plantaris"	KPP		2461420, 16831889	Standard	NM_000421		Approved	K10, CK10	uc002hvi.3	P13645	OTTHUMG00000133368	ENST00000269576.5:c.1472A>C	chr17.hg19:g.38975315T>G	ENSP00000269576:p.His491Pro	67.0	0.0		106.0	10.0	NM_000421	Q14664|Q8N175	Missense_Mutation	SNP	ENST00000269576.5	hg19	CCDS11377.1	.	.	.	.	.	.	.	.	.	.	T	15.71	2.913887	0.52439	.	.	ENSG00000186395	ENST00000269576	D	0.83591	-1.74	5.21	1.74	0.24563	.	2.489830	0.01848	N	0.035767	T	0.68118	0.2966	N	0.08118	0	0.09310	N	1	B	0.22080	0.064	B	0.23018	0.043	T	0.56366	-0.7991	10	0.19147	T	0.46	.	6.4997	0.22162	0.0:0.4912:0.0:0.5088	.	491	P13645	K1C10_HUMAN	P	491	ENSP00000269576:H491P	ENSP00000269576:H491P	H	-	2	0	KRT10	36228841	0.000000	0.05858	0.003000	0.11579	0.038000	0.13279	-3.316000	0.00515	0.176000	0.19873	0.491000	0.48974	CAC	.	.		0.806	KRT10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257875.1	NM_000421		G	38975315	T	G	38975315	3	3	251	1	0	0	0	0	1	0	0	0	8457	1696	59	5	290	5	KRT10	17	38975315	Missense_Mutation	SNP	T	TCGA-ED-A97K-01A-21D-A382-10	4902695	38975315	42219895	51	34127	174	2								
KRT10	3858	hgsc.bcm.edu	37	chr17	38975319	38975319	+	Missense_Mutation	SNP	C	C	T													0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	gccggaactgccgccgtggcCgccgccgtggccgccgccgg							TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr17:38975319C>T	ENST00000269576.5	-	7	1477	c.1468G>A	c.(1468-1470)Ggc>Agc	p.G490S	TMEM99_ENST00000301665.3_5'Flank	NM_000421.3	NP_000412	P13645	K1C10_HUMAN	keratin 10	490	Gly-rich.|Ser-rich.|Tail.			Missing (in Ref. 8; AAA59199). {ECO:0000305}.	cellular response to calcium ion (GO:0071277)|keratinocyte differentiation (GO:0030216)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of epidermis (GO:0030280)			NS(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	11		Breast(137;0.000301)				ccgccgtggccgccgccgtgg	0.791																																					p.G490S		Atlas-SNP	.											.	KRT10	56	.	0			c.G1468A						.																																			SO:0001583	missense	3858	exon7			CGTGGCCGCCGCC	J04029	CCDS11377.1	17q21.2	2013-06-20	2008-08-01		ENSG00000186395	ENSG00000186395		"-", "Intermediate filaments type I, keratins (acidic)"	6413	protein-coding gene	gene with protein product	"cytokeratin 10", "epidermolytic hyperkeratosis"	148080	"keratosis palmaris et plantaris"	KPP		2461420, 16831889	Standard	NM_000421		Approved	K10, CK10	uc002hvi.3	P13645	OTTHUMG00000133368	ENST00000269576.5:c.1468G>A	chr17.hg19:g.38975319C>T	ENSP00000269576:p.Gly490Ser	64.0	0.0		109.0	10.0	NM_000421	Q14664|Q8N175	Missense_Mutation	SNP	ENST00000269576.5	hg19	CCDS11377.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.546565	0.86022	.	.	ENSG00000186395	ENST00000269576	D	0.96587	-4.06	4.38	4.38	0.52667	.	0.845686	0.09879	N	0.743932	D	0.94778	0.8314	N	0.08118	0	0.27860	N	0.940431	D	0.89917	1.0	D	0.76071	0.987	D	0.87790	0.2618	10	0.18710	T	0.47	.	12.7512	0.57310	0.0:1.0:0.0:0.0	.	490	P13645	K1C10_HUMAN	S	490	ENSP00000269576:G490S	ENSP00000269576:G490S	G	-	1	0	KRT10	36228845	0.019000	0.18553	0.876000	0.34364	0.184000	0.23303	0.448000	0.21726	2.739000	0.93911	0.603000	0.83216	GGC	.	.		0.791	KRT10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257875.1	NM_000421		T	38975319	C	T	38975319	3	4	251	1	0	0	0	0	1	0	0	0	8457	652	23	1	294	1	KRT10	17	38975319	Missense_Mutation	SNP	C	TCGA-ED-A97K-01A-21D-A382-10	4	38975319	42219891	52	34128	174	2								
PRKCA	5578	hgsc.bcm.edu	37	chr17	64302214	64302214	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	ttcttgtttttgtttttcagGgggtttgggaaacaaggctt	12	4	2	0			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr17:64302214G>C	ENST00000413366.3	+	2	200	c.174G>C	c.(172-174)tgG>tgC	p.W58C	PRKCA_ENST00000583361.1_3'UTR	NM_002737.2	NP_002728	P17252	KPCA_HUMAN	protein kinase C, alpha	58					activation of adenylate cyclase activity (GO:0007190)|activation of phospholipase C activity (GO:0007202)|angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|cellular response to carbohydrate stimulus (GO:0071322)|chondrocyte differentiation (GO:0002062)|desmosome assembly (GO:0002159)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|histone H3-T6 phosphorylation (GO:0035408)|inactivation of MAPK activity (GO:0000188)|induction of positive chemotaxis (GO:0050930)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|mRNA metabolic process (GO:0016071)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of glucose import (GO:0046325)|negative regulation of insulin receptor signaling pathway (GO:0046627)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|peptidyl-serine autophosphorylation (GO:0036289)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell migration (GO:0030335)|positive regulation of dense core granule biogenesis (GO:2000707)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of inflammatory response (GO:0050729)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of protein phosphorylation (GO:0001934)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|regulation of muscle contraction (GO:0006937)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of the force of heart contraction (GO:0002026)|response to interleukin-1 (GO:0070555)|rhodopsin mediated signaling pathway (GO:0016056)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|enzyme binding (GO:0019899)|histone kinase activity (H3-T6 specific) (GO:0035403)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38			BRCA - Breast invasive adenocarcinoma(6;4.68e-09)		Ingenol Mebutate(DB05013)|Phosphatidylserine(DB00144)|Tamoxifen(DB00675)|Vitamin E(DB00163)	TGTTTTTCAGGGGGTTTGGGA	0.333																																					p.W58C		Atlas-SNP	.											.	PRKCA	82	.	0			c.G174C						.						142	139	140					17																	64302214		2203	4300	6503	SO:0001630	splice_region_variant	5578	exon2			TTTCAGGGGGTTT		CCDS11664.1	17q22-q24	2009-07-10				ENSG00000154229	2.7.11.1		9393	protein-coding gene	gene with protein product		176960		PKCA			Standard	NM_002737		Approved		uc002jfp.1	P17252		ENST00000413366.3:c.174-1G>C	chr17.hg19:g.64302214G>C		56.0	0.0		75.0	10.0	NM_002737	B5BU22|Q15137|Q32M72|Q96RE4	Missense_Mutation	SNP	ENST00000413366.3	hg19	CCDS11664.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.937995	0.73557	.	.	ENSG00000154229	ENST00000413366	D	0.83673	-1.75	4.8	4.8	0.61643	Protein kinase C-like, phorbol ester/diacylglycerol binding (4);Diacylglycerol/phorbol-ester binding (1);	0.000000	0.53938	U	0.000041	D	0.93390	0.7892	M	0.93462	3.42	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	D	0.95158	0.8279	9	.	.	.	.	17.794	0.88564	0.0:0.0:1.0:0.0	.	58	P17252	KPCA_HUMAN	C	58	ENSP00000408695:W58C	.	W	+	3	0	PRKCA	61732676	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.984000	0.93482	2.369000	0.80426	0.655000	0.94253	TGG	.	.		0.333	PRKCA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446976.1		Missense_Mutation	C	64302214	G	C	64302214	5	2	251	1	0	0	0	0	0	0	1	0	12519	1246	43	4	180	4	PRKCA	17	64302214	Splice_Site	SNP	G	TCGA-ED-A97K-01A-21D-A382-10	25326895	64302214	16892996	53	34129										
RYR1	6261	hgsc.bcm.edu	37	chr19	39055854	39055854	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	ccacggcggcggcgggggcgAcggcgcgggttgtggcggcc	23	13	0	0			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr19:39055854A>G	ENST00000359596.3	+	91	12880	c.12880A>G	c.(12880-12882)Acg>Gcg	p.T4294A	RYR1_ENST00000360985.3_Missense_Mutation_p.T4289A|RYR1_ENST00000355481.4_Missense_Mutation_p.T4289A			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	4294					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	ggcgggggcgacggcgCGGGT	0.846																																					p.T4294A		Atlas-SNP	.											.	RYR1	708	.	0			c.A12880G						.						1	1	1					19																	39055854		18	18	36	SO:0001583	missense	6261	exon91			GGGGCGACGGCGC	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.12880A>G	chr19.hg19:g.39055854A>G	ENSP00000352608:p.Thr4294Ala	6.0	0.0		13.0	5.0	NM_000540	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	A	9.104	1.004863	0.19199	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.96427	-4.01;-4.01;-4.01	2.88	-1.87	0.07737	.	0.322035	0.24873	U	0.034918	D	0.86180	0.5871	N	0.14661	0.345	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.74919	-0.3500	10	0.17832	T	0.49	.	0.7381	0.00969	0.4141:0.1519:0.1138:0.3202	.	4289;4289;4294	P21817-3;P21817-2;P21817	.;.;RYR1_HUMAN	A	4294;4289;4289	ENSP00000352608:T4294A;ENSP00000347667:T4289A;ENSP00000354254:T4289A	ENSP00000347667:T4289A	T	+	1	0	RYR1	43747694	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-0.092000	0.11129	-0.236000	0.09753	0.156000	0.16432	ACG	.	.		0.846	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			G	39055854	A	G	39055854	3	3	251	1	0	0	0	0	1	0	0	0	13783	275	10	2	13242	2	RYR1	19	39055854	Missense_Mutation	SNP	A	TCGA-ED-A97K-01A-21D-A382-10		39055854	20073129	54	34130										
ZBTB45	84878	hgsc.bcm.edu	37	chr19	59027809	59027809	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	agtttttccgggagctgaacGtcttgcgacagtggctgcac	13	10	1	1			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr19:59027809G>A	ENST00000594051.1	-	2	1712	c.1232C>T	c.(1231-1233)aCg>aTg	p.T411M	ZBTB45_ENST00000600990.1_Missense_Mutation_p.T411M|ZBTB45_ENST00000354590.3_Missense_Mutation_p.T411M			Q96K62	ZBT45_HUMAN	zinc finger and BTB domain containing 45	411					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|lung(5)|urinary_tract(1)	11		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0165)|Lung(386;0.18)		GGAGCTGAACGTCTTGCGACA	0.622																																					p.T411M	NSCLC(164;1383 2017 5233 27540 46677)	Atlas-SNP	.											.	ZBTB45	37	.	0			c.C1232T						.						79	76	77					19																	59027809		2203	4300	6503	SO:0001583	missense	84878	exon2			CTGAACGTCTTGC	AK027392	CCDS12984.1	19q13.43	2013-10-10	2006-09-19	2006-09-19	ENSG00000119574	ENSG00000119574		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	23715	protein-coding gene	gene with protein product			"zinc finger protein 499"	ZNF499			Standard	NM_032792		Approved	FLJ14486	uc002qtd.3	Q96K62	OTTHUMG00000183545	ENST00000594051.1:c.1232C>T	chr19.hg19:g.59027809G>A	ENSP00000469089:p.Thr411Met	36.0	0.0		59.0	17.0	NM_032792		Missense_Mutation	SNP	ENST00000594051.1	hg19	CCDS12984.1	.	.	.	.	.	.	.	.	.	.	g	18.74	3.688847	0.68271	.	.	ENSG00000119574	ENST00000354590	T	0.35048	1.33	3.41	3.41	0.39046	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.205916	0.29631	N	0.011608	T	0.50480	0.1618	L	0.47078	1.49	0.31546	N	0.65939	D	0.89917	1.0	D	0.74674	0.984	T	0.57516	-0.7798	10	0.87932	D	0	.	13.1018	0.59224	0.0:0.0:1.0:0.0	.	411	Q96K62	ZBT45_HUMAN	M	411	ENSP00000346603:T411M	ENSP00000346603:T411M	T	-	2	0	ZBTB45	63719621	0.999000	0.42202	1.000000	0.80357	0.970000	0.65996	2.835000	0.48175	2.221000	0.72209	0.467000	0.42956	ACG	.	.		0.622	ZBTB45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467067.1	NM_032792		A	59027809	G	A	59027809	3	1	251	1	0	0	0	0	1	0	0	0	17561	1145	40	1	311	1	ZBTB45	19	59027809	Missense_Mutation	SNP	G	TCGA-ED-A97K-01A-21D-A382-10	19971955	59027809	101174	55	34131										
RASSF2	9770	hgsc.bcm.edu	37	chr20	4771204	4771204	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	acgcaccccaacatcactgcGtgtgcgcatcagctgtgggg	12	14	2	0			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr20:4771204G>A	ENST00000379400.3	-	7	625	c.430C>T	c.(430-432)Cgc>Tgc	p.R144C	RASSF2_ENST00000379376.2_Missense_Mutation_p.R144C|RASSF2_ENST00000478553.1_5'UTR	NM_014737.2	NP_055552.1	P50749	RASF2_HUMAN	Ras association (RalGDS/AF-6) domain family member 2	144			R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		bone remodeling (GO:0046849)|cell cycle (GO:0007049)|epidermal growth factor receptor signaling pathway via I-kappaB kinase/NF-kappaB cascade (GO:0038168)|homeostasis of number of cells (GO:0048872)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|ossification (GO:0001503)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(3)|kidney(2)|large_intestine(8)|lung(12)|ovary(3)|pancreas(2)|prostate(2)|skin(2)	34						ACATCACTGCGTGTGCGCATC	0.597																																					p.R144C	Melanoma(158;1891 3343 50738)	Atlas-SNP	.											.	RASSF2	75	.	0			c.C430T						.						76	60	65					20																	4771204		2203	4300	6503	SO:0001583	missense	9770	exon7			CACTGCGTGTGCG	D79990	CCDS13083.1	20p13	2011-08-12	2008-02-22		ENSG00000101265	ENSG00000101265			9883	protein-coding gene	gene with protein product	"centromere protein 34"	609492				8724849, 15806169	Standard	NM_014737		Approved	KIAA0168, CENP-34	uc002wld.3	P50749	OTTHUMG00000031790	ENST00000379400.3:c.430C>T	chr20.hg19:g.4771204G>A	ENSP00000368710:p.Arg144Cys	48.0	0.0		57.0	19.0	NM_014737	A6NIX9|A8K5Z3|Q17S06|Q53HD0|Q6AHZ2|Q8IZA5	Missense_Mutation	SNP	ENST00000379400.3	hg19	CCDS13083.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.532830	0.85812	.	.	ENSG00000101265	ENST00000379400;ENST00000379376	T;T	0.10573	2.86;2.86	5.2	5.2	0.72013	.	0.102570	0.64402	D	0.000005	T	0.18964	0.0455	M	0.75264	2.295	0.58432	D	0.999999	D	0.58620	0.983	P	0.46208	0.507	T	0.00518	-1.1693	10	0.62326	D	0.03	.	12.5495	0.56218	0.0:0.0:0.8336:0.1664	.	144	P50749	RASF2_HUMAN	C	144	ENSP00000368710:R144C;ENSP00000368684:R144C	ENSP00000368684:R144C	R	-	1	0	RASSF2	4719204	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	5.623000	0.67757	2.706000	0.92434	0.563000	0.77884	CGC	.	.		0.597	RASSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077828.1	NM_014737		A	4771204	G	A	4771204	3	1	251	1	0	0	0	0	1	0	0	0	13101	1145	40	1	574	1	RASSF2	20	4771204	Missense_Mutation	SNP	G	TCGA-ED-A97K-01A-21D-A382-10		4771204	58254316	56	34132										
CDK5RAP1	51654	hgsc.bcm.edu	37	chr20	31973469	31973469	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	tcttcacctgctcagaaagcTtcttcacttcctctagaatg	5	13	6	2			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chr20:31973469T>C	ENST00000357886.4	-	7	1016	c.863A>G	c.(862-864)aAg>aGg	p.K288R	CDK5RAP1_ENST00000473997.1_Missense_Mutation_p.K198R|CDK5RAP1_ENST00000339269.5_Missense_Mutation_p.K288R|CDK5RAP1_ENST00000477105.1_5'UTR|CDK5RAP1_ENST00000346416.2_Missense_Mutation_p.K288R|CDK5RAP1_ENST00000544843.1_Missense_Mutation_p.K288R			Q96SZ6	CK5P1_HUMAN	CDK5 regulatory subunit associated protein 1	288					brain development (GO:0007420)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|regulation of neuron differentiation (GO:0045664)|tRNA modification (GO:0006400)	cytoplasm (GO:0005737)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|transferase activity (GO:0016740)			endometrium(2)|kidney(2)|large_intestine(3)|lung(12)|ovary(3)|skin(3)|urinary_tract(1)	26						CTCAGAAAGCTTCTTCACTTC	0.498																																					p.K288R		Atlas-SNP	.											.	CDK5RAP1	62	.	0			c.A863G						.						109	103	105					20																	31973469		2203	4300	6503	SO:0001583	missense	51654	exon7			GAAAGCTTCTTCA	AF152097	CCDS13219.1, CCDS63255.1	20q11.21	2012-09-20	2002-07-22	2002-07-26	ENSG00000101391	ENSG00000101391			15880	protein-coding gene	gene with protein product		608200	"chromosome 20 open reading frame 34"	C20orf34		10721722, 11882646, 15329498	Standard	NM_016408		Approved	CGI-05, HSPC167, C42	uc002wyy.4	Q96SZ6	OTTHUMG00000032256	ENST00000357886.4:c.863A>G	chr20.hg19:g.31973469T>C	ENSP00000350558:p.Lys288Arg	82.0	0.0		113.0	24.0	NM_016408	A8K7R0|Q5QP46|Q5QP47|Q5QP48|Q675N4|Q675N5|Q9BVG6|Q9BWZ5|Q9H859|Q9NZZ9|Q9Y3F0	Missense_Mutation	SNP	ENST00000357886.4	hg19		.	.	.	.	.	.	.	.	.	.	T	12.54	1.967991	0.34754	.	.	ENSG00000101391	ENST00000346416;ENST00000357886;ENST00000339269;ENST00000452723;ENST00000544843	T;T;T;T;T	0.80480	-1.38;-1.38;-1.38;-1.38;-1.38	4.82	4.82	0.62117	Elongator protein 3/MiaB/NifB (1);Radical SAM, alpha/beta horseshoe (1);Radical SAM (1);	0.269001	0.44285	D	0.000467	T	0.52933	0.1765	N	0.01705	-0.755	0.29462	N	0.857665	B;B;B;B;B;B;B	0.27416	0.0;0.178;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B	0.27380	0.004;0.079;0.004;0.004;0.004;0.002;0.001	T	0.50642	-0.8804	10	0.16420	T	0.52	-20.3103	7.8385	0.29384	0.1847:0.0:0.0:0.8153	.	288;288;288;288;288;288;198	Q675N4;Q96SZ6-4;Q96SZ6;Q675N5;Q53H36;Q96SZ6-3;Q96SZ6-2	.;.;CK5P1_HUMAN;.;.;.;.	R	288;288;288;198;288	ENSP00000217372:K288R;ENSP00000350558:K288R;ENSP00000341840:K288R;ENSP00000408133:K198R;ENSP00000439034:K288R	ENSP00000341840:K288R	K	-	2	0	CDK5RAP1	31437130	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	5.213000	0.65230	2.019000	0.59389	0.460000	0.39030	AAG	.	.		0.498	CDK5RAP1-011	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000078697.1	NM_016408		C	31973469	T	C	31973469	3	2	251	1	0	0	0	0	1	0	0	0	3147	1609	56	2	932	2	CDK5RAP1	20	31973469	Missense_Mutation	SNP	T	TCGA-ED-A97K-01A-21D-A382-10	27202265	31973469	31052051	57	34133										
USP11	8237	hgsc.bcm.edu	37	chrX	47104422	47104422	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	ccctcacccccagcccagccGtacattgctatcgactggga	8	18	1	0			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chrX:47104422G>A	ENST00000218348.3	+	16	2223	c.2223G>A	c.(2221-2223)ccG>ccA	p.P741P	USP11_ENST00000377107.2_Silent_p.P698P	NM_004651.3	NP_004642.2	P51784	UBP11_HUMAN	ubiquitin specific peptidase 11	741	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|ovary(3)|pancreas(1)|stomach(1)	40						CAGCCCAGCCGTACATTGCTA	0.567																																					p.P741P		Atlas-SNP	.											.	USP11	93	.	0			c.G2223A						.						64	55	58					X																	47104422		2203	4300	6503	SO:0001819	synonymous_variant	8237	exon16			CCAGCCGTACATT	U44839	CCDS14277.1	Xp11.23	2008-02-05	2005-08-08		ENSG00000102226	ENSG00000102226		"Ubiquitin-specific peptidases"	12609	protein-coding gene	gene with protein product		300050	"ubiquitin specific protease 11"			12838346	Standard	XM_005272674		Approved	UHX1	uc004dhp.3	P51784	OTTHUMG00000021437	ENST00000218348.3:c.2223G>A	chrX.hg19:g.47104422G>A		53.0	0.0		72.0	31.0	NM_004651	B2RTX1|Q8IUG6|Q9BWE1	Silent	SNP	ENST00000218348.3	hg19	CCDS14277.1																																																																																			.	.		0.567	USP11-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_004651		A	47104422	G	A	47104422	2	1	251	1	0	0	0	0	0	0	0	1	17057	1132	40	1		1	USP11	23	47104422	Silent	SNP	G	TCGA-ED-A97K-01A-21D-A382-10		47104422	108166138	58	34134										
SLITRK4	139065	hgsc.bcm.edu	37	chrX	142718491	142718491	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0350877192982456	2	1	0.573015873015873	0	0.594238683127572	0.444444444444444	1	0	tgaaggctcctcgttcaataTacttgattaaattgtagtca	7	7	2	2			TCGA-ED-A97K-01A-21D-A382-10	TCGA-ED-A97K-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f0404ca-e297-4913-86a1-c140b47e98fd	228563d9-a759-4c83-93c8-8ceb4c9e0e9f	g.chrX:142718491T>C	ENST00000381779.4	-	2	659	c.434A>G	c.(433-435)tAt>tGt	p.Y145C	SLITRK4_ENST00000356928.1_Missense_Mutation_p.Y145C|SLITRK4_ENST00000338017.4_Missense_Mutation_p.Y145C	NM_001184749.2|NM_001184750.1|NM_173078.4	NP_001171678.1|NP_001171679.1|NP_775101.1	Q8IW52	SLIK4_HUMAN	SLIT and NTRK-like family, member 4	145						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(27)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	60	Acute lymphoblastic leukemia(192;6.56e-05)					TCGTTCAATATACTTGATTAA	0.373																																					p.Y145C		Atlas-SNP	.											.	SLITRK4	162	.	0			c.A434G						.						81	82	82					X																	142718491		2203	4300	6503	SO:0001583	missense	139065	exon2			TCAATATACTTGA	BC040986	CCDS14679.1	Xq27.3	2004-06-23			ENSG00000179542	ENSG00000179542			23502	protein-coding gene	gene with protein product		300562				14557068	Standard	NM_001184749		Approved	DKFZp547M2010	uc004fby.3	Q8IW52	OTTHUMG00000022580	ENST00000381779.4:c.434A>G	chrX.hg19:g.142718491T>C	ENSP00000371198:p.Tyr145Cys	117.0	0.0		120.0	19.0	NM_001184750	Q5JXG3|Q8TCM8|Q96DL3	Missense_Mutation	SNP	ENST00000381779.4	hg19	CCDS14679.1	.	.	.	.	.	.	.	.	.	.	T	9.541	1.113419	0.20795	.	.	ENSG00000179542	ENST00000381779;ENST00000356928;ENST00000338017	T;T;T	0.58506	0.33;0.33;0.33	5.37	5.37	0.77165	.	0.358748	0.29501	N	0.011971	T	0.59636	0.2208	L	0.39020	1.185	0.39439	D	0.96721	B	0.33022	0.394	P	0.49637	0.617	T	0.61327	-0.7085	10	0.36615	T	0.2	-9.3469	9.2396	0.37489	0.1637:0.0:0.0:0.8363	.	145	Q8IW52	SLIK4_HUMAN	C	145	ENSP00000371198:Y145C;ENSP00000349400:Y145C;ENSP00000336627:Y145C	ENSP00000336627:Y145C	Y	-	2	0	SLITRK4	142546157	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.685000	0.37659	1.788000	0.52465	0.486000	0.48141	TAT	.	.		0.373	SLITRK4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058617.1	NM_173078		C	142718491	T	C	142718491	3	2	251	1	0	0	0	0	1	0	0	0	14760	1406	49	2	2083	2	SLITRK4	23	142718491	Missense_Mutation	SNP	T	TCGA-ED-A97K-01A-21D-A382-10	95614069	142718491	12552069	59	34135										
NRD1	4898	hgsc.bcm.edu	37	chr1	52306079	52306079	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	catcatcttcttcttcttccTccacctcctcttcttcttca	0	18	9	0	rs62648104		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr1:52306079T>A	ENST00000354831.7	-	2	638	c.449A>T	c.(448-450)gAg>gTg	p.E150V	NRD1_ENST00000539524.1_Missense_Mutation_p.E18V|NRD1_ENST00000544028.1_Missense_Mutation_p.E18V|NRD1_ENST00000352171.7_Missense_Mutation_p.E150V|NRD1_ENST00000485608.1_5'UTR	NM_002525.2	NP_002516.2	O43847	NRDC_HUMAN	nardilysin (N-arginine dibasic convertase)	0	Asp/Glu-rich (highly acidic).|Poly-Glu.				cell migration (GO:0016477)|cell proliferation (GO:0008283)|neuromuscular junction development (GO:0007528)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)	cell surface (GO:0009986)|cytosol (GO:0005829)	epidermal growth factor binding (GO:0048408)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)	27						ttcttcttcctccacctcctc	0.378																																					p.E150V		Atlas-SNP	.											.	NRD1	89	.	0			c.A449T						.						163	138	146					1																	52306079		2203	4300	6503	SO:0001583	missense	4898	exon2			TCTTCCTCCACCT	X93207	CCDS559.1, CCDS41335.1, CCDS55599.1	1p32.2-p32.1	2008-07-18			ENSG00000078618	ENSG00000078618			7995	protein-coding gene	gene with protein product		602651				9581555, 9479496	Standard	NM_002525		Approved	hNRD1, hNRD2	uc001ctc.4	O43847	OTTHUMG00000008278	ENST00000354831.7:c.449A>T	chr1.hg19:g.52306079T>A	ENSP00000346890:p.Glu150Val	111.0	0.0		298.0	18.0	NM_002525	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	Missense_Mutation	SNP	ENST00000354831.7	hg19	CCDS559.1	.	.	.	.	.	.	.	.	.	.	T	3.056	-0.194350	0.06259	.	.	ENSG00000078618	ENST00000352171;ENST00000354831;ENST00000539524;ENST00000546169;ENST00000544028	T;T;T;T	0.38240	1.31;3.15;1.15;1.22	5.25	2.92	0.33932	Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.525899	0.19688	N	0.108344	T	0.18341	0.0440	N	0.14661	0.345	0.09310	N	1	B;B;B	0.23650	0.062;0.089;0.01	B;B;B	0.17098	0.017;0.007;0.007	T	0.14755	-1.0461	10	0.38643	T	0.18	-0.0317	5.1939	0.15225	0.0:0.1704:0.2022:0.6274	rs62648104	150;150;150	F5H6R2;O43847;B1AKJ5	.;NRDC_HUMAN;.	V	150;150;18;150;18	ENSP00000262679:E150V;ENSP00000346890:E150V;ENSP00000444416:E18V;ENSP00000442262:E18V	ENSP00000262679:E150V	E	-	2	0	NRD1	52078667	0.129000	0.22400	0.012000	0.15200	0.145000	0.21501	0.870000	0.28010	0.317000	0.23160	0.454000	0.30748	GAG	.	T|0.024;A|0.976		0.378	NRD1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023045.1	NM_002525		A	52306079	T	A	52306079	3	1	252	1	0	0	0	0	1	0	0	0	10654	1551	54	4	3338	4	NRD1	1	52306079	Missense_Mutation	SNP	T	TCGA-EP-A12J-01A-11D-A12Z-10		52306079	196944542	1	34136										
PTPN22	26191	hgsc.bcm.edu	37	chr1	114380291	114380291	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	aaagaatcatgtgaattgtaAtaagagaagagggatgtaga	12	1	1	5			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr1:114380291A>G	ENST00000359785.5	-	13	1866	c.1731T>C	c.(1729-1731)taT>taC	p.Y577Y	PTPN22_ENST00000525799.1_Silent_p.Y450Y|PTPN22_ENST00000528414.1_Silent_p.Y522Y|PTPN22_ENST00000460620.1_Intron|PTPN22_ENST00000420377.2_Silent_p.Y577Y|PTPN22_ENST00000538253.1_Silent_p.Y333Y	NM_001193431.1|NM_015967.5	NP_001180360.1|NP_057051	Q9Y2R2	PTN22_HUMAN	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	577					negative regulation of T cell activation (GO:0050868)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphoanandamide dephosphorylation (GO:0035644)|protein dephosphorylation (GO:0006470)|regulation of B cell receptor signaling pathway (GO:0050855)|regulation of innate immune response (GO:0045088)|regulation of natural killer cell proliferation (GO:0032817)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	kinase binding (GO:0019900)|protein tyrosine phosphatase activity (GO:0004725)|SH3 domain binding (GO:0017124)			NS(1)|breast(1)|kidney(3)|large_intestine(4)|lung(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GTGAATTGTAATAAGAGAAGA	0.363																																					p.Y577Y		Atlas-SNP	.											.	PTPN22	90	.	0			c.T1731C						.						97	98	98					1																	114380291		2203	4300	6503	SO:0001819	synonymous_variant	26191	exon13			ATTGTAATAAGAG	AF001846	CCDS863.1, CCDS864.1, CCDS864.2	1p13.2	2011-06-09	2005-02-02		ENSG00000134242	ENSG00000134242		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9652	protein-coding gene	gene with protein product		600716	"protein tyrosine phosphatase, non-receptor type 8"	PTPN8		10068674, 1373816	Standard	NM_015967		Approved	Lyp, Lyp1, Lyp2	uc001eds.3	Q9Y2R2	OTTHUMG00000011936	ENST00000359785.5:c.1731T>C	chr1.hg19:g.114380291A>G		63.0	0.0		162.0	60.0	NM_015967	A0N0K6|B1ALC8|D4NZ71|E9PLD8|E9PPI1|O95063|O95064|Q6IPX8|Q8WVM1	Silent	SNP	ENST00000359785.5	hg19	CCDS863.1																																																																																			.	.		0.363	PTPN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033015.1	NM_015967		G	114380291	A	G	114380291	2	3	252	1	0	0	0	0	0	0	0	1	12802	108	4	2		2	PTPN22	1	114380291	Silent	SNP	A	TCGA-EP-A12J-01A-11D-A12Z-10	62074212	114380291	134870330	2	34137										
SYCP1	6847	hgsc.bcm.edu	37	chr1	115524051	115524051	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	tgtatctcgaaatttcacatCagttgatcatggcatatcca	6	9	4	1			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr1:115524051C>T	ENST00000369522.3	+	29	2717	c.2477C>T	c.(2476-2478)tCa>tTa	p.S826L	SYCP1_ENST00000477590.1_3'UTR|SYCP1_ENST00000369518.1_Missense_Mutation_p.S826L	NM_001282541.1|NM_003176.2	NP_001269470.1|NP_003167.2	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1	826					chiasma assembly (GO:0051026)|lateral element assembly (GO:0051878)|meiotic DNA repair synthesis (GO:0000711)|reciprocal meiotic recombination (GO:0007131)|regulation of protein localization (GO:0032880)|sperm chromatin condensation (GO:0035092)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)|male germ cell nucleus (GO:0001673)|transverse filament (GO:0000802)	DNA binding (GO:0003677)		RGS22/SYCP1(2)	NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		AATTTCACATCAGTTGATCAT	0.333																																					p.S826L		Atlas-SNP	.											.	SYCP1	149	.	0			c.C2477T						.						92	92	92					1																	115524051		2203	4297	6500	SO:0001583	missense	6847	exon29			TCACATCAGTTGA	D67035	CCDS879.1, CCDS72840.1	1p13-p12	2009-03-12			ENSG00000198765	ENSG00000198765			11487	protein-coding gene	gene with protein product	"cancer/testis antigen 8"	602162				9560255	Standard	XM_005271154		Approved	HOM-TES-14, SCP1, CT8	uc001efr.3	Q15431	OTTHUMG00000012057	ENST00000369522.3:c.2477C>T	chr1.hg19:g.115524051C>T	ENSP00000358535:p.Ser826Leu	74.0	0.0		215.0	96.0	NM_003176	O14963|Q5VXJ6	Missense_Mutation	SNP	ENST00000369522.3	hg19	CCDS879.1	.	.	.	.	.	.	.	.	.	.	C	11.12	1.545076	0.27652	.	.	ENSG00000198765	ENST00000369522;ENST00000369518	T;T	0.34072	1.38;1.38	5.52	5.52	0.82312	.	0.552403	0.19046	N	0.124171	T	0.30727	0.0774	M	0.62723	1.935	0.32710	N	0.511757	D;D	0.54047	0.964;0.964	P;P	0.45310	0.476;0.476	T	0.34725	-0.9817	10	0.72032	D	0.01	-3.8726	14.9278	0.70893	0.0:1.0:0.0:0.0	.	826;826	B7ZLS9;Q15431	.;SYCP1_HUMAN	L	826	ENSP00000358535:S826L;ENSP00000358531:S826L	ENSP00000358531:S826L	S	+	2	0	SYCP1	115325574	0.949000	0.32298	0.813000	0.32504	0.039000	0.13416	2.043000	0.41231	2.609000	0.88269	0.591000	0.81541	TCA	.	.		0.333	SYCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033386.1	NM_003176		T	115524051	C	T	115524051	3	4	252	1	0	0	0	0	1	0	0	0	15446	838	29	3	2587	3	SYCP1	1	115524051	Missense_Mutation	SNP	C	TCGA-EP-A12J-01A-11D-A12Z-10	1143760	115524051	133726570	3	34138										
FCGR3B	2214	hgsc.bcm.edu	37	chr1	161596059	161596059	+	Intron	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	tggaagtcagaattatgatgAaaatacttcctgtctttgcc	8	7	2	3			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr1:161596059A>C	ENST00000540048.1	-	2	94				FCGR3B_ENST00000367964.2_Missense_Mutation_p.F151L|FCGR3B_ENST00000531221.1_Missense_Mutation_p.F187L|FCGR2B_ENST00000367962.4_Intron|FCGR2B_ENST00000428605.2_Intron|FCGR2B_ENST00000367960.5_Intron|FCGR3B_ENST00000294800.3_Missense_Mutation_p.F151L|FCGR2B_ENST00000403078.3_Intron			P08637	FCG3A_HUMAN	Fc fragment of IgG, low affinity IIIa, receptor (CD16a)						Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of immune response (GO:0050776)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	24	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	AATTATGATGAAAATACTTCC	0.443																																					p.F187L		Atlas-SNP	.											.	FCGR3B	35	.	0			c.T561G						.						152	151	151					1																	161596059		2191	4299	6490	SO:0001627	intron_variant	2215	exon4			ATGATGAAAATAC	BC036723	CCDS1232.1, CCDS44266.1	1q23	2014-09-17	2005-02-02		ENSG00000203747	ENSG00000203747		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3619	protein-coding gene	gene with protein product		146740	"Fc fragment of IgG, low affinity IIIa, receptor for (CD16)"	FCGR3, FCG3		2139735	Standard	NM_001127592		Approved	CD16, CD16a	uc001gar.3	P08637	OTTHUMG00000034466	ENST00000540048.1:c.61+4098T>G	chr1.hg19:g.161596059A>C		100.0	0.0		199.0	160.0	NM_001244753	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Missense_Mutation	SNP	ENST00000540048.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	7.898|7.898	0.733772|0.733772	0.15574|0.15574	.|.	.|.	ENSG00000162747|ENSG00000162747	ENST00000367964;ENST00000294800;ENST00000531221|ENST00000421702	T;T;T|.	0.11821|.	2.74;2.74;2.74|.	2.35|2.35	-2.11|-2.11	0.07187|0.07187	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);|.	0.778704|.	0.10279|.	U|.	0.693741|.	T|T	0.10766|0.10766	0.0263|0.0263	L|L	0.39898|0.39898	1.24|1.24	0.09310|0.09310	N|N	1|1	D|.	0.56287|.	0.975|.	P|.	0.48677|.	0.586|.	T|T	0.34477|0.34477	-0.9827|-0.9827	10|5	0.25106|.	T|.	0.35|.	.|.	2.9454|2.9454	0.05845|0.05845	0.3664:0.2608:0.3728:0.0|0.3664:0.2608:0.3728:0.0	.|.	151|.	O75015|.	FCG3B_HUMAN|.	L|A	151;151;187|172	ENSP00000356941:F151L;ENSP00000294800:F151L;ENSP00000433642:F187L|.	ENSP00000294800:F151L|.	F|S	-|-	3|1	2|0	FCGR3B|FCGR3B	159862683|159862683	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.098000|0.098000	0.18820|0.18820	-0.432000|-0.432000	0.06956|0.06956	-0.170000|-0.170000	0.10816|0.10816	0.155000|0.155000	0.16302|0.16302	TTT|TCA	.	.		0.443	FCGR3A-203	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_000569		C	161596059	A	C	161596059	1	2	252	0	1	0	0	0	0	0	0	0	5793	243	9	5		5	FCGR3B	1	161596059	Intron	SNP	A	TCGA-EP-A12J-01A-11D-A12Z-10	46072008	161596059	87654562	4	34139										
C1orf25	81627	hgsc.bcm.edu	37	chr1	185089286	185089287	+	Frame_Shift_Ins	INS	-	-	A													0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	aggtgggggtgctgtactttINSaaaaggatagatttaaactg							TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr1:185089286_185089287insA	ENST00000367506.5	-	15	2334_2335	c.2066_2067insT	c.(2065-2067)ttafs	p.L689fs	TRMT1L_ENST00000465827.1_5'UTR|TRMT1L_ENST00000367504.3_3'UTR	NM_001202423.1|NM_030934.4	NP_001189352.1|NP_112196.3	Q7Z2T5	TRM1L_HUMAN	tRNA methyltransferase 1 homolog (S. cerevisiae)-like	689					adult locomotory behavior (GO:0008344)		metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|tRNA (guanine-N2-)-methyltransferase activity (GO:0004809)|tRNA binding (GO:0000049)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	21						TGCTGTACTTTAAAAGGATAGA	0.441																																					p.L689fs		Atlas-Indel,Pindel	.											.	TRMT1L	50	.	0			c.2067_2068insT						.																																			SO:0001589	frameshift_variant	81627	exon15			.	AF288399	CCDS1366.1	1q25.2	2012-06-29	2012-06-29	2011-01-24	ENSG00000121486	ENSG00000121486			16782	protein-coding gene	gene with protein product	"TRM1-like"	611673	"chromosome 1 open reading frame 25", "TRM1 tRNA methyltransferase 1-like"	C1orf25		11318611, 17198746	Standard	NM_030934		Approved		uc001grf.4	Q7Z2T5	OTTHUMG00000035389	ENST00000367506.5:c.2067dupT	chr1.hg19:g.185089290_185089290dupA	ENSP00000356476:p.Leu689fs	84.0	0.0		412.0	102.0	NM_030934	Q5TEN0|Q6ZMX0|Q8IWH5|Q8NC68|Q9BZQ1	Frame_Shift_Ins	INS	ENST00000367506.5	hg19	CCDS1366.1																																																																																			.	.		0.441	TRMT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085787.1	NM_030934		A	185089287	-	A	185089286	7	5	252	1	0	1	1	0	0	0	0	0	2036	1751	61	0	138	0	C1orf25	1	185089286	Frame_Shift_Ins	INS	-	TCGA-EP-A12J-01A-11D-A12Z-10	23493227	185089286	64161335	5	34140										
GPR137B	7107	hgsc.bcm.edu	37	chr1	236368456	236368456	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	gaatggtccccagccatggaTtcagtcccagatcttatttc	8	12	2	1			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr1:236368456T>A	ENST00000366592.3	+	6	1088	c.997T>A	c.(997-999)Ttc>Atc	p.F333I	GPR137B_ENST00000477559.1_3'UTR	NM_003272.3	NP_003263.1	O60478	G137B_HUMAN	G protein-coupled receptor 137B	333						integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|membrane (GO:0016020)				endometrium(2)|large_intestine(1)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.197)|Prostate(94;0.219)|Acute lymphoblastic leukemia(190;0.226)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)			CAGCCATGGATTCAGTCCCAG	0.463																																					p.F333I		Atlas-SNP	.											.	GPR137B	57	.	0			c.T997A						.						181	179	180					1																	236368456		2203	4300	6503	SO:0001583	missense	7107	exon6			CATGGATTCAGTC	AF027826	CCDS1609.1	1q42-q43	2012-08-10	2006-01-26	2006-01-26	ENSG00000077585	ENSG00000077585			11862	protein-coding gene	gene with protein product		604658	"transmembrane 7 superfamily member 1 (upregulated in kidney)"	TM7SF1		9521871	Standard	NM_003272		Approved		uc001hxq.3	O60478	OTTHUMG00000037994	ENST00000366592.3:c.997T>A	chr1.hg19:g.236368456T>A	ENSP00000355551:p.Phe333Ile	47.0	0.0		151.0	56.0	NM_003272	Q53EK7|Q5TAE6|Q6FHI3	Missense_Mutation	SNP	ENST00000366592.3	hg19	CCDS1609.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	32|32	5.128649|5.128649	0.94473|0.94473	.|.	.|.	ENSG00000077585|ENSG00000077585	ENST00000454895|ENST00000366592;ENST00000391852;ENST00000419162	.|T;T	.|0.48836	.|0.8;0.82	5.9|5.9	5.9|5.9	0.94986|0.94986	.|.	.|0.049214	.|0.85682	.|D	.|0.000000	T|T	0.59729|0.59729	0.2215|0.2215	M|M	0.78049|0.78049	2.395|2.395	0.80722|0.80722	D|D	1|1	.|P;P	.|0.51537	.|0.775;0.946	.|B;P	.|0.48840	.|0.225;0.592	T|T	0.65672|0.65672	-0.6111|-0.6111	5|10	.|0.62326	.|D	.|0.03	-35.2765|-35.2765	15.9906|15.9906	0.80202|0.80202	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|196;333	.|Q5TAF1;O60478	.|.;G137B_HUMAN	E|I	196|333;332;115	.|ENSP00000355551:F333I;ENSP00000401841:F115I	.|ENSP00000355551:F333I	D|F	+|+	3|1	2|0	GPR137B|GPR137B	234435079|234435079	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.977000|0.977000	0.68977|0.68977	3.697000|3.697000	0.54764|0.54764	2.257000|2.257000	0.74773|0.74773	0.528000|0.528000	0.53228|0.53228	GAT|TTC	.	.		0.463	GPR137B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092761.1	NM_003272		A	236368456	T	A	236368456	3	1	252	1	0	0	0	0	1	0	0	0	6654	1493	52	4	1019	4	GPR137B	1	236368456	Missense_Mutation	SNP	T	TCGA-EP-A12J-01A-11D-A12Z-10	51279170	236368456	12882165	6	34141										
RYR2	6262	hgsc.bcm.edu	37	chr1	237774079	237774079	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	tagaatgtgatgcctctctcGgcgggattattcaagagtga	12	7	2	4			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr1:237774079G>T	ENST00000366574.2	+	36	5018	c.4701G>T	c.(4699-4701)tcG>tcT	p.S1567S	RYR2_ENST00000542537.1_Silent_p.S1551S|RYR2_ENST00000360064.6_Silent_p.S1565S	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1567	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TGCCTCTCTCGGCGGGATTAT	0.532																																					p.S1567S		Atlas-SNP	.											.	RYR2	1273	.	0			c.G4701T						.						34	34	34					1																	237774079		1897	4104	6001	SO:0001819	synonymous_variant	6262	exon36			TCTCTCGGCGGGA	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.4701G>T	chr1.hg19:g.237774079G>T		67.0	0.0		181.0	52.0	NM_001035	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	hg19	CCDS55691.1																																																																																			.	.		0.532	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		T	237774079	G	T	237774079	2	4	252	1	0	0	0	0	0	0	0	1	13784	1103	39	1		1	RYR2	1	237774079	Silent	SNP	G	TCGA-EP-A12J-01A-11D-A12Z-10	1405623	237774079	11476542	7	34142										
OR2L13	284521	hgsc.bcm.edu	37	chr1	248263611	248263611	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	ggatattctctttcctgaaaGaataatcatggccatcccca	6	11	2	2			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr1:248263611G>T	ENST00000358120.2	+	2	1079	c.934G>T	c.(934-936)Gaa>Taa	p.E312*	OR2L13_ENST00000366478.2_Nonsense_Mutation_p.E312*			Q8N349	OR2LD_HUMAN	olfactory receptor, family 2, subfamily L, member 13	312						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(12)|lung(32)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	59	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0132)			TTTCCTGAAAGAATAATCATG	0.433																																					p.E312X		Atlas-SNP	.											.	OR2L13	261	.	0			c.G934T						.						29	31	30					1																	248263611		2203	4300	6503	SO:0001587	stop_gained	284521	exon3			CTGAAAGAATAAT	BC028158	CCDS1637.1	1q44	2012-08-09			ENSG00000196071	ENSG00000196071		"GPCR / Class A : Olfactory receptors"	19578	protein-coding gene	gene with protein product				OR2L14			Standard	NM_175911		Approved		uc001ids.3	Q8N349	OTTHUMG00000040446	ENST00000358120.2:c.934G>T	chr1.hg19:g.248263611G>T	ENSP00000350836:p.Glu312*	32.0	0.0		110.0	27.0	NM_175911	Q5VUR5	Nonsense_Mutation	SNP	ENST00000358120.2	hg19	CCDS1637.1	.	.	.	.	.	.	.	.	.	.	G	16.12	3.032243	0.54790	.	.	ENSG00000196071	ENST00000366478;ENST00000358120	.	.	.	4.12	-8.23	0.01033	.	1.716890	0.03777	N	0.260790	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.13470	T	0.59	.	1.9389	0.03342	0.1185:0.2183:0.185:0.4783	.	.	.	.	X	312	.	ENSP00000350836:E312X	E	+	1	0	OR2L13	246330234	0.001000	0.12720	0.000000	0.03702	0.011000	0.07611	0.013000	0.13310	-2.305000	0.00654	-1.036000	0.02392	GAA	.	.		0.433	OR2L13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097342.1	NM_175911		T	248263611	G	T	248263611	4	4	252	1	0	0	0	0	0	1	0	0	11015	943	33	3	936	3	OR2L13	1	248263611	Nonsense_Mutation	SNP	G	TCGA-EP-A12J-01A-11D-A12Z-10	10489532	248263611	987010	8	34143										
OR2T4	127074	hgsc.bcm.edu	37	chr1	248525404	248525404	+	Silent	SNP	C	C	T													0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	atgaaccatagggtgtgtctCttcctgtcatcaggctgctg							TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr1:248525404C>T	ENST00000366475.1	+	1	522	c.522C>T	c.(520-522)ctC>ctT	p.L174L		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	174						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GGGTGTGTCTCTTCCTGTCAT	0.542																																					p.L174L		Atlas-SNP	.											.	OR2T4	126	.	0			c.C522T						.						270	235	247					1																	248525404		2203	4300	6503	SO:0001819	synonymous_variant	127074	exon1			GTGTCTCTTCCTG	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"GPCR / Class A : Olfactory receptors"	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.522C>T	chr1.hg19:g.248525404C>T		172.0	0.0		1540.0	69.0	NM_001004696	Q6IEZ8	Silent	SNP	ENST00000366475.1	hg19	CCDS31113.1																																																																																			.	.		0.542	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696		T	248525404	C	T	248525404	2	4	252	1	0	0	0	0	0	0	0	1	11036	900	32	3		3	OR2T4	1	248525404	Silent	SNP	C	TCGA-EP-A12J-01A-11D-A12Z-10	261793	248525404	725217	9	34144	175	2								
OR2T4	127074	hgsc.bcm.edu	37	chr1	248525411	248525411	+	Missense_Mutation	SNP	T	T	G													0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	atagggtgtgtctcttcctgTcatcaggctgctggttcctg							TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr1:248525411T>G	ENST00000366475.1	+	1	529	c.529T>G	c.(529-531)Tca>Gca	p.S177A		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	177						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TCTCTTCCTGTCATCAGGCTG	0.532																																					p.S177A		Atlas-SNP	.											.	OR2T4	126	.	0			c.T529G						.						266	232	243					1																	248525411		2203	4300	6503	SO:0001583	missense	127074	exon1			TTCCTGTCATCAG	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"GPCR / Class A : Olfactory receptors"	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.529T>G	chr1.hg19:g.248525411T>G	ENSP00000355431:p.Ser177Ala	174.0	0.0		1529.0	62.0	NM_001004696	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	hg19	CCDS31113.1	.	.	.	.	.	.	.	.	.	.	T	0	-2.746146	0.00087	.	.	ENSG00000196944	ENST00000366475	T	0.36699	1.24	3.48	0.418	0.16429	GPCR, rhodopsin-like superfamily (1);	1.058640	0.07443	N	0.897735	T	0.07503	0.0189	N	0.00321	-1.65	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.33599	-0.9862	10	0.05959	T	0.93	.	2.6302	0.04941	0.3488:0.0:0.4402:0.2111	.	177	Q8NH00	OR2T4_HUMAN	A	177	ENSP00000355431:S177A	ENSP00000355431:S177A	S	+	1	0	OR2T4	246592034	0.197000	0.23362	0.009000	0.14445	0.004000	0.04260	0.693000	0.25497	0.026000	0.15269	-0.359000	0.07587	TCA	.	.		0.532	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696		G	248525411	T	G	248525411	3	3	252	1	0	0	0	0	1	0	0	0	11036	1667	58	5	531	5	OR2T4	1	248525411	Missense_Mutation	SNP	T	TCGA-EP-A12J-01A-11D-A12Z-10	7	248525411	725210	10	34145	175	2								
APOB	338	hgsc.bcm.edu	37	chr2	21231993	21231994	+	Frame_Shift_Ins	INS	-	-	CTCTACC													0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	tcaggaacagtgaacccttgINSctctaccaatgctttcatac							TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr2:21231993_21231994insCTCTACC	ENST00000233242.1	-	26	7873_7874	c.7746_7747insGGTAGAG	c.(7744-7749)gagcaafs	p.Q2583fs		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	2583					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GTGAACCCTTGCTCTACCAATG	0.45																																					p.Q2583fs		Atlas-Indel,Pindel	.											.	APOB	761	.	0			c.7747_7748insGGTAGAG						.																																			SO:0001589	frameshift_variant	338	exon26			.	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.7740_7746dupGGTAGAG	chr2.hg19:g.21231994_21232000dupCTCTACC	ENSP00000233242:p.Gln2583fs	59.0	0.0		146.0	33.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Frame_Shift_Ins	INS	ENST00000233242.1	hg19	CCDS1703.1																																																																																			.	.		0.45	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			CTCTACC	21231994	-	CTCTACC	21231993	7	5	252	1	0	1	1	0	0	0	0	0	785	1328	46	0	5960	0	APOB	2	21231993	Frame_Shift_Ins	INS	-	TCGA-EP-A12J-01A-11D-A12Z-10		21231993	221967380	11	34146										
CLEC4F	165530	hgsc.bcm.edu	37	chr2	71047619	71047619	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	ggggtgcagggagacacactGgttatctgtgcagaagcgga	17	7	1	2	rs575554427		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr2:71047619G>T	ENST00000272367.2	-	1	113	c.37C>A	c.(37-39)Cag>Aag	p.Q13K	CLEC4F_ENST00000426626.1_Missense_Mutation_p.Q13K	NM_001258027.1|NM_173535.2	NP_001244956.1|NP_775806.2	Q8N1N0	CLC4F_HUMAN	C-type lectin domain family 4, member F	13					endocytosis (GO:0006897)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			endometrium(1)|large_intestine(5)|lung(18)|ovary(5)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	37						GAGACACACTGGTTATCTGTG	0.617																																					p.Q13K	Colon(107;10 2157 6841 26035)	Atlas-SNP	.											.	CLEC4F	95	.	0			c.C37A						.						109	78	89					2																	71047619		2203	4299	6502	SO:0001583	missense	165530	exon1			CACACTGGTTATC	AK096429	CCDS1910.1	2p13.3	2008-02-05	2005-02-09	2005-02-11	ENSG00000152672	ENSG00000152672		"C-type lectin domain containing"	25357	protein-coding gene	gene with protein product			"C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 13"	CLECSF13		8889548, 1846367	Standard	NM_001258027		Approved	FLJ39110, KCLR	uc002shf.3	Q8N1N0	OTTHUMG00000129713	ENST00000272367.2:c.37C>A	chr2.hg19:g.71047619G>T	ENSP00000272367:p.Gln13Lys	54.0	0.0		100.0	49.0	NM_173535	A4QPA5	Missense_Mutation	SNP	ENST00000272367.2	hg19	CCDS1910.1	.	.	.	.	.	.	.	.	.	.	G	15.10	2.734209	0.48939	.	.	ENSG00000152672	ENST00000272367;ENST00000426626	T;T	0.03330	3.99;3.97	3.36	2.44	0.29823	.	.	.	.	.	T	0.05547	0.0146	L	0.52573	1.65	0.09310	N	0.999999	P;P	0.51057	0.941;0.941	B;B	0.44224	0.444;0.444	T	0.33650	-0.9860	9	0.87932	D	0	.	8.4551	0.32895	0.0:0.2405:0.7595:0.0	.	13;13	B7ZMM1;Q8N1N0	.;CLC4F_HUMAN	K	13	ENSP00000272367:Q13K;ENSP00000390581:Q13K	ENSP00000272367:Q13K	Q	-	1	0	CLEC4F	70901127	0.418000	0.25440	0.167000	0.22817	0.294000	0.27393	2.075000	0.41538	0.954000	0.37851	0.467000	0.42956	CAG	.	.		0.617	CLEC4F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251922.1	NM_173535		T	71047619	G	T	71047619	3	4	252	1	0	0	0	0	1	0	0	0	3518	1357	47	3	1760	3	CLEC4F	2	71047619	Missense_Mutation	SNP	G	TCGA-EP-A12J-01A-11D-A12Z-10	49815626	71047619	172151754	12	34147										
DNAH6	1768	hgsc.bcm.edu	37	chr2	85043137	85043137	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	gaaccacaacaaaactataaGccaagcccaacactttacca	3	14	0	0			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr2:85043137G>A	ENST00000237449.6	+	75	12311	c.12303G>A	c.(12301-12303)aaG>aaA	p.K4101K	DNAH6_ENST00000389394.3_Silent_p.K4101K			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	4101					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						AAAACTATAAGCCAAGCCCAA	0.458																																					p.K4101K		Atlas-SNP	.											.	DNAH6	194	.	0			c.G12303A						.						163	143	149					2																	85043137		692	1591	2283	SO:0001819	synonymous_variant	1768	exon76			CTATAAGCCAAGC	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.12303G>A	chr2.hg19:g.85043137G>A		75.0	0.0		228.0	85.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	hg19	CCDS46348.1																																																																																			.	.		0.458	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		A	85043137	G	A	85043137	2	1	252	1	0	0	0	0	0	0	0	1	4607	962	34	3		3	DNAH6	2	85043137	Silent	SNP	G	TCGA-EP-A12J-01A-11D-A12Z-10	13995518	85043137	158156236	13	34148										
C2orf62	375307	hgsc.bcm.edu	37	chr2	219222268	219222286	+	Frame_Shift_Del	DEL	CTACAGATGCTGTTCTTCT	CTACAGATGCTGTTCTTCT	-													0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	tcaccccagacaaggaggagCtacagatgctgttcttctct					rs376076590		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	CTACAGATGCTGTTCTTCT	CTACAGATGCTGTTCTTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr2:219222268_219222286delCTACAGATGCTGTTCTTCT	ENST00000289388.3	+	3	159_177	c.130_148delCTACAGATGCTGTTCTTCT	c.(130-150)ctacagatgctgttcttctctfs	p.LQMLFFS44fs	AC021016.8_ENST00000411433.1_RNA	NM_198559.1	NP_940961.1	Q7Z7H3	CATIP_HUMAN		44					actin filament polymerization (GO:0030041)|cilium organization (GO:0044782)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.L44L(1)		endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	16		Renal(207;0.0915)		Epithelial(149;8.08e-07)|all cancers(144;0.000146)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CAAGGAGGAGCTACAGATGCTGTTCTTCTCTGAGACGCT	0.589																																					p.43_49del		Atlas-INDEL	.											.	C2orf62	28	.	1	Substitution - coding silent(1)	endometrium(1)	c.129_147del						.																																			SO:0001589	frameshift_variant	375307	exon3			.																												ENST00000289388.3:c.130_148delCTACAGATGCTGTTCTTCT	chr2.hg19:g.219222268_219222286delCTACAGATGCTGTTCTTCT	ENSP00000289388:p.Leu44fs	37.0	0.0		41.0	16.0	NM_198559		Frame_Shift_Del	DEL	ENST00000289388.3	hg19	CCDS2414.1																																																																																			.	.		0.589	C2orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256771.1			-	219222286	CTACAGATGCTGTTCTTCT	-	219222268	7	5	252	1	0	1	0	1	0	0	0	0	2183	796	28	0	140	0	C2orf62	2	219222268	Frame_Shift_Del	DEL	CTACAGATGCTGTTCTTCT	TCGA-EP-A12J-01A-11D-A12Z-10	134179131	219222268	23977105	14	34149	176	2								
C2orf62	375307	hgsc.bcm.edu	37	chr2	219222270	219222288	+	Frame_Shift_Del	DEL	ACAGATGCTGTTCTTCTCT	ACAGATGCTGTTCTTCTCT	-													0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	accccagacaaggaggagctAcagatgctgttcttctctga							TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	ACAGATGCTGTTCTTCTCT	ACAGATGCTGTTCTTCTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr2:219222270_219222288delACAGATGCTGTTCTTCTCT	ENST00000289388.3	+	3	161_179	c.132_150delACAGATGCTGTTCTTCTCT	c.(130-150)ctacagatgctgttcttctctfs	p.LQMLFFS44fs	AC021016.8_ENST00000411433.1_RNA	NM_198559.1	NP_940961.1	Q7Z7H3	CATIP_HUMAN		44					actin filament polymerization (GO:0030041)|cilium organization (GO:0044782)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.L44L(1)		endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	16		Renal(207;0.0915)		Epithelial(149;8.08e-07)|all cancers(144;0.000146)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGGAGGAGCTACAGATGCTGTTCTTCTCTGAGACGCTGG	0.584																																					p.44_50del		Pindel	.											.	C2orf62	28	.	1	Substitution - coding silent(1)	endometrium(1)	c.131_149del						.																																			SO:0001589	frameshift_variant	375307	exon3			.																												ENST00000289388.3:c.132_150delACAGATGCTGTTCTTCTCT	chr2.hg19:g.219222270_219222288delACAGATGCTGTTCTTCTCT	ENSP00000289388:p.Leu44fs	0.0	0.0		10.0	10.0	NM_198559		Frame_Shift_Del	DEL	ENST00000289388.3	hg19	CCDS2414.1																																																																																			.	.		0.584	C2orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256771.1			-	219222288	ACAGATGCTGTTCTTCTCT	-	219222270	7	5	252	1	0	1	0	1	0	0	0	0	2183	378	14	0	142	0	C2orf62	2	219222270	Frame_Shift_Del	DEL	ACAGATGCTGTTCTTCTCT	TCGA-EP-A12J-01A-11D-A12Z-10	2	219222270	23977103	15	34150	176	2								
CHL1	10752	hgsc.bcm.edu	37	chr3	440785	440785	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	gctcttctcacactactattAttaactgtttgctttgtgaa	5	9	2	1			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr3:440785A>T	ENST00000256509.2	+	26	3981	c.3339A>T	c.(3337-3339)ttA>ttT	p.L1113F	CHL1_ENST00000397491.2_Missense_Mutation_p.L1097F	NM_001253387.1|NM_001253388.1|NM_006614.3	NP_001240316.1|NP_001240317.1|NP_006605.2	Q96FC9	DDX11_HUMAN	cell adhesion molecule L1-like	0					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			NS(1)|central_nervous_system(5)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|lung(31)|ovary(1)|prostate(4)|skin(10)|stomach(1)	93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		CACTACTATTATTAACTGTTT	0.358																																					p.L1113F		Atlas-SNP	.											.	CHL1	242	.	0			c.A3339T						.						196	188	190					3																	440785		2203	4300	6503	SO:0001583	missense	10752	exon26			ACTATTATTAACT	AF002246	CCDS2556.1, CCDS58812.1, CCDS74887.1	3p26	2013-05-01	2013-05-01		ENSG00000134121	ENSG00000134121		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	1939	protein-coding gene	gene with protein product	"neural cell adhesion molecule", "close homolog of L1"	607416	"cell adhesion molecule with homology to L1CAM (close homologue of L1)", "cell adhesion molecule with homology to L1CAM (close homolog of L1)"			9799093	Standard	NM_006614		Approved	CALL, L1CAM2, FLJ44930, MGC132578	uc003bot.3	O00533	OTTHUMG00000090601	ENST00000256509.2:c.3339A>T	chr3.hg19:g.440785A>T	ENSP00000256509:p.Leu1113Phe	120.0	0.0		456.0	196.0	NM_006614	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000256509.2	hg19	CCDS2556.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.92|17.92	3.505650|3.505650	0.64410|0.64410	.|.	.|.	ENSG00000134121|ENSG00000134121	ENST00000256509;ENST00000397491|ENST00000445697	T;T|.	0.70631|.	-0.5;-0.47|.	5.45|5.45	2.24|2.24	0.28232|0.28232	.|.	0.081995|.	0.51477|.	D|.	0.000098|.	T|T	0.63486|0.63486	0.2515|0.2515	M|M	0.63428|0.63428	1.95|1.95	0.39107|0.39107	D|D	0.961404|0.961404	D;D;D|.	0.89917|.	1.0;1.0;0.996|.	D;D;D|.	0.87578|.	0.998;0.993;0.974|.	T|T	0.63976|0.63976	-0.6515|-0.6515	10|5	0.87932|.	D|.	0|.	.|.	12.3397|12.3397	0.55087|0.55087	0.2175:0.0:0.7825:0.0|0.2175:0.0:0.7825:0.0	.|.	1097;1097;1113|.	B3KX75;O00533;O00533-2|.	.;CHL1_HUMAN;.|.	F|F	1113;1097|247	ENSP00000256509:L1113F;ENSP00000380628:L1097F|.	ENSP00000256509:L1113F|.	L|Y	+|+	3|2	2|0	CHL1|CHL1	415785|415785	1.000000|1.000000	0.71417|0.71417	0.160000|0.160000	0.22671|0.22671	0.875000|0.875000	0.50365|0.50365	1.949000|1.949000	0.40313|0.40313	0.672000|0.672000	0.31204|0.31204	-0.146000|-0.146000	0.13790|0.13790	TTA|TAT	.	.		0.358	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614		T	440785	A	T	440785	3	4	252	1	0	0	0	0	1	0	0	0	3351	446	16	4	3433	4	CHL1	3	440785	Missense_Mutation	SNP	A	TCGA-EP-A12J-01A-11D-A12Z-10		440785	197581645	16	34151										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266100	41266100	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	agcaacagtcttacctggacTctggaatccattctggtgcc	9	12	3	0	rs121913416		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr3:41266100T>G	ENST00000349496.5	+	3	377	c.97T>G	c.(97-99)Tct>Gct	p.S33A	CTNNB1_ENST00000453024.1_Missense_Mutation_p.S26A|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S33A|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S33A|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S33A	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	33			Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> F (in PTR, MDB and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10666372}.|S -> L (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> Y (in colorectal cancer and PTR; enhances transactivation of target genes). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:9065402}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.S33P(47)|p.S33A(16)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.W25_D32del(4)|p.S33L(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S33N(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.D32fs*9(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.S29_H36del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.D32_S33insS(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.S33T(1)|p.D32_H36>D(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TTACCTGGACTCTGGAATCCA	0.488		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S33A	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,-1,1	CTNNB1	4904	.	212	Deletion - In frame(115)|Substitution - Missense(70)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)|Insertion - In frame(1)	liver(130)|large_intestine(20)|endometrium(14)|stomach(10)|pituitary(9)|pancreas(9)|central_nervous_system(8)|adrenal_gland(2)|small_intestine(2)|biliary_tract(2)|skin(2)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|breast(1)	c.T97G						.						93	77	82					3																	41266100		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	CTGGACTCTGGAA	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.97T>G	chr3.hg19:g.41266100T>G	ENSP00000344456:p.Ser33Ala	89.0	0.0		238.0	105.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.317386	0.81469	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.70281	0.3206	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.74509	-0.3642	10	0.87932	D	0	-10.7796	16.0677	0.80897	0.0:0.0:0.0:1.0	.	33	P35222	CTNB1_HUMAN	A	26;33;33;33;33;26;33;33;33	ENSP00000400508:S26A;ENSP00000385604:S33A;ENSP00000412219:S33A;ENSP00000379486:S33A;ENSP00000344456:S33A;ENSP00000411226:S26A;ENSP00000379488:S33A;ENSP00000409302:S33A;ENSP00000401599:S33A	ENSP00000344456:S33A	S	+	1	0	CTNNB1	41241104	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.201000	0.70794	0.533000	0.62120	TCT	.	.		0.488	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266100	T	G	41266100	3	3	252	1	0	0	0	0	1	0	0	0	4018	1551	54	5	103	5	CTNNB1	3	41266100	Missense_Mutation	SNP	T	TCGA-EP-A12J-01A-11D-A12Z-10	40825315	41266100	156756330	17	34152										
PLXNA1	5361	hgsc.bcm.edu	37	chr3	126733602	126733602	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	tccgtgcgtgcccatgacgcCctggtggaggtgtgtgtgcg	17	11	0	1			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr3:126733602C>A	ENST00000393409.2	+	13	2805	c.2805C>A	c.(2803-2805)gcC>gcA	p.A935A	PLXNA1_ENST00000251772.4_Silent_p.A912A	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	935	IPT/TIG 1.				axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)			breast(3)|central_nervous_system(5)|endometrium(10)|kidney(5)|large_intestine(4)|lung(32)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	67				GBM - Glioblastoma multiforme(114;0.155)		CCCATGACGCCCTGGTGGAGG	0.692																																					p.A935A		Atlas-SNP	.											.	PLXNA1	185	.	0			c.C2805A						.						62	47	52					3																	126733602		2202	4299	6501	SO:0001819	synonymous_variant	5361	exon13			TGACGCCCTGGTG	X87832	CCDS33847.1, CCDS33847.2	3q21.2	2006-12-19				ENSG00000114554		"Plexins"	9099	protein-coding gene	gene with protein product		601055		PLXN1		8570614	Standard	NM_032242		Approved	NOV	uc003ejg.3	Q9UIW2		ENST00000393409.2:c.2805C>A	chr3.hg19:g.126733602C>A		31.0	0.0		87.0	37.0	NM_032242		Silent	SNP	ENST00000393409.2	hg19	CCDS33847.2																																																																																			.	.		0.692	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356451.1	NM_032242		A	126733602	C	A	126733602	2	1	252	1	0	0	0	0	0	0	0	1	12128	610	22	3		3	PLXNA1	3	126733602	Silent	SNP	C	TCGA-EP-A12J-01A-11D-A12Z-10	85467502	126733602	71288828	18	34153										
TSC22D2	9819	hgsc.bcm.edu	37	chr3	150128513	150128513	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	tcagccgactggagtgccccCggctactgtgggaggcgtgg	17	12	1	0			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr3:150128513C>T	ENST00000361875.3	+	1	2392	c.1376C>T	c.(1375-1377)cCg>cTg	p.P459L	TSC22D2_ENST00000361136.2_Missense_Mutation_p.P459L	NM_014779.2	NP_055594.1	O75157	T22D2_HUMAN	TSC22 domain family, member 2	459					response to osmotic stress (GO:0006970)		sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	18			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			GGAGTGCCCCCGGCTACTGTG	0.736																																					p.P459L		Atlas-SNP	.											.	TSC22D2	42	.	0			c.C1376T						.						8	10	9					3																	150128513		2174	4252	6426	SO:0001583	missense	9819	exon1			TGCCCCCGGCTAC	AB014569	CCDS3149.1	3q25.1	2005-03-01			ENSG00000196428	ENSG00000196428			29095	protein-coding gene	gene with protein product						9734811	Standard	NM_014779		Approved	KIAA0669, TILZ4a, TILZ4b, TILZ4c	uc003exv.3	O75157	OTTHUMG00000159744	ENST00000361875.3:c.1376C>T	chr3.hg19:g.150128513C>T	ENSP00000354543:p.Pro459Leu	7.0	0.0		40.0	19.0	NM_014779	D3DNI5|Q6PI50|Q9H2Z6|Q9H2Z7|Q9H2Z8	Missense_Mutation	SNP	ENST00000361875.3	hg19	CCDS3149.1	.	.	.	.	.	.	.	.	.	.	C	6.916	0.538699	0.13250	.	.	ENSG00000196428	ENST00000361875;ENST00000361136	T;T	0.35048	1.37;1.33	3.01	-0.242	0.13039	.	1.000620	0.08065	N	0.998965	T	0.19485	0.0468	N	0.12182	0.205	0.09310	N	0.999993	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.24512	-1.0158	10	0.46703	T	0.11	.	6.0063	0.19549	0.3438:0.5554:0.0:0.1008	.	459;459	O75157-2;O75157	.;T22D2_HUMAN	L	459	ENSP00000354543:P459L;ENSP00000354893:P459L	ENSP00000354893:P459L	P	+	2	0	TSC22D2	151611203	0.000000	0.05858	0.170000	0.22879	0.812000	0.45895	0.083000	0.14871	-0.060000	0.13132	0.557000	0.71058	CCG	.	.		0.736	TSC22D2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357123.2	NM_014779		T	150128513	C	T	150128513	3	4	252	1	0	0	0	0	1	0	0	0	16623	652	23	1	1378	1	TSC22D2	3	150128513	Missense_Mutation	SNP	C	TCGA-EP-A12J-01A-11D-A12Z-10	23394911	150128513	47893917	19	34154										
FNDC3B	64778	hgsc.bcm.edu	37	chr3	172098773	172098773	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	cagcacctcgagtaacacagTtagaaggaaattcatgtgaa	9	8	1	2			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr3:172098773T>C	ENST00000336824.4	+	25	3292	c.3193T>C	c.(3193-3195)Tta>Cta	p.L1065L	FNDC3B_ENST00000415807.2_Silent_p.L1065L|FNDC3B_ENST00000416957.1_Silent_p.L1065L	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	1065	Fibronectin type-III 9. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell migration (GO:0016477)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast proliferation (GO:0048146)|substrate adhesion-dependent cell spreading (GO:0034446)|Type II pneumocyte differentiation (GO:0060510)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(26)|ovary(3)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	69	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		AGTAACACAGTTAGAAGGAAA	0.378																																					p.L1065L		Atlas-SNP	.											.	FNDC3B	118	.	0			c.T3193C						.						168	161	163					3																	172098773		2203	4300	6503	SO:0001819	synonymous_variant	64778	exon25			ACACAGTTAGAAG	AF543840	CCDS3217.1	3q26.31	2013-11-06			ENSG00000075420	ENSG00000075420		"Fibronectin type III domain containing"	24670	protein-coding gene	gene with protein product		611909				15527760	Standard	NM_022763		Approved	FAD104, DKFZp762K137, FLJ23399, PRO4979, YVTM2421	uc003fhy.3	Q53EP0	OTTHUMG00000156761	ENST00000336824.4:c.3193T>C	chr3.hg19:g.172098773T>C		51.0	0.0		101.0	31.0	NM_001135095	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Silent	SNP	ENST00000336824.4	hg19	CCDS3217.1																																																																																			.	.		0.378	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763		C	172098773	T	C	172098773	2	2	252	1	0	0	0	0	0	0	0	1	5978	1722	60	2		2	FNDC3B	3	172098773	Silent	SNP	T	TCGA-EP-A12J-01A-11D-A12Z-10	21970260	172098773	25923657	20	34155										
RFC1	5981	hgsc.bcm.edu	37	chr4	39310299	39310299	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	ctcttttgccagtttcggagCcagcgtaggagtttgttggc	13	9	1	0			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr4:39310299C>A	ENST00000381897.1	-	13	1975	c.1842G>T	c.(1840-1842)tgG>tgT	p.W614C	RFC1_ENST00000349703.2_Missense_Mutation_p.W614C	NM_001204747.1|NM_002913.4	NP_001191676.1|NP_002904.3	P35251	RFC1_HUMAN	replication factor C (activator 1) 1, 145kDa	614					DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription, DNA-templated (GO:0045893)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|telomere maintenance via telomerase (GO:0007004)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	cell junction (GO:0030054)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA clamp loader activity (GO:0003689)|double-stranded DNA binding (GO:0003690)|enzyme activator activity (GO:0008047)|sequence-specific DNA binding (GO:0043565)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16						AGTTTCGGAGCCAGCGTAGGA	0.428																																					p.W614C	Colon(109;59 1555 12203 17579 39824)|Esophageal Squamous(18;360 542 16186 28570 51157)	Atlas-SNP	.											.	RFC1	114	.	0			c.G1842T						.						159	166	164					4																	39310299		2203	4300	6503	SO:0001583	missense	5981	exon13			TCGGAGCCAGCGT	L23320	CCDS3450.1, CCDS56329.1	4p14-p13	2010-04-21	2002-08-29		ENSG00000035928	ENSG00000035928		"ATPases / AAA-type"	9969	protein-coding gene	gene with protein product		102579	"replication factor C (activator 1) 1 (145kD)"			8114700	Standard	NM_002913		Approved	A1, PO-GA, RFC140, MHCBFB	uc003gty.2	P35251	OTTHUMG00000099363	ENST00000381897.1:c.1842G>T	chr4.hg19:g.39310299C>A	ENSP00000371321:p.Trp614Cys	141.0	0.0		563.0	248.0	NM_002913	A8K6E7|Q5XKF5|Q6PKU0|Q86V41|Q86V46	Missense_Mutation	SNP	ENST00000381897.1	hg19	CCDS56329.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.611366	0.87258	.	.	ENSG00000035928	ENST00000381897;ENST00000349703	T;T	0.17854	2.25;2.25	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.54398	0.1856	M	0.90922	3.16	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.62548	-0.6831	10	0.87932	D	0	-6.9473	20.3053	0.98627	0.0:1.0:0.0:0.0	.	614;614	P35251;P35251-2	RFC1_HUMAN;.	C	614	ENSP00000371321:W614C;ENSP00000261424:W614C	ENSP00000261424:W614C	W	-	3	0	RFC1	38986694	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.502000	0.81614	2.808000	0.96608	0.655000	0.94253	TGG	.	.		0.428	RFC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216808.1	NM_002913		A	39310299	C	A	39310299	3	1	252	1	0	0	0	0	1	0	0	0	13259	740	26	3	1653	3	RFC1	4	39310299	Missense_Mutation	SNP	C	TCGA-EP-A12J-01A-11D-A12Z-10		39310299	151843977	21	34156										
EDNRA	1909	hgsc.bcm.edu	37	chr4	148457097	148457097	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	atgcccttggtgtgcactgcGatcttctacaccctcatgac	8	14	3	1	rs200693894		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr4:148457097G>A	ENST00000324300.5	+	5	1331	c.816G>A	c.(814-816)gcG>gcA	p.A272A	EDNRA_ENST00000503721.1_3'UTR|EDNRA_ENST00000511804.1_Silent_p.A47A|EDNRA_ENST00000358556.4_Silent_p.A163A|EDNRA_ENST00000506066.1_Silent_p.A163A|EDNRA_ENST00000339690.5_3'UTR	NM_001957.3	NP_001948.1	P25101	EDNRA_HUMAN	endothelin receptor type A	272					activation of adenylate cyclase activity (GO:0007190)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|artery smooth muscle contraction (GO:0014824)|cell proliferation (GO:0008283)|cellular response to mechanical stimulus (GO:0071260)|endothelin receptor signaling pathway (GO:0086100)|enteric nervous system development (GO:0048484)|fibroblast proliferation (GO:0048144)|G-protein coupled receptor signaling pathway (GO:0007186)|glomerular filtration (GO:0003094)|glucose transport (GO:0015758)|head development (GO:0060322)|heart development (GO:0007507)|histamine secretion (GO:0001821)|in utero embryonic development (GO:0001701)|maternal process involved in parturition (GO:0060137)|metabolic process (GO:0008152)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cAMP biosynthetic process (GO:0030818)|neural crest cell development (GO:0014032)|patterning of blood vessels (GO:0001569)|penile erection (GO:0043084)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of inflammatory response (GO:0050729)|positive regulation of kidney development (GO:0090184)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of odontogenesis (GO:0042482)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of blood pressure (GO:0008217)|regulation of epithelial cell proliferation (GO:0050678)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to morphine (GO:0043278)|Rho protein signal transduction (GO:0007266)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|smooth muscle cell proliferation (GO:0048659)|smooth muscle contraction (GO:0006939)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)	endothelin receptor activity (GO:0004962)|phosphatidylinositol phospholipase C activity (GO:0004435)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(3)|ovary(1)	17	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.154)	Acetylsalicylic acid(DB00945)|Bosentan(DB00559)|MACITENTAN(DB08932)|Sitaxentan(DB06268)	TGTGCACTGCGATCTTCTACA	0.418																																					p.A272A		Atlas-SNP	.											.	EDNRA	48	.	0			c.G816A						.						220	205	210					4																	148457097		2203	4300	6503	SO:0001819	synonymous_variant	1909	exon5			CACTGCGATCTTC	D90348	CCDS3769.1, CCDS54810.1, CCDS58927.1	4q31.22	2013-09-20			ENSG00000151617	ENSG00000151617		"GPCR / Class A : Endothelin receptors"	3179	protein-coding gene	gene with protein product		131243				1659806	Standard	NM_001957		Approved		uc003iky.3	P25101	OTTHUMG00000161354	ENST00000324300.5:c.816G>A	chr4.hg19:g.148457097G>A		109.0	0.0		297.0	127.0	NM_001957	B2R723|B4E2V6|B7Z9G6|D3DP03|E7ER36|O43441|Q16432|Q16433|Q8TBH2	Silent	SNP	ENST00000324300.5	hg19	CCDS3769.1																																																																																			.	.		0.418	EDNRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364635.1			A	148457097	G	A	148457097	2	1	252	1	0	0	0	0	0	0	0	1	4921	1045	37	1		1	EDNRA	4	148457097	Silent	SNP	G	TCGA-EP-A12J-01A-11D-A12Z-10	109146798	148457097	42697179	22	34157										
TNPO1	3842	hgsc.bcm.edu	37	chr5	72168474	72168474	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	ctttgtttctaggtctcacgCtgttgcatgtgtcaatcagt	9	9	4	0			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr5:72168474C>T	ENST00000337273.5	+	7	1031	c.605C>T	c.(604-606)gCt>gTt	p.A202V	TNPO1_ENST00000447967.2_Silent_p.L114L|TNPO1_ENST00000454282.1_Missense_Mutation_p.A152V|TNPO1_ENST00000523768.1_Missense_Mutation_p.A152V|TNPO1_ENST00000506351.2_Missense_Mutation_p.A194V	NM_002270.3	NP_002261.3	Q92973	TNPO1_HUMAN	transportin 1	202					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|protein import into nucleus, translocation (GO:0000060)|RNA metabolic process (GO:0016070)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(6)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	36		Lung NSC(167;0.0053)|Ovarian(174;0.0175)		OV - Ovarian serous cystadenocarcinoma(47;6.14e-54)		AGGTCTCACGCTGTTGCATGT	0.328																																					p.A202V		Atlas-SNP	.											TNPO1,colon,carcinoma,0,1	TNPO1	90	.	0			c.C605T						.						145	127	133					5																	72168474		2203	4300	6503	SO:0001583	missense	3842	exon7			CTCACGCTGTTGC	U70322	CCDS4016.1, CCDS43329.1	5q13.1	2009-01-12	2004-01-29	2004-01-30	ENSG00000083312	ENSG00000083312		"Importins"	6401	protein-coding gene	gene with protein product	"importin 2"	602901	"karyopherin (importin) beta 2"	KPNB2		8808633, 9144189	Standard	NM_153188		Approved	MIP, TRN, IPO2, MIP1	uc003kci.4	Q92973	OTTHUMG00000100967	ENST00000337273.5:c.605C>T	chr5.hg19:g.72168474C>T	ENSP00000336712:p.Ala202Val	96.0	0.0		223.0	100.0	NM_002270	B4DVC6|Q92957|Q92975	Missense_Mutation	SNP	ENST00000337273.5	hg19	CCDS43329.1	.	.	.	.	.	.	.	.	.	.	C	34	5.336982	0.95758	.	.	ENSG00000083312	ENST00000337273;ENST00000454282;ENST00000523768;ENST00000506351	T;T;T;T	0.73152	-0.72;-0.72;-0.72;-0.72	5.25	5.25	0.73442	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.89114	0.6623	H	0.95780	3.72	0.80722	D	1	D;D	0.67145	0.996;0.992	D;P	0.70487	0.969;0.808	D	0.92131	0.5712	10	0.87932	D	0	-14.3056	19.1933	0.93675	0.0:1.0:0.0:0.0	.	152;202	Q92973-3;Q92973	.;TNPO1_HUMAN	V	202;152;152;194	ENSP00000336712:A202V;ENSP00000398524:A152V;ENSP00000428899:A152V;ENSP00000425118:A194V	ENSP00000336712:A202V	A	+	2	0	TNPO1	72204230	1.000000	0.71417	0.999000	0.59377	0.976000	0.68499	5.756000	0.68757	2.626000	0.88956	0.591000	0.81541	GCT	.	.		0.328	TNPO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000218577.3	NM_002270		T	72168474	C	T	72168474	3	4	252	1	0	0	0	0	1	0	0	0	16350	797	28	3	631	3	TNPO1	5	72168474	Missense_Mutation	SNP	C	TCGA-EP-A12J-01A-11D-A12Z-10		72168474	108746786	23	34158										
TTC37	9652	hgsc.bcm.edu	37	chr5	94839530	94839530	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	atacttacctttgctgctctCtttataaagccccttcatga	4	12	2	1			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr5:94839530C>T	ENST00000358746.2	-	31	3503	c.3205G>A	c.(3205-3207)Gag>Aag	p.E1069K		NM_014639.3	NP_055454.1	Q6PGP7	TTC37_HUMAN	tetratricopeptide repeat domain 37	1069						cytoplasm (GO:0005737)|nucleus (GO:0005634)|Ski complex (GO:0055087)|transcriptionally active chromatin (GO:0035327)				breast(2)|endometrium(6)|kidney(3)|large_intestine(13)|liver(1)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	47						TTGCTGCTCTCTTTATAAAGC	0.363																																					p.E1069K		Atlas-SNP	.											.	TTC37	128	.	0			c.G3205A						.						122	121	121					5																	94839530		2203	4300	6503	SO:0001583	missense	9652	exon31			TGCTCTCTTTATA	AB002370	CCDS4072.1	5q15	2014-09-17	2008-06-11	2008-06-11	ENSG00000198677	ENSG00000198677		"Tetratricopeptide (TTC) repeat domain containing"	23639	protein-coding gene	gene with protein product		614589	"KIAA0372"	KIAA0372		9205841	Standard	NM_014639		Approved		uc003klb.3	Q6PGP7	OTTHUMG00000121165	ENST00000358746.2:c.3205G>A	chr5.hg19:g.94839530C>T	ENSP00000351596:p.Glu1069Lys	86.0	0.0		154.0	63.0	NM_014639	O15077|Q6PJI3	Missense_Mutation	SNP	ENST00000358746.2	hg19	CCDS4072.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.496049	0.85069	.	.	ENSG00000198677	ENST00000358746	T	0.54675	0.56	5.7	5.7	0.88788	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.56187	0.1968	M	0.77616	2.38	0.80722	D	1	P	0.40731	0.728	B	0.36092	0.217	T	0.57768	-0.7754	10	0.29301	T	0.29	.	20.2096	0.98287	0.0:1.0:0.0:0.0	.	1069	Q6PGP7	TTC37_HUMAN	K	1069	ENSP00000351596:E1069K	ENSP00000351596:E1069K	E	-	1	0	TTC37	94865286	1.000000	0.71417	1.000000	0.80357	0.802000	0.45316	6.497000	0.73674	2.841000	0.97950	0.637000	0.83480	GAG	.	.		0.363	TTC37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241651.1	NM_014639		T	94839530	C	T	94839530	3	4	252	1	0	0	0	0	1	0	0	0	16720	922	32	3	1541	3	TTC37	5	94839530	Missense_Mutation	SNP	C	TCGA-EP-A12J-01A-11D-A12Z-10	22671056	94839530	86075730	24	34159										
CDO1	1036	hgsc.bcm.edu	37	chr5	115146946	115146946	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	ttgtcaggccaggcaaataaTgtctcctttagatttccctg	8	10	2	1			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr5:115146946T>C	ENST00000250535.4	-	3	871	c.315A>G	c.(313-315)acA>acG	p.T105T	CDO1_ENST00000502631.1_5'UTR	NM_001801.2	NP_001792.2	Q16878	CDO1_HUMAN	cysteine dioxygenase type 1	105					cellular nitrogen compound metabolic process (GO:0034641)|cysteine metabolic process (GO:0006534)|inflammatory response (GO:0006954)|L-cysteine catabolic process (GO:0019448)|lactation (GO:0007595)|oxidation-reduction process (GO:0055114)|response to amino acid (GO:0043200)|response to cAMP (GO:0051591)|response to ethanol (GO:0045471)|response to glucagon (GO:0033762)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)|sulfur amino acid biosynthetic process (GO:0000097)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)|taurine biosynthetic process (GO:0042412)	cytosol (GO:0005829)	cysteine dioxygenase activity (GO:0017172)|ferrous iron binding (GO:0008198)			breast(1)|endometrium(1)|large_intestine(3)|lung(1)|skin(5)	11		all_cancers(142;0.0046)|all_epithelial(76;0.000161)|Prostate(80;0.0132)|Ovarian(225;0.0776)		OV - Ovarian serous cystadenocarcinoma(64;7.8e-08)|Epithelial(69;7.32e-07)|all cancers(49;3.24e-05)	L-Cysteine(DB00151)	AGGCAAATAATGTCTCCTTTA	0.393																																					p.T105T		Atlas-SNP	.											CDO1,NS,carcinoma,0,1	CDO1	29	.	0			c.A315G						.						218	209	212					5																	115146946		2202	4300	6502	SO:0001819	synonymous_variant	1036	exon3			AAATAATGTCTCC		CCDS4121.1	5q23.2	2013-06-11	2013-06-11		ENSG00000129596	ENSG00000129596	1.13.11.20		1795	protein-coding gene	gene with protein product		603943	"cysteine dioxygenase, type I"			7524679	Standard	NM_001801		Approved		uc003krg.3	Q16878	OTTHUMG00000128891	ENST00000250535.4:c.315A>G	chr5.hg19:g.115146946T>C		106.0	0.0		302.0	120.0	NM_001801	B2RAK4|P78513|Q6FHZ8|Q8TB64	Silent	SNP	ENST00000250535.4	hg19	CCDS4121.1																																																																																			.	.		0.393	CDO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250853.2	NM_001801		C	115146946	T	C	115146946	2	2	252	1	0	0	0	0	0	0	0	1	3171	1451	51	2		2	CDO1	5	115146946	Silent	SNP	T	TCGA-EP-A12J-01A-11D-A12Z-10	20307416	115146946	65768314	25	34160										
PCDHA3	56145	hgsc.bcm.edu	37	chr5	140182753	140182753	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	gtgaaggaccacggtgaaccCtcattgaccgccacggccac	11	15	1	3			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr5:140182753C>G	ENST00000522353.2	+	1	1971	c.1971C>G	c.(1969-1971)ccC>ccG	p.P657P	PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000520672.2_Intron|PCDHA3_ENST00000532566.2_Silent_p.P657P	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	657	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACGGTGAACCCTCATTGACCG	0.692																																					p.P657P		Atlas-SNP	.											.	PCDHA3	396	.	0			c.C1971G						.						60	61	61					5																	140182753		2203	4300	6503	SO:0001819	synonymous_variant	56145	exon1			TGAACCCTCATTG	AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"Cadherins / Protocadherins : Clustered"	8669	other	complex locus constituent	"KIAA0345-like 11"	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.1971C>G	chr5.hg19:g.140182753C>G		50.0	0.0		106.0	48.0	NM_031497	O75286	Silent	SNP	ENST00000522353.2	hg19	CCDS54915.1																																																																																			.	.		0.692	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906		G	140182753	C	G	140182753	2	3	252	1	0	0	0	0	0	0	0	1	11534	668	24	4		4	PCDHA3	5	140182753	Silent	SNP	C	TCGA-EP-A12J-01A-11D-A12Z-10	25035807	140182753	40732507	26	34161										
LCP2	3937	hgsc.bcm.edu	37	chr5	169685155	169685155	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	gaagtagtgctggctggggcAaaggtctctgatgcactgtg	16	7	1	1			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr5:169685155A>G	ENST00000046794.5	-	16	1601	c.986T>C	c.(985-987)tTg>tCg	p.L329S	LCP2_ENST00000521416.1_Missense_Mutation_p.L124S	NM_005565.3	NP_005556.1	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte protein of 76kDa)	329					blood coagulation (GO:0007596)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|innate immune response (GO:0045087)|mast cell activation (GO:0045576)|platelet activation (GO:0030168)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)				cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	23	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.247)		TGGCTGGGGCAAAGGTCTCTG	0.498																																					p.L329S		Atlas-SNP	.											.	LCP2	133	.	0			c.T986C						.						175	173	174					5																	169685155		1945	4144	6089	SO:0001583	missense	3937	exon16			TGGGGCAAAGGTC		CCDS47339.1	5q35.1	2013-02-14	2002-08-29		ENSG00000043462	ENSG00000043462		"SH2 domain containing"	6529	protein-coding gene	gene with protein product	"76 kDa tyrosine phosphoprotein", "SH2 domain-containing leukocyte protein of 76kD"	601603	"lymphocyte cytosolic protein 2 (SH2 domain-containing leukocyte protein of 76kD)"	SLP76		7706237	Standard	NM_005565		Approved	SLP-76	uc003man.1	Q13094	OTTHUMG00000163121	ENST00000046794.5:c.986T>C	chr5.hg19:g.169685155A>G	ENSP00000046794:p.Leu329Ser	75.0	0.0		154.0	63.0	NM_005565	A8KA25|Q53XV4	Missense_Mutation	SNP	ENST00000046794.5	hg19	CCDS47339.1	.	.	.	.	.	.	.	.	.	.	A	14.72	2.620395	0.46736	.	.	ENSG00000043462	ENST00000046794;ENST00000521416;ENST00000520344	T;T	0.48836	0.82;0.8	5.72	4.56	0.56223	.	0.301944	0.29073	N	0.013231	T	0.42494	0.1205	L	0.50333	1.59	0.36232	D	0.852709	P;P	0.44776	0.843;0.469	B;B	0.42653	0.394;0.209	T	0.50988	-0.8762	9	.	.	.	-5.6214	9.5973	0.39582	0.92:0.0:0.08:0.0	.	124;329	E7ESF6;Q13094	.;LCP2_HUMAN	S	329;124;96	ENSP00000046794:L329S;ENSP00000428871:L124S	.	L	-	2	0	LCP2	169617733	0.999000	0.42202	0.984000	0.44739	0.744000	0.42396	2.971000	0.49248	1.108000	0.41662	0.533000	0.62120	TTG	.	.		0.498	LCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371727.1	NM_005565		G	169685155	A	G	169685155	3	3	252	1	0	0	0	0	1	0	0	0	8701	131	5	2	639	2	LCP2	5	169685155	Missense_Mutation	SNP	A	TCGA-EP-A12J-01A-11D-A12Z-10	29502402	169685155	11230105	27	34162										
C5orf25	375484	hgsc.bcm.edu	37	chr5	175772304	175772305	+	Missense_Mutation	DNP	CC	CC	AA													0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	gagaagcagattgaggccttCcgcagccgcctgatccagat							TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr5:175772304_175772305CC>AA	ENST00000443967.1	+	12	2882_2883	c.2475_2476CC>AA	c.(2473-2478)ttCCgc>ttAAgc	p.825_826FR>LS	KIAA1191_ENST00000393728.2_5'Flank|SIMC1_ENST00000341199.6_Missense_Mutation_p.410_411FR>LS|SIMC1_ENST00000332772.4_Missense_Mutation_p.286_287FR>LS|SIMC1_ENST00000430704.2_Missense_Mutation_p.410_411FR>LS|RP11-843P14.2_ENST00000508187.1_RNA			Q8NDZ2	SIMC1_HUMAN	SUMO-interacting motifs containing 1	825							SUMO polymer binding (GO:0032184)										TTGAGGCCTTCCGCAGCCGCCT	0.51																																					p.F410L|p.R411S		Atlas-SNP	.											.	.	.	.	0			c.C1230A|c.C1231A						.																																			SO:0001583	missense	375484	exon9			GGCCTTCCGCAGC|GCCTTCCGCAGCC	BC037298	CCDS4398.2	5q35.2	2013-08-14	2012-11-14	2012-11-14	ENSG00000170085	ENSG00000170085			24779	protein-coding gene	gene with protein product	"oocyte maturation associated 1", "platform element for inhibition of autolytic degradation"		"chromosome 5 open reading frame 25"	C5orf25		23086935, 23707407	Standard	NM_198567		Approved	FLJ44216, OOMA1, PLEIAD	uc003mds.4	Q8NDZ2	OTTHUMG00000130663	Exception_encountered	chr5.hg19:g.175772304_175772305delinsAA	ENSP00000406571:p.F825_R826delinsLS	73.0|72.0	0.0		191.0|193.0	81.0|80.0	NM_198567	J3KQQ8|Q6NXN8|Q6ZTU4|Q8IZ15	Missense_Mutation	SNP	ENST00000443967.1	hg19																																																																																				.	.		0.51	SIMC1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000253155.2	NM_198567		AA	175772305	CC	AA	175772304	3	1	252	1	0	0	0	0	1	0	0	0	2290	854	30	3	1264	3	C5orf25	5	175772304	Missense_Mutation	DNP	CC	TCGA-EP-A12J-01A-11D-A12Z-10	6087149	175772304	5142956	28	34163										
TRIM52	84851	hgsc.bcm.edu	37	chr5	180687428	180687428	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	aggtaatagtcctgatcttcCtcttcttcttcttcctcctc	4	14	5	1	rs200454506|rs3073543|rs33972170	byFrequency	TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr5:180687428C>T	ENST00000327767.4	-	1	691	c.387G>A	c.(385-387)gaG>gaA	p.E129E	TRIM52-AS1_ENST00000507434.1_RNA|TRIM52_ENST00000514805.1_5'UTR|CTC-338M12.4_ENST00000511331.1_RNA|CTC-338M12.4_ENST00000505151.1_RNA|TRIM52-AS1_ENST00000509252.1_RNA|TRIM52-AS1_ENST00000514146.1_RNA|CTC-338M12.4_ENST00000417281.2_RNA	NM_032765.2	NP_116154.1	Q96A61	TRI52_HUMAN	tripartite motif containing 52	129	Glu-rich.				positive regulation of NF-kappaB transcription factor activity (GO:0051092)	intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(3)|skin(1)|stomach(1)	8	all_cancers(89;8.79e-06)|all_epithelial(37;1.13e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0654)	all_cancers(40;0.0106)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.0588)|all_lung(500;0.149)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.232)		CCTGATCTTCCTCTTCTTCTT	0.458																																					p.E129E		Atlas-SNP	.											.	TRIM52	20	.	0			c.G387A						.						187	165	173					5																	180687428		2203	4300	6503	SO:0001819	synonymous_variant	84851	exon1			ATCTTCCTCTTCT		CCDS4467.1	5q35.3	2013-01-09	2011-01-25		ENSG00000183718	ENSG00000183718		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19024	protein-coding gene	gene with protein product			"tripartite motif-containing 52"				Standard	NM_032765		Approved	RNF102	uc003mnp.3	Q96A61	OTTHUMG00000130964	ENST00000327767.4:c.387G>A	chr5.hg19:g.180687428C>T		59.0	0.0		184.0	18.0	NM_032765		Silent	SNP	ENST00000327767.4	hg19	CCDS4467.1																																																																																			.	.		0.458	TRIM52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253572.3	NM_032765		T	180687428	C	T	180687428	2	4	252	1	0	0	0	0	0	0	0	1	16542	680	24	3		3	TRIM52	5	180687428	Silent	SNP	C	TCGA-EP-A12J-01A-11D-A12Z-10	4915124	180687428	227832	29	34164										
ITPR3	3710	hgsc.bcm.edu	37	chr6	33657110	33657110	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	agcgctacagcatccgccccCtcatcgtggcgctcatcctg	9	18	2	0			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr6:33657110C>A	ENST00000374316.5	+	51	7850	c.6790C>A	c.(6790-6792)Ctc>Atc	p.L2264I	ITPR3_ENST00000605930.1_Missense_Mutation_p.L2264I			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	2264					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	CATCCGCCCCCTCATCGTGGC	0.612																																					p.L2264I		Atlas-SNP	.											.	ITPR3	409	.	0			c.C6790A						.						133	112	119					6																	33657110		2203	4300	6503	SO:0001583	missense	3710	exon50			CGCCCCCTCATCG	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"Ion channels / Inositol triphosphate receptors"	6182	protein-coding gene	gene with protein product		147267	"inositol 1,4,5-triphosphate receptor, type 3"			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.6790C>A	chr6.hg19:g.33657110C>A	ENSP00000363435:p.Leu2264Ile	57.0	0.0		75.0	32.0	NM_002224	Q14649|Q5TAQ2	Missense_Mutation	SNP	ENST00000374316.5	hg19	CCDS4783.1	.	.	.	.	.	.	.	.	.	.	C	16.21	3.060027	0.55325	.	.	ENSG00000096433	ENST00000374316	D	0.92249	-3.0	5.07	4.17	0.49024	.	0.201739	0.42821	D	0.000658	D	0.87708	0.6245	L	0.58669	1.825	0.45464	D	0.998435	B;B	0.22346	0.028;0.068	B;B	0.35312	0.2;0.132	D	0.86469	0.1784	10	0.52906	T	0.07	-35.9732	10.4156	0.44320	0.0:0.7737:0.1477:0.0786	.	2264;1934	Q14573;Q59ES2	ITPR3_HUMAN;.	I	2264	ENSP00000363435:L2264I	ENSP00000363435:L2264I	L	+	1	0	ITPR3	33765088	0.978000	0.34361	1.000000	0.80357	0.960000	0.62799	2.274000	0.43390	2.653000	0.90120	0.561000	0.74099	CTC	.	.		0.612	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224		A	33657110	C	A	33657110	3	1	252	1	0	0	0	0	1	0	0	0	7931	681	24	3	6988	3	ITPR3	6	33657110	Missense_Mutation	SNP	C	TCGA-EP-A12J-01A-11D-A12Z-10		33657110	137457957	30	34165										
CYP39A1	51302	hgsc.bcm.edu	37	chr6	46607278	46607278	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	ccatgagtgcctaaattctcCagttgttcatgtaattcttc	6	10	3	1			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr6:46607278C>T	ENST00000275016.2	-	3	644	c.441G>A	c.(439-441)ctG>ctA	p.L147L		NM_016593.3	NP_057677.2	Q9NYL5	CP39A_HUMAN	cytochrome P450, family 39, subfamily A, polypeptide 1	147					bile acid biosynthetic process (GO:0006699)|bile acid catabolic process (GO:0030573)|bile acid metabolic process (GO:0008206)|cholesterol catabolic process (GO:0006707)|digestion (GO:0007586)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	24-hydroxycholesterol 7alpha-hydroxylase activity (GO:0033782)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxysterol 7-alpha-hydroxylase activity (GO:0008396)|steroid 7-alpha-hydroxylase activity (GO:0008387)		EIF3K/CYP39A1(2)	NS(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(2)	21						CTAAATTCTCCAGTTGTTCAT	0.353																																					p.L147L		Atlas-SNP	.											.	CYP39A1	41	.	0			c.G441A						.						139	131	134					6																	46607278		2203	4300	6503	SO:0001819	synonymous_variant	51302	exon3			ATTCTCCAGTTGT	AF237982	CCDS4916.1, CCDS75465.1	6p21.1-p11.2	2008-02-05	2003-01-14		ENSG00000146233	ENSG00000146233		"Cytochrome P450s"	17449	protein-coding gene	gene with protein product		605994	"cytochrome P450, subfamily XXXIX (oxysterol 7 alpha-hydroxylase), polypeptide 1"			10748047	Standard	NM_016593		Approved		uc003oyf.1	Q9NYL5	OTTHUMG00000014785	ENST00000275016.2:c.441G>A	chr6.hg19:g.46607278C>T		108.0	0.0		336.0	138.0	NM_016593	Q5VTT0|Q96FW5	Silent	SNP	ENST00000275016.2	hg19	CCDS4916.1																																																																																			.	.		0.353	CYP39A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040787.1			T	46607278	C	T	46607278	2	4	252	1	0	0	0	0	0	0	0	1	4179	581	21	3		3	CYP39A1	6	46607278	Silent	SNP	C	TCGA-EP-A12J-01A-11D-A12Z-10	12950168	46607278	124507789	31	34166										
CDK13	8621	hgsc.bcm.edu	37	chr7	40085553	40085553	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	atgagacagctcatggagggTctggattattgtcataagaa	12	5	3	2			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr7:40085553T>C	ENST00000181839.4	+	6	3077	c.2472T>C	c.(2470-2472)ggT>ggC	p.G824G	CDK13_ENST00000340829.5_Silent_p.G824G|CDK13_ENST00000484589.1_3'UTR	NM_003718.4|NM_031267.3	NP_003709.3|NP_112557.2	Q14004	CDK13_HUMAN	cyclin-dependent kinase 13	824	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				alternative mRNA splicing, via spliceosome (GO:0000380)|hemopoiesis (GO:0030097)|multicellular organismal development (GO:0007275)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|positive regulation of cell proliferation (GO:0008284)|regulation of mitosis (GO:0007088)|viral process (GO:0016032)	cyclin K-CDK13 complex (GO:0002945)|extracellular space (GO:0005615)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(2)|prostate(2)|skin(5)|stomach(2)|urinary_tract(1)	49						TCATGGAGGGTCTGGATTATT	0.313																																					p.G824G		Atlas-SNP	.											.	CDK13	114	.	0			c.T2472C						.						131	139	136					7																	40085553		2203	4300	6503	SO:0001819	synonymous_variant	8621	exon6			GGAGGGTCTGGAT	M80629	CCDS5461.1, CCDS5462.1	7p14.1	2011-11-08	2009-12-16	2009-12-16	ENSG00000065883	ENSG00000065883		"Cyclin-dependent kinases"	1733	protein-coding gene	gene with protein product	"cholinesterase-related cell division controller"	603309	"cell division cycle 2-like 5 (cholinesterase-related cell division controller)"	CDC2L5		1731328, 19884882	Standard	NM_003718		Approved	CHED, CDC2L, KIAA1791	uc003thh.4	Q14004	OTTHUMG00000023726	ENST00000181839.4:c.2472T>C	chr7.hg19:g.40085553T>C		60.0	0.0		154.0	74.0	NM_003718	Q53G78|Q6DKQ9|Q75MH4|Q75MH5|Q96JN4|Q9H4A0|Q9H4A1|Q9UDR4	Silent	SNP	ENST00000181839.4	hg19	CCDS5461.1																																																																																			.	.		0.313	CDK13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250726.2	NM_003718		C	40085553	T	C	40085553	2	2	252	1	0	0	0	0	0	0	0	1	3131	1654	58	2		2	CDK13	7	40085553	Silent	SNP	T	TCGA-EP-A12J-01A-11D-A12Z-10		40085553	119053110	32	34167										
PHTF2	57157	hgsc.bcm.edu	37	chr7	77569480	77569480	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	actcacagcacattctgcttCagaactttatgtgattgcat	6	10	3	2			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr7:77569480C>A	ENST00000248550.7	+	13	1677	c.1601C>A	c.(1600-1602)tCa>tAa	p.S534*	PHTF2_ENST00000307305.8_Nonsense_Mutation_p.S496*|PHTF2_ENST00000422959.2_Nonsense_Mutation_p.S500*|PHTF2_ENST00000424760.1_Nonsense_Mutation_p.S496*|PHTF2_ENST00000275575.7_Nonsense_Mutation_p.S496*|PHTF2_ENST00000416283.2_Nonsense_Mutation_p.S500*			Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2	534					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	19						CATTCTGCTTCAGAACTTTAT	0.373																																					p.S500X		Atlas-SNP	.											.	PHTF2	104	.	0			c.C1499A						.						126	116	119					7																	77569480		1862	4106	5968	SO:0001587	stop_gained	57157	exon12			CTGCTTCAGAACT	AL136883	CCDS47621.1, CCDS47622.1, CCDS47623.1, CCDS47624.1	7q11.23-q21	2008-02-01			ENSG00000006576	ENSG00000006576			13411	protein-coding gene	gene with protein product						10729229	Standard	NM_020432		Approved	DKFZp434D166	uc003ugq.4	Q8N3S3	OTTHUMG00000155557	ENST00000248550.7:c.1601C>A	chr7.hg19:g.77569480C>A	ENSP00000248550:p.Ser534*	126.0	0.0		495.0	183.0	NM_001127357	A0JP04|A0JP05|A4D1C2|E9PEE3|G5E9H7|Q6NW35|Q8TBW4|Q9H099	Nonsense_Mutation	SNP	ENST00000248550.7	hg19		.	.	.	.	.	.	.	.	.	.	C	38	6.899107	0.97920	.	.	ENSG00000006576	ENST00000427986;ENST00000422959;ENST00000307305;ENST00000424760;ENST00000275575;ENST00000416283;ENST00000248550	.	.	.	5.67	5.67	0.87782	.	0.344882	0.27482	N	0.019166	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.3448	13.9903	0.64362	0.0:0.9275:0.0:0.0725	.	.	.	.	X	500;500;496;496;496;500;534	.	ENSP00000248550:S534X	S	+	2	0	PHTF2	77407416	0.990000	0.36364	0.995000	0.50966	0.969000	0.65631	1.485000	0.35519	2.665000	0.90641	0.557000	0.71058	TCA	.	.		0.373	PHTF2-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000340638.2	NM_020432		A	77569480	C	A	77569480	4	1	252	1	0	0	0	0	0	1	0	0	11872	838	29	3	1599	3	PHTF2	7	77569480	Nonsense_Mutation	SNP	C	TCGA-EP-A12J-01A-11D-A12Z-10	37483927	77569480	81569183	33	34168										
SMURF1	57154	hgsc.bcm.edu	37	chr7	98655111	98655111	+	Frame_Shift_Del	DEL	T	T	-													0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	cccaggaagccagctccctgTttcttgtgaattttcttatg							TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr7:98655111delT	ENST00000361125.1	-	4	586	c.267delA	c.(265-267)aaafs	p.K89fs	SMURF1_ENST00000480055.1_5'UTR|SMURF1_ENST00000361368.2_Frame_Shift_Del_p.K89fs	NM_020429.2	NP_065162.1	Q9HCE7	SMUF1_HUMAN	SMAD specific E3 ubiquitin protein ligase 1	89	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				BMP signaling pathway (GO:0030509)|cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of ossification (GO:0030279)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein export from nucleus (GO:0006611)|protein localization to cell surface (GO:0034394)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	activin binding (GO:0048185)|I-SMAD binding (GO:0070411)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|urinary_tract(1)	25	all_cancers(62;1.05e-08)|all_epithelial(64;4.34e-09)|Lung NSC(181;0.00902)|all_lung(186;0.0145)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)|Lung(104;0.224)			CAGCTCCCTGTTTCTTGTGAA	0.423																																					p.Q90fs		Atlas-Indel,Pindel	.											.	SMURF1	58	.	0			c.268delC						.						124	132	129					7																	98655111		2203	4300	6503	SO:0001589	frameshift_variant	57154	exon4			.	AB046845	CCDS34689.1, CCDS34690.1	7q21.1-q31.1	2004-07-29			ENSG00000198742	ENSG00000198742			16807	protein-coding gene	gene with protein product		605568				10458166	Standard	NM_020429		Approved	KIAA1625	uc003upu.2	Q9HCE7	OTTHUMG00000150272	ENST00000361125.1:c.267delA	chr7.hg19:g.98655111delT	ENSP00000354621:p.Lys89fs	93.0	0.0		247.0	89.0	NM_020429	A4D279|B7ZMB6|B9EGV3|O75853|Q547Q3|Q9UJT8	Frame_Shift_Del	DEL	ENST00000361125.1	hg19	CCDS34690.1																																																																																			.	.		0.423	SMURF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000335001.2	NM_020429		-	98655111	T	-	98655111	7	5	252	1	0	1	0	1	0	0	0	0	14834	1722	60	0	2070	0	SMURF1	7	98655111	Frame_Shift_Del	DEL	T	TCGA-EP-A12J-01A-11D-A12Z-10	21085631	98655111	60483552	34	34169										
MUC17	140453	hgsc.bcm.edu	37	chr7	100678724	100678724	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	gaactcctttaacaagtataCctgtcaacaccacactggtg	6	12	1	0			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr7:100678724C>A	ENST00000306151.4	+	3	4091	c.4027C>A	c.(4027-4029)Cct>Act	p.P1343T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1343	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					AACAAGTATACCTGTCAACAC	0.463																																					p.P1343T		Atlas-SNP	.											.	MUC17	804	.	0			c.C4027A						.						231	226	228					7																	100678724		2203	4300	6503	SO:0001583	missense	140453	exon3			AGTATACCTGTCA	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.4027C>A	chr7.hg19:g.100678724C>A	ENSP00000302716:p.Pro1343Thr	66.0	0.0		198.0	10.0	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	c	0.046	-1.266293	0.01433	.	.	ENSG00000169876	ENST00000306151	T	0.03212	4.01	0.656	-0.414	0.12359	.	.	.	.	.	T	0.02342	0.0072	L	0.29908	0.895	0.09310	N	1	B	0.24576	0.106	B	0.16722	0.016	T	0.48758	-0.9007	8	0.08381	T	0.77	.	.	.	.	.	1343	Q685J3	MUC17_HUMAN	T	1343	ENSP00000302716:P1343T	ENSP00000302716:P1343T	P	+	1	0	MUC17	100465444	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-3.852000	0.00350	-0.128000	0.11641	-1.404000	0.01136	CCT	.	.		0.463	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		A	100678724	C	A	100678724	3	1	252	1	0	0	0	0	1	0	0	0	9983	507	18	3	4037	3	MUC17	7	100678724	Missense_Mutation	SNP	C	TCGA-EP-A12J-01A-11D-A12Z-10	2023613	100678724	58459939	35	34170										
BCAP29	55973	hgsc.bcm.edu	37	chr7	107254121	107254122	+	Intron	INS	-	-	A													0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	tccagttttggtgaatttttINSaagcaaaagaagccacaaaa					rs576177767	byFrequency	TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr7:107254121_107254122insA	ENST00000005259.4	+	7	1029				BCAP29_ENST00000379121.2_Intron|BCAP29_ENST00000379117.2_Intron|BCAP29_ENST00000465919.1_Intron|BCAP29_ENST00000445771.2_Frame_Shift_Ins_p.S239fs|BCAP29_ENST00000379119.2_Frame_Shift_Ins_p.S239fs|BCAP29_ENST00000494086.1_Intron	NM_018844.3	NP_061332.2	Q9UHQ4	BAP29_HUMAN	B-cell receptor-associated protein 29						apoptotic process (GO:0006915)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|osteoblast differentiation (GO:0001649)|protein localization to endoplasmic reticulum exit site (GO:0070973)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				cervix(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	14						GGTGAATTTTTAAGCAAAAGAA	0.366																																					p.L238fs		Atlas-INDEL	.											.	BCAP29	46	.	0			c.713_714insA						.																																			SO:0001627	intron_variant	55973	exon7			.		CCDS34730.1, CCDS34731.1	7q22.3	2012-09-20			ENSG00000075790	ENSG00000075790			24131	protein-coding gene	gene with protein product						12477932	Standard	NM_018844		Approved	BAP29, DKFZp686M2086	uc011kma.1	Q9UHQ4	OTTHUMG00000154770	ENST00000005259.4:c.690+244->A	chr7.hg19:g.107254123_107254123dupA		72.0	0.0		199.0	15.0	NM_001008405	G5E9L4|O95003	Frame_Shift_Ins	INS	ENST00000005259.4	hg19	CCDS34731.1																																																																																			.	.		0.366	BCAP29-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337011.2	NM_018844		A	107254122	-	A	107254121	6	5	252	0	1	1	1	0	0	0	0	0	1346	1764	61	0		0	BCAP29	7	107254121	Intron	INS	-	TCGA-EP-A12J-01A-11D-A12Z-10	6575397	107254121	51884542	36	34171										
NRCAM	4897	hgsc.bcm.edu	37	chr7	107824934	107824934	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	atgctgttcactgccatcacGcggaaggagtagttcacgta	11	10	3	0			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr7:107824934G>A	ENST00000425651.2	-	18	2159	c.2160C>T	c.(2158-2160)cgC>cgT	p.R720R	NRCAM_ENST00000379024.4_Silent_p.R701R|NRCAM_ENST00000351718.4_Silent_p.R704R|NRCAM_ENST00000379028.3_Silent_p.R720R|NRCAM_ENST00000413765.2_Silent_p.R701R|NRCAM_ENST00000379022.4_Silent_p.R720R	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	720	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						CTGCCATCACGCGGAAGGAGT	0.547																																					p.R720R		Atlas-SNP	.											.	NRCAM	267	.	0			c.C2160T						.						99	91	94					7																	107824934		2203	4300	6503	SO:0001819	synonymous_variant	4897	exon18			CATCACGCGGAAG		CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7994	protein-coding gene	gene with protein product	"NgCAM-related cell adhesion molecule"	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.2160C>T	chr7.hg19:g.107824934G>A		42.0	0.0		106.0	39.0	NM_001037132	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Silent	SNP	ENST00000425651.2	hg19	CCDS47686.1																																																																																			.	.		0.547	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132		A	107824934	G	A	107824934	2	1	252	1	0	0	0	0	0	0	0	1	10653	1074	38	1		1	NRCAM	7	107824934	Silent	SNP	G	TCGA-EP-A12J-01A-11D-A12Z-10	570813	107824934	51313729	37	34172										
HYAL4	23553	hgsc.bcm.edu	37	chr7	123508467	123508467	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	tccaatttatcaaaggaaacCttttatagctgcttggaatg	7	7	1	0			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr7:123508467C>A	ENST00000223026.4	+	3	778	c.140C>A	c.(139-141)cCt>cAt	p.P47H	HYAL4_ENST00000476325.1_Missense_Mutation_p.P47H	NM_012269.2	NP_036401.2	Q2M3T9	HYAL4_HUMAN	hyaluronoglucosaminidase 4	47					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate catabolic process (GO:0030207)|glycosaminoglycan catabolic process (GO:0006027)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)	hyalurononglucosaminidase activity (GO:0004415)	p.P47L(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	23						CAAAGGAAACCTTTTATAGCT	0.353																																					p.P47H		Atlas-SNP	.											HYAL4,NS,carcinoma,0,1	HYAL4	65	.	1	Substitution - Missense(1)	endometrium(1)	c.C140A						.						72	77	75					7																	123508467		2203	4300	6503	SO:0001583	missense	23553	exon3			GGAAACCTTTTAT	AF009010	CCDS5789.1	7q31.3	2010-01-14			ENSG00000106302	ENSG00000106302			5323	protein-coding gene	gene with protein product	"hyaluronidase 4"	604510				10493834	Standard	NM_012269		Approved		uc003vlc.3	Q2M3T9	OTTHUMG00000157349	ENST00000223026.4:c.140C>A	chr7.hg19:g.123508467C>A	ENSP00000223026:p.Pro47His	60.0	0.0		162.0	70.0	NM_012269	D0VXG1|Q9UL99|Q9Y6T9	Missense_Mutation	SNP	ENST00000223026.4	hg19	CCDS5789.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.090318	0.76756	.	.	ENSG00000106302	ENST00000489978;ENST00000223026;ENST00000476325	T;T	0.55052	0.54;0.54	5.73	5.73	0.89815	Aldolase-type TIM barrel (1);Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	T	0.71324	0.3326	M	0.83483	2.645	0.47621	D	0.999479	P;D	0.56746	0.887;0.977	P;P	0.59546	0.657;0.859	T	0.75593	-0.3264	10	0.87932	D	0	-0.4856	14.5749	0.68238	0.1453:0.8547:0.0:0.0	.	47;47	F8WDH9;Q2M3T9	.;HYAL4_HUMAN	H	47	ENSP00000223026:P47H;ENSP00000417186:P47H	ENSP00000223026:P47H	P	+	2	0	HYAL4	123295703	1.000000	0.71417	0.979000	0.43373	0.964000	0.63967	4.591000	0.61019	2.698000	0.92095	0.655000	0.94253	CCT	.	.		0.353	HYAL4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348545.1	NM_012269		A	123508467	C	A	123508467	3	1	252	1	0	0	0	0	1	0	0	0	7475	681	24	3	142	3	HYAL4	7	123508467	Missense_Mutation	SNP	C	TCGA-EP-A12J-01A-11D-A12Z-10	15683533	123508467	35630196	38	34173										
METTL2B	55798	hgsc.bcm.edu	37	chr7	128140982	128140983	+	Frame_Shift_Del	DEL	TG	TG	-													0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	tgtctatctggaaatttctaTgtgagaggtgatggaaccag					rs10257897|rs139332186	byFrequency	TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr7:128140982_128140983delTG	ENST00000262432.8	+	8	979_980	c.942_943delTG	c.(940-945)tatgtgfs	p.V315fs	METTL2B_ENST00000480046.1_Frame_Shift_Del_p.V250fs	NM_018396.2	NP_060866.2	Q6P1Q9	MET2B_HUMAN	methyltransferase like 2B	315					tRNA methylation (GO:0030488)		tRNA (cytosine) methyltransferase activity (GO:0016427)			breast(1)|cervix(1)|large_intestine(2)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						GAAATTTCTATGTGAGAGGTGA	0.396																																					p.314_314del		Pindel	.											.	METTL2B	34	.	0			c.941_942del						.																																			SO:0001589	frameshift_variant	55798	exon8			.	AK002212	CCDS5803.2	7q32.2	2012-06-12	2006-02-09	2006-02-09	ENSG00000165055	ENSG00000165055			18272	protein-coding gene	gene with protein product		607846	"methyltransferase like 2"	METTL2		11738826	Standard	NM_018396		Approved	METL, FLJ11350	uc003vnf.3	Q6P1Q9	OTTHUMG00000143738	ENST00000262432.8:c.942_943delTG	chr7.hg19:g.128140984_128140985delTG	ENSP00000262432:p.Val315fs	0.0	0.0		25.0	25.0	NM_018396	B4DZ68|Q0IJ54|Q3B7J1	Frame_Shift_Del	DEL	ENST00000262432.8	hg19	CCDS5803.2																																																																																			.	.		0.396	METTL2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289817.1	NM_018396		-	128140983	TG	-	128140982	7	5	252	1	0	1	0	1	0	0	0	0	9509	1471	51	0	972	0	METTL2B	7	128140982	Frame_Shift_Del	DEL	TG	TCGA-EP-A12J-01A-11D-A12Z-10	4632515	128140982	30997681	39	34174	177	2								
METTL2B	55798	hgsc.bcm.edu	37	chr7	128140983	128140984	+	Frame_Shift_Ins	INS	-	-	T													0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	tctatctggaaatttctatgINStgagaggtgatggaaccaga					rs139332186	byFrequency	TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr7:128140983_128140984insT	ENST00000262432.8	+	8	980_981	c.943_944insT	c.(943-945)gtgfs	p.V315fs	METTL2B_ENST00000480046.1_Frame_Shift_Ins_p.V250fs	NM_018396.2	NP_060866.2	Q6P1Q9	MET2B_HUMAN	methyltransferase like 2B	315					tRNA methylation (GO:0030488)		tRNA (cytosine) methyltransferase activity (GO:0016427)			breast(1)|cervix(1)|large_intestine(2)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						AAATTTCTATGTGAGAGGTGAT	0.396																																					p.V315fs		Atlas-INDEL	.											.	METTL2B	34	.	0			c.943_944insT						.																																			SO:0001589	frameshift_variant	55798	exon8			.	AK002212	CCDS5803.2	7q32.2	2012-06-12	2006-02-09	2006-02-09	ENSG00000165055	ENSG00000165055			18272	protein-coding gene	gene with protein product		607846	"methyltransferase like 2"	METTL2		11738826	Standard	NM_018396		Approved	METL, FLJ11350	uc003vnf.3	Q6P1Q9	OTTHUMG00000143738	ENST00000262432.8:c.944dupT	chr7.hg19:g.128140984_128140984dupT	ENSP00000262432:p.Val315fs	79.0	0.0		254.0	41.0	NM_018396	B4DZ68|Q0IJ54|Q3B7J1	Frame_Shift_Ins	INS	ENST00000262432.8	hg19	CCDS5803.2																																																																																			.	.		0.396	METTL2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289817.1	NM_018396		T	128140984	-	T	128140983	7	5	252	1	0	1	1	0	0	0	0	0	9509	1377	48	0	973	0	METTL2B	7	128140983	Frame_Shift_Ins	INS	-	TCGA-EP-A12J-01A-11D-A12Z-10	1	128140983	30997680	40	34175	177	2								
MLL3	58508	hgsc.bcm.edu	37	chr7	151962169	151962169	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	aggacattgccaacctgcacGttttaatggagtaaccgcta	9	10	0	0			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr7:151962169G>A	ENST00000262189.6	-	8	1356	c.1138C>T	c.(1138-1140)Cgt>Tgt	p.R380C	KMT2C_ENST00000355193.2_Missense_Mutation_p.R380C	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	380					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.R380C(2)									CAACCTGCACGTTTTAATGGA	0.448																																					p.R380C		Atlas-SNP	.											MLL3_ENST00000355193,extremity,malignant_melanoma,+1,2	MLL3	1564	.	2	Substitution - Missense(2)	central_nervous_system(2)	c.C1138T						.						418	376	390					7																	151962169		2203	4300	6503	SO:0001583	missense	58508	exon8			CTGCACGTTTTAA	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.1138C>T	chr7.hg19:g.151962169G>A	ENSP00000262189:p.Arg380Cys	134.0	0.0		367.0	16.0	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	hg19	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	G	12.17	1.858881	0.32884	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.98926	-5.24;-5.24	4.65	4.65	0.58169	Zinc finger, PHD-finger (1);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, PHD-type (1);Protein kinase C-like, phorbol ester/diacylglycerol binding (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.38548	U	0.001645	D	0.99039	0.9671	M	0.83223	2.63	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.99437	1.0937	10	0.87932	D	0	.	14.4119	0.67119	0.0:0.0:0.852:0.148	.	380	Q8NEZ4	MLL3_HUMAN	C	380	ENSP00000262189:R380C;ENSP00000347325:R380C	ENSP00000262189:R380C	R	-	1	0	MLL3	151593102	1.000000	0.71417	1.000000	0.80357	0.490000	0.33462	3.895000	0.56258	2.271000	0.75665	0.557000	0.71058	CGT	.	.		0.448	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			A	151962169	G	A	151962169	3	1	252	1	0	0	0	0	1	0	0	0	9631	1145	40	1	13805	1	MLL3	7	151962169	Missense_Mutation	SNP	G	TCGA-EP-A12J-01A-11D-A12Z-10	23821186	151962169	7176494	41	34176										
CDHR1	92211	hgsc.bcm.edu	37	chr10	85960359	85960359	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	tggctgtgaccccctcaggaCatacctgctgggagcatcat	11	13	2	1			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr10:85960359C>T	ENST00000372117.3	+	6	544	c.441C>T	c.(439-441)gaC>gaT	p.D147D	CDHR1_ENST00000440770.2_5'Flank|CDHR1_ENST00000332904.3_Silent_p.D147D	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1	147	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cellular process (GO:0009987)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						CCCCTCAGGACATACCTGCTG	0.592																																					p.D147D		Atlas-SNP	.											.	CDHR1	122	.	0			c.C441T						.						79	58	65					10																	85960359		2203	4300	6503	SO:0001819	synonymous_variant	92211	exon6			TCAGGACATACCT	AB053448	CCDS7372.1, CCDS53548.1	10q23.1	2014-01-28	2010-01-25	2010-01-25	ENSG00000148600	ENSG00000148600		"Cadherins / Cadherin-related"	14550	protein-coding gene	gene with protein product		609502	"protocadherin 21"	PCDH21		11597768	Standard	NM_001171971		Approved	KIAA1775, CORD15, RP65	uc001kcv.3	Q96JP9	OTTHUMG00000018634	ENST00000372117.3:c.441C>T	chr10.hg19:g.85960359C>T		76.0	0.0		123.0	62.0	NM_001171971	Q69YZ8|Q8IXY5	Silent	SNP	ENST00000372117.3	hg19	CCDS7372.1																																																																																			.	.		0.592	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100		T	85960359	C	T	85960359	2	4	252	1	0	0	0	0	0	0	0	1	3120	477	17	3		3	CDHR1	10	85960359	Silent	SNP	C	TCGA-EP-A12J-01A-11D-A12Z-10		85960359	49574388	42	34177										
CUTC	51076	hgsc.bcm.edu	37	chr10	101503802	101503802	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	ttctttttatagctatttgcCgccctctgccagtcactttc	5	13	3	0			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr10:101503802C>T	ENST00000370476.5	+	5	541	c.412C>T	c.(412-414)Cgc>Tgc	p.R138C		NM_015960.2	NP_057044.2	Q9NTM9	CUTC_HUMAN	cutC copper transporter	138					copper ion homeostasis (GO:0055070)|copper ion transport (GO:0006825)|protein tetramerization (GO:0051262)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	copper ion binding (GO:0005507)	p.R138G(1)|p.R138C(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14		Colorectal(252;0.234)		Epithelial(162;3e-10)|all cancers(201;2.37e-08)		AGCTATTTGCCGCCCTCTGCC	0.338																																					p.R138C		Atlas-SNP	.											CUTC,NS,carcinoma,0,2	CUTC	32	.	2	Substitution - Missense(2)	prostate(1)|lung(1)	c.C412T						.						130	123	126					10																	101503802		2203	4300	6503	SO:0001583	missense	51076	exon5			ATTTGCCGCCCTC	AF132966	CCDS7483.1	10q24.31	2013-07-31	2013-07-31		ENSG00000119929	ENSG00000119929			24271	protein-coding gene	gene with protein product		610101	"cutC copper transporter homolog (E. coli)"			16182249	Standard	NM_015960		Approved	CGI-32	uc001kqd.4	Q9NTM9	OTTHUMG00000018889	ENST00000370476.5:c.412C>T	chr10.hg19:g.101503802C>T	ENSP00000359507:p.Arg138Cys	62.0	0.0		174.0	85.0	NM_015960	Q5TCZ8|Q9Y321	Missense_Mutation	SNP	ENST00000370476.5	hg19	CCDS7483.1	.	.	.	.	.	.	.	.	.	.	C	15.42	2.828442	0.50845	.	.	ENSG00000119929	ENST00000370476;ENST00000370472	.	.	.	4.97	4.97	0.65823	Copper homeostasis CutC domain (2);	0.051997	0.85682	D	0.000000	T	0.63780	0.2540	M	0.83223	2.63	0.80722	D	1	P;B	0.36027	0.533;0.101	B;B	0.24269	0.052;0.03	T	0.70092	-0.4967	9	0.48119	T	0.1	-9.0535	18.7716	0.91894	0.0:1.0:0.0:0.0	.	138;138	B4DYM2;Q9NTM9	.;CUTC_HUMAN	C	138;75	.	ENSP00000359503:R75C	R	+	1	0	CUTC	101493792	1.000000	0.71417	1.000000	0.80357	0.569000	0.35902	6.643000	0.74334	2.727000	0.93392	0.591000	0.81541	CGC	.	.		0.338	CUTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049811.1	NM_015960		T	101503802	C	T	101503802	3	4	252	1	0	0	0	0	1	0	0	0	4065	652	23	1	430	1	CUTC	10	101503802	Missense_Mutation	SNP	C	TCGA-EP-A12J-01A-11D-A12Z-10	15543443	101503802	34030945	43	34178										
MUC6	4588	hgsc.bcm.edu	37	chr11	1016851	1016851	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	ctggaaggatgttgcagtcaTaggacctgtggaagagaagg	16	5	1	1			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr11:1016851T>C	ENST00000421673.2	-	31	6000	c.5950A>G	c.(5950-5952)Atg>Gtg	p.M1984V		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1984	Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GTTGCAGTCATAGGACCTGTG	0.582																																					p.M1984V		Atlas-SNP	.											.	MUC6	408	.	0			c.A5950G						.						1531	1522	1525					11																	1016851		2203	4298	6501	SO:0001583	missense	4588	exon31			CAGTCATAGGACC	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"Mucins"	7517	protein-coding gene	gene with protein product		158374	"mucin 6, gastric"			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.5950A>G	chr11.hg19:g.1016851T>C	ENSP00000406861:p.Met1984Val	186.0	0.0		1978.0	89.0	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	hg19	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	C	1.757	-0.487796	0.04352	.	.	ENSG00000184956	ENST00000421673	T	0.17370	2.28	2.75	-1.23	0.09465	.	.	.	.	.	T	0.10809	0.0264	L	0.43152	1.355	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45205	-0.9277	9	0.06365	T	0.9	.	7.0983	0.25321	0.0:0.1589:0.2688:0.5723	.	1984	Q6W4X9	MUC6_HUMAN	V	1984	ENSP00000406861:M1984V	ENSP00000406861:M1984V	M	-	1	0	MUC6	1006851	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.137000	0.00588	-0.732000	0.04856	-2.319000	0.00253	ATG	.	.		0.582	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540		C	1016851	T	C	1016851	3	2	252	1	0	0	0	0	1	0	0	0	9989	1406	49	2	1381	2	MUC6	11	1016851	Missense_Mutation	SNP	T	TCGA-EP-A12J-01A-11D-A12Z-10		1016851	133989665	44	34179										
EFEMP2	30008	hgsc.bcm.edu	37	chr11	65638628	65638628	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	ccagagcagtccccactcacCcacacagctgtcctgatcgt	7	18	1	2			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr11:65638628C>A	ENST00000307998.6	-	4	597	c.367G>T	c.(367-369)Gat>Tat	p.D123Y	EFEMP2_ENST00000528176.1_Splice_Site_p.D123Y	NM_016938.4	NP_058634.4	O95967	FBLN4_HUMAN	EGF containing fibulin-like extracellular matrix protein 2	123	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				blood coagulation (GO:0007596)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21				READ - Rectum adenocarcinoma(159;0.169)		CCCCACTCACCCACACAGCTG	0.632																																					p.D123Y		Atlas-SNP	.											.	EFEMP2	42	.	0			c.G367T						.						58	56	57					11																	65638628		2201	4296	6497	SO:0001630	splice_region_variant	30008	exon4			ACTCACCCACACA	AF109121	CCDS8116.1	11q13	2011-06-17	2011-01-25		ENSG00000172638	ENSG00000172638		"Fibulins"	3219	protein-coding gene	gene with protein product	"fibulin 4"	604633	"EGF-containing fibulin-like extracellular matrix protein 2"			10601734, 10982184	Standard	NR_037718		Approved	FBLN4, UPH1	uc001ofy.4	O95967	OTTHUMG00000166664	ENST00000307998.6:c.367+1G>T	chr11.hg19:g.65638628C>A		23.0	0.0		58.0	20.0	NM_016938	A8K7R4|B3KM31|B3KQT1|O75967	Missense_Mutation	SNP	ENST00000307998.6	hg19	CCDS8116.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.308672	0.81247	.	.	ENSG00000172638	ENST00000528176;ENST00000307998;ENST00000526624;ENST00000527378	D;D;D;D	0.99080	-5.4;-5.4;-5.4;-5.4	4.58	4.58	0.56647	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.39834	N	0.001260	D	0.99408	0.9791	M	0.93241	3.395	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.70487	0.969;0.966	D	0.98440	1.0586	9	.	.	.	.	14.88	0.70525	0.0:1.0:0.0:0.0	.	123;123	E9PRU1;O95967	.;FBLN4_HUMAN	Y	123	ENSP00000434151:D123Y;ENSP00000309953:D123Y;ENSP00000435419:D123Y;ENSP00000435963:D123Y	.	D	-	1	0	EFEMP2	65395204	1.000000	0.71417	1.000000	0.80357	0.818000	0.46254	5.096000	0.64535	2.361000	0.80049	0.655000	0.94253	GAT	.	.		0.632	EFEMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391047.4	NM_016938	Missense_Mutation	A	65638628	C	A	65638628	5	1	252	1	0	0	0	0	0	0	1	0	4944	637	22	3	996	3	EFEMP2	11	65638628	Splice_Site	SNP	C	TCGA-EP-A12J-01A-11D-A12Z-10	64621777	65638628	69367888	45	34180										
NCAM1	4684	hgsc.bcm.edu	37	chr11	112832332	112832363	+	5'UTR	DEL	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	-													0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	ccctcccagccagcagattaCaatgctgccaaactaaggat					rs6589347|rs11284059|rs559828324|rs201772924|rs563686839|rs7105734|rs112306738		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr11:112832332_112832363delCATCCCTCCCAGCCAGCAGATTACAATGCTGC	ENST00000533760.1	+	0	243_274				NCAM1_ENST00000397957.4_3'UTR|RP11-629G13.1_ENST00000532002.1_RNA|RP11-629G13.1_ENST00000500537.2_RNA	NM_001242608.1	NP_001229537.1	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		CAGCAGATTACAATGCTGCCAAACTAAGGATTTCATTTGGACTTTGTTTTTC	0.491																																					.		Pindel	.											.	NCAM1	372	.	0			.						.																																			SO:0001623	5_prime_UTR_variant	4684	wholegene			.		CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000533760.1:c.-326CATCCCTCCCAGCCAGCAGATTACAATGCTGC>-	chr11.hg19:g.112832332_112832363delCATCCCTCCCAGCCAGCAGATTACAATGCTGC		0.0	0.0		27.0	27.0	NM_001242607	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Frame_Shift_Del	DEL	ENST00000533760.1	hg19																																																																																				.	.		0.491	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394068.2	NM_000615		-	112832363	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	-	112832332	6	5	252	0	1	1	0	1	0	0	0	0	10211	493	17	0		0	NCAM1	11	112832332	5'UTR	DEL	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	TCGA-EP-A12J-01A-11D-A12Z-10	47193704	112832332	22174184	46	34181										
DDX11	1663	hgsc.bcm.edu	37	chr12	31255209	31255209	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	cctaagagcgcacaccaggtGgagcaggtgctgctggcata	14	11	0	1	rs571690896	byFrequency	TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr12:31255209G>A	ENST00000407793.2	+	22	2486	c.2235G>A	c.(2233-2235)gtG>gtA	p.V745V	DDX11_ENST00000545668.1_Silent_p.V745V|DDX11_ENST00000542838.1_Silent_p.V745V|DDX11_ENST00000228264.6_Silent_p.V719V|DDX11_ENST00000251758.5_3'UTR|DDX11_ENST00000350437.4_Silent_p.V695V	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	745					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					CACACCAGGTGGAGCAGGTGC	0.587										Multiple Myeloma(12;0.14)			G|||	11	0.00219649	8e-04	0.0014	5008	,	,		21388	0.003		0.002	False		,,,				2504	0.0041				p.V745V		Atlas-SNP	.											.	DDX11	188	.	0			c.G2235A						.						80	87	85					12																	31255209		2203	4300	6503	SO:0001819	synonymous_variant	1663	exon22			CCAGGTGGAGCAG	U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573		"DEAD-boxes"	2736	protein-coding gene	gene with protein product	"CHL1-like helicase homolog (S. cerevisiae)"	601150	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase)", "DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11"				Standard	NM_030653		Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000407793.2:c.2235G>A	chr12.hg19:g.31255209G>A		105.0	0.0		236.0	12.0	NM_030653	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Silent	SNP	ENST00000407793.2	hg19	CCDS44856.1	.	.	.	.	.	.	.	.	.	.	G	7.213	0.595897	0.13875	.	.	ENSG00000013573	ENST00000539702	.	.	.	3.85	2.93	0.34026	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.3677	0.44035	0.0:0.0:0.8026:0.1974	.	.	.	.	X	3	.	.	W	+	2	0	DDX11	31146476	1.000000	0.71417	1.000000	0.80357	0.636000	0.38137	3.612000	0.54142	0.793000	0.33875	0.603000	0.83216	TGG	.	G|0.500;A|0.500		0.587	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653		A	31255209	G	A	31255209	2	1	252	1	0	0	0	0	0	0	0	1	4345	1335	47	3		3	DDX11	12	31255209	Silent	SNP	G	TCGA-EP-A12J-01A-11D-A12Z-10		31255209	102596686	47	34182										
TMTC2	160335	hgsc.bcm.edu	37	chr12	83358835	83358835	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	ccaggagaacagcaggtttgCagaagcactacattattata	9	8	0	2			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr12:83358835C>G	ENST00000321196.3	+	5	2338	c.1631C>G	c.(1630-1632)gCa>gGa	p.A544G	TMTC2_ENST00000548305.1_Missense_Mutation_p.A544G|TMTC2_ENST00000549919.1_Missense_Mutation_p.A538G	NM_152588.1	NP_689801.1	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat containing 2	544					calcium ion homeostasis (GO:0055074)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|urinary_tract(1)	39						AGCAGGTTTGCAGAAGCACTA	0.348																																					p.A544G		Atlas-SNP	.											.	TMTC2	100	.	0			c.C1631G						.						95	103	101					12																	83358835		2203	4300	6503	SO:0001583	missense	160335	exon5			GGTTTGCAGAAGC	AK074634	CCDS9025.1	12q21.31	2014-06-09			ENSG00000179104	ENSG00000179104		"Tetratricopeptide (TTC) repeat domain containing"	25440	protein-coding gene	gene with protein product		615856				24764305	Standard	NM_152588		Approved	DKFZp762A217	uc001szt.3	Q8N394	OTTHUMG00000169736	ENST00000321196.3:c.1631C>G	chr12.hg19:g.83358835C>G	ENSP00000322300:p.Ala544Gly	131.0	0.0		498.0	193.0	NM_152588	B2RCU7|Q8N2K8	Missense_Mutation	SNP	ENST00000321196.3	hg19	CCDS9025.1	.	.	.	.	.	.	.	.	.	.	C	18.98	3.737144	0.69304	.	.	ENSG00000179104	ENST00000321196;ENST00000548305;ENST00000549919;ENST00000546590	T;T;T	0.76578	-1.03;-0.04;-1.03	5.92	5.92	0.95590	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.275758	0.43416	D	0.000577	T	0.74718	0.3753	L	0.45581	1.43	0.40649	D	0.982014	B;B;B	0.17038	0.003;0.006;0.02	B;B;B	0.18871	0.014;0.016;0.023	T	0.67554	-0.5641	10	0.30854	T	0.27	-4.1126	20.3343	0.98733	0.0:1.0:0.0:0.0	.	544;299;544	Q8N394;F8VRQ2;F8VSH2	TMTC2_HUMAN;.;.	G	544;544;538;299	ENSP00000322300:A544G;ENSP00000448292:A544G;ENSP00000447609:A538G	ENSP00000322300:A544G	A	+	2	0	TMTC2	81882966	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	5.727000	0.68523	2.822000	0.97130	0.650000	0.86243	GCA	.	.		0.348	TMTC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405663.1	NM_152588		G	83358835	C	G	83358835	3	3	252	1	0	0	0	0	1	0	0	0	16276	710	25	4	1649	4	TMTC2	12	83358835	Missense_Mutation	SNP	C	TCGA-EP-A12J-01A-11D-A12Z-10	52103626	83358835	50493060	48	34183										
GALNT4	8693	hgsc.bcm.edu	37	chr12	89916794	89916794	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	caattttgcattcccacataAtttttttgctcaggtacctc	4	11	1	0			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr12:89916794A>C	ENST00000529983.2	-	1	1789	c.1533T>G	c.(1531-1533)aaT>aaG	p.N511K	POC1B_ENST00000541909.1_Intron|POC1B_ENST00000393179.4_Intron|POC1B-GALNT4_ENST00000548729.1_Missense_Mutation_p.N508K|POC1B-GALNT4_ENST00000547474.1_3'UTR|GALNT4_ENST00000413530.1_Missense_Mutation_p.N339K|POC1B_ENST00000549504.1_Intron|RP11-734K2.4_ENST00000605233.1_RNA|POC1B_ENST00000549035.1_Intron|POC1B_ENST00000313546.3_Intron	NM_003774.4	NP_003765.2	Q8N4A0	GALT4_HUMAN	polypeptide N-acetylgalactosaminyltransferase 4	511	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			endometrium(4)|kidney(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)	14						TTCCCACATAATTTTTTTGCT	0.363																																					p.N511K		Atlas-SNP	.											.	GALNT4	38	.	0			c.T1533G						.						65	62	63					12																	89916794		1832	4085	5917	SO:0001583	missense	8693	exon1			CACATAATTTTTT	Y08564	CCDS53817.1	12q21.33	2014-03-13	2014-03-13		ENSG00000257594	ENSG00000257594	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4126	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 4"	603565	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 4 (GalNAc-T4)"			9804815	Standard	NM_003774		Approved	GalNAc-T4	uc001tbd.3	Q8N4A0	OTTHUMG00000166292	ENST00000529983.2:c.1533T>G	chr12.hg19:g.89916794A>C	ENSP00000436604:p.Asn511Lys	59.0	0.0		169.0	85.0	NM_003774	B2R775|B4DMX6|O00208	Missense_Mutation	SNP	ENST00000529983.2	hg19	CCDS53817.1	.	.	.	.	.	.	.	.	.	.	A	8.561	0.877726	0.17395	.	.	ENSG00000259075;ENSG00000259075;ENSG00000257594	ENST00000548729;ENST00000413530;ENST00000529983	T;T;T	0.32023	1.47;1.47;1.47	5.93	-0.841	0.10752	Ricin B-related lectin (1);Ricin B lectin (3);	.	.	.	.	T	0.09730	0.0239	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.001	T	0.29305	-1.0016	9	0.21014	T	0.42	.	0.3181	0.00298	0.3187:0.265:0.1911:0.2253	.	508;511	F8VUJ3;Q8N4A0	.;GALT4_HUMAN	K	508;339;511	ENSP00000447852:N508K;ENSP00000389686:N339K;ENSP00000436604:N511K	ENSP00000436604:N511K	N	-	3	2	GALNT4;RP11-1109F11.4	88440925	0.000000	0.05858	0.000000	0.03702	0.954000	0.61252	-0.508000	0.06344	-0.144000	0.11314	0.482000	0.46254	AAT	.	.		0.363	GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388973.2	NM_003774		C	89916794	A	C	89916794	3	2	252	1	0	0	0	0	1	0	0	0	6223	98	4	5	207	5	GALNT4	12	89916794	Missense_Mutation	SNP	A	TCGA-EP-A12J-01A-11D-A12Z-10	6557959	89916794	43935101	49	34184										
NOS1	4842	hgsc.bcm.edu	37	chr12	117768410	117768410	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	gcatgctgaggcccattcccGggacccgaggccccatccac	11	18	0	1	rs369224010		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr12:117768410G>A	ENST00000338101.4	-	1	469	c.465C>T	c.(463-465)ccC>ccT	p.P155P	NOS1_ENST00000317775.6_Silent_p.P155P|NOS1_ENST00000344089.3_Silent_p.P155P|NOS1_ENST00000549189.1_5'Flank			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0	Ala-rich.				cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		GCCCATTCCCGGGACCCGAGG	0.701																																					p.P155P	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											.	NOS1	240	.	0			c.C465T						.	G	,	1,3821		0,1,1910	39	44	42		465,465	-9.5	0	12		42	1,8233		0,1,4116	no	coding-synonymous,coding-synonymous	NOS1	NM_000620.4,NM_001204218.1	,	0,2,6026	AA,AG,GG		0.0121,0.0262,0.0166	,	155/1435,155/1469	117768410	2,12054	1911	4117	6028	SO:0001819	synonymous_variant	4842	exon2			ATTCCCGGGACCC		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.465C>T	chr12.hg19:g.117768410G>A		25.0	0.0		55.0	22.0	NM_000620		Silent	SNP	ENST00000338101.4	hg19	CCDS55890.1																																																																																			.	.		0.701	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1			A	117768410	G	A	117768410	2	1	252	1	0	0	0	0	0	0	0	1	10550	1103	39	1		1	NOS1	12	117768410	Silent	SNP	G	TCGA-EP-A12J-01A-11D-A12Z-10	27851616	117768410	16083485	50	34185										
DHX37	57647	hgsc.bcm.edu	37	chr12	125453127	125453127	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	agaccttccggaagcactcgCcactgtagtcttccagcggt	10	14	1	1			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr12:125453127C>A	ENST00000308736.2	-	10	1459	c.1361G>T	c.(1360-1362)gGc>gTc	p.G454V	DHX37_ENST00000544745.1_Missense_Mutation_p.G241V	NM_032656.3	NP_116045.2	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	454							ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(5)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|liver(1)|lung(27)|ovary(1)|prostate(2)|skin(3)	65	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)		GAAGCACTCGCCACTGTAGTC	0.612																																					p.G454V		Atlas-SNP	.											.	DHX37	114	.	0			c.G1361T						.						133	133	133					12																	125453127		2203	4300	6503	SO:0001583	missense	57647	exon10			CACTCGCCACTGT	AB040950	CCDS9261.1	12q24.31	2004-03-25	2003-06-13	2003-06-20		ENSG00000150990		"DEAH-boxes"	17210	protein-coding gene	gene with protein product			"DEAD/DEAH box helicase DDX37"	DDX37		10819331	Standard	NM_032656		Approved	KIAA1517, MGC4322, MGC2695	uc001ugy.3	Q8IY37		ENST00000308736.2:c.1361G>T	chr12.hg19:g.125453127C>A	ENSP00000311135:p.Gly454Val	19.0	0.0		32.0	16.0	NM_032656	Q9BUI7|Q9P211	Missense_Mutation	SNP	ENST00000308736.2	hg19	CCDS9261.1	.	.	.	.	.	.	.	.	.	.	C	11.83	1.756702	0.31137	.	.	ENSG00000150990	ENST00000308736;ENST00000544745	T;T	0.03831	3.79;3.79	4.6	4.6	0.57074	.	0.104012	0.64402	D	0.000003	T	0.07773	0.0195	M	0.63428	1.95	0.80722	D	1	B	0.14438	0.01	B	0.17098	0.017	T	0.12372	-1.0550	10	0.32370	T	0.25	-27.7653	13.9708	0.64240	0.0:0.847:0.153:0.0	.	454	Q8IY37	DHX37_HUMAN	V	454;241	ENSP00000311135:G454V;ENSP00000439009:G241V	ENSP00000311135:G454V	G	-	2	0	DHX37	124019080	0.998000	0.40836	0.770000	0.31555	0.759000	0.43091	3.530000	0.53539	2.263000	0.75096	0.561000	0.74099	GGC	.	.		0.612	DHX37-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032656		A	125453127	C	A	125453127	3	1	252	1	0	0	0	0	1	0	0	0	4512	739	26	3	2184	3	DHX37	12	125453127	Missense_Mutation	SNP	C	TCGA-EP-A12J-01A-11D-A12Z-10	7684717	125453127	8398768	51	34186										
TMEM90A	646658	hgsc.bcm.edu	37	chr14	74876039	74876039	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	tcatgcactcacctcctcttCctcctggtcatcctcctggt	5	18	4	0			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr14:74876039C>T	ENST00000554823.1	-	1	470	c.409G>A	c.(409-411)Gaa>Aaa	p.E137K	SYNDIG1L_ENST00000331628.3_Missense_Mutation_p.E137K			A6NDD5	SYN1L_HUMAN	synapse differentiation inducing 1-like	137					response to biotic stimulus (GO:0009607)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|lung(8)|pancreas(1)|prostate(1)|skin(1)	14						ACCTCCTCTTCCTCCTGGTCA	0.512																																					p.E137K		Atlas-SNP	.											.	SYNDIG1L	24	.	0			c.G409A						.						88	94	92					14																	74876039		2055	4180	6235	SO:0001583	missense	646658	exon2			CCTCTTCCTCCTG		CCDS41970.1	14q24.3	2011-06-30	2011-06-30	2011-06-30		ENSG00000183379			32388	protein-coding gene	gene with protein product	"caudate-and putamen-enriched sequence", "interferon induced transmembrane protein domain containing 4"	609999	"transmembrane protein 90A"	TMEM90A		16359841	Standard	NM_001105579		Approved	capucin, IFITMD4	uc001xpx.2	A6NDD5		ENST00000554823.1:c.409G>A	chr14.hg19:g.74876039C>T	ENSP00000450439:p.Glu137Lys	72.0	0.0		88.0	54.0	NM_001105579		Missense_Mutation	SNP	ENST00000554823.1	hg19	CCDS41970.1	.	.	.	.	.	.	.	.	.	.	C	13.81	2.348504	0.41599	.	.	ENSG00000183379	ENST00000331628;ENST00000554823	D;D	0.95821	-3.82;-3.82	4.63	2.81	0.32909	.	0.406089	0.25857	N	0.027842	D	0.90181	0.6931	L	0.38175	1.15	0.22001	N	0.999422	B	0.18310	0.027	B	0.14023	0.01	T	0.80236	-0.1466	10	0.35671	T	0.21	-10.8241	6.4673	0.21990	0.0:0.7047:0.0:0.2953	.	137	A6NDD5	SYN1L_HUMAN	K	137	ENSP00000331474:E137K;ENSP00000450439:E137K	ENSP00000331474:E137K	E	-	1	0	SYNDIG1L	73945792	.	.	0.957000	0.39632	0.148000	0.21650	.	.	0.578000	0.29487	-0.373000	0.07131	GAA	.	.		0.512	SYNDIG1L-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412341.1	XM_938515		T	74876039	C	T	74876039	3	4	252	1	0	0	0	0	1	0	0	0	16233	864	30	3	319	3	TMEM90A	14	74876039	Missense_Mutation	SNP	C	TCGA-EP-A12J-01A-11D-A12Z-10		74876039	32473501	52	34187										
MYH11	4629	hgsc.bcm.edu	37	chr16	15808930	15808930	+	Frame_Shift_Del	DEL	T	T	-													0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	tgcttgaccctggcattgccTttctctgcctgtcgcggaga							TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr16:15808930delT	ENST00000300036.5	-	40	5731	c.5622delA	c.(5620-5622)aaafs	p.K1874fs	MYH11_ENST00000576790.2_Frame_Shift_Del_p.K1874fs|NDE1_ENST00000396354.1_Intron|NDE1_ENST00000342673.5_Intron|MYH11_ENST00000452625.2_Frame_Shift_Del_p.K1881fs|NDE1_ENST00000396355.1_Intron|MYH11_ENST00000396324.3_Frame_Shift_Del_p.K1881fs	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	1874					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						TGGCATTGCCTTTCTCTGCCT	0.672			T	CBFB	AML																																p.G1882fs		Atlas-Indel,Pindel	.		Dom	yes		16	16p13.13-p13.12	4629	"myosin, heavy polypeptide 11, smooth muscle"		L	.	MYH11	520	.	0			c.5644delG						.						105	101	102					16																	15808930		2197	4300	6497	SO:0001589	frameshift_variant	4629	exon41			.	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"Myosins / Myosin superfamily : Class II"	7569	protein-coding gene	gene with protein product		160745	"myosin, heavy polypeptide 11, smooth muscle"			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.5622delA	chr16.hg19:g.15808930delT	ENSP00000300036:p.Lys1874fs	49.0	0.0		92.0	39.0	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Frame_Shift_Del	DEL	ENST00000300036.5	hg19	CCDS10565.1																																																																																			.	.		0.672	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113		-	15808930	T	-	15808930	7	5	252	1	0	1	0	1	0	0	0	0	10040	1606	56	0	339	0	MYH11	16	15808930	Frame_Shift_Del	DEL	T	TCGA-EP-A12J-01A-11D-A12Z-10		15808930	74545823	53	34188										
CTU2	348180	hgsc.bcm.edu	37	chr16	88776355	88776355	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	ctgtgttgcagggactgtttCaaggccttctacgtccacaa	10	11	2	0			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr16:88776355C>T	ENST00000453996.2	+	3	221	c.153C>T	c.(151-153)ttC>ttT	p.F51F	CTU2_ENST00000312060.5_Silent_p.F51F|CTU2_ENST00000378384.3_Intron|CTU2_ENST00000567949.1_Silent_p.F51F	NM_001012759.1	NP_001012777.1			cytosolic thiouridylase subunit 2 homolog (S. pombe)											NS(1)|breast(1)|endometrium(1)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	11						GGGACTGTTTCAAGGCCTTCT	0.597																																					p.F51F		Atlas-SNP	.											.	CTU2	66	.	0			c.C153T						.						170	166	167					16																	88776355		2198	4300	6498	SO:0001819	synonymous_variant	348180	exon3			CTGTTTCAAGGCC	BC021056	CCDS32506.1, CCDS45545.1	16q24.3	2013-10-11	2009-08-19	2009-08-19		ENSG00000174177			28005	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 84"	C16orf84		19017811	Standard	NM_001012759		Approved	NCS2	uc002flm.3	Q2VPK5		ENST00000453996.2:c.153C>T	chr16.hg19:g.88776355C>T		62.0	0.0		102.0	44.0	NM_001012759		Silent	SNP	ENST00000453996.2	hg19	CCDS45545.1																																																																																			.	.		0.597	CTU2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423025.1	NM_001012762		T	88776355	C	T	88776355	2	4	252	1	0	0	0	0	0	0	0	1	4050	825	29	3		3	CTU2	16	88776355	Silent	SNP	C	TCGA-EP-A12J-01A-11D-A12Z-10	72967425	88776355	1578398	54	34189										
DLG4	1742	hgsc.bcm.edu	37	chr17	7097812	7097812	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	tcttgtcgtaatcaaacaggGccctggagggcaagtggcta	13	9	2	0			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr17:7097812G>A	ENST00000399506.2	-	12	1495	c.1304C>T	c.(1303-1305)gCc>gTc	p.A435V	DLG4_ENST00000399510.2_Missense_Mutation_p.A478V|DLG4_ENST00000302955.6_Missense_Mutation_p.A432V			P78352	DLG4_HUMAN	discs, large homolog 4 (Drosophila)	435	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|axon guidance (GO:0007411)|dendritic spine morphogenesis (GO:0060997)|establishment of protein localization (GO:0045184)|learning (GO:0007612)|locomotory exploration behavior (GO:0035641)|negative regulation of receptor internalization (GO:0002091)|nervous system development (GO:0007399)|neuromuscular process controlling balance (GO:0050885)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synaptic transmission (GO:0050806)|protein complex assembly (GO:0006461)|protein localization to synapse (GO:0035418)|receptor localization to synapse (GO:0097120)|regulation of grooming behavior (GO:2000821)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|signal transduction (GO:0007165)|social behavior (GO:0035176)|synaptic transmission (GO:0007268)|synaptic vesicle maturation (GO:0016188)|vocalization behavior (GO:0071625)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|cerebellar mossy fiber (GO:0044300)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|dendrite cytoplasm (GO:0032839)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|juxtaparanode region of axon (GO:0044224)|neuron projection terminus (GO:0044306)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	acetylcholine receptor binding (GO:0033130)|beta-1 adrenergic receptor binding (GO:0031697)|D1 dopamine receptor binding (GO:0031748)|ionotropic glutamate receptor binding (GO:0035255)|P2Y1 nucleotide receptor binding (GO:0031812)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein phosphatase binding (GO:0019903)|scaffold protein binding (GO:0097110)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)	18					Guanidine(DB00536)	ATCAAACAGGGCCCTGGAGGG	0.597																																					p.A478V		Atlas-SNP	.											.	DLG4	110	.	0			c.C1433T						.						28	32	31					17																	7097812		2041	4198	6239	SO:0001583	missense	1742	exon14			AACAGGGCCCTGG	U83192	CCDS45599.1, CCDS45600.1	17p13.1	2008-12-15	2001-12-04		ENSG00000132535	ENSG00000132535			2903	protein-coding gene	gene with protein product		602887				9286702	Standard	NM_001128827		Approved	PSD-95, PSD95, SAP90, SAP-90	uc010cly.3	P78352	OTTHUMG00000134327	ENST00000399506.2:c.1304C>T	chr17.hg19:g.7097812G>A	ENSP00000382425:p.Ala435Val	35.0	0.0		45.0	30.0	NM_001365	B7Z1S1|G5E939|Q92941|Q9UKK8	Missense_Mutation	SNP	ENST00000399506.2	hg19		.	.	.	.	.	.	.	.	.	.	G	35	5.555178	0.96514	.	.	ENSG00000132535	ENST00000399506;ENST00000302955;ENST00000399510;ENST00000293813;ENST00000380912;ENST00000539674	T;T;T	0.80304	-1.36;-1.36;-1.36	5.3	5.3	0.74995	Src homology-3 domain (4);	.	.	.	.	D	0.91358	0.7274	M	0.90309	3.105	0.80722	D	1	D;D;D;D	0.76494	0.995;0.999;0.998;0.989	D;D;D;D	0.79784	0.953;0.972;0.985;0.993	D	0.92680	0.6157	9	0.87932	D	0	.	16.5016	0.84259	0.0:0.0:1.0:0.0	.	475;435;432;478	B9EGL1;P78352;G5E939;P78352-2	.;DLG4_HUMAN;.;.	V	435;432;478;478;375;478	ENSP00000382425:A435V;ENSP00000307471:A432V;ENSP00000382428:A478V	ENSP00000293813:A478V	A	-	2	0	DLG4	7038536	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.601000	0.98297	2.769000	0.95229	0.655000	0.94253	GCC	.	.		0.597	DLG4-002	KNOWN	non_canonical_TEC|not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000259419.2	NM_001365		A	7097812	G	A	7097812	3	1	252	1	0	0	0	0	1	0	0	0	4559	1203	42	3	906	3	DLG4	17	7097812	Missense_Mutation	SNP	G	TCGA-EP-A12J-01A-11D-A12Z-10		7097812	74097398	55	34190										
KRT33B	3884	hgsc.bcm.edu	37	chr17	39525703	39525703	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	aagtaggactggtagctgggGcacagcaagggctcctgctg	16	9	0	0	rs386797081|rs532358097	byFrequency	TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr17:39525703G>A	ENST00000251646.3	-	1	349	c.300C>T	c.(298-300)tgC>tgT	p.C100C		NM_002279.4	NP_002270.1	Q14525	KT33B_HUMAN	keratin 33B	100	Linker 1.|Rod.				aging (GO:0007568)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|lung(6)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)	21		Breast(137;0.000496)				GGTAGCTGGGGCACAGCAAGG	0.572													G|||	3	0.000599042	0.0023	0	5008	,	,		18426	0		0	False		,,,				2504	0				p.C100C		Atlas-SNP	.											.	KRT33B	46	.	0			c.C300T						.						69	68	68					17																	39525703		2191	4300	6491	SO:0001819	synonymous_variant	3884	exon1			GCTGGGGCACAGC	X82634	CCDS11389.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000131738	ENSG00000131738		"-", "Intermediate filaments type I, keratins (acidic)"	6451	protein-coding gene	gene with protein product	"hard keratin type I 3II"	602762	"keratin, hair, acidic, 3B"	KRTHA3B		7565656, 16831889	Standard	NM_002279		Approved	Ha-3II	uc002hwl.4	Q14525	OTTHUMG00000133429	ENST00000251646.3:c.300C>T	chr17.hg19:g.39525703G>A		40.0	0.0		112.0	10.0	NM_002279	O76010	Silent	SNP	ENST00000251646.3	hg19	CCDS11389.1																																																																																			.	.		0.572	KRT33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257292.1	NM_002279		A	39525703	G	A	39525703	2	1	252	1	0	0	0	0	0	0	0	1	8479	1195	42	3		3	KRT33B	17	39525703	Silent	SNP	G	TCGA-EP-A12J-01A-11D-A12Z-10	32427891	39525703	41669507	56	34191										
CDC27	996	hgsc.bcm.edu	37	chr17	45234594	45234729	+	Splice_Site	DEL	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	-													0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	cactagaatataagacacttAcaattgtgtcctggggtgtt					rs149474782|rs113608268|rs370849730|rs78395997|rs76624491|rs370261409|rs75353677|rs368304141|rs376818791|rs372212798|rs375653477|rs374472811|rs76359747|rs147617501|rs374614181|rs78108688|rs142987740|rs143453365|rs75990396|rs144985864|rs367644695|rs202182614|rs139751753|rs11570485|rs372926889|rs140171160|rs368750026|rs201098929|rs199899451|rs75175938|rs200340309|rs537990668	byFrequency	TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr17:45234594_45234729delCTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	ENST00000066544.3	-	6	590_724	c.497_631delAGTTCTTACGGAAACACCCCAGGACACAATTGTAAGTGTCTTATATTCTAGTGTTCAAAATATTATGAAAACTACAAAGAATGATCTGAACTAAATAATATATTGTGAATGACTTGGTAGAAATTTTCTGTTTCAG	c.(496-633)cagttcttacggaaacaccccaggacacaattgtaagtgtcttatattctagtgttcaaaatattatgaaaactacaaagaatgatctgaactaaataatatattgtgaatgacttggtagaaattttctgtttcaga>cga	p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF166fs	CDC27_ENST00000527547.1_Splice_Site_p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF166fs|CDC27_ENST00000446365.2_Splice_Site_p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF105fs|CDC27_ENST00000531206.1_Splice_Site_p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF166fs|CDC27_ENST00000528748.1_5'UTR	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	166					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)	p.T167T(7)|p.T171T(3)|p.V201I(2)|p.E199E(2)|p.T200T(2)|p.L173S(1)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACTGTCTCAGGCTGTCTGTGAGATAAACTATGATTAGGTACTTGTGTTGTGCAAGAGTTGGGCAGACAGTTGCTAAAGTTCTGTAAAGATGTGAATTTAAATGTTTGGTCAGGATC	0.342																																					p.201_211del		Pindel	.											.	CDC27	337	.	17	Substitution - coding silent(14)|Substitution - Missense(3)	large_intestine(6)|prostate(6)|kidney(4)|NS(1)	c.601_631del						.																																			SO:0001630	splice_region_variant	996	exon6			.	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1728	protein-coding gene	gene with protein product	"anaphase promoting complex subunit 3"	116946	"cell division cycle 27", "cell division cycle 27 homolog (S. cerevisiae)"	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.631-104AGTTCTTACGGAAACACCCCAGGACACAATTGTAAGTGTCTTATATTCTAGTGTTCAAAATATTATGAAAACTACAAAGAATGATCTGAACTAAATAATATATTGTGAATGACTTGGTAGAAATTTTCTGTTTCAG>-	chr17.hg19:g.45234594_45234729delCTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT		0.0	0.0		19.0	19.0	NM_001114091	G3V1C4|Q16349|Q96F35	Frame_Shift_Del	DEL	ENST00000066544.3	hg19	CCDS11509.1																																																																																			.	.		0.342	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		Frame_Shift_Del	-	45234729	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	-	45234594	8	5	252	1	0	1	0	1	0	0	1	0	3068	405	14	0	1916	0	CDC27	17	45234594	Splice_Site	DEL	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	TCGA-EP-A12J-01A-11D-A12Z-10	5708891	45234594	35960616	57	34192										
CCDC57	284001	hgsc.bcm.edu	37	chr17	80115731	80115731	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	cttccccagctcagccacctGcttccgcagctccaaaacct	5	20	1	0			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr17:80115731G>A	ENST00000389641.4	-	14	2170	c.2134C>T	c.(2134-2136)Cag>Tag	p.Q712*	CCDC57_ENST00000392343.3_Nonsense_Mutation_p.Q712*|RP11-1376P16.1_ENST00000582774.1_RNA|CCDC57_ENST00000327026.3_5'UTR|CCDC57_ENST00000392347.1_Nonsense_Mutation_p.Q712*			Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57	712										endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	16	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)			TCAGCCACCTGCTTCCGCAGC	0.682																																					p.Q712X		Atlas-SNP	.											.	CCDC57	102	.	0			c.C2134T						.						25	29	27					17																	80115731		1989	4159	6148	SO:0001587	stop_gained	284001	exon14			CCACCTGCTTCCG	BC040264		17q25.3	2006-03-08			ENSG00000176155	ENSG00000176155			27564	protein-coding gene	gene with protein product						12477932	Standard	XM_006722279		Approved	FLJ00130, FLJ23754	uc002kdx.1	Q2TAC2	OTTHUMG00000140396	ENST00000389641.4:c.2134C>T	chr17.hg19:g.80115731G>A	ENSP00000374292:p.Gln712*	25.0	0.0		49.0	28.0	NM_198082	A6NP51|A8MQC7|Q8IWG2|Q8TER3	Nonsense_Mutation	SNP	ENST00000389641.4	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	35|35	5.540187|5.540187	0.96474|0.96474	.|.	.|.	ENSG00000176155|ENSG00000176155	ENST00000419322|ENST00000389641;ENST00000392347;ENST00000327026;ENST00000392343	.|.	.|.	.|.	3.19|3.19	2.15|2.15	0.27550|0.27550	.|.	.|0.000000	.|0.38959	.|N	.|0.001517	T|.	0.60932|.	0.2307|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.58918|.	-0.7551|.	4|.	.|0.49607	.|T	.|0.09	-22.0135|-22.0135	8.1007|8.1007	0.30854|0.30854	0.0:0.2506:0.7494:0.0|0.0:0.2506:0.7494:0.0	.|.	.|.	.|.	.|.	V|X	57|712;712;220;712	.|.	.|ENSP00000315967:Q220X	A|Q	-|-	2|1	0|0	CCDC57|CCDC57	77709020|77709020	0.988000|0.988000	0.35896|0.35896	0.645000|0.645000	0.29479|0.29479	0.176000|0.176000	0.22953|0.22953	2.236000|2.236000	0.43052|0.43052	0.612000|0.612000	0.30071|0.30071	0.462000|0.462000	0.41574|0.41574	GCA|CAG	.	.		0.682	CCDC57-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000277182.3	NM_198082		A	80115731	G	A	80115731	4	1	252	1	0	0	0	0	0	1	0	0	2829	1328	46	3	629	3	CCDC57	17	80115731	Nonsense_Mutation	SNP	G	TCGA-EP-A12J-01A-11D-A12Z-10	34881137	80115731	1079479	58	34193										
APCDD1	147495	hgsc.bcm.edu	37	chr18	10471887	10471887	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	ggctgtgagtgcaccaaggcCgtgaactttgccatgcatga	13	10	0	3	rs145453912		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr18:10471887C>T	ENST00000355285.5	+	3	957	c.603C>T	c.(601-603)gcC>gcT	p.A201A	APCDD1_ENST00000578882.1_Intron	NM_153000.4	NP_694545.1			adenomatosis polyposis coli down-regulated 1											NS(1)|breast(1)|endometrium(3)|large_intestine(5)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22				READ - Rectum adenocarcinoma(15;0.08)		GCACCAAGGCCGTGAACTTTG	0.607																																					p.A201A		Atlas-SNP	.											APCDD1,NS,carcinoma,0,1	APCDD1	57	.	0			c.C603T						.						144	132	136					18																	10471887		2203	4300	6503	SO:0001819	synonymous_variant	147495	exon3			CAAGGCCGTGAAC	AB056722	CCDS11849.1	18p11.21	2006-07-07			ENSG00000154856	ENSG00000154856			15718	protein-coding gene	gene with protein product		607479				12384519	Standard	NM_153000		Approved	B7323	uc002kom.4	Q8J025	OTTHUMG00000131635	ENST00000355285.5:c.603C>T	chr18.hg19:g.10471887C>T		30.0	0.0		69.0	26.0	NM_153000		Silent	SNP	ENST00000355285.5	hg19	CCDS11849.1																																																																																			.	C|1.000;G|0.000		0.607	APCDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254529.2	NM_153000		T	10471887	C	T	10471887	2	4	252	1	0	0	0	0	0	0	0	1	765	639	23	1		1	APCDD1	18	10471887	Silent	SNP	C	TCGA-EP-A12J-01A-11D-A12Z-10		10471887	67605361	59	34194										
ZNF527	84503	hgsc.bcm.edu	37	chr19	37879212	37879212	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	tcttgatatttttcagactgGgagtcttggtgtgaaattga	11	4	3	4			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr19:37879212G>T	ENST00000436120.2	+	5	368	c.261G>T	c.(259-261)tgG>tgT	p.W87C	ZNF527_ENST00000587349.1_Intron	NM_032453.1	NP_115829.1	Q8NB42	ZN527_HUMAN	zinc finger protein 527	87	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	33			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TTTCAGACTGGGAGTCTTGGT	0.383																																					p.W87C		Atlas-SNP	.											.	ZNF527	78	.	0			c.G261T						.						44	42	42					19																	37879212		1822	4086	5908	SO:0001583	missense	84503	exon5			AGACTGGGAGTCT	AB058732, AK091585	CCDS42559.1	19q13.1	2013-01-08			ENSG00000189164	ENSG00000189164		"Zinc fingers, C2H2-type", "-"	29385	protein-coding gene	gene with protein product						11347906	Standard	NM_032453		Approved	KIAA1829	uc010efk.1	Q8NB42	OTTHUMG00000048173	ENST00000436120.2:c.261G>T	chr19.hg19:g.37879212G>T	ENSP00000390179:p.Trp87Cys	88.0	0.0		240.0	92.0	NM_032453	B4DVL5	Missense_Mutation	SNP	ENST00000436120.2	hg19	CCDS42559.1	.	.	.	.	.	.	.	.	.	.	G	14.03	2.413878	0.42817	.	.	ENSG00000189164	ENST00000356178;ENST00000317566;ENST00000436120	.	.	.	4.72	3.62	0.41486	.	0.000000	0.30501	N	0.009483	T	0.39306	0.1073	N	0.16862	0.45	0.80722	D	1	B;B	0.20988	0.03;0.05	B;B	0.21151	0.015;0.033	T	0.35226	-0.9797	9	0.51188	T	0.08	.	10.1897	0.43019	0.0:0.0:0.8027:0.1973	.	87;55	Q8NB42;Q8NB42-2	ZN527_HUMAN;.	C	87;55;35	.	ENSP00000325231:W55C	W	+	3	0	ZNF527	42571052	0.786000	0.28738	1.000000	0.80357	0.991000	0.79684	0.462000	0.21956	2.455000	0.83008	0.655000	0.94253	TGG	.	.		0.383	ZNF527-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458434.1	NM_032453		T	37879212	G	T	37879212	3	4	252	1	0	0	0	0	1	0	0	0	17983	1241	43	3	275	3	ZNF527	19	37879212	Missense_Mutation	SNP	G	TCGA-EP-A12J-01A-11D-A12Z-10		37879212	21249771	60	34195										
HNRNPL	3191	hgsc.bcm.edu	37	chr19	39328060	39328060	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	gtaatggttcaggaagcccaGagtctccagggcatcgctct	12	11	3	1			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr19:39328060G>C	ENST00000221419.5	-	12	2041	c.1675C>G	c.(1675-1677)Ctg>Gtg	p.L559V	AC104534.3_ENST00000594769.1_Silent_p.L175L|HNRNPL_ENST00000600873.1_Missense_Mutation_p.L426V	NM_001533.2	NP_001524.2	P14866	HNRPL_HUMAN	heterogeneous nuclear ribonucleoprotein L	559	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)			AGGAAGCCCAGAGTCTCCAGG	0.522																																					p.L559V		Atlas-SNP	.											.	HNRNPL	67	.	0			c.C1675G						.						86	82	83					19																	39328060		2203	4300	6503	SO:0001583	missense	3191	exon12			AGCCCAGAGTCTC	X16135	CCDS33015.1, CCDS33016.1	19q13.2	2013-06-12		2007-08-16	ENSG00000104824	ENSG00000104824		"RNA binding motif (RRM) containing"	5045	protein-coding gene	gene with protein product		603083		HNRPL		2687284	Standard	NM_001533		Approved		uc021uuh.1	P14866	OTTHUMG00000182612	ENST00000221419.5:c.1675C>G	chr19.hg19:g.39328060G>C	ENSP00000221419:p.Leu559Val	69.0	0.0		172.0	68.0	NM_001533	A6ND69|A6NIT8|Q9H3P3	Missense_Mutation	SNP	ENST00000221419.5	hg19	CCDS33015.1	.	.	.	.	.	.	.	.	.	.	G	13.95	2.390924	0.42410	.	.	ENSG00000104824	ENST00000221419;ENST00000388749;ENST00000388750	.	.	.	6.06	-3.63	0.04529	Nucleotide-binding, alpha-beta plait (1);	0.129890	0.52532	D	0.000079	T	0.75206	0.3818	M	0.68593	2.085	0.45261	D	0.998266	P;P;D	0.62365	0.869;0.951;0.991	P;P;D	0.72625	0.775;0.701;0.978	T	0.78378	-0.2227	9	0.87932	D	0	.	20.3926	0.98949	0.1295:0.0:0.8705:0.0	.	559;528;542	P14866;B2R959;Q6NTA2	HNRPL_HUMAN;.;.	V	559;426;426	.	ENSP00000221419:L559V	L	-	1	2	HNRNPL	44019900	0.981000	0.34729	0.133000	0.22050	0.921000	0.55340	1.881000	0.39638	-0.563000	0.06078	-0.302000	0.09304	CTG	.	.		0.522	HNRNPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462670.1			C	39328060	G	C	39328060	3	2	252	1	0	0	0	0	1	0	0	0	7279	933	33	4	102	4	HNRNPL	19	39328060	Missense_Mutation	SNP	G	TCGA-EP-A12J-01A-11D-A12Z-10	1448848	39328060	19800923	61	34196										
OSCAR	126014	hgsc.bcm.edu	37	chr19	54602893	54602893	+	Intron	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	gtactcacctataatggccaCtaaggggaatgagaaaagaa	10	7	1	2			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr19:54602893C>A	ENST00000284648.6	-	3	268				OSCAR_ENST00000359649.4_Splice_Site|OSCAR_ENST00000351806.4_Intron|OSCAR_ENST00000391761.1_Intron|OSCAR_ENST00000356532.3_Splice_Site|OSCAR_ENST00000358375.4_Intron|OSCAR_ENST00000391760.1_Intron			Q8IYS5	OSCAR_HUMAN	osteoclast associated, immunoglobulin-like receptor							extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				large_intestine(1)|skin(1)	2	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)					ataatgGCCACTAAGgggaat	0.428																																					.		Atlas-SNP	.											.	OSCAR	22	.	0			c.71-1G>T						.						86	81	83					19																	54602893		2203	4300	6503	SO:0001627	intron_variant	126014	exon4			TGGCCACTAAGGG	AK130199	CCDS12873.1, CCDS12874.1, CCDS12875.1, CCDS12876.1, CCDS62789.1, CCDS74444.1	19q13.42	2013-01-29			ENSG00000170909	ENSG00000170909		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29960	protein-coding gene	gene with protein product		606862				11805147	Standard	NM_206818		Approved		uc002qda.3	Q8IYS5	OTTHUMG00000064966	ENST00000284648.6:c.70+145G>T	chr19.hg19:g.54602893C>A		44.0	0.0		117.0	50.0	NM_130771	B7WNS2|Q5GRG5|Q8N763|Q8NHL4|Q8WXQ0|Q8WXQ1|Q8WXQ2	Splice_Site	SNP	ENST00000284648.6	hg19		.	.	.	.	.	.	.	.	.	.	C	5.864	0.343657	0.11126	.	.	ENSG00000170909	ENST00000356532;ENST00000359649	.	.	.	2.17	2.17	0.27698	.	.	.	.	.	.	.	.	.	.	.	0.20403	N	0.99991	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.9473	0.29993	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	OSCAR	59294705	0.015000	0.18098	0.013000	0.15412	0.087000	0.18053	0.337000	0.19841	1.558000	0.49541	0.456000	0.33151	.	.	.		0.428	OSCAR-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000139493.4	NM_133169		A	54602893	C	A	54602893	1	1	252	0	1	0	0	0	0	0	0	0	11294	579	20	3		3	OSCAR	19	54602893	Intron	SNP	C	TCGA-EP-A12J-01A-11D-A12Z-10	15274833	54602893	4526090	62	34197										
COX4I2	84701	hgsc.bcm.edu	37	chr20	30227827	30227827	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	cccttctgcacagaactcaaCgctgaggagcaggccctgaa	10	14	2	3	rs539460095		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr20:30227827C>T	ENST00000376075.3	+	3	249	c.174C>T	c.(172-174)aaC>aaT	p.N58N	COX4I2_ENST00000490030.1_3'UTR	NM_032609.2	NP_115998.2	Q96KJ9	COX42_HUMAN	cytochrome c oxidase subunit IV isoform 2 (lung)	58					cellular respiration (GO:0045333)|generation of precursor metabolites and energy (GO:0006091)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)	mitochondrial respiratory chain complex IV (GO:0005751)	cytochrome-c oxidase activity (GO:0004129)			breast(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)	11	all_cancers(5;7.12e-06)|Lung NSC(7;3.95e-06)|all_epithelial(3;4.36e-06)|all_lung(7;6.68e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Epithelial(4;1.01e-05)|all cancers(5;9.46e-05)|OV - Ovarian serous cystadenocarcinoma(3;0.00121)|Colorectal(19;0.0055)|COAD - Colon adenocarcinoma(19;0.0264)			CAGAACTCAACGCTGAGGAGC	0.612													C|||	1	0.000199681	0	0	5008	,	,		16861	0.001		0	False		,,,				2504	0				p.N58N		Atlas-SNP	.											.	COX4I2	18	.	0			c.C174T						.						61	51	54					20																	30227827		2203	4300	6503	SO:0001819	synonymous_variant	84701	exon3			ACTCAACGCTGAG	AF257180	CCDS13187.1	20q11.21	2011-07-04	2004-08-11		ENSG00000131055	ENSG00000131055		"Mitochondrial respiratory chain complex / Complex IV"	16232	protein-coding gene	gene with protein product	"cytochrome c oxidase subunit IV-like 2"	607976	"cytochrome c oxidase subunit IV isoform 2"	COX4L2		11311561, 17937768	Standard	NM_032609		Approved	COXIV-2, COX4B, dJ857M17.2, COX4-2	uc002wwj.1	Q96KJ9	OTTHUMG00000032180	ENST00000376075.3:c.174C>T	chr20.hg19:g.30227827C>T		15.0	0.0		22.0	11.0	NM_032609	Q6GTF4|Q9H0Z4	Silent	SNP	ENST00000376075.3	hg19	CCDS13187.1																																																																																			.	.		0.612	COX4I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078548.1	NM_032609		T	30227827	C	T	30227827	2	4	252	1	0	0	0	0	0	0	0	1	3772	535	19	1		1	COX4I2	20	30227827	Silent	SNP	C	TCGA-EP-A12J-01A-11D-A12Z-10		30227827	32797693	63	34198										
TRPC4AP	26133	hgsc.bcm.edu	37	chr20	33598060	33598060	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	gatggcactgagttcattcaGctcctggttgttgagtaaca	11	8	2	2			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr20:33598060G>C	ENST00000252015.2	-	12	1530	c.1441C>G	c.(1441-1443)Ctg>Gtg	p.L481V	TRPC4AP_ENST00000432634.2_Missense_Mutation_p.L442V|TRPC4AP_ENST00000451813.2_Missense_Mutation_p.L473V|TRPC4AP_ENST00000539834.1_Missense_Mutation_p.L83V			Q8TEL6	TP4AP_HUMAN	transient receptor potential cation channel, subfamily C, member 4 associated protein	481					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|protein ubiquitination (GO:0016567)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process (GO:0006511)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|plasma membrane (GO:0005886)	phosphatase binding (GO:0019902)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|skin(1)|stomach(1)|urinary_tract(1)	32			BRCA - Breast invasive adenocarcinoma(18;0.00936)			AGTTCATTCAGCTCCTGGTTG	0.532																																					p.L481V		Atlas-SNP	.											.	TRPC4AP	64	.	0			c.C1441G						.						234	162	186					20																	33598060		2203	4300	6503	SO:0001583	missense	26133	exon12			CATTCAGCTCCTG	AF055022	CCDS13246.1, CCDS46591.1	20q11.23	2014-06-13	2003-10-06	2003-10-08	ENSG00000100991	ENSG00000100991			16181	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 158"	608430	"chromosome 20 open reading frame 188"	C20orf188			Standard	NM_015638		Approved	DKFZP727M231, DKFZp586C1223, dJ756N5.2, TRRP4AP, PPP1R158	uc002xbk.3	Q8TEL6	OTTHUMG00000032319	ENST00000252015.2:c.1441C>G	chr20.hg19:g.33598060G>C	ENSP00000252015:p.Leu481Val	106.0	0.0		277.0	107.0	NM_015638	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Missense_Mutation	SNP	ENST00000252015.2	hg19	CCDS13246.1	.	.	.	.	.	.	.	.	.	.	G	16.55	3.155652	0.57259	.	.	ENSG00000100991	ENST00000252015;ENST00000451813;ENST00000539834;ENST00000432634;ENST00000541994	.	.	.	5.67	4.72	0.59763	.	0.000000	0.85682	D	0.000000	T	0.62539	0.2436	M	0.62723	1.935	0.53688	D	0.999975	B;B;B	0.29481	0.245;0.201;0.201	B;B;B	0.35182	0.197;0.138;0.138	T	0.63497	-0.6624	9	0.52906	T	0.07	.	12.8124	0.57647	0.0758:0.0:0.9242:0.0	.	442;473;481	B4E0Q1;E1P5Q0;Q8TEL6	.;.;TP4AP_HUMAN	V	481;473;83;442;466	.	ENSP00000252015:L481V	L	-	1	2	TRPC4AP	33061721	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.846000	0.62860	1.399000	0.46721	0.555000	0.69702	CTG	.	.		0.532	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638		C	33598060	G	C	33598060	3	2	252	1	0	0	0	0	1	0	0	0	16596	962	34	4	984	4	TRPC4AP	20	33598060	Missense_Mutation	SNP	G	TCGA-EP-A12J-01A-11D-A12Z-10	3370233	33598060	29427460	64	34199										
LCA5L	150082	hgsc.bcm.edu	37	chr21	40800132	40800132	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	attttagaaacattatacttTttcttctccttttcttttac	1	8	3	1			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr21:40800132T>C	ENST00000358268.2	-	4	816	c.288A>G	c.(286-288)aaA>aaG	p.K96K	LCA5L_ENST00000485895.2_Silent_p.K96K|LCA5L_ENST00000288350.3_Silent_p.K96K|LCA5L_ENST00000380671.2_Silent_p.K96K			O95447	LCA5L_HUMAN	Leber congenital amaurosis 5-like	96										breast(1)|cervix(1)|endometrium(3)|large_intestine(8)|lung(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	24		Prostate(19;1.2e-06)				CATTATACTTTTTCTTCTCCT	0.313																																					p.K96K		Atlas-SNP	.											.	LCA5L	57	.	0			c.A288G						.						57	63	61					21																	40800132		2201	4297	6498	SO:0001819	synonymous_variant	150082	exon4			ATACTTTTTCTTC	AF121781	CCDS13665.1	21q22.2	2007-12-18	2007-12-18	2007-12-18	ENSG00000157578	ENSG00000157578			1255	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 13"	C21orf13			Standard	XM_005260926		Approved	MGC33295	uc002yxu.3	O95447	OTTHUMG00000066280	ENST00000358268.2:c.288A>G	chr21.hg19:g.40800132T>C		109.0	0.0		303.0	123.0	NM_152505	D3DSI0|Q3ZCT0	Silent	SNP	ENST00000358268.2	hg19	CCDS13665.1																																																																																			.	.		0.313	LCA5L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141807.2	NM_152505		C	40800132	T	C	40800132	2	2	252	1	0	0	0	0	0	0	0	1	8666	1838	64	2		2	LCA5L	21	40800132	Silent	SNP	T	TCGA-EP-A12J-01A-11D-A12Z-10		40800132	7329763	65	34200										
PCNT	5116	hgsc.bcm.edu	37	chr21	47773060	47773060	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	gcgcacctctcgtgtggaagAtttagaacagctgaagcagc	12	10	1	3			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr21:47773060A>G	ENST00000359568.5	+	10	1606	c.1499A>G	c.(1498-1500)gAt>gGt	p.D500G	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	500	Glu-rich.				brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					CGTGTGGAAGATTTAGAACAG	0.473																																					p.D500G		Atlas-SNP	.											.	PCNT	283	.	0			c.A1499G						.						56	60	59					21																	47773060		2203	4300	6503	SO:0001583	missense	5116	exon10			TGGAAGATTTAGA	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"kendrin", "Seckel syndrome 4"	605925	"pericentrin 2 (kendrin)"	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.1499A>G	chr21.hg19:g.47773060A>G	ENSP00000352572:p.Asp500Gly	56.0	0.0		92.0	25.0	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	hg19	CCDS33592.1	.	.	.	.	.	.	.	.	.	.	A	12.10	1.836279	0.32421	.	.	ENSG00000160299	ENST00000359568;ENST00000337772	T	0.02709	4.19	4.68	4.68	0.58851	.	.	.	.	.	T	0.03564	0.0102	L	0.43152	1.355	0.32642	N	0.520569	P;P	0.38978	0.531;0.652	B;B	0.32762	0.152;0.073	T	0.18116	-1.0347	9	0.56958	D	0.05	.	13.3185	0.60421	1.0:0.0:0.0:0.0	.	382;500	O95613-2;O95613	.;PCNT_HUMAN	G	500;487	ENSP00000352572:D500G	ENSP00000338675:D487G	D	+	2	0	PCNT	46597488	0.999000	0.42202	0.024000	0.17045	0.011000	0.07611	4.493000	0.60341	1.732000	0.51606	0.460000	0.39030	GAT	.	.		0.473	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031		G	47773060	A	G	47773060	3	3	252	1	0	0	0	0	1	0	0	0	11599	333	12	2	1537	2	PCNT	21	47773060	Missense_Mutation	SNP	A	TCGA-EP-A12J-01A-11D-A12Z-10	6972928	47773060	356835	66	34201										
NEFH	4744	hgsc.bcm.edu	37	chr22	29885573	29885574	+	In_Frame_Ins	INS	-	-	CCTGAGAAGGCCAAGTCC													0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	cgaaggaggaagcaaagtccINScctgagaaggccaagtcccc					rs541596221		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr22:29885573_29885574insCCTGAGAAGGCCAAGTCC	ENST00000310624.6	+	4	1977_1978	c.1944_1945insCCTGAGAAGGCCAAGTCC	c.(1945-1947)cct>CCTGAGAAGGCCAAGTCCcct	p.649_649P>PEKAKSP		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	655	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.			Missing (in Ref. 1; CAA33366 and 5; AC000035). {ECO:0000305}.	axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AAGCAAAGTCCCCTGAGAAGGC	0.569																																					p.S648delinsSPEKAKS		Atlas-INDEL	.											.	NEFH	178	.	0			c.1944_1945insCCTGAGAAGGCCAAGTCC						.																																			SO:0001652	inframe_insertion	4744	exon4			.		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1945_1962dupCCTGAGAAGGCCAAGTCC	chr22.hg19:g.29885573_29885574insCCTGAGAAGGCCAAGTCC	Exception_encountered	46.0	0.0		152.0	19.0	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Ins	INS	ENST00000310624.6	hg19	CCDS13858.1																																																																																			.	.		0.569	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		CCTGAGAAGGCCAAGTCC	29885574	-	CCTGAGAAGGCCAAGTCC	29885573	7	5	252	1	0	1	1	0	0	0	0	0	10323	610	22	0	1958	0	NEFH	22	29885573	In_Frame_Ins	INS	-	TCGA-EP-A12J-01A-11D-A12Z-10		29885573	21418993	67	34202										
C22orf30	253143	hgsc.bcm.edu	37	chr22	32111160	32111160	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	gctactggaggtgtgaatggTtttgtttgaaattccactat	11	5	0	2			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr22:32111160T>G	ENST00000327423.6	-	4	2854	c.2665A>C	c.(2665-2667)Acc>Ccc	p.T889P	PRR14L_ENST00000461722.1_5'Flank|PRR14L_ENST00000397493.2_Missense_Mutation_p.T889P|PRR14L_ENST00000434485.1_Missense_Mutation_p.T889P	NM_173566.2	NP_775837.2	Q5THK1	PR14L_HUMAN	proline rich 14-like	889										endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(5)|skin(1)|urinary_tract(2)	14						GTGTGAATGGTTTTGTTTGAA	0.408																																					p.T889P		Atlas-SNP	.											.	PRR14L	198	.	0			c.A2665C						.						199	149	164					22																	32111160		692	1591	2283	SO:0001583	missense	253143	exon4			GAATGGTTTTGTT	BC040859	CCDS13900.2	22q12.2	2011-01-25	2011-01-25	2011-01-25	ENSG00000183530	ENSG00000183530			28738	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 30"	C22orf30		12477932	Standard	NM_173566		Approved	MGC50372	uc003alp.4	Q5THK1	OTTHUMG00000030139	ENST00000327423.6:c.2665A>C	chr22.hg19:g.32111160T>G	ENSP00000331845:p.Thr889Pro	123.0	0.0		438.0	208.0	NM_173566	Q5THK4|Q6ZNN1|Q6ZWH0|Q8IW74|Q9H5T4	Missense_Mutation	SNP	ENST00000327423.6	hg19	CCDS13900.2	.	.	.	.	.	.	.	.	.	.	T	11.09	1.536073	0.27475	.	.	ENSG00000183530	ENST00000397493;ENST00000327423;ENST00000434485	T;T;T	0.06849	3.25;3.26;3.25	5.36	-1.29	0.09288	.	0.425905	0.19729	N	0.107386	T	0.06188	0.0160	L	0.47716	1.5	0.09310	N	1	P;B;P	0.35656	0.514;0.226;0.514	B;B;B	0.34138	0.176;0.176;0.176	T	0.29397	-1.0013	9	.	.	.	1.1631	4.9926	0.14222	0.1423:0.3861:0.0:0.4716	.	889;889;889	Q5THK1-2;Q5THK1;Q5THK1-4	.;PR14L_HUMAN;.	P	889	ENSP00000380630:T889P;ENSP00000331845:T889P;ENSP00000388314:T889P	.	T	-	1	0	PRR14L	30441160	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-0.068000	0.11561	-0.326000	0.08564	-0.263000	0.10527	ACC	.	.		0.408	PRR14L-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074993.2	NM_173566		G	32111160	T	G	32111160	3	3	252	1	0	0	0	0	1	0	0	0	2144	1725	60	5	3814	5	C22orf30	22	32111160	Missense_Mutation	SNP	T	TCGA-EP-A12J-01A-11D-A12Z-10	2225587	32111160	19193406	68	34203										
CRELD2	79174	hgsc.bcm.edu	37	chr22	50315943	50315980	+	Intron	DEL	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	-													0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	cgattcttacgcccctcagcAgtcaggaccggcctctccga					rs377640443|rs562885075|rs542695980|rs113299196|rs7410276|rs12160965|rs386822607|rs386822606|rs564615833|rs368043307|rs71805922|rs386822608|rs73891177	byFrequency	TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr22:50315943_50315980delCCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	ENST00000328268.4	+	6	666				CRELD2_ENST00000403427.3_Intron|CRELD2_ENST00000404488.3_Splice_Site_p.PQQSGPASPILTR198fs|CRELD2_ENST00000407217.3_Intron|CRELD2_ENST00000444954.1_Intron	NM_024324.3	NP_077300.3	Q6UXH1	CREL2_HUMAN	cysteine-rich with EGF-like domains 2							endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|stomach(3)	9		all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.198)|LUAD - Lung adenocarcinoma(64;0.247)		GCCCCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCGCCTTGCTGTCTGTCTCT	0.618																																					p.198_207del		Atlas-Indel,Pindel	.											.	CRELD2	57	.	0			c.593_620del						.																																			SO:0001627	intron_variant	79174	exon6			.	BC050675	CCDS14082.1, CCDS46730.1, CCDS63515.1, CCDS63516.1	22q13.33	2005-12-08			ENSG00000184164	ENSG00000184164			28150	protein-coding gene	gene with protein product		607171				12137942	Standard	XM_005261737		Approved	MGC11256	uc010hal.2	Q6UXH1	OTTHUMG00000150292	ENST00000328268.4:c.593-280CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG>-	chr22.hg19:g.50315943_50315980delCCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG		33.0	0.0		77.0	23.0	NM_001135101	A5GZA2|A5GZA3|A5GZA4|A5GZA5|A5GZA6|Q4W0V0|Q86UC0|Q9BU47	Frame_Shift_Del	DEL	ENST00000328268.4	hg19	CCDS14082.1																																																																																			.	.		0.618	CRELD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317409.1	NM_024324		-	50315980	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	-	50315943	6	5	252	0	1	1	0	1	0	0	0	0	3869	202	7	0		0	CRELD2	22	50315943	Intron	DEL	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	TCGA-EP-A12J-01A-11D-A12Z-10	18204783	50315943	988623	69	34204										
PNMA3	29944	hgsc.bcm.edu	37	chrX	152225435	152225435	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0597014925373134	4	1	1.05853658536585	1.65396341463415	0.945121951219512	0.545454545454546	1	0	gccgttgaccttgttacaggActggtgtcggggggaacacc	15	10	0	1			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chrX:152225435A>G	ENST00000370264.4	+	1	49	c.23A>G	c.(22-24)gAc>gGc	p.D8G	PNMA3_ENST00000447306.1_Missense_Mutation_p.D8G|PNMA3_ENST00000370265.4_Missense_Mutation_p.D8G			Q9UL41	PNMA3_HUMAN	paraneoplastic Ma antigen 3	8					positive regulation of apoptotic process (GO:0043065)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)	16	Acute lymphoblastic leukemia(192;6.56e-05)					ttgttacaggactggtgtcgg	0.567																																					p.D8G		Atlas-SNP	.											.	PNMA3	81	.	0			c.A23G						.						111	87	95					X																	152225435		2203	4300	6503	SO:0001583	missense	29944	exon2			TACAGGACTGGTG	AF083116	CCDS35435.2, CCDS65344.1	Xq28	2012-02-09	2012-02-09		ENSG00000183837	ENSG00000183837		"Paraneoplastic Ma antigens"	18742	protein-coding gene	gene with protein product	"paraneoplastic cancer-testis-brain antigen"	300675	"paraneoplastic antigen MA3"			11558790	Standard	NM_013364		Approved	MA5, MA3, MGC132756, MGC132758	uc004fhc.2	Q9UL41	OTTHUMG00000024195	ENST00000370264.4:c.23A>G	chrX.hg19:g.152225435A>G	ENSP00000359286:p.Asp8Gly	40.0	0.0		117.0	104.0	NM_013364	D3DWT7|Q9H0A4	Missense_Mutation	SNP	ENST00000370264.4	hg19	CCDS35435.2	.	.	.	.	.	.	.	.	.	.	a	14.75	2.627457	0.46944	.	.	ENSG00000183837	ENST00000370265;ENST00000447306;ENST00000370264	T;T;T	0.31769	1.48;1.48;1.48	1.93	1.93	0.25924	.	.	.	.	.	T	0.49660	0.1570	M	0.75085	2.285	0.20703	N	0.999864	D	0.89917	1.0	D	0.91635	0.999	T	0.22730	-1.0208	9	0.72032	D	0.01	.	5.3241	0.15896	1.0:0.0:0.0:0.0	.	8	Q9UL41	PNMA3_HUMAN	G	8	ENSP00000359288:D8G;ENSP00000407642:D8G;ENSP00000359286:D8G	ENSP00000359286:D8G	D	+	2	0	PNMA3	151976091	0.998000	0.40836	0.468000	0.27192	0.004000	0.04260	1.432000	0.34936	1.028000	0.39785	0.336000	0.21669	GAC	.	.		0.567	PNMA3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060946.2	NM_013364		G	152225435	A	G	152225435	3	3	252	1	0	0	0	0	1	0	0	0	12164	275	10	2	25	2	PNMA3	23	152225435	Missense_Mutation	SNP	A	TCGA-EP-A12J-01A-11D-A12Z-10		152225435	3045125	70	34205										
OR10Z1	128368	hgsc.bcm.edu	37	chr1	158576688	158576688	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	cttccttcctgactggatacCtctttggactgggaatgaca	9	11	1	2			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr1:158576688C>T	ENST00000361284.1	+	1	460	c.460C>T	c.(460-462)Ctc>Ttc	p.L154F		NM_001004478.1	NP_001004478.1	Q8NGY1	O10Z1_HUMAN	olfactory receptor, family 10, subfamily Z, member 1	154						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(6)|lung(21)|pancreas(1)|prostate(3)|skin(4)	37	all_hematologic(112;0.0378)					GACTGGATACCTCTTTGGACT	0.498																																					p.L154F		Atlas-SNP	.											.	OR10Z1	99	.	0			c.C460T						.						105	100	102					1																	158576688		2203	4300	6503	SO:0001583	missense	128368	exon1			GGATACCTCTTTG	AB065635	CCDS30901.1	1q23.1	2012-08-23			ENSG00000198967	ENSG00000198967		"GPCR / Class A : Olfactory receptors"	14996	protein-coding gene	gene with protein product							Standard	NM_001004478		Approved		uc010pio.2	Q8NGY1	OTTHUMG00000019637	ENST00000361284.1:c.460C>T	chr1.hg19:g.158576688C>T	ENSP00000354707:p.Leu154Phe	135.0	0.0		171.0	44.0	NM_001004478	Q5VYL0|Q6IFR7	Missense_Mutation	SNP	ENST00000361284.1	hg19	CCDS30901.1	.	.	.	.	.	.	.	.	.	.	C	0.519	-0.862988	0.02610	.	.	ENSG00000198967	ENST00000361284	T	0.46451	0.87	5.36	-1.87	0.07737	GPCR, rhodopsin-like superfamily (1);	0.887851	0.09141	N	0.843040	T	0.10337	0.0253	L	0.31752	0.955	0.09310	N	1	B	0.10296	0.003	B	0.20577	0.03	T	0.35699	-0.9778	10	0.33940	T	0.23	.	4.9305	0.13914	0.2362:0.287:0.0:0.4769	.	154	Q8NGY1	O10Z1_HUMAN	F	154	ENSP00000354707:L154F	ENSP00000354707:L154F	L	+	1	0	OR10Z1	156843312	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.264000	0.02847	-0.522000	0.06417	-0.982000	0.02568	CTC	.	.		0.498	OR10Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051853.1	NM_001004478		T	158576688	C	T	158576688	3	4	253	1	0	0	0	0	1	0	0	0	10932	681	24	3	462	3	OR10Z1	1	158576688	Missense_Mutation	SNP	C	TCGA-EP-A26S-01A-11D-A16V-10		158576688	90673933	1	34206										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158605719	158605719	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	tcaccgggccttggccaactCtttgagcttctcccagtgtt	9	14	3	1			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr1:158605719C>G	ENST00000368147.4	-	38	5596	c.5416G>C	c.(5416-5418)Gag>Cag	p.E1806Q		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1806					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TTGGCCAACTCTTTGAGCTTC	0.537																																					p.E1806Q		Atlas-SNP	.											.	SPTA1	720	.	0			c.G5416C						.						90	93	92					1																	158605719		1942	4139	6081	SO:0001583	missense	6708	exon38			CCAACTCTTTGAG	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.5416G>C	chr1.hg19:g.158605719C>G	ENSP00000357129:p.Glu1806Gln	48.0	0.0		72.0	55.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	C	11.09	1.536202	0.27475	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.51574	0.7;0.7	5.65	3.8	0.43715	.	0.266274	0.19779	N	0.106267	T	0.19765	0.0475	L	0.59967	1.855	0.32110	N	0.589433	B	0.30973	0.302	B	0.30401	0.115	T	0.09228	-1.0684	10	0.12766	T	0.61	.	7.8794	0.29614	0.0:0.7181:0.1338:0.1481	.	1806	P02549	SPTA1_HUMAN	Q	1806	ENSP00000357130:E1806Q;ENSP00000357129:E1806Q	ENSP00000357129:E1806Q	E	-	1	0	SPTA1	156872343	0.998000	0.40836	0.998000	0.56505	0.993000	0.82548	3.002000	0.49496	0.944000	0.37579	0.655000	0.94253	GAG	.	.		0.537	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		G	158605719	C	G	158605719	3	3	253	1	0	0	0	0	1	0	0	0	15131	922	32	4	1903	4	SPTA1	1	158605719	Missense_Mutation	SNP	C	TCGA-EP-A26S-01A-11D-A16V-10	29031	158605719	90644902	2	34207										
OR6K2	81448	hgsc.bcm.edu	37	chr1	158670099	158670099	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	agtggtcaaaggccataactGtcaagagacacacctcacag	9	11	3	1			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr1:158670099G>C	ENST00000359610.2	-	1	387	c.344C>G	c.(343-345)aCa>aGa	p.T115R		NM_001005279.1	NP_001005279.1	Q8NGY2	OR6K2_HUMAN	olfactory receptor, family 6, subfamily K, member 2	115						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	46	all_hematologic(112;0.0378)					GGCCATAACTGTCAAGAGACA	0.478																																					p.T115R		Atlas-SNP	.											.	OR6K2	104	.	0			c.C344G						.						112	102	105					1																	158670099		2203	4300	6503	SO:0001583	missense	81448	exon1			ATAACTGTCAAGA	BK004196	CCDS30902.1	1q23.1	2012-08-09			ENSG00000196171	ENSG00000196171		"GPCR / Class A : Olfactory receptors"	15029	protein-coding gene	gene with protein product							Standard	NM_001005279		Approved		uc001fsu.1	Q8NGY2	OTTHUMG00000022768	ENST00000359610.2:c.344C>G	chr1.hg19:g.158670099G>C	ENSP00000352626:p.Thr115Arg	90.0	0.0		103.0	56.0	NM_001005279	B9EH33|Q6IFR6	Missense_Mutation	SNP	ENST00000359610.2	hg19	CCDS30902.1	.	.	.	.	.	.	.	.	.	.	G	17.83	3.484518	0.63962	.	.	ENSG00000196171	ENST00000359610	T	0.01359	4.98	4.7	3.76	0.43208	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39341	N	0.001389	T	0.05914	0.0154	H	0.95224	3.64	0.31333	N	0.684559	D	0.60575	0.988	P	0.59825	0.864	T	0.00918	-1.1515	10	0.87932	D	0	-4.7894	12.2266	0.54463	0.0863:0.0:0.9137:0.0	.	115	Q8NGY2	OR6K2_HUMAN	R	115	ENSP00000352626:T115R	ENSP00000352626:T115R	T	-	2	0	OR6K2	156936723	0.009000	0.17119	1.000000	0.80357	0.973000	0.67179	1.689000	0.37700	2.413000	0.81919	0.650000	0.86243	ACA	.	.		0.478	OR6K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059061.1	NM_001005279		C	158670099	G	C	158670099	3	2	253	1	0	0	0	0	1	0	0	0	11211	1377	48	4	634	4	OR6K2	1	158670099	Missense_Mutation	SNP	G	TCGA-EP-A26S-01A-11D-A16V-10	64380	158670099	90580522	3	34208										
DCAF6	55827	hgsc.bcm.edu	37	chr1	167971772	167971772	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	tcgtggtgattggtcagataCtggacccagagcaaggccgg	15	9	1	3			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr1:167971772C>T	ENST00000312263.6	+	8	1160	c.956C>T	c.(955-957)aCt>aTt	p.T319I	DCAF6_ENST00000432587.2_Missense_Mutation_p.T288I|DCAF6_ENST00000367843.3_Missense_Mutation_p.T319I|DCAF6_ENST00000367840.3_Missense_Mutation_p.T319I	NM_001017977.2	NP_001017977.1	Q58WW2	DCAF6_HUMAN	DDB1 and CUL4 associated factor 6	319					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	36						TGGTCAGATACTGGACCCAGA	0.373																																					p.T319I		Atlas-SNP	.											.	DCAF6	99	.	0			c.C956T						.						153	154	154					1																	167971772		2203	4300	6503	SO:0001583	missense	55827	exon8			CAGATACTGGACC	AL136738	CCDS1267.2, CCDS30933.1, CCDS55657.1, CCDS55658.1	1q23.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000143164	ENSG00000143164		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	30002	protein-coding gene	gene with protein product		610494	"IQ motif and WD repeats 1"	IQWD1		12032826	Standard	NM_018442		Approved	PC326	uc001gex.3	Q58WW2	OTTHUMG00000034572	ENST00000312263.6:c.956C>T	chr1.hg19:g.167971772C>T	ENSP00000311949:p.Thr319Ile	234.0	0.0		237.0	64.0	NM_001198956	A2A295|B4DNB8|Q7L8I0|Q8IXH3|Q8TB19	Missense_Mutation	SNP	ENST00000312263.6	hg19	CCDS30933.1	.	.	.	.	.	.	.	.	.	.	C	32	5.183393	0.94885	.	.	ENSG00000143164	ENST00000367843;ENST00000432587;ENST00000312263;ENST00000367840	D;T;D;D	0.84660	-1.8;-0.17;-1.79;-1.88	5.56	5.56	0.83823	WD40 repeat-like-containing domain (1);	0.048107	0.85682	D	0.000000	D	0.91640	0.7358	M	0.74647	2.275	0.45076	D	0.998099	D;D;D;D	0.76494	0.999;0.999;0.994;0.997	D;D;P;D	0.78314	0.991;0.972;0.836;0.914	D	0.91405	0.5146	9	0.66056	D	0.02	.	19.8925	0.96935	0.0:1.0:0.0:0.0	.	288;319;319;319	B4DNB8;Q58WW2-3;Q58WW2;Q58WW2-2	.;.;DCAF6_HUMAN;.	I	319;288;319;319	ENSP00000356817:T319I;ENSP00000396238:T288I;ENSP00000311949:T319I;ENSP00000356814:T319I	ENSP00000311949:T319I	T	+	2	0	DCAF6	166238396	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.890000	0.75633	2.787000	0.95880	0.650000	0.86243	ACT	.	.		0.373	DCAF6-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083661.2	NM_018442		T	167971772	C	T	167971772	3	4	253	1	0	0	0	0	1	0	0	0	4276	565	20	3	986	3	DCAF6	1	167971772	Missense_Mutation	SNP	C	TCGA-EP-A26S-01A-11D-A16V-10	9301673	167971772	81278849	4	34209										
C1orf14	81626	hgsc.bcm.edu	37	chr1	182873386	182873386	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	aacacacactcctgttccttCacattttaatatgcagtttt	3	11	1	0			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr1:182873386C>T	ENST00000367547.3	-	8	1752	c.1516G>A	c.(1516-1518)Gaa>Aaa	p.E506K	SHCBP1L_ENST00000488956.1_5'UTR|SHCBP1L_ENST00000423786.1_Missense_Mutation_p.E387K	NM_030933.2	NP_112195.2	Q9BZQ2	SHP1L_HUMAN	SHC SH2-domain binding protein 1-like	578										breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|pancreas(1)|prostate(1)|skin(2)	15						CCTGTTCCTTCACATTTTAAT	0.413																																					p.E506K		Atlas-SNP	.											.	SHCBP1L	64	.	0			c.G1516A						.						157	153	154					1																	182873386		2203	4300	6503	SO:0001583	missense	81626	exon8			TTCCTTCACATTT	AF288397	CCDS30955.1	1q25	2011-01-24	2011-01-24	2011-01-24	ENSG00000157060	ENSG00000157060			16788	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 14"	C1orf14		11318611	Standard	NM_030933		Approved		uc001gpu.3	Q9BZQ2	OTTHUMG00000035419	ENST00000367547.3:c.1516G>A	chr1.hg19:g.182873386C>T	ENSP00000356518:p.Glu506Lys	75.0	0.0		111.0	24.0	NM_030933	Q4G195|Q9BZQ3|Q9H2B6	Missense_Mutation	SNP	ENST00000367547.3	hg19	CCDS30955.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.664124	0.88251	.	.	ENSG00000157060	ENST00000367547;ENST00000287709;ENST00000423786	T;T	0.41065	1.01;1.01	5.55	5.55	0.83447	Pectin lyase fold/virulence factor (1);Carbohydrate-binding/sugar hydrolysis domain (1);Pectin lyase fold (1);	0.000000	0.64402	D	0.000014	T	0.57770	0.2076	L	0.47190	1.495	0.39150	D	0.962202	D;D;D	0.71674	0.998;0.991;0.998	D;P;D	0.79108	0.992;0.86;0.986	T	0.55786	-0.8086	10	0.38643	T	0.18	-27.4096	16.4312	0.83844	0.0:1.0:0.0:0.0	.	578;387;506	Q9BZQ2;Q9BZQ2-2;Q9BZQ2-3	SHP1L_HUMAN;.;.	K	506;575;387	ENSP00000356518:E506K;ENSP00000397308:E387K	ENSP00000287709:E575K	E	-	1	0	SHCBP1L	181140009	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.085000	0.64468	2.618000	0.88619	0.655000	0.94253	GAA	.	.		0.413	SHCBP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085956.1	NM_030933		T	182873386	C	T	182873386	3	4	253	1	0	0	0	0	1	0	0	0	2002	835	29	3	457	3	C1orf14	1	182873386	Missense_Mutation	SNP	C	TCGA-EP-A26S-01A-11D-A16V-10	14901614	182873386	66377235	5	34210										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186097385	186097385	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	agctactggtattccattgcCcaaattaacatggaccttca	6	11	1	0			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr1:186097385C>T	ENST00000271588.4	+	83	13095	c.12866C>T	c.(12865-12867)cCc>cTc	p.P4289L	HMCN1_ENST00000367492.2_Missense_Mutation_p.P4289L	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	4289	Ig-like C2-type 42.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						ATTCCATTGCCCAAATTAACA	0.378																																					p.P4289L		Atlas-SNP	.											.	HMCN1	797	.	0			c.C12866T						.						89	84	86					1																	186097385		2203	4300	6503	SO:0001583	missense	83872	exon83			CATTGCCCAAATT	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.12866C>T	chr1.hg19:g.186097385C>T	ENSP00000271588:p.Pro4289Leu	37.0	0.0		57.0	23.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	C	29.4	5.000600	0.93227	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.71461	-0.57;-0.57	5.36	5.36	0.76844	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.89150	0.6633	H	0.96518	3.835	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89548	0.3797	10	0.27785	T	0.31	.	19.0722	0.93143	0.0:1.0:0.0:0.0	.	4289	Q96RW7	HMCN1_HUMAN	L	4289	ENSP00000271588:P4289L;ENSP00000356462:P4289L	ENSP00000271588:P4289L	P	+	2	0	HMCN1	184364008	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.469000	0.80959	2.502000	0.84385	0.585000	0.79938	CCC	.	.		0.378	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		T	186097385	C	T	186097385	3	4	253	1	0	0	0	0	1	0	0	0	7229	623	22	3	13196	3	HMCN1	1	186097385	Missense_Mutation	SNP	C	TCGA-EP-A26S-01A-11D-A16V-10	3223999	186097385	63153236	6	34211										
MAPKAPK2	9261	hgsc.bcm.edu	37	chr1	206902164	206902166	+	In_Frame_Del	DEL	GGA	GGA	-													0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	gtacgagaatctgtacgcagGgaggaagtgcctgctgattg							TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr1:206902164_206902166delGGA	ENST00000367103.3	+	2	582_584	c.389_391delGGA	c.(388-393)gggagg>ggg	p.R131del	MAPKAPK2_ENST00000294981.4_In_Frame_Del_p.R131del	NM_004759.4|NM_032960.3	NP_004750.1|NP_116584.2	P49137	MAPK2_HUMAN	mitogen-activated protein kinase-activated protein kinase 2	131	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|activation of MAPK activity (GO:0000187)|arachidonic acid metabolic process (GO:0019369)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|G2 DNA damage checkpoint (GO:0031572)|gene expression (GO:0010467)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|leukotriene metabolic process (GO:0006691)|macropinocytosis (GO:0044351)|MAPK cascade (GO:0000165)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of interleukin-6 production (GO:0032675)|regulation of tumor necrosis factor production (GO:0032680)|response to cytokine (GO:0034097)|response to lipopolysaccharide (GO:0032496)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	19	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.211)			CTGTACGCAGGGAGGAAGTGCCT	0.611																																					p.130_130del		Atlas-Indel,Pindel	.											.	MAPKAPK2	45	.	0			c.388_390del						.																																			SO:0001651	inframe_deletion	9261	exon2			.	U12779	CCDS1466.1, CCDS31001.1	1q32	2008-02-05			ENSG00000162889	ENSG00000162889			6887	protein-coding gene	gene with protein product		602006				8179591, 8280084	Standard	NM_004759		Approved		uc001hem.2	P49137	OTTHUMG00000036342	ENST00000367103.3:c.389_391delGGA	chr1.hg19:g.206902167_206902169delGGA	ENSP00000356070:p.Arg131del	73.0	0.0		62.0	15.0	NM_004759	Q5SY30|Q5SY41|Q8IYD6	In_Frame_Del	DEL	ENST00000367103.3	hg19	CCDS31001.1																																																																																			.	.		0.611	MAPKAPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088465.1	NM_004759		-	206902166	GGA	-	206902164	7	5	253	1	0	1	0	1	0	0	0	0	9298	1232	43	0	395	0	MAPKAPK2	1	206902164	In_Frame_Del	DEL	GGA	TCGA-EP-A26S-01A-11D-A16V-10	20804779	206902164	42348457	7	34212										
IFT172	26160	hgsc.bcm.edu	37	chr2	27688641	27688641	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	gttgccatcatcaatggctgTtccaaactcgatgaggccct	9	12	2	1			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr2:27688641T>G	ENST00000260570.3	-	17	1904	c.1801A>C	c.(1801-1803)Aca>Cca	p.T601P		NM_015662.1	NP_056477.1	Q9UG01	IF172_HUMAN	intraflagellar transport 172	601					bone development (GO:0060348)|brain development (GO:0007420)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|epidermis development (GO:0008544)|heart looping (GO:0001947)|hindgut development (GO:0061525)|left/right axis specification (GO:0070986)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)	axoneme (GO:0005930)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|sperm midpiece (GO:0097225)|sperm principal piece (GO:0097228)|vesicle (GO:0031982)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(17)|lung(17)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	43	Acute lymphoblastic leukemia(172;0.155)					TCAATGGCTGTTCCAAACTCG	0.567																																					p.T601P		Atlas-SNP	.											.	IFT172	119	.	0			c.A1801C						.						389	367	375					2																	27688641		2203	4300	6503	SO:0001583	missense	26160	exon17			TGGCTGTTCCAAA	AB033005	CCDS1755.1	2p23.3	2014-07-03	2014-07-03		ENSG00000138002	ENSG00000138002		"Intraflagellar transport homologs", "WD repeat domain containing"	30391	protein-coding gene	gene with protein product	"wimple homolog"	607386	"intraflagellar transport 172 homolog (Chlamydomonas)"			10788441, 10574461, 24140113	Standard	XM_005264254		Approved	SLB, wim, osm-1, NPHP17	uc002rku.3	Q9UG01	OTTHUMG00000128425	ENST00000260570.3:c.1801A>C	chr2.hg19:g.27688641T>G	ENSP00000260570:p.Thr601Pro	75.0	0.0		67.0	33.0	NM_015662	A5PKZ0|B2RNU5|Q86X44|Q96HW4|Q9UFJ9|Q9ULP1	Missense_Mutation	SNP	ENST00000260570.3	hg19	CCDS1755.1	.	.	.	.	.	.	.	.	.	.	T	31	5.065895	0.93898	.	.	ENSG00000138002	ENST00000260570	T	0.63580	-0.05	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.79215	0.4408	M	0.85373	2.75	0.80722	D	1	D	0.64830	0.994	P	0.61800	0.894	T	0.82916	-0.0220	10	0.72032	D	0.01	-10.8715	14.679	0.69004	0.0:0.0:0.0:1.0	.	601	Q9UG01	IF172_HUMAN	P	601	ENSP00000260570:T601P	ENSP00000260570:T601P	T	-	1	0	IFT172	27542145	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.281000	0.78621	2.157000	0.67596	0.533000	0.62120	ACA	.	.		0.567	IFT172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250213.2	NM_015662		G	27688641	T	G	27688641	3	3	253	1	0	0	0	0	1	0	0	0	7566	1725	60	5	3576	5	IFT172	2	27688641	Missense_Mutation	SNP	T	TCGA-EP-A26S-01A-11D-A16V-10		27688641	215510732	8	34213										
ABCG8	64241	hgsc.bcm.edu	37	chr2	44099245	44099245	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	tttctatggaaagcagagacGaaggatcttgacgaggacac	12	7	2	2			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr2:44099245G>T	ENST00000272286.2	+	7	1185	c.1095G>T	c.(1093-1095)acG>acT	p.T365T		NM_022437.2	NP_071882.1	Q9H221	ABCG8_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 8	365					ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|excretion (GO:0007588)|intestinal cholesterol absorption (GO:0030299)|negative regulation of intestinal cholesterol absorption (GO:0045796)|negative regulation of intestinal phytosterol absorption (GO:0010949)|phospholipid transport (GO:0015914)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|protein heterodimerization activity (GO:0046982)|sterol transporter activity (GO:0015248)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(21)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	45		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)			Ezetimibe(DB00973)	AAGCAGAGACGAAGGATCTTG	0.552																																					p.T365T		Atlas-SNP	.											.	ABCG8	98	.	0			c.G1095T						.						119	116	117					2																	44099245		2203	4300	6503	SO:0001819	synonymous_variant	64241	exon7			AGAGACGAAGGAT	AF320294	CCDS1815.1	2p21	2012-03-14	2008-07-31		ENSG00000143921	ENSG00000143921		"ATP binding cassette transporters / subfamily G"	13887	protein-coding gene	gene with protein product	"gallbladder disease 4", "sterolin 2"	605460	"ATP-binding cassette, sub-family G (WHITE), member 8 (sterolin 2)"			11099417, 17626266	Standard	NM_022437		Approved	GBD4	uc002rtq.3	Q9H221	OTTHUMG00000128756	ENST00000272286.2:c.1095G>T	chr2.hg19:g.44099245G>T		61.0	0.0		75.0	31.0	NM_022437	Q53QN8	Silent	SNP	ENST00000272286.2	hg19	CCDS1815.1																																																																																			.	.		0.552	ABCG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250671.1	NM_022437		T	44099245	G	T	44099245	2	4	253	1	0	0	0	0	0	0	0	1	72	1045	37	1		1	ABCG8	2	44099245	Silent	SNP	G	TCGA-EP-A26S-01A-11D-A16V-10	16410604	44099245	199100128	9	34214										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168100450	168100450	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	ggatgtttgaaacccagccaTtagacattctaaaagaagtt	8	7	1	3			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr2:168100450T>C	ENST00000409195.1	+	9	2637	c.2548T>C	c.(2548-2550)Tta>Cta	p.L850L	XIRP2_ENST00000409273.1_Silent_p.L628L|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000295237.9_Silent_p.L850L|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	675					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AACCCAGCCATTAGACATTCT	0.368																																					p.L850L		Atlas-SNP	.											.	XIRP2	914	.	0			c.T2548C						.						106	105	105					2																	168100450		1837	4093	5930	SO:0001819	synonymous_variant	129446	exon9			CAGCCATTAGACA	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.2548T>C	chr2.hg19:g.168100450T>C		173.0	0.0		135.0	55.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent	SNP	ENST00000409195.1	hg19	CCDS42769.1																																																																																			.	.		0.368	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		C	168100450	T	C	168100450	2	2	253	1	0	0	0	0	0	0	0	1	17445	1490	52	2		2	XIRP2	2	168100450	Silent	SNP	T	TCGA-EP-A26S-01A-11D-A16V-10	124001205	168100450	75098923	10	34215										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168104420	168104420	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	tccagtcagcatgccagttgGaggaacttacgacctttcag	10	11	2	0	rs375925351		TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr2:168104420G>T	ENST00000409195.1	+	9	6607	c.6518G>T	c.(6517-6519)gGa>gTa	p.G2173V	XIRP2_ENST00000409273.1_Missense_Mutation_p.G1951V|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.G2173V|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1998	Pro-rich.				actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						ATGCCAGTTGGAGGAACTTAC	0.353																																					p.G2173V		Atlas-SNP	.											.	XIRP2	914	.	0			c.G6518T						.						41	39	40					2																	168104420		1843	4084	5927	SO:0001583	missense	129446	exon9			CAGTTGGAGGAAC	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.6518G>T	chr2.hg19:g.168104420G>T	ENSP00000386840:p.Gly2173Val	124.0	0.0		116.0	55.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	hg19	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	G	13.51	2.259266	0.39995	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.21734	1.99;1.99;1.99	5.84	0.185	0.15096	.	1.178370	0.05809	N	0.613663	T	0.17534	0.0421	L	0.54323	1.7	0.09310	N	1	B;B;B	0.18610	0.017;0.029;0.029	B;B;B	0.21151	0.008;0.018;0.033	T	0.34030	-0.9845	10	0.21540	T	0.41	-2.0792	1.5813	0.02635	0.3283:0.1381:0.3935:0.1401	.	1998;1998;1951	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	V	2173;2173;1951	ENSP00000386840:G2173V;ENSP00000295237:G2173V;ENSP00000387255:G1951V	ENSP00000295237:G2173V	G	+	2	0	XIRP2	167812666	0.000000	0.05858	0.001000	0.08648	0.618000	0.37518	0.543000	0.23237	0.096000	0.17463	-0.142000	0.14014	GGA	.	.		0.353	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		T	168104420	G	T	168104420	3	4	253	1	0	0	0	0	1	0	0	0	17445	1174	41	3	6548	3	XIRP2	2	168104420	Missense_Mutation	SNP	G	TCGA-EP-A26S-01A-11D-A16V-10	3970	168104420	75094953	11	34216										
TTN	7273	hgsc.bcm.edu	37	chr2	179560596	179560596	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	ttcagtttatacataccttcAtagacctccttttgaacttg	4	10	2	2			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr2:179560596A>G	ENST00000591111.1	-	112	30476	c.30252T>C	c.(30250-30252)taT>taC	p.Y10084Y	TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Silent_p.Y10401Y|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Silent_p.Y9157Y			Q8WZ42	TITIN_HUMAN	titin	0	Glu-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACATACCTTCATAGACCTCCT	0.373																																					p.Y10401Y		Atlas-SNP	.											.	TTN	18412	.	0			c.T31203C						.						122	117	118					2																	179560596		1346	2805	4151	SO:0001819	synonymous_variant	7273	exon114			ACCTTCATAGACC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.30252T>C	chr2.hg19:g.179560596A>G		236.0	0.0		190.0	85.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.373	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179560596	A	G	179560596	2	3	253	1	0	0	0	0	0	0	0	1	16750	224	8	2		2	TTN	2	179560596	Silent	SNP	A	TCGA-EP-A26S-01A-11D-A16V-10	11456176	179560596	63638777	12	34217										
SF3B1	23451	hgsc.bcm.edu	37	chr2	198267360	198267360	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	tagctatctgttgtacaatcTtaataccagtgtgtctcgct	7	9	3	0	rs374250186		TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr2:198267360T>G	ENST00000335508.6	-	14	2088	c.1997A>C	c.(1996-1998)aAg>aCg	p.K666T	SF3B1_ENST00000462613.1_5'Flank|SNORA4_ENST00000365564.1_RNA	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	666					anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)	p.K666R(7)|p.K666T(6)|p.K666M(6)		NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			TTGTACAATCTTAATACCAGT	0.413			Mis		myelodysplastic syndrome																																p.K666T		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	SF3B1,NS,malignant_melanoma,0,27	SF3B1	1038	.	19	Substitution - Missense(19)	haematopoietic_and_lymphoid_tissue(18)|NS(1)	c.A1997C						.						116	116	116					2																	198267360		2203	4300	6503	SO:0001583	missense	23451	exon14			ACAATCTTAATAC	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"splicing factor 3b, subunit 1, 155kD"			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.1997A>C	chr2.hg19:g.198267360T>G	ENSP00000335321:p.Lys666Thr	120.0	0.0		128.0	58.0	NM_012433	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	hg19	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	T	26.4	4.736206	0.89482	.	.	ENSG00000115524	ENST00000335508	T	0.65549	-0.16	5.68	5.68	0.88126	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.85208	0.5644	H	0.95645	3.7	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.89754	0.3942	10	0.87932	D	0	.	15.938	0.79729	0.0:0.0:0.0:1.0	.	666	O75533	SF3B1_HUMAN	T	666	ENSP00000335321:K666T	ENSP00000335321:K666T	K	-	2	0	SF3B1	197975605	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.877000	0.87225	2.167000	0.68274	0.459000	0.35465	AAG	.	.		0.413	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			G	198267360	T	G	198267360	3	3	253	1	0	0	0	0	1	0	0	0	14164	1609	56	5	1965	5	SF3B1	2	198267360	Missense_Mutation	SNP	T	TCGA-EP-A26S-01A-11D-A16V-10	18706764	198267360	44932013	13	34218										
TRAK2	66008	hgsc.bcm.edu	37	chr2	202245316	202245316	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	tgaggatgtgcaaactggggCagcaaagctacccattatga	12	8	0	2			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr2:202245316C>G	ENST00000332624.3	-	16	3123	c.2695G>C	c.(2695-2697)Gcc>Ccc	p.A899P		NM_015049.2	NP_055864.2	O60296	TRAK2_HUMAN	trafficking protein, kinesin binding 2	899					protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|endosome (GO:0005768)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GABA receptor binding (GO:0050811)|receptor binding (GO:0005102)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	23						CAAACTGGGGCAGCAAAGCTA	0.423																																					p.A899P		Atlas-SNP	.											.	TRAK2	62	.	0			c.G2695C						.						66	59	61					2																	202245316		2203	4300	6503	SO:0001583	missense	66008	exon16			CTGGGGCAGCAAA	AB038951	CCDS2347.1	2q33.1	2012-03-05	2005-12-13	2005-12-13	ENSG00000115993	ENSG00000115993			13206	protein-coding gene	gene with protein product	"gamma-aminobutyric acid(A) receptor-interacting factor", "milton homolog 2 (Drosophila)", "O-linked N-acetylglucosamine transferase interacting protein 98"	607334	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 3"	ALS2CR3		11161814, 16380713, 20230862	Standard	NM_015049		Approved	CALS-C, KIAA0549, GRIF-1, OIP98, MILT2	uc002uyb.4	O60296	OTTHUMG00000132822	ENST00000332624.3:c.2695G>C	chr2.hg19:g.202245316C>G	ENSP00000328875:p.Ala899Pro	118.0	0.0		99.0	42.0	NM_015049	E7EV21|Q8WVH7|Q96NS2|Q9C0K5|Q9C0K6	Missense_Mutation	SNP	ENST00000332624.3	hg19	CCDS2347.1	.	.	.	.	.	.	.	.	.	.	C	11.99	1.802824	0.31869	.	.	ENSG00000115993	ENST00000332624	T	0.09723	2.95	6.03	-2.93	0.05598	.	0.524458	0.19144	N	0.121611	T	0.05227	0.0139	N	0.17082	0.46	0.28565	N	0.910905	B	0.06786	0.001	B	0.04013	0.001	T	0.21245	-1.0251	10	0.46703	T	0.11	.	6.8752	0.24143	0.0:0.4932:0.2116:0.2952	.	899	O60296	TRAK2_HUMAN	P	899	ENSP00000328875:A899P	ENSP00000328875:A899P	A	-	1	0	TRAK2	201953561	0.632000	0.27172	0.013000	0.15412	0.864000	0.49448	0.786000	0.26844	-0.451000	0.07097	-0.768000	0.03414	GCC	.	.		0.423	TRAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256284.3	NM_015049		G	202245316	C	G	202245316	3	3	253	1	0	0	0	0	1	0	0	0	16465	710	25	4	53	4	TRAK2	2	202245316	Missense_Mutation	SNP	C	TCGA-EP-A26S-01A-11D-A16V-10	3977956	202245316	40954057	14	34219										
HACL1	26061	hgsc.bcm.edu	37	chr3	15604875	15604875	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	ctgtatttacctgggccttcCgtgtggcttgtggctcaatc	11	11	1	0	rs149555880	byFrequency	TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr3:15604875C>G	ENST00000321169.5	-	16	2061	c.1694G>C	c.(1693-1695)cGg>cCg	p.R565P	HACL1_ENST00000435217.2_Missense_Mutation_p.R324P|HACL1_ENST00000457447.2_Missense_Mutation_p.R505P|HACL1_ENST00000456194.2_Missense_Mutation_p.R538P|HACL1_ENST00000451445.2_Missense_Mutation_p.R483P	NM_012260.2	NP_036392.2	Q9UJ83	HACL1_HUMAN	2-hydroxyacyl-CoA lyase 1	565					cellular lipid metabolic process (GO:0044255)|fatty acid alpha-oxidation (GO:0001561)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carbon-carbon lyase activity (GO:0016830)|cofactor binding (GO:0048037)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|receptor binding (GO:0005102)|thiamine pyrophosphate binding (GO:0030976)			NS(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|skin(1)	16						CTGGGCCTTCCGTGTGGCTTG	0.453																																					p.R565P		Atlas-SNP	.											.	HACL1	33	.	0			c.G1694C						.						187	171	176					3																	15604875		2203	4300	6503	SO:0001583	missense	26061	exon16			GCCTTCCGTGTGG	AJ131753	CCDS2627.1, CCDS68360.1, CCDS68361.1, CCDS68362.1	3p24.3	2009-01-14	2006-05-16	2006-05-16	ENSG00000131373	ENSG00000131373	4.1.-.-		17856	protein-coding gene	gene with protein product		604300	"2-hydroxyphytanoyl-CoA lyase"	HPCL		10468558, 15644336	Standard	NM_001284416		Approved	2-HPCL, PHYH2	uc003caf.3	Q9UJ83	OTTHUMG00000129862	ENST00000321169.5:c.1694G>C	chr3.hg19:g.15604875C>G	ENSP00000323811:p.Arg565Pro	327.0	0.0		259.0	132.0	NM_012260	B4DWI1|B4DXI5|E9PEN4|Q9BV42|Q9P0A2	Missense_Mutation	SNP	ENST00000321169.5	hg19	CCDS2627.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.886169	0.91814	.	.	ENSG00000131373	ENST00000321169;ENST00000435217;ENST00000451445;ENST00000456194;ENST00000457447	T;T;T;T;T	0.47528	1.44;0.84;1.43;1.44;0.89	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.72045	0.3412	M	0.78916	2.43	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.998;0.998;0.996;1.0;0.998	T	0.73347	-0.4011	10	0.66056	D	0.02	.	20.093	0.97828	0.0:1.0:0.0:0.0	.	483;505;538;324;565	B4DXI5;E9PEN4;B4DWI1;B3KPX4;Q9UJ83	.;.;.;.;HACL1_HUMAN	P	565;324;483;538;505	ENSP00000323811:R565P;ENSP00000395278:R324P;ENSP00000403656:R483P;ENSP00000390699:R538P;ENSP00000404883:R505P	ENSP00000323811:R565P	R	-	2	0	HACL1	15579879	0.994000	0.37717	0.568000	0.28447	0.925000	0.55904	4.108000	0.57817	2.756000	0.94617	0.561000	0.74099	CGG	.	C|1.000;T|0.000		0.453	HACL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252104.3	NM_012260		G	15604875	C	G	15604875	3	3	253	1	0	0	0	0	1	0	0	0	6950	652	23	4	50	4	HACL1	3	15604875	Missense_Mutation	SNP	C	TCGA-EP-A26S-01A-11D-A16V-10		15604875	182417555	15	34220										
KCNH8	131096	hgsc.bcm.edu	37	chr3	19554731	19554731	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	accaagcaggaaattgacccCcccaaccataataaaaggaa	6	12	0	1			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr3:19554731C>T	ENST00000328405.2	+	13	2615	c.2349C>T	c.(2347-2349)ccC>ccT	p.P783P		NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	783					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(3)|lung(37)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	77						AAATTGACCCCCCCAACCATA	0.458																																					p.P783P	NSCLC(124;1625 1765 8018 24930 42026)	Atlas-SNP	.											.	KCNH8	189	.	0			c.C2349T						.						80	87	85					3																	19554731		2203	4300	6503	SO:0001819	synonymous_variant	131096	exon13			TGACCCCCCCAAC	AY053503	CCDS2632.1	3p24.3	2012-07-05			ENSG00000183960	ENSG00000183960		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18864	protein-coding gene	gene with protein product		608260				16382104	Standard	NM_144633		Approved	Kv12.1, elk3	uc003cbk.1	Q96L42	OTTHUMG00000129891	ENST00000328405.2:c.2349C>T	chr3.hg19:g.19554731C>T		130.0	0.0		99.0	31.0	NM_144633	B7Z2I7|Q59GQ6	Silent	SNP	ENST00000328405.2	hg19	CCDS2632.1																																																																																			.	.		0.458	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	NM_144633		T	19554731	C	T	19554731	2	4	253	1	0	0	0	0	0	0	0	1	8047	610	22	3		3	KCNH8	3	19554731	Silent	SNP	C	TCGA-EP-A26S-01A-11D-A16V-10	3949856	19554731	178467699	16	34221										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266125	41266125	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	aatccattctggtgccactaCcacagctccttctctgagtg	7	14	2	1	rs121913413		TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr3:41266125C>T	ENST00000349496.5	+	3	402	c.122C>T	c.(121-123)aCc>aTc	p.T41I	CTNNB1_ENST00000453024.1_Missense_Mutation_p.T34I|CTNNB1_ENST00000405570.1_Missense_Mutation_p.T41I|CTNNB1_ENST00000396183.3_Missense_Mutation_p.T41I|CTNNB1_ENST00000396185.3_Missense_Mutation_p.T41I	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	41			T -> A (in hepatoblastoma and hepatocellular carcinoma; also in a desmoid tumor; strongly reduces phosphorylation and degradation; abolishes phosphorylation on Ser-33 and Ser-37 and enhances transactivation of target genes). {ECO:0000269|PubMed:10391090, ECO:0000269|PubMed:10398436, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10655994, ECO:0000269|PubMed:9927029}.|T -> I (in PTR, hepatocellular carcinoma and ovarian cancer). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10391090, ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.T41I(74)|p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.T41N(6)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T41S(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.T40_L46del(1)|p.A20_N141del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.I35_T41del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A39_T42del(1)|p.A20_S111del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GGTGCCACTACCACAGCTCCT	0.507		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.T41I	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,+1,98	CTNNB1	4904	.	204	Deletion - In frame(95)|Substitution - Missense(83)|Complex - deletion inframe(17)|Unknown(7)|Deletion - Frameshift(2)	liver(105)|large_intestine(24)|pituitary(20)|endometrium(14)|stomach(8)|skin(6)|biliary_tract(5)|haematopoietic_and_lymphoid_tissue(4)|soft_tissue(3)|pancreas(3)|thyroid(2)|small_intestine(2)|prostate(2)|ovary(2)|bone(2)|adrenal_gland(1)|cervix(1)	c.C122T						.						90	77	81					3																	41266125		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	CCACTACCACAGC	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.122C>T	chr3.hg19:g.41266125C>T	ENSP00000344456:p.Thr41Ile	121.0	0.0		111.0	53.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.568904	0.86439	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.71082	0.3298	M	0.79258	2.445	0.80722	D	1	D	0.67145	0.996	D	0.68039	0.955	T	0.72893	-0.4154	10	0.87932	D	0	-8.9189	20.2983	0.98569	0.0:1.0:0.0:0.0	.	41	P35222	CTNB1_HUMAN	I	34;41;41;41;41;34;41;41;41	ENSP00000400508:T34I;ENSP00000385604:T41I;ENSP00000412219:T41I;ENSP00000379486:T41I;ENSP00000344456:T41I;ENSP00000411226:T34I;ENSP00000379488:T41I;ENSP00000409302:T41I;ENSP00000401599:T41I	ENSP00000344456:T41I	T	+	2	0	CTNNB1	41241129	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.818000	0.86416	2.802000	0.96397	0.655000	0.94253	ACC	.	.		0.507	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41266125	C	T	41266125	3	4	253	1	0	0	0	0	1	0	0	0	4018	507	18	3	128	3	CTNNB1	3	41266125	Missense_Mutation	SNP	C	TCGA-EP-A26S-01A-11D-A16V-10	21711394	41266125	156756305	17	34222										
TRAIP	10293	hgsc.bcm.edu	37	chr3	49867199	49867199	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	acccagtgagagctgggactCctgcagggaagaccccaggg	15	12	0	2			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr3:49867199C>T	ENST00000331456.2	-	13	1200	c.1087G>A	c.(1087-1089)Gag>Aag	p.E363K	TRAIP_ENST00000469027.1_Splice_Site_p.E208K	NM_005879.2	NP_005870.2	Q9BWF2	TRAIP_HUMAN	TRAF interacting protein	363	Interaction with CYLD.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|receptor signaling protein activity (GO:0005057)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(9)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		AGCTGGGACTCCTGCAGGGAA	0.567																																					p.E363K		Atlas-SNP	.											.	TRAIP	47	.	0			c.G1087A						.						31	31	31					3																	49867199		2203	4300	6503	SO:0001630	splice_region_variant	10293	exon13			GGGACTCCTGCAG	BC019283	CCDS2806.1	3p21.31	2013-01-09			ENSG00000183763	ENSG00000183763		"RING-type (C3HC4) zinc fingers"	30764	protein-coding gene	gene with protein product	"ring finger protein 206"	605958				9104814	Standard	NM_005879		Approved	TRIP, RNF206	uc003cxs.1	Q9BWF2	OTTHUMG00000158269	ENST00000331456.2:c.1087-1G>A	chr3.hg19:g.49867199C>T		31.0	0.0		19.0	11.0	NM_005879	B5BU84|B5BUL3|O00467	Missense_Mutation	SNP	ENST00000331456.2	hg19	CCDS2806.1	.	.	.	.	.	.	.	.	.	.	C	12.13	1.844797	0.32606	.	.	ENSG00000183763	ENST00000331456;ENST00000469027	T	0.44881	0.91	5.08	4.21	0.49690	.	0.512387	0.20570	N	0.089742	T	0.31071	0.0785	L	0.51422	1.61	0.35350	D	0.787276	B;B	0.18610	0.001;0.029	B;B	0.14023	0.002;0.01	T	0.24835	-1.0149	10	0.06236	T	0.91	-14.4236	9.2917	0.37791	0.0:0.9033:0.0:0.0967	.	363;363	A8K807;Q9BWF2	.;TRAIP_HUMAN	K	363;208	ENSP00000420085:E208K	ENSP00000328203:E363K	E	-	1	0	TRAIP	49842203	0.998000	0.40836	0.993000	0.49108	0.134000	0.20937	1.262000	0.32992	1.376000	0.46267	0.561000	0.74099	GAG	.	.		0.567	TRAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350518.1	NM_005879	Missense_Mutation	T	49867199	C	T	49867199	5	4	253	1	0	0	0	0	0	0	1	0	16463	869	30	3	334	3	TRAIP	3	49867199	Splice_Site	SNP	C	TCGA-EP-A26S-01A-11D-A16V-10	8601074	49867199	148155231	18	34223										
ADAMTS9	56999	hgsc.bcm.edu	37	chr3	64582656	64582656	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	cgctgggatccgccagcacaGgtactggaacactaaacaca	10	13	0	0			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr3:64582656G>C	ENST00000498707.1	-	27	4371	c.4029C>G	c.(4027-4029)acC>acG	p.T1343T	ADAMTS9_ENST00000295903.4_Silent_p.T1315T	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	1343	TSP type-1 9. {ECO:0000255|PROSITE- ProRule:PRU00210}.				glycoprotein catabolic process (GO:0006516)|multicellular organismal development (GO:0007275)|positive regulation of melanocyte differentiation (GO:0045636)|protein transport (GO:0015031)|proteolysis (GO:0006508)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(17)|liver(4)|lung(43)|ovary(3)|prostate(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	100		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		CGCCAGCACAGGTACTGGAAC	0.468																																					p.T1343T		Atlas-SNP	.											.	ADAMTS9	206	.	0			c.C4029G						.						95	92	93					3																	64582656		2203	4300	6503	SO:0001819	synonymous_variant	56999	exon27			AGCACAGGTACTG	AF261918	CCDS2903.1	3p14.1	2008-05-15	2005-08-19		ENSG00000163638	ENSG00000163638		"ADAM metallopeptidases with thrombospondin type 1 motif"	13202	protein-coding gene	gene with protein product		605421	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 9"			10936055	Standard	NM_182920		Approved	KIAA1312	uc003dmg.3	Q9P2N4	OTTHUMG00000158722	ENST00000498707.1:c.4029C>G	chr3.hg19:g.64582656G>C		72.0	0.0		60.0	33.0	NM_182920	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	Silent	SNP	ENST00000498707.1	hg19	CCDS2903.1	.	.	.	.	.	.	.	.	.	.	G	9.122	1.009253	0.19277	.	.	ENSG00000163638	ENST00000481060	.	.	.	5.4	1.43	0.22495	.	.	.	.	.	T	0.46658	0.1404	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33266	-0.9875	4	.	.	.	.	4.4167	0.11459	0.0737:0.1726:0.4512:0.3025	.	.	.	.	R	399	.	.	P	-	2	0	ADAMTS9	64557696	0.743000	0.28239	1.000000	0.80357	0.994000	0.84299	-0.209000	0.09358	0.820000	0.34516	0.591000	0.81541	CCT	.	.		0.468	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351891.1			C	64582656	G	C	64582656	2	2	253	1	0	0	0	0	0	0	0	1	273	987	35	4		4	ADAMTS9	3	64582656	Silent	SNP	G	TCGA-EP-A26S-01A-11D-A16V-10	14715457	64582656	133439774	19	34224										
CADM2	253559	hgsc.bcm.edu	37	chr3	85984981	85984981	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	gaaggacagcctttaattttGacttgtgaatccaaaggaaa	9	6	0	2			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr3:85984981G>T	ENST00000407528.2	+	6	800	c.738G>T	c.(736-738)ttG>ttT	p.L246F	CADM2_ENST00000405615.2_Missense_Mutation_p.L248F|CADM2_ENST00000383699.3_Missense_Mutation_p.L255F	NM_001167674.1	NP_001161146.1	Q8N3J6	CADM2_HUMAN	cell adhesion molecule 2	246	Ig-like C2-type 2.				adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|synapse (GO:0045202)				endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(1)|prostate(1)|skin(4)	38		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		CTTTAATTTTGACTTGTGAAT	0.308																																					p.L255F		Atlas-SNP	.											.	CADM2	195	.	0			c.G765T						.						96	102	100					3																	85984981		2203	4297	6500	SO:0001583	missense	253559	exon7			AATTTTGACTTGT	AF538973	CCDS33792.1, CCDS54613.1, CCDS54614.1	3p12.2	2013-01-11	2007-02-07	2007-02-07	ENSG00000175161	ENSG00000175161		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing"	29849	protein-coding gene	gene with protein product	"nectin-like 3"	609938	"immunoglobulin superfamily, member 4D"	IGSF4D			Standard	NM_153184		Approved	NECL3, Necl-3, SynCAM2	uc003dqj.3	Q8N3J6	OTTHUMG00000158990	ENST00000407528.2:c.738G>T	chr3.hg19:g.85984981G>T	ENSP00000384575:p.Leu246Phe	218.0	0.0		213.0	93.0	NM_001167675	G3XHN7|G3XHN8|Q3KQY9|Q658Q7|Q8IZP8	Missense_Mutation	SNP	ENST00000407528.2	hg19	CCDS54614.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.155619	0.78114	.	.	ENSG00000175161	ENST00000383699;ENST00000407528;ENST00000405615	D;T;T	0.89415	-2.51;-1.48;-1.48	5.77	5.77	0.91146	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.92280	0.7551	L	0.43554	1.36	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.999	D	0.89344	0.3656	10	0.23302	T	0.38	.	19.9785	0.97317	0.0:0.0:1.0:0.0	.	248;255;246	Q8N3J6-3;G3XHN4;Q8N3J6	.;.;CADM2_HUMAN	F	255;246;248	ENSP00000373200:L255F;ENSP00000384575:L246F;ENSP00000384193:L248F	ENSP00000373200:L255F	L	+	3	2	CADM2	86067671	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.778000	0.75043	2.724000	0.93272	0.650000	0.86243	TTG	.	.		0.308	CADM2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352822.1	NM_153184		T	85984981	G	T	85984981	3	4	253	1	0	0	0	0	1	0	0	0	2569	1281	45	3	831	3	CADM2	3	85984981	Missense_Mutation	SNP	G	TCGA-EP-A26S-01A-11D-A16V-10	21402325	85984981	112037449	20	34225										
PCDH7	5099	hgsc.bcm.edu	37	chr4	30726038	30726038	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	ctggcaaggcattacaaatcTagttccccattgcctactgt	7	12	1	0			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr4:30726038T>A	ENST00000361762.2	+	1	4002	c.2994T>A	c.(2992-2994)tcT>tcA	p.S998S	PCDH7_ENST00000543491.1_Silent_p.S998S	NM_002589.2	NP_002580.2	O60245	PCDH7_HUMAN	protocadherin 7	998					homophilic cell adhesion (GO:0007156)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(8)|liver(1)|lung(26)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	55						ATTACAAATCTAGTTCCCCAT	0.517																																					p.S998S		Atlas-SNP	.											.	PCDH7	215	.	0			c.T2994A						.						95	95	95					4																	30726038		2203	4300	6503	SO:0001819	synonymous_variant	5099	exon1			CAAATCTAGTTCC	AB006755	CCDS33971.1, CCDS75116.1	4p15	2014-06-13	2007-02-12			ENSG00000169851		"Cadherins / Protocadherins : Non-clustered"	8659	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 120"	602988	"BH-protocadherin (brain-heart)"			9615233	Standard	NM_002589		Approved	BH-Pcdh, PPP1R120	uc021xnd.1	O60245		ENST00000361762.2:c.2994T>A	chr4.hg19:g.30726038T>A		42.0	0.0		64.0	22.0	NM_032457	O60246|O60247|Q4W5C4	Silent	SNP	ENST00000361762.2	hg19	CCDS33971.1	.	.	.	.	.	.	.	.	.	.	T	5.757	0.324047	0.10900	.	.	ENSG00000169851	ENST00000511884	.	.	.	5.08	-7.67	0.01272	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.8975	0.86104	0.0:0.7091:0.1904:0.1005	.	.	.	.	K	688	.	.	X	+	1	0	PCDH7	30335136	0.000000	0.05858	0.860000	0.33809	0.989000	0.77384	-1.924000	0.01565	-1.434000	0.01975	-0.379000	0.06801	TAG	.	.		0.517	PCDH7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360366.1	NM_032457, NM_002589		A	30726038	T	A	30726038	2	1	253	1	0	0	0	0	0	0	0	1	11525	1509	53	4		4	PCDH7	4	30726038	Silent	SNP	T	TCGA-EP-A26S-01A-11D-A16V-10		30726038	160428238	21	34226										
C4orf34	201895	hgsc.bcm.edu	37	chr4	39553765	39553765	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	gttagtccacaggaggagctGgtggatcttgtccctggcat	14	9	1	0			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr4:39553765G>A	ENST00000295958.5	-	5	667	c.281C>T	c.(280-282)cCa>cTa	p.P94L	SMIM14_ENST00000510628.1_5'UTR|SMIM14_ENST00000511809.1_Silent_p.T46T|UGDH-AS1_ENST00000504032.1_RNA	NM_174921.1	NP_777581.1	Q96QK8	SIM14_HUMAN	small integral membrane protein 14	94						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											AGGAGGAGCTGGTGGATCTTG	0.318																																					p.P94L		Atlas-SNP	.											.	.	.	.	0			c.C281T						.						95	84	88					4																	39553765		2203	4300	6503	SO:0001583	missense	201895	exon5			GGAGCTGGTGGAT	BC008502	CCDS3456.1	4p14	2014-02-10	2012-12-03	2012-12-03	ENSG00000163683	ENSG00000163683			27321	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 34"	C4orf34		15231747, 24499674, 23759569	Standard	NM_174921		Approved	FLJ13289	uc003guo.3	Q96QK8	OTTHUMG00000128581	ENST00000295958.5:c.281C>T	chr4.hg19:g.39553765G>A	ENSP00000295958:p.Pro94Leu	251.0	1.0		205.0	88.0	NM_174921		Missense_Mutation	SNP	ENST00000295958.5	hg19	CCDS3456.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.133107	0.77662	.	.	ENSG00000163683	ENST00000295958	.	.	.	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.64735	0.2625	.	.	.	0.80722	D	1	P	0.47604	0.898	P	0.48089	0.566	T	0.68093	-0.5500	8	0.72032	D	0.01	-6.657	17.1564	0.86792	0.0:0.0:1.0:0.0	.	94	Q96QK8	CD034_HUMAN	L	94	.	ENSP00000295958:P94L	P	-	2	0	C4orf34	39230160	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.293000	0.72731	2.802000	0.96397	0.655000	0.94253	CCA	.	.		0.318	SMIM14-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000250434.4	NM_174921		A	39553765	G	A	39553765	3	1	253	1	0	0	0	0	1	0	0	0	2266	1348	47	3	22	3	C4orf34	4	39553765	Missense_Mutation	SNP	G	TCGA-EP-A26S-01A-11D-A16V-10	8827727	39553765	151600511	22	34227										
GABRA2	2555	hgsc.bcm.edu	37	chr4	46390679	46390679	+	Frame_Shift_Del	DEL	A	A	-													0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	gggtcccacaccaagaaaacAaaaagcaggaactgcatgtt							TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr4:46390679delA	ENST00000510861.1	-	2	218	c.45delT	c.(43-45)tttfs	p.F15fs	RP11-436F23.1_ENST00000502455.1_RNA|GABRA2_ENST00000540012.1_5'UTR|GABRA2_ENST00000507460.1_Frame_Shift_Del_p.F15fs|GABRA2_ENST00000507069.1_Frame_Shift_Del_p.F15fs|GABRA2_ENST00000515082.1_Frame_Shift_Del_p.F15fs|GABRA2_ENST00000381620.4_Frame_Shift_Del_p.F15fs|GABRA2_ENST00000514090.1_Frame_Shift_Del_p.F15fs|GABRA2_ENST00000356504.1_Frame_Shift_Del_p.F15fs|GABRA2_ENST00000509716.1_5'UTR			P47869	GBRA2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 2	15					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|neurotransmitter transport (GO:0006836)|regulation of neurotransmitter levels (GO:0001505)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of synaptic vesicle membrane (GO:0030285)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(9)|lung(33)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	56					Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zolpidem(DB00425)|Zopiclone(DB01198)	CCAAGAAAACAAAAAGCAGGA	0.373																																					p.V16fs		Atlas-Indel,Pindel	.											.	GABRA2	134	.	0			c.46delG						.						157	155	156					4																	46390679		2203	4300	6503	SO:0001589	frameshift_variant	2555	exon1			.		CCDS3471.1	4p12	2012-06-22			ENSG00000151834	ENSG00000151834		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4076	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 2"	137140					Standard	NM_000807		Approved		uc010igc.2	P47869	OTTHUMG00000044266	ENST00000510861.1:c.45delT	chr4.hg19:g.46390679delA	ENSP00000421828:p.Phe15fs	306.0	0.0		311.0	137.0	NM_001114175	A8K0U7|B7Z1H8|Q59G14	Frame_Shift_Del	DEL	ENST00000510861.1	hg19	CCDS3471.1																																																																																			.	.		0.373	GABRA2-005	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360848.2			-	46390679	A	-	46390679	7	5	253	1	0	1	0	1	0	0	0	0	6169	127	5	0	1346	0	GABRA2	4	46390679	Frame_Shift_Del	DEL	A	TCGA-EP-A26S-01A-11D-A16V-10	6836914	46390679	144763597	23	34228	178	2								
GABRA2	2555	hgsc.bcm.edu	37	chr4	46390684	46390684	+	Missense_Mutation	SNP	G	G	T													0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	ccacaccaagaaaacaaaaaGcaggaactgcatgttgtaga							TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr4:46390684G>T	ENST00000510861.1	-	2	213	c.40C>A	c.(40-42)Ctt>Att	p.L14I	RP11-436F23.1_ENST00000502455.1_RNA|GABRA2_ENST00000540012.1_5'UTR|GABRA2_ENST00000507460.1_Missense_Mutation_p.L14I|GABRA2_ENST00000507069.1_Missense_Mutation_p.L14I|GABRA2_ENST00000515082.1_Missense_Mutation_p.L14I|GABRA2_ENST00000381620.4_Missense_Mutation_p.L14I|GABRA2_ENST00000514090.1_Missense_Mutation_p.L14I|GABRA2_ENST00000356504.1_Missense_Mutation_p.L14I|GABRA2_ENST00000509716.1_5'UTR			P47869	GBRA2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 2	14					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|neurotransmitter transport (GO:0006836)|regulation of neurotransmitter levels (GO:0001505)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of synaptic vesicle membrane (GO:0030285)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(9)|lung(33)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	56					Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zolpidem(DB00425)|Zopiclone(DB01198)	AAAACAAAAAGCAGGAACTGC	0.378																																					p.L14I		Atlas-SNP	.											.	GABRA2	134	.	0			c.C40A						.						159	157	158					4																	46390684		2203	4300	6503	SO:0001583	missense	2555	exon2			CAAAAAGCAGGAA		CCDS3471.1	4p12	2012-06-22			ENSG00000151834	ENSG00000151834		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4076	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 2"	137140					Standard	NM_000807		Approved		uc010igc.2	P47869	OTTHUMG00000044266	ENST00000510861.1:c.40C>A	chr4.hg19:g.46390684G>T	ENSP00000421828:p.Leu14Ile	302.0	1.0		309.0	139.0	NM_000807	A8K0U7|B7Z1H8|Q59G14	Missense_Mutation	SNP	ENST00000510861.1	hg19	CCDS3471.1	.	.	.	.	.	.	.	.	.	.	G	17.15	3.315639	0.60524	.	.	ENSG00000151834	ENST00000510861;ENST00000514090;ENST00000381620;ENST00000356504;ENST00000507069;ENST00000515082;ENST00000503806;ENST00000506961;ENST00000507460	T;T;T;T;T;D;T;T	0.81908	-1.34;-1.34;-1.34;-1.34;-1.49;-1.55;-1.17;-1.17	5.0	5.0	0.66597	.	1.271310	0.05211	N	0.506821	D	0.87621	0.6223	N	0.24115	0.695	0.26319	N	0.9777	D;P;P	0.67145	0.996;0.927;0.458	D;D;P	0.80764	0.994;0.953;0.745	T	0.79650	-0.1715	10	0.72032	D	0.01	.	15.9563	0.79889	0.0:0.0:1.0:0.0	.	14;14;14	D6RAA9;G5E9Z6;P47869	.;.;GBRA2_HUMAN	I	14	ENSP00000421828:L14I;ENSP00000421300:L14I;ENSP00000371033:L14I;ENSP00000348897:L14I;ENSP00000427603:L14I;ENSP00000423840:L14I;ENSP00000424362:L14I;ENSP00000424093:L14I	ENSP00000348897:L14I	L	-	1	0	GABRA2	46085441	0.998000	0.40836	0.269000	0.24586	0.582000	0.36321	2.893000	0.48633	2.746000	0.94184	0.561000	0.74099	CTT	.	.		0.378	GABRA2-005	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360848.2			T	46390684	G	T	46390684	3	4	253	1	0	0	0	0	1	0	0	0	6169	971	34	3	1351	3	GABRA2	4	46390684	Missense_Mutation	SNP	G	TCGA-EP-A26S-01A-11D-A16V-10	5	46390684	144763592	24	34229	178	2								
ANKRD17	26057	hgsc.bcm.edu	37	chr4	73990633	73990633	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	ctaaggggaaacattacctcCtgtcttcccccagaacaagc	7	14	1	1			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr4:73990633C>T	ENST00000358602.4	-	18	3605	c.3489G>A	c.(3487-3489)caG>caA	p.Q1163Q	ANKRD17_ENST00000509867.2_Silent_p.Q1050Q|ANKRD17_ENST00000330838.6_Silent_p.Q912Q|ANKRD17_ENST00000514252.1_5'UTR	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	1163				Q -> P (in Ref. 1; AAG48253). {ECO:0000305}.	blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			ACATTACCTCCTGTCTTCCCC	0.408																																					p.Q1163Q		Atlas-SNP	.											.	ANKRD17	214	.	0			c.G3489A						.						119	110	113					4																	73990633		2203	4300	6503	SO:0001819	synonymous_variant	26057	exon18			TACCTCCTGTCTT	AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"Ankyrin repeat domain containing"	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.3489G>A	chr4.hg19:g.73990633C>T		57.0	0.0		45.0	18.0	NM_032217	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Silent	SNP	ENST00000358602.4	hg19	CCDS34004.1																																																																																			.	.		0.408	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217		T	73990633	C	T	73990633	2	4	253	1	0	0	0	0	0	0	0	1	646	680	24	3		3	ANKRD17	4	73990633	Silent	SNP	C	TCGA-EP-A26S-01A-11D-A16V-10	27599949	73990633	117163643	25	34230										
ALB	213	hgsc.bcm.edu	37	chr4	74279198	74279198	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	ctccagtaaactgaaggaatGctgtgaaaaacctctgttgg	10	8	1	2			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr4:74279198G>T	ENST00000503124.1	+	6	662	c.455G>T	c.(454-456)tGc>tTc	p.C152F	ALB_ENST00000401494.3_Missense_Mutation_p.C187F|ALB_ENST00000505649.1_3'UTR|ALB_ENST00000509063.1_Missense_Mutation_p.C302F|ALB_ENST00000295897.4_Missense_Mutation_p.C302F|ALB_ENST00000415165.2_Missense_Mutation_p.C110F			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CTGAAGGAATGCTGTGAAAAA	0.408																																					p.C302F		Atlas-SNP	.											.	ALB	132	.	0			c.G905T						.						120	115	117					4																	74279198		2203	4300	6503	SO:0001583	missense	213	exon8			AGGAATGCTGTGA	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.455G>T	chr4.hg19:g.74279198G>T	ENSP00000421027:p.Cys152Phe	62.0	0.0		69.0	30.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000503124.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.5|20.5	3.993248|3.993248	0.74703|0.74703	.|.	.|.	ENSG00000163631|ENSG00000163631	ENST00000295897;ENST00000415165;ENST00000503124;ENST00000509063;ENST00000401494;ENST00000430202|ENST00000511370	D;D;D;D;D|.	0.99637|.	-6.29;-6.29;-6.29;-6.29;-6.29|.	5.98|5.98	5.98|5.98	0.97165|0.97165	Serum albumin-like (1);Serum albumin, N-terminal (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.87204|0.87204	0.6119|0.6119	M|M	0.93420|0.93420	3.415|3.415	0.80722|0.80722	D|D	1|1	D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D|.	0.97110|.	1.0;1.0;1.0;1.0;1.0|.	D|D	0.89545|0.89545	0.3795|0.3795	10|5	0.87932|.	D|.	0|.	-14.7984|-14.7984	19.0219|19.0219	0.92919|0.92919	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	187;110;152;302;302|.	B7WNR0;C9JKR2;D6RHD5;A6NBZ8;P02768|.	.;.;.;.;ALBU_HUMAN|.	F|I	302;110;152;302;187;311|146	ENSP00000295897:C302F;ENSP00000401820:C110F;ENSP00000421027:C152F;ENSP00000422784:C302F;ENSP00000384695:C187F|.	ENSP00000295897:C302F|.	C|M	+|+	2|3	0|0	ALB|ALB	74498062|74498062	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.775000|0.775000	0.43874|0.43874	6.394000|6.394000	0.73223|0.73223	2.835000|2.835000	0.97688|0.97688	0.650000|0.650000	0.86243|0.86243	TGC|ATG	.	.		0.408	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		T	74279198	G	T	74279198	3	4	253	1	0	0	0	0	1	0	0	0	486	1319	46	3	935	3	ALB	4	74279198	Missense_Mutation	SNP	G	TCGA-EP-A26S-01A-11D-A16V-10	288565	74279198	116875078	26	34231										
ANXA3	306	hgsc.bcm.edu	37	chr4	79494388	79494388	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	actttagcccatcagtggatGctgaagctattcagaaagca	9	9	2	2			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr4:79494388G>T	ENST00000264908.6	+	3	449	c.70G>T	c.(70-72)Gct>Tct	p.A24S	ANXA3_ENST00000503570.2_5'UTR|ANXA3_ENST00000512884.1_Intron	NM_005139.2	NP_005130.1	P12429	ANXA3_HUMAN	annexin A3	24					defense response to bacterium (GO:0042742)|neutrophil degranulation (GO:0043312)|phagocytosis (GO:0006909)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|specific granule (GO:0042581)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|phospholipase A2 inhibitor activity (GO:0019834)			NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	15						ATCAGTGGATGCTGAAGCTAT	0.373																																					p.A24S	GBM(2;126 157 27790 28920 42492)	Atlas-SNP	.											.	ANXA3	35	.	0			c.G70T						.						117	110	112					4																	79494388		2203	4300	6503	SO:0001583	missense	306	exon3			GTGGATGCTGAAG	M63310	CCDS3584.1	4q21.21	2009-07-10			ENSG00000138772	ENSG00000138772	3.1.4.43	"Annexins"	541	protein-coding gene	gene with protein product		106490		ANX3		1830024	Standard	XM_005262973		Approved		uc003hld.3	P12429	OTTHUMG00000130198	ENST00000264908.6:c.70G>T	chr4.hg19:g.79494388G>T	ENSP00000264908:p.Ala24Ser	43.0	0.0		27.0	13.0	NM_005139	B2R9W6|Q6LET2	Missense_Mutation	SNP	ENST00000264908.6	hg19	CCDS3584.1	.	.	.	.	.	.	.	.	.	.	G	18.21	3.572749	0.65765	.	.	ENSG00000138772	ENST00000264908;ENST00000512373;ENST00000514171;ENST00000508214	T;T;T;T	0.09073	3.02;3.02;3.02;3.02	4.89	4.89	0.63831	.	0.057085	0.64402	D	0.000002	T	0.33789	0.0875	M	0.85859	2.78	0.80722	D	1	D	0.60575	0.988	D	0.75020	0.985	T	0.13683	-1.0500	10	0.72032	D	0.01	.	17.3412	0.87297	0.0:0.0:1.0:0.0	.	24	P12429	ANXA3_HUMAN	S	24	ENSP00000264908:A24S;ENSP00000424584:A24S;ENSP00000421512:A24S;ENSP00000422281:A24S	ENSP00000264908:A24S	A	+	1	0	ANXA3	79713412	1.000000	0.71417	1.000000	0.80357	0.392000	0.30506	5.386000	0.66238	2.689000	0.91719	0.591000	0.81541	GCT	.	.		0.373	ANXA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252516.3	NM_005139		T	79494388	G	T	79494388	3	4	253	1	0	0	0	0	1	0	0	0	719	1319	46	3	76	3	ANXA3	4	79494388	Missense_Mutation	SNP	G	TCGA-EP-A26S-01A-11D-A16V-10	5215190	79494388	111659888	27	34232										
ODZ3	55714	hgsc.bcm.edu	37	chr4	183267884	183267884	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	cattttgtgcggaaatggggCtccctcacagaggttactct	11	10	2	1			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr4:183267884C>T	ENST00000511685.1	+	3	436	c.313C>T	c.(313-315)Ctc>Ttc	p.L105F	TENM3_ENST00000406950.2_Missense_Mutation_p.L105F			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	105	Teneurin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00694}.				camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										GGAAATGGGGCTCCCTCACAG	0.488																																					p.L105F		Atlas-SNP	.											.	.	.	.	0			c.C313T						.						53	53	53					4																	183267884		1908	4123	6031	SO:0001583	missense	55714	exon2			ATGGGGCTCCCTC	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.313C>T	chr4.hg19:g.183267884C>T	ENSP00000424226:p.Leu105Phe	92.0	0.0		71.0	31.0	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	hg19	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.632750	0.87660	.	.	ENSG00000218336	ENST00000512480;ENST00000511685;ENST00000406950	T;T;T	0.39787	1.06;1.06;1.06	5.15	5.15	0.70609	Teneurin intracellular, N-terminal (2);	.	.	.	.	T	0.63248	0.2495	M	0.65975	2.015	0.47374	D	0.999401	D;D	0.63046	0.991;0.992	D;P	0.65987	0.94;0.898	T	0.64968	-0.6282	9	0.62326	D	0.03	.	18.8123	0.92063	0.0:1.0:0.0:0.0	.	105;105	D6RGC5;Q9P273	.;TEN3_HUMAN	F	105	ENSP00000421320:L105F;ENSP00000424226:L105F;ENSP00000385276:L105F	ENSP00000385276:L105F	L	+	1	0	ODZ3	183504878	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.589000	0.61006	2.681000	0.91329	0.563000	0.77884	CTC	.	.		0.488	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			T	183267884	C	T	183267884	3	4	253	1	0	0	0	0	1	0	0	0	10845	797	28	3	319	3	ODZ3	4	183267884	Missense_Mutation	SNP	C	TCGA-EP-A26S-01A-11D-A16V-10	103773496	183267884	7886392	28	34233										
MYO10	4651	hgsc.bcm.edu	37	chr5	16701447	16701447	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	ctggtccggatgccacttgtTcgctggtctgagtggccgtg	15	11	1	1	rs372673284		TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr5:16701447T>C	ENST00000513610.1	-	25	3511	c.3057A>G	c.(3055-3057)cgA>cgG	p.R1019R	MYO10_ENST00000274203.9_Silent_p.R376R|MYO10_ENST00000512061.1_5'Flank|MYO10_ENST00000505695.1_Silent_p.R358R|MYO10_ENST00000515803.1_Silent_p.R358R|MYO10_ENST00000427430.2_Silent_p.R376R	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	1019					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						TGCCACTTGTTCGCTGGTCTG	0.637																																					p.R1019R		Atlas-SNP	.											.	MYO10	198	.	0			c.A3057G						.						46	52	50					5																	16701447		2173	4267	6440	SO:0001819	synonymous_variant	4651	exon25			ACTTGTTCGCTGG	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"Myosins / Myosin superfamily : Class X", "Pleckstrin homology (PH) domain containing"	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.3057A>G	chr5.hg19:g.16701447T>C		57.0	0.0		61.0	28.0	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Silent	SNP	ENST00000513610.1	hg19	CCDS54834.1																																																																																			.	.		0.637	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		C	16701447	T	C	16701447	2	2	253	1	0	0	0	0	0	0	0	1	10071	1770	62	2		2	MYO10	5	16701447	Silent	SNP	T	TCGA-EP-A26S-01A-11D-A16V-10		16701447	164213813	29	34234										
GDNF	2668	hgsc.bcm.edu	37	chr5	37815756	37815756	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	agtctctggagccggagtcaGatacatccacaccttttagc	9	12	2	1	rs121918536		TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr5:37815756G>A	ENST00000326524.2	-	3	832	c.633C>T	c.(631-633)atC>atT	p.I211I	GDNF_ENST00000515058.1_Silent_p.I185I|GDNF_ENST00000381826.4_Silent_p.I202I|GDNF_ENST00000427982.1_Silent_p.I228I|GDNF_ENST00000344622.4_Silent_p.I185I	NM_000514.3	NP_000505.1	P39905	GDNF_HUMAN	glial cell derived neurotrophic factor	211			I -> M (in HSCR3). {ECO:0000269|PubMed:10917288}.		adult locomotory behavior (GO:0008344)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|enteric nervous system development (GO:0048484)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|metanephros development (GO:0001656)|mRNA stabilization (GO:0048255)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neuron projection development (GO:0031175)|organ induction (GO:0001759)|peristalsis (GO:0030432)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0072108)|positive regulation of monooxygenase activity (GO:0032770)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of ureteric bud formation (GO:0072107)|postganglionic parasympathetic nervous system development (GO:0021784)|postsynaptic membrane organization (GO:0001941)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of morphogenesis of a branching structure (GO:0060688)|signal transduction (GO:0007165)|sympathetic nervous system development (GO:0048485)|ureteric bud formation (GO:0060676)	extracellular region (GO:0005576)	protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			NS(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(8)|skin(2)	15	all_lung(31;0.00118)					GCCGGAGTCAGATACATCCAC	0.458																																					p.I228I		Atlas-SNP	.											.	GDNF	56	.	0			c.C684T						.						104	93	96					5																	37815756		2203	4300	6503	SO:0001819	synonymous_variant	2668	exon3			GAGTCAGATACAT		CCDS3922.1, CCDS3923.1, CCDS54845.1, CCDS54846.1, CCDS75237.1	5p13.1-p12	2014-01-30			ENSG00000168621	ENSG00000168621		"Endogenous ligands"	4232	protein-coding gene	gene with protein product	"astrocyte-derived trophic factor", "glial cell line derived neurotrophic factor", "glial derived neurotrophic factor"	600837				8493557	Standard	NM_199231		Approved	ATF1, ATF2, HFB1-GDNF	uc011cpg.2	P39905	OTTHUMG00000090809	ENST00000326524.2:c.633C>T	chr5.hg19:g.37815756G>A		112.0	0.0		93.0	25.0	NM_001190468	B7WPK7|O95448|O95449|O95986|Q6FH33|Q96L44|Q9UD32|Q9UD33|Q9UMV2|Q9UP67|Q9UP97	Silent	SNP	ENST00000326524.2	hg19	CCDS3922.1																																																																																			.	.		0.458	GDNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207606.1	NM_000514		A	37815756	G	A	37815756	2	1	253	1	0	0	0	0	0	0	0	1	6330	932	33	3		3	GDNF	5	37815756	Silent	SNP	G	TCGA-EP-A26S-01A-11D-A16V-10	21114309	37815756	143099504	30	34235										
SKIV2L2	23517	hgsc.bcm.edu	37	chr5	54637586	54637586	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	atatttgatgaaattcattaTatgagagattcaggtatatt	7	2	2	4			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr5:54637586T>C	ENST00000230640.5	+	7	1022	c.768T>C	c.(766-768)taT>taC	p.Y256Y	SKIV2L2_ENST00000545714.1_Silent_p.Y155Y	NM_015360.4	NP_056175.3	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2 (S. cerevisiae)	256	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				maturation of 5.8S rRNA (GO:0000460)|mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			NS(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|lung(12)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)				AAATTCATTATATGAGAGATT	0.299																																					p.Y256Y	Melanoma(2;92 134 23744 29976 33782)	Atlas-SNP	.											.	SKIV2L2	104	.	0			c.T768C						.						88	92	91					5																	54637586		2202	4297	6499	SO:0001819	synonymous_variant	23517	exon7			TCATTATATGAGA	D29641	CCDS3967.1	5q11.2	2008-11-25	2005-02-18	2005-02-18	ENSG00000039123	ENSG00000039123			18734	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 118"		"KIAA0052"	KIAA0052			Standard	NM_015360		Approved	Mtr4, Dob1, fSAP118	uc003jpy.4	P42285	OTTHUMG00000097019	ENST00000230640.5:c.768T>C	chr5.hg19:g.54637586T>C		99.0	0.0		102.0	42.0	NM_015360	Q2M386|Q6MZZ8|Q6P170|Q8N5R0|Q8TAG2	Silent	SNP	ENST00000230640.5	hg19	CCDS3967.1																																																																																			.	.		0.299	SKIV2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214108.1			C	54637586	T	C	54637586	2	2	253	1	0	0	0	0	0	0	0	1	14375	1413	49	2		2	SKIV2L2	5	54637586	Silent	SNP	T	TCGA-EP-A26S-01A-11D-A16V-10	16821830	54637586	126277674	31	34236										
GRAMD3	65983	hgsc.bcm.edu	37	chr5	125819257	125819257	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	ctcaaactcctgaatctgagAactctcgaggtttgggaaat	9	9	3	2			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr5:125819257A>C	ENST00000285689.3	+	9	1299	c.838A>C	c.(838-840)Aac>Cac	p.N280H	RP11-517I3.1_ENST00000512500.1_RNA|RP11-517I3.1_ENST00000515808.1_RNA|GRAMD3_ENST00000542322.1_Missense_Mutation_p.N288H|GRAMD3_ENST00000515200.1_Missense_Mutation_p.N257H|GRAMD3_ENST00000511134.1_Missense_Mutation_p.N264H|GRAMD3_ENST00000543198.1_Missense_Mutation_p.N257H|GRAMD3_ENST00000544396.1_Missense_Mutation_p.N176H|GRAMD3_ENST00000502348.1_Missense_Mutation_p.N171H|GRAMD3_ENST00000513040.1_Missense_Mutation_p.N295H	NM_023927.2	NP_076416.2	Q96HH9	GRAM3_HUMAN	GRAM domain containing 3	280						cytoplasmic microtubule (GO:0005881)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		Prostate(80;0.0928)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0401)|OV - Ovarian serous cystadenocarcinoma(64;0.0604)|all cancers(49;0.108)		TGAATCTGAGAACTCTCGAGG	0.373																																					p.N295H		Atlas-SNP	.											.	GRAMD3	30	.	0			c.A883C						.						77	74	75					5																	125819257		2203	4300	6503	SO:0001583	missense	65983	exon9			TCTGAGAACTCTC	BC008590	CCDS4136.1, CCDS54891.1, CCDS54892.1, CCDS54893.1, CCDS54894.1	5q23.2	2014-02-12	2005-11-03		ENSG00000155324	ENSG00000155324			24911	protein-coding gene	gene with protein product	"HCV NS3 transactivated protein 2"					12477932	Standard	NM_023927		Approved	NS3TP2, FLJ21313	uc011cwt.2	Q96HH9	OTTHUMG00000128943	ENST00000285689.3:c.838A>C	chr5.hg19:g.125819257A>C	ENSP00000285689:p.Asn280His	39.0	0.0		43.0	18.0	NM_001146319	B7Z1F2|B7Z3R1|B7Z6D8|B7Z8T2|D3DSZ3|Q9H753	Missense_Mutation	SNP	ENST00000285689.3	hg19	CCDS4136.1	.	.	.	.	.	.	.	.	.	.	A	14.03	2.414771	0.42817	.	.	ENSG00000155324	ENST00000513040;ENST00000543367;ENST00000285689;ENST00000515200;ENST00000542322;ENST00000544396;ENST00000543198;ENST00000502348;ENST00000511134	T;T;T;T;T;T;T;T	0.34859	1.34;1.34;1.37;1.34;1.38;1.39;1.38;1.36	6.07	4.92	0.64577	.	0.465860	0.26099	N	0.026350	T	0.37598	0.1009	M	0.66939	2.045	0.36831	D	0.886889	B;B;B;B;B	0.16166	0.005;0.003;0.004;0.016;0.005	B;B;B;B;B	0.11329	0.006;0.004;0.006;0.004;0.004	T	0.33137	-0.9880	10	0.37606	T	0.19	.	12.7036	0.57046	0.6522:0.3478:0.0:0.0	.	264;176;288;295;280	B7Z8T2;B7Z1F2;B7Z3R1;B7Z6D8;Q96HH9	.;.;.;.;GRAM3_HUMAN	H	295;264;280;257;288;176;257;171;264	ENSP00000426120:N295H;ENSP00000285689:N280H;ENSP00000426143:N257H;ENSP00000441876:N288H;ENSP00000444049:N176H;ENSP00000442902:N257H;ENSP00000427596:N171H;ENSP00000426088:N264H	ENSP00000285689:N280H	N	+	1	0	GRAMD3	125847156	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.939000	0.48995	1.111000	0.41721	0.533000	0.62120	AAC	.	.		0.373	GRAMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250922.2	NM_023927		C	125819257	A	C	125819257	3	2	253	1	0	0	0	0	1	0	0	0	6760	246	9	5	1086	5	GRAMD3	5	125819257	Missense_Mutation	SNP	A	TCGA-EP-A26S-01A-11D-A16V-10	71181671	125819257	55096003	32	34237										
NSD1	64324	hgsc.bcm.edu	37	chr5	176562164	176562164	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	ctgcccttttccaatccagtGaatttagatgcccctgaaga	7	12	0	4			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr5:176562164G>A	ENST00000439151.2	+	2	105	c.60G>A	c.(58-60)gtG>gtA	p.V20V	NSD1_ENST00000347982.4_5'UTR|NSD1_ENST00000354179.4_5'UTR|NSD1_ENST00000361032.4_Silent_p.V20V|NSD1_ENST00000511258.1_5'UTR	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	20					gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		CCAATCCAGTGAATTTAGATG	0.463			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.V20V		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.G60A						.						122	120	121					5																	176562164		2203	4300	6503	SO:0001819	synonymous_variant	64324	exon2	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	TCCAGTGAATTTA	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	14234	protein-coding gene	gene with protein product		606681	"Sotos syndrome"	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.60G>A	chr5.hg19:g.176562164G>A		63.0	0.0		56.0	18.0	NM_022455	Q96PD8|Q96RN7	Silent	SNP	ENST00000439151.2	hg19	CCDS4412.1																																																																																			.	.		0.463	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349		A	176562164	G	A	176562164	2	1	253	1	0	0	0	0	0	0	0	1	10678	1277	45	3		3	NSD1	5	176562164	Silent	SNP	G	TCGA-EP-A26S-01A-11D-A16V-10	50742907	176562164	4353096	33	34238										
COL11A2	1302	hgsc.bcm.edu	37	chr6	33144048	33144048	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	gtgctcaccttctcacccttAtgacccttcagaccccgaat	5	17	3	2			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr6:33144048A>T	ENST00000374708.4	-	26	2202	c.1944T>A	c.(1942-1944)caT>caA	p.H648Q	COL11A2_ENST00000477772.1_Intron|COL11A2_ENST00000374712.1_Missense_Mutation_p.H653Q|COL11A2_ENST00000361917.1_Missense_Mutation_p.H627Q|COL11A2_ENST00000357486.1_Missense_Mutation_p.H713Q|COL11A2_ENST00000374713.1_Missense_Mutation_p.H687Q|COL11A2_ENST00000395197.1_Missense_Mutation_p.H674Q|COL11A2_ENST00000341947.2_Missense_Mutation_p.H734Q|COL11A2_ENST00000374714.1_Missense_Mutation_p.H708Q	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	734	Triple-helical region.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						TCTCACCCTTATGACCCTTCA	0.587																																					p.H734Q	Melanoma(1;90 116 3946 5341 17093)	Atlas-SNP	.											.	COL11A2	124	.	0			c.T2202A						.						75	43	54					6																	33144048		1511	2709	4220	SO:0001583	missense	1302	exon28			ACCCTTATGACCC	U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"Collagens"	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000374708.4:c.1944T>A	chr6.hg19:g.33144048A>T	ENSP00000363840:p.His648Gln	81.0	0.0		82.0	36.0	NM_080680	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Missense_Mutation	SNP	ENST00000374708.4	hg19	CCDS43452.1	.	.	.	.	.	.	.	.	.	.	A	11.80	1.747069	0.30955	.	.	ENSG00000204248	ENST00000374708;ENST00000341947;ENST00000357486;ENST00000374714;ENST00000374713;ENST00000395197;ENST00000374712;ENST00000361917	D;D;D;D;D;D;D;D	0.95069	-3.35;-3.35;-3.35;-3.6;-3.35;-3.35;-3.35;-3.35	4.88	-0.479	0.12089	.	0.000000	0.85682	D	0.000000	T	0.81555	0.4847	N	0.03281	-0.365	0.47905	D	0.999546	P;P;D	0.57257	0.756;0.748;0.979	P;P;P	0.55055	0.583;0.583;0.767	T	0.78393	-0.2221	10	0.20519	T	0.43	.	8.0482	0.30562	0.4656:0.0:0.5344:0.0	.	627;648;734	P13942-8;P13942-6;P13942	.;.;COBA2_HUMAN	Q	648;734;713;708;687;674;653;627	ENSP00000363840:H648Q;ENSP00000339915:H734Q;ENSP00000350079:H713Q;ENSP00000363846:H708Q;ENSP00000363845:H687Q;ENSP00000378623:H674Q;ENSP00000363844:H653Q;ENSP00000355123:H627Q	ENSP00000339915:H734Q	H	-	3	2	COL11A2	33252026	0.998000	0.40836	0.994000	0.49952	0.997000	0.91878	0.360000	0.20250	-0.219000	0.10003	0.448000	0.29417	CAT	.	.		0.587	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2			T	33144048	A	T	33144048	3	4	253	1	0	0	0	0	1	0	0	0	3670	446	16	4	3164	4	COL11A2	6	33144048	Missense_Mutation	SNP	A	TCGA-EP-A26S-01A-11D-A16V-10		33144048	137971019	34	34239										
SLC35B2	347734	hgsc.bcm.edu	37	chr6	44223037	44223037	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	gtcaggtactcccagtgttcGtagctgcgccgagacacaag	12	12	1	1	rs538318523	byFrequency	TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr6:44223037G>A	ENST00000393812.3	-	4	848	c.705C>T	c.(703-705)taC>taT	p.Y235Y	SLC35B2_ENST00000538577.1_Silent_p.Y142Y|SLC35B2_ENST00000537814.1_Silent_p.Y102Y|SLC35B2_ENST00000393810.1_3'UTR|MIR4647_ENST00000583964.1_RNA|SLC35B2_ENST00000495706.1_5'UTR	NM_178148.2	NP_835361.1	Q8TB61	S35B2_HUMAN	solute carrier family 35 (adenosine 3'-phospho 5'-phosphosulfate transporter), member B2	235					3'-phospho-5'-adenylyl sulfate transmembrane transport (GO:1902559)|3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|3'-phosphoadenosine 5'-phosphosulfate transport (GO:0046963)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3'-phosphoadenosine 5'-phosphosulfate transmembrane transporter activity (GO:0046964)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|kidney(3)|large_intestine(2)|lung(4)|ovary(2)|urinary_tract(1)	15	all_cancers(18;2e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CCCAGTGTTCGTAGCTGCGCC	0.587													g|||	2	0.000399361	0.0015	0	5008	,	,		19503	0		0	False		,,,				2504	0				p.Y235Y		Atlas-SNP	.											.	SLC35B2	40	.	0			c.C705T						.						82	80	81					6																	44223037		2203	4300	6503	SO:0001819	synonymous_variant	347734	exon4			GTGTTCGTAGCTG	AK075456	CCDS34462.1, CCDS69127.1, CCDS75462.1, CCDS75463.1	6p12.1-p11.21	2013-07-17	2013-07-17		ENSG00000157593	ENSG00000157593		"Solute carriers"	16872	protein-coding gene	gene with protein product		610788	"solute carrier family 35, member B2"				Standard	NM_001286517		Approved	UGTrel4	uc003oxd.3	Q8TB61	OTTHUMG00000014760	ENST00000393812.3:c.705C>T	chr6.hg19:g.44223037G>A		77.0	0.0		63.0	28.0	NM_178148	B4DDU9|F5H7Y9|Q2VY06|Q53GA3|Q5T9W1|Q5T9W2|Q7Z2G3|Q8NBK6|Q96AR6	Silent	SNP	ENST00000393812.3	hg19	CCDS34462.1																																																																																			.	.		0.587	SLC35B2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040724.2			A	44223037	G	A	44223037	2	1	253	1	0	0	0	0	0	0	0	1	14591	1140	40	1		1	SLC35B2	6	44223037	Silent	SNP	G	TCGA-EP-A26S-01A-11D-A16V-10	11078989	44223037	126892030	35	34240										
FBXL4	26235	hgsc.bcm.edu	37	chr6	99322272	99322272	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	gtaaagaaagatctttacaaGattccaggagttttcttaag	8	5	2	3			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr6:99322272G>T	ENST00000369244.2	-	10	2176	c.1748C>A	c.(1747-1749)tCt>tAt	p.S583Y	FBXL4_ENST00000229971.1_Missense_Mutation_p.S583Y	NM_001278716.1	NP_001265645.1	Q9UKA2	FBXL4_HUMAN	F-box and leucine-rich repeat protein 4	583					ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(4)|prostate(3)|skin(2)	18		all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197)		BRCA - Breast invasive adenocarcinoma(108;0.0413)		ATCTTTACAAGATTCCAGGAG	0.343																																					p.S583Y		Atlas-SNP	.											.	FBXL4	54	.	0			c.C1748A						.						119	123	122					6																	99322272		2203	4300	6503	SO:0001583	missense	26235	exon9			TTACAAGATTCCA	AF176699	CCDS5041.1	6q16.1-q16.3	2011-06-09			ENSG00000112234	ENSG00000112234		"F-boxes / Leucine-rich repeats"	13601	protein-coding gene	gene with protein product		605654				10531035	Standard	NM_012160		Approved	FBL4, FBL5	uc003ppf.1	Q9UKA2	OTTHUMG00000015259	ENST00000369244.2:c.1748C>A	chr6.hg19:g.99322272G>T	ENSP00000358247:p.Ser583Tyr	116.0	0.0		108.0	49.0	NM_012160	B2R7Q5|E1P530|O95919|Q5BJH0|Q9UJU0	Missense_Mutation	SNP	ENST00000369244.2	hg19	CCDS5041.1	.	.	.	.	.	.	.	.	.	.	G	15.27	2.783913	0.49891	.	.	ENSG00000112234	ENST00000369244;ENST00000229971	T;T	0.19105	2.17;2.17	5.95	5.08	0.68730	.	0.166936	0.53938	D	0.000042	T	0.11707	0.0285	L	0.40543	1.245	0.45867	D	0.998725	P	0.36789	0.57	B	0.40101	0.319	T	0.04796	-1.0926	10	0.30854	T	0.27	.	15.774	0.78193	0.0:0.3814:0.6186:0.0	.	583	Q9UKA2	FBXL4_HUMAN	Y	583	ENSP00000358247:S583Y;ENSP00000229971:S583Y	ENSP00000229971:S583Y	S	-	2	0	FBXL4	99428993	1.000000	0.71417	0.990000	0.47175	0.999000	0.98932	4.331000	0.59273	1.504000	0.48704	0.655000	0.94253	TCT	.	.		0.343	FBXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041587.2			T	99322272	G	T	99322272	3	4	253	1	0	0	0	0	1	0	0	0	5729	942	33	3	121	3	FBXL4	6	99322272	Missense_Mutation	SNP	G	TCGA-EP-A26S-01A-11D-A16V-10	55099235	99322272	71792795	36	34241										
RPF2	84154	hgsc.bcm.edu	37	chr6	111318428	111318428	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	attgttctttattcatgtttGgctcccataataagaagcgg	8	7	2	1			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr6:111318428G>A	ENST00000441448.2	+	5	369	c.277G>A	c.(277-279)Ggc>Agc	p.G93S		NM_032194.1	NP_115570.1	Q9H7B2	RPF2_HUMAN	ribosome production factor 2 homolog (S. cerevisiae)	93	Brix. {ECO:0000255|PROSITE- ProRule:PRU00034}.					nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|ovary(2)	7						ATTCATGTTTGGCTCCCATAA	0.299																																					p.G93S		Atlas-SNP	.											.	RPF2	26	.	0			c.G277A						.						71	66	68					6																	111318428		2202	4298	6500	SO:0001583	missense	84154	exon5			ATGTTTGGCTCCC	AK024740	CCDS5088.1	6q21	2009-09-25	2009-09-25	2009-09-25	ENSG00000197498	ENSG00000197498			20870	protein-coding gene	gene with protein product	"ribosomal processing factor 2 homolog (S. cerevisiae)"		"brix domain containing 1"	BXDC1		12048200	Standard	NM_032194		Approved	FLJ21087, bA397G5.4	uc003pun.3	Q9H7B2	OTTHUMG00000015368	ENST00000441448.2:c.277G>A	chr6.hg19:g.111318428G>A	ENSP00000402338:p.Gly93Ser	122.0	0.0		95.0	36.0	NM_032194	Q5VXN1|Q8N4A1	Missense_Mutation	SNP	ENST00000441448.2	hg19	CCDS5088.1	.	.	.	.	.	.	.	.	.	.	g	23.9	4.467411	0.84533	.	.	ENSG00000197498	ENST00000441448;ENST00000368864;ENST00000425871	T;T;T	0.41400	1.0;1.0;1.0	5.12	5.12	0.69794	Brix domain (3);	0.000000	0.85682	D	0.000000	T	0.52805	0.1757	L	0.60957	1.885	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.65573	0.936;0.936	T	0.53308	-0.8457	10	0.54805	T	0.06	-32.9184	17.7258	0.88365	0.0:0.0:1.0:0.0	.	93;93	A8K800;Q9H7B2	.;RPF2_HUMAN	S	93;54;60	ENSP00000402338:G93S;ENSP00000357857:G54S;ENSP00000414026:G60S	ENSP00000357857:G54S	G	+	1	0	RPF2	111425121	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	6.901000	0.75693	2.542000	0.85734	0.655000	0.94253	GGC	.	.		0.299	RPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041813.2	NM_032194		A	111318428	G	A	111318428	3	1	253	1	0	0	0	0	1	0	0	0	13562	1348	47	3	295	3	RPF2	6	111318428	Missense_Mutation	SNP	G	TCGA-EP-A26S-01A-11D-A16V-10	11996156	111318428	59796639	37	34242										
PLEKHG1	57480	hgsc.bcm.edu	37	chr6	151161944	151161944	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	tgacaaactgaatgactatcTttggagggggccatctccca	10	10	2	3			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr6:151161944T>G	ENST00000358517.2	+	16	4281	c.4070T>G	c.(4069-4071)cTt>cGt	p.L1357R	PLEKHG1_ENST00000367328.1_Missense_Mutation_p.L1357R			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	1357							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(19)|ovary(5)|prostate(4)|stomach(1)|urinary_tract(3)	53			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		AATGACTATCTTTGGAGGGGG	0.408																																					p.L1357R		Atlas-SNP	.											.	PLEKHG1	97	.	0			c.T4070G						.						86	87	86					6																	151161944		2203	4300	6503	SO:0001583	missense	57480	exon17			ACTATCTTTGGAG	AB033035	CCDS34552.1	6q25.1	2013-01-11			ENSG00000120278	ENSG00000120278		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	20884	protein-coding gene	gene with protein product						10574462	Standard	XM_005267064		Approved	KIAA1209, ARHGEF41	uc003qny.1	Q9ULL1	OTTHUMG00000015824	ENST00000358517.2:c.4070T>G	chr6.hg19:g.151161944T>G	ENSP00000351318:p.Leu1357Arg	94.0	0.0		65.0	26.0	NM_001029884	Q5T1F2	Missense_Mutation	SNP	ENST00000358517.2	hg19	CCDS34552.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.366450	0.82463	.	.	ENSG00000120278	ENST00000367328;ENST00000358517	T;T	0.71934	-0.61;-0.61	5.7	5.7	0.88788	.	0.175401	0.51477	D	0.000093	T	0.79516	0.4459	M	0.66939	2.045	0.48571	D	0.99967	D;D	0.89917	1.0;0.998	D;D	0.76575	0.988;0.915	T	0.82540	-0.0406	10	0.87932	D	0	.	15.9568	0.79893	0.0:0.0:0.0:1.0	.	1164;1357	Q5EBL9;Q9ULL1	.;PKHG1_HUMAN	R	1357	ENSP00000356297:L1357R;ENSP00000351318:L1357R	ENSP00000351318:L1357R	L	+	2	0	PLEKHG1	151203637	1.000000	0.71417	0.992000	0.48379	0.984000	0.73092	7.170000	0.77587	2.160000	0.67779	0.533000	0.62120	CTT	.	.		0.408	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042691.1			G	151161944	T	G	151161944	3	3	253	1	0	0	0	0	1	0	0	0	12077	1609	56	5	4128	5	PLEKHG1	6	151161944	Missense_Mutation	SNP	T	TCGA-EP-A26S-01A-11D-A16V-10	39843516	151161944	19953123	38	34243										
RSPH10B	222967	hgsc.bcm.edu	37	chr7	5967916	5967916	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	cttattttctccttgatagcTtcttcacgtttatacgcatg	5	10	3	1			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr7:5967916T>C	ENST00000405415.1	-	19	2729	c.2343A>G	c.(2341-2343)gaA>gaG	p.E781E	RSPH10B_ENST00000535104.1_5'UTR|RSPH10B_ENST00000404406.1_Silent_p.E781E|RSPH10B_ENST00000539903.1_3'UTR|RSPH10B_ENST00000337579.3_Silent_p.E781E|RSPH10B_ENST00000441023.2_Silent_p.E781E			P0C881	R10B1_HUMAN	radial spoke head 10 homolog B (Chlamydomonas)	781										breast(1)|kidney(1)|lung(4)|ovary(1)|skin(4)	11		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0974)		CCTTGATAGCTTCTTCACGTT	0.463																																					p.E781E		Atlas-SNP	.											.	RSPH10B	28	.	0			c.A2343G						.						187	173	177					7																	5967916		2202	4298	6500	SO:0001819	synonymous_variant	222967	exon20			GATAGCTTCTTCA		CCDS34598.1	7p22.2	2008-07-04			ENSG00000155026	ENSG00000155026			27362	protein-coding gene	gene with protein product						16507594	Standard	NM_173565		Approved		uc003sph.1	P0C881	OTTHUMG00000152378	ENST00000405415.1:c.2343A>G	chr7.hg19:g.5967916T>C		667.0	0.0		465.0	135.0	NM_173565	A6NMW7|Q86ST9|Q8NE68	Silent	SNP	ENST00000405415.1	hg19	CCDS34598.1																																																																																			.	.		0.463	RSPH10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325465.2	NM_173565		C	5967916	T	C	5967916	2	2	253	1	0	0	0	0	0	0	0	1	13718	1606	56	2		2	RSPH10B	7	5967916	Silent	SNP	T	TCGA-EP-A26S-01A-11D-A16V-10		5967916	153170747	39	34244										
MPP6	51678	hgsc.bcm.edu	37	chr7	24705683	24705683	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	agcaaaaaaaagaaaaagatGatgtatctcacaaccagaaa	6	6	1	4			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr7:24705683G>C	ENST00000222644.5	+	8	1177	c.927G>C	c.(925-927)atG>atC	p.M309I	MPP6_ENST00000396475.2_Missense_Mutation_p.M309I|MPP6_ENST00000409761.1_Missense_Mutation_p.M197I			Q99547	MPH6_HUMAN	membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6)	0					maturation of 5.8S rRNA (GO:0000460)	cytoplasm (GO:0005737)|exosome (RNase complex) (GO:0000178)|nucleolus (GO:0005730)|nucleus (GO:0005634)	RNA binding (GO:0003723)	p.M309I(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|pancreas(1)|skin(2)	20						AGAAAAAGATGATGTATCTCA	0.303																																					p.M309I		Atlas-SNP	.											.	MPP6	62	.	1	Substitution - Missense(1)	lung(1)	c.G927C						.						92	107	102					7																	24705683		2197	4293	6490	SO:0001583	missense	51678	exon9			AAAGATGATGTAT	AF162130	CCDS5388.1	7p15	2007-08-01			ENSG00000105926	ENSG00000105926			18167	protein-coding gene	gene with protein product		606959				10753959, 11311936	Standard	NM_016447		Approved	PALS2, VAM-1, p55T	uc003swx.3	Q9NZW5	OTTHUMG00000023507	ENST00000222644.5:c.927G>C	chr7.hg19:g.24705683G>C	ENSP00000222644:p.Met309Ile	76.0	0.0		87.0	40.0	NM_016447	B2RAF0	Missense_Mutation	SNP	ENST00000222644.5	hg19	CCDS5388.1	.	.	.	.	.	.	.	.	.	.	G	14.74	2.624452	0.46840	.	.	ENSG00000105926	ENST00000222644;ENST00000409761;ENST00000396475	D;D;D	0.82167	-1.58;-1.58;-1.58	5.32	5.32	0.75619	Src homology-3 domain (1);	0.000000	0.64402	D	0.000002	T	0.73877	0.3643	N	0.16743	0.435	0.80722	D	1	B	0.17268	0.021	B	0.12156	0.007	T	0.67707	-0.5601	10	0.36615	T	0.2	.	18.9769	0.92740	0.0:0.0:1.0:0.0	.	309	Q9NZW5	MPP6_HUMAN	I	309;197;309	ENSP00000222644:M309I;ENSP00000386262:M197I;ENSP00000379737:M309I	ENSP00000222644:M309I	M	+	3	0	MPP6	24672208	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.794000	0.85869	2.477000	0.83638	0.591000	0.81541	ATG	.	.		0.303	MPP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250272.4			C	24705683	G	C	24705683	3	2	253	1	0	0	0	0	1	0	0	0	9747	1290	45	4	953	4	MPP6	7	24705683	Missense_Mutation	SNP	G	TCGA-EP-A26S-01A-11D-A16V-10	18737767	24705683	134432980	40	34245										
ABCB4	5244	hgsc.bcm.edu	37	chr7	87051459	87051459	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	gaaggaagaaagtaaaaaaaGaaataattcccagaaataag	8	3	0	3			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr7:87051459G>A	ENST00000265723.4	-	18	2405	c.2294C>T	c.(2293-2295)tCt>tTt	p.S765F	ABCB4_ENST00000358400.3_Missense_Mutation_p.S765F|ABCB4_ENST00000359206.3_Missense_Mutation_p.S765F|ABCB4_ENST00000545634.1_Missense_Mutation_p.S765F|ABCB4_ENST00000453593.1_Missense_Mutation_p.S765F	NM_000443.3|NM_018849.2	NP_000434.1|NP_061337.1	P21439	MDR3_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 4	765	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular lipid metabolic process (GO:0044255)|lipid metabolic process (GO:0006629)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|xenobiotic-transporting ATPase activity (GO:0008559)			breast(5)|endometrium(7)|kidney(2)|large_intestine(15)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				Colchicine(DB01394)|Etravirine(DB06414)|Silodosin(DB06207)	AGTAAAAAAAGAAATAATTCC	0.318																																					p.S765F		Atlas-SNP	.											.	ABCB4	177	.	0			c.C2294T						.						43	45	45					7																	87051459		2203	4300	6503	SO:0001583	missense	5244	exon18			AAAAAAGAAATAA	M23234	CCDS5605.1, CCDS5606.1, CCDS5607.1	7q21	2012-03-14			ENSG00000005471	ENSG00000005471		"ATP binding cassette transporters / subfamily B"	45	protein-coding gene	gene with protein product		171060		PGY3, MDR3		2892668, 11313316	Standard	NM_018850		Approved	MDR2, PFIC-3, GBD1	uc003uiv.1	P21439	OTTHUMG00000023396	ENST00000265723.4:c.2294C>T	chr7.hg19:g.87051459G>A	ENSP00000265723:p.Ser765Phe	195.0	0.0		273.0	76.0	NM_018850	A0A2V7|A4D1D3|A4D1D4|A4D1D5|D6W5P3|D6W5P4|Q14813	Missense_Mutation	SNP	ENST00000265723.4	hg19	CCDS5606.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.529316	0.85706	.	.	ENSG00000005471	ENST00000359206;ENST00000358400;ENST00000265723;ENST00000453593;ENST00000545634	D;D;D;D;D	0.88818	-2.43;-2.43;-2.43;-2.43;-2.43	5.99	5.99	0.97316	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.053448	0.85682	D	0.000000	D	0.94843	0.8334	M	0.82517	2.595	0.80722	D	1	B;D;D	0.61697	0.357;0.987;0.99	B;D;D	0.70935	0.301;0.952;0.971	D	0.94818	0.7984	10	0.72032	D	0.01	-16.5265	18.2507	0.90002	0.0:0.0:1.0:0.0	.	765;765;765	A4D1D5;P21439-2;P21439	.;.;MDR3_HUMAN	F	765	ENSP00000352135:S765F;ENSP00000351172:S765F;ENSP00000265723:S765F;ENSP00000392983:S765F;ENSP00000437465:S765F	ENSP00000265723:S765F	S	-	2	0	ABCB4	86889395	1.000000	0.71417	0.972000	0.41901	0.987000	0.75469	6.605000	0.74155	2.840000	0.97914	0.655000	0.94253	TCT	.	.		0.318	ABCB4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000336083.1	NM_000443		A	87051459	G	A	87051459	3	1	253	1	0	0	0	0	1	0	0	0	43	942	33	3	1610	3	ABCB4	7	87051459	Missense_Mutation	SNP	G	TCGA-EP-A26S-01A-11D-A16V-10	62345776	87051459	72087204	41	34246										
PVRIG	79037	hgsc.bcm.edu	37	chr7	99818613	99818613	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	gccactatcaacaccagctgCcgcccagctactttggacac	7	17	1	0			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr7:99818613C>A	ENST00000317271.2	+	6	1083	c.720C>A	c.(718-720)tgC>tgA	p.C240*	GATS_ENST00000436886.2_Intron|GATS_ENST00000543273.1_RNA|AC005071.1_ENST00000410550.1_RNA	NM_024070.3	NP_076975.2	Q6DKI7	PVRIG_HUMAN	poliovirus receptor related immunoglobulin domain containing	240						integral component of membrane (GO:0016021)				breast(1)|endometrium(3)|kidney(1)|lung(3)|prostate(1)|skin(2)	11	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					ACACCAGCTGCCGCCCAGCTA	0.677																																					p.C240X		Atlas-SNP	.											.	PVRIG	20	.	0			c.C720A						.						65	70	68					7																	99818613		2203	4300	6503	SO:0001587	stop_gained	79037	exon6			CAGCTGCCGCCCA	BC001129	CCDS5690.1	7q22.1	2013-06-26			ENSG00000213413	ENSG00000213413			32190	protein-coding gene	gene with protein product						16926269	Standard	NM_024070		Approved	MGC2463, C7orf15	uc003uuf.1	Q6DKI7	OTTHUMG00000156798	ENST00000317271.2:c.720C>A	chr7.hg19:g.99818613C>A	ENSP00000316675:p.Cys240*	100.0	0.0		102.0	30.0	NM_024070	D6W5U9|Q9BVK3	Nonsense_Mutation	SNP	ENST00000317271.2	hg19	CCDS5690.1	.	.	.	.	.	.	.	.	.	.	c	26.9	4.780649	0.90195	.	.	ENSG00000213413	ENST00000317271	.	.	.	3.01	3.01	0.34805	.	.	.	.	.	.	.	.	.	.	.	0.35377	D	0.789556	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	.	9.7879	0.40688	0.0:1.0:0.0:0.0	.	.	.	.	X	240	.	ENSP00000316675:C240X	C	+	3	2	PVRIG	99656549	0.001000	0.12720	0.004000	0.12327	0.149000	0.21700	0.819000	0.27308	2.010000	0.58986	0.505000	0.49811	TGC	.	.		0.677	PVRIG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345870.2	NM_024070		A	99818613	C	A	99818613	4	1	253	1	0	0	0	0	0	1	0	0	12853	747	26	3	738	3	PVRIG	7	99818613	Nonsense_Mutation	SNP	C	TCGA-EP-A26S-01A-11D-A16V-10	12767154	99818613	59320050	42	34247										
PNPLA8	50640	hgsc.bcm.edu	37	chr7	108131857	108131857	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	agagactctaagcttaccttAggacatgtggggtttcttgc	11	8	2	1			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr7:108131857A>T	ENST00000422087.1	-	9	2086	c.1680T>A	c.(1678-1680)ccT>ccA	p.P560P	PNPLA8_ENST00000453144.1_Silent_p.P460P|PNPLA8_ENST00000388728.5_Silent_p.P560P|PNPLA8_ENST00000257694.8_Silent_p.P560P|PNPLA8_ENST00000436062.1_Silent_p.P560P|PNPLA8_ENST00000426128.2_Silent_p.P560P	NM_015723.3	NP_056538.1	Q9NP80	PLPL8_HUMAN	patatin-like phospholipase domain containing 8	560	Patatin.				arachidonic acid metabolic process (GO:0019369)|arachidonic acid secretion (GO:0050482)|cell death (GO:0008219)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|linoleic acid metabolic process (GO:0043651)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylcholine catabolic process (GO:0034638)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylethanolamine catabolic process (GO:0046338)|phospholipid metabolic process (GO:0006644)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|calcium-independent phospholipase A2 activity (GO:0047499)|lysophospholipase activity (GO:0004622)			breast(5)|endometrium(1)|kidney(3)|large_intestine(5)|lung(12)|upper_aerodigestive_tract(3)	29						AGCTTACCTTAGGACATGTGG	0.343																																					p.P560P		Atlas-SNP	.											.	PNPLA8	82	.	0			c.T1680A						.						139	134	136					7																	108131857		2203	4300	6503	SO:0001819	synonymous_variant	50640	exon7			TACCTTAGGACAT	AF217519	CCDS34733.1, CCDS59075.1, CCDS59508.1	7q31	2012-07-31			ENSG00000135241	ENSG00000135241		"Patatin-like phospholipase domain containing"	28900	protein-coding gene	gene with protein product		612123				10744668, 10833412, 16799181, 19029121	Standard	NM_015723		Approved	IPLA2G, IPLA2-2, iPLA2gamma	uc003vfj.2	Q9NP80	OTTHUMG00000154870	ENST00000422087.1:c.1680T>A	chr7.hg19:g.108131857A>T		115.0	0.0		147.0	56.0	NM_001256008	A4D0S1|C9JZI4|O95035|Q8N3I3|Q9H7T5|Q9NR17|Q9NUN2|Q9NZ79	Silent	SNP	ENST00000422087.1	hg19	CCDS34733.1																																																																																			.	.		0.343	PNPLA8-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337475.1	NM_015723		T	108131857	A	T	108131857	2	4	253	1	0	0	0	0	0	0	0	1	12180	407	15	4		4	PNPLA8	7	108131857	Silent	SNP	A	TCGA-EP-A26S-01A-11D-A16V-10	8313244	108131857	51006806	43	34248										
C9orf170	401535	hgsc.bcm.edu	37	chr9	89763702	89763702	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	cccctgcatctcctcctgggGgtgtgggggccgagtgggag	18	12	1	0			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr9:89763702G>T	ENST00000375941.2	+	1	144	c.57G>T	c.(55-57)ggG>ggT	p.G19G		NM_001001709.2	NP_001001709.1	A2RU37	CI170_HUMAN	chromosome 9 open reading frame 170	19										large_intestine(3)|lung(2)|prostate(1)	6						TCCTCCTGGGGGTGTGGGGGC	0.711																																					p.G19G		Atlas-SNP	.											.	C9orf170	17	.	0			c.G57T						.						16	19	18					9																	89763702		2202	4296	6498	SO:0001819	synonymous_variant	401535	exon1			CCTGGGGGTGTGG	AK127445	CCDS35058.1	9q21.33	2009-02-11			ENSG00000204446	ENSG00000204446			33817	protein-coding gene	gene with protein product							Standard	NM_001001709		Approved	FLJ45537	uc004apa.1	A2RU37	OTTHUMG00000159587	ENST00000375941.2:c.57G>T	chr9.hg19:g.89763702G>T		34.0	0.0		27.0	14.0	NM_001001709		Silent	SNP	ENST00000375941.2	hg19	CCDS35058.1																																																																																			.	.		0.711	C9orf170-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356346.1	NM_001001709		T	89763702	G	T	89763702	2	4	253	1	0	0	0	0	0	0	0	1	2471	1219	43	3		3	C9orf170	9	89763702	Silent	SNP	G	TCGA-EP-A26S-01A-11D-A16V-10		89763702	51449729	44	34249										
PSAP	5660	hgsc.bcm.edu	37	chr10	73610968	73610968	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	ggaggctggccaggaggaagAgggcgtacatagcgccgtct	18	9	1	1			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr10:73610968A>T	ENST00000394936.3	-	1	158	c.11T>A	c.(10-12)cTc>cAc	p.L4H	PSAP_ENST00000394934.1_Missense_Mutation_p.L4H			P07602	SAP_HUMAN	prosaposin	4					blood coagulation (GO:0007596)|cellular response to organic substance (GO:0071310)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|glycosphingolipid metabolic process (GO:0006687)|lipid transport (GO:0006869)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of catalytic activity (GO:0043085)|prostate gland growth (GO:0060736)|regulation of lipid metabolic process (GO:0019216)|regulation of MAPK cascade (GO:0043408)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|lipid binding (GO:0008289)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	13						CAGGAGGAAGAGGGCGTACAT	0.652																																					p.L4H		Atlas-SNP	.											.	PSAP	43	.	0			c.T11A						.						26	22	23					10																	73610968		1904	3576	5480	SO:0001583	missense	5660	exon1			AGGAAGAGGGCGT	BC004275	CCDS7311.1	10q21-q22	2014-01-30	2008-07-31		ENSG00000197746	ENSG00000197746		"Endogenous ligands"	9498	protein-coding gene	gene with protein product	"variant Gaucher disease and variant metachromatic leukodystrophy"	176801	"sphingolipid activator protein-1"	SAP1, GLBA		2717620	Standard	NM_001042465		Approved		uc001jsm.3	P07602	OTTHUMG00000018429	ENST00000394936.3:c.11T>A	chr10.hg19:g.73610968A>T	ENSP00000378394:p.Leu4His	54.0	0.0		56.0	32.0	NM_001042466	P07292|P15793|P78538|P78541|P78546|P78547|P78558|Q53Y86|Q6IBQ6|Q92739|Q92740|Q92741|Q92742	Missense_Mutation	SNP	ENST00000394936.3	hg19	CCDS7311.1	.	.	.	.	.	.	.	.	.	.	A	13.98	2.399257	0.42512	.	.	ENSG00000197746	ENST00000394936;ENST00000373120;ENST00000357471;ENST00000394934;ENST00000394929;ENST00000404083	T;T	0.76578	-1.02;-1.03	4.97	4.97	0.65823	.	0.992181	0.08197	N	0.982913	D	0.82637	0.5080	M	0.69358	2.11	0.09310	N	1	D	0.59767	0.986	P	0.51453	0.67	T	0.71517	-0.4569	10	0.87932	D	0	-15.3803	11.3155	0.49390	1.0:0.0:0.0:0.0	.	4	P07602	SAP_HUMAN	H	4;4;4;4;4;7	ENSP00000378394:L4H;ENSP00000378392:L4H	ENSP00000350063:L4H	L	-	2	0	PSAP	73280974	0.029000	0.19370	0.003000	0.11579	0.484000	0.33280	3.955000	0.56715	1.980000	0.57719	0.397000	0.26171	CTC	.	.		0.652	PSAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048553.1	NM_002778		T	73610968	A	T	73610968	3	4	253	1	0	0	0	0	1	0	0	0	12655	304	11	4	1635	4	PSAP	10	73610968	Missense_Mutation	SNP	A	TCGA-EP-A26S-01A-11D-A16V-10		73610968	61923779	45	34250										
PLEKHA1	59338	hgsc.bcm.edu	37	chr10	124166157	124166157	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	agcaggacctagtggaatggGtaaatgtgttaaacaaagct	12	5	0	0			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr10:124166157G>T	ENST00000368990.3	+	5	441	c.310G>T	c.(310-312)Gta>Tta	p.V104L	PLEKHA1_ENST00000538022.1_Missense_Mutation_p.V104L|PLEKHA1_ENST00000433307.1_Missense_Mutation_p.V104L|PLEKHA1_ENST00000368988.1_Missense_Mutation_p.V104L|PLEKHA1_ENST00000494222.1_Intron|PLEKHA1_ENST00000368989.2_Missense_Mutation_p.V104L	NM_001001974.2	NP_001001974.1	Q9HB21	PKHA1_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1	104	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				androgen metabolic process (GO:0008209)|B cell receptor signaling pathway (GO:0050853)|cellular response to hydrogen peroxide (GO:0070301)|establishment of protein localization (GO:0045184)|estrogen metabolic process (GO:0008210)|face morphogenesis (GO:0060325)|Leydig cell differentiation (GO:0033327)|luteinization (GO:0001553)|multicellular organism growth (GO:0035264)|negative regulation of protein kinase B signaling (GO:0051898)|palate development (GO:0060021)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic development (GO:0009791)|ruffle organization (GO:0031529)|skeletal system morphogenesis (GO:0048705)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|urinary_tract(1)	13		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				AGTGGAATGGGTAAATGTGTT	0.313																																					p.V104L		Atlas-SNP	.											.	PLEKHA1	33	.	0			c.G310T						.						133	134	133					10																	124166157		2203	4300	6503	SO:0001583	missense	59338	exon5			GAATGGGTAAATG	AF286160	CCDS7629.1, CCDS55730.1	10q26.3	2013-01-10	2002-01-14		ENSG00000107679	ENSG00000107679		"Pleckstrin homology (PH) domain containing"	14335	protein-coding gene	gene with protein product	"tandem PH domain containing protein-1"	607772	"pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 1"			11001876, 15485858	Standard	NM_001001974		Approved	TAPP1	uc001lge.2	Q9HB21	OTTHUMG00000019184	ENST00000368990.3:c.310G>T	chr10.hg19:g.124166157G>T	ENSP00000357986:p.Val104Leu	149.0	0.0		139.0	62.0	NM_021622	B3KQ55|D3DRE2|Q9BVK0	Missense_Mutation	SNP	ENST00000368990.3	hg19	CCDS7629.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.082336	0.76528	.	.	ENSG00000107679	ENST00000368990;ENST00000368989;ENST00000409427;ENST00000368988;ENST00000538022;ENST00000392799;ENST00000433307	T;T;T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13;-1.13;-1.13	6.17	5.25	0.73442	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.112241	0.64402	D	0.000010	D	0.84534	0.5493	M	0.65498	2.005	0.54753	D	0.999983	B;D	0.53619	0.012;0.961	B;D	0.63597	0.096;0.916	D	0.84930	0.0859	10	0.52906	T	0.07	-12.7731	10.9078	0.47090	0.1466:0.0:0.8534:0.0	.	104;104	B3KQ55;Q9HB21	.;PKHA1_HUMAN	L	104	ENSP00000357986:V104L;ENSP00000357985:V104L;ENSP00000357984:V104L;ENSP00000438608:V104L;ENSP00000376547:V104L;ENSP00000394416:V104L	ENSP00000357984:V104L	V	+	1	0	PLEKHA1	124156147	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.489000	0.60309	1.561000	0.49584	0.655000	0.94253	GTA	.	.		0.313	PLEKHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050783.1	NM_001001974		T	124166157	G	T	124166157	3	4	253	1	0	0	0	0	1	0	0	0	12064	1261	44	3	324	3	PLEKHA1	10	124166157	Missense_Mutation	SNP	G	TCGA-EP-A26S-01A-11D-A16V-10	50555189	124166157	11368590	46	34251										
MOB2	81532	hgsc.bcm.edu	37	chr11	1491556	1491556	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	ggtccagcaggttgaactccCgagcaaagaggatgaagtgg	15	8	0	3	rs565130082	byFrequency	TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr11:1491556C>T	ENST00000329957.6	-	5	842	c.653G>A	c.(652-654)cGg>cAg	p.R218Q	MOB2_ENST00000526462.1_5'UTR	NM_001172223.1	NP_001165694.1	Q70IA6	MOB2_HUMAN	MOB kinase activator 2	187					actin cytoskeleton organization (GO:0030036)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein phosphorylation (GO:0001934)	cytoplasm (GO:0005737)|neuron projection terminus (GO:0044306)|nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|kidney(2)|lung(1)	4						GTTGAACTCCCGAGCAAAGAG	0.627													C|||	2	0.000399361	0	0	5008	,	,		14614	0.002		0	False		,,,				2504	0				p.R218Q		Atlas-SNP	.											.	MOB2	23	.	0			c.G653A						.						124	134	131					11																	1491556		2107	4223	6330	SO:0001583	missense	81532	exon5			AACTCCCGAGCAA		CCDS53591.1	11p15.5	2011-09-28			ENSG00000182208	ENSG00000182208		"MOB kinase activators"	24904	protein-coding gene	gene with protein product	"MOB2 Mps One Binder homolog (yeast)"	611969				11223154, 15067004	Standard	NM_053005		Approved	HCCA2	uc010qwz.2	Q70IA6	OTTHUMG00000165545	ENST00000329957.6:c.653G>A	chr11.hg19:g.1491556C>T	ENSP00000328694:p.Arg218Gln	86.0	0.0		61.0	24.0	NM_001172223	B4DKP3|Q96M67	Missense_Mutation	SNP	ENST00000329957.6	hg19	CCDS53591.1	.	.	.	.	.	.	.	.	.	.	C	15.59	2.877643	0.51801	.	.	ENSG00000182208	ENST00000329957	.	.	.	4.18	4.18	0.49190	.	0.055833	0.64402	D	0.000005	T	0.60945	0.2308	L	0.28400	0.85	0.80722	D	1	P;D	0.89917	0.784;1.0	B;D	0.72982	0.364;0.979	T	0.54057	-0.8350	9	0.06757	T	0.87	-38.8627	16.7007	0.85349	0.0:1.0:0.0:0.0	.	218;187	E9PDA5;Q70IA6	.;MOB2_HUMAN	Q	218	.	ENSP00000328694:R218Q	R	-	2	0	AC091196.1	1448132	1.000000	0.71417	0.791000	0.31998	0.346000	0.29079	7.154000	0.77437	2.176000	0.68965	0.563000	0.77884	CGG	.	.		0.627	MOB2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000384770.1	NM_053005		T	1491556	C	T	1491556	3	4	253	1	0	0	0	0	1	0	0	0	9690	652	23	1	157	1	MOB2	11	1491556	Missense_Mutation	SNP	C	TCGA-EP-A26S-01A-11D-A16V-10		1491556	133514960	47	34252										
HNRNPUL2	221092	hgsc.bcm.edu	37	chr11	62491884	62491884	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	tgctggttttgacttttcacTatcctggtcatctcctacaa	6	11	3	1			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr11:62491884T>G	ENST00000301785.5	-	2	745	c.553A>C	c.(553-555)Agt>Cgt	p.S185R	HNRNPUL2-BSCL2_ENST00000403734.2_Missense_Mutation_p.S185R	NM_001079559.2	NP_001073027.1	Q1KMD3	HNRL2_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 2	185	Glu-rich. {ECO:0000255}.					membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						GACTTTTCACTATCCTGGTCA	0.458																																					p.S185R		Atlas-SNP	.											.	HNRNPUL2	41	.	0			c.A553C						.						105	103	104					11																	62491884		1875	4120	5995	SO:0001583	missense	221092	exon2			TTTCACTATCCTG		CCDS41659.1	11q12	2013-07-16		2008-04-18	ENSG00000214753	ENSG00000214753			25451	protein-coding gene	gene with protein product				HNRPUL2			Standard	NM_001079559		Approved	DKFZp762N1910	uc001nuw.3	Q1KMD3	OTTHUMG00000167773	ENST00000301785.5:c.553A>C	chr11.hg19:g.62491884T>G	ENSP00000301785:p.Ser185Arg	122.0	0.0		88.0	42.0	NM_001079559	Q8N3B3	Missense_Mutation	SNP	ENST00000301785.5	hg19	CCDS41659.1	.	.	.	.	.	.	.	.	.	.	T	12.95	2.091707	0.36952	.	.	ENSG00000214753	ENST00000301785	T	0.43294	0.95	5.08	5.08	0.68730	.	0.541134	0.20885	N	0.083924	T	0.22975	0.0555	N	0.14661	0.345	0.36983	D	0.894393	P	0.39551	0.678	B	0.33799	0.17	T	0.18681	-1.0329	10	0.15499	T	0.54	-9.8168	12.8404	0.57800	0.0:0.0:0.0:1.0	.	185	Q1KMD3	HNRL2_HUMAN	R	185	ENSP00000301785:S185R	ENSP00000301785:S185R	S	-	1	0	HNRNPUL2	62248460	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.933000	0.40153	2.140000	0.66376	0.533000	0.62120	AGT	.	.		0.458	HNRNPUL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396208.2	XM_495877		G	62491884	T	G	62491884	3	3	253	1	0	0	0	0	1	0	0	0	7284	1522	53	5	1742	5	HNRNPUL2	11	62491884	Missense_Mutation	SNP	T	TCGA-EP-A26S-01A-11D-A16V-10	61000328	62491884	72514632	48	34253										
MRPL21	219927	hgsc.bcm.edu	37	chr11	68664055	68664055	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	aagatcaggtcttcagaggtCaccttccactggcggctggc	12	12	4	2			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr11:68664055C>G	ENST00000362034.2	-	4	333	c.324G>C	c.(322-324)gtG>gtC	p.V108V	MRPL21_ENST00000450904.2_Silent_p.V23V|MRPL21_ENST00000567045.1_Silent_p.V23V	NM_181514.1|NM_181515.1	NP_852615.1|NP_852616.1	Q7Z2W9	RM21_HUMAN	mitochondrial ribosomal protein L21	108					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			large_intestine(1)|lung(6)|prostate(1)	8			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			CTTCAGAGGTCACCTTCCACT	0.527																																					p.V108V		Atlas-SNP	.											.	MRPL21	13	.	0			c.G324C						.						163	152	156					11																	68664055		2200	4294	6494	SO:0001819	synonymous_variant	219927	exon4			AGAGGTCACCTTC	AK096756	CCDS8186.1, CCDS44662.1	11q13.3	2012-09-13			ENSG00000197345	ENSG00000197345		"Mitochondrial ribosomal proteins / large subunits"	14479	protein-coding gene	gene with protein product		611834				11551941	Standard	NM_181514		Approved		uc001ooi.3	Q7Z2W9	OTTHUMG00000167893	ENST00000362034.2:c.324G>C	chr11.hg19:g.68664055C>G		77.0	0.0		69.0	30.0	NM_181514	A6NKU0|C9JPR2	Silent	SNP	ENST00000362034.2	hg19	CCDS8186.1																																																																																			.	.		0.527	MRPL21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396856.1	NM_181512		G	68664055	C	G	68664055	2	3	253	1	0	0	0	0	0	0	0	1	9796	813	29	4		4	MRPL21	11	68664055	Silent	SNP	C	TCGA-EP-A26S-01A-11D-A16V-10	6172171	68664055	66342461	49	34254										
NOX4	50507	hgsc.bcm.edu	37	chr11	89069054	89069054	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	tcatcaaacaaaagtttccaCcgaggacgtcctataaacag	6	11	2	0			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr11:89069054C>G	ENST00000263317.4	-	17	1813	c.1575G>C	c.(1573-1575)cgG>cgC	p.R525R	NOX4_ENST00000413594.2_Silent_p.R546R|NOX4_ENST00000343727.5_Silent_p.R501R|NOX4_ENST00000528341.1_Silent_p.R500R|NOX4_ENST00000534731.1_Silent_p.R485R|NOX4_ENST00000542487.1_Silent_p.R501R|NOX4_ENST00000531342.1_Silent_p.R178R|NOX4_ENST00000375979.3_Silent_p.R218R|NOX4_ENST00000527956.1_Silent_p.R501R|NOX4_ENST00000535633.1_Silent_p.R501R|NOX4_ENST00000527626.1_Silent_p.R338R|NOX4_ENST00000424319.1_Silent_p.R501R|NOX4_ENST00000525196.1_Silent_p.R289R|NOX4_ENST00000532825.1_Silent_p.R461R			Q9NPH5	NOX4_HUMAN	NADPH oxidase 4	525	Mediates interaction with TLR4.				bone resorption (GO:0045453)|cardiac muscle cell differentiation (GO:0055007)|cell aging (GO:0007569)|cell morphogenesis (GO:0000902)|cellular response to cAMP (GO:0071320)|cellular response to gamma radiation (GO:0071480)|cellular response to glucose stimulus (GO:0071333)|cellular response to transforming growth factor beta stimulus (GO:0071560)|homocysteine metabolic process (GO:0050667)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|oxidation-reduction process (GO:0055114)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of stress fiber assembly (GO:0051496)|reactive oxygen species metabolic process (GO:0072593)|response to hypoxia (GO:0001666)|superoxide anion generation (GO:0042554)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|modified amino acid binding (GO:0072341)|NAD(P)H oxidase activity (GO:0016174)|nucleotide binding (GO:0000166)|oxygen sensor activity (GO:0019826)|superoxide-generating NADPH oxidase activity (GO:0016175)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(20)|ovary(2)|prostate(3)|skin(2)	44		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)				AAAGTTTCCACCGAGGACGTC	0.289																																					p.R525R		Atlas-SNP	.											.	NOX4	101	.	0			c.G1575C						.						70	72	72					11																	89069054		2201	4296	6497	SO:0001819	synonymous_variant	50507	exon17			TTTCCACCGAGGA	AF254621	CCDS8285.1, CCDS44695.1, CCDS44696.1, CCDS73361.1, CCDS73362.1	11q14.2-q21	2008-02-05			ENSG00000086991	ENSG00000086991			7891	protein-coding gene	gene with protein product		605261					Standard	NM_001143837		Approved	KOX-1, KOX	uc001pct.3	Q9NPH5	OTTHUMG00000167298	ENST00000263317.4:c.1575G>C	chr11.hg19:g.89069054C>G		455.0	0.0		418.0	181.0	NM_016931	A8K715|B7Z520|E7EMD7|Q5K3R4|Q5K3R5|Q5K3R6|Q5K3R8|Q7Z7G3|Q86V92	Silent	SNP	ENST00000263317.4	hg19	CCDS8285.1																																																																																			.	.		0.289	NOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394054.1	NM_016931		G	89069054	C	G	89069054	2	3	253	1	0	0	0	0	0	0	0	1	10567	494	18	4		4	NOX4	11	89069054	Silent	SNP	C	TCGA-EP-A26S-01A-11D-A16V-10	20404999	89069054	45937462	50	34255										
HMBS	3145	hgsc.bcm.edu	37	chr11	118963906	118963907	+	Frame_Shift_Del	DEL	CT	CT	-													0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	ccccagttggctgcccagaaCttgggcatcagcctggccaa							TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr11:118963906_118963907delCT	ENST00000278715.3	+	14	1150_1151	c.999_1000delCT	c.(997-1002)aacttgfs	p.L334fs	HMBS_ENST00000537841.1_Frame_Shift_Del_p.L317fs|HMBS_ENST00000543090.1_Frame_Shift_Del_p.L303fs|HMBS_ENST00000442944.2_Frame_Shift_Del_p.L317fs|HMBS_ENST00000544387.1_Frame_Shift_Del_p.L294fs|HMBS_ENST00000542729.1_Frame_Shift_Del_p.L277fs|HMBS_ENST00000392841.1_Frame_Shift_Del_p.L317fs	NM_000190.3	NP_000181.2	P08397	HEM3_HUMAN	hydroxymethylbilane synthase	334					heme biosynthetic process (GO:0006783)|peptidyl-pyrromethane cofactor linkage (GO:0018160)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	hydroxymethylbilane synthase activity (GO:0004418)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|urinary_tract(1)	15	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.72e-05)		CTGCCCAGAACTTGGGCATCAG	0.545																																					p.333_333del		Atlas-INDEL	.											.	HMBS	27	.	0			c.998_999del	GRCh37	CD085816	HMBS	D		.																																			SO:0001589	frameshift_variant	3145	exon14			.	X04808	CCDS8409.1, CCDS41726.1, CCDS58186.1, CCDS58187.1	11q23.3	2013-07-10			ENSG00000256269	ENSG00000256269	2.5.1.61		4982	protein-coding gene	gene with protein product		609806	"uroporphyrinogen I synthase", "porphobilinogen deaminase", "porphyria, acute; Chester type"	PBGD, UPS, PORC		8432552, 17298217	Standard	NM_001258208		Approved		uc001puz.1	P08397	OTTHUMG00000168295	ENST00000278715.3:c.999_1000delCT	chr11.hg19:g.118963906_118963907delCT	ENSP00000278715:p.Leu334fs	26.0	0.0		31.0	14.0	NM_000190	A8K2L0|G3V1P4|G5EA58|P08396|Q16012	Frame_Shift_Del	DEL	ENST00000278715.3	hg19	CCDS8409.1																																																																																			.	.		0.545	HMBS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399188.1	NM_000190		-	118963907	CT	-	118963906	7	5	253	1	0	1	0	1	0	0	0	0	7228	564	20	0	1053	0	HMBS	11	118963906	Frame_Shift_Del	DEL	CT	TCGA-EP-A26S-01A-11D-A16V-10	29894852	118963906	16042610	51	34256										
TMTC1	83857	hgsc.bcm.edu	37	chr12	29659790	29659790	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	acggtggtgctatgtttgatCcttttctcgaacttcttgta	9	8	2	1			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr12:29659790C>T	ENST00000539277.1	-	18	2696	c.2638G>A	c.(2638-2640)Gat>Aat	p.D880N	TMTC1_ENST00000552618.1_Missense_Mutation_p.D904N|TMTC1_ENST00000319685.8_5'UTR|TMTC1_ENST00000256062.5_Missense_Mutation_p.D772N|TMTC1_ENST00000551659.1_Missense_Mutation_p.D942N	NM_001193451.1	NP_001180380.1	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat containing 1	880						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(1)|endometrium(4)|kidney(3)|large_intestine(17)|lung(45)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					TATGTTTGATCCTTTTCTCGA	0.473																																					p.D880N		Atlas-SNP	.											.	TMTC1	147	.	0			c.G2638A						.						291	275	281					12																	29659790		2203	4300	6503	SO:0001583	missense	83857	exon18			TTTGATCCTTTTC		CCDS8718.1, CCDS53772.1	12p11.22	2014-06-09	2006-01-06			ENSG00000133687		"Tetratricopeptide (TTC) repeat domain containing"	24099	protein-coding gene	gene with protein product		615855				24764305	Standard	NM_001193451		Approved	ARG99, OLF, FLJ31400, FLJ41625	uc021qwi.1	Q8IUR5	OTTHUMG00000169324	ENST00000539277.1:c.2638G>A	chr12.hg19:g.29659790C>T	ENSP00000442046:p.Asp880Asn	149.0	0.0		119.0	47.0	NM_001193451	D0EP37|F5H8B5|Q6PIU4|Q6ZSM5|Q96N52|Q9BXM2	Missense_Mutation	SNP	ENST00000539277.1	hg19	CCDS53772.1	.	.	.	.	.	.	.	.	.	.	C	16.41	3.115963	0.56505	.	.	ENSG00000133687	ENST00000540901;ENST00000256062;ENST00000551659;ENST00000552618;ENST00000539277	T;T;T;T	0.69435	-0.39;-0.27;-0.4;-0.28	5.13	4.24	0.50183	.	0.315023	0.29876	N	0.010975	T	0.50905	0.1643	L	0.36672	1.1	0.80722	D	1	B;B;B	0.14438	0.001;0.001;0.01	B;B;B	0.14023	0.003;0.002;0.01	T	0.43212	-0.9405	10	0.02654	T	1	-11.0509	12.379	0.55295	0.0:0.9176:0.0:0.0824	.	880;942;225	Q8IUR5;F8VTQ9;Q8IUR5-4	TMTC1_HUMAN;.;.	N	643;772;942;904;880	ENSP00000256062:D772N;ENSP00000448112:D942N;ENSP00000449043:D904N;ENSP00000442046:D880N	ENSP00000256062:D772N	D	-	1	0	TMTC1	29551057	1.000000	0.71417	0.974000	0.42286	0.969000	0.65631	2.244000	0.43124	1.164000	0.42652	0.650000	0.86243	GAT	.	.		0.473	TMTC1-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403509.1	NM_031920		T	29659790	C	T	29659790	3	4	253	1	0	0	0	0	1	0	0	0	16275	855	30	3	14	3	TMTC1	12	29659790	Missense_Mutation	SNP	C	TCGA-EP-A26S-01A-11D-A16V-10		29659790	104192105	52	34257										
KRT1	3848	hgsc.bcm.edu	37	chr12	53071186	53071186	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	gacctcagcaatgatgctgtCcaggtcgagactgcggttgt	13	10	1	2			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr12:53071186C>A	ENST00000252244.3	-	5	1100	c.1042G>T	c.(1042-1044)Gac>Tac	p.D348Y		NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1	348	Linker 12.|Rod.				complement activation, lectin pathway (GO:0001867)|establishment of skin barrier (GO:0061436)|fibrinolysis (GO:0042730)|negative regulation of inflammatory response (GO:0050728)|regulation of angiogenesis (GO:0045765)|response to oxidative stress (GO:0006979)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(7)|skin(3)	39						ATGATGCTGTCCAGGTCGAGA	0.493																																					p.D348Y		Atlas-SNP	.											.	KRT1	110	.	0			c.G1042T						.						130	121	124					12																	53071186		2203	4300	6503	SO:0001583	missense	3848	exon5			TGCTGTCCAGGTC	X69725	CCDS8836.1	12q13.13	2014-06-05	2008-08-01		ENSG00000167768	ENSG00000167768		"-", "Intermediate filaments type II, keratins (basic)"	6412	protein-coding gene	gene with protein product		139350	"epidermolytic hyperkeratosis 1"	EHK1		2461420, 2470667, 16831889	Standard	NM_006121		Approved	KRT1A	uc001sau.1	P04264	OTTHUMG00000169749	ENST00000252244.3:c.1042G>T	chr12.hg19:g.53071186C>A	ENSP00000252244:p.Asp348Tyr	64.0	0.0		57.0	26.0	NM_006121	B2RA01|P85925|P86104|Q14720|Q6GSJ0|Q9H298	Missense_Mutation	SNP	ENST00000252244.3	hg19	CCDS8836.1	.	.	.	.	.	.	.	.	.	.	C	15.84	2.951589	0.53186	.	.	ENSG00000167768	ENST00000252244	D	0.83673	-1.75	5.22	0.0563	0.14319	Filament (1);	.	.	.	.	D	0.92835	0.7721	H	0.98466	4.24	0.38381	D	0.945122	D	0.89917	1.0	D	0.91635	0.999	D	0.89538	0.3790	9	0.87932	D	0	.	5.7045	0.17901	0.1216:0.537:0.0:0.3414	.	348	P04264	K2C1_HUMAN	Y	348	ENSP00000252244:D348Y	ENSP00000252244:D348Y	D	-	1	0	KRT1	51357453	0.929000	0.31497	0.887000	0.34795	0.800000	0.45204	0.456000	0.21859	0.037000	0.15575	-1.202000	0.01658	GAC	.	.		0.493	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1	NM_006121		A	53071186	C	A	53071186	3	1	253	1	0	0	0	0	1	0	0	0	8456	855	30	3	912	3	KRT1	12	53071186	Missense_Mutation	SNP	C	TCGA-EP-A26S-01A-11D-A16V-10	23411396	53071186	80780709	53	34258										
RAB3IP	117177	hgsc.bcm.edu	37	chr12	70149324	70149324	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	tcatctaccggccacaccctTcagctttatcctctgtacct	4	17	4	0			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr12:70149324T>G	ENST00000247833.7	+	2	512	c.136T>G	c.(136-138)Tca>Gca	p.S46A	RAB3IP_ENST00000362025.5_Missense_Mutation_p.S62A|RAB3IP_ENST00000550536.1_Missense_Mutation_p.S62A|RAB3IP_ENST00000325555.9_5'UTR|RAB3IP_ENST00000378815.6_Missense_Mutation_p.S46A|RAB3IP_ENST00000483530.2_Missense_Mutation_p.S46A					RAB3A interacting protein											NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	22	Esophageal squamous(21;0.187)		Lung(24;0.000381)|OV - Ovarian serous cystadenocarcinoma(12;0.00168)|STAD - Stomach adenocarcinoma(21;0.00694)			GCCACACCCTTCAGCTTTATC	0.468																																					p.S62A		Atlas-SNP	.											.	RAB3IP	48	.	0			c.T184G						.						175	156	162					12																	70149324		2203	4300	6503	SO:0001583	missense	117177	exon2			CACCCTTCAGCTT		CCDS8993.1, CCDS8995.1, CCDS8996.1, CCDS41811.1, CCDS44942.1	12q15	2013-01-22	2013-01-22		ENSG00000127328	ENSG00000127328			16508	protein-coding gene	gene with protein product	"rabin3"	608686					Standard	NM_175623		Approved	RABIN3	uc001svm.3	Q96QF0	OTTHUMG00000169437	ENST00000247833.7:c.136T>G	chr12.hg19:g.70149324T>G	ENSP00000247833:p.Ser46Ala	84.0	0.0		106.0	37.0	NM_175623		Missense_Mutation	SNP	ENST00000247833.7	hg19	CCDS8995.1	.	.	.	.	.	.	.	.	.	.	T	13.74	2.326084	0.41197	.	.	ENSG00000127328	ENST00000247833;ENST00000378815;ENST00000483530;ENST00000549760;ENST00000550536;ENST00000362025	T;T	0.44482	0.92;0.92	5.2	4.03	0.46877	.	0.321368	0.34067	N	0.004296	T	0.27134	0.0665	N	0.24115	0.695	0.80722	D	1	B;B;B;B	0.10296	0.003;0.0;0.002;0.0	B;B;B;B	0.11329	0.005;0.001;0.006;0.001	T	0.05582	-1.0876	10	0.38643	T	0.18	-5.4128	8.1652	0.31222	0.0:0.0714:0.136:0.7926	.	62;62;46;46	Q96QF0-4;Q96QF0;Q96QF0-3;Q96QF0-7	.;RAB3I_HUMAN;.;.	A	46;46;46;46;62;62	ENSP00000247833:S46A;ENSP00000447300:S62A	ENSP00000247833:S46A	S	+	1	0	RAB3IP	68435591	1.000000	0.71417	0.953000	0.39169	0.933000	0.57130	1.874000	0.39568	1.033000	0.39918	0.533000	0.62120	TCA	.	.		0.468	RAB3IP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280671.2	NM_022456		G	70149324	T	G	70149324	3	3	253	1	0	0	0	0	1	0	0	0	12953	1783	62	5	190	5	RAB3IP	12	70149324	Missense_Mutation	SNP	T	TCGA-EP-A26S-01A-11D-A16V-10	17078138	70149324	63702571	54	34259										
DCN	1634	hgsc.bcm.edu	37	chr12	91558424	91558424	+	Frame_Shift_Del	DEL	G	G	-													0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	aagtctccatctttgatttcGgttattttgttgttttgcag					rs3138221	byFrequency	TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr12:91558424delG	ENST00000052754.5	-	3	783	c.282delC	c.(280-282)accfs	p.T94fs	DCN_ENST00000547568.2_Intron|DCN_ENST00000420120.2_Intron|DCN_ENST00000228329.5_Intron|DCN_ENST00000393155.1_Frame_Shift_Del_p.T94fs|DCN_ENST00000441303.2_Frame_Shift_Del_p.T94fs|DCN_ENST00000303320.3_Frame_Shift_Del_p.T94fs|DCN_ENST00000456569.2_Intron|DCN_ENST00000425043.1_Intron|DCN_ENST00000552962.1_Frame_Shift_Del_p.T94fs	NM_001920.3	NP_001911.1	P07585	PGS2_HUMAN	decorin	94					aging (GO:0007568)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|kidney development (GO:0001822)|organ morphogenesis (GO:0009887)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|placenta development (GO:0001890)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|skeletal muscle tissue development (GO:0007519)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	collagen type VI trimer (GO:0005589)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|glycosaminoglycan binding (GO:0005539)|poly(A) RNA binding (GO:0044822)			central_nervous_system(2)|cervix(1)|kidney(2)|large_intestine(4)|liver(1)|lung(8)|ovary(1)|skin(1)	20						CTTTGATTTCGGTTATTTTGT	0.378																																					p.E95fs		Atlas-Indel,Pindel	.											DCN,NS,carcinoma,0,3	DCN	61	.	0			c.283delG						.						153	137	142					12																	91558424		2203	4300	6503	SO:0001589	frameshift_variant	1634	exon2			.	AF138300	CCDS9039.1, CCDS9040.1, CCDS9041.1, CCDS9042.1, CCDS44951.1	12q21.33	2014-04-16			ENSG00000011465	ENSG00000011465		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	2705	protein-coding gene	gene with protein product	"decorin proteoglycan"	125255				8432526	Standard	NM_133507		Approved	DSPG2, SLRR1B	uc001tbt.3	P07585	OTTHUMG00000169998	ENST00000052754.5:c.282delC	chr12.hg19:g.91558424delG	ENSP00000052754:p.Thr94fs	203.0	0.0		145.0	60.0	NM_133506	Q9P0Z0|Q9P0Z1|Q9Y5N8|Q9Y5N9	Frame_Shift_Del	DEL	ENST00000052754.5	hg19	CCDS9039.1																																																																																			.	.		0.378	DCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406799.3	NM_133507		-	91558424	G	-	91558424	7	5	253	1	0	1	0	1	0	0	0	0	4299	1103	39	0	821	0	DCN	12	91558424	Frame_Shift_Del	DEL	G	TCGA-EP-A26S-01A-11D-A16V-10	21409100	91558424	42293471	55	34260										
TMPO	7112	hgsc.bcm.edu	37	chr12	98938066	98938066	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	aagtggatcttcaaaaggcgGacctctgcaggcattaacta	10	9	3	0			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr12:98938066G>A	ENST00000556029.1	+	5	1078	c.722G>A	c.(721-723)gGa>gAa	p.G241E	TMPO_ENST00000393053.2_Intron|TMPO_ENST00000548223.1_3'UTR|TMPO_ENST00000343315.5_Intron	NM_001032283.2	NP_001027454.1	P42167	LAP2B_HUMAN	thymopoietin	241	NAKAP95-binding N.|Nucleoplasmic. {ECO:0000255}.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)|lamin binding (GO:0005521)			breast(2)|endometrium(1)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						TCAAAAGGCGGACCTCTGCAG	0.408																																					p.G241E		Atlas-SNP	.											.	TMPO	111	.	0			c.G722A						.						86	87	87					12																	98938066		2203	4300	6503	SO:0001583	missense	7112	exon5			AAGGCGGACCTCT		CCDS9064.1, CCDS31879.1, CCDS31880.1	12q22	2014-09-17			ENSG00000120802	ENSG00000120802			11875	protein-coding gene	gene with protein product	"LEM domain containing 4"	188380				7517549	Standard	NM_003276		Approved	TP, LAP2, LEMD4	uc001tfh.2	P42166	OTTHUMG00000170210	ENST00000556029.1:c.722G>A	chr12.hg19:g.98938066G>A	ENSP00000450627:p.Gly241Glu	117.0	0.0		112.0	57.0	NM_001032283	A2T926|Q14861	Missense_Mutation	SNP	ENST00000556029.1	hg19	CCDS31879.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.187716	0.78789	.	.	ENSG00000120802	ENST00000556029	T	0.71579	-0.58	5.75	5.75	0.90469	.	.	.	.	.	T	0.81735	0.4885	L	0.53249	1.67	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.77167	-0.2687	9	0.28530	T	0.3	.	19.9478	0.97189	0.0:0.0:1.0:0.0	.	241	P42167	LAP2B_HUMAN	E	241	ENSP00000450627:G241E	ENSP00000340251:G241E	G	+	2	0	TMPO	97462197	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.473000	0.73572	2.712000	0.92718	0.591000	0.81541	GGA	.	.		0.408	TMPO-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407973.2	NM_003276		A	98938066	G	A	98938066	3	1	253	1	0	0	0	0	1	0	0	0	16252	1174	41	3	2264	3	TMPO	12	98938066	Missense_Mutation	SNP	G	TCGA-EP-A26S-01A-11D-A16V-10	7379642	98938066	34913829	56	34261										
KIAA1033	23325	hgsc.bcm.edu	37	chr12	105557965	105557965	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	tggttccagtctgttagagaGaaatacctgaaggagataag	12	5	1	4			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr12:105557965G>A	ENST00000332180.5	+	31	3321	c.3234G>A	c.(3232-3234)gaG>gaA	p.E1078E	KIAA1033_ENST00000547171.1_3'UTR	NM_015275.1	NP_056090.1			KIAA1033											breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(15)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	41						CTGTTAGAGAGAAATACCTGA	0.418																																					p.E1078E		Atlas-SNP	.											.	KIAA1033	83	.	0			c.G3234A						.						130	119	122					12																	105557965		1876	4110	5986	SO:0001819	synonymous_variant	23325	exon31			TAGAGAGAAATAC	AB028956	CCDS41826.1, CCDS73514.1	12q24.11	2014-05-09				ENSG00000136051			29174	protein-coding gene	gene with protein product		615748				20376207, 20498093, 21498477	Standard	XM_005268742		Approved	SWIP	uc001tld.3	Q2M389		ENST00000332180.5:c.3234G>A	chr12.hg19:g.105557965G>A		106.0	0.0		77.0	31.0	NM_015275		Silent	SNP	ENST00000332180.5	hg19	CCDS41826.1																																																																																			.	.		0.418	KIAA1033-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406138.4	NM_015275		A	105557965	G	A	105557965	2	1	253	1	0	0	0	0	0	0	0	1	8215	933	33	3		3	KIAA1033	12	105557965	Silent	SNP	G	TCGA-EP-A26S-01A-11D-A16V-10	6619899	105557965	28293930	57	34262										
DNAH10	196385	hgsc.bcm.edu	37	chr12	124377824	124377824	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	aagaggagaaagagtctatcCtgagtcagattggacaggaa	13	5	2	5			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr12:124377824C>T	ENST00000409039.3	+	52	8711	c.8686C>T	c.(8686-8688)Ctg>Ttg	p.L2896L		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2896	AAA 4. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		AGAGTCTATCCTGAGTCAGAT	0.498																																					p.L2896L		Atlas-SNP	.											.	DNAH10	888	.	0			c.C8686T						.						64	67	66					12																	124377824		2006	4194	6200	SO:0001819	synonymous_variant	196385	exon52			TCTATCCTGAGTC	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.8686C>T	chr12.hg19:g.124377824C>T		90.0	0.0		67.0	28.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	hg19	CCDS9255.2																																																																																			.	.		0.498	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			T	124377824	C	T	124377824	2	4	253	1	0	0	0	0	0	0	0	1	4600	680	24	3		3	DNAH10	12	124377824	Silent	SNP	C	TCGA-EP-A26S-01A-11D-A16V-10	18819859	124377824	9474071	58	34263										
ZMYM2	7750	hgsc.bcm.edu	37	chr13	20567272	20567272	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	cagactcctgttttattaggGagtacggccatggcaactag	11	9	0	1			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr13:20567272G>A	ENST00000382874.2	+	4	250	c.60G>A	c.(58-60)ggG>ggA	p.G20G	ZMYM2_ENST00000382871.2_Silent_p.G20G|ZMYM2_ENST00000382881.3_Silent_p.G20G|ZMYM2_ENST00000382869.3_Silent_p.G20G	NM_001190964.1	NP_001177893.1	Q9UBW7	ZMYM2_HUMAN	zinc finger, MYM-type 2	20					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|PML body (GO:0016605)	ubiquitin conjugating enzyme binding (GO:0031624)|zinc ion binding (GO:0008270)			large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	10		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)		TTTTATTAGGGAGTACGGCCA	0.393																																					p.G20G		Atlas-SNP	.											.	ZMYM2	191	.	0			c.G60A						.						141	140	140					13																	20567272		2062	4244	6306	SO:0001819	synonymous_variant	7750	exon4			ATTAGGGAGTACG	AF012126	CCDS45016.1	13q11-q12	2013-01-08	2006-07-13	2006-07-13	ENSG00000121741	ENSG00000121741		"Zinc fingers, MYM type"	12989	protein-coding gene	gene with protein product		602221	"zinc finger protein 198"	ZNF198		9499416, 9425908	Standard	XM_005266517		Approved	RAMP, FIM, MYM	uc001ums.3	Q9UBW7	OTTHUMG00000016507	ENST00000382874.2:c.60G>A	chr13.hg19:g.20567272G>A		99.0	0.0		123.0	54.0	NM_001190964	A6NDG0|A6NI02|O43212|O43434|O60898|Q5W0Q4|Q5W0T3|Q63HP0|Q8NE39|Q9H0V5|Q9H538|Q9UEU2	Silent	SNP	ENST00000382874.2	hg19	CCDS45016.1																																																																																			.	.		0.393	ZMYM2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044051.2	NM_003453		A	20567272	G	A	20567272	2	1	253	1	0	0	0	0	0	0	0	1	17715	1161	41	3		3	ZMYM2	13	20567272	Silent	SNP	G	TCGA-EP-A26S-01A-11D-A16V-10		20567272	94602606	59	34264										
FARP1	10160	hgsc.bcm.edu	37	chr13	98896898	98896898	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	ttacaggctctatttcttacAcaaactgggctggaagtaga	9	8	2	1			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr13:98896898A>G	ENST00000319562.6	+	2	436				FARP1_ENST00000376586.2_Intron|FARP1_ENST00000595437.1_Intron|FARP1_ENST00000376581.5_Missense_Mutation_p.T109A	NM_005766.2	NP_005757.1	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)						dendrite morphogenesis (GO:0048813)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|synapse assembly (GO:0007416)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|synapse (GO:0045202)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|endometrium(6)|kidney(6)|large_intestine(13)|lung(16)|ovary(1)|skin(3)|urinary_tract(1)	49	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			TATTTCTTACACAAACTGGGC	0.418																																					p.T109A		Atlas-SNP	.											.	FARP1	207	.	0			c.A325G						.						117	116	116					13																	98896898		2203	4300	6503	SO:0001627	intron_variant	10160	exon3			TCTTACACAAACT	AB008430	CCDS9487.1, CCDS32000.1, CCDS66572.1	13q32.2	2013-01-10			ENSG00000152767	ENSG00000152767		"Rho guanine nucleotide exchange factors", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Pleckstrin homology (PH) domain containing"	3591	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 75"	602654				9425278	Standard	NM_005766		Approved	CDEP, PLEKHC2, MGC87400, PPP1R75	uc001vnj.3	Q9Y4F1	OTTHUMG00000017248	ENST00000319562.6:c.171+31231A>G	chr13.hg19:g.98896898A>G		57.0	0.0		57.0	32.0	NM_001001715	Q5JVI9|Q6IQ29	Missense_Mutation	SNP	ENST00000319562.6	hg19	CCDS9487.1	.	.	.	.	.	.	.	.	.	.	A	4.838	0.155825	0.09236	.	.	ENSG00000152767	ENST00000376581	T	0.49432	0.78	3.2	-4.09	0.03951	.	.	.	.	.	T	0.21590	0.0520	N	0.08118	0	0.09310	N	1	B	0.11235	0.004	B	0.09377	0.004	T	0.15549	-1.0433	9	0.87932	D	0	.	3.4211	0.07393	0.2581:0.0:0.394:0.3479	.	109	Q5JVI9	.	A	109	ENSP00000365765:T109A	ENSP00000365765:T109A	T	+	1	0	FARP1	97694899	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.013000	0.03645	-0.871000	0.04042	-0.403000	0.06358	ACA	.	.		0.418	FARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045541.3	NM_005766		G	98896898	A	G	98896898	1	3	253	0	1	0	0	0	0	0	0	0	5684	159	6	2		2	FARP1	13	98896898	Intron	SNP	A	TCGA-EP-A26S-01A-11D-A16V-10	78329626	98896898	16272980	60	34265										
NOVA1	4857	hgsc.bcm.edu	37	chr14	26917704	26917704	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	acctaaacctaaagtgttgaGattatatccatagctggcta	7	8	0	1			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr14:26917704G>T	ENST00000539517.2	-	5	1302	c.985C>A	c.(985-987)Ctc>Atc	p.L329I	NOVA1_ENST00000465357.2_Missense_Mutation_p.L305I|NOVA1_ENST00000267422.7_Missense_Mutation_p.L207I	NM_002515.2	NP_002506.2	P51513	NOVA1_HUMAN	neuro-oncological ventral antigen 1	332	Ala-rich.				locomotory behavior (GO:0007626)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA metabolic process (GO:0051252)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(265;0.0135)		AAAGTGTTGAGATTATATCCA	0.502																																					p.L329I		Atlas-SNP	.											.	NOVA1	146	.	0			c.C985A						.						52	48	50					14																	26917704		2203	4300	6503	SO:0001583	missense	4857	exon5			TGTTGAGATTATA	U04840	CCDS9635.1, CCDS32060.1, CCDS32061.1	14q12	2006-06-09			ENSG00000139910	ENSG00000139910			7886	protein-coding gene	gene with protein product		602157				8558240	Standard	NM_006489		Approved		uc001wpy.3	P51513	OTTHUMG00000029385	ENST00000539517.2:c.985C>A	chr14.hg19:g.26917704G>T	ENSP00000438875:p.Leu329Ile	26.0	0.0		20.0	11.0	NM_002515	A8K0S4|A8K4Q7|D3DS81|D3DS82|Q6B004	Missense_Mutation	SNP	ENST00000539517.2	hg19	CCDS32061.1	.	.	.	.	.	.	.	.	.	.	G	4.892	0.165831	0.09339	.	.	ENSG00000139910	ENST00000465357;ENST00000539517;ENST00000267422	T;T;T	0.34472	1.37;1.36;1.37	5.93	5.93	0.95920	.	0.168630	0.41712	D	0.000828	T	0.20251	0.0487	N	0.08118	0	0.53005	D	0.999967	B;B;P	0.35872	0.092;0.256;0.525	B;B;B	0.30572	0.018;0.055;0.117	T	0.09530	-1.0670	10	0.10902	T	0.67	-5.7973	20.3363	0.98740	0.0:0.0:1.0:0.0	.	332;305;329	P51513;D3DS81;P51513-4	NOVA1_HUMAN;.;.	I	305;329;207	ENSP00000447391:L305I;ENSP00000438875:L329I;ENSP00000267422:L207I	ENSP00000267422:L207I	L	-	1	0	NOVA1	25987544	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.392000	0.79840	2.814000	0.96858	0.563000	0.77884	CTC	.	.		0.502	NOVA1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000073261.3	NM_006491		T	26917704	G	T	26917704	3	4	253	1	0	0	0	0	1	0	0	0	10563	942	33	3	542	3	NOVA1	14	26917704	Missense_Mutation	SNP	G	TCGA-EP-A26S-01A-11D-A16V-10		26917704	80431836	61	34266										
C14orf101	54916	hgsc.bcm.edu	37	chr14	57070549	57070549	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	gcaggctttctggctcatctGctggaggaatccttgctgcg	13	11	3	0			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr14:57070549G>A	ENST00000261556.6	+	4	483	c.361G>A	c.(361-363)Gct>Act	p.A121T	TMEM260_ENST00000536419.1_Intron|TMEM260_ENST00000538838.1_Missense_Mutation_p.A121T	NM_017799.3	NP_060269.3	Q9NX78	TM260_HUMAN	transmembrane protein 260	121						integral component of membrane (GO:0016021)											TGGCTCATCTGCTGGAGGAAT	0.413																																					p.A121T		Atlas-SNP	.											.	.	.	.	0			c.G361A						.						104	107	106					14																	57070549		2203	4300	6503	SO:0001583	missense	0	exon4			TCATCTGCTGGAG	AK000399	CCDS9727.2	14q22.2	2013-03-08	2013-03-08	2013-03-08	ENSG00000070269	ENSG00000070269			20185	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 101"	C14orf101			Standard	XR_245695		Approved	FLJ20392	uc001xcm.3	Q9NX78	OTTHUMG00000152337	ENST00000261556.6:c.361G>A	chr14.hg19:g.57070549G>A	ENSP00000261556:p.Ala121Thr	223.0	0.0		174.0	67.0	NM_017799	A8KAN4|B3KPF5|Q86XE1	Missense_Mutation	SNP	ENST00000261556.6	hg19	CCDS9727.2	.	.	.	.	.	.	.	.	.	.	G	22.3	4.273708	0.80580	.	.	ENSG00000070269	ENST00000261556;ENST00000538838	T;T	0.49432	1.37;0.78	5.88	5.88	0.94601	.	0.054747	0.64402	D	0.000001	T	0.46927	0.1418	L	0.45051	1.395	0.80722	D	1	P	0.43477	0.808	B	0.43082	0.407	T	0.19745	-1.0296	10	0.20046	T	0.44	-11.5948	20.2381	0.98363	0.0:0.0:1.0:0.0	.	121	Q9NX78	CN101_HUMAN	T	121	ENSP00000261556:A121T;ENSP00000441934:A121T	ENSP00000261556:A121T	A	+	1	0	C14orf101	56140302	1.000000	0.71417	0.980000	0.43619	0.994000	0.84299	6.781000	0.75068	2.779000	0.95612	0.650000	0.86243	GCT	.	.		0.413	TMEM260-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276924.1	NM_017799		A	57070549	G	A	57070549	3	1	253	1	0	0	0	0	1	0	0	0	1736	1319	46	3	375	3	C14orf101	14	57070549	Missense_Mutation	SNP	G	TCGA-EP-A26S-01A-11D-A16V-10	30152845	57070549	50278991	62	34267										
SYT16	83851	hgsc.bcm.edu	37	chr14	62550920	62550920	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	ttcttcccctccagagtggaGggtctccgctcagcccatct	9	16	4	1			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr14:62550920G>T	ENST00000430451.2	+	5	1638	c.1441G>T	c.(1441-1443)Ggg>Tgg	p.G481W		NM_031914.2	NP_114120.2	Q17RD7	SYT16_HUMAN	synaptotagmin XVI	481					exocytosis (GO:0006887)					central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	35				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)		CCAGAGTGGAGGGTCTCCGCT	0.527																																					p.G481W		Atlas-SNP	.											.	SYT16	144	.	0			c.G1441T						.						99	96	97					14																	62550920		1973	4154	6127	SO:0001583	missense	83851	exon5			AGTGGAGGGTCTC	BC040924	CCDS45121.1	14q23.2	2014-07-02	2005-07-15	2005-07-15	ENSG00000139973	ENSG00000139973		"Synaptotagmins"	23142	protein-coding gene	gene with protein product	"synaptotagmin XIV-related", " chr14 synaptotagmin"	610950	"synaptotagmin XIV-like"	SYT14L		11543631	Standard	NM_031914		Approved	yt14r, CHR14SYT, Strep14	uc001xfu.1	Q17RD7	OTTHUMG00000171106	ENST00000430451.2:c.1441G>T	chr14.hg19:g.62550920G>T	ENSP00000394700:p.Gly481Trp	81.0	0.0		71.0	26.0	NM_031914	B4DZH2|B7ZL60|C9J8I3|Q707N2|Q7Z441|Q8IUU0|Q9BQR8	Missense_Mutation	SNP	ENST00000430451.2	hg19	CCDS45121.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.137384	0.77775	.	.	ENSG00000139973	ENST00000430451	T	0.04406	3.63	5.44	5.44	0.79542	.	0.294878	0.36234	N	0.002719	T	0.10809	0.0264	L	0.29908	0.895	0.80722	D	1	P	0.49783	0.928	P	0.54060	0.741	T	0.01951	-1.1241	10	0.62326	D	0.03	-6.1342	19.4718	0.94966	0.0:0.0:1.0:0.0	.	481	Q17RD7	SYT16_HUMAN	W	481	ENSP00000394700:G481W	ENSP00000394700:G481W	G	+	1	0	SYT16	61620673	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.333000	0.79214	2.831000	0.97527	0.643000	0.83706	GGG	.	.		0.527	SYT16-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000411700.1	NM_031914		T	62550920	G	T	62550920	3	4	253	1	0	0	0	0	1	0	0	0	15487	1000	35	3	1459	3	SYT16	14	62550920	Missense_Mutation	SNP	G	TCGA-EP-A26S-01A-11D-A16V-10	5480371	62550920	44798620	63	34268										
PPP2R5E	5529	hgsc.bcm.edu	37	chr14	63858560	63858560	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	tttgactacatgttttaggcCaaaatttcattaacccccta	4	10	1	1			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr14:63858560C>T	ENST00000337537.3	-	10	1531	c.929G>A	c.(928-930)tGg>tAg	p.W310*	PPP2R5E_ENST00000553266.1_5'UTR|PPP2R5E_ENST00000555899.1_Nonsense_Mutation_p.W310*|PPP2R5E_ENST00000422769.2_Nonsense_Mutation_p.W234*	NM_001282179.1|NM_001282180.1|NM_001282181.1|NM_001282182.1|NM_006246.2	NP_001269108.1|NP_001269109.1|NP_001269110.1|NP_001269111.1|NP_006237.1	Q16537	2A5E_HUMAN	protein phosphatase 2, regulatory subunit B', epsilon isoform	310					regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|soft_tissue(1)	15				OV - Ovarian serous cystadenocarcinoma(108;0.00197)|all cancers(60;0.0153)|BRCA - Breast invasive adenocarcinoma(234;0.128)		TGTTTTAGGCCAAAATTTCAT	0.338																																					p.W310X		Atlas-SNP	.											.	PPP2R5E	43	.	0			c.G929A						.						81	81	81					14																	63858560		2203	4300	6503	SO:0001587	stop_gained	5529	exon10			TTAGGCCAAAATT	L76703	CCDS9758.1, CCDS61467.1, CCDS61468.1	14q23.2	2010-06-18	2007-01-22		ENSG00000154001	ENSG00000154001		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9313	protein-coding gene	gene with protein product		601647	"protein phosphatase 2, regulatory subunit B (B56), epsilon isoform"			7592815	Standard	NM_006246		Approved		uc001xgd.1	Q16537	OTTHUMG00000140341	ENST00000337537.3:c.929G>A	chr14.hg19:g.63858560C>T	ENSP00000337641:p.Trp310*	121.0	0.0		88.0	34.0	NM_006246	A4FU37|B7ZAW5|B7ZKK8|B7ZKK9|J3KQN6|Q52LW4	Nonsense_Mutation	SNP	ENST00000337537.3	hg19	CCDS9758.1	.	.	.	.	.	.	.	.	.	.	C	43	9.954419	0.99304	.	.	ENSG00000154001	ENST00000337537;ENST00000555899;ENST00000422769	.	.	.	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.5188	19.5064	0.95118	0.0:1.0:0.0:0.0	.	.	.	.	X	310;310;234	.	ENSP00000337641:W310X	W	-	2	0	PPP2R5E	62928313	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.716000	0.84723	2.672000	0.90937	0.655000	0.94253	TGG	.	.		0.338	PPP2R5E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276973.1	NM_006246		T	63858560	C	T	63858560	4	4	253	1	0	0	0	0	0	1	0	0	12408	595	21	3	494	3	PPP2R5E	14	63858560	Nonsense_Mutation	SNP	C	TCGA-EP-A26S-01A-11D-A16V-10	1307640	63858560	43490980	64	34269										
STON2	85439	hgsc.bcm.edu	37	chr14	81737182	81737182	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	tcccggtcagagccgagttcAaggtggcaaaagaaacagtg	13	9	2	2			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr14:81737182A>C	ENST00000267540.2	-	5	2645	c.2445T>G	c.(2443-2445)ctT>ctG	p.L815L	STON2_ENST00000555447.1_Silent_p.L815L	NM_033104.3	NP_149095.2	Q8WXE9	STON2_HUMAN	stonin 2	815	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				hematopoietic progenitor cell differentiation (GO:0002244)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleolus (GO:0005730)|synaptic vesicle (GO:0008021)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|pancreas(2)|prostate(1)|skin(5)	34				BRCA - Breast invasive adenocarcinoma(234;0.0348)		AGCCGAGTTCAAGGTGGCAAA	0.498																																					p.L815L		Atlas-SNP	.											.	STON2	94	.	0			c.T2445G						.						87	75	79					14																	81737182		2203	4300	6503	SO:0001819	synonymous_variant	85439	exon7			GAGTTCAAGGTGG	AB208948	CCDS9875.1, CCDS58332.1	14q31.1	2007-08-01				ENSG00000140022			30652	protein-coding gene	gene with protein product	"stoned B homolog 2 (Drosophila)"	608467				11381094, 11454741	Standard	NM_033104		Approved	STNB2, STN2	uc001xvk.2	Q8WXE9		ENST00000267540.2:c.2445T>G	chr14.hg19:g.81737182A>C		46.0	0.0		34.0	11.0	NM_001256430	G3V2T7|Q17R24|Q59H11|Q6NT47|Q96RI7|Q96RU6	Silent	SNP	ENST00000267540.2	hg19	CCDS9875.1	.	.	.	.	.	.	.	.	.	.	A	10.11	1.259519	0.23051	.	.	ENSG00000140022	ENST00000553821	T	0.26957	1.7	5.79	3.26	0.37387	.	0.000000	0.64402	D	0.000003	T	0.29423	0.0733	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.02617	-1.1133	6	.	.	.	-21.4275	7.9458	0.29985	0.4081:0.4586:0.0:0.1332	.	.	.	.	W	23	ENSP00000450577:L23W	.	L	-	2	0	STON2	80806935	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.141000	0.31528	0.984000	0.38629	0.533000	0.62120	TTG	.	.		0.498	STON2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413317.1	NM_033104		C	81737182	A	C	81737182	2	2	253	1	0	0	0	0	0	0	0	1	15333	117	5	5		5	STON2	14	81737182	Silent	SNP	A	TCGA-EP-A26S-01A-11D-A16V-10	17878622	81737182	25612358	65	34270										
RPS6KA5	9252	hgsc.bcm.edu	37	chr14	91338575	91338575	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	tgctgcgcgtctcggtactgGtgctagtctttttcattttt	10	9	3	0			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr14:91338575G>C	ENST00000261991.3	-	17	2425	c.2252C>G	c.(2251-2253)aCc>aGc	p.T751S	RPS6KA5_ENST00000536315.2_Missense_Mutation_p.T672S	NM_004755.2	NP_004746.2	O75582	KS6A5_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 5	751					axon guidance (GO:0007411)|epidermal growth factor receptor signaling pathway (GO:0007173)|histone H2A-S1 phosphorylation (GO:0043990)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-S28 phosphorylation (GO:0043988)|histone phosphorylation (GO:0016572)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|intracellular signal transduction (GO:0035556)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cytokine production (GO:0001818)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			endometrium(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	24		all_cancers(154;0.0148)|Melanoma(154;0.099)|all_epithelial(191;0.146)		Epithelial(152;0.182)|BRCA - Breast invasive adenocarcinoma(234;0.201)		CTCGGTACTGGTGCTAGTCTT	0.483																																					p.T751S		Atlas-SNP	.											.	RPS6KA5	135	.	0			c.C2252G						.						129	114	119					14																	91338575		2203	4300	6503	SO:0001583	missense	9252	exon17			GTACTGGTGCTAG	AF074393	CCDS9893.1, CCDS45149.1	14q31-q32.1	2011-04-05	2002-08-29			ENSG00000100784			10434	protein-coding gene	gene with protein product		603607	"ribosomal protein S6 kinase, 90kD, polypeptide 5"			9687510, 10702687	Standard	NM_004755		Approved	MSK1, RLPK	uc001xys.2	O75582		ENST00000261991.3:c.2252C>G	chr14.hg19:g.91338575G>C	ENSP00000261991:p.Thr751Ser	215.0	0.0		224.0	108.0	NM_004755	O95316|Q96AF7	Missense_Mutation	SNP	ENST00000261991.3	hg19	CCDS9893.1	.	.	.	.	.	.	.	.	.	.	G	10.45	1.354677	0.24512	.	.	ENSG00000100784	ENST00000261991;ENST00000536315	T;T	0.66815	-0.23;-0.23	5.25	5.25	0.73442	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.70290	0.3207	L	0.33485	1.01	0.80722	D	1	P	0.52842	0.956	D	0.65010	0.931	T	0.61959	-0.6955	10	0.05959	T	0.93	.	19.2225	0.93803	0.0:0.0:1.0:0.0	.	751	O75582	KS6A5_HUMAN	S	751;672	ENSP00000261991:T751S;ENSP00000442803:T672S	ENSP00000261991:T751S	T	-	2	0	RPS6KA5	90408328	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.813000	0.99286	2.611000	0.88343	0.655000	0.94253	ACC	.	.		0.483	RPS6KA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411442.2	NM_004755		C	91338575	G	C	91338575	3	2	253	1	0	0	0	0	1	0	0	0	13669	1261	44	4	160	4	RPS6KA5	14	91338575	Missense_Mutation	SNP	G	TCGA-EP-A26S-01A-11D-A16V-10	9601393	91338575	16010965	66	34271										
DUOXA2	405753	hgsc.bcm.edu	37	chr15	45408389	45408389	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	acatcctacaaagccttcagCgcagcgcgcgttacagcccg	9	16	1	0			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr15:45408389C>A	ENST00000323030.5	+	3	558	c.273C>A	c.(271-273)agC>agA	p.S91R	DUOX2_ENST00000603300.1_5'Flank|DUOX2_ENST00000389039.6_5'Flank	NM_207581.3	NP_997464.2	Q1HG44	DOXA2_HUMAN	dual oxidase maturation factor 2	91					hydrogen peroxide metabolic process (GO:0042743)|protein transport (GO:0015031)|regulation of inflammatory response (GO:0050727)|regulation of thyroid hormone generation (GO:2000609)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)							all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;2.88e-18)|GBM - Glioblastoma multiforme(94;3.95e-07)|COAD - Colon adenocarcinoma(120;0.0652)|Colorectal(133;0.0659)		AAGCCTTCAGCGCAGCGCGCG	0.572																																					p.S91R		Atlas-SNP	.											.	DUOXA2	38	.	0			c.C273A						.						139	132	134					15																	45408389		2002	4151	6153	SO:0001583	missense	405753	exon3			CTTCAGCGCAGCG	BX537581	CCDS10118.2	15q21.1	2008-10-30		2006-07-25	ENSG00000140274	ENSG00000140274			32698	protein-coding gene	gene with protein product		612772				16651268	Standard	NM_207581		Approved		uc001zuo.3	Q1HG44	OTTHUMG00000131354	ENST00000323030.5:c.273C>A	chr15.hg19:g.45408389C>A	ENSP00000319705:p.Ser91Arg	41.0	0.0		43.0	26.0	NM_207581	B2RPI9|H0YNQ6	Missense_Mutation	SNP	ENST00000323030.5	hg19	CCDS10118.2	.	.	.	.	.	.	.	.	.	.	C	14.81	2.646005	0.47258	.	.	ENSG00000140274	ENST00000323030	T	0.67865	-0.29	5.41	-9.39	0.00619	.	0.117307	0.85682	D	0.000000	T	0.78742	0.4331	M	0.79123	2.44	0.31474	N	0.668055	D	0.76494	0.999	D	0.71870	0.975	T	0.82678	-0.0338	10	0.72032	D	0.01	-18.1639	23.4889	0.99983	0.0:0.8007:0.0:0.1993	.	91	Q1HG44	DOXA2_HUMAN	R	91	ENSP00000319705:S91R	ENSP00000319705:S91R	S	+	3	2	DUOXA2	43195681	0.000000	0.05858	0.000000	0.03702	0.112000	0.19704	-0.207000	0.09384	-2.250000	0.00701	-1.267000	0.01435	AGC	.	.		0.572	DUOXA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254142.1	NM_207581		A	45408389	C	A	45408389	3	1	253	1	0	0	0	0	1	0	0	0	4805	767	27	1	283	1	DUOXA2	15	45408389	Missense_Mutation	SNP	C	TCGA-EP-A26S-01A-11D-A16V-10		45408389	57123003	67	34272										
SETD1A	9739	hgsc.bcm.edu	37	chr16	30977205	30977205	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	ctccttggagctcatggaccGacttggggctcagtggggag	16	10	2	0			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr16:30977205G>T	ENST00000262519.8	+	8	2689	c.2003G>T	c.(2002-2004)cGa>cTa	p.R668L		NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A	668					histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(21)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	59						CTCATGGACCGACTTGGGGCT	0.617																																					p.R668L		Atlas-SNP	.											.	SETD1A	143	.	0			c.G2003T						.						76	73	74					16																	30977205		2197	4300	6497	SO:0001583	missense	9739	exon8			TGGACCGACTTGG	AB002337	CCDS32435.1	16p11.2	2013-02-12			ENSG00000099381	ENSG00000099381		"Chromatin-modifying enzymes / K-methyltransferases", "RNA binding motif (RRM) containing"	29010	protein-coding gene	gene with protein product		611052				9205841, 12670868	Standard	XM_005255723		Approved	KIAA0339, Set1, KMT2F	uc002ead.1	O15047	OTTHUMG00000150474	ENST00000262519.8:c.2003G>T	chr16.hg19:g.30977205G>T	ENSP00000262519:p.Arg668Leu	113.0	0.0		113.0	48.0	NM_014712	A6NP62|Q6PIF3|Q8TAJ6	Missense_Mutation	SNP	ENST00000262519.8	hg19	CCDS32435.1	.	.	.	.	.	.	.	.	.	.	G	11.63	1.694952	0.30052	.	.	ENSG00000099381	ENST00000262519	D	0.94000	-3.33	4.67	4.67	0.58626	.	0.084306	0.49916	D	0.000124	D	0.92093	0.7494	N	0.19112	0.55	0.46356	D	0.999007	D	0.63880	0.993	D	0.74023	0.982	D	0.87573	0.2479	10	0.02654	T	1	.	16.5112	0.84286	0.0:0.0:1.0:0.0	.	668	O15047	SET1A_HUMAN	L	668	ENSP00000262519:R668L	ENSP00000262519:R668L	R	+	2	0	SETD1A	30884706	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	2.187000	0.42602	2.434000	0.82447	0.655000	0.94253	CGA	.	.		0.617	SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318244.2	NM_014712		T	30977205	G	T	30977205	3	4	253	1	0	0	0	0	1	0	0	0	14145	1058	37	1	2029	1	SETD1A	16	30977205	Missense_Mutation	SNP	G	TCGA-EP-A26S-01A-11D-A16V-10		30977205	59377548	68	34273										
DNAH2	146754	hgsc.bcm.edu	37	chr17	7734001	7734001	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	agaaaacttgctgagcctctAtctcgatgagtacgaggaga	11	8	2	4			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr17:7734001A>G	ENST00000572933.1	+	79	13531	c.12071A>G	c.(12070-12072)tAt>tGt	p.Y4024C	DNAH2_ENST00000389173.2_Missense_Mutation_p.Y4024C			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	4024					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				CTGAGCCTCTATCTCGATGAG	0.542																																					p.Y4024C		Atlas-SNP	.											.	DNAH2	498	.	0			c.A12071G						.						75	73	74					17																	7734001		2203	4300	6503	SO:0001583	missense	146754	exon78			GCCTCTATCTCGA	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.12071A>G	chr17.hg19:g.7734001A>G	ENSP00000458355:p.Tyr4024Cys	99.0	0.0		62.0	24.0	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	hg19	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	A	19.18	3.777868	0.70107	.	.	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.13657	2.57	5.84	5.84	0.93424	Dynein heavy chain (1);	0.000000	0.85682	D	0.000000	T	0.51924	0.1703	H	0.96547	3.84	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.67937	-0.5541	10	0.87932	D	0	.	15.1984	0.73116	1.0:0.0:0.0:0.0	.	3985;4024	Q9P225-2;Q9P225	.;DYH2_HUMAN	C	3985;4024	ENSP00000373825:Y4024C	ENSP00000353818:Y3985C	Y	+	2	0	DNAH2	7674726	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	5.509000	0.67012	2.243000	0.73865	0.533000	0.62120	TAT	.	.		0.542	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		G	7734001	A	G	7734001	3	3	253	1	0	0	0	0	1	0	0	0	4604	449	16	2	12381	2	DNAH2	17	7734001	Missense_Mutation	SNP	A	TCGA-EP-A26S-01A-11D-A16V-10		7734001	73461209	69	34274										
DLX4	1748	hgsc.bcm.edu	37	chr17	48046980	48046980	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	ccaatttgtcctactccaggCcgtatggccacctcctgtct	7	16	1	0			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr17:48046980C>T	ENST00000240306.3	+	1	443	c.148C>T	c.(148-150)Ccg>Tcg	p.P50S	DLX4_ENST00000505318.2_Missense_Mutation_p.P50S|DLX4_ENST00000503410.1_3'UTR	NM_138281.2	NP_612138.1	Q92988	DLX4_HUMAN	distal-less homeobox 4	50				MTSLPCPLPGRDASKAVFPDLAPVPSVAAAYPLGLSPTTAA SPNLSYSRPYGHLLSYPYTEPANPGDSYLSCQQPAALSQPL CGPAEHPQELEA -> GGSLSLPPEPLCARCPTKEGAAPRR PGFWGSLETQAATVWRGRHGHFSCRVRLSRGAARYSRRGQG KPGVTISAARLVFKVLSAGPLTHPAGRSRRLPRGHRLKPLS IALSLCLQCPSSVISRPRLSPGPSLSAPPYPKLAPPPVAEL RPPTAGAAVPWLWPSARFLPRVTGPIRVGAPLGAELRLVSP GAVNVGVETLHAE (in Ref. 9). {ECO:0000305}.	multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(3)	10						CTACTCCAGGCCGTATGGCCA	0.652																																					p.P50S		Atlas-SNP	.											DLX4,caecum,carcinoma,0,1	DLX4	25	.	0			c.C148T						.						99	100	100					17																	48046980		2203	4300	6503	SO:0001583	missense	1748	exon1			TCCAGGCCGTATG		CCDS11555.1, CCDS45728.1	17q21.33	2011-06-20			ENSG00000108813	ENSG00000108813		"Homeoboxes / ANTP class : NKL subclass"	2917	protein-coding gene	gene with protein product		601911		DLX7, DLX9			Standard	NM_138281		Approved	DLX8, BP1	uc002ipv.3	Q92988	OTTHUMG00000161839	ENST00000240306.3:c.148C>T	chr17.hg19:g.48046980C>T	ENSP00000240306:p.Pro50Ser	33.0	0.0		26.0	12.0	NM_138281	D3DTX2|D3DTX3|O60480|Q13265|Q6PJK0|Q9HBE0	Missense_Mutation	SNP	ENST00000240306.3	hg19	CCDS11555.1	.	.	.	.	.	.	.	.	.	.	C	11.51	1.660455	0.29515	.	.	ENSG00000108813	ENST00000240306	D	0.91351	-2.83	3.88	0.596	0.17496	.	.	.	.	.	T	0.75027	0.3794	N	0.14661	0.345	0.09310	N	0.999997	B	0.09022	0.002	B	0.04013	0.001	T	0.61098	-0.7131	9	0.02654	T	1	-0.3069	3.3909	0.07289	0.2023:0.5656:0.0:0.2321	.	50	Q92988	DLX4_HUMAN	S	50	ENSP00000240306:P50S	ENSP00000240306:P50S	P	+	1	0	DLX4	45401979	0.007000	0.16637	0.006000	0.13384	0.898000	0.52572	1.018000	0.30002	0.304000	0.22809	0.313000	0.20887	CCG	.	.		0.652	DLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366214.1			T	48046980	C	T	48046980	3	4	253	1	0	0	0	0	1	0	0	0	4575	739	26	3	150	3	DLX4	17	48046980	Missense_Mutation	SNP	C	TCGA-EP-A26S-01A-11D-A16V-10	40312979	48046980	33148230	70	34275										
VEZF1	7716	hgsc.bcm.edu	37	chr17	56056601	56056601	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	gtcacatgttgttgttgttgTtgttgctgctgctgctgctg	13	7	1	0			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr17:56056601T>C	ENST00000581208.1	-	5	1090	c.1050A>G	c.(1048-1050)caA>caG	p.Q350Q	VEZF1_ENST00000584396.1_Silent_p.Q341Q	NM_007146.2	NP_009077.2	Q14119	VEZF1_HUMAN	vascular endothelial zinc finger 1	350	Poly-Gln.			Missing (in Ref. 1; BAA05663). {ECO:0000305}.	angiogenesis (GO:0001525)|cellular defense response (GO:0006968)|endothelial cell development (GO:0001885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(2)|lung(5)|ovary(1)	10						gttgttgttgttgttgctgct	0.473																																					p.Q350Q		Atlas-SNP	.											.	VEZF1	50	.	0			c.A1050G						.						173	159	164					17																	56056601		2203	4300	6503	SO:0001819	synonymous_variant	7716	exon5			TTGTTGTTGTTGC	D28118	CCDS32687.1	17q22	2012-10-05	2006-08-16	2006-08-16	ENSG00000136451	ENSG00000136451		"Zinc fingers, C2H2-type"	12949	protein-coding gene	gene with protein product		606747	"zinc finger protein 161"	ZNF161		8035792	Standard	XM_005257643		Approved	DB1	uc002ivf.1	Q14119	OTTHUMG00000178777	ENST00000581208.1:c.1050A>G	chr17.hg19:g.56056601T>C		84.0	0.0		112.0	10.0	NM_007146		Silent	SNP	ENST00000581208.1	hg19	CCDS32687.1																																																																																			.	.		0.473	VEZF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443321.1			C	56056601	T	C	56056601	2	2	253	1	0	0	0	0	0	0	0	1	17170	1722	60	2		2	VEZF1	17	56056601	Silent	SNP	T	TCGA-EP-A26S-01A-11D-A16V-10	8009621	56056601	25138609	71	34276										
CD300LF	146722	hgsc.bcm.edu	37	chr17	72700898	72700898	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	cacactgcacggtcaaggagCcccgctccaagccattcact	8	17	2	0	rs146550147		TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr17:72700898C>A	ENST00000326165.6	-	2	212	c.101G>T	c.(100-102)gGc>gTc	p.G34V	CD300LF_ENST00000301573.9_Missense_Mutation_p.G34V|CD300LF_ENST00000469092.1_Missense_Mutation_p.G37V|CD300LF_ENST00000361254.4_Missense_Mutation_p.G37V|RAB37_ENST00000340415.3_Intron|CD300LF_ENST00000343125.4_Missense_Mutation_p.G37V|CD300LF_ENST00000583937.1_Missense_Mutation_p.G34V|CD300LF_ENST00000464910.1_Missense_Mutation_p.G37V|RAB37_ENST00000402449.4_Intron|CD300LF_ENST00000581500.1_Missense_Mutation_p.G37V	NM_139018.3	NP_620587.2	Q8TDQ1	CLM1_HUMAN	CD300 molecule-like family member f	34	Ig-like V-type.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|large_intestine(1)|lung(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	12						GGTCAAGGAGCCCCGCTCCAA	0.512																																					p.G34V		Atlas-SNP	.											.	CD300LF	55	.	0			c.G101T						.	C	VAL/GLY,	1,4405	2.1+/-5.4	0,1,2202	85	79	81		101,	4.4	0.1	17	dbSNP_134	81	0,8600		0,0,4300	no	missense,intron	CD300LF,RAB37	NM_139018.3,NM_175738.4	109,	0,1,6502	AA,AC,CC		0.0,0.0227,0.0077	probably-damaging,	34/291,	72700898	1,13005	2203	4300	6503	SO:0001583	missense	146722	exon2			AAGGAGCCCCGCT	BC028199	CCDS11704.1, CCDS74148.1, CCDS74149.1, CCDS74150.1, CCDS74151.1, CCDS74152.1	17q25.2	2013-01-11	2006-03-29		ENSG00000186074	ENSG00000186074		"Immunoglobulin superfamily / V-set domain containing"	29883	protein-coding gene	gene with protein product		609807	"CD300 antigen like family member F"			12975309	Standard	NM_139018		Approved	IREM1, NKIR, IGSF13, CD300f, CLM1	uc002jlg.3	Q8TDQ1	OTTHUMG00000067609	ENST00000326165.6:c.101G>T	chr17.hg19:g.72700898C>A	ENSP00000327075:p.Gly34Val	90.0	0.0		84.0	35.0	NM_139018	B2RCL2|C9JDN3|Q3Y6P0|Q6UX24|Q7Z6A6|Q7Z7I4|Q7Z7I5|Q8N6D0|Q8NAF5	Missense_Mutation	SNP	ENST00000326165.6	hg19	CCDS11704.1	.	.	.	.	.	.	.	.	.	.	C	15.31	2.795488	0.50208	2.27E-4	0.0	ENSG00000186074	ENST00000301573;ENST00000361254;ENST00000343125;ENST00000326165	T;T;T;T	0.05081	3.5;3.5;3.5;3.5	5.35	4.38	0.52667	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.374624	0.23091	N	0.052033	T	0.31702	0.0805	H	0.94264	3.515	0.22851	N	0.998652	D;D;D;D;D;D	0.89917	0.994;1.0;0.967;1.0;1.0;1.0	D;D;P;D;D;D	0.87578	0.951;0.996;0.853;0.997;0.998;0.993	T	0.33266	-0.9875	10	0.87932	D	0	.	8.4986	0.33144	0.0:0.8221:0.0:0.1779	.	34;37;37;34;34;37	E7EME0;Q8TDQ1-2;Q8TDQ1-4;Q8TDQ1-5;Q8TDQ1;Q8TDQ1-6	.;.;.;.;CLM1_HUMAN;.	V	34;37;37;34	ENSP00000301573:G34V;ENSP00000355294:G37V;ENSP00000343751:G37V;ENSP00000327075:G34V	ENSP00000301573:G34V	G	-	2	0	CD300LF	70212493	0.000000	0.05858	0.078000	0.20375	0.024000	0.10985	-0.163000	0.09997	1.381000	0.46364	0.561000	0.74099	GGC	.	C|1.000;A|0.000		0.512	CD300LF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000145085.1	NM_139018		A	72700898	C	A	72700898	3	1	253	1	0	0	0	0	1	0	0	0	3003	739	26	3	795	3	CD300LF	17	72700898	Missense_Mutation	SNP	C	TCGA-EP-A26S-01A-11D-A16V-10	16644297	72700898	8494312	72	34277										
MCART2	147407	hgsc.bcm.edu	37	chr18	29339767	29339767	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	aagaactcataagttgcattGattatgccccaagagatgag	9	7	1	4			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr18:29339767G>A	ENST00000579441.2	-	1	857	c.858C>T	c.(856-858)atC>atT	p.I286I	SLC25A52_ENST00000269205.5_Silent_p.I296I			Q3SY17	S2552_HUMAN	solute carrier family 25, member 52	286					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)											AAGTTGCATTGATTATGCCCC	0.363																																					p.I296I		Atlas-SNP	.											.	.	.	.	0			c.C888T						.						44	47	46					18																	29339767		2198	4296	6494	SO:0001819	synonymous_variant	147407	exon1			TGCATTGATTATG		CCDS32812.1, CCDS32812.2	18q12.1	2013-07-15	2012-03-29	2012-03-29	ENSG00000141437	ENSG00000141437		"Solute carriers"	23324	protein-coding gene	gene with protein product			"mitochondrial carrier triple repeat 2"	MCART2			Standard	NM_001034172		Approved		uc002kxa.3	Q3SY17	OTTHUMG00000179617	ENST00000579441.2:c.858C>T	chr18.hg19:g.29339767G>A		132.0	0.0		131.0	46.0	NM_001034172		Silent	SNP	ENST00000579441.2	hg19																																																																																				.	.		0.363	SLC25A52-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_084000		A	29339767	G	A	29339767	2	1	253	1	0	0	0	0	0	0	0	1	9379	1280	45	3		3	MCART2	18	29339767	Silent	SNP	G	TCGA-EP-A26S-01A-11D-A16V-10		29339767	48737481	73	34278										
SERPINB13	5275	hgsc.bcm.edu	37	chr18	61255920	61255920	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	tcatggattcacttggcgccGtcagcactcgacttgggttt	11	11	3	0	rs139825462		TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr18:61255920G>A	ENST00000344731.5	+	2	121	c.19G>A	c.(19-21)Gtc>Atc	p.V7I	SERPINB13_ENST00000269489.5_Missense_Mutation_p.V7I	NM_012397.3	NP_036529.1	Q9UIV8	SPB13_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 13	7					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)|response to UV (GO:0009411)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.V7I(3)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|urinary_tract(1)	25						ACTTGGCGCCGTCAGCACTCG	0.418																																					p.V7I		Atlas-SNP	.											SERPINB13,NS,carcinoma,0,3	SERPINB13	51	.	3	Substitution - Missense(3)	prostate(2)|kidney(1)	c.G19A						.	G	ILE/VAL	3,4403	6.2+/-15.9	0,3,2200	94	90	91		19	2.1	0	18	dbSNP_134	91	0,8600		0,0,4300	no	missense	SERPINB13	NM_012397.3	29	0,3,6500	AA,AG,GG		0.0,0.0681,0.0231	benign	7/392	61255920	3,13003	2203	4300	6503	SO:0001583	missense	5275	exon2			GGCGCCGTCAGCA	AF169949, BC101821	CCDS11985.1	18q21.33	2014-02-18	2005-08-18		ENSG00000197641	ENSG00000197641		"Serine (or cysteine) peptidase inhibitors"	8944	protein-coding gene	gene with protein product		604445	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 13"	PI13		9297979, 10512713, 24172014	Standard	NM_012397		Approved	HUR7, hurpin, headpin	uc002ljc.3	Q9UIV8	OTTHUMG00000060406	ENST00000344731.5:c.19G>A	chr18.hg19:g.61255920G>A	ENSP00000341584:p.Val7Ile	156.0	1.0		128.0	68.0	NM_012397	A8K2Q8|Q3MII2|Q9HCX1|Q9UBW1|Q9UKG0	Missense_Mutation	SNP	ENST00000344731.5	hg19	CCDS11985.1	.	.	.	.	.	.	.	.	.	.	G	10.55	1.380737	0.24944	6.81E-4	0.0	ENSG00000197641	ENST00000431153;ENST00000269489;ENST00000539341;ENST00000344731	T;T;D	0.82081	-0.79;2.82;-1.57	4.89	2.12	0.27331	Serpin domain (1);	0.365172	0.23587	N	0.046598	T	0.69178	0.3082	N	0.20881	0.62	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.10450	0.005;0.003	T	0.59547	-0.7434	10	0.59425	D	0.04	.	6.7555	0.23512	0.0764:0.1282:0.6636:0.1318	.	7;7	B7ZKV6;Q9UIV8	.;SPB13_HUMAN	I	37;7;7;7	ENSP00000388300:V37I;ENSP00000269489:V7I;ENSP00000341584:V7I	ENSP00000269489:V7I	V	+	1	0	SERPINB13	59406900	0.005000	0.15991	0.000000	0.03702	0.000000	0.00434	0.742000	0.26216	0.261000	0.21753	-1.149000	0.01842	GTC	.	G|1.000;A|0.000		0.418	SERPINB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133798.1	NM_012397		A	61255920	G	A	61255920	3	1	253	1	0	0	0	0	1	0	0	0	14115	1145	40	1	21	1	SERPINB13	18	61255920	Missense_Mutation	SNP	G	TCGA-EP-A26S-01A-11D-A16V-10	31916153	61255920	16821328	74	34279										
SALL3	27164	hgsc.bcm.edu	37	chr18	76754127	76754127	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	ccgttcaagtgcaagatctgCggccgcgccttcaccaccaa	9	16	3	1			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr18:76754127C>T	ENST00000537592.2	+	2	2136	c.2136C>T	c.(2134-2136)tgC>tgT	p.C712C	SALL3_ENST00000536229.3_Silent_p.C579C|SALL3_ENST00000575389.2_Silent_p.C712C	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	712					forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|negative regulation of smoothened signaling pathway (GO:0045879)|olfactory bulb interneuron development (GO:0021891)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(40)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)		GCAAGATCTGCGGCCGCGCCT	0.662																																					p.C712C		Atlas-SNP	.											.	SALL3	162	.	0			c.C2136T						.						36	33	34					18																	76754127		2203	4299	6502	SO:0001819	synonymous_variant	27164	exon2			GATCTGCGGCCGC	AJ007421	CCDS12013.1	18q23	2013-10-17	2013-10-17		ENSG00000256463	ENSG00000256463		"Zinc fingers, C2H2-type"	10527	protein-coding gene	gene with protein product		605079	"sal (Drosophila)-like 3", "sal-like 3 (Drosophila)"			10610715	Standard	NM_171999		Approved	ZNF796	uc002lmt.3	Q9BXA9	OTTHUMG00000132896	ENST00000537592.2:c.2136C>T	chr18.hg19:g.76754127C>T		33.0	0.0		21.0	9.0	NM_171999	Q9UGH1	Silent	SNP	ENST00000537592.2	hg19	CCDS12013.1																																																																																			.	.		0.662	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256397.1	NM_171999		T	76754127	C	T	76754127	2	4	253	1	0	0	0	0	0	0	0	1	13827	776	27	1		1	SALL3	18	76754127	Silent	SNP	C	TCGA-EP-A26S-01A-11D-A16V-10	15498207	76754127	1323121	75	34280										
CLEC17A	388512	hgsc.bcm.edu	37	chr19	14705334	14705334	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	gcttctcttctccaggttcaAgtgctccaccaagacctcca	6	16	3	1			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr19:14705334A>T	ENST00000417570.1	+	5	321	c.283A>T	c.(283-285)Agt>Tgt	p.S95C	CLEC17A_ENST00000397439.2_Missense_Mutation_p.S78C|CLEC17A_ENST00000547437.1_Missense_Mutation_p.S95C	NM_001204118.1	NP_001191047.1	Q6ZS10	CL17A_HUMAN	C-type lectin domain family 17, member A	95						cell surface (GO:0009986)|integral component of membrane (GO:0016021)	fucose binding (GO:0042806)|mannose binding (GO:0005537)|metal ion binding (GO:0046872)										TCCAGGTTCAAGTGCTCCACC	0.582																																					p.S95C		Atlas-SNP	.											.	CLEC17A	27	.	0			c.A283T						.						40	41	40					19																	14705334		1957	4146	6103	SO:0001583	missense	388512	exon5			GGTTCAAGTGCTC	AK127809	CCDS46002.1, CCDS46002.2, CCDS56087.1	19p13.12	2009-06-26			ENSG00000187912	ENSG00000187912		"C-type lectin domain containing"	34520	protein-coding gene	gene with protein product	"prolectin"					19419970	Standard	NM_207390		Approved	FLJ45910	uc010dzn.2	Q6ZS10		ENST00000417570.1:c.283A>T	chr19.hg19:g.14705334A>T	ENSP00000393719:p.Ser95Cys	57.0	0.0		66.0	31.0	NM_207390	A8MX68|B2RTX0|B7ZMM4	Missense_Mutation	SNP	ENST00000417570.1	hg19	CCDS56087.1	.	.	.	.	.	.	.	.	.	.	a	7.414	0.635337	0.14322	.	.	ENSG00000187912	ENST00000547437;ENST00000397439;ENST00000417570	T;T;T	0.64618	-0.11;2.22;-0.11	3.18	-6.36	0.01969	.	.	.	.	.	T	0.30603	0.0770	N	0.08118	0	0.09310	N	1	P;P;P;P	0.46327	0.876;0.768;0.804;0.768	B;B;B;B	0.40982	0.345;0.26;0.187;0.26	T	0.34004	-0.9846	9	0.41790	T	0.15	-36.3205	0.4882	0.00559	0.2203:0.2181:0.2921:0.2695	.	95;95;95;95	Q6ZS10-2;Q6ZS10-3;Q6ZS10;F8W1T8	.;.;CL17A_HUMAN;.	C	95;78;95	ENSP00000450065:S95C;ENSP00000380581:S78C;ENSP00000393719:S95C	ENSP00000341620:S95C	S	+	1	0	CLEC17A	14566334	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.707000	0.05041	-3.115000	0.00240	-1.668000	0.00747	AGT	.	.		0.582	CLEC17A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403400.1	NM_207390		T	14705334	A	T	14705334	3	4	253	1	0	0	0	0	1	0	0	0	3503	72	3	4	246	4	CLEC17A	19	14705334	Missense_Mutation	SNP	A	TCGA-EP-A26S-01A-11D-A16V-10		14705334	44423649	76	34281										
JAK3	3718	hgsc.bcm.edu	37	chr19	17950393	17950393	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	ctcgaagactgctgtggggtCggctgaggccaaccagaagg	16	10	0	3			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr19:17950393C>T	ENST00000527670.1	-	9	1363	c.1334G>A	c.(1333-1335)cGa>cAa	p.R445Q	JAK3_ENST00000534444.1_Missense_Mutation_p.R445Q|JAK3_ENST00000458235.1_Missense_Mutation_p.R445Q|JAK3_ENST00000526008.1_5'UTR			P52333	JAK3_HUMAN	Janus kinase 3	445	SH2; atypical.				B cell differentiation (GO:0030183)|enzyme linked receptor protein signaling pathway (GO:0007167)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of dendritic cell cytokine production (GO:0002731)|negative regulation of FasL biosynthetic process (GO:0045221)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of T cell activation (GO:0050868)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|negative regulation of thymocyte apoptotic process (GO:0070244)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of T cell apoptotic process (GO:0070232)|response to interleukin-15 (GO:0070672)|response to interleukin-2 (GO:0070669)|response to interleukin-4 (GO:0070670)|response to interleukin-9 (GO:0071104)|STAT protein import into nucleus (GO:0007262)|T cell homeostasis (GO:0043029)|tyrosine phosphorylation of STAT protein (GO:0007260)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(85)|kidney(4)|large_intestine(11)|lung(22)|ovary(3)|prostate(5)|skin(1)|stomach(2)|upper_aerodigestive_tract(5)	147					Tofacitinib(DB08895)	GCTGTGGGGTCGGCTGAGGCC	0.612		2	Mis		"acute megakaryocytic leukemia, ETP ALL"																																p.R445Q		Atlas-SNP	.		Dom	yes		19	19p13.1	3718	Janus kinase 3		L	.	JAK3	341	.	0			c.G1334A						.						36	31	33					19																	17950393		2203	4300	6503	SO:0001583	missense	3718	exon10			TGGGGTCGGCTGA	U31601	CCDS12366.1	19p13-p12	2014-09-17	2009-04-23		ENSG00000105639	ENSG00000105639	2.7.10.1		6193	protein-coding gene	gene with protein product	"tyrosine-protein kinase JAK3", "leukocyte Janus kinase"	600173				8921370, 9226382	Standard	NM_000215		Approved	L-JAK, JAKL, LJAK, JAK3_HUMAN, JAK-3	uc002nhn.4	P52333	OTTHUMG00000165648	ENST00000527670.1:c.1334G>A	chr19.hg19:g.17950393C>T	ENSP00000432511:p.Arg445Gln	15.0	0.0		20.0	8.0	NM_000215	Q13259|Q13260|Q13611|Q8N1E8|Q99699|Q9Y6S2	Missense_Mutation	SNP	ENST00000527670.1	hg19	CCDS12366.1	.	.	.	.	.	.	.	.	.	.	C	4.419	0.077400	0.08485	.	.	ENSG00000105639	ENST00000458235;ENST00000428406;ENST00000527670;ENST00000534444	T;T;T	0.26518	1.73;1.73;1.73	3.7	-1.12	0.09808	SH2 motif (2);	0.386456	0.26297	N	0.025183	T	0.12390	0.0301	N	0.19112	0.55	0.09310	N	1	B;B;B	0.23891	0.093;0.085;0.023	B;B;B	0.15870	0.011;0.014;0.003	T	0.14811	-1.0459	10	0.42905	T	0.14	-4.1589	6.6306	0.22855	0.0:0.511:0.0:0.489	.	445;445;445	B4DK43;P52333-2;P52333	.;.;JAK3_HUMAN	Q	445	ENSP00000391676:R445Q;ENSP00000432511:R445Q;ENSP00000436421:R445Q	ENSP00000413248:R445Q	R	-	2	0	JAK3	17811393	0.000000	0.05858	0.098000	0.21074	0.002000	0.02628	-0.150000	0.10189	-0.030000	0.13804	-0.463000	0.05309	CGA	.	.		0.612	JAK3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385549.1	NM_000215		T	17950393	C	T	17950393	3	4	253	1	0	0	0	0	1	0	0	0	7948	884	31	1	2100	1	JAK3	19	17950393	Missense_Mutation	SNP	C	TCGA-EP-A26S-01A-11D-A16V-10	3245059	17950393	41178590	77	34282										
ZNF676	163223	hgsc.bcm.edu	37	chr19	22363944	22363944	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	atttgtagggtttctctccaGtatgaatactcttataataa	6	6	2	1			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr19:22363944G>T	ENST00000397121.2	-	3	892	c.575C>A	c.(574-576)aCt>aAt	p.T192N		NM_001001411.2	NP_001001411.2	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	192					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(49)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	67		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				TTTCTCTCCAGTATGAATACT	0.348																																					p.T192N		Atlas-SNP	.											.	ZNF676	146	.	0			c.C575A						.						52	56	55					19																	22363944		2031	4219	6250	SO:0001583	missense	163223	exon3			TCTCCAGTATGAA	AK097798	CCDS42539.1	19p12	2013-01-08				ENSG00000196109		"Zinc fingers, C2H2-type"	20429	protein-coding gene	gene with protein product							Standard	NM_001001411		Approved		uc002nqs.1	Q8N7Q3		ENST00000397121.2:c.575C>A	chr19.hg19:g.22363944G>T	ENSP00000380310:p.Thr192Asn	46.0	0.0		55.0	29.0	NM_001001411	A8MVX5	Missense_Mutation	SNP	ENST00000397121.2	hg19	CCDS42539.1	.	.	.	.	.	.	.	.	.	.	.	7.323	0.617441	0.14129	.	.	ENSG00000196109	ENST00000397121	T	0.26067	1.76	1.03	-2.06	0.07298	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.33644	0.0870	M	0.71036	2.16	0.21933	N	0.999468	P	0.46987	0.888	P	0.52386	0.697	T	0.23332	-1.0191	9	0.72032	D	0.01	.	3.9636	0.09421	0.1909:0.0:0.5787:0.2305	.	192	Q8N7Q3	ZN676_HUMAN	N	192	ENSP00000380310:T192N	ENSP00000380310:T192N	T	-	2	0	ZNF676	22155784	0.799000	0.28903	0.005000	0.12908	0.031000	0.12232	1.222000	0.32515	-0.631000	0.05560	0.195000	0.17529	ACT	.	.		0.348	ZNF676-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464392.1	NM_001001411		T	22363944	G	T	22363944	3	4	253	1	0	0	0	0	1	0	0	0	18098	1029	36	3	1195	3	ZNF676	19	22363944	Missense_Mutation	SNP	G	TCGA-EP-A26S-01A-11D-A16V-10	4413551	22363944	36765039	78	34283										
HIPK4	147746	hgsc.bcm.edu	37	chr19	40895613	40895613	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	tgacgtgggcctcttcagggTctaggcctcgcatgcagtgc	14	12	3	1			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr19:40895613T>C	ENST00000291823.2	-	1	481	c.197A>G	c.(196-198)gAc>gGc	p.D66G		NM_144685.3	NP_653286.2	Q8NE63	HIPK4_HUMAN	homeodomain interacting protein kinase 4	66	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				histone phosphorylation (GO:0016572)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|regulation of signal transduction by p53 class mediator (GO:1901796)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	20			Lung(22;4.95e-05)|LUSC - Lung squamous cell carcinoma(20;0.000292)			CTCTTCAGGGTCTAGGCCTCG	0.547																																					p.D66G		Atlas-SNP	.											.	HIPK4	100	.	0			c.A197G						.						160	141	147					19																	40895613		2203	4300	6503	SO:0001583	missense	147746	exon1			TCAGGGTCTAGGC	BC034501	CCDS12555.1	19q13.2	2008-02-05				ENSG00000160396			19007	protein-coding gene	gene with protein product		611712					Standard	NM_144685		Approved	FLJ32818	uc002onp.3	Q8NE63		ENST00000291823.2:c.197A>G	chr19.hg19:g.40895613T>C	ENSP00000291823:p.Asp66Gly	118.0	0.0		70.0	33.0	NM_144685	A8K863|Q96M54	Missense_Mutation	SNP	ENST00000291823.2	hg19	CCDS12555.1	.	.	.	.	.	.	.	.	.	.	T	18.48	3.633943	0.67130	.	.	ENSG00000160396	ENST00000291823;ENST00000452139	T	0.20738	2.05	4.76	4.76	0.60689	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.53938	D	0.000060	T	0.40119	0.1104	M	0.79343	2.45	0.40835	D	0.983623	D	0.56746	0.977	P	0.60012	0.867	T	0.40194	-0.9576	10	0.87932	D	0	.	8.1293	0.31018	0.0:0.0917:0.0:0.9083	.	66	Q8NE63	HIPK4_HUMAN	G	66;31	ENSP00000291823:D66G	ENSP00000291823:D66G	D	-	2	0	HIPK4	45587453	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	4.587000	0.60991	1.987000	0.57996	0.460000	0.39030	GAC	.	.		0.547	HIPK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462593.1	NM_144685		C	40895613	T	C	40895613	3	2	253	1	0	0	0	0	1	0	0	0	7128	1667	58	2	1669	2	HIPK4	19	40895613	Missense_Mutation	SNP	T	TCGA-EP-A26S-01A-11D-A16V-10	18531669	40895613	18233370	79	34284										
TBC1D17	79735	hgsc.bcm.edu	37	chr19	50387721	50387721	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	cccatgtccccccaggctacGtccagggcatgagtgatctt	10	15	1	2			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr19:50387721G>A	ENST00000221543.5	+	12	1548	c.1249G>A	c.(1249-1251)Gtc>Atc	p.V417I	TBC1D17_ENST00000535102.2_Missense_Mutation_p.V384I	NM_024682.2	NP_078958	Q9HA65	TBC17_HUMAN	TBC1 domain family, member 17	417	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				autophagy (GO:0006914)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	Rab GTPase activator activity (GO:0005097)			NS(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	15		all_lung(116;0.000338)|Lung NSC(112;0.000446)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.017)		CCCAGGCTACGTCCAGGGCAT	0.642																																					p.V417I		Atlas-SNP	.											TBC1D17,NS,carcinoma,0,1	TBC1D17	39	.	0			c.G1249A						.						171	160	164					19																	50387721		2203	4300	6503	SO:0001583	missense	79735	exon12			GGCTACGTCCAGG	AK090606	CCDS12785.1, CCDS54294.1	19q13.33	2013-07-09				ENSG00000104946			25699	protein-coding gene	gene with protein product						22854040	Standard	NM_024682		Approved	FLJ12168	uc002pqo.3	Q9HA65		ENST00000221543.5:c.1249G>A	chr19.hg19:g.50387721G>A	ENSP00000221543:p.Val417Ile	87.0	0.0		80.0	39.0	NM_024682	B4DT12|B9A6L8|F5H1W7	Missense_Mutation	SNP	ENST00000221543.5	hg19	CCDS12785.1	.	.	.	.	.	.	.	.	.	.	G	31	5.068829	0.93950	.	.	ENSG00000104946	ENST00000221543;ENST00000535102	T;T	0.12984	2.63;2.63	5.22	5.22	0.72569	Rab-GAP/TBC domain (4);	0.000000	0.64402	D	0.000001	T	0.45256	0.1333	M	0.91768	3.24	0.80722	D	1	D;D	0.76494	0.999;0.999	P;D	0.67900	0.88;0.954	T	0.54931	-0.8219	10	0.52906	T	0.07	-43.7203	16.2481	0.82460	0.0:0.0:1.0:0.0	.	384;417	F5H1W7;Q9HA65	.;TBC17_HUMAN	I	417;384	ENSP00000221543:V417I;ENSP00000446323:V384I	ENSP00000221543:V417I	V	+	1	0	TBC1D17	55079533	1.000000	0.71417	0.990000	0.47175	0.956000	0.61745	9.097000	0.94193	2.424000	0.82194	0.561000	0.74099	GTC	.	.		0.642	TBC1D17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466404.1	NM_024682		A	50387721	G	A	50387721	3	1	253	1	0	0	0	0	1	0	0	0	15621	1145	40	1	1295	1	TBC1D17	19	50387721	Missense_Mutation	SNP	G	TCGA-EP-A26S-01A-11D-A16V-10	9492108	50387721	8741262	80	34285										
ZSCAN5A	79149	hgsc.bcm.edu	37	chr19	56735066	56735066	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	cggtgggcctggccttccccTggacgcatctggttcaccga	13	15	2	0	rs199886337		TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr19:56735066T>C	ENST00000587340.1	-	5	1217	c.522A>G	c.(520-522)ccA>ccG	p.P174P	ZSCAN5A_ENST00000254165.3_Silent_p.P57P|ZSCAN5A_ENST00000587492.1_Silent_p.P28P|ZSCAN5A_ENST00000391713.1_Silent_p.P174P|ZSCAN5A_ENST00000592355.1_Silent_p.P174P			Q9BUG6	ZSA5A_HUMAN	zinc finger and SCAN domain containing 5A	174					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(1)|lung(12)|ovary(1)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						GGCCTTCCCCTGGACGCATCT	0.612																																					p.P174P		Atlas-SNP	.											.	ZSCAN5A	118	.	0			c.A522G						.						67	60	62					19																	56735066		2203	4300	6503	SO:0001819	synonymous_variant	79149	exon3			TTCCCCTGGACGC	AK098700	CCDS12941.1	19q13.43	2013-01-08	2008-06-10	2008-06-10	ENSG00000131848	ENSG00000131848		"-", "Zinc fingers, C2H2-type"	23710	protein-coding gene	gene with protein product			"zinc finger protein 495", "zinc finger and SCAN domain containing 5"	ZNF495, ZSCAN5			Standard	NM_024303		Approved	MGC4161	uc002qmq.3	Q9BUG6		ENST00000587340.1:c.522A>G	chr19.hg19:g.56735066T>C		44.0	0.0		32.0	16.0	NM_024303	B4DX98|Q49A73|Q53F04|Q8N7B3	Silent	SNP	ENST00000587340.1	hg19	CCDS12941.1																																																																																			.	T|0.999;C|0.001		0.612	ZSCAN5A-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458110.1	NM_024303		C	56735066	T	C	56735066	2	2	253	1	0	0	0	0	0	0	0	1	18253	1567	55	2		2	ZSCAN5A	19	56735066	Silent	SNP	T	TCGA-EP-A26S-01A-11D-A16V-10	6347345	56735066	2393917	81	34286										
ZNF71	58491	hgsc.bcm.edu	37	chr19	57133787	57133787	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	agcaccagcgcatccacaccGgcgagaagccctacgagtgc	11	16	0	1			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr19:57133787G>T	ENST00000328070.6	+	3	1366	c.1132G>T	c.(1132-1134)Ggc>Tgc	p.G378C		NM_021216.4	NP_067039.1	Q9NQZ8	ZNF71_HUMAN	zinc finger protein 71	378					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			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)		CATCCACACCGGCGAGAAGCC	0.627																																					p.G378C		Atlas-SNP	.											.	ZNF71	69	.	0			c.G1132T						.						94	79	84					19																	57133787		2203	4300	6503	SO:0001583	missense	58491	exon3			CACACCGGCGAGA	X60074	CCDS12947.1	19q13.4	2013-01-08	2006-05-12			ENSG00000197951		"Zinc fingers, C2H2-type"	13141	protein-coding gene	gene with protein product		194545	"zinc finger protein 71 (Cos26)"			1639391	Standard	NM_021216		Approved	Cos26, EZFIT	uc002qnm.4	Q9NQZ8		ENST00000328070.6:c.1132G>T	chr19.hg19:g.57133787G>T	ENSP00000328245:p.Gly378Cys	118.0	0.0		78.0	30.0	NM_021216	Q15919|Q9UC09|Q9UQD3	Missense_Mutation	SNP	ENST00000328070.6	hg19	CCDS12947.1	.	.	.	.	.	.	.	.	.	.	G	14.89	2.670820	0.47781	.	.	ENSG00000197951	ENST00000328070	T	0.26660	1.72	3.58	3.58	0.41010	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.47875	0.1469	M	0.79258	2.445	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.27262	-1.0079	9	0.87932	D	0	.	6.744	0.23451	0.1285:0.0:0.8715:0.0	.	378	Q9NQZ8	ZNF71_HUMAN	C	378	ENSP00000328245:G378C	ENSP00000328245:G378C	G	+	1	0	ZNF71	61825599	0.994000	0.37717	0.049000	0.19019	0.895000	0.52256	4.080000	0.57620	1.815000	0.52974	0.561000	0.74099	GGC	.	.		0.627	ZNF71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459798.2	NM_021216		T	57133787	G	T	57133787	3	4	253	1	0	0	0	0	1	0	0	0	18129	1116	39	1	1134	1	ZNF71	19	57133787	Missense_Mutation	SNP	G	TCGA-EP-A26S-01A-11D-A16V-10	398721	57133787	1995196	82	34287										
SCARF2	91179	hgsc.bcm.edu	37	chr22	20784723	20784723	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	ccggggcactcactggggccCgtggacgccagggctgcaca	16	15	1	0			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr22:20784723C>T	ENST00000266214.5	-	6	1299	c.1195G>A	c.(1195-1197)Ggg>Agg	p.G399R	SCARF2_ENST00000405555.3_Missense_Mutation_p.G399R	NM_153334.4	NP_699165.2	Q96GP6	SREC2_HUMAN	scavenger receptor class F, member 2	399	EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell adhesion (GO:0007155)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|skin(2)	10	Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.219)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)			CACTGGGGCCCGTGGACGCCA	0.716																																					p.G399R		Atlas-SNP	.											.	SCARF2	23	.	0			c.G1195A						.						6	7	7					22																	20784723		2139	4207	6346	SO:0001583	missense	91179	exon6			GGGGCCCGTGGAC	AF522196	CCDS13779.1, CCDS46666.1	22q11.21	2011-10-10			ENSG00000244486	ENSG00000244486			19869	protein-coding gene	gene with protein product		613619				12154095	Standard	XM_006724364		Approved	SREC-II, SREC2, HUMZD58C02	uc002zsk.2	Q96GP6	OTTHUMG00000150779	ENST00000266214.5:c.1195G>A	chr22.hg19:g.20784723C>T	ENSP00000266214:p.Gly399Arg	19.0	0.0		22.0	14.0	NM_182895	E5RFB8|Q58A83|Q8IXF3|Q9BW74	Missense_Mutation	SNP	ENST00000266214.5	hg19	CCDS13779.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.556727	0.86231	.	.	ENSG00000244486	ENST00000405555;ENST00000341328;ENST00000266214	T;T	0.72394	-0.65;-0.65	4.45	4.45	0.53987	EGF-like region, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.83138	0.5189	M	0.75085	2.285	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.85718	0.1323	10	0.87932	D	0	-21.5452	14.9433	0.71012	0.0:1.0:0.0:0.0	.	399;399	E5RFB8;Q96GP6	.;SREC2_HUMAN	R	399	ENSP00000385589:G399R;ENSP00000266214:G399R	ENSP00000266214:G399R	G	-	1	0	SCARF2	19114723	1.000000	0.71417	1.000000	0.80357	0.862000	0.49288	6.737000	0.74816	2.188000	0.69820	0.561000	0.74099	GGG	.	.		0.716	SCARF2-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320047.1			T	20784723	C	T	20784723	3	4	253	1	0	0	0	0	1	0	0	0	13899	652	23	1	1441	1	SCARF2	22	20784723	Missense_Mutation	SNP	C	TCGA-EP-A26S-01A-11D-A16V-10		20784723	30519843	83	34288										
TRIOBP	11078	hgsc.bcm.edu	37	chr22	38120914	38120914	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	tcccaggacctcctctcccaAtagagccacacgagacaacc	6	18	1	2			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr22:38120914A>G	ENST00000406386.3	+	7	2606	c.2351A>G	c.(2350-2352)aAt>aGt	p.N784S		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	784					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					TCCTCTCCCAATAGAGCCACA	0.562																																					p.N784S		Atlas-SNP	.											.	TRIOBP	262	.	0			c.A2351G						.						136	147	143					22																	38120914		1980	4156	6136	SO:0001583	missense	11078	exon7			CTCCCAATAGAGC	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"Pleckstrin homology (PH) domain containing"	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.2351A>G	chr22.hg19:g.38120914A>G	ENSP00000384312:p.Asn784Ser	148.0	0.0		138.0	69.0	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	hg19	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	A	7.619	0.676520	0.14841	.	.	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.19394	2.15	3.65	-1.7	0.08159	.	.	.	.	.	T	0.11750	0.0286	L	0.34521	1.04	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.32587	-0.9901	9	0.33940	T	0.23	.	1.5067	0.02488	0.3434:0.3775:0.1108:0.1683	.	784	Q9H2D6	TARA_HUMAN	S	784	ENSP00000384312:N784S	ENSP00000384312:N784S	N	+	2	0	TRIOBP	36450860	0.075000	0.21258	0.003000	0.11579	0.028000	0.11728	-0.418000	0.07080	-0.145000	0.11294	-0.560000	0.04181	AAT	.	.		0.562	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2			G	38120914	A	G	38120914	3	3	253	1	0	0	0	0	1	0	0	0	16568	101	4	2	2369	2	TRIOBP	22	38120914	Missense_Mutation	SNP	A	TCGA-EP-A26S-01A-11D-A16V-10	17336191	38120914	13183652	84	34289										
EP300	2033	hgsc.bcm.edu	37	chr22	41560092	41560092	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	agagtgcggaagaaagatgcAtcagatctgtgtccttcacc	11	9	3	4			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr22:41560092A>T	ENST00000263253.7	+	22	4983	c.3764A>T	c.(3763-3765)cAt>cTt	p.H1255L		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	1255					apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						AGAAAGATGCATCAGATCTGT	0.388			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																												p.H1255L		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	.	EP300	367	.	0			c.A3764T						.						229	201	211					22																	41560092		2203	4300	6503	SO:0001583	missense	2033	exon22	Familial Cancer Database	Broad Thumb-Hallux syndrome	AGATGCATCAGAT	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.3764A>T	chr22.hg19:g.41560092A>T	ENSP00000263253:p.His1255Leu	232.0	0.0		217.0	98.0	NM_001429	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	hg19	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.457081	0.84317	.	.	ENSG00000100393	ENST00000263253	D	0.97941	-4.62	5.59	5.59	0.84812	.	0.000000	0.47852	D	0.000207	D	0.99026	0.9667	M	0.93328	3.405	0.54753	D	0.999986	D	0.76494	0.999	D	0.78314	0.991	D	0.99533	1.0961	10	0.87932	D	0	-13.0515	15.7693	0.78152	1.0:0.0:0.0:0.0	.	1255	Q09472	EP300_HUMAN	L	1255	ENSP00000263253:H1255L	ENSP00000263253:H1255L	H	+	2	0	EP300	39890038	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	9.339000	0.96797	2.125000	0.65367	0.459000	0.35465	CAT	.	.		0.388	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		T	41560092	A	T	41560092	3	4	253	1	0	0	0	0	1	0	0	0	5150	217	8	4	3850	4	EP300	22	41560092	Missense_Mutation	SNP	A	TCGA-EP-A26S-01A-11D-A16V-10	3439178	41560092	9744474	85	34290										
CPT1B	1375	hgsc.bcm.edu	37	chr22	51010728	51010728	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	gaaatgagagtgaaggatttGtcaaaccacctgcaggaaga	12	6	1	3			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chr22:51010728G>C	ENST00000360719.2	-	12	1499	c.1362C>G	c.(1360-1362)gaC>gaG	p.D454E	CPT1B_ENST00000440709.1_Missense_Mutation_p.D373E|CPT1B_ENST00000395650.2_Missense_Mutation_p.D454E|CHKB-CPT1B_ENST00000453634.1_3'UTR|CPT1B_ENST00000434492.2_Missense_Mutation_p.D251E|CPT1B_ENST00000312108.7_Missense_Mutation_p.D454E|CPT1B_ENST00000405237.3_Missense_Mutation_p.D454E|CPT1B_ENST00000457250.1_Missense_Mutation_p.D420E	NM_001145135.1|NM_152245.2	NP_001138607.1|NP_689451.1	Q92523	CPT1B_HUMAN	carnitine palmitoyltransferase 1B (muscle)	454					carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	carnitine O-palmitoyltransferase activity (GO:0004095)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22		all_cancers(38;8.8e-15)|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)		all cancers(3;3.56e-77)|OV - Ovarian serous cystadenocarcinoma(4;5.39e-74)|Epithelial(4;5.58e-70)|GBM - Glioblastoma multiforme(4;5.59e-08)|LUAD - Lung adenocarcinoma(64;0.0016)|Lung(4;0.00942)|BRCA - Breast invasive adenocarcinoma(115;0.207)		TGAAGGATTTGTCAAACCACC	0.498																																					p.D454E	Esophageal Squamous(170;988 1933 25577 30295 48163)	Atlas-SNP	.											.	CPT1B	61	.	0			c.C1362G						.						66	59	61					22																	51010728		2203	4298	6501	SO:0001583	missense	1375	exon12			GGATTTGTCAAAC	U62733	CCDS14098.1, CCDS46734.1	22q13.33	2007-07-26			ENSG00000205560	ENSG00000205560			2329	protein-coding gene	gene with protein product		601987				9070950	Standard	NM_152245		Approved	M-CPT1, CPT1-M	uc003bmm.3	Q92523	OTTHUMG00000137390	ENST00000360719.2:c.1362C>G	chr22.hg19:g.51010728G>C	ENSP00000353945:p.Asp454Glu	54.0	0.0		34.0	16.0	NM_001145135	B7Z4U4|B7Z5T8|E9PCP2|Q13389|Q99655|Q9BY90	Missense_Mutation	SNP	ENST00000360719.2	hg19	CCDS14098.1	.	.	.	.	.	.	.	.	.	.	G	16.92	3.255430	0.59321	.	.	ENSG00000205560	ENST00000405237;ENST00000312108;ENST00000360719;ENST00000457250;ENST00000440709;ENST00000434492;ENST00000395650	D;D;D;D;D;D;D	0.97598	-4.45;-4.45;-4.45;-4.45;-4.45;-4.45;-4.45	5.51	3.42	0.39159	.	0.000000	0.85682	D	0.000000	D	0.98661	0.9551	H	0.96748	3.875	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;0.998;0.998	D;D;D;D	0.91635	0.998;0.999;0.971;0.971	D	0.97931	1.0320	10	0.87932	D	0	-39.6839	7.2184	0.25973	0.2329:0.0:0.7671:0.0	.	373;420;251;454	E9PCP2;B7Z4U4;A2RRE8;Q92523	.;.;.;CPT1B_HUMAN	E	454;454;454;420;373;251;454	ENSP00000385486:D454E;ENSP00000312189:D454E;ENSP00000353945:D454E;ENSP00000409342:D420E;ENSP00000414713:D373E;ENSP00000410966:D251E;ENSP00000379011:D454E	ENSP00000312189:D454E	D	-	3	2	CPT1B	49357594	1.000000	0.71417	1.000000	0.80357	0.584000	0.36387	1.093000	0.30939	2.586000	0.87340	0.561000	0.74099	GAC	.	.		0.498	CPT1B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317264.5	NM_152246		C	51010728	G	C	51010728	3	2	253	1	0	0	0	0	1	0	0	0	3834	1368	48	4	988	4	CPT1B	22	51010728	Missense_Mutation	SNP	G	TCGA-EP-A26S-01A-11D-A16V-10	9450636	51010728	293838	86	34291										
GDPD2	54857	hgsc.bcm.edu	37	chrX	69644840	69644840	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.104651162790698	9	1	1.50599760095962	2.05819672131148	1.32786885245902	0.400323058285099	1	0	ccccaggccttcaccatggcCgagtcccccggctgctgctc	10	20	1	0			TCGA-EP-A26S-01A-11D-A16V-10	TCGA-EP-A26S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	463bf060-8ba6-4a73-8173-172025f7b527	b2075602-828f-4788-9c30-978a3ca744bd	g.chrX:69644840C>T	ENST00000374382.3	+	2	257	c.6C>T	c.(4-6)gcC>gcT	p.A2A	GDPD2_ENST00000453994.2_Silent_p.A2A|GDPD2_ENST00000536730.1_Intron|GDPD2_ENST00000538649.1_Intron	NM_017711.3	NP_060181.2	Q9HCC8	GDPD2_HUMAN	glycerophosphodiester phosphodiesterase domain containing 2	2					glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycerophosphodiester phosphodiesterase activity (GO:0008889)|glycerophosphoinositol inositolphosphodiesterase activity (GO:0047394)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(6)|large_intestine(8)|lung(3)|ovary(2)	22	Renal(35;0.156)					TCACCATGGCCGAGTCCCCCG	0.647																																					p.A2A		Atlas-SNP	.											.	GDPD2	80	.	0			c.C6T						.						17	13	14					X																	69644840		2197	4287	6484	SO:0001819	synonymous_variant	54857	exon2			CATGGCCGAGTCC	AK000214	CCDS14402.1, CCDS55437.1, CCDS55438.1	Xq13.1	2011-01-25			ENSG00000130055	ENSG00000130055			25974	protein-coding gene	gene with protein product	"osteoblast differentiation promoting factor"					12975309	Standard	NM_017711		Approved	OBDPF, FLJ20207, GDE3	uc011mpk.2	Q9HCC8	OTTHUMG00000021776	ENST00000374382.3:c.6C>T	chrX.hg19:g.69644840C>T		46.0	0.0		46.0	43.0	NM_017711	B4DRH4|B4DVC9|Q9NXJ6	Silent	SNP	ENST00000374382.3	hg19	CCDS14402.1																																																																																			.	.		0.647	GDPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057070.1	NM_017711		T	69644840	C	T	69644840	2	4	253	1	0	0	0	0	0	0	0	1	6332	639	23	1		1	GDPD2	23	69644840	Silent	SNP	C	TCGA-EP-A26S-01A-11D-A16V-10		69644840	85625720	87	34292										
ACAP3	116983	hgsc.bcm.edu	37	chr1	1231249	1231249	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cttggggcctccagggctggTgccatgggcgccttccgcag	16	14	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:1231249T>C	ENST00000354700.5	-	18	1774	c.1572A>G	c.(1570-1572)gcA>gcG	p.A524A	ACAP3_ENST00000379037.2_5'Flank|ACAP3_ENST00000353662.3_Silent_p.A482A	NM_030649.2	NP_085152.2	Q96P50	ACAP3_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 3	524	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			endometrium(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	14						CCAGGGCTGGTGCCATGGGCG	0.657																																					p.A524A		Atlas-SNP	.											.	ACAP3	87	.	0			c.A1572G						.						49	61	57					1																	1231249		2201	4298	6499	SO:0001819	synonymous_variant	116983	exon18			GGCTGGTGCCATG	AF411981	CCDS19.2	1p36	2013-01-10	2008-09-22	2008-09-22	ENSG00000131584	ENSG00000131584		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16754	protein-coding gene	gene with protein product			"centaurin, beta 5"	CENTB5			Standard	NM_030649		Approved	KIAA1716	uc001aeb.2	Q96P50	OTTHUMG00000002235	ENST00000354700.5:c.1572A>G	chr1.hg19:g.1231249T>C		110.0	0.0		83.0	4.0	NM_030649	B1AMF5|Q5TA42|Q5TA43|Q86UT3|Q9BSR9|Q9C0E7	Silent	SNP	ENST00000354700.5	hg19	CCDS19.2																																																																																			.	.		0.657	ACAP3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006366.2	NM_030649		C	1231249	T	C	1231249	2	2	254	1	0	0	0	0	0	0	0	1	120	1683	59	2		2	ACAP3	1	1231249	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10		1231249	248019372	1	34293										
NADK	65220	hgsc.bcm.edu	37	chr1	1685559	1685559	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgggggcagatgggcgtgatCatgatggccggcacgttggg	20	7	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:1685559C>A	ENST00000341426.5	-	10	1253	c.1032G>T	c.(1030-1032)atG>atT	p.M344I	NADK_ENST00000492768.1_5'Flank|NADK_ENST00000378625.1_Missense_Mutation_p.M489I|NADK_ENST00000344463.4_Missense_Mutation_p.M489I|NADK_ENST00000342348.5_Missense_Mutation_p.M312I|NADK_ENST00000341991.3_Missense_Mutation_p.M344I	NM_023018.4	NP_075394.3	O95544	NADK_HUMAN	NAD kinase	344					ATP metabolic process (GO:0046034)|NAD metabolic process (GO:0019674)|NADP biosynthetic process (GO:0006741)|phosphorylation (GO:0016310)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			NS(1)|autonomic_ganglia(1)|endometrium(4)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)|stomach(1)|urinary_tract(1)	17	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.61e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;8.75e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.33e-23)|GBM - Glioblastoma multiforme(42;1.35e-07)|Colorectal(212;0.000203)|COAD - Colon adenocarcinoma(227;0.000225)|Kidney(185;0.00265)|STAD - Stomach adenocarcinoma(132;0.00655)|BRCA - Breast invasive adenocarcinoma(365;0.00855)|KIRC - Kidney renal clear cell carcinoma(229;0.0382)|Lung(427;0.207)		TGGGCGTGATCATGATGGCCG	0.662																																					p.M489I		Atlas-SNP	.											.	NADK	79	.	0			c.G1467T						.						52	63	59					1																	1685559		2203	4300	6503	SO:0001583	missense	65220	exon12			CGTGATCATGATG	BC001709	CCDS30565.1, CCDS55561.1, CCDS55562.1	1p36.33	2013-04-29			ENSG00000008130	ENSG00000008130	2.7.1.23		29831	protein-coding gene	gene with protein product		611616				11594753	Standard	NM_023018		Approved	FLJ13052	uc001aie.3	O95544	OTTHUMG00000000942	ENST00000341426.5:c.1032G>T	chr1.hg19:g.1685559C>A	ENSP00000341679:p.Met344Ile	190.0	0.0		117.0	5.0	NM_001198994	A6NNN3|A8K296|B7Z434|F5GXR5|Q5QPS4|Q9H2P2|Q9H931	Missense_Mutation	SNP	ENST00000341426.5	hg19	CCDS30565.1	.	.	.	.	.	.	.	.	.	.	C	28.7	4.943976	0.92593	.	.	ENSG00000008130	ENST00000341426;ENST00000341991;ENST00000378625;ENST00000344463;ENST00000342348	T;T;T;T;T	0.38887	1.11;1.11;1.11;1.11;1.11	5.27	4.33	0.51752	ATP-NAD kinase, PpnK-type, all-beta (1);ATP-NAD kinase, PpnK-type (1);	0.000000	0.85682	D	0.000000	T	0.44850	0.1313	N	0.21545	0.675	0.58432	D	0.999995	P;P;P	0.51240	0.86;0.939;0.943	P;P;P	0.57548	0.661;0.771;0.823	T	0.40079	-0.9582	10	0.44086	T	0.13	-56.1128	14.1061	0.65091	0.1517:0.8483:0.0:0.0	.	312;489;344	F5GXR5;Q5QPS4;O95544	.;.;NADK_HUMAN	I	344;344;489;489;312	ENSP00000341679:M344I;ENSP00000344340:M344I;ENSP00000367890:M489I;ENSP00000340925:M489I;ENSP00000339727:M312I	ENSP00000341679:M344I	M	-	3	0	NADK	1675419	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	7.288000	0.78691	1.309000	0.44985	0.561000	0.74099	ATG	.	.		0.662	NADK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002769.1	NM_023018		A	1685559	C	A	1685559	3	1	254	1	0	0	0	0	1	0	0	0	10146	826	29	3	320	3	NADK	1	1685559	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	454310	1685559	247565062	2	34294										
PANK4	55229	hgsc.bcm.edu	37	chr1	2451799	2451799	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agcgccaagcccccagaaggTgccgcctccaatggagctgc	12	16	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:2451799T>C	ENST00000378466.3	-	5	673	c.661A>G	c.(661-663)Acc>Gcc	p.T221A	PANK4_ENST00000435556.3_Missense_Mutation_p.T182A|PANK4_ENST00000491212.1_5'Flank	NM_018216.1	NP_060686.1	Q9NVE7	PANK4_HUMAN	pantothenate kinase 4	221					coenzyme A biosynthetic process (GO:0015937)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)			breast(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	23	all_cancers(77;0.000158)|all_epithelial(69;8.01e-05)|all_lung(157;0.0212)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.18e-20)|all_lung(118;1.67e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;1.54e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.95e-23)|GBM - Glioblastoma multiforme(42;2.81e-08)|Colorectal(212;4.25e-05)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.00445)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.201)		CCCCAGAAGGTGCCGCCTCCA	0.647																																					p.T221A		Atlas-SNP	.											.	PANK4	64	.	0			c.A661G						.						53	52	52					1																	2451799		2202	4300	6502	SO:0001583	missense	55229	exon5			AGAAGGTGCCGCC	AK001644	CCDS42.1	1p36.32	2008-02-05			ENSG00000157881	ENSG00000157881			19366	protein-coding gene	gene with protein product		606162				11479594	Standard	XR_241034		Approved	FLJ10782	uc001ajm.1	Q9NVE7	OTTHUMG00000000791	ENST00000378466.3:c.661A>G	chr1.hg19:g.2451799T>C	ENSP00000367727:p.Thr221Ala	104.0	0.0		82.0	4.0	NM_018216	B9DI84|Q53EU3|Q5TA84|Q7RTX3|Q9H3X5	Missense_Mutation	SNP	ENST00000378466.3	hg19	CCDS42.1	.	.	.	.	.	.	.	.	.	.	T	18.74	3.687746	0.68157	.	.	ENSG00000157881	ENST00000378466;ENST00000435556	D;D	0.99652	-6.3;-6.3	4.78	4.78	0.61160	.	0.000000	0.85682	D	0.000000	D	0.99405	0.9790	M	0.90198	3.095	0.80722	D	1	P;P	0.45569	0.861;0.861	P;P	0.48840	0.592;0.592	D	0.98376	1.0556	10	0.72032	D	0.01	-33.4976	13.4557	0.61197	0.0:0.0:0.0:1.0	.	182;221	E9PHT6;Q9NVE7	.;PANK4_HUMAN	A	221;182	ENSP00000367727:T221A;ENSP00000421433:T182A	ENSP00000367727:T221A	T	-	1	0	PANK4	2441659	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.595000	0.67563	1.784000	0.52394	0.455000	0.32223	ACC	.	.		0.647	PANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002082.1			C	2451799	T	C	2451799	3	2	254	1	0	0	0	0	1	0	0	0	11428	1696	59	2	1720	2	PANK4	1	2451799	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	766240	2451799	246798822	3	34295										
TPRG1L	127262	hgsc.bcm.edu	37	chr1	3544177	3544177	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgccactttcacagaacaccCgatggctggcgcagatgaga	11	12	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:3544177C>A	ENST00000378344.2	+	4	655	c.584C>A	c.(583-585)cCg>cAg	p.P195Q	RP11-46F15.2_ENST00000435049.1_RNA|TPRG1L_ENST00000344579.5_Missense_Mutation_p.P136Q	NM_182752.3	NP_877429.2	Q5T0D9	TPRGL_HUMAN	tumor protein p63 regulated 1-like	195						cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|synaptic vesicle (GO:0008021)				endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|prostate(1)	8	all_cancers(77;0.0119)|all_epithelial(69;0.00481)|Ovarian(185;0.0634)|Lung NSC(156;0.162)|all_lung(157;0.172)	all_epithelial(116;7.37e-22)|all_lung(118;8.23e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.41e-38)|OV - Ovarian serous cystadenocarcinoma(86;3.83e-22)|GBM - Glioblastoma multiforme(42;4.77e-14)|Colorectal(212;1.12e-05)|COAD - Colon adenocarcinoma(227;5.61e-05)|Kidney(185;0.000351)|BRCA - Breast invasive adenocarcinoma(365;0.000688)|KIRC - Kidney renal clear cell carcinoma(229;0.00553)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.201)		ACAGAACACCCGATGGCTGGC	0.537																																					p.P195Q		Atlas-SNP	.											.	TPRG1L	24	.	0			c.C584A						.						144	145	145					1																	3544177		2203	4300	6503	SO:0001583	missense	127262	exon4			AACACCCGATGGC	BC019034	CCDS47.1	1p36.32	2008-02-05	2008-01-16	2008-01-16	ENSG00000158109	ENSG00000158109			27007	protein-coding gene	gene with protein product		611460	"family with sequence similarity 79, member A"	FAM79A		12477932	Standard	NM_182752		Approved	RP11-46F15.3, FLJ21811	uc001akm.3	Q5T0D9	OTTHUMG00000000609	ENST00000378344.2:c.584C>A	chr1.hg19:g.3544177C>A	ENSP00000367595:p.Pro195Gln	118.0	0.0		95.0	4.0	NM_182752	A8K1K4|Q8WV04	Missense_Mutation	SNP	ENST00000378344.2	hg19	CCDS47.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.343531	0.82022	.	.	ENSG00000158109	ENST00000378344;ENST00000456805;ENST00000344579	.	.	.	4.93	4.93	0.64822	.	0.000000	0.85682	D	0.000000	D	0.83248	0.5213	M	0.83223	2.63	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.86311	0.1686	9	0.87932	D	0	-0.7616	17.1228	0.86706	0.0:1.0:0.0:0.0	.	136;195	Q5T0D9-2;Q5T0D9	.;TPRGL_HUMAN	Q	195;152;136	.	ENSP00000339714:P136Q	P	+	2	0	TPRG1L	3534037	1.000000	0.71417	0.980000	0.43619	0.972000	0.66771	5.803000	0.69129	2.282000	0.76494	0.563000	0.77884	CCG	.	.		0.537	TPRG1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001466.1	NM_182752		A	3544177	C	A	3544177	3	1	254	1	0	0	0	0	1	0	0	0	16434	652	23	1	598	1	TPRG1L	1	3544177	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1092378	3544177	245706444	4	34296										
H6PD	9563	hgsc.bcm.edu	37	chr1	9324411	9324411	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cacgcacctgtggctggttgAcgagcgctgcgtcccactct	12	15	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:9324411A>G	ENST00000377403.2	+	5	2161	c.1859A>G	c.(1858-1860)gAc>gGc	p.D620G	H6PD_ENST00000602477.1_Missense_Mutation_p.D631G	NM_001282587.1|NM_004285.3	NP_001269516.1|NP_004276.2	O95479	G6PE_HUMAN	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	620	6-phosphogluconolactonase.				pentose-phosphate shunt (GO:0006098)|response to alcohol (GO:0097305)	endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	6-phosphogluconolactonase activity (GO:0017057)|carbohydrate binding (GO:0030246)|glucose 1-dehydrogenase [NAD(P)] activity (GO:0047936)|glucose-6-phosphate dehydrogenase activity (GO:0004345)|NADP binding (GO:0050661)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	all_lung(157;0.23)	all_epithelial(116;1.28e-19)|all_lung(118;5.22e-06)|Lung NSC(185;1.98e-05)|Renal(390;0.000147)|Breast(348;0.00109)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.88e-07)|COAD - Colon adenocarcinoma(227;7.47e-05)|Kidney(185;0.000244)|KIRC - Kidney renal clear cell carcinoma(229;0.000905)|STAD - Stomach adenocarcinoma(132;0.00176)|BRCA - Breast invasive adenocarcinoma(304;0.00183)|READ - Rectum adenocarcinoma(331;0.0419)		TGGCTGGTTGACGAGCGCTGC	0.682																																					p.D620G		Atlas-SNP	.											H6PD,NS,carcinoma,0,1	H6PD	71	.	0			c.A1859G						.						19	20	20					1																	9324411		2193	4287	6480	SO:0001583	missense	9563	exon5			TGGTTGACGAGCG	AJ012590	CCDS101.1, CCDS72697.1	1p36	2008-02-05	2003-10-10		ENSG00000049239	ENSG00000049239	1.1.1.47		4795	protein-coding gene	gene with protein product		138090	"glucose dehyrogenase"	GDH		10349511	Standard	NM_001282587		Approved		uc001apt.3	O95479	OTTHUMG00000001768	ENST00000377403.2:c.1859A>G	chr1.hg19:g.9324411A>G	ENSP00000366620:p.Asp620Gly	109.0	2.0		60.0	4.0	NM_004285	Q4TT33|Q66I35|Q68DT3	Missense_Mutation	SNP	ENST00000377403.2	hg19	CCDS101.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.149643	0.78001	.	.	ENSG00000049239	ENST00000377403	T	0.73575	-0.76	5.16	5.16	0.70880	Glucosamine/galactosamine-6-phosphate isomerase (1);6-phosphogluconolactonase, DevB-type (1);	0.000000	0.85682	D	0.000000	D	0.91676	0.7369	H	0.98918	4.37	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94719	0.7899	10	0.87932	D	0	-40.0579	14.1988	0.65688	1.0:0.0:0.0:0.0	.	620	O95479	G6PE_HUMAN	G	620	ENSP00000366620:D620G	ENSP00000366620:D620G	D	+	2	0	H6PD	9246998	1.000000	0.71417	0.894000	0.35097	0.950000	0.60333	8.774000	0.91767	1.961000	0.56991	0.459000	0.35465	GAC	.	.		0.682	H6PD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004928.2	NM_004285		G	9324411	A	G	9324411	3	3	254	1	0	0	0	0	1	0	0	0	6945	275	10	2	1873	2	H6PD	1	9324411	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	5780234	9324411	239926210	5	34297										
TMEM201	199953	hgsc.bcm.edu	37	chr1	9662234	9662234	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcctagctggctagacacgcTcaagttcagcaccacatctt	8	14	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:9662234T>C	ENST00000340381.6	+	6	1073	c.1064T>C	c.(1063-1065)cTc>cCc	p.L355P	TMEM201_ENST00000377376.4_Missense_Mutation_p.L355P|TMEM201_ENST00000340305.5_Missense_Mutation_p.L355P	NM_001130924.2	NP_001124396.2	Q5SNT2	TM201_HUMAN	transmembrane protein 201	355					fibroblast migration (GO:0010761)|nuclear migration (GO:0007097)	integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)				lung(3)|upper_aerodigestive_tract(1)	4	all_lung(157;0.222)	all_epithelial(116;2.09e-14)|Renal(390;0.000469)|all_lung(118;0.000521)|Lung NSC(185;0.000744)|Colorectal(325;0.0062)|Breast(348;0.0157)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.5e-08)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|STAD - Stomach adenocarcinoma(132;0.00345)|READ - Rectum adenocarcinoma(331;0.0419)		CTAGACACGCTCAAGTTCAGC	0.652																																					p.L355P		Atlas-SNP	.											.	TMEM201	63	.	0			c.T1064C						.						44	38	40					1																	9662234		2203	4300	6503	SO:0001583	missense	199953	exon6			ACACGCTCAAGTT		CCDS30579.1, CCDS44055.1, CCDS44055.2	1p36.22	2009-11-06			ENSG00000188807	ENSG00000188807			33719	protein-coding gene	gene with protein product							Standard	NM_001130924		Approved	RP13-15M17.2, NET5	uc021ofy.1	Q5SNT2	OTTHUMG00000057457	ENST00000340381.6:c.1064T>C	chr1.hg19:g.9662234T>C	ENSP00000344503:p.Leu355Pro	185.0	0.0		97.0	4.0	NM_001010866	B9EH90|Q5SNT3	Missense_Mutation	SNP	ENST00000340381.6	hg19	CCDS44055.2	.	.	.	.	.	.	.	.	.	.	t	10.85	1.467908	0.26335	.	.	ENSG00000188807	ENST00000377376;ENST00000340305;ENST00000340381	.	.	.	4.65	3.52	0.40303	.	0.414815	0.22632	N	0.057562	T	0.31857	0.0810	L	0.27053	0.805	0.46028	D	0.998826	B;P	0.42123	0.005;0.771	B;B	0.39840	0.017;0.311	T	0.07481	-1.0770	9	0.56958	D	0.05	-21.7504	5.9072	0.19008	0.0:0.2218:0.0:0.7782	.	355;355	E9PBR6;Q5SNT2-2	.;.	P	355	.	ENSP00000344772:L355P	L	+	2	0	TMEM201	9584821	0.991000	0.36638	0.926000	0.36857	0.719000	0.41307	2.453000	0.44970	0.658000	0.30925	0.375000	0.23000	CTC	.	.		0.652	TMEM201-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127672.1	NM_001010866		C	9662234	T	C	9662234	3	2	254	1	0	0	0	0	1	0	0	0	16141	1551	54	2	1086	2	TMEM201	1	9662234	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	337823	9662234	239588387	6	34298										
MTOR	2475	hgsc.bcm.edu	37	chr1	11186822	11186822	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cccggcacatcagaagttttGgggaaacatattgcagctct	10	10	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:11186822G>A	ENST00000361445.4	-	46	6459	c.6383C>T	c.(6382-6384)cCa>cTa	p.P2128L	MTOR_ENST00000376838.1_Missense_Mutation_p.P333L	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	2128	Sufficient for interaction with the FKBP1A/rapamycin complex. {ECO:0000250}.				cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	CAGAAGTTTTGGGGAAACATA	0.428																																					p.P2128L		Atlas-SNP	.											.	MTOR	327	.	0			c.C6383T						.						107	105	106					1																	11186822		2203	4300	6503	SO:0001583	missense	2475	exon46			AGTTTTGGGGAAA	L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"FK506 binding protein 12-rapamycin associated protein 2", "rapamycin target protein", "FKBP12-rapamycin complex-associated protein 1", "FKBP-rapamycin associated protein", "rapamycin associated protein FRAP2", "dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)", "rapamycin and FKBP12 target 1", "mammalian target of rapamycin"	601231	"FK506 binding protein 12-rapamycin associated protein 1"	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.6383C>T	chr1.hg19:g.11186822G>A	ENSP00000354558:p.Pro2128Leu	125.0	0.0		93.0	4.0	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Missense_Mutation	SNP	ENST00000361445.4	hg19	CCDS127.1	.	.	.	.	.	.	.	.	.	.	G	31	5.086473	0.94100	.	.	ENSG00000198793	ENST00000361445;ENST00000376838	T;T	0.80909	-1.43;-1.43	5.4	5.4	0.78164	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	D	0.93115	0.7808	H	0.95402	3.665	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.94890	0.8047	10	0.87932	D	0	-19.6508	19.196	0.93689	0.0:0.0:1.0:0.0	.	2128	P42345	MTOR_HUMAN	L	2128;333	ENSP00000354558:P2128L;ENSP00000366034:P333L	ENSP00000354558:P2128L	P	-	2	0	MTOR	11109409	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.434000	0.97515	2.531000	0.85337	0.650000	0.86243	CCA	.	.		0.428	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958		A	11186822	G	A	11186822	3	1	254	1	0	0	0	0	1	0	0	0	9963	1348	47	3	1318	3	MTOR	1	11186822	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1524588	11186822	238063799	7	34299										
VPS13D	55187	hgsc.bcm.edu	37	chr1	12516140	12516140	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tacatcaggtaccatgcagcCacaagtggtgaacaccttgt	9	11	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:12516140C>A	ENST00000358136.3	+	66	12550	c.12420C>A	c.(12418-12420)gcC>gcA	p.A4140A	VPS13D_ENST00000356315.4_Silent_p.A4115A|VPS13D_ENST00000496628.1_Intron|VPS13D_ENST00000543766.1_Silent_p.A138A	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		ACCATGCAGCCACAAGTGGTG	0.527																																					p.A4140A		Atlas-SNP	.											.	VPS13D	316	.	0			c.C12420A						.						112	83	93					1																	12516140		2203	4300	6503	SO:0001819	synonymous_variant	55187	exon66			TGCAGCCACAAGT	AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"vacuolar protein sorting 13D (yeast)"				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.12420C>A	chr1.hg19:g.12516140C>A		84.0	0.0		62.0	4.0	NM_015378		Silent	SNP	ENST00000358136.3	hg19	CCDS30588.1	.	.	.	.	.	.	.	.	.	.	C	9.015	0.983490	0.18889	.	.	ENSG00000048707	ENST00000011700	.	.	.	5.84	0.112	0.14623	.	.	.	.	.	T	0.42268	0.1195	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.21245	-1.0251	4	.	.	.	.	2.0973	0.03671	0.3234:0.3773:0.0836:0.2157	.	.	.	.	Q	2962	.	.	P	+	2	0	VPS13D	12438727	1.000000	0.71417	0.932000	0.37286	0.788000	0.44548	1.310000	0.33551	-0.099000	0.12263	-0.813000	0.03139	CCA	.	.		0.527	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		A	12516140	C	A	12516140	2	1	254	1	0	0	0	0	0	0	0	1	17207	581	21	3		3	VPS13D	1	12516140	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1329318	12516140	236734481	8	34300										
CROCC	9696	hgsc.bcm.edu	37	chr1	17265407	17265407	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccctcccccaccctcaggccGtcttgtcagactctgagagc	8	19	4	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:17265407G>A	ENST00000375541.5	+	12	1447	c.1378G>A	c.(1378-1380)Gtc>Atc	p.V460I	CROCC_ENST00000467938.1_3'UTR	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		CCCTCAGGCCGTCTTGTCAGA	0.687																																					p.V460I		Atlas-SNP	.											.	CROCC	185	.	0			c.G1378A						.						29	28	29					1																	17265407		2200	4293	6493	SO:0001583	missense	9696	exon12			CAGGCCGTCTTGT	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"rootletin, ciliary rootlet protein"	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.1378G>A	chr1.hg19:g.17265407G>A	ENSP00000364691:p.Val460Ile	129.0	0.0		80.0	4.0	NM_014675		Missense_Mutation	SNP	ENST00000375541.5	hg19	CCDS30616.1	.	.	.	.	.	.	.	.	.	.	G	12.50	1.955289	0.34471	.	.	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.14640	2.49	5.39	5.39	0.77823	.	.	.	.	.	T	0.15998	0.0385	L	0.38838	1.175	0.35922	D	0.831901	P;D;P	0.58620	0.839;0.983;0.939	B;P;B	0.44696	0.186;0.458;0.357	T	0.05666	-1.0871	9	0.39692	T	0.17	.	18.0808	0.89440	0.0:0.0:1.0:0.0	.	323;323;460	A1L0S8;A1L0S9;Q5TZA2	.;.;CROCC_HUMAN	I	460;341	ENSP00000364691:V460I	ENSP00000364691:V460I	V	+	1	0	CROCC	17137994	1.000000	0.71417	0.845000	0.33349	0.037000	0.13140	6.294000	0.72738	2.702000	0.92279	0.561000	0.74099	GTC	.	.		0.687	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675		A	17265407	G	A	17265407	3	1	254	1	0	0	0	0	1	0	0	0	3895	1145	40	1	1424	1	CROCC	1	17265407	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	4749267	17265407	231985214	9	34301										
PADI4	23569	hgsc.bcm.edu	37	chr1	17674451	17674451	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cacaggatgaaatggagatcGgctacatccaagccccacac	9	13	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:17674451G>T	ENST00000375448.4	+	10	1089	c.1063G>T	c.(1063-1065)Ggc>Tgc	p.G355C	PADI4_ENST00000487048.1_3'UTR|AC004824.2_ENST00000602074.1_Intron	NM_012387.2	NP_036519.2	Q9UM07	PADI4_HUMAN	peptidyl arginine deiminase, type IV	355					cellular protein modification process (GO:0006464)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|histone citrullination (GO:0036414)|histone H3-R26 citrullination (GO:0036413)|innate immune response (GO:0045087)|nucleosome assembly (GO:0006334)|protein citrullination (GO:0018101)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	arginine deiminase activity (GO:0016990)|calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(13)|ovary(2)|skin(2)|urinary_tract(3)	26		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000338)|Lung NSC(340;0.00042)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00537)|BRCA - Breast invasive adenocarcinoma(304;8.54e-06)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(64;0.000223)|KIRC - Kidney renal clear cell carcinoma(64;0.00313)|STAD - Stomach adenocarcinoma(196;0.00707)|READ - Rectum adenocarcinoma(331;0.0689)|Lung(427;0.199)	L-Citrulline(DB00155)	AATGGAGATCGGCTACATCCA	0.587																																					p.G355C		Atlas-SNP	.											.	PADI4	70	.	0			c.G1063T						.						108	91	97					1																	17674451		2203	4300	6503	SO:0001583	missense	23569	exon10			GAGATCGGCTACA	AB017919	CCDS180.1	1p36.13	2014-06-06	2003-02-12		ENSG00000159339	ENSG00000159339	3.5.3.15	"Peptidyl arginine deiminases"	18368	protein-coding gene	gene with protein product		605347	"peptidyl arginine deiminase, type V"	PADI5		10488123	Standard	NM_012387		Approved	PAD, PDI5, PDI4	uc001baj.2	Q9UM07	OTTHUMG00000002371	ENST00000375448.4:c.1063G>T	chr1.hg19:g.17674451G>T	ENSP00000364597:p.Gly355Cys	119.0	0.0		65.0	4.0	NM_012387	A8K392|B2RBW0|Q5VTZ8|Q70SX4	Missense_Mutation	SNP	ENST00000375448.4	hg19	CCDS180.1	.	.	.	.	.	.	.	.	.	.	-	20.7	4.033983	0.75504	.	.	ENSG00000159339	ENST00000375448	T	0.39787	1.06	5.47	5.47	0.80525	Protein-arginine deiminase, C-terminal (1);	0.000000	0.64402	D	0.000001	T	0.67163	0.2864	M	0.83692	2.655	0.44539	D	0.997494	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.67647	-0.5617	10	0.39692	T	0.17	-37.6537	16.1026	0.81194	0.0:0.0:1.0:0.0	.	355;355	A8K392;Q9UM07	.;PADI4_HUMAN	C	355	ENSP00000364597:G355C	ENSP00000364597:G355C	G	+	1	0	PADI4	17547038	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	8.773000	0.91762	2.582000	0.87167	0.518000	0.50308	GGC	.	.		0.587	PADI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006799.1	NM_012387		T	17674451	G	T	17674451	3	4	254	1	0	0	0	0	1	0	0	0	11389	1116	39	1	1101	1	PADI4	1	17674451	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	409044	17674451	231576170	10	34302										
KLHDC7A	127707	hgsc.bcm.edu	37	chr1	18807714	18807714	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tggggtgctcctgagggggcCaagacgtcggaggagcagca	19	9	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:18807714C>T	ENST00000400664.1	+	1	291	c.239C>T	c.(238-240)cCa>cTa	p.P80L		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	80						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		CTGAGGGGGCCAAGACGTCGG	0.647																																					p.P80L		Atlas-SNP	.											.	KLHDC7A	60	.	0			c.C239T						.						18	21	20					1																	18807714		1994	4158	6152	SO:0001583	missense	127707	exon1			GGGGGCCAAGACG	AK096072	CCDS185.2	1p36.13	2008-02-05			ENSG00000179023	ENSG00000179023			26791	protein-coding gene	gene with protein product							Standard	NM_152375		Approved	FLJ38753	uc001bax.3	Q5VTJ3	OTTHUMG00000002431	ENST00000400664.1:c.239C>T	chr1.hg19:g.18807714C>T	ENSP00000383505:p.Pro80Leu	125.0	0.0		97.0	4.0	NM_152375	Q8N8W6	Missense_Mutation	SNP	ENST00000400664.1	hg19	CCDS185.2	.	.	.	.	.	.	.	.	.	.	C	2.644	-0.283498	0.05642	.	.	ENSG00000179023	ENST00000400664;ENST00000540290	T	0.69685	-0.42	5.63	-4.18	0.03846	.	.	.	.	.	T	0.39572	0.1083	N	0.08118	0	0.09310	N	1	B	0.12013	0.005	B	0.11329	0.006	T	0.19778	-1.0295	9	0.27082	T	0.32	.	8.0909	0.30801	0.0:0.3593:0.1094:0.5313	.	80	Q5VTJ3	KLD7A_HUMAN	L	80;17	ENSP00000383505:P80L	ENSP00000383505:P80L	P	+	2	0	KLHDC7A	18680301	0.000000	0.05858	0.001000	0.08648	0.033000	0.12548	-1.542000	0.02196	-0.764000	0.04651	0.591000	0.81541	CCA	.	.		0.647	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375		T	18807714	C	T	18807714	3	4	254	1	0	0	0	0	1	0	0	0	8369	594	21	3	241	3	KLHDC7A	1	18807714	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1133263	18807714	230442907	11	34303										
UBR4	23352	hgsc.bcm.edu	37	chr1	19407897	19407897	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcgaggtcaccaacagcctcCgcaagatttccacacgtgtg	10	14	1	1	rs372882903		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:19407897C>T	ENST00000375254.3	-	103	15206	c.15179G>A	c.(15178-15180)cGg>cAg	p.R5060Q	UBR4_ENST00000375225.3_Missense_Mutation_p.R135Q|AL137127.1_ENST00000582644.1_RNA|UBR4_ENST00000375217.2_Missense_Mutation_p.R5053Q|UBR4_ENST00000375226.2_Missense_Mutation_p.R5036Q|UBR4_ENST00000375267.2_Missense_Mutation_p.R5060Q|UBR4_ENST00000375224.1_Missense_Mutation_p.R767Q|UBR4_ENST00000543981.1_Missense_Mutation_p.R724Q|UBR4_ENST00000429347.2_Missense_Mutation_p.R583Q	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	5060					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		CAACAGCCTCCGCAAGATTTC	0.587																																					p.R5060Q		Atlas-SNP	.											.	UBR4	415	.	0			c.G15179A						.	C	GLN/ARG	0,4406		0,0,2203	99	104	103		15179	2.5	1	1		103	1,8599	1.2+/-3.3	0,1,4299	no	missense	UBR4	NM_020765.2	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	5060/5184	19407897	1,13005	2203	4300	6503	SO:0001583	missense	23352	exon103			AGCCTCCGCAAGA	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.15179G>A	chr1.hg19:g.19407897C>T	ENSP00000364403:p.Arg5060Gln	93.0	0.0		103.0	11.0	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	hg19	CCDS189.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.255837	0.80135	0.0	1.16E-4	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000375225;ENST00000375224;ENST00000429347;ENST00000543981	T;T;T;T;T;T;T;T	0.29397	1.57;1.57;1.57;1.57;1.57;1.57;1.57;1.57	5.69	2.48	0.30137	.	0.060957	0.64402	N	0.000002	T	0.19446	0.0467	L	0.27053	0.805	0.50313	D	0.999865	B;B;B;B	0.15719	0.001;0.001;0.014;0.003	B;B;B;B	0.08055	0.002;0.002;0.002;0.003	T	0.05419	-1.0886	10	0.25106	T	0.35	.	10.6625	0.45710	0.0:0.744:0.0:0.256	.	724;583;5060;5036	B4DYV5;B4DPF6;Q5T4S7;Q5T4S7-3	.;.;UBR4_HUMAN;.	Q	5060;5060;5053;5036;135;767;583;724	ENSP00000364403:R5060Q;ENSP00000364416:R5060Q;ENSP00000364365:R5053Q;ENSP00000364374:R5036Q;ENSP00000364373:R135Q;ENSP00000364372:R767Q;ENSP00000394173:R583Q;ENSP00000444070:R724Q	ENSP00000364365:R5053Q	R	-	2	0	UBR4	19280484	0.691000	0.27709	1.000000	0.80357	0.984000	0.73092	1.169000	0.31871	0.630000	0.30394	0.462000	0.41574	CGG	.	.		0.587	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		T	19407897	C	T	19407897	3	4	254	1	0	0	0	0	1	0	0	0	16919	652	23	1	388	1	UBR4	1	19407897	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	600183	19407897	229842724	12	34304										
UBR4	23352	hgsc.bcm.edu	37	chr1	19433073	19433073	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggccactcacttgtcgcagcCagttgttatgccccagtttg	10	13	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:19433073C>A	ENST00000375254.3	-	83	12410	c.12383G>T	c.(12382-12384)tGg>tTg	p.W4128L	UBR4_ENST00000375217.2_Missense_Mutation_p.W4121L|UBR4_ENST00000375226.2_Missense_Mutation_p.W4104L|UBR4_ENST00000375267.2_Missense_Mutation_p.W4128L|UBR4_ENST00000375224.1_5'Flank	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	4128					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		TTGTCGCAGCCAGTTGTTATG	0.552																																					p.W4128L		Atlas-SNP	.											.	UBR4	415	.	0			c.G12383T						.						90	83	85					1																	19433073		2203	4300	6503	SO:0001583	missense	23352	exon83			CGCAGCCAGTTGT	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.12383G>T	chr1.hg19:g.19433073C>A	ENSP00000364403:p.Trp4128Leu	46.0	0.0		30.0	4.0	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	hg19	CCDS189.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.902347	0.92035	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226	T;T;T;T	0.49139	0.8;0.79;0.85;0.86	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.65026	0.2652	M	0.64997	1.995	0.80722	D	1	D	0.54601	0.967	P	0.62382	0.901	T	0.67154	-0.5742	10	0.87932	D	0	.	17.5745	0.87944	0.0:1.0:0.0:0.0	.	4128	Q5T4S7	UBR4_HUMAN	L	4128;4128;4121;4104	ENSP00000364403:W4128L;ENSP00000364416:W4128L;ENSP00000364365:W4121L;ENSP00000364374:W4104L	ENSP00000364365:W4121L	W	-	2	0	UBR4	19305660	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.320000	0.79064	2.733000	0.93635	0.561000	0.74099	TGG	.	.		0.552	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		A	19433073	C	A	19433073	3	1	254	1	0	0	0	0	1	0	0	0	16919	595	21	3	3264	3	UBR4	1	19433073	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	25176	19433073	229817548	13	34305										
UBR4	23352	hgsc.bcm.edu	37	chr1	19501462	19501462	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tagtaccacagaatcaagtcGgttcaaatcatcctctgagg	8	10	4	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:19501462G>T	ENST00000375254.3	-	21	2866	c.2839C>A	c.(2839-2841)Cga>Aga	p.R947R	UBR4_ENST00000375217.2_Silent_p.R947R|UBR4_ENST00000375226.2_Silent_p.R947R|UBR4_ENST00000375267.2_Silent_p.R947R	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	947					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		GAATCAAGTCGGTTCAAATCA	0.443																																					p.R947R		Atlas-SNP	.											.	UBR4	415	.	0			c.C2839A						.						102	94	97					1																	19501462		2203	4300	6503	SO:0001819	synonymous_variant	23352	exon21			CAAGTCGGTTCAA	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.2839C>A	chr1.hg19:g.19501462G>T		133.0	0.0		109.0	5.0	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Silent	SNP	ENST00000375254.3	hg19	CCDS189.1																																																																																			.	.		0.443	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		T	19501462	G	T	19501462	2	4	254	1	0	0	0	0	0	0	0	1	16919	1124	39	1		1	UBR4	1	19501462	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	68389	19501462	229749159	14	34306										
PLA2G2F	64600	hgsc.bcm.edu	37	chr1	20466705	20466705	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcaccgtggccatccttgctGgcagcggtgagtaaagactc	12	12	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:20466705G>A	ENST00000375102.3	+	2	265	c.163G>A	c.(163-165)Ggc>Agc	p.G55S		NM_022819.3	NP_073730.3	Q9BZM2	PA2GF_HUMAN	phospholipase A2, group IIF	12					glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	15		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000247)|Lung NSC(340;0.000285)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;8.01e-05)|Kidney(64;0.00017)|GBM - Glioblastoma multiforme(114;0.000524)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.198)		CATCCTTGCTGGCAGCGGTGA	0.592																																					p.G55S		Atlas-SNP	.											.	PLA2G2F	28	.	0			c.G163A						.						138	122	128					1																	20466705		2203	4300	6503	SO:0001583	missense	64600	exon2			CTTGCTGGCAGCG	AL158172	CCDS204.2	1p35	2008-09-19			ENSG00000158786	ENSG00000158786	3.1.1.4		30040	protein-coding gene	gene with protein product						11112443	Standard	NM_022819		Approved		uc009vpp.1	Q9BZM2	OTTHUMG00000002704	ENST00000375102.3:c.163G>A	chr1.hg19:g.20466705G>A	ENSP00000364243:p.Gly55Ser	108.0	0.0		64.0	4.0	NM_022819	Q5R385|Q8N217|Q9H506	Missense_Mutation	SNP	ENST00000375102.3	hg19	CCDS204.2	.	.	.	.	.	.	.	.	.	.	G	2.466	-0.323005	0.05350	.	.	ENSG00000158786	ENST00000375102	T	0.27890	1.64	4.76	-2.07	0.07276	.	0.459946	0.20406	N	0.092947	T	0.12774	0.0310	N	0.14661	0.345	0.09310	N	0.999998	P	0.35628	0.513	B	0.26202	0.067	T	0.16394	-1.0404	10	0.26408	T	0.33	-10.5336	10.6333	0.45549	0.5084:0.0:0.4916:0.0	.	55	Q9BZM2-2	.	S	55	ENSP00000364243:G55S	ENSP00000364243:G55S	G	+	1	0	PLA2G2F	20339292	0.006000	0.16342	0.016000	0.15963	0.000000	0.00434	-0.216000	0.09266	-1.046000	0.03246	-2.069000	0.00389	GGC	.	.		0.592	PLA2G2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007687.1	NM_022819		A	20466705	G	A	20466705	3	1	254	1	0	0	0	0	1	0	0	0	12008	1348	47	3	169	3	PLA2G2F	1	20466705	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	965243	20466705	228783916	15	34307										
PINK1	65018	hgsc.bcm.edu	37	chr1	20971140	20971140	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctgaaggcctgggccatggcCggacgctgttcctcgttatg	14	12	0	1	rs536146282		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:20971140C>T	ENST00000321556.4	+	4	1028	c.934C>T	c.(934-936)Cgg>Tgg	p.R312W	PINK1-AS_ENST00000451424.1_RNA|PINK1_ENST00000492302.1_3'UTR	NM_032409.2	NP_115785.1	Q9BXM7	PINK1_HUMAN	PTEN induced putative kinase 1	312	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159, ECO:0000305}.				activation of protein kinase B activity (GO:0032148)|cell death (GO:0008219)|cellular response to hypoxia (GO:0071456)|cellular response to toxic substance (GO:0097237)|intracellular signal transduction (GO:0035556)|mitochondrion degradation (GO:0000422)|mitochondrion organization (GO:0007005)|negative regulation of gene expression (GO:0010629)|negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway (GO:1903384)|negative regulation of JNK cascade (GO:0046329)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced cell death (GO:1903202)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of oxidative stress-induced neuron death (GO:1903204)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|peptidyl-serine autophosphorylation (GO:0036289)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial electron transport, NADH to ubiquinone (GO:1902958)|positive regulation of peptidase activity (GO:0010952)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of mitochondrion degradation (GO:1903146)|regulation of protein complex assembly (GO:0043254)|regulation of protein ubiquitination (GO:0031396)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|TORC2 signaling (GO:0038203)|ubiquitin-dependent protein catabolic process (GO:0006511)	astrocyte projection (GO:0097449)|axon (GO:0030424)|cell body (GO:0044297)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of mitochondrial outer membrane (GO:0031307)|Lewy body (GO:0097413)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|C3HC4-type RING finger domain binding (GO:0055131)|calcium-dependent protein kinase activity (GO:0010857)|kinase activity (GO:0016301)|magnesium ion binding (GO:0000287)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)|protein kinase B binding (GO:0043422)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)	14		all_lung(284;2.72e-05)|Lung NSC(340;2.94e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.21e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000146)|Kidney(64;0.000182)|GBM - Glioblastoma multiforme(114;0.000497)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GGGCCATGGCCGGACGCTGTT	0.647													C|||	1	0.000199681	0	0	5008	,	,		18286	0		0	False		,,,				2504	0.001				p.R312W	Esophageal Squamous(145;853 1803 8146 34412 35011)	Atlas-SNP	.											PINK1,NS,carcinoma,0,1	PINK1	37	.	0			c.C934T						.						63	58	60					1																	20971140		2203	4300	6503	SO:0001583	missense	65018	exon4			CATGGCCGGACGC	AB053323	CCDS211.1	1p36.12	2011-07-21			ENSG00000158828	ENSG00000158828		"Parkinson disease"	14581	protein-coding gene	gene with protein product		608309	"Parkinson disease (autosomal recessive) 6"	PARK6		11494141, 15349860	Standard	NM_032409		Approved		uc001bdm.3	Q9BXM7	OTTHUMG00000002841	ENST00000321556.4:c.934C>T	chr1.hg19:g.20971140C>T	ENSP00000364204:p.Arg312Trp	57.0	0.0		47.0	2.0	NM_032409	Q8N6T9|Q8NBU3|Q96DE4	Missense_Mutation	SNP	ENST00000321556.4	hg19	CCDS211.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.711168	0.89112	.	.	ENSG00000158828	ENST00000321556	T	0.74421	-0.84	6.07	5.14	0.70334	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.104529	0.64402	D	0.000002	D	0.86510	0.5950	M	0.85041	2.73	0.49915	D	0.999839	D	0.89917	1.0	D	0.77004	0.989	D	0.88162	0.2858	10	0.66056	D	0.02	-21.5917	12.5324	0.56122	0.1666:0.8334:0.0:0.0	.	312	Q9BXM7	PINK1_HUMAN	W	312	ENSP00000364204:R312W	ENSP00000364204:R312W	R	+	1	2	PINK1	20843727	1.000000	0.71417	0.912000	0.35992	0.982000	0.71751	4.948000	0.63590	1.533000	0.49186	0.655000	0.94253	CGG	.	.		0.647	PINK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007954.1	NM_032409		T	20971140	C	T	20971140	3	4	254	1	0	0	0	0	1	0	0	0	11941	643	23	1	948	1	PINK1	1	20971140	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	504435	20971140	228279481	16	34308										
ALPL	249	hgsc.bcm.edu	37	chr1	21902359	21902359	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	actctgaccgtggtcactgcGgaccattcccacgtcttcac	8	16	4	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:21902359G>T	ENST00000374840.3	+	10	1381	c.1131G>T	c.(1129-1131)gcG>gcT	p.A377A	ALPL_ENST00000374829.1_Silent_p.A23A|ALPL_ENST00000374832.1_Silent_p.A377A|ALPL_ENST00000539907.1_Silent_p.A300A|ALPL_ENST00000374830.1_Silent_p.A23A|ALPL_ENST00000540617.1_Silent_p.A322A|ALPL_ENST00000425315.2_Silent_p.A377A	NM_000478.4	NP_000469.3	P05186	PPBT_HUMAN	alkaline phosphatase, liver/bone/kidney	377					cellular response to organic cyclic compound (GO:0071407)|cementum mineralization (GO:0071529)|developmental process involved in reproduction (GO:0003006)|endochondral ossification (GO:0001958)|osteoblast differentiation (GO:0001649)|response to antibiotic (GO:0046677)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to vitamin D (GO:0033280)|skeletal system development (GO:0001501)	anchored component of membrane (GO:0031225)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	26		all_lung(284;2.19e-05)|Lung NSC(340;2.22e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;8.7e-28)|COAD - Colon adenocarcinoma(152;1.57e-05)|GBM - Glioblastoma multiforme(114;2.66e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000177)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00856)|READ - Rectum adenocarcinoma(331;0.0623)|Lung(427;0.146)	Amifostine(DB01143)|Fospropofol(DB06716)	TGGTCACTGCGGACCATTCCC	0.607																																					p.A377A		Atlas-SNP	.											.	ALPL	50	.	0			c.G1131T						.						167	158	161					1																	21902359		2203	4300	6503	SO:0001819	synonymous_variant	249	exon10			CACTGCGGACCAT	BC021289	CCDS217.1, CCDS53274.1, CCDS53275.1	1p36.12	2008-02-05			ENSG00000162551	ENSG00000162551	3.1.3.1		438	protein-coding gene	gene with protein product		171760		HOPS		3532105, 3446011	Standard	NM_001127501		Approved	TNSALP	uc001bet.3	P05186	OTTHUMG00000002949	ENST00000374840.3:c.1131G>T	chr1.hg19:g.21902359G>T		129.0	0.0		108.0	5.0	NM_000478	A1A4E7|B2RMP8|B7Z387|B7Z4Y6|O75090|Q2TAI7|Q59EJ7|Q5BKZ5|Q5VTG5|Q6NZI8|Q8WU32|Q9UBK0	Silent	SNP	ENST00000374840.3	hg19	CCDS217.1																																																																																			.	.		0.607	ALPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000008202.1	NM_000478		T	21902359	G	T	21902359	2	4	254	1	0	0	0	0	0	0	0	1	547	1103	39	1		1	ALPL	1	21902359	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	931219	21902359	227348262	17	34309										
HSPG2	3339	hgsc.bcm.edu	37	chr1	22170757	22170757	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttctgccactcgggaggaggAgggctcgatgcggatgggtg	19	8	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:22170757A>G	ENST00000374695.3	-	65	8579	c.8500T>C	c.(8500-8502)Tcc>Ccc	p.S2834P		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2834	Ig-like C2-type 14.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	CGGGAGGAGGAGGGCTCGATG	0.677																																					p.S2834P		Atlas-SNP	.											.	HSPG2	311	.	0			c.T8500C						.						57	59	58					1																	22170757		2203	4300	6503	SO:0001583	missense	3339	exon65			AGGAGGAGGGCTC	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"Proteoglycans / Extracellular Matrix : Other", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5273	protein-coding gene	gene with protein product	"perlecan proteoglycan"	142461	"Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.8500T>C	chr1.hg19:g.22170757A>G	ENSP00000363827:p.Ser2834Pro	184.0	0.0		105.0	5.0	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	hg19	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	A	17.44	3.389311	0.61956	.	.	ENSG00000142798	ENST00000374695	T	0.68479	-0.33	4.65	4.65	0.58169	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.37577	N	0.002034	T	0.79246	0.4413	M	0.79614	2.46	0.43211	D	0.995072	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.998	T	0.77175	-0.2684	10	0.21540	T	0.41	.	12.0553	0.53531	1.0:0.0:0.0:0.0	.	774;2834	Q59EG0;P98160	.;PGBM_HUMAN	P	2834	ENSP00000363827:S2834P	ENSP00000363827:S2834P	S	-	1	0	HSPG2	22043344	1.000000	0.71417	0.970000	0.41538	0.893000	0.52053	4.846000	0.62860	1.724000	0.51502	0.459000	0.35465	TCC	.	.		0.677	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		G	22170757	A	G	22170757	3	3	254	1	0	0	0	0	1	0	0	0	7439	304	11	2	4807	2	HSPG2	1	22170757	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	268398	22170757	227079864	18	34310										
HSPG2	3339	hgsc.bcm.edu	37	chr1	22175467	22175467	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gctgccgaccacacggcacaCgtactcccctgaatcagctg	9	17	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:22175467C>T	ENST00000374695.3	-	58	7583	c.7504G>A	c.(7504-7506)Gtg>Atg	p.V2502M	HSPG2_ENST00000430507.1_3'UTR	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2502	Ig-like C2-type 10.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	ACACGGCACACGTACTCCCCT	0.642																																					p.V2502M		Atlas-SNP	.											.	HSPG2	311	.	0			c.G7504A						.						146	138	140					1																	22175467		2203	4300	6503	SO:0001583	missense	3339	exon58			GGCACACGTACTC	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"Proteoglycans / Extracellular Matrix : Other", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5273	protein-coding gene	gene with protein product	"perlecan proteoglycan"	142461	"Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.7504G>A	chr1.hg19:g.22175467C>T	ENSP00000363827:p.Val2502Met	130.0	0.0		97.0	4.0	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	hg19	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	C	13.38	2.219229	0.39201	.	.	ENSG00000142798	ENST00000374695	T	0.16073	2.37	4.96	4.05	0.47172	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.276156	0.19533	N	0.111990	T	0.35740	0.0942	M	0.66378	2.025	0.26627	N	0.97254	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.09640	-1.0665	10	0.52906	T	0.07	.	7.8077	0.29213	0.0:0.8108:0.0:0.1892	.	442;2502	Q59EG0;P98160	.;PGBM_HUMAN	M	2502	ENSP00000363827:V2502M	ENSP00000363827:V2502M	V	-	1	0	HSPG2	22048054	0.943000	0.32029	0.980000	0.43619	0.097000	0.18754	1.915000	0.39976	1.080000	0.41073	0.561000	0.74099	GTG	.	.		0.642	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		T	22175467	C	T	22175467	3	4	254	1	0	0	0	0	1	0	0	0	7439	536	19	1	5831	1	HSPG2	1	22175467	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	4710	22175467	227075154	19	34311										
EPHB2	2048	hgsc.bcm.edu	37	chr1	23110887	23110887	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cgagcattttacccacagtgGgaagaggtgagtggctacga	14	8	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:23110887G>T	ENST00000400191.3	+	3	147	c.129G>T	c.(127-129)tgG>tgT	p.W43C	EPHB2_ENST00000544305.1_Missense_Mutation_p.W43C|EPHB2_ENST00000374627.1_Missense_Mutation_p.W37C|EPHB2_ENST00000374630.3_Missense_Mutation_p.W43C|EPHB2_ENST00000374632.3_Missense_Mutation_p.W43C	NM_004442.6|NM_017449.3	NP_004433.2|NP_059145.2	P29323	EPHB2_HUMAN	EPH receptor B2	43	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|camera-type eye morphogenesis (GO:0048593)|central nervous system projection neuron axonogenesis (GO:0021952)|commissural neuron axon guidance (GO:0071679)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|ephrin receptor signaling pathway (GO:0048013)|inner ear morphogenesis (GO:0042472)|learning (GO:0007612)|negative regulation of axonogenesis (GO:0050771)|nervous system development (GO:0007399)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse assembly (GO:0051965)|regulation of body fluid levels (GO:0050878)|retinal ganglion cell axon guidance (GO:0031290)|urogenital system development (GO:0001655)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|protein tyrosine kinase activity (GO:0004713)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(8)|stomach(1)|urinary_tract(1)	56		Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153)		ACCCACAGTGGGAAGAGGTGA	0.542																																					p.W43C		Atlas-SNP	.											.	EPHB2	257	.	0			c.G129T						.						87	74	78					1																	23110887		2203	4300	6503	SO:0001583	missense	2048	exon3			ACAGTGGGAAGAG	AF025304	CCDS229.2, CCDS230.1	1p36.1-p35	2014-09-17	2004-10-28		ENSG00000133216	ENSG00000133216	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3393	protein-coding gene	gene with protein product		600997	"EphB2"	DRT, ERK, EPHT3		1648701	Standard	NM_017449		Approved	Hek5, Tyro5	uc001bge.3	P29323	OTTHUMG00000002881	ENST00000400191.3:c.129G>T	chr1.hg19:g.23110887G>T	ENSP00000383053:p.Trp43Cys	151.0	0.0		97.0	4.0	NM_004442	O43477|Q5T0U6|Q5T0U7|Q5T0U8	Missense_Mutation	SNP	ENST00000400191.3	hg19		.	.	.	.	.	.	.	.	.	.	G	19.79	3.893633	0.72639	.	.	ENSG00000133216	ENST00000374625;ENST00000544305;ENST00000374630;ENST00000400191;ENST00000374632;ENST00000374627	T;T;T;T;T	0.20200	2.09;2.09;2.09;2.09;2.09	5.19	5.19	0.71726	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	T	0.58623	0.2135	M	0.93978	3.48	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	T	0.69928	-0.5012	10	0.87932	D	0	.	17.4346	0.87548	0.0:0.0:1.0:0.0	.	43;43;61;43	A6NJM0;P29323;Q4LE53;P29323-3	.;EPHB2_HUMAN;.;.	C	43;43;43;43;43;37	ENSP00000444174:W43C;ENSP00000363761:W43C;ENSP00000383053:W43C;ENSP00000363763:W43C;ENSP00000363758:W37C	ENSP00000363755:W43C	W	+	3	0	EPHB2	22983474	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.578000	0.98200	2.704000	0.92352	0.484000	0.47621	TGG	.	.		0.542	EPHB2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000008060.2	NM_017449		T	23110887	G	T	23110887	3	4	254	1	0	0	0	0	1	0	0	0	5177	1241	43	3	139	3	EPHB2	1	23110887	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	935420	23110887	226139734	20	34312										
TCEA3	6920	hgsc.bcm.edu	37	chr1	23710837	23710837	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggaaatacataaacatacagAccttccagcgattgccacat	6	11	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:23710837A>G	ENST00000450454.2	-	10	1145		c.e10+1			NM_003196.1	NP_003187.1	O75764	TCEA3_HUMAN	transcription elongation factor A (SII), 3						regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|urinary_tract(1)	7		Colorectal(325;3.46e-05)|Lung NSC(340;4.16e-05)|all_lung(284;6.68e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.0054)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.6e-25)|Colorectal(126;8.32e-08)|COAD - Colon adenocarcinoma(152;4.29e-06)|GBM - Glioblastoma multiforme(114;9e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00424)|STAD - Stomach adenocarcinoma(196;0.0145)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0963)|LUSC - Lung squamous cell carcinoma(448;0.198)		AAACATACAGACCTTCCAGCG	0.507																																					.		Atlas-SNP	.											.	TCEA3	20	.	0			c.1038+2T>C						.						159	161	161					1																	23710837		2143	4265	6408	SO:0001630	splice_region_variant	6920	exon11			ATACAGACCTTCC	AJ223473	CCDS44086.1	1p36.11	2011-01-25			ENSG00000204219	ENSG00000204219			11615	protein-coding gene	gene with protein product		604128				9790746	Standard	NM_003196		Approved	TFIIS.H	uc021oig.1	O75764	OTTHUMG00000003233	ENST00000450454.2:c.1038+1T>C	chr1.hg19:g.23710837A>G		91.0	0.0		55.0	4.0	NM_003196	A8K2K7|Q5DR83	Splice_Site	SNP	ENST00000450454.2	hg19	CCDS44086.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.252025	0.80135	.	.	ENSG00000204219	ENST00000450454	.	.	.	5.37	5.37	0.77165	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5294	0.67915	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TCEA3	23583424	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	8.804000	0.91921	2.189000	0.69895	0.459000	0.35465	.	.	.		0.507	TCEA3-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008911.2	NM_003196	Intron	G	23710837	A	G	23710837	5	3	254	1	0	0	0	0	0	0	1	0	15684	289	10	2	14	2	TCEA3	1	23710837	Splice_Site	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	599950	23710837	225539784	21	34313										
FUCA1	2517	hgsc.bcm.edu	37	chr1	24186295	24186295	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tataatcacataccttgacaGggctgtcattgtagagccat	8	9	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:24186295G>T	ENST00000374479.3	-	4	768	c.761C>A	c.(760-762)cCt>cAt	p.P254H		NM_000147.4	NP_000138.2	P04066	FUCO_HUMAN	fucosidase, alpha-L- 1, tissue	254					fucose metabolic process (GO:0006004)|glycosaminoglycan catabolic process (GO:0006027)|glycoside catabolic process (GO:0016139)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-L-fucosidase activity (GO:0004560)|fucose binding (GO:0042806)			breast(1)|endometrium(1)|large_intestine(3)|lung(3)	8		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.00957)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-24)|Colorectal(126;5.69e-08)|COAD - Colon adenocarcinoma(152;3.15e-06)|GBM - Glioblastoma multiforme(114;9.04e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|KIRC - Kidney renal clear cell carcinoma(1967;0.00342)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.144)		TACCTTGACAGGGCTGTCATT	0.418																																					p.P254H		Atlas-SNP	.											.	FUCA1	24	.	0			c.C761A						.						93	87	89					1																	24186295		2203	4300	6503	SO:0001583	missense	2517	exon4			TTGACAGGGCTGT	BC017338	CCDS244.2	1p34	2012-10-02			ENSG00000179163	ENSG00000179163	3.2.1.51		4006	protein-coding gene	gene with protein product		612280				2803312	Standard	NM_000147		Approved		uc001bie.3	P04066	OTTHUMG00000002965	ENST00000374479.3:c.761C>A	chr1.hg19:g.24186295G>T	ENSP00000363603:p.Pro254His	90.0	0.0		73.0	4.0	NM_000147	B2RBG3|Q14334|Q14335|Q3LID0|Q8NAC2	Missense_Mutation	SNP	ENST00000374479.3	hg19	CCDS244.2	.	.	.	.	.	.	.	.	.	.	G	17.63	3.437118	0.62955	.	.	ENSG00000179163	ENST00000374479;ENST00000374475	T	0.66638	-0.22	6.16	6.16	0.99307	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	D	0.88081	0.6341	H	0.94542	3.55	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.89805	0.3978	10	0.87932	D	0	-15.2455	20.8598	0.99761	0.0:0.0:1.0:0.0	.	254	P04066	FUCO_HUMAN	H	254;43	ENSP00000363603:P254H	ENSP00000363599:P43H	P	-	2	0	FUCA1	24058882	1.000000	0.71417	0.954000	0.39281	0.054000	0.15201	9.283000	0.95860	2.937000	0.99478	0.650000	0.86243	CCT	.	.		0.418	FUCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008259.2	NM_000147		T	24186295	G	T	24186295	3	4	254	1	0	0	0	0	1	0	0	0	6102	1000	35	3	659	3	FUCA1	1	24186295	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	475458	24186295	225064326	22	34314										
WDTC1	23038	hgsc.bcm.edu	37	chr1	27627864	27627864	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gagtgcctggacgacttcaaAgggaaatttccggagcaggc	14	9	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:27627864A>G	ENST00000319394.3	+	13	1915	c.1380A>G	c.(1378-1380)aaA>aaG	p.K460K	WDTC1_ENST00000361771.3_Silent_p.K459K	NM_001276252.1|NM_015023.3	NP_001263181.1|NP_055838.2	Q8N5D0	WDTC1_HUMAN	WD and tetratricopeptide repeats 1	460					cellular chemical homeostasis (GO:0055082)|cellular response to insulin stimulus (GO:0032869)|glucose metabolic process (GO:0006006)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|regulation of cell size (GO:0008361)	cytosol (GO:0005829)|nucleus (GO:0005634)	enzyme inhibitor activity (GO:0004857)			central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|skin(1)	21		all_cancers(24;3.12e-19)|all_epithelial(13;4.18e-18)|Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.00257)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0443)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;1.02e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00201)|STAD - Stomach adenocarcinoma(196;0.00321)|READ - Rectum adenocarcinoma(331;0.0476)		ACGACTTCAAAGGGAAATTTC	0.572											OREG0013280	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K460K		Atlas-SNP	.											.	WDTC1	69	.	0			c.A1380G						.						70	68	69					1																	27627864		2203	4300	6503	SO:0001819	synonymous_variant	23038	exon13			CTTCAAAGGGAAA	AK023778	CCDS296.1, CCDS60044.1	1p35.3	2013-01-11			ENSG00000142784	ENSG00000142784		"DDB1 and CUL4 associated factors", "WD repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29175	protein-coding gene	gene with protein product	"adipose homolog (Drosophila)", "DDB1 and CUL4 associated factor 9"					12717455, 19238144	Standard	NM_015023		Approved	KIAA1037, ADP, DCAF9	uc009vst.3	Q8N5D0	OTTHUMG00000004273	ENST00000319394.3:c.1380A>G	chr1.hg19:g.27627864A>G		116.0	0.0	795	74.0	4.0	NM_001276252	D3DPL5|Q5SSC5|Q9NV87|Q9UPW4	Silent	SNP	ENST00000319394.3	hg19																																																																																				.	.		0.572	WDTC1-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015023		G	27627864	A	G	27627864	2	3	254	1	0	0	0	0	0	0	0	1	17357	69	3	2		2	WDTC1	1	27627864	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	3441569	27627864	221622757	23	34315										
AHDC1	27245	hgsc.bcm.edu	37	chr1	27876114	27876114	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cgagcagcgagcgaaagtagCcggtgaagaggttttggcgc	17	8	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:27876114C>T	ENST00000247087.5	-	5	3109	c.2513G>A	c.(2512-2514)gGc>gAc	p.G838D	AHDC1_ENST00000374011.2_Missense_Mutation_p.G838D			Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	838							DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)		GCGAAAGTAGCCGGTGAAGAG	0.627																																					p.G838D		Atlas-SNP	.											.	AHDC1	98	.	0			c.G2513A						.						46	51	50					1																	27876114		2193	4286	6479	SO:0001583	missense	27245	exon6			AAGTAGCCGGTGA	AK125431	CCDS30652.1	1p36.13	2008-02-05			ENSG00000126705	ENSG00000126705			25230	protein-coding gene	gene with protein product		615790				8619474, 9110174	Standard	XM_005245848		Approved	DJ159A19.3, RP1-159A19.1	uc009vsy.3	Q5TGY3	OTTHUMG00000003398	ENST00000247087.5:c.2513G>A	chr1.hg19:g.27876114C>T	ENSP00000247087:p.Gly838Asp	170.0	0.0		99.0	4.0	NM_001029882	Q5TGY4|Q6PJK1|Q6ZUQ6|Q99769|Q9NUF5	Missense_Mutation	SNP	ENST00000247087.5	hg19	CCDS30652.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.308244	0.81247	.	.	ENSG00000126705	ENST00000247087;ENST00000374011	T;T	0.71222	-0.55;-0.55	5.77	5.77	0.91146	.	0.000000	0.64402	D	0.000010	T	0.76399	0.3982	N	0.24115	0.695	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.76462	-0.2950	10	0.44086	T	0.13	-16.5503	18.7552	0.91830	0.0:1.0:0.0:0.0	.	838	Q5TGY3	AHDC1_HUMAN	D	838	ENSP00000247087:G838D;ENSP00000363123:G838D	ENSP00000247087:G838D	G	-	2	0	AHDC1	27748701	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	6.987000	0.76206	2.723000	0.93209	0.655000	0.94253	GGC	.	.		0.627	AHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009523.3			T	27876114	C	T	27876114	3	4	254	1	0	0	0	0	1	0	0	0	412	739	26	3	2302	3	AHDC1	1	27876114	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	248250	27876114	221374507	24	34316										
CSMD2	114784	hgsc.bcm.edu	37	chr1	34033348	34033348	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtccgttgacaatgggctcaGgagtcccacagtgtccagct	12	12	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:34033348G>T	ENST00000373381.4	-	53	8401	c.8225C>A	c.(8224-8226)cCt>cAt	p.P2742H		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	2719	Sushi 18. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				AATGGGCTCAGGAGTCCCACA	0.532																																					p.P2719H		Atlas-SNP	.											.	CSMD2	946	.	0			c.C8156A						.						98	83	88					1																	34033348		2203	4300	6503	SO:0001583	missense	114784	exon54			GGCTCAGGAGTCC	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.8225C>A	chr1.hg19:g.34033348G>T	ENSP00000362479:p.Pro2742His	142.0	0.0		125.0	5.0	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373381.4	hg19		.	.	.	.	.	.	.	.	.	.	G	18.06	3.540138	0.65085	.	.	ENSG00000121904	ENST00000373381	D	0.84873	-1.91	5.07	5.07	0.68467	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.85682	D	0.000000	D	0.95881	0.8659	H	0.98701	4.305	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.991;1.0	D	0.97764	1.0222	10	0.87932	D	0	.	17.7969	0.88575	0.0:0.0:1.0:0.0	.	2719;2742	Q7Z408;E7EUA6	CSMD2_HUMAN;.	H	2742	ENSP00000362479:P2742H	ENSP00000241312:P2719H	P	-	2	0	CSMD2	33805935	1.000000	0.71417	0.868000	0.34077	0.776000	0.43924	9.809000	0.99208	2.539000	0.85634	0.655000	0.94253	CCT	.	.		0.532	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896		T	34033348	G	T	34033348	3	4	254	1	0	0	0	0	1	0	0	0	3947	1000	35	3	2371	3	CSMD2	1	34033348	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	6157234	34033348	215217273	25	34317										
CSMD2	114784	hgsc.bcm.edu	37	chr1	34080170	34080170	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggggtagttgcctgggaagcCggggctcaggatcaccccct	16	12	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:34080170C>A	ENST00000373380.1	-	19	2906	c.2686G>T	c.(2686-2688)Ggc>Tgc	p.G896C	CSMD2_ENST00000373381.4_Missense_Mutation_p.G2023C|CSMD2_ENST00000373388.2_Missense_Mutation_p.G122C|CSMD2_ENST00000373377.1_Missense_Mutation_p.G122C			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1983	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.G1983S(1)		NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				CCTGGGAAGCCGGGGCTCAGG	0.572																																					p.G1983C		Atlas-SNP	.											CSMD2,caecum,carcinoma,0,1	CSMD2	946	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5947T						.						90	83	85					1																	34080170		2203	4300	6503	SO:0001583	missense	114784	exon40			GGAAGCCGGGGCT	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373380.1:c.2686G>T	chr1.hg19:g.34080170C>A	ENSP00000362478:p.Gly896Cys	71.0	1.0		61.0	3.0	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373380.1	hg19		.	.	.	.	.	.	.	.	.	.	C	29.0	4.966772	0.92855	.	.	ENSG00000121904	ENST00000373381;ENST00000373380;ENST00000373377;ENST00000373388	T;T;T;T	0.33865	1.39;1.39;1.39;1.39	5.47	5.47	0.80525	CUB (5);	0.000000	0.85682	D	0.000000	T	0.68742	0.3034	M	0.90542	3.125	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.75795	-0.3192	10	0.87932	D	0	.	18.323	0.90244	0.0:1.0:0.0:0.0	.	896;1983;2023	Q7Z408-2;Q7Z408;E7EUA6	.;CSMD2_HUMAN;.	C	2023;896;122;122	ENSP00000362479:G2023C;ENSP00000362478:G896C;ENSP00000362475:G122C;ENSP00000362486:G122C	ENSP00000241312:G1983C	G	-	1	0	CSMD2	33852757	1.000000	0.71417	0.930000	0.37139	0.992000	0.81027	7.818000	0.86416	2.570000	0.86706	0.655000	0.94253	GGC	.	.		0.572	CSMD2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000030635.4	NM_052896		A	34080170	C	A	34080170	3	1	254	1	0	0	0	0	1	0	0	0	3947	652	23	1	4636	1	CSMD2	1	34080170	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	46822	34080170	215170451	26	34318										
CSMD2	114784	hgsc.bcm.edu	37	chr1	34089068	34089068	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	caaaactgacaacttggatcTgggaagggagaagagtgaat	13	5	1	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:34089068T>C	ENST00000373380.1	-	15	2465		c.e15-2		CSMD2_ENST00000373381.4_Splice_Site|CSMD2_ENST00000373388.2_Splice_Site|CSMD2_ENST00000373377.1_Splice_Site			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				AACTTGGATCTGGGAAGGGAG	0.483																																					.		Atlas-SNP	.											.	CSMD2	946	.	0			c.5506-2A>G						.						100	86	91					1																	34089068		2203	4300	6503	SO:0001630	splice_region_variant	114784	exon37			TGGATCTGGGAAG	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373380.1:c.2245-2A>G	chr1.hg19:g.34089068T>C		136.0	0.0		113.0	5.0	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Splice_Site	SNP	ENST00000373380.1	hg19		.	.	.	.	.	.	.	.	.	.	T	14.26	2.481768	0.44147	.	.	ENSG00000121904	ENST00000373381;ENST00000373380	.	.	.	5.69	5.69	0.88448	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7749	0.69724	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	CSMD2	33861655	1.000000	0.71417	1.000000	0.80357	0.283000	0.27025	7.669000	0.83911	2.170000	0.68504	0.459000	0.35465	.	.	.		0.483	CSMD2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000030635.4	NM_052896	Intron	C	34089068	T	C	34089068	5	2	254	1	0	0	0	0	0	0	1	0	3947	1594	55	2	5095	2	CSMD2	1	34089068	Splice_Site	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	8898	34089068	215161553	27	34319										
MAP7D1	55700	hgsc.bcm.edu	37	chr1	36636731	36636731	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcagctcccactggaaccagAgagcccctcagggcaggtcg	13	15	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:36636731A>G	ENST00000373151.2	+	2	422	c.206A>G	c.(205-207)gAg>gGg	p.E69G	MAP7D1_ENST00000373150.4_Missense_Mutation_p.E69G|MAP7D1_ENST00000316156.4_Missense_Mutation_p.E69G	NM_018067.3	NP_060537.3	Q3KQU3	MA7D1_HUMAN	MAP7 domain containing 1	69	Pro-rich.				microtubule cytoskeleton organization (GO:0000226)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)				breast(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	19		Myeloproliferative disorder(586;0.0393)				CTGGAACCAGAGAGCCCCTCA	0.652																																					p.E69G		Atlas-SNP	.											.	MAP7D1	62	.	0			c.A206G						.						52	58	56					1																	36636731		2203	4300	6503	SO:0001583	missense	55700	exon2			AACCAGAGAGCCC	AK096341	CCDS30673.1, CCDS65492.1, CCDS65493.1	1p34.3	2008-02-05	2007-02-08	2007-02-08	ENSG00000116871	ENSG00000116871			25514	protein-coding gene	gene with protein product			"proline arginine rich coiled coil 1", "arginine/proline rich coiled-coil 1"	PARCC1, RPRC1		10574461	Standard	XM_005271024		Approved	FLJ10350, FLJ39022	uc001bzz.3	Q3KQU3	OTTHUMG00000007714	ENST00000373151.2:c.206A>G	chr1.hg19:g.36636731A>G	ENSP00000362244:p.Glu69Gly	119.0	0.0		77.0	4.0	NM_018067	D3DPS4|Q7L8J5|Q8N905|Q8TAK0|Q9HBQ2|Q9NW29|Q9ULN3	Missense_Mutation	SNP	ENST00000373151.2	hg19	CCDS30673.1	.	.	.	.	.	.	.	.	.	.	A	12.81	2.049010	0.36181	.	.	ENSG00000116871	ENST00000429533;ENST00000316156;ENST00000373150;ENST00000373151;ENST00000530729	T;T;T;T;T	0.05319	3.46;3.46;3.46;3.46;3.46	4.62	-0.754	0.11065	.	0.351134	0.20847	N	0.084582	T	0.02494	0.0076	N	0.08118	0	0.80722	D	1	B;B;B	0.15719	0.0;0.0;0.014	B;B;B	0.09377	0.001;0.001;0.004	T	0.48790	-0.9004	10	0.40728	T	0.16	-5.5227	2.306	0.04174	0.4741:0.2962:0.0843:0.1455	.	69;69;69	Q3KQU3-2;Q3KQU3-4;Q3KQU3	.;.;MA7D1_HUMAN	G	30;69;69;69;30	ENSP00000390091:E30G;ENSP00000320228:E69G;ENSP00000362243:E69G;ENSP00000362244:E69G;ENSP00000435126:E30G	ENSP00000320228:E69G	E	+	2	0	MAP7D1	36409318	0.511000	0.26179	0.687000	0.30102	0.929000	0.56500	0.815000	0.27253	-0.199000	0.10317	0.379000	0.24179	GAG	.	.		0.652	MAP7D1-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382095.1	NM_018067		G	36636731	A	G	36636731	3	3	254	1	0	0	0	0	1	0	0	0	9276	304	11	2	212	2	MAP7D1	1	36636731	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	2547663	36636731	212613890	28	34320										
C1orf113	79729	hgsc.bcm.edu	37	chr1	36785547	36785547	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tccggaggacaaggcttctaTcccagagaactccatcatcc	8	14	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:36785547T>C	ENST00000426732.2	+	13	1220	c.935T>C	c.(934-936)aTc>aCc	p.I312T	SH3D21_ENST00000312808.4_Missense_Mutation_p.I74T|SH3D21_ENST00000453908.2_Missense_Mutation_p.I428T|SH3D21_ENST00000505871.1_Missense_Mutation_p.I317T|EVA1B_ENST00000490466.1_5'Flank			A4FU49	SH321_HUMAN	SH3 domain containing 21	312						extracellular vesicular exosome (GO:0070062)				endometrium(1)|large_intestine(6)|lung(4)|pancreas(1)	12						AAGGCTTCTATCCCAGAGAAC	0.572																																					p.I428T		Atlas-SNP	.											.	SH3D21	73	.	0			c.T1283C						.						55	60	59					1																	36785547		2203	4300	6503	SO:0001583	missense	79729	exon14			CTTCTATCCCAGA	AK056459	CCDS30674.1, CCDS30674.2	1p34.3	2011-02-21	2011-02-21	2011-02-21	ENSG00000214193	ENSG00000214193			26236	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 113"	C1orf113		12477932	Standard	NM_024676		Approved	FLJ22938	uc010oia.1	A4FU49	OTTHUMG00000007868	ENST00000426732.2:c.935T>C	chr1.hg19:g.36785547T>C	ENSP00000408613:p.Ile312Thr	83.0	0.0		69.0	5.0	NM_001162530	B4DLI6|D3DPS6|J3KQM5|Q5VTK7|Q86XZ6|Q8N445|Q96DN4|Q9H5W5	Missense_Mutation	SNP	ENST00000426732.2	hg19		.	.	.	.	.	.	.	.	.	.	T	5.827	0.336767	0.11013	.	.	ENSG00000214193	ENST00000453908;ENST00000426732;ENST00000312808;ENST00000505871	T;T;T;T	0.45276	1.43;1.88;0.9;1.89	2.83	-4.09	0.03951	.	.	.	.	.	T	0.23451	0.0567	N	0.22421	0.69	0.09310	N	1	B;B	0.22346	0.068;0.018	B;B	0.17098	0.017;0.005	T	0.22906	-1.0203	8	.	.	.	.	8.9418	0.35733	0.0:0.3146:0.5794:0.106	.	317;312	A4FU49-3;A4FU49	.;SH321_HUMAN	T	428;312;74;317	ENSP00000403476:I428T;ENSP00000408613:I312T;ENSP00000321936:I74T;ENSP00000421294:I317T	.	I	+	2	0	SH3D21	36558134	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-2.065000	0.01386	-0.907000	0.03862	0.260000	0.18958	ATC	.	.		0.572	SH3D21-202	KNOWN	basic	protein_coding	protein_coding		NM_024676		C	36785547	T	C	36785547	3	2	254	1	0	0	0	0	1	0	0	0	1988	1435	50	2	1337	2	C1orf113	1	36785547	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	148816	36785547	212465074	29	34321										
KCNQ4	9132	hgsc.bcm.edu	37	chr1	41285131	41285131	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctcctcctacgccgactcgcTctggtgggggacggtgcgtg	15	14	1	0	rs80358276		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:41285131T>C	ENST00000347132.5	+	5	903	c.821T>C	c.(820-822)cTc>cCc	p.L274P	KCNQ4_ENST00000509682.2_Missense_Mutation_p.L274P|KCNQ4_ENST00000506017.1_3'UTR	NM_004700.3|NM_172163.2	NP_004691.2|NP_751895.1	P56696	KCNQ4_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 4	274			L -> H (in DFNA2A). {ECO:0000269|PubMed:10925378}.		inner ear morphogenesis (GO:0042472)|potassium ion transport (GO:0006813)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(13)|skin(1)	26	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.38e-17)		Ezogabine(DB04953)	GCCGACTCGCTCTGGTGGGGG	0.622																																					p.L274P		Atlas-SNP	.											.	KCNQ4	58	.	0			c.T821C	GRCh37	CM001721	KCNQ4	M	rs80358276	.						116	101	106					1																	41285131		2203	4300	6503	SO:0001583	missense	9132	exon5			ACTCGCTCTGGTG	AF105202	CCDS456.1	1p34	2012-07-05			ENSG00000117013	ENSG00000117013		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6298	protein-coding gene	gene with protein product		603537		DFNA2		10025409, 16382104	Standard	NM_004700		Approved	Kv7.4	uc001cgh.2	P56696	OTTHUMG00000007730	ENST00000347132.5:c.821T>C	chr1.hg19:g.41285131T>C	ENSP00000262916:p.Leu274Pro	237.0	0.0		137.0	6.0	NM_004700	O96025	Missense_Mutation	SNP	ENST00000347132.5	hg19	CCDS456.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.621136	0.87460	.	.	ENSG00000117013	ENST00000347132;ENST00000509682	D;D	0.98926	-5.24;-5.24	5.08	5.08	0.68730	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99254	0.9740	M	0.92649	3.33	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.99150	1.0858	10	0.87932	D	0	-28.9565	12.801	0.57586	0.0:0.0:0.0:1.0	.	274;274	P56696-2;P56696	.;KCNQ4_HUMAN	P	274	ENSP00000262916:L274P;ENSP00000423756:L274P	ENSP00000262916:L274P	L	+	2	0	KCNQ4	41057718	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	8.040000	0.89188	1.907000	0.55213	0.460000	0.39030	CTC	.	.		0.622	KCNQ4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000020812.1	NM_004700		C	41285131	T	C	41285131	3	2	254	1	0	0	0	0	1	0	0	0	8094	1551	54	2	839	2	KCNQ4	1	41285131	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	4499584	41285131	207965490	30	34322										
PTPRF	5792	hgsc.bcm.edu	37	chr1	44083444	44083444	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tacatcaatgccaactacatCgatggctaccgcaagcagaa	7	12	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:44083444C>A	ENST00000359947.4	+	25	4573	c.4233C>A	c.(4231-4233)atC>atA	p.I1411I	PTPRF_ENST00000438120.1_Silent_p.I1402I|PTPRF_ENST00000496447.1_3'UTR|PTPRF_ENST00000422171.2_Silent_p.I770I|PTPRF_ENST00000372413.3_Silent_p.I1402I|PTPRF_ENST00000372414.3_Silent_p.I1411I	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	1411	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|negative regulation of receptor binding (GO:1900121)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(24)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)	72	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				CCAACTACATCGATGGCTACC	0.602																																					p.I1411I		Atlas-SNP	.											PTPRF,colon,carcinoma,0,1	PTPRF	172	.	0			c.C4233A						.						63	62	62					1																	44083444		2203	4300	6503	SO:0001819	synonymous_variant	5792	exon25			CTACATCGATGGC	Y00815	CCDS489.2, CCDS490.2	1p34	2013-02-11			ENSG00000142949	ENSG00000142949		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9670	protein-coding gene	gene with protein product		179590		LAR		7558042	Standard	NM_130440		Approved		uc001cjr.3	P10586	OTTHUMG00000007501	ENST00000359947.4:c.4233C>A	chr1.hg19:g.44083444C>A		144.0	0.0		116.0	6.0	NM_002840	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Silent	SNP	ENST00000359947.4	hg19	CCDS489.2	.	.	.	.	.	.	.	.	.	.	C	9.798	1.179769	0.21787	.	.	ENSG00000142949	ENST00000429895	.	.	.	5.58	-0.477	0.12097	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.5273	0.11988	0.226:0.3766:0.0:0.3974	.	.	.	.	X	1057	.	.	S	+	2	0	PTPRF	43856031	0.000000	0.05858	1.000000	0.80357	0.977000	0.68977	-2.533000	0.00942	0.237000	0.21200	-0.727000	0.03589	TCG	.	.		0.602	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1			A	44083444	C	A	44083444	2	1	254	1	0	0	0	0	0	0	0	1	12816	874	31	1		1	PTPRF	1	44083444	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	2798313	44083444	205167177	31	34323										
RNF220	55182	hgsc.bcm.edu	37	chr1	45115396	45115396	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gctcgggtcagagaacttgaAcggcagctatctcgtgggga	15	9	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:45115396A>G	ENST00000355387.2	+	13	1959	c.1509A>G	c.(1507-1509)gaA>gaG	p.E503E	TMEM53_ENST00000372244.3_Intron|RNF220_ENST00000361799.2_Silent_p.E503E|RNF220_ENST00000372247.2_Silent_p.E503E|RNF220_ENST00000443020.2_Silent_p.E290E|TMEM53_ENST00000372242.3_Intron|RNF220_ENST00000480686.1_3'UTR|TMEM53_ENST00000372243.3_Intron			Q5VTB9	RN220_HUMAN	ring finger protein 220	503					protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(1)|large_intestine(3)|lung(13)|ovary(2)|skin(2)|urinary_tract(2)	29						GAGAACTTGAACGGCAGCTAT	0.547																																					p.E503E		Atlas-SNP	.											.	RNF220	56	.	0			c.A1509G						.						139	131	134					1																	45115396		2203	4300	6503	SO:0001819	synonymous_variant	55182	exon13			ACTTGAACGGCAG	AK056424	CCDS510.1	1p34.1	2008-06-13	2008-06-13	2008-06-13	ENSG00000187147	ENSG00000187147		"RING-type (C3HC4) zinc fingers"	25552	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 164"	C1orf164		11042152	Standard	NM_018150		Approved	FLJ10597	uc001clv.1	Q5VTB9	OTTHUMG00000007697	ENST00000355387.2:c.1509A>G	chr1.hg19:g.45115396A>G		122.0	0.0		97.0	4.0	NM_018150	B3KPJ3|B4DLZ9|E9PCS1|Q4KMX2|Q9NVP6	Silent	SNP	ENST00000355387.2	hg19	CCDS510.1																																																																																			.	.		0.547	RNF220-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000020683.4	NM_018150		G	45115396	A	G	45115396	2	3	254	1	0	0	0	0	0	0	0	1	13498	40	2	2		2	RNF220	1	45115396	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	1031952	45115396	204135225	32	34324										
MUTYH	4595	hgsc.bcm.edu	37	chr1	45797951	45797951	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttggttgaaatctcctggccGggctgggtccaccagctgct	13	12	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:45797951G>T	ENST00000372098.3	-	10	944	c.811C>A	c.(811-813)Cgg>Agg	p.R271R	MUTYH_ENST00000372104.1_Silent_p.R246R|MUTYH_ENST00000372110.3_Silent_p.R261R|MUTYH_ENST00000528013.2_Silent_p.R260R|MUTYH_ENST00000528332.2_Intron|MUTYH_ENST00000531105.1_Intron|MUTYH_ENST00000355498.2_Silent_p.R246R|MUTYH_ENST00000448481.1_Silent_p.R257R|MUTYH_ENST00000456914.2_Silent_p.R246R|MUTYH_ENST00000488731.2_Intron|MUTYH_ENST00000354383.6_Silent_p.R247R|MUTYH_ENST00000372100.5_Silent_p.R257R|MUTYH_ENST00000450313.1_Silent_p.R274R|MUTYH_ENST00000529984.1_Intron|MUTYH_ENST00000372115.3_Silent_p.R260R			Q9UIF7	MUTYH_HUMAN	mutY homolog	271					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depurination (GO:0045007)|DNA repair (GO:0006281)|mismatch repair (GO:0006298)	mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|hydrolase activity, acting on glycosyl bonds (GO:0016798)|metal ion binding (GO:0046872)|MutSalpha complex binding (GO:0032407)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.155)					TCTCCTGGCCGGGCTGGGTCC	0.612			Mis			colorectal		Base excision repair (BER), DNA glycosylases	MUTYH-associated polyposis																												p.R274R		Atlas-SNP	.	yes	Rec		Adenomatous polyposis coli	1	1p34.3-1p32.1	4595	mutY homolog (E. coli)		E	MUTYH,NS,chondrosarcoma,0,1	MUTYH	38	.	0			c.C820A	GRCh37	CM053996	MUTYH	M		.						29	31	30					1																	45797951		2203	4300	6503	SO:0001819	synonymous_variant	4595	exon10	Familial Cancer Database	MAP, MYH-associated polyposis	CTGGCCGGGCTGG	U63329	CCDS520.1, CCDS41320.1, CCDS41321.1, CCDS41322.1, CCDS72776.1, CCDS72777.1	1p34.1	2014-09-17	2013-09-12		ENSG00000132781	ENSG00000132781			7527	protein-coding gene	gene with protein product		604933	"mutY (E. coli) homolog", "mutY homolog (E. coli)"			7823963, 10684930	Standard	NM_012222		Approved	MYH	uc009vxp.3	Q9UIF7	OTTHUMG00000007682	ENST00000372098.3:c.811C>A	chr1.hg19:g.45797951G>T		87.0	0.0		51.0	3.0	NM_001128425	D3DPZ4|Q15830|Q9UBP2|Q9UBS7|Q9UIF4|Q9UIF5|Q9UIF6	Silent	SNP	ENST00000372098.3	hg19	CCDS520.1																																																																																			.	.		0.612	MUTYH-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000020529.1	NM_012222		T	45797951	G	T	45797951	2	4	254	1	0	0	0	0	0	0	0	1	10002	1115	39	1		1	MUTYH	1	45797951	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	682555	45797951	203452670	33	34325										
CYP4B1	1580	hgsc.bcm.edu	37	chr1	47264911	47264911	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cccagggcctcccacccactGgctttttggacatgccctcg	9	18	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:47264911G>A	ENST00000271153.4	+	1	194	c.158G>A	c.(157-159)tGg>tAg	p.W53*	CYP4B1_ENST00000371919.4_Nonsense_Mutation_p.W53*|CYP4B1_ENST00000371923.4_Nonsense_Mutation_p.W53*|CYP4B1_ENST00000546128.1_Intron			P13584	CP4B1_HUMAN	cytochrome P450, family 4, subfamily B, polypeptide 1	53					biphenyl metabolic process (GO:0018879)|exogenous drug catabolic process (GO:0042738)|fluorene metabolic process (GO:0018917)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|fluorene oxygenase activity (GO:0018585)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)	p.W53*(1)		NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	36	Acute lymphoblastic leukemia(166;0.155)				Midazolam(DB00683)|Phenobarbital(DB01174)|Thiamine(DB00152)	CCCACCCACTGGCTTTTTGGA	0.557																																					p.W53X		Atlas-SNP	.											CYP4B1,extremity,malignant_melanoma,0,1	CYP4B1	81	.	1	Substitution - Nonsense(1)	skin(1)	c.G158A						.						35	31	33					1																	47264911		2203	4300	6503	SO:0001587	stop_gained	1580	exon1			CCCACTGGCTTTT	BC017758	CCDS542.1, CCDS41328.1	1p33	2013-11-11	2003-01-14		ENSG00000142973	ENSG00000142973		"Cytochrome P450s"	2644	protein-coding gene	gene with protein product		124075	"cytochrome P450, subfamily IVB, polypeptide 1"				Standard	NM_000779		Approved		uc001cqn.4	P13584	OTTHUMG00000007984	ENST00000271153.4:c.158G>A	chr1.hg19:g.47264911G>A	ENSP00000271153:p.Trp53*	137.0	0.0		70.0	25.0	NM_000779	Q1HBI2|Q8TD85|Q8WWF2|Q8WWU9|Q8WWV0	Nonsense_Mutation	SNP	ENST00000271153.4	hg19	CCDS542.1	.	.	.	.	.	.	.	.	.	.	G	18.83	3.707124	0.68615	.	.	ENSG00000142973	ENST00000371923;ENST00000271153;ENST00000371919	.	.	.	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.5952	0.76574	0.0:0.0:1.0:0.0	.	.	.	.	X	53	.	ENSP00000271153:W53X	W	+	2	0	CYP4B1	47037498	1.000000	0.71417	1.000000	0.80357	0.067000	0.16453	4.702000	0.61817	2.753000	0.94483	0.467000	0.42956	TGG	.	.		0.557	CYP4B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021911.1	NM_000779		A	47264911	G	A	47264911	4	1	254	1	0	0	0	0	0	1	0	0	4187	1357	47	3	160	3	CYP4B1	1	47264911	Nonsense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1466960	47264911	201985710	34	34326										
C8B	732	hgsc.bcm.edu	37	chr1	57399139	57399139	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aggcaaaatctgtggctgtcActagttcatacagaggctcc	10	10	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:57399139A>G	ENST00000371237.4	-	10	1487	c.1421T>C	c.(1420-1422)gTg>gCg	p.V474A	C8B_ENST00000543257.1_Missense_Mutation_p.V422A|C8B_ENST00000535057.1_Missense_Mutation_p.V412A	NM_000066.2	NP_000057	P07358	CO8B_HUMAN	complement component 8, beta polypeptide	474	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane attack complex (GO:0005579)|vesicle (GO:0031982)				breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	52						TGTGGCTGTCACTAGTTCATA	0.438																																					p.V474A		Atlas-SNP	.											.	C8B	107	.	0			c.T1421C						.						78	70	73					1																	57399139		2203	4300	6503	SO:0001583	missense	732	exon10			GCTGTCACTAGTT	M16973	CCDS30730.1, CCDS60151.1, CCDS60152.1	1p32.2	2014-09-17			ENSG00000021852	ENSG00000021852		"Complement system"	1353	protein-coding gene	gene with protein product		120960					Standard	NM_000066		Approved		uc001cyp.3	P07358	OTTHUMG00000008305	ENST00000371237.4:c.1421T>C	chr1.hg19:g.57399139A>G	ENSP00000360281:p.Val474Ala	100.0	0.0		88.0	5.0	NM_000066	A1L4K7	Missense_Mutation	SNP	ENST00000371237.4	hg19	CCDS30730.1	.	.	.	.	.	.	.	.	.	.	A	16.34	3.094834	0.56075	.	.	ENSG00000021852	ENST00000371237;ENST00000543257;ENST00000535057	D;D;D	0.86030	-2.06;-2.06;-2.06	5.08	3.88	0.44766	Membrane attack complex component/perforin (MACPF) domain (3);	0.117394	0.56097	D	0.000024	D	0.87989	0.6317	M	0.82517	2.595	0.58432	D	0.999999	P;D;P	0.55385	0.868;0.971;0.892	B;P;P	0.48488	0.443;0.562;0.579	D	0.90070	0.4162	10	0.87932	D	0	-20.4023	12.5995	0.56489	0.8624:0.1376:0.0:0.0	.	422;412;474	F5H7G1;F5GY80;P07358	.;.;CO8B_HUMAN	A	474;422;412	ENSP00000360281:V474A;ENSP00000442548:V422A;ENSP00000440113:V412A	ENSP00000360281:V474A	V	-	2	0	C8B	57171727	1.000000	0.71417	1.000000	0.80357	0.329000	0.28539	5.809000	0.69172	2.264000	0.75181	0.533000	0.62120	GTG	.	.		0.438	C8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022886.2			G	57399139	A	G	57399139	3	3	254	1	0	0	0	0	1	0	0	0	2419	159	6	2	366	2	C8B	1	57399139	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	10134228	57399139	191851482	35	34327										
KANK4	163782	hgsc.bcm.edu	37	chr1	62739434	62739434	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gaggccattctcctctcctcGgtgcccccagctttcagact	8	17	3	1	rs370065609		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:62739434G>T	ENST00000371153.4	-	3	1720	c.1342C>A	c.(1342-1344)Cga>Aga	p.R448R	KANK4_ENST00000371150.1_5'Flank|KANK4_ENST00000354381.3_Intron	NM_181712.4	NP_859063.3	Q5T7N3	KANK4_HUMAN	KN motif and ankyrin repeat domains 4	448						cytoplasm (GO:0005737)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(49)|ovary(3)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	81						TCCTCTCCTCGGTGCCCCCAG	0.557																																					p.R448R		Atlas-SNP	.											.	KANK4	135	.	0			c.C1342A						.						164	161	162					1																	62739434		2203	4300	6503	SO:0001819	synonymous_variant	163782	exon3			CTCCTCGGTGCCC	AK096259	CCDS620.1	1p31.3	2013-10-11	2008-01-29	2008-01-29	ENSG00000132854	ENSG00000132854		"KN motif and ankyrin repeat domain containing", "Ankyrin repeat domain containing"	27263	protein-coding gene	gene with protein product		614612	"ankyrin repeat domain 38"	ANKRD38		17996375, 19554261	Standard	NM_181712		Approved	KIAA0172	uc001dah.4	Q5T7N3	OTTHUMG00000008971	ENST00000371153.4:c.1342C>A	chr1.hg19:g.62739434G>T		140.0	0.0		113.0	5.0	NM_181712	B1ALP7|Q6P9A0|Q86T71|Q86VE6|Q8NAX3	Silent	SNP	ENST00000371153.4	hg19	CCDS620.1																																																																																			.	.		0.557	KANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024877.1	NM_181712		T	62739434	G	T	62739434	2	4	254	1	0	0	0	0	0	0	0	1	7988	1124	39	1		1	KANK4	1	62739434	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	5340295	62739434	186511187	36	34328										
PGM1	5236	hgsc.bcm.edu	37	chr1	64114221	64114221	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccgtgagaaagatggactgtGggctgtccttgcctggctct	14	10	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:64114221G>T	ENST00000371084.3	+	8	1391	c.1178G>T	c.(1177-1179)tGg>tTg	p.W393L	PGM1_ENST00000540265.1_Missense_Mutation_p.W196L|PGM1_ENST00000371083.4_Missense_Mutation_p.W411L	NM_002633.2	NP_002624.2	P36871	PGM1_HUMAN	phosphoglucomutase 1	393					carbohydrate metabolic process (GO:0005975)|galactose catabolic process (GO:0019388)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	magnesium ion binding (GO:0000287)|phosphoglucomutase activity (GO:0004614)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20						GATGGACTGTGGGCTGTCCTT	0.522																																					p.W411L		Atlas-SNP	.											.	PGM1	75	.	0			c.G1232T						.						83	69	74					1																	64114221		2203	4300	6503	SO:0001583	missense	5236	exon8			GACTGTGGGCTGT	BC019920	CCDS625.1, CCDS53323.1, CCDS53324.1	1p22.1	2012-10-02			ENSG00000079739	ENSG00000079739	5.4.2.2		8905	protein-coding gene	gene with protein product		171900				4517931, 1530890	Standard	NM_002633		Approved		uc010ooz.2	P36871	OTTHUMG00000008968	ENST00000371084.3:c.1178G>T	chr1.hg19:g.64114221G>T	ENSP00000360125:p.Trp393Leu	70.0	0.0		59.0	4.0	NM_001172818	B2R5N9|B4DPV0|Q16105|Q16106|Q5BKZ9|Q6NW22|Q86U74|Q96J40|Q9NTY4	Missense_Mutation	SNP	ENST00000371084.3	hg19	CCDS625.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.726226	0.89298	.	.	ENSG00000079739	ENST00000538673;ENST00000371084;ENST00000540265;ENST00000371083	T;T;T	0.38077	1.16;1.16;1.16	6.06	6.06	0.98353	Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III (2);Alpha-D-phosphohexomutase, alpha/beta/alpha domain III (1);	0.000000	0.85682	D	0.000000	T	0.58652	0.2137	M	0.75884	2.315	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.59402	-0.7461	10	0.87932	D	0	-33.0953	20.6208	0.99490	0.0:0.0:1.0:0.0	.	411;393	P36871-2;P36871	.;PGM1_HUMAN	L	369;393;196;411	ENSP00000360125:W393L;ENSP00000443449:W196L;ENSP00000360124:W411L	ENSP00000360124:W411L	W	+	2	0	PGM1	63886809	1.000000	0.71417	1.000000	0.80357	0.614000	0.37383	9.869000	0.99810	2.882000	0.98803	0.655000	0.94253	TGG	.	.		0.522	PGM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024868.1	NM_002633		T	64114221	G	T	64114221	3	4	254	1	0	0	0	0	1	0	0	0	11806	1357	47	3	1512	3	PGM1	1	64114221	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1374787	64114221	185136400	37	34329										
DIRAS3	9077	hgsc.bcm.edu	37	chr1	68512864	68512864	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcggtgccgactaccacgacGcggtaatctctgatcttcct	10	14	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:68512864G>A	ENST00000370981.1	-	4	753	c.117C>T	c.(115-117)cgC>cgT	p.R39R	GNG12-AS1_ENST00000413628.1_RNA|GNG12-AS1_ENST00000420587.1_RNA|DIRAS3_ENST00000395201.1_Silent_p.R39R			O95661	DIRA3_HUMAN	DIRAS family, GTP-binding RAS-like 3	39					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of gene expression by genetic imprinting (GO:0006349)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|cervix(1)|endometrium(2)|large_intestine(1)|lung(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						CTACCACGACGCGGTAATCTC	0.582																																					p.R39R		Atlas-SNP	.											.	DIRAS3	31	.	0			c.C117T						.						68	72	71					1																	68512864		2203	4300	6503	SO:0001819	synonymous_variant	9077	exon2			CACGACGCGGTAA	U96750	CCDS641.1	1p31	2014-05-09		2005-01-27	ENSG00000162595	ENSG00000162595			687	protein-coding gene	gene with protein product		605193	"ras homolog gene family, member I"	ARHI		9874798	Standard	XM_006711027		Approved	NOEY2	uc001ded.3	O95661	OTTHUMG00000009544	ENST00000370981.1:c.117C>T	chr1.hg19:g.68512864G>A		147.0	0.0		106.0	30.0	NM_004675	B3KMP3	Silent	SNP	ENST00000370981.1	hg19	CCDS641.1																																																																																			.	.		0.582	DIRAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026354.2	NM_004675		A	68512864	G	A	68512864	2	1	254	1	0	0	0	0	0	0	0	1	4534	1074	38	1		1	DIRAS3	1	68512864	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	4398643	68512864	180737757	38	34330										
LRRC7	57554	hgsc.bcm.edu	37	chr1	70504859	70504859	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctagagcttacagaggatacCcaccgatggagcaaatgttt	10	9	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:70504859C>A	ENST00000035383.5	+	19	3268	c.3238C>A	c.(3238-3240)Cca>Aca	p.P1080T	LRRC7_ENST00000310961.5_Missense_Mutation_p.P1085T|LRRC7_ENST00000415775.2_Missense_Mutation_p.P364T	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	1080						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)				breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						CAGAGGATACCCACCGATGGA	0.512																																					p.P1080T		Atlas-SNP	.											.	LRRC7	400	.	0			c.C3238A						.						68	72	71					1																	70504859		2203	4300	6503	SO:0001583	missense	57554	exon19			GGATACCCACCGA		CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.3238C>A	chr1.hg19:g.70504859C>A	ENSP00000035383:p.Pro1080Thr	121.0	0.0		93.0	4.0	NM_020794	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Missense_Mutation	SNP	ENST00000035383.5	hg19	CCDS645.1	.	.	.	.	.	.	.	.	.	.	C	9.110	1.006281	0.19199	.	.	ENSG00000033122	ENST00000310961;ENST00000035383;ENST00000415775;ENST00000370957	T;T;T	0.39406	1.08;1.15;2.26	5.76	2.77	0.32553	.	0.118903	0.64402	D	0.000020	T	0.44787	0.1310	L	0.40543	1.245	0.47659	D	0.999489	P;B;D	0.89917	0.952;0.221;1.0	P;B;D	0.80764	0.732;0.244;0.994	T	0.47812	-0.9088	10	0.49607	T	0.09	.	17.496	0.87717	0.0:0.526:0.474:0.0	.	364;1080;1080	F8WE45;Q96NW7-2;Q96NW7	.;.;LRRC7_HUMAN	T	1085;1080;364;903	ENSP00000309245:P1085T;ENSP00000035383:P1080T;ENSP00000394867:P364T	ENSP00000035383:P1080T	P	+	1	0	LRRC7	70277447	1.000000	0.71417	0.951000	0.38953	0.001000	0.01503	3.007000	0.49536	0.319000	0.23209	-0.955000	0.02649	CCA	.	.		0.512	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794		A	70504859	C	A	70504859	3	1	254	1	0	0	0	0	1	0	0	0	9029	623	22	3	3312	3	LRRC7	1	70504859	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1991995	70504859	178745762	39	34331										
SFRS11	9295	hgsc.bcm.edu	37	chr1	70710417	70710417	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	acattctaagtctaggagtcGgcgacgatccaaaagcccaa	9	11	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:70710417G>T	ENST00000370950.3	+	9	933	c.851G>T	c.(850-852)cGg>cTg	p.R284L	SRSF11_ENST00000484162.1_3'UTR|SRSF11_ENST00000405432.1_Missense_Mutation_p.R284L|SRSF11_ENST00000370949.1_Missense_Mutation_p.R224L|SRSF11_ENST00000370951.1_Missense_Mutation_p.R284L			Q05519	SRS11_HUMAN	serine/arginine-rich splicing factor 11	284	10 X 8 AA approximate repeats of R-R-S-R- S-R-S-R.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			large_intestine(3)|ovary(2)|skin(1)	6						TCTAGGAGTCGGCGACGATCC	0.443																																					p.R284L		Atlas-SNP	.											.	SRSF11	68	.	0			c.G851T						.						94	90	91					1																	70710417		2203	4300	6503	SO:0001583	missense	9295	exon9			GGAGTCGGCGACG	M74002	CCDS647.1, CCDS53332.1	1p31.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000116754	ENSG00000116754		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10782	protein-coding gene	gene with protein product	"SR splicing factor 11"	602010	"splicing factor, arginine/serine-rich 11"	SFRS11		1896467, 20516191	Standard	NM_004768		Approved	p54, NET2	uc001des.3	Q05519	OTTHUMG00000009342	ENST00000370950.3:c.851G>T	chr1.hg19:g.70710417G>T	ENSP00000359988:p.Arg284Leu	129.0	0.0		115.0	6.0	NM_001190987	Q5T758|Q8IWE6	Missense_Mutation	SNP	ENST00000370950.3	hg19	CCDS647.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.201992	0.79127	.	.	ENSG00000116754	ENST00000370951;ENST00000370950;ENST00000405432;ENST00000395136;ENST00000370949	D;D;D;T;T	0.82167	-1.58;-1.58;-1.58;2.56;-0.45	5.53	5.53	0.82687	.	0.038654	0.85682	D	0.000000	D	0.89591	0.6759	M	0.82517	2.595	0.80722	D	1	D;D;D;D	0.60575	0.988;0.983;0.983;0.958	P;P;P;P	0.57911	0.829;0.549;0.549;0.451	D	0.90381	0.4388	10	0.87932	D	0	.	19.8223	0.96603	0.0:0.0:1.0:0.0	.	224;284;284;284	Q5T757;Q6PJB9;Q8IWE6;Q05519	.;.;.;SRS11_HUMAN	L	284;284;284;284;224	ENSP00000359989:R284L;ENSP00000359988:R284L;ENSP00000384357:R284L;ENSP00000378568:R284L;ENSP00000359987:R224L	ENSP00000359987:R224L	R	+	2	0	SRSF11	70483005	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	6.281000	0.72632	2.763000	0.94921	0.555000	0.69702	CGG	.	.		0.443	SRSF11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025889.1	NM_004768		T	70710417	G	T	70710417	3	4	254	1	0	0	0	0	1	0	0	0	14181	1116	39	1	881	1	SFRS11	1	70710417	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	205558	70710417	178540204	40	34332										
LPAR3	23566	hgsc.bcm.edu	37	chr1	85331068	85331068	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcttgggtcctcttacctacCtaagacagtcatcaccgtct	7	14	4	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:85331068C>A	ENST00000440886.1	-	1	774	c.736G>T	c.(736-738)Ggg>Tgg	p.G246W	LPAR3_ENST00000491034.1_5'UTR|LPAR3_ENST00000370611.3_Splice_Site_p.G246W			Q9UBY5	LPAR3_HUMAN	lysophosphatidic acid receptor 3	246					activation of MAPK activity (GO:0000187)|bleb assembly (GO:0032060)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|synaptic transmission (GO:0007268)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)|lysophosphatidic acid receptor activity (GO:0070915)|phospholipid binding (GO:0005543)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|urinary_tract(1)	24						TCTTACCTACCTAAGACAGTC	0.498																																					p.G246W		Atlas-SNP	.											.	LPAR3	53	.	0			c.G736T						.						54	41	46					1																	85331068		2203	4300	6503	SO:0001630	splice_region_variant	23566	exon2			ACCTACCTAAGAC	AF127138	CCDS700.1	1p22.3	2012-08-08	2008-04-11	2008-04-11	ENSG00000171517	ENSG00000171517		"GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"	14298	protein-coding gene	gene with protein product		605106	"endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 7"	EDG7		10488122	Standard	NM_012152		Approved	LP-A3, Edg-7, RP4-678I3, HOFNH30, LPA3	uc009wcj.1	Q9UBY5	OTTHUMG00000009925	ENST00000440886.1:c.736+1G>T	chr1.hg19:g.85331068C>A		118.0	0.0		71.0	4.0	NM_012152	A0AVA3	Missense_Mutation	SNP	ENST00000440886.1	hg19	CCDS700.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.142484	0.77888	.	.	ENSG00000171517	ENST00000440886;ENST00000370611	T;T	0.38560	1.13;1.13	5.2	5.2	0.72013	GPCR, rhodopsin-like superfamily (1);	0.110306	0.64402	D	0.000008	T	0.73651	0.3614	H	0.97077	3.935	0.80722	D	1	D	0.76494	0.999	D	0.74348	0.983	D	0.83863	0.0269	9	.	.	.	.	18.7607	0.91849	0.0:1.0:0.0:0.0	.	246	Q9UBY5	LPAR3_HUMAN	W	246	ENSP00000395389:G246W;ENSP00000359643:G246W	.	G	-	1	0	LPAR3	85103656	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	7.792000	0.85828	2.437000	0.82529	0.650000	0.86243	GGG	.	.		0.498	LPAR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027467.1	NM_012152	Missense_Mutation	A	85331068	C	A	85331068	5	1	254	1	0	0	0	0	0	0	1	0	8915	695	24	3	333	3	LPAR3	1	85331068	Splice_Site	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	14620651	85331068	163919553	41	34333										
COL24A1	255631	hgsc.bcm.edu	37	chr1	86340972	86340972	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aaggttacctttgcacctggTtcaccttgcagaccagactc	8	13	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:86340972T>C	ENST00000370571.2	-	34	3438	c.3072A>G	c.(3070-3072)gaA>gaG	p.E1024E	COL24A1_ENST00000436319.1_Silent_p.E1024E	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	1024	Collagen-like 9.				extracellular matrix organization (GO:0030198)|hematopoietic progenitor cell differentiation (GO:0002244)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			NS(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(9)|liver(1)|lung(56)|ovary(4)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	101				all cancers(265;0.0627)|Epithelial(280;0.0689)		TTGCACCTGGTTCACCTTGCA	0.413																																					p.E1024E		Atlas-SNP	.											.	COL24A1	202	.	0			c.A3072G						.						79	77	78					1																	86340972		1875	4107	5982	SO:0001819	synonymous_variant	255631	exon34			ACCTGGTTCACCT	AF410793	CCDS41353.1	1p22.3-p22.2	2013-01-16			ENSG00000171502	ENSG00000171502		"Collagens"	20821	protein-coding gene	gene with protein product		610025					Standard	NM_152890		Approved		uc001dlj.3	Q17RW2	OTTHUMG00000010629	ENST00000370571.2:c.3072A>G	chr1.hg19:g.86340972T>C		220.0	0.0		108.0	5.0	NM_152890	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Silent	SNP	ENST00000370571.2	hg19	CCDS41353.1																																																																																			.	.		0.413	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	NM_152890		C	86340972	T	C	86340972	2	2	254	1	0	0	0	0	0	0	0	1	3685	1722	60	2		2	COL24A1	1	86340972	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	1009904	86340972	162909649	42	34334										
GBP7	388646	hgsc.bcm.edu	37	chr1	89607318	89607318	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtgactgcaggaagctctggAggacctcgtctgcctgaaga	14	10	2	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:89607318A>G	ENST00000294671.2	-	9	1517	c.1379T>C	c.(1378-1380)cTc>cCc	p.L460P		NM_207398.2	NP_997281.2	Q8N8V2	GBP7_HUMAN	guanylate binding protein 7	460						membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Lung NSC(277;0.0908)		all cancers(265;0.00835)|Epithelial(280;0.0322)		GAAGCTCTGGAGGACCTCGTC	0.498																																					p.L460P		Atlas-SNP	.											.	GBP7	57	.	0			c.T1379C						.						113	104	107					1																	89607318		2203	4300	6503	SO:0001583	missense	388646	exon9			CTCTGGAGGACCT	AK096141	CCDS720.1	1p22.2	2008-02-05			ENSG00000213512	ENSG00000213512			29606	protein-coding gene	gene with protein product		612468					Standard	NM_207398		Approved	FLJ38822, GBP4L	uc001dna.2	Q8N8V2	OTTHUMG00000010659	ENST00000294671.2:c.1379T>C	chr1.hg19:g.89607318A>G	ENSP00000294671:p.Leu460Pro	148.0	0.0		100.0	4.0	NM_207398		Missense_Mutation	SNP	ENST00000294671.2	hg19	CCDS720.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.241778	0.79912	.	.	ENSG00000213512	ENST00000294671	T	0.73152	-0.72	4.14	4.14	0.48551	Guanylate-binding protein, C-terminal (3);	0.000000	0.64402	D	0.000003	D	0.85128	0.5626	H	0.95539	3.685	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	D	0.88657	0.3186	10	0.87932	D	0	.	11.1443	0.48422	1.0:0.0:0.0:0.0	.	460	Q8N8V2	GBP7_HUMAN	P	460	ENSP00000294671:L460P	ENSP00000294671:L460P	L	-	2	0	GBP7	89379906	1.000000	0.71417	0.930000	0.37139	0.704000	0.40688	5.607000	0.67648	1.745000	0.51790	0.477000	0.44152	CTC	.	.		0.498	GBP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029401.1	NM_207398		G	89607318	A	G	89607318	3	3	254	1	0	0	0	0	1	0	0	0	6287	304	11	2	549	2	GBP7	1	89607318	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	3266346	89607318	159643303	43	34335										
GLMN	11146	hgsc.bcm.edu	37	chr1	92712653	92712653	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	caggaggcatattagggatcTcttctccacttacagttata	8	9	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:92712653T>C	ENST00000370360.3	-	18	1715	c.1634A>G	c.(1633-1635)gAg>gGg	p.E545G	GLMN_ENST00000534881.1_Missense_Mutation_p.E531G	NM_053274.2	NP_444504.1	Q92990	GLMN_HUMAN	glomulin, FKBP associated protein	545					muscle cell differentiation (GO:0042692)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of T cell proliferation (GO:0042130)|neural tube closure (GO:0001843)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of phosphorylation (GO:0042327)|regulation of gene expression, epigenetic (GO:0040029)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|vasculogenesis (GO:0001570)	Cul2-RING ubiquitin ligase complex (GO:0031462)|Cul3-RING ubiquitin ligase complex (GO:0031463)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|cullin-RING ubiquitin ligase complex (GO:0031461)|intracellular (GO:0005622)	hepatocyte growth factor receptor binding (GO:0005171)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase inhibitor activity (GO:0055105)			endometrium(5)|kidney(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)	17		all_lung(203;0.00827)|Lung NSC(277;0.0295)		all cancers(265;0.00702)|GBM - Glioblastoma multiforme(16;0.0381)|Epithelial(280;0.0989)		ATTAGGGATCTCTTCTCCACT	0.368									Multiple Glomus Tumors (of the Skin), Familial																												p.E545G		Atlas-SNP	.											GLMN,NS,carcinoma,0,1	GLMN	37	.	0			c.A1634G						.						138	145	142					1																	92712653		2203	4300	6503	SO:0001583	missense	11146	exon18	Familial Cancer Database	Multiple Familial Glomangiomas, Hereditary Multiple Glomus Tumors, Familial Multiple Glomangiomatosis, Inherited Cutaneous Venous Anomalies, incl. Familial Multiple Glomangiomyoma	GGGATCTCTTCTC	U73704	CCDS738.1	1p22.1	2008-02-05	2004-07-01		ENSG00000174842	ENSG00000174842			14373	protein-coding gene	gene with protein product		601749	"venous malformation with glomus cells"	VMGLOM		8955134	Standard	XM_005270400		Approved	FAP48, GLML, GVM, FKBPAP	uc001dor.3	Q92990	OTTHUMG00000010283	ENST00000370360.3:c.1634A>G	chr1.hg19:g.92712653T>C	ENSP00000359385:p.Glu545Gly	47.0	0.0		24.0	2.0	NM_053274	Q5VVC3|Q9BVE8	Missense_Mutation	SNP	ENST00000370360.3	hg19	CCDS738.1	.	.	.	.	.	.	.	.	.	.	T	15.40	2.823688	0.50739	.	.	ENSG00000174842	ENST00000370360;ENST00000534881	T;T	0.46451	0.87;0.87	6.17	5.03	0.67393	.	0.175572	0.64402	D	0.000012	T	0.21145	0.0509	L	0.36672	1.1	0.36542	D	0.871352	B;B	0.24317	0.101;0.081	B;B	0.28465	0.09;0.061	T	0.07328	-1.0778	10	0.62326	D	0.03	-3.7276	12.8097	0.57634	0.1226:0.0:0.0:0.8774	.	531;545	B4DJ85;Q92990	.;GLMN_HUMAN	G	545;531	ENSP00000359385:E545G;ENSP00000440156:E531G	ENSP00000359385:E545G	E	-	2	0	GLMN	92485241	1.000000	0.71417	0.984000	0.44739	0.703000	0.40648	5.467000	0.66737	1.111000	0.41721	0.533000	0.62120	GAG	.	.		0.368	GLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028358.1	NM_007070		C	92712653	T	C	92712653	3	2	254	1	0	0	0	0	1	0	0	0	6456	1551	54	2	158	2	GLMN	1	92712653	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	3105335	92712653	156537968	44	34336										
CCDC18	343099	hgsc.bcm.edu	37	chr1	93677670	93677670	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgtgccagaattaagcttgcAataaaagaggcagaaattca	9	6	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:93677670A>G	ENST00000343253.7	+	11	1849	c.1347A>G	c.(1345-1347)gcA>gcG	p.A449A	CCDC18_ENST00000401026.3_Silent_p.A449A|CCDC18_ENST00000334652.5_5'UTR|CCDC18_ENST00000338949.4_Silent_p.A248A|CCDC18_ENST00000557479.1_Silent_p.A567A			Q5T9S5	CCD18_HUMAN	coiled-coil domain containing 18	449										breast(5)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)		TTAAGCTTGCAATAAAAGAGG	0.313																																					p.A449A		Atlas-SNP	.											.	CCDC18	93	.	0			c.A1347G						.						101	99	99					1																	93677670		1803	4063	5866	SO:0001819	synonymous_variant	343099	exon11			GCTTGCAATAAAA			1p22.1	2008-02-05			ENSG00000122483	ENSG00000122483			30370	protein-coding gene	gene with protein product						12601173	Standard	XM_006710609		Approved	NY-SAR-41	uc021opx.1	Q5T9S5	OTTHUMG00000010598	ENST00000343253.7:c.1347A>G	chr1.hg19:g.93677670A>G		142.0	0.0		98.0	4.0	NM_206886	Q6ZU17	Silent	SNP	ENST00000343253.7	hg19		.	.	.	.	.	.	.	.	.	.	A	10.04	1.242781	0.22796	.	.	ENSG00000122483	ENST00000370276	.	.	.	5.62	5.62	0.85841	.	.	.	.	.	T	0.64216	0.2578	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.64689	-0.6348	4	.	.	.	.	15.8222	0.78662	1.0:0.0:0.0:0.0	.	.	.	.	R	503	.	.	Q	+	2	0	CCDC18	93450258	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.267000	0.58877	2.123000	0.65237	0.460000	0.39030	CAA	.	.		0.313	CCDC18-008	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000382327.1	NM_206886		G	93677670	A	G	93677670	2	3	254	1	0	0	0	0	0	0	0	1	2796	117	5	2		2	CCDC18	1	93677670	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	965017	93677670	155572951	45	34337										
ABCA4	24	hgsc.bcm.edu	37	chr1	94520858	94520858	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgccaaatccaaatgccaccGgagacagtaagctctgcagt	9	12	1	1	rs542919944|rs281865399		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:94520858G>T	ENST00000370225.3	-	16	2482	c.2396C>A	c.(2395-2397)cCg>cAg	p.P799Q	ABCA4_ENST00000535735.1_Missense_Mutation_p.P725Q	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	799					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			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)		AAATGCCACCGGAGACAGTAA	0.567																																					p.P799Q		Atlas-SNP	.											.	ABCA4	275	.	0			c.C2396A						.						62	57	59					1																	94520858		2203	4300	6503	SO:0001583	missense	24	exon16			GCCACCGGAGACA	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.2396C>A	chr1.hg19:g.94520858G>T	ENSP00000359245:p.Pro799Gln	69.0	0.0		64.0	4.0	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	hg19	CCDS747.1	.	.	.	.	.	.	.	.	.	.	G	10.56	1.385296	0.25031	.	.	ENSG00000198691	ENST00000370225;ENST00000535735	D;T	0.87256	-2.23;-0.57	5.55	5.55	0.83447	.	0.263117	0.38164	N	0.001788	T	0.72503	0.3468	N	0.26092	0.79	0.35233	D	0.777139	B;B	0.23591	0.088;0.001	B;B	0.21917	0.037;0.016	T	0.71879	-0.4459	10	0.46703	T	0.11	.	15.0531	0.71891	0.0:0.0:0.8574:0.1426	.	725;799	F5H6E5;P78363	.;ABCA4_HUMAN	Q	799;725	ENSP00000359245:P799Q;ENSP00000437682:P725Q	ENSP00000359245:P799Q	P	-	2	0	ABCA4	94293446	1.000000	0.71417	0.996000	0.52242	0.239000	0.25481	2.783000	0.47766	2.626000	0.88956	0.650000	0.86243	CCG	.	.		0.567	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		T	94520858	G	T	94520858	3	4	254	1	0	0	0	0	1	0	0	0	34	1116	39	1	4565	1	ABCA4	1	94520858	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	843188	94520858	154729763	46	34338										
LPPR5	163404	hgsc.bcm.edu	37	chr1	99418828	99418828	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gatttcctgtgactacttgtCcagcatttacaaagatatct	6	9	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:99418828C>A	ENST00000263177.4	-	3	640	c.419G>T	c.(418-420)gGa>gTa	p.G140V	LPPR5_ENST00000370188.3_Missense_Mutation_p.G140V	NM_001037317.1	NP_001032394.1	Q32ZL2	LPPR5_HUMAN		140						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)										GACTACTTGTCCAGCATTTAC	0.403																																					p.G140V		Atlas-SNP	.											.	.	.	.	0			c.G419T						.						79	78	79					1																	99418828		2203	4300	6503	SO:0001583	missense	0	exon3			ACTTGTCCAGCAT																												ENST00000263177.4:c.419G>T	chr1.hg19:g.99418828C>A	ENSP00000263177:p.Gly140Val	91.0	0.0		79.0	4.0	NM_001037317	A8MPX4|B7UCH3|Q32ZD0|Q3ZCU7	Missense_Mutation	SNP	ENST00000263177.4	hg19	CCDS30778.1	.	.	.	.	.	.	.	.	.	.	C	16.56	3.156654	0.57259	.	.	ENSG00000117598	ENST00000370188;ENST00000263177	T;T	0.74209	-0.82;-0.82	4.9	4.9	0.64082	.	0.158353	0.56097	D	0.000028	T	0.73590	0.3606	L	0.49778	1.585	0.80722	D	1	D;D	0.65815	0.994;0.995	P;D	0.64595	0.88;0.927	T	0.69781	-0.5052	10	0.10111	T	0.7	.	17.4358	0.87552	0.0:1.0:0.0:0.0	.	140;140	Q32ZL2-2;Q32ZL2	.;LPPR5_HUMAN	V	140	ENSP00000359207:G140V;ENSP00000263177:G140V	ENSP00000263177:G140V	G	-	2	0	AL161744.1	99191416	1.000000	0.71417	0.991000	0.47740	0.736000	0.42039	7.442000	0.80503	2.407000	0.81776	0.655000	0.94253	GGA	.	.		0.403	LPPR5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393221.1			A	99418828	C	A	99418828	3	1	254	1	0	0	0	0	1	0	0	0	8937	855	30	3	562	3	LPPR5	1	99418828	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	4897970	99418828	149831793	47	34339										
PALMD	54873	hgsc.bcm.edu	37	chr1	100154877	100154877	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aatgactccttgggaagaatCgaatgtcatgcaggacaaag	11	7	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:100154877C>A	ENST00000263174.4	+	7	1436	c.1061C>A	c.(1060-1062)tCg>tAg	p.S354*	PALMD_ENST00000605497.1_Nonsense_Mutation_p.S354*	NM_017734.4	NP_060204.1	Q9NP74	PALMD_HUMAN	palmdelphin	354					regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|membrane (GO:0016020)				central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(8)|ovary(6)|pancreas(1)|prostate(2)	31		all_epithelial(167;0.000813)|all_lung(203;0.0214)|Lung NSC(277;0.0216)		Epithelial(280;0.067)|all cancers(265;0.117)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)		TGGGAAGAATCGAATGTCATG	0.493																																					p.S354X		Atlas-SNP	.											.	PALMD	64	.	0			c.C1061A						.						59	55	56					1																	100154877		2203	4300	6503	SO:0001587	stop_gained	54873	exon7			AAGAATCGAATGT	AJ312214	CCDS758.1	1p22-p21	2008-07-18			ENSG00000099260	ENSG00000099260			15846	protein-coding gene	gene with protein product		610182		C1orf11		11478809	Standard	NM_017734		Approved	FLJ20271, PALML	uc001dsg.3	Q9NP74	OTTHUMG00000010764	ENST00000263174.4:c.1061C>A	chr1.hg19:g.100154877C>A	ENSP00000263174:p.Ser354*	92.0	0.0		91.0	5.0	NM_017734	Q9H7E6|Q9NPM5|Q9NPM6|Q9NPS0	Nonsense_Mutation	SNP	ENST00000263174.4	hg19	CCDS758.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.043021	0.93685	.	.	ENSG00000099260	ENST00000263174	.	.	.	5.93	5.93	0.95920	.	1.348970	0.04374	N	0.359659	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.0E-4	14.0993	0.65044	0.0:0.8066:0.1934:0.0	.	.	.	.	X	354	.	ENSP00000263174:S354X	S	+	2	0	PALMD	99927465	0.003000	0.15002	0.015000	0.15790	0.012000	0.07955	1.649000	0.37281	2.802000	0.96397	0.563000	0.77884	TCG	.	.		0.493	PALMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029672.1	NM_017734		A	100154877	C	A	100154877	4	1	254	1	0	0	0	0	0	1	0	0	11420	893	31	1	1087	1	PALMD	1	100154877	Nonsense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	736049	100154877	149095744	48	34340										
ATXN7L2	127002	hgsc.bcm.edu	37	chr1	110032963	110032963	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccgccggctggaccggttctGctcagcactcagctccatgc	11	17	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:110032963G>T	ENST00000369870.3	+	9	1322	c.1307G>T	c.(1306-1308)tGc>tTc	p.C436F		NM_153340.4	NP_699171.3	Q5T6C5	AT7L2_HUMAN	ataxin 7-like 2	436										breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)	17		all_epithelial(167;0.00197)|all_lung(203;0.00291)|Lung NSC(277;0.00453)		Colorectal(144;0.0129)|Lung(183;0.0426)|Epithelial(280;0.0675)|READ - Rectum adenocarcinoma(129;0.0693)|all cancers(265;0.071)|LUSC - Lung squamous cell carcinoma(189;0.228)		GACCGGTTCTGCTCAGCACTC	0.552											OREG0013635	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C436F		Atlas-SNP	.											.	ATXN7L2	60	.	0			c.G1307T						.						82	76	78					1																	110032963		2203	4300	6503	SO:0001583	missense	127002	exon9			GGTTCTGCTCAGC	BC037582	CCDS30794.1	1p13.2	2008-02-05			ENSG00000162650	ENSG00000162650			28713	protein-coding gene	gene with protein product						12477932	Standard	NM_153340		Approved	MGC46534, FLJ00381	uc001dxr.3	Q5T6C5	OTTHUMG00000011027	ENST00000369870.3:c.1307G>T	chr1.hg19:g.110032963G>T	ENSP00000358886:p.Cys436Phe	75.0	0.0	1424	70.0	4.0	NM_153340		Missense_Mutation	SNP	ENST00000369870.3	hg19	CCDS30794.1	.	.	.	.	.	.	.	.	.	.	G	16.71	3.199607	0.58126	.	.	ENSG00000162650	ENST00000369870;ENST00000541125;ENST00000369869	T	0.41065	1.01	5.97	5.97	0.96955	.	0.000000	0.64402	D	0.000001	T	0.50394	0.1613	L	0.47716	1.5	0.52099	D	0.999944	D	0.67145	0.996	D	0.67725	0.953	T	0.45366	-0.9266	10	0.56958	D	0.05	-12.0532	17.3447	0.87307	0.0:0.0:1.0:0.0	.	436	Q5T6C5	AT7L2_HUMAN	F	436;436;63	ENSP00000358886:C436F	ENSP00000358885:C63F	C	+	2	0	ATXN7L2	109834486	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.622000	0.90953	2.837000	0.97791	0.655000	0.94253	TGC	.	.		0.552	ATXN7L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030331.1	NM_153340		T	110032963	G	T	110032963	3	4	254	1	0	0	0	0	1	0	0	0	1217	1319	46	3	1341	3	ATXN7L2	1	110032963	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	9878086	110032963	139217658	49	34341										
KCNA10	3744	hgsc.bcm.edu	37	chr1	111061042	111061042	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aatactcatttctcatggagTcaaagaactgcatccttttt	5	9	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:111061042T>C	ENST00000369771.2	-	1	755	c.368A>G	c.(367-369)gAc>gGc	p.D123G		NM_005549.2	NP_005540.1	Q16322	KCA10_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 10	123					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|intracellular cyclic nucleotide activated cation channel activity (GO:0005221)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(3)|skin(1)|urinary_tract(1)	35		all_cancers(81;4.57e-06)|all_epithelial(167;1.52e-05)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0238)|all cancers(265;0.0874)|Colorectal(144;0.103)|Epithelial(280;0.116)|LUSC - Lung squamous cell carcinoma(189;0.134)	Dalfampridine(DB06637)	TCTCATGGAGTCAAAGAACTG	0.468																																					p.D123G		Atlas-SNP	.											.	KCNA10	92	.	0			c.A368G						.						68	72	70					1																	111061042		2203	4300	6503	SO:0001583	missense	3744	exon1			ATGGAGTCAAAGA	U96110	CCDS826.1	1p13.1	2012-07-05			ENSG00000143105	ENSG00000143105		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6219	protein-coding gene	gene with protein product		602420				16382104	Standard	NM_005549		Approved	Kv1.8	uc001dzt.1	Q16322	OTTHUMG00000022785	ENST00000369771.2:c.368A>G	chr1.hg19:g.111061042T>C	ENSP00000358786:p.Asp123Gly	42.0	0.0		29.0	5.0	NM_005549		Missense_Mutation	SNP	ENST00000369771.2	hg19	CCDS826.1	.	.	.	.	.	.	.	.	.	.	T	19.01	3.743242	0.69418	.	.	ENSG00000143105	ENST00000369771	T	0.78126	-1.15	5.72	5.72	0.89469	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.000000	0.85682	D	0.000000	D	0.92198	0.7526	H	0.98883	4.36	0.58432	D	0.999996	D	0.89917	1.0	D	0.97110	1.0	D	0.95141	0.8264	10	0.87932	D	0	.	14.8223	0.70082	0.0:0.0:0.0:1.0	.	123	Q16322	KCA10_HUMAN	G	123	ENSP00000358786:D123G	ENSP00000358786:D123G	D	-	2	0	KCNA10	110862565	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.171000	0.68590	0.533000	0.62120	GAC	.	.		0.468	KCNA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059081.1	NM_005549		C	111061042	T	C	111061042	3	2	254	1	0	0	0	0	1	0	0	0	8011	1667	58	2	1171	2	KCNA10	1	111061042	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	1028079	111061042	138189579	50	34342										
CHI3L2	1117	hgsc.bcm.edu	37	chr1	111773369	111773369	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttcactctactccaggatctGcctacaaactggtttgctac	6	13	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:111773369G>A	ENST00000445067.2	+	5	847	c.76G>A	c.(76-78)Gcc>Acc	p.A26T	CHI3L2_ENST00000369744.2_Missense_Mutation_p.A16T|CHI3L2_ENST00000524472.1_5'UTR|CHI3L2_ENST00000369748.4_Missense_Mutation_p.A26T|CHI3L2_ENST00000466741.1_5'UTR			Q15782	CH3L2_HUMAN	chitinase 3-like 2	26					carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)	extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(8)|prostate(1)	19		all_cancers(81;1.89e-05)|all_epithelial(167;7.36e-06)|all_lung(203;0.00018)|Lung NSC(277;0.000359)		Lung(183;0.0171)|Colorectal(144;0.0387)|all cancers(265;0.0464)|LUSC - Lung squamous cell carcinoma(189;0.0872)|Epithelial(280;0.0994)|COAD - Colon adenocarcinoma(174;0.141)		TCCAGGATCTGCCTACAAACT	0.488																																					p.A26T		Atlas-SNP	.											.	CHI3L2	38	.	0			c.G76A						.						72	68	69					1																	111773369		2203	4300	6503	SO:0001583	missense	1117	exon3			GGATCTGCCTACA	U49835	CCDS30802.1, CCDS30803.1, CCDS41367.1	1p13.3	2008-02-05			ENSG00000064886	ENSG00000064886			1933	protein-coding gene	gene with protein product		601526				8702629	Standard	NM_001025197		Approved	YKL-39, YKL39	uc001eam.3	Q15782	OTTHUMG00000012174	ENST00000445067.2:c.76G>A	chr1.hg19:g.111773369G>A	ENSP00000437082:p.Ala26Thr	77.0	0.0		60.0	4.0	NM_004000	A6NNY3|B4DPR7|Q15749|Q15783|Q5VUV7|Q96F97	Missense_Mutation	SNP	ENST00000445067.2	hg19	CCDS30802.1	.	.	.	.	.	.	.	.	.	.	G	15.12	2.738828	0.49045	.	.	ENSG00000064886	ENST00000445067;ENST00000528451;ENST00000486561;ENST00000369744;ENST00000369748;ENST00000474304	T;T;T;T;T	0.15139	3.3;2.49;2.45;3.3;3.3	4.09	2.22	0.28083	.	0.000000	0.40554	N	0.001067	T	0.07458	0.0188	L	0.43757	1.38	0.21184	N	0.999761	D;D	0.54397	0.966;0.966	P;P	0.48227	0.571;0.571	T	0.18650	-1.0330	10	0.36615	T	0.2	-2.6827	8.0089	0.30342	0.2034:0.0:0.7966:0.0	.	16;26	A6NNY3;Q15782	.;CH3L2_HUMAN	T	26;26;26;16;26;26	ENSP00000437082:A26T;ENSP00000436077:A26T;ENSP00000431968:A26T;ENSP00000358759:A16T;ENSP00000358763:A26T	ENSP00000358759:A16T	A	+	1	0	CHI3L2	111574892	0.931000	0.31567	0.645000	0.29479	0.962000	0.63368	0.718000	0.25866	0.371000	0.24564	0.655000	0.94253	GCC	.	.		0.488	CHI3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033669.4	NM_004000		A	111773369	G	A	111773369	3	1	254	1	0	0	0	0	1	0	0	0	3343	1319	46	3	86	3	CHI3L2	1	111773369	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	712327	111773369	137477252	51	34343										
CHIA	27159	hgsc.bcm.edu	37	chr1	111857977	111857977	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgcgccagtatgagtttgacGggctggactttgactgggag	16	7	0	3	rs551479392		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:111857977G>T	ENST00000369740.1	+	6	503	c.400G>T	c.(400-402)Ggg>Tgg	p.G134W	CHIA_ENST00000343320.6_Missense_Mutation_p.G134W|CHIA_ENST00000451398.2_5'UTR|CHIA_ENST00000483391.1_Intron|CHIA_ENST00000430615.1_Missense_Mutation_p.G26W|CHIA_ENST00000353665.6_Intron|RP5-1125M8.2_ENST00000426321.1_RNA	NM_001258001.1|NM_201653.3	NP_001244930.1|NP_970615.2	Q9BZP6	CHIA_HUMAN	chitinase, acidic	134					apoptotic process (GO:0006915)|cell wall chitin metabolic process (GO:0006037)|chitin catabolic process (GO:0006032)|chitin metabolic process (GO:0006030)|digestion (GO:0007586)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|positive regulation of chemokine secretion (GO:0090197)|production of molecular mediator involved in inflammatory response (GO:0002532)|response to fungus (GO:0009620)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|chitinase activity (GO:0004568)|kinase binding (GO:0019900)|lysozyme activity (GO:0003796)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		all_cancers(81;3.23e-05)|all_epithelial(167;1.2e-05)|all_lung(203;0.000154)|Lung NSC(277;0.000304)		Colorectal(144;0.0115)|Lung(183;0.0292)|COAD - Colon adenocarcinoma(174;0.0314)|all cancers(265;0.0477)|Epithelial(280;0.0918)|LUSC - Lung squamous cell carcinoma(189;0.154)		TGAGTTTGACGGGCTGGACTT	0.547																																					p.G134W		Atlas-SNP	.											.	CHIA	115	.	0			c.G400T						.						96	91	93					1																	111857977		2203	4300	6503	SO:0001583	missense	27159	exon6			TTTGACGGGCTGG	AF290004	CCDS832.1, CCDS41368.1, CCDS58017.1	1p13.2	2008-05-14			ENSG00000134216	ENSG00000134216			17432	protein-coding gene	gene with protein product		606080				11085997	Standard	NM_021797		Approved	AMCase, TSA1902, CHIT2	uc001eas.4	Q9BZP6	OTTHUMG00000011165	ENST00000369740.1:c.400G>T	chr1.hg19:g.111857977G>T	ENSP00000358755:p.Gly134Trp	133.0	0.0		91.0	4.0	NM_201653	Q32W79|Q32W80|Q3B866|Q5U5Z5|Q5VUV4|Q86UD8|Q9ULY3|Q9ULY4	Missense_Mutation	SNP	ENST00000369740.1	hg19	CCDS41368.1	.	.	.	.	.	.	.	.	.	.	G	18.58	3.654769	0.67472	.	.	ENSG00000134216	ENST00000422815;ENST00000369740;ENST00000343320;ENST00000430615	T;T;T;T	0.39592	1.07;1.07;1.07;1.07	4.72	3.8	0.43715	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.64402	D	0.000003	T	0.73953	0.3653	H	0.99752	4.75	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.83514	0.0082	10	0.87932	D	0	-8.8093	11.22	0.48848	0.0925:0.0:0.9075:0.0	.	134	Q9BZP6	CHIA_HUMAN	W	78;134;134;26	ENSP00000387671:G78W;ENSP00000358755:G134W;ENSP00000341828:G134W;ENSP00000391132:G26W	ENSP00000341828:G134W	G	+	1	0	CHIA	111659500	1.000000	0.71417	0.840000	0.33206	0.817000	0.46193	5.612000	0.67681	1.096000	0.41439	0.655000	0.94253	GGG	.	.		0.547	CHIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030710.1			T	111857977	G	T	111857977	3	4	254	1	0	0	0	0	1	0	0	0	3344	1116	39	1	418	1	CHIA	1	111857977	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	84608	111857977	137392644	52	34344										
HIPK1	204851	hgsc.bcm.edu	37	chr1	114499248	114499248	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	attctgaattttctttggaaGgtgaatatgtctacagacct	8	6	3	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:114499248G>T	ENST00000369558.1	+	6	1639		c.e6-1		HIPK1_ENST00000369554.2_Splice_Site|HIPK1_ENST00000369553.1_Splice_Site|HIPK1_ENST00000406344.1_Splice_Site|HIPK1_ENST00000369561.4_Splice_Site|HIPK1_ENST00000369555.2_Splice_Site|HIPK1_ENST00000369559.4_Splice_Site|HIPK1_ENST00000340480.4_Splice_Site|HIPK1_ENST00000426820.2_Splice_Site			Q86Z02	HIPK1_HUMAN	homeodomain interacting protein kinase 1						anterior/posterior pattern specification (GO:0009952)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|neuron differentiation (GO:0030182)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|retina layer formation (GO:0010842)|smoothened signaling pathway (GO:0007224)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(15)|ovary(4)|prostate(2)	39	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTCTTTGGAAGGTGAATATGT	0.388																																					.		Atlas-SNP	.											.	HIPK1	195	.	0			c.1408-1G>T						.						66	63	64					1																	114499248		2203	4300	6503	SO:0001630	splice_region_variant	204851	exon6			TTGGAAGGTGAAT	AB089957	CCDS867.1, CCDS868.1, CCDS869.1, CCDS41370.1	1p13.1	2008-02-05			ENSG00000163349	ENSG00000163349			19006	protein-coding gene	gene with protein product		608003					Standard	NM_198268		Approved	KIAA0630, Myak, MGC26642, Nbak2, MGC33446, MGC33548	uc001eem.3	Q86Z02	OTTHUMG00000011983	ENST00000369558.1:c.1408-1G>T	chr1.hg19:g.114499248G>T		95.0	0.0		60.0	4.0	NM_152696	A6NJ34|O75125|Q5SQL2|Q5SQL4|Q5SQL5|Q8IYD7|Q8NDN5|Q8NEB6|Q8TBZ1	Splice_Site	SNP	ENST00000369558.1	hg19	CCDS867.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.967471	0.74131	.	.	ENSG00000163349	ENST00000426820;ENST00000369559;ENST00000443627;ENST00000369554;ENST00000369555;ENST00000369558;ENST00000369561;ENST00000340480;ENST00000369553;ENST00000406344	.	.	.	5.08	5.08	0.68730	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.6579	0.91460	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	HIPK1	114300771	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	9.657000	0.98554	2.646000	0.89796	0.650000	0.86243	.	.	.		0.388	HIPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000033127.1	NM_198268	Intron	T	114499248	G	T	114499248	5	4	254	1	0	0	0	0	0	0	1	0	7125	1014	35	3	1443	3	HIPK1	1	114499248	Splice_Site	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	2641271	114499248	134751373	53	34345										
ATP1A1	476	hgsc.bcm.edu	37	chr1	116942136	116942136	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agacaaacttgtgaatgagcGgctgatcagcatggcctatg	12	8	1	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:116942136G>T	ENST00000295598.5	+	18	2795	c.2543G>T	c.(2542-2544)cGg>cTg	p.R848L	ATP1A1_ENST00000537345.1_Missense_Mutation_p.R848L|ATP1A1_ENST00000369496.4_Missense_Mutation_p.R817L	NM_000701.7	NP_000692.2	P05023	AT1A1_HUMAN	ATPase, Na+/K+ transporting, alpha 1 polypeptide	848					ATP biosynthetic process (GO:0006754)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|membrane hyperpolarization (GO:0060081)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of glucocorticoid biosynthetic process (GO:0031947)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart contraction (GO:0045823)|positive regulation of striated muscle contraction (GO:0045989)|potassium ion import (GO:0010107)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of sodium ion transport (GO:0002028)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|chaperone binding (GO:0051087)|phosphatase activity (GO:0016791)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(2)|breast(2)|cervix(3)|endometrium(2)|kidney(5)|large_intestine(9)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47	Lung SC(450;0.225)	all_cancers(81;1.28e-06)|all_epithelial(167;3.48e-07)|all_lung(203;2.64e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0164)|LUSC - Lung squamous cell carcinoma(189;0.0548)|Colorectal(144;0.0825)|COAD - Colon adenocarcinoma(174;0.127)|all cancers(265;0.24)	Acetyldigitoxin(DB00511)|Almitrine(DB01430)|Aluminium(DB01370)|Bepridil(DB01244)|Bretylium(DB01158)|Ciclopirox(DB01188)|Deslanoside(DB01078)|Diazoxide(DB01119)|Digitoxin(DB01396)|Digoxin(DB00390)|Ethacrynic acid(DB00903)|Hydroflumethiazide(DB00774)|Ouabain(DB01092)|Trichlormethiazide(DB01021)	GTGAATGAGCGGCTGATCAGC	0.532																																					p.R848L		Atlas-SNP	.											.	ATP1A1	87	.	0			c.G2543T						.						88	78	81					1																	116942136		2203	4300	6503	SO:0001583	missense	476	exon18			ATGAGCGGCTGAT	D00099	CCDS887.1, CCDS53351.1, CCDS53352.1	1p13	2012-10-22			ENSG00000163399	ENSG00000163399	3.6.3.9	"ATPases / P-type"	799	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-1", "sodium pump subunit alpha-1", "sodium-potassium ATPase catalytic subunit alpha-1"	182310					Standard	NM_000701		Approved		uc001ege.3	P05023	OTTHUMG00000012109	ENST00000295598.5:c.2543G>T	chr1.hg19:g.116942136G>T	ENSP00000295598:p.Arg848Leu	116.0	0.0		92.0	4.0	NM_001160233	B2RBR6|B7Z2T5|B7Z3U6|F5H3A1|Q16689|Q6LDM4|Q9UCN1|Q9UJ20|Q9UJ21	Missense_Mutation	SNP	ENST00000295598.5	hg19	CCDS887.1	.	.	.	.	.	.	.	.	.	.	G	33	5.280459	0.95489	.	.	ENSG00000163399	ENST00000295598;ENST00000445896;ENST00000537345;ENST00000369496;ENST00000440951	D;D;D;D	0.96041	-3.89;-3.89;-3.89;-3.89	5.04	5.04	0.67666	ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.98588	0.9528	H	0.97103	3.94	0.80722	D	1	D;D	0.64830	0.993;0.994	D;D	0.71870	0.958;0.975	D	0.99624	1.0984	10	0.87932	D	0	.	18.5698	0.91130	0.0:0.0:1.0:0.0	.	848;848	F5H3A1;P05023	.;AT1A1_HUMAN	L	848;17;848;817;15	ENSP00000295598:R848L;ENSP00000445306:R848L;ENSP00000358508:R817L;ENSP00000396236:R15L	ENSP00000295598:R848L	R	+	2	0	ATP1A1	116743659	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	7.823000	0.86660	2.611000	0.88343	0.655000	0.94253	CGG	.	.		0.532	ATP1A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033481.5	NM_001160233		T	116942136	G	T	116942136	3	4	254	1	0	0	0	0	1	0	0	0	1128	1116	39	1	2629	1	ATP1A1	1	116942136	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	2442888	116942136	132308485	54	34346										
VTCN1	79679	hgsc.bcm.edu	37	chr1	117690333	117690333	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aagtgcccagctgatggcaaAgaaagaagagacacacagag	12	8	0	5			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:117690333A>G	ENST00000369458.3	-	5	874	c.796T>C	c.(796-798)Ttt>Ctt	p.F266L	VTCN1_ENST00000328189.3_Missense_Mutation_p.F150L|VTCN1_ENST00000539893.1_Missense_Mutation_p.F171L|VTCN1_ENST00000359008.4_Missense_Mutation_p.F269L	NM_024626.3	NP_078902.2			V-set domain containing T cell activation inhibitor 1									p.F265fs*14(1)		large_intestine(7)|lung(4)|upper_aerodigestive_tract(1)	12	Lung SC(450;0.225)	all_cancers(81;6.05e-06)|all_epithelial(167;5.59e-07)|all_lung(203;2.85e-06)|Lung NSC(69;2e-05)		Lung(183;0.0664)|LUSC - Lung squamous cell carcinoma(189;0.214)|Colorectal(144;0.23)		CTGATGGCAAAGAAAGAAGAG	0.458																																					p.F266L		Atlas-SNP	.											.	VTCN1	26	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.T796C						.						114	108	110					1																	117690333		2203	4300	6503	SO:0001583	missense	79679	exon5			TGGCAAAGAAAGA	BX648021	CCDS894.1, CCDS58019.1, CCDS58020.1	1p12	2013-01-29			ENSG00000134258	ENSG00000134258		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	28873	protein-coding gene	gene with protein product	"B7 family member, H4", "B7 superfamily member 1"	608162				12818165, 12818166	Standard	NM_024626		Approved	B7-H4, FLJ22418, B7S1, B7X, B7H4	uc001ehb.3	Q7Z7D3	OTTHUMG00000012118	ENST00000369458.3:c.796T>C	chr1.hg19:g.117690333A>G	ENSP00000358470:p.Phe266Leu	94.0	0.0		58.0	4.0	NM_024626		Missense_Mutation	SNP	ENST00000369458.3	hg19	CCDS894.1	.	.	.	.	.	.	.	.	.	.	A	0.007	-2.005974	0.00426	.	.	ENSG00000134258	ENST00000369458;ENST00000359008;ENST00000328189;ENST00000539893	T;T;T;T	0.20332	3.54;3.53;2.08;3.77	5.49	-0.842	0.10748	.	0.988038	0.08242	N	0.975883	T	0.03053	0.0090	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46331	-0.9199	10	0.23891	T	0.37	-15.0185	6.6871	0.23152	0.5635:0.1474:0.2891:0.0	.	150;266	Q7Z7D3-2;Q7Z7D3	.;VTCN1_HUMAN	L	266;269;150;171	ENSP00000358470:F266L;ENSP00000351899:F269L;ENSP00000328168:F150L;ENSP00000444724:F171L	ENSP00000328168:F150L	F	-	1	0	VTCN1	117491856	0.000000	0.05858	0.000000	0.03702	0.067000	0.16453	-0.344000	0.07780	-0.609000	0.05724	-2.096000	0.00365	TTT	.	.		0.458	VTCN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000033500.2	NM_024626		G	117690333	A	G	117690333	3	3	254	1	0	0	0	0	1	0	0	0	17249	72	3	2	56	2	VTCN1	1	117690333	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	748197	117690333	131560288	55	34347										
VPS72	6944	hgsc.bcm.edu	37	chr1	151150609	151150609	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tctttttatcagcctcgagcCgctcatatgtctctttaggg	8	11	4	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:151150609C>A	ENST00000354473.4	-	5	611	c.575G>T	c.(574-576)cGg>cTg	p.R192L	VPS72_ENST00000496809.1_5'UTR|TMOD4_ENST00000416280.2_5'Flank|TMOD4_ENST00000601585.1_5'Flank			Q15906	VPS72_HUMAN	vacuolar protein sorting 72 homolog (S. cerevisiae)	192					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(6)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	14	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			AGCCTCGAGCCGCTCATATGT	0.478																																					p.R192L	Pancreas(109;1131 2287 3209 24201)	Atlas-SNP	.											.	VPS72	31	.	0			c.G575T						.						68	65	66					1																	151150609		2203	4300	6503	SO:0001583	missense	6944	exon5			TCGAGCCGCTCAT	D43642	CCDS989.1, CCDS59201.1	1q21	2008-02-05	2006-12-19	2005-09-08	ENSG00000163159	ENSG00000163159			11644	protein-coding gene	gene with protein product		600607	"transcription factor-like 1", "vacuolar protein sorting 72 (yeast)"	TCFL1		7702631	Standard	NM_001271087		Approved	YL-1, YL1, Swc2	uc001exe.2	Q15906	OTTHUMG00000012345	ENST00000354473.4:c.575G>T	chr1.hg19:g.151150609C>A	ENSP00000346464:p.Arg192Leu	71.0	0.0		78.0	4.0	NM_001271087	A6NLK9|A6PW55|Q53GJ2|Q5U0R4	Missense_Mutation	SNP	ENST00000354473.4	hg19	CCDS59201.1	.	.	.	.	.	.	.	.	.	.	.	24.0	4.483923	0.84854	.	.	ENSG00000163159	ENST00000368892;ENST00000354473	.	.	.	5.18	4.26	0.50523	.	0.000000	0.85682	D	0.000000	T	0.60650	0.2285	L	0.56769	1.78	0.80722	D	1	D	0.76494	0.999	D	0.66602	0.945	T	0.64305	-0.6439	9	0.51188	T	0.08	-6.3222	12.1919	0.54277	0.171:0.829:0.0:0.0	.	192	Q15906	VPS72_HUMAN	L	192	.	ENSP00000346464:R192L	R	-	2	0	VPS72	149417233	1.000000	0.71417	0.218000	0.23776	0.990000	0.78478	7.188000	0.77739	1.388000	0.46506	0.655000	0.94253	CGG	.	.		0.478	VPS72-002	NOVEL	mRNA_start_NF|basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000034394.3	NM_005997		A	151150609	C	A	151150609	3	1	254	1	0	0	0	0	1	0	0	0	17232	652	23	1	527	1	VPS72	1	151150609	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	33460276	151150609	98100012	56	34348										
RORC	6097	hgsc.bcm.edu	37	chr1	151779983	151779983	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cacaggtgactcggtttcagTgctgaagagctccttgtaga	12	9	1	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:151779983T>C	ENST00000318247.6	-	11	1629	c.1522A>G	c.(1522-1524)Act>Gct	p.T508A	LINGO4_ENST00000368820.3_5'Flank|RORC_ENST00000356728.6_Missense_Mutation_p.T487A|RORC_ENST00000480719.1_5'UTR|RORC_ENST00000392697.3_Missense_Mutation_p.T562A	NM_005060.3	NP_005051.2	P51449	RORG_HUMAN	RAR-related orphan receptor C	508	Ligand-binding.				adipose tissue development (GO:0060612)|cellular response to sterol (GO:0036315)|circadian regulation of gene expression (GO:0032922)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|lymph node development (GO:0048535)|negative regulation of thymocyte apoptotic process (GO:0070244)|Peyer's patch development (GO:0048541)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of fat cell differentiation (GO:0045598)|regulation of gamma-delta T cell differentiation (GO:0045586)|regulation of glucose metabolic process (GO:0010906)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription involved in cell fate commitment (GO:0060850)|T cell differentiation in thymus (GO:0033077)|T-helper 17 cell differentiation (GO:0072539)|T-helper cell differentiation (GO:0042093)|transcription initiation from RNA polymerase II promoter (GO:0006367)|xenobiotic metabolic process (GO:0006805)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	direct ligand regulated sequence-specific DNA binding transcription factor activity (GO:0098531)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|oxysterol binding (GO:0008142)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(4)|large_intestine(1)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			TCGGTTTCAGTGCTGAAGAGC	0.602																																					p.T508A		Atlas-SNP	.											.	RORC	70	.	0			c.A1522G						.						110	99	103					1																	151779983		2203	4300	6503	SO:0001583	missense	6097	exon11			TTTCAGTGCTGAA	U16997	CCDS1004.1, CCDS30856.1	1q21	2013-01-16			ENSG00000143365	ENSG00000143365		"Nuclear hormone receptors"	10260	protein-coding gene	gene with protein product		602943				7811290	Standard	NM_005060		Approved	RZRG, RORG, NR1F3, TOR	uc001ezh.3	P51449	OTTHUMG00000013053	ENST00000318247.6:c.1522A>G	chr1.hg19:g.151779983T>C	ENSP00000327025:p.Thr508Ala	73.0	0.0		76.0	4.0	NM_005060	Q5SZR9|Q8N5V7|Q8NCY8	Missense_Mutation	SNP	ENST00000318247.6	hg19	CCDS1004.1	.	.	.	.	.	.	.	.	.	.	T	16.37	3.103716	0.56291	.	.	ENSG00000143365	ENST00000356728;ENST00000392697;ENST00000318247	D;D;D	0.94046	-3.31;-3.34;-3.32	5.5	4.38	0.52667	Nuclear hormone receptor, ligand-binding (2);	0.314066	0.26159	U	0.025996	T	0.81749	0.4888	L	0.54323	1.7	0.29163	N	0.877634	B;B;B;B	0.28998	0.112;0.23;0.057;0.1	B;B;B;B	0.26864	0.05;0.05;0.05;0.074	T	0.71334	-0.4624	10	0.28530	T	0.3	.	4.3785	0.11283	0.1745:0.0903:0.0:0.7352	.	496;562;508;487	B6ZGS6;B4DPR1;P51449;F1D8P6	.;.;RORG_HUMAN;.	A	487;562;508	ENSP00000349164:T487A;ENSP00000376461:T562A;ENSP00000327025:T508A	ENSP00000327025:T508A	T	-	1	0	RORC	150046607	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.453000	0.35167	2.085000	0.62840	0.533000	0.62120	ACT	.	.		0.602	RORC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036626.1			C	151779983	T	C	151779983	3	2	254	1	0	0	0	0	1	0	0	0	13545	1696	59	2	38	2	RORC	1	151779983	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	629374	151779983	97470638	57	34349										
SPRR2A	6700	hgsc.bcm.edu	37	chr1	153029108	153029108	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gacactttggtggtgggcagGgctcagggcacttcgggggt	19	8	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:153029108G>T	ENST00000392653.2	-	2	189	c.104C>A	c.(103-105)cCc>cAc	p.P35H		NM_005988.2	NP_005979.1	P35326	SPR2A_HUMAN	small proline-rich protein 2A	35	3 X 9 AA tandem repeats of P-K-C-P-[EQ]- P-C-P-P.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)				large_intestine(2)|ovary(1)	3	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			TGGTGGGCAGGGCTCAGGGCA	0.607																																					p.P35H		Atlas-SNP	.											.	SPRR2A	9	.	0			c.C104A						.						68	65	66					1																	153029108		2202	4278	6480	SO:0001583	missense	6700	exon2			GGGCAGGGCTCAG	X53064	CCDS1034.1	1q21-q22	2008-02-05			ENSG00000241794	ENSG00000241794			11261	protein-coding gene	gene with protein product		182267				8325635	Standard	NM_005988		Approved		uc001fbd.3	P35326	OTTHUMG00000014395	ENST00000392653.2:c.104C>A	chr1.hg19:g.153029108G>T	ENSP00000376423:p.Pro35His	183.0	0.0		183.0	34.0	NM_005988	B2R4T3|D3DV35|Q5T529	Missense_Mutation	SNP	ENST00000392653.2	hg19	CCDS1034.1	.	.	.	.	.	.	.	.	.	.	G	9.563	1.118924	0.20877	.	.	ENSG00000241794	ENST00000392653	T	0.53857	0.6	2.79	2.79	0.32731	.	0.000000	0.32671	N	0.005794	T	0.56717	0.2004	.	.	.	0.18873	N	0.999981	D	0.89917	1.0	D	0.87578	0.998	T	0.44065	-0.9352	9	0.87932	D	0	.	9.1956	0.37226	0.0:0.0:1.0:0.0	.	35	P35326	SPR2A_HUMAN	H	35	ENSP00000376423:P35H	ENSP00000376423:P35H	P	-	2	0	SPRR2A	151295732	1.000000	0.71417	0.419000	0.26584	0.386000	0.30323	4.127000	0.57944	1.551000	0.49450	0.400000	0.26472	CCC	.	.		0.607	SPRR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040049.1	NM_005988		T	153029108	G	T	153029108	3	4	254	1	0	0	0	0	1	0	0	0	15112	1232	43	3	118	3	SPRR2A	1	153029108	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1249125	153029108	96221513	58	34350										
DENND4B	9909	hgsc.bcm.edu	37	chr1	153903278	153903278	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agcactgactccaacagtgcCaaactaagggatgcaggtac	10	11	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:153903278C>A	ENST00000361217.4	-	26	4588	c.4170G>T	c.(4168-4170)ttG>ttT	p.L1390F	DENND4B_ENST00000474386.1_5'UTR	NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	1390					positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab protein signal transduction (GO:0032483)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	36	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			CCAACAGTGCCAAACTAAGGG	0.597																																					p.L1390F		Atlas-SNP	.											.	DENND4B	210	.	0			c.G4170T						.						22	23	23					1																	153903278		2001	4185	6186	SO:0001583	missense	9909	exon26			CAGTGCCAAACTA	AB007945	CCDS44228.1	1q21.3	2012-10-03	2006-01-27	2006-01-27	ENSG00000198837	ENSG00000198837		"DENN/MADD domain containing"	29044	protein-coding gene	gene with protein product			"KIAA0476"	KIAA0476		9455484, 12906859	Standard	NM_014856		Approved		uc001fdd.1	O75064	OTTHUMG00000037157	ENST00000361217.4:c.4170G>T	chr1.hg19:g.153903278C>A	ENSP00000354597:p.Leu1390Phe	49.0	0.0		100.0	4.0	NM_014856	Q5T4K0	Missense_Mutation	SNP	ENST00000361217.4	hg19	CCDS44228.1	.	.	.	.	.	.	.	.	.	.	C	9.859	1.195729	0.22037	.	.	ENSG00000198837	ENST00000361217	T	0.07567	3.18	5.14	1.93	0.25924	.	0.184794	0.26400	N	0.024593	T	0.02767	0.0083	L	0.36672	1.1	0.38547	D	0.949367	P	0.41748	0.761	B	0.41571	0.36	T	0.46162	-0.9211	10	0.56958	D	0.05	-1.5912	4.6914	0.12783	0.2682:0.531:0.1205:0.0803	.	1390	O75064	DEN4B_HUMAN	F	1390	ENSP00000354597:L1390F	ENSP00000354597:L1390F	L	-	3	2	DENND4B	152169902	0.906000	0.30813	0.263000	0.24496	0.779000	0.44077	1.166000	0.31834	0.708000	0.31955	0.563000	0.77884	TTG	.	.		0.597	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806		A	153903278	C	A	153903278	3	1	254	1	0	0	0	0	1	0	0	0	4436	593	21	3	332	3	DENND4B	1	153903278	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	874170	153903278	95347343	59	34351										
FDPS	2224	hgsc.bcm.edu	37	chr1	155289468	155289468	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgctggagatgggggagttcTttcagattcaggtaagaagg	16	4	3	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:155289468T>C	ENST00000356657.6	+	9	1075	c.913T>C	c.(913-915)Ttt>Ctt	p.F305L	RUSC1-AS1_ENST00000450199.1_RNA|RUSC1-AS1_ENST00000543656.1_RNA|RUSC1_ENST00000368354.3_5'Flank|FDPS_ENST00000447866.1_Missense_Mutation_p.F239L|FDPS_ENST00000368356.4_Missense_Mutation_p.F305L|RUSC1_ENST00000368352.5_5'Flank|RUSC1-AS1_ENST00000446880.1_RNA|RUSC1-AS1_ENST00000443642.1_RNA	NM_001135821.1	NP_001129293.1	P14324	FPPS_HUMAN	farnesyl diphosphate synthase	305					cholesterol biosynthetic process (GO:0006695)|farnesyl diphosphate biosynthetic process (GO:0045337)|geranyl diphosphate biosynthetic process (GO:0033384)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	dimethylallyltranstransferase activity (GO:0004161)|geranyltranstransferase activity (GO:0004337)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)	10	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;2.03e-10)|all cancers(21;5.23e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)		Alendronate(DB00630)|Ibandronate(DB00710)|Pamidronate(DB00282)|Risedronate(DB00884)|Zoledronate(DB00399)	GGGGGAGTTCTTTCAGATTCA	0.547																																					p.F305L		Atlas-SNP	.											.	FDPS	41	.	0			c.T913C						.						79	80	80					1																	155289468		2203	4300	6503	SO:0001583	missense	2224	exon9			GAGTTCTTTCAGA	J05262	CCDS1110.1, CCDS44241.1, CCDS72940.1	1q22	2012-07-13	2010-06-24		ENSG00000160752	ENSG00000160752	2.5.1.1, 2.5.1.10		3631	protein-coding gene	gene with protein product	"farnesyl pyrophosphate synthetase, dimethylallyltranstransferase, geranyltranstransferase"	134629				1968462	Standard	NM_002004		Approved		uc001fkc.2	P14324	OTTHUMG00000013909	ENST00000356657.6:c.913T>C	chr1.hg19:g.155289468T>C	ENSP00000349078:p.Phe305Leu	118.0	0.0		88.0	4.0	NM_001135821	D3DV91|E9PCI9|Q96G29	Missense_Mutation	SNP	ENST00000356657.6	hg19	CCDS1110.1	.	.	.	.	.	.	.	.	.	.	T	27.9	4.876048	0.91664	.	.	ENSG00000160752	ENST00000447866;ENST00000368356;ENST00000356657	D;D;D	0.82526	-1.62;-1.62;-1.62	4.06	4.06	0.47325	Terpenoid synthase (2);	0.000000	0.45126	D	0.000394	D	0.91188	0.7224	M	0.93594	3.435	0.80722	D	1	D	0.61080	0.989	D	0.66979	0.948	D	0.93060	0.6473	10	0.87932	D	0	-16.4506	12.9405	0.58340	0.0:0.0:0.0:1.0	.	305	P14324	FPPS_HUMAN	L	239;305;305	ENSP00000391755:F239L;ENSP00000357340:F305L;ENSP00000349078:F305L	ENSP00000349078:F305L	F	+	1	0	FDPS	153556092	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.711000	0.84669	2.066000	0.61787	0.459000	0.35465	TTT	.	.		0.547	FDPS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039053.1	NM_002004		C	155289468	T	C	155289468	3	2	254	1	0	0	0	0	1	0	0	0	5811	1609	56	2	943	2	FDPS	1	155289468	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	1386190	155289468	93961153	60	34352										
CCT3	7203	hgsc.bcm.edu	37	chr1	156280946	156280946	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gagggtccaggagaacattgCgacacacttgcatggcatcc	12	11	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:156280946C>T	ENST00000295688.3	-	12	1476	c.1196G>A	c.(1195-1197)cGc>cAc	p.R399H	CCT3_ENST00000472765.2_Missense_Mutation_p.R354H|CCT3_ENST00000368259.2_Missense_Mutation_p.R361H|CCT3_ENST00000368261.3_Missense_Mutation_p.R354H	NM_005998.4	NP_005989.3	P49368	TCPG_HUMAN	chaperonin containing TCP1, subunit 3 (gamma)	399					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			endometrium(4)|large_intestine(1)|liver(1)|lung(11)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	22	Hepatocellular(266;0.158)					GAGAACATTGCGACACACTTG	0.537																																					p.R399H		Atlas-SNP	.											.	CCT3	61	.	0			c.G1196A						.						76	73	74					1																	156280946		2203	4300	6503	SO:0001583	missense	7203	exon12			ACATTGCGACACA	BC008019	CCDS1140.2, CCDS30888.1	1q23	2011-09-02			ENSG00000163468	ENSG00000163468		"Heat Shock Proteins / Chaperonins"	1616	protein-coding gene	gene with protein product		600114		TRIC5		8110840	Standard	NM_005998		Approved	Cctg	uc001fol.2	P49368	OTTHUMG00000024061	ENST00000295688.3:c.1196G>A	chr1.hg19:g.156280946C>T	ENSP00000295688:p.Arg399His	141.0	0.0		157.0	23.0	NM_005998	A6NE14|Q5SZY1|Q9BR64	Missense_Mutation	SNP	ENST00000295688.3	hg19	CCDS1140.2	.	.	.	.	.	.	.	.	.	.	C	33	5.252956	0.95336	.	.	ENSG00000163468	ENST00000295688;ENST00000368259;ENST00000368261;ENST00000472765	T;T;T;T	0.80994	-1.44;-1.44;-1.44;-1.44	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	D	0.92740	0.7692	H	0.96805	3.885	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.73708	0.96;0.981;0.972	D	0.94427	0.7646	10	0.72032	D	0.01	-9.7785	17.4945	0.87713	0.0:1.0:0.0:0.0	.	361;398;399	P49368-2;E9PAQ6;P49368	.;.;TCPG_HUMAN	H	399;361;354;354	ENSP00000295688:R399H;ENSP00000357242:R361H;ENSP00000357244:R354H;ENSP00000431543:R354H	ENSP00000295688:R399H	R	-	2	0	CCT3	154547570	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.441000	0.80485	2.726000	0.93360	0.650000	0.86243	CGC	.	.		0.537	CCT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060602.3	NM_005998		T	156280946	C	T	156280946	3	4	254	1	0	0	0	0	1	0	0	0	2956	768	27	1	453	1	CCT3	1	156280946	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	991478	156280946	92969675	61	34353										
C1orf66	51093	hgsc.bcm.edu	37	chr1	156703277	156703277	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcctggaccaggagcttctgCaggctctggagaaagaggag	16	9	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:156703277C>T	ENST00000368216.4	+	5	1231	c.601C>T	c.(601-603)Cag>Tag	p.Q201*	RRNAD1_ENST00000368218.4_Nonsense_Mutation_p.Q201*|RRNAD1_ENST00000476229.1_Nonsense_Mutation_p.Q78*	NM_015997.3	NP_057081.3	Q96FB5	RRNAD_HUMAN	ribosomal RNA adenine dimethylase domain containing 1	201						integral component of membrane (GO:0016021)	rRNA (adenine-N6,N6-)-dimethyltransferase activity (GO:0000179)			NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(3)	9						GGAGCTTCTGCAGGCTCTGGA	0.607																																					p.Q201X		Atlas-SNP	.											.	RRNAD1	39	.	0			c.C601T						.						72	83	79					1																	156703277		2203	4300	6503	SO:0001587	stop_gained	51093	exon5			CTTCTGCAGGCTC	BC011382	CCDS1154.1, CCDS44246.1	1q23.1	2011-01-28	2011-01-28	2011-01-28	ENSG00000143303	ENSG00000143303			24273	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 66"	C1orf66		10810093, 310876	Standard	NM_015997		Approved	CGI-41	uc001fpu.3	Q96FB5	OTTHUMG00000041302	ENST00000368216.4:c.601C>T	chr1.hg19:g.156703277C>T	ENSP00000357199:p.Gln201*	77.0	0.0		75.0	4.0	NM_015997	D3DVC7|Q4VX71|Q5SZ03|Q9Y358	Nonsense_Mutation	SNP	ENST00000368216.4	hg19	CCDS1154.1	.	.	.	.	.	.	.	.	.	.	C	16.53	3.148138	0.57151	.	.	ENSG00000143303	ENST00000368218;ENST00000368216;ENST00000519086;ENST00000484742;ENST00000476229	.	.	.	4.75	2.68	0.31781	.	0.580363	0.19514	N	0.112445	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.3672	7.1541	0.25626	0.3157:0.5962:0.0:0.0881	.	.	.	.	X	201;201;180;99;78	.	ENSP00000357199:Q201X	Q	+	1	0	RRNAD1	154969901	0.550000	0.26489	1.000000	0.80357	0.974000	0.67602	0.677000	0.25262	1.213000	0.43380	0.555000	0.69702	CAG	.	.		0.607	RRNAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098973.1	NM_015997		T	156703277	C	T	156703277	4	4	254	1	0	0	0	0	0	1	0	0	2058	711	25	3	619	3	C1orf66	1	156703277	Nonsense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	422331	156703277	92547344	62	34354										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158641151	158641151	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	actatgatcttctcttcctgGgcagtaaaggcttcctcaaa	7	11	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:158641151G>T	ENST00000368147.4	-	12	1761	c.1581C>A	c.(1579-1581)gcC>gcA	p.A527A		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	527					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TCTCTTCCTGGGCAGTAAAGG	0.468																																					p.A527A		Atlas-SNP	.											.	SPTA1	720	.	0			c.C1581A						.						103	98	99					1																	158641151		1849	4092	5941	SO:0001819	synonymous_variant	6708	exon12			TTCCTGGGCAGTA	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.1581C>A	chr1.hg19:g.158641151G>T		141.0	0.0		203.0	9.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Silent	SNP	ENST00000368147.4	hg19	CCDS41423.1																																																																																			.	.		0.468	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		T	158641151	G	T	158641151	2	4	254	1	0	0	0	0	0	0	0	1	15131	1219	43	3		3	SPTA1	1	158641151	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1937874	158641151	90609470	63	34355										
APCS	325	hgsc.bcm.edu	37	chr1	159558025	159558025	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtgatctctctcgtgcctacAgcctcttctcctacaatacc	5	16	4	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:159558025A>T	ENST00000255040.2	+	2	296	c.199A>T	c.(199-201)Agc>Tgc	p.S67C		NM_001639.3	NP_001630.1	P02743	SAMP_HUMAN	amyloid P component, serum	67	Pentaxin.				acute-phase response (GO:0006953)|chaperone-mediated protein complex assembly (GO:0051131)|innate immune response (GO:0045087)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of exo-alpha-sialidase activity (GO:1903016)|negative regulation of glycoprotein metabolic process (GO:1903019)|negative regulation of monocyte differentiation (GO:0045656)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral process (GO:0048525)|negative regulation of wound healing (GO:0061045)|protein folding (GO:0006457)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|complement component C1q binding (GO:0001849)|unfolded protein binding (GO:0051082)|virion binding (GO:0046790)			breast(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(2)	20	all_hematologic(112;0.0429)					TCGTGCCTACAGCCTCTTCTC	0.413																																					p.S67C		Atlas-SNP	.											.	APCS	48	.	0			c.A199T						.						116	115	115					1																	159558025		2203	4300	6503	SO:0001583	missense	325	exon2			GCCTACAGCCTCT		CCDS1186.1	1q21-q23	2012-10-02			ENSG00000132703	ENSG00000132703			584	protein-coding gene	gene with protein product	"pentaxin-related", "9.5S alpha-1-glycoprotein"	104770				2987268	Standard	NM_001639		Approved	SAP, PTX2, MGC88159	uc001ftv.3	P02743	OTTHUMG00000022741	ENST00000255040.2:c.199A>T	chr1.hg19:g.159558025A>T	ENSP00000255040:p.Ser67Cys	90.0	0.0		179.0	14.0	NM_001639		Missense_Mutation	SNP	ENST00000255040.2	hg19	CCDS1186.1	.	.	.	.	.	.	.	.	.	.	A	13.84	2.358230	0.41801	.	.	ENSG00000132703	ENST00000255040	T	0.09817	2.94	4.45	4.45	0.53987	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.268199	0.41294	D	0.000916	T	0.27384	0.0672	M	0.91300	3.195	0.41910	D	0.990463	D	0.89917	1.0	D	0.91635	0.999	T	0.12941	-1.0528	10	0.87932	D	0	-18.5039	7.5418	0.27742	0.8092:0.0:0.0:0.1908	.	67	P02743	SAMP_HUMAN	C	67	ENSP00000255040:S67C	ENSP00000255040:S67C	S	+	1	0	APCS	157824649	0.957000	0.32711	0.895000	0.35142	0.023000	0.10783	2.214000	0.42853	1.984000	0.57885	0.533000	0.62120	AGC	.	.		0.413	APCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059024.2	NM_001639		T	159558025	A	T	159558025	3	4	254	1	0	0	0	0	1	0	0	0	767	188	7	4	205	4	APCS	1	159558025	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	916874	159558025	89692596	64	34356										
CD84	8832	hgsc.bcm.edu	37	chr1	160519720	160519720	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gggttaccttatcagcaaacTgcacttcggaataaactgtg	9	9	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:160519720T>C	ENST00000311224.4	-	7	1025	c.959A>G	c.(958-960)cAg>cGg	p.Q320R	CD84_ENST00000368051.3_Silent_p.A270A|CD84_ENST00000534968.1_Missense_Mutation_p.Q189R|CD84_ENST00000368048.3_Missense_Mutation_p.Q314R|RP11-528G1.2_ENST00000446952.1_RNA|CD84_ENST00000368054.3_Missense_Mutation_p.Q303R	NM_001184879.1	NP_001171808.1	Q9UIB8	SLAF5_HUMAN	CD84 molecule	320					blood coagulation (GO:0007596)|defense response (GO:0006952)|homophilic cell adhesion (GO:0007156)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.Q303L(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(1)	24	all_cancers(52;3.62e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			ATCAGCAAACTGCACTTCGGA	0.512																																					p.Q320R		Atlas-SNP	.											CD84_ENST00000311224,NS,carcinoma,0,2	CD84	71	.	1	Substitution - Missense(1)	lung(1)	c.A959G						.						127	115	119					1																	160519720		2203	4300	6503	SO:0001583	missense	8832	exon7			GCAAACTGCACTT	AF054816	CCDS1206.1, CCDS53395.1, CCDS53396.1, CCDS53397.1	1q24	2013-01-11	2006-03-31		ENSG00000066294	ENSG00000066294		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1704	protein-coding gene	gene with protein product		604513	"CD84 antigen (leukocyte antigen)", "CD84 molecule "			9310491	Standard	NM_003874		Approved	SLAMF5, hCD84, mCD84	uc001fwh.4	Q9UIB8	OTTHUMG00000022788	ENST00000311224.4:c.959A>G	chr1.hg19:g.160519720T>C	ENSP00000312367:p.Gln320Arg	90.0	0.0		69.0	3.0	NM_001184879	B2R8T1|B7Z3R8|O15430|O95266|O95660|Q5H9R1|Q6FHA8|Q8WLP1|Q8WWI8|Q9UF04|Q9UIB6|Q9UIB7|Q9UIT7	Missense_Mutation	SNP	ENST00000311224.4	hg19	CCDS53396.1	.	.	.	.	.	.	.	.	.	.	T	13.79	2.343616	0.41498	.	.	ENSG00000066294	ENST00000534968;ENST00000368054;ENST00000368048;ENST00000311224	T;T;T;T	0.63913	2.11;-0.07;-0.02;0.01	4.51	3.38	0.38709	.	0.349704	0.25549	N	0.029904	T	0.33498	0.0865	.	.	.	0.31601	N	0.652746	B;P;P;P	0.45474	0.202;0.779;0.859;0.859	B;B;B;B	0.41571	0.111;0.197;0.36;0.36	T	0.14117	-1.0484	9	0.39692	T	0.17	-2.9994	6.8508	0.24014	0.0:0.1056:0.0:0.8944	.	189;320;314;303	Q9UIB8-7;Q9UIB8;Q9UIB8-2;Q9UIB8-3	.;SLAF5_HUMAN;.;.	R	189;303;314;320	ENSP00000442845:Q189R;ENSP00000357033:Q303R;ENSP00000357027:Q314R;ENSP00000312367:Q320R	ENSP00000312367:Q320R	Q	-	2	0	CD84	158786344	0.987000	0.35691	0.684000	0.30055	0.020000	0.10135	1.959000	0.40412	0.864000	0.35578	0.460000	0.39030	CAG	.	.		0.512	CD84-003	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059092.1	NM_003874		C	160519720	T	C	160519720	3	2	254	1	0	0	0	0	1	0	0	0	3044	1580	55	2	86	2	CD84	1	160519720	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	961695	160519720	88730901	65	34357										
CD48	962	hgsc.bcm.edu	37	chr1	160648872	160648872	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aacaggccaagaatggtgggCaccgtgaccactagccaact	11	12	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:160648872C>T	ENST00000368046.3	-	4	789	c.702G>A	c.(700-702)gtG>gtA	p.V234V	RP11-404F10.2_ENST00000443928.2_RNA|RP11-404F10.2_ENST00000588034.1_RNA|RP11-404F10.2_ENST00000598917.2_RNA	NM_001778.3	NP_001769.2	P09326	CD48_HUMAN	CD48 molecule	234					blood coagulation (GO:0007596)|defense response (GO:0006952)|leukocyte migration (GO:0050900)|mast cell activation (GO:0045576)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	anchored component of plasma membrane (GO:0046658)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(2)|endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|stomach(1)	10	all_cancers(52;2.18e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			GAATGGTGGGCACCGTGACCA	0.453																																					p.V234V		Atlas-SNP	.											.	CD48	31	.	0			c.G702A						.						120	112	115					1																	160648872		2203	4300	6503	SO:0001819	synonymous_variant	962	exon4			GGTGGGCACCGTG	BC016182	CCDS1208.1, CCDS72955.1	1q21.3-q22	2013-01-29	2006-03-31		ENSG00000117091	ENSG00000117091		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1683	protein-coding gene	gene with protein product		109530	"CD48 antigen (B-cell membrane protein)", "CD48 molecule "	BCM1		2828034	Standard	NM_001256030		Approved	BLAST, mCD48, hCD48, SLAMF2	uc001fwo.2	P09326	OTTHUMG00000024009	ENST00000368046.3:c.702G>A	chr1.hg19:g.160648872C>T		134.0	0.0		136.0	44.0	NM_001778	Q5U055|Q8MGR0	Silent	SNP	ENST00000368046.3	hg19	CCDS1208.1																																																																																			.	.		0.453	CD48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060471.1	NM_001778		T	160648872	C	T	160648872	2	4	254	1	0	0	0	0	0	0	0	1	3022	697	25	3		3	CD48	1	160648872	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	129152	160648872	88601749	66	34358										
PPOX	5498	hgsc.bcm.edu	37	chr1	161138329	161138329	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctcttccaagctgagcaaacCcatcgttccatattactggg	7	13	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:161138329C>A	ENST00000367999.4	+	6	845	c.579C>A	c.(577-579)acC>acA	p.T193T	PPOX_ENST00000495483.1_3'UTR|PPOX_ENST00000535223.1_Intron|PPOX_ENST00000432542.2_Intron|B4GALT3_ENST00000470882.1_5'Flank|PPOX_ENST00000544598.1_Intron|PPOX_ENST00000352210.5_Silent_p.T193T	NM_001122764.1	NP_001116236.1	P50336	PPOX_HUMAN	protoporphyrinogen oxidase	193					heme biosynthetic process (GO:0006783)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound biosynthetic process (GO:0006779)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)	integral component of mitochondrial inner membrane (GO:0031305)|intrinsic component of mitochondrial inner membrane (GO:0031304)|mitochondrial intermembrane space (GO:0005758)|mitochondrial membrane (GO:0031966)	flavin adenine dinucleotide binding (GO:0050660)|oxygen-dependent protoporphyrinogen oxidase activity (GO:0004729)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(3)	15	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			CTGAGCAAACCCATCGTTCCA	0.547																																					p.T193T		Atlas-SNP	.											.	PPOX	34	.	0			c.C579A						.						100	87	91					1																	161138329		2203	4300	6503	SO:0001819	synonymous_variant	5498	exon6			GCAAACCCATCGT	BC002357	CCDS1221.1	1q22	2008-02-05			ENSG00000143224	ENSG00000143224	1.3.3.4		9280	protein-coding gene	gene with protein product		600923	"variegate porphyria"	VP		8575762, 10457135	Standard	NM_000309		Approved	PPO	uc001fyg.2	P50336	OTTHUMG00000034342	ENST00000367999.4:c.579C>A	chr1.hg19:g.161138329C>A		106.0	0.0		94.0	4.0	NM_000309	D3DVG0|Q5VTW8	Silent	SNP	ENST00000367999.4	hg19	CCDS1221.1	.	.	.	.	.	.	.	.	.	.	C	9.098	1.003320	0.19121	.	.	ENSG00000143224	ENST00000537523	.	.	.	5.23	-0.285	0.12866	.	.	.	.	.	T	0.36331	0.0963	.	.	.	0.58432	D	0.999998	.	.	.	.	.	.	T	0.26087	-1.0113	4	.	.	.	-24.08	6.4416	0.21853	0.6146:0.2279:0.0:0.1574	.	.	.	.	H	6	.	.	P	+	2	0	PPOX	159404953	0.000000	0.05858	0.985000	0.45067	0.987000	0.75469	-0.749000	0.04813	0.067000	0.16545	-0.188000	0.12872	CCC	.	.		0.547	PPOX-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082993.1	NM_000309		A	161138329	C	A	161138329	2	1	254	1	0	0	0	0	0	0	0	1	12360	610	22	3		3	PPOX	1	161138329	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	489457	161138329	88112292	67	34359										
DDR2	4921	hgsc.bcm.edu	37	chr1	162743270	162743270	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tttgtctaggttcatctctgTgaagtggagggaatggaaaa	13	4	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:162743270T>C	ENST00000367922.3	+	15	2178	c.1740T>C	c.(1738-1740)tgT>tgC	p.C580C	DDR2_ENST00000367921.3_Silent_p.C580C	NM_001014796.1	NP_001014796.1	Q16832	DDR2_HUMAN	discoidin domain receptor tyrosine kinase 2	580	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|chondrocyte proliferation (GO:0035988)|collagen fibril organization (GO:0030199)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|endochondral bone growth (GO:0003416)|extracellular matrix organization (GO:0030198)|ossification (GO:0001503)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of extracellular matrix disassembly (GO:0090091)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autophosphorylation (GO:0046777)|regulation of bone mineralization (GO:0030500)|regulation of extracellular matrix disassembly (GO:0010715)|signal transduction (GO:0007165)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(2)|kidney(1)|lung(2)|ovary(1)|skin(1)	7	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.113)		Regorafenib(DB08896)	TTCATCTCTGTGAAGTGGAGG	0.448																																					p.C580C	NSCLC(161;314 2006 8283 19651 23192)	Atlas-SNP	.											.	DDR2	228	.	0			c.T1740C						.						114	109	111					1																	162743270		2203	4300	6503	SO:0001819	synonymous_variant	4921	exon15			TCTCTGTGAAGTG	AK095975	CCDS1241.1	1q12-q23	2009-07-10	2008-01-23		ENSG00000162733	ENSG00000162733	2.7.10.1		2731	protein-coding gene	gene with protein product		191311	"discoidin domain receptor family, member 2"	TYRO10, NTRKR3		9659899	Standard	XM_005245221		Approved	TKT	uc001gcg.3	Q16832	OTTHUMG00000034423	ENST00000367922.3:c.1740T>C	chr1.hg19:g.162743270T>C		112.0	0.0		117.0	5.0	NM_001014796	Q7Z730	Silent	SNP	ENST00000367922.3	hg19	CCDS1241.1																																																																																			.	.		0.448	DDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083213.2	NM_006182		C	162743270	T	C	162743270	2	2	254	1	0	0	0	0	0	0	0	1	4339	1702	59	2		2	DDR2	1	162743270	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	1604941	162743270	86507351	68	34360										
ALDH9A1	223	hgsc.bcm.edu	37	chr1	165664622	165664622	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctcctgaacatgtgaaagtaGctatcactcggcctataaag	8	10	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:165664622G>T	ENST00000354775.4	-	2	498	c.194C>A	c.(193-195)gCt>gAt	p.A65D	ALDH9A1_ENST00000538148.1_5'UTR|ALDH9A1_ENST00000461664.1_5'UTR	NM_000696.3	NP_000687.3	P49189	AL9A1_HUMAN	aldehyde dehydrogenase 9 family, member A1	41					carnitine biosynthetic process (GO:0045329)|cellular aldehyde metabolic process (GO:0006081)|cellular nitrogen compound metabolic process (GO:0034641)|hormone metabolic process (GO:0042445)|kidney development (GO:0001822)|liver development (GO:0001889)|neurotransmitter biosynthetic process (GO:0042136)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	1-pyrroline dehydrogenase activity (GO:0033737)|3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|4-trimethylammoniobutyraldehyde dehydrogenase activity (GO:0047105)|aldehyde dehydrogenase (NAD) activity (GO:0004029)|amine binding (GO:0043176)|aminobutyraldehyde dehydrogenase activity (GO:0019145)|NAD binding (GO:0051287)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	21	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)					TGTGAAAGTAGCTATCACTCG	0.343																																					p.A65D	Ovarian(179;1583 2014 18106 33801 42447)	Atlas-SNP	.											.	ALDH9A1	75	.	0			c.C194A						.						92	92	92					1																	165664622		2203	4300	6503	SO:0001583	missense	223	exon2			AAAGTAGCTATCA	U34252	CCDS1250.2	1q22-q23	2008-02-05			ENSG00000143149	ENSG00000143149		"Aldehyde dehydrogenases"	412	protein-coding gene	gene with protein product		602733		ALDH7, ALDH4, ALDH9		8112751, 8786138	Standard	NM_000696		Approved	E3	uc001gdh.1	P49189	OTTHUMG00000034677	ENST00000354775.4:c.194C>A	chr1.hg19:g.165664622G>T	ENSP00000346827:p.Ala65Asp	98.0	0.0		96.0	4.0	NM_000696	B2R6X1|B4DXY7|Q5VV90|Q6LCL1|Q9NZT7	Missense_Mutation	SNP	ENST00000354775.4	hg19	CCDS1250.2	.	.	.	.	.	.	.	.	.	.	G	17.63	3.437233	0.62955	.	.	ENSG00000143149	ENST00000354775	T	0.79247	-1.25	5.44	4.52	0.55395	.	0.149162	0.64402	D	0.000010	T	0.78824	0.4344	M	0.76170	2.325	0.33790	D	0.625315	D;D	0.56035	0.974;0.974	P;P	0.53809	0.645;0.735	T	0.82948	-0.0204	9	0.72032	D	0.01	.	13.8734	0.63634	0.0:0.1542:0.8458:0.0	.	55;65	B4DX14;B9EKV4	.;.	D	65	ENSP00000346827:A65D	ENSP00000346827:A65D	A	-	2	0	ALDH9A1	163931246	0.511000	0.26179	0.961000	0.40146	0.730000	0.41778	1.493000	0.35605	1.256000	0.44068	0.655000	0.94253	GCT	.	.		0.343	ALDH9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083899.1			T	165664622	G	T	165664622	3	4	254	1	0	0	0	0	1	0	0	0	506	971	34	3	1402	3	ALDH9A1	1	165664622	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	2921352	165664622	83585999	69	34361										
DPT	1805	hgsc.bcm.edu	37	chr1	168670334	168670334	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aatcatgtccatttcctcacCatagtgacctggatattctg	6	11	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:168670334C>A	ENST00000367817.3	-	3	549	c.460G>T	c.(460-462)Ggt>Tgt	p.G154C		NM_001937.4	NP_001928.2	Q07507	DERM_HUMAN	dermatopontin	154	2 X 53-55 AA tandem repeats.|3 X 6 AA repeats of D-R-[EQ]-W-[NQK]- [FY].				cell adhesion (GO:0007155)|collagen fibril organization (GO:0030199)|negative regulation of cell proliferation (GO:0008285)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)	12	all_hematologic(923;0.208)					ATTTCCTCACCATAGTGACCT	0.418																																					p.G154C		Atlas-SNP	.											.	DPT	29	.	0			c.G460T						.						197	186	190					1																	168670334		2203	4300	6503	SO:0001583	missense	1805	exon3			CCTCACCATAGTG	BC033736	CCDS1275.1	1q12-q23	2008-02-05			ENSG00000143196	ENSG00000143196			3011	protein-coding gene	gene with protein product		125597				8104875	Standard	NM_001937		Approved		uc001gfp.3	Q07507	OTTHUMG00000034554	ENST00000367817.3:c.460G>T	chr1.hg19:g.168670334C>A	ENSP00000356791:p.Gly154Cys	98.0	0.0		94.0	5.0	NM_001937	A8K981|Q8N4R2|Q9UIX8	Missense_Mutation	SNP	ENST00000367817.3	hg19	CCDS1275.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.166262	0.78339	.	.	ENSG00000143196	ENST00000367817	T	0.46819	0.86	5.72	5.72	0.89469	.	0.099859	0.64402	D	0.000002	T	0.54303	0.1850	L	0.51422	1.61	0.43199	D	0.995045	D	0.71674	0.998	D	0.64237	0.923	T	0.45160	-0.9280	9	0.36615	T	0.2	-18.1772	18.7179	0.91682	0.0:1.0:0.0:0.0	.	154	Q07507	DERM_HUMAN	C	154	ENSP00000356791:G154C	ENSP00000356791:G154C	G	-	1	0	DPT	166936958	1.000000	0.71417	0.982000	0.44146	0.999000	0.98932	4.649000	0.61433	2.697000	0.92050	0.644000	0.83932	GGT	.	.		0.418	DPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083618.1	NM_001937		A	168670334	C	A	168670334	3	1	254	1	0	0	0	0	1	0	0	0	4741	594	21	3	153	3	DPT	1	168670334	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	3005712	168670334	80580287	70	34362										
C1orf112	55732	hgsc.bcm.edu	37	chr1	169806089	169806089	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tggagtttatccagaaatttTccccaaaagaagcagaaaat	7	7	0	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:169806089T>C	ENST00000286031.6	+	17	2261	c.1561T>C	c.(1561-1563)Tcc>Ccc	p.S521P	C1orf112_ENST00000359326.4_Missense_Mutation_p.S521P|C1orf112_ENST00000498289.1_3'UTR	NM_018186.2	NP_060656.2	Q9NSG2	CA112_HUMAN	chromosome 1 open reading frame 112	521										breast(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|stomach(1)	34	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					CCAGAAATTTTCCCCAAAAGA	0.398																																					p.S521P		Atlas-SNP	.											.,1	C1orf112	74	.	0			c.T1561C						.						49	49	49					1																	169806089		2203	4300	6503	SO:0001583	missense	55732	exon17			AAATTTTCCCCAA	AL354614	CCDS1285.1	1q24.2	2012-06-26			ENSG00000000460	ENSG00000000460			25565	protein-coding gene	gene with protein product						12477932	Standard	NM_018186		Approved	FLJ10706	uc001ggq.3	Q9NSG2	OTTHUMG00000035821	ENST00000286031.6:c.1561T>C	chr1.hg19:g.169806089T>C	ENSP00000286031:p.Ser521Pro	34.0	0.0		36.0	2.0	NM_018186	A6NFP1|B3KU42|Q3KNQ1|Q9H8L5|Q9NVJ0	Missense_Mutation	SNP	ENST00000286031.6	hg19	CCDS1285.1	.	.	.	.	.	.	.	.	.	.	T	13.06	2.122968	0.37436	.	.	ENSG00000000460	ENST00000359326;ENST00000286031	T;T	0.47528	0.84;0.84	6.03	-4.92	0.03075	.	0.250031	0.47852	N	0.000209	T	0.06188	0.0160	N	0.05351	-0.065	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.003	T	0.37549	-0.9701	10	0.02654	T	1	-0.5306	9.9667	0.41730	0.0:0.5133:0.1127:0.374	.	463;521	B4DGF2;Q9NSG2	.;CA112_HUMAN	P	521	ENSP00000352276:S521P;ENSP00000286031:S521P	ENSP00000286031:S521P	S	+	1	0	C1orf112	168072713	0.031000	0.19500	0.800000	0.32199	0.962000	0.63368	-0.984000	0.03755	-0.669000	0.05289	0.533000	0.62120	TCC	.	.		0.398	C1orf112-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087126.3	NM_018186		C	169806089	T	C	169806089	3	2	254	1	0	0	0	0	1	0	0	0	1987	1783	62	2	1619	2	C1orf112	1	169806089	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	1135755	169806089	79444532	71	34363										
FMO3	2328	hgsc.bcm.edu	37	chr1	171076816	171076816	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tctttctgtatttctcttagAcatttgtatccagtgtaaat	5	7	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:171076816A>G	ENST00000367755.4	+	4	433	c.322A>G	c.(322-324)Aca>Gca	p.T108A	FMO3_ENST00000392085.2_Splice_Site_p.T108A|FMO3_ENST00000542847.1_Splice_Site_p.T88A|FMO3_ENST00000538429.1_Splice_Site_p.T45A	NM_001002294.2	NP_001002294.1	P31513	FMO3_HUMAN	flavin containing monooxygenase 3	108					drug metabolic process (GO:0017144)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	amino acid binding (GO:0016597)|flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)|trimethylamine monooxygenase activity (GO:0034899)			endometrium(1)|kidney(1)|large_intestine(12)|lung(12)|skin(1)|stomach(2)|urinary_tract(2)	31	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)				Almotriptan(DB00918)|Cimetidine(DB00501)|Clozapine(DB00363)|Dapsone(DB00250)|Dasatinib(DB01254)|Olanzapine(DB00334)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582)	TTTCTCTTAGACATTTGTATC	0.348																																					p.T108A		Atlas-SNP	.											.	FMO3	73	.	0			c.A322G						.						78	78	78					1																	171076816		2203	4300	6503	SO:0001630	splice_region_variant	2328	exon4			TCTTAGACATTTG	BC032016	CCDS1292.1	1q24.3	2013-10-01			ENSG00000007933	ENSG00000007933	2.6.1.16		3771	protein-coding gene	gene with protein product		136132				8486388, 9417913	Standard	NM_001002294		Approved		uc001ghh.3	P31513	OTTHUMG00000035505	ENST00000367755.4:c.322-1A>G	chr1.hg19:g.171076816A>G		156.0	0.0		143.0	6.0	NM_006894	B2R816|Q14854|Q8N5N5	Missense_Mutation	SNP	ENST00000367755.4	hg19	CCDS1292.1	.	.	.	.	.	.	.	.	.	.	A	19.75	3.885920	0.72410	.	.	ENSG00000007933	ENST00000367755;ENST00000392085;ENST00000542847;ENST00000538429	T;T;T;T	0.61392	0.11;0.11;0.11;0.11	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	T	0.71945	0.3400	M	0.88640	2.97	0.58432	D	0.999994	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.87578	0.998;0.985;0.996	T	0.77539	-0.2550	9	.	.	.	-13.2412	10.0866	0.42421	0.8497:0.0:0.0:0.1503	.	45;88;108	F5H261;F5GZZ8;P31513	.;.;FMO3_HUMAN	A	108;108;88;45	ENSP00000356729:T108A;ENSP00000375935:T108A;ENSP00000444073:T88A;ENSP00000439500:T45A	.	T	+	1	0	FMO3	169343440	1.000000	0.71417	0.998000	0.56505	0.895000	0.52256	7.079000	0.76829	1.787000	0.52448	0.482000	0.46254	ACA	.	.		0.348	FMO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086219.1	NM_006894	Missense_Mutation	G	171076816	A	G	171076816	5	3	254	1	0	0	0	0	0	0	1	0	5964	289	10	2	332	2	FMO3	1	171076816	Splice_Site	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	1270727	171076816	78173805	72	34364										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181684513	181684513	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agaaaataaaaatgctggaaCatccgccttagaaggtaagg	10	6	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:181684513C>T	ENST00000367573.2	+	9	1211	c.1211C>T	c.(1210-1212)aCa>aTa	p.T404I	CACNA1E_ENST00000358338.5_Missense_Mutation_p.T355I|CACNA1E_ENST00000526775.1_Missense_Mutation_p.T404I|CACNA1E_ENST00000367570.1_Missense_Mutation_p.T404I|CACNA1E_ENST00000367567.4_Missense_Mutation_p.T11I|CACNA1E_ENST00000360108.3_Missense_Mutation_p.T404I|CACNA1E_ENST00000357570.5_Missense_Mutation_p.T355I	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	404					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						AATGCTGGAACATCCGCCTTA	0.378																																					p.T404I		Atlas-SNP	.											.	CACNA1E	778	.	0			c.C1211T						.						56	54	55					1																	181684513		1850	4114	5964	SO:0001583	missense	777	exon9			CTGGAACATCCGC	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.1211C>T	chr1.hg19:g.181684513C>T	ENSP00000356545:p.Thr404Ile	67.0	0.0		96.0	5.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.227589	0.79576	.	.	ENSG00000198216	ENST00000524607;ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D;D	0.96265	-3.21;-3.21;-3.21;-3.21;-3.21;-3.96;-3.21;-3.21	5.36	5.36	0.76844	.	0.861229	0.10542	N	0.662567	D	0.94637	0.8271	N	0.17474	0.49	0.42244	D	0.991947	D;D	0.53745	0.962;0.962	P;P	0.49276	0.605;0.605	D	0.93198	0.6589	10	0.46703	T	0.11	.	19.0518	0.93050	0.0:1.0:0.0:0.0	.	404;404	Q15878-2;Q15878-3	.;.	I	404;404;404;355;355;11;404;404	ENSP00000432038:T404I;ENSP00000356542:T404I;ENSP00000434814:T404I;ENSP00000350183:T355I;ENSP00000351101:T355I;ENSP00000356539:T11I;ENSP00000353222:T404I;ENSP00000356545:T404I	ENSP00000350183:T355I	T	+	2	0	CACNA1E	179951136	0.880000	0.30214	0.253000	0.24343	0.823000	0.46562	2.290000	0.43531	2.673000	0.90976	0.650000	0.86243	ACA	.	.		0.378	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		T	181684513	C	T	181684513	3	4	254	1	0	0	0	0	1	0	0	0	2544	478	17	3	1245	3	CACNA1E	1	181684513	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	10607697	181684513	67566108	73	34365										
LAMC1	3915	hgsc.bcm.edu	37	chr1	183086467	183086467	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	acctgcagatgaggatgggtGgcgtgcggaacagagagatg	18	6	0	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:183086467G>T	ENST00000258341.4	+	9	1834	c.1577G>T	c.(1576-1578)tGg>tTg	p.W526L		NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	526	Laminin IV type A. {ECO:0000255|PROSITE- ProRule:PRU00458}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						GAGGATGGGTGGCGTGCGGAA	0.473																																					p.W526L		Atlas-SNP	.											.	LAMC1	176	.	0			c.G1577T						.						134	116	122					1																	183086467		2203	4300	6503	SO:0001583	missense	3915	exon9			ATGGGTGGCGTGC	J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"Laminins"	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.1577G>T	chr1.hg19:g.183086467G>T	ENSP00000258341:p.Trp526Leu	93.0	0.0		87.0	5.0	NM_002293	Q5VYE7	Missense_Mutation	SNP	ENST00000258341.4	hg19	CCDS1351.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.982234	0.93044	.	.	ENSG00000135862	ENST00000258341	T	0.32753	1.44	5.04	5.04	0.67666	Laminin B type IV (1);	0.117057	0.64402	D	0.000007	T	0.61664	0.2365	M	0.91140	3.18	0.80722	D	1	D	0.69078	0.997	P	0.59643	0.861	T	0.72404	-0.4304	10	0.62326	D	0.03	.	18.3933	0.90490	0.0:0.0:1.0:0.0	.	526	P11047	LAMC1_HUMAN	L	526	ENSP00000258341:W526L	ENSP00000258341:W526L	W	+	2	0	LAMC1	181353090	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.013000	0.93629	2.338000	0.79540	0.591000	0.81541	TGG	.	.		0.473	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293		T	183086467	G	T	183086467	3	4	254	1	0	0	0	0	1	0	0	0	8623	1357	47	3	1611	3	LAMC1	1	183086467	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1401954	183086467	66164154	74	34366										
CAMSAP1L1	23271	hgsc.bcm.edu	37	chr1	200708967	200708967	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cggtgaaagatgggggatgcTgcagaccccagggagatgag	18	7	0	5			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:200708967T>C	ENST00000236925.4	+	1	61	c.12T>C	c.(10-12)gcT>gcC	p.A4A	CAMSAP2_ENST00000413307.2_Silent_p.A4A|CAMSAP2_ENST00000358823.2_Silent_p.A4A			Q08AD1	CAMP2_HUMAN	calmodulin regulated spectrin-associated protein family, member 2	4					microtubule cytoskeleton organization (GO:0000226)|regulation of organelle organization (GO:0033043)	cytoplasm (GO:0005737)|microtubule minus-end (GO:0036449)	microtubule minus-end binding (GO:0051011)										TGGGGGATGCTGCAGACCCCA	0.592																																					p.A4A		Atlas-SNP	.											.	.	.	.	0			c.T12C						.						91	74	80					1																	200708967		2203	4300	6503	SO:0001819	synonymous_variant	23271	exon1			GGATGCTGCAGAC	AB029001	CCDS1404.1, CCDS72998.1, CCDS72999.1	1q32	2011-08-18	2011-08-18	2011-08-18	ENSG00000118200	ENSG00000118200			29188	protein-coding gene	gene with protein product		613775	"calmodulin regulated spectrin-associated protein 1-like 1"	CAMSAP1L1		15897902, 19508979	Standard	XM_005245040		Approved	KIAA1078	uc001gvk.3	Q08AD1	OTTHUMG00000035740	ENST00000236925.4:c.12T>C	chr1.hg19:g.200708967T>C		175.0	0.0		184.0	8.0	NM_203459	B1APG6|Q08AD2|Q6PGN8|Q96FB3|Q9UG20|Q9UPS4	Silent	SNP	ENST00000236925.4	hg19																																																																																				.	.		0.592	CAMSAP2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086956.2	NM_203459		C	200708967	T	C	200708967	2	2	254	1	0	0	0	0	0	0	0	1	2614	1567	55	2		2	CAMSAP1L1	1	200708967	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	17622500	200708967	48541654	75	34367										
CAMSAP1L1	23271	hgsc.bcm.edu	37	chr1	200817629	200817629	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	atagtcaagaaatgagtatcTtaaattcaaatatcaagtta	5	4	4	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:200817629T>C	ENST00000236925.4	+	12	1814	c.1765T>C	c.(1765-1767)Tta>Cta	p.L589L	CAMSAP2_ENST00000413307.2_Silent_p.L562L|CAMSAP2_ENST00000358823.2_Silent_p.L578L			Q08AD1	CAMP2_HUMAN	calmodulin regulated spectrin-associated protein family, member 2	589					microtubule cytoskeleton organization (GO:0000226)|regulation of organelle organization (GO:0033043)	cytoplasm (GO:0005737)|microtubule minus-end (GO:0036449)	microtubule minus-end binding (GO:0051011)										AATGAGTATCTTAAATTCAAA	0.348																																					p.L578L		Atlas-SNP	.											.	.	.	.	0			c.T1732C						.						44	45	45					1																	200817629		2202	4298	6500	SO:0001819	synonymous_variant	23271	exon11			AGTATCTTAAATT	AB029001	CCDS1404.1, CCDS72998.1, CCDS72999.1	1q32	2011-08-18	2011-08-18	2011-08-18	ENSG00000118200	ENSG00000118200			29188	protein-coding gene	gene with protein product		613775	"calmodulin regulated spectrin-associated protein 1-like 1"	CAMSAP1L1		15897902, 19508979	Standard	XM_005245040		Approved	KIAA1078	uc001gvk.3	Q08AD1	OTTHUMG00000035740	ENST00000236925.4:c.1765T>C	chr1.hg19:g.200817629T>C		103.0	0.0		100.0	4.0	NM_203459	B1APG6|Q08AD2|Q6PGN8|Q96FB3|Q9UG20|Q9UPS4	Silent	SNP	ENST00000236925.4	hg19																																																																																				.	.		0.348	CAMSAP2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086956.2	NM_203459		C	200817629	T	C	200817629	2	2	254	1	0	0	0	0	0	0	0	1	2614	1606	56	2		2	CAMSAP1L1	1	200817629	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	108662	200817629	48432992	76	34368										
DYRK3	8444	hgsc.bcm.edu	37	chr1	206822049	206822049	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	atagagttcttgaaaaggtgTcttcactgggacccctctgc	10	10	4	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:206822049T>C	ENST00000367109.2	+	3	1674	c.1506T>C	c.(1504-1506)tgT>tgC	p.C502C	DYRK3_ENST00000367106.1_Silent_p.C482C|DYRK3_ENST00000367108.3_Silent_p.C482C|DYRK3_ENST00000489878.1_Intron	NM_003582.2	NP_003573.2	O43781	DYRK3_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3	502	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				erythrocyte differentiation (GO:0030218)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(9)|lung(8)|skin(1)|stomach(2)	25	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)			TGAAAAGGTGTCTTCACTGGG	0.532																																					p.C502C	Melanoma(164;427 2622 26826 51707)	Atlas-SNP	.											.	DYRK3	146	.	0			c.T1506C						.						56	57	57					1																	206822049		2203	4300	6503	SO:0001819	synonymous_variant	8444	exon3			AAGGTGTCTTCAC	Y12735	CCDS30999.1, CCDS31000.1	1q32	2008-07-18			ENSG00000143479	ENSG00000143479	2.7.12.1		3094	protein-coding gene	gene with protein product	"regulatory erythroid kinase", "dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 5", "protein kinase Dyrk3"	603497				9748265	Standard	NM_003582		Approved	RED, REDK, hYAK3-2	uc001hej.3	O43781	OTTHUMG00000036339	ENST00000367109.2:c.1506T>C	chr1.hg19:g.206822049T>C		138.0	0.0		111.0	5.0	NM_003582	D3DT79|Q7Z752|Q9HBY6|Q9HBY7	Silent	SNP	ENST00000367109.2	hg19	CCDS30999.1																																																																																			.	.		0.532	DYRK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088458.1	NM_003582		C	206822049	T	C	206822049	2	2	254	1	0	0	0	0	0	0	0	1	4859	1673	58	2		2	DYRK3	1	206822049	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	6004420	206822049	42428572	77	34369										
C1orf116	79098	hgsc.bcm.edu	37	chr1	207195943	207195943	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gagctgcaggctgagccagaCctggagctggggacagatgc	17	10	0	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:207195943C>A	ENST00000359470.5	-	4	1415	c.1166G>T	c.(1165-1167)gGt>gTt	p.G389V	C1orf116_ENST00000461135.2_Missense_Mutation_p.G143V	NM_023938.5	NP_076427.2	Q9BW04	SARG_HUMAN	chromosome 1 open reading frame 116	389	Ala-rich.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)		p.G389A(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(4)|stomach(1)	29	Prostate(682;0.19)					ctgagccagacctggagctgg	0.622																																					p.G389V		Atlas-SNP	.											C1orf116,NS,carcinoma,0,1	C1orf116	64	.	1	Substitution - Missense(1)	lung(1)	c.G1166T						.						50	56	54					1																	207195943		2201	4300	6501	SO:0001583	missense	79098	exon4			GCCAGACCTGGAG		CCDS1475.1, CCDS44306.1	1q32.1	2012-06-26			ENSG00000182795	ENSG00000182795			28667	protein-coding gene	gene with protein product	"specifically androgen-regulated gene"	611680				15525603, 9389513	Standard	NM_023938		Approved	SARG, FLJ36507, MGC2742, MGC4309	uc001hfd.2	Q9BW04	OTTHUMG00000036580	ENST00000359470.5:c.1166G>T	chr1.hg19:g.207195943C>A	ENSP00000352447:p.Gly389Val	49.0	0.0		40.0	2.0	NM_023938	C9JV41|Q658X3	Missense_Mutation	SNP	ENST00000359470.5	hg19	CCDS1475.1	.	.	.	.	.	.	.	.	.	.	C	5.692	0.312305	0.10789	.	.	ENSG00000182795	ENST00000359470;ENST00000461135	T;T	0.16897	3.17;2.31	4.95	0.726	0.18248	.	1.401590	0.04545	N	0.388796	T	0.10852	0.0265	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34329	-0.9833	10	0.22109	T	0.4	2.5361	8.4468	0.32847	0.0:0.1417:0.3254:0.533	.	389	Q9BW04	SARG_HUMAN	V	389;143	ENSP00000352447:G389V;ENSP00000436862:G143V	ENSP00000352447:G389V	G	-	2	0	C1orf116	205262566	0.002000	0.14202	0.000000	0.03702	0.000000	0.00434	0.643000	0.24750	0.172000	0.19760	-3.036000	0.00072	GGT	.	.		0.622	C1orf116-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088973.1	NM_024115		A	207195943	C	A	207195943	3	1	254	1	0	0	0	0	1	0	0	0	1991	507	18	3	643	3	C1orf116	1	207195943	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	373894	207195943	42054678	78	34370										
IRF6	3664	hgsc.bcm.edu	37	chr1	209974642	209974642	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgccgggtggcatgtttccaGggaatctggaagcgtttaga	15	7	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:209974642G>A	ENST00000367021.3	-	3	289	c.117C>T	c.(115-117)ccC>ccT	p.P39P	IRF6_ENST00000542854.1_Intron	NM_006147.3	NP_006138.1	O14896	IRF6_HUMAN	interferon regulatory factor 6	39			P -> A (in VWS1). {ECO:0000269|PubMed:12219090}.		cell cycle arrest (GO:0007050)|cell development (GO:0048468)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|keratinocyte differentiation (GO:0030216)|keratinocyte proliferation (GO:0043616)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell proliferation (GO:0008285)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|large_intestine(4)|lung(12)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	28				OV - Ovarian serous cystadenocarcinoma(81;0.0351)		CATGTTTCCAGGGAATCTGGA	0.502										HNSCC(57;0.16)																											p.P39P		Atlas-SNP	.											.	IRF6	65	.	0			c.C117T						.						88	94	92					1																	209974642		2203	4300	6503	SO:0001819	synonymous_variant	3664	exon3			TTTCCAGGGAATC	AL022398	CCDS1492.1, CCDS55681.1	1q32.2-q32.3	2011-02-10			ENSG00000117595	ENSG00000117595			6121	protein-coding gene	gene with protein product		607199	"Van der Woude syndrome"	VWS, LPS		12219090	Standard	NM_006147		Approved	OFC6, VWS1	uc001hhq.2	O14896	OTTHUMG00000036521	ENST00000367021.3:c.117C>T	chr1.hg19:g.209974642G>A		101.0	0.0		79.0	4.0	NM_006147	B4DLE2|D3DT90|F5GWX8|G0ZTL0	Silent	SNP	ENST00000367021.3	hg19	CCDS1492.1																																																																																			.	.		0.502	IRF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088827.1	NM_006147		A	209974642	G	A	209974642	2	1	254	1	0	0	0	0	0	0	0	1	7843	987	35	3		3	IRF6	1	209974642	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	2778699	209974642	39275979	79	34371										
RPS6KC1	26750	hgsc.bcm.edu	37	chr1	213349823	213349823	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aaggccttcagagtccttggGgtgattgacaaggtaattct	12	7	2	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:213349823G>T	ENST00000366960.3	+	8	1182	c.1032G>T	c.(1030-1032)ggG>ggT	p.G344G	RPS6KC1_ENST00000366959.3_Silent_p.G332G|RPS6KC1_ENST00000543354.1_Silent_p.G47G|RPS6KC1_ENST00000543470.1_Intron|RPS6KC1_ENST00000490299.1_3'UTR	NM_012424.3	NP_036556.2	Q96S38	KS6C1_HUMAN	ribosomal protein S6 kinase, 52kDa, polypeptide 1	344	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(6)|kidney(4)|large_intestine(8)|liver(2)|lung(15)|ovary(3)|prostate(1)|urinary_tract(3)	43				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)		GAGTCCTTGGGGTGATTGACA	0.453																																					p.G344G		Atlas-SNP	.											.	RPS6KC1	114	.	0			c.G1032T						.						126	121	123					1																	213349823		2203	4300	6503	SO:0001819	synonymous_variant	26750	exon8			CCTTGGGGTGATT	AF037447	CCDS1513.1, CCDS44317.1, CCDS73028.1, CCDS73029.1, CCDS73030.1	1q41	2011-04-05	2002-08-29		ENSG00000136643	ENSG00000136643			10439	protein-coding gene	gene with protein product			"ribosomal protein S6 kinase, 52kD, polypeptide 1"			10552933	Standard	XM_005273095		Approved	humS6PKh1	uc010ptr.2	Q96S38	OTTHUMG00000036926	ENST00000366960.3:c.1032G>T	chr1.hg19:g.213349823G>T		111.0	0.0		123.0	5.0	NM_012424	B1APS8|B3KVM4|D3DTA4|Q8TDD3|Q9NSF4|Q9UL66	Silent	SNP	ENST00000366960.3	hg19	CCDS1513.1																																																																																			.	.		0.453	RPS6KC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089690.3	NM_012424		T	213349823	G	T	213349823	2	4	254	1	0	0	0	0	0	0	0	1	13673	1219	43	3		3	RPS6KC1	1	213349823	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	3375181	213349823	35900798	80	34372										
HHIPL2	79802	hgsc.bcm.edu	37	chr1	222717113	222717113	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gttgctccaggcgactcccaTcagggaggtagacccacacc	11	15	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:222717113T>C	ENST00000343410.6	-	2	798	c.740A>G	c.(739-741)gAt>gGt	p.D247G		NM_024746.3	NP_079022.2	Q6UWX4	HIPL2_HUMAN	HHIP-like 2	247					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)			NS(2)|endometrium(8)|kidney(4)|large_intestine(7)|lung(28)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59				GBM - Glioblastoma multiforme(131;0.0185)		GCGACTCCCATCAGGGAGGTA	0.592																																					p.D247G		Atlas-SNP	.											.	HHIPL2	122	.	0			c.A740G						.						85	79	81					1																	222717113		2203	4300	6503	SO:0001583	missense	79802	exon2			CTCCCATCAGGGA	BC007638	CCDS1530.2	1q41	2008-02-05	2008-01-16	2008-01-16	ENSG00000143512	ENSG00000143512			25842	protein-coding gene	gene with protein product			"KIAA1822-like"	KIAA1822L		12975309	Standard	NM_024746		Approved	FLJ13840	uc001hnh.1	Q6UWX4	OTTHUMG00000037545	ENST00000343410.6:c.740A>G	chr1.hg19:g.222717113T>C	ENSP00000342118:p.Asp247Gly	101.0	0.0		87.0	4.0	NM_024746	Q6GU65|Q96BT4|Q96BU5|Q9H8A0	Missense_Mutation	SNP	ENST00000343410.6	hg19	CCDS1530.2	.	.	.	.	.	.	.	.	.	.	T	13.39	2.223114	0.39300	.	.	ENSG00000143512	ENST00000343410	T	0.15256	2.44	5.31	4.18	0.49190	Soluble quinoprotein glucose/sorbosone dehydrogenase (1);Six-bladed beta-propeller, TolB-like (1);	0.099910	0.64402	N	0.000004	T	0.27832	0.0685	L	0.58669	1.825	0.49483	D	0.999797	P	0.46142	0.873	P	0.51945	0.685	T	0.01111	-1.1448	10	0.59425	D	0.04	-18.5314	10.4995	0.44798	0.0:0.0772:0.0:0.9228	.	247	Q6UWX4	HIPL2_HUMAN	G	247	ENSP00000342118:D247G	ENSP00000342118:D247G	D	-	2	0	HHIPL2	220783736	1.000000	0.71417	0.919000	0.36401	0.578000	0.36192	3.916000	0.56416	0.850000	0.35239	0.383000	0.25322	GAT	.	.		0.592	HHIPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091499.2	NM_024746		C	222717113	T	C	222717113	3	2	254	1	0	0	0	0	1	0	0	0	7103	1435	50	2	1466	2	HHIPL2	1	222717113	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	9367290	222717113	26533508	81	34373										
NVL	4931	hgsc.bcm.edu	37	chr1	224475675	224475675	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcttggtctcttagcaacccCagcagcctttgtaattcatc	6	13	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:224475675C>A	ENST00000281701.6	-	14	1855	c.1596G>T	c.(1594-1596)ctG>ctT	p.L532L	NVL_ENST00000361463.3_Silent_p.L426L|NVL_ENST00000340871.4_Silent_p.L343L|NVL_ENST00000482491.1_Silent_p.L256L|NVL_ENST00000391875.2_Silent_p.L426L|NVL_ENST00000469075.1_Silent_p.L441L	NM_002533.3	NP_002524.2	O15381	NVL_HUMAN	nuclear VCP-like	532						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|prostate(1)|skin(4)|soft_tissue(1)|urinary_tract(1)	42				GBM - Glioblastoma multiforme(131;0.00501)		TTAGCAACCCCAGCAGCCTTT	0.408																																					p.L532L		Atlas-SNP	.											.	NVL	74	.	0			c.G1596T						.						61	61	61					1																	224475675		2203	4300	6503	SO:0001819	synonymous_variant	4931	exon14			CAACCCCAGCAGC	U78772	CCDS1541.1, CCDS1542.1, CCDS58062.1, CCDS58063.1	1q41-q42.2	2010-04-21			ENSG00000143748	ENSG00000143748		"ATPases / AAA-type"	8070	protein-coding gene	gene with protein product	"Nuclear valosin-containing protein-like", "nuclear VCP-like protein"	602426				9286697	Standard	NM_002533		Approved		uc001hok.3	O15381	OTTHUMG00000037536	ENST00000281701.6:c.1596G>T	chr1.hg19:g.224475675C>A		66.0	0.0		70.0	4.0	NM_002533	B4DMC4|B4DP98|Q96EM7	Silent	SNP	ENST00000281701.6	hg19	CCDS1541.1	.	.	.	.	.	.	.	.	.	.	C	6.827	0.521689	0.13005	.	.	ENSG00000143748	ENST00000469968	.	.	.	5.58	3.38	0.38709	.	.	.	.	.	T	0.59004	0.2162	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55976	-0.8055	4	.	.	.	-9.0371	9.1489	0.36951	0.0:0.6816:0.1209:0.1976	.	.	.	.	W	415	.	.	G	-	1	0	NVL	222542298	0.950000	0.32346	0.830000	0.32933	0.843000	0.47879	2.100000	0.41777	1.358000	0.45922	-0.150000	0.13652	GGG	.	.		0.408	NVL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091453.2	NM_002533		A	224475675	C	A	224475675	2	1	254	1	0	0	0	0	0	0	0	1	10789	581	21	3		3	NVL	1	224475675	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1758562	224475675	24774946	82	34374										
EPHX1	2052	hgsc.bcm.edu	37	chr1	226027000	226027000	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gaattctacattcaaggaggGgactgggggtccctgatctg	14	8	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:226027000G>T	ENST00000366837.4	+	5	871	c.675G>T	c.(673-675)ggG>ggT	p.G225G	EPHX1_ENST00000272167.5_Silent_p.G225G|RP11-285F7.2_ENST00000424332.1_RNA	NM_000120.3	NP_000111.1	P07099	HYEP_HUMAN	epoxide hydrolase 1, microsomal (xenobiotic)	225					aromatic compound catabolic process (GO:0019439)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cis-stilbene-oxide hydrolase activity (GO:0033961)|epoxide hydrolase activity (GO:0004301)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(7)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	28	Breast(184;0.197)					TTCAAGGAGGGGACTGGGGGT	0.567																																					p.G225G		Atlas-SNP	.											.	EPHX1	57	.	0			c.G675T						.						75	83	80					1																	226027000		2203	4300	6503	SO:0001819	synonymous_variant	2052	exon5			AGGAGGGGACTGG	J03518	CCDS1547.1	1q42.1	2009-07-10			ENSG00000143819	ENSG00000143819	3.3.2.9		3401	protein-coding gene	gene with protein product		132810		EPHX		9925921	Standard	NM_000120		Approved		uc001hpk.3	P07099	OTTHUMG00000037743	ENST00000366837.4:c.675G>T	chr1.hg19:g.226027000G>T		151.0	0.0		133.0	6.0	NM_001136018	B2R8N0|Q5VTJ6|Q9NP75|Q9NPE7|Q9NQU6|Q9NQU7|Q9NQU8|Q9NQU9|Q9NQV0|Q9NQV1|Q9NQV2	Silent	SNP	ENST00000366837.4	hg19	CCDS1547.1																																																																																			.	.		0.567	EPHX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092064.1	NM_000120		T	226027000	G	T	226027000	2	4	254	1	0	0	0	0	0	0	0	1	5181	1219	43	3		3	EPHX1	1	226027000	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1551325	226027000	23223621	83	34375										
CNST	163882	hgsc.bcm.edu	37	chr1	246784775	246784775	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctttaatgcaagaaaaagtaCtaagcgcagtcacatatgct	7	8	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:246784775C>T	ENST00000366513.4	+	3	693	c.424C>T	c.(424-426)Cta>Tta	p.L142L	CNST_ENST00000366512.3_Silent_p.L142L|CNST_ENST00000483271.1_3'UTR	NM_152609.2	NP_689822.2	Q6PJW8	CNST_HUMAN	consortin, connexin sorting protein	142					negative regulation of phosphatase activity (GO:0010923)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)	connexin binding (GO:0071253)|phosphatase binding (GO:0019902)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|prostate(1)|urinary_tract(2)	28						AGAAAAAGTACTAAGCGCAGT	0.398																																					p.L142L		Atlas-SNP	.											.	CNST	73	.	0			c.C424T						.						201	207	205					1																	246784775		2203	4300	6503	SO:0001819	synonymous_variant	163882	exon3			AAAGTACTAAGCG	AK056563	CCDS1628.1, CCDS44343.1	1q44	2012-04-17	2009-11-03	2009-11-03	ENSG00000162852	ENSG00000162852		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	26486	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 64"	613439	"chromosome 1 open reading frame 71"	C1orf71		19864490	Standard	NM_152609		Approved	FLJ32001, PPP1R64	uc001ibp.3	Q6PJW8	OTTHUMG00000040090	ENST00000366513.4:c.424C>T	chr1.hg19:g.246784775C>T		68.0	0.0		92.0	4.0	NM_152609	Q5VSY9|Q5VTM7|Q8IYA9|Q8N3L5|Q8NB09|Q8TEI2|Q96MR5	Silent	SNP	ENST00000366513.4	hg19	CCDS1628.1																																																																																			.	.		0.398	CNST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096780.1	NM_152609		T	246784775	C	T	246784775	2	4	254	1	0	0	0	0	0	0	0	1	3636	564	20	3		3	CNST	1	246784775	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	20757775	246784775	2465846	84	34376										
OR6F1	343169	hgsc.bcm.edu	37	chr1	247875382	247875382	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	actggcagaggggatcctgaGgatggtgctgatgatgtaca	16	6	0	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr1:247875382G>T	ENST00000302084.2	-	1	723	c.676C>A	c.(676-678)Ctc>Atc	p.L226I	RP11-634B7.4_ENST00000449298.1_RNA	NM_001005286.1	NP_001005286.1	Q8NGZ6	OR6F1_HUMAN	olfactory receptor, family 6, subfamily F, member 1	226						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(1)|large_intestine(5)|lung(34)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)	47	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.0168)			GGGATCCTGAGGATGGTGCTG	0.522																																					p.L226I		Atlas-SNP	.											.	OR6F1	88	.	0			c.C676A						.						126	113	117					1																	247875382		2203	4300	6503	SO:0001583	missense	343169	exon1			TCCTGAGGATGGT	BK004460	CCDS31095.1	1q44	2012-08-09			ENSG00000169214	ENSG00000169214		"GPCR / Class A : Olfactory receptors"	15027	protein-coding gene	gene with protein product							Standard	NM_001005286		Approved	OST731	uc001idj.1	Q8NGZ6	OTTHUMG00000040213	ENST00000302084.2:c.676C>A	chr1.hg19:g.247875382G>T	ENSP00000305640:p.Leu226Ile	95.0	0.0		97.0	4.0	NM_001005286	B2RNV6|Q6IF02|Q96R39	Missense_Mutation	SNP	ENST00000302084.2	hg19	CCDS31095.1	.	.	.	.	.	.	.	.	.	.	G	4.335	0.061550	0.08339	.	.	ENSG00000169214	ENST00000302084	T	0.00302	8.2	3.72	-2.46	0.06461	GPCR, rhodopsin-like superfamily (1);	0.428415	0.17142	N	0.185383	T	0.00178	0.0005	L	0.58510	1.815	0.20703	N	0.999865	B	0.12630	0.006	B	0.16722	0.016	T	0.45440	-0.9261	10	0.54805	T	0.06	-23.7073	2.7977	0.05406	0.1689:0.253:0.4493:0.1288	.	226	Q8NGZ6	OR6F1_HUMAN	I	226	ENSP00000305640:L226I	ENSP00000305640:L226I	L	-	1	0	OR6F1	245942005	0.000000	0.05858	0.006000	0.13384	0.023000	0.10783	-2.281000	0.01157	-0.241000	0.09681	0.591000	0.81541	CTC	.	.		0.522	OR6F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096870.1	NM_001005286		T	247875382	G	T	247875382	3	4	254	1	0	0	0	0	1	0	0	0	11210	1000	35	3	254	3	OR6F1	1	247875382	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1090607	247875382	1375239	85	34377										
KIDINS220	57498	hgsc.bcm.edu	37	chr2	8919191	8919191	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aagcacactattgaggttctGgttaattgcctttatgataa	8	6	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:8919191G>T	ENST00000256707.3	-	19	2630	c.2449C>A	c.(2449-2451)Cag>Aag	p.Q817K	KIDINS220_ENST00000427284.1_Missense_Mutation_p.Q817K|KIDINS220_ENST00000319688.5_Missense_Mutation_p.Q818K|KIDINS220_ENST00000473731.1_Missense_Mutation_p.Q817K|KIDINS220_ENST00000418530.1_Missense_Mutation_p.Q775K	NM_020738.2	NP_065789.1	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate, 220kDa	817	KAP NTPase.				activation of MAPKK activity (GO:0000186)|cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|dendrite morphogenesis (GO:0048813)|in utero embryonic development (GO:0001701)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of neuron projection development (GO:0010976)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|protein complex (GO:0043234)	PDZ domain binding (GO:0030165)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(25)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	60	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					TTGAGGTTCTGGTTAATTGCC	0.418																																					p.Q817K		Atlas-SNP	.											.	KIDINS220	136	.	0			c.C2449A						.						210	189	195					2																	8919191		1858	4111	5969	SO:0001583	missense	57498	exon19			GGTTCTGGTTAAT	AK025528	CCDS42650.1	2p24	2013-01-10			ENSG00000134313	ENSG00000134313		"Ankyrin repeat domain containing"	29508	protein-coding gene	gene with protein product	"ankyrin repeat-rich membrane-spanning protein"	615759				10998417, 10574462	Standard	NM_020738		Approved	ARMS	uc002qzc.2	Q9ULH0	OTTHUMG00000151658	ENST00000256707.3:c.2449C>A	chr2.hg19:g.8919191G>T	ENSP00000256707:p.Gln817Lys	137.0	0.0		81.0	4.0	NM_020738	A1L4N4|Q4VC08|Q6MZU2|Q9H889|Q9H9E4|Q9NT37|Q9UF42	Missense_Mutation	SNP	ENST00000256707.3	hg19	CCDS42650.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.939734	0.92526	.	.	ENSG00000134313	ENST00000496383;ENST00000541927;ENST00000256707;ENST00000427284;ENST00000418530;ENST00000473731;ENST00000489024;ENST00000319688	T;T;T;T;T;T;T	0.28069	1.63;1.63;1.63;1.63;1.63;1.63;1.63	5.64	5.64	0.86602	KAP P-loop (1);	0.000000	0.85682	D	0.000000	T	0.53029	0.1771	L	0.53249	1.67	0.80722	D	1	D;D;D;D	0.69078	0.985;0.971;0.997;0.996	D;P;D;D	0.83275	0.981;0.796;0.992;0.996	T	0.32771	-0.9894	10	0.33940	T	0.23	.	20.0769	0.97748	0.0:0.0:1.0:0.0	.	818;818;775;817	B4DK94;E9PH70;Q9ULH0-2;Q9ULH0	.;.;.;KDIS_HUMAN	K	564;501;817;817;775;817;818;818	ENSP00000420364:Q564K;ENSP00000256707:Q817K;ENSP00000411849:Q817K;ENSP00000414923:Q775K;ENSP00000418974:Q817K;ENSP00000419964:Q818K;ENSP00000319947:Q818K	ENSP00000256707:Q817K	Q	-	1	0	KIDINS220	8836642	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.506000	0.97992	2.820000	0.97059	0.650000	0.86243	CAG	.	.		0.418	KIDINS220-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323408.2	NM_020738		T	8919191	G	T	8919191	3	4	254	1	0	0	0	0	1	0	0	0	8280	1357	47	3	2914	3	KIDINS220	2	8919191	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10		8919191	234280182	86	34378										
WDR35	57539	hgsc.bcm.edu	37	chr2	20133274	20133274	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	caaacatttgtgctatttccTgtacaaacaaaacaatacta	3	9	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:20133274T>C	ENST00000345530.3	-	23	2696		c.e23-2		WDR35_ENST00000416055.2_Intron|WDR35_ENST00000281405.4_Splice_Site	NM_001006657.1	NP_001006658.1	Q9P2L0	WDR35_HUMAN	WD repeat domain 35						cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)				breast(1)|endometrium(5)|kidney(8)|large_intestine(8)|lung(16)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGCTATTTCCTGTACAAACAA	0.343																																					.		Atlas-SNP	.											.	WDR35	92	.	0			c.2548-2A>G						.						99	86	91					2																	20133274		2203	4300	6503	SO:0001630	splice_region_variant	57539	exon23			ATTTCCTGTACAA	AB037757	CCDS1695.1, CCDS33152.1	2p24.3	2014-02-21			ENSG00000118965	ENSG00000118965		"WD repeat domain containing", "Intraflagellar transport homologs"	29250	protein-coding gene	gene with protein product		613602				10718198	Standard	NM_001006657		Approved	MGC33196, KIAA1336, IFT121, IFTA1	uc002rdi.3	Q9P2L0	OTTHUMG00000090737	ENST00000345530.3:c.2581-2A>G	chr2.hg19:g.20133274T>C		63.0	0.0		91.0	4.0	NM_020779	B3KVI5|Q4ZG01|Q8NE11	Splice_Site	SNP	ENST00000345530.3	hg19	CCDS33152.1	.	.	.	.	.	.	.	.	.	.	T	19.98	3.926318	0.73327	.	.	ENSG00000118965	ENST00000345530;ENST00000281405	.	.	.	5.1	5.1	0.69264	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3615	0.66773	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	WDR35	19996755	1.000000	0.71417	0.997000	0.53966	0.857000	0.48899	7.661000	0.83786	2.049000	0.60858	0.460000	0.39030	.	.	.		0.343	WDR35-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000207472.2	NM_020779	Intron	C	20133274	T	C	20133274	5	2	254	1	0	0	0	0	0	0	1	0	17304	1594	55	2	990	2	WDR35	2	20133274	Splice_Site	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	11214083	20133274	223066099	87	34379										
C2orf44	80304	hgsc.bcm.edu	37	chr2	24261602	24261602	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	atccatagagcgtacttcacCaataactggtaaagcatacg	7	10	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:24261602C>A	ENST00000295148.4	-	2	820	c.763G>T	c.(763-765)Ggt>Tgt	p.G255C	C2orf44_ENST00000406895.3_Missense_Mutation_p.G255C	NM_025203.2	NP_079479.1	Q9H6R7	CB044_HUMAN	chromosome 2 open reading frame 44	255									C2orf44/ALK(2)	breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CGTACTTCACCAATAACTGGT	0.378			T	ALK	NSCLC																																p.G255C		Atlas-SNP	.		Dom	yes		2	2p23.3	80304	chromosome 2 open reading frame 44		E	.	C2orf44	56	.	0			c.G763T						.						84	83	84					2																	24261602		2203	4300	6503	SO:0001583	missense	80304	exon2			CTTCACCAATAAC	AK025598	CCDS1705.1, CCDS46229.1	2p23.3	2012-07-30			ENSG00000163026	ENSG00000163026			26157	protein-coding gene	gene with protein product						22327622	Standard	NM_025203		Approved	FLJ21945	uc002rep.2	Q9H6R7	OTTHUMG00000125498	ENST00000295148.4:c.763G>T	chr2.hg19:g.24261602C>A	ENSP00000295148:p.Gly255Cys	121.0	0.0		112.0	5.0	NM_025203	D6W532|Q8IYK0|Q9HBP5	Missense_Mutation	SNP	ENST00000295148.4	hg19	CCDS1705.1	.	.	.	.	.	.	.	.	.	.	C	10.57	1.387681	0.25031	.	.	ENSG00000163026	ENST00000295148;ENST00000406895	T;T	0.48201	0.82;0.82	5.51	1.67	0.24075	WD40/YVTN repeat-like-containing domain (1);	0.820821	0.11399	N	0.568010	T	0.38453	0.1041	N	0.08118	0	0.09310	N	1	D;D	0.63046	0.992;0.992	P;P	0.53360	0.724;0.724	T	0.33599	-0.9862	10	0.62326	D	0.03	-0.0589	10.773	0.46334	0.0:0.7279:0.0:0.2721	.	255;255	Q9H6R7-2;Q9H6R7	.;CB044_HUMAN	C	255	ENSP00000295148:G255C;ENSP00000385816:G255C	ENSP00000295148:G255C	G	-	1	0	C2orf44	24115106	0.001000	0.12720	0.000000	0.03702	0.010000	0.07245	1.518000	0.35877	0.394000	0.25230	-0.136000	0.14681	GGT	.	.		0.378	C2orf44-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246825.1	NM_025203		A	24261602	C	A	24261602	3	1	254	1	0	0	0	0	1	0	0	0	2170	594	21	3	1414	3	C2orf44	2	24261602	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	4128328	24261602	218937771	88	34380										
HADHA	3030	hgsc.bcm.edu	37	chr2	26453120	26453120	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgccctgtctgcacgaatgcTtctaccagtcagcatcatgt	8	13	4	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:26453120T>C	ENST00000380649.3	-	7	745	c.616A>G	c.(616-618)Agc>Ggc	p.S206G	HADHA_ENST00000461025.1_5'Flank|HADHA_ENST00000457468.2_Missense_Mutation_p.S119G	NM_000182.4	NP_000173.2	P40939	ECHA_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), alpha subunit	206				S -> N (in Ref. 2; AAA56664). {ECO:0000305}.	cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acetyltransferase activity (GO:0003985)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)			autonomic_ganglia(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(4)|skin(1)	30	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCACGAATGCTTCTACCAGTC	0.458																																					p.S206G		Atlas-SNP	.											.	HADHA	87	.	0			c.A616G						.						192	173	179					2																	26453120		2203	4300	6503	SO:0001583	missense	3030	exon7			GAATGCTTCTACC	D16480	CCDS1721.1	2p23	2014-09-17	2010-04-30		ENSG00000084754	ENSG00000084754	1.1.1.211, 4.2.1.17		4801	protein-coding gene	gene with protein product	"gastrin-binding protein", "long-chain-3-hydroxyacyl-CoA dehydrogenase", "long-chain 2-enoyl-CoA hydratase", "mitochondrial trifunctional protein, alpha subunit"	600890	"hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit"			9605857, 7918661	Standard	NM_000182		Approved	GBP, LCEH, LCHAD, MTPA	uc002rgy.3	P40939	OTTHUMG00000096979	ENST00000380649.3:c.616A>G	chr2.hg19:g.26453120T>C	ENSP00000370023:p.Ser206Gly	108.0	0.0		82.0	4.0	NM_000182	B2R7L4|B4DYP2|Q16679|Q53T69|Q53TA2|Q96GT7|Q9UQC5	Missense_Mutation	SNP	ENST00000380649.3	hg19	CCDS1721.1	.	.	.	.	.	.	.	.	.	.	T	15.76	2.928614	0.52759	.	.	ENSG00000084754	ENST00000380649;ENST00000457468	T;T	0.69306	-0.39;-0.39	5.94	3.42	0.39159	Crotonase, core (1);	0.216560	0.53938	N	0.000041	T	0.56761	0.2007	L	0.46885	1.475	0.19775	N	0.999953	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.10450	0.005;0.0;0.0	T	0.51988	-0.8635	10	0.49607	T	0.09	-28.0796	9.0929	0.36621	0.0:0.1646:0.0:0.8354	.	119;206;206	B4DYP2;E9KL44;P40939	.;.;ECHA_HUMAN	G	206;119	ENSP00000370023:S206G;ENSP00000405344:S119G	ENSP00000370023:S206G	S	-	1	0	HADHA	26306624	1.000000	0.71417	0.983000	0.44433	0.985000	0.73830	3.037000	0.49775	0.998000	0.38996	0.455000	0.32223	AGC	.	.		0.458	HADHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214051.1	NM_000182		C	26453120	T	C	26453120	3	2	254	1	0	0	0	0	1	0	0	0	6952	1609	56	2	1731	2	HADHA	2	26453120	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	2191518	26453120	216746253	89	34381										
C2orf39	92749	hgsc.bcm.edu	37	chr2	26624926	26624926	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cacttgtccacccagattctCgcgccctcggtccactccga	7	19	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:26624926C>T	ENST00000288710.2	+	1	143	c.69C>T	c.(67-69)ctC>ctT	p.L23L		NM_145038.2	NP_659475.2	Q96MC2	DRC1_HUMAN	dynein regulatory complex subunit 1	23					axonemal dynein complex assembly (GO:0070286)|bacterial-type flagellum-dependent cell motility (GO:0071973)|cilium-dependent cell motility (GO:0060285)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)											CCCAGATTCTCGCGCCCTCGG	0.697																																					p.L23L		Atlas-SNP	.											.	CCDC164	84	.	0			c.C69T						.						35	31	32					2																	26624926		2203	4300	6503	SO:0001819	synonymous_variant	92749	exon1			GATTCTCGCGCCC	AL833892	CCDS1723.1	2p23.3	2014-07-18	2014-07-18	2013-03-14	ENSG00000157856	ENSG00000157856			24245	protein-coding gene	gene with protein product		615288	"chromosome 2 open reading frame 39", "coiled-coil domain containing 164", "dynein regulatory complex subunit 1 homolog (Chlamydomonas)"	C2orf39, CCDC164		23354437	Standard	NM_145038		Approved	MGC16372, FLJ32660, CILD21	uc002rhg.2	Q96MC2	OTTHUMG00000125531	ENST00000288710.2:c.69C>T	chr2.hg19:g.26624926C>T		122.0	0.0		64.0	4.0	NM_145038	A8K1N8|Q53R91|Q53TA3|Q8NDI5	Silent	SNP	ENST00000288710.2	hg19	CCDS1723.1																																																																																			.	.		0.697	DRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246862.1	NM_145038		T	26624926	C	T	26624926	2	4	254	1	0	0	0	0	0	0	0	1	2166	871	31	1		1	C2orf39	2	26624926	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	171806	26624926	216574447	90	34382										
TMEM214	54867	hgsc.bcm.edu	37	chr2	27258128	27258128	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctacaagctcctctaagtgaAcccacgctgagccagcatac	7	15	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:27258128A>G	ENST00000238788.9	+	3	539	c.477A>G	c.(475-477)gaA>gaG	p.E159E	TMEM214_ENST00000404032.3_Silent_p.E159E	NM_017727.4	NP_060197.4	Q6NUQ4	TM214_HUMAN	transmembrane protein 214	159					apoptotic process (GO:0006915)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)	18						CTCTAAGTGAACCCACGCTGA	0.468																																					p.E159E		Atlas-SNP	.											.	TMEM214	41	.	0			c.A477G						.						85	84	84					2																	27258128		1975	4168	6143	SO:0001819	synonymous_variant	54867	exon3			AAGTGAACCCACG		CCDS42664.1, CCDS46242.1	2p23.3	2013-06-19			ENSG00000119777	ENSG00000119777			25983	protein-coding gene	gene with protein product						23661706	Standard	NM_001083590		Approved	FLJ20254	uc002ria.4	Q6NUQ4	OTTHUMG00000151999	ENST00000238788.9:c.477A>G	chr2.hg19:g.27258128A>G		150.0	0.0		96.0	4.0	NM_017727	A6NNF2|B3KUI9|B5MCD8|D6W547|Q53SW1|Q69YH4|Q8NC45|Q8WZ37|Q9NXH2	Silent	SNP	ENST00000238788.9	hg19	CCDS42664.1																																																																																			.	.		0.468	TMEM214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324748.1	NM_017727		G	27258128	A	G	27258128	2	3	254	1	0	0	0	0	0	0	0	1	16152	40	2	2		2	TMEM214	2	27258128	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	633202	27258128	215941245	91	34383										
CAD	790	hgsc.bcm.edu	37	chr2	27465209	27465209	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggaggccagtgatcaatgctGgggatggggtcggagagcac	19	7	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:27465209G>T	ENST00000403525.1	+	39	6091	c.5947G>T	c.(5947-5949)Ggg>Tgg	p.G1983W	CAD_ENST00000264705.4_Missense_Mutation_p.G2046W			O76075	DFFB_HUMAN	carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	0					apoptotic chromosome condensation (GO:0030263)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			NS(1)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(40)|ovary(6)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	92	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GATCAATGCTGGGGATGGGGT	0.617																																					p.G2046W		Atlas-SNP	.											.	CAD	199	.	0			c.G6136T						.						33	36	35					2																	27465209		2203	4300	6503	SO:0001583	missense	790	exon40			AATGCTGGGGATG	D78586	CCDS1742.1	2p22-p21	2012-10-02			ENSG00000084774	ENSG00000084774	2.1.3.2, 3.5.2.-		1424	protein-coding gene	gene with protein product		114010				8619816, 2565865	Standard	NM_004341		Approved		uc002rji.3	P27708	OTTHUMG00000097070	ENST00000403525.1:c.5947G>T	chr2.hg19:g.27465209G>T	ENSP00000384510:p.Gly1983Trp	91.0	0.0		60.0	4.0	NM_004341	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Missense_Mutation	SNP	ENST00000403525.1	hg19		.	.	.	.	.	.	.	.	.	.	G	25.3	4.623149	0.87460	.	.	ENSG00000084774	ENST00000264705;ENST00000403525	D;D	0.99220	-5.58;-5.58	4.88	4.88	0.63580	Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding (1);	0.000000	0.85682	D	0.000000	D	0.99764	0.9904	H	0.99800	4.79	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96579	0.9429	10	0.87932	D	0	-11.1868	16.5999	0.84810	0.0:0.0:1.0:0.0	.	1983;2046	F8VPD4;P27708	.;PYR1_HUMAN	W	2046;1983	ENSP00000264705:G2046W;ENSP00000384510:G1983W	ENSP00000264705:G2046W	G	+	1	0	CAD	27318713	1.000000	0.71417	0.836000	0.33094	0.947000	0.59692	9.106000	0.94253	2.239000	0.73571	0.491000	0.48974	GGG	.	.		0.617	CAD-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000324970.1			T	27465209	G	T	27465209	3	4	254	1	0	0	0	0	1	0	0	0	2567	1348	47	3	6294	3	CAD	2	27465209	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	207081	27465209	215734164	92	34384										
GTF3C2	2976	hgsc.bcm.edu	37	chr2	27551011	27551011	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agcagaagaatggtctggacCttcaggactgtcctgatacg	12	9	2	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:27551011C>A	ENST00000359541.2	-	17	2731	c.2302G>T	c.(2302-2304)Ggt>Tgt	p.G768C	GTF3C2_ENST00000264720.3_Missense_Mutation_p.G768C|MPV17_ENST00000357186.6_5'Flank			Q8WUA4	TF3C2_HUMAN	general transcription factor IIIC, polypeptide 2, beta 110kDa	768					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)				central_nervous_system(4)|endometrium(6)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	38	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGGTCTGGACCTTCAGGACTG	0.433																																					p.P768S		Atlas-SNP	.											.	GTF3C2	73	.	0			c.C2302T						.						93	89	90					2																	27551011		2203	4300	6503	SO:0001583	missense	2976	exon18			CTGGACCTTCAGG	D13636	CCDS1749.1	2p23.3	2013-01-10	2002-08-29		ENSG00000115207	ENSG00000115207		"General transcription factors", "WD repeat domain containing"	4665	protein-coding gene	gene with protein product		604883	"general transcription factor IIIC, polypeptide 2 (beta subunit, 110kD)"			7729686	Standard	NM_001521		Approved	KIAA0011, TFIIIC110	uc002rjw.2	Q8WUA4	OTTHUMG00000097785	ENST00000359541.2:c.2302G>T	chr2.hg19:g.27551011C>A	ENSP00000352536:p.Gly768Cys	98.0	0.0		100.0	4.0	NM_001521	D6W557|Q16632|Q9BWI7	Missense_Mutation	SNP	ENST00000359541.2	hg19	CCDS1749.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	18.46|18.46|18.46	3.628299|3.628299|3.628299	0.67015|0.67015|0.67015	.|.|.	.|.|.	ENSG00000115207|ENSG00000115207|ENSG00000115207	ENST00000359541;ENST00000264720|ENST00000454704;ENST00000415683|ENST00000457098	T;T|.|.	0.72942|.|.	-0.7;-0.7|.|.	5.16|5.16|5.16	5.16|5.16|5.16	0.70880|0.70880|0.70880	WD40 repeat-like-containing domain (1);|.|.	1.082350|.|.	0.06921|.|.	N|.|.	0.809368|.|.	T|T|T	0.32852|0.32852|0.32852	0.0843|0.0843|0.0843	N|N|N	0.08118|0.08118|0.08118	0|0|0	0.32594|0.32594|0.32594	N|N|N	0.526821|0.526821|0.526821	P|.|.	0.51791|.|.	0.948|.|.	B|.|.	0.43155|.|.	0.41|.|.	T|T|T	0.40887|0.40887|0.40887	-0.9539|-0.9539|-0.9539	10|5|5	0.56958|.|.	D|.|.	0.05|.|.	0.0308|0.0308|0.0308	14.1451|14.1451|14.1451	0.65347|0.65347|0.65347	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	768|.|.	Q8WUA4|.|.	TF3C2_HUMAN|.|.	C|N|M	768|276;190|61	ENSP00000352536:G768C;ENSP00000264720:G768C|.|.	ENSP00000264720:G768C|.|.	G|K|R	-|-|-	1|3|2	0|2|0	GTF3C2|GTF3C2|GTF3C2	27404515|27404515|27404515	0.676000|0.676000|0.676000	0.27567|0.27567|0.27567	0.961000|0.961000|0.961000	0.40146|0.40146|0.40146	0.956000|0.956000|0.956000	0.61745|0.61745|0.61745	3.374000|3.374000|3.374000	0.52402|0.52402|0.52402	2.399000|2.399000|2.399000	0.81585|0.81585|0.81585	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	GGT|AAG|AGG	.	.		0.433	GTF3C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215028.2			A	27551011	C	A	27551011	3	1	254	1	0	0	0	0	1	0	0	0	6882	681	24	3	445	3	GTF3C2	2	27551011	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	85802	27551011	215648362	93	34385										
SNX17	9784	hgsc.bcm.edu	37	chr2	27597622	27597622	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggcctgaacctgctttatgcTcaggtgagcttggagctgcc	13	11	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:27597622T>C	ENST00000233575.2	+	8	900	c.678T>C	c.(676-678)gcT>gcC	p.A226A	ZNF513_ENST00000491924.1_5'Flank|SNX17_ENST00000542478.1_Silent_p.A12A|SNX17_ENST00000543024.1_Silent_p.A12A|SNX17_ENST00000537606.1_Silent_p.A201A	NM_001267059.1|NM_001267061.1|NM_014748.3	NP_001253988.1|NP_001253990.1|NP_055563.1	Q15036	SNX17_HUMAN	sorting nexin 17	226	FERM-like.				cholesterol catabolic process (GO:0006707)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|receptor-mediated endocytosis (GO:0006898)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|protein complex (GO:0043234)	low-density lipoprotein particle receptor binding (GO:0050750)|phosphatidylinositol binding (GO:0035091)|protein C-terminus binding (GO:0008022)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)	14	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGCTTTATGCTCAGGTGAGCT	0.517																																					p.A226A		Atlas-SNP	.											.	SNX17	40	.	0			c.T678C						.						152	138	143					2																	27597622		2203	4300	6503	SO:0001819	synonymous_variant	9784	exon8			TTATGCTCAGGTG	D31764	CCDS1750.1, CCDS58704.1	2p23-p22	2008-05-21			ENSG00000115234	ENSG00000115234		"Sorting nexins"	14979	protein-coding gene	gene with protein product		605963				12169628, 15769472	Standard	NM_014748		Approved	KIAA0064	uc002rkg.2	Q15036	OTTHUMG00000097781	ENST00000233575.2:c.678T>C	chr2.hg19:g.27597622T>C		110.0	0.0		89.0	4.0	NM_014748	B4DQM7|Q53HN7|Q6IAS3	Silent	SNP	ENST00000233575.2	hg19	CCDS1750.1																																																																																			.	.		0.517	SNX17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215024.1	NM_014748		C	27597622	T	C	27597622	2	2	254	1	0	0	0	0	0	0	0	1	14903	1538	54	2		2	SNX17	2	27597622	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	46611	27597622	215601751	94	34386										
IFT172	26160	hgsc.bcm.edu	37	chr2	27679376	27679376	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gagagaaagcttggggcctcAccaattgtctgcagcgtggt	14	9	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:27679376A>G	ENST00000260570.3	-	30	3475		c.e30+1			NM_015662.1	NP_056477.1	Q9UG01	IF172_HUMAN	intraflagellar transport 172						bone development (GO:0060348)|brain development (GO:0007420)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|epidermis development (GO:0008544)|heart looping (GO:0001947)|hindgut development (GO:0061525)|left/right axis specification (GO:0070986)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)	axoneme (GO:0005930)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|sperm midpiece (GO:0097225)|sperm principal piece (GO:0097228)|vesicle (GO:0031982)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(17)|lung(17)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	43	Acute lymphoblastic leukemia(172;0.155)					TTGGGGCCTCACCAATTGTCT	0.512																																					.		Atlas-SNP	.											.	IFT172	119	.	0			c.3371+2T>C						.						90	88	89					2																	27679376		2203	4300	6503	SO:0001630	splice_region_variant	26160	exon31			GGCCTCACCAATT	AB033005	CCDS1755.1	2p23.3	2014-07-03	2014-07-03		ENSG00000138002	ENSG00000138002		"Intraflagellar transport homologs", "WD repeat domain containing"	30391	protein-coding gene	gene with protein product	"wimple homolog"	607386	"intraflagellar transport 172 homolog (Chlamydomonas)"			10788441, 10574461, 24140113	Standard	XM_005264254		Approved	SLB, wim, osm-1, NPHP17	uc002rku.3	Q9UG01	OTTHUMG00000128425	ENST00000260570.3:c.3371+1T>C	chr2.hg19:g.27679376A>G		120.0	0.0		106.0	5.0	NM_015662	A5PKZ0|B2RNU5|Q86X44|Q96HW4|Q9UFJ9|Q9ULP1	Splice_Site	SNP	ENST00000260570.3	hg19	CCDS1755.1	.	.	.	.	.	.	.	.	.	.	A	13.01	2.110658	0.37242	.	.	ENSG00000138002	ENST00000260570	.	.	.	5.99	5.99	0.97316	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2885	0.73849	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	IFT172	27532880	1.000000	0.71417	1.000000	0.80357	0.047000	0.14425	8.841000	0.92131	2.292000	0.77174	0.533000	0.62120	.	.	.		0.512	IFT172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250213.2	NM_015662	Intron	G	27679376	A	G	27679376	5	3	254	1	0	0	0	0	0	0	1	0	7566	173	6	2	1952	2	IFT172	2	27679376	Splice_Site	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	81754	27679376	215519997	95	34387										
IFT172	26160	hgsc.bcm.edu	37	chr2	27703934	27703934	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgtcataacttcctagcacaAcagactggcccccaggactt	7	14	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:27703934A>G	ENST00000260570.3	-	8	867	c.764T>C	c.(763-765)gTt>gCt	p.V255A	IFT172_ENST00000416524.2_Missense_Mutation_p.V234A|IFT172_ENST00000359466.6_Missense_Mutation_p.V255A	NM_015662.1	NP_056477.1	Q9UG01	IF172_HUMAN	intraflagellar transport 172	255					bone development (GO:0060348)|brain development (GO:0007420)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|epidermis development (GO:0008544)|heart looping (GO:0001947)|hindgut development (GO:0061525)|left/right axis specification (GO:0070986)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)	axoneme (GO:0005930)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|sperm midpiece (GO:0097225)|sperm principal piece (GO:0097228)|vesicle (GO:0031982)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(17)|lung(17)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	43	Acute lymphoblastic leukemia(172;0.155)					TCCTAGCACAACAGACTGGCC	0.468																																					p.V255A		Atlas-SNP	.											.	IFT172	119	.	0			c.T764C						.						70	63	66					2																	27703934		2203	4300	6503	SO:0001583	missense	26160	exon8			AGCACAACAGACT	AB033005	CCDS1755.1	2p23.3	2014-07-03	2014-07-03		ENSG00000138002	ENSG00000138002		"Intraflagellar transport homologs", "WD repeat domain containing"	30391	protein-coding gene	gene with protein product	"wimple homolog"	607386	"intraflagellar transport 172 homolog (Chlamydomonas)"			10788441, 10574461, 24140113	Standard	XM_005264254		Approved	SLB, wim, osm-1, NPHP17	uc002rku.3	Q9UG01	OTTHUMG00000128425	ENST00000260570.3:c.764T>C	chr2.hg19:g.27703934A>G	ENSP00000260570:p.Val255Ala	117.0	0.0		83.0	4.0	NM_015662	A5PKZ0|B2RNU5|Q86X44|Q96HW4|Q9UFJ9|Q9ULP1	Missense_Mutation	SNP	ENST00000260570.3	hg19	CCDS1755.1	.	.	.	.	.	.	.	.	.	.	A	31	5.084199	0.94100	.	.	ENSG00000138002	ENST00000260570;ENST00000359466;ENST00000416524	T;T;T	0.69306	-0.39;-0.39;1.38	5.85	5.85	0.93711	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.174068	0.50627	D	0.000118	T	0.81969	0.4935	M	0.87900	2.915	0.58432	D	0.999995	D;D;D;D	0.57899	0.969;0.967;0.969;0.981	P;P;P;P	0.61070	0.766;0.883;0.766;0.851	D	0.83873	0.0275	10	0.46703	T	0.11	-14.9757	15.0355	0.71744	1.0:0.0:0.0:0.0	.	255;255;255;255	A5PKZ0;Q9UG01-2;E7EP25;Q9UG01	.;.;.;IF172_HUMAN	A	255;255;234	ENSP00000260570:V255A;ENSP00000352443:V255A;ENSP00000407408:V234A	ENSP00000260570:V255A	V	-	2	0	IFT172	27557438	1.000000	0.71417	0.998000	0.56505	0.970000	0.65996	8.581000	0.90788	2.227000	0.72691	0.455000	0.32223	GTT	.	.		0.468	IFT172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250213.2	NM_015662		G	27703934	A	G	27703934	3	3	254	1	0	0	0	0	1	0	0	0	7566	43	2	2	4649	2	IFT172	2	27703934	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	24558	27703934	215495439	96	34388										
GPN1	79635	hgsc.bcm.edu	37	chr2	27852779	27852779	+	5'Flank	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccaccgtatgtgatcaacctGgatccagcagtacatgaagt	9	11	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:27852779G>T	ENST00000324364.3	-	0	0				GPN1_ENST00000458167.2_5'UTR|RP11-158I13.2_ENST00000505973.1_RNA|CCDC121_ENST00000394775.3_5'Flank|GPN1_ENST00000264718.3_Silent_p.L69L|ZNF512_ENST00000556601.1_3'UTR|GPN1_ENST00000503738.1_5'UTR|GPN1_ENST00000515877.1_5'UTR|GPN1_ENST00000407583.3_Silent_p.L43L|GPN1_ENST00000424214.1_5'UTR|GPN1_ENST00000610189.1_Silent_p.L55L|GPN1_ENST00000461249.1_3'UTR	NM_024584.4	NP_078860.2	Q6ZUS5	CC121_HUMAN	coiled-coil domain containing 121											breast(1)|endometrium(3)|large_intestine(2)|lung(6)|prostate(2)	14	Acute lymphoblastic leukemia(172;0.155)					TGATCAACCTGGATCCAGCAG	0.493																																					p.L69L		Atlas-SNP	.											.	GPN1	28	.	0			c.G207T						.						143	115	124					2																	27852779		2203	4300	6503	SO:0001631	upstream_gene_variant	11321	exon2			CAACCTGGATCCA	AK125354	CCDS1759.1, CCDS46247.1	2p23.2	2008-02-05			ENSG00000176714	ENSG00000176714			25833	protein-coding gene	gene with protein product							Standard	NM_024584		Approved	FLJ43364, FLJ13646	uc002rld.3	Q6ZUS5	OTTHUMG00000128427		chr2.hg19:g.27852779G>T	Exception_encountered	148.0	0.0		121.0	5.0	NM_007266	B3KW66|J3KQZ8|Q9H8G6	Silent	SNP	ENST00000324364.3	hg19	CCDS1759.1																																																																																			.	.		0.493	CCDC121-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250215.1	NM_024584		T	27852779	G	T	27852779	1	4	254	0	1	0	0	0	0	0	0	0	6625	1335	47	3		3	GPN1	2	27852779	5'Flank	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	148845	27852779	215346594	97	34389										
BIRC6	57448	hgsc.bcm.edu	37	chr2	32678911	32678911	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtagttgcacagctgctgagGgtagtttcacatctctcact	10	10	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:32678911G>T	ENST00000421745.2	+	23	4788	c.4654G>T	c.(4654-4656)Ggt>Tgt	p.G1552C		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	1552					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					AGCTGCTGAGGGTAGTTTCAC	0.388																																					p.G1552C	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.G4654T						.						205	190	195					2																	32678911		2203	4300	6503	SO:0001583	missense	57448	exon23			GCTGAGGGTAGTT	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.4654G>T	chr2.hg19:g.32678911G>T	ENSP00000393596:p.Gly1552Cys	176.0	0.0		152.0	8.0	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	hg19	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	G	20.8	4.045012	0.75846	.	.	ENSG00000115760	ENST00000421745	T	0.74947	-0.89	5.51	5.51	0.81932	.	0.063521	0.64402	D	0.000009	T	0.80633	0.4660	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.68765	0.96	T	0.80251	-0.1460	10	0.45353	T	0.12	.	19.4105	0.94670	0.0:0.0:1.0:0.0	.	1552	Q9NR09	BIRC6_HUMAN	C	1552	ENSP00000393596:G1552C	ENSP00000393596:G1552C	G	+	1	0	BIRC6	32532415	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.987000	0.88182	2.593000	0.87608	0.585000	0.79938	GGT	.	.		0.388	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		T	32678911	G	T	32678911	3	4	254	1	0	0	0	0	1	0	0	0	1438	1232	43	3	4744	3	BIRC6	2	32678911	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	4826132	32678911	210520462	98	34390										
LTBP1	4052	hgsc.bcm.edu	37	chr2	33526595	33526595	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tctcttgctcatagacattgAtgaatgccagcaccgtcatc	7	12	3	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:33526595A>G	ENST00000404816.2	+	22	3718	c.3365A>G	c.(3364-3366)gAt>gGt	p.D1122G	LTBP1_ENST00000390003.4_Missense_Mutation_p.D797G|LTBP1_ENST00000402934.1_Missense_Mutation_p.D743G|LTBP1_ENST00000407925.1_Missense_Mutation_p.D796G|LTBP1_ENST00000418533.2_Missense_Mutation_p.D796G|LTBP1_ENST00000272273.5_Missense_Mutation_p.D62G|LTBP1_ENST00000354476.3_Missense_Mutation_p.D1123G|LTBP1_ENST00000404525.1_Missense_Mutation_p.D743G|LTBP1_ENST00000498013.1_3'UTR			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	1122	EGF-like 10; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				ATAGACATTGATGAATGCCAG	0.438																																					p.D1122G		Atlas-SNP	.											.	LTBP1	317	.	0			c.A3365G						.						154	147	149					2																	33526595		2203	4300	6503	SO:0001583	missense	4052	exon22			ACATTGATGAATG		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"Latent transforming growth factor, beta binding proteins"	6714	protein-coding gene	gene with protein product	"TGF-beta1-BP-1"	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.3365A>G	chr2.hg19:g.33526595A>G	ENSP00000386043:p.Asp1122Gly	118.0	0.0		94.0	4.0	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	hg19	CCDS33177.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.26|12.26	1.885121|1.885121	0.33255|0.33255	.|.	.|.	ENSG00000049323|ENSG00000049323	ENST00000404816;ENST00000354476;ENST00000390003;ENST00000418533;ENST00000402934;ENST00000404525;ENST00000407925;ENST00000272273|ENST00000415140	D;D;D;D;D;D;D;D|.	0.95588|.	-3.75;-3.75;-3.75;-3.75;-3.75;-3.75;-3.75;-3.75|.	5.36|5.36	5.36|5.36	0.76844|0.76844	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);|.	.|.	.|.	.|.	.|.	D|D	0.86760|0.86760	0.6010|0.6010	H|H	0.95437|0.95437	3.67|3.67	0.46564|0.46564	D|D	0.999104|0.999104	P;B;P;P;B;B;B|.	0.49090|.	0.778;0.438;0.587;0.919;0.239;0.15;0.384|.	P;P;B;P;B;B;B|.	0.54238|.	0.484;0.559;0.336;0.746;0.304;0.226;0.423|.	D|D	0.90634|0.90634	0.4569|0.4569	9|5	0.72032|.	D|.	0.01|.	.|.	14.3408|14.3408	0.66624|0.66624	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	62;1122;796;743;796;797;1123|.	E7EUU6;Q14766;E7EV71;Q14766-3;Q14766-2;Q14766-5;Q14766-4|.	.;LTBP1_HUMAN;.;.;.;.;.|.	G|V	1122;1123;797;796;743;743;796;62|84	ENSP00000386043:D1122G;ENSP00000346467:D1123G;ENSP00000374653:D797G;ENSP00000393057:D796G;ENSP00000384373:D743G;ENSP00000385359:D743G;ENSP00000384091:D796G;ENSP00000272273:D62G|.	ENSP00000272273:D62G|.	D|M	+|+	2|1	0|0	LTBP1|LTBP1	33380099|33380099	1.000000|1.000000	0.71417|0.71417	0.970000|0.970000	0.41538|0.41538	0.092000|0.092000	0.18411|0.18411	7.408000|7.408000	0.80041|0.80041	2.029000|2.029000	0.59856|0.59856	0.460000|0.460000	0.39030|0.39030	GAT|ATG	.	.		0.438	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943		G	33526595	A	G	33526595	3	3	254	1	0	0	0	0	1	0	0	0	9082	333	12	2	3506	2	LTBP1	2	33526595	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	847684	33526595	209672778	99	34391										
FAM82A1	151393	hgsc.bcm.edu	37	chr2	38178622	38178622	+	Intron	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggatttcaaaaaagaaatgcTtccccttactggcaacaaag	7	9	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:38178622T>A	ENST00000406384.1	+	2	646				RMDN2_ENST00000417700.2_Intron|RMDN2_ENST00000234195.3_Silent_p.A88A|RMDN2_ENST00000407257.1_Silent_p.A88A|RMDN2-AS1_ENST00000414365.2_RNA|RMDN2_ENST00000354545.2_Intron|RMDN2_ENST00000402091.3_Silent_p.A88A	NM_001170792.1	NP_001164263.1	Q96LZ7	RMD2_HUMAN	regulator of microtubule dynamics 2							cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)|mitochondrion (GO:0005739)											AAAGAAATGCTTCCCCTTACT	0.353																																					p.A88A		Atlas-SNP	.											.	.	.	.	0			c.T264A						.						83	87	86					2																	38178622		2203	4300	6503	SO:0001627	intron_variant	151393	exon2			AAATGCTTCCCCT	AK057516	CCDS1792.1, CCDS54351.1, CCDS54352.1	2p22.2	2013-01-11	2013-01-11	2013-01-11	ENSG00000115841	ENSG00000115841			26567	protein-coding gene	gene with protein product		611872	"family with sequence similarity 82, member A1"	FAM82A, FAM82A1		12477932	Standard	XM_005264161		Approved	FLJ32954, RMD2	uc002rqn.2	Q96LZ7	OTTHUMG00000128487	ENST00000406384.1:c.452+21750T>A	chr2.hg19:g.38178622T>A		76.0	0.0		54.0	4.0	NM_144713	A9UMZ7|A9UN00|Q4ZG33|Q6UXN4|Q8N657|Q8N9A2|Q8NCV6|Q8NHM0	Silent	SNP	ENST00000406384.1	hg19	CCDS54351.1																																																																																			.	.		0.353	RMDN2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325577.1	NM_144713		A	38178622	T	A	38178622	1	1	254	0	1	0	0	0	0	0	0	0	5638	1596	56	4		4	FAM82A1	2	38178622	Intron	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	4652027	38178622	205020751	100	34392										
EPAS1	2034	hgsc.bcm.edu	37	chr2	46605102	46605102	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cccgagccagccatgggccaCggagttgaggagccacagca	14	14	0	1	rs540130771	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:46605102C>A	ENST00000263734.3	+	10	1829	c.1319C>A	c.(1318-1320)aCg>aAg	p.T440K		NM_001430.4	NP_001421.2	Q99814	EPAS1_HUMAN	endothelial PAS domain protein 1	440					angiogenesis (GO:0001525)|blood vessel remodeling (GO:0001974)|cell maturation (GO:0048469)|cellular response to hypoxia (GO:0071456)|embryonic placenta development (GO:0001892)|erythrocyte differentiation (GO:0030218)|lung development (GO:0030324)|mitochondrion organization (GO:0007005)|myoblast fate commitment (GO:0048625)|norepinephrine metabolic process (GO:0042415)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of heart rate (GO:0002027)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|surfactant homeostasis (GO:0043129)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|histone acetyltransferase binding (GO:0035035)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	LUSC - Lung squamous cell carcinoma(58;0.151)			CCATGGGCCACGGAGTTGAGG	0.672																																					p.T440K		Atlas-SNP	.											.	EPAS1	83	.	0			c.C1319A						.						20	18	19					2																	46605102		2177	4261	6438	SO:0001583	missense	2034	exon10			GGGCCACGGAGTT	U81984	CCDS1825.1	2p21-p16	2013-05-21			ENSG00000116016	ENSG00000116016		"Basic helix-loop-helix proteins"	3374	protein-coding gene	gene with protein product	"HIF-1 alpha-like factor"	603349				9000051, 9079689, 18378852	Standard	NM_001430		Approved	MOP2, PASD2, HIF2A, HLF, bHLHe73	uc002ruv.3	Q99814	OTTHUMG00000128818	ENST00000263734.3:c.1319C>A	chr2.hg19:g.46605102C>A	ENSP00000263734:p.Thr440Lys	141.0	0.0		100.0	4.0	NM_001430	Q86VA2|Q99630	Missense_Mutation	SNP	ENST00000263734.3	hg19	CCDS1825.1	.	.	.	.	.	.	.	.	.	.	C	0.010	-1.747677	0.00669	.	.	ENSG00000116016	ENST00000263734	T	0.45276	0.9	5.58	-1.3	0.09259	.	4.242400	0.00166	N	0.000006	T	0.16257	0.0391	N	0.04203	-0.255	0.09310	N	1	B	0.17038	0.02	B	0.13407	0.009	T	0.20672	-1.0268	10	0.02654	T	1	.	1.6473	0.02764	0.2761:0.3684:0.197:0.1585	.	440	Q99814	EPAS1_HUMAN	K	440	ENSP00000263734:T440K	ENSP00000263734:T440K	T	+	2	0	EPAS1	46458606	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-0.372000	0.07504	-0.082000	0.12640	0.655000	0.94253	ACG	.	.		0.672	EPAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250752.2	NM_001430		A	46605102	C	A	46605102	3	1	254	1	0	0	0	0	1	0	0	0	5152	536	19	1	1357	1	EPAS1	2	46605102	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	8426480	46605102	196594271	101	34393										
MSH2	4436	hgsc.bcm.edu	37	chr2	47703706	47703706	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgttggaaactgcttctatcCtcaggtaagtgcatctccta	8	10	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:47703706C>A	ENST00000233146.2	+	13	2429	c.2206C>A	c.(2206-2208)Ctc>Atc	p.L736I	MSH2_ENST00000543555.1_Missense_Mutation_p.L670I|MSH2_ENST00000406134.1_Missense_Mutation_p.L736I	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2	736					ATP catabolic process (GO:0006200)|B cell differentiation (GO:0030183)|B cell mediated immunity (GO:0019724)|cell cycle arrest (GO:0007050)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|intra-S DNA damage checkpoint (GO:0031573)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|isotype switching (GO:0045190)|maintenance of DNA repeat elements (GO:0043570)|male gonad development (GO:0008584)|meiotic gene conversion (GO:0006311)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reciprocal meiotic recombination (GO:0045128)|oxidative phosphorylation (GO:0006119)|positive regulation of helicase activity (GO:0051096)|postreplication repair (GO:0006301)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSalpha complex (GO:0032301)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|guanine/thymine mispair binding (GO:0032137)|heteroduplex DNA loop binding (GO:0000404)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|Y-form DNA binding (GO:0000403)	p.0?(2)|p.?(2)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(5)|large_intestine(50)|lung(18)|ovary(5)|prostate(2)|skin(3)|small_intestine(1)|stomach(2)|urinary_tract(1)	112		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TGCTTCTATCCTCAGGTAAGT	0.438			"D, Mis, N, F, S"		"colorectal, endometrial, ovarian"	"colorectal, endometrial, ovarian"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.L736I		Atlas-SNP	.	yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p22-p21	4436	mutS homolog 2 (E. coli)		E	MSH2,NS,carcinoma,0,1	MSH2	198	.	4	Whole gene deletion(2)|Unknown(2)	haematopoietic_and_lymphoid_tissue(3)|prostate(1)	c.C2206A						.						129	117	121					2																	47703706		2203	4300	6503	SO:0001583	missense	4436	exon13	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	TCTATCCTCAGGT	U03911	CCDS1834.1, CCDS58709.1	2p21	2014-09-17	2013-09-12		ENSG00000095002	ENSG00000095002			7325	protein-coding gene	gene with protein product		609309	"mutS (E. coli) homolog 2 (colon cancer, nonpolyposis type 1)", "mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)"	COCA1		8484120, 9843200	Standard	NM_000251		Approved	HNPCC, HNPCC1	uc002rvy.2	P43246	OTTHUMG00000128861	ENST00000233146.2:c.2206C>A	chr2.hg19:g.47703706C>A	ENSP00000233146:p.Leu736Ile	64.0	0.0		42.0	2.0	NM_000251	B4E2Z2|O75488	Missense_Mutation	SNP	ENST00000233146.2	hg19	CCDS1834.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.352194	0.82132	.	.	ENSG00000095002	ENST00000233146;ENST00000543555;ENST00000406134;ENST00000419559;ENST00000413880	D;D;D	0.91068	-2.78;-2.78;-2.78	6.17	6.17	0.99709	DNA mismatch repair protein MutS, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.95796	0.8632	M	0.81341	2.54	0.80722	D	1	D;D;P	0.89917	1.0;1.0;0.95	D;D;P	0.91635	0.999;0.999;0.823	D	0.94587	0.7784	10	0.49607	T	0.09	-10.741	20.8794	0.99867	0.0:1.0:0.0:0.0	.	670;736;736	B4E2Z2;E9PHA6;P43246	.;.;MSH2_HUMAN	I	736;670;736;736;522	ENSP00000233146:L736I;ENSP00000442697:L670I;ENSP00000384199:L736I	ENSP00000233146:L736I	L	+	1	0	MSH2	47557210	1.000000	0.71417	1.000000	0.80357	0.586000	0.36452	4.626000	0.61269	2.941000	0.99782	0.655000	0.94253	CTC	.	.		0.438	MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3			A	47703706	C	A	47703706	3	1	254	1	0	0	0	0	1	0	0	0	9879	681	24	3	2256	3	MSH2	2	47703706	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1098604	47703706	195495667	102	34394										
FAM161A	84140	hgsc.bcm.edu	37	chr2	62067708	62067708	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggtgataggagttcttttctGatacagatctaaatgagaag	11	4	3	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:62067708G>A	ENST00000405894.3	-	3	532	c.431C>T	c.(430-432)tCa>tTa	p.S144L	FAM161A_ENST00000404929.1_Missense_Mutation_p.S144L	NM_032180.2	NP_115556.2	Q3B820	F161A_HUMAN	family with sequence similarity 161, member A	144					cilium assembly (GO:0042384)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(5)|large_intestine(8)|lung(4)|ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						GTTCTTTTCTGATACAGATCT	0.343																																					p.S144L		Atlas-SNP	.											.	FAM161A	200	.	0			c.C431T						.						67	59	61					2																	62067708		1833	4086	5919	SO:0001583	missense	84140	exon3			TTTTCTGATACAG		CCDS42687.2, CCDS56120.1	2p15	2011-03-15			ENSG00000170264	ENSG00000170264			25808	protein-coding gene	gene with protein product		613596	"retinitis pigmentosa 28 (autosomal recessive)"	RP28		10507729, 20705278, 20705279	Standard	NM_032180		Approved	FLJ13305	uc002sbm.4	Q3B820	OTTHUMG00000152165	ENST00000405894.3:c.431C>T	chr2.hg19:g.62067708G>A	ENSP00000385893:p.Ser144Leu	200.0	0.0		159.0	76.0	NM_032180	B4DJV7|Q9H8R2	Missense_Mutation	SNP	ENST00000405894.3	hg19	CCDS42687.2	.	.	.	.	.	.	.	.	.	.	G	13.01	2.110039	0.37242	.	.	ENSG00000170264	ENST00000404929;ENST00000405894	T;T	0.25250	2.62;1.81	4.66	1.63	0.23807	.	0.372310	0.26453	N	0.024295	T	0.21921	0.0528	L	0.56769	1.78	0.09310	N	1	P;B	0.50156	0.932;0.274	B;B	0.44278	0.445;0.084	T	0.13019	-1.0525	9	.	.	.	-9.5961	2.1742	0.03858	0.1828:0.2952:0.3944:0.1276	.	144;144	Q3B820;Q3B820-3	F161A_HUMAN;.	L	144	ENSP00000385158:S144L;ENSP00000385893:S144L	.	S	-	2	0	FAM161A	61921212	0.997000	0.39634	0.163000	0.22734	0.918000	0.54935	1.814000	0.38972	0.513000	0.28278	0.563000	0.77884	TCA	.	.		0.343	FAM161A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325537.2	NM_032180		A	62067708	G	A	62067708	3	1	254	1	0	0	0	0	1	0	0	0	5477	1294	45	3	1567	3	FAM161A	2	62067708	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	14364002	62067708	181131665	103	34395										
EHBP1	23301	hgsc.bcm.edu	37	chr2	62998523	62998523	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agagtggacatttgtcatagAaaatgtaagctaatggcaaa	10	4	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:62998523A>C	ENST00000263991.5	+	5	790	c.308A>C	c.(307-309)gAa>gCa	p.E103A	EHBP1_ENST00000354487.3_Missense_Mutation_p.E103A|EHBP1_ENST00000405289.1_Missense_Mutation_p.E103A|EHBP1_ENST00000431489.1_Missense_Mutation_p.E103A|EHBP1_ENST00000405015.3_Missense_Mutation_p.E103A	NM_015252.3	NP_056067.2	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1	103						cytoplasm (GO:0005737)|membrane (GO:0016020)				biliary_tract(1)|breast(3)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(22)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	47	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			TTTGTCATAGAAAATGTAAGC	0.333																																					p.E103A		Atlas-SNP	.											.	EHBP1	127	.	0			c.A308C						.						114	113	113					2																	62998523		2203	4296	6499	SO:0001583	missense	23301	exon5			TCATAGAAAATGT	AL833968	CCDS1872.1, CCDS46299.1, CCDS46300.1	2p15	2008-02-05			ENSG00000115504	ENSG00000115504			29144	protein-coding gene	gene with protein product		609922				10048485	Standard	NM_015252		Approved	KIAA0903, NACSIN	uc002sby.3	Q8NDI1	OTTHUMG00000129453	ENST00000263991.5:c.308A>C	chr2.hg19:g.62998523A>C	ENSP00000263991:p.Glu103Ala	152.0	0.0		145.0	26.0	NM_001142616	O94977|Q53TG7|Q53TV6|Q580X2|Q6NX72|Q6PIT3|Q6QNV2|Q9NWI9	Missense_Mutation	SNP	ENST00000263991.5	hg19	CCDS1872.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.618486	0.87359	.	.	ENSG00000115504	ENST00000405015;ENST00000413434;ENST00000405482;ENST00000431489;ENST00000263991;ENST00000354487;ENST00000405289	T;T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97;0.97	5.06	5.06	0.68205	.	0.122342	0.56097	D	0.000023	T	0.68513	0.3009	M	0.87180	2.865	0.80722	D	1	P;D;D;P	0.71674	0.726;0.979;0.998;0.689	P;D;D;P	0.81914	0.525;0.973;0.995;0.73	T	0.75539	-0.3282	10	0.87932	D	0	.	14.5025	0.67732	1.0:0.0:0.0:0.0	.	103;103;103;103	Q8NDI1-2;A8K930;Q8NDI1-3;Q8NDI1	.;.;.;EHBP1_HUMAN	A	103;71;103;103;103;103;103	ENSP00000384143:E103A;ENSP00000392192:E71A;ENSP00000384829:E103A;ENSP00000403783:E103A;ENSP00000263991:E103A;ENSP00000346482:E103A;ENSP00000385524:E103A	ENSP00000263991:E103A	E	+	2	0	EHBP1	62852027	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.964000	0.93389	1.909000	0.55274	0.528000	0.53228	GAA	.	.		0.333	EHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251616.1	NM_015252		C	62998523	A	C	62998523	3	2	254	1	0	0	0	0	1	0	0	0	4977	246	9	5	322	5	EHBP1	2	62998523	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	930815	62998523	180200850	104	34396										
PLEK	5341	hgsc.bcm.edu	37	chr2	68607861	68607861	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gttttgattttcagtttgtgTttaagatcactacgaccaaa	7	6	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:68607861T>C	ENST00000234313.7	+	3	384	c.205T>C	c.(205-207)Ttt>Ctt	p.F69L		NM_002664.2	NP_002655.2	P08567	PLEK_HUMAN	pleckstrin	69	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton reorganization (GO:0031532)|blood coagulation (GO:0007596)|cell projection organization (GO:0030030)|cortical actin cytoskeleton organization (GO:0030866)|hematopoietic progenitor cell differentiation (GO:0002244)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of calcium-mediated signaling (GO:0050849)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of inositol phosphate biosynthetic process (GO:0010920)|phosphatidylinositol metabolic process (GO:0046488)|phospholipase C-inhibiting G-protein coupled receptor signaling pathway (GO:0030845)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of inositol-polyphosphate 5-phosphatase activity (GO:0010925)|positive regulation of integrin activation (GO:0033625)|positive regulation of platelet activation (GO:0010572)|protein kinase C signaling (GO:0070528)|protein secretion by platelet (GO:0070560)|regulation of cell diameter (GO:0060305)|ruffle organization (GO:0031529)|thrombin receptor signaling pathway (GO:0070493)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|membrane (GO:0016020)|ruffle membrane (GO:0032587)	phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)			autonomic_ganglia(1)|endometrium(3)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	24		Ovarian(717;0.0129)		STAD - Stomach adenocarcinoma(1183;0.00159)|READ - Rectum adenocarcinoma(193;0.0419)		TCAGTTTGTGTTTAAGATCAC	0.478																																					p.F69L		Atlas-SNP	.											.	PLEK	64	.	0			c.T205C						.						116	115	115					2																	68607861		2203	4300	6503	SO:0001583	missense	5341	exon3			TTTGTGTTTAAGA	X07743	CCDS1887.1	2p13.3	2013-01-10			ENSG00000115956	ENSG00000115956		"Pleckstrin homology (PH) domain containing"	9070	protein-coding gene	gene with protein product		173570				2897630, 12054651	Standard	NM_002664		Approved	P47	uc002sen.4	P08567	OTTHUMG00000129562	ENST00000234313.7:c.205T>C	chr2.hg19:g.68607861T>C	ENSP00000234313:p.Phe69Leu	111.0	0.0		95.0	5.0	NM_002664	B2R9E8|Q53SU8|Q6FGM8|Q6FGQ1|Q8WV81	Missense_Mutation	SNP	ENST00000234313.7	hg19	CCDS1887.1	.	.	.	.	.	.	.	.	.	.	T	17.66	3.445498	0.63178	.	.	ENSG00000115956	ENST00000234313	T	0.35236	1.32	5.79	5.79	0.91817	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.042653	0.85682	N	0.000000	T	0.42988	0.1227	M	0.74258	2.255	0.80722	D	1	B;B	0.13145	0.007;0.004	B;B	0.17433	0.018;0.015	T	0.30679	-0.9970	10	0.46703	T	0.11	.	16.1338	0.81465	0.0:0.0:0.0:1.0	.	87;69	Q59GZ2;P08567	.;PLEK_HUMAN	L	69	ENSP00000234313:F69L	ENSP00000234313:F69L	F	+	1	0	PLEK	68461365	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.676000	0.84012	2.216000	0.71823	0.528000	0.53228	TTT	.	.		0.478	PLEK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251755.1	NM_002664		C	68607861	T	C	68607861	3	2	254	1	0	0	0	0	1	0	0	0	12062	1725	60	2	215	2	PLEK	2	68607861	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	5609338	68607861	174591512	105	34397										
SFXN5	94097	hgsc.bcm.edu	37	chr2	73247367	73247367	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcctttgaaggtaacacttaCaattggcgtcccaaaaggaa	8	9	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:73247367C>T	ENST00000272433.2	-	6	488		c.e6+1		SFXN5_ENST00000474528.1_Splice_Site|SFXN5_ENST00000410065.1_Splice_Site	NM_144579.2	NP_653180.1	Q8TD22	SFXN5_HUMAN	sideroflexin 5						iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)|citrate transmembrane transporter activity (GO:0015137)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)	9						GTAACACTTACAATTGGCGTC	0.383																																					.		Atlas-SNP	.											.	SFXN5	31	.	0			c.357+1G>A						.						87	86	86					2																	73247367		2203	4300	6503	SO:0001630	splice_region_variant	94097	exon7			CACTTACAATTGG	AY044437	CCDS1922.1	2p13	2008-05-21			ENSG00000144040	ENSG00000144040		"Sideroflexins"	16073	protein-coding gene	gene with protein product		615572				12039050, 12150972	Standard	XM_005264648		Approved	BBG-TCC	uc002siq.3	Q8TD22	OTTHUMG00000129775	ENST00000272433.2:c.357+1G>A	chr2.hg19:g.73247367C>T		126.0	0.0		89.0	4.0	NM_144579	A8K116|Q494Y3|Q53T29	Splice_Site	SNP	ENST00000272433.2	hg19	CCDS1922.1	.	.	.	.	.	.	.	.	.	.	C	18.10	3.547892	0.65311	.	.	ENSG00000144040	ENST00000272433;ENST00000411783;ENST00000410065;ENST00000442582	.	.	.	4.94	4.94	0.65067	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.8549	0.63519	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SFXN5	73100875	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	4.640000	0.61368	2.726000	0.93360	0.655000	0.94253	.	.	.		0.383	SFXN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251991.1	NM_144579	Intron	T	73247367	C	T	73247367	5	4	254	1	0	0	0	0	0	0	1	0	14213	492	17	3	700	3	SFXN5	2	73247367	Splice_Site	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	4639506	73247367	169952006	106	34398										
FBXO41	150726	hgsc.bcm.edu	37	chr2	73496418	73496418	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cgccggggaagtgggcgaggGgagcgtggtgatggtggtgg	25	5	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:73496418G>A	ENST00000521871.1	-	2	756	c.341C>T	c.(340-342)cCc>cTc	p.P114L	FBXO41_ENST00000520186.1_5'Flank|FBXO41_ENST00000520530.2_Missense_Mutation_p.P114L|FBXO41_ENST00000295133.5_Missense_Mutation_p.P175L			Q8TF61	FBX41_HUMAN	F-box protein 41	114										breast(2)|central_nervous_system(1)|endometrium(1)|lung(6)|pancreas(1)|prostate(1)|skin(1)	13						GTGGGCGAGGGGAGCGTGGTG	0.726																																					p.P114L		Atlas-SNP	.											.	FBXO41	82	.	0			c.C341T						.						1	2	2					2																	73496418		1163	2298	3461	SO:0001583	missense	150726	exon1			GCGAGGGGAGCGT	AB075820	CCDS46337.1, CCDS46337.2	2p13.2	2004-08-24				ENSG00000163013		"F-boxes /  "other""	29409	protein-coding gene	gene with protein product		609108				11853319	Standard	NM_001080410		Approved	KIAA1940, Fbx41	uc021vjh.1	Q8TF61		ENST00000521871.1:c.341C>T	chr2.hg19:g.73496418G>A	ENSP00000428646:p.Pro114Leu	129.0	0.0		60.0	4.0	NM_001080410	G3V0Z7|Q2M1V8	Missense_Mutation	SNP	ENST00000521871.1	hg19	CCDS46337.2	.	.	.	.	.	.	.	.	.	.	G	15.39	2.820856	0.50633	.	.	ENSG00000163013	ENST00000295133;ENST00000521871;ENST00000520530	.	.	.	4.4	4.4	0.53042	.	0.144200	0.32503	N	0.006007	T	0.37265	0.0997	N	0.08118	0	0.41524	D	0.988414	B	0.15141	0.012	B	0.09377	0.004	T	0.33650	-0.9860	9	0.66056	D	0.02	-14.6849	12.6472	0.56742	0.0:0.0:1.0:0.0	.	114	Q8TF61	FBX41_HUMAN	L	175;114;175	.	ENSP00000295133:P175L	P	-	2	0	FBXO41	73349926	0.998000	0.40836	1.000000	0.80357	0.962000	0.63368	-0.033000	0.12246	2.428000	0.82296	0.462000	0.41574	CCC	.	.		0.726	FBXO41-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377381.1			A	73496418	G	A	73496418	3	1	254	1	0	0	0	0	1	0	0	0	5758	1232	43	3	2334	3	FBXO41	2	73496418	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	249051	73496418	169702955	107	34399										
DNAH6	1768	hgsc.bcm.edu	37	chr2	84822786	84822786	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	atagtccaaatttgattgccTggatccagaagtcctaaacg	8	9	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:84822786T>C	ENST00000237449.6	+	17	2749	c.2741T>C	c.(2740-2742)cTg>cCg	p.L914P	DNAH6_ENST00000389394.3_Missense_Mutation_p.L914P|DNAH6_ENST00000398278.2_Missense_Mutation_p.L914P			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	914	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						TTTGATTGCCTGGATCCAGAA	0.333																																					p.L914P		Atlas-SNP	.											.	DNAH6	194	.	0			c.T2741C						.						57	48	51					2																	84822786		692	1591	2283	SO:0001583	missense	1768	exon18			ATTGCCTGGATCC	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.2741T>C	chr2.hg19:g.84822786T>C	ENSP00000237449:p.Leu914Pro	54.0	0.0		93.0	4.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	hg19	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	T	19.81	3.896152	0.72639	.	.	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.66460	-0.21;-0.21;-0.21	5.82	5.82	0.92795	Dynein heavy chain, domain-2 (1);	.	.	.	.	D	0.86548	0.5959	H	0.94183	3.505	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	D	0.90224	0.4274	9	0.87932	D	0	.	15.159	0.72767	0.0:0.0:0.0:1.0	.	914	Q9C0G6	DYH6_HUMAN	P	914	ENSP00000374045:L914P;ENSP00000381326:L914P;ENSP00000237449:L914P	ENSP00000237449:L914P	L	+	2	0	DNAH6	84676297	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	6.206000	0.72154	2.215000	0.71742	0.528000	0.53228	CTG	.	.		0.333	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		C	84822786	T	C	84822786	3	2	254	1	0	0	0	0	1	0	0	0	4607	1580	55	2	2807	2	DNAH6	2	84822786	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	11326368	84822786	158376587	108	34400										
DNAH6	1768	hgsc.bcm.edu	37	chr2	84955003	84955003	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctgaatggaatttctttctcCgaggttctgcaggattggaa	11	7	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:84955003C>A	ENST00000237449.6	+	60	10191	c.10183C>A	c.(10183-10185)Cga>Aga	p.R3395R	DNAH6_ENST00000389394.3_Silent_p.R3395R			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	3395					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						TTTCTTTCTCCGAGGTTCTGC	0.413																																					p.R3395R		Atlas-SNP	.											.	DNAH6	194	.	0			c.C10183A						.						102	83	89					2																	84955003		692	1591	2283	SO:0001819	synonymous_variant	1768	exon61			TTTCTCCGAGGTT	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.10183C>A	chr2.hg19:g.84955003C>A		103.0	0.0		91.0	4.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	hg19	CCDS46348.1																																																																																			.	.		0.413	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		A	84955003	C	A	84955003	2	1	254	1	0	0	0	0	0	0	0	1	4607	644	23	1		1	DNAH6	2	84955003	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	132217	84955003	158244370	109	34401										
GNLY	10578	hgsc.bcm.edu	37	chr2	85922521	85922521	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgatgaggagaaatcctgccCgtgcctggcccaggagggcc	15	12	0	3	rs573832985		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:85922521C>T	ENST00000263863.4	+	2	259	c.131C>T	c.(130-132)cCg>cTg	p.P44L	GNLY_ENST00000533041.1_3'UTR|GNLY_ENST00000409696.3_Missense_Mutation_p.P29L|GNLY_ENST00000524600.1_Missense_Mutation_p.P71L	NM_006433.3	NP_006424.2	P22749	GNLY_HUMAN	granulysin	44					cellular defense response (GO:0006968)|defense response to bacterium (GO:0042742)|defense response to fungus (GO:0050832)|killing of cells of other organism (GO:0031640)	extracellular space (GO:0005615)				endometrium(4)|kidney(10)|large_intestine(1)|lung(1)|skin(2)|upper_aerodigestive_tract(1)	19						AAATCCTGCCCGTGCCTGGCC	0.622													C|||	1	0.000199681	8e-04	0	5008	,	,		18397	0		0	False		,,,				2504	0				p.P44L		Atlas-SNP	.											.	GNLY	29	.	0			c.C131T						.						77	64	69					2																	85922521		2203	4300	6503	SO:0001583	missense	10578	exon2			CCTGCCCGTGCCT	X54101	CCDS1984.1, CCDS46354.1	2p12-q11	2008-02-05			ENSG00000115523	ENSG00000115523			4414	protein-coding gene	gene with protein product	"T-lymphocyte activation gene 519"	188855		LAG2		2212946, 2434598	Standard	NM_012483		Approved	NKG5, LAG-2, D2S69E, TLA519	uc002sql.4	P22749	OTTHUMG00000130179	ENST00000263863.4:c.131C>T	chr2.hg19:g.85922521C>T	ENSP00000263863:p.Pro44Leu	78.0	0.0		84.0	4.0	NM_006433	P09325|Q6GU08	Missense_Mutation	SNP	ENST00000263863.4	hg19	CCDS1984.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.649|8.649	0.897716|0.897716	0.17686|0.17686	.|.	.|.	ENSG00000115523|ENSG00000115523	ENST00000263863;ENST00000524600;ENST00000409696|ENST00000526018	T;T;T|.	0.48201|.	0.87;0.82;0.87|.	1.64|1.64	-3.28|-3.28	0.05033|0.05033	.|.	2.881540|.	0.01470|.	U|.	0.016250|.	T|T	0.17280|0.17280	0.0415|0.0415	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	P;P|.	0.46512|.	0.879;0.879|.	B;B|.	0.26517|.	0.07;0.07|.	T|T	0.23226|0.23226	-1.0194|-1.0194	10|5	0.33141|.	T|.	0.24|.	.|.	5.7405|5.7405	0.18092|0.18092	0.2475:0.5939:0.1586:0.0|0.2475:0.5939:0.1586:0.0	.|.	71;44|.	B4E3H9;P22749|.	.;GNLY_HUMAN|.	L|C	44;71;29|11	ENSP00000263863:P44L;ENSP00000436423:P71L;ENSP00000387116:P29L|.	ENSP00000263863:P44L|.	P|R	+|+	2|1	0|0	GNLY|GNLY	85776032|85776032	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.125000|0.125000	0.20455|0.20455	-0.562000|-0.562000	0.05950|0.05950	-1.619000|-1.619000	0.01566|0.01566	0.306000|0.306000	0.20318|0.20318	CCG|CGT	.	.		0.622	GNLY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252497.1	NM_006433		T	85922521	C	T	85922521	3	4	254	1	0	0	0	0	1	0	0	0	6547	652	23	1	148	1	GNLY	2	85922521	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	967518	85922521	157276852	110	34402										
MRPS5	64969	hgsc.bcm.edu	37	chr2	95756225	95756225	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgtctttgatgccaatgagcCggcagatggtgatgatggcc	14	8	1	5			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:95756225C>T	ENST00000272418.2	-	11	1182	c.974G>A	c.(973-975)cGg>cAg	p.R325Q		NM_031902.3	NP_114108.1	P82675	RT05_HUMAN	mitochondrial ribosomal protein S5	325					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	20						GCCAATGAGCCGGCAGATGGT	0.572																																					p.R325Q		Atlas-SNP	.											.	MRPS5	52	.	0			c.G974A						.						99	100	100					2																	95756225		2203	4300	6503	SO:0001583	missense	64969	exon11			ATGAGCCGGCAGA	AB049940	CCDS2010.1	2p11.2-q11.2	2012-09-13			ENSG00000144029	ENSG00000144029		"Mitochondrial ribosomal proteins / small subunits"	14498	protein-coding gene	gene with protein product	"mitochondrial 28S ribosomal protein S5"	611972					Standard	NM_031902		Approved	MRP-S5, S5mt	uc002sub.3	P82675	OTTHUMG00000130394	ENST00000272418.2:c.974G>A	chr2.hg19:g.95756225C>T	ENSP00000272418:p.Arg325Gln	122.0	0.0		87.0	24.0	NM_031902	Q4ZFY5|Q96LJ6|Q9BWI4|Q9BYC4	Missense_Mutation	SNP	ENST00000272418.2	hg19	CCDS2010.1	.	.	.	.	.	.	.	.	.	.	C	14.83	2.652325	0.47362	.	.	ENSG00000144029	ENST00000272418	.	.	.	5.09	4.0	0.46444	Ribosomal protein S5 domain 2-type fold (1);Ribosomal protein S5, C-terminal (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);	0.122060	0.51477	D	0.000094	T	0.26521	0.0648	N	0.25144	0.715	0.26531	N	0.974258	B	0.20261	0.043	B	0.15484	0.013	T	0.11203	-1.0597	9	0.52906	T	0.07	-10.0992	7.817	0.29265	0.0:0.8007:0.0:0.1993	.	325	P82675	RT05_HUMAN	Q	325	.	ENSP00000272418:R325Q	R	-	2	0	MRPS5	95119952	0.993000	0.37304	1.000000	0.80357	0.998000	0.95712	2.213000	0.42844	2.360000	0.80028	0.591000	0.81541	CGG	.	.		0.572	MRPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252772.1	NM_031902		T	95756225	C	T	95756225	3	4	254	1	0	0	0	0	1	0	0	0	9855	652	23	1	326	1	MRPS5	2	95756225	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	9833704	95756225	147443148	111	34403										
FAHD2A	51011	hgsc.bcm.edu	37	chr2	96078508	96078508	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	caggaaacctcctgtctttcTcaaggtaggttagcgaaaag	10	9	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:96078508T>C	ENST00000233379.4	+	7	1031	c.878T>C	c.(877-879)cTc>cCc	p.L293P	FAHD2A_ENST00000447036.1_Missense_Mutation_p.L293P	NM_016044.2	NP_057128.2	Q96GK7	FAH2A_HUMAN	fumarylacetoacetate hydrolase domain containing 2A	293							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|lung(3)|ovary(1)	8						CCTGTCTTTCTCAAGGTAGGT	0.517																																					p.L293P		Atlas-SNP	.											.	FAHD2A	25	.	0			c.T878C						.						37	37	37					2																	96078508		2203	4300	6503	SO:0001583	missense	51011	exon7			TCTTTCTCAAGGT	AF151863	CCDS2014.1	2q11.2	2008-02-05			ENSG00000115042	ENSG00000115042			24252	protein-coding gene	gene with protein product							Standard	NM_016044		Approved	CGI-105	uc002sur.3	Q96GK7	OTTHUMG00000130397	ENST00000233379.4:c.878T>C	chr2.hg19:g.96078508T>C	ENSP00000233379:p.Leu293Pro	105.0	0.0		98.0	4.0	NM_016044	Q9Y3B0	Missense_Mutation	SNP	ENST00000233379.4	hg19	CCDS2014.1	.	.	.	.	.	.	.	.	.	.	T	19.38	3.816199	0.70912	.	.	ENSG00000115042	ENST00000447036;ENST00000233379	D;D	0.98633	-5.04;-5.04	3.38	3.38	0.38709	Fumarylacetoacetase, C-terminal-related (2);Fumarylacetoacetase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.99429	0.9798	H	0.98996	4.395	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98190	1.0462	10	0.87932	D	0	.	10.0306	0.42099	0.0:0.0:0.0:1.0	.	293	Q96GK7	FAH2A_HUMAN	P	293	ENSP00000406424:L293P;ENSP00000233379:L293P	ENSP00000233379:L293P	L	+	2	0	FAHD2A	95442235	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	6.987000	0.76206	1.527000	0.49086	0.402000	0.26972	CTC	.	.		0.517	FAHD2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252778.1	NM_016044		C	96078508	T	C	96078508	3	2	254	1	0	0	0	0	1	0	0	0	5378	1551	54	2	900	2	FAHD2A	2	96078508	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	322283	96078508	147120865	112	34404										
KIAA1310	55683	hgsc.bcm.edu	37	chr2	97302719	97302719	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcgggtggggcgggcactacTggcatctgggtgggcactcc	19	11	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:97302719T>C	ENST00000431828.1	-	2	230	c.154A>G	c.(154-156)Agt>Ggt	p.S52G	KANSL3_ENST00000435669.1_5'UTR|KANSL3_ENST00000487070.1_5'UTR|KANSL3_ENST00000599854.1_5'UTR|KANSL3_ENST00000441706.2_5'UTR|KANSL3_ENST00000440133.1_5'UTR			Q9P2N6	KANL3_HUMAN	KAT8 regulatory NSL complex subunit 3	52					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											CGGGCACTACTGGCATCTGGG	0.582																																					p.S52G		Atlas-SNP	.											.	.	.	.	0			c.A154G						.						54	47	49					2																	97302719		692	1591	2283	SO:0001583	missense	55683	exon2			CACTACTGGCATC	BC063792	CCDS46361.1	2q11.2	2011-10-31	2011-10-31	2011-10-31	ENSG00000114982	ENSG00000114982			25473	protein-coding gene	gene with protein product			"KIAA1310"	KIAA1310			Standard	NM_001115016		Approved	FLJ10081, Rcd1, NSL3	uc002swn.5	Q9P2N6	OTTHUMG00000155249	ENST00000431828.1:c.154A>G	chr2.hg19:g.97302719T>C	ENSP00000396749:p.Ser52Gly	161.0	0.0		101.0	5.0	NM_001115016	A1L184|D3DXH3|D3DXH4|Q05BU4|Q6P3X2|Q6PJH6|Q86T19|Q96L64|Q9H0C9|Q9H8C9|Q9HAP8|Q9NWE5	Missense_Mutation	SNP	ENST00000431828.1	hg19	CCDS46361.1	.	.	.	.	.	.	.	.	.	.	T	17.07	3.295076	0.60086	.	.	ENSG00000114982	ENST00000431828	T	0.69561	-0.41	4.73	4.73	0.59995	.	.	.	.	.	T	0.64713	0.2623	L	0.58101	1.795	0.80722	D	1	B	0.23128	0.08	B	0.29440	0.102	T	0.66551	-0.5895	9	0.87932	D	0	.	12.218	0.54416	0.0:0.0:0.0:1.0	.	52	Q9P2N6-3	.	G	52	ENSP00000396749:S52G	ENSP00000410775:S52G	S	-	1	0	KIAA1310	96666446	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.087000	0.76893	1.982000	0.57802	0.460000	0.39030	AGT	.	.		0.582	KANSL3-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339040.2	NM_017991		C	97302719	T	C	97302719	3	2	254	1	0	0	0	0	1	0	0	0	8231	1580	55	2	2562	2	KIAA1310	2	97302719	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	1224211	97302719	145896654	113	34405										
ZAP70	7535	hgsc.bcm.edu	37	chr2	98349776	98349776	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccaggggctgctgctcccacActcccagcccacccatccac	7	22	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:98349776A>G	ENST00000264972.5	+	7	1022	c.807A>G	c.(805-807)acA>acG	p.T269T	ZAP70_ENST00000442208.1_Silent_p.T143T|ZAP70_ENST00000463643.1_3'UTR|ZAP70_ENST00000451498.2_5'Flank	NM_001079.3	NP_001070.2	P43403	ZAP70_HUMAN	zeta-chain (TCR) associated protein kinase 70kDa	269	Interdomain B.				adaptive immune response (GO:0002250)|B cell activation (GO:0042113)|beta selection (GO:0043366)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative thymic T cell selection (GO:0045060)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of T cell differentiation (GO:0045582)|positive thymic T cell selection (GO:0045059)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell activation (GO:0042110)|T cell aggregation (GO:0070489)|T cell differentiation (GO:0030217)|T cell migration (GO:0072678)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	29						CTGCTCCCACACTCCCAGCCC	0.706																																					p.T269T		Atlas-SNP	.											.	ZAP70	77	.	0			c.A807G						.						18	18	18					2																	98349776		2203	4297	6500	SO:0001819	synonymous_variant	7535	exon7			TCCCACACTCCCA	L05148	CCDS33254.1, CCDS33255.1	2q11-q13	2014-09-17	2002-08-29		ENSG00000115085	ENSG00000115085		"SH2 domain containing"	12858	protein-coding gene	gene with protein product		176947	"zeta-chain (TCR) associated protein kinase (70 kD)"	SRK		1423621	Standard	NM_001079		Approved	ZAP-70, STD	uc002syd.1	P43403	OTTHUMG00000153060	ENST00000264972.5:c.807A>G	chr2.hg19:g.98349776A>G		191.0	0.0		124.0	6.0	NM_001079	A6NFP4|Q6PIA4|Q8IXD6|Q9UBS6	Silent	SNP	ENST00000264972.5	hg19	CCDS33254.1																																																																																			.	.		0.706	ZAP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329278.1			G	98349776	A	G	98349776	2	3	254	1	0	0	0	0	0	0	0	1	17529	146	6	2		2	ZAP70	2	98349776	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	1047057	98349776	144849597	114	34406										
LYG2	254773	hgsc.bcm.edu	37	chr2	99870712	99870712	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	attagtccccaaaacaccacGgaggataacatggcggggaa	11	10	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:99870712G>T	ENST00000409238.1	-	1	32	c.12C>A	c.(10-12)tcC>tcA	p.S4S	LYG2_ENST00000409679.1_Silent_p.S4S|LYG2_ENST00000423800.1_Silent_p.S4S|LYG2_ENST00000333017.2_Silent_p.S4S			Q86SG7	LYG2_HUMAN	lysozyme G-like 2	4					cell wall macromolecule catabolic process (GO:0016998)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)	lysozyme activity (GO:0003796)			large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(1)|stomach(1)	12						AAAACACCACGGAGGATAACA	0.398																																					p.S4S		Atlas-SNP	.											.	LYG2	26	.	0			c.C12A						.						119	109	112					2																	99870712		2203	4300	6503	SO:0001819	synonymous_variant	254773	exon2			CACCACGGAGGAT	AF323919	CCDS2042.1	2q11.2	2008-02-05			ENSG00000185674	ENSG00000185674			29615	protein-coding gene	gene with protein product						8889548, 12574869	Standard	NM_175735		Approved	LYGH	uc002szw.1	Q86SG7	OTTHUMG00000130643	ENST00000409238.1:c.12C>A	chr2.hg19:g.99870712G>T		73.0	0.0		57.0	5.0	NM_175735	Q496G2|Q53RW0	Silent	SNP	ENST00000409238.1	hg19	CCDS2042.1																																																																																			.	.		0.398	LYG2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330307.1	NM_175735		T	99870712	G	T	99870712	2	4	254	1	0	0	0	0	0	0	0	1	9114	1103	39	1		1	LYG2	2	99870712	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1520936	99870712	143328661	115	34407										
AFF3	3899	hgsc.bcm.edu	37	chr2	100185316	100185316	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gaaagaaaagggtctcaccaTtgcatctgctttatgcttca	8	9	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:100185316T>C	ENST00000409236.2	-	17	3092	c.2980A>G	c.(2980-2982)Atg>Gtg	p.M994V	AFF3_ENST00000317233.4_Missense_Mutation_p.M994V|AFF3_ENST00000409579.1_Missense_Mutation_p.M1019V|AFF3_ENST00000356421.2_Missense_Mutation_p.M1019V			P51826	AFF3_HUMAN	AF4/FMR2 family, member 3	994					embryonic hindlimb morphogenesis (GO:0035116)|regulation of transcription, DNA-templated (GO:0006355)|response to tumor necrosis factor (GO:0034612)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)	p.M1019V(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(9)|kidney(4)|large_intestine(20)|liver(1)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(3)	86						GGTCTCACCATTGCATCTGCT	0.383																																					p.M1019V		Atlas-SNP	.											AFF3,NS,carcinoma,0,1	AFF3	164	.	1	Substitution - Missense(1)	breast(1)	c.A3055G						.						208	190	197					2																	100185316		2203	4300	6503	SO:0001583	missense	3899	exon18			TCACCATTGCATC	U34360	CCDS33258.1, CCDS42723.1	2q11.2-q12	2008-02-05	2005-06-27	2005-06-27	ENSG00000144218	ENSG00000144218			6473	protein-coding gene	gene with protein product		601464	"lymphoid nuclear protein related to AF4"	LAF4		8662235, 8555498	Standard	XM_005263945		Approved	MLLT2-like	uc002taf.3	P51826	OTTHUMG00000153011	ENST00000409236.2:c.2980A>G	chr2.hg19:g.100185316T>C	ENSP00000387207:p.Met994Val	125.0	0.0		121.0	6.0	NM_001025108	B7ZM46|B9EGL9|D3DVI6|Q53RD6|Q53S47|Q53SI6|Q53TB9|Q59F27|Q8IWJ5	Missense_Mutation	SNP	ENST00000409236.2	hg19	CCDS42723.1	.	.	.	.	.	.	.	.	.	.	T	18.71	3.681634	0.68042	.	.	ENSG00000144218	ENST00000317233;ENST00000356421;ENST00000409579;ENST00000409236;ENST00000445815	T;T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19;-0.19	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.71492	0.3346	M	0.63428	1.95	0.50813	D	0.999892	B;P	0.51147	0.237;0.942	B;P	0.53649	0.387;0.731	T	0.72704	-0.4213	10	0.49607	T	0.09	.	16.383	0.83481	0.0:0.0:0.0:1.0	.	994;1019	P51826;P51826-2	AFF3_HUMAN;.	V	994;1019;1019;994;36	ENSP00000317421:M994V;ENSP00000348793:M1019V;ENSP00000386834:M1019V;ENSP00000387207:M994V;ENSP00000416685:M36V	ENSP00000317421:M994V	M	-	1	0	AFF3	99551748	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.842000	0.62831	2.326000	0.78906	0.533000	0.62120	ATG	.	.		0.383	AFF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328982.3	NM_002285		C	100185316	T	C	100185316	3	2	254	1	0	0	0	0	1	0	0	0	358	1493	52	2	728	2	AFF3	2	100185316	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	314604	100185316	143014057	116	34408										
IL1R1	3554	hgsc.bcm.edu	37	chr2	102791944	102791944	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgtttttcctttagcttcagAtggaaagacctatgacgcat	8	8	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:102791944A>G	ENST00000410023.1	+	11	1460	c.1142A>G	c.(1141-1143)gAt>gGt	p.D381G	IL1R1_ENST00000409929.1_Intron|IL1R1_ENST00000424272.1_Missense_Mutation_p.D381G|AC007271.3_ENST00000428188.1_RNA|IL1R1_ENST00000409329.1_Missense_Mutation_p.D381G|IL1R1_ENST00000233946.3_Missense_Mutation_p.D381G|IL1R1_ENST00000409288.1_Missense_Mutation_p.D381G|IL1R1_ENST00000409589.1_Intron			P14778	IL1R1_HUMAN	interleukin 1 receptor, type I	381					cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|interleukin-1-mediated signaling pathway (GO:0070498)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)	cell surface (GO:0009986)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type I, activating receptor activity (GO:0004909)|platelet-derived growth factor receptor binding (GO:0005161)|signal transducer activity (GO:0004871)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|prostate(2)|skin(3)	19					Anakinra(DB00026)	TTAGCTTCAGATGGAAAGACC	0.348																																					p.D381G		Atlas-SNP	.											.	IL1R1	52	.	0			c.A1142G						.						228	214	219					2																	102791944		2203	4300	6503	SO:0001583	missense	3554	exon10			CTTCAGATGGAAA	M27492	CCDS2055.1, CCDS74547.1	2q12	2013-01-29			ENSG00000115594	ENSG00000115594		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5993	protein-coding gene	gene with protein product		147810		IL1R, IL1RA		1833184, 10191101	Standard	XM_005263929		Approved	D2S1473, CD121A	uc002tbr.3	P14778	OTTHUMG00000130783	ENST00000410023.1:c.1142A>G	chr2.hg19:g.102791944A>G	ENSP00000386380:p.Asp381Gly	555.0	0.0		557.0	109.0	NM_000877	Q587I7	Missense_Mutation	SNP	ENST00000410023.1	hg19	CCDS2055.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.079933	0.76528	.	.	ENSG00000115594	ENST00000424272;ENST00000409329;ENST00000428279;ENST00000409288;ENST00000410023;ENST00000233946	T;T;T;T;T;T	0.02606	4.23;4.23;4.23;4.23;4.23;4.23	5.23	5.23	0.72850	Toll/interleukin-1 receptor homology (TIR) domain (1);	0.155915	0.56097	D	0.000030	T	0.19406	0.0466	M	0.88450	2.955	0.53005	D	0.999968	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.01245	-1.1407	10	0.87932	D	0	.	15.4254	0.75045	1.0:0.0:0.0:0.0	.	381;381	P14778;B8ZZ73	IL1R1_HUMAN;.	G	381;381;237;381;381;381	ENSP00000415366:D381G;ENSP00000387131:D381G;ENSP00000410461:D237G;ENSP00000386478:D381G;ENSP00000386380:D381G;ENSP00000233946:D381G	ENSP00000233946:D381G	D	+	2	0	IL1R1	102158376	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.777000	0.62361	2.104000	0.64026	0.456000	0.33151	GAT	.	.		0.348	IL1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253299.1			G	102791944	A	G	102791944	3	3	254	1	0	0	0	0	1	0	0	0	7667	333	12	2	1176	2	IL1R1	2	102791944	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	2606628	102791944	140407429	117	34409										
NCK2	8440	hgsc.bcm.edu	37	chr2	106498261	106498261	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggagaacgaccccgagtggtGgaaatgcaaaaatgcccggg	15	9	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:106498261G>A	ENST00000233154.4	+	4	1146	c.704G>A	c.(703-705)tGg>tAg	p.W235*	NCK2_ENST00000522586.1_Intron|NCK2_ENST00000393349.2_Nonsense_Mutation_p.W235*|NCK2_ENST00000451463.2_Intron	NM_003581.4	NP_003572.2	O43639	NCK2_HUMAN	NCK adaptor protein 2	235	SH3 3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin filament organization (GO:0007015)|axon guidance (GO:0007411)|cell migration (GO:0016477)|epidermal growth factor receptor signaling pathway (GO:0007173)|lamellipodium assembly (GO:0030032)|negative regulation of cell proliferation (GO:0008285)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of translation (GO:0006417)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|vesicle membrane (GO:0012506)	cytoskeletal adaptor activity (GO:0008093)|receptor signaling complex scaffold activity (GO:0030159)			endometrium(1)|lung(3)|ovary(1)	5						CCCGAGTGGTGGAAATGCAAA	0.622																																					p.W235X		Atlas-SNP	.											.	NCK2	75	.	0			c.G704A						.						73	81	78					2																	106498261		2203	4300	6503	SO:0001587	stop_gained	8440	exon3			AGTGGTGGAAATG	AF043119	CCDS33266.1	2q12	2013-02-14			ENSG00000071051	ENSG00000071051		"SH2 domain containing"	7665	protein-coding gene	gene with protein product		604930				9737977, 16752908	Standard	NM_001004720		Approved	NCKbeta	uc002tdi.3	O43639	OTTHUMG00000153116	ENST00000233154.4:c.704G>A	chr2.hg19:g.106498261G>A	ENSP00000233154:p.Trp235*	118.0	0.0		91.0	5.0	NM_001004720	D3DVK1|Q9BWN9|Q9UIC3	Nonsense_Mutation	SNP	ENST00000233154.4	hg19	CCDS33266.1	.	.	.	.	.	.	.	.	.	.	G	40	8.081717	0.98643	.	.	ENSG00000071051	ENST00000233154;ENST00000393349	.	.	.	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.6619	19.782	0.96420	0.0:0.0:1.0:0.0	.	.	.	.	X	235	.	ENSP00000233154:W235X	W	+	2	0	NCK2	105864693	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.354000	0.97083	2.757000	0.94681	0.462000	0.41574	TGG	.	.		0.622	NCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329634.1	NM_003581		A	106498261	G	A	106498261	4	1	254	1	0	0	0	0	0	1	0	0	10229	1357	47	3	710	3	NCK2	2	106498261	Nonsense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	3706317	106498261	136701112	118	34410										
TFCP2L1	29842	hgsc.bcm.edu	37	chr2	121991665	121991665	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agctctgctccccacaactcAccagacaggttgctgtctcc	7	17	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:121991665A>T	ENST00000263707.5	-	12	1296		c.e12+1			NM_014553.2	NP_055368.1	Q9NZI6	TF2L1_HUMAN	transcription factor CP2-like 1						cell morphogenesis (GO:0000902)|cytoplasm organization (GO:0007028)|determination of adult lifespan (GO:0008340)|epithelial cell maturation (GO:0002070)|female pregnancy (GO:0007565)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of growth (GO:0045927)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|salivary gland development (GO:0007431)|steroid biosynthetic process (GO:0006694)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(4)|large_intestine(5)|lung(7)|ovary(1)|pancreas(2)|skin(1)|stomach(1)	22	Renal(3;0.01)					CCCACAACTCACCAGACAGGT	0.577																																					.		Atlas-SNP	.											.	TFCP2L1	54	.	0			c.1198+2T>A						.						95	87	90					2																	121991665		2203	4300	6503	SO:0001630	splice_region_variant	29842	exon13			CAACTCACCAGAC	AF198488	CCDS2134.1	2q14	2008-02-05			ENSG00000115112	ENSG00000115112			17925	protein-coding gene	gene with protein product		609785				10644752, 11073954	Standard	NM_014553		Approved	LBP-9, CRTR1	uc002tmx.3	Q9NZI6	OTTHUMG00000131443	ENST00000263707.5:c.1198+1T>A	chr2.hg19:g.121991665A>T		61.0	0.0		56.0	4.0	NM_014553	Q4ZG43	Splice_Site	SNP	ENST00000263707.5	hg19	CCDS2134.1	.	.	.	.	.	.	.	.	.	.	A	10.27	1.303855	0.23736	.	.	ENSG00000115112	ENST00000263707	.	.	.	5.53	4.39	0.52855	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.2086	0.48784	0.9282:0.0:0.0718:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TFCP2L1	121708135	1.000000	0.71417	0.994000	0.49952	0.064000	0.16182	4.675000	0.61619	0.955000	0.37878	0.448000	0.29417	.	.	.		0.577	TFCP2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338539.1	NM_014553	Intron	T	121991665	A	T	121991665	5	4	254	1	0	0	0	0	0	0	1	0	15811	173	6	4	255	4	TFCP2L1	2	121991665	Splice_Site	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	15493404	121991665	121207708	119	34411										
PROC	5624	hgsc.bcm.edu	37	chr2	128186178	128186178	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gctggggctaccacagcagcCgagagaaggaggccaagaga	16	10	0	2	rs121918141		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:128186178C>A	ENST00000234071.3	+	9	1129	c.1042C>A	c.(1042-1044)Cga>Aga	p.R348R	PROC_ENST00000409048.1_Silent_p.R382R|PROC_ENST00000422777.3_Silent_p.R348R|PROC_ENST00000453608.2_Silent_p.R403R	NM_000312.3	NP_000303.1	P04070	PROC_HUMAN	protein C (inactivator of coagulation factors Va and VIIIa)	348	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood coagulation (GO:0030195)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)	15	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0673)	Antihemophilic Factor(DB00025)|Menadione(DB00170)|Sodium Tetradecyl Sulfate(DB00464)	CCACAGCAGCCGAGAGAAGGA	0.612																																					p.R348R		Atlas-SNP	.											.	PROC	31	.	0			c.C1042A	GRCh37	CM870018	PROC	M	rs121918141	.						101	116	111					2																	128186178		2203	4300	6503	SO:0001819	synonymous_variant	5624	exon9			AGCAGCCGAGAGA	X02750	CCDS2145.1	2q13-q14	2014-01-30			ENSG00000115718	ENSG00000115718		"Endogenous ligands"	9451	protein-coding gene	gene with protein product	"prepro-protein C"	612283				2991887, 2437584	Standard	NM_000312		Approved		uc002tok.3	P04070	OTTHUMG00000131528	ENST00000234071.3:c.1042C>A	chr2.hg19:g.128186178C>A		131.0	0.0		67.0	4.0	NM_000312	B4DPQ7|Q15189|Q15190|Q16001|Q53S74|Q9UC55	Silent	SNP	ENST00000234071.3	hg19	CCDS2145.1																																																																																			.	.		0.612	PROC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254385.2	NM_000312		A	128186178	C	A	128186178	2	1	254	1	0	0	0	0	0	0	0	1	12557	644	23	1		1	PROC	2	128186178	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	6194513	128186178	115013195	120	34412										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141773444	141773444	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctcaatccttcccacgctgtCatctatttcatcttcctccc	2	18	5	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:141773444C>A	ENST00000389484.3	-	13	2982	c.2011G>T	c.(2011-2013)Gac>Tac	p.D671Y		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	671					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CCCACGCTGTCATCTATTTCA	0.408										TSP Lung(27;0.18)																											p.D671Y	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.G2011T						.						156	152	154					2																	141773444		2203	4300	6503	SO:0001583	missense	53353	exon13			CGCTGTCATCTAT	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.2011G>T	chr2.hg19:g.141773444C>A	ENSP00000374135:p.Asp671Tyr	322.0	0.0		238.0	72.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.031998	0.75504	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.90197	-2.63	5.75	5.75	0.90469	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.000000	0.85682	U	0.000000	D	0.93148	0.7818	L	0.50333	1.59	0.52099	D	0.999946	P	0.50066	0.931	P	0.57152	0.814	D	0.92568	0.6064	10	0.54805	T	0.06	.	20.312	0.98644	0.0:1.0:0.0:0.0	.	671	Q9NZR2	LRP1B_HUMAN	Y	671;609	ENSP00000374135:D671Y	ENSP00000374135:D671Y	D	-	1	0	LRP1B	141489914	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.951000	0.56684	2.866000	0.98385	0.650000	0.86243	GAC	.	.		0.408	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		A	141773444	C	A	141773444	3	1	254	1	0	0	0	0	1	0	0	0	8964	826	29	3	12104	3	LRP1B	2	141773444	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	13587266	141773444	101425929	121	34413										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141777526	141777526	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	accacaattcctctgggatgAgacatttcaccctctaaaag	6	12	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:141777526A>G	ENST00000389484.3	-	12	2906	c.1935T>C	c.(1933-1935)tcT>tcC	p.S645S		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	645					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CTCTGGGATGAGACATTTCAC	0.373										TSP Lung(27;0.18)																											p.S645S	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.T1935C						.						92	93	93					2																	141777526		2203	4300	6503	SO:0001819	synonymous_variant	53353	exon12			GGGATGAGACATT	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.1935T>C	chr2.hg19:g.141777526A>G		100.0	0.0		84.0	5.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	hg19	CCDS2182.1																																																																																			.	.		0.373	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		G	141777526	A	G	141777526	2	3	254	1	0	0	0	0	0	0	0	1	8964	291	11	2		2	LRP1B	2	141777526	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	4082	141777526	101421847	122	34414										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168107554	168107554	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggtctgaaatcatcatgtctCctgcaacacttcgtcgtcaa	7	12	5	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:168107554C>T	ENST00000409195.1	+	9	9741	c.9652C>T	c.(9652-9654)Cct>Tct	p.P3218S	XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.P2996S|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.P3218S|XIRP2_ENST00000420519.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	3043					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						CATCATGTCTCCTGCAACACT	0.448																																					p.P3218S		Atlas-SNP	.											.	XIRP2	914	.	0			c.C9652T						.						70	69	69					2																	168107554		1927	4131	6058	SO:0001583	missense	129446	exon9			ATGTCTCCTGCAA	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.9652C>T	chr2.hg19:g.168107554C>T	ENSP00000386840:p.Pro3218Ser	140.0	0.0		101.0	5.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	hg19	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.346807	0.82022	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273;ENST00000413534	T;T;T	0.02763	4.18;4.18;4.17	5.45	5.45	0.79879	.	0.369002	0.30840	N	0.008776	T	0.15565	0.0375	M	0.72894	2.215	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.993	T	0.00026	-1.2309	10	0.66056	D	0.02	-15.7534	18.4306	0.90624	0.0:1.0:0.0:0.0	.	3043;3043;2996	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	S	3218;3218;2996;632	ENSP00000386840:P3218S;ENSP00000295237:P3218S;ENSP00000387255:P2996S	ENSP00000295237:P3218S	P	+	1	0	XIRP2	167815800	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	6.782000	0.75073	2.729000	0.93468	0.460000	0.39030	CCT	.	.		0.448	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		T	168107554	C	T	168107554	3	4	254	1	0	0	0	0	1	0	0	0	17445	855	30	3	9682	3	XIRP2	2	168107554	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	26330028	168107554	75091819	123	34415										
LRP2	4036	hgsc.bcm.edu	37	chr2	170044602	170044602	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gacacgtgggttctggggtgTggcacaggtgcatcagctca	16	9	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:170044602T>A	ENST00000263816.3	-	49	9491	c.9206A>T	c.(9205-9207)cAc>cTc	p.H3069L		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	3069	LDL-receptor class A 24. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	TTCTGGGGTGTGGCACAGGTG	0.512																																					p.H3069L		Atlas-SNP	.											.	LRP2	751	.	0			c.A9206T						.						162	136	145					2																	170044602		2203	4300	6503	SO:0001583	missense	4036	exon49			GGGGTGTGGCACA		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.9206A>T	chr2.hg19:g.170044602T>A	ENSP00000263816:p.His3069Leu	318.0	0.0		196.0	49.0	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	hg19	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	T	3.858	-0.030439	0.07543	.	.	ENSG00000081479	ENST00000263816	D	0.90444	-2.67	5.68	0.456	0.16655	.	0.717713	0.14809	N	0.297148	T	0.80665	0.4666	L	0.37630	1.12	0.09310	N	1	B	0.28552	0.215	B	0.25614	0.062	T	0.65705	-0.6103	10	0.27785	T	0.31	.	1.9714	0.03406	0.1242:0.3487:0.254:0.2731	.	3069	P98164	LRP2_HUMAN	L	3069	ENSP00000263816:H3069L	ENSP00000263816:H3069L	H	-	2	0	LRP2	169752848	0.000000	0.05858	0.143000	0.22291	0.045000	0.14185	-0.678000	0.05209	0.408000	0.25621	0.528000	0.53228	CAC	.	.		0.512	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		A	170044602	T	A	170044602	3	1	254	1	0	0	0	0	1	0	0	0	8965	1696	59	4	4885	4	LRP2	2	170044602	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	1937048	170044602	73154771	124	34416										
TTN	7273	hgsc.bcm.edu	37	chr2	179577619	179577619	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gctaacactgaaaggaggtgTtccttttacgatacttgtga	10	7	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:179577619T>C	ENST00000591111.1	-	92	26406	c.26182A>G	c.(26182-26184)Aca>Gca	p.T8728A	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.T7801A|TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.T9045A|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000359218.5_Intron			Q8WZ42	TITIN_HUMAN	titin	12884	Ig-like 70.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AAAGGAGGTGTTCCTTTTACG	0.423																																					p.T9045A		Atlas-SNP	.											.	TTN	18412	.	0			c.A27133G						.						59	54	55					2																	179577619		1925	4121	6046	SO:0001583	missense	7273	exon94			GAGGTGTTCCTTT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.26182A>G	chr2.hg19:g.179577619T>C	ENSP00000465570:p.Thr8728Ala	59.0	0.0		84.0	4.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	11.08	1.533562	0.27387	.	.	ENSG00000155657	ENST00000342992	T	0.66995	-0.24	5.48	4.3	0.51218	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.60077	0.2241	L	0.52266	1.64	0.80722	D	1	B	0.06786	0.001	B	0.12156	0.007	T	0.58381	-0.7646	9	0.87932	D	0	.	10.4484	0.44507	0.3117:0.0:0.0:0.6883	.	8728	Q8WZ42	TITIN_HUMAN	A	7801	ENSP00000343764:T7801A	ENSP00000343764:T7801A	T	-	1	0	TTN	179285864	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	2.774000	0.47694	0.973000	0.38340	0.533000	0.62120	ACA	.	.		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179577619	T	C	179577619	3	2	254	1	0	0	0	0	1	0	0	0	16750	1725	60	2	77472	2	TTN	2	179577619	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	9533017	179577619	63621754	125	34417										
HECW2	57520	hgsc.bcm.edu	37	chr2	197172805	197172805	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tggctgtcaatgcgtgcctcCcagtctaaatggcagtgagg	13	10	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:197172805C>T	ENST00000260983.3	-	11	2621	c.2439G>A	c.(2437-2439)tgG>tgA	p.W813*	HECW2_ENST00000409111.1_Nonsense_Mutation_p.W457*	NM_020760.1	NP_065811.1	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	813	Interaction with TP73.|WW 1. {ECO:0000255|PROSITE- ProRule:PRU00224}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(24)|lung(45)|ovary(5)|pancreas(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	113						TGCGTGCCTCCCAGTCTAAAT	0.527																																					p.W813X		Atlas-SNP	.											.	HECW2	239	.	0			c.G2439A						.						44	42	43					2																	197172805		2203	4300	6503	SO:0001587	stop_gained	57520	exon11			TGCCTCCCAGTCT	AL390186	CCDS33354.1	2q32.3	2004-12-13			ENSG00000138411	ENSG00000138411			29853	protein-coding gene	gene with protein product						10718198, 12890487	Standard	NM_020760		Approved	KIAA1301, NEDL2	uc002utm.1	Q9P2P5	OTTHUMG00000154435	ENST00000260983.3:c.2439G>A	chr2.hg19:g.197172805C>T	ENSP00000260983:p.Trp813*	68.0	0.0		89.0	4.0	NM_020760	B8ZZB4|Q17RT5|Q68DF8|Q9NPS9	Nonsense_Mutation	SNP	ENST00000260983.3	hg19	CCDS33354.1	.	.	.	.	.	.	.	.	.	.	C	43	9.939275	0.99300	.	.	ENSG00000138411	ENST00000409111;ENST00000260983	.	.	.	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.8496	0.92222	0.0:1.0:0.0:0.0	.	.	.	.	X	457;813	.	ENSP00000260983:W813X	W	-	3	0	HECW2	196881050	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.320000	0.79064	2.692000	0.91855	0.555000	0.69702	TGG	.	.		0.527	HECW2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335199.3	NM_020760		T	197172805	C	T	197172805	4	4	254	1	0	0	0	0	0	1	0	0	7052	624	22	3	2355	3	HECW2	2	197172805	Nonsense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	17595186	197172805	46026568	126	34418										
PARD3B	117583	hgsc.bcm.edu	37	chr2	205912377	205912377	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gatacccagccaagcgcttcAcaccctggtggccagagtct	10	15	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:205912377A>G	ENST00000406610.2	+	4	675	c.468A>G	c.(466-468)tcA>tcG	p.S156S	PARD3B_ENST00000462231.1_Silent_p.S156S|PARD3B_ENST00000351153.1_Silent_p.S156S|PARD3B_ENST00000358768.2_Silent_p.S156S|PARD3B_ENST00000349953.3_Silent_p.S156S	NM_057177.6|NM_152526.5|NM_205863.3	NP_476518.4|NP_689739.4|NP_995585.2	Q8TEW8	PAR3L_HUMAN	par-3 family cell polarity regulator beta	156					cell cycle (GO:0007049)|cell division (GO:0051301)	membrane (GO:0016020)|tight junction (GO:0005923)				breast(1)|endometrium(9)|kidney(2)|large_intestine(6)|liver(4)|lung(33)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	65		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		CAAGCGCTTCACACCCTGGTG	0.532																																					p.S156S		Atlas-SNP	.											.	PARD3B	314	.	0			c.A468G						.						37	41	40					2																	205912377		1907	3991	5898	SO:0001819	synonymous_variant	117583	exon4			CGCTTCACACCCT	AB053321	CCDS42804.1, CCDS42805.1, CCDS42806.1	2q33.3	2013-08-28	2013-08-28	2006-09-28	ENSG00000116117	ENSG00000116117			14446	protein-coding gene	gene with protein product			"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 19", "par-3 partitioning defective 3 homolog B (C. elegans)"	ALS2CR19		11586298, 12459187	Standard	NM_057177		Approved	Par3L, PAR3beta	uc002vap.2	Q8TEW8	OTTHUMG00000154562	ENST00000406610.2:c.468A>G	chr2.hg19:g.205912377A>G		130.0	0.0		75.0	4.0	NM_205863	E9PE87|Q8IUC7|Q8IUC9|Q96DK9|Q96N09|Q96NX6|Q96NX7|Q96Q29	Silent	SNP	ENST00000406610.2	hg19																																																																																				.	.		0.532	PARD3B-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000335992.1	NM_057177		G	205912377	A	G	205912377	2	3	254	1	0	0	0	0	0	0	0	1	11453	146	6	2		2	PARD3B	2	205912377	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	8739572	205912377	37286996	127	34419										
GPR1	2825	hgsc.bcm.edu	37	chr2	207041152	207041152	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	atggtgggaatagctattgtGgtgaatggtgagctcccaaa	14	5	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:207041152G>T	ENST00000407325.2	-	3	1182	c.820C>A	c.(820-822)Cac>Aac	p.H274N	GPR1_ENST00000437420.1_Missense_Mutation_p.H274N	NM_001098199.1|NM_001261452.1|NM_001261453.1|NM_001261454.1|NM_001261455.1|NM_005279.3	NP_001091669.1|NP_001248381.1|NP_001248382.1|NP_001248383.1|NP_001248384.1|NP_005270.2	P46091	GPR1_HUMAN	G protein-coupled receptor 1	274					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(1)	18		Lung NSC(271;7.93e-06)|Renal(323;0.000147)|Hepatocellular(293;0.000888)		UCEC - Uterine corpus endometrioid carcinoma (47;0.000241)|Epithelial(149;1.91e-37)|STAD - Stomach adenocarcinoma(1183;0.00178)|Lung(261;0.111)|LUSC - Lung squamous cell carcinoma(261;0.184)		TAGCTATTGTGGTGAATGGTG	0.478																																					p.H274N		Atlas-SNP	.											.	GPR1	38	.	0			c.C820A						.						107	101	103					2																	207041152		2203	4300	6503	SO:0001583	missense	2825	exon3			TATTGTGGTGAAT		CCDS2368.1	2q33.3	2014-01-30			ENSG00000183671	ENSG00000183671		"GPCR / Class A : Orphans"	4463	protein-coding gene	gene with protein product		600239				7851889	Standard	NM_005279		Approved		uc031rqv.1	P46091	OTTHUMG00000132894	ENST00000407325.2:c.820C>A	chr2.hg19:g.207041152G>T	ENSP00000384345:p.His274Asn	127.0	0.0		83.0	4.0	NM_001098199	A5JUU6|A8K4L1|Q53TR9|Q6NVX4	Missense_Mutation	SNP	ENST00000407325.2	hg19	CCDS2368.1	.	.	.	.	.	.	.	.	.	.	G	16.33	3.091780	0.55968	.	.	ENSG00000183671	ENST00000407325;ENST00000437420	T;T	0.71341	-0.56;-0.56	5.7	4.82	0.62117	GPCR, rhodopsin-like superfamily (1);	0.118678	0.56097	D	0.000023	T	0.72463	0.3463	L	0.31526	0.94	0.47094	D	0.999318	D	0.57257	0.979	P	0.57846	0.828	T	0.74763	-0.3555	10	0.52906	T	0.07	.	14.7805	0.69764	0.0693:0.0:0.9307:0.0	.	274	P46091	GPR1_HUMAN	N	274	ENSP00000384345:H274N;ENSP00000397535:H274N	ENSP00000384345:H274N	H	-	1	0	GPR1	206749397	1.000000	0.71417	0.997000	0.53966	0.652000	0.38707	3.569000	0.53827	1.415000	0.47037	0.655000	0.94253	CAC	.	.		0.478	GPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256394.2	NM_001098199		T	207041152	G	T	207041152	3	4	254	1	0	0	0	0	1	0	0	0	6629	1348	47	3	251	3	GPR1	2	207041152	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1128775	207041152	36158221	128	34420										
SMARCAL1	50485	hgsc.bcm.edu	37	chr2	217303199	217303199	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cgctgtcgagcagctatgccGgtcctaaaggtgagtacttc	12	11	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:217303199G>T	ENST00000357276.4	+	10	2031	c.1701G>T	c.(1699-1701)ccG>ccT	p.P567P	SMARCAL1_ENST00000358207.5_Silent_p.P567P	NM_014140.3	NP_054859.2	Q9NZC9	SMAL1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a-like 1	567	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA metabolic process (GO:0006259)|DNA strand renaturation (GO:0000733)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|replication fork processing (GO:0031297)	nucleus (GO:0005634)|site of double-strand break (GO:0035861)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(15)|ovary(3)|prostate(1)|skin(1)	42		Renal(323;0.0458)		Epithelial(149;9.48e-06)|all cancers(144;0.000621)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0111)		CAGCTATGCCGGTCCTAAAGG	0.488									Schimke Immuno-Osseous Dysplasia																												p.P567P		Atlas-SNP	.											SMARCAL1,colon,carcinoma,0,1	SMARCAL1	93	.	0			c.G1701T						.						76	68	71					2																	217303199		2203	4300	6503	SO:0001819	synonymous_variant	50485	exon10	Familial Cancer Database	SIOD	TATGCCGGTCCTA	AF210833	CCDS2403.1	2q35	2014-09-17			ENSG00000138375	ENSG00000138375			11102	protein-coding gene	gene with protein product	"HepA-related protein", "ATP-driven annealing helicase"	606622				10713074, 10857751, 18974355	Standard	NM_014140		Approved	HHARP, HARP	uc002vgd.4	Q9NZC9	OTTHUMG00000133055	ENST00000357276.4:c.1701G>T	chr2.hg19:g.217303199G>T		56.0	0.0		40.0	2.0	NM_014140	A6NEH0|Q53R00|Q96AY1|Q9NXQ5|Q9UFH3|Q9UI93	Silent	SNP	ENST00000357276.4	hg19	CCDS2403.1	.	.	.	.	.	.	.	.	.	.	G	5.189	0.220328	0.09863	.	.	ENSG00000138375	ENST00000445153	.	.	.	4.69	1.8	0.24995	.	.	.	.	.	T	0.54078	0.1836	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42766	-0.9432	4	.	.	.	-24.6343	6.5006	0.22166	0.0:0.3516:0.4695:0.1789	.	.	.	.	L	125	.	.	R	+	2	0	SMARCAL1	217011444	0.993000	0.37304	0.891000	0.34965	0.552000	0.35366	0.451000	0.21779	0.258000	0.21686	-0.311000	0.09066	CGG	.	.		0.488	SMARCAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256671.2			T	217303199	G	T	217303199	2	4	254	1	0	0	0	0	0	0	0	1	14788	1103	39	1		1	SMARCAL1	2	217303199	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	10262047	217303199	25896174	129	34421										
C2orf62	375307	hgsc.bcm.edu	37	chr2	219222293	219222293	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gatgctgttcttctctgagaCgctggccatggtctcagaca	11	11	3	2	rs369378162		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:219222293C>T	ENST00000289388.3	+	3	184	c.155C>T	c.(154-156)aCg>aTg	p.T52M	AC021016.8_ENST00000411433.1_RNA	NM_198559.1	NP_940961.1	Q7Z7H3	CATIP_HUMAN		52					actin filament polymerization (GO:0030041)|cilium organization (GO:0044782)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	16		Renal(207;0.0915)		Epithelial(149;8.08e-07)|all cancers(144;0.000146)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TTCTCTGAGACGCTGGCCATG	0.577																																					p.T52M		Atlas-SNP	.											.	C2orf62	28	.	0			c.C155T						.	C	MET/THR	1,4405	2.1+/-5.4	0,1,2202	43	40	41		155	4.3	0.9	2		41	0,8600		0,0,4300	no	missense	C2orf62	NM_198559.1	81	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	52/388	219222293	1,13005	2203	4300	6503	SO:0001583	missense	375307	exon3			CTGAGACGCTGGC																												ENST00000289388.3:c.155C>T	chr2.hg19:g.219222293C>T	ENSP00000289388:p.Thr52Met	111.0	0.0		109.0	13.0	NM_198559		Missense_Mutation	SNP	ENST00000289388.3	hg19	CCDS2414.1	.	.	.	.	.	.	.	.	.	.	C	13.91	2.378286	0.42207	2.27E-4	0.0	ENSG00000158428	ENST00000289388	.	.	.	4.32	4.32	0.51571	.	0.058136	0.64402	D	0.000001	T	0.68650	0.3024	M	0.67953	2.075	0.33075	D	0.535836	D	0.89917	1.0	D	0.91635	0.999	T	0.77571	-0.2538	9	0.87932	D	0	-18.5541	12.4741	0.55803	0.0:1.0:0.0:0.0	.	52	Q7Z7H3	CB062_HUMAN	M	52	.	ENSP00000289388:T52M	T	+	2	0	C2orf62	218930537	0.953000	0.32496	0.900000	0.35374	0.025000	0.11179	2.350000	0.44063	2.398000	0.81561	0.462000	0.41574	ACG	.	.		0.577	C2orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256771.1			T	219222293	C	T	219222293	3	4	254	1	0	0	0	0	1	0	0	0	2183	536	19	1	165	1	C2orf62	2	219222293	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1919094	219222293	23977080	130	34422										
CRYBA2	1412	hgsc.bcm.edu	37	chr2	219856962	219856962	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcggggtactcaaaggccacCcaactggaaaaggagaagag	13	9	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:219856962C>A	ENST00000295728.2	-	2	401	c.165G>T	c.(163-165)tgG>tgT	p.W55C	CRYBA2_ENST00000487181.1_5'Flank|CRYBA2_ENST00000392096.2_Missense_Mutation_p.W55C	NM_057093.1	NP_476434.1	P53672	CRBA2_HUMAN	crystallin, beta A2	55	Beta/gamma crystallin 'Greek key' 2. {ECO:0000255|PROSITE-ProRule:PRU00028}.				lens development in camera-type eye (GO:0002088)		structural constituent of eye lens (GO:0005212)			endometrium(1)|lung(3)|prostate(1)	5		Renal(207;0.0474)		Epithelial(149;9.77e-07)|all cancers(144;0.000167)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CAAAGGCCACCCAACTGGAAA	0.582																																					p.W55C		Atlas-SNP	.											.	CRYBA2	13	.	0			c.G165T						.						40	42	41					2																	219856962		2203	4300	6503	SO:0001583	missense	1412	exon3			GGCCACCCAACTG		CCDS2429.1	2q35	2013-02-14			ENSG00000163499	ENSG00000163499			2395	protein-coding gene	gene with protein product		600836				7490092, 12907171	Standard	NM_057093		Approved		uc002vjj.1	P53672	OTTHUMG00000133084	ENST00000295728.2:c.165G>T	chr2.hg19:g.219856962C>A	ENSP00000295728:p.Trp55Cys	87.0	0.0		84.0	4.0	NM_057094	Q4ZFX0|Q9Y562	Missense_Mutation	SNP	ENST00000295728.2	hg19	CCDS2429.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.052241	0.75960	.	.	ENSG00000163499	ENST00000392096;ENST00000295728;ENST00000453769	D;D;D	0.85702	-2.02;-2.02;-2.02	4.46	4.46	0.54185	Beta/gamma crystallin (5);Gamma-crystallin-related (1);	0.000000	0.85682	D	0.000000	D	0.94398	0.8198	H	0.94847	3.59	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95841	0.8866	10	0.87932	D	0	.	16.4349	0.83872	0.0:1.0:0.0:0.0	.	55	P53672	CRBA2_HUMAN	C	55	ENSP00000375946:W55C;ENSP00000295728:W55C;ENSP00000395120:W55C	ENSP00000295728:W55C	W	-	3	0	CRYBA2	219565206	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	7.373000	0.79623	2.476000	0.83614	0.655000	0.94253	TGG	.	.		0.582	CRYBA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336424.1	NM_057093		A	219856962	C	A	219856962	3	1	254	1	0	0	0	0	1	0	0	0	3910	624	22	3	440	3	CRYBA2	2	219856962	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	634669	219856962	23342411	131	34423										
ATG9A	79065	hgsc.bcm.edu	37	chr2	220089453	220089453	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	caccatgtagttctggaaacGgaggatgcggtggtagatgt	15	6	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:220089453G>T	ENST00000409618.1	-	8	1079	c.640C>A	c.(640-642)Cgt>Agt	p.R214S	ATG9A_ENST00000396761.2_Missense_Mutation_p.R214S|ATG9A_ENST00000409422.1_Missense_Mutation_p.R153S|ATG9A_ENST00000361242.4_Missense_Mutation_p.R214S|AC068946.1_ENST00000408417.1_RNA|ATG9A_ENST00000488833.1_5'Flank			Q7Z3C6	ATG9A_HUMAN	autophagy related 9A	214					autophagic vacuole assembly (GO:0000045)|late nucleophagy (GO:0044805)|mitochondrion degradation (GO:0000422)|piecemeal microautophagy of nucleus (GO:0034727)|protein localization to pre-autophagosomal structure (GO:0034497)|protein transport (GO:0015031)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)				endometrium(2)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|stomach(1)	13		Renal(207;0.0474)		Epithelial(149;1.37e-06)|all cancers(144;0.000222)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TTCTGGAAACGGAGGATGCGG	0.577																																					p.R214S		Atlas-SNP	.											.	ATG9A	50	.	0			c.C640A						.						115	118	117					2																	220089453		2134	4241	6375	SO:0001583	missense	79065	exon8			GGAAACGGAGGAT	AK021732	CCDS42820.1	2q35	2014-02-12	2012-06-06	2005-09-11	ENSG00000198925	ENSG00000198925			22408	protein-coding gene	gene with protein product		612204	"APG9 autophagy 9-like 1 (S. cerevisiae)", "ATG9 autophagy related 9 homolog A (S. cerevisiae)"	APG9L1			Standard	NM_024085		Approved	FLJ22169	uc002vkf.1	Q7Z3C6	OTTHUMG00000154557	ENST00000409618.1:c.640C>A	chr2.hg19:g.220089453G>T	ENSP00000386710:p.Arg214Ser	165.0	0.0		98.0	4.0	NM_001077198	Q3ZAQ6|Q6P0N7|Q7Z317|Q7Z320|Q8NDK6|Q8WU65|Q9BVL5|Q9H6L1|Q9HAG7	Missense_Mutation	SNP	ENST00000409618.1	hg19	CCDS42820.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.178098	0.78564	.	.	ENSG00000198925	ENST00000396761;ENST00000409618;ENST00000361242;ENST00000409422;ENST00000431715	T;T;T;T	0.62364	0.47;0.47;0.47;0.03	5.28	5.28	0.74379	.	0.157884	0.56097	D	0.000021	T	0.73473	0.3591	H	0.95260	3.645	0.80722	D	1	P	0.39282	0.666	B	0.33521	0.165	T	0.82723	-0.0316	10	0.87932	D	0	.	18.5131	0.90925	0.0:0.0:1.0:0.0	.	214	Q7Z3C6	ATG9A_HUMAN	S	214;214;214;153;118	ENSP00000379983:R214S;ENSP00000386710:R214S;ENSP00000355173:R214S;ENSP00000386535:R153S	ENSP00000355173:R214S	R	-	1	0	ATG9A	219797697	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	9.819000	0.99357	2.449000	0.82847	0.655000	0.94253	CGT	.	.		0.577	ATG9A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335930.1	NM_024085		T	220089453	G	T	220089453	3	4	254	1	0	0	0	0	1	0	0	0	1102	1116	39	1	1915	1	ATG9A	2	220089453	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	232491	220089453	23109920	132	34424										
GMPPA	29926	hgsc.bcm.edu	37	chr2	220366718	220366718	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgagtgctatgttggaagccCaccgacgccagcgtcaccct	11	14	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:220366718C>T	ENST00000358215.3	+	5	757	c.388C>T	c.(388-390)Cac>Tac	p.H130Y	GMPPA_ENST00000373908.1_Missense_Mutation_p.H130Y|GMPPA_ENST00000313597.5_Missense_Mutation_p.H130Y|GMPPA_ENST00000341142.3_Missense_Mutation_p.H130Y|AC053503.11_ENST00000429882.1_RNA|GMPPA_ENST00000373917.3_Missense_Mutation_p.H130Y	NM_205847.2	NP_995319.1	Q96IJ6	GMPPA_HUMAN	GDP-mannose pyrophosphorylase A	130					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotidyltransferase activity (GO:0016779)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(6)|prostate(1)|skin(1)	20		Renal(207;0.0183)		Epithelial(149;3.82e-10)|all cancers(144;6.25e-08)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00807)|READ - Rectum adenocarcinoma(5;0.148)		GTTGGAAGCCCACCGACGCCA	0.587																																					p.H130Y		Atlas-SNP	.											.	GMPPA	50	.	0			c.C388T						.						185	168	174					2																	220366718		2203	4300	6503	SO:0001583	missense	29926	exon5			GAAGCCCACCGAC	AF135422	CCDS2441.1	2q36.1	2008-02-05			ENSG00000144591	ENSG00000144591			22923	protein-coding gene	gene with protein product		615495					Standard	NM_205847		Approved		uc002vlr.3	Q96IJ6	OTTHUMG00000058922	ENST00000358215.3:c.388C>T	chr2.hg19:g.220366718C>T	ENSP00000350949:p.His130Tyr	115.0	0.0		65.0	6.0	NM_205847	A6NJ74|A8K3Q6|B3KMT4|Q53GI0|Q9NWC3|Q9Y5P5	Missense_Mutation	SNP	ENST00000358215.3	hg19	CCDS2441.1	.	.	.	.	.	.	.	.	.	.	C	15.87	2.961313	0.53400	.	.	ENSG00000144591	ENST00000313597;ENST00000373917;ENST00000358215;ENST00000373908;ENST00000455657;ENST00000435316;ENST00000341142;ENST00000373924	D;D;D;D;T;T;D	0.94862	-3.54;-3.54;-3.54;-3.54;-0.93;-0.93;-3.54	4.89	3.98	0.46160	Nucleotidyl transferase (1);	0.119716	0.56097	N	0.000021	D	0.94145	0.8122	M	0.71036	2.16	0.42599	D	0.993274	B;B	0.31227	0.011;0.314	B;B	0.39935	0.029;0.314	D	0.92724	0.6194	10	0.51188	T	0.08	-24.9987	12.0301	0.53394	0.0:0.9114:0.0:0.0886	.	130;130	Q96IJ6-2;Q96IJ6	.;GMPPA_HUMAN	Y	130;130;130;130;130;95;130;60	ENSP00000315925:H130Y;ENSP00000363027:H130Y;ENSP00000350949:H130Y;ENSP00000363016:H130Y;ENSP00000392465:H130Y;ENSP00000411060:H95Y;ENSP00000340760:H130Y	ENSP00000315925:H130Y	H	+	1	0	GMPPA	220074962	0.999000	0.42202	0.996000	0.52242	0.809000	0.45718	2.616000	0.46376	0.999000	0.39023	0.561000	0.74099	CAC	.	.		0.587	GMPPA-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130230.1	NM_013335		T	220366718	C	T	220366718	3	4	254	1	0	0	0	0	1	0	0	0	6502	594	21	3	402	3	GMPPA	2	220366718	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	277265	220366718	22832655	133	34425										
OBSL1	23363	hgsc.bcm.edu	37	chr2	220422083	220422083	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	accttccacgctgacaaggaAgatgcggctgtcctggggcg	14	12	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:220422083A>G	ENST00000404537.1	-	12	4104	c.4048T>C	c.(4048-4050)Ttc>Ctc	p.F1350L	OBSL1_ENST00000265318.4_Missense_Mutation_p.F1258L|OBSL1_ENST00000373876.1_Intron|OBSL1_ENST00000265317.5_Intron|RP11-256I23.2_ENST00000597192.1_RNA|OBSL1_ENST00000603926.1_Missense_Mutation_p.F1350L	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	1350	Ig-like 11.				cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)						Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		CTGACAAGGAAGATGCGGCTG	0.667																																					p.F1350L		Atlas-SNP	.											.	OBSL1	120	.	0			c.T4048C						.						17	21	20					2																	220422083		2175	4243	6418	SO:0001583	missense	23363	exon12			CAAGGAAGATGCG	BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.4048T>C	chr2.hg19:g.220422083A>G	ENSP00000385636:p.Phe1350Leu	54.0	0.0		38.0	4.0	NM_001173431	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Missense_Mutation	SNP	ENST00000404537.1	hg19	CCDS46520.1	.	.	.	.	.	.	.	.	.	.	a	21.6	4.169419	0.78452	.	.	ENSG00000124006	ENST00000265318;ENST00000404537	T;T	0.04603	3.59;3.59	3.89	3.89	0.44902	Immunoglobulin subtype (1);	.	.	.	.	T	0.19967	0.0480	M	0.82132	2.575	0.48975	D	0.999734	D;D	0.61080	0.989;0.979	D;D	0.74348	0.983;0.983	T	0.01488	-1.1342	9	0.35671	T	0.21	.	12.9034	0.58139	1.0:0.0:0.0:0.0	.	1351;1350	A4KVA4;O75147	.;OBSL1_HUMAN	L	1258;1350	ENSP00000265318:F1258L;ENSP00000385636:F1350L	ENSP00000265318:F1258L	F	-	1	0	OBSL1	220130327	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	4.183000	0.58317	1.643000	0.50594	0.375000	0.23000	TTC	.	.		0.667	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1			G	220422083	A	G	220422083	3	3	254	1	0	0	0	0	1	0	0	0	10822	72	3	2	1705	2	OBSL1	2	220422083	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	55365	220422083	22777290	134	34426										
PAX3	5077	hgsc.bcm.edu	37	chr2	223066865	223066865	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gagagcgcgtaatcagtctgGggctgatgaggtaccccacc	14	11	2	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:223066865G>T	ENST00000350526.4	-	8	1354	c.1218C>A	c.(1216-1218)ccC>ccA	p.P406P	PAX3_ENST00000336840.6_Intron|PAX3_ENST00000392070.2_Silent_p.P406P|PAX3_ENST00000464706.1_5'UTR|PAX3_ENST00000392069.2_Silent_p.P406P|PAX3_ENST00000409551.3_Silent_p.P405P|PAX3_ENST00000344493.4_Intron	NM_181457.3	NP_852122.1	P23760	PAX3_HUMAN	paired box 3	406					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|developmental pigmentation (GO:0048066)|heart development (GO:0007507)|mammary gland specification (GO:0060594)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|neuron fate commitment (GO:0048663)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of somitogenesis (GO:0014807)|sensory perception of sound (GO:0007605)|spinal cord association neuron differentiation (GO:0021527)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)		PAX3/NCOA2(4)|PAX3/NCOA1(8)|PAX3/FOXO1(749)	NS(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(13)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	38		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;1.85e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AATCAGTCTGGGGCTGATGAG	0.542			T	"FOXO1A, NCOA1"	alveolar rhabdomyosarcoma		Waardenburg syndrome; craniofacial-deafness-hand syndrome																														p.P406P		Atlas-SNP	.		Dom	yes		2	2q35	5077	paired box gene 3	yes	M	.	PAX3	106	.	0			c.C1218A						.						64	63	63					2																	223066865		2203	4300	6503	SO:0001819	synonymous_variant	5077	exon8			AGTCTGGGGCTGA		CCDS2449.1, CCDS2450.1, CCDS2451.1, CCDS42825.1, CCDS2448.1, CCDS42826.1, CCDS46522.1, CCDS46523.1	2q36.1	2011-06-20	2007-07-12		ENSG00000135903	ENSG00000135903		"Paired boxes", "Homeoboxes / PRD class"	8617	protein-coding gene	gene with protein product		606597	"Waardenburg syndrome 1", "paired box gene 3 (Waardenburg syndrome 1)"	WS1		1347149	Standard	NM_181461		Approved	HUP2	uc002vmt.2	P23760	OTTHUMG00000133157	ENST00000350526.4:c.1218C>A	chr2.hg19:g.223066865G>T		115.0	0.0		81.0	4.0	NM_181457	G5E9C1|Q16448|Q494Z3|Q494Z4|Q53T90|Q6GSJ9|Q86UQ2|Q86UQ3	Silent	SNP	ENST00000350526.4	hg19	CCDS42826.1																																																																																			.	.		0.542	PAX3-006	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328670.1			T	223066865	G	T	223066865	2	4	254	1	0	0	0	0	0	0	0	1	11489	1219	43	3		3	PAX3	2	223066865	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	2644782	223066865	20132508	135	34427										
CUL3	8452	hgsc.bcm.edu	37	chr2	225376256	225376256	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tagcttctactttctttataTatactgaagcactattttct	3	8	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:225376256T>C	ENST00000264414.4	-	6	1036	c.698A>G	c.(697-699)tAt>tGt	p.Y233C	CUL3_ENST00000409777.1_Missense_Mutation_p.Y209C|CUL3_ENST00000409096.1_Missense_Mutation_p.Y209C|CUL3_ENST00000432260.2_5'Flank|CUL3_ENST00000344951.4_Missense_Mutation_p.Y167C	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3	233					cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|COPII vesicle coating (GO:0048208)|cyclin catabolic process (GO:0008054)|embryonic cleavage (GO:0040016)|ER to Golgi vesicle-mediated transport (GO:0006888)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation (GO:0007369)|integrin-mediated signaling pathway (GO:0007229)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic metaphase plate congression (GO:0007080)|negative regulation of Rho protein signal transduction (GO:0035024)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|stem cell division (GO:0017145)|stress fiber assembly (GO:0043149)|trophectodermal cellular morphogenesis (GO:0001831)|Wnt signaling pathway (GO:0016055)	Cul3-RING ubiquitin ligase complex (GO:0031463)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|nucleus (GO:0005634)|polar microtubule (GO:0005827)	POZ domain binding (GO:0031208)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	46		all_lung(227;0.00877)|Lung NSC(271;0.011)|Renal(207;0.0112)|all_hematologic(139;0.138)		Epithelial(121;1.58e-11)|all cancers(144;1.43e-08)|Lung(261;0.00863)|LUSC - Lung squamous cell carcinoma(224;0.00902)		TTTCTTTATATATACTGAAGC	0.308																																					p.Y239C		Atlas-SNP	.											.	CUL3	96	.	0			c.A716G						.						117	118	118					2																	225376256		2202	4299	6501	SO:0001583	missense	8452	exon6			TTTATATATACTG	U58089	CCDS2462.1, CCDS58751.1	2q36.2	2011-05-24			ENSG00000036257	ENSG00000036257			2553	protein-coding gene	gene with protein product		603136				8681378, 17192413	Standard	NM_003590		Approved		uc002vny.3	Q13618	OTTHUMG00000133167	ENST00000264414.4:c.698A>G	chr2.hg19:g.225376256T>C	ENSP00000264414:p.Tyr233Cys	110.0	0.0		118.0	5.0	NM_001257198	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	Missense_Mutation	SNP	ENST00000264414.4	hg19	CCDS2462.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.395818	0.83011	.	.	ENSG00000036257	ENST00000264414;ENST00000344951;ENST00000409096;ENST00000409777	T;T;T;T	0.61510	0.1;0.1;0.1;0.1	5.64	5.64	0.86602	Cullin, N-terminal (1);Cullin repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.83741	0.5320	H	0.95950	3.745	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.89060	0.3462	10	0.87932	D	0	.	16.1486	0.81594	0.0:0.0:0.0:1.0	.	167;211;233	Q13618-3;Q53S54;Q13618	.;.;CUL3_HUMAN	C	233;167;209;209	ENSP00000264414:Y233C;ENSP00000343601:Y167C;ENSP00000387200:Y209C;ENSP00000386525:Y209C	ENSP00000264414:Y233C	Y	-	2	0	CUL3	225084500	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.655000	0.83696	2.265000	0.75225	0.482000	0.46254	TAT	.	.		0.308	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256871.2			C	225376256	T	C	225376256	3	2	254	1	0	0	0	0	1	0	0	0	4058	1406	49	2	1652	2	CUL3	2	225376256	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	2309391	225376256	17823117	136	34428										
DOCK10	55619	hgsc.bcm.edu	37	chr2	225751231	225751231	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aggaatgtgaaggaagcttcTctggtttgtattctgctctg	12	6	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:225751231T>C	ENST00000258390.7	-	5	501	c.434A>G	c.(433-435)gAg>gGg	p.E145G	DOCK10_ENST00000409592.3_Missense_Mutation_p.E139G	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	145					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		AGGAAGCTTCTCTGGTTTGTA	0.328																																					p.E145G		Atlas-SNP	.											.	DOCK10	308	.	0			c.A434G						.						91	85	87					2																	225751231		1836	4073	5909	SO:0001583	missense	55619	exon5			AGCTTCTCTGGTT	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"Pleckstrin homology (PH) domain containing"	23479	protein-coding gene	gene with protein product	"zizimin3"	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.434A>G	chr2.hg19:g.225751231T>C	ENSP00000258390:p.Glu145Gly	95.0	0.0		73.0	4.0	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Missense_Mutation	SNP	ENST00000258390.7	hg19	CCDS46528.1	.	.	.	.	.	.	.	.	.	.	T	24.5	4.532934	0.85812	.	.	ENSG00000135905	ENST00000409592;ENST00000258390	T;T	0.48201	0.82;0.82	5.69	5.69	0.88448	.	0.106120	0.64402	D	0.000006	T	0.68366	0.2993	M	0.70842	2.15	0.52501	D	0.999958	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.999	T	0.71020	-0.4713	10	0.59425	D	0.04	.	15.9476	0.79806	0.0:0.0:0.0:1.0	.	145;145;139	Q96BY6;Q96BY6-2;B3FL70	DOC10_HUMAN;.;.	G	139;145	ENSP00000386694:E139G;ENSP00000258390:E145G	ENSP00000258390:E145G	E	-	2	0	DOCK10	225459475	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.698000	0.84413	2.173000	0.68751	0.533000	0.62120	GAG	.	.		0.328	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1			C	225751231	T	C	225751231	3	2	254	1	0	0	0	0	1	0	0	0	4687	1551	54	2	6334	2	DOCK10	2	225751231	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	374975	225751231	17448142	137	34429										
DOCK10	55619	hgsc.bcm.edu	37	chr2	225796364	225796364	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agtctcataatccaaaggctCgagaagcctaggcttttctt	8	10	2	1	rs186136248	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:225796364C>A	ENST00000258390.7	-	2	212	c.145G>T	c.(145-147)Gag>Tag	p.E49*	DOCK10_ENST00000474102.1_5'UTR|DOCK10_ENST00000409592.3_Nonsense_Mutation_p.E43*	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	49					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		TCCAAAGGCTCGAGAAGCCTA	0.398																																					p.E49X		Atlas-SNP	.											.	DOCK10	308	.	0			c.G145T						.						88	85	86					2																	225796364		1860	4104	5964	SO:0001587	stop_gained	55619	exon2			AAGGCTCGAGAAG	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"Pleckstrin homology (PH) domain containing"	23479	protein-coding gene	gene with protein product	"zizimin3"	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.145G>T	chr2.hg19:g.225796364C>A	ENSP00000258390:p.Glu49*	81.0	0.0		50.0	4.0	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Nonsense_Mutation	SNP	ENST00000258390.7	hg19	CCDS46528.1	.	.	.	.	.	.	.	.	.	.	C	32	5.174291	0.94807	.	.	ENSG00000135905	ENST00000409592;ENST00000258390	.	.	.	5.59	4.71	0.59529	.	0.148988	0.64402	D	0.000013	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	16.6234	0.84935	0.0:0.8698:0.1302:0.0	.	.	.	.	X	43;49	.	ENSP00000258390:E49X	E	-	1	0	DOCK10	225504608	0.993000	0.37304	0.864000	0.33941	0.695000	0.40330	3.186000	0.50942	1.499000	0.48617	0.563000	0.77884	GAG	.	C|0.999;T|0.001		0.398	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1			A	225796364	C	A	225796364	4	1	254	1	0	0	0	0	0	1	0	0	4687	893	31	1	6635	1	DOCK10	2	225796364	Nonsense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	45133	225796364	17403009	138	34430										
KIAA1486	57624	hgsc.bcm.edu	37	chr2	226378371	226378371	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agccagtaagagcgggaaaaCccctgagaggactgaaggta	14	8	0	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:226378371C>T	ENST00000272907.6	+	3	919	c.506C>T	c.(505-507)aCc>aTc	p.T169I	NYAP2_ENST00000409269.2_Intron	NM_020864.1	NP_065915.1	Q9P242	NYAP2_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	169					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												AGCGGGAAAACCCCTGAGAGG	0.542																																					p.T169I		Atlas-SNP	.											.	.	.	.	0			c.C506T						.						60	73	69					2																	226378371		2051	4207	6258	SO:0001583	missense	57624	exon3			GGAAAACCCCTGA	AB040919	CCDS46529.1	2q36.3	2011-11-30	2011-11-30	2011-11-30	ENSG00000144460	ENSG00000144460			29291	protein-coding gene	gene with protein product		615478	"KIAA1486"	KIAA1486		10819331, 21946561	Standard	NM_020864		Approved		uc002voe.2	Q9P242	OTTHUMG00000153450	ENST00000272907.6:c.506C>T	chr2.hg19:g.226378371C>T	ENSP00000272907:p.Thr169Ile	86.0	0.0		67.0	14.0	NM_020864	A2RRN4|Q96NL2	Missense_Mutation	SNP	ENST00000272907.6	hg19	CCDS46529.1	.	.	.	.	.	.	.	.	.	.	C	15.32	2.799329	0.50208	.	.	ENSG00000144460	ENST00000272907	T	0.42900	0.96	5.46	-3.88	0.04205	.	1.155810	0.06302	N	0.701107	T	0.25865	0.0630	N	0.22421	0.69	0.09310	N	0.999998	B	0.06786	0.001	B	0.04013	0.001	T	0.25745	-1.0123	10	0.34782	T	0.22	0.1231	7.788	0.29103	0.0:0.128:0.5199:0.3521	.	169	Q9P242	K1486_HUMAN	I	169	ENSP00000272907:T169I	ENSP00000272907:T169I	T	+	2	0	KIAA1486	226086615	0.000000	0.05858	0.000000	0.03702	0.969000	0.65631	0.510000	0.22723	-0.592000	0.05851	0.563000	0.77884	ACC	.	.		0.542	NYAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331258.1	NM_020864		T	226378371	C	T	226378371	3	4	254	1	0	0	0	0	1	0	0	0	8246	507	18	3	512	3	KIAA1486	2	226378371	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	582007	226378371	16821002	139	34431										
KIAA1486	57624	hgsc.bcm.edu	37	chr2	226447056	226447056	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcctgacttggacttcgccaAggcctcagtgccatgccccc	10	17	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:226447056A>G	ENST00000272907.6	+	4	1336	c.923A>G	c.(922-924)aAg>aGg	p.K308R	NYAP2_ENST00000409269.2_Intron	NM_020864.1	NP_065915.1	Q9P242	NYAP2_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	308					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												GACTTCGCCAAGGCCTCAGTG	0.597																																					p.K308R		Atlas-SNP	.											.	.	.	.	0			c.A923G						.						64	67	66					2																	226447056		2069	4190	6259	SO:0001583	missense	57624	exon4			TCGCCAAGGCCTC	AB040919	CCDS46529.1	2q36.3	2011-11-30	2011-11-30	2011-11-30	ENSG00000144460	ENSG00000144460			29291	protein-coding gene	gene with protein product		615478	"KIAA1486"	KIAA1486		10819331, 21946561	Standard	NM_020864		Approved		uc002voe.2	Q9P242	OTTHUMG00000153450	ENST00000272907.6:c.923A>G	chr2.hg19:g.226447056A>G	ENSP00000272907:p.Lys308Arg	114.0	0.0		117.0	27.0	NM_020864	A2RRN4|Q96NL2	Missense_Mutation	SNP	ENST00000272907.6	hg19	CCDS46529.1	.	.	.	.	.	.	.	.	.	.	A	11.36	1.615003	0.28712	.	.	ENSG00000144460	ENST00000272907	T	0.44482	0.92	5.84	3.49	0.39957	.	0.212320	0.41294	N	0.000920	T	0.31606	0.0802	L	0.45137	1.4	0.80722	D	1	B	0.15930	0.015	B	0.15870	0.014	T	0.06917	-1.0800	10	0.15499	T	0.54	-20.2547	10.2151	0.43164	0.8774:0.0:0.1226:0.0	.	308	Q9P242	K1486_HUMAN	R	308	ENSP00000272907:K308R	ENSP00000272907:K308R	K	+	2	0	KIAA1486	226155300	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.141000	0.42168	0.487000	0.27698	0.528000	0.53228	AAG	.	.		0.597	NYAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331258.1	NM_020864		G	226447056	A	G	226447056	3	3	254	1	0	0	0	0	1	0	0	0	8246	72	3	2	933	2	KIAA1486	2	226447056	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	68685	226447056	16752317	140	34432										
TRIP12	9320	hgsc.bcm.edu	37	chr2	230643664	230643664	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tctctgtagttcctgagataCaagcgcataaaactccagtg	8	10	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:230643664C>T	ENST00000283943.5	-	34	5090	c.4912G>A	c.(4912-4914)Gta>Ata	p.V1638I	TRIP12_ENST00000389044.4_Missense_Mutation_p.V1686I|TRIP12_ENST00000389045.3_Missense_Mutation_p.V1368I	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	1638					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		TCCTGAGATACAAGCGCATAA	0.398																																					p.V1638I		Atlas-SNP	.											.	TRIP12	207	.	0			c.G4912A						.						168	167	167					2																	230643664		2203	4300	6503	SO:0001583	missense	9320	exon34			GAGATACAAGCGC	L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.4912G>A	chr2.hg19:g.230643664C>T	ENSP00000283943:p.Val1638Ile	106.0	0.0		82.0	4.0	NM_004238	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Missense_Mutation	SNP	ENST00000283943.5	hg19	CCDS33391.1	.	.	.	.	.	.	.	.	.	.	C	34	5.393726	0.96009	.	.	ENSG00000153827	ENST00000283943;ENST00000389045;ENST00000389044	T;T;T	0.43294	0.95;0.95;0.95	6.03	6.03	0.97812	HECT (4);	0.000000	0.85682	D	0.000000	T	0.62648	0.2445	L	0.54965	1.715	0.80722	D	1	P;D;P	0.54601	0.92;0.967;0.92	D;D;D	0.70716	0.956;0.97;0.956	T	0.58399	-0.7643	10	0.52906	T	0.07	.	20.1617	0.98138	0.0:1.0:0.0:0.0	.	1368;1686;1638	Q14CF1;Q14CA3;Q14669	.;.;TRIPC_HUMAN	I	1638;1368;1686	ENSP00000283943:V1638I;ENSP00000373697:V1368I;ENSP00000373696:V1686I	ENSP00000283943:V1638I	V	-	1	0	TRIP12	230351908	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.405000	0.80007	2.854000	0.98071	0.655000	0.94253	GTA	.	.		0.398	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238		T	230643664	C	T	230643664	3	4	254	1	0	0	0	0	1	0	0	0	16571	478	17	3	1098	3	TRIP12	2	230643664	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	4196608	230643664	12555709	141	34433										
DIS3L2	129563	hgsc.bcm.edu	37	chr2	232880358	232880358	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aggaggatgtttcagaaggcTtgaagagaggaacactcatc	13	6	2	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:232880358T>C	ENST00000409307.1	+	2	187	c.187T>C	c.(187-189)Ttg>Ctg	p.L63L	DIS3L2_ENST00000273009.6_Silent_p.L63L|DIS3L2_ENST00000360410.4_Silent_p.L63L|DIS3L2_ENST00000409401.3_Silent_p.L63L|AC105461.1_ENST00000413841.1_RNA|DIS3L2_ENST00000325385.7_Silent_p.L63L					DIS3 like 3'-5' exoribonuclease 2											breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(2)|urinary_tract(1)	40		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)		TTCAGAAGGCTTGAAGAGAGG	0.403																																					p.L63L		Atlas-SNP	.											.	DIS3L2	77	.	0			c.T187C						.						114	102	106					2																	232880358		1885	4121	6006	SO:0001819	synonymous_variant	129563	exon3			GAAGGCTTGAAGA	BC026166	CCDS42834.1, CCDS58752.1, CCDS58753.1	2q37.1	2014-09-17	2014-03-05		ENSG00000144535	ENSG00000144535			28648	protein-coding gene	gene with protein product		614184	"family with sequence similarity 6, member A", "DIS3 mitotic control homolog (S. cerevisiae)-like 2"	FAM6A		22306653, 23503588	Standard	NM_152383		Approved	FLJ36974, MGC42174	uc010fxz.3	Q8IYB7	OTTHUMG00000153385	ENST00000409307.1:c.187T>C	chr2.hg19:g.232880358T>C		128.0	0.0		102.0	5.0	NM_001257282		Silent	SNP	ENST00000409307.1	hg19	CCDS42834.1																																																																																			.	.		0.403	DIS3L2-015	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330988.1	NM_152383		C	232880358	T	C	232880358	2	2	254	1	0	0	0	0	0	0	0	1	4539	1606	56	2		2	DIS3L2	2	232880358	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	2236694	232880358	10319015	142	34434										
AGXT	189	hgsc.bcm.edu	37	chr2	241813425	241813425	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cctgtactcgggctcccagaAggccctgaacgcccctccag	10	18	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr2:241813425A>G	ENST00000307503.3	+	6	1013	c.626A>G	c.(625-627)aAg>aGg	p.K209R		NM_000030.2	NP_000021.1	P21549	SPYA_HUMAN	alanine-glyoxylate aminotransferase	209					cellular nitrogen compound metabolic process (GO:0034641)|glycine biosynthetic process, by transamination of glyoxylate (GO:0019265)|glyoxylate catabolic process (GO:0009436)|glyoxylate metabolic process (GO:0046487)|L-alanine catabolic process (GO:0042853)|L-cysteine catabolic process (GO:0019448)|oxalic acid secretion (GO:0046724)|pyruvate biosynthetic process (GO:0042866)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	alanine-glyoxylate transaminase activity (GO:0008453)|amino acid binding (GO:0016597)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|receptor binding (GO:0005102)|serine-pyruvate transaminase activity (GO:0004760)|transaminase activity (GO:0008483)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)	18		all_epithelial(40;1.61e-15)|Breast(86;2.35e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;8.14e-32)|all cancers(36;4.77e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;4.88e-06)|Lung(119;0.000452)|LUSC - Lung squamous cell carcinoma(224;0.00415)|Colorectal(34;0.021)|COAD - Colon adenocarcinoma(134;0.15)	Glycine(DB00145)|L-Alanine(DB00160)|L-Serine(DB00133)	GGCTCCCAGAAGGCCCTGAAC	0.632																																					p.K209R		Atlas-SNP	.											.	AGXT	50	.	0			c.A626G						.						108	95	100					2																	241813425		2203	4300	6503	SO:0001583	missense	189	exon6			CCCAGAAGGCCCT	D13368	CCDS2543.1	2q37.3	2008-02-05	2007-04-13		ENSG00000172482	ENSG00000172482	2.6.1.44, 2.6.1.51		341	protein-coding gene	gene with protein product	"oxalosis I", "primary hyperoxaluria type 1", "L-alanine: glyoxylate aminotransferase 1", "serine:pyruvate aminotransferase", "glycolicaciduria"	604285		SPAT		2039493, 2045108	Standard	NM_000030		Approved	AGXT1, PH1, AGT, SPT, AGT1	uc002waa.4	P21549	OTTHUMG00000133354	ENST00000307503.3:c.626A>G	chr2.hg19:g.241813425A>G	ENSP00000302620:p.Lys209Arg	74.0	0.0		52.0	4.0	NM_000030	Q53QU6	Missense_Mutation	SNP	ENST00000307503.3	hg19	CCDS2543.1	.	.	.	.	.	.	.	.	.	.	A	16.52	3.145225	0.57044	.	.	ENSG00000172482	ENST00000307503	D	0.99474	-5.97	4.1	4.1	0.47936	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	0.095585	0.64402	D	0.000001	D	0.99687	0.9882	H	0.97465	4.01	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97383	0.9984	10	0.87932	D	0	-39.91	13.3954	0.60849	1.0:0.0:0.0:0.0	.	209	P21549	SPYA_HUMAN	R	209	ENSP00000302620:K209R	ENSP00000302620:K209R	K	+	2	0	AGXT	241462098	1.000000	0.71417	1.000000	0.80357	0.036000	0.12997	5.335000	0.65929	1.634000	0.50500	0.472000	0.43445	AAG	.	.		0.632	AGXT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257186.1	NM_000030		G	241813425	A	G	241813425	3	3	254	1	0	0	0	0	1	0	0	0	404	72	3	2	648	2	AGXT	2	241813425	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	8933067	241813425	1385948	143	34435										
ITPR1	3708	hgsc.bcm.edu	37	chr3	4730230	4730230	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggttggctcatgaatttttgCagaatttctgcgcaggcaac	11	8	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:4730230C>T	ENST00000443694.2	+	28	3709	c.3709C>T	c.(3709-3711)Cag>Tag	p.Q1237*	ITPR1_ENST00000357086.4_Nonsense_Mutation_p.Q1243*|ITPR1_ENST00000423119.2_Nonsense_Mutation_p.Q1243*|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000354582.6_Nonsense_Mutation_p.Q1252*|ITPR1_ENST00000302640.8_Nonsense_Mutation_p.Q1237*|ITPR1_ENST00000456211.2_Nonsense_Mutation_p.Q1228*			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	1252					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	TGAATTTTTGCAGAATTTCTG	0.468																																					p.Q1243X		Atlas-SNP	.											.	ITPR1	659	.	0			c.C3727T						.						120	118	119					3																	4730230		1904	4124	6028	SO:0001587	stop_gained	3708	exon31			TTTTTGCAGAATT	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"Ion channels / Inositol triphosphate receptors"	6180	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 94"	147265	"spinocerebellar ataxia 15", "spinocerebellar ataxia 16", "spinocerebellar ataxia 29"	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.3709C>T	chr3.hg19:g.4730230C>T	ENSP00000401671:p.Gln1237*	139.0	0.0		97.0	4.0	NM_001099952	E7EPX7|E9PDE9|Q14660|Q99897	Nonsense_Mutation	SNP	ENST00000443694.2	hg19	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	C	44	10.686949	0.99450	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000357086;ENST00000456211;ENST00000443694	.	.	.	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	.	19.1808	0.93622	0.0:1.0:0.0:0.0	.	.	.	.	X	1252;1237;1252;1243;1243;1228;1237	.	ENSP00000306253:Q1237X	Q	+	1	0	ITPR1	4705230	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.673000	0.83973	2.518000	0.84900	0.655000	0.94253	CAG	.	.		0.468	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		T	4730230	C	T	4730230	4	4	254	1	0	0	0	0	0	1	0	0	7929	711	25	3	3868	3	ITPR1	3	4730230	Nonsense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10		4730230	193292200	144	34436										
ITPR1	3708	hgsc.bcm.edu	37	chr3	4735176	4735176	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	accctgttctttatgtagctGgtcaattcgggagaggatgt	12	7	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:4735176G>T	ENST00000443694.2	+	30	3987	c.3987G>T	c.(3985-3987)ctG>ctT	p.L1329L	ITPR1_ENST00000357086.4_Silent_p.L1335L|ITPR1_ENST00000423119.2_Silent_p.L1335L|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000354582.6_Silent_p.L1344L|ITPR1_ENST00000302640.8_Silent_p.L1329L|ITPR1_ENST00000456211.2_Silent_p.L1320L			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	1344					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	TTATGTAGCTGGTCAATTCGG	0.483																																					p.L1335L		Atlas-SNP	.											.	ITPR1	659	.	0			c.G4005T						.						267	246	253					3																	4735176		1908	4138	6046	SO:0001819	synonymous_variant	3708	exon33			GTAGCTGGTCAAT	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"Ion channels / Inositol triphosphate receptors"	6180	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 94"	147265	"spinocerebellar ataxia 15", "spinocerebellar ataxia 16", "spinocerebellar ataxia 29"	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.3987G>T	chr3.hg19:g.4735176G>T		122.0	0.0		98.0	4.0	NM_001099952	E7EPX7|E9PDE9|Q14660|Q99897	Silent	SNP	ENST00000443694.2	hg19	CCDS54551.1																																																																																			.	.		0.483	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		T	4735176	G	T	4735176	2	4	254	1	0	0	0	0	0	0	0	1	7929	1335	47	3		3	ITPR1	3	4735176	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	4946	4735176	193287254	145	34437										
ITPR1	3708	hgsc.bcm.edu	37	chr3	4747895	4747895	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccgtggacctggacagccaaGtcaacaacctctttctcaag	8	14	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:4747895G>A	ENST00000443694.2	+	34	4657	c.4657G>A	c.(4657-4659)Gtc>Atc	p.V1553I	ITPR1_ENST00000357086.4_Missense_Mutation_p.V1559I|ITPR1_ENST00000423119.2_Missense_Mutation_p.V1559I|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000354582.6_Missense_Mutation_p.V1568I|ITPR1_ENST00000302640.8_Missense_Mutation_p.V1553I|ITPR1_ENST00000456211.2_Missense_Mutation_p.V1544I			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	1568					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	GGACAGCCAAGTCAACAACCT	0.562																																					p.V1559I		Atlas-SNP	.											.	ITPR1	659	.	0			c.G4675A						.						62	65	64					3																	4747895		2008	4163	6171	SO:0001583	missense	3708	exon37			AGCCAAGTCAACA	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"Ion channels / Inositol triphosphate receptors"	6180	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 94"	147265	"spinocerebellar ataxia 15", "spinocerebellar ataxia 16", "spinocerebellar ataxia 29"	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.4657G>A	chr3.hg19:g.4747895G>A	ENSP00000401671:p.Val1553Ile	135.0	0.0		86.0	4.0	NM_001099952	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	hg19	CCDS54551.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.4|20.4	3.986143|3.986143	0.74589|0.74589	.|.	.|.	ENSG00000150995|ENSG00000150995	ENST00000426160|ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000357086;ENST00000456211;ENST00000443694	.|T;T;T;T;T;T	.|0.63255	.|-0.03;-0.03;-0.03;-0.03;-0.03;-0.03	5.36|5.36	5.36|5.36	0.76844|0.76844	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.54431|0.54431	0.1858|0.1858	L|L	0.52573|0.52573	1.65|1.65	0.80722|0.80722	D|D	1|1	.|P;B	.|0.40909	.|0.732;0.065	.|B;B	.|0.33254	.|0.16;0.03	T|T	0.54009|0.54009	-0.8357|-0.8357	6|10	0.72032|0.18276	D|T	0.01|0.48	.|.	19.4633|19.4633	0.94927|0.94927	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1568;1559	.|Q14643;G5E9P1	.|ITPR1_HUMAN;.	N|I	15|1568;1553;1568;1559;1559;1544;1553	.|ENSP00000306253:V1553I;ENSP00000346595:V1568I;ENSP00000405934:V1559I;ENSP00000349597:V1559I;ENSP00000397885:V1544I;ENSP00000401671:V1553I	ENSP00000409258:S15N|ENSP00000306253:V1553I	S|V	+|+	2|1	0|0	ITPR1|ITPR1	4722895|4722895	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.994000|0.994000	0.84299|0.84299	9.571000|9.571000	0.98176|0.98176	2.666000|2.666000	0.90696|0.90696	0.655000|0.655000	0.94253|0.94253	AGT|GTC	.	.		0.562	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		A	4747895	G	A	4747895	3	1	254	1	0	0	0	0	1	0	0	0	7929	1029	36	3	4840	3	ITPR1	3	4747895	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	12719	4747895	193274535	146	34438										
ITPR1	3708	hgsc.bcm.edu	37	chr3	4774886	4774886	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cactgtcagcaggaggacccGgcaagcccgggggaggaggt	18	11	1	0	rs369108656		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:4774886G>T	ENST00000443694.2	+	40	5290	c.5290G>T	c.(5290-5292)Ggc>Tgc	p.G1764C	ITPR1_ENST00000357086.4_Missense_Mutation_p.G1731C|ITPR1_ENST00000423119.2_Missense_Mutation_p.G1731C|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000354582.6_Missense_Mutation_p.G1764C|ITPR1_ENST00000302640.8_Missense_Mutation_p.G1764C|ITPR1_ENST00000456211.2_Missense_Mutation_p.G1716C			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	1779					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	AGGAGGACCCGGCAAGCCCGG	0.522																																					p.G1764C		Atlas-SNP	.											.	ITPR1	659	.	0			c.G5290T						.						63	70	67					3																	4774886		1985	4142	6127	SO:0001583	missense	3708	exon42			GGACCCGGCAAGC	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"Ion channels / Inositol triphosphate receptors"	6180	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 94"	147265	"spinocerebellar ataxia 15", "spinocerebellar ataxia 16", "spinocerebellar ataxia 29"	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.5290G>T	chr3.hg19:g.4774886G>T	ENSP00000401671:p.Gly1764Cys	59.0	0.0		52.0	4.0	NM_001168272	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	hg19	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	A	17.75	3.465638	0.63513	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000426160;ENST00000357086;ENST00000456211;ENST00000443694	D;D;D;D;D;D	0.91945	-2.94;-2.82;-2.88;-2.88;-2.88;-2.94	5.56	3.15	0.36227	.	0.213424	0.49916	D	0.000133	D	0.89760	0.6808	N	0.19112	0.55	0.80722	D	1	D;D	0.61080	0.989;0.971	P;P	0.58077	0.832;0.753	D	0.87355	0.2340	10	0.54805	T	0.06	.	9.5	0.39011	0.6366:0.0:0.3634:0.0	.	1779;1731	Q14643;G5E9P1	ITPR1_HUMAN;.	C	1779;1764;1764;1731;225;1731;1716;1764	ENSP00000306253:G1764C;ENSP00000346595:G1764C;ENSP00000405934:G1731C;ENSP00000349597:G1731C;ENSP00000397885:G1716C;ENSP00000401671:G1764C	ENSP00000306253:G1764C	G	+	1	0	ITPR1	4749886	0.234000	0.23783	1.000000	0.80357	0.973000	0.67179	0.394000	0.20834	0.137000	0.18759	-0.332000	0.08345	GGC	.	.		0.522	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		T	4774886	G	T	4774886	3	4	254	1	0	0	0	0	1	0	0	0	7929	1116	39	1	5497	1	ITPR1	3	4774886	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	26991	4774886	193247544	147	34439										
HRH1	3269	hgsc.bcm.edu	37	chr3	11302057	11302057	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgccttctgcaagaactgttGcaatgaacatttgcacatgt	8	9	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:11302057G>T	ENST00000397056.1	+	3	1525	c.1334G>T	c.(1333-1335)tGc>tTc	p.C445F	HRH1_ENST00000438284.2_Missense_Mutation_p.C445F|HRH1_ENST00000431010.2_Missense_Mutation_p.C445F	NM_000861.3|NM_001098211.1	NP_000852.1|NP_001091681.1	P35367	HRH1_HUMAN	histamine receptor H1	445					cellular response to histamine (GO:0071420)|eosinophil chemotaxis (GO:0048245)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|inositol phosphate-mediated signaling (GO:0048016)|memory (GO:0007613)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of vasoconstriction (GO:0045907)|regulation of synaptic plasticity (GO:0048167)|regulation of vascular permeability (GO:0043114)|visual learning (GO:0008542)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|histamine receptor activity (GO:0004969)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25					Aceprometazine(DB01615)|Alcaftadine(DB06766)|Alimemazine(DB01246)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Antazoline(DB08799)|Aripiprazole(DB01238)|Asenapine(DB06216)|Astemizole(DB00637)|Azatadine(DB00719)|Azelastine(DB00972)|Benzatropine(DB00245)|Bepotastine(DB04890)|Betahistine(DB06698)|Bromodiphenhydramine(DB01237)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbinoxamine(DB00748)|Cetirizine(DB00341)|Chlorcyclizine(DB08936)|Chloropyramine(DB08800)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Citalopram(DB00215)|Clemastine(DB00283)|Clofedanol(DB04837)|Clozapine(DB00363)|Cyclizine(DB01176)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexbrompheniramine(DB00405)|Dimenhydrinate(DB00985)|Dimetindene(DB08801)|Diphenhydramine(DB01075)|Diphenylpyraline(DB01146)|Doxepin(DB01142)|Doxylamine(DB00366)|Emedastine(DB01084)|Epinastine(DB00751)|Escitalopram(DB01175)|Fexofenadine(DB00950)|Flunarizine(DB04841)|Histamine Phosphate(DB00667)|Hydroxyzine(DB00557)|Iloperidone(DB04946)|Imipramine(DB00458)|Isothipendyl(DB08802)|Ketotifen(DB00920)|Levocabastine(DB01106)|Loratadine(DB00455)|Loxapine(DB00408)|Maprotiline(DB00934)|Meclizine(DB00737)|Mepyramine(DB06691)|Mequitazine(DB01071)|Methdilazine(DB00902)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Olopatadine(DB00768)|Orphenadrine(DB01173)|Paliperidone(DB01267)|Phenindamine(DB01619)|Pheniramine(DB01620)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Tolazoline(DB00797)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Ziprasidone(DB00246)	AAGAACTGTTGCAATGAACAT	0.468																																					p.C445F		Atlas-SNP	.											HRH1,NS,carcinoma,0,1	HRH1	58	.	0			c.G1334T						.						240	246	244					3																	11302057		2203	4300	6503	SO:0001583	missense	3269	exon3			ACTGTTGCAATGA		CCDS2604.1	3p25	2012-11-12			ENSG00000196639	ENSG00000196639		"GPCR / Class A : Histamine receptors"	5182	protein-coding gene	gene with protein product		600167				8003029	Standard	NM_001098211		Approved		uc010hds.3	P35367	OTTHUMG00000129719	ENST00000397056.1:c.1334G>T	chr3.hg19:g.11302057G>T	ENSP00000380247:p.Cys445Phe	70.0	0.0		54.0	3.0	NM_000861	A8K047|Q6P9E5	Missense_Mutation	SNP	ENST00000397056.1	hg19	CCDS2604.1	.	.	.	.	.	.	.	.	.	.	G	1.722	-0.496430	0.04291	.	.	ENSG00000196639	ENST00000438284;ENST00000431010;ENST00000397056	T;T;T	0.71103	-0.54;-0.54;-0.54	6.08	3.26	0.37387	GPCR, rhodopsin-like superfamily (1);	0.264594	0.38492	N	0.001674	T	0.58836	0.2150	L	0.50333	1.59	0.40591	D	0.981485	B	0.13145	0.007	B	0.12837	0.008	T	0.52419	-0.8578	10	0.41790	T	0.15	-14.0251	4.0971	0.09996	0.0858:0.2332:0.4409:0.24	.	445	P35367	HRH1_HUMAN	F	445	ENSP00000406705:C445F;ENSP00000397028:C445F;ENSP00000380247:C445F	ENSP00000380247:C445F	C	+	2	0	HRH1	11277057	0.000000	0.05858	0.438000	0.26821	0.200000	0.23975	-0.089000	0.11180	0.424000	0.26061	0.655000	0.94253	TGC	.	.		0.468	HRH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251928.2			T	11302057	G	T	11302057	3	4	254	1	0	0	0	0	1	0	0	0	7364	1319	46	3	1336	3	HRH1	3	11302057	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	6527171	11302057	186720373	148	34440										
NUP210	23225	hgsc.bcm.edu	37	chr3	13413453	13413453	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgaggccactgatcctcaggGgcagctccagggcctggccc	14	15	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:13413453G>A	ENST00000254508.5	-	13	1749	c.1667C>T	c.(1666-1668)cCc>cTc	p.P556L		NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	556					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|ovary(7)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	66	all_neural(104;0.187)					GATCCTCAGGGGCAGCTCCAG	0.647																																					p.P556L		Atlas-SNP	.											.	NUP210	182	.	0			c.C1667T						.						25	21	23					3																	13413453		2202	4299	6501	SO:0001583	missense	23225	exon13			CTCAGGGGCAGCT	AB020713	CCDS33704.1	3p25	2008-02-05			ENSG00000132182	ENSG00000132182			30052	protein-coding gene	gene with protein product		607703				2184032, 7504063	Standard	NM_024923		Approved	GP210, POM210, FLJ22389, KIAA0906	uc003bxv.1	Q8TEM1	OTTHUMG00000157268	ENST00000254508.5:c.1667C>T	chr3.hg19:g.13413453G>A	ENSP00000254508:p.Pro556Leu	130.0	0.0		94.0	5.0	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Missense_Mutation	SNP	ENST00000254508.5	hg19	CCDS33704.1	.	.	.	.	.	.	.	.	.	.	G	34	5.324811	0.95708	.	.	ENSG00000132182	ENST00000254508	T	0.05447	3.44	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	T	0.30262	0.0759	M	0.80183	2.485	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.00611	-1.1645	10	0.59425	D	0.04	-30.4294	20.1865	0.98220	0.0:0.0:1.0:0.0	.	556;556	Q8TEM1-2;Q8TEM1	.;PO210_HUMAN	L	556	ENSP00000254508:P556L	ENSP00000254508:P556L	P	-	2	0	NUP210	13388453	1.000000	0.71417	1.000000	0.80357	0.869000	0.49853	9.837000	0.99465	2.775000	0.95449	0.655000	0.94253	CCC	.	.		0.647	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923		A	13413453	G	A	13413453	3	1	254	1	0	0	0	0	1	0	0	0	10769	1232	43	3	4108	3	NUP210	3	13413453	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	2111396	13413453	184608977	149	34441										
NUP210	23225	hgsc.bcm.edu	37	chr3	13429809	13429809	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cgccccaggcccaccttgtaGacagcctcctggatgcgagc	11	17	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:13429809G>T	ENST00000254508.5	-	5	760	c.678C>A	c.(676-678)gtC>gtA	p.V226V		NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	226					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|ovary(7)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	66	all_neural(104;0.187)					CCACCTTGTAGACAGCCTCCT	0.592																																					p.V226V		Atlas-SNP	.											NUP210,NS,carcinoma,0,1	NUP210	182	.	0			c.C678A						.						82	80	81					3																	13429809		2203	4300	6503	SO:0001819	synonymous_variant	23225	exon5			CTTGTAGACAGCC	AB020713	CCDS33704.1	3p25	2008-02-05			ENSG00000132182	ENSG00000132182			30052	protein-coding gene	gene with protein product		607703				2184032, 7504063	Standard	NM_024923		Approved	GP210, POM210, FLJ22389, KIAA0906	uc003bxv.1	Q8TEM1	OTTHUMG00000157268	ENST00000254508.5:c.678C>A	chr3.hg19:g.13429809G>T		77.0	0.0		44.0	2.0	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Silent	SNP	ENST00000254508.5	hg19	CCDS33704.1																																																																																			.	.		0.592	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923		T	13429809	G	T	13429809	2	4	254	1	0	0	0	0	0	0	0	1	10769	929	33	3		3	NUP210	3	13429809	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	16356	13429809	184592621	150	34442										
WNT7A	7476	hgsc.bcm.edu	37	chr3	13860913	13860913	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	attccagcttcatgttctccTccaggatctgcaggggaggg	12	11	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:13860913T>C	ENST00000285018.4	-	4	882	c.578A>G	c.(577-579)gAg>gGg	p.E193G		NM_004625.3	NP_004616.2	O00755	WNT7A_HUMAN	wingless-type MMTV integration site family, member 7A	193					asymmetric protein localization (GO:0008105)|canonical Wnt signaling pathway (GO:0060070)|cartilage condensation (GO:0001502)|cell fate commitment (GO:0045165)|cell proliferation in forebrain (GO:0021846)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system vasculogenesis (GO:0022009)|cerebellar granule cell differentiation (GO:0021707)|chondrocyte differentiation (GO:0002062)|dorsal/ventral pattern formation (GO:0009953)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|establishment of cell polarity (GO:0030010)|lens fiber cell development (GO:0070307)|negative regulation of apoptotic process (GO:0043066)|negative regulation of neurogenesis (GO:0050768)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|non-canonical Wnt signaling pathway (GO:0035567)|oviduct development (GO:0060066)|palate development (GO:0060021)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|positive regulation of JNK cascade (GO:0046330)|positive regulation of synapse assembly (GO:0051965)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of axon diameter (GO:0031133)|response to estradiol (GO:0032355)|sex differentiation (GO:0007548)|skeletal muscle satellite cell activation (GO:0014719)|skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration (GO:0014834)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|stem cell development (GO:0048864)|synapse organization (GO:0050808)|uterus morphogenesis (GO:0061038)|Wnt signaling pathway involved in wound healing, spreading of epidermal cells (GO:0035659)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|receptor binding (GO:0005102)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	24						CATGTTCTCCTCCAGGATCTG	0.657																																					p.E193G		Atlas-SNP	.											.	WNT7A	70	.	0			c.A578G						.						88	85	86					3																	13860913		2203	4300	6503	SO:0001583	missense	7476	exon4			TTCTCCTCCAGGA	D83175	CCDS2616.1	3p25	2008-07-18			ENSG00000154764	ENSG00000154764		"Wingless-type MMTV integration sites"	12786	protein-coding gene	gene with protein product	"proto-oncogene Wnt7a protein"	601570				8893824, 9161407	Standard	NM_004625		Approved		uc003bye.1	O00755	OTTHUMG00000129803	ENST00000285018.4:c.578A>G	chr3.hg19:g.13860913T>C	ENSP00000285018:p.Glu193Gly	62.0	0.0		59.0	4.0	NM_004625	Q96H90|Q9Y560	Missense_Mutation	SNP	ENST00000285018.4	hg19	CCDS2616.1	.	.	.	.	.	.	.	.	.	.	t	18.65	3.670592	0.67814	.	.	ENSG00000154764	ENST00000285018	T	0.76578	-1.03	4.29	4.29	0.51040	.	0.170785	0.49916	D	0.000132	T	0.78685	0.4322	M	0.77820	2.39	0.80722	D	1	B	0.30973	0.302	B	0.36186	0.219	T	0.76397	-0.2974	10	0.27082	T	0.32	.	13.7615	0.62968	0.0:0.0:0.0:1.0	.	193	O00755	WNT7A_HUMAN	G	193	ENSP00000285018:E193G	ENSP00000285018:E193G	E	-	2	0	WNT7A	13835914	1.000000	0.71417	1.000000	0.80357	0.828000	0.46876	8.032000	0.88838	1.724000	0.51502	0.456000	0.33151	GAG	.	.		0.657	WNT7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252031.2	NM_004625		C	13860913	T	C	13860913	3	2	254	1	0	0	0	0	1	0	0	0	17409	1551	54	2	475	2	WNT7A	3	13860913	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	431104	13860913	184161517	151	34443										
SLC6A6	6533	hgsc.bcm.edu	37	chr3	14526411	14526411	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgaccccaagggaacccaacCgctgggctgtggagcgcgag	15	13	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:14526411C>T	ENST00000454876.2	+	15	2088	c.1759C>T	c.(1759-1761)Cgc>Tgc	p.R587C	SLC6A6_ENST00000360861.3_Missense_Mutation_p.R587C			P31641	SC6A6_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 6	587					amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|taurine transport (GO:0015734)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)|taurine binding (GO:0030977)|taurine:sodium symporter activity (GO:0005369)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|skin(2)	28						GGAACCCAACCGCTGGGCTGT	0.607																																					p.R587C		Atlas-SNP	.											.	SLC6A6	58	.	0			c.C1759T						.						56	48	50					3																	14526411		2203	4300	6503	SO:0001583	missense	6533	exon15			CCCAACCGCTGGG		CCDS33705.1, CCDS46765.1	3p25.1	2013-07-19	2013-07-19		ENSG00000131389	ENSG00000131389		"Solute carriers"	11052	protein-coding gene	gene with protein product	"taurine transporter"	186854	"solute carrier family 6 (neurotransmitter transporter, taurine), member 6"			8010975, 8382624	Standard	XM_006713307		Approved	TAUT	uc010heg.4	P31641	OTTHUMG00000155525	ENST00000454876.2:c.1759C>T	chr3.hg19:g.14526411C>T	ENSP00000398063:p.Arg587Cys	117.0	0.0		68.0	4.0	NM_003043	B2RNU7|Q9BRI2|Q9BXB0	Missense_Mutation	SNP	ENST00000454876.2	hg19	CCDS33705.1	.	.	.	.	.	.	.	.	.	.	C	19.82	3.899168	0.72754	.	.	ENSG00000131389	ENST00000454876;ENST00000360861	T;T	0.73047	-0.71;-0.71	5.17	2.17	0.27698	.	0.626892	0.16013	N	0.233707	T	0.59676	0.2211	N	0.24115	0.695	0.45852	D	0.998718	D	0.62365	0.991	P	0.45660	0.489	T	0.63287	-0.6671	10	0.54805	T	0.06	.	12.4998	0.55950	0.1125:0.5636:0.3239:0.0	.	587	P31641	SC6A6_HUMAN	C	587	ENSP00000398063:R587C;ENSP00000354107:R587C	ENSP00000354107:R587C	R	+	1	0	SLC6A6	14501415	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	0.702000	0.25631	1.132000	0.42129	0.313000	0.20887	CGC	.	.		0.607	SLC6A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340507.1	NM_003043		T	14526411	C	T	14526411	3	4	254	1	0	0	0	0	1	0	0	0	14703	652	23	1	1813	1	SLC6A6	3	14526411	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	665498	14526411	183496019	152	34444										
FGD5	152273	hgsc.bcm.edu	37	chr3	14958766	14958766	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctctctccagatgaacgatgTgctcctgtacacctatcccc	6	16	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:14958766T>C	ENST00000285046.5	+	12	3526	c.3416T>C	c.(3415-3417)gTg>gCg	p.V1139A	FGD5_ENST00000543601.1_Missense_Mutation_p.V898A|FGD5_ENST00000476851.1_3'UTR	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	1139	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			NS(2)|breast(2)|endometrium(3)|kidney(5)|large_intestine(10)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(1)	54						ATGAACGATGTGCTCCTGTAC	0.567																																					p.V1139A		Atlas-SNP	.											.	FGD5	248	.	0			c.T3416C						.						60	60	60					3																	14958766		1921	4125	6046	SO:0001583	missense	152273	exon12			ACGATGTGCTCCT	AK097276	CCDS46767.1	3p25.1	2013-01-10			ENSG00000154783	ENSG00000154783		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	19117	protein-coding gene	gene with protein product		614788					Standard	NM_152536		Approved	ZFYVE23, FLJ39957, FLJ00274	uc003bzc.3	Q6ZNL6	OTTHUMG00000155556	ENST00000285046.5:c.3416T>C	chr3.hg19:g.14958766T>C	ENSP00000285046:p.Val1139Ala	121.0	0.0		84.0	4.0	NM_152536	B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	Missense_Mutation	SNP	ENST00000285046.5	hg19	CCDS46767.1	.	.	.	.	.	.	.	.	.	.	T	11.81	1.750753	0.31046	.	.	ENSG00000154783	ENST00000285046;ENST00000543601	T;T	0.76316	-1.01;-1.01	4.42	3.26	0.37387	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.614817	0.14306	N	0.327976	T	0.78868	0.4351	L	0.54908	1.71	0.23003	N	0.998443	P;P	0.44877	0.845;0.845	P;P	0.53360	0.724;0.724	T	0.65352	-0.6189	10	0.33141	T	0.24	-5.6493	7.4459	0.27211	0.0:0.1039:0.0:0.8961	.	898;1139	B7ZM68;Q6ZNL6	.;FGD5_HUMAN	A	1139;898	ENSP00000285046:V1139A;ENSP00000445949:V898A	ENSP00000285046:V1139A	V	+	2	0	FGD5	14933770	0.994000	0.37717	0.400000	0.26346	0.772000	0.43724	2.551000	0.45820	0.589000	0.29677	0.482000	0.46254	GTG	.	.		0.567	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340628.1	NM_152536		C	14958766	T	C	14958766	3	2	254	1	0	0	0	0	1	0	0	0	5844	1696	59	2	3462	2	FGD5	3	14958766	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	432355	14958766	183063664	153	34445										
TBC1D5	9779	hgsc.bcm.edu	37	chr3	17333464	17333464	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgggtaatgcatcagaaggcCgagacaggtctggtagttac	14	7	2	2	rs143029277		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:17333464C>A	ENST00000253692.7	-	15	2832	c.1168G>T	c.(1168-1170)Ggc>Tgc	p.G390C	TBC1D5_ENST00000446818.2_Missense_Mutation_p.G390C|TBC1D5_ENST00000429383.4_Missense_Mutation_p.G390C|TBC1D5_ENST00000414318.2_Intron|TBC1D5_ENST00000429924.2_Missense_Mutation_p.G342C	NM_014744.2	NP_055559.1	Q92609	TBCD5_HUMAN	TBC1 domain family, member 5	390						retromer complex (GO:0030904)	Rab GTPase activator activity (GO:0005097)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	36						ATCAGAAGGCCGAGACAGGTC	0.383																																					p.G390C		Atlas-SNP	.											.	TBC1D5	69	.	0			c.G1168T						.						89	87	88					3																	17333464		2203	4300	6503	SO:0001583	missense	9779	exon15			GAAGGCCGAGACA	D86965	CCDS33714.1, CCDS46770.1	3p24.3	2013-07-09			ENSG00000131374	ENSG00000131374			19166	protein-coding gene	gene with protein product		615740				19531583	Standard	NM_014744		Approved	KIAA0210	uc003cbe.3	Q92609	OTTHUMG00000155488	ENST00000253692.7:c.1168G>T	chr3.hg19:g.17333464C>A	ENSP00000253692:p.Gly390Cys	103.0	0.0		72.0	4.0	NM_014744	A6NP25|C9JP52	Missense_Mutation	SNP	ENST00000253692.7	hg19	CCDS33714.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.962192	0.74016	.	.	ENSG00000131374	ENST00000253692;ENST00000429383;ENST00000446818;ENST00000429924	T;T;T;T	0.21932	1.98;1.98;1.98;1.98	6.03	6.03	0.97812	Rab-GAP/TBC domain (1);	0.000000	0.85682	D	0.000000	T	0.34687	0.0906	M	0.61703	1.905	0.80722	D	1	B;P;P	0.44241	0.345;0.801;0.829	B;P;P	0.46253	0.2;0.509;0.509	T	0.02081	-1.1217	10	0.62326	D	0.03	-19.4637	20.1672	0.98154	0.0:1.0:0.0:0.0	.	342;390;390	C9J3F6;C9JP52;Q92609	.;.;TBCD5_HUMAN	C	390;390;390;342	ENSP00000253692:G390C;ENSP00000398127:G390C;ENSP00000402935:G390C;ENSP00000411925:G342C	ENSP00000253692:G390C	G	-	1	0	TBC1D5	17308468	1.000000	0.71417	0.976000	0.42696	0.993000	0.82548	7.284000	0.78650	2.861000	0.98227	0.655000	0.94253	GGC	.	C|1.000;T|0.000		0.383	TBC1D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340301.3	NM_014744		A	17333464	C	A	17333464	3	1	254	1	0	0	0	0	1	0	0	0	15638	652	23	1	1321	1	TBC1D5	3	17333464	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	2374698	17333464	180688966	154	34446										
SATB1	6304	hgsc.bcm.edu	37	chr3	18393620	18393620	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	accttcggatcatggagaggTtctcccacagggttctgttt	11	10	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:18393620T>C	ENST00000338745.6	-	10	3377	c.1643A>G	c.(1642-1644)aAc>aGc	p.N548S	SATB1_ENST00000417717.2_Missense_Mutation_p.N548S|TBC1D5_ENST00000414318.2_Intron|SATB1_ENST00000454909.2_Missense_Mutation_p.N548S	NM_002971.4	NP_002962.1	Q01826	SATB1_HUMAN	SATB homeobox 1	548					activated T cell proliferation (GO:0050798)|apoptotic process (GO:0006915)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|epidermis development (GO:0008544)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|reflex (GO:0060004)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(2)|endometrium(6)|large_intestine(4)|lung(10)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	32						CATGGAGAGGTTCTCCCACAG	0.517																																					p.N548S		Atlas-SNP	.											.	SATB1	96	.	0			c.A1643G						.						103	96	98					3																	18393620		2203	4300	6503	SO:0001583	missense	6304	exon10			GAGAGGTTCTCCC		CCDS2631.1, CCDS56242.1	3p24.3	2011-07-19	2007-02-15		ENSG00000182568	ENSG00000182568		"Homeoboxes / CUT class"	10541	protein-coding gene	gene with protein product		602075	"special AT-rich sequence binding protein 1 (binds to nuclear matrix/scaffold-associating DNA)"			1505028	Standard	NM_002971		Approved		uc003cbj.3	Q01826	OTTHUMG00000129890	ENST00000338745.6:c.1643A>G	chr3.hg19:g.18393620T>C	ENSP00000341024:p.Asn548Ser	220.0	0.0		146.0	6.0	NM_002971	B3KXF1|C9JTR6|Q59EQ0	Missense_Mutation	SNP	ENST00000338745.6	hg19	CCDS2631.1	.	.	.	.	.	.	.	.	.	.	T	27.9	4.870657	0.91587	.	.	ENSG00000182568	ENST00000338745;ENST00000454909;ENST00000417717	T;T;T	0.63255	-0.01;-0.01;-0.03	5.52	5.52	0.82312	Homeodomain protein CUT (2);Lambda repressor-like, DNA-binding (2);	0.000000	0.85682	D	0.000000	T	0.79015	0.4375	M	0.74258	2.255	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.81457	-0.0924	10	0.66056	D	0.02	-19.5847	15.6295	0.76893	0.0:0.0:0.0:1.0	.	548;548	Q01826-2;Q01826	.;SATB1_HUMAN	S	548	ENSP00000341024:N548S;ENSP00000399708:N548S;ENSP00000399518:N548S	ENSP00000341024:N548S	N	-	2	0	SATB1	18368624	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.013000	0.88655	2.091000	0.63221	0.533000	0.62120	AAC	.	.		0.517	SATB1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252138.4	NM_001131010		C	18393620	T	C	18393620	3	2	254	1	0	0	0	0	1	0	0	0	13868	1725	60	2	656	2	SATB1	3	18393620	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	1060156	18393620	179628810	155	34447										
KAT2B	8850	hgsc.bcm.edu	37	chr3	20153102	20153102	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcacaggtggctgtgttactGcaacgtgccacagttctgcg	12	11	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:20153102G>A	ENST00000263754.4	+	6	1321	c.866G>A	c.(865-867)tGc>tAc	p.C289Y		NM_003884.4	NP_003875.3	Q92831	KAT2B_HUMAN	K(lysine) acetyltransferase 2B	289					cell cycle arrest (GO:0007050)|cellular response to insulin stimulus (GO:0032869)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|histone H3-K9 acetylation (GO:0043970)|internal peptidyl-lysine acetylation (GO:0018393)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|Notch signaling pathway (GO:0007219)|peptidyl-lysine acetylation (GO:0018394)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein acetylation (GO:0006473)|regulation of protein ADP-ribosylation (GO:0010835)|rhythmic process (GO:0048511)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	A band (GO:0031672)|actomyosin (GO:0042641)|Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|I band (GO:0031674)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)	acetyltransferase activity (GO:0016407)|cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|histone acetyltransferase activity (GO:0004402)|histone deacetylase binding (GO:0042826)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	40						CTGTGTTACTGCAACGTGCCA	0.458																																					p.C289Y		Atlas-SNP	.											.	KAT2B	73	.	0			c.G866A						.						137	118	125					3																	20153102		2203	4300	6503	SO:0001583	missense	8850	exon6			GTTACTGCAACGT	U57316	CCDS2634.1	3p24	2011-07-01	2008-07-04	2008-07-04	ENSG00000114166	ENSG00000114166		"Chromatin-modifying enzymes / K-acetyltransferases"	8638	protein-coding gene	gene with protein product		602303	"p300/CBP-associated factor"	PCAF		8684459, 9722949	Standard	NM_003884		Approved	P/CAF, GCN5, GCN5L	uc003cbq.3	Q92831	OTTHUMG00000130481	ENST00000263754.4:c.866G>A	chr3.hg19:g.20153102G>A	ENSP00000263754:p.Cys289Tyr	86.0	0.0		73.0	4.0	NM_003884	Q6NSK1	Missense_Mutation	SNP	ENST00000263754.4	hg19	CCDS2634.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.856854	0.91433	.	.	ENSG00000114166	ENST00000263754	T	0.39787	1.06	5.7	5.7	0.88788	PCAF, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.69993	0.3173	M	0.84082	2.675	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.73544	-0.3949	10	0.87932	D	0	-18.9628	19.8232	0.96605	0.0:0.0:1.0:0.0	.	289	Q92831	KAT2B_HUMAN	Y	289	ENSP00000263754:C289Y	ENSP00000263754:C289Y	C	+	2	0	KAT2B	20128106	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	9.734000	0.98822	2.684000	0.91462	0.650000	0.86243	TGC	.	.		0.458	KAT2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252880.1	NM_003884		A	20153102	G	A	20153102	3	1	254	1	0	0	0	0	1	0	0	0	7991	1319	46	3	888	3	KAT2B	3	20153102	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1759482	20153102	177869328	156	34448										
NGLY1	55768	hgsc.bcm.edu	37	chr3	25778936	25778936	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgtttccaaaagtttctcagGgttattatatctggtttaaa	7	5	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:25778936G>T	ENST00000280700.5	-	6	1052	c.892C>A	c.(892-894)Cct>Act	p.P298T	NGLY1_ENST00000396649.3_Missense_Mutation_p.P298T|NGLY1_ENST00000428257.1_Missense_Mutation_p.P298T|NGLY1_ENST00000417874.2_Missense_Mutation_p.P256T|NGLY1_ENST00000422724.2_Silent_p.T146T	NM_018297.3	NP_060767.2	Q96IV0	NGLY1_HUMAN	N-glycanase 1	298					glycoprotein catabolic process (GO:0006516)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity (GO:0000224)			breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(2)|skin(1)	18						AGTTTCTCAGGGTTATTATAT	0.353																																					p.P298T		Atlas-SNP	.											.	NGLY1	57	.	0			c.C892A						.						65	65	65					3																	25778936		2203	4300	6503	SO:0001583	missense	55768	exon6			TCTCAGGGTTATT	AF250924	CCDS33719.1, CCDS46777.1, CCDS46778.1, CCDS46779.1	3p23	2006-08-30			ENSG00000151092	ENSG00000151092			17646	protein-coding gene	gene with protein product		610661					Standard	NM_018297		Approved	FLJ11005, PNG1	uc003cdl.3	Q96IV0	OTTHUMG00000155600	ENST00000280700.5:c.892C>A	chr3.hg19:g.25778936G>T	ENSP00000280700:p.Pro298Thr	52.0	0.0		45.0	4.0	NM_018297	B4DJE9|Q59FB1|Q6PJD8|Q9BVR8|Q9NR70	Missense_Mutation	SNP	ENST00000280700.5	hg19	CCDS33719.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.681043	0.88542	.	.	ENSG00000151092	ENST00000428257;ENST00000280700;ENST00000396649;ENST00000308710;ENST00000417874	T;T;T;T;T	0.24538	1.85;1.85;1.85;1.85;1.85	5.48	5.48	0.80851	Transglutaminase-like (1);	0.000000	0.85682	D	0.000000	T	0.56124	0.1964	M	0.80616	2.505	0.80722	D	1	D;D;D;D	0.89917	0.979;0.987;0.987;1.0	D;P;D;D	0.87578	0.938;0.905;0.929;0.998	T	0.55958	-0.8058	9	.	.	.	-17.0907	19.7098	0.96094	0.0:0.0:1.0:0.0	.	256;298;298;298	B4DJE9;Q96IV0-2;Q96IV0-3;Q96IV0	.;.;.;NGLY1_HUMAN	T	298;298;298;295;256	ENSP00000387430:P298T;ENSP00000280700:P298T;ENSP00000379886:P298T;ENSP00000307980:P295T;ENSP00000389888:P256T	.	P	-	1	0	NGLY1	25753940	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.524000	0.98036	2.713000	0.92767	0.655000	0.94253	CCT	.	.		0.353	NGLY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340832.2			T	25778936	G	T	25778936	3	4	254	1	0	0	0	0	1	0	0	0	10407	1232	43	3	1196	3	NGLY1	3	25778936	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	5625834	25778936	172243494	157	34449										
AZI2	64343	hgsc.bcm.edu	37	chr3	28368437	28368437	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccagtatgcatgctgcatatTatcactgaaataaatttttt	5	7	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:28368437T>C	ENST00000479665.1	-	7	1183	c.652A>G	c.(652-654)Aat>Gat	p.N218D	AZI2_ENST00000295748.3_5'UTR	NM_022461.3	NP_071906.1	Q9H6S1	AZI2_HUMAN	5-azacytidine induced 2	218	Interaction with TBK1 and IKBKE.				dendritic cell differentiation (GO:0097028)|dendritic cell proliferation (GO:0044565)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|interferon-alpha production (GO:0032607)|interferon-gamma production (GO:0032609)|interleukin-6 production (GO:0032635)|mitotic cell cycle (GO:0000278)|T cell activation (GO:0042110)|tumor necrosis factor production (GO:0032640)	cytoplasm (GO:0005737)				cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	15						TGCTGCATATTATCACTGAAA	0.318																																					p.N218D		Atlas-SNP	.											.	AZI2	33	.	0			c.A652G						.						82	77	79					3																	28368437		2203	4299	6502	SO:0001583	missense	64343	exon7			GCATATTATCACT	AC093142	CCDS2647.1, CCDS46782.1, CCDS46783.1	3p23	2006-03-01			ENSG00000163512	ENSG00000163512			24002	protein-coding gene	gene with protein product		609916				10580148	Standard	NM_001134432		Approved	NAP1, FLJ21939, AZ2	uc003ceb.4	Q9H6S1	OTTHUMG00000130573	ENST00000479665.1:c.652A>G	chr3.hg19:g.28368437T>C	ENSP00000419371:p.Asn218Asp	105.0	0.0		92.0	4.0	NM_022461	A8K3M2|C9JB40|H7BXU6|Q86W99|Q9BQF1	Missense_Mutation	SNP	ENST00000479665.1	hg19	CCDS2647.1	.	.	.	.	.	.	.	.	.	.	T	13.17	2.157028	0.38119	.	.	ENSG00000163512	ENST00000479665	.	.	.	5.83	2.15	0.27550	Tbk1/Ikki binding domain (1);	0.240399	0.46145	N	0.000306	T	0.41903	0.1179	L	0.35723	1.085	0.80722	D	1	B	0.02656	0.0	B	0.11329	0.006	T	0.17289	-1.0374	9	0.36615	T	0.2	-12.0707	6.3789	0.21523	0.0:0.1408:0.134:0.7252	.	218	Q9H6S1	AZI2_HUMAN	D	218	.	ENSP00000419371:N218D	N	-	1	0	AZI2	28343441	0.999000	0.42202	0.921000	0.36526	0.977000	0.68977	1.856000	0.39389	0.444000	0.26612	0.528000	0.53228	AAT	.	.		0.318	AZI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252998.2	NM_203326		C	28368437	T	C	28368437	3	2	254	1	0	0	0	0	1	0	0	0	1241	1754	61	2	534	2	AZI2	3	28368437	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	2589501	28368437	169653993	158	34450										
LRRFIP2	9209	hgsc.bcm.edu	37	chr3	37107332	37107332	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tctcctgctgactccaagacCtgagcagcttcctgagacac	8	15	1	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:37107332C>A	ENST00000336686.4	-	23	1748	c.1668G>T	c.(1666-1668)caG>caT	p.Q556H	LRRFIP2_ENST00000440230.1_Missense_Mutation_p.Q259H|LRRFIP2_ENST00000354379.4_Missense_Mutation_p.Q235H|MLH1_ENST00000536378.1_3'UTR|LRRFIP2_ENST00000421276.2_Missense_Mutation_p.Q259H|LRRFIP2_ENST00000421307.1_Missense_Mutation_p.Q556H|LRRFIP2_ENST00000396428.2_Missense_Mutation_p.Q338H			Q9Y608	LRRF2_HUMAN	leucine rich repeat (in FLII) interacting protein 2	556					Wnt signaling pathway (GO:0016055)		LRR domain binding (GO:0030275)	p.0?(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22						ACTCCAAGACCTGAGCAGCTT	0.463																																					p.Q556H		Atlas-SNP	.											.	LRRFIP2	71	.	1	Whole gene deletion(1)	ovary(1)	c.G1668T						.						103	102	102					3																	37107332		2203	4300	6503	SO:0001583	missense	9209	exon24			CAAGACCTGAGCA	AF115509	CCDS2664.1, CCDS2665.1, CCDS46791.1, CCDS63592.1	3p22.1	2008-07-18			ENSG00000093167	ENSG00000093167			6703	protein-coding gene	gene with protein product		614043				10366446	Standard	NM_017724		Approved	HUFI-2	uc003cgp.2	Q9Y608	OTTHUMG00000130796	ENST00000336686.4:c.1668G>T	chr3.hg19:g.37107332C>A	ENSP00000338727:p.Gln556His	167.0	0.0		137.0	6.0	NM_006309	A8K649|A8MXR0|B4DY63|Q68CV3|Q9NXH5	Missense_Mutation	SNP	ENST00000336686.4	hg19	CCDS2664.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.48|14.48	2.547956|2.547956	0.45383|0.45383	.|.	.|.	ENSG00000093167|ENSG00000093167	ENST00000440742|ENST00000421307;ENST00000354379;ENST00000336686;ENST00000421276;ENST00000396428;ENST00000440230	.|T;T;T;T;T;T	.|0.46451	.|0.87;0.87;0.87;0.87;0.87;0.87	6.17|6.17	3.3|3.3	0.37823|0.37823	.|.	.|0.099259	.|0.64402	.|D	.|0.000001	T|T	0.24198|0.24198	0.0586|0.0586	N|N	0.21583|0.21583	0.68|0.68	0.52099|0.52099	D|D	0.999946|0.999946	.|B;B;B;B	.|0.14805	.|0.005;0.001;0.0;0.011	.|B;B;B;B	.|0.20384	.|0.029;0.005;0.008;0.029	T|T	0.10154|0.10154	-1.0642|-1.0642	5|10	.|0.45353	.|T	.|0.12	-14.5176|-14.5176	2.4894|2.4894	0.04607|0.04607	0.1332:0.5163:0.1293:0.2213|0.1332:0.5163:0.1293:0.2213	.|.	.|338;235;259;556	.|A8MXR0;Q9Y608-2;Q9Y608-4;Q9Y608	.|.;.;.;LRRF2_HUMAN	C|H	138|556;235;556;259;338;259	.|ENSP00000392217:Q556H;ENSP00000346349:Q235H;ENSP00000338727:Q556H;ENSP00000416364:Q259H;ENSP00000379705:Q338H;ENSP00000405480:Q259H	.|ENSP00000338727:Q556H	G|Q	-|-	1|3	0|2	LRRFIP2|LRRFIP2	37082336|37082336	0.999000|0.999000	0.42202|0.42202	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	0.667000|0.667000	0.25112|0.25112	0.938000|0.938000	0.37419|0.37419	0.655000|0.655000	0.94253|0.94253	GGT|CAG	.	.		0.463	LRRFIP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253335.3	NM_006309		A	37107332	C	A	37107332	3	1	254	1	0	0	0	0	1	0	0	0	9037	680	24	3	521	3	LRRFIP2	3	37107332	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	8738895	37107332	160915098	159	34451										
VILL	50853	hgsc.bcm.edu	37	chr3	38044030	38044030	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tccagtgacatcttcttgctGgtcacagccagcgtctgcta	9	13	4	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:38044030G>T	ENST00000283713.6	+	14	1889	c.1623G>T	c.(1621-1623)ctG>ctT	p.L541L	VILL_ENST00000383759.2_Silent_p.L541L|VILL_ENST00000465644.1_Silent_p.L259L			O15195	VILL_HUMAN	villin-like	541					actin filament capping (GO:0051693)|cytoskeleton organization (GO:0007010)	actin cytoskeleton (GO:0015629)	structural constituent of cytoskeleton (GO:0005200)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(3)|stomach(3)|urinary_tract(2)	28				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)		TCTTCTTGCTGGTCACAGCCA	0.577																																					p.L541L		Atlas-SNP	.											.	VILL	61	.	0			c.G1623T						.						153	118	130					3																	38044030		2203	4300	6503	SO:0001819	synonymous_variant	50853	exon13			CTTGCTGGTCACA		CCDS2670.2	3p21	2004-07-28			ENSG00000136059	ENSG00000136059			30906	protein-coding gene	gene with protein product						9179494	Standard	XM_005265191		Approved		uc003chl.3	O15195	OTTHUMG00000130814	ENST00000283713.6:c.1623G>T	chr3.hg19:g.38044030G>T		87.0	0.0		119.0	7.0	NM_015873	A8MZP1|Q9BT80|Q9BWH7	Silent	SNP	ENST00000283713.6	hg19	CCDS2670.2																																																																																			.	.		0.577	VILL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253360.3	NM_015873		T	38044030	G	T	38044030	2	4	254	1	0	0	0	0	0	0	0	1	17180	1335	47	3		3	VILL	3	38044030	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	936698	38044030	159978400	160	34452										
CSRNP1	64651	hgsc.bcm.edu	37	chr3	39184971	39184971	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	atccaggacgcctgatgtgaAgctacagccagaatagctgt	11	10	0	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:39184971A>G	ENST00000273153.5	-	5	1522	c.1345T>C	c.(1345-1347)Ttc>Ctc	p.F449L	CSRNP1_ENST00000514182.1_Missense_Mutation_p.F449L	NM_033027.3	NP_149016.2	Q96S65	CSRN1_HUMAN	cysteine-serine-rich nuclear protein 1	449					apoptotic process (GO:0006915)|face morphogenesis (GO:0060325)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|skeletal system morphogenesis (GO:0048705)	nucleus (GO:0005634)	RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(5)|lung(3)|ovary(5)|skin(3)	24						CCTGATGTGAAGCTACAGCCA	0.567																																					p.F449L		Atlas-SNP	.											.	CSRNP1	59	.	0			c.T1345C						.						64	62	63					3																	39184971		2203	4300	6503	SO:0001583	missense	64651	exon5			ATGTGAAGCTACA	AB053121	CCDS2682.1	3p22	2009-04-17	2009-04-17	2009-04-17	ENSG00000144655	ENSG00000144655			14300	protein-coding gene	gene with protein product		606458	"AXIN1 up-regulated 1"	AXUD1		11526492, 17726538	Standard	NM_033027		Approved	URAX1, DKFZp566F164, FAM130B, TAIP-3	uc003cjg.3	Q96S65	OTTHUMG00000131293	ENST00000273153.5:c.1345T>C	chr3.hg19:g.39184971A>G	ENSP00000273153:p.Phe449Leu	124.0	0.0		88.0	5.0	NM_033027	Q69YY5	Missense_Mutation	SNP	ENST00000273153.5	hg19	CCDS2682.1	.	.	.	.	.	.	.	.	.	.	A	0.010	-1.793807	0.00623	.	.	ENSG00000144655	ENST00000273153;ENST00000514182;ENST00000318290	T;T	0.39406	1.08;1.08	4.52	-0.818	0.10833	.	1.069230	0.07196	N	0.856677	T	0.10594	0.0259	N	0.00347	-1.61	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.29518	-1.0009	10	0.10636	T	0.68	-16.6951	6.468	0.21993	0.3045:0.1212:0.5743:0.0	.	449	Q96S65	CSRN1_HUMAN	L	449;449;107	ENSP00000273153:F449L;ENSP00000422532:F449L	ENSP00000273153:F449L	F	-	1	0	CSRNP1	39159975	0.989000	0.36119	0.014000	0.15608	0.327000	0.28475	0.309000	0.19332	0.001000	0.14605	-0.242000	0.12053	TTC	.	.		0.567	CSRNP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254061.1	NM_033027		G	39184971	A	G	39184971	3	3	254	1	0	0	0	0	1	0	0	0	3965	72	3	2	428	2	CSRNP1	3	39184971	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	1140941	39184971	158837459	161	34453										
CSRNP1	64651	hgsc.bcm.edu	37	chr3	39185786	39185786	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgaagccctcagcagagctcGacgtcgccgggctgggtagg	16	12	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:39185786G>T	ENST00000273153.5	-	4	799	c.622C>A	c.(622-624)Cga>Aga	p.R208R	CSRNP1_ENST00000514182.1_Silent_p.R208R	NM_033027.3	NP_149016.2	Q96S65	CSRN1_HUMAN	cysteine-serine-rich nuclear protein 1	208					apoptotic process (GO:0006915)|face morphogenesis (GO:0060325)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|skeletal system morphogenesis (GO:0048705)	nucleus (GO:0005634)	RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(5)|lung(3)|ovary(5)|skin(3)	24						AGCAGAGCTCGACGTCGCCGG	0.627																																					p.R208R		Atlas-SNP	.											.	CSRNP1	59	.	0			c.C622A						.						76	72	73					3																	39185786		2203	4300	6503	SO:0001819	synonymous_variant	64651	exon4			GAGCTCGACGTCG	AB053121	CCDS2682.1	3p22	2009-04-17	2009-04-17	2009-04-17	ENSG00000144655	ENSG00000144655			14300	protein-coding gene	gene with protein product		606458	"AXIN1 up-regulated 1"	AXUD1		11526492, 17726538	Standard	NM_033027		Approved	URAX1, DKFZp566F164, FAM130B, TAIP-3	uc003cjg.3	Q96S65	OTTHUMG00000131293	ENST00000273153.5:c.622C>A	chr3.hg19:g.39185786G>T		146.0	0.0		90.0	6.0	NM_033027	Q69YY5	Silent	SNP	ENST00000273153.5	hg19	CCDS2682.1																																																																																			.	.		0.627	CSRNP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254061.1	NM_033027		T	39185786	G	T	39185786	2	4	254	1	0	0	0	0	0	0	0	1	3965	1066	37	1		1	CSRNP1	3	39185786	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	815	39185786	158836644	162	34454										
XIRP1	165904	hgsc.bcm.edu	37	chr3	39229162	39229162	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cgaacaaccaccggatggtcTgcacatcgccctttgggggt	12	13	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:39229162T>C	ENST00000340369.3	-	2	2003	c.1775A>G	c.(1774-1776)cAg>cGg	p.Q592R	XIRP1_ENST00000396251.1_Missense_Mutation_p.Q592R|XIRP1_ENST00000421646.1_Intron	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	592	Interaction with CTNNB1. {ECO:0000250}.				cardiac muscle cell development (GO:0055013)|negative regulation of cell proliferation (GO:0008285)|regulation of membrane potential (GO:0042391)|sarcomere organization (GO:0045214)	fascia adherens (GO:0005916)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(14)|lung(22)|ovary(4)|pancreas(1)|prostate(2)|skin(6)	71				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		CCGGATGGTCTGCACATCGCC	0.587																																					p.Q592R		Atlas-SNP	.											.	XIRP1	173	.	0			c.A1775G						.						74	63	67					3																	39229162		2203	4300	6503	SO:0001583	missense	165904	exon2			ATGGTCTGCACAT	AW755250	CCDS2683.1, CCDS56245.1	3p21.33	2008-02-05	2007-06-27	2007-06-27	ENSG00000168334	ENSG00000168334			14301	protein-coding gene	gene with protein product		609777	"cardiomyopathy associated 1"	CMYA1		12203715, 15454575	Standard	NM_001198621		Approved	DKFZp451D042, Xin	uc003cjk.2	Q702N8	OTTHUMG00000131297	ENST00000340369.3:c.1775A>G	chr3.hg19:g.39229162T>C	ENSP00000343140:p.Gln592Arg	189.0	0.0		134.0	8.0	NM_001198621	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Missense_Mutation	SNP	ENST00000340369.3	hg19	CCDS2683.1	.	.	.	.	.	.	.	.	.	.	T	14.75	2.629289	0.46944	.	.	ENSG00000168334	ENST00000396251;ENST00000340369	T;T	0.36520	1.25;1.25	4.8	-1.23	0.09465	.	0.246709	0.38005	N	0.001842	T	0.30916	0.0780	L	0.55103	1.725	0.80722	D	1	B;D	0.57899	0.012;0.981	B;P	0.48454	0.018;0.578	T	0.13656	-1.0501	10	0.56958	D	0.05	.	2.4487	0.04512	0.1401:0.0845:0.2887:0.4867	.	592;592	Q702N8;Q702N8-2	XIRP1_HUMAN;.	R	592	ENSP00000379550:Q592R;ENSP00000343140:Q592R	ENSP00000343140:Q592R	Q	-	2	0	XIRP1	39204166	1.000000	0.71417	0.986000	0.45419	0.622000	0.37654	3.934000	0.56553	-0.037000	0.13646	0.379000	0.24179	CAG	.	.		0.587	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522		C	39229162	T	C	39229162	3	2	254	1	0	0	0	0	1	0	0	0	17444	1580	55	2	3760	2	XIRP1	3	39229162	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	43376	39229162	158793268	163	34455										
ZNF620	253639	hgsc.bcm.edu	37	chr3	40558019	40558019	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agaagctctatgaatgtaacGaatgttggaaaactttcagt	9	5	2	2	rs377575762		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:40558019G>T	ENST00000314529.6	+	5	1083	c.934G>T	c.(934-936)Gaa>Taa	p.E312*	ZNF620_ENST00000418905.1_Nonsense_Mutation_p.E198*	NM_175888.3	NP_787084.1	Q6ZNG0	ZN620_HUMAN	zinc finger protein 620	312					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|ovary(1)|urinary_tract(1)	11				KIRC - Kidney renal clear cell carcinoma(284;0.0519)|Kidney(284;0.0653)		TGAATGTAACGAATGTTGGAA	0.473																																					p.E312X		Atlas-SNP	.											ZNF620,NS,carcinoma,0,1	ZNF620	38	.	0			c.G934T						.						60	61	60					3																	40558019		2203	4300	6503	SO:0001587	stop_gained	253639	exon5			TGTAACGAATGTT	AK093599	CCDS33740.1, CCDS58825.1	3p21.33	2013-01-08			ENSG00000177842	ENSG00000177842		"Zinc fingers, C2H2-type", "-"	28742	protein-coding gene	gene with protein product						12477932	Standard	NM_175888		Approved	MGC50836	uc003ckk.4	Q6ZNG0	OTTHUMG00000156044	ENST00000314529.6:c.934G>T	chr3.hg19:g.40558019G>T	ENSP00000322265:p.Glu312*	27.0	0.0		40.0	2.0	NM_175888	Q8N223	Nonsense_Mutation	SNP	ENST00000314529.6	hg19	CCDS33740.1	.	.	.	.	.	.	.	.	.	.	G	12.44	1.938329	0.34189	.	.	ENSG00000177842	ENST00000314529;ENST00000418905	.	.	.	2.65	1.72	0.24424	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.1546	0.06500	0.1502:0.0:0.5563:0.2934	.	.	.	.	X	312;198	.	.	E	+	1	0	ZNF620	40533023	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	0.244000	0.18124	0.395000	0.25257	0.591000	0.81541	GAA	.	.		0.473	ZNF620-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342824.1	XM_171060		T	40558019	G	T	40558019	4	4	254	1	0	0	0	0	0	1	0	0	18059	1059	37	1	948	1	ZNF620	3	40558019	Nonsense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1328857	40558019	157464411	164	34456										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41275034	41275034	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccataggaagggatggaaggTctccttgggactcttgttca	13	8	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:41275034T>C	ENST00000349496.5	+	9	1480	c.1200T>C	c.(1198-1200)ggT>ggC	p.G400G	CTNNB1_ENST00000453024.1_Silent_p.G393G|CTNNB1_ENST00000396183.3_Silent_p.G400G|CTNNB1_ENST00000396185.3_Silent_p.G400G|CTNNB1_ENST00000405570.1_Silent_p.G400G	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	400					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GGATGGAAGGTCTCCTTGGGA	0.413		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.G400G	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	.	CTNNB1	4904	.	0			c.T1200C						.						142	135	137					3																	41275034		2203	4300	6503	SO:0001819	synonymous_variant	1499	exon9	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	GGAAGGTCTCCTT	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.1200T>C	chr3.hg19:g.41275034T>C		107.0	0.0		97.0	5.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Silent	SNP	ENST00000349496.5	hg19	CCDS2694.1																																																																																			.	.		0.413	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41275034	T	C	41275034	2	2	254	1	0	0	0	0	0	0	0	1	4018	1654	58	2		2	CTNNB1	3	41275034	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	717015	41275034	156747396	165	34457										
CCDC13	152206	hgsc.bcm.edu	37	chr3	42754719	42754719	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctggctccaggcgtatcttcTccagatgttgctccagcacc	9	15	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:42754719T>C	ENST00000310232.6	-	14	1891	c.1808A>G	c.(1807-1809)gAg>gGg	p.E603G		NM_144719.3	NP_653320.3	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13	603										endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	25						GCGTATCTTCTCCAGATGTTG	0.607																																					p.E603G		Atlas-SNP	.											.	CCDC13	71	.	0			c.A1808G						.						123	111	115					3																	42754719		2203	4300	6503	SO:0001583	missense	152206	exon14			ATCTTCTCCAGAT	AK058196	CCDS2705.1	3p22.1	2005-01-25			ENSG00000244607	ENSG00000244607			26358	protein-coding gene	gene with protein product						12477932	Standard	NM_144719		Approved	FLJ25467	uc003cly.4	Q8IYE1	OTTHUMG00000133046	ENST00000310232.6:c.1808A>G	chr3.hg19:g.42754719T>C	ENSP00000309836:p.Glu603Gly	122.0	0.0		80.0	5.0	NM_144719		Missense_Mutation	SNP	ENST00000310232.6	hg19	CCDS2705.1	.	.	.	.	.	.	.	.	.	.	T	14.17	2.455851	0.43634	.	.	ENSG00000244607	ENST00000310232	T	0.12569	2.67	4.99	3.84	0.44239	.	0.057010	0.64402	N	0.000003	T	0.29321	0.0730	M	0.79475	2.455	0.37976	D	0.933447	D	0.57257	0.979	P	0.56563	0.801	T	0.12502	-1.0545	10	0.52906	T	0.07	.	9.5852	0.39512	0.0:0.085:0.0:0.915	.	603	Q8IYE1	CCD13_HUMAN	G	603	ENSP00000309836:E603G	ENSP00000309836:E603G	E	-	2	0	CCDC13	42729723	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	1.739000	0.38217	0.762000	0.33152	0.482000	0.46254	GAG	.	.		0.607	CCDC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256652.1	NM_144719		C	42754719	T	C	42754719	3	2	254	1	0	0	0	0	1	0	0	0	2767	1551	54	2	351	2	CCDC13	3	42754719	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	1479685	42754719	155267711	166	34458										
ANO10	55129	hgsc.bcm.edu	37	chr3	43621859	43621859	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	acatacctatgggctgatacTtcaaagcaaaccgagtgtac	8	10	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:43621859T>C	ENST00000292246.3	-	5	748	c.578A>G	c.(577-579)aAg>aGg	p.K193R	ANO10_ENST00000396091.3_Missense_Mutation_p.K127R|ANO10_ENST00000350459.4_Missense_Mutation_p.K193R|ANO10_ENST00000414522.2_Missense_Mutation_p.K193R|ANO10_ENST00000451430.2_Missense_Mutation_p.K82R	NM_018075.3	NP_060545.3	Q9NW15	ANO10_HUMAN	anoctamin 10	193					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell death (GO:0008219)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)			NS(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(9)|ovary(3)|prostate(3)|skin(3)	29						GGGCTGATACTTCAAAGCAAA	0.483																																					p.K193R		Atlas-SNP	.											ANO10,NS,carcinoma,0,1	ANO10	70	.	0			c.A578G						.						213	176	188					3																	43621859		2203	4300	6503	SO:0001583	missense	55129	exon5			TGATACTTCAAAG	AL832508	CCDS2710.2, CCDS56247.1, CCDS56248.1, CCDS56249.1, CCDS56250.1	3p22.1-p21.33	2014-04-09	2008-08-28	2008-08-28	ENSG00000160746	ENSG00000160746		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	25519	protein-coding gene	gene with protein product		613726	"transmembrane protein 16K"	TMEM16K		12477932, 24692353	Standard	NM_001204831		Approved	FLJ10375, MGC47890, SCAR10	uc003cmv.3	Q9NW15	OTTHUMG00000133044	ENST00000292246.3:c.578A>G	chr3.hg19:g.43621859T>C	ENSP00000292246:p.Lys193Arg	38.0	0.0		30.0	4.0	NM_018075	A8K8K3|A8MV74|B3KTZ1|B3KY93|B4DJ83|B4DNK2|B7WP12|C9JHS1|Q8IXX9	Missense_Mutation	SNP	ENST00000292246.3	hg19	CCDS2710.2	.	.	.	.	.	.	.	.	.	.	T	8.029	0.761378	0.15914	.	.	ENSG00000160746	ENST00000292246;ENST00000350459;ENST00000396091;ENST00000414522;ENST00000451430;ENST00000428472	T;T;T;T;T;T	0.67865	-0.01;-0.09;0.0;0.03;-0.17;-0.29	5.98	4.82	0.62117	.	0.289920	0.39615	N	0.001311	T	0.59459	0.2195	L	0.58101	1.795	0.09310	N	1	B;B;B;B;B	0.21452	0.004;0.001;0.056;0.001;0.0	B;B;B;B;B	0.30251	0.005;0.002;0.113;0.005;0.001	T	0.53056	-0.8492	10	0.35671	T	0.21	.	4.3114	0.10972	0.0:0.1996:0.1707:0.6297	.	82;193;193;127;193	Q9NW15-4;C9JHS1;Q9NW15-2;Q9NW15-3;Q9NW15	.;.;.;.;ANO10_HUMAN	R	193;193;127;193;82;82	ENSP00000292246:K193R;ENSP00000327767:K193R;ENSP00000379398:K127R;ENSP00000396990:K193R;ENSP00000394119:K82R;ENSP00000416266:K82R	ENSP00000292246:K193R	K	-	2	0	ANO10	43596863	0.906000	0.30813	0.099000	0.21106	0.625000	0.37756	2.544000	0.45761	1.091000	0.41335	0.482000	0.46254	AAG	.	.		0.483	ANO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256649.2	NM_018075		C	43621859	T	C	43621859	3	2	254	1	0	0	0	0	1	0	0	0	696	1609	56	2	1440	2	ANO10	3	43621859	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	867140	43621859	154400571	167	34459										
CCR9	10803	hgsc.bcm.edu	37	chr3	45942794	45942794	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcaaaatggtttgctttaccAtctgggtattggcagctgct	11	8	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:45942794A>G	ENST00000357632.2	+	3	694	c.514A>G	c.(514-516)Atc>Gtc	p.I172V	LZTFL1_ENST00000536047.1_Intron|LZTFL1_ENST00000539217.1_Intron|CCR9_ENST00000395963.2_Missense_Mutation_p.I160V|CCR9_ENST00000422395.1_3'UTR|CCR9_ENST00000355983.2_Missense_Mutation_p.I160V|Y_RNA_ENST00000364765.1_RNA	NM_001256369.1|NM_031200.2	NP_001243298.1|NP_112477.1	P51686	CCR9_HUMAN	chemokine (C-C motif) receptor 9	172					cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)			breast(1)|endometrium(4)|large_intestine(8)|lung(2)|ovary(2)|prostate(2)|skin(1)	20				BRCA - Breast invasive adenocarcinoma(193;0.00118)|KIRC - Kidney renal clear cell carcinoma(197;0.0182)|Kidney(197;0.0214)		TTGCTTTACCATCTGGGTATT	0.488																																					p.I172V		Atlas-SNP	.											CCR9,NS,carcinoma,0,1	CCR9	45	.	0			c.A514G						.						77	78	78					3																	45942794		2203	4300	6503	SO:0001583	missense	10803	exon3			TTTACCATCTGGG	AJ132337	CCDS2732.1, CCDS2733.1	3p21.31	2012-09-20			ENSG00000173585	ENSG00000173585		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1610	protein-coding gene	gene with protein product		604738		GPR28		10229797	Standard	NM_006641		Approved	GPR-9-6, CDw199	uc003coz.2	P51686	OTTHUMG00000133450	ENST00000357632.2:c.514A>G	chr3.hg19:g.45942794A>G	ENSP00000350256:p.Ile172Val	106.0	0.0		72.0	20.0	NM_031200	Q4VBM3|Q549E0|Q9UQQ6	Missense_Mutation	SNP	ENST00000357632.2	hg19	CCDS2732.1	.	.	.	.	.	.	.	.	.	.	A	0.011	-1.737593	0.00681	.	.	ENSG00000173585	ENST00000357632;ENST00000395963;ENST00000355983	T;T;T	0.70282	-0.47;-0.47;-0.47	4.96	-1.93	0.07594	GPCR, rhodopsin-like superfamily (1);	0.392917	0.25860	N	0.027824	T	0.41743	0.1172	N	0.10664	0.02	0.21355	N	0.999711	B	0.02656	0.0	B	0.12156	0.007	T	0.35500	-0.9786	10	0.02654	T	1	.	12.8268	0.57725	0.3575:0.0:0.6425:0.0	.	172	P51686	CCR9_HUMAN	V	172;160;160	ENSP00000350256:I172V;ENSP00000379292:I160V;ENSP00000348260:I160V	ENSP00000348260:I160V	I	+	1	0	CCR9	45917798	0.726000	0.28059	0.013000	0.15412	0.503000	0.33858	1.040000	0.30278	-0.630000	0.05567	-0.376000	0.06991	ATC	.	.		0.488	CCR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257323.2			G	45942794	A	G	45942794	3	3	254	1	0	0	0	0	1	0	0	0	2950	217	8	2	520	2	CCR9	3	45942794	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	2320935	45942794	152079636	168	34460										
NBEAL2	23218	hgsc.bcm.edu	37	chr3	47046023	47046023	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	atatccaacttcgagtacttGatgcaactcaacaccattgc	5	12	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:47046023G>T	ENST00000450053.3	+	38	6416	c.6237G>T	c.(6235-6237)ttG>ttT	p.L2079F	NBEAL2_ENST00000292309.5_Missense_Mutation_p.L1895F|NBEAL2_ENST00000383740.2_Missense_Mutation_p.L358F	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	2079	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.				blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		TCGAGTACTTGATGCAACTCA	0.582																																					p.L2079F		Atlas-SNP	.											.	NBEAL2	267	.	0			c.G6237T						.						100	111	107					3																	47046023		2099	4220	6319	SO:0001583	missense	23218	exon38			GTACTTGATGCAA	AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"WD repeat domain containing"	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.6237G>T	chr3.hg19:g.47046023G>T	ENSP00000415034:p.Leu2079Phe	139.0	0.0		74.0	4.0	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Missense_Mutation	SNP	ENST00000450053.3	hg19	CCDS46817.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	19.40|19.40|19.40	3.820435|3.820435|3.820435	0.71028|0.71028|0.71028	.|.|.	.|.|.	ENSG00000160796|ENSG00000160796|ENSG00000160796	ENST00000443829|ENST00000292309;ENST00000383740;ENST00000450053;ENST00000445550|ENST00000416683	.|D;D;D|.	.|0.88201|.	.|-2.35;-2.35;-2.35|.	4.96|4.96|4.96	4.08|4.08|4.08	0.47627|0.47627|0.47627	.|BEACH domain (4);|.	.|0.147291|.	.|0.45606|.	.|D|.	.|0.000344|.	D|D|.	0.88991|0.88991|.	0.6588|0.6588|.	H|H|H	0.99286|0.99286|0.99286	4.5|4.5|4.5	0.58432|0.58432|0.58432	D|D|D	0.999996|0.999996|0.999996	.|D;D|.	.|0.89917|.	.|1.0;1.0|.	.|D;D|.	.|0.97110|.	.|0.999;1.0|.	D|D|.	0.92912|0.92912|.	0.6348|0.6348|.	5|10|.	.|0.87932|.	.|D|.	.|0|.	.|.|.	13.6862|13.6862|13.6862	0.62517|0.62517|0.62517	0.0:0.2934:0.7065:0.0|0.0:0.2934:0.7065:0.0|0.0:0.2934:0.7065:0.0	.|.|.	.|1895;2079|.	.|Q6ZNJ1-2;Q6ZNJ1|.	.|.;NBEL2_HUMAN|.	Y|F|L	448|1895;358;2079;22|1367	.|ENSP00000292309:L1895F;ENSP00000373246:L358F;ENSP00000415034:L2079F|.	.|ENSP00000292309:L1895F|.	D|L|X	+|+|+	1|3|2	0|2|2	NBEAL2|NBEAL2|NBEAL2	47021027|47021027|47021027	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.998000|0.998000|0.998000	0.95712|0.95712|0.95712	2.988000|2.988000|2.988000	0.49386|0.49386|0.49386	1.296000|1.296000|1.296000	0.44742|0.44742|0.44742	0.561000|0.561000|0.561000	0.74099|0.74099|0.74099	GAT|TTG|TGA	.	.		0.582	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064		T	47046023	G	T	47046023	3	4	254	1	0	0	0	0	1	0	0	0	10198	1281	45	3	6387	3	NBEAL2	3	47046023	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1103229	47046023	150976407	169	34461										
PLXNB1	5364	hgsc.bcm.edu	37	chr3	48465517	48465517	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctgctggtgtatcctcgcccCacaaacaggaggggctcccc	11	16	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:48465517C>T	ENST00000358536.4	-	3	773	c.504G>A	c.(502-504)gtG>gtA	p.V168V	PLXNB1_ENST00000448774.2_Intron|PLXNB1_ENST00000358459.4_Silent_p.V168V|PLXNB1_ENST00000456774.1_Silent_p.V168V|PLXNB1_ENST00000296440.6_Silent_p.V168V	NM_002673.4	NP_002664.2	O43157	PLXB1_HUMAN	plexin B1	168	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast proliferation (GO:0033689)|neuron projection morphogenesis (GO:0048812)|ossification involved in bone maturation (GO:0043931)|positive regulation of axonogenesis (GO:0050772)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	GTPase activating protein binding (GO:0032794)|receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		ATCCTCGCCCCACAAACAGGA	0.662																																					p.V168V		Atlas-SNP	.											.	PLXNB1	150	.	0			c.G504A						.						9	12	11					3																	48465517		2175	4250	6425	SO:0001819	synonymous_variant	5364	exon3			TCGCCCCACAAAC	X87904	CCDS2765.1	3p21.31	2008-07-18			ENSG00000164050	ENSG00000164050		"Plexins"	9103	protein-coding gene	gene with protein product		601053		PLXN5		8570614, 11035813	Standard	XM_005265234		Approved	SEP, KIAA0407	uc003csw.2	O43157	OTTHUMG00000133527	ENST00000358536.4:c.504G>A	chr3.hg19:g.48465517C>T		91.0	0.0		88.0	4.0	NM_001130082	A6H8Y2|Q6NY20|Q9UIV7|Q9UJ92|Q9UJ93	Silent	SNP	ENST00000358536.4	hg19	CCDS2765.1																																																																																			.	.		0.662	PLXNB1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344454.1	NM_002673		T	48465517	C	T	48465517	2	4	254	1	0	0	0	0	0	0	0	1	12132	581	21	3		3	PLXNB1	3	48465517	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1419494	48465517	149556913	170	34462										
SLC26A6	65010	hgsc.bcm.edu	37	chr3	48669737	48669737	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctgtacccgggcagcatctcTggctgtctcattgatcatgg	11	12	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:48669737T>A	ENST00000395550.2	-	5	573	c.526A>T	c.(526-528)Aga>Tga	p.R176*	SLC26A6_ENST00000455886.2_Intron|SLC26A6_ENST00000337000.8_Intron|SLC26A6_ENST00000482282.1_5'UTR|SLC26A6_ENST00000383733.3_Nonsense_Mutation_p.R176*|SLC26A6_ENST00000358747.6_Nonsense_Mutation_p.R155*|SLC26A6_ENST00000420764.2_Nonsense_Mutation_p.R176*			Q9BXS9	S26A6_HUMAN	solute carrier family 26 (anion exchanger), member 6	176					angiotensin-activated signaling pathway (GO:0038166)|anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|cellular response to cAMP (GO:0071320)|cellular response to fructose stimulus (GO:0071332)|cellular response to interferon-gamma (GO:0071346)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|epithelial fluid transport (GO:0042045)|formate transport (GO:0015724)|intestinal absorption (GO:0050892)|intracellular pH elevation (GO:0051454)|ion transport (GO:0006811)|mannitol transport (GO:0015797)|oxalate transport (GO:0019532)|oxalic acid secretion (GO:0046724)|positive regulation of dipeptide transmembrane transport (GO:2001150)|protein kinase C signaling (GO:0070528)|regulation of intracellular pH (GO:0051453)|sperm capacitation (GO:0048240)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transepithelial chloride transport (GO:0030321)|transepithelial transport (GO:0070633)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|chloride channel complex (GO:0034707)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane-bounded vesicle (GO:0031988)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)|vesicle membrane (GO:0012506)	anion:anion antiporter activity (GO:0015301)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride channel activity (GO:0005254)|chloride transmembrane transporter activity (GO:0015108)|efflux transmembrane transporter activity (GO:0015562)|formate efflux transmembrane transporter activity (GO:0015660)|formate transmembrane transporter activity (GO:0015499)|formate uptake transmembrane transporter activity (GO:0015659)|oxalate transmembrane transporter activity (GO:0019531)|PDZ domain binding (GO:0030165)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)		SLC26A6/PRKAR2A(2)	NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(1)|lung(11)|ovary(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00609)		GCAGCATCTCTGGCTGTCTCA	0.582																																					p.R176X	NSCLC(13;369 479 28271 30152 44026)	Atlas-SNP	.											.	SLC26A6	45	.	0			c.A526T						.						63	70	68					3																	48669737		2132	4239	6371	SO:0001587	stop_gained	65010	exon5			CATCTCTGGCTGT	AF279265	CCDS43087.1, CCDS46824.1, CCDS46825.1, CCDS46826.1, CCDS63627.1, CCDS63628.1	3p21.31	2013-08-05	2013-07-18		ENSG00000225697	ENSG00000225697		"Solute carriers"	14472	protein-coding gene	gene with protein product	"pendrin-like protein 1", "pendrin L1", "sulfate anion transporter", "anion transporter 1"	610068	"solute carrier family 26, member 6"			11087667, 11247665	Standard	NM_022911		Approved	DKFZp586E1422		Q9BXS9	OTTHUMG00000186381	ENST00000395550.2:c.526A>T	chr3.hg19:g.48669737T>A	ENSP00000378920:p.Arg176*	340.0	0.0		262.0	109.0	NM_022911	B4DMZ1|Q548A7|Q96Q90|Q9NQU1	Nonsense_Mutation	SNP	ENST00000395550.2	hg19	CCDS43087.1	.	.	.	.	.	.	.	.	.	.	T	13.10	2.136113	0.37728	.	.	ENSG00000225697	ENST00000420764;ENST00000395550;ENST00000383733;ENST00000447978;ENST00000358747;ENST00000421649	.	.	.	3.87	0.197	0.15164	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.0949	0.14727	0.0:0.2673:0.1592:0.5734	.	.	.	.	X	176;176;176;189;155;22	.	ENSP00000351597:R155X	R	-	1	2	SLC26A6	48644741	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	0.144000	0.16135	-0.123000	0.11745	0.455000	0.32223	AGA	.	.		0.582	SLC26A6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345040.1	NM_022911		A	48669737	T	A	48669737	4	1	254	1	0	0	0	0	0	1	0	0	14536	1588	55	4	1857	4	SLC26A6	3	48669737	Nonsense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	204220	48669737	149352693	171	34463										
WDR6	11180	hgsc.bcm.edu	37	chr3	49049708	49049708	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctgcgagtgcctgggggtcgGgtgcagaatattgggcactg	18	8	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:49049708G>T	ENST00000608424.1	+	2	780	c.741G>T	c.(739-741)cgG>cgT	p.R247R	WDR6_ENST00000415265.2_Intron|WDR6_ENST00000395474.3_Silent_p.R277R|WDR6_ENST00000448293.1_Silent_p.R196R|WDR6_ENST00000489684.1_3'UTR			Q9NNW5	WDR6_HUMAN	WD repeat domain 6	247					cell cycle arrest (GO:0007050)|negative regulation of autophagy (GO:0010507)|negative regulation of cell proliferation (GO:0008285)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(1)|liver(1)|lung(9)|ovary(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26				Kidney(197;9.12e-07)|KIRC - Kidney renal clear cell carcinoma(197;1.32e-05)|BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000155)		CTGGGGGTCGGGTGCAGAATA	0.552																																					p.R277R		Atlas-SNP	.											.	WDR6	79	.	0			c.G831T						.						92	96	95					3																	49049708		2203	4300	6503	SO:0001819	synonymous_variant	11180	exon2			GGGTCGGGTGCAG	AF099100	CCDS2782.2	3p21.31	2013-01-09			ENSG00000178252	ENSG00000178252		"WD repeat domain containing"	12758	protein-coding gene	gene with protein product		606031					Standard	NM_018031		Approved		uc003cvj.2	Q9NNW5	OTTHUMG00000133546	ENST00000608424.1:c.741G>T	chr3.hg19:g.49049708G>T		147.0	0.0		117.0	5.0	NM_018031	B4DHK2|Q3MIT1|Q9UF63	Silent	SNP	ENST00000608424.1	hg19																																																																																				.	.		0.552	WDR6-024	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471652.1			T	49049708	G	T	49049708	2	4	254	1	0	0	0	0	0	0	0	1	17325	1219	43	3		3	WDR6	3	49049708	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	379971	49049708	148972722	172	34464										
WDR6	11180	hgsc.bcm.edu	37	chr3	49051271	49051271	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggctcagcccacgcactcacAgctgtttgtaaccatatctc	7	15	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:49051271A>G	ENST00000608424.1	+	2	2343	c.2304A>G	c.(2302-2304)acA>acG	p.T768T	WDR6_ENST00000415265.2_Silent_p.T216T|WDR6_ENST00000395474.3_Silent_p.T798T|WDR6_ENST00000448293.1_Silent_p.T717T			Q9NNW5	WDR6_HUMAN	WD repeat domain 6	768					cell cycle arrest (GO:0007050)|negative regulation of autophagy (GO:0010507)|negative regulation of cell proliferation (GO:0008285)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(1)|liver(1)|lung(9)|ovary(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26				Kidney(197;9.12e-07)|KIRC - Kidney renal clear cell carcinoma(197;1.32e-05)|BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000155)		ACGCACTCACAGCTGTTTGTA	0.577											OREG0015565	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T798T		Atlas-SNP	.											.	WDR6	79	.	0			c.A2394G						.						86	80	82					3																	49051271		2203	4300	6503	SO:0001819	synonymous_variant	11180	exon2			ACTCACAGCTGTT	AF099100	CCDS2782.2	3p21.31	2013-01-09			ENSG00000178252	ENSG00000178252		"WD repeat domain containing"	12758	protein-coding gene	gene with protein product		606031					Standard	NM_018031		Approved		uc003cvj.2	Q9NNW5	OTTHUMG00000133546	ENST00000608424.1:c.2304A>G	chr3.hg19:g.49051271A>G		99.0	0.0	959	84.0	4.0	NM_018031	B4DHK2|Q3MIT1|Q9UF63	Silent	SNP	ENST00000608424.1	hg19																																																																																				.	.		0.577	WDR6-024	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471652.1			G	49051271	A	G	49051271	2	3	254	1	0	0	0	0	0	0	0	1	17325	175	7	2		2	WDR6	3	49051271	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	1563	49051271	148971159	173	34465										
CCDC36	339834	hgsc.bcm.edu	37	chr3	49293752	49293752	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gacagtgcttctcagacgtcGccacctttggcccagagcct	10	15	1	2	rs143925037	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:49293752G>T	ENST00000438782.1	+	8	1058	c.822G>T	c.(820-822)tcG>tcT	p.S274S	CCDC36_ENST00000296449.5_Silent_p.S274S|CCDC36_ENST00000452691.2_Silent_p.S274S			Q8IYA8	CCD36_HUMAN	coiled-coil domain containing 36	274										endometrium(1)|kidney(2)|large_intestine(3)|liver(1)|lung(3)|ovary(1)|urinary_tract(3)	14				BRCA - Breast invasive adenocarcinoma(193;9.11e-05)|Kidney(197;0.00248)|KIRC - Kidney renal clear cell carcinoma(197;0.00262)		CTCAGACGTCGCCACCTTTGG	0.542																																					p.S274S		Atlas-SNP	.											CCDC36_ENST00000438782,NS,carcinoma,0,2	CCDC36	77	.	0			c.G822T						.						65	63	64					3																	49293752		2203	4300	6503	SO:0001819	synonymous_variant	339834	exon8			GACGTCGCCACCT	AK058049	CCDS33755.2	3p21.31	2009-08-06			ENSG00000173421	ENSG00000173421			27945	protein-coding gene	gene with protein product	"cancer/testis antigen 74"						Standard	NM_178173		Approved	FLJ25320, CT74	uc011bck.1	Q8IYA8	OTTHUMG00000155920	ENST00000438782.1:c.822G>T	chr3.hg19:g.49293752G>T		42.0	0.0		47.0	2.0	NM_001135197	C9JJL0|Q05DG9|Q96LP7	Silent	SNP	ENST00000438782.1	hg19	CCDS33755.2																																																																																			.	G|1.000;A|0.000		0.542	CCDC36-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342332.1	NM_178173		T	49293752	G	T	49293752	2	4	254	1	0	0	0	0	0	0	0	1	2810	1074	38	1		1	CCDC36	3	49293752	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	242481	49293752	148728678	174	34466										
C3orf54	7318	hgsc.bcm.edu	37	chr3	49841899	49841899	+	IGR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aggaagaactgcctgtatccCagcgcccagcaccctcagca	9	16	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:49841899C>T	ENST00000333486.3	-	0	3299				FAM212A_ENST00000333323.4_Nonsense_Mutation_p.Q115*|MIR5193_ENST00000584510.1_RNA	NM_003335.2	NP_003326.2	P41226	UBA7_HUMAN	ubiquitin-like modifier activating enzyme 7						cellular protein modification process (GO:0006464)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|modification-dependent protein catabolic process (GO:0019941)|negative regulation of type I interferon production (GO:0032480)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ISG15 activating enzyme activity (GO:0019782)|ubiquitin activating enzyme activity (GO:0004839)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(15)|large_intestine(4)|lung(7)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;3.58e-06)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		GCCTGTATCCCAGCGCCCAGC	0.647																																					p.Q115X		Atlas-SNP	.											.	.	.	.	0			c.C343T						.						96	92	93					3																	49841899		2203	4300	6503	SO:0001628	intergenic_variant	389119	exon2			GTATCCCAGCGCC	BC006378	CCDS2805.1	3p21	2007-11-30	2007-11-30	2007-11-30	ENSG00000182179	ENSG00000182179		"Ubiquitin-like modifier activating enzymes"	12471	protein-coding gene	gene with protein product	"UBA1, ubiquitin-activating enzyme E1 homolog B (yeast)", "UBA7, ubiquitin-activating enzyme E1"	191325	"ubiquitin-activating enzyme E1-like"	UBE1L		8327486	Standard	NM_003335		Approved	D8, UBE2, UBA1B	uc003cxr.3	P41226	OTTHUMG00000158267		chr3.hg19:g.49841899C>T		124.0	0.0		83.0	4.0	NM_203370	Q9BRB2	Nonsense_Mutation	SNP	ENST00000333486.3	hg19	CCDS2805.1	.	.	.	.	.	.	.	.	.	.	C	8.961	0.970684	0.18659	.	.	ENSG00000185614	ENST00000333323	.	.	.	4.9	4.9	0.64082	.	0.717703	0.12099	N	0.499647	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	.	7.9022	0.29742	0.0:0.8223:0.0:0.1777	.	.	.	.	X	115	.	ENSP00000329735:Q115X	Q	+	1	0	C3orf54	49816903	0.706000	0.27856	0.052000	0.19188	0.021000	0.10359	2.036000	0.41165	2.430000	0.82344	0.561000	0.74099	CAG	.	.		0.647	UBA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350503.1	NM_003335		T	49841899	C	T	49841899	1	4	254	0	1	0	0	0	0	0	0	0	2235	595	21	3		3	C3orf54	3	49841899	IGR	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	548147	49841899	148180531	175	34467										
CYB561D2	11068	hgsc.bcm.edu	37	chr3	50390719	50390719	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctggtgttttctcctgagagTtcgctgctgcactccctctc	9	14	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:50390719T>C	ENST00000418577.1	+	3	789	c.213T>C	c.(211-213)agT>agC	p.S71S	CYB561D2_ENST00000425346.1_Silent_p.S71S|CYB561D2_ENST00000419046.1_3'UTR|CYB561D2_ENST00000424512.1_Silent_p.S71S|XXcos-LUCA11.5_ENST00000606589.1_Intron|CYB561D2_ENST00000232508.5_Silent_p.S71S|NPRL2_ENST00000232501.3_5'Flank			O14569	C56D2_HUMAN	cytochrome b561 family, member D2	71	Cytochrome b561. {ECO:0000255|PROSITE- ProRule:PRU00242}.				oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			endometrium(1)|lung(1)|urinary_tract(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		CTCCTGAGAGTTCGCTGCTGC	0.607																																					p.S71S		Atlas-SNP	.											.	CYB561D2	13	.	0			c.T213C						.						110	107	108					3																	50390719		2203	4300	6503	SO:0001819	synonymous_variant	11068	exon4			TGAGAGTTCGCTG	AF040704	CCDS2827.1	3p21.3	2013-03-14	2013-03-14		ENSG00000114395	ENSG00000114395		"Cytochrome b genes"	30253	protein-coding gene	gene with protein product	"putative tumor suppressor 101F6"	607068	"cytochrome b-561 domain containing 2"			9122200, 11085536, 23249217	Standard	XM_005264832		Approved	101F6, TSP10	uc003dal.3	O14569	OTTHUMG00000156813	ENST00000418577.1:c.213T>C	chr3.hg19:g.50390719T>C		86.0	0.0		91.0	4.0	NM_007022	A8K552	Silent	SNP	ENST00000418577.1	hg19	CCDS2827.1																																																																																			.	.		0.607	CYB561D2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345973.1	NM_007022		C	50390719	T	C	50390719	2	2	254	1	0	0	0	0	0	0	0	1	4123	1722	60	2		2	CYB561D2	3	50390719	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	548820	50390719	147631711	176	34468										
DOCK3	1795	hgsc.bcm.edu	37	chr3	51376393	51376393	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	acaaatctgagattaacaagGaagaaatgtatatccgctac	7	7	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:51376393G>A	ENST00000266037.9	+	37	3723	c.3700G>A	c.(3700-3702)Gaa>Aaa	p.E1234K		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	1234	DHR-2.				small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		GATTAACAAGGAAGAAATGTA	0.448																																					p.E1234K		Atlas-SNP	.											.	DOCK3	397	.	0			c.G3700A						.						48	47	47					3																	51376393		1909	4140	6049	SO:0001583	missense	1795	exon37			AACAAGGAAGAAA	AB002297	CCDS46835.1	3p21	2008-02-01			ENSG00000088538	ENSG00000088538			2989	protein-coding gene	gene with protein product		603123	"dedicator of cyto-kinesis 3"			9205841	Standard	NM_004947		Approved	KIAA0299, MOCA, PBP	uc011bds.2	Q8IZD9	OTTHUMG00000156892	ENST00000266037.9:c.3700G>A	chr3.hg19:g.51376393G>A	ENSP00000266037:p.Glu1234Lys	108.0	0.0		98.0	4.0	NM_004947	O15017	Missense_Mutation	SNP	ENST00000266037.9	hg19	CCDS46835.1	.	.	.	.	.	.	.	.	.	.	G	19.39	3.817569	0.70912	.	.	ENSG00000088538	ENST00000266037;ENST00000402669	T	0.56776	0.44	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.44350	0.1289	L	0.37800	1.135	0.80722	D	1	B	0.24675	0.109	B	0.26614	0.071	T	0.31530	-0.9940	10	0.12103	T	0.63	.	18.4995	0.90876	0.0:0.0:1.0:0.0	.	1234	Q8IZD9	DOCK3_HUMAN	K	1234;30	ENSP00000266037:E1234K	ENSP00000266037:E1234K	E	+	1	0	DOCK3	51351433	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.657000	0.98554	2.606000	0.88127	0.650000	0.86243	GAA	.	.		0.448	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947		A	51376393	G	A	51376393	3	1	254	1	0	0	0	0	1	0	0	0	4690	1175	41	3	3846	3	DOCK3	3	51376393	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	985674	51376393	146646037	177	34469										
VPRBP	9730	hgsc.bcm.edu	37	chr3	51505002	51505002	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	acgatactcttcagtttcttTttcaatcaattgagacatcc	4	10	5	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:51505002T>C	ENST00000335891.5	-	2	139	c.130A>G	c.(130-132)Aaa>Gaa	p.K44E				Q9Y4B6	VPRBP_HUMAN	Vpr (HIV-1) binding protein	44					B cell differentiation (GO:0030183)|cell competition in a multicellular organism (GO:0035212)|histone H2A-T120 phosphorylation (GO:1990245)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|transcription, DNA-templated (GO:0006351)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone kinase activity (H2A-T120 specific) (GO:1990244)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(193;0.000272)|Kidney(197;0.000729)|KIRC - Kidney renal clear cell carcinoma(197;0.000875)		TCAGTTTCTTTTTCAATCAAT	0.393																																					p.K44E		Atlas-SNP	.											.	VPRBP	107	.	0			c.A130G						.						105	94	97					3																	51505002		1850	4100	5950	SO:0001583	missense	9730	exon4			TTTCTTTTTCAAT	AB018343	CCDS74943.1, CCDS74944.1	3p21.2	2011-06-17			ENSG00000145041	ENSG00000145041		"DDB1 and CUL4 associated factors"	30911	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 1"					8195203, 11223251	Standard	NM_014703		Approved	KIAA0800, MGC102804, DCAF1	uc003dbe.2	Q9Y4B6	OTTHUMG00000156895	ENST00000335891.5:c.130A>G	chr3.hg19:g.51505002T>C	ENSP00000338857:p.Lys44Glu	119.0	0.0		99.0	4.0	NM_014703	Q2YD74|Q8TBD9|Q9HCA1|Q9UG37	Missense_Mutation	SNP	ENST00000335891.5	hg19		.	.	.	.	.	.	.	.	.	.	T	14.84	2.655051	0.47467	.	.	ENSG00000145041	ENST00000335891;ENST00000504652	T;T	0.55413	0.52;0.9	4.93	4.93	0.64822	.	0.103596	0.64402	D	0.000005	T	0.40839	0.1133	N	0.26042	0.785	0.25380	N	0.98862	P	0.35714	0.517	B	0.37239	0.244	T	0.30238	-0.9985	10	0.28530	T	0.3	-2.9551	13.6041	0.62037	0.0:0.0:0.0:1.0	.	44	Q9Y4B6	VPRBP_HUMAN	E	44	ENSP00000338857:K44E;ENSP00000421724:K44E	ENSP00000338857:K44E	K	-	1	0	VPRBP	51480042	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.300000	0.65721	1.849000	0.53698	0.369000	0.22263	AAA	.	.		0.393	VPRBP-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014703		C	51505002	T	C	51505002	3	2	254	1	0	0	0	0	1	0	0	0	17200	1850	64	2	4318	2	VPRBP	3	51505002	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	128609	51505002	146517428	178	34470										
GLT8D1	55830	hgsc.bcm.edu	37	chr3	52730329	52730329	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggcaagtagaaccttgcaaaGgttaactggaaaaggaaaga	12	5	0	2	rs371584519		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:52730329G>T	ENST00000407584.3	-	7	1303	c.453C>A	c.(451-453)acC>acA	p.T151T	GLT8D1_ENST00000463827.1_5'UTR|GLT8D1_ENST00000491606.1_Silent_p.T151T|GLT8D1_ENST00000478968.2_Silent_p.T151T|GLT8D1_ENST00000266014.5_Silent_p.T151T|GLT8D1_ENST00000394783.3_Silent_p.T151T	NM_001010983.1|NM_001278280.1	NP_001010983.1|NP_001265209.1	Q68CQ7	GL8D1_HUMAN	glycosyltransferase 8 domain containing 1	151						integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|endometrium(1)|kidney(3)|large_intestine(3)	8				BRCA - Breast invasive adenocarcinoma(193;6.78e-05)|Kidney(197;0.000618)|KIRC - Kidney renal clear cell carcinoma(197;0.000779)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		ACCTTGCAAAGGTTAACTGGA	0.408																																					p.T151T		Atlas-SNP	.											.	GLT8D1	28	.	0			c.C453A						.						84	77	79					3																	52730329		2203	4300	6503	SO:0001819	synonymous_variant	55830	exon6			TGCAAAGGTTAAC	AY358579	CCDS2862.1	3p21.1	2013-02-22			ENSG00000016864	ENSG00000016864		"Glycosyltransferase family 8 domain containing"	24870	protein-coding gene	gene with protein product						12975309	Standard	NM_152932		Approved	AD-017, FLJ14611	uc003dfi.4	Q68CQ7	OTTHUMG00000158759	ENST00000407584.3:c.453C>A	chr3.hg19:g.52730329G>T		128.0	0.0		90.0	4.0	NM_152932	Q7Z4D1|Q8N2J6|Q9P0I5	Silent	SNP	ENST00000407584.3	hg19	CCDS2862.1																																																																																			.	.		0.408	GLT8D1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352065.3	NM_152932		T	52730329	G	T	52730329	2	4	254	1	0	0	0	0	0	0	0	1	6477	987	35	3		3	GLT8D1	3	52730329	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1225327	52730329	145292101	179	34471										
TMEM110	375346	hgsc.bcm.edu	37	chr3	52874604	52874604	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccacgtcggactcctccatcTcatcatccgctgagatcagg	8	16	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:52874604T>C	ENST00000355083.5	-	8	936	c.791A>G	c.(790-792)gAg>gGg	p.E264G	TMEM110-MUSTN1_ENST00000504329.1_Missense_Mutation_p.E264G|TMEM110_ENST00000464769.1_5'UTR	NM_198563.2	NP_940965.1	Q86TL2	TM110_HUMAN	transmembrane protein 110	264						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(1)|lung(2)	4				BRCA - Breast invasive adenocarcinoma(193;7.72e-05)|Kidney(197;0.000777)|KIRC - Kidney renal clear cell carcinoma(197;0.000915)|OV - Ovarian serous cystadenocarcinoma(275;0.0541)		CTCCTCCATCTCATCATCCGC	0.592																																					p.E264G		Atlas-SNP	.											.	.	.	.	0			c.A791G						.						87	92	90					3																	52874604		2203	4300	6503	SO:0001583	missense	100526772	exon8			TCCATCTCATCAT	BC047015	CCDS2866.1	3p21.1	2010-08-13			ENSG00000213533	ENSG00000213533			30526	protein-coding gene	gene with protein product						12477932	Standard	NM_198563		Approved	MGC52022		Q86TL2	OTTHUMG00000150346	ENST00000355083.5:c.791A>G	chr3.hg19:g.52874604T>C	ENSP00000347195:p.Glu264Gly	66.0	0.0		55.0	4.0	NM_001198974		Missense_Mutation	SNP	ENST00000355083.5	hg19	CCDS2866.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.7|20.7	4.027780|4.027780	0.75390|0.75390	.|.	.|.	ENSG00000248592;ENSG00000213533;ENSG00000213533|ENSG00000248592	ENST00000504329;ENST00000482155;ENST00000355083|ENST00000514466	.|.	.|.	.|.	5.58|5.58	4.4|4.4	0.53042|0.53042	.|.	0.000000|.	0.85682|.	U|.	0.000000|.	T|T	0.51449|0.51449	0.1675|0.1675	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	D|D	1|1	D;D|.	0.67145|.	0.99;0.996|.	P;P|.	0.60012|.	0.815;0.867|.	T|T	0.42413|0.42413	-0.9453|-0.9453	9|5	0.38643|.	T|.	0.18|.	-11.2934|-11.2934	11.9796|11.9796	0.53113|0.53113	0.13:0.0:0.0:0.87|0.13:0.0:0.0:0.87	.|.	264;264|.	Q86TL2;A8MSY1|.	TM110_HUMAN;.|.	G|G	264;7;264|54	.|.	ENSP00000347195:E264G|.	E|R	-|-	2|1	0|2	TMEM110-MUSTN1;TMEM110|TMEM110-MUSTN1	52849644|52849644	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.597000|0.597000	0.36814|0.36814	7.441000|7.441000	0.80485|0.80485	0.932000|0.932000	0.37266|0.37266	0.496000|0.496000	0.49642|0.49642	GAG|AGA	.	.		0.592	TMEM110-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352949.2	NM_198563		C	52874604	T	C	52874604	3	2	254	1	0	0	0	0	1	0	0	0	16042	1551	54	2	97	2	TMEM110	3	52874604	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	144275	52874604	145147826	180	34472										
TKT	7086	hgsc.bcm.edu	37	chr3	53289863	53289863	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cgcactcacccagagcccgcCgcagtggtggcctggatgga	14	15	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:53289863C>T	ENST00000462138.1	-	1	184	c.96G>A	c.(94-96)gcG>gcA	p.A32A	TKT_ENST00000423525.2_Silent_p.A32A|TKT_ENST00000296289.6_5'UTR|TKT_ENST00000423516.1_Silent_p.A32A			P29401	TKT_HUMAN	transketolase	32					carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|glyceraldehyde-3-phosphate biosynthetic process (GO:0046166)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, non-oxidative branch (GO:0009052)|regulation of growth (GO:0040008)|small molecule metabolic process (GO:0044281)|xylulose biosynthetic process (GO:0005999)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|peroxisome (GO:0005777)|vesicle (GO:0031982)	cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|transketolase activity (GO:0004802)			endometrium(5)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17		Prostate(884;0.0959)		BRCA - Breast invasive adenocarcinoma(193;0.000159)|OV - Ovarian serous cystadenocarcinoma(275;0.000314)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)		CAGAGCCCGCCGCAGTGGTGG	0.731																																					p.A32A	Colon(133;1506 2347 35238 42177)	Atlas-SNP	.											.	TKT	38	.	0			c.G96A						.						35	32	33					3																	53289863		2202	4300	6502	SO:0001819	synonymous_variant	7086	exon1			GCCCGCCGCAGTG		CCDS2871.1, CCDS58834.1	3p14.3	2008-07-31	2008-07-31		ENSG00000163931	ENSG00000163931	2.2.1.1		11834	protein-coding gene	gene with protein product	"Wernicke-Korsakoff syndrome"	606781				1567394	Standard	NM_001064		Approved		uc011beq.2	P29401	OTTHUMG00000158192	ENST00000462138.1:c.96G>A	chr3.hg19:g.53289863C>T		148.0	0.0		80.0	4.0	NM_001258028	A8K089|B4DE31|E7EPA7|Q8TBA3|Q96HH3	Silent	SNP	ENST00000462138.1	hg19	CCDS2871.1																																																																																			.	.		0.731	TKT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350356.1			T	53289863	C	T	53289863	2	4	254	1	0	0	0	0	0	0	0	1	15949	639	23	1		1	TKT	3	53289863	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	415259	53289863	144732567	181	34473										
CACNA1D	776	hgsc.bcm.edu	37	chr3	53815596	53815596	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttgttttttgaatccagggaAcctggagcaagctaatgaag	11	6	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:53815596A>G	ENST00000350061.5	+	39	5205	c.4694A>G	c.(4693-4695)aAc>aGc	p.N1565S	CACNA1D_ENST00000422281.2_Missense_Mutation_p.N1550S|CACNA1D_ENST00000540742.1_Missense_Mutation_p.N457S|CACNA1D_ENST00000288139.4_Missense_Mutation_p.N1585S	NM_001128840.1	NP_001122312.1	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type, alpha 1D subunit	1565					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|energy reserve metabolic process (GO:0006112)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during SA node cell action potential (GO:0086052)|positive regulation of calcium ion transport (GO:0051928)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|ankyrin binding (GO:0030506)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)|voltage-gated calcium channel activity involved in cardiac muscle cell action potential (GO:0086007)|voltage-gated calcium channel activity involved SA node cell action potential (GO:0086059)			breast(3)|central_nervous_system(9)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(13)|liver(1)|lung(29)|ovary(6)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	90				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	AATCCAGGGAACCTGGAGCAA	0.473																																					p.N1585S		Atlas-SNP	.											.	CACNA1D	324	.	0			c.A4754G						.						79	82	81					3																	53815596		2203	4300	6503	SO:0001583	missense	776	exon40			CAGGGAACCTGGA	AB209171	CCDS2872.1, CCDS46848.1, CCDS46849.1	3p14.3	2012-03-07			ENSG00000157388	ENSG00000157388		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1391	protein-coding gene	gene with protein product		114206		CCHL1A2, CACNL1A2		1664412	Standard	NM_000720		Approved	Cav1.3, CACH3, CACN4	uc003dgu.5	Q01668	OTTHUMG00000158278	ENST00000350061.5:c.4694A>G	chr3.hg19:g.53815596A>G	ENSP00000288133:p.Asn1565Ser	176.0	0.0		117.0	5.0	NM_000720	B0FYA3|Q13916|Q13931|Q71UT1|Q9UDC3	Missense_Mutation	SNP	ENST00000350061.5	hg19	CCDS46848.1	.	.	.	.	.	.	.	.	.	.	A	16.25	3.070312	0.55539	.	.	ENSG00000157388	ENST00000350061;ENST00000288139;ENST00000422281;ENST00000481478;ENST00000540742	D;D;D;T;T	0.96427	-3.97;-4.01;-4.01;3.03;3.03	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	D	0.92912	0.7745	N	0.25890	0.77	0.80722	D	1	B;B;P;B;B	0.41188	0.031;0.004;0.741;0.007;0.234	B;B;B;B;B	0.39419	0.017;0.012;0.299;0.009;0.272	D	0.93357	0.6723	10	0.49607	T	0.09	.	15.7098	0.77615	1.0:0.0:0.0:0.0	.	1550;457;1258;1565;1585	B0FYA3;F5H313;Q59GD8;Q01668;Q01668-2	.;.;.;CAC1D_HUMAN;.	S	1565;1585;1550;1258;457	ENSP00000288133:N1565S;ENSP00000288139:N1585S;ENSP00000409174:N1550S;ENSP00000418014:N1258S;ENSP00000438229:N457S	ENSP00000288139:N1585S	N	+	2	0	CACNA1D	53790636	1.000000	0.71417	1.000000	0.80357	0.842000	0.47809	9.241000	0.95402	2.179000	0.69175	0.528000	0.53228	AAC	.	.		0.473	CACNA1D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350557.1	NM_000720		G	53815596	A	G	53815596	3	3	254	1	0	0	0	0	1	0	0	0	2543	43	2	2	5020	2	CACNA1D	3	53815596	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	525733	53815596	144206834	182	34474										
ROBO2	6092	hgsc.bcm.edu	37	chr3	77617564	77617564	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccagttgtgctgactcccacCacggttcaggtcacatggac	10	14	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:77617564C>A	ENST00000461745.1	+	13	2850	c.1950C>A	c.(1948-1950)acC>acA	p.T650T	ROBO2_ENST00000332191.8_Silent_p.T650T|ROBO2_ENST00000487694.3_Silent_p.T666T	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	650	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)			NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		TGACTCCCACCACGGTTCAGG	0.458																																					p.T650T		Atlas-SNP	.											.	ROBO2	527	.	0			c.C1950A						.						108	106	107					3																	77617564		2075	4212	6287	SO:0001819	synonymous_variant	6092	exon13			TCCCACCACGGTT	AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10250	protein-coding gene	gene with protein product		602431	"roundabout (axon guidance receptor, Drosophila) homolog 2"			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.1950C>A	chr3.hg19:g.77617564C>A		108.0	0.0		95.0	4.0	NM_002942	O43608|Q19AB4|Q19AB5	Silent	SNP	ENST00000461745.1	hg19	CCDS43109.1																																																																																			.	.		0.458	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		A	77617564	C	A	77617564	2	1	254	1	0	0	0	0	0	0	0	1	13529	581	21	3		3	ROBO2	3	77617564	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	23801968	77617564	120404866	183	34475										
STX19	415117	hgsc.bcm.edu	37	chr3	93733245	93733245	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttctttattttgagctacagCatggacagcaccaacaacac	6	11	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:93733245C>T	ENST00000315099.2	-	2	1125	c.869G>A	c.(868-870)tGc>tAc	p.C290Y	ARL13B_ENST00000539730.1_Intron|ARL13B_ENST00000394222.3_Intron|ARL13B_ENST00000303097.7_Intron|ARL13B_ENST00000471138.1_Intron|ARL13B_ENST00000535334.1_Intron|ARL13B_ENST00000486562.1_Intron	NM_001001850.2	NP_001001850.1	Q8N4C7	STX19_HUMAN	syntaxin 19	290	Cys-rich.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	integral component of membrane (GO:0016021)				kidney(2)|large_intestine(2)|lung(4)|prostate(1)	9						TGAGCTACAGCATGGACAGCA	0.318																																					p.C290Y		Atlas-SNP	.											.	STX19	19	.	0			c.G869A						.						46	43	44					3																	93733245		2203	4298	6501	SO:0001583	missense	415117	exon2			CTACAGCATGGAC	AF461456	CCDS33793.1	3q11	2005-12-30			ENSG00000178750	ENSG00000178750			19300	protein-coding gene	gene with protein product							Standard	NM_001001850		Approved	MGC21382	uc003drh.1	Q8N4C7	OTTHUMG00000159013	ENST00000315099.2:c.869G>A	chr3.hg19:g.93733245C>T	ENSP00000320679:p.Cys290Tyr	99.0	0.0		84.0	5.0	NM_001001850		Missense_Mutation	SNP	ENST00000315099.2	hg19	CCDS33793.1	.	.	.	.	.	.	.	.	.	.	C	14.16	2.453435	0.43531	.	.	ENSG00000178750	ENST00000315099	T	0.50548	0.74	5.2	5.2	0.72013	.	0.103138	0.64402	D	0.000002	T	0.49321	0.1550	M	0.69358	2.11	0.39259	D	0.964184	B	0.31054	0.306	B	0.27500	0.08	T	0.54964	-0.8214	10	0.54805	T	0.06	-5.212	18.6137	0.91295	0.0:1.0:0.0:0.0	.	290	Q8N4C7	STX19_HUMAN	Y	290	ENSP00000320679:C290Y	ENSP00000320679:C290Y	C	-	2	0	STX19	95215935	0.677000	0.27577	0.959000	0.39883	0.983000	0.72400	1.587000	0.36622	2.805000	0.96524	0.655000	0.94253	TGC	.	.		0.318	STX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352909.1	NM_001001850		T	93733245	C	T	93733245	3	4	254	1	0	0	0	0	1	0	0	0	15357	710	25	3	19	3	STX19	3	93733245	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	16115681	93733245	104289185	184	34476										
DHFRL1	200895	hgsc.bcm.edu	37	chr3	93779792	93779792	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aaccagaaaacaccttcataTtaatcatccttctcacatac	1	13	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:93779792T>C	ENST00000394221.2	-	2	1013	c.564A>G	c.(562-564)taA>taG	p.*188*	DHFRL1_ENST00000314636.2_Silent_p.*188*|DHFRL1_ENST00000481631.1_Intron|NSUN3_ENST00000314622.4_5'Flank	NM_001195643.1	NP_001182572.1	Q86XF0	DYRL1_HUMAN	dihydrofolate reductase-like 1	0					glycine biosynthetic process (GO:0006545)|nucleotide biosynthetic process (GO:0009165)|one-carbon metabolic process (GO:0006730)|tetrahydrofolate biosynthetic process (GO:0046654)|tetrahydrofolate metabolic process (GO:0046653)|thymidine biosynthetic process (GO:0046105)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	dihydrofolate reductase activity (GO:0004146)|mRNA binding (GO:0003729)|NADP binding (GO:0050661)			kidney(1)|large_intestine(2)|lung(3)|skin(1)|stomach(1)	8						CACCTTCATATTAATCATCCT	0.378																																					p.X188X		Atlas-SNP	.											.	DHFRL1	25	.	0			c.A564G						.						88	83	84					3																	93779792		2203	4300	6503	SO:0001819	synonymous_variant	200895	exon2			TTCATATTAATCA	AL832912	CCDS2926.1	3q11.2	2005-08-16	2005-02-07		ENSG00000178700	ENSG00000178700			27309	protein-coding gene	gene with protein product			"dihydrofolate reductase pseudogene 4"	DHFRP4		12477932	Standard	NM_001195643		Approved	FLJ16119	uc003drj.3	Q86XF0	OTTHUMG00000159014	ENST00000394221.2:c.564A>G	chr3.hg19:g.93779792T>C		122.0	0.0		125.0	5.0	NM_001195643	D3DN30|Q6P4I9	Silent	SNP	ENST00000394221.2	hg19	CCDS2926.1																																																																																			.	.		0.378	DHFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352910.1	NM_176815		C	93779792	T	C	93779792	2	2	254	1	0	0	0	0	0	0	0	1	4484	1500	52	2		2	DHFRL1	3	93779792	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	46547	93779792	104242638	185	34477										
RG9MTD1	54931	hgsc.bcm.edu	37	chr3	101284095	101284095	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggaaatgaaagcagcagcaaGggaagaagcaaaaaatatca	11	5	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:101284095G>T	ENST00000309922.6	+	2	624	c.470G>T	c.(469-471)aGg>aTg	p.R157M		NM_017819.2	NP_060289.2	Q7L0Y3	MRRP1_HUMAN	tRNA methyltransferase 10 homolog C (S. cerevisiae)	157					mitochondrial RNA 5'-end processing (GO:0000964)|tRNA processing (GO:0008033)	mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)										GCAGCAGCAAGGGAAGAAGCA	0.308																																					p.R157M		Atlas-SNP	.											.	.	.	.	0			c.G470T						.						44	43	43					3																	101284095		1809	4076	5885	SO:0001583	missense	54931	exon2			CAGCAAGGGAAGA	AK000439	CCDS43122.1	3q12.3	2012-06-28	2012-06-28	2012-06-28	ENSG00000174173	ENSG00000174173			26022	protein-coding gene	gene with protein product	"mitochondrial RNase P subunit 1"	615423	"RNA (guanine-9-) methyltransferase domain containing 1"	RG9MTD1		18984158	Standard	NM_017819		Approved	FLJ20432, MRPP1	uc003duz.4	Q7L0Y3	OTTHUMG00000159114	ENST00000309922.6:c.470G>T	chr3.hg19:g.101284095G>T	ENSP00000312356:p.Arg157Met	69.0	0.0		50.0	4.0	NM_017819	Q9NRG5|Q9NX54|Q9Y596	Missense_Mutation	SNP	ENST00000309922.6	hg19	CCDS43122.1	.	.	.	.	.	.	.	.	.	.	G	8.347	0.830109	0.16749	.	.	ENSG00000174173	ENST00000309922;ENST00000495642	T;T	0.47528	0.84;0.84	5.74	-6.52	0.01872	.	1.047670	0.07392	N	0.889222	T	0.33789	0.0875	L	0.36672	1.1	0.28829	N	0.897279	B	0.27229	0.172	B	0.25140	0.058	T	0.34304	-0.9834	10	0.41790	T	0.15	-11.2128	11.4372	0.50074	0.1091:0.0:0.7029:0.1879	.	157	Q7L0Y3	MRRP1_HUMAN	M	157	ENSP00000312356:R157M;ENSP00000419389:R157M	ENSP00000312356:R157M	R	+	2	0	RG9MTD1	102766785	0.041000	0.20044	0.325000	0.25375	0.388000	0.30384	-0.434000	0.06939	-0.877000	0.04012	0.655000	0.94253	AGG	.	.		0.308	TRMT10C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353400.2	NM_017819		T	101284095	G	T	101284095	3	4	254	1	0	0	0	0	1	0	0	0	13286	1000	35	3	472	3	RG9MTD1	3	101284095	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	7504303	101284095	96738335	186	34478										
PLCXD2	257068	hgsc.bcm.edu	37	chr3	111432801	111432801	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtggccaggaaagaagattcCagcgccctgggcaaacacca	12	12	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:111432801C>A	ENST00000477665.1	+	3	1016	c.692C>A	c.(691-693)cCa>cAa	p.P231Q	PLCXD2_ENST00000393934.3_Missense_Mutation_p.P231Q|PLCXD2_ENST00000472215.1_3'UTR	NM_001185106.1	NP_001172035.1	Q0VAA5	PLCX2_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 2	231					lipid catabolic process (GO:0016042)		phosphoric diester hydrolase activity (GO:0008081)|signal transducer activity (GO:0004871)			endometrium(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)	17						AAGAAGATTCCAGCGCCCTGG	0.498																																					p.P231Q		Atlas-SNP	.											.	PLCXD2	36	.	0			c.C692A						.						79	80	80					3																	111432801		2203	4300	6503	SO:0001583	missense	257068	exon3			AGATTCCAGCGCC	AK056141	CCDS2961.1, CCDS54619.1	3q13.2	2004-09-09			ENSG00000240891	ENSG00000240891			26462	protein-coding gene	gene with protein product							Standard	NM_001185106		Approved	FLJ31579	uc003dxz.3	Q0VAA5	OTTHUMG00000159279	ENST00000477665.1:c.692C>A	chr3.hg19:g.111432801C>A	ENSP00000420686:p.Pro231Gln	98.0	0.0		52.0	4.0	NM_001185106	Q96N12	Missense_Mutation	SNP	ENST00000477665.1	hg19	CCDS54619.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.441884	0.83993	.	.	ENSG00000240891	ENST00000393934;ENST00000477665	.	.	.	5.39	5.39	0.77823	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);	.	.	.	.	T	0.79100	0.4389	M	0.83483	2.645	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.75903	-0.3153	8	0.14656	T	0.56	-9.4779	16.6677	0.85257	0.0:1.0:0.0:0.0	.	231;231	Q0VAA5;Q0VAA5-2	PLCX2_HUMAN;.	Q	231	.	ENSP00000377511:P231Q	P	+	2	0	PLCXD2	112915491	1.000000	0.71417	0.985000	0.45067	0.955000	0.61496	7.376000	0.79658	2.512000	0.84698	0.563000	0.77884	CCA	.	.		0.498	PLCXD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354322.1	NM_153268		A	111432801	C	A	111432801	3	1	254	1	0	0	0	0	1	0	0	0	12051	594	21	3	702	3	PLCXD2	3	111432801	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	10148706	111432801	86589629	187	34479										
SLC9A10	285335	hgsc.bcm.edu	37	chr3	111985087	111985089	+	In_Frame_Del	DEL	AAG	AAG	-													0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aatatgctatccacttactcAagaagaagtgtttcttcaat					rs557883834	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:111985087_111985089delAAG	ENST00000305815.5	-	8	1126_1128	c.874_876delCTT	c.(874-876)cttdel	p.L292del	SLC9C1_ENST00000487372.1_In_Frame_Del_p.L292del	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	292					cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										CCACTTACTCAAGAAGAAGTGTT	0.315														4	0.000798722	0.003	0	5008	,	,		14903	0		0	False		,,,				2504	0				p.292_293del		Pindel	.											.	.	.	.	0			c.875_877del						.																																			SO:0001651	inframe_deletion	285335	exon8			.	AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"Solute carriers"	31401	protein-coding gene	gene with protein product	"sperm-NHE"	612738	"solute carrier family 9, isoform 10", "solute carrier family 9, member 10"	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.874_876delCTT	chr3.hg19:g.111985093_111985095delAAG	ENSP00000306627:p.Leu292del	420.0	0.0		423.0	87.0	NM_183061	Q6ZRP4|Q7RTP2	In_Frame_Del	DEL	ENST00000305815.5	hg19	CCDS33817.1																																																																																			.	.		0.315	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061		-	111985089	AAG	-	111985087	7	5	254	1	0	1	0	1	0	0	0	0	14725	117	5	0	2745	0	SLC9A10	3	111985087	In_Frame_Del	DEL	AAG	TCGA-EP-A2KA-01A-11D-A183-10	552286	111985087	86037343	188	34480										
BOC	91653	hgsc.bcm.edu	37	chr3	112987288	112987288	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	caagagtggctggaggcctcCagaggtgagtgggcaggagc	19	8	0	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:112987288C>T	ENST00000495514.1	+	5	1223	c.519C>T	c.(517-519)tcC>tcT	p.S173S	BOC_ENST00000273395.4_Silent_p.S173S|BOC_ENST00000355385.3_Silent_p.S173S			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	173	Ig-like C2-type 2.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			TGGAGGCCTCCAGAGGTGAGT	0.622																																					p.S173S		Atlas-SNP	.											.	BOC	139	.	0			c.C519T						.						51	47	48					3																	112987288		2203	4300	6503	SO:0001819	synonymous_variant	91653	exon5			GGCCTCCAGAGGT	AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	17173	protein-coding gene	gene with protein product	"brother of CDO", "brother of CDON", "cell adhesion associated, oncogene regulated 2"	608708	"Boc homolog (mouse)"			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.519C>T	chr3.hg19:g.112987288C>T		65.0	0.0		68.0	16.0	NM_033254	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Silent	SNP	ENST00000495514.1	hg19	CCDS2971.1																																																																																			.	.		0.622	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254		T	112987288	C	T	112987288	2	4	254	1	0	0	0	0	0	0	0	1	1481	581	21	3		3	BOC	3	112987288	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1002201	112987288	85035142	189	34481										
KIAA1407	57577	hgsc.bcm.edu	37	chr3	113737567	113737567	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tttccaaggcttgagtctccCgctccaacttctggaatctt	7	13	3	1	rs76418892	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:113737567C>A	ENST00000295878.3	-	8	1267	c.1121G>T	c.(1120-1122)cGg>cTg	p.R374L	KIAA1407_ENST00000545063.1_Missense_Mutation_p.R205L	NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	374			R -> W (in dbSNP:rs17603649).							endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						TTGAGTCTCCCGCTCCAACTT	0.448																																					p.R374L		Atlas-SNP	.											.	KIAA1407	80	.	0			c.G1121T						.						172	186	182					3																	113737567		2203	4300	6503	SO:0001583	missense	57577	exon8			GTCTCCCGCTCCA	AF509494	CCDS2977.1	3q13.31	2005-01-10			ENSG00000163617	ENSG00000163617			29272	protein-coding gene	gene with protein product						10718198	Standard	NM_020817		Approved		uc003eax.3	Q8NCU4	OTTHUMG00000159337	ENST00000295878.3:c.1121G>T	chr3.hg19:g.113737567C>A	ENSP00000295878:p.Arg374Leu	93.0	0.0		81.0	4.0	NM_020817	B4DYL1|Q9P2E0	Missense_Mutation	SNP	ENST00000295878.3	hg19	CCDS2977.1	.	.	.	.	.	.	.	.	.	.	C	17.59	3.427362	0.62733	.	.	ENSG00000163617	ENST00000295878;ENST00000545063;ENST00000491000	T;T;T	0.59502	0.98;0.26;0.48	5.76	3.98	0.46160	.	0.292319	0.33199	N	0.005167	T	0.67306	0.2879	M	0.71581	2.175	0.80722	D	1	D;D;D	0.69078	0.994;0.997;0.997	P;P;P	0.58172	0.706;0.834;0.773	T	0.68439	-0.5408	10	0.72032	D	0.01	.	8.7673	0.34711	0.0:0.7174:0.0:0.2826	.	361;250;374	C9JA89;B4DIZ9;Q8NCU4	.;.;K1407_HUMAN	L	374;205;361	ENSP00000295878:R374L;ENSP00000446381:R205L;ENSP00000418099:R361L	ENSP00000295878:R374L	R	-	2	0	KIAA1407	115220257	0.996000	0.38824	0.966000	0.40874	0.818000	0.46254	1.382000	0.34374	0.797000	0.33971	-0.140000	0.14226	CGG	.	C|0.991;T|0.009		0.448	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817		A	113737567	C	A	113737567	3	1	254	1	0	0	0	0	1	0	0	0	8238	652	23	1	1729	1	KIAA1407	3	113737567	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	750279	113737567	84284863	190	34482										
QTRTD1	79691	hgsc.bcm.edu	37	chr3	113789666	113789666	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tttcttggataactgtctgcGgctgcaggaagagtcagagg	14	7	3	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:113789666G>T	ENST00000493014.1	+	2	277	c.209G>T	c.(208-210)cGg>cTg	p.R70L	QTRTD1_ENST00000479882.1_Missense_Mutation_p.R53L|QTRTD1_ENST00000281273.4_Missense_Mutation_p.R176L|QTRTD1_ENST00000485050.1_Missense_Mutation_p.R188L	NM_001256836.1	NP_001243765.1			queuine tRNA-ribosyltransferase domain containing 1											central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|skin(2)	10						AACTGTCTGCGGCTGCAGGAA	0.458																																					p.R188L		Atlas-SNP	.											.	QTRTD1	29	.	0			c.G563T						.						72	70	71					3																	113789666		2203	4300	6503	SO:0001583	missense	79691	exon5			GTCTGCGGCTGCA	AK023022	CCDS33828.1, CCDS58846.1, CCDS58845.1, CCDS58844.1	3q13.31	2010-11-16			ENSG00000151576	ENSG00000151576			25771	protein-coding gene	gene with protein product						12477932	Standard	NM_024638		Approved	FLJ12960	uc003eaz.4	Q9H974	OTTHUMG00000159336	ENST00000493014.1:c.209G>T	chr3.hg19:g.113789666G>T	ENSP00000419169:p.Arg70Leu	57.0	0.0		93.0	4.0	NM_001256835		Missense_Mutation	SNP	ENST00000493014.1	hg19	CCDS58845.1	.	.	.	.	.	.	.	.	.	.	G	8.134	0.783777	0.16189	.	.	ENSG00000151576	ENST00000485050;ENST00000281273;ENST00000479882;ENST00000493014	.	.	.	5.5	-0.545	0.11843	.	0.756596	0.12397	N	0.472504	T	0.14485	0.0350	N	0.08118	0	0.25024	N	0.99132	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.0	T	0.26916	-1.0089	8	.	.	.	-0.1312	4.6807	0.12734	0.6221:0.0:0.2063:0.1716	.	70;53;176	B7Z472;B7Z5R2;Q9H974	.;.;QTRD1_HUMAN	L	188;176;53;70	.	.	R	+	2	0	QTRTD1	115272356	0.883000	0.30277	0.889000	0.34880	0.277000	0.26821	1.041000	0.30291	-0.008000	0.14320	0.561000	0.74099	CGG	.	.		0.458	QTRTD1-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000354711.1	NM_024638		T	113789666	G	T	113789666	3	4	254	1	0	0	0	0	1	0	0	0	12901	1116	39	1	541	1	QTRTD1	3	113789666	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	52099	113789666	84232764	191	34483										
POPDC2	64091	hgsc.bcm.edu	37	chr3	119378819	119378819	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	acaggcggttgatgggtgtcTcaccctccacagcataggtc	12	12	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:119378819T>C	ENST00000264231.3	-	1	618	c.452A>G	c.(451-453)gAg>gGg	p.E151G	POPDC2_ENST00000468801.1_Missense_Mutation_p.E151G|POPDC2_ENST00000474523.1_5'UTR|POPDC2_ENST00000538678.1_Missense_Mutation_p.E151G|POPDC2_ENST00000493094.1_Missense_Mutation_p.E151G	NM_022135.2	NP_071418.2	Q9HBU9	POPD2_HUMAN	popeye domain containing 2	151					regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sinoatrial node cell development (GO:0060931)	integral component of membrane (GO:0016021)	cAMP binding (GO:0030552)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	13				GBM - Glioblastoma multiforme(114;0.242)		GATGGGTGTCTCACCCTCCAC	0.542																																					p.E151G		Atlas-SNP	.											.	POPDC2	36	.	0			c.A452G						.						134	132	133					3																	119378819		2203	4300	6503	SO:0001583	missense	64091	exon1			GGTGTCTCACCCT	AF204173	CCDS2992.1	3q13.33	2004-01-15			ENSG00000121577	ENSG00000121577			17648	protein-coding gene	gene with protein product		605823				10882522	Standard	NM_022135		Approved	POP2	uc031sbc.1	Q9HBU9	OTTHUMG00000159438	ENST00000264231.3:c.452A>G	chr3.hg19:g.119378819T>C	ENSP00000264231:p.Glu151Gly	96.0	0.0		76.0	5.0	NM_022135	Q86UE7	Missense_Mutation	SNP	ENST00000264231.3	hg19	CCDS2992.1	.	.	.	.	.	.	.	.	.	.	T	28.2	4.903812	0.92035	.	.	ENSG00000121577	ENST00000264231;ENST00000493094;ENST00000468801;ENST00000538678	T;T;T;T	0.31510	1.49;1.49;1.49;1.49	5.69	5.69	0.88448	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);	0.046397	0.85682	D	0.000000	T	0.42314	0.1197	L	0.34521	1.04	0.80722	D	1	D;D	0.67145	0.996;0.986	P;P	0.62813	0.857;0.907	T	0.15607	-1.0431	10	0.35671	T	0.21	.	15.9315	0.79663	0.0:0.0:0.0:1.0	.	151;151	Q9HBU9-2;Q9HBU9	.;POPD2_HUMAN	G	151	ENSP00000264231:E151G;ENSP00000417250:E151G;ENSP00000420715:E151G;ENSP00000438271:E151G	ENSP00000264231:E151G	E	-	2	0	POPDC2	120861509	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.136000	0.71703	2.162000	0.67917	0.533000	0.62120	GAG	.	.		0.542	POPDC2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000355378.1	NM_022135		C	119378819	T	C	119378819	3	2	254	1	0	0	0	0	1	0	0	0	12264	1551	54	2	658	2	POPDC2	3	119378819	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	5589153	119378819	78643611	192	34484										
PARP14	54625	hgsc.bcm.edu	37	chr3	122419215	122419215	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	taagcgcattgaagttgagaAcaaagaagttcttcatggca	10	6	2	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:122419215A>G	ENST00000474629.2	+	6	2080	c.1814A>G	c.(1813-1815)aAc>aGc	p.N605S		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	605					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		GAAGTTGAGAACAAAGAAGTT	0.388																																					p.N605S		Atlas-SNP	.											.	PARP14	242	.	0			c.A1814G						.						37	36	36					3																	122419215		1869	4091	5960	SO:0001583	missense	54625	exon6			TTGAGAACAAAGA	AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"Poly (ADP-ribose) polymerases"	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.1814A>G	chr3.hg19:g.122419215A>G	ENSP00000418194:p.Asn605Ser	92.0	0.0		79.0	4.0	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Missense_Mutation	SNP	ENST00000474629.2	hg19	CCDS46894.1	.	.	.	.	.	.	.	.	.	.	A	13.35	2.209543	0.39003	.	.	ENSG00000173193	ENST00000474629;ENST00000398162	T	0.08370	3.1	5.22	2.88	0.33553	.	0.342378	0.27056	N	0.021143	T	0.05547	0.0146	N	0.22421	0.69	0.25439	N	0.98811	B;B	0.29716	0.005;0.255	B;B	0.22152	0.004;0.038	T	0.30937	-0.9961	10	0.72032	D	0.01	.	8.4903	0.33095	0.8411:0.0:0.1589:0.0	.	605;605	Q460N5-4;Q460N5	.;PAR14_HUMAN	S	605;524	ENSP00000418194:N605S	ENSP00000381228:N524S	N	+	2	0	PARP14	123901905	1.000000	0.71417	0.122000	0.21767	0.004000	0.04260	5.648000	0.67930	0.465000	0.27167	-0.376000	0.06991	AAC	.	.		0.388	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554		G	122419215	A	G	122419215	3	3	254	1	0	0	0	0	1	0	0	0	11467	43	2	2	1836	2	PARP14	3	122419215	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	3040396	122419215	75603215	193	34485										
CCDC14	64770	hgsc.bcm.edu	37	chr3	123634090	123634090	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agctgctcttatttgtggctGaggggatagtctcttagaaa	12	6	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:123634090G>T	ENST00000488653.2	-	13	2488	c.2398C>A	c.(2398-2400)Cag>Aag	p.Q800K	CCDC14_ENST00000310351.4_Missense_Mutation_p.Q640K|CCDC14_ENST00000489746.1_Missense_Mutation_p.Q600K|CCDC14_ENST00000483247.1_5'UTR|CCDC14_ENST00000433542.2_Missense_Mutation_p.Q759K|CCDC14_ENST00000485727.1_Missense_Mutation_p.Q600K			Q49A88	CCD14_HUMAN	coiled-coil domain containing 14	800					substantia nigra development (GO:0021762)	centrosome (GO:0005813)				NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)	21		Lung NSC(201;0.0371)|Prostate(884;0.0405)|Myeloproliferative disorder(1037;0.205)		Lung(219;0.00942)|GBM - Glioblastoma multiforme(114;0.159)		ATTTGTGGCTGAGGGGATAGT	0.388																																					p.Q759K		Atlas-SNP	.											.	CCDC14	97	.	0			c.C2275A						.						74	75	74					3																	123634090		2203	4300	6503	SO:0001583	missense	64770	exon12			GTGGCTGAGGGGA	AL122079	CCDS3025.2	3q21.1	2014-03-20			ENSG00000175455	ENSG00000175455			25766	protein-coding gene	gene with protein product						12477932	Standard	NM_022757		Approved	FLJ12892, DKFZp434L1050	uc010hrt.3	Q49A88	OTTHUMG00000153005	ENST00000488653.2:c.2398C>A	chr3.hg19:g.123634090G>T	ENSP00000420180:p.Gln800Lys	109.0	0.0		76.0	4.0	NM_022757	B7Z2T2|B8ZZ41|B8ZZ58|D3DN98|Q7Z3N3|Q86T30|Q8IWF8|Q8WUJ8|Q96K47|Q9H9A3|Q9UFH0	Missense_Mutation	SNP	ENST00000488653.2	hg19		.	.	.	.	.	.	.	.	.	.	G	0.053	-1.243834	0.01481	.	.	ENSG00000175455	ENST00000488653;ENST00000310351;ENST00000485727;ENST00000489746;ENST00000433542;ENST00000409697;ENST00000419247	T;T;T;T;T;T;T	0.44482	0.95;0.95;0.95;0.95;0.95;0.95;0.92	5.05	4.09	0.47781	.	0.121048	0.36854	N	0.002369	T	0.47135	0.1429	L	0.56769	1.78	0.09310	N	1	D;D;D	0.56035	0.974;0.974;0.974	P;P;P	0.53861	0.736;0.736;0.736	T	0.30851	-0.9964	10	0.24483	T	0.36	.	9.7046	0.40207	0.0839:0.0:0.7706:0.1455	.	800;759;641	Q49A88;Q49A88-6;Q49A88-5	CCD14_HUMAN;.;.	K	800;640;600;600;759;781;298	ENSP00000420180:Q800K;ENSP00000312031:Q640K;ENSP00000418002:Q600K;ENSP00000418403:Q600K;ENSP00000395706:Q759K;ENSP00000386866:Q781K;ENSP00000400957:Q298K	ENSP00000312031:Q640K	Q	-	1	0	CCDC14	125116780	0.249000	0.23941	0.435000	0.26784	0.035000	0.12851	1.936000	0.40183	2.623000	0.88846	0.591000	0.81541	CAG	.	.		0.388	CCDC14-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_022757		T	123634090	G	T	123634090	3	4	254	1	0	0	0	0	1	0	0	0	2775	1299	45	3	467	3	CCDC14	3	123634090	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1214875	123634090	74388340	194	34486										
HEG1	57493	hgsc.bcm.edu	37	chr3	124732817	124732817	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agctgtgccacgcacttgacCgtagctaatcccagcgactg	10	14	0	1	rs574836585		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:124732817C>A	ENST00000311127.4	-	6	1673	c.1606G>T	c.(1606-1608)Ggt>Tgt	p.G536C	HEG1_ENST00000477536.1_5'UTR	NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	536	Ser-rich.				cardiac atrium morphogenesis (GO:0003209)|cell-cell junction assembly (GO:0007043)|endothelial cell morphogenesis (GO:0001886)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|lymph circulation (GO:0003017)|lymph vessel development (GO:0001945)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|post-embryonic development (GO:0009791)|regulation of body fluid levels (GO:0050878)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|ventricular septum development (GO:0003281)	cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)	p.G536C(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(24)|ovary(2)|urinary_tract(4)	47						CGCACTTGACCGTAGCTAATC	0.443																																					p.G536C		Atlas-SNP	.											HEG1,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	HEG1	109	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.G1606T						.						91	84	86					3																	124732817		1934	4143	6077	SO:0001583	missense	57493	exon6			CTTGACCGTAGCT	AK074987	CCDS46898.1	3q21.2	2013-03-08	2013-03-08		ENSG00000173706	ENSG00000173706			29227	protein-coding gene	gene with protein product	"heart of glass"	614182	"HEG homolog 1 (zebrafish)"			10574462, 19151727, 23007647	Standard	NM_020733		Approved	KIAA1237, HEG	uc003ehs.4	Q9ULI3	OTTHUMG00000159486	ENST00000311127.4:c.1606G>T	chr3.hg19:g.124732817C>A	ENSP00000311502:p.Gly536Cys	44.0	1.0		46.0	3.0	NM_020733	Q6NX66|Q8NC40|Q9BSV0	Missense_Mutation	SNP	ENST00000311127.4	hg19	CCDS46898.1	.	.	.	.	.	.	.	.	.	.	C	18.62	3.662490	0.67700	.	.	ENSG00000173706	ENST00000311127	D	0.88277	-2.36	5.54	0.0224	0.14133	.	.	.	.	.	D	0.86260	0.5890	N	0.22421	0.69	0.09310	N	1	D;D	0.69078	0.997;0.997	P;P	0.60682	0.878;0.758	T	0.75522	-0.3288	9	0.66056	D	0.02	.	5.0469	0.14488	0.0:0.3339:0.2895:0.3766	.	536;536	Q9ULI3-2;Q9ULI3	.;HEG1_HUMAN	C	536	ENSP00000311502:G536C	ENSP00000311502:G536C	G	-	1	0	HEG1	126215507	0.000000	0.05858	0.000000	0.03702	0.512000	0.34134	-0.074000	0.11450	-0.195000	0.10382	-0.150000	0.13652	GGT	.	.		0.443	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386		A	124732817	C	A	124732817	3	1	254	1	0	0	0	0	1	0	0	0	7053	652	23	1	2587	1	HEG1	3	124732817	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1098727	124732817	73289613	195	34487										
IFT122	55764	hgsc.bcm.edu	37	chr3	129238004	129238004	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctccatcggagatgaggaccCgttcacagctaagctgagct	11	12	1	3	rs373326394		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:129238004C>A	ENST00000348417.2	+	28	3523	c.3446C>A	c.(3445-3447)cCg>cAg	p.P1149Q	IFT122_ENST00000504021.1_Missense_Mutation_p.P1026Q|IFT122_ENST00000296266.3_Missense_Mutation_p.P1200Q|IFT122_ENST00000347300.2_Missense_Mutation_p.P1090Q|IFT122_ENST00000431818.2_Missense_Mutation_p.P999Q|IFT122_ENST00000440957.2_Missense_Mutation_p.P940Q|IFT122_ENST00000349441.2_Missense_Mutation_p.P1039Q|IFT122_ENST00000507564.1_Missense_Mutation_p.P1142Q	NM_052989.1	NP_443715.1	Q9HBG6	IF122_HUMAN	intraflagellar transport 122	1149					camera-type eye morphogenesis (GO:0048593)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|establishment of protein localization to organelle (GO:0072594)|intraciliary anterograde transport (GO:0035720)|intraciliary retrograde transport (GO:0035721)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|protein localization to cilium (GO:0061512)|signal transduction downstream of smoothened (GO:0007227)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|intraciliary transport particle A (GO:0030991)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)		p.P1200Q(1)		breast(3)|cervix(1)|endometrium(9)|large_intestine(10)|lung(21)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	52						GATGAGGACCCGTTCACAGCT	0.587																																					p.P1200Q		Atlas-SNP	.											.	IFT122	117	.	1	Substitution - Missense(1)	lung(1)	c.C3599A						.						120	111	114					3																	129238004		2203	4300	6503	SO:0001583	missense	55764	exon29			AGGACCCGTTCAC	AF244930	CCDS3059.1, CCDS3060.1, CCDS3061.1, CCDS3062.1, CCDS63770.1, CCDS63772.1, CCDS63773.1	3q21	2014-07-03	2014-07-03	2005-11-02	ENSG00000163913	ENSG00000163913		"WD repeat domain containing", "Intraflagellar transport homologs"	13556	protein-coding gene	gene with protein product		606045	"WD repeat domain 10", "intraflagellar transport 122 homolog (Chlamydomonas)"	WDR10		11242542	Standard	NM_052985		Approved	WDR140, WDR10p, SPG	uc003emm.3	Q9HBG6	OTTHUMG00000159516	ENST00000348417.2:c.3446C>A	chr3.hg19:g.129238004C>A	ENSP00000324005:p.Pro1149Gln	145.0	0.0		93.0	5.0	NM_052985	B3KW53|B4DEY9|B4DPW7|E7EQF4|E9PDG2|E9PDX2|G3XAB1|H7C3C0|Q53G36|Q8TC06|Q9BTB9|Q9BTY4|Q9HAT9|Q9HBG5|Q9NV68|Q9UF80	Missense_Mutation	SNP	ENST00000348417.2	hg19	CCDS3061.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.998072	0.74818	.	.	ENSG00000163913	ENST00000347300;ENST00000296266;ENST00000507564;ENST00000431818;ENST00000504021;ENST00000349441;ENST00000348417;ENST00000446384;ENST00000440957	T;T;T;T;T;T;T;T	0.62498	0.66;0.02;0.14;0.19;0.81;0.8;0.64;0.22	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.72898	0.3518	L	0.34521	1.04	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.988;1.0;1.0;0.997;1.0;1.0	D;D;D;D;P;D;D;D;D;D	0.91635	0.999;0.999;0.997;0.996;0.708;0.995;0.991;0.932;0.999;0.999	T	0.72690	-0.4217	10	0.52906	T	0.07	-15.0043	20.1054	0.97890	0.0:1.0:0.0:0.0	.	940;475;1142;537;1026;991;1039;1090;1149;1200	E9PDG2;B3KUD1;E7EQF4;B3KT43;B4DEY9;B4DPW7;Q9BTY4;Q9HBG6-3;Q9HBG6;G3XAB1	.;.;.;.;.;.;.;.;IF122_HUMAN;.	Q	1090;1200;1142;999;1026;1039;1149;991;940	ENSP00000323973:P1090Q;ENSP00000296266:P1200Q;ENSP00000425536:P1142Q;ENSP00000410946:P999Q;ENSP00000422179:P1026Q;ENSP00000324165:P1039Q;ENSP00000324005:P1149Q;ENSP00000401569:P940Q	ENSP00000296266:P1200Q	P	+	2	0	IFT122	130720694	1.000000	0.71417	0.965000	0.40720	0.359000	0.29487	7.025000	0.76449	2.757000	0.94681	0.655000	0.94253	CCG	.	.		0.587	IFT122-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355852.1	NM_018262		A	129238004	C	A	129238004	3	1	254	1	0	0	0	0	1	0	0	0	7564	652	23	1	3716	1	IFT122	3	129238004	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	4505187	129238004	68784426	196	34488										
PLXND1	23129	hgsc.bcm.edu	37	chr3	129279245	129279245	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tggctctgccggtgagacttCttgggctccgccagctcgtc	13	14	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:129279245C>G	ENST00000324093.4	-	31	5239	c.5061G>C	c.(5059-5061)aaG>aaC	p.K1687N	PLXND1_ENST00000393239.1_Missense_Mutation_p.K1687N	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1687					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)		PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						GGTGAGACTTCTTGGGCTCCG	0.667																																					p.K1687N	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											.	PLXND1	149	.	0			c.G5061C						.						70	58	62					3																	129279245		2203	4299	6502	SO:0001583	missense	23129	exon31			AGACTTCTTGGGC	AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"Plexins"	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.5061G>C	chr3.hg19:g.129279245C>G	ENSP00000317128:p.Lys1687Asn	197.0	0.0		117.0	5.0	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Missense_Mutation	SNP	ENST00000324093.4	hg19	CCDS33854.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.62|12.62	1.993734|1.993734	0.35131|0.35131	.|.	.|.	ENSG00000004399|ENSG00000004399	ENST00000506979|ENST00000324093;ENST00000393239	.|T;T	.|0.12774	.|2.65;2.65	5.0|5.0	3.17|3.17	0.36434|0.36434	.|Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	.|0.348813	.|0.29814	.|N	.|0.011130	T|T	0.13157|0.13157	0.0319|0.0319	N|N	0.05280|0.05280	-0.08|-0.08	0.50813|0.50813	D|D	0.999894|0.999894	.|B;D	.|0.64830	.|0.322;0.994	.|B;P	.|0.61003	.|0.126;0.882	T|T	0.13150|0.13150	-1.0520|-1.0520	5|10	.|0.87932	.|D	.|0	.|.	8.321|8.321	0.32130|0.32130	0.0:0.6927:0.0:0.3073|0.0:0.6927:0.0:0.3073	.|.	.|282;1687	.|B4DRU3;Q9Y4D7	.|.;PLXD1_HUMAN	Q|N	31|1687	.|ENSP00000317128:K1687N;ENSP00000376931:K1687N	.|ENSP00000317128:K1687N	E|K	-|-	1|3	0|2	PLXND1|PLXND1	130761935|130761935	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.495000|0.495000	0.33615|0.33615	2.562000|2.562000	0.45914|0.45914	1.107000|1.107000	0.41642|0.41642	0.462000|0.462000	0.41574|0.41574	GAA|AAG	.	.		0.667	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103		G	129279245	C	G	129279245	3	3	254	1	0	0	0	0	1	0	0	0	12136	912	32	4	740	4	PLXND1	3	129279245	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	41241	129279245	68743185	197	34489										
DNAJC13	23317	hgsc.bcm.edu	37	chr3	132193831	132193831	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggaatttcaaaacacgagaaGaactgaaagatactcttgaa	8	6	2	5			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:132193831G>T	ENST00000260818.6	+	22	2595	c.2347G>T	c.(2347-2349)Gaa>Taa	p.E783*		NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	783					osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						AACACGAGAAGAACTGAAAGA	0.383																																					p.E783X		Atlas-SNP	.											.	DNAJC13	253	.	0			c.G2347T						.						107	112	110					3																	132193831		2203	4300	6503	SO:0001587	stop_gained	23317	exon22			CGAGAAGAACTGA	AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"Heat shock proteins / DNAJ (HSP40)"	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.2347G>T	chr3.hg19:g.132193831G>T	ENSP00000260818:p.Glu783*	102.0	0.0		86.0	4.0	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Nonsense_Mutation	SNP	ENST00000260818.6	hg19	CCDS33857.1	.	.	.	.	.	.	.	.	.	.	G	43	10.191783	0.99355	.	.	ENSG00000138246	ENST00000260818	.	.	.	5.68	4.81	0.61882	.	0.121103	0.56097	D	0.000040	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	14.1936	0.65654	0.0712:0.0:0.9288:0.0	.	.	.	.	X	783	.	ENSP00000260818:E783X	E	+	1	0	DNAJC13	133676521	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.623000	0.98386	1.413000	0.46997	0.650000	0.86243	GAA	.	.		0.383	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268		T	132193831	G	T	132193831	4	4	254	1	0	0	0	0	0	1	0	0	4634	943	33	3	2429	3	DNAJC13	3	132193831	Nonsense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	2914586	132193831	65828599	198	34490										
CEP63	80254	hgsc.bcm.edu	37	chr3	134264444	134264444	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctaggctcagcttgtcaatcGgaaacagaaattagagtctg	10	8	3	2	rs529386244		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:134264444G>T	ENST00000337090.3	+	7	745	c.572G>T	c.(571-573)cGg>cTg	p.R191L	CEP63_ENST00000332047.5_Missense_Mutation_p.R191L|CEP63_ENST00000513612.2_Missense_Mutation_p.R191L|CEP63_ENST00000606977.1_Missense_Mutation_p.R191L|CEP63_ENST00000354446.3_Missense_Mutation_p.R191L|CEP63_ENST00000383229.3_Missense_Mutation_p.R191L			Q96MT8	CEP63_HUMAN	centrosomal protein 63kDa	191					centriole replication (GO:0007099)|DNA damage checkpoint (GO:0000077)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|signal transduction in response to DNA damage (GO:0042770)|spindle assembly (GO:0051225)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|spindle pole (GO:0000922)				kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						CTTGTCAATCGGAAACAGAAA	0.353																																					p.R191L		Atlas-SNP	.											.	CEP63	56	.	0			c.G572T						.						79	75	76					3																	134264444		2203	4300	6503	SO:0001583	missense	80254	exon7			TCAATCGGAAACA	AK056465	CCDS3086.1, CCDS43152.1, CCDS43153.1, CCDS43154.1	3q22.1	2014-02-20			ENSG00000182923	ENSG00000182923			25815	protein-coding gene	gene with protein product		614724				14654843, 24240477	Standard	NM_001042383		Approved	FLJ13386	uc003eqo.1	Q96MT8	OTTHUMG00000159725	ENST00000337090.3:c.572G>T	chr3.hg19:g.134264444G>T	ENSP00000336524:p.Arg191Leu	105.0	0.0		78.0	4.0	NM_001042383	D3DND8|D3DND9|D3DNE0|Q96CR0|Q9H8F5|Q9H8N0	Missense_Mutation	SNP	ENST00000337090.3	hg19	CCDS3086.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	27.2|27.2	4.811746|4.811746	0.90707|0.90707	.|.	.|.	ENSG00000182923|ENSG00000182923	ENST00000508778|ENST00000332047;ENST00000354446;ENST00000337090;ENST00000383229;ENST00000513612	.|T;T;T;T;T	.|0.36157	.|1.93;1.66;1.92;1.27;1.92	6.1|6.1	6.1|6.1	0.99115|0.99115	.|.	.|0.068772	.|0.64402	.|D	.|0.000016	.|T	.|0.60431	.|0.2268	M|M	0.68952|0.68952	2.095|2.095	0.53688|0.53688	D|D	0.999977|0.999977	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;0.997	.|D;D;D;P	.|0.91635	.|0.999;0.985;0.985;0.898	.|T	.|0.47275	.|-0.9130	.|10	.|0.23891	.|T	.|0.37	-13.8266|-13.8266	20.7146|20.7146	0.99709|0.99709	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|191;191;191;191	.|Q96MT8;Q96MT8-2;Q96MT8-4;Q96MT8-3	.|CEP63_HUMAN;.;.;.	X|L	97|191	.|ENSP00000328382:R191L;ENSP00000346432:R191L;ENSP00000336524:R191L;ENSP00000372716:R191L;ENSP00000426129:R191L	.|ENSP00000328382:R191L	G|R	+|+	1|2	0|0	CEP63|CEP63	135747134|135747134	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.969000|0.969000	0.65631|0.65631	6.717000|6.717000	0.74707|0.74707	2.902000|2.902000	0.99343|0.99343	0.650000|0.650000	0.86243|0.86243	GGA|CGG	.	.		0.353	CEP63-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000470139.1	NM_025180		T	134264444	G	T	134264444	3	4	254	1	0	0	0	0	1	0	0	0	3259	1116	39	1	594	1	CEP63	3	134264444	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	2070613	134264444	63757986	199	34491										
CLSTN2	64084	hgsc.bcm.edu	37	chr3	140251313	140251313	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tagccatgcaactcacagtcGgcgcttgttggcaaggtaat	11	10	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:140251313G>T	ENST00000458420.3	+	9	1682	c.1492G>T	c.(1492-1494)Ggc>Tgc	p.G498C		NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	498					homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						ACTCACAGTCGGCGCTTGTTG	0.443										HNSCC(16;0.037)																											p.G498C	GBM(45;858 913 3709 36904 37282)	Atlas-SNP	.											.	CLSTN2	190	.	0			c.G1492T						.						136	113	121					3																	140251313		2203	4300	6503	SO:0001583	missense	64084	exon9			ACAGTCGGCGCTT	AJ278018	CCDS3112.1	3q23	2011-07-01			ENSG00000158258	ENSG00000158258		"Cadherins / Cadherin-related"	17448	protein-coding gene	gene with protein product	"cadherin-related family member 13"	611323				12498782	Standard	NM_022131		Approved	CSTN2, CS2, FLJ39113, CDHR13	uc003etn.3	Q9H4D0	OTTHUMG00000160139	ENST00000458420.3:c.1492G>T	chr3.hg19:g.140251313G>T	ENSP00000402460:p.Gly498Cys	122.0	0.0		91.0	5.0	NM_022131	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Missense_Mutation	SNP	ENST00000458420.3	hg19	CCDS3112.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.499134	0.85069	.	.	ENSG00000158258	ENST00000458420	D	0.89270	-2.49	5.67	5.67	0.87782	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.000000	0.85682	D	0.000000	D	0.94974	0.8374	M	0.86097	2.795	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94871	0.8030	9	.	.	.	-12.4934	17.2644	0.87081	0.0:0.0:1.0:0.0	.	498	Q9H4D0	CSTN2_HUMAN	C	498	ENSP00000402460:G498C	.	G	+	1	0	CLSTN2	141734003	1.000000	0.71417	0.971000	0.41717	0.880000	0.50808	9.869000	0.99810	2.697000	0.92050	0.655000	0.94253	GGC	.	.		0.443	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131		T	140251313	G	T	140251313	3	4	254	1	0	0	0	0	1	0	0	0	3564	1116	39	1	1526	1	CLSTN2	3	140251313	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	5986869	140251313	57771117	200	34492										
EIF2A	83939	hgsc.bcm.edu	37	chr3	150285799	150285799	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gctaataaaagtttctttaaGgcagataaagttacaatgct	7	5	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:150285799G>A	ENST00000460851.1	+	8	769	c.660G>A	c.(658-660)aaG>aaA	p.K220K	EIF2A_ENST00000487799.1_Silent_p.K195K|SERP1_ENST00000479209.1_Intron|EIF2A_ENST00000273435.5_Silent_p.K215K|SERP1_ENST00000490945.1_Intron|EIF2A_ENST00000383043.3_Splice_Site|EIF2A_ENST00000406576.3_Silent_p.K159K			Q9BY44	EIF2A_HUMAN	eukaryotic translation initiation factor 2A, 65kDa	220					positive regulation of signal transduction (GO:0009967)|protein phosphorylation (GO:0006468)|regulation of translation (GO:0006417)|ribosome assembly (GO:0042255)|SREBP signaling pathway (GO:0032933)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|eukaryotic translation initiation factor 2 complex (GO:0005850)|extracellular space (GO:0005615)	ribosome binding (GO:0043022)|translation initiation factor activity (GO:0003743)|tRNA binding (GO:0000049)			cervix(1)|endometrium(2)|kidney(1)|lung(3)	7		Melanoma(1037;0.0575)	LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			GTTTCTTTAAGGCAGATAAAG	0.338																																					p.K220K		Atlas-SNP	.											.	EIF2A	59	.	0			c.G660A						.						65	61	62					3																	150285799		1824	4087	5911	SO:0001819	synonymous_variant	83939	exon8			CTTTAAGGCAGAT	AF212241	CCDS46935.1	3q25.1	2011-01-19	2006-01-24		ENSG00000144895	ENSG00000144895			3254	protein-coding gene	gene with protein product		609234				12133843, 1620067	Standard	NM_032025		Approved	EIF-2A	uc003eya.3	Q9BY44	OTTHUMG00000159775	ENST00000460851.1:c.660G>A	chr3.hg19:g.150285799G>A		61.0	0.0		61.0	19.0	NM_032025	A8MPS6|B4DF96|B4DQ14|D3DNI9|Q5QTR2|Q7Z4E9|Q8NFM1|Q96EW9|Q96K81	Silent	SNP	ENST00000460851.1	hg19	CCDS46935.1	.	.	.	.	.	.	.	.	.	.	G	15.40	2.822993	0.50739	.	.	ENSG00000144895	ENST00000383043	.	.	.	6.07	3.18	0.36537	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.1513	0.20313	0.5938:0.0:0.4062:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	EIF2A	151768489	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.664000	0.46783	0.796000	0.33947	0.655000	0.94253	.	.	.		0.338	EIF2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000357259.2	NM_032025		A	150285799	G	A	150285799	2	1	254	1	0	0	0	0	0	0	0	1	4997	991	35	3		3	EIF2A	3	150285799	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	10034486	150285799	47736631	201	34493										
SGEF	26084	hgsc.bcm.edu	37	chr3	153840716	153840716	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agggtctctgcggagaggctTgcggtccacgtcttatcgca	14	11	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:153840716T>C	ENST00000356448.4	+	2	1219	c.935T>C	c.(934-936)tTg>tCg	p.L312S	ARHGEF26-AS1_ENST00000479270.1_RNA|ARHGEF26-AS1_ENST00000467912.1_RNA|ARHGEF26_ENST00000465093.1_Missense_Mutation_p.L312S|ARHGEF26_ENST00000465817.1_Missense_Mutation_p.L312S|ARHGEF26-AS1_ENST00000480639.1_RNA|ARHGEF26-AS1_ENST00000491862.1_RNA	NM_001251962.1	NP_001238891.1	Q96DR7	ARHGQ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 26	312					endothelial cell morphogenesis (GO:0001886)|ruffle assembly (GO:0097178)	cell projection (GO:0042995)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	23						CGGAGAGGCTTGCGGTCCACG	0.577																																					p.L312S	GBM(163;191 2003 24758 29593 48540)|Ovarian(152;631 1885 20165 22910 51013)	Atlas-SNP	.											.	ARHGEF26	158	.	0			c.T935C						.						44	61	55					3																	153840716		2035	4194	6229	SO:0001583	missense	26084	exon2			GAGGCTTGCGGTC	BC016628	CCDS46938.1, CCDS58858.1	3q25.2	2013-01-10			ENSG00000114790	ENSG00000114790		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	24490	protein-coding gene	gene with protein product	"Src homology 3 domain-containing guanine nucleotide exchange factor"					15133129, 12697679	Standard	NM_015595		Approved	DKFZP434D146, SGEF	uc021xgc.1	Q96DR7	OTTHUMG00000159098	ENST00000356448.4:c.935T>C	chr3.hg19:g.153840716T>C	ENSP00000348828:p.Leu312Ser	160.0	0.0		95.0	4.0	NM_001251962	B3KVP8|E9PBD0|Q68CL1|Q6AZ96|Q6Q8Q8|Q96AW8|Q96DR6|Q9H9D7|Q9H9R2|Q9UFW5	Missense_Mutation	SNP	ENST00000356448.4	hg19	CCDS46938.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.761436	0.89932	.	.	ENSG00000114790	ENST00000356448;ENST00000465093;ENST00000465817	T;T;T	0.63417	-0.04;-0.04;1.39	5.29	5.29	0.74685	.	0.000000	0.64402	D	0.000001	T	0.77471	0.4135	M	0.65498	2.005	0.58432	D	0.999992	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.80118	-0.1516	10	0.72032	D	0.01	-11.9824	15.2386	0.73450	0.0:0.0:0.0:1.0	.	312;312	E9PBD0;Q96DR7	.;ARHGQ_HUMAN	S	312	ENSP00000348828:L312S;ENSP00000423418:L312S;ENSP00000423295:L312S	ENSP00000348828:L312S	L	+	2	0	ARHGEF26	155323406	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	6.967000	0.76079	2.005000	0.58758	0.454000	0.30748	TTG	.	.		0.577	ARHGEF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353287.3	NM_015595		C	153840716	T	C	153840716	3	2	254	1	0	0	0	0	1	0	0	0	14220	1821	63	2	937	2	SGEF	3	153840716	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	3554917	153840716	44181714	202	34494										
GPR149	344758	hgsc.bcm.edu	37	chr3	154145382	154145382	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cacagggcaagtgggtccagCgtttggacaagacaaacact	12	10	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:154145382C>T	ENST00000389740.2	-	2	1196	c.1097G>A	c.(1096-1098)cGc>cAc	p.R366H		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	366					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			GTGGGTCCAGCGTTTGGACAA	0.527																																					p.R366H		Atlas-SNP	.											GPR149,NS,carcinoma,0,1	GPR149	134	.	0			c.G1097A						.						71	75	74					3																	154145382		2024	4194	6218	SO:0001583	missense	344758	exon2			GTCCAGCGTTTGG	AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"GPCR / Class A : Orphans"	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.1097G>A	chr3.hg19:g.154145382C>T	ENSP00000374390:p.Arg366His	116.0	0.0		71.0	3.0	NM_001038705		Missense_Mutation	SNP	ENST00000389740.2	hg19	CCDS43162.1	.	.	.	.	.	.	.	.	.	.	C	13.87	2.366027	0.41902	.	.	ENSG00000174948	ENST00000389740	.	.	.	6.03	2.79	0.32731	.	0.203131	0.53938	N	0.000058	T	0.38026	0.1025	L	0.27053	0.805	0.44956	D	0.99797	B	0.19445	0.036	B	0.10450	0.005	T	0.08932	-1.0698	9	0.18276	T	0.48	-12.0261	7.941	0.29959	0.0:0.5739:0.0:0.4261	.	366	Q86SP6	GP149_HUMAN	H	366	.	ENSP00000374390:R366H	R	-	2	0	GPR149	155628076	0.996000	0.38824	1.000000	0.80357	0.996000	0.88848	0.448000	0.21726	0.605000	0.29947	0.655000	0.94253	CGC	.	.		0.527	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580		T	154145382	C	T	154145382	3	4	254	1	0	0	0	0	1	0	0	0	6662	768	27	1	1110	1	GPR149	3	154145382	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	304666	154145382	43877048	203	34495										
KCNAB1	7881	hgsc.bcm.edu	37	chr3	155838515	155838515	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	acaaatctcccaagaaagccTcagaaaacgctaaagacagc	6	12	2	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:155838515T>C	ENST00000490337.1	+	1	179	c.115T>C	c.(115-117)Tca>Cca	p.S39P	KCNAB1_ENST00000389636.5_Missense_Mutation_p.S39P	NM_172160.2	NP_751892.1	Q14722	KCAB1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, beta member 1	39					learning or memory (GO:0007611)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	28			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			CAAGAAAGCCTCAGAAAACGC	0.542																																					p.S39P		Atlas-SNP	.											.	KCNAB1	176	.	0			c.T115C						.						76	80	79					3																	155838515		2203	4300	6503	SO:0001583	missense	7881	exon1			AAAGCCTCAGAAA	U33428	CCDS3174.1, CCDS3175.1, CCDS33882.1	3q26.1	2006-11-29			ENSG00000169282	ENSG00000169282		"Potassium channels", "Aldo-keto reductases"	6228	protein-coding gene	gene with protein product		601141				8838324, 7499366	Standard	NM_172160		Approved	AKR6A3, KCNA1B, hKvBeta3, Kvb1.3, hKvb3	uc003far.2	Q14722	OTTHUMG00000158552	ENST00000490337.1:c.115T>C	chr3.hg19:g.155838515T>C	ENSP00000419952:p.Ser39Pro	197.0	0.0		137.0	6.0	NM_172160	A8K9H8|A8KAD4|B3KPZ4|Q13031|Q13302|Q16547|Q6PI60|Q99869	Missense_Mutation	SNP	ENST00000490337.1	hg19	CCDS3174.1	.	.	.	.	.	.	.	.	.	.	T	12.88	2.070024	0.36566	.	.	ENSG00000169282	ENST00000490337;ENST00000389636	T;T	0.11821	3.16;2.74	5.47	-3.34	0.04943	.	.	.	.	.	T	0.04815	0.0130	N	0.08118	0	0.41283	D	0.986929	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33266	-0.9875	9	0.35671	T	0.21	-7.1239	2.5176	0.04672	0.1268:0.3006:0.3317:0.241	.	39;39	B7Z8E5;Q14722	.;KCAB1_HUMAN	P	39	ENSP00000419952:S39P;ENSP00000374287:S39P	ENSP00000374287:S39P	S	+	1	0	KCNAB1	157321209	0.000000	0.05858	0.656000	0.29637	0.979000	0.70002	-1.078000	0.03413	-0.474000	0.06862	0.455000	0.32223	TCA	.	.		0.542	KCNAB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351411.1	NM_003471		C	155838515	T	C	155838515	3	2	254	1	0	0	0	0	1	0	0	0	8018	1551	54	2	117	2	KCNAB1	3	155838515	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	1693133	155838515	42183915	204	34496										
TRIM59	286827	hgsc.bcm.edu	37	chr3	160155954	160155954	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gagtatcgacatcagtattaCtgaaattaatgtaactacaa	6	6	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:160155954C>G	ENST00000309784.4	-	3	1203	c.1018G>C	c.(1018-1020)Gta>Cta	p.V340L	RP11-432B6.3_ENST00000483754.1_Intron|TRIM59_ENST00000543469.1_Intron	NM_173084.2	NP_775107.1	Q8IWR1	TRI59_HUMAN	tripartite motif containing 59	340					innate immune response (GO:0045087)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of viral entry into host cell (GO:0046597)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|urinary_tract(3)	15			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			ATCAGTATTACTGAAATTAAT	0.308																																					p.V340L		Atlas-SNP	.											.	TRIM59	42	.	0			c.G1018C						.						59	62	61					3																	160155954		2201	4297	6498	SO:0001583	missense	286827	exon3			GTATTACTGAAAT	AY159379	CCDS3190.1	3q26	2013-01-09	2011-01-25		ENSG00000213186	ENSG00000213186		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	30834	protein-coding gene	gene with protein product			"tripartite motif-containing 57", "tripartite motif-containing 59"	TRIM57		12095697	Standard	NM_173084		Approved	TSBF1, Mrf1, RNF104	uc003fdm.3	Q8IWR1	OTTHUMG00000159034	ENST00000309784.4:c.1018G>C	chr3.hg19:g.160155954C>G	ENSP00000311219:p.Val340Leu	299.0	0.0		271.0	85.0	NM_173084	A8K5G9|D3DNL9	Missense_Mutation	SNP	ENST00000309784.4	hg19	CCDS3190.1	.	.	.	.	.	.	.	.	.	.	C	6.199	0.404851	0.11754	.	.	ENSG00000213186	ENST00000309784	T	0.22539	1.95	5.77	1.75	0.24633	.	0.507764	0.20377	N	0.093523	T	0.12732	0.0309	L	0.40543	1.245	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.22730	-1.0208	9	.	.	.	-1.2124	2.1154	0.03713	0.2416:0.3814:0.2378:0.1392	.	340	Q8IWR1	TRI59_HUMAN	L	340	ENSP00000311219:V340L	.	V	-	1	0	TRIM59	161638648	0.000000	0.05858	0.724000	0.30704	0.843000	0.47879	0.012000	0.13287	0.334000	0.23590	0.561000	0.74099	GTA	.	.		0.308	TRIM59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352963.1	NM_173084		G	160155954	C	G	160155954	3	3	254	1	0	0	0	0	1	0	0	0	16547	565	20	4	197	4	TRIM59	3	160155954	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	4317439	160155954	37866476	205	34497										
SPATA16	83893	hgsc.bcm.edu	37	chr3	172835323	172835323	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttgtttttctttgatgccctTtgtcatttttgttctttcaa	5	7	4	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:172835323T>C	ENST00000351008.3	-	2	382	c.199A>G	c.(199-201)Aag>Gag	p.K67E		NM_031955.5	NP_114161.3	Q9BXB7	SPT16_HUMAN	spermatogenesis associated 16	67					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)				breast(2)|cervix(1)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	43	Ovarian(172;0.00319)|Breast(254;0.197)		LUSC - Lung squamous cell carcinoma(14;1.48e-14)|Lung(28;6.63e-14)			TTGATGCCCTTTGTCATTTTT	0.388																																					p.K67E		Atlas-SNP	.											.	SPATA16	111	.	0			c.A199G						.						340	323	329					3																	172835323		2203	4300	6503	SO:0001583	missense	83893	exon2			TGCCCTTTGTCAT	AF345909	CCDS3221.1	3q26.31	2009-01-05			ENSG00000144962	ENSG00000144962			29935	protein-coding gene	gene with protein product		609856				12529416, 17847006	Standard	NM_031955		Approved	NYD-SP12	uc003fin.4	Q9BXB7	OTTHUMG00000156865	ENST00000351008.3:c.199A>G	chr3.hg19:g.172835323T>C	ENSP00000341765:p.Lys67Glu	696.0	0.0		1219.0	190.0	NM_031955	Q0R0N4|Q0R0S0|Q0R0W2|Q0R129|Q0R131|Q0R140|Q0R1B8|Q0R1G5|Q0R1I2|Q0R1J6|Q0R1S4|Q0R202|Q0R280|Q0R2F8|Q0R2N6|Q0R2N7|Q0R2R0|Q0R2R1|Q0R2S3|Q0R2S4|Q0R2S5|Q0R2T4|Q0R2T7|Q0R2U2|Q0R2U8|Q0R2U9|Q0R2V5|Q0R2V7|Q8NE67	Missense_Mutation	SNP	ENST00000351008.3	hg19	CCDS3221.1	.	.	.	.	.	.	.	.	.	.	T	15.03	2.710873	0.48517	.	.	ENSG00000144962	ENST00000351008	T	0.16196	2.36	5.27	5.27	0.74061	.	0.107922	0.41396	D	0.000884	T	0.09862	0.0242	N	0.17082	0.46	0.32811	D	0.501493	B	0.31318	0.319	B	0.26416	0.069	T	0.13388	-1.0511	10	0.38643	T	0.18	-15.4234	9.0924	0.36619	0.0:0.0845:0.0:0.9155	.	67	Q9BXB7	SPT16_HUMAN	E	67	ENSP00000341765:K67E	ENSP00000341765:K67E	K	-	1	0	SPATA16	174318017	0.897000	0.30589	1.000000	0.80357	0.976000	0.68499	1.652000	0.37313	1.985000	0.57927	0.528000	0.53228	AAG	.	.		0.388	SPATA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346322.1	NM_031955		C	172835323	T	C	172835323	3	2	254	1	0	0	0	0	1	0	0	0	15016	1850	64	2	1550	2	SPATA16	3	172835323	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	12679369	172835323	25187107	206	34498										
YEATS2	55689	hgsc.bcm.edu	37	chr3	183521785	183521785	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tttttttaagtggcaaagagCaatgacaatgcgaaaagtct	9	5	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:183521785C>A	ENST00000305135.5	+	27	3788	c.3593C>A	c.(3592-3594)gCa>gAa	p.A1198E	YEATS2-AS1_ENST00000425008.3_RNA|AC131160.1_ENST00000401347.1_RNA	NM_018023.4	NP_060493.3	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	1198					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|mitotic spindle (GO:0072686)	TBP-class protein binding (GO:0017025)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(24)|ovary(3)|prostate(2)|skin(3)	49	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			TGGCAAAGAGCAATGACAATG	0.408																																					p.A1198E		Atlas-SNP	.											.	YEATS2	111	.	0			c.C3593A						.						58	57	57					3																	183521785		1889	4122	6011	SO:0001583	missense	55689	exon27			AAAGAGCAATGAC	AB033023	CCDS43175.1	3q27.3	2004-08-18			ENSG00000163872	ENSG00000163872			25489	protein-coding gene	gene with protein product		613373				10574462	Standard	NM_018023		Approved	FLJ10201, FLJ12841, FLJ13308, KIAA1197	uc003fly.2	Q9ULM3	OTTHUMG00000156898	ENST00000305135.5:c.3593C>A	chr3.hg19:g.183521785C>A	ENSP00000306983:p.Ala1198Glu	129.0	0.0		111.0	5.0	NM_018023	A7E2B9|D3DNS9|Q641P6|Q9NW96	Missense_Mutation	SNP	ENST00000305135.5	hg19	CCDS43175.1	.	.	.	.	.	.	.	.	.	.	C	31	5.101983	0.94245	.	.	ENSG00000163872	ENST00000421660;ENST00000305135	D	0.86627	-2.15	5.25	5.25	0.73442	.	0.000000	0.64402	D	0.000001	D	0.93667	0.7977	M	0.77820	2.39	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.94294	0.7531	10	0.87932	D	0	-20.758	18.8616	0.92275	0.0:1.0:0.0:0.0	.	1198	Q9ULM3	YETS2_HUMAN	E	1198	ENSP00000306983:A1198E	ENSP00000306983:A1198E	A	+	2	0	YEATS2	185004479	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.065000	0.76727	2.444000	0.82710	0.655000	0.94253	GCA	.	.		0.408	YEATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346507.2	NM_018023		A	183521785	C	A	183521785	3	1	254	1	0	0	0	0	1	0	0	0	17487	710	25	3	3695	3	YEATS2	3	183521785	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	10686462	183521785	14500645	207	34499										
EIF4G1	1981	hgsc.bcm.edu	37	chr3	184049840	184049840	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctacaggcgctctacgccctCcaggcccttgtagtgacctt	9	16	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:184049840C>A	ENST00000346169.2	+	32	4855	c.4584C>A	c.(4582-4584)ctC>ctA	p.L1528L	EIF4G1_ENST00000382330.3_Silent_p.L1535L|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000352767.3_Silent_p.L1535L|EIF4G1_ENST00000441154.1_Silent_p.L1365L|EIF4G1_ENST00000392537.2_Silent_p.L1441L|EIF4G1_ENST00000427845.1_Silent_p.L1442L|EIF4G1_ENST00000342981.4_Silent_p.L1529L|EIF4G1_ENST00000434061.2_Silent_p.L1333L|EIF4G1_ENST00000319274.6_Silent_p.L1528L|EIF4G1_ENST00000350481.5_Silent_p.L1364L|EIF4G1_ENST00000414031.1_Silent_p.L1488L|EIF4G1_ENST00000411531.1_Silent_p.L1489L|EIF4G1_ENST00000424196.1_Silent_p.L1535L|EIF4G1_ENST00000435046.2_Silent_p.L1332L	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	1528	EIF4A-binding.|W2. {ECO:0000255|PROSITE- ProRule:PRU00695}.				cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|response to ethanol (GO:0045471)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	75	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TCTACGCCCTCCAGGCCCTTG	0.612																																					p.L1535L		Atlas-SNP	.											.	EIF4G1	151	.	0			c.C4605A						.						54	51	52					3																	184049840		2203	4300	6503	SO:0001819	synonymous_variant	1981	exon33			CGCCCTCCAGGCC	D12686	CCDS3259.1, CCDS3260.1, CCDS3261.1, CCDS46970.1, CCDS46970.2, CCDS54687.1, CCDS54688.1	3q27.1	2013-09-19			ENSG00000114867	ENSG00000114867		"Parkinson disease"	3296	protein-coding gene	gene with protein product		600495		EIF4G, EIF4F		1429670, 9372926, 21907011	Standard	NM_182917		Approved	p220, PARK18	uc010hxy.3	Q04637	OTTHUMG00000156784	ENST00000346169.2:c.4584C>A	chr3.hg19:g.184049840C>A		86.0	0.0		78.0	4.0	NM_001194946	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Silent	SNP	ENST00000346169.2	hg19	CCDS3259.1																																																																																			.	.		0.612	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917		A	184049840	C	A	184049840	2	1	254	1	0	0	0	0	0	0	0	1	5038	842	30	3		3	EIF4G1	3	184049840	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	528055	184049840	13972590	208	34500										
SENP2	59343	hgsc.bcm.edu	37	chr3	185316214	185316214	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttctagattgctttattcacCaagtgaaaaacagtctctac	5	9	3	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:185316214C>A	ENST00000296257.5	+	3	412	c.172C>A	c.(172-174)Caa>Aaa	p.Q58K	SENP2_ENST00000465201.1_3'UTR|SENP2_ENST00000545472.1_Missense_Mutation_p.Q48K|SENP2_ENST00000427465.2_5'UTR	NM_021627.2	NP_067640.2	Q9HC62	SENP2_HUMAN	SUMO1/sentrin/SMT3 specific peptidase 2	58					cellular protein metabolic process (GO:0044267)|dorsal/ventral axis specification (GO:0009950)|heart development (GO:0007507)|labyrinthine layer development (GO:0060711)|mRNA transport (GO:0051028)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of protein binding (GO:0032091)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-translational protein modification (GO:0043687)|protein desumoylation (GO:0016926)|protein sumoylation (GO:0016925)|protein transport (GO:0015031)|regulation of DNA endoreduplication (GO:0032875)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of Wnt signaling pathway (GO:0030111)|spongiotrophoblast layer development (GO:0060712)|trophoblast giant cell differentiation (GO:0060707)|Wnt signaling pathway (GO:0016055)	cytoplasmic vesicle (GO:0031410)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	SUMO-specific protease activity (GO:0016929)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|skin(3)	12	all_cancers(143;1.28e-10)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;1.31e-21)			CTTTATTCACCAAGTGAAAAA	0.368																																					p.Q58K		Atlas-SNP	.											.	SENP2	88	.	0			c.C172A						.						64	63	63					3																	185316214		2203	4300	6503	SO:0001583	missense	59343	exon3			ATTCACCAAGTGA	AF151697	CCDS33902.1	3q28	2005-08-17	2005-08-17		ENSG00000163904	ENSG00000163904			23116	protein-coding gene	gene with protein product		608261	"SUMO1/sentrin/SMT3 specific protease 2"			11896061, 11489887	Standard	XM_005247690		Approved	SMT3IP2, KIAA1331, DKFZp762A2316, AXAM2	uc003fpn.3	Q9HC62	OTTHUMG00000156658	ENST00000296257.5:c.172C>A	chr3.hg19:g.185316214C>A	ENSP00000296257:p.Gln58Lys	186.0	0.0		175.0	7.0	NM_021627	B4DQ42|Q8IW97|Q96SR2|Q9P2L5	Missense_Mutation	SNP	ENST00000296257.5	hg19	CCDS33902.1	.	.	.	.	.	.	.	.	.	.	C	19.91	3.914001	0.72983	.	.	ENSG00000163904	ENST00000430355;ENST00000545472;ENST00000296257;ENST00000437107	T;T	0.22945	1.93;1.94	4.98	4.98	0.66077	.	0.177411	0.27636	N	0.018485	T	0.15696	0.0378	N	0.14661	0.345	0.80722	D	1	B;B	0.23316	0.083;0.034	B;B	0.22601	0.04;0.025	T	0.08764	-1.0706	10	0.21014	T	0.42	-5.4854	13.9415	0.64057	0.0:1.0:0.0:0.0	.	48;58	B4DQ42;Q9HC62	.;SENP2_HUMAN	K	112;48;58;58	ENSP00000439653:Q48K;ENSP00000296257:Q58K	ENSP00000296257:Q58K	Q	+	1	0	SENP2	186798908	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.109000	0.41863	2.739000	0.93911	0.650000	0.86243	CAA	.	.		0.368	SENP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345159.1	NM_021627		A	185316214	C	A	185316214	3	1	254	1	0	0	0	0	1	0	0	0	14062	595	21	3	182	3	SENP2	3	185316214	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1266374	185316214	12706216	209	34501										
LPP	4026	hgsc.bcm.edu	37	chr3	188327323	188327323	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgtccacctccttcaacacgGggaggcatggattatgccta	10	12	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:188327323G>T	ENST00000312675.4	+	6	1050	c.804G>T	c.(802-804)cgG>cgT	p.R268R	LPP_ENST00000448637.1_Silent_p.R268R|LPP_ENST00000543006.1_Silent_p.R268R|LPP_ENST00000471917.1_3'UTR	NM_001167672.1|NM_005578.3	NP_001161144.1|NP_005569.1	Q93052	LPP_HUMAN	LIM domain containing preferred translocation partner in lipoma	268	Pro-rich.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)		HMGA2/LPP(161)	NS(1)|breast(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		CTTCAACACGGGGAGGCATGG	0.557			T	"HMGA2, MLL, C12orf9"	"lipoma, leukemia"																																p.R268R		Atlas-SNP	.		Dom	yes		3	3q28	4026	LIM domain containing preferred translocation partner in lipoma		"L, M"	.	LPP	72	.	0			c.G804T						.						77	68	71					3																	188327323		2203	4300	6503	SO:0001819	synonymous_variant	4026	exon6			AACACGGGGAGGC	AL833171	CCDS3291.1	3q27-q28	2004-03-02	2002-01-14		ENSG00000145012	ENSG00000145012			6679	protein-coding gene	gene with protein product		600700	"LIM domain-containing preferred translocation partner in lipoma"			8812423	Standard	XM_005247453		Approved		uc003frs.2	Q93052	OTTHUMG00000156387	ENST00000312675.4:c.804G>T	chr3.hg19:g.188327323G>T		119.0	0.0		89.0	4.0	NM_005578	A1L4L6|D3DNV6|Q8NFX5	Silent	SNP	ENST00000312675.4	hg19	CCDS3291.1																																																																																			.	.		0.557	LPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344030.1	NM_005578		T	188327323	G	T	188327323	2	4	254	1	0	0	0	0	0	0	0	1	8932	1219	43	3		3	LPP	3	188327323	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	3011109	188327323	9695107	210	34502										
LPP	4026	hgsc.bcm.edu	37	chr3	188592145	188592145	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctttactgttctaggattgcGgtggtctcctgtctgaagga	12	8	3	1	rs9830664	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:188592145G>T	ENST00000312675.4	+	11	1963	c.1717G>T	c.(1717-1719)Ggt>Tgt	p.G573C	LPP_ENST00000543006.1_Missense_Mutation_p.G573C	NM_001167672.1|NM_005578.3	NP_001161144.1|NP_005569.1	Q93052	LPP_HUMAN	LIM domain containing preferred translocation partner in lipoma	573	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)		HMGA2/LPP(161)	NS(1)|breast(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		CTAGGATTGCGGTGGTCTCCT	0.488			T	"HMGA2, MLL, C12orf9"	"lipoma, leukemia"																																p.G573C		Atlas-SNP	.		Dom	yes		3	3q28	4026	LIM domain containing preferred translocation partner in lipoma		"L, M"	.	LPP	72	.	0			c.G1717T						.						187	165	172					3																	188592145		2203	4300	6503	SO:0001583	missense	4026	exon11			GATTGCGGTGGTC	AL833171	CCDS3291.1	3q27-q28	2004-03-02	2002-01-14		ENSG00000145012	ENSG00000145012			6679	protein-coding gene	gene with protein product		600700	"LIM domain-containing preferred translocation partner in lipoma"			8812423	Standard	XM_005247453		Approved		uc003frs.2	Q93052	OTTHUMG00000156387	ENST00000312675.4:c.1717G>T	chr3.hg19:g.188592145G>T	ENSP00000318089:p.Gly573Cys	67.0	0.0		79.0	4.0	NM_005578	A1L4L6|D3DNV6|Q8NFX5	Missense_Mutation	SNP	ENST00000312675.4	hg19	CCDS3291.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.149572	0.78001	.	.	ENSG00000145012	ENST00000312675;ENST00000543006	D;D	0.88354	-2.37;-2.37	5.79	5.79	0.91817	Zinc finger, LIM-type (4);	0.045098	0.85682	D	0.000000	D	0.96185	0.8756	M	0.93283	3.4	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.987;0.999	D	0.96557	0.9412	10	0.66056	D	0.02	.	19.0299	0.92952	0.0:0.0:1.0:0.0	.	426;573	B7Z8W0;Q93052	.;LPP_HUMAN	C	573	ENSP00000318089:G573C;ENSP00000438891:G573C	ENSP00000318089:G573C	G	+	1	0	LPP	190074839	1.000000	0.71417	0.996000	0.52242	0.611000	0.37282	9.750000	0.98875	2.736000	0.93811	0.655000	0.94253	GGT	.	G|0.998;A|0.002		0.488	LPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344030.1	NM_005578		T	188592145	G	T	188592145	3	4	254	1	0	0	0	0	1	0	0	0	8932	1116	39	1	1751	1	LPP	3	188592145	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	264822	188592145	9430285	211	34503										
CPN2	1370	hgsc.bcm.edu	37	chr3	194062557	194062557	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tatgggtcagagacaggccaAccaggcacggggtgtgggca	17	9	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:194062557A>G	ENST00000323830.3	-	2	964	c.875T>C	c.(874-876)gTt>gCt	p.V292A	CPN2_ENST00000429275.1_Missense_Mutation_p.V292A	NM_001080513.2	NP_001073982	P22792	CPN2_HUMAN	carboxypeptidase N, polypeptide 2	292					protein stabilization (GO:0050821)|regulation of catalytic activity (GO:0050790)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	enzyme regulator activity (GO:0030234)			breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|ovary(5)|prostate(1)	27	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.65e-05)		AGACAGGCCAACCAGGCACGG	0.577																																					p.V292A		Atlas-SNP	.											.	CPN2	56	.	0			c.T875C						.						51	49	50					3																	194062557		2203	4300	6503	SO:0001583	missense	1370	exon2			AGGCCAACCAGGC	J05158	CCDS33920.1	3q29	2012-02-10	2007-02-23		ENSG00000178772	ENSG00000178772	3.4.17.3		2313	protein-coding gene	gene with protein product		603104	"carboxypeptidase N, polypeptide 2, 83kD"	ACBP		2378615, 9628828	Standard	XM_005269280		Approved		uc003fts.3	P22792	OTTHUMG00000156047	ENST00000323830.3:c.875T>C	chr3.hg19:g.194062557A>G	ENSP00000319464:p.Val292Ala	146.0	0.0		97.0	4.0	NM_001080513	B2RPE7|Q86SU4|Q8N5V4	Missense_Mutation	SNP	ENST00000323830.3	hg19	CCDS33920.1	.	.	.	.	.	.	.	.	.	.	A	0.524	-0.860978	0.02610	.	.	ENSG00000178772	ENST00000323830;ENST00000429275	T;T	0.24723	1.84;1.84	5.01	-0.324	0.12706	.	0.530450	0.14094	N	0.341800	T	0.13713	0.0332	L	0.37850	1.14	0.09310	N	1	B	0.09022	0.002	B	0.12156	0.007	T	0.33317	-0.9873	10	0.09084	T	0.74	.	3.8831	0.09086	0.5414:0.0:0.2233:0.2352	.	292	P22792	CPN2_HUMAN	A	292	ENSP00000319464:V292A;ENSP00000402232:V292A	ENSP00000319464:V292A	V	-	2	0	CPN2	195544252	0.000000	0.05858	0.021000	0.16686	0.111000	0.19643	-1.910000	0.01584	0.319000	0.23209	0.459000	0.35465	GTT	.	.		0.577	CPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342856.2	NM_001080513		G	194062557	A	G	194062557	3	3	254	1	0	0	0	0	1	0	0	0	3812	43	2	2	766	2	CPN2	3	194062557	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	5470412	194062557	3959873	212	34504										
OSTalpha	200931	hgsc.bcm.edu	37	chr3	195944788	195944788	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgcttctctcagcctcccacAgcagcccaactcctgagagg	8	17	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr3:195944788A>G	ENST00000296327.5	+	2	323	c.114A>G	c.(112-114)acA>acG	p.T38T		NM_152672.5	NP_689885.4	Q86UW1	OSTA_HUMAN	solute carrier family 51, alpha subunit	38					bile acid and bile salt transport (GO:0015721)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)									Conjugated Estrogens(DB00286)|Digoxin(DB00390)|Dinoprostone(DB00917)	AGCCTCCCACAGCAGCCCAAC	0.607																																					p.T38T		Atlas-SNP	.											.	.	.	.	0			c.A114G						.						51	46	48					3																	195944788		2203	4300	6503	SO:0001819	synonymous_variant	200931	exon2			TCCCACAGCAGCC		CCDS3314.1	3q29	2013-05-22			ENSG00000163959	ENSG00000163959		"Solute carriers"	29955	protein-coding gene	gene with protein product	"organic solute transporter, alpha subunit"	612084				12719432, 20538072	Standard	NM_152672		Approved	OSTalpha	uc003fwd.3	Q86UW1	OTTHUMG00000155684	ENST00000296327.5:c.114A>G	chr3.hg19:g.195944788A>G		85.0	0.0		43.0	5.0	NM_152672	Q6ZMC7	Silent	SNP	ENST00000296327.5	hg19	CCDS3314.1	.	.	.	.	.	.	.	.	.	.	A	4.040	0.005065	0.07866	.	.	ENSG00000163959	ENST00000428985	.	.	.	5.89	-11.8	0.00035	.	.	.	.	.	T	0.30510	0.0767	.	.	.	0.53005	D	0.999965	.	.	.	.	.	.	T	0.38824	-0.9643	4	.	.	.	.	1.3954	0.02260	0.4026:0.1863:0.2685:0.1426	.	.	.	.	R	9	.	.	Q	+	2	0	AC069257.9	197429185	0.000000	0.05858	0.326000	0.25389	0.519000	0.34347	-4.969000	0.00165	-2.420000	0.00564	-0.908000	0.02827	CAG	.	.		0.607	SLC51A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341253.1	NM_152672		G	195944788	A	G	195944788	2	3	254	1	0	0	0	0	0	0	0	1	11309	175	7	2		2	OSTalpha	3	195944788	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	1882231	195944788	2077642	213	34505										
MFSD7	84179	hgsc.bcm.edu	37	chr4	678289	678289	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cacactggagtggccgcttgCacagaggatctgctccagga	13	12	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:678289C>T	ENST00000404286.2	-	6	841	c.826G>A	c.(826-828)Gca>Aca	p.A276T	MFSD7_ENST00000347950.5_Missense_Mutation_p.A157T|MFSD7_ENST00000515118.1_Missense_Mutation_p.A179T|MFSD7_ENST00000322224.4_Missense_Mutation_p.A275T|MFSD7_ENST00000513740.1_5'Flank|MFSD7_ENST00000503156.1_Missense_Mutation_p.A211T	NM_032219.2	NP_115595.2	Q6UXD7	MFSD7_HUMAN	major facilitator superfamily domain containing 7	276					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				cervix(1)|kidney(2)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	11						TGGCCGCTTGCACAGAGGATC	0.637											OREG0016025	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A275T		Atlas-SNP	.											.	MFSD7	50	.	0			c.G823A						.						77	80	79					4																	678289		2203	4300	6503	SO:0001583	missense	84179	exon6			CGCTTGCACAGAG	AK025922	CCDS3338.1, CCDS75086.1	4p16.3	2013-05-22			ENSG00000169026	ENSG00000169026		"Solute carriers"	26177	protein-coding gene	gene with protein product						12975309	Standard	XM_005272295		Approved	FLJ22269, LP2561	uc003gax.3	Q6UXD7	OTTHUMG00000119001	ENST00000404286.2:c.826G>A	chr4.hg19:g.678289C>T	ENSP00000384616:p.Ala276Thr	125.0	0.0	590	79.0	4.0	NM_032219	A8K7J5|Q6XYD4|Q8N6H1|Q9H6H6	Missense_Mutation	SNP	ENST00000404286.2	hg19		.	.	.	.	.	.	.	.	.	.	C	10.70	1.423382	0.25639	.	.	ENSG00000169026	ENST00000347950;ENST00000322224;ENST00000404286;ENST00000515118;ENST00000503156;ENST00000507165	T;T;T;T;T;T	0.80480	0.33;0.33;0.33;0.33;0.33;-1.38	4.73	4.73	0.59995	Major facilitator superfamily domain, general substrate transporter (1);	0.520933	0.18640	N	0.135310	T	0.67998	0.2953	N	0.11927	0.2	0.26626	N	0.972569	B;P;P;B;P	0.45672	0.1;0.864;0.864;0.157;0.726	B;B;B;B;B	0.43867	0.063;0.434;0.434;0.105;0.146	T	0.61739	-0.7001	10	0.31617	T	0.26	-15.0889	13.1096	0.59267	0.0:1.0:0.0:0.0	.	211;179;157;276;275	D6RIZ6;D6R9R0;Q6UXD7-3;Q6UXD7;Q6UXD7-2	.;.;.;MFSD7_HUMAN;.	T	157;275;276;179;211;212	ENSP00000307545:A157T;ENSP00000320234:A275T;ENSP00000384616:A276T;ENSP00000423204:A179T;ENSP00000425753:A211T;ENSP00000424556:A212T	ENSP00000320234:A275T	A	-	1	0	MFSD7	668289	0.030000	0.19436	0.275000	0.24674	0.012000	0.07955	2.116000	0.41930	2.460000	0.83146	0.460000	0.39030	GCA	.	.		0.637	MFSD7-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000358585.1	NM_032219		T	678289	C	T	678289	3	4	254	1	0	0	0	0	1	0	0	0	9546	710	25	3	876	3	MFSD7	4	678289	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10		678289	190475987	214	34506										
GAK	2580	hgsc.bcm.edu	37	chr4	843758	843758	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gccaccaggtcggccatgccCacgggcgtccagcggctctc	13	18	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:843758C>T	ENST00000314167.4	-	27	3866	c.3756G>A	c.(3754-3756)gtG>gtA	p.V1252V	GAK_ENST00000511163.1_Silent_p.V1173V|GAK_ENST00000509566.1_5'UTR	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	1252	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				cell cycle (GO:0007049)|cell development (GO:0048468)|clathrin coat disassembly (GO:0072318)|clathrin-mediated endocytosis (GO:0072583)|endoplasmic reticulum organization (GO:0007029)|epidermal cell differentiation (GO:0009913)|establishment of skin barrier (GO:0061436)|forebrain morphogenesis (GO:0048853)|Golgi organization (GO:0007030)|intrahepatic bile duct development (GO:0035622)|positive regulation of neural precursor cell proliferation (GO:2000179)	cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(16)|skin(7)|urinary_tract(2)	39				Colorectal(103;0.219)		CGGCCATGCCCACGGGCGTCC	0.677																																					p.V1252V		Atlas-SNP	.											.	GAK	104	.	0			c.G3756A						.						24	24	24					4																	843758		2202	4298	6500	SO:0001819	synonymous_variant	2580	exon27			CATGCCCACGGGC	D88435	CCDS3340.1	4p16	2011-09-07			ENSG00000178950	ENSG00000178950		"Heat shock proteins / DNAJ (HSP40)"	4113	protein-coding gene	gene with protein product	"auxilin-2"	602052				9299234	Standard	NM_005255		Approved	DNAJC26	uc003gbm.4	O14976	OTTHUMG00000088301	ENST00000314167.4:c.3756G>A	chr4.hg19:g.843758C>T		94.0	0.0		84.0	4.0	NM_005255	Q5U4P5|Q9BVY6	Silent	SNP	ENST00000314167.4	hg19	CCDS3340.1	.	.	.	.	.	.	.	.	.	.	C	1.760	-0.486963	0.04352	.	.	ENSG00000178950	ENST00000511980	.	.	.	4.77	3.78	0.43462	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-26.3922	6.7194	0.23323	0.2491:0.5863:0.1646:0.0	.	.	.	.	X	408	.	.	W	-	2	0	GAK	833758	0.998000	0.40836	0.994000	0.49952	0.016000	0.09150	0.661000	0.25023	2.338000	0.79540	0.637000	0.83480	TGG	.	.		0.677	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239188.1	NM_005255		T	843758	C	T	843758	2	4	254	1	0	0	0	0	0	0	0	1	6203	581	21	3		3	GAK	4	843758	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	165469	843758	190310518	215	34507										
SLC26A1	10861	hgsc.bcm.edu	37	chr4	984946	984946	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccggtcatcagcgtgagggcGgtggcgacacggatggcgta	18	10	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:984946G>T	ENST00000361661.2	-	3	923	c.546C>A	c.(544-546)acC>acA	p.T182T	IDUA_ENST00000453894.1_Intron|SLC26A1_ENST00000398520.2_Silent_p.T182T|SLC26A1_ENST00000513138.1_5'UTR|IDUA_ENST00000247933.4_Intron|SLC26A1_ENST00000398516.2_Silent_p.T182T	NM_213613.2	NP_998778.1	Q9H2B4	S26A1_HUMAN	solute carrier family 26 (anion exchanger), member 1	182					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|chloride transport (GO:0006821)|glycosaminoglycan metabolic process (GO:0030203)|ion transport (GO:0006811)|oxalate transport (GO:0019532)|small molecule metabolic process (GO:0044281)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|chloride transmembrane transporter activity (GO:0015108)|oxalate transmembrane transporter activity (GO:0019531)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			central_nervous_system(1)|endometrium(4)|pancreas(1)|prostate(1)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GCGTGAGGGCGGTGGCGACAC	0.687																																					p.T182T		Atlas-SNP	.											.	SLC26A1	44	.	0			c.C546A						.						31	33	32					4																	984946		2201	4293	6494	SO:0001819	synonymous_variant	10861	exon2			GAGGGCGGTGGCG	AF297659	CCDS33933.1, CCDS33934.1	4p16.3	2013-07-18	2013-07-18		ENSG00000145217	ENSG00000145217		"Solute carriers"	10993	protein-coding gene	gene with protein product		610130	"solute carrier family 26 (sulfate transporter), member 1"				Standard	NM_213613		Approved	SAT-1, EDM4	uc003gcc.3	Q9H2B4	OTTHUMG00000160003	ENST00000361661.2:c.546C>A	chr4.hg19:g.984946G>T		156.0	0.0		121.0	5.0	NM_022042	A8K9N2|Q7Z5R3|Q96BK0	Silent	SNP	ENST00000361661.2	hg19	CCDS33934.1																																																																																			.	.		0.687	SLC26A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358783.1	NM_022042, NM_134425		T	984946	G	T	984946	2	4	254	1	0	0	0	0	0	0	0	1	14529	1103	39	1		1	SLC26A1	4	984946	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	141188	984946	190169330	216	34508										
HTT	3064	hgsc.bcm.edu	37	chr4	3131704	3131704	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctgcagattggacagccccaGgatgaagatgaggaagccac	13	10	0	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:3131704G>T	ENST00000355072.5	+	13	1942	c.1797G>T	c.(1795-1797)caG>caT	p.Q599H		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	599					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		GACAGCCCCAGGATGAAGATG	0.507																																					p.Q599H		Atlas-SNP	.											HTT,NS,carcinoma,0,1	HTT	221	.	0			c.G1797T						.						89	88	88					4																	3131704		1897	4136	6033	SO:0001583	missense	3064	exon13			GCCCCAGGATGAA	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.1797G>T	chr4.hg19:g.3131704G>T	ENSP00000347184:p.Gln599His	100.0	0.0		99.0	6.0	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	hg19	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	G	13.29	2.194400	0.38806	.	.	ENSG00000197386	ENST00000355072	T	0.06371	3.31	4.5	3.64	0.41730	Armadillo-type fold (1);	0.244527	0.42964	D	0.000623	T	0.06325	0.0163	L	0.38175	1.15	0.52099	D	0.999946	P	0.39326	0.668	B	0.41088	0.347	T	0.31280	-0.9949	10	0.66056	D	0.02	.	5.4243	0.16417	0.1627:0.0:0.672:0.1652	.	599	P42858	HD_HUMAN	H	599	ENSP00000347184:Q599H	ENSP00000347184:Q599H	Q	+	3	2	HTT	3101502	1.000000	0.71417	0.702000	0.30337	0.041000	0.13682	1.226000	0.32563	1.003000	0.39130	-0.314000	0.08810	CAG	.	.		0.507	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		T	3131704	G	T	3131704	3	4	254	1	0	0	0	0	1	0	0	0	7466	991	35	3	1847	3	HTT	4	3131704	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	2146758	3131704	188022572	217	34509										
HTT	3064	hgsc.bcm.edu	37	chr4	3225849	3225849	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctgtcccttctctgtctccgGctactacaggtacctgaggg	10	14	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:3225849G>T	ENST00000355072.5	+	56	7901	c.7756G>T	c.(7756-7758)Gct>Tct	p.A2586S		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	2586					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		TCTGTCTCCGGCTACTACAGG	0.507																																					p.A2586S		Atlas-SNP	.											.	HTT	221	.	0			c.G7756T						.						130	144	139					4																	3225849		2141	4261	6402	SO:0001583	missense	3064	exon56			TCTCCGGCTACTA	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.7756G>T	chr4.hg19:g.3225849G>T	ENSP00000347184:p.Ala2586Ser	98.0	0.0		98.0	35.0	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	hg19	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	G	6.407	0.443274	0.12164	.	.	ENSG00000197386	ENST00000355072	T	0.05447	3.44	5.53	4.64	0.57946	.	0.202412	0.43747	D	0.000527	T	0.05227	0.0139	L	0.29908	0.895	0.31287	N	0.689856	B	0.19331	0.035	B	0.14023	0.01	T	0.07616	-1.0763	10	0.28530	T	0.3	.	9.8937	0.41304	0.0:0.1293:0.6232:0.2475	.	2586	P42858	HD_HUMAN	S	2586	ENSP00000347184:A2586S	ENSP00000347184:A2586S	A	+	1	0	HTT	3195647	1.000000	0.71417	0.429000	0.26710	0.156000	0.22039	3.703000	0.54808	2.611000	0.88343	0.650000	0.86243	GCT	.	.		0.507	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		T	3225849	G	T	3225849	3	4	254	1	0	0	0	0	1	0	0	0	7466	1203	42	3	7978	3	HTT	4	3225849	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	94145	3225849	187928427	218	34510										
HTT	3064	hgsc.bcm.edu	37	chr4	3241606	3241606	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	atcagcaggatgggcaagctGgagcaggtggacgtgaacct	16	8	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:3241606G>T	ENST00000355072.5	+	67	9394	c.9249G>T	c.(9247-9249)ctG>ctT	p.L3083L		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	3083					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		TGGGCAAGCTGGAGCAGGTGG	0.582																																					p.L3083L		Atlas-SNP	.											.	HTT	221	.	0			c.G9249T						.						29	31	30					4																	3241606		2151	4240	6391	SO:0001819	synonymous_variant	3064	exon67			CAAGCTGGAGCAG	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.9249G>T	chr4.hg19:g.3241606G>T		91.0	0.0		92.0	4.0	NM_002111	Q9UQB7	Silent	SNP	ENST00000355072.5	hg19	CCDS43206.1																																																																																			.	.		0.582	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		T	3241606	G	T	3241606	2	4	254	1	0	0	0	0	0	0	0	1	7466	1335	47	3		3	HTT	4	3241606	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	15757	3241606	187912670	219	34511										
RGS12	6002	hgsc.bcm.edu	37	chr4	3424105	3424105	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgtctcgctgctccccagtcGgaggcctgcaggactttggc	13	14	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:3424105G>T	ENST00000344733.5	+	11	3745	c.2841G>T	c.(2839-2841)tcG>tcT	p.S947S	RGS12_ENST00000508158.1_3'UTR|RGS12_ENST00000336727.3_Silent_p.S947S|RGS12_ENST00000306648.7_Silent_p.S345S|RGS12_ENST00000382788.3_Silent_p.S947S|RGS12_ENST00000338806.4_Silent_p.S299S|RGS12_ENST00000538395.1_Silent_p.S289S	NM_198229.2	NP_937872.1	O14924	RGS12_HUMAN	regulator of G-protein signaling 12	947					positive regulation of GTPase activity (GO:0043547)|regulation of catalytic activity (GO:0050790)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|GTPase regulator activity (GO:0030695)|receptor signaling protein activity (GO:0005057)			autonomic_ganglia(1)|breast(4)|endometrium(3)|kidney(2)|large_intestine(9)|lung(16)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		CTCCCCAGTCGGAGGCCTGCA	0.667																																					p.S947S		Atlas-SNP	.											.	RGS12	128	.	0			c.G2841T						.						43	38	40					4																	3424105		2198	4297	6495	SO:0001819	synonymous_variant	6002	exon11			CCAGTCGGAGGCC	AF035152	CCDS3366.1, CCDS3367.1, CCDS3368.1	4p16.3	2008-02-05	2007-08-14		ENSG00000159788	ENSG00000159788		"Regulators of G-protein signaling"	9994	protein-coding gene	gene with protein product		602512	"regulator of G-protein signalling 12"			9651375	Standard	NM_198229		Approved		uc003ggw.3	O14924	OTTHUMG00000090277	ENST00000344733.5:c.2841G>T	chr4.hg19:g.3424105G>T		141.0	0.0		122.0	5.0	NM_002926	B1AQ30|B1AQ31|B1AQ32|B7Z764|E7EMN9|O14922|O14923|O43510|O75338|Q147X0|Q8WX95	Silent	SNP	ENST00000344733.5	hg19	CCDS3366.1																																																																																			.	.		0.667	RGS12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206602.1	NM_002926		T	3424105	G	T	3424105	2	4	254	1	0	0	0	0	0	0	0	1	13310	1103	39	1		1	RGS12	4	3424105	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	182499	3424105	187730171	220	34512										
HGFAC	3083	hgsc.bcm.edu	37	chr4	3443800	3443800	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cccttcctcctcctcctcctGctgctgctgctgctgccacg	7	21	0	0	rs372137428		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:3443800G>C	ENST00000382774.3	+	1	187	c.72G>C	c.(70-72)ctG>ctC	p.L24L	HGFAC_ENST00000511533.1_Silent_p.L24L	NM_001528.2	NP_001519.1	Q04756	HGFA_HUMAN	HGF activator	24					proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|rough endoplasmic reticulum (GO:0005791)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		TCCTCCTCCTGCTGCTGCTGC	0.716													G|||	1	0.000199681	8e-04	0	5008	,	,		13355	0		0	False		,,,				2504	0				p.L24L		Atlas-SNP	.											.	HGFAC	69	.	0			c.G72C						.	G		5,3433		0,5,1714	13	16	15		72	0.1	1	4		15	0,7164		0,0,3582	no	coding-synonymous	HGFAC	NM_001528.2		0,5,5296	CC,CG,GG		0.0,0.1454,0.0472		24/656	3443800	5,10597	1719	3582	5301	SO:0001819	synonymous_variant	3083	exon1			CCTCCTGCTGCTG	D14012	CCDS3369.1, CCDS75098.1	4p16	2008-02-07			ENSG00000109758	ENSG00000109758	3.4.21.-		4894	protein-coding gene	gene with protein product		604552				7683665, 8226803	Standard	XM_005247966		Approved	HGFAP, HGFA	uc003ghc.3	Q04756	OTTHUMG00000090281	ENST00000382774.3:c.72G>C	chr4.hg19:g.3443800G>C		27.0	0.0		22.0	4.0	NM_001528	Q14726|Q2M1W7|Q53X47	Silent	SNP	ENST00000382774.3	hg19	CCDS3369.1																																																																																			.	.		0.716	HGFAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206607.3			C	3443800	G	C	3443800	2	2	254	1	0	0	0	0	0	0	0	1	7095	1306	46	4		4	HGFAC	4	3443800	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	19695	3443800	187710476	221	34513										
STK32B	55351	hgsc.bcm.edu	37	chr4	5399971	5399971	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	atatcctgctggatgaacacGgtaagcctgctactaatcct	8	11	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:5399971G>T	ENST00000282908.5	+	5	894	c.472G>T	c.(472-474)Gga>Tga	p.G158*	STK32B_ENST00000510398.1_Splice_Site_p.G111*|STK32B_ENST00000512636.1_Splice_Site_p.A111S	NM_018401.1	NP_060871.1			serine/threonine kinase 32B											breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	39						GGATGAACACGGTAAGCCTGC	0.488																																					p.G158X		Atlas-SNP	.											STK32B,NS,carcinoma,0,1	STK32B	87	.	0			c.G472T						.						134	126	129					4																	5399971		2203	4300	6503	SO:0001630	splice_region_variant	55351	exon5			GAACACGGTAAGC	AJ250839	CCDS3380.1	4p16	2009-09-30			ENSG00000152953	ENSG00000152953			14217	protein-coding gene	gene with protein product						10700184	Standard	XM_005247982		Approved	STKG6, YANK2, STK32, HSA250839	uc003gih.1	Q9NY57	OTTHUMG00000090423	ENST00000282908.5:c.472+1G>T	chr4.hg19:g.5399971G>T		146.0	0.0		96.0	4.0	NM_018401		Nonsense_Mutation	SNP	ENST00000282908.5	hg19	CCDS3380.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	36|36	5.808128|5.808128	0.96967|0.96967	.|.	.|.	ENSG00000152953|ENSG00000152953	ENST00000512636|ENST00000282908;ENST00000510398	T|.	0.46063|.	0.88|.	4.4|4.4	4.4|4.4	0.53042|0.53042	.|.	.|0.000000	.|0.39475	.|U	.|0.001358	T|.	0.67429|.	0.2892|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.77822|.	-0.2445|.	5|.	0.87932|0.87932	D|D	0|0	.|.	12.6557|12.6557	0.56786|0.56786	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	S|X	111|158;111	ENSP00000423209:A111S|.	ENSP00000423209:A111S|ENSP00000282908:G158X	A|G	+|+	1|1	0|0	STK32B|STK32B	5450872|5450872	0.997000|0.997000	0.39634|0.39634	0.988000|0.988000	0.46212|0.46212	0.563000|0.563000	0.35712|0.35712	3.880000|3.880000	0.56145|0.56145	2.440000|2.440000	0.82611|0.82611	0.655000|0.655000	0.94253|0.94253	GCT|GGA	.	.		0.488	STK32B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206854.4	NM_018401	Nonsense_Mutation	T	5399971	G	T	5399971	5	4	254	1	0	0	0	0	0	0	1	0	15313	1130	39	1	490	1	STK32B	4	5399971	Splice_Site	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1956171	5399971	185754305	222	34514										
SORCS2	57537	hgsc.bcm.edu	37	chr4	7735080	7735080	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	catccagcaggtgctgaacgCacagaagatcagcttcctcc	9	14	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:7735080C>T	ENST00000507866.2	+	24	3249	c.3140C>T	c.(3139-3141)gCa>gTa	p.A1047V	SORCS2_ENST00000329016.9_Missense_Mutation_p.A875V	NM_020777.2	NP_065828.2	Q96PQ0	SORC2_HUMAN	sortilin-related VPS10 domain containing receptor 2	1047					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(8)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	42						GTGCTGAACGCACAGAAGATC	0.652																																					p.A1047V		Atlas-SNP	.											.	SORCS2	98	.	0			c.C3140T						.						14	18	17					4																	7735080		2019	4143	6162	SO:0001583	missense	57537	exon24			TGAACGCACAGAA	AB037750	CCDS47008.1	4p16.1	2008-02-05			ENSG00000184985	ENSG00000184985			16698	protein-coding gene	gene with protein product		606284				11499680	Standard	NM_020777		Approved	KIAA1329	uc003gkb.4	Q96PQ0	OTTHUMG00000159981	ENST00000507866.2:c.3140C>T	chr4.hg19:g.7735080C>T	ENSP00000422185:p.Ala1047Val	117.0	0.0		107.0	5.0	NM_020777	Q9P2L7	Missense_Mutation	SNP	ENST00000507866.2	hg19	CCDS47008.1	.	.	.	.	.	.	.	.	.	.	C	5.234	0.228737	0.09916	.	.	ENSG00000184985	ENST00000507866;ENST00000329016	T;T	0.14893	2.47;2.48	3.97	2.19	0.27852	.	0.625527	0.14631	N	0.307817	T	0.13756	0.0333	L	0.46157	1.445	0.09310	N	1	B;B	0.33583	0.418;0.363	B;B	0.32533	0.147;0.118	T	0.21042	-1.0257	10	0.66056	D	0.02	.	4.6175	0.12433	0.215:0.6683:0.0:0.1167	.	875;1047	B5MED8;Q96PQ0	.;SORC2_HUMAN	V	1047;875	ENSP00000422185:A1047V;ENSP00000329124:A875V	ENSP00000329124:A875V	A	+	2	0	SORCS2	7785980	0.004000	0.15560	0.008000	0.14137	0.006000	0.05464	0.390000	0.20768	0.323000	0.23307	-0.357000	0.07601	GCA	.	.		0.652	SORCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358685.4	NM_020777		T	7735080	C	T	7735080	3	4	254	1	0	0	0	0	1	0	0	0	14946	710	25	3	3234	3	SORCS2	4	7735080	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	2335109	7735080	183419196	223	34515										
WDR1	9948	hgsc.bcm.edu	37	chr4	10100740	10100740	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctccttctgcgtggtatcccAgatcctcagcttcccagaca	7	16	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:10100740A>G	ENST00000499869.2	-	4	446	c.253T>C	c.(253-255)Tgg>Cgg	p.W85R	WDR1_ENST00000382451.2_Intron|WDR1_ENST00000382452.2_Missense_Mutation_p.W85R|WDR1_ENST00000502702.1_Intron			O75083	WDR1_HUMAN	WD repeat domain 1	85					blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|sensory perception of sound (GO:0007605)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)				endometrium(3)|lung(5)|ovary(2)|pancreas(1)|urinary_tract(1)	12				STAD - Stomach adenocarcinoma(129;0.000703)|Colorectal(103;0.0057)|LUSC - Lung squamous cell carcinoma(721;0.0232)		GTGGTATCCCAGATCCTCAGC	0.592																																					p.W85R		Atlas-SNP	.											.	WDR1	93	.	0			c.T253C						.						79	77	78					4																	10100740		1936	4128	6064	SO:0001583	missense	9948	exon4			TATCCCAGATCCT	AF020260	CCDS54739.1, CCDS54740.1	4p16.1	2013-01-09			ENSG00000071127	ENSG00000071127		"WD repeat domain containing"	12754	protein-coding gene	gene with protein product		604734				10036186	Standard	NM_017491		Approved		uc021xlv.1	O75083	OTTHUMG00000160253	ENST00000499869.2:c.253T>C	chr4.hg19:g.10100740A>G	ENSP00000427687:p.Trp85Arg	173.0	0.0		99.0	4.0	NM_017491	A8K6E9|A8MPU4|O75313|Q8N6E5|Q9UG05|Q9UG78|Q9UQE0	Missense_Mutation	SNP	ENST00000499869.2	hg19	CCDS54740.1	.	.	.	.	.	.	.	.	.	.	A	29.0	4.967437	0.92855	.	.	ENSG00000071127	ENST00000499869;ENST00000382452;ENST00000508079	D;D;D	0.83506	-1.73;-1.73;-1.73	5.7	5.7	0.88788	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.95043	0.8395	H	0.99811	4.8	0.80722	D	1	P	0.44260	0.83	P	0.57502	0.822	D	0.96868	0.9637	10	0.87932	D	0	-5.8267	15.1289	0.72503	1.0:0.0:0.0:0.0	.	85	O75083	WDR1_HUMAN	R	85;85;89	ENSP00000427687:W85R;ENSP00000371890:W85R;ENSP00000425481:W89R	ENSP00000371890:W85R	W	-	1	0	WDR1	9709838	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.836000	0.92105	2.169000	0.68431	0.533000	0.62120	TGG	.	.		0.592	WDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359877.1			G	10100740	A	G	10100740	3	3	254	1	0	0	0	0	1	0	0	0	17287	188	7	2	1615	2	WDR1	4	10100740	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	2365660	10100740	181053536	224	34516										
BOD1L	259282	hgsc.bcm.edu	37	chr4	13603749	13603749	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cctctgtgacaacagccccaCcttcttcagctgcagcaaaa	6	16	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:13603749C>T	ENST00000040738.5	-	10	4910	c.4775G>A	c.(4774-4776)gGt>gAt	p.G1592D		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	1592						nucleus (GO:0005634)	DNA binding (GO:0003677)										AACAGCCCCACCTTCTTCAGC	0.483																																					p.G1592D		Atlas-SNP	.											.	.	.	.	0			c.G4775A						.						52	50	51					4																	13603749		2203	4300	6503	SO:0001583	missense	259282	exon10			GCCCCACCTTCTT	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.4775G>A	chr4.hg19:g.13603749C>T	ENSP00000040738:p.Gly1592Asp	123.0	0.0		95.0	4.0	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	hg19	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	C	16.68	3.191206	0.58017	.	.	ENSG00000038219	ENST00000040738	T	0.13420	2.59	5.23	5.23	0.72850	.	0.000000	0.56097	D	0.000033	T	0.29458	0.0734	L	0.36672	1.1	0.44668	D	0.997655	D	0.89917	1.0	D	0.87578	0.998	T	0.01583	-1.1319	10	0.66056	D	0.02	-10.5684	16.9701	0.86296	0.0:1.0:0.0:0.0	.	1592	Q8NFC6	BOD1L_HUMAN	D	1592	ENSP00000040738:G1592D	ENSP00000040738:G1592D	G	-	2	0	BOD1L	13212847	0.996000	0.38824	0.823000	0.32752	0.382000	0.30200	3.261000	0.51530	2.429000	0.82318	0.650000	0.86243	GGT	.	.		0.483	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		T	13603749	C	T	13603749	3	4	254	1	0	0	0	0	1	0	0	0	1483	507	18	3	4448	3	BOD1L	4	13603749	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	3503009	13603749	177550527	225	34517										
KCNIP4	80333	hgsc.bcm.edu	37	chr4	20852249	20852249	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aagctcaagggcttcaggccGatgcctgacggtggccatct	13	12	3	1	rs548454366		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:20852249G>A	ENST00000382152.2	-	3	372	c.205C>T	c.(205-207)Cgg>Tgg	p.R69W	KCNIP4_ENST00000382150.4_Missense_Mutation_p.R48W|KCNIP4_ENST00000447367.2_Missense_Mutation_p.R35W|KCNIP4_ENST00000359001.5_Missense_Mutation_p.R7W|KCNIP4_ENST00000509207.1_Missense_Mutation_p.R7W|KCNIP4_ENST00000382149.4_5'UTR|KCNIP4_ENST00000382148.3_Missense_Mutation_p.R44W	NM_025221.5	NP_079497.2	Q6PIL6	KCIP4_HUMAN	Kv channel interacting protein 4	69	EF-hand 1; degenerate. {ECO:0000255|PROSITE-ProRule:PRU00448}.					dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13		Breast(46;0.134)				GCTTCAGGCCGATGCCTGACG	0.468													G|||	1	0.000199681	0	0	5008	,	,		18121	0		0	False		,,,				2504	0.001				p.R49W		Atlas-SNP	.											KCNIP4_ENST00000447367,NS,carcinoma,+1,4	KCNIP4	85	.	0			c.C145T						.						70	69	69					4																	20852249		2203	4300	6503	SO:0001583	missense	80333	exon2			CAGGCCGATGCCT	AF453244	CCDS3428.1, CCDS43215.1, CCDS43216.1, CCDS43217.1, CCDS47035.1	4p15.32	2013-01-10			ENSG00000185774	ENSG00000185774		"EF-hand domain containing"	30083	protein-coding gene	gene with protein product		608182				11805342, 11847232	Standard	XM_005248190		Approved	CALP, KCHIP4, MGC44947	uc003gqh.1	Q6PIL6	OTTHUMG00000128557	ENST00000382152.2:c.205C>T	chr4.hg19:g.20852249G>A	ENSP00000371587:p.Arg69Trp	57.0	0.0		43.0	2.0	NM_025221	Q3YAB8|Q3YAB9|Q3YAC0|Q3YAC1|Q3YAC2|Q4W5G8|Q8NEU0|Q9BWT2|Q9H294|Q9H2A4	Missense_Mutation	SNP	ENST00000382152.2	hg19	CCDS43216.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.241883	0.79912	.	.	ENSG00000185774	ENST00000382148;ENST00000447367;ENST00000382150;ENST00000413487;ENST00000382152;ENST00000509207;ENST00000359001	T;T;T;T;T;T	0.68479	-0.33;1.93;-0.33;1.93;-0.33;-0.33	5.42	5.42	0.78866	.	0.228508	0.44688	D	0.000434	D	0.82595	0.5071	M	0.84326	2.69	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;P;D;D	0.75484	0.934;0.871;0.934;0.986	D	0.85146	0.0983	10	0.87932	D	0	.	14.9878	0.71362	0.0:0.0:0.8486:0.1514	.	44;48;52;69	Q3YAB9;Q3YAC0;Q3YAB7;Q6PIL6	.;.;.;KCIP4_HUMAN	W	44;35;48;7;69;7;7	ENSP00000371583:R44W;ENSP00000399080:R35W;ENSP00000371585:R48W;ENSP00000371587:R69W;ENSP00000423257:R7W;ENSP00000351892:R7W	ENSP00000351892:R7W	R	-	1	2	KCNIP4	20461347	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.259000	0.65485	2.521000	0.84997	0.655000	0.94253	CGG	.	.		0.468	KCNIP4-004	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360407.3	NM_025221		A	20852249	G	A	20852249	3	1	254	1	0	0	0	0	1	0	0	0	8051	1057	37	1	575	1	KCNIP4	4	20852249	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	7248500	20852249	170302027	226	34518										
LGI2	55203	hgsc.bcm.edu	37	chr4	25005815	25005815	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cgtatttgtaaatgtgagagCcaccgaagagctgggctacc	12	9	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:25005815C>A	ENST00000382114.4	-	8	1081	c.896G>T	c.(895-897)gGc>gTc	p.G299V		NM_018176.3	NP_060646.2	Q8N0V4	LGI2_HUMAN	leucine-rich repeat LGI family, member 2	299						extracellular region (GO:0005576)				breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(15)|prostate(1)|skin(3)|stomach(2)	33		Breast(46;0.173)				AATGTGAGAGCCACCGAAGAG	0.473																																					p.G299V		Atlas-SNP	.											.	LGI2	62	.	0			c.G896T						.						177	180	179					4																	25005815		2203	4300	6503	SO:0001583	missense	55203	exon8			TGAGAGCCACCGA	AJ487516	CCDS3431.1	4p15.31	2008-07-28			ENSG00000153012	ENSG00000153012			18710	protein-coding gene	gene with protein product		608301				12023020, 16014869	Standard	NM_018176		Approved	KIAA1916, FLJ10675	uc003grf.2	Q8N0V4	OTTHUMG00000097749	ENST00000382114.4:c.896G>T	chr4.hg19:g.25005815C>A	ENSP00000371548:p.Gly299Val	152.0	0.0		89.0	4.0	NM_018176	Q3MIN2|Q8NDW6|Q96PX2|Q9NVK4	Missense_Mutation	SNP	ENST00000382114.4	hg19	CCDS3431.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.551812	0.86127	.	.	ENSG00000153012	ENST00000382114	D	0.81499	-1.5	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.89413	0.6708	M	0.68317	2.08	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89676	0.3887	10	0.87932	D	0	-37.1251	19.8769	0.96880	0.0:1.0:0.0:0.0	.	299	Q8N0V4	LGI2_HUMAN	V	299	ENSP00000371548:G299V	ENSP00000371548:G299V	G	-	2	0	LGI2	24614913	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.776000	0.85560	2.767000	0.95098	0.557000	0.71058	GGC	.	.		0.473	LGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214978.1			A	25005815	C	A	25005815	3	1	254	1	0	0	0	0	1	0	0	0	8761	739	26	3	745	3	LGI2	4	25005815	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	4153566	25005815	166148461	227	34519										
SLAIN2	57606	hgsc.bcm.edu	37	chr4	48422205	48422205	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tttggctcttcggcaaccagTgaaagcatttagtaaccatg	9	9	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:48422205T>C	ENST00000264313.6	+	7	1842	c.1424T>C	c.(1423-1425)gTg>gCg	p.V475A	SLAIN2_ENST00000512093.1_Missense_Mutation_p.V308A	NM_020846.1	NP_065897.1	Q9P270	SLAI2_HUMAN	SLAIN motif family, member 2	475					cytoplasmic microtubule organization (GO:0031122)|microtubule nucleation (GO:0007020)|positive regulation of microtubule polymerization (GO:0031116)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|prostate(1)	13						CGGCAACCAGTGAAAGCATTT	0.498																																					p.V475A		Atlas-SNP	.											.	SLAIN2	31	.	0			c.T1424C						.						99	95	96					4																	48422205		1996	4163	6159	SO:0001583	missense	57606	exon7			AACCAGTGAAAGC	BC006139	CCDS47051.1	4p12	2008-02-05	2006-09-12	2006-09-12	ENSG00000109171	ENSG00000109171			29282	protein-coding gene	gene with protein product		610492	"KIAA1458"	KIAA1458		16546155	Standard	NM_020846		Approved	FLJ21611	uc003gya.4	Q9P270	OTTHUMG00000161701	ENST00000264313.6:c.1424T>C	chr4.hg19:g.48422205T>C	ENSP00000264313:p.Val475Ala	178.0	0.0		96.0	4.0	NM_020846	A8K4P1|Q8N5R3	Missense_Mutation	SNP	ENST00000264313.6	hg19	CCDS47051.1	.	.	.	.	.	.	.	.	.	.	T	15.77	2.930569	0.52866	.	.	ENSG00000109171	ENST00000264313;ENST00000512093	.	.	.	5.02	5.02	0.67125	.	0.389109	0.28425	N	0.015390	T	0.53965	0.1829	L	0.43152	1.355	0.49130	D	0.999756	P	0.41450	0.75	B	0.41917	0.37	T	0.59506	-0.7442	9	0.62326	D	0.03	-3.3571	14.7394	0.69442	0.0:0.0:0.0:1.0	.	475	Q9P270	SLAI2_HUMAN	A	475;308	.	ENSP00000264313:V475A	V	+	2	0	SLAIN2	48116962	1.000000	0.71417	1.000000	0.80357	0.522000	0.34438	6.610000	0.74178	1.901000	0.55032	0.455000	0.32223	GTG	.	.		0.498	SLAIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365807.4	NM_020846		C	48422205	T	C	48422205	3	2	254	1	0	0	0	0	1	0	0	0	14381	1696	59	2	1450	2	SLAIN2	4	48422205	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	23416390	48422205	142732071	228	34520										
ANKRD17	26057	hgsc.bcm.edu	37	chr4	74005966	74005966	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgtacatcctggctgtttgcTggcaaatggctgctggactt	12	9	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:74005966T>C	ENST00000358602.4	-	15	2483	c.2367A>G	c.(2365-2367)ccA>ccG	p.P789P	ANKRD17_ENST00000330838.6_Intron|ANKRD17_ENST00000509867.2_Silent_p.P676P|ANKRD17_ENST00000514252.1_5'UTR	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	789					blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GGCTGTTTGCTGGCAAATGGC	0.453																																					p.P789P		Atlas-SNP	.											.	ANKRD17	214	.	0			c.A2367G						.						65	65	65					4																	74005966		2203	4300	6503	SO:0001819	synonymous_variant	26057	exon15			GTTTGCTGGCAAA	AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"Ankyrin repeat domain containing"	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.2367A>G	chr4.hg19:g.74005966T>C		89.0	0.0		84.0	4.0	NM_032217	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Silent	SNP	ENST00000358602.4	hg19	CCDS34004.1																																																																																			.	.		0.453	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217		C	74005966	T	C	74005966	2	2	254	1	0	0	0	0	0	0	0	1	646	1567	55	2		2	ANKRD17	4	74005966	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	25583761	74005966	117148310	229	34521										
G3BP2	9908	hgsc.bcm.edu	37	chr4	76573877	76573877	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttctctaggtcgttgttcacGcacacgaggtggctgagatt	12	9	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:76573877G>A	ENST00000359707.4	-	9	1659	c.874C>T	c.(874-876)Cgt>Tgt	p.R292C	G3BP2_ENST00000357854.3_Missense_Mutation_p.R259C|G3BP2_ENST00000395719.3_Missense_Mutation_p.R292C	NM_203505.2	NP_987101.1	Q9UN86	G3BP2_HUMAN	GTPase activating protein (SH3 domain) binding protein 2	292					cytoplasmic sequestering of NF-kappaB (GO:0007253)|mRNA transport (GO:0051028)|Ras protein signal transduction (GO:0007265)	cytoplasm (GO:0005737)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|receptor signaling complex scaffold activity (GO:0030159)			breast(3)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	27			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			CGTTGTTCACGCACACGAGGT	0.408																																					p.R292C		Atlas-SNP	.											.	G3BP2	52	.	0			c.C874T						.						102	92	96					4																	76573877		2203	4300	6503	SO:0001583	missense	9908	exon9			GTTCACGCACACG	AB014560	CCDS3571.1, CCDS3572.1	4q21.1	2013-02-12	2006-11-01		ENSG00000138757	ENSG00000138757		"RNA binding motif (RRM) containing"	30291	protein-coding gene	gene with protein product	"Ras-GTPase activating protein SH3 domain-binding protein 2"					9734811, 9575347	Standard	NM_203504		Approved	KIAA0660	uc003his.3	Q9UN86	OTTHUMG00000130097	ENST00000359707.4:c.874C>T	chr4.hg19:g.76573877G>A	ENSP00000352738:p.Arg292Cys	34.0	0.0		35.0	4.0	NM_012297	A8K6X1|O60606|O75149|Q9UPA1	Missense_Mutation	SNP	ENST00000359707.4	hg19	CCDS3571.1	.	.	.	.	.	.	.	.	.	.	G	16.28	3.077733	0.55753	.	.	ENSG00000138757	ENST00000395719;ENST00000359707;ENST00000357854	T;T;T	0.78707	-1.19;-1.19;-1.2	5.96	5.96	0.96718	.	0.050014	0.85682	D	0.000000	D	0.86053	0.5841	M	0.61703	1.905	0.80722	D	1	D;D	0.89917	0.993;1.0	P;D	0.74023	0.489;0.982	D	0.86364	0.1719	10	0.66056	D	0.02	.	15.1472	0.72667	0.0:0.0:0.8588:0.1412	.	259;292	Q9UN86-2;Q9UN86	.;G3BP2_HUMAN	C	292;292;259	ENSP00000379069:R292C;ENSP00000352738:R292C;ENSP00000350518:R259C	ENSP00000350518:R259C	R	-	1	0	G3BP2	76792901	1.000000	0.71417	1.000000	0.80357	0.126000	0.20510	4.978000	0.63799	2.813000	0.96785	0.655000	0.94253	CGT	.	.		0.408	G3BP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252399.2	NM_012297		A	76573877	G	A	76573877	3	1	254	1	0	0	0	0	1	0	0	0	6150	1087	38	1	590	1	G3BP2	4	76573877	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	2567911	76573877	114580399	230	34522										
SCD5	79966	hgsc.bcm.edu	37	chr4	83582036	83582036	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tctcttctgaccttcagaatAcctccagggacacagaaaga	7	12	3	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:83582036A>G	ENST00000319540.4	-	3	889				SCD5_ENST00000273908.4_Missense_Mutation_p.V255A	NM_001037582.2	NP_001032671.2	Q86SK9	SCD5_HUMAN	stearoyl-CoA desaturase 5						fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	iron ion binding (GO:0005506)|stearoyl-CoA 9-desaturase activity (GO:0004768)			endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)	13		Colorectal(4;0.0323)|Hepatocellular(203;0.115)				CCTTCAGAATACCTCCAGGGA	0.463																																					p.V255A		Atlas-SNP	.											.	SCD5	58	.	0			c.T764C						.						120	116	117					4																	83582036		2203	4300	6503	SO:0001627	intron_variant	79966	exon4			CAGAATACCTCCA	AF389338	CCDS3595.1, CCDS34024.1	4q21.3	2013-01-25	2005-06-09	2005-06-09	ENSG00000145284	ENSG00000145284		"Fatty acid desaturases"	21088	protein-coding gene	gene with protein product		608370	"stearoyl-CoA desaturase 4"	SCD4		12477932	Standard	NM_024906		Approved	ACOD4, FLJ21032, FADS4, HSCD5	uc003hna.2	Q86SK9	OTTHUMG00000130293	ENST00000319540.4:c.569+19823T>C	chr4.hg19:g.83582036A>G		114.0	0.0		99.0	4.0	NM_024906	B2RPG0|Q4W5Q5|Q8NDS0|Q9H7D1	Missense_Mutation	SNP	ENST00000319540.4	hg19	CCDS34024.1	.	.	.	.	.	.	.	.	.	.	A	7.564	0.665249	0.14710	.	.	ENSG00000145284	ENST00000273908	.	.	.	3.92	1.46	0.22682	.	.	.	.	.	T	0.28134	0.0694	.	.	.	0.09310	N	1	B	0.13145	0.007	B	0.12156	0.007	T	0.29274	-1.0017	7	0.87932	D	0	.	3.1377	0.06444	0.6794:0.0:0.1128:0.2079	.	255	Q86SK9-2	.	A	255	.	ENSP00000273908:V255A	V	-	2	0	SCD5	83801060	0.000000	0.05858	0.003000	0.11579	0.050000	0.14768	-0.029000	0.12329	0.338000	0.23692	0.477000	0.44152	GTA	.	.		0.463	SCD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252635.1	NM_024906		G	83582036	A	G	83582036	1	3	254	0	1	0	0	0	0	0	0	0	13902	391	14	2		2	SCD5	4	83582036	Intron	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	7008159	83582036	107572240	231	34523										
PTPN13	5783	hgsc.bcm.edu	37	chr4	87690933	87690933	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tttctccagaaaatacatttGaggtaaaattatttaaaaat	4	4	1	2	rs549399227		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:87690933G>T	ENST00000411767.2	+	29	4564	c.4501G>T	c.(4501-4503)Gag>Tag	p.E1501*	PTPN13_ENST00000316707.6_Nonsense_Mutation_p.E1310*|PTPN13_ENST00000427191.2_Nonsense_Mutation_p.E1482*|PTPN13_ENST00000511467.1_Nonsense_Mutation_p.E1506*|PTPN13_ENST00000436978.1_Nonsense_Mutation_p.E1506*			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	1501	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		AAATACATTTGAGGTAAAATT	0.284																																					p.E1506X		Atlas-SNP	.											.	PTPN13	203	.	0			c.G4516T						.						21	21	21					4																	87690933		1779	4047	5826	SO:0001587	stop_gained	5783	exon29			ACATTTGAGGTAA		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.4501G>T	chr4.hg19:g.87690933G>T	ENSP00000407249:p.Glu1501*	81.0	0.0		93.0	4.0	NM_080685	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Nonsense_Mutation	SNP	ENST00000411767.2	hg19	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	G	48	14.498267	0.99798	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	.	.	.	5.74	5.74	0.90152	.	0.000000	0.50627	D	0.000103	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.9357	0.97140	0.0:0.0:1.0:0.0	.	.	.	.	X	1482;1506;1310;1501;1506;1450	.	ENSP00000322675:E1310X	E	+	1	0	PTPN13	87909957	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.188000	0.94921	2.715000	0.92844	0.655000	0.94253	GAG	.	.		0.284	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			T	87690933	G	T	87690933	4	4	254	1	0	0	0	0	0	1	0	0	12795	1291	45	3	4626	3	PTPN13	4	87690933	Nonsense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	4108897	87690933	103463343	232	34524										
HERC6	55008	hgsc.bcm.edu	37	chr4	89356960	89356960	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttaaatgttgctaaccttccTttcccactggctctgtataa	5	11	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:89356960T>C	ENST00000264346.7	+	18	2393	c.2334T>C	c.(2332-2334)ccT>ccC	p.P778P	HERC6_ENST00000380265.5_Silent_p.P742P	NM_017912.3	NP_060382.3	Q8IVU3	HERC6_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 6	778	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				hematopoietic progenitor cell differentiation (GO:0002244)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)	11		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000222)		CTAACCTTCCTTTCCCACTGG	0.368																																					p.P778P		Atlas-SNP	.											.	HERC6	104	.	0			c.T2334C						.						60	56	57					4																	89356960		1910	4180	6090	SO:0001819	synonymous_variant	55008	exon18			CCTTCCTTTCCCA	AF336798	CCDS47098.1, CCDS54777.1	4q22	2012-02-23	2012-02-23		ENSG00000138642	ENSG00000138642			26072	protein-coding gene	gene with protein product		609249	"hect domain and RLD 6"				Standard	NM_001165136		Approved	FLJ20637	uc011cdi.2	Q8IVU3	OTTHUMG00000160983	ENST00000264346.7:c.2334T>C	chr4.hg19:g.89356960T>C		129.0	0.0		104.0	5.0	NM_017912	B4DIY5|Q5GC90|Q5GRH3|Q5HYM6|Q5JPB6|Q6PIF4|Q8NAN3|Q9NWS4	Silent	SNP	ENST00000264346.7	hg19	CCDS47098.1																																																																																			.	.		0.368	HERC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363259.2			C	89356960	T	C	89356960	2	2	254	1	0	0	0	0	0	0	0	1	7071	1596	56	2		2	HERC6	4	89356960	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	1666027	89356960	101797316	233	34525										
UNC5C	8633	hgsc.bcm.edu	37	chr4	96104119	96104119	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccgcacacagagtttgcaaaCcagctccactgtgttcaggc	9	14	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:96104119C>T	ENST00000453304.1	-	14	2728	c.2380G>A	c.(2380-2382)Gtt>Att	p.V794I		NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	794					anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|brain development (GO:0007420)|positive regulation of apoptotic process (GO:0043065)|regulation of cell migration (GO:0030334)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(14)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	55		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)		AGTTTGCAAACCAGCTCCACT	0.488																																					p.V794I		Atlas-SNP	.											.	UNC5C	141	.	0			c.G2380A						.						155	132	140					4																	96104119		2203	4300	6503	SO:0001583	missense	8633	exon14			TGCAAACCAGCTC	AF055634	CCDS3643.1	4q21-q23	2013-01-11	2001-11-28		ENSG00000182168	ENSG00000182168		"Immunoglobulin superfamily / I-set domain containing"	12569	protein-coding gene	gene with protein product		603610	"unc5 (C.elegans homolog) c"			9126742, 9782087	Standard	NM_003728		Approved		uc003hto.3	O95185	OTTHUMG00000130989	ENST00000453304.1:c.2380G>A	chr4.hg19:g.96104119C>T	ENSP00000406022:p.Val794Ile	155.0	0.0		98.0	4.0	NM_003728	Q8IUT0	Missense_Mutation	SNP	ENST00000453304.1	hg19	CCDS3643.1	.	.	.	.	.	.	.	.	.	.	C	17.19	3.326783	0.60743	.	.	ENSG00000182168	ENST00000453304;ENST00000331502	T	0.47869	0.83	5.83	5.83	0.93111	.	0.233837	0.40469	N	0.001086	T	0.41880	0.1178	L	0.36672	1.1	0.80722	D	1	B	0.29716	0.255	B	0.19148	0.024	T	0.31475	-0.9942	10	0.66056	D	0.02	.	20.1338	0.98010	0.0:1.0:0.0:0.0	.	794	O95185	UNC5C_HUMAN	I	794;753	ENSP00000406022:V794I	ENSP00000328673:V753I	V	-	1	0	UNC5C	96323142	0.984000	0.35163	1.000000	0.80357	0.985000	0.73830	1.925000	0.40074	2.770000	0.95276	0.655000	0.94253	GTT	.	.		0.488	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728		T	96104119	C	T	96104119	3	4	254	1	0	0	0	0	1	0	0	0	17008	507	18	3	427	3	UNC5C	4	96104119	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	6747159	96104119	95050157	234	34526										
TET2	54790	hgsc.bcm.edu	37	chr4	106155605	106155605	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tttcaccagtttttcaacacAtaactgcagtgggcctgaaa	7	10	2	1	rs545616524		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:106155605A>T	ENST00000540549.1	+	3	1366	c.506A>T	c.(505-507)cAt>cTt	p.H169L	TET2_ENST00000380013.4_Missense_Mutation_p.H169L|TET2_ENST00000545826.1_Missense_Mutation_p.H169L|TET2_ENST00000305737.2_Missense_Mutation_p.H169L|TET2_ENST00000513237.1_Missense_Mutation_p.H190L|TET2_ENST00000394764.1_Missense_Mutation_p.H169L|TET2_ENST00000413648.2_Missense_Mutation_p.H169L			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	169					5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		TTTTCAACACATAACTGCAGT	0.388			"Mis N, F"		MDS																																p.H169L		Atlas-SNP	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	.	TET2	1762	.	0			c.A506T						.						44	42	43					4																	106155605		2203	4300	6503	SO:0001583	missense	54790	exon3			CAACACATAACTG	AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"KIAA1546", "tet oncogene family member 2"	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.506A>T	chr4.hg19:g.106155605A>T	ENSP00000442788:p.His169Leu	220.0	0.0		149.0	43.0	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Missense_Mutation	SNP	ENST00000540549.1	hg19	CCDS47120.1	.	.	.	.	.	.	.	.	.	.	A	7.287	0.610195	0.14066	.	.	ENSG00000168769	ENST00000305737;ENST00000540549;ENST00000545826;ENST00000513237;ENST00000380013;ENST00000394764;ENST00000413648;ENST00000535110	T;T;T;T;T;T;T	0.03717	3.83;4.5;3.83;4.5;4.5;3.83;3.84	5.28	-3.22	0.05125	.	14.800100	0.00728	N	0.000920	T	0.03348	0.0097	N	0.19112	0.55	0.09310	N	1	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.06405	0.0;0.0;0.002	T	0.46938	-0.9155	10	0.56958	D	0.05	.	8.0142	0.30372	0.3563:0.0:0.5205:0.1233	.	190;169;169	E7EQS8;Q6N021;Q6N021-2	.;TET2_HUMAN;.	L	169;169;169;190;169;169;169;169	ENSP00000306705:H169L;ENSP00000442788:H169L;ENSP00000442867:H169L;ENSP00000425443:H190L;ENSP00000369351:H169L;ENSP00000378245:H169L;ENSP00000391448:H169L	ENSP00000265149:H169L	H	+	2	0	TET2	106375054	0.000000	0.05858	0.002000	0.10522	0.219000	0.24729	-0.261000	0.08694	-0.319000	0.08652	0.533000	0.62120	CAT	.	.		0.388	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628		T	106155605	A	T	106155605	3	4	254	1	0	0	0	0	1	0	0	0	15785	217	8	4	508	4	TET2	4	106155605	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	10051486	106155605	84998671	235	34527										
SGMS2	166929	hgsc.bcm.edu	37	chr4	108824505	108824505	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttcctcttcagcggtcacacGgttacgctgacactgactta	8	13	3	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:108824505G>T	ENST00000394684.4	+	5	1247	c.690G>T	c.(688-690)acG>acT	p.T230T	RP11-286E11.1_ENST00000513071.1_RNA|RP11-286E11.1_ENST00000499098.1_RNA|SGMS2_ENST00000359079.4_Silent_p.T230T|SGMS2_ENST00000394686.3_Silent_p.T230T	NM_001136258.1	NP_001129730.1	Q8NHU3	SMS2_HUMAN	sphingomyelin synthase 2	230					small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)	Golgi apparatus (GO:0005794)|integral component of cell outer membrane (GO:0045203)|integral component of Golgi membrane (GO:0030173)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ceramide cholinephosphotransferase activity (GO:0047493)|kinase activity (GO:0016301)|sphingomyelin synthase activity (GO:0033188)			central_nervous_system(1)|endometrium(2)|large_intestine(8)|liver(2)|lung(6)|prostate(1)	20				OV - Ovarian serous cystadenocarcinoma(123;2.95e-05)		GCGGTCACACGGTTACGCTGA	0.453																																					p.T230T		Atlas-SNP	.											.	SGMS2	39	.	0			c.G690T						.						149	137	141					4																	108824505		2203	4300	6503	SO:0001819	synonymous_variant	166929	exon4			TCACACGGTTACG	BC041369	CCDS3677.1	4q25	2008-02-05			ENSG00000164023	ENSG00000164023	2.7.8.27		28395	protein-coding gene	gene with protein product		611574				14685263	Standard	NM_152621		Approved	MGC26963, SMS2	uc003hyl.4	Q8NHU3	OTTHUMG00000131811	ENST00000394684.4:c.690G>T	chr4.hg19:g.108824505G>T		92.0	0.0		98.0	4.0	NM_001136257	A8K2S9|B2RA61	Silent	SNP	ENST00000394684.4	hg19	CCDS3677.1																																																																																			.	.		0.453	SGMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254752.1	NM_152621		T	108824505	G	T	108824505	2	4	254	1	0	0	0	0	0	0	0	1	14230	1103	39	1		1	SGMS2	4	108824505	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	2668900	108824505	82329771	236	34528										
ELOVL6	79071	hgsc.bcm.edu	37	chr4	111119423	111119423	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cagttttcctgcatccattgGatggcttcattctcgttgaa	8	10	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:111119423G>A	ENST00000394607.3	-	2	232	c.69C>T	c.(67-69)atC>atT	p.I23I	ELOVL6_ENST00000302274.3_Silent_p.I23I|ELOVL6_ENST00000506461.1_5'UTR			Q9H5J4	ELOV6_HUMAN	ELOVL fatty acid elongase 6	23					cellular lipid metabolic process (GO:0044255)|fatty acid elongation, saturated fatty acid (GO:0019367)|long-chain fatty acid biosynthetic process (GO:0042759)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	transferase activity, transferring acyl groups other than amino-acyl groups (GO:0016747)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	8				OV - Ovarian serous cystadenocarcinoma(123;0.00462)		GCATCCATTGGATGGCTTCAT	0.493																																					p.I23I		Atlas-SNP	.											.	ELOVL6	27	.	0			c.C69T						.						236	200	213					4																	111119423		2203	4300	6503	SO:0001819	synonymous_variant	79071	exon2			CCATTGGATGGCT	AK027031	CCDS3690.1	4q25	2011-05-25	2011-05-25		ENSG00000170522	ENSG00000170522			15829	protein-coding gene	gene with protein product		611546	"ELOVL family member 6, elongation of long chain fatty acids (FEN1/Elo2, SUR4/Elo3-like, yeast)"			11567032	Standard	NM_024090		Approved	FLJ23378, MGC5487, LCE	uc003hzz.3	Q9H5J4	OTTHUMG00000132547	ENST00000394607.3:c.69C>T	chr4.hg19:g.111119423G>A		140.0	0.0		78.0	5.0	NM_001130721	Q4W5L0|Q8NCD1	Silent	SNP	ENST00000394607.3	hg19	CCDS3690.1																																																																																			.	.		0.493	ELOVL6-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255748.1	NM_024090		A	111119423	G	A	111119423	2	1	254	1	0	0	0	0	0	0	0	1	5080	1164	41	3		3	ELOVL6	4	111119423	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	2294918	111119423	80034853	237	34529										
ANXA5	308	hgsc.bcm.edu	37	chr4	122607464	122607464	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	caagcctttcatagccttccGaagagtttctgcatcagccc	7	14	3	1	rs370872365		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:122607464G>T	ENST00000296511.5	-	3	358	c.73C>A	c.(73-75)Cgg>Agg	p.R25R	ANXA5_ENST00000509016.1_5'UTR|ANXA5_ENST00000501272.2_Intron|ANXA5_ENST00000515017.1_Silent_p.R25R	NM_001154.3	NP_001145.1	P08758	ANXA5_HUMAN	annexin A5	25					blood coagulation (GO:0007596)|negative regulation of apoptotic process (GO:0043066)|negative regulation of catalytic activity (GO:0043086)|negative regulation of coagulation (GO:0050819)|response to organic substance (GO:0010033)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|endothelial microparticle (GO:0072563)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipase inhibitor activity (GO:0004859)|phospholipid binding (GO:0005543)			NS(1)|breast(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)	15						ATAGCCTTCCGAAGAGTTTCT	0.378																																					p.R25R	Pancreas(191;1279 2147 16046 17806 52646)|GBM(88;628 1285 16585 32846 50188)	Atlas-SNP	.											.	ANXA5	29	.	0			c.C73A						.						95	93	94					4																	122607464		2203	4300	6503	SO:0001819	synonymous_variant	308	exon3			CCTTCCGAAGAGT	U05770	CCDS3720.1	4q27	2008-02-05			ENSG00000164111	ENSG00000164111		"Annexins"	543	protein-coding gene	gene with protein product		131230		ENX2, ANX5		2960376	Standard	NM_001154		Approved		uc003idv.4	P08758	OTTHUMG00000133034	ENST00000296511.5:c.73C>A	chr4.hg19:g.122607464G>T		124.0	0.0		80.0	4.0	NM_001154	D3DNW7|Q6FHB3|Q6FI16|Q8WV69|Q9UDH9	Silent	SNP	ENST00000296511.5	hg19	CCDS3720.1																																																																																			.	.		0.378	ANXA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256636.2	NM_001154		T	122607464	G	T	122607464	2	4	254	1	0	0	0	0	0	0	0	1	721	1057	37	1		1	ANXA5	4	122607464	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	11488041	122607464	68546812	238	34530										
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123274969	123274969	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtatttttattttgttgtagGctccagtgatcattctacat	7	6	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:123274969G>T	ENST00000264501.4	+	82	14475	c.14102G>T	c.(14101-14103)gGc>gTc	p.G4701V	KIAA1109_ENST00000388738.3_Splice_Site_p.G4701V			Q2LD37	K1109_HUMAN	KIAA1109	4701					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						TTTGTTGTAGGCTCCAGTGAT	0.318																																					p.G4701V		Atlas-SNP	.											.	KIAA1109	424	.	0			c.G14102T						.						61	56	58					4																	123274969		1800	4073	5873	SO:0001630	splice_region_variant	84162	exon80			TTGTAGGCTCCAG	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.14102-1G>T	chr4.hg19:g.123274969G>T		132.0	0.0		87.0	4.0	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.55|14.55	2.568440|2.568440	0.45798|0.45798	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000306802|ENST00000264501;ENST00000388738;ENST00000438707;ENST00000431755	.|T;T;T	.|0.31247	.|2.48;2.48;1.5	5.47|5.47	5.47|5.47	0.80525|0.80525	.|Fragile site-associated protein, C-terminal (1);	.|0.164157	.|0.53938	.|D	.|0.000047	T|T	0.50667|0.50667	0.1629|0.1629	L|L	0.47716|0.47716	1.5|1.5	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|0.999;1.0	.|D;D	.|0.77557	.|0.964;0.99	T|T	0.30387|0.30387	-0.9980|-0.9980	5|9	.|.	.|.	.|.	.|.	19.7313|19.7313	0.96182|0.96182	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|4700;4701	.|Q2LD37-4;Q2LD37	.|.;K1109_HUMAN	S|V	1077|4701;4701;1370;302	.|ENSP00000264501:G4701V;ENSP00000373390:G4701V;ENSP00000410874:G1370V	.|.	A|G	+|+	1|2	0|0	KIAA1109|KIAA1109	123494419|123494419	1.000000|1.000000	0.71417|0.71417	0.987000|0.987000	0.45799|0.45799	0.653000|0.653000	0.38743|0.38743	6.746000|6.746000	0.74866|0.74866	2.761000|2.761000	0.94854|0.94854	0.650000|0.650000	0.86243|0.86243	GCT|GGC	.	.		0.318	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797	Missense_Mutation	T	123274969	G	T	123274969	5	4	254	1	0	0	0	0	0	0	1	0	8217	1217	42	3	14420	3	KIAA1109	4	123274969	Splice_Site	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	667505	123274969	67879307	239	34531										
GAB1	2549	hgsc.bcm.edu	37	chr4	144378898	144378898	+	Intron	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gaactgattcacaaaccataGgtgactttgctacaagaaga	8	8	1	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:144378898G>T	ENST00000262994.4	+	7	1887				GAB1_ENST00000505913.1_Intron|GAB1_ENST00000262995.4_Missense_Mutation_p.G551C	NM_002039.3	NP_002030.2	Q13480	GAB1_HUMAN	GRB2-associated binding protein 1						activation of JUN kinase activity (GO:0007257)|cell proliferation (GO:0008283)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis development (GO:0008544)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|interleukin-6-mediated signaling pathway (GO:0070102)|labyrinthine layer development (GO:0060711)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|regulation of cell migration (GO:0030334)|response to oxidative stress (GO:0006979)	cytosol (GO:0005829)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			breast(3)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	30	all_hematologic(180;0.158)					ACAAACCATAGGTGACTTTGC	0.338																																					p.G551C		Atlas-SNP	.											.	GAB1	80	.	0			c.G1651T						.						58	53	55					4																	144378898		2203	4298	6501	SO:0001627	intron_variant	2549	exon7			ACCATAGGTGACT	U43885	CCDS3759.1, CCDS3760.1	4q31.1	2013-01-10			ENSG00000109458	ENSG00000109458		"Pleckstrin homology (PH) domain containing"	4066	protein-coding gene	gene with protein product		604439				8596638	Standard	NM_207123		Approved		uc003ijd.3	Q13480	OTTHUMG00000161432	ENST00000262994.4:c.1586-1640G>T	chr4.hg19:g.144378898G>T		112.0	0.0		87.0	4.0	NM_207123	A8K152|Q4W5G2|Q6P1W2	Missense_Mutation	SNP	ENST00000262994.4	hg19	CCDS3759.1	.	.	.	.	.	.	.	.	.	.	G	19.86	3.906295	0.72868	.	.	ENSG00000109458	ENST00000262995	T	0.15603	2.41	5.18	4.33	0.51752	.	0.075533	0.50627	D	0.000105	T	0.27419	0.0673	N	0.22421	0.69	0.80722	D	1	D	0.69078	0.997	D	0.65874	0.939	T	0.07635	-1.0762	10	0.87932	D	0	-5.757	15.6984	0.77517	0.0:0.1372:0.8628:0.0	.	551	Q13480-2	.	C	551	ENSP00000262995:G551C	ENSP00000262995:G551C	G	+	1	0	GAB1	144598348	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.356000	0.79445	1.162000	0.42619	0.655000	0.94253	GGT	.	.		0.338	GAB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364998.1	NM_002039		T	144378898	G	T	144378898	1	4	254	0	1	0	0	0	0	0	0	0	6156	1000	35	3		3	GAB1	4	144378898	Intron	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	21103929	144378898	46775378	240	34532										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155244428	155244428	+	Intron	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgtttgtttgtttgtttgttTtttgcacgactgcttcccaa	8	7	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:155244428T>G	ENST00000357232.4	-	13	2653				DCHS2_ENST00000339452.1_Missense_Mutation_p.K1358Q	NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2						homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		tttgtttgttttttgCACGAC	0.383																																					p.K1358Q		Atlas-SNP	.											DCHS2_ENST00000339452,NS,carcinoma,0,1	DCHS2	594	.	0			c.A4072C						.						86	65	71					4																	155244428		692	1591	2283	SO:0001627	intron_variant	54798	exon8			TTTGTTTTTTGCA	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.2654-788A>C	chr4.hg19:g.155244428T>G		53.0	1.0		81.0	5.0	NM_001142552	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	hg19	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	T	5.448	0.267684	0.10294	.	.	ENSG00000197410	ENST00000339452	T	0.59083	0.29	1.19	-2.19	0.07015	.	.	.	.	.	T	0.29321	0.0730	N	0.14661	0.345	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.16867	-1.0388	9	0.13470	T	0.59	.	2.2509	0.04043	0.0:0.2273:0.3135:0.4592	.	1358	E9PC11	.	Q	1358	ENSP00000345062:K1358Q	ENSP00000345062:K1358Q	K	-	1	0	DCHS2	155463878	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.498000	0.02287	-0.611000	0.05709	-0.579000	0.04138	AAA	.	.		0.383	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		G	155244428	T	G	155244428	1	3	254	0	1	0	0	0	0	0	0	0	4290	1850	64	5		5	DCHS2	4	155244428	Intron	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	10865530	155244428	35909848	241	34533										
ANXA10	11199	hgsc.bcm.edu	37	chr4	169060641	169060641	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tattattcttttccagactgTgacaaagacatgctgatcaa	6	8	2	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:169060641T>C	ENST00000359299.3	+	3	291	c.105T>C	c.(103-105)tgT>tgC	p.C35C		NM_007193.4	NP_009124.2	Q9UJ72	ANX10_HUMAN	annexin A10	35						mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)			endometrium(1)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)|stomach(2)	16		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0325)		TTCCAGACTGTGACAAAGACA	0.413																																					p.C35C		Atlas-SNP	.											.	ANXA10	44	.	0			c.T105C						.						89	87	88					4																	169060641		2203	4300	6503	SO:0001819	synonymous_variant	11199	exon3			AGACTGTGACAAA	AJ238979	CCDS34096.1	4q32.3	2008-02-05			ENSG00000109511	ENSG00000109511		"Annexins"	534	protein-coding gene	gene with protein product		608008				10458909	Standard	NM_007193		Approved	ANX14	uc003irm.3	Q9UJ72	OTTHUMG00000161275	ENST00000359299.3:c.105T>C	chr4.hg19:g.169060641T>C		146.0	0.0		100.0	4.0	NM_007193	Q96IQ5|Q9UJV4	Silent	SNP	ENST00000359299.3	hg19	CCDS34096.1																																																																																			.	.		0.413	ANXA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364348.2	NM_007193		C	169060641	T	C	169060641	2	2	254	1	0	0	0	0	0	0	0	1	715	1702	59	2		2	ANXA10	4	169060641	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	13816213	169060641	22093635	242	34534										
CBR4	84869	hgsc.bcm.edu	37	chr4	169931172	169931172	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gccagtcggtagcctttccgGgccattaactgggccacagc	12	14	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:169931172G>T	ENST00000306193.3	-	1	237	c.69C>A	c.(67-69)gcC>gcA	p.A23A	CBR4_ENST00000504480.1_Silent_p.A23A|RP11-483A20.3_ENST00000506933.1_RNA	NM_032783.4	NP_116172.2	Q8N4T8	CBR4_HUMAN	carbonyl reductase 4	23					daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|fatty acid biosynthetic process (GO:0006633)|protein homotetramerization (GO:0051289)	mitochondrial matrix (GO:0005759)	NAD(P)H dehydrogenase (quinone) activity (GO:0003955)|NADPH binding (GO:0070402)|NADPH dehydrogenase (quinone) activity (GO:0008753)|quinone binding (GO:0048038)			kidney(1)|large_intestine(2)|lung(2)	5		Prostate(90;0.00263)|Renal(120;0.0183)|Melanoma(52;0.123)		GBM - Glioblastoma multiforme(119;0.0321)		AGCCTTTCCGGGCCATTAACT	0.582											OREG0016397	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A23A		Atlas-SNP	.											.	CBR4	15	.	0			c.C69A						.						39	43	42					4																	169931172		2203	4300	6503	SO:0001819	synonymous_variant	84869	exon1			TTTCCGGGCCATT	BC021973	CCDS3812.1	4q32.3	2013-10-11			ENSG00000145439	ENSG00000145439	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	25891	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 45C, member 1"					19027726	Standard	NM_032783		Approved	FLJ14431, SDR45C1	uc003iry.3	Q8N4T8	OTTHUMG00000161025	ENST00000306193.3:c.69C>A	chr4.hg19:g.169931172G>T		116.0	0.0	1881	93.0	4.0	NM_032783	Q8WTW8|Q96K93	Silent	SNP	ENST00000306193.3	hg19	CCDS3812.1																																																																																			.	.		0.582	CBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363441.2	NM_032783		T	169931172	G	T	169931172	2	4	254	1	0	0	0	0	0	0	0	1	2712	1219	43	3		3	CBR4	4	169931172	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	870531	169931172	21223104	243	34535										
GALNTL6	442117	hgsc.bcm.edu	37	chr4	173730515	173730515	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctctacttcctacctagaacAcctgaaggataaattggaag	7	10	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:173730515A>G	ENST00000506823.1	+	6	1214	c.557A>G	c.(556-558)cAc>cGc	p.H186R	GALNTL6_ENST00000508122.1_Missense_Mutation_p.H169R	NM_001034845.2	NP_001030017.2	Q49A17	GLTL6_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 6	186	Catalytic subdomain A.				protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(2)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	45						TACCTAGAACACCTGAAGGAT	0.433																																					p.H186R		Atlas-SNP	.											.	GALNTL6	102	.	0			c.A557G						.						91	88	89					4																	173730515		2203	4300	6503	SO:0001583	missense	442117	exon6			TAGAACACCTGAA		CCDS34104.1	4q34.1	2014-03-13	2014-03-13		ENSG00000174473	ENSG00000174473		"Glycosyltransferase family 2 domain containing"	33844	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase-like 6"	615138	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 6"				Standard	NM_001034845		Approved	GALNT17, GalNAc-T6L	uc003isv.3	Q49A17	OTTHUMG00000160807	ENST00000506823.1:c.557A>G	chr4.hg19:g.173730515A>G	ENSP00000423313:p.His186Arg	138.0	0.0		94.0	4.0	NM_001034845	Q2L4S6	Missense_Mutation	SNP	ENST00000506823.1	hg19	CCDS34104.1	.	.	.	.	.	.	.	.	.	.	A	13.38	2.220922	0.39201	.	.	ENSG00000174473	ENST00000506823;ENST00000404275;ENST00000508122	T;T	0.58940	0.3;0.3	5.45	5.45	0.79879	Glycosyl transferase, family 2 (1);	0.000000	0.64402	D	0.000003	T	0.72358	0.3450	L	0.58510	1.815	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	T	0.74191	-0.3745	10	0.56958	D	0.05	.	15.7979	0.78424	1.0:0.0:0.0:0.0	.	186	Q49A17	GLTL6_HUMAN	R	186;186;169	ENSP00000423313:H186R;ENSP00000423827:H169R	ENSP00000385382:H186R	H	+	2	0	GALNTL6	173967090	1.000000	0.71417	0.999000	0.59377	0.013000	0.08279	9.287000	0.95975	2.196000	0.70406	0.402000	0.26972	CAC	.	.		0.433	GALNTL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362395.1	NM_001034845		G	173730515	A	G	173730515	3	3	254	1	0	0	0	0	1	0	0	0	6233	159	6	2	575	2	GALNTL6	4	173730515	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	3799343	173730515	17423761	244	34536										
STOX2	56977	hgsc.bcm.edu	37	chr4	184930350	184930350	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agaaattctgcggcacacgcTgaacacgctggtacgggaga	13	10	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr4:184930350T>C	ENST00000308497.4	+	3	1794	c.359T>C	c.(358-360)cTg>cCg	p.L120P	STOX2_ENST00000438269.1_Missense_Mutation_p.L120P	NM_020225.1	NP_064610.1	Q9P2F5	STOX2_HUMAN	storkhead box 2	120					embryo development (GO:0009790)|maternal placenta development (GO:0001893)					breast(1)|endometrium(7)|lung(6)	14		all_lung(41;1.89e-12)|Lung NSC(41;3.48e-12)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|all_hematologic(60;0.027)|Prostate(90;0.0283)		all cancers(43;2.85e-26)|Epithelial(43;2.27e-22)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-10)|Colorectal(24;8.23e-06)|GBM - Glioblastoma multiforme(59;1.64e-05)|STAD - Stomach adenocarcinoma(60;3.6e-05)|COAD - Colon adenocarcinoma(29;4.37e-05)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.227)		CGGCACACGCTGAACACGCTG	0.443																																					p.L120P		Atlas-SNP	.											.	STOX2	142	.	0			c.T359C						.						53	48	50					4																	184930350		1920	4156	6076	SO:0001583	missense	56977	exon3			ACACGCTGAACAC	AB037813	CCDS47167.1	4q35.1	2014-09-11			ENSG00000173320	ENSG00000173320			25450	protein-coding gene	gene with protein product							Standard	XM_005263142		Approved	DKFZp762K222	uc003ivz.1	Q9P2F5	OTTHUMG00000160618	ENST00000308497.4:c.359T>C	chr4.hg19:g.184930350T>C	ENSP00000311257:p.Leu120Pro	91.0	0.0		86.0	5.0	NM_020225	A6H8U4|Q9NPS8	Missense_Mutation	SNP	ENST00000308497.4	hg19	CCDS47167.1	.	.	.	.	.	.	.	.	.	.	T	27.1	4.803740	0.90623	.	.	ENSG00000173320	ENST00000308497;ENST00000438269;ENST00000512520	D;D;D	0.88586	-2.4;-2.4;-2.4	5.55	5.55	0.83447	Storkhead-box protein, winged-helix domain (1);	0.000000	0.64402	D	0.000001	D	0.93858	0.8035	M	0.72353	2.195	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94443	0.7660	10	0.87932	D	0	-13.753	15.8615	0.79026	0.0:0.0:0.0:1.0	.	120	Q9P2F5	STOX2_HUMAN	P	120;120;58	ENSP00000311257:L120P;ENSP00000390127:L120P;ENSP00000425388:L58P	ENSP00000311257:L120P	L	+	2	0	STOX2	185167344	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	7.868000	0.87116	2.333000	0.79357	0.533000	0.62120	CTG	.	.		0.443	STOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361433.3	NM_020225		C	184930350	T	C	184930350	3	2	254	1	0	0	0	0	1	0	0	0	15335	1580	55	2	369	2	STOX2	4	184930350	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	11199835	184930350	6223926	245	34537										
PDZD2	23037	hgsc.bcm.edu	37	chr5	32098708	32098708	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	caatgggaagggtttgctgtCcagaaagaccatccccctgg	12	11	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:32098708C>A	ENST00000438447.1	+	23	8574	c.8186C>A	c.(8185-8187)tCc>tAc	p.S2729Y	PDZD2_ENST00000282493.3_Missense_Mutation_p.S2729Y			O15018	PDZD2_HUMAN	PDZ domain containing 2	2729					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				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						GGTTTGCTGTCCAGAAAGACC	0.547																																					p.S2729Y		Atlas-SNP	.											.	PDZD2	306	.	0			c.C8186A						.						46	44	44					5																	32098708		2203	4300	6503	SO:0001583	missense	23037	exon22			TGCTGTCCAGAAA	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"PDZ domain containing 3"	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.8186C>A	chr5.hg19:g.32098708C>A	ENSP00000402033:p.Ser2729Tyr	67.0	0.0		65.0	4.0	NM_178140	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	hg19	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.088140	0.76642	.	.	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.08102	3.13;3.13	5.22	4.34	0.51931	.	0.253674	0.28521	N	0.015043	T	0.12944	0.0314	L	0.32530	0.975	0.27874	N	0.939914	D	0.56521	0.976	P	0.53450	0.726	T	0.02288	-1.1182	10	0.66056	D	0.02	.	11.9527	0.52964	0.0:0.8256:0.1744:0.0	.	2729	O15018	PDZD2_HUMAN	Y	2729;2530;2729	ENSP00000402033:S2729Y;ENSP00000282493:S2729Y	ENSP00000282493:S2729Y	S	+	2	0	PDZD2	32134465	0.869000	0.29996	0.591000	0.28745	0.683000	0.39861	1.531000	0.36018	1.152000	0.42452	0.655000	0.94253	TCC	.	.		0.547	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			A	32098708	C	A	32098708	3	1	254	1	0	0	0	0	1	0	0	0	11710	855	30	3	8272	3	PDZD2	5	32098708	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10		32098708	148816552	246	34538										
C5orf33	133686	hgsc.bcm.edu	37	chr5	36217963	36217963	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cagtcccttcaaggtataacCtgattctctgcctccacaac	5	15	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:36217963C>A	ENST00000381937.4	-	6	667	c.668G>T	c.(667-669)aGg>aTg	p.R223M	NADK2_ENST00000514504.1_Missense_Mutation_p.R223M|NADK2_ENST00000282512.3_Missense_Mutation_p.R60M|NADK2_ENST00000506945.1_Missense_Mutation_p.R60M|NADK2_ENST00000397338.1_Missense_Mutation_p.R60M	NM_001085411.1	NP_001078880.1	Q4G0N4	NAKD2_HUMAN	NAD kinase 2, mitochondrial	223					NAD metabolic process (GO:0019674)|NADP biosynthetic process (GO:0006741)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|NAD+ kinase activity (GO:0003951)|protein homodimerization activity (GO:0042803)										AAGGTATAACCTGATTCTCTG	0.368																																					p.R223M		Atlas-SNP	.											.	NADKD1	47	.	0			c.G668T						.						120	106	111					5																	36217963		2203	4300	6503	SO:0001583	missense	133686	exon6			TATAACCTGATTC	BC062567	CCDS3917.1, CCDS47197.1, CCDS75235.1	5p13.2	2013-04-30	2013-04-30	2013-04-30	ENSG00000152620	ENSG00000152620			26404	protein-coding gene	gene with protein product	"mitochondrial NAD kinase"	615787	"chromosome 5 open reading frame 33", "NAD kinase domain containing 1"	C5orf33, NADKD1		23616928	Standard	NM_001085411		Approved	FLJ30596, MNADK	uc003jkf.4	Q4G0N4	OTTHUMG00000131105	ENST00000381937.4:c.668G>T	chr5.hg19:g.36217963C>A	ENSP00000371362:p.Arg223Met	164.0	0.0		103.0	5.0	NM_001085411	B5MC93|Q6UTX5|Q96NM0	Missense_Mutation	SNP	ENST00000381937.4	hg19	CCDS47197.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.781693	0.90282	.	.	ENSG00000152620	ENST00000397338;ENST00000282512;ENST00000381937;ENST00000506945;ENST00000514504;ENST00000511088	T;T;T;T;T;T	0.45668	0.89;0.89;0.94;0.89;0.89;0.89	6.08	5.22	0.72569	ATP-NAD kinase, PpnK-type, alpha/beta (1);ATP-NAD kinase, PpnK-type (1);	0.000000	0.85682	D	0.000000	T	0.67664	0.2917	M	0.82323	2.585	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.998	T	0.73754	-0.3883	10	0.87932	D	0	-10.8315	15.1343	0.72552	0.0:0.932:0.0:0.068	.	60;223;223	B7Z8V7;Q4G0N4-2;Q4G0N4	.;.;NAKD1_HUMAN	M	60;60;223;60;223;60	ENSP00000380499:R60M;ENSP00000282512:R60M;ENSP00000371362:R223M;ENSP00000422250:R60M;ENSP00000421029:R223M;ENSP00000426084:R60M	ENSP00000282512:R60M	R	-	2	0	NADKD1	36253720	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.938000	0.75904	1.595000	0.50050	0.591000	0.81541	AGG	.	.		0.368	NADK2-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367541.1	NM_153013		A	36217963	C	A	36217963	3	1	254	1	0	0	0	0	1	0	0	0	2294	681	24	3	688	3	C5orf33	5	36217963	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	4119255	36217963	144697297	247	34539										
MAST4	375449	hgsc.bcm.edu	37	chr5	66459398	66459398	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	caagaagcacctgtgctcccGcaagcacagcctggaggtga	12	13	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:66459398G>A	ENST00000403625.2	+	29	4686	c.4391G>A	c.(4390-4392)cGc>cAc	p.R1464H	MAST4_ENST00000261569.7_Missense_Mutation_p.R1270H|MAST4_ENST00000405643.1_Missense_Mutation_p.R1285H|MAST4_ENST00000403666.1_Missense_Mutation_p.R1275H|MAST4_ENST00000404260.3_Missense_Mutation_p.R1467H	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	1467						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		CTGTGCTCCCGCAAGCACAGC	0.667																																					p.R1464H		Atlas-SNP	.											.	MAST4	218	.	0			c.G4391A						.						13	18	16					5																	66459398		2090	4194	6284	SO:0001583	missense	375449	exon29			GCTCCCGCAAGCA	AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.4391G>A	chr5.hg19:g.66459398G>A	ENSP00000385727:p.Arg1464His	88.0	0.0		62.0	4.0	NM_001164664	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	ENST00000403625.2	hg19	CCDS54861.1	.	.	.	.	.	.	.	.	.	.	G	33	5.194465	0.94960	.	.	ENSG00000069020	ENST00000404260;ENST00000403625;ENST00000403666;ENST00000405643;ENST00000380908;ENST00000261569	T;T;T;T;T	0.72394	-0.63;-0.63;-0.65;-0.65;-0.62	5.92	5.05	0.67936	.	0.000000	0.85682	D	0.000000	D	0.84506	0.5487	M	0.83953	2.67	0.39097	D	0.96121	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.993	D	0.86817	0.2002	10	0.66056	D	0.02	-21.9289	14.5277	0.67900	0.0697:0.0:0.9303:0.0	.	1467;1275	O15021;O15021-3	MAST4_HUMAN;.	H	1467;1464;1275;1285;1285;1270	ENSP00000385048:R1467H;ENSP00000385727:R1464H;ENSP00000384313:R1275H;ENSP00000384099:R1285H;ENSP00000261569:R1270H	ENSP00000261569:R1270H	R	+	2	0	MAST4	66495154	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.643000	0.98464	2.818000	0.97014	0.655000	0.94253	CGC	.	.		0.667	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			A	66459398	G	A	66459398	3	1	254	1	0	0	0	0	1	0	0	0	9336	1087	38	1	4635	1	MAST4	5	66459398	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	30241435	66459398	114455862	248	34540										
CARTPT	9607	hgsc.bcm.edu	37	chr5	71015234	71015234	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gagctccagccccgagccctGgacatctactctgccgtgga	11	16	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:71015234G>T	ENST00000296777.4	+	1	245	c.114G>T	c.(112-114)ctG>ctT	p.L38L		NM_004291.3	NP_004282.1	Q16568	CART_HUMAN	CART prepropeptide	38					activation of MAPKK activity (GO:0000186)|adult feeding behavior (GO:0008343)|cell-cell signaling (GO:0007267)|cellular glucose homeostasis (GO:0001678)|cellular response to starvation (GO:0009267)|circadian regulation of gene expression (GO:0032922)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of appetite (GO:0032099)|negative regulation of bone resorption (GO:0045779)|negative regulation of glucagon secretion (GO:0070093)|negative regulation of osteoclast differentiation (GO:0045671)|neuropeptide signaling pathway (GO:0007218)|positive regulation of blood pressure (GO:0045777)|positive regulation of epinephrine secretion (GO:0032812)|positive regulation of transmission of nerve impulse (GO:0051971)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|somatostatin secretion (GO:0070253)|synaptic transmission (GO:0007268)	extracellular space (GO:0005615)|secretory granule (GO:0030141)				large_intestine(1)|lung(2)|ovary(1)	4		Lung NSC(167;0.00153)|Ovarian(174;0.0175)|Prostate(74;0.11)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;8.4e-56)	Amphetamine(DB00182)	CCCGAGCCCTGGACATCTACT	0.652																																					p.L38L		Atlas-SNP	.											.	CARTPT	10	.	0			c.G114T						.						72	70	70					5																	71015234		2203	4300	6503	SO:0001819	synonymous_variant	9607	exon1			AGCCCTGGACATC	U16826	CCDS4011.1	5q13.2	2008-02-05			ENSG00000164326	ENSG00000164326			24323	protein-coding gene	gene with protein product	"cocaine and amphetamine regulated transcript"	602606				9590691, 8647455	Standard	NM_004291		Approved	CART	uc003kbv.2	Q16568	OTTHUMG00000131261	ENST00000296777.4:c.114G>T	chr5.hg19:g.71015234G>T		104.0	0.0		95.0	4.0	NM_004291	Q6FG92	Silent	SNP	ENST00000296777.4	hg19	CCDS4011.1																																																																																			.	.		0.652	CARTPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254029.2	NM_004291		T	71015234	G	T	71015234	2	4	254	1	0	0	0	0	0	0	0	1	2661	1335	47	3		3	CARTPT	5	71015234	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	4555836	71015234	109900026	249	34541										
ENC1	8507	hgsc.bcm.edu	37	chr5	73930624	73930624	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggtgatgctgttccacacgtCtaatgttggatcgtagcagt	12	8	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:73930624C>A	ENST00000302351.4	-	2	2817	c.1687G>T	c.(1687-1689)Gac>Tac	p.D563Y	ENC1_ENST00000510316.1_Missense_Mutation_p.D490Y|ENC1_ENST00000509284.1_5'Flank|ENC1_ENST00000537006.1_Missense_Mutation_p.D563Y	NM_003633.3	NP_003624.1	O14682	ENC1_HUMAN	ectodermal-neural cortex 1 (with BTB domain)	563				YTAAAVLGNQIFIMGGDTEFSACSAYKFNSETYQWTKVGDV TAKRMSCHAVASGNKLYVVGGYFGIQRCKTLDCYDPTLDVW NSITTVPYSLIPTAFVSTWKHLPS -> IHSQASCPGGTQD FLLWGVIQNFSACFCL (in Ref. 1; AAC39532). {ECO:0000305}.	multicellular organismal development (GO:0007275)|negative regulation of translation (GO:0017148)|nervous system development (GO:0007399)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	20		all_lung(232;0.0154)|Lung NSC(167;0.0331)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;1.45e-59)		TTCCACACGTCTAATGTTGGA	0.478																																					p.D563Y		Atlas-SNP	.											.	ENC1	56	.	0			c.G1687T						.						116	88	97					5																	73930624		2203	4300	6503	SO:0001583	missense	8507	exon2			ACACGTCTAATGT	AF059611	CCDS4021.1, CCDS58958.1	5q13	2013-01-30	2013-01-30		ENSG00000171617	ENSG00000171617		"Kelch-like", "BTB/POZ domain containing"	3345	protein-coding gene	gene with protein product	"kelch-like family member 37"	605173	"ectodermal-neural cortex 1 (with BTB-like domain)"	NRPB		9305847, 9566959	Standard	NM_003633		Approved	PIG10, ENC-1, TP53I10, KLHL37	uc003kdc.5	O14682	OTTHUMG00000102059	ENST00000302351.4:c.1687G>T	chr5.hg19:g.73930624C>A	ENSP00000306356:p.Asp563Tyr	150.0	0.0		100.0	4.0	NM_003633	B4DHJ1|E9PFU0|O75464|Q9UPG9	Missense_Mutation	SNP	ENST00000302351.4	hg19	CCDS4021.1	.	.	.	.	.	.	.	.	.	.	C	18.47	3.630395	0.67015	.	.	ENSG00000171617	ENST00000302351;ENST00000510316;ENST00000537006	T;T;T	0.80304	-1.36;-1.36;-1.36	5.75	5.75	0.90469	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	D	0.92629	0.7658	M	0.92923	3.36	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93679	0.6997	10	0.87932	D	0	.	19.9421	0.97168	0.0:1.0:0.0:0.0	.	563	O14682	ENC1_HUMAN	Y	563;490;563	ENSP00000306356:D563Y;ENSP00000423804:D490Y;ENSP00000446289:D563Y	ENSP00000306356:D563Y	D	-	1	0	ENC1	73966380	1.000000	0.71417	0.229000	0.23960	0.898000	0.52572	7.818000	0.86416	2.714000	0.92807	0.561000	0.74099	GAC	.	.		0.478	ENC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219862.2	NM_003633		A	73930624	C	A	73930624	3	1	254	1	0	0	0	0	1	0	0	0	5115	913	32	3	86	3	ENC1	5	73930624	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	2915390	73930624	106984636	250	34542										
GFM2	84340	hgsc.bcm.edu	37	chr5	74028915	74028915	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctgaagacatttcaacgcatGttccaaatctatgggataaa	7	8	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:74028915G>T	ENST00000296805.3	-	16	1976	c.1519C>A	c.(1519-1521)Cat>Aat	p.H507N	GFM2_ENST00000509430.1_Missense_Mutation_p.H507N|GFM2_ENST00000345239.2_Missense_Mutation_p.H460N|GFM2_ENST00000515125.1_5'UTR	NM_032380.3	NP_115756.2			G elongation factor, mitochondrial 2											breast(2)|endometrium(2)|large_intestine(4)|lung(5)|prostate(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)		TTCAACGCATGTTCCAAATCT	0.343																																					p.H507N		Atlas-SNP	.											.	GFM2	38	.	0			c.C1519A						.						117	110	112					5																	74028915		2203	4300	6503	SO:0001583	missense	84340	exon16			ACGCATGTTCCAA	AF111808	CCDS4023.1, CCDS4024.1, CCDS47232.1	5q13	2008-02-05			ENSG00000164347	ENSG00000164347			29682	protein-coding gene	gene with protein product		606544				11735030	Standard	NM_001281302		Approved	EFG2, FLJ21661	uc003kdh.1	Q969S9	OTTHUMG00000102058	ENST00000296805.3:c.1519C>A	chr5.hg19:g.74028915G>T	ENSP00000296805:p.His507Asn	108.0	0.0		84.0	4.0	NM_032380		Missense_Mutation	SNP	ENST00000296805.3	hg19	CCDS4023.1	.	.	.	.	.	.	.	.	.	.	G	6.267	0.417379	0.11870	.	.	ENSG00000164347	ENST00000296805;ENST00000345239;ENST00000546082;ENST00000509430	T;T;T	0.70749	-0.51;-0.51;-0.51	5.07	4.17	0.49024	Elongation factor G/III/V (1);	0.246709	0.38663	N	0.001603	T	0.47040	0.1424	N	0.10874	0.06	0.80722	D	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.06405	0.001;0.002;0.001	T	0.31971	-0.9924	10	0.31617	T	0.26	-8.6912	6.5471	0.22412	0.0955:0.0:0.6032:0.3013	.	507;460;507	Q969S9-3;Q969S9-2;Q969S9	.;.;RRF2M_HUMAN	N	507;460;507;507	ENSP00000296805:H507N;ENSP00000296804:H460N;ENSP00000427004:H507N	ENSP00000296805:H507N	H	-	1	0	GFM2	74064671	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	3.058000	0.49939	1.067000	0.40740	0.557000	0.71058	CAT	.	.		0.343	GFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219860.2	NM_032380		T	74028915	G	T	74028915	3	4	254	1	0	0	0	0	1	0	0	0	6350	1377	48	3	844	3	GFM2	5	74028915	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	98291	74028915	106886345	251	34543										
JMY	133746	hgsc.bcm.edu	37	chr5	78533050	78533050	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctgggacggtctccgaggagAtagaggtgctggaaatggtg	18	6	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:78533050A>G	ENST00000396137.4	+	1	1039	c.577A>G	c.(577-579)Ata>Gta	p.I193V	DMGDH_ENST00000520388.1_5'Flank	NM_152405.4	NP_689618.4	Q8N9B5	JMY_HUMAN	junction mediating and regulatory protein, p53 cofactor	193					'de novo' actin filament nucleation (GO:0070060)|actin polymerization-dependent cell motility (GO:0070358)|Arp2/3 complex-mediated actin nucleation (GO:0034314)|cell cycle arrest (GO:0007050)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of apoptotic process (GO:0043065)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			endometrium(4)|kidney(2)|large_intestine(2)|lung(6)|skin(1)|urinary_tract(1)	16		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;4.45e-45)|Epithelial(54;5.85e-40)|all cancers(79;2.89e-35)		CTCCGAGGAGATAGAGGTGCT	0.701																																					p.I193V		Atlas-SNP	.											.	JMY	82	.	0			c.A577G						.						14	20	18					5																	78533050		692	1590	2282	SO:0001583	missense	133746	exon1			GAGGAGATAGAGG	AK095189	CCDS4047.3	5q14.1	2010-03-23			ENSG00000152409	ENSG00000152409			28916	protein-coding gene	gene with protein product		604279				10518217	Standard	NM_152405		Approved	FLJ37870	uc003kfx.4	Q8N9B5	OTTHUMG00000131301	ENST00000396137.4:c.577A>G	chr5.hg19:g.78533050A>G	ENSP00000379441:p.Ile193Val	206.0	0.0		121.0	5.0	NM_152405	A1L4P5|B5MDS2|B5MDT0	Missense_Mutation	SNP	ENST00000396137.4	hg19	CCDS4047.3	.	.	.	.	.	.	.	.	.	.	A	16.82	3.229082	0.58777	.	.	ENSG00000152409	ENST00000282259;ENST00000396137	T	0.08008	3.14	3.84	2.65	0.31530	.	2.723900	0.02643	U	0.105502	T	0.12860	0.0312	L	0.54323	1.7	0.25529	N	0.987294	B	0.20780	0.048	B	0.24541	0.054	T	0.35001	-0.9806	10	0.54805	T	0.06	.	8.3538	0.32318	0.7999:0.2001:0.0:0.0	.	193	Q8N9B5	JMY_HUMAN	V	193	ENSP00000379441:I193V	ENSP00000282259:I193V	I	+	1	0	JMY	78568806	1.000000	0.71417	0.049000	0.19019	0.904000	0.53231	1.637000	0.37155	0.524000	0.28502	0.379000	0.24179	ATA	.	.		0.701	JMY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254070.4	NM_152405		G	78533050	A	G	78533050	3	3	254	1	0	0	0	0	1	0	0	0	7966	333	12	2	579	2	JMY	5	78533050	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	4504135	78533050	102382210	252	34544										
CMYA5	202333	hgsc.bcm.edu	37	chr5	79034137	79034137	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtcattgatccagaatttctGgaggagccacctgcacttgc	10	11	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:79034137G>T	ENST00000446378.2	+	2	9580	c.9549G>T	c.(9547-9549)ctG>ctT	p.L3183L		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	3183					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		CAGAATTTCTGGAGGAGCCAC	0.428																																					p.L3183L		Atlas-SNP	.											.	CMYA5	643	.	0			c.G9549T						.						46	46	46					5																	79034137		1850	4093	5943	SO:0001819	synonymous_variant	202333	exon2			ATTTCTGGAGGAG	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.9549G>T	chr5.hg19:g.79034137G>T		111.0	0.0		86.0	4.0	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Silent	SNP	ENST00000446378.2	hg19	CCDS47238.1																																																																																			.	.		0.428	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		T	79034137	G	T	79034137	2	4	254	1	0	0	0	0	0	0	0	1	3592	1335	47	3		3	CMYA5	5	79034137	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	501087	79034137	101881123	253	34545										
THBS4	7060	hgsc.bcm.edu	37	chr5	79351663	79351663	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	catttggtggttttcaacaaCctgcagctggcagacggaag	12	9	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:79351663C>T	ENST00000350881.2	+	3	538	c.348C>T	c.(346-348)aaC>aaT	p.N116N	CTD-2201I18.1_ENST00000503007.1_RNA|THBS4_ENST00000511733.1_Silent_p.N25N	NM_003248.4	NP_003239.2	P35443	TSP4_HUMAN	thrombospondin 4	116	Laminin G-like.				behavioral response to pain (GO:0048266)|endothelial cell-cell adhesion (GO:0071603)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|positive regulation of cell division (GO:0051781)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of tissue remodeling (GO:0034103)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)|tissue remodeling (GO:0048771)	basement membrane (GO:0005604)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)|integrin binding (GO:0005178)			breast(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|stomach(3)	34		Lung NSC(167;0.00328)|all_lung(232;0.00355)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;6.3e-45)|Epithelial(54;1.77e-39)|all cancers(79;3.2e-34)		TTTTCAACAACCTGCAGCTGG	0.567																																					p.N116N		Atlas-SNP	.											.	THBS4	82	.	0			c.C348T						.						166	171	169					5																	79351663		2203	4300	6503	SO:0001819	synonymous_variant	7060	exon3			CAACAACCTGCAG		CCDS4049.1	5q13	2008-05-15			ENSG00000113296	ENSG00000113296			11788	protein-coding gene	gene with protein product		600715				7852353	Standard	NM_003248		Approved		uc021yaw.1	P35443	OTTHUMG00000108173	ENST00000350881.2:c.348C>T	chr5.hg19:g.79351663C>T		151.0	0.0		82.0	4.0	NM_003248	B2R909|Q86TG2	Silent	SNP	ENST00000350881.2	hg19	CCDS4049.1																																																																																			.	.		0.567	THBS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226977.1			T	79351663	C	T	79351663	2	4	254	1	0	0	0	0	0	0	0	1	15871	506	18	3		3	THBS4	5	79351663	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	317526	79351663	101563597	254	34546										
THBS4	7060	hgsc.bcm.edu	37	chr5	79355537	79355537	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tttctctaggtcctctcaagTttcagtctccgaccccaagc	6	15	4	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:79355537T>C	ENST00000350881.2	+	7	986	c.796T>C	c.(796-798)Ttt>Ctt	p.F266L	CTD-2201I18.1_ENST00000503007.1_RNA|THBS4_ENST00000511733.1_Missense_Mutation_p.F175L	NM_003248.4	NP_003239.2	P35443	TSP4_HUMAN	thrombospondin 4	266					behavioral response to pain (GO:0048266)|endothelial cell-cell adhesion (GO:0071603)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|positive regulation of cell division (GO:0051781)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of tissue remodeling (GO:0034103)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)|tissue remodeling (GO:0048771)	basement membrane (GO:0005604)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)|integrin binding (GO:0005178)			breast(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|stomach(3)	34		Lung NSC(167;0.00328)|all_lung(232;0.00355)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;6.3e-45)|Epithelial(54;1.77e-39)|all cancers(79;3.2e-34)		TCCTCTCAAGTTTCAGTCTCC	0.527																																					p.F266L		Atlas-SNP	.											.	THBS4	82	.	0			c.T796C						.						118	118	118					5																	79355537		2203	4300	6503	SO:0001583	missense	7060	exon7			CTCAAGTTTCAGT		CCDS4049.1	5q13	2008-05-15			ENSG00000113296	ENSG00000113296			11788	protein-coding gene	gene with protein product		600715				7852353	Standard	NM_003248		Approved		uc021yaw.1	P35443	OTTHUMG00000108173	ENST00000350881.2:c.796T>C	chr5.hg19:g.79355537T>C	ENSP00000339730:p.Phe266Leu	94.0	0.0		54.0	4.0	NM_003248	B2R909|Q86TG2	Missense_Mutation	SNP	ENST00000350881.2	hg19	CCDS4049.1	.	.	.	.	.	.	.	.	.	.	T	2.198	-0.383767	0.04966	.	.	ENSG00000113296	ENST00000350881;ENST00000511733	T;T	0.27890	1.64;1.64	5.23	-3.23	0.05109	.	1.179790	0.05785	N	0.609271	T	0.12390	0.0301	N	0.08118	0	0.09310	N	0.999998	B	0.02656	0.0	B	0.01281	0.0	T	0.28681	-1.0036	10	0.11794	T	0.64	-1.5851	5.1683	0.15098	0.1103:0.0745:0.4831:0.3322	.	266	P35443	TSP4_HUMAN	L	266;175	ENSP00000339730:F266L;ENSP00000422298:F175L	ENSP00000339730:F266L	F	+	1	0	THBS4	79391293	0.172000	0.23043	0.346000	0.25655	0.151000	0.21798	0.047000	0.14056	-0.130000	0.11599	-0.316000	0.08728	TTT	.	.		0.527	THBS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226977.1			C	79355537	T	C	79355537	3	2	254	1	0	0	0	0	1	0	0	0	15871	1725	60	2	822	2	THBS4	5	79355537	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	3874	79355537	101559723	255	34547										
ARRDC3	57561	hgsc.bcm.edu	37	chr5	90670966	90670966	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cattcgggaagagcagttctCaatctcagcaaatatctgaa	8	9	3	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:90670966C>T	ENST00000265138.3	-	5	909	c.643G>A	c.(643-645)Gag>Aag	p.E215K	ARRDC3_ENST00000503192.1_5'Flank	NM_020801.2	NP_065852.1	Q96B67	ARRD3_HUMAN	arrestin domain containing 3	215					fat pad development (GO:0060613)|negative regulation of heat generation (GO:0031651)|negative regulation of locomotion involved in locomotory behavior (GO:0090327)|negative regulation of multicellular organismal metabolic process (GO:0044252)|positive regulation of adrenergic receptor signaling pathway (GO:0071879)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|skin development (GO:0043588)|temperature homeostasis (GO:0001659)	endosome (GO:0005768)|plasma membrane (GO:0005886)	beta-3 adrenergic receptor binding (GO:0031699)			breast(2)|endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	18		all_cancers(142;2.22e-05)|all_epithelial(76;1.58e-07)|all_lung(232;0.000521)|Lung NSC(167;0.000548)|Ovarian(174;0.0798)|Colorectal(57;0.207)		OV - Ovarian serous cystadenocarcinoma(54;4.56e-30)|Epithelial(54;7.55e-26)|all cancers(79;3.63e-22)		GAGCAGTTCTCAATCTCAGCA	0.388																																					p.E215K		Atlas-SNP	.											ARRDC3,bladder,carcinoma,0,1	ARRDC3	56	.	0			c.G643A						.						59	54	56					5																	90670966		2203	4300	6503	SO:0001583	missense	57561	exon5			AGTTCTCAATCTC	AB037797	CCDS34202.1	5q14.3	2013-10-11			ENSG00000113369	ENSG00000113369			29263	protein-coding gene	gene with protein product	"alpha-arrestin 3"	612464				10718198, 19605364	Standard	NM_020801		Approved	KIAA1376	uc003kjz.2	Q96B67	OTTHUMG00000162616	ENST00000265138.3:c.643G>A	chr5.hg19:g.90670966C>T	ENSP00000265138:p.Glu215Lys	51.0	0.0		64.0	3.0	NM_020801	A8K6T8|Q9P2H1	Missense_Mutation	SNP	ENST00000265138.3	hg19	CCDS34202.1	.	.	.	.	.	.	.	.	.	.	C	37	6.148985	0.97324	.	.	ENSG00000113369	ENST00000265138	T	0.06933	3.24	6.08	6.08	0.98989	Immunoglobulin E-set (1);Arrestin, C-terminal (1);Arrestin-like, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.36663	0.0975	M	0.87827	2.91	0.80722	D	1	D	0.69078	0.997	D	0.79108	0.992	T	0.02950	-1.1090	10	0.34782	T	0.22	-17.7314	20.6721	0.99693	0.0:1.0:0.0:0.0	.	215	Q96B67	ARRD3_HUMAN	K	215	ENSP00000265138:E215K	ENSP00000265138:E215K	E	-	1	0	ARRDC3	90706722	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.786000	0.85741	2.894000	0.99253	0.591000	0.81541	GAG	.	.		0.388	ARRDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369763.2	NM_020801		T	90670966	C	T	90670966	3	4	254	1	0	0	0	0	1	0	0	0	984	835	29	3	617	3	ARRDC3	5	90670966	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	11315429	90670966	90244294	256	34548										
MCTP1	79772	hgsc.bcm.edu	37	chr5	94275844	94275844	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gactgagagcaaaatgattcCaagatcatggtcaggataat	10	6	2	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:94275844C>A	ENST00000515393.1	-	5	1116	c.1117G>T	c.(1117-1119)Gga>Tga	p.G373*	MCTP1_ENST00000312216.8_Nonsense_Mutation_p.G152*|MCTP1_ENST00000505208.1_Nonsense_Mutation_p.G152*|MCTP1_ENST00000429576.2_Nonsense_Mutation_p.G152*	NM_024717.4	NP_078993.4	Q6DN14	MCTP1_HUMAN	multiple C2 domains, transmembrane 1	373					calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(13)|liver(2)|lung(13)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	41		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)		AAAATGATTCCAAGATCATGG	0.408																																					p.G373X		Atlas-SNP	.											.	MCTP1	110	.	0			c.G1117T						.						170	172	171					5																	94275844		2203	4300	6503	SO:0001587	stop_gained	79772	exon5			TGATTCCAAGATC		CCDS34203.1, CCDS47247.1, CCDS75275.1	5q15	2008-02-05			ENSG00000175471	ENSG00000175471			26183	protein-coding gene	gene with protein product						15528213	Standard	XM_005272082		Approved	FLJ22344	uc003kkx.2	Q6DN14	OTTHUMG00000162742	ENST00000515393.1:c.1117G>T	chr5.hg19:g.94275844C>A	ENSP00000424126:p.Gly373*	124.0	0.0		82.0	4.0	NM_024717	Q6DN13|Q8N2W1|Q8NBA2|Q96LX0|Q9H6E8	Nonsense_Mutation	SNP	ENST00000515393.1	hg19	CCDS34203.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	40|40	7.936443|7.936443	0.98571|0.98571	.|.	.|.	ENSG00000175471|ENSG00000175471	ENST00000515393;ENST00000429576;ENST00000312216;ENST00000508509;ENST00000512425;ENST00000505208;ENST00000506568;ENST00000415885;ENST00000507214;ENST00000514780|ENST00000503301	.|.	.|.	.|.	5.63|5.63	5.63|5.63	0.86233|0.86233	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.79992	.|0.4542	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.77593	.|-0.2530	.|3	0.66056|.	D|.	0.02|.	-12.3737|-12.3737	20.0396|20.0396	0.97574|0.97574	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|L	373;152;152;152;34;152;13;114;134;133|181	.|.	ENSP00000308957:G152X|.	G|W	-|-	1|2	0|0	MCTP1|MCTP1	94301600|94301600	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.958000|0.958000	0.62258|0.62258	6.394000|6.394000	0.73223|0.73223	2.814000|2.814000	0.96858|0.96858	0.563000|0.563000	0.77884|0.77884	GGA|TGG	.	.		0.408	MCTP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370280.3	NM_024717		A	94275844	C	A	94275844	4	1	254	1	0	0	0	0	0	1	0	0	9409	603	21	3	1958	3	MCTP1	5	94275844	Nonsense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	3604878	94275844	86639416	257	34549										
ARSK	153642	hgsc.bcm.edu	37	chr5	94939217	94939217	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcttaaaacccatatgaatcCaagagcagtttgaacaaaaa	6	8	0	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:94939217C>A	ENST00000380009.4	+	8	1803	c.1598C>A	c.(1597-1599)cCa>cAa	p.P533Q		NM_198150.2	NP_937793.1	Q6UWY0	ARSK_HUMAN	arylsulfatase family, member K	533					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|pancreas(1)|skin(1)	16		all_cancers(142;3.38e-06)|all_epithelial(76;6.57e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.00473)		all cancers(79;6.5e-16)		CATATGAATCCAAGAGCAGTT	0.303																																					p.P533Q		Atlas-SNP	.											.	ARSK	29	.	0			c.C1598A						.						38	38	38					5																	94939217		2203	4299	6502	SO:0001583	missense	153642	exon8			TGAATCCAAGAGC		CCDS4073.1	5q15	2013-02-14	2006-03-07		ENSG00000164291	ENSG00000164291		"Arylsulfatase family"	25239	protein-coding gene	gene with protein product		610011	"arylsulfatase K"			12975309, 16174644	Standard	NM_198150		Approved	DKFZp313G1735, TSULF	uc003kld.3	Q6UWY0	OTTHUMG00000121166	ENST00000380009.4:c.1598C>A	chr5.hg19:g.94939217C>A	ENSP00000369346:p.Pro533Gln	74.0	0.0		73.0	4.0	NM_198150	A2BDE3|B4E1I4|Q3ZCW3|Q8N3Q8	Missense_Mutation	SNP	ENST00000380009.4	hg19	CCDS4073.1	.	.	.	.	.	.	.	.	.	.	C	9.667	1.145640	0.21288	.	.	ENSG00000164291	ENST00000380009	D	0.98362	-4.89	4.86	1.47	0.22746	.	1.526730	0.03754	N	0.257001	D	0.95089	0.8409	L	0.44542	1.39	0.09310	N	1	B	0.28512	0.214	B	0.23574	0.047	D	0.87413	0.2377	10	0.29301	T	0.29	0.1729	0.0796	0.00030	0.2785:0.2289:0.2308:0.2618	.	533	Q6UWY0	ARSK_HUMAN	Q	533	ENSP00000369346:P533Q	ENSP00000369346:P533Q	P	+	2	0	ARSK	94964973	0.084000	0.21492	0.000000	0.03702	0.026000	0.11368	0.067000	0.14510	0.548000	0.28955	-0.137000	0.14449	CCA	.	.		0.303	ARSK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241652.2	NM_198150		A	94939217	C	A	94939217	3	1	254	1	0	0	0	0	1	0	0	0	996	594	21	3	1628	3	ARSK	5	94939217	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	663373	94939217	85976043	258	34550										
TRPC7	57113	hgsc.bcm.edu	37	chr5	135692571	135692571	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctggcagtgcgccgccaggaTgatgggcgtgatgtcgtggg	19	9	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:135692571T>C	ENST00000513104.1	-	2	787	c.505A>G	c.(505-507)Atc>Gtc	p.I169V	TRPC7_ENST00000355180.3_Missense_Mutation_p.I169V|TRPC7_ENST00000426057.2_Missense_Mutation_p.I169V	NM_020389.2	NP_065122.1	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel, subfamily C, member 7	169					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|manganese ion transport (GO:0006828)|platelet activation (GO:0030168)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(3)	46			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GCCGCCAGGATGATGGGCGTG	0.637																																					p.I169V		Atlas-SNP	.											.	TRPC7	126	.	0			c.A505G						.						132	142	138					5																	135692571		2203	4300	6503	SO:0001583	missense	57113	exon2			CCAGGATGATGGG	AJ272034	CCDS47267.1, CCDS47267.2, CCDS54905.1, CCDS54906.1	5q31.2	2011-12-14			ENSG00000069018	ENSG00000069018		"Voltage-gated ion channels / Transient receptor potential cation channels"	20754	protein-coding gene	gene with protein product						11805119, 16382100	Standard	NM_020389		Approved		uc003lbn.2	Q9HCX4	OTTHUMG00000162035	ENST00000513104.1:c.505A>G	chr5.hg19:g.135692571T>C	ENSP00000426070:p.Ile169Val	116.0	0.0		93.0	4.0	NM_001167576	A1A4Z4|F5H5U9|Q70T26|Q8IWP7	Missense_Mutation	SNP	ENST00000513104.1	hg19	CCDS47267.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.55|16.55	3.154030|3.154030	0.57259|0.57259	.|.	.|.	ENSG00000069018|ENSG00000069018	ENST00000352189;ENST00000378459;ENST00000502753|ENST00000355180;ENST00000426057;ENST00000513104;ENST00000265193	.|T;T;T	.|0.70869	.|-0.52;-0.52;-0.52	5.26|5.26	5.26|5.26	0.73747|0.73747	.|Ankyrin repeat-containing domain (2);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.76248|0.76248	0.3961|0.3961	M|M	0.79475|0.79475	2.455|2.455	0.29723|0.29723	N|N	0.838498|0.838498	.|B;D;B;B	.|0.55385	.|0.001;0.971;0.032;0.032	.|B;P;B;B	.|0.47603	.|0.001;0.551;0.071;0.102	T|T	0.77955|0.77955	-0.2393|-0.2393	5|10	.|0.56958	.|D	.|0.05	-22.9787|-22.9787	15.3565|15.3565	0.74431|0.74431	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|169;169;169;169	.|Q8IWP7;F5H5U9;Q70T25;Q9HCX4	.|.;.;.;TRPC7_HUMAN	R|V	168|169	.|ENSP00000347312:I169V;ENSP00000441628:I169V;ENSP00000426070:I169V	.|ENSP00000265193:I169V	H|I	-|-	2|1	0|0	TRPC7|TRPC7	135720470|135720470	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	5.022000|5.022000	0.64078|0.64078	2.205000|2.205000	0.71048|0.71048	0.528000|0.528000	0.53228|0.53228	CAT|ATC	.	.		0.637	TRPC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366975.1	NM_020389		C	135692571	T	C	135692571	3	2	254	1	0	0	0	0	1	0	0	0	16599	1464	51	2	2127	2	TRPC7	5	135692571	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	40753354	135692571	45222689	259	34551										
KIF20A	10112	hgsc.bcm.edu	37	chr5	137518950	137518950	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggatctcattctttgagatcTacaacgaactgctttatgac	7	9	3	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:137518950T>C	ENST00000394894.3	+	8	1151	c.925T>C	c.(925-927)Tac>Cac	p.Y309H	KIF20A_ENST00000508792.1_Missense_Mutation_p.Y291H	NM_005733.2	NP_005724.1	O95235	KI20A_HUMAN	kinesin family member 20A	309	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cytokinesis (GO:0000910)|metabolic process (GO:0008152)|microtubule bundle formation (GO:0001578)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)|transporter activity (GO:0005215)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|liver(2)|lung(9)|prostate(2)|upper_aerodigestive_tract(1)	27			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			CTTTGAGATCTACAACGAACT	0.493																																					p.Y309H		Atlas-SNP	.											.	KIF20A	53	.	0			c.T925C						.						66	63	64					5																	137518950		2203	4300	6503	SO:0001583	missense	10112	exon8			GAGATCTACAACG	AF070672	CCDS4199.1	5q31	2008-02-05	2003-01-13	2003-01-17	ENSG00000112984	ENSG00000112984		"Kinesins"	9787	protein-coding gene	gene with protein product		605664	"RAB6 interacting, kinesin-like (rabkinesin6)"	RAB6KIFL		11416179, 10806357	Standard	NM_005733		Approved		uc003lcj.3	O95235	OTTHUMG00000129195	ENST00000394894.3:c.925T>C	chr5.hg19:g.137518950T>C	ENSP00000378356:p.Tyr309His	83.0	0.0		84.0	4.0	NM_005733	B4DL79|D3DQB6	Missense_Mutation	SNP	ENST00000394894.3	hg19	CCDS4199.1	.	.	.	.	.	.	.	.	.	.	T	18.77	3.694220	0.68386	.	.	ENSG00000112984	ENST00000394894;ENST00000508792	D;D	0.87334	-2.24;-2.24	5.4	5.4	0.78164	Kinesin, motor domain (4);	0.000000	0.40908	D	0.000992	D	0.93471	0.7917	M	0.80616	2.505	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.94349	0.7577	10	0.87932	D	0	-11.4603	15.4415	0.75187	0.0:0.0:0.0:1.0	.	291;309	B4DL79;O95235	.;KI20A_HUMAN	H	309;291	ENSP00000378356:Y309H;ENSP00000420880:Y291H	ENSP00000378356:Y309H	Y	+	1	0	KIF20A	137546849	1.000000	0.71417	1.000000	0.80357	0.691000	0.40173	7.698000	0.84413	2.061000	0.61500	0.533000	0.62120	TAC	.	.		0.493	KIF20A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251272.1	NM_005733		C	137518950	T	C	137518950	3	2	254	1	0	0	0	0	1	0	0	0	8295	1522	53	2	951	2	KIF20A	5	137518950	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	1826379	137518950	43396310	260	34552										
ETF1	2107	hgsc.bcm.edu	37	chr5	137844000	137844000	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cccatgtcgactacctagtaGtcatcaaggtcaaaaaattc	6	11	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:137844000G>A	ENST00000360541.5	-	11	1529	c.1308C>T	c.(1306-1308)gaC>gaT	p.D436D	ETF1_ENST00000503014.1_Silent_p.D422D|ETF1_ENST00000499810.2_Silent_p.D403D	NM_004730.3	NP_004721.1	P62495	ERF1_HUMAN	eukaryotic translation termination factor 1	436					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein methylation (GO:0006479)|regulation of translational termination (GO:0006449)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational termination (GO:0006415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|RNA binding (GO:0003723)|translation release factor activity (GO:0003747)|translation release factor activity, codon specific (GO:0016149)|translation termination factor activity (GO:0008079)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)|urinary_tract(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CTACCTAGTAGTCATCAAGGT	0.488																																					p.D436D		Atlas-SNP	.											.	ETF1	38	.	0			c.C1308T						.						56	47	50					5																	137844000		2203	4300	6503	SO:0001819	synonymous_variant	2107	exon11			CTAGTAGTCATCA	AF095901	CCDS4207.1, CCDS75313.1, CCDS75314.1	5q31.2	2008-02-05			ENSG00000120705	ENSG00000120705			3477	protein-coding gene	gene with protein product	"sup45 (yeast omnipotent suppressor 45) homolog-like 1", "polypeptide chain release factor 1"	600285		SUP45L1, ERF1, ERF		1546371, 7990965	Standard	NM_004730		Approved	eRF1, TB3-1, RF1	uc003ldc.5	P62495	OTTHUMG00000129199	ENST00000360541.5:c.1308C>T	chr5.hg19:g.137844000G>A		96.0	0.0		124.0	19.0	NM_004730	B2R6B4|D3DQC1|P46055|Q5M7Z7|Q96CG1	Silent	SNP	ENST00000360541.5	hg19	CCDS4207.1																																																																																			.	.		0.488	ETF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251276.2	NM_004730		A	137844000	G	A	137844000	2	1	254	1	0	0	0	0	0	0	0	1	5270	1020	36	3		3	ETF1	5	137844000	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	325050	137844000	43071260	261	34553										
PSD2	84249	hgsc.bcm.edu	37	chr5	139189371	139189371	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	atgcttccaggagcctctacCcagatgctgaggaccctcag	10	14	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:139189371C>A	ENST00000274710.3	+	2	551	c.346C>A	c.(346-348)Cca>Aca	p.P116T		NM_032289.2	NP_115665.1	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	116					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(10)|liver(2)|lung(15)|ovary(1)|prostate(2)	38			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAGCCTCTACCCAGATGCTGA	0.592																																					p.P116T		Atlas-SNP	.											.	PSD2	88	.	0			c.C346A						.						65	73	71					5																	139189371		2203	4300	6503	SO:0001583	missense	84249	exon2			CTCTACCCAGATG	AL136559	CCDS4216.1	5q31.3	2013-01-10			ENSG00000146005	ENSG00000146005		"Pleckstrin homology (PH) domain containing"	19092	protein-coding gene	gene with protein product							Standard	NM_032289		Approved	DKFZp761B0514	uc003leu.1	Q9BQI7	OTTHUMG00000129240	ENST00000274710.3:c.346C>A	chr5.hg19:g.139189371C>A	ENSP00000274710:p.Pro116Thr	64.0	0.0		113.0	5.0	NM_032289	D3DQD3|Q8N3J8	Missense_Mutation	SNP	ENST00000274710.3	hg19	CCDS4216.1	.	.	.	.	.	.	.	.	.	.	C	2.704	-0.270254	0.05716	.	.	ENSG00000146005	ENST00000274710	T	0.26223	1.75	4.75	-1.13	0.09775	.	1.428600	0.04426	N	0.368474	T	0.17365	0.0417	N	0.19112	0.55	0.09310	N	1	B	0.13594	0.008	B	0.14578	0.011	T	0.30119	-0.9989	10	0.25106	T	0.35	.	9.8505	0.41055	0.0:0.3107:0.5936:0.0957	.	116	Q9BQI7	PSD2_HUMAN	T	116	ENSP00000274710:P116T	ENSP00000274710:P116T	P	+	1	0	PSD2	139169555	0.001000	0.12720	0.000000	0.03702	0.004000	0.04260	0.314000	0.19432	-0.331000	0.08501	-0.367000	0.07326	CCA	.	.		0.592	PSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251339.1	NM_032289		A	139189371	C	A	139189371	3	1	254	1	0	0	0	0	1	0	0	0	12659	623	22	3	348	3	PSD2	5	139189371	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1345371	139189371	41725889	262	34554										
PCDHAC2	56134	hgsc.bcm.edu	37	chr5	140347691	140347691	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agccacagatgggggaatacCgcagctcacatccctgcgta	11	13	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:140347691C>A	ENST00000289269.5	+	1	1872	c.1340C>A	c.(1339-1341)cCg>cAg	p.P447Q	PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHAC1_ENST00000253807.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA13_ENST00000289272.2_Intron	NM_018899.5|NM_031883.2	NP_061722.1|NP_114089.1	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2	447	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|liver(2)|lung(9)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	45			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGGGGAATACCGCAGCTCACA	0.537																																					p.P447Q	Melanoma(190;638 2083 3390 11909 52360)	Atlas-SNP	.											.	PCDHAC2	142	.	0			c.C1340A						.						110	113	112					5																	140347691		2203	4300	6503	SO:0001583	missense	56134	exon1			GAATACCGCAGCT	AF152474	CCDS4242.1	5q31	2010-11-26			ENSG00000243232	ENSG00000243232		"Cadherins / Protocadherins : Clustered"	8677	other	complex locus constituent		606321				10380929	Standard	NM_031883		Approved	PCDH-ALPHA-C2		Q9Y5I4	OTTHUMG00000129607	ENST00000289269.5:c.1340C>A	chr5.hg19:g.140347691C>A	ENSP00000289269:p.Pro447Gln	151.0	0.0		87.0	5.0	NM_031883	Q2M3V1|Q9Y5F4	Missense_Mutation	SNP	ENST00000289269.5	hg19	CCDS4242.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.977428	0.74360	.	.	ENSG00000243232	ENST00000289269	T	0.55588	0.51	5.92	5.92	0.95590	Cadherin (4);Cadherin-like (1);	0.000000	0.41712	D	0.000834	D	0.82838	0.5124	H	0.96460	3.825	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.87312	0.2312	10	0.87932	D	0	.	20.3248	0.98698	0.0:1.0:0.0:0.0	.	447;447	Q9Y5I4-2;Q9Y5I4	.;PCDC2_HUMAN	Q	447	ENSP00000289269:P447Q	ENSP00000289269:P447Q	P	+	2	0	PCDHAC2	140327875	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.818000	0.86416	2.818000	0.97014	0.655000	0.94253	CCG	.	.		0.537	PCDHAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251802.2	NM_018899		A	140347691	C	A	140347691	3	1	254	1	0	0	0	0	1	0	0	0	11542	652	23	1	1342	1	PCDHAC2	5	140347691	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1158320	140347691	40567569	263	34555										
PCDHGA2	56113	hgsc.bcm.edu	37	chr5	140719523	140719523	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aggatggtccgggccttctaAccagagcgaaggttatcgtc	13	10	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:140719523A>G	ENST00000394576.2	+	1	985	c.985A>G	c.(985-987)Acc>Gcc	p.T329A	PCDHGA1_ENST00000517417.1_Intron	NM_018915.2	NP_061738.1	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2	329	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(32)|ovary(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGGCCTTCTAACCAGAGCGAA	0.428																																					p.T329A		Atlas-SNP	.											.	PCDHGA2	205	.	0			c.A985G						.						154	159	157					5																	140719523		2203	4300	6503	SO:0001583	missense	56113	exon1			CTTCTAACCAGAG	AF152508	CCDS47289.1	5q31	2011-03-28			ENSG00000081853	ENSG00000081853		"Cadherins / Protocadherins : Clustered"	8700	other	protocadherin		606289				10380929	Standard	NM_018915		Approved	PCDH-GAMMA-A2		Q9Y5H1	OTTHUMG00000163679	ENST00000394576.2:c.985A>G	chr5.hg19:g.140719523A>G	ENSP00000378077:p.Thr329Ala	149.0	0.0		98.0	4.0	NM_018915	Q52LL6|Q9Y5D5	Missense_Mutation	SNP	ENST00000394576.2	hg19	CCDS47289.1	.	.	.	.	.	.	.	.	.	.	.	0.392	-0.922845	0.02377	.	.	ENSG00000081853	ENST00000394576	T	0.02709	4.19	5.26	4.09	0.47781	Cadherin (4);Cadherin-like (1);	0.590193	0.13742	U	0.365898	T	0.01287	0.0042	N	0.04043	-0.29	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.13407	0.005;0.009	T	0.47935	-0.9078	10	0.02654	T	1	.	5.6812	0.17776	0.7463:0.0:0.2537:0.0	.	329;329	Q9Y5H1-2;Q9Y5H1	.;PCDG2_HUMAN	A	329	ENSP00000378077:T329A	ENSP00000378077:T329A	T	+	1	0	PCDHGA2	140699707	0.000000	0.05858	1.000000	0.80357	0.688000	0.40055	-0.472000	0.06623	2.125000	0.65367	0.533000	0.62120	ACC	.	.		0.428	PCDHGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374738.1	NM_018915		G	140719523	A	G	140719523	3	3	254	1	0	0	0	0	1	0	0	0	11563	43	2	2	987	2	PCDHGA2	5	140719523	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	371832	140719523	40195737	264	34556										
PCDHGA6	56109	hgsc.bcm.edu	37	chr5	140754660	140754660	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agcgaaagtcttaataactaTcttggatgtcaatgataatg	8	5	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:140754660T>C	ENST00000517434.1	+	1	1010	c.1010T>C	c.(1009-1011)aTc>aCc	p.I337T	PCDHGB2_ENST00000522605.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA4_ENST00000571252.1_Intron	NM_018919.2|NM_032086.1	NP_061742.1|NP_114475.1	Q9Y5G7	PCDG6_HUMAN	protocadherin gamma subfamily A, 6	337	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|large_intestine(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTAATAACTATCTTGGATGTC	0.443																																					p.I337T		Atlas-SNP	.											.	PCDHGA6	219	.	0			c.T1010C						.						149	156	154					5																	140754660		1912	4114	6026	SO:0001583	missense	56109	exon1			TAACTATCTTGGA	AF152513	CCDS54926.1, CCDS75335.1	5q31	2010-01-26				ENSG00000253731		"Cadherins / Protocadherins : Clustered"	8704	other	protocadherin		606293				10380929	Standard	NM_018919		Approved	PCDH-GAMMA-A6		Q9Y5G7		ENST00000517434.1:c.1010T>C	chr5.hg19:g.140754660T>C	ENSP00000429601:p.Ile337Thr	151.0	0.0		98.0	6.0	NM_018919	A6H8K7|B2RN55|Q9Y5D1	Missense_Mutation	SNP	ENST00000517434.1	hg19	CCDS54926.1	.	.	.	.	.	.	.	.	.	.	.	18.57	3.651515	0.67472	.	.	ENSG00000253731	ENST00000517434	T	0.58940	0.3	5.25	5.25	0.73442	Cadherin (5);Cadherin conserved site (1);Cadherin-like (1);	0.677552	0.11059	U	0.604160	T	0.74741	0.3756	M	0.81942	2.565	0.09310	N	1	P;P	0.45634	0.731;0.863	P;P	0.54590	0.462;0.756	T	0.67221	-0.5725	10	0.87932	D	0	.	15.6084	0.76692	0.0:0.0:0.0:1.0	.	337;337	Q9Y5G7-2;Q9Y5G7	.;PCDG6_HUMAN	T	337	ENSP00000429601:I337T	ENSP00000429601:I337T	I	+	2	0	PCDHGA6	140734844	0.237000	0.23815	0.984000	0.44739	0.976000	0.68499	3.360000	0.52299	2.326000	0.78906	0.533000	0.62120	ATC	.	.		0.443	PCDHGA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374743.1	NM_018919		C	140754660	T	C	140754660	3	2	254	1	0	0	0	0	1	0	0	0	11567	1435	50	2	1012	2	PCDHGA6	5	140754660	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	35137	140754660	40160600	265	34557										
PCDHGA7	56108	hgsc.bcm.edu	37	chr5	140762724	140762724	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cgcagcggcagcttggtcacTgcgggcaggatagaccggga	17	11	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:140762724T>C	ENST00000518325.1	+	1	258	c.258T>C	c.(256-258)acT>acC	p.T86T	PCDHGB2_ENST00000522605.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA6_ENST00000517434.1_Intron	NM_018920.2	NP_061743.1	Q9Y5G6	PCDG7_HUMAN	protocadherin gamma subfamily A, 7	86	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|biliary_tract(1)|endometrium(8)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|skin(1)|stomach(3)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCTTGGTCACTGCGGGCAGGA	0.577																																					p.T86T		Atlas-SNP	.											.	PCDHGA7	130	.	0			c.T258C						.						49	58	55					5																	140762724		2191	4296	6487	SO:0001819	synonymous_variant	56108	exon1			GGTCACTGCGGGC	AF152514	CCDS54927.1, CCDS75336.1	5q31	2010-01-26				ENSG00000253537		"Cadherins / Protocadherins : Clustered"	8705	other	protocadherin		606294				10380929	Standard	NM_018920		Approved	PCDH-GAMMA-A7		Q9Y5G6		ENST00000518325.1:c.258T>C	chr5.hg19:g.140762724T>C		160.0	0.0		97.0	4.0	NM_032087	B2RN87|Q9Y5D0	Silent	SNP	ENST00000518325.1	hg19	CCDS54927.1																																																																																			.	.		0.577	PCDHGA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374744.1	NM_018920		C	140762724	T	C	140762724	2	2	254	1	0	0	0	0	0	0	0	1	11568	1567	55	2		2	PCDHGA7	5	140762724	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	8064	140762724	40152536	266	34558										
PCDHGB4	8641	hgsc.bcm.edu	37	chr5	140768682	140768682	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cagatgctgttctagaccgcGagcagaatccagagtacaat	10	10	1	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:140768682G>T	ENST00000519479.1	+	1	1231	c.1231G>T	c.(1231-1233)Gag>Tag	p.E411*	PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron	NM_003736.2|NM_018925.2|NM_032098.1	NP_003727.1|NP_061748.1|NP_115269.1	Q9UN71	PCDGG_HUMAN	protocadherin gamma subfamily B, 4	411	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(9)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(2)	37			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTAGACCGCGAGCAGAATCC	0.433																																					p.E411X		Atlas-SNP	.											PCDHGB4,NS,carcinoma,0,1	PCDHGB4	125	.	0			c.G1231T						.						133	135	134					5																	140768682		1941	4139	6080	SO:0001587	stop_gained	8641	exon1			GACCGCGAGCAGA	AF152520	CCDS54928.1, CCDS75337.1	5q31	2010-01-26				ENSG00000253953		"Cadherins / Protocadherins : Clustered"	8711	other	protocadherin	"fibroblast cadherin FIB2", "cadherin 20"	603058				10380929	Standard	NM_003736		Approved	FIB2, CDH20, PCDH-GAMMA-B4		Q9UN71		ENST00000519479.1:c.1231G>T	chr5.hg19:g.140768682G>T	ENSP00000428288:p.Glu411*	92.0	0.0		83.0	4.0	NM_032098	O15099|Q2M267|Q9UN64	Nonsense_Mutation	SNP	ENST00000519479.1	hg19	CCDS54928.1	.	.	.	.	.	.	.	.	.	.	.	21.5	4.164694	0.78339	.	.	ENSG00000253953	ENST00000519479	.	.	.	5.14	4.27	0.50696	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	13.6028	0.62029	0.0758:0.0:0.9242:0.0	.	.	.	.	X	411	.	ENSP00000428288:E411X	E	+	1	0	PCDHGB4	140748866	1.000000	0.71417	0.024000	0.17045	0.048000	0.14542	9.706000	0.98722	1.304000	0.44892	0.650000	0.86243	GAG	.	.		0.433	PCDHGB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374745.1	NM_003736		T	140768682	G	T	140768682	4	4	254	1	0	0	0	0	0	1	0	0	11574	1059	37	1	1233	1	PCDHGB4	5	140768682	Nonsense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	5958	140768682	40146578	267	34559										
PCDHGB4	8641	hgsc.bcm.edu	37	chr5	140769224	140769224	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttggtgaccaaggtagtggcGgtggacgcagactcaggaca	16	8	1	2	rs372714152	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:140769224G>T	ENST00000519479.1	+	1	1773	c.1773G>T	c.(1771-1773)gcG>gcT	p.A591A	PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron	NM_003736.2|NM_018925.2|NM_032098.1	NP_003727.1|NP_061748.1|NP_115269.1	Q9UN71	PCDGG_HUMAN	protocadherin gamma subfamily B, 4	591	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(9)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(2)	37			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGTAGTGGCGGTGGACGCAG	0.672																																					p.A591A		Atlas-SNP	.											PCDHGB4,colon,carcinoma,0,1	PCDHGB4	125	.	0			c.G1773T						.						40	47	45					5																	140769224		2189	4291	6480	SO:0001819	synonymous_variant	8641	exon1			AGTGGCGGTGGAC	AF152520	CCDS54928.1, CCDS75337.1	5q31	2010-01-26				ENSG00000253953		"Cadherins / Protocadherins : Clustered"	8711	other	protocadherin	"fibroblast cadherin FIB2", "cadherin 20"	603058				10380929	Standard	NM_003736		Approved	FIB2, CDH20, PCDH-GAMMA-B4		Q9UN71		ENST00000519479.1:c.1773G>T	chr5.hg19:g.140769224G>T		81.0	0.0		63.0	3.0	NM_032098	O15099|Q2M267|Q9UN64	Silent	SNP	ENST00000519479.1	hg19	CCDS54928.1																																																																																			.	.		0.672	PCDHGB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374745.1	NM_003736		T	140769224	G	T	140769224	2	4	254	1	0	0	0	0	0	0	0	1	11574	1103	39	1		1	PCDHGB4	5	140769224	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	542	140769224	40146036	268	34560										
DIAPH1	1729	hgsc.bcm.edu	37	chr5	140953135	140953135	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttaatccaaatggcagaactGgggctgcaggaactccaaat	10	9	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:140953135G>T	ENST00000398557.4	-	16	2422	c.2282C>A	c.(2281-2283)cCa>cAa	p.P761Q	DIAPH1_ENST00000389057.5_Missense_Mutation_p.P752Q|DIAPH1_ENST00000389054.3_Missense_Mutation_p.P761Q|DIAPH1_ENST00000518047.1_Missense_Mutation_p.P752Q|DIAPH1_ENST00000253811.6_Missense_Mutation_p.P761Q|DIAPH1_ENST00000398566.3_Missense_Mutation_p.P752Q|DIAPH1_ENST00000398562.2_Missense_Mutation_p.P740Q|DIAPH1_ENST00000520569.1_Missense_Mutation_p.P707Q	NM_005219.4	NP_005210.3	O60610	DIAP1_HUMAN	diaphanous-related formin 1	761	FH1.				actin filament polymerization (GO:0030041)|cellular response to histamine (GO:0071420)|cytoskeleton organization (GO:0007010)|positive regulation of cell migration (GO:0030335)|protein localization to microtubule (GO:0035372)|regulation of cell shape (GO:0008360)|regulation of microtubule-based process (GO:0032886)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|mitotic spindle (GO:0072686)|ruffle membrane (GO:0032587)	ion channel binding (GO:0044325)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(12)|pancreas(1)|skin(2)|stomach(2)	23			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGCAGAACTGGGGCTGCAGG	0.542																																					p.P761Q		Atlas-SNP	.											.	DIAPH1	64	.	0			c.C2282A						.						50	54	53					5																	140953135		1849	4093	5942	SO:0001583	missense	1729	exon16			AGAACTGGGGCTG	BC007411		5q31	2013-05-24	2013-05-24		ENSG00000131504	ENSG00000131504			2876	protein-coding gene	gene with protein product		602121	"diaphanous (Drosophila, homolog) 1", "diaphanous homolog 1 (Drosophila)"	DFNA1		9360932, 1350680	Standard	NM_005219		Approved	hDIA1, LFHL1	uc003llb.4	O60610	OTTHUMG00000149893	ENST00000398557.4:c.2282C>A	chr5.hg19:g.140953135G>T	ENSP00000381565:p.Pro761Gln	133.0	0.0		94.0	5.0	NM_005219	A6NF18|B7ZKW2|E9PEZ2|Q17RN4|Q59FH8|Q9UC76	Missense_Mutation	SNP	ENST00000398557.4	hg19	CCDS43374.1	.	.	.	.	.	.	.	.	.	.	G	17.34	3.365931	0.61513	.	.	ENSG00000131504	ENST00000389054;ENST00000520569;ENST00000398562;ENST00000389057;ENST00000398566;ENST00000398557;ENST00000253811;ENST00000518047;ENST00000546094	T;T;T;T;T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17;-0.17;-0.17;-0.17;-0.17	4.65	4.65	0.58169	Actin-binding FH2 (1);Formin Homology 1 (1);	0.000000	0.64402	D	0.000007	T	0.77751	0.4177	M	0.75777	2.31	0.58432	D	0.999995	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.75830	-0.3179	10	0.29301	T	0.29	.	16.4522	0.83994	0.0:0.0:1.0:0.0	.	707;752;761	E7ERW8;E9PEZ2;O60610	.;.;DIAP1_HUMAN	Q	761;707;740;752;752;761;761;752;200	ENSP00000373706:P761Q;ENSP00000429282:P707Q;ENSP00000381570:P740Q;ENSP00000373709:P752Q;ENSP00000381572:P752Q;ENSP00000381565:P761Q;ENSP00000253811:P761Q;ENSP00000428268:P752Q	ENSP00000253811:P761Q	P	-	2	0	DIAPH1	140933319	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.136000	0.71703	2.418000	0.82041	0.591000	0.81541	CCA	.	.		0.542	DIAPH1-203	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_005219		T	140953135	G	T	140953135	3	4	254	1	0	0	0	0	1	0	0	0	4520	1348	47	3	1588	3	DIAPH1	5	140953135	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	183911	140953135	39962125	269	34561										
PDE6A	5145	hgsc.bcm.edu	37	chr5	149278051	149278051	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aggatttaagacagaccagcCcagaaattgagtcaaagact	9	8	1	5			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:149278051C>A	ENST00000255266.5	-	10	1401	c.1282G>T	c.(1282-1284)Ggc>Tgc	p.G428C		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	428	GAF 2.				cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	44			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Caffeine(DB00201)	ACAGACCAGCCCAGAAATTGA	0.358																																					p.G428C		Atlas-SNP	.											.	PDE6A	98	.	0			c.G1282T						.						65	64	65					5																	149278051		2203	4300	6503	SO:0001583	missense	5145	exon10			ACCAGCCCAGAAA		CCDS4299.1	5q31.2-q34	2013-02-14			ENSG00000132915	ENSG00000132915	3.1.4.17	"Phosphodiesterases"	8785	protein-coding gene	gene with protein product		180071		PDEA		2155175	Standard	NM_000440		Approved	RP43	uc003lrg.4	P16499	OTTHUMG00000130047	ENST00000255266.5:c.1282G>T	chr5.hg19:g.149278051C>A	ENSP00000255266:p.Gly428Cys	52.0	0.0		57.0	4.0	NM_000440	Q0P638	Missense_Mutation	SNP	ENST00000255266.5	hg19	CCDS4299.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.205999	0.79127	.	.	ENSG00000132915	ENST00000255266	T	0.70399	-0.48	5.74	4.87	0.63330	GAF (2);	0.000000	0.85682	D	0.000000	D	0.86867	0.6036	M	0.92268	3.29	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89634	0.3857	10	0.87932	D	0	.	12.7212	0.57144	0.0:0.9205:0.0:0.0795	.	428	P16499	PDE6A_HUMAN	C	428	ENSP00000255266:G428C	ENSP00000255266:G428C	G	-	1	0	PDE6A	149258244	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.427000	0.80284	1.574000	0.49760	0.561000	0.74099	GGC	.	.		0.358	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2			A	149278051	C	A	149278051	3	1	254	1	0	0	0	0	1	0	0	0	11654	623	22	3	1352	3	PDE6A	5	149278051	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	8324916	149278051	31637209	270	34562										
NDST1	3340	hgsc.bcm.edu	37	chr5	149927823	149927823	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agtggccctaaagtacacctTccatgaggtgattaccgccg	10	12	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:149927823T>C	ENST00000261797.6	+	12	2691	c.2189T>C	c.(2188-2190)tTc>tCc	p.F730S	NDST1_ENST00000523767.1_Intron	NM_001543.4	NP_001534.1	P52848	NDST1_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1	730	Heparan sulfate N-sulfotransferase 1.				carbohydrate metabolic process (GO:0005975)|embryonic neurocranium morphogenesis (GO:0048702)|embryonic viscerocranium morphogenesis (GO:0048703)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)|inflammatory response (GO:0006954)|MAPK cascade (GO:0000165)|midbrain development (GO:0030901)|polysaccharide biosynthetic process (GO:0000271)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)|smoothened signaling pathway (GO:0007224)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			breast(2)|central_nervous_system(3)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	34		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AAGTACACCTTCCATGAGGTG	0.617																																					p.F730S		Atlas-SNP	.											.	NDST1	79	.	0			c.T2189C						.						87	61	70					5																	149927823		2203	4300	6503	SO:0001583	missense	3340	exon12			ACACCTTCCATGA	U18918	CCDS34277.1, CCDS75358.1	5q33.1	2008-02-05				ENSG00000070614		"Sulfotransferases, membrane-bound"	7680	protein-coding gene	gene with protein product		600853		HSST		7601448, 9230113	Standard	NM_001543		Approved	NST1	uc003lsk.4	P52848		ENST00000261797.6:c.2189T>C	chr5.hg19:g.149927823T>C	ENSP00000261797:p.Phe730Ser	133.0	0.0		104.0	5.0	NM_001543	Q96E57	Missense_Mutation	SNP	ENST00000261797.6	hg19	CCDS34277.1	.	.	.	.	.	.	.	.	.	.	T	26.2	4.711708	0.89112	.	.	ENSG00000070614	ENST00000261797	T	0.58210	0.35	4.76	4.76	0.60689	Sulfotransferase domain (1);	0.043601	0.85682	D	0.000000	T	0.72244	0.3436	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75485	-0.3301	10	0.52906	T	0.07	.	14.6042	0.68466	0.0:0.0:0.0:1.0	.	730	P52848	NDST1_HUMAN	S	730	ENSP00000261797:F730S	ENSP00000261797:F730S	F	+	2	0	NDST1	149908016	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.989000	0.88205	1.909000	0.55274	0.533000	0.62120	TTC	.	.		0.617	NDST1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374314.2	NM_001543		C	149927823	T	C	149927823	3	2	254	1	0	0	0	0	1	0	0	0	10264	1783	62	2	2231	2	NDST1	5	149927823	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	649772	149927823	30987437	271	34563										
TIMD4	91937	hgsc.bcm.edu	37	chr5	156349214	156349214	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tttcattcttcattgacatgGgtattccatccatctgatgg	7	9	4	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:156349214G>T	ENST00000274532.2	-	7	964	c.908C>A	c.(907-909)cCc>cAc	p.P303H	TIMD4_ENST00000406964.1_Missense_Mutation_p.P5H|TIMD4_ENST00000407087.3_Missense_Mutation_p.P275H	NM_138379.2	NP_612388.2	Q96H15	TIMD4_HUMAN	T-cell immunoglobulin and mucin domain containing 4	303						integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(23)|ovary(2)|skin(2)	37	Renal(175;0.00488)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CATTGACATGGGTATTCCATC	0.502																																					p.P303H		Atlas-SNP	.											.	TIMD4	94	.	0			c.C908A						.						191	172	178					5																	156349214		2203	4300	6503	SO:0001583	missense	91937	exon7			GACATGGGTATTC	BC008988	CCDS4332.1, CCDS54943.1	5q33.3	2013-01-11			ENSG00000145850	ENSG00000145850		"Immunoglobulin superfamily / V-set domain containing"	25132	protein-coding gene	gene with protein product		610096				12477932	Standard	NM_001146726		Approved		uc003lwh.2	Q96H15	OTTHUMG00000130244	ENST00000274532.2:c.908C>A	chr5.hg19:g.156349214G>T	ENSP00000274532:p.Pro303His	125.0	0.0		82.0	5.0	NM_138379	B5MCL9	Missense_Mutation	SNP	ENST00000274532.2	hg19	CCDS4332.1	.	.	.	.	.	.	.	.	.	.	G	9.327	1.059540	0.19987	.	.	ENSG00000145850	ENST00000274532;ENST00000406964;ENST00000407087	T;T;T	0.70631	-0.5;-0.5;-0.5	1.27	-1.17	0.09648	.	24.147000	0.00807	U	0.001463	T	0.66963	0.2843	N	0.19112	0.55	0.09310	N	1	D;D	0.67145	0.996;0.996	P;P	0.56823	0.807;0.807	T	0.55347	-0.8155	10	0.59425	D	0.04	.	3.8138	0.08808	0.5788:0.0:0.4212:0.0	.	275;303	B5MCL9;Q96H15	.;TIMD4_HUMAN	H	303;5;275	ENSP00000274532:P303H;ENSP00000385882:P5H;ENSP00000385973:P275H	ENSP00000274532:P303H	P	-	2	0	TIMD4	156281792	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.761000	0.04751	-0.270000	0.09285	-0.266000	0.10368	CCC	.	.		0.502	TIMD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252568.1	NM_138379		T	156349214	G	T	156349214	3	4	254	1	0	0	0	0	1	0	0	0	15918	1232	43	3	240	3	TIMD4	5	156349214	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	6421391	156349214	24566046	272	34564										
GABRA1	2554	hgsc.bcm.edu	37	chr5	161300201	161300201	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aaggacctatgacagtcctcCggttaaataacctaatggca	8	10	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:161300201C>A	ENST00000428797.2	+	6	689	c.334C>A	c.(334-336)Cgg>Agg	p.R112R	GABRA1_ENST00000023897.6_Silent_p.R112R|GABRA1_ENST00000444819.1_Silent_p.R112R|GABRA1_ENST00000437025.2_Silent_p.R112R|GABRA1_ENST00000420560.1_Silent_p.R112R|GABRA1_ENST00000393943.4_Silent_p.R112R	NM_001127643.1	NP_001121115.1	P14867	GBRA1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 1	112			R -> Q (in EIEE19). {ECO:0000269|PubMed:24623842}.		gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|drug binding (GO:0008144)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|endometrium(2)|kidney(3)|large_intestine(4)|liver(1)|lung(22)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(1)	42	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.228)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethanol(DB00898)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methohexital(DB00474)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Prazepam(DB01588)|Primidone(DB00794)|Progabide(DB00837)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiamylal(DB01154)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zaleplon(DB00962)|Zolpidem(DB00425)|Zopiclone(DB01198)	GACAGTCCTCCGGTTAAATAA	0.388																																					p.R112R		Atlas-SNP	.											.	GABRA1	132	.	0			c.C334A						.						80	82	81					5																	161300201		2203	4300	6503	SO:0001819	synonymous_variant	2554	exon6			GTCCTCCGGTTAA		CCDS4357.1	5q34	2012-06-22			ENSG00000022355	ENSG00000022355		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4075	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 1"	137160				1330891	Standard	NM_000806		Approved	EJM5	uc003lyx.4	P14867	OTTHUMG00000163586	ENST00000428797.2:c.334C>A	chr5.hg19:g.161300201C>A		167.0	0.0		133.0	42.0	NM_001127643	D3DQK6|Q8N629	Silent	SNP	ENST00000428797.2	hg19	CCDS4357.1																																																																																			.	.		0.388	GABRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252702.2	NM_000806.5		A	161300201	C	A	161300201	2	1	254	1	0	0	0	0	0	0	0	1	6168	643	23	1		1	GABRA1	5	161300201	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	4950987	161300201	19615059	273	34565										
ODZ2	57451	hgsc.bcm.edu	37	chr5	167675305	167675305	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cgtgggcaaggagccggcccCctttaacctgtatatgttca	11	12	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:167675305C>T	ENST00000518659.1	+	27	7400	c.7361C>T	c.(7360-7362)cCc>cTc	p.P2454L	TENM2_ENST00000519204.1_Missense_Mutation_p.P2333L|TENM2_ENST00000545108.1_Missense_Mutation_p.P2453L|TENM2_ENST00000403607.2_Missense_Mutation_p.P2278L|TENM2_ENST00000520394.1_Missense_Mutation_p.P2215L	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	2454					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										GAGCCGGCCCCCTTTAACCTG	0.512																																					p.P2445L		Atlas-SNP	.											.	.	.	.	0			c.C7334T						.						60	61	60					5																	167675305		1934	4131	6065	SO:0001583	missense	57451	exon27			CGGCCCCCTTTAA	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"odz, odd Oz/ten-m homolog 2 (Drosophila)"	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.7361C>T	chr5.hg19:g.167675305C>T	ENSP00000429430:p.Pro2454Leu	144.0	0.0		98.0	4.0	NM_001122679	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	hg19		.	.	.	.	.	.	.	.	.	.	C	20.3	3.974209	0.74246	.	.	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	D;D;D;D;D	0.89875	-2.11;-2.1;-2.21;-2.55;-2.58	4.95	4.95	0.65309	Rhs repeat-associated core (1);	0.000000	0.85682	D	0.000000	D	0.95611	0.8573	M	0.90595	3.13	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.996	D	0.96330	0.9243	10	0.72032	D	0.01	.	18.6074	0.91271	0.0:1.0:0.0:0.0	.	2453;2454;2215	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	L	2454;2453;2333;2215;2278	ENSP00000429430:P2454L;ENSP00000438635:P2453L;ENSP00000428964:P2333L;ENSP00000427874:P2215L;ENSP00000384905:P2278L	ENSP00000384905:P2278L	P	+	2	0	ODZ2	167607883	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.773000	0.85462	2.475000	0.83589	0.556000	0.70494	CCC	.	.		0.512	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		T	167675305	C	T	167675305	3	4	254	1	0	0	0	0	1	0	0	0	10844	623	22	3	7440	3	ODZ2	5	167675305	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	6375104	167675305	13239955	274	34566										
ODZ2	57451	hgsc.bcm.edu	37	chr5	167689229	167689229	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtttgccatcaaagaagggcGggtgaccacgggcgtgtcca	15	10	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:167689229G>T	ENST00000518659.1	+	29	7778	c.7739G>T	c.(7738-7740)cGg>cTg	p.R2580L	TENM2_ENST00000519204.1_Missense_Mutation_p.R2459L|TENM2_ENST00000545108.1_Missense_Mutation_p.R2579L|TENM2_ENST00000403607.2_Missense_Mutation_p.R2404L|TENM2_ENST00000520394.1_Missense_Mutation_p.R2341L	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	2580					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										AAAGAAGGGCGGGTGACCACG	0.557																																					p.R2571L		Atlas-SNP	.											.	.	.	.	0			c.G7712T						.						29	33	32					5																	167689229		2034	4204	6238	SO:0001583	missense	57451	exon29			AAGGGCGGGTGAC	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"odz, odd Oz/ten-m homolog 2 (Drosophila)"	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.7739G>T	chr5.hg19:g.167689229G>T	ENSP00000429430:p.Arg2580Leu	115.0	0.0		89.0	6.0	NM_001122679	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	hg19		.	.	.	.	.	.	.	.	.	.	G	12.85	2.062122	0.36373	.	.	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	D;D;D;D;D	0.90197	-2.15;-2.14;-2.26;-2.61;-2.63	5.42	4.53	0.55603	.	0.108147	0.64402	D	0.000006	D	0.86422	0.5929	L	0.49126	1.545	0.35424	D	0.793446	B;B;P	0.35226	0.125;0.076;0.491	B;B;B	0.33521	0.165;0.079;0.092	D	0.88191	0.2877	10	0.48119	T	0.1	.	10.0276	0.42081	0.1599:0.0:0.8401:0.0	.	2579;2580;2341	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	L	2580;2579;2459;2341;2404	ENSP00000429430:R2580L;ENSP00000438635:R2579L;ENSP00000428964:R2459L;ENSP00000427874:R2341L;ENSP00000384905:R2404L	ENSP00000384905:R2404L	R	+	2	0	ODZ2	167621807	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.017000	0.64047	1.349000	0.45751	0.655000	0.94253	CGG	.	.		0.557	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		T	167689229	G	T	167689229	3	4	254	1	0	0	0	0	1	0	0	0	10844	1116	39	1	7826	1	ODZ2	5	167689229	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	13924	167689229	13226031	275	34567										
CDHR2	54825	hgsc.bcm.edu	37	chr5	175995734	175995734	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gacaatgaccctctgacctaTgggatgagcggccccaatgc	11	13	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:175995734T>C	ENST00000510636.1	+	4	454	c.180T>C	c.(178-180)taT>taC	p.Y60Y	CDHR2_ENST00000261944.5_Silent_p.Y60Y|CDHR2_ENST00000506348.1_Silent_p.Y60Y	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	60	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|liver(1)|lung(23)|ovary(3)|prostate(5)|skin(4)|urinary_tract(1)	56						CTCTGACCTATGGGATGAGCG	0.602																																					p.Y60Y		Atlas-SNP	.											.	CDHR2	152	.	0			c.T180C						.						109	102	104					5																	175995734		2203	4300	6503	SO:0001819	synonymous_variant	54825	exon4			GACCTATGGGATG	AB047004	CCDS34297.1	5q35.2	2011-07-01	2010-01-25	2010-01-25		ENSG00000074276		"Cadherins / Cadherin-related"	18231	protein-coding gene	gene with protein product	"protocadherin LKC"		"protocadherin 24"	PCDH24		11082270, 12117771	Standard	NM_001171976		Approved	PC-LKC, FLJ20124, FLJ20383, PCLKC	uc003mem.2	Q9BYE9		ENST00000510636.1:c.180T>C	chr5.hg19:g.175995734T>C		121.0	0.0		98.0	4.0	NM_017675	A1L3U4|A6NC80|Q9NXP8	Silent	SNP	ENST00000510636.1	hg19	CCDS34297.1																																																																																			.	.		0.602	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675		C	175995734	T	C	175995734	2	2	254	1	0	0	0	0	0	0	0	1	3121	1471	51	2		2	CDHR2	5	175995734	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	8306505	175995734	4919526	276	34568										
UIMC1	51720	hgsc.bcm.edu	37	chr5	176396709	176396709	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	catcagaaggccggcaactcTgaaacaagtgatcccatacc	8	13	2	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:176396709T>C	ENST00000377227.4	-	5	490		c.e5-2		UIMC1_ENST00000511320.1_Splice_Site|UIMC1_ENST00000506128.1_Splice_Site|UIMC1_ENST00000377219.2_Splice_Site|UIMC1_ENST00000503273.1_5'Flank			Q96RL1	UIMC1_HUMAN	ubiquitin interaction motif containing 1						double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|histone H2A K63-linked deubiquitination (GO:0070537)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of DNA repair (GO:0045739)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)	BRCA1-A complex (GO:0070531)|nucleus (GO:0005634)	histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)			NS(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(5)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	21	all_cancers(89;7.96e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	Medulloblastoma(196;0.0145)|all_neural(177;0.0325)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCGGCAACTCTGAAACAAGTG	0.483																																					.		Atlas-SNP	.											.	UIMC1	55	.	0			c.358-2A>G						.						86	83	84					5																	176396709		2203	4300	6503	SO:0001630	splice_region_variant	51720	exon6			CAACTCTGAAACA	AF349313	CCDS4408.1	5q35.2	2008-02-05			ENSG00000087206	ENSG00000087206			30298	protein-coding gene	gene with protein product	"receptor associated protein 80"	609433				12080054	Standard	NM_001199297		Approved	RAP80	uc021yin.1	Q96RL1	OTTHUMG00000130852	ENST00000377227.4:c.358-2A>G	chr5.hg19:g.176396709T>C		107.0	0.0		89.0	4.0	NM_016290	A8MSA1|B3KMZ1|B4E3N2|Q5XKQ1|Q7Z3W7|Q8N5B9|Q9BZR1|Q9BZR5|Q9UHX7	Splice_Site	SNP	ENST00000377227.4	hg19	CCDS4408.1	.	.	.	.	.	.	.	.	.	.	T	16.71	3.199603	0.58126	.	.	ENSG00000087206	ENST00000377227;ENST00000377219;ENST00000511320;ENST00000506128;ENST00000377220;ENST00000509236	.	.	.	5.83	5.83	0.93111	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7632	0.69619	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	UIMC1	176329315	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.803000	0.62546	2.226000	0.72624	0.459000	0.35465	.	.	.		0.483	UIMC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253422.1	NM_016290	Intron	C	176396709	T	C	176396709	5	2	254	1	0	0	0	0	0	0	1	0	16986	1594	55	2	1847	2	UIMC1	5	176396709	Splice_Site	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	400975	176396709	4518551	277	34569										
ZNF346	23567	hgsc.bcm.edu	37	chr5	176477805	176477805	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	acaagttctgcagcctctgcCatgcaactttcaacgaccct	6	15	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:176477805C>T	ENST00000358149.3	+	5	614	c.571C>T	c.(571-573)Cat>Tat	p.H191Y	ZNF346_ENST00000506693.1_Missense_Mutation_p.H93Y|ZNF346_ENST00000503039.1_Missense_Mutation_p.H216Y|ZNF346_ENST00000261948.4_Missense_Mutation_p.H216Y|ZNF346_ENST00000503425.1_Missense_Mutation_p.H159Y|ZNF346_ENST00000512315.1_Intron|ZNF346-IT1_ENST00000515264.1_RNA|ZNF346_ENST00000511834.1_Missense_Mutation_p.H207Y	NM_012279.2	NP_036411.1	Q9UL40	ZN346_HUMAN	zinc finger protein 346	191					positive regulation of apoptotic process (GO:0043065)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|prostate(1)|urinary_tract(1)	14	all_cancers(89;6.3e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CAGCCTCTGCCATGCAACTTT	0.483																																					p.H191Y		Atlas-SNP	.											.	ZNF346	24	.	0			c.C571T						.						119	110	113					5																	176477805		2203	4300	6503	SO:0001583	missense	23567	exon5			CTCTGCCATGCAA	AF083340	CCDS4409.1	5q35.3	2012-10-05			ENSG00000113761	ENSG00000113761			16403	protein-coding gene	gene with protein product		605308				10488071	Standard	NM_012279		Approved	JAZ, Zfp346	uc003mfi.3	Q9UL40	OTTHUMG00000130848	ENST00000358149.3:c.571C>T	chr5.hg19:g.176477805C>T	ENSP00000350869:p.His191Tyr	129.0	0.0		71.0	4.0	NM_012279	B7Z367|Q68CV9|Q6ZMW1	Missense_Mutation	SNP	ENST00000358149.3	hg19	CCDS4409.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.461267	0.84317	.	.	ENSG00000113761	ENST00000358149;ENST00000506693;ENST00000503425;ENST00000261948;ENST00000511834;ENST00000503039	T;T;T;T;T;T	0.22134	1.97;1.97;1.97;1.97;1.97;1.97	5.47	4.59	0.56863	Zinc finger, C2H2-like (1);Zinc finger, U1-type (1);Zinc finger, C2H2 (1);	0.261330	0.45606	D	0.000360	T	0.38401	0.1039	L	0.54323	1.7	0.38262	D	0.941917	P;P;D;P	0.62365	0.945;0.954;0.991;0.953	P;P;P;P	0.59221	0.74;0.816;0.854;0.768	T	0.42699	-0.9436	10	0.72032	D	0.01	.	16.2029	0.82102	0.0:0.8666:0.1334:0.0	.	93;159;216;191	B7Z4J8;B7Z367;Q9UL40-2;Q9UL40	.;.;.;ZN346_HUMAN	Y	191;93;159;216;207;216	ENSP00000350869:H191Y;ENSP00000423515:H93Y;ENSP00000421212:H159Y;ENSP00000261948:H216Y;ENSP00000425725:H207Y;ENSP00000424495:H216Y	ENSP00000261948:H216Y	H	+	1	0	ZNF346	176410411	1.000000	0.71417	0.913000	0.36048	0.952000	0.60782	5.175000	0.65021	1.266000	0.44231	0.655000	0.94253	CAT	.	.		0.483	ZNF346-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253415.2	NM_012279		T	176477805	C	T	176477805	3	4	254	1	0	0	0	0	1	0	0	0	17875	594	21	3	589	3	ZNF346	5	176477805	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	81096	176477805	4437455	278	34570										
FGFR4	2264	hgsc.bcm.edu	37	chr5	176523334	176523334	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcccgaggccttgtttgaccGggtgtacacacaccagagtg	13	12	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:176523334G>T	ENST00000292408.4	+	15	2236	c.1991G>T	c.(1990-1992)cGg>cTg	p.R664L	FGFR4_ENST00000292410.3_Missense_Mutation_p.R624L|FGFR4_ENST00000393648.2_Missense_Mutation_p.R596L|FGFR4_ENST00000393637.1_Missense_Mutation_p.R624L|FGFR4_ENST00000502906.1_Missense_Mutation_p.R664L	NM_002011.3|NM_213647.1	NP_002002.3|NP_998812.1	P22455	FGFR4_HUMAN	fibroblast growth factor receptor 4	664	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				alveolar secondary septum development (GO:0061144)|cell migration (GO:0016477)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphate ion homeostasis (GO:0055062)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of proteolysis (GO:0045862)|protein autophosphorylation (GO:0046777)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cholesterol homeostasis (GO:2000188)|regulation of extracellular matrix disassembly (GO:0010715)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	34	all_cancers(89;5.93e-05)|Renal(175;0.000269)|Lung NSC(126;0.0088)|all_lung(126;0.0142)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Palifermin(DB00039)|Ponatinib(DB08901)	TTGTTTGACCGGGTGTACACA	0.642										TSP Lung(9;0.080)																											p.R664L		Atlas-SNP	.											FGFR4_ENST00000292408,colon,carcinoma,0,2	FGFR4	174	.	0			c.G1991T						.						81	79	80					5																	176523334		2203	4300	6503	SO:0001583	missense	2264	exon15			TTGACCGGGTGTA	AF202063	CCDS4410.1, CCDS4411.1	5q35.2	2013-09-19			ENSG00000160867	ENSG00000160867		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3691	protein-coding gene	gene with protein product		134935					Standard	XM_005265837		Approved	JTK2, CD334	uc003mfm.3	P22455	OTTHUMG00000151523	ENST00000292408.4:c.1991G>T	chr5.hg19:g.176523334G>T	ENSP00000292408:p.Arg664Leu	127.0	0.0		75.0	3.0	NM_002011	G3JVM2|G3JVM5|G3JVM7|G3JVM9|O43785|Q14309|Q71TW8|Q8TDA0|Q96KE5	Missense_Mutation	SNP	ENST00000292408.4	hg19	CCDS4410.1	.	.	.	.	.	.	.	.	.	.	g	29.8	5.033067	0.93575	.	.	ENSG00000160867	ENST00000292408;ENST00000393648;ENST00000502906;ENST00000292410;ENST00000393637;ENST00000377207	D;D;D;D;D	0.82526	-1.62;-1.62;-1.62;-1.62;-1.62	4.65	4.65	0.58169	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.87370	0.6160	L	0.37800	1.135	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	D	0.89220	0.3570	10	0.87932	D	0	.	17.1688	0.86824	0.0:0.0:1.0:0.0	.	596;624;664	B4DVP5;P22455-2;P22455	.;.;FGFR4_HUMAN	L	664;596;664;624;624;892	ENSP00000292408:R664L;ENSP00000377259:R596L;ENSP00000424960:R664L;ENSP00000292410:R624L;ENSP00000377254:R624L	ENSP00000292408:R664L	R	+	2	0	FGFR4	176455940	1.000000	0.71417	0.988000	0.46212	0.843000	0.47879	9.866000	0.99616	2.142000	0.66516	0.556000	0.70494	CGG	.	.		0.642	FGFR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253410.1			T	176523334	G	T	176523334	3	4	254	1	0	0	0	0	1	0	0	0	5876	1116	39	1	2115	1	FGFR4	5	176523334	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	45529	176523334	4391926	279	34571										
NSD1	64324	hgsc.bcm.edu	37	chr5	176722236	176722236	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agttggtaaccacagagcaaAgtccctgggccctgggaaaa	12	10	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:176722236A>C	ENST00000439151.2	+	23	7912	c.7867A>C	c.(7867-7869)Agt>Cgt	p.S2623R	NSD1_ENST00000347982.4_Missense_Mutation_p.S2354R|NSD1_ENST00000361032.4_Missense_Mutation_p.S2520R|NSD1_ENST00000354179.4_Missense_Mutation_p.S2354R	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	2623					gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		CACAGAGCAAAGTCCCTGGGC	0.587			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.S2623R		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.A7867C						.						67	70	69					5																	176722236		2203	4300	6503	SO:0001583	missense	64324	exon23	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	GAGCAAAGTCCCT	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	14234	protein-coding gene	gene with protein product		606681	"Sotos syndrome"	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.7867A>C	chr5.hg19:g.176722236A>C	ENSP00000395929:p.Ser2623Arg	151.0	0.0		110.0	39.0	NM_022455	Q96PD8|Q96RN7	Missense_Mutation	SNP	ENST00000439151.2	hg19	CCDS4412.1	.	.	.	.	.	.	.	.	.	.	A	11.83	1.756162	0.31137	.	.	ENSG00000165671	ENST00000354179;ENST00000439151;ENST00000347982;ENST00000361032	D;D;D;D	0.93604	-3.15;-3.15;-3.15;-3.25	4.71	3.54	0.40534	.	0.227351	0.31636	N	0.007312	D	0.86936	0.6053	N	0.19112	0.55	0.27574	N	0.949798	B;B	0.21905	0.062;0.037	B;B	0.26969	0.075;0.048	T	0.79820	-0.1642	10	0.42905	T	0.14	.	11.1301	0.48341	0.835:0.165:0.0:0.0	.	2354;2623	Q96L73-2;Q96L73	.;NSD1_HUMAN	R	2354;2623;2354;2520	ENSP00000346111:S2354R;ENSP00000395929:S2623R;ENSP00000343209:S2354R;ENSP00000354310:S2520R	ENSP00000343209:S2354R	S	+	1	0	NSD1	176654842	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	2.691000	0.47010	1.980000	0.57719	0.379000	0.24179	AGT	.	.		0.587	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349		C	176722236	A	C	176722236	3	2	254	1	0	0	0	0	1	0	0	0	10678	72	3	5	7953	5	NSD1	5	176722236	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	198902	176722236	4193024	280	34572										
NSD1	64324	hgsc.bcm.edu	37	chr5	176722361	176722361	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttggcacagacttgctggtcTcttggaagagggcaagaccc	13	10	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:176722361T>C	ENST00000439151.2	+	23	8037	c.7992T>C	c.(7990-7992)tcT>tcC	p.S2664S	NSD1_ENST00000347982.4_Silent_p.S2395S|NSD1_ENST00000361032.4_Silent_p.S2561S|NSD1_ENST00000354179.4_Silent_p.S2395S	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	2664					gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		CTTGCTGGTCTCTTGGAAGAG	0.537			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.S2664S		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.T7992C						.						67	71	70					5																	176722361		2203	4300	6503	SO:0001819	synonymous_variant	64324	exon23	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	CTGGTCTCTTGGA	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	14234	protein-coding gene	gene with protein product		606681	"Sotos syndrome"	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.7992T>C	chr5.hg19:g.176722361T>C		139.0	0.0		96.0	5.0	NM_022455	Q96PD8|Q96RN7	Silent	SNP	ENST00000439151.2	hg19	CCDS4412.1																																																																																			.	.		0.537	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349		C	176722361	T	C	176722361	2	2	254	1	0	0	0	0	0	0	0	1	10678	1538	54	2		2	NSD1	5	176722361	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	125	176722361	4192899	281	34573										
F12	2161	hgsc.bcm.edu	37	chr5	176833015	176833015	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	acatttgtggtacagctgccGgtggtactggaaggggaagt	16	6	0	0	rs201132135		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:176833015G>T	ENST00000253496.3	-	3	211	c.163C>A	c.(163-165)Cgg>Agg	p.R55R	F12_ENST00000514943.1_5'Flank	NM_000505.3	NP_000496.2	P00748	FA12_HUMAN	coagulation factor XII (Hageman factor)	55	Fibronectin type-II. {ECO:0000255|PROSITE-ProRule:PRU00478, ECO:0000255|PROSITE-ProRule:PRU00479}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|Factor XII activation (GO:0002542)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|plasma kallikrein-kinin cascade (GO:0002353)|positive regulation of blood coagulation (GO:0030194)|positive regulation of fibrinolysis (GO:0051919)|positive regulation of plasminogen activation (GO:0010756)|protein autoprocessing (GO:0016540)|protein processing (GO:0016485)|response to misfolded protein (GO:0051788)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	misfolded protein binding (GO:0051787)|serine-type aminopeptidase activity (GO:0070009)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	12	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Ethanolamine Oleate(DB06689)	TACAGCTGCCGGTGGTACTGG	0.607									Hereditary Angioedema																												p.R55R		Atlas-SNP	.											.	F12	35	.	0			c.C163A						.						93	96	95					5																	176833015		2203	4300	6503	SO:0001819	synonymous_variant	2161	exon3	Familial Cancer Database	HAE, type I-III, Hereditary Angioneurotic Edema, HANE,	GCTGCCGGTGGTA	M31315	CCDS34302.1	5q35.3	2014-09-17			ENSG00000131187	ENSG00000131187	3.4.21.38		3530	protein-coding gene	gene with protein product		610619					Standard	NM_000505		Approved		uc003mgo.4	P00748	OTTHUMG00000163403	ENST00000253496.3:c.163C>A	chr5.hg19:g.176833015G>T		127.0	0.0		87.0	4.0	NM_000505	P78339	Silent	SNP	ENST00000253496.3	hg19	CCDS34302.1																																																																																			.	.		0.607	F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373217.1			T	176833015	G	T	176833015	2	4	254	1	0	0	0	0	0	0	0	1	5341	1115	39	1		1	F12	5	176833015	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	110654	176833015	4082245	282	34574										
ZNF354C	30832	hgsc.bcm.edu	37	chr5	178506014	178506014	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	caatatgtattatacatttgGgaaagattttaaacagaatt	6	3	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:178506014G>T	ENST00000315475.6	+	5	887	c.581G>T	c.(580-582)gGg>gTg	p.G194V		NM_014594.1	NP_055409.1	Q86Y25	Z354C_HUMAN	zinc finger protein 354C	194					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|urinary_tract(3)	30	all_cancers(89;0.00065)|all_epithelial(37;0.000153)|Renal(175;0.000159)|Lung NSC(126;0.00175)|all_lung(126;0.00309)	all_cancers(40;0.19)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.247)		TATACATTTGGGAAAGATTTT	0.363																																					p.G194V		Atlas-SNP	.											.	ZNF354C	77	.	0			c.G581T						.						54	58	57					5																	178506014		2201	4299	6500	SO:0001583	missense	30832	exon5			CATTTGGGAAAGA		CCDS4443.1	5q35	2013-01-08			ENSG00000177932	ENSG00000177932		"Zinc fingers, C2H2-type", "-"	16736	protein-coding gene	gene with protein product						10786630	Standard	NM_014594		Approved	KID3	uc003mju.3	Q86Y25	OTTHUMG00000130888	ENST00000315475.6:c.581G>T	chr5.hg19:g.178506014G>T	ENSP00000324064:p.Gly194Val	71.0	0.0		70.0	5.0	NM_014594	Q6P4P9|Q8NFX1	Missense_Mutation	SNP	ENST00000315475.6	hg19	CCDS4443.1	.	.	.	.	.	.	.	.	.	.	G	15.14	2.743763	0.49151	.	.	ENSG00000177932	ENST00000315475	T	0.36520	1.25	3.94	1.59	0.23543	.	.	.	.	.	T	0.57417	0.2052	M	0.90870	3.155	0.53688	D	0.999975	D	0.63880	0.993	P	0.59012	0.85	T	0.58306	-0.7659	9	0.66056	D	0.02	-4.7609	6.9571	0.24578	0.2915:0.0:0.7085:0.0	.	194	Q86Y25	Z354C_HUMAN	V	194	ENSP00000324064:G194V	ENSP00000324064:G194V	G	+	2	0	ZNF354C	178438620	1.000000	0.71417	0.004000	0.12327	0.011000	0.07611	3.680000	0.54641	0.202000	0.20498	-0.229000	0.12294	GGG	.	.		0.363	ZNF354C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253473.2			T	178506014	G	T	178506014	3	4	254	1	0	0	0	0	1	0	0	0	17881	1232	43	3	595	3	ZNF354C	5	178506014	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1672999	178506014	2409246	283	34575										
MGAT1	4245	hgsc.bcm.edu	37	chr5	180219412	180219412	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccagcgcccagcggtagtggCgcgcgatcttgtagtagccc	14	14	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:180219412C>A	ENST00000446023.2	-	3	1310	c.560G>T	c.(559-561)cGc>cTc	p.R187L	MGAT1_ENST00000307826.4_Missense_Mutation_p.R187L|MGAT1_ENST00000427865.2_Missense_Mutation_p.R187L|MGAT1_ENST00000393340.3_Missense_Mutation_p.R187L|MGAT1_ENST00000333055.3_Missense_Mutation_p.R187L	NM_001114617.1|NM_001114618.1	NP_001108089.1|NP_001108090.1	P26572	MGAT1_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,2-N-acetylglucosaminyltransferase	187					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine catabolic process (GO:0006049)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982)	acetylglucosaminyltransferase activity (GO:0008375)|alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity (GO:0003827)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	13	all_cancers(89;1.11e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.0027)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00356)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCGGTAGTGGCGCGCGATCTT	0.682																																					p.R187L		Atlas-SNP	.											.	MGAT1	48	.	0			c.G560T						.						39	46	44					5																	180219412		2201	4296	6497	SO:0001583	missense	4245	exon3			TAGTGGCGCGCGA	M61829	CCDS4458.1	5q35.3	2013-02-25			ENSG00000131446	ENSG00000131446	2.4.1.101	"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	7044	protein-coding gene	gene with protein product		160995		MGAT, GLYT1		1827260	Standard	NM_002406		Approved	GNT-1, GLCNAC-TI	uc003mmg.4	P26572	OTTHUMG00000130937	ENST00000446023.2:c.560G>T	chr5.hg19:g.180219412C>A	ENSP00000404718:p.Arg187Leu	110.0	0.0		91.0	30.0	NM_001114617	A8K404|B3KRU8|D3DWR1|Q6IBE3	Missense_Mutation	SNP	ENST00000446023.2	hg19	CCDS4458.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.640519	0.87859	.	.	ENSG00000131446	ENST00000333055;ENST00000307826;ENST00000446023;ENST00000393340;ENST00000427865;ENST00000504671	D;D;D;D;D;D	0.88586	-2.4;-2.4;-2.4;-2.4;-2.4;-2.4	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	D	0.94182	0.8133	M	0.77820	2.39	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.94464	0.7679	10	0.87932	D	0	-28.1319	16.3966	0.83607	0.0:1.0:0.0:0.0	.	187	P26572	MGAT1_HUMAN	L	187	ENSP00000332073:R187L;ENSP00000311888:R187L;ENSP00000404718:R187L;ENSP00000377010:R187L;ENSP00000402838:R187L;ENSP00000424891:R187L	ENSP00000311888:R187L	R	-	2	0	MGAT1	180152018	0.815000	0.29118	0.614000	0.29051	0.849000	0.48306	6.801000	0.75170	2.811000	0.96726	0.655000	0.94253	CGC	.	.		0.682	MGAT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368189.1	NM_001114618		A	180219412	C	A	180219412	3	1	254	1	0	0	0	0	1	0	0	0	9551	768	27	1	781	1	MGAT1	5	180219412	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1713398	180219412	695848	284	34576										
TRIM41	90933	hgsc.bcm.edu	37	chr5	180651055	180651055	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gacccttcaggaggaggcggTgtgcgccatctgcctcgatt	14	12	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:180651055T>C	ENST00000315073.5	+	1	766	c.56T>C	c.(55-57)gTg>gCg	p.V19A	CTC-338M12.7_ENST00000499096.2_RNA|MIR4638_ENST00000581158.1_RNA|TRIM41_ENST00000351937.5_Missense_Mutation_p.V19A	NM_033549.4	NP_291027.3	Q8WV44	TRI41_HUMAN	tripartite motif containing 41	19					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(3)|prostate(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	26	all_cancers(89;9.17e-06)|all_epithelial(37;1.19e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0684)	all_cancers(40;0.000209)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GAGGAGGCGGTGTGCGCCATC	0.617																																					p.V19A		Atlas-SNP	.											.	TRIM41	96	.	0			c.T56C						.						55	47	50					5																	180651055		2203	4300	6503	SO:0001583	missense	90933	exon1			AGGCGGTGTGCGC	AF258579	CCDS4465.1, CCDS4466.1	5q35.3	2013-01-09	2011-01-25		ENSG00000146063	ENSG00000146063		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19013	protein-coding gene	gene with protein product	"RING-finger protein that interacts with C kinase"	610530	"tripartite motif-containing 41"			16022281	Standard	NM_033549		Approved	MGC1127, RINCK	uc003mne.2	Q8WV44	OTTHUMG00000130965	ENST00000315073.5:c.56T>C	chr5.hg19:g.180651055T>C	ENSP00000320869:p.Val19Ala	115.0	0.0		100.0	4.0	NM_201627	B3KNJ6|D3DWR9|Q5BKT0|Q7L484|Q96Q10|Q9BSL8	Missense_Mutation	SNP	ENST00000315073.5	hg19	CCDS4466.1	.	.	.	.	.	.	.	.	.	.	T	17.80	3.478351	0.63849	.	.	ENSG00000146063	ENST00000351937;ENST00000315073;ENST00000421508	D;D	0.83673	-1.75;-1.75	4.65	4.65	0.58169	Zinc finger, RING/FYVE/PHD-type (1);	0.181068	0.26442	N	0.024350	T	0.72374	0.3452	N	0.11892	0.195	0.28931	N	0.891565	P;P;P	0.49783	0.779;0.859;0.928	B;P;P	0.47573	0.348;0.55;0.55	T	0.69537	-0.5119	10	0.56958	D	0.05	.	8.4849	0.33065	0.0:0.0:0.1968:0.8032	.	19;19;19	Q8WV44;Q8WV44-2;Q8WV44-4	TRI41_HUMAN;.;.	A	19;19;6	ENSP00000336749:V19A;ENSP00000320869:V19A	ENSP00000320869:V19A	V	+	2	0	TRIM41	180583661	0.970000	0.33590	1.000000	0.80357	0.975000	0.68041	1.108000	0.31123	1.720000	0.51447	0.260000	0.18958	GTG	.	.		0.617	TRIM41-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253574.3	NM_201627		C	180651055	T	C	180651055	3	2	254	1	0	0	0	0	1	0	0	0	16531	1696	59	2	58	2	TRIM41	5	180651055	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	431643	180651055	264205	285	34577										
GNB2L1	10399	hgsc.bcm.edu	37	chr5	180668513	180668513	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tggacagtgtatttgcacacAcccagggtattccatagctt	9	10	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr5:180668513A>G	ENST00000512805.1	-	3	816	c.408T>C	c.(406-408)ggT>ggC	p.G136G	GNB2L1_ENST00000511566.1_Silent_p.G136G|GNB2L1_ENST00000456394.2_Silent_p.G136G|GNB2L1_ENST00000376817.4_Silent_p.G92G|SNORD96A_ENST00000606577.1_RNA|GNB2L1_ENST00000504726.1_Intron|GNB2L1_ENST00000505461.1_5'UTR|GNB2L1_ENST00000511900.1_Intron|SNORD95_ENST00000579879.1_RNA|GNB2L1_ENST00000514455.1_5'Flank	NM_006098.4	NP_006089.1	P63244	GBLP_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 2-like 1	136					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cell cycle (GO:0007049)|gastrulation (GO:0007369)|negative regulation of cell growth (GO:0030308)|negative regulation of gene expression (GO:0010629)|negative regulation of hydrogen peroxide-induced neuron death (GO:1903208)|negative regulation of phagocytosis (GO:0050765)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein tyrosine kinase activity (GO:0061099)|negative regulation of translation (GO:0017148)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP catabolic process (GO:0030822)|positive regulation of cell migration (GO:0030335)|positive regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051343)|positive regulation of gastrulation (GO:2000543)|positive regulation of GTPase activity (GO:0043547)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein homooligomerization (GO:0032464)|positive regulation of protein phosphorylation (GO:0001934)|regulation of cell cycle (GO:0051726)|regulation of cell division (GO:0051302)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|regulation of protein localization (GO:0032880)|rhythmic process (GO:0048511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|midbody (GO:0030496)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|phagocytic cup (GO:0001891)|small ribosomal subunit (GO:0015935)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|ion channel inhibitor activity (GO:0008200)|poly(A) RNA binding (GO:0044822)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase inhibitor activity (GO:0030292)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|SH2 domain binding (GO:0042169)			lung(3)|skin(2)	5	all_cancers(89;8.79e-06)|all_epithelial(37;1.13e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0654)	all_cancers(40;0.000209)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.101)|all cancers(165;0.11)		ATTTGCACACACCCAGGGTAT	0.458																																					p.G136G		Atlas-SNP	.											.	GNB2L1	22	.	0			c.T408C						.						148	156	153					5																	180668513		2203	4300	6503	SO:0001819	synonymous_variant	10399	exon3			GCACACACCCAGG	M24194	CCDS34324.1	5q35.3	2013-01-10				ENSG00000204628		"WD repeat domain containing"	4399	protein-coding gene	gene with protein product	"Receptor for Activated C Kinase 1"	176981				8302854, 2499885	Standard	NM_006098		Approved	Gnb2-rs1, RACK1, H12.3	uc003mni.1	P63244		ENST00000512805.1:c.408T>C	chr5.hg19:g.180668513A>G		76.0	0.0		76.0	5.0	NM_006098	B3KTJ0|D3DWS0|P25388|P99049|Q53HU2|Q5J8M6|Q5VLR4|Q6FH47	Silent	SNP	ENST00000512805.1	hg19	CCDS34324.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.36|11.36	1.616192|1.616192	0.28801|0.28801	.|.	.|.	ENSG00000204628|ENSG00000204628	ENST00000502905;ENST00000504128|ENST00000507756;ENST00000512968	.|T	.|0.53206	.|0.63	5.88|5.88	0.607|0.607	0.17564|0.17564	.|.	.|.	.|.	.|.	.|.	T|T	0.35248|0.35248	0.0925|0.0925	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.16158|0.16158	-1.0412|-1.0412	4|5	.|.	.|.	.|.	-19.8633|-19.8633	0.5266|0.5266	0.00621|0.00621	0.4199:0.1374:0.1534:0.2893|0.4199:0.1374:0.1534:0.2893	.|.	.|.	.|.	.|.	R|A	54;43|67;111	.|ENSP00000425008:V111A	.|.	C|V	-|-	1|2	0|0	GNB2L1|GNB2L1	180601119|180601119	0.086000|0.086000	0.21541|0.21541	0.930000|0.930000	0.37139|0.37139	0.968000|0.968000	0.65278|0.65278	-0.529000|-0.529000	0.06186|0.06186	-0.121000|-0.121000	0.11787|0.11787	-0.290000|-0.290000	0.09829|0.09829	TGT|GTG	.	.		0.458	GNB2L1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372943.2	NM_006098		G	180668513	A	G	180668513	2	3	254	1	0	0	0	0	0	0	0	1	6526	146	6	2		2	GNB2L1	5	180668513	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	17458	180668513	246747	286	34578										
SLC22A23	63027	hgsc.bcm.edu	37	chr6	3416016	3416016	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgcatccagttattaggtagCcaaagattaatccaaccagt	7	9	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:3416016C>T	ENST00000406686.3	-	2	727	c.728G>A	c.(727-729)gGc>gAc	p.G243D	SLC22A23_ENST00000380298.2_Missense_Mutation_p.G243D|SLC22A23_ENST00000490273.1_5'UTR|SLC22A23_ENST00000436008.2_Missense_Mutation_p.G243D|SLC22A23_ENST00000380302.4_5'UTR	NM_015482.1	NP_056297.1	A1A5C7	S22AN_HUMAN	solute carrier family 22, member 23	243					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)	14	Ovarian(93;0.0493)	all_hematologic(90;0.0905)				TATTAGGTAGCCAAAGATTAA	0.458																																					p.G243D		Atlas-SNP	.											.	SLC22A23	89	.	0			c.G728A						.						164	144	150					6																	3416016		692	1591	2283	SO:0001583	missense	63027	exon2			AGGTAGCCAAAGA	AJ420525	CCDS34331.1, CCDS47363.1, CCDS75389.1	6p25.2	2013-05-22	2008-01-11	2008-01-11	ENSG00000137266	ENSG00000137266		"Solute carriers"	21106	protein-coding gene	gene with protein product		611697	"chromosome 6 open reading frame 85"	C6orf85		17714910	Standard	NM_015482		Approved	FLJ22174	uc003mvm.3	A1A5C7	OTTHUMG00000014144	ENST00000406686.3:c.728G>A	chr6.hg19:g.3416016C>T	ENSP00000385028:p.Gly243Asp	174.0	0.0		104.0	5.0	NM_015482	A1A5C8|Q5T8B8|Q6ZMH3|Q8IW73	Missense_Mutation	SNP	ENST00000406686.3	hg19	CCDS47363.1	.	.	.	.	.	.	.	.	.	.	C	31	5.102966	0.94245	.	.	ENSG00000137266	ENST00000436008;ENST00000406686;ENST00000485307;ENST00000467177;ENST00000380298	D;D;D;D;D	0.89810	-2.57;-2.57;-2.57;-2.57;-2.57	5.4	5.4	0.78164	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	.	.	.	.	D	0.94335	0.8179	M	0.79926	2.475	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.94692	0.7875	9	0.87932	D	0	-17.0608	19.1812	0.93623	0.0:1.0:0.0:0.0	.	243;243	C9J4Z0;A1A5C7	.;S22AN_HUMAN	D	243;243;71;69;243	ENSP00000410245:G243D;ENSP00000385028:G243D;ENSP00000418134:G71D;ENSP00000418985:G69D;ENSP00000369653:G243D	ENSP00000369653:G243D	G	-	2	0	SLC22A23	3361015	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.313000	0.78978	2.530000	0.85305	0.563000	0.77884	GGC	.	.		0.458	SLC22A23-006	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353059.1	NM_021945		T	3416016	C	T	3416016	3	4	254	1	0	0	0	0	1	0	0	0	14467	739	26	3	1368	3	SLC22A23	6	3416016	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10		3416016	167699051	287	34579										
GCNT2	2651	hgsc.bcm.edu	37	chr6	10621632	10621632	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctggactggaaacctcagagCtataaagtggagtgacatgg	13	7	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:10621632C>T	ENST00000379597.3	+	2	1530	c.974C>T	c.(973-975)gCt>gTt	p.A325V	GCNT2_ENST00000316170.3_Missense_Mutation_p.A323V|GCNT2_ENST00000495262.1_Missense_Mutation_p.A325V|GCNT2_ENST00000410107.1_Missense_Mutation_p.A39V|GCNT2_ENST00000265012.4_Missense_Mutation_p.A325V|GCNT2_ENST00000397423.2_3'UTR			Q8N0V5	GNT2A_HUMAN	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group)	325					maintenance of lens transparency (GO:0036438)|negative regulation of cell-substrate adhesion (GO:0010812)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of protein kinase B signaling (GO:0051897)|posttranscriptional regulation of gene expression (GO:0010608)|protein glycosylation (GO:0006486)|transforming growth factor beta receptor signaling pathway (GO:0007179)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)			endometrium(2)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)	12	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)		AACCTCAGAGCTATAAAGTGG	0.512																																					p.A325V		Atlas-SNP	.											.	GCNT2	123	.	0			c.C974T						.						94	80	85					6																	10621632		2203	4300	6503	SO:0001583	missense	2651	exon4			TCAGAGCTATAAA	L41605	CCDS4512.1, CCDS4513.1, CCDS34338.1	6p24.2	2014-07-18	2006-02-23		ENSG00000111846	ENSG00000111846	2.4.1.150	"Blood group antigens", "Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	4204	protein-coding gene	gene with protein product	"Ii blood group", "unassigned linkage group 3"	600429	"glucosaminyl (N-acetyl) transferase 5", "glucosaminyl (N-acetyl) transferase 2, I-branching enzyme", "glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (Ii blood group)", "cataract, congenital"	NACGT1, II, GCNT5, CCAT		8449405, 9915862	Standard	NM_145649		Approved	IGNT, NAGCT1, bA421M1.1, bA360O19.2, ULG3	uc003mze.3	Q06430	OTTHUMG00000014244	ENST00000379597.3:c.974C>T	chr6.hg19:g.10621632C>T	ENSP00000368917:p.Ala325Val	90.0	0.0		87.0	4.0	NM_145649		Missense_Mutation	SNP	ENST00000379597.3	hg19	CCDS34338.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.896631	0.91962	.	.	ENSG00000111846	ENST00000410107;ENST00000495262;ENST00000379597;ENST00000316170;ENST00000265012	T;T;T;T;T	0.42900	0.96;2.84;2.84;2.84;2.84	5.51	5.51	0.81932	.	0.000000	0.56097	D	0.000032	T	0.56645	0.1999	M	0.72118	2.19	0.51482	D	0.999925	P;D;P;B	0.89917	0.885;1.0;0.885;0.392	P;D;P;B	0.91635	0.823;0.999;0.771;0.349	T	0.52328	-0.8590	10	0.35671	T	0.21	-24.6358	17.2045	0.86914	0.0:1.0:0.0:0.0	.	325;39;325;323	Q8N0V5;B7ZBL3;Q8NFS9;Q06430	GNT2A_HUMAN;.;GNT2C_HUMAN;GNT2B_HUMAN	V	39;325;325;323;325	ENSP00000386321:A39V;ENSP00000419411:A325V;ENSP00000368917:A325V;ENSP00000314844:A323V;ENSP00000265012:A325V	ENSP00000265012:A325V	A	+	2	0	GCNT2	10729618	0.999000	0.42202	0.955000	0.39395	0.897000	0.52465	5.198000	0.65147	2.600000	0.87896	0.655000	0.94253	GCT	.	.		0.512	GCNT2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327912.3	NM_145649		T	10621632	C	T	10621632	3	4	254	1	0	0	0	0	1	0	0	0	6309	797	28	3	2832	3	GCNT2	6	10621632	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	7205616	10621632	160493435	288	34580										
TBC1D7	51256	hgsc.bcm.edu	37	chr6	13316857	13316857	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aattggttcacaaagcgtcgGgtgatccagtaacagtcgac	11	9	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:13316857G>T	ENST00000379300.3	-	5	708	c.465C>A	c.(463-465)acC>acA	p.T155T	TBC1D7_ENST00000607658.1_Silent_p.T128T|TBC1D7_ENST00000343141.4_Intron|TBC1D7_ENST00000607532.1_5'UTR|TBC1D7_ENST00000379307.2_Silent_p.T128T|TBC1D7_ENST00000356436.4_Silent_p.T155T	NM_001143964.2|NM_016495.4	NP_001137436.1|NP_057579.1	Q9P0N9	TBCD7_HUMAN	TBC1 domain family, member 7	155	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				activation of Rho GTPase activity (GO:0032862)|negative regulation of cilium assembly (GO:1902018)|negative regulation of TOR signaling (GO:0032007)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of Rab GTPase activity (GO:0032851)|response to growth factor (GO:0070848)	ciliary basal body (GO:0036064)|cytoplasmic vesicle (GO:0031410)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(1)|large_intestine(4)|lung(14)|ovary(1)|stomach(1)	22	Breast(50;0.0296)|Ovarian(93;0.0339)	all_hematologic(90;0.135)	Epithelial(50;0.0784)|BRCA - Breast invasive adenocarcinoma(129;0.13)|all cancers(50;0.21)			CAAAGCGTCGGGTGATCCAGT	0.423																																					p.T155T		Atlas-SNP	.											.	TBC1D7	34	.	0			c.C465A						.						196	204	201					6																	13316857		2203	4300	6503	SO:0001819	synonymous_variant	51256	exon5			GCGTCGGGTGATC	AF151073	CCDS4523.1, CCDS47376.1, CCDS58995.1	6p23	2013-07-10			ENSG00000145979	ENSG00000145979			21066	protein-coding gene	gene with protein product		612655				11042152, 17646400	Standard	XM_005249163		Approved	dJ257A7.3, FLJ32666	uc003nan.3	Q9P0N9	OTTHUMG00000014272	ENST00000379300.3:c.465C>A	chr6.hg19:g.13316857G>T		101.0	0.0		96.0	4.0	NM_001143965	E7EV96|Q2TU37|Q53F44|Q5SZL7|Q86VM8|Q96MB8	Silent	SNP	ENST00000379300.3	hg19	CCDS4523.1																																																																																			.	.		0.423	TBC1D7-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039896.2	NM_016495		T	13316857	G	T	13316857	2	4	254	1	0	0	0	0	0	0	0	1	15639	1219	43	3		3	TBC1D7	6	13316857	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	2695225	13316857	157798210	289	34581										
SOX4	6659	hgsc.bcm.edu	37	chr6	21595158	21595158	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gactacaagtaccggcccagGaagaaggtgaagtccggcaa	13	10	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:21595158G>A	ENST00000244745.1	+	1	1187	c.393G>A	c.(391-393)agG>agA	p.R131R	SOX4_ENST00000543472.1_Silent_p.R131R	NM_003107.2	NP_003098.1	Q06945	SOX4_HUMAN	SRY (sex determining region Y)-box 4	131					ascending aorta morphogenesis (GO:0035910)|atrial septum primum morphogenesis (GO:0003289)|canonical Wnt signaling pathway (GO:0060070)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac ventricle formation (GO:0003211)|cellular response to glucose stimulus (GO:0071333)|DNA damage response, detection of DNA damage (GO:0042769)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|endocrine pancreas development (GO:0031018)|glial cell development (GO:0021782)|glial cell proliferation (GO:0014009)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|kidney morphogenesis (GO:0060993)|limb bud formation (GO:0060174)|mitral valve morphogenesis (GO:0003183)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein export from nucleus (GO:0046826)|negative regulation of protein ubiquitination (GO:0031397)|neural tube formation (GO:0001841)|neuroepithelial cell differentiation (GO:0060563)|noradrenergic neuron differentiation (GO:0003357)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin secretion (GO:0032024)|positive regulation of N-terminal peptidyl-lysine acetylation (GO:2000761)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|positive regulation of Wnt signaling pathway (GO:0030177)|pro-B cell differentiation (GO:0002328)|protein stabilization (GO:0050821)|regulation of protein stability (GO:0031647)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|spinal cord development (GO:0021510)|spinal cord motor neuron differentiation (GO:0021522)|sympathetic nervous system development (GO:0048485)|T cell differentiation (GO:0030217)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			kidney(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	6	Ovarian(93;0.163)		all cancers(50;0.0751)|Epithelial(50;0.155)			ACCGGCCCAGGAAGAAGGTGA	0.642																																					p.R131R		Atlas-SNP	.											SOX4,bladder,carcinoma,0,1	SOX4	11	.	0			c.G393A						.						21	26	25					6																	21595158		2202	4299	6501	SO:0001819	synonymous_variant	6659	exon1			GCCCAGGAAGAAG	AF070669	CCDS4547.1	6p22.3	2008-02-05			ENSG00000124766	ENSG00000124766		"SRY (sex determining region Y)-boxes"	11200	protein-coding gene	gene with protein product		184430				8268656, 9730625	Standard	NM_003107		Approved		uc003ndi.3	Q06945	OTTHUMG00000016101	ENST00000244745.1:c.393G>A	chr6.hg19:g.21595158G>A		96.0	0.0		59.0	4.0	NM_003107		Silent	SNP	ENST00000244745.1	hg19	CCDS4547.1																																																																																			.	.		0.642	SOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043301.1	NM_003107		A	21595158	G	A	21595158	2	1	254	1	0	0	0	0	0	0	0	1	14968	1165	41	3		3	SOX4	6	21595158	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	8278301	21595158	149519909	290	34582										
HIST1H2BA	255626	hgsc.bcm.edu	37	chr6	25727451	25727451	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcagtgcgcttgctactgccGggagagctggctaaacatgc	14	11	0	1	rs145569895		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:25727451G>T	ENST00000274764.2	+	1	315	c.315G>T	c.(313-315)ccG>ccT	p.P105P	HIST1H2AA_ENST00000297012.3_5'Flank	NM_170610.2	NP_733759.1	Q96A08	H2B1A_HUMAN	histone cluster 1, H2ba	105					cellular response to acid chemical (GO:0071229)|chromatin organization (GO:0006325)|inflammatory response (GO:0006954)|mononuclear cell migration (GO:0071674)|nucleosome assembly (GO:0006334)|nucleosome disassembly (GO:0006337)|plasminogen activation (GO:0031639)|positive regulation of binding (GO:0051099)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)	extrinsic component of plasma membrane (GO:0019897)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|kidney(1)	2						TGCTACTGCCGGGAGAGCTGG	0.517																																					p.P105P		Atlas-SNP	.											.	HIST1H2BA	25	.	0			c.G315T						.						271	196	221					6																	25727451		2203	4300	6503	SO:0001819	synonymous_variant	255626	exon1			ACTGCCGGGAGAG	AF397301	CCDS4563.1	6p22.2	2011-01-27	2006-10-11		ENSG00000146047	ENSG00000146047		"Histones / Replication-dependent"	18730	protein-coding gene	gene with protein product		609904	"H2B histone family, member U, (testis-specific)", "histone 1, H2ba"			12408966, 12213818	Standard	NM_170610		Approved	bA317E16.3, STBP, TSH2B, H2BFU	uc003nfd.3	Q96A08	OTTHUMG00000014408	ENST00000274764.2:c.315G>T	chr6.hg19:g.25727451G>T		124.0	0.0		125.0	6.0	NM_170610	B2R544|Q6NZ98|Q6NZA0|Q6NZA1	Silent	SNP	ENST00000274764.2	hg19	CCDS4563.1																																																																																			.	G|1.000;C|0.000		0.517	HIST1H2BA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040066.1	NM_170610		T	25727451	G	T	25727451	2	4	254	1	0	0	0	0	0	0	0	1	7149	1103	39	1		1	HIST1H2BA	6	25727451	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	4132293	25727451	145387616	291	34583										
ATP6V1G2	534	hgsc.bcm.edu	37	chr6	31513188	31513188	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	caggccctacggtggccctaGgcagaaatccggtagttggg	15	11	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:31513188G>T	ENST00000303892.5	-	3	638	c.354C>A	c.(352-354)gcC>gcA	p.A118A	ATP6V1G2_ENST00000376151.4_Silent_p.A78A|ATP6V1G2_ENST00000483251.1_Silent_p.A77A|DDX39B-AS1_ENST00000420520.1_RNA|DDX39B-AS1_ENST00000416684.1_RNA|ATP6V1G2-DDX39B_ENST00000475917.1_Intron|DDX39B_ENST00000458640.1_5'Flank|NFKBIL1_ENST00000376148.4_5'Flank|ATP6V1G2-DDX39B_ENST00000376185.1_Intron|ATP6V1G2_ENST00000483170.1_5'UTR|DDX39B_ENST00000396172.1_5'Flank|DDX39B_ENST00000417556.2_5'Flank|NFKBIL1_ENST00000376145.4_5'Flank	NM_130463.3|NM_138282.2	NP_569730.1|NP_612139.1	O95670	VATG2_HUMAN	ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G2	118					cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances (GO:0016820)			breast(1)|large_intestine(2)|lung(1)|prostate(1)	5						GGTGGCCCTAGGCAGAAATCC	0.567																																					p.A118A		Atlas-SNP	.											.	ATP6V1G2	15	.	0			c.C354A						.						44	39	40					6																	31513188		2203	4300	6503	SO:0001819	synonymous_variant	534	exon3			GCCCTAGGCAGAA	Y14768	CCDS4698.1, CCDS4699.1, CCDS56413.1	6p21.3	2011-03-29	2006-01-13	2002-05-10	ENSG00000213760	ENSG00000213760		"ATPases / V-type"	862	protein-coding gene	gene with protein product		606853	"ATPase, H+ transporting, lysosomal (vacuolar proton pump)", "ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G isoform 2"	ATP6G, ATP6G2		10202016	Standard	NM_138282		Approved	Vma10, NG38, Em:AC004181.3	uc003nua.3	O95670	OTTHUMG00000166618	ENST00000303892.5:c.354C>A	chr6.hg19:g.31513188G>T		56.0	0.0		58.0	4.0	NM_130463	B5MEF0|Q2L6F8|Q5HYU8|Q5RJ63	Silent	SNP	ENST00000303892.5	hg19	CCDS4698.1																																																																																			.	.		0.567	ATP6V1G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076399.3	NM_130463		T	31513188	G	T	31513188	2	4	254	1	0	0	0	0	0	0	0	1	1187	987	35	3		3	ATP6V1G2	6	31513188	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	5785737	31513188	139601879	292	34584										
TNF	7124	hgsc.bcm.edu	37	chr6	31544346	31544346	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tctctaatcagccctctggcCcaggcagtcagtaagtgtct	9	13	5	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:31544346C>A	ENST00000449264.2	+	2	397	c.222C>A	c.(220-222)gcC>gcA	p.A74A		NM_000594.3	NP_000585.2	P01375	TNFA_HUMAN	tumor necrosis factor	74					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPK activity (GO:0000187)|activation of MAPKKK activity (GO:0000185)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|calcium-mediated signaling (GO:0019722)|cell activation (GO:0001775)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nicotine (GO:0071316)|cellular response to organic cyclic compound (GO:0071407)|chronic inflammatory response to antigenic stimulus (GO:0002439)|defense response to Gram-positive bacterium (GO:0050830)|embryonic digestive tract development (GO:0048566)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|glucose metabolic process (GO:0006006)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|JNK cascade (GO:0007254)|leukocyte tethering or rolling (GO:0050901)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MAPK cascade (GO:0000165)|necroptotic signaling pathway (GO:0097527)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of branching involved in lung morphogenesis (GO:0061048)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gene expression (GO:0010629)|negative regulation of glucose import (GO:0046325)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of L-glutamate transport (GO:0002037)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of lipid storage (GO:0010888)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|organ morphogenesis (GO:0009887)|osteoclast differentiation (GO:0030316)|positive regulation of apoptotic process (GO:0043065)|positive regulation of calcidiol 1-monooxygenase activity (GO:0060559)|positive regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000343)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of chemokine production (GO:0032722)|positive regulation of chronic inflammatory response to antigenic stimulus (GO:0002876)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fever generation (GO:0031622)|positive regulation of gene expression (GO:0010628)|positive regulation of hair follicle development (GO:0051798)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of mitosis (GO:0045840)|positive regulation of mononuclear cell migration (GO:0071677)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of podosome assembly (GO:0071803)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein complex disassembly (GO:0043243)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein localization to cell surface (GO:2000010)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein transport (GO:0051222)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of synaptic transmission (GO:0050806)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translational initiation by iron (GO:0045994)|positive regulation of vitamin D biosynthetic process (GO:0060557)|protein import into nucleus, translocation (GO:0000060)|protein kinase B signaling (GO:0043491)|receptor biosynthetic process (GO:0032800)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of immunoglobulin secretion (GO:0051023)|regulation of insulin secretion (GO:0050796)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to salt stress (GO:0009651)|response to virus (GO:0009615)|sequestering of triglyceride (GO:0030730)|skeletal muscle contraction (GO:0003009)|transformed cell apoptotic process (GO:0006927)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	cytokine activity (GO:0005125)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|transcription regulatory region DNA binding (GO:0044212)|tumor necrosis factor receptor binding (GO:0005164)			large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|skin(3)	8		Ovarian(999;0.00556)			Adalimumab(DB00051)|Amrinone(DB01427)|Certolizumab pegol(DB08904)|Chloroquine(DB00608)|Clenbuterol(DB01407)|Epinephrine(DB00668)|Etanercept(DB00005)|Glucosamine(DB01296)|golimumab(DB06674)|Infliximab(DB00065)|Pomalidomide(DB08910)|Pranlukast(DB01411)|Pseudoephedrine(DB00852)|Thalidomide(DB01041)	GCCCTCTGGCCCAGGCAGTCA	0.517									Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of																												p.A74A		Atlas-SNP	.											.	TNF	15	.	0			c.C222A						.						113	109	111					6																	31544346		2203	4300	6503	SO:0001819	synonymous_variant	7124	exon2	Familial Cancer Database	incl.: Familial Head and Neck Cancer	TCTGGCCCAGGCA	X02910	CCDS4702.1	6p21.3	2013-05-22	2010-05-04		ENSG00000232810	ENSG00000232810		"Tumor necrosis factor (ligand) superfamily"	11892	protein-coding gene	gene with protein product	"TNF superfamily, member 2"	191160	"tumor necrosis factor (TNF superfamily, member 2)"	TNFA		2413547, 6392892	Standard	NM_000594		Approved	TNFSF2, DIF, TNF-alpha	uc003nui.4	P01375	OTTHUMG00000031194	ENST00000449264.2:c.222C>A	chr6.hg19:g.31544346C>A		73.0	0.0		74.0	4.0	NM_000594	O43647|Q9P1Q2|Q9UIV3	Silent	SNP	ENST00000449264.2	hg19	CCDS4702.1																																																																																			.	.		0.517	TNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076390.2			A	31544346	C	A	31544346	2	1	254	1	0	0	0	0	0	0	0	1	16286	610	22	3		3	TNF	6	31544346	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	31158	31544346	139570721	293	34585										
CLIC1	1192	hgsc.bcm.edu	37	chr6	31698776	31698776	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	atccccggtacttcttacacAccacctgaggatggggagag	11	12	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:31698776A>G	ENST00000375780.2	-	7	1141	c.569T>C	c.(568-570)gTg>gCg	p.V190A	CLIC1_ENST00000375784.3_Missense_Mutation_p.V190A|CLIC1_ENST00000375779.2_Missense_Mutation_p.V190A|DDAH2_ENST00000375787.2_5'Flank|DDAH2_ENST00000375792.3_5'Flank|DDAH2_ENST00000480913.1_5'Flank|DDAH2_ENST00000375789.2_5'Flank|CLIC1_ENST00000395892.1_Missense_Mutation_p.V190A			O00299	CLIC1_HUMAN	chloride intracellular channel 1	190	GST C-terminal.				chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|platelet aggregation (GO:0070527)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of mitochondrial membrane potential (GO:0051881)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|brush border (GO:0005903)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			central_nervous_system(1)|endometrium(1)|lung(3)|ovary(1)|skin(1)	7						CTTCTTACACACCACCTGAGG	0.572																																					p.V190A		Atlas-SNP	.											.	CLIC1	15	.	0			c.T569C						.						43	33	37					6																	31698776		1510	2708	4218	SO:0001583	missense	1192	exon6			TTACACACCACCT	U93205	CCDS4719.1	6p21.3	2012-09-26			ENSG00000213719	ENSG00000213719		"Ion channels / Chloride channels : Intracellular"	2062	protein-coding gene	gene with protein product		602872				9139710	Standard	NM_001288		Approved	NCC27, p64CLCP	uc003nwr.3	O00299	OTTHUMG00000031103	ENST00000375780.2:c.569T>C	chr6.hg19:g.31698776A>G	ENSP00000364935:p.Val190Ala	96.0	0.0		123.0	5.0	NM_001288	Q15089|Q502X1	Missense_Mutation	SNP	ENST00000375780.2	hg19	CCDS4719.1	.	.	.	.	.	.	.	.	.	.	A	15.54	2.865033	0.51482	.	.	ENSG00000213719	ENST00000375784;ENST00000375779;ENST00000375780;ENST00000395892	D;D;D;D	0.92858	-3.12;-3.12;-3.12;-3.12	4.64	4.64	0.57946	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);	0.000000	0.64402	U	0.000015	T	0.76227	0.3958	N	0.25144	0.715	0.80722	D	1	B	0.32507	0.373	B	0.37888	0.26	T	0.75701	-0.3226	10	0.02654	T	1	-10.7814	12.0341	0.53415	1.0:0.0:0.0:0.0	.	190	O00299	CLIC1_HUMAN	A	190	ENSP00000364940:V190A;ENSP00000364934:V190A;ENSP00000364935:V190A;ENSP00000379229:V190A	ENSP00000364934:V190A	V	-	2	0	CLIC1	31806755	1.000000	0.71417	0.987000	0.45799	0.960000	0.62799	5.679000	0.68160	1.948000	0.56530	0.459000	0.35465	GTG	.	.		0.572	CLIC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076167.3	NM_001288		G	31698776	A	G	31698776	3	3	254	1	0	0	0	0	1	0	0	0	3527	159	6	2	160	2	CLIC1	6	31698776	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	154430	31698776	139416291	294	34586										
TNXB	7148	hgsc.bcm.edu	37	chr6	32029479	32029479	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgctgggttctgtggggctgGgggtctcttcctctgcagct	16	10	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:32029479G>T	ENST00000375244.3	-	21	7388	c.7187C>A	c.(7186-7188)cCc>cAc	p.P2396H	TNXB_ENST00000375247.2_Missense_Mutation_p.P2396H			P22105	TENX_HUMAN	tenascin XB	2456	Fibronectin type-III 16. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						TGTGGGGCTGGGGGTCTCTTC	0.627																																					p.P2396H		Atlas-SNP	.											.	TNXB	553	.	0			c.C7187A						.						45	55	52					6																	32029479		1204	2520	3724	SO:0001583	missense	7148	exon21			GGGCTGGGGGTCT	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.7187C>A	chr6.hg19:g.32029479G>T	ENSP00000364393:p.Pro2396His	131.0	0.0		115.0	5.0	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	hg19		.	.	.	.	.	.	.	.	.	.	G	17.77	3.471565	0.63737	.	.	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.59772	0.42;0.24	3.99	3.99	0.46301	.	0.113838	0.39475	N	0.001348	T	0.61413	0.2345	M	0.86028	2.79	0.23838	N	0.996701	P	0.45176	0.852	P	0.53549	0.729	T	0.56463	-0.7975	10	0.56958	D	0.05	.	11.4331	0.50052	0.0:0.0:1.0:0.0	.	2396	P22105-3	.	H	2396	ENSP00000364393:P2396H;ENSP00000364396:P2396H	ENSP00000364393:P2396H	P	-	2	0	TNXB	32137457	0.990000	0.36364	0.937000	0.37676	0.947000	0.59692	2.392000	0.44433	2.033000	0.60031	0.585000	0.79938	CCC	.	.		0.627	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		T	32029479	G	T	32029479	3	4	254	1	0	0	0	0	1	0	0	0	16361	1232	43	3	7622	3	TNXB	6	32029479	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	330703	32029479	139085588	295	34587										
TNXB	7148	hgsc.bcm.edu	37	chr6	32038106	32038106	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccctcaggaaccgtccaggaGaggcgcagtgagtctggggt	16	11	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:32038106G>T	ENST00000375244.3	-	14	5277	c.5076C>A	c.(5074-5076)ctC>ctA	p.L1692L	TNXB_ENST00000375247.2_Silent_p.L1692L			P22105	TENX_HUMAN	tenascin XB	1774	Fibronectin type-III 9. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						CCGTCCAGGAGAGGCGCAGTG	0.657																																					p.L1692L		Atlas-SNP	.											.	TNXB	553	.	0			c.C5076A						.						20	21	21					6																	32038106		1915	4123	6038	SO:0001819	synonymous_variant	7148	exon14			CCAGGAGAGGCGC	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.5076C>A	chr6.hg19:g.32038106G>T		187.0	0.0		166.0	31.0	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Silent	SNP	ENST00000375244.3	hg19																																																																																				.	.		0.657	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		T	32038106	G	T	32038106	2	4	254	1	0	0	0	0	0	0	0	1	16361	929	33	3		3	TNXB	6	32038106	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	8627	32038106	139076961	296	34588										
RNF5	6048	hgsc.bcm.edu	37	chr6	32148076	32148076	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttcctgtttctcgccatcttCttctttttttggctgctcag	6	12	5	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:32148076C>T	ENST00000375094.3	+	6	674	c.516C>T	c.(514-516)ttC>ttT	p.F172F	RNF5_ENST00000427134.2_Intron|AGPAT1_ENST00000336984.6_5'Flank|AGPAT1_ENST00000490711.1_5'Flank|AGPAT1_ENST00000395497.1_5'Flank|AGPAT1_ENST00000375104.2_5'Flank	NM_006913.3	NP_008844.1	Q99942	RNF5_HUMAN	ring finger protein 5, E3 ubiquitin protein ligase	172					cellular protein catabolic process (GO:0044257)|ER-associated misfolded protein catabolic process (GO:0071712)|negative regulation of autophagy (GO:0010507)|protein destabilization (GO:0031648)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|regulation of autophagic vacuole assembly (GO:2000785)|response to bacterium (GO:0009617)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|lung(7)|urinary_tract(2)	10						TCGCCATCTTCTTCTTTTTTT	0.537																																					p.F172F		Atlas-SNP	.											.	RNF5	16	.	0			c.C516T						.						170	184	179					6																	32148076		1511	2708	4219	SO:0001819	synonymous_variant	6048	exon6			CATCTTCTTCTTT	U89336	CCDS4745.1	6p21.31	2013-01-09	2012-02-23			ENSG00000204308		"RING-type (C3HC4) zinc fingers"	10068	protein-coding gene	gene with protein product		602677	"ring finger protein 5"			9533025	Standard	NM_006913		Approved	NG2, G16, RING5, RMA1	uc031snv.1	Q99942	OTTHUMG00000031093	ENST00000375094.3:c.516C>T	chr6.hg19:g.32148076C>T		44.0	0.0		63.0	4.0	NM_006913	A2BFI6|B2R4K3|Q0VDB7|Q9UMQ2	Silent	SNP	ENST00000375094.3	hg19	CCDS4745.1																																																																																			.	.		0.537	RNF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076133.2	NM_006913		T	32148076	C	T	32148076	2	4	254	1	0	0	0	0	0	0	0	1	13512	912	32	3		3	RNF5	6	32148076	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	109970	32148076	138966991	297	34589										
SLC39A7	7922	hgsc.bcm.edu	37	chr6	33170874	33170874	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttggtccagtctggctgcagCaaaaagcaggttggtgatgt	14	7	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:33170874C>A	ENST00000374677.3	+	6	1501	c.1128C>A	c.(1126-1128)agC>agA	p.S376R	RXRB_ENST00000374685.4_5'Flank|RXRB_ENST00000374680.3_5'Flank|RXRB_ENST00000544186.1_5'Flank|SLC39A7_ENST00000374675.3_Missense_Mutation_p.S376R|SLC39A7_ENST00000463972.1_3'UTR|HSD17B8_ENST00000374662.3_5'Flank|RXRB_ENST00000413614.2_5'Flank	NM_006979.2	NP_008910.2	Q92504	S39A7_HUMAN	solute carrier family 39 (zinc transporter), member 7	376				S -> T (in Ref. 1; BAA11528 and 2; AAD12305). {ECO:0000305}.	transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metal ion transmembrane transporter activity (GO:0046873)			NS(1)|breast(3)|endometrium(2)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						CTGGCTGCAGCAAAAAGCAGG	0.527																																					p.S376R		Atlas-SNP	.											.	SLC39A7	32	.	0			c.C1128A						.						113	131	124					6																	33170874		1399	2635	4034	SO:0001583	missense	7922	exon6			CTGCAGCAAAAAG	AF117221	CCDS43453.1	6p21.3	2014-01-28		2003-10-27	ENSG00000112473	ENSG00000112473		"Solute carriers"	4927	protein-coding gene	gene with protein product		601416	"HLA class II region expressed gene KE4"	HKE4		8812499, 1855816, 19246244, 15705588	Standard	NM_006979		Approved	H2-KE4, D6S2244E, KE4, RING5, ZIP7	uc003odf.3	Q92504	OTTHUMG00000031238	ENST00000374677.3:c.1128C>A	chr6.hg19:g.33170874C>A	ENSP00000363809:p.Ser376Arg	119.0	0.0		84.0	4.0	NM_006979	B0UXF6|Q5STP8|Q9UIQ0	Missense_Mutation	SNP	ENST00000374677.3	hg19	CCDS43453.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.136882	0.77662	.	.	ENSG00000112473	ENST00000374675;ENST00000446283;ENST00000445037;ENST00000374677	T;T	0.53206	0.63;0.63	5.02	5.02	0.67125	.	0.051265	0.85682	D	0.000000	T	0.58864	0.2152	M	0.83483	2.645	0.52099	D	0.999942	P;D	0.55172	0.885;0.97	P;P	0.60415	0.833;0.874	T	0.64317	-0.6436	10	0.62326	D	0.03	-9.1565	11.5361	0.50639	0.0:0.8195:0.1805:0.0	.	357;376	B4DVK8;Q92504	.;S39A7_HUMAN	R	376;357;281;376	ENSP00000363807:S376R;ENSP00000363809:S376R	ENSP00000363807:S376R	S	+	3	2	SLC39A7	33278852	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.542000	0.53625	2.603000	0.88011	0.448000	0.29417	AGC	.	.		0.527	SLC39A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076499.2	NM_006979		A	33170874	C	A	33170874	3	1	254	1	0	0	0	0	1	0	0	0	14638	709	25	3	1150	3	SLC39A7	6	33170874	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1022798	33170874	137944193	298	34590										
DEF6	50619	hgsc.bcm.edu	37	chr6	35288753	35288753	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	catccaattgagcctggaggTgagaaggaatagactctgga	13	7	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:35288753T>A	ENST00000316637.5	+	10	1677		c.e10+2		DEF6_ENST00000542066.1_Splice_Site	NM_022047.3	NP_071330.3	Q9H4E7	DEFI6_HUMAN	differentially expressed in FDCP 6 homolog (mouse)							cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				cervix(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)	15						AGCCTGGAGGTGAGAAGGAAT	0.572																																					.		Atlas-SNP	.											.	DEF6	36	.	0			c.1672+2T>A						.						54	51	52					6																	35288753		2203	4300	6503	SO:0001630	splice_region_variant	50619	exon10			TGGAGGTGAGAAG	AJ276095	CCDS4802.1	6p21.33-p21.1	2013-01-10	2001-11-28		ENSG00000023892	ENSG00000023892		"Pleckstrin homology (PH) domain containing"	2760	protein-coding gene	gene with protein product	"SWAP-70-like adaptor protein of T cells"	610094	"differentially expressed in FDCP (mouse homolog) 6"			19251698	Standard	NM_022047		Approved	IBP, SLAT, SWAP70L	uc003okk.3	Q9H4E7	OTTHUMG00000014563	ENST00000316637.5:c.1672+2T>A	chr6.hg19:g.35288753T>A		134.0	0.0		93.0	4.0	NM_022047	Q86VF4	Splice_Site	SNP	ENST00000316637.5	hg19	CCDS4802.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.081657	0.76528	.	.	ENSG00000023892	ENST00000542066;ENST00000316637	.	.	.	5.42	4.25	0.50352	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.6434	0.56721	0.0:0.0:0.1381:0.8619	.	.	.	.	.	-1	.	.	.	+	.	.	DEF6	35396731	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	5.789000	0.69029	0.877000	0.35895	0.459000	0.35465	.	.	.		0.572	DEF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040276.1	NM_022047	Intron	A	35288753	T	A	35288753	5	1	254	1	0	0	0	0	0	0	1	0	4388	1710	59	4	1712	4	DEF6	6	35288753	Splice_Site	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	2117879	35288753	135826314	299	34591										
FKBP5	2289	hgsc.bcm.edu	37	chr6	35604882	35604882	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tttcctttgtaatggacataAactttgtctccaatcatcgg	6	9	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:35604882A>C	ENST00000539068.1	-	3	361	c.159T>G	c.(157-159)gtT>gtG	p.V53V	FKBP5_ENST00000536438.1_Silent_p.V53V|FKBP5_ENST00000357266.4_Silent_p.V53V|FKBP5_ENST00000540787.1_Intron|FKBP5_ENST00000542713.1_Silent_p.V53V	NM_001145776.1	NP_001139248.1	Q13451	FKBP5_HUMAN	FK506 binding protein 5	53	PPIase FKBP-type 1. {ECO:0000255|PROSITE- ProRule:PRU00277}.				chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	FK506 binding (GO:0005528)|heat shock protein binding (GO:0031072)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(3)|urinary_tract(2)	17						AATGGACATAAACTTTGTCTC	0.363																																					p.V53V		Atlas-SNP	.											.	FKBP5	64	.	0			c.T159G						.						112	102	105					6																	35604882		2203	4300	6503	SO:0001819	synonymous_variant	2289	exon4			GACATAAACTTTG	U42031	CCDS4808.1, CCDS54996.1	6p21.31	2013-01-10	2001-11-28		ENSG00000096060	ENSG00000096060		"Tetratricopeptide (TTC) repeat domain containing"	3721	protein-coding gene	gene with protein product		602623	"FK506-binding protein 5"			9001212	Standard	NM_004117		Approved	FKBP51, FKBP54, PPIase, P54, Ptg-10	uc003okx.2	Q13451	OTTHUMG00000014576	ENST00000539068.1:c.159T>G	chr6.hg19:g.35604882A>C		204.0	0.0		117.0	40.0	NM_001145775	F5H7R1|Q59EB8|Q5TGM6	Silent	SNP	ENST00000539068.1	hg19	CCDS4808.1																																																																																			.	.		0.363	FKBP5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040309.2			C	35604882	A	C	35604882	2	2	254	1	0	0	0	0	0	0	0	1	5919	1	1	5		5	FKBP5	6	35604882	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	316129	35604882	135510185	300	34592										
SLC26A8	116369	hgsc.bcm.edu	37	chr6	35918964	35918964	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tctgtttctgagtaggtttcCcgtatcactgtctcggattc	9	10	4	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:35918964C>A	ENST00000490799.1	-	19	2801	c.2448G>T	c.(2446-2448)cgG>cgT	p.R816R	SLC26A8_ENST00000355574.2_Silent_p.R816R|SLC26A8_ENST00000394602.2_Silent_p.R711R	NM_052961.3	NP_443193.1			solute carrier family 26 (anion exchanger), member 8											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(6)|lung(16)|ovary(3)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	46						AGTAGGTTTCCCGTATCACTG	0.542																																					p.R816R		Atlas-SNP	.											.	SLC26A8	95	.	0			c.G2448T						.						140	119	126					6																	35918964		2203	4300	6503	SO:0001819	synonymous_variant	116369	exon19			GGTTTCCCGTATC	AF331522	CCDS4813.1, CCDS4814.1	6p21	2013-07-18	2013-07-18		ENSG00000112053	ENSG00000112053		"Solute carriers"	14468	protein-coding gene	gene with protein product		608480	"solute carrier family 26, member 8"			11834742, 11829495	Standard	NM_001193476		Approved		uc003olm.3	Q96RN1	OTTHUMG00000014586	ENST00000490799.1:c.2448G>T	chr6.hg19:g.35918964C>A		146.0	0.0		99.0	4.0	NM_052961		Silent	SNP	ENST00000490799.1	hg19	CCDS4813.1																																																																																			.	.		0.542	SLC26A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040325.2			A	35918964	C	A	35918964	2	1	254	1	0	0	0	0	0	0	0	1	14538	610	22	3		3	SLC26A8	6	35918964	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	314082	35918964	135196103	301	34593										
TREM2	54209	hgsc.bcm.edu	37	chr6	41130810	41130810	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agagtaagatgagcagccggAgaggctccatgccacccttc	12	12	0	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:41130810A>G	ENST00000373113.3	-	1	104	c.11T>C	c.(10-12)cTc>cCc	p.L4P	TREM2_ENST00000338469.3_Missense_Mutation_p.L4P|TREM2_ENST00000373122.4_Missense_Mutation_p.L4P	NM_018965.2	NP_061838.1	Q9NZC2	TREM2_HUMAN	triggering receptor expressed on myeloid cells 2	4					axon guidance (GO:0007411)|dendritic cell differentiation (GO:0097028)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|positive regulation of antigen processing and presentation of peptide antigen via MHC class II (GO:0002588)|positive regulation of C-C chemokine receptor CCR7 signaling pathway (GO:1903082)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of CD40 signaling pathway (GO:2000350)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein localization to plasma membrane (GO:1903078)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lipopolysaccharide binding (GO:0001530)|receptor activity (GO:0004872)|scaffold protein binding (GO:0097110)			breast(1)|endometrium(2)|large_intestine(4)|lung(2)|ovary(1)|pancreas(1)	11	Ovarian(28;0.0418)|Colorectal(47;0.196)					GAGCAGCCGGAGAGGCTCCAT	0.567																																					p.L4P		Atlas-SNP	.											.	TREM2	35	.	0			c.T11C						.						118	89	99					6																	41130810		2203	4300	6503	SO:0001583	missense	54209	exon1			AGCCGGAGAGGCT	AF213457	CCDS4852.1, CCDS64422.1	6p21.1	2014-09-17	2002-08-15		ENSG00000095970	ENSG00000095970		"Immunoglobulin superfamily / V-set domain containing"	17761	protein-coding gene	gene with protein product		605086	"triggering receptor expressed on myeloid cells 2a"			10799849, 12080485	Standard	NM_001271821		Approved	TREM-2, Trem2a, Trem2b, Trem2c	uc003opy.3	Q9NZC2	OTTHUMG00000014671	ENST00000373113.3:c.11T>C	chr6.hg19:g.41130810A>G	ENSP00000362205:p.Leu4Pro	139.0	0.0		88.0	4.0	NM_018965	Q8N5H8|Q8WYN6	Missense_Mutation	SNP	ENST00000373113.3	hg19	CCDS4852.1	.	.	.	.	.	.	.	.	.	.	A	15.00	2.703761	0.48412	.	.	ENSG00000095970	ENST00000373113;ENST00000338469;ENST00000373122	T;T;T	0.59224	0.28;0.56;0.39	4.8	2.36	0.29203	.	.	.	.	.	T	0.53738	0.1815	L	0.53249	1.67	0.21652	N	0.999608	D;D;B	0.76494	0.999;0.997;0.011	D;D;B	0.67548	0.952;0.931;0.008	T	0.38845	-0.9642	9	0.87932	D	0	19.6202	7.4957	0.27487	0.8232:0.0:0.1768:0.0	.	4;4;4	Q9NZC2-2;Q9NZC2-3;Q9NZC2	.;.;TREM2_HUMAN	P	4	ENSP00000362205:L4P;ENSP00000342651:L4P;ENSP00000362214:L4P	ENSP00000342651:L4P	L	-	2	0	TREM2	41238788	0.152000	0.22762	0.025000	0.17156	0.155000	0.21991	2.089000	0.41672	0.863000	0.35553	0.459000	0.35465	CTC	.	.		0.567	TREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040499.1	NM_018965		G	41130810	A	G	41130810	3	3	254	1	0	0	0	0	1	0	0	0	16486	304	11	2	701	2	TREM2	6	41130810	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	5211846	41130810	129984257	302	34594										
KLHL31	401265	hgsc.bcm.edu	37	chr6	53516499	53516499	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	acacgccgacagtggcctcgGgtagctcgtcgtcctccgtc	12	16	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:53516499G>T	ENST00000407079.1	-	2	1801	c.1802C>A	c.(1801-1803)cCc>cAc	p.P601H	KLHL31_ENST00000370905.3_Missense_Mutation_p.P601H			Q9H511	KLH31_HUMAN	kelch-like family member 31	601					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					autonomic_ganglia(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|prostate(3)	20	Lung NSC(77;0.0158)					AGTGGCCTCGGGTAGCTCGTC	0.607											OREG0017507	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P601H		Atlas-SNP	.											.	KLHL31	48	.	0			c.C1802A						.						121	105	110					6																	53516499		2203	4300	6503	SO:0001583	missense	401265	exon3			GCCTCGGGTAGCT		CCDS34478.1	6p12.1	2013-09-27	2013-02-22	2007-01-09	ENSG00000124743	ENSG00000124743		"Kelch-like", "BTB/POZ domain containing"	21353	protein-coding gene	gene with protein product		610749	"kelch repeat and BTB (POZ) domain containing 1", "kelch-like 31 (Drosophila)"	KBTBD1			Standard	NM_001003760		Approved	bA345L23.2, BKLHD6	uc003pcb.4	Q9H511	OTTHUMG00000014882	ENST00000407079.1:c.1802C>A	chr6.hg19:g.53516499G>T	ENSP00000384644:p.Pro601His	133.0	0.0	993	88.0	5.0	NM_001003760	A6N9J2|B2RP49	Missense_Mutation	SNP	ENST00000407079.1	hg19	CCDS34478.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.519413	0.85495	.	.	ENSG00000124743	ENST00000370905;ENST00000407079	T;T	0.71341	-0.56;-0.56	5.77	5.77	0.91146	Galactose oxidase, beta-propeller (1);	0.000000	0.85682	D	0.000000	T	0.78836	0.4346	M	0.71206	2.165	0.80722	D	1	D	0.76494	0.999	D	0.64042	0.921	T	0.72017	-0.4417	10	0.23891	T	0.37	.	20.3473	0.98799	0.0:0.0:1.0:0.0	.	601	Q9H511	KLH31_HUMAN	H	601	ENSP00000359942:P601H;ENSP00000384644:P601H	ENSP00000359942:P601H	P	-	2	0	KLHL31	53624458	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.868000	0.87116	2.884000	0.98904	0.655000	0.94253	CCC	.	.		0.607	KLHL31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040965.1	NM_001003760		T	53516499	G	T	53516499	3	4	254	1	0	0	0	0	1	0	0	0	8394	1232	43	3	106	3	KLHL31	6	53516499	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	12385689	53516499	117598568	303	34595										
DST	667	hgsc.bcm.edu	37	chr6	56350122	56350122	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aacaataccttgtgattatcGatcagattcatcaccaaatc	4	10	3	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:56350122G>T	ENST00000361203.3	-	83	20242	c.20235C>A	c.(20233-20235)atC>atA	p.I6745I	DST_ENST00000244364.6_Silent_p.I4442I|DST_ENST00000312431.6_3'UTR|DST_ENST00000370769.4_Silent_p.I6856I|DST_ENST00000370754.5_Silent_p.I7034I|DST_ENST00000421834.2_Silent_p.I4768I|DST_ENST00000370788.2_Silent_p.I4659I|DST_ENST00000446842.2_Silent_p.I6530I			Q03001	DYST_HUMAN	dystonin	6744					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)	p.I6856I(1)		NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TGTGATTATCGATCAGATTCA	0.363																																					p.I4442I		Atlas-SNP	.											DST_ENST00000370769,pharynx,carcinoma,0,1	DST	1427	.	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.C13326A						.						128	122	124					6																	56350122		1841	4084	5925	SO:0001819	synonymous_variant	667	exon69			ATTATCGATCAGA	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.20235C>A	chr6.hg19:g.56350122G>T		150.0	0.0		106.0	5.0	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000361203.3	hg19																																																																																				.	.		0.363	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		T	56350122	G	T	56350122	2	4	254	1	0	0	0	0	0	0	0	1	4785	1048	37	1		1	DST	6	56350122	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	2833623	56350122	114764945	304	34596										
DST	667	hgsc.bcm.edu	37	chr6	56365936	56365936	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctcctccaacaggtttctgcTcacttagcaagccctcggtg	8	15	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:56365936T>C	ENST00000361203.3	-	75	18885	c.18878A>G	c.(18877-18879)gAg>gGg	p.E6293G	DST_ENST00000244364.6_Missense_Mutation_p.E3990G|DST_ENST00000312431.6_3'UTR|DST_ENST00000340834.4_5'UTR|DST_ENST00000370769.4_Missense_Mutation_p.E6404G|DST_ENST00000370754.5_Missense_Mutation_p.E6582G|DST_ENST00000421834.2_Missense_Mutation_p.E4316G|DST_ENST00000370788.2_Missense_Mutation_p.E4207G|DST_ENST00000446842.2_Missense_Mutation_p.E6078G			Q03001	DYST_HUMAN	dystonin	6292					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			AGGTTTCTGCTCACTTAGCAA	0.478																																					p.E3990G		Atlas-SNP	.											.	DST	1427	.	0			c.A11969G						.						99	96	97					6																	56365936		1947	4142	6089	SO:0001583	missense	667	exon61			TTCTGCTCACTTA	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.18878A>G	chr6.hg19:g.56365936T>C	ENSP00000354508:p.Glu6293Gly	103.0	0.0		77.0	5.0	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	hg19		.	.	.	.	.	.	.	.	.	.	T	17.02	3.283157	0.59867	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T	0.53206	0.63;0.63;0.63;0.63;0.63;0.63;0.63	5.88	5.88	0.94601	.	0.000000	0.53938	D	0.000042	T	0.57755	0.2075	M	0.62154	1.92	0.33747	D	0.620107	D;D;D;P;B	0.69078	0.96;0.997;0.993;0.896;0.093	P;D;D;P;B	0.73380	0.859;0.98;0.926;0.562;0.059	T	0.57837	-0.7742	9	0.39692	T	0.17	.	16.2744	0.82636	0.0:0.0:0.0:1.0	.	4316;6404;6582;6402;3990	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	G	3990;6582;6404;4316;6078;4207;6293	ENSP00000244364:E3990G;ENSP00000359790:E6582G;ENSP00000359805:E6404G;ENSP00000400883:E4316G;ENSP00000393645:E6078G;ENSP00000359824:E4207G;ENSP00000354508:E6293G	ENSP00000244364:E3990G	E	-	2	0	DST	56473895	1.000000	0.71417	0.957000	0.39632	0.686000	0.39977	5.093000	0.64517	2.237000	0.73441	0.482000	0.46254	GAG	.	.		0.478	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		C	56365936	T	C	56365936	3	2	254	1	0	0	0	0	1	0	0	0	4785	1551	54	2	3642	2	DST	6	56365936	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	15814	56365936	114749131	305	34597										
DST	667	hgsc.bcm.edu	37	chr6	56376052	56376052	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcacgctttttgacatcttcTttaatttgactgtaaagggt	8	7	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:56376052T>C	ENST00000361203.3	-	68	17770	c.17763A>G	c.(17761-17763)aaA>aaG	p.K5921K	DST_ENST00000244364.6_Silent_p.K3618K|DST_ENST00000312431.6_3'UTR|DST_ENST00000340834.4_5'UTR|DST_ENST00000370769.4_Silent_p.K6032K|DST_ENST00000370754.5_Silent_p.K6210K|DST_ENST00000421834.2_Silent_p.K3944K|DST_ENST00000370788.2_Silent_p.K3835K|DST_ENST00000446842.2_Silent_p.K5706K			Q03001	DYST_HUMAN	dystonin	5922					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TGACATCTTCTTTAATTTGAC	0.428																																					p.K3618K		Atlas-SNP	.											.	DST	1427	.	0			c.A10854G						.						61	56	58					6																	56376052		1882	4109	5991	SO:0001819	synonymous_variant	667	exon54			ATCTTCTTTAATT	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.17763A>G	chr6.hg19:g.56376052T>C		164.0	0.0		132.0	6.0	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000361203.3	hg19																																																																																				.	.		0.428	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		C	56376052	T	C	56376052	2	2	254	1	0	0	0	0	0	0	0	1	4785	1606	56	2		2	DST	6	56376052	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	10116	56376052	114739015	306	34598										
EYS	346007	hgsc.bcm.edu	37	chr6	66094343	66094343	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agttgatgctgagcagtttaCagtggtcaattgctttctca	10	7	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:66094343C>T	ENST00000370621.3	-	8	1761	c.1235G>A	c.(1234-1236)tGt>tAt	p.C412Y	EYS_ENST00000393380.2_Missense_Mutation_p.C412Y|EYS_ENST00000370618.3_Missense_Mutation_p.C412Y|EYS_ENST00000503581.1_Missense_Mutation_p.C412Y|EYS_ENST00000342421.5_Missense_Mutation_p.C412Y|EYS_ENST00000370616.2_Missense_Mutation_p.C412Y			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	412					detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						GAGCAGTTTACAGTGGTCAAT	0.299																																					p.C412Y		Atlas-SNP	.											.	EYS	527	.	0			c.G1235A						.						101	98	99					6																	66094343		2202	4295	6497	SO:0001583	missense	346007	exon8			AGTTTACAGTGGT		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.1235G>A	chr6.hg19:g.66094343C>T	ENSP00000359655:p.Cys412Tyr	131.0	0.0		83.0	4.0	NM_001142801	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	hg19		.	.	.	.	.	.	.	.	.	.	C	15.44	2.834902	0.50951	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616;ENST00000393380;ENST00000342421;ENST00000370618	T;T;T;D;D;D	0.96685	1.35;1.35;1.35;-4.09;-4.09;-4.09	6.07	5.21	0.72293	.	.	.	.	.	D	0.98365	0.9457	H	0.95645	3.7	0.30964	N	0.723299	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.74023	0.962;0.982;0.96	D	0.97376	0.9979	9	0.87932	D	0	.	14.343	0.66641	0.0:0.9296:0.0:0.0704	.	412;412;412	Q5T1H1-1;Q5T1H1-2;Q5SZM4	.;.;.	Y	412	ENSP00000424243:C412Y;ENSP00000359655:C412Y;ENSP00000359650:C412Y;ENSP00000377042:C412Y;ENSP00000341818:C412Y;ENSP00000359652:C412Y	ENSP00000341818:C412Y	C	-	2	0	EYS	66151064	1.000000	0.71417	0.008000	0.14137	0.409000	0.31022	5.635000	0.67841	1.578000	0.49821	0.655000	0.94253	TGT	.	.		0.299	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		T	66094343	C	T	66094343	3	4	254	1	0	0	0	0	1	0	0	0	5334	478	17	3	8305	3	EYS	6	66094343	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	9718291	66094343	105020724	307	34599										
BAI3	577	hgsc.bcm.edu	37	chr6	69666002	69666002	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agcagagaagccggcagtgcActgcagctgcccatggaggc	15	12	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:69666002A>G	ENST00000370598.1	+	7	2103	c.1282A>G	c.(1282-1284)Act>Gct	p.T428A		NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	428	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				CCGGCAGTGCACTGCAGCTGC	0.542																																					p.T428A		Atlas-SNP	.											.	BAI3	451	.	0			c.A1282G						.						76	68	71					6																	69666002		2203	4300	6503	SO:0001583	missense	577	exon7			CAGTGCACTGCAG	AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"-", "GPCR / Class B : Orphans"	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.1282A>G	chr6.hg19:g.69666002A>G	ENSP00000359630:p.Thr428Ala	93.0	0.0		70.0	4.0	NM_001704	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	ENST00000370598.1	hg19	CCDS4968.1	.	.	.	.	.	.	.	.	.	.	A	14.81	2.646796	0.47258	.	.	ENSG00000135298	ENST00000370598	T	0.50548	0.74	5.71	4.53	0.55603	.	0.127331	0.53938	D	0.000049	T	0.22975	0.0555	L	0.37697	1.125	0.80722	D	1	B	0.11235	0.004	B	0.11329	0.006	T	0.07462	-1.0771	10	0.54805	T	0.06	.	12.2372	0.54522	0.8725:0.0:0.0:0.1275	.	428	O60242	BAI3_HUMAN	A	428	ENSP00000359630:T428A	ENSP00000359630:T428A	T	+	1	0	BAI3	69722723	1.000000	0.71417	1.000000	0.80357	0.815000	0.46073	5.837000	0.69381	0.976000	0.38417	0.482000	0.46254	ACT	.	.		0.542	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			G	69666002	A	G	69666002	3	3	254	1	0	0	0	0	1	0	0	0	1300	159	6	2	1300	2	BAI3	6	69666002	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	3571659	69666002	101449065	308	34600										
COL19A1	1310	hgsc.bcm.edu	37	chr6	70897949	70897949	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccaggcatccctggcattccGgtaagtagtgctaagacgct	11	12	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:70897949G>T	ENST00000322773.4	+	47	3129	c.3027G>T	c.(3025-3027)ccG>ccT	p.P1009P	COL19A1_ENST00000393344.1_Splice_Site_p.P631P	NM_001858.4	NP_001849.2	Q14993	COJA1_HUMAN	collagen, type XIX, alpha 1	1009	Triple-helical region 5 (COL5).				cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)|skeletal muscle tissue development (GO:0007519)|skeletal system development (GO:0001501)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(8)|lung(54)|ovary(3)|prostate(2)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	109						CTGGCATTCCGGTAAGTAGTG	0.522																																					p.P1009P		Atlas-SNP	.											COL19A1,right_upper_lobe,carcinoma,+1,1	COL19A1	232	.	0			c.G3027T						.						43	43	43					6																	70897949		2203	4300	6503	SO:0001630	splice_region_variant	1310	exon47			CATTCCGGTAAGT		CCDS4970.1	6q12-q13	2013-01-16			ENSG00000082293	ENSG00000082293		"Collagens"	2196	protein-coding gene	gene with protein product		120165				7916703, 9143499	Standard	NM_001858		Approved		uc003pfc.1	Q14993	OTTHUMG00000014987	ENST00000322773.4:c.3027+1G>T	chr6.hg19:g.70897949G>T		120.0	1.0		97.0	4.0	NM_001858	Q00559|Q05850|Q12885|Q13676|Q14DH1|Q5JUF0|Q5T424|Q9H572|Q9NPZ2|Q9NQP2	Silent	SNP	ENST00000322773.4	hg19	CCDS4970.1																																																																																			.	.		0.522	COL19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041127.1		Silent	T	70897949	G	T	70897949	5	4	254	1	0	0	0	0	0	0	1	0	3678	1130	39	1	3209	1	COL19A1	6	70897949	Splice_Site	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1231947	70897949	100217118	309	34601										
TMEM30A	55754	hgsc.bcm.edu	37	chr6	75970580	75970580	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	atagctccacaaggagcaatTggtttgtcttcatttcttcg	8	9	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:75970580T>C	ENST00000230461.6	-	4	830	c.501A>G	c.(499-501)ccA>ccG	p.P167P	TMEM30A_ENST00000475111.2_Silent_p.P131P|TMEM30A_ENST00000370050.5_Silent_p.P48P	NM_018247.3	NP_060717.1	Q9NV96	CC50A_HUMAN	transmembrane protein 30A	167					drug transmembrane transport (GO:0006855)|phospholipid translocation (GO:0045332)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endosome (GO:0036010)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(1)|haematopoietic_and_lymphoid_tissue(8)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						AAGGAGCAATTGGTTTGTCTT	0.338																																					p.P167P		Atlas-SNP	.											.	TMEM30A	40	.	0			c.A501G						.						165	151	156					6																	75970580		2203	4300	6503	SO:0001819	synonymous_variant	55754	exon4			AGCAATTGGTTTG	AK001718	CCDS4983.1, CCDS47453.1	6q14.1	2014-01-28	2004-06-17	2004-06-18	ENSG00000112697	ENSG00000112697			16667	protein-coding gene	gene with protein product		611028	"chromosome 6 open reading frame 67"	C6orf67		15375526	Standard	NM_001143958		Approved	FLJ10856, CDC50A	uc003phw.2	Q9NV96	OTTHUMG00000015050	ENST00000230461.6:c.501A>G	chr6.hg19:g.75970580T>C		263.0	0.0		189.0	69.0	NM_018247	A8K9V8|E1P539|Q658Z3|Q96H09|Q9NSL9	Silent	SNP	ENST00000230461.6	hg19	CCDS4983.1																																																																																			.	.		0.338	TMEM30A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041248.2	NM_018247		C	75970580	T	C	75970580	2	2	254	1	0	0	0	0	0	0	0	1	16168	1799	63	2		2	TMEM30A	6	75970580	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	5072631	75970580	95144487	310	34602										
MYO6	4646	hgsc.bcm.edu	37	chr6	76542624	76542624	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctatcattgtatctggagaaTcaggagccggcaaaacagaa	10	8	3	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:76542624T>A	ENST00000369977.3	+	6	596	c.457T>A	c.(457-459)Tca>Aca	p.S153T	MYO6_ENST00000369985.4_Missense_Mutation_p.S153T|MYO6_ENST00000369981.3_Missense_Mutation_p.S153T|MYO6_ENST00000369975.1_Missense_Mutation_p.S153T	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI	153	Myosin motor.				actin filament-based movement (GO:0030048)|auditory receptor cell differentiation (GO:0042491)|cellular response to electrical stimulus (GO:0071257)|dendrite development (GO:0016358)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|endocytosis (GO:0006897)|glutamate secretion (GO:0014047)|inner ear morphogenesis (GO:0042472)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein targeting (GO:0006605)|regulation of secretion (GO:0051046)|regulation of synaptic plasticity (GO:0048167)|response to drug (GO:0042493)|sensory perception of sound (GO:0007605)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell cortex (GO:0005938)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microvillus (GO:0005902)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|unconventional myosin complex (GO:0016461)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|minus-end directed microfilament motor activity (GO:0060001)|motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(16)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	58		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		ATCTGGAGAATCAGGAGCCGG	0.373																																					p.S153T		Atlas-SNP	.											.	MYO6	124	.	0			c.T457A						.						83	89	87					6																	76542624		2203	4300	6503	SO:0001583	missense	4646	exon6			GGAGAATCAGGAG	U90236, AB002387	CCDS34487.1, CCDS75481.1	6q14.1	2014-09-17	2004-05-19		ENSG00000196586	ENSG00000196586		"Myosins / Myosin superfamily : Class VI"	7605	protein-coding gene	gene with protein product		600970	"deafness, autosomal recessive 37"	DFNA22, DFNB37		9259267, 11468689	Standard	XM_005248719		Approved	KIAA0389	uc003pih.1	Q9UM54	OTTHUMG00000015061	ENST00000369977.3:c.457T>A	chr6.hg19:g.76542624T>A	ENSP00000358994:p.Ser153Thr	109.0	0.0		84.0	4.0	NM_004999	A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	Missense_Mutation	SNP	ENST00000369977.3	hg19	CCDS34487.1	.	.	.	.	.	.	.	.	.	.	T	27.7	4.852950	0.91355	.	.	ENSG00000196586	ENST00000428345;ENST00000369981;ENST00000369985;ENST00000369977;ENST00000369975	D;D;D;D	0.96136	-3.92;-3.92;-3.92;-3.92	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	D	0.98614	0.9536	H	0.97896	4.1	0.80722	D	1	D;D	0.71674	0.998;0.96	D;D	0.79108	0.992;0.923	D	0.99802	1.1036	10	0.87932	D	0	.	15.8146	0.78589	0.0:0.0:0.0:1.0	.	153;153	Q9UM54-2;Q9UM54-1	.;.	T	153	ENSP00000358998:S153T;ENSP00000359002:S153T;ENSP00000358994:S153T;ENSP00000358992:S153T	ENSP00000358992:S153T	S	+	1	0	MYO6	76599344	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	7.630000	0.83225	2.193000	0.70182	0.528000	0.53228	TCA	.	.		0.373	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041279.2	NM_004999		A	76542624	T	A	76542624	3	1	254	1	0	0	0	0	1	0	0	0	10090	1435	50	4	475	4	MYO6	6	76542624	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	572044	76542624	94572443	311	34603										
SNAP91	9892	hgsc.bcm.edu	37	chr6	84300973	84300973	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gatgaactagaagcagcctgAgatgcaggttggggttcaga	15	6	1	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:84300973A>G	ENST00000439399.2	-	22	2287	c.1971T>C	c.(1969-1971)tcT>tcC	p.S657S	SNAP91_ENST00000437520.1_Intron|SNAP91_ENST00000521743.1_Silent_p.S657S|SNAP91_ENST00000520213.1_Intron|SNAP91_ENST00000521485.1_Silent_p.S657S|SNAP91_ENST00000195649.6_Silent_p.S657S|SNAP91_ENST00000369694.2_Silent_p.S657S|SNAP91_ENST00000520302.1_Silent_p.S627S|SNAP91_ENST00000428679.2_Silent_p.S657S	NM_014841.2	NP_055656.1	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa	657					clathrin coat assembly (GO:0048268)|protein transport (GO:0015031)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|protein kinase binding (GO:0019901)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(22)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		AAGCAGCCTGAGATGCAGGTT	0.363																																					p.S657S		Atlas-SNP	.											.	SNAP91	199	.	0			c.T1971C						.						124	118	120					6																	84300973		1865	4103	5968	SO:0001819	synonymous_variant	9892	exon21			AGCCTGAGATGCA	AB014556	CCDS47455.1, CCDS56437.1, CCDS56438.1	6q15	2012-12-07	2012-12-07		ENSG00000065609	ENSG00000065609			14986	protein-coding gene	gene with protein product		607923	"synaptosomal-associated protein, 91 kDa (mouse) homolog", "synaptosomal-associated protein, 91kDa homolog (mouse)"			9734811, 12493563, 10436022	Standard	NM_014841		Approved	KIAA0656, AP180, CALM	uc003pka.3	O60641	OTTHUMG00000015114	ENST00000439399.2:c.1971T>C	chr6.hg19:g.84300973A>G		87.0	0.0		44.0	4.0	NM_001242792	A8K0L7|E5RI02|Q5JX13|Q68DL9|Q6P9D3|Q9NTY7	Silent	SNP	ENST00000439399.2	hg19	CCDS47455.1																																																																																			.	.		0.363	SNAP91-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375296.1			G	84300973	A	G	84300973	2	3	254	1	0	0	0	0	0	0	0	1	14848	291	11	2		2	SNAP91	6	84300973	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	7758349	84300973	86814094	312	34604										
CASP8AP2	9994	hgsc.bcm.edu	37	chr6	90577355	90577355	+	RNA	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctctttaacagtaccatcgcCtctgaagtcagatggtcatc	7	12	4	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:90577355C>T	ENST00000551025.1	+	0	5783									caspase 8 associated protein 2											NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2)	51		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		GTACCATCGCCTCTGAAGTCA	0.398																																					p.P1449L	Colon(187;1656 2025 17045 31481 39901)	Atlas-SNP	.											.	CASP8AP2	108	.	0			c.C4346T						.						91	89	90					6																	90577355		1890	4110	6000			9994	exon8			CATCGCCTCTGAA	AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"FLICE-associated huge protein"	606880	"CASP8 associated protein 2"			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		chr6.hg19:g.90577355C>T		105.0	0.0		79.0	4.0	NM_001137667		Missense_Mutation	SNP	ENST00000551025.1	hg19																																																																																				.	.		0.398	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667		T	90577355	C	T	90577355	1	4	254	0	1	0	0	0	0	0	0	0	2680	681	24	3		3	CASP8AP2	6	90577355	RNA	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	6276382	90577355	80537712	313	34605										
BACH2	60468	hgsc.bcm.edu	37	chr6	90661010	90661010	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gctcacttttaatctgccccCtggcaagccccggcttgagg	10	15	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:90661010C>A	ENST00000257749.4	-	7	1522	c.815G>T	c.(814-816)aGg>aTg	p.R272M	BACH2_ENST00000343122.3_Missense_Mutation_p.R272M|RP3-512E2.2_ENST00000445838.1_RNA|RP3-512E2.2_ENST00000413986.1_RNA|BACH2_ENST00000537989.1_Missense_Mutation_p.R272M	NM_021813.2	NP_068585.1	Q9BYV9	BACH2_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 2	272						cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	45		all_cancers(76;7.37e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.0063)		BRCA - Breast invasive adenocarcinoma(108;0.0799)		AATCTGCCCCCTGGCAAGCCC	0.532																																					p.R272M		Atlas-SNP	.											.	BACH2	224	.	0			c.G815T						.						76	78	77					6																	90661010		2203	4300	6503	SO:0001583	missense	60468	exon5			TGCCCCCTGGCAA	AL121787	CCDS5026.1	6q15	2013-01-10			ENSG00000112182	ENSG00000112182		"BTB/POZ domain containing", "basic leucine zipper proteins"	14078	protein-coding gene	gene with protein product		605394				10949928, 12829606	Standard	NM_001170794		Approved	BTBD25	uc003pnw.3	Q9BYV9	OTTHUMG00000015216	ENST00000257749.4:c.815G>T	chr6.hg19:g.90661010C>A	ENSP00000257749:p.Arg272Met	135.0	0.0		95.0	4.0	NM_001170794	E1P518|Q59H70|Q5T793|Q9NTS5	Missense_Mutation	SNP	ENST00000257749.4	hg19	CCDS5026.1	.	.	.	.	.	.	.	.	.	.	C	1.851	-0.464926	0.04476	.	.	ENSG00000112182	ENST00000257749;ENST00000537989;ENST00000343122	T;T;T	0.35605	1.3;1.3;1.3	5.03	1.12	0.20585	.	0.868689	0.10677	N	0.646818	T	0.06781	0.0173	N	0.03608	-0.345	0.23607	N	0.997304	B	0.02656	0.0	B	0.01281	0.0	T	0.39251	-0.9623	10	0.45353	T	0.12	-22.7857	12.7214	0.57144	0.5957:0.4043:0.0:0.0	.	272	Q9BYV9	BACH2_HUMAN	M	272	ENSP00000257749:R272M;ENSP00000437473:R272M;ENSP00000345642:R272M	ENSP00000257749:R272M	R	-	2	0	BACH2	90717731	0.997000	0.39634	0.726000	0.30738	0.426000	0.31534	2.704000	0.47118	0.051000	0.15978	-1.321000	0.01291	AGG	.	.		0.532	BACH2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041522.2	NM_021813		A	90661010	C	A	90661010	3	1	254	1	0	0	0	0	1	0	0	0	1284	681	24	3	1722	3	BACH2	6	90661010	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	83655	90661010	80454057	314	34606										
MANEA	79694	hgsc.bcm.edu	37	chr6	96034523	96034523	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agagtgacagaatcaacagtGaaacaaataccaagaattta	7	6	1	5			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:96034523G>A	ENST00000358812.4	+	2	342	c.208G>A	c.(208-210)Gaa>Aaa	p.E70K	MANEA_ENST00000369293.1_Missense_Mutation_p.E70K	NM_024641.3	NP_078917.2	Q5SRI9	MANEA_HUMAN	mannosidase, endo-alpha	70	Catalytic. {ECO:0000305}.				cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	glycoprotein endo-alpha-1,2-mannosidase activity (GO:0004569)			breast(2)|endometrium(3)|kidney(2)|liver(2)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26		all_cancers(76;1.01e-06)|Acute lymphoblastic leukemia(125;3.58e-09)|all_hematologic(75;1.22e-06)|all_epithelial(107;0.00433)|Colorectal(196;0.0341)		BRCA - Breast invasive adenocarcinoma(108;0.148)		AATCAACAGTGAAACAAATAC	0.358																																					p.E70K		Atlas-SNP	.											.	MANEA	58	.	0			c.G208A						.						83	86	85					6																	96034523		2203	4300	6503	SO:0001583	missense	79694	exon2			AACAGTGAAACAA	AK022900	CCDS5032.1	6q16.2	2008-02-05			ENSG00000172469	ENSG00000172469			21072	protein-coding gene	gene with protein product		612327					Standard	NM_024641		Approved	FLJ12838, mandaselin	uc003poo.2	Q5SRI9	OTTHUMG00000016296	ENST00000358812.4:c.208G>A	chr6.hg19:g.96034523G>A	ENSP00000351669:p.Glu70Lys	111.0	0.0		96.0	4.0	NM_024641	A6H8M6|Q5SRJ0|Q6MZV0|Q70JE9|Q7Z3V7|Q8WWX5|Q9H9D2	Missense_Mutation	SNP	ENST00000358812.4	hg19	CCDS5032.1	.	.	.	.	.	.	.	.	.	.	G	13.90	2.374741	0.42105	.	.	ENSG00000172469	ENST00000358812;ENST00000369293;ENST00000542500	.	.	.	5.82	4.77	0.60923	.	0.314947	0.38548	N	0.001645	T	0.33614	0.0869	L	0.57536	1.79	0.43317	D	0.995333	B;P	0.38597	0.041;0.639	B;B	0.34652	0.048;0.187	T	0.30534	-0.9975	9	0.07482	T	0.82	-23.6425	14.8901	0.70604	0.0804:0.0:0.9196:0.0	.	70;70	Q5SRI9;Q8WWX4	MANEA_HUMAN;.	K	70	.	ENSP00000351669:E70K	E	+	1	0	MANEA	96141244	0.998000	0.40836	1.000000	0.80357	0.995000	0.86356	1.586000	0.36611	2.754000	0.94517	0.650000	0.86243	GAA	.	.		0.358	MANEA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043644.1	NM_024641		A	96034523	G	A	96034523	3	1	254	1	0	0	0	0	1	0	0	0	9230	1291	45	3	210	3	MANEA	6	96034523	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	5373513	96034523	75080544	315	34607										
BEND3	57673	hgsc.bcm.edu	37	chr6	107390471	107390471	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cgtgtcccggcgccggcagcGctcatccagtttgcccacga	12	17	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:107390471G>T	ENST00000369042.1	-	4	2114	c.1924C>A	c.(1924-1926)Cgc>Agc	p.R642S	BEND3_ENST00000429433.2_Missense_Mutation_p.R642S			Q5T5X7	BEND3_HUMAN	BEN domain containing 3	642	BEN 3. {ECO:0000255|PROSITE- ProRule:PRU00784}.									central_nervous_system(1)|cervix(2)|endometrium(3)|large_intestine(7)|lung(10)|ovary(4)|prostate(3)	30						CGCCGGCAGCGCTCATCCAGT	0.637																																					p.R642S		Atlas-SNP	.											.	BEND3	70	.	0			c.C1924A						.						23	26	25					6																	107390471		2202	4299	6501	SO:0001583	missense	57673	exon5			GGCAGCGCTCATC	AB046773	CCDS34507.1	6q21	2012-11-22	2008-10-03	2008-10-03	ENSG00000178409	ENSG00000178409		"BEN domain containing"	23040	protein-coding gene	gene with protein product			"KIAA1553"	KIAA1553			Standard	NM_001080450		Approved		uc003prs.2	Q5T5X7	OTTHUMG00000015308	ENST00000369042.1:c.1924C>A	chr6.hg19:g.107390471G>T	ENSP00000358038:p.Arg642Ser	94.0	0.0		77.0	4.0	NM_001080450	A2RRH2|Q9HCL9	Missense_Mutation	SNP	ENST00000369042.1	hg19	CCDS34507.1	.	.	.	.	.	.	.	.	.	.	G	12.41	1.928665	0.34002	.	.	ENSG00000178409	ENST00000369042;ENST00000429433	T;T	0.44083	0.93;0.93	4.62	2.61	0.31194	BEN domain (2);	0.000000	0.85682	D	0.000000	T	0.20700	0.0498	L	0.29908	0.895	0.49915	D	0.999832	P	0.43909	0.821	P	0.46237	0.508	T	0.04565	-1.0942	10	0.72032	D	0.01	-8.309	6.9748	0.24669	0.0:0.1256:0.4778:0.3965	.	642	Q5T5X7	BEND3_HUMAN	S	642	ENSP00000358038:R642S;ENSP00000411268:R642S	ENSP00000358038:R642S	R	-	1	0	BEND3	107497164	1.000000	0.71417	1.000000	0.80357	0.425000	0.31504	2.710000	0.47169	1.126000	0.42016	0.555000	0.69702	CGC	.	.		0.637	BEND3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041686.1	NM_020913		T	107390471	G	T	107390471	3	4	254	1	0	0	0	0	1	0	0	0	1399	1087	38	1	566	1	BEND3	6	107390471	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	11355948	107390471	63724596	316	34608										
WASF1	8936	hgsc.bcm.edu	37	chr6	110426738	110426738	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cgccgcctgtcatgaggtgcTcttggcactttttctggttc	11	12	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:110426738T>C	ENST00000392589.1	-	8	1421	c.585A>G	c.(583-585)agA>agG	p.R195R	WASF1_ENST00000359451.2_Silent_p.R195R|WASF1_ENST00000392586.1_Silent_p.R195R|WASF1_ENST00000392587.2_Silent_p.R195R|WASF1_ENST00000392588.1_Silent_p.R195R	NM_003931.2	NP_003922.1	Q92558	WASF1_HUMAN	WAS protein family, member 1	195					actin filament polymerization (GO:0030041)|cellular component movement (GO:0006928)|lamellipodium morphogenesis (GO:0072673)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|protein complex assembly (GO:0006461)|Rac protein signal transduction (GO:0016601)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytoskeleton (GO:0005856)|lamellipodium (GO:0030027)|mitochondrial outer membrane (GO:0005741)|SCAR complex (GO:0031209)|synapse (GO:0045202)	protein complex binding (GO:0032403)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	16		all_cancers(87;1.18e-05)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488)		OV - Ovarian serous cystadenocarcinoma(136;0.0364)|Epithelial(106;0.051)|all cancers(137;0.0687)		CATGAGGTGCTCTTGGCACTT	0.418																																					p.R195R		Atlas-SNP	.											.	WASF1	35	.	0			c.A585G						.						101	96	98					6																	110426738		2203	4300	6503	SO:0001819	synonymous_variant	8936	exon7			AGGTGCTCTTGGC	D87459	CCDS5080.1	6q21	2010-08-20			ENSG00000112290	ENSG00000112290		"A-kinase anchor proteins"	12732	protein-coding gene	gene with protein product		605035				9843499, 9889097	Standard	XM_005267204		Approved	WAVE1, SCAR1, KIAA0269, WAVE	uc003pty.1	Q92558	OTTHUMG00000015357	ENST00000392589.1:c.585A>G	chr6.hg19:g.110426738T>C		103.0	0.0		95.0	4.0	NM_001024935	E1P5F2|Q5SZK7	Silent	SNP	ENST00000392589.1	hg19	CCDS5080.1																																																																																			.	.		0.418	WASF1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041784.3	NM_003931		C	110426738	T	C	110426738	2	2	254	1	0	0	0	0	0	0	0	1	17267	1548	54	2		2	WASF1	6	110426738	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	3036267	110426738	60688329	317	34609										
HS3ST5	222537	hgsc.bcm.edu	37	chr6	114383915	114383915	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcacccacctatccaagctcCcaactctggcgactagatac	6	17	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:114383915C>A	ENST00000312719.5	-	4	1283	c.95G>T	c.(94-96)gGg>gTg	p.G32V	HS3ST5_ENST00000411826.1_Missense_Mutation_p.G32V|RP3-399L15.3_ENST00000523087.1_RNA|RP3-399L15.3_ENST00000519104.1_RNA|RP3-399L15.3_ENST00000519270.1_RNA			Q8IZT8	HS3S5_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	32					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|negative regulation of coagulation (GO:0050819)|protein sulfation (GO:0006477)|regulation of viral entry into host cell (GO:0046596)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)			breast(4)|endometrium(2)|kidney(1)|large_intestine(7)|lung(17)|ovary(1)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	41		all_cancers(87;0.0587)|Colorectal(196;0.0676)|all_epithelial(87;0.154)		OV - Ovarian serous cystadenocarcinoma(136;0.00937)|all cancers(137;0.0117)|Epithelial(106;0.0274)|GBM - Glioblastoma multiforme(226;0.143)		ATCCAAGCTCCCAACTCTGGC	0.478																																					p.G32V		Atlas-SNP	.											.	HS3ST5	80	.	0			c.G95T						.						153	152	152					6																	114383915		2203	4300	6503	SO:0001583	missense	222537	exon1			AAGCTCCCAACTC	AF503292	CCDS34517.1	6q21	2011-11-16			ENSG00000249853	ENSG00000249853		"Sulfotransferases, membrane-bound"	19419	protein-coding gene	gene with protein product		609407				12138164	Standard	NM_153612		Approved	3-OST-5	uc003pwg.4	Q8IZT8	OTTHUMG00000015412	ENST00000312719.5:c.95G>T	chr6.hg19:g.114383915C>A	ENSP00000427888:p.Gly32Val	125.0	0.0		100.0	4.0	NM_153612	A8K1J2|Q52LI2|Q8N285	Missense_Mutation	SNP	ENST00000312719.5	hg19	CCDS34517.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.371444	0.82573	.	.	ENSG00000249853	ENST00000312719;ENST00000411826	T;T	0.48836	0.8;0.8	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.50222	0.1603	N	0.19112	0.55	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.53725	-0.8398	10	0.56958	D	0.05	.	20.6593	0.99626	0.0:1.0:0.0:0.0	.	32	Q8IZT8	HS3S5_HUMAN	V	32	ENSP00000427888:G32V;ENSP00000440332:G32V	ENSP00000427888:G32V	G	-	2	0	HS3ST5	114490608	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.022000	0.76431	2.885000	0.99019	0.655000	0.94253	GGG	.	.		0.478	HS3ST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041911.2	NM_153612		A	114383915	C	A	114383915	3	1	254	1	0	0	0	0	1	0	0	0	7377	623	22	3	953	3	HS3ST5	6	114383915	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	3957177	114383915	56731152	318	34610										
ZUFSP	221302	hgsc.bcm.edu	37	chr6	116988328	116988328	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtctggttctgaggttactgTttcaccacaaatattacagg	9	8	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:116988328T>C	ENST00000368576.3	-	2	271	c.28A>G	c.(28-30)Aca>Gca	p.T10A	ZUFSP_ENST00000471919.1_Intron|ZUFSP_ENST00000368573.1_Missense_Mutation_p.T10A	NM_145062.2	NP_659499.2	Q96AP4	ZUFSP_HUMAN	zinc finger with UFM1-specific peptidase domain	10							metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(6)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	21				GBM - Glioblastoma multiforme(226;0.0258)|all cancers(137;0.0368)|OV - Ovarian serous cystadenocarcinoma(136;0.0464)|Epithelial(106;0.186)		GAGGTTACTGTTTCACCACAA	0.328																																					p.T10A		Atlas-SNP	.											.	ZUFSP	46	.	0			c.A28G						.						72	74	74					6																	116988328		2187	4291	6478	SO:0001583	missense	221302	exon2			TTACTGTTTCACC	AK054582	CCDS5110.1	6q22.31	2013-01-28	2008-03-25	2008-03-25	ENSG00000153975	ENSG00000153975		"Zinc fingers, C2H2-type"	21224	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 113"	C6orf113			Standard	NM_145062		Approved	dJ412I7.3	uc003pxf.2	Q96AP4	OTTHUMG00000015445	ENST00000368576.3:c.28A>G	chr6.hg19:g.116988328T>C	ENSP00000357565:p.Thr10Ala	120.0	0.0		99.0	4.0	NM_145062	Q5TD92|Q6PJH7|Q96NV6	Missense_Mutation	SNP	ENST00000368576.3	hg19	CCDS5110.1	.	.	.	.	.	.	.	.	.	.	T	12.13	1.846093	0.32606	.	.	ENSG00000153975	ENST00000368576;ENST00000368573	T;T	0.41400	1.0;1.67	5.94	3.47	0.39725	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	0.317816	0.34484	N	0.003921	T	0.09158	0.0226	L	0.29908	0.895	0.25697	N	0.985626	B	0.26400	0.148	B	0.22386	0.039	T	0.18085	-1.0348	10	0.10902	T	0.67	-10.347	4.3961	0.11363	0.0:0.1566:0.1762:0.6671	.	10	Q96AP4	ZUFSP_HUMAN	A	10	ENSP00000357565:T10A;ENSP00000357562:T10A	ENSP00000357562:T10A	T	-	1	0	ZUFSP	117095021	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	1.412000	0.34714	2.272000	0.75746	0.459000	0.35465	ACA	.	.		0.328	ZUFSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041961.1	NM_145062		C	116988328	T	C	116988328	3	2	254	1	0	0	0	0	1	0	0	0	18261	1725	60	2	1744	2	ZUFSP	6	116988328	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	2604413	116988328	54126739	319	34611										
GOPC	57120	hgsc.bcm.edu	37	chr6	117884507	117884507	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcacttgcagtgcccaggtcTccattttcatgtgtgtcagt	9	11	4	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:117884507T>C	ENST00000368498.2	-	9	1374	c.1299A>G	c.(1297-1299)ggA>ggG	p.G433G	GOPC_ENST00000535237.1_Silent_p.G433G|GOPC_ENST00000467125.1_Intron|DCBLD1_ENST00000296955.8_Intron|GOPC_ENST00000052569.6_Silent_p.G425G	NM_020399.3	NP_065132.1	Q9HD26	GOPC_HUMAN	golgi-associated PDZ and coiled-coil motif containing	433					apical protein localization (GO:0045176)|cytoplasmic sequestering of CFTR protein (GO:0043004)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi to plasma membrane transport (GO:0006893)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)|spermatid nucleus differentiation (GO:0007289)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|trans-Golgi network transport vesicle (GO:0030140)	ion channel binding (GO:0044325)|small GTPase regulator activity (GO:0005083)		GOPC/ROS1(14)	endometrium(1)|large_intestine(3)|lung(4)|ovary(1)	9		all_cancers(87;0.00844)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0363)|OV - Ovarian serous cystadenocarcinoma(136;0.0821)|all cancers(137;0.0976)		TGCCCAGGTCTCCATTTTCAT	0.363			O	ROS1	glioblastoma																																p.G433G		Atlas-SNP	.		Dom	yes		6	6q21	57120	golgi associated PDZ and coiled-coil motif containing		O	.	GOPC	29	.	0			c.A1299G						.						132	123	126					6																	117884507		2203	4300	6503	SO:0001819	synonymous_variant	57120	exon9			CAGGTCTCCATTT	AF287894	CCDS5117.1, CCDS34523.1	6q21	2010-02-12	2010-02-12		ENSG00000047932	ENSG00000047932			17643	protein-coding gene	gene with protein product		606845				11162552, 11520064	Standard	NM_020399		Approved	dJ94G16.2, PIST, FIG, GOPC1, CAL		Q9HD26	OTTHUMG00000015457	ENST00000368498.2:c.1299A>G	chr6.hg19:g.117884507T>C		129.0	0.0		96.0	4.0	NM_020399	A6NM30|Q59FS4|Q969U8	Silent	SNP	ENST00000368498.2	hg19	CCDS5117.1																																																																																			.	.		0.363	GOPC-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041988.1	NM_020399		C	117884507	T	C	117884507	2	2	254	1	0	0	0	0	0	0	0	1	6581	1538	54	2		2	GOPC	6	117884507	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	896179	117884507	53230560	320	34612										
RNF146	81847	hgsc.bcm.edu	37	chr6	127607967	127607967	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agcttcatggcttggaaagcGgtgtgctctttgtcgacaag	13	8	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:127607967G>T	ENST00000368314.1	+	3	633	c.209G>T	c.(208-210)cGg>cTg	p.R70L	RNF146_ENST00000477776.1_3'UTR|RNF146_ENST00000309649.3_Missense_Mutation_p.R69L|RNF146_ENST00000608991.1_Missense_Mutation_p.R69L|RNF146_ENST00000480444.1_3'UTR|RNF146_ENST00000610153.1_Missense_Mutation_p.R70L|RNF146_ENST00000356799.2_3'UTR|RNF146_ENST00000489534.1_3'UTR|RNF146_ENST00000476956.1_3'UTR	NM_001242850.1|NM_001242851.1	NP_001229779.1|NP_001229780.1	Q9NTX7	RN146_HUMAN	ring finger protein 146	70					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein autoubiquitination (GO:0051865)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly-ADP-D-ribose binding (GO:0072572)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	10				GBM - Glioblastoma multiforme(226;0.0407)|all cancers(137;0.2)		CTTGGAAAGCGGTGTGCTCTT	0.458																																					p.R70L		Atlas-SNP	.											.	RNF146	31	.	0			c.G209T						.						136	116	123					6																	127607967		2203	4300	6503	SO:0001583	missense	81847	exon3			GAAAGCGGTGTGC	AK027558	CCDS5136.1, CCDS56449.1	6q22.1-q22.33	2008-02-05			ENSG00000118518	ENSG00000118518		"RING-type (C3HC4) zinc fingers"	21336	protein-coding gene	gene with protein product		612137					Standard	NM_001242844		Approved	DKFZp434O1427, dactylidin, dJ351K20.1	uc021zes.1	Q9NTX7	OTTHUMG00000015522	ENST00000368314.1:c.209G>T	chr6.hg19:g.127607967G>T	ENSP00000357297:p.Arg70Leu	243.0	0.0		200.0	9.0	NM_001242850	E1P572|Q6FIB2|Q7L8H4|Q96K03|Q96T06|Q9NTX6	Missense_Mutation	SNP	ENST00000368314.1	hg19	CCDS56449.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.545107	0.86022	.	.	ENSG00000118518	ENST00000368314;ENST00000356799;ENST00000309649	D;D;D	0.86097	-2.07;-2.07;-2.07	5.8	5.8	0.92144	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.000000	0.85682	D	0.000000	D	0.87775	0.6262	L	0.38733	1.17	0.80722	D	1	D	0.71674	0.998	D	0.69142	0.962	D	0.88401	0.3015	10	0.72032	D	0.01	1.2613	20.0734	0.97734	0.0:0.0:1.0:0.0	.	70	Q9NTX7	RN146_HUMAN	L	70;69;69	ENSP00000357297:R70L;ENSP00000349253:R69L;ENSP00000309365:R69L	ENSP00000309365:R69L	R	+	2	0	RNF146	127649660	1.000000	0.71417	0.998000	0.56505	0.957000	0.61999	9.809000	0.99208	2.748000	0.94277	0.655000	0.94253	CGG	.	.		0.458	RNF146-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042112.1	NM_030963		T	127607967	G	T	127607967	3	4	254	1	0	0	0	0	1	0	0	0	13463	1116	39	1	208	1	RNF146	6	127607967	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	9723460	127607967	43507100	321	34613										
THEMIS	387357	hgsc.bcm.edu	37	chr6	128134090	128134090	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggttagcagggttaactttgTttcctctactgaggggtgtt	13	6	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:128134090T>C	ENST00000368248.2	-	4	1844	c.1696A>G	c.(1696-1698)Aca>Gca	p.T566A	THEMIS_ENST00000368250.1_Missense_Mutation_p.T487A|THEMIS_ENST00000537166.1_Missense_Mutation_p.T531A|THEMIS_ENST00000543064.1_Missense_Mutation_p.T566A	NM_001010923.2	NP_001010923.1	Q8N1K5	THMS1_HUMAN	thymocyte selection associated	566					negative T cell selection (GO:0043383)|positive T cell selection (GO:0043368)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(3)	60						GTTAACTTTGTTTCCTCTACT	0.483																																					p.T566A		Atlas-SNP	.											.	THEMIS	168	.	0			c.A1696G						.						140	143	142					6																	128134090		2203	4300	6503	SO:0001583	missense	387357	exon4			ACTTTGTTTCCTC	AK094863	CCDS34534.1, CCDS55055.1	6q22.33	2012-02-08	2009-06-25	2009-06-25	ENSG00000172673	ENSG00000172673			21569	protein-coding gene	gene with protein product	"thymocyte expressed molecule involved in selection"	613607	"chromosome 6 open reading frame 207", "chromosome 6 open reading frame 190", "thymocyte selection pathway associated"	C6orf207, C6orf190, TSEPA		19597499, 19597498, 19597497	Standard	NM_001010923		Approved	bA325O24.4, FLJ40584, bA325O24.3	uc011ebt.2	Q8N1K5	OTTHUMG00000015534	ENST00000368248.2:c.1696A>G	chr6.hg19:g.128134090T>C	ENSP00000357231:p.Thr566Ala	88.0	0.0		95.0	4.0	NM_001010923	A1L4F0|A8K7N1|B3KT31|B3KW32|B3KY07|F5H1J9|Q5T3C4|Q5T3C5|Q6MZT7	Missense_Mutation	SNP	ENST00000368248.2	hg19	CCDS34534.1	.	.	.	.	.	.	.	.	.	.	T	0.006	-2.041446	0.00402	.	.	ENSG00000172673	ENST00000368250;ENST00000543064;ENST00000368248;ENST00000537166	T;T;T;T	0.17054	2.3;2.31;2.3;2.3	5.96	2.33	0.28932	.	0.600804	0.16591	N	0.207743	T	0.03095	0.0091	L	0.40543	1.245	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.06405	0.002;0.001	T	0.46816	-0.9164	10	0.11182	T	0.66	-0.125	5.2204	0.15366	0.0:0.3037:0.1454:0.5509	.	566;566	F5H1J9;Q8N1K5	.;THMS1_HUMAN	A	487;566;566;531	ENSP00000357233:T487A;ENSP00000439594:T566A;ENSP00000357231:T566A;ENSP00000439863:T531A	ENSP00000357231:T566A	T	-	1	0	THEMIS	128175783	0.006000	0.16342	0.001000	0.08648	0.023000	0.10783	1.016000	0.29976	0.171000	0.19730	0.533000	0.62120	ACA	.	.		0.483	THEMIS-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_001010923		C	128134090	T	C	128134090	3	2	254	1	0	0	0	0	1	0	0	0	15875	1725	60	2	362	2	THEMIS	6	128134090	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	526123	128134090	42980977	322	34614										
ENPP3	5169	hgsc.bcm.edu	37	chr6	131996238	131996238	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agatgtggctgacagcaatgTatcaaggtttaaaagccgct	11	7	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:131996238T>C	ENST00000414305.1	+	10	1109	c.781T>C	c.(781-783)Tat>Cat	p.Y261H	ENPP3_ENST00000543135.1_Missense_Mutation_p.Y227H|ENPP3_ENST00000427148.2_3'UTR|ENPP3_ENST00000358229.5_Missense_Mutation_p.Y261H|ENPP3_ENST00000357639.3_Missense_Mutation_p.Y261H			O14638	ENPP3_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 3	261	Phosphodiesterase.				immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)	metal ion binding (GO:0046872)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0252)|OV - Ovarian serous cystadenocarcinoma(155;0.0511)		GACAGCAATGTATCAAGGTTT	0.398																																					p.Y261H		Atlas-SNP	.											.	ENPP3	117	.	0			c.T781C						.						92	88	89					6																	131996238		2203	4300	6503	SO:0001583	missense	5169	exon9			GCAATGTATCAAG	AF005632	CCDS5148.1	6q22	2010-06-23			ENSG00000154269	ENSG00000154269	3.1.4.1, 3.6.1.9	"CD molecules"	3358	protein-coding gene	gene with protein product		602182		PDNP3		9344668	Standard	NM_005021		Approved	PD-IBETA, gp130RB13-6, B10, CD203c	uc003qcv.3	O14638	OTTHUMG00000016292	ENST00000414305.1:c.781T>C	chr6.hg19:g.131996238T>C	ENSP00000406261:p.Tyr261His	92.0	0.0		84.0	4.0	NM_005021	Q5JTL3	Missense_Mutation	SNP	ENST00000414305.1	hg19	CCDS5148.1	.	.	.	.	.	.	.	.	.	.	T	12.38	1.921957	0.33908	.	.	ENSG00000154269	ENST00000414305;ENST00000357639;ENST00000543135;ENST00000358229	T;T;T;T	0.72051	-0.62;-0.62;-0.62;-0.62	5.52	1.65	0.23941	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.203901	0.34178	N	0.004181	T	0.33118	0.0852	N	0.25286	0.73	0.80722	D	1	B	0.15719	0.014	B	0.23852	0.049	T	0.09271	-1.0682	10	0.29301	T	0.29	-11.3445	6.093	0.20005	0.2494:0.0713:0.0:0.6794	.	261	O14638	ENPP3_HUMAN	H	261;261;227;261	ENSP00000406261:Y261H;ENSP00000350265:Y261H;ENSP00000440810:Y227H;ENSP00000350964:Y261H	ENSP00000350265:Y261H	Y	+	1	0	ENPP3	132037931	1.000000	0.71417	0.998000	0.56505	0.887000	0.51463	1.583000	0.36579	0.356000	0.24157	0.363000	0.22086	TAT	.	.		0.398	ENPP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043627.2			C	131996238	T	C	131996238	3	2	254	1	0	0	0	0	1	0	0	0	5133	1638	57	2	815	2	ENPP3	6	131996238	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	3862148	131996238	39118829	323	34615										
ENPP3	5169	hgsc.bcm.edu	37	chr6	132068028	132068028	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggcttgacttctatcaggatAaagtgcagcctgtctctgaa	10	9	3	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:132068028A>G	ENST00000414305.1	+	26	2888	c.2560A>G	c.(2560-2562)Aaa>Gaa	p.K854E	ENPP3_ENST00000358229.5_3'UTR|ENPP3_ENST00000357639.3_Missense_Mutation_p.K854E			O14638	ENPP3_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 3	854	Nuclease.				immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)	metal ion binding (GO:0046872)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0252)|OV - Ovarian serous cystadenocarcinoma(155;0.0511)		CTATCAGGATAAAGTGCAGCC	0.363																																					p.K854E		Atlas-SNP	.											.	ENPP3	117	.	0			c.A2560G						.						67	70	69					6																	132068028		2203	4300	6503	SO:0001583	missense	5169	exon25			CAGGATAAAGTGC	AF005632	CCDS5148.1	6q22	2010-06-23			ENSG00000154269	ENSG00000154269	3.1.4.1, 3.6.1.9	"CD molecules"	3358	protein-coding gene	gene with protein product		602182		PDNP3		9344668	Standard	NM_005021		Approved	PD-IBETA, gp130RB13-6, B10, CD203c	uc003qcv.3	O14638	OTTHUMG00000016292	ENST00000414305.1:c.2560A>G	chr6.hg19:g.132068028A>G	ENSP00000406261:p.Lys854Glu	217.0	0.0		151.0	37.0	NM_005021	Q5JTL3	Missense_Mutation	SNP	ENST00000414305.1	hg19	CCDS5148.1	.	.	.	.	.	.	.	.	.	.	A	8.833	0.940494	0.18281	.	.	ENSG00000154269	ENST00000414305;ENST00000357639	T;T	0.73258	-0.73;-0.73	5.45	5.45	0.79879	DNA/RNA non-specific endonuclease (1);Extracellular Endonuclease, subunit A (1);	0.249386	0.35378	N	0.003250	T	0.59702	0.2213	M	0.68317	2.08	0.30983	N	0.722258	B	0.32467	0.372	B	0.39771	0.309	T	0.61382	-0.7074	10	0.37606	T	0.19	-20.724	11.7667	0.51935	0.8531:0.1469:0.0:0.0	.	854	O14638	ENPP3_HUMAN	E	854	ENSP00000406261:K854E;ENSP00000350265:K854E	ENSP00000350265:K854E	K	+	1	0	ENPP3	132109721	0.430000	0.25538	0.028000	0.17463	0.009000	0.06853	3.820000	0.55693	2.190000	0.69967	0.482000	0.46254	AAA	.	.		0.363	ENPP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043627.2			G	132068028	A	G	132068028	3	3	254	1	0	0	0	0	1	0	0	0	5133	363	13	2	2658	2	ENPP3	6	132068028	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	71790	132068028	39047039	324	34616										
VNN2	8875	hgsc.bcm.edu	37	chr6	133071001	133071001	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tttgcacttcagcagtgtgcAgacctatgtggaacaaacgc	10	10	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:133071001A>G	ENST00000326499.6	-	6	1328	c.1204T>C	c.(1204-1206)Tgc>Cgc	p.C402R	VNN2_ENST00000525289.1_Missense_Mutation_p.C181R|RP1-55C23.7_ENST00000430895.1_RNA|VNN2_ENST00000525270.1_Missense_Mutation_p.C349R	NM_004665.2	NP_004656	O95498	VNN2_HUMAN	vanin 2	402					cellular component movement (GO:0006928)|pantothenate metabolic process (GO:0015939)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	pantetheine hydrolase activity (GO:0017159)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(155;0.00237)|GBM - Glioblastoma multiforme(226;0.0267)		AGCAGTGTGCAGACCTATGTG	0.403																																					p.C402R		Atlas-SNP	.											.	VNN2	83	.	0			c.T1204C						.						84	75	78					6																	133071001		2203	4300	6503	SO:0001583	missense	8875	exon6			GTGTGCAGACCTA	AB026705	CCDS5161.1, CCDS5162.1, CCDS56451.1	6q23-q24	2013-02-13			ENSG00000112303	ENSG00000112303	3.5.1.92	"Vanins"	12706	protein-coding gene	gene with protein product	"pantetheinase"	603571				9790769, 11491533	Standard	NM_078488		Approved	FOAP-4, GPI-80	uc003qdt.3	O95498	OTTHUMG00000015588	ENST00000326499.6:c.1204T>C	chr6.hg19:g.133071001A>G	ENSP00000322276:p.Cys402Arg	115.0	0.0		93.0	4.0	NM_004665	A0AUZ3|A6NDY1|A8K4E3|A8K7W0|B2DFZ0|B2DFZ1|B2DFZ2|B2DFZ3|F6XL73|Q2XUN1|Q9UJF3|Q9UMW2	Missense_Mutation	SNP	ENST00000326499.6	hg19	CCDS5161.1	.	.	.	.	.	.	.	.	.	.	A	16.97	3.268007	0.59540	.	.	ENSG00000112303	ENST00000326499;ENST00000525270;ENST00000525289	D;D;D	0.96041	-3.89;-3.89;-3.89	5.2	5.2	0.72013	.	0.000000	0.64402	D	0.000002	D	0.98134	0.9384	H	0.94264	3.515	0.44643	D	0.997629	D;D	0.89917	1.0;1.0	D;D	0.91635	0.967;0.999	D	0.99466	1.0944	10	0.87932	D	0	-10.9792	14.0292	0.64604	1.0:0.0:0.0:0.0	.	181;402	O95498-2;O95498	.;VNN2_HUMAN	R	402;349;181	ENSP00000322276:C402R;ENSP00000436822:C349R;ENSP00000436935:C181R	ENSP00000322276:C402R	C	-	1	0	VNN2	133112694	1.000000	0.71417	0.119000	0.21687	0.003000	0.03518	5.911000	0.69939	1.967000	0.57214	0.533000	0.62120	TGC	.	.		0.403	VNN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042264.2			G	133071001	A	G	133071001	3	3	254	1	0	0	0	0	1	0	0	0	17198	188	7	2	366	2	VNN2	6	133071001	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	1002973	133071001	38044066	325	34617										
PEX7	5191	hgsc.bcm.edu	37	chr6	137193356	137193356	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttttcaccatttcatgcttcTgtgctggcctcttgctcgta	7	12	4	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:137193356T>C	ENST00000318471.4	+	8	849	c.768T>C	c.(766-768)tcT>tcC	p.S256S	PEX7_ENST00000541292.1_3'UTR	NM_000288.3	NP_000279.1	O00628	PEX7_HUMAN	peroxisomal biogenesis factor 7	256					endochondral ossification (GO:0001958)|ether lipid biosynthetic process (GO:0008611)|fatty acid beta-oxidation (GO:0006635)|neuron migration (GO:0001764)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)	cytosol (GO:0005829)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	enzyme binding (GO:0019899)|peroxisome matrix targeting signal-2 binding (GO:0005053)|protein homodimerization activity (GO:0042803)			lung(7)|prostate(1)	8	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000257)|OV - Ovarian serous cystadenocarcinoma(155;0.00492)		TTCATGCTTCTGTGCTGGCCT	0.323																																					p.S256S		Atlas-SNP	.											.	PEX7	24	.	0			c.T768C						.						144	148	147					6																	137193356		2202	4297	6499	SO:0001819	synonymous_variant	5191	exon8			TGCTTCTGTGCTG	AF180814	CCDS5180.1	6q21-q22.2	2013-01-10			ENSG00000112357	ENSG00000112357		"WD repeat domain containing"	8860	protein-coding gene	gene with protein product	"Refsum disease"	601757				9090381, 10673331	Standard	NM_000288		Approved	PTS2R, RD	uc003qhd.3	O00628	OTTHUMG00000015650	ENST00000318471.4:c.768T>C	chr6.hg19:g.137193356T>C		100.0	0.0		92.0	5.0	NM_000288	C0H5X6	Silent	SNP	ENST00000318471.4	hg19	CCDS5180.1																																																																																			.	.		0.323	PEX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042387.2	NM_000288		C	137193356	T	C	137193356	2	2	254	1	0	0	0	0	0	0	0	1	11760	1567	55	2		2	PEX7	6	137193356	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	4122355	137193356	33921711	326	34618										
PLEKHG1	57480	hgsc.bcm.edu	37	chr6	151152098	151152098	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agtgctggggagagcaacacAtgccctcctgaaataggaac	12	10	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:151152098A>G	ENST00000358517.2	+	15	2062	c.1851A>G	c.(1849-1851)acA>acG	p.T617T	PLEKHG1_ENST00000367328.1_Silent_p.T617T			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	617							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(19)|ovary(5)|prostate(4)|stomach(1)|urinary_tract(3)	53			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		AGAGCAACACATGCCCTCCTG	0.557																																					p.T617T		Atlas-SNP	.											.	PLEKHG1	97	.	0			c.A1851G						.						60	55	57					6																	151152098		2203	4300	6503	SO:0001819	synonymous_variant	57480	exon16			CAACACATGCCCT	AB033035	CCDS34552.1	6q25.1	2013-01-11			ENSG00000120278	ENSG00000120278		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	20884	protein-coding gene	gene with protein product						10574462	Standard	XM_005267064		Approved	KIAA1209, ARHGEF41	uc003qny.1	Q9ULL1	OTTHUMG00000015824	ENST00000358517.2:c.1851A>G	chr6.hg19:g.151152098A>G		114.0	0.0		62.0	4.0	NM_001029884	Q5T1F2	Silent	SNP	ENST00000358517.2	hg19	CCDS34552.1																																																																																			.	.		0.557	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042691.1			G	151152098	A	G	151152098	2	3	254	1	0	0	0	0	0	0	0	1	12077	204	8	2		2	PLEKHG1	6	151152098	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	13958742	151152098	19962969	327	34619										
ARID1B	57492	hgsc.bcm.edu	37	chr6	157502170	157502170	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cgagctggggaatgagccagAgagaaagctctgggtcgacc	16	9	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:157502170A>G	ENST00000350026.5	+	11	3165	c.3164A>G	c.(3163-3165)gAg>gGg	p.E1055G	ARID1B_ENST00000275248.4_Missense_Mutation_p.E1050G|ARID1B_ENST00000478761.2_3'UTR|ARID1B_ENST00000367148.1_Missense_Mutation_p.E1108G|ARID1B_ENST00000346085.5_Missense_Mutation_p.E1068G	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1055	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.				chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		AATGAGCCAGAGAGAAAGCTC	0.577																																					p.E1068G		Atlas-SNP	.											.	ARID1B	320	.	0			c.A3203G						.						92	76	82					6																	157502170		2203	4296	6499	SO:0001583	missense	57492	exon12			AGCCAGAGAGAAA	AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"-"	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.3164A>G	chr6.hg19:g.157502170A>G	ENSP00000055163:p.Glu1055Gly	73.0	0.0		38.0	4.0	NM_020732	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Missense_Mutation	SNP	ENST00000350026.5	hg19	CCDS5251.2	.	.	.	.	.	.	.	.	.	.	A	28.7	4.946609	0.92593	.	.	ENSG00000049618	ENST00000346085;ENST00000350026;ENST00000367148;ENST00000275248;ENST00000354354;ENST00000414678;ENST00000319584;ENST00000400790	T;T;T;T;T;T;T	0.48522	0.81;0.81;0.81;0.81;0.81;0.81;0.81	5.76	5.76	0.90799	ARID/BRIGHT DNA-binding domain (5);	0.000000	0.85682	D	0.000000	T	0.61223	0.2330	M	0.68317	2.08	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.91635	0.998;0.999;0.998;0.998	T	0.66432	-0.5925	10	0.87932	D	0	.	16.0796	0.80995	1.0:0.0:0.0:0.0	.	305;1055;1068;1050	Q8NFD5-4;Q8NFD5;Q8NFD5-2;G3XAA0	.;ARI1B_HUMAN;.;.	G	1068;1055;1108;1050;525;577;530;122	ENSP00000344546:E1068G;ENSP00000055163:E1055G;ENSP00000356116:E1108G;ENSP00000275248:E1050G;ENSP00000412835:E577G;ENSP00000313006:E530G;ENSP00000383596:E122G	ENSP00000275248:E1050G	E	+	2	0	ARID1B	157543862	1.000000	0.71417	0.990000	0.47175	0.994000	0.84299	9.339000	0.96797	2.195000	0.70347	0.528000	0.53228	GAG	.	.		0.577	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732		G	157502170	A	G	157502170	3	3	254	1	0	0	0	0	1	0	0	0	914	304	11	2	3249	2	ARID1B	6	157502170	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	6350072	157502170	13612897	328	34620										
ARID1B	57492	hgsc.bcm.edu	37	chr6	157502190	157502190	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agagaaagctctgggtcgacCgatacctcaccttcatggaa	10	11	3	1	rs387907144		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:157502190C>A	ENST00000350026.5	+	11	3185	c.3184C>A	c.(3184-3186)Cga>Aga	p.R1062R	ARID1B_ENST00000275248.4_Silent_p.R1057R|ARID1B_ENST00000478761.2_3'UTR|ARID1B_ENST00000367148.1_Silent_p.R1115R|ARID1B_ENST00000346085.5_Silent_p.R1075R	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1062	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.				chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		CTGGGTCGACCGATACCTCAC	0.562																																					p.R1075R		Atlas-SNP	.											ARID1B_ENST00000346085,NS,adenocarcinoma,0,2	ARID1B	320	.	0			c.C3223A						.						96	81	86					6																	157502190		2203	4296	6499	SO:0001819	synonymous_variant	57492	exon12			GTCGACCGATACC	AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"-"	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.3184C>A	chr6.hg19:g.157502190C>A		78.0	0.0		43.0	3.0	NM_020732	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Silent	SNP	ENST00000350026.5	hg19	CCDS5251.2																																																																																			.	.		0.562	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732		A	157502190	C	A	157502190	2	1	254	1	0	0	0	0	0	0	0	1	914	644	23	1		1	ARID1B	6	157502190	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	20	157502190	13612877	329	34621										
FNDC1	84624	hgsc.bcm.edu	37	chr6	159618551	159618551	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gacccacccaaagatgctacCagtagacctgtggagcatta	9	12	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:159618551C>A	ENST00000297267.9	+	2	398	c.198C>A	c.(196-198)acC>acA	p.T66T	FNDC1_ENST00000340366.6_Silent_p.T66T	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	66	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		AAGATGCTACCAGTAGACCTG	0.463																																					p.T66T		Atlas-SNP	.											.	FNDC1	250	.	0			c.C198A						.						170	162	165					6																	159618551		1965	4150	6115	SO:0001819	synonymous_variant	84624	exon2			TGCTACCAGTAGA	AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"Fibronectin type III domain containing"	21184	protein-coding gene	gene with protein product		609991	"fibronectin type III domain containing 2"	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.198C>A	chr6.hg19:g.159618551C>A		134.0	0.0		96.0	4.0	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Silent	SNP	ENST00000297267.9	hg19	CCDS47512.1	.	.	.	.	.	.	.	.	.	.	C	10.48	1.361524	0.24684	.	.	ENSG00000164694	ENST00000329629	.	.	.	6.11	6.11	0.99139	.	.	.	.	.	T	0.66366	0.2782	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63056	-0.6722	4	.	.	.	-7.2994	16.3193	0.82939	0.0:1.0:0.0:0.0	.	.	.	.	K	25	.	.	Q	+	1	0	FNDC1	159538539	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.939000	0.63526	2.928000	0.99379	0.638000	0.83543	CAG	.	.		0.463	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532		A	159618551	C	A	159618551	2	1	254	1	0	0	0	0	0	0	0	1	5976	581	21	3		3	FNDC1	6	159618551	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	2116361	159618551	11496516	330	34622										
IGF2R	3482	hgsc.bcm.edu	37	chr6	160450671	160450671	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gactattacatttgtttgccCgtcggagcggagagaggtaa	13	7	0	1	rs373279911		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:160450671C>A	ENST00000356956.1	+	7	1014	c.866C>A	c.(865-867)cCg>cAg	p.P289Q		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	289					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	TTTGTTTGCCCGTCGGAGCGG	0.562																																					p.P289Q		Atlas-SNP	.											.	IGF2R	251	.	0			c.C866A						.						115	94	101					6																	160450671		2203	4300	6503	SO:0001583	missense	3482	exon7			TTTGCCCGTCGGA	J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"CD molecules"	5467	protein-coding gene	gene with protein product	"cation-independent mannose-6 phosphate receptor"	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.866C>A	chr6.hg19:g.160450671C>A	ENSP00000349437:p.Pro289Gln	168.0	0.0		125.0	5.0	NM_000876	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	hg19	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	C	17.53	3.411954	0.62511	.	.	ENSG00000197081	ENST00000356956	T	0.13657	2.57	4.91	4.91	0.64330	Mannose-6-phosphate receptor, binding (1);	0.000000	0.85682	D	0.000000	T	0.36744	0.0978	M	0.87827	2.91	0.48830	D	0.999717	D	0.89917	1.0	D	0.97110	1.0	T	0.40997	-0.9533	10	0.66056	D	0.02	-32.3188	17.4451	0.87575	0.0:1.0:0.0:0.0	.	289	P11717	MPRI_HUMAN	Q	289	ENSP00000349437:P289Q	ENSP00000349437:P289Q	P	+	2	0	IGF2R	160370661	1.000000	0.71417	0.042000	0.18584	0.322000	0.28314	5.926000	0.70070	2.433000	0.82419	0.655000	0.94253	CCG	.	.		0.562	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876		A	160450671	C	A	160450671	3	1	254	1	0	0	0	0	1	0	0	0	7585	652	23	1	892	1	IGF2R	6	160450671	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	832120	160450671	10664396	331	34623										
SLC22A2	6582	hgsc.bcm.edu	37	chr6	160663434	160663434	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	taatttttagccattgtagaTctaagagggaaaagaacagt	9	4	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:160663434T>C	ENST00000366953.3	-	8	1538	c.1280A>G	c.(1279-1281)gAt>gGt	p.D427G	SLC22A2_ENST00000491092.1_5'UTR	NM_003058.3	NP_003049.2	O15244	S22A2_HUMAN	solute carrier family 22 (organic cation transporter), member 2	427					body fluid secretion (GO:0007589)|drug transmembrane transport (GO:0006855)|histamine transport (GO:0051608)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|organic cation transport (GO:0015695)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	choline transmembrane transporter activity (GO:0015220)|organic cation transmembrane transporter activity (GO:0015101)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|steroid binding (GO:0005496)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(16)|prostate(2)|skin(1)	27		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.28e-17)|BRCA - Breast invasive adenocarcinoma(81;6.29e-06)	Amantadine(DB00915)|Amiloride(DB00594)|Aminohippurate(DB00345)|Chlorphenamine(DB01114)|Choline(DB00122)|Cimetidine(DB00501)|Cisplatin(DB00515)|Cladribine(DB00242)|Cocaine(DB00907)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Desipramine(DB01151)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Diphenhydramine(DB01075)|Disopyramide(DB00280)|Dopamine(DB00988)|Epinephrine(DB00668)|Estradiol(DB00783)|Famotidine(DB00927)|Flurazepam(DB00690)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Imatinib(DB00619)|Imipramine(DB00458)|Lamivudine(DB00709)|Levofloxacin(DB01137)|Memantine(DB01043)|Metformin(DB00331)|Metoprolol(DB00264)|Nicotine(DB00184)|Norepinephrine(DB00368)|Oxaliplatin(DB00526)|Oxprenolol(DB01580)|Pancuronium(DB01337)|Phenformin(DB00914)|Phenoxybenzamine(DB00925)|Pramipexole(DB00413)|Prazosin(DB00457)|Probenecid(DB01032)|Procainamide(DB01035)|Progesterone(DB00396)|Propranolol(DB00571)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Reserpine(DB00206)|Thiamine(DB00152)|Tubocurarine(DB01199)|Vinblastine(DB00570)|Zidovudine(DB00495)	CCATTGTAGATCTAAGAGGGA	0.448																																					p.D427G		Atlas-SNP	.											.	SLC22A2	78	.	0			c.A1280G						.						128	117	120					6																	160663434		2203	4300	6503	SO:0001630	splice_region_variant	6582	exon8			TGTAGATCTAAGA	X98333	CCDS5276.1	6q25.3	2013-05-22			ENSG00000112499	ENSG00000112499		"Solute carriers"	10966	protein-coding gene	gene with protein product		602608				9605850	Standard	NM_003058		Approved	OCT2	uc003qtf.3	O15244	OTTHUMG00000015950	ENST00000366953.3:c.1280-1A>G	chr6.hg19:g.160663434T>C		124.0	0.0		61.0	4.0	NM_003058	Q5T7Q6|Q6PIQ8|Q8NG62|Q9NQB9	Missense_Mutation	SNP	ENST00000366953.3	hg19	CCDS5276.1	.	.	.	.	.	.	.	.	.	.	T	2.403	-0.337027	0.05278	.	.	ENSG00000112499	ENST00000366953	T	0.57107	0.42	5.13	2.71	0.32032	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.432615	0.27442	N	0.019345	T	0.21631	0.0521	L	0.48218	1.51	0.80722	D	1	B	0.17038	0.02	B	0.17979	0.02	T	0.06734	-1.0810	10	0.31617	T	0.26	.	4.3124	0.10977	0.1234:0.0688:0.1288:0.679	.	427	O15244	S22A2_HUMAN	G	427	ENSP00000355920:D427G	ENSP00000355920:D427G	D	-	2	0	SLC22A2	160583424	0.803000	0.28956	0.490000	0.27465	0.006000	0.05464	0.922000	0.28734	0.490000	0.27771	-0.336000	0.08194	GAT	.	.		0.448	SLC22A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042943.1	NM_003058	Missense_Mutation	C	160663434	T	C	160663434	5	2	254	1	0	0	0	0	0	0	1	0	14465	1449	50	2	403	2	SLC22A2	6	160663434	Splice_Site	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	212763	160663434	10451633	332	34624										
SLC22A2	6582	hgsc.bcm.edu	37	chr6	160666525	160666525	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tctgaggagttctgaccaagTcaagaaatgaagggttcaat	11	6	4	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:160666525T>C	ENST00000366953.3	-	6	1268	c.1010A>G	c.(1009-1011)gAc>gGc	p.D337G	SLC22A2_ENST00000491092.1_5'UTR|SLC22A2_ENST00000366952.1_Missense_Mutation_p.D316G	NM_003058.3	NP_003049.2	O15244	S22A2_HUMAN	solute carrier family 22 (organic cation transporter), member 2	337					body fluid secretion (GO:0007589)|drug transmembrane transport (GO:0006855)|histamine transport (GO:0051608)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|organic cation transport (GO:0015695)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	choline transmembrane transporter activity (GO:0015220)|organic cation transmembrane transporter activity (GO:0015101)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|steroid binding (GO:0005496)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(16)|prostate(2)|skin(1)	27		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.28e-17)|BRCA - Breast invasive adenocarcinoma(81;6.29e-06)	Amantadine(DB00915)|Amiloride(DB00594)|Aminohippurate(DB00345)|Chlorphenamine(DB01114)|Choline(DB00122)|Cimetidine(DB00501)|Cisplatin(DB00515)|Cladribine(DB00242)|Cocaine(DB00907)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Desipramine(DB01151)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Diphenhydramine(DB01075)|Disopyramide(DB00280)|Dopamine(DB00988)|Epinephrine(DB00668)|Estradiol(DB00783)|Famotidine(DB00927)|Flurazepam(DB00690)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Imatinib(DB00619)|Imipramine(DB00458)|Lamivudine(DB00709)|Levofloxacin(DB01137)|Memantine(DB01043)|Metformin(DB00331)|Metoprolol(DB00264)|Nicotine(DB00184)|Norepinephrine(DB00368)|Oxaliplatin(DB00526)|Oxprenolol(DB01580)|Pancuronium(DB01337)|Phenformin(DB00914)|Phenoxybenzamine(DB00925)|Pramipexole(DB00413)|Prazosin(DB00457)|Probenecid(DB01032)|Procainamide(DB01035)|Progesterone(DB00396)|Propranolol(DB00571)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Reserpine(DB00206)|Thiamine(DB00152)|Tubocurarine(DB01199)|Vinblastine(DB00570)|Zidovudine(DB00495)	TCTGACCAAGTCAAGAAATGA	0.358																																					p.D337G		Atlas-SNP	.											.	SLC22A2	78	.	0			c.A1010G						.						98	92	94					6																	160666525		2203	4300	6503	SO:0001583	missense	6582	exon6			ACCAAGTCAAGAA	X98333	CCDS5276.1	6q25.3	2013-05-22			ENSG00000112499	ENSG00000112499		"Solute carriers"	10966	protein-coding gene	gene with protein product		602608				9605850	Standard	NM_003058		Approved	OCT2	uc003qtf.3	O15244	OTTHUMG00000015950	ENST00000366953.3:c.1010A>G	chr6.hg19:g.160666525T>C	ENSP00000355920:p.Asp337Gly	85.0	0.0		79.0	4.0	NM_003058	Q5T7Q6|Q6PIQ8|Q8NG62|Q9NQB9	Missense_Mutation	SNP	ENST00000366953.3	hg19	CCDS5276.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.439366	0.83885	.	.	ENSG00000112499	ENST00000366953;ENST00000366952	T;T	0.73897	-0.79;-0.79	5.17	5.17	0.71159	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.88336	0.6409	H	0.94620	3.56	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	D	0.91638	0.5324	10	0.87932	D	0	.	15.1705	0.72869	0.0:0.0:0.0:1.0	.	337;337	O15244;O15244-2	S22A2_HUMAN;.	G	337;316	ENSP00000355920:D337G;ENSP00000355919:D316G	ENSP00000355919:D316G	D	-	2	0	SLC22A2	160586515	1.000000	0.71417	0.978000	0.43139	0.755000	0.42902	7.593000	0.82686	2.159000	0.67721	0.533000	0.62120	GAC	.	.		0.358	SLC22A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042943.1	NM_003058		C	160666525	T	C	160666525	3	2	254	1	0	0	0	0	1	0	0	0	14465	1667	58	2	681	2	SLC22A2	6	160666525	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	3091	160666525	10448542	333	34625										
MAP3K4	4216	hgsc.bcm.edu	37	chr6	161508771	161508771	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgtttgttccagacactcttGctgaggagaagagtattatt	10	6	1	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:161508771G>A	ENST00000392142.4	+	10	2756	c.2608G>A	c.(2608-2610)Gct>Act	p.A870T	MAP3K4_ENST00000366919.2_Missense_Mutation_p.A870T|MAP3K4_ENST00000366920.2_Missense_Mutation_p.A870T|MAP3K4_ENST00000348824.7_Missense_Mutation_p.A870T	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	870					activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		AGACACTCTTGCTGAGGAGAA	0.393																																					p.A870T		Atlas-SNP	.											.	MAP3K4	364	.	0			c.G2608A						.						103	102	102					6																	161508771		2203	4300	6503	SO:0001583	missense	4216	exon10			ACTCTTGCTGAGG	AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.2608G>A	chr6.hg19:g.161508771G>A	ENSP00000375986:p.Ala870Thr	129.0	0.0		92.0	4.0	NM_006724	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Missense_Mutation	SNP	ENST00000392142.4	hg19	CCDS34565.1	.	.	.	.	.	.	.	.	.	.	G	13.67	2.306302	0.40795	.	.	ENSG00000085511	ENST00000366919;ENST00000392142;ENST00000540111;ENST00000366920;ENST00000348824	T;T;T;T	0.71461	-0.57;-0.57;-0.57;-0.57	5.73	4.84	0.62591	.	0.382460	0.27544	N	0.018900	T	0.34337	0.0894	N	0.16478	0.41	0.09310	N	0.999998	B;B;B	0.15473	0.013;0.013;0.008	B;B;B	0.14023	0.007;0.01;0.005	T	0.11348	-1.0591	10	0.21014	T	0.42	-22.1873	13.8761	0.63653	0.0:0.0:0.7222:0.2778	.	870;870;870	F5H538;Q9Y6R4-2;Q9Y6R4	.;.;M3K4_HUMAN	T	870	ENSP00000355886:A870T;ENSP00000375986:A870T;ENSP00000355887:A870T;ENSP00000297332:A870T	ENSP00000297332:A870T	A	+	1	0	MAP3K4	161428761	0.990000	0.36364	0.265000	0.24526	0.964000	0.63967	3.493000	0.53266	1.514000	0.48869	0.655000	0.94253	GCT	.	.		0.393	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3			A	161508771	G	A	161508771	3	1	254	1	0	0	0	0	1	0	0	0	9261	1319	46	3	2646	3	MAP3K4	6	161508771	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	842246	161508771	9606296	334	34626										
RNASET2	8635	hgsc.bcm.edu	37	chr6	167356557	167356557	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	attacgtcaggccagtatgcCctcatttctggcaaaagatc	8	11	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr6:167356557C>T	ENST00000508775.1	-	5	801	c.282G>A	c.(280-282)agG>agA	p.R94R	RP11-514O12.4_ENST00000507747.1_Missense_Mutation_p.G75E|RNASET2_ENST00000496851.2_5'UTR|RNASET2_ENST00000476238.2_Silent_p.R94R|RNASET2_ENST00000366855.6_Silent_p.R56R	NM_003730.4	NP_003721.2	O00584	RNT2_HUMAN	ribonuclease T2	94					RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	ribonuclease activity (GO:0004540)|ribonuclease T2 activity (GO:0033897)|RNA binding (GO:0003723)			large_intestine(4)|lung(4)	8		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;1.53e-19)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00665)		GCCAGTATGCCCTCATTTCTG	0.413																																					p.R94R		Atlas-SNP	.											.	RNASET2	18	.	0			c.G282A						.						71	64	66					6																	167356557		2203	4300	6503	SO:0001819	synonymous_variant	8635	exon5			GTATGCCCTCATT	AJ419866	CCDS5295.1	6q27	2014-05-20			ENSG00000026297	ENSG00000026297			21686	protein-coding gene	gene with protein product		612944				9192857	Standard	NM_003730		Approved	RNASE6PL, FLJ10907, bA514O12.3	uc003qve.3	O00584	OTTHUMG00000016009	ENST00000508775.1:c.282G>A	chr6.hg19:g.167356557C>T		72.0	0.0		70.0	4.0	NM_003730	B2RDA7|E1P5C3|Q5T8Q0|Q8TCU2|Q9BZ46|Q9BZ47	Silent	SNP	ENST00000508775.1	hg19	CCDS5295.1	.	.	.	.	.	.	.	.	.	.	C	0.403	-0.917518	0.02396	.	.	ENSG00000249141	ENST00000507747	.	.	.	4.62	2.73	0.32206	.	.	.	.	.	T	0.31544	0.0800	.	.	.	0.53005	D	0.999961	.	.	.	.	.	.	T	0.21484	-1.0244	4	.	.	.	-5.6199	3.7476	0.08554	0.1703:0.5676:0.1657:0.0964	.	.	.	.	E	75	.	.	G	-	2	0	RP11-514O12.4	167276547	0.053000	0.20554	0.532000	0.27989	0.056000	0.15407	0.540000	0.23191	1.009000	0.39289	0.655000	0.94253	GGG	.	.		0.413	RNASET2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043089.2	NM_003730		T	167356557	C	T	167356557	2	4	254	1	0	0	0	0	0	0	0	1	13433	622	22	3		3	RNASET2	6	167356557	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	5847786	167356557	3758510	335	34627										
ADAP1	11033	hgsc.bcm.edu	37	chr7	975141	975141	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgtaggaggcccagtcgggaTctgcaagggaaagccggacg	17	9	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:975141T>C	ENST00000265846.5	-	2	302	c.83A>G	c.(82-84)gAt>gGt	p.D28G	ADAP1_ENST00000539900.1_Splice_Site_p.D39G|ADAP1_ENST00000463358.1_5'UTR	NM_001284308.1|NM_001284309.1|NM_001284311.1|NM_006869.2	NP_001271237.1|NP_001271238.1|NP_001271240.1|NP_006860	O75689	ADAP1_HUMAN	ArfGAP with dual PH domains 1	28	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				cell surface receptor signaling pathway (GO:0007166)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF GTPase activity (GO:0032312)|regulation of GTPase activity (GO:0043087)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|lung(3)|upper_aerodigestive_tract(1)	6						CCAGTCGGGATCTGCAAGGGA	0.662																																					p.D28G		Atlas-SNP	.											.	ADAP1	23	.	0			c.A83G						.						39	38	39					7																	975141		2189	4272	6461	SO:0001630	splice_region_variant	11033	exon2			TCGGGATCTGCAA	AJ006422	CCDS5318.1, CCDS64576.1, CCDS64577.1, CCDS75558.1	7p22.3	2013-01-10	2008-09-22	2008-09-22	ENSG00000105963	ENSG00000105963		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	16486	protein-coding gene	gene with protein product		608114	"centaurin, alpha 1"	CENTA1		10333475	Standard	NM_006869		Approved	GCS1L	uc003sjo.4	O75689	OTTHUMG00000023380	ENST00000265846.5:c.83-1A>G	chr7.hg19:g.975141T>C		143.0	0.0		93.0	4.0	NM_006869	A4D2Q2|B3KRZ4|B4DVA6|F6XZ68|H7C2Q4	Missense_Mutation	SNP	ENST00000265846.5	hg19	CCDS5318.1	.	.	.	.	.	.	.	.	.	.	T	11.18	1.563398	0.27915	.	.	ENSG00000105963	ENST00000265846;ENST00000539900;ENST00000435943	T;T;T	0.42131	0.98;0.98;0.98	4.62	3.37	0.38596	.	0.119179	0.53938	U	0.000044	T	0.33933	0.0880	L	0.49513	1.565	0.80722	D	1	B	0.02656	0.0	B	0.12837	0.008	T	0.12192	-1.0557	10	0.19147	T	0.46	.	10.8326	0.46669	0.0:0.0:0.1584:0.8416	.	28	O75689	ADAP1_HUMAN	G	28;39;15	ENSP00000265846:D28G;ENSP00000442682:D39G;ENSP00000394973:D15G	ENSP00000265846:D28G	D	-	2	0	ADAP1	941667	1.000000	0.71417	0.971000	0.41717	0.351000	0.29236	2.828000	0.48120	1.716000	0.51395	0.454000	0.30748	GAT	.	.		0.662	ADAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059701.2	NM_006869	Missense_Mutation	C	975141	T	C	975141	5	2	254	1	0	0	0	0	0	0	1	0	279	1449	50	2	1081	2	ADAP1	7	975141	Splice_Site	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10		975141	158163522	336	34628										
IQCE	23288	hgsc.bcm.edu	37	chr7	2644523	2644523	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cttccctgacaggcggctgtGgtgcttcaggcagctttcag	13	12	2	1	rs201471152		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:2644523G>A	ENST00000402050.2	+	19	1825	c.1641G>A	c.(1639-1641)gtG>gtA	p.V547V	IQCE_ENST00000325979.7_Silent_p.V482V|IQCE_ENST00000438376.2_Silent_p.V531V|IQCE_ENST00000404984.1_Silent_p.V496V	NM_001100390.1|NM_152558.3	NP_001093860.1|NP_689771.3	Q6IPM2	IQCE_HUMAN	IQ motif containing E	547	IQ 1. {ECO:0000255|PROSITE- ProRule:PRU00116}.					mitochondrion (GO:0005739)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;1.23e-13)		AGGCGGCTGTGGTGCTTCAGG	0.642																																					p.V547V		Atlas-SNP	.											.	IQCE	66	.	0			c.G1641A						.						41	48	46					7																	2644523		2081	4219	6300	SO:0001819	synonymous_variant	23288	exon19			GGCTGTGGTGCTT	AL136792	CCDS43542.1, CCDS47527.1, CCDS47527.2, CCDS75559.1, CCDS75560.1	7p22.3	2006-04-12			ENSG00000106012	ENSG00000106012			29171	protein-coding gene	gene with protein product						10470851	Standard	XR_242067		Approved	KIAA1023	uc003smo.4	Q6IPM2	OTTHUMG00000152047	ENST00000402050.2:c.1641G>A	chr7.hg19:g.2644523G>A		111.0	0.0		91.0	4.0	NM_152558	Q4G0P7|Q6P7T4|Q9H0H7|Q9UPX7	Silent	SNP	ENST00000402050.2	hg19	CCDS43542.1																																																																																			.	G|1.000;T|0.000		0.642	IQCE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325063.2	NM_152558		A	2644523	G	A	2644523	2	1	254	1	0	0	0	0	0	0	0	1	7815	1335	47	3		3	IQCE	7	2644523	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1669382	2644523	156494140	337	34629										
RADIL	55698	hgsc.bcm.edu	37	chr7	4917718	4917718	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	acaacagctggctctgccgcTtcagtttgctcttggtgggc	12	12	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:4917718T>C	ENST00000399583.3	-	2	240	c.53A>G	c.(52-54)aAg>aGg	p.K18R	RADIL_ENST00000536091.1_Missense_Mutation_p.K18R	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	18					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		GCTCTGCCGCTTCAGTTTGCT	0.587																																					p.K18R		Atlas-SNP	.											.	RADIL	110	.	0			c.A53G						.						22	26	24					7																	4917718		2085	4204	6289	SO:0001583	missense	55698	exon2			TGCCGCTTCAGTT	AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.53A>G	chr7.hg19:g.4917718T>C	ENSP00000382492:p.Lys18Arg	98.0	0.0		83.0	4.0	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	hg19	CCDS43544.1	.	.	.	.	.	.	.	.	.	.	T	17.84	3.487848	0.64074	.	.	ENSG00000157927	ENST00000399583;ENST00000536091;ENST00000457174	T;T	0.26660	3.11;1.72	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.28764	0.0713	L	0.43152	1.355	0.35318	D	0.784559	P	0.48503	0.911	P	0.49387	0.609	T	0.18429	-1.0337	10	0.10377	T	0.69	-53.8006	13.9572	0.64157	0.0:0.0:0.0:1.0	.	18	Q96JH8	RADIL_HUMAN	R	18	ENSP00000382492:K18R;ENSP00000442533:K18R	ENSP00000382492:K18R	K	-	2	0	RADIL	4884244	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	4.365000	0.59486	2.235000	0.73313	0.459000	0.35465	AAG	.	.		0.587	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059		C	4917718	T	C	4917718	3	2	254	1	0	0	0	0	1	0	0	0	13012	1609	56	2	3230	2	RADIL	7	4917718	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	2273195	4917718	154220945	338	34630										
C7orf70	84792	hgsc.bcm.edu	37	chr7	6370275	6370275	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cttgggaaaagcacttggtgGgtcatcctgaaaacttccca	10	10	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:6370275G>T	ENST00000313324.4	-	2	978	c.511C>A	c.(511-513)Cca>Aca	p.P171T	FAM220A_ENST00000533877.1_5'Flank	NM_001037163.1	NP_001032240.1	Q7Z4H9	F220A_HUMAN	family with sequence similarity 220, member A	171						nucleus (GO:0005634)											GCACTTGGTGGGTCATCCTGA	0.577																																					p.P171T		Atlas-SNP	.											.	.	.	.	0			c.C511A						.						56	67	63					7																	6370275		2203	4300	6503	SO:0001583	missense	84792	exon2			TTGGTGGGTCATC	BC006110	CCDS34599.1	7p22.1	2012-03-19	2012-03-19	2012-03-19	ENSG00000178397	ENSG00000178397			22422	protein-coding gene	gene with protein product	"STAT3-interacting protein as a repressor"		"chromosome 7 open reading frame 70"	C7orf70			Standard	NM_001037163		Approved	SIPAR, MGC12966	uc003spu.3	Q7Z4H9	OTTHUMG00000122091	ENST00000313324.4:c.511C>A	chr7.hg19:g.6370275G>T	ENSP00000317289:p.Pro171Thr	139.0	0.0		118.0	5.0	NM_001037163	Q75ML2|Q8NA52|Q9BRR7	Missense_Mutation	SNP	ENST00000313324.4	hg19	CCDS34599.1	.	.	.	.	.	.	.	.	.	.	G	4.819	0.152269	0.09185	.	.	ENSG00000178397	ENST00000313324	T	0.08896	3.04	5.28	4.4	0.53042	.	0.732533	0.11678	U	0.540083	T	0.14356	0.0347	L	0.55481	1.735	0.09310	N	1	D	0.58268	0.982	P	0.52189	0.692	T	0.17961	-1.0352	10	0.42905	T	0.14	-1.7872	6.0625	0.19846	0.1679:0.1552:0.6769:0.0	.	171	Q7Z4H9	SIPAR_HUMAN	T	171	ENSP00000317289:P171T	ENSP00000317289:P171T	P	-	1	0	C7orf70	6336800	0.003000	0.15002	0.001000	0.08648	0.067000	0.16453	0.920000	0.28705	1.211000	0.43351	0.655000	0.94253	CCA	.	.		0.577	FAM220A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000242853.2	NM_001037163		T	6370275	G	T	6370275	3	4	254	1	0	0	0	0	1	0	0	0	2417	1232	43	3	272	3	C7orf70	7	6370275	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1452557	6370275	152768388	339	34631										
DAGLB	221955	hgsc.bcm.edu	37	chr7	6474496	6474496	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcttgattctggtttcccacAcgcttgtagctgctgtcttg	10	11	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:6474496A>G	ENST00000297056.6	-	4	744	c.575T>C	c.(574-576)gTg>gCg	p.V192A	DAGLB_ENST00000425398.2_Intron|DAGLB_ENST00000421761.2_Intron|DAGLB_ENST00000428902.2_Missense_Mutation_p.V65A|DAGLB_ENST00000479922.2_5'Flank|DAGLB_ENST00000436575.1_Missense_Mutation_p.V151A	NM_139179.3	NP_631918.3	Q8NCG7	DGLB_HUMAN	diacylglycerol lipase, beta	192					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|lipid catabolic process (GO:0016042)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|urinary_tract(2)	26		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.102)		GGTTTCCCACACGCTTGTAGC	0.502																																					p.V192A		Atlas-SNP	.											.	DAGLB	74	.	0			c.T575C						.						165	159	161					7																	6474496		2203	4300	6503	SO:0001583	missense	221955	exon4			TCCCACACGCTTG	AF450090	CCDS5350.1, CCDS47536.1	7p22.1	2008-03-18			ENSG00000164535	ENSG00000164535	3.1.1.-		28923	protein-coding gene	gene with protein product		614016					Standard	NM_139179		Approved	KCCR13L, DAGLBETA	uc003sqa.3	Q8NCG7	OTTHUMG00000125513	ENST00000297056.6:c.575T>C	chr7.hg19:g.6474496A>G	ENSP00000297056:p.Val192Ala	190.0	0.0		114.0	6.0	NM_139179	A4D2P3|B3KV90|B4DQU0|Q6PIX3|Q8N2N2|Q8N9S1|Q8TED3|Q8WXE6	Missense_Mutation	SNP	ENST00000297056.6	hg19	CCDS5350.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.361846	0.82353	.	.	ENSG00000164535	ENST00000297056;ENST00000436575;ENST00000471132;ENST00000428902	T;T	0.44083	0.94;0.93	5.37	5.37	0.77165	.	0.068629	0.64402	D	0.000019	T	0.49372	0.1553	M	0.78637	2.42	0.80722	D	1	D	0.53745	0.962	P	0.46389	0.515	T	0.51371	-0.8714	10	0.16420	T	0.52	.	15.3683	0.74541	1.0:0.0:0.0:0.0	.	192	Q8NCG7	DGLB_HUMAN	A	192;151;192;65	ENSP00000297056:V192A;ENSP00000404785:V151A	ENSP00000297056:V192A	V	-	2	0	DAGLB	6441021	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.834000	0.92094	2.024000	0.59613	0.482000	0.46254	GTG	.	.		0.502	DAGLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246840.2	NM_139179		G	6474496	A	G	6474496	3	3	254	1	0	0	0	0	1	0	0	0	4229	159	6	2	1491	2	DAGLB	7	6474496	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	104221	6474496	152664167	340	34632										
ITGB8	3696	hgsc.bcm.edu	37	chr7	20444277	20444277	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gagagtgtgaagcaggcagaTgccaatgcttcagtggctgg	16	7	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:20444277T>C	ENST00000222573.4	+	11	2398	c.1714T>C	c.(1714-1716)Tgc>Cgc	p.C572R	ITGB8_ENST00000537992.1_Missense_Mutation_p.C437R	NM_002214.2	NP_002205.1	P26012	ITB8_HUMAN	integrin, beta 8	572	Cysteine-rich tandem repeats.				cartilage development (GO:0051216)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|ganglioside metabolic process (GO:0001573)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of gene expression (GO:0010629)|placenta blood vessel development (GO:0060674)|positive regulation of gene expression (GO:0010628)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	extracellular matrix protein binding (GO:1990430)|receptor activity (GO:0004872)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(4)|stomach(2)|urinary_tract(1)	37						AGCAGGCAGATGCCAATGCTT	0.522																																					p.C572R		Atlas-SNP	.											.	ITGB8	159	.	0			c.T1714C						.						117	97	104					7																	20444277		2203	4300	6503	SO:0001583	missense	3696	exon11			GGCAGATGCCAAT		CCDS5370.1	7p15.3	2010-03-23			ENSG00000105855	ENSG00000105855		"Integrins"	6163	protein-coding gene	gene with protein product		604160					Standard	XM_005249751		Approved		uc003suu.3	P26012	OTTHUMG00000023594	ENST00000222573.4:c.1714T>C	chr7.hg19:g.20444277T>C	ENSP00000222573:p.Cys572Arg	136.0	0.0		100.0	6.0	NM_002214	A4D133|B4DHD4	Missense_Mutation	SNP	ENST00000222573.4	hg19	CCDS5370.1	.	.	.	.	.	.	.	.	.	.	T	24.5	4.543454	0.86022	.	.	ENSG00000105855	ENST00000537992;ENST00000222573	D;D	0.99724	-3.57;-6.54	5.77	5.77	0.91146	EGF, extracellular (1);Epidermal growth factor-like (1);EGF-like region, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.99813	0.9918	H	0.95260	3.645	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96891	0.9653	10	0.87932	D	0	.	16.3818	0.83467	0.0:0.0:0.0:1.0	.	572	P26012	ITB8_HUMAN	R	437;572	ENSP00000441561:C437R;ENSP00000222573:C572R	ENSP00000222573:C572R	C	+	1	0	ITGB8	20410802	1.000000	0.71417	0.997000	0.53966	0.950000	0.60333	7.348000	0.79366	2.330000	0.79161	0.528000	0.53228	TGC	.	.		0.522	ITGB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059915.3	NM_002214		C	20444277	T	C	20444277	3	2	254	1	0	0	0	0	1	0	0	0	7910	1464	51	2	1756	2	ITGB8	7	20444277	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	13969781	20444277	138694386	341	34633										
CBX3	11335	hgsc.bcm.edu	37	chr7	26248156	26248156	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgaatctgatgacagcaaatCaaagaagaaaagagatgctg	10	5	2	6			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:26248156C>A	ENST00000337620.4	+	4	739	c.311C>A	c.(310-312)tCa>tAa	p.S104*	CBX3_ENST00000396386.2_Nonsense_Mutation_p.S104*|CBX3_ENST00000409747.1_Missense_Mutation_p.Q80K|CBX3_ENST00000497498.1_3'UTR	NM_007276.4	NP_009207.2	Q13185	CBX3_HUMAN	chromobox homolog 3	104					chromatin remodeling (GO:0006338)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|condensed chromosome, centromeric region (GO:0000779)|nuclear envelope (GO:0005635)|nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nuclear inner membrane (GO:0005637)|nuclear pericentric heterochromatin (GO:0031618)|nucleus (GO:0005634)|spindle (GO:0005819)	enzyme binding (GO:0019899)|histone methyltransferase binding (GO:1990226)|identical protein binding (GO:0042802)|protein domain specific binding (GO:0019904)			endometrium(4)|large_intestine(2)|lung(2)|ovary(1)	9						GACAGCAAATCAAAGAAGAAA	0.328																																					p.S104X		Atlas-SNP	.											.	CBX3	25	.	0			c.C311A						.						36	39	38					7																	26248156		2200	4298	6498	SO:0001587	stop_gained	11335	exon4			GCAAATCAAAGAA	U26312	CCDS5398.1	7p15.2	2010-07-06	2010-06-24		ENSG00000122565	ENSG00000122565			1553	protein-coding gene	gene with protein product	"HP1 gamma homolog (Drosophila)"	604477	"chromobox homolog 3 (Drosophila HP1 gamma)"			8663349	Standard	NM_016587		Approved	HP1Hs-gamma	uc003sxu.3	Q13185	OTTHUMG00000022911	ENST00000337620.4:c.311C>A	chr7.hg19:g.26248156C>A	ENSP00000336687:p.Ser104*	139.0	0.0		116.0	5.0	NM_016587	Q96CD7|Q99409|Q9BVS3|Q9P0Z6	Nonsense_Mutation	SNP	ENST00000337620.4	hg19	CCDS5398.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	39|39	7.650357|7.650357	0.98412|0.98412	.|.	.|.	ENSG00000122565|ENSG00000122565	ENST00000409747|ENST00000337620;ENST00000396386	.|.	.|.	.|.	5.35|5.35	5.35|5.35	0.76521|0.76521	.|.	.|0.228637	.|0.43260	.|D	.|0.000594	T|.	0.27489|.	0.0675|.	.|.	.|.	.|.	0.26827|0.26827	N|N	0.968673|0.968673	B|.	0.12630|.	0.006|.	B|.	0.11329|.	0.006|.	T|.	0.13872|.	-1.0493|.	7|.	0.30078|0.02654	T|T	0.28|1	.|.	19.424|19.424	0.94734|0.94734	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	80|.	B8ZZ43|.	.|.	K|X	80|104	.|.	ENSP00000387348:Q80K|ENSP00000336687:S104X	Q|S	+|+	1|2	0|0	CBX3|CBX3	26214681|26214681	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	2.507000|2.507000	0.45442|0.45442	2.661000|2.661000	0.90470|0.90470	0.655000|0.655000	0.94253|0.94253	CAA|TCA	.	.		0.328	CBX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214117.1	NM_007276		A	26248156	C	A	26248156	4	1	254	1	0	0	0	0	0	1	0	0	2721	838	29	3	321	3	CBX3	7	26248156	Nonsense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	5803879	26248156	132890507	342	34634										
SKAP2	8935	hgsc.bcm.edu	37	chr7	26779530	26779530	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tctgcgtttttcaaggtagcCagcctttagaacaaaaggaa	9	8	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:26779530C>T	ENST00000345317.2	-	5	674	c.361G>A	c.(361-363)Ggc>Agc	p.G121S	SKAP2_ENST00000489977.1_5'UTR|SKAP2_ENST00000539623.1_5'UTR	NM_003930.3	NP_003921.2	O75563	SKAP2_HUMAN	src kinase associated phosphoprotein 2	121	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				B cell activation (GO:0042113)|negative regulation of cell proliferation (GO:0008285)|positive regulation of signal transduction (GO:0009967)|protein complex assembly (GO:0006461)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|skin(3)	17						TCAAGGTAGCCAGCCTTTAGA	0.373																																					p.G121S		Atlas-SNP	.											.	SKAP2	40	.	0			c.G361A						.						75	71	72					7																	26779530		2203	4300	6503	SO:0001583	missense	8935	exon5			GGTAGCCAGCCTT		CCDS5400.1	7p15.2	2013-01-10	2006-09-28	2006-09-28	ENSG00000005020	ENSG00000005020		"Pleckstrin homology (PH) domain containing"	15687	protein-coding gene	gene with protein product		605215	"src family associated phosphoprotein 2"	SCAP2		9837776, 9755858	Standard	NM_003930		Approved	RA70, SKAP-HOM, SKAP55R, SAPS	uc003syc.3	O75563	OTTHUMG00000023495	ENST00000345317.2:c.361G>A	chr7.hg19:g.26779530C>T	ENSP00000005587:p.Gly121Ser	162.0	0.0		99.0	4.0	NM_003930	A4D173|Q53GP6|Q75MK6|Q75MZ4|Q9UBZ3|Q9UED8	Missense_Mutation	SNP	ENST00000345317.2	hg19	CCDS5400.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.844708	0.91197	.	.	ENSG00000005020	ENST00000345317;ENST00000535331;ENST00000432747	T;T	0.73897	-0.79;-0.79	5.81	4.93	0.64822	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.045894	0.85682	D	0.000000	D	0.87265	0.6134	H	0.96996	3.92	0.80722	D	1	P;D	0.54397	0.887;0.966	P;P	0.54270	0.457;0.747	D	0.90186	0.4246	10	0.72032	D	0.01	-4.3258	11.4594	0.50202	0.0:0.9166:0.0:0.0834	.	106;121	B7Z5N4;O75563	.;SKAP2_HUMAN	S	121;106;106	ENSP00000005587:G121S;ENSP00000408163:G106S	ENSP00000005587:G121S	G	-	1	0	SKAP2	26746055	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.209000	0.58493	2.746000	0.94184	0.591000	0.81541	GGC	.	.		0.373	SKAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214128.1			T	26779530	C	T	26779530	3	4	254	1	0	0	0	0	1	0	0	0	14371	594	21	3	750	3	SKAP2	7	26779530	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	531374	26779530	132359133	343	34635										
CREB5	9586	hgsc.bcm.edu	37	chr7	28547292	28547292	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gaggaggtgggcctcttcagCgagctggactgctccctgga	16	11	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:28547292C>A	ENST00000357727.2	+	4	618	c.228C>A	c.(226-228)agC>agA	p.S76R	CREB5_ENST00000409603.1_Missense_Mutation_p.S43R|CREB5_ENST00000396299.2_Missense_Mutation_p.S43R|CREB5_ENST00000396300.2_Missense_Mutation_p.S69R	NM_182898.2	NP_878901.2	Q02930	CREB5_HUMAN	cAMP responsive element binding protein 5	76					adipose tissue development (GO:0060612)|fat cell differentiation (GO:0045444)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S76S(1)		breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(13)|prostate(1)|skin(3)	32						GCCTCTTCAGCGAGCTGGACT	0.547																																					p.S76R		Atlas-SNP	.											CREB5,colon,carcinoma,0,2	CREB5	115	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C228A						.						106	112	110					7																	28547292		2203	4300	6503	SO:0001583	missense	9586	exon4			CTTCAGCGAGCTG	L05515	CCDS5417.1, CCDS5418.1, CCDS43562.1, CCDS43563.1	7p15	2013-01-10			ENSG00000146592	ENSG00000146592		"basic leucine zipper proteins"	16844	protein-coding gene	gene with protein product	"cAMP response element binding protein CRE-Bpa"					8378084, 8440710	Standard	XM_005249906		Approved	H_GS165L15.1, CRE-BPA	uc003szr.3	Q02930	OTTHUMG00000097081	ENST00000357727.2:c.228C>A	chr7.hg19:g.28547292C>A	ENSP00000350359:p.Ser76Arg	162.0	0.0		119.0	5.0	NM_182898	A8KA51|B4DU13|B5BUH3|C9JK47|Q05886|Q06246|Q75N02|Q86UJ9	Missense_Mutation	SNP	ENST00000357727.2	hg19	CCDS5417.1	.	.	.	.	.	.	.	.	.	.	C	11.61	1.691046	0.30052	.	.	ENSG00000146592	ENST00000396299;ENST00000424599;ENST00000357727;ENST00000396300;ENST00000409603	T;T;T;T;T	0.28454	1.61;1.61;1.61;1.61;1.61	5.6	-6.46	0.01908	.	0.415223	0.29676	N	0.011491	T	0.19886	0.0478	L	0.29908	0.895	0.80722	D	1	B	0.21520	0.057	B	0.17433	0.018	T	0.01130	-1.1442	10	0.72032	D	0.01	0.5969	16.2367	0.82380	0.0:0.6286:0.0:0.3714	.	76	Q02930	CREB5_HUMAN	R	43;69;76;69;43	ENSP00000379593:S43R;ENSP00000394088:S69R;ENSP00000350359:S76R;ENSP00000379594:S69R;ENSP00000387197:S43R	ENSP00000350359:S76R	S	+	3	2	CREB5	28513817	0.011000	0.17503	0.003000	0.11579	0.417000	0.31264	-0.458000	0.06737	-1.555000	0.01697	-0.793000	0.03317	AGC	.	.		0.547	CREB5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214204.4	NM_004904		A	28547292	C	A	28547292	3	1	254	1	0	0	0	0	1	0	0	0	3862	767	27	1	242	1	CREB5	7	28547292	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1767762	28547292	130591371	344	34636										
VPS41	27072	hgsc.bcm.edu	37	chr7	38798051	38798051	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgaattattatacagatctcCaggccattctcggatcaatg	7	9	3	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:38798051C>A	ENST00000310301.4	-	18	1507	c.1453G>T	c.(1453-1455)Gga>Tga	p.G485*	VPS41_ENST00000395969.2_Nonsense_Mutation_p.G460*	NM_014396.3	NP_055211.2	P49754	VPS41_HUMAN	vacuolar protein sorting 41 homolog (S. cerevisiae)	485					Golgi vesicle transport (GO:0048193)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	cytosol (GO:0005829)|early endosome (GO:0005769)|Golgi-associated vesicle (GO:0005798)|HOPS complex (GO:0030897)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	44						TACAGATCTCCAGGCCATTCT	0.358																																					p.G485X		Atlas-SNP	.											.	VPS41	102	.	0			c.G1453T						.						133	129	130					7																	38798051		2203	4300	6503	SO:0001587	stop_gained	27072	exon18			GATCTCCAGGCCA	U87309	CCDS5457.1, CCDS5458.2	7p14.1-p13	2009-05-08	2006-12-19		ENSG00000006715	ENSG00000006715			12713	protein-coding gene	gene with protein product		605485	"vacuolar protein sorting 41 (yeast homolog)", "vacuolar protein sorting 41 (yeast)"			9159129	Standard	NM_080631		Approved	HVSP41	uc003tgy.3	P49754	OTTHUMG00000023629	ENST00000310301.4:c.1453G>T	chr7.hg19:g.38798051C>A	ENSP00000309457:p.Gly485*	150.0	0.0		95.0	4.0	NM_014396	E9PF36|Q86TP8|Q99851|Q99852	Nonsense_Mutation	SNP	ENST00000310301.4	hg19	CCDS5457.1	.	.	.	.	.	.	.	.	.	.	C	38	7.054453	0.98032	.	.	ENSG00000006715	ENST00000310301;ENST00000395969	.	.	.	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13853	T	0.58	-28.0693	20.6439	0.99570	0.0:1.0:0.0:0.0	.	.	.	.	X	485;460	.	ENSP00000309457:G485X	G	-	1	0	VPS41	38764576	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.818000	0.86416	2.884000	0.98904	0.655000	0.94253	GGA	.	.		0.358	VPS41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226986.3			A	38798051	C	A	38798051	4	1	254	1	0	0	0	0	0	1	0	0	17225	603	21	3	1159	3	VPS41	7	38798051	Nonsense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	10250759	38798051	120340612	345	34637										
INHBA	3624	hgsc.bcm.edu	37	chr7	41729530	41729530	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	atgatccagtcattccagccGatgtccttgaaactgacaaa	7	11	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:41729530G>T	ENST00000242208.4	-	3	1245	c.999C>A	c.(997-999)atC>atA	p.I333I	AC005027.3_ENST00000416150.1_RNA|INHBA_ENST00000464515.1_5'UTR|INHBA_ENST00000442711.1_Silent_p.I333I	NM_002192.2	NP_002183.1	P08476	INHBA_HUMAN	inhibin, beta A	333					activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to cholesterol (GO:0071397)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|defense response (GO:0006952)|endodermal cell differentiation (GO:0035987)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|eyelid development in camera-type eye (GO:0061029)|G1/S transition of mitotic cell cycle (GO:0000082)|growth (GO:0040007)|hair follicle development (GO:0001942)|hematopoietic progenitor cell differentiation (GO:0002244)|hemoglobin biosynthetic process (GO:0042541)|male gonad development (GO:0008584)|mesodermal cell differentiation (GO:0048333)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of phosphorylation (GO:0042326)|nervous system development (GO:0007399)|odontogenesis (GO:0042476)|ovarian follicle development (GO:0001541)|palate development (GO:0060021)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|positive regulation of ovulation (GO:0060279)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone secretion (GO:0042701)|regulation of follicle-stimulating hormone secretion (GO:0046880)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)	activin A complex (GO:0043509)|extracellular region (GO:0005576)|inhibin A complex (GO:0043512)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|hormone activity (GO:0005179)|identical protein binding (GO:0042802)|peptide hormone binding (GO:0017046)|type II activin receptor binding (GO:0070699)	p.I333I(1)		biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(15)|lung(26)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						CATTCCAGCCGATGTCCTTGA	0.557										TSP Lung(11;0.080)																											p.I333I		Atlas-SNP	.											INHBA,NS,carcinoma,0,1	INHBA	118	.	1	Substitution - coding silent(1)	lung(1)	c.C999A						.						123	123	123					7																	41729530		2203	4300	6503	SO:0001819	synonymous_variant	3624	exon3			CCAGCCGATGTCC		CCDS5464.1	7p15-p13	2014-01-30	2007-07-30		ENSG00000122641	ENSG00000122641		"Endogenous ligands"	6066	protein-coding gene	gene with protein product		147290	"inhibin, beta A (activin A, activin AB alpha polypeptide)"			3345731	Standard	NM_002192		Approved		uc003thr.3	P08476	OTTHUMG00000023574	ENST00000242208.4:c.999C>A	chr7.hg19:g.41729530G>T		50.0	1.0		32.0	2.0	NM_002192	Q14599	Silent	SNP	ENST00000242208.4	hg19	CCDS5464.1																																																																																			.	.		0.557	INHBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250793.1			T	41729530	G	T	41729530	2	4	254	1	0	0	0	0	0	0	0	1	7750	1048	37	1		1	INHBA	7	41729530	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	2931479	41729530	117409133	346	34638										
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47870945	47870945	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tagtccctccaaaccactgcTgggtgctgcggaagagtagg	13	11	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:47870945T>C	ENST00000289672.2	-	42	6393	c.6343A>G	c.(6343-6345)Agc>Ggc	p.S2115G		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	2115					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						AAACCACTGCTGGGTGCTGCG	0.577																																					p.S2115G		Atlas-SNP	.											.	PKD1L1	328	.	0			c.A6343G						.						76	72	73					7																	47870945		2203	4300	6503	SO:0001583	missense	168507	exon42			CACTGCTGGGTGC	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"polycystin-1L1"	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.6343A>G	chr7.hg19:g.47870945T>C	ENSP00000289672:p.Ser2115Gly	129.0	0.0		92.0	4.0	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	hg19	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	T	7.042	0.562675	0.13498	.	.	ENSG00000158683	ENST00000289672	T	0.19532	2.14	4.96	-9.93	0.00452	.	3.234350	0.00899	N	0.002326	T	0.06645	0.0170	N	0.04508	-0.205	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.21314	-1.0249	10	0.20046	T	0.44	0.9118	2.2761	0.04103	0.1146:0.358:0.2339:0.2935	.	2115	Q8TDX9	PK1L1_HUMAN	G	2115	ENSP00000289672:S2115G	ENSP00000289672:S2115G	S	-	1	0	PKD1L1	47837470	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-1.638000	0.02013	-1.574000	0.01657	0.379000	0.24179	AGC	.	.		0.577	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		C	47870945	T	C	47870945	3	2	254	1	0	0	0	0	1	0	0	0	11973	1580	55	2	2270	2	PKD1L1	7	47870945	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	6141415	47870945	111267718	347	34639										
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47874578	47874578	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	catttaccatggggtgcctcGgtctgtgctcctcctctaag	10	13	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:47874578G>T	ENST00000289672.2	-	39	6164	c.6114C>A	c.(6112-6114)acC>acA	p.T2038T		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	2038					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						GGGGTGCCTCGGTCTGTGCTC	0.527																																					p.T2038T		Atlas-SNP	.											.	PKD1L1	328	.	0			c.C6114A						.						80	86	84					7																	47874578		2203	4300	6503	SO:0001819	synonymous_variant	168507	exon39			TGCCTCGGTCTGT	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"polycystin-1L1"	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.6114C>A	chr7.hg19:g.47874578G>T		109.0	0.0		84.0	4.0	NM_138295	Q6UWK1	Silent	SNP	ENST00000289672.2	hg19	CCDS34633.1																																																																																			.	.		0.527	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		T	47874578	G	T	47874578	2	4	254	1	0	0	0	0	0	0	0	1	11973	1103	39	1		1	PKD1L1	7	47874578	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	3633	47874578	111264085	348	34640										
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47898327	47898327	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	atgtcgatagacttcctcctTcgagttttcttgctcagaga	8	10	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:47898327T>C	ENST00000289672.2	-	27	4356	c.4306A>G	c.(4306-4308)Aag>Gag	p.K1436E		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	1436	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						ACTTCCTCCTTCGAGTTTTCT	0.428																																					p.K1436E		Atlas-SNP	.											.	PKD1L1	328	.	0			c.A4306G						.						176	174	175					7																	47898327		2203	4300	6503	SO:0001583	missense	168507	exon27			CCTCCTTCGAGTT	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"polycystin-1L1"	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.4306A>G	chr7.hg19:g.47898327T>C	ENSP00000289672:p.Lys1436Glu	80.0	0.0		77.0	4.0	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	hg19	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	T	10.93	1.489285	0.26686	.	.	ENSG00000158683	ENST00000289672	T	0.19250	2.16	5.03	-0.218	0.13142	Egg jelly receptor, REJ-like (1);	1.115740	0.06704	N	0.771982	T	0.11495	0.0280	L	0.34521	1.04	0.09310	N	1	B	0.28082	0.2	B	0.23716	0.048	T	0.26883	-1.0090	10	0.05436	T	0.98	-8.1515	4.2509	0.10695	0.0:0.1874:0.3461:0.4665	.	1436	Q8TDX9	PK1L1_HUMAN	E	1436	ENSP00000289672:K1436E	ENSP00000289672:K1436E	K	-	1	0	PKD1L1	47864852	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.309000	0.19332	0.020000	0.15106	-0.321000	0.08615	AAG	.	.		0.428	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		C	47898327	T	C	47898327	3	2	254	1	0	0	0	0	1	0	0	0	11973	1792	62	2	4367	2	PKD1L1	7	47898327	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	23749	47898327	111240336	349	34641										
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47947753	47947753	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gagttcatgaacgcagacacGgcctcatggccaatctccac	9	14	3	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:47947753G>T	ENST00000289672.2	-	9	1373	c.1323C>A	c.(1321-1323)gcC>gcA	p.A441A		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	441					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						ACGCAGACACGGCCTCATGGC	0.458																																					p.A441A		Atlas-SNP	.											.	PKD1L1	328	.	0			c.C1323A						.						118	102	107					7																	47947753		2203	4300	6503	SO:0001819	synonymous_variant	168507	exon9			AGACACGGCCTCA	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"polycystin-1L1"	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.1323C>A	chr7.hg19:g.47947753G>T		75.0	0.0		75.0	4.0	NM_138295	Q6UWK1	Silent	SNP	ENST00000289672.2	hg19	CCDS34633.1																																																																																			.	.		0.458	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		T	47947753	G	T	47947753	2	4	254	1	0	0	0	0	0	0	0	1	11973	1103	39	1		1	PKD1L1	7	47947753	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	49426	47947753	111190910	350	34642										
ZNF107	51427	hgsc.bcm.edu	37	chr7	64166707	64166707	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttttatttctttcagtaatgTcttttcattttgcccaagac	4	8	4	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:64166707T>C	ENST00000395391.1	+	4	1400	c.25T>C	c.(25-27)Tct>Cct	p.S9P	ZNF107_ENST00000423627.1_Missense_Mutation_p.S9P|ZNF107_ENST00000344930.3_Missense_Mutation_p.S9P			Q9UII5	ZN107_HUMAN	zinc finger protein 107	9					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(18)|ovary(1)|stomach(1)	37		Lung NSC(55;0.00948)|all_lung(88;0.0249)				TTCAGTAATGTCTTTTCATTT	0.299																																					p.S9P		Atlas-SNP	.											.	ZNF107	107	.	0			c.T25C						.						39	40	40					7																	64166707		2194	4295	6489	SO:0001583	missense	51427	exon7			GTAATGTCTTTTC	AB027251	CCDS5527.1, CCDS75605.1, CCDS75606.1	7q11.2	2013-01-08	2007-06-26			ENSG00000196247		"Zinc fingers, C2H2-type"	12887	protein-coding gene	gene with protein product		603989	"zinc finger protein 588", "zinc finger protein 107 (Y8)"	ZNF588		8467795	Standard	NM_016220		Approved	ZFD25, smap-7	uc003tte.3	Q9UII5		ENST00000395391.1:c.25T>C	chr7.hg19:g.64166707T>C	ENSP00000378789:p.Ser9Pro	78.0	0.0		63.0	4.0	NM_016220		Missense_Mutation	SNP	ENST00000395391.1	hg19	CCDS5527.1	.	.	.	.	.	.	.	.	.	.	.	9.217	1.032386	0.19590	.	.	ENSG00000196247	ENST00000541526;ENST00000360117;ENST00000344930;ENST00000423627;ENST00000395391	T;T;T;T	0.08370	4.81;3.1;3.1;3.1	0.596	0.596	0.17496	.	.	.	.	.	T	0.07007	0.0178	L	0.38175	1.15	0.23628	N	0.997252	B	0.02656	0.0	B	0.01281	0.0	T	0.32877	-0.9890	8	0.59425	D	0.04	.	.	.	.	.	9	Q9UII5	ZN107_HUMAN	P	9	ENSP00000353234:S9P;ENSP00000343443:S9P;ENSP00000400037:S9P;ENSP00000378789:S9P	ENSP00000343443:S9P	S	+	1	0	ZNF107	63804142	0.000000	0.05858	0.057000	0.19452	0.129000	0.20672	-0.013000	0.12678	0.478000	0.27488	0.254000	0.18369	TCT	.	.		0.299	ZNF107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251593.1	NM_016220		C	64166707	T	C	64166707	3	2	254	1	0	0	0	0	1	0	0	0	17730	1667	58	2	31	2	ZNF107	7	64166707	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	16218954	64166707	94971956	351	34643										
GUSB	2990	hgsc.bcm.edu	37	chr7	65435344	65435344	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tccaaggatttggtgtgagcGatcaccatcctgtccacaaa	9	11	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:65435344G>T	ENST00000304895.4	-	9	1531	c.1401C>A	c.(1399-1401)atC>atA	p.I467I	GUSB_ENST00000421103.1_Silent_p.I321I|GUSB_ENST00000345660.6_Silent_p.I416I	NM_000181.3	NP_000172.2	P08236	BGLR_HUMAN	glucuronidase, beta	467					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-glucuronidase activity (GO:0004566)			breast(1)|cervix(2)|kidney(2)|large_intestine(4)|lung(10)|skin(1)	20						TGGTGTGAGCGATCACCATCC	0.577																																					p.I467I		Atlas-SNP	.											.	GUSB	52	.	0			c.C1401A						.						85	82	83					7																	65435344		2203	4300	6503	SO:0001819	synonymous_variant	2990	exon9			GTGAGCGATCACC	M15182	CCDS5530.1, CCDS64665.1	7q11.21	2012-10-02			ENSG00000169919	ENSG00000169919	3.2.1.31		4696	protein-coding gene	gene with protein product		611499				3468507	Standard	NM_000181		Approved		uc003tun.3	P08236	OTTHUMG00000023735	ENST00000304895.4:c.1401C>A	chr7.hg19:g.65435344G>T		82.0	0.0		89.0	5.0	NM_000181	B4E1F6|E9PCV0|Q549U0|Q96CL9	Silent	SNP	ENST00000304895.4	hg19	CCDS5530.1																																																																																			.	.		0.577	GUSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251637.3	NM_000181		T	65435344	G	T	65435344	2	4	254	1	0	0	0	0	0	0	0	1	6911	1048	37	1		1	GUSB	7	65435344	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1268637	65435344	93703319	352	34644										
WBSCR17	64409	hgsc.bcm.edu	37	chr7	70880904	70880904	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aggtccccctagaggagtatGtccacaaacgctaccccggg	11	14	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:70880904G>A	ENST00000333538.5	+	4	1253	c.619G>A	c.(619-621)Gtc>Atc	p.V207I	WBSCR17_ENST00000498380.2_3'UTR	NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17	207	Catalytic subdomain A.				protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(5)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(7)|large_intestine(22)|lung(45)|ovary(2)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	100		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				AGAGGAGTATGTCCACAAACG	0.507																																					p.V207I		Atlas-SNP	.											.	WBSCR17	208	.	0			c.G619A						.						72	67	69					7																	70880904		2203	4300	6503	SO:0001583	missense	64409	exon4			GAGTATGTCCACA	AF410457	CCDS5540.1	7q11.23	2014-03-13			ENSG00000185274	ENSG00000185274		"Glycosyltransferase family 2 domain containing"	16347	protein-coding gene	gene with protein product	"polypeptide N-acetylgalactosaminyltransferase-like 3", "polypeptide GalNAc transferase 3"	615137				12073013, 15744064, 22787146	Standard	NM_022479		Approved	GALNTL3, GalNAc-T5L	uc003tvy.4	Q6IS24	OTTHUMG00000129783	ENST00000333538.5:c.619G>A	chr7.hg19:g.70880904G>A	ENSP00000329654:p.Val207Ile	154.0	0.0		86.0	21.0	NM_022479	Q8NFV9|Q9NTA8	Missense_Mutation	SNP	ENST00000333538.5	hg19	CCDS5540.1	.	.	.	.	.	.	.	.	.	.	G	19.88	3.908797	0.72868	.	.	ENSG00000185274	ENST00000333538;ENST00000447516	T;T	0.61040	0.31;0.14	5.17	4.23	0.50019	Glycosyl transferase, family 2 (1);	0.000000	0.85682	D	0.000000	T	0.65260	0.2674	L	0.43646	1.37	0.58432	D	0.999996	D	0.76494	0.999	D	0.73708	0.981	T	0.58951	-0.7545	10	0.20519	T	0.43	.	13.5761	0.61875	0.0:0.0:0.8442:0.1558	.	207	Q6IS24	GLTL3_HUMAN	I	207;185	ENSP00000329654:V207I;ENSP00000392019:V185I	ENSP00000329654:V207I	V	+	1	0	WBSCR17	70518840	1.000000	0.71417	0.994000	0.49952	0.944000	0.59088	7.462000	0.80851	2.421000	0.82119	0.563000	0.77884	GTC	.	.		0.507	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252006.1	NM_022479		A	70880904	G	A	70880904	3	1	254	1	0	0	0	0	1	0	0	0	17279	1377	48	3	633	3	WBSCR17	7	70880904	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	5445560	70880904	88257759	353	34645										
FGL2	10875	hgsc.bcm.edu	37	chr7	76828978	76828978	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctcttcgcatttccctctgcTttctagtctcactgggcaga	7	14	4	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:76828978T>C	ENST00000248598.5	-	1	165	c.133A>G	c.(133-135)Agc>Ggc	p.S45G	CCDC146_ENST00000431197.1_Intron|CCDC146_ENST00000285871.4_Intron|RP11-467H10.2_ENST00000459742.1_RNA	NM_006682.2	NP_006673.1	Q14314	FGL2_HUMAN	fibrinogen-like 2	45						extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)				breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|skin(2)	13						TTCCCTCTGCTTTCTAGTCTC	0.498																																					p.S45G		Atlas-SNP	.											.	FGL2	40	.	0			c.A133G						.						120	116	118					7																	76828978		2203	4300	6503	SO:0001583	missense	10875	exon1			CTCTGCTTTCTAG	Z36531	CCDS5591.1	7q11.23	2013-02-06			ENSG00000127951	ENSG00000127951		"Fibrinogen C domain containing"	3696	protein-coding gene	gene with protein product		605351				7642106	Standard	NM_006682		Approved	pT49, T49	uc003ugb.3	Q14314	OTTHUMG00000130681	ENST00000248598.5:c.133A>G	chr7.hg19:g.76828978T>C	ENSP00000248598:p.Ser45Gly	112.0	0.0		89.0	4.0	NM_006682		Missense_Mutation	SNP	ENST00000248598.5	hg19	CCDS5591.1	.	.	.	.	.	.	.	.	.	.	T	2.182	-0.387245	0.04932	.	.	ENSG00000127951	ENST00000248598	T	0.58210	0.35	5.38	0.0476	0.14281	.	0.335611	0.39274	N	0.001418	T	0.25121	0.0610	N	0.11560	0.145	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.11767	-1.0574	10	0.21014	T	0.42	.	5.6955	0.17853	0.0:0.2206:0.1313:0.6481	.	45	Q14314	FGL2_HUMAN	G	45	ENSP00000248598:S45G	ENSP00000248598:S45G	S	-	1	0	FGL2	76666914	0.206000	0.23470	0.051000	0.19133	0.454000	0.32378	-0.074000	0.11450	0.114000	0.18032	-1.054000	0.02325	AGC	.	.		0.498	FGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253176.1	NM_006682		C	76828978	T	C	76828978	3	2	254	1	0	0	0	0	1	0	0	0	5881	1609	56	2	1194	2	FGL2	7	76828978	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	5948074	76828978	82309685	354	34646										
AKAP9	10142	hgsc.bcm.edu	37	chr7	91652178	91652178	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgcaagatcttgaaaaaactAaacttgaagaacaagttcaa	6	6	2	4	rs111673064|rs10644111|rs397825978	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:91652178A>C	ENST00000359028.2	+	15	4264	c.4039A>C	c.(4039-4041)Aaa>Caa	p.K1347Q	AKAP9_ENST00000356239.3_Missense_Mutation_p.K1335Q|AKAP9_ENST00000358100.2_Missense_Mutation_p.K1347Q			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	1347			K -> KQ. {ECO:0000269|PubMed:10202149}.		G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)	p.K1335_L1336insQ(1)|p.K1347_L1348insQ(1)		NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TGAAAAAACTAAACTTGAAGA	0.313			T	BRAF	papillary thyroid																																p.K1335Q		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.,2	AKAP9	788	.	2	Insertion - In frame(2)	ovary(2)	c.A4003C						.						45	46	46					7																	91652178		2203	4300	6503	SO:0001583	missense	10142	exon14			AAAACTAAACTTG	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	379	protein-coding gene	gene with protein product	"A-kinase anchoring protein 450", "AKAP9-BRAF fusion protein", "AKAP120-like protein", "centrosome- and golgi-localized protein kinase N-associated protein", "protein kinase A anchoring protein 9", "A-kinase anchor protein, 350kDa", "protein phosphatase 1, regulatory subunit 45", "yotiao"	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.4039A>C	chr7.hg19:g.91652178A>C	ENSP00000351922:p.Lys1347Gln	50.0	2.0		116.0	7.0	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	hg19		.	.	.	.	.	.	.	.	.	.	A	0.162	-1.080695	0.01888	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394565	T;T;T	0.02974	4.09;4.09;4.1	4.68	2.19	0.27852	.	0.840174	0.09958	N	0.733777	T	0.01254	0.0041	N	0.00210	-1.845	0.09310	N	1	P;B;B;B	0.51791	0.948;0.004;0.02;0.115	P;B;B;B	0.49528	0.614;0.007;0.037;0.083	T	0.50625	-0.8806	10	0.23302	T	0.38	.	8.1855	0.31337	0.7884:0.134:0.0775:0.0	.	1347;1335;1335;1347	Q99996;Q99996-2;Q99996-3;A4D1E4	AKAP9_HUMAN;.;.;.	Q	1335;1347;1347;1347;1347	ENSP00000348573:K1335Q;ENSP00000351922:K1347Q;ENSP00000350813:K1347Q	ENSP00000348573:K1335Q	K	+	1	0	AKAP9	91490114	0.545000	0.26449	0.005000	0.12908	0.028000	0.11728	2.404000	0.44539	0.033000	0.15463	-1.431000	0.01090	AAA	.	.		0.313	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751		C	91652178	A	C	91652178	3	2	254	1	0	0	0	0	1	0	0	0	459	363	13	5	4057	5	AKAP9	7	91652178	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	14823200	91652178	67486485	355	34647										
CDK6	1021	hgsc.bcm.edu	37	chr7	92300836	92300836	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agacttcgggtgctctgtacCacagcgtgacgacctgcaat	11	12	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:92300836C>T	ENST00000265734.4	-	5	962	c.551G>A	c.(550-552)tGg>tAg	p.W184*	CDK6_ENST00000424848.2_Nonsense_Mutation_p.W184*	NM_001259.6	NP_001250.1	Q00534	CDK6_HUMAN	cyclin-dependent kinase 6	184	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				astrocyte development (GO:0014002)|cell cycle arrest (GO:0007050)|cell dedifferentiation (GO:0043697)|cell division (GO:0051301)|dentate gyrus development (GO:0021542)|G1/S transition of mitotic cell cycle (GO:0000082)|generation of neurons (GO:0048699)|gliogenesis (GO:0042063)|hematopoietic stem cell differentiation (GO:0060218)|lateral ventricle development (GO:0021670)|mitotic cell cycle (GO:0000278)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell differentiation (GO:0045596)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular senescence (GO:2000773)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of osteoblast differentiation (GO:0045668)|Notch signaling pathway (GO:0007219)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of gene expression (GO:0010628)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of erythrocyte differentiation (GO:0045646)|regulation of gene expression (GO:0010468)|response to virus (GO:0009615)|T cell differentiation in thymus (GO:0033077)|type B pancreatic cell development (GO:0003323)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|ruffle (GO:0001726)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|urinary_tract(1)	11	all_cancers(62;8.72e-12)|all_epithelial(64;3.65e-10)|Breast(17;0.000675)|all_lung(186;0.0392)|Lung NSC(181;0.053)|all_neural(327;0.219)|all_hematologic(106;0.237)		STAD - Stomach adenocarcinoma(4;6.16e-07)|GBM - Glioblastoma multiforme(5;1.2e-06)|all cancers(6;3.1e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			TGCTCTGTACCACAGCGTGAC	0.502			T	MLLT10	ALL																																p.W184X		Atlas-SNP	.		Dom	yes		7	7q21-q22	1021	cyclin-dependent kinase 6		L	.	CDK6	30	.	0			c.G551A						.						103	89	94					7																	92300836		2203	4300	6503	SO:0001587	stop_gained	1021	exon5			CTGTACCACAGCG		CCDS5628.1	7q21-q22	2011-11-08			ENSG00000105810	ENSG00000105810		"Cyclin-dependent kinases"	1777	protein-coding gene	gene with protein product		603368				1639063	Standard	NM_001259		Approved	PLSTIRE	uc010lez.3	Q00534	OTTHUMG00000131697	ENST00000265734.4:c.551G>A	chr7.hg19:g.92300836C>T	ENSP00000265734:p.Trp184*	92.0	0.0		137.0	6.0	NM_001259	A4D1G0	Nonsense_Mutation	SNP	ENST00000265734.4	hg19	CCDS5628.1	.	.	.	.	.	.	.	.	.	.	C	39	7.555246	0.98355	.	.	ENSG00000105810	ENST00000265734;ENST00000424848	.	.	.	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-21.1808	19.1725	0.93585	0.0:1.0:0.0:0.0	.	.	.	.	X	184	.	ENSP00000265734:W184X	W	-	2	0	CDK6	92138772	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	7.746000	0.85057	2.620000	0.88729	0.305000	0.20034	TGG	.	.		0.502	CDK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254605.2			T	92300836	C	T	92300836	4	4	254	1	0	0	0	0	0	1	0	0	3150	595	21	3	445	3	CDK6	7	92300836	Nonsense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	648658	92300836	66837827	356	34648										
ARPC1B	10095	hgsc.bcm.edu	37	chr7	98988562	98988562	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tggaggaacggccggcacccAccccgtggggctccaagatg	15	14	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:98988562A>G	ENST00000451682.1	+	8	856	c.547A>G	c.(547-549)Acc>Gcc	p.T183A	ARPC1B_ENST00000252725.5_Missense_Mutation_p.T183A|PDAP1_ENST00000496335.1_5'Flank			O15143	ARC1B_HUMAN	actin related protein 2/3 complex, subunit 1B, 41kDa	183					Arp2/3 complex-mediated actin nucleation (GO:0034314)|cellular component movement (GO:0006928)	actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|liver(2)|lung(1)	11	all_cancers(62;3.49e-09)|all_epithelial(64;2.57e-10)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			GCCGGCACCCACCCCGTGGGG	0.592																																					p.T183A		Atlas-SNP	.											.	ARPC1B	41	.	0			c.A547G						.						48	48	48					7																	98988562		2203	4300	6503	SO:0001583	missense	10095	exon6			GCACCCACCCCGT	AF006084	CCDS5661.1	7q22.1	2013-03-14	2002-08-29		ENSG00000130429	ENSG00000130429		"Actin related protein 2/3 complex subunits", "WD repeat domain containing"	704	protein-coding gene	gene with protein product	"ARP2/3 protein complex subunit p41", "actin related protein 2/3 complex, subunit 1A (41 kD)"	604223	"actin related protein 2/3 complex, subunit 1B (41 kD)"			9230079, 9359840	Standard	NM_005720		Approved	ARC41, p40-ARC, p41-ARC	uc003upz.3	O15143	OTTHUMG00000154552	ENST00000451682.1:c.547A>G	chr7.hg19:g.98988562A>G	ENSP00000389631:p.Thr183Ala	36.0	0.0		70.0	4.0	NM_005720	Q9BU00	Missense_Mutation	SNP	ENST00000451682.1	hg19	CCDS5661.1	.	.	.	.	.	.	.	.	.	.	A	28.2	4.902590	0.92035	.	.	ENSG00000130429	ENST00000252725;ENST00000451682	T;T	0.65364	-0.15;-0.15	5.69	5.69	0.88448	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.69824	0.3154	M	0.81497	2.545	0.80722	D	1	P;P	0.45715	0.865;0.865	P;P	0.45829	0.494;0.494	T	0.73104	-0.4088	10	0.44086	T	0.13	-49.599	15.6192	0.76793	1.0:0.0:0.0:0.0	.	183;183	A4D275;O15143	.;ARC1B_HUMAN	A	183	ENSP00000252725:T183A;ENSP00000389631:T183A	ENSP00000252725:T183A	T	+	1	0	ARPC1B	98826498	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	7.373000	0.79623	2.176000	0.68965	0.459000	0.35465	ACC	.	.		0.592	ARPC1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335894.1	NM_005720		G	98988562	A	G	98988562	3	3	254	1	0	0	0	0	1	0	0	0	970	159	6	2	565	2	ARPC1B	7	98988562	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	6687726	98988562	60150101	357	34649										
ZNF655	79027	hgsc.bcm.edu	37	chr7	99169920	99169920	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	attcctaagcagaaaatttcGgaagaagtgcattcatacaa	7	7	1	2	rs531904406		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:99169920G>T	ENST00000394163.2	+	3	372	c.189G>T	c.(187-189)tcG>tcT	p.S63S	ZNF655_ENST00000425063.1_3'UTR|ZNF655_ENST00000252713.4_Silent_p.S63S|ZNF655_ENST00000419215.2_3'UTR|GS1-259H13.10_ENST00000455905.1_Intron|GS1-259H13.10_ENST00000486324.1_Intron|ZNF655_ENST00000424881.1_Silent_p.S98S|ZNF655_ENST00000493277.1_Silent_p.S98S	NM_001009960.1|NM_138494.2	NP_001009960.1|NP_612503.1	Q8N720	ZN655_HUMAN	zinc finger protein 655	63					negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	16	all_epithelial(64;3.19e-09)|Lung NSC(181;0.0066)|all_lung(186;0.011)|Esophageal squamous(72;0.0166)					AGAAAATTTCGGAAGAAGTGC	0.378																																					p.S98S		Atlas-SNP	.											.	ZNF655	75	.	0			c.G294T						.						82	85	84					7																	99169920		2203	4300	6503	SO:0001819	synonymous_variant	79027	exon4			AATTTCGGAAGAA	AY099353	CCDS5669.1, CCDS5670.1, CCDS34695.1, CCDS47655.1	7q22.1	2013-01-08			ENSG00000197343	ENSG00000197343		"Zinc fingers, C2H2-type", "-"	30899	protein-coding gene	gene with protein product						11179890, 15558030	Standard	NM_001083956		Approved	VIK-1, VIK	uc010lgc.3	Q8N720	OTTHUMG00000156637	ENST00000394163.2:c.189G>T	chr7.hg19:g.99169920G>T		64.0	0.0		123.0	5.0	NM_001085368	A4D291|A6NGD3|B4E3M4|B7Z9Q9|D6W5T4|Q8IV00|Q8TA89|Q96EZ3|Q9BQ85	Silent	SNP	ENST00000394163.2	hg19	CCDS5669.1																																																																																			.	.		0.378	ZNF655-009	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000344929.1	NM_138494		T	99169920	G	T	99169920	2	4	254	1	0	0	0	0	0	0	0	1	18083	1103	39	1		1	ZNF655	7	99169920	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	181358	99169920	59968743	358	34650										
TAF6	6878	hgsc.bcm.edu	37	chr7	99709449	99709449	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gttctgaaccacgttcacacGgacctgtgggagggagaagt	14	9	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:99709449G>T	ENST00000344095.4	-	9	1327	c.802C>A	c.(802-804)Cgt>Agt	p.R268S	TAF6_ENST00000472509.1_Missense_Mutation_p.R325S|TAF6_ENST00000453269.2_Missense_Mutation_p.R268S|TAF6_ENST00000497233.1_5'Flank|TAF6_ENST00000452041.1_Missense_Mutation_p.R268S|TAF6_ENST00000437822.2_Missense_Mutation_p.R305S|TAF6_ENST00000418432.2_Missense_Mutation_p.R192S	NM_005641.3	NP_005632.1	P49848	TAF6_HUMAN	TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80kDa	268					DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R268C(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(2)	26	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					ACGTTCACACGGACCTGTGGG	0.567																																					p.R305S		Atlas-SNP	.											TAF6,NS,carcinoma,0,1	TAF6	55	.	1	Substitution - Missense(1)	breast(1)	c.C913A						.						116	107	110					7																	99709449		2203	4300	6503	SO:0001583	missense	6878	exon9			TCACACGGACCTG		CCDS5686.1, CCDS55135.1	7q	2010-02-26	2002-08-29	2001-12-07	ENSG00000106290	ENSG00000106290			11540	protein-coding gene	gene with protein product	"TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80 kD", "transcription initiation factor TFIID 70 kD subunit"	602955	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, E, 70/85kD"	TAF2E		826207	Standard	NM_139315		Approved	TAFII70, TAFII80, MGC:8964, TAFII85	uc011kji.2	P49848	OTTHUMG00000154771	ENST00000344095.4:c.802C>A	chr7.hg19:g.99709449G>T	ENSP00000344537:p.Arg268Ser	154.0	0.0		125.0	5.0	NM_001190415	A4D2B2|A4D2B3|B4DT11|D6W5U2|Q6AI29	Missense_Mutation	SNP	ENST00000344095.4	hg19	CCDS5686.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.588749	0.86851	.	.	ENSG00000106290	ENST00000453269;ENST00000472509;ENST00000452041;ENST00000344095;ENST00000418432;ENST00000437822	T;T;T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01;-0.01;-0.01	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.71384	0.3333	L	0.47190	1.495	0.80722	D	1	D;D;D;P;D	0.67145	0.994;0.996;0.994;0.897;0.994	P;D;P;P;P	0.65874	0.871;0.939;0.871;0.462;0.871	T	0.64198	-0.6464	10	0.18276	T	0.48	-11.6477	17.4922	0.87707	0.0:0.0:1.0:0.0	.	305;268;258;268;192	B4DT11;P49848-2;A4D299;P49848;B3KUR4	.;.;.;TAF6_HUMAN;.	S	268;325;268;268;192;305	ENSP00000389575:R268S;ENSP00000419760:R325S;ENSP00000416396:R268S;ENSP00000344537:R268S;ENSP00000407980:R192S;ENSP00000399982:R305S	ENSP00000344537:R268S	R	-	1	0	TAF6	99547385	1.000000	0.71417	1.000000	0.80357	0.493000	0.33554	7.345000	0.79337	2.724000	0.93272	0.561000	0.74099	CGT	.	.		0.567	TAF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337024.2	NM_005641		T	99709449	G	T	99709449	3	4	254	1	0	0	0	0	1	0	0	0	15545	1116	39	1	1259	1	TAF6	7	99709449	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	539529	99709449	59429214	359	34651										
C7orf43	55262	hgsc.bcm.edu	37	chr7	99754538	99754538	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agttgtgttcctccagggcaTtcagcgggcaggggaagcag	16	9	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:99754538T>C	ENST00000316937.3	-	6	1108	c.923A>G	c.(922-924)aAt>aGt	p.N308S	C7orf43_ENST00000419841.1_Missense_Mutation_p.N76S|C7orf43_ENST00000394035.2_5'Flank|MIR4658_ENST00000584344.1_RNA|C7orf43_ENST00000457641.1_Missense_Mutation_p.N39S|C7orf43_ENST00000498638.1_5'UTR	NM_018275.3	NP_060745.3	Q8WVR3	CG043_HUMAN	chromosome 7 open reading frame 43	308										breast(1)|endometrium(3)|large_intestine(3)|lung(2)|prostate(1)	10	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CTCCAGGGCATTCAGCGGGCA	0.602																																					p.N308S		Atlas-SNP	.											.	C7orf43	28	.	0			c.A923G						.						58	69	65					7																	99754538		2203	4300	6503	SO:0001583	missense	55262	exon6			AGGGCATTCAGCG		CCDS5687.1	7q22.1	2011-11-25			ENSG00000146826	ENSG00000146826			25604	protein-coding gene	gene with protein product						12477932	Standard	NM_018275		Approved	FLJ10925	uc003utr.3	Q8WVR3	OTTHUMG00000154862	ENST00000316937.3:c.923A>G	chr7.hg19:g.99754538T>C	ENSP00000324741:p.Asn308Ser	53.0	0.0		58.0	4.0	NM_018275	A4D2A9|D6W5U4|Q9BQJ1|Q9BUB6|Q9NV47	Missense_Mutation	SNP	ENST00000316937.3	hg19	CCDS5687.1	.	.	.	.	.	.	.	.	.	.	T	2.682	-0.275060	0.05679	.	.	ENSG00000146826	ENST00000457641;ENST00000316937;ENST00000419841	T;T;T	0.27104	1.69;1.69;1.69	5.58	2.78	0.32641	.	0.106937	0.64402	N	0.000011	T	0.07593	0.0191	N	0.02539	-0.55	0.25997	N	0.982169	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36939	-0.9727	10	0.07030	T	0.85	-0.7826	6.4336	0.21811	0.0:0.6983:0.0:0.3017	.	76;308	E9PFF9;Q8WVR3	.;CG043_HUMAN	S	39;308;76	ENSP00000396432:N39S;ENSP00000324741:N308S;ENSP00000406326:N76S	ENSP00000324741:N308S	N	-	2	0	C7orf43	99592474	0.987000	0.35691	0.993000	0.49108	0.850000	0.48378	1.049000	0.30392	0.714000	0.32081	-0.464000	0.05259	AAT	.	.		0.602	C7orf43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337395.2	NM_018275		C	99754538	T	C	99754538	3	2	254	1	0	0	0	0	1	0	0	0	2395	1493	52	2	843	2	C7orf43	7	99754538	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	45089	99754538	59384125	360	34652										
AGFG2	3268	hgsc.bcm.edu	37	chr7	100161852	100161852	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gccccctaggctcttccttcGgggacttaggatcagccaag	11	14	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:100161852G>T	ENST00000300176.4	+	11	1434	c.1312G>T	c.(1312-1314)Ggg>Tgg	p.G438W	AGFG2_ENST00000262935.4_3'UTR|AGFG2_ENST00000474713.1_Intron	NM_006076.4	NP_006067.3	O95081	AGFG2_HUMAN	ArfGAP with FG repeats 2	438					regulation of ARF GTPase activity (GO:0032312)	membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						CTCTTCCTTCGGGGACTTAGG	0.627											OREG0018204	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G438W		Atlas-SNP	.											.	AGFG2	44	.	0			c.G1312T						.						41	35	37					7																	100161852		2203	4300	6503	SO:0001583	missense	3268	exon11			TCCTTCGGGGACT	AF015042	CCDS5697.1	7q22.1	2008-09-22	2008-09-22	2008-09-22	ENSG00000106351	ENSG00000106351		"ADP-ribosylation factor GTPase activating proteins"	5177	protein-coding gene	gene with protein product		604019	"HIV-1 Rev binding protein-like"	HRBL		9799793	Standard	XM_005250306		Approved	RABR	uc003uvf.3	O95081	OTTHUMG00000156029	ENST00000300176.4:c.1312G>T	chr7.hg19:g.100161852G>T	ENSP00000300176:p.Gly438Trp	117.0	0.0	1349	93.0	4.0	NM_006076	O75429|Q96AB9|Q96GL4	Missense_Mutation	SNP	ENST00000300176.4	hg19	CCDS5697.1	.	.	.	.	.	.	.	.	.	.	G	17.54	3.416311	0.62511	.	.	ENSG00000106351	ENST00000300176	T	0.23552	1.9	4.59	3.62	0.41486	.	0.455087	0.21940	N	0.066882	T	0.34106	0.0886	L	0.36672	1.1	0.80722	D	1	D	0.71674	0.998	D	0.64410	0.925	T	0.08229	-1.0732	10	0.87932	D	0	-0.6479	7.1738	0.25732	0.1344:0.0:0.8656:0.0	.	438	O95081	AGFG2_HUMAN	W	438	ENSP00000300176:G438W	ENSP00000300176:G438W	G	+	1	0	AGFG2	99999788	0.079000	0.21365	0.974000	0.42286	0.912000	0.54170	1.019000	0.30014	0.995000	0.38917	0.555000	0.69702	GGG	.	.		0.627	AGFG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342769.1	NM_006076		T	100161852	G	T	100161852	3	4	254	1	0	0	0	0	1	0	0	0	381	1116	39	1	1354	1	AGFG2	7	100161852	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	407314	100161852	58976811	361	34653										
LRCH4	4034	hgsc.bcm.edu	37	chr7	100175328	100175328	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	atcctccccggggacatggcTgtcgatgaagtcaatctgca	11	12	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:100175328T>C	ENST00000310300.6	-	9	1127	c.1075A>G	c.(1075-1077)Agc>Ggc	p.S359G	LRCH4_ENST00000497245.1_5'UTR	NM_002319.3	NP_002310.2	O75427	LRCH4_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 4	359					nervous system development (GO:0007399)	PML body (GO:0016605)				NS(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	23	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GGGACATGGCTGTCGATGAAG	0.667																																					p.S359G		Atlas-SNP	.											.	LRCH4	53	.	0			c.A1075G						.						117	102	107					7																	100175328		2203	4300	6503	SO:0001583	missense	4034	exon9			CATGGCTGTCGAT	AF053356	CCDS34706.1	7q22	2008-05-20	2004-05-27	2004-05-28	ENSG00000077454	ENSG00000077454			6691	protein-coding gene	gene with protein product				LRN, LRRN1		9799793	Standard	XM_005250346		Approved		uc003uvj.3	O75427	OTTHUMG00000159544	ENST00000310300.6:c.1075A>G	chr7.hg19:g.100175328T>C	ENSP00000309689:p.Ser359Gly	67.0	0.0		72.0	4.0	NM_002319	A4D2D5|Q8WV85|Q96ID0	Missense_Mutation	SNP	ENST00000310300.6	hg19	CCDS34706.1	.	.	.	.	.	.	.	.	.	.	T	17.60	3.429146	0.62844	.	.	ENSG00000077454	ENST00000310300	T	0.36340	1.26	5.52	3.0	0.34707	.	0.141094	0.64402	N	0.000006	T	0.48187	0.1486	M	0.76170	2.325	0.80722	D	1	D	0.60160	0.987	P	0.57101	0.813	T	0.46261	-0.9204	10	0.54805	T	0.06	-4.1156	6.4083	0.21676	0.0:0.0849:0.1586:0.7565	.	359	O75427	LRCH4_HUMAN	G	359	ENSP00000309689:S359G	ENSP00000309689:S359G	S	-	1	0	LRCH4	100013264	1.000000	0.71417	1.000000	0.80357	0.521000	0.34408	3.290000	0.51755	0.931000	0.37242	0.439000	0.28862	AGC	.	.		0.667	LRCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356110.1	NM_002319		C	100175328	T	C	100175328	3	2	254	1	0	0	0	0	1	0	0	0	8944	1580	55	2	1016	2	LRCH4	7	100175328	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	13476	100175328	58963335	362	34654										
SLC12A9	56996	hgsc.bcm.edu	37	chr7	100454532	100454532	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccgggtcctgccccagggctAcggctggaacctgctgtatg	14	14	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:100454532A>G	ENST00000354161.3	+	5	616	c.491A>G	c.(490-492)tAc>tGc	p.Y164C	SLC12A9_ENST00000275729.3_Missense_Mutation_p.Y75C|SLC12A9_ENST00000428758.1_Missense_Mutation_p.Y164C|SLC12A9_ENST00000415287.1_Missense_Mutation_p.Y75C|SLC12A9_ENST00000540482.1_Missense_Mutation_p.Y164C	NM_020246.3	NP_064631.2	Q9BXP2	S12A9_HUMAN	solute carrier family 12, member 9	164					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation:chloride symporter activity (GO:0015377)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(20)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	41	Lung NSC(181;0.041)|all_lung(186;0.0581)					CCCCAGGGCTACGGCTGGAAC	0.662																																					p.Y164C		Atlas-SNP	.											.	SLC12A9	81	.	0			c.A491G						.						52	54	54					7																	100454532		2203	4300	6503	SO:0001583	missense	56996	exon5			AGGGCTACGGCTG	AF284422	CCDS5707.1, CCDS59068.1, CCDS59069.1	7q22	2013-07-18	2013-07-18		ENSG00000146828	ENSG00000146828		"Solute carriers"	17435	protein-coding gene	gene with protein product	"cation-chloride cotransporter-interacting protein"					10871601, 11239002	Standard	NM_020246		Approved	CIP1	uc003uwp.4	Q9BXP2	OTTHUMG00000156045	ENST00000354161.3:c.491A>G	chr7.hg19:g.100454532A>G	ENSP00000275730:p.Tyr164Cys	83.0	0.0		84.0	4.0	NM_001267812	B7Z740|D6W5X0|D6W5X2|F5H8C2|Q9BWL2|Q9BXP1|Q9BYI0|Q9NQR5	Missense_Mutation	SNP	ENST00000354161.3	hg19	CCDS5707.1	.	.	.	.	.	.	.	.	.	.	A	18.66	3.671349	0.67814	.	.	ENSG00000146828	ENST00000540482;ENST00000428758;ENST00000275729;ENST00000415287;ENST00000354161	D;D;D;D;D	0.98835	-2.65;-2.65;-5.17;-5.17;-2.94	4.62	4.62	0.57501	Amino acid permease domain (1);	0.000000	0.64402	D	0.000001	D	0.99007	0.9661	M	0.85197	2.74	0.58432	D	0.999994	D;P	0.89917	1.0;0.83	D;P	0.87578	0.998;0.676	D	0.99346	1.0913	10	0.46703	T	0.11	.	11.9565	0.52984	1.0:0.0:0.0:0.0	.	75;164	Q9BXP2-2;Q9BXP2	.;S12A9_HUMAN	C	164;164;75;75;164	ENSP00000443702:Y164C;ENSP00000408301:Y164C;ENSP00000275729:Y75C;ENSP00000413796:Y75C;ENSP00000275730:Y164C	ENSP00000275729:Y75C	Y	+	2	0	SLC12A9	100292468	1.000000	0.71417	0.998000	0.56505	0.960000	0.62799	8.795000	0.91872	1.711000	0.51337	0.379000	0.24179	TAC	.	.		0.662	SLC12A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342837.1	NM_020246		G	100454532	A	G	100454532	3	3	254	1	0	0	0	0	1	0	0	0	14405	391	14	2	505	2	SLC12A9	7	100454532	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	279204	100454532	58684131	363	34655										
MUC17	140453	hgsc.bcm.edu	37	chr7	100675798	100675798	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	accagcacacttgtgaccacTtctactgaacccagttcact	5	15	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:100675798T>C	ENST00000306151.4	+	3	1165	c.1101T>C	c.(1099-1101)acT>acC	p.T367T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	367	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					TTGTGACCACTTCTACTGAAC	0.468																																					p.T367T		Atlas-SNP	.											.	MUC17	804	.	0			c.T1101C						.						189	196	194					7																	100675798		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			GACCACTTCTACT	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.1101T>C	chr7.hg19:g.100675798T>C		70.0	0.0		83.0	4.0	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	hg19	CCDS34711.1																																																																																			.	.		0.468	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		C	100675798	T	C	100675798	2	2	254	1	0	0	0	0	0	0	0	1	9983	1596	56	2		2	MUC17	7	100675798	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	221266	100675798	58462865	364	34656										
CUX1	1523	hgsc.bcm.edu	37	chr7	101840082	101840082	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcaagactttttcagctcatCcctggcaagccccagcctac	6	16	3	1	rs569218052		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:101840082C>A	ENST00000292535.7	+	15	1429	c.1391C>A	c.(1390-1392)tCc>tAc	p.S464Y	SNORA48_ENST00000517015.1_RNA|CUX1_ENST00000437600.4_Intron|CUX1_ENST00000292538.4_Intron|CUX1_ENST00000393824.3_Intron|CUX1_ENST00000547394.2_Intron|CUX1_ENST00000549414.2_Missense_Mutation_p.S464Y|CUX1_ENST00000425244.2_Intron|CUX1_ENST00000556210.1_Intron|CUX1_ENST00000360264.3_Missense_Mutation_p.S475Y|CUX1_ENST00000550008.2_Missense_Mutation_p.S464Y|CUX1_ENST00000560541.1_Intron|CUX1_ENST00000546411.2_Intron	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	464					auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						TTCAGCTCATCCCTGGCAAGC	0.532													C|||	1	0.000199681	8e-04	0	5008	,	,		16575	0		0	False		,,,				2504	0				p.S475Y		Atlas-SNP	.											.	CUX1	253	.	0			c.C1424A						.						70	73	72					7																	101840082		2203	4300	6503	SO:0001583	missense	1523	exon15			GCTCATCCCTGGC	M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923		"Homeoboxes / CUT class"	2557	protein-coding gene	gene with protein product	"golgi integral membrane protein 6"	116896	"cut (Drosophila)-like 1 (CCAAT displacement protein)", "cut-like 1, CCAAT displacement protein (Drosophila)"	CUTL1		8468066, 9799793, 15004235	Standard	NM_001202543		Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000292535.7:c.1391C>A	chr7.hg19:g.101840082C>A	ENSP00000292535:p.Ser464Tyr	162.0	0.0		146.0	6.0	NM_001202543	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Missense_Mutation	SNP	ENST00000292535.7	hg19	CCDS5721.1	.	.	.	.	.	.	.	.	.	.	C	14.24	2.476486	0.44044	.	.	ENSG00000257923	ENST00000360264;ENST00000292535;ENST00000549414;ENST00000550008	T;T;T;T	0.60797	0.18;0.17;0.16;0.17	5.71	4.8	0.61643	.	0.294006	0.28635	N	0.014644	T	0.52500	0.1738	N	0.22421	0.69	0.80722	D	1	P;P	0.42649	0.681;0.786	B;P	0.47251	0.254;0.542	T	0.53012	-0.8498	10	0.40728	T	0.16	-6.8901	15.6421	0.77012	0.1423:0.8577:0.0:0.0	.	464;475	P39880;P39880-3	CUX1_HUMAN;.	Y	475;464;464;464	ENSP00000353401:S475Y;ENSP00000292535:S464Y;ENSP00000446630:S464Y;ENSP00000447373:S464Y	ENSP00000292535:S464Y	S	+	2	0	CUX1	101626802	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.111000	0.50360	1.350000	0.45770	0.561000	0.74099	TCC	.	.		0.532	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913		A	101840082	C	A	101840082	3	1	254	1	0	0	0	0	1	0	0	0	4066	855	30	3	1516	3	CUX1	7	101840082	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1164284	101840082	57298581	365	34657										
LAMB4	22798	hgsc.bcm.edu	37	chr7	107706357	107706357	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aggatttccatagtaaccatCaatacacctgtcaagacaat	5	10	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:107706357C>A	ENST00000388781.3	-	21	2769	c.2686G>T	c.(2686-2688)Gat>Tat	p.D896Y	LAMB4_ENST00000388780.3_Missense_Mutation_p.D896Y|LAMB4_ENST00000205386.4_Missense_Mutation_p.D896Y	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	896	Laminin EGF-like 8. {ECO:0000255|PROSITE- ProRule:PRU00460}.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)				NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						TAGTAACCATCAATACACCTG	0.428																																					p.D896Y		Atlas-SNP	.											.	LAMB4	253	.	0			c.G2686T						.						114	113	113					7																	107706357		2203	4300	6503	SO:0001583	missense	22798	exon21			AACCATCAATACA	AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"Laminins"	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.2686G>T	chr7.hg19:g.107706357C>A	ENSP00000373433:p.Asp896Tyr	65.0	0.0		81.0	5.0	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Missense_Mutation	SNP	ENST00000388781.3	hg19	CCDS34732.1	.	.	.	.	.	.	.	.	.	.	C	15.68	2.904909	0.52333	.	.	ENSG00000091128	ENST00000205386;ENST00000388781;ENST00000388780	T;T;T	0.64991	-0.13;-0.13;-0.13	4.69	1.83	0.25207	EGF-like, laminin (4);	0.116598	0.38005	N	0.001844	T	0.75064	0.3799	M	0.83692	2.655	0.80722	D	1	D	0.89917	1.0	D	0.72982	0.979	T	0.72557	-0.4257	10	0.66056	D	0.02	.	6.1473	0.20293	0.0:0.6432:0.1348:0.222	.	896	A4D0S4	LAMB4_HUMAN	Y	896	ENSP00000205386:D896Y;ENSP00000373433:D896Y;ENSP00000373432:D896Y	ENSP00000205386:D896Y	D	-	1	0	LAMB4	107493593	0.864000	0.29904	0.925000	0.36789	0.932000	0.56968	1.861000	0.39438	0.277000	0.22141	0.563000	0.77884	GAT	.	.		0.428	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857		A	107706357	C	A	107706357	3	1	254	1	0	0	0	0	1	0	0	0	8622	826	29	3	2655	3	LAMB4	7	107706357	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	5866275	107706357	51432306	366	34658										
LAMB4	22798	hgsc.bcm.edu	37	chr7	107720067	107720067	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgggtttcatagtgaatggcAatggtgaagtccacaggaaa	13	5	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:107720067A>G	ENST00000388781.3	-	15	1949	c.1866T>C	c.(1864-1866)atT>atC	p.I622I	LAMB4_ENST00000414450.2_Silent_p.I622I|LAMB4_ENST00000388780.3_Silent_p.I622I|LAMB4_ENST00000418464.1_Silent_p.I622I|LAMB4_ENST00000205386.4_Silent_p.I622I	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	622	Laminin IV type B. {ECO:0000255|PROSITE- ProRule:PRU00462}.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)				NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						AGTGAATGGCAATGGTGAAGT	0.463																																					p.I622I		Atlas-SNP	.											.	LAMB4	253	.	0			c.T1866C						.						93	86	89					7																	107720067		2203	4300	6503	SO:0001819	synonymous_variant	22798	exon15			AATGGCAATGGTG	AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"Laminins"	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.1866T>C	chr7.hg19:g.107720067A>G		74.0	0.0		49.0	4.0	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Silent	SNP	ENST00000388781.3	hg19	CCDS34732.1																																																																																			.	.		0.463	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857		G	107720067	A	G	107720067	2	3	254	1	0	0	0	0	0	0	0	1	8622	126	5	2		2	LAMB4	7	107720067	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	13710	107720067	51418596	367	34659										
IMPDH1	3614	hgsc.bcm.edu	37	chr7	128034563	128034563	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tggcagccgtgttggatgccTgctatgaggtagggcacgaa	16	8	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:128034563T>C	ENST00000480861.1	-	12	1448	c.1371A>G	c.(1369-1371)gcA>gcG	p.A457A	IMPDH1_ENST00000419067.2_Silent_p.A514A|IMPDH1_ENST00000496200.1_Silent_p.A437A|IMPDH1_ENST00000338791.6_Silent_p.A547A|IMPDH1_ENST00000348127.6_Silent_p.A511A|IMPDH1_ENST00000470772.1_Silent_p.A461A|IMPDH1_ENST00000354269.5_Silent_p.A537A|IMPDH1_ENST00000343214.4_Silent_p.A437A|IMPDH1_ENST00000378717.4_Silent_p.A478A	NM_001142574.1	NP_001136046.1			IMP (inosine 5'-monophosphate) dehydrogenase 1											breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(3)	22						GTTGGATGCCTGCTATGAGGT	0.597																																					p.A547A		Atlas-SNP	.											.	IMPDH1	38	.	0			c.A1641G						.						84	81	82					7																	128034563		2203	4300	6503	SO:0001819	synonymous_variant	3614	exon15			GATGCCTGCTATG		CCDS34748.1, CCDS34749.1, CCDS43643.1, CCDS47699.1, CCDS47700.1, CCDS55161.1	7q31.3-q32	2013-01-08	2010-04-29		ENSG00000106348	ENSG00000106348	1.1.1.205		6052	protein-coding gene	gene with protein product		146690	"retinitis pigmentosa 10 (autosomal dominant)", "IMP (inosine monophosphate) dehydrogenase 1"	RP10		1969416, 11875049, 11875050	Standard	NM_000883		Approved	sWSS2608, LCA11	uc003vmu.2	P20839	OTTHUMG00000157713	ENST00000480861.1:c.1371A>G	chr7.hg19:g.128034563T>C		96.0	0.0		91.0	4.0	NM_000883		Silent	SNP	ENST00000480861.1	hg19	CCDS55161.1																																																																																			.	.		0.597	IMPDH1-009	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000349462.1	NM_000883		C	128034563	T	C	128034563	2	2	254	1	0	0	0	0	0	0	0	1	7735	1567	55	2		2	IMPDH1	7	128034563	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	20314496	128034563	31104100	368	34660										
FLNC	2318	hgsc.bcm.edu	37	chr7	128494726	128494726	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gggctggagcgaggtgtggcCggcgtgccaggtaaggggca	22	8	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:128494726C>A	ENST00000325888.8	+	41	7248	c.6987C>A	c.(6985-6987)gcC>gcA	p.A2329A	RP11-309L24.2_ENST00000469965.1_RNA|FLNC_ENST00000346177.6_Silent_p.A2296A	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	2329					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						GAGGTGTGGCCGGCGTGCCAG	0.672																																					p.A2329A		Atlas-SNP	.											.	FLNC	339	.	0			c.C6987A						.						16	20	19					7																	128494726		2172	4257	6429	SO:0001819	synonymous_variant	2318	exon41			TGTGGCCGGCGTG	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"actin binding protein 280"	102565	"filamin C, gamma (actin binding protein 280)"	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.6987C>A	chr7.hg19:g.128494726C>A		113.0	0.0		95.0	4.0	NM_001458	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Silent	SNP	ENST00000325888.8	hg19	CCDS43644.1																																																																																			.	.		0.672	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3			A	128494726	C	A	128494726	2	1	254	1	0	0	0	0	0	0	0	1	5943	639	23	1		1	FLNC	7	128494726	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	460163	128494726	30643937	369	34661										
KIAA1549	57670	hgsc.bcm.edu	37	chr7	138554406	138554406	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtgtcgcccgaggacaggtcGtctaccaccgggaactcgta	13	13	1	0	rs575482000		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:138554406G>A	ENST00000422774.1	-	14	4701	c.4653C>T	c.(4651-4653)gaC>gaT	p.D1551D	KIAA1549_ENST00000242365.4_Silent_p.D1501D|KIAA1549_ENST00000440172.1_Silent_p.D1551D			Q9HCM3	K1549_HUMAN	KIAA1549	1551						integral component of membrane (GO:0016021)			KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						AGGACAGGTCGTCTACCACCG	0.652			O	BRAF	pilocytic astrocytoma								g|||	1	0.000199681	0	0	5008	,	,		15717	0		0	False		,,,				2504	0.001				p.D1551D	NSCLC(119;1534 1718 44213 46230 50068)	Atlas-SNP	.		Dom	yes		7	7q34	57670	KIAA1549		O	KIAA1549_ENST00000422774,NS,carcinoma,0,2	KIAA1549	314	.	0			c.C4653T						.						39	48	45					7																	138554406		2066	4198	6264	SO:0001819	synonymous_variant	57670	exon14			CAGGTCGTCTACC		CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.4653C>T	chr7.hg19:g.138554406G>A		161.0	0.0		194.0	31.0	NM_020910	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Silent	SNP	ENST00000422774.1	hg19	CCDS56513.1																																																																																			.	.		0.652	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1			A	138554406	G	A	138554406	2	1	254	1	0	0	0	0	0	0	0	1	8253	1136	40	1		1	KIAA1549	7	138554406	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	10059680	138554406	20584257	370	34662										
TRPV6	55503	hgsc.bcm.edu	37	chr7	142574527	142574527	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cccggatgtcagctccatgcTcaatgagcagccgcacgatc	10	15	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:142574527T>C	ENST00000359396.3	-	5	796	c.551A>G	c.(550-552)gAg>gGg	p.E184G	RP11-114L10.2_ENST00000438839.1_RNA	NM_018646.3	NP_061116	Q9H1D0	TRPV6_HUMAN	transient receptor potential cation channel, subfamily V, member 6	184					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|regulation of calcium ion-dependent exocytosis (GO:0017158)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)			breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	42	Melanoma(164;0.059)					AGCTCCATGCTCAATGAGCAG	0.597																																					p.E184G		Atlas-SNP	.											.	TRPV6	108	.	0			c.A551G						.						101	89	93					7																	142574527		2203	4300	6503	SO:0001583	missense	55503	exon5			CCATGCTCAATGA	AJ277909	CCDS5874.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000165125	ENSG00000165125		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	14006	protein-coding gene	gene with protein product		606680	"epithelial calcium channel 2"	ECAC2		11097838, 11549322, 16382100, 16717058	Standard	NM_018646		Approved	CaT1	uc003wbx.2	Q9H1D0	OTTHUMG00000157158	ENST00000359396.3:c.551A>G	chr7.hg19:g.142574527T>C	ENSP00000352358:p.Glu184Gly	148.0	0.0		119.0	5.0	NM_018646	A4D2I8|Q8TDL3|Q8WXR8|Q96LC5|Q9H1D1|Q9H296	Missense_Mutation	SNP	ENST00000359396.3	hg19	CCDS5874.1	.	.	.	.	.	.	.	.	.	.	T	14.89	2.669128	0.47677	.	.	ENSG00000165125	ENST00000359396	T	0.68765	-0.35	4.67	3.52	0.40303	Ankyrin repeat-containing domain (4);	0.340540	0.33834	N	0.004503	T	0.64907	0.2641	M	0.69823	2.125	0.41978	D	0.990788	B	0.21381	0.055	B	0.28709	0.093	T	0.62895	-0.6757	10	0.59425	D	0.04	-12.3191	9.3236	0.37980	0.0:0.0857:0.0:0.9143	.	184	Q9H1D0	TRPV6_HUMAN	G	184	ENSP00000352358:E184G	ENSP00000352358:E184G	E	-	2	0	TRPV6	142284649	0.999000	0.42202	0.984000	0.44739	0.861000	0.49209	6.011000	0.70760	0.657000	0.30906	-0.250000	0.11733	GAG	.	.		0.597	TRPV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347662.1	NM_014274		C	142574527	T	C	142574527	3	2	254	1	0	0	0	0	1	0	0	0	16615	1551	54	2	1670	2	TRPV6	7	142574527	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	4020121	142574527	16564136	371	34663										
AGAP3	116988	hgsc.bcm.edu	37	chr7	150814236	150814236	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccctggtgcaccgctatctgAcggggacctatgtccaggag	13	13	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:150814236A>G	ENST00000397238.2	+	3	445	c.445A>G	c.(445-447)Acg>Gcg	p.T149A	AGAP3_ENST00000335367.3_Missense_Mutation_p.T329A|AGAP3_ENST00000463381.1_5'UTR|AGAP3_ENST00000479901.1_Missense_Mutation_p.T149A|AGAP3_ENST00000473312.1_Missense_Mutation_p.T149A|AGAP3_ENST00000476375.1_3'UTR	NM_031946.4	NP_114152.3	Q96P47	AGAP3_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 3	113	Small GTPase-like.				cellular response to reactive oxygen species (GO:0034614)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein import into nucleus, translocation (GO:0000060)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|liver(2)|lung(9)|ovary(2)|prostate(3)|urinary_tract(1)	28						CCGCTATCTGACGGGGACCTA	0.662																																					p.T149A		Atlas-SNP	.											.	AGAP3	121	.	0			c.A445G						.						57	61	60					7																	150814236		2099	4266	6365	SO:0001583	missense	116988	exon3			TATCTGACGGGGA	AF413079	CCDS43681.1, CCDS55185.1, CCDS64802.1	7q36.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000133612	ENSG00000133612		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16923	protein-coding gene	gene with protein product			"centaurin, gamma 3"	CENTG3			Standard	NM_001042535		Approved		uc003wjg.1	Q96P47	OTTHUMG00000158724	ENST00000397238.2:c.445A>G	chr7.hg19:g.150814236A>G	ENSP00000380413:p.Thr149Ala	121.0	0.0		100.0	4.0	NM_001042535	B3KNZ8|E9PAL8|Q59EN0|Q96RK3	Missense_Mutation	SNP	ENST00000397238.2	hg19	CCDS43681.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	28.4|28.4	4.917500|4.917500	0.92249|0.92249	.|.	.|.	ENSG00000133612|ENSG00000133612	ENST00000473312;ENST00000479901;ENST00000397238;ENST00000335355;ENST00000335367|ENST00000469901	T;T;T;T|.	0.22743|.	1.94;1.94;1.94;1.94|.	4.42|4.42	4.42|4.42	0.53409|0.53409	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.80834|.	0.4699|.	M|M	0.91717|0.91717	3.235|3.235	0.80722|0.80722	D|D	1|1	P;P;P;D|.	0.58268|.	0.843;0.648;0.774;0.982|.	P;P;B;P|.	0.58130|.	0.68;0.538;0.307;0.833|.	D|.	0.85152|.	0.0987|.	10|.	0.87932|.	D|.	0|.	.|.	13.0143|13.0143	0.58749|0.58749	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	149;329;149;149|.	C9J975;E7ESL9;Q96P47-4;E9PAL8|.	.;.;.;.|.	A|W	149;149;149;113;329|84	ENSP00000418921:T149A;ENSP00000418125:T149A;ENSP00000380413:T149A;ENSP00000335589:T329A|.	ENSP00000334157:T113A|.	T|X	+|+	1|3	0|0	AGAP3|AGAP3	150445169|150445169	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.986000|0.986000	0.74619|0.74619	9.039000|9.039000	0.93777|0.93777	1.868000|1.868000	0.54150|0.54150	0.334000|0.334000	0.21626|0.21626	ACG|TGA	.	.		0.662	AGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351908.3	NM_031946		G	150814236	A	G	150814236	3	3	254	1	0	0	0	0	1	0	0	0	369	275	10	2	455	2	AGAP3	7	150814236	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	8239709	150814236	8324427	372	34664										
ASB10	136371	hgsc.bcm.edu	37	chr7	150878505	150878505	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctcttcttcctcggaccgacCatccactctcgctccaaacc	4	20	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:150878505C>A	ENST00000420175.2	-	3	649	c.625G>T	c.(625-627)Ggt>Tgt	p.G209C	ASB10_ENST00000422024.1_Missense_Mutation_p.G254C|ASB10_ENST00000275838.1_Missense_Mutation_p.G209C|ASB10_ENST00000434669.1_Missense_Mutation_p.G254C|ASB10_ENST00000377867.3_Missense_Mutation_p.G194C			Q8WXI3	ASB10_HUMAN	ankyrin repeat and SOCS box containing 10	209					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(2)|lung(7)|skin(2)	12			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TCGGACCGACCATCCACTCTC	0.632																																					p.G209C		Atlas-SNP	.											.	ASB10	99	.	0			c.G625T						.						27	25	26					7																	150878505		2200	4291	6491	SO:0001583	missense	136371	exon3			ACCGACCATCCAC	AK055536	CCDS5921.2, CCDS47749.1, CCDS47750.1, CCDS47749.2, CCDS47750.2	7q35	2014-02-04	2011-01-25		ENSG00000146926	ENSG00000146926		"Ankyrin repeat domain containing"	17185	protein-coding gene	gene with protein product		615054	"ankyrin repeat and SOCS box-containing 10", "glaucoma 1, open angle, F (adult-onset)"	GLC1F		22156576	Standard	NM_080871		Approved		uc003wjm.1	Q8WXI3	OTTHUMG00000157013	ENST00000420175.2:c.625G>T	chr7.hg19:g.150878505C>A	ENSP00000391137:p.Gly209Cys	120.0	0.0		94.0	4.0	NM_001142459	A0AVH0|Q6ZUL6	Missense_Mutation	SNP	ENST00000420175.2	hg19	CCDS47750.2	.	.	.	.	.	.	.	.	.	.	C	16.85	3.236302	0.58886	.	.	ENSG00000146926	ENST00000275838;ENST00000377867;ENST00000422024;ENST00000434669;ENST00000420175	T;T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1;-0.1	5.14	5.14	0.70334	Ankyrin repeat-containing domain (4);	0.054132	0.85682	D	0.000000	T	0.53753	0.1816	N	0.02697	-0.525	0.50039	D	0.999842	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.996;0.995;0.999	T	0.61869	-0.6974	10	0.62326	D	0.03	-9.5834	7.2454	0.26119	0.0:0.7308:0.1744:0.0948	.	194;209;254	Q8WXI3-3;Q8WXI3;D5MNW9	.;ASB10_HUMAN;.	C	209;194;254;254;209	ENSP00000275838:G209C;ENSP00000367098:G194C;ENSP00000401369:G254C;ENSP00000398247:G254C;ENSP00000391137:G209C	ENSP00000275838:G209C	G	-	1	0	ASB10	150509438	0.161000	0.22892	0.996000	0.52242	0.637000	0.38172	1.447000	0.35101	2.549000	0.85964	0.655000	0.94253	GGT	.	.		0.632	ASB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347096.3	NM_080871		A	150878505	C	A	150878505	3	1	254	1	0	0	0	0	1	0	0	0	1014	594	21	3	790	3	ASB10	7	150878505	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	64269	150878505	8260158	373	34665										
PAXIP1	22976	hgsc.bcm.edu	37	chr7	154738503	154738503	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agacttgggcagattccaggTgtgatgtaaaaatattttgc	11	5	0	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:154738503T>C	ENST00000404141.1	-	18	3097	c.2943A>G	c.(2941-2943)acA>acG	p.T981T	PAXIP1_ENST00000473219.1_5'UTR|PAXIP1_ENST00000397192.1_Silent_p.T981T			Q6ZW49	PAXI1_HUMAN	PAX interacting (with transcription-activation domain) protein 1	981	BRCT 6. {ECO:0000255|PROSITE- ProRule:PRU00033}.|Interaction with TP53BP1.				adipose tissue development (GO:0060612)|chorion development (GO:0060717)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|endothelial cell migration (GO:0043542)|histone H3-K4 methylation (GO:0051568)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K36 methylation (GO:0000416)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of isotype switching (GO:0045830)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	33	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0296)	UCEC - Uterine corpus endometrioid carcinoma (81;0.178)		AGATTCCAGGTGTGATGTAAA	0.363																																					p.T981T		Atlas-SNP	.											.	PAXIP1	150	.	0			c.A2943G						.						50	45	46					7																	154738503		1845	4112	5957	SO:0001819	synonymous_variant	22976	exon18			TCCAGGTGTGATG	U80735	CCDS47753.1	7q36	2007-07-06	2005-04-05	2005-04-05	ENSG00000157212	ENSG00000157212			8624	protein-coding gene	gene with protein product		608254	"PAX transcription activation domain interacting protein 1 like"	PAXIP1L		9225980	Standard	XM_005249539		Approved	CAGF29, CAGF28, TNRC2, PTIP	uc022aqf.1	Q6ZW49	OTTHUMG00000151322	ENST00000404141.1:c.2943A>G	chr7.hg19:g.154738503T>C		44.0	0.0		49.0	4.0	NM_007349	O15404|Q6N099|Q6ZWH9|Q7Z315|Q86UN0|Q8N4P9|Q96HP2	Silent	SNP	ENST00000404141.1	hg19	CCDS47753.1																																																																																			.	.		0.363	PAXIP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322223.1	NM_007349		C	154738503	T	C	154738503	2	2	254	1	0	0	0	0	0	0	0	1	11496	1683	59	2		2	PAXIP1	7	154738503	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	3859998	154738503	4400160	374	34666										
UBE3C	9690	hgsc.bcm.edu	37	chr7	156961778	156961778	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgaaaaatgcaataattatcCagtcatttattcgaggctat	6	6	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:156961778C>A	ENST00000348165.5	+	3	517	c.157C>A	c.(157-159)Cag>Aag	p.Q53K	UBE3C_ENST00000389103.4_Intron	NM_014671.2	NP_055486.2	Q15386	UBE3C_HUMAN	ubiquitin protein ligase E3C	53	Cis-determinant of acceptor ubiquitin- binding.|IQ. {ECO:0000255|PROSITE- ProRule:PRU00116}.				protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(2)|endometrium(3)|kidney(16)|large_intestine(13)|lung(25)|ovary(2)|prostate(1)|urinary_tract(1)	63		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)		AATAATTATCCAGTCATTTAT	0.358																																					p.Q53K		Atlas-SNP	.											.	UBE3C	124	.	0			c.C157A						.						97	93	95					7																	156961778		2203	4300	6503	SO:0001583	missense	9690	exon3			ATTATCCAGTCAT	AK127280	CCDS34789.1	7q36.3	2004-05-04			ENSG00000009335	ENSG00000009335			16803	protein-coding gene	gene with protein product		614454				7584026, 11278995	Standard	NM_014671		Approved	KIAA0010, KIAA10	uc010lqs.3	Q15386	OTTHUMG00000157239	ENST00000348165.5:c.157C>A	chr7.hg19:g.156961778C>A	ENSP00000309198:p.Gln53Lys	90.0	0.0		73.0	4.0	NM_014671	A4D235|A6NCP3|Q8TC15|Q96CR4|Q9UDU3	Missense_Mutation	SNP	ENST00000348165.5	hg19	CCDS34789.1	.	.	.	.	.	.	.	.	.	.	C	19.61	3.860561	0.71834	.	.	ENSG00000009335	ENST00000348165	T	0.75154	-0.91	4.63	4.63	0.57726	.	0.000000	0.85682	D	0.000000	D	0.82430	0.5035	M	0.80422	2.495	0.80722	D	1	P;D	0.53312	0.748;0.959	B;P	0.51079	0.318;0.658	D	0.86368	0.1721	10	0.87932	D	0	.	17.8605	0.88779	0.0:1.0:0.0:0.0	.	53;53	Q15386;Q15386-2	UBE3C_HUMAN;.	K	53	ENSP00000309198:Q53K	ENSP00000309198:Q53K	Q	+	1	0	UBE3C	156654539	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.994000	0.70623	2.273000	0.75805	0.655000	0.94253	CAG	.	.		0.358	UBE3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348108.1	NM_014671		A	156961778	C	A	156961778	3	1	254	1	0	0	0	0	1	0	0	0	16896	595	21	3	167	3	UBE3C	7	156961778	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	2223275	156961778	2176885	375	34667										
PTPRN2	5799	hgsc.bcm.edu	37	chr7	157959974	157959974	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	caggatgctctcggagaagcGgtcatcaccctgaaggaaag	13	10	3	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr7:157959974G>T	ENST00000389418.4	-	6	568	c.559C>A	c.(559-561)Cgc>Agc	p.R187S	PTPRN2_ENST00000409483.1_Missense_Mutation_p.R149S|PTPRN2_ENST00000389413.3_Missense_Mutation_p.R187S|PTPRN2_ENST00000404321.2_Missense_Mutation_p.R210S|PTPRN2_ENST00000389416.4_Missense_Mutation_p.R170S	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	187					negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		TCGGAGAAGCGGTCATCACCC	0.597																																					p.R187S		Atlas-SNP	.											.	PTPRN2	243	.	0			c.C559A						.						64	64	64					7																	157959974		2203	4300	6503	SO:0001583	missense	5799	exon6			AGAAGCGGTCATC	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9677	protein-coding gene	gene with protein product	"IAR PTPRP"	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.559C>A	chr7.hg19:g.157959974G>T	ENSP00000374069:p.Arg187Ser	71.0	0.0		95.0	5.0	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Missense_Mutation	SNP	ENST00000389418.4	hg19	CCDS5947.1	.	.	.	.	.	.	.	.	.	.	G	0.003	-2.531298	0.00145	.	.	ENSG00000155093	ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321	T;T;T;T;T	0.02656	4.22;4.23;4.22;4.22;4.21	4.3	-5.53	0.02552	.	1.669860	0.04103	N	0.313279	T	0.00936	0.0031	N	0.02539	-0.55	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.0;0.001;0.0;0.0	T	0.44329	-0.9335	10	0.07482	T	0.82	.	0.1714	0.00113	0.2905:0.266:0.1773:0.2662	.	210;149;187;170;187	Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932	.;.;.;.;PTPR2_HUMAN	S	149;187;170;187;210	ENSP00000387114:R149S;ENSP00000374064:R187S;ENSP00000374067:R170S;ENSP00000374069:R187S;ENSP00000385464:R210S	ENSP00000374064:R187S	R	-	1	0	PTPRN2	157652735	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.298000	0.08265	-0.884000	0.03976	-0.266000	0.10368	CGC	.	.		0.597	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1			T	157959974	G	T	157959974	3	4	254	1	0	0	0	0	1	0	0	0	12823	1116	39	1	2560	1	PTPRN2	7	157959974	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	998196	157959974	1178689	376	34668										
CSMD1	64478	hgsc.bcm.edu	37	chr8	2967694	2967694	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcataccaaacagcaatgtaAtcgttgacagcttccgtctg	7	11	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:2967694A>G	ENST00000520002.1	-	44	7152	c.6597T>C	c.(6595-6597)gaT>gaC	p.D2199D	CSMD1_ENST00000602723.1_Silent_p.D2199D|CSMD1_ENST00000400186.3_Silent_p.D2199D|CSMD1_ENST00000542608.1_Silent_p.D2198D|CSMD1_ENST00000602557.1_Silent_p.D2199D|CSMD1_ENST00000537824.1_Silent_p.D2198D			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	2199	CUB 13. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CAGCAATGTAATCGTTGACAG	0.433																																					p.D2198D		Atlas-SNP	.											.	CSMD1	1469	.	0			c.T6594C						.						89	87	88					8																	2967694		1947	4132	6079	SO:0001819	synonymous_variant	64478	exon43			AATGTAATCGTTG			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.6597T>C	chr8.hg19:g.2967694A>G		72.0	0.0		52.0	4.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	hg19																																																																																				.	.		0.433	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		G	2967694	A	G	2967694	2	3	254	1	0	0	0	0	0	0	0	1	3946	98	4	2		2	CSMD1	8	2967694	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10		2967694	143396328	377	34669										
SGK223	157285	hgsc.bcm.edu	37	chr8	8185764	8185764	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agtggcttaggttcagcttgGggcttgctgttccgggcttg	16	8	1	0	rs150737128	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:8185764G>T	ENST00000520004.1	-	5	2792	c.2528C>A	c.(2527-2529)cCc>cAc	p.P843H	SGK223_ENST00000330777.4_Missense_Mutation_p.P843H			Q86YV5	SG223_HUMAN		845							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										GTTCAGCTTGGGGCTTGCTGT	0.587																																					p.P843H	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.C2528A						.						135	147	143					8																	8185764		1988	4147	6135	SO:0001583	missense	0	exon4			AGCTTGGGGCTTG																												ENST00000520004.1:c.2528C>A	chr8.hg19:g.8185764G>T	ENSP00000428054:p.Pro843His	149.0	0.0		72.0	4.0	NM_001080826	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	hg19	CCDS43706.1	.	.	.	.	.	.	.	.	.	.	G	16.22	3.063106	0.55432	.	.	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.65364	-0.15;-0.15	4.97	4.97	0.65823	.	0.081584	0.48286	D	0.000185	T	0.76723	0.4027	M	0.63843	1.955	0.51767	D	0.999935	D	0.89917	1.0	D	0.91635	0.999	T	0.78540	-0.2165	10	0.87932	D	0	.	15.906	0.79430	0.0:0.0:1.0:0.0	.	843	Q86YV5	SG223_HUMAN	H	843	ENSP00000330930:P843H;ENSP00000428054:P843H	ENSP00000330930:P843H	P	-	2	0	AC068353.1	8223174	1.000000	0.71417	1.000000	0.80357	0.242000	0.25591	5.320000	0.65841	2.751000	0.94390	0.563000	0.77884	CCC	.	G|1.000;A|0.000		0.587	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1			T	8185764	G	T	8185764	3	4	254	1	0	0	0	0	1	0	0	0	14225	1232	43	3	1688	3	SGK223	8	8185764	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	5218070	8185764	138178258	378	34670										
RP1L1	94137	hgsc.bcm.edu	37	chr8	10468763	10468763	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agcctctggagacgagcgggGcagagagctgggtgacacac	17	10	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:10468763G>A	ENST00000382483.3	-	4	3068	c.2845C>T	c.(2845-2847)Ccc>Tcc	p.P949S		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	949					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		GACGAGCGGGGCAGAGAGCTG	0.642																																					p.P949S		Atlas-SNP	.											RP1L1,right_upper_lobe,carcinoma,0,1	RP1L1	453	.	0			c.C2845T						.						41	49	46					8																	10468763		2021	4171	6192	SO:0001583	missense	94137	exon4			AGCGGGGCAGAGA	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.2845C>T	chr8.hg19:g.10468763G>A	ENSP00000371923:p.Pro949Ser	103.0	0.0		44.0	2.0	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	hg19	CCDS43708.1	.	.	.	.	.	.	.	.	.	.	G	16.13	3.035997	0.54896	.	.	ENSG00000183638	ENST00000382483	T	0.76186	-1.0	4.73	4.73	0.59995	.	0.000000	0.34628	N	0.003817	T	0.79851	0.4517	L	0.32530	0.975	0.45899	D	0.99874	D	0.89917	1.0	D	0.91635	0.999	T	0.82163	-0.0593	10	0.87932	D	0	-24.7821	14.9928	0.71401	0.0:0.0:1.0:0.0	.	949	A6NKC6	.	S	949	ENSP00000371923:P949S	ENSP00000371923:P949S	P	-	1	0	RP1L1	10506173	1.000000	0.71417	0.994000	0.49952	0.020000	0.10135	6.864000	0.75494	2.441000	0.82636	0.462000	0.41574	CCC	.	.		0.642	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			A	10468763	G	A	10468763	3	1	254	1	0	0	0	0	1	0	0	0	13548	1203	42	3	4361	3	RP1L1	8	10468763	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	2282999	10468763	135895259	379	34671										
MSR1	4481	hgsc.bcm.edu	37	chr8	15967718	15967718	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	acacttcattcagccatattGgaccagtacctgcaataatg	6	11	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:15967718G>A	ENST00000262101.5	-	10	1353	c.1232C>T	c.(1231-1233)cCa>cTa	p.P411L	MSR1_ENST00000445506.2_Missense_Mutation_p.P429L|MSR1_ENST00000350896.3_Missense_Mutation_p.P348L|MSR1_ENST00000355282.2_Missense_Mutation_p.P348L			P21757	MSRE_HUMAN	macrophage scavenger receptor 1	411	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				cholesterol transport (GO:0030301)|lipoprotein transport (GO:0042953)|plasma lipoprotein particle clearance (GO:0034381)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|receptor-mediated endocytosis (GO:0006898)	collagen trimer (GO:0005581)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|plasma membrane (GO:0005886)	low-density lipoprotein particle binding (GO:0030169)|scavenger receptor activity (GO:0005044)	p.P411Q(1)		haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(7)|lung(14)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	37				Colorectal(111;0.00475)|COAD - Colon adenocarcinoma(73;0.0164)		CAGCCATATTGGACCAGTACC	0.373																																					p.P411L		Atlas-SNP	.											MSR1,NS,carcinoma,0,1	MSR1	140	.	1	Substitution - Missense(1)	lung(1)	c.C1232T						.						91	94	93					8																	15967718		2203	4300	6503	SO:0001583	missense	4481	exon10			CATATTGGACCAG	D13263	CCDS5995.1, CCDS5996.1, CCDS5997.1	8p22	2006-02-22			ENSG00000038945	ENSG00000038945		"CD molecules"	7376	protein-coding gene	gene with protein product		153622				2251254	Standard	NM_138715		Approved	SCARA1, CD204	uc003wwz.3	P21757	OTTHUMG00000094809	ENST00000262101.5:c.1232C>T	chr8.hg19:g.15967718G>A	ENSP00000262101:p.Pro411Leu	132.0	0.0		73.0	3.0	NM_138715	D3DSP3|O60505|P21759|Q45F10	Missense_Mutation	SNP	ENST00000262101.5	hg19	CCDS5995.1	.	.	.	.	.	.	.	.	.	.	G	15.15	2.748979	0.49257	.	.	ENSG00000038945	ENST00000350896;ENST00000262101;ENST00000445506;ENST00000355282	T;T;T;T	0.35973	1.28;1.28;1.28;1.28	5.08	4.19	0.49359	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.000000	0.48286	D	0.000194	T	0.54759	0.1878	M	0.74546	2.27	0.80722	D	1	D;D;D	0.89917	0.997;0.999;1.0	D;D;D	0.75484	0.95;0.973;0.986	T	0.50651	-0.8803	10	0.30854	T	0.27	.	10.1036	0.42519	0.0983:0.0:0.9017:0.0	.	429;348;411	B4DDJ5;P21757-3;P21757	.;.;MSRE_HUMAN	L	348;411;429;348	ENSP00000262100:P348L;ENSP00000262101:P411L;ENSP00000405453:P429L;ENSP00000347430:P348L	ENSP00000262101:P411L	P	-	2	0	MSR1	16012089	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.821000	0.39041	2.515000	0.84797	0.650000	0.86243	CCA	.	.		0.373	MSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211627.2			A	15967718	G	A	15967718	3	1	254	1	0	0	0	0	1	0	0	0	9895	1348	47	3	127	3	MSR1	8	15967718	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	5498955	15967718	130396304	380	34672										
EFHA2	286097	hgsc.bcm.edu	37	chr8	16921741	16921741	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggctgttacaacagatgagcCcaaaggtaagtacacttttg	10	8	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:16921741C>A	ENST00000318063.5	+	2	572	c.530C>A	c.(529-531)cCc>cAc	p.P177H		NM_181723.2	NP_859074.1	Q86XE3	MICU3_HUMAN	mitochondrial calcium uptake family, member 3	177						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)										ACAGATGAGCCCAAAGGTAAG	0.338																																					p.P177H		Atlas-SNP	.											.	EFHA2	60	.	0			c.C530A						.						92	84	87					8																	16921741		2203	4300	6503	SO:0001583	missense	286097	exon2			ATGAGCCCAAAGG	BC032868	CCDS5999.1	8p22	2013-03-26	2013-03-26	2013-03-14	ENSG00000155970	ENSG00000155970		"EF-hand domain containing"	27820	protein-coding gene	gene with protein product		610633	"EF hand domain family A2", "EF-hand domain family, member A2"	EFHA2		23409044	Standard	NM_181723		Approved	DKFZp313A0139	uc003wxd.2	Q86XE3	OTTHUMG00000096965	ENST00000318063.5:c.530C>A	chr8.hg19:g.16921741C>A	ENSP00000321455:p.Pro177His	130.0	0.0		87.0	4.0	NM_181723	Q8IYZ3	Missense_Mutation	SNP	ENST00000318063.5	hg19	CCDS5999.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.29|17.29	3.352511|3.352511	0.61293|0.61293	.|.	.|.	ENSG00000155970|ENSG00000155970	ENST00000318063|ENST00000519044	D|D	0.90620|0.90444	-2.7|-2.67	4.83|4.83	3.92|3.92	0.45320|0.45320	.|.	0.114638|0.114638	0.64402|0.64402	D|D	0.000011|0.000011	D|D	0.93785|0.93785	0.8013|0.8013	M|M	0.81942|0.81942	2.565|2.565	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.87578|.	0.998|.	D|D	0.93055|0.93055	0.6469|0.6469	10|8	0.72032|0.35671	D|T	0.01|0.21	-21.2422|-21.2422	15.3036|15.3036	0.73976|0.73976	0.0:0.8587:0.1413:0.0|0.0:0.8587:0.1413:0.0	.|.	177|.	Q86XE3|.	EFHA2_HUMAN|.	H|T	177|35	ENSP00000321455:P177H|ENSP00000427765:P35T	ENSP00000321455:P177H|ENSP00000427765:P35T	P|P	+|+	2|1	0|0	EFHA2|EFHA2	16966112|16966112	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.896000|0.896000	0.52359|0.52359	6.206000|6.206000	0.72154|0.72154	1.297000|1.297000	0.44761|0.44761	0.591000|0.591000	0.81541|0.81541	CCC|CCA	.	.		0.338	MICU3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214031.1	NM_181723		A	16921741	C	A	16921741	3	1	254	1	0	0	0	0	1	0	0	0	4946	623	22	3	536	3	EFHA2	8	16921741	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	954023	16921741	129442281	381	34673										
VPS37A	137492	hgsc.bcm.edu	37	chr8	17126365	17126365	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcatgtattgttactttcagTttacaatgcactcagatctt	5	8	4	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:17126365T>C	ENST00000324849.4	+	4	990	c.316T>C	c.(316-318)Ttt>Ctt	p.F106L	VPS37A_ENST00000521829.1_Splice_Site_p.F81L|VPS37A_ENST00000324815.3_Splice_Site_p.F106L	NM_001145152.1|NM_152415.2	NP_001138624.1|NP_689628.2	Q8NEZ2	VP37A_HUMAN	vacuolar protein sorting 37 homolog A (S. cerevisiae)	106					cell death (GO:0008219)|endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|membrane organization (GO:0061024)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)				autonomic_ganglia(1)|breast(1)|kidney(2)|large_intestine(1)|lung(4)|skin(1)	10				Colorectal(111;0.0553)|COAD - Colon adenocarcinoma(73;0.212)		TTACTTTCAGTTTACAATGCA	0.333																																					p.F106L		Atlas-SNP	.											.	VPS37A	22	.	0			c.T316C						.						86	84	85					8																	17126365		2203	4297	6500	SO:0001630	splice_region_variant	137492	exon4			TTTCAGTTTACAA		CCDS6001.1, CCDS47811.1	8p22	2012-06-29	2006-04-04		ENSG00000155975	ENSG00000155975			24928	protein-coding gene	gene with protein product	"hepatocellular carcinoma related protein 1"	609927	"vacuolar protein sorting 37A (yeast)", "polyglutamine binding protein 2"	PQBP2		15240819, 15218037, 22717650	Standard	NM_152415		Approved	FLJ32642, HCRP1, SPG53	uc003wxj.3	Q8NEZ2	OTTHUMG00000130785	ENST00000324849.4:c.316-1T>C	chr8.hg19:g.17126365T>C		117.0	0.0		79.0	4.0	NM_152415	Q336D5|Q6NW27|Q8N3D7|Q8TBL7|Q96DL9	Missense_Mutation	SNP	ENST00000324849.4	hg19	CCDS6001.1	.	.	.	.	.	.	.	.	.	.	T	28.2	4.897638	0.91962	.	.	ENSG00000155975	ENST00000324849;ENST00000324815;ENST00000521829	T;T	0.65549	-0.16;-0.08	5.0	5.0	0.66597	Ubiquitin-conjugating enzyme/RWD-like (2);	0.000000	0.85682	D	0.000000	T	0.66107	0.2756	M	0.71581	2.175	0.80722	D	1	P;B	0.48230	0.907;0.412	P;B	0.45712	0.491;0.134	T	0.69101	-0.5234	9	.	.	.	-17.9103	15.0191	0.71613	0.0:0.0:0.0:1.0	.	81;106	Q8NEZ2-2;Q8NEZ2	.;VP37A_HUMAN	L	106;106;81	ENSP00000318629:F106L;ENSP00000429680:F81L	.	F	+	1	0	VPS37A	17170736	1.000000	0.71417	1.000000	0.80357	0.794000	0.44872	7.262000	0.78410	2.011000	0.59026	0.533000	0.62120	TTT	.	.		0.333	VPS37A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253301.2	NM_152415	Missense_Mutation	C	17126365	T	C	17126365	5	2	254	1	0	0	0	0	0	0	1	0	17220	1739	60	2	330	2	VPS37A	8	17126365	Splice_Site	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	204624	17126365	129237657	382	34674										
EGR3	1960	hgsc.bcm.edu	37	chr8	22548215	22548215	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggtcgctgcggctgaagctcCgcatgcagatccggcactgg	15	13	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:22548215C>T	ENST00000317216.2	-	2	1292	c.935G>A	c.(934-936)cGg>cAg	p.R312Q	EGR3_ENST00000519492.1_3'UTR|RP11-459E5.1_ENST00000523627.1_RNA|EGR3_ENST00000524088.1_5'UTR|EGR3_ENST00000522910.1_Missense_Mutation_p.R274Q	NM_001199881.1|NM_004430.2	NP_001186810.1|NP_004421.2	Q06889	EGR3_HUMAN	early growth response 3	312					cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to gonadotropin stimulus (GO:0071371)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|circadian rhythm (GO:0007623)|endothelial cell chemotaxis (GO:0035767)|muscle organ development (GO:0007517)|negative regulation of apoptotic process (GO:0043066)|neuromuscular synaptic transmission (GO:0007274)|peripheral nervous system development (GO:0007422)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of T cell differentiation in thymus (GO:0033089)|regulation of gamma-delta T cell differentiation (GO:0045586)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	10		Prostate(55;0.0421)|Breast(100;0.102)		Colorectal(74;0.0145)|BRCA - Breast invasive adenocarcinoma(99;0.053)|COAD - Colon adenocarcinoma(73;0.0608)		GCTGAAGCTCCGCATGCAGAT	0.667																																					p.R312Q		Atlas-SNP	.											.	EGR3	33	.	0			c.G935A						.						62	63	63					8																	22548215		2203	4300	6503	SO:0001583	missense	1960	exon2			AAGCTCCGCATGC	X63741	CCDS6033.1, CCDS56528.1	8p23-p21	2013-01-08			ENSG00000179388	ENSG00000179388		"Zinc fingers, C2H2-type"	3240	protein-coding gene	gene with protein product	"zinc finger protein pilot"	602419				1906159, 11909874	Standard	NM_004430		Approved	PILOT	uc003xcm.1	Q06889	OTTHUMG00000097825	ENST00000317216.2:c.935G>A	chr8.hg19:g.22548215C>T	ENSP00000318057:p.Arg312Gln	207.0	0.0		100.0	4.0	NM_004430	A8K8U9|B4DHJ5|E7EW38|Q2M3W2	Missense_Mutation	SNP	ENST00000317216.2	hg19	CCDS6033.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.770789	0.90108	.	.	ENSG00000179388	ENST00000317216;ENST00000522910;ENST00000435199	T;T	0.18960	2.18;2.18	5.62	5.62	0.85841	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.41903	0.1179	L	0.48877	1.53	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.15983	-1.0418	10	0.87932	D	0	-12.7178	17.155	0.86788	0.0:1.0:0.0:0.0	.	274;312	E7EW38;Q06889	.;EGR3_HUMAN	Q	312;274;153	ENSP00000318057:R312Q;ENSP00000430310:R274Q	ENSP00000318057:R312Q	R	-	2	0	EGR3	22604160	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.976000	0.63785	2.643000	0.89663	0.655000	0.94253	CGG	.	.		0.667	EGR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215098.1	NM_004430		T	22548215	C	T	22548215	3	4	254	1	0	0	0	0	1	0	0	0	4975	652	23	1	232	1	EGR3	8	22548215	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	5421850	22548215	123815807	383	34675										
TNFRSF10D	8793	hgsc.bcm.edu	37	chr8	23003279	23003279	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctaaaaccactatgatgataAggtagtgatagggagaggca	12	5	0	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:23003279A>G	ENST00000312584.3	-	5	732	c.638T>C	c.(637-639)cTt>cCt	p.L213P		NM_003840.4	NP_003831.2	Q9UBN6	TR10D_HUMAN	tumor necrosis factor receptor superfamily, member 10d, decoy with truncated death domain	213					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0147)|COAD - Colon adenocarcinoma(73;0.0612)		TATGATGATAAGGTAGTGATA	0.468																																					p.L213P		Atlas-SNP	.											.	TNFRSF10D	21	.	0			c.T638C						.						144	128	134					8																	23003279		2203	4300	6503	SO:0001583	missense	8793	exon5			ATGATAAGGTAGT	AF029761	CCDS6038.1	8p21	2006-02-22			ENSG00000173530	ENSG00000173530		"Tumor necrosis factor receptor superfamily", "CD molecules"	11907	protein-coding gene	gene with protein product		603614				9382840, 9537512	Standard	NM_003840		Approved	DcR2, TRUNDD, TRAILR4, CD264	uc003xcz.2	Q9UBN6	OTTHUMG00000097845	ENST00000312584.3:c.638T>C	chr8.hg19:g.23003279A>G	ENSP00000310263:p.Leu213Pro	101.0	0.0		56.0	4.0	NM_003840	B2R8W0|Q9Y6Q4	Missense_Mutation	SNP	ENST00000312584.3	hg19	CCDS6038.1	.	.	.	.	.	.	.	.	.	.	a	3.465	-0.109254	0.06924	.	.	ENSG00000173530	ENST00000312584	D	0.83755	-1.76	1.38	-1.89	0.07689	.	.	.	.	.	T	0.67144	0.2862	N	0.22421	0.69	0.09310	N	0.999997	B	0.24651	0.108	B	0.23018	0.043	T	0.50857	-0.8778	9	0.36615	T	0.2	.	5.2822	0.15682	0.5563:0.0:0.4437:0.0	.	213	Q9UBN6	TR10D_HUMAN	P	213	ENSP00000310263:L213P	ENSP00000310263:L213P	L	-	2	0	TNFRSF10D	23059224	0.042000	0.20092	0.000000	0.03702	0.000000	0.00434	0.003000	0.13083	-0.687000	0.05162	-1.587000	0.00848	CTT	.	.		0.468	TNFRSF10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215135.1			G	23003279	A	G	23003279	3	3	254	1	0	0	0	0	1	0	0	0	16298	72	3	2	542	2	TNFRSF10D	8	23003279	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	455064	23003279	123360743	384	34676										
DPYSL2	1808	hgsc.bcm.edu	37	chr8	26439530	26439530	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtaaaattgttaatgatgacCagtcgttctatgcagacata	8	6	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:26439530C>A	ENST00000311151.5	+	2	497	c.85C>A	c.(85-87)Cag>Aag	p.Q29K	DPYSL2_ENST00000521913.1_5'UTR|DPYSL2_ENST00000523027.1_5'UTR	NM_001386.5	NP_001377.1	Q16555	DPYL2_HUMAN	dihydropyrimidinase-like 2	29					axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|endocytosis (GO:0006897)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|olfactory bulb development (GO:0021772)|positive regulation of glutamate secretion (GO:0014049)|pyrimidine nucleobase catabolic process (GO:0006208)|regulation of neuron differentiation (GO:0045664)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|signal transduction (GO:0007165)|spinal cord development (GO:0021510)|synaptic vesicle transport (GO:0048489)	axon (GO:0030424)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	dihydropyrimidinase activity (GO:0004157)			breast(1)|endometrium(5)|large_intestine(8)|lung(3)|prostate(1)|skin(1)|stomach(1)	20		all_cancers(63;0.121)|Ovarian(32;2.68e-05)|all_epithelial(46;0.116)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;3.33e-10)|Colorectal(74;0.183)		TAATGATGACCAGTCGTTCTA	0.398																																					p.Q134K		Atlas-SNP	.											.	DPYSL2	49	.	0			c.C400A						.						152	128	136					8																	26439530		2203	4300	6503	SO:0001583	missense	1808	exon2			GATGACCAGTCGT	D78013	CCDS6051.1, CCDS59096.1	8p22-p21	2011-09-28			ENSG00000092964	ENSG00000092964			3014	protein-coding gene	gene with protein product		602463				8973361	Standard	NM_001197293		Approved	DRP-2, DHPRP2, CRMP2, DRP2	uc003xfa.3	Q16555	OTTHUMG00000099439	ENST00000311151.5:c.85C>A	chr8.hg19:g.26439530C>A	ENSP00000309539:p.Gln29Lys	126.0	0.0		85.0	4.0	NM_001197293	A8K5H2|B4DR31|D3DSS7|O00424	Missense_Mutation	SNP	ENST00000311151.5	hg19	CCDS6051.1	.	.	.	.	.	.	.	.	.	.	C	19.38	3.816092	0.70912	.	.	ENSG00000092964	ENST00000493789;ENST00000311151;ENST00000522745	D;D;D	0.86627	-2.15;-1.92;-1.92	5.13	5.13	0.70059	Metal-dependent hydrolase, composite domain (1);	0.000000	0.85682	D	0.000000	D	0.87148	0.6105	L	0.35593	1.075	0.80722	D	1	B;P;P	0.49961	0.032;0.732;0.93	B;P;P	0.57679	0.009;0.625;0.825	T	0.81927	-0.0709	10	0.07325	T	0.83	-19.4567	18.7656	0.91871	0.0:1.0:0.0:0.0	.	29;29;85	Q53ET2;Q16555;Q59GB4	.;DPYL2_HUMAN;.	K	101;29;29	ENSP00000427954:Q101K;ENSP00000309539:Q29K;ENSP00000428909:Q29K	ENSP00000309539:Q29K	Q	+	1	0	DPYSL2	26495447	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.647000	0.83462	2.666000	0.90696	0.561000	0.74099	CAG	.	.		0.398	DPYSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216904.3	NM_001386		A	26439530	C	A	26439530	3	1	254	1	0	0	0	0	1	0	0	0	4749	595	21	3	91	3	DPYSL2	8	26439530	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	3436251	26439530	119924492	385	34677										
CHRNA2	1135	hgsc.bcm.edu	37	chr8	27320754	27320754	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tccacgttgctctccagccaGtgataagaggggctgagctt	12	11	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:27320754G>A	ENST00000520933.2	-	5	1359	c.1206C>T	c.(1204-1206)caC>caT	p.H402H	CHRNA2_ENST00000407991.1_Silent_p.H402H|CHRNA2_ENST00000240132.2_Silent_p.H387H			Q15822	ACHA2_HUMAN	cholinergic receptor, nicotinic, alpha 2 (neuronal)	402					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transport (GO:0006811)|protein heterooligomerization (GO:0051291)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|drug binding (GO:0008144)			breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	23		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0208)|Epithelial(17;2.77e-10)|Colorectal(74;0.136)	Atracurium(DB00732)|Biperiden(DB00810)|Carbachol(DB00411)|Cisatracurium Besylate(DB00565)|Decamethonium(DB01245)|Dextromethorphan(DB00514)|Doxacurium chloride(DB01135)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Mecamylamine(DB00657)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicotine(DB00184)|Pancuronium(DB01337)|Pipecuronium(DB01338)|Procaine(DB00721)|Rocuronium(DB00728)|Tubocurarine(DB01199)|Vecuronium(DB01339)	TCTCCAGCCAGTGATAAGAGG	0.657																																					p.H402H		Atlas-SNP	.											.	CHRNA2	48	.	0			c.C1206T						.						71	64	66					8																	27320754		2203	4300	6503	SO:0001819	synonymous_variant	1135	exon6			CAGCCAGTGATAA	U62431	CCDS6059.1, CCDS64856.1	8p21	2012-02-11	2006-02-01		ENSG00000120903	ENSG00000120903		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1956	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 2 (neuronal)"	118502	"cholinergic receptor, nicotinic, alpha polypeptide 2 (neuronal)"			1505988	Standard	NM_000742		Approved		uc010lur.3	Q15822	OTTHUMG00000102083	ENST00000520933.2:c.1206C>T	chr8.hg19:g.27320754G>A		79.0	0.0		37.0	4.0	NM_000742	A8KAX3|B4DK19|J3KMY9|Q9HAQ3	Silent	SNP	ENST00000520933.2	hg19	CCDS6059.1																																																																																			.	.		0.657	CHRNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376125.4			A	27320754	G	A	27320754	2	1	254	1	0	0	0	0	0	0	0	1	3385	1020	36	3		3	CHRNA2	8	27320754	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	881224	27320754	119043268	386	34678										
ESCO2	157570	hgsc.bcm.edu	37	chr8	27633887	27633887	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttctttttatagccttttacActtcactgaaaatctgtttc	3	9	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:27633887A>G	ENST00000305188.8	+	3	300	c.62A>G	c.(61-63)cAc>cGc	p.H21R	RNU6-1276P_ENST00000365372.1_RNA|ESCO2_ENST00000397418.2_5'UTR	NM_001017420.2	NP_001017420.1	Q56NI9	ESCO2_HUMAN	establishment of sister chromatid cohesion N-acetyltransferase 2	21					chromosome segregation (GO:0007059)|double-strand break repair (GO:0006302)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|post-translational protein acetylation (GO:0034421)|protein localization to chromatin (GO:0071168)|regulation of DNA replication (GO:0006275)	chromatin (GO:0000785)|chromocenter (GO:0010369)|Golgi apparatus (GO:0005794)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|XY body (GO:0001741)	lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|KIRC - Kidney renal clear cell carcinoma(542;0.0955)|Kidney(114;0.115)|Colorectal(74;0.132)		AGCCTTTTACACTTCACTGAA	0.308									SC Phocomelia syndrome																												p.H21R		Atlas-SNP	.											.	ESCO2	50	.	0			c.A62G						.						27	29	28					8																	27633887		2199	4299	6498	SO:0001583	missense	157570	exon3	Familial Cancer Database	SC-Pseudothalidomide s., incl.: Roberts s.	TTTTACACTTCAC	AF306679	CCDS34872.1	8p21.1	2013-05-02	2013-05-02		ENSG00000171320	ENSG00000171320			27230	protein-coding gene	gene with protein product		609353	"Roberts syndrome", "establishment of cohesion 1 homolog 2 (S. cerevisiae)"	RBS		15958495, 16775838, 15821733, 16380922	Standard	XR_247122		Approved	EFO2	uc003xgg.3	Q56NI9	OTTHUMG00000163901	ENST00000305188.8:c.62A>G	chr8.hg19:g.27633887A>G	ENSP00000306999:p.His21Arg	143.0	0.0		79.0	4.0	NM_001017420	B3KW59|Q49AP4	Missense_Mutation	SNP	ENST00000305188.8	hg19	CCDS34872.1	.	.	.	.	.	.	.	.	.	.	A	0.055	-1.237731	0.01493	.	.	ENSG00000171320	ENST00000523566;ENST00000305188;ENST00000519637	T;T;T	0.61742	1.09;0.08;1.09	5.02	2.6	0.31112	.	2.157160	0.02081	N	0.052398	T	0.31358	0.0794	N	0.02539	-0.55	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.37197	-0.9716	10	0.16896	T	0.51	6.3879	4.5927	0.12315	0.7389:0.0:0.0925:0.1686	.	21;21	E5RFE4;Q56NI9	.;ESCO2_HUMAN	R	21	ENSP00000428435:H21R;ENSP00000306999:H21R;ENSP00000428027:H21R	ENSP00000306999:H21R	H	+	2	0	ESCO2	27689806	0.765000	0.28485	0.046000	0.18839	0.224000	0.24922	0.774000	0.26675	0.329000	0.23460	-1.114000	0.02060	CAC	.	.		0.308	ESCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376276.1	NM_001017420		G	27633887	A	G	27633887	3	3	254	1	0	0	0	0	1	0	0	0	5251	159	6	2	68	2	ESCO2	8	27633887	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	313133	27633887	118730135	387	34679										
HTRA4	203100	hgsc.bcm.edu	37	chr8	38845473	38845473	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agctctggattgagagatcaCgatgtaattgtcaacataaa	9	6	3	2	rs576647651		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:38845473C>T	ENST00000302495.4	+	9	1387	c.1287C>T	c.(1285-1287)caC>caT	p.H429H		NM_153692.3	NP_710159.1	P83105	HTRA4_HUMAN	HtrA serine peptidase 4	429	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|upper_aerodigestive_tract(1)	11		all_lung(54;0.0344)|Hepatocellular(245;0.0512)|Lung NSC(58;0.0955)	LUSC - Lung squamous cell carcinoma(45;1.5e-07)			TGAGAGATCACGATGTAATTG	0.358																																					p.H429H		Atlas-SNP	.											.	HTRA4	25	.	0			c.C1287T						.						103	89	94					8																	38845473		2203	4300	6503	SO:0001819	synonymous_variant	203100	exon9			AGATCACGATGTA	AK075205	CCDS6110.1	8p11.23	2008-02-05			ENSG00000169495	ENSG00000169495			26909	protein-coding gene	gene with protein product		610700					Standard	NM_153692		Approved	FLJ90724	uc003xmj.3	P83105	OTTHUMG00000164070	ENST00000302495.4:c.1287C>T	chr8.hg19:g.38845473C>T		87.0	0.0		46.0	4.0	NM_153692	Q542Z4|Q6PF13	Silent	SNP	ENST00000302495.4	hg19	CCDS6110.1																																																																																			.	.		0.358	HTRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377077.1	NM_153692		T	38845473	C	T	38845473	2	4	254	1	0	0	0	0	0	0	0	1	7465	535	19	1		1	HTRA4	8	38845473	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	11211586	38845473	107518549	388	34680										
ADAM9	8754	hgsc.bcm.edu	37	chr8	38934925	38934925	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aaggcacaaaatgtggtgctGgaaaggtaatcaaaatattt	10	4	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:38934925G>A	ENST00000487273.2	+	16	1954	c.1876G>A	c.(1876-1878)Gga>Aga	p.G626R	ADAM9_ENST00000484143.1_3'UTR	NM_003816.2	NP_003807.1	Q13443	ADAM9_HUMAN	ADAM metallopeptidase domain 9	626	Cys-rich.				activation of MAPKK activity (GO:0000186)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cellular response to lipopolysaccharide (GO:0071222)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte activation (GO:0042117)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein secretion (GO:0050714)|response to calcium ion (GO:0051592)|response to glucocorticoid (GO:0051384)|response to hydrogen peroxide (GO:0042542)|response to laminar fluid shear stress (GO:0034616)|response to manganese ion (GO:0010042)|response to tumor necrosis factor (GO:0034612)|transforming growth factor beta receptor signaling pathway (GO:0007179)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of external side of plasma membrane (GO:0031233)	collagen binding (GO:0005518)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein kinase C binding (GO:0005080)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.0153)	LUSC - Lung squamous cell carcinoma(45;2.74e-07)			ATGTGGTGCTGGAAAGGTAAT	0.348																																					p.G626R		Atlas-SNP	.											.	ADAM9	66	.	0			c.G1876A						.						52	49	50					8																	38934925		2203	4300	6503	SO:0001583	missense	8754	exon16			GGTGCTGGAAAGG	U41766	CCDS6112.1	8p11.23	2011-03-18	2010-06-24		ENSG00000168615	ENSG00000168615		"ADAM metallopeptidase domain containing"	216	protein-coding gene	gene with protein product	"meltrin gamma"	602713	"a disintegrin and metalloproteinase domain 9 (meltrin gamma)", "cone rod dystrophy 9"	CORD9		8647900, 11581183, 19409519	Standard	NR_027638		Approved	MDC9, KIAA0021, MCMP, Mltng	uc003xmr.3	Q13443	OTTHUMG00000159783	ENST00000487273.2:c.1876G>A	chr8.hg19:g.38934925G>A	ENSP00000419446:p.Gly626Arg	173.0	0.0		85.0	4.0	NM_003816	B7ZLN7|Q10718|Q8NFM6	Missense_Mutation	SNP	ENST00000487273.2	hg19	CCDS6112.1	.	.	.	.	.	.	.	.	.	.	G	15.38	2.816101	0.50527	.	.	ENSG00000168615	ENST00000487273	T	0.16597	2.33	5.55	5.55	0.83447	ADAM, cysteine-rich (1);	0.251101	0.40728	N	0.001028	T	0.37598	0.1009	L	0.58428	1.81	0.40269	D	0.978263	D	0.54772	0.968	P	0.59703	0.862	T	0.02901	-1.1096	10	0.54805	T	0.06	.	19.8769	0.96880	0.0:0.0:1.0:0.0	.	626	Q13443	ADAM9_HUMAN	R	626	ENSP00000419446:G626R	ENSP00000369249:G626R	G	+	1	0	ADAM9	39054082	1.000000	0.71417	0.886000	0.34754	0.278000	0.26855	6.128000	0.71650	2.767000	0.95098	0.557000	0.71058	GGA	.	.		0.348	ADAM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357291.2			A	38934925	G	A	38934925	3	1	254	1	0	0	0	0	1	0	0	0	253	1349	47	3	1938	3	ADAM9	8	38934925	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	89452	38934925	107429097	389	34681										
ADAM2	2515	hgsc.bcm.edu	37	chr8	39678655	39678655	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgaagactccaggggttctaTtccataactaacattttcaa	6	9	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:39678655T>C	ENST00000265708.4	-	6	482	c.379A>G	c.(379-381)Ata>Gta	p.I127V	ADAM2_ENST00000347580.4_Missense_Mutation_p.I127V|ADAM2_ENST00000523181.1_5'UTR|ADAM2_ENST00000521880.1_Missense_Mutation_p.I127V|ADAM2_ENST00000379853.2_Missense_Mutation_p.I127V	NM_001464.3	NP_001455.3	Q99965	ADAM2_HUMAN	ADAM metallopeptidase domain 2	127					adult behavior (GO:0030534)|binding of sperm to zona pellucida (GO:0007339)|cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|visual learning (GO:0008542)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(29)|ovary(3)|prostate(1)|skin(5)|urinary_tract(1)	53		all_cancers(7;2.38e-28)|all_epithelial(6;8.85e-21)|all_lung(54;1.24e-07)|Lung NSC(58;1.94e-07)|Hepatocellular(245;0.00745)|Breast(189;0.00908)|Renal(179;0.0183)|Colorectal(162;0.246)	LUSC - Lung squamous cell carcinoma(45;0.000149)	READ - Rectum adenocarcinoma(644;0.0689)|Kidney(114;0.162)		AGGGGTTCTATTCCATAACTA	0.318																																					p.I127V		Atlas-SNP	.											.	ADAM2	124	.	0			c.A379G						.						49	49	49					8																	39678655		2203	4297	6500	SO:0001583	missense	2515	exon6			GTTCTATTCCATA	U52370	CCDS34884.1, CCDS64882.1, CCDS64883.1	8p11.2	2009-03-25	2008-07-31		ENSG00000104755	ENSG00000104755		"ADAM metallopeptidase domain containing"	198	protein-coding gene	gene with protein product	"cancer/testis antigen 15"	601533	"fertilin beta"	FTNB		8702389, 9070941	Standard	NM_001278113		Approved	PH-30b, PH30, CT15	uc003xnj.4	Q99965	OTTHUMG00000164041	ENST00000265708.4:c.379A>G	chr8.hg19:g.39678655T>C	ENSP00000265708:p.Ile127Val	163.0	0.0		99.0	5.0	NM_001464	P78326|Q9UQQ8	Missense_Mutation	SNP	ENST00000265708.4	hg19	CCDS34884.1	.	.	.	.	.	.	.	.	.	.	T	19.65	3.867809	0.72065	.	.	ENSG00000104755	ENST00000347580;ENST00000379853;ENST00000265708;ENST00000521880	T;T;T;T	0.13901	2.55;2.55;2.55;2.55	5.47	5.47	0.80525	Peptidase M12B, propeptide (1);	.	.	.	.	T	0.41419	0.1158	M	0.84585	2.705	0.36139	D	0.846633	D;D;D;D	0.76494	0.999;0.998;0.999;0.999	D;D;D;D	0.85130	0.99;0.995;0.993;0.997	T	0.56565	-0.7958	8	.	.	.	.	13.5152	0.61537	0.0:0.0:0.0:1.0	.	127;127;127;127	B4DWY7;Q6P2G0;Q99965-2;Q99965	.;.;.;ADAM2_HUMAN	V	127	ENSP00000343854:I127V;ENSP00000369182:I127V;ENSP00000265708:I127V;ENSP00000429352:I127V	.	I	-	1	0	ADAM2	39797812	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	3.868000	0.56055	2.076000	0.62316	0.533000	0.62120	ATA	.	.		0.318	ADAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376926.1	NM_001464		C	39678655	T	C	39678655	3	2	254	1	0	0	0	0	1	0	0	0	241	1493	52	2	1888	2	ADAM2	8	39678655	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	743730	39678655	106685367	390	34682										
MYST3	7994	hgsc.bcm.edu	37	chr8	41790607	41790607	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gatcataggagctggggtgaAactgttattcatactacact	10	7	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:41790607A>G	ENST00000396930.3	-	18	5674	c.5131T>C	c.(5131-5133)Ttc>Ctc	p.F1711L	KAT6A_ENST00000265713.2_Missense_Mutation_p.F1711L|KAT6A_ENST00000406337.1_Missense_Mutation_p.F1711L	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	1711	Interaction with PML.				aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										GCTGGGGTGAAACTGTTATTC	0.572																																					p.F1711L		Atlas-SNP	.											.	.	.	.	0			c.T5131C						.						75	78	77					8																	41790607		2203	4300	6503	SO:0001583	missense	7994	exon18			GGGTGAAACTGTT	U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	13013	protein-coding gene	gene with protein product	"Monocytic leukemia zinc finger protein"	601408	"runt-related transcription factor binding protein 2", "MYST histone acetyltransferase (monocytic leukemia) 3"	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.5131T>C	chr8.hg19:g.41790607A>G	ENSP00000380136:p.Phe1711Leu	185.0	0.0		72.0	4.0	NM_001099412	Q76L81	Missense_Mutation	SNP	ENST00000396930.3	hg19	CCDS6124.1	.	.	.	.	.	.	.	.	.	.	A	6.821	0.520527	0.13005	.	.	ENSG00000083168	ENST00000265713;ENST00000406337;ENST00000396930	T;T;T	0.67523	-0.27;-0.27;-0.27	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.70798	0.3265	L	0.34521	1.04	0.58432	D	0.999996	D	0.69078	0.997	D	0.70716	0.97	T	0.65179	-0.6231	10	0.10636	T	0.68	-17.5726	15.8462	0.78895	1.0:0.0:0.0:0.0	.	1711	Q92794	KAT6A_HUMAN	L	1711	ENSP00000265713:F1711L;ENSP00000385888:F1711L;ENSP00000380136:F1711L	ENSP00000265713:F1711L	F	-	1	0	KAT6A	41909764	1.000000	0.71417	1.000000	0.80357	0.239000	0.25481	8.890000	0.92477	2.136000	0.66102	0.528000	0.53228	TTC	.	.		0.572	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766		G	41790607	A	G	41790607	3	3	254	1	0	0	0	0	1	0	0	0	10113	14	1	2	887	2	MYST3	8	41790607	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	2111952	41790607	104573415	391	34683										
POLB	5423	hgsc.bcm.edu	37	chr8	42214709	42214709	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	attttggggactttgaaaaaAgaattcctcgtgaagagatg	11	4	0	4	rs200554507		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:42214709A>G	ENST00000265421.4	+	8	615	c.445A>G	c.(445-447)Aga>Gga	p.R149G	POLB_ENST00000538005.1_5'UTR	NM_002690.2	NP_002681.1	P06746	DPOLB_HUMAN	polymerase (DNA directed), beta	149					base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|neuron apoptotic process (GO:0051402)|pyrimidine dimer repair (GO:0006290)|response to ethanol (GO:0045471)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|enzyme binding (GO:0019899)|lyase activity (GO:0016829)|metal ion binding (GO:0046872)|microtubule binding (GO:0008017)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(5)|ovary(1)	16	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;2.58e-12)|Lung NSC(13;4.24e-11)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.1)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;3.18e-11)|Lung(22;0.00467)|OV - Ovarian serous cystadenocarcinoma(14;0.00523)|LUSC - Lung squamous cell carcinoma(45;0.024)		Cytarabine(DB00987)	CTTTGAAAAAAGAATTCCTCG	0.289								DNA polymerases (catalytic subunits)																													p.R149G		Atlas-SNP	.											.	POLB	60	.	0			c.A445G						.																																			SO:0001583	missense	5423	exon8			GAAAAAAGAATTC		CCDS6129.1	8p12-p11	2012-10-02			ENSG00000070501	ENSG00000070501	2.7.7.7	"DNA polymerases"	9174	protein-coding gene	gene with protein product		174760					Standard	NM_002690		Approved		uc003xoz.2	P06746	OTTHUMG00000164093	ENST00000265421.4:c.445A>G	chr8.hg19:g.42214709A>G	ENSP00000265421:p.Arg149Gly	181.0	0.0		99.0	4.0	NM_002690	B2RC78|Q3KP48|Q6FI34	Missense_Mutation	SNP	ENST00000265421.4	hg19	CCDS6129.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.87|16.87	3.242315|3.242315	0.58995|0.58995	.|.	.|.	ENSG00000070501|ENSG00000070501	ENST00000521290|ENST00000532157;ENST00000265421;ENST00000518925	T|T;T	0.14391|0.51071	2.51|0.72;0.72	5.93|5.93	5.93|5.93	0.95920|0.95920	.|DNA-directed DNA polymerase X (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.53753|0.53753	0.1816|0.1816	M|M	0.85945|0.85945	2.785|2.785	0.80722|0.80722	D|D	1|1	.|B;B	.|0.28055	.|0.199;0.166	.|B;B	.|0.30782	.|0.12;0.06	T|T	0.59434|0.59434	-0.7455|-0.7455	7|10	0.54805|0.87932	T|D	0.06|0	-0.5562|-0.5562	10.3894|10.3894	0.44160|0.44160	0.8359:0.1641:0.0:0.0|0.8359:0.1641:0.0:0.0	.|.	.|149;149	.|Q53EV2;P06746	.|.;DPOLB_HUMAN	R|G	79|35;149;184	ENSP00000429597:K79R|ENSP00000265421:R149G;ENSP00000430784:R184G	ENSP00000429597:K79R|ENSP00000265421:R149G	K|R	+|+	2|1	0|2	POLB|POLB	42333866|42333866	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.963000|0.963000	0.63663|0.63663	6.432000|6.432000	0.73400|0.73400	2.263000|2.263000	0.75096|0.75096	0.533000|0.533000	0.62120|0.62120	AAG|AGA	.	A|0.999;G|0.001		0.289	POLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377242.1	NM_002690		G	42214709	A	G	42214709	3	3	254	1	0	0	0	0	1	0	0	0	12198	64	3	2	475	2	POLB	8	42214709	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	424102	42214709	104149313	392	34684										
PRKDC	5591	hgsc.bcm.edu	37	chr8	48707064	48707064	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agcagggaacggaagagatcTaaaacagagagctgaaactt	12	6	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:48707064T>A	ENST00000523565.1	-	74	10514		c.e74-2		PRKDC_ENST00000338368.3_Splice_Site|PRKDC_ENST00000314191.2_Splice_Site			P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic polypeptide						B cell lineage commitment (GO:0002326)|brain development (GO:0007420)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|ectopic germ cell programmed cell death (GO:0035234)|heart development (GO:0007507)|immunoglobulin V(D)J recombination (GO:0033152)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of protein phosphorylation (GO:0001933)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|pro-B cell differentiation (GO:0002328)|protein destabilization (GO:0031648)|regulation of circadian rhythm (GO:0042752)|response to gamma radiation (GO:0010332)|rhythmic process (GO:0048511)|signal transduction involved in mitotic G1 DNA damage checkpoint (GO:0072431)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell receptor V(D)J recombination (GO:0033153)|telomere maintenance (GO:0000723)	cytosol (GO:0005829)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription factor binding (GO:0008134)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(9)|cervix(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(30)|lung(56)|ovary(6)|pancreas(1)|prostate(8)|skin(7)	147		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)			Caffeine(DB00201)	GGAAGAGATCTAAAACAGAGA	0.408								Non-homologous end-joining																													.	Esophageal Squamous(79;1091 1253 12329 31680 40677)	Atlas-SNP	.											.	PRKDC	394	.	0			c.10458-2A>T						.						54	50	52					8																	48707064		1894	4133	6027	SO:0001630	splice_region_variant	5591	exon75			GAGATCTAAAACA		CCDS75734.1, CCDS75735.1	8q11	2014-09-17				ENSG00000253729	2.7.11.1		9413	protein-coding gene	gene with protein product		600899		HYRC, HYRC1		7638222	Standard	NM_001081640		Approved	DNPK1, p350, DNAPK, XRCC7, DNA-PKcs	uc003xqi.3	P78527		ENST00000523565.1:c.2995-2A>T	chr8.hg19:g.48707064T>A		81.0	0.0		73.0	4.0	NM_001081640	P78528|Q13327|Q13337|Q14175|Q59H99|Q7Z611|Q96SE6|Q9UME3	Splice_Site	SNP	ENST00000523565.1	hg19		.	.	.	.	.	.	.	.	.	.	T	13.85	2.361541	0.41801	.	.	ENSG00000253729	ENST00000314191;ENST00000338368	.	.	.	5.6	5.6	0.85130	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7929	0.78380	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	PRKDC	48869617	1.000000	0.71417	0.911000	0.35937	0.077000	0.17291	7.358000	0.79466	2.123000	0.65237	0.533000	0.62120	.	.	.		0.408	PRKDC-002	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000377896.1	NM_001081640	Intron	A	48707064	T	A	48707064	5	1	254	1	0	0	0	0	0	0	1	0	12533	1536	53	4	1981	4	PRKDC	8	48707064	Splice_Site	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	6492355	48707064	97656958	393	34685										
CHD7	55636	hgsc.bcm.edu	37	chr8	61765595	61765595	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccgagacttgctggttggtgCtgctaaacacggggtcagtc	14	10	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:61765595C>T	ENST00000423902.2	+	31	6790	c.6311C>T	c.(6310-6312)gCt>gTt	p.A2104V	CHD7_ENST00000524602.1_Intron	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	2104					adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			CTGGTTGGTGCTGCTAAACAC	0.537																																					p.A2104V		Atlas-SNP	.											.	CHD7	534	.	0			c.C6311T						.						103	114	111					8																	61765595		2074	4209	6283	SO:0001583	missense	55636	exon31			TTGGTGCTGCTAA	AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"CHARGE association"	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.6311C>T	chr8.hg19:g.61765595C>T	ENSP00000392028:p.Ala2104Val	241.0	1.0		220.0	95.0	NM_017780	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Missense_Mutation	SNP	ENST00000423902.2	hg19	CCDS47865.1	.	.	.	.	.	.	.	.	.	.	C	16.54	3.153143	0.57259	.	.	ENSG00000171316	ENST00000307121;ENST00000423902	D	0.87966	-2.32	5.41	4.52	0.55395	.	0.063732	0.64402	D	0.000007	D	0.83303	0.5225	L	0.28115	0.83	0.58432	D	0.999999	B	0.25169	0.119	B	0.36885	0.235	T	0.78909	-0.2018	10	0.34782	T	0.22	-14.0265	16.0296	0.80570	0.0:0.8653:0.1347:0.0	.	2104	Q9P2D1	CHD7_HUMAN	V	2104	ENSP00000392028:A2104V	ENSP00000307304:A2104V	A	+	2	0	CHD7	61928149	1.000000	0.71417	0.583000	0.28640	0.991000	0.79684	6.090000	0.71397	1.252000	0.44001	0.655000	0.94253	GCT	.	.		0.537	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762		T	61765595	C	T	61765595	3	4	254	1	0	0	0	0	1	0	0	0	3332	797	28	3	6429	3	CHD7	8	61765595	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	13058531	61765595	84598427	394	34686										
RRS1	23212	hgsc.bcm.edu	37	chr8	67342183	67342183	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agaaccagttggagctgcttCgtgtcatgaacagcaagaag	12	8	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:67342183C>T	ENST00000320270.2	+	1	921	c.817C>T	c.(817-819)Cgt>Tgt	p.R273C	ADHFE1_ENST00000379385.4_5'Flank|RP11-346I3.4_ENST00000499642.1_lincRNA|ADHFE1_ENST00000396623.3_5'Flank|ADHFE1_ENST00000415254.1_5'Flank	NM_015169.3	NP_055984.1	Q15050	RRS1_HUMAN	RRS1 ribosome biogenesis regulator homolog (S. cerevisiae)	273					hematopoietic progenitor cell differentiation (GO:0002244)|mitotic metaphase plate congression (GO:0007080)|ribosome biogenesis (GO:0042254)	condensed nuclear chromosome (GO:0000794)|endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			kidney(2)|lung(2)	4		Lung NSC(129;0.197)	Epithelial(68;0.0391)|all cancers(69;0.0898)|BRCA - Breast invasive adenocarcinoma(89;0.111)|OV - Ovarian serous cystadenocarcinoma(28;0.226)			GGAGCTGCTTCGTGTCATGAA	0.557																																					p.R273C		Atlas-SNP	.											.	RRS1	13	.	0			c.C817T						.						26	31	29					8																	67342183		2203	4300	6503	SO:0001583	missense	23212	exon1			CTGCTTCGTGTCA	BC001811	CCDS6189.1	8q13.1	2013-10-22			ENSG00000179041	ENSG00000179041			17083	protein-coding gene	gene with protein product						7788527, 10688653	Standard	NM_015169		Approved	KIAA0112	uc003xwa.3	Q15050	OTTHUMG00000164765	ENST00000320270.2:c.817C>T	chr8.hg19:g.67342183C>T	ENSP00000322396:p.Arg273Cys	58.0	0.0		73.0	5.0	NM_015169	Q9BUX8	Missense_Mutation	SNP	ENST00000320270.2	hg19	CCDS6189.1	.	.	.	.	.	.	.	.	.	.	C	14.28	2.486862	0.44249	.	.	ENSG00000179041	ENST00000320270	D	0.86497	-2.13	5.26	3.33	0.38152	.	0.132508	0.48286	D	0.000193	D	0.88676	0.6501	L	0.47716	1.5	0.49915	D	0.999839	D	0.76494	0.999	P	0.58391	0.838	D	0.89186	0.3547	10	0.62326	D	0.03	-4.8295	12.8419	0.57809	0.3984:0.6016:0.0:0.0	.	273	Q15050	RRS1_HUMAN	C	273	ENSP00000322396:R273C	ENSP00000322396:R273C	R	+	1	0	RRS1	67504737	1.000000	0.71417	0.998000	0.56505	0.454000	0.32378	1.181000	0.32017	1.343000	0.45638	0.650000	0.86243	CGT	.	.		0.557	RRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380126.1	NM_015169		T	67342183	C	T	67342183	3	4	254	1	0	0	0	0	1	0	0	0	13707	884	31	1	819	1	RRS1	8	67342183	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	5576588	67342183	79021839	395	34687										
PREX2	80243	hgsc.bcm.edu	37	chr8	69104651	69104651	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccaagcgcacagctgcctgtGcaaacacagcttgcagtgct	10	14	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:69104651G>A	ENST00000288368.4	+	37	4772	c.4495G>A	c.(4495-4497)Gca>Aca	p.A1499T		NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	1499					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						AGCTGCCTGTGCAAACACAGC	0.537																																					p.A1499T		Atlas-SNP	.											PREX2,colon,carcinoma,0,1	PREX2	614	.	0			c.G4495A						.						78	64	69					8																	69104651		2203	4300	6503	SO:0001583	missense	80243	exon37			GCCTGTGCAAACA	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.4495G>A	chr8.hg19:g.69104651G>A	ENSP00000288368:p.Ala1499Thr	73.0	0.0		68.0	17.0	NM_024870	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	hg19	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	G	18.50	3.636432	0.67130	.	.	ENSG00000046889	ENST00000288368	T	0.59906	0.23	4.89	4.89	0.63831	.	0.494062	0.21652	N	0.071168	T	0.42539	0.1207	N	0.11560	0.145	0.35876	D	0.828574	B	0.10296	0.003	B	0.17098	0.017	T	0.45056	-0.9287	10	0.39692	T	0.17	.	18.4181	0.90577	0.0:0.0:1.0:0.0	.	1499	Q70Z35	PREX2_HUMAN	T	1499	ENSP00000288368:A1499T	ENSP00000288368:A1499T	A	+	1	0	PREX2	69267205	0.992000	0.36948	0.982000	0.44146	0.991000	0.79684	5.460000	0.66691	2.427000	0.82271	0.467000	0.42956	GCA	.	.		0.537	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		A	69104651	G	A	69104651	3	1	254	1	0	0	0	0	1	0	0	0	12489	1319	46	3	4870	3	PREX2	8	69104651	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1762468	69104651	77259371	396	34688										
LY96	23643	hgsc.bcm.edu	37	chr8	74941217	74941217	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tacaaatgtgttgttgaagcTatttctgggagcccagaaga	11	6	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:74941217T>C	ENST00000284818.2	+	5	502	c.411T>C	c.(409-411)gcT>gcC	p.A137A	LY96_ENST00000518893.1_Silent_p.A107A	NM_015364.4	NP_056179	Q9Y6Y9	LY96_HUMAN	lymphocyte antigen 96	137					cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|detection of lipopolysaccharide (GO:0032497)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|response to lipopolysaccharide (GO:0032496)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	endosome membrane (GO:0010008)|extracellular region (GO:0005576)|lipopolysaccharide receptor complex (GO:0046696)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)|lipopolysaccharide receptor activity (GO:0001875)			endometrium(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	5	Breast(64;0.0311)		Epithelial(68;0.0208)|BRCA - Breast invasive adenocarcinoma(89;0.0499)|all cancers(69;0.0619)			TTGTTGAAGCTATTTCTGGGA	0.299																																					p.A137A	GBM(131;1357 1748 34893 50149 52212)	Atlas-SNP	.											.	LY96	17	.	0			c.T411C						.						76	77	77					8																	74941217		2203	4298	6501	SO:0001819	synonymous_variant	23643	exon5			TGAAGCTATTTCT	AB018549	CCDS6216.1, CCDS56540.1	8q13.3	2004-01-22			ENSG00000154589	ENSG00000154589			17156	protein-coding gene	gene with protein product		605243				10359581, 11466383	Standard	NM_015364		Approved	MD-2	uc003yad.3	Q9Y6Y9	OTTHUMG00000164504	ENST00000284818.2:c.411T>C	chr8.hg19:g.74941217T>C		84.0	0.0		94.0	4.0	NM_015364	B3Y6A5|E5RJJ7	Silent	SNP	ENST00000284818.2	hg19	CCDS6216.1																																																																																			.	.		0.299	LY96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379032.2	NM_015364		C	74941217	T	C	74941217	2	2	254	1	0	0	0	0	0	0	0	1	9111	1509	53	2		2	LY96	8	74941217	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	5836566	74941217	71422805	397	34689										
MRPS28	28957	hgsc.bcm.edu	37	chr8	80942312	80942312	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctgtagaagctccgagtgccGctccaacgcgctcgcgaaac	11	15	0	1	rs147337080	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:80942312G>T	ENST00000276585.4	-	1	194	c.172C>A	c.(172-174)Cgg>Agg	p.R58R	MRPS28_ENST00000521605.1_Silent_p.R58R|MRPS28_ENST00000522987.1_5'UTR|MRPS28_ENST00000521434.1_5'Flank|RP11-92K15.3_ENST00000607017.1_lincRNA|TPD52_ENST00000537855.1_Intron	NM_014018.2	NP_054737.1	Q9Y2Q9	RT28_HUMAN	mitochondrial ribosomal protein S28	58						mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(2)|skin(1)	5	Lung NSC(7;1.86e-06)|all_lung(9;6.91e-06)		BRCA - Breast invasive adenocarcinoma(6;0.00769)|Epithelial(68;0.0208)|all cancers(69;0.0805)			TCCGAGTGCCGCTCCAACGCG	0.642																																					p.R58R		Atlas-SNP	.											.	MRPS28	11	.	0			c.C172A						.						30	30	30					8																	80942312		2203	4300	6503	SO:0001819	synonymous_variant	28957	exon1			AGTGCCGCTCCAA	AB061209	CCDS6226.1	8q21.1-q21.2	2012-09-13			ENSG00000147586	ENSG00000147586		"Mitochondrial ribosomal proteins / small subunits"	14513	protein-coding gene	gene with protein product		611990				11279123, 11042152	Standard	NM_014018		Approved	MRP-S28, HSPC007, MRPS35	uc003ybp.3	Q9Y2Q9	OTTHUMG00000164642	ENST00000276585.4:c.172C>A	chr8.hg19:g.80942312G>T		58.0	0.0		89.0	4.0	NM_014018	B2RDZ7|Q96Q21	Silent	SNP	ENST00000276585.4	hg19	CCDS6226.1	.	.	.	.	.	.	.	.	.	.	G	5.653	0.305105	0.10678	.	.	ENSG00000147586	ENST00000518271	.	.	.	5.28	4.4	0.53042	.	.	.	.	.	T	0.62466	0.2430	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60964	-0.7158	4	.	.	.	.	11.0826	0.48068	0.0:0.0:0.8152:0.1847	.	.	.	.	R	52	.	.	S	-	3	2	MRPS28	81104867	0.743000	0.28239	0.992000	0.48379	0.229000	0.25112	0.950000	0.29122	1.442000	0.47568	0.655000	0.94253	AGC	.	G|0.997;A|0.003		0.642	MRPS28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379526.1	NM_014018		T	80942312	G	T	80942312	2	4	254	1	0	0	0	0	0	0	0	1	9848	1086	38	1		1	MRPS28	8	80942312	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	6001095	80942312	65421710	398	34690										
WWP1	11059	hgsc.bcm.edu	37	chr8	87439874	87439874	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	attgtttacttgtggtagttGggaaagaagagttgatgatc	13	2	0	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:87439874G>T	ENST00000517970.1	+	11	1467	c.1160G>T	c.(1159-1161)tGg>tTg	p.W387L	WWP1_ENST00000349423.2_Missense_Mutation_p.W169L|WWP1_ENST00000265428.4_Missense_Mutation_p.W387L|WWP1_ENST00000341922.2_Missense_Mutation_p.W257L	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	387	WW 2. {ECO:0000255|PROSITE- ProRule:PRU00224}.				central nervous system development (GO:0007417)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(9)|liver(4)|lung(10)|prostate(2)|urinary_tract(1)	31						TGTGGTAGTTGGGAAAGAAGA	0.338																																					p.W387L		Atlas-SNP	.											.	WWP1	97	.	0			c.G1160T						.						116	120	119					8																	87439874		2203	4300	6503	SO:0001583	missense	11059	exon11			GTAGTTGGGAAAG	AY043361	CCDS6242.1	8q21.3	2013-07-22			ENSG00000123124	ENSG00000123124			17004	protein-coding gene	gene with protein product		602307				9169421, 9647693	Standard	NM_007013		Approved	AIP5, DKFZP434D2111	uc003ydt.3	Q9H0M0	OTTHUMG00000163690	ENST00000517970.1:c.1160G>T	chr8.hg19:g.87439874G>T	ENSP00000427793:p.Trp387Leu	129.0	0.0		130.0	6.0	NM_007013	O00307|Q5YLC1|Q96BP4	Missense_Mutation	SNP	ENST00000517970.1	hg19	CCDS6242.1	.	.	.	.	.	.	.	.	.	.	G	31	5.083754	0.94050	.	.	ENSG00000123124	ENST00000517970;ENST00000265428;ENST00000341922;ENST00000349423	D;D;D;D	0.99766	-6.69;-6.69;-6.69;-6.69	5.54	5.54	0.83059	WW/Rsp5/WWP (6);	0.000000	0.85682	D	0.000000	D	0.99898	0.9951	H	0.98951	4.38	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96263	0.9192	10	0.72032	D	0.01	.	19.4875	0.95035	0.0:0.0:1.0:0.0	.	169;387	Q9H0M0-6;Q9H0M0	.;WWP1_HUMAN	L	387;387;257;169	ENSP00000427793:W387L;ENSP00000265428:W387L;ENSP00000340564:W257L;ENSP00000342665:W169L	ENSP00000265428:W387L	W	+	2	0	WWP1	87508990	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.813000	0.99286	2.585000	0.87301	0.650000	0.86243	TGG	.	.		0.338	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374755.1	NM_007013		T	87439874	G	T	87439874	3	4	254	1	0	0	0	0	1	0	0	0	17430	1357	47	3	1194	3	WWP1	8	87439874	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	6497562	87439874	58924148	399	34691										
KIAA1429	25962	hgsc.bcm.edu	37	chr8	95531221	95531221	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtaggaaattaccccaaggcTtctttggaatagtactccat	8	9	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:95531221T>C	ENST00000297591.5	-	9	2580	c.2505A>G	c.(2503-2505)gaA>gaG	p.E835E	KIAA1429_ENST00000437199.1_Silent_p.E835E|KIAA1429_ENST00000421249.2_Silent_p.E835E	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	835					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			ACCCCAAGGCTTCTTTGGAAT	0.333																																					p.E835E		Atlas-SNP	.											.	KIAA1429	176	.	0			c.A2505G						.						50	56	54					8																	95531221		2191	4299	6490	SO:0001819	synonymous_variant	25962	exon9			CAAGGCTTCTTTG	AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 121"					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.2505A>G	chr8.hg19:g.95531221T>C		64.0	0.0		68.0	4.0	NM_015496	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Silent	SNP	ENST00000297591.5	hg19	CCDS34923.1																																																																																			.	.		0.333	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496		C	95531221	T	C	95531221	2	2	254	1	0	0	0	0	0	0	0	1	8240	1606	56	2		2	KIAA1429	8	95531221	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	8091347	95531221	50832801	400	34692										
MTDH	92140	hgsc.bcm.edu	37	chr8	98656988	98656988	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccgcaaaaagcggaggagccCgccccgcaagcgggaggagg	17	13	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:98656988C>T	ENST00000336273.3	+	1	582	c.254C>T	c.(253-255)cCg>cTg	p.P85L	MTDH_ENST00000519934.1_Missense_Mutation_p.P62L	NM_178812.3	NP_848927.2	Q86UE4	LYRIC_HUMAN	metadherin	85	Interaction with BCCIP.				lipopolysaccharide-mediated signaling pathway (GO:0031663)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of angiogenesis (GO:0045766)|positive regulation of autophagy (GO:0010508)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase B signaling (GO:0051897)|tight junction assembly (GO:0070830)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intercellular canaliculus (GO:0046581)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|tight junction (GO:0005923)	double-stranded RNA binding (GO:0003725)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(5)|liver(1)|lung(8)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	Breast(36;2.56e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.178)			CGGAGGAGCCCGCCCCGCAAG	0.711																																					p.P85L		Atlas-SNP	.											.	MTDH	54	.	0			c.C254T						.						5	7	6					8																	98656988		1866	3849	5715	SO:0001583	missense	92140	exon1			GGAGCCCGCCCCG	AF411226	CCDS6274.1	8q22.1	2014-07-14			ENSG00000147649	ENSG00000147649			29608	protein-coding gene	gene with protein product	"astrocyte elevated gene 1"	610323				15093543	Standard	NM_178812		Approved	LYRIC, 3D3, AEG-1	uc003yhz.3	Q86UE4	OTTHUMG00000164692	ENST00000336273.3:c.254C>T	chr8.hg19:g.98656988C>T	ENSP00000338235:p.Pro85Leu	28.0	0.0		32.0	4.0	NM_178812	Q05DH2|Q52QU9|Q6PK07|Q8TCX3	Missense_Mutation	SNP	ENST00000336273.3	hg19	CCDS6274.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.434272	0.83776	.	.	ENSG00000147649	ENST00000336273;ENST00000519934	T;T	0.09723	2.95;2.95	5.32	4.44	0.53790	.	0.263023	0.37715	N	0.001978	T	0.08935	0.0221	L	0.29908	0.895	0.50313	D	0.999863	B	0.15141	0.012	B	0.08055	0.003	T	0.11817	-1.0572	10	0.44086	T	0.13	-4.4925	11.3329	0.49487	0.0:0.9141:0.0:0.0859	.	85	Q86UE4	LYRIC_HUMAN	L	85;62	ENSP00000338235:P85L;ENSP00000428168:P62L	ENSP00000338235:P85L	P	+	2	0	MTDH	98726164	0.079000	0.21365	1.000000	0.80357	0.994000	0.84299	0.365000	0.20348	1.371000	0.46172	0.591000	0.81541	CCG	.	.		0.711	MTDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379772.2			T	98656988	C	T	98656988	3	4	254	1	0	0	0	0	1	0	0	0	9926	652	23	1	256	1	MTDH	8	98656988	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	3125767	98656988	47707034	401	34693										
FBXO43	286151	hgsc.bcm.edu	37	chr8	101153750	101153750	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gatatacattcaacttcaaaTaggctacaatcatctttgga	5	8	4	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:101153750T>A	ENST00000428847.2	-	2	1048	c.732A>T	c.(730-732)ctA>ctT	p.L244L		NM_001029860.3	NP_001025031.2	Q4G163	FBX43_HUMAN	F-box protein 43	244					meiotic nuclear division (GO:0007126)|negative regulation of meiosis (GO:0045835)|negative regulation of protein catabolic process (GO:0042177)|protein ubiquitination (GO:0016567)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(5)|lung(14)|prostate(1)|skin(5)|urinary_tract(1)	31	all_cancers(14;0.000139)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000274)|all_lung(17;0.000798)		Epithelial(11;1.17e-09)|all cancers(13;1.34e-07)|OV - Ovarian serous cystadenocarcinoma(57;3.82e-05)|STAD - Stomach adenocarcinoma(118;0.0957)			CAACTTCAAATAGGCTACAAT	0.323																																					p.L244L		Atlas-SNP	.											FBXO43_ENST00000428847,colon,carcinoma,0,3	FBXO43	155	.	0			c.A732T						.						37	38	38					8																	101153750		1808	3958	5766	SO:0001819	synonymous_variant	286151	exon2			TTCAAATAGGCTA	BC028709	CCDS47904.1	8q22.3	2004-08-24			ENSG00000156509	ENSG00000156509		"F-boxes /  "other""	28521	protein-coding gene	gene with protein product		609110					Standard	NR_036491		Approved	Fbx43	uc003yjd.3	Q4G163	OTTHUMG00000164803	ENST00000428847.2:c.732A>T	chr8.hg19:g.101153750T>A		50.0	1.0		50.0	2.0	NM_001029860		Silent	SNP	ENST00000428847.2	hg19	CCDS47904.1																																																																																			.	.		0.323	FBXO43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380380.1	XM_209918		A	101153750	T	A	101153750	2	1	254	1	0	0	0	0	0	0	0	1	5760	1393	49	4		4	FBXO43	8	101153750	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	2496762	101153750	45210272	402	34694										
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110457403	110457403	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctgtaaaagttcttattgaaGgagaaggtttggggactgtt	13	3	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:110457403G>T	ENST00000378402.5	+	38	5409	c.5305G>T	c.(5305-5307)Gga>Tga	p.G1769*		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	1769	IPT/TIG 10.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			TCTTATTGAAGGAGAAGGTTT	0.398										HNSCC(38;0.096)																											p.G1769X		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.G5305T						.						82	77	78					8																	110457403		1874	4111	5985	SO:0001587	stop_gained	93035	exon38			ATTGAAGGAGAAG	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.5305G>T	chr8.hg19:g.110457403G>T	ENSP00000367655:p.Gly1769*	62.0	0.0		59.0	4.0	NM_177531	Q567P2|Q9UF27	Nonsense_Mutation	SNP	ENST00000378402.5	hg19	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	G	46	12.168009	0.99643	.	.	ENSG00000205038	ENST00000378402	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	18.3732	0.90420	0.0:0.0:1.0:0.0	.	.	.	.	X	1769	.	ENSP00000367655:G1769X	G	+	1	0	PKHD1L1	110526579	1.000000	0.71417	1.000000	0.80357	0.760000	0.43138	7.545000	0.82128	2.941000	0.99782	0.655000	0.94253	GGA	.	.		0.398	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		T	110457403	G	T	110457403	4	4	254	1	0	0	0	0	0	1	0	0	11981	1001	35	3	5455	3	PKHD1L1	8	110457403	Nonsense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	9303653	110457403	35906619	403	34695										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113650925	113650925	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tttgttttttattttctcacCagagaatgttatgttaaatc	5	5	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:113650925C>T	ENST00000297405.5	-	21	3770	c.3526G>A	c.(3526-3528)Gaa>Aaa	p.E1176K	CSMD3_ENST00000455883.2_Splice_Site_p.E1072K|CSMD3_ENST00000343508.3_Splice_Site_p.E1136K|CSMD3_ENST00000352409.3_Splice_Site_p.E1176K	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1176	CUB 6. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						ATTTTCTCACCAGAGAATGTT	0.308										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.E1176K		Atlas-SNP	.											CSMD3_ENST00000343508,left_upper_lobe,carcinoma,0,2	CSMD3	2325	.	0			c.G3526A						.						33	36	35					8																	113650925		2201	4300	6501	SO:0001630	splice_region_variant	114788	exon21			TCTCACCAGAGAA	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.3526+1G>A	chr8.hg19:g.113650925C>T		26.0	0.0		25.0	2.0	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.960401	0.92791	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.28895	1.59;1.59;1.59;1.59;1.59	4.91	4.91	0.64330	CUB (3);	0.000000	0.64402	D	0.000001	T	0.58466	0.2124	M	0.79258	2.445	0.49213	D	0.999763	D;D;D	0.76494	0.999;0.998;0.997	D;D;D	0.85130	0.997;0.993;0.977	T	0.60875	-0.7176	9	.	.	.	.	18.4581	0.90728	0.0:1.0:0.0:0.0	.	1072;1176;1136	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	K	1136;1176;516;1072;1176	ENSP00000345799:E1136K;ENSP00000297405:E1176K;ENSP00000341558:E516K;ENSP00000412263:E1072K;ENSP00000343124:E1176K	.	E	-	1	0	CSMD3	113720101	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.750000	0.85110	2.448000	0.82819	0.491000	0.48974	GAA	.	.		0.308	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	Missense_Mutation	T	113650925	C	T	113650925	5	4	254	1	0	0	0	0	0	0	1	0	3948	608	21	3	7801	3	CSMD3	8	113650925	Splice_Site	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	3193522	113650925	32713097	404	34696										
KIAA0196	9897	hgsc.bcm.edu	37	chr8	126093910	126093910	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agcccaggaatacctgtatcGgtagtaagaaaccagcatcc	9	11	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:126093910G>T	ENST00000318410.7	-	5	860	c.511C>A	c.(511-513)Cga>Aga	p.R171R	KIAA0196_ENST00000521109.1_5'Flank|KIAA0196_ENST00000517845.1_Silent_p.R23R	NM_014846.3	NP_055661.3	Q12768	STRUM_HUMAN	KIAA0196	171					cell death (GO:0008219)|endosomal transport (GO:0016197)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|WASH complex (GO:0071203)				NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	42	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)			TACCTGTATCGGTAGTAAGAA	0.428																																					p.R171R		Atlas-SNP	.											.	KIAA0196	90	.	0			c.C511A						.						207	164	179					8																	126093910		2203	4300	6503	SO:0001819	synonymous_variant	9897	exon5			TGTATCGGTAGTA		CCDS6355.1	8q24.13	2014-05-09			ENSG00000164961	ENSG00000164961			28984	protein-coding gene	gene with protein product	"strumpellin"	610657	"spastic paraplegia 8 (autosomal dominant)"	SPG8		9973294, 17160902, 23085491	Standard	NM_014846		Approved		uc003yrt.3	Q12768	OTTHUMG00000164991	ENST00000318410.7:c.511C>A	chr8.hg19:g.126093910G>T		114.0	0.0		121.0	5.0	NM_014846	A8K4R7|Q3KQX5|Q8TBQ2	Silent	SNP	ENST00000318410.7	hg19	CCDS6355.1																																																																																			.	.		0.428	KIAA0196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381369.1	NM_014846		T	126093910	G	T	126093910	2	4	254	1	0	0	0	0	0	0	0	1	8170	1124	39	1		1	KIAA0196	8	126093910	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	12442985	126093910	20270112	405	34697										
ADCY8	114	hgsc.bcm.edu	37	chr8	131833641	131833641	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	catggccatcagtagcagtgAtacctccttggtccccagga	10	13	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:131833641A>G	ENST00000286355.5	-	13	4793	c.2701T>C	c.(2701-2703)Tca>Cca	p.S901P	ADCY8_ENST00000377928.3_Missense_Mutation_p.S770P	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	901					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			AGTAGCAGTGATACCTCCTTG	0.463										HNSCC(32;0.087)																											p.S901P		Atlas-SNP	.											.	ADCY8	291	.	0			c.T2701C						.						100	78	86					8																	131833641		2203	4300	6503	SO:0001583	missense	114	exon13			GCAGTGATACCTC	Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"Adenylate cyclases"	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.2701T>C	chr8.hg19:g.131833641A>G	ENSP00000286355:p.Ser901Pro	88.0	0.0		97.0	4.0	NM_001115		Missense_Mutation	SNP	ENST00000286355.5	hg19	CCDS6363.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.367570	0.82463	.	.	ENSG00000155897	ENST00000286355;ENST00000377928	T;T	0.79653	-1.29;-1.28	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	D	0.84615	0.5511	L	0.50333	1.59	0.42160	D	0.991596	P;D	0.69078	0.937;0.997	P;P	0.59221	0.671;0.854	D	0.83803	0.0237	10	0.35671	T	0.21	.	15.5593	0.76229	1.0:0.0:0.0:0.0	.	770;901	E7EVL1;P40145	.;ADCY8_HUMAN	P	901;770	ENSP00000286355:S901P;ENSP00000367161:S770P	ENSP00000286355:S901P	S	-	1	0	ADCY8	131902823	1.000000	0.71417	0.111000	0.21465	0.636000	0.38137	8.811000	0.91954	2.277000	0.76020	0.528000	0.53228	TCA	.	.		0.463	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			G	131833641	A	G	131833641	3	3	254	1	0	0	0	0	1	0	0	0	300	333	12	2	1078	2	ADCY8	8	131833641	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	5739731	131833641	14530381	406	34698										
KCNQ3	3786	hgsc.bcm.edu	37	chr8	133153569	133153569	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cgaacccgatccaagagaccCagcttttggctacaaaataa	7	12	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:133153569C>T	ENST00000388996.4	-	10	1692	c.1272G>A	c.(1270-1272)ctG>ctA	p.L424L	KCNQ3_ENST00000519445.1_Silent_p.L424L|KCNQ3_ENST00000521134.1_Silent_p.L304L	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	424					axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	70	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	CCAAGAGACCCAGCTTTTGGC	0.423																																					p.L424L		Atlas-SNP	.											.	KCNQ3	164	.	0			c.G1272A						.						66	69	68					8																	133153569		2203	4300	6503	SO:0001819	synonymous_variant	3786	exon10			GAGACCCAGCTTT	AB208890	CCDS34943.1, CCDS56554.1	8q24	2012-07-05			ENSG00000184156	ENSG00000184156		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6297	protein-coding gene	gene with protein product		602232		EBN2		9425900, 16382104	Standard	NM_004519		Approved	Kv7.3	uc003ytj.3	O43525	OTTHUMG00000137472	ENST00000388996.4:c.1272G>A	chr8.hg19:g.133153569C>T		85.0	0.0		105.0	50.0	NM_004519	A2VCT8|B4DJY4|E7EQ89	Silent	SNP	ENST00000388996.4	hg19	CCDS34943.1																																																																																			.	.		0.423	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519		T	133153569	C	T	133153569	2	4	254	1	0	0	0	0	0	0	0	1	8093	581	21	3		3	KCNQ3	8	133153569	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1319928	133153569	13210453	407	34699										
PTK2	5747	hgsc.bcm.edu	37	chr8	141753415	141753415	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttgaggacaccagaacattcCgagcagcaatgtccctgata	9	11	0	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:141753415C>A	ENST00000522684.1	-	20	1878	c.1649G>T	c.(1648-1650)cGg>cTg	p.R550L	PTK2_ENST00000340930.3_Missense_Mutation_p.R550L|PTK2_ENST00000517887.1_Missense_Mutation_p.R594L|PTK2_ENST00000521059.1_Missense_Mutation_p.R550L|PTK2_ENST00000519465.1_Missense_Mutation_p.R178L|PTK2_ENST00000519419.1_Missense_Mutation_p.R594L|PTK2_ENST00000538769.1_Missense_Mutation_p.R218L|PTK2_ENST00000520151.1_3'UTR|PTK2_ENST00000535192.1_Missense_Mutation_p.R550L|PTK2_ENST00000395218.2_Missense_Mutation_p.R550L	NM_153831.3	NP_722560.1	Q05397	FAK1_HUMAN	protein tyrosine kinase 2	550	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell motility (GO:0048870)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|central nervous system neuron axonogenesis (GO:0021955)|embryo development (GO:0009790)|endothelial cell migration (GO:0043542)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|establishment of nucleus localization (GO:0040023)|extracellular matrix organization (GO:0030198)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|growth hormone receptor signaling pathway (GO:0060396)|heart morphogenesis (GO:0003007)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of organ growth (GO:0046621)|negative regulation of synapse assembly (GO:0051964)|netrin-activated signaling pathway (GO:0038007)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|placenta development (GO:0001890)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|regulation of endothelial cell migration (GO:0010594)|regulation of focal adhesion assembly (GO:0051893)|regulation of osteoblast differentiation (GO:0045667)|regulation of Rho GTPase activity (GO:0032319)|signal complex assembly (GO:0007172)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)	apical plasma membrane (GO:0016324)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|stress fiber (GO:0001725)	actin binding (GO:0003779)|ATP binding (GO:0005524)|JUN kinase binding (GO:0008432)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(6)|lung(23)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	48	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)			CAGAACATTCCGAGCAGCAAT	0.338																																					p.R572L		Atlas-SNP	.											.	PTK2	311	.	0			c.G1715T						.						105	102	103					8																	141753415		2203	4300	6503	SO:0001583	missense	5747	exon20			ACATTCCGAGCAG	L13616	CCDS6381.1, CCDS56557.1	8q24.3	2013-02-18	2013-02-18		ENSG00000169398	ENSG00000169398	2.7.10.1	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9611	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 71"	600758	"PTK2 protein tyrosine kinase 2"			8422239	Standard	NM_153831		Approved	FAK, FADK, FAK1, PPP1R71	uc003yvt.3	Q05397	OTTHUMG00000067438	ENST00000522684.1:c.1649G>T	chr8.hg19:g.141753415C>A	ENSP00000429911:p.Arg550Leu	76.0	0.0		91.0	4.0	NM_005607	B4E2N6|F5H4S4|Q14291|Q9UD85	Missense_Mutation	SNP	ENST00000522684.1	hg19	CCDS6381.1	.	.	.	.	.	.	.	.	.	.	C	34	5.346651	0.95807	.	.	ENSG00000169398	ENST00000522684;ENST00000535192;ENST00000519465;ENST00000517887;ENST00000521059;ENST00000395214;ENST00000395218;ENST00000354438;ENST00000395221;ENST00000523539;ENST00000340930;ENST00000538769;ENST00000519419;ENST00000521986;ENST00000342207	D;D;D;D;D;D;D;D;D;D;D	0.87729	-2.29;-2.29;-2.29;-2.29;-2.29;-2.29;-2.29;-2.29;-2.29;-2.29;-2.29	5.2	5.2	0.72013	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.94499	0.8229	M	0.86864	2.845	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;1.0;0.999;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D	0.97110	0.999;0.997;0.999;0.996;1.0;0.996;0.996;0.999;0.999;0.996	D	0.95265	0.8372	10	0.87932	D	0	.	18.7608	0.91849	0.0:1.0:0.0:0.0	.	550;245;470;550;572;550;502;398;218;178	B4E2N6;B4DH13;Q59GN8;Q05397;Q658W2;Q8IYN9;Q59GM6;Q05397-2;Q8N9D7;E9PEI4	.;.;.;FAK1_HUMAN;.;.;.;.;.;.	L	550;550;178;594;550;502;550;471;245;222;550;218;594;248;396	ENSP00000429911:R550L;ENSP00000438009:R550L;ENSP00000429170:R178L;ENSP00000429082:R594L;ENSP00000429474:R550L;ENSP00000378644:R550L;ENSP00000428492:R222L;ENSP00000341189:R550L;ENSP00000445742:R218L;ENSP00000429129:R594L;ENSP00000430603:R248L	ENSP00000341189:R550L	R	-	2	0	PTK2	141822597	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.642000	0.83385	2.442000	0.82660	0.591000	0.81541	CGG	.	.		0.338	PTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378054.5	NM_005607		A	141753415	C	A	141753415	3	1	254	1	0	0	0	0	1	0	0	0	12775	652	23	1	1561	1	PTK2	8	141753415	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	8599846	141753415	4610607	408	34700										
GPR20	2843	hgsc.bcm.edu	37	chr8	142366956	142366956	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agccctgctgactaagcctcGggcccattagccagggcctg	12	15	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:142366956G>T	ENST00000377741.3	-	2	1158	c.1068C>A	c.(1066-1068)ccC>ccA	p.P356P	CTD-3064M3.3_ENST00000562459.1_RNA	NM_005293.2	NP_005284.2	Q99678	GPR20_HUMAN	G protein-coupled receptor 20	356					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(3)|lung(4)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	15	all_cancers(97;4.32e-16)|all_epithelial(106;6.61e-14)|Lung NSC(106;9.4e-06)|all_lung(105;1.35e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0415)			ACTAAGCCTCGGGCCCATTAG	0.652																																					p.P356P		Atlas-SNP	.											.	GPR20	43	.	0			c.C1068A						.						25	25	25					8																	142366956		2203	4299	6502	SO:0001819	synonymous_variant	2843	exon2			AGCCTCGGGCCCA	U66579	CCDS34949.1	8q24.3	2012-08-21				ENSG00000204882		"GPCR / Class A : Orphans"	4475	protein-coding gene	gene with protein product		601908				18347022	Standard	NM_005293		Approved		uc003ywf.3	Q99678		ENST00000377741.3:c.1068C>A	chr8.hg19:g.142366956G>T		57.0	0.0		73.0	5.0	NM_005293	Q17R96	Silent	SNP	ENST00000377741.3	hg19	CCDS34949.1																																																																																			.	.		0.652	GPR20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378968.1	NM_005293		T	142366956	G	T	142366956	2	4	254	1	0	0	0	0	0	0	0	1	6688	1103	39	1		1	GPR20	8	142366956	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	613541	142366956	3997066	409	34701										
TSNARE1	203062	hgsc.bcm.edu	37	chr8	143436037	143436037	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tctcgaaggtcccccgaaagGgccacggctccccaggccac	11	18	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:143436037G>A	ENST00000307180.3	-	2	166	c.49C>T	c.(49-51)Cct>Tct	p.P17S	TSNARE1_ENST00000524325.1_Missense_Mutation_p.P17S|TSNARE1_ENST00000519651.1_Missense_Mutation_p.P17S|TSNARE1_ENST00000520166.1_Missense_Mutation_p.P17S	NM_145003.3	NP_659440.2	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1	17					intracellular protein transport (GO:0006886)|synaptic vesicle exocytosis (GO:0016079)	integral component of membrane (GO:0016021)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)			breast(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(6)|ovary(2)|stomach(2)|urinary_tract(1)	20	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					CCCCCGAAAGGGCCACGGCTC	0.607																																					p.P17S		Atlas-SNP	.											.	TSNARE1	59	.	0			c.C49T						.						51	46	47					8																	143436037		2203	4300	6503	SO:0001583	missense	203062	exon2			CGAAAGGGCCACG			8q24.3	2005-08-18							26437	protein-coding gene	gene with protein product						14702039	Standard	XM_005250828		Approved	FLJ31164	uc003ywk.3	Q96NA8		ENST00000307180.3:c.49C>T	chr8.hg19:g.143436037G>A	ENSP00000303437:p.Pro17Ser	58.0	0.0		64.0	5.0	NM_145003	B7ZLB0|Q14D03	Missense_Mutation	SNP	ENST00000307180.3	hg19	CCDS6384.1	.	.	.	.	.	.	.	.	.	.	G	10.59	1.392290	0.25118	.	.	ENSG00000171045	ENST00000524325;ENST00000307180;ENST00000520166;ENST00000519651;ENST00000520462;ENST00000518720	T;T;T;T;T;T	0.28666	2.21;2.19;2.21;1.6;1.88;1.85	3.47	2.57	0.30868	.	0.000000	0.32970	U	0.005437	T	0.20251	0.0487	L	0.32530	0.975	0.09310	N	1	B;B;B;B	0.29862	0.141;0.259;0.141;0.141	B;B;B;B	0.26614	0.043;0.071;0.043;0.043	T	0.17961	-1.0352	10	0.87932	D	0	-3.3269	7.0289	0.24956	0.1369:0.0:0.8631:0.0	.	17;17;17;17	B7ZLB0;E5RHT3;Q96NA8;A0AVG3	.;.;TSNA1_HUMAN;.	S	17;17;17;17;17;33	ENSP00000428763:P17S;ENSP00000303437:P17S;ENSP00000427770:P17S;ENSP00000429679:P17S;ENSP00000429626:P17S;ENSP00000430789:P33S	ENSP00000303437:P17S	P	-	1	0	TSNARE1	143433944	0.145000	0.22656	0.002000	0.10522	0.641000	0.38312	0.823000	0.27366	0.728000	0.32382	0.563000	0.77884	CCT	.	.		0.607	TSNARE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_145003		A	143436037	G	A	143436037	3	1	254	1	0	0	0	0	1	0	0	0	16645	1232	43	3	1540	3	TSNARE1	8	143436037	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1069081	143436037	2927985	410	34702										
BAI1	575	hgsc.bcm.edu	37	chr8	143603470	143603470	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcaagcgcttcctctgcctgGgctggggtgagccgcggcct	16	14	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:143603470G>A	ENST00000517894.1	+	21	4063	c.3169G>A	c.(3169-3171)Ggc>Agc	p.G1057S	BAI1_ENST00000323289.5_Missense_Mutation_p.G1057S			O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1	1057					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)|signal transduction (GO:0007165)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(28)|ovary(4)|pancreas(1)|prostate(7)	57	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					CCTCTGCCTGGGCTGGGGTGA	0.672																																					p.G1057S		Atlas-SNP	.											.	BAI1	146	.	0			c.G3169A						.						32	40	38					8																	143603470		2196	4296	6492	SO:0001583	missense	575	exon20			TGCCTGGGCTGGG	AB005297	CCDS64985.1	8q24.3	2014-08-08			ENSG00000181790	ENSG00000181790		"-", "GPCR / Class B : Orphans"	943	protein-coding gene	gene with protein product		602682				9533023	Standard	NM_001702		Approved		uc003ywm.3	O14514	OTTHUMG00000164732	ENST00000517894.1:c.3169G>A	chr8.hg19:g.143603470G>A	ENSP00000430945:p.Gly1057Ser	64.0	0.0		57.0	4.0	NM_001702		Missense_Mutation	SNP	ENST00000517894.1	hg19		.	.	.	.	.	.	.	.	.	.	G	16.06	3.016528	0.54468	.	.	ENSG00000181790	ENST00000517894;ENST00000323289	D;D	0.84516	-1.86;-1.86	3.78	3.78	0.43462	.	0.151741	0.43260	U	0.000583	D	0.86969	0.6061	M	0.84219	2.685	0.58432	D	0.999999	B	0.24533	0.105	B	0.30401	0.115	D	0.87356	0.2341	10	0.72032	D	0.01	.	14.6053	0.68475	0.0:0.0:1.0:0.0	.	1057	E9PBK0	.	S	1057	ENSP00000430945:G1057S;ENSP00000313046:G1057S	ENSP00000313046:G1057S	G	+	1	0	BAI1	143600472	1.000000	0.71417	1.000000	0.80357	0.388000	0.30384	9.490000	0.97952	1.641000	0.50575	0.305000	0.20034	GGC	.	.		0.672	BAI1-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379963.3	NM_001702		A	143603470	G	A	143603470	3	1	254	1	0	0	0	0	1	0	0	0	1298	1232	43	3	3247	3	BAI1	8	143603470	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	167433	143603470	2760552	411	34703										
LYNX1	66004	hgsc.bcm.edu	37	chr8	143846491	143846491	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cagtgggtggagtccctcagGcatctggatccatgggagca	15	10	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:143846491G>A	ENST00000335822.5	-	4	849	c.222C>T	c.(220-222)tgC>tgT	p.C74C	RP11-706C16.7_ENST00000523657.1_RNA|LYNX1_ENST00000523332.1_Missense_Mutation_p.A82V|LYNX1_ENST00000317543.7_Silent_p.C40C	NM_023946.2	NP_076435.1	Q9BZG9	LYNX1_HUMAN	Ly6/neurotoxin 1	74	UPAR/Ly6.					anchored component of membrane (GO:0031225)|cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)		p.C74W(1)|p.C40W(1)		endometrium(1)|lung(2)|skin(1)	4	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					AGTCCCTCAGGCATCTGGATC	0.617																																					p.C74C		Atlas-SNP	.											LYNX1_ENST00000317543,NS,carcinoma,0,2	LYNX1	40	.	2	Substitution - Missense(2)	lung(2)	c.C222T						.						76	56	63					8																	143846491		2203	4300	6503	SO:0001819	synonymous_variant	66004	exon4			CCTCAGGCATCTG	AF321824	CCDS6389.1, CCDS34951.1, CCDS34952.1	8q24.3	2008-03-12			ENSG00000180155	ENSG00000180155			29604	protein-coding gene	gene with protein product		606110				12573258, 10402197	Standard	NM_023946		Approved	SLURP2	uc003yxd.1	Q9BZG9	OTTHUMG00000164694	ENST00000335822.5:c.222C>T	chr8.hg19:g.143846491G>A		71.0	0.0		39.0	3.0	NM_023946	D3DWI7|G3XAC2|Q86SR0	Silent	SNP	ENST00000335822.5	hg19	CCDS34951.1	.	.	.	.	.	.	.	.	.	.	G	7.555	0.663421	0.14710	.	.	ENSG00000180155	ENST00000523332	T	0.52754	0.65	3.73	0.841	0.18918	.	.	.	.	.	T	0.45558	0.1348	.	.	.	0.20489	N	0.999892	.	.	.	.	.	.	T	0.42865	-0.9426	6	0.87932	D	0	.	6.5234	0.22287	0.3369:0.0:0.6631:0.0	.	.	.	.	V	82	ENSP00000428713:A82V	ENSP00000428713:A82V	A	-	2	0	LYNX1	143843493	0.881000	0.30235	0.017000	0.16124	0.007000	0.05969	1.215000	0.32431	0.025000	0.15241	-0.492000	0.04666	GCC	.	.		0.617	LYNX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000379786.3	NM_177476		A	143846491	G	A	143846491	2	1	254	1	0	0	0	0	0	0	0	1	9117	1195	42	3		3	LYNX1	8	143846491	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	243021	143846491	2517531	412	34704										
PUF60	22827	hgsc.bcm.edu	37	chr8	144904074	144904074	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cccgttctccatcttgatggAgtctgtgccctggtaaggga	12	11	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:144904074A>G	ENST00000526683.1	-	3	676	c.121T>C	c.(121-123)Tcc>Ccc	p.S41P	PUF60_ENST00000313352.7_5'UTR|PUF60_ENST00000349157.6_Missense_Mutation_p.S41P|PUF60_ENST00000524570.1_5'UTR|PUF60_ENST00000456095.2_Missense_Mutation_p.S12P|PUF60_ENST00000527197.1_Missense_Mutation_p.S12P|PUF60_ENST00000453551.2_5'UTR	NM_001271098.1|NM_078480.2	NP_001258027.1|NP_510965.1	Q9UHX1	PUF60_HUMAN	poly-U binding splicing factor 60KDa	41	Inhibits homodimerization.				apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(1)|kidney(3)|lung(7)|prostate(2)	14	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;6.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			ATCTTGATGGAGTCTGTGCCC	0.632																																					p.S41P		Atlas-SNP	.											.	PUF60	26	.	0			c.T121C						.						30	35	33					8																	144904074		2050	4183	6233	SO:0001583	missense	22827	exon3			TGATGGAGTCTGT	AF114818	CCDS47933.1, CCDS47934.1, CCDS47935.1, CCDS59514.1, CCDS59515.1, CCDS59516.1	8q24.3	2013-02-12	2007-07-27		ENSG00000179950	ENSG00000179950		"RNA binding motif (RRM) containing"	17042	protein-coding gene	gene with protein product	"siah binding protein 1", "FBP interacting repressor", "pyrimidine tract binding splicing factor", "Ro ribonucleoprotein binding protein 1"	604819				10668799, 10882074, 17579712	Standard	NM_078480		Approved	FIR, SIAHBP1, RoBPI	uc003yzs.4	Q9UHX1	OTTHUMG00000165155	ENST00000526683.1:c.121T>C	chr8.hg19:g.144904074A>G	ENSP00000434359:p.Ser41Pro	61.0	0.0		61.0	4.0	NM_078480	A8K8K8|Q969E7|Q96D94|Q96H63|Q99628|Q9NZA0|Q9UJY7	Missense_Mutation	SNP	ENST00000526683.1	hg19	CCDS47934.1	.	.	.	.	.	.	.	.	.	.	A	15.62	2.888214	0.52014	.	.	ENSG00000179950	ENST00000526683;ENST00000456095;ENST00000349157;ENST00000527197;ENST00000526459;ENST00000529999;ENST00000531897;ENST00000533162	T;T;T;T;T;T;T;T	0.21543	2.53;2.59;2.42;2.51;2.59;3.43;3.35;2.0	5.13	-2.14	0.07123	.	.	.	.	.	T	0.08492	0.0211	N	0.08118	0	0.35256	D	0.779152	P;B;P	0.52316	0.952;0.0;0.92	B;B;B	0.44315	0.446;0.0;0.178	T	0.42292	-0.9460	9	0.39692	T	0.17	.	0.7891	0.01054	0.4676:0.1478:0.1474:0.2372	.	12;41;41	Q9UHX1-5;Q9UHX1-2;Q9UHX1	.;.;PUF60_HUMAN	P	41;12;41;12;40;78;78;78	ENSP00000434359:S41P;ENSP00000395417:S12P;ENSP00000322036:S41P;ENSP00000431960:S12P;ENSP00000432610:S40P;ENSP00000434863:S78P;ENSP00000437309:S78P;ENSP00000433403:S78P	ENSP00000322036:S41P	S	-	1	0	PUF60	144976062	0.849000	0.29639	0.513000	0.27749	0.942000	0.58702	0.603000	0.24149	-0.654000	0.05394	0.460000	0.39030	TCC	.	.		0.632	PUF60-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382222.1	NM_014281		G	144904074	A	G	144904074	3	3	254	1	0	0	0	0	1	0	0	0	12839	304	11	2	1598	2	PUF60	8	144904074	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	1057583	144904074	1459948	413	34705										
EPPK1	83481	hgsc.bcm.edu	37	chr8	144942463	144942463	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgctgcccggtataggggtcGgtgtagccggtgacggcgcg	19	10	0	1	rs377506188		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:144942463G>T	ENST00000525985.1	-	2	5030	c.4959C>A	c.(4957-4959)acC>acA	p.T1653T				P58107	EPIPL_HUMAN	epiplakin 1	1653						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TATAGGGGTCGGTGTAGCCGG	0.632																																					p.T1653T		Atlas-SNP	.											.	EPPK1	199	.	0			c.C4959A						.						64	75	71					8																	144942463		1996	4154	6150	SO:0001819	synonymous_variant	83481	exon1			GGGGTCGGTGTAG	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"epidermal autoantigen 450K"	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.4959C>A	chr8.hg19:g.144942463G>T		146.0	0.0		152.0	7.0	NM_031308	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	hg19																																																																																				.	.		0.632	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		T	144942463	G	T	144942463	2	4	254	1	0	0	0	0	0	0	0	1	5192	1103	39	1		1	EPPK1	8	144942463	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	38389	144942463	1421559	414	34706										
PLEC	5339	hgsc.bcm.edu	37	chr8	144996328	144996328	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	catgctgccgccgccgcgccTcctccatgctggccaccagc	10	21	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:144996328T>C	ENST00000322810.4	-	32	8241	c.8072A>G	c.(8071-8073)gAg>gGg	p.E2691G	PLEC_ENST00000357649.2_Missense_Mutation_p.E2558G|PLEC_ENST00000398774.2_Missense_Mutation_p.E2522G|PLEC_ENST00000436759.2_Missense_Mutation_p.E2581G|PLEC_ENST00000356346.3_Missense_Mutation_p.E2540G|PLEC_ENST00000345136.3_Missense_Mutation_p.E2554G|PLEC_ENST00000354589.3_Missense_Mutation_p.E2554G|PLEC_ENST00000527096.1_Missense_Mutation_p.E2577G|PLEC_ENST00000354958.2_Missense_Mutation_p.E2532G	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	2691	Central fibrous rod domain.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						CCGCCGCGCCTCCTCCATGCT	0.711																																					p.E2691G		Atlas-SNP	.											.	PLEC	1144	.	0			c.A8072G						.						8	8	8					8																	144996328		2098	4151	6249	SO:0001583	missense	5339	exon32			CGCGCCTCCTCCA	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"plectin 1, intermediate filament binding protein, 500kD", "epidermolysis bullosa simplex 1 (Ogna)", "plectin 1, intermediate filament binding protein 500kDa"	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.8072A>G	chr8.hg19:g.144996328T>C	ENSP00000323856:p.Glu2691Gly	50.0	0.0		48.0	4.0	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	hg19	CCDS43772.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	7.992|7.992	0.753435|0.753435	0.15778|0.15778	.|.	.|.	ENSG00000178209|ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096|ENST00000527303	T;T;T;T;T;T;T;T;T|.	0.77229|.	-1.04;-1.04;-1.08;-1.08;-1.06;-1.04;-1.04;-1.04;-1.04|.	4.19|4.19	4.19|4.19	0.49359|0.49359	.|.	0.367509|.	0.19788|.	U|.	0.106041|.	T|T	0.58424|0.58424	0.2121|0.2121	L|L	0.43152|0.43152	1.355|1.355	0.36059|0.36059	D|D	0.841329|0.841329	P;P;P;P;P;P;P;P|.	0.42296|.	0.775;0.775;0.775;0.666;0.775;0.775;0.775;0.775|.	B;B;B;B;B;B;B;B|.	0.41412|.	0.356;0.356;0.356;0.194;0.356;0.356;0.356;0.356|.	T|T	0.64601|0.64601	-0.6369|-0.6369	10|5	0.72032|.	D|.	0.01|.	.|.	13.0896|13.0896	0.59160|0.59160	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	2581;2540;2532;2691;2522;2554;2558;2554|.	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4|.	.;.;.;PLEC_HUMAN;.;.;.;.|.	G|G	2554;2558;2554;2522;2691;2532;2540;2581;2577|124	ENSP00000344848:E2554G;ENSP00000350277:E2558G;ENSP00000346602:E2554G;ENSP00000381756:E2522G;ENSP00000323856:E2691G;ENSP00000347044:E2532G;ENSP00000348702:E2540G;ENSP00000388180:E2581G;ENSP00000434583:E2577G|.	ENSP00000323856:E2691G|.	E|R	-|-	2|1	0|2	PLEC|PLEC	145068316|145068316	0.954000|0.954000	0.32549|0.32549	1.000000|1.000000	0.80357|0.80357	0.415000|0.415000	0.31203|0.31203	2.021000|2.021000	0.41020|0.41020	1.773000|1.773000	0.52216|0.52216	0.364000|0.364000	0.22116|0.22116	GAG|AGG	.	.		0.711	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		C	144996328	T	C	144996328	3	2	254	1	0	0	0	0	1	0	0	0	12061	1551	54	2	5986	2	PLEC	8	144996328	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	53865	144996328	1367694	415	34707										
EXOSC4	54512	hgsc.bcm.edu	37	chr8	145135446	145135446	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgcccgagatgtgcacacccTcttagatcgagtggtccggc	12	13	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:145135446T>C	ENST00000316052.5	+	3	783	c.680T>C	c.(679-681)cTc>cCc	p.L227P	GPAA1_ENST00000361036.6_5'Flank|GPAA1_ENST00000355091.4_5'Flank|CTD-3065J16.9_ENST00000524499.1_RNA	NM_019037.2	NP_061910.1	Q9NPD3	EXOS4_HUMAN	exosome component 4	227					defense response to virus (GO:0051607)|DNA deamination (GO:0045006)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|maturation of 5.8S rRNA (GO:0000460)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of cell growth (GO:0030307)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	3'-5'-exoribonuclease activity (GO:0000175)|AU-rich element binding (GO:0017091)			lung(4)|prostate(1)|upper_aerodigestive_tract(2)	7	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;3.48e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GTGCACACCCTCTTAGATCGA	0.622																																					p.L227P		Atlas-SNP	.											.	EXOSC4	19	.	0			c.T680C						.						56	64	62					8																	145135446		2203	4300	6503	SO:0001583	missense	54512	exon3			ACACCCTCTTAGA	AF281133	CCDS6414.1	8q24.3	2004-03-26			ENSG00000178896	ENSG00000178896			18189	protein-coding gene	gene with protein product	"exosome component Rrp41"	606491				11110791	Standard	NM_019037		Approved	hRrp41p, FLJ20591, Rrp41p, RRP41, RRP41A, Ski6p, SKI6, p12A	uc003zau.3	Q9NPD3	OTTHUMG00000165437	ENST00000316052.5:c.680T>C	chr8.hg19:g.145135446T>C	ENSP00000315476:p.Leu227Pro	71.0	0.0		54.0	6.0	NM_019037		Missense_Mutation	SNP	ENST00000316052.5	hg19	CCDS6414.1	.	.	.	.	.	.	.	.	.	.	T	16.90	3.249010	0.59103	.	.	ENSG00000178896	ENST00000316052;ENST00000527954	T	0.74421	-0.84	5.38	5.38	0.77491	Exoribonuclease, phosphorolytic domain 2 (1);	0.384150	0.21994	N	0.066109	T	0.78780	0.4337	L	0.39898	1.24	0.80722	D	1	P	0.36944	0.574	P	0.54026	0.74	T	0.78229	-0.2285	10	0.46703	T	0.11	-32.6333	13.3251	0.60454	0.0:0.0:0.0:1.0	.	227	Q9NPD3	EXOS4_HUMAN	P	227;250	ENSP00000315476:L227P	ENSP00000315476:L227P	L	+	2	0	EXOSC4	145207434	1.000000	0.71417	0.299000	0.25016	0.529000	0.34654	5.537000	0.67186	2.046000	0.60703	0.459000	0.35465	CTC	.	.		0.622	EXOSC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384065.1	NM_019037		C	145135446	T	C	145135446	3	2	254	1	0	0	0	0	1	0	0	0	5319	1551	54	2	690	2	EXOSC4	8	145135446	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	139118	145135446	1228576	416	34708										
CPSF1	29894	hgsc.bcm.edu	37	chr8	145622853	145622853	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccgaatccccatacagcatcTcctcctcgtcatccactgtg	5	18	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:145622853T>C	ENST00000349769.3	-	22	2328	c.2234A>G	c.(2233-2235)gAg>gGg	p.E745G	MIR1234_ENST00000408875.1_RNA	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1, 160kDa	745					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	mRNA 3'-UTR binding (GO:0003730)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			ATACAGCATCTCCTCCTCGTC	0.692																																					p.E745G	NSCLC(133;1088 1848 27708 34777 35269)	Atlas-SNP	.											.	CPSF1	92	.	0			c.A2234G						.						50	58	55					8																	145622853		2201	4296	6497	SO:0001583	missense	29894	exon22			AGCATCTCCTCCT	U37012	CCDS34966.1	8q24	2014-05-06	2002-08-29		ENSG00000071894	ENSG00000071894			2324	protein-coding gene	gene with protein product		606027	"cleavage and polyadenylation specific factor 1, 160kD subunit"			7651824, 7590244	Standard	NM_013291		Approved		uc003zcj.3	Q10570	OTTHUMG00000174612	ENST00000349769.3:c.2234A>G	chr8.hg19:g.145622853T>C	ENSP00000339353:p.Glu745Gly	70.0	0.0		78.0	4.0	NM_013291	Q96AF0	Missense_Mutation	SNP	ENST00000349769.3	hg19	CCDS34966.1	.	.	.	.	.	.	.	.	.	.	T	29.6	5.021539	0.93462	.	.	ENSG00000071894	ENST00000349769	T	0.32515	1.45	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.40067	0.1102	L	0.58101	1.795	0.80722	D	1	P	0.51933	0.949	P	0.52343	0.696	T	0.14117	-1.0484	10	0.18276	T	0.48	-6.8196	13.3392	0.60535	0.0:0.0:0.0:1.0	.	745	Q10570	CPSF1_HUMAN	G	745	ENSP00000339353:E745G	ENSP00000339353:E745G	E	-	2	0	CPSF1	145593661	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	7.114000	0.77103	2.051000	0.60960	0.402000	0.26972	GAG	.	.		0.692	CPSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382422.2	NM_013291		C	145622853	T	C	145622853	3	2	254	1	0	0	0	0	1	0	0	0	3826	1551	54	2	2165	2	CPSF1	8	145622853	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	487407	145622853	741169	417	34709										
SLC39A4	55630	hgsc.bcm.edu	37	chr8	145640174	145640174	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aggtgcaggctccactcagcTgctgttggagcagggcaggg	17	10	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:145640174T>C	ENST00000301305.3	-	5	1016	c.911A>G	c.(910-912)cAg>cGg	p.Q304R	SLC39A4_ENST00000531013.1_5'Flank|SLC39A4_ENST00000276833.5_Missense_Mutation_p.Q279R	NM_130849.2	NP_570901	Q6P5W5	S39A4_HUMAN	solute carrier family 39 (zinc transporter), member 4	304					cellular response to zinc ion starvation (GO:0034224)|cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	14	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;1.12e-40)|all cancers(56;8.17e-36)|BRCA - Breast invasive adenocarcinoma(115;0.0407)|Colorectal(110;0.055)			TCCACTCAGCTGCTGTTGGAG	0.657																																					p.Q304R		Atlas-SNP	.											SLC39A4_ENST00000276833,NS,carcinoma,0,2	SLC39A4	54	.	0			c.A911G						.						52	54	53					8																	145640174		2203	4300	6503	SO:0001583	missense	55630	exon5			CTCAGCTGCTGTT	AK025537	CCDS6424.1, CCDS43782.1	8q24.3	2013-05-22			ENSG00000147804	ENSG00000147804		"Solute carriers"	17129	protein-coding gene	gene with protein product		607059	"acrodermatitis enteropathica, zinc-deficiency type"	AEZ		12801924, 12659941, 14709598	Standard	NM_017767		Approved	ZIP4, AWMS2	uc003zcq.3	Q6P5W5		ENST00000301305.3:c.911A>G	chr8.hg19:g.145640174T>C	ENSP00000301305:p.Gln304Arg	94.0	1.0		75.0	3.0	NM_130849	Q7L5S5|Q9H6T8|Q9NXC4	Missense_Mutation	SNP	ENST00000301305.3	hg19	CCDS6424.1	.	.	.	.	.	.	.	.	.	.	T	19.09	3.760629	0.69763	.	.	ENSG00000147804	ENST00000276833;ENST00000301305	T;T	0.60920	0.15;0.34	4.98	4.98	0.66077	.	0.373720	0.26828	N	0.022284	T	0.64549	0.2608	M	0.62723	1.935	0.31638	N	0.648231	B;D	0.67145	0.275;0.996	B;P	0.53649	0.047;0.731	T	0.73116	-0.4084	10	0.72032	D	0.01	-19.829	11.0906	0.48113	0.0:0.0:0.0:1.0	.	304;279	Q6P5W5;A6NDY5	S39A4_HUMAN;.	R	279;304	ENSP00000276833:Q279R;ENSP00000301305:Q304R	ENSP00000276833:Q279R	Q	-	2	0	SLC39A4	145610982	0.996000	0.38824	1.000000	0.80357	0.915000	0.54546	1.317000	0.33631	1.903000	0.55091	0.444000	0.29173	CAG	.	.		0.657	SLC39A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382688.1			C	145640174	T	C	145640174	3	2	254	1	0	0	0	0	1	0	0	0	14635	1580	55	2	1064	2	SLC39A4	8	145640174	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	17321	145640174	723848	418	34710										
NFKBIL2	4796	hgsc.bcm.edu	37	chr8	145659654	145659654	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cacggcctgcagcacctgttGgtgctcccctgcgggaggga	15	14	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr8:145659654G>T	ENST00000409379.3	-	21	3123	c.3094C>A	c.(3094-3096)Caa>Aaa	p.Q1032K	AC084125.4_ENST00000544423.1_RNA	NM_013432.4	NP_038460.4	Q96HA7	TONSL_HUMAN	tonsoku-like, DNA repair protein	1032					cytoplasmic sequestering of transcription factor (GO:0042994)|double-strand break repair via homologous recombination (GO:0000724)|regulation of RNA biosynthetic process (GO:2001141)|replication fork processing (GO:0031297)	cytoplasm (GO:0005737)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	histone binding (GO:0042393)|transcription corepressor activity (GO:0003714)			biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|lung(14)|ovary(3)|prostate(1)|skin(1)	26						AGCACCTGTTGGTGCTCCCCT	0.662																																					p.Q1032K		Atlas-SNP	.											.	TONSL	128	.	0			c.C3094A						.						14	14	14					8																	145659654		2181	4275	6456	SO:0001583	missense	4796	exon21			CCTGTTGGTGCTC		CCDS34968.2	8q24.3	2013-01-10	2010-12-02	2010-11-30	ENSG00000160949	ENSG00000160949		"Ankyrin repeat domain containing"	7801	protein-coding gene	gene with protein product		604546	"nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 2"	NFKBIL2		7738005, 11246458	Standard	NM_013432		Approved	IKBR	uc011llg.2	Q96HA7	OTTHUMG00000153122	ENST00000409379.3:c.3094C>A	chr8.hg19:g.145659654G>T	ENSP00000386239:p.Gln1032Lys	125.0	0.0		90.0	4.0	NM_013432	B5MDP0|C9JKB1|C9JNV8|Q13006|Q9UGJ2	Missense_Mutation	SNP	ENST00000409379.3	hg19	CCDS34968.2	.	.	.	.	.	.	.	.	.	.	G	0.058	-1.230958	0.01518	.	.	ENSG00000160949	ENST00000409379;ENST00000422691	T	0.38722	1.12	5.08	4.19	0.49359	.	0.894593	0.09740	N	0.761961	T	0.38799	0.1054	L	0.50333	1.59	0.31259	N	0.693062	B	0.15473	0.013	B	0.11329	0.006	T	0.39078	-0.9631	10	0.16896	T	0.51	-1.0722	13.1015	0.59222	0.0:0.1628:0.8372:0.0	.	1032	Q96HA7	TONSL_HUMAN	K	1032;1031	ENSP00000386239:Q1032K	ENSP00000386239:Q1032K	Q	-	1	0	TONSL	145630462	0.997000	0.39634	0.229000	0.23960	0.055000	0.15305	2.490000	0.45294	1.102000	0.41551	0.462000	0.41574	CAA	.	.		0.662	TONSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329668.2	NM_013432		T	145659654	G	T	145659654	3	4	254	1	0	0	0	0	1	0	0	0	10391	1357	47	3	1066	3	NFKBIL2	8	145659654	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	19480	145659654	704368	419	34711										
SMARCA2	6595	hgsc.bcm.edu	37	chr9	2056807	2056807	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agaagctggagaagcagcagAagattgagcaggagaggaaa	16	4	0	6			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:2056807A>G	ENST00000382203.1	+	7	1518	c.1309A>G	c.(1309-1311)Aag>Gag	p.K437E	SMARCA2_ENST00000357248.2_Missense_Mutation_p.K437E|SMARCA2_ENST00000382194.1_Missense_Mutation_p.K437E|SMARCA2_ENST00000349721.2_Missense_Mutation_p.K437E			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	437	HSA. {ECO:0000255|PROSITE- ProRule:PRU00549}.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|chromatin remodeling (GO:0006338)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		GAAGCAGCAGAAGATTGAGCA	0.532																																					p.K437E		Atlas-SNP	.											.	SMARCA2	313	.	0			c.A1309G						.						82	77	79					9																	2056807		2203	4300	6503	SO:0001583	missense	6595	exon7			CAGCAGAAGATTG	D26155	CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1	9p24.3	2008-11-11	2006-11-09		ENSG00000080503	ENSG00000080503			11098	protein-coding gene	gene with protein product		600014		SNF2L2		8012116	Standard	NM_003070		Approved	BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2	uc003zhc.3	P51531	OTTHUMG00000019445	ENST00000382203.1:c.1309A>G	chr9.hg19:g.2056807A>G	ENSP00000371638:p.Lys437Glu	107.0	0.0		65.0	4.0	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Missense_Mutation	SNP	ENST00000382203.1	hg19	CCDS34977.1	.	.	.	.	.	.	.	.	.	.	A	27.8	4.860069	0.91433	.	.	ENSG00000080503	ENST00000349721;ENST00000357248;ENST00000450198;ENST00000382203;ENST00000382194	T;T;T;T;T	0.72051	-0.62;-0.62;-0.62;-0.62;-0.62	5.17	5.17	0.71159	Helicase/SANT-associated, DNA binding (1);HAS subgroup (1);HSA (1);	0.000000	0.85682	D	0.000000	D	0.85287	0.5662	M	0.86343	2.81	0.80722	D	1	D;D;D	0.69078	0.992;0.996;0.997	D;D;D	0.79108	0.933;0.987;0.992	D	0.86819	0.2003	10	0.46703	T	0.11	-33.2005	14.69	0.69080	1.0:0.0:0.0:0.0	.	38;437;437	B4DK35;P51531-2;P51531	.;.;SMCA2_HUMAN	E	437	ENSP00000265773:K437E;ENSP00000349788:K437E;ENSP00000392081:K437E;ENSP00000371638:K437E;ENSP00000371629:K437E	ENSP00000265773:K437E	K	+	1	0	SMARCA2	2046807	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.305000	0.96197	1.946000	0.56461	0.533000	0.62120	AAG	.	.		0.532	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070		G	2056807	A	G	2056807	3	3	254	1	0	0	0	0	1	0	0	0	14784	247	9	2	1331	2	SMARCA2	9	2056807	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10		2056807	139156624	420	34712										
ERMP1	79956	hgsc.bcm.edu	37	chr9	5830996	5830996	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctggacttcctgtagtcctgGggccaatggaggttatgtgt	14	8	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:5830996G>T	ENST00000339450.5	-	2	460	c.371C>A	c.(370-372)cCc>cAc	p.P124H	ERMP1_ENST00000214893.5_5'UTR|ERMP1_ENST00000381506.3_5'Flank	NM_024896.2	NP_079172.2	Q7Z2K6	ERMP1_HUMAN	endoplasmic reticulum metallopeptidase 1	124						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			endometrium(2)|kidney(1)|large_intestine(9)|lung(4)|ovary(1)|prostate(2)|skin(1)	20		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00115)|Lung(218;0.111)		TGTAGTCCTGGGGCCAATGGA	0.393																																					p.P124H		Atlas-SNP	.											.	ERMP1	63	.	0			c.C371A						.						98	97	97					9																	5830996		2203	4300	6503	SO:0001583	missense	79956	exon2			GTCCTGGGGCCAA	AB058718	CCDS34983.1	9p24	2008-02-05	2007-07-05	2007-07-05	ENSG00000099219	ENSG00000099219			23703	protein-coding gene	gene with protein product	"Felix-ina"	611156	"KIAA1815"	KIAA1815		11347906	Standard	XM_005251587		Approved	FLJ23309, FXNA	uc003zjm.1	Q7Z2K6	OTTHUMG00000019508	ENST00000339450.5:c.371C>A	chr9.hg19:g.5830996G>T	ENSP00000340427:p.Pro124His	134.0	0.0		89.0	4.0	NM_024896	B2RNA4|B3KSB1|Q8N5T5|Q9H5M1	Missense_Mutation	SNP	ENST00000339450.5	hg19	CCDS34983.1	.	.	.	.	.	.	.	.	.	.	G	20.0	3.929829	0.73327	.	.	ENSG00000099219	ENST00000339450	T	0.55930	0.49	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.62816	0.2459	M	0.73319	2.225	0.80722	D	1	D;P	0.53462	0.96;0.941	P;P	0.48425	0.46;0.577	T	0.61515	-0.7047	10	0.36615	T	0.2	-15.9811	20.0124	0.97464	0.0:0.0:1.0:0.0	.	124;124	E7ER77;Q7Z2K6	.;ERMP1_HUMAN	H	124	ENSP00000340427:P124H	ENSP00000340427:P124H	P	-	2	0	ERMP1	5820996	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.476000	0.97823	2.749000	0.94314	0.655000	0.94253	CCC	.	.		0.393	ERMP1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354877.1	NM_024896		T	5830996	G	T	5830996	3	4	254	1	0	0	0	0	1	0	0	0	5238	1232	43	3	2399	3	ERMP1	9	5830996	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	3774189	5830996	135382435	421	34713										
BNC2	54796	hgsc.bcm.edu	37	chr9	16552604	16552604	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgtgcagtacctcctcttgcTtcaggacgctgaagagacgg	12	11	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:16552604T>C	ENST00000380672.4	-	5	650	c.593A>G	c.(592-594)aAg>aGg	p.K198R	BNC2_ENST00000380666.2_Missense_Mutation_p.K198R|BNC2_ENST00000380667.2_Missense_Mutation_p.K131R|BNC2_ENST00000545497.1_Missense_Mutation_p.K103R	NM_017637.5	NP_060107.3			basonuclin 2											NS(2)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(16)|liver(1)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(50;9.01e-08)		CTCCTCTTGCTTCAGGACGCT	0.562																																					p.K198R		Atlas-SNP	.											.	BNC2	166	.	0			c.A593G						.						111	81	91					9																	16552604		2203	4300	6503	SO:0001583	missense	54796	exon5			TCTTGCTTCAGGA	AK092247	CCDS6482.2	9p22.2	2013-05-20			ENSG00000173068	ENSG00000173068		"Zinc fingers, C2H2-type"	30988	protein-coding gene	gene with protein product		608669				14702039	Standard	XM_006716784		Approved	BSN2, FLJ20043	uc003zml.3	Q6ZN30	OTTHUMG00000019593	ENST00000380672.4:c.593A>G	chr9.hg19:g.16552604T>C	ENSP00000370047:p.Lys198Arg	163.0	0.0		77.0	5.0	NM_017637		Missense_Mutation	SNP	ENST00000380672.4	hg19	CCDS6482.2	.	.	.	.	.	.	.	.	.	.	T	35	5.446621	0.96205	.	.	ENSG00000173068	ENST00000380672;ENST00000418777;ENST00000456672;ENST00000436939;ENST00000380667;ENST00000545497;ENST00000544198;ENST00000380666;ENST00000540340	T;T;T;T;T	0.03772	3.81;3.81;3.81;3.81;3.81	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.18759	0.0450	L	0.53249	1.67	0.80722	D	1	D;B;D;D;D;D;B	0.89917	0.999;0.127;0.992;0.996;1.0;0.993;0.272	D;B;D;D;D;D;B	0.91635	0.994;0.109;0.984;0.99;0.999;0.956;0.153	T	0.00054	-1.2182	10	0.66056	D	0.02	-25.3735	16.6512	0.85203	0.0:0.0:0.0:1.0	.	103;131;235;198;24;156;198	F5H586;B1APH0;Q06HC4;Q6ZN30-2;B4E3J2;Q5H9S4;Q6ZN30	.;.;.;.;.;.;BNC2_HUMAN	R	198;155;235;226;131;103;24;198;198	ENSP00000370047:K198R;ENSP00000408370:K155R;ENSP00000370042:K131R;ENSP00000444640:K103R;ENSP00000370041:K198R	ENSP00000370041:K198R	K	-	2	0	BNC2	16542604	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.040000	0.89188	2.333000	0.79357	0.482000	0.46254	AAG	.	.		0.562	BNC2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216901.5	NM_017637		C	16552604	T	C	16552604	3	2	254	1	0	0	0	0	1	0	0	0	1475	1609	56	2	2718	2	BNC2	9	16552604	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	10721608	16552604	124660827	422	34714										
CNTLN	54875	hgsc.bcm.edu	37	chr9	17332673	17332673	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agactcagaagagctacagaAgctgagaaaagctgaaagaa	11	6	1	7			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:17332673A>G	ENST00000380647.3	+	10	1673	c.1589A>G	c.(1588-1590)aAg>aGg	p.K530R	CNTLN_ENST00000425824.1_Missense_Mutation_p.K530R|CNTLN_ENST00000262360.5_Missense_Mutation_p.K530R			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	530					centriole-centriole cohesion (GO:0010457)|protein localization to organelle (GO:0033365)	centriole (GO:0005814)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)|protein binding, bridging (GO:0030674)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(6)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53				GBM - Glioblastoma multiforme(50;6.14e-10)		GAGCTACAGAAGCTGAGAAAA	0.383																																					p.K530R		Atlas-SNP	.											.	CNTLN	128	.	0			c.A1589G						.						73	69	70					9																	17332673		1836	4082	5918	SO:0001583	missense	54875	exon10			TACAGAAGCTGAG	AK000283	CCDS43789.1, CCDS47953.1	9p22.2-p22.1	2008-11-11	2008-02-08	2008-02-08	ENSG00000044459	ENSG00000044459			23432	protein-coding gene	gene with protein product		611870	"chromosome 9 open reading frame 101", "chromosome 9 open reading frame 39"	C9orf101, C9orf39		18086554	Standard	XM_005251492		Approved	FLJ20276, bA340N12.1, OTTHUMG00000019597	uc003zmy.3	Q9NXG0	OTTHUMG00000019599	ENST00000380647.3:c.1589A>G	chr9.hg19:g.17332673A>G	ENSP00000370021:p.Lys530Arg	244.0	0.0		137.0	6.0	NM_017738	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Missense_Mutation	SNP	ENST00000380647.3	hg19	CCDS43789.1	.	.	.	.	.	.	.	.	.	.	A	11.40	1.626434	0.28978	.	.	ENSG00000044459	ENST00000380647;ENST00000425824;ENST00000262360	T;T;T	0.13307	2.6;2.6;2.6	5.54	5.54	0.83059	.	.	.	.	.	T	0.16557	0.0398	L	0.34521	1.04	0.31547	N	0.659277	P;P;P	0.42692	0.787;0.787;0.787	P;P;P	0.46758	0.526;0.526;0.526	T	0.04635	-1.0937	9	0.20519	T	0.43	.	15.3261	0.74164	1.0:0.0:0.0:0.0	.	530;530;530	Q9NXG0;C9J1F9;Q9NXG0-2	CNTLN_HUMAN;.;.	R	530	ENSP00000370021:K530R;ENSP00000392798:K530R;ENSP00000262360:K530R	ENSP00000262360:K530R	K	+	2	0	CNTLN	17322673	1.000000	0.71417	0.986000	0.45419	0.780000	0.44128	3.434000	0.52841	2.098000	0.63641	0.482000	0.46254	AAG	.	.		0.383	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738		G	17332673	A	G	17332673	3	3	254	1	0	0	0	0	1	0	0	0	3641	72	3	2	1657	2	CNTLN	9	17332673	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	780069	17332673	123880758	423	34715										
SH3GL2	6456	hgsc.bcm.edu	37	chr9	17791315	17791315	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cagatcctgcagcaagtcacGgtcagactggaagaaaggta	12	9	2	3	rs150625805	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:17791315G>T	ENST00000380607.4	+	7	831	c.711G>T	c.(709-711)acG>acT	p.T237T	SH3GL2_ENST00000537391.1_Silent_p.T190T	NM_003026.2	NP_003017.1	Q99962	SH3G2_HUMAN	SH3-domain GRB2-like 2	237	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|central nervous system development (GO:0007417)|epidermal growth factor receptor signaling pathway (GO:0007173)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of receptor internalization (GO:0002090)|signal transduction (GO:0007165)|synaptic vesicle endocytosis (GO:0048488)	clathrin-coated endocytic vesicle membrane (GO:0030669)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)			NS(1)|breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(11)|skin(3)|upper_aerodigestive_tract(1)	26				GBM - Glioblastoma multiforme(50;2.71e-10)|Lung(42;0.203)		AGCAAGTCACGGTCAGACTGG	0.423																																					p.T237T		Atlas-SNP	.											.	SH3GL2	60	.	0			c.G711T						.						143	132	136					9																	17791315		2203	4300	6503	SO:0001819	synonymous_variant	6456	exon7			AGTCACGGTCAGA	X99657	CCDS6483.1	9p22	2008-02-05			ENSG00000107295	ENSG00000107295			10831	protein-coding gene	gene with protein product		604465				9169142	Standard	XM_005251549		Approved	SH3P4, SH3D2A, CNSA2, EEN-B1	uc003zna.3	Q99962	OTTHUMG00000019601	ENST00000380607.4:c.711G>T	chr9.hg19:g.17791315G>T		234.0	0.0		91.0	4.0	NM_003026	B2R618|Q9NQK5	Silent	SNP	ENST00000380607.4	hg19	CCDS6483.1																																																																																			.	G|0.998;A|0.002		0.423	SH3GL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051796.1	NM_003026		T	17791315	G	T	17791315	2	4	254	1	0	0	0	0	0	0	0	1	14266	1103	39	1		1	SH3GL2	9	17791315	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	458642	17791315	123422116	424	34716										
KIAA1797	54914	hgsc.bcm.edu	37	chr9	20907148	20907148	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgtggtacatttttcccataGgttcatatccagctttcaga	7	9	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:20907148G>T	ENST00000380249.1	+	24	2989		c.e24-1		FOCAD_ENST00000605086.1_Splice_Site|FOCAD_ENST00000338382.6_Splice_Site	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin							focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)											ttttcccataggttcatatcc	0.363																																					.		Atlas-SNP	.											.	.	.	.	0			c.2626-1G>T						.						116	107	110					9																	20907148		2203	4300	6503	SO:0001630	splice_region_variant	54914	exon24			CCCATAGGTTCAT	AB058700	CCDS34993.1	9p21	2012-03-23	2012-03-23	2012-03-23	ENSG00000188352	ENSG00000188352			23377	protein-coding gene	gene with protein product		614606	"KIAA1797"	KIAA1797		22427331	Standard	XM_006716794		Approved	FLJ20375	uc003zog.1	Q5VW36	OTTHUMG00000066930	ENST00000380249.1:c.2626-1G>T	chr9.hg19:g.20907148G>T		80.0	0.0		64.0	4.0	NM_017794	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Splice_Site	SNP	ENST00000380249.1	hg19	CCDS34993.1																																																																																			.	.		0.363	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794	Intron	T	20907148	G	T	20907148	5	4	254	1	0	0	0	0	0	0	1	0	8267	1014	35	3	2707	3	KIAA1797	9	20907148	Splice_Site	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	3115833	20907148	120306283	425	34717										
TEK	7010	hgsc.bcm.edu	37	chr9	27212778	27212778	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cttcgcaagagccgtgtgctGgagacggacccagcatttgc	13	12	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:27212778G>T	ENST00000380036.4	+	17	3202	c.2760G>T	c.(2758-2760)ctG>ctT	p.L920L	TEK_ENST00000519097.1_Silent_p.L772L|TEK_ENST00000406359.4_Silent_p.L877L	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	920	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	GCCGTGTGCTGGAGACGGACC	0.597																																					p.L920L		Atlas-SNP	.											.	TEK	250	.	0			c.G2760T						.						97	76	83					9																	27212778		2203	4300	6503	SO:0001819	synonymous_variant	7010	exon17			TGTGCTGGAGACG	L06139	CCDS6519.1, CCDS75825.1	9p21	2013-02-11	2008-07-31		ENSG00000120156	ENSG00000120156		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	11724	protein-coding gene	gene with protein product		600221	"venous malformations, multiple cutaneous and mucosal"	VMCM		1312667, 7833915	Standard	XM_005251561		Approved	TIE2, TIE-2, VMCM1, CD202b	uc003zqi.4	Q02763	OTTHUMG00000019712	ENST00000380036.4:c.2760G>T	chr9.hg19:g.27212778G>T		141.0	0.0		84.0	4.0	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Silent	SNP	ENST00000380036.4	hg19	CCDS6519.1																																																																																			.	.		0.597	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3			T	27212778	G	T	27212778	2	4	254	1	0	0	0	0	0	0	0	1	15766	1335	47	3		3	TEK	9	27212778	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	6305630	27212778	114000653	426	34718										
NFX1	4799	hgsc.bcm.edu	37	chr9	33364038	33364038	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gaggcatttcatatcagtgaGgattctgatcctttcaatat	8	7	4	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:33364038G>T	ENST00000379540.3	+	20	2966	c.2904G>T	c.(2902-2904)gaG>gaT	p.E968D	NFX1_ENST00000379521.4_Missense_Mutation_p.E968D	NM_002504.4	NP_002495.2	Q12986	NFX1_HUMAN	nuclear transcription factor, X-box binding 1	968					inflammatory response (GO:0006954)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25			LUSC - Lung squamous cell carcinoma(29;0.00506)	GBM - Glioblastoma multiforme(74;0.224)		ATATCAGTGAGGATTCTGATC	0.403																																					p.E968D		Atlas-SNP	.											.	NFX1	85	.	0			c.G2904T						.						142	130	134					9																	33364038		2203	4300	6503	SO:0001583	missense	4799	exon20			CAGTGAGGATTCT	U19759	CCDS6538.1, CCDS6539.1, CCDS6540.1	9p12	2013-12-13			ENSG00000086102	ENSG00000086102			7803	protein-coding gene	gene with protein product		603255				7964459, 2511169	Standard	NM_002504		Approved	NFX2, MGC20369, Tex42, TEG-42	uc003zsq.3	Q12986	OTTHUMG00000019772	ENST00000379540.3:c.2904G>T	chr9.hg19:g.33364038G>T	ENSP00000368856:p.Glu968Asp	173.0	0.0		136.0	6.0	NM_147133	A8K6H8|Q5VXW6|Q96EL5|Q9BXI1	Missense_Mutation	SNP	ENST00000379540.3	hg19	CCDS6538.1	.	.	.	.	.	.	.	.	.	.	G	8.494	0.862744	0.17178	.	.	ENSG00000086102	ENST00000379540;ENST00000379521	T;T	0.22743	2.27;1.94	6.08	-12.2	0.00006	.	0.561473	0.20789	N	0.085649	T	0.04407	0.0121	N	0.05467	-0.045	0.38185	D	0.939728	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.42865	-0.9426	10	0.12430	T	0.62	-1.2131	1.8683	0.03203	0.3128:0.3206:0.2358:0.1309	.	968;968	Q12986;Q12986-2	NFX1_HUMAN;.	D	968	ENSP00000368856:E968D;ENSP00000368836:E968D	ENSP00000368836:E968D	E	+	3	2	NFX1	33354038	0.000000	0.05858	0.495000	0.27527	0.918000	0.54935	-2.966000	0.00670	-2.052000	0.00902	-0.282000	0.10007	GAG	.	.		0.403	NFX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052069.1			T	33364038	G	T	33364038	3	4	254	1	0	0	0	0	1	0	0	0	10396	991	35	3	3064	3	NFX1	9	33364038	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	6151260	33364038	107849393	427	34719										
FRMPD1	22844	hgsc.bcm.edu	37	chr9	37737222	37737222	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gaaacaaacaacaagcgcacCgggtatctgcagaagaaggt	11	9	1	2	rs550100323		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:37737222C>A	ENST00000539465.1	+	14	2124	c.1531C>A	c.(1531-1533)Cgg>Agg	p.R511R	FRMPD1_ENST00000541302.1_Silent_p.R380R|FRMPD1_ENST00000377765.3_Silent_p.R511R|FRMPD1_ENST00000536622.1_Silent_p.R333R|RP11-613M10.9_ENST00000540557.1_Intron			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	511						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		ACAAGCGCACCGGGTATCTGC	0.537																																					p.R511R		Atlas-SNP	.											.	FRMPD1	237	.	0			c.C1531A						.						80	73	75					9																	37737222		2203	4300	6503	SO:0001819	synonymous_variant	22844	exon14			GCGCACCGGGTAT	AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.1531C>A	chr9.hg19:g.37737222C>A		122.0	0.0		106.0	5.0	NM_014907	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Silent	SNP	ENST00000539465.1	hg19	CCDS6612.1																																																																																			.	.		0.537	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907		A	37737222	C	A	37737222	2	1	254	1	0	0	0	0	0	0	0	1	6065	643	23	1		1	FRMPD1	9	37737222	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	4373184	37737222	103476209	428	34720										
TJP2	9414	hgsc.bcm.edu	37	chr9	71842715	71842715	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gagtcaaaccgatcattttcTccagaggagagacgtcatca	9	10	5	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:71842715T>C	ENST00000377245.4	+	8	1453	c.1245T>C	c.(1243-1245)tcT>tcC	p.S415S	TJP2_ENST00000453658.2_Silent_p.S392S|TJP2_ENST00000348208.4_Silent_p.S415S|TJP2_ENST00000265384.7_Silent_p.S415S|TJP2_ENST00000535702.1_Silent_p.S419S|TJP2_ENST00000539225.1_Silent_p.S446S	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	415					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|hippo signaling (GO:0035329)|nucleotide phosphorylation (GO:0046939)|response to organic substance (GO:0010033)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	guanylate kinase activity (GO:0004385)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(5)|lung(9)|prostate(3)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	35						GATCATTTTCTCCAGAGGAGA	0.318																																					p.S446S		Atlas-SNP	.											.	TJP2	120	.	0			c.T1338C						.						76	71	73					9																	71842715		2203	4300	6503	SO:0001819	synonymous_variant	9414	exon8			ATTTTCTCCAGAG	L27476	CCDS6627.1, CCDS6628.1, CCDS55314.1, CCDS55315.1, CCDS55316.1, CCDS55317.1	9q13-q21	2012-07-12	2012-07-12		ENSG00000119139	ENSG00000119139			11828	protein-coding gene	gene with protein product	"Friedreich ataxia region gene X104 (tight junction protein ZO-2)", "zona occludens 2"	607709	"deafness, autosomal dominant 51"	DFNA51		7951235, 20602916	Standard	NM_001170630		Approved	ZO-2, X104, ZO2	uc011lrv.2	Q9UDY2	OTTHUMG00000019978	ENST00000377245.4:c.1245T>C	chr9.hg19:g.71842715T>C		142.0	0.0		91.0	5.0	NM_001170416	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Silent	SNP	ENST00000377245.4	hg19	CCDS6627.1																																																																																			.	.		0.318	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629		C	71842715	T	C	71842715	2	2	254	1	0	0	0	0	0	0	0	1	15945	1538	54	2		2	TJP2	9	71842715	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	34105493	71842715	69370716	429	34721										
FAM189A2	9413	hgsc.bcm.edu	37	chr9	72003281	72003281	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	catgaccccagacatccatgAacttgtagaaaacattaaat	5	10	0	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:72003281A>G	ENST00000257515.8	+	10	1484	c.1064A>G	c.(1063-1065)gAa>gGa	p.E355G	FAM189A2_ENST00000455972.1_Missense_Mutation_p.E355G|FAM189A2_ENST00000303068.7_Missense_Mutation_p.E190G|FAM189A2_ENST00000377216.3_Missense_Mutation_p.E142G|FAM189A2_ENST00000469179.1_3'UTR	NM_004816.3	NP_004807.3	Q15884	F1892_HUMAN	family with sequence similarity 189, member A2	355						integral component of membrane (GO:0016021)				endometrium(3)|large_intestine(5)|liver(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	12						GACATCCATGAACTTGTAGAA	0.438																																					p.E355G		Atlas-SNP	.											.	FAM189A2	55	.	0			c.A1064G						.						61	58	59					9																	72003281		2203	4300	6503	SO:0001583	missense	9413	exon10			TCCATGAACTTGT	L27479	CCDS6629.1	9q21.11	2009-07-09	2009-07-09	2009-07-09	ENSG00000135063	ENSG00000135063			24820	protein-coding gene	gene with protein product		607710	"chromosome 9 open reading frame 61"	C9orf61		7951235	Standard	NM_004816		Approved	X123	uc010mon.1	Q15884	OTTHUMG00000019979	ENST00000257515.8:c.1064A>G	chr9.hg19:g.72003281A>G	ENSP00000257515:p.Glu355Gly	140.0	0.0		94.0	4.0	NM_004816	Q14CN5|Q5T6C8|Q5T6C9|Q6ZTX4|Q96N10	Missense_Mutation	SNP	ENST00000257515.8	hg19	CCDS6629.1	.	.	.	.	.	.	.	.	.	.	A	28.5	4.924268	0.92319	.	.	ENSG00000135063	ENST00000455972;ENST00000257515;ENST00000303068;ENST00000377225;ENST00000377216	T;T;T	0.35605	2.35;2.35;1.3	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.58524	0.2128	M	0.62723	1.935	0.58432	D	0.999998	D	0.89917	1.0	D	0.78314	0.991	T	0.61068	-0.7137	10	0.72032	D	0.01	-19.6869	16.1549	0.81657	1.0:0.0:0.0:0.0	.	355	Q15884	F1892_HUMAN	G	355;355;190;354;142	ENSP00000395675:E355G;ENSP00000257515:E355G;ENSP00000304435:E190G	ENSP00000257515:E355G	E	+	2	0	FAM189A2	71193101	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.210000	0.95106	2.209000	0.71365	0.533000	0.62120	GAA	.	.		0.438	FAM189A2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052576.2	NM_004816		G	72003281	A	G	72003281	3	3	254	1	0	0	0	0	1	0	0	0	5521	246	9	2	1098	2	FAM189A2	9	72003281	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	160566	72003281	69210150	430	34722										
MAMDC2	256691	hgsc.bcm.edu	37	chr9	72728033	72728033	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttctcccacaggatcacaccTtcaagagtgaactgggtgag	10	11	3	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:72728033T>C	ENST00000377182.4	+	5	1245	c.628T>C	c.(628-630)Ttc>Ctc	p.F210L	MAMDC2-AS1_ENST00000414515.3_RNA|MAMDC2-AS1_ENST00000591368.1_RNA	NM_153267.4	NP_694999.3	Q7Z304	MAMC2_HUMAN	MAM domain containing 2	210	MAM 2. {ECO:0000255|PROSITE- ProRule:PRU00128}.				peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)	endoplasmic reticulum (GO:0005783)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	glycosaminoglycan binding (GO:0005539)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)	14						GGATCACACCTTCAAGAGTGA	0.493																																					p.F210L		Atlas-SNP	.											.	MAMDC2	55	.	0			c.T628C						.						92	82	86					9																	72728033		2203	4300	6503	SO:0001583	missense	256691	exon5			CACACCTTCAAGA	BC040299	CCDS6631.1	9q21.2	2008-02-05			ENSG00000165072	ENSG00000165072			23673	protein-coding gene	gene with protein product		612879					Standard	NM_153267		Approved	MGC21981	uc004ahm.2	Q7Z304	OTTHUMG00000019990	ENST00000377182.4:c.628T>C	chr9.hg19:g.72728033T>C	ENSP00000366387:p.Phe210Leu	120.0	0.0		96.0	4.0	NM_153267	Q5VW47|Q8WX43|Q96BM4	Missense_Mutation	SNP	ENST00000377182.4	hg19	CCDS6631.1	.	.	.	.	.	.	.	.	.	.	T	2.869	-0.234515	0.05983	.	.	ENSG00000165072	ENST00000377182	T	0.01804	4.63	5.72	3.39	0.38822	Concanavalin A-like lectin/glucanase (1);MAM domain (3);	0.662303	0.16615	N	0.206726	T	0.00580	0.0019	N	0.00690	-1.25	0.24804	N	0.992684	B	0.02656	0.0	B	0.08055	0.003	T	0.45264	-0.9273	10	0.07325	T	0.83	-11.9473	4.5903	0.12304	0.0:0.4564:0.0:0.5436	.	210	Q7Z304	MAMC2_HUMAN	L	210	ENSP00000366387:F210L	ENSP00000366387:F210L	F	+	1	0	MAMDC2	71917853	0.475000	0.25894	0.714000	0.30535	0.704000	0.40688	0.784000	0.26816	1.001000	0.39076	0.379000	0.24179	TTC	.	.		0.493	MAMDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052600.1	NM_153267		C	72728033	T	C	72728033	3	2	254	1	0	0	0	0	1	0	0	0	9212	1609	56	2	646	2	MAMDC2	9	72728033	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	724752	72728033	68485398	431	34723										
PCSK5	5125	hgsc.bcm.edu	37	chr9	78749051	78749051	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tctgacctggagagacgtacAgcatgttattgtcaggactt	11	8	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:78749051A>G	ENST00000545128.1	+	10	1773	c.1235A>G	c.(1234-1236)cAg>cGg	p.Q412R	PCSK5_ENST00000376767.3_Missense_Mutation_p.Q412R|PCSK5_ENST00000376752.4_Missense_Mutation_p.Q412R	NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	412	Peptidase S8.				anterior/posterior pattern specification (GO:0009952)|cell-cell signaling (GO:0007267)|cytokine biosynthetic process (GO:0042089)|embryo implantation (GO:0007566)|embryonic digestive tract development (GO:0048566)|embryonic skeletal system development (GO:0048706)|heart development (GO:0007507)|kidney development (GO:0001822)|limb morphogenesis (GO:0035108)|nerve growth factor processing (GO:0032455)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|protein processing (GO:0016485)|renin secretion into blood stream (GO:0002001)|respiratory tube development (GO:0030323)|signal peptide processing (GO:0006465)|viral life cycle (GO:0019058)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|secretory granule (GO:0030141)	peptidase activity (GO:0008233)|peptide binding (GO:0042277)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|liver(2)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55						AGAGACGTACAGCATGTTATT	0.433																																					p.Q412R		Atlas-SNP	.											.	PCSK5	329	.	0			c.A1235G						.						133	123	126					9																	78749051		2203	4300	6503	SO:0001583	missense	5125	exon10			ACGTACAGCATGT		CCDS6652.1, CCDS55320.1	9q21.13	2013-09-24			ENSG00000099139	ENSG00000099139			8747	protein-coding gene	gene with protein product		600488				7782070	Standard	NM_001190482		Approved	PC5, PC6, SPC6	uc004akc.2	Q92824	OTTHUMG00000020039	ENST00000545128.1:c.1235A>G	chr9.hg19:g.78749051A>G	ENSP00000446280:p.Gln412Arg	73.0	0.0		72.0	4.0	NM_006200	F5H2G7|Q13527|Q96EP4	Missense_Mutation	SNP	ENST00000545128.1	hg19	CCDS55320.1	.	.	.	.	.	.	.	.	.	.	A	25.7	4.661280	0.88154	.	.	ENSG00000099139	ENST00000545128;ENST00000376754;ENST00000376767;ENST00000396108;ENST00000376752;ENST00000424854	D;D;D;D	0.86164	-2.08;-2.08;-2.08;-2.08	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	D	0.93148	0.7818	M	0.76328	2.33	0.58432	D	0.999995	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.93660	0.6981	10	0.66056	D	0.02	-22.4224	16.3426	0.83092	1.0:0.0:0.0:0.0	.	412;412	Q92824-2;B1AMG5	.;.	R	412;115;412;412;412;85	ENSP00000446280:Q412R;ENSP00000365958:Q412R;ENSP00000365943:Q412R;ENSP00000411654:Q85R	ENSP00000365943:Q412R	Q	+	2	0	PCSK5	77938871	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.910000	0.92685	2.317000	0.78254	0.460000	0.39030	CAG	.	.		0.433	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				G	78749051	A	G	78749051	3	3	254	1	0	0	0	0	1	0	0	0	11612	188	7	2	1273	2	PCSK5	9	78749051	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	6021018	78749051	62464380	432	34724										
FLJ46321	389763	hgsc.bcm.edu	37	chr9	84608274	84608274	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aaagatggggtctctaagtcCcgtagtcgaagcacttttca	10	9	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:84608274C>A	ENST00000344803.2	+	4	2936	c.2889C>A	c.(2887-2889)tcC>tcA	p.S963S		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	963					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											TCTCTAAGTCCCGTAGTCGAA	0.507																																					p.S963S		Atlas-SNP	.											.	.	.	.	0			c.C2889A						.						102	99	100					9																	84608274		1885	4128	6013	SO:0001819	synonymous_variant	389763	exon4			TAAGTCCCGTAGT		CCDS47986.1	9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000214929	ENSG00000214929			37283	protein-coding gene	gene with protein product			"family with sequence similarity 75, member D1"	FAM75D1			Standard	NM_001001670		Approved	FLJ46321	uc004amn.3	Q6ZQQ2	OTTHUMG00000169122	ENST00000344803.2:c.2889C>A	chr9.hg19:g.84608274C>A		107.0	0.0		89.0	4.0	NM_001001670		Silent	SNP	ENST00000344803.2	hg19	CCDS47986.1																																																																																			.	.		0.507	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		A	84608274	C	A	84608274	2	1	254	1	0	0	0	0	0	0	0	1	5940	610	22	3		3	FLJ46321	9	84608274	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	5859223	84608274	56605157	433	34725										
NTRK2	4915	hgsc.bcm.edu	37	chr9	87339221	87339221	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gaagcagatctcttgtgtggCggaaaatcttgtaggagaag	14	5	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:87339221C>T	ENST00000323115.4	+	7	1156	c.803C>T	c.(802-804)gCg>gTg	p.A268V	NTRK2_ENST00000359847.3_Missense_Mutation_p.A268V|NTRK2_ENST00000376208.1_Missense_Mutation_p.A268V|NTRK2_ENST00000376213.1_Missense_Mutation_p.A268V|NTRK2_ENST00000395866.2_Missense_Mutation_p.A112V|NTRK2_ENST00000376214.1_Missense_Mutation_p.A268V|NTRK2_ENST00000395882.1_Missense_Mutation_p.A268V|NTRK2_ENST00000304053.6_Missense_Mutation_p.A268V|NTRK2_ENST00000277120.3_Missense_Mutation_p.A268V			Q16620	NTRK2_HUMAN	neurotrophic tyrosine kinase, receptor, type 2	268	Ig-like C2-type 1.				activation of adenylate cyclase activity (GO:0007190)|aging (GO:0007568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|central nervous system neuron development (GO:0021954)|cerebral cortex development (GO:0021987)|circadian rhythm (GO:0007623)|feeding behavior (GO:0007631)|glutamate secretion (GO:0014047)|learning (GO:0007612)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mechanoreceptor differentiation (GO:0042490)|negative regulation of anoikis (GO:2000811)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular junction development (GO:0007528)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peripheral nervous system neuron development (GO:0048935)|positive regulation of axonogenesis (GO:0050772)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|regulation of dendrite development (GO:0050773)|regulation of neurotransmitter secretion (GO:0046928)|regulation of protein kinase B signaling (GO:0051896)|regulation of Rac GTPase activity (GO:0032314)|response to auditory stimulus (GO:0010996)|retinal rod cell development (GO:0046548)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vasculogenesis (GO:0001570)	cell surface (GO:0009986)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endosome (GO:0005768)|excitatory synapse (GO:0060076)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|receptor complex (GO:0043235)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|brain-derived neurotrophic factor binding (GO:0048403)|brain-derived neurotrophic factor-activated receptor activity (GO:0060175)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	46					Amitriptyline(DB00321)	TCTTGTGTGGCGGAAAATCTT	0.408										TSP Lung(25;0.17)																											p.A268V		Atlas-SNP	.											.	NTRK2	331	.	0			c.C803T						.						215	204	208					9																	87339221		2203	4300	6503	SO:0001583	missense	4915	exon8			GTGTGGCGGAAAA	AF410902	CCDS6671.1, CCDS35050.1, CCDS35051.1, CCDS35052.1, CCDS35053.1	9q22.1	2013-01-11			ENSG00000148053	ENSG00000148053	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing"	8032	protein-coding gene	gene with protein product		600456				7789988	Standard	NM_001018065		Approved	TRKB	uc004anz.1	Q16620	OTTHUMG00000020120	ENST00000323115.4:c.803C>T	chr9.hg19:g.87339221C>T	ENSP00000314586:p.Ala268Val	188.0	0.0		140.0	35.0	NM_001018065	B1ANZ4|B4DFV9|Q16675|Q59GJ1|Q8WXJ5|Q8WXJ6|Q8WXJ7	Missense_Mutation	SNP	ENST00000323115.4	hg19	CCDS35050.1	.	.	.	.	.	.	.	.	.	.	C	31	5.067874	0.93950	.	.	ENSG00000148053	ENST00000376214;ENST00000376213;ENST00000395882;ENST00000376208;ENST00000304053;ENST00000277120;ENST00000323115;ENST00000359847;ENST00000395866	T;T;T;T;T;T;T;T;T	0.72505	-0.66;-0.66;-0.66;-0.66;-0.66;-0.66;-0.66;-0.66;-0.66	5.27	5.27	0.74061	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.054584	0.64402	D	0.000001	D	0.84566	0.5500	M	0.83692	2.655	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.91635	0.999;0.995;0.995;0.997;0.987;0.977;0.999;0.995	T	0.80966	-0.1146	10	0.15952	T	0.53	.	19.2585	0.93957	0.0:1.0:0.0:0.0	.	112;268;268;268;268;268;314;268	B4DFV9;Q16620-3;Q16620-5;Q5VWE5;Q16620;Q16620-4;Q59GJ1;Q16620-2	.;.;.;.;NTRK2_HUMAN;.;.;.	V	268;268;268;268;268;268;268;268;112	ENSP00000365387:A268V;ENSP00000365386:A268V;ENSP00000379221:A268V;ENSP00000365381:A268V;ENSP00000306167:A268V;ENSP00000277120:A268V;ENSP00000314586:A268V;ENSP00000352906:A268V;ENSP00000379207:A112V	ENSP00000277120:A268V	A	+	2	0	NTRK2	86529041	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.453000	0.73488	2.627000	0.88993	0.460000	0.39030	GCG	.	.		0.408	NTRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052882.1			T	87339221	C	T	87339221	3	4	254	1	0	0	0	0	1	0	0	0	10716	768	27	1	829	1	NTRK2	9	87339221	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	2730947	87339221	53874210	434	34726										
WNK2	65268	hgsc.bcm.edu	37	chr9	96079837	96079837	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcaggagtggggatgccacgTctgcccccagcgcccggccc	15	17	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:96079837T>C	ENST00000297954.4	+	29	6663	c.6663T>C	c.(6661-6663)cgT>cgC	p.R2221R	WNK2_ENST00000395477.2_Silent_p.R2184R|WNK2_ENST00000356055.3_3'UTR|WNK2_ENST00000471076.1_3'UTR|WNK2_ENST00000395475.2_3'UTR|WNK2_ENST00000349097.3_Silent_p.R1833R|WNK2_ENST00000427277.2_Silent_p.R1796R	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	2221					intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						GGATGCCACGTCTGCCCCCAG	0.637																																					p.R2184R		Atlas-SNP	.											.	WNK2	277	.	0			c.T6552C						.						79	70	73					9																	96079837		2203	4300	6503	SO:0001819	synonymous_variant	65268	exon28			GCCACGTCTGCCC	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"serologically defined colon cancer antigen 43"	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.6663T>C	chr9.hg19:g.96079837T>C		131.0	0.0		96.0	4.0	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Silent	SNP	ENST00000297954.4	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.231|9.231	1.035854|1.035854	0.19590|0.19590	.|.	.|.	ENSG00000165238|ENSG00000165238	ENST00000411624|ENST00000432730;ENST00000448251	.|.	.|.	.|.	5.53|5.53	0.617|0.617	0.17619|0.17619	.|.	.|.	.|.	.|.	.|.	T|T	0.34687|0.34687	0.0906|0.0906	.|.	.|.	.|.	0.23036|0.23036	N|N	0.998394|0.998394	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.28202|0.28202	-1.0051|-1.0051	4|4	.|.	.|.	.|.	.|.	9.2033|9.2033	0.37272|0.37272	0.0:0.4499:0.0:0.5501|0.0:0.4499:0.0:0.5501	.|.	.|.	.|.	.|.	P|A	1676|2180;981	.|.	.|.	S|V	+|+	1|2	0|0	WNK2|WNK2	95119658|95119658	0.878000|0.878000	0.30173|0.30173	0.136000|0.136000	0.22124|0.22124	0.825000|0.825000	0.46686|0.46686	0.410000|0.410000	0.21098|0.21098	-0.118000|-0.118000	0.11851|0.11851	0.528000|0.528000	0.53228|0.53228	TCT|GTC	.	.		0.637	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648		C	96079837	T	C	96079837	2	2	254	1	0	0	0	0	0	0	0	1	17393	1654	58	2		2	WNK2	9	96079837	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	8740616	96079837	45133594	435	34727										
HIATL1	84641	hgsc.bcm.edu	37	chr9	97218607	97218607	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcgtctctcggaatgcagagTcagatcagcaaggtgaggtc	13	9	3	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:97218607T>C	ENST00000375344.3	+	10	1383	c.1114T>C	c.(1114-1116)Tca>Cca	p.S372P	HIATL1_ENST00000428393.2_Intron	NM_032558.2	NP_115947.2	Q5SR56	HIAL1_HUMAN	hippocampus abundant transcript-like 1	372					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|pancreas(1)	11		Acute lymphoblastic leukemia(62;0.136)				GAATGCAGAGTCAGATCAGCA	0.567																																					p.S372P	Pancreas(77;1260 1915 1973 10423)	Atlas-SNP	.											.	HIATL1	31	.	0			c.T1114C						.						115	90	99					9																	97218607		2203	4300	6503	SO:0001583	missense	84641	exon10			GCAGAGTCAGATC	AK027659	CCDS6710.2	9q22.32	2009-12-04			ENSG00000148110	ENSG00000148110			23376	protein-coding gene	gene with protein product							Standard	XM_005252277		Approved	FLJ14753	uc004aur.3	Q5SR56	OTTHUMG00000020265	ENST00000375344.3:c.1114T>C	chr9.hg19:g.97218607T>C	ENSP00000364493:p.Ser372Pro	112.0	0.0		84.0	4.0	NM_032558	B4DUE6|E9PD58|Q3KQT4|Q53GU5|Q8WU95|Q96SM4	Missense_Mutation	SNP	ENST00000375344.3	hg19	CCDS6710.2	.	.	.	.	.	.	.	.	.	.	T	3.671	-0.067489	0.07273	.	.	ENSG00000148110	ENST00000375344;ENST00000277183	T	0.54071	0.59	4.96	1.4	0.22301	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.122256	0.36338	N	0.002646	T	0.17238	0.0414	N	0.01431	-0.87	0.80722	D	1	B	0.06786	0.001	B	0.13407	0.009	T	0.05194	-1.0900	10	0.09338	T	0.73	-1.2852	3.9325	0.09292	0.0:0.3154:0.1895:0.4951	.	372	Q5SR56	HIAL1_HUMAN	P	372;77	ENSP00000364493:S372P	ENSP00000277183:S77P	S	+	1	0	HIATL1	96258428	0.620000	0.27068	1.000000	0.80357	0.993000	0.82548	0.504000	0.22626	0.468000	0.27243	0.533000	0.62120	TCA	.	.		0.567	HIATL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053184.1	NM_032558		C	97218607	T	C	97218607	3	2	254	1	0	0	0	0	1	0	0	0	7107	1667	58	2	1152	2	HIATL1	9	97218607	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	1138770	97218607	43994824	436	34728										
C9orf102	375748	hgsc.bcm.edu	37	chr9	98643510	98643510	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aaggaacccggtttctttatGgacactacatccatggagga	10	9	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:98643510G>A	ENST00000288985.7	+	2	744	c.439G>A	c.(439-441)Gga>Aga	p.G147R	ERCC6L2_ENST00000466840.1_3'UTR	NM_001010895.2	NP_001010895.1	Q5T890	ER6L2_HUMAN	excision repair cross-complementation group 6-like 2	147	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				DNA repair (GO:0006281)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)										GTTTCTTTATGGACACTACAT	0.373																																					p.G147R		Atlas-SNP	.											.	.	.	.	0			c.G439A						.						78	79	79					9																	98643510		2203	4300	6503	SO:0001583	missense	375748	exon2			CTTTATGGACACT	BC022957	CCDS35072.1	9q22.32	2014-03-07	2014-03-07	2012-03-30	ENSG00000182150	ENSG00000182150			26922	protein-coding gene	gene with protein product		615667	"chromosome 9 open reading frame 102", "excision repair cross-complementing rodent repair deficiency, complementation group 6-like 2"	C9orf102			Standard	NM_001010895		Approved	FLJ37706, RAD26L	uc004avt.4	Q5T890	OTTHUMG00000020289	ENST00000288985.7:c.439G>A	chr9.hg19:g.98643510G>A	ENSP00000288985:p.Gly147Arg	96.0	0.0		79.0	4.0	NM_001010895	A4D997|B2RTP8|Q49AM9|Q5T892|Q8N663|Q8N9D0|Q9NPM7	Missense_Mutation	SNP	ENST00000288985.7	hg19	CCDS35072.1	.	.	.	.	.	.	.	.	.	.	G	1.646	-0.515159	0.04200	.	.	ENSG00000182150	ENST00000288985	D	0.92397	-3.03	5.32	2.49	0.30216	DEAD-like helicase (2);SNF2-related (1);	0.740189	0.12278	N	0.483201	T	0.73837	0.3638	N	0.01297	-0.9	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.60989	-0.7153	10	0.16420	T	0.52	-1.7485	4.7574	0.13092	0.3734:0.0:0.4875:0.1391	.	147	Q5T890	RAD26_HUMAN	R	147	ENSP00000288985:G147R	ENSP00000288985:G147R	G	+	1	0	C9orf102	97683331	0.999000	0.42202	0.990000	0.47175	0.841000	0.47740	0.630000	0.24553	0.376000	0.24707	0.591000	0.81541	GGA	.	.		0.373	ERCC6L2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053247.2	NM_001010895		A	98643510	G	A	98643510	3	1	254	1	0	0	0	0	1	0	0	0	2447	1349	47	3	445	3	C9orf102	9	98643510	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1424903	98643510	42569921	437	34729										
KIAA1529	100499483	hgsc.bcm.edu	37	chr9	100080840	100080840	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gaacgtcctgcagcaaaggcGgctgaagcatctctgcacca	11	13	1	1	rs368120179		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:100080840G>T	ENST00000357054.1	+	24	2539	c.1604G>T	c.(1603-1605)cGg>cTg	p.R535L	RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000395220.1_Intron|CCDC180_ENST00000460482.2_3'UTR|CCDC180_ENST00000375202.2_Missense_Mutation_p.R396L|CCDC180_ENST00000411667.2_Missense_Mutation_p.R393L|CCDC180_ENST00000529487.1_Missense_Mutation_p.R396L			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	535						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.R535Q(1)									CAGCAAAGGCGGCTGAAGCAT	0.602																																					p.R396L		Atlas-SNP	.											KIAA1529,colon,carcinoma,0,1	.	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1187T						.						78	63	68					9																	100080840		2203	4300	6503	SO:0001583	missense	0	exon10			AAAGGCGGCTGAA	AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"Behcet's Disease Associated Gene 1"		"KIAA1529", "chromosome 9 open reading frame 174"	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.1604G>T	chr9.hg19:g.100080840G>T	ENSP00000349562:p.Arg535Leu	36.0	0.0		26.0	2.0	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Missense_Mutation	SNP	ENST00000357054.1	hg19		.	.	.	.	.	.	.	.	.	.	G	15.93	2.977491	0.53720	.	.	ENSG00000197816	ENST00000357054;ENST00000375202;ENST00000411667;ENST00000541524;ENST00000529487	T;T;T;T	0.24350	1.86;1.86;1.86;1.86	4.61	4.61	0.57282	.	0.229630	0.36409	N	0.002610	T	0.48822	0.1521	M	0.74258	2.255	0.20307	N	0.999916	D;D;D;D	0.89917	0.962;1.0;1.0;1.0	B;D;D;D	0.91635	0.358;0.999;0.999;0.999	T	0.34925	-0.9809	10	0.37606	T	0.19	-25.4457	13.1516	0.59492	0.0:0.0:1.0:0.0	.	393;535;396;535	F5H149;B7ZMG3;Q9P1Z9-2;Q9P1Z9	.;.;.;CI174_HUMAN	L	535;396;393;419;396	ENSP00000349562:R535L;ENSP00000364348:R396L;ENSP00000414000:R393L;ENSP00000434727:R396L	ENSP00000349562:R535L	R	+	2	0	C9orf174	99120661	0.860000	0.29831	0.335000	0.25508	0.014000	0.08584	3.458000	0.53014	2.548000	0.85928	0.563000	0.77884	CGG	.	.		0.602	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893		T	100080840	G	T	100080840	3	4	254	1	0	0	0	0	1	0	0	0	8249	1116	39	1	1654	1	KIAA1529	9	100080840	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1437330	100080840	41132591	438	34730										
C9orf156	51531	hgsc.bcm.edu	37	chr9	100667081	100667081	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	acaggctcagaagccggcttGatcctcagcacctctgcaaa	9	14	3	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:100667081G>T	ENST00000375119.3	-	5	1336	c.1260C>A	c.(1258-1260)atC>atA	p.I420I		NM_016481.3	NP_057565.3	Q9BU70	NAP1_HUMAN	chromosome 9 open reading frame 156	420					viral process (GO:0016032)		hydrolase activity (GO:0016787)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|prostate(1)|skin(1)	13		Acute lymphoblastic leukemia(62;0.158)				AAGCCGGCTTGATCCTCAGCA	0.522																																					p.I420I		Atlas-SNP	.											.	C9orf156	35	.	0			c.C1260A						.						111	104	106					9																	100667081		2203	4300	6503	SO:0001819	synonymous_variant	51531	exon5			CGGCTTGATCCTC	AK023069	CCDS6730.1	9q31.1	2011-03-02			ENSG00000136932	ENSG00000136932			30967	protein-coding gene	gene with protein product	"Nef (lentivirus myristoylated factor) associated protein 1"						Standard	NM_016481		Approved	HSPC219, NAP1	uc004axv.1	Q9BU70	OTTHUMG00000021007	ENST00000375119.3:c.1260C>A	chr9.hg19:g.100667081G>T		122.0	0.0		106.0	6.0	NM_016481	Q5T113|Q86SK0|Q9NXJ7|Q9P0Q7	Silent	SNP	ENST00000375119.3	hg19	CCDS6730.1																																																																																			.	.		0.522	C9orf156-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055401.1	NM_016481		T	100667081	G	T	100667081	2	4	254	1	0	0	0	0	0	0	0	1	2467	1280	45	3		3	C9orf156	9	100667081	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	586241	100667081	40546350	439	34731										
TEX10	54881	hgsc.bcm.edu	37	chr9	103090232	103090232	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gccagccaacgggataacacTttactacgatatcttagaaa	7	10	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:103090232T>C	ENST00000374902.4	-	8	1814	c.1638A>G	c.(1636-1638)aaA>aaG	p.K546K	TEX10_ENST00000535814.1_Silent_p.K549K	NM_017746.3	NP_060216.2	Q9NXF1	TEX10_HUMAN	testis expressed 10	546						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|MLL1 complex (GO:0071339)				NS(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	38		Acute lymphoblastic leukemia(62;0.0527)		OV - Ovarian serous cystadenocarcinoma(323;0.157)		GGGATAACACTTTACTACGAT	0.348																																					p.K549K		Atlas-SNP	.											.	TEX10	99	.	0			c.A1647G						.						79	67	71					9																	103090232		2203	4300	6503	SO:0001819	synonymous_variant	54881	exon8			TAACACTTTACTA	AB060968	CCDS6748.1, CCDS55330.1	9q31.1	2012-05-02	2007-03-13		ENSG00000136891	ENSG00000136891			25988	protein-coding gene	gene with protein product			"testis expressed gene 10", "testis expressed sequence 10"			12477932	Standard	NM_017746		Approved	FLJ20287, bA208F1.2, Ipi1	uc004bas.3	Q9NXF1	OTTHUMG00000020366	ENST00000374902.4:c.1638A>G	chr9.hg19:g.103090232T>C		113.0	0.0		113.0	5.0	NM_001161584	B4DYV2|Q5T722|Q5T723|Q8NCN8|Q8TDY0	Silent	SNP	ENST00000374902.4	hg19	CCDS6748.1																																																																																			.	.		0.348	TEX10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053416.1	NM_017746		C	103090232	T	C	103090232	2	2	254	1	0	0	0	0	0	0	0	1	15787	1606	56	2		2	TEX10	9	103090232	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	2423151	103090232	38123199	440	34732										
CYLC2	1539	hgsc.bcm.edu	37	chr9	105767096	105767096	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gccaggaggcagcctctcaaAccaactcgtactgtcgaggt	11	13	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:105767096A>G	ENST00000374798.3	+	4	370	c.300A>G	c.(298-300)aaA>aaG	p.K100K	CYLC2_ENST00000487798.1_Silent_p.K100K	NM_001340.3	NP_001331.1	Q14093	CYLC2_HUMAN	cylicin, basic protein of sperm head cytoskeleton 2	100	31 X 3 AA repeats of K-K-X.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(14)|ovary(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)	41		all_hematologic(171;0.125)				AGCCTCTCAAACCAACTCGTA	0.378																																					p.K100K		Atlas-SNP	.											CYLC2,NS,carcinoma,0,1	CYLC2	109	.	0			c.A300G						.						60	60	60					9																	105767096		2203	4300	6503	SO:0001819	synonymous_variant	1539	exon4			TCTCAAACCAACT	Z46788	CCDS35085.1	9q31.2	2008-07-21			ENSG00000155833	ENSG00000155833			2583	protein-coding gene	gene with protein product		604035				7737358	Standard	NM_001340		Approved		uc004bbs.2	Q14093	OTTHUMG00000020396	ENST00000374798.3:c.300A>G	chr9.hg19:g.105767096A>G		65.0	0.0		46.0	2.0	NM_001340	B2R8F4|Q5VVJ9	Silent	SNP	ENST00000374798.3	hg19	CCDS35085.1																																																																																			.	.		0.378	CYLC2-001	KNOWN	alternative_3_UTR|NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053463.3	NM_001340		G	105767096	A	G	105767096	2	3	254	1	0	0	0	0	0	0	0	1	4144	40	2	2		2	CYLC2	9	105767096	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	2676864	105767096	35446335	441	34733										
SMC2	10592	hgsc.bcm.edu	37	chr9	106877083	106877083	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gaattagtggctggagaacgActctacaatgttgtagtaga	12	5	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:106877083A>G	ENST00000286398.7	+	13	1932	c.1644A>G	c.(1642-1644)cgA>cgG	p.R548R	SMC2_ENST00000374793.3_Silent_p.R548R|SMC2_ENST00000303219.8_Silent_p.R548R|SMC2_ENST00000374787.3_Silent_p.R548R	NM_001042551.1|NM_001265602.1|NM_006444.2	NP_001036016.1|NP_001252531.1|NP_006435.2	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2	548	Flexible hinge.				kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(14)|ovary(5)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	48						CTGGAGAACGACTCTACAATG	0.338																																					p.R548R		Atlas-SNP	.											SMC2L1,NS,carcinoma,0,2	SMC2	127	.	0			c.A1644G						.						91	87	89					9																	106877083		2203	4300	6503	SO:0001819	synonymous_variant	10592	exon13			AGAACGACTCTAC	AF092563	CCDS35086.1	9q31.1	2008-05-14	2006-07-06	2006-07-06	ENSG00000136824	ENSG00000136824		"Structural maintenance of chromosomes proteins"	14011	protein-coding gene	gene with protein product		605576	"SMC2 (structural maintenance of chromosomes 2, yeast)-like 1", "SMC2 structural maintenance of chromosomes 2-like 1 (yeast)"	SMC2L1		9789013	Standard	NM_006444		Approved	hCAP-E, CAP-E	uc011lvl.2	O95347	OTTHUMG00000020401	ENST00000286398.7:c.1644A>G	chr9.hg19:g.106877083A>G		99.0	2.0		81.0	4.0	NM_006444	Q6IEE0|Q9P1P2	Silent	SNP	ENST00000286398.7	hg19	CCDS35086.1																																																																																			.	.		0.338	SMC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053470.1			G	106877083	A	G	106877083	2	3	254	1	0	0	0	0	0	0	0	1	14798	262	10	2		2	SMC2	9	106877083	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	1109987	106877083	34336348	442	34734										
OR13D1	286365	hgsc.bcm.edu	37	chr9	107457666	107457666	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	caatgttaaatcccatcatcTatagcctcaggaataaagag	6	9	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:107457666T>C	ENST00000318763.5	+	1	1007	c.964T>C	c.(964-966)Tat>Cat	p.Y322H		NM_001004484.1	NP_001004484.1	Q8NGV5	O13D1_HUMAN	olfactory receptor, family 13, subfamily D, member 1	322						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(4)|lung(10)|ovary(1)|prostate(2)|skin(2)	19						TCCCATCATCTATAGCCTCAG	0.388																																					p.Y322H		Atlas-SNP	.											.	OR13D1	42	.	0			c.T964C						.						87	90	89					9																	107457666		2203	4300	6503	SO:0001583	missense	286365	exon1			ATCATCTATAGCC		CCDS35094.1	9q31.1	2013-09-24			ENSG00000179055	ENSG00000179055		"GPCR / Class A : Olfactory receptors"	14695	protein-coding gene	gene with protein product							Standard	NM_001004484		Approved		uc011lvs.2	Q8NGV5	OTTHUMG00000020412	ENST00000318763.5:c.964T>C	chr9.hg19:g.107457666T>C	ENSP00000317357:p.Tyr322His	137.0	0.0		90.0	4.0	NM_001004484	B9EIS1|Q6IFL1	Missense_Mutation	SNP	ENST00000318763.5	hg19	CCDS35094.1	.	.	.	.	.	.	.	.	.	.	T	12.31	1.899063	0.33535	.	.	ENSG00000179055	ENST00000318763	T	0.61859	0.07	3.65	3.65	0.41850	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41294	D	0.000901	T	0.76659	0.4018	M	0.92026	3.265	0.41997	D	0.990879	D	0.76494	0.999	D	0.67103	0.949	T	0.80317	-0.1433	10	0.87932	D	0	.	8.5813	0.33630	0.0:0.0:0.0:1.0	.	322	Q8NGV5	O13D1_HUMAN	H	322	ENSP00000317357:Y322H	ENSP00000317357:Y322H	Y	+	1	0	OR13D1	106497487	1.000000	0.71417	0.264000	0.24511	0.100000	0.18952	5.656000	0.67988	1.515000	0.48885	0.418000	0.28097	TAT	.	.		0.388	OR13D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053483.1			C	107457666	T	C	107457666	3	2	254	1	0	0	0	0	1	0	0	0	10949	1522	53	2	966	2	OR13D1	9	107457666	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	580583	107457666	33755765	443	34735										
RAD23B	5887	hgsc.bcm.edu	37	chr9	110045933	110045933	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcaggtcaccctgaagacccTccagcagcagaccttcaaga	9	15	2	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:110045933T>C	ENST00000358015.3	+	1	374	c.23T>C	c.(22-24)cTc>cCc	p.L8P	RAD23B_ENST00000416373.2_5'Flank	NM_001244713.1|NM_002874.4	NP_001231642.1|NP_002865.1	P54727	RD23B_HUMAN	RAD23 homolog B (S. cerevisiae)	8	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				DNA repair (GO:0006281)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage recognition (GO:0000715)|nucleotide-excision repair, DNA damage removal (GO:0000718)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|XPC complex (GO:0071942)	damaged DNA binding (GO:0003684)|polyubiquitin binding (GO:0031593)|single-stranded DNA binding (GO:0003697)			breast(3)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14						CTGAAGACCCTCCAGCAGCAG	0.756								Direct reversal of damage;Nucleotide excision repair (NER)																													p.L8P		Atlas-SNP	.											.	RAD23B	31	.	0			c.T23C						.						9	7	8					9																	110045933		2060	4010	6070	SO:0001583	missense	5887	exon1			AGACCCTCCAGCA		CCDS6769.1, CCDS59138.1	9q31.2	2008-07-21	2001-11-28		ENSG00000119318	ENSG00000119318			9813	protein-coding gene	gene with protein product	"XP-C repair complementing protein", "XP-C repair complementing complex 58 kDa"	600062	"RAD23 (S. cerevisiae) homolog B"			7851894, 8168482	Standard	NM_002874		Approved	HHR23B, P58, HR23B	uc004bde.3	P54727	OTTHUMG00000020446	ENST00000358015.3:c.23T>C	chr9.hg19:g.110045933T>C	ENSP00000350708:p.Leu8Pro	76.0	0.0		39.0	4.0	NM_002874	B3KWK8|G5E9P0|Q7Z5K8|Q8WUB0	Missense_Mutation	SNP	ENST00000358015.3	hg19	CCDS6769.1	.	.	.	.	.	.	.	.	.	.	t	11.88	1.769288	0.31320	.	.	ENSG00000119318	ENST00000419616;ENST00000358015	T;T	0.75821	-0.97;-0.97	4.3	4.3	0.51218	Ubiquitin supergroup (1);Ubiquitin (2);	0.000000	0.64402	D	0.000004	D	0.88998	0.6590	H	0.95402	3.665	0.80722	D	1	D;D	0.69078	0.997;0.993	D;D	0.81914	0.995;0.995	D	0.91075	0.4895	10	0.87932	D	0	-6.4507	11.0015	0.47609	0.0:0.0:0.0:1.0	.	8;8	B4DEA3;P54727	.;RD23B_HUMAN	P	8	ENSP00000416868:L8P;ENSP00000350708:L8P	ENSP00000350708:L8P	L	+	2	0	RAD23B	109085754	1.000000	0.71417	0.996000	0.52242	0.045000	0.14185	3.417000	0.52714	1.575000	0.49775	0.451000	0.29950	CTC	.	.		0.756	RAD23B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053548.1	NM_002874		C	110045933	T	C	110045933	3	2	254	1	0	0	0	0	1	0	0	0	12998	1551	54	2	25	2	RAD23B	9	110045933	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	2588267	110045933	31167498	444	34736										
IKBKAP	8518	hgsc.bcm.edu	37	chr9	111665171	111665171	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgcatggataaggaaaccgaAcaggaaatccaccagagttc	10	9	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:111665171A>G	ENST00000374647.5	-	16	2109	c.1802T>C	c.(1801-1803)gTt>gCt	p.V601A	IKBKAP_ENST00000537196.1_Missense_Mutation_p.V252A	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein	601					chromatin organization (GO:0006325)|immune response (GO:0006955)|positive regulation of cell migration (GO:0030335)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	phosphorylase kinase regulator activity (GO:0008607)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						AGGAAACCGAACAGGAAATCC	0.453																																					p.V601A		Atlas-SNP	.											.	IKBKAP	122	.	0			c.T1802C						.						115	114	114					9																	111665171		2203	4300	6503	SO:0001583	missense	8518	exon16			AACCGAACAGGAA	AF044195	CCDS6773.1	9q31	2014-09-17	2003-12-02		ENSG00000070061	ENSG00000070061		"Elongator acetyltransferase complex subunits"	5959	protein-coding gene	gene with protein product	"elongator acetyltransferase complex subunit 1"	603722	"dysautonomia (Riley-Day syndrome, hereditary sensory autonomic neuropathy type III)"	DYS		9751059, 11179008	Standard	NM_003640		Approved	IKAP, TOT1, ELP1, IKI3	uc004bdm.4	O95163	OTTHUMG00000020465	ENST00000374647.5:c.1802T>C	chr9.hg19:g.111665171A>G	ENSP00000363779:p.Val601Ala	175.0	0.0		120.0	6.0	NM_003640	Q5JSV2|Q9H327|Q9UG87	Missense_Mutation	SNP	ENST00000374647.5	hg19	CCDS6773.1	.	.	.	.	.	.	.	.	.	.	A	19.33	3.807873	0.70797	.	.	ENSG00000070061	ENST00000374647;ENST00000537196	T;T	0.26957	1.7;1.7	5.52	5.52	0.82312	.	0.267708	0.35970	N	0.002871	T	0.31199	0.0789	L	0.60904	1.88	0.23528	N	0.99749	P	0.45283	0.855	P	0.44447	0.45	T	0.22941	-1.0202	10	0.41790	T	0.15	-7.0671	13.5958	0.61988	1.0:0.0:0.0:0.0	.	601	O95163	ELP1_HUMAN	A	601;252	ENSP00000363779:V601A;ENSP00000439367:V252A	ENSP00000363779:V601A	V	-	2	0	IKBKAP	110704992	0.994000	0.37717	0.074000	0.20217	0.751000	0.42716	7.128000	0.77217	2.096000	0.63516	0.454000	0.30748	GTT	.	.		0.453	IKBKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053574.1			G	111665171	A	G	111665171	3	3	254	1	0	0	0	0	1	0	0	0	7619	43	2	2	2284	2	IKBKAP	9	111665171	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	1619238	111665171	29548260	445	34737										
IKBKAP	8518	hgsc.bcm.edu	37	chr9	111685163	111685163	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttgtctgccttctgatccatGgaactgtgtctccttcctac	7	13	3	1	rs202179488		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:111685163G>A	ENST00000374647.5	-	6	818	c.511C>T	c.(511-513)Cat>Tat	p.H171Y	IKBKAP_ENST00000537196.1_Intron	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein	171					chromatin organization (GO:0006325)|immune response (GO:0006955)|positive regulation of cell migration (GO:0030335)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	phosphorylase kinase regulator activity (GO:0008607)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						TCTGATCCATGGAACTGTGTC	0.408																																					p.H171Y		Atlas-SNP	.											.	IKBKAP	122	.	0			c.C511T						.						214	188	196					9																	111685163		2203	4300	6503	SO:0001583	missense	8518	exon6			ATCCATGGAACTG	AF044195	CCDS6773.1	9q31	2014-09-17	2003-12-02		ENSG00000070061	ENSG00000070061		"Elongator acetyltransferase complex subunits"	5959	protein-coding gene	gene with protein product	"elongator acetyltransferase complex subunit 1"	603722	"dysautonomia (Riley-Day syndrome, hereditary sensory autonomic neuropathy type III)"	DYS		9751059, 11179008	Standard	NM_003640		Approved	IKAP, TOT1, ELP1, IKI3	uc004bdm.4	O95163	OTTHUMG00000020465	ENST00000374647.5:c.511C>T	chr9.hg19:g.111685163G>A	ENSP00000363779:p.His171Tyr	110.0	0.0		100.0	4.0	NM_003640	Q5JSV2|Q9H327|Q9UG87	Missense_Mutation	SNP	ENST00000374647.5	hg19	CCDS6773.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.773896	0.90108	.	.	ENSG00000070061	ENST00000374647	T	0.30182	1.54	5.62	5.62	0.85841	.	0.044217	0.85682	D	0.000000	T	0.64405	0.2595	M	0.90542	3.125	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.71431	-0.4595	10	0.72032	D	0.01	-9.2614	17.1551	0.86790	0.0:0.0:1.0:0.0	.	171	O95163	ELP1_HUMAN	Y	171	ENSP00000363779:H171Y	ENSP00000363779:H171Y	H	-	1	0	IKBKAP	110724984	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.088000	0.94132	2.639000	0.89480	0.650000	0.86243	CAT	.	G|0.999;C|0.001		0.408	IKBKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053574.1			A	111685163	G	A	111685163	3	1	254	1	0	0	0	0	1	0	0	0	7619	1348	47	3	3615	3	IKBKAP	9	111685163	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	19992	111685163	29528268	446	34738										
EPB41L4B	54566	hgsc.bcm.edu	37	chr9	112013790	112013790	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gctgctatcactgggttgctTgctataaaggaaaaacagaa	10	7	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:112013790T>C	ENST00000374566.3	-	13	1798	c.1281A>G	c.(1279-1281)gcA>gcG	p.A427A	EPB41L4B_ENST00000374557.4_Splice_Site_p.A427A	NM_019114.3	NP_061987.3	Q9H329	E41LB_HUMAN	erythrocyte membrane protein band 4.1 like 4B	427					actomyosin structure organization (GO:0031032)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)	structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CTGGGTTGCTTGCTATAAAGG	0.428																																					p.A427A		Atlas-SNP	.											.	EPB41L4B	111	.	0			c.A1281G						.						145	152	150					9																	112013790		1958	4155	6113	SO:0001630	splice_region_variant	54566	exon13			GTTGCTTGCTATA	AB032179	CCDS43859.1, CCDS43860.1	9q22.1-q22.3	2008-02-05			ENSG00000095203	ENSG00000095203			19818	protein-coding gene	gene with protein product		610340				10783258	Standard	NM_018424		Approved	EHM2	uc004bdz.1	Q9H329	OTTHUMG00000020470	ENST00000374566.3:c.1280-1A>G	chr9.hg19:g.112013790T>C		135.0	0.0		121.0	5.0	NM_019114	Q5T4G5|Q5T4G6|Q9H328|Q9P2V3	Silent	SNP	ENST00000374566.3	hg19	CCDS43859.1																																																																																			.	.		0.428	EPB41L4B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053592.1	NM_018424	Silent	C	112013790	T	C	112013790	5	2	254	1	0	0	0	0	0	0	1	0	5158	1826	63	2	1629	2	EPB41L4B	9	112013790	Splice_Site	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	328627	112013790	29199641	447	34739										
AKAP2	11217	hgsc.bcm.edu	37	chr9	112899145	112899145	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aatactgcattagaaaagtgAggccttcagaggagatgctg	12	6	1	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:112899145A>G	ENST00000259318.7	+	2	835	c.628A>G	c.(628-630)Agg>Ggg	p.R210G	AKAP2_ENST00000374525.1_Missense_Mutation_p.R299G|AKAP2_ENST00000434623.2_Missense_Mutation_p.R299G|PALM2-AKAP2_ENST00000374530.3_Missense_Mutation_p.R441G|PALM2-AKAP2_ENST00000302798.7_Missense_Mutation_p.R441G|AKAP2_ENST00000555236.1_Missense_Mutation_p.R441G|AKAP2_ENST00000510514.5_Missense_Mutation_p.R441G	NM_001136562.2	NP_001130034.1	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2	210										breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	33						TAGAAAAGTGAGGCCTTCAGA	0.512																																					p.R441G		Atlas-SNP	.											.	PALM2-AKAP2	117	.	0			c.A1321G						.						66	68	67					9																	112899145		2203	4300	6503	SO:0001583	missense	445815	exon8			AAAGTGAGGCCTT	AB023137	CCDS43861.1, CCDS48003.1, CCDS56581.1	9q31.3	2009-10-16			ENSG00000241978	ENSG00000241978		"A-kinase anchor proteins"	372	protein-coding gene	gene with protein product	"protein kinase A2"	604582		PRKA2		10231032	Standard	NM_001136562		Approved	AKAP-KL, KIAA0920, DKFZp564L0716		Q9Y2D5	OTTHUMG00000156811	ENST00000259318.7:c.628A>G	chr9.hg19:g.112899145A>G	ENSP00000259318:p.Arg210Gly	130.0	0.0		93.0	4.0	NM_007203	B1ALX9|B2RTU4|B3KQ00|B4DTZ2|B7ZW07|B9EJB5|Q9UG26	Missense_Mutation	SNP	ENST00000259318.7	hg19	CCDS48003.1	.	.	.	.	.	.	.	.	.	.	A	11.08	1.533409	0.27387	.	.	ENSG00000157654;ENSG00000157654;ENSG00000241978;ENSG00000241978;ENSG00000241978;ENSG00000241978;ENSG00000241978;ENSG00000241978	ENST00000374530;ENST00000302798;ENST00000555236;ENST00000510514;ENST00000434623;ENST00000374525;ENST00000480388;ENST00000259318	T;T;T;T;T;T;T;T	0.51325	0.71;0.71;0.71;0.71;0.71;0.71;0.71;0.71	6.16	3.81	0.43845	.	0.044099	0.85682	D	0.000000	T	0.66157	0.2761	M	0.70275	2.135	0.49798	D	0.999821	D;D;D;D;D;D;D;D	0.89917	0.999;1.0;0.993;1.0;0.999;0.996;0.996;0.993	D;D;P;D;D;P;P;P	0.85130	0.996;0.997;0.782;0.997;0.994;0.892;0.892;0.782	T	0.67484	-0.5659	10	0.72032	D	0.01	-29.5922	12.6715	0.56870	0.7178:0.2822:0.0:0.0	.	210;299;293;299;300;441;441;259	Q9Y2D5;Q9Y2D5-7;B4E2K2;Q9Y2D5-5;B1ALY1;Q9Y2D5-6;Q9Y2D5-4;C9JVY5	AKAP2_HUMAN;.;.;.;.;.;.;.	G	441;441;441;441;299;299;259;210	ENSP00000363654:R441G;ENSP00000305861:R441G;ENSP00000451476:R441G;ENSP00000421522:R441G;ENSP00000404782:R299G;ENSP00000363649:R299G;ENSP00000419268:R259G;ENSP00000259318:R210G	ENSP00000259318:R210G	R	+	1	2	PALM2-AKAP2;AKAP2	111938966	1.000000	0.71417	1.000000	0.80357	0.032000	0.12392	3.660000	0.54496	0.544000	0.28883	-0.319000	0.08680	AGG	.	.		0.512	AKAP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346067.3	NM_001004065		G	112899145	A	G	112899145	3	3	254	1	0	0	0	0	1	0	0	0	451	295	11	2	901	2	AKAP2	9	112899145	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	885355	112899145	28314286	448	34740										
KIAA0368	23392	hgsc.bcm.edu	37	chr9	114172333	114172333	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aaacttaccttatttgtttcTttactggaaggtattctact	5	7	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:114172333T>C	ENST00000338205.5	-	22	2757	c.2538A>G	c.(2536-2538)aaA>aaG	p.K846K	RNA5SP294_ENST00000411306.1_RNA|KIAA0368_ENST00000259335.4_Silent_p.K1024K|KIAA0368_ENST00000374378.3_5'Flank			Q5VYK3	ECM29_HUMAN	KIAA0368	852					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)				NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						TATTTGTTTCTTTACTGGAAG	0.353																																					p.K1024K		Atlas-SNP	.											.	KIAA0368	144	.	0			c.A3072G						.						24	23	23					9																	114172333		1812	4073	5885	SO:0001819	synonymous_variant	23392	exon24			TGTTTCTTTACTG	AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"ECM29 homolog (S. cerevisiae)"					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.2538A>G	chr9.hg19:g.114172333T>C		109.0	0.0		122.0	5.0	NM_001080398	O15074|Q8WU82	Silent	SNP	ENST00000338205.5	hg19																																																																																				.	.		0.353	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686		C	114172333	T	C	114172333	2	2	254	1	0	0	0	0	0	0	0	1	8180	1606	56	2		2	KIAA0368	9	114172333	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	1273188	114172333	27041098	449	34741										
C9orf84	158401	hgsc.bcm.edu	37	chr9	114480520	114480520	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctctaattgttaccagaagaTgtaagagagcggcatgcttg	11	7	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:114480520T>C	ENST00000318737.4	-	14	2116	c.1988A>G	c.(1987-1989)cAt>cGt	p.H663R	C9orf84_ENST00000394777.4_Intron|C9orf84_ENST00000374287.3_Missense_Mutation_p.H663R|C9orf84_ENST00000394779.3_Missense_Mutation_p.H624R	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	663										breast(1)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(10)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						TACCAGAAGATGTAAGAGAGC	0.333																																					p.H663R		Atlas-SNP	.											.	C9orf84	207	.	0			c.A1988G						.						106	99	101					9																	114480520		2203	4300	6503	SO:0001583	missense	158401	exon14			AGAAGATGTAAGA	AL833535	CCDS6781.3, CCDS43863.1	9q32	2012-03-16			ENSG00000165181	ENSG00000165181			26535	protein-coding gene	gene with protein product							Standard	XM_005251738		Approved	FLJ32779	uc004bfr.3	Q5VXU9	OTTHUMG00000020495	ENST00000318737.4:c.1988A>G	chr9.hg19:g.114480520T>C	ENSP00000322108:p.His663Arg	133.0	0.0		80.0	4.0	NM_173521	A2A2V3|Q2M1H8|Q96M73	Missense_Mutation	SNP	ENST00000318737.4	hg19	CCDS6781.3	.	.	.	.	.	.	.	.	.	.	T	14.69	2.611816	0.46631	.	.	ENSG00000165181	ENST00000394779;ENST00000394778;ENST00000374287;ENST00000318737	T;T;T	0.07567	3.18;3.19;3.19	5.25	5.25	0.73442	.	0.000000	0.52532	D	0.000062	T	0.19927	0.0479	L	0.34521	1.04	0.32601	N	0.525949	D;D	0.89917	1.0;0.992	D;P	0.85130	0.997;0.868	T	0.07829	-1.0752	10	0.87932	D	0	-9.0295	15.1394	0.72599	0.0:0.0:0.0:1.0	.	663;624	Q5VXU9;A2A2V3	CI084_HUMAN;.	R	624;277;663;663	ENSP00000378259:H624R;ENSP00000363405:H663R;ENSP00000322108:H663R	ENSP00000322108:H663R	H	-	2	0	C9orf84	113520341	1.000000	0.71417	1.000000	0.80357	0.116000	0.19942	5.371000	0.66150	1.987000	0.57996	0.482000	0.46254	CAT	.	.		0.333	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521		C	114480520	T	C	114480520	3	2	254	1	0	0	0	0	1	0	0	0	2502	1464	51	2	2398	2	C9orf84	9	114480520	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	308187	114480520	26732911	450	34742										
PRPF4	9128	hgsc.bcm.edu	37	chr9	116053881	116053881	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcctagatatttcttccgatGggcagctcatagccacttgc	9	12	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:116053881G>A	ENST00000374198.4	+	14	1612	c.1510G>A	c.(1510-1512)Ggg>Agg	p.G504R	PRPF4_ENST00000374199.4_Missense_Mutation_p.G503R	NM_001244926.1|NM_004697.4	NP_001231855.1|NP_004688.2	O43172	PRP4_HUMAN	pre-mRNA processing factor 4	504					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U4/U6 snRNP (GO:0071001)				NS(1)|breast(2)|endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|prostate(2)	23						TTCTTCCGATGGGCAGCTCAT	0.512																																					p.G504R		Atlas-SNP	.											.	PRPF4	56	.	0			c.G1510A						.						95	87	90					9																	116053881		2203	4300	6503	SO:0001583	missense	9128	exon14			TCCGATGGGCAGC	AF001687	CCDS6791.1, CCDS59142.1	9q31-q33	2013-10-03	2013-10-03		ENSG00000136875	ENSG00000136875		"WD repeat domain containing"	17349	protein-coding gene	gene with protein product	"PRP4/STK/WD splicing factor", "U4/U6 small nuclear ribonucleoprotein Prp4"	607795	"PRP4 pre-mRNA processing factor 4 homolog (yeast)"			9257651, 9404889	Standard	NM_004697		Approved	Prp4p, HPRP4, HPRP4P, PRP4, SNRNP60	uc004bgx.3	O43172	OTTHUMG00000020517	ENST00000374198.4:c.1510G>A	chr9.hg19:g.116053881G>A	ENSP00000363313:p.Gly504Arg	135.0	0.0		78.0	4.0	NM_004697	O43445|O43864|Q5T1M8|Q96DG2|Q96IK4	Missense_Mutation	SNP	ENST00000374198.4	hg19	CCDS6791.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.893442	0.91889	.	.	ENSG00000136875	ENST00000374199;ENST00000374198	T;T	0.65549	-0.16;-0.16	5.8	5.8	0.92144	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.097634	0.64402	D	0.000001	D	0.84151	0.5409	M	0.93978	3.48	0.80722	D	1	D;D	0.63880	0.987;0.993	D;D	0.63703	0.909;0.917	D	0.87581	0.2484	10	0.72032	D	0.01	.	19.0588	0.93078	0.0:0.0:1.0:0.0	.	519;504	Q59EL4;O43172	.;PRP4_HUMAN	R	503;504	ENSP00000363315:G503R;ENSP00000363313:G504R	ENSP00000363313:G504R	G	+	1	0	PRPF4	115093702	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	9.102000	0.94226	2.744000	0.94065	0.655000	0.94253	GGG	.	.		0.512	PRPF4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053708.2	NM_004697		A	116053881	G	A	116053881	3	1	254	1	0	0	0	0	1	0	0	0	12582	1348	47	3	1564	3	PRPF4	9	116053881	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1573361	116053881	25159550	451	34743										
COL27A1	85301	hgsc.bcm.edu	37	chr9	117068856	117068856	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggaggagagatctttaaaacCttacactacctcagcaacct	7	11	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:117068856C>A	ENST00000356083.3	+	58	5386	c.4995C>A	c.(4993-4995)acC>acA	p.T1665T		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	1665	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						TCTTTAAAACCTTACACTACC	0.567											OREG0019417	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T1665T		Atlas-SNP	.											.	COL27A1	200	.	0			c.C4995A						.						77	77	77					9																	117068856		2203	4300	6503	SO:0001819	synonymous_variant	85301	exon58			TAAAACCTTACAC	AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"Collagens"	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.4995C>A	chr9.hg19:g.117068856C>A		77.0	0.0	1478	84.0	4.0	NM_032888	Q66K43|Q96JF7	Silent	SNP	ENST00000356083.3	hg19	CCDS6802.1																																																																																			.	.		0.567	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888		A	117068856	C	A	117068856	2	1	254	1	0	0	0	0	0	0	0	1	3687	668	24	3		3	COL27A1	9	117068856	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1014975	117068856	24144575	452	34744										
FBXW2	26190	hgsc.bcm.edu	37	chr9	123526947	123526947	+	Missense_Mutation	SNP	C	C	T													0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tccattcagccaggatgcttCgcctgccaggaagcttgagc					rs374464211		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:123526947C>T	ENST00000608872.1	-	8	1442	c.1255G>A	c.(1255-1257)Gaa>Aaa	p.E419K	FBXW2_ENST00000493559.1_Intron|FBXW2_ENST00000340778.5_Missense_Mutation_p.E354K	NM_012164.3	NP_036296.2	Q9UKT8	FBXW2_HUMAN	F-box and WD repeat domain containing 2	419					cellular protein modification process (GO:0006464)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	ubiquitin-protein transferase activity (GO:0004842)			ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	4						CAGGATGCTTCGCCTGCCAGG	0.542																																					p.E419K		Atlas-SNP	.											.	FBXW2	34	.	0			c.G1255A						.	C	LYS/GLU	1,4167		0,1,2083	127	137	134		1255	4.9	1	9		134	0,8458		0,0,4229	no	missense	FBXW2	NM_012164.3	56	0,1,6312	TT,TC,CC		0.0,0.024,0.0079	benign	419/455	123526947	1,12625	2084	4229	6313	SO:0001583	missense	26190	exon8			ATGCTTCGCCTGC	AF129531	CCDS43872.1	9q34	2013-01-09	2007-02-08		ENSG00000119402	ENSG00000119402		"F-boxes / WD-40 domains", "WD repeat domain containing"	13608	protein-coding gene	gene with protein product		609071	"F-box and WD-40 domain protein 2"			10531035, 10828603	Standard	NM_012164		Approved	FBW2, Md6, Fwd2	uc004bkm.1	Q9UKT8	OTTHUMG00000020576	ENST00000608872.1:c.1255G>A	chr9.hg19:g.123526947C>T	ENSP00000476369:p.Glu419Lys	115.0	0.0		95.0	5.0	NM_012164	B3KRL8|Q4VXH2|Q7Z4V6|Q8WV51|Q9HA09|Q9UKA3	Missense_Mutation	SNP	ENST00000608872.1	hg19	CCDS43872.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.000785	0.74818	2.4E-4	0.0	ENSG00000119402	ENST00000373926;ENST00000340778;ENST00000444833	T;T	0.80480	0.29;-1.38	4.95	4.95	0.65309	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.106728	0.64402	D	0.000005	T	0.66386	0.2784	N	0.22421	0.69	0.53688	D	0.999978	P;P;B	0.43352	0.774;0.804;0.428	B;B;B	0.29716	0.106;0.039;0.027	T	0.74426	-0.3669	10	0.72032	D	0.01	-8.1105	16.037	0.80638	0.0:1.0:0.0:0.0	.	354;419;419	Q9UKT8-2;B2RAW3;Q9UKT8	.;.;FBXW2_HUMAN	K	419;354;419	ENSP00000363036:E419K;ENSP00000341161:E354K	ENSP00000341161:E354K	E	-	1	0	FBXW2	122566768	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.978000	0.70501	2.447000	0.82792	0.563000	0.77884	GAA	.	.		0.542	FBXW2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053834.2			T	123526947	C	T	123526947	3	4	254	1	0	0	0	0	1	0	0	0	5774	893	31	1	113	1	FBXW2	9	123526947	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	6458091	123526947	17686484	453	34745	179	2								
FBXW2	26190	hgsc.bcm.edu	37	chr9	123526956	123526956	+	Missense_Mutation	SNP	G	G	T													0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccaggatgcttcgcctgccaGgaagcttgagcctctctttg							TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:123526956G>T	ENST00000608872.1	-	8	1433	c.1246C>A	c.(1246-1248)Ctg>Atg	p.L416M	FBXW2_ENST00000493559.1_Intron|FBXW2_ENST00000340778.5_Missense_Mutation_p.L351M	NM_012164.3	NP_036296.2	Q9UKT8	FBXW2_HUMAN	F-box and WD repeat domain containing 2	416					cellular protein modification process (GO:0006464)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	ubiquitin-protein transferase activity (GO:0004842)			ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	4						TCGCCTGCCAGGAAGCTTGAG	0.542																																					p.L416M		Atlas-SNP	.											.	FBXW2	34	.	0			c.C1246A						.						136	142	140					9																	123526956		2032	4212	6244	SO:0001583	missense	26190	exon8			CTGCCAGGAAGCT	AF129531	CCDS43872.1	9q34	2013-01-09	2007-02-08		ENSG00000119402	ENSG00000119402		"F-boxes / WD-40 domains", "WD repeat domain containing"	13608	protein-coding gene	gene with protein product		609071	"F-box and WD-40 domain protein 2"			10531035, 10828603	Standard	NM_012164		Approved	FBW2, Md6, Fwd2	uc004bkm.1	Q9UKT8	OTTHUMG00000020576	ENST00000608872.1:c.1246C>A	chr9.hg19:g.123526956G>T	ENSP00000476369:p.Leu416Met	105.0	0.0		96.0	4.0	NM_012164	B3KRL8|Q4VXH2|Q7Z4V6|Q8WV51|Q9HA09|Q9UKA3	Missense_Mutation	SNP	ENST00000608872.1	hg19	CCDS43872.1	.	.	.	.	.	.	.	.	.	.	G	16.14	3.038947	0.55003	.	.	ENSG00000119402	ENST00000373926;ENST00000340778;ENST00000444833	T;D	0.83992	-0.09;-1.79	4.95	3.8	0.43715	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.84492	0.5484	L	0.44542	1.39	0.51482	D	0.999925	D;D;D	0.71674	0.994;0.998;0.994	P;D;D	0.77557	0.827;0.99;0.99	D	0.84080	0.0384	10	0.87932	D	0	-2.4718	5.0892	0.14698	0.2566:0.0:0.7434:0.0	.	351;416;416	Q9UKT8-2;B2RAW3;Q9UKT8	.;.;FBXW2_HUMAN	M	416;351;416	ENSP00000363036:L416M;ENSP00000341161:L351M	ENSP00000341161:L351M	L	-	1	2	FBXW2	122566777	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.734000	0.55037	2.447000	0.82792	0.563000	0.77884	CTG	.	.		0.542	FBXW2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053834.2			T	123526956	G	T	123526956	3	4	254	1	0	0	0	0	1	0	0	0	5774	991	35	3	122	3	FBXW2	9	123526956	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	9	123526956	17686475	454	34746	179	2								
PHF19	26147	hgsc.bcm.edu	37	chr9	123636996	123636996	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccataggagtcccgagtcccTggatccagagctcgattctc	10	14	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:123636996T>C	ENST00000373896.3	-	2	276	c.24A>G	c.(22-24)ccA>ccG	p.P8P	PHF19_ENST00000312189.6_Silent_p.P8P	NM_015651.1	NP_056466.1	Q5T6S3	PHF19_HUMAN	PHD finger protein 19	8					chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K27 methylation (GO:0061087)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)	methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|endometrium(3)|large_intestine(1)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						CCCGAGTCCCTGGATCCAGAG	0.552																																					p.P8P		Atlas-SNP	.											.	PHF19	47	.	0			c.A24G						.						77	78	78					9																	123636996		2203	4300	6503	SO:0001819	synonymous_variant	26147	exon2			AGTCCCTGGATCC	BX640713	CCDS35116.1, CCDS35117.1, CCDS69648.1, CCDS75889.1	9q34.11	2013-01-28			ENSG00000119403	ENSG00000119403		"Tudor domain containing", "Zinc fingers, PHD-type"	24566	protein-coding gene	gene with protein product	"polycomb-like 3", "tudor domain containing 19B"	609740				15563832	Standard	XM_005251906		Approved	DKFZP727G051, PCL3, MTF2L1, TDRD19B	uc004bks.1	Q5T6S3	OTTHUMG00000020577	ENST00000373896.3:c.24A>G	chr9.hg19:g.123636996T>C		58.0	0.0		63.0	4.0	NM_015651	Q32NF2|Q5T6S4|Q6N038|Q8TBL6|Q9UFS9	Silent	SNP	ENST00000373896.3	hg19	CCDS35116.1																																																																																			.	.		0.552	PHF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053838.3	XM_045308		C	123636996	T	C	123636996	2	2	254	1	0	0	0	0	0	0	0	1	11838	1567	55	2		2	PHF19	9	123636996	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	110040	123636996	17576435	455	34747										
SCAI	286205	hgsc.bcm.edu	37	chr9	127781126	127781126	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcgtcagccagagacaactgTcccacaatcatgccctgttc	8	15	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:127781126T>C	ENST00000336505.6	-	9	871	c.813A>G	c.(811-813)ggA>ggG	p.G271G	SCAI_ENST00000373549.4_Silent_p.G294G	NM_001144877.2	NP_001138349.1	Q8N9R8	SCAI_HUMAN	suppressor of cancer cell invasion	271					negative regulation of cell migration (GO:0030336)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|prostate(5)|stomach(1)|urinary_tract(1)	35						GAGACAACTGTCCCACAATCA	0.383																																					p.G294G		Atlas-SNP	.											.	SCAI	84	.	0			c.A882G						.						114	109	111					9																	127781126		1952	4147	6099	SO:0001819	synonymous_variant	286205	exon10			CAACTGTCCCACA	AK093983	CCDS43877.1, CCDS48017.1	9q34.11	2009-11-06	2009-07-09	2009-07-09	ENSG00000173611	ENSG00000173611			26709	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 126"	C9orf126			Standard	NM_173690		Approved	FLJ36664, NET40	uc004bpd.3	Q8N9R8	OTTHUMG00000020667	ENST00000336505.6:c.813A>G	chr9.hg19:g.127781126T>C		105.0	0.0		82.0	4.0	NM_173690	Q3SXZ1|Q3SXZ2|Q5T163|Q8N1I4	Silent	SNP	ENST00000336505.6	hg19	CCDS48017.1																																																																																			.	.		0.383	SCAI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054055.3	NM_173690		C	127781126	T	C	127781126	2	2	254	1	0	0	0	0	0	0	0	1	13884	1654	58	2		2	SCAI	9	127781126	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	4144130	127781126	13432305	456	34748										
FAM129B	64855	hgsc.bcm.edu	37	chr9	130272586	130272586	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctggacatggttccgcacgcAcacctctgccttggggagga	13	13	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:130272586A>G	ENST00000373312.3	-	9	1213	c.1000T>C	c.(1000-1002)Tgc>Cgc	p.C334R	FAM129B_ENST00000373314.3_Missense_Mutation_p.C321R|FAM129B_ENST00000468379.1_Intron	NM_022833.2	NP_073744.2	Q96TA1	NIBL1_HUMAN	family with sequence similarity 129, member B	334					negative regulation of apoptotic process (GO:0043066)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25						TTCCGCACGCACACCTCTGCC	0.642																																					p.C334R		Atlas-SNP	.											.	FAM129B	84	.	0			c.T1000C						.						106	102	103					9																	130272586		2203	4300	6503	SO:0001583	missense	64855	exon9			GCACGCACACCTC	AF151783	CCDS35144.1, CCDS35145.1	9q34.13	2010-02-01	2006-11-23	2006-11-23	ENSG00000136830	ENSG00000136830			25282	protein-coding gene	gene with protein product		614045	"chromosome 9 open reading frame 88"	C9orf88		14702039, 19362540	Standard	XM_005252135		Approved	DKFZP434H0820, FLJ13518, FLJ22151, FLJ22298, bA356B19.6, MINERVA	uc004brh.3	Q96TA1	OTTHUMG00000020705	ENST00000373312.3:c.1000T>C	chr9.hg19:g.130272586A>G	ENSP00000362409:p.Cys334Arg	108.0	0.0		66.0	4.0	NM_022833	Q4LE55|Q5VVW6|Q5VVW7|Q9BUS2|Q9NT35	Missense_Mutation	SNP	ENST00000373312.3	hg19	CCDS35145.1	.	.	.	.	.	.	.	.	.	.	A	8.958	0.969866	0.18659	.	.	ENSG00000136830	ENST00000373314;ENST00000373312	T;T	0.26067	1.77;1.76	6.04	6.04	0.98038	.	0.174286	0.51477	D	0.000096	T	0.23210	0.0561	L	0.40543	1.245	0.80722	D	1	P;P	0.39094	0.659;0.659	B;B	0.37943	0.261;0.261	T	0.02625	-1.1132	10	0.26408	T	0.33	-23.0447	14.5284	0.67905	1.0:0.0:0.0:0.0	.	321;334	Q96TA1-2;Q96TA1	.;NIBL1_HUMAN	R	321;334	ENSP00000362411:C321R;ENSP00000362409:C334R	ENSP00000362409:C334R	C	-	1	0	FAM129B	129312407	1.000000	0.71417	1.000000	0.80357	0.049000	0.14656	3.207000	0.51106	2.317000	0.78254	0.459000	0.35465	TGC	.	.		0.642	FAM129B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054196.1	NM_022833		G	130272586	A	G	130272586	3	3	254	1	0	0	0	0	1	0	0	0	5442	159	6	2	1264	2	FAM129B	9	130272586	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	2491460	130272586	10940845	457	34749										
C9orf117	286207	hgsc.bcm.edu	37	chr9	130473684	130473684	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gctgcaggagaatgagcagcTcaagggaagacagaacaatc	13	8	1	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:130473684T>C	ENST00000373295.2	+	4	804	c.764T>C	c.(763-765)cTc>cCc	p.L255P	C9orf117_ENST00000373293.5_5'Flank	NM_001012502.2	NP_001012520.2	Q5JU67	CI117_HUMAN	chromosome 9 open reading frame 117	255										breast(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	6						AATGAGCAGCTCAAGGGAAGA	0.557																																					p.L255P		Atlas-SNP	.											.	C9orf117	21	.	0			c.T764C						.						68	70	69					9																	130473684		2018	4194	6212	SO:0001583	missense	286207	exon4			AGCAGCTCAAGGG	AK094948	CCDS43878.1	9q34.11	2012-04-02			ENSG00000160401	ENSG00000160401			27843	protein-coding gene	gene with protein product							Standard	NM_001012502		Approved		uc004brn.1	Q5JU67	OTTHUMG00000020709	ENST00000373295.2:c.764T>C	chr9.hg19:g.130473684T>C	ENSP00000362392:p.Leu255Pro	121.0	0.0		70.0	4.0	NM_001012502	A5D8T9	Missense_Mutation	SNP	ENST00000373295.2	hg19	CCDS43878.1	.	.	.	.	.	.	.	.	.	.	T	15.23	2.773137	0.49680	.	.	ENSG00000160401	ENST00000373295	T	0.45276	0.9	5.44	5.44	0.79542	.	0.075738	0.56097	D	0.000029	T	0.64136	0.2571	M	0.75264	2.295	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.68198	-0.5472	10	0.72032	D	0.01	-22.8891	13.4422	0.61119	0.0:0.0:0.0:1.0	.	255	Q5JU67	CI117_HUMAN	P	255	ENSP00000362392:L255P	ENSP00000362392:L255P	L	+	2	0	C9orf117	129513505	1.000000	0.71417	0.963000	0.40424	0.423000	0.31445	4.822000	0.62686	2.064000	0.61679	0.454000	0.30748	CTC	.	.		0.557	C9orf117-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054215.2	NM_001012502		C	130473684	T	C	130473684	3	2	254	1	0	0	0	0	1	0	0	0	2453	1551	54	2	778	2	C9orf117	9	130473684	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	201098	130473684	10739747	458	34750										
LCN2	3934	hgsc.bcm.edu	37	chr9	130911932	130911932	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccctctgcagcagaacttccAggacaaccaagtaaggggcc	10	14	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:130911932A>G	ENST00000373017.1	+	2	365	c.128A>G	c.(127-129)cAg>cGg	p.Q43R	LCN2_ENST00000540948.1_Missense_Mutation_p.Q43R|LCN2_ENST00000277480.2_Missense_Mutation_p.Q43R|LCN2_ENST00000372998.1_Missense_Mutation_p.Q43R|LCN2_ENST00000470902.1_3'UTR|LCN2_ENST00000373013.2_Missense_Mutation_p.Q43R			P80188	NGAL_HUMAN	lipocalin 2	43					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|ion transport (GO:0006811)|iron ion homeostasis (GO:0055072)|siderophore transport (GO:0015891)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|small molecule binding (GO:0036094)|transporter activity (GO:0005215)			central_nervous_system(1)|lung(3)|prostate(2)|skin(1)|urinary_tract(1)	8						CAGAACTTCCAGGACAACCAA	0.627																																					p.Q43R		Atlas-SNP	.											.	LCN2	12	.	0			c.A128G						.						63	64	63					9																	130911932		2203	4300	6503	SO:0001583	missense	3934	exon1			ACTTCCAGGACAA		CCDS6892.1	9q34	2011-10-24	2007-12-18		ENSG00000148346	ENSG00000148346		"Lipocalins"	6526	protein-coding gene	gene with protein product	"oncogene 24p3", "neutrophil gelatinase-associated lipocalin", "siderocalin"	600181	"lipocalin 2 (oncogene 24p3)"			7683678	Standard	NM_005564		Approved	NGAL, 24p3	uc004bto.1	P80188	OTTHUMG00000020734	ENST00000373017.1:c.128A>G	chr9.hg19:g.130911932A>G	ENSP00000362108:p.Gln43Arg	110.0	0.0		99.0	5.0	NM_005564	A6NII8|B4DWV4|B7ZAA2|P30150|Q5SYV9|Q5SYW0|Q6FGL5|Q92683	Missense_Mutation	SNP	ENST00000373017.1	hg19	CCDS6892.1	.	.	.	.	.	.	.	.	.	.	A	10.10	1.256384	0.22965	.	.	ENSG00000148346	ENST00000373017;ENST00000277480;ENST00000373013;ENST00000540948;ENST00000372998	T;T;T;T;T	0.24538	1.87;1.87;1.85;1.86;1.86	3.45	2.32	0.28847	Lipocalin conserved site (1);Calycin-like (1);Calycin (1);	0.875580	0.09640	N	0.775100	T	0.17109	0.0411	L	0.38175	1.15	0.09310	N	1	B;B;B	0.29253	0.239;0.041;0.041	B;B;B	0.24269	0.052;0.035;0.035	T	0.24835	-1.0149	10	0.38643	T	0.18	-6.123	3.66	0.08236	0.7502:0.0:0.2498:0.0	.	43;44;43	P80188-2;B2ZDQ1;P80188	.;.;NGAL_HUMAN	R	43	ENSP00000362108:Q43R;ENSP00000277480:Q43R;ENSP00000362104:Q43R;ENSP00000441666:Q43R;ENSP00000362089:Q43R	ENSP00000277480:Q43R	Q	+	2	0	LCN2	129951753	0.088000	0.21588	0.219000	0.23793	0.625000	0.37756	1.313000	0.33585	0.715000	0.32103	0.374000	0.22700	CAG	.	.		0.627	LCN2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054375.1	NM_005564		G	130911932	A	G	130911932	3	3	254	1	0	0	0	0	1	0	0	0	8693	188	7	2	130	2	LCN2	9	130911932	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	438248	130911932	10301499	459	34751										
SPTAN1	6709	hgsc.bcm.edu	37	chr9	131337065	131337065	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgcagtacttacgagaatgtGaggacgtgatggactggatc	14	6	0	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:131337065G>T	ENST00000372731.4	+	4	585	c.475G>T	c.(475-477)Gag>Tag	p.E159*	SPTAN1_ENST00000358161.5_Nonsense_Mutation_p.E159*|SPTAN1_ENST00000372739.3_Nonsense_Mutation_p.E159*	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	159					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						ACGAGAATGTGAGGACGTGAT	0.473																																					p.E159X	NSCLC(120;833 1744 2558 35612 37579)	Atlas-SNP	.											.	SPTAN1	266	.	0			c.G475T						.						164	162	162					9																	131337065		2203	4300	6503	SO:0001587	stop_gained	6709	exon4			GAATGTGAGGACG	M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"EF-hand domain containing"	11273	protein-coding gene	gene with protein product	"alpha-fodrin"	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.475G>T	chr9.hg19:g.131337065G>T	ENSP00000361816:p.Glu159*	124.0	0.0		100.0	4.0	NM_003127	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Nonsense_Mutation	SNP	ENST00000372731.4	hg19	CCDS6905.1	.	.	.	.	.	.	.	.	.	.	G	37	6.473816	0.97594	.	.	ENSG00000197694	ENST00000358161;ENST00000372731;ENST00000372739;ENST00000372719	.	.	.	6.08	6.08	0.98989	.	0.046712	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	19.6516	0.95815	0.0:0.0:1.0:0.0	.	.	.	.	X	159	.	ENSP00000350882:E159X	E	+	1	0	SPTAN1	130376886	1.000000	0.71417	1.000000	0.80357	0.828000	0.46876	9.430000	0.97488	2.894000	0.99253	0.655000	0.94253	GAG	.	.		0.473	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127		T	131337065	G	T	131337065	4	4	254	1	0	0	0	0	0	1	0	0	15132	1291	45	3	485	3	SPTAN1	9	131337065	Nonsense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	425133	131337065	9876366	460	34752										
NUP188	23511	hgsc.bcm.edu	37	chr9	131765691	131765691	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cagctctctaacttcatgaaGgagtggcacttccacctgcc	8	14	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:131765691G>T	ENST00000372577.2	+	38	4413	c.4392G>T	c.(4390-4392)aaG>aaT	p.K1464N	RP11-167N5.5_ENST00000594418.1_lincRNA	NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	1464					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				breast(2)|central_nervous_system(3)|endometrium(6)|kidney(4)|large_intestine(9)|lung(20)|ovary(6)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	60						ACTTCATGAAGGAGTGGCACT	0.582																																					p.K1464N		Atlas-SNP	.											.	NUP188	140	.	0			c.G4392T						.						118	110	113					9																	131765691		2203	4300	6503	SO:0001583	missense	23511	exon38			CATGAAGGAGTGG	D79991	CCDS35156.1	9q34.13	2014-01-28	2004-03-19	2004-03-24	ENSG00000095319	ENSG00000095319			17859	protein-coding gene	gene with protein product		615587	"KIAA0169"	KIAA0169		11029043	Standard	NM_015354		Approved		uc004bws.2	Q5SRE5	OTTHUMG00000020768	ENST00000372577.2:c.4392G>T	chr9.hg19:g.131765691G>T	ENSP00000361658:p.Lys1464Asn	67.0	0.0		46.0	4.0	NM_015354	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Missense_Mutation	SNP	ENST00000372577.2	hg19	CCDS35156.1	.	.	.	.	.	.	.	.	.	.	G	19.31	3.803502	0.70682	.	.	ENSG00000095319	ENST00000356693;ENST00000372577	T	0.33438	1.41	5.8	3.93	0.45458	.	0.000000	0.85682	D	0.000000	T	0.46073	0.1374	L	0.53249	1.67	0.80722	D	1	P;D	0.76494	0.784;0.999	B;D	0.78314	0.312;0.991	T	0.32428	-0.9907	10	0.39692	T	0.17	-8.8756	9.7807	0.40647	0.2141:0.0:0.7859:0.0	.	797;1464	E9PET9;Q5SRE5	.;NU188_HUMAN	N	1353;1464	ENSP00000361658:K1464N	ENSP00000349125:K1353N	K	+	3	2	NUP188	130805512	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.477000	0.45180	1.455000	0.47813	0.561000	0.74099	AAG	.	.		0.582	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2			T	131765691	G	T	131765691	3	4	254	1	0	0	0	0	1	0	0	0	10767	991	35	3	4542	3	NUP188	9	131765691	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	428626	131765691	9447740	461	34753										
USP20	10868	hgsc.bcm.edu	37	chr9	132642472	132642472	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtggccccgagattgccatcCgccagagtgtggcgcagccg	15	14	0	2	rs200854092	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:132642472C>A	ENST00000315480.4	+	25	2823	c.2665C>A	c.(2665-2667)Cgc>Agc	p.R889S	USP20_ENST00000372429.3_Missense_Mutation_p.R889S|USP20_ENST00000472108.1_3'UTR|USP20_ENST00000358355.1_Missense_Mutation_p.R889S			Q9Y2K6	UBP20_HUMAN	ubiquitin specific peptidase 20	889	DUSP 2. {ECO:0000255|PROSITE- ProRule:PRU00613}.				endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|urinary_tract(1)	11		Ovarian(14;0.00556)				GATTGCCATCCGCCAGAGTGT	0.632																																					p.R889S		Atlas-SNP	.											.	USP20	186	.	0			c.C2665A						.						32	43	39					9																	132642472		2066	4205	6271	SO:0001583	missense	10868	exon25			GCCATCCGCCAGA	AB023220	CCDS43892.1	9q34.2	2014-07-15	2005-08-08		ENSG00000136878	ENSG00000136878		"Ubiquitin-specific peptidases"	12619	protein-coding gene	gene with protein product		615143	"ubiquitin specific protease 20"			12838346	Standard	NM_006676		Approved	KIAA1003	uc004byr.3	Q9Y2K6	OTTHUMG00000020793	ENST00000315480.4:c.2665C>A	chr9.hg19:g.132642472C>A	ENSP00000313811:p.Arg889Ser	112.0	0.0		50.0	4.0	NM_001008563	Q541F1|Q8IXQ1|Q96LG5|Q9UQN8|Q9UQP0	Missense_Mutation	SNP	ENST00000315480.4	hg19	CCDS43892.1	.	.	.	.	.	.	.	.	.	.	C	15.54	2.863098	0.51482	.	.	ENSG00000136878	ENST00000372429;ENST00000315480;ENST00000358355	T;T;T	0.18657	2.2;2.2;2.2	5.11	5.11	0.69529	Peptidase C19, ubiquitin-specific peptidase, DUSP domain (2);	0.000000	0.85682	D	0.000000	T	0.48714	0.1515	M	0.83953	2.67	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.51631	-0.8681	10	0.54805	T	0.06	.	13.2032	0.59780	0.1698:0.8302:0.0:0.0	.	889	Q9Y2K6	UBP20_HUMAN	S	889	ENSP00000361506:R889S;ENSP00000313811:R889S;ENSP00000351122:R889S	ENSP00000313811:R889S	R	+	1	0	USP20	131682293	1.000000	0.71417	0.998000	0.56505	0.054000	0.15201	1.766000	0.38491	2.387000	0.81309	0.655000	0.94253	CGC	.	C|1.000;T|0.000		0.632	USP20-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054604.2			A	132642472	C	A	132642472	3	1	254	1	0	0	0	0	1	0	0	0	17067	652	23	1	2755	1	USP20	9	132642472	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	876781	132642472	8570959	462	34754										
NUP214	8021	hgsc.bcm.edu	37	chr9	134049687	134049687	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tggttcatggttcttcacctGgtgtgatgggaacttcaggt	13	7	4	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:134049687G>A	ENST00000359428.5	+	22	3283	c.3139G>A	c.(3139-3141)Ggt>Agt	p.G1047S	NUP214_ENST00000451030.1_Missense_Mutation_p.G1048S|NUP214_ENST00000411637.2_Missense_Mutation_p.G1037S			P35658	NU214_HUMAN	nucleoporin 214kDa	1047	11 X 5 AA approximate repeats.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		TTCTTCACCTGGTGTGATGGG	0.483			T	"DEK, SET, ABL1"	"AML, T-ALL"																																p.G1047S	Pancreas(4;24 48 25510 30394 32571)	Atlas-SNP	.		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.	NUP214	166	.	0			c.G3139A						.						78	68	71					9																	134049687		2203	4300	6503	SO:0001583	missense	8021	exon22			TCACCTGGTGTGA	X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"nuclear pore complex protein Nup214", "CAN protein, putative oncogene"	114350	"nucleoporin 214kD (CAIN)"			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.3139G>A	chr9.hg19:g.134049687G>A	ENSP00000352400:p.Gly1047Ser	153.0	0.0		93.0	4.0	NM_005085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Missense_Mutation	SNP	ENST00000359428.5	hg19	CCDS6940.1	.	.	.	.	.	.	.	.	.	.	G	14.69	2.611743	0.46631	.	.	ENSG00000126883	ENST00000359428;ENST00000411637;ENST00000451030;ENST00000541375;ENST00000540899;ENST00000438605	T;T;T	0.31510	1.49;1.49;1.49	5.81	1.13	0.20643	.	0.672958	0.12990	N	0.422559	T	0.10637	0.0260	N	0.08118	0	0.22710	N	0.998825	B;B;B;B	0.16603	0.001;0.0;0.018;0.0	B;B;B;B	0.17722	0.004;0.003;0.015;0.019	T	0.34378	-0.9831	10	0.05525	T	0.97	-5.2842	2.9419	0.05833	0.3673:0.0:0.4403:0.1924	.	1036;641;1037;1047	P35658-2;Q5JUP9;P35658-4;P35658	.;.;.;NU214_HUMAN	S	1047;1037;1048;1036;641;476	ENSP00000352400:G1047S;ENSP00000396576:G1037S;ENSP00000405014:G1048S	ENSP00000352400:G1047S	G	+	1	0	NUP214	133039508	0.780000	0.28664	0.018000	0.16275	0.853000	0.48598	1.415000	0.34748	0.301000	0.22738	-0.982000	0.02568	GGT	.	.		0.483	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085		A	134049687	G	A	134049687	3	1	254	1	0	0	0	0	1	0	0	0	10771	1348	47	3	3225	3	NUP214	9	134049687	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1407215	134049687	7163744	463	34755										
SETX	23064	hgsc.bcm.edu	37	chr9	135218087	135218087	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcacactcaccatttcattgGgatggactaaaaacaaatag	6	9	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:135218087G>T	ENST00000224140.5	-	5	670	c.488C>A	c.(487-489)cCc>cAc	p.P163H	SETX_ENST00000372169.2_Missense_Mutation_p.P163H|SETX_ENST00000393220.1_Missense_Mutation_p.P163H	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	163					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		CATTTCATTGGGATGGACTAA	0.398																																					p.P163H		Atlas-SNP	.											.	SETX	234	.	0			c.C488A						.						202	209	207					9																	135218087		2203	4300	6503	SO:0001583	missense	23064	exon5			TCATTGGGATGGA	AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"amyotrophic lateral sclerosis 4", "spinocerebellar ataxia, recessive, non-Friedreich type 1"	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.488C>A	chr9.hg19:g.135218087G>T	ENSP00000224140:p.Pro163His	104.0	0.0		74.0	5.0	NM_015046	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Missense_Mutation	SNP	ENST00000224140.5	hg19	CCDS6947.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.258512	0.80246	.	.	ENSG00000107290	ENST00000224140;ENST00000372169;ENST00000393220	D;D;D	0.89196	-2.48;-2.48;-2.48	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	D	0.91845	0.7419	L	0.34521	1.04	0.42482	D	0.992865	D	0.89917	1.0	D	0.91635	0.999	D	0.92843	0.6290	10	0.87932	D	0	.	18.6094	0.91279	0.0:0.0:1.0:0.0	.	163	Q7Z333	SETX_HUMAN	H	163	ENSP00000224140:P163H;ENSP00000361242:P163H;ENSP00000376913:P163H	ENSP00000224140:P163H	P	-	2	0	SETX	134207908	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.041000	0.64196	2.636000	0.89361	0.557000	0.71058	CCC	.	.		0.398	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046		T	135218087	G	T	135218087	3	4	254	1	0	0	0	0	1	0	0	0	14156	1232	43	3	7633	3	SETX	9	135218087	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1168400	135218087	5995344	464	34756										
TSC1	7248	hgsc.bcm.edu	37	chr9	135779080	135779080	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agagctgctgctttgatcacCttgcggaggagccgcctgtt	13	11	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:135779080C>A	ENST00000298552.3	-	17	2387	c.2166G>T	c.(2164-2166)aaG>aaT	p.K722N	TSC1_ENST00000545250.1_Missense_Mutation_p.K671N|TSC1_ENST00000440111.2_Missense_Mutation_p.K722N	NM_000368.4|NM_001162426.1|NM_001162427.1	NP_000359.1|NP_001155898.1|NP_001155899.1	Q92574	TSC1_HUMAN	tuberous sclerosis 1	722					activation of Rho GTPase activity (GO:0032862)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|insulin receptor signaling pathway (GO:0008286)|kidney development (GO:0001822)|myelination (GO:0042552)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of TOR signaling (GO:0032007)|negative regulation of translation (GO:0017148)|neural tube closure (GO:0001843)|positive regulation of focal adhesion assembly (GO:0051894)|potassium ion transport (GO:0006813)|protein heterooligomerization (GO:0051291)|protein stabilization (GO:0050821)|regulation of cell cycle (GO:0051726)|regulation of cell-matrix adhesion (GO:0001952)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of protein kinase activity (GO:0045859)|regulation of stress fiber assembly (GO:0051492)|regulation of translation (GO:0006417)|response to insulin (GO:0032868)|rRNA export from nucleus (GO:0006407)|synapse organization (GO:0050808)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|lamellipodium (GO:0030027)|membrane (GO:0016020)|protein complex (GO:0043234)|TSC1-TSC2 complex (GO:0033596)	chaperone binding (GO:0051087)|GTPase regulator activity (GO:0030695)|protein N-terminus binding (GO:0047485)	p.R721fs*9(1)|p.?(1)		NS(1)|bone(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(9)|lung(20)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	65				OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06)		CTTTGATCACCTTGCGGAGGA	0.537			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.K722N		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 1	9	9q34	7248	tuberous sclerosis 1 gene		"E, O"	.	TSC1	167	.	2	Unknown(1)|Deletion - Frameshift(1)	ovary(1)|bone(1)	c.G2166T						.						69	70	70					9																	135779080		2203	4300	6503	SO:0001583	missense	7248	exon17	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	GATCACCTTGCGG	AF013168	CCDS6956.1, CCDS55350.1	9q34	2014-09-17			ENSG00000165699	ENSG00000165699			12362	protein-coding gene	gene with protein product		605284		TSC		9242607, 10806479	Standard	NM_000368		Approved	KIAA0243, LAM, hamartin	uc004cca.2	Q92574	OTTHUMG00000020844	ENST00000298552.3:c.2166G>T	chr9.hg19:g.135779080C>A	ENSP00000298552:p.Lys722Asn	94.0	0.0		82.0	33.0	NM_000368	B7Z897|Q5VVN5	Missense_Mutation	SNP	ENST00000298552.3	hg19	CCDS6956.1	.	.	.	.	.	.	.	.	.	.	C	16.30	3.085869	0.55861	.	.	ENSG00000165699	ENST00000298552;ENST00000440111;ENST00000545250	D;D;D	0.85339	-1.97;-1.97;-1.84	5.32	3.47	0.39725	.	0.209808	0.49916	D	0.000125	T	0.73976	0.3656	L	0.27053	0.805	0.80722	D	1	P;P	0.36753	0.568;0.568	B;B	0.37550	0.253;0.253	T	0.72887	-0.4156	10	0.66056	D	0.02	-7.8598	5.4933	0.16789	0.0:0.6389:0.0:0.3611	.	671;722	B7Z897;Q92574	.;TSC1_HUMAN	N	722;722;671	ENSP00000298552:K722N;ENSP00000394524:K722N;ENSP00000444017:K671N	ENSP00000298552:K722N	K	-	3	2	TSC1	134768901	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	0.810000	0.27183	1.242000	0.43836	0.650000	0.86243	AAG	.	.		0.537	TSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054799.1			A	135779080	C	A	135779080	3	1	254	1	0	0	0	0	1	0	0	0	16620	680	24	3	1356	3	TSC1	9	135779080	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	560993	135779080	5434351	465	34757										
GBGT1	26301	hgsc.bcm.edu	37	chr9	136029419	136029419	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gaagaggtagtccacctcccGgtgagccctcttagcaatgt	11	12	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:136029419G>T	ENST00000372040.3	-	7	900	c.589C>A	c.(589-591)Cgg>Agg	p.R197R	GBGT1_ENST00000372043.3_Silent_p.T190T|GBGT1_ENST00000540636.1_Silent_p.R180R|RALGDS_ENST00000542690.1_Intron|GBGT1_ENST00000472281.1_5'UTR	NM_001282629.1	NP_001269558.1	Q8N5D6	GBGT1_HUMAN	globoside alpha-1,3-N-acetylgalactosaminyltransferase 1	197					glycolipid biosynthetic process (GO:0009247)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	globoside alpha-N-acetylgalactosaminyltransferase activity (GO:0047277)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(4)|lung(2)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(145;3.49e-06)|Epithelial(140;2.59e-05)		TCCACCTCCCGGTGAGCCCTC	0.602																																					p.R197R		Atlas-SNP	.											.,1	GBGT1	25	.	0			c.C589A						.						91	72	78					9																	136029419		2203	4300	6503	SO:0001819	synonymous_variant	26301	exon7			CCTCCCGGTGAGC	AY358175	CCDS6960.1, CCDS65175.1, CCDS65176.1	9q34.13-q34.3	2014-07-18			ENSG00000148288	ENSG00000148288		"Glycosyltransferase family 6 domain containing"	20460	protein-coding gene	gene with protein product	"Forssman glycolipid synthetase (FS)", "Forssman synthetase"	606074				10506200, 8855242	Standard	NM_021996		Approved	UDP-GalNAc, A3GALNT, MGC44848, FS		Q8N5D6	OTTHUMG00000020853	ENST00000372040.3:c.589C>A	chr9.hg19:g.136029419G>T		114.0	0.0		99.0	4.0	NM_021996	A8K633|B2RA95|B7Z8S5|Q45F07|Q5T7U9|Q5T7V1|Q8N2K4|Q9UKI5	Silent	SNP	ENST00000372040.3	hg19	CCDS6960.1																																																																																			.	.		0.602	GBGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054815.1	NM_021996		T	136029419	G	T	136029419	2	4	254	1	0	0	0	0	0	0	0	1	6280	1115	39	1		1	GBGT1	9	136029419	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	250339	136029419	5184012	466	34758										
GBGT1	26301	hgsc.bcm.edu	37	chr9	136031411	136031411	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agtctccttaccataccacgGgctggagtggcttctccctc	9	15	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:136031411G>T	ENST00000372040.3	-	4	490	c.179C>A	c.(178-180)cCc>cAc	p.P60H	GBGT1_ENST00000372043.3_Missense_Mutation_p.P60H|GBGT1_ENST00000540636.1_Intron|GBGT1_ENST00000372038.3_Silent_p.A72A|RALGDS_ENST00000542690.1_Silent_p.A72A|GBGT1_ENST00000472281.1_5'UTR	NM_001282629.1	NP_001269558.1	Q8N5D6	GBGT1_HUMAN	globoside alpha-1,3-N-acetylgalactosaminyltransferase 1	60					glycolipid biosynthetic process (GO:0009247)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	globoside alpha-N-acetylgalactosaminyltransferase activity (GO:0047277)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(4)|lung(2)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(145;3.49e-06)|Epithelial(140;2.59e-05)		CCATACCACGGGCTGGAGTGG	0.552																																					p.P60H		Atlas-SNP	.											.	GBGT1	25	.	0			c.C179A						.						145	121	129					9																	136031411		2203	4300	6503	SO:0001583	missense	26301	exon4			ACCACGGGCTGGA	AY358175	CCDS6960.1, CCDS65175.1, CCDS65176.1	9q34.13-q34.3	2014-07-18			ENSG00000148288	ENSG00000148288		"Glycosyltransferase family 6 domain containing"	20460	protein-coding gene	gene with protein product	"Forssman glycolipid synthetase (FS)", "Forssman synthetase"	606074				10506200, 8855242	Standard	NM_021996		Approved	UDP-GalNAc, A3GALNT, MGC44848, FS		Q8N5D6	OTTHUMG00000020853	ENST00000372040.3:c.179C>A	chr9.hg19:g.136031411G>T	ENSP00000361110:p.Pro60His	149.0	0.0		83.0	4.0	NM_021996	A8K633|B2RA95|B7Z8S5|Q45F07|Q5T7U9|Q5T7V1|Q8N2K4|Q9UKI5	Missense_Mutation	SNP	ENST00000372040.3	hg19	CCDS6960.1	.	.	.	.	.	.	.	.	.	.	G	8.952	0.968524	0.18659	.	.	ENSG00000148288	ENST00000372043;ENST00000372040	T;T	0.01228	5.14;5.14	4.65	3.75	0.43078	.	0.357573	0.26279	N	0.025296	T	0.05090	0.0136	M	0.66939	2.045	0.24795	N	0.992734	D;D	0.76494	0.999;0.98	D;P	0.66351	0.943;0.845	T	0.23226	-1.0194	10	0.36615	T	0.2	-13.5243	7.5864	0.27995	0.1982:0.0:0.8018:0.0	.	60;60	Q8N5D6-2;Q8N5D6	.;GBGT1_HUMAN	H	60	ENSP00000361113:P60H;ENSP00000361110:P60H	ENSP00000361110:P60H	P	-	2	0	GBGT1	135021232	0.992000	0.36948	0.060000	0.19600	0.002000	0.02628	2.534000	0.45676	1.068000	0.40764	-0.136000	0.14681	CCC	.	.		0.552	GBGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054815.1	NM_021996		T	136031411	G	T	136031411	3	4	254	1	0	0	0	0	1	0	0	0	6280	1232	43	3	880	3	GBGT1	9	136031411	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1992	136031411	5182020	467	34759										
C9orf7	11094	hgsc.bcm.edu	37	chr9	136328625	136328625	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cttgcgcgatctctggcctcTtcaactgcatcaccatccac	6	17	4	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:136328625T>C	ENST00000316948.4	+	2	222	c.142T>C	c.(142-144)Ttc>Ctc	p.F48L	CACFD1_ENST00000489519.1_3'UTR|CACFD1_ENST00000291722.7_Missense_Mutation_p.F48L|CACFD1_ENST00000542192.1_Missense_Mutation_p.F48L|CACFD1_ENST00000540581.1_Missense_Mutation_p.F48L	NM_017586.3	NP_060056.1	Q9UGQ2	FLOWR_HUMAN	calcium channel flower domain containing 1	48					synaptic vesicle endocytosis (GO:0048488)	integral component of synaptic vesicle membrane (GO:0030285)	calcium channel activity (GO:0005262)										CTCTGGCCTCTTCAACTGCAT	0.622																																					p.F48L		Atlas-SNP	.											.	CACFD1	1	.	0			c.T142C						.						157	146	150					9																	136328625		2203	4300	6503	SO:0001583	missense	11094	exon2			GGCCTCTTCAACT		CCDS6974.1, CCDS48051.1, CCDS56591.1, CCDS56592.1	9q34	2012-03-06	2012-03-06	2012-03-06	ENSG00000160325	ENSG00000160325			1365	protein-coding gene	gene with protein product		613104	"chromosome 9 open reading frame 7"	C9orf7		19737521	Standard	NM_001242370		Approved	D9S2135, flower	uc011mdh.1	Q9UGQ2	OTTHUMG00000020875	ENST00000316948.4:c.142T>C	chr9.hg19:g.136328625T>C	ENSP00000317121:p.Phe48Leu	119.0	0.0		93.0	4.0	NM_001242370	B7Z3T8|B7Z5E1|F5GXX4|Q5SXD4|Q8NBM6	Missense_Mutation	SNP	ENST00000316948.4	hg19	CCDS6974.1	.	.	.	.	.	.	.	.	.	.	T	15.93	2.978155	0.53720	.	.	ENSG00000160325	ENST00000291722;ENST00000535514;ENST00000316948;ENST00000540581;ENST00000542192;ENST00000444798	D;T;T;T;T	0.87887	-2.31;1.07;1.07;0.98;1.07	4.81	4.81	0.61882	Membrane protein, Golgi apparatus TVP18/Calcium channel flower (1);	0.177896	0.52532	D	0.000065	T	0.78842	0.4347	N	0.19112	0.55	0.45390	D	0.998373	B;B;B;B	0.31817	0.15;0.119;0.003;0.341	B;B;B;B	0.31101	0.027;0.019;0.016;0.124	T	0.79259	-0.1877	10	0.52906	T	0.07	-31.3281	13.8451	0.63463	0.0:0.0:0.0:1.0	.	48;48;48;48	B7Z5E1;F5GXX4;Q9UGQ2;Q9UGQ2-2	.;.;FLOWR_HUMAN;.	L	48;38;48;48;48;20	ENSP00000291722:F48L;ENSP00000317121:F48L;ENSP00000440832:F48L;ENSP00000444328:F48L;ENSP00000414495:F20L	ENSP00000291722:F48L	F	+	1	0	C9orf7	135318446	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	7.550000	0.82173	1.940000	0.56252	0.402000	0.26972	TTC	.	.		0.622	CACFD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054915.1	NM_017586		C	136328625	T	C	136328625	3	2	254	1	0	0	0	0	1	0	0	0	2495	1609	56	2	148	2	C9orf7	9	136328625	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	297214	136328625	4884806	468	34760										
GPSM1	26086	hgsc.bcm.edu	37	chr9	139250846	139250846	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gaggaattcttcgacctcatCgccagctcccagagccgccg	10	16	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:139250846C>T	ENST00000440944.1	+	13	1885	c.1665C>T	c.(1663-1665)atC>atT	p.I555I	GPSM1_ENST00000392944.1_Silent_p.I46I|GPSM1_ENST00000429455.1_Silent_p.I46I	NM_001145638.1	NP_001139110	Q86YR5	GPSM1_HUMAN	G-protein signaling modulator 1	555	GoLoco 2. {ECO:0000255|PROSITE- ProRule:PRU00097}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	GDP-dissociation inhibitor activity (GO:0005092)			biliary_tract(1)|endometrium(1)|kidney(2)|lung(4)|upper_aerodigestive_tract(1)	9		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.39e-06)|Epithelial(140;3.24e-06)		TCGACCTCATCGCCAGCTCCC	0.711																																					p.I555I		Atlas-SNP	.											.	GPSM1	50	.	0			c.C1665T						.						16	20	19					9																	139250846		2195	4291	6486	SO:0001819	synonymous_variant	26086	exon13			CCTCATCGCCAGC	AI272212	CCDS6996.2, CCDS48055.1, CCDS48056.1	9q34.3	2013-01-10	2010-06-24		ENSG00000160360	ENSG00000160360		"Tetratricopeptide (TTC) repeat domain containing"	17858	protein-coding gene	gene with protein product	"AGS3 homolog (C. elegans)"	609491	"G-protein signalling modulator 1 (AGS3-like, C. elegans)"			11278352, 10969064	Standard	NM_001145639		Approved	AGS3, DKFZP727I051	uc004chd.2	Q86YR5	OTTHUMG00000020930	ENST00000440944.1:c.1665C>T	chr9.hg19:g.139250846C>T		76.0	0.0		65.0	19.0	NM_001145638	A9Z1X4|B1B0W3|Q86SR5|Q969T1|Q9UFS8	Silent	SNP	ENST00000440944.1	hg19	CCDS48055.1																																																																																			.	.		0.711	GPSM1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015597		T	139250846	C	T	139250846	2	4	254	1	0	0	0	0	0	0	0	1	6743	874	31	1		1	GPSM1	9	139250846	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	2922221	139250846	1962585	469	34761										
SEC16A	9919	hgsc.bcm.edu	37	chr9	139370230	139370230	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	caactaagtgagattttaccGgttcgaaagaactatttgca	8	7	0	2	rs371898934		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:139370230G>T	ENST00000371706.3	-	1	1337	c.1304C>A	c.(1303-1305)cCg>cAg	p.P435Q	SEC16A_ENST00000290037.6_Missense_Mutation_p.P435Q|SEC16A_ENST00000313050.7_Missense_Mutation_p.P613Q|SEC16A_ENST00000431893.2_Missense_Mutation_p.P435Q			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	435					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|protein transport (GO:0015031)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)				breast(1)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(15)|lung(14)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)		AGATTTTACCGGTTCGAAAGA	0.522																																					p.P613Q		Atlas-SNP	.											.	SEC16A	249	.	0			c.C1838A						.						36	38	37					9																	139370230		2061	4198	6259	SO:0001583	missense	9919	exon3			TTTACCGGTTCGA	AK074565	CCDS55351.1, CCDS75936.1	9q34.3	2007-06-20	2007-06-20	2007-06-20	ENSG00000148396	ENSG00000148396			29006	protein-coding gene	gene with protein product		612854	"KIAA0310"	KIAA0310		9205841	Standard	NM_014866		Approved	p250	uc004chx.3	O15027	OTTHUMG00000020932	ENST00000371706.3:c.1304C>A	chr9.hg19:g.139370230G>T	ENSP00000360771:p.Pro435Gln	84.0	0.0		51.0	4.0	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Missense_Mutation	SNP	ENST00000371706.3	hg19		.	.	.	.	.	.	.	.	.	.	G	26.6	4.749388	0.89753	.	.	ENSG00000148396	ENST00000313050;ENST00000371706;ENST00000290037;ENST00000431893;ENST00000404925	T;T;T;T	0.42900	0.96;1.0;0.98;1.0	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.66167	0.2762	M	0.72894	2.215	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	T	0.67639	-0.5619	10	0.87932	D	0	-15.3679	18.9459	0.92622	0.0:0.0:1.0:0.0	.	613;435;435;240	F1T0I1;O15027-5;O15027-4;A4QN19	.;.;.;.	Q	613;435;435;435;240	ENSP00000325827:P613Q;ENSP00000360771:P435Q;ENSP00000290037:P435Q;ENSP00000387583:P435Q	ENSP00000290037:P435Q	P	-	2	0	SEC16A	138490051	1.000000	0.71417	0.997000	0.53966	0.856000	0.48823	7.833000	0.86765	2.796000	0.96246	0.650000	0.86243	CCG	.	.		0.522	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459		T	139370230	G	T	139370230	3	4	254	1	0	0	0	0	1	0	0	0	14001	1116	39	1	5355	1	SEC16A	9	139370230	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	119384	139370230	1843201	470	34762										
GRIN1	2902	hgsc.bcm.edu	37	chr9	140036523	140036523	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cgaccacttcactcccacccCtgtctcctacacagccggct	5	21	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:140036523C>T	ENST00000371561.3	+	2	1414	c.317C>T	c.(316-318)cCt>cTt	p.P106L	GRIN1_ENST00000371553.3_Missense_Mutation_p.P106L|GRIN1_ENST00000315048.3_Missense_Mutation_p.P106L|GRIN1_ENST00000350902.5_Missense_Mutation_p.P106L|GRIN1_ENST00000371560.3_Missense_Mutation_p.P106L|GRIN1_ENST00000371559.4_Missense_Mutation_p.P106L|GRIN1_ENST00000371555.4_Missense_Mutation_p.P106L|GRIN1_ENST00000371546.4_Missense_Mutation_p.P106L|GRIN1_ENST00000371550.4_Missense_Mutation_p.P106L|GRIN1_ENST00000471122.1_3'UTR	NM_007327.3	NP_015566.1	Q05586	NMDZ1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 1	106					adult locomotory behavior (GO:0008344)|calcium ion homeostasis (GO:0055074)|calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular calcium ion homeostasis (GO:0006874)|cellular response to manganese ion (GO:0071287)|cerebral cortex development (GO:0021987)|conditioned taste aversion (GO:0001661)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|male mating behavior (GO:0060179)|negative regulation of neuron apoptotic process (GO:0043524)|olfactory learning (GO:0008355)|pons maturation (GO:0021586)|positive regulation of apoptotic process (GO:0043065)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prepulse inhibition (GO:0060134)|propylene metabolic process (GO:0018964)|protein tetramerization (GO:0051262)|regulation of axonogenesis (GO:0050770)|regulation of dendrite morphogenesis (GO:0048814)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of membrane potential (GO:0042391)|regulation of respiratory gaseous exchange (GO:0043576)|regulation of synapse assembly (GO:0051963)|respiratory gaseous exchange (GO:0007585)|response to amphetamine (GO:0001975)|response to calcium ion (GO:0051592)|response to ethanol (GO:0045471)|response to fungicide (GO:0060992)|response to morphine (GO:0043278)|rhythmic process (GO:0048511)|sensory perception of pain (GO:0019233)|social behavior (GO:0035176)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)|synaptic cleft (GO:0043083)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate binding (GO:0016595)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|voltage-gated cation channel activity (GO:0022843)			NS(1)|breast(1)|endometrium(1)|kidney(1)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;6.87e-05)|Epithelial(140;0.00095)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	ACTCCCACCCCTGTCTCCTAC	0.592																																					p.P106L	NSCLC(113;717 1653 2089 20474 37618)	Atlas-SNP	.											.	GRIN1	51	.	0			c.C317T						.						380	298	326					9																	140036523		2203	4300	6503	SO:0001583	missense	2902	exon2			CCACCCCTGTCTC		CCDS7031.1, CCDS7032.1, CCDS43910.1, CCDS55354.1, CCDS55355.1	9q34.3	2013-01-11			ENSG00000176884	ENSG00000176884		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4584	protein-coding gene	gene with protein product		138249	"N-methyl-D-aspartate receptor subunit NR1"	NMDAR1		1350383	Standard	NM_000832		Approved	GluN1	uc004cln.3	Q05586	OTTHUMG00000020976	ENST00000371561.3:c.317C>T	chr9.hg19:g.140036523C>T	ENSP00000360616:p.Pro106Leu	287.0	0.0		191.0	32.0	NM_000832	A6NLK7|A6NLR1|C9K0X1|P35437|Q12867|Q12868|Q5VSF3|Q5VSF4|Q5VSF5|Q5VSF6|Q5VSF7|Q5VSF8|Q9UPF8|Q9UPF9	Missense_Mutation	SNP	ENST00000371561.3	hg19	CCDS7031.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.457243	0.84317	.	.	ENSG00000176884	ENST00000371561;ENST00000315048;ENST00000350902;ENST00000371550;ENST00000371546;ENST00000371555;ENST00000371553;ENST00000371559;ENST00000371560	D;D;D;D;D;D;D;D;D	0.83755	-1.76;-1.76;-1.76;-1.76;-1.76;-1.76;-1.76;-1.76;-1.76	3.37	3.37	0.38596	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.84826	0.5558	L	0.29908	0.895	0.80722	D	1	D;B;D;D;D;D	0.89917	0.999;0.144;1.0;1.0;1.0;0.995	D;B;D;D;D;D	0.85130	0.984;0.27;0.995;0.995;0.997;0.956	D	0.84739	0.0750	10	0.41790	T	0.15	.	13.8091	0.63252	0.0:1.0:0.0:0.0	.	106;106;106;106;106;106	Q5VSF4;Q5VSF5;Q05586-2;Q05586-3;Q05586;A2AVK2	.;.;.;.;NMDZ1_HUMAN;.	L	106	ENSP00000360616:P106L;ENSP00000316696:P106L;ENSP00000316915:P106L;ENSP00000360605:P106L;ENSP00000360601:P106L;ENSP00000360610:P106L;ENSP00000360608:P106L;ENSP00000360614:P106L;ENSP00000360615:P106L	ENSP00000316696:P106L	P	+	2	0	GRIN1	139156344	1.000000	0.71417	0.997000	0.53966	0.989000	0.77384	7.016000	0.76393	1.887000	0.54652	0.462000	0.41574	CCT	.	.		0.592	GRIN1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055267.3	NM_007327		T	140036523	C	T	140036523	3	4	254	1	0	0	0	0	1	0	0	0	6787	681	24	3	323	3	GRIN1	9	140036523	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	666293	140036523	1176908	471	34763										
ANAPC2	29882	hgsc.bcm.edu	37	chr9	140077667	140077667	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccttgatggcagagatatagAgggtgatgatgtcacacgtg	14	6	1	5			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:140077667A>G	ENST00000323927.2	-	6	1200	c.1196T>C	c.(1195-1197)cTc>cCc	p.L399P		NM_013366.3	NP_037498.1	Q9UJX6	ANC2_HUMAN	anaphase promoting complex subunit 2	399					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of axon extension (GO:0045773)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)				breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	15	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.000858)		AGAGATATAGAGGGTGATGAT	0.622																																					p.L399P		Atlas-SNP	.											.	ANAPC2	57	.	0			c.T1196C						.						144	141	142					9																	140077667		2203	4299	6502	SO:0001583	missense	29882	exon6			ATATAGAGGGTGA	AB037827	CCDS7033.1	9q34.3	2011-06-15			ENSG00000176248	ENSG00000176248		"Anaphase promoting complex subunits"	19989	protein-coding gene	gene with protein product		606946				11739784	Standard	NM_013366		Approved	APC2, KIAA1406	uc004clr.1	Q9UJX6	OTTHUMG00000020983	ENST00000323927.2:c.1196T>C	chr9.hg19:g.140077667A>G	ENSP00000314004:p.Leu399Pro	136.0	0.0		93.0	5.0	NM_013366	Q5VSG1|Q96DG5|Q96GG4|Q9P2E1	Missense_Mutation	SNP	ENST00000323927.2	hg19	CCDS7033.1	.	.	.	.	.	.	.	.	.	.	A	17.71	3.456193	0.63401	.	.	ENSG00000176248	ENST00000323927	T	0.03124	4.04	4.83	4.83	0.62350	.	0.066268	0.64402	D	0.000019	T	0.11239	0.0274	L	0.55990	1.75	0.80722	D	1	D;D	0.64830	0.994;0.993	P;P	0.62491	0.903;0.843	T	0.07233	-1.0783	10	0.33940	T	0.23	-28.7388	12.3771	0.55285	1.0:0.0:0.0:0.0	.	399;396	Q9UJX6;Q9UJX6-2	ANC2_HUMAN;.	P	399	ENSP00000314004:L399P	ENSP00000314004:L399P	L	-	2	0	ANAPC2	139197488	1.000000	0.71417	0.981000	0.43875	0.988000	0.76386	8.545000	0.90657	2.034000	0.60081	0.459000	0.35465	CTC	.	.		0.622	ANAPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055315.1	NM_013366		G	140077667	A	G	140077667	3	3	254	1	0	0	0	0	1	0	0	0	603	304	11	2	1304	2	ANAPC2	9	140077667	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	41144	140077667	1135764	472	34764										
ANAPC2	29882	hgsc.bcm.edu	37	chr9	140082090	140082090	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cccttccagttccgggtctgTgcccccttcccccttcctct	6	21	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:140082090T>C	ENST00000323927.2	-	2	587	c.583A>G	c.(583-585)Aca>Gca	p.T195A	SSNA1_ENST00000322310.5_5'Flank	NM_013366.3	NP_037498.1	Q9UJX6	ANC2_HUMAN	anaphase promoting complex subunit 2	195					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of axon extension (GO:0045773)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)				breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	15	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.000858)		TCCGGGTCTGTGCCCCCTTCC	0.587																																					p.T195A		Atlas-SNP	.											.	ANAPC2	57	.	0			c.A583G						.						78	78	78					9																	140082090		2203	4300	6503	SO:0001583	missense	29882	exon2			GGTCTGTGCCCCC	AB037827	CCDS7033.1	9q34.3	2011-06-15			ENSG00000176248	ENSG00000176248		"Anaphase promoting complex subunits"	19989	protein-coding gene	gene with protein product		606946				11739784	Standard	NM_013366		Approved	APC2, KIAA1406	uc004clr.1	Q9UJX6	OTTHUMG00000020983	ENST00000323927.2:c.583A>G	chr9.hg19:g.140082090T>C	ENSP00000314004:p.Thr195Ala	148.0	0.0		95.0	4.0	NM_013366	Q5VSG1|Q96DG5|Q96GG4|Q9P2E1	Missense_Mutation	SNP	ENST00000323927.2	hg19	CCDS7033.1	.	.	.	.	.	.	.	.	.	.	T	10.29	1.308976	0.23821	.	.	ENSG00000176248	ENST00000323927	T	0.76186	-1.0	4.56	4.56	0.56223	.	0.373064	0.32608	N	0.005880	T	0.52917	0.1764	N	0.22421	0.69	0.27736	N	0.944655	B;B	0.24920	0.001;0.114	B;B	0.24394	0.001;0.053	T	0.41342	-0.9514	10	0.06757	T	0.87	-10.2173	6.7051	0.23246	0.0:0.1043:0.0:0.8957	.	195;195	Q9UJX6;Q9UJX6-2	ANC2_HUMAN;.	A	195	ENSP00000314004:T195A	ENSP00000314004:T195A	T	-	1	0	ANAPC2	139201911	0.973000	0.33851	0.994000	0.49952	0.946000	0.59487	1.708000	0.37899	1.915000	0.55452	0.459000	0.35465	ACA	.	.		0.587	ANAPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055315.1	NM_013366		C	140082090	T	C	140082090	3	2	254	1	0	0	0	0	1	0	0	0	603	1696	59	2	1933	2	ANAPC2	9	140082090	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	4423	140082090	1131341	473	34765										
C9orf167	54863	hgsc.bcm.edu	37	chr9	140173587	140173587	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cgataacgcgcagcgctatgAcctcgacgggctggagaaag	14	11	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr9:140173587A>G	ENST00000357503.2	+	2	642	c.446A>G	c.(445-447)gAc>gGc	p.D149G		NM_017723.2	NP_060193.2	Q9NXH8	TOR4A_HUMAN	torsin family 4, member A	149					chaperone mediated protein folding requiring cofactor (GO:0051085)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)										CAGCGCTATGACCTCGACGGG	0.652																																					p.D149G		Atlas-SNP	.											.	.	.	.	0			c.A446G						.						17	15	15					9																	140173587		2196	4296	6492	SO:0001583	missense	54863	exon2			GCTATGACCTCGA	AK023361	CCDS7041.1	9q34.3	2012-04-03	2012-04-03	2012-04-03	ENSG00000198113	ENSG00000198113			25981	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 167"	C9orf167			Standard	NM_017723		Approved	FLJ20245	uc004cmn.3	Q9NXH8	OTTHUMG00000131779	ENST00000357503.2:c.446A>G	chr9.hg19:g.140173587A>G	ENSP00000350102:p.Asp149Gly	97.0	0.0		67.0	4.0	NM_017723	A2BFA4	Missense_Mutation	SNP	ENST00000357503.2	hg19	CCDS7041.1	.	.	.	.	.	.	.	.	.	.	A	18.84	3.708706	0.68615	.	.	ENSG00000198113	ENST00000357503	T	0.46063	0.88	4.76	4.76	0.60689	.	0.000000	0.85682	D	0.000000	T	0.62551	0.2437	M	0.72894	2.215	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.66492	-0.5910	10	0.66056	D	0.02	-8.8223	13.0926	0.59174	1.0:0.0:0.0:0.0	.	149	Q9NXH8	CI167_HUMAN	G	149	ENSP00000350102:D149G	ENSP00000350102:D149G	D	+	2	0	C9orf167	139293408	1.000000	0.71417	1.000000	0.80357	0.723000	0.41478	4.678000	0.61641	1.770000	0.52166	0.459000	0.35465	GAC	.	.		0.652	TOR4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254711.1	NM_017723		G	140173587	A	G	140173587	3	3	254	1	0	0	0	0	1	0	0	0	2470	275	10	2	448	2	C9orf167	9	140173587	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	91497	140173587	1039844	474	34766										
AKR1E2	83592	hgsc.bcm.edu	37	chr10	4879675	4879675	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tggaggacctggtgatcaccGggctggtgaagaacatcggg	17	8	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:4879675G>T	ENST00000298375.7	+	5	555	c.484G>T	c.(484-486)Ggg>Tgg	p.G162W	AKR1E2_ENST00000334019.4_Missense_Mutation_p.G162W|AKR1E2_ENST00000345253.5_Intron|AKR1E2_ENST00000532248.1_Missense_Mutation_p.G162W|AKR1E2_ENST00000525281.1_3'UTR	NM_001040177.2	NP_001035267.1	Q96JD6	AKCL2_HUMAN	aldo-keto reductase family 1, member E2	162						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	1,5-anhydro-D-fructose reductase activity (GO:0050571)			NS(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)	15						GGTGATCACCGGGCTGGTGAA	0.507																																					p.G162W	NSCLC(43;343 1097 20371 28813 45509)	Atlas-SNP	.											.	AKR1E2	30	.	0			c.G484T						.						101	95	97					10																	4879675		2203	4300	6503	SO:0001583	missense	83592	exon5			ATCACCGGGCTGG	AB040820	CCDS31134.1, CCDS59210.1, CCDS59209.1	10p15.2	2009-09-09	2009-09-09	2009-09-09	ENSG00000165568	ENSG00000165568		"Aldo-keto reductases"	23437	protein-coding gene	gene with protein product			"aldo-keto reductase family 1, member C-like 2"	AKRDC1, AKR1CL2			Standard	NM_001271021		Approved	MGC10612	uc001ihi.4	Q96JD6	OTTHUMG00000017577	ENST00000298375.7:c.484G>T	chr10.hg19:g.4879675G>T	ENSP00000298375:p.Gly162Trp	98.0	0.0		81.0	4.0	NM_001040177	Q86Z16|Q86Z17|Q86Z18|Q9BU71	Missense_Mutation	SNP	ENST00000298375.7	hg19	CCDS31134.1	.	.	.	.	.	.	.	.	.	.	G	13.20	2.166273	0.38217	.	.	ENSG00000165568	ENST00000462718;ENST00000533295;ENST00000298375;ENST00000532248;ENST00000334019	D;T;T;T	0.87887	-2.31;-0.72;-0.72;-0.72	4.2	3.27	0.37495	Aldo/keto reductase, conserved site (1);NADP-dependent oxidoreductase domain (3);	0.000000	0.85682	D	0.000000	D	0.95671	0.8592	H	0.98333	4.205	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.96091	0.9061	10	0.87932	D	0	.	11.5482	0.50706	0.0:0.0:0.8199:0.1801	.	123;162;162;162	B7Z7K2;Q96JD6-2;Q96JD6;Q96JD6-3	.;.;AKCL2_HUMAN;.	W	58;166;162;162;162	ENSP00000435436:G166W;ENSP00000298375:G162W;ENSP00000432947:G162W;ENSP00000335034:G162W	ENSP00000298375:G162W	G	+	1	0	AKR1E2	4869675	1.000000	0.71417	0.557000	0.28306	0.012000	0.07955	6.848000	0.75409	1.314000	0.45095	0.455000	0.32223	GGG	.	.		0.507	AKR1E2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046520.4	NM_031436		T	4879675	G	T	4879675	3	4	254	1	0	0	0	0	1	0	0	0	474	1116	39	1	502	1	AKR1E2	10	4879675	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10		4879675	130655072	475	34767										
ITIH2	3698	hgsc.bcm.edu	37	chr10	7751027	7751027	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tttatagctataaagtccagTctactattacttctcggatg	6	8	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:7751027T>C	ENST00000358415.4	+	4	401	c.235T>C	c.(235-237)Tct>Cct	p.S79P	ITIH2_ENST00000480387.1_Intron|ITIH2_ENST00000379587.4_Missense_Mutation_p.S68P	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	79	VIT. {ECO:0000255|PROSITE- ProRule:PRU00801}.				hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(2)|breast(1)|endometrium(8)|kidney(1)|large_intestine(17)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64						TAAAGTCCAGTCTACTATTAC	0.418																																					p.S79P		Atlas-SNP	.											.	ITIH2	144	.	0			c.T235C						.						150	148	149					10																	7751027		2203	4300	6503	SO:0001583	missense	3698	exon4			GTCCAGTCTACTA	X07173	CCDS31141.1	10p14	2011-10-26	2011-10-26		ENSG00000151655	ENSG00000151655			6167	protein-coding gene	gene with protein product		146640	"inter-alpha (globulin) inhibitor, H2 polypeptide"			1385302, 10100603	Standard	NM_002216		Approved	H2P	uc001ijs.3	P19823	OTTHUMG00000017633	ENST00000358415.4:c.235T>C	chr10.hg19:g.7751027T>C	ENSP00000351190:p.Ser79Pro	107.0	0.0		91.0	4.0	NM_002216	Q14659|Q15484|Q5T986	Missense_Mutation	SNP	ENST00000358415.4	hg19	CCDS31141.1	.	.	.	.	.	.	.	.	.	.	T	13.22	2.171990	0.38315	.	.	ENSG00000151655	ENST00000358415;ENST00000429820;ENST00000379587	T;T;T	0.28895	1.59;1.59;1.59	5.5	5.5	0.81552	Vault protein inter-alpha-trypsin (2);Vault protein inter-alpha-trypsin, metazoa (1);	0.099413	0.64402	D	0.000001	T	0.60715	0.2290	M	0.90369	3.11	0.54753	D	0.999981	D	0.76494	0.999	D	0.76575	0.988	T	0.67546	-0.5643	10	0.56958	D	0.05	-23.9638	11.6215	0.51121	0.1331:0.0:0.0:0.8669	.	79	P19823	ITIH2_HUMAN	P	79;54;68	ENSP00000351190:S79P;ENSP00000388826:S54P;ENSP00000368906:S68P	ENSP00000351190:S79P	S	+	1	0	ITIH2	7791033	1.000000	0.71417	1.000000	0.80357	0.037000	0.13140	4.079000	0.57613	2.214000	0.71695	0.482000	0.46254	TCT	.	.		0.418	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	NM_002216		C	7751027	T	C	7751027	3	2	254	1	0	0	0	0	1	0	0	0	7913	1667	58	2	249	2	ITIH2	10	7751027	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	2871352	7751027	127783720	476	34768										
NUDT5	11164	hgsc.bcm.edu	37	chr10	12219831	12219831	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtagccccccattggtggtcGgaactgtttcaccagaacga	11	12	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:12219831G>T	ENST00000491614.1	-	5	645	c.250C>A	c.(250-252)Cga>Aga	p.R84R	NUDT5_ENST00000378940.3_Silent_p.R84R|NUDT5_ENST00000378952.3_5'UTR|NUDT5_ENST00000537776.1_Silent_p.R84R|NUDT5_ENST00000378927.3_Silent_p.R84R|NUDT5_ENST00000378937.3_Silent_p.R97R			Q9UKK9	NUDT5_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 5	84	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				D-ribose catabolic process (GO:0019303)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|ribonucleoside diphosphate catabolic process (GO:0009191)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	ADP-ribose diphosphatase activity (GO:0047631)|ADP-sugar diphosphatase activity (GO:0019144)|magnesium ion binding (GO:0000287)|nucleoside-diphosphatase activity (GO:0017110)|snoRNA binding (GO:0030515)			breast(1)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)	8		Renal(717;0.228)				ATTGGTGGTCGGAACTGTTTC	0.522																																					p.R84R		Atlas-SNP	.											NUDT5,caecum,carcinoma,0,1	NUDT5	10	.	0			c.C250A						.						115	89	98					10																	12219831		2203	4300	6503	SO:0001819	synonymous_variant	11164	exon5			GTGGTCGGAACTG	AF155832	CCDS7089.1	10p14	2008-05-14			ENSG00000165609	ENSG00000165609		"Nudix motif containing"	8052	protein-coding gene	gene with protein product		609230				10373642	Standard	NM_014142		Approved	hYSAH1, YSA1H	uc001ilj.3	Q9UKK9	OTTHUMG00000017682	ENST00000491614.1:c.250C>A	chr10.hg19:g.12219831G>T		91.0	0.0		54.0	4.0	NM_014142	A8K516|Q6IAG0|Q9UH49	Silent	SNP	ENST00000491614.1	hg19	CCDS7089.1																																																																																			.	.		0.522	NUDT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046811.1			T	12219831	G	T	12219831	2	4	254	1	0	0	0	0	0	0	0	1	10751	1124	39	1		1	NUDT5	10	12219831	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	4468804	12219831	123314916	477	34769										
NUDT5	11164	hgsc.bcm.edu	37	chr10	12219892	12219892	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctctgcagcacggggatgacCgcgacacctgtcaccaggaa	12	14	2	1	rs371734243		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:12219892C>A	ENST00000491614.1	-	5	584	c.189G>T	c.(187-189)gcG>gcT	p.A63A	NUDT5_ENST00000378940.3_Silent_p.A63A|NUDT5_ENST00000378952.3_5'UTR|NUDT5_ENST00000537776.1_Silent_p.A63A|NUDT5_ENST00000378927.3_Silent_p.A63A|NUDT5_ENST00000378937.3_Silent_p.A76A			Q9UKK9	NUDT5_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 5	63	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				D-ribose catabolic process (GO:0019303)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|ribonucleoside diphosphate catabolic process (GO:0009191)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	ADP-ribose diphosphatase activity (GO:0047631)|ADP-sugar diphosphatase activity (GO:0019144)|magnesium ion binding (GO:0000287)|nucleoside-diphosphatase activity (GO:0017110)|snoRNA binding (GO:0030515)			breast(1)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)	8		Renal(717;0.228)				CGGGGATGACCGCGACACCTG	0.502																																					p.A63A		Atlas-SNP	.											.	NUDT5	10	.	0			c.G189T						.						84	65	72					10																	12219892		2203	4300	6503	SO:0001819	synonymous_variant	11164	exon5			GATGACCGCGACA	AF155832	CCDS7089.1	10p14	2008-05-14			ENSG00000165609	ENSG00000165609		"Nudix motif containing"	8052	protein-coding gene	gene with protein product		609230				10373642	Standard	NM_014142		Approved	hYSAH1, YSA1H	uc001ilj.3	Q9UKK9	OTTHUMG00000017682	ENST00000491614.1:c.189G>T	chr10.hg19:g.12219892C>A		57.0	0.0		48.0	4.0	NM_014142	A8K516|Q6IAG0|Q9UH49	Silent	SNP	ENST00000491614.1	hg19	CCDS7089.1																																																																																			.	.		0.502	NUDT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046811.1			A	12219892	C	A	12219892	2	1	254	1	0	0	0	0	0	0	0	1	10751	639	23	1		1	NUDT5	10	12219892	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	61	12219892	123314855	478	34770										
FAM188A	80013	hgsc.bcm.edu	37	chr10	15821138	15821138	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcagtcccttctacgtacatGacctgttgaacaaaataaag	7	10	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:15821138G>T	ENST00000277632.3	-	15	1411	c.1191C>A	c.(1189-1191)gtC>gtA	p.V397V	FAM188A_ENST00000477891.1_5'UTR|FAM188A_ENST00000378036.1_Silent_p.V102V	NM_024948.2	NP_079224.1	Q9H8M7	F188A_HUMAN	family with sequence similarity 188, member A	397					apoptotic process (GO:0006915)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(2)|endometrium(5)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	22						CTACGTACATGACCTGTTGAA	0.398																																					p.V397V	Pancreas(159;946 1953 2111 4475 22008)	Atlas-SNP	.											.	FAM188A	44	.	0			c.C1191A						.						109	86	93					10																	15821138		2202	4300	6502	SO:0001819	synonymous_variant	80013	exon15			GTACATGACCTGT	AK023459	CCDS7110.1	10p13	2009-07-14	2009-07-14	2009-07-14	ENSG00000148481	ENSG00000148481			23578	protein-coding gene	gene with protein product	"caspase recruitment domain containing pro-apoptotic protein", "CARD-containing protein"	611649	"chromosome 10 open reading frame 97"	C10orf97		12054670, 17652099	Standard	XM_005252600		Approved	FLJ13397, CARP, my042, DERP5	uc001iod.1	Q9H8M7	OTTHUMG00000017734	ENST00000277632.3:c.1191C>A	chr10.hg19:g.15821138G>T		112.0	0.0		69.0	4.0	NM_024948	Q5SZ68|Q5SZ69|Q5SZ70|Q6IA40|Q6P7P0|Q7Z2S1|Q8WUF1|Q9H3I4	Silent	SNP	ENST00000277632.3	hg19	CCDS7110.1																																																																																			.	.		0.398	FAM188A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046990.2	NM_024948		T	15821138	G	T	15821138	2	4	254	1	0	0	0	0	0	0	0	1	5519	1277	45	3		3	FAM188A	10	15821138	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	3601246	15821138	119713609	479	34771										
CUBN	8029	hgsc.bcm.edu	37	chr10	17127716	17127716	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gacagagaaagtggtgcagaActtcccaagaagggggtcct	14	8	0	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:17127716A>G	ENST00000377833.4	-	16	2055	c.1990T>C	c.(1990-1992)Ttc>Ctc	p.F664L		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	664	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GTGGTGCAGAACTTCCCAAGA	0.448																																					p.F664L		Atlas-SNP	.											.	CUBN	515	.	0			c.T1990C						.						78	78	78					10																	17127716		2203	4300	6503	SO:0001583	missense	8029	exon16			TGCAGAACTTCCC	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.1990T>C	chr10.hg19:g.17127716A>G	ENSP00000367064:p.Phe664Leu	152.0	0.0		87.0	4.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	A	17.03	3.283422	0.59867	.	.	ENSG00000107611	ENST00000377833	T	0.19394	2.15	5.83	4.69	0.59074	CUB (5);	0.000000	0.44285	D	0.000471	T	0.16128	0.0388	L	0.31207	0.915	0.80722	D	1	P	0.35894	0.526	B	0.34301	0.179	T	0.02966	-1.1088	10	0.54805	T	0.06	.	11.6014	0.51006	0.9298:0.0:0.0702:0.0	.	664	O60494	CUBN_HUMAN	L	664	ENSP00000367064:F664L	ENSP00000367064:F664L	F	-	1	0	CUBN	17167722	1.000000	0.71417	0.942000	0.38095	0.327000	0.28475	6.043000	0.71004	1.031000	0.39867	0.533000	0.62120	TTC	.	.		0.448	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		G	17127716	A	G	17127716	3	3	254	1	0	0	0	0	1	0	0	0	4053	43	2	2	9089	2	CUBN	10	17127716	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	1306578	17127716	118407031	480	34772										
STAM	8027	hgsc.bcm.edu	37	chr10	17747603	17747603	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcagaaaacattcagaactcTcagaacttaatgtgaaagtg	7	7	3	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:17747603T>C	ENST00000377524.3	+	12	1287	c.1072T>C	c.(1072-1074)Tca>Cca	p.S358P	STAM_ENST00000540523.1_Missense_Mutation_p.S247P	NM_003473.3	NP_003464.1	Q92783	STAM1_HUMAN	signal transducing adaptor molecule (SH3 domain and ITAM motif) 1	358					endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	26						TTCAGAACTCTCAGAACTTAA	0.323																																					p.S358P		Atlas-SNP	.											STAM,colon,carcinoma,0,1	STAM	60	.	0			c.T1072C						.						91	90	90					10																	17747603		2202	4300	6502	SO:0001583	missense	8027	exon12			GAACTCTCAGAAC	U43899	CCDS7122.1	10p14-p13	2009-04-29			ENSG00000136738	ENSG00000136738			11357	protein-coding gene	gene with protein product	"HSE1 homolog (S. cerevisiae)"	601899				8780729	Standard	NM_003473		Approved	STAM1	uc001ipj.2	Q92783	OTTHUMG00000017749	ENST00000377524.3:c.1072T>C	chr10.hg19:g.17747603T>C	ENSP00000366746:p.Ser358Pro	82.0	0.0		59.0	3.0	NM_003473	B0YJ99|D3DRU5|Q8N6D9	Missense_Mutation	SNP	ENST00000377524.3	hg19	CCDS7122.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.680564	0.88542	.	.	ENSG00000136738	ENST00000377524;ENST00000540523	T;T	0.42513	1.31;0.97	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.65749	0.2721	M	0.78049	2.395	0.80722	D	1	D	0.71674	0.998	D	0.75484	0.986	T	0.68081	-0.5503	10	0.49607	T	0.09	-18.014	15.8513	0.78934	0.0:0.0:0.0:1.0	.	358	Q92783	STAM1_HUMAN	P	358;247	ENSP00000366746:S358P;ENSP00000438073:S247P	ENSP00000366746:S358P	S	+	1	0	STAM	17787609	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	2.152000	0.67230	0.533000	0.62120	TCA	.	.		0.323	STAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047039.1	NM_003473		C	17747603	T	C	17747603	3	2	254	1	0	0	0	0	1	0	0	0	15263	1551	54	2	1118	2	STAM	10	17747603	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	619887	17747603	117787144	481	34773										
ARL5B	221079	hgsc.bcm.edu	37	chr10	18963040	18963040	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcatccatggcacattcaatCctgctgtgctctcacaggag	8	13	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:18963040C>A	ENST00000377275.3	+	5	700	c.467C>A	c.(466-468)tCc>tAc	p.S156Y		NM_178815.3	NP_848930.1	Q96KC2	ARL5B_HUMAN	ADP-ribosylation factor-like 5B	156					small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)			lung(1)|ovary(1)	2						CACATTCAATCCTGCTGTGCT	0.413																																					p.S156Y		Atlas-SNP	.											.	ARL5B	12	.	0			c.C467A						.						108	94	98					10																	18963040		2203	4300	6503	SO:0001583	missense	221079	exon5			TTCAATCCTGCTG	AF494061	CCDS7131.1	10p13	2014-05-09	2005-11-03	2005-11-03	ENSG00000165997	ENSG00000165997		"ADP-ribosylation factors-like", "ADP-ribosylation factors"	23052	protein-coding gene	gene with protein product		608909	"ADP-ribosylation factor-like 8"	ARL8		12853149	Standard	XM_005252400		Approved		uc001iqd.1	Q96KC2	OTTHUMG00000017765	ENST00000377275.3:c.467C>A	chr10.hg19:g.18963040C>A	ENSP00000366487:p.Ser156Tyr	85.0	0.0		64.0	4.0	NM_178815		Missense_Mutation	SNP	ENST00000377275.3	hg19	CCDS7131.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.739167	0.89573	.	.	ENSG00000165997	ENST00000377275	D	0.82255	-1.59	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	D	0.89787	0.6816	M	0.67517	2.055	0.80722	D	1	D	0.63046	0.992	P	0.61722	0.893	D	0.90363	0.4375	10	0.87932	D	0	-3.4532	19.6088	0.95594	0.0:1.0:0.0:0.0	.	156	Q96KC2	ARL5B_HUMAN	Y	156	ENSP00000366487:S156Y	ENSP00000366487:S156Y	S	+	2	0	ARL5B	19003046	1.000000	0.71417	1.000000	0.80357	0.805000	0.45488	7.760000	0.85248	2.636000	0.89361	0.467000	0.42956	TCC	.	.		0.413	ARL5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047078.1	NM_178815		A	18963040	C	A	18963040	3	1	254	1	0	0	0	0	1	0	0	0	940	855	30	3	485	3	ARL5B	10	18963040	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1215437	18963040	116571707	482	34774										
NEBL	10529	hgsc.bcm.edu	37	chr10	21104614	21104614	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcaggagttacacttaaagtGgtagctcttcccagctgacc	9	11	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:21104614G>T	ENST00000377122.4	-	22	2577	c.2181C>A	c.(2179-2181)acC>acA	p.T727T	NEBL_ENST00000417816.2_Intron|NEBL_ENST00000377159.4_Intron	NM_006393.2	NP_006384.1	O76041	NEBL_HUMAN	nebulette	727					cardiac muscle thin filament assembly (GO:0071691)	extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|cytoskeletal protein binding (GO:0008092)|filamin binding (GO:0031005)|structural constituent of muscle (GO:0008307)|tropomyosin binding (GO:0005523)			NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						CACTTAAAGTGGTAGCTCTTC	0.323																																					p.T727T		Atlas-SNP	.											.	NEBL	199	.	0			c.C2181A						.						118	113	114					10																	21104614		2203	4300	6503	SO:0001819	synonymous_variant	10529	exon22			TAAAGTGGTAGCT	Y16241	CCDS7133.1, CCDS7134.1	10p12	2014-09-17			ENSG00000078114	ENSG00000078114			16932	protein-coding gene	gene with protein product		605491				9733644, 10470015	Standard	NM_213569		Approved		uc001iqi.3	O76041	OTTHUMG00000017788	ENST00000377122.4:c.2181C>A	chr10.hg19:g.21104614G>T		139.0	0.0		92.0	4.0	NM_006393	B0YJ45|Q2TBD0|Q70I54|Q9UIC4	Silent	SNP	ENST00000377122.4	hg19	CCDS7134.1																																																																																			.	.		0.323	NEBL-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047113.1	NM_006393		T	21104614	G	T	21104614	2	4	254	1	0	0	0	0	0	0	0	1	10312	1335	47	3		3	NEBL	10	21104614	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	2141574	21104614	114430133	483	34775										
MLLT10	8028	hgsc.bcm.edu	37	chr10	21884283	21884283	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gggcccatgtggtttgtgccCtgtatattccagaggtacaa	12	9	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:21884283C>T	ENST00000307729.7	+	5	497	c.319C>T	c.(319-321)Ctg>Ttg	p.L107L	MLLT10_ENST00000377059.3_Silent_p.L107L|MLLT10_ENST00000446906.2_Silent_p.L107L|MLLT10_ENST00000377072.3_Silent_p.L107L|MLLT10_ENST00000495130.1_3'UTR			P55197	AF10_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10	107	Self-association.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6						GGTTTGTGCCCTGTATATTCC	0.353			T	"MLL, PICALM, CDK6"	AL																																p.L107L		Atlas-SNP	.		Dom	yes		10	10p12	8028	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10 (AF10)"		L	MLLT10_ENST00000377072,colon,carcinoma,0,2	MLLT10	183	.	0			c.C319T						.						100	93	96					10																	21884283		2203	4300	6503	SO:0001819	synonymous_variant	8028	exon4			TGTGCCCTGTATA	U13948	CCDS7135.1, CCDS55706.1, CCDS55707.1, CCDS55708.1	10p12	2013-01-28	2001-11-28		ENSG00000078403	ENSG00000078403		"Zinc fingers, PHD-type"	16063	protein-coding gene	gene with protein product		602409	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 10"			7888665	Standard	NM_004641		Approved	AF10	uc021pny.1	P55197	OTTHUMG00000017799	ENST00000307729.7:c.319C>T	chr10.hg19:g.21884283C>T		128.0	0.0		98.0	5.0	NM_001195626	B1ANA8|Q5JT37|Q5VX90|Q66K63	Silent	SNP	ENST00000307729.7	hg19	CCDS55708.1																																																																																			.	.		0.353	MLLT10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047136.1			T	21884283	C	T	21884283	2	4	254	1	0	0	0	0	0	0	0	1	9635	680	24	3		3	MLLT10	10	21884283	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	779669	21884283	113650464	484	34776										
PIP4K2A	5305	hgsc.bcm.edu	37	chr10	22880591	22880591	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttcaggatgttgtgcatttcGgccacgtcttcactggtaat	10	9	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:22880591G>T	ENST00000376573.4	-	4	687	c.459C>A	c.(457-459)gcC>gcA	p.A153A	PIP4K2A_ENST00000323883.7_5'UTR|PIP4K2A_ENST00000422321.1_5'UTR|PIP4K2A_ENST00000545335.1_Silent_p.A94A	NM_005028.4	NP_005019.2	P48426	PI42A_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, alpha	153	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				megakaryocyte development (GO:0035855)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|1-phosphatidylinositol-5-phosphate 4-kinase activity (GO:0016309)|ATP binding (GO:0005524)			endometrium(4)|kidney(13)|large_intestine(4)|lung(6)|ovary(1)|skin(1)	29						TGTGCATTTCGGCCACGTCTT	0.453																																					p.A153A		Atlas-SNP	.											.	PIP4K2A	59	.	0			c.C459A						.						135	123	127					10																	22880591		2203	4300	6503	SO:0001819	synonymous_variant	5305	exon4			CATTTCGGCCACG	S78798	CCDS7141.1	10p12.2	2007-08-21	2007-08-14	2007-08-14	ENSG00000150867	ENSG00000150867			8997	protein-coding gene	gene with protein product		603140	"phosphatidylinositol-4-phosphate 5-kinase, type II, alpha"	PIP5K2A		7852364, 9367159	Standard	NM_005028		Approved	PIP5KIIA, PIP5KIIalpha	uc001irl.4	P48426	OTTHUMG00000017810	ENST00000376573.4:c.459C>A	chr10.hg19:g.22880591G>T		125.0	0.0		120.0	6.0	NM_005028	B0YJ66|B4DGX2|D3DRV1|P53807|Q5VUX3	Silent	SNP	ENST00000376573.4	hg19	CCDS7141.1																																																																																			.	.		0.453	PIP4K2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047193.1	NM_005028		T	22880591	G	T	22880591	2	4	254	1	0	0	0	0	0	0	0	1	11945	1103	39	1		1	PIP4K2A	10	22880591	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	996308	22880591	112654156	485	34777										
APBB1IP	54518	hgsc.bcm.edu	37	chr10	26825148	26825148	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	acccaaaggaaagactaaggTcagaaaaaaaaaaaaaaaag	7	5	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:26825148T>C	ENST00000376236.4	+	10	1499		c.e10+2			NM_019043.3	NP_061916.3	Q7Z5R6	AB1IP_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein						blood coagulation (GO:0007596)|platelet activation (GO:0030168)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(27)|skin(7)|upper_aerodigestive_tract(1)	45						AAGACTAAGGTCAGAAAAAAA	0.333																																					.		Atlas-SNP	.											.	APBB1IP	117	.	0			c.1044+2T>C						.						64	79	74					10																	26825148		2193	4294	6487	SO:0001630	splice_region_variant	54518	exon10			CTAAGGTCAGAAA	AB085852	CCDS31167.1	10p12.1	2013-01-10			ENSG00000077420	ENSG00000077420		"Pleckstrin homology (PH) domain containing"	17379	protein-coding gene	gene with protein product	"Rap1-GTP-interacting adaptor molecule"	609036				9407065	Standard	NM_019043		Approved	INAG1, RIAM	uc001iss.3	Q7Z5R6	OTTHUMG00000017841	ENST00000376236.4:c.1044+2T>C	chr10.hg19:g.26825148T>C		73.0	0.0		80.0	4.0	NM_019043	Q8IWS8|Q8IYL7|Q8IZZ7	Splice_Site	SNP	ENST00000376236.4	hg19	CCDS31167.1	.	.	.	.	.	.	.	.	.	.	T	17.96	3.517084	0.64634	.	.	ENSG00000077420	ENST00000445780;ENST00000376236	.	.	.	5.93	4.8	0.61643	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.6743	0.56884	0.1238:0.0:0.0:0.8762	.	.	.	.	.	-1	.	.	.	+	.	.	APBB1IP	26865154	1.000000	0.71417	1.000000	0.80357	0.748000	0.42578	8.040000	0.89188	1.073000	0.40885	-0.258000	0.10820	.	.	.		0.333	APBB1IP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047270.1	NM_019043	Intron	C	26825148	T	C	26825148	5	2	254	1	0	0	0	0	0	0	1	0	760	1681	58	2	1076	2	APBB1IP	10	26825148	Splice_Site	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	3944557	26825148	108709599	486	34778										
ZNF248	57209	hgsc.bcm.edu	37	chr10	38126943	38126943	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aagattgctataattttccaGgatcacatctctgtatagaa	6	7	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:38126943G>T	ENST00000395867.3	-	4	662	c.112C>A	c.(112-114)Ctg>Atg	p.L38M	ZNF248_ENST00000494133.1_5'UTR|ZNF248_ENST00000374648.3_Missense_Mutation_p.L38M|ZNF248_ENST00000357328.4_Missense_Mutation_p.L38M	NM_001267605.1|NM_001267606.1|NM_001267607.1|NM_021045.2	NP_001254534.1|NP_001254535.1|NP_001254536.1|NP_066383.1	Q8NDW4	ZN248_HUMAN	zinc finger protein 248	38	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(2)|urinary_tract(1)	20						TAATTTTCCAGGATCACATCT	0.418																																					p.L38M		Atlas-SNP	.											.	ZNF248	61	.	0			c.C112A						.						159	151	153					10																	38126943		2203	4300	6503	SO:0001583	missense	57209	exon4			TTTCCAGGATCAC	AJ491695	CCDS7194.1, CCDS58077.1, CCDS73087.1	10p11.21	2013-01-08			ENSG00000198105	ENSG00000198105		"Zinc fingers, C2H2-type", "-"	13041	protein-coding gene	gene with protein product						12566394	Standard	NM_021045		Approved	bA162G10.3	uc010qeu.2	Q8NDW4	OTTHUMG00000017980	ENST00000395867.3:c.112C>A	chr10.hg19:g.38126943G>T	ENSP00000379208:p.Leu38Met	148.0	0.0		96.0	4.0	NM_001267597	Q8NDV8|Q9UMP3	Missense_Mutation	SNP	ENST00000395867.3	hg19	CCDS7194.1	.	.	.	.	.	.	.	.	.	.	G	13.50	2.255122	0.39896	.	.	ENSG00000198105	ENST00000395867;ENST00000374648;ENST00000357328;ENST00000395873;ENST00000395874	T;T;T;T;T	0.58506	4.03;0.33;4.03;0.33;0.33	4.43	3.53	0.40419	Krueppel-associated box (4);	0.000000	0.35495	N	0.003172	T	0.79143	0.4396	M	0.93016	3.37	0.33771	D	0.623008	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.86561	0.1841	10	0.87932	D	0	.	10.4631	0.44592	0.097:0.0:0.903:0.0	.	38;38	Q8NDW4;Q8NDV8	ZN248_HUMAN;.	M	38	ENSP00000379208:L38M;ENSP00000363778:L38M;ENSP00000349882:L38M;ENSP00000379214:L38M;ENSP00000379215:L38M	ENSP00000349882:L38M	L	-	1	2	ZNF248	38166949	1.000000	0.71417	0.999000	0.59377	0.244000	0.25665	1.997000	0.40786	1.213000	0.43380	0.563000	0.77884	CTG	.	.		0.418	ZNF248-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047609.1	NM_021045		T	38126943	G	T	38126943	3	4	254	1	0	0	0	0	1	0	0	0	17808	991	35	3	1639	3	ZNF248	10	38126943	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	11301795	38126943	97407804	487	34779										
ZNF33A	7581	hgsc.bcm.edu	37	chr10	38343701	38343701	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agaagattcaaactttagagCacaattttgaatacagtata	6	5	1	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:38343701C>A	ENST00000458705.2	+	5	804	c.646C>A	c.(646-648)Cac>Aac	p.H216N	ZNF33A_ENST00000374618.3_Missense_Mutation_p.H217N|ZNF33A_ENST00000307441.9_Missense_Mutation_p.H216N|ZNF33A_ENST00000469037.2_Intron|ZNF33A_ENST00000432900.2_Missense_Mutation_p.H223N			Q06730	ZN33A_HUMAN	zinc finger protein 33A	216					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(2)|large_intestine(8)|liver(2)|lung(27)|ovary(2)|prostate(1)|skin(2)	46						AACTTTAGAGCACAATTTTGA	0.353																																					p.H217N		Atlas-SNP	.											.	ZNF33A	103	.	0			c.C649A						.						83	82	82					10																	38343701		2203	4300	6503	SO:0001583	missense	7581	exon5			TTAGAGCACAATT	D31763	CCDS31182.1, CCDS60514.1, CCDS73088.1, CCDS73089.1	10p11.2	2013-01-08	2005-03-18		ENSG00000189180	ENSG00000189180		"Zinc fingers, C2H2-type", "-"	13096	protein-coding gene	gene with protein product	"zinc finger and ZAK associated protein with KRAB domain"	194521	"zinc finger protein 33a (KOX 31)", "zinc finger protein 11A"	ZNF33, ZNF11A		2014798, 8464732	Standard	NM_006974		Approved	KOX5, KOX31, KIAA0065, FLJ23404, ZZAPK	uc031pui.1	Q06730	OTTHUMG00000017983	ENST00000458705.2:c.646C>A	chr10.hg19:g.38343701C>A	ENSP00000387713:p.His216Asn	142.0	0.0		118.0	5.0	NM_006954	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Missense_Mutation	SNP	ENST00000458705.2	hg19	CCDS31182.1	.	.	.	.	.	.	.	.	.	.	C	12.64	1.998246	0.35226	.	.	ENSG00000189180	ENST00000374618;ENST00000432900;ENST00000458705;ENST00000307441	T;T;T;T	0.05139	3.52;3.49;3.49;3.49	2.26	-0.992	0.10232	.	0.469523	0.15964	N	0.236124	T	0.03263	0.0095	N	0.22421	0.69	0.21841	N	0.999518	B;B;B	0.32467	0.372;0.097;0.184	B;B;B	0.26094	0.051;0.023;0.066	T	0.38178	-0.9673	10	0.56958	D	0.05	.	3.3177	0.07039	0.5539:0.2845:0.0:0.1616	.	223;216;217	F6TH33;Q06730;F8WAJ5	.;ZN33A_HUMAN;.	N	217;223;216;216	ENSP00000363747:H217N;ENSP00000402467:H223N;ENSP00000387713:H216N;ENSP00000304268:H216N	ENSP00000304268:H216N	H	+	1	0	ZNF33A	38383707	0.001000	0.12720	0.344000	0.25628	0.542000	0.35054	-0.069000	0.11542	0.085000	0.17107	0.460000	0.39030	CAC	.	.		0.353	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974		A	38343701	C	A	38343701	3	1	254	1	0	0	0	0	1	0	0	0	17869	710	25	3	663	3	ZNF33A	10	38343701	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	216758	38343701	97191046	488	34780										
ZNF33B	7582	hgsc.bcm.edu	37	chr10	43088543	43088543	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agtgagttgtgacttctggcAgaaggtttttccacattcat	10	7	2	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:43088543A>G	ENST00000359467.3	-	5	1969	c.1855T>C	c.(1855-1857)Tgc>Cgc	p.C619R	ZNF33B_ENST00000486187.1_RNA	NM_006955.1	NP_008886.1	Q06732	ZN33B_HUMAN	zinc finger protein 33B	619					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(15)|skin(1)|stomach(1)	29						GACTTCTGGCAGAAGGTTTTT	0.373																																					p.C619R	Melanoma(137;1247 1767 16772 25727 43810)	Atlas-SNP	.											.	ZNF33B	78	.	0			c.T1855C						.						95	95	95					10																	43088543		2203	4300	6503	SO:0001583	missense	7582	exon5			TCTGGCAGAAGGT	X68688, AJ491697	CCDS7198.1	10q11.2	2013-01-08	2005-03-18		ENSG00000196693	ENSG00000196693		"Zinc fingers, C2H2-type", "-"	13097	protein-coding gene	gene with protein product		194522	"zinc finger protein 33b (KOX 31)", "zinc finger protein 11B"	ZNF11B		2014798	Standard	NM_006955		Approved	KOX31, KOX2	uc001jaf.1	Q06732	OTTHUMG00000018014	ENST00000359467.3:c.1855T>C	chr10.hg19:g.43088543A>G	ENSP00000352444:p.Cys619Arg	129.0	0.0		121.0	5.0	NM_006955	Q06731|Q32MA2|Q86XY8|Q8NDW3	Missense_Mutation	SNP	ENST00000359467.3	hg19	CCDS7198.1	.	.	.	.	.	.	.	.	.	.	A	2.623	-0.288063	0.05605	.	.	ENSG00000196693	ENST00000359467;ENST00000395836	T	0.07327	3.2	2.58	2.58	0.30949	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.36740	N	0.002422	T	0.03783	0.0107	N	0.02202	-0.64	0.37728	D	0.925189	B	0.28552	0.215	B	0.34590	0.186	T	0.47497	-0.9113	10	0.35671	T	0.21	.	9.025	0.36224	1.0:0.0:0.0:0.0	.	619	Q06732	ZN33B_HUMAN	R	619;585	ENSP00000352444:C619R	ENSP00000352444:C619R	C	-	1	0	ZNF33B	42408549	0.012000	0.17670	0.995000	0.50966	0.982000	0.71751	0.506000	0.22658	1.446000	0.47643	0.336000	0.21669	TGC	.	.		0.373	ZNF33B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_006955		G	43088543	A	G	43088543	3	3	254	1	0	0	0	0	1	0	0	0	17870	188	7	2	485	2	ZNF33B	10	43088543	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	4744842	43088543	92446204	489	34781										
RASGEF1A	221002	hgsc.bcm.edu	37	chr10	43698747	43698747	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cagccaggccccgcctcaccTtttcaggcccggcttccagc	9	20	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:43698747T>C	ENST00000395809.1	-	3	2826	c.320A>G	c.(319-321)aAg>aGg	p.K107R	RASGEF1A_ENST00000374459.1_Splice_Site_p.K115R|RASGEF1A_ENST00000395810.1_Splice_Site_p.K107R|RASGEF1A_ENST00000472864.1_5'UTR			Q8N9B8	RGF1A_HUMAN	RasGEF domain family, member 1A	107	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				cell migration (GO:0016477)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	Ras guanyl-nucleotide exchange factor activity (GO:0005088)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(2)	11						CCGCCTCACCTTTTCAGGCCC	0.697																																					p.K107R		Atlas-SNP	.											.	RASGEF1A	66	.	0			c.A320G						.						8	8	8					10																	43698747		2136	4212	6348	SO:0001630	splice_region_variant	221002	exon3			CTCACCTTTTCAG	AK095136	CCDS7202.2, CCDS60517.1	10q11.21	2006-01-11			ENSG00000198915	ENSG00000198915			24246	protein-coding gene	gene with protein product		614531				12477932	Standard	XM_005271808		Approved	CG4853, FLJ37817	uc001jap.1	Q8N9B8	OTTHUMG00000018025	ENST00000395809.1:c.321+1A>G	chr10.hg19:g.43698747T>C		91.0	0.0		100.0	4.0	NM_145313	Q8TBF1	Missense_Mutation	SNP	ENST00000395809.1	hg19	CCDS7202.2	.	.	.	.	.	.	.	.	.	.	T	14.62	2.590975	0.46214	.	.	ENSG00000198915	ENST00000374459;ENST00000395810;ENST00000395809	T;T;T	0.51574	0.7;0.7;0.7	5.33	5.33	0.75918	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (3);	0.071891	0.56097	D	0.000027	T	0.43299	0.1241	L	0.48642	1.525	0.53688	D	0.999972	B;B	0.12630	0.006;0.005	B;B	0.20767	0.031;0.018	T	0.28038	-1.0056	10	0.35671	T	0.21	.	14.4595	0.67440	0.0:0.0:0.0:1.0	.	107;115	Q8N9B8;Q8N9B8-2	RGF1A_HUMAN;.	R	115;107;107	ENSP00000363583:K115R;ENSP00000379155:K107R;ENSP00000379154:K107R	ENSP00000363583:K115R	K	-	2	0	RASGEF1A	43018753	1.000000	0.71417	0.988000	0.46212	0.061000	0.15899	6.668000	0.74457	2.017000	0.59298	0.402000	0.26972	AAG	.	.		0.697	RASGEF1A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000313989.1	NM_145313	Missense_Mutation	C	43698747	T	C	43698747	5	2	254	1	0	0	0	0	0	0	1	0	13084	1623	56	2	1169	2	RASGEF1A	10	43698747	Splice_Site	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	610204	43698747	91836000	490	34782										
TMEM72	643236	hgsc.bcm.edu	37	chr10	45429084	45429084	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	acctggactccctctccccaGgtgtcaaccagggtccctgg	10	17	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:45429084G>T	ENST00000544540.1	+	3	339		c.e3-1		TMEM72-AS1_ENST00000450287.2_RNA			A0PK05	TMM72_HUMAN	transmembrane protein 72							integral component of membrane (GO:0016021)				breast(2)|kidney(1)|large_intestine(2)|lung(10)	15						CCTCTCCCCAGGTGTCAACCA	0.607																																					.		Atlas-SNP	.											.	TMEM72	25	.	0			c.210-1G>T						.						59	60	59					10																	45429084		1568	3582	5150	SO:0001630	splice_region_variant	643236	exon4			TCCCCAGGTGTCA	AB235418	CCDS41504.1	10q11.21	2008-10-24	2008-08-21	2008-08-21	ENSG00000187783	ENSG00000187783			31658	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 127"	C10orf127			Standard	NM_001123376		Approved	bA285G1.3, KSP37	uc001jbn.2	A0PK05	OTTHUMG00000018067	ENST00000544540.1:c.-145-1G>T	chr10.hg19:g.45429084G>T		63.0	0.0		52.0	4.0	NM_001123376	A1L181|Q5T740	Splice_Site	SNP	ENST00000544540.1	hg19		.	.	.	.	.	.	.	.	.	.	G	10.78	1.447607	0.26074	.	.	ENSG00000187783	ENST00000389583	.	.	.	5.58	5.58	0.84498	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4359	0.75146	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TMEM72	44749090	1.000000	0.71417	0.999000	0.59377	0.127000	0.20565	6.353000	0.73032	2.788000	0.95919	0.650000	0.86243	.	.	.		0.607	TMEM72-201	KNOWN	basic	protein_coding	protein_coding		NM_001123376	Intron	T	45429084	G	T	45429084	5	4	254	1	0	0	0	0	0	0	1	0	16216	1014	35	3	223	3	TMEM72	10	45429084	Splice_Site	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1730337	45429084	90105663	491	34783										
C10orf71	118461	hgsc.bcm.edu	37	chr10	50532329	50532329	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gaaggaccctacagctgaccCcagtgagccctctgcagaca	10	15	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:50532329C>T	ENST00000374144.3	+	3	2027	c.1739C>T	c.(1738-1740)cCc>cTc	p.P580L	C10orf71_ENST00000323868.4_Missense_Mutation_p.P580L			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	580										endometrium(1)	1						ACAGCTGACCCCAGTGAGCCC	0.547																																					p.P580L		Atlas-SNP	.											.	C10orf71	179	.	0			c.C1739T						.						41	42	42					10																	50532329		1996	4173	6169	SO:0001583	missense	118461	exon3			CTGACCCCAGTGA	AL833265	CCDS44387.1	10q11.23	2012-05-31			ENSG00000177354	ENSG00000177354			26973	protein-coding gene	gene with protein product							Standard	NM_001135196		Approved	FLJ45913	uc021pqa.2	Q711Q0	OTTHUMG00000018190	ENST00000374144.3:c.1739C>T	chr10.hg19:g.50532329C>T	ENSP00000363259:p.Pro580Leu	133.0	0.0		86.0	4.0	NM_001135196	A0AVL8	Missense_Mutation	SNP	ENST00000374144.3	hg19	CCDS44387.1	.	.	.	.	.	.	.	.	.	.	C	14.18	2.457083	0.43634	.	.	ENSG00000177354	ENST00000323868;ENST00000374144	T;T	0.13196	2.61;3.72	5.48	4.47	0.54385	.	0.470679	0.15889	N	0.239636	T	0.08044	0.0201	L	0.36672	1.1	0.09310	N	1	B	0.20988	0.05	B	0.17722	0.019	T	0.45963	-0.9225	10	0.02654	T	1	.	4.8407	0.13489	0.0:0.792:0.0:0.208	.	580	Q711Q0-3	.	L	580	ENSP00000318713:P580L;ENSP00000363259:P580L	ENSP00000318713:P580L	P	+	2	0	C10orf71	50202335	0.006000	0.16342	0.006000	0.13384	0.239000	0.25481	1.931000	0.40134	2.587000	0.87381	0.591000	0.81541	CCC	.	.		0.547	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459		T	50532329	C	T	50532329	3	4	254	1	0	0	0	0	1	0	0	0	1616	623	22	3	1741	3	C10orf71	10	50532329	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	5103245	50532329	85002418	492	34784										
CHAT	1103	hgsc.bcm.edu	37	chr10	50833615	50833615	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttctcctcctaccggctcccCggccatacccaggacacgct	7	20	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:50833615C>A	ENST00000337653.2	+	6	1002	c.849C>A	c.(847-849)ccC>ccA	p.P283P	CHAT_ENST00000455728.2_Silent_p.P165P|CHAT_ENST00000395559.2_Silent_p.P165P|CHAT_ENST00000351556.3_Silent_p.P165P|CHAT_ENST00000339797.1_Silent_p.P165P|CHAT_ENST00000395562.2_Silent_p.P201P	NM_001142929.1|NM_020549.4	NP_001136401.1|NP_065574	P28329	CLAT_HUMAN	choline O-acetyltransferase	283					adult walking behavior (GO:0007628)|dendrite development (GO:0016358)|establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|rhythmic behavior (GO:0007622)|rhythmic excitation (GO:0043179)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	choline O-acetyltransferase activity (GO:0004102)	p.P283P(1)		central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(11)|lung(34)|prostate(3)|urinary_tract(1)	56		all_neural(218;0.107)		GBM - Glioblastoma multiforme(2;0.000585)	Choline(DB00122)|Nicotine(DB00184)	ACCGGCTCCCCGGCCATACCC	0.587																																					p.P283P		Atlas-SNP	.											CHAT,NS,carcinoma,0,1	CHAT	162	.	1	Substitution - coding silent(1)	kidney(1)	c.C849A						.						47	36	40					10																	50833615		2203	4300	6503	SO:0001819	synonymous_variant	1103	exon6			GCTCCCCGGCCAT	AF305907	CCDS7232.1, CCDS7233.1, CCDS44389.1	10q11.2	2010-05-11	2010-05-11		ENSG00000070748	ENSG00000070748	2.3.1.6		1912	protein-coding gene	gene with protein product		118490	"choline acetyltransferase"			1840566	Standard	NM_020984		Approved		uc001jhz.2	P28329	OTTHUMG00000018198	ENST00000337653.2:c.849C>A	chr10.hg19:g.50833615C>A		108.0	0.0		71.0	4.0	NM_020549	A2BDF4|A2BDF5|Q16488|Q9BQ23|Q9BQ35|Q9BQE1	Silent	SNP	ENST00000337653.2	hg19	CCDS7232.1																																																																																			.	.		0.587	CHAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047997.1	NM_020549		A	50833615	C	A	50833615	2	1	254	1	0	0	0	0	0	0	0	1	3315	639	23	1		1	CHAT	10	50833615	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	301286	50833615	84701132	493	34785										
OGDHL	55753	hgsc.bcm.edu	37	chr10	50948862	50948862	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctgcggtcaacctcctggtcAtggagaacatggtgccggtg	14	11	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:50948862A>G	ENST00000374103.4	-	16	2119	c.2034T>C	c.(2032-2034)caT>caC	p.H678H	OGDHL_ENST00000419399.1_Silent_p.H621H|OGDHL_ENST00000432695.1_Silent_p.H469H|OGDHL_ENST00000490844.1_5'Flank	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	678					glycolytic process (GO:0006096)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	61						CCTCCTGGTCATGGAGAACAT	0.632																																					p.H678H		Atlas-SNP	.											.	OGDHL	149	.	0			c.T2034C						.						126	95	105					10																	50948862		2203	4300	6503	SO:0001819	synonymous_variant	55753	exon16			CTGGTCATGGAGA	AK001713	CCDS7234.1, CCDS44390.1, CCDS44391.1	10q11.23	2013-09-20			ENSG00000197444	ENSG00000197444			25590	protein-coding gene	gene with protein product						10574462	Standard	NM_018245		Approved	FLJ10851	uc001jie.3	Q9ULD0	OTTHUMG00000018200	ENST00000374103.4:c.2034T>C	chr10.hg19:g.50948862A>G		67.0	0.0		47.0	4.0	NM_018245	A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	Silent	SNP	ENST00000374103.4	hg19	CCDS7234.1																																																																																			.	.		0.632	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1	NM_018245		G	50948862	A	G	50948862	2	3	254	1	0	0	0	0	0	0	0	1	10849	214	8	2		2	OGDHL	10	50948862	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	115247	50948862	84585885	494	34786										
SGMS1	259230	hgsc.bcm.edu	37	chr10	52066912	52066912	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgtacagctgttatgtgtcaTtcaccagccggctgtattta	9	9	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:52066912T>C	ENST00000361781.2	-	11	2191	c.1232A>G	c.(1231-1233)aAt>aGt	p.N411S	SGMS1_ENST00000429490.1_Missense_Mutation_p.N242S	NM_147156.3	NP_671512.1	Q86VZ5	SMS1_HUMAN	sphingomyelin synthase 1	417					apoptotic process (GO:0006915)|cell growth (GO:0016049)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|Golgi trans cisterna (GO:0000138)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ceramide cholinephosphotransferase activity (GO:0047493)|kinase activity (GO:0016301)|sphingomyelin synthase activity (GO:0033188)			endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	16						TTATGTGTCATTCACCAGCCG	0.448																																					p.N411S		Atlas-SNP	.											.	SGMS1	40	.	0			c.A1232G						.						100	86	91					10																	52066912		2203	4300	6503	SO:0001583	missense	259230	exon11			GTGTCATTCACCA	AY280959	CCDS7240.1	10q11.2	2013-01-10	2007-03-16	2007-03-16	ENSG00000198964	ENSG00000198964	2.7.8.27	"Sterile alpha motif (SAM) domain containing"	29799	protein-coding gene	gene with protein product		611573	"transmembrane protein 23"	TMEM23		11841947, 14976195	Standard	NM_147156		Approved	MOB, MGC17342, SMS1	uc001jje.3	Q86VZ5	OTTHUMG00000018231	ENST00000361781.2:c.1232A>G	chr10.hg19:g.52066912T>C	ENSP00000354829:p.Asn411Ser	223.0	0.0		149.0	6.0	NM_147156	Q68U43|Q6EKK0|Q75SP1	Missense_Mutation	SNP	ENST00000361781.2	hg19	CCDS7240.1	.	.	.	.	.	.	.	.	.	.	T	9.604	1.129421	0.21041	.	.	ENSG00000198964	ENST00000412547;ENST00000361781;ENST00000429490	T	0.41400	1.0	5.58	3.22	0.36961	.	0.198210	0.47093	D	0.000258	T	0.17323	0.0416	N	0.03608	-0.345	0.80722	D	1	B;B	0.17038	0.02;0.002	B;B	0.12837	0.008;0.001	T	0.04386	-1.0955	10	0.26408	T	0.33	-11.3741	6.6094	0.22743	0.0:0.2538:0.0:0.7462	.	242;417	B4DJU2;Q86VZ5	.;SMS1_HUMAN	S	211;411;242	ENSP00000354829:N411S	ENSP00000354829:N411S	N	-	2	0	SGMS1	51736918	0.997000	0.39634	1.000000	0.80357	0.995000	0.86356	0.505000	0.22642	1.027000	0.39758	0.533000	0.62120	AAT	.	.		0.448	SGMS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048074.2	NM_147156		C	52066912	T	C	52066912	3	2	254	1	0	0	0	0	1	0	0	0	14229	1493	52	2	13	2	SGMS1	10	52066912	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	1118050	52066912	83467835	495	34787										
A1CF	29974	hgsc.bcm.edu	37	chr10	52619608	52619608	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcacaagttcctacctggacCaagctatatcctgtgcgctg	8	13	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:52619608C>A	ENST00000373993.1	-	1	137	c.93G>T	c.(91-93)ttG>ttT	p.L31F	A1CF_ENST00000374001.2_Missense_Mutation_p.L31F|A1CF_ENST00000395495.1_Missense_Mutation_p.L31F|A1CF_ENST00000373997.3_Missense_Mutation_p.L31F|A1CF_ENST00000282641.2_Missense_Mutation_p.L31F|A1CF_ENST00000373995.3_5'UTR|A1CF_ENST00000395489.2_5'UTR			Q9NQ94	A1CF_HUMAN	APOBEC1 complementation factor	31					cytidine to uridine editing (GO:0016554)|gene expression (GO:0010467)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|protein stabilization (GO:0050821)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			NS(1)|breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(14)|prostate(2)|skin(3)	29						CTACCTGGACCAAGCTATATC	0.502																																					p.L31F		Atlas-SNP	.											.	A1CF	190	.	0			c.G93T						.						84	74	78					10																	52619608		2203	4300	6503	SO:0001583	missense	29974	exon3			CTGGACCAAGCTA	AF271790	CCDS7241.1, CCDS7242.1, CCDS7243.1, CCDS73133.1	10q21.1	2013-02-12			ENSG00000148584	ENSG00000148584		"RNA binding motif (RRM) containing"	24086	protein-coding gene	gene with protein product						11815617, 11072063	Standard	NM_014576		Approved	ACF, ASP, ACF64, ACF65, APOBEC1CF	uc001jjj.3	Q9NQ94	OTTHUMG00000018240	ENST00000373993.1:c.93G>T	chr10.hg19:g.52619608C>A	ENSP00000363105:p.Leu31Phe	105.0	0.0		80.0	4.0	NM_138932	A1L4F2|A8K7G7|B7ZM14|Q5SZQ0|Q9NQ93|Q9NQX8|Q9NQX9|Q9NXC9|Q9NZD3	Missense_Mutation	SNP	ENST00000373993.1	hg19	CCDS7242.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.242686	0.79912	.	.	ENSG00000148584	ENST00000374001;ENST00000373993;ENST00000373997;ENST00000282641;ENST00000395495;ENST00000414883	T;T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;2.54;1.91	5.83	5.83	0.93111	.	0.644585	0.15345	N	0.267300	T	0.58177	0.2104	M	0.82630	2.6	0.80722	D	1	P;P	0.49783	0.846;0.928	B;P	0.47573	0.398;0.55	T	0.64385	-0.6420	10	0.72032	D	0.01	.	17.6277	0.88097	0.0:1.0:0.0:0.0	.	31;31	Q9NQ94;Q9NQ94-2	A1CF_HUMAN;.	F	31	ENSP00000363113:L31F;ENSP00000363105:L31F;ENSP00000363109:L31F;ENSP00000282641:L31F;ENSP00000378873:L31F;ENSP00000397953:L31F	ENSP00000282641:L31F	L	-	3	2	A1CF	52289614	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.253000	0.65452	2.770000	0.95276	0.655000	0.94253	TTG	.	.		0.502	A1CF-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048086.2	NM_014576		A	52619608	C	A	52619608	3	1	254	1	0	0	0	0	1	0	0	0	2	593	21	3	1862	3	A1CF	10	52619608	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	552696	52619608	82915139	496	34788										
EGR2	1959	hgsc.bcm.edu	37	chr10	64575711	64575711	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggcggcgaggtcctccaccgGgtagatgttgtcagacagct	15	11	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:64575711G>T	ENST00000242480.3	-	1	404	c.79C>A	c.(79-81)Ccg>Acg	p.P27T	EGR2_ENST00000493899.2_5'UTR|EGR2_ENST00000411732.1_5'UTR|EGR2_ENST00000439032.1_Missense_Mutation_p.P27T	NM_000399.3|NM_001136177.1	NP_000390.2|NP_001129649.1	P11161	EGR2_HUMAN	early growth response 2	27					brain development (GO:0007420)|brain segmentation (GO:0035284)|cell death (GO:0008219)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|facial nerve structural organization (GO:0021612)|fat cell differentiation (GO:0045444)|learning or memory (GO:0007611)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of apoptotic process (GO:0043066)|peripheral nervous system development (GO:0007422)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein export from nucleus (GO:0006611)|protein sumoylation (GO:0016925)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of ossification (GO:0030278)|response to insulin (GO:0032868)|rhombomere 3 formation (GO:0021660)|rhombomere 5 formation (GO:0021666)|rhythmic behavior (GO:0007622)|Schwann cell differentiation (GO:0014037)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|lung(13)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)	36	Prostate(12;0.0297)|all_hematologic(501;0.228)					TCCTCCACCGGGTAGATGTTG	0.582																																					p.P27T		Atlas-SNP	.											.	EGR2	77	.	0			c.C79A						.						183	166	172					10																	64575711		2203	4300	6503	SO:0001583	missense	1959	exon1			CCACCGGGTAGAT	BC035625	CCDS7267.1, CCDS44409.1	10q21.1	2014-09-17	2009-04-23		ENSG00000122877	ENSG00000122877		"Zinc fingers, C2H2-type"	3239	protein-coding gene	gene with protein product	"Krox-20 homolog, Drosophila"	129010	"early growth response 2 (Krox-20 homolog, Drosophila)"	KROX20			Standard	NM_000399		Approved		uc001jmi.3	P11161	OTTHUMG00000018308	ENST00000242480.3:c.79C>A	chr10.hg19:g.64575711G>T	ENSP00000242480:p.Pro27Thr	178.0	0.0		122.0	5.0	NM_000399	B2R724|B3KRD7|Q68CZ5|Q8IV26|Q9UNA6	Missense_Mutation	SNP	ENST00000242480.3	hg19	CCDS7267.1	.	.	.	.	.	.	.	.	.	.	G	17.07	3.296360	0.60086	.	.	ENSG00000122877	ENST00000242480;ENST00000439032;ENST00000432380	T;T	0.14766	2.48;2.48	5.1	5.1	0.69264	.	0.131508	0.53938	D	0.000058	T	0.14527	0.0351	L	0.59436	1.845	0.80722	D	1	P	0.43024	0.798	B	0.36289	0.221	T	0.01371	-1.1372	10	0.87932	D	0	-15.2967	11.9405	0.52899	0.0851:0.0:0.9149:0.0	.	27	P11161	EGR2_HUMAN	T	27;27;40	ENSP00000242480:P27T;ENSP00000402040:P27T	ENSP00000242480:P27T	P	-	1	0	EGR2	64245717	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.627000	0.54252	2.548000	0.85928	0.556000	0.70494	CCG	.	.		0.582	EGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048245.2	NM_000399		T	64575711	G	T	64575711	3	4	254	1	0	0	0	0	1	0	0	0	4974	1232	43	3	1359	3	EGR2	10	64575711	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	11956103	64575711	70959036	497	34789										
STOX1	219736	hgsc.bcm.edu	37	chr10	70645469	70645469	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gagaccaaacagactccgcaTagtctgccatcacgaggtgc	10	13	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:70645469T>C	ENST00000298596.6	+	3	2000	c.1917T>C	c.(1915-1917)caT>caC	p.H639H	STOX1_ENST00000399162.2_Intron|STOX1_ENST00000399169.4_Silent_p.H639H|STOX1_ENST00000399165.4_Intron|STOX1_ENST00000421961.2_Silent_p.H529H	NM_152709.4	NP_689922.3	Q6ZVD7	STOX1_HUMAN	storkhead box 1	639						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|prostate(1)|skin(3)	28						AGACTCCGCATAGTCTGCCAT	0.438																																					p.H639H		Atlas-SNP	.											.	STOX1	75	.	0			c.T1917C						.						128	121	123					10																	70645469		1926	4141	6067	SO:0001819	synonymous_variant	219736	exon3			TCCGCATAGTCTG	AK057891	CCDS41535.1, CCDS44416.1, CCDS44417.1	10q22.1	2005-11-29	2005-04-04	2005-04-04	ENSG00000165730	ENSG00000165730			23508	protein-coding gene	gene with protein product		609397	"chromosome 10 open reading frame 24"	C10orf24			Standard	NM_152709		Approved	FLJ25162	uc001joq.3	Q6ZVD7	OTTHUMG00000018367	ENST00000298596.6:c.1917T>C	chr10.hg19:g.70645469T>C		60.0	0.0		54.0	4.0	NM_152709	A2A3Q9|A5D6Y7|B0QZA4|B0QZA5|B0QZA6|Q4F8Q6|Q5I946|Q5I947|Q5I948|Q5VX38|Q5VX39|Q6ZRY3|Q96LR3|Q96LS0	Silent	SNP	ENST00000298596.6	hg19	CCDS41535.1																																																																																			.	.		0.438	STOX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276849.3	NM_152709		C	70645469	T	C	70645469	2	2	254	1	0	0	0	0	0	0	0	1	15334	1403	49	2		2	STOX1	10	70645469	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	6069758	70645469	64889278	498	34790										
PRF1	5551	hgsc.bcm.edu	37	chr10	72357906	72357906	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctcccaggtggggcaagcacCtggcatgatagcggaatttt	13	10	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:72357906C>A	ENST00000441259.1	-	3	1731	c.1571G>T	c.(1570-1572)aGg>aTg	p.R524M	PRF1_ENST00000373209.2_Missense_Mutation_p.R524M	NM_001083116.1|NM_005041.4	NP_001076585.1|NP_005032.2	P14222	PERF_HUMAN	perforin 1 (pore forming protein)	524					apoptotic process (GO:0006915)|cellular defense response (GO:0006968)|cytolysis (GO:0019835)|defense response to tumor cell (GO:0002357)|defense response to virus (GO:0051607)|immune response to tumor cell (GO:0002418)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)	cytolytic granule (GO:0044194)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|wide pore channel activity (GO:0022829)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(3)|urinary_tract(3)	23						GGGCAAGCACCTGGCATGATA	0.582			M			"various leukaemia, lymphoma"	Type 2 familial hemophagocytic lymphohistiocytosis		Familial Hemophagocytic Lymphohistiocytosis																												p.R524M		Atlas-SNP	.	yes	Rec			10	10q22	5551	perforin 1 (pore forming protein)		L	.	PRF1	64	.	0			c.G1571T						.						106	100	102					10																	72357906		2203	4300	6503	SO:0001583	missense	5551	exon3	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	AAGCACCTGGCAT	BC047695	CCDS7305.1	10q22	2014-09-17			ENSG00000180644	ENSG00000180644			9360	protein-coding gene	gene with protein product	"Perforin", "perforin 1 (preforming protein)"	170280				1505959, 2592021	Standard	NM_005041		Approved	PFP, P1, HPLH2	uc001jrf.4	P14222	OTTHUMG00000018412	ENST00000441259.1:c.1571G>T	chr10.hg19:g.72357906C>A	ENSP00000398568:p.Arg524Met	88.0	0.0		79.0	6.0	NM_001083116	B2R6X4|Q59F57|Q86WX7	Missense_Mutation	SNP	ENST00000441259.1	hg19	CCDS7305.1	.	.	.	.	.	.	.	.	.	.	C	11.54	1.667704	0.29604	.	.	ENSG00000180644	ENST00000373209;ENST00000441259;ENST00000318971	D;D	0.91237	-2.81;-2.81	5.97	-11.9	0.00025	.	1.068430	0.07158	N	0.850236	T	0.78553	0.4301	N	0.14661	0.345	0.09310	N	1	B	0.13145	0.007	B	0.11329	0.006	T	0.65849	-0.6068	10	0.49607	T	0.09	-3.7194	12.2817	0.54767	0.0714:0.196:0.6362:0.0964	.	524	P14222	PERF_HUMAN	M	524	ENSP00000362305:R524M;ENSP00000398568:R524M	ENSP00000316746:R524M	R	-	2	0	PRF1	72027912	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.888000	0.01616	-2.925000	0.00303	-2.226000	0.00293	AGG	.	.		0.582	PRF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048517.2	NM_005041		A	72357906	C	A	72357906	3	1	254	1	0	0	0	0	1	0	0	0	12490	681	24	3	100	3	PRF1	10	72357906	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1712437	72357906	63176841	499	34791										
PSAP	5660	hgsc.bcm.edu	37	chr10	73585601	73585601	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccgtgccacctaccatgtgcAtcatcatctggatagcaatt	7	13	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:73585601A>G	ENST00000394936.3	-	7	917	c.770T>C	c.(769-771)aTg>aCg	p.M257T	PSAP_ENST00000394934.1_Missense_Mutation_p.M257T			P07602	SAP_HUMAN	prosaposin	257	Saposin B-type 2. {ECO:0000255|PROSITE- ProRule:PRU00415}.				blood coagulation (GO:0007596)|cellular response to organic substance (GO:0071310)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|glycosphingolipid metabolic process (GO:0006687)|lipid transport (GO:0006869)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of catalytic activity (GO:0043085)|prostate gland growth (GO:0060736)|regulation of lipid metabolic process (GO:0019216)|regulation of MAPK cascade (GO:0043408)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|lipid binding (GO:0008289)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	13						TACCATGTGCATCATCATCTG	0.388																																					p.M257T		Atlas-SNP	.											.	PSAP	43	.	0			c.T770C						.						101	96	98					10																	73585601		2203	4300	6503	SO:0001583	missense	5660	exon7			ATGTGCATCATCA	BC004275	CCDS7311.1	10q21-q22	2014-01-30	2008-07-31		ENSG00000197746	ENSG00000197746		"Endogenous ligands"	9498	protein-coding gene	gene with protein product	"variant Gaucher disease and variant metachromatic leukodystrophy"	176801	"sphingolipid activator protein-1"	SAP1, GLBA		2717620	Standard	NM_001042465		Approved		uc001jsm.3	P07602	OTTHUMG00000018429	ENST00000394936.3:c.770T>C	chr10.hg19:g.73585601A>G	ENSP00000378394:p.Met257Thr	102.0	0.0		88.0	4.0	NM_001042466	P07292|P15793|P78538|P78541|P78546|P78547|P78558|Q53Y86|Q6IBQ6|Q92739|Q92740|Q92741|Q92742	Missense_Mutation	SNP	ENST00000394936.3	hg19	CCDS7311.1	.	.	.	.	.	.	.	.	.	.	A	19.50	3.839762	0.71488	.	.	ENSG00000197746	ENST00000394936;ENST00000373120;ENST00000357471;ENST00000394934;ENST00000404083;ENST00000394940	T;T	0.74842	-0.88;-0.88	5.3	5.3	0.74995	Saposin-like (2);Saposin-like type B, 2 (1);Saposin B (2);	0.077004	0.85682	D	0.000000	T	0.79839	0.4515	M	0.76002	2.32	0.58432	D	0.999997	P	0.47191	0.891	P	0.48873	0.593	T	0.81651	-0.0836	10	0.49607	T	0.09	-28.0768	15.2039	0.73162	1.0:0.0:0.0:0.0	.	257	P07602	SAP_HUMAN	T	257;257;257;257;260;182	ENSP00000378394:M257T;ENSP00000378392:M257T	ENSP00000350063:M257T	M	-	2	0	PSAP	73255607	1.000000	0.71417	1.000000	0.80357	0.638000	0.38207	4.259000	0.58828	2.143000	0.66587	0.459000	0.35465	ATG	.	.		0.388	PSAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048553.1	NM_002778		G	73585601	A	G	73585601	3	3	254	1	0	0	0	0	1	0	0	0	12655	217	8	2	852	2	PSAP	10	73585601	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	1227695	73585601	61949146	500	34792										
SEC24C	9632	hgsc.bcm.edu	37	chr10	75526220	75526220	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agccacagatgatggttgtgTctgatgtggctgacatgttt	13	6	1	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:75526220T>C	ENST00000339365.2	+	13	1882	c.1720T>C	c.(1720-1722)Tct>Cct	p.S574P	SEC24C_ENST00000345254.4_Missense_Mutation_p.S574P|SEC24C_ENST00000411652.2_Missense_Mutation_p.S455P|SEC24C_ENST00000540668.1_Intron|SEC24C_ENST00000546025.1_3'UTR|SEC24C_ENST00000535742.1_Intron	NM_004922.3	NP_004913.2	P53992	SC24C_HUMAN	SEC24 family member C	574					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(3)|lung(12)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	Prostate(51;0.0112)					GATGGTTGTGTCTGATGTGGC	0.502																																					p.S574P		Atlas-SNP	.											.	SEC24C	86	.	0			c.T1720C						.						100	83	89					10																	75526220		2203	4300	6503	SO:0001583	missense	9632	exon12			GTTGTGTCTGATG	D38555	CCDS7332.1	10q22	2013-10-21	2013-10-21		ENSG00000176986	ENSG00000176986			10705	protein-coding gene	gene with protein product		607185	"SEC24 (S. cerevisiae) related gene family, member C", "SEC24 family, member C (S. cerevisiae)"			10214955, 7584044	Standard	NM_004922		Approved	KIAA0079	uc001jux.3	P53992	OTTHUMG00000018476	ENST00000339365.2:c.1720T>C	chr10.hg19:g.75526220T>C	ENSP00000343405:p.Ser574Pro	69.0	0.0		50.0	4.0	NM_198597	B4DZT4|Q8WV25	Missense_Mutation	SNP	ENST00000339365.2	hg19	CCDS7332.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.229951	0.79688	.	.	ENSG00000176986	ENST00000345254;ENST00000339365;ENST00000411652	T;T;T	0.76186	-1.0;-1.0;-1.0	5.93	5.93	0.95920	Sec23/Sec24, trunk domain (1);	0.000000	0.85682	D	0.000000	T	0.79992	0.4542	L	0.39245	1.2	0.80722	D	1	D;D;D	0.64830	0.987;0.992;0.994	P;P;D	0.68943	0.82;0.874;0.961	T	0.75952	-0.3136	10	0.21014	T	0.42	-20.5737	16.3798	0.83452	0.0:0.0:0.0:1.0	.	455;574;574	E7EP00;G5EA31;P53992	.;.;SC24C_HUMAN	P	574;574;455	ENSP00000321845:S574P;ENSP00000343405:S574P;ENSP00000402913:S455P	ENSP00000343405:S574P	S	+	1	0	SEC24C	75196226	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	8.040000	0.89188	2.271000	0.75665	0.533000	0.62120	TCT	.	.		0.502	SEC24C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048679.1			C	75526220	T	C	75526220	3	2	254	1	0	0	0	0	1	0	0	0	14011	1667	58	2	1762	2	SEC24C	10	75526220	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	1940619	75526220	60008527	501	34793										
CAMK2G	818	hgsc.bcm.edu	37	chr10	75602229	75602229	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cactcaccttcagttttctcCgggcattgaacttgcgcaaa	7	13	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:75602229C>A	ENST00000351293.3	-	11	947	c.890G>T	c.(889-891)cGg>cTg	p.R297L	CAMK2G_ENST00000423381.1_Missense_Mutation_p.R297L|CAMK2G_ENST00000372765.1_Missense_Mutation_p.R297L|CAMK2G_ENST00000444854.2_Silent_p.P97P|CAMK2G_ENST00000394762.2_Missense_Mutation_p.R297L|CAMK2G_ENST00000322635.3_Missense_Mutation_p.R297L|CAMK2G_ENST00000322680.3_Missense_Mutation_p.R297L|CAMK2G_ENST00000472912.1_5'UTR|CAMK2G_ENST00000305762.7_Missense_Mutation_p.R297L|RP11-574K11.8_ENST00000446730.2_RNA	NM_001222.3|NM_172173.2	NP_001213.2|NP_751913.1	Q13555	KCC2G_HUMAN	calcium/calmodulin-dependent protein kinase II gamma	297	Calmodulin-binding.|Calmodulin-binding. {ECO:0000250}.				calcium ion transport (GO:0006816)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|dephosphorylation (GO:0016311)|G1/S transition of mitotic cell cycle (GO:0000082)|insulin secretion (GO:0030073)|interferon-gamma-mediated signaling pathway (GO:0060333)|nervous system development (GO:0007399)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of calcium ion transport (GO:0051924)|regulation of relaxation of cardiac muscle (GO:1901897)|regulation of skeletal muscle adaptation (GO:0014733)|synaptic transmission (GO:0007268)	calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-dependent protein serine/threonine phosphatase activity (GO:0004723)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|protein homodimerization activity (GO:0042803)			kidney(2)|large_intestine(2)|lung(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	15	Prostate(51;0.0112)				Bosutinib(DB06616)	CAGTTTTCTCCGGGCATTGAA	0.542																																					p.R297L		Atlas-SNP	.											.	CAMK2G	79	.	0			c.G890T						.						128	115	120					10																	75602229		2203	4300	6503	SO:0001583	missense	818	exon11			TTTCTCCGGGCAT	U81554	CCDS7336.1, CCDS7337.1, CCDS7338.1, CCDS73153.1	10q22	2008-10-30	2008-10-30		ENSG00000148660	ENSG00000148660			1463	protein-coding gene	gene with protein product		602123	"calcium/calmodulin-dependent protein kinase (CaM kinase) II gamma"	CAMKG		8287681	Standard	NM_001204492		Approved		uc001jvm.2	Q13555	OTTHUMG00000018492	ENST00000351293.3:c.890G>T	chr10.hg19:g.75602229C>A	ENSP00000277853:p.Arg297Leu	110.0	0.0		91.0	5.0	NM_172170	O00561|O15378|Q13279|Q13282|Q13556|Q5SQZ3|Q5SQZ4|Q5SWX4|Q7KYX5|Q8N4I3|Q8NIA4	Missense_Mutation	SNP	ENST00000351293.3	hg19	CCDS7336.1	.	.	.	.	.	.	.	.	.	.	C	36	5.757903	0.96898	.	.	ENSG00000148660	ENST00000351293;ENST00000322635;ENST00000423381;ENST00000394763;ENST00000322680;ENST00000394762;ENST00000433289;ENST00000305762;ENST00000372765	T;T;T;T;T;T;T;T	0.70045	-0.38;1.96;-0.39;-0.36;-0.39;-0.45;-0.4;1.96	5.87	5.87	0.94306	Protein kinase-like domain (1);	0.000000	0.64402	D	0.000001	D	0.83362	0.5238	M	0.86178	2.8	0.80722	D	1	P;P;P;P;B;B;P;D;D	0.60575	0.935;0.807;0.935;0.878;0.186;0.128;0.661;0.975;0.988	P;B;P;P;B;B;B;P;P	0.61477	0.569;0.274;0.569;0.464;0.037;0.04;0.33;0.622;0.889	D	0.85128	0.0973	10	0.87932	D	0	.	20.2079	0.98282	0.0:1.0:0.0:0.0	.	297;289;297;297;297;297;297;297;297	Q13555-2;B3KY86;Q13555-4;Q13555-6;Q13555-10;A8K6N9;Q13555;Q13555-5;Q13555-8	.;.;.;.;.;.;KCC2G_HUMAN;.;.	L	297;297;297;297;297;297;232;297;297	ENSP00000277853:R297L;ENSP00000315599:R297L;ENSP00000410298:R297L;ENSP00000319060:R297L;ENSP00000378243:R297L;ENSP00000393784:R232L;ENSP00000307082:R297L;ENSP00000361851:R297L	ENSP00000307082:R297L	R	-	2	0	CAMK2G	75272235	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.810000	0.86072	2.781000	0.95711	0.655000	0.94253	CGG	.	.		0.542	CAMK2G-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048715.1	NM_172169		A	75602229	C	A	75602229	3	1	254	1	0	0	0	0	1	0	0	0	2604	652	23	1	924	1	CAMK2G	10	75602229	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	76009	75602229	59932518	502	34794										
C10orf55	414236	hgsc.bcm.edu	37	chr10	75671984	75671984	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tctctccagcgaactgtgacTgtctaaatggaggaacatgt	10	9	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:75671984T>C	ENST00000409178.1	-	4	359	c.19A>G	c.(19-21)Agt>Ggt	p.S7G	PLAU_ENST00000372764.3_Missense_Mutation_p.C33R|PLAU_ENST00000446342.1_Missense_Mutation_p.C16R|C10orf55_ENST00000412307.2_Missense_Mutation_p.S7G|PLAU_ENST00000494287.1_3'UTR|PLAU_ENST00000372762.4_Intron	NM_001001791.2	NP_001001791.2	Q5SWW7	CJ055_HUMAN	chromosome 10 open reading frame 55	7										endometrium(1)	1	Prostate(51;0.0112)					GAACTGTGACTGTCTAAATGG	0.537																																					p.C33R		Atlas-SNP	.											.	PLAU	47	.	0			c.T97C						.						106	95	99					10																	75671984		2203	4300	6503	SO:0001583	missense	5328	exon4			TGTGACTGTCTAA		CCDS53541.1	10q22.2	2012-05-24			ENSG00000222047	ENSG00000222047			31008	protein-coding gene	gene with protein product							Standard	NM_001001791		Approved	bA417O11.3	uc001jvz.2	Q5SWW7	OTTHUMG00000018496	ENST00000409178.1:c.19A>G	chr10.hg19:g.75671984T>C	ENSP00000386960:p.Ser7Gly	94.0	0.0		93.0	4.0	NM_002658	Q3KRG4|Q8NAK4	Missense_Mutation	SNP	ENST00000409178.1	hg19	CCDS53541.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.64|15.64	2.891905|2.891905	0.52014|0.52014	.|.	.|.	ENSG00000122861|ENSG00000222047	ENST00000446342;ENST00000372764|ENST00000409178;ENST00000412307	D;D|.	0.89123|.	-2.37;-2.47|.	5.84|5.84	5.84|5.84	0.93424|0.93424	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.40067|0.40067	0.1102|0.1102	N|N	0.08118|0.08118	0|0	0.26793|0.26793	N|N	0.969365|0.969365	D;D;D|D	0.89917|0.89917	1.0;1.0;1.0|1.0	D;D;D|D	0.97110|0.72338	0.998;0.998;1.0|0.977	T|T	0.41342|0.41342	-0.9514|-0.9514	9|8	.|0.87932	.|D	.|0	.|.	12.6036|12.6036	0.56511|0.56511	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	16;33;33|7	E7ET40;B2R7F2;P00749|Q5SWW7	.;.;UROK_HUMAN|CJ055_HUMAN	R|G	16;33|7	ENSP00000388474:C16R;ENSP00000361850:C33R|.	.|ENSP00000386960:S7G	C|S	+|-	1|1	0|0	PLAU|C10orf55	75341990|75341990	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.144000|0.144000	0.21451|0.21451	4.825000|4.825000	0.62708|0.62708	2.234000|2.234000	0.73211|0.73211	0.402000|0.402000	0.26972|0.26972	TGT|AGT	.	.		0.537	C10orf55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048746.1	NM_001001791		C	75671984	T	C	75671984	3	2	254	1	0	0	0	0	1	0	0	0	1610	1580	55	2	444	2	C10orf55	10	75671984	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	69755	75671984	59862763	503	34795										
MAT1A	4143	hgsc.bcm.edu	37	chr10	82039957	82039957	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tagagtcaggccgcagccagGggaggaggccggagcgcctg	19	11	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:82039957G>T	ENST00000372213.3	-	5	781	c.521C>A	c.(520-522)cCc>cAc	p.P174H		NM_000429.2	NP_000420.1	Q00266	METK1_HUMAN	methionine adenosyltransferase I, alpha	174					cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|S-adenosylmethionine biosynthetic process (GO:0006556)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methionine adenosyltransferase activity (GO:0004478)			endometrium(4)|large_intestine(7)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26			Colorectal(32;0.229)		L-Methionine(DB00134)|S-Adenosylmethionine(DB00118)	CCGCAGCCAGGGGAGGAGGCC	0.567																																					p.P174H		Atlas-SNP	.											.	MAT1A	52	.	0			c.C521A						.						67	76	73					10																	82039957		2203	4300	6503	SO:0001583	missense	4143	exon5			AGCCAGGGGAGGA		CCDS7365.1	10q22	2008-08-01			ENSG00000151224	ENSG00000151224			6903	protein-coding gene	gene with protein product	"S-adenosylmethionine synthetase"	610550				8393662	Standard	XM_005269842		Approved	MAT, SAMS, MATA1, SAMS1	uc001kbw.3	Q00266	OTTHUMG00000018613	ENST00000372213.3:c.521C>A	chr10.hg19:g.82039957G>T	ENSP00000361287:p.Pro174His	100.0	0.0		70.0	19.0	NM_000429	D3DWD5|Q5QP09	Missense_Mutation	SNP	ENST00000372213.3	hg19	CCDS7365.1	.	.	.	.	.	.	.	.	.	.	G	18.96	3.732975	0.69189	.	.	ENSG00000151224	ENST00000372213;ENST00000372206;ENST00000455001	D;D	0.83250	-1.7;-1.7	4.91	4.91	0.64330	S-adenosylmethionine synthetase, central domain (1);S-adenosylmethionine synthetase superfamily (1);	0.000000	0.85682	D	0.000000	D	0.89866	0.6839	M	0.88512	2.96	0.80722	D	1	P	0.52692	0.955	P	0.52909	0.713	D	0.92061	0.5656	10	0.87932	D	0	-27.5525	15.935	0.79694	0.0:0.0:1.0:0.0	.	174	Q00266	METK1_HUMAN	H	174;174;111	ENSP00000361287:P174H;ENSP00000414961:P111H	ENSP00000361280:P174H	P	-	2	0	MAT1A	82029937	1.000000	0.71417	0.997000	0.53966	0.655000	0.38815	7.528000	0.81941	2.442000	0.82660	0.655000	0.94253	CCC	.	.		0.567	MAT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049070.1	NM_000429		T	82039957	G	T	82039957	3	4	254	1	0	0	0	0	1	0	0	0	9338	1232	43	3	686	3	MAT1A	10	82039957	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	6367973	82039957	53494790	504	34796										
TSPAN14	81619	hgsc.bcm.edu	37	chr10	82275975	82275975	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgcagctgaagagcaagtggGatgagtccatcttcacgaaa	12	8	2	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:82275975G>T	ENST00000429989.3	+	8	860	c.637G>T	c.(637-639)Gat>Tat	p.D213Y	TSPAN14_ENST00000372164.3_Missense_Mutation_p.D196Y|TSPAN14_ENST00000372156.1_Missense_Mutation_p.D213Y|TSPAN14_ENST00000481124.1_Missense_Mutation_p.D90Y|TSPAN14_ENST00000341863.6_Missense_Mutation_p.D156Y|TSPAN14_ENST00000265450.5_3'UTR|TSPAN14_ENST00000372158.1_Missense_Mutation_p.D213Y	NM_030927.2	NP_112189.2	Q8NG11	TSN14_HUMAN	tetraspanin 14	213					establishment of protein localization to plasma membrane (GO:0090002)|positive regulation of Notch signaling pathway (GO:0045747)|protein maturation (GO:0051604)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	enzyme binding (GO:0019899)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	7			Colorectal(32;0.229)			GAGCAAGTGGGATGAGTCCAT	0.562																																					p.D213Y		Atlas-SNP	.											.	TSPAN14	29	.	0			c.G637T						.						135	120	125					10																	82275975		2203	4300	6503	SO:0001583	missense	81619	exon8			AAGTGGGATGAGT	AF311903	CCDS7369.1, CCDS44448.1	10q23.1	2013-02-14	2005-03-21	2005-03-21	ENSG00000108219	ENSG00000108219		"Tetraspanins"	23303	protein-coding gene	gene with protein product			"transmembrane 4 superfamily member 14"	TM4SF14		11230166	Standard	NM_030927		Approved	DC-TM4F2, MGC11352	uc001kcj.4	Q8NG11	OTTHUMG00000018615	ENST00000429989.3:c.637G>T	chr10.hg19:g.82275975G>T	ENSP00000396270:p.Asp213Tyr	154.0	0.0		83.0	4.0	NM_030927	A6NHE1|B4DHY6|D3DWD7|D3DWD8|Q567U7|Q9BU34|Q9H0U1	Missense_Mutation	SNP	ENST00000429989.3	hg19	CCDS7369.1	.	.	.	.	.	.	.	.	.	.	G	17.89	3.500877	0.64298	.	.	ENSG00000108219	ENST00000429989;ENST00000481124;ENST00000372157;ENST00000372164;ENST00000372158;ENST00000341863;ENST00000372156	T;T;T;T;T;T;T	0.79554	-1.28;-1.28;-1.28;-1.28;-1.28;-1.28;-1.28	5.57	5.57	0.84162	Tetraspanin, EC2 domain (1);	0.523983	0.22284	N	0.062088	T	0.78585	0.4306	N	0.17082	0.46	0.42227	D	0.991878	D;P;P	0.61697	0.99;0.903;0.94	P;P;P	0.60236	0.871;0.722;0.601	T	0.80341	-0.1423	10	0.66056	D	0.02	-21.4631	10.4742	0.44655	0.088:0.0:0.912:0.0	.	90;213;196	B4DHY6;Q8NG11;Q8NG11-2	.;TSN14_HUMAN;.	Y	213;90;183;196;213;156;213	ENSP00000396270:D213Y;ENSP00000418195:D90Y;ENSP00000361230:D183Y;ENSP00000361237:D196Y;ENSP00000361231:D213Y;ENSP00000344076:D156Y;ENSP00000361229:D213Y	ENSP00000344076:D156Y	D	+	1	0	TSPAN14	82265955	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	3.381000	0.52455	2.643000	0.89663	0.591000	0.81541	GAT	.	.		0.562	TSPAN14-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049081.2	NM_030927		T	82275975	G	T	82275975	3	4	254	1	0	0	0	0	1	0	0	0	16653	1174	41	3	663	3	TSPAN14	10	82275975	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	236018	82275975	53258772	505	34797										
IFIT2	3433	hgsc.bcm.edu	37	chr10	91066851	91066851	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tccatctgcggtatggcaacTttcagctgtaccaaatgaag	9	10	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:91066851T>C	ENST00000371826.3	+	2	1307	c.1138T>C	c.(1138-1140)Ttt>Ctt	p.F380L	LIPA_ENST00000487618.1_Intron|LIPA_ENST00000371837.1_Intron	NM_001547.4	NP_001538.4	P09913	IFIT2_HUMAN	interferon-induced protein with tetratricopeptide repeats 2	380					apoptotic mitochondrial changes (GO:0008637)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|negative regulation of protein binding (GO:0032091)|positive regulation of apoptotic process (GO:0043065)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|skin(1)	12		Colorectal(252;0.0161)				GTATGGCAACTTTCAGCTGTA	0.408																																					p.F380L		Atlas-SNP	.											.	IFIT2	39	.	0			c.T1138C						.						93	87	89					10																	91066851		1914	4128	6042	SO:0001583	missense	3433	exon2			GGCAACTTTCAGC	M14660	CCDS41548.1	10q23.31	2013-01-11			ENSG00000119922	ENSG00000119922		"Tetratricopeptide (TTC) repeat domain containing"	5409	protein-coding gene	gene with protein product		147040		IFI54, G10P2		3175763, 3360121	Standard	NM_001547		Approved	IFI-54, ISG-54K, cig42, GARG-39	uc009xts.3	P09913	OTTHUMG00000018707	ENST00000371826.3:c.1138T>C	chr10.hg19:g.91066851T>C	ENSP00000360891:p.Phe380Leu	96.0	0.0		91.0	4.0	NM_001547	Q5T767	Missense_Mutation	SNP	ENST00000371826.3	hg19	CCDS41548.1	.	.	.	.	.	.	.	.	.	.	T	19.00	3.741715	0.69304	.	.	ENSG00000119922	ENST00000371826	T	0.20463	2.07	4.58	2.12	0.27331	Tetratricopeptide-like helical (1);	0.078649	0.52532	U	0.000072	T	0.24236	0.0587	L	0.58969	1.84	0.41503	D	0.988297	D	0.54397	0.966	P	0.48598	0.583	T	0.02031	-1.1226	10	0.42905	T	0.14	-8.7326	7.5678	0.27890	0.1403:0.0:0.1468:0.7129	.	380	P09913	IFIT2_HUMAN	L	380	ENSP00000360891:F380L	ENSP00000360891:F380L	F	+	1	0	IFIT2	91056831	0.976000	0.34144	0.994000	0.49952	0.994000	0.84299	2.922000	0.48860	0.449000	0.26747	0.533000	0.62120	TTT	.	.		0.408	IFIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049293.1	NM_001547		C	91066851	T	C	91066851	3	2	254	1	0	0	0	0	1	0	0	0	7532	1609	56	2	1144	2	IFIT2	10	91066851	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	8790876	91066851	44467896	506	34798										
IDE	3416	hgsc.bcm.edu	37	chr10	94291601	94291601	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	catcacattcttctcatgttCtgaatcaactgcattcacct	3	13	6	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:94291601C>A	ENST00000265986.6	-	4	621	c.565G>T	c.(565-567)Gaa>Taa	p.E189*		NM_004969.3	NP_004960.2	P14735	IDE_HUMAN	insulin-degrading enzyme	189					beta-amyloid metabolic process (GO:0050435)|bradykinin catabolic process (GO:0010815)|determination of adult lifespan (GO:0008340)|hormone catabolic process (GO:0042447)|insulin catabolic process (GO:1901143)|insulin metabolic process (GO:1901142)|insulin receptor signaling pathway (GO:0008286)|negative regulation of proteolysis (GO:0045861)|positive regulation of protein oligomerization (GO:0032461)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein homotetramerization (GO:0051289)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|ubiquitin homeostasis (GO:0010992)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|beta-amyloid binding (GO:0001540)|beta-endorphin binding (GO:0031626)|glycoprotein binding (GO:0001948)|insulin binding (GO:0043559)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|urinary_tract(2)	33					"""Insulin(DB00071)|Bacitracin(DB00626)|Insulin Regular(DB00030)"	TTCTCATGTTCTGAATCAACT	0.398																																					p.E189X		Atlas-SNP	.											.	IDE	77	.	0			c.G565T						.						98	90	92					10																	94291601		2203	4300	6503	SO:0001587	stop_gained	3416	exon4			CATGTTCTGAATC	M21188	CCDS7421.1, CCDS53554.1	10q23-q25	2007-03-27			ENSG00000119912	ENSG00000119912			5381	protein-coding gene	gene with protein product	"insulysin"	146680				2293021	Standard	NM_004969		Approved		uc001kia.3	P14735	OTTHUMG00000018759	ENST00000265986.6:c.565G>T	chr10.hg19:g.94291601C>A	ENSP00000265986:p.Glu189*	114.0	0.0		76.0	5.0	NM_004969	B2R721|B7ZAU2|D3DR35|Q5T5N2	Nonsense_Mutation	SNP	ENST00000265986.6	hg19	CCDS7421.1	.	.	.	.	.	.	.	.	.	.	C	35	5.577823	0.96565	.	.	ENSG00000119912	ENST00000265986;ENST00000436178	.	.	.	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-16.124	19.6584	0.95853	0.0:1.0:0.0:0.0	.	.	.	.	X	189;175	.	ENSP00000265986:E189X	E	-	1	0	IDE	94281581	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.747000	0.85070	2.646000	0.89796	0.655000	0.94253	GAA	.	.		0.398	IDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049393.1	NM_004969		A	94291601	C	A	94291601	4	1	254	1	0	0	0	0	0	1	0	0	7502	922	32	3	2582	3	IDE	10	94291601	Nonsense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	3224750	94291601	41243146	507	34799										
HPS1	3257	hgsc.bcm.edu	37	chr10	100182230	100182230	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctgcccagtggtgcggtccaCatagatgaagtgcaccaagc	12	12	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:100182230C>T	ENST00000325103.6	-	17	1872	c.1639G>A	c.(1639-1641)Gtg>Atg	p.V547M	HPS1_ENST00000361490.4_Missense_Mutation_p.V547M|HPS1_ENST00000467246.1_5'UTR	NM_000195.3	NP_000186.2	Q92902	HPS1_HUMAN	Hermansky-Pudlak syndrome 1	547					blood coagulation (GO:0007596)|eye pigmentation (GO:0048069)|lysosome organization (GO:0007040)|melanocyte differentiation (GO:0030318)|positive regulation of natural killer cell activation (GO:0032816)|retina development in camera-type eye (GO:0060041)|secretion of lysosomal enzymes (GO:0033299)|visual perception (GO:0007601)	BLOC-3 complex (GO:0031085)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	protein dimerization activity (GO:0046983)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	23		Colorectal(252;0.234)		Epithelial(162;3.87e-12)|all cancers(201;5.63e-10)		GTGCGGTCCACATAGATGAAG	0.572									Hermansky-Pudlak syndrome																												p.V547M		Atlas-SNP	.											.	HPS1	65	.	0			c.G1639A						.						114	111	112					10																	100182230		2203	4300	6503	SO:0001583	missense	3257	exon17	Familial Cancer Database	HPS, HPS1-8	GGTCCACATAGAT	U79136	CCDS7475.1, CCDS7476.1	10q23.1-q23.3	2014-06-18		2002-05-01	ENSG00000107521	ENSG00000107521			5163	protein-coding gene	gene with protein product		604982	"Hermansky-Pudlak syndrome"	HPS		8541858, 7573033	Standard	NM_182639		Approved		uc021pwv.1	Q92902	OTTHUMG00000018876	ENST00000325103.6:c.1639G>A	chr10.hg19:g.100182230C>T	ENSP00000326649:p.Val547Met	87.0	0.0		89.0	4.0	NM_000195	A8MRT2|O15402|O15502|Q5TAA3|Q8WXE5	Missense_Mutation	SNP	ENST00000325103.6	hg19	CCDS7475.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.965098	0.74131	.	.	ENSG00000107521	ENST00000325103;ENST00000361490;ENST00000407891	T;T	0.32988	1.43;1.43	5.37	1.48	0.22813	.	0.062767	0.64402	D	0.000004	T	0.54727	0.1876	M	0.86178	2.8	0.80722	D	1	D;D;D	0.89917	0.994;1.0;0.994	P;D;P	0.91635	0.894;0.999;0.894	T	0.54139	-0.8338	10	0.59425	D	0.04	.	9.8855	0.41260	0.0:0.7252:0.0:0.2748	.	514;547;548	Q92902-2;Q8WXE5;D3DR62	.;.;.	M	547;547;514	ENSP00000326649:V547M;ENSP00000355310:V547M	ENSP00000326649:V547M	V	-	1	0	HPS1	100172220	1.000000	0.71417	0.927000	0.36925	0.822000	0.46500	4.434000	0.59935	0.012000	0.14892	0.561000	0.74099	GTG	.	.		0.572	HPS1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049776.1	NM_000195, NM_182637, NM_182638, NM_182639		T	100182230	C	T	100182230	3	4	254	1	0	0	0	0	1	0	0	0	7348	478	17	3	479	3	HPS1	10	100182230	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	5890629	100182230	35352517	508	34800										
ABCC2	1244	hgsc.bcm.edu	37	chr10	101567952	101567952	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tatcctgcgctttcccctgaGcatgcttcccatgatgatct	7	14	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:101567952G>A	ENST00000370449.4	+	13	1894	c.1781G>A	c.(1780-1782)aGc>aAc	p.S594N		NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	594	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular chloride ion homeostasis (GO:0030644)|drug transmembrane transport (GO:0006855)|prostaglandin transport (GO:0015732)|response to arsenic-containing substance (GO:0046685)|response to estrogen (GO:0043627)|response to heat (GO:0009408)|response to methotrexate (GO:0031427)|response to oxidative stress (GO:0006979)|thyroid hormone transport (GO:0070327)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(5)|endometrium(9)|kidney(2)|large_intestine(20)|liver(1)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	67		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Aminohippurate(DB00345)|Arsenic trioxide(DB01169)|Atorvastatin(DB01076)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carboplatin(DB00958)|Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Eprosartan(DB00876)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Ezetimibe(DB00973)|Furosemide(DB00695)|Fusidic Acid(DB02703)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Leucovorin(DB00650)|Levetiracetam(DB01202)|Lomefloxacin(DB00978)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nifedipine(DB01115)|Norgestimate(DB00957)|Ofloxacin(DB01165)|Olmesartan(DB00275)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Ritonavir(DB00503)|Saquinavir(DB01232)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Sulfasalazine(DB00795)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Tenofovir(DB00300)|Tetrahydrofolic acid(DB00116)|Ursodeoxycholic acid(DB01586)|Vasopressin(DB00067)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	TTTCCCCTGAGCATGCTTCCC	0.473																																					p.S594N		Atlas-SNP	.											.	ABCC2	160	.	0			c.G1781A						.						241	210	221					10																	101567952		2203	4300	6503	SO:0001583	missense	1244	exon13			CCCTGAGCATGCT	U63970	CCDS7484.1	10q24	2012-03-14			ENSG00000023839	ENSG00000023839		"ATP binding cassette transporters / subfamily C"	53	protein-coding gene	gene with protein product		601107	"canalicular multispecific organic anion transporter 1"	CMOAT		8797578, 9284939	Standard	XM_006717630		Approved	DJS, MRP2, cMRP	uc001kqf.2	Q92887	OTTHUMG00000018895	ENST00000370449.4:c.1781G>A	chr10.hg19:g.101567952G>A	ENSP00000359478:p.Ser594Asn	160.0	0.0		115.0	39.0	NM_000392	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Missense_Mutation	SNP	ENST00000370449.4	hg19	CCDS7484.1	.	.	.	.	.	.	.	.	.	.	G	2.621	-0.288648	0.05605	.	.	ENSG00000023839	ENST00000370449	T	0.29142	1.58	5.63	1.32	0.21799	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);	0.767826	0.12970	N	0.424253	T	0.22859	0.0552	N	0.25789	0.76	0.58432	D	0.999999	B	0.30326	0.276	B	0.28709	0.093	T	0.14008	-1.0488	10	0.07813	T	0.8	-12.9795	20.8761	0.99795	0.0:0.8123:0.1877:0.0	.	594	Q92887	MRP2_HUMAN	N	594	ENSP00000359478:S594N	ENSP00000359478:S594N	S	+	2	0	ABCC2	101557942	0.003000	0.15002	0.157000	0.22605	0.964000	0.63967	0.116000	0.15561	0.253000	0.21552	0.491000	0.48974	AGC	.	.		0.473	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392		A	101567952	G	A	101567952	3	1	254	1	0	0	0	0	1	0	0	0	53	971	34	3	1831	3	ABCC2	10	101567952	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1385722	101567952	33966795	509	34801										
CPN1	1369	hgsc.bcm.edu	37	chr10	101824984	101824984	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcaggcgtgggggtgctggcGgtgcggcggacccctcggac	20	12	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:101824984G>T	ENST00000370418.3	-	4	971	c.720C>A	c.(718-720)acC>acA	p.T240T		NM_001308.2	NP_001299.1	P15169	CBPN_HUMAN	carboxypeptidase N, polypeptide 1	240	Catalytic.				response to glucocorticoid (GO:0051384)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	33		Colorectal(252;0.234)		Epithelial(162;4.77e-10)|all cancers(201;3.82e-08)		GGGTGCTGGCGGTGCGGCGGA	0.602																																					p.T240T		Atlas-SNP	.											.	CPN1	62	.	0			c.C720A						.						61	65	64					10																	101824984		2203	4300	6503	SO:0001819	synonymous_variant	1369	exon4			GCTGGCGGTGCGG	X14329	CCDS7486.1	10q24.2	2012-02-10	2007-02-23		ENSG00000120054	ENSG00000120054	3.4.17.3		2312	protein-coding gene	gene with protein product	"anaphylatoxin inactivator", "arginine carboxypeptidase", "carboxypeptidase K", "kininase I", "lysine carboxypeptidase"	603103	"carboxypeptidase N, polypeptide 1, 50kD"			9628828, 2912725	Standard	NM_001308		Approved		uc001kql.2	P15169	OTTHUMG00000018896	ENST00000370418.3:c.720C>A	chr10.hg19:g.101824984G>T		96.0	0.0		87.0	4.0	NM_001308	B1AP59	Silent	SNP	ENST00000370418.3	hg19	CCDS7486.1																																																																																			.	.		0.602	CPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049828.1	NM_001308		T	101824984	G	T	101824984	2	4	254	1	0	0	0	0	0	0	0	1	3811	1103	39	1		1	CPN1	10	101824984	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	257032	101824984	33709763	510	34802										
CHUK	1147	hgsc.bcm.edu	37	chr10	101964400	101964400	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttgttaagttagcattatatCtaagaagacttaacctaaac	5	6	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:101964400C>A	ENST00000370397.7	-	13	1456	c.1370G>T	c.(1369-1371)aGa>aTa	p.R457I		NM_001278.3	NP_001269.3	O15111	IKKA_HUMAN	conserved helix-loop-helix ubiquitous kinase	457	Leucine-zipper.				anatomical structure morphogenesis (GO:0009653)|cellular response to tumor necrosis factor (GO:0071356)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|morphogenesis of an epithelial sheet (GO:0002011)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hydroperoxide (GO:0033194)|response to lipopolysaccharide (GO:0032496)|response to toxic substance (GO:0009636)|response to virus (GO:0009615)|Rho protein signal transduction (GO:0007266)|skeletal muscle contraction (GO:0003009)|striated muscle cell differentiation (GO:0051146)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|scaffold protein binding (GO:0097110)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(9)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	27		Colorectal(252;0.117)		Epithelial(162;2.05e-10)|all cancers(201;1.91e-08)	Acetylcysteine(DB06151)|Aminosalicylic Acid(DB00233)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	AGCATTATATCTAAGAAGACT	0.289																																					p.R457I	Ovarian(159;52 1904 10536 35305 37148)	Atlas-SNP	.											.	CHUK	71	.	0			c.G1370T						.						89	83	85					10																	101964400		2202	4300	6502	SO:0001583	missense	1147	exon13			TTATATCTAAGAA	AF009225	CCDS7488.1	10q24-q25	2008-08-01			ENSG00000213341	ENSG00000213341			1974	protein-coding gene	gene with protein product		600664		TCF16		7558004, 16902410	Standard	XR_246062		Approved	IKK1, IKK-alpha, IkBKA, NFKBIKA, IKKA	uc001kqp.3	O15111	OTTHUMG00000018899	ENST00000370397.7:c.1370G>T	chr10.hg19:g.101964400C>A	ENSP00000359424:p.Arg457Ile	104.0	0.0		115.0	5.0	NM_001278	O14666|Q13132|Q5W0I4|Q92467	Missense_Mutation	SNP	ENST00000370397.7	hg19	CCDS7488.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.893339	0.91889	.	.	ENSG00000213341	ENST00000370397	T	0.77489	-1.1	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	D	0.87152	0.6106	M	0.68593	2.085	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.87874	0.2673	10	0.87932	D	0	-18.3766	17.3158	0.87224	0.0:1.0:0.0:0.0	.	457	O15111	IKKA_HUMAN	I	457	ENSP00000359424:R457I	ENSP00000359424:R457I	R	-	2	0	CHUK	101954390	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.818000	0.86416	2.696000	0.92011	0.650000	0.86243	AGA	.	.		0.289	CHUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049836.1	NM_001278		A	101964400	C	A	101964400	3	1	254	1	0	0	0	0	1	0	0	0	3418	913	32	3	903	3	CHUK	10	101964400	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	139416	101964400	33570347	511	34803										
CHUK	1147	hgsc.bcm.edu	37	chr10	101982628	101982628	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aaacatccacactacctttcGgagatctcctccagaacagt	5	14	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:101982628G>T	ENST00000370397.7	-	3	396	c.310C>A	c.(310-312)Cga>Aga	p.R104R		NM_001278.3	NP_001269.3	O15111	IKKA_HUMAN	conserved helix-loop-helix ubiquitous kinase	104	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				anatomical structure morphogenesis (GO:0009653)|cellular response to tumor necrosis factor (GO:0071356)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|morphogenesis of an epithelial sheet (GO:0002011)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hydroperoxide (GO:0033194)|response to lipopolysaccharide (GO:0032496)|response to toxic substance (GO:0009636)|response to virus (GO:0009615)|Rho protein signal transduction (GO:0007266)|skeletal muscle contraction (GO:0003009)|striated muscle cell differentiation (GO:0051146)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|scaffold protein binding (GO:0097110)	p.R104*(1)		breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(9)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	27		Colorectal(252;0.117)		Epithelial(162;2.05e-10)|all cancers(201;1.91e-08)	Acetylcysteine(DB06151)|Aminosalicylic Acid(DB00233)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	ACTACCTTTCGGAGATCTCCT	0.353																																					p.R104R	Ovarian(159;52 1904 10536 35305 37148)	Atlas-SNP	.											CHUK,NS,carcinoma,0,1	CHUK	71	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C310A						.						110	96	101					10																	101982628		2203	4300	6503	SO:0001819	synonymous_variant	1147	exon3			CCTTTCGGAGATC	AF009225	CCDS7488.1	10q24-q25	2008-08-01			ENSG00000213341	ENSG00000213341			1974	protein-coding gene	gene with protein product		600664		TCF16		7558004, 16902410	Standard	XR_246062		Approved	IKK1, IKK-alpha, IkBKA, NFKBIKA, IKKA	uc001kqp.3	O15111	OTTHUMG00000018899	ENST00000370397.7:c.310C>A	chr10.hg19:g.101982628G>T		86.0	1.0		98.0	4.0	NM_001278	O14666|Q13132|Q5W0I4|Q92467	Silent	SNP	ENST00000370397.7	hg19	CCDS7488.1																																																																																			.	.		0.353	CHUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049836.1	NM_001278		T	101982628	G	T	101982628	2	4	254	1	0	0	0	0	0	0	0	1	3418	1124	39	1		1	CHUK	10	101982628	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	18228	101982628	33552119	512	34804										
OBFC1	79991	hgsc.bcm.edu	37	chr10	105652001	105652001	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cttggaagtggtgtccttctTaaaattcacctgtaaagaga	9	7	2	1	rs553430081		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:105652001T>C	ENST00000224950.3	-	8	930	c.763A>G	c.(763-765)Aag>Gag	p.K255E	OBFC1_ENST00000369764.1_Missense_Mutation_p.K255E|OBFC1_ENST00000466828.1_5'UTR	NM_024928.4	NP_079204.2	Q9H668	STN1_HUMAN	oligonucleotide/oligosaccharide-binding fold containing 1	255	Winged helix-turn-helix (wHTH) 1.				positive regulation of DNA replication (GO:0045740)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromosome, telomeric region (GO:0000784)|nucleolus (GO:0005730)|nucleus (GO:0005634)|Stn1-Ten1 complex (GO:0070188)	single-stranded DNA binding (GO:0003697)|single-stranded telomeric DNA binding (GO:0043047)			large_intestine(3)|lung(7)|ovary(1)|pancreas(2)	13		Colorectal(252;0.178)		Epithelial(162;3.39e-10)|all cancers(201;1.32e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0151)		GTGTCCTTCTTAAAATTCACC	0.363													T|||	1	0.000199681	8e-04	0	5008	,	,		17281	0		0	False		,,,				2504	0				p.K255E		Atlas-SNP	.											.	OBFC1	33	.	0			c.A763G						.						75	76	76					10																	105652001		2203	4300	6503	SO:0001583	missense	79991	exon8			CCTTCTTAAAATT	BC017400	CCDS7552.1	10q25.1	2011-06-14				ENSG00000107960			26200	protein-coding gene	gene with protein product		613128				12477932	Standard	NM_024928		Approved	FLJ22559, bA541N10.2	uc001kxm.3	Q9H668		ENST00000224950.3:c.763A>G	chr10.hg19:g.105652001T>C	ENSP00000224950:p.Lys255Glu	77.0	0.0		93.0	4.0	NM_024928	D3DR99|Q5TCZ0	Missense_Mutation	SNP	ENST00000224950.3	hg19	CCDS7552.1	.	.	.	.	.	.	.	.	.	.	T	0.046	-1.266407	0.01433	.	.	ENSG00000107960	ENST00000224950;ENST00000369764	T;T	0.43294	0.95;0.95	5.23	2.82	0.32997	Domain of unknown function DUF1879, CTS complex STN1 subunit (1);	0.768337	0.13102	N	0.413671	T	0.29749	0.0743	L	0.37561	1.115	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.17258	-1.0375	10	0.27785	T	0.31	-13.7692	7.0044	0.24828	0.0:0.0838:0.1523:0.7639	.	255	Q9H668	STN1_HUMAN	E	255	ENSP00000224950:K255E;ENSP00000358779:K255E	ENSP00000224950:K255E	K	-	1	0	OBFC1	105641991	0.410000	0.25376	0.292000	0.24919	0.203000	0.24098	0.817000	0.27281	0.903000	0.36546	-0.466000	0.05196	AAG	.	.		0.363	OBFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050174.1	NM_024928		C	105652001	T	C	105652001	3	2	254	1	0	0	0	0	1	0	0	0	10816	1763	61	2	355	2	OBFC1	10	105652001	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	3669373	105652001	29882746	513	34805										
VWA2	340706	hgsc.bcm.edu	37	chr10	116045927	116045927	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtgcctgacctggtctggagCctcgatggcattcccttccg	12	14	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:116045927C>T	ENST00000392982.3	+	11	1477	c.1227C>T	c.(1225-1227)agC>agT	p.S409S	VWA2_ENST00000603594.1_Silent_p.S409S			Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	409	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				calcium-independent cell-matrix adhesion (GO:0007161)|protein homooligomerization (GO:0051260)|regulation of insulin receptor signaling pathway (GO:0046626)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Epithelial(162;0.036)|all cancers(201;0.0793)		TGGTCTGGAGCCTCGATGGCA	0.687																																					p.S409S		Atlas-SNP	.											.	VWA2	64	.	0			c.C1227T						.						78	71	73					10																	116045927		2203	4300	6503	SO:0001819	synonymous_variant	340706	exon11			CTGGAGCCTCGAT	AK127756	CCDS7589.1, CCDS7589.2	10q25.3	2009-11-06			ENSG00000165816	ENSG00000165816			24709	protein-coding gene	gene with protein product						15580307, 14506275	Standard	NM_001272046		Approved	FLJ45857, FLJ16213, CCSP-2, AMACO, NET42	uc001lbl.2	Q5GFL6	OTTHUMG00000019082	ENST00000392982.3:c.1227C>T	chr10.hg19:g.116045927C>T		159.0	0.0		85.0	4.0	NM_001272046	A1A5D4|B5MDJ8|Q6ZS39|Q6ZWJ7|Q708C5|Q70UZ8	Silent	SNP	ENST00000392982.3	hg19																																																																																				.	.		0.687	VWA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050456.3	NM_198496		T	116045927	C	T	116045927	2	4	254	1	0	0	0	0	0	0	0	1	17254	738	26	3		3	VWA2	10	116045927	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	10393926	116045927	19488820	514	34806										
BTBD16	118663	hgsc.bcm.edu	37	chr10	124096039	124096039	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	acacagacctggaatctcccTctgcggtctacgagcacaac	8	15	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:124096039T>C	ENST00000260723.4	+	15	1545	c.1294T>C	c.(1294-1296)Tct>Cct	p.S432P	BTBD16_ENST00000495370.2_3'UTR|BTBD16_ENST00000368994.2_Missense_Mutation_p.S433P	NM_144587.2	NP_653188.2	Q32M84	BTBDG_HUMAN	BTB (POZ) domain containing 16	432										breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(3)|skin(2)|stomach(1)|urinary_tract(1)	15		all_neural(114;0.107)|Lung NSC(174;0.175)|all_lung(145;0.222)|Breast(234;0.238)				GGAATCTCCCTCTGCGGTCTA	0.562																																					p.S432P		Atlas-SNP	.											.	BTBD16	44	.	0			c.T1294C						.						69	59	62					10																	124096039		2203	4300	6503	SO:0001583	missense	118663	exon15			TCTCCCTCTGCGG	AK058088	CCDS31301.1	10q26.13	2013-01-24	2006-07-04	2006-07-04	ENSG00000138152	ENSG00000138152		"BTB/POZ domain containing"	26340	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 87"	C10orf87			Standard	NM_144587		Approved	FLJ25359, Em:AC061711.1	uc001lgc.1	Q32M84	OTTHUMG00000019182	ENST00000260723.4:c.1294T>C	chr10.hg19:g.124096039T>C	ENSP00000260723:p.Ser432Pro	121.0	0.0		93.0	4.0	NM_144587	A6NM63|Q4VXL1|Q96LN0	Missense_Mutation	SNP	ENST00000260723.4	hg19	CCDS31301.1	.	.	.	.	.	.	.	.	.	.	T	10.22	1.289154	0.23478	.	.	ENSG00000138152	ENST00000260723;ENST00000368994	T;T	0.18502	2.21;2.21	5.49	-3.99	0.04069	.	0.836862	0.10391	N	0.680466	T	0.08268	0.0206	N	0.19112	0.55	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.09377	0.004;0.004	T	0.33929	-0.9849	10	0.35671	T	0.21	-8.1829	5.1317	0.14913	0.1138:0.0769:0.5034:0.3059	.	433;432	Q32M84-2;Q32M84	.;BTBDG_HUMAN	P	432;433	ENSP00000260723:S432P;ENSP00000357990:S433P	ENSP00000260723:S432P	S	+	1	0	BTBD16	124086029	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.710000	0.05024	-0.257000	0.09459	-0.331000	0.08364	TCT	.	.		0.562	BTBD16-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050780.3	NM_144587		C	124096039	T	C	124096039	3	2	254	1	0	0	0	0	1	0	0	0	1543	1551	54	2	1348	2	BTBD16	10	124096039	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	8050112	124096039	11438708	515	34807										
DMBT1	1755	hgsc.bcm.edu	37	chr10	124380739	124380739	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggctgtggctgggccatgtcGgccccaggaaatgcccggtt	16	12	0	0	rs374741257		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:124380739G>T	ENST00000338354.3	+	41	5170	c.5064G>T	c.(5062-5064)tcG>tcT	p.S1688S	DMBT1_ENST00000359586.6_Intron|DMBT1_ENST00000368955.3_Silent_p.S1678S|DMBT1_ENST00000368956.2_Silent_p.S1060S|DMBT1_ENST00000344338.3_Silent_p.S1678S|DMBT1_ENST00000330163.4_Silent_p.S1060S|DMBT1_ENST00000368909.3_Silent_p.S1688S			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	1688	SRCR 13. {ECO:0000255|PROSITE- ProRule:PRU00196}.				defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				GGGCCATGTCGGCCCCAGGAA	0.612																																					p.S1688S	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											DMBT1_ENST00000368915,NS,carcinoma,0,3	DMBT1	677	.	0			c.G5064T						.						156	159	158					10																	124380739		1972	4162	6134	SO:0001819	synonymous_variant	1755	exon41			CATGTCGGCCCCA		CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.5064G>T	chr10.hg19:g.124380739G>T		102.0	1.0		49.0	3.0	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Silent	SNP	ENST00000338354.3	hg19																																																																																				.	.		0.612	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406		T	124380739	G	T	124380739	2	4	254	1	0	0	0	0	0	0	0	1	4579	1103	39	1		1	DMBT1	10	124380739	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	284700	124380739	11154008	516	34808										
GPR123	84435	hgsc.bcm.edu	37	chr10	134910585	134910585	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgcctcctggcctccttcgtCacctacatcgtgcaccagag	8	17	1	1	rs62624493	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:134910585C>T	ENST00000392607.3	+	3	547	c.111C>T	c.(109-111)gtC>gtT	p.V37V	GPR123_ENST00000607359.1_Silent_p.V757V	NM_001083909.1	NP_001077378.1	Q86SQ6	GP123_HUMAN	G protein-coupled receptor 123	37					G-protein coupled receptor signaling pathway (GO:0007186)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(3)	14		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)		CCTCCTTCGTCACCTACATCG	0.627																																					p.V37V		Atlas-SNP	.											.	GPR123	118	.	0			c.C111T						.						124	101	109					10																	134910585		2203	4300	6503	SO:0001819	synonymous_variant	84435	exon3			CTTCGTCACCTAC	AB058731	CCDS41580.1	10q26	2014-08-08			ENSG00000197177	ENSG00000197177		"-", "GPCR / Class B : Orphans"	13838	protein-coding gene	gene with protein product		612302				12565841	Standard	XM_005252695		Approved	KIAA1828	uc001llw.3	Q86SQ6	OTTHUMG00000019304	ENST00000392607.3:c.111C>T	chr10.hg19:g.134910585C>T		35.0	0.0		36.0	8.0	NM_001083909	A5HL16|A6NG50|Q5T234|Q86SN7|Q96JJ9	Silent	SNP	ENST00000392607.3	hg19	CCDS41580.1																																																																																			.	C|0.993;G|0.007		0.627	GPR123-003	NOVEL	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051113.2			T	134910585	C	T	134910585	2	4	254	1	0	0	0	0	0	0	0	1	6645	813	29	3		3	GPR123	10	134910585	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	10529846	134910585	624162	517	34809										
ADAM8	101	hgsc.bcm.edu	37	chr10	135087474	135087474	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cctgcccgcgaggctgctccGtcacctcggagccattggca	12	17	1	0	rs375135486		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:135087474G>A	ENST00000445355.3	-	4	337	c.287C>T	c.(286-288)aCg>aTg	p.T96M	ADAM8_ENST00000559180.1_5'UTR|ADAM8_ENST00000415217.3_Missense_Mutation_p.T96M|ADAM8_ENST00000485491.2_Silent_p.D61D	NM_001109.4	NP_001100.3	P78325	ADAM8_HUMAN	ADAM metallopeptidase domain 8	96					activation of MAPK activity involved in innate immune response (GO:0035419)|angiogenesis (GO:0001525)|cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|leukocyte migration involved in inflammatory response (GO:0002523)|lymphocyte chemotaxis (GO:0048247)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of bone resorption (GO:0045780)|positive regulation of cell adhesion (GO:0045785)|positive regulation of eosinophil migration (GO:2000418)|positive regulation of fibronectin-dependent thymocyte migration (GO:2000415)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of neutrophil extravasation (GO:2000391)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein processing (GO:0010954)|positive regulation of protein secretion (GO:0050714)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000309)|regulation of cell-cell adhesion (GO:0022407)|single organismal cell-cell adhesion (GO:0016337)	alpha9-beta1 integrin-ADAM8 complex (GO:0071133)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dense core granule membrane (GO:0032127)|integral component of plasma membrane (GO:0005887)|phagolysosome (GO:0032010)|plasma membrane (GO:0005886)|podosome (GO:0002102)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein self-association (GO:0043621)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)	17		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		all cancers(32;7.72e-06)|OV - Ovarian serous cystadenocarcinoma(35;8.23e-06)|Epithelial(32;1.02e-05)		AGGCTGCTCCGTCACCTCGGA	0.701																																					p.T96M		Atlas-SNP	.											.	ADAM8	41	.	0			c.C287T						.		MET/THR,MET/THR,	0,4354		0,0,2177	28	29	29		287,287,183	0.2	0.2	10		29	3,8577		0,3,4287	no	missense,missense,coding-synonymous	ADAM8	NM_001109.4,NM_001164489.1,NM_001164490.1	81,81,	0,3,6464	AA,AG,GG		0.035,0.0,0.0232	probably-damaging,probably-damaging,	96/825,96/743,61/734	135087474	3,12931	2177	4290	6467	SO:0001583	missense	101	exon4			TGCTCCGTCACCT	D26579	CCDS31319.2, CCDS58102.1, CCDS58103.1	10q26.3	2014-03-20	2005-08-18		ENSG00000151651	ENSG00000151651		"ADAM metallopeptidase domain containing", "CD molecules"	215	protein-coding gene	gene with protein product		602267	"a disintegrin and metalloproteinase domain 8"			9126482	Standard	NM_001109		Approved	CD156, MS2, CD156a	uc021qbe.1	P78325	OTTHUMG00000019309	ENST00000445355.3:c.287C>T	chr10.hg19:g.135087474G>A	ENSP00000453302:p.Thr96Met	101.0	0.0		62.0	17.0	NM_001164489	B4DVM6|H0YL36|H0YLR0|H0YN39	Missense_Mutation	SNP	ENST00000445355.3	hg19	CCDS31319.2																																																																																			.	.		0.701	ADAM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051118.4	NM_001109		A	135087474	G	A	135087474	3	1	254	1	0	0	0	0	1	0	0	0	252	1145	40	1	2185	1	ADAM8	10	135087474	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	176889	135087474	447273	518	34810										
ECHS1	1892	hgsc.bcm.edu	37	chr10	135182430	135182430	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	acagtgtcactctttacctgGgatggttcctattaagatct	8	9	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr10:135182430G>T	ENST00000368547.3	-	4	866	c.511C>A	c.(511-513)Cca>Aca	p.P171T	MIR3944_ENST00000581277.1_RNA	NM_004092.3	NP_004083.3	P30084	ECHM_HUMAN	enoyl CoA hydratase, short chain, 1, mitochondrial	171					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enoyl-CoA hydratase activity (GO:0004300)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)|skin(1)	10		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		all cancers(32;1.62e-06)|OV - Ovarian serous cystadenocarcinoma(35;5.75e-06)|Epithelial(32;7.58e-06)		TCTTTACCTGGGATGGTTCCT	0.512																																					p.P171T	GBM(132;1720 1771 5373 10277 21402)	Atlas-SNP	.											.	ECHS1	31	.	0			c.C511A						.						126	112	116					10																	135182430		2202	4298	6500	SO:0001583	missense	1892	exon4			TACCTGGGATGGT		CCDS7681.1	10q26.2-q26.3	2010-05-04	2010-04-30		ENSG00000127884	ENSG00000127884	4.2.1.17		3151	protein-coding gene	gene with protein product		602292	"enoyl Coenzyme A hydratase, short chain, 1, mitochondrial"			8012501	Standard	NM_004092		Approved	SCEH	uc001lmu.3	P30084	OTTHUMG00000019320	ENST00000368547.3:c.511C>A	chr10.hg19:g.135182430G>T	ENSP00000357535:p.Pro171Thr	135.0	0.0		109.0	6.0	NM_004092	O00739|Q5VWY1|Q96H54	Missense_Mutation	SNP	ENST00000368547.3	hg19	CCDS7681.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.085421	0.76642	.	.	ENSG00000127884	ENST00000368547	T	0.77229	-1.08	5.81	5.81	0.92471	Crotonase, core (1);	0.000000	0.85682	D	0.000000	D	0.91240	0.7239	M	0.93978	3.48	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.92823	0.6274	10	0.72032	D	0.01	.	17.6318	0.88111	0.0:0.0:1.0:0.0	.	171	P30084	ECHM_HUMAN	T	171	ENSP00000357535:P171T	ENSP00000357535:P171T	P	-	1	0	ECHS1	135032420	1.000000	0.71417	1.000000	0.80357	0.538000	0.34931	6.633000	0.74286	2.763000	0.94921	0.650000	0.86243	CCA	.	.		0.512	ECHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051156.1			T	135182430	G	T	135182430	3	4	254	1	0	0	0	0	1	0	0	0	4898	1232	43	3	381	3	ECHS1	10	135182430	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	94956	135182430	352317	519	34811										
PHRF1	57661	hgsc.bcm.edu	37	chr11	607103	607103	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cgaaactcaggcagtctgtcCagaggggaagaaggattcaa	13	8	3	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:607103C>A	ENST00000264555.5	+	14	1775	c.1647C>A	c.(1645-1647)tcC>tcA	p.S549S	PHRF1_ENST00000416188.2_Silent_p.S548S|PHRF1_ENST00000413872.2_Silent_p.S547S|PHRF1_ENST00000533464.1_Silent_p.S545S	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	549					mRNA processing (GO:0006397)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)	RNA polymerase binding (GO:0070063)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|urinary_tract(2)	28						GCAGTCTGTCCAGAGGGGAAG	0.542																																					p.S548S		Atlas-SNP	.											.	PHRF1	188	.	0			c.C1644A						.						54	52	53					11																	607103		1870	4102	5972	SO:0001819	synonymous_variant	57661	exon14			TCTGTCCAGAGGG	BC004950	CCDS44507.1, CCDS65987.1, CCDS65988.1, CCDS65989.1	11p15.5	2014-06-13			ENSG00000070047	ENSG00000070047		"RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	24351	protein-coding gene	gene with protein product	"CTD binding SR like protein rA9", "protein phosphatase 1, regulatory subunit 125"	611780		RNF221			Standard	XM_005253027		Approved	KIAA1542, PPP1R125	uc010qwc.2	Q9P1Y6	OTTHUMG00000165141	ENST00000264555.5:c.1647C>A	chr11.hg19:g.607103C>A		93.0	0.0		85.0	4.0	NM_020901	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Silent	SNP	ENST00000264555.5	hg19																																																																																				.	.		0.542	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901		A	607103	C	A	607103	2	1	254	1	0	0	0	0	0	0	0	1	11870	581	21	3		3	PHRF1	11	607103	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10		607103	134399413	520	34812										
OSBPL5	114879	hgsc.bcm.edu	37	chr11	3143580	3143580	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccccgggcccgggctcacctTgagagtctccttcttggtga	12	15	3	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:3143580T>C	ENST00000263650.7	-	4	457	c.298A>G	c.(298-300)Aag>Gag	p.K100E	OSBPL5_ENST00000389989.3_Missense_Mutation_p.K100E|OSBPL5_ENST00000542243.1_Missense_Mutation_p.Q15R|OSBPL5_ENST00000525498.1_Missense_Mutation_p.K52E|OSBPL5_ENST00000348039.5_Missense_Mutation_p.K100E	NM_020896.3	NP_065947.1	Q9H0X9	OSBL5_HUMAN	oxysterol binding protein-like 5	100					cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|Golgi to plasma membrane transport (GO:0006893)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	cholesterol binding (GO:0015485)|oxysterol binding (GO:0008142)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	25		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)		GGGCTCACCTTGAGAGTCTCC	0.622																																					p.K100E		Atlas-SNP	.											.	OSBPL5	78	.	0			c.A298G						.						54	44	48					11																	3143580		2202	4298	6500	SO:0001583	missense	114879	exon4			TCACCTTGAGAGT	AF392453	CCDS31343.1, CCDS31344.1	11p15.4	2013-01-10			ENSG00000021762	ENSG00000021762		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16392	protein-coding gene	gene with protein product		606733					Standard	NM_145638		Approved	KIAA1534, ORP5	uc001lxk.2	Q9H0X9	OTTHUMG00000011702	ENST00000263650.7:c.298A>G	chr11.hg19:g.3143580T>C	ENSP00000263650:p.Lys100Glu	107.0	0.0		80.0	4.0	NM_145638	A6NDP0|A6NJS8|Q54A90|Q8N596|Q9BZB0|Q9P1Z4	Missense_Mutation	SNP	ENST00000263650.7	hg19	CCDS31344.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.4|25.4	4.630835|4.630835	0.87660|0.87660	.|.	.|.	ENSG00000021762|ENSG00000021762	ENST00000263650;ENST00000389989;ENST00000525498;ENST00000348039;ENST00000533234;ENST00000526122|ENST00000542243	T;T;T;T;T;T|T	0.58210|0.43294	1.02;0.85;0.94;0.85;0.44;0.35|0.95	4.32|4.32	4.32|4.32	0.51571|0.51571	.|.	0.142736|.	0.46145|.	N|.	0.000318|.	T|T	0.53530|0.53530	0.1802|0.1802	M|M	0.66939|0.66939	2.045|2.045	0.30506|0.30506	N|N	0.769943|0.769943	D;D;D;D|.	0.89917|.	1.0;0.997;1.0;1.0|.	D;D;D;D|.	0.85130|.	0.976;0.945;0.997;0.976|.	T|T	0.58629|0.58629	-0.7603|-0.7603	10|7	0.87932|0.59425	D|D	0|0.04	13.4107|13.4107	12.7833|12.7833	0.57489|0.57489	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	52;61;100;100|.	B4DVB0;E7EP03;Q8N596;Q9H0X9|.	.;.;.;OSBL5_HUMAN|.	E|R	100;100;52;100;100;100|15	ENSP00000263650:K100E;ENSP00000374639:K100E;ENSP00000433342:K52E;ENSP00000302872:K100E;ENSP00000436950:K100E;ENSP00000433754:K100E|ENSP00000441551:Q15R	ENSP00000263650:K100E|ENSP00000441551:Q15R	K|Q	-|-	1|2	0|0	OSBPL5|OSBPL5	3100156|3100156	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.741000|0.741000	0.42261|0.42261	7.255000|7.255000	0.78338|0.78338	1.817000|1.817000	0.53016|0.53016	0.459000|0.459000	0.35465|0.35465	AAG|CAA	.	.		0.622	OSBPL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032332.2			C	3143580	T	C	3143580	3	2	254	1	0	0	0	0	1	0	0	0	11289	1821	63	2	2417	2	OSBPL5	11	3143580	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	2536477	3143580	131862936	521	34813										
OR52A1	23538	hgsc.bcm.edu	37	chr11	5173434	5173434	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtacaagggctcatggagacTgcgctcagatttgatgatgc	13	8	2	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:5173434T>C	ENST00000380367.1	-	2	583	c.166A>G	c.(166-168)Agt>Ggt	p.S56G	OR52A1_ENST00000328942.1_Missense_Mutation_p.S56G			Q9UKL2	O52A1_HUMAN	olfactory receptor, family 52, subfamily A, member 1	56					sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	19		Medulloblastoma(188;0.00106)|Breast(177;0.0155)|all_neural(188;0.0189)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCATGGAGACTGCGCTCAGAT	0.438																																					p.S56G		Atlas-SNP	.											.	OR52A1	58	.	0			c.A166G						.						79	74	76					11																	5173434		2201	4297	6498	SO:0001583	missense	23538	exon1			GGAGACTGCGCTC	AF154673	CCDS31374.1	11p15.4	2012-08-09			ENSG00000182070	ENSG00000182070		"GPCR / Class A : Olfactory receptors"	8318	protein-coding gene	gene with protein product						10512676	Standard	NM_012375		Approved	HPFH1OR	uc010qyy.2	Q9UKL2	OTTHUMG00000066603	ENST00000380367.1:c.166A>G	chr11.hg19:g.5173434T>C	ENSP00000369725:p.Ser56Gly	132.0	0.0		112.0	5.0	NM_012375	Q6IF31	Missense_Mutation	SNP	ENST00000380367.1	hg19	CCDS31374.1	.	.	.	.	.	.	.	.	.	.	T	13.67	2.307509	0.40795	.	.	ENSG00000182070	ENST00000380367;ENST00000328942	T;T	0.00464	7.24;7.24	5.37	5.37	0.77165	GPCR, rhodopsin-like superfamily (1);	0.209000	0.33732	N	0.004619	T	0.00815	0.0027	M	0.88181	2.935	0.34100	D	0.661778	B	0.15719	0.014	B	0.14578	0.011	T	0.15178	-1.0446	10	0.66056	D	0.02	.	14.3488	0.66685	0.0:0.0:0.0:1.0	.	56	Q9UKL2	O52A1_HUMAN	G	56	ENSP00000369725:S56G;ENSP00000333684:S56G	ENSP00000333684:S56G	S	-	1	0	OR52A1	5130010	0.751000	0.28327	0.984000	0.44739	0.472000	0.32918	3.145000	0.50623	2.257000	0.74773	0.533000	0.62120	AGT	.	.		0.438	OR52A1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142810.2	NM_012375		C	5173434	T	C	5173434	3	2	254	1	0	0	0	0	1	0	0	0	11117	1580	55	2	774	2	OR52A1	11	5173434	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	2029854	5173434	129833082	522	34814										
RRP8	23378	hgsc.bcm.edu	37	chr11	6622399	6622399	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cgctggcgaagatccctggcGatgcggtccactggctgcag	15	13	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:6622399G>T	ENST00000254605.6	-	3	1014	c.897C>A	c.(895-897)atC>atA	p.I299I	ILK_ENST00000537806.1_5'Flank|ILK_ENST00000528995.1_5'Flank|RP11-732A19.8_ENST00000527191.1_RNA|RRP8_ENST00000534343.1_Intron|ILK_ENST00000396751.2_5'Flank|ILK_ENST00000420936.2_5'Flank|ILK_ENST00000299421.4_5'Flank	NM_015324.3	NP_056139.1	O43159	RRP8_HUMAN	ribosomal RNA processing 8, methyltransferase, homolog (yeast)	299					cellular response to glucose starvation (GO:0042149)|chromatin modification (GO:0016568)|chromatin silencing at rDNA (GO:0000183)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription by glucose (GO:0046015)|rRNA processing (GO:0006364)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|rDNA heterochromatin (GO:0033553)	methylated histone binding (GO:0035064)|poly(A) RNA binding (GO:0044822)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)	13						GATCCCTGGCGATGCGGTCCA	0.577																																					p.I299I		Atlas-SNP	.											RRP8,NS,adenocarcinoma,0,1	RRP8	40	.	0			c.C897A						.						28	28	28					11																	6622399		2201	4296	6497	SO:0001819	synonymous_variant	23378	exon3			CCTGGCGATGCGG	AB007869	CCDS31411.1	11p15.4	2009-02-23	2009-02-23	2009-02-23	ENSG00000132275	ENSG00000132275			29030	protein-coding gene	gene with protein product	RRP8 methyltransferase homolog (S. cerevisiae)	615818	"KIAA0409"	KIAA0409		9455477	Standard	NM_015324		Approved		uc001med.3	O43159		ENST00000254605.6:c.897C>A	chr11.hg19:g.6622399G>T		54.0	1.0		41.0	2.0	NM_015324	Q7KZ78|Q9BVM6	Silent	SNP	ENST00000254605.6	hg19	CCDS31411.1																																																																																			.	.		0.577	RRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384505.1	NM_015324		T	6622399	G	T	6622399	2	4	254	1	0	0	0	0	0	0	0	1	13705	1048	37	1		1	RRP8	11	6622399	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1448965	6622399	128384117	523	34815										
DCHS1	8642	hgsc.bcm.edu	37	chr11	6653382	6653382	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gactcggcccacgctggtccCtgggggctggttctcagcca	14	15	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:6653382C>T	ENST00000299441.3	-	6	3772	c.3361G>A	c.(3361-3363)Ggg>Agg	p.G1121R	RP11-732A19.6_ENST00000526633.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	1121	Cadherin 11. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ACGCTGGTCCCTGGGGGCTGG	0.597																																					p.G1121R		Atlas-SNP	.											.	DCHS1	277	.	0			c.G3361A						.						62	62	62					11																	6653382		2201	4295	6496	SO:0001583	missense	8642	exon6			TGGTCCCTGGGGG	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"Cadherins / Cadherin-related"	13681	protein-coding gene	gene with protein product	"cadherin-related family member 6"	603057	"protocadherin 16", "dachsous 1 (Drosophila)"	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.3361G>A	chr11.hg19:g.6653382C>T	ENSP00000299441:p.Gly1121Arg	128.0	0.0		112.0	5.0	NM_003737	O15098	Missense_Mutation	SNP	ENST00000299441.3	hg19	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	C	19.73	3.881772	0.72294	.	.	ENSG00000166341	ENST00000299441	T	0.69806	-0.43	4.66	4.66	0.58398	Cadherin (3);Cadherin-like (1);	0.000000	0.47093	D	0.000245	D	0.86264	0.5891	M	0.94101	3.495	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89686	0.3894	10	0.66056	D	0.02	.	17.0688	0.86567	0.0:1.0:0.0:0.0	.	1121	Q96JQ0	PCD16_HUMAN	R	1121	ENSP00000299441:G1121R	ENSP00000299441:G1121R	G	-	1	0	DCHS1	6609958	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.297000	0.78799	2.584000	0.87258	0.561000	0.74099	GGG	.	.		0.597	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		T	6653382	C	T	6653382	3	4	254	1	0	0	0	0	1	0	0	0	4289	681	24	3	6599	3	DCHS1	11	6653382	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	30983	6653382	128353134	524	34816										
NLRP14	338323	hgsc.bcm.edu	37	chr11	7091661	7091661	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttatataaagtcttgaagtcTcctaagtgtaaactacaagt	6	6	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:7091661T>C	ENST00000299481.4	+	11	3466	c.3120T>C	c.(3118-3120)tcT>tcC	p.S1040S		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	1040					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)			breast(3)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	21				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		TCTTGAAGTCTCCTAAGTGTA	0.393																																					p.S1040S		Atlas-SNP	.											.	NLRP14	187	.	0			c.T3120C						.						88	90	89					11																	7091661		2201	4296	6497	SO:0001819	synonymous_variant	338323	exon11			GAAGTCTCCTAAG	BK001107	CCDS7776.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000158077		"Nucleotide-binding domain and leucine rich repeat containing"	22939	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 14"	609665	"NACHT, leucine rich repeat and PYD containing 14"	NALP14		12563287	Standard	NM_176822		Approved	NOD5, GC-LRR, Nalp-iota, PAN8, CLR11.2	uc001mfb.1	Q86W24		ENST00000299481.4:c.3120T>C	chr11.hg19:g.7091661T>C		139.0	0.0		96.0	4.0	NM_176822	Q7RTR6	Silent	SNP	ENST00000299481.4	hg19	CCDS7776.1																																																																																			.	.		0.393	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822		C	7091661	T	C	7091661	2	2	254	1	0	0	0	0	0	0	0	1	10485	1538	54	2		2	NLRP14	11	7091661	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	438279	7091661	127914855	525	34817										
OR10A3	26496	hgsc.bcm.edu	37	chr11	7960614	7960614	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cacagtagccaccatgatccCtgagatccatgagaatatta	7	11	0	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:7960614C>A	ENST00000360759.3	-	1	527	c.454G>T	c.(454-456)Ggg>Tgg	p.G152W		NM_001003745.1	NP_001003745.1	P58181	O10A3_HUMAN	olfactory receptor, family 10, subfamily A, member 3	152					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(5)|lung(12)|pancreas(1)|skin(2)	21				Epithelial(150;1.38e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		ACCATGATCCCTGAGATCCAT	0.428																																					p.G152W		Atlas-SNP	.											.	OR10A3	54	.	0			c.G454T						.						54	52	53					11																	7960614		2201	4296	6497	SO:0001583	missense	26496	exon1			TGATCCCTGAGAT	BK004404	CCDS31421.1	11p15.4	2012-08-09			ENSG00000170683	ENSG00000170683		"GPCR / Class A : Olfactory receptors"	8162	protein-coding gene	gene with protein product						1370859	Standard	NM_001003745		Approved	HTPCRX12, HSHTPCRX12	uc010rbi.2	P58181	OTTHUMG00000165672	ENST00000360759.3:c.454G>T	chr11.hg19:g.7960614C>A	ENSP00000353988:p.Gly152Trp	117.0	0.0		129.0	6.0	NM_001003745	B9EH39|Q6IF58|Q96R11	Missense_Mutation	SNP	ENST00000360759.3	hg19	CCDS31421.1	.	.	.	.	.	.	.	.	.	.	C	4.878	0.163194	0.09287	.	.	ENSG00000170683	ENST00000360759	T	0.40756	1.02	4.95	1.97	0.26223	GPCR, rhodopsin-like superfamily (1);	0.376015	0.18862	N	0.129105	T	0.59224	0.2178	H	0.97732	4.065	0.09310	N	1	B	0.25007	0.116	B	0.35278	0.199	T	0.60316	-0.7287	10	0.72032	D	0.01	.	6.3974	0.21620	0.1471:0.6892:0.0:0.1637	.	152	P58181	O10A3_HUMAN	W	152	ENSP00000353988:G152W	ENSP00000353988:G152W	G	-	1	0	OR10A3	7917190	0.000000	0.05858	0.069000	0.20011	0.056000	0.15407	0.321000	0.19558	0.344000	0.23847	0.650000	0.86243	GGG	.	.		0.428	OR10A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385704.1	NM_001003745		A	7960614	C	A	7960614	3	1	254	1	0	0	0	0	1	0	0	0	10900	681	24	3	493	3	OR10A3	11	7960614	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	868953	7960614	127045902	526	34818										
DKK3	27122	hgsc.bcm.edu	37	chr11	11988502	11988502	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctgaggggaggccactcaccTctctggaaggcacagcacag	13	13	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:11988502T>C	ENST00000396505.2	-	6	910	c.672A>G	c.(670-672)agA>agG	p.R224R	DKK3_ENST00000450094.2_Splice_Site_p.R196R|DKK3_ENST00000527132.1_Intron|DKK3_ENST00000525493.1_Splice_Site_p.R224R|DKK3_ENST00000326932.4_Splice_Site_p.R224R	NM_015881.5	NP_056965.3	Q9UBP4	DKK3_HUMAN	dickkopf WNT signaling pathway inhibitor 3	224	DKK-type Cys-2.				adrenal gland development (GO:0030325)|anatomical structure morphogenesis (GO:0009653)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of transcription, DNA-templated (GO:0045892)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)				breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(1)|pancreas(1)	8				Epithelial(150;0.000502)		GCCACTCACCTCTCTGGAAGG	0.607											OREG0020766	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R224R		Atlas-SNP	.											.	DKK3	35	.	0			c.A672G						.						77	75	76					11																	11988502		2201	4294	6495	SO:0001630	splice_region_variant	27122	exon5			CTCACCTCTCTGG	AF177396	CCDS7808.1	11p15.3	2013-05-15	2013-05-15		ENSG00000050165	ENSG00000050165			2893	protein-coding gene	gene with protein product	"regulated in glioma"	605416	"dickkopf (Xenopus laevis) homolog 3", "dickkopf 3 homolog (Xenopus laevis)"			10570958	Standard	XM_006718177		Approved	REIC, RIG	uc001mjv.3	Q9UBP4	OTTHUMG00000165709	ENST00000396505.2:c.673+1A>G	chr11.hg19:g.11988502T>C		232.0	0.0	676	129.0	6.0	NM_001018057	A8K1I2|D3DQW1|Q9ULB7	Silent	SNP	ENST00000396505.2	hg19	CCDS7808.1																																																																																			.	.		0.607	DKK3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385863.1	NM_013253	Silent	C	11988502	T	C	11988502	5	2	254	1	0	0	0	0	0	0	1	0	4548	1565	54	2	392	2	DKK3	11	11988502	Splice_Site	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	4027888	11988502	123018014	527	34819										
TEAD1	7003	hgsc.bcm.edu	37	chr11	12904610	12904610	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggcaaggtcgctccattggcAcaaccaagcttcgcctggtg	12	13	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:12904610A>G	ENST00000526600.1	+	4	572	c.349A>G	c.(349-351)Aca>Gca	p.T117A	TEAD1_ENST00000527575.1_Missense_Mutation_p.T213A|TEAD1_ENST00000361905.4_Missense_Mutation_p.T198A|TEAD1_ENST00000527636.1_Missense_Mutation_p.T213A|TEAD1_ENST00000334310.6_Missense_Mutation_p.T202A|TEAD1_ENST00000361985.2_Missense_Mutation_p.T213A			P28347	TEAD1_HUMAN	TEA domain family member 1 (SV40 transcriptional enhancer factor)	213					gene expression (GO:0010467)|hippo signaling (GO:0035329)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)	17				Epithelial(150;0.00223)|BRCA - Breast invasive adenocarcinoma(625;0.236)		CTCCATTGGCACAACCAAGCT	0.562																																					p.T213A		Atlas-SNP	.											.	TEAD1	40	.	0			c.A637G						.						124	107	113					11																	12904610		2200	4294	6494	SO:0001583	missense	7003	exon9			ATTGGCACAACCA	X84839	CCDS7810.1, CCDS7810.2	11p15.4	2008-11-12				ENSG00000187079			11714	protein-coding gene	gene with protein product		189967	"atrophia areata, peripapillary chorioretinal degeneration"	TCF13, AA		1851669, 9889009, 15016762	Standard	NM_021961		Approved	TEF-1	uc021qdx.1	P28347		ENST00000526600.1:c.349A>G	chr11.hg19:g.12904610A>G	ENSP00000435393:p.Thr117Ala	137.0	0.0		97.0	4.0	NM_021961	A4FUP2|E7EV65	Missense_Mutation	SNP	ENST00000526600.1	hg19		.	.	.	.	.	.	.	.	.	.	A	18.73	3.686755	0.68157	.	.	ENSG00000187079	ENST00000361905;ENST00000527636;ENST00000527575;ENST00000334310;ENST00000361985;ENST00000526600	T;T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54;1.54	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.44891	0.1315	M	0.76002	2.32	0.80722	D	1	D;B;B	0.54397	0.966;0.237;0.024	P;B;B	0.50934	0.654;0.318;0.108	T	0.38394	-0.9663	10	0.28530	T	0.3	-10.2993	15.4426	0.75200	1.0:0.0:0.0:0.0	.	202;117;213	A4FUP2;E9PKB7;P28347	.;.;TEAD1_HUMAN	A	198;213;213;202;213;117	ENSP00000355332:T198A;ENSP00000435233:T213A;ENSP00000435977:T213A;ENSP00000334754:T202A;ENSP00000354588:T213A;ENSP00000435393:T117A	ENSP00000334754:T202A	T	+	1	0	TEAD1	12861186	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.339000	0.96797	2.123000	0.65237	0.533000	0.62120	ACA	.	.		0.562	TEAD1-007	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000387220.1	NM_021961		G	12904610	A	G	12904610	3	3	254	1	0	0	0	0	1	0	0	0	15753	159	6	2	663	2	TEAD1	11	12904610	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	916108	12904610	122101906	528	34820										
ARNTL	406	hgsc.bcm.edu	37	chr11	13408153	13408153	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cctcccacaggtgagaacccCcacataggtatagacatgat	8	13	0	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:13408153C>A	ENST00000403290.1	+	20	2086	c.1731C>A	c.(1729-1731)ccC>ccA	p.P577P	ARNTL_ENST00000389707.4_Silent_p.P576P|ARNTL_ENST00000403482.3_Silent_p.P575P|ARNTL_ENST00000361003.4_Silent_p.P459P|ARNTL_ENST00000403510.3_Silent_p.P533P|ARNTL_ENST00000396441.3_Silent_p.P576P|ARNTL_ENST00000389708.3_3'UTR|ARNTL_ENST00000401424.1_Silent_p.P534P			O00327	BMAL1_HUMAN	aryl hydrocarbon receptor nuclear translocator-like	577	Interaction with CIART. {ECO:0000250|UniProtKB:Q9WTL8}.				circadian regulation of gene expression (GO:0032922)|circadian rhythm (GO:0007623)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription, DNA-templated (GO:0045892)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of skeletal muscle cell differentiation (GO:2001016)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein import into nucleus, translocation (GO:0000060)|regulation of cell cycle (GO:0051726)|regulation of cellular senescence (GO:2000772)|regulation of hair cycle (GO:0042634)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|regulation of type B pancreatic cell development (GO:2000074)|response to redox state (GO:0051775)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|nuclear body (GO:0016604)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor binding (GO:0017162)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|Hsp90 protein binding (GO:0051879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|signal transducer activity (GO:0004871)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|endometrium(2)|large_intestine(11)|lung(5)|upper_aerodigestive_tract(1)	20				Epithelial(150;0.0243)		GTGAGAACCCCCACATAGGTA	0.413																																					p.P576P		Atlas-SNP	.											.	ARNTL	46	.	0			c.C1728A						.						100	99	99					11																	13408153		2200	4294	6494	SO:0001819	synonymous_variant	406	exon19			GAACCCCCACATA	D89722	CCDS31430.1, CCDS44543.1, CCDS73259.1	11p15	2013-05-21			ENSG00000133794	ENSG00000133794		"Basic helix-loop-helix proteins"	701	protein-coding gene	gene with protein product		602550				9144434, 9079689	Standard	XM_005252930		Approved	MOP3, JAP3, BMAL1, PASD3, bHLHe5	uc001mkp.3	O00327	OTTHUMG00000150623	ENST00000403290.1:c.1731C>A	chr11.hg19:g.13408153C>A		103.0	0.0		72.0	4.0	NM_001030272	A2I2N6|A8K645|B5ME11|B7WPG7|D3DQW6|O00313|O00314|O00315|O00316|O00317|Q4G136|Q8IUT4|Q99631|Q99649	Silent	SNP	ENST00000403290.1	hg19																																																																																				.	.		0.413	ARNTL-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000319173.1	NM_001178		A	13408153	C	A	13408153	2	1	254	1	0	0	0	0	0	0	0	1	967	610	22	3		3	ARNTL	11	13408153	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	503543	13408153	121598363	529	34821										
C11orf58	10944	hgsc.bcm.edu	37	chr11	16774369	16774369	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	attaatgaagaactggagtcTcaatatcagcaaagtatgga	9	5	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:16774369T>C	ENST00000228136.4	+	4	624	c.246T>C	c.(244-246)tcT>tcC	p.S82S	C11orf58_ENST00000422258.2_Silent_p.S38S|C11orf58_ENST00000525684.1_Missense_Mutation_p.L62P			O00193	SMAP_HUMAN	chromosome 11 open reading frame 58	82										NS(1)|endometrium(1)|lung(3)|prostate(1)|skin(1)	7						AACTGGAGTCTCAATATCAGC	0.348																																					p.S82S		Atlas-SNP	.											C11orf58,bladder,carcinoma,+1,1	C11orf58	14	.	0			c.T246C						.						124	118	120					11																	16774369		2200	4294	6494	SO:0001819	synonymous_variant	10944	exon4			GGAGTCTCAATAT	BC007103	CCDS7822.1	11p15.1	2012-05-30			ENSG00000110696	ENSG00000110696			16990	protein-coding gene	gene with protein product	"small acidic protein"					9263035	Standard	NM_014267		Approved	SMAP	uc001mmk.2	O00193	OTTHUMG00000165910	ENST00000228136.4:c.246T>C	chr11.hg19:g.16774369T>C		145.0	0.0		98.0	5.0	NM_014267	B2RD28	Silent	SNP	ENST00000228136.4	hg19	CCDS7822.1	.	.	.	.	.	.	.	.	.	.	T	9.867	1.197999	0.22037	.	.	ENSG00000110696	ENST00000525684	.	.	.	5.57	1.74	0.24563	.	.	.	.	.	T	0.58466	0.2124	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58411	-0.7641	5	0.59425	D	0.04	.	5.4834	0.16737	0.0:0.1384:0.2831:0.5785	.	.	.	.	P	62	.	ENSP00000432534:L62P	L	+	2	0	C11orf58	16730945	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	0.984000	0.29565	0.902000	0.36520	0.533000	0.62120	CTC	.	.		0.348	C11orf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387023.2	NM_014267		C	16774369	T	C	16774369	2	2	254	1	0	0	0	0	0	0	0	1	1653	1538	54	2		2	C11orf58	11	16774369	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	3366216	16774369	118232147	530	34822										
SAA4	6291	hgsc.bcm.edu	37	chr11	18253136	18253136	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcagctttctcgttggacttCgagtcctccaatacagtgct	8	12	2	0	rs201938371		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:18253136C>A	ENST00000278222.4	-	4	486	c.306G>T	c.(304-306)tcG>tcT	p.S102S	SAA2-SAA4_ENST00000524555.1_RNA	NM_006512.3	NP_006503.2	P35542	SAA4_HUMAN	serum amyloid A4, constitutive	102					acute-phase response (GO:0006953)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)		p.S102S(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(6)|skin(1)|stomach(1)	13						CGTTGGACTTCGAGTCCTCCA	0.517																																					p.S180S		Atlas-SNP	.											SAA4,colon,carcinoma,0,1	.	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G540T						.						105	105	105					11																	18253136		2199	4293	6492	SO:0001819	synonymous_variant	100528017	exon6			GGACTTCGAGTCC	M81349	CCDS7832.1	11p15.1-p14	2008-07-21			ENSG00000148965	ENSG00000148965			10516	protein-coding gene	gene with protein product		104752				8325654	Standard	NM_006512		Approved	C-SAA, CSAA		P35542	OTTHUMG00000166483	ENST00000278222.4:c.306G>T	chr11.hg19:g.18253136C>A		169.0	0.0		111.0	28.0	NM_001199744	Q6FHJ4	Silent	SNP	ENST00000278222.4	hg19	CCDS7832.1																																																																																			.	C|1.000;T|0.000		0.517	SAA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389988.1	NM_006512		A	18253136	C	A	18253136	2	1	254	1	0	0	0	0	0	0	0	1	13815	871	31	1		1	SAA4	11	18253136	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1478767	18253136	116753380	531	34823										
IGSF22	283284	hgsc.bcm.edu	37	chr11	18732375	18732375	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gggaggcaaaaccaggaggcTctgtgggggaaagagagagt	19	5	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:18732375T>C	ENST00000513874.1	-	16	2538	c.2399A>G	c.(2398-2400)gAg>gGg	p.E800G	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	800										NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						ACCAGGAGGCTCTGTGGGGGA	0.537																																					p.E800G		Atlas-SNP	.											.	IGSF22	211	.	0			c.A2399G						.						42	43	43					11																	18732375		1943	4139	6082	SO:0001630	splice_region_variant	283284	exon16			GGAGGCTCTGTGG	AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	26750	protein-coding gene	gene with protein product							Standard	NM_173588		Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.2399-1A>G	chr11.hg19:g.18732375T>C		137.0	0.0		132.0	6.0	NM_173588	A6NNA0|D6RGV7	Missense_Mutation	SNP	ENST00000513874.1	hg19	CCDS41625.2	.	.	.	.	.	.	.	.	.	.	T	16.17	3.046319	0.55110	.	.	ENSG00000179057	ENST00000513874	T	0.53640	0.61	4.5	4.5	0.54988	.	0.202751	0.24136	U	0.041218	T	0.23806	0.0576	N	0.03608	-0.345	0.20638	N	0.999878	P	0.38922	0.651	B	0.33521	0.165	T	0.17776	-1.0358	10	0.66056	D	0.02	.	12.1657	0.54129	0.0:0.0:0.0:1.0	.	800	D6RGV7	.	G	800	ENSP00000421191:E800G	ENSP00000322422:E699G	E	-	2	0	IGSF22	18688951	0.815000	0.29118	0.990000	0.47175	0.580000	0.36256	0.999000	0.29757	1.884000	0.54569	0.460000	0.39030	GAG	.	.		0.537	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588	Missense_Mutation	C	18732375	T	C	18732375	5	2	254	1	0	0	0	0	0	0	1	0	7609	1565	54	2	1613	2	IGSF22	11	18732375	Splice_Site	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	479239	18732375	116274141	532	34824										
LUZP2	338645	hgsc.bcm.edu	37	chr11	24759781	24759781	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aaatagagaagaaatgaagtCtcttcaggaggccctgcaaa	10	7	2	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:24759781C>G	ENST00000336930.6	+	4	332	c.266C>G	c.(265-267)tCt>tGt	p.S89C	LUZP2_ENST00000531187.1_3'UTR|LUZP2_ENST00000533227.1_Missense_Mutation_p.S3C			Q86TE4	LUZP2_HUMAN	leucine zipper protein 2	89						extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(11)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	32						GAAATGAAGTCTCTTCAGGAG	0.358																																					p.S89C		Atlas-SNP	.											LUZP2,colon,carcinoma,0,1	LUZP2	90	.	0			c.C266G						.						66	69	68					11																	24759781		2203	4300	6503	SO:0001583	missense	338645	exon4			TGAAGTCTCTTCA	AL832641	CCDS31446.1, CCDS58128.1	11p14.3	2005-09-18			ENSG00000187398	ENSG00000187398			23206	protein-coding gene	gene with protein product		608178				12856284	Standard	NM_001009909		Approved		uc001mqs.3	Q86TE4	OTTHUMG00000166109	ENST00000336930.6:c.266C>G	chr11.hg19:g.24759781C>G	ENSP00000336817:p.Ser89Cys	251.0	1.0		183.0	55.0	NM_001252010	A2RUB8|E9PN53|Q6UXE7|Q6ZS65	Missense_Mutation	SNP	ENST00000336930.6	hg19	CCDS31446.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.072033	0.76415	.	.	ENSG00000187398	ENST00000336930;ENST00000529015;ENST00000533227	T;T;T	0.25749	1.78;1.78;1.78	5.76	5.76	0.90799	.	0.200304	0.43416	D	0.000574	T	0.47710	0.1460	L	0.60455	1.87	0.41438	D	0.987905	D;D	0.89917	1.0;0.999	D;D	0.66351	0.943;0.943	T	0.41034	-0.9531	10	0.72032	D	0.01	-6.6251	17.4398	0.87562	0.0:1.0:0.0:0.0	.	3;89	E9PN53;Q86TE4	.;LUZP2_HUMAN	C	89;89;3	ENSP00000336817:S89C;ENSP00000437032:S89C;ENSP00000432952:S3C	ENSP00000336817:S89C	S	+	2	0	LUZP2	24716357	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.098000	0.71458	2.721000	0.93114	0.650000	0.86243	TCT	.	.		0.358	LUZP2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387861.1	NM_001009909		G	24759781	C	G	24759781	3	3	254	1	0	0	0	0	1	0	0	0	9096	913	32	4	280	4	LUZP2	11	24759781	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	6027406	24759781	110246735	533	34825										
LDLRAD3	143458	hgsc.bcm.edu	37	chr11	36250861	36250861	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcctgagcgtggaagacaccAgccacagcccggggcagcct	13	15	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:36250861A>G	ENST00000315571.5	+	6	973	c.952A>G	c.(952-954)Agc>Ggc	p.S318G	LDLRAD3_ENST00000528989.1_Missense_Mutation_p.S269G|LDLRAD3_ENST00000524419.1_Missense_Mutation_p.S308G	NM_174902.2	NP_777562.1	Q86YD5	LRAD3_HUMAN	low density lipoprotein receptor class A domain containing 3	318					receptor-mediated endocytosis (GO:0006898)|regulation of protein processing (GO:0070613)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(14)|prostate(7)|skin(1)	28	all_lung(20;0.089)|Lung NSC(22;0.175)|all_epithelial(35;0.177)	all_hematologic(20;0.124)				GGAAGACACCAGCCACAGCCC	0.662																																					p.S318G		Atlas-SNP	.											.	LDLRAD3	52	.	0			c.A952G						.						56	67	63					11																	36250861		2201	4292	6493	SO:0001583	missense	143458	exon6			GACACCAGCCACA	AK075546	CCDS31462.1	11p13	2014-06-05			ENSG00000179241	ENSG00000179241			27046	protein-coding gene	gene with protein product						21795536	Standard	NM_174902		Approved	LRAD3	uc001mwk.1	Q86YD5	OTTHUMG00000166313	ENST00000315571.5:c.952A>G	chr11.hg19:g.36250861A>G	ENSP00000318607:p.Ser318Gly	127.0	0.0		90.0	4.0	NM_174902	B7Z1U3|B9EG81|Q8NBJ0	Missense_Mutation	SNP	ENST00000315571.5	hg19	CCDS31462.1	.	.	.	.	.	.	.	.	.	.	A	0.016	-1.525352	0.00959	.	.	ENSG00000179241	ENST00000528989;ENST00000524419;ENST00000315571	D;D;D	0.94280	-3.39;-3.25;-3.15	5.12	-10.2	0.00374	.	1.204760	0.05640	N	0.583225	D	0.83385	0.5243	N	0.14661	0.345	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.71652	-0.4528	10	0.33141	T	0.24	.	10.2419	0.43316	0.6743:0.1099:0.1507:0.0651	.	308;269;318	E9PR86;B7Z1U3;Q86YD5	.;.;LRAD3_HUMAN	G	269;308;318	ENSP00000433954:S269G;ENSP00000434313:S308G;ENSP00000318607:S318G	ENSP00000318607:S318G	S	+	1	0	LDLRAD3	36207437	0.000000	0.05858	0.000000	0.03702	0.079000	0.17450	-1.570000	0.02140	-2.955000	0.00292	-2.346000	0.00244	AGC	.	.		0.662	LDLRAD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389085.1	NM_174902		G	36250861	A	G	36250861	3	3	254	1	0	0	0	0	1	0	0	0	8716	188	7	2	974	2	LDLRAD3	11	36250861	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	11491080	36250861	98755655	534	34826										
ACCS	84680	hgsc.bcm.edu	37	chr11	44089232	44089232	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccaccacctgtctgggccccAcctgcatgcaggacctgggc	11	18	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:44089232A>G	ENST00000263776.8	+	2	489	c.55A>G	c.(55-57)Acc>Gcc	p.T19A	ACCS_ENST00000432284.2_Missense_Mutation_p.T19A|ACCS_ENST00000533208.1_3'UTR	NM_001127219.1|NM_032592.3	NP_001120691.1|NP_115981.1	Q96QU6	1A1L1_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)	19					biosynthetic process (GO:0009058)		catalytic activity (GO:0003824)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)	p.T19A(1)		breast(4)|endometrium(3)|large_intestine(11)|lung(15)|ovary(1)|skin(1)	35						TCTGGGCCCCACCTGCATGCA	0.557																																					p.T19A	Esophageal Squamous(158;148 1889 8077 23160 41213)	Atlas-SNP	.											ACCS,rectum,carcinoma,0,1	ACCS	64	.	1	Substitution - Missense(1)	large_intestine(1)	c.A55G						.						69	73	72					11																	44089232		2203	4300	6503	SO:0001583	missense	84680	exon2			GGCCCCACCTGCA	AY026508	CCDS7907.1	11p11	2008-03-12	2008-01-28		ENSG00000110455	ENSG00000110455			23989	protein-coding gene	gene with protein product		608405				11470512	Standard	NM_032592		Approved	PHACS, ACS	uc009yks.1	Q96QU6	OTTHUMG00000166427	ENST00000263776.8:c.55A>G	chr11.hg19:g.44089232A>G	ENSP00000263776:p.Thr19Ala	127.0	0.0		112.0	5.0	NM_032592	B4E219|Q8WUL4|Q96LX5	Missense_Mutation	SNP	ENST00000263776.8	hg19	CCDS7907.1	.	.	.	.	.	.	.	.	.	.	G	0.417	-0.910247	0.02434	.	.	ENSG00000110455	ENST00000524990;ENST00000263776;ENST00000432284;ENST00000533404	T;T;T;T	0.59364	0.97;0.27;0.97;1.07	5.43	0.0996	0.14503	.	0.861636	0.10406	N	0.678505	T	0.26738	0.0654	N	0.03115	-0.41	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.22836	-1.0205	10	0.07030	T	0.85	-0.427	7.4529	0.27248	0.2042:0.1334:0.6623:0.0	.	19;19	B4E219;Q96QU6	.;1A1L1_HUMAN	A	19	ENSP00000434156:T19A;ENSP00000263776:T19A;ENSP00000391775:T19A;ENSP00000435919:T19A	ENSP00000263776:T19A	T	+	1	0	ACCS	44045808	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.167000	0.09940	-0.164000	0.10927	-3.370000	0.00041	ACC	.	.		0.557	ACCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389721.1	NM_032592		G	44089232	A	G	44089232	3	3	254	1	0	0	0	0	1	0	0	0	133	159	6	2	57	2	ACCS	11	44089232	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	7838371	44089232	90917284	535	34827										
C11orf94	143678	hgsc.bcm.edu	37	chr11	45928125	45928125	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tatgagggccttgggtcataGgtgtgcatcatagtaatact	12	6	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:45928125G>T	ENST00000449465.1	-	3	328	c.292C>A	c.(292-294)Cta>Ata	p.L98I	RP11-618K13.2_ENST00000533218.1_RNA	NM_001080446.2	NP_001073915.2	C9JXX5	CK094_HUMAN	chromosome 11 open reading frame 94	98						extracellular region (GO:0005576)				NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|ovary(1)|pancreas(1)|prostate(1)	7						TTGGGTCATAGGTGTGCATCA	0.617																																					p.L98I		Atlas-SNP	.											.	C11orf94	13	.	0			c.C292A						.						94	96	96					11																	45928125		1938	4124	6062	SO:0001583	missense	143678	exon3			GTCATAGGTGTGC		CCDS44577.1	11p11.2	2012-08-10			ENSG00000234776	ENSG00000234776			37213	protein-coding gene	gene with protein product							Standard	NM_001080446		Approved		uc001nbs.4	C9JXX5	OTTHUMG00000167004	ENST00000449465.1:c.292C>A	chr11.hg19:g.45928125G>T	ENSP00000401498:p.Leu98Ile	87.0	0.0		82.0	4.0	NM_001080446		Missense_Mutation	SNP	ENST00000449465.1	hg19	CCDS44577.1	.	.	.	.	.	.	.	.	.	.	G	15.69	2.908906	0.52439	.	.	ENSG00000234776	ENST00000449465	T	0.55052	0.54	4.66	0.388	0.16264	.	.	.	.	.	T	0.34803	0.0910	.	.	.	0.09310	N	1	B	0.21821	0.061	B	0.19148	0.024	T	0.34551	-0.9824	8	0.87932	D	0	-1.7759	1.1397	0.01762	0.2163:0.3268:0.2903:0.1666	.	98	C9JXX5	CK094_HUMAN	I	98	ENSP00000401498:L98I	ENSP00000401498:L98I	L	-	1	2	C11orf94	45884701	0.000000	0.05858	0.032000	0.17829	0.020000	0.10135	0.050000	0.14120	-0.075000	0.12798	-0.181000	0.13052	CTA	.	.		0.617	C11orf94-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392395.1	NM_001080446		T	45928125	G	T	45928125	3	4	254	1	0	0	0	0	1	0	0	0	1675	991	35	3	8	3	C11orf94	11	45928125	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1838893	45928125	89078391	536	34828										
LRP4	4038	hgsc.bcm.edu	37	chr11	46896443	46896443	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttgttgagctcaggaacaggGacatgcacatcggtgtggtc	14	8	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:46896443G>T	ENST00000378623.1	-	28	4379	c.4137C>A	c.(4135-4137)gtC>gtA	p.V1379V	LRP4-AS1_ENST00000531719.1_RNA|LRP4-AS1_ENST00000502049.2_RNA	NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	1379					dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			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)		CAGGAACAGGGACATGCACAT	0.527																																					p.V1379V		Atlas-SNP	.											.	LRP4	160	.	0			c.C4137A						.						163	132	142					11																	46896443		2201	4299	6500	SO:0001819	synonymous_variant	4038	exon28			AACAGGGACATGC	AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"Low density lipoprotein receptors"	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.4137C>A	chr11.hg19:g.46896443G>T		134.0	0.0		114.0	31.0	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Silent	SNP	ENST00000378623.1	hg19	CCDS31478.1																																																																																			.	.		0.527	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334		T	46896443	G	T	46896443	2	4	254	1	0	0	0	0	0	0	0	1	8968	1161	41	3		3	LRP4	11	46896443	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	968318	46896443	88110073	537	34829										
PACSIN3	29763	hgsc.bcm.edu	37	chr11	47199984	47199984	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agtgccctcacccgaaccccGgtggcagccttccggggact	12	17	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:47199984G>T	ENST00000539589.1	-	10	1434	c.1092C>A	c.(1090-1092)acC>acA	p.T364T	ARFGAP2_ENST00000395449.3_5'Flank|ARFGAP2_ENST00000524782.1_5'Flank|ARFGAP2_ENST00000419701.2_5'Flank|PACSIN3_ENST00000298838.6_Silent_p.T364T|ARFGAP2_ENST00000426335.2_5'Flank|ARFGAP2_ENST00000319543.6_5'Flank	NM_001184975.1	NP_001171904.1	Q9UKS6	PACN3_HUMAN	protein kinase C and casein kinase substrate in neurons 3	364	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of endocytosis (GO:0045806)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium channel inhibitor activity (GO:0019855)|cytoskeletal protein binding (GO:0008092)|lipid binding (GO:0008289)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)	11						CCCGAACCCCGGTGGCAGCCT	0.617																																					p.T364T		Atlas-SNP	.											.	PACSIN3	28	.	0			c.C1092A						.						69	69	69					11																	47199984		2201	4298	6499	SO:0001819	synonymous_variant	29763	exon10			AACCCCGGTGGCA	AF130979	CCDS31481.1	11p12-p11	2008-02-05				ENSG00000165912			8572	protein-coding gene	gene with protein product	"syndapin III"	606513				10531379	Standard	NM_016223		Approved	SDPIII	uc001ndx.3	Q9UKS6		ENST00000539589.1:c.1092C>A	chr11.hg19:g.47199984G>T		155.0	0.0		87.0	4.0	NM_016223	A6NH84|Q9H331|Q9NWV9	Silent	SNP	ENST00000539589.1	hg19	CCDS31481.1																																																																																			.	.		0.617	PACSIN3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391632.1	NM_016223		T	47199984	G	T	47199984	2	4	254	1	0	0	0	0	0	0	0	1	11385	1103	39	1		1	PACSIN3	11	47199984	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	303541	47199984	87806532	538	34830										
MADD	8567	hgsc.bcm.edu	37	chr11	47307982	47307982	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcttgcaccctccccttgatAggcagcctctatcggaacca	7	16	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:47307982A>G	ENST00000311027.5	+	15	2716		c.e15-1		MADD_ENST00000342922.4_Splice_Site|MADD_ENST00000395336.3_Splice_Site|MADD_ENST00000395344.3_Splice_Site|MADD_ENST00000406482.1_Splice_Site|MADD_ENST00000402192.2_Splice_Site|MADD_ENST00000407859.3_Splice_Site|MADD_ENST00000349238.3_Splice_Site|MADD_ENST00000402799.1_Splice_Site	NM_003682.3	NP_003673.3			MAP-kinase activating death domain											breast(7)|central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(19)|lung(26)|ovary(6)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	84				Lung(87;0.182)		TCCCCTTGATAGGCAGCCTCT	0.517																																					.		Atlas-SNP	.											.	MADD	172	.	0			c.2552-2A>G						.						197	171	180					11																	47307982		2201	4298	6499	SO:0001630	splice_region_variant	8567	exon15			CTTGATAGGCAGC	AB002356	CCDS7930.1, CCDS7931.1, CCDS7932.1, CCDS41642.1, CCDS44586.1, CCDS44587.1, CCDS44588.1, CCDS44589.1, CCDS44590.1	11p11.2	2012-10-04			ENSG00000110514	ENSG00000110514		"DENN/MADD domain containing"	6766	protein-coding gene	gene with protein product		603584				9115275, 9796103	Standard	NM_130476		Approved	DENN, KIAA0358, RAB3GEP	uc001ner.1	Q8WXG6	OTTHUMG00000150350	ENST00000311027.5:c.2552-1A>G	chr11.hg19:g.47307982A>G		102.0	0.0		69.0	4.0	NM_130470		Splice_Site	SNP	ENST00000311027.5	hg19	CCDS7930.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.579730	0.86645	.	.	ENSG00000110514	ENST00000342922;ENST00000395342;ENST00000402799;ENST00000406482;ENST00000349238;ENST00000311027;ENST00000407859;ENST00000395344;ENST00000395336;ENST00000402192	.	.	.	5.93	5.93	0.95920	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.379	0.83439	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MADD	47264558	1.000000	0.71417	0.936000	0.37596	0.992000	0.81027	8.698000	0.91311	2.268000	0.75426	0.455000	0.32223	.	.	.		0.517	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1		Intron	G	47307982	A	G	47307982	5	3	254	1	0	0	0	0	0	0	1	0	9161	434	15	2	2604	2	MADD	11	47307982	Splice_Site	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	107998	47307982	87698534	539	34831										
TNKS1BP1	85456	hgsc.bcm.edu	37	chr11	57069548	57069548	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aaataatacatcagccctacCtgtagagtcctggaacaggt	8	10	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:57069548C>A	ENST00000532437.1	-	7	5145	c.4834G>T	c.(4834-4836)Gag>Tag	p.E1612*	TNKS1BP1_ENST00000358252.3_Splice_Site_p.E1612*			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	1612	Arg/Glu/Lys-rich (charged).				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)			breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				TCAGCCCTACCTGTAGAGTCC	0.592																																					p.E1612X		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.G4834T						.						131	128	129					11																	57069548		2201	4296	6497	SO:0001630	splice_region_variant	85456	exon8			CCCTACCTGTAGA	AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.4834+1G>T	chr11.hg19:g.57069548C>A		94.0	0.0		82.0	4.0	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Nonsense_Mutation	SNP	ENST00000532437.1	hg19	CCDS7951.1	.	.	.	.	.	.	.	.	.	.	C	48	13.939359	0.99771	.	.	ENSG00000149115	ENST00000358252;ENST00000532437	.	.	.	5.22	5.22	0.72569	.	0.128563	0.51477	D	0.000091	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-22.6828	15.687	0.77418	0.0:1.0:0.0:0.0	.	.	.	.	X	1612	.	.	E	-	1	0	TNKS1BP1	56826124	0.988000	0.35896	0.564000	0.28396	0.775000	0.43874	3.002000	0.49496	2.432000	0.82394	0.561000	0.74099	GAG	.	.		0.592	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396	Nonsense_Mutation	A	57069548	C	A	57069548	5	1	254	1	0	0	0	0	0	0	1	0	16335	695	24	3	371	3	TNKS1BP1	11	57069548	Splice_Site	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	9761566	57069548	77936968	540	34832										
P2RX3	5024	hgsc.bcm.edu	37	chr11	57115686	57115686	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gaactacagctctgtgctccGgacctgtgagatccagggct	12	12	1	1	rs115850675	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:57115686G>T	ENST00000263314.2	+	5	468	c.434G>T	c.(433-435)cGg>cTg	p.R145L		NM_002559.3	NP_002550.2	P56373	P2RX3_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 3	145					behavioral response to pain (GO:0048266)|cation transmembrane transport (GO:0098655)|neuromuscular synaptic transmission (GO:0007274)|neuronal action potential (GO:0019228)|peristalsis (GO:0030432)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of synaptic plasticity (GO:0048167)|response to ATP (GO:0033198)|response to carbohydrate (GO:0009743)|response to cold (GO:0009409)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)|transport (GO:0006810)|urinary bladder smooth muscle contraction (GO:0014832)	dendritic spine (GO:0043197)|Golgi apparatus (GO:0005794)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|purinergic nucleotide receptor activity (GO:0001614)			endometrium(4)|kidney(2)|large_intestine(4)|lung(15)|prostate(1)	26						TCTGTGCTCCGGACCTGTGAG	0.627																																					p.R145L		Atlas-SNP	.											.	P2RX3	55	.	0			c.G434T						.						39	32	34					11																	57115686		2200	4296	6496	SO:0001583	missense	5024	exon5			TGCTCCGGACCTG	Y07683	CCDS7953.1	11q12	2012-01-17			ENSG00000109991	ENSG00000109991		"Purinergic receptors", "Ligand-gated ion channels / Purinergic receptors, ionotropic"	8534	protein-coding gene	gene with protein product		600843				9221902	Standard	NM_002559		Approved	P2X3	uc001nju.3	P56373	OTTHUMG00000167025	ENST00000263314.2:c.434G>T	chr11.hg19:g.57115686G>T	ENSP00000263314:p.Arg145Leu	57.0	0.0		68.0	5.0	NM_002559	Q6DK37|Q9UQB6	Missense_Mutation	SNP	ENST00000263314.2	hg19	CCDS7953.1	.	.	.	.	.	.	.	.	.	.	G	11.37	1.620038	0.28801	.	.	ENSG00000109991	ENST00000439993;ENST00000263314	T	0.04603	3.59	4.79	0.744	0.18353	.	0.837269	0.10699	N	0.644320	T	0.05227	0.0139	L	0.41492	1.28	0.09310	N	1	B	0.31256	0.316	B	0.31946	0.138	T	0.38045	-0.9679	10	0.72032	D	0.01	-3.417	8.0811	0.30746	0.3492:0.0:0.6508:0.0	.	145	P56373	P2RX3_HUMAN	L	145	ENSP00000263314:R145L	ENSP00000263314:R145L	R	+	2	0	P2RX3	56872262	0.002000	0.14202	0.466000	0.27168	0.373000	0.29922	0.350000	0.20079	0.444000	0.26612	-0.258000	0.10820	CGG	.	G|0.996;A|0.004		0.627	P2RX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392465.1	NM_002559		T	57115686	G	T	57115686	3	4	254	1	0	0	0	0	1	0	0	0	11350	1116	39	1	452	1	P2RX3	11	57115686	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	46138	57115686	77890830	541	34833										
MS4A13	503497	hgsc.bcm.edu	37	chr11	60292725	60292725	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcatctgcataattactacaAttactgcagtaactctaaca	3	10	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:60292725A>T	ENST00000378186.2	+	5	555	c.232A>T	c.(232-234)Att>Ttt	p.I78F	MS4A13_ENST00000527948.1_Intron|MS4A13_ENST00000437058.2_Intron|MS4A13_ENST00000378185.2_Intron	NM_001012417.2	NP_001012417.2	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member 13	122						integral component of membrane (GO:0016021)				endometrium(3)|large_intestine(1)|lung(2)|skin(2)	8						AATTACTACAATTACTGCAGT	0.303																																					p.I78F		Atlas-SNP	.											.	MS4A13	27	.	0			c.A232T						.						41	43	42					11																	60292725		2197	4274	6471	SO:0001583	missense	503497	exon5			ACTACAATTACTG	AY324188	CCDS31571.1, CCDS41653.1, CCDS60801.1	11q12.2	2005-12-05	2005-12-05		ENSG00000204979	ENSG00000204979			16674	protein-coding gene	gene with protein product							Standard	NM_001012417		Approved		uc001nps.3	Q5J8X5	OTTHUMG00000167615	ENST00000378186.2:c.232A>T	chr11.hg19:g.60292725A>T	ENSP00000367428:p.Ile78Phe	409.0	0.0		373.0	126.0	NM_001012417	E9PJE3|Q2TVT5|Q3B7W3|Q86XH8|Q9NTC2	Missense_Mutation	SNP	ENST00000378186.2	hg19	CCDS31571.1	.	.	.	.	.	.	.	.	.	.	A	14.62	2.588705	0.46110	.	.	ENSG00000204979	ENST00000378186	T	0.02525	4.26	4.55	-5.16	0.02857	.	0.554719	0.14962	N	0.288332	T	0.02083	0.0065	L	0.43757	1.38	0.09310	N	1	B	0.18863	0.031	B	0.20767	0.031	T	0.41858	-0.9485	10	0.27785	T	0.31	-10.0673	3.3356	0.07100	0.2504:0.1477:0.4578:0.1441	.	78	Q5J8X5	M4A13_HUMAN	F	78	ENSP00000367428:I78F	ENSP00000367428:I78F	I	+	1	0	MS4A13	60049301	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-2.314000	0.01125	-0.906000	0.03866	0.477000	0.44152	ATT	.	.		0.303	MS4A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395408.1	NM_001012417		T	60292725	A	T	60292725	3	4	254	1	0	0	0	0	1	0	0	0	9866	101	4	4	242	4	MS4A13	11	60292725	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	3177039	60292725	74713791	542	34834										
PRPF19	27339	hgsc.bcm.edu	37	chr11	60666657	60666657	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctcaggagatagtcgccagtGgcatgaaggctgaggcctgt	15	9	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:60666657G>T	ENST00000227524.4	-	11	1153	c.948C>A	c.(946-948)gcC>gcA	p.A316A		NM_014502.4	NP_055317.1			pre-mRNA processing factor 19											haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|urinary_tract(1)	22						AGTCGCCAGTGGCATGAAGGC	0.612											OREG0020994	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A316A		Atlas-SNP	.											.	PRPF19	62	.	0			c.C948A						.						53	42	46					11																	60666657		2203	4299	6502	SO:0001819	synonymous_variant	27339	exon11			GCCAGTGGCATGA	BC018698	CCDS7995.1	11q12.2	2014-05-20	2013-06-10	2005-04-01	ENSG00000110107	ENSG00000110107		"WD repeat domain containing", "U-box domain containing"	17896	protein-coding gene	gene with protein product	"nuclear matrix protein NMP200 related to splicing factor PRP19", "psoralen 4"	608330	"PRP19/PSO4 homolog (S. cerevisiae)", "PRP19/PSO4 pre-mRNA processing factor 19 homolog (S. cerevisiae)"	PRP19		12960389	Standard	NM_014502		Approved	UBOX4, NMP200, PSO4, hPSO4	uc001nqf.3	Q9UMS4	OTTHUMG00000167798	ENST00000227524.4:c.948C>A	chr11.hg19:g.60666657G>T		110.0	0.0	1047	77.0	4.0	NM_014502		Silent	SNP	ENST00000227524.4	hg19	CCDS7995.1																																																																																			.	.		0.612	PRPF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396334.1	NM_014502		T	60666657	G	T	60666657	2	4	254	1	0	0	0	0	0	0	0	1	12576	1335	47	3		3	PRPF19	11	60666657	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	373932	60666657	74339859	543	34835										
TUT1	64852	hgsc.bcm.edu	37	chr11	62346379	62346379	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aaagtccagggcttcagaatCctggggagaagcaggaggtt	15	7	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:62346379C>A	ENST00000476907.1	-	5	1505	c.814G>T	c.(814-816)Gat>Tat	p.D272Y	TUT1_ENST00000308436.7_Missense_Mutation_p.D310Y|MIR3654_ENST00000496634.2_Missense_Mutation_p.D272Y			Q9H6E5	STPAP_HUMAN	terminal uridylyl transferase 1, U6 snRNA-specific	272	Pro-rich.				mRNA cleavage (GO:0006379)|mRNA polyadenylation (GO:0006378)|snRNA processing (GO:0016180)	intercellular bridge (GO:0045171)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|mRNA 3'-UTR binding (GO:0003730)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)|RNA uridylyltransferase activity (GO:0050265)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						GCTTCAGAATCCTGGGGAGAA	0.627																																					p.D310Y		Atlas-SNP	.											.	TUT1	122	.	0			c.G928T						.						43	50	48					11																	62346379		2202	4299	6501	SO:0001583	missense	64852	exon5			CAGAATCCTGGGG	BC005013	CCDS8021.1, CCDS8021.2	11q12.2	2014-03-05	2006-10-06	2006-10-06	ENSG00000149016	ENSG00000149016	2.7.7.52	"RNA binding motif (RRM) containing"	26184	protein-coding gene	gene with protein product	"RNA uridylyltransferase", "U6 TUTase", "TUTase 6"	610641	"RNA binding motif protein 21"	RBM21		16790842	Standard	NM_022830		Approved	FLJ22347, FLJ22267, FLJ21850, PAPD2, TUTase	uc001nto.2	Q9H6E5	OTTHUMG00000158564	ENST00000476907.1:c.814G>T	chr11.hg19:g.62346379C>A	ENSP00000419607:p.Asp272Tyr	140.0	0.0		91.0	4.0	NM_022830	A1A527|A8K995|Q2NL65|Q7L583|Q9H6H7	Missense_Mutation	SNP	ENST00000476907.1	hg19		.	.	.	.	.	.	.	.	.	.	C	19.39	3.818019	0.71028	.	.	ENSG00000149016	ENST00000308436;ENST00000476907;ENST00000278279	T;T	0.39592	1.07;1.09	5.44	5.44	0.79542	.	0.628774	0.14934	N	0.289938	T	0.42899	0.1223	N	0.22421	0.69	0.25198	N	0.99008	P	0.49559	0.925	P	0.51355	0.667	T	0.37753	-0.9692	10	0.72032	D	0.01	-0.4185	14.7726	0.69691	0.0:1.0:0.0:0.0	.	310	F5H0R1	.	Y	310;272;133	ENSP00000308000:D310Y;ENSP00000419607:D272Y	ENSP00000441670:D272Y	D	-	1	0	TUT1	62102955	0.093000	0.21703	0.981000	0.43875	0.978000	0.69477	2.409000	0.44583	2.561000	0.86390	0.563000	0.77884	GAT	.	.		0.627	TUT1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000351319.2	NM_022830		A	62346379	C	A	62346379	3	1	254	1	0	0	0	0	1	0	0	0	16795	855	30	3	1830	3	TUT1	11	62346379	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1679722	62346379	72660137	544	34836										
HNRNPUL2	221092	hgsc.bcm.edu	37	chr11	62488867	62488867	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aaaggtctcggcttttggggTccatctctggctcctcgaga	12	11	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:62488867T>C	ENST00000301785.5	-	9	1703	c.1511A>G	c.(1510-1512)gAc>gGc	p.D504G	HNRNPUL2-BSCL2_ENST00000403734.2_Missense_Mutation_p.D504G	NM_001079559.2	NP_001073027.1	Q1KMD3	HNRL2_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 2	504						membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						GCTTTTGGGGTCCATCTCTGG	0.433																																					p.D504G		Atlas-SNP	.											.	HNRNPUL2	41	.	0			c.A1511G						.						151	156	154					11																	62488867		1850	4095	5945	SO:0001583	missense	221092	exon9			TTGGGGTCCATCT		CCDS41659.1	11q12	2013-07-16		2008-04-18	ENSG00000214753	ENSG00000214753			25451	protein-coding gene	gene with protein product				HNRPUL2			Standard	NM_001079559		Approved	DKFZp762N1910	uc001nuw.3	Q1KMD3	OTTHUMG00000167773	ENST00000301785.5:c.1511A>G	chr11.hg19:g.62488867T>C	ENSP00000301785:p.Asp504Gly	132.0	0.0		90.0	4.0	NM_001079559	Q8N3B3	Missense_Mutation	SNP	ENST00000301785.5	hg19	CCDS41659.1	.	.	.	.	.	.	.	.	.	.	T	13.58	2.278462	0.40294	.	.	ENSG00000214753	ENST00000301785	T	0.43688	0.94	5.99	5.99	0.97316	Zeta toxin domain (1);	0.158080	0.56097	D	0.000037	T	0.50051	0.1593	L	0.41961	1.31	0.46542	D	0.999093	D	0.59767	0.986	P	0.59595	0.86	T	0.36261	-0.9755	10	0.15952	T	0.53	-26.4567	14.4463	0.67352	0.0:0.0:0.0:1.0	.	504	Q1KMD3	HNRL2_HUMAN	G	504	ENSP00000301785:D504G	ENSP00000301785:D504G	D	-	2	0	HNRNPUL2	62245443	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.648000	0.67930	2.291000	0.77112	0.533000	0.62120	GAC	.	.		0.433	HNRNPUL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396208.2	XM_495877		C	62488867	T	C	62488867	3	2	254	1	0	0	0	0	1	0	0	0	7284	1667	58	2	756	2	HNRNPUL2	11	62488867	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	142488	62488867	72517649	545	34837										
FLRT1	28992	hgsc.bcm.edu	37	chr11	63884020	63884020	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cctgcagaacaaccagatcaAcaacgccggcatcccccagg	8	17	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:63884020A>G	ENST00000255681.6	-	3	584				RP11-21A7A.3_ENST00000543817.1_RNA|FLRT1_ENST00000246841.3_Missense_Mutation_p.N94S	NM_014067.3	NP_054786.2	Q9BQ69	MACD1_HUMAN	MACRO domain containing 1						cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(1)|large_intestine(3)|lung(6)|skin(1)	11						AACCAGATCAACAACGCCGGC	0.562																																					p.N94S		Atlas-SNP	.											.	FLRT1	46	.	0			c.A281G						.						91	70	77					11																	63884020		2201	4297	6498	SO:0001627	intron_variant	23769	exon2			AGATCAACAACGC	AF202922	CCDS8056.1	11q13.1	2007-07-24	2007-06-11		ENSG00000133315	ENSG00000133315			29598	protein-coding gene	gene with protein product		610400				15691879	Standard	NM_014067		Approved	LRP16	uc001nyh.3	Q9BQ69	OTTHUMG00000167843	ENST00000255681.6:c.517+34690T>C	chr11.hg19:g.63884020A>G		65.0	0.0		61.0	5.0	NM_013280	Q9UH96	Missense_Mutation	SNP	ENST00000255681.6	hg19	CCDS8056.1	.	.	.	.	.	.	.	.	.	.	A	10.49	1.365961	0.24684	.	.	ENSG00000126500	ENST00000246841	T	0.02032	4.49	5.57	0.773	0.18516	.	0.315459	0.31660	N	0.007277	T	0.01730	0.0055	L	0.34521	1.04	0.38044	D	0.935546	B	0.21606	0.058	B	0.15052	0.012	T	0.53885	-0.8375	10	0.23891	T	0.37	-34.1717	5.8822	0.18862	0.6576:0.1347:0.2077:0.0	.	66	Q9NZU1	FLRT1_HUMAN	S	94	ENSP00000246841:N94S	ENSP00000246841:N94S	N	+	2	0	FLRT1	63640596	0.999000	0.42202	1.000000	0.80357	0.941000	0.58515	1.347000	0.33975	0.394000	0.25230	0.459000	0.35465	AAC	.	.		0.562	MACROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396570.1	NM_014067		G	63884020	A	G	63884020	1	3	254	0	1	0	0	0	0	0	0	0	5946	43	2	2		2	FLRT1	11	63884020	Intron	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	1395153	63884020	71122496	546	34838										
STIP1	10963	hgsc.bcm.edu	37	chr11	63962047	63962047	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	actcagtgatcctacctaccGggagctgatagagcagctac	10	12	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:63962047G>T	ENST00000305218.4	+	4	605	c.458G>T	c.(457-459)cGg>cTg	p.R153L	STIP1_ENST00000538945.1_Missense_Mutation_p.R129L|STIP1_ENST00000358794.5_Missense_Mutation_p.R200L|STIP1_ENST00000540501.1_3'UTR|STIP1_ENST00000543847.1_Missense_Mutation_p.R153L	NM_006819.2	NP_006810.1	P31948	STIP1_HUMAN	stress-induced phosphoprotein 1	153	STI1 1.				response to stress (GO:0006950)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(4)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(1)|skin(1)	27						CCTACCTACCGGGAGCTGATA	0.483																																					p.R153L		Atlas-SNP	.											.	STIP1	63	.	0			c.G458T						.						102	86	91					11																	63962047		2201	4297	6498	SO:0001583	missense	10963	exon4			CCTACCGGGAGCT	BC039299	CCDS8058.1, CCDS60827.1, CCDS60828.1	11q13	2014-01-13	2014-01-13		ENSG00000168439	ENSG00000168439		"Tetratricopeptide (TTC) repeat domain containing"	11387	protein-coding gene	gene with protein product	"Hsp70/Hsp90-organizing protein"	605063	"stress-induced-phosphoprotein 1"			1569099	Standard	NM_006819		Approved	HOP, STI1	uc001nyk.1	P31948	OTTHUMG00000167789	ENST00000305218.4:c.458G>T	chr11.hg19:g.63962047G>T	ENSP00000305958:p.Arg153Leu	134.0	0.0		93.0	5.0	NM_006819	B4DM70|F5H0T1|G3XAD8|Q3ZCU9|Q5TZU9	Missense_Mutation	SNP	ENST00000305218.4	hg19	CCDS8058.1	.	.	.	.	.	.	.	.	.	.	G	11.76	1.734182	0.30684	.	.	ENSG00000168439	ENST00000358794;ENST00000305218;ENST00000538945;ENST00000543847	T;T;T;T	0.22336	2.63;2.87;2.68;1.96	5.57	4.45	0.53987	Heat shock chaperonin-binding (1);	0.062752	0.56097	D	0.000021	T	0.14830	0.0358	L	0.41236	1.265	0.51012	D	0.9999	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.09377	0.0;0.0;0.004	T	0.07385	-1.0775	10	0.16420	T	0.52	-16.3185	8.2957	0.31984	0.1974:0.0:0.8026:0.0	.	129;153;153	F5H0T1;P31948;F5H783	.;STIP1_HUMAN;.	L	200;153;129;153	ENSP00000351646:R200L;ENSP00000305958:R153L;ENSP00000445957:R129L;ENSP00000442704:R153L	ENSP00000305958:R153L	R	+	2	0	STIP1	63718623	1.000000	0.71417	1.000000	0.80357	0.431000	0.31685	3.088000	0.50175	2.788000	0.95919	0.650000	0.86243	CGG	.	.		0.483	STIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396289.2	NM_006819		T	63962047	G	T	63962047	3	4	254	1	0	0	0	0	1	0	0	0	15300	1116	39	1	472	1	STIP1	11	63962047	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	78027	63962047	71044469	547	34839										
CDC42BPG	55561	hgsc.bcm.edu	37	chr11	64599915	64599915	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctcaccctaaagatgcgtggCaggtccctggattgggcatg	13	11	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:64599915C>T	ENST00000342711.5	-	27	3071	c.3072G>A	c.(3070-3072)ctG>ctA	p.L1024L	CDC42BPG_ENST00000491280.1_5'UTR	NM_017525.2	NP_059995.2			CDC42 binding protein kinase gamma (DMPK-like)											central_nervous_system(1)|lung(3)	4						AGATGCGTGGCAGGTCCCTGG	0.592																																					p.L1024L		Atlas-SNP	.											.	CDC42BPG	101	.	0			c.G3072A						.						63	66	65					11																	64599915		2201	4297	6498	SO:0001819	synonymous_variant	55561	exon27			GCGTGGCAGGTCC	AY648038	CCDS31601.1	11q13	2013-01-10			ENSG00000171219	ENSG00000171219		"Pleckstrin homology (PH) domain containing"	29829	protein-coding gene	gene with protein product		613991				9341881, 15194684	Standard	NM_017525		Approved	HSMDPKIN, MRCKgamma, DMPK2, kappa-200	uc001obs.4	Q6DT37	OTTHUMG00000045365	ENST00000342711.5:c.3072G>A	chr11.hg19:g.64599915C>T		119.0	0.0		75.0	4.0	NM_017525		Silent	SNP	ENST00000342711.5	hg19	CCDS31601.1																																																																																			.	.		0.592	CDC42BPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105352.4	XM_290516		T	64599915	C	T	64599915	2	4	254	1	0	0	0	0	0	0	0	1	3076	697	25	3		3	CDC42BPG	11	64599915	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	637868	64599915	70406601	548	34840										
MAP3K11	4296	hgsc.bcm.edu	37	chr11	65373551	65373551	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tggcctggctctgcaggctcCactgcaggggaaaccgatga	14	12	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:65373551C>T	ENST00000530153.1	-	7	1355	c.834G>A	c.(832-834)ttG>ttA	p.L278L	MAP3K11_ENST00000532507.1_5'UTR|MAP3K11_ENST00000534432.1_5'UTR|MAP3K11_ENST00000309100.3_Splice_Site_p.L535L					mitogen-activated protein kinase kinase kinase 11											breast(3)|central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(14)|skin(1)	24						CTGCAGGCTCCACTGCAGGGG	0.577																																					p.L535L		Atlas-SNP	.											.	MAP3K11	67	.	0			c.G1605A						.						15	18	17					11																	65373551		2199	4296	6495	SO:0001630	splice_region_variant	4296	exon7			AGGCTCCACTGCA		CCDS8107.1	11q13.1-q13.3	2011-06-09			ENSG00000173327	ENSG00000173327	2.7.10.1	"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6850	protein-coding gene	gene with protein product		600050		MLK3, PTK1		9267807, 8183572	Standard	NM_002419		Approved	SPRK, MEKK11	uc001oew.3	Q16584	OTTHUMG00000166529	ENST00000530153.1:c.833-1G>A	chr11.hg19:g.65373551C>T		48.0	0.0		58.0	4.0	NM_002419		Silent	SNP	ENST00000530153.1	hg19																																																																																				.	.		0.577	MAP3K11-004	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000390233.2		Silent	T	65373551	C	T	65373551	5	4	254	1	0	0	0	0	0	0	1	0	9254	608	21	3	954	3	MAP3K11	11	65373551	Splice_Site	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	773636	65373551	69632965	549	34841										
KLC2	64837	hgsc.bcm.edu	37	chr11	66031564	66031564	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gccaagcagctcagcaacctGgccctgctgtgccagaacca	10	16	1	1	rs556408432		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:66031564G>T	ENST00000417856.1	+	8	1233	c.990G>T	c.(988-990)ctG>ctT	p.L330L	KLC2_ENST00000394065.2_Silent_p.L191L|KLC2_ENST00000316924.5_Silent_p.L330L|RP11-867G23.1_ENST00000530805.1_RNA|RP11-755F10.3_ENST00000533576.1_RNA|KLC2_ENST00000394066.2_Silent_p.L253L|KLC2_ENST00000394078.1_Intron|KLC2_ENST00000421552.1_Silent_p.L253L|KLC2_ENST00000394067.2_Silent_p.L330L	NM_001134775.1	NP_001128247.1	Q9H0B6	KLC2_HUMAN	kinesin light chain 2	330					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon cargo transport (GO:0008088)|blood coagulation (GO:0007596)|microtubule-based movement (GO:0007018)	ciliary rootlet (GO:0035253)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinesin I complex (GO:0016938)|membrane (GO:0016020)|microtubule (GO:0005874)|neuron projection (GO:0043005)|protein complex (GO:0043234)	kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)			breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	24						TCAGCAACCTGGCCCTGCTGT	0.637																																					p.L330L		Atlas-SNP	.											.	KLC2	50	.	0			c.G990T						.						27	26	26					11																	66031564		2200	4294	6494	SO:0001819	synonymous_variant	64837	exon8			CAACCTGGCCCTG	AK022449	CCDS8130.1, CCDS44653.1	11q13.1	2013-01-10			ENSG00000174996	ENSG00000174996		"Tetratricopeptide (TTC) repeat domain containing"	20716	protein-coding gene	gene with protein product		611729				9624122	Standard	NM_022822		Approved	FLJ12387	uc001ohb.2	Q9H0B6	OTTHUMG00000133757	ENST00000417856.1:c.990G>T	chr11.hg19:g.66031564G>T		118.0	0.0		142.0	18.0	NM_022822	A8MXL7|B2RDY4|Q9H9C8|Q9HA20	Silent	SNP	ENST00000417856.1	hg19	CCDS8130.1																																																																																			.	.		0.637	KLC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258200.1	NM_022822		T	66031564	G	T	66031564	2	4	254	1	0	0	0	0	0	0	0	1	8343	1335	47	3		3	KLC2	11	66031564	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	658013	66031564	68974952	550	34842										
BBS1	582	hgsc.bcm.edu	37	chr11	66283057	66283057	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggagatgctggagagcatccGgtgagaggctgccttcccct	15	11	0	3	rs376894444		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:66283057G>T	ENST00000318312.7	+	5	530	c.479G>T	c.(478-480)cGg>cTg	p.R160L	BBS1_ENST00000537537.1_Intron|BBS1_ENST00000455748.2_Intron|BBS1_ENST00000393994.2_Splice_Site_p.R160L|CTD-3074O7.11_ENST00000419755.3_Splice_Site_p.R197L|BBS1_ENST00000529766.1_3'UTR	NM_024649.4	NP_078925.3	Q8NFJ9	BBS1_HUMAN	Bardet-Biedl syndrome 1	160			R -> Q (in BBS1). {ECO:0000269|PubMed:15770229, ECO:0000269|PubMed:21344540}.		cilium assembly (GO:0042384)|Golgi to plasma membrane protein transport (GO:0043001)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	BBSome (GO:0034464)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	patched binding (GO:0005113)|RNA polymerase II repressing transcription factor binding (GO:0001103)|smoothened binding (GO:0005119)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(2)|urinary_tract(1)	28						GAGAGCATCCGGTGAGAGGCT	0.587									Bardet-Biedl syndrome																												p.R160L	GBM(152;173 2612 9770 10137)	Atlas-SNP	.											.	BBS1	58	.	0			c.G479T						.						112	101	105					11																	66283057		2200	4295	6495	SO:0001630	splice_region_variant	582	exon5	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	GCATCCGGTGAGA	AF503941	CCDS8142.1	11q13	2013-01-08			ENSG00000174483	ENSG00000174483			966	protein-coding gene	gene with protein product		209901				9039982, 12567324	Standard	NM_024649		Approved	FLJ23590	uc001oij.1	Q8NFJ9	OTTHUMG00000167110	ENST00000318312.7:c.479+1G>T	chr11.hg19:g.66283057G>T		132.0	0.0		195.0	8.0	NM_024649	Q32MM9|Q32MN0|Q96SN4	Missense_Mutation	SNP	ENST00000318312.7	hg19	CCDS8142.1	.	.	.	.	.	.	.	.	.	.	G	32	5.135798	0.94517	.	.	ENSG00000256349;ENSG00000174483;ENSG00000174483;ENSG00000174483;ENSG00000174483	ENST00000419755;ENST00000318312;ENST00000525809;ENST00000393994;ENST00000524705	D;D;D;D;D	0.91577	-2.87;-2.87;-2.87;-2.87;-2.87	5.25	5.25	0.73442	.	.	.	.	.	D	0.94528	0.8238	M	0.67569	2.06	0.80722	D	1	D;D;D;D	0.76494	0.996;0.992;0.999;0.999	D;D;D;D	0.79108	0.992;0.91;0.977;0.977	D	0.94926	0.8078	9	0.72032	D	0.01	.	16.4108	0.83712	0.0:0.0:1.0:0.0	.	160;48;160;197	Q32MM9;Q4G0L2;Q8NFJ9;Q8NFJ9-2	.;.;BBS1_HUMAN;.	L	197;160;69;160;67	ENSP00000398526:R197L;ENSP00000317469:R160L;ENSP00000431187:R69L;ENSP00000377563:R160L;ENSP00000436927:R67L	ENSP00000317469:R160L	R	+	2	0	BBS1;CTD-3074O7.11	66039633	1.000000	0.71417	1.000000	0.80357	0.814000	0.46013	7.932000	0.87634	2.452000	0.82932	0.558000	0.71614	CGG	.	.		0.587	BBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393235.2		Missense_Mutation	T	66283057	G	T	66283057	5	4	254	1	0	0	0	0	0	0	1	0	1335	1130	39	1	497	1	BBS1	11	66283057	Splice_Site	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	251493	66283057	68723459	551	34843										
RBM14	10432	hgsc.bcm.edu	37	chr11	66392658	66392658	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcctatgtggcacagccagcCacagctgctgcctatgccag	11	15	0	0	rs375934305		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:66392658C>A	ENST00000310137.4	+	2	1450	c.1311C>A	c.(1309-1311)gcC>gcA	p.A437A	RBM14_ENST00000409738.4_Intron|RBM14-RBM4_ENST00000511114.1_Intron|RBM14_ENST00000393979.3_Intron|RBM14-RBM4_ENST00000412278.2_Intron|RBM4_ENST00000503028.2_Intron|RBM14-RBM4_ENST00000500635.2_Intron|RBM4_ENST00000514361.3_Intron	NM_006328.3	NP_006319.1	Q96PK6	RBM14_HUMAN	RNA binding motif protein 14	437	Ala-rich.				DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|glucocorticoid receptor signaling pathway (GO:0042921)|histone deacetylation (GO:0016575)|intracellular estrogen receptor signaling pathway (GO:0030520)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to hormone (GO:0009725)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor complex (GO:0005667)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)		RBM14/PACS1(2)	breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17						CACAGCCAGCCACAGCTGCTG	0.637																																					p.A437A		Atlas-SNP	.											.	RBM14	59	.	0			c.C1311A						.						68	71	70					11																	66392658		2187	4264	6451	SO:0001819	synonymous_variant	10432	exon2			GCCAGCCACAGCT	AF080561	CCDS8147.1, CCDS55772.1, CCDS55773.1	11q13.2	2013-02-12			ENSG00000239306	ENSG00000239306		"RNA binding motif (RRM) containing"	14219	protein-coding gene	gene with protein product	"coactivator activator", "SYT interacting protein"	612409				9285794	Standard	NM_006328		Approved	SIP, SYTIP1, COAA, DKFZp779J0927	uc001oit.3	Q96PK6	OTTHUMG00000140380	ENST00000310137.4:c.1311C>A	chr11.hg19:g.66392658C>A		40.0	0.0		75.0	4.0	NM_006328	B0LM41|B3KMN4|D6RGD8|O75932|Q2PYN1|Q53GV1|Q68DQ9|Q96PK5	Silent	SNP	ENST00000310137.4	hg19	CCDS8147.1																																																																																			.	.		0.637	RBM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277128.1	NM_006328		A	66392658	C	A	66392658	2	1	254	1	0	0	0	0	0	0	0	1	13130	581	21	3		3	RBM14	11	66392658	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	109601	66392658	68613858	552	34844										
RBM14	10432	hgsc.bcm.edu	37	chr11	66392968	66392968	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cccaggctgctgcctcctacCgcggccagccaggcaatgcc	11	19	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:66392968C>A	ENST00000310137.4	+	2	1760	c.1621C>A	c.(1621-1623)Cgc>Agc	p.R541S	RBM14_ENST00000409738.4_Intron|RBM14-RBM4_ENST00000511114.1_Intron|RBM14_ENST00000393979.3_Intron|RBM14-RBM4_ENST00000412278.2_Intron|RBM4_ENST00000503028.2_Intron|RBM14-RBM4_ENST00000500635.2_Intron|RBM4_ENST00000514361.3_Intron	NM_006328.3	NP_006319.1	Q96PK6	RBM14_HUMAN	RNA binding motif protein 14	541	Ala-rich.				DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|glucocorticoid receptor signaling pathway (GO:0042921)|histone deacetylation (GO:0016575)|intracellular estrogen receptor signaling pathway (GO:0030520)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to hormone (GO:0009725)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor complex (GO:0005667)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)		RBM14/PACS1(2)	breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17						TGCCTCCTACCGCGGCCAGCC	0.652																																					p.R541S		Atlas-SNP	.											.	RBM14	59	.	0			c.C1621A						.						41	36	38					11																	66392968		2200	4295	6495	SO:0001583	missense	10432	exon2			TCCTACCGCGGCC	AF080561	CCDS8147.1, CCDS55772.1, CCDS55773.1	11q13.2	2013-02-12			ENSG00000239306	ENSG00000239306		"RNA binding motif (RRM) containing"	14219	protein-coding gene	gene with protein product	"coactivator activator", "SYT interacting protein"	612409				9285794	Standard	NM_006328		Approved	SIP, SYTIP1, COAA, DKFZp779J0927	uc001oit.3	Q96PK6	OTTHUMG00000140380	ENST00000310137.4:c.1621C>A	chr11.hg19:g.66392968C>A	ENSP00000311747:p.Arg541Ser	88.0	0.0		126.0	6.0	NM_006328	B0LM41|B3KMN4|D6RGD8|O75932|Q2PYN1|Q53GV1|Q68DQ9|Q96PK5	Missense_Mutation	SNP	ENST00000310137.4	hg19	CCDS8147.1	.	.	.	.	.	.	.	.	.	.	C	12.15	1.851892	0.32699	.	.	ENSG00000239306	ENST00000310137	D	0.83837	-1.77	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.81226	0.4778	N	0.08118	0	0.80722	D	1	D	0.53745	0.962	D	0.65010	0.931	D	0.84711	0.0734	10	0.87932	D	0	-2.0699	14.1553	0.65413	0.0:1.0:0.0:0.0	.	541	Q96PK6	RBM14_HUMAN	S	541	ENSP00000311747:R541S	ENSP00000311747:R541S	R	+	1	0	RBM14	66149544	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.116000	0.31221	2.720000	0.93068	0.655000	0.94253	CGC	.	.		0.652	RBM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277128.1	NM_006328		A	66392968	C	A	66392968	3	1	254	1	0	0	0	0	1	0	0	0	13130	652	23	1	1627	1	RBM14	11	66392968	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	310	66392968	68613548	553	34845										
KDM2A	22992	hgsc.bcm.edu	37	chr11	67017960	67017960	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	atccattgtgcccaagctgcAggccatcacggcctcctctg	9	16	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:67017960A>G	ENST00000529006.2	+	17	2905	c.2459A>G	c.(2458-2460)cAg>cGg	p.Q820R	KDM2A_ENST00000530342.1_Missense_Mutation_p.Q381R|KDM2A_ENST00000398645.2_Intron|KDM2A_ENST00000308783.5_Missense_Mutation_p.Q278R|KDM2A_ENST00000526258.1_3'UTR	NM_012308.2	NP_036440.1	Q9Y2K7	KDM2A_HUMAN	lysine (K)-specific demethylase 2A	820					histone H3-K36 demethylation (GO:0070544)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K36 specific) (GO:0051864)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|skin(1)|urinary_tract(2)	36						CCCAAGCTGCAGGCCATCACG	0.622																																					p.Q820R		Atlas-SNP	.											.	KDM2A	80	.	0			c.A2459G						.						52	59	56					11																	67017960		2131	4233	6364	SO:0001583	missense	22992	exon17			AGCTGCAGGCCAT	BC047486	CCDS44657.1, CCDS58148.1	11q13.1	2014-02-18	2009-04-06	2009-04-06	ENSG00000173120	ENSG00000173120		"F-boxes / Leucine-rich repeats", "Chromatin-modifying enzymes / K-demethylases"	13606	protein-coding gene	gene with protein product	"F-box protein FBL11", "jumonji C domain-containing histone demethylase 1A"	605657	"F-box and leucine-rich repeat protein 11"	FBXL11		10231032, 10531037	Standard	NM_012308		Approved	KIAA1004, FBL11, LILINA, DKFZP434M1735, FBL7, FLJ00115, CXXC8, JHDM1A	uc001ojw.3	Q9Y2K7	OTTHUMG00000167103	ENST00000529006.2:c.2459A>G	chr11.hg19:g.67017960A>G	ENSP00000432786:p.Gln820Arg	107.0	0.0		85.0	4.0	NM_012308	D4QA03|E9PIL6|I3VM55|Q49A21|Q4G0M3|Q69YY8|Q9BVH5|Q9H7H5|Q9UK66	Missense_Mutation	SNP	ENST00000529006.2	hg19	CCDS44657.1	.	.	.	.	.	.	.	.	.	.	A	16.15	3.041105	0.55003	.	.	ENSG00000173120	ENST00000529006;ENST00000530342;ENST00000308783	T;T;T	0.24723	2.21;1.84;1.89	5.91	5.91	0.95273	.	0.104270	0.64402	D	0.000003	T	0.12817	0.0311	N	0.08118	0	0.58432	D	0.999997	P;P	0.42409	0.779;0.779	B;B	0.34873	0.191;0.145	T	0.17289	-1.0374	9	.	.	.	-6.2752	14.9163	0.70801	1.0:0.0:0.0:0.0	.	278;820	D4QA03;Q9Y2K7	.;KDM2A_HUMAN	R	820;381;278	ENSP00000432786:Q820R;ENSP00000435776:Q381R;ENSP00000309302:Q278R	.	Q	+	2	0	KDM2A	66774536	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.149000	0.64863	2.261000	0.74972	0.533000	0.62120	CAG	.	.		0.622	KDM2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393140.2	NM_012308		G	67017960	A	G	67017960	3	3	254	1	0	0	0	0	1	0	0	0	8133	188	7	2	2521	2	KDM2A	11	67017960	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	624992	67017960	67988556	554	34846										
ACY3	91703	hgsc.bcm.edu	37	chr11	67410349	67410349	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	actctccctcatagagcaggTcctccccactgaacatctgg	7	16	3	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:67410349T>C	ENST00000255082.3	-	8	976	c.806A>G	c.(805-807)gAc>gGc	p.D269G	ACY3_ENST00000529256.1_Missense_Mutation_p.D148G	NM_080658.1	NP_542389.1	Q96HD9	ACY3_HUMAN	aspartoacylase (aminocyclase) 3	269	Shielding domain. {ECO:0000250}.				viral process (GO:0016032)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	aminoacylase activity (GO:0004046)|hydrolase activity, acting on ester bonds (GO:0016788)|metal ion binding (GO:0046872)			endometrium(1)|lung(5)|prostate(2)	8					L-Aspartic Acid(DB00128)	ATAGAGCAGGTCCTCCCCACT	0.572																																					p.D269G	GBM(56;346 1011 27014 29495 46841)	Atlas-SNP	.											.	ACY3	27	.	0			c.A806G						.						83	65	71					11																	67410349		2200	4294	6494	SO:0001583	missense	91703	exon8			AGCAGGTCCTCCC	BC008689	CCDS8175.1	11q13.2	2014-08-08			ENSG00000132744	ENSG00000132744			24104	protein-coding gene	gene with protein product		614413				14656720	Standard	NM_080658		Approved	HCBP1, MGC9740, ACY-3	uc001omq.3	Q96HD9	OTTHUMG00000167283	ENST00000255082.3:c.806A>G	chr11.hg19:g.67410349T>C	ENSP00000255082:p.Asp269Gly	73.0	0.0		91.0	4.0	NM_080658		Missense_Mutation	SNP	ENST00000255082.3	hg19	CCDS8175.1	.	.	.	.	.	.	.	.	.	.	T	11.86	1.765609	0.31228	.	.	ENSG00000132744	ENST00000255082;ENST00000529256	D;D	0.97752	-4.52;-4.52	4.36	3.23	0.37069	.	0.262355	0.36628	N	0.002490	D	0.95595	0.8568	M	0.72353	2.195	0.39880	D	0.973625	B	0.20368	0.044	B	0.19391	0.025	D	0.91543	0.5251	10	0.17832	T	0.49	.	9.0536	0.36392	0.0:0.0914:0.0:0.9086	.	269	Q96HD9	ACY3_HUMAN	G	269;148	ENSP00000255082:D269G;ENSP00000434270:D148G	ENSP00000255082:D269G	D	-	2	0	ACY3	67166925	0.167000	0.22975	0.084000	0.20598	0.021000	0.10359	1.494000	0.35616	0.663000	0.31027	0.448000	0.29417	GAC	.	.		0.572	ACY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394002.1	NM_080658		C	67410349	T	C	67410349	3	2	254	1	0	0	0	0	1	0	0	0	227	1667	58	2	157	2	ACY3	11	67410349	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	392389	67410349	67596167	555	34847										
TCIRG1	10312	hgsc.bcm.edu	37	chr11	67818045	67818045	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gctgtggtgctggtccccatCtttgccgcctttgccgtgat	12	13	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:67818045C>A	ENST00000265686.3	+	19	2436	c.2328C>A	c.(2326-2328)atC>atA	p.I776I	TCIRG1_ENST00000532635.1_Silent_p.I560I|RP11-802E16.3_ENST00000526897.1_RNA|TCIRG1_ENST00000530802.1_Intron|CHKA_ENST00000533728.1_5'Flank|RP11-802E16.3_ENST00000534517.1_RNA|RP11-802E16.3_ENST00000529934.1_RNA	NM_006019.3	NP_006010.2	Q13488	VPP3_HUMAN	T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 subunit A3	776					ATP hydrolysis coupled proton transport (GO:0015991)|cellular defense response (GO:0006968)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of cell proliferation (GO:0008284)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	hydrogen ion transmembrane transporter activity (GO:0015078)|transporter activity (GO:0005215)			breast(1)|endometrium(4)|large_intestine(3)|lung(4)|ovary(3)|prostate(1)	16						TGGTCCCCATCTTTGCCGCCT	0.662																																					p.I776I		Atlas-SNP	.											.	TCIRG1	40	.	0			c.C2328A						.						108	118	115					11																	67818045		2200	4294	6494	SO:0001819	synonymous_variant	10312	exon19			CCCCATCTTTGCC	AF025374	CCDS8177.1, CCDS53670.1	11q13.2	2014-09-17	2006-01-20		ENSG00000110719	ENSG00000110719		"ATPases / V-type"	11647	protein-coding gene	gene with protein product	"T-cell immune response cDNA 7"	604592	"T-cell, immune regulator 1", "T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein a isoform 3", "T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3"			8579597, 9806637	Standard	NM_006019		Approved	TIRC7, OC-116, OC116, ATP6N1C, Atp6i, a3, ATP6V0A3	uc001one.3	Q13488	OTTHUMG00000167358	ENST00000265686.3:c.2328C>A	chr11.hg19:g.67818045C>A		433.0	1.0		386.0	167.0	NM_006019	O75877|Q8WVC5	Silent	SNP	ENST00000265686.3	hg19	CCDS8177.1																																																																																			.	.		0.662	TCIRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394305.1	NM_006019		A	67818045	C	A	67818045	2	1	254	1	0	0	0	0	0	0	0	1	15718	903	32	3		3	TCIRG1	11	67818045	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	407696	67818045	67188471	556	34848										
SHANK2	22941	hgsc.bcm.edu	37	chr11	70332784	70332784	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gatcaagcagccgccctgtgAgtgggtggacataattcccg	13	11	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:70332784A>G	ENST00000423696.2	-	15	2513	c.2477T>C	c.(2476-2478)cTc>cCc	p.L826P	SHANK2_ENST00000338508.4_Missense_Mutation_p.L1206P|SHANK2_ENST00000409161.1_Missense_Mutation_p.L609P|SHANK2_ENST00000449833.2_Missense_Mutation_p.L610P			Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2	826					adult behavior (GO:0030534)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|ionotropic glutamate receptor binding (GO:0035255)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(30)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			CCGCCCTGTGAGTGGGTGGAC	0.677																																					p.L617P		Atlas-SNP	.											.	SHANK2	340	.	0			c.T1850C						.						29	36	34					11																	70332784		2199	4294	6493	SO:0001583	missense	22941	exon10			CCTGTGAGTGGGT	AF141901		11q13.2	2013-01-10			ENSG00000162105	ENSG00000162105		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	14295	protein-coding gene	gene with protein product		603290	"cortactin binding protein 1"	CORTBP1		10506216	Standard	XM_005277930		Approved	CTTNBP1, ProSAP1, SHANK, SPANK-3	uc001oqc.3	Q9UPX8	OTTHUMG00000154615	ENST00000423696.2:c.2477T>C	chr11.hg19:g.70332784A>G	ENSP00000394536:p.Leu826Pro	87.0	0.0		101.0	5.0	NM_133266	C0SPG8|C0SPG9|Q3Y8G9|Q52LK2|Q9UKP1	Missense_Mutation	SNP	ENST00000423696.2	hg19		.	.	.	.	.	.	.	.	.	.	A	11.91	1.781106	0.31502	.	.	ENSG00000162105	ENST00000449833;ENST00000409161;ENST00000424924;ENST00000338508;ENST00000423696;ENST00000433693;ENST00000294018	T;T;T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04;-0.04;-0.04	4.88	4.88	0.63580	.	0.056200	0.64402	D	0.000001	T	0.76990	0.4065	M	0.78049	2.395	0.80722	D	1	D;D;D	0.67145	0.986;0.992;0.996	P;P;P	0.62089	0.828;0.898;0.898	T	0.81048	-0.1109	10	0.87932	D	0	.	14.486	0.67616	1.0:0.0:0.0:0.0	.	826;1205;610	Q9UPX8;Q9UPX8-3;Q9UPX8-4	SHAN2_HUMAN;.;.	P	610;609;484;1206;826;844;829	ENSP00000399423:L610P;ENSP00000386491:L609P;ENSP00000402944:L484P;ENSP00000345193:L1206P;ENSP00000394536:L826P;ENSP00000294018:L829P	ENSP00000294018:L829P	L	-	2	0	SHANK2	70010432	1.000000	0.71417	1.000000	0.80357	0.318000	0.28184	8.722000	0.91452	1.819000	0.53055	0.459000	0.35465	CTC	.	.		0.677	SHANK2-203	KNOWN	basic	protein_coding	protein_coding		NM_012309		G	70332784	A	G	70332784	3	3	254	1	0	0	0	0	1	0	0	0	14280	304	11	2	1943	2	SHANK2	11	70332784	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	2514739	70332784	64673732	557	34849										
P2RY2	5029	hgsc.bcm.edu	37	chr11	72946264	72946264	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agaggatagaagatgtgttgGgcagcagtgaggactctagg	17	4	1	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:72946264G>T	ENST00000311131.2	+	3	1527	c.1060G>T	c.(1060-1062)Ggc>Tgc	p.G354C	P2RY2_ENST00000393596.2_Missense_Mutation_p.G354C|P2RY2_ENST00000393597.2_Missense_Mutation_p.G354C	NM_002564.2|NM_176072.1	NP_002555|NP_788086	P41231	P2RY2_HUMAN	purinergic receptor P2Y, G-protein coupled, 2	354					cellular ion homeostasis (GO:0006873)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of mucus secretion (GO:0070257)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|receptor activity (GO:0004872)			endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	25					Suramin(DB04786)	AGATGTGTTGGGCAGCAGTGA	0.622																																					p.G354C		Atlas-SNP	.											.	P2RY2	54	.	0			c.G1060T						.						84	87	86					11																	72946264		2191	4272	6463	SO:0001583	missense	5029	exon3			GTGTTGGGCAGCA	U07225	CCDS8219.1	11q13.5-q14.1	2012-08-08				ENSG00000175591		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	8541	protein-coding gene	gene with protein product		600041				8159738, 9286708	Standard	NM_002564		Approved	P2U	uc001otj.4	P41231		ENST00000311131.2:c.1060G>T	chr11.hg19:g.72946264G>T	ENSP00000310305:p.Gly354Cys	127.0	0.0		94.0	4.0	NM_176071	B2R9W3|Q96EM8	Missense_Mutation	SNP	ENST00000311131.2	hg19	CCDS8219.1	.	.	.	.	.	.	.	.	.	.	G	3.668	-0.068213	0.07228	.	.	ENSG00000175591	ENST00000393597;ENST00000311131;ENST00000393596	T;T;T	0.73047	-0.71;-0.71;-0.71	4.43	-0.178	0.13303	.	2.032220	0.03119	N	0.163493	T	0.49167	0.1541	N	0.08118	0	0.09310	N	1	P	0.35527	0.507	B	0.33196	0.159	T	0.46105	-0.9215	10	0.56958	D	0.05	.	4.6964	0.12806	0.2125:0.3375:0.4499:0.0	.	354	P41231	P2RY2_HUMAN	C	354	ENSP00000377222:G354C;ENSP00000310305:G354C;ENSP00000377221:G354C	ENSP00000310305:G354C	G	+	1	0	P2RY2	72623912	0.000000	0.05858	0.013000	0.15412	0.210000	0.24377	0.270000	0.18607	-0.104000	0.12154	0.561000	0.74099	GGC	.	.		0.622	P2RY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397336.1	NM_176072		T	72946264	G	T	72946264	3	4	254	1	0	0	0	0	1	0	0	0	11361	1232	43	3	1062	3	P2RY2	11	72946264	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	2613480	72946264	62060252	558	34850										
C2CD3	26005	hgsc.bcm.edu	37	chr11	73796884	73796884	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tggtgacagaggcattgaccCcgactgtggcactaaactgt	12	10	0	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:73796884C>A	ENST00000334126.7	-	21	3915	c.3689G>T	c.(3688-3690)gGg>gTg	p.G1230V	C2CD3_ENST00000313663.7_Missense_Mutation_p.G1230V			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1230	C2 1.				brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					GGCATTGACCCCGACTGTGGC	0.537																																					p.G1230V		Atlas-SNP	.											.	C2CD3	288	.	0			c.G3689T						.						74	67	69					11																	73796884		2200	4293	6493	SO:0001583	missense	26005	exon21			TTGACCCCGACTG	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.3689G>T	chr11.hg19:g.73796884C>A	ENSP00000334379:p.Gly1230Val	178.0	0.0		116.0	5.0	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	hg19		.	.	.	.	.	.	.	.	.	.	C	34	5.363126	0.95877	.	.	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681;ENST00000414160	T;T;T	0.59906	0.23;0.36;0.37	5.8	5.8	0.92144	.	0.104717	0.64402	D	0.000004	T	0.75796	0.3898	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.73616	-0.3926	9	.	.	.	-14.677	19.6402	0.95754	0.0:1.0:0.0:0.0	.	1230	Q4AC94-1	.	V	1230;1230;1230;38	ENSP00000334379:G1230V;ENSP00000323339:G1230V;ENSP00000388750:G38V	.	G	-	2	0	C2CD3	73474532	1.000000	0.71417	0.991000	0.47740	0.991000	0.79684	7.273000	0.78527	2.742000	0.94016	0.655000	0.94253	GGG	.	.		0.537	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531		A	73796884	C	A	73796884	3	1	254	1	0	0	0	0	1	0	0	0	2156	623	22	3	2246	3	C2CD3	11	73796884	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	850620	73796884	61209632	559	34851										
PICALM	8301	hgsc.bcm.edu	37	chr11	85701369	85701369	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	atggaaaggtgaacatcaccActactttttgtgaggaaagg	11	6	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:85701369A>G	ENST00000393346.3	-	13	1480	c.1332T>C	c.(1330-1332)agT>agC	p.S444S	PICALM_ENST00000356360.5_Silent_p.S444S|PICALM_ENST00000526033.1_Silent_p.S437S|PICALM_ENST00000532317.1_Intron|PICALM_ENST00000528398.1_Intron			Q13492	PICAL_HUMAN	phosphatidylinositol binding clathrin assembly protein	444					axonogenesis (GO:0007409)|cargo loading into vesicle (GO:0035459)|cell proliferation (GO:0008283)|clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|hemopoiesis (GO:0030097)|iron ion homeostasis (GO:0055072)|iron ion import into cell (GO:0097459)|negative regulation of gene expression (GO:0010629)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of receptor-mediated endocytosis (GO:0048261)|positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902961)|positive regulation of beta-amyloid formation (GO:1902004)|positive regulation of neuron death (GO:1901216)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902959)|regulation of endocytosis (GO:0030100)|regulation of protein localization (GO:0032880)|synaptic vesicle maturation (GO:0016188)|vesicle-mediated transport (GO:0016192)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neurofibrillary tangle (GO:0097418)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|vesicle (GO:0031982)	1-phosphatidylinositol binding (GO:0005545)|clathrin adaptor activity (GO:0035615)|clathrin binding (GO:0030276)|clathrin heavy chain binding (GO:0032050)			endometrium(1)|kidney(2)|large_intestine(2)|liver(1)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	19		Acute lymphoblastic leukemia(157;7.42e-07)|all_hematologic(158;0.00092)				GAACATCACCACTACTTTTTG	0.363			T	"MLLT10, MLL"	"TALL, AML, "																																p.S444S		Atlas-SNP	.		Dom	yes		11	11q14	8301	phosphatidylinositol binding clathrin assembly protein (CALM)		L	.	PICALM	82	.	0			c.T1332C						.						129	121	124					11																	85701369		2203	4299	6502	SO:0001819	synonymous_variant	8301	exon13			ATCACCACTACTT	BC048259	CCDS8272.1, CCDS31653.1, CCDS55783.1, CCDS55784.1	11q14	2008-02-01			ENSG00000073921	ENSG00000073921			15514	protein-coding gene	gene with protein product		603025				8643484	Standard	NM_001206947		Approved	CALM, CLTH	uc001pbm.3	Q13492	OTTHUMG00000166981	ENST00000393346.3:c.1332T>C	chr11.hg19:g.85701369A>G		131.0	0.0		100.0	4.0	NM_007166	B4DTM3|E9PN05|F8VPG7|O60700|Q4LE54|Q6GMQ6|Q86XZ9	Silent	SNP	ENST00000393346.3	hg19	CCDS8272.1	.	.	.	.	.	.	.	.	.	.	A	9.246	1.039433	0.19669	.	.	ENSG00000073921	ENST00000526961;ENST00000530542	.	.	.	6.07	6.07	0.98685	.	.	.	.	.	T	0.60340	0.2261	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60352	-0.7280	4	.	.	.	-10.4418	8.5418	0.33397	0.8543:0.0:0.1457:0.0	.	.	.	.	R	53;147	.	.	W	-	1	0	PICALM	85379017	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.239000	0.43079	2.326000	0.78906	0.533000	0.62120	TGG	.	.		0.363	PICALM-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392224.1	NM_007166		G	85701369	A	G	85701369	2	3	254	1	0	0	0	0	0	0	0	1	11889	156	6	2		2	PICALM	11	85701369	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	11904485	85701369	49305147	560	34852										
FAT3	120114	hgsc.bcm.edu	37	chr11	92616016	92616016	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cgccgggctacgtgggccagTactgcgggctgcgccccgtg	17	15	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:92616016T>C	ENST00000298047.6	+	23	12411	c.12394T>C	c.(12394-12396)Tac>Cac	p.Y4132H	FAT3_ENST00000409404.2_Missense_Mutation_p.Y4132H|FAT3_ENST00000533797.1_Missense_Mutation_p.Y467H|FAT3_ENST00000525166.1_Missense_Mutation_p.Y3982H			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	4132	EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				CGTGGGCCAGTACTGCGGGCT	0.622										TCGA Ovarian(4;0.039)																											p.Y4132H		Atlas-SNP	.											.	FAT3	1822	.	0			c.T12394C						.						61	79	73					11																	92616016		2093	4213	6306	SO:0001583	missense	120114	exon23			GGCCAGTACTGCG	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.12394T>C	chr11.hg19:g.92616016T>C	ENSP00000298047:p.Tyr4132His	130.0	0.0		76.0	22.0	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	hg19		.	.	.	.	.	.	.	.	.	.	T	0.836	-0.743501	0.03088	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166;ENST00000533797	D;D;D;D	0.91577	-2.24;-2.24;-2.24;-2.87	5.55	-1.56	0.08532	EGF-like region, conserved site (2);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	T	0.75642	0.3877	N	0.10837	0.055	0.80722	D	1	B;B	0.09022	0.002;0.0	B;B	0.09377	0.002;0.004	T	0.62267	-0.6890	9	0.02654	T	1	.	11.637	0.51209	0.0:0.4332:0.0:0.5668	.	4132;4132	Q8TDW7-3;Q8TDW7	.;FAT3_HUMAN	H	4132;4132;3982;467	ENSP00000298047:Y4132H;ENSP00000387040:Y4132H;ENSP00000432586:Y3982H;ENSP00000436399:Y467H	ENSP00000298047:Y4132H	Y	+	1	0	FAT3	92255664	0.940000	0.31905	0.676000	0.29932	0.598000	0.36846	0.132000	0.15891	-0.451000	0.07097	-0.250000	0.11733	TAC	.	.		0.622	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		C	92616016	T	C	92616016	3	2	254	1	0	0	0	0	1	0	0	0	5699	1638	57	2	12484	2	FAT3	11	92616016	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	6914647	92616016	42390500	561	34853										
HEPHL1	341208	hgsc.bcm.edu	37	chr11	93844139	93844139	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccaaaccattgaactgtttgCagatcacccagggacatggc	9	12	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:93844139C>T	ENST00000315765.9	+	18	3124	c.3116C>T	c.(3115-3117)gCa>gTa	p.A1039V		NM_001098672.1	NP_001092142.1	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	1039	Plastocyanin-like 6.				copper ion transport (GO:0006825)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	61		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				GAACTGTTTGCAGATCACCCA	0.438																																					p.A1039V		Atlas-SNP	.											.	HEPHL1	144	.	0			c.C3116T						.						84	84	84					11																	93844139		2096	4250	6346	SO:0001583	missense	341208	exon18			TGTTTGCAGATCA	BX641008	CCDS44710.1	11q21	2008-02-05			ENSG00000181333	ENSG00000181333			30477	protein-coding gene	gene with protein product							Standard	NM_001098672		Approved	DKFZp686F22190	uc001pep.2	Q6MZM0	OTTHUMG00000167751	ENST00000315765.9:c.3116C>T	chr11.hg19:g.93844139C>T	ENSP00000313699:p.Ala1039Val	112.0	0.0		91.0	4.0	NM_001098672	Q3C1W7	Missense_Mutation	SNP	ENST00000315765.9	hg19	CCDS44710.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.535694	0.85812	.	.	ENSG00000181333	ENST00000315765	D	0.99758	-6.65	5.97	4.1	0.47936	Cupredoxin (2);Multicopper oxidase, type 2 (1);	0.000000	0.85682	D	0.000000	D	0.99658	0.9873	M	0.84846	2.72	0.42291	D	0.992134	P	0.48294	0.908	P	0.58391	0.838	D	0.97475	1.0043	10	0.54805	T	0.06	-2.2986	13.3983	0.60868	0.0:0.8701:0.0:0.1299	.	1039	Q6MZM0	HPHL1_HUMAN	V	1039	ENSP00000313699:A1039V	ENSP00000313699:A1039V	A	+	2	0	HEPHL1	93483787	0.997000	0.39634	0.980000	0.43619	0.998000	0.95712	3.633000	0.54295	1.544000	0.49359	0.655000	0.94253	GCA	.	.		0.438	HEPHL1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396103.2	XM_291947		T	93844139	C	T	93844139	3	4	254	1	0	0	0	0	1	0	0	0	7064	710	25	3	3186	3	HEPHL1	11	93844139	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1228123	93844139	41162377	562	34854										
CNTN5	53942	hgsc.bcm.edu	37	chr11	100141826	100141826	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tttccttcctttctatagtcCcagaaatcataacaggggac	6	11	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:100141826C>T	ENST00000524871.1	+	18	2457	c.2167C>T	c.(2167-2169)Cca>Tca	p.P723S	CNTN5_ENST00000527185.1_Missense_Mutation_p.P723S|CNTN5_ENST00000418526.2_Missense_Mutation_p.P649S|CNTN5_ENST00000279463.3_Missense_Mutation_p.P723S|CNTN5_ENST00000528682.1_Missense_Mutation_p.P723S|CNTN5_ENST00000524560.1_3'UTR	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	723	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(12)|lung(38)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	81		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		TTCTATAGTCCCAGAAATCAT	0.423																																					p.P723S		Atlas-SNP	.											.	CNTN5	324	.	0			c.C2167T						.						75	76	76					11																	100141826		1909	4134	6043	SO:0001583	missense	53942	exon17			ATAGTCCCAGAAA	AB013802	CCDS53696.1, CCDS53697.1, CCDS58168.1	11q22.1	2013-02-11			ENSG00000149972	ENSG00000149972		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2175	protein-coding gene	gene with protein product		607219					Standard	NM_014361		Approved	NB-2, hNB-2	uc021qpb.1	O94779	OTTHUMG00000167579	ENST00000524871.1:c.2167C>T	chr11.hg19:g.100141826C>T	ENSP00000435637:p.Pro723Ser	89.0	0.0		70.0	4.0	NM_001243270	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Missense_Mutation	SNP	ENST00000524871.1	hg19	CCDS53696.1	.	.	.	.	.	.	.	.	.	.	C	17.75	3.466543	0.63625	.	.	ENSG00000149972	ENST00000527185;ENST00000528682;ENST00000524871;ENST00000418526;ENST00000279463	T;T;T;T;T	0.59083	0.29;0.33;0.33;0.34;0.33	5.73	5.73	0.89815	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.75997	0.3926	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.77278	-0.2647	10	0.87932	D	0	.	18.9016	0.92444	0.0:1.0:0.0:0.0	.	649;723	O94779-2;O94779	.;CNTN5_HUMAN	S	723;723;723;649;723	ENSP00000433575:P723S;ENSP00000436185:P723S;ENSP00000435637:P723S;ENSP00000393229:P649S;ENSP00000279463:P723S	ENSP00000279463:P723S	P	+	1	0	CNTN5	99647036	1.000000	0.71417	0.996000	0.52242	0.210000	0.24377	7.382000	0.79729	2.708000	0.92522	0.467000	0.42956	CCA	.	.		0.423	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361		T	100141826	C	T	100141826	3	4	254	1	0	0	0	0	1	0	0	0	3646	623	22	3	2229	3	CNTN5	11	100141826	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	6297687	100141826	34864690	563	34855										
BIRC2	329	hgsc.bcm.edu	37	chr11	102221307	102221307	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgatgctatgtcagaacaccGgaggcattttcccaactgtc	9	11	1	2	rs144530384		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:102221307G>T	ENST00000227758.2	+	2	2121	c.722G>T	c.(721-723)cGg>cTg	p.R241L	BIRC2_ENST00000532672.1_Missense_Mutation_p.R220L|BIRC2_ENST00000527910.1_3'UTR|BIRC2_ENST00000530675.1_Missense_Mutation_p.R192L	NM_001166.4|NM_001256163.1	NP_001157.1|NP_001243092.1	Q13490	BIRC2_HUMAN	baculoviral IAP repeat containing 2	241					apoptotic process (GO:0006915)|cell surface receptor signaling pathway (GO:0007166)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein K48-linked ubiquitination (GO:1902524)|positive regulation of protein K63-linked ubiquitination (GO:1902523)|positive regulation of protein monoubiquitination (GO:1902527)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cell cycle (GO:0051726)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|regulation of cysteine-type endopeptidase activity (GO:2000116)|regulation of inflammatory response (GO:0050727)|regulation of innate immune response (GO:0045088)|regulation of necroptotic process (GO:0060544)|regulation of nucleotide-binding oligomerization domain containing signaling pathway (GO:0070424)|regulation of RIG-I signaling pathway (GO:0039535)|regulation of toll-like receptor signaling pathway (GO:0034121)|regulation of transcription, DNA-templated (GO:0006355)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|protein N-terminus binding (GO:0047485)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|liver(2)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|Epithelial(9;0.11)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0144)		TCAGAACACCGGAGGCATTTT	0.443																																					p.R241L		Atlas-SNP	.											.	BIRC2	51	.	0			c.G722T						.						91	96	94					11																	102221307		2203	4299	6502	SO:0001583	missense	329	exon2			AACACCGGAGGCA	L49431	CCDS8316.1, CCDS58169.1	11q22	2011-01-25	2011-01-25		ENSG00000110330	ENSG00000110330		"Baculoviral IAP repeat containing", "RING-type (C3HC4) zinc fingers"	590	protein-coding gene	gene with protein product	"NFR2-TRAF signalling complex protein", "apoptosis inhibitor 1"	601712	"baculoviral IAP repeat-containing 2"	API1		8552191, 8548810	Standard	NM_001166		Approved	cIAP1, hiap-2, MIHB, RNF48, c-IAP1	uc010ruq.3	Q13490	OTTHUMG00000167325	ENST00000227758.2:c.722G>T	chr11.hg19:g.102221307G>T	ENSP00000227758:p.Arg241Leu	82.0	0.0		83.0	4.0	NM_001256163	B4E026|Q16516|Q4TTG0	Missense_Mutation	SNP	ENST00000227758.2	hg19	CCDS8316.1	.	.	.	.	.	.	.	.	.	.	G	14.03	2.414163	0.42817	.	.	ENSG00000110330	ENST00000530675;ENST00000227758;ENST00000541741;ENST00000532672	T;T;T	0.70164	-0.46;-0.46;-0.46	5.71	4.8	0.61643	Baculoviral inhibition of apoptosis protein repeat (5);	0.052408	0.85682	D	0.000000	T	0.54111	0.1838	N	0.20483	0.58	0.49130	D	0.999752	B	0.14805	0.011	B	0.24701	0.055	T	0.49854	-0.8895	10	0.39692	T	0.17	-9.9057	14.7345	0.69406	0.0694:0.0:0.9306:0.0	.	241	Q13490	BIRC2_HUMAN	L	192;241;241;220	ENSP00000431723:R192L;ENSP00000227758:R241L;ENSP00000434979:R220L	ENSP00000227758:R241L	R	+	2	0	BIRC2	101726517	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.959000	0.49153	1.427000	0.47276	0.655000	0.94253	CGG	.	G|1.000;A|0.000		0.443	BIRC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394170.1	NM_001166		T	102221307	G	T	102221307	3	4	254	1	0	0	0	0	1	0	0	0	1435	1116	39	1	724	1	BIRC2	11	102221307	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	2079481	102221307	32785209	564	34856										
TMEM123	114908	hgsc.bcm.edu	37	chr11	102272281	102272281	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aaaacttacatggttcgataCcgaatgcctcttcttgagta	7	9	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:102272281C>T	ENST00000398136.2	-	4	1011	c.591G>A	c.(589-591)cgG>cgA	p.R197R	TMEM123_ENST00000532161.1_Silent_p.R109R|TMEM123_ENST00000525577.1_5'Flank|TMEM123_ENST00000361236.3_Silent_p.R178R	NM_052932.2	NP_443164.2	Q8N131	PORIM_HUMAN	transmembrane protein 123	197					oncosis (GO:0070267)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(3)|kidney(1)|large_intestine(1)|lung(3)|urinary_tract(1)	9	all_cancers(8;0.00027)|all_epithelial(12;0.0021)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0314)|Lung(13;0.109)|all cancers(10;0.12)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0149)		TGGTTCGATACCGAATGCCTC	0.358																																					p.R197R		Atlas-SNP	.											.	TMEM123	16	.	0			c.G591A						.						95	91	92					11																	102272281		1821	4080	5901	SO:0001819	synonymous_variant	114908	exon4			TCGATACCGAATG	AL050161	CCDS41702.1	11q22.1	2014-01-02			ENSG00000152558	ENSG00000152558			30138	protein-coding gene	gene with protein product	"pro oncosis receptor inducing membrane injury gene"	606356				11481458, 24318988	Standard	NM_052932		Approved	PORIMIN, KCT3	uc001pha.3	Q8N131	OTTHUMG00000167326	ENST00000398136.2:c.591G>A	chr11.hg19:g.102272281C>T		108.0	0.0		90.0	5.0	NM_052932	Q8IWS2|Q96QV2	Silent	SNP	ENST00000398136.2	hg19	CCDS41702.1																																																																																			.	.		0.358	TMEM123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394178.1	NM_052932		T	102272281	C	T	102272281	2	4	254	1	0	0	0	0	0	0	0	1	16051	494	18	3		3	TMEM123	11	102272281	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	50974	102272281	32734235	565	34857										
KBTBD3	143879	hgsc.bcm.edu	37	chr11	105924774	105924774	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctaaggacaactttcagtacCatttcttcttcaggaacatt	5	10	4	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:105924774C>T	ENST00000526793.1	-	3	801	c.642G>A	c.(640-642)atG>atA	p.M214I	KBTBD3_ENST00000534815.1_Missense_Mutation_p.M135I|KBTBD3_ENST00000531837.1_Missense_Mutation_p.M214I	NM_152433.3	NP_689646.2	Q8NAB2	KBTB3_HUMAN	kelch repeat and BTB (POZ) domain containing 3	210	BACK.									NS(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|prostate(1)	25		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.43e-05)|Epithelial(105;0.00418)|all cancers(92;0.0299)		CTTTCAGTACCATTTCTTCTT	0.313																																					p.M214I		Atlas-SNP	.											.	KBTBD3	59	.	0			c.G642A						.						63	67	66					11																	105924774		2201	4298	6499	SO:0001583	missense	143879	exon3			CAGTACCATTTCT	AK055247	CCDS8334.1	11q22.3	2013-01-08	2003-12-12	2003-12-17		ENSG00000182359		"BTB/POZ domain containing"	22934	protein-coding gene	gene with protein product			"BTB and kelch domain containing 3"	BKLHD3			Standard	NM_198439		Approved		uc001pjb.3	Q8NAB2		ENST00000526793.1:c.642G>A	chr11.hg19:g.105924774C>T	ENSP00000436262:p.Met214Ile	88.0	0.0		92.0	4.0	NM_152433	Q6N066|Q86X38|Q96NK5	Missense_Mutation	SNP	ENST00000526793.1	hg19	CCDS8334.1	.	.	.	.	.	.	.	.	.	.	C	10.10	1.256678	0.22965	.	.	ENSG00000182359	ENST00000534815;ENST00000526793;ENST00000531837	T;T;T	0.68181	-0.31;-0.31;-0.31	5.71	-7.6	0.01303	BTB/Kelch-associated (2);	0.506452	0.24258	N	0.040120	T	0.31009	0.0783	N	0.08118	0	0.26322	N	0.977669	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.04693	-1.0933	10	0.45353	T	0.12	.	1.2847	0.02048	0.2642:0.2301:0.3144:0.1913	.	214;210	A8K1K0;Q8NAB2	.;KBTB3_HUMAN	I	135;214;214	ENSP00000431910:M135I;ENSP00000436262:M214I;ENSP00000432163:M214I	ENSP00000436262:M214I	M	-	3	0	KBTBD3	105429984	0.001000	0.12720	0.536000	0.28039	0.963000	0.63663	-1.398000	0.02509	-1.616000	0.01572	-0.312000	0.09012	ATG	.	.		0.313	KBTBD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388705.2	NM_152433		T	105924774	C	T	105924774	3	4	254	1	0	0	0	0	1	0	0	0	8003	594	21	3	1200	3	KBTBD3	11	105924774	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	3652493	105924774	29081742	566	34858										
CWF19L2	143884	hgsc.bcm.edu	37	chr11	107263571	107263571	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggtgtgttcacaggccatacTcttccagactgatctgttct	9	11	4	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:107263571T>C	ENST00000282251.5	-	11	1695	c.1668A>G	c.(1666-1668)agA>agG	p.R556R	CWF19L2_ENST00000433523.1_Silent_p.R556R	NM_152434.2	NP_689647.2	Q2TBE0	C19L2_HUMAN	CWF19-like 2, cell cycle control (S. pombe)	556							catalytic activity (GO:0003824)			endometrium(4)|kidney(2)|large_intestine(13)|lung(21)	40		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)		CAGGCCATACTCTTCCAGACT	0.348																																					p.R556R		Atlas-SNP	.											.	CWF19L2	135	.	0			c.A1668G						.						116	111	113					11																	107263571		2201	4298	6499	SO:0001819	synonymous_variant	143884	exon11			CCATACTCTTCCA	AK056905	CCDS8336.2	11q23.1	2005-09-22			ENSG00000152404	ENSG00000152404			26508	protein-coding gene	gene with protein product						14702039	Standard	NM_152434		Approved	FLJ32343	uc010rvp.2	Q2TBE0	OTTHUMG00000152975	ENST00000282251.5:c.1668A>G	chr11.hg19:g.107263571T>C		108.0	0.0		86.0	4.0	NM_152434	A4FU66|A4FU67|A4FU68|Q6PHW1|Q96MI1	Silent	SNP	ENST00000282251.5	hg19	CCDS8336.2																																																																																			.	.		0.348	CWF19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328825.2	NM_152434		C	107263571	T	C	107263571	2	2	254	1	0	0	0	0	0	0	0	1	4074	1548	54	2		2	CWF19L2	11	107263571	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	1338797	107263571	27742945	567	34859										
C11orf88	399949	hgsc.bcm.edu	37	chr11	111385715	111385715	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcgtctgccggtggcgcggcCcaggaggagcagagggtctg	20	11	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:111385715C>A	ENST00000375618.4	+	1	206	c.206C>A	c.(205-207)cCc>cAc	p.P69H	RP11-794P6.6_ENST00000530283.1_RNA|BTG4_ENST00000525791.1_5'Flank|MIR34B_ENST00000385076.1_RNA|C11orf88_ENST00000529167.1_Missense_Mutation_p.P69H|BTG4_ENST00000356018.2_5'Flank|C11orf88_ENST00000332814.6_Missense_Mutation_p.P69H|MIR34C_ENST00000384831.1_RNA	NM_001100388.1	NP_001093858.1	Q6PI97	CK088_HUMAN	chromosome 11 open reading frame 88	69										endometrium(1)|large_intestine(3)|lung(2)	6						GTGGCGCGGCCCAGGAGGAGC	0.602											OREG0021329	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P69H		Atlas-SNP	.											.	C11orf88	37	.	0			c.C206A						.						36	42	40					11																	111385715		2153	4278	6431	SO:0001583	missense	399949	exon1			CGCGGCCCAGGAG	BC039505, AK128145	CCDS41712.1, CCDS41713.1	11q23.1	2012-08-10			ENSG00000183644	ENSG00000183644			25061	protein-coding gene	gene with protein product	"hypothetical gene supported by BC039505"					12477932	Standard	NM_001100388		Approved	FLJ46266	uc009yyd.3	Q6PI97	OTTHUMG00000166720	ENST00000375618.4:c.206C>A	chr11.hg19:g.111385715C>A	ENSP00000364768:p.Pro69His	74.0	0.0	1434	65.0	5.0	NM_001100388	E9PAN0|Q6ZRL3	Missense_Mutation	SNP	ENST00000375618.4	hg19	CCDS41713.1	.	.	.	.	.	.	.	.	.	.	C	10.29	1.309148	0.23821	.	.	ENSG00000183644	ENST00000375618;ENST00000529167;ENST00000332814	.	.	.	5.09	-1.95	0.07548	.	1.790330	0.02949	N	0.141429	T	0.36496	0.0969	L	0.43152	1.355	0.09310	N	1	P;B	0.34780	0.468;0.12	B;B	0.32289	0.143;0.087	T	0.36407	-0.9749	9	0.46703	T	0.11	2.5614	10.6724	0.45766	0.2192:0.3744:0.4064:0.0	.	69;69	E9PAN0;Q6PI97	.;CK088_HUMAN	H	69	.	ENSP00000333845:P69H	P	+	2	0	C11orf88	110890925	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.351000	0.20096	-0.880000	0.03997	-2.498000	0.00192	CCC	.	.		0.602	C11orf88-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391181.1	NM_001100388		A	111385715	C	A	111385715	3	1	254	1	0	0	0	0	1	0	0	0	1672	623	22	3	208	3	C11orf88	11	111385715	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	4122144	111385715	23620801	568	34860										
PTS	5805	hgsc.bcm.edu	37	chr11	112104184	112104184	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aaatgtagctgtttatatctGggacaacctccagaaagttc	8	8	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:112104184G>T	ENST00000280362.3	+	6	423	c.344G>T	c.(343-345)tGg>tTg	p.W115L	PTS_ENST00000524931.1_Missense_Mutation_p.W47L|PTS_ENST00000525803.1_3'UTR	NM_000317.2	NP_000308.1	Q03393	PTPS_HUMAN	6-pyruvoyltetrahydropterin synthase	115					cellular amino acid metabolic process (GO:0006520)|central nervous system development (GO:0007417)|nitric oxide metabolic process (GO:0046209)|regulation of nitric-oxide synthase activity (GO:0050999)|small molecule metabolic process (GO:0044281)|tetrahydrobiopterin biosynthetic process (GO:0006729)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)	6-pyruvoyltetrahydropterin synthase activity (GO:0003874)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			breast(1)|large_intestine(1)	2		all_cancers(61;2.51e-14)|all_epithelial(67;1.64e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;1.27e-06)|BRCA - Breast invasive adenocarcinoma(274;1.43e-06)|all cancers(92;2.1e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0519)		GTTTATATCTGGGACAACCTC	0.274																																					p.W115L		Atlas-SNP	.											.	PTS	7	.	0			c.G344T						.						41	44	43					11																	112104184		2199	4296	6495	SO:0001583	missense	5805	exon6			ATATCTGGGACAA	U63382	CCDS8359.1	11q22.3	2014-04-01				ENSG00000150787	4.2.3.12		9689	protein-coding gene	gene with protein product		612719				8188266	Standard	NM_000317		Approved	PTPS	uc001pnj.4	Q03393		ENST00000280362.3:c.344G>T	chr11.hg19:g.112104184G>T	ENSP00000280362:p.Trp115Leu	114.0	0.0		93.0	5.0	NM_000317	B0YJ87|Q8WVG8	Missense_Mutation	SNP	ENST00000280362.3	hg19	CCDS8359.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.910445	0.92107	.	.	ENSG00000150787	ENST00000280362;ENST00000524931	D;D	0.99311	-5.73;-5.73	6.01	6.01	0.97437	.	0.054479	0.85682	D	0.000000	D	0.99417	0.9794	M	0.83852	2.665	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.99047	1.0826	10	0.72032	D	0.01	-6.6916	17.2452	0.87026	0.0:0.0:1.0:0.0	.	115	Q03393	PTPS_HUMAN	L	115;47	ENSP00000280362:W115L;ENSP00000434688:W47L	ENSP00000280362:W115L	W	+	2	0	PTS	111609394	1.000000	0.71417	1.000000	0.80357	0.819000	0.46315	8.828000	0.92047	2.845000	0.97973	0.643000	0.83706	TGG	.	.		0.274	PTS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393541.1	NM_000317		T	112104184	G	T	112104184	3	4	254	1	0	0	0	0	1	0	0	0	12833	1357	47	3	366	3	PTS	11	112104184	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	718469	112104184	22902332	569	34861										
USP28	57646	hgsc.bcm.edu	37	chr11	113694377	113694377	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcctccttcaactttcgaatAcactctctcttatttcgaat	2	13	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:113694377A>G	ENST00000003302.4	-	12	1301	c.1233T>C	c.(1231-1233)tgT>tgC	p.C411C	USP28_ENST00000537706.1_Silent_p.C411C|USP28_ENST00000545540.1_Silent_p.C286C|RP11-667M19.10_ENST00000399123.2_RNA|USP28_ENST00000260188.5_Silent_p.C411C|USP28_ENST00000544967.1_Silent_p.C119C	NM_020886.2	NP_065937.1	Q96RU2	UBP28_HUMAN	ubiquitin specific peptidase 28	411	USP.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|protein deubiquitination (GO:0016579)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(4)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(24)|ovary(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	59		all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|Epithelial(105;0.000122)|all cancers(92;0.00104)		ACTTTCGAATACACTCTCTCT	0.303																																					p.C411C	Melanoma(4;162 555 7664)|GBM(79;500 2010 17506)|Esophageal Squamous(9;463 924 15765)	Atlas-SNP	.											.	USP28	135	.	0			c.T1233C						.						97	90	93					11																	113694377		2200	4296	6496	SO:0001819	synonymous_variant	57646	exon12			TCGAATACACTCT	AB040948	CCDS31680.1, CCDS73394.1	11q23	2008-04-11	2005-08-08		ENSG00000048028	ENSG00000048028		"Ubiquitin-specific peptidases"	12625	protein-coding gene	gene with protein product		610748	"ubiquitin specific protease 28"			12838346, 11597335	Standard	XM_005271630		Approved	KIAA1515	uc001poh.3	Q96RU2	OTTHUMG00000168205	ENST00000003302.4:c.1233T>C	chr11.hg19:g.113694377A>G		92.0	0.0		89.0	4.0	NM_020886	B0YJC0|B0YJC1|Q9P213	Silent	SNP	ENST00000003302.4	hg19	CCDS31680.1																																																																																			.	.		0.303	USP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398789.1			G	113694377	A	G	113694377	2	3	254	1	0	0	0	0	0	0	0	1	17073	389	14	2		2	USP28	11	113694377	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	1590193	113694377	21312139	570	34862										
CADM1	23705	hgsc.bcm.edu	37	chr11	115109361	115109361	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	attcagcaactgaaacctgcTgtccttcaaagctgtgaaac	7	11	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:115109361T>C	ENST00000452722.3	-	3	303	c.283A>G	c.(283-285)Agc>Ggc	p.S95G	CADM1_ENST00000537140.1_5'UTR|CADM1_ENST00000537058.1_Missense_Mutation_p.S95G|CADM1_ENST00000542447.2_Missense_Mutation_p.S95G|CADM1_ENST00000536727.1_Missense_Mutation_p.S95G|CADM1_ENST00000331581.6_Missense_Mutation_p.S95G	NM_014333.3	NP_055148.3			cell adhesion molecule 1											cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(9)|ovary(2)|skin(1)	32	all_hematologic(175;0.0628)	all_cancers(61;2.98e-14)|all_epithelial(67;2.64e-08)|all_hematologic(158;0.000154)|Melanoma(852;0.000952)|Acute lymphoblastic leukemia(157;0.00101)|Breast(348;0.0102)|Medulloblastoma(222;0.0429)|Prostate(24;0.145)|all_neural(223;0.237)		BRCA - Breast invasive adenocarcinoma(274;5.01e-06)|Epithelial(105;0.000305)|all cancers(92;0.00303)		TGAAACCTGCTGTCCTTCAAA	0.373																																					p.S95G		Atlas-SNP	.											.	CADM1	74	.	0			c.A283G						.						69	69	69					11																	115109361		2201	4296	6497	SO:0001583	missense	23705	exon3			ACCTGCTGTCCTT	AB017563	CCDS8373.1, CCDS53711.1, CCDS73397.1, CCDS73398.1, CCDS73399.1	11q23.2	2013-01-29	2007-02-07	2007-02-07	ENSG00000182985	ENSG00000182985		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5951	protein-coding gene	gene with protein product	"nectin-like 2"	605686	"tumor suppressor in lung cancer 1", "immunoglobulin superfamily, member 4"	TSLC1, IGSF4		10610705	Standard	NM_014333		Approved	NECL2, ST17, BL2, SYNCAM, IGSF4A, Necl-2, SYNCAM1, RA175	uc001ppi.4	Q9BY67	OTTHUMG00000168202	ENST00000452722.3:c.283A>G	chr11.hg19:g.115109361T>C	ENSP00000395359:p.Ser95Gly	129.0	0.0		86.0	4.0	NM_014333		Missense_Mutation	SNP	ENST00000452722.3	hg19	CCDS8373.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.01|17.01	3.280362|3.280362	0.59758|0.59758	.|.	.|.	ENSG00000182985|ENSG00000182985	ENST00000545380|ENST00000542447;ENST00000452722;ENST00000537058;ENST00000536727;ENST00000404468;ENST00000331581;ENST00000545094	.|T;T;T;T;T;T	.|0.59364	.|0.27;0.27;0.27;0.27;0.27;0.27	5.81|5.81	5.81|5.81	0.92471|0.92471	.|Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.|0.173783	.|0.64402	.|D	.|0.000010	T|T	0.62551|0.62551	0.2437|0.2437	M|M	0.62723|0.62723	1.935|1.935	0.51482|0.51482	D|D	0.99992|0.99992	.|P;D;P;B;P	.|0.52996	.|0.942;0.957;0.866;0.447;0.649	.|P;P;P;B;B	.|0.49276	.|0.543;0.57;0.605;0.439;0.222	T|T	0.60058|0.60058	-0.7337|-0.7337	5|10	.|0.22109	.|T	.|0.4	.|.	16.167|16.167	0.81768|0.81768	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|95;95;96;95;95	.|Q9BY67-2;F5H0J4;A4FVB5;Q9BY67;A0A4Z1	.|.;.;.;CADM1_HUMAN;.	R|G	93|95;95;95;95;54;95;62	.|ENSP00000439176:S95G;ENSP00000395359:S95G;ENSP00000439817:S95G;ENSP00000440322:S95G;ENSP00000329797:S95G;ENSP00000439696:S62G	.|ENSP00000329797:S95G	Q|S	-|-	2|1	0|0	CADM1|CADM1	114614571|114614571	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	2.046000|2.046000	0.41260|0.41260	2.214000|2.214000	0.71695|0.71695	0.528000|0.528000	0.53228|0.53228	CAG|AGC	.	.		0.373	CADM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398753.2	NM_014333		C	115109361	T	C	115109361	3	2	254	1	0	0	0	0	1	0	0	0	2568	1580	55	2	1077	2	CADM1	11	115109361	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	1414984	115109361	19897155	571	34863										
SIK3	23387	hgsc.bcm.edu	37	chr11	116746722	116746722	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	atcataggcatctgatcttaAtgactaccaagagagaaggg	10	7	3	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:116746722A>G	ENST00000292055.4	-	9	960	c.925T>C	c.(925-927)Tta>Cta	p.L309L	SIK3_ENST00000375288.1_5'UTR|SIK3_ENST00000542607.1_Intron|SIK3_ENST00000434315.2_Silent_p.L208L|SIK3_ENST00000375300.1_Silent_p.L367L|SIK3_ENST00000446921.2_Intron	NM_025164.3	NP_079440.3	Q9Y2K2	SIK3_HUMAN	SIK family kinase 3	309	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.				protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	57						TCTGATCTTAATGACTACCAA	0.433																																					p.L309L		Atlas-SNP	.											.	SIK3	112	.	0			c.T925C						.						81	75	77					11																	116746722		2201	4296	6497	SO:0001819	synonymous_variant	23387	exon9			ATCTTAATGACTA	AB023216	CCDS8379.1, CCDS60974.1, CCDS8379.2	11q23.3	2010-02-17			ENSG00000160584	ENSG00000160584			29165	protein-coding gene	gene with protein product		614776				10231032, 8889548	Standard	NM_025164		Approved	FLJ12240, L19, KIAA0999, QSK	uc001ppy.3	Q9Y2K2	OTTHUMG00000066628	ENST00000292055.4:c.925T>C	chr11.hg19:g.116746722A>G		101.0	0.0		76.0	4.0	NM_025164	A1A5A8|Q59FY2|Q5M9N1|Q6P3R6|Q8IYM8|Q9HA50	Silent	SNP	ENST00000292055.4	hg19	CCDS8379.1	.	.	.	.	.	.	.	.	.	.	A	9.192	1.026248	0.19512	.	.	ENSG00000160584	ENST00000445177;ENST00000413553	.	.	.	5.45	3.17	0.36434	.	.	.	.	.	T	0.55832	0.1945	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52808	-0.8526	4	.	.	.	.	6.9859	0.24727	0.7012:0.0:0.2988:0.0	.	.	.	.	T	360;269	.	.	I	-	2	0	SIK3	116251932	0.993000	0.37304	1.000000	0.80357	0.996000	0.88848	2.547000	0.45786	2.062000	0.61559	0.454000	0.30748	ATT	.	.		0.433	SIK3-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_025164		G	116746722	A	G	116746722	2	3	254	1	0	0	0	0	0	0	0	1	14334	98	4	2		2	SIK3	11	116746722	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	1637361	116746722	18259794	572	34864										
BACE1	23621	hgsc.bcm.edu	37	chr11	117161738	117161739	+	Frame_Shift_Ins	INS	-	-	C													0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cacaccagctgctctcctagINSccagaaaccatcagggaact							TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:117161738_117161739insC	ENST00000313005.6	-	7	1429_1430	c.969_970insG	c.(967-972)tggctafs	p.L324fs	BACE1_ENST00000513780.1_Frame_Shift_Ins_p.L299fs|BACE1_ENST00000445823.2_Frame_Shift_Ins_p.L280fs|BACE1_ENST00000428381.2_Frame_Shift_Ins_p.L255fs|BACE1_ENST00000392937.6_Frame_Shift_Ins_p.L224fs|BACE1_ENST00000514464.1_5'Flank|BACE1_ENST00000510630.1_Frame_Shift_Ins_p.L199fs|BACE1_ENST00000528053.1_Frame_Shift_Ins_p.L290fs	NM_012104.4|NM_138971.3|NM_138972.3|NM_138973.3	NP_036236|NP_620427.1|NP_620428.1|NP_620429.1	P56817	BACE1_HUMAN	beta-site APP-cleaving enzyme 1	324					beta-amyloid metabolic process (GO:0050435)|membrane protein ectodomain proteolysis (GO:0006509)|proteolysis (GO:0006508)	axon (GO:0030424)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	aspartic-type endopeptidase activity (GO:0004190)|beta-amyloid binding (GO:0001540)|beta-aspartyl-peptidase activity (GO:0008798)|enzyme binding (GO:0019899)			breast(2)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)	19	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.69e-05)|Epithelial(105;0.000563)|all cancers(92;0.0032)		TGCTCTCCTAGCCAGAAACCAT	0.505																																					p.L324fs		Pindel	.											.	BACE1	33	.	0			c.970_971insG						.																																			SO:0001589	frameshift_variant	23621	exon7			.	AF190725	CCDS8383.1, CCDS44739.1, CCDS44740.1, CCDS44741.1, CCDS55787.1, CCDS55786.1	11q23-q24	2011-07-27	2004-04-02	2004-04-02	ENSG00000186318	ENSG00000186318			933	protein-coding gene	gene with protein product		604252	"beta-site APP-cleaving enzyme"	BACE		10531052	Standard	NM_012104		Approved		uc001pqz.3	P56817	OTTHUMG00000160636	ENST00000313005.6:c.970dupG	chr11.hg19:g.117161740_117161740dupC	ENSP00000318585:p.Leu324fs	145.0	0.0		72.0	17.0	NM_012104	A0M8W7|B0YIU9|E9PE65|H7BXJ9|Q9BYB9|Q9BYC0|Q9BYC1|Q9UJT5|Q9ULS1	Frame_Shift_Ins	INS	ENST00000313005.6	hg19	CCDS8383.1																																																																																			.	.		0.505	BACE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361505.1			C	117161739	-	C	117161738	7	5	254	1	0	1	1	0	0	0	0	0	1281	962	34	0	547	0	BACE1	11	117161738	Frame_Shift_Ins	INS	-	TCGA-EP-A2KA-01A-11D-A183-10	415016	117161738	17844778	573	34865										
DSCAML1	57453	hgsc.bcm.edu	37	chr11	117374691	117374691	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgttgggcaggatctggatgCggccagtgaggggcacaggg	20	7	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:117374691C>T	ENST00000321322.6	-	11	2409	c.2408G>A	c.(2407-2409)cGc>cAc	p.R803H	DSCAML1_ENST00000527706.1_Missense_Mutation_p.R533H	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	743	Ig-like C2-type 9.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		GATCTGGATGCGGCCAGTGAG	0.632																																					p.R803H		Atlas-SNP	.											DSCAML1,NS,carcinoma,0,1	DSCAML1	286	.	0			c.G2408A						.						104	94	97					11																	117374691		2201	4296	6497	SO:0001583	missense	57453	exon11			TGGATGCGGCCAG		CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.2408G>A	chr11.hg19:g.117374691C>T	ENSP00000315465:p.Arg803His	194.0	0.0		134.0	40.0	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Missense_Mutation	SNP	ENST00000321322.6	hg19	CCDS8384.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.619302	0.87460	.	.	ENSG00000177103	ENST00000527706;ENST00000321322;ENST00000446508	D;D	0.84800	-1.9;-1.9	4.29	4.29	0.51040	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.88280	0.6394	L	0.35854	1.095	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	D	0.87355	0.2340	9	0.34782	T	0.22	.	16.9369	0.86205	0.0:1.0:0.0:0.0	.	743	Q8TD84	DSCL1_HUMAN	H	533;803;510	ENSP00000434335:R533H;ENSP00000315465:R803H	ENSP00000315465:R803H	R	-	2	0	DSCAML1	116879901	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.605000	0.82844	2.237000	0.73441	0.462000	0.41574	CGC	.	.		0.632	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693		T	117374691	C	T	117374691	3	4	254	1	0	0	0	0	1	0	0	0	4771	768	27	1	4025	1	DSCAML1	11	117374691	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	212953	117374691	17631825	574	34866										
DSCAML1	57453	hgsc.bcm.edu	37	chr11	117392100	117392100	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggtcttcagcttctttggtgTcagggtcacatgaaggggat	14	7	5	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:117392100T>A	ENST00000321322.6	-	6	1139	c.1138A>T	c.(1138-1140)Aca>Tca	p.T380S	DSCAML1_ENST00000527706.1_Missense_Mutation_p.T110S	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	320	Ig-like C2-type 4.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		TTCTTTGGTGTCAGGGTCACA	0.582																																					p.T380S		Atlas-SNP	.											.	DSCAML1	286	.	0			c.A1138T						.						30	30	30					11																	117392100		2201	4296	6497	SO:0001583	missense	57453	exon6			TTGGTGTCAGGGT		CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.1138A>T	chr11.hg19:g.117392100T>A	ENSP00000315465:p.Thr380Ser	109.0	0.0		80.0	4.0	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Missense_Mutation	SNP	ENST00000321322.6	hg19	CCDS8384.1	.	.	.	.	.	.	.	.	.	.	T	4.454	0.084126	0.08583	.	.	ENSG00000177103	ENST00000527706;ENST00000321322;ENST00000446508	T;T	0.66638	-0.22;-0.22	4.65	4.65	0.58169	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.32852	0.0843	N	0.01493	-0.835	0.34265	D	0.680376	B;B	0.06786	0.001;0.001	B;B	0.14023	0.006;0.01	T	0.40496	-0.9560	9	0.02654	T	1	.	9.6215	0.39723	0.1557:0.0:0.0:0.8443	.	110;320	G3V1B5;Q8TD84	.;DSCL1_HUMAN	S	110;380;87	ENSP00000434335:T110S;ENSP00000315465:T380S	ENSP00000315465:T380S	T	-	1	0	DSCAML1	116897310	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.112000	0.50368	1.955000	0.56771	0.496000	0.49642	ACA	.	.		0.582	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693		A	117392100	T	A	117392100	3	1	254	1	0	0	0	0	1	0	0	0	4771	1667	58	4	5315	4	DSCAML1	11	117392100	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	17409	117392100	17614416	575	34867										
TMPRSS13	84000	hgsc.bcm.edu	37	chr11	117780678	117780678	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cccggtcatggccctcagtcCgcagtctggagggaaggagt	15	12	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:117780678C>A	ENST00000430170.2	-	8	1039	c.952G>T	c.(952-954)Gga>Tga	p.G318*	TMPRSS13_ENST00000528626.1_Nonsense_Mutation_p.G283*|TMPRSS13_ENST00000445164.2_Nonsense_Mutation_p.G318*|TMPRSS13_ENST00000524993.1_Nonsense_Mutation_p.G318*|TMPRSS13_ENST00000526090.1_Nonsense_Mutation_p.G318*	NM_001244995.1	NP_001231924.1	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	318	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.					blood microparticle (GO:0072562)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|pancreas(1)|prostate(1)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.00106)		GCCCTCAGTCCGCAGTCTGGA	0.617																																					p.G318X		Atlas-SNP	.											.	TMPRSS13	75	.	0			c.G952T						.						53	57	56					11																	117780678		2079	4201	6280	SO:0001587	stop_gained	84000	exon8			TCAGTCCGCAGTC	AB048796	CCDS41721.1, CCDS55788.1, CCDS55789.1, CCDS58185.1	11q23	2010-04-13	2005-03-11	2005-03-12	ENSG00000137747	ENSG00000137747		"Serine peptidases / Transmembrane"	29808	protein-coding gene	gene with protein product		610050	"transmembrane protease, serine 11"	TMPRSS11		11267681	Standard	NM_001077263		Approved	MSPL	uc001prs.2	Q9BYE2	OTTHUMG00000166992	ENST00000430170.2:c.952G>T	chr11.hg19:g.117780678C>A	ENSP00000387702:p.Gly318*	97.0	0.0		73.0	5.0	NM_001206790	B4DTM9|E9PIJ5|F8WAJ3|Q86YM4|Q96JY8|Q9BYE1	Nonsense_Mutation	SNP	ENST00000430170.2	hg19	CCDS58185.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.405168	0.83230	.	.	ENSG00000137747	ENST00000528626;ENST00000336500;ENST00000524993;ENST00000430170;ENST00000445164;ENST00000526090	.	.	.	4.41	4.41	0.53225	.	0.347098	0.24606	N	0.037092	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	16.7676	0.85528	0.0:1.0:0.0:0.0	.	.	.	.	X	283;313;318;318;318;318	.	ENSP00000337113:G313X	G	-	1	0	TMPRSS13	117285888	1.000000	0.71417	0.995000	0.50966	0.074000	0.17049	5.332000	0.65911	2.265000	0.75225	0.561000	0.74099	GGA	.	.		0.617	TMPRSS13-006	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000392318.1	NM_032046		A	117780678	C	A	117780678	4	1	254	1	0	0	0	0	0	1	0	0	16260	661	23	1	775	1	TMPRSS13	11	117780678	Nonsense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	388578	117780678	17225838	576	34868										
MLL	4297	hgsc.bcm.edu	37	chr11	118377325	118377325	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttcttctgaagcacacattcCagaccaagaaacgacatccc	5	14	2	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:118377325C>T	ENST00000389506.5	+	27	10709	c.10709C>T	c.(10708-10710)cCa>cTa	p.P3570L	KMT2A_ENST00000354520.4_Missense_Mutation_p.P3532L|KMT2A_ENST00000534358.1_Missense_Mutation_p.P3573L			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	3570					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										GCACACATTCCAGACCAAGAA	0.473																																					p.P3573L		Atlas-SNP	.											.	MLL	548	.	0			c.C10718T						.						96	93	94					11																	118377325		2200	4295	6495	SO:0001583	missense	4297	exon27			ACATTCCAGACCA	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.10709C>T	chr11.hg19:g.118377325C>T	ENSP00000374157:p.Pro3570Leu	104.0	0.0		51.0	4.0	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Missense_Mutation	SNP	ENST00000389506.5	hg19	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	C	16.02	3.004395	0.54254	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313	D;D;D	0.82167	-1.58;-1.58;-1.54	5.85	5.85	0.93711	.	0.117165	0.64402	D	0.000011	D	0.84777	0.5547	L	0.36672	1.1	0.54753	D	0.999987	D;D	0.63880	0.993;0.993	P;P	0.53954	0.738;0.738	D	0.83952	0.0317	10	0.44086	T	0.13	.	20.1663	0.98152	0.0:1.0:0.0:0.0	.	3573;3570	E9PQG7;Q03164	.;MLL1_HUMAN	L	3573;3570;3532;2480	ENSP00000436786:P3573L;ENSP00000374157:P3570L;ENSP00000346516:P3532L	ENSP00000346516:P3532L	P	+	2	0	MLL	117882535	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.231000	0.51294	2.773000	0.95371	0.585000	0.79938	CCA	.	.		0.473	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		T	118377325	C	T	118377325	3	4	254	1	0	0	0	0	1	0	0	0	9629	594	21	3	10815	3	MLL	11	118377325	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	596647	118377325	16629191	577	34869										
HSPA8	3312	hgsc.bcm.edu	37	chr11	122930222	122930222	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	catcagggttgatgctcttaTtcagttcttttccattgaag	8	8	4	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:122930222T>C	ENST00000532636.1	-	5	1198	c.1079A>G	c.(1078-1080)aAt>aGt	p.N360S	HSPA8_ENST00000227378.3_Missense_Mutation_p.N360S|HSPA8_ENST00000534624.1_Missense_Mutation_p.N360S|SNORD14E_ENST00000364009.1_RNA|HSPA8_ENST00000526862.1_5'UTR|SNORD14C_ENST00000365382.1_RNA|HSPA8_ENST00000526110.1_Missense_Mutation_p.N341S|SNORD14D_ENST00000384390.1_RNA|HSPA8_ENST00000534319.1_Missense_Mutation_p.N124S|HSPA8_ENST00000533540.1_Missense_Mutation_p.N214S|HSPA8_ENST00000453788.2_Missense_Mutation_p.N360S			P11142	HSP7C_HUMAN	heat shock 70kDa protein 8	360	Interaction with BAG1.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone mediated protein folding requiring cofactor (GO:0051085)|clathrin coat disassembly (GO:0072318)|gene expression (GO:0010467)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|negative regulation of fibril organization (GO:1902904)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotransmitter secretion (GO:0007269)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|protein refolding (GO:0042026)|regulation of cell cycle (GO:0051726)|response to unfolded protein (GO:0006986)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	blood microparticle (GO:0072562)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Prp19 complex (GO:0000974)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|MHC class II protein complex binding (GO:0023026)|poly(A) RNA binding (GO:0044822)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)			breast(1)|central_nervous_system(7)|endometrium(1)|kidney(9)|large_intestine(4)|lung(13)|upper_aerodigestive_tract(1)	36		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		GATGCTCTTATTCAGTTCTTT	0.448																																					p.N360S	Colon(21;486 594 5900 6733 14272)	Atlas-SNP	.											.	HSPA8	168	.	0			c.A1079G						.						113	108	110					11																	122930222		2202	4299	6501	SO:0001583	missense	3312	exon5			CTCTTATTCAGTT	Y00371	CCDS8440.1, CCDS44754.1	11q24.1	2011-09-02	2002-08-29		ENSG00000109971	ENSG00000109971		"Heat shock proteins / HSP70"	5241	protein-coding gene	gene with protein product		600816	"heat shock 70kD protein 8"	HSPA10		8530083, 3037489	Standard	NM_006597		Approved	HSC71, HSC70, HSP73	uc001pyo.3	P11142	OTTHUMG00000166030	ENST00000532636.1:c.1079A>G	chr11.hg19:g.122930222T>C	ENSP00000437125:p.Asn360Ser	146.0	0.0		122.0	12.0	NM_006597	Q9H3R6	Missense_Mutation	SNP	ENST00000532636.1	hg19	CCDS8440.1	.	.	.	.	.	.	.	.	.	.	T	24.5	4.539880	0.85917	.	.	ENSG00000109971	ENST00000532636;ENST00000533540;ENST00000534624;ENST00000453788;ENST00000227378;ENST00000534319;ENST00000526110;ENST00000528292	T;T;T;T;T;T;T;T	0.00912	5.55;5.55;5.55;5.55;5.55;5.55;5.55;5.55	4.65	4.65	0.58169	.	0.000000	0.85682	D	0.000000	T	0.03053	0.0090	L	0.41236	1.265	0.80722	D	1	D;D;D;D	0.58970	0.984;0.966;0.958;0.984	P;D;P;P	0.65684	0.896;0.937;0.896;0.896	T	0.59473	-0.7448	10	0.87932	D	0	-19.7226	14.4185	0.67168	0.0:0.0:0.0:1.0	.	360;360;360;360	Q53GZ6;E7ET08;P11142-2;P11142	.;.;.;HSP7C_HUMAN	S	360;214;360;360;360;124;341;300	ENSP00000437125:N360S;ENSP00000437189:N214S;ENSP00000432083:N360S;ENSP00000404372:N360S;ENSP00000227378:N360S;ENSP00000433316:N124S;ENSP00000433584:N341S;ENSP00000432884:N300S	ENSP00000227378:N360S	N	-	2	0	HSPA8	122435432	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.064000	0.71169	1.871000	0.54225	0.454000	0.30748	AAT	.	.		0.448	HSPA8-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387515.1			C	122930222	T	C	122930222	3	2	254	1	0	0	0	0	1	0	0	0	7425	1493	52	2	881	2	HSPA8	11	122930222	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	4552897	122930222	12076294	578	34870										
OR10G8	219869	hgsc.bcm.edu	37	chr11	123901212	123901212	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccctgaggaacaaggaggtgAagaaagctctgttgaagctg	14	7	1	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:123901212A>T	ENST00000431524.1	+	1	916	c.883A>T	c.(883-885)Aag>Tag	p.K295*		NM_001004464.1	NP_001004464.1	Q8NGN5	O10G8_HUMAN	olfactory receptor, family 10, subfamily G, member 8	295						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(7)|large_intestine(2)|lung(21)|ovary(1)|prostate(5)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	44		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		CAAGGAGGTGAAGAAAGCTCT	0.468																																					p.K295X		Atlas-SNP	.											.	OR10G8	132	.	0			c.A883T						.						102	96	98					11																	123901212		2201	4299	6500	SO:0001587	stop_gained	219869	exon1			GAGGTGAAGAAAG	AB065755	CCDS31704.1	11q24.1	2012-08-09			ENSG00000234560	ENSG00000234560		"GPCR / Class A : Olfactory receptors"	14845	protein-coding gene	gene with protein product							Standard	NM_001004464		Approved		uc001pzp.1	Q8NGN5	OTTHUMG00000165968	ENST00000431524.1:c.883A>T	chr11.hg19:g.123901212A>T	ENSP00000389072:p.Lys295*	284.0	0.0		201.0	63.0	NM_001004464	B2RNJ3|Q6IEV2	Nonsense_Mutation	SNP	ENST00000431524.1	hg19	CCDS31704.1	.	.	.	.	.	.	.	.	.	.	A	11.97	1.797584	0.31777	.	.	ENSG00000234560	ENST00000431524	.	.	.	2.91	0.326	0.15908	.	0.161493	0.28927	N	0.013682	.	.	.	.	.	.	0.36812	D	0.885947	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.3731	0.16150	0.7224:0.1757:0.1019:0.0	.	.	.	.	X	295	.	ENSP00000389072:K295X	K	+	1	0	OR10G8	123406422	0.044000	0.20184	0.982000	0.44146	0.346000	0.29079	1.529000	0.35996	-0.064000	0.13043	-0.385000	0.06624	AAG	.	.		0.468	OR10G8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387270.1	NM_001004464		T	123901212	A	T	123901212	4	4	254	1	0	0	0	0	0	1	0	0	10912	247	9	4	885	4	OR10G8	11	123901212	Nonsense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	970990	123901212	11105304	579	34871										
OR8G5	219865	hgsc.bcm.edu	37	chr11	124134976	124134976	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gggcatgatcacactgattgGgctcagttctcacctgcaca	10	12	3	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:124134976G>A	ENST00000524943.2	+	1	254	c.254G>A	c.(253-255)gGg>gAg	p.G85E	OR8G1_ENST00000341493.2_RNA	NM_001005198.1	NP_001005198.1	Q8NG78	OR8G5_HUMAN	olfactory receptor, family 8, subfamily G, member 5	85						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)						Breast(109;0.0157)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0523)		ACACTGATTGGGCTCAGTTCT	0.507																																					p.G85E	Ovarian(169;523 1969 8640 31295 51256)	Atlas-SNP	.											.	.	.	.	0			c.G254A						.						122	114	117					11																	124134976		2174	4282	6456	SO:0001583	missense	219865	exon1			TGATTGGGCTCAG	BK004516	CCDS66256.1	11q24.1	2014-04-17		2004-03-10	ENSG00000255298	ENSG00000255298		"GPCR / Class A : Olfactory receptors"	19622	protein-coding gene	gene with protein product				OR8G5P, OR8G6			Standard	NM_001005198		Approved			Q8NG78	OTTHUMG00000186059	ENST00000524943.2:c.254G>A	chr11.hg19:g.124134976G>A	ENSP00000477014:p.Gly85Glu	137.0	0.0		123.0	34.0	NM_001005198	B2RND3|Q6IEU6	Missense_Mutation	SNP	ENST00000524943.2	hg19																																																																																				.	.		0.507	OR8G5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000387283.2	NM_001005198		A	124134976	G	A	124134976	3	1	254	1	0	0	0	0	1	0	0	0	11245	1232	43	3	256	3	OR8G5	11	124134976	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	233764	124134976	10871540	580	34872										
OR8B8	26493	hgsc.bcm.edu	37	chr11	124310838	124310838	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aagtgagagttgagccttatCagggttatcaagcccaggtt	12	7	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr11:124310838C>T	ENST00000328064.2	-	1	216	c.144G>A	c.(142-144)ctG>ctA	p.L48L		NM_012378.1	NP_036510.1	Q15620	OR8B8_HUMAN	olfactory receptor, family 8, subfamily B, member 8	48					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		TGAGCCTTATCAGGGTTATCA	0.483																																					p.L48L		Atlas-SNP	.											.	OR8B8	76	.	0			c.G144A						.						111	113	112					11																	124310838		2201	4299	6500	SO:0001819	synonymous_variant	26493	exon1			CCTTATCAGGGTT	AF238488	CCDS8446.1	11q24.2	2012-08-09			ENSG00000197125	ENSG00000197125		"GPCR / Class A : Olfactory receptors"	8477	protein-coding gene	gene with protein product						9119360	Standard	NM_012378		Approved	TPCR85	uc010sal.2	Q15620	OTTHUMG00000165917	ENST00000328064.2:c.144G>A	chr11.hg19:g.124310838C>T		148.0	0.0		84.0	4.0	NM_012378	A1L446|Q96RC8	Silent	SNP	ENST00000328064.2	hg19	CCDS8446.1																																																																																			.	.		0.483	OR8B8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387056.1	NM_012378		T	124310838	C	T	124310838	2	4	254	1	0	0	0	0	0	0	0	1	11239	813	29	3		3	OR8B8	11	124310838	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	175862	124310838	10695678	581	34873										
WNK1	65125	hgsc.bcm.edu	37	chr12	988759	988759	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cttccagtttcccagccagtAccaactatccaaggcgaacc	6	16	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:988759A>G	ENST00000315939.6	+	11	3037	c.2394A>G	c.(2392-2394)gtA>gtG	p.V798V	WNK1_ENST00000537687.1_Intron|WNK1_ENST00000340908.4_Silent_p.V391V|WNK1_ENST00000535572.1_Intron|WNK1_ENST00000530271.2_Silent_p.V1296V	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	798					intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			CCCAGCCAGTACCAACTATCC	0.463																																					p.V798V	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											WNK1,colon,carcinoma,0,1	WNK1	403	.	0			c.A2394G						.						81	76	77					12																	988759		2203	4300	6503	SO:0001819	synonymous_variant	65125	exon11			GCCAGTACCAACT	AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 167"	605232	"protein kinase, lysine deficient 1", "hereditary sensory neuropathy, type II"	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.2394A>G	chr12.hg19:g.988759A>G		103.0	0.0		98.0	4.0	NM_018979	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Silent	SNP	ENST00000315939.6	hg19	CCDS8506.1																																																																																			.	.		0.463	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979		G	988759	A	G	988759	2	3	254	1	0	0	0	0	0	0	0	1	17392	378	14	2		2	WNK1	12	988759	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10		988759	132863136	582	34874										
KCNA5	3741	hgsc.bcm.edu	37	chr12	5153812	5153812	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggaacgagtacttcttcgacCgcaaccggcccagcttcgac	10	15	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:5153812C>T	ENST00000252321.3	+	1	728	c.499C>T	c.(499-501)Cgc>Tgc	p.R167C		NM_002234.3	NP_002225.2	P22460	KCNA5_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 5	167					atrial cardiac muscle cell action potential (GO:0086014)|membrane hyperpolarization (GO:0060081)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of potassium ion transport (GO:0043267)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of myoblast proliferation (GO:2000288)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transport (GO:0043266)|regulation of vasoconstriction (GO:0019229)|response to hypoxia (GO:0001666)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|intracellular canaliculus (GO:0046691)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|potassium channel inhibitor activity (GO:0019870)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization (GO:0086089)			NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(21)|ovary(5)|prostate(2)|upper_aerodigestive_tract(2)	52					Dalfampridine(DB06637)	CTTCTTCGACCGCAACCGGCC	0.662																																					p.R167C		Atlas-SNP	.											.	KCNA5	138	.	0			c.C499T						.						38	41	40					12																	5153812		2203	4300	6503	SO:0001583	missense	3741	exon1			TTCGACCGCAACC	M83254	CCDS8536.1	12p13	2012-07-05				ENSG00000130037		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6224	protein-coding gene	gene with protein product		176267				16382104	Standard	NM_002234		Approved	Kv1.5, HK2, HPCN1	uc001qni.4	P22460		ENST00000252321.3:c.499C>T	chr12.hg19:g.5153812C>T	ENSP00000252321:p.Arg167Cys	98.0	0.0		63.0	26.0	NM_002234	Q4KKT8|Q4VAJ1|Q4VAJ2|Q9UDA4	Missense_Mutation	SNP	ENST00000252321.3	hg19	CCDS8536.1	.	.	.	.	.	.	.	.	.	.	C	19.90	3.912344	0.72983	.	.	ENSG00000130037	ENST00000252321	D	0.90324	-2.65	4.7	4.7	0.59300	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.000000	0.64402	U	0.000001	D	0.97729	0.9255	H	0.99650	4.68	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99564	1.0969	10	0.87932	D	0	.	16.8208	0.85745	0.0:1.0:0.0:0.0	.	167	P22460	KCNA5_HUMAN	C	167	ENSP00000252321:R167C	ENSP00000252321:R167C	R	+	1	0	KCNA5	5024073	0.999000	0.42202	1.000000	0.80357	0.998000	0.95712	1.820000	0.39032	2.443000	0.82685	0.511000	0.50034	CGC	.	.		0.662	KCNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398925.2	NM_002234		T	5153812	C	T	5153812	3	4	254	1	0	0	0	0	1	0	0	0	8015	652	23	1	501	1	KCNA5	12	5153812	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	4165053	5153812	128698083	583	34875										
C12orf53	196500	hgsc.bcm.edu	37	chr12	6804636	6804636	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agcccccttggggtggggcaTcccaggccggggtccccctc	15	17	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:6804636T>C	ENST00000540656.1	-	5	1125	c.787A>G	c.(787-789)Atg>Gtg	p.M263V	PIANP_ENST00000320591.5_Missense_Mutation_p.M263V|PIANP_ENST00000534837.1_Missense_Mutation_p.M263V	NM_001244015.1	NP_001230944.1	Q8IYJ0	PIANP_HUMAN	PILR alpha associated neural protein	263						integral component of membrane (GO:0016021)											GGGTGGGGCATCCCAGGCCGG	0.667																																					p.M263V		Atlas-SNP	.											.	.	.	.	0			c.A787G						.						19	21	20					12																	6804636		1851	4075	5926	SO:0001583	missense	196500	exon5			GGGGCATCCCAGG	BC035736	CCDS44818.1, CCDS58205.1	12p13.31	2012-08-17	2012-08-17	2012-08-17	ENSG00000139200	ENSG00000139200			25338	protein-coding gene	gene with protein product	"PILR-associating neural protein"		"chromosome 12 open reading frame 53"	C12orf53		12975309	Standard	NM_153685		Approved	DKFZp547D2210, PANP	uc001qqf.2	Q8IYJ0	OTTHUMG00000168664	ENST00000540656.1:c.787A>G	chr12.hg19:g.6804636T>C	ENSP00000442157:p.Met263Val	135.0	0.0		84.0	4.0	NM_001244014	A8K0T3|B3KPF7|B3KRI6|Q6UX35	Missense_Mutation	SNP	ENST00000540656.1	hg19	CCDS44818.1	.	.	.	.	.	.	.	.	.	.	T	0.037	-1.304093	0.01353	.	.	ENSG00000139200	ENST00000540656;ENST00000320591;ENST00000534837;ENST00000439553	T;T;T	0.39787	1.06;1.06;1.06	3.73	2.55	0.30701	.	0.399158	0.24178	U	0.040823	T	0.15262	0.0368	N	0.08118	0	0.23468	N	0.997619	B	0.02656	0.0	B	0.06405	0.002	T	0.08700	-1.0709	10	0.14656	T	0.56	-6.8587	0.3592	0.00362	0.1888:0.1829:0.2285:0.3998	.	263	Q8IYJ0	CL053_HUMAN	V	263;263;263;237	ENSP00000442157:M263V;ENSP00000317818:M263V;ENSP00000443919:M263V	ENSP00000317818:M263V	M	-	1	0	C12orf53	6674897	0.999000	0.42202	1.000000	0.80357	0.983000	0.72400	0.285000	0.18883	1.562000	0.49601	0.260000	0.18958	ATG	.	.		0.667	PIANP-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400524.1	NM_153685		C	6804636	T	C	6804636	3	2	254	1	0	0	0	0	1	0	0	0	1700	1435	50	2	69	2	C12orf53	12	6804636	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	1650824	6804636	127047259	584	34876										
USP5	8078	hgsc.bcm.edu	37	chr12	6968664	6968664	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aagctggagaagatcttccaGaatgccccgacggaccctac	10	13	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:6968664G>T	ENST00000229268.8	+	9	1141	c.1089G>T	c.(1087-1089)caG>caT	p.Q363H	USP5_ENST00000389231.5_Missense_Mutation_p.Q363H	NM_001098536.1	NP_001092006.1	P45974	UBP5_HUMAN	ubiquitin specific peptidase 5 (isopeptidase T)	363	USP.				positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)	lysosome (GO:0005764)	cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin thiolesterase activity (GO:0004221)|zinc ion binding (GO:0008270)			breast(6)|endometrium(4)|kidney(2)|large_intestine(6)|lung(14)|skin(2)|urinary_tract(2)	36						AGATCTTCCAGAATGCCCCGA	0.527																																					p.Q363H		Atlas-SNP	.											.	USP5	124	.	0			c.G1089T						.						95	86	89					12																	6968664		2203	4300	6503	SO:0001583	missense	8078	exon9			CTTCCAGAATGCC	U35116	CCDS31733.1, CCDS41743.1	12p13	2007-03-02	2005-08-08		ENSG00000111667	ENSG00000111667		"Ubiquitin-specific peptidases"	12628	protein-coding gene	gene with protein product		601447	"ubiquitin specific protease 5 (isopeptidase T)"			12838346, 8723724	Standard	NM_003481		Approved	IsoT	uc001qri.4	P45974	OTTHUMG00000169233	ENST00000229268.8:c.1089G>T	chr12.hg19:g.6968664G>T	ENSP00000229268:p.Gln363His	106.0	0.0		84.0	4.0	NM_003481	D3DUS7|D3DUS8|Q96J22	Missense_Mutation	SNP	ENST00000229268.8	hg19	CCDS41743.1	.	.	.	.	.	.	.	.	.	.	G	14.89	2.669371	0.47677	.	.	ENSG00000111667	ENST00000229268;ENST00000389231	T;T	0.31769	1.48;1.48	5.38	5.38	0.77491	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.105540	0.64402	D	0.000003	T	0.23410	0.0566	L	0.28192	0.835	0.53688	D	0.999978	B;B	0.10296	0.003;0.002	B;B	0.12837	0.008;0.005	T	0.02560	-1.1141	10	0.48119	T	0.1	-7.2631	13.0182	0.58771	0.0826:0.0:0.9174:0.0	.	363;363	P45974;P45974-2	UBP5_HUMAN;.	H	363	ENSP00000229268:Q363H;ENSP00000373883:Q363H	ENSP00000229268:Q363H	Q	+	3	2	USP5	6838925	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.041000	0.49807	2.793000	0.96121	0.655000	0.94253	CAG	.	.		0.527	USP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402982.1			T	6968664	G	T	6968664	3	4	254	1	0	0	0	0	1	0	0	0	17096	933	33	3	1123	3	USP5	12	6968664	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	164028	6968664	126883231	585	34877										
AICDA	57379	hgsc.bcm.edu	37	chr12	8759503	8759503	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tccagtgaaaaggatgtagcActgtcacgcctcttcactac	8	12	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:8759503A>G	ENST00000229335.6	-	2	217	c.114T>C	c.(112-114)agT>agC	p.S38S	AICDA_ENST00000537228.1_Silent_p.S38S	NM_020661.2	NP_065712.1	Q9GZX7	AICDA_HUMAN	activation-induced cytidine deaminase	38					B cell differentiation (GO:0030183)|cellular response to lipopolysaccharide (GO:0071222)|DNA demethylation (GO:0080111)|isotype switching (GO:0045190)|mRNA processing (GO:0006397)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|somatic diversification of immunoglobulins (GO:0016445)|somatic hypermutation of immunoglobulin genes (GO:0016446)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cytidine deaminase activity (GO:0004126)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(4)|ovary(2)|pancreas(1)	16	Lung SC(5;0.184)					AGGATGTAGCACTGTCACGCC	0.448																																					p.S38S	GBM(62;896 1067 5527 26594 30137)	Atlas-SNP	.											.	AICDA	37	.	0			c.T114C						.						92	89	90					12																	8759503		1988	4152	6140	SO:0001819	synonymous_variant	57379	exon2			TGTAGCACTGTCA	AB040430	CCDS41747.1	12p13	2014-09-17			ENSG00000111732	ENSG00000111732		"Apolipoprotein B mRNA editing enzymes"	13203	protein-coding gene	gene with protein product		605257					Standard	NM_020661		Approved	HIGM2, CDA2, ARP2, AID	uc001qur.2	Q9GZX7	OTTHUMG00000168676	ENST00000229335.6:c.114T>C	chr12.hg19:g.8759503A>G		71.0	0.0		57.0	4.0	NM_020661	Q6QJ81|Q8NFC1	Silent	SNP	ENST00000229335.6	hg19	CCDS41747.1	.	.	.	.	.	.	.	.	.	.	A	10.86	1.469819	0.26423	.	.	ENSG00000111732	ENST00000543081;ENST00000544516;ENST00000545512	.	.	.	5.36	-4.59	0.03400	.	.	.	.	.	T	0.63010	0.2475	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63395	-0.6647	4	.	.	.	-18.6705	14.4911	0.67651	0.4192:0.0:0.5808:0.0	.	.	.	.	A	37	.	.	V	-	2	0	AICDA	8650770	0.000000	0.05858	0.946000	0.38457	0.880000	0.50808	-2.820000	0.00749	-0.834000	0.04239	0.383000	0.25322	GTG	.	.		0.448	AICDA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400575.1	NM_020661		G	8759503	A	G	8759503	2	3	254	1	0	0	0	0	0	0	0	1	422	156	6	2		2	AICDA	12	8759503	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	1790839	8759503	125092392	586	34878										
PHC1	1911	hgsc.bcm.edu	37	chr12	9086863	9086863	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aatctgtgtttgttttccagAaaaagctgaatcagtggcta	9	6	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:9086863A>G	ENST00000543824.1	+	11	2374	c.2042A>G	c.(2041-2043)gAa>gGa	p.E681G	PHC1_ENST00000544916.1_Splice_Site_p.E681G|PHC1_ENST00000433083.2_Splice_Site_p.E636G|PHC1_ENST00000536844.1_Splice_Site_p.E287G			P78364	PHC1_HUMAN	polyhomeotic homolog 1 (Drosophila)	681					cellular response to retinoic acid (GO:0071300)|histone ubiquitination (GO:0016574)|multicellular organismal development (GO:0007275)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|large_intestine(8)|liver(2)|lung(3)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	27						TGTTTTCCAGAAAAAGCTGAA	0.438																																					p.E681G		Atlas-SNP	.											.	PHC1	67	.	0			c.A2042G						.						68	65	66					12																	9086863		2203	4300	6503	SO:0001630	splice_region_variant	1911	exon10			TTCCAGAAAAAGC	U89277	CCDS8597.1	12p13	2013-01-10	2006-09-12	2002-11-15	ENSG00000111752	ENSG00000111752		"Sterile alpha motif (SAM) domain containing"	3182	protein-coding gene	gene with protein product		602978	"early development regulator 1 (homolog of polyhomeotic 1)", "polyhomeotic-like 1 (Drosophila)"	EDR1		9121482	Standard	XM_005253334		Approved	HPH1, RAE28	uc001qvd.3	P78364	OTTHUMG00000168275	ENST00000543824.1:c.2042-1A>G	chr12.hg19:g.9086863A>G		58.0	0.0		84.0	4.0	NM_004426	D3DUV4|Q8WVM3|Q9BU63	Missense_Mutation	SNP	ENST00000543824.1	hg19	CCDS8597.1	.	.	.	.	.	.	.	.	.	.	A	13.38	2.220598	0.39201	.	.	ENSG00000111752	ENST00000543824;ENST00000251757;ENST00000433083;ENST00000544916;ENST00000536844	T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91	5.7	5.7	0.88788	.	0.215097	0.40728	N	0.001026	T	0.26738	0.0654	N	0.14661	0.345	0.42241	D	0.99193	B	0.17667	0.023	B	0.16289	0.015	T	0.10776	-1.0615	9	.	.	.	.	14.1997	0.65693	1.0:0.0:0.0:0.0	.	681	P78364	PHC1_HUMAN	G	681;681;636;681;287	ENSP00000440674:E681G;ENSP00000251757:E681G;ENSP00000399194:E636G;ENSP00000437659:E681G;ENSP00000440488:E287G	.	E	+	2	0	PHC1	8978130	1.000000	0.71417	1.000000	0.80357	0.715000	0.41141	4.639000	0.61361	2.183000	0.69458	0.533000	0.62120	GAA	.	.		0.438	PHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399115.1	NM_004426	Missense_Mutation	G	9086863	A	G	9086863	5	3	254	1	0	0	0	0	0	0	1	0	11825	260	9	2	2076	2	PHC1	12	9086863	Splice_Site	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	327360	9086863	124765032	587	34879										
TAS2R43	259289	hgsc.bcm.edu	37	chr12	11244577	11244577	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	atcactgcccagatattataAgcagtagttcttacttctac	5	10	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:11244577A>G	ENST00000531678.1	-	1	335	c.252T>C	c.(250-252)gcT>gcC	p.A84A	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176884.2	NP_795365.2	P59537	T2R43_HUMAN	taste receptor, type 2, member 43	84					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			endometrium(1)|ovary(1)|prostate(2)|urinary_tract(1)	5			OV - Ovarian serous cystadenocarcinoma(49;0.0344)	BRCA - Breast invasive adenocarcinoma(232;0.196)		AGATATTATAAGCAGTAGTTC	0.378																																					p.A84A		Atlas-SNP	.											.	TAS2R43	19	.	0			c.T252C						.						52	45	48					12																	11244577		1879	3859	5738	SO:0001819	synonymous_variant	259289	exon1			ATTATAAGCAGTA	AF494237	CCDS53749.1	12p13.2	2012-08-22				ENSG00000255374		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	18875	protein-coding gene	gene with protein product		612668				12379855	Standard	NM_176884		Approved	T2R52	uc001qzq.1	P59537		ENST00000531678.1:c.252T>C	chr12.hg19:g.11244577A>G		152.0	0.0		107.0	6.0	NM_176884	P59546|Q645X4	Silent	SNP	ENST00000531678.1	hg19	CCDS53749.1																																																																																			.	.		0.378	TAS2R43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383561.1	NM_176884		G	11244577	A	G	11244577	2	3	254	1	0	0	0	0	0	0	0	1	15596	59	3	2		2	TAS2R43	12	11244577	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	2157714	11244577	122607318	588	34880										
GSG1	57613	hgsc.bcm.edu	37	chr12	13238130	13238130	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcctggtgtacgtgttgaagGtggtgacagccgacgccatg	15	9	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:13238130G>A	ENST00000197268.8	+	0	4808				GSG1_ENST00000396310.2_Missense_Mutation_p.T198I|GSG1_ENST00000324458.8_Missense_Mutation_p.T265I|GSG1_ENST00000457134.2_Missense_Mutation_p.T178I|GSG1_ENST00000396302.3_Silent_p.H270H|GSG1_ENST00000537302.1_Missense_Mutation_p.T201I|GSG1_ENST00000351606.6_Silent_p.H306H|GSG1_ENST00000432710.2_Missense_Mutation_p.T242I|GSG1_ENST00000337630.6_Missense_Mutation_p.T229I	NM_020853.1	NP_065904.1	A2RU67	K1467_HUMAN	KIAA1467							integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|prostate(1)|skin(4)	36		Prostate(47;0.184)		BRCA - Breast invasive adenocarcinoma(232;0.157)		CGTGTTGAAGGTGGTGACAGC	0.493																																					p.T265I		Atlas-SNP	.											.	GSG1	62	.	0			c.C794T						.						93	64	74					12																	13238130		2203	4300	6503	SO:0001628	intergenic_variant	83445	exon7			TTGAAGGTGGTGA	AB040900	CCDS31750.1	12p13.1	2006-01-23				ENSG00000084444			29288	protein-coding gene	gene with protein product						10819331	Standard	XM_005253450		Approved		uc001rbi.3	A2RU67			chr12.hg19:g.13238130G>A		172.0	0.0		99.0	4.0	NM_001080555	Q49AF2|Q5CZ81|Q6ZUV7|Q9P261	Missense_Mutation	SNP	ENST00000197268.8	hg19	CCDS31750.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.983277	0.93044	.	.	ENSG00000111305	ENST00000337630;ENST00000324458;ENST00000396310;ENST00000457134;ENST00000432710;ENST00000537302	T;T;T;T;T;T	0.43294	0.98;0.97;0.98;1.0;0.95;0.98	5.66	5.66	0.87406	.	0.187618	0.32120	U	0.006558	T	0.71533	0.3351	M	0.86651	2.83	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;0.999;0.999;0.998	D;D;D;D;D	0.83275	0.995;0.996;0.955;0.974;0.987	T	0.76085	-0.3088	10	0.87932	D	0	.	19.7398	0.96223	0.0:0.0:1.0:0.0	.	242;252;178;201;229	Q2KHT4-6;Q2KHT4;Q2KHT4-5;Q2KHT4-2;F1T0A1	.;GSG1_HUMAN;.;.;.	I	229;265;198;178;242;201	ENSP00000336816:T229I;ENSP00000320838:T265I;ENSP00000379604:T198I;ENSP00000398384:T178I;ENSP00000405032:T242I;ENSP00000441718:T201I	ENSP00000320838:T265I	T	-	2	0	GSG1	13129397	1.000000	0.71417	1.000000	0.80357	0.855000	0.48748	7.980000	0.88113	2.665000	0.90641	0.561000	0.74099	ACC	.	.		0.493	KIAA1467-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401007.1	NM_020853		A	13238130	G	A	13238130	1	1	254	0	1	0	0	0	0	0	0	0	6829	1261	44	3		3	GSG1	12	13238130	IGR	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1993553	13238130	120613765	589	34881										
PLEKHA5	54477	hgsc.bcm.edu	37	chr12	19489449	19489449	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttaacactttttggttttagGaattggaacgagcatggaga	11	4	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:19489449G>T	ENST00000299275.6	+	16	2146	c.2140G>T	c.(2140-2142)Gaa>Taa	p.E714*	PLEKHA5_ENST00000429027.2_Splice_Site_p.E817*|PLEKHA5_ENST00000355397.3_Splice_Site_p.E772*|PLEKHA5_ENST00000317589.4_Splice_Site_p.E714*|PLEKHA5_ENST00000539256.1_Splice_Site_p.E472*|PLEKHA5_ENST00000538714.1_Splice_Site_p.E772*|PLEKHA5_ENST00000359180.3_Splice_Site_p.E714*|PLEKHA5_ENST00000424268.1_Splice_Site_p.E645*|PLEKHA5_ENST00000543806.1_Splice_Site_p.E633*	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5	714					reproductive system development (GO:0061458)	cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					TTGGTTTTAGGAATTGGAACG	0.353																																					p.E817X	Pancreas(196;329 2193 11246 14234 19524)	Atlas-SNP	.											.	PLEKHA5	198	.	0			c.G2449T						.						90	93	92					12																	19489449		2203	4300	6503	SO:0001630	splice_region_variant	54477	exon21			TTTTAGGAATTGG	AF302150	CCDS8682.1, CCDS44840.1, CCDS44840.2, CCDS55809.1, CCDS58213.1, CCDS58214.1	12p12	2013-01-10			ENSG00000052126	ENSG00000052126		"Pleckstrin homology (PH) domain containing"	30036	protein-coding gene	gene with protein product		607770				11214970, 11001876	Standard	NM_001143821		Approved	PEPP2, KIAA1686, FLJ10667	uc031qgo.1	Q9HAU0	OTTHUMG00000167921	ENST00000299275.6:c.2140-1G>T	chr12.hg19:g.19489449G>T		72.0	0.0		87.0	4.0	NM_001256470	A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	Nonsense_Mutation	SNP	ENST00000299275.6	hg19	CCDS8682.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.428455	0.83667	.	.	ENSG00000052126	ENST00000317589;ENST00000355397;ENST00000359180;ENST00000542828;ENST00000429027;ENST00000299275;ENST00000539256;ENST00000538714;ENST00000424268;ENST00000543806;ENST00000536974;ENST00000538972	.	.	.	4.78	4.78	0.61160	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-15.8883	17.4031	0.87466	0.0:0.0:1.0:0.0	.	.	.	.	X	714;772;714;818;817;714;472;772;645;633;606;51	.	.	E	+	1	0	PLEKHA5	19380716	1.000000	0.71417	1.000000	0.80357	0.839000	0.47603	6.667000	0.74451	2.204000	0.70986	0.467000	0.42956	GAA	.	.		0.353	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	NM_019012	Nonsense_Mutation	T	19489449	G	T	19489449	5	4	254	1	0	0	0	0	0	0	1	0	12068	1188	41	3	2327	3	PLEKHA5	12	19489449	Splice_Site	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	6251319	19489449	114362446	590	34882										
PDE3A	5139	hgsc.bcm.edu	37	chr12	20769196	20769196	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agtttgcctcctggcttgttGagacgagtttcttccacttg	10	10	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:20769196G>T	ENST00000359062.3	+	4	1342	c.1302G>T	c.(1300-1302)ttG>ttT	p.L434F	PDE3A_ENST00000544307.1_3'UTR	NM_000921.4|NM_001244683.1	NP_000912.3|NP_001231612.1	Q14432	PDE3A_HUMAN	phosphodiesterase 3A, cGMP-inhibited	434					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP-mediated signaling (GO:0019934)|diterpenoid metabolic process (GO:0016101)|lipid metabolic process (GO:0006629)|negative regulation of apoptotic process (GO:0043066)|negative regulation of vascular permeability (GO:0043116)|oocyte maturation (GO:0001556)|positive regulation of oocyte development (GO:0060282)|positive regulation of vascular permeability (GO:0043117)|regulation of meiosis (GO:0040020)|response to cAMP (GO:0051591)|response to drug (GO:0042493)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(7)|lung(29)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	58	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Caffeine(DB00201)|Cilostazol(DB01166)|Enoximone(DB04880)|Ibudilast(DB05266)|Levosimendan(DB00922)|Milrinone(DB00235)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Tofisopam(DB08811)	CTGGCTTGTTGAGACGAGTTT	0.473																																					p.L434F		Atlas-SNP	.											PDE3A,lower_third,carcinoma,0,1	PDE3A	184	.	0			c.G1302T						.						115	109	111					12																	20769196		2203	4300	6503	SO:0001583	missense	5139	exon4			CTTGTTGAGACGA		CCDS31754.1	12p12.2	2011-04-15			ENSG00000172572	ENSG00000172572	3.1.4.17	"Phosphodiesterases"	8778	protein-coding gene	gene with protein product		123805				1315035, 10679291	Standard	NM_000921		Approved	CGI-PDE	uc001reh.2	Q14432	OTTHUMG00000168962	ENST00000359062.3:c.1302G>T	chr12.hg19:g.20769196G>T	ENSP00000351957:p.Leu434Phe	49.0	0.0		39.0	3.0	NM_000921	O60865|Q13348|Q17RD1	Missense_Mutation	SNP	ENST00000359062.3	hg19	CCDS31754.1	.	.	.	.	.	.	.	.	.	.	G	19.81	3.896170	0.72639	.	.	ENSG00000172572	ENST00000359062	T	0.55234	0.53	5.43	3.61	0.41365	.	2.081570	0.02009	N	0.046881	T	0.74313	0.3700	M	0.70595	2.14	0.45227	D	0.998231	D	0.76494	0.999	D	0.87578	0.998	T	0.50389	-0.8834	10	0.72032	D	0.01	.	10.16	0.42847	0.2144:0.0:0.7856:0.0	.	434	Q14432	PDE3A_HUMAN	F	434	ENSP00000351957:L434F	ENSP00000351957:L434F	L	+	3	2	PDE3A	20660463	1.000000	0.71417	0.997000	0.53966	0.987000	0.75469	0.758000	0.26447	0.782000	0.33613	0.655000	0.94253	TTG	.	.		0.473	PDE3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401756.2			T	20769196	G	T	20769196	3	4	254	1	0	0	0	0	1	0	0	0	11646	1281	45	3	1316	3	PDE3A	12	20769196	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1279747	20769196	113082699	591	34883										
ABCC9	10060	hgsc.bcm.edu	37	chr12	21962812	21962812	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctccaggtagagatttgaccAtattcttcagctgagcaatt	8	9	2	3	rs144125604		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:21962812A>G	ENST00000261201.4	-	35	4288	c.4289T>C	c.(4288-4290)aTg>aCg	p.M1430T	ABCC9_ENST00000345162.2_Missense_Mutation_p.M1394T|ABCC9_ENST00000261200.4_Missense_Mutation_p.M1430T	NM_005691.2	NP_005682.2	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	1430	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				defense response to virus (GO:0051607)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	ATP-sensitive potassium channel complex (GO:0008282)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcomere (GO:0030017)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|sulfonylurea receptor activity (GO:0008281)|transporter activity (GO:0005215)			NS(2)|breast(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|lung(56)|ovary(4)|pancreas(1)|prostate(4)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(5)	118					Adenosine triphosphate(DB00171)|Glyburide(DB01016)	AGATTTGACCATATTCTTCAG	0.333																																					p.M1430T		Atlas-SNP	.											.	ABCC9	411	.	0			c.T4289C						.	A	THR/MET,THR/MET	0,4406		0,0,2203	97	100	99		4289,4289	5.3	1	12	dbSNP_134	99	1,8597	1.2+/-3.3	0,1,4298	no	missense,missense	ABCC9	NM_005691.2,NM_020297.2	81,81	0,1,6501	GG,GA,AA		0.0116,0.0,0.0077	benign,benign	1430/1550,1430/1550	21962812	1,13003	2203	4299	6502	SO:0001583	missense	10060	exon35			TTGACCATATTCT	AF061323	CCDS8693.1, CCDS8694.1	12p12.1	2014-09-17			ENSG00000069431	ENSG00000069431		"ATP binding cassette transporters / subfamily C"	60	protein-coding gene	gene with protein product	"sulfonylurea receptor 2"	601439				9457174, 15034580	Standard	NM_020297		Approved	SUR2, CMD1O	uc001rfh.3	O60706	OTTHUMG00000169094	ENST00000261201.4:c.4289T>C	chr12.hg19:g.21962812A>G	ENSP00000261201:p.Met1430Thr	60.0	0.0		45.0	4.0	NM_005691	O60707	Missense_Mutation	SNP	ENST00000261201.4	hg19	CCDS8694.1	.	.	.	.	.	.	.	.	.	.	A	14.78	2.636999	0.47049	0.0	1.16E-4	ENSG00000069431	ENST00000261200;ENST00000544039;ENST00000261201;ENST00000345162	D;D;D;D	0.90133	-2.62;-2.62;-2.62;-2.62	5.29	5.29	0.74685	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.039691	0.85682	D	0.000000	T	0.80899	0.4712	N	0.05031	-0.125	0.58432	D	0.999998	B;B	0.14012	0.004;0.009	B;B	0.20384	0.029;0.013	T	0.76353	-0.2990	10	0.35671	T	0.21	-18.5984	13.954	0.64135	1.0:0.0:0.0:0.0	.	1430;1430	O60706;O60706-2	ABCC9_HUMAN;.	T	1430;1057;1430;1394	ENSP00000261200:M1430T;ENSP00000440521:M1057T;ENSP00000261201:M1430T;ENSP00000261202:M1394T	ENSP00000261200:M1430T	M	-	2	0	ABCC9	21854079	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	8.688000	0.91260	2.213000	0.71641	0.528000	0.53228	ATG	.	A|1.000;G|0.000		0.333	ABCC9-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402230.1	NM_005691		G	21962812	A	G	21962812	3	3	254	1	0	0	0	0	1	0	0	0	59	217	8	2	518	2	ABCC9	12	21962812	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	1193616	21962812	111889083	592	34884										
ITPR2	3709	hgsc.bcm.edu	37	chr12	26732975	26732975	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cttacctggaggctggtactAttgtctgaaaagggagaatt	12	6	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:26732975A>T	ENST00000381340.3	-	33	4910	c.4494T>A	c.(4492-4494)aaT>aaA	p.N1498K		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1498					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	GGCTGGTACTATTGTCTGAAA	0.373																																					p.N1498K		Atlas-SNP	.											.	ITPR2	270	.	0			c.T4494A						.						111	100	103					12																	26732975		1809	4071	5880	SO:0001583	missense	3709	exon33			GGTACTATTGTCT	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"Ion channels / Inositol triphosphate receptors"	6181	protein-coding gene	gene with protein product	"cilia and flagella associated protein 48"	600144	"inositol 1,4,5-triphosphate receptor, type 2"			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.4494T>A	chr12.hg19:g.26732975A>T	ENSP00000370744:p.Asn1498Lys	99.0	0.0		124.0	5.0	NM_002223	O94773	Missense_Mutation	SNP	ENST00000381340.3	hg19	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	A	12.89	2.074147	0.36566	.	.	ENSG00000123104	ENST00000381340	T	0.68331	-0.32	5.17	3.18	0.36537	.	0.042649	0.85682	D	0.000000	T	0.65112	0.2660	M	0.63428	1.95	0.80722	D	1	B	0.27117	0.168	B	0.38842	0.283	T	0.62779	-0.6782	10	0.37606	T	0.19	.	8.009	0.30342	0.0738:0.0:0.6515:0.2747	.	1498	Q14571	ITPR2_HUMAN	K	1498	ENSP00000370744:N1498K	ENSP00000370744:N1498K	N	-	3	2	ITPR2	26624242	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	0.719000	0.25881	1.394000	0.46624	-0.177000	0.13119	AAT	.	.		0.373	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		T	26732975	A	T	26732975	3	4	254	1	0	0	0	0	1	0	0	0	7930	446	16	4	3711	4	ITPR2	12	26732975	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	4770163	26732975	107118920	593	34885										
STK38L	23012	hgsc.bcm.edu	37	chr12	27475143	27475143	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cttcaaattttgatgacttcCctgaatctgatattttacaa	4	8	2	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:27475143C>T	ENST00000389032.3	+	13	1412	c.1243C>T	c.(1243-1245)Cct>Tct	p.P415S	STK38L_ENST00000539577.1_Missense_Mutation_p.P322S	NM_015000.3	NP_055815.1			serine/threonine kinase 38 like											breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)|skin(1)	12	Colorectal(261;0.0847)					TGATGACTTCCCTGAATCTGA	0.328																																					p.P415S		Atlas-SNP	.											.	STK38L	44	.	0			c.C1243T						.						103	116	112					12																	27475143		2203	4299	6502	SO:0001583	missense	23012	exon13			GACTTCCCTGAAT	AB023182	CCDS31761.1	12p11.23	2014-04-23			ENSG00000211455	ENSG00000211455			17848	protein-coding gene	gene with protein product	"nuclear Dbf2-related 2"	615836				16488889	Standard	NM_015000		Approved	KIAA0965, NDR2	uc001rhr.3	Q9Y2H1	OTTHUMG00000169284	ENST00000389032.3:c.1243C>T	chr12.hg19:g.27475143C>T	ENSP00000373684:p.Pro415Ser	75.0	0.0		58.0	5.0	NM_015000		Missense_Mutation	SNP	ENST00000389032.3	hg19	CCDS31761.1	.	.	.	.	.	.	.	.	.	.	C	17.93	3.509477	0.64522	.	.	ENSG00000211455	ENST00000389032;ENST00000539577	T;T	0.56941	0.43;0.43	4.98	4.98	0.66077	Protein kinase, C-terminal (1);AGC-kinase, C-terminal (2);	0.000000	0.85682	D	0.000000	T	0.71651	0.3365	M	0.71871	2.18	0.80722	D	1	D;D	0.67145	0.996;0.988	D;P	0.68039	0.955;0.904	T	0.74990	-0.3475	10	0.66056	D	0.02	.	18.6314	0.91361	0.0:1.0:0.0:0.0	.	322;415	B4E3J8;Q9Y2H1	.;ST38L_HUMAN	S	415;322	ENSP00000373684:P415S;ENSP00000446386:P322S	ENSP00000373684:P415S	P	+	1	0	STK38L	27366410	1.000000	0.71417	1.000000	0.80357	0.838000	0.47535	5.671000	0.68095	2.477000	0.83638	0.305000	0.20034	CCT	.	.		0.328	STK38L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403297.1	NM_015000		T	27475143	C	T	27475143	3	4	254	1	0	0	0	0	1	0	0	0	15319	623	22	3	1289	3	STK38L	12	27475143	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	742168	27475143	106376752	594	34886										
SLC2A13	114134	hgsc.bcm.edu	37	chr12	40158289	40158289	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgtaagatactctgctgtgtGtaaaaatgttagtgaaacca	9	5	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:40158289G>A	ENST00000280871.4	-	9	1743	c.1693C>T	c.(1693-1695)Cac>Tac	p.H565Y		NM_052885.3	NP_443117.3	Q96QE2	MYCT_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 13	565					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	29		Lung NSC(34;0.105)|all_lung(34;0.123)				TCTGCTGTGTGTAAAAATGTT	0.289										HNSCC(50;0.14)																											p.H565Y		Atlas-SNP	.											.	SLC2A13	91	.	0			c.C1693T						.						86	86	86					12																	40158289		2203	4300	6503	SO:0001583	missense	114134	exon9			CTGTGTGTAAAAA	AJ315644	CCDS8736.2	12q12	2013-05-22			ENSG00000151229	ENSG00000151229		"Solute carriers"	15956	protein-coding gene	gene with protein product	"H(+)-myo-inositol symporter"	611036				11500374	Standard	NM_052885		Approved	HMIT	uc010skm.2	Q96QE2	OTTHUMG00000059743	ENST00000280871.4:c.1693C>T	chr12.hg19:g.40158289G>A	ENSP00000280871:p.His565Tyr	158.0	0.0		89.0	4.0	NM_052885	Q17S07	Missense_Mutation	SNP	ENST00000280871.4	hg19	CCDS8736.2	.	.	.	.	.	.	.	.	.	.	G	24.6	4.545889	0.86022	.	.	ENSG00000151229	ENST00000280871	T	0.72394	-0.65	5.63	5.63	0.86233	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.53916	0.1826	N	0.10707	0.03	0.80722	D	1	D	0.60160	0.987	B	0.41723	0.365	T	0.58042	-0.7706	10	0.29301	T	0.29	-23.9392	19.6978	0.96034	0.0:0.0:1.0:0.0	.	565	Q96QE2	MYCT_HUMAN	Y	565	ENSP00000280871:H565Y	ENSP00000280871:H565Y	H	-	1	0	SLC2A13	38444556	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.389000	0.97243	2.649000	0.89929	0.650000	0.86243	CAC	.	.		0.289	SLC2A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132849.2			A	40158289	G	A	40158289	3	1	254	1	0	0	0	0	1	0	0	0	14557	1377	48	3	261	3	SLC2A13	12	40158289	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	12683146	40158289	93693606	595	34887										
ANO6	196527	hgsc.bcm.edu	37	chr12	45742051	45742051	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	accggatgaatgatttttacAtagttgatagagatgctttc	9	5	0	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:45742051A>T	ENST00000320560.8	+	5	788	c.586A>T	c.(586-588)Ata>Tta	p.I196L	ANO6_ENST00000425752.2_Missense_Mutation_p.I196L|ANO6_ENST00000426898.2_3'UTR|ANO6_ENST00000441606.2_Missense_Mutation_p.I178L|ANO6_ENST00000423947.3_Missense_Mutation_p.I217L|ANO6_ENST00000435642.1_Missense_Mutation_p.I196L	NM_001025356.2	NP_001020527.2	Q4KMQ2	ANO6_HUMAN	anoctamin 6	196					activation of blood coagulation via clotting cascade (GO:0002543)|blood coagulation (GO:0007596)|bone mineralization involved in bone maturation (GO:0035630)|calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|phosphatidylserine exposure on blood platelet (GO:0097045)|phospholipid scrambling (GO:0017121)|positive regulation of endothelial cell apoptotic process (GO:2000353)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)|voltage-gated chloride channel activity (GO:0005247)|voltage-gated ion channel activity (GO:0005244)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						TGATTTTTACATAGTTGATAG	0.423																																					p.I217L		Atlas-SNP	.											.	ANO6	163	.	0			c.A649T						.						115	117	116					12																	45742051		2203	4300	6503	SO:0001583	missense	196527	exon6			TTTTACATAGTTG	AL832340	CCDS31782.1, CCDS44865.1, CCDS44866.1, CCDS55819.1	12q12-q13.11	2014-09-17	2008-08-28	2008-08-28				"Ion channels / Chloride channels : Calcium activated : Anoctamins"	25240	protein-coding gene	gene with protein product		608663	"transmembrane protein 16F"	TMEM16F		15067359, 24692353	Standard	NM_001025356		Approved	DKFZp313M0720	uc010slf.2	Q4KMQ2	OTTHUMG00000169564	ENST00000320560.8:c.586A>T	chr12.hg19:g.45742051A>T	ENSP00000320087:p.Ile196Leu	275.0	0.0		213.0	16.0	NM_001204803	A6NNM6|B9EGG0|E7ENK4|E9PB30|E9PCT2|Q8N3Q2	Missense_Mutation	SNP	ENST00000320560.8	hg19	CCDS31782.1	.	.	.	.	.	.	.	.	.	.	A	15.30	2.793353	0.50102	.	.	ENSG00000177119	ENST00000425752;ENST00000423947;ENST00000435642;ENST00000320560;ENST00000441606	T;T;T;T;T	0.70282	-0.47;-0.47;-0.47;-0.47;-0.47	5.3	5.3	0.74995	.	0.109289	0.64402	D	0.000009	T	0.62171	0.2406	L	0.45352	1.415	0.48040	D	0.999571	B;B;B;B	0.33022	0.394;0.013;0.019;0.013	B;B;B;B	0.31245	0.126;0.022;0.017;0.026	T	0.59359	-0.7469	10	0.17832	T	0.49	.	15.9619	0.79936	1.0:0.0:0.0:0.0	.	178;217;196;196	E9PB30;B9EGG0;E9PCT2;Q4KMQ2	.;.;.;ANO6_HUMAN	L	196;217;196;196;178	ENSP00000391417:I196L;ENSP00000409126:I217L;ENSP00000413840:I196L;ENSP00000320087:I196L;ENSP00000413137:I178L	ENSP00000320087:I196L	I	+	1	0	ANO6	44028318	1.000000	0.71417	0.919000	0.36401	0.787000	0.44495	4.247000	0.58750	2.308000	0.77769	0.533000	0.62120	ATA	.	.		0.423	ANO6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404822.1	XM_113743		T	45742051	A	T	45742051	3	4	254	1	0	0	0	0	1	0	0	0	701	217	8	4	624	4	ANO6	12	45742051	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	5583762	45742051	88109844	596	34888										
SENP1	29843	hgsc.bcm.edu	37	chr12	48491823	48491823	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cctctggaaaacctgtttgtGgcaggaggtgggttttgaat	14	6	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:48491823G>A	ENST00000004980.5	-	3	567	c.89C>T	c.(88-90)cCa>cTa	p.P30L	SENP1_ENST00000549595.1_Missense_Mutation_p.P30L|SENP1_ENST00000547886.1_5'Flank|SENP1_ENST00000551330.1_Missense_Mutation_p.P30L|SENP1_ENST00000448372.1_Missense_Mutation_p.P30L|SENP1_ENST00000549518.1_Missense_Mutation_p.P30L|SENP1_ENST00000339976.6_Missense_Mutation_p.P62L			Q9P0U3	SENP1_HUMAN	SUMO1/sentrin specific peptidase 1	30					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic signaling pathway (GO:0097190)|cellular protein metabolic process (GO:0044267)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-translational protein modification (GO:0043687)|protein desumoylation (GO:0016926)|protein sumoylation (GO:0016925)|proteolysis (GO:0006508)|regulation of definitive erythrocyte differentiation (GO:0010724)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endopeptidase activity (GO:0004175)|SUMO-specific protease activity (GO:0016929)			large_intestine(3)|lung(1)|pancreas(2)|stomach(1)	7		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)				ACCTGTTTGTGGCAGGAGGTG	0.433																																					p.P30L		Atlas-SNP	.											.	SENP1	44	.	0			c.C89T						.						83	93	90					12																	48491823		1880	4109	5989	SO:0001583	missense	29843	exon3			GTTTGTGGCAGGA	AF149770	CCDS44868.1, CCDS44868.2	12q13.1	2008-02-05	2005-08-17			ENSG00000079387			17927	protein-coding gene	gene with protein product		612157	"SUMO1/sentrin specific protease 1"			10652325, 14563852	Standard	NM_001267595		Approved		uc009zkx.4	Q9P0U3	OTTHUMG00000169896	ENST00000004980.5:c.89C>T	chr12.hg19:g.48491823G>A	ENSP00000004980:p.Pro30Leu	106.0	0.0		73.0	4.0	NM_001267594	A8K7P5|Q86XC8	Missense_Mutation	SNP	ENST00000004980.5	hg19	CCDS44868.2	.	.	.	.	.	.	.	.	.	.	G	12.78	2.040593	0.35989	.	.	ENSG00000079387	ENST00000004980;ENST00000339976;ENST00000448372;ENST00000551330;ENST00000549595;ENST00000549518;ENST00000551798	T;T;T;T;T	0.15952	2.38;2.38;2.38;2.38;2.38	4.69	1.74	0.24563	.	1.314310	0.05034	N	0.475024	T	0.14657	0.0354	N	0.19112	0.55	0.30326	N	0.787074	B;B	0.11235	0.002;0.004	B;B	0.13407	0.004;0.009	T	0.33979	-0.9847	10	0.56958	D	0.05	3.0118	12.1929	0.54280	0.0:0.0:0.3573:0.6427	.	30;30	Q9P0U3;Q9P0U3-2	SENP1_HUMAN;.	L	30;62;30;30;30;30;23	ENSP00000004980:P30L;ENSP00000394791:P30L;ENSP00000446681:P30L;ENSP00000450076:P30L;ENSP00000447328:P30L	ENSP00000004980:P30L	P	-	2	0	SENP1	46778090	1.000000	0.71417	0.946000	0.38457	0.795000	0.44927	0.748000	0.26305	0.393000	0.25203	-0.274000	0.10170	CCA	.	.		0.433	SENP1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406471.1	NM_014554		A	48491823	G	A	48491823	3	1	254	1	0	0	0	0	1	0	0	0	14061	1348	47	3	1906	3	SENP1	12	48491823	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	2749772	48491823	85360072	597	34889										
SENP1	29843	hgsc.bcm.edu	37	chr12	48491866	48491866	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggagttgtggttcactaaagTcacttctccagcatccatcc	8	12	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:48491866T>C	ENST00000004980.5	-	3	524	c.46A>G	c.(46-48)Act>Gct	p.T16A	SENP1_ENST00000549595.1_Missense_Mutation_p.T16A|SENP1_ENST00000547886.1_5'Flank|SENP1_ENST00000551330.1_Missense_Mutation_p.T16A|SENP1_ENST00000448372.1_Missense_Mutation_p.T16A|SENP1_ENST00000549518.1_Missense_Mutation_p.T16A|SENP1_ENST00000339976.6_Missense_Mutation_p.T48A			Q9P0U3	SENP1_HUMAN	SUMO1/sentrin specific peptidase 1	16					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic signaling pathway (GO:0097190)|cellular protein metabolic process (GO:0044267)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-translational protein modification (GO:0043687)|protein desumoylation (GO:0016926)|protein sumoylation (GO:0016925)|proteolysis (GO:0006508)|regulation of definitive erythrocyte differentiation (GO:0010724)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endopeptidase activity (GO:0004175)|SUMO-specific protease activity (GO:0016929)			large_intestine(3)|lung(1)|pancreas(2)|stomach(1)	7		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)				TTCACTAAAGTCACTTCTCCA	0.443																																					p.T16A		Atlas-SNP	.											.	SENP1	44	.	0			c.A46G						.						95	102	99					12																	48491866		1934	4143	6077	SO:0001583	missense	29843	exon3			CTAAAGTCACTTC	AF149770	CCDS44868.1, CCDS44868.2	12q13.1	2008-02-05	2005-08-17			ENSG00000079387			17927	protein-coding gene	gene with protein product		612157	"SUMO1/sentrin specific protease 1"			10652325, 14563852	Standard	NM_001267595		Approved		uc009zkx.4	Q9P0U3	OTTHUMG00000169896	ENST00000004980.5:c.46A>G	chr12.hg19:g.48491866T>C	ENSP00000004980:p.Thr16Ala	117.0	0.0		81.0	4.0	NM_001267594	A8K7P5|Q86XC8	Missense_Mutation	SNP	ENST00000004980.5	hg19	CCDS44868.2	.	.	.	.	.	.	.	.	.	.	T	16.27	3.074817	0.55646	.	.	ENSG00000079387	ENST00000004980;ENST00000339976;ENST00000448372;ENST00000551330;ENST00000549595;ENST00000549518;ENST00000551798	T;T;T;T;T	0.16324	2.35;2.35;2.35;2.35;2.35	5.09	5.09	0.68999	.	0.000000	0.64402	D	0.000005	T	0.11110	0.0271	N	0.19112	0.55	0.20703	N	0.999865	B;B	0.25007	0.071;0.116	B;B	0.26969	0.034;0.075	T	0.15065	-1.0450	10	0.52906	T	0.07	-12.3831	7.7073	0.28657	0.0:0.092:0.0:0.908	.	16;16	Q9P0U3;Q9P0U3-2	SENP1_HUMAN;.	A	16;48;16;16;16;16;9	ENSP00000004980:T16A;ENSP00000394791:T16A;ENSP00000446681:T16A;ENSP00000450076:T16A;ENSP00000447328:T16A	ENSP00000004980:T16A	T	-	1	0	SENP1	46778133	0.958000	0.32768	0.973000	0.42090	0.992000	0.81027	1.176000	0.31957	2.272000	0.75746	0.460000	0.39030	ACT	.	.		0.443	SENP1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406471.1	NM_014554		C	48491866	T	C	48491866	3	2	254	1	0	0	0	0	1	0	0	0	14061	1667	58	2	1949	2	SENP1	12	48491866	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	43	48491866	85360029	598	34890										
CACNB3	784	hgsc.bcm.edu	37	chr12	49221409	49221409	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cgtggcgaggagcactccccCcttgagcgggacagcttgat	14	13	0	2	rs191174951	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:49221409C>T	ENST00000301050.2	+	13	1381	c.1182C>T	c.(1180-1182)ccC>ccT	p.P394P	CACNB3_ENST00000540990.1_Silent_p.P381P|CACNB3_ENST00000547230.1_Silent_p.P353P|CACNB3_ENST00000547392.1_Silent_p.P367P|CACNB3_ENST00000536187.2_Silent_p.P393P	NM_000725.3	NP_000716.2	P54284	CACB3_HUMAN	calcium channel, voltage-dependent, beta 3 subunit	394					axon guidance (GO:0007411)|calcium ion transport (GO:0006816)|membrane depolarization (GO:0051899)|synaptic transmission (GO:0007268)|T cell receptor signaling pathway (GO:0050852)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|membrane (GO:0016020)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			autonomic_ganglia(1)|breast(1)|large_intestine(5)|lung(4)|prostate(1)	12					Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	AGCACTCCCCCCTTGAGCGGG	0.632																																					p.P394P		Atlas-SNP	.											.	CACNB3	51	.	0			c.C1182T						.																																			SO:0001819	synonymous_variant	784	exon13			CTCCCCCCTTGAG		CCDS8769.1, CCDS55821.1, CCDS55822.1, CCDS55823.1	12q13	2008-05-02				ENSG00000167535		"Calcium channel subunits"	1403	protein-coding gene	gene with protein product		601958		CACNLB3		8119293	Standard	NM_000725		Approved		uc010sly.2	P54284		ENST00000301050.2:c.1182C>T	chr12.hg19:g.49221409C>T		91.0	0.0		51.0	4.0	NM_000725	A8K0Z4|B7Z4Q1|B7Z973|B7ZAK8|F5GZW7|F5H2P6|F8VSG3|Q13913	Silent	SNP	ENST00000301050.2	hg19	CCDS8769.1																																																																																			.	C|1.000;A|0.000		0.632	CACNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408886.1			T	49221409	C	T	49221409	2	4	254	1	0	0	0	0	0	0	0	1	2556	610	22	3		3	CACNB3	12	49221409	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	729543	49221409	84630486	599	34891										
SPATS2	65244	hgsc.bcm.edu	37	chr12	49854820	49854820	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccaggaaacagaaccagaagGgtaagattacatgtgggcat	12	7	0	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:49854820G>T	ENST00000553127.1	+	4	538	c.25G>T	c.(25-27)Gat>Tat	p.D9Y	SPATS2_ENST00000552918.1_Splice_Site_p.D9Y|SPATS2_ENST00000547865.1_Splice_Site_p.G9*|SPATS2_ENST00000321898.6_Splice_Site_p.D9Y			Q86XZ4	SPAS2_HUMAN	spermatogenesis associated, serine-rich 2	9						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(1)|prostate(1)|urinary_tract(4)	21						GAACCAGAAGGGTAAGATTAC	0.338																																					p.D9Y		Atlas-SNP	.											.	SPATS2	43	.	0			c.G25T						.						103	102	102					12																	49854820		2203	4300	6503	SO:0001630	splice_region_variant	65244	exon3			CAGAAGGGTAAGA	AK023179	CCDS31794.1	12q13.12	2009-06-12							18650	protein-coding gene	gene with protein product		611667				11944913, 17989879	Standard	NM_023071		Approved	SPATA10, SCR59, FLJ13117	uc001rud.2	Q86XZ4		ENST00000553127.1:c.25+1G>T	chr12.hg19:g.49854820G>T		272.0	0.0		211.0	9.0	NM_023071	A8K8G9|Q9H7D4|Q9H8Y7|Q9H8Z8	Missense_Mutation	SNP	ENST00000553127.1	hg19	CCDS31794.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	37|37	6.583770|6.583770	0.97684|0.97684	.|.	.|.	ENSG00000123352|ENSG00000123352	ENST00000550997;ENST00000549538;ENST00000550643;ENST00000548710;ENST00000549298;ENST00000553127;ENST00000321898;ENST00000551540;ENST00000552918;ENST00000548777;ENST00000552171|ENST00000547865	.|.	.|.	.|.	5.85|5.85	5.85|5.85	0.93711|0.93711	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.70378|.	0.3217|.	L|L	0.50333|0.50333	1.59|1.59	0.80722|0.80722	D|D	1|1	B|.	0.11235|.	0.004|.	B|.	0.09377|.	0.004|.	T|.	0.71859|.	-0.4465|.	9|.	0.87932|0.87932	D|D	0|0	-10.8084|-10.8084	15.6543|15.6543	0.77121|0.77121	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	9|.	Q86XZ4|.	SPAS2_HUMAN|.	Y|X	9|9	.|.	ENSP00000326841:D9Y|ENSP00000449615:G9X	D|G	+|+	1|1	0|0	SPATS2|SPATS2	48141087|48141087	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.947000|0.947000	0.59692|0.59692	4.219000|4.219000	0.58561|0.58561	2.767000|2.767000	0.95098|0.95098	0.563000|0.563000	0.77884|0.77884	GAT|GGA	.	.		0.338	SPATS2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404023.1	NM_023071	Missense_Mutation	T	49854820	G	T	49854820	5	4	254	1	0	0	0	0	0	0	1	0	15034	1246	43	3	27	3	SPATS2	12	49854820	Splice_Site	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	633411	49854820	83997075	600	34892										
LARP4	113251	hgsc.bcm.edu	37	chr12	50822725	50822725	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtctttaatacaggtaatgcAgagctctcagaagatatatg	9	6	2	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:50822725A>G	ENST00000398473.2	+	3	286	c.174A>G	c.(172-174)gcA>gcG	p.A58A	LARP4_ENST00000293618.8_Silent_p.A58A|LARP4_ENST00000429001.3_Silent_p.A64A|LARP4_ENST00000518561.1_5'UTR|LARP4_ENST00000522085.1_Silent_p.A58A|LARP4_ENST00000347328.5_Silent_p.A58A|LARP4_ENST00000518444.1_Silent_p.A57A	NM_052879.4|NM_199188.2	NP_443111.4|NP_954658.2	Q71RC2	LARP4_HUMAN	La ribonucleoprotein domain family, member 4	58					cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(1)|skin(2)|urinary_tract(1)	23						CAGGTAATGCAGAGCTCTCAG	0.328																																					p.A58A		Atlas-SNP	.											.	LARP4	58	.	0			c.A174G						.						68	65	66					12																	50822725		1813	4064	5877	SO:0001819	synonymous_variant	113251	exon3			TAATGCAGAGCTC	AY004310	CCDS41782.1, CCDS44879.1, CCDS44880.1, CCDS44879.2, CCDS53789.1, CCDS53790.1	12q13.12	2005-08-09			ENSG00000161813	ENSG00000161813		"La ribonucleoprotein domain containing"	24320	protein-coding gene	gene with protein product						12477932	Standard	NM_052879		Approved	PP13296	uc001rwp.2	Q71RC2	OTTHUMG00000163724	ENST00000398473.2:c.174A>G	chr12.hg19:g.50822725A>G		85.0	0.0		86.0	4.0	NM_001170808	A8K6T1|E9PDG5|G3XAA8|G5E976|Q5CZ97|Q6ZV14|Q96NF9	Silent	SNP	ENST00000398473.2	hg19	CCDS41782.1																																																																																			.	.		0.328	LARP4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374981.1	NM_052879		G	50822725	A	G	50822725	2	3	254	1	0	0	0	0	0	0	0	1	8639	175	7	2		2	LARP4	12	50822725	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	967905	50822725	83029170	601	34893										
KRT75	9119	hgsc.bcm.edu	37	chr12	52826983	52826983	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtcctggagccctgctcctgCaggagggcccacttggtctc	13	15	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:52826983C>A	ENST00000252245.5	-	2	772	c.552G>T	c.(550-552)ctG>ctT	p.L184L		NM_004693.2	NP_004684.2	O95678	K2C75_HUMAN	keratin 75	184	Coil 1A.|Rod.				hematopoietic progenitor cell differentiation (GO:0002244)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(10)|prostate(1)|skin(1)	28				BRCA - Breast invasive adenocarcinoma(357;0.192)		CCTGCTCCTGCAGGAGGGCCC	0.562																																					p.L184L		Atlas-SNP	.											.	KRT75	75	.	0			c.G552T						.						77	79	79					12																	52826983		2203	4300	6503	SO:0001819	synonymous_variant	9119	exon2			CTCCTGCAGGAGG	Y19212	CCDS8827.1	12q13.13	2013-06-25			ENSG00000170454	ENSG00000170454		"-", "Intermediate filaments type II, keratins (basic)"	24431	protein-coding gene	gene with protein product		609025				9856802, 10692104, 16831889	Standard	NM_004693		Approved	K6HF	uc001saj.2	O95678	OTTHUMG00000169592	ENST00000252245.5:c.552G>T	chr12.hg19:g.52826983C>A		100.0	0.0		69.0	4.0	NM_004693	B4DQU4|Q9NSA9	Silent	SNP	ENST00000252245.5	hg19	CCDS8827.1																																																																																			.	.		0.562	KRT75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404968.1	NM_004693		A	52826983	C	A	52826983	2	1	254	1	0	0	0	0	0	0	0	1	8497	697	25	3		3	KRT75	12	52826983	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	2004258	52826983	81024912	602	34894										
KRT79	338785	hgsc.bcm.edu	37	chr12	53217754	53217754	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctcgttcttggtgtcccgcaGgttgtccccatgcttcccag	10	15	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:53217754G>T	ENST00000330553.5	-	6	1097	c.1063C>A	c.(1063-1065)Ctg>Atg	p.L355M		NM_175834.2	NP_787028.1	Q5XKE5	K2C79_HUMAN	keratin 79	355	Coil 2.|Rod.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	enzyme binding (GO:0019899)|structural molecule activity (GO:0005198)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GTGTCCCGCAGGTTGTCCCCA	0.602																																					p.L355M		Atlas-SNP	.											.	KRT79	78	.	0			c.C1063A						.						87	68	74					12																	53217754		2203	4300	6503	SO:0001583	missense	338785	exon6			CCCGCAGGTTGTC	AJ564105	CCDS8839.1	12q13.13	2014-02-12	2007-07-03		ENSG00000185640	ENSG00000185640		"-", "Intermediate filaments type II, keratins (basic)"	28930	protein-coding gene	gene with protein product	"keratin 6-like"	611160				11683385	Standard	NM_175834		Approved	K6L, KRT6L	uc001sbb.3	Q5XKE5	OTTHUMG00000169878	ENST00000330553.5:c.1063C>A	chr12.hg19:g.53217754G>T	ENSP00000328358:p.Leu355Met	140.0	0.0		87.0	4.0	NM_175834	Q6P465|Q7Z793	Missense_Mutation	SNP	ENST00000330553.5	hg19	CCDS8839.1	.	.	.	.	.	.	.	.	.	.	G	16.91	3.252877	0.59212	.	.	ENSG00000185640	ENST00000330553	D	0.81908	-1.55	3.9	2.07	0.26955	Filament (1);	0.000000	0.37530	N	0.002059	D	0.89715	0.6795	M	0.84219	2.685	0.37103	D	0.900001	D	0.89917	1.0	D	0.81914	0.995	D	0.90586	0.4533	10	0.87932	D	0	.	9.6816	0.40074	0.1773:0.0:0.8227:0.0	.	355	Q5XKE5	K2C79_HUMAN	M	355	ENSP00000328358:L355M	ENSP00000328358:L355M	L	-	1	2	KRT79	51504021	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.123000	0.77176	0.611000	0.30052	-0.350000	0.07774	CTG	.	.		0.602	KRT79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406376.1	NM_175834		T	53217754	G	T	53217754	3	4	254	1	0	0	0	0	1	0	0	0	8501	991	35	3	560	3	KRT79	12	53217754	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	390771	53217754	80634141	603	34895										
AAAS	8086	hgsc.bcm.edu	37	chr12	53701649	53701649	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cacactgagcagggccccttTgttgaaggaaggatggaaag	14	8	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:53701649T>C	ENST00000209873.4	-	15	1561	c.1396A>G	c.(1396-1398)Aaa>Gaa	p.K466E	AAAS_ENST00000549983.1_5'Flank|AAAS_ENST00000394384.3_Missense_Mutation_p.K433E|AAAS_ENST00000550286.1_Missense_Mutation_p.K342E	NM_015665.5	NP_056480.1	Q9NRG9	AAAS_HUMAN	achalasia, adrenocortical insufficiency, alacrimia	466					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|fertilization (GO:0009566)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|learning (GO:0007612)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nucleocytoplasmic transport (GO:0006913)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|regulation of nucleocytoplasmic transport (GO:0046822)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(2)	20						AGGGCCCCTTTGTTGAAGGAA	0.597																																					p.K466E		Atlas-SNP	.											.	AAAS	46	.	0			c.A1396G						.						72	73	73					12																	53701649		2203	4300	6503	SO:0001583	missense	8086	exon15			CCCCTTTGTTGAA	AJ289841	CCDS8856.1, CCDS53797.1	12q13	2013-06-27	2010-06-24		ENSG00000094914	ENSG00000094914		"WD repeat domain containing"	13666	protein-coding gene	gene with protein product	"aladin", "Allgrove, triple-A"	605378	"achalasia, adrenocortical insufficiency, alacrimia (Allgrove, triple-A)"			11062474	Standard	NM_015665		Approved		uc001scr.4	Q9NRG9	OTTHUMG00000169729	ENST00000209873.4:c.1396A>G	chr12.hg19:g.53701649T>C	ENSP00000209873:p.Lys466Glu	101.0	0.0		100.0	4.0	NM_015665	Q5JB47|Q9NWI6|Q9UG19	Missense_Mutation	SNP	ENST00000209873.4	hg19	CCDS8856.1	.	.	.	.	.	.	.	.	.	.	T	15.92	2.974536	0.53720	.	.	ENSG00000094914	ENST00000209873;ENST00000394384;ENST00000550286	D;D;D	0.95690	-3.78;-3.78;-3.78	4.54	4.54	0.55810	.	0.100290	0.64402	D	0.000002	D	0.88837	0.6545	N	0.14661	0.345	0.39203	D	0.963188	D;B	0.53151	0.958;0.231	B;B	0.44224	0.444;0.039	D	0.87097	0.2176	10	0.10902	T	0.67	-19.0471	10.4798	0.44687	0.0:0.0:0.0:1.0	.	433;466	Q5JB47;Q9NRG9	.;AAAS_HUMAN	E	466;433;342	ENSP00000209873:K466E;ENSP00000377908:K433E;ENSP00000446885:K342E	ENSP00000209873:K466E	K	-	1	0	AAAS	51987916	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.743000	0.55104	2.054000	0.61138	0.533000	0.62120	AAA	.	.		0.597	AAAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405632.1			C	53701649	T	C	53701649	3	2	254	1	0	0	0	0	1	0	0	0	8	1821	63	2	252	2	AAAS	12	53701649	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	483895	53701649	80150246	604	34896										
NFE2	4778	hgsc.bcm.edu	37	chr12	54686181	54686181	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtctgtggcctccatcttggTcccccggggcacaaggaaga	13	13	2	1	rs373651500		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:54686181T>C	ENST00000540264.2	-	2	1608	c.1099A>G	c.(1099-1101)Acc>Gcc	p.T367A	NFE2_ENST00000553070.1_Missense_Mutation_p.T367A|RP11-968A15.8_ENST00000553061.1_RNA|NFE2_ENST00000435572.2_Missense_Mutation_p.T367A|NFE2_ENST00000312156.4_Missense_Mutation_p.T367A			Q16621	NFE2_HUMAN	nuclear factor, erythroid 2	367					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|hemostasis (GO:0007599)|labyrinthine layer blood vessel development (GO:0060716)|multicellular organismal development (GO:0007275)|negative regulation of bone mineralization (GO:0030502)|negative regulation of syncytium formation by plasma membrane fusion (GO:0034242)|nucleosome disassembly (GO:0006337)|positive regulation of peptidyl-lysine acetylation (GO:2000758)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein N-terminus binding (GO:0047485)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|WW domain binding (GO:0050699)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(7)|upper_aerodigestive_tract(2)	16						TCCATCTTGGTCCCCCGGGGC	0.567																																					p.T367A		Atlas-SNP	.											.	NFE2	28	.	0			c.A1099G						.						55	52	53					12																	54686181		2203	4300	6503	SO:0001583	missense	4778	exon4			TCTTGGTCCCCCG	BC005044	CCDS8876.1	12q13	2013-08-23	2013-08-23			ENSG00000123405		"basic leucine zipper proteins"	7780	protein-coding gene	gene with protein product		601490	"nuclear factor (erythroid-derived 2), 45kD", "nuclear factor (erythroid-derived 2), 45kDa"			8355703	Standard	NM_001136023		Approved	NF-E2	uc001sfr.5	Q16621		ENST00000540264.2:c.1099A>G	chr12.hg19:g.54686181T>C	ENSP00000439120:p.Thr367Ala	130.0	0.0		121.0	5.0	NM_001261461	Q07720|Q6ICV9	Missense_Mutation	SNP	ENST00000540264.2	hg19	CCDS8876.1	.	.	.	.	.	.	.	.	.	.	t	12.20	1.866560	0.32977	.	.	ENSG00000123405	ENST00000312156;ENST00000435572;ENST00000540264;ENST00000553070	.	.	.	5.27	-6.02	0.02192	.	1.192680	0.06002	N	0.647924	T	0.21718	0.0523	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.17592	-1.0364	9	0.36615	T	0.2	-0.6578	2.1584	0.03819	0.105:0.2082:0.3223:0.3645	.	367	Q16621	NFE2_HUMAN	A	367	.	ENSP00000312436:T367A	T	-	1	0	NFE2	52972448	0.000000	0.05858	0.011000	0.14972	0.976000	0.68499	-0.150000	0.10189	-0.814000	0.04352	-1.060000	0.02296	ACC	.	.		0.567	NFE2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405747.1	NM_006163		C	54686181	T	C	54686181	3	2	254	1	0	0	0	0	1	0	0	0	10375	1667	58	2	26	2	NFE2	12	54686181	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	984532	54686181	79165714	605	34897										
GPR84	53831	hgsc.bcm.edu	37	chr12	54757304	54757304	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtcccagtgcgatgaggcagAgggtcaggatggagacagaa	17	7	1	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:54757304A>G	ENST00000551809.1	-	1	967	c.332T>C	c.(331-333)cTc>cCc	p.L111P	RP11-753H16.3_ENST00000550474.1_RNA|GPR84_ENST00000267015.3_Missense_Mutation_p.L111P|RP11-753H16.5_ENST00000552785.1_RNA			Q9NQS5	GPR84_HUMAN	G protein-coupled receptor 84	111						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(2)|kidney(2)|large_intestine(6)|lung(5)|skin(1)|urinary_tract(1)	18						GATGAGGCAGAGGGTCAGGAT	0.577																																					p.L111P		Atlas-SNP	.											.	GPR84	38	.	0			c.T332C						.						94	85	88					12																	54757304		2203	4300	6503	SO:0001583	missense	53831	exon2			AGGCAGAGGGTCA	AF237762	CCDS8878.1	12q13.13	2012-08-20						"GPCR / Class A : Fatty acid receptors"	4535	protein-coding gene	gene with protein product		606383				11273702	Standard	NM_020370		Approved	EX33	uc001sfu.3	Q9NQS5		ENST00000551809.1:c.332T>C	chr12.hg19:g.54757304A>G	ENSP00000450310:p.Leu111Pro	96.0	0.0		98.0	4.0	NM_020370	B6V9G7	Missense_Mutation	SNP	ENST00000551809.1	hg19	CCDS8878.1	.	.	.	.	.	.	.	.	.	.	A	19.99	3.928176	0.73327	.	.	ENSG00000139572	ENST00000267015;ENST00000551809	D;D	0.81659	-1.52;-1.52	5.21	5.21	0.72293	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000071	D	0.91226	0.7235	M	0.90977	3.165	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92965	0.6392	10	0.87932	D	0	-17.6368	13.3521	0.60607	1.0:0.0:0.0:0.0	.	111	Q9NQS5	GPR84_HUMAN	P	111	ENSP00000267015:L111P;ENSP00000450310:L111P	ENSP00000267015:L111P	L	-	2	0	GPR84	53043571	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	6.700000	0.74619	2.104000	0.64026	0.454000	0.30748	CTC	.	.		0.577	GPR84-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406156.1			G	54757304	A	G	54757304	3	3	254	1	0	0	0	0	1	0	0	0	6722	304	11	2	862	2	GPR84	12	54757304	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	71123	54757304	79094591	606	34898										
OR6C4	341418	hgsc.bcm.edu	37	chr12	55945361	55945361	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tacctcctggcctccatgtcTtatgatcgttatgtggccat	8	12	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:55945361T>C	ENST00000394256.2	+	1	379	c.351T>C	c.(349-351)tcT>tcC	p.S117S	RP11-110A12.2_ENST00000555138.1_RNA|RP11-110A12.2_ENST00000556750.1_RNA	NM_001005494.1	NP_001005494.1	Q8NGE1	OR6C4_HUMAN	olfactory receptor, family 6, subfamily C, member 4	117						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|skin(1)	11						CCTCCATGTCTTATGATCGTT	0.443																																					p.S117S		Atlas-SNP	.											.	OR6C4	34	.	0			c.T351C						.						99	102	101					12																	55945361		2203	4300	6503	SO:0001819	synonymous_variant	341418	exon1			CATGTCTTATGAT	BK004261	CCDS31827.1	12q14.2	2012-08-09				ENSG00000179626		"GPCR / Class A : Olfactory receptors"	19632	protein-coding gene	gene with protein product							Standard	NM_001005494		Approved		uc010spp.2	Q8NGE1	OTTHUMG00000169959	ENST00000394256.2:c.351T>C	chr12.hg19:g.55945361T>C		137.0	0.0		120.0	6.0	NM_001005494	A8MZG7|B2RNN2|Q6IFK1	Silent	SNP	ENST00000394256.2	hg19	CCDS31827.1																																																																																			.	.		0.443	OR6C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406678.1			C	55945361	T	C	55945361	2	2	254	1	0	0	0	0	0	0	0	1	11202	1596	56	2		2	OR6C4	12	55945361	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	1188057	55945361	77906534	607	34899										
DNAJC14	85406	hgsc.bcm.edu	37	chr12	56221087	56221087	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agttcaacatctgatgctgtGgcctcaacccccagtacatg	8	13	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:56221087G>T	ENST00000357606.3	-	3	1645	c.1356C>A	c.(1354-1356)gcC>gcA	p.A452A	DNAJC14_ENST00000317269.3_Silent_p.A452A|RP11-762I7.5_ENST00000546837.1_Missense_Mutation_p.H82N|DNAJC14_ENST00000317287.5_Silent_p.A452A|TMEM198B_ENST00000478241.1_RNA			Q6Y2X3	DJC14_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 14	452	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(2)|kidney(1)|large_intestine(8)|lung(7)|ovary(3)|prostate(1)|skin(1)	23						CTGATGCTGTGGCCTCAACCC	0.502																																					p.A452A		Atlas-SNP	.											.	DNAJC14	52	.	0			c.C1356A						.						193	174	181					12																	56221087		2203	4300	6503	SO:0001819	synonymous_variant	85406	exon2			TGCTGTGGCCTCA	AF141342	CCDS8894.1	12q12	2011-09-02				ENSG00000135392		"Heat shock proteins / DNAJ (HSP40)"	24581	protein-coding gene	gene with protein product		606092				11331877, 11984006	Standard	NM_032364		Approved	DNAJ, DRIP78, HDJ3, LIP6, FLJ32792	uc001shu.2	Q6Y2X3		ENST00000357606.3:c.1356C>A	chr12.hg19:g.56221087G>T		111.0	0.0		83.0	4.0	NM_032364	A5YM67|Q17RY2|Q66K17|Q96N59|Q96T63	Silent	SNP	ENST00000357606.3	hg19	CCDS8894.1	.	.	.	.	.	.	.	.	.	.	G	6.381	0.438489	0.12104	.	.	ENSG00000257390	ENST00000546837	.	.	.	4.7	2.73	0.32206	.	.	.	.	.	T	0.47173	0.1431	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.31971	-0.9924	4	.	.	.	-1.7081	4.1991	0.10457	0.2291:0.1879:0.5829:0.0	.	.	.	.	N	82	.	.	H	-	1	0	RP11-762I7.5	54507354	0.998000	0.40836	1.000000	0.80357	0.931000	0.56810	0.515000	0.22801	0.611000	0.30052	-0.367000	0.07326	CAC	.	.		0.502	DNAJC14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409095.1	NM_032364		T	56221087	G	T	56221087	2	4	254	1	0	0	0	0	0	0	0	1	4635	1335	47	3		3	DNAJC14	12	56221087	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	275726	56221087	77630808	608	34900										
MMP19	4327	hgsc.bcm.edu	37	chr12	56234506	56234506	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tggcggccatggaaggagagGcggatgtcagccgcaccagc	17	11	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:56234506G>T	ENST00000322569.4	-	4	556	c.465C>A	c.(463-465)cgC>cgA	p.R155R	MMP19_ENST00000394182.1_5'Flank|MMP19_ENST00000548629.1_Silent_p.R132R|MMP19_ENST00000547487.1_5'Flank|MMP19_ENST00000409200.3_Silent_p.R155R	NM_002429.4	NP_002420.1	Q99542	MMP19_HUMAN	matrix metallopeptidase 19	155					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|luteolysis (GO:0001554)|ovarian follicle development (GO:0001541)|ovulation from ovarian follicle (GO:0001542)|proteolysis (GO:0006508)|response to cAMP (GO:0051591)|response to hormone (GO:0009725)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(2)|skin(2)	26					Marimastat(DB00786)	GGAAGGAGAGGCGGATGTCAG	0.577																																					p.R155R		Atlas-SNP	.											.	MMP19	61	.	0			c.C465A						.						89	87	88					12																	56234506		2203	4300	6503	SO:0001819	synonymous_variant	4327	exon4			GGAGAGGCGGATG	X92521	CCDS8895.1, CCDS61146.1	12q14	2005-08-08	2005-08-08			ENSG00000123342			7165	protein-coding gene	gene with protein product		601807	"matrix metalloproteinase 19"	MMP18		9232430	Standard	NM_002429		Approved	RASI-1	uc001sib.4	Q99542	OTTHUMG00000170216	ENST00000322569.4:c.465C>A	chr12.hg19:g.56234506G>T		98.0	0.0		89.0	4.0	NM_001272101	B4E030|O15278|O95606|Q99580	Silent	SNP	ENST00000322569.4	hg19	CCDS8895.1																																																																																			.	.		0.577	MMP19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408023.1	NM_002429		T	56234506	G	T	56234506	2	4	254	1	0	0	0	0	0	0	0	1	9666	1190	42	3		3	MMP19	12	56234506	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	13419	56234506	77617389	609	34901										
ERBB3	2065	hgsc.bcm.edu	37	chr12	56487950	56487950	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cggaatgccaacccatggagGgcactgccacatgcaatggc	12	13	0	0	rs202048840		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:56487950G>T	ENST00000267101.3	+	14	2121	c.1681G>T	c.(1681-1683)Ggc>Tgc	p.G561C	ERBB3_ENST00000553131.1_5'Flank|ERBB3_ENST00000415288.2_Missense_Mutation_p.G502C|ERBB3_ENST00000450146.2_Intron	NM_001982.3	NP_001973.2	P21860	ERBB3_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3	561					cranial nerve development (GO:0021545)|endocardial cushion development (GO:0003197)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of cell adhesion (GO:0007162)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of secretion (GO:0051048)|negative regulation of signal transduction (GO:0009968)|neuron apoptotic process (GO:0051402)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell proliferation (GO:0042127)|Schwann cell differentiation (GO:0014037)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein tyrosine kinase activator activity (GO:0030296)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			ACCCATGGAGGGCACTGCCAC	0.562																																					p.G561C		Atlas-SNP	.											.	ERBB3	350	.	0			c.G1681T						.						65	63	63					12																	56487950		2203	4300	6503	SO:0001583	missense	2065	exon14			ATGGAGGGCACTG	M34309	CCDS31833.1, CCDS44918.1	12q13	2013-07-09	2013-07-09			ENSG00000065361			3431	protein-coding gene	gene with protein product		190151	"lethal congenital contracture syndrome 2"	LCCS2			Standard	NM_001982		Approved	HER3	uc001sjh.3	P21860	OTTHUMG00000170140	ENST00000267101.3:c.1681G>T	chr12.hg19:g.56487950G>T	ENSP00000267101:p.Gly561Cys	68.0	0.0		52.0	4.0	NM_001982	A8K6L6|B4DIK7|B4DV32|E9PDT8|Q9BUD7	Missense_Mutation	SNP	ENST00000267101.3	hg19	CCDS31833.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.586656	0.86851	.	.	ENSG00000065361	ENST00000267101;ENST00000415288	T;T	0.45276	0.9;0.9	5.48	5.48	0.80851	Growth factor, receptor (1);	0.000000	0.64402	D	0.000004	T	0.67970	0.2950	M	0.81942	2.565	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.968;0.995	T	0.72171	-0.4371	10	0.87932	D	0	.	18.1181	0.89563	0.0:0.0:1.0:0.0	.	502;561	P21860-4;P21860	.;ERBB3_HUMAN	C	561;502	ENSP00000267101:G561C;ENSP00000408340:G502C	ENSP00000267101:G561C	G	+	1	0	ERBB3	54774217	1.000000	0.71417	0.993000	0.49108	0.975000	0.68041	5.651000	0.67951	2.570000	0.86706	0.561000	0.74099	GGC	.	G|0.999;A|0.001		0.562	ERBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407619.3			T	56487950	G	T	56487950	3	4	254	1	0	0	0	0	1	0	0	0	5210	1232	43	3	1866	3	ERBB3	12	56487950	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	253444	56487950	77363945	610	34902										
LRP1	4035	hgsc.bcm.edu	37	chr12	57573622	57573622	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctcccgaaacctgttctggaCaagctatgacaccaataaga	7	12	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:57573622C>G	ENST00000243077.3	+	30	5490	c.5024C>G	c.(5023-5025)aCa>aGa	p.T1675R		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	1675					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	CTGTTCTGGACAAGCTATGAC	0.587																																					p.T1675R		Atlas-SNP	.											.	LRP1	428	.	0			c.C5024G						.						127	128	127					12																	57573622		2203	4300	6503	SO:0001583	missense	4035	exon30			TCTGGACAAGCTA	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"CD molecules", "Low density lipoprotein receptors"	6692	protein-coding gene	gene with protein product		107770	"alpha-2-macroglobulin receptor"	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.5024C>G	chr12.hg19:g.57573622C>G	ENSP00000243077:p.Thr1675Arg	89.0	0.0		72.0	16.0	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	hg19	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	C	16.08	3.020624	0.54576	.	.	ENSG00000123384	ENST00000243077	D	0.92446	-3.04	4.57	4.57	0.56435	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	D	0.000002	D	0.96867	0.8977	M	0.93106	3.38	0.80722	D	1	D	0.71674	0.998	D	0.78314	0.991	D	0.97868	1.0284	10	0.87932	D	0	.	16.2887	0.82737	0.0:1.0:0.0:0.0	.	1675	Q07954	LRP1_HUMAN	R	1675	ENSP00000243077:T1675R	ENSP00000243077:T1675R	T	+	2	0	LRP1	55859889	0.998000	0.40836	0.941000	0.38009	0.983000	0.72400	3.928000	0.56506	2.383000	0.81215	0.655000	0.94253	ACA	.	.		0.587	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		G	57573622	C	G	57573622	3	3	254	1	0	0	0	0	1	0	0	0	8960	478	17	4	5142	4	LRP1	12	57573622	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1085672	57573622	76278273	611	34903										
LRP1	4035	hgsc.bcm.edu	37	chr12	57592334	57592334	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccgcagcgtcatcgtggacaCcaagatcacatggcccaatg	10	14	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:57592334C>A	ENST00000243077.3	+	60	10023	c.9557C>A	c.(9556-9558)aCc>aAc	p.T3186N		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	3186					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	ATCGTGGACACCAAGATCACA	0.592																																					p.T3186N		Atlas-SNP	.											.	LRP1	428	.	0			c.C9557A						.						99	72	81					12																	57592334		2203	4300	6503	SO:0001583	missense	4035	exon60			TGGACACCAAGAT	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"CD molecules", "Low density lipoprotein receptors"	6692	protein-coding gene	gene with protein product		107770	"alpha-2-macroglobulin receptor"	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.9557C>A	chr12.hg19:g.57592334C>A	ENSP00000243077:p.Thr3186Asn	65.0	0.0		84.0	4.0	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	hg19	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	C	15.69	2.906710	0.52333	.	.	ENSG00000123384	ENST00000243077	D	0.95554	-3.74	4.39	4.39	0.52855	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.149041	0.44688	D	0.000432	D	0.91526	0.7324	L	0.28192	0.835	0.80722	D	1	B	0.27013	0.166	B	0.31946	0.138	D	0.88543	0.3111	10	0.20046	T	0.44	.	16.2482	0.82460	0.0:1.0:0.0:0.0	.	3186	Q07954	LRP1_HUMAN	N	3186	ENSP00000243077:T3186N	ENSP00000243077:T3186N	T	+	2	0	LRP1	55878601	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.782000	0.55401	2.434000	0.82447	0.561000	0.74099	ACC	.	.		0.592	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		A	57592334	C	A	57592334	3	1	254	1	0	0	0	0	1	0	0	0	8960	507	18	3	9795	3	LRP1	12	57592334	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	18712	57592334	76259561	612	34904										
SHMT2	6472	hgsc.bcm.edu	37	chr12	57627867	57627867	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tatagatgaaggggtcaacaTtggcttagaggtgaagagca	14	4	1	5			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:57627867T>C	ENST00000328923.3	+	11	1813	c.1361T>C	c.(1360-1362)aTt>aCt	p.I454T	SHMT2_ENST00000449049.3_Missense_Mutation_p.I433T|SHMT2_ENST00000553474.1_Missense_Mutation_p.I433T|SHMT2_ENST00000557487.1_Missense_Mutation_p.I444T|SHMT2_ENST00000414700.3_Missense_Mutation_p.I433T|SHMT2_ENST00000393827.4_Missense_Mutation_p.I358T	NM_001166356.1|NM_005412.5	NP_001159828.1|NP_005403.2	P34897	GLYM_HUMAN	serine hydroxymethyltransferase 2 (mitochondrial)	454					glycine biosynthetic process from serine (GO:0019264)|L-serine biosynthetic process (GO:0006564)|one-carbon metabolic process (GO:0006730)|positive regulation of cell proliferation (GO:0008284)|protein homotetramerization (GO:0051289)|tetrahydrofolate interconversion (GO:0035999)	extracellular vesicular exosome (GO:0070062)|microtubule cytoskeleton (GO:0015630)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|chromatin binding (GO:0003682)|glycine hydroxymethyltransferase activity (GO:0004372)|L-allo-threonine aldolase activity (GO:0008732)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(1)|large_intestine(4)|liver(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	15					Glycine(DB00145)|Tetrahydrofolic acid(DB00116)	GGGGTCAACATTGGCTTAGAG	0.567																																					p.I454T	Esophageal Squamous(150;1369 2416 49071 49364)	Atlas-SNP	.											.	SHMT2	40	.	0			c.T1361C						.						88	92	91					12																	57627867		2203	4300	6503	SO:0001583	missense	6472	exon11			TCAACATTGGCTT	AK223555	CCDS8934.1, CCDS53805.1, CCDS55837.1	12q12-q14	2006-03-27				ENSG00000182199	2.1.2.1		10852	protein-coding gene	gene with protein product		138450		SHMT		8999870	Standard	NM_005412		Approved		uc001snf.2	P34897		ENST00000328923.3:c.1361T>C	chr12.hg19:g.57627867T>C	ENSP00000333667:p.Ile454Thr	98.0	0.0		94.0	5.0	NM_005412	B7Z9F1|E7EQ19|E7EU43|O00740|Q8N1A5	Missense_Mutation	SNP	ENST00000328923.3	hg19	CCDS8934.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.287601	0.80803	.	.	ENSG00000182199	ENST00000328923;ENST00000557487;ENST00000414700;ENST00000553474;ENST00000449049;ENST00000393827	T;T;T;T;T;T	0.35421	1.52;1.38;1.52;1.52;1.52;1.31	4.98	4.98	0.66077	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	T	0.67832	0.2935	M	0.93150	3.385	0.80722	D	1	P;P;D;D;D	0.76494	0.944;0.895;0.999;0.972;0.996	P;P;D;P;P	0.73380	0.696;0.652;0.98;0.778;0.894	T	0.77035	-0.2737	10	0.87932	D	0	-12.3206	12.9362	0.58316	0.0:0.0:0.0:1.0	.	463;444;358;385;454	B4DWA7;Q8N1A5;B4DLV4;B4DP88;P34897	.;.;.;.;GLYM_HUMAN	T	454;444;433;433;433;358	ENSP00000333667:I454T;ENSP00000452315:I444T;ENSP00000406881:I433T;ENSP00000452419:I433T;ENSP00000413770:I433T;ENSP00000377413:I358T	ENSP00000333667:I454T	I	+	2	0	SHMT2	55914134	0.999000	0.42202	0.588000	0.28705	0.936000	0.57629	4.989000	0.63870	2.011000	0.59026	0.533000	0.62120	ATT	.	.		0.567	SHMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412525.2	NM_005412		C	57627867	T	C	57627867	3	2	254	1	0	0	0	0	1	0	0	0	14301	1493	52	2	1403	2	SHMT2	12	57627867	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	35533	57627867	76224028	613	34905										
HELB	92797	hgsc.bcm.edu	37	chr12	66698763	66698763	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgttaataaatttttaacatGggtaaaggaggtatcaaact	8	3	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:66698763G>T	ENST00000247815.4	+	2	499	c.440G>T	c.(439-441)tGg>tTg	p.W147L		NM_033647.3	NP_387467.2	Q8NG08	HELB_HUMAN	helicase (DNA) B	147					DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication, synthesis of RNA primer (GO:0006269)		ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|single-stranded DNA-dependent ATP-dependent DNA helicase activity (GO:0017116)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	40			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)		TTTTTAACATGGGTAAAGGAG	0.353																																					p.W147L		Atlas-SNP	.											.	HELB	90	.	0			c.G440T						.						75	74	74					12																	66698763		2203	4300	6503	SO:0001583	missense	92797	exon2			TAACATGGGTAAA	AF319995	CCDS8976.1	12q14.2	2009-01-15			ENSG00000127311	ENSG00000127311			17196	protein-coding gene	gene with protein product		614539				12181327	Standard	NM_033647		Approved		uc001sti.3	Q8NG08	OTTHUMG00000169006	ENST00000247815.4:c.440G>T	chr12.hg19:g.66698763G>T	ENSP00000247815:p.Trp147Leu	164.0	0.0		100.0	5.0	NM_033647	A8K4C9|Q4G0T2|Q9H7L5	Missense_Mutation	SNP	ENST00000247815.4	hg19	CCDS8976.1	.	.	.	.	.	.	.	.	.	.	G	19.98	3.926937	0.73327	.	.	ENSG00000127311	ENST00000247815	T	0.15372	2.43	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.40909	0.1136	M	0.68593	2.085	0.49687	D	0.999811	D	0.89917	1.0	D	0.66716	0.946	T	0.10941	-1.0608	9	.	.	.	-9.7652	18.835	0.92159	0.0:0.0:1.0:0.0	.	147	Q8NG08	HELB_HUMAN	L	147	ENSP00000247815:W147L	.	W	+	2	0	HELB	64985030	1.000000	0.71417	0.670000	0.29842	0.015000	0.08874	5.458000	0.66679	2.438000	0.82558	0.455000	0.32223	TGG	.	.		0.353	HELB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401919.1			T	66698763	G	T	66698763	3	4	254	1	0	0	0	0	1	0	0	0	7054	1357	47	3	446	3	HELB	12	66698763	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	9070896	66698763	67153132	614	34906										
HELB	92797	hgsc.bcm.edu	37	chr12	66725244	66725244	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgtagtcacagaccacgccaTgacaaatgatgtcacctgga	9	11	2	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:66725244T>C	ENST00000247815.4	+	12	3040	c.2981T>C	c.(2980-2982)aTg>aCg	p.M994T		NM_033647.3	NP_387467.2	Q8NG08	HELB_HUMAN	helicase (DNA) B	994					DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication, synthesis of RNA primer (GO:0006269)		ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|single-stranded DNA-dependent ATP-dependent DNA helicase activity (GO:0017116)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	40			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)		GACCACGCCATGACAAATGAT	0.537																																					p.M994T		Atlas-SNP	.											.	HELB	90	.	0			c.T2981C						.						88	66	73					12																	66725244		2203	4300	6503	SO:0001583	missense	92797	exon12			ACGCCATGACAAA	AF319995	CCDS8976.1	12q14.2	2009-01-15			ENSG00000127311	ENSG00000127311			17196	protein-coding gene	gene with protein product		614539				12181327	Standard	NM_033647		Approved		uc001sti.3	Q8NG08	OTTHUMG00000169006	ENST00000247815.4:c.2981T>C	chr12.hg19:g.66725244T>C	ENSP00000247815:p.Met994Thr	81.0	0.0		85.0	4.0	NM_033647	A8K4C9|Q4G0T2|Q9H7L5	Missense_Mutation	SNP	ENST00000247815.4	hg19	CCDS8976.1	.	.	.	.	.	.	.	.	.	.	T	5.190	0.220595	0.09863	.	.	ENSG00000127311	ENST00000247815	T	0.10763	2.84	4.6	-9.2	0.00682	.	2.051000	0.02191	N	0.061329	T	0.03871	0.0109	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.32534	-0.9903	9	.	.	.	1.0983	2.6293	0.04939	0.1254:0.3382:0.3622:0.1741	.	994	Q8NG08	HELB_HUMAN	T	994	ENSP00000247815:M994T	.	M	+	2	0	HELB	65011511	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.082000	0.03400	-2.008000	0.00955	-0.366000	0.07423	ATG	.	.		0.537	HELB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401919.1			C	66725244	T	C	66725244	3	2	254	1	0	0	0	0	1	0	0	0	7054	1464	51	2	3027	2	HELB	12	66725244	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	26481	66725244	67126651	615	34907										
HELB	92797	hgsc.bcm.edu	37	chr12	66731843	66731843	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agactgaataatttaattccCaggcaacttttcaagcccac	5	11	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:66731843C>A	ENST00000247815.4	+	13	3284	c.3225C>A	c.(3223-3225)ccC>ccA	p.P1075P		NM_033647.3	NP_387467.2	Q8NG08	HELB_HUMAN	helicase (DNA) B	1075					DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication, synthesis of RNA primer (GO:0006269)		ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|single-stranded DNA-dependent ATP-dependent DNA helicase activity (GO:0017116)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	40			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)		ATTTAATTCCCAGGCAACTTT	0.323																																					p.P1075P		Atlas-SNP	.											.	HELB	90	.	0			c.C3225A						.						68	72	70					12																	66731843		2203	4299	6502	SO:0001819	synonymous_variant	92797	exon13			AATTCCCAGGCAA	AF319995	CCDS8976.1	12q14.2	2009-01-15			ENSG00000127311	ENSG00000127311			17196	protein-coding gene	gene with protein product		614539				12181327	Standard	NM_033647		Approved		uc001sti.3	Q8NG08	OTTHUMG00000169006	ENST00000247815.4:c.3225C>A	chr12.hg19:g.66731843C>A		140.0	0.0		98.0	4.0	NM_033647	A8K4C9|Q4G0T2|Q9H7L5	Silent	SNP	ENST00000247815.4	hg19	CCDS8976.1																																																																																			.	.		0.323	HELB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401919.1			A	66731843	C	A	66731843	2	1	254	1	0	0	0	0	0	0	0	1	7054	581	21	3		3	HELB	12	66731843	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	6599	66731843	67120052	616	34908										
LGR5	8549	hgsc.bcm.edu	37	chr12	71976289	71976289	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttgaggaagacctgaaagccCttcattcagtgcagtgttca	10	9	3	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:71976289C>A	ENST00000266674.5	+	17	1917	c.1606C>A	c.(1606-1608)Ctt>Att	p.L536I	LGR5_ENST00000540815.2_Missense_Mutation_p.L512I|LGR5_ENST00000536515.1_Missense_Mutation_p.L464I|RP11-186F10.2_ENST00000546601.1_RNA			O75473	LGR5_HUMAN	leucine-rich repeat containing G protein-coupled receptor 5	536					G-protein coupled receptor signaling pathway (GO:0007186)|inner ear development (GO:0048839)|positive regulation of canonical Wnt signaling pathway (GO:0090263)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)		NUP107/LGR5(2)	endometrium(2)|kidney(3)|large_intestine(2)|lung(24)|ovary(1)|pancreas(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(3)	48						CCTGAAAGCCCTTCATTCAGT	0.443																																					p.L536I		Atlas-SNP	.											.	LGR5	103	.	0			c.C1606A						.						149	123	132					12																	71976289		2203	4300	6503	SO:0001583	missense	8549	exon17			AAAGCCCTTCATT	AF062006	CCDS9000.1, CCDS61194.1, CCDS61195.1	12q22-q23	2012-08-21	2011-01-25	2004-11-12				"GPCR / Class A : Orphans"	4504	protein-coding gene	gene with protein product		606667	"G protein-coupled receptor 49", "leucine-rich repeat-containing G protein-coupled receptor 5"	GPR67, GPR49		9642114	Standard	NM_003667		Approved	HG38, FEX	uc001swl.4	O75473	OTTHUMG00000169543	ENST00000266674.5:c.1606C>A	chr12.hg19:g.71976289C>A	ENSP00000266674:p.Leu536Ile	161.0	0.0		114.0	5.0	NM_003667	D8MCT0|Q4VAM0|Q4VAM2|Q9UP75	Missense_Mutation	SNP	ENST00000266674.5	hg19	CCDS9000.1	.	.	.	.	.	.	.	.	.	.	C	15.50	2.851439	0.51270	.	.	ENSG00000139292	ENST00000266674;ENST00000451585;ENST00000536515;ENST00000540815	T;T;T	0.22134	1.97;1.97;1.97	5.36	4.41	0.53225	.	0.209998	0.33057	N	0.005322	T	0.20820	0.0501	L	0.47716	1.5	0.28130	N	0.93022	P;P	0.40875	0.731;0.592	B;B	0.39660	0.306;0.162	T	0.09079	-1.0691	10	0.22109	T	0.4	.	15.8484	0.78907	0.0:0.8643:0.1357:0.0	.	512;536	O75473-2;O75473	.;LGR5_HUMAN	I	536;536;464;512	ENSP00000266674:L536I;ENSP00000443033:L464I;ENSP00000441035:L512I	ENSP00000266674:L536I	L	+	1	0	LGR5	70262556	1.000000	0.71417	0.999000	0.59377	0.963000	0.63663	3.410000	0.52664	2.668000	0.90789	0.650000	0.86243	CTT	.	.		0.443	LGR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404744.1	NM_003667		A	71976289	C	A	71976289	3	1	254	1	0	0	0	0	1	0	0	0	8766	681	24	3	1672	3	LGR5	12	71976289	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	5244446	71976289	61875606	617	34909										
ZFC3H1	196441	hgsc.bcm.edu	37	chr12	72057219	72057219	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	accgccccgggccgagtgagGaggccttcgccgcggatagg	17	14	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:72057219G>T	ENST00000378743.3	-	1	530	c.172C>A	c.(172-174)Cct>Act	p.P58T	ZFC3H1_ENST00000552037.1_Missense_Mutation_p.P58T|THAP2_ENST00000547843.1_5'Flank|THAP2_ENST00000308086.2_5'UTR|ZFC3H1_ENST00000549407.1_5'Flank|ZFC3H1_ENST00000548100.1_Missense_Mutation_p.P58T	NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	58	Ser-rich.				RNA processing (GO:0006396)	extracellular space (GO:0005615)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.P58S(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						GCCGAGTGAGGAGGCCTTCGC	0.632											OREG0021993	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P58T		Atlas-SNP	.											ZFC3H1,NS,carcinoma,0,1	ZFC3H1	172	.	1	Substitution - Missense(1)	lung(1)	c.C172A						.						41	51	48					12																	72057219		2042	4188	6230	SO:0001583	missense	196441	exon1			AGTGAGGAGGCCT	AB011118	CCDS41813.1	12q21.1	2013-01-25	2008-10-01	2008-10-01		ENSG00000133858		"Zinc finger, C3H1-type containing"	28328	protein-coding gene	gene with protein product			"proline/serine-rich coiled-coil 2", "coiled-coil domain containing 131"	PSRC2, CCDC131		9628581	Standard	NM_144982		Approved	MGC23401, KIAA0546	uc001swo.2	O60293	OTTHUMG00000169545	ENST00000378743.3:c.172C>A	chr12.hg19:g.72057219G>T	ENSP00000368017:p.Pro58Thr	70.0	0.0	1134	43.0	2.0	NM_144982	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Missense_Mutation	SNP	ENST00000378743.3	hg19	CCDS41813.1	.	.	.	.	.	.	.	.	.	.	G	17.69	3.452917	0.63290	.	.	ENSG00000133858	ENST00000378743;ENST00000548100;ENST00000552037	T	0.33654	1.4	4.66	4.66	0.58398	.	0.310293	0.23694	N	0.045485	T	0.27241	0.0668	N	0.14661	0.345	0.80722	D	1	P;P;P	0.44946	0.846;0.603;0.535	B;B;B	0.42738	0.396;0.396;0.151	T	0.12116	-1.0560	10	0.52906	T	0.07	.	15.8933	0.79318	0.0:0.0:1.0:0.0	.	58;58;58	G3V1X1;O60293-4;O60293	.;.;ZC3H1_HUMAN	T	58	ENSP00000368017:P58T	ENSP00000368017:P58T	P	-	1	0	ZFC3H1	70343486	0.999000	0.42202	0.995000	0.50966	0.977000	0.68977	2.343000	0.44001	2.427000	0.82271	0.455000	0.32223	CCT	.	.		0.632	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982		T	72057219	G	T	72057219	3	4	254	1	0	0	0	0	1	0	0	0	17648	1174	41	3	5937	3	ZFC3H1	12	72057219	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	80930	72057219	61794676	618	34910										
TPH2	121278	hgsc.bcm.edu	37	chr12	72416258	72416258	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tggagcaggactcctttcctCcattggagaattaaaggtat	10	8	0	1	rs371065822		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:72416258C>A	ENST00000333850.3	+	9	1289	c.1148C>A	c.(1147-1149)tCc>tAc	p.S383Y		NM_173353.3	NP_775489.2	Q8IWU9	TPH2_HUMAN	tryptophan hydroxylase 2	383					aromatic amino acid family metabolic process (GO:0009072)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to lithium ion (GO:0071285)|circadian rhythm (GO:0007623)|indolalkylamine biosynthetic process (GO:0046219)|response to activity (GO:0014823)|response to calcium ion (GO:0051592)|response to estrogen (GO:0043627)|response to glucocorticoid (GO:0051384)|response to nutrient levels (GO:0031667)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|neuron projection (GO:0043005)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|tryptophan 5-monooxygenase activity (GO:0004510)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	41					L-Tryptophan(DB00150)	CTCCTTTCCTCCATTGGAGAA	0.418																																					p.S383Y		Atlas-SNP	.											.	TPH2	81	.	0			c.C1148A						.						101	95	97					12																	72416258		2203	4300	6503	SO:0001583	missense	121278	exon9			TTTCCTCCATTGG	AY098914	CCDS31859.1	12q15	2008-02-07				ENSG00000139287	1.14.16.4		20692	protein-coding gene	gene with protein product		607478				12511643	Standard	NM_173353		Approved	NTPH, FLJ37295	uc009zrw.1	Q8IWU9		ENST00000333850.3:c.1148C>A	chr12.hg19:g.72416258C>A	ENSP00000329093:p.Ser383Tyr	111.0	0.0		74.0	4.0	NM_173353	A6NGA4|Q14CB0	Missense_Mutation	SNP	ENST00000333850.3	hg19	CCDS31859.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.690515	0.88735	.	.	ENSG00000139287	ENST00000333850	D	0.99801	-6.81	5.98	5.98	0.97165	Aromatic amino acid hydroxylase, C-terminal (4);	0.000000	0.85682	D	0.000000	D	0.99891	0.9948	H	0.98218	4.175	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	D	0.96636	0.9470	10	0.87932	D	0	-25.8637	20.452	0.99131	0.0:1.0:0.0:0.0	.	383	Q8IWU9	TPH2_HUMAN	Y	383	ENSP00000329093:S383Y	ENSP00000329093:S383Y	S	+	2	0	TPH2	70702525	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.818000	0.86416	2.838000	0.97847	0.591000	0.81541	TCC	.	.		0.418	TPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405234.1	NM_173353		A	72416258	C	A	72416258	3	1	254	1	0	0	0	0	1	0	0	0	16417	855	30	3	1182	3	TPH2	12	72416258	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	359039	72416258	61435637	619	34911										
CAPS2	84698	hgsc.bcm.edu	37	chr12	75683540	75683540	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gaacacctcttttatgtagtTtttcttttagcacatctgtt	5	8	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:75683540T>C	ENST00000409445.3	-	15	1509	c.1313A>G	c.(1312-1314)aAa>aGa	p.K438R	CAPS2_ENST00000393284.3_Missense_Mutation_p.K206R|CAPS2_ENST00000409004.1_5'UTR|CAPS2_ENST00000409799.1_Missense_Mutation_p.K356R|CAPS2_ENST00000442339.2_Missense_Mutation_p.K28R|RP11-560G2.1_ENST00000549953.1_RNA	NM_032606.3	NP_115995.2	Q9BXY5	CAYP2_HUMAN	calcyphosine 2	438							calcium ion binding (GO:0005509)			endometrium(2)|large_intestine(1)|lung(4)|ovary(2)|skin(1)	10						TTTATGTAGTTTTTCTTTTAG	0.313																																					p.K438R		Atlas-SNP	.											.	CAPS2	96	.	0			c.A1313G						.						98	99	99					12																	75683540		2201	4299	6500	SO:0001583	missense	84698	exon15			TGTAGTTTTTCTT	AF251056	CCDS9008.2, CCDS66424.1, CCDS73497.1	12q14.1	2013-01-10	2005-05-09		ENSG00000180881	ENSG00000180881		"EF-hand domain containing"	16471	protein-coding gene	gene with protein product		607724	"calcyphosphine 2"			11846421	Standard	NM_032606		Approved		uc001sxk.4	Q9BXY5	OTTHUMG00000152787	ENST00000409445.3:c.1313A>G	chr12.hg19:g.75683540T>C	ENSP00000386959:p.Lys438Arg	107.0	0.0		98.0	4.0	NM_032606	Q6PH84|Q8N242|Q8NAY5	Missense_Mutation	SNP	ENST00000409445.3	hg19	CCDS9008.2	.	.	.	.	.	.	.	.	.	.	T	12.25	1.880475	0.33255	.	.	ENSG00000180881	ENST00000409799;ENST00000409445;ENST00000378703;ENST00000393284;ENST00000442339	T;T;T;T	0.24908	1.91;1.88;1.88;1.83	5.58	5.58	0.84498	.	0.373187	0.26995	N	0.021444	T	0.16811	0.0404	N	0.15975	0.35	0.24863	N	0.992339	B;B;B;B;B	0.17852	0.002;0.004;0.016;0.008;0.024	B;B;B;B;B	0.29077	0.021;0.025;0.02;0.046;0.098	T	0.24512	-1.0158	10	0.16420	T	0.52	-1.8459	12.507	0.55987	0.0:0.0:0.1486:0.8513	.	28;206;174;438;356	A2RRN2;Q9BXY5-2;Q9BXY5-3;Q9BXY5;B9A061	.;.;.;CAYP2_HUMAN;.	R	356;438;174;206;28	ENSP00000386977:K356R;ENSP00000386959:K438R;ENSP00000376963:K206R;ENSP00000389633:K28R	ENSP00000367975:K174R	K	-	2	0	CAPS2	73969807	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	2.585000	0.46111	2.120000	0.65058	0.533000	0.62120	AAA	.	.		0.313	CAPS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000327880.2			C	75683540	T	C	75683540	3	2	254	1	0	0	0	0	1	0	0	0	2640	1841	64	2	376	2	CAPS2	12	75683540	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	3267282	75683540	58168355	620	34912										
NAV3	89795	hgsc.bcm.edu	37	chr12	78513068	78513068	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aggaaaagctcccctaaaagGatcatctctacaaagatctc	6	11	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:78513068G>T	ENST00000397909.2	+	15	3265	c.3092G>T	c.(3091-3093)gGa>gTa	p.G1031V	NAV3_ENST00000228327.6_Missense_Mutation_p.G1031V|NAV3_ENST00000536525.2_Missense_Mutation_p.G1031V|NAV3_ENST00000266692.7_Missense_Mutation_p.G1031V			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1031						membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						CCCCTAAAAGGATCATCTCTA	0.443										HNSCC(70;0.22)																											p.G1031V		Atlas-SNP	.											.	NAV3	506	.	0			c.G3092T						.						120	115	116					12																	78513068		1859	4096	5955	SO:0001583	missense	89795	exon15			TAAAAGGATCATC	AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.3092G>T	chr12.hg19:g.78513068G>T	ENSP00000381007:p.Gly1031Val	98.0	0.0		83.0	4.0	NM_014903	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.63|19.63	3.864159|3.864159	0.71949|0.71949	.|.	.|.	ENSG00000067798|ENSG00000067798	ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692|ENST00000552895	T;T;T;T|.	0.29142|.	1.58;1.58;1.58;1.58|.	6.0|6.0	5.09|5.09	0.68999|0.68999	.|.	0.000000|.	0.39341|.	U|.	0.001388|.	T|T	0.59404|0.59404	0.2191|0.2191	L|L	0.36672|0.36672	1.1|1.1	0.80722|0.80722	D|D	1|1	P;D;D;B|.	0.89917|.	0.895;1.0;0.998;0.328|.	B;D;P;B|.	0.74348|.	0.392;0.983;0.859;0.155|.	T|T	0.55742|0.55742	-0.8093|-0.8093	10|5	0.52906|.	T|.	0.07|.	-10.147|-10.147	17.1406|17.1406	0.86752|0.86752	0.0:0.1265:0.8735:0.0|0.0:0.1265:0.8735:0.0	.|.	1031;1031;1031;1031|.	E7EUC6;Q8IVL0-3;Q8IVL0;Q8IVL0-2|.	.;.;NAV3_HUMAN;.|.	V|S	1031|102	ENSP00000446132:G1031V;ENSP00000381007:G1031V;ENSP00000228327:G1031V;ENSP00000266692:G1031V|.	ENSP00000228327:G1031V|.	G|R	+|+	2|3	0|2	NAV3|NAV3	77037199|77037199	1.000000|1.000000	0.71417|0.71417	0.915000|0.915000	0.36163|0.36163	0.982000|0.982000	0.71751|0.71751	7.597000|7.597000	0.82733|0.82733	1.496000|1.496000	0.48567|0.48567	0.655000|0.655000	0.94253|0.94253	GGA|AGG	.	.		0.443	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		T	78513068	G	T	78513068	3	4	254	1	0	0	0	0	1	0	0	0	10194	1174	41	3	3150	3	NAV3	12	78513068	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	2829528	78513068	55338827	621	34913										
PAWR	5074	hgsc.bcm.edu	37	chr12	80007382	80007382	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	atctgcctgaaactgttctaGgtggctcctgcaaagtaaaa	9	9	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:80007382G>T	ENST00000328827.4	-	4	1028	c.656C>A	c.(655-657)cCt>cAt	p.P219H		NM_002583.2	NP_002574.2	Q96IZ0	PAWR_HUMAN	PRKC, apoptosis, WT1, regulator	219					actin filament bundle assembly (GO:0051017)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|interleukin-2 biosynthetic process (GO:0042094)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of amyloid precursor protein biosynthetic process (GO:0042986)|positive regulation of apoptotic process (GO:0043065)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|enzyme binding (GO:0019899)|leucine zipper domain binding (GO:0043522)|transcription corepressor activity (GO:0003714)			NS(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	8						AACTGTTCTAGGTGGCTCCTG	0.289																																					p.P219H		Atlas-SNP	.											.	PAWR	14	.	0			c.C656A						.						113	116	115					12																	80007382		2203	4299	6502	SO:0001583	missense	5074	exon4			GTTCTAGGTGGCT	U63809	CCDS31863.1	12q21.2	2013-03-07			ENSG00000177425	ENSG00000177425			8614	protein-coding gene	gene with protein product	"prostate apoptosis response-4"	601936				8943350, 9790775	Standard	NM_002583		Approved	par-4, PAR4	uc001syx.3	Q96IZ0	OTTHUMG00000170080	ENST00000328827.4:c.656C>A	chr12.hg19:g.80007382G>T	ENSP00000328088:p.Pro219His	137.0	0.0		98.0	6.0	NM_002583	O75796|Q6FHY9|Q8N700	Missense_Mutation	SNP	ENST00000328827.4	hg19	CCDS31863.1	.	.	.	.	.	.	.	.	.	.	G	9.493	1.101312	0.20632	.	.	ENSG00000177425	ENST00000328827	T	0.18016	2.24	4.68	4.68	0.58851	.	1.160130	0.06516	N	0.738775	T	0.15565	0.0375	N	0.14661	0.345	0.25000	N	0.991474	P	0.36249	0.545	B	0.41236	0.351	T	0.23261	-1.0193	9	.	.	.	0.4321	13.2844	0.60235	0.0:0.0:1.0:0.0	.	219	Q96IZ0	PAWR_HUMAN	H	219	ENSP00000328088:P219H	.	P	-	2	0	PAWR	78531513	1.000000	0.71417	1.000000	0.80357	0.336000	0.28762	4.020000	0.57189	2.587000	0.87381	0.655000	0.94253	CCT	.	.		0.289	PAWR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407175.1	NM_002583		T	80007382	G	T	80007382	3	4	254	1	0	0	0	0	1	0	0	0	11486	1000	35	3	382	3	PAWR	12	80007382	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1494314	80007382	53844513	622	34914										
TMTC2	160335	hgsc.bcm.edu	37	chr12	83526015	83526015	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gctgctttgatgaacctgggAgccattctgcacctcaatgg	11	11	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:83526015A>G	ENST00000321196.3	+	12	3065	c.2358A>G	c.(2356-2358)ggA>ggG	p.G786G	TMTC2_ENST00000549919.1_Silent_p.G780G	NM_152588.1	NP_689801.1	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat containing 2	786					calcium ion homeostasis (GO:0055074)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|urinary_tract(1)	39						TGAACCTGGGAGCCATTCTGC	0.498																																					p.G786G		Atlas-SNP	.											.	TMTC2	100	.	0			c.A2358G						.						97	87	91					12																	83526015		2203	4300	6503	SO:0001819	synonymous_variant	160335	exon12			CCTGGGAGCCATT	AK074634	CCDS9025.1	12q21.31	2014-06-09			ENSG00000179104	ENSG00000179104		"Tetratricopeptide (TTC) repeat domain containing"	25440	protein-coding gene	gene with protein product		615856				24764305	Standard	NM_152588		Approved	DKFZp762A217	uc001szt.3	Q8N394	OTTHUMG00000169736	ENST00000321196.3:c.2358A>G	chr12.hg19:g.83526015A>G		139.0	0.0		124.0	5.0	NM_152588	B2RCU7|Q8N2K8	Silent	SNP	ENST00000321196.3	hg19	CCDS9025.1																																																																																			.	.		0.498	TMTC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405663.1	NM_152588		G	83526015	A	G	83526015	2	3	254	1	0	0	0	0	0	0	0	1	16276	291	11	2		2	TMTC2	12	83526015	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	3518633	83526015	50325880	623	34915										
ATP2B1	490	hgsc.bcm.edu	37	chr12	90015326	90015326	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aattatttcaaaaaccttacCaatatttttgatgtataagc	3	6	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:90015326C>A	ENST00000428670.3	-	10	2043	c.1587G>T	c.(1585-1587)ttG>ttT	p.L529F	ATP2B1_ENST00000261173.2_Splice_Site_p.L529F|ATP2B1_ENST00000359142.3_Splice_Site_p.L529F|ATP2B1_ENST00000348959.3_Splice_Site_p.L529F|ATP2B1_ENST00000393164.2_Splice_Site_p.L272F			P20020	AT2B1_HUMAN	ATPase, Ca++ transporting, plasma membrane 1	529					blood coagulation (GO:0007596)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	45						AAAACCTTACCAATATTTTTG	0.279																																					p.L529F		Atlas-SNP	.											.	ATP2B1	191	.	0			c.G1587T						.						33	33	33					12																	90015326		2181	4276	6457	SO:0001630	splice_region_variant	490	exon9			CCTTACCAATATT	J04027	CCDS9035.1, CCDS41817.1	12q21.33	2010-04-20			ENSG00000070961	ENSG00000070961	3.6.3.8	"ATPases / P-type"	814	protein-coding gene	gene with protein product	"plasma membrane calcium-transporting ATPase 1"	108731				1674727	Standard	NM_001682		Approved	PMCA1	uc001tbh.3	P20020		ENST00000428670.3:c.1587+1G>T	chr12.hg19:g.90015326C>A		115.0	0.0		81.0	4.0	NM_001001323	Q12992|Q12993|Q13819|Q13820|Q13821|Q16504|Q93082	Missense_Mutation	SNP	ENST00000428670.3	hg19	CCDS9035.1	.	.	.	.	.	.	.	.	.	.	C	18.41	3.618329	0.66787	.	.	ENSG00000070961	ENST00000261173;ENST00000348959;ENST00000359142;ENST00000428670;ENST00000393164	T;T;T;T;T	0.70516	-0.49;-0.49;-0.49;-0.49;-0.49	5.85	4.96	0.65561	.	0.054532	0.64402	D	0.000001	T	0.69387	0.3105	L	0.28054	0.825	0.80722	D	1	P;P;P	0.46512	0.879;0.855;0.486	B;P;B	0.53809	0.408;0.735;0.347	T	0.67715	-0.5599	9	.	.	.	-13.6016	15.0228	0.71643	0.0:0.9319:0.0:0.0681	.	529;529;529	P20020-3;P20020-2;P20020-6	.;.;.	F	529;529;529;529;272	ENSP00000261173:L529F;ENSP00000343599:L529F;ENSP00000352054:L529F;ENSP00000392043:L529F;ENSP00000376869:L272F	.	L	-	3	2	ATP2B1	88539457	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.487000	0.81328	1.487000	0.48415	0.563000	0.77884	TTG	.	.		0.279	ATP2B1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406653.1	NM_001682	Missense_Mutation	A	90015326	C	A	90015326	5	1	254	1	0	0	0	0	0	0	1	0	1139	608	21	3	2281	3	ATP2B1	12	90015326	Splice_Site	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	6489311	90015326	43836569	624	34916										
APAF1	317	hgsc.bcm.edu	37	chr12	99056270	99056270	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gatgatgtttgggactcttgGgtgttgaaagcttttgacag	14	4	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:99056270G>T	ENST00000551964.1	+	6	1483	c.747G>T	c.(745-747)tgG>tgT	p.W249C	APAF1_ENST00000357310.1_Missense_Mutation_p.W249C|APAF1_ENST00000333991.1_Missense_Mutation_p.W249C|APAF1_ENST00000552268.1_Missense_Mutation_p.W249C|APAF1_ENST00000339433.3_Missense_Mutation_p.W249C|APAF1_ENST00000550527.1_Missense_Mutation_p.W238C|APAF1_ENST00000549007.1_Missense_Mutation_p.W249C|APAF1_ENST00000547045.1_Missense_Mutation_p.W249C|APAF1_ENST00000359972.2_Missense_Mutation_p.W238C	NM_181861.1	NP_863651.1	O14727	APAF_HUMAN	apoptotic peptidase activating factor 1	249	NB-ARC.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|forebrain development (GO:0030900)|intrinsic apoptotic signaling pathway (GO:0097193)|nervous system development (GO:0007399)|neural tube closure (GO:0001843)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|regulation of apoptotic DNA fragmentation (GO:1902510)|regulation of apoptotic process (GO:0042981)|response to G1 DNA damage checkpoint signaling (GO:0072432)	apoptosome (GO:0043293)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(1)	42					Adenosine triphosphate(DB00171)	GGGACTCTTGGGTGTTGAAAG	0.323																																					p.W249C		Atlas-SNP	.											.	APAF1	111	.	0			c.G747T						.						118	114	115					12																	99056270		2203	4299	6502	SO:0001583	missense	317	exon6			CTCTTGGGTGTTG	AF013263	CCDS9069.1, CCDS9070.1, CCDS9071.1, CCDS55862.1, CCDS55863.1	12q23	2013-01-10	2006-10-23			ENSG00000120868		"WD repeat domain containing"	576	protein-coding gene	gene with protein product		602233	"apoptotic protease activating factor", "apoptotic peptidase activating factor"			9267021, 10702682	Standard	NM_181861		Approved	CED4, APAF-1	uc001tfz.3	O14727	OTTHUMG00000170214	ENST00000551964.1:c.747G>T	chr12.hg19:g.99056270G>T	ENSP00000448165:p.Trp249Cys	173.0	0.0		122.0	5.0	NM_181868	B2RMX8|O43297|Q7Z438|Q9BXZ6|Q9UBZ5|Q9UGN8|Q9UGN9|Q9UGP0|Q9UJ58|Q9UJ59|Q9UJ60|Q9UJ61|Q9UJ62|Q9UJ63|Q9UJ64|Q9UJ65|Q9UJ66|Q9UJ67|Q9UNC9	Missense_Mutation	SNP	ENST00000551964.1	hg19	CCDS9069.1	.	.	.	.	.	.	.	.	.	.	G	15.60	2.881118	0.51801	.	.	ENSG00000120868	ENST00000551964;ENST00000359972;ENST00000357310;ENST00000339433;ENST00000333991;ENST00000552268;ENST00000550527;ENST00000547045;ENST00000549007	T;T;T;T;T;T;T;T;T	0.81078	-1.45;-1.45;-1.45;-1.45;-1.45;-1.45;-1.45;-1.45;-1.45	5.77	5.77	0.91146	NB-ARC (1);	0.159535	0.64402	D	0.000019	D	0.87912	0.6297	L	0.52573	1.65	0.80722	D	1	D;D;D;D;D	0.89917	0.999;1.0;0.999;1.0;0.999	D;D;D;D;P	0.78314	0.945;0.977;0.945;0.991;0.871	D	0.87585	0.2487	10	0.59425	D	0.04	-15.6004	19.9859	0.97351	0.0:0.0:1.0:0.0	.	249;249;238;249;238	O14727-6;O14727-4;O14727-3;O14727;O14727-2	.;.;.;APAF_HUMAN;.	C	249;238;249;249;249;249;238;249;249	ENSP00000448165:W249C;ENSP00000353059:W238C;ENSP00000349862:W249C;ENSP00000341830:W249C;ENSP00000334558:W249C;ENSP00000448826:W249C;ENSP00000448449:W238C;ENSP00000449791:W249C;ENSP00000448161:W249C	ENSP00000334558:W249C	W	+	3	0	APAF1	97580401	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	3.509000	0.53386	2.729000	0.93468	0.655000	0.94253	TGG	.	.		0.323	APAF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408006.1	NM_181861.1		T	99056270	G	T	99056270	3	4	254	1	0	0	0	0	1	0	0	0	755	1241	43	3	765	3	APAF1	12	99056270	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	9040944	99056270	34795625	625	34917										
MYBPC1	4604	hgsc.bcm.edu	37	chr12	102067212	102067212	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tctttctttttagggaaaacCaagaccagaattaacttgga	7	7	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:102067212C>T	ENST00000550270.1	+	24	2600	c.2600C>T	c.(2599-2601)cCa>cTa	p.P867L	MYBPC1_ENST00000547509.1_Missense_Mutation_p.P835L|MYBPC1_ENST00000452455.2_Missense_Mutation_p.P867L|MYBPC1_ENST00000360610.2_Missense_Mutation_p.P867L|MYBPC1_ENST00000550501.1_Intron|MYBPC1_ENST00000361466.2_Missense_Mutation_p.P874L|MYBPC1_ENST00000545503.2_Missense_Mutation_p.P849L|MYBPC1_ENST00000541119.1_Missense_Mutation_p.P837L|MYBPC1_ENST00000549145.1_Missense_Mutation_p.P880L|MYBPC1_ENST00000392934.3_Missense_Mutation_p.P836L|MYBPC1_ENST00000361685.2_Missense_Mutation_p.P874L|MYBPC1_ENST00000441232.1_Missense_Mutation_p.P867L|MYBPC1_ENST00000536007.1_Missense_Mutation_p.P830L|MYBPC1_ENST00000553190.1_Missense_Mutation_p.P849L|MYBPC1_ENST00000547405.1_Missense_Mutation_p.P823L|MYBPC1_ENST00000551300.1_Missense_Mutation_p.P750L			Q00872	MYPC1_HUMAN	myosin binding protein C, slow type	867	Ig-like C2-type 6.				cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myofibril (GO:0030016)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	57						TAGGGAAAACCAAGACCAGAA	0.343																																					p.P874L		Atlas-SNP	.											.	MYBPC1	235	.	0			c.C2621T						.						103	108	106					12																	102067212		2203	4300	6503	SO:0001583	missense	4604	exon25			GAAAACCAAGACC		CCDS9083.1, CCDS9084.1, CCDS9085.1, CCDS55877.1, CCDS58268.1, CCDS58269.1, CCDS58270.1, CCDS58271.1, CCDS58272.1, CCDS58273.1	12q23.2	2013-02-11	2001-11-28		ENSG00000196091	ENSG00000196091		"Myosin binding proteins", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7549	protein-coding gene	gene with protein product		160794	"myosin-binding protein C, slow-type"			8375400, 16918501	Standard	NM_002465		Approved		uc010svs.2	Q00872	OTTHUMG00000170274	ENST00000550270.1:c.2600C>T	chr12.hg19:g.102067212C>T	ENSP00000449702:p.Pro867Leu	113.0	0.0		92.0	4.0	NM_206819	B4DKR5|B7Z8G8|B7ZL02|B7ZL09|B7ZL10|E7ESM5|E7EWS6|G3XAE8|Q15497|Q17RR7|Q569K7|Q86T48|Q86TC8|Q8N3L2	Missense_Mutation	SNP	ENST00000550270.1	hg19	CCDS9085.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.995554	0.93167	.	.	ENSG00000196091	ENST00000547405;ENST00000452455;ENST00000441232;ENST00000360610;ENST00000392934;ENST00000547509;ENST00000361685;ENST00000549145;ENST00000553190;ENST00000545503;ENST00000536007;ENST00000541119;ENST00000361466;ENST00000551300;ENST00000550270	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.74526	-0.85;-0.85;-0.85;-0.85;-0.85;-0.85;-0.85;-0.85;-0.85;-0.85;-0.85;-0.85;-0.85;-0.85;-0.85	5.75	5.75	0.90469	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.49916	D	0.000140	D	0.91036	0.7180	H	0.95816	3.725	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;0.996;0.999;1.0;1.0;1.0;0.999;1.0	D	0.93019	0.6438	10	0.87932	D	0	.	19.9379	0.97147	0.0:1.0:0.0:0.0	.	830;837;867;849;836;823;849;867;874;874	B7ZL02;B7ZL10;E7EWS6;B7ZL09;E7ESM5;Q17RR7;Q00872-3;Q00872;G3XAE8;Q00872-2	.;.;.;.;.;.;.;MYPC1_HUMAN;.;.	L	823;867;867;867;836;835;874;880;849;849;830;837;874;750;867	ENSP00000448175:P823L;ENSP00000400908:P867L;ENSP00000388989:P867L;ENSP00000353822:P867L;ENSP00000376665:P836L;ENSP00000447362:P835L;ENSP00000354845:P874L;ENSP00000447660:P880L;ENSP00000447900:P849L;ENSP00000440034:P849L;ENSP00000446128:P830L;ENSP00000442847:P837L;ENSP00000354849:P874L;ENSP00000447116:P750L;ENSP00000449702:P867L	ENSP00000353822:P867L	P	+	2	0	MYBPC1	100591343	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.400000	0.79949	2.710000	0.92621	0.555000	0.69702	CCA	.	.		0.343	MYBPC1-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000408806.1			T	102067212	C	T	102067212	3	4	254	1	0	0	0	0	1	0	0	0	10020	594	21	3	2777	3	MYBPC1	12	102067212	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	3010942	102067212	31784683	626	34918										
KIAA1033	23325	hgsc.bcm.edu	37	chr12	105534742	105534742	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtgctctctgctctagttttGgctgaaaacactctaaatgg	9	9	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:105534742G>T	ENST00000332180.5	+	17	1713	c.1626G>T	c.(1624-1626)ttG>ttT	p.L542F		NM_015275.1	NP_056090.1			KIAA1033											breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(15)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	41						CTCTAGTTTTGGCTGAAAACA	0.373																																					p.L542F		Atlas-SNP	.											.	KIAA1033	83	.	0			c.G1626T						.						167	157	160					12																	105534742		1889	4129	6018	SO:0001583	missense	23325	exon17			AGTTTTGGCTGAA	AB028956	CCDS41826.1, CCDS73514.1	12q24.11	2014-05-09				ENSG00000136051			29174	protein-coding gene	gene with protein product		615748				20376207, 20498093, 21498477	Standard	XM_005268742		Approved	SWIP	uc001tld.3	Q2M389		ENST00000332180.5:c.1626G>T	chr12.hg19:g.105534742G>T	ENSP00000328062:p.Leu542Phe	162.0	0.0		103.0	5.0	NM_015275		Missense_Mutation	SNP	ENST00000332180.5	hg19	CCDS41826.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.145255	0.77888	.	.	ENSG00000136051	ENST00000332180	T	0.51325	0.71	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	T	0.68677	0.3027	M	0.65975	2.015	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.72982	0.979;0.979	T	0.70597	-0.4828	10	0.72032	D	0.01	.	19.5261	0.95208	0.0:0.0:1.0:0.0	.	543;542	B7ZKT9;Q2M389	.;WASH7_HUMAN	F	542	ENSP00000328062:L542F	ENSP00000328062:L542F	L	+	3	2	KIAA1033	104058872	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.275000	0.51639	2.668000	0.90789	0.650000	0.86243	TTG	.	.		0.373	KIAA1033-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406138.4	NM_015275		T	105534742	G	T	105534742	3	4	254	1	0	0	0	0	1	0	0	0	8215	1339	47	3	1692	3	KIAA1033	12	105534742	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	3467530	105534742	28317153	627	34919										
TCP11L2	255394	hgsc.bcm.edu	37	chr12	106740234	106740234	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aagtgtatggaccattttatGcaaatatacttcgaaagctg	8	6	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:106740234G>T	ENST00000299045.3	+	10	1660	c.1486G>T	c.(1486-1488)Gca>Tca	p.A496S		NM_152772.1	NP_689985.1	Q8N4U5	T11L2_HUMAN	t-complex 11, testis-specific-like 2	496										endometrium(2)|kidney(2)|large_intestine(5)|ovary(3)|prostate(1)|urinary_tract(2)	15						ACCATTTTATGCAAATATACT	0.443																																					p.A496S		Atlas-SNP	.											.	TCP11L2	59	.	0			c.G1486T						.						88	82	84					12																	106740234		2203	4300	6503	SO:0001583	missense	255394	exon10			TTTTATGCAAATA	BC033617	CCDS9104.1, CCDS66456.1	12q23.3	2014-08-12	2012-09-20		ENSG00000166046	ENSG00000166046			28627	protein-coding gene	gene with protein product			"t-complex 11 (mouse) like 2", "t-complex 11 (mouse)-like 2"				Standard	XM_005268769		Approved	MGC40368	uc001tln.3	Q8N4U5	OTTHUMG00000170087	ENST00000299045.3:c.1486G>T	chr12.hg19:g.106740234G>T	ENSP00000299045:p.Ala496Ser	109.0	0.0		69.0	4.0	NM_152772	B2RA65|G3V1Y9	Missense_Mutation	SNP	ENST00000299045.3	hg19	CCDS9104.1	.	.	.	.	.	.	.	.	.	.	G	15.24	2.774837	0.49786	.	.	ENSG00000166046	ENST00000299045	T	0.11385	2.78	5.69	5.69	0.88448	.	0.108901	0.64402	D	0.000008	T	0.28200	0.0696	M	0.64170	1.965	0.80722	D	1	D	0.56521	0.976	D	0.65140	0.932	T	0.02893	-1.1097	10	0.10377	T	0.69	-13.0341	19.812	0.96551	0.0:0.0:1.0:0.0	.	496	Q8N4U5	T11L2_HUMAN	S	496	ENSP00000299045:A496S	ENSP00000299045:A496S	A	+	1	0	TCP11L2	105264364	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.423000	0.66458	2.685000	0.91497	0.655000	0.94253	GCA	.	.		0.443	TCP11L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407206.1	NM_152772		T	106740234	G	T	106740234	3	4	254	1	0	0	0	0	1	0	0	0	15730	1319	46	3	1520	3	TCP11L2	12	106740234	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1205492	106740234	27111661	628	34920										
RIC8B	55188	hgsc.bcm.edu	37	chr12	107209055	107209055	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aaagctctcttcaatgtgacGgtagacagttggaaggtgca	12	7	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:107209055G>T	ENST00000392839.2	+	3	820	c.714G>T	c.(712-714)acG>acT	p.T238T	RIC8B_ENST00000355478.2_Silent_p.T198T|RIC8B_ENST00000392837.4_Silent_p.T238T|RIC8B_ENST00000549643.1_Intron	NM_018157.2	NP_060627.2	Q9NVN3	RIC8B_HUMAN	RIC8 guanine nucleotide exchange factor B	238					regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	G-protein alpha-subunit binding (GO:0001965)|guanyl-nucleotide exchange factor activity (GO:0005085)	p.T238T(1)		kidney(2)|large_intestine(5)|lung(10)|ovary(1)|urinary_tract(1)	19						TCAATGTGACGGTAGACAGTT	0.473																																					p.T238T		Atlas-SNP	.											RIC8B_ENST00000355478,NS,carcinoma,0,2	RIC8B	51	.	1	Substitution - coding silent(1)	lung(1)	c.G714T						.						122	118	120					12																	107209055		2203	4300	6503	SO:0001819	synonymous_variant	55188	exon3			TGTGACGGTAGAC	AK128102	CCDS9109.2	12q23.3	2013-08-05	2013-08-05		ENSG00000111785	ENSG00000111785			25555	protein-coding gene	gene with protein product		609147	"resistance to inhibitors of cholinesterase 8 homolog B (C. elegans)"				Standard	XM_005268998		Approved	FLJ10620, hSyn, RIC8	uc001tlx.3	Q9NVN3	OTTHUMG00000144188	ENST00000392839.2:c.714G>T	chr12.hg19:g.107209055G>T		90.0	0.0		45.0	3.0	NM_018157	A2RTZ0|Q4G103|Q6ZRN4|Q86WD3	Silent	SNP	ENST00000392839.2	hg19	CCDS9109.2																																																																																			.	.		0.473	RIC8B-006	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000291398.2	NM_018157		T	107209055	G	T	107209055	2	4	254	1	0	0	0	0	0	0	0	1	13371	1103	39	1		1	RIC8B	12	107209055	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	468821	107209055	26642840	629	34921										
DAO	1610	hgsc.bcm.edu	37	chr12	109278816	109278816	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgattggagcaggagtcatcGggctgtccaccgccctctgc	13	13	2	1	rs373913310		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:109278816G>T	ENST00000228476.3	+	2	238	c.34G>T	c.(34-36)Ggg>Tgg	p.G12W	DAO_ENST00000551281.1_Missense_Mutation_p.G12W	NM_001917.4	NP_001908.3	P14920	OXDA_HUMAN	D-amino-acid oxidase	12					cellular nitrogen compound metabolic process (GO:0034641)|D-alanine catabolic process (GO:0055130)|D-serine catabolic process (GO:0036088)|D-serine metabolic process (GO:0070178)|dopamine biosynthetic process (GO:0042416)|glyoxylate metabolic process (GO:0046487)|leucine metabolic process (GO:0006551)|proline catabolic process (GO:0006562)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	cofactor binding (GO:0048037)|D-amino-acid oxidase activity (GO:0003884)|FAD binding (GO:0071949)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|prostate(2)|skin(1)	26					Flavin adenine dinucleotide(DB03147)	AGGAGTCATCGGGCTGTCCAC	0.577																																					p.G12W		Atlas-SNP	.											DAO,caecum,carcinoma,0,2	DAO	58	.	0			c.G34T						.	G	TRP/GLY	0,4406		0,0,2203	154	115	128		34	5.4	1	12		128	1,8599	1.2+/-3.3	0,1,4299	no	missense	DAO	NM_001917.4	184	0,1,6502	TT,TG,GG		0.0116,0.0,0.0077	probably-damaging	12/348	109278816	1,13005	2203	4300	6503	SO:0001583	missense	1610	exon2			GTCATCGGGCTGT	D11370	CCDS9122.1	12q24.11	2013-09-20			ENSG00000110887	ENSG00000110887	1.4.3.3		2671	protein-coding gene	gene with protein product		124050				1356107, 8182053	Standard	NM_001917		Approved	DAMOX	uc001tnr.4	P14920	OTTHUMG00000169360	ENST00000228476.3:c.34G>T	chr12.hg19:g.109278816G>T	ENSP00000228476:p.Gly12Trp	54.0	0.0		86.0	4.0	NM_001917	B2R7I5|Q16758|Q8N6R2	Missense_Mutation	SNP	ENST00000228476.3	hg19	CCDS9122.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.990236	0.74589	0.0	1.16E-4	ENSG00000110887	ENST00000551281;ENST00000228476;ENST00000547166	D;D;D	0.98400	-3.55;-3.55;-4.91	5.44	5.44	0.79542	FAD dependent oxidoreductase (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99366	0.9777	H	0.96805	3.885	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98614	1.0664	10	0.87932	D	0	-23.0601	17.8335	0.88689	0.0:0.0:1.0:0.0	.	12;12	P14920;Q7Z312	OXDA_HUMAN;.	W	12	ENSP00000446853:G12W;ENSP00000228476:G12W;ENSP00000447104:G12W	ENSP00000228476:G12W	G	+	1	0	DAO	107802945	1.000000	0.71417	0.965000	0.40720	0.534000	0.34807	9.777000	0.99008	2.541000	0.85698	0.591000	0.81541	GGG	.	.		0.577	DAO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403682.1			T	109278816	G	T	109278816	3	4	254	1	0	0	0	0	1	0	0	0	4233	1116	39	1	36	1	DAO	12	109278816	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	2069761	109278816	24573079	630	34922										
ACACB	32	hgsc.bcm.edu	37	chr12	109660331	109660331	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggatgagctgtgtggcccagAcccttccctgtcggacgagc	14	13	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:109660331A>G	ENST00000338432.7	+	25	3703	c.3584A>G	c.(3583-3585)gAc>gGc	p.D1195G	ACACB_ENST00000377854.5_Missense_Mutation_p.D1125G|ACACB_ENST00000377848.3_Missense_Mutation_p.D1195G			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	1195					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	TGTGGCCCAGACCCTTCCCTG	0.572																																					p.D1195G		Atlas-SNP	.											.	ACACB	330	.	0			c.A3584G						.						95	91	92					12																	109660331		2203	4300	6503	SO:0001583	missense	32	exon24			GCCCAGACCCTTC	U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 2"	601557	"acetyl-Coenzyme A carboxylase beta"			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.3584A>G	chr12.hg19:g.109660331A>G	ENSP00000341044:p.Asp1195Gly	132.0	0.0		88.0	4.0	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	hg19	CCDS31898.1	.	.	.	.	.	.	.	.	.	.	A	15.78	2.935008	0.52866	.	.	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854;ENST00000390027	T;T;T	0.44881	0.91;0.91;0.91	5.17	5.17	0.71159	Acetyl-CoA carboxylase, central domain (1);	0.046636	0.85682	D	0.000000	T	0.42268	0.1195	L	0.59436	1.845	0.80722	D	1	B	0.14805	0.011	B	0.20577	0.03	T	0.27606	-1.0069	10	0.36615	T	0.2	.	15.2981	0.73925	1.0:0.0:0.0:0.0	.	1195	O00763	ACACB_HUMAN	G	1195;1195;1125;426	ENSP00000341044:D1195G;ENSP00000367079:D1195G;ENSP00000367085:D1125G	ENSP00000341044:D1195G	D	+	2	0	ACACB	108144714	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.172000	0.94808	2.074000	0.62210	0.528000	0.53228	GAC	.	.		0.572	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093		G	109660331	A	G	109660331	3	3	254	1	0	0	0	0	1	0	0	0	107	275	10	2	3678	2	ACACB	12	109660331	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	381515	109660331	24191564	631	34923										
TCHP	84260	hgsc.bcm.edu	37	chr12	110340853	110340853	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tggcgctcccgacgctgccgTcctactggtgcagccagcag	13	16	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:110340853T>C	ENST00000312777.5	+	2	236	c.22T>C	c.(22-24)Tcc>Ccc	p.S8P	TCHP_ENST00000405876.4_Missense_Mutation_p.S8P	NM_032300.4	NP_115676.1			trichoplein, keratin filament binding											NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|skin(2)	22						GACGCTGCCGTCCTACTGGTG	0.602																																					p.S8P		Atlas-SNP	.											.	TCHP	45	.	0			c.T22C						.						49	51	50					12																	110340853		2203	4300	6503	SO:0001583	missense	84260	exon2			CTGCCGTCCTACT	AK092736	CCDS9137.1	12q24.11	2011-08-25	2006-01-27			ENSG00000139437			28135	protein-coding gene	gene with protein product	"mitostatin"	612654				15731013, 20930847	Standard	NM_032300		Approved	MGC10854, TpMs	uc001tpn.3	Q9BT92		ENST00000312777.5:c.22T>C	chr12.hg19:g.110340853T>C	ENSP00000324404:p.Ser8Pro	149.0	0.0		87.0	4.0	NM_001143852		Missense_Mutation	SNP	ENST00000312777.5	hg19	CCDS9137.1	.	.	.	.	.	.	.	.	.	.	T	10.65	1.411064	0.25465	.	.	ENSG00000139437	ENST00000405876;ENST00000536868;ENST00000312777;ENST00000536408	T;T;T	0.51071	1.37;1.37;0.72	4.81	3.66	0.41972	.	0.317802	0.34245	N	0.004123	T	0.39172	0.1068	L	0.55103	1.725	0.40394	D	0.979571	B	0.09022	0.002	B	0.06405	0.002	T	0.18650	-1.0330	10	0.25751	T	0.34	-0.7753	8.5903	0.33684	0.0:0.093:0.0:0.907	.	8	Q9BT92	TCHP_HUMAN	P	8	ENSP00000384520:S8P;ENSP00000324404:S8P;ENSP00000441835:S8P	ENSP00000324404:S8P	S	+	1	0	TCHP	108825236	0.010000	0.17322	0.930000	0.37139	0.076000	0.17211	1.235000	0.32671	0.710000	0.31997	0.369000	0.22263	TCC	.	.		0.602	TCHP-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403289.1	NM_032300		C	110340853	T	C	110340853	3	2	254	1	0	0	0	0	1	0	0	0	15717	1667	58	2	24	2	TCHP	12	110340853	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	680522	110340853	23511042	632	34924										
OAS1	4938	hgsc.bcm.edu	37	chr12	113357204	113357204	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	accctttcaggctgaaagcaAcagtgcagacgatgagaccg	11	11	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:113357204A>G	ENST00000202917.5	+	6	1312	c.1049A>G	c.(1048-1050)aAc>aGc	p.N350S	RP1-71H24.1_ENST00000552784.1_RNA|OAS1_ENST00000445409.2_Intron|OAS1_ENST00000551241.1_Intron	NM_016816.2	NP_058132.2	P00973	OAS1_HUMAN	2'-5'-oligoadenylate synthetase 1, 40/46kDa	350					cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|protein oligomerization (GO:0051259)|purine nucleotide biosynthetic process (GO:0006164)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(2)|skin(1)	16						GCTGAAAGCAACAGTGCAGAC	0.483																																					p.N350S		Atlas-SNP	.											.	OAS1	128	.	0			c.A1049G						.						83	82	83					12																	113357204		2203	4300	6503	SO:0001583	missense	4938	exon6			AAAGCAACAGTGC	X04371	CCDS31905.1, CCDS41838.1, CCDS44980.1	12q24.2	2014-05-21	2011-07-21				2.7.7.-		8086	protein-coding gene	gene with protein product		164350	"2',5'-oligoadenylate synthetase 1 (40-46 kD)"	OIAS		9344649, 9325053	Standard	XM_006719434		Approved	OIASI, IFI-4	uc001tud.3	P00973		ENST00000202917.5:c.1049A>G	chr12.hg19:g.113357204A>G	ENSP00000202917:p.Asn350Ser	93.0	0.0		92.0	5.0	NM_016816	A8K4N8|P04820|P29080|P29081|P78485|P78486|Q16700|Q16701|Q1PG42|Q3ZM01|Q53GC5|Q53YA4|Q6A1Z3|Q6IPC6|Q6P7N9|Q96J61	Missense_Mutation	SNP	ENST00000202917.5	hg19	CCDS41838.1	.	.	.	.	.	.	.	.	.	.	A	2.929	-0.221556	0.06061	.	.	ENSG00000089127	ENST00000202917	T	0.04502	3.61	1.9	1.9	0.25705	.	.	.	.	.	T	0.02193	0.0068	N	0.08118	0	0.09310	N	0.999991	B	0.02656	0.0	B	0.04013	0.001	T	0.48031	-0.9070	9	0.09590	T	0.72	.	5.8476	0.18675	1.0:0.0:0.0:0.0	.	350	P00973	OAS1_HUMAN	S	350	ENSP00000202917:N350S	ENSP00000202917:N350S	N	+	2	0	OAS1	111841587	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.024000	0.12435	1.136000	0.42199	0.455000	0.32223	AAC	.	.		0.483	OAS1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405896.2			G	113357204	A	G	113357204	3	3	254	1	0	0	0	0	1	0	0	0	10808	43	2	2	1128	2	OAS1	12	113357204	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	3016351	113357204	20494691	633	34925										
LHX5	64211	hgsc.bcm.edu	37	chr12	113901182	113901182	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggtgcgagatcatgtcggtgAacctggggttgtccgcggcg	18	9	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:113901182A>G	ENST00000261731.3	-	5	1595	c.1022T>C	c.(1021-1023)tTc>tCc	p.F341S		NM_022363.2	NP_071758.1	Q9H2C1	LHX5_HUMAN	LIM homeobox 5	341					cell proliferation in forebrain (GO:0021846)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation (GO:0021937)|forebrain neuron differentiation (GO:0021879)|hippocampus development (GO:0021766)|positive regulation of transcription, DNA-templated (GO:0045893)|spinal cord association neuron differentiation (GO:0021527)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	10						CATGTCGGTGAACCTGGGGTT	0.751																																					p.F341S		Atlas-SNP	.											.	LHX5	39	.	0			c.T1022C						.						11	14	13					12																	113901182		2037	3996	6033	SO:0001583	missense	64211	exon5			TCGGTGAACCTGG	AF291181	CCDS9171.1	12q24.13	2014-01-15			ENSG00000089116	ENSG00000089116		"Homeoboxes / LIM class"	14216	protein-coding gene	gene with protein product		605992					Standard	NM_022363		Approved		uc001tvj.1	Q9H2C1	OTTHUMG00000169552	ENST00000261731.3:c.1022T>C	chr12.hg19:g.113901182A>G	ENSP00000261731:p.Phe341Ser	118.0	0.0		88.0	6.0	NM_022363	Q32MA4	Missense_Mutation	SNP	ENST00000261731.3	hg19	CCDS9171.1	.	.	.	.	.	.	.	.	.	.	A	16.80	3.223565	0.58668	.	.	ENSG00000089116	ENST00000261731	D	0.91407	-2.84	4.08	1.05	0.20165	.	0.279818	0.24983	N	0.034052	D	0.86896	0.6043	L	0.57536	1.79	0.40601	D	0.981589	P	0.43938	0.822	B	0.43809	0.432	T	0.81355	-0.0970	10	0.22706	T	0.39	.	8.4052	0.32610	0.3463:0.0:0.0:0.6537	.	341	Q9H2C1	LHX5_HUMAN	S	341	ENSP00000261731:F341S	ENSP00000261731:F341S	F	-	2	0	LHX5	112385565	1.000000	0.71417	0.996000	0.52242	0.994000	0.84299	1.711000	0.37930	0.538000	0.28769	0.459000	0.35465	TTC	.	.		0.751	LHX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404788.3	NM_022363		G	113901182	A	G	113901182	3	3	254	1	0	0	0	0	1	0	0	0	8783	246	9	2	190	2	LHX5	12	113901182	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	543978	113901182	19950713	634	34926										
CIT	11113	hgsc.bcm.edu	37	chr12	120151337	120151337	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctccttggtctggagacctgGggagttcattttgtcacggc	13	10	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:120151337G>T	ENST00000261833.7	-	33	4349	c.4297C>A	c.(4297-4299)Cca>Aca	p.P1433T	CIT_ENST00000392521.2_Missense_Mutation_p.P1475T|CIT_ENST00000537607.1_5'UTR|MIR1178_ENST00000408396.1_RNA	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	1433					cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		TGGAGACCTGGGGAGTTCATT	0.607																																					p.P1475T		Atlas-SNP	.											.	CIT	535	.	0			c.C4423A						.						73	62	66					12																	120151337		2203	4300	6503	SO:0001583	missense	11113	exon34			GACCTGGGGAGTT	AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966			1985	protein-coding gene	gene with protein product	"serine/threonine kinase 21"	605629	"citron (rho-interacting, serine/threonine kinase 21)"			9792683	Standard	NM_001206999		Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000261833.7:c.4297C>A	chr12.hg19:g.120151337G>T	ENSP00000261833:p.Pro1433Thr	149.0	0.0		119.0	5.0	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Missense_Mutation	SNP	ENST00000261833.7	hg19	CCDS9192.1	.	.	.	.	.	.	.	.	.	.	G	15.31	2.796029	0.50208	.	.	ENSG00000122966	ENST00000392521;ENST00000261833	T;T	0.65178	-0.12;-0.14	6.07	6.07	0.98685	.	0.059274	0.64402	D	0.000002	T	0.55752	0.1940	L	0.43152	1.355	0.58432	D	0.999998	P;P;B	0.45126	0.851;0.851;0.148	B;B;B	0.37550	0.162;0.253;0.033	T	0.52631	-0.8550	10	0.24483	T	0.36	.	20.6439	0.99570	0.0:0.0:1.0:0.0	.	1475;1433;951	Q2M5E1;O14578;O14578-3	.;CTRO_HUMAN;.	T	1475;1433	ENSP00000376306:P1475T;ENSP00000261833:P1433T	ENSP00000261833:P1433T	P	-	1	0	CIT	118635720	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	6.443000	0.73447	2.884000	0.98904	0.655000	0.94253	CCA	.	.		0.607	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174		T	120151337	G	T	120151337	3	4	254	1	0	0	0	0	1	0	0	0	3440	1232	43	3	1846	3	CIT	12	120151337	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	6250155	120151337	13700558	635	34927										
GCN1L1	10985	hgsc.bcm.edu	37	chr12	120572406	120572406	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agagggggtccaccttaatgTggatggaaatgagcttcccc	13	9	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:120572406T>C	ENST00000300648.6	-	52	7145	c.7133A>G	c.(7132-7134)cAc>cGc	p.H2378R		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	2378					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CACCTTAATGTGGATGGAAAT	0.622																																					p.H2378R		Atlas-SNP	.											.	GCN1L1	207	.	0			c.A7133G						.						75	79	78					12																	120572406		1972	4157	6129	SO:0001583	missense	10985	exon52			TTAATGTGGATGG	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.7133A>G	chr12.hg19:g.120572406T>C	ENSP00000300648:p.His2378Arg	145.0	0.0		95.0	5.0	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Missense_Mutation	SNP	ENST00000300648.6	hg19	CCDS41847.1	.	.	.	.	.	.	.	.	.	.	T	28.3	4.905149	0.92035	.	.	ENSG00000089154	ENST00000300648	T	0.63255	-0.03	5.64	5.64	0.86602	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.81721	0.4882	M	0.86953	2.85	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.84824	0.0798	10	0.62326	D	0.03	-18.4244	15.8461	0.78890	0.0:0.0:0.0:1.0	.	2378	Q92616	GCN1L_HUMAN	R	2378	ENSP00000300648:H2378R	ENSP00000300648:H2378R	H	-	2	0	GCN1L1	119056789	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.490000	0.81461	2.151000	0.67156	0.496000	0.49642	CAC	.	.		0.622	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1			C	120572406	T	C	120572406	3	2	254	1	0	0	0	0	1	0	0	0	6307	1696	59	2	910	2	GCN1L1	12	120572406	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	421069	120572406	13279489	636	34928										
GCN1L1	10985	hgsc.bcm.edu	37	chr12	120600885	120600885	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gccacggacctaaggatgggTggtgggagatgatcagcatt	16	7	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:120600885T>C	ENST00000300648.6	-	19	2039	c.2027A>G	c.(2026-2028)cAc>cGc	p.H676R		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	676					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TAAGGATGGGTGGTGGGAGAT	0.597																																					p.H676R		Atlas-SNP	.											.	GCN1L1	207	.	0			c.A2027G						.						90	88	89					12																	120600885		2070	4198	6268	SO:0001583	missense	10985	exon19			GATGGGTGGTGGG	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.2027A>G	chr12.hg19:g.120600885T>C	ENSP00000300648:p.His676Arg	108.0	0.0		92.0	4.0	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Missense_Mutation	SNP	ENST00000300648.6	hg19	CCDS41847.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.505128	0.85282	.	.	ENSG00000089154	ENST00000300648	T	0.04654	3.58	5.71	5.71	0.89125	Domain of unknown function DUF3554 (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.20129	0.0484	M	0.65975	2.015	0.80722	D	1	D	0.76494	0.999	D	0.74674	0.984	T	0.00109	-1.2049	10	0.72032	D	0.01	.	15.9958	0.80243	0.0:0.0:0.0:1.0	.	676	Q92616	GCN1L_HUMAN	R	676	ENSP00000300648:H676R	ENSP00000300648:H676R	H	-	2	0	GCN1L1	119085268	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.249000	0.78278	2.188000	0.69820	0.533000	0.62120	CAC	.	.		0.597	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1			C	120600885	T	C	120600885	3	2	254	1	0	0	0	0	1	0	0	0	6307	1696	59	2	6148	2	GCN1L1	12	120600885	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	28479	120600885	13251010	637	34929										
MSI1	4440	hgsc.bcm.edu	37	chr12	120795696	120795696	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	actctcaaacgtgacaaaccCgaaccctagaggttggacaa	8	12	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:120795696C>A	ENST00000257552.2	-	8	545	c.457G>T	c.(457-459)Ggg>Tgg	p.G153W	MSI1_ENST00000546622.1_5'UTR	NM_002442.3	NP_002433.1	O43347	MSI1H_HUMAN	musashi RNA-binding protein 1	153	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				epithelial cell differentiation (GO:0030855)|nervous system development (GO:0007399)|response to hormone (GO:0009725)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|polysome (GO:0005844)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)			breast(4)|central_nervous_system(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(5)|skin(2)	19	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GTGACAAACCCGAACCCTAGA	0.493																																					p.G153W		Atlas-SNP	.											MSI1,NS,carcinoma,0,1	MSI1	40	.	0			c.G457T						.						107	86	93					12																	120795696		2203	4300	6503	SO:0001583	missense	4440	exon8			CAAACCCGAACCC	AB012851	CCDS9196.1	12q24	2013-07-16	2012-12-13					"RNA binding motif (RRM) containing"	7330	protein-coding gene	gene with protein product		603328	"Musashi (Drosophila) homolog 1", "musashi homolog 1 (Drosophila)"			9790759	Standard	NM_002442		Approved		uc001tye.2	O43347	OTTHUMG00000169344	ENST00000257552.2:c.457G>T	chr12.hg19:g.120795696C>A	ENSP00000257552:p.Gly153Trp	140.0	1.0		85.0	5.0	NM_002442	Q96PU0|Q96PU1|Q96PU2|Q96PU3	Missense_Mutation	SNP	ENST00000257552.2	hg19	CCDS9196.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.483654	0.84854	.	.	ENSG00000135097	ENST00000257552	T	0.80480	-1.38	5.27	5.27	0.74061	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.64402	D	0.000001	D	0.94679	0.8284	H	0.99074	4.42	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96861	0.9632	10	0.87932	D	0	.	19.2695	0.94003	0.0:1.0:0.0:0.0	.	153	O43347	MSI1H_HUMAN	W	153	ENSP00000257552:G153W	ENSP00000257552:G153W	G	-	1	0	MSI1	119280079	1.000000	0.71417	0.998000	0.56505	0.818000	0.46254	7.455000	0.80726	2.637000	0.89404	0.462000	0.41574	GGG	.	.		0.493	MSI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403629.1	NM_002442		A	120795696	C	A	120795696	3	1	254	1	0	0	0	0	1	0	0	0	9884	652	23	1	659	1	MSI1	12	120795696	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	194811	120795696	13056199	638	34930										
P2RX4	5025	hgsc.bcm.edu	37	chr12	121648016	121648016	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccttcctgttcgagtacgacAcgccgcgcatcgtgctcatc	9	16	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:121648016A>G	ENST00000337233.4	+	1	357	c.49A>G	c.(49-51)Acg>Gcg	p.T17A	P2RX4_ENST00000359949.7_Missense_Mutation_p.T17A|P2RX4_ENST00000543171.1_5'UTR|P2RX4_ENST00000541532.1_Missense_Mutation_p.T17A|P2RX4_ENST00000540930.1_3'UTR	NM_001261397.1|NM_001261398.1|NM_002560.2	NP_001248326.1|NP_001248327.1|NP_002551.2	Q99571	P2RX4_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 4	17					apoptotic signaling pathway (GO:0097190)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cellular response to ATP (GO:0071318)|endothelial cell activation (GO:0042118)|ion transmembrane transport (GO:0034220)|membrane depolarization (GO:0051899)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|neuronal action potential (GO:0019228)|nitric oxide biosynthetic process (GO:0006809)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of prostaglandin secretion (GO:0032308)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction (GO:0055117)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sodium ion transport (GO:0002028)|relaxation of cardiac muscle (GO:0055119)|response to ATP (GO:0033198)|response to fluid shear stress (GO:0034405)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|tissue homeostasis (GO:0001894)|transport (GO:0006810)|vasodilation (GO:0042311)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|cadherin binding (GO:0045296)|copper ion binding (GO:0005507)|drug binding (GO:0008144)|extracellular ATP-gated cation channel activity (GO:0004931)|protein homodimerization activity (GO:0042803)|purinergic nucleotide receptor activity (GO:0001614)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			breast(1)|kidney(4)|large_intestine(4)|lung(7)|prostate(1)	17	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CGAGTACGACACGCCGCGCAT	0.711																																					p.T17A		Atlas-SNP	.											.	P2RX4	27	.	0			c.A49G						.						20	19	20					12																	121648016		2197	4295	6492	SO:0001583	missense	5025	exon1			TACGACACGCCGC	Y07684	CCDS9214.1, CCDS58282.1	12q24.32	2012-01-17			ENSG00000135124	ENSG00000135124		"Purinergic receptors", "Ligand-gated ion channels / Purinergic receptors, ionotropic"	8535	protein-coding gene	gene with protein product		600846				9016352	Standard	NM_002560		Approved	P2X4	uc031qjt.1	Q99571	OTTHUMG00000169155	ENST00000337233.4:c.49A>G	chr12.hg19:g.121648016A>G	ENSP00000336607:p.Thr17Ala	72.0	0.0		93.0	4.0	NM_001261398	E7EPF7|F6RU17|O00450|O14722|Q5U089|Q5U090|Q8N4N1|Q9UBG9	Missense_Mutation	SNP	ENST00000337233.4	hg19	CCDS9214.1	.	.	.	.	.	.	.	.	.	.	A	19.06	3.753047	0.69648	.	.	ENSG00000135124	ENST00000337233;ENST00000359949;ENST00000541532;ENST00000538701;ENST00000542067	T;T;T;T;T	0.10668	2.85;2.85;2.85;2.85;2.85	3.78	2.62	0.31277	.	0.000000	0.85682	D	0.000000	T	0.38081	0.1027	M	0.93678	3.445	0.43399	D	0.995524	D;P;D	0.76494	0.999;0.929;0.999	D;P;D	0.81914	0.991;0.803;0.995	T	0.32402	-0.9908	10	0.87932	D	0	-18.2534	8.4382	0.32799	0.904:0.0:0.096:0.0	.	17;17;17	F6RU17;E7EPF7;Q99571	.;.;P2RX4_HUMAN	A	17	ENSP00000336607:T17A;ENSP00000353032:T17A;ENSP00000443115:T17A;ENSP00000444033:T17A;ENSP00000438329:T17A	ENSP00000336607:T17A	T	+	1	0	P2RX4	120132399	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.154000	0.64894	0.629000	0.30376	0.172000	0.16884	ACG	.	.		0.711	P2RX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402545.1	NM_175567		G	121648016	A	G	121648016	3	3	254	1	0	0	0	0	1	0	0	0	11351	159	6	2	51	2	P2RX4	12	121648016	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	852320	121648016	12203879	639	34931										
CAMKK2	10645	hgsc.bcm.edu	37	chr12	121701741	121701741	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtgcctcggggtggagggcgAcctgaaggaaacaaaaacag	16	8	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:121701741A>G	ENST00000324774.5	-	6	1455	c.627T>C	c.(625-627)cgT>cgC	p.R209R	CAMKK2_ENST00000392473.2_Splice_Site_p.R209R|CAMKK2_ENST00000404169.3_Splice_Site_p.R209R|CAMKK2_ENST00000392474.2_Splice_Site_p.R209R|CAMKK2_ENST00000538733.1_Splice_Site_p.R209R|CAMKK2_ENST00000535524.1_Intron|CAMKK2_ENST00000337174.3_Splice_Site_p.R209R|CAMKK2_ENST00000412367.2_Splice_Site_p.R209R|CAMKK2_ENST00000347034.2_Splice_Site_p.R209R|CAMKK2_ENST00000446440.2_Splice_Site_p.R209R|CAMKK2_ENST00000402834.4_Splice_Site_p.R209R	NM_006549.3	NP_006540.3	Q96RR4	KKCC2_HUMAN	calcium/calmodulin-dependent protein kinase kinase 2, beta	209	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|RP domain.				calcium-mediated signaling (GO:0019722)|MAPK cascade (GO:0000165)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of protein kinase activity (GO:0045859)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	17	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					GTGGAGGGCGACCTGAAGGAA	0.602																																					p.R209R		Atlas-SNP	.											.	CAMKK2	87	.	0			c.T627C						.						20	19	19					12																	121701741		2203	4297	6500	SO:0001630	splice_region_variant	10645	exon6			AGGGCGACCTGAA	AF101264	CCDS9216.1, CCDS9217.1, CCDS9218.1, CCDS9219.1, CCDS44999.1, CCDS53837.1, CCDS58283.1	12q24.2	2002-08-13				ENSG00000110931			1470	protein-coding gene	gene with protein product		615002				9662074	Standard	NM_172226		Approved	CAMKK, KIAA0787, CAMKKB, MGC15254	uc001tzu.3	Q96RR4		ENST00000324774.5:c.626-1T>C	chr12.hg19:g.121701741A>G		62.0	0.0		76.0	4.0	NM_153500	A8K7Q7|O94883|Q8IUG2|Q8IUG3|Q8N3I4|Q8WY03|Q8WY04|Q8WY05|Q8WY06|Q96RP1|Q96RP2|Q96RR3|Q9BWE9|Q9UER3|Q9UES2|Q9Y5N2	Silent	SNP	ENST00000324774.5	hg19	CCDS9216.1																																																																																			.	.		0.602	CAMKK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402563.1	NM_172226	Silent	G	121701741	A	G	121701741	5	3	254	1	0	0	0	0	0	0	1	0	2609	289	10	2	1197	2	CAMKK2	12	121701741	Splice_Site	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	53725	121701741	12150154	640	34932										
LRRC43	254050	hgsc.bcm.edu	37	chr12	122669301	122669301	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cttcttctactcctacttccGgtccctgcgggtaatagaca	7	14	2	1	rs372181783		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:122669301G>T	ENST00000339777.4	+	2	414	c.386G>T	c.(385-387)cGg>cTg	p.R129L	LRRC43_ENST00000425921.1_5'UTR	NM_152759.4	NP_689972.3	Q8N309	LRC43_HUMAN	leucine rich repeat containing 43	129										NS(1)|endometrium(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(2)	19	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000312)|Epithelial(86;0.000539)|BRCA - Breast invasive adenocarcinoma(302;0.225)		TCCTACTTCCGGTCCCTGCGG	0.562																																					p.R129L		Atlas-SNP	.											.	LRRC43	105	.	0			c.G386T						.	G	LEU/ARG,	0,3986		0,0,1993	25	26	26		386,	1.3	1	12		26	1,8349		0,1,4174	no	missense,utr-5	LRRC43	NM_001098519.1,NM_152759.4	102,	0,1,6167	TT,TG,GG		0.012,0.0,0.0081	possibly-damaging,	129/657,	122669301	1,12335	1993	4175	6168	SO:0001583	missense	254050	exon2			ACTTCCGGTCCCT	AK124107	CCDS45001.1	12q24.31	2014-09-11			ENSG00000158113	ENSG00000158113			28562	protein-coding gene	gene with protein product						12477932	Standard	NM_152759		Approved	MGC35140	uc009zxm.3	Q8N309	OTTHUMG00000168915	ENST00000339777.4:c.386G>T	chr12.hg19:g.122669301G>T	ENSP00000344233:p.Arg129Leu	192.0	0.0		144.0	6.0	NM_001098519	Q6ZVT9	Missense_Mutation	SNP	ENST00000339777.4	hg19	CCDS45001.1	.	.	.	.	.	.	.	.	.	.	G	19.79	3.892321	0.72524	0.0	1.2E-4	ENSG00000158113	ENST00000339777	T	0.58358	0.34	4.9	1.34	0.21922	.	.	.	.	.	T	0.60209	0.2251	M	0.62723	1.935	0.39919	D	0.974138	D	0.65815	0.995	P	0.60682	0.878	T	0.62779	-0.6782	9	0.66056	D	0.02	-19.8237	6.3874	0.21568	0.2552:0.1498:0.595:0.0	.	129	Q8N309	LRC43_HUMAN	L	129	ENSP00000344233:R129L	ENSP00000344233:R129L	R	+	2	0	LRRC43	121235254	0.937000	0.31787	0.983000	0.44433	0.867000	0.49689	0.382000	0.20635	1.069000	0.40788	0.462000	0.41574	CGG	.	.		0.562	LRRC43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401589.1	NM_152759		T	122669301	G	T	122669301	3	4	254	1	0	0	0	0	1	0	0	0	9010	1116	39	1	392	1	LRRC43	12	122669301	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	967560	122669301	11182594	641	34933										
SETD8	387893	hgsc.bcm.edu	37	chr12	123880916	123880924	+	In_Frame_Del	DEL	TCGCAAACT	TCGCAAACT	-													0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	caaggaaaaacgcaacagaaTcgcaaacttacggatttcta					rs148212570|rs372757608|rs77198130	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	TCGCAAACT	TCGCAAACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:123880916_123880924delTCGCAAACT	ENST00000402868.3	+	5	960_968	c.534_542delTCGCAAACT	c.(532-543)aatcgcaaactt>aat	p.RKL179del	SETD8_ENST00000478781.2_3'UTR|SETD8_ENST00000330479.4_In_Frame_Del_p.RKL179del			Q9NQR1	SETD8_HUMAN	SET domain containing (lysine methyltransferase) 8	220					histone lysine methylation (GO:0034968)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine monomethylation (GO:0018026)|regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043516)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|urinary_tract(1)	13	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.00101)|Epithelial(86;0.00425)		CGCAACAGAATCGCAAACTTACGGATTTC	0.502																																					p.178_181del		Pindel	.											.	SETD8	35	.	0			c.533_541del						.																																			SO:0001651	inframe_deletion	387893	exon5			.	AY102937	CCDS9247.1	12q24.31	2011-07-01			ENSG00000183955	ENSG00000183955		"Chromatin-modifying enzymes / K-methyltransferases"	29489	protein-coding gene	gene with protein product		607240				15933070, 12086618, 12121615	Standard	NM_020382		Approved	SET8, SET07, PR-Set7, KMT5A	uc001uew.3	Q9NQR1	OTTHUMG00000150477	ENST00000402868.3:c.534_542delTCGCAAACT	chr12.hg19:g.123880916_123880924delTCGCAAACT	ENSP00000384629:p.Arg179_Leu181del	102.0	0.0		63.0	17.0	NM_020382	A8K9D0|Q86W83|Q8TD09	In_Frame_Del	DEL	ENST00000402868.3	hg19	CCDS9247.1																																																																																			.	.		0.502	SETD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318263.1	NM_020382		-	123880924	TCGCAAACT	-	123880916	7	5	254	1	0	1	0	1	0	0	0	0	14152	1432	50	0	552	0	SETD8	12	123880916	In_Frame_Del	DEL	TCGCAAACT	TCGA-EP-A2KA-01A-11D-A183-10	1211615	123880916	9970979	642	34934										
SFRS8	6433	hgsc.bcm.edu	37	chr12	132283969	132283969	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgtgtctcgccctgcacaggAtctcatggccaaagtcagag	11	12	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:132283969A>G	ENST00000261674.4	+	18	2933	c.2792A>G	c.(2791-2793)gAt>gGt	p.D931G	SFSWAP_ENST00000539506.1_3'UTR|RNA5SP378_ENST00000363646.1_RNA|SFSWAP_ENST00000541286.1_Splice_Site_p.D983G	NM_004592.3	NP_004583.2	Q12872	SFSWA_HUMAN	splicing factor, suppressor of white-apricot family	931	Arg/Ser-rich (RS domain).				mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	RNA binding (GO:0003723)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(8)|ovary(1)|skin(2)	25						CCTGCACAGGATCTCATGGCC	0.577																																					p.D983G		Atlas-SNP	.											.	SFSWAP	69	.	0			c.A2948G						.						61	54	57					12																	132283969		2203	4300	6503	SO:0001630	splice_region_variant	6433	exon19			CACAGGATCTCAT	U08377	CCDS9273.1, CCDS58290.1	12q24.33	2014-04-14	2014-04-14	2010-09-15	ENSG00000061936	ENSG00000061936			10790	protein-coding gene	gene with protein product		601945	"splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot, Drosophila homolog)", "splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot homolog, Drosophila)", "splicing factor, suppressor of white-apricot homolog (Drosophila)"	SFRS8		8940107	Standard	NM_004592		Approved	SWAP	uc010tbn.2	Q12872	OTTHUMG00000168319	ENST00000261674.4:c.2791-1A>G	chr12.hg19:g.132283969A>G		140.0	0.0		81.0	4.0	NM_001261411	B2RN45|B7ZM97|F5H6B8|Q6PJF7	Missense_Mutation	SNP	ENST00000261674.4	hg19	CCDS9273.1	.	.	.	.	.	.	.	.	.	.	A	15.92	2.975453	0.53720	.	.	ENSG00000061936	ENST00000261674;ENST00000541286	T;T	0.20332	2.25;2.08	5.14	5.14	0.70334	.	0.140754	0.64402	D	0.000006	T	0.42562	0.1208	L	0.56769	1.78	0.80722	D	1	D;D	0.67145	0.996;0.993	D;D	0.79784	0.993;0.984	T	0.33317	-0.9873	10	0.72032	D	0.01	-32.0351	14.2322	0.65901	1.0:0.0:0.0:0.0	.	983;931	F5H6B8;Q12872	.;SFSWA_HUMAN	G	931;983	ENSP00000261674:D931G;ENSP00000437738:D983G	ENSP00000261674:D931G	D	+	2	0	SFSWAP	130849922	1.000000	0.71417	1.000000	0.80357	0.702000	0.40608	5.904000	0.69886	2.064000	0.61679	0.454000	0.30748	GAT	.	.		0.577	SFSWAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399276.1	NM_004592	Missense_Mutation	G	132283969	A	G	132283969	5	3	254	1	0	0	0	0	0	0	1	0	14198	347	12	2	2862	2	SFRS8	12	132283969	Splice_Site	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	8403053	132283969	1567926	643	34935										
EP400	57634	hgsc.bcm.edu	37	chr12	132549272	132549272	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cccccgcagcccccaccgccAcaggcccagtctgcgccccc	8	26	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:132549272A>G	ENST00000333577.4	+	49	8611	c.8502A>G	c.(8500-8502)ccA>ccG	p.P2834P	EP400_ENST00000389561.2_Silent_p.P2798P|EP400_ENST00000389562.2_Silent_p.P2797P|EP400_ENST00000330386.6_Silent_p.P2717P|EP400_ENST00000332482.4_Silent_p.P2761P			Q96L91	EP400_HUMAN	E1A binding protein p400	2834	Poly-Pro.				chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		CCCCACCGCCACAGGCCCAGT	0.592																																					p.P2798P		Atlas-SNP	.											.	EP400	370	.	0			c.A8394G						.						32	47	42					12																	132549272		2200	4298	6498	SO:0001819	synonymous_variant	57634	exon48			ACCGCCACAGGCC	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"trinucleotide repeat containing 12"	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.8502A>G	chr12.hg19:g.132549272A>G		100.0	0.0		73.0	4.0	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	hg19																																																																																				.	.		0.592	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		G	132549272	A	G	132549272	2	3	254	1	0	0	0	0	0	0	0	1	5151	146	6	2		2	EP400	12	132549272	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	265303	132549272	1302623	644	34936										
ZNF10	7556	hgsc.bcm.edu	37	chr12	133732852	133732852	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tctcaccttgttactcatcaGagaactcatacaggagacaa	6	11	4	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr12:133732852G>T	ENST00000248211.6	+	5	1242	c.1020G>T	c.(1018-1020)caG>caT	p.Q340H	CTD-2140B24.4_ENST00000540096.2_Intron|ZNF268_ENST00000416488.1_Intron|ZNF10_ENST00000426665.2_Missense_Mutation_p.Q340H|ZNF10_ENST00000402932.2_Missense_Mutation_p.Q206H	NM_015394.4	NP_056209.2	P21506	ZNF10_HUMAN	zinc finger protein 10	340					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|prostate(1)|skin(5)|urinary_tract(1)	26	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;1.28e-06)|all_epithelial(31;0.0051)|Lung NSC(355;0.00948)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		TTACTCATCAGAGAACTCATA	0.418																																					p.Q340H		Atlas-SNP	.											.	ZNF10	58	.	0			c.G1020T						.						114	122	119					12																	133732852		2203	4300	6503	SO:0001583	missense	7556	exon5			TCATCAGAGAACT	X52332, BC024182	CCDS9283.1	12q24.33	2013-01-08	2005-05-22		ENSG00000256223	ENSG00000256223		"Zinc fingers, C2H2-type", "-"	12879	protein-coding gene	gene with protein product		194538	"zinc finger protein 10 (KOX 1)"			7865130, 8262519	Standard	NM_015394		Approved	KOX1	uc001ulq.3	P21506	OTTHUMG00000167944	ENST00000248211.6:c.1020G>T	chr12.hg19:g.133732852G>T	ENSP00000248211:p.Gln340His	100.0	0.0		75.0	4.0	NM_015394	B2RBS1|Q8TC91	Missense_Mutation	SNP	ENST00000248211.6	hg19	CCDS9283.1	.	.	.	.	.	.	.	.	.	.	G	11.14	1.550609	0.27739	.	.	ENSG00000256223	ENST00000248211;ENST00000426665;ENST00000402932	T;T;T	0.18502	3.18;3.18;2.21	3.6	2.69	0.31865	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.314161	0.18298	N	0.145506	T	0.12518	0.0304	L	0.44542	1.39	0.80722	D	1	B	0.20164	0.042	B	0.17433	0.018	T	0.08086	-1.0739	9	.	.	.	.	6.506	0.22196	0.1092:0.1899:0.7009:0.0	.	340	P21506	ZNF10_HUMAN	H	340;340;206	ENSP00000248211:Q340H;ENSP00000393814:Q340H;ENSP00000384893:Q206H	.	Q	+	3	2	ZNF10	132242925	0.291000	0.24352	1.000000	0.80357	0.996000	0.88848	0.875000	0.28079	2.012000	0.59069	0.655000	0.94253	CAG	.	.		0.418	ZNF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397182.1	NM_015394		T	133732852	G	T	133732852	3	4	254	1	0	0	0	0	1	0	0	0	17727	933	33	3	1034	3	ZNF10	12	133732852	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1183580	133732852	119043	645	34937										
SACS	26278	hgsc.bcm.edu	37	chr13	23908202	23908202	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cagtcttttagagtatcaacAacaatgtcaaatgttggttt	7	6	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:23908202A>G	ENST00000382292.3	-	9	10086	c.9813T>C	c.(9811-9813)gtT>gtC	p.V3271V	SACS_ENST00000382298.3_Silent_p.V3271V|SACS_ENST00000402364.1_Silent_p.V2521V			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	3271					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		GAGTATCAACAACAATGTCAA	0.398																																					p.V3271V		Atlas-SNP	.											.	SACS	871	.	0			c.T9813C						.						107	99	102					13																	23908202		2203	4299	6502	SO:0001819	synonymous_variant	26278	exon10			ATCAACAACAATG	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.9813T>C	chr13.hg19:g.23908202A>G		98.0	0.0		84.0	4.0	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	hg19	CCDS9300.2																																																																																			.	.		0.398	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		G	23908202	A	G	23908202	2	3	254	1	0	0	0	0	0	0	0	1	13819	117	5	2		2	SACS	13	23908202	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10		23908202	91261676	646	34938										
SLC46A3	283537	hgsc.bcm.edu	37	chr13	29286871	29286871	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggtcatagccattcctgtcaTcgtggtaaaaatcccaatga	8	10	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:29286871T>C	ENST00000266943.6	-	3	1375	c.1006A>G	c.(1006-1008)Atg>Gtg	p.M336V	SLC46A3_ENST00000380814.4_Missense_Mutation_p.M336V	NM_001135919.1|NM_181785.3	NP_001129391.1|NP_861450.1	Q7Z3Q1	S46A3_HUMAN	solute carrier family 46, member 3	336					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(2)|prostate(1)|skin(1)	15		Lung SC(185;0.0367)		all cancers(112;0.159)		ATTCCTGTCATCGTGGTAAAA	0.373																																					p.M336V		Atlas-SNP	.											.	SLC46A3	86	.	0			c.A1006G						.						89	86	87					13																	29286871		2203	4300	6503	SO:0001583	missense	283537	exon3			CTGTCATCGTGGT		CCDS9332.1, CCDS45021.1	13q12.3	2013-05-22	2007-03-29		ENSG00000139508	ENSG00000139508		"Solute carriers"	27501	protein-coding gene	gene with protein product							Standard	NM_001135919		Approved	DKFZp686A1775, FLJ42613	uc001usj.3	Q7Z3Q1	OTTHUMG00000016650	ENST00000266943.6:c.1006A>G	chr13.hg19:g.29286871T>C	ENSP00000266943:p.Met336Val	154.0	0.0		112.0	5.0	NM_181785	Q3ZCV8|Q6NUK5|Q6P9B3|Q6ZVG5|Q96QA1	Missense_Mutation	SNP	ENST00000266943.6	hg19	CCDS9332.1	.	.	.	.	.	.	.	.	.	.	T	3.555	-0.090823	0.07053	.	.	ENSG00000139508	ENST00000266943;ENST00000380814	T;T	0.56103	0.48;0.48	5.43	4.23	0.50019	Major facilitator superfamily domain, general substrate transporter (1);	0.578774	0.20321	N	0.094629	T	0.41166	0.1147	L	0.44542	1.39	0.28488	N	0.914614	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.002	T	0.28776	-1.0033	10	0.10111	T	0.7	-16.2244	11.7366	0.51769	0.0:0.0699:0.0:0.9301	.	261;336;336	B5MEH0;Q7Z3Q1-2;Q7Z3Q1	.;.;S46A3_HUMAN	V	336	ENSP00000266943:M336V;ENSP00000370192:M336V	ENSP00000266943:M336V	M	-	1	0	SLC46A3	28184871	0.511000	0.26179	0.958000	0.39756	0.526000	0.34562	0.376000	0.20535	0.982000	0.38575	0.533000	0.62120	ATG	.	.		0.373	SLC46A3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276111.1	NM_181785		C	29286871	T	C	29286871	3	2	254	1	0	0	0	0	1	0	0	0	14661	1435	50	2	409	2	SLC46A3	13	29286871	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	5378669	29286871	85883007	647	34939										
STARD13	90627	hgsc.bcm.edu	37	chr13	33681005	33681005	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	acaccacccaggagctgggcTtcctcatgctccacggagag	11	15	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:33681005T>C	ENST00000336934.5	-	13	3230	c.3114A>G	c.(3112-3114)gaA>gaG	p.E1038E	STARD13_ENST00000255486.4_Silent_p.E1030E|STARD13_ENST00000399365.3_Silent_p.E920E	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	1038	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	40	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		GGAGCTGGGCTTCCTCATGCT	0.532																																					p.E1038E		Atlas-SNP	.											.	STARD13	100	.	0			c.A3114G						.						134	123	127					13																	33681005		2203	4300	6503	SO:0001819	synonymous_variant	90627	exon13			CTGGGCTTCCTCA	AL049801	CCDS9348.1, CCDS9349.1, CCDS9350.1	13q13.1	2013-08-13	2007-08-16		ENSG00000133121	ENSG00000133121		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	19164	protein-coding gene	gene with protein product		609866	"START domain containing 13", "long intergenic non-protein coding RNA 464"	LINC00464		8812419	Standard	NM_178006		Approved	GT650, DLC2, ARHGAP37	uc001uuw.3	Q9Y3M8	OTTHUMG00000016708	ENST00000336934.5:c.3114A>G	chr13.hg19:g.33681005T>C		132.0	0.0		97.0	4.0	NM_178006	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Silent	SNP	ENST00000336934.5	hg19	CCDS9348.1																																																																																			.	.		0.532	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2	NM_001243466		C	33681005	T	C	33681005	2	2	254	1	0	0	0	0	0	0	0	1	15271	1606	56	2		2	STARD13	13	33681005	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	4394134	33681005	81488873	648	34940										
NBEA	26960	hgsc.bcm.edu	37	chr13	36239245	36239245	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	actatccggcaccaagagccGtcctcacaggccatgaccat	8	16	1	2	rs368581341		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:36239245G>A	ENST00000400445.3	+	55	8857	c.8323G>A	c.(8323-8325)Gtc>Atc	p.V2775I	NBEA_ENST00000537702.1_Missense_Mutation_p.V568I|NBEA_ENST00000310336.4_Missense_Mutation_p.V2775I|NBEA_ENST00000540320.1_Missense_Mutation_p.V2775I|NBEA_ENST00000379922.3_Missense_Mutation_p.V353I|NBEA_ENST00000379939.2_Missense_Mutation_p.V2772I	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	2775					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		ACCAAGAGCCGTCCTCACAGG	0.483																																					p.V2775I		Atlas-SNP	.											.	NBEA	340	.	0			c.G8323A						.	G	ILE/VAL,ILE/VAL	0,4088		0,0,2044	83	83	83		1702,8323	4.7	1	13		83	1,8379		0,1,4189	no	missense,missense	NBEA	NM_001204197.1,NM_015678.4	29,29	0,1,6233	AA,AG,GG		0.0119,0.0,0.0080	benign,benign	568/740,2775/2947	36239245	1,12467	2044	4190	6234	SO:0001583	missense	26960	exon55			AGAGCCGTCCTCA	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.8323G>A	chr13.hg19:g.36239245G>A	ENSP00000383295:p.Val2775Ile	282.0	0.0		177.0	53.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	G	6.332	0.429400	0.11987	0.0	1.19E-4	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336;ENST00000422518;ENST00000402346;ENST00000537702;ENST00000379922	T;T;T;T;T;T	0.29655	1.56;1.56;1.56;1.56;1.56;1.56	5.52	4.66	0.58398	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.08044	0.0201	N	0.00427	-1.505	0.54753	D	0.999987	B;B;B	0.21905	0.062;0.006;0.038	B;B;B	0.16289	0.015;0.004;0.005	T	0.33137	-0.9880	10	0.02654	T	1	.	14.7267	0.69349	0.0709:0.0:0.9291:0.0	.	2775;353;2772	Q8NFP9;Q8NFP9-2;Q5T321	NBEA_HUMAN;.;.	I	2775;2775;2772;2775;1404;353;568;353	ENSP00000440951:V2775I;ENSP00000383295:V2775I;ENSP00000369271:V2772I;ENSP00000308534:V2775I;ENSP00000440233:V568I;ENSP00000369254:V353I	ENSP00000308534:V2775I	V	+	1	0	NBEA	35137245	1.000000	0.71417	1.000000	0.80357	0.637000	0.38172	7.210000	0.77924	2.582000	0.87167	0.655000	0.94253	GTC	.	.		0.483	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		A	36239245	G	A	36239245	3	1	254	1	0	0	0	0	1	0	0	0	10196	1145	40	1	8541	1	NBEA	13	36239245	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	2558240	36239245	78930633	649	34941										
KBTBD7	84078	hgsc.bcm.edu	37	chr13	41768100	41768100	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tacatgccacctgtgaacatGctcttgaagtagggacacgc	10	11	1	2	rs138677495		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:41768100G>T	ENST00000379483.3	-	1	602	c.294C>A	c.(292-294)agC>agA	p.S98R		NM_032138.4	NP_115514.2	Q8WVZ9	KBTB7_HUMAN	kelch repeat and BTB (POZ) domain containing 7	98	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.									central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(8)|ovary(4)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24		Lung NSC(96;0.000105)|Breast(139;0.00715)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.21e-09)|Epithelial(112;6.99e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000196)|GBM - Glioblastoma multiforme(144;0.000857)|BRCA - Breast invasive adenocarcinoma(63;0.0669)		CTGTGAACATGCTCTTGAAGT	0.607																																					p.S98R		Atlas-SNP	.											.	KBTBD7	60	.	0			c.C294A						.						83	55	64					13																	41768100		2203	4300	6503	SO:0001583	missense	84078	exon1			GAACATGCTCTTG	AL136782	CCDS9377.1	13q13.3	2013-01-08			ENSG00000120696	ENSG00000120696		"BTB/POZ domain containing"	25266	protein-coding gene	gene with protein product						11230166	Standard	NM_032138		Approved	DKFZP434E2318	uc001uxw.1	Q8WVZ9	OTTHUMG00000016789	ENST00000379483.3:c.294C>A	chr13.hg19:g.41768100G>T	ENSP00000368797:p.Ser98Arg	153.0	0.0		99.0	4.0	NM_032138	B5TZ86|Q5T6Y7|Q8NB99|Q9H0I6	Missense_Mutation	SNP	ENST00000379483.3	hg19	CCDS9377.1	.	.	.	.	.	.	.	.	.	.	G	16.79	3.221378	0.58560	.	.	ENSG00000120696	ENST00000379483	T	0.68025	-0.3	4.79	3.04	0.35103	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	U	0.000000	T	0.78033	0.4220	M	0.72894	2.215	0.45979	D	0.99879	D	0.89917	1.0	D	0.91635	0.999	T	0.77490	-0.2568	10	0.87932	D	0	.	9.5678	0.39409	0.178:0.0:0.822:0.0	.	98	Q8WVZ9	KBTB7_HUMAN	R	98	ENSP00000368797:S98R	ENSP00000368797:S98R	S	-	3	2	KBTBD7	40666100	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.262000	0.58847	0.534000	0.28695	0.563000	0.77884	AGC	.	G|1.000;A|0.000		0.607	KBTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044660.1	NM_032138		T	41768100	G	T	41768100	3	4	254	1	0	0	0	0	1	0	0	0	8007	1310	46	3	1764	3	KBTBD7	13	41768100	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	5528855	41768100	73401778	650	34942										
COG3	83548	hgsc.bcm.edu	37	chr13	46085936	46085936	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gattatcacaggaagcattgTctgcctgcattcagtcctta	8	10	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:46085936T>C	ENST00000349995.5	+	16	1868	c.1756T>C	c.(1756-1758)Tct>Cct	p.S586P	COG3_ENST00000465942.1_3'UTR	NM_031431.3	NP_113619	Q96JB2	COG3_HUMAN	component of oligomeric golgi complex 3	586					ER to Golgi vesicle-mediated transport (GO:0006888)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|stomach(1)	24		Lung NSC(96;0.000145)|Breast(56;0.000596)|Prostate(109;0.00438)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000124)		GGAAGCATTGTCTGCCTGCAT	0.398																																					p.S586P	Ovarian(150;1048 1859 18083 21577 42700)	Atlas-SNP	.											.	COG3	52	.	0			c.T1756C						.						136	122	127					13																	46085936		2203	4300	6503	SO:0001583	missense	83548	exon16			GCATTGTCTGCCT	AF131829	CCDS9398.1	13q14.11	2008-02-05			ENSG00000136152	ENSG00000136152		"Components of oligomeric golgi complex"	18619	protein-coding gene	gene with protein product		606975				11980916	Standard	NM_031431		Approved	SEC34	uc001vak.3	Q96JB2	OTTHUMG00000016855	ENST00000349995.5:c.1756T>C	chr13.hg19:g.46085936T>C	ENSP00000258654:p.Ser586Pro	105.0	0.0		91.0	5.0	NM_031431	B2RAW5|Q5VT70|Q8IXX4|Q9BZ92	Missense_Mutation	SNP	ENST00000349995.5	hg19	CCDS9398.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.030526	0.75504	.	.	ENSG00000136152	ENST00000349995	T	0.46819	0.86	5.41	4.22	0.49857	.	0.110324	0.64402	D	0.000004	T	0.59046	0.2165	M	0.79475	2.455	0.80722	D	1	P;D	0.67145	0.653;0.996	B;P	0.53912	0.243;0.737	T	0.59606	-0.7423	10	0.31617	T	0.26	-10.3941	12.056	0.53536	0.0:0.0:0.144:0.8559	.	423;586	B4E2F3;Q96JB2	.;COG3_HUMAN	P	586	ENSP00000258654:S586P	ENSP00000258654:S586P	S	+	1	0	COG3	44983937	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.814000	0.69208	1.058000	0.40530	0.482000	0.46254	TCT	.	.		0.398	COG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044777.2			C	46085936	T	C	46085936	3	2	254	1	0	0	0	0	1	0	0	0	3661	1667	58	2	1818	2	COG3	13	46085936	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	4317836	46085936	69083942	651	34943										
INTS6	26512	hgsc.bcm.edu	37	chr13	51961531	51961531	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctggtacttactagtgttggCgaattttgatctggccaaaa	10	7	1	1	rs142545429		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:51961531C>A	ENST00000311234.4	-	7	1357	c.885G>T	c.(883-885)tcG>tcT	p.S295S	INTS6_ENST00000425000.1_5'UTR|INTS6_ENST00000490542.1_5'Flank|INTS6_ENST00000420668.2_3'UTR|INTS6_ENST00000497989.1_Silent_p.S117S|INTS6_ENST00000398119.2_Silent_p.S282S|INTS6_ENST00000463928.1_Intron	NM_012141.2	NP_036273.1	Q9UL03	INT6_HUMAN	integrator complex subunit 6	295					signal transduction (GO:0007165)|snRNA processing (GO:0016180)	actin cytoskeleton (GO:0015629)|integrator complex (GO:0032039)|nucleus (GO:0005634)	transmembrane signaling receptor activity (GO:0004888)	p.S295S(1)		NS(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31		Breast(56;0.000286)|Lung NSC(96;0.00145)|Prostate(109;0.00403)|Hepatocellular(98;0.065)|Myeloproliferative disorder(33;0.163)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;7.7e-08)		CTAGTGTTGGCGAATTTTGAT	0.378																																					p.S295S		Atlas-SNP	.											INTS6,NS,carcinoma,-1,1	INTS6	72	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G885T						.						95	87	90					13																	51961531		2203	4300	6503	SO:0001819	synonymous_variant	26512	exon7			TGTTGGCGAATTT	AF097645	CCDS9428.1, CCDS41890.1, CCDS45048.1	13q14.3	2010-08-20	2006-03-15	2006-03-15	ENSG00000102786	ENSG00000102786		"DEAD-boxes"	14879	protein-coding gene	gene with protein product		604331	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 26"	DDX26		10467397, 16239144	Standard	XM_005266340		Approved	DICE1, HDB, Notchl2, DBI-1, DDX26A, INT6	uc001vfk.3	Q9UL03	OTTHUMG00000016945	ENST00000311234.4:c.885G>T	chr13.hg19:g.51961531C>A		68.0	0.0		57.0	3.0	NM_012141	Q0P664|Q6PJP4|Q9UFK0|Q9Y5M9	Silent	SNP	ENST00000311234.4	hg19	CCDS9428.1																																																																																			.	C|1.000;T|0.000		0.378	INTS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045023.1	NM_012141		A	51961531	C	A	51961531	2	1	254	1	0	0	0	0	0	0	0	1	7791	755	27	1		1	INTS6	13	51961531	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	5875595	51961531	63208347	652	34944										
ATP7B	540	hgsc.bcm.edu	37	chr13	52539142	52539142	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tttggactctatgttgtggaCacaggacgcgcaggtcatcc	12	10	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:52539142C>T	ENST00000242839.4	-	5	1891	c.1735G>A	c.(1735-1737)Gtc>Atc	p.V579I	ATP7B_ENST00000542656.1_Intron|ATP7B_ENST00000448424.2_Missense_Mutation_p.V579I|ATP7B_ENST00000400366.3_Missense_Mutation_p.V468I|ATP7B_ENST00000344297.5_Missense_Mutation_p.V579I|ATP7B_ENST00000400370.3_Intron|ATP7B_ENST00000482841.1_5'UTR|ATP7B_ENST00000418097.2_Missense_Mutation_p.V579I	NM_000053.3	NP_000044.2	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	579	HMA 6. {ECO:0000255|PROSITE- ProRule:PRU00280}.				cellular copper ion homeostasis (GO:0006878)|cellular zinc ion homeostasis (GO:0006882)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|intracellular copper ion transport (GO:0015680)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|response to copper ion (GO:0046688)|sequestering of calcium ion (GO:0051208)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|mitochondrion (GO:0005739)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper-exporting ATPase activity (GO:0004008)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(23)|ovary(1)|prostate(3)|skin(4)|stomach(2)	55		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)	Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	ATGTTGTGGACACAGGACGCG	0.527									Wilson disease																												p.V579I		Atlas-SNP	.											.	ATP7B	123	.	0			c.G1735A						.						87	89	89					13																	52539142		2064	4209	6273	SO:0001583	missense	540	exon5	Familial Cancer Database		TGTGGACACAGGA	U11700	CCDS41892.1, CCDS45049.1, CCDS58293.1	13q14.3	2012-10-22	2005-11-29		ENSG00000123191	ENSG00000123191	3.6.3.4	"ATPases / P-type"	870	protein-coding gene	gene with protein product	"Wilson disease", "copper pump 2", "copper-transporting ATPase 2"	606882	"ATPase, Cu++ transporting, beta polypeptide (Wilson disease)"	WND		8298641, 8298639	Standard	NM_000053		Approved		uc001vfw.2	P35670	OTTHUMG00000017406	ENST00000242839.4:c.1735G>A	chr13.hg19:g.52539142C>T	ENSP00000242839:p.Val579Ile	108.0	0.0		88.0	4.0	NM_000053	Q16318|Q16319|Q4U3V3|Q59FJ9|Q5T7X7	Missense_Mutation	SNP	ENST00000242839.4	hg19	CCDS41892.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.761702	0.89932	.	.	ENSG00000123191	ENST00000242839;ENST00000400366;ENST00000344297;ENST00000448424;ENST00000418097	D;D;D;D;D	0.86694	-2.16;-2.16;-2.16;-2.16;-2.16	5.95	5.95	0.96441	Heavy metal-associated domain, HMA (3);Heavy metal-associated domain, copper ion-binding (1);Heavy-metal-associated, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.94578	0.8253	M	0.85630	2.765	0.80722	D	1	B;B;D;P;P;B	0.76494	0.016;0.407;0.999;0.937;0.868;0.037	B;B;D;P;P;B	0.85130	0.013;0.33;0.997;0.72;0.513;0.174	D	0.94398	0.7620	10	0.72032	D	0.01	-29.5788	20.3932	0.98965	0.0:1.0:0.0:0.0	.	579;579;579;468;579;579	E7ET55;B7ZLR4;F5H748;P35670-3;P35670-2;P35670	.;.;.;.;.;ATP7B_HUMAN	I	579;468;579;579;579	ENSP00000242839:V579I;ENSP00000383217:V468I;ENSP00000342559:V579I;ENSP00000416738:V579I;ENSP00000393343:V579I	ENSP00000242839:V579I	V	-	1	0	ATP7B	51437143	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.735000	0.68587	2.824000	0.97209	0.655000	0.94253	GTC	.	.		0.527	ATP7B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045981.1	NM_000053		T	52539142	C	T	52539142	3	4	254	1	0	0	0	0	1	0	0	0	1191	478	17	3	2730	3	ATP7B	13	52539142	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	577611	52539142	62630736	653	34945										
PCDH20	64881	hgsc.bcm.edu	37	chr13	61987996	61987996	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccaggctgccgatgagcaccCccgcgggtagtccctcgttt	12	16	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:61987996C>A	ENST00000409186.1	-	5	2341	c.236G>T	c.(235-237)gGg>gTg	p.G79V	PCDH20_ENST00000409204.4_Missense_Mutation_p.G79V			Q8N6Y1	PCD20_HUMAN	protocadherin 20	79	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(14)|liver(1)|lung(23)|ovary(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	58		Breast(118;0.195)|Prostate(109;0.229)		GBM - Glioblastoma multiforme(99;0.000118)		GATGAGCACCCCCGCGGGTAG	0.662																																					p.G79V		Atlas-SNP	.											.	PCDH20	265	.	0			c.G236T						.						14	15	14					13																	61987996		2195	4289	6484	SO:0001583	missense	64881	exon2			AGCACCCCCGCGG	AF169693	CCDS9442.2	13q21	2010-01-26			ENSG00000197991	ENSG00000197991		"Cadherins / Protocadherins : Non-clustered"	14257	protein-coding gene	gene with protein product		614449					Standard	NM_022843		Approved	PCDH13, FLJ22218	uc001vid.4	Q8N6Y1	OTTHUMG00000017012	ENST00000409186.1:c.236G>T	chr13.hg19:g.61987996C>A	ENSP00000386653:p.Gly79Val	102.0	0.0		83.0	4.0	NM_022843	A8K1K9|B1AQU2|Q8NDN4|Q9NRT9	Missense_Mutation	SNP	ENST00000409186.1	hg19	CCDS9442.2	.	.	.	.	.	.	.	.	.	.	c	29.1	4.976742	0.92982	.	.	ENSG00000197991	ENST00000409204;ENST00000409186	T;T	0.60548	0.18;0.18	5.19	5.19	0.71726	.	0.000000	0.64402	D	0.000015	D	0.83830	0.5339	H	0.95224	3.64	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89023	0.3436	10	0.87932	D	0	.	18.6958	0.91600	0.0:1.0:0.0:0.0	.	79	A8K1K9	.	V	79	ENSP00000387250:G79V;ENSP00000386653:G79V	ENSP00000386653:G79V	G	-	2	0	PCDH20	60885997	1.000000	0.71417	0.906000	0.35671	0.982000	0.71751	7.507000	0.81676	2.413000	0.81919	0.591000	0.81541	GGG	.	.		0.662	PCDH20-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333054.2	NM_022843		A	61987996	C	A	61987996	3	1	254	1	0	0	0	0	1	0	0	0	11524	623	22	3	2623	3	PCDH20	13	61987996	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	9448854	61987996	53181882	654	34946										
KLF12	11278	hgsc.bcm.edu	37	chr13	74420058	74420058	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gctgtgtagacaacaggcacCgactgtaccaccacggggat	12	12	0	1	rs200955639		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:74420058C>A	ENST00000377669.2	-	3	602	c.576G>T	c.(574-576)tcG>tcT	p.S192S	KLF12_ENST00000377666.4_Silent_p.S192S|KLF12_ENST00000472022.1_5'UTR	NM_007249.4	NP_009180.3	Q9Y4X4	KLF12_HUMAN	Kruppel-like factor 12	192					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.S192S(1)		central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	16		Prostate(6;0.00217)|Breast(118;0.0838)		GBM - Glioblastoma multiforme(99;0.00677)		CAACAGGCACCGACTGTACCA	0.488																																					p.S192S		Atlas-SNP	.											.	KLF12	42	.	1	Substitution - coding silent(1)	lung(1)	c.G576T						.						122	101	108					13																	74420058		2203	4300	6503	SO:0001819	synonymous_variant	11278	exon4			AGGCACCGACTGT	AJ243274	CCDS9449.1	13q22	2013-01-08			ENSG00000118922	ENSG00000118922		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	6346	protein-coding gene	gene with protein product	"KLF12 zinc finger transcriptional repressor", "AP-2rep transcription factor", "AP-2 repressor"	607531				10704285	Standard	NM_007249		Approved	AP-2rep, HSPC122, AP2REP	uc001vjf.3	Q9Y4X4	OTTHUMG00000017078	ENST00000377669.2:c.576G>T	chr13.hg19:g.74420058C>A		166.0	0.0		137.0	7.0	NM_007249	A8K5T2|L0R3J4|Q5VZM7|Q9UHZ0	Silent	SNP	ENST00000377669.2	hg19	CCDS9449.1																																																																																			.	C|1.000;T|0.000		0.488	KLF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045271.2	NM_007249		A	74420058	C	A	74420058	2	1	254	1	0	0	0	0	0	0	0	1	8349	639	23	1		1	KLF12	13	74420058	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	12432062	74420058	40749820	655	34947										
POU4F1	5457	hgsc.bcm.edu	37	chr13	79175920	79175920	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtgagcccacgcccgggatcTtgaggttggccagcgccgag	16	13	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:79175920T>C	ENST00000377208.5	-	2	1101	c.890A>G	c.(889-891)aAg>aGg	p.K297R	RNF219-AS1_ENST00000430549.2_RNA|RNF219-AS1_ENST00000606376.1_RNA|RNF219-AS1_ENST00000607220.1_RNA|RNF219-AS1_ENST00000607860.1_RNA|RP11-52L5.6_ENST00000607269.1_RNA|RNF219-AS1_ENST00000444769.3_RNA|RNF219-AS1_ENST00000607205.1_RNA|RNF219-AS1_ENST00000560584.2_RNA|RNF219-AS1_ENST00000606124.1_RNA|RNF219-AS1_ENST00000560209.2_RNA|RNF219-AS1_ENST00000606429.1_RNA	NM_006237.3	NP_006228.3	Q01851	PO4F1_HUMAN	POU class 4 homeobox 1	297	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.				axonogenesis (GO:0007409)|cell migration in hindbrain (GO:0021535)|central nervous system neuron differentiation (GO:0021953)|habenula development (GO:0021986)|innervation (GO:0060384)|mesoderm development (GO:0007498)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron fate specification (GO:0048665)|peripheral nervous system neuron development (GO:0048935)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proprioception involved in equilibrioception (GO:0051355)|regulation of neurogenesis (GO:0050767)|sensory system development (GO:0048880)|suckling behavior (GO:0001967)|synapse assembly (GO:0007416)|transcription from RNA polymerase II promoter (GO:0006366)|trigeminal nerve development (GO:0021559)|ventricular compact myocardium morphogenesis (GO:0003223)	neuron projection (GO:0043005)|nuclear chromatin (GO:0000790)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)			central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(5)|ovary(1)	16		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.129)		GCCCGGGATCTTGAGGTTGGC	0.667																																					p.K297R	Melanoma(109;347 2166 14574 42843)|Ovarian(81;1394 1854 22417 48351)	Atlas-SNP	.											.	POU4F1	43	.	0			c.A890G						.						33	30	31					13																	79175920		2202	4300	6502	SO:0001583	missense	5457	exon2			GGGATCTTGAGGT	X64624	CCDS31996.1	13q31.1	2011-06-20	2007-07-13		ENSG00000152192	ENSG00000152192		"Homeoboxes / POU class"	9218	protein-coding gene	gene with protein product		601632	"POU domain class 4, transcription factor 1"	BRN3A		1357630	Standard	NM_006237		Approved	RDC-1	uc001vkv.3	Q01851	OTTHUMG00000017119	ENST00000377208.5:c.890A>G	chr13.hg19:g.79175920T>C	ENSP00000366413:p.Lys297Arg	126.0	0.0		91.0	4.0	NM_006237	Q14986|Q15318|Q5T227	Missense_Mutation	SNP	ENST00000377208.5	hg19	CCDS31996.1	.	.	.	.	.	.	.	.	.	.	T	13.92	2.381290	0.42207	.	.	ENSG00000152192	ENST00000377208	D	0.83673	-1.75	3.21	3.21	0.36854	POU-specific (3);Lambda repressor-like, DNA-binding (2);	0.000000	0.85682	U	0.000000	D	0.86965	0.6060	L	0.59912	1.85	0.53688	D	0.999971	D	0.65815	0.995	D	0.64410	0.925	D	0.87137	0.2200	10	0.59425	D	0.04	.	10.9225	0.47174	0.0:0.0:0.0:1.0	.	297	Q01851	PO4F1_HUMAN	R	297	ENSP00000366413:K297R	ENSP00000366413:K297R	K	-	2	0	POU4F1	78073921	1.000000	0.71417	1.000000	0.80357	0.832000	0.47134	7.606000	0.82863	1.473000	0.48159	0.323000	0.21402	AAG	.	.		0.667	POU4F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045360.3			C	79175920	T	C	79175920	3	2	254	1	0	0	0	0	1	0	0	0	12287	1609	56	2	373	2	POU4F1	13	79175920	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	4755862	79175920	35993958	656	34948										
DOCK9	23348	hgsc.bcm.edu	37	chr13	99536145	99536145	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tctacccatttaatttccggAccataatgctaaaaaaaata	3	9	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:99536145A>G	ENST00000376460.1	-	22	2471	c.2391T>C	c.(2389-2391)ggT>ggC	p.G797G	DOCK9_ENST00000448493.2_Silent_p.G809G|DOCK9_ENST00000442173.1_Silent_p.G797G|DOCK9_ENST00000339416.2_Silent_p.G798G	NM_001130048.1|NM_015296.2	NP_001123520.1|NP_056111.1	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9	798	DHR-1.				blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(18)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					TAATTTCCGGACCATAATGCT	0.373																																					p.G798G		Atlas-SNP	.											.	DOCK9	311	.	0			c.T2394C						.						56	55	55					13																	99536145		1846	4090	5936	SO:0001819	synonymous_variant	23348	exon22			TTCCGGACCATAA	AF527605	CCDS45062.1	13q32.3	2013-01-10			ENSG00000088387	ENSG00000088387		"Pleckstrin homology (PH) domain containing"	14132	protein-coding gene	gene with protein product	"zizimin1"	607325				12172552, 12432077	Standard	NM_015296		Approved	KIAA1058, ZIZ1	uc001vnt.2	Q9BZ29	OTTHUMG00000017260	ENST00000376460.1:c.2391T>C	chr13.hg19:g.99536145A>G		73.0	0.0		72.0	4.0	NM_001130049	B3KX25|E9PFM9|Q5JUD4|Q5JUD6|Q5T2Q1|Q5TAN8|Q9BZ25|Q9BZ26|Q9BZ27|Q9BZ28|Q9UPU4	Silent	SNP	ENST00000376460.1	hg19	CCDS45062.1																																																																																			.	.		0.373	DOCK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045566.1	NM_015296		G	99536145	A	G	99536145	2	3	254	1	0	0	0	0	0	0	0	1	4696	262	10	2		2	DOCK9	13	99536145	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	20360225	99536145	15633733	657	34949										
COL4A1	1282	hgsc.bcm.edu	37	chr13	110831299	110831299	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccggtggtccctgtcctccaGggggacccctagctccaggg	14	16	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:110831299G>T	ENST00000375820.4	-	31	2550	c.2429C>A	c.(2428-2430)cCt>cAt	p.P810H		NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	810	Triple-helical region.				axon guidance (GO:0007411)|basement membrane organization (GO:0071711)|blood vessel morphogenesis (GO:0048514)|brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)|patterning of blood vessels (GO:0001569)|renal tubule morphogenesis (GO:0061333)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)|platelet-derived growth factor binding (GO:0048407)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	105	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			CTGTCCTCCAGGGGGACCCCT	0.572																																					p.P810H		Atlas-SNP	.											.	COL4A1	372	.	0			c.C2429A						.						15	17	16					13																	110831299		2202	4298	6500	SO:0001583	missense	1282	exon31			CCTCCAGGGGGAC	J04217	CCDS9511.1	13q34	2013-09-05			ENSG00000187498	ENSG00000187498		"Collagens"	2202	protein-coding gene	gene with protein product		120130				3691802	Standard	NM_001845		Approved		uc001vqw.4	P02462	OTTHUMG00000017342	ENST00000375820.4:c.2429C>A	chr13.hg19:g.110831299G>T	ENSP00000364979:p.Pro810His	69.0	0.0		52.0	4.0	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Missense_Mutation	SNP	ENST00000375820.4	hg19	CCDS9511.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.480937	0.84747	.	.	ENSG00000187498	ENST00000375820	D	0.98701	-5.08	4.89	4.89	0.63831	.	0.206902	0.43260	D	0.000594	D	0.99312	0.9759	M	0.92219	3.285	0.80722	D	1	D	0.76494	0.999	D	0.75484	0.986	D	0.98931	1.0787	10	0.54805	T	0.06	.	17.4237	0.87521	0.0:0.0:1.0:0.0	.	810	P02462	CO4A1_HUMAN	H	810	ENSP00000364979:P810H	ENSP00000364979:P810H	P	-	2	0	COL4A1	109629300	1.000000	0.71417	0.999000	0.59377	0.928000	0.56348	5.705000	0.68355	2.431000	0.82371	0.655000	0.94253	CCT	.	.		0.572	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3			T	110831299	G	T	110831299	3	4	254	1	0	0	0	0	1	0	0	0	3691	1000	35	3	2668	3	COL4A1	13	110831299	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	11295154	110831299	4338579	658	34950										
COL4A2	1284	hgsc.bcm.edu	37	chr13	111144454	111144454	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gggcctccagggtcgcagggAgagctggggcggattggact	20	9	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:111144454A>G	ENST00000360467.5	+	38	3798	c.3492A>G	c.(3490-3492)ggA>ggG	p.G1164G		NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	1164	Triple-helical region.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	extracellular matrix structural constituent (GO:0005201)			NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	80	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			GGTCGCAGGGAGAGCTGGGGC	0.612																																					p.G1164G		Atlas-SNP	.											.	COL4A2	178	.	0			c.A3492G						.						28	38	34					13																	111144454		1946	4068	6014	SO:0001819	synonymous_variant	1284	exon38			GCAGGGAGAGCTG	AK025912	CCDS41907.1	13q34	2013-09-05			ENSG00000134871	ENSG00000134871		"Collagens"	2203	protein-coding gene	gene with protein product	"canstatin", "collagen type IV alpha 2"	120090				2439508, 3025878	Standard	NM_001846		Approved	FLJ22259, DKFZp686I14213	uc001vqx.3	P08572	OTTHUMG00000017344	ENST00000360467.5:c.3492A>G	chr13.hg19:g.111144454A>G		84.0	0.0		57.0	4.0	NM_001846	Q14052|Q548C3|Q5VZA9|Q66K23	Silent	SNP	ENST00000360467.5	hg19	CCDS41907.1																																																																																			.	.		0.612	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846		G	111144454	A	G	111144454	2	3	254	1	0	0	0	0	0	0	0	1	3692	291	11	2		2	COL4A2	13	111144454	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	313155	111144454	4025424	659	34951										
TUBGCP3	10426	hgsc.bcm.edu	37	chr13	113174218	113174218	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	acctccagcagccgcacgtcCagccttcgcaggatctcagg	10	17	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:113174218C>T	ENST00000261965.3	-	15	2049	c.1863G>A	c.(1861-1863)ctG>ctA	p.L621L	TUBGCP3_ENST00000462580.1_5'Flank|TUBGCP3_ENST00000375669.3_Silent_p.L621L	NM_006322.4	NP_006313.1	Q96CW5	GCP3_HUMAN	tubulin, gamma complex associated protein 3	621					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|single fertilization (GO:0007338)	centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|polar microtubule (GO:0005827)|spindle (GO:0005819)	gamma-tubulin binding (GO:0043015)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|prostate(3)|urinary_tract(1)	25	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)					GCCGCACGTCCAGCCTTCGCA	0.582																																					p.L621L		Atlas-SNP	.											.	TUBGCP3	74	.	0			c.G1863A						.						92	92	92					13																	113174218		2203	4300	6503	SO:0001819	synonymous_variant	10426	exon15			CACGTCCAGCCTT	AF042378	CCDS9525.1, CCDS66584.1, CCDS73599.1	13q34	2008-07-18			ENSG00000126216	ENSG00000126216			18598	protein-coding gene	gene with protein product	"spindle pole body protein"					9566967, 9566969	Standard	XM_005268293		Approved	GCP3, Spc98p, SPBC98	uc001vse.1	Q96CW5	OTTHUMG00000017367	ENST00000261965.3:c.1863G>A	chr13.hg19:g.113174218C>T		97.0	0.0		92.0	4.0	NM_006322	O43631|O60852|O60853|Q5T8L2|Q7Z4K1|Q96I79	Silent	SNP	ENST00000261965.3	hg19	CCDS9525.1																																																																																			.	.		0.582	TUBGCP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045825.2	NM_006322		T	113174218	C	T	113174218	2	4	254	1	0	0	0	0	0	0	0	1	16782	581	21	3		3	TUBGCP3	13	113174218	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	2029764	113174218	1995660	660	34952										
ATP11A	23250	hgsc.bcm.edu	37	chr13	113512575	113512575	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	atttttattacattaggatcTctgagctcgtgcagtacttc	7	8	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:113512575T>C	ENST00000487903.1	+	22	2726	c.2638T>C	c.(2638-2640)Tct>Cct	p.S880P	ATP11A_ENST00000375630.2_Missense_Mutation_p.S880P|ATP11A_ENST00000375645.3_Missense_Mutation_p.S880P|ATP11A_ENST00000283558.8_Missense_Mutation_p.S880P			P98196	AT11A_HUMAN	ATPase, class VI, type 11A	880					phospholipid translocation (GO:0045332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(12)|lung(17)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	51	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)				CATTAGGATCTCTGAGCTCGT	0.522																																					p.S880P		Atlas-SNP	.											.	ATP11A	225	.	0			c.T2638C						.						94	92	93					13																	113512575		2203	4300	6503	SO:0001583	missense	23250	exon22			AGGATCTCTGAGC	AB028944	CCDS32011.1	13q34	2010-04-20	2007-09-19		ENSG00000068650	ENSG00000068650	3.6.3.1	"ATPases / P-type"	13552	protein-coding gene	gene with protein product	"potential phospholipid-transporting ATPase IH", "phospholipid-translocating ATPase"	605868	"ATPase, Class VI, type 11A"			11015572	Standard	NM_032189		Approved	ATPIH, ATPIS, KIAA1021	uc001vsj.4	P98196	OTTHUMG00000017371	ENST00000487903.1:c.2638T>C	chr13.hg19:g.113512575T>C	ENSP00000420387:p.Ser880Pro	168.0	0.0		121.0	5.0	NM_032189	Q5VXT2	Missense_Mutation	SNP	ENST00000487903.1	hg19	CCDS32011.1	.	.	.	.	.	.	.	.	.	.	T	15.69	2.907221	0.52333	.	.	ENSG00000068650	ENST00000487903;ENST00000375630;ENST00000375645;ENST00000283558;ENST00000432166	T;T;T;T	0.60299	0.2;0.2;0.2;0.2	5.62	-2.64	0.06114	.	0.220919	0.47852	D	0.000217	T	0.70413	0.3221	M	0.91090	3.175	0.45390	D	0.998376	P;P;B	0.45715	0.865;0.559;0.18	P;P;P	0.49192	0.544;0.602;0.474	T	0.81446	-0.0929	10	0.66056	D	0.02	.	16.7801	0.85561	0.0:0.0:0.5845:0.4155	.	880;880;880	E9PCW5;E9PEJ6;P98196	.;.;AT11A_HUMAN	P	880;880;880;880;321	ENSP00000420387:S880P;ENSP00000364781:S880P;ENSP00000364796:S880P;ENSP00000283558:S880P	ENSP00000283558:S880P	S	+	1	0	ATP11A	112560576	0.991000	0.36638	0.003000	0.11579	0.294000	0.27393	1.459000	0.35234	-0.241000	0.09681	0.533000	0.62120	TCT	.	.		0.522	ATP11A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045834.3	NM_015205		C	113512575	T	C	113512575	3	2	254	1	0	0	0	0	1	0	0	0	1119	1551	54	2	2724	2	ATP11A	13	113512575	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	338357	113512575	1657303	661	34953										
RASA3	22821	hgsc.bcm.edu	37	chr13	114780788	114780788	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	atggcgtggaagacgcggtcCacatactgccgtaggttctc	13	11	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:114780788C>T	ENST00000334062.7	-	14	1423	c.1302G>A	c.(1300-1302)gtG>gtA	p.V434V	RASA3_ENST00000389544.4_Silent_p.V402V	NM_007368.2	NP_031394.2	Q14644	RASA3_HUMAN	RAS p21 protein activator 3	434	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				calcium ion transmembrane transport (GO:0070588)|intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	calcium-release channel activity (GO:0015278)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|Ras GTPase activator activity (GO:0005099)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(20)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	47	Lung NSC(43;0.00814)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.016)|all_epithelial(44;0.00577)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.188)	BRCA - Breast invasive adenocarcinoma(86;0.128)			AGACGCGGTCCACATACTGCC	0.662																																					p.V434V		Atlas-SNP	.											.	RASA3	83	.	0			c.G1302A						.						109	91	97					13																	114780788		2203	4299	6502	SO:0001819	synonymous_variant	22821	exon14			GCGGTCCACATAC		CCDS32016.1	13q34	2013-01-10			ENSG00000185989	ENSG00000185989		"Pleckstrin homology (PH) domain containing"	20331	protein-coding gene	gene with protein product		605182				7637787, 9382842	Standard	NM_007368		Approved	GAP1IP4BP, GAPIII	uc001vui.3	Q14644	OTTHUMG00000017399	ENST00000334062.7:c.1302G>A	chr13.hg19:g.114780788C>T		81.0	0.0		59.0	4.0	NM_007368	A6NL15|F8W6X8|Q8IUY2	Silent	SNP	ENST00000334062.7	hg19	CCDS32016.1																																																																																			.	.		0.662	RASA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045957.2	NM_007368		T	114780788	C	T	114780788	2	4	254	1	0	0	0	0	0	0	0	1	13077	581	21	3		3	RASA3	13	114780788	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1268213	114780788	389090	662	34954										
CDC16	8881	hgsc.bcm.edu	37	chr13	115002339	115002339	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cagcacaatatcacagagccGcccatgcacttcggtcacga	8	15	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr13:115002339G>T	ENST00000356221.3	+	3	277	c.169G>T	c.(169-171)Gcc>Tcc	p.A57S	CDC16_ENST00000375308.1_5'UTR|CDC16_ENST00000375312.3_5'UTR|CDC16_ENST00000375310.1_5'UTR|CDC16_ENST00000252458.6_5'UTR|CDC16_ENST00000252457.5_Missense_Mutation_p.A56S|CDC16_ENST00000360383.3_Missense_Mutation_p.A57S			Q13042	CDC16_HUMAN	cell division cycle 16	57					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of mitosis (GO:0007088)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|spindle (GO:0005819)				endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)			TCACAGAGCCGCCCATGCACT	0.453																																					p.A57S		Atlas-SNP	.											.	CDC16	50	.	0			c.G169T						.						83	80	81					13																	115002339		2203	4300	6503	SO:0001583	missense	8881	exon3			AGAGCCGCCCATG	U18291	CCDS9542.2	13q34	2013-01-17	2013-01-17		ENSG00000130177	ENSG00000130177		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1720	protein-coding gene	gene with protein product	"anaphase-promoting complex, subunit 6"	603461	"CDC16 (cell division cycle 16, S. cerevisiae, homolog)", "CDC16 cell division cycle 16 homolog (S. cerevisiae)", "cell division cycle 16 homolog (S. cerevisiae)"			7736578	Standard	NM_001078645		Approved	APC6, ANAPC6, CUT9	uc001vul.1	Q13042	OTTHUMG00000017402	ENST00000356221.3:c.169G>T	chr13.hg19:g.115002339G>T	ENSP00000348554:p.Ala57Ser	116.0	0.0		90.0	4.0	NM_003903	A2A365|Q5T8C8|Q96AE6|Q9Y564	Missense_Mutation	SNP	ENST00000356221.3	hg19	CCDS9542.2	.	.	.	.	.	.	.	.	.	.	G	5.183	0.219273	0.09863	.	.	ENSG00000130177	ENST00000360383;ENST00000356221;ENST00000252457	T;T;T	0.38240	1.15;1.15;1.15	5.29	5.29	0.74685	Tetratricopeptide-like helical (1);	0.050215	0.85682	D	0.000000	T	0.20941	0.0504	N	0.10972	0.075	0.80722	D	1	B;B;B;B	0.19445	0.036;0.005;0.002;0.009	B;B;B;B	0.25506	0.058;0.026;0.026;0.061	T	0.09509	-1.0671	9	.	.	.	-4.5644	13.1066	0.59252	0.0:0.0:0.84:0.1599	.	57;56;56;57	B4DK74;Q13042-3;Q13042-2;Q13042	.;.;.;CDC16_HUMAN	S	57;57;56	ENSP00000353549:A57S;ENSP00000348554:A57S;ENSP00000252457:A56S	.	A	+	1	0	CDC16	114020441	1.000000	0.71417	1.000000	0.80357	0.038000	0.13279	4.801000	0.62532	2.756000	0.94617	0.561000	0.74099	GCC	.	.		0.453	CDC16-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276737.1	NM_003903		T	115002339	G	T	115002339	3	4	254	1	0	0	0	0	1	0	0	0	3060	1087	38	1	179	1	CDC16	13	115002339	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	221551	115002339	167539	663	34955										
OR4K14	122740	hgsc.bcm.edu	37	chr14	20483233	20483233	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	accaaaatgagaaggttaccCagcataatggccacatagac	8	10	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:20483233C>A	ENST00000305045.2	-	1	119	c.120G>T	c.(118-120)ctG>ctT	p.L40L		NM_001004712.1	NP_001004712.1	Q8NGD5	OR4KE_HUMAN	olfactory receptor, family 4, subfamily K, member 14	40						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(20)|skin(6)	37	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2e-06)	GBM - Glioblastoma multiforme(265;0.00124)		GAAGGTTACCCAGCATAATGG	0.448																																					p.L40L		Atlas-SNP	.											.	OR4K14	86	.	0			c.G120T						.						73	68	70					14																	20483233		2203	4300	6503	SO:0001819	synonymous_variant	122740	exon1			GTTACCCAGCATA		CCDS32027.1	14q11.2	2013-09-23			ENSG00000169484	ENSG00000169484		"GPCR / Class A : Olfactory receptors"	15352	protein-coding gene	gene with protein product							Standard	NM_001004712		Approved		uc010tky.2	Q8NGD5	OTTHUMG00000170780	ENST00000305045.2:c.120G>T	chr14.hg19:g.20483233C>A		296.0	0.0		224.0	78.0	NM_001004712	Q6IEU1|Q96R71	Silent	SNP	ENST00000305045.2	hg19	CCDS32027.1																																																																																			.	.		0.448	OR4K14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410343.1			A	20483233	C	A	20483233	2	1	254	1	0	0	0	0	0	0	0	1	11078	581	21	3		3	OR4K14	14	20483233	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10		20483233	86866307	664	34956										
TEP1	7011	hgsc.bcm.edu	37	chr14	20848600	20848600	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aacactgcaacgtcagcctcGgggagcttttgttcctcttt	9	12	2	0	rs200043242		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:20848600G>T	ENST00000262715.5	-	34	4837	c.4797C>A	c.(4795-4797)ccC>ccA	p.P1599P	TEP1_ENST00000545983.1_5'UTR|TEP1_ENST00000556935.1_Silent_p.P1491P	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1599					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		CGTCAGCCTCGGGGAGCTTTT	0.587																																					p.P1599P		Atlas-SNP	.											TEP1,bladder,carcinoma,0,1	TEP1	224	.	0			c.C4797A						.						50	51	51					14																	20848600		2203	4300	6503	SO:0001819	synonymous_variant	7011	exon34			AGCCTCGGGGAGC		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"WD repeat domain containing"	11726	protein-coding gene	gene with protein product	"TROVE domain family, member 1"	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.4797C>A	chr14.hg19:g.20848600G>T		70.0	0.0		54.0	4.0	NM_007110	A0AUV9	Silent	SNP	ENST00000262715.5	hg19	CCDS9548.1																																																																																			.	G|1.000;A|0.000		0.587	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		T	20848600	G	T	20848600	2	4	254	1	0	0	0	0	0	0	0	1	15774	1103	39	1		1	TEP1	14	20848600	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	365367	20848600	86500940	665	34957										
TEP1	7011	hgsc.bcm.edu	37	chr14	20872802	20872802	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agccacctggatccagtcagAaggcagctggacaatggcac	12	12	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:20872802A>G	ENST00000262715.5	-	5	1040	c.1000T>C	c.(1000-1002)Tct>Cct	p.S334P	TEP1_ENST00000556935.1_Intron	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	334	TROVE. {ECO:0000255|PROSITE- ProRule:PRU00343}.				RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		ATCCAGTCAGAAGGCAGCTGG	0.537																																					p.S334P		Atlas-SNP	.											.	TEP1	224	.	0			c.T1000C						.						72	65	67					14																	20872802		2203	4300	6503	SO:0001583	missense	7011	exon5			AGTCAGAAGGCAG		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"WD repeat domain containing"	11726	protein-coding gene	gene with protein product	"TROVE domain family, member 1"	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.1000T>C	chr14.hg19:g.20872802A>G	ENSP00000262715:p.Ser334Pro	114.0	0.0		92.0	4.0	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	hg19	CCDS9548.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.532968	0.85812	.	.	ENSG00000129566	ENST00000262715;ENST00000359243	T	0.16073	2.37	5.55	5.55	0.83447	TROVE (2);	0.066420	0.64402	D	0.000010	T	0.43612	0.1255	M	0.82323	2.585	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.44937	-0.9295	10	0.87932	D	0	-18.4815	10.8794	0.46929	0.8425:0.1575:0.0:0.0	.	334	Q99973	TEP1_HUMAN	P	334	ENSP00000262715:S334P	ENSP00000262715:S334P	S	-	1	0	TEP1	19942642	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.952000	0.63618	2.333000	0.79357	0.533000	0.62120	TCT	.	.		0.537	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		G	20872802	A	G	20872802	3	3	254	1	0	0	0	0	1	0	0	0	15774	246	9	2	7087	2	TEP1	14	20872802	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	24202	20872802	86476738	666	34958										
RNASE1	6035	hgsc.bcm.edu	37	chr14	21270132	21270132	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgccgctggaatttcttggcCcgggattccttgcccaggga	13	12	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:21270132C>A	ENST00000397967.4	-	2	602	c.96G>T	c.(94-96)cgG>cgT	p.R32R	RNASE1_ENST00000555698.1_5'UTR|RNASE1_ENST00000397970.4_Silent_p.R32R|RNASE1_ENST00000340900.3_Silent_p.R32R|RNASE1_ENST00000412779.2_Silent_p.R32R	NM_002933.4	NP_002924.1	P07998	RNAS1_HUMAN	ribonuclease, RNase A family, 1 (pancreatic)	32					RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	extracellular vesicular exosome (GO:0070062)	nucleic acid binding (GO:0003676)|pancreatic ribonuclease activity (GO:0004522)			central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	5	all_cancers(95;0.00671)	all_lung(585;0.235)	Epithelial(56;9.21e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0126)	Guanidine(DB00536)|L-Aspartic Acid(DB00128)	ATTTCTTGGCCCGGGATTCCT	0.577																																					p.R32R		Atlas-SNP	.											.	RNASE1	14	.	0			c.G96T						.						43	44	44					14																	21270132		2203	4300	6503	SO:0001819	synonymous_variant	6035	exon3			CTTGGCCCGGGAT	BC005324	CCDS9559.1	14q11.2	2014-03-13			ENSG00000129538	ENSG00000129538	3.1.27.5	"Ribonucleases, RNase A"	10044	protein-coding gene	gene with protein product		180440		RNS1		8588814	Standard	NM_002933		Approved		uc001vyi.3	P07998	OTTHUMG00000029603	ENST00000397967.4:c.96G>T	chr14.hg19:g.21270132C>A		92.0	0.0		96.0	4.0	NM_198235	B2R589|D3DS06|Q16830|Q16869|Q1KHR2|Q6ICS5|Q9UCB4|Q9UCB5	Silent	SNP	ENST00000397967.4	hg19	CCDS9559.1																																																																																			.	.		0.577	RNASE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073791.3			A	21270132	C	A	21270132	2	1	254	1	0	0	0	0	0	0	0	1	13414	610	22	3		3	RNASE1	14	21270132	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	397330	21270132	86079408	667	34959										
FLJ10357	55701	hgsc.bcm.edu	37	chr14	21547122	21547122	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttgtgcgcctctccaacctgCacgtgcagcagcaagagcag	11	14	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:21547122C>A	ENST00000298694.4	+	11	2453	c.2326C>A	c.(2326-2328)Cac>Aac	p.H776N	ARHGEF40_ENST00000298693.3_Missense_Mutation_p.H776N			Q8TER5	ARH40_HUMAN	Rho guanine nucleotide exchange factor (GEF) 40	776						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.H776N(1)		large_intestine(4)|ovary(3)|upper_aerodigestive_tract(2)	9						CTCCAACCTGCACGTGCAGCA	0.627																																					p.H776N		Atlas-SNP	.											ARHGEF40,NS,carcinoma,0,1	ARHGEF40	84	.	1	Substitution - Missense(1)	ovary(1)	c.C2326A						.						61	55	57					14																	21547122		2203	4300	6503	SO:0001583	missense	55701	exon11			AACCTGCACGTGC		CCDS32041.1	14q11.2	2012-07-24			ENSG00000165801	ENSG00000165801		"Rho guanine nucleotide exchange factors"	25516	protein-coding gene	gene with protein product		610018				16143467	Standard	NM_001278529		Approved	solo, FLJ10357	uc001vzp.3	Q8TER5		ENST00000298694.4:c.2326C>A	chr14.hg19:g.21547122C>A	ENSP00000298694:p.His776Asn	60.0	0.0		56.0	3.0	NM_018071	A5PL07|Q9BWP5|Q9H7L6|Q9NTF9|Q9NW24	Missense_Mutation	SNP	ENST00000298694.4	hg19	CCDS32041.1	.	.	.	.	.	.	.	.	.	.	C	11.88	1.770771	0.31320	.	.	ENSG00000165801	ENST00000298694;ENST00000298693	T;T	0.02216	4.45;4.39	5.3	4.33	0.51752	.	0.411593	0.21075	N	0.080583	T	0.02193	0.0068	L	0.36672	1.1	0.09310	N	1	B;B	0.18310	0.027;0.009	B;B	0.16289	0.015;0.007	T	0.43245	-0.9403	10	0.27785	T	0.31	.	7.9979	0.30280	0.0:0.8892:0.0:0.1108	.	776;776	Q8TER5-4;Q8TER5	.;ARH40_HUMAN	N	776	ENSP00000298694:H776N;ENSP00000298693:H776N	ENSP00000298693:H776N	H	+	1	0	ARHGEF40	20616962	0.020000	0.18652	0.398000	0.26321	0.969000	0.65631	0.979000	0.29500	2.756000	0.94617	0.563000	0.77884	CAC	.	.		0.627	ARHGEF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413122.1			A	21547122	C	A	21547122	3	1	254	1	0	0	0	0	1	0	0	0	5934	710	25	3	2368	3	FLJ10357	14	21547122	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	276990	21547122	85802418	668	34960										
OXA1L	5018	hgsc.bcm.edu	37	chr14	23237290	23237290	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcttcgctgaactggggctgGggtcatacaccccagtggga	15	11	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:23237290G>T	ENST00000604262.1	+	3	372	c.349G>T	c.(349-351)Ggg>Tgg	p.G117W	OXA1L_ENST00000412791.1_Missense_Mutation_p.G117W|CTD-2555K7.2_ENST00000553792.1_RNA|CTD-2555K7.2_ENST00000554857.1_RNA|CTD-2555K7.2_ENST00000554730.1_RNA|OXA1L_ENST00000285848.5_Missense_Mutation_p.G177W|OXA1L_ENST00000358043.5_Missense_Mutation_p.G101W			Q15070	OXA1L_HUMAN	oxidase (cytochrome c) assembly 1-like	117					aerobic respiration (GO:0009060)|mitochondrial proton-transporting ATP synthase complex assembly (GO:0033615)|mitochondrial respiratory chain complex I assembly (GO:0032981)|mitochondrial respiratory chain complex I biogenesis (GO:0097031)|negative regulation of ATPase activity (GO:0032780)|negative regulation of oxidoreductase activity (GO:0051354)|oxidation-reduction process (GO:0055114)|protein complex assembly (GO:0006461)|protein insertion into membrane (GO:0051205)|protein tetramerization (GO:0051262)	integral component of mitochondrial membrane (GO:0032592)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	mitochondrial ribosome binding (GO:0097177)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(5)|skin(2)	19	all_cancers(95;8.44e-05)			GBM - Glioblastoma multiforme(265;0.0096)		ACTGGGGCTGGGGTCATACAC	0.542																																					p.G177W		Atlas-SNP	.											.	OXA1L	49	.	0			c.G529T						.						56	53	54					14																	23237290		2203	4300	6503	SO:0001583	missense	5018	exon3			GGGCTGGGGTCAT		CCDS9573.1	14q11.2	2009-05-26			ENSG00000155463	ENSG00000155463			8526	protein-coding gene	gene with protein product		601066				8586451, 19349278	Standard	NM_005015		Approved	MGC133129, OXA1	uc001wgn.2	Q15070	OTTHUMG00000028691	ENST00000604262.1:c.349G>T	chr14.hg19:g.23237290G>T	ENSP00000474623:p.Gly117Trp	113.0	0.0		68.0	4.0	NM_005015	B4DPA2	Missense_Mutation	SNP	ENST00000604262.1	hg19		.	.	.	.	.	.	.	.	.	.	G	18.53	3.644409	0.67244	.	.	ENSG00000155463	ENST00000285848;ENST00000412791;ENST00000358043	T;T;T	0.35048	1.33;1.38;1.36	5.76	4.87	0.63330	.	0.208448	0.49305	D	0.000155	T	0.62563	0.2438	M	0.83953	2.67	0.50313	D	0.999866	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.997;0.999;0.999;0.998	T	0.68025	-0.5518	10	0.62326	D	0.03	-11.0391	13.612	0.62086	0.0757:0.0:0.9243:0.0	.	117;117;117;177	B4DGZ2;E7EVY0;Q15070;Q2M1J6	.;.;OXA1L_HUMAN;.	W	177;117;101	ENSP00000285848:G177W;ENSP00000387601:G117W;ENSP00000350740:G101W	ENSP00000285848:G177W	G	+	1	0	OXA1L	22307130	1.000000	0.71417	0.815000	0.32552	0.641000	0.38312	6.169000	0.71913	1.432000	0.47375	0.655000	0.94253	GGG	.	.		0.542	OXA1L-012	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000468876.1	NM_005015		T	23237290	G	T	23237290	3	4	254	1	0	0	0	0	1	0	0	0	11337	1232	43	3	539	3	OXA1L	14	23237290	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1690168	23237290	84112250	669	34961										
MMP14	4323	hgsc.bcm.edu	37	chr14	23314461	23314461	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttcctttccccttccccaggTactaccgtttcaacgaagag	6	15	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:23314461T>C	ENST00000311852.6	+	9	1564	c.1303T>C	c.(1303-1305)Tac>Cac	p.Y435H	MMP14_ENST00000548162.1_3'UTR	NM_004995.2	NP_004986.1	P50281	MMP14_HUMAN	matrix metallopeptidase 14 (membrane-inserted)	435					angiogenesis (GO:0001525)|astrocyte cell migration (GO:0043615)|branching morphogenesis of an epithelial tube (GO:0048754)|chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|endodermal cell differentiation (GO:0035987)|endothelial cell proliferation (GO:0001935)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|male gonad development (GO:0008584)|negative regulation of focal adhesion assembly (GO:0051895)|ovarian follicle development (GO:0001541)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|proteolysis (GO:0006508)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to oxidative stress (GO:0006979)|tissue remodeling (GO:0048771)|zymogen activation (GO:0031638)	extracellular matrix (GO:0031012)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|peptidase activator activity (GO:0016504)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	20	all_cancers(95;9.47e-05)			GBM - Glioblastoma multiforme(265;0.00551)	Marimastat(DB00786)	CTTCCCCAGGTACTACCGTTT	0.572																																					p.Y435H		Atlas-SNP	.											.	MMP14	40	.	0			c.T1303C						.						56	45	49					14																	23314461		2203	4299	6502	SO:0001630	splice_region_variant	4323	exon9			CCCAGGTACTACC		CCDS9577.1	14q11-q12	2011-06-29	2005-08-08		ENSG00000157227	ENSG00000157227			7160	protein-coding gene	gene with protein product	"membrane type 1 metalloprotease"	600754	"matrix metalloproteinase 14 (membrane-inserted)"			8015608	Standard	NM_004995		Approved	MT1-MMP	uc001whc.3	P50281	OTTHUMG00000028704	ENST00000311852.6:c.1302-1T>C	chr14.hg19:g.23314461T>C		40.0	0.0		49.0	4.0	NM_004995	A8K5L0|Q6GSF3|Q92678	Missense_Mutation	SNP	ENST00000311852.6	hg19	CCDS9577.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.423028	0.83559	.	.	ENSG00000157227	ENST00000311852	T	0.06849	3.25	5.45	5.45	0.79879	Hemopexin/matrixin (2);	0.000000	0.85682	D	0.000000	T	0.39384	0.1076	M	0.93283	3.4	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.53229	-0.8468	10	0.87932	D	0	.	14.4911	0.67651	0.0:0.0:0.0:1.0	.	435	P50281	MMP14_HUMAN	H	435	ENSP00000308208:Y435H	ENSP00000308208:Y435H	Y	+	1	0	MMP14	22384301	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.944000	0.87722	2.076000	0.62316	0.455000	0.32223	TAC	.	.		0.572	MMP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071660.3	NM_004995	Missense_Mutation	C	23314461	T	C	23314461	5	2	254	1	0	0	0	0	0	0	1	0	9662	1652	57	2	1337	2	MMP14	14	23314461	Splice_Site	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	77171	23314461	84035079	670	34962										
SLC7A8	23428	hgsc.bcm.edu	37	chr14	23598939	23598939	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gaccccatagaagaggtagtTgatgaagcccacatagttga	11	8	0	5			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:23598939T>C	ENST00000316902.7	-	9	1908	c.1183A>G	c.(1183-1185)Aac>Gac	p.N395D	SLC7A8_ENST00000422941.2_Missense_Mutation_p.N171D|SLC7A8_ENST00000529705.2_Missense_Mutation_p.N290D|SLC7A8_ENST00000469263.1_Intron|SLC7A8_ENST00000453702.1_Missense_Mutation_p.N192D	NM_012244.3	NP_036376.2	Q9UHI5	LAT2_HUMAN	solute carrier family 7 (amino acid transporter light chain, L system), member 8	395					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|metal ion homeostasis (GO:0055065)|neutral amino acid transport (GO:0015804)|organic cation transport (GO:0015695)|response to toxic substance (GO:0009636)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-amino acid transmembrane transporter activity (GO:0015179)|neutral amino acid transmembrane transporter activity (GO:0015175)|organic cation transmembrane transporter activity (GO:0015101)|peptide antigen binding (GO:0042605)|toxin transporter activity (GO:0019534)			autonomic_ganglia(1)|endometrium(6)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|skin(1)	24	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.00809)	L-Alanine(DB00160)|L-DOPA(DB01235)|L-Glutamine(DB00130)|L-Phenylalanine(DB00120)	AAGAGGTAGTTGATGAAGCCC	0.532																																					p.N395D		Atlas-SNP	.											.	SLC7A8	54	.	0			c.A1183G						.						250	215	227					14																	23598939		2203	4300	6503	SO:0001583	missense	23428	exon9			GGTAGTTGATGAA	Y18483	CCDS9590.1, CCDS41924.1, CCDS58304.1, CCDS58305.1	14q11.2	2013-05-22	2011-07-12		ENSG00000092068	ENSG00000092068		"Solute carriers"	11066	protein-coding gene	gene with protein product		604235				10080183, 10391915	Standard	NM_001267036		Approved	LPI-PC1, LAT2	uc001wiz.4	Q9UHI5	OTTHUMG00000028720	ENST00000316902.7:c.1183A>G	chr14.hg19:g.23598939T>C	ENSP00000320378:p.Asn395Asp	165.0	0.0		80.0	4.0	NM_012244	B2R8Q4|B4DKT4|B4DTV6|D3DS46|F2Z2J4|Q86U05|Q9UKQ6|Q9UKQ7|Q9UKQ8|Q9Y445	Missense_Mutation	SNP	ENST00000316902.7	hg19	CCDS9590.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	24.9|24.9	4.583889|4.583889	0.86748|0.86748	.|.	.|.	ENSG00000092068|ENSG00000092068	ENST00000316902;ENST00000453702;ENST00000529705;ENST00000422941;ENST00000206514|ENST00000334354	D;D;D;D|.	0.89939|.	-2.59;-2.59;-2.59;-2.59|.	5.86|5.86	5.86|5.86	0.93980|0.93980	Amino acid permease domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.70263|0.70263	0.3204|0.3204	L|L	0.55103|0.55103	1.725|1.725	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	0.999;0.999;1.0|.	D;D;D|.	0.77557|.	0.988;0.984;0.99|.	T|T	0.71293|0.71293	-0.4636|-0.4636	10|6	0.21540|0.52906	T|T	0.41|0.07	.|.	15.2376|15.2376	0.73443|0.73443	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	290;171;395|.	B4DKT4;B4DTV6;Q9UHI5|.	.;.;LAT2_HUMAN|.	D|R	395;192;290;171;192|191	ENSP00000320378:N395D;ENSP00000391577:N192D;ENSP00000434345:N290D;ENSP00000416398:N171D|.	ENSP00000206514:N192D|ENSP00000334744:Q191R	N|Q	-|-	1|2	0|0	SLC7A8|SLC7A8	22668779|22668779	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	7.767000|7.767000	0.85331|0.85331	2.240000|2.240000	0.73641|0.73641	0.533000|0.533000	0.62120|0.62120	AAC|CAA	.	.		0.532	SLC7A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071718.3			C	23598939	T	C	23598939	3	2	254	1	0	0	0	0	1	0	0	0	14719	1812	63	2	436	2	SLC7A8	14	23598939	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	284478	23598939	83750601	671	34963										
PABPN1	8106	hgsc.bcm.edu	37	chr14	23790983	23790983	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccaagaggaggaggaggagcCgggactggtcgagggtgacc	20	8	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:23790983C>T	ENST00000216727.4	+	1	486	c.305C>T	c.(304-306)cCg>cTg	p.P102L	PABPN1_ENST00000557702.1_5'Flank|BCL2L2-PABPN1_ENST00000553781.1_Intron|BCL2L2-PABPN1_ENST00000557008.1_Intron|PABPN1_ENST00000556821.1_5'UTR|AL049829.1_ENST00000594872.1_Silent_p.P45P|PABPN1_ENST00000397276.2_Missense_Mutation_p.P102L	NM_004643.3	NP_004634.1	Q86U42	PABP2_HUMAN	poly(A) binding protein, nuclear 1	102	Interacts with SKIP.				gene expression (GO:0010467)|modification by virus of host mRNA processing (GO:0046778)|modulation by virus of host morphology or physiology (GO:0019048)|modulation by virus of host process (GO:0019054)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|muscle contraction (GO:0006936)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)|viral life cycle (GO:0019058)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			large_intestine(1)|lung(1)|ovary(2)	4	all_cancers(95;6.69e-06)			GBM - Glioblastoma multiforme(265;0.00643)		GAGGAGGAGCCGGGACTGGTC	0.781																																					p.P102L		Atlas-SNP	.											.	PABPN1	18	.	0			c.C305T						.						5	6	6					14																	23790983		1931	3826	5757	SO:0001583	missense	8106	exon1			AGGAGCCGGGACT	AF026029	CCDS9592.1	14q11.2	2013-02-12	2001-11-28		ENSG00000100836	ENSG00000100836		"RNA binding motif (RRM) containing"	8565	protein-coding gene	gene with protein product		602279	"poly(A)-binding protein, nuclear 1"	OPMD, PABP2		7795598	Standard	NM_004643		Approved	PAB2		Q86U42	OTTHUMG00000028739	ENST00000216727.4:c.305C>T	chr14.hg19:g.23790983C>T	ENSP00000216727:p.Pro102Leu	176.0	0.0		102.0	5.0	NM_004643	D3DS49|O43484	Missense_Mutation	SNP	ENST00000216727.4	hg19	CCDS9592.1	.	.	.	.	.	.	.	.	.	.	C	15.90	2.970224	0.53614	.	.	ENSG00000100836	ENST00000216727;ENST00000397276	T;T	0.57436	0.4;0.81	3.65	3.65	0.41850	.	0.000000	0.44902	U	0.000406	T	0.31796	0.0808	.	.	.	0.80722	D	1	P;P	0.40197	0.581;0.706	B;B	0.20384	0.013;0.029	T	0.24728	-1.0152	9	0.40728	T	0.16	-8.0E-4	10.1285	0.42665	0.2006:0.7994:0.0:0.0	.	102;102	Q86U42;Q86U42-2	PABP2_HUMAN;.	L	102	ENSP00000216727:P102L;ENSP00000380446:P102L	ENSP00000216727:P102L	P	+	2	0	PABPN1	22860823	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	1.852000	0.39348	2.049000	0.60858	0.456000	0.33151	CCG	.	.		0.781	PABPN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071767.4	NM_004643		T	23790983	C	T	23790983	3	4	254	1	0	0	0	0	1	0	0	0	11377	652	23	1	307	1	PABPN1	14	23790983	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	192044	23790983	83558557	672	34964										
MYH6	4624	hgsc.bcm.edu	37	chr14	23866382	23866382	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtcttctcctggctcacctgGagccttccgctcattgggga	11	14	4	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:23866382G>T	ENST00000356287.3	-	16	2076	c.2047C>A	c.(2047-2049)Cca>Aca	p.P683T	MYH6_ENST00000405093.3_Missense_Mutation_p.P683T			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	683	Myosin motor.				adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)			breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		GGCTCACCTGGAGCCTTCCGC	0.547																																					p.P683T		Atlas-SNP	.											.	MYH6	274	.	0			c.C2047A						.						143	141	141					14																	23866382		2203	4300	6503	SO:0001583	missense	4624	exon17			CACCTGGAGCCTT	D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"Myosins / Myosin superfamily : Class II"	7576	protein-coding gene	gene with protein product	"cardiomyopathy, hypertrophic 1"	160710	"myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.2047C>A	chr14.hg19:g.23866382G>T	ENSP00000348634:p.Pro683Thr	110.0	0.0		93.0	4.0	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Missense_Mutation	SNP	ENST00000356287.3	hg19	CCDS9600.1	.	.	.	.	.	.	.	.	.	.	.	17.87	3.494992	0.64186	.	.	ENSG00000197616	ENST00000405093;ENST00000356287	T;T	0.74526	-0.85;-0.85	4.14	3.25	0.37280	Myosin head, motor domain (2);	.	.	.	.	D	0.89093	0.6617	H	0.98802	4.335	0.58432	D	0.999998	P	0.38420	0.63	P	0.51135	0.66	D	0.91006	0.4846	9	0.62326	D	0.03	.	12.3534	0.55161	0.0837:0.0:0.9163:0.0	.	683	P13533	MYH6_HUMAN	T	683	ENSP00000386041:P683T;ENSP00000348634:P683T	ENSP00000348634:P683T	P	-	1	0	MYH6	22936222	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	8.819000	0.91997	1.094000	0.41399	-0.157000	0.13467	CCA	.	.		0.547	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3			T	23866382	G	T	23866382	3	4	254	1	0	0	0	0	1	0	0	0	10047	1174	41	3	3864	3	MYH6	14	23866382	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	75399	23866382	83483158	673	34965										
MYH7	4625	hgsc.bcm.edu	37	chr14	23890225	23890225	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gggcctgttcatcctcaatcCttgcgttgagagcattcagc	10	12	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:23890225C>A	ENST00000355349.3	-	26	3440	c.3278G>T	c.(3277-3279)aGg>aTg	p.R1093M	MIR208B_ENST00000401172.1_RNA	NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	1093					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		ATCCTCAATCCTTGCGTTGAG	0.587																																					p.R1093M		Atlas-SNP	.											.	MYH7	349	.	0			c.G3278T						.						94	86	89					14																	23890225		2203	4300	6503	SO:0001583	missense	4625	exon26			TCAATCCTTGCGT	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.3278G>T	chr14.hg19:g.23890225C>A	ENSP00000347507:p.Arg1093Met	160.0	0.0		100.0	5.0	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Missense_Mutation	SNP	ENST00000355349.3	hg19	CCDS9601.1	.	.	.	.	.	.	.	.	.	.	C	19.21	3.783576	0.70222	.	.	ENSG00000092054	ENST00000355349;ENST00000544444	D	0.83591	-1.74	5.55	4.66	0.58398	Myosin tail (1);	.	.	.	.	D	0.89928	0.6857	M	0.87547	2.89	0.46849	D	0.999221	P	0.40266	0.71	P	0.55455	0.776	D	0.90717	0.4632	9	0.87932	D	0	.	9.774	0.40607	0.0:0.7863:0.0:0.2137	.	1093	P12883	MYH7_HUMAN	M	1093	ENSP00000347507:R1093M	ENSP00000347507:R1093M	R	-	2	0	MYH7	22960065	0.199000	0.23386	0.995000	0.50966	0.932000	0.56968	0.984000	0.29565	1.575000	0.49775	0.655000	0.94253	AGG	.	.		0.587	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257		A	23890225	C	A	23890225	3	1	254	1	0	0	0	0	1	0	0	0	10048	681	24	3	2589	3	MYH7	14	23890225	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	23843	23890225	83459315	674	34966										
TM9SF1	10548	hgsc.bcm.edu	37	chr14	24662037	24662037	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtaccgagccaggtcattccGaagcacacgcattagaatga	10	11	1	2	rs533902919		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:24662037G>T	ENST00000261789.4	-	3	1142	c.784C>A	c.(784-786)Cgg>Agg	p.R262R	TM9SF1_ENST00000396854.4_Silent_p.R262R|RP11-468E2.2_ENST00000561419.1_5'Flank|TM9SF1_ENST00000556387.1_Silent_p.R471R|TM9SF1_ENST00000528669.1_Silent_p.R262R|TM9SF1_ENST00000524835.1_Silent_p.R175R|TM9SF1_ENST00000530611.1_Silent_p.R471R	NM_006405.5	NP_006396.2	O15321	TM9S1_HUMAN	transmembrane 9 superfamily member 1	262					autophagy (GO:0006914)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)				NS(1)|breast(4)|endometrium(3)|large_intestine(11)|lung(4)|ovary(1)	24				GBM - Glioblastoma multiforme(265;0.0183)		AGGTCATTCCGAAGCACACGC	0.473																																					p.R262R		Atlas-SNP	.											.	TM9SF1	58	.	0			c.C784A						.						126	111	116					14																	24662037		2203	4300	6503	SO:0001819	synonymous_variant	10548	exon3			CATTCCGAAGCAC	U94831	CCDS9617.1, CCDS41934.1, CCDS73623.1	14q11.2	2005-10-11			ENSG00000100926	ENSG00000100926			11864	protein-coding gene	gene with protein product						9332367	Standard	NM_006405		Approved	MP70, HMP70	uc010tob.1	O15321	OTTHUMG00000029322	ENST00000261789.4:c.784C>A	chr14.hg19:g.24662037G>T		144.0	0.0		100.0	4.0	NM_001014842	D3DS65|Q86SZ6|Q96FI8	Silent	SNP	ENST00000261789.4	hg19	CCDS9617.1																																																																																			.	.		0.473	TM9SF1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073136.2	NM_006405		T	24662037	G	T	24662037	2	4	254	1	0	0	0	0	0	0	0	1	15992	1057	37	1		1	TM9SF1	14	24662037	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	771812	24662037	82687503	675	34967										
RIPK3	11035	hgsc.bcm.edu	37	chr14	24808320	24808320	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aggtaaaacatcccaagcacCacttctttcagcaggcggca	8	13	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:24808320C>A	ENST00000216274.5	-	3	590	c.372G>T	c.(370-372)gtG>gtT	p.V124V	RIPK3_ENST00000554338.1_5'Flank|RP11-934B9.3_ENST00000555591.1_5'Flank	NM_006871.3	NP_006862.2	Q9Y572	RIPK3_HUMAN	receptor-interacting serine-threonine kinase 3	124	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|amyloid fibril formation (GO:1990000)|apoptotic signaling pathway (GO:0097190)|cellular protein modification process (GO:0006464)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|lymph node development (GO:0048535)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of ligase activity (GO:0051351)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phosphatase activity (GO:0010922)|positive regulation of protein deacetylation (GO:0090312)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of type I interferon production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of activated T cell proliferation (GO:0046006)|regulation of activation-induced cell death of T cells (GO:0070235)|regulation of adaptive immune response (GO:0002819)|regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation (GO:2000452)|regulation of interferon-gamma production (GO:0032649)|regulation of T cell mediated cytotoxicity (GO:0001914)|signal transduction (GO:0007165)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|NF-kappaB-inducing kinase activity (GO:0004704)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				GBM - Glioblastoma multiforme(265;0.0181)		TCCCAAGCACCACTTCTTTCA	0.612																																					p.V124V	Pancreas(58;918 1191 4668 13304 15331)	Atlas-SNP	.											.	RIPK3	43	.	0			c.G372T						.						60	66	64					14																	24808320		2203	4300	6503	SO:0001819	synonymous_variant	11035	exon3			AAGCACCACTTCT	AF156884	CCDS9628.1	14q12	2006-05-15			ENSG00000129465	ENSG00000129465			10021	protein-coding gene	gene with protein product		605817				10339433, 10358032	Standard	NM_006871		Approved	RIP3	uc001wpb.3	Q9Y572	OTTHUMG00000029349	ENST00000216274.5:c.372G>T	chr14.hg19:g.24808320C>A		103.0	0.0		67.0	4.0	NM_006871	B4DJL9|C4AM87|Q5J795|Q5J796|Q6P5Y1	Silent	SNP	ENST00000216274.5	hg19	CCDS9628.1																																																																																			.	.		0.612	RIPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073203.4	NM_006871		A	24808320	C	A	24808320	2	1	254	1	0	0	0	0	0	0	0	1	13397	581	21	3		3	RIPK3	14	24808320	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	146283	24808320	82541220	676	34968										
PRKD1	5587	hgsc.bcm.edu	37	chr14	30066937	30066937	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agacttctctccaatgatccGggcaaaaccaaaatcacaaa	5	12	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:30066937G>A	ENST00000331968.5	-	16	2423	c.2194C>T	c.(2194-2196)Cgg>Tgg	p.R732W	PRKD1_ENST00000415220.2_Missense_Mutation_p.R740W	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	732	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to oxidative stress (GO:0034599)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|negative regulation of cell death (GO:0060548)|negative regulation of endocytosis (GO:0045806)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein autophosphorylation (GO:0046777)|regulation of integrin-mediated signaling pathway (GO:2001044)|regulation of keratinocyte proliferation (GO:0010837)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|lung(32)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	78	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		CCAATGATCCGGGCAAAACCA	0.473																																					p.R732W		Atlas-SNP	.											PRKD1_ENST00000331968,right_upper_lobe,carcinoma,0,4	PRKD1	316	.	0			c.C2194T						.						50	55	53					14																	30066937		2203	4300	6503	SO:0001583	missense	5587	exon16			TGATCCGGGCAAA		CCDS9637.1	14q11	2013-01-10	2004-10-28	2004-10-30	ENSG00000184304	ENSG00000184304	2.7.11.1	"Pleckstrin homology (PH) domain containing"	9407	protein-coding gene	gene with protein product		605435	"protein kinase C, mu"	PRKCM		8119958, 10965134	Standard	NM_002742		Approved	PKCM, PKD, PKC-mu	uc001wqh.3	Q15139	OTTHUMG00000140203	ENST00000331968.5:c.2194C>T	chr14.hg19:g.30066937G>A	ENSP00000333568:p.Arg732Trp	34.0	0.0		24.0	2.0	NM_002742	A6NL64|B2RAF6	Missense_Mutation	SNP	ENST00000331968.5	hg19	CCDS9637.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.454641	0.84209	.	.	ENSG00000184304	ENST00000331968;ENST00000415220	D;D	0.84873	-1.91;-1.91	5.72	3.76	0.43208	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000002	D	0.92286	0.7553	M	0.82433	2.59	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93616	0.6943	10	0.87932	D	0	-11.0088	14.7829	0.69779	0.0:0.0:0.7372:0.2628	.	732	Q15139	KPCD1_HUMAN	W	732;740	ENSP00000333568:R732W;ENSP00000390535:R740W	ENSP00000333568:R732W	R	-	1	2	PRKD1	29136688	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.632000	0.67819	1.523000	0.49018	0.650000	0.86243	CGG	.	.		0.473	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2	NM_002742		A	30066937	G	A	30066937	3	1	254	1	0	0	0	0	1	0	0	0	12530	1115	39	1	556	1	PRKD1	14	30066937	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	5258617	30066937	77282603	677	34969										
PRKD1	5587	hgsc.bcm.edu	37	chr14	30068321	30068321	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	taaaatgaaggtgccgcaaaGccacgagtatctgtaaagaa	10	7	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:30068321G>A	ENST00000331968.5	-	15	2307	c.2078C>T	c.(2077-2079)gCt>gTt	p.A693V	PRKD1_ENST00000415220.2_Missense_Mutation_p.A701V	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	693	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to oxidative stress (GO:0034599)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|negative regulation of cell death (GO:0060548)|negative regulation of endocytosis (GO:0045806)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein autophosphorylation (GO:0046777)|regulation of integrin-mediated signaling pathway (GO:2001044)|regulation of keratinocyte proliferation (GO:0010837)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|lung(32)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	78	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		GTGCCGCAAAGCCACGAGTAT	0.358																																					p.A693V		Atlas-SNP	.											.	PRKD1	316	.	0			c.C2078T						.						90	89	89					14																	30068321		2203	4300	6503	SO:0001583	missense	5587	exon15			CGCAAAGCCACGA		CCDS9637.1	14q11	2013-01-10	2004-10-28	2004-10-30	ENSG00000184304	ENSG00000184304	2.7.11.1	"Pleckstrin homology (PH) domain containing"	9407	protein-coding gene	gene with protein product		605435	"protein kinase C, mu"	PRKCM		8119958, 10965134	Standard	NM_002742		Approved	PKCM, PKD, PKC-mu	uc001wqh.3	Q15139	OTTHUMG00000140203	ENST00000331968.5:c.2078C>T	chr14.hg19:g.30068321G>A	ENSP00000333568:p.Ala693Val	101.0	0.0		70.0	4.0	NM_002742	A6NL64|B2RAF6	Missense_Mutation	SNP	ENST00000331968.5	hg19	CCDS9637.1	.	.	.	.	.	.	.	.	.	.	G	34	5.352183	0.95830	.	.	ENSG00000184304	ENST00000331968;ENST00000415220	D;D	0.88124	-2.34;-2.34	5.58	5.58	0.84498	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.94618	0.8265	M	0.87269	2.87	0.80722	D	1	D	0.76494	0.999	D	0.75484	0.986	D	0.94831	0.7996	10	0.87932	D	0	-15.3433	19.9348	0.97133	0.0:0.0:1.0:0.0	.	693	Q15139	KPCD1_HUMAN	V	693;701	ENSP00000333568:A693V;ENSP00000390535:A701V	ENSP00000333568:A693V	A	-	2	0	PRKD1	29138072	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.740000	0.98839	2.789000	0.95967	0.591000	0.81541	GCT	.	.		0.358	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2	NM_002742		A	30068321	G	A	30068321	3	1	254	1	0	0	0	0	1	0	0	0	12530	971	34	3	676	3	PRKD1	14	30068321	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1384	30068321	77281219	678	34970										
FBXO33	254170	hgsc.bcm.edu	37	chr14	39900875	39900875	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcctcgacttcctcccctccAgtcccggtgtccgcgccacc	8	22	0	0	rs377484603		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:39900875A>G	ENST00000298097.7	-	1	829	c.492T>C	c.(490-492)acT>acC	p.T164T	FBXO33_ENST00000554190.1_Silent_p.T36T	NM_203301.3	NP_976046.1	Q7Z6M2	FBX33_HUMAN	F-box protein 33	164					protein ubiquitination (GO:0016567)					endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|urinary_tract(1)	9	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00121)|Epithelial(34;0.169)	GBM - Glioblastoma multiforme(112;0.0425)		CCTCCCCTCCAGTCCCGGTGT	0.652																																					p.T164T		Atlas-SNP	.											.	FBXO33	21	.	0			c.T492C						.						38	42	41					14																	39900875		2203	4300	6503	SO:0001819	synonymous_variant	254170	exon1			CCCTCCAGTCCCG	BI460761	CCDS9677.1	14q13.3	2004-08-24	2004-06-15		ENSG00000165355	ENSG00000165355		"F-boxes /  "other""	19833	protein-coding gene	gene with protein product		609103	"F-box only protein 33"				Standard	NM_203301		Approved	Fbx33	uc001wvk.3	Q7Z6M2	OTTHUMG00000140257	ENST00000298097.7:c.492T>C	chr14.hg19:g.39900875A>G		94.0	0.0		70.0	4.0	NM_203301	Q6PIR2|Q86TR2|Q86YE0	Silent	SNP	ENST00000298097.7	hg19	CCDS9677.1																																																																																			.	.		0.652	FBXO33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276769.2			G	39900875	A	G	39900875	2	3	254	1	0	0	0	0	0	0	0	1	5751	175	7	2		2	FBXO33	14	39900875	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	9832554	39900875	67448665	679	34971										
FBXO33	254170	hgsc.bcm.edu	37	chr14	39900902	39900902	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtgtccgcgccacctccgtcCcctgggccaccgccgctcag	11	21	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:39900902C>T	ENST00000298097.7	-	1	802	c.465G>A	c.(463-465)ggG>ggA	p.G155G	FBXO33_ENST00000554190.1_Silent_p.G27G	NM_203301.3	NP_976046.1	Q7Z6M2	FBX33_HUMAN	F-box protein 33	155					protein ubiquitination (GO:0016567)					endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|urinary_tract(1)	9	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00121)|Epithelial(34;0.169)	GBM - Glioblastoma multiforme(112;0.0425)		CACCTCCGTCCCCTGGGCCAC	0.652																																					p.G155G		Atlas-SNP	.											.	FBXO33	21	.	0			c.G465A						.						33	39	37					14																	39900902		2201	4300	6501	SO:0001819	synonymous_variant	254170	exon1			TCCGTCCCCTGGG	BI460761	CCDS9677.1	14q13.3	2004-08-24	2004-06-15		ENSG00000165355	ENSG00000165355		"F-boxes /  "other""	19833	protein-coding gene	gene with protein product		609103	"F-box only protein 33"				Standard	NM_203301		Approved	Fbx33	uc001wvk.3	Q7Z6M2	OTTHUMG00000140257	ENST00000298097.7:c.465G>A	chr14.hg19:g.39900902C>T		110.0	0.0		83.0	4.0	NM_203301	Q6PIR2|Q86TR2|Q86YE0	Silent	SNP	ENST00000298097.7	hg19	CCDS9677.1																																																																																			.	.		0.652	FBXO33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276769.2			T	39900902	C	T	39900902	2	4	254	1	0	0	0	0	0	0	0	1	5751	610	22	3		3	FBXO33	14	39900902	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	27	39900902	67448638	680	34972										
FAM179B	23116	hgsc.bcm.edu	37	chr14	45465036	45465036	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	atttatgttttagcagaaaaAgagtatcaagaaacttattt	6	3	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:45465036A>G	ENST00000361577.3	+	2	2348	c.2134A>G	c.(2134-2136)Aga>Gga	p.R712G	FAM179B_ENST00000382233.2_Missense_Mutation_p.R712G|FAM179B_ENST00000361462.2_Missense_Mutation_p.R712G|KLHL28_ENST00000553817.1_Intron	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	712										endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						TAGCAGAAAAAGAGTATCAAG	0.343																																					p.R712G		Atlas-SNP	.											.	FAM179B	115	.	0			c.A2134G						.						102	99	100					14																	45465036		2203	4300	6503	SO:0001583	missense	23116	exon2			AGAAAAAGAGTAT	AB007883	CCDS9681.1	14q21.3	2008-07-21	2008-07-21	2008-07-21	ENSG00000198718	ENSG00000198718			19959	protein-coding gene	gene with protein product			"KIAA0423"	KIAA0423			Standard	XM_005267451		Approved		uc001wvv.3	Q9Y4F4	OTTHUMG00000140264	ENST00000361577.3:c.2134A>G	chr14.hg19:g.45465036A>G	ENSP00000355045:p.Arg712Gly	148.0	0.0		110.0	5.0	NM_015091	Q68D66|Q6PG27	Missense_Mutation	SNP	ENST00000361577.3	hg19	CCDS9681.1	.	.	.	.	.	.	.	.	.	.	A	18.46	3.629626	0.67015	.	.	ENSG00000198718	ENST00000429476;ENST00000361577;ENST00000361462;ENST00000382233;ENST00000555874	T;T;T;T	0.04015	3.73;3.73;3.73;3.73	5.42	5.42	0.78866	Armadillo-type fold (1);	0.174903	0.39687	N	0.001294	T	0.09642	0.0237	L	0.27053	0.805	0.37052	D	0.897644	D;D;D;D	0.67145	0.991;0.974;0.996;0.991	P;P;P;P	0.61874	0.801;0.731;0.895;0.801	T	0.15065	-1.0450	10	0.87932	D	0	-18.5762	9.6499	0.39890	0.8249:0.1751:0.0:0.0	.	712;712;712;712	Q9Y4F4-3;G3XAE9;Q9Y4F4;Q9Y4F4-2	.;.;F179B_HUMAN;.	G	712;712;712;712;31	ENSP00000355045:R712G;ENSP00000354917:R712G;ENSP00000371668:R712G;ENSP00000451141:R31G	ENSP00000354917:R712G	R	+	1	2	FAM179B	44534786	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.163000	0.64948	2.064000	0.61679	0.477000	0.44152	AGA	.	.		0.343	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781		G	45465036	A	G	45465036	3	3	254	1	0	0	0	0	1	0	0	0	5511	64	3	2	2140	2	FAM179B	14	45465036	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	5564134	45465036	61884504	681	34973										
FANCM	57697	hgsc.bcm.edu	37	chr14	45633698	45633698	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cccaattcgtcttgtacaacGaatgggtagaactggccgta	10	10	1	1	rs550238354		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:45633698G>T	ENST00000267430.5	+	10	1803	c.1718G>T	c.(1717-1719)cGa>cTa	p.R573L	FANCM_ENST00000556036.1_Missense_Mutation_p.R573L|FANCM_ENST00000542564.2_Missense_Mutation_p.R547L	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	573	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						CTTGTACAACGAATGGGTAGA	0.423								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.R573L		Atlas-SNP	.											.	FANCM	225	.	0			c.G1718T						.						76	74	74					14																	45633698		2203	4300	6503	SO:0001583	missense	57697	exon10	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TACAACGAATGGG	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"Fanconi anemia, complementation groups"	23168	protein-coding gene	gene with protein product		609644	"KIAA1596"	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.1718G>T	chr14.hg19:g.45633698G>T	ENSP00000267430:p.Arg573Leu	128.0	0.0		80.0	4.0	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	hg19	CCDS32070.1	.	.	.	.	.	.	.	.	.	.	G	34	5.394071	0.96009	.	.	ENSG00000187790	ENST00000556036;ENST00000267430;ENST00000542564	D;D;D	0.81908	-1.55;-1.55;-1.55	6.07	6.07	0.98685	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.95677	0.8594	H	0.99325	4.515	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.96905	0.9663	10	0.87932	D	0	.	20.2544	0.98414	0.0:0.0:1.0:0.0	.	547;573;573	B2RTQ9;Q8IYD8;Q8IYD8-2	.;FANCM_HUMAN;.	L	573;573;547	ENSP00000450596:R573L;ENSP00000267430:R573L;ENSP00000442493:R547L	ENSP00000267430:R573L	R	+	2	0	FANCM	44703448	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	9.432000	0.97498	2.885000	0.99019	0.655000	0.94253	CGA	.	.		0.423	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		T	45633698	G	T	45633698	3	4	254	1	0	0	0	0	1	0	0	0	5679	1058	37	1	1756	1	FANCM	14	45633698	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	168662	45633698	61715842	682	34974										
MDGA2	161357	hgsc.bcm.edu	37	chr14	47613426	47613426	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttctctcatagtaaaattgtTctttagcttcacctatactt	3	9	4	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:47613426T>C	ENST00000399232.2	-	4	804	c.440A>G	c.(439-441)gAa>gGa	p.E147G	MDGA2_ENST00000439988.3_Missense_Mutation_p.E216G|MDGA2_ENST00000426342.1_5'UTR|MDGA2_ENST00000357362.3_5'UTR	NM_001113498.2	NP_001106970.3	Q7Z553	MDGA2_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 2	147	Ig-like 2.				pattern specification process (GO:0007389)|spinal cord motor neuron differentiation (GO:0021522)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(3)|endometrium(4)|kidney(2)|large_intestine(14)|lung(41)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(5)	76						GTAAAATTGTTCTTTAGCTTC	0.408																																					p.E216G		Atlas-SNP	.											.	MDGA2	470	.	0			c.A647G						.						147	132	136					14																	47613426		692	1591	2283	SO:0001583	missense	161357	exon4			AATTGTTCTTTAG	AI859192	CCDS41948.1, CCDS45098.1, CCDS45098.2, CCDS45098.3	14q21.2	2013-01-29	2007-04-03	2007-04-03	ENSG00000139915	ENSG00000139915		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19835	protein-coding gene	gene with protein product		611128	"MAM domain containing 1"	MAMDC1		15019943	Standard	NM_001113498		Approved		uc001wwj.4	Q7Z553	OTTHUMG00000029429	ENST00000399232.2:c.440A>G	chr14.hg19:g.47613426T>C	ENSP00000382178:p.Glu147Gly	146.0	0.0		112.0	5.0	NM_001113498	F6W3S7|J3KPX6	Missense_Mutation	SNP	ENST00000399232.2	hg19		.	.	.	.	.	.	.	.	.	.	T	16.63	3.175804	0.57692	.	.	ENSG00000139915	ENST00000439988;ENST00000399232	T;T	0.42900	0.96;0.96	5.52	5.52	0.82312	Immunoglobulin subtype (1);Immunoglobulin-like (1);	0.000000	0.52532	U	0.000071	T	0.28599	0.0708	N	0.17474	0.49	0.80722	D	1	B	0.14012	0.009	B	0.22880	0.042	T	0.09509	-1.0671	10	0.17832	T	0.49	.	14.4758	0.67546	0.0:0.0:0.0:1.0	.	147	Q7Z553	MDGA2_HUMAN	G	147;216	ENSP00000400011:E147G;ENSP00000382178:E216G	ENSP00000382178:E216G	E	-	2	0	MDGA2	46683176	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.621000	0.83083	2.108000	0.64289	0.477000	0.44152	GAA	.	.		0.408	MDGA2-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000073352.5	NM_182830		C	47613426	T	C	47613426	3	2	254	1	0	0	0	0	1	0	0	0	9416	1783	62	2	2486	2	MDGA2	14	47613426	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	1979728	47613426	59736114	683	34975										
NID2	22795	hgsc.bcm.edu	37	chr14	52509008	52509008	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggtccacatcagtgaagtgcAcgggtgtatggcccacgtgg	15	10	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:52509008A>G	ENST00000216286.5	-	7	1639	c.1640T>C	c.(1639-1641)gTg>gCg	p.V547A	NID2_ENST00000541773.1_Missense_Mutation_p.V494A	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	547	Nidogen G2 beta-barrel. {ECO:0000255|PROSITE-ProRule:PRU00348}.				basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					AGTGAAGTGCACGGGTGTATG	0.577																																					p.V547A		Atlas-SNP	.											.	NID2	201	.	0			c.T1640C						.						139	141	140					14																	52509008		2203	4300	6503	SO:0001583	missense	22795	exon7			AAGTGCACGGGTG	AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.1640T>C	chr14.hg19:g.52509008A>G	ENSP00000216286:p.Val547Ala	137.0	0.0		82.0	5.0	NM_007361	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	hg19	CCDS9706.1	.	.	.	.	.	.	.	.	.	.	A	16.55	3.155519	0.57259	.	.	ENSG00000087303	ENST00000216286;ENST00000316204;ENST00000541773;ENST00000395707	T;T	0.35236	1.32;1.32	6.17	6.17	0.99709	G2 nidogen/fibulin G2F (3);Green fluorescent protein-like (1);	0.052456	0.85682	D	0.000000	T	0.64918	0.2642	M	0.84326	2.69	0.42283	D	0.992109	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.97110	0.995;0.992;1.0;0.998	T	0.69892	-0.5022	10	0.72032	D	0.01	.	16.4837	0.84171	1.0:0.0:0.0:0.0	.	141;494;549;547	E7EPP3;Q14112-2;Q5CZI2;Q14112	.;.;.;NID2_HUMAN	A	547;141;494;549	ENSP00000216286:V547A;ENSP00000443730:V494A	ENSP00000216286:V547A	V	-	2	0	NID2	51578758	1.000000	0.71417	0.990000	0.47175	0.009000	0.06853	8.901000	0.92560	2.371000	0.80710	0.533000	0.62120	GTG	.	.		0.577	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1			G	52509008	A	G	52509008	3	3	254	1	0	0	0	0	1	0	0	0	10424	159	6	2	2551	2	NID2	14	52509008	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	4895582	52509008	54840532	684	34976										
WDHD1	11169	hgsc.bcm.edu	37	chr14	55434060	55434060	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cttaaaggataatatagcaaCagcagggcgtggaagggttg	14	5	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:55434060C>T	ENST00000360586.3	-	17	2181	c.2116G>A	c.(2116-2118)Gtt>Att	p.V706I	WDHD1_ENST00000421192.1_Missense_Mutation_p.V583I|WDHD1_ENST00000359167.4_Missense_Mutation_p.V224I|WDHD1_ENST00000420358.2_Missense_Mutation_p.V583I	NM_007086.3	NP_009017.1	O75717	WDHD1_HUMAN	WD repeat and HMG-box DNA binding protein 1	706					heterochromatin maintenance (GO:0070829)|regulation of chromosome organization (GO:0033044)|RNA processing (GO:0006396)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA binding (GO:0003723)			breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(2)	42						AATATAGCAACAGCAGGGCGT	0.388																																					p.V706I		Atlas-SNP	.											.	WDHD1	82	.	0			c.G2116A						.						96	94	95					14																	55434060		2203	4300	6503	SO:0001583	missense	11169	exon17			TAGCAACAGCAGG	AJ006266	CCDS9721.1, CCDS41955.1	14q22.2	2013-01-09			ENSG00000198554	ENSG00000198554		"WD repeat domain containing"	23170	protein-coding gene	gene with protein product	"CTF4, chromosome transmission fidelity factor 4 homolog (S. cerevisiae)"	608126				9175701, 20028748	Standard	NM_007086		Approved	AND-1, CTF4, CHTF4	uc001xbm.2	O75717	OTTHUMG00000140304	ENST00000360586.3:c.2116G>A	chr14.hg19:g.55434060C>T	ENSP00000353793:p.Val706Ile	101.0	0.0		82.0	4.0	NM_007086	C9JW18|F6W0U7	Missense_Mutation	SNP	ENST00000360586.3	hg19	CCDS9721.1	.	.	.	.	.	.	.	.	.	.	C	12.03	1.815286	0.32053	.	.	ENSG00000198554	ENST00000360586;ENST00000359167;ENST00000421192	T;T;T	0.62232	0.42;0.83;0.04	5.34	3.54	0.40534	.	0.137252	0.48286	N	0.000181	T	0.52125	0.1715	L	0.40543	1.245	0.54753	D	0.999984	B;B	0.22414	0.069;0.006	B;B	0.27715	0.082;0.006	T	0.40590	-0.9555	10	0.27082	T	0.32	.	11.7104	0.51623	0.0:0.8575:0.0:0.1425	.	224;706	F8W7P7;O75717	.;WDHD1_HUMAN	I	706;224;583	ENSP00000353793:V706I;ENSP00000352085:V224I;ENSP00000391049:V583I	ENSP00000352085:V224I	V	-	1	0	WDHD1	54503810	0.996000	0.38824	0.679000	0.29978	0.438000	0.31896	2.338000	0.43957	0.643000	0.30638	0.655000	0.94253	GTT	.	.		0.388	WDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276897.2	NM_007086		T	55434060	C	T	55434060	3	4	254	1	0	0	0	0	1	0	0	0	17286	478	17	3	1313	3	WDHD1	14	55434060	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	2925052	55434060	51915480	685	34977										
SLC38A6	145389	hgsc.bcm.edu	37	chr14	61550393	61550393	+	Missense_Mutation	SNP	T	T	C													0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	caaacgtgtccacaccttgaTcttgcacttcccaacctcca							TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:61550393T>C	ENST00000354886.2	+	17	1693	c.1529T>C	c.(1528-1530)aTc>aCc	p.I510T	SLC38A6_ENST00000456840.2_3'UTR	NM_001172702.1	NP_001166173.1	Q8IZM9	S38A6_HUMAN	solute carrier family 38, member 6	346					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(108;0.0981)		cacaccttgatcttgcacttc	0.463																																					p.I510T		Atlas-SNP	.											.	SLC38A6	87	.	0			c.T1529C						.																																			SO:0001583	missense	145389	exon17			CCTTGATCTTGCA	AF070578	CCDS9751.1, CCDS53900.1	14q23.1	2013-05-22			ENSG00000139974	ENSG00000139974		"Solute carriers"	19863	protein-coding gene	gene with protein product							Standard	NM_153811		Approved	NAT-1	uc001xfh.2	Q8IZM9	OTTHUMG00000140335	ENST00000354886.2:c.1529T>C	chr14.hg19:g.61550393T>C	ENSP00000346959:p.Ile510Thr	99.0	0.0		92.0	4.0	NM_001172702	C9JWA6|Q86SY5	Missense_Mutation	SNP	ENST00000354886.2	hg19	CCDS53900.1	.	.	.	.	.	.	.	.	.	.	T	5.651	0.304812	0.10678	.	.	ENSG00000139974	ENST00000354886;ENST00000451406	T;T	0.06142	3.34;3.34	2.8	-2.93	0.05598	.	.	.	.	.	T	0.04634	0.0126	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38887	-0.9640	8	0.87932	D	0	.	4.0768	0.09908	0.1611:0.3483:0.0:0.4905	.	510	Q8IZM9-2	.	T	510;505	ENSP00000346959:I510T;ENSP00000395851:I505T	ENSP00000346959:I510T	I	+	2	0	SLC38A6	60620146	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.840000	0.04363	-1.120000	0.02953	-1.162000	0.01777	ATC	.	.		0.463	SLC38A6-201	KNOWN	basic|CCDS	protein_coding	protein_coding				C	61550393	T	C	61550393	3	2	254	1	0	0	0	0	1	0	0	0	14623	1435	50	2	1680	2	SLC38A6	14	61550393	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	6116333	61550393	45799147	686	34978	180	3								
SLC38A6	145389	hgsc.bcm.edu	37	chr14	61550399	61550399	+	Missense_Mutation	SNP	A	A	G													0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgtccacaccttgatcttgcActtcccaacctccagaactg							TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:61550399A>G	ENST00000354886.2	+	17	1699	c.1535A>G	c.(1534-1536)cAc>cGc	p.H512R	SLC38A6_ENST00000456840.2_3'UTR	NM_001172702.1	NP_001166173.1	Q8IZM9	S38A6_HUMAN	solute carrier family 38, member 6	348					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(108;0.0981)		ttgatcttgcacttcccaacc	0.458																																					p.H512R		Atlas-SNP	.											.	SLC38A6	87	.	0			c.A1535G						.																																			SO:0001583	missense	145389	exon17			TCTTGCACTTCCC	AF070578	CCDS9751.1, CCDS53900.1	14q23.1	2013-05-22			ENSG00000139974	ENSG00000139974		"Solute carriers"	19863	protein-coding gene	gene with protein product							Standard	NM_153811		Approved	NAT-1	uc001xfh.2	Q8IZM9	OTTHUMG00000140335	ENST00000354886.2:c.1535A>G	chr14.hg19:g.61550399A>G	ENSP00000346959:p.His512Arg	96.0	0.0		84.0	5.0	NM_001172702	C9JWA6|Q86SY5	Missense_Mutation	SNP	ENST00000354886.2	hg19	CCDS53900.1	.	.	.	.	.	.	.	.	.	.	A	8.343	0.829158	0.16749	.	.	ENSG00000139974	ENST00000354886;ENST00000451406	T;T	0.05139	3.49;3.49	2.9	-0.921	0.10472	.	.	.	.	.	T	0.04724	0.0128	.	.	.	0.09310	N	1	B	0.25169	0.119	B	0.23574	0.047	T	0.40961	-0.9535	8	0.87932	D	0	.	3.0296	0.06102	0.5001:0.2305:0.2694:0.0	.	512	Q8IZM9-2	.	R	512;507	ENSP00000346959:H512R;ENSP00000395851:H507R	ENSP00000346959:H512R	H	+	2	0	SLC38A6	60620152	0.000000	0.05858	0.003000	0.11579	0.032000	0.12392	-0.124000	0.10595	-0.173000	0.10761	0.528000	0.53228	CAC	.	.		0.458	SLC38A6-201	KNOWN	basic|CCDS	protein_coding	protein_coding				G	61550399	A	G	61550399	3	3	254	1	0	0	0	0	1	0	0	0	14623	159	6	2	1686	2	SLC38A6	14	61550399	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	6	61550399	45799141	687	34979	180	3								
SLC38A6	145389	hgsc.bcm.edu	37	chr14	61550409	61550409	+	Silent	SNP	C	C	A													0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttgatcttgcacttcccaacCtccagaactgtgagcaaata							TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:61550409C>A	ENST00000354886.2	+	17	1709	c.1545C>A	c.(1543-1545)acC>acA	p.T515T	SLC38A6_ENST00000456840.2_3'UTR	NM_001172702.1	NP_001166173.1	Q8IZM9	S38A6_HUMAN	solute carrier family 38, member 6	351					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(108;0.0981)		acttcccaacctccagaactg	0.448																																					p.T515T		Atlas-SNP	.											.	SLC38A6	87	.	0			c.C1545A						.																																			SO:0001819	synonymous_variant	145389	exon17			CCCAACCTCCAGA	AF070578	CCDS9751.1, CCDS53900.1	14q23.1	2013-05-22			ENSG00000139974	ENSG00000139974		"Solute carriers"	19863	protein-coding gene	gene with protein product							Standard	NM_153811		Approved	NAT-1	uc001xfh.2	Q8IZM9	OTTHUMG00000140335	ENST00000354886.2:c.1545C>A	chr14.hg19:g.61550409C>A		87.0	0.0		79.0	4.0	NM_001172702	C9JWA6|Q86SY5	Silent	SNP	ENST00000354886.2	hg19	CCDS53900.1																																																																																			.	.		0.448	SLC38A6-201	KNOWN	basic|CCDS	protein_coding	protein_coding				A	61550409	C	A	61550409	2	1	254	1	0	0	0	0	0	0	0	1	14623	668	24	3		3	SLC38A6	14	61550409	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	10	61550409	45799131	688	34980	180	3								
PRKCH	5583	hgsc.bcm.edu	37	chr14	61920071	61920071	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggaaatatttctccaacctcGgtgagactttgctttttttc	7	9	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:61920071G>T	ENST00000332981.5	+	7	1345	c.960G>T	c.(958-960)tcG>tcT	p.S320S	PRKCH_ENST00000555082.1_Splice_Site_p.S159S	NM_006255.3	NP_006246.2	P24723	KPCL_HUMAN	protein kinase C, eta	320					blood coagulation (GO:0007596)|negative regulation of glial cell apoptotic process (GO:0034351)|platelet activation (GO:0030168)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein kinase C signaling (GO:0070528)|protein phosphorylation (GO:0006468)|regulation of tight junction assembly (GO:2000810)|signal transduction (GO:0007165)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(4)|ovary(2)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25				OV - Ovarian serous cystadenocarcinoma(108;0.045)|BRCA - Breast invasive adenocarcinoma(234;0.0906)|KIRC - Kidney renal clear cell carcinoma(182;0.182)		CTCCAACCTCGGTGAGACTTT	0.483																																					p.S320S	Melanoma(135;863 1779 8064 14443 26348)	Atlas-SNP	.											.	PRKCH	89	.	0			c.G960T						.						76	64	68					14																	61920071		2203	4300	6503	SO:0001630	splice_region_variant	5583	exon7			AACCTCGGTGAGA	M55284	CCDS9752.1	14q23.1	2009-07-10			ENSG00000027075	ENSG00000027075	2.7.11.1		9403	protein-coding gene	gene with protein product		605437		PRKCL		1986216, 1545821	Standard	NM_006255		Approved	PKC-L, PKCL	uc001xfn.3	P24723	OTTHUMG00000152341	ENST00000332981.5:c.960+1G>T	chr14.hg19:g.61920071G>T		114.0	0.0		112.0	5.0	NM_006255	B4DJN5|Q16246|Q8NE03	Silent	SNP	ENST00000332981.5	hg19	CCDS9752.1																																																																																			.	.		0.483	PRKCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276974.2	NM_006255	Silent	T	61920071	G	T	61920071	5	4	254	1	0	0	0	0	0	0	1	0	12525	1130	39	1	986	1	PRKCH	14	61920071	Splice_Site	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	369662	61920071	45429469	689	34981										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64641845	64641845	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agatgattaagcagttccagAgcactgtagaggtaaactca	10	7	1	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:64641845A>G	ENST00000344113.4	+	95	17631	c.17419A>G	c.(17419-17421)Agc>Ggc	p.S5807G	SYNE2_ENST00000358025.3_Missense_Mutation_p.S5807G|SYNE2_ENST00000357395.3_Missense_Mutation_p.S2192G|SYNE2_ENST00000394768.2_Missense_Mutation_p.S2192G|SYNE2_ENST00000555002.1_Missense_Mutation_p.S2441G|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000554584.1_Missense_Mutation_p.S5672G	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	5807					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		GCAGTTCCAGAGCACTGTAGA	0.413																																					p.S5807G		Atlas-SNP	.											.	SYNE2	577	.	0			c.A17419G						.						71	73	72					14																	64641845		2203	4300	6503	SO:0001583	missense	23224	exon95			TTCCAGAGCACTG	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.17419A>G	chr14.hg19:g.64641845A>G	ENSP00000341781:p.Ser5807Gly	88.0	0.0		113.0	5.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	hg19	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	A	9.500	1.103026	0.20632	.	.	ENSG00000054654	ENST00000358025;ENST00000357395;ENST00000344113;ENST00000554584;ENST00000261678;ENST00000555002;ENST00000394768	T;T;T;T;T;T	0.75589	1.31;1.31;1.31;-0.95;1.31;1.31	5.46	3.09	0.35607	.	0.395446	0.23847	N	0.043988	T	0.60143	0.2246	L	0.52364	1.645	0.41980	D	0.990793	B;B;B;B;B	0.18310	0.003;0.001;0.004;0.004;0.027	B;B;B;B;B	0.15484	0.011;0.003;0.006;0.005;0.013	T	0.49244	-0.8960	10	0.02654	T	1	.	7.6073	0.28110	0.8192:0.0:0.1808:0.0	.	2192;195;5672;5807;5807	Q8WXH0-7;Q7Z362;G3V5X4;Q8WXH0;Q8WXH0-2	.;.;.;SYNE2_HUMAN;.	G	5807;2192;5807;5672;5678;2441;2192	ENSP00000350719:S5807G;ENSP00000349969:S2192G;ENSP00000341781:S5807G;ENSP00000452570:S5672G;ENSP00000450831:S2441G;ENSP00000378249:S2192G	ENSP00000261678:S5678G	S	+	1	0	SYNE2	63711598	0.975000	0.34042	0.703000	0.30354	0.173000	0.22820	1.135000	0.31454	0.446000	0.26666	0.482000	0.46254	AGC	.	.		0.413	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		G	64641845	A	G	64641845	3	3	254	1	0	0	0	0	1	0	0	0	15461	304	11	2	17793	2	SYNE2	14	64641845	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	2721774	64641845	42707695	690	34982										
RAB15	376267	hgsc.bcm.edu	37	chr14	65417736	65417736	+	Intron	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcccatctggccctcgccttGccttccccggtgaggcaccc	9	20	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:65417736G>T	ENST00000533601.2	-	4	662				FNTB_ENST00000542227.1_Intron|RAB15_ENST00000267512.5_Missense_Mutation_p.A127E|RAB15_ENST00000426039.3_Intron|RAB15_ENST00000436278.2_Missense_Mutation_p.A81E|CHURC1-FNTB_ENST00000549987.1_Intron|FNTB_ENST00000447296.2_Intron			P59190	RAB15_HUMAN	RAB15, member RAS oncogene family						protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	GTP binding (GO:0005525)			endometrium(1)|large_intestine(2)|lung(4)|ovary(1)	8				all cancers(60;0.00136)|OV - Ovarian serous cystadenocarcinoma(108;0.00593)|BRCA - Breast invasive adenocarcinoma(234;0.0102)		CCCTCGCCTTGCCTTCCCCGG	0.582																																					p.A127E		Atlas-SNP	.											.	RAB15	23	.	0			c.C380A						.						68	61	63					14																	65417736		2203	4300	6503	SO:0001627	intron_variant	376267	exon4			CGCCTTGCCTTCC	BC014511	CCDS9768.1	14q23.2	2012-02-28	2012-02-28		ENSG00000139998	ENSG00000139998		"RAB, member RAS oncogene"	20150	protein-coding gene	gene with protein product						11697911	Standard	NM_198686		Approved		uc001xhz.2	P59190	OTTHUMG00000142810	ENST00000533601.2:c.324+55C>A	chr14.hg19:g.65417736G>T		31.0	0.0		35.0	5.0	NM_198686	G5EMR7|Q86TX7|Q8IW89	Missense_Mutation	SNP	ENST00000533601.2	hg19		.	.	.	.	.	.	.	.	.	.	G	9.336	1.061676	0.19987	.	.	ENSG00000139998	ENST00000267512	T	0.66099	-0.19	4.44	0.293	0.15742	.	0.752556	0.10886	N	0.623228	T	0.29976	0.0750	N	0.04768	-0.165	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.17289	-1.0374	10	0.10636	T	0.68	.	0.8357	0.01140	0.262:0.1695:0.395:0.1735	.	127	P59190-2	.	E	127	ENSP00000267512:A127E	ENSP00000267512:A127E	A	-	2	0	RAB15	64487489	0.000000	0.05858	0.001000	0.08648	0.125000	0.20455	-0.067000	0.11579	0.066000	0.16515	0.462000	0.41574	GCA	.	.		0.582	RAB15-003	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000390443.2	NM_198686		T	65417736	G	T	65417736	1	4	254	0	1	0	0	0	0	0	0	0	12916	1319	46	3		3	RAB15	14	65417736	Intron	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	775891	65417736	41931804	691	34983										
FUT8	2530	hgsc.bcm.edu	37	chr14	66083023	66083023	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agtgaattgaagaaattaaaGaacttagaaggaaatgaact	9	2	0	6			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:66083023G>T	ENST00000360689.5	+	5	2141	c.414G>T	c.(412-414)aaG>aaT	p.K138N	FUT8_ENST00000394585.1_Missense_Mutation_p.K138N|FUT8_ENST00000358307.2_5'UTR|FUT8_ENST00000394586.2_Missense_Mutation_p.K138N|FUT8_ENST00000557164.1_5'UTR	NM_004480.4|NM_178155.2	NP_004471.4|NP_835368.1	Q9BYC5	FUT8_HUMAN	fucosyltransferase 8 (alpha (1,6) fucosyltransferase)	138					cell migration (GO:0016477)|cellular protein metabolic process (GO:0044267)|GDP-L-fucose metabolic process (GO:0046368)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|L-fucose catabolic process (GO:0042355)|N-glycan fucosylation (GO:0036071)|N-glycan processing (GO:0006491)|oligosaccharide biosynthetic process (GO:0009312)|post-translational protein modification (GO:0043687)|protein glycosylation in Golgi (GO:0033578)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|receptor metabolic process (GO:0043112)|respiratory gaseous exchange (GO:0007585)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycoprotein 6-alpha-L-fucosyltransferase activity (GO:0008424)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	22				all cancers(60;0.00109)|OV - Ovarian serous cystadenocarcinoma(108;0.00242)|BRCA - Breast invasive adenocarcinoma(234;0.0114)		AGAAATTAAAGAACTTAGAAG	0.378																																					p.K138N		Atlas-SNP	.											FUT8_ENST00000360689,NS,carcinoma,0,4	FUT8	101	.	0			c.G414T						.						66	72	70					14																	66083023		2203	4299	6502	SO:0001583	missense	2530	exon5			ATTAAAGAACTTA	AB049740	CCDS9775.1, CCDS9776.1, CCDS9776.2	14q24.3	2013-02-26			ENSG00000033170	ENSG00000033170		"Fucosyltransferases"	4019	protein-coding gene	gene with protein product		602589				9368041	Standard	NM_178155		Approved		uc001xio.3	Q9BYC5	OTTHUMG00000142818	ENST00000360689.5:c.414G>T	chr14.hg19:g.66083023G>T	ENSP00000353910:p.Lys138Asn	115.0	0.0		86.0	4.0	NM_178155	B4DFS7|G3V5N0|O00235|Q8IUA5|Q9BYC6|Q9P2U5|Q9P2U6	Missense_Mutation	SNP	ENST00000360689.5	hg19	CCDS9775.1	.	.	.	.	.	.	.	.	.	.	G	13.05	2.120068	0.37436	.	.	ENSG00000033170	ENST00000360689;ENST00000394586;ENST00000394585	T;T;T	0.21031	2.03;2.03;2.03	5.81	1.49	0.22878	.	0.315147	0.38111	N	0.001818	T	0.14874	0.0359	L	0.35854	1.095	0.80722	D	1	B	0.25719	0.132	B	0.21546	0.035	T	0.06881	-1.0802	10	0.62326	D	0.03	-12.1693	7.9475	0.29995	0.4102:0.0:0.5898:0.0	.	138	Q9BYC5	FUT8_HUMAN	N	138	ENSP00000353910:K138N;ENSP00000378087:K138N;ENSP00000378086:K138N	ENSP00000345865:K138N	K	+	3	2	FUT8	65152776	1.000000	0.71417	0.997000	0.53966	0.942000	0.58702	1.151000	0.31651	0.393000	0.25203	0.557000	0.71058	AAG	.	.		0.378	FUT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286406.1	NM_004480		T	66083023	G	T	66083023	3	4	254	1	0	0	0	0	1	0	0	0	6118	933	33	3	424	3	FUT8	14	66083023	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	665287	66083023	41266517	692	34984										
RDH11	51109	hgsc.bcm.edu	37	chr14	68157901	68157901	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tctcaaagccatctgctgtcTtcgagtacggacacatcatc	7	13	4	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:68157901T>C	ENST00000381346.4	-	4	520	c.410A>G	c.(409-411)aAg>aGg	p.K137R	RDH11_ENST00000428130.2_Missense_Mutation_p.K137R|RDH11_ENST00000553384.1_Missense_Mutation_p.K124R|RP11-1012A1.4_ENST00000553306.1_5'Flank|RP11-1012A1.4_ENST00000554493.1_5'Flank	NM_001252650.1|NM_016026.3	NP_001239579.1|NP_057110.3	Q8TC12	RDH11_HUMAN	retinol dehydrogenase 11 (all-trans/9-cis/11-cis)	137					adaptation of rhodopsin mediated signaling (GO:0016062)|phototransduction, visible light (GO:0007603)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|photoreceptor inner segment (GO:0001917)	NADP-retinol dehydrogenase activity (GO:0052650)|retinol dehydrogenase activity (GO:0004745)			breast(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(3)|ovary(1)	12				all cancers(60;0.00047)|OV - Ovarian serous cystadenocarcinoma(108;0.00206)|BRCA - Breast invasive adenocarcinoma(234;0.00924)	Vitamin A(DB00162)	ATCTGCTGTCTTCGAGTACGG	0.478																																					p.K137R		Atlas-SNP	.											.	RDH11	21	.	0			c.A410G						.						271	252	258					14																	68157901		2203	4300	6503	SO:0001583	missense	51109	exon4			GCTGTCTTCGAGT	AF151840	CCDS32104.1, CCDS58326.1	14q24.1	2013-10-15	2006-05-09		ENSG00000072042	ENSG00000072042	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	17964	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 7C, member 1", "androgen-regulated short-chain dehydrogenase/reductase 1"	607849	"retinol dehydrogenase 11 (all-trans and 9-cis)"			12226107, 8018917, 19027726	Standard	NM_016026		Approved	MDT1, SDR7C1, ARSDR1	uc001xjv.4	Q8TC12	OTTHUMG00000171196	ENST00000381346.4:c.410A>G	chr14.hg19:g.68157901T>C	ENSP00000370750:p.Lys137Arg	129.0	0.0		89.0	4.0	NM_001252650	A6NDK3|A8K062|B2RB26|B4DDW0|Q0QD40|Q6IAH5|Q9NRW0|Q9Y391	Missense_Mutation	SNP	ENST00000381346.4	hg19	CCDS32104.1	.	.	.	.	.	.	.	.	.	.	T	16.29	3.082882	0.55861	.	.	ENSG00000072042	ENST00000381346;ENST00000553384;ENST00000428130;ENST00000554035;ENST00000557726	D;D;D;D;D	0.87491	-2.26;-2.26;-2.26;-2.26;-2.26	5.85	5.85	0.93711	NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.83524	0.5273	N	0.14661	0.345	0.48632	D	0.999686	P;P;P	0.51240	0.943;0.889;0.91	P;P;P	0.53912	0.733;0.618;0.737	T	0.80832	-0.1206	10	0.12766	T	0.61	.	16.2365	0.82377	0.0:0.0:0.0:1.0	.	137;124;137	B4DDW0;Q8TC12-2;Q8TC12	.;.;RDH11_HUMAN	R	137;124;137;36;85	ENSP00000370750:K137R;ENSP00000452079:K124R;ENSP00000416395:K137R;ENSP00000450802:K36R;ENSP00000450435:K85R	ENSP00000370750:K137R	K	-	2	0	RDH11	67227654	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.054000	0.64275	2.238000	0.73509	0.477000	0.44152	AAG	.	.		0.478	RDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412257.3			C	68157901	T	C	68157901	3	2	254	1	0	0	0	0	1	0	0	0	13205	1609	56	2	562	2	RDH11	14	68157901	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	2074878	68157901	39191639	693	34985										
PAPLN	89932	hgsc.bcm.edu	37	chr14	73720573	73720573	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggcatccaggaggccgtggaGgaggctgagtgtgccgggct	20	9	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:73720573G>T	ENST00000554301.1	+	11	1369	c.1206G>T	c.(1204-1206)gaG>gaT	p.E402D	PAPLN_ENST00000555445.1_Missense_Mutation_p.E402D|PAPLN_ENST00000340738.5_Missense_Mutation_p.E375D|PAPLN_ENST00000427855.1_Missense_Mutation_p.E402D|PAPLN_ENST00000381166.3_Missense_Mutation_p.E402D			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	402	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.					basement membrane (GO:0005604)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(3)	42				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)		AGGCCGTGGAGGAGGCTGAGT	0.692																																					p.E375D		Atlas-SNP	.											.	PAPLN	180	.	0			c.G1125T						.						35	37	36					14																	73720573		2202	4300	6502	SO:0001583	missense	89932	exon11			CGTGGAGGAGGCT	BC042057	CCDS32114.1	14q24.2	2013-01-11				ENSG00000100767		"Immunoglobulin superfamily / I-set domain containing"	19262	protein-coding gene	gene with protein product						11076767, 19734141	Standard	NM_173462		Approved	MGC50452	uc001xnw.4	O95428		ENST00000554301.1:c.1206G>T	chr14.hg19:g.73720573G>T	ENSP00000451803:p.Glu402Asp	145.0	0.0		94.0	4.0	NM_173462	B4DES8|B4DGE6|Q659F2|Q6UXJ4|Q6ZNM1|Q6ZUJ0|Q7Z681|Q8IVU0	Missense_Mutation	SNP	ENST00000554301.1	hg19		.	.	.	.	.	.	.	.	.	.	G	1.192	-0.634944	0.03584	.	.	ENSG00000100767	ENST00000340738;ENST00000427855;ENST00000381166;ENST00000554301;ENST00000555445	T;T;T;T;T	0.60040	0.22;0.22;0.22;0.22;0.22	5.1	-3.13	0.05266	.	.	.	.	.	T	0.22666	0.0547	N	0.04320	-0.23	0.20196	N	0.999923	B;B;B	0.28933	0.011;0.014;0.228	B;B;B	0.24541	0.006;0.01;0.054	T	0.20773	-1.0265	9	0.10111	T	0.7	.	2.3034	0.04168	0.1429:0.3301:0.2631:0.2639	.	402;402;375	O95428-5;O95428;O95428-6	.;PPN_HUMAN;.	D	375;402;402;402;402	ENSP00000345395:E375D;ENSP00000403403:E402D;ENSP00000370558:E402D;ENSP00000451803:E402D;ENSP00000451729:E402D	ENSP00000216658:E402D	E	+	3	2	PAPLN	72790326	0.978000	0.34361	0.016000	0.15963	0.099000	0.18886	0.119000	0.15626	-0.359000	0.08150	-0.379000	0.06801	GAG	.	.		0.692	PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	NM_173462		T	73720573	G	T	73720573	3	4	254	1	0	0	0	0	1	0	0	0	11437	991	35	3	1163	3	PAPLN	14	73720573	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	5562672	73720573	33628967	694	34986										
HEATR4	399671	hgsc.bcm.edu	37	chr14	73969702	73969702	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	attccacatcagctggatcaActtatgtttcatatcctata	4	10	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:73969702A>G	ENST00000553558.1	-	11	2323	c.2002T>C	c.(2002-2004)Ttg>Ctg	p.L668L	HEATR4_ENST00000560393.1_Silent_p.L621L|HEATR4_ENST00000334988.2_Silent_p.L668L	NM_001220484.1	NP_001207413.1	Q86WZ0	HEAT4_HUMAN	HEAT repeat containing 4	668										breast(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00386)|OV - Ovarian serous cystadenocarcinoma(108;0.0719)		AGCTGGATCAACTTATGTTTC	0.403																																					p.L668L		Atlas-SNP	.											.	HEATR4	126	.	0			c.T2002C						.						109	98	101					14																	73969702		2203	4300	6503	SO:0001819	synonymous_variant	399671	exon10			GGATCAACTTATG	BC047590	CCDS9815.1, CCDS9815.2	14q24.3	2013-09-20			ENSG00000187105	ENSG00000187105			16761	protein-coding gene	gene with protein product						15489334	Standard	NM_203309		Approved	MGC48595	uc021rwf.2	Q86WZ0	OTTHUMG00000171602	ENST00000553558.1:c.2002T>C	chr14.hg19:g.73969702A>G		84.0	0.0		88.0	4.0	NM_203309	B7Z7V9|E9KL41	Silent	SNP	ENST00000553558.1	hg19	CCDS9815.2																																																																																			.	.		0.403	HEATR4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414422.2	NM_203309		G	73969702	A	G	73969702	2	3	254	1	0	0	0	0	0	0	0	1	7039	40	2	2		2	HEATR4	14	73969702	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	249129	73969702	33379838	695	34987										
ALDH6A1	4329	hgsc.bcm.edu	37	chr14	74534081	74534081	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggcaagtcaggtgattgattAcctgcattgactctcaggtt	11	8	2	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:74534081A>G	ENST00000553458.1	-	8	1141		c.e8+1		ALDH6A1_ENST00000555126.1_Splice_Site|CCDC176_ENST00000553773.1_Intron|AC005484.5_ENST00000492026.1_RNA|ALDH6A1_ENST00000350259.4_Splice_Site	NM_001278593.1|NM_005589.2	NP_001265522.1|NP_005580.1	Q02252	MMSA_HUMAN	aldehyde dehydrogenase 6 family, member A1						branched-chain amino acid catabolic process (GO:0009083)|brown fat cell differentiation (GO:0050873)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|thymine catabolic process (GO:0006210)|thymine metabolic process (GO:0019859)|valine catabolic process (GO:0006574)|valine metabolic process (GO:0006573)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	fatty-acyl-CoA binding (GO:0000062)|malonate-semialdehyde dehydrogenase (acetylating) activity (GO:0018478)|methylmalonate-semialdehyde dehydrogenase (acylating) activity (GO:0004491)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|prostate(3)|skin(3)	21				BRCA - Breast invasive adenocarcinoma(234;0.00354)		GTGATTGATTACCTGCATTGA	0.507																																					.		Atlas-SNP	.											.	ALDH6A1	42	.	0			c.1042+2T>C						.						72	71	71					14																	74534081		2203	4300	6503	SO:0001630	splice_region_variant	4329	exon9			TTGATTACCTGCA	M93405	CCDS9826.1, CCDS61501.1	14q24.3	2014-02-03			ENSG00000119711	ENSG00000119711	1.2.1.27	"Aldehyde dehydrogenases"	7179	protein-coding gene	gene with protein product		603178		MMSDH		1527093	Standard	NM_005589		Approved		uc001xpo.3	Q02252	OTTHUMG00000171203	ENST00000553458.1:c.1042+1T>C	chr14.hg19:g.74534081A>G		63.0	0.0		73.0	4.0	NM_005589	B2R609|B4DFS8|J3KNU8|Q9UKM8	Splice_Site	SNP	ENST00000553458.1	hg19	CCDS9826.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.007886	0.75046	.	.	ENSG00000119711	ENST00000553458;ENST00000350259;ENST00000555126	.	.	.	4.55	4.55	0.56014	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.9558	0.71113	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ALDH6A1	73603834	1.000000	0.71417	0.935000	0.37517	0.955000	0.61496	9.084000	0.94076	2.270000	0.75569	0.482000	0.46254	.	.	.		0.507	ALDH6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412309.1		Intron	G	74534081	A	G	74534081	5	3	254	1	0	0	0	0	0	0	1	0	503	405	14	2	583	2	ALDH6A1	14	74534081	Splice_Site	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	564379	74534081	32815459	696	34988										
ADCK1	57143	hgsc.bcm.edu	37	chr14	78374194	78374194	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cggagcgggtcctcctgatgGagtttgtggatggcgggcag	19	8	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:78374194G>T	ENST00000238561.5	+	7	889	c.790G>T	c.(790-792)Gag>Tag	p.E264*	ADCK1_ENST00000341211.5_Nonsense_Mutation_p.E196*	NM_020421.3	NP_065154.2	Q86TW2	ADCK1_HUMAN	aarF domain containing kinase 1	271	Protein kinase.					extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(2)|stomach(2)	25			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0376)		CCTCCTGATGGAGTTTGTGGA	0.592																																					p.E264X		Atlas-SNP	.											.	ADCK1	81	.	0			c.G790T						.						104	90	95					14																	78374194		2203	4300	6503	SO:0001587	stop_gained	57143	exon7			CTGATGGAGTTTG	AK096919	CCDS9869.1, CCDS45144.1	14q24	2005-10-30							19038	protein-coding gene	gene with protein product						12471243	Standard	NM_020421		Approved	FLJ39600	uc001xui.3	Q86TW2		ENST00000238561.5:c.790G>T	chr14.hg19:g.78374194G>T	ENSP00000238561:p.Glu264*	147.0	0.0		71.0	5.0	NM_020421	B3KUD5|Q6PD65|Q9UIE6	Nonsense_Mutation	SNP	ENST00000238561.5	hg19	CCDS9869.1	.	.	.	.	.	.	.	.	.	.	G	39	7.883161	0.98542	.	.	ENSG00000063761	ENST00000238561;ENST00000341211	.	.	.	4.76	4.76	0.60689	.	0.048925	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-40.5031	17.9868	0.89158	0.0:0.0:1.0:0.0	.	.	.	.	X	264;196	.	ENSP00000238561:E264X	E	+	1	0	ADCK1	77443947	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.411000	0.97342	2.473000	0.83533	0.561000	0.74099	GAG	.	.		0.592	ADCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413864.1	NM_020421		T	78374194	G	T	78374194	4	4	254	1	0	0	0	0	0	1	0	0	288	1175	41	3	812	3	ADCK1	14	78374194	Nonsense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	3840113	78374194	28975346	697	34989										
NRXN3	9369	hgsc.bcm.edu	37	chr14	80130289	80130289	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cagtgaatgaacattatcctAcaggtacatgttgttcgctc	8	9	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:80130289A>G	ENST00000557594.1	+	3	1551	c.598A>G	c.(598-600)Aca>Gca	p.T200A	NRXN3_ENST00000554719.1_Missense_Mutation_p.T832A|RP11-242P2.1_ENST00000553322.1_RNA|NRXN3_ENST00000556003.1_3'UTR|NRXN3_ENST00000281127.7_Missense_Mutation_p.T200A|NRXN3_ENST00000335750.5_Missense_Mutation_p.T832A|NRXN3_ENST00000428277.2_Missense_Mutation_p.T200A	NM_001272020.1	NP_001258949.1	Q9HDB5	NRX3B_HUMAN	neurexin 3	200	Laminin G-like. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|angiogenesis (GO:0001525)|learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(23)|lung(40)|ovary(3)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(9)|urinary_tract(1)	104		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		ACATTATCCTACAGGTACATG	0.478																																					p.T832A		Atlas-SNP	.											.	NRXN3	342	.	0			c.A2494G						.						120	109	113					14																	80130289		2203	4300	6503	SO:0001583	missense	9369	exon14			TATCCTACAGGTA	AB018286	CCDS9870.1, CCDS9871.1, CCDS45145.1, CCDS61515.1	14q31	2010-01-19				ENSG00000021645			8010	protein-coding gene	gene with protein product		600567	"chromosome 14 open reading frame 60"	C14orf60		11944992, 12379233	Standard	NM_004796		Approved	KIAA0743	uc001xun.4	Q9HDB5		ENST00000557594.1:c.598A>G	chr14.hg19:g.80130289A>G	ENSP00000451672:p.Thr200Ala	115.0	0.0		93.0	4.0	NM_004796	A5PKW8|A8MPU5|B3KPM7|Q6NUR0|Q8IUD8	Missense_Mutation	SNP	ENST00000557594.1	hg19		.	.	.	.	.	.	.	.	.	.	A	3.606	-0.080515	0.07141	.	.	ENSG00000021645	ENST00000330071;ENST00000332068;ENST00000554719;ENST00000335750;ENST00000557594;ENST00000281127;ENST00000428277	T;T;T;T;T	0.77877	-1.13;-1.13;-1.05;-1.05;-1.05	5.38	4.1	0.47936	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.270973	0.35013	N	0.003515	T	0.52256	0.1723	N	0.04335	-0.225	0.27521	N	0.951405	B;B;B;B	0.15473	0.013;0.0;0.0;0.0	B;B;B;B	0.24701	0.055;0.0;0.001;0.0	T	0.37220	-0.9715	9	.	.	.	.	5.9111	0.19029	0.6982:0.0:0.0813:0.2204	.	200;200;200;832	Q9HDB5-4;Q9HDB5-2;Q9HDB5;Q9Y4C0-3	.;.;NRX3B_HUMAN;.	A	1205;1194;832;832;200;200;200	ENSP00000451648:T832A;ENSP00000338349:T832A;ENSP00000451672:T200A;ENSP00000281127:T200A;ENSP00000394426:T200A	.	T	+	1	0	NRXN3	79200042	0.492000	0.26027	1.000000	0.80357	0.861000	0.49209	1.248000	0.32827	2.159000	0.67721	0.379000	0.24179	ACA	.	.		0.478	NRXN3-004	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000413790.1	NM_001105250		G	80130289	A	G	80130289	3	3	254	1	0	0	0	0	1	0	0	0	10676	391	14	2	2791	2	NRXN3	14	80130289	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	1756095	80130289	27219251	698	34990										
C14orf145	145508	hgsc.bcm.edu	37	chr14	80971326	80971326	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aagaggatgagtgatctaacCcacgagtgtgggaaccttcc	12	9	1	3	rs377362585		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:80971326C>A	ENST00000555265.1	-	24	3485	c.3110G>T	c.(3109-3111)gGg>gTg	p.G1037V	CEP128_ENST00000553717.1_5'UTR|CEP128_ENST00000281129.3_Missense_Mutation_p.G1037V			Q6ZU80	CE128_HUMAN	centrosomal protein 128kDa	1037						centriole (GO:0005814)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	51						GTGATCTAACCCACGAGTGTG	0.423																																					p.G1037V		Atlas-SNP	.											.	CEP128	146	.	0			c.G3110T						.	C	VAL/GLY	1,4405	2.1+/-5.4	0,1,2202	68	65	66		3110	3.4	0	14		66	0,8600		0,0,4300	no	missense	CEP128	NM_152446.3	109	0,1,6502	AA,AC,CC		0.0,0.0227,0.0077	benign	1037/1095	80971326	1,13005	2203	4300	6503	SO:0001583	missense	145508	exon23			TCTAACCCACGAG	AK056756	CCDS32130.1	14q31.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000100629	ENSG00000100629			20359	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 61", "chromosome 14 open reading frame 145"	C14orf61, C14orf145		21399614	Standard	NM_152446		Approved		uc001xux.2	Q6ZU80		ENST00000555265.1:c.3110G>T	chr14.hg19:g.80971326C>A	ENSP00000451162:p.Gly1037Val	78.0	0.0		60.0	4.0	NM_152446	B9EK52|Q86X97|Q96ML4	Missense_Mutation	SNP	ENST00000555265.1	hg19	CCDS32130.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.36|11.36	1.615669|1.615669	0.28801|0.28801	2.27E-4|2.27E-4	0.0|0.0	ENSG00000100629|ENSG00000100629	ENST00000281129;ENST00000555265|ENST00000556061	T;T|.	0.33216|.	1.42;1.42|.	5.32|5.32	3.38|3.38	0.38709|0.38709	.|.	0.718872|.	0.12773|.	N|.	0.440346|.	T|T	0.23965|0.23965	0.0580|0.0580	N|N	0.24115|0.24115	0.695|0.695	0.09310|0.09310	N|N	0.999999|0.999999	B|.	0.16603|.	0.018|.	B|.	0.19946|.	0.027|.	T|T	0.19386|0.19386	-1.0307|-1.0307	10|5	0.37606|.	T|.	0.19|.	.|.	5.7203|5.7203	0.17982|0.17982	0.187:0.7092:0.0:0.1037|0.187:0.7092:0.0:0.1037	.|.	1037|.	Q6ZU80|.	CE128_HUMAN|.	V|C	1037|102	ENSP00000281129:G1037V;ENSP00000451162:G1037V|.	ENSP00000281129:G1037V|.	G|W	-|-	2|3	0|0	CEP128|CEP128	80041079|80041079	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.167000|0.167000	0.22549|0.22549	0.136000|0.136000	0.15974|0.15974	0.708000|0.708000	0.31955|0.31955	-0.355000|-0.355000	0.07637|0.07637	GGG|TGG	.	.		0.423	CEP128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413415.1	NM_152446		A	80971326	C	A	80971326	3	1	254	1	0	0	0	0	1	0	0	0	1751	623	22	3	182	3	C14orf145	14	80971326	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	841037	80971326	26378214	699	34991										
PTPN21	11099	hgsc.bcm.edu	37	chr14	88974267	88974267	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tatgaattgatcttatttacCttgaacagctaagcctgcta	6	8	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:88974267C>T	ENST00000556564.1	-	4	732	c.448G>A	c.(448-450)Gcg>Acg	p.A150T	RP11-507K2.2_ENST00000555444.1_RNA|PTPN21_ENST00000554628.1_5'UTR|PTPN21_ENST00000328736.3_Splice_Site_p.A150T	NM_007039.3	NP_008970.2	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type 21	150	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|liver(1)|lung(7)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						TCTTATTTACCTTGAACAGCT	0.313																																					p.A150T		Atlas-SNP	.											.	PTPN21	113	.	0			c.G448A						.						73	68	70					14																	88974267		2202	4299	6501	SO:0001630	splice_region_variant	11099	exon4			ATTTACCTTGAAC	X79510	CCDS9884.1	14q31	2011-06-09				ENSG00000070778		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9651	protein-coding gene	gene with protein product		603271				7519780	Standard	NM_007039		Approved	PTPD1, PTPRL10	uc001xwv.4	Q16825		ENST00000556564.1:c.448+1G>A	chr14.hg19:g.88974267C>T		95.0	0.0		79.0	4.0	NM_007039		Missense_Mutation	SNP	ENST00000556564.1	hg19	CCDS9884.1	.	.	.	.	.	.	.	.	.	.	C	35	5.508892	0.96386	.	.	ENSG00000070778	ENST00000328736;ENST00000556564;ENST00000555243	T;T;T	0.79554	-1.28;-1.28;-1.28	5.36	5.36	0.76844	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.137638	0.48767	D	0.000178	D	0.92080	0.7490	M	0.91510	3.215	0.53005	D	0.999963	D;P	0.89917	1.0;0.875	D;P	0.78314	0.991;0.672	D	0.93399	0.6758	9	.	.	.	.	19.0908	0.93225	0.0:1.0:0.0:0.0	.	150;150	G3V3S6;Q16825	.;PTN21_HUMAN	T	150	ENSP00000330276:A150T;ENSP00000452414:A150T;ENSP00000451401:A150T	.	A	-	1	0	PTPN21	88044020	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.818000	0.86416	2.498000	0.84270	0.591000	0.81541	GCG	.	.		0.313	PTPN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410303.1		Missense_Mutation	T	88974267	C	T	88974267	5	4	254	1	0	0	0	0	0	0	1	0	12801	695	24	3	3140	3	PTPN21	14	88974267	Splice_Site	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	8002941	88974267	18375273	700	34992										
GPR68	8111	hgsc.bcm.edu	37	chr14	91700499	91700499	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccaggcaggccccgcggaggCgggccaggtcccggtgggtg	20	14	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:91700499C>T	ENST00000531499.2	-	2	1235	c.896G>A	c.(895-897)cGc>cAc	p.R299H	GPR68_ENST00000238699.3_Missense_Mutation_p.R309H|GPR68_ENST00000529300.1_5'Flank|GPR68_ENST00000535815.1_Missense_Mutation_p.R299H			Q15743	OGR1_HUMAN	G protein-coupled receptor 68	299					cellular response to pH (GO:0071467)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of osteoclast development (GO:2001206)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(2)|endometrium(1)|kidney(1)|lung(2)|skin(1)|urinary_tract(1)	8		all_cancers(154;0.0555)		COAD - Colon adenocarcinoma(157;0.21)		CCCGCGGAGGCGGGCCAGGTC	0.711																																					p.R299H		Atlas-SNP	.											GPR68,colon,carcinoma,0,1	GPR68	32	.	0			c.G896A						.						8	12	11					14																	91700499		2110	4150	6260	SO:0001583	missense	8111	exon2			CGGAGGCGGGCCA	U48405	CCDS9894.1, CCDS9894.2	14q31	2012-08-21				ENSG00000119714		"GPCR / Class A : Orphans"	4519	protein-coding gene	gene with protein product		601404				8661159	Standard	NM_001177676		Approved	OGR1	uc001xzg.3	Q15743		ENST00000531499.2:c.896G>A	chr14.hg19:g.91700499C>T	ENSP00000434045:p.Arg299His	40.0	0.0		32.0	11.0	NM_001177676	Q13334|Q4VBB4|Q6IX34	Missense_Mutation	SNP	ENST00000531499.2	hg19	CCDS9894.2	.	.	.	.	.	.	.	.	.	.	C	18.93	3.728328	0.69074	.	.	ENSG00000119714	ENST00000531499;ENST00000238699;ENST00000535815;ENST00000529102	T;T;T;T	0.40756	1.02;1.02;1.02;1.02	5.26	5.26	0.73747	.	0.226361	0.35739	N	0.003009	T	0.45915	0.1366	L	0.27053	0.805	0.30915	N	0.728668	D;D	0.89917	1.0;1.0	D;D	0.65443	0.935;0.935	T	0.51474	-0.8701	10	0.66056	D	0.02	.	8.091	0.30801	0.0:0.8617:0.0:0.1383	.	299;299	Q6NWR5;Q15743	.;OGR1_HUMAN	H	299;309;299;299	ENSP00000434045:R299H;ENSP00000238699:R309H;ENSP00000440797:R299H;ENSP00000432740:R299H	ENSP00000238699:R309H	R	-	2	0	GPR68	90770252	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.952000	0.63618	2.457000	0.83068	0.555000	0.69702	CGC	.	.		0.711	GPR68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395245.2			T	91700499	C	T	91700499	3	4	254	1	0	0	0	0	1	0	0	0	6715	768	27	1	205	1	GPR68	14	91700499	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	2726232	91700499	15649041	701	34993										
KIAA1409	57578	hgsc.bcm.edu	37	chr14	94158258	94158258	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	attttggagtagggtgacacCcagcatccttcagctaatgg	11	9	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:94158258C>A	ENST00000393151.2	+	47	7553	c.7553C>A	c.(7552-7554)cCc>cAc	p.P2518H	UNC79_ENST00000553484.1_Missense_Mutation_p.P2540H|UNC79_ENST00000555664.1_Missense_Mutation_p.P2479H|UNC79_ENST00000256339.4_Missense_Mutation_p.P2341H			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	2518					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						AGGGTGACACCCAGCATCCTT	0.463																																					p.P2341H		Atlas-SNP	.											.	UNC79	366	.	0			c.C7022A						.						139	126	130					14																	94158258		2203	4300	6503	SO:0001583	missense	57578	exon47			TGACACCCAGCAT	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"KIAA1409"	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.7553C>A	chr14.hg19:g.94158258C>A	ENSP00000376858:p.Pro2518His	173.0	0.0		138.0	8.0	NM_020818	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	hg19		.	.	.	.	.	.	.	.	.	.	C	26.9	4.783060	0.90282	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.33438	1.42;1.47;1.41;1.42	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.59662	0.2210	M	0.74647	2.275	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.60984	-0.7154	10	0.87932	D	0	-20.8729	20.0784	0.97758	0.0:1.0:0.0:0.0	.	2540	C9JQL1	.	H	2341;2479;2540;2518;2540	ENSP00000256339:P2341H;ENSP00000450868:P2479H;ENSP00000451360:P2540H;ENSP00000376858:P2518H	ENSP00000256339:P2341H	P	+	2	0	KIAA1409	93228011	1.000000	0.71417	0.992000	0.48379	0.993000	0.82548	7.818000	0.86416	2.736000	0.93811	0.655000	0.94253	CCC	.	.		0.463	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		A	94158258	C	A	94158258	3	1	254	1	0	0	0	0	1	0	0	0	8239	623	22	3	7196	3	KIAA1409	14	94158258	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	2457759	94158258	13191282	702	34994										
DEGS2	51466	hgsc.bcm.edu	37	chr14	100613207	100613207	+	IGR	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcacccaggagtggtgctgcGgcaggtggtcgtagtactcg	16	10	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:100613207G>T	ENST00000402714.2	+	0	2353				DEGS2_ENST00000305631.5_Missense_Mutation_p.P288Q|DEGS2_ENST00000557117.1_5'Flank|DEGS2_ENST00000553834.1_Silent_p.A40A			Q9UI08	EVL_HUMAN	Enah/Vasp-like						actin filament organization (GO:0007015)|actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ruffle assembly (GO:1900028)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of stress fiber assembly (GO:0051496)|protein homotetramerization (GO:0051289)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|membrane (GO:0016020)	profilin binding (GO:0005522)|SH3 domain binding (GO:0017124)			cervix(1)|large_intestine(5)|lung(3)|ovary(3)|urinary_tract(2)	14		Melanoma(154;0.152)				GTGGTGCTGCGGCAGGTGGTC	0.637																																					p.P288Q		Atlas-SNP	.											.	DEGS2	25	.	0			c.C863A						.						105	103	104					14																	100613207		2203	4300	6503	SO:0001628	intergenic_variant	123099	exon3			TGCTGCGGCAGGT	AF112209	CCDS9955.1	14q32.2	2014-08-13			ENSG00000196405	ENSG00000196405			20234	protein-coding gene	gene with protein product						10945997, 10993894	Standard	NM_016337		Approved	RNB6	uc001ygu.3	Q9UI08	OTTHUMG00000171530		chr14.hg19:g.100613207G>T		114.0	0.0		75.0	4.0	NM_206918	A8K105|O95884|Q7Z522|Q8TBV1|Q9UF25|Q9UIC2	Missense_Mutation	SNP	ENST00000402714.2	hg19		.	.	.	.	.	.	.	.	.	.	G	27.1	4.802559	0.90623	.	.	ENSG00000168350	ENST00000305631	T	0.33216	1.42	4.86	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.66858	0.2832	M	0.93594	3.435	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.76841	-0.2810	10	0.56958	D	0.05	-8.3096	17.986	0.89156	0.0:0.0:1.0:0.0	.	288	Q6QHC5	DEGS2_HUMAN	Q	288	ENSP00000307126:P288Q	ENSP00000307126:P288Q	P	-	2	0	DEGS2	99682960	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.714000	0.98744	2.251000	0.74343	0.561000	0.74099	CCG	.	.		0.637	EVL-006	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000413958.1			T	100613207	G	T	100613207	1	4	254	0	1	0	0	0	0	0	0	0	4425	1116	39	1		1	DEGS2	14	100613207	IGR	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	6454949	100613207	6736333	703	34995										
DYNC1H1	1778	hgsc.bcm.edu	37	chr14	102446804	102446804	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccgcatccaggagaaacgggAgagcccggaagttctcctga	13	12	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:102446804A>G	ENST00000360184.4	+	5	1042	c.878A>G	c.(877-879)gAg>gGg	p.E293G		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	293	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						GAGAAACGGGAGAGCCCGGAA	0.473																																					p.E293G		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.A878G						.						81	81	81					14																	102446804		2203	4300	6503	SO:0001583	missense	1778	exon5			AACGGGAGAGCCC	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"Cytoplasmic dyneins"	2961	protein-coding gene	gene with protein product		600112	"dynein, cytoplasmic, heavy polypeptide 1"	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.878A>G	chr14.hg19:g.102446804A>G	ENSP00000348965:p.Glu293Gly	113.0	0.0		102.0	6.0	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	hg19	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	A	17.47	3.398526	0.62177	.	.	ENSG00000197102	ENST00000360184	T	0.56941	0.43	5.24	5.24	0.73138	Dynein heavy chain, domain-1 (1);	0.000000	0.85682	D	0.000000	T	0.63379	0.2506	M	0.69248	2.105	0.80722	D	1	P	0.46020	0.871	P	0.52343	0.696	T	0.62774	-0.6783	10	0.35671	T	0.21	.	15.421	0.75011	1.0:0.0:0.0:0.0	.	293	Q14204	DYHC1_HUMAN	G	293	ENSP00000348965:E293G	ENSP00000348965:E293G	E	+	2	0	DYNC1H1	101516557	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.833000	0.92089	2.102000	0.63906	0.482000	0.46254	GAG	.	.		0.473	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		G	102446804	A	G	102446804	3	3	254	1	0	0	0	0	1	0	0	0	4843	304	11	2	896	2	DYNC1H1	14	102446804	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	1833597	102446804	4902736	704	34996										
DYNC1H1	1778	hgsc.bcm.edu	37	chr14	102494143	102494143	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggagggactcaaggaccgggCagctacatcaccagcacttt	12	12	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:102494143C>A	ENST00000360184.4	+	47	9400	c.9236C>A	c.(9235-9237)gCa>gAa	p.A3079E		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	3079	AAA 4. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						AAGGACCGGGCAGCTACATCA	0.562																																					p.A3079E		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.C9236A						.						130	124	126					14																	102494143		2203	4300	6503	SO:0001583	missense	1778	exon47			ACCGGGCAGCTAC	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"Cytoplasmic dyneins"	2961	protein-coding gene	gene with protein product		600112	"dynein, cytoplasmic, heavy polypeptide 1"	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.9236C>A	chr14.hg19:g.102494143C>A	ENSP00000348965:p.Ala3079Glu	88.0	0.0		59.0	14.0	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	hg19	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.721168	0.89205	.	.	ENSG00000197102	ENST00000360184	T	0.49139	0.79	5.78	5.78	0.91487	Dynein heavy chain, P-loop containing D4 domain (1);ATPase, AAA+ type, core (1);	0.112123	0.64402	D	0.000011	T	0.79100	0.4389	H	0.96943	3.91	0.80722	D	1	D	0.63046	0.992	P	0.61275	0.886	D	0.85690	0.1306	10	0.72032	D	0.01	.	20.0203	0.97492	0.0:1.0:0.0:0.0	.	3079	Q14204	DYHC1_HUMAN	E	3079	ENSP00000348965:A3079E	ENSP00000348965:A3079E	A	+	2	0	DYNC1H1	101563896	1.000000	0.71417	0.944000	0.38274	0.889000	0.51656	7.554000	0.82212	2.730000	0.93505	0.655000	0.94253	GCA	.	.		0.562	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		A	102494143	C	A	102494143	3	1	254	1	0	0	0	0	1	0	0	0	4843	710	25	3	9422	3	DYNC1H1	14	102494143	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	47339	102494143	4855397	705	34997										
ZNF839	55778	hgsc.bcm.edu	37	chr14	102805186	102805186	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	taggaatcacagaattcctaCggaagaaagaaatacaccca	7	9	1	3	rs535523717		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:102805186C>A	ENST00000558850.1	+	6	1695	c.1345C>A	c.(1345-1347)Cgg>Agg	p.R449R	AL137229.1_ENST00000577622.1_RNA|ZNF839_ENST00000420933.2_3'UTR|ZNF839_ENST00000559185.1_Silent_p.R449R|ZNF839_ENST00000442396.2_Silent_p.R565R|ZNF839_ENST00000262236.5_Silent_p.R449R	NM_001267827.1	NP_001254756.1	A8K0R7	ZN839_HUMAN	zinc finger protein 839	449							metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						AGAATTCCTACGGAAGAAAGA	0.502																																					p.R565R		Atlas-SNP	.											.	ZNF839	41	.	0			c.C1693A						.						95	93	94					14																	102805186		1960	4144	6104	SO:0001819	synonymous_variant	55778	exon6			TTCCTACGGAAGA	AK093342	CCDS45164.1, CCDS58336.1	14q32.32	2010-05-06	2008-06-23	2008-06-23	ENSG00000022976	ENSG00000022976			20345	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 131"	C14orf131			Standard	NM_018335		Approved		uc010awk.2	A8K0R7		ENST00000558850.1:c.1345C>A	chr14.hg19:g.102805186C>A		217.0	0.0		149.0	35.0	NM_018335	B3KSD2|Q53FH5|Q6GPI5|Q86TU1|Q9BQ86|Q9NUU3	Silent	SNP	ENST00000558850.1	hg19	CCDS58336.1																																																																																			.	.		0.502	ZNF839-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000415492.2	NM_018335		A	102805186	C	A	102805186	2	1	254	1	0	0	0	0	0	0	0	1	18203	527	19	1		1	ZNF839	14	102805186	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	311043	102805186	4544354	706	34998										
AMN	81693	hgsc.bcm.edu	37	chr14	103396365	103396365	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtgctggtggagaatgggccCgagacaggcggagcggggcg	22	8	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:103396365C>A	ENST00000299155.5	+	9	981	c.948C>A	c.(946-948)ccC>ccA	p.P316P		NM_030943.3	NP_112205.2	Q9BXJ7	AMNLS_HUMAN	amnion associated transmembrane protein	316					cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|excretion (GO:0007588)|Golgi to plasma membrane protein transport (GO:0043001)|lipoprotein metabolic process (GO:0042157)|multicellular organismal development (GO:0007275)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			kidney(2)|large_intestine(1)|lung(2)|skin(1)	6				Colorectal(3;0.00739)|READ - Rectum adenocarcinoma(2;0.0336)|Epithelial(152;0.0363)|all cancers(159;0.147)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	AGAATGGGCCCGAGACAGGCG	0.746																																					p.P316P		Atlas-SNP	.											.	AMN	13	.	0			c.C948A						.						9	10	10					14																	103396365		2102	4163	6265	SO:0001819	synonymous_variant	81693	exon9			TGGGCCCGAGACA	AF328788	CCDS9977.1	14q32.32	2014-09-17	2012-12-07		ENSG00000166126	ENSG00000166126			14604	protein-coding gene	gene with protein product		605799	"amnionless homolog (mouse)"			11279523	Standard	NM_030943		Approved	amnionless	uc001ymg.4	Q9BXJ7		ENST00000299155.5:c.948C>A	chr14.hg19:g.103396365C>A		114.0	0.0		76.0	4.0	NM_030943	Q6UX83	Silent	SNP	ENST00000299155.5	hg19	CCDS9977.1																																																																																			.	.		0.746	AMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415704.1			A	103396365	C	A	103396365	2	1	254	1	0	0	0	0	0	0	0	1	580	639	23	1		1	AMN	14	103396365	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	591179	103396365	3953175	707	34999										
C14orf2	9556	hgsc.bcm.edu	37	chr14	104379023	104379023	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttagtgatgaccaggagcagGcgctgaagcttttgaaagag	14	6	0	5			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:104379023G>A	ENST00000554880.1	-	4	310	c.157C>T	c.(157-159)Cct>Tct	p.P53S	C14orf2_ENST00000286953.3_Missense_Mutation_p.P53S|C14orf2_ENST00000555030.1_3'UTR|C14orf2_ENST00000557040.1_Missense_Mutation_p.P53S|C14orf2_ENST00000553430.1_3'UTR|C14orf2_ENST00000414262.2_Missense_Mutation_p.P70S|C14orf2_ENST00000553449.1_5'UTR			P56378	68MP_HUMAN	chromosome 14 open reading frame 2	53						integral component of membrane (GO:0016021)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)				kidney(1)	1				Epithelial(152;0.223)		CCAGGAGCAGGCGCTGAAGCT	0.378																																					p.P70S		Atlas-SNP	.											.	C14orf2	7	.	0			c.C208T						.						146	140	142					14																	104379023		2203	4300	6503	SO:0001583	missense	9556	exon5			GAGCAGGCGCTGA	AF054175	CCDS9986.1, CCDS45169.1	14q32.33	2013-02-18			ENSG00000156411	ENSG00000156411			1188	protein-coding gene	gene with protein product	"6.8 kDa mitochondrial proteolipid"	604573				9653160	Standard	NM_001127393		Approved	MP68	uc001yoi.4	P56378	OTTHUMG00000171601	ENST00000554880.1:c.157C>T	chr14.hg19:g.104379023G>A	ENSP00000452133:p.Pro53Ser	72.0	0.0		66.0	4.0	NM_001127393	B2R588|G3V5Q3|Q86TT7	Missense_Mutation	SNP	ENST00000554880.1	hg19	CCDS9986.1	.	.	.	.	.	.	.	.	.	.	G	9.555	1.117061	0.20795	.	.	ENSG00000156411	ENST00000286953;ENST00000554880;ENST00000414262;ENST00000557040	T;T;T;T	0.45276	0.9;0.9;0.9;0.9	3.8	1.9	0.25705	.	0.301114	0.23838	N	0.044066	T	0.25865	0.0630	.	.	.	0.09310	N	0.999999	B	0.16166	0.016	B	0.12837	0.008	T	0.13176	-1.0519	9	0.38643	T	0.18	.	5.3066	0.15807	0.1167:0.2081:0.6752:0.0	.	53	P56378	68MP_HUMAN	S	53;53;70;53	ENSP00000286953:P53S;ENSP00000452133:P53S;ENSP00000401770:P70S;ENSP00000450894:P53S	ENSP00000286953:P53S	P	-	1	0	C14orf2	103448776	0.872000	0.30054	0.002000	0.10522	0.228000	0.25075	0.895000	0.28363	0.377000	0.24735	0.655000	0.94253	CCT	.	.		0.378	C14orf2-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414398.1	NM_001127393		A	104379023	G	A	104379023	3	1	254	1	0	0	0	0	1	0	0	0	1770	1203	42	3	23	3	C14orf2	14	104379023	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	982658	104379023	2970517	708	35000										
TDRD9	122402	hgsc.bcm.edu	37	chr14	104470585	104470585	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcctttgaaggccgtgctggAcgagtgtctagagggtactg	15	8	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:104470585A>G	ENST00000409874.4	+	14	1542	c.1494A>G	c.(1492-1494)ggA>ggG	p.G498G	TDRD9_ENST00000339063.5_Silent_p.G498G	NM_153046.2	NP_694591.2	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	498	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|piP-body (GO:0071547)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				GCCGTGCTGGACGAGTGTCTA	0.408																																					p.G498G		Atlas-SNP	.											.	TDRD9	175	.	0			c.A1494G						.						112	86	95					14																	104470585		2203	4300	6503	SO:0001819	synonymous_variant	122402	exon14			TGCTGGACGAGTG	AK093483	CCDS9987.2	14q32.33	2013-01-23	2004-04-01	2004-04-02	ENSG00000156414	ENSG00000156414		"Tudor domain containing"	20122	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 75"	C14orf75			Standard	NM_153046		Approved	DKFZp434N0820, FLJ36164, NET54	uc001yom.4	Q8NDG6	OTTHUMG00000152876	ENST00000409874.4:c.1494A>G	chr14.hg19:g.104470585A>G		137.0	0.0		91.0	4.0	NM_153046	A1A4S7|Q6ZU54|Q8N7T3|Q8N827|Q8N9V5|Q96AS9	Silent	SNP	ENST00000409874.4	hg19	CCDS9987.2	.	.	.	.	.	.	.	.	.	.	A	10.50	1.368680	0.24771	.	.	ENSG00000156414	ENST00000557332	.	.	.	5.87	-2.58	0.06228	.	.	.	.	.	T	0.51924	0.1703	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47736	-0.9094	4	.	.	.	.	8.437	0.32793	0.4929:0.107:0.4001:0.0	.	.	.	.	A	225	.	.	T	+	1	0	TDRD9	103540338	0.281000	0.24258	0.963000	0.40424	0.943000	0.58893	-0.382000	0.07408	-0.394000	0.07727	-0.250000	0.11733	ACG	.	.		0.408	TDRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328325.3	NM_153046		G	104470585	A	G	104470585	2	3	254	1	0	0	0	0	0	0	0	1	15751	262	10	2		2	TDRD9	14	104470585	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	91562	104470585	2878955	709	35001										
GPR132	29933	hgsc.bcm.edu	37	chr14	105517772	105517772	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttcaccttggccttctgggcAgcgcttaagcccatgctctg	10	14	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr14:105517772A>G	ENST00000329797.3	-	4	1613	c.702T>C	c.(700-702)gcT>gcC	p.A234A	GPR132_ENST00000546679.1_5'Flank|GPR132_ENST00000392585.2_Silent_p.A225A|GPR132_ENST00000539291.2_Silent_p.A234A	NM_001278694.1|NM_001278696.1|NM_013345.2	NP_001265623.1|NP_001265625.1|NP_037477.1	Q9UNW8	GP132_HUMAN	G protein-coupled receptor 132	234					G1/S transition of mitotic cell cycle (GO:0000082)|response to stress (GO:0006950)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)	18		all_cancers(154;0.0953)|Melanoma(154;0.155)|all_epithelial(191;0.219)	OV - Ovarian serous cystadenocarcinoma(23;0.00778)|all cancers(16;0.00936)|Epithelial(46;0.0227)	Epithelial(152;0.02)|all cancers(159;0.0419)|OV - Ovarian serous cystadenocarcinoma(161;0.0521)		CCTTCTGGGCAGCGCTTAAGC	0.582																																					p.A234A		Atlas-SNP	.											.	GPR132	40	.	0			c.T702C						.						97	89	91					14																	105517772		2203	4300	6503	SO:0001819	synonymous_variant	29933	exon4			CTGGGCAGCGCTT	AF083955	CCDS9997.1, CCDS61567.1	14q32.3	2012-08-21			ENSG00000183484	ENSG00000183484		"GPCR / Class A : Orphans"	17482	protein-coding gene	gene with protein product	"G2 accumulation"	606167				12086852	Standard	NM_013345		Approved	G2A	uc001yqd.3	Q9UNW8	OTTHUMG00000140173	ENST00000329797.3:c.702T>C	chr14.hg19:g.105517772A>G		152.0	0.0		99.0	4.0	NM_013345	A8K7X7|B4E144|Q9BSU2	Silent	SNP	ENST00000329797.3	hg19	CCDS9997.1																																																																																			.	.		0.582	GPR132-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409278.1	NM_013345		G	105517772	A	G	105517772	2	3	254	1	0	0	0	0	0	0	0	1	6650	175	7	2		2	GPR132	14	105517772	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	1047187	105517772	1831768	710	35002										
TUBGCP5	114791	hgsc.bcm.edu	37	chr15	22873209	22873209	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	attcttcccacagtggaatcTctagcgttgtcactcatggc	8	12	4	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:22873209T>C	ENST00000283645.4	+	23	3166	c.3036T>C	c.(3034-3036)tcT>tcC	p.S1012S		NM_052903.4	NP_443135.3	Q96RT8	GCP5_HUMAN	tubulin, gamma complex associated protein 5	1012					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gamma-tubulin ring complex (GO:0008274)|microtubule (GO:0005874)|nucleus (GO:0005634)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(5)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(23)|prostate(1)|skin(2)|urinary_tract(1)	46		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.86e-06)|Epithelial(43;2.63e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000949)		CAGTGGAATCTCTAGCGTTGT	0.373																																					p.S1012S		Atlas-SNP	.											.	TUBGCP5	82	.	0			c.T3036C						.						130	130	130					15																	22873209		2203	4300	6503	SO:0001819	synonymous_variant	114791	exon23			GGAATCTCTAGCG	AB067486	CCDS73697.1, CCDS73698.1	15q11.1	2014-04-17			ENSG00000153575	ENSG00000275835			18600	protein-coding gene	gene with protein product	"gamma-tubulin complex component GCP5"	608147				11694571	Standard	NM_052903		Approved	GCP5, KIAA1899	uc001yur.4	Q96RT8	OTTHUMG00000188371	ENST00000283645.4:c.3036T>C	chr15.hg19:g.22873209T>C		100.0	0.0		100.0	4.0	NM_052903	E9PB12|Q6IQ52|Q96PY8	Silent	SNP	ENST00000283645.4	hg19	CCDS10008.1																																																																																			.	.		0.373	TUBGCP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250998.2	NM_052903		C	22873209	T	C	22873209	2	2	254	1	0	0	0	0	0	0	0	1	16784	1538	54	2		2	TUBGCP5	15	22873209	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10		22873209	79658183	711	35003										
GABRB3	2562	hgsc.bcm.edu	37	chr15	26812847	26812847	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agtatccaatgttcctcttcAaccgaaagctcagtgacagt	7	11	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:26812847A>G	ENST00000311550.5	-	7	827	c.716T>C	c.(715-717)tTg>tCg	p.L239S	GABRB3_ENST00000400188.3_Missense_Mutation_p.L168S|GABRB3_ENST00000545868.1_Missense_Mutation_p.L154S|GABRB3_ENST00000541819.2_Missense_Mutation_p.L295S|GABRB3_ENST00000299267.4_Missense_Mutation_p.L239S	NM_000814.5|NM_001278631.1	NP_000805.1|NP_001265560.1	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 3	239					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|GABA-gated chloride ion channel activity (GO:0022851)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(41)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	68		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ivermectin(DB00602)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Piperazine(DB00592)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GTTCCTCTTCAACCGAAAGCT	0.423																																					p.L239S		Atlas-SNP	.											.	GABRB3	338	.	0			c.T716C						.						127	108	115					15																	26812847		2203	4300	6503	SO:0001583	missense	2562	exon7			CTCTTCAACCGAA		CCDS10018.1, CCDS10019.1, CCDS53920.1, CCDS53921.1	15q12	2012-06-22			ENSG00000166206	ENSG00000166206		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4083	protein-coding gene	gene with protein product	"GABA(A) receptor, beta 3"	137192					Standard	NM_000814		Approved		uc001zaz.3	P28472	OTTHUMG00000129231	ENST00000311550.5:c.716T>C	chr15.hg19:g.26812847A>G	ENSP00000308725:p.Leu239Ser	103.0	0.0		80.0	4.0	NM_021912	B7Z2W1|B7Z825|F5H3D2|H7BYV8|Q14352|Q96FM5	Missense_Mutation	SNP	ENST00000311550.5	hg19	CCDS10019.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.677285	0.88445	.	.	ENSG00000166206	ENST00000311550;ENST00000541819;ENST00000299267;ENST00000400188;ENST00000545868	D;D;D;D;D	0.83914	-1.78;-1.78;-1.78;-1.78;-1.78	6.06	6.06	0.98353	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	D	0.94218	0.8144	H	0.96833	3.89	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.81914	0.988;0.991;0.995	D	0.95891	0.8907	10	0.87932	D	0	.	15.7938	0.78394	1.0:0.0:0.0:0.0	.	295;239;239	F5H7N0;P28472-2;P28472	.;.;GBRB3_HUMAN	S	239;295;239;168;154	ENSP00000308725:L239S;ENSP00000442408:L295S;ENSP00000299267:L239S;ENSP00000383049:L168S;ENSP00000439169:L154S	ENSP00000299267:L239S	L	-	2	0	GABRB3	24363940	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.204000	0.95041	2.322000	0.78497	0.528000	0.53228	TTG	.	.		0.423	GABRB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251352.2			G	26812847	A	G	26812847	3	3	254	1	0	0	0	0	1	0	0	0	6176	131	5	2	717	2	GABRB3	15	26812847	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	3939638	26812847	75718545	712	35004										
TRPM1	4308	hgsc.bcm.edu	37	chr15	31360167	31360167	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccaaagacttgtttcagcttGggctgcatctcaaagttctg	9	10	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:31360167G>A	ENST00000256552.6	-	5	555	c.408C>T	c.(406-408)ccC>ccT	p.P136P	MIR211_ENST00000384969.1_RNA|TRPM1_ENST00000397795.2_Silent_p.P114P|TRPM1_ENST00000542188.1_Silent_p.P153P	NM_001252024.1	NP_001238953.1			transient receptor potential cation channel, subfamily M, member 1											NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		GTTTCAGCTTGGGCTGCATCT	0.542																																					p.P153P		Atlas-SNP	.											.	TRPM1	183	.	0			c.C459T						.						119	118	118					15																	31360167		1898	4128	6026	SO:0001819	synonymous_variant	4308	exon4			CAGCTTGGGCTGC	AF071787	CCDS10024.2, CCDS58345.1, CCDS58346.1, CCDS58347.1	15q13.3	2014-01-28		2002-01-18	ENSG00000134160	ENSG00000134160		"Voltage-gated ion channels / Transient receptor potential cation channels"	7146	protein-coding gene	gene with protein product		603576	"melastatin 1"	MLSN1		9806836, 9537257, 16382100	Standard	NM_001252020		Approved	LTRPC1, CSNB1C	uc021sia.1	Q7Z4N2	OTTHUMG00000129267	ENST00000256552.6:c.408C>T	chr15.hg19:g.31360167G>A		101.0	0.0		99.0	4.0	NM_001252020		Silent	SNP	ENST00000256552.6	hg19	CCDS58346.1																																																																																			.	.		0.542	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420		A	31360167	G	A	31360167	2	1	254	1	0	0	0	0	0	0	0	1	16600	1335	47	3		3	TRPM1	15	31360167	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	4547320	31360167	71171225	713	35005										
RYR3	6263	hgsc.bcm.edu	37	chr15	33855056	33855056	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aggaactcaaggagaaattaGactccagtcacaagcgagac	10	9	2	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:33855056G>T	ENST00000389232.4	+	11	1061	c.991G>T	c.(991-993)Gac>Tac	p.D331Y	RYR3_ENST00000415757.3_Missense_Mutation_p.D331Y	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	331	MIR 4. {ECO:0000255|PROSITE- ProRule:PRU00131}.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			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)		GGAGAAATTAGACTCCAGTCA	0.393																																					p.D331Y		Atlas-SNP	.											.	RYR3	760	.	0			c.G991T						.						66	65	65					15																	33855056		1862	4106	5968	SO:0001583	missense	6263	exon11			AAATTAGACTCCA		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.991G>T	chr15.hg19:g.33855056G>T	ENSP00000373884:p.Asp331Tyr	120.0	0.0		86.0	30.0	NM_001243996	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	hg19	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.335986	0.81801	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D;D	0.93953	-3.32;-3.32	5.27	5.27	0.74061	MIR motif (2);MIR (2);	0.118731	0.56097	D	0.000026	D	0.95573	0.8561	L	0.54323	1.7	0.58432	D	0.999998	D;D	0.67145	0.996;0.989	D;P	0.65874	0.939;0.883	D	0.95691	0.8740	10	0.72032	D	0.01	.	18.6774	0.91534	0.0:0.0:1.0:0.0	.	331;331	Q15413-2;Q15413	.;RYR3_HUMAN	Y	331	ENSP00000373884:D331Y;ENSP00000399610:D331Y	ENSP00000354735:D331Y	D	+	1	0	RYR3	31642348	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.491000	0.97954	2.748000	0.94277	0.655000	0.94253	GAC	.	.		0.393	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			T	33855056	G	T	33855056	3	4	254	1	0	0	0	0	1	0	0	0	13785	942	33	3	1033	3	RYR3	15	33855056	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	2494889	33855056	68676336	714	35006										
AQR	9716	hgsc.bcm.edu	37	chr15	35182513	35182513	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgccatgattttctcaaacaActggtttagggcctagacaa	8	9	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:35182513A>G	ENST00000156471.5	-	24	2809	c.2584T>C	c.(2584-2586)Ttg>Ctg	p.L862L		NM_014691.2	NP_055506.1	O60306	AQR_HUMAN	aquarius intron-binding spliceosomal factor	862					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(10)|lung(18)|ovary(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	57		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		TTCTCAAACAACTGGTTTAGG	0.423																																					p.L862L		Atlas-SNP	.											.	AQR	139	.	0			c.T2584C						.						155	145	148					15																	35182513		1901	4121	6022	SO:0001819	synonymous_variant	9716	exon24			CAAACAACTGGTT	AB011132	CCDS42013.1	15q13	2013-09-12	2013-09-12			ENSG00000021776			29513	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 164"	610548	"aquarius homolog (mouse)"			9626505, 16949364	Standard	NM_014691		Approved	KIAA0560, fSAP164, IBP160	uc001ziv.3	O60306		ENST00000156471.5:c.2584T>C	chr15.hg19:g.35182513A>G		147.0	0.0		97.0	4.0	NM_014691	A0JP17|A5YKK3|Q2YDX9|Q6IRU8|Q6PIC8	Silent	SNP	ENST00000156471.5	hg19	CCDS42013.1																																																																																			.	.		0.423	AQR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417526.2	NM_014691		G	35182513	A	G	35182513	2	3	254	1	0	0	0	0	0	0	0	1	835	40	2	2		2	AQR	15	35182513	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	1327457	35182513	67348879	715	35007										
AQR	9716	hgsc.bcm.edu	37	chr15	35212582	35212582	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aagttgtgtcttcatttttaGgaagagttggcaacaagcag	11	5	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:35212582G>T	ENST00000156471.5	-	14	1397	c.1172C>A	c.(1171-1173)cCt>cAt	p.P391H		NM_014691.2	NP_055506.1	O60306	AQR_HUMAN	aquarius intron-binding spliceosomal factor	391					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(10)|lung(18)|ovary(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	57		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		TTCATTTTTAGGAAGAGTTGG	0.338																																					p.P391H		Atlas-SNP	.											.	AQR	139	.	0			c.C1172A						.						77	74	75					15																	35212582		1819	4083	5902	SO:0001583	missense	9716	exon14			TTTTTAGGAAGAG	AB011132	CCDS42013.1	15q13	2013-09-12	2013-09-12			ENSG00000021776			29513	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 164"	610548	"aquarius homolog (mouse)"			9626505, 16949364	Standard	NM_014691		Approved	KIAA0560, fSAP164, IBP160	uc001ziv.3	O60306		ENST00000156471.5:c.1172C>A	chr15.hg19:g.35212582G>T	ENSP00000156471:p.Pro391His	92.0	0.0		88.0	4.0	NM_014691	A0JP17|A5YKK3|Q2YDX9|Q6IRU8|Q6PIC8	Missense_Mutation	SNP	ENST00000156471.5	hg19	CCDS42013.1	.	.	.	.	.	.	.	.	.	.	G	18.73	3.685655	0.68157	.	.	ENSG00000021776	ENST00000156471;ENST00000543879	D	0.94138	-3.36	5.16	5.16	0.70880	.	0.097095	0.64402	D	0.000001	D	0.94404	0.8200	M	0.87097	2.86	0.49798	D	0.999827	P	0.44344	0.833	B	0.40659	0.336	D	0.95277	0.8382	10	0.62326	D	0.03	-17.0567	18.8265	0.92121	0.0:0.0:1.0:0.0	.	391	O60306	AQR_HUMAN	H	391	ENSP00000156471:P391H	ENSP00000156471:P391H	P	-	2	0	AQR	32999874	1.000000	0.71417	0.998000	0.56505	0.599000	0.36880	7.335000	0.79234	2.688000	0.91661	0.563000	0.77884	CCT	.	.		0.338	AQR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417526.2	NM_014691		T	35212582	G	T	35212582	3	4	254	1	0	0	0	0	1	0	0	0	835	1000	35	3	3373	3	AQR	15	35212582	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	30069	35212582	67318810	716	35008										
EIF2AK4	440275	hgsc.bcm.edu	37	chr15	40301931	40301931	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	attattctgtatgatgctgtGgtaagcatttaattacttat	7	4	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:40301931G>A	ENST00000263791.5	+	26	3736	c.3693G>A	c.(3691-3693)gtG>gtA	p.V1231V	EIF2AK4_ENST00000382727.2_Splice_Site_p.V1203V	NM_001013703.2	NP_001013725.2	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha kinase 4	1231	Histidyl-tRNA synthetase-like.				cellular response to starvation (GO:0009267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of translation (GO:0017148)|protein phosphorylation (GO:0006468)|regulation of translational initiation (GO:0006446)|regulation of translational initiation in response to stress (GO:0043558)	cytosolic ribosome (GO:0022626)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)	40		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		ATGATGCTGTGGTAAGCATTT	0.323																																					p.V1231V		Atlas-SNP	.											.	EIF2AK4	107	.	0			c.G3693A						.						92	89	90					15																	40301931		1857	4097	5954	SO:0001630	splice_region_variant	440275	exon26			TGCTGTGGTAAGC	AB037759	CCDS42016.1	15q13.3	2008-08-18				ENSG00000128829			19687	protein-coding gene	gene with protein product		609280				10504407	Standard	XM_005254392		Approved	GCN2, KIAA1338	uc001zkm.1	Q9P2K8		ENST00000263791.5:c.3693+1G>A	chr15.hg19:g.40301931G>A		138.0	0.0		96.0	4.0	NM_001013703	C9JEC4|Q69YL7|Q6DC97|Q96GN6|Q9H5K1|Q9NSQ3|Q9NSZ5|Q9UJ56	Silent	SNP	ENST00000263791.5	hg19	CCDS42016.1																																																																																			.	.		0.323	EIF2AK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418395.1		Silent	A	40301931	G	A	40301931	5	1	254	1	0	0	0	0	0	0	1	0	5001	1362	47	3	3795	3	EIF2AK4	15	40301931	Splice_Site	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	5089349	40301931	62229461	717	35009										
PAK6	56924	hgsc.bcm.edu	37	chr15	40565184	40565184	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agggaggagccctcacagacAtcgtctcccaagtcaggtgg	13	12	3	1	rs140245743		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:40565184A>G	ENST00000542403.2	+	5	1585	c.1474A>G	c.(1474-1476)Atc>Gtc	p.I492V	PAK6_ENST00000453867.1_Missense_Mutation_p.I492V|PAK6_ENST00000260404.4_Missense_Mutation_p.I492V|PAK6_ENST00000455577.2_Missense_Mutation_p.I492V|RP11-133K1.2_ENST00000558658.1_3'UTR|PAK6_ENST00000560346.1_Missense_Mutation_p.I492V|PAK6_ENST00000441369.1_Missense_Mutation_p.I492V	NM_001276717.1	NP_001263646.1	Q9NQU5	PAK6_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 6	492	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cytoskeleton organization (GO:0007010)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(11)|ovary(2)|prostate(1)|skin(2)	24		all_cancers(109;1.13e-18)|all_epithelial(112;1.62e-15)|Lung NSC(122;5.67e-11)|all_lung(180;1.41e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0823)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.51e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0544)		CCTCACAGACATCGTCTCCCA	0.622																																					p.I492V		Atlas-SNP	.											.	PAK6	49	.	0			c.A1474G						.	A	VAL/ILE,VAL/ILE,VAL/ILE	0,4406		0,0,2203	129	114	119		1474,1474,1474	4.7	1	15	dbSNP_134	119	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	PAK6	NM_001128628.1,NM_001128629.1,NM_020168.4	29,29,29	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging	492/682,492/682,492/682	40565184	1,13005	2203	4300	6503	SO:0001583	missense	56924	exon6			ACAGACATCGTCT	AF276893	CCDS10054.1, CCDS61590.1	15q14	2008-06-17	2008-06-17		ENSG00000137843	ENSG00000137843			16061	protein-coding gene	gene with protein product		608110	"p21(CDKN1A)-activated kinase 6"			11278661	Standard	NM_020168		Approved	PAK5	uc001zlb.3	Q9NQU5	OTTHUMG00000129921	ENST00000542403.2:c.1474A>G	chr15.hg19:g.40565184A>G	ENSP00000439597:p.Ile492Val	66.0	0.0		70.0	4.0	NM_001128629	A8K2G2|B3KYB0|G5E9R2	Missense_Mutation	SNP	ENST00000542403.2	hg19	CCDS10054.1	.	.	.	.	.	.	.	.	.	.	A	18.04	3.535649	0.64972	0.0	1.16E-4	ENSG00000137843	ENST00000441369;ENST00000453867;ENST00000455577;ENST00000260404;ENST00000542403	T;T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11;-0.11	4.69	4.69	0.59074	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.052324	0.85682	D	0.000000	T	0.62708	0.2450	N	0.11892	0.195	0.80722	D	1	P;P	0.46656	0.882;0.639	D;B	0.68765	0.96;0.172	T	0.63363	-0.6654	10	0.30854	T	0.27	.	14.342	0.66633	1.0:0.0:0.0:0.0	.	492;492	Q9NQU5;G5E9R2	PAK6_HUMAN;.	V	492	ENSP00000406873:I492V;ENSP00000401153:I492V;ENSP00000409465:I492V;ENSP00000260404:I492V;ENSP00000439597:I492V	ENSP00000260404:I492V	I	+	1	0	PAK6	38352476	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.139000	0.94554	1.974000	0.57490	0.533000	0.62120	ATC	.	A|1.000;G|0.000		0.622	PAK6-004	NOVEL	alternative_3_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000418355.1			G	40565184	A	G	40565184	3	3	254	1	0	0	0	0	1	0	0	0	11413	217	8	2	1488	2	PAK6	15	40565184	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	263253	40565184	61966208	718	35010										
VPS18	57617	hgsc.bcm.edu	37	chr15	41187016	41187016	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctcgctgtcccgctcggccgTcttgcagcccggctgcccta	11	19	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:41187016T>C	ENST00000220509.5	+	1	389	c.50T>C	c.(49-51)gTc>gCc	p.V17A	VPS18_ENST00000558474.1_Missense_Mutation_p.V17A	NM_020857.2	NP_065908.1	Q9P253	VPS18_HUMAN	vacuolar protein sorting 18 homolog (S. cerevisiae)	17					endosome organization (GO:0007032)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|vesicle-mediated transport (GO:0016192)|viral entry into host cell (GO:0046718)	actin filament (GO:0005884)|early endosome (GO:0005769)|HOPS complex (GO:0030897)|lysosomal membrane (GO:0005765)	metal ion binding (GO:0046872)			autonomic_ganglia(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	28		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;1.07e-05)|COAD - Colon adenocarcinoma(120;0.15)|BRCA - Breast invasive adenocarcinoma(123;0.164)		CGCTCGGCCGTCTTGCAGCCC	0.652											OREG0023068	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V17A		Atlas-SNP	.											.	VPS18	67	.	0			c.T50C						.						21	19	20					15																	41187016		2169	4246	6415	SO:0001583	missense	57617	exon1			CGGCCGTCTTGCA	AF308802	CCDS10069.1	15q14-q15	2006-12-19	2006-12-19		ENSG00000104142	ENSG00000104142			15972	protein-coding gene	gene with protein product		608551	"vacuolar protein sorting protein 18"			11250079, 16203730	Standard	NM_020857		Approved	KIAA1475, PEP3	uc001zne.3	Q9P253	OTTHUMG00000130135	ENST00000220509.5:c.50T>C	chr15.hg19:g.41187016T>C	ENSP00000220509:p.Val17Ala	127.0	0.0	899	48.0	4.0	NM_020857	Q8TCG0|Q96DI3|Q9H268	Missense_Mutation	SNP	ENST00000220509.5	hg19	CCDS10069.1	.	.	.	.	.	.	.	.	.	.	T	7.813	0.716130	0.15306	.	.	ENSG00000104142	ENST00000220509	T	0.41758	0.99	4.68	3.56	0.40772	.	0.384243	0.29972	N	0.010740	T	0.18467	0.0443	N	0.08118	0	0.26613	N	0.972797	B	0.10296	0.003	B	0.08055	0.003	T	0.16276	-1.0408	10	0.16896	T	0.51	-51.0287	5.667	0.17700	0.0:0.254:0.0:0.746	.	17	Q9P253	VPS18_HUMAN	A	17	ENSP00000220509:V17A	ENSP00000220509:V17A	V	+	2	0	VPS18	38974308	0.874000	0.30092	1.000000	0.80357	0.181000	0.23173	1.022000	0.30052	0.941000	0.37499	0.402000	0.26972	GTC	.	.		0.652	VPS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252443.2			C	41187016	T	C	41187016	3	2	254	1	0	0	0	0	1	0	0	0	17209	1667	58	2	52	2	VPS18	15	41187016	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	621832	41187016	61344376	719	35011										
NDUFAF1	51103	hgsc.bcm.edu	37	chr15	41687071	41687071	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgttaccttgacctcctgccAgtagggtcccccgcgggtga	12	14	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:41687071A>G	ENST00000260361.4	-	3	1126	c.745T>C	c.(745-747)Tgg>Cgg	p.W249R		NM_016013.3	NP_057097.2	Q9Y375	CIA30_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 1	249					mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|mitochondrial respiratory chain complex I (GO:0005747)	unfolded protein binding (GO:0051082)			endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	12		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;8e-17)|GBM - Glioblastoma multiforme(113;1.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.114)		ACCTCCTGCCAGTAGGGTCCC	0.478																																					p.W249R		Atlas-SNP	.											.	NDUFAF1	39	.	0			c.T745C						.						76	73	74					15																	41687071		2203	4300	6503	SO:0001583	missense	51103	exon3			CCTGCCAGTAGGG	AF151823	CCDS10075.1	15q11.2-q21.3	2012-10-12	2012-05-08		ENSG00000137806	ENSG00000137806		"Mitochondrial respiratory chain complex assembly factors"	18828	protein-coding gene	gene with protein product		606934				11935339, 10810093	Standard	NM_016013		Approved	CIA30, CGI-65	uc001znx.3	Q9Y375	OTTHUMG00000130340	ENST00000260361.4:c.745T>C	chr15.hg19:g.41687071A>G	ENSP00000260361:p.Trp249Arg	95.0	0.0		71.0	4.0	NM_016013	Q9BVZ5	Missense_Mutation	SNP	ENST00000260361.4	hg19	CCDS10075.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.522096	0.85600	.	.	ENSG00000137806	ENST00000260361	D	0.82619	-1.63	5.52	5.52	0.82312	NADH:ubiquinone oxidoreductase intermediate-associated protein 30 (1);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	D	0.93344	0.7878	M	0.94021	3.485	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94959	0.8106	10	0.87932	D	0	-20.7997	15.9772	0.80079	1.0:0.0:0.0:0.0	.	249	Q9Y375	CIA30_HUMAN	R	249	ENSP00000260361:W249R	ENSP00000260361:W249R	W	-	1	0	NDUFAF1	39474363	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	9.047000	0.93823	2.235000	0.73313	0.451000	0.29950	TGG	.	.		0.478	NDUFAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252692.2	NM_016013		G	41687071	A	G	41687071	3	3	254	1	0	0	0	0	1	0	0	0	10283	188	7	2	250	2	NDUFAF1	15	41687071	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	500055	41687071	60844321	720	35012										
LTK	4058	hgsc.bcm.edu	37	chr15	41801262	41801262	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	caggaagagctcgctgctggGgtgtatgaaggatactccat	14	8	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:41801262G>T	ENST00000263800.6	-	8	1159	c.1063C>A	c.(1063-1065)Ccc>Acc	p.P355T	LTK_ENST00000561619.1_Missense_Mutation_p.P37T|LTK_ENST00000453182.2_Missense_Mutation_p.P294T|LTK_ENST00000355166.5_Missense_Mutation_p.P294T	NM_002344.5	NP_002335.2	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase	355					cell proliferation (GO:0008283)|cellular response to retinoic acid (GO:0071300)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of neuron projection development (GO:0010976)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(16)|skin(3)|urinary_tract(1)	26		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		TCGCTGCTGGGGTGTATGAAG	0.587										TSP Lung(18;0.14)																											p.P355T		Atlas-SNP	.											.	LTK	117	.	0			c.C1063A						.						95	92	93					15																	41801262		2203	4300	6503	SO:0001583	missense	4058	exon8			TGCTGGGGTGTAT	D16105	CCDS10077.1, CCDS10078.1, CCDS45237.1	15q15.1-q21.1	2009-07-10	2008-01-23		ENSG00000062524	ENSG00000062524	2.7.10.1		6721	protein-coding gene	gene with protein product		151520	"leukocyte tyrosine kinase"			2320375	Standard	NM_206961		Approved	TYK1	uc001zoa.3	P29376	OTTHUMG00000130339	ENST00000263800.6:c.1063C>A	chr15.hg19:g.41801262G>T	ENSP00000263800:p.Pro355Thr	238.0	0.0		163.0	7.0	NM_002344	A6NNJ8|B4DL89|E9PFX4	Missense_Mutation	SNP	ENST00000263800.6	hg19	CCDS10077.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.253548	0.80135	.	.	ENSG00000062524	ENST00000360087;ENST00000355166;ENST00000263800;ENST00000453182	T;T;D	0.81659	-1.07;1.2;-1.52	5.33	4.42	0.53409	.	0.000000	0.33364	U	0.004998	D	0.87807	0.6270	M	0.72118	2.19	0.28559	N	0.911205	P;D;D;D	0.89917	0.915;0.999;1.0;1.0	P;D;D;D	0.87578	0.468;0.921;0.996;0.998	T	0.82552	-0.0400	10	0.48119	T	0.1	.	12.4858	0.55872	0.0816:0.0:0.9184:0.0	.	294;294;294;355	E9PFX4;B4DL89;P29376-4;P29376	.;.;.;LTK_HUMAN	T	355;294;355;294	ENSP00000347293:P294T;ENSP00000263800:P355T;ENSP00000392196:P294T	ENSP00000263800:P355T	P	-	1	0	LTK	39588554	1.000000	0.71417	0.603000	0.28903	0.989000	0.77384	6.530000	0.73816	1.233000	0.43693	0.491000	0.48974	CCC	.	.		0.587	LTK-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252690.2			T	41801262	G	T	41801262	3	4	254	1	0	0	0	0	1	0	0	0	9089	1232	43	3	1583	3	LTK	15	41801262	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	114191	41801262	60730130	721	35013										
MGA	23269	hgsc.bcm.edu	37	chr15	41989188	41989188	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aagcctgatctggaagatgtGgatggtgttctctttgtttc	12	6	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:41989188G>T	ENST00000570161.1	+	2	1980	c.1980G>T	c.(1978-1980)gtG>gtT	p.V660V	MGA_ENST00000389936.4_Silent_p.V660V|MGA_ENST00000545763.1_Silent_p.V660V|MGA_ENST00000219905.7_Silent_p.V660V|MGA_ENST00000566586.1_Silent_p.V660V			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	Maltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TGGAAGATGTGGATGGTGTTC	0.378																																					p.V660V		Atlas-SNP	.											.	MGA	264	.	0			c.G1980T						.						16	15	16					15																	41989188		1840	4001	5841	SO:0001819	synonymous_variant	23269	exon3			AGATGTGGATGGT	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.1980G>T	chr15.hg19:g.41989188G>T		88.0	0.0		86.0	4.0	NM_001080541	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000570161.1	hg19	CCDS55959.1																																																																																			.	.		0.378	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		T	41989188	G	T	41989188	2	4	254	1	0	0	0	0	0	0	0	1	9549	1335	47	3		3	MGA	15	41989188	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	187926	41989188	60542204	722	35014										
SPTBN5	51332	hgsc.bcm.edu	37	chr15	42182404	42182404	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccgatgagtggtactggcacCtgtgggcacagttggatggg	17	8	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:42182404C>A	ENST00000320955.6	-	4	612		c.e4-1		RP11-23P13.6_ENST00000309874.2_RNA|RP11-23P13.6_ENST00000564432.2_RNA	NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5						actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		GTACTGGCACCTGTGGGCACA	0.577																																					.		Atlas-SNP	.											.	SPTBN5	171	.	0			c.280-1G>T						.						93	94	93					15																	42182404		2058	4200	6258	SO:0001630	splice_region_variant	51332	exon5			TGGCACCTGTGGG	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"beta V spectrin"	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.385-1G>T	chr15.hg19:g.42182404C>A		147.0	0.0		90.0	4.0	NM_016642		Splice_Site	SNP	ENST00000320955.6	hg19		.	.	.	.	.	.	.	.	.	.	C	19.25	3.790500	0.70337	.	.	ENSG00000137877	ENST00000320955	.	.	.	4.89	3.98	0.46160	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.5858	0.56416	0.0:0.9188:0.0:0.0812	.	.	.	.	.	-1	.	.	.	-	.	.	SPTBN5	39969696	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	6.357000	0.73051	1.048000	0.40298	0.655000	0.94253	.	.	.		0.577	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	Intron	A	42182404	C	A	42182404	5	1	254	1	0	0	0	0	0	0	1	0	15137	695	24	3	10900	3	SPTBN5	15	42182404	Splice_Site	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	193216	42182404	60348988	723	35015										
TMEM87A	25963	hgsc.bcm.edu	37	chr15	42529654	42529654	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttctcctttgtatcggatatTctgaaattccgcatagaaga	7	8	2	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:42529654T>C	ENST00000389834.4	-	9	1108	c.844A>G	c.(844-846)Aat>Gat	p.N282D	TMEM87A_ENST00000448392.1_Missense_Mutation_p.N221D	NM_015497.3	NP_056312.2	Q8NBN3	TM87A_HUMAN	transmembrane protein 87A	282						integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(4)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	24		all_cancers(109;4.28e-16)|all_epithelial(112;1.04e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;1.03e-06)		TATCGGATATTCTGAAATTCC	0.428																																					p.N282D		Atlas-SNP	.											.	TMEM87A	56	.	0			c.A844G						.						105	98	100					15																	42529654		2203	4299	6502	SO:0001583	missense	25963	exon9			GGATATTCTGAAA	AF132733	CCDS32205.1, CCDS45243.1, CCDS66742.1	15q15.1	2005-10-30				ENSG00000103978			24522	protein-coding gene	gene with protein product						12477932	Standard	XM_005254287		Approved	DKFZP564G2022	uc021sjr.1	Q8NBN3		ENST00000389834.4:c.844A>G	chr15.hg19:g.42529654T>C	ENSP00000374484:p.Asn282Asp	101.0	0.0		89.0	4.0	NM_015497	Q6NT77|Q8NCA4|Q9BS46|Q9P103|Q9Y3Y7	Missense_Mutation	SNP	ENST00000389834.4	hg19	CCDS32205.1	.	.	.	.	.	.	.	.	.	.	T	33	5.205764	0.95033	.	.	ENSG00000103978	ENST00000389834;ENST00000448392;ENST00000535305	.	.	.	5.8	5.8	0.92144	.	0.047282	0.85682	D	0.000000	T	0.66386	0.2784	M	0.63428	1.95	0.50171	D	0.999859	D;P	0.53312	0.959;0.544	P;B	0.52343	0.696;0.341	T	0.65817	-0.6076	9	0.37606	T	0.19	-16.717	16.1464	0.81575	0.0:0.0:0.0:1.0	.	282;221	Q8NBN3;Q8NBN3-3	TM87A_HUMAN;.	D	282;221;258	.	ENSP00000374484:N282D	N	-	1	0	TMEM87A	40316946	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	8.040000	0.89188	2.220000	0.72140	0.383000	0.25322	AAT	.	.		0.428	TMEM87A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420482.2	NM_015497		C	42529654	T	C	42529654	3	2	254	1	0	0	0	0	1	0	0	0	16225	1783	62	2	871	2	TMEM87A	15	42529654	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	347250	42529654	60001738	724	35016										
SERINC4	619189	hgsc.bcm.edu	37	chr15	44089116	44089116	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cagctgatgacagaagcttgTaggaggccagagcggggttg	17	7	0	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:44089116T>A	ENST00000319327.6	-	7	1101	c.867A>T	c.(865-867)ctA>ctT	p.L289L	SERF2_ENST00000594896.1_Intron|HYPK_ENST00000406925.1_5'UTR|SERINC4_ENST00000249714.3_Silent_p.L45L|SERF2_ENST00000409646.1_Intron|SERF2_ENST00000409291.1_Intron|SERINC4_ENST00000299969.6_Intron|RP11-296A16.1_ENST00000417761.2_Missense_Mutation_p.T98S	NM_001258031.1	NP_001244960.1	A6NH21	SERC4_HUMAN	serine incorporator 4	289					phospholipid biosynthetic process (GO:0008654)	integral component of membrane (GO:0016021)				central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)	6		all_cancers(109;3.26e-11)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.61e-06)|all_lung(180;1.5e-05)|Melanoma(134;0.0417)		GBM - Glioblastoma multiforme(94;7.81e-07)		CAGAAGCTTGTAGGAGGCCAG	0.493																																					p.L289L		Atlas-SNP	.											.	SERINC4	18	.	0			c.A867T						.						133	137	136					15																	44089116		2198	4298	6496	SO:0001819	synonymous_variant	619189	exon7			AGCTTGTAGGAGG	DQ103711	CCDS58360.1	15q15.3	2013-09-25			ENSG00000184716	ENSG00000184716			32237	protein-coding gene	gene with protein product		614550					Standard	NM_001258031		Approved	FLJ40363	uc031qrp.1	A6NH21	OTTHUMG00000060144	ENST00000319327.6:c.867A>T	chr15.hg19:g.44089116T>A		175.0	0.0		121.0	5.0	NM_001258031	B2RN41|Q3YL75	Silent	SNP	ENST00000319327.6	hg19	CCDS58360.1																																																																																			.	.		0.493	SERINC4-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133485.2			A	44089116	T	A	44089116	2	1	254	1	0	0	0	0	0	0	0	1	14097	1625	57	4		4	SERINC4	15	44089116	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	1559462	44089116	58442276	725	35017										
SPG11	80208	hgsc.bcm.edu	37	chr15	44876208	44876208	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	actctacttgcttcatgcacAcagccatcatccagtaggcg	7	14	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:44876208A>G	ENST00000261866.7	-	30	5686	c.5670T>C	c.(5668-5670)tgT>tgC	p.C1890C	SPG11_ENST00000558253.1_5'Flank|SPG11_ENST00000427534.2_Silent_p.C1890C|SPG11_ENST00000535302.2_Silent_p.C1890C|SPG11_ENST00000558319.1_Silent_p.C1890C	NM_025137.3	NP_079413.3	Q96JI7	SPTCS_HUMAN	spastic paraplegia 11 (autosomal recessive)	1890					cell death (GO:0008219)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	72		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		CTTCATGCACACAGCCATCAT	0.453																																					p.C1890C		Atlas-SNP	.											.	SPG11	207	.	0			c.T5670C						.						120	99	106					15																	44876208		2198	4298	6496	SO:0001819	synonymous_variant	80208	exon30			ATGCACACAGCCA		CCDS10112.1, CCDS53939.1	15q13-q15	2007-11-13			ENSG00000104133	ENSG00000104133			11226	protein-coding gene	gene with protein product	"spatacsin"	610844	"KIAA1840"	KIAA1840		10408536, 17322883	Standard	NM_001160227		Approved	FLJ21439	uc001ztx.3	Q96JI7	OTTHUMG00000131199	ENST00000261866.7:c.5670T>C	chr15.hg19:g.44876208A>G		102.0	0.0		98.0	5.0	NM_025137	A8KAX9|B9EK60|F5H3N6|Q4VC11|Q58G86|Q69YG6|Q6NW01|Q8N270|Q8TBU9|Q9H734	Silent	SNP	ENST00000261866.7	hg19	CCDS10112.1																																																																																			.	.		0.453	SPG11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253927.1			G	44876208	A	G	44876208	2	3	254	1	0	0	0	0	0	0	0	1	15056	157	6	2		2	SPG11	15	44876208	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	787092	44876208	57655184	726	35018										
SPATA5L1	79029	hgsc.bcm.edu	37	chr15	45713246	45713246	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cttgtctcttaataggctgcTttgctggctctgcaagaaaa	9	9	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:45713246T>C	ENST00000305560.6	+	8	2199	c.2100T>C	c.(2098-2100)gcT>gcC	p.A700A	SPATA5L1_ENST00000533841.1_3'UTR	NM_024063.2	NP_076968.2	Q9BVQ7	SPA5L_HUMAN	spermatogenesis associated 5-like 1	700						cytoplasm (GO:0005737)	ATP binding (GO:0005524)			kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	14		Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;7.31e-17)|GBM - Glioblastoma multiforme(94;6.28e-07)		AATAGGCTGCTTTGCTGGCTC	0.403																																					p.A700A		Atlas-SNP	.											.	SPATA5L1	40	.	0			c.T2100C						.						52	53	53					15																	45713246		2198	4298	6496	SO:0001819	synonymous_variant	79029	exon8			GGCTGCTTTGCTG	AK023232	CCDS10123.1	15q15.1	2010-04-21			ENSG00000171763	ENSG00000171763		"ATPases / AAA-type"	28762	protein-coding gene	gene with protein product						12477932	Standard	NM_024063		Approved	MGC5347, FLJ12286	uc001zve.3	Q9BVQ7	OTTHUMG00000131425	ENST00000305560.6:c.2100T>C	chr15.hg19:g.45713246T>C		43.0	0.0		60.0	4.0	NM_024063	C9JHR5|Q9H8W7|Q9HA41	Silent	SNP	ENST00000305560.6	hg19	CCDS10123.1	.	.	.	.	.	.	.	.	.	.	T	9.528	1.110046	0.20714	.	.	ENSG00000171763	ENST00000531624	.	.	.	5.6	2.22	0.28083	.	.	.	.	.	T	0.58264	0.2110	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53143	-0.8480	4	.	.	.	-26.8576	9.1663	0.37054	0.0:0.6612:0.0:0.3388	.	.	.	.	P	205	.	.	L	+	2	0	SPATA5L1	43500538	0.966000	0.33281	1.000000	0.80357	0.980000	0.70556	-0.056000	0.11787	0.705000	0.31890	-0.366000	0.07423	CTT	.	.		0.403	SPATA5L1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254218.1	NM_024063		C	45713246	T	C	45713246	2	2	254	1	0	0	0	0	0	0	0	1	15027	1596	56	2		2	SPATA5L1	15	45713246	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	837038	45713246	56818146	727	35019										
SLC12A1	6557	hgsc.bcm.edu	37	chr15	48519318	48519318	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cctaagtgtggtagtaacgaCactcacaggtatttctatgt	9	8	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:48519318C>T	ENST00000558405.1	+	4	738				SLC12A1_ENST00000396577.3_Missense_Mutation_p.T224I|SLC12A1_ENST00000380993.3_Intron|SLC12A1_ENST00000330289.6_Intron|SLC12A1_ENST00000559723.1_Intron			Q13621	S12A1_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 1						cell death (GO:0008219)|chemical homeostasis (GO:0048878)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|kidney development (GO:0001822)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:potassium:chloride symporter activity (GO:0008511)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|prostate(2)|skin(1)	59		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Potassium Chloride(DB00761)|Quinethazone(DB01325)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	GTAGTAACGACACTCACAGGT	0.418																																					p.T224I		Atlas-SNP	.											.	SLC12A1	243	.	0			c.C671T						.						255	210	223					15																	48519318		687	1588	2275	SO:0001627	intron_variant	6557	exon5			TAACGACACTCAC		CCDS10129.2, CCDS53940.1	15q15-q21	2013-07-18	2013-07-18		ENSG00000074803	ENSG00000074803		"Solute carriers"	10910	protein-coding gene	gene with protein product		600839				8640224	Standard	NM_000338		Approved	NKCC2	uc010bem.3	Q13621	OTTHUMG00000131495	ENST00000558405.1:c.724+550C>T	chr15.hg19:g.48519318C>T		155.0	0.0		99.0	4.0	NM_001184832	A8JYA2|E9PDW4	Missense_Mutation	SNP	ENST00000558405.1	hg19	CCDS10129.2	.	.	.	.	.	.	.	.	.	.	C	17.66	3.443428	0.63067	.	.	ENSG00000074803	ENST00000396577	D	0.98617	-5.03	5.77	5.77	0.91146	.	0.212326	0.49916	D	0.000122	D	0.98701	0.9564	L	0.57130	1.785	0.80722	D	1	.	.	.	.	.	.	D	0.99709	1.1006	8	0.72032	D	0.01	.	20.3473	0.98799	0.0:1.0:0.0:0.0	.	.	.	.	I	224	ENSP00000379822:T224I	ENSP00000379822:T224I	T	+	2	0	SLC12A1	46306610	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.428000	0.52792	2.884000	0.98904	0.655000	0.94253	ACA	.	.		0.418	SLC12A1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417131.1			T	48519318	C	T	48519318	1	4	254	0	1	0	0	0	0	0	0	0	14397	478	17	3		3	SLC12A1	15	48519318	Intron	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	2806072	48519318	54012074	728	35020										
SLC12A1	6557	hgsc.bcm.edu	37	chr15	48539187	48539187	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tctcctccgccctggcctccCttgtcagcgcacccaaagtg	8	19	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:48539187C>T	ENST00000558405.1	+	11	1548	c.1534C>T	c.(1534-1536)Ctt>Ttt	p.L512F	SLC12A1_ENST00000396577.3_Missense_Mutation_p.L512F|SLC12A1_ENST00000380993.3_Missense_Mutation_p.L512F			Q13621	S12A1_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 1	512					cell death (GO:0008219)|chemical homeostasis (GO:0048878)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|kidney development (GO:0001822)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:potassium:chloride symporter activity (GO:0008511)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|prostate(2)|skin(1)	59		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Potassium Chloride(DB00761)|Quinethazone(DB01325)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	CCTGGCCTCCCTTGTCAGCGC	0.498																																					p.L512F		Atlas-SNP	.											.	SLC12A1	243	.	0			c.C1534T						.						220	203	209					15																	48539187		2198	4297	6495	SO:0001583	missense	6557	exon12			GCCTCCCTTGTCA		CCDS10129.2, CCDS53940.1	15q15-q21	2013-07-18	2013-07-18		ENSG00000074803	ENSG00000074803		"Solute carriers"	10910	protein-coding gene	gene with protein product		600839				8640224	Standard	NM_000338		Approved	NKCC2	uc010bem.3	Q13621	OTTHUMG00000131495	ENST00000558405.1:c.1534C>T	chr15.hg19:g.48539187C>T	ENSP00000453409:p.Leu512Phe	138.0	0.0		98.0	4.0	NM_001184832	A8JYA2|E9PDW4	Missense_Mutation	SNP	ENST00000558405.1	hg19	CCDS10129.2	.	.	.	.	.	.	.	.	.	.	C	26.1	4.707984	0.89018	.	.	ENSG00000074803	ENST00000428362;ENST00000380993;ENST00000396577	D;D	0.99129	-5.46;-5.46	4.98	4.98	0.66077	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.99275	0.9747	M	0.80847	2.515	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.99429	1.0935	10	0.87932	D	0	.	18.4428	0.90673	0.0:1.0:0.0:0.0	.	512;512	E9PDW4;Q13621	.;S12A1_HUMAN	F	325;512;512	ENSP00000370381:L512F;ENSP00000379822:L512F	ENSP00000370381:L512F	L	+	1	0	SLC12A1	46326479	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	5.890000	0.69774	2.582000	0.87167	0.655000	0.94253	CTT	.	.		0.498	SLC12A1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417131.1			T	48539187	C	T	48539187	3	4	254	1	0	0	0	0	1	0	0	0	14397	681	24	3	1676	3	SLC12A1	15	48539187	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	19869	48539187	53992205	729	35021										
SECISBP2L	9728	hgsc.bcm.edu	37	chr15	49320786	49320786	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cactagaagattcagcagtaGggtgggatgctcttcttctc	11	9	4	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:49320786G>C	ENST00000559471.1	-	5	1021	c.758C>G	c.(757-759)cCt>cGt	p.P253R	SECISBP2L_ENST00000261847.3_Missense_Mutation_p.P253R	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	253							poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(8)|large_intestine(12)|lung(11)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	46						TTCAGCAGTAGGGTGGGATGC	0.498																																					p.P253R		Atlas-SNP	.											.	SECISBP2L	118	.	0			c.C758G						.						144	129	134					15																	49320786		2197	4295	6492	SO:0001583	missense	9728	exon5			GCAGTAGGGTGGG	BC033001	CCDS32234.1, CCDS53942.1	15q21.1	2014-02-12				ENSG00000138593			28997	protein-coding gene	gene with protein product		615756					Standard	NM_001193489		Approved	KIAA0256	uc001zxe.2	Q93073		ENST00000559471.1:c.758C>G	chr15.hg19:g.49320786G>C	ENSP00000453854:p.Pro253Arg	218.0	0.0		140.0	51.0	NM_001193489	Q8N767	Missense_Mutation	SNP	ENST00000559471.1	hg19	CCDS53942.1	.	.	.	.	.	.	.	.	.	.	G	15.67	2.900694	0.52227	.	.	ENSG00000138593	ENST00000261847;ENST00000380927	D	0.88741	-2.42	5.78	5.78	0.91487	.	0.062479	0.64402	D	0.000004	D	0.91057	0.7186	L	0.29908	0.895	0.45295	D	0.998295	D;D	0.71674	0.998;0.996	P;P	0.62813	0.873;0.907	D	0.91760	0.5419	10	0.72032	D	0.01	.	20.0278	0.97529	0.0:0.0:1.0:0.0	.	253;253	Q93073;Q93073-2	SBP2L_HUMAN;.	R	253	ENSP00000261847:P253R	ENSP00000261847:P253R	P	-	2	0	SECISBP2L	47108078	1.000000	0.71417	0.959000	0.39883	0.299000	0.27559	5.734000	0.68580	2.732000	0.93576	0.655000	0.94253	CCT	.	.		0.498	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417277.1	NM_014701		C	49320786	G	C	49320786	3	2	254	1	0	0	0	0	1	0	0	0	14022	1000	35	4	2464	4	SECISBP2L	15	49320786	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	781599	49320786	53210606	730	35022										
GALK2	2585	hgsc.bcm.edu	37	chr15	49611880	49611880	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctccagtttaagaagatatgTgaagaagcacctgaaaacat	8	7	0	5			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:49611880T>C	ENST00000560031.1	+	9	1354	c.1047T>C	c.(1045-1047)tgT>tgC	p.C349C	GALK2_ENST00000327171.3_Silent_p.C338C|GALK2_ENST00000544523.1_Silent_p.C325C|GALK2_ENST00000543495.1_3'UTR|GALK2_ENST00000559454.1_Silent_p.C325C|GALK2_ENST00000396509.2_Silent_p.C325C|GALK2_ENST00000561014.1_3'UTR			Q01415	GALK2_HUMAN	galactokinase 2	349					carbohydrate metabolic process (GO:0005975)|galactose metabolic process (GO:0006012)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|galactokinase activity (GO:0004335)|N-acetylgalactosamine kinase activity (GO:0033858)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|liver(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		all_lung(180;0.000325)		all cancers(107;3.71e-08)|GBM - Glioblastoma multiforme(94;7e-05)		AGAAGATATGTGAAGAAGCAC	0.537																																					p.C349C		Atlas-SNP	.											.	GALK2	78	.	0			c.T1047C						.						87	79	82					15																	49611880		2196	4295	6491	SO:0001819	synonymous_variant	2585	exon9			GATATGTGAAGAA		CCDS32236.1, CCDS42034.1, CCDS73724.1	15q21.1-q21.2	2013-09-20			ENSG00000156958	ENSG00000156958	2.7.1.6		4119	protein-coding gene	gene with protein product		137028					Standard	XM_005254279		Approved	GK2	uc001zxj.1	Q01415	OTTHUMG00000172325	ENST00000560031.1:c.1047T>C	chr15.hg19:g.49611880T>C		135.0	0.0		100.0	4.0	NM_002044	Q7Z4Q4	Silent	SNP	ENST00000560031.1	hg19	CCDS42034.1																																																																																			.	.		0.537	GALK2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417854.1			C	49611880	T	C	49611880	2	2	254	1	0	0	0	0	0	0	0	1	6212	1702	59	2		2	GALK2	15	49611880	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	291094	49611880	52919512	731	35023										
UNC13C	440279	hgsc.bcm.edu	37	chr15	54307628	54307628	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	atctcaatcaactgcaaatgAgtcaagtaccacacttgact	5	11	3	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:54307628A>G	ENST00000260323.11	+	1	2528	c.2528A>G	c.(2527-2529)gAg>gGg	p.E843G	UNC13C_ENST00000537900.1_Missense_Mutation_p.E843G|UNC13C_ENST00000545554.1_Missense_Mutation_p.E843G	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	843					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		ACTGCAAATGAGTCAAGTACC	0.428																																					p.E843G		Atlas-SNP	.											UNC13C_ENST00000260323,colon,carcinoma,0,2	UNC13C	674	.	0			c.A2528G						.						79	77	78					15																	54307628		1954	4144	6098	SO:0001583	missense	440279	exon1			CAAATGAGTCAAG	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.2528A>G	chr15.hg19:g.54307628A>G	ENSP00000260323:p.Glu843Gly	76.0	1.0		69.0	3.0	NM_001080534	Q0P613|Q8ND48|Q96NP3	Missense_Mutation	SNP	ENST00000260323.11	hg19	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	A	14.65	2.597578	0.46318	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	T;T;T	0.80653	-1.4;-1.4;-1.4	5.42	5.42	0.78866	.	.	.	.	.	T	0.70727	0.3257	L	0.29908	0.895	0.30377	N	0.78235	P	0.35844	0.524	B	0.28849	0.095	T	0.73119	-0.4083	9	0.59425	D	0.04	.	14.6463	0.68764	1.0:0.0:0.0:0.0	.	843	Q8NB66	UN13C_HUMAN	G	843	ENSP00000260323:E843G;ENSP00000438156:E843G;ENSP00000442569:E843G	ENSP00000260323:E843G	E	+	2	0	UNC13C	52094920	1.000000	0.71417	0.986000	0.45419	0.985000	0.73830	3.973000	0.56845	2.047000	0.60756	0.528000	0.53228	GAG	.	.		0.428	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		G	54307628	A	G	54307628	3	3	254	1	0	0	0	0	1	0	0	0	17001	304	11	2	2530	2	UNC13C	15	54307628	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	4695748	54307628	48223764	732	35024										
CCPG1	9236	hgsc.bcm.edu	37	chr15	55664085	55664085	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aactgacgtttactcaactcCttagaaggttcagtttcttg	7	9	3	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:55664085C>T	ENST00000310958.6	-	6	910	c.612G>A	c.(610-612)aaG>aaA	p.K204K	CCPG1_ENST00000569205.1_Silent_p.K204K|CCPG1_ENST00000425574.3_Silent_p.K204K|MIR628_ENST00000385229.1_RNA|DYX1C1-CCPG1_ENST00000565113.1_RNA|CCPG1_ENST00000442196.3_Silent_p.K204K	NM_001204450.1|NM_001204451.1|NM_004748.4|NM_020739.3	NP_001191379.1|NP_001191380.1|NP_004739.3|NP_065790.2	Q9ULG6	CCPG1_HUMAN	cell cycle progression 1	204	Interaction with MCF2L and SRC. {ECO:0000250}.				cell cycle (GO:0007049)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001106)	integral component of membrane (GO:0016021)				autonomic_ganglia(1)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|stomach(3)	30				all cancers(107;0.0354)		TACTCAACTCCTTAGAAGGTT	0.448																																					p.K204K		Atlas-SNP	.											.	CCPG1	74	.	0			c.G612A						.						114	103	106					15																	55664085		1876	4107	5983	SO:0001819	synonymous_variant	9236	exon6			CAACTCCTTAGAA	AF212228	CCDS42039.1, CCDS55966.1, CCDS55967.1	15q21.1	2011-04-20				ENSG00000260916			24227	protein-coding gene	gene with protein product		611326				9383053, 10574462	Standard	NM_004748		Approved	KIAA1254, CPR8	uc010bfk.2	Q9ULG6		ENST00000310958.6:c.612G>A	chr15.hg19:g.55664085C>T		271.0	0.0		204.0	34.0	NM_020739	A0PJH3|A8K9T0|O14712|Q05DG4|Q5U5S7|Q8IYV8|Q9BY53|Q9HA17	Silent	SNP	ENST00000310958.6	hg19	CCDS42039.1																																																																																			.	.		0.448	CCPG1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419850.1	NM_004748		T	55664085	C	T	55664085	2	4	254	1	0	0	0	0	0	0	0	1	2940	680	24	3		3	CCPG1	15	55664085	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1356457	55664085	46867307	733	35025										
VPS13C	54832	hgsc.bcm.edu	37	chr15	62202491	62202491	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgcctgacaaactttctggcCaaaatggaaggcactaaaaa	8	9	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:62202491C>A	ENST00000261517.5	-	64	8802	c.8729G>T	c.(8728-8730)tGg>tTg	p.W2910L	VPS13C_ENST00000395896.4_Missense_Mutation_p.W2910L|VPS13C_ENST00000395898.3_Missense_Mutation_p.W2867L|VPS13C_ENST00000249837.3_Missense_Mutation_p.W2867L	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						ACTTTCTGGCCAAAATGGAAG	0.333																																					p.W2910L		Atlas-SNP	.											.	VPS13C	506	.	0			c.G8729T						.						48	50	49					15																	62202491		2203	4300	6503	SO:0001583	missense	54832	exon64			TCTGGCCAAAATG	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"vacuolar protein sorting 13C (yeast)"				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.8729G>T	chr15.hg19:g.62202491C>A	ENSP00000261517:p.Trp2910Leu	100.0	0.0		78.0	4.0	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	hg19	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.903713	0.92035	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.30448	1.53;1.53;1.53	5.85	5.85	0.93711	Vacuolar protein sorting-associated protein (1);	0.000000	0.85682	D	0.000000	T	0.64114	0.2569	M	0.88310	2.945	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.998;0.998;0.998;0.998;0.999	T	0.63576	-0.6606	10	0.33940	T	0.23	.	20.1649	0.98147	0.0:1.0:0.0:0.0	.	2910;2867;2910;2867;2910	F5GZG8;Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;.;VP13C_HUMAN	L	2867;2910;2910;2910	ENSP00000249837:W2867L;ENSP00000261517:W2910L;ENSP00000379233:W2910L	ENSP00000249837:W2867L	W	-	2	0	VPS13C	59989783	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.766000	0.74970	2.753000	0.94483	0.655000	0.94253	TGG	.	.		0.333	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		A	62202491	C	A	62202491	3	1	254	1	0	0	0	0	1	0	0	0	17206	595	21	3	2648	3	VPS13C	15	62202491	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	6538406	62202491	40328901	734	35026										
FBXL22	283807	hgsc.bcm.edu	37	chr15	63889776	63889776	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttccctcactgaactccagaAggacaacttcctcctgggcc	7	16	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:63889776A>G	ENST00000360587.2	+	1	225	c.185A>G	c.(184-186)aAg>aGg	p.K62R	USP3-AS1_ENST00000560622.1_RNA|FBXL22_ENST00000534939.1_Missense_Mutation_p.K62R|FBXL22_ENST00000539570.3_Missense_Mutation_p.K56R|USP3-AS1_ENST00000559861.1_RNA|USP3-AS1_ENST00000561191.1_RNA|USP3-AS1_ENST00000560962.1_RNA|USP3-AS1_ENST00000559737.1_RNA|USP3-AS1_ENST00000561256.1_RNA|USP3-AS1_ENST00000558831.1_RNA	NM_203373.2	NP_976307.2	Q6P050	FXL22_HUMAN	F-box and leucine-rich repeat protein 22	62					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				lung(4)	4						GAACTCCAGAAGGACAACTTC	0.627																																					p.K62R		Atlas-SNP	.											.	FBXL22	4	.	0			c.A185G						.						62	50	54					15																	63889776		2203	4300	6503	SO:0001583	missense	283807	exon1			TCCAGAAGGACAA	BC065833	CCDS10187.1, CCDS10187.2	15q22.1	2012-04-05			ENSG00000197361	ENSG00000197361		"F-boxes / Leucine-rich repeats"	27537	protein-coding gene	gene with protein product		609088				12477932	Standard	NM_203373		Approved	Fbl22, FLJ39626	uc002amn.4	Q6P050	OTTHUMG00000132905	ENST00000360587.2:c.185A>G	chr15.hg19:g.63889776A>G	ENSP00000353794:p.Lys62Arg	80.0	0.0		83.0	4.0	NM_203373		Missense_Mutation	SNP	ENST00000360587.2	hg19	CCDS10187.2	.	.	.	.	.	.	.	.	.	.	A	21.4	4.138354	0.77775	.	.	ENSG00000197361	ENST00000360587;ENST00000539570	T;T	0.39056	1.1;1.1	5.49	5.49	0.81192	.	0.158011	0.56097	D	0.000032	T	0.29684	0.0741	L	0.41824	1.3	0.33837	D	0.630966	P	0.43750	0.816	B	0.32762	0.152	T	0.52290	-0.8595	10	0.52906	T	0.07	-11.311	10.7624	0.46272	0.9261:0.0:0.0739:0.0	.	56	Q6P050	FXL22_HUMAN	R	62;56	ENSP00000353794:K62R;ENSP00000442112:K56R	ENSP00000353794:K62R	K	+	2	0	FBXL22	61676829	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.369000	0.44231	2.090000	0.63153	0.460000	0.39030	AAG	.	.		0.627	FBXL22-001	KNOWN	downstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256412.4	NM_203373		G	63889776	A	G	63889776	3	3	254	1	0	0	0	0	1	0	0	0	5727	72	3	2	169	2	FBXL22	15	63889776	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	1687285	63889776	38641616	735	35027										
PARP16	54956	hgsc.bcm.edu	37	chr15	65578651	65578651	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcggggaagggccgcagcacCgagtcgcgcttgtagctctg	17	12	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:65578651C>A	ENST00000444347.2	-	1	530	c.114G>T	c.(112-114)tcG>tcT	p.S38S	PARP16_ENST00000261888.6_Silent_p.S38S|SNORA24_ENST00000384176.1_RNA|PARP16_ENST00000558873.1_Intron			Q8N5Y8	PAR16_HUMAN	poly (ADP-ribose) polymerase family, member 16	38	PARP alpha-helical.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of cell death (GO:0060548)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum tubular network (GO:0071782)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)	kinase binding (GO:0019900)|NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|protein serine/threonine kinase activator activity (GO:0043539)			kidney(1)|large_intestine(1)|lung(5)|prostate(1)|skin(1)	9						GCCGCAGCACCGAGTCGCGCT	0.716																																					p.S38S	NSCLC(50;885 1163 13509 21242 41978)	Atlas-SNP	.											.	PARP16	23	.	0			c.G114T						.						15	17	16					15																	65578651		2197	4295	6492	SO:0001819	synonymous_variant	54956	exon1			CAGCACCGAGTCG	AK000516	CCDS10204.1	15q22.2	2010-02-16	2004-08-25	2004-08-25	ENSG00000138617	ENSG00000138617		"Poly (ADP-ribose) polymerases"	26040	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 30"	C15orf30		15273990	Standard	NM_017851		Approved	FLJ20509, FLJ25281, pART15	uc002aoq.3	Q8N5Y8	OTTHUMG00000133138	ENST00000444347.2:c.114G>T	chr15.hg19:g.65578651C>A		68.0	0.0		78.0	4.0	NM_017851	Q6PK64|Q9NX03	Silent	SNP	ENST00000444347.2	hg19																																																																																				.	.		0.716	PARP16-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000418174.1	NM_017851		A	65578651	C	A	65578651	2	1	254	1	0	0	0	0	0	0	0	1	11469	639	23	1		1	PARP16	15	65578651	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1688875	65578651	36952741	736	35028										
IGDCC3	9543	hgsc.bcm.edu	37	chr15	65621487	65621487	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcgggggctgcaggatcctgCtggggaaagagcccgtcaca	17	11	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:65621487C>A	ENST00000327987.4	-	14	2457		c.e14-1		IGDCC3_ENST00000559231.1_5'Flank	NM_004884.3	NP_004875.2	Q8IVU1	IGDC3_HUMAN	immunoglobulin superfamily, DCC subclass, member 3						neuromuscular process controlling balance (GO:0050885)	integral component of plasma membrane (GO:0005887)				breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(9)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						CAGGATCCTGCTGGGGAAAGA	0.667																																					.		Atlas-SNP	.											.	IGDCC3	82	.	0			c.2206-1G>T						.						14	17	16					15																	65621487		2201	4297	6498	SO:0001630	splice_region_variant	9543	exon15			ATCCTGCTGGGGA	AF063936	CCDS10205.1	15q22.3-q23	2013-02-11	2009-01-08	2009-01-08	ENSG00000174498	ENSG00000174498		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9700	protein-coding gene	gene with protein product		604184	"putative neuronal cell adhesion molecule"	PUNC		9922388	Standard	NM_004884		Approved	HsT18880	uc002aos.2	Q8IVU1	OTTHUMG00000133137	ENST00000327987.4:c.2206-1G>T	chr15.hg19:g.65621487C>A		51.0	0.0		46.0	16.0	NM_004884	O95215	Splice_Site	SNP	ENST00000327987.4	hg19	CCDS10205.1	.	.	.	.	.	.	.	.	.	.	C	11.79	1.743246	0.30865	.	.	ENSG00000174498	ENST00000327987	.	.	.	5.45	2.48	0.30137	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.3969	0.16275	0.1661:0.6644:0.0:0.1695	.	.	.	.	.	-1	.	.	.	-	.	.	IGDCC3	63408540	0.073000	0.21202	0.343000	0.25615	0.045000	0.14185	0.301000	0.19174	0.242000	0.21303	0.555000	0.69702	.	.	.		0.667	IGDCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256826.1	NM_004884	Intron	A	65621487	C	A	65621487	5	1	254	1	0	0	0	0	0	0	1	0	7577	811	28	3	243	3	IGDCC3	15	65621487	Splice_Site	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	42836	65621487	36909905	737	35029										
ARIH1	25820	hgsc.bcm.edu	37	chr15	72767267	72767267	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cgggccggggcatgagcaggAggaggattaccgctacgagg	19	9	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:72767267A>G	ENST00000379887.4	+	1	601	c.287A>G	c.(286-288)gAg>gGg	p.E96G	RP11-1007O24.3_ENST00000565181.1_lincRNA	NM_005744.3	NP_005735.2	Q9Y4X5	ARI1_HUMAN	ariadne RBR E3 ubiquitin protein ligase 1	96					cytokine-mediated signaling pathway (GO:0019221)|protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|ubiquitin ligase complex (GO:0000151)	small conjugating protein ligase activity (GO:0019787)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(3)|lung(4)|prostate(1)|skin(1)	14						CATGAGCAGGAGGAGGATTAC	0.711																																					p.E96G		Atlas-SNP	.											.	ARIH1	42	.	0			c.A287G						.						19	13	15					15																	72767267		2072	4097	6169	SO:0001583	missense	25820	exon1			AGCAGGAGGAGGA	AF072832	CCDS10244.1	15q24	2013-10-03	2013-10-03		ENSG00000166233	ENSG00000166233			689	protein-coding gene	gene with protein product	"ariadne, Drosophila, homolog of"	605624	"ariadne (Drosophila) homolog, ubiquitin-conjugating enzyme E2-binding protein, 1", "ariadne homolog, ubiquitin-conjugating enzyme E2 binding protein, 1 (Drosophila)"			10521492, 24058416	Standard	NM_005744		Approved	HARI, HHARI, UBCH7BP, ARI	uc002aut.4	Q9Y4X5	OTTHUMG00000133474	ENST00000379887.4:c.287A>G	chr15.hg19:g.72767267A>G	ENSP00000369217:p.Glu96Gly	86.0	0.0		79.0	4.0	NM_005744	B2R6U3|O76026|Q9H3T6|Q9UEN0|Q9UP39	Missense_Mutation	SNP	ENST00000379887.4	hg19	CCDS10244.1	.	.	.	.	.	.	.	.	.	.	A	17.05	3.291195	0.59976	.	.	ENSG00000166233	ENST00000379887	D	0.88664	-2.41	4.06	4.06	0.47325	.	0.157254	0.39274	N	0.001416	T	0.77260	0.4104	N	0.19112	0.55	0.44762	D	0.997764	P	0.36199	0.543	B	0.25987	0.065	T	0.76410	-0.2969	10	0.33940	T	0.23	.	11.2844	0.49214	1.0:0.0:0.0:0.0	.	96	Q9Y4X5	ARI1_HUMAN	G	96	ENSP00000369217:E96G	ENSP00000369217:E96G	E	+	2	0	ARIH1	70554321	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.672000	0.68102	1.603000	0.50134	0.459000	0.35465	GAG	.	.		0.711	ARIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257350.1	NM_005744		G	72767267	A	G	72767267	3	3	254	1	0	0	0	0	1	0	0	0	923	304	11	2	289	2	ARIH1	15	72767267	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	7145780	72767267	29764125	738	35030										
PML	5371	hgsc.bcm.edu	37	chr15	74327563	74327563	+	Intron	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cagtcctcgccagcccactcCtcgccagcccactcctcgcc	6	24	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:74327563C>A	ENST00000268058.3	+	7	1806				PML_ENST00000565898.1_Intron|PML_ENST00000268059.6_Silent_p.S587S|PML_ENST00000563500.1_3'UTR|PML_ENST00000569477.1_Missense_Mutation_p.L601I|PML_ENST00000569965.1_Intron|PML_ENST00000395135.3_Intron|PML_ENST00000395132.2_Intron|PML_ENST00000354026.6_Silent_p.S539S|PML_ENST00000436891.3_3'UTR|PML_ENST00000564428.1_Intron|PML_ENST00000359928.4_Intron|PML_ENST00000435786.2_3'UTR	NM_033238.2	NP_150241.2	P29590	PML_HUMAN	promyelocytic leukemia						activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell cycle arrest (GO:0007050)|cell fate commitment (GO:0045165)|cellular response to interleukin-4 (GO:0071353)|cellular senescence (GO:0090398)|circadian regulation of gene expression (GO:0032922)|common-partner SMAD protein phosphorylation (GO:0007182)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|entrainment of circadian clock by photoperiod (GO:0043153)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|maintenance of protein location in nucleus (GO:0051457)|myeloid cell differentiation (GO:0030099)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation in response to oxidative stress (GO:0032938)|negative regulation of viral release from host cell (GO:1902187)|PML body organization (GO:0030578)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of histone deacetylation (GO:0031065)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)|regulation of calcium ion transport into cytosol (GO:0010522)|regulation of circadian rhythm (GO:0042752)|regulation of double-strand break repair (GO:2000779)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of protein phosphorylation (GO:0001932)|regulation of transcription, DNA-templated (GO:0006355)|response to cytokine (GO:0034097)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|retinoic acid receptor signaling pathway (GO:0048384)|SMAD protein import into nucleus (GO:0007184)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	cobalt ion binding (GO:0050897)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|SUMO binding (GO:0032183)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	31						CAGCCCACTCCTCGCCAGCCC	0.647			T	"RARA, PAX5"	"APL, ALL"																																p.S587S		Atlas-SNP	.		Dom	yes		15	15q22	5371	promyelocytic leukemia		L	.	PML	169	.	0			c.C1761A						.						100	116	110					15																	74327563		2198	4297	6495	SO:0001627	intron_variant	5371	exon8			CCACTCCTCGCCA	AB208950	CCDS10255.1, CCDS10256.1, CCDS10257.1, CCDS10258.1, CCDS45297.1, CCDS45298.1, CCDS45299.1, CCDS45300.1, CCDS58386.1	15q24.1	2011-04-21			ENSG00000140464	ENSG00000140464		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	9113	protein-coding gene	gene with protein product		102578					Standard	NM_033244		Approved	MYL, TRIM19, RNF71	uc002awv.3	P29590	OTTHUMG00000137607	ENST00000268058.3:c.1710+692C>A	chr15.hg19:g.74327563C>A		159.0	0.0		94.0	4.0	NM_033239	E9PBR7|P29591|P29592|P29593|Q00755|Q15959|Q59FP9|Q8WUA0|Q96S41|Q9BPW2|Q9BWP7|Q9BZX6|Q9BZX7|Q9BZX8|Q9BZX9|Q9BZY0|Q9BZY2|Q9BZY3	Silent	SNP	ENST00000268058.3	hg19	CCDS10255.1																																																																																			.	.		0.647	PML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269021.3	NM_002675		A	74327563	C	A	74327563	1	1	254	0	1	0	0	0	0	0	0	0	12144	668	24	3		3	PML	15	74327563	Intron	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1560296	74327563	28203829	739	35031										
CYP1A1	1543	hgsc.bcm.edu	37	chr15	75015213	75015213	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gggtgtggagccaattcggaTctgcagcacgtccccatact	12	12	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:75015213T>C	ENST00000379727.3	-	2	424	c.226A>G	c.(226-228)Atc>Gtc	p.I76V	CYP1A1_ENST00000564596.1_Intron|CYP1A1_ENST00000395049.4_Missense_Mutation_p.I76V|CYP1A1_ENST00000567032.1_Missense_Mutation_p.I76V|CYP1A1_ENST00000395048.2_Missense_Mutation_p.I76V			P04798	CP1A1_HUMAN	cytochrome P450, family 1, subfamily A, polypeptide 1	76					9-cis-retinoic acid biosynthetic process (GO:0042904)|aging (GO:0007568)|amine metabolic process (GO:0009308)|arachidonic acid metabolic process (GO:0019369)|camera-type eye development (GO:0043010)|cell proliferation (GO:0008283)|cellular lipid metabolic process (GO:0044255)|cellular response to organic cyclic compound (GO:0071407)|coumarin metabolic process (GO:0009804)|dibenzo-p-dioxin catabolic process (GO:0019341)|digestive tract development (GO:0048565)|drug metabolic process (GO:0017144)|embryo development ending in birth or egg hatching (GO:0009792)|epoxygenase P450 pathway (GO:0019373)|flavonoid metabolic process (GO:0009812)|hepatocyte differentiation (GO:0070365)|hydrogen peroxide biosynthetic process (GO:0050665)|insecticide metabolic process (GO:0017143)|maternal process involved in parturition (GO:0060137)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound metabolic process (GO:0006778)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|response to antibiotic (GO:0046677)|response to arsenic-containing substance (GO:0046685)|response to drug (GO:0042493)|response to food (GO:0032094)|response to herbicide (GO:0009635)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to iron(III) ion (GO:0010041)|response to lipopolysaccharide (GO:0032496)|response to nematode (GO:0009624)|response to virus (GO:0009615)|response to vitamin A (GO:0033189)|response to wounding (GO:0009611)|small molecule metabolic process (GO:0044281)|vitamin D metabolic process (GO:0042359)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|demethylase activity (GO:0032451)|flavonoid 3'-monooxygenase activity (GO:0016711)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on diphenols and related substances as donors (GO:0016679)|oxygen binding (GO:0019825)|steroid hydroxylase activity (GO:0008395)|vitamin D 24-hydroxylase activity (GO:0070576)			autonomic_ganglia(1)|breast(2)|endometrium(1)|large_intestine(7)|lung(13)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34					Acetaminophen(DB00316)|Albendazole(DB00518)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Arsenic trioxide(DB01169)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bezafibrate(DB01393)|Bortezomib(DB00188)|Caffeine(DB00201)|Carvedilol(DB01136)|Chloroquine(DB00608)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Cinnarizine(DB00568)|Clenbuterol(DB01407)|Clobetasol propionate(DB01013)|Clofibrate(DB00636)|Clomifene(DB00882)|Clonidine(DB00575)|Clozapine(DB00363)|Dacarbazine(DB00851)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Dexamethasone(DB01234)|Dexmedetomidine(DB00633)|Diclofenac(DB00586)|Dicyclomine(DB00804)|Dronabinol(DB00470)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Ethanol(DB00898)|Flunarizine(DB04841)|Fluorescein(DB00693)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Granisetron(DB00889)|Haloperidol(DB00502)|Isoprenaline(DB01064)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Lorcaserin(DB04871)|Mebendazole(DB00643)|Melatonin(DB01065)|Menadione(DB00170)|Methoxsalen(DB00553)|Nicotine(DB00184)|Nifedipine(DB01115)|Nitroprusside(DB00325)|Norfloxacin(DB01059)|Omeprazole(DB00338)|Ouabain(DB01092)|Oxaliplatin(DB00526)|Pentamidine(DB00738)|Phenobarbital(DB01174)|Prazosin(DB00457)|Primaquine(DB01087)|Progesterone(DB00396)|Propofol(DB00818)|Propranolol(DB00571)|Pyridoxine(DB00165)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Riluzole(DB00740)|Sildenafil(DB00203)|Streptozocin(DB00428)|Sulindac(DB00605)|Tamoxifen(DB00675)|Testosterone(DB00624)|Thalidomide(DB01041)|Theophylline(DB00277)|Thiabendazole(DB00730)|Ticlopidine(DB00208)|Toremifene(DB00539)|Tretinoin(DB00755)|Vitamin A(DB00162)|Warfarin(DB00682)	CCAATTCGGATCTGCAGCACG	0.647									Endometrial Cancer, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia																												p.I76V		Atlas-SNP	.											.	CYP1A1	60	.	0			c.A226G						.						64	54	57					15																	75015213		2197	4296	6493	SO:0001583	missense	1543	exon2	Familial Cancer Database	;AIMAH, Cushing disease, Adrenal, Familial	TTCGGATCTGCAG	BC023019	CCDS10268.1	15q24.1	2007-12-14	2003-01-14		ENSG00000140465	ENSG00000140465	1.14.14.1	"Cytochrome P450s"	2595	protein-coding gene	gene with protein product		108330	"cytochrome P450, subfamily I (aromatic compound-inducible), polypeptide 1"	CYP1		15128046	Standard	NM_000499		Approved	P450DX, P1-450, P450-C, CP11	uc002ayp.4	P04798	OTTHUMG00000142812	ENST00000379727.3:c.226A>G	chr15.hg19:g.75015213T>C	ENSP00000369050:p.Ile76Val	142.0	0.0		99.0	5.0	NM_000499	A4F3V9|A4F3W0|Q53G18	Missense_Mutation	SNP	ENST00000379727.3	hg19	CCDS10268.1	.	.	.	.	.	.	.	.	.	.	T	9.329	1.060079	0.19987	.	.	ENSG00000140465	ENST00000379727;ENST00000395048;ENST00000395049;ENST00000268062	T;T;T	0.68181	-0.31;-0.31;-0.31	5.23	2.95	0.34219	.	0.157502	0.56097	N	0.000024	T	0.50292	0.1607	N	0.24115	0.695	0.50171	D	0.999851	B;B	0.24368	0.102;0.012	B;B	0.30495	0.116;0.048	T	0.42068	-0.9473	10	0.40728	T	0.16	.	7.5077	0.27555	0.0:0.2876:0.0:0.7124	.	76;76	E7EMT5;P04798	.;CP1A1_HUMAN	V	76	ENSP00000369050:I76V;ENSP00000378488:I76V;ENSP00000378489:I76V	ENSP00000268062:I76V	I	-	1	0	CYP1A1	72802266	1.000000	0.71417	0.998000	0.56505	0.333000	0.28666	3.388000	0.52509	0.833000	0.34828	0.379000	0.24179	ATC	.	.		0.647	CYP1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286396.1	NM_000499		C	75015213	T	C	75015213	3	2	254	1	0	0	0	0	1	0	0	0	4151	1435	50	2	1336	2	CYP1A1	15	75015213	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	687650	75015213	27516179	740	35032										
NEIL1	79661	hgsc.bcm.edu	37	chr15	75647049	75647049	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	acgaagggcaaagagagaccTtcctaagaggactgcaaccc	11	11	0	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:75647049T>C	ENST00000564784.1	+	10	1621	c.992T>C	c.(991-993)cTt>cCt	p.L331P	NEIL1_ENST00000569035.1_Missense_Mutation_p.L331P|MIR631_ENST00000384904.1_RNA|RP11-817O13.6_ENST00000563660.1_lincRNA|NEIL1_ENST00000355059.4_Missense_Mutation_p.L331P			Q96FI4	NEIL1_HUMAN	nei endonuclease VIII-like 1 (E. coli)	331					base-excision repair (GO:0006284)|negative regulation of nuclease activity (GO:0032074)|nucleotide-excision repair (GO:0006289)|response to oxidative stress (GO:0006979)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|hydrolase activity, acting on glycosyl bonds (GO:0016798)|protein C-terminus binding (GO:0008022)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|large_intestine(4)|lung(4)|ovary(1)	13						AAGAGAGACCTTCCTAAGAGG	0.622								Base excision repair (BER), DNA glycosylases																													p.L417P		Atlas-SNP	.											.	NEIL1	36	.	0			c.T1250C						.						50	55	53					15																	75647049		2197	4294	6491	SO:0001583	missense	79661	exon9			GAGACCTTCCTAA	AK026055	CCDS10278.1	15q33.33	2008-07-18			ENSG00000140398	ENSG00000140398			18448	protein-coding gene	gene with protein product		608844				11904416	Standard	NM_024608		Approved	FLJ22402, hFPG1, NEI1, FPG1	uc002bae.4	Q96FI4	OTTHUMG00000142821	ENST00000564784.1:c.992T>C	chr15.hg19:g.75647049T>C	ENSP00000457352:p.Leu331Pro	82.0	0.0		66.0	4.0	NM_001256552	D3DW75|Q6ZRA7|Q86XW7|Q9H6C3	Missense_Mutation	SNP	ENST00000564784.1	hg19	CCDS10278.1	.	.	.	.	.	.	.	.	.	.	T	6.154	0.396553	0.11638	.	.	ENSG00000140398	ENST00000355059	T	0.12672	2.66	3.65	-0.0446	0.13855	.	1.484880	0.03689	N	0.246787	T	0.09949	0.0244	N	0.25647	0.755	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.32981	-0.9886	10	0.44086	T	0.13	-2.4153	3.3161	0.07034	0.0:0.2306:0.2096:0.5598	.	331	Q96FI4	NEIL1_HUMAN	P	331	ENSP00000347170:L331P	ENSP00000347170:L331P	L	+	2	0	NEIL1	73434102	0.000000	0.05858	0.001000	0.08648	0.098000	0.18820	-0.118000	0.10692	-0.015000	0.14150	0.454000	0.30748	CTT	.	.		0.622	NEIL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419885.1	NM_024608		C	75647049	T	C	75647049	3	2	254	1	0	0	0	0	1	0	0	0	10327	1609	56	2	1022	2	NEIL1	15	75647049	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	631836	75647049	26884343	741	35033										
ACSBG1	23205	hgsc.bcm.edu	37	chr15	78474373	78474373	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctggatgcctgtccacaggtCgtagatctgggcggcaatat	13	10	1	1	rs372447099		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:78474373C>A	ENST00000258873.4	-	8	1214	c.1009G>T	c.(1009-1011)Gac>Tac	p.D337Y	ACSBG1_ENST00000560817.1_Missense_Mutation_p.D95Y|ACSBG1_ENST00000541759.1_Missense_Mutation_p.D95Y	NM_001199377.1|NM_015162.4	NP_001186306.1|NP_055977.3	Q96GR2	ACBG1_HUMAN	acyl-CoA synthetase bubblegum family member 1	337					long-chain fatty acid metabolic process (GO:0001676)|myelination (GO:0042552)|ovarian follicle atresia (GO:0001552)|response to glucocorticoid (GO:0051384)|very long-chain fatty acid metabolic process (GO:0000038)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			endometrium(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	37						GTCCACAGGTCGTAGATCTGG	0.637																																					p.D337Y		Atlas-SNP	.											.	ACSBG1	79	.	0			c.G1009T						.						83	69	74					15																	78474373		2196	4293	6489	SO:0001583	missense	23205	exon8			ACAGGTCGTAGAT	AB014531	CCDS10298.1	15q23-q24	2006-02-09			ENSG00000103740	ENSG00000103740		"Acyl-CoA synthetase family"	29567	protein-coding gene	gene with protein product	"bubblegum", "very long-chain acyl-CoA synthetase", "lipidosin"	614362				9734811, 10954726	Standard	NM_015162		Approved	BGM, FLJ30320, MGC14352, BG1, KIAA0631, hBG1, hsBG	uc002bdh.3	Q96GR2	OTTHUMG00000143734	ENST00000258873.4:c.1009G>T	chr15.hg19:g.78474373C>A	ENSP00000258873:p.Asp337Tyr	70.0	0.0		48.0	4.0	NM_015162	B2RB61|O75126|Q76N27|Q9HC26	Missense_Mutation	SNP	ENST00000258873.4	hg19	CCDS10298.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.922995	0.92319	.	.	ENSG00000103740	ENST00000258873;ENST00000541759	T;T	0.42131	0.98;0.98	5.32	5.32	0.75619	AMP-dependent synthetase/ligase (1);	0.117935	0.53938	D	0.000044	T	0.71099	0.3300	M	0.88640	2.97	0.80722	D	1	D;D	0.89917	1.0;0.996	D;D	0.77004	0.989;0.974	T	0.77453	-0.2582	10	0.87932	D	0	-46.0626	18.0808	0.89440	0.0:1.0:0.0:0.0	.	333;337	B7Z2Y6;Q96GR2	.;ACBG1_HUMAN	Y	337;95	ENSP00000258873:D337Y;ENSP00000439955:D95Y	ENSP00000258873:D337Y	D	-	1	0	ACSBG1	76261428	1.000000	0.71417	0.986000	0.45419	0.986000	0.74619	7.736000	0.84948	2.512000	0.84698	0.650000	0.86243	GAC	.	.		0.637	ACSBG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289802.2	NM_015162		A	78474373	C	A	78474373	3	1	254	1	0	0	0	0	1	0	0	0	173	884	31	1	1193	1	ACSBG1	15	78474373	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	2827324	78474373	24057019	742	35034										
ADAMTSL3	57188	hgsc.bcm.edu	37	chr15	84561455	84561455	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gctgggaacataatccttggActgcatgttccgtgtcctgt	11	10	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:84561455A>G	ENST00000286744.5	+	13	1506	c.1282A>G	c.(1282-1284)Act>Gct	p.T428A	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.T428A	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	428	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			TAATCCTTGGACTGCATGTTC	0.408																																					p.T428A		Atlas-SNP	.											.	ADAMTSL3	290	.	0			c.A1282G						.						131	117	122					15																	84561455		2203	4300	6503	SO:0001583	missense	57188	exon13			CCTTGGACTGCAT	AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.1282A>G	chr15.hg19:g.84561455A>G	ENSP00000286744:p.Thr428Ala	120.0	0.0		91.0	4.0	NM_207517	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	hg19	CCDS10326.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.448979	0.84101	.	.	ENSG00000156218	ENST00000286744	T	0.53423	0.62	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.66297	0.2775	M	0.62088	1.915	0.58432	D	0.999999	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.996	T	0.69723	-0.5068	10	0.72032	D	0.01	.	15.2316	0.73395	1.0:0.0:0.0:0.0	.	428;428	P82987-2;P82987	.;ATL3_HUMAN	A	428	ENSP00000286744:T428A	ENSP00000286744:T428A	T	+	1	0	ADAMTSL3	82352459	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.858000	0.92256	1.994000	0.58287	0.533000	0.62120	ACT	.	.		0.408	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517		G	84561455	A	G	84561455	3	3	254	1	0	0	0	0	1	0	0	0	276	275	10	2	1328	2	ADAMTSL3	15	84561455	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	6087082	84561455	17969937	743	35035										
NTRK3	4916	hgsc.bcm.edu	37	chr15	88679734	88679734	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gactgcagcccagtgactatCcagtccacatcaggaagggg	12	12	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:88679734C>G	ENST00000360948.2	-	7	890	c.729G>C	c.(727-729)tgG>tgC	p.W243C	NTRK3_ENST00000317501.3_Missense_Mutation_p.W243C|NTRK3_ENST00000394480.2_Missense_Mutation_p.W243C|NTRK3_ENST00000557856.1_Missense_Mutation_p.W243C|NTRK3_ENST00000540489.2_Missense_Mutation_p.W243C|NTRK3_ENST00000357724.2_Missense_Mutation_p.W243C|NTRK3_ENST00000558676.1_Missense_Mutation_p.W243C|NTRK3_ENST00000355254.2_Missense_Mutation_p.W243C|NTRK3_ENST00000542733.2_Missense_Mutation_p.W145C	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	243	Ig-like C2-type 1.				activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|cochlea development (GO:0090102)|lens fiber cell differentiation (GO:0070306)|mechanoreceptor differentiation (GO:0042490)|modulation by virus of host transcription (GO:0019056)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell death (GO:0060548)|negative regulation of protein phosphorylation (GO:0001933)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|neurotrophin signaling pathway (GO:0038179)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of axon extension involved in regeneration (GO:0048691)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of positive chemotaxis (GO:0050927)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|neurotrophin binding (GO:0043121)|neurotrophin receptor activity (GO:0005030)|p53 binding (GO:0002039)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.W243C(3)	ETV6/NTRK3(238)	breast(3)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(22)|lung(63)|ovary(6)|pancreas(3)|prostate(1)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)	119			BRCA - Breast invasive adenocarcinoma(143;0.211)			CAGTGACTATCCAGTCCACAT	0.547			T	ETV6	"congenital fibrosarcoma, Secretory breast "					TSP Lung(13;0.10)																											p.W243C		Atlas-SNP	.		Dom	yes		15	15q25	4916	"neurotrophic tyrosine kinase, receptor, type 3"		"E, M"	NTRK3_ENST00000360948,NS,carcinoma,0,3	NTRK3	587	.	3	Substitution - Missense(3)	lung(3)	c.G729C						.						151	97	115					15																	88679734		2201	4299	6500	SO:0001583	missense	4916	exon8			GACTATCCAGTCC	U05012	CCDS10340.1, CCDS32322.1, CCDS32323.1, CCDS58399.1	15q24-q25	2013-01-11			ENSG00000140538	ENSG00000140538	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing"	8033	protein-coding gene	gene with protein product		191316				7806211	Standard	NM_001012338		Approved	TRKC	uc002bme.2	Q16288	OTTHUMG00000148677	ENST00000360948.2:c.729G>C	chr15.hg19:g.88679734C>G	ENSP00000354207:p.Trp243Cys	134.0	0.0		75.0	4.0	NM_001243101	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Missense_Mutation	SNP	ENST00000360948.2	hg19	CCDS32322.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.440008	0.83993	.	.	ENSG00000140538	ENST00000394480;ENST00000360948;ENST00000357724;ENST00000355254;ENST00000542733;ENST00000540489;ENST00000317501	D;D;D;D;D;D;D	0.96300	-3.97;-3.97;-3.97;-3.97;-3.97;-3.97;-3.97	5.64	5.64	0.86602	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.98566	0.9521	M	0.91354	3.2	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.999;0.999;1.0;0.999;0.996;1.0	D	0.99461	1.0943	10	0.87932	D	0	.	18.6884	0.91574	0.0:1.0:0.0:0.0	.	145;243;243;243;243;243	B7Z7U4;E9PG56;B7Z4C5;Q96CY4;Q16288-3;Q16288	.;.;.;.;.;NTRK3_HUMAN	C	243;243;243;243;145;243;243	ENSP00000377990:W243C;ENSP00000354207:W243C;ENSP00000350356:W243C;ENSP00000347397:W243C;ENSP00000437773:W145C;ENSP00000444673:W243C;ENSP00000318328:W243C	ENSP00000318328:W243C	W	-	3	0	NTRK3	86480738	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.359000	0.79477	2.657000	0.90304	0.655000	0.94253	TGG	.	.		0.547	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding				G	88679734	C	G	88679734	3	3	254	1	0	0	0	0	1	0	0	0	10717	856	30	4	2104	4	NTRK3	15	88679734	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	4118279	88679734	13851658	744	35036										
MFGE8	4240	hgsc.bcm.edu	37	chr15	89442944	89442944	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cagttcgcactgtcattactGtaggcaaccttgtaggatgc	10	10	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:89442944G>T	ENST00000566497.1	-	7	1030	c.969C>A	c.(967-969)taC>taA	p.Y323*	MFGE8_ENST00000268150.8_Nonsense_Mutation_p.Y323*|MFGE8_ENST00000539437.1_Nonsense_Mutation_p.Y315*|MFGE8_ENST00000542878.1_Nonsense_Mutation_p.Y279*|MFGE8_ENST00000268151.7_Intron			Q08431	MFGM_HUMAN	milk fat globule-EGF factor 8 protein	323	F5/8 type C 2. {ECO:0000255|PROSITE- ProRule:PRU00081}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|phagocytosis, engulfment (GO:0006911)|phagocytosis, recognition (GO:0006910)|positive regulation of apoptotic cell clearance (GO:2000427)|single fertilization (GO:0007338)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|vesicle (GO:0031982)	phosphatidylethanolamine binding (GO:0008429)|phosphatidylserine binding (GO:0001786)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	22	Lung NSC(78;0.0392)|all_lung(78;0.077)					TGTCATTACTGTAGGCAACCT	0.567																																					p.Y323X		Atlas-SNP	.											.	MFGE8	60	.	0			c.C969A						.						106	87	93					15																	89442944		2200	4299	6499	SO:0001587	stop_gained	4240	exon7			ATTACTGTAGGCA	U58516	CCDS10347.1, CCDS45345.1	15q25	2009-03-25			ENSG00000140545	ENSG00000140545			7036	protein-coding gene	gene with protein product	"sperm surface protein hP47"	602281	"sperm associated antigen 10"	SPAG10		9027496, 19204935	Standard	NM_005928		Approved	SED1, EDIL1, BA46, OAcGD3S, HsT19888, MFG-E8, hP47	uc002bng.4	Q08431	OTTHUMG00000148682	ENST00000566497.1:c.969C>A	chr15.hg19:g.89442944G>T	ENSP00000456281:p.Tyr323*	125.0	0.0		97.0	4.0	NM_005928	B2R6M7|Q53FU9|Q7Z3D2|Q9BTL9	Nonsense_Mutation	SNP	ENST00000566497.1	hg19	CCDS10347.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.922032	0.92319	.	.	ENSG00000140545	ENST00000268150;ENST00000539437;ENST00000542878	.	.	.	5.03	2.04	0.26737	.	0.437377	0.27315	N	0.019926	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.7146	8.9969	0.36059	0.2572:0.0:0.7428:0.0	.	.	.	.	X	323;315;279	.	ENSP00000268150:Y323X	Y	-	3	2	MFGE8	87243948	1.000000	0.71417	0.989000	0.46669	0.888000	0.51559	2.796000	0.47869	0.524000	0.28502	0.485000	0.47835	TAC	.	.		0.567	MFGE8-015	NOVEL	alternative_3_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000432804.1	NM_005928		T	89442944	G	T	89442944	4	4	254	1	0	0	0	0	0	1	0	0	9529	1372	48	3	202	3	MFGE8	15	89442944	Nonsense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	763210	89442944	13088448	745	35037										
RLBP1	6017	hgsc.bcm.edu	37	chr15	89760380	89760380	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gctcataggcacggcccacgTtgaacttccgtgcgcggatg	13	13	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:89760380T>C	ENST00000268125.5	-	5	756	c.317A>G	c.(316-318)aAc>aGc	p.N106S		NM_000326.4	NP_000317.1	P12271	RLBP1_HUMAN	retinaldehyde binding protein 1	106					phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	cell body (GO:0044297)|cytosol (GO:0005829)	11-cis retinal binding (GO:0005502)|retinol binding (GO:0019841)|transporter activity (GO:0005215)	p.N106S(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(1)|prostate(1)|skin(1)	18	Lung NSC(78;0.0472)|all_lung(78;0.089)				Vitamin A(DB00162)	ACGGCCCACGTTGAACTTCCG	0.657																																					p.N106S		Atlas-SNP	.											RLBP1,face,carcinoma,0,1	RLBP1	34	.	1	Substitution - Missense(1)	skin(1)	c.A317G						.						42	43	43					15																	89760380		2200	4299	6499	SO:0001583	missense	6017	exon5			CCCACGTTGAACT	BC004199	CCDS32324.1	15q26.1	2007-07-16	2001-11-28			ENSG00000140522			10024	protein-coding gene	gene with protein product		180090	"retinaldehyde-binding protein 1"			1733864, 9326942	Standard	NM_000326		Approved	CRALBP	uc002bnl.3	P12271		ENST00000268125.5:c.317A>G	chr15.hg19:g.89760380T>C	ENSP00000268125:p.Asn106Ser	108.0	0.0		74.0	3.0	NM_000326	B2R667	Missense_Mutation	SNP	ENST00000268125.5	hg19	CCDS32324.1	.	.	.	.	.	.	.	.	.	.	T	16.57	3.159036	0.57368	.	.	ENSG00000140522	ENST00000268125	D	0.87179	-2.22	5.03	5.03	0.67393	Phosphatidylinositol transfer protein-like, N-terminal (1);Cellular retinaldehyde-binding/triple function, N-terminal (1);	0.208161	0.49305	D	0.000145	T	0.74435	0.3716	N	0.10837	0.055	0.28284	N	0.923864	B	0.12630	0.006	B	0.08055	0.003	T	0.58956	-0.7544	10	0.13853	T	0.58	-20.6791	14.7632	0.69619	0.0:0.0:0.0:1.0	.	106	P12271	RLBP1_HUMAN	S	106	ENSP00000268125:N106S	ENSP00000268125:N106S	N	-	2	0	RLBP1	87561384	0.987000	0.35691	0.890000	0.34922	0.832000	0.47134	7.419000	0.80179	1.898000	0.54952	0.459000	0.35465	AAC	.	.		0.657	RLBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421135.1	NM_000326		C	89760380	T	C	89760380	3	2	254	1	0	0	0	0	1	0	0	0	13403	1725	60	2	656	2	RLBP1	15	89760380	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	317436	89760380	12771012	746	35038										
C15orf42	90381	hgsc.bcm.edu	37	chr15	90142664	90142664	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gctcgaaacatgatctcaacCgttaaaatgttcctaaaatc	5	10	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:90142664C>A	ENST00000268138.7	+	8	2115	c.2010C>A	c.(2008-2010)acC>acA	p.T670T	TICRR_ENST00000560985.1_Silent_p.T669T			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	670					cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|formation of translation preinitiation complex (GO:0001731)|mitotic DNA replication checkpoint (GO:0033314)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)	chromatin binding (GO:0003682)										TGATCTCAACCGTTAAAATGT	0.403																																					p.T670T		Atlas-SNP	.											.	.	.	.	0			c.C2010A						.						102	94	96					15																	90142664		1867	4112	5979	SO:0001819	synonymous_variant	90381	exon8			CTCAACCGTTAAA	AK123612	CCDS10352.2	15q26.1	2012-07-11	2012-07-11	2012-07-11	ENSG00000140534	ENSG00000140534			28704	protein-coding gene	gene with protein product	"TOPBP1-interacting replication-stimulating protein", "SLD3 homolog (S. cerevisiae)"	613298	"chromosome 15 open reading frame 42"	C15orf42		20116089, 20080954	Standard	NM_152259		Approved	MGC45866, FLJ41618, Treslin, SLD3	uc002boe.3	Q7Z2Z1	OTTHUMG00000149648	ENST00000268138.7:c.2010C>A	chr15.hg19:g.90142664C>A		144.0	0.0		92.0	4.0	NM_152259	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Silent	SNP	ENST00000268138.7	hg19	CCDS10352.2																																																																																			.	.		0.403	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259		A	90142664	C	A	90142664	2	1	254	1	0	0	0	0	0	0	0	1	1798	639	23	1		1	C15orf42	15	90142664	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	382284	90142664	12388728	747	35039										
VPS33B	26276	hgsc.bcm.edu	37	chr15	91549273	91549273	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cattggagaagtgctcgttcCgaatctcattaaacacctgt	8	10	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:91549273C>T	ENST00000333371.3	-	12	1222	c.869G>A	c.(868-870)cGg>cAg	p.R290Q	VPS33B_ENST00000535906.1_Missense_Mutation_p.R263Q|VPS33B_ENST00000535843.1_Missense_Mutation_p.R199Q	NM_018668.3	NP_061138.3	Q9H267	VP33B_HUMAN	vacuolar protein sorting 33 homolog B (yeast)	290					lysosome localization (GO:0032418)|melanosome localization (GO:0032400)|membrane fusion (GO:0061025)|platelet alpha granule organization (GO:0070889)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule (GO:0031091)				central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|stomach(2)	16	Lung NSC(78;0.0987)|all_lung(78;0.175)					GTGCTCGTTCCGAATCTCATT	0.483																																					p.R290Q		Atlas-SNP	.											.	VPS33B	42	.	0			c.G869A						.						59	55	56					15																	91549273		2198	4298	6496	SO:0001583	missense	26276	exon12			TCGTTCCGAATCT	AF201694	CCDS10369.1, CCDS73783.1	15q26.1	2006-12-19	2006-12-19		ENSG00000184056	ENSG00000184056			12712	protein-coding gene	gene with protein product		608552	"vacuolar protein sorting 33B (yeast homolog)"			8996080	Standard	XM_005254887		Approved	FLJ14848	uc002bqp.1	Q9H267	OTTHUMG00000149835	ENST00000333371.3:c.869G>A	chr15.hg19:g.91549273C>T	ENSP00000327650:p.Arg290Gln	113.0	0.0		110.0	5.0	NM_018668	B3KQF6|Q96K14|Q9NRP6|Q9NSF3	Missense_Mutation	SNP	ENST00000333371.3	hg19	CCDS10369.1	.	.	.	.	.	.	.	.	.	.	C	32	5.134609	0.94517	.	.	ENSG00000184056	ENST00000333371;ENST00000535906;ENST00000535843;ENST00000537510	T;T;T	0.80909	-1.43;-1.43;-1.43	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	D	0.92057	0.7483	M	0.90922	3.16	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.72982	0.979;0.979	D	0.93060	0.6473	10	0.87932	D	0	-10.9832	19.2714	0.94011	0.0:1.0:0.0:0.0	.	263;290	F5H008;Q9H267	.;VP33B_HUMAN	Q	290;263;199;245	ENSP00000327650:R290Q;ENSP00000444053:R263Q;ENSP00000446267:R199Q	ENSP00000327650:R290Q	R	-	2	0	VPS33B	89350277	1.000000	0.71417	0.971000	0.41717	0.575000	0.36095	6.684000	0.74538	2.884000	0.98904	0.655000	0.94253	CGG	.	.		0.483	VPS33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313496.1	NM_018668		T	91549273	C	T	91549273	3	4	254	1	0	0	0	0	1	0	0	0	17217	652	23	1	1032	1	VPS33B	15	91549273	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1406609	91549273	10982119	748	35040										
NR2F2	7026	hgsc.bcm.edu	37	chr15	96877485	96877485	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcagcccaacaacatcatggGtatcgagaacatttgcgaac	9	11	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr15:96877485G>T	ENST00000394166.3	+	2	2012	c.623G>T	c.(622-624)gGt>gTt	p.G208V	NR2F2_ENST00000421109.2_Missense_Mutation_p.G75V|NR2F2_ENST00000453270.2_Missense_Mutation_p.G55V|MIR1469_ENST00000410719.1_RNA|NR2F2_ENST00000394171.2_Missense_Mutation_p.G55V	NM_021005.3	NP_066285.1	P24468	COT2_HUMAN	nuclear receptor subfamily 2, group F, member 2	208	Interaction with ZFPM2. {ECO:0000250}.|Ligand-binding. {ECO:0000250}.				anterior/posterior pattern specification (GO:0009952)|blood vessel morphogenesis (GO:0048514)|fertilization (GO:0009566)|forebrain development (GO:0030900)|intracellular receptor signaling pathway (GO:0030522)|limb development (GO:0060173)|lipid metabolic process (GO:0006629)|maternal placenta development (GO:0001893)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron migration (GO:0001764)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|radial pattern formation (GO:0009956)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription involved in lymphatic endothelial cell fate commitment (GO:0060849)|response to estradiol (GO:0032355)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|liver(2)|lung(3)|ovary(2)|urinary_tract(1)	17	Lung NSC(78;0.0186)|Melanoma(26;0.0195)|all_lung(78;0.0297)		OV - Ovarian serous cystadenocarcinoma(32;0.0856)			AACATCATGGGTATCGAGAAC	0.602																																					p.G208V		Atlas-SNP	.											.	NR2F2	35	.	0			c.G623T						.						166	159	162					15																	96877485		2197	4298	6495	SO:0001583	missense	7026	exon2			TCATGGGTATCGA	M64497	CCDS10375.1, CCDS45358.1, CCDS45359.1	15q26	2013-01-16			ENSG00000185551	ENSG00000185551		"Nuclear hormone receptors"	7976	protein-coding gene	gene with protein product		107773		ARP1, TFCOUP2		8530078, 11544252	Standard	NM_021005		Approved	COUP-TFII, COUPTFB, SVP40, NF-E3	uc010uri.2	P24468	OTTHUMG00000149848	ENST00000394166.3:c.623G>T	chr15.hg19:g.96877485G>T	ENSP00000377721:p.Gly208Val	135.0	0.0		112.0	5.0	NM_021005	B4DQJ2|B6ZGU1|Q03754|Q3KQR7	Missense_Mutation	SNP	ENST00000394166.3	hg19	CCDS10375.1	.	.	.	.	.	.	.	.	.	.	G	31	5.089585	0.94149	.	.	ENSG00000185551	ENST00000421109;ENST00000394166;ENST00000394171;ENST00000453270	D;D;D;D	0.96992	-4.2;-4.2;-4.2;-4.2	4.96	4.96	0.65561	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (1);	0.000000	0.85682	D	0.000000	D	0.97723	0.9253	M	0.69248	2.105	0.80722	D	1	D;D	0.89917	1.0;0.992	D;D	0.97110	1.0;0.948	D	0.98080	1.0403	10	0.51188	T	0.08	.	18.1811	0.89779	0.0:0.0:1.0:0.0	.	208;75	P24468;Q3KQR7	COT2_HUMAN;.	V	75;208;55;55	ENSP00000401674:G75V;ENSP00000377721:G208V;ENSP00000377726:G55V;ENSP00000389853:G55V	ENSP00000377721:G208V	G	+	2	0	NR2F2	94678489	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.866000	0.99616	2.306000	0.77630	0.561000	0.74099	GGT	.	.		0.602	NR2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313534.1			T	96877485	G	T	96877485	3	4	254	1	0	0	0	0	1	0	0	0	10637	1261	44	3	676	3	NR2F2	15	96877485	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	5328212	96877485	5653907	749	35041										
CACNA1H	8912	hgsc.bcm.edu	37	chr16	1261545	1261545	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gaacatctccaccaaggcacAgtgccgggccgcccactacc	9	18	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:1261545A>G	ENST00000348261.5	+	23	4663	c.4415A>G	c.(4414-4416)cAg>cGg	p.Q1472R	CACNA1H_ENST00000358590.4_Missense_Mutation_p.Q1472R|CACNA1H_ENST00000565831.1_Missense_Mutation_p.Q1472R	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	1472					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	ACCAAGGCACAGTGCCGGGCC	0.682																																					p.Q1472R		Atlas-SNP	.											.	CACNA1H	317	.	0			c.A4415G						.						33	39	37					16																	1261545		2017	4161	6178	SO:0001583	missense	8912	exon23			AGGCACAGTGCCG	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.4415A>G	chr16.hg19:g.1261545A>G	ENSP00000334198:p.Gln1472Arg	137.0	0.0		89.0	4.0	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	hg19	CCDS45375.1	.	.	.	.	.	.	.	.	.	.	A	16.55	3.154628	0.57259	.	.	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.96554	-4.05;-4.01	3.99	3.99	0.46301	Ion transport (1);	0.333388	0.30686	N	0.009086	D	0.93367	0.7885	L	0.48218	1.51	0.29692	N	0.840876	B;B;B;B;B	0.32031	0.174;0.095;0.352;0.072;0.101	B;B;B;B;B	0.29440	0.042;0.102;0.102;0.062;0.102	D	0.91848	0.5489	10	0.87932	D	0	.	12.4821	0.55850	1.0:0.0:0.0:0.0	.	213;213;213;1472;1472	A2SX38;A2SX35;A2SX37;O95180-2;O95180	.;.;.;.;CAC1H_HUMAN	R	1472	ENSP00000334198:Q1472R;ENSP00000351401:Q1472R	ENSP00000334198:Q1472R	Q	+	2	0	CACNA1H	1201546	1.000000	0.71417	1.000000	0.80357	0.543000	0.35085	7.127000	0.77210	1.789000	0.52484	0.402000	0.26972	CAG	.	.		0.682	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407		G	1261545	A	G	1261545	3	3	254	1	0	0	0	0	1	0	0	0	2547	188	7	2	4501	2	CACNA1H	16	1261545	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10		1261545	89093208	750	35042										
CACNA1H	8912	hgsc.bcm.edu	37	chr16	1270004	1270004	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gctgtgcacaccgattccttGgaagggaagattgacagccc	12	11	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:1270004G>A	ENST00000348261.5	+	35	6320	c.6072G>A	c.(6070-6072)ttG>ttA	p.L2024L	CACNA1H_ENST00000358590.4_Silent_p.L2018L|CACNA1H_ENST00000565831.1_Silent_p.L2018L	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	2024					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	CCGATTCCTTGGAAGGGAAGA	0.662																																					p.L2024L		Atlas-SNP	.											.	CACNA1H	317	.	0			c.G6072A						.						16	19	18					16																	1270004		1916	4114	6030	SO:0001819	synonymous_variant	8912	exon35			TTCCTTGGAAGGG	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.6072G>A	chr16.hg19:g.1270004G>A		118.0	0.0		99.0	4.0	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Silent	SNP	ENST00000348261.5	hg19	CCDS45375.1																																																																																			.	.		0.662	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407		A	1270004	G	A	1270004	2	1	254	1	0	0	0	0	0	0	0	1	2547	1339	47	3		3	CACNA1H	16	1270004	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	8459	1270004	89084749	751	35043										
TBL3	10607	hgsc.bcm.edu	37	chr16	2024958	2024958	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cttccacccggaccctacacGcctgctgctcttctcctcgg	7	20	2	0	rs541759826		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:2024958G>T	ENST00000568546.1	+	7	622	c.494G>T	c.(493-495)cGc>cTc	p.R165L		NM_006453.2	NP_006444.2	Q12788	TBL3_HUMAN	transducin (beta)-like 3	165					G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|intracellular signal transduction (GO:0035556)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)	p.R165H(1)		breast(1)|endometrium(2)|kidney(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	18						GACCCTACACGCCTGCTGCTC	0.677																																					p.R165L	Melanoma(118;616 1651 35077 38081 48633)	Atlas-SNP	.											TBL3,NS,carcinoma,0,1	TBL3	54	.	1	Substitution - Missense(1)	lung(1)	c.G494T						.						69	53	59					16																	2024958		2197	4299	6496	SO:0001583	missense	10607	exon7			CTACACGCCTGCT	U02609	CCDS10453.1	16p13.3	2013-01-10			ENSG00000183751	ENSG00000183751		"WD repeat domain containing"	11587	protein-coding gene	gene with protein product		605915				8307582	Standard	NM_006453		Approved	SAZD, UTP13	uc002cnu.1	Q12788	OTTHUMG00000128710	ENST00000568546.1:c.494G>T	chr16.hg19:g.2024958G>T	ENSP00000454836:p.Arg165Leu	109.0	1.0		56.0	3.0	NM_006453	Q59GD6|Q8IVB7|Q96A78	Missense_Mutation	SNP	ENST00000568546.1	hg19	CCDS10453.1	.	.	.	.	.	.	.	.	.	.	G	15.70	2.912003	0.52439	.	.	ENSG00000183751	ENST00000332704	.	.	.	5.32	4.15	0.48705	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	1.547110	0.03341	N	0.194821	T	0.65913	0.2737	M	0.63208	1.945	0.54753	D	0.999985	B	0.20780	0.048	B	0.22753	0.041	T	0.47368	-0.9123	9	0.42905	T	0.14	-25.763	13.9416	0.64059	0.0875:0.0:0.9125:0.0	.	165	Q12788	TBL3_HUMAN	L	165	.	ENSP00000331815:R165L	R	+	2	0	TBL3	1964959	0.990000	0.36364	0.993000	0.49108	0.690000	0.40134	1.546000	0.36179	2.484000	0.83849	0.561000	0.74099	CGC	.	.		0.677	TBL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250615.3	NM_006453		T	2024958	G	T	2024958	3	4	254	1	0	0	0	0	1	0	0	0	15658	1087	38	1	520	1	TBL3	16	2024958	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	754954	2024958	88329795	752	35044										
TBL3	10607	hgsc.bcm.edu	37	chr16	2027159	2027159	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccacagtgccagctgctgggTgtcttctcaggccaccggcg	13	15	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:2027159T>C	ENST00000568546.1	+	15	1673	c.1545T>C	c.(1543-1545)ggT>ggC	p.G515G		NM_006453.2	NP_006444.2	Q12788	TBL3_HUMAN	transducin (beta)-like 3	515					G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|intracellular signal transduction (GO:0035556)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)			breast(1)|endometrium(2)|kidney(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	18						AGCTGCTGGGTGTCTTCTCAG	0.652																																					p.G515G	Melanoma(118;616 1651 35077 38081 48633)	Atlas-SNP	.											.	TBL3	54	.	0			c.T1545C						.						41	41	41					16																	2027159		2198	4300	6498	SO:0001819	synonymous_variant	10607	exon15			GCTGGGTGTCTTC	U02609	CCDS10453.1	16p13.3	2013-01-10			ENSG00000183751	ENSG00000183751		"WD repeat domain containing"	11587	protein-coding gene	gene with protein product		605915				8307582	Standard	NM_006453		Approved	SAZD, UTP13	uc002cnu.1	Q12788	OTTHUMG00000128710	ENST00000568546.1:c.1545T>C	chr16.hg19:g.2027159T>C		57.0	0.0		40.0	4.0	NM_006453	Q59GD6|Q8IVB7|Q96A78	Silent	SNP	ENST00000568546.1	hg19	CCDS10453.1																																																																																			.	.		0.652	TBL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250615.3	NM_006453		C	2027159	T	C	2027159	2	2	254	1	0	0	0	0	0	0	0	1	15658	1683	59	2		2	TBL3	16	2027159	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	2201	2027159	88327594	753	35045										
ABCA3	21	hgsc.bcm.edu	37	chr16	2339468	2339468	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttgacagcggtgcgctcctcCtcgatgagggctccaatgcc	12	14	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:2339468C>T	ENST00000301732.5	-	20	3367	c.2667G>A	c.(2665-2667)gaG>gaA	p.E889E	ABCA3_ENST00000382381.3_Silent_p.E831E	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	889					response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	alveolar lamellar body (GO:0097208)|alveolar lamellar body membrane (GO:0097233)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(7)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(7)|prostate(5)|skin(6)|upper_aerodigestive_tract(1)	70		Ovarian(90;0.17)			Imatinib(DB00619)	TGCGCTCCTCCTCGATGAGGG	0.677																																					p.E889E		Atlas-SNP	.											.	ABCA3	176	.	0			c.G2667A						.						29	27	28					16																	2339468		2195	4298	6493	SO:0001819	synonymous_variant	21	exon20			CTCCTCCTCGATG	U78735	CCDS10466.1	16p13.3	2012-03-14			ENSG00000167972	ENSG00000167972		"ATP binding cassette transporters / subfamily A"	33	protein-coding gene	gene with protein product		601615		ABC3		8706931	Standard	NM_001089		Approved	ABC-C, EST111653, LBM180	uc002cpy.1	Q99758	OTTHUMG00000128845	ENST00000301732.5:c.2667G>A	chr16.hg19:g.2339468C>T		110.0	0.0		67.0	16.0	NM_001089	B2RU09|Q54A95|Q6P5P9|Q92473	Silent	SNP	ENST00000301732.5	hg19	CCDS10466.1																																																																																			.	.		0.677	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089		T	2339468	C	T	2339468	2	4	254	1	0	0	0	0	0	0	0	1	33	680	24	3		3	ABCA3	16	2339468	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	312309	2339468	88015285	754	35046										
SRRM2	23524	hgsc.bcm.edu	37	chr16	2812361	2812361	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcggtctagaacaccagcccGgaggggcaggtctcggtcta	14	12	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:2812361G>T	ENST00000301740.8	+	11	2381	c.1832G>T	c.(1831-1833)cGg>cTg	p.R611L		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	611	Arg-rich.|Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						ACACCAGCCCGGAGGGGCAGG	0.622																																					p.R611L		Atlas-SNP	.											.	SRRM2	263	.	0			c.G1832T						.						57	59	58					16																	2812361		2198	4300	6498	SO:0001583	missense	23524	exon11			CAGCCCGGAGGGG	AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.1832G>T	chr16.hg19:g.2812361G>T	ENSP00000301740:p.Arg611Leu	89.0	0.0		54.0	5.0	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	hg19	CCDS32373.1	.	.	.	.	.	.	.	.	.	.	G	11.09	1.536390	0.27475	.	.	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000426305	T	0.26223	1.75	5.91	5.91	0.95273	.	0.000000	0.56097	D	0.000031	T	0.35248	0.0925	L	0.27053	0.805	0.36903	D	0.890505	D	0.63880	0.993	D	0.74023	0.982	T	0.23619	-1.0183	10	0.44086	T	0.13	-8.1276	11.1017	0.48179	0.0836:0.0:0.9164:0.0	.	611	Q9UQ35	SRRM2_HUMAN	L	611;611;576	ENSP00000301740:R611L	ENSP00000301740:R611L	R	+	2	0	SRRM2	2752362	0.139000	0.22563	0.924000	0.36721	0.284000	0.27059	3.181000	0.50903	2.801000	0.96364	0.655000	0.94253	CGG	.	.		0.622	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			T	2812361	G	T	2812361	3	4	254	1	0	0	0	0	1	0	0	0	15184	1116	39	1	1870	1	SRRM2	16	2812361	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	472893	2812361	87542392	755	35047										
CCDC64B	146439	hgsc.bcm.edu	37	chr16	3078749	3078749	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gggcactgtgcagggcctccCcagggtcttcctgcgcccgc	14	17	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:3078749C>A	ENST00000572449.1	-	8	1252	c.1190G>T	c.(1189-1191)gGg>gTg	p.G397V	CCDC64B_ENST00000573514.1_Missense_Mutation_p.G190V|CCDC64B_ENST00000389347.4_Missense_Mutation_p.G397V			A1A5D9	BICR2_HUMAN	coiled-coil domain containing 64B	397										breast(1)|endometrium(2)|large_intestine(1)	4						CAGGGCCTCCCCAGGGTCTTC	0.672																																					p.G397V		Atlas-SNP	.											.	CCDC64B	19	.	0			c.G1190T						.						28	38	35					16																	3078749		2037	4159	6196	SO:0001583	missense	146439	exon7			GCCTCCCCAGGGT	BC128602	CCDS45393.1	16p13.3	2008-07-04				ENSG00000162069			33584	protein-coding gene	gene with protein product							Standard	NM_001103175		Approved		uc002ctf.4	A1A5D9		ENST00000572449.1:c.1190G>T	chr16.hg19:g.3078749C>A	ENSP00000459043:p.Gly397Val	143.0	0.0		118.0	6.0	NM_001103175	Q658L9	Missense_Mutation	SNP	ENST00000572449.1	hg19	CCDS45393.1	.	.	.	.	.	.	.	.	.	.	C	8.389	0.839369	0.16891	.	.	ENSG00000162069	ENST00000389347	T	0.30981	1.51	4.81	-1.42	0.08913	.	0.734974	0.12341	N	0.477507	T	0.18299	0.0439	N	0.24115	0.695	0.09310	N	0.999993	B	0.26195	0.144	B	0.29942	0.109	T	0.24621	-1.0155	10	0.56958	D	0.05	-3.5455	5.365	0.16109	0.0:0.3698:0.1541:0.4762	.	397	A1A5D9	BICR2_HUMAN	V	397	ENSP00000373998:G397V	ENSP00000373998:G397V	G	-	2	0	CCDC64B	3018750	0.000000	0.05858	0.031000	0.17742	0.014000	0.08584	0.335000	0.19806	-0.324000	0.08589	-0.367000	0.07326	GGG	.	.		0.672	CCDC64B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436991.1			A	3078749	C	A	3078749	3	1	254	1	0	0	0	0	1	0	0	0	2838	623	22	3	348	3	CCDC64B	16	3078749	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	266388	3078749	87276004	756	35048										
ZNF75A	7627	hgsc.bcm.edu	37	chr16	3367499	3367499	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gaaaaccttcagagttagctCtgaccttattaagcaccaaa	6	10	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:3367499C>G	ENST00000574298.1	+	6	994	c.521C>G	c.(520-522)tCt>tGt	p.S174C	ZNF75A_ENST00000498240.2_3'UTR	NM_153028.2	NP_694573.1	Q96N20	ZN75A_HUMAN	zinc finger protein 75a	174					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|large_intestine(3)|lung(7)|prostate(1)	12						AGAGTTAGCTCTGACCTTATT	0.383																																					p.S174C		Atlas-SNP	.											.	ZNF75A	34	.	0			c.C521G						.						81	79	79					16																	3367499		2197	4300	6497	SO:0001583	missense	7627	exon6			TTAGCTCTGACCT	X91826	CCDS10501.1	16p13.11	2013-01-08			ENSG00000162086	ENSG00000162086		"Zinc fingers, C2H2-type", "-"	13146	protein-coding gene	gene with protein product		601473				8661144	Standard	NM_153028		Approved	FLJ31529	uc002cut.4	Q96N20	OTTHUMG00000129356	ENST00000574298.1:c.521C>G	chr16.hg19:g.3367499C>G	ENSP00000459566:p.Ser174Cys	220.0	0.0		199.0	62.0	NM_153028	Q0VDI8|Q92669	Missense_Mutation	SNP	ENST00000574298.1	hg19	CCDS10501.1	.	.	.	.	.	.	.	.	.	.	C	16.73	3.202946	0.58234	.	.	ENSG00000162086	ENST00000293995	.	.	.	4.57	3.6	0.41247	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.44285	D	0.000464	T	0.54775	0.1879	M	0.80028	2.48	0.26965	N	0.96573	B	0.22414	0.069	B	0.19946	0.027	T	0.56649	-0.7944	9	0.66056	D	0.02	.	12.5959	0.56470	0.0:0.8312:0.1688:0.0	.	174	Q96N20	ZN75A_HUMAN	C	174	.	ENSP00000293995:S174C	S	+	2	0	ZNF75A	3307500	0.000000	0.05858	1.000000	0.80357	0.996000	0.88848	0.207000	0.17395	1.253000	0.44018	0.557000	0.71058	TCT	.	.		0.383	ZNF75A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251506.2	NM_153028		G	3367499	C	G	3367499	3	3	254	1	0	0	0	0	1	0	0	0	18148	913	32	4	531	4	ZNF75A	16	3367499	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	288750	3367499	86987254	757	35049										
CREBBP	1387	hgsc.bcm.edu	37	chr16	3778391	3778391	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gccatgcccccagccatgccGgcactcccttgctgctgctg	10	19	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:3778391G>T	ENST00000262367.5	-	31	7466	c.6657C>A	c.(6655-6657)gcC>gcA	p.A2219A	CREBBP_ENST00000382070.3_Silent_p.A2181A	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	2219					cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		CAGCCATGCCGGCACTCCCTt	0.642			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																														p.A2219A		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP	546	.	0			c.C6657A						.						33	30	31					16																	3778391		2196	4300	6496	SO:0001819	synonymous_variant	1387	exon31			CATGCCGGCACTC	U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.6657C>A	chr16.hg19:g.3778391G>T		82.0	0.0		76.0	5.0	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Silent	SNP	ENST00000262367.5	hg19	CCDS10509.1																																																																																			.	.		0.642	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		T	3778391	G	T	3778391	2	4	254	1	0	0	0	0	0	0	0	1	3863	1103	39	1		1	CREBBP	16	3778391	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	410892	3778391	86576362	758	35050										
DNAJA3	9093	hgsc.bcm.edu	37	chr16	4500484	4500484	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggggacggtgaacggcgtcaCcctcaccagctctggtaagg	15	12	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:4500484C>T	ENST00000262375.6	+	10	1402	c.1325C>T	c.(1324-1326)aCc>aTc	p.T442I	DNAJA3_ENST00000431375.2_Missense_Mutation_p.T289I|DNAJA3_ENST00000355296.4_Missense_Mutation_p.T442I	NM_005147.5	NP_005138.3	Q96EY1	DNJA3_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 3	442					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation-induced cell death of T cells (GO:0006924)|cell aging (GO:0007569)|mitochondrial DNA replication (GO:0006264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of programmed cell death (GO:0043069)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell proliferation (GO:0042102)|protein folding (GO:0006457)|protein stabilization (GO:0050821)|response to heat (GO:0009408)|response to interferon-gamma (GO:0034341)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|small GTPase mediated signal transduction (GO:0007264)|T cell differentiation in thymus (GO:0033077)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of plasma membrane (GO:0019897)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|interferon-gamma receptor binding (GO:0005133)|metal ion binding (GO:0046872)|NF-kappaB binding (GO:0051059)|protein kinase binding (GO:0019901)|small GTPase regulator activity (GO:0005083)|transcription factor binding (GO:0008134)			NS(1)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|upper_aerodigestive_tract(2)	15						AACGGCGTCACCCTCACCAGC	0.612																																					p.T442I		Atlas-SNP	.											.	DNAJA3	52	.	0			c.C1325T						.						45	35	38					16																	4500484		2197	4296	6493	SO:0001583	missense	9093	exon10			GCGTCACCCTCAC	AF061749	CCDS10515.1, CCDS45400.1, CCDS66930.1	16p13.3	2011-09-02			ENSG00000103423	ENSG00000103423		"Heat shock proteins / DNAJ (HSP40)"	11808	protein-coding gene	gene with protein product		608382		TID1		9683573	Standard	NM_005147		Approved	hTid-1	uc002cwk.3	Q96EY1	OTTHUMG00000129470	ENST00000262375.6:c.1325C>T	chr16.hg19:g.4500484C>T	ENSP00000262375:p.Thr442Ile	72.0	0.0		66.0	4.0	NM_001135110	B2RAJ5|B4DI33|E7ES32|O75472|Q8WUJ6|Q8WXJ3|Q96D76|Q96IV1|Q9NYH8	Missense_Mutation	SNP	ENST00000262375.6	hg19	CCDS10515.1	.	.	.	.	.	.	.	.	.	.	C	18.48	3.633660	0.67015	.	.	ENSG00000103423	ENST00000262375;ENST00000355296;ENST00000431375	T;T;T	0.65364	-0.11;-0.15;0.84	5.63	5.63	0.86233	.	0.046583	0.85682	D	0.000000	T	0.71921	0.3397	M	0.62723	1.935	0.80722	D	1	D;D;D	0.62365	0.991;0.963;0.967	P;P;P	0.52672	0.606;0.706;0.606	T	0.75082	-0.3443	10	0.87932	D	0	-26.8186	18.6707	0.91510	0.0:1.0:0.0:0.0	.	289;442;442	E7ES32;Q96EY1-2;Q96EY1	.;.;DNJA3_HUMAN	I	442;442;289	ENSP00000262375:T442I;ENSP00000347445:T442I;ENSP00000393970:T289I	ENSP00000262375:T442I	T	+	2	0	DNAJA3	4440485	1.000000	0.71417	0.999000	0.59377	0.683000	0.39861	4.787000	0.62432	2.659000	0.90383	0.561000	0.74099	ACC	.	.		0.612	DNAJA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251633.1			T	4500484	C	T	4500484	3	4	254	1	0	0	0	0	1	0	0	0	4615	507	18	3	1363	3	DNAJA3	16	4500484	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	722093	4500484	85854269	759	35051										
ABAT	18	hgsc.bcm.edu	37	chr16	8866644	8866644	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctttgggatccaggtggaggAtctgattgtgaaatatcgga	14	5	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:8866644A>G	ENST00000396600.2	+	12	1762	c.824A>G	c.(823-825)gAt>gGt	p.D275G	ABAT_ENST00000425191.2_Missense_Mutation_p.D275G|ABAT_ENST00000268251.8_Missense_Mutation_p.D275G|ABAT_ENST00000567812.1_Missense_Mutation_p.D290G|ABAT_ENST00000569156.1_Missense_Mutation_p.D275G	NM_000663.4	NP_000654.2	P80404	GABT_HUMAN	4-aminobutyrate aminotransferase	275					behavioral response to cocaine (GO:0048148)|copulation (GO:0007620)|gamma-aminobutyric acid catabolic process (GO:0009450)|locomotory behavior (GO:0007626)|negative regulation of blood pressure (GO:0045776)|neurotransmitter catabolic process (GO:0042135)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to iron ion (GO:0010039)|response to nicotine (GO:0035094)|synaptic transmission (GO:0007268)	4-aminobutyrate transaminase complex (GO:0032144)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	(S)-3-amino-2-methylpropionate transaminase activity (GO:0047298)|4-aminobutyrate transaminase activity (GO:0003867)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|succinate-semialdehyde dehydrogenase binding (GO:0032145)			breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|skin(3)|upper_aerodigestive_tract(2)	26					L-Alanine(DB00160)|Phenelzine(DB00780)|Pyruvic acid(DB00119)|Valproic Acid(DB00313)|Vigabatrin(DB01080)	CAGGTGGAGGATCTGATTGTG	0.552																																					p.D275G		Atlas-SNP	.											.	ABAT	46	.	0			c.A824G						.						77	71	73					16																	8866644		2197	4300	6497	SO:0001583	missense	18	exon12			TGGAGGATCTGAT	L32961	CCDS10534.1	16p13.2	2011-01-10			ENSG00000183044	ENSG00000183044	2.6.1.19		23	protein-coding gene	gene with protein product	"4-aminobutyrate transaminase"	137150				7721088	Standard	NM_020686		Approved	GABAT	uc002czc.4	P80404	OTTHUMG00000048201	ENST00000396600.2:c.824A>G	chr16.hg19:g.8866644A>G	ENSP00000379845:p.Asp275Gly	103.0	0.0		100.0	4.0	NM_001127448	A8K386|Q16260|Q8N5W2|Q96BG2|Q99800	Missense_Mutation	SNP	ENST00000396600.2	hg19	CCDS10534.1	.	.	.	.	.	.	.	.	.	.	A	12.50	1.956399	0.34565	.	.	ENSG00000183044	ENST00000268251;ENST00000396600;ENST00000425191	T;T;T	0.77229	-1.08;-1.08;-1.08	4.94	4.94	0.65067	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	T	0.74581	0.3735	L	0.53780	1.695	0.80722	D	1	B	0.22146	0.065	B	0.28232	0.087	T	0.71974	-0.4430	10	0.41790	T	0.15	.	13.7814	0.63085	1.0:0.0:0.0:0.0	.	275	P80404	GABT_HUMAN	G	275	ENSP00000268251:D275G;ENSP00000379845:D275G;ENSP00000411916:D275G	ENSP00000268251:D275G	D	+	2	0	ABAT	8774145	1.000000	0.71417	0.999000	0.59377	0.253000	0.25986	9.083000	0.94067	1.847000	0.53656	0.459000	0.35465	GAT	.	.		0.552	ABAT-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433620.2	NM_020686		G	8866644	A	G	8866644	3	3	254	1	0	0	0	0	1	0	0	0	27	333	12	2	866	2	ABAT	16	8866644	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	4366160	8866644	81488109	760	35052										
USP7	7874	hgsc.bcm.edu	37	chr16	9015082	9015082	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gaacaaatgactaatacgacGactgaacgacttttcatcat	6	9	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:9015082G>T	ENST00000344836.4	-	4	652	c.454C>A	c.(454-456)Cgt>Agt	p.R152S	USP7_ENST00000566224.1_5'Flank|USP7_ENST00000535863.1_Missense_Mutation_p.R53S|USP7_ENST00000381886.4_Missense_Mutation_p.R136S	NM_003470.2	NP_003461.2	Q93009	UBP7_HUMAN	ubiquitin specific peptidase 7 (herpes virus-associated)	152	Interaction with TSPYL5.|Interaction with p53/TP53, MDM2 and EBNA1.|MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.|Necessary for nuclear localization.				maintenance of DNA methylation (GO:0010216)|multicellular organismal development (GO:0007275)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|protein deubiquitination (GO:0016579)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|transcription-coupled nucleotide-excision repair (GO:0006283)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|p53 binding (GO:0002039)|protein C-terminus binding (GO:0008022)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(13)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	48						CTAATACGACGACTGAACGAC	0.358																																					p.R152S		Atlas-SNP	.											.	USP7	116	.	0			c.C454A						.						95	86	89					16																	9015082		2197	4300	6497	SO:0001583	missense	7874	exon4			TACGACGACTGAA	Z72499	CCDS32385.1, CCDS66941.1	16p13.3	2008-04-11	2005-08-08			ENSG00000187555		"Ubiquitin-specific peptidases"	12630	protein-coding gene	gene with protein product		602519	"ubiquitin specific protease 7 (herpes virus-associated)"	HAUSP		12838346, 9925944	Standard	NM_003470		Approved		uc002czl.2	Q93009		ENST00000344836.4:c.454C>A	chr16.hg19:g.9015082G>T	ENSP00000343535:p.Arg152Ser	148.0	0.0		135.0	8.0	NM_003470	A6NMY8|B7Z815|H0Y3G8	Missense_Mutation	SNP	ENST00000344836.4	hg19	CCDS32385.1	.	.	.	.	.	.	.	.	.	.	G	16.64	3.179091	0.57692	.	.	ENSG00000187555	ENST00000344836;ENST00000381886;ENST00000535863;ENST00000544549;ENST00000542333	T;T;T	0.42131	0.98;0.98;0.98	5.9	5.9	0.94986	TRAF-like (1);MATH (3);	0.000000	0.85682	D	0.000000	T	0.63570	0.2522	M	0.86420	2.815	0.80722	D	1	P;P	0.44946	0.846;0.846	P;P	0.51550	0.673;0.673	T	0.61466	-0.7057	10	0.29301	T	0.29	.	20.3398	0.98759	0.0:0.0:1.0:0.0	.	152;136	Q93009;B7Z815	UBP7_HUMAN;.	S	152;160;53;53;94	ENSP00000343535:R152S;ENSP00000443646:R53S;ENSP00000439272:R94S	ENSP00000343535:R152S	R	-	1	0	USP7	8922583	1.000000	0.71417	0.801000	0.32222	0.921000	0.55340	9.509000	0.98002	2.817000	0.96982	0.552000	0.68991	CGT	.	.		0.358	USP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434268.2			T	9015082	G	T	9015082	3	4	254	1	0	0	0	0	1	0	0	0	17103	1058	37	1	2966	1	USP7	16	9015082	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	148438	9015082	81339671	761	35053										
GRIN2A	2903	hgsc.bcm.edu	37	chr16	9934644	9934644	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agccaactgccatgactgccCgttgatagaccacctggatg	10	13	0	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:9934644C>A	ENST00000396573.2	-	8	1820	c.1511G>T	c.(1510-1512)cGg>cTg	p.R504L	GRIN2A_ENST00000396575.2_Missense_Mutation_p.R504L|GRIN2A_ENST00000562109.1_Missense_Mutation_p.R504L|GRIN2A_ENST00000535259.1_Missense_Mutation_p.R347L|GRIN2A_ENST00000404927.2_Missense_Mutation_p.R504L|GRIN2A_ENST00000330684.3_Missense_Mutation_p.R504L	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	504			R -> W (in FESD). {ECO:0000269|PubMed:23933820}.		directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CATGACTGCCCGTTGATAGAC	0.448																																					p.R504L		Atlas-SNP	.											.	GRIN2A	366	.	0			c.G1511T						.						80	63	69					16																	9934644		2197	4300	6497	SO:0001583	missense	2903	exon8			ACTGCCCGTTGAT		CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.1511G>T	chr16.hg19:g.9934644C>A	ENSP00000379818:p.Arg504Leu	109.0	0.0		72.0	4.0	NM_000833	O00669|Q17RZ6	Missense_Mutation	SNP	ENST00000396573.2	hg19	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	C	13.72	2.322313	0.41096	.	.	ENSG00000183454	ENST00000396573;ENST00000404927;ENST00000535259;ENST00000330684;ENST00000396575	T;T;T;T;T	0.55052	0.54;0.54;0.54;0.54;0.54	5.3	5.3	0.74995	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (1);	0.126603	0.53938	D	0.000051	T	0.54806	0.1881	M	0.66560	2.04	0.49687	D	0.999818	B;P;P	0.41710	0.307;0.76;0.758	B;B;B	0.40228	0.071;0.187;0.323	T	0.57015	-0.7883	9	.	.	.	.	17.9735	0.89120	0.0:1.0:0.0:0.0	.	347;504;504	F5GZ52;Q17RZ6;Q12879	.;.;NMDE1_HUMAN	L	504;504;347;504;504	ENSP00000379818:R504L;ENSP00000385872:R504L;ENSP00000441572:R347L;ENSP00000332549:R504L;ENSP00000379820:R504L	.	R	-	2	0	GRIN2A	9842145	1.000000	0.71417	0.610000	0.28997	0.282000	0.26991	4.425000	0.59875	2.469000	0.83416	0.655000	0.94253	CGG	.	.		0.448	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			A	9934644	C	A	9934644	3	1	254	1	0	0	0	0	1	0	0	0	6788	652	23	1	2911	1	GRIN2A	16	9934644	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	919562	9934644	80420109	762	35054										
PDXDC1	23042	hgsc.bcm.edu	37	chr16	15127208	15127208	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aacgtcgatgctgctgagctCgtggagaccattgcggccac	13	12	0	2	rs151129728	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:15127208C>A	ENST00000396410.4	+	19	1861	c.1764C>A	c.(1762-1764)ctC>ctA	p.L588L	PDXDC1_ENST00000535621.2_Intron|PDXDC1_ENST00000325823.7_Silent_p.L573L|PDXDC1_ENST00000450288.2_Silent_p.L560L|PDXDC1_ENST00000569715.1_Silent_p.L561L|PDXDC1_ENST00000563679.1_Silent_p.L606L|PDXDC1_ENST00000447912.2_Silent_p.L497L	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	588					carboxylic acid metabolic process (GO:0019752)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(10)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CTGCTGAGCTCGTGGAGACCA	0.537																																					p.L588L		Atlas-SNP	.											.	PDXDC1	59	.	0			c.C1764A						.						145	130	135					16																	15127208		2197	4300	6497	SO:0001819	synonymous_variant	23042	exon19			TGAGCTCGTGGAG	AK025504, BX647809	CCDS32393.1, CCDS66954.1, CCDS66957.1, CCDS73830.1, CCDS73831.1	16p13.11	2008-02-05							28995	protein-coding gene	gene with protein product		614244					Standard	XM_005255173		Approved	KIAA0251	uc002dda.4	Q6P996	OTTHUMG00000166304	ENST00000396410.4:c.1764C>A	chr16.hg19:g.15127208C>A		86.0	0.0		72.0	4.0	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Silent	SNP	ENST00000396410.4	hg19	CCDS32393.1																																																																																			.	C|1.000;T|0.000		0.537	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027		A	15127208	C	A	15127208	2	1	254	1	0	0	0	0	0	0	0	1	11705	871	31	1		1	PDXDC1	16	15127208	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	5192564	15127208	75227545	763	35055										
USP31	57478	hgsc.bcm.edu	37	chr16	23080459	23080459	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcgctctgatccacataagcGatctgattattgttatcaaa	6	9	3	2	rs201814190		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:23080459G>T	ENST00000219689.7	-	16	2966	c.2967C>A	c.(2965-2967)atC>atA	p.I989I	USP31_ENST00000567975.1_Silent_p.I282I	NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	0	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)	p.I989I(1)		breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	57				GBM - Glioblastoma multiforme(48;0.0187)		CCACATAAGCGATCTGATTAT	0.522																																					p.I989I		Atlas-SNP	.											USP31,leg,malignant_melanoma,0,1	USP31	122	.	1	Substitution - coding silent(1)	skin(1)	c.C2967A						.						78	82	81					16																	23080459		2197	4300	6497	SO:0001819	synonymous_variant	57478	exon16			ATAAGCGATCTGA	AB033029	CCDS10607.1	16p12.3	2008-02-05	2005-08-08		ENSG00000103404	ENSG00000103404		"Ubiquitin-specific peptidases"	20060	protein-coding gene	gene with protein product			"ubiquitin specific protease 31"			12838346	Standard	NM_020718		Approved	KIAA1203	uc002dll.3	Q70CQ4	OTTHUMG00000094793	ENST00000219689.7:c.2967C>A	chr16.hg19:g.23080459G>T		50.0	0.0		27.0	4.0	NM_020718	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Silent	SNP	ENST00000219689.7	hg19	CCDS10607.1																																																																																			.	G|1.000;A|0.000		0.522	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718		T	23080459	G	T	23080459	2	4	254	1	0	0	0	0	0	0	0	1	17077	1048	37	1		1	USP31	16	23080459	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	7953251	23080459	67274294	764	35056										
USP31	57478	hgsc.bcm.edu	37	chr16	23080589	23080589	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	attcgtctttgaacacgcctTccatgacagccagaggggcc	10	13	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:23080589T>C	ENST00000219689.7	-	16	2836	c.2837A>G	c.(2836-2838)gAa>gGa	p.E946G	USP31_ENST00000567975.1_Missense_Mutation_p.E239G	NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	0	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	57				GBM - Glioblastoma multiforme(48;0.0187)		GAACACGCCTTCCATGACAGC	0.577																																					p.E946G		Atlas-SNP	.											.	USP31	122	.	0			c.A2837G						.						85	87	86					16																	23080589		2197	4300	6497	SO:0001583	missense	57478	exon16			ACGCCTTCCATGA	AB033029	CCDS10607.1	16p12.3	2008-02-05	2005-08-08		ENSG00000103404	ENSG00000103404		"Ubiquitin-specific peptidases"	20060	protein-coding gene	gene with protein product			"ubiquitin specific protease 31"			12838346	Standard	NM_020718		Approved	KIAA1203	uc002dll.3	Q70CQ4	OTTHUMG00000094793	ENST00000219689.7:c.2837A>G	chr16.hg19:g.23080589T>C	ENSP00000219689:p.Glu946Gly	103.0	0.0		96.0	5.0	NM_020718	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Missense_Mutation	SNP	ENST00000219689.7	hg19	CCDS10607.1	.	.	.	.	.	.	.	.	.	.	T	18.66	3.672299	0.67928	.	.	ENSG00000103404	ENST00000219689;ENST00000381162	T	0.12039	2.72	6.16	6.16	0.99307	.	0.649429	0.13781	N	0.363238	T	0.35480	0.0933	L	0.56769	1.78	0.58432	D	0.999999	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.81914	0.994;0.986;0.995	T	0.00484	-1.1712	10	0.37606	T	0.19	-15.1034	15.9872	0.80168	0.0:0.0:0.0:1.0	.	249;946;239	Q70CQ4-2;Q70CQ4;B3KS48	.;UBP31_HUMAN;.	G	946;249	ENSP00000219689:E946G	ENSP00000219689:E946G	E	-	2	0	USP31	22988090	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.665000	0.83852	2.367000	0.80283	0.528000	0.53228	GAA	.	.		0.577	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718		C	23080589	T	C	23080589	3	2	254	1	0	0	0	0	1	0	0	0	17077	1783	62	2	1225	2	USP31	16	23080589	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	130	23080589	67274164	765	35057										
USP31	57478	hgsc.bcm.edu	37	chr16	23091273	23091273	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctcacactgcagacctgtgtAgtgccccccttgcatggtgc	10	15	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:23091273A>G	ENST00000219689.7	-	13	2169	c.2170T>C	c.(2170-2172)Tac>Cac	p.Y724H		NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	354	DUSP 3. {ECO:0000255|PROSITE- ProRule:PRU00613}.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	57				GBM - Glioblastoma multiforme(48;0.0187)		AGACCTGTGTAGTGCCCCCCT	0.577																																					p.Y724H		Atlas-SNP	.											.	USP31	122	.	0			c.T2170C						.						84	66	72					16																	23091273		2197	4300	6497	SO:0001583	missense	57478	exon13			CTGTGTAGTGCCC	AB033029	CCDS10607.1	16p12.3	2008-02-05	2005-08-08		ENSG00000103404	ENSG00000103404		"Ubiquitin-specific peptidases"	20060	protein-coding gene	gene with protein product			"ubiquitin specific protease 31"			12838346	Standard	NM_020718		Approved	KIAA1203	uc002dll.3	Q70CQ4	OTTHUMG00000094793	ENST00000219689.7:c.2170T>C	chr16.hg19:g.23091273A>G	ENSP00000219689:p.Tyr724His	116.0	0.0		75.0	4.0	NM_020718	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Missense_Mutation	SNP	ENST00000219689.7	hg19	CCDS10607.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.602357	0.87157	.	.	ENSG00000103404	ENST00000219689	T	0.21361	2.01	5.11	5.11	0.69529	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site (1);Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.64402	D	0.000001	T	0.60741	0.2292	H	0.96720	3.87	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.75260	-0.3380	10	0.87932	D	0	-13.1175	14.0861	0.64957	1.0:0.0:0.0:0.0	.	724	Q70CQ4	UBP31_HUMAN	H	724	ENSP00000219689:Y724H	ENSP00000219689:Y724H	Y	-	1	0	USP31	22998774	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.958000	0.93099	1.917000	0.55516	0.455000	0.32223	TAC	.	.		0.577	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718		G	23091273	A	G	23091273	3	3	254	1	0	0	0	0	1	0	0	0	17077	420	15	2	1904	2	USP31	16	23091273	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	10684	23091273	67263480	766	35058										
XPO6	23214	hgsc.bcm.edu	37	chr16	28167437	28167437	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgctcttcactgtgtgggcaTtgttatccttggtgattttc	10	8	2	1	rs369899782		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:28167437T>A	ENST00000304658.5	-	7	1555	c.1055A>T	c.(1054-1056)aAt>aTt	p.N352I	XPO6_ENST00000565698.1_Missense_Mutation_p.N338I|XPO6_ENST00000561488.1_5'UTR	NM_015171.3	NP_055986.1	Q96QU8	XPO6_HUMAN	exportin 6	352					protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	25						TGTGTGGGCATTGTTATCCTT	0.478																																					p.N352I		Atlas-SNP	.											.	XPO6	177	.	0			c.A1055T						.						108	95	100					16																	28167437		1963	4151	6114	SO:0001583	missense	23214	exon7			TGGGCATTGTTAT	AY026388	CCDS42135.1, CCDS59266.1	16p11.2	2011-04-13	2003-03-11	2003-03-14		ENSG00000169180		"Exportins"	19733	protein-coding gene	gene with protein product		608411	"RAN binding protein 20"	RANBP20		14592989	Standard	NM_001270940		Approved	KIAA0370, FLJ22519	uc002dpa.2	Q96QU8		ENST00000304658.5:c.1055A>T	chr16.hg19:g.28167437T>A	ENSP00000302790:p.Asn352Ile	773.0	0.0		544.0	173.0	NM_015171	A1L3W4|D3DWF9|Q2YDX3|Q53G88|Q68G50|Q76N88|Q96CP8|Q9BT21	Missense_Mutation	SNP	ENST00000304658.5	hg19	CCDS42135.1	.	.	.	.	.	.	.	.	.	.	T	14.32	2.500126	0.44455	.	.	ENSG00000169180	ENST00000304658	T	0.51071	0.72	5.87	5.87	0.94306	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.43389	0.1245	L	0.46157	1.445	0.80722	D	1	P;P	0.51933	0.949;0.893	B;B	0.40901	0.343;0.343	T	0.48969	-0.8987	10	0.72032	D	0.01	-17.8237	14.5226	0.67863	0.0:0.0:0.0:1.0	.	352;352	B7ZM10;Q96QU8	.;XPO6_HUMAN	I	352	ENSP00000302790:N352I	ENSP00000302790:N352I	N	-	2	0	XPO6	28074938	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.997000	0.88414	2.371000	0.80710	0.533000	0.62120	AAT	.	.		0.478	XPO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433732.1	XM_055195		A	28167437	T	A	28167437	3	1	254	1	0	0	0	0	1	0	0	0	17463	1493	52	4	2394	4	XPO6	16	28167437	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	5076164	28167437	62187316	767	35059										
TUFM	25970	hgsc.bcm.edu	37	chr16	28856082	28856082	+	5'Flank	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcccctttatagccaaactcGgtgagcagctcccggatctc	8	15	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:28856082G>T	ENST00000322610.8	+	0	0				TUFM_ENST00000313511.3_Silent_p.T207T|MIR4721_ENST00000577590.1_RNA			Q9NRF2	SH2B1_HUMAN	SH2B adaptor protein 1						blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|intracellular signal transduction (GO:0035556)|lamellipodium assembly (GO:0030032)|positive regulation of mitosis (GO:0045840)|regulation of DNA biosynthetic process (GO:2000278)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25						AGCCAAACTCGGTGAGCAGCT	0.592																																					p.T207T		Atlas-SNP	.											TUFM,rectum,carcinoma,0,1	TUFM	33	.	0			c.C621A						.						110	103	106					16																	28856082		2197	4300	6497	SO:0001631	upstream_gene_variant	7284	exon5			AAACTCGGTGAGC	AK055104	CCDS32424.1, CCDS53996.1, CCDS53997.1	16p11.2	2013-02-14						"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	30417	protein-coding gene	gene with protein product	"SH2-B homolog"	608937				11827956, 10594240	Standard	NM_001145812		Approved	FLJ30542, SH2B	uc002drl.3	Q9NRF2			chr16.hg19:g.28856082G>T	Exception_encountered	126.0	0.0		100.0	4.0	NM_003321	A8K2R7|Q96FK3|Q96SX3|Q9NRF1|Q9NRF3|Q9P2P7|Q9Y3Y3	Silent	SNP	ENST00000322610.8	hg19	CCDS53996.1																																																																																			.	.		0.592	SH2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000432666.1	NM_015503		T	28856082	G	T	28856082	1	4	254	0	1	0	0	0	0	0	0	0	16786	1103	39	1		1	TUFM	16	28856082	5'Flank	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	688645	28856082	61498671	768	35060										
SPN	6693	hgsc.bcm.edu	37	chr16	29675060	29675060	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttgcctggaaatggccacgcTtctccttctccttggggtgc	11	13	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:29675060T>C	ENST00000360121.3	+	2	103	c.11T>C	c.(10-12)cTt>cCt	p.L4P	SPN_ENST00000395389.2_Missense_Mutation_p.L4P	NM_001030288.2|NM_003123.4	NP_001025459.1|NP_003114.1	O75398	DEAF1_HUMAN	sialophorin	0	Ala-rich.				anatomical structure morphogenesis (GO:0009653)|embryonic skeletal system development (GO:0048706)|germ cell development (GO:0007281)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|skin(2)|stomach(1)	15						ATGGCCACGCTTCTCCTTCTC	0.627																																					p.L4P		Atlas-SNP	.											.	SPN	44	.	0			c.T11C						.						118	129	125					16																	29675060		2197	4300	6497	SO:0001583	missense	6693	exon2			CCACGCTTCTCCT	J04536	CCDS10650.1	16p11.2	2008-07-31	2008-07-31		ENSG00000197471	ENSG00000197471		"CD molecules"	11249	protein-coding gene	gene with protein product	"leukosialin"	182160	"sialophorin (gpL115, leukosialin, CD43)"			2784859, 2521952	Standard	NM_001030288		Approved	LSN, CD43, GPL115	uc002dtm.4	P16150	OTTHUMG00000097765	ENST00000360121.3:c.11T>C	chr16.hg19:g.29675060T>C	ENSP00000353238:p.Leu4Pro	122.0	0.0		104.0	5.0	NM_001030288	A8K1F8|A8K5R8|C7T5V5|O15152|O75399|O75510|O75511|O75512|O75513|Q9UET1	Missense_Mutation	SNP	ENST00000360121.3	hg19	CCDS10650.1	.	.	.	.	.	.	.	.	.	.	.	13.37	2.217088	0.39201	.	.	ENSG00000197471	ENST00000395389;ENST00000436527;ENST00000360121	T;T;T	0.47869	0.87;0.83;0.87	4.51	3.42	0.39159	.	0.203527	0.24481	N	0.038145	T	0.34978	0.0916	L	0.39898	1.24	0.20638	N	0.999877	B	0.31931	0.347	B	0.29176	0.099	T	0.32107	-0.9919	10	0.87932	D	0	-6.7037	7.0944	0.25301	0.0:0.1065:0.0:0.8935	.	4	P16150	LEUK_HUMAN	P	4	ENSP00000378787:L4P;ENSP00000412907:L4P;ENSP00000353238:L4P	ENSP00000353238:L4P	L	+	2	0	SPN	29582561	0.012000	0.17670	0.124000	0.21820	0.011000	0.07611	1.911000	0.39937	0.839000	0.34971	0.459000	0.35465	CTT	.	.		0.627	SPN-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215001.2			C	29675060	T	C	29675060	3	2	254	1	0	0	0	0	1	0	0	0	15088	1609	56	2	13	2	SPN	16	29675060	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	818978	29675060	60679693	769	35061										
MAZ	4150	hgsc.bcm.edu	37	chr16	29820871	29820871	+	Intron	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cccccaataggcttcaccacGgcagcatacctgcgcatcca	7	18	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:29820871G>T	ENST00000322945.6	+	5	1444				AC009133.20_ENST00000569039.1_RNA|AC009133.15_ENST00000566537.1_RNA|PRRT2_ENST00000358758.7_5'Flank|PRRT2_ENST00000300797.6_5'Flank|MAZ_ENST00000563402.1_Intron|AC009133.14_ENST00000563806.1_RNA|MAZ_ENST00000562337.1_Intron|MAZ_ENST00000568544.1_Intron|PRRT2_ENST00000567659.1_5'Flank|AC009133.14_ENST00000569981.1_RNA|MAZ_ENST00000219782.6_Silent_p.T430T|MAZ_ENST00000568282.1_Silent_p.T31T|MAZ_ENST00000545521.1_Intron|MAZ_ENST00000566906.2_Intron	NM_002383.2	NP_002374.2	P56270	MAZ_HUMAN	MYC-associated zinc finger protein (purine-binding transcription factor)						positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|termination of RNA polymerase II transcription (GO:0006369)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			endometrium(3)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	10						GCTTCACCACGGCAGCATACC	0.682																																					p.T430T	Colon(72;875 1167 15364 30899 37091)	Atlas-SNP	.											.	MAZ	48	.	0			c.G1290T						.						22	23	22					16																	29820871		1987	4123	6110	SO:0001627	intron_variant	4150	exon5			CACCACGGCAGCA	M93339	CCDS42143.1, CCDS42144.1, CCDS61902.1, CCDS61903.1	16p11.2	2013-01-08			ENSG00000103495	ENSG00000103495		"Zinc fingers, C2H2-type"	6914	protein-coding gene	gene with protein product		600999				1567856, 1502157	Standard	NM_001276275		Approved	ZF87, Pur-1, Zif87, ZNF801	uc002dtx.4	P56270	OTTHUMG00000132119	ENST00000322945.6:c.1280-527G>T	chr16.hg19:g.29820871G>T		141.0	0.0		125.0	5.0	NM_001042539	A8QJL9|C6G496|G5E927|H3BQD6|Q15703|Q8NFN7|Q99443	Silent	SNP	ENST00000322945.6	hg19	CCDS42143.1																																																																																			.	.		0.682	MAZ-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000435536.1	NM_002383		T	29820871	G	T	29820871	1	4	254	0	1	0	0	0	0	0	0	0	9349	1103	39	1		1	MAZ	16	29820871	Intron	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	145811	29820871	60533882	770	35062										
TAOK2	8479	hgsc.bcm.edu	37	chr16	30002499	30002499	+	IGR	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggcttctccagcatggctctGgggggcatcccggctgaagc	15	13	2	1	rs138517482		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:30002499G>T	ENST00000279392.3	-	0	3385				TAOK2_ENST00000279394.3_Silent_p.L920L	NM_003609.4	NP_003600.2	Q9BW71	HIRP3_HUMAN	HIRA interacting protein 3						chromatin assembly or disassembly (GO:0006333)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(1)|lung(9)	17						GCATGGCTCTGGGGGGCATCC	0.677																																					p.L920L		Atlas-SNP	.											.	TAOK2	142	.	0			c.G2760T						.						57	61	59					16																	30002499		2197	4300	6497	SO:0001628	intergenic_variant	9344	exon19			GGCTCTGGGGGGC	AJ223351	CCDS10664.1, CCDS58449.1	16p12.1	2008-02-05	2001-11-29		ENSG00000149929	ENSG00000149929			4917	protein-coding gene	gene with protein product		603365	"HIRA-interacting protein 3"			9710638	Standard	NM_003609		Approved		uc002dve.3	Q9BW71	OTTHUMG00000132118		chr16.hg19:g.30002499G>T		97.0	0.0		79.0	4.0	NM_004783	H3BSR3|O75707|O75708	Silent	SNP	ENST00000279392.3	hg19	CCDS10664.1																																																																																			.	G|1.000;C|0.000		0.677	HIRIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255160.2	NM_003609		T	30002499	G	T	30002499	1	4	254	0	1	0	0	0	0	0	0	0	15563	1335	47	3		3	TAOK2	16	30002499	IGR	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	181628	30002499	60352254	771	35063										
DOC2A	8448	hgsc.bcm.edu	37	chr16	30020840	30020840	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtgcagagtgcaggaggcccGgtcgtagagaaggtcaaact	16	8	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:30020840G>T	ENST00000350119.4	-	3	491	c.301C>A	c.(301-303)Cgg>Agg	p.R101R	DOC2A_ENST00000564944.1_Silent_p.R101R|DOC2A_ENST00000564979.1_Silent_p.R101R|DOC2A_ENST00000567824.1_5'Flank	NM_001282062.1|NM_001282063.1|NM_001282068.1|NM_003586.2	NP_001268991.1|NP_001268992.1|NP_001268997.1|NP_003577.2	Q14183	DOC2A_HUMAN	double C2-like domains, alpha	101	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				nervous system development (GO:0007399)|regulation of calcium ion-dependent exocytosis (GO:0017158)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|lysosome (GO:0005764)|membrane (GO:0016020)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)	9						CAGGAGGCCCGGTCGTAGAGA	0.657																																					p.R101R		Atlas-SNP	.											.	DOC2A	40	.	0			c.C301A						.						47	40	42					16																	30020840		1910	3689	5599	SO:0001819	synonymous_variant	8448	exon3			AGGCCCGGTCGTA	D31897	CCDS10666.1	16p11.2	2014-07-02			ENSG00000149927	ENSG00000149927		"Synaptotagmins"	2985	protein-coding gene	gene with protein product		604567				7826360, 9736751	Standard	NM_003586		Approved		uc002dvn.3	Q14183	OTTHUMG00000132109	ENST00000350119.4:c.301C>A	chr16.hg19:g.30020840G>T		58.0	0.0		57.0	4.0	NM_003586	B4DEJ2|H3BNH6|Q6P4G4|Q7Z5G0|Q8IVX0	Silent	SNP	ENST00000350119.4	hg19	CCDS10666.1																																																																																			.	.		0.657	DOC2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255148.2	NM_003586		T	30020840	G	T	30020840	2	4	254	1	0	0	0	0	0	0	0	1	4685	1115	39	1		1	DOC2A	16	30020840	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	18341	30020840	60333913	772	35064										
GDPD3	79153	hgsc.bcm.edu	37	chr16	30124047	30124047	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	caggttctcatcatgtgacaCcaccaccactctgtcccgtg	7	16	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:30124047C>T	ENST00000406256.3	-	3	627	c.250G>A	c.(250-252)Gtg>Atg	p.V84M	RP11-455F5.4_ENST00000566190.1_RNA|MAPK3_ENST00000494643.1_5'Flank	NM_024307.2	NP_077283.2	Q7L5L3	GDPD3_HUMAN	glycerophosphodiester phosphodiesterase domain containing 3	84	GP-PDE.				glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)|metal ion binding (GO:0046872)			biliary_tract(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(6)	11						TCATGTGACACCACCACCACT	0.667											OREG0023731	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V84M		Atlas-SNP	.											.	GDPD3	23	.	0			c.G250A						.						69	61	64					16																	30124047		2197	4300	6497	SO:0001583	missense	79153	exon3			GTGACACCACCAC	AK026256	CCDS10671.2	16p11.2	2008-02-05			ENSG00000102886	ENSG00000102886			28638	protein-coding gene	gene with protein product							Standard	NM_024307		Approved	MGC4171	uc002dwp.3	Q7L5L3	OTTHUMG00000132106	ENST00000406256.3:c.250G>A	chr16.hg19:g.30124047C>T	ENSP00000384363:p.Val84Met	52.0	0.0	814	40.0	13.0	NM_024307	Q9H652	Missense_Mutation	SNP	ENST00000406256.3	hg19	CCDS10671.2	.	.	.	.	.	.	.	.	.	.	C	18.59	3.655806	0.67586	.	.	ENSG00000102886	ENST00000406256;ENST00000360688	T	0.19532	2.14	5.57	4.61	0.57282	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);	0.059458	0.64402	D	0.000003	T	0.51702	0.1690	M	0.91196	3.185	0.48571	D	0.999676	D	0.76494	0.999	D	0.66602	0.945	T	0.62765	-0.6785	10	0.87932	D	0	.	12.4157	0.55492	0.0:0.8309:0.1691:0.0	.	84	Q7L5L3	GDPD3_HUMAN	M	84;22	ENSP00000384363:V84M	ENSP00000353909:V22M	V	-	1	0	GDPD3	30031548	0.999000	0.42202	0.998000	0.56505	0.529000	0.34654	4.175000	0.58263	1.318000	0.45170	0.563000	0.77884	GTG	.	.		0.667	GDPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255144.1	NM_024307		T	30124047	C	T	30124047	3	4	254	1	0	0	0	0	1	0	0	0	6333	507	18	3	738	3	GDPD3	16	30124047	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	103207	30124047	60230706	773	35065										
ZNF629	23361	hgsc.bcm.edu	37	chr16	30793344	30793344	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggccctgcaatctgagcagcGgtagggtctggcccccaggg	16	13	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:30793344G>T	ENST00000262525.4	-	3	2512	c.2305C>A	c.(2305-2307)Cgc>Agc	p.R769S	RP11-2C24.6_ENST00000575562.1_RNA	NM_001080417.1	NP_001073886.1	Q9UEG4	ZN629_HUMAN	zinc finger protein 629	769					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(3)|urinary_tract(1)	22			Colorectal(24;0.198)			TCTGAGCAGCGGTAGGGTCTG	0.657																																					p.R769S		Atlas-SNP	.											.	ZNF629	44	.	0			c.C2305A						.						63	74	71					16																	30793344		1896	4104	6000	SO:0001583	missense	23361	exon3			AGCAGCGGTAGGG	AB002324	CCDS45463.1	16p11.2	2013-01-08				ENSG00000102870		"Zinc fingers, C2H2-type"	29008	protein-coding gene	gene with protein product			"zinc finger protein 65"	ZNF65		9205841	Standard	NM_001080417		Approved	KIAA0326	uc002dzs.1	Q9UEG4		ENST00000262525.4:c.2305C>A	chr16.hg19:g.30793344G>T	ENSP00000262525:p.Arg769Ser	89.0	0.0		89.0	4.0	NM_001080417	Q15938	Missense_Mutation	SNP	ENST00000262525.4	hg19	CCDS45463.1	.	.	.	.	.	.	.	.	.	.	g	3.042	-0.197282	0.06259	.	.	ENSG00000102870	ENST00000262525	T	0.14893	2.47	5.65	4.56	0.56223	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.126886	0.35970	N	0.002877	T	0.09468	0.0233	N	0.11255	0.115	0.21802	N	0.999535	B	0.02656	0.0	B	0.01281	0.0	T	0.26677	-1.0096	10	0.29301	T	0.29	-18.3376	11.3261	0.49450	0.0:0.0:0.1532:0.8468	.	769	Q9UEG4	ZN629_HUMAN	S	769	ENSP00000262525:R769S	ENSP00000262525:R769S	R	-	1	0	ZNF629	30700845	0.583000	0.26757	1.000000	0.80357	0.938000	0.57974	0.401000	0.20948	0.984000	0.38629	-0.367000	0.07326	CGC	.	.		0.657	ZNF629-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434291.1	NM_015309		T	30793344	G	T	30793344	3	4	254	1	0	0	0	0	1	0	0	0	18068	1116	39	1	308	1	ZNF629	16	30793344	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	669297	30793344	59561409	774	35066										
SETD1A	9739	hgsc.bcm.edu	37	chr16	30976649	30976649	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggccagagatacagggagtgAggtgccttctgggtcagggc	18	8	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:30976649A>G	ENST00000262519.8	+	7	2272	c.1586A>G	c.(1585-1587)gAg>gGg	p.E529G		NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A	529	Pro-rich. {ECO:0000255}.				histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(21)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	59						ACAGGGAGTGAGGTGCCTTCT	0.612																																					p.E529G		Atlas-SNP	.											.	SETD1A	143	.	0			c.A1586G						.						58	63	61					16																	30976649		2197	4300	6497	SO:0001583	missense	9739	exon7			GGAGTGAGGTGCC	AB002337	CCDS32435.1	16p11.2	2013-02-12			ENSG00000099381	ENSG00000099381		"Chromatin-modifying enzymes / K-methyltransferases", "RNA binding motif (RRM) containing"	29010	protein-coding gene	gene with protein product		611052				9205841, 12670868	Standard	XM_005255723		Approved	KIAA0339, Set1, KMT2F	uc002ead.1	O15047	OTTHUMG00000150474	ENST00000262519.8:c.1586A>G	chr16.hg19:g.30976649A>G	ENSP00000262519:p.Glu529Gly	133.0	0.0		101.0	5.0	NM_014712	A6NP62|Q6PIF3|Q8TAJ6	Missense_Mutation	SNP	ENST00000262519.8	hg19	CCDS32435.1	.	.	.	.	.	.	.	.	.	.	A	12.51	1.960356	0.34565	.	.	ENSG00000099381	ENST00000262519	D	0.94862	-3.54	5.53	5.53	0.82687	.	0.282904	0.32161	N	0.006486	D	0.87981	0.6315	N	0.11427	0.14	0.36161	D	0.848091	B	0.18610	0.029	B	0.17433	0.018	D	0.86817	0.2002	10	0.48119	T	0.1	.	13.5996	0.62011	1.0:0.0:0.0:0.0	.	529	O15047	SET1A_HUMAN	G	529	ENSP00000262519:E529G	ENSP00000262519:E529G	E	+	2	0	SETD1A	30884150	0.998000	0.40836	0.997000	0.53966	0.637000	0.38172	2.181000	0.42547	2.100000	0.63781	0.459000	0.35465	GAG	.	.		0.612	SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318244.2	NM_014712		G	30976649	A	G	30976649	3	3	254	1	0	0	0	0	1	0	0	0	14145	304	11	2	1608	2	SETD1A	16	30976649	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	183305	30976649	59378104	775	35067										
HSD3B7	80270	hgsc.bcm.edu	37	chr16	30997766	30997766	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	acccggaacgtgatcgaggcTtgtgtgcagaccggaacacg	14	11	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:30997766T>C	ENST00000297679.5	+	4	438	c.345T>C	c.(343-345)gcT>gcC	p.A115A	AC135048.1_ENST00000602217.1_5'Flank|HSD3B7_ENST00000262520.6_Silent_p.A115A|HSD3B7_ENST00000353250.5_Silent_p.A115A	NM_025193.3	NP_079469.2	Q9H2F3	3BHS7_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 7	115					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|cholest-5-ene-3-beta,7-alpha-diol 3-beta-dehydrogenase activity (GO:0047016)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						TGATCGAGGCTTGTGTGCAGA	0.597																																					p.A115A		Atlas-SNP	.											.	HSD3B7	33	.	0			c.T345C						.						96	81	86					16																	30997766		2197	4300	6497	SO:0001819	synonymous_variant	80270	exon4			CGAGGCTTGTGTG	AF277719	CCDS10698.1, CCDS45466.1	16p11.2	2011-09-14			ENSG00000099377	ENSG00000099377	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Extended SDR fold"	18324	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 11E, member 3"	607764				11067870, 19027726	Standard	NM_001142777		Approved	C(27)-3BETA-HSD, SDR11E3	uc002eaf.2	Q9H2F3	OTTHUMG00000132417	ENST00000297679.5:c.345T>C	chr16.hg19:g.30997766T>C		96.0	0.0		123.0	6.0	NM_025193	Q96M28|Q9BSN9	Silent	SNP	ENST00000297679.5	hg19	CCDS10698.1																																																																																			.	.		0.597	HSD3B7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255554.2			C	30997766	T	C	30997766	2	2	254	1	0	0	0	0	0	0	0	1	7401	1596	56	2		2	HSD3B7	16	30997766	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	21117	30997766	59356987	776	35068										
BCKDK	10295	hgsc.bcm.edu	37	chr16	31123498	31123498	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggagtacctcggtgggtctcTgcagctgcagtccctgcagg	15	12	1	0	rs398124213		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:31123498T>C	ENST00000394951.1	+	13	1774	c.1151T>C	c.(1150-1152)cTg>cCg	p.L384P	BCKDK_ENST00000394950.3_3'UTR|BCKDK_ENST00000219794.6_Missense_Mutation_p.L384P|BCKDK_ENST00000287507.3_3'UTR|AC135050.1_ENST00000517000.2_RNA			O14874	BCKD_HUMAN	branched chain ketoacid dehydrogenase kinase	384	Histidine kinase. {ECO:0000255|PROSITE- ProRule:PRU00107}.				branched-chain amino acid catabolic process (GO:0009083)|cellular amino acid catabolic process (GO:0009063)|phosphorylation (GO:0016310)|protein phosphorylation (GO:0006468)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrion (GO:0005739)	[3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity (GO:0047323)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|stomach(1)	2						GGTGGGTCTCTGCAGCTGCAG	0.657																																					p.L384P		Atlas-SNP	.											.	BCKDK	52	.	0			c.T1151C						.						68	65	66					16																	31123498		2197	4300	6497	SO:0001583	missense	10295	exon12			GGTCTCTGCAGCT	AF026548	CCDS10705.1, CCDS45467.1, CCDS61917.1	16p11.2	2008-05-14			ENSG00000103507	ENSG00000103507			16902	protein-coding gene	gene with protein product		614901				1889817	Standard	NM_005881		Approved		uc002eaw.5	O14874	OTTHUMG00000047356	ENST00000394951.1:c.1151T>C	chr16.hg19:g.31123498T>C	ENSP00000378405:p.Leu384Pro	90.0	0.0		90.0	4.0	NM_005881	A8MY43|Q6FGL4|Q96G95|Q96IN5	Missense_Mutation	SNP	ENST00000394951.1	hg19	CCDS10705.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.848931	0.91277	.	.	ENSG00000103507	ENST00000394951;ENST00000219794	D;D	0.81739	-1.53;-1.53	5.66	5.66	0.87406	Signal transduction histidine kinase, core (1);ATPase-like, ATP-binding domain (4);	0.000000	0.85682	D	0.000000	D	0.91499	0.7316	M	0.91612	3.225	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.93269	0.6650	10	0.87932	D	0	-19.1152	14.8634	0.70397	0.0:0.0:0.0:1.0	.	384	O14874	BCKD_HUMAN	P	384	ENSP00000378405:L384P;ENSP00000219794:L384P	ENSP00000219794:L384P	L	+	2	0	BCKDK	31030999	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	7.682000	0.84083	2.158000	0.67659	0.482000	0.46254	CTG	.	.		0.657	BCKDK-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108514.1	NM_005881		C	31123498	T	C	31123498	3	2	254	1	0	0	0	0	1	0	0	0	1361	1580	55	2	1197	2	BCKDK	16	31123498	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	125732	31123498	59231255	777	35069										
ZNF267	10308	hgsc.bcm.edu	37	chr16	31926476	31926476	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agctataacaaatatgataaAgatcttagtcagtcatcaaa	5	6	4	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:31926476A>G	ENST00000300870.10	+	4	1115	c.906A>G	c.(904-906)aaA>aaG	p.K302K		NM_001265588.1|NM_003414.5	NP_001252517.1|NP_003405	Q14586	ZN267_HUMAN	zinc finger protein 267	302					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(5)|kidney(1)|large_intestine(14)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	41						AATATGATAAAGATCTTAGTC	0.313																																					p.K302K		Atlas-SNP	.											ZNF267,right_upper_lobe,carcinoma,0,1	ZNF267	94	.	0			c.A906G						.						63	67	65					16																	31926476		2197	4297	6494	SO:0001819	synonymous_variant	10308	exon4			TGATAAAGATCTT	X78925	CCDS32440.1	16p11.2	2013-01-08			ENSG00000185947	ENSG00000185947		"Zinc fingers, C2H2-type", "-"	13060	protein-coding gene	gene with protein product		604752				7865130	Standard	NM_003414		Approved	HZF2	uc002ecs.5	Q14586		ENST00000300870.10:c.906A>G	chr16.hg19:g.31926476A>G		99.0	0.0		72.0	3.0	NM_003414	A0JNZ9|Q8NE41|Q9NRJ0	Silent	SNP	ENST00000300870.10	hg19	CCDS32440.1																																																																																			.	.		0.313	ZNF267-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432446.2	NM_003414		G	31926476	A	G	31926476	2	3	254	1	0	0	0	0	0	0	0	1	17821	69	3	2		2	ZNF267	16	31926476	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	802978	31926476	58428277	778	35070										
SHCBP1	79801	hgsc.bcm.edu	37	chr16	46633834	46633834	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tccacaaaagtgtcgcctttGcccctcttttctatcacaat	4	14	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:46633834G>T	ENST00000303383.3	-	9	1520	c.1254C>A	c.(1252-1254)ggC>ggA	p.G418G		NM_024745.4	NP_079021	Q8NEM2	SHCBP_HUMAN	SHC SH2-domain binding protein 1	418					fibroblast growth factor receptor signaling pathway (GO:0008543)|regulation of neural precursor cell proliferation (GO:2000177)					breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		all_cancers(37;0.00404)|all_epithelial(9;0.00527)|all_lung(18;0.0413)|Lung NSC(13;0.213)				TGTCGCCTTTGCCCCTCTTTT	0.413																																					p.G418G		Atlas-SNP	.											.	SHCBP1	54	.	0			c.C1254A						.						91	84	86					16																	46633834		2203	4300	6503	SO:0001819	synonymous_variant	79801	exon9			GCCTTTGCCCCTC	AK055931	CCDS10720.1	16q11	2008-02-05			ENSG00000171241	ENSG00000171241			29547	protein-coding gene	gene with protein product		611027				10086341	Standard	NM_024745		Approved	FLJ22009	uc002eec.4	Q8NEM2	OTTHUMG00000132540	ENST00000303383.3:c.1254C>A	chr16.hg19:g.46633834G>T		110.0	0.0		70.0	4.0	NM_024745	Q96N60|Q9BVS0|Q9H6P6	Silent	SNP	ENST00000303383.3	hg19	CCDS10720.1																																																																																			.	.		0.413	SHCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255740.1	NM_024745		T	46633834	G	T	46633834	2	4	254	1	0	0	0	0	0	0	0	1	14289	1306	46	3		3	SHCBP1	16	46633834	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	14707358	46633834	43720919	779	35071										
NLRC5	84166	hgsc.bcm.edu	37	chr16	57113154	57113154	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttggcggaaaacaacctggcTggaggggtcctgcgtttctg	15	9	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:57113154T>C	ENST00000262510.6	+	45	5412	c.5187T>C	c.(5185-5187)gcT>gcC	p.A1729A	NLRC5_ENST00000436936.1_3'UTR|NLRC5_ENST00000539144.1_Silent_p.A1700A|NLRC5_ENST00000308149.7_Silent_p.A1700A	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	1729					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				ACAACCTGGCTGGAGGGGTCC	0.642																																					p.A1729A		Atlas-SNP	.											.	NLRC5	186	.	0			c.T5187C						.						52	53	53					16																	57113154		2198	4300	6498	SO:0001819	synonymous_variant	84166	exon44			CCTGGCTGGAGGG	AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"Nucleotide-binding domain and leucine rich repeat containing"	29933	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5", "NOD-like receptor C5"	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.5187T>C	chr16.hg19:g.57113154T>C		142.0	0.0		100.0	4.0	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Silent	SNP	ENST00000262510.6	hg19	CCDS10773.1																																																																																			.	.		0.642	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206		C	57113154	T	C	57113154	2	2	254	1	0	0	0	0	0	0	0	1	10479	1567	55	2		2	NLRC5	16	57113154	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	10479320	57113154	33241599	780	35072										
C16orf80	29105	hgsc.bcm.edu	37	chr16	58150036	58150036	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcgtcttcttggggtctgcaGggcatgtgatatatgtggtg	16	6	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:58150036G>T	ENST00000262498.3	-	3	519	c.185C>A	c.(184-186)cCt>cAt	p.P62H	C16orf80_ENST00000562443.1_5'Flank|CTB-134F13.1_ENST00000564672.1_RNA	NM_013242.2	NP_037374.1														kidney(1)|large_intestine(1)|lung(1)|prostate(1)	4						GGGGTCTGCAGGGCATGTGAT	0.418																																					p.P62H	Pancreas(103;1212 1612 18629 30162 52390)	Atlas-SNP	.											.	C16orf80	17	.	0			c.C185A						.						116	113	114					16																	58150036		2198	4300	6498	SO:0001583	missense	29105	exon3			TCTGCAGGGCATG																												ENST00000262498.3:c.185C>A	chr16.hg19:g.58150036G>T	ENSP00000262498:p.Pro62His	170.0	0.0		96.0	4.0	NM_013242		Missense_Mutation	SNP	ENST00000262498.3	hg19	CCDS10793.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.970315	0.92919	.	.	ENSG00000070761	ENST00000262498	T	0.56275	0.47	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	T	0.81927	0.4926	H	0.96142	3.775	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87069	0.2158	10	0.87932	D	0	-10.1419	17.3425	0.87301	0.0:0.0:1.0:0.0	.	62	Q9Y6A4	CP080_HUMAN	H	62	ENSP00000262498:P62H	ENSP00000262498:P62H	P	-	2	0	C16orf80	56707537	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.226000	0.95229	2.775000	0.95449	0.655000	0.94253	CCT	.	.		0.418	C16orf80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257388.2			T	58150036	G	T	58150036	3	4	254	1	0	0	0	0	1	0	0	0	1839	1000	35	3	412	3	C16orf80	16	58150036	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1036882	58150036	32204717	781	35073										
DYNC1LI2	1783	hgsc.bcm.edu	37	chr16	66764024	66764024	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tctttgactacctttctcacGggaggtttcacaataaagtc	7	10	3	1	rs145562779		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:66764024G>T	ENST00000258198.2	-	8	1238	c.1032C>A	c.(1030-1032)ccC>ccA	p.P344P	DYNC1LI2_ENST00000379482.2_Intron|DYNC1LI2_ENST00000443351.2_Silent_p.P267P|DYNC1LI2_ENST00000570201.1_5'UTR|RP11-63M22.2_ENST00000569274.1_RNA	NM_006141.2	NP_006132.1	O43237	DC1L2_HUMAN	dynein, cytoplasmic 1, light intermediate chain 2	344					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|centrosome localization (GO:0051642)|microtubule cytoskeleton organization (GO:0000226)|microtubule-based movement (GO:0007018)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.P344P(1)		central_nervous_system(3)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(4)|stomach(1)	15		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0907)|Epithelial(162;0.212)		CCTTTCTCACGGGAGGTTTCA	0.468																																					p.P344P		Atlas-SNP	.											.	DYNC1LI2	37	.	1	Substitution - coding silent(1)	lung(1)	c.C1032A						.						72	66	68					16																	66764024		2200	4300	6500	SO:0001819	synonymous_variant	1783	exon8			TCTCACGGGAGGT	AF035812	CCDS10818.1, CCDS67049.1	16q22.1	2008-02-05	2005-11-25	2005-11-25	ENSG00000135720	ENSG00000135720		"Cytoplasmic dyneins"	2966	protein-coding gene	gene with protein product		611406	"dynein, cytoplasmic, light intermediate polypeptide 2"	DNCLI2		16260502	Standard	NM_006141		Approved		uc002eqb.1	O43237	OTTHUMG00000137523	ENST00000258198.2:c.1032C>A	chr16.hg19:g.66764024G>T		105.0	0.0		79.0	4.0	NM_006141	A8K6V1|B4DZP4|Q8TAT3	Silent	SNP	ENST00000258198.2	hg19	CCDS10818.1																																																																																			.	G|1.000;A|0.000		0.468	DYNC1LI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268846.1	NM_006141		T	66764024	G	T	66764024	2	4	254	1	0	0	0	0	0	0	0	1	4847	1103	39	1		1	DYNC1LI2	16	66764024	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	8613988	66764024	23590729	782	35074										
ZDHHC1	29800	hgsc.bcm.edu	37	chr16	67432186	67432186	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cttggcctcctgtggtgggcGgtgctgcacgatgtactcat	14	11	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:67432186G>T	ENST00000348579.2	-	8	1197	c.856C>A	c.(856-858)Cgc>Agc	p.R286S	ZDHHC1_ENST00000566075.1_5'Flank	NM_013304.2	NP_037436.1	Q8WTX9	ZDHC1_HUMAN	zinc finger, DHHC-type containing 1	286					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(1)|urinary_tract(1)	10		Ovarian(137;0.223)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0178)|all cancers(182;5.71e-53)|Epithelial(162;4.73e-52)|OV - Ovarian serous cystadenocarcinoma(108;1.53e-29)|Kidney(780;4.37e-05)|BRCA - Breast invasive adenocarcinoma(181;5.8e-05)|GBM - Glioblastoma multiforme(240;0.0022)		TGTGGTGGGCGGTGCTGCACG	0.622																																					p.R286S		Atlas-SNP	.											.	ZDHHC1	28	.	0			c.C856A						.						119	100	107					16																	67432186		2198	4300	6498	SO:0001583	missense	29800	exon8			GTGGGCGGTGCTG	U90653	CCDS10836.1	16q22.1	2010-03-25	2003-01-27		ENSG00000159714	ENSG00000159714		"Zinc fingers, DHHC-type"	17916	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 1"	C16orf1		10395086	Standard	NM_013304		Approved	HSU90653, ZNF377	uc010vjm.2	Q8WTX9	OTTHUMG00000137522	ENST00000348579.2:c.856C>A	chr16.hg19:g.67432186G>T	ENSP00000340299:p.Arg286Ser	78.0	0.0		61.0	4.0	NM_013304	O15461	Missense_Mutation	SNP	ENST00000348579.2	hg19	CCDS10836.1	.	.	.	.	.	.	.	.	.	.	G	33	5.262895	0.95399	.	.	ENSG00000159714	ENST00000348579	T	0.42513	0.97	5.46	5.46	0.80206	.	0.682773	0.14213	N	0.333908	T	0.56093	0.1962	L	0.29908	0.895	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.54741	-0.8248	10	0.51188	T	0.08	.	18.2808	0.90097	0.0:0.0:1.0:0.0	.	286	Q8WTX9	ZDHC1_HUMAN	S	286	ENSP00000340299:R286S	ENSP00000340299:R286S	R	-	1	0	ZDHHC1	65989687	1.000000	0.71417	0.996000	0.52242	0.981000	0.71138	5.438000	0.66550	2.563000	0.86464	0.407000	0.27541	CGC	.	.		0.622	ZDHHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268845.1	NM_013304		T	67432186	G	T	67432186	3	4	254	1	0	0	0	0	1	0	0	0	17615	1116	39	1	617	1	ZDHHC1	16	67432186	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	668162	67432186	22922567	783	35075										
RLTPR	146206	hgsc.bcm.edu	37	chr16	67679452	67679452	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cccttccacaggcgagatcaCcaggttcctgtggcccaaag	10	15	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:67679452C>T	ENST00000334583.6	+	2	378	c.50C>T	c.(49-51)aCc>aTc	p.T17I	RLTPR_ENST00000545661.1_Missense_Mutation_p.T17I	NM_001013838.1	NP_001013860.1	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing	17					cell migration (GO:0016477)|establishment of protein localization (GO:0045184)|homeostasis of number of cells (GO:0048872)|maintenance of cell polarity (GO:0030011)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma secretion (GO:1902715)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|F-actin capping protein complex (GO:0008290)|immunological synapse (GO:0001772)|membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(4)|kidney(1)|lung(9)|urinary_tract(2)	18		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)		GGCGAGATCACCAGGTTCCTG	0.622																																					p.T17I		Atlas-SNP	.											.	RLTPR	124	.	0			c.C50T						.																																			SO:0001583	missense	146206	exon2			AGATCACCAGGTT	AB113647	CCDS45513.1	16q22.1	2010-09-10				ENSG00000159753			27089	protein-coding gene	gene with protein product	"RGD, leucine-rich repeat, tropomodulin and proline-rich containing protein", "leucine rich repeat containing 16C"	610859				15588584, 19846667	Standard	XM_005255807		Approved	LRRC16C, CARMIL2	uc002etn.3	Q6F5E8		ENST00000334583.6:c.50C>T	chr16.hg19:g.67679452C>T	ENSP00000334958:p.Thr17Ile	109.0	0.0		75.0	4.0	NM_001013838	B8X2Z3	Missense_Mutation	SNP	ENST00000334583.6	hg19	CCDS45513.1	.	.	.	.	.	.	.	.	.	.	c	20.2	3.951096	0.73787	.	.	ENSG00000159753	ENST00000334583;ENST00000545661	T;T	0.16324	2.35;2.38	4.5	3.55	0.40652	.	1.135210	0.06547	N	0.744305	T	0.13841	0.0335	N	0.22421	0.69	0.32048	N	0.597355	B;P	0.43477	0.007;0.808	B;B	0.39590	0.007;0.304	T	0.14282	-1.0478	10	0.45353	T	0.12	-8.4582	9.8859	0.41262	0.0:0.9031:0.0:0.0969	.	17;17	B8X2Z3;Q6F5E8	.;LR16C_HUMAN	I	17	ENSP00000334958:T17I;ENSP00000441481:T17I	ENSP00000334958:T17I	T	+	2	0	RLTPR	66236953	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	2.862000	0.48388	1.253000	0.44018	0.556000	0.70494	ACC	.	.		0.622	RLTPR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467858.1	NM_001013838		T	67679452	C	T	67679452	3	4	254	1	0	0	0	0	1	0	0	0	13409	507	18	3	56	3	RLTPR	16	67679452	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	247266	67679452	22675301	784	35076										
TSNAXIP1	80152	hgsc.bcm.edu	37	chr16	67859899	67859899	+	IGR	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gctgcacatgagcacgctgaAggaacgggaccaattcttct	11	11	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:67859899A>G	ENST00000562787.1	-	0	2345				TSNAXIP1_ENST00000561639.1_Missense_Mutation_p.K355R|TSNAXIP1_ENST00000388833.3_Missense_Mutation_p.K301R|TSNAXIP1_ENST00000415766.3_Missense_Mutation_p.K286R	NM_025082.3	NP_079358.3	Q96BT3	CENPT_HUMAN	centromere protein T						chromosome organization (GO:0051276)|chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|lung(6)|urinary_tract(1)	10		Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00429)|Epithelial(162;0.019)|all cancers(182;0.124)		AGCACGCTGAAGGAACGGGAC	0.612																																					p.K301R		Atlas-SNP	.											.	TSNAXIP1	66	.	0			c.A902G						.						62	51	55					16																	67859899		2198	4300	6498	SO:0001628	intergenic_variant	55815	exon9			CGCTGAAGGAACG	AK056097	CCDS42182.1	16q22.1	2013-11-05	2006-06-15	2006-06-15		ENSG00000102901			25787	protein-coding gene	gene with protein product		611510	"chromosome 16 open reading frame 56"	C16orf56		16622420, 16622419	Standard	NM_025082		Approved	FLJ13111, CENP-T	uc002eun.4	Q96BT3			chr16.hg19:g.67859899A>G		94.0	0.0		64.0	4.0	NM_018430	Q96I29|Q96IC6|Q96NK9|Q9H901	Missense_Mutation	SNP	ENST00000562787.1	hg19	CCDS42182.1	.	.	.	.	.	.	.	.	.	.	A	15.18	2.757646	0.49468	.	.	ENSG00000102904	ENST00000415766;ENST00000388833;ENST00000431934	.	.	.	5.8	3.53	0.40419	.	0.312152	0.31233	N	0.008006	T	0.52289	0.1725	L	0.60455	1.87	0.28676	N	0.9054	B;B;B;B;B;D	0.63880	0.037;0.037;0.02;0.197;0.02;0.993	B;B;B;B;B;P	0.60789	0.039;0.027;0.016;0.062;0.027;0.879	T	0.46735	-0.9170	9	0.46703	T	0.11	-33.0536	9.0471	0.36354	0.8511:0.0:0.1489:0.0	.	286;355;91;9;301;286	E7ENJ7;B4DXD0;B4DY78;Q2TAA8-2;Q2TAA8;B4E1H3	.;.;.;.;TXIP1_HUMAN;.	R	286;301;91	.	ENSP00000373485:K301R	K	+	2	0	TSNAXIP1	66417400	1.000000	0.71417	1.000000	0.80357	0.174000	0.22865	1.883000	0.39658	1.018000	0.39521	0.533000	0.62120	AAG	.	.		0.612	CENPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422020.1	NM_025082		G	67859899	A	G	67859899	1	3	254	0	1	0	0	0	0	0	0	0	16647	72	3	2		2	TSNAXIP1	16	67859899	IGR	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	180447	67859899	22494854	785	35077										
ESRP2	80004	hgsc.bcm.edu	37	chr16	68269764	68269764	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	accctacctggcggctccgcGgctcaaccacttgccaaact	8	18	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:68269764G>T	ENST00000565858.1	-	1	271	c.185C>A	c.(184-186)cCg>cAg	p.P62Q	ESRP2_ENST00000473183.2_Missense_Mutation_p.P62Q|RP11-96D1.6_ENST00000564147.1_RNA	NM_024939.2	NP_079215.2	Q9H6T0	ESRP2_HUMAN	epithelial splicing regulatory protein 2	62					mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)	16						GCGGCTCCGCGGCTCAACCAC	0.672																																					p.P62Q		Atlas-SNP	.											.	ESRP2	118	.	0			c.C185A						.						22	18	20					16																	68269764		2184	4274	6458	SO:0001583	missense	80004	exon1			CTCCGCGGCTCAA	AK025571	CCDS10863.1	16q22.1	2013-02-12	2009-03-10	2009-03-10	ENSG00000103067	ENSG00000103067		"RNA binding motif (RRM) containing"	26152	protein-coding gene	gene with protein product		612960	"RNA binding motif protein 35B"	RBM35B		12477932	Standard	NM_024939		Approved	FLJ21918	uc002evq.1	Q9H6T0	OTTHUMG00000137557	ENST00000565858.1:c.185C>A	chr16.hg19:g.68269764G>T	ENSP00000454554:p.Pro62Gln	138.0	0.0		85.0	4.0	NM_024939	Q8N6H8|Q8WZ15|Q9H6I4	Missense_Mutation	SNP	ENST00000565858.1	hg19		.	.	.	.	.	.	.	.	.	.	G	20.1	3.937974	0.73557	.	.	ENSG00000103067	ENST00000473183	T	0.44482	0.92	4.26	2.29	0.28610	.	0.068424	0.64402	D	0.000008	T	0.30293	0.0760	N	0.22421	0.69	0.29787	N	0.833503	P;P	0.49447	0.924;0.908	B;P	0.47206	0.339;0.541	T	0.16571	-1.0398	10	0.59425	D	0.04	-12.6571	5.9021	0.18972	0.2339:0.0:0.7661:0.0	.	62;62	Q9H6T0;Q9H6T0-2	ESRP2_HUMAN;.	Q	62	ENSP00000418748:P62Q	ENSP00000418748:P62Q	P	-	2	0	ESRP2	66827265	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	5.212000	0.65225	1.160000	0.42584	0.555000	0.69702	CCG	.	.		0.672	ESRP2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000433083.1	NM_024939		T	68269764	G	T	68269764	3	4	254	1	0	0	0	0	1	0	0	0	5261	1116	39	1	2028	1	ESRP2	16	68269764	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	409865	68269764	22084989	786	35078										
MTSS1L	92154	hgsc.bcm.edu	37	chr16	70698860	70698860	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	caggggacatccggggtcgcGgtgcctcttccccgctgggg	17	14	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:70698860G>T	ENST00000338779.6	-	13	1542	c.1268C>A	c.(1267-1269)cCg>cAg	p.P423Q	FLJ00418_ENST00000597002.1_Missense_Mutation_p.G57C	NM_138383.2	NP_612392.1	Q765P7	MTSSL_HUMAN	metastasis suppressor 1-like	423					filopodium assembly (GO:0046847)|signal transduction (GO:0007165)					breast(1)|central_nervous_system(2)|endometrium(1)|liver(1)|lung(1)|skin(1)	7						CCGGGGTCGCGGTGCCTCTTC	0.716																																					p.P423Q		Atlas-SNP	.											MTSS1L,NS,carcinoma,0,1	MTSS1L	22	.	0			c.C1268A						.						11	12	12					16																	70698860		2181	4287	6468	SO:0001583	missense	92154	exon13			GGTCGCGGTGCCT		CCDS32476.1	16q22.1	2008-12-16				ENSG00000132613			25094	protein-coding gene	gene with protein product	"actin-bundling protein with BAIAP2 homology"					12477932	Standard	XM_006721335		Approved	ABBA-1, LOC92154	uc002ezj.3	Q765P7		ENST00000338779.6:c.1268C>A	chr16.hg19:g.70698860G>T	ENSP00000341171:p.Pro423Gln	93.0	0.0		62.0	3.0	NM_138383	A6NJI7|Q9BUA8	Missense_Mutation	SNP	ENST00000338779.6	hg19	CCDS32476.1	.	.	.	.	.	.	.	.	.	.	G	1.520	-0.547286	0.04024	.	.	ENSG00000132613	ENST00000338779	T	0.28069	1.63	4.87	4.87	0.63330	.	0.134525	0.50627	D	0.000117	T	0.18002	0.0432	N	0.17082	0.46	0.35561	D	0.80467	B	0.18610	0.029	B	0.11329	0.006	T	0.17349	-1.0372	10	0.13108	T	0.6	-12.5589	12.6841	0.56938	0.0:0.0:0.8346:0.1654	.	423	Q765P7	MTSSL_HUMAN	Q	423	ENSP00000341171:P423Q	ENSP00000341171:P423Q	P	-	2	0	MTSS1L	69256361	1.000000	0.71417	0.047000	0.18901	0.286000	0.27126	5.692000	0.68256	2.233000	0.73108	0.313000	0.20887	CCG	.	.		0.716	MTSS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434927.3	NM_138383		T	70698860	G	T	70698860	3	4	254	1	0	0	0	0	1	0	0	0	9972	1116	39	1	987	1	MTSS1L	16	70698860	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	2429096	70698860	19655893	787	35079										
PMFBP1	83449	hgsc.bcm.edu	37	chr16	72163129	72163129	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tttgatggagccttgctcccTgtgctgaaaaaataaagact	9	8	0	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:72163129T>C	ENST00000237353.10	-	13	2047	c.1786A>G	c.(1786-1788)Agg>Ggg	p.R596G	PMFBP1_ENST00000355636.6_Missense_Mutation_p.R451G|PMFBP1_ENST00000537465.1_Missense_Mutation_p.R601G	NM_031293.2	NP_112583.2	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	601						cytoplasm (GO:0005737)				NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	45		Ovarian(137;0.179)				CCTTGCTCCCTGTGCTGAAAA	0.433																																					p.R596G		Atlas-SNP	.											.	PMFBP1	101	.	0			c.A1786G						.						167	173	171					16																	72163129		2198	4300	6498	SO:0001583	missense	83449	exon13			GCTCCCTGTGCTG	AF239683	CCDS32483.1	16q23.1	2008-08-04			ENSG00000118557	ENSG00000118557			17728	protein-coding gene	gene with protein product						11468771	Standard	NM_031293		Approved		uc002fcd.3	Q8TBY8	OTTHUMG00000167827	ENST00000237353.10:c.1786A>G	chr16.hg19:g.72163129T>C	ENSP00000237353:p.Arg596Gly	103.0	0.0		84.0	4.0	NM_031293	B3KVI9|H7BY07|Q8NA09|Q9BY16|Q9H0H4	Missense_Mutation	SNP	ENST00000237353.10	hg19	CCDS32483.1	.	.	.	.	.	.	.	.	.	.	T	13.35	2.211638	0.39102	.	.	ENSG00000118557	ENST00000537465;ENST00000237353;ENST00000355636	T;T;T	0.12984	2.63;2.64;2.63	4.31	4.31	0.51392	.	0.382752	0.22695	N	0.056780	T	0.14874	0.0359	L	0.34521	1.04	0.09310	N	1	P;P;P	0.40731	0.728;0.728;0.728	B;P;B	0.46076	0.297;0.503;0.297	T	0.06972	-1.0797	10	0.59425	D	0.04	-14.5575	10.1548	0.42816	0.0:0.0:0.0:1.0	rs34703574	601;596;601	Q8TBY8;Q8TBY8-2;G3V1Q7	PMFBP_HUMAN;.;.	G	601;596;451	ENSP00000443817:R601G;ENSP00000237353:R596G;ENSP00000347854:R451G	ENSP00000237353:R596G	R	-	1	2	PMFBP1	70720630	0.351000	0.24887	0.090000	0.20809	0.145000	0.21501	1.818000	0.39012	2.175000	0.68902	0.533000	0.62120	AGG	.	.		0.433	PMFBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396473.2	NM_031293		C	72163129	T	C	72163129	3	2	254	1	0	0	0	0	1	0	0	0	12143	1579	55	2	1333	2	PMFBP1	16	72163129	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	1464269	72163129	18191624	788	35080										
PMFBP1	83449	hgsc.bcm.edu	37	chr16	72184647	72184647	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggcgatcttgtccccggccaAggcgagttgctcctgcgcca	13	15	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:72184647A>G	ENST00000237353.10	-	5	757	c.496T>C	c.(496-498)Ttg>Ctg	p.L166L	PMFBP1_ENST00000355636.6_Silent_p.L21L|PMFBP1_ENST00000537465.1_Silent_p.L166L	NM_031293.2	NP_112583.2	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	166						cytoplasm (GO:0005737)				NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	45		Ovarian(137;0.179)				TCCCCGGCCAAGGCGAGTTGC	0.488																																					p.L166L		Atlas-SNP	.											.	PMFBP1	101	.	0			c.T496C						.						119	110	113					16																	72184647		2198	4300	6498	SO:0001819	synonymous_variant	83449	exon5			CGGCCAAGGCGAG	AF239683	CCDS32483.1	16q23.1	2008-08-04			ENSG00000118557	ENSG00000118557			17728	protein-coding gene	gene with protein product						11468771	Standard	NM_031293		Approved		uc002fcd.3	Q8TBY8	OTTHUMG00000167827	ENST00000237353.10:c.496T>C	chr16.hg19:g.72184647A>G		111.0	0.0		94.0	4.0	NM_031293	B3KVI9|H7BY07|Q8NA09|Q9BY16|Q9H0H4	Silent	SNP	ENST00000237353.10	hg19	CCDS32483.1																																																																																			.	.		0.488	PMFBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396473.2	NM_031293		G	72184647	A	G	72184647	2	3	254	1	0	0	0	0	0	0	0	1	12143	69	3	2		2	PMFBP1	16	72184647	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	21518	72184647	18170106	789	35081										
CMIP	80790	hgsc.bcm.edu	37	chr16	81654516	81654516	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctgcgagaccagtggttccaTtctctgcaatggaaggtaag	12	9	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:81654516T>C	ENST00000537098.3	+	3	534	c.462T>C	c.(460-462)caT>caC	p.H154H	CMIP_ENST00000539778.2_Silent_p.H60H|CMIP_ENST00000566513.1_3'UTR	NM_198390.2	NP_938204.2	Q8IY22	CMIP_HUMAN	c-Maf inducing protein	154	PH.					cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(5)|kidney(1)|lung(7)	13						AGTGGTTCCATTCTCTGCAAT	0.512																																					p.H154H		Atlas-SNP	.											.	CMIP	37	.	0			c.T462C						.						118	115	116					16																	81654516		2031	4208	6239	SO:0001819	synonymous_variant	80790	exon3			GTTCCATTCTCTG	AB051481	CCDS54044.1, CCDS54045.1	16q23	2011-08-04			ENSG00000153815	ENSG00000153815			24319	protein-coding gene	gene with protein product		610112				11214970, 12939343	Standard	NM_030629		Approved		uc002fgp.3	Q8IY22		ENST00000537098.3:c.462T>C	chr16.hg19:g.81654516T>C		125.0	0.0		98.0	4.0	NM_198390	Q9C0G9	Silent	SNP	ENST00000537098.3	hg19	CCDS54044.1																																																																																			.	.		0.512	CMIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432399.2	NM_030629		C	81654516	T	C	81654516	2	2	254	1	0	0	0	0	0	0	0	1	3580	1490	52	2		2	CMIP	16	81654516	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	9469869	81654516	8700237	790	35082										
MBTPS1	8720	hgsc.bcm.edu	37	chr16	84097002	84097002	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gaatctgataaagtcccaaaAtggggacgttttcaacaact	8	8	2	1	rs138967616		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:84097002A>G	ENST00000343411.3	-	19	2975	c.2480T>C	c.(2479-2481)aTt>aCt	p.I827T		NM_003791.2	NP_003782.1	Q14703	MBTP1_HUMAN	membrane-bound transcription factor peptidase, site 1	827					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cholesterol metabolic process (GO:0008203)|endoplasmic reticulum unfolded protein response (GO:0030968)|lipid metabolic process (GO:0006629)|lysosome organization (GO:0007040)|proteolysis (GO:0006508)|regulation of transcription factor import into nucleus (GO:0042990)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(10)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						AAGTCCCAAAATGGGGACGTT	0.463											OREG0023981	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I827T		Atlas-SNP	.											.	MBTPS1	85	.	0			c.T2480C						.	A	THR/ILE	1,4399	2.1+/-5.4	0,1,2199	85	81	82		2480	5.4	1	16	dbSNP_134	82	0,8600		0,0,4300	no	missense	MBTPS1	NM_003791.2	89	0,1,6499	GG,GA,AA		0.0,0.0227,0.0077	possibly-damaging	827/1053	84097002	1,12999	2200	4300	6500	SO:0001583	missense	8720	exon19			CCCAAAATGGGGA	D42053	CCDS10941.1	16q24	2008-08-04	2005-08-17		ENSG00000140943	ENSG00000140943			15456	protein-coding gene	gene with protein product		603355	"membrane-bound transcription factor protease, site 1"			9809072, 10944850	Standard	NM_003791		Approved	S1P, KIAA0091, SKI-1, PCSK8	uc002fhi.3	Q14703	OTTHUMG00000137639	ENST00000343411.3:c.2480T>C	chr16.hg19:g.84097002A>G	ENSP00000344223:p.Ile827Thr	143.0	0.0	1226	121.0	5.0	NM_003791	A8K6V8|Q24JQ2|Q9UF67	Missense_Mutation	SNP	ENST00000343411.3	hg19	CCDS10941.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.410106	0.83340	2.27E-4	0.0	ENSG00000140943	ENST00000343411;ENST00000347334	T	0.35236	1.32	5.44	5.44	0.79542	.	0.201589	0.52532	D	0.000064	T	0.43986	0.1272	M	0.67569	2.06	0.58432	D	0.999991	P	0.43938	0.822	B	0.43575	0.424	T	0.49799	-0.8901	10	0.87932	D	0	-16.8187	15.7875	0.78319	1.0:0.0:0.0:0.0	.	827	Q14703	MBTP1_HUMAN	T	827;272	ENSP00000344223:I827T	ENSP00000344223:I827T	I	-	2	0	MBTPS1	82654503	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	9.275000	0.95738	2.197000	0.70478	0.402000	0.26972	ATT	.	A|1.000;G|0.000		0.463	MBTPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269080.2	NM_003791		G	84097002	A	G	84097002	3	3	254	1	0	0	0	0	1	0	0	0	9370	101	4	2	698	2	MBTPS1	16	84097002	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	2442486	84097002	6257751	791	35083										
TAF1C	9013	hgsc.bcm.edu	37	chr16	84212983	84212983	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aggcagcccctcggcctgccCaggcttcccccaggcgctca	11	20	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:84212983C>T	ENST00000567759.1	-	14	2356	c.2174G>A	c.(2173-2175)tGg>tAg	p.W725*	TAF1C_ENST00000570117.1_Nonsense_Mutation_p.W393*|TAF1C_ENST00000566732.1_Nonsense_Mutation_p.W699*|TAF1C_ENST00000378541.4_Nonsense_Mutation_p.W725*|TAF1C_ENST00000341690.6_Nonsense_Mutation_p.W631*|TAF1C_ENST00000541676.1_Nonsense_Mutation_p.W632*	NM_005679.3	NP_005670	Q15572	TAF1C_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kDa	725					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	26						TCGGCCTGCCCAGGCTTCCCC	0.716																																					p.W725X		Atlas-SNP	.											.	TAF1C	60	.	0			c.G2174A						.						17	21	20					16																	84212983		2198	4292	6490	SO:0001587	stop_gained	9013	exon14			CCTGCCCAGGCTT	L39059	CCDS32496.1, CCDS45535.1, CCDS58488.1, CCDS58489.1	16q24	2008-02-05	2002-08-29			ENSG00000103168			11534	protein-coding gene	gene with protein product		604905	"TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kD"			7801123	Standard	NM_005679		Approved	TAFI110, TAFI95, SL1, MGC:39976	uc010vnx.2	Q15572		ENST00000567759.1:c.2174G>A	chr16.hg19:g.84212983C>T	ENSP00000455265:p.Trp725*	122.0	0.0		84.0	4.0	NM_005679	B7Z5K5|B7Z5S4|B7Z908|B7Z9L7|Q59F67|Q8N6V3	Nonsense_Mutation	SNP	ENST00000567759.1	hg19	CCDS32496.1	.	.	.	.	.	.	.	.	.	.	C	33	5.274598	0.95459	.	.	ENSG00000103168	ENST00000378541;ENST00000541676;ENST00000341690;ENST00000544090	.	.	.	5.14	5.14	0.70334	.	0.101272	0.43579	D	0.000553	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.0209	14.0909	0.64990	0.0:1.0:0.0:0.0	.	.	.	.	X	725;632;631;248	.	ENSP00000345305:W631X	W	-	2	0	TAF1C	82770484	0.533000	0.26354	1.000000	0.80357	0.981000	0.71138	1.161000	0.31773	2.390000	0.81377	0.561000	0.74099	TGG	.	.		0.716	TAF1C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000433045.2	NM_139353		T	84212983	C	T	84212983	4	4	254	1	0	0	0	0	0	1	0	0	15536	595	21	3	439	3	TAF1C	16	84212983	Nonsense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	115981	84212983	6141770	792	35084										
GALNS	2588	hgsc.bcm.edu	37	chr16	88909227	88909227	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctccatacaccccgaggtcaCcccatcccatctgcagggaa	7	18	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr16:88909227C>T	ENST00000268695.5	-	2	219	c.131G>A	c.(130-132)gGt>gAt	p.G44D	GALNS_ENST00000542788.1_Intron|GALNS_ENST00000565364.1_5'UTR	NM_000512.4	NP_000503.1	P34059	GALNS_HUMAN	galactosamine (N-acetyl)-6-sulfatase	44	Catalytic domain.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	metal ion binding (GO:0046872)|N-acetylgalactosamine-4-sulfatase activity (GO:0003943)|N-acetylgalactosamine-6-sulfatase activity (GO:0043890)|sulfuric ester hydrolase activity (GO:0008484)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(8)	22				BRCA - Breast invasive adenocarcinoma(80;0.0496)		CCCGAGGTCACCCCATCCCAT	0.607																																					p.G44D	GBM(129;1929 2344 25209 33204)	Atlas-SNP	.											.	GALNS	37	.	0			c.G131A						.						49	45	47					16																	88909227		2197	4300	6497	SO:0001583	missense	2588	exon2			AGGTCACCCCATC	D17629	CCDS10970.1	16q24.3	2014-07-03	2014-07-03		ENSG00000141012	ENSG00000141012	3.1.6.4	"Arylsulfatase family"	4122	protein-coding gene	gene with protein product	"Morquio syndrome", "mucopolysaccharidosis type IVA"	612222	"galactosamine (N-acetyl)-6-sulfate sulfatase"			1755850	Standard	NM_000512		Approved	GAS, GALNAC6S	uc002fly.4	P34059	OTTHUMG00000137862	ENST00000268695.5:c.131G>A	chr16.hg19:g.88909227C>T	ENSP00000268695:p.Gly44Asp	92.0	0.0		84.0	4.0	NM_000512	Q86VK3	Missense_Mutation	SNP	ENST00000268695.5	hg19	CCDS10970.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.545763	0.86022	.	.	ENSG00000141012	ENST00000268695	D	0.92911	-3.13	4.8	4.8	0.61643	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	D	0.96827	0.8964	M	0.90595	3.13	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97729	1.0201	10	0.87932	D	0	.	18.2008	0.89838	0.0:1.0:0.0:0.0	.	44;44	B2R6P1;P34059	.;GALNS_HUMAN	D	44	ENSP00000268695:G44D	ENSP00000268695:G44D	G	-	2	0	GALNS	87436728	1.000000	0.71417	0.955000	0.39395	0.615000	0.37417	7.383000	0.79741	2.388000	0.81334	0.561000	0.74099	GGT	.	.		0.607	GALNS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269543.1			T	88909227	C	T	88909227	3	4	254	1	0	0	0	0	1	0	0	0	6214	507	18	3	1489	3	GALNS	16	88909227	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	4696244	88909227	1445526	793	35085										
METT10D	79066	hgsc.bcm.edu	37	chr17	2323799	2323799	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gctgtctcacacgctctcttTtctttctccttaaatgaatc	4	13	4	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:2323799T>C	ENST00000263092.6	-	10	1281	c.1154A>G	c.(1153-1155)aAa>aGa	p.K385R	METTL16_ENST00000571669.2_5'UTR|METTL16_ENST00000538844.1_Missense_Mutation_p.K167R	NM_024086.3	NP_076991.3	Q86W50	MET16_HUMAN	methyltransferase like 16	385							methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)			kidney(2)|large_intestine(9)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	19						ACGCTCTCTTTTCTTTCTCCT	0.488																																					p.K385R		Atlas-SNP	.											.	METTL16	75	.	0			c.A1154G						.						78	82	80					17																	2323799		1867	4100	5967	SO:0001583	missense	79066	exon10			TCTCTTTTCTTTC	AK027410	CCDS42232.1	17p13.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000127804	ENSG00000127804			28484	protein-coding gene	gene with protein product			"methyltransferase 10 domain containing"	METT10D		18021804	Standard	NM_024086		Approved	MGC3329	uc002fut.3	Q86W50		ENST00000263092.6:c.1154A>G	chr17.hg19:g.2323799T>C	ENSP00000263092:p.Lys385Arg	50.0	0.0		74.0	4.0	NM_024086	D3DTI8|Q86TE5|Q96T16|Q9BVG7	Missense_Mutation	SNP	ENST00000263092.6	hg19	CCDS42232.1	.	.	.	.	.	.	.	.	.	.	T	3.059	-0.193714	0.06259	.	.	ENSG00000127804	ENST00000263092;ENST00000537138;ENST00000538844	T;T	0.38077	1.16;1.36	5.75	2.37	0.29283	.	0.182120	0.64402	N	0.000015	T	0.15696	0.0378	N	0.13235	0.315	0.28140	N	0.929833	B	0.06786	0.001	B	0.06405	0.002	T	0.34378	-0.9831	10	0.02654	T	1	-0.1836	7.5271	0.27662	0.0:0.3501:0.0:0.6498	.	385	Q86W50	MET16_HUMAN	R	385;65;167	ENSP00000263092:K385R;ENSP00000443633:K167R	ENSP00000263092:K385R	K	-	2	0	METTL16	2270549	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	2.049000	0.41288	0.131000	0.18576	-0.256000	0.11100	AAA	.	.		0.488	METTL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437653.2	NM_024086		C	2323799	T	C	2323799	3	2	254	1	0	0	0	0	1	0	0	0	9499	1841	64	2	538	2	METT10D	17	2323799	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10		2323799	78871411	794	35086										
KIAA0664	23277	hgsc.bcm.edu	37	chr17	2599486	2599486	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tggcaggagagcaggaaggcAgccgcgtccttcagcagctg	16	11	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:2599486A>G	ENST00000570628.2	-	13	2346	c.2241T>C	c.(2239-2241)gcT>gcC	p.A747A	CLUH_ENST00000538975.1_Silent_p.A747A|CLUH_ENST00000435359.1_Silent_p.A747A			O75153	CLU_HUMAN	clustered mitochondria (cluA/CLU1) homolog	747					intracellular distribution of mitochondria (GO:0048312)	cytoplasm (GO:0005737)											GCAGGAAGGCAGCCGCGTCCT	0.647																																					p.A747A		Atlas-SNP	.											.	.	.	.	0			c.T2241C						.						22	26	25					17																	2599486		1985	4147	6132	SO:0001819	synonymous_variant	23277	exon13			GAAGGCAGCCGCG	AB014564	CCDS45572.1	17p13.3	2012-12-18	2012-11-30	2012-11-30	ENSG00000132361	ENSG00000132361			29094	protein-coding gene	gene with protein product			"KIAA0664"	KIAA0664			Standard	XM_005256567		Approved	CLU1	uc002fuy.1	O75153	OTTHUMG00000177575	ENST00000570628.2:c.2241T>C	chr17.hg19:g.2599486A>G		158.0	0.0		99.0	6.0	NM_015229	Q6AHY2|Q6P3X7|Q6ZUG8|Q8N4U7|Q9BTA3|Q9H979	Silent	SNP	ENST00000570628.2	hg19	CCDS45572.1																																																																																			.	.		0.647	CLUH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437807.2	NM_015229		G	2599486	A	G	2599486	2	3	254	1	0	0	0	0	0	0	0	1	8198	175	7	2		2	KIAA0664	17	2599486	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	275687	2599486	78595724	795	35087										
RAP1GAP2	23108	hgsc.bcm.edu	37	chr17	2921396	2921396	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cactccatggagaccatggtGggcggccagaagaagtcgca	14	11	0	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:2921396G>A	ENST00000254695.8	+	18	1626	c.1536G>A	c.(1534-1536)gtG>gtA	p.V512V	RAP1GAP2_ENST00000540393.2_Silent_p.V493V|RAP1GAP2_ENST00000366401.4_Silent_p.V497V|RAP1GAP2_ENST00000542807.1_Silent_p.V512V	NM_015085.4	NP_055900.4	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2	512					negative regulation of neuron projection development (GO:0010977)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|nuclear membrane (GO:0031965)	Rap GTPase activator activity (GO:0046582)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	11						AGACCATGGTGGGCGGCCAGA	0.637																																					p.V512V		Atlas-SNP	.											.	RAP1GAP2	90	.	0			c.G1536A						.						17	21	20					17																	2921396		2075	4190	6265	SO:0001819	synonymous_variant	23108	exon18			CATGGTGGGCGGC	AB028962	CCDS45573.1, CCDS45574.1	17p13.3	2009-09-14	2009-09-14	2009-09-14		ENSG00000132359			29176	protein-coding gene	gene with protein product			"GTPase activating RANGAP domain-like 4", "GTPase activating Rap/RanGAP domain-like 4"	GARNL4		15632203	Standard	NM_015085		Approved	KIAA1039	uc010ckd.3	Q684P5		ENST00000254695.8:c.1536G>A	chr17.hg19:g.2921396G>A		77.0	0.0		54.0	4.0	NM_015085	B2RTY5|Q684P4|Q6AI00|Q6ZVF0|Q9UPW2	Silent	SNP	ENST00000254695.8	hg19	CCDS45573.1																																																																																			.	.		0.637	RAP1GAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438208.2			A	2921396	G	A	2921396	2	1	254	1	0	0	0	0	0	0	0	1	13053	1335	47	3		3	RAP1GAP2	17	2921396	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	321910	2921396	78273814	796	35088										
GSG2	83903	hgsc.bcm.edu	37	chr17	3628016	3628016	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	attctgagtttcgggcagatGggaagaatatgagagagtcc	14	5	1	5			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:3628016G>T	ENST00000325418.4	+	1	806	c.787G>T	c.(787-789)Ggg>Tgg	p.G263W	CTD-3195I5.3_ENST00000571741.1_RNA|ITGAE_ENST00000571185.1_5'UTR|ITGAE_ENST00000263087.4_Intron	NM_031965.2	NP_114171.2	Q8TF76	HASP_HUMAN	germ cell associated 2 (haspin)	263					histone H3-T3 phosphorylation involved in chromosome passenger complex localization to kinetochore (GO:2000751)|intracellular signal transduction (GO:0035556)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|protein localization to chromosome, centromeric region (GO:0071459)|protein phosphorylation (GO:0006468)|regulation of spindle checkpoint (GO:0090231)	centrosome (GO:0005813)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|histone kinase activity (H3-T3 specific) (GO:0072354)|protein kinase activity (GO:0004672)										TCGGGCAGATGGGAAGAATAT	0.552																																					p.G263W		Atlas-SNP	.											.	GSG2	48	.	0			c.G787T						.						61	71	68					17																	3628016		2203	4300	6503	SO:0001583	missense	83903	exon1			GCAGATGGGAAGA	AB039834	CCDS11036.1	17p13	2005-01-19			ENSG00000177602	ENSG00000177602			19682	protein-coding gene	gene with protein product		609240					Standard	NM_031965		Approved	haspin	uc002fwp.3	Q8TF76	OTTHUMG00000090703	ENST00000325418.4:c.787G>T	chr17.hg19:g.3628016G>T	ENSP00000325290:p.Gly263Trp	110.0	0.0		75.0	4.0	NM_031965	Q5U5K3|Q96MN1|Q9BXS7	Missense_Mutation	SNP	ENST00000325418.4	hg19	CCDS11036.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.042756	0.75732	.	.	ENSG00000177602	ENST00000325418	T	0.08282	3.11	3.95	3.95	0.45737	.	0.196377	0.25194	N	0.032424	T	0.17023	0.0409	L	0.27053	0.805	0.26655	N	0.972021	D	0.89917	1.0	D	0.85130	0.997	T	0.01583	-1.1319	10	0.87932	D	0	-50.6244	13.7897	0.63133	0.0:0.0:1.0:0.0	.	263	Q8TF76	HASP_HUMAN	W	263	ENSP00000325290:G263W	ENSP00000325290:G263W	G	+	1	0	GSG2	3574765	0.558000	0.26554	0.239000	0.24122	0.277000	0.26821	0.708000	0.25719	2.470000	0.83445	0.655000	0.94253	GGG	.	.		0.552	GSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207391.1	NM_031965		T	3628016	G	T	3628016	3	4	254	1	0	0	0	0	1	0	0	0	6831	1348	47	3	789	3	GSG2	17	3628016	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	706620	3628016	77567194	797	35089										
MYBBP1A	10514	hgsc.bcm.edu	37	chr17	4458458	4458458	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agatactccagcagcttctcCgtggccgcaagtcgcgtctc	10	15	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:4458458C>T	ENST00000254718.4	-	1	468	c.162G>A	c.(160-162)acG>acA	p.T54T	MYBBP1A_ENST00000381556.2_Silent_p.T54T			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	54	Interaction with MYB. {ECO:0000250}.				cellular response to glucose starvation (GO:0042149)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|osteoblast differentiation (GO:0001649)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|NLS-dependent protein nuclear import complex (GO:0042564)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)	24						GCAGCTTCTCCGTGGCCGCAA	0.647																																					p.T54T		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.G162A						.						19	18	19					17																	4458458		2197	4299	6496	SO:0001819	synonymous_variant	10514	exon1			CTTCTCCGTGGCC	AF147709	CCDS11046.1, CCDS42238.1	17p13.3	2008-07-18			ENSG00000132382	ENSG00000132382			7546	protein-coding gene	gene with protein product	"p53-activated protein-2"	604885				10644447	Standard	NM_014520		Approved	P160, PAP2, FLJ37886	uc002fxz.4	Q9BQG0	OTTHUMG00000090747	ENST00000254718.4:c.162G>A	chr17.hg19:g.4458458C>T		82.0	0.0		77.0	4.0	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Silent	SNP	ENST00000254718.4	hg19	CCDS11046.1																																																																																			.	.		0.647	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520		T	4458458	C	T	4458458	2	4	254	1	0	0	0	0	0	0	0	1	10017	639	23	1		1	MYBBP1A	17	4458458	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	830442	4458458	76736752	798	35090										
MINK1	50488	hgsc.bcm.edu	37	chr17	4793904	4793904	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcctacctcaagtccctgcaGcagcagcaacagcagcagca	9	16	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:4793904G>T	ENST00000355280.6	+	14	1636	c.1440G>T	c.(1438-1440)caG>caT	p.Q480H	MINK1_ENST00000453408.3_Missense_Mutation_p.Q480H|MINK1_ENST00000347992.7_Missense_Mutation_p.Q480H	NM_001024937.3|NM_015716.4|NM_153827.4	NP_001020108.1|NP_056531.1|NP_722549.2			misshapen-like kinase 1											central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)|stomach(1)	6						AGTCCCTgcagcagcagcaac	0.612																																					p.Q480H		Atlas-SNP	.											.	MINK1	110	.	0			c.G1440T						.						16	21	19					17																	4793904		2177	4255	6432	SO:0001583	missense	50488	exon14			CCTGCAGCAGCAG	AY775058	CCDS45588.1, CCDS45589.1, CCDS45590.1	17p13.2	2011-04-14	2010-06-24		ENSG00000141503	ENSG00000141503			17565	protein-coding gene	gene with protein product	"misshapen/NIK-related kinase"	609426	"misshapen-like kinase 1 (zebrafish)"			10708748, 12087176	Standard	NM_015716		Approved	B55, MINK, ZC3, MAP4K6, YSK2	uc010vsl.2	Q8N4C8		ENST00000355280.6:c.1440G>T	chr17.hg19:g.4793904G>T	ENSP00000347427:p.Gln480His	72.0	0.0		64.0	4.0	NM_170663		Missense_Mutation	SNP	ENST00000355280.6	hg19	CCDS45588.1	.	.	.	.	.	.	.	.	.	.	G	14.08	2.427383	0.43122	.	.	ENSG00000141503	ENST00000355280;ENST00000453408;ENST00000347992	T;T;T	0.52057	0.68;0.68;0.68	4.89	3.93	0.45458	.	0.068143	0.64402	D	0.000015	T	0.64616	0.2614	M	0.70842	2.15	0.49051	D	0.999743	D;D;D;D	0.60575	0.988;0.988;0.98;0.988	D;D;D;D	0.72338	0.977;0.977;0.948;0.977	T	0.67296	-0.5706	10	0.66056	D	0.02	.	11.0187	0.47705	0.0906:0.0:0.9094:0.0	.	480;480;480;480	Q8N4C8-2;Q8N4C8-4;Q8N4C8;Q8N4C8-3	.;.;MINK1_HUMAN;.	H	480	ENSP00000347427:Q480H;ENSP00000406487:Q480H;ENSP00000269296:Q480H	ENSP00000269296:Q480H	Q	+	3	2	MINK1	4734686	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.607000	0.61133	1.293000	0.44690	-0.258000	0.10820	CAG	.	.		0.612	MINK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439801.1	NM_015716		T	4793904	G	T	4793904	3	4	254	1	0	0	0	0	1	0	0	0	9596	962	34	3	1233	3	MINK1	17	4793904	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	335446	4793904	76401306	799	35091										
GPR172B	55065	hgsc.bcm.edu	37	chr17	4936582	4936582	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gaccacccctgcagtggtgcCcaccaggggtgggcaggggc	17	14	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:4936582C>A	ENST00000424747.1	-	4	1820	c.1108G>T	c.(1108-1110)Ggc>Tgc	p.G370C	SLC52A1_ENST00000512825.2_Intron|SLC52A1_ENST00000254853.5_Missense_Mutation_p.G370C	NM_001104577.1	NP_001098047.1	Q9NWF4	S52A1_HUMAN	solute carrier family 52 (riboflavin transporter), member 1	370					riboflavin transport (GO:0032218)	integral component of plasma membrane (GO:0005887)	riboflavin transporter activity (GO:0032217)|virus receptor activity (GO:0001618)										GCAGTGGTGCCCACCAGGGGT	0.627																																					p.G370C		Atlas-SNP	.											.	.	.	.	0			c.G1108T						.						74	86	82					17																	4936582		2203	4300	6503	SO:0001583	missense	55065	exon4			TGGTGCCCACCAG	AY070775	CCDS11066.1	17p13.3	2013-07-17	2013-07-17	2012-02-29	ENSG00000132517	ENSG00000132517		"Solute carriers"	30225	protein-coding gene	gene with protein product	"riboflavin transporter 1"	607883	"G protein-coupled receptor 172B"	GPR172B		12740431, 18632736	Standard	NM_001104577		Approved	FLJ10060, GPCR42, PAR2, hRFT1, RFVT1	uc002gao.4	Q9NWF4	OTTHUMG00000099448	ENST00000424747.1:c.1108G>T	chr17.hg19:g.4936582C>A	ENSP00000399979:p.Gly370Cys	105.0	0.0		88.0	4.0	NM_017986	B5MEV1|B5MEV2|Q6P9E0|Q86UT0	Missense_Mutation	SNP	ENST00000424747.1	hg19	CCDS11066.1	.	.	.	.	.	.	.	.	.	.	C	19.37	3.815482	0.70912	.	.	ENSG00000132517	ENST00000254853;ENST00000424747	T;T	0.72615	-0.67;-0.67	0.913	-0.217	0.13149	.	0.000000	0.85682	D	0.000000	T	0.80149	0.4570	M	0.83603	2.65	0.58432	D	0.999995	D	0.89917	1.0	D	0.80764	0.994	T	0.76350	-0.2991	10	0.66056	D	0.02	.	5.7669	0.18231	0.3146:0.6853:0.0:0.0	.	370	Q9NWF4	RFT_HUMAN	C	370	ENSP00000254853:G370C;ENSP00000399979:G370C	ENSP00000254853:G370C	G	-	1	0	GPR172B	4877306	0.599000	0.26891	0.766000	0.31476	0.882000	0.50991	2.005000	0.40864	-0.059000	0.13154	-0.181000	0.13052	GGC	.	.		0.627	SLC52A1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216913.1	NM_017986		A	4936582	C	A	4936582	3	1	254	1	0	0	0	0	1	0	0	0	6678	623	22	3	246	3	GPR172B	17	4936582	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	142678	4936582	76258628	800	35092										
RABEP1	9135	hgsc.bcm.edu	37	chr17	5283729	5283729	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aataaagatcagtttggaagAgcagttaaagaaagagactg	11	3	1	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:5283729A>G	ENST00000546142.2	+	16	2529	c.2342A>G	c.(2341-2343)gAg>gGg	p.E781G	NUP88_ENST00000573169.1_Intron|RABEP1_ENST00000341923.6_Intron|RABEP1_ENST00000262477.6_Missense_Mutation_p.E781G|RABEP1_ENST00000537505.1_Missense_Mutation_p.E738G|RABEP1_ENST00000408982.2_Intron			Q15276	RABE1_HUMAN	rabaptin, RAB GTPase binding effector protein 1	781					apoptotic process (GO:0006915)|endocytosis (GO:0006897)|membrane fusion (GO:0061025)|protein transport (GO:0015031)	early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)|protein homodimerization activity (GO:0042803)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	8						AGTTTGGAAGAGCAGTTAAAG	0.373																																					p.E781G		Atlas-SNP	.											.	RABEP1	59	.	0			c.A2342G						.						68	61	63					17																	5283729		1822	4078	5900	SO:0001583	missense	9135	exon16			TGGAAGAGCAGTT	AF098638	CCDS42243.1, CCDS45592.1	17p13.2	2008-02-05				ENSG00000029725			17677	protein-coding gene	gene with protein product		603616				8521472	Standard	NM_001291582		Approved	neurocrescin, RAB5EP, RABPT5, rabaptin-5	uc002gbm.4	Q15276		ENST00000546142.2:c.2342A>G	chr17.hg19:g.5283729A>G	ENSP00000437701:p.Glu781Gly	107.0	0.0		75.0	4.0	NM_004703	B2RAG7|O95369|Q8IVX3	Missense_Mutation	SNP	ENST00000546142.2	hg19	CCDS45592.1	.	.	.	.	.	.	.	.	.	.	A	16.28	3.078022	0.55753	.	.	ENSG00000029725	ENST00000262477;ENST00000546142;ENST00000537505	T;T;T	0.46451	0.87;0.87;0.87	5.21	5.21	0.72293	Rabaptin, GTPase-Rab5 binding (1);	0.273852	0.40640	N	0.001049	T	0.29126	0.0724	N	0.19112	0.55	0.80722	D	1	B;B	0.24823	0.112;0.029	B;B	0.20955	0.032;0.017	T	0.06698	-1.0812	10	0.32370	T	0.25	-10.4351	14.3671	0.66812	1.0:0.0:0.0:0.0	.	738;781	F5H355;Q15276	.;RABE1_HUMAN	G	781;781;738	ENSP00000262477:E781G;ENSP00000437701:E781G;ENSP00000445408:E738G	ENSP00000262477:E781G	E	+	2	0	RABEP1	5224453	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	7.114000	0.77103	2.326000	0.78906	0.533000	0.62120	GAG	.	.		0.373	RABEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439349.1	NM_004703		G	5283729	A	G	5283729	3	3	254	1	0	0	0	0	1	0	0	0	12976	304	11	2	2404	2	RABEP1	17	5283729	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	347147	5283729	75911481	801	35093										
NUP88	4927	hgsc.bcm.edu	37	chr17	5317451	5317451	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aatctctccgcaactggagtGgtactaaaataaagataata	7	7	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:5317451G>T	ENST00000573584.1	-	3	980	c.471C>A	c.(469-471)acC>acA	p.T157T		NM_002532.4	NP_002523.2	Q99567	NUP88_HUMAN	nucleoporin 88kDa	157					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	transporter activity (GO:0005215)			endometrium(4)|kidney(4)|large_intestine(4)|lung(3)	15						CAACTGGAGTGGTACTAAAAT	0.383																																					p.T157T		Atlas-SNP	.											.	NUP88	47	.	0			c.C471A						.						56	53	54					17																	5317451		2203	4300	6503	SO:0001819	synonymous_variant	4927	exon3			TGGAGTGGTACTA	Y08612	CCDS11070.1	17p13	2004-02-18	2002-08-29		ENSG00000108559	ENSG00000108559			8067	protein-coding gene	gene with protein product		602552	"nucleoporin 88kD"			9049309	Standard	NM_002532		Approved	MGC8530	uc002gbo.2	Q99567	OTTHUMG00000099453	ENST00000573584.1:c.471C>A	chr17.hg19:g.5317451G>T		62.0	0.0		66.0	4.0	NM_002532	D3DTM2|Q9BWE5	Silent	SNP	ENST00000573584.1	hg19	CCDS11070.1																																																																																			.	.		0.383	NUP88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216918.3	NM_002532		T	5317451	G	T	5317451	2	4	254	1	0	0	0	0	0	0	0	1	10780	1335	47	3		3	NUP88	17	5317451	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	33722	5317451	75877759	802	35094										
TEKT1	83659	hgsc.bcm.edu	37	chr17	6716342	6716342	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttctccacattggtgctggaGaagtccaaccagtcttccag	9	12	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:6716342G>T	ENST00000338694.2	-	6	789	c.660C>A	c.(658-660)ttC>ttA	p.F220L	TEKT1_ENST00000535086.1_Missense_Mutation_p.F74L	NM_053285.1	NP_444515.1	Q969V4	TEKT1_HUMAN	tektin 1	220						cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)	20		Myeloproliferative disorder(207;0.0255)				TGGTGCTGGAGAAGTCCAACC	0.547																																					p.F220L		Atlas-SNP	.											.	TEKT1	49	.	0			c.C660A						.						76	68	71					17																	6716342		2203	4300	6503	SO:0001583	missense	83659	exon6			GCTGGAGAAGTCC		CCDS11083.1	17p13.2	2011-05-23			ENSG00000167858	ENSG00000167858			15534	protein-coding gene	gene with protein product		609002				11606253	Standard	NM_053285		Approved		uc002gdt.3	Q969V4	OTTHUMG00000102063	ENST00000338694.2:c.660C>A	chr17.hg19:g.6716342G>T	ENSP00000341346:p.Phe220Leu	95.0	0.0		65.0	4.0	NM_053285	D3DTM7	Missense_Mutation	SNP	ENST00000338694.2	hg19	CCDS11083.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.311936	0.81358	.	.	ENSG00000167858	ENST00000338694;ENST00000535086	T;T	0.02916	4.11;4.11	4.96	4.96	0.65561	.	0.237839	0.43747	D	0.000533	T	0.09730	0.0239	M	0.87900	2.915	0.34957	D	0.751854	B	0.24576	0.106	B	0.34452	0.183	T	0.02546	-1.1143	10	0.44086	T	0.13	.	16.0725	0.80946	0.0:0.0:1.0:0.0	.	220	Q969V4	TEKT1_HUMAN	L	220;74	ENSP00000341346:F220L;ENSP00000444142:F74L	ENSP00000341346:F220L	F	-	3	2	TEKT1	6657066	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.093000	0.57714	2.458000	0.83093	0.591000	0.81541	TTC	.	.		0.547	TEKT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219867.2	NM_053285		T	6716342	G	T	6716342	3	4	254	1	0	0	0	0	1	0	0	0	15767	933	33	3	608	3	TEKT1	17	6716342	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1398891	6716342	74478868	803	35095										
DVL2	1856	hgsc.bcm.edu	37	chr17	7132581	7132581	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	caacaatggagatacccaggAagttgtacttctctgtggag	11	8	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:7132581A>G	ENST00000005340.5	-	8	1112	c.830T>C	c.(829-831)tTc>tCc	p.F277S	DVL2_ENST00000575458.1_Missense_Mutation_p.F271S|DVL2_ENST00000574642.1_5'UTR	NM_004422.2	NP_004413.1	O14641	DVL2_HUMAN	dishevelled segment polarity protein 2	277	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration in hindbrain (GO:0021535)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|convergent extension involved in neural plate elongation (GO:0022007)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hippo signaling (GO:0035329)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|segment specification (GO:0007379)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|clathrin-coated endocytic vesicle (GO:0045334)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|identical protein binding (GO:0042802)			breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(7)|skin(1)	25						GATACCCAGGAAGTTGTACTT	0.622																																					p.F277S		Atlas-SNP	.											.	DVL2	49	.	0			c.T830C						.						81	85	84					17																	7132581		2203	4300	6503	SO:0001583	missense	1856	exon8			CCCAGGAAGTTGT	BC014844	CCDS11091.1	17p13.1	2013-05-22	2013-05-22		ENSG00000004975	ENSG00000004975		"Dishevelled homologs"	3086	protein-coding gene	gene with protein product		602151	"dishevelled 2 (homologous to Drosophila dsh)", "dishevelled, dsh homolog 2 (Drosophila)"			8662242	Standard	NM_004422		Approved		uc002gez.1	O14641	OTTHUMG00000102155	ENST00000005340.5:c.830T>C	chr17.hg19:g.7132581A>G	ENSP00000005340:p.Phe277Ser	115.0	0.0		79.0	4.0	NM_004422	D3DTN3|Q53XM0	Missense_Mutation	SNP	ENST00000005340.5	hg19	CCDS11091.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.060179	0.76074	.	.	ENSG00000004975	ENST00000005340	T	0.14640	2.49	5.11	5.11	0.69529	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.21921	0.0528	N	0.16233	0.39	0.80722	D	1	P;D	0.89917	0.946;1.0	P;D	0.87578	0.869;0.998	T	0.05920	-1.0856	10	0.87932	D	0	-17.7532	12.856	0.57886	1.0:0.0:0.0:0.0	.	271;277	B4DLQ0;O14641	.;DVL2_HUMAN	S	277	ENSP00000005340:F277S	ENSP00000005340:F277S	F	-	2	0	DVL2	7073305	1.000000	0.71417	1.000000	0.80357	0.774000	0.43823	9.307000	0.96226	1.938000	0.56188	0.459000	0.35465	TTC	.	.		0.622	DVL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219999.2	NM_004422		G	7132581	A	G	7132581	3	3	254	1	0	0	0	0	1	0	0	0	4838	246	9	2	1412	2	DVL2	17	7132581	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	416239	7132581	74062629	804	35096										
DVL2	1856	hgsc.bcm.edu	37	chr17	7133190	7133190	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tctccagctcgctggtcatgAgggtagaggagctctcgtat	13	10	3	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:7133190A>G	ENST00000005340.5	-	5	875	c.593T>C	c.(592-594)cTc>cCc	p.L198P	DVL2_ENST00000575458.1_Missense_Mutation_p.L192P|DVL2_ENST00000574642.1_5'UTR	NM_004422.2	NP_004413.1	O14641	DVL2_HUMAN	dishevelled segment polarity protein 2	198					canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration in hindbrain (GO:0021535)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|convergent extension involved in neural plate elongation (GO:0022007)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hippo signaling (GO:0035329)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|segment specification (GO:0007379)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|clathrin-coated endocytic vesicle (GO:0045334)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|identical protein binding (GO:0042802)			breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(7)|skin(1)	25						GCTGGTCATGAGGGTAGAGGA	0.647																																					p.L198P		Atlas-SNP	.											.	DVL2	49	.	0			c.T593C						.						69	72	71					17																	7133190		2203	4300	6503	SO:0001583	missense	1856	exon5			GTCATGAGGGTAG	BC014844	CCDS11091.1	17p13.1	2013-05-22	2013-05-22		ENSG00000004975	ENSG00000004975		"Dishevelled homologs"	3086	protein-coding gene	gene with protein product		602151	"dishevelled 2 (homologous to Drosophila dsh)", "dishevelled, dsh homolog 2 (Drosophila)"			8662242	Standard	NM_004422		Approved		uc002gez.1	O14641	OTTHUMG00000102155	ENST00000005340.5:c.593T>C	chr17.hg19:g.7133190A>G	ENSP00000005340:p.Leu198Pro	93.0	0.0		50.0	4.0	NM_004422	D3DTN3|Q53XM0	Missense_Mutation	SNP	ENST00000005340.5	hg19	CCDS11091.1	.	.	.	.	.	.	.	.	.	.	A	19.64	3.864584	0.71949	.	.	ENSG00000004975	ENST00000005340	T	0.04917	3.53	5.18	5.18	0.71444	Dishevelled protein domain (1);	0.137790	0.49305	D	0.000146	T	0.23410	0.0566	M	0.74881	2.28	0.80722	D	1	D;D;D	0.76494	0.999;0.994;0.994	D;D;D	0.71184	0.972;0.961;0.961	T	0.00557	-1.1672	10	0.72032	D	0.01	-21.0209	12.972	0.58517	1.0:0.0:0.0:0.0	.	105;192;198	B4DM44;B4DLQ0;O14641	.;.;DVL2_HUMAN	P	198	ENSP00000005340:L198P	ENSP00000005340:L198P	L	-	2	0	DVL2	7073914	1.000000	0.71417	0.998000	0.56505	0.807000	0.45602	8.930000	0.92872	1.961000	0.56991	0.418000	0.28097	CTC	.	.		0.647	DVL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219999.2	NM_004422		G	7133190	A	G	7133190	3	3	254	1	0	0	0	0	1	0	0	0	4838	304	11	2	1661	2	DVL2	17	7133190	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	609	7133190	74062020	805	35097										
TNK1	8711	hgsc.bcm.edu	37	chr17	7290400	7290400	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgacgctggcagatgcggggGgcttgccagccacccgtcca	15	14	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:7290400G>T	ENST00000576812.1	+	9	1708	c.1339G>T	c.(1339-1341)Ggc>Tgc	p.G447C	TNK1_ENST00000570896.1_Missense_Mutation_p.G442C|TNK1_ENST00000311668.2_Missense_Mutation_p.G442C	NM_001251902.1	NP_001238831.1			tyrosine kinase, non-receptor, 1											central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(2)|pancreas(1)	16		Prostate(122;0.157)				AGATGCGGGGGGCTTGCCAGC	0.632																																					p.G447C		Atlas-SNP	.											.	TNK1	31	.	0			c.G1339T						.						24	24	24					17																	7290400		1934	4122	6056	SO:0001583	missense	8711	exon9			GCGGGGGGCTTGC	U43408	CCDS45602.1, CCDS58510.1	17p13.1	2005-09-22				ENSG00000174292			11940	protein-coding gene	gene with protein product		608076				8632913	Standard	NM_003985		Approved		uc002ggi.4	Q13470		ENST00000576812.1:c.1339G>T	chr17.hg19:g.7290400G>T	ENSP00000459799:p.Gly447Cys	97.0	0.0		67.0	4.0	NM_001251902		Missense_Mutation	SNP	ENST00000576812.1	hg19	CCDS58510.1	.	.	.	.	.	.	.	.	.	.	G	14.75	2.628971	0.46944	.	.	ENSG00000174292	ENST00000311668	T	0.76709	-1.04	4.2	3.21	0.36854	.	0.174595	0.27851	N	0.017593	T	0.68988	0.3061	L	0.29908	0.895	0.21445	N	0.999684	P;P	0.48407	0.91;0.855	P;B	0.46758	0.526;0.326	T	0.61466	-0.7057	10	0.54805	T	0.06	.	8.5117	0.33222	0.1142:0.0:0.8858:0.0	.	442;447	Q13470-2;Q13470	.;TNK1_HUMAN	C	442	ENSP00000312309:G442C	ENSP00000312309:G442C	G	+	1	0	TNK1	7231124	0.104000	0.21937	0.330000	0.25442	0.325000	0.28411	0.758000	0.26447	1.100000	0.41517	0.313000	0.20887	GGC	.	.		0.632	TNK1-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000440832.2	NM_003985		T	7290400	G	T	7290400	3	4	254	1	0	0	0	0	1	0	0	0	16332	1232	43	3	1354	3	TNK1	17	7290400	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	157210	7290400	73904810	806	35098										
ZBTB4	57659	hgsc.bcm.edu	37	chr17	7370026	7370026	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgtctccggctatgagggtgAcgtcacagaagaggccacgg	15	10	2	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:7370026A>G	ENST00000311403.4	-	3	434	c.95T>C	c.(94-96)gTc>gCc	p.V32A	ZBTB4_ENST00000380599.4_Missense_Mutation_p.V32A	NM_020899.3	NP_065950.2	Q9P1Z0	ZBTB4_HUMAN	zinc finger and BTB domain containing 4	32	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				cellular response to DNA damage stimulus (GO:0006974)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)|methyl-CpNpG binding (GO:0010428)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|prostate(3)|skin(6)	36		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)		COAD - Colon adenocarcinoma(228;4.1e-06)|READ - Rectum adenocarcinoma(115;0.0642)		TATGAGGGTGACGTCACAGAA	0.647																																					p.V32A		Atlas-SNP	.											.	ZBTB4	163	.	0			c.T95C						.						47	36	40					17																	7370026		2203	4300	6503	SO:0001583	missense	57659	exon3			AGGGTGACGTCAC	AB040971	CCDS11107.1	17p13.2	2013-01-09			ENSG00000174282	ENSG00000174282		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	23847	protein-coding gene	gene with protein product		612308				12477932	Standard	NM_020899		Approved	KIAA1538, KAISO-L1, ZNF903	uc002ghd.4	Q9P1Z0	OTTHUMG00000108137	ENST00000311403.4:c.95T>C	chr17.hg19:g.7370026A>G	ENSP00000307858:p.Val32Ala	113.0	0.0		67.0	4.0	NM_001128833	B3KVL6|Q7Z697|Q86XJ4|Q8N4V8	Missense_Mutation	SNP	ENST00000311403.4	hg19	CCDS11107.1	.	.	.	.	.	.	.	.	.	.	A	18.46	3.628141	0.66901	.	.	ENSG00000174282	ENST00000311403;ENST00000380599	T;T	0.77750	-1.12;-1.12	4.91	4.91	0.64330	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.086330	0.44483	D	0.000452	D	0.83741	0.5320	L	0.49699	1.58	0.44129	D	0.996917	D	0.71674	0.998	D	0.69654	0.965	D	0.85411	0.1137	10	0.72032	D	0.01	-22.8599	13.6415	0.62253	1.0:0.0:0.0:0.0	.	32	Q9P1Z0	ZBTB4_HUMAN	A	32	ENSP00000307858:V32A;ENSP00000369973:V32A	ENSP00000307858:V32A	V	-	2	0	ZBTB4	7310750	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.423000	0.90264	2.060000	0.61445	0.459000	0.35465	GTC	.	.		0.647	ZBTB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226940.2	NM_020899		G	7370026	A	G	7370026	3	3	254	1	0	0	0	0	1	0	0	0	17556	275	10	2	2954	2	ZBTB4	17	7370026	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	79626	7370026	73825184	807	35099										
SENP3	26168	hgsc.bcm.edu	37	chr17	7466514	7466514	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggcccccacctcccaaacccCgactcaagtcaggtggaggg	11	17	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:7466514C>A	ENST00000429205.2	+	2	170	c.121C>A	c.(121-123)Cga>Aga	p.R41R	SENP3-EIF4A1_ENST00000579777.1_RNA|SENP3_ENST00000578868.1_3'UTR|SENP3_ENST00000321337.7_Silent_p.R41R			Q9H4L4	SENP3_HUMAN	SUMO1/sentrin/SMT3 specific peptidase 3	41	Pro-rich.					cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)	cysteine-type peptidase activity (GO:0008234)			central_nervous_system(1)|ovary(1)	2		Prostate(122;0.157)				TCCCAAACCCCGACTCAAGTC	0.662																																					p.R41R		Atlas-SNP	.											.	SENP3	18	.	0			c.C121A						.						11	14	13					17																	7466514		1972	4133	6105	SO:0001819	synonymous_variant	26168	exon2			AAACCCCGACTCA	AK000923	CCDS73958.1	17p13	2012-05-02	2005-08-17			ENSG00000161956			17862	protein-coding gene	gene with protein product		612844	"SUMO1/sentrin/SMT3 specific protease 3"			10806345, 11230166	Standard	NM_015670		Approved	DKFZP586K0919, SSP3, DKFZp762A152, SMT3IP1, Ulp1	uc002ghm.3	Q9H4L4		ENST00000429205.2:c.121C>A	chr17.hg19:g.7466514C>A		91.0	0.0		83.0	4.0	NM_015670	Q66K15|Q86VS7|Q96PS4|Q9Y3W9	Silent	SNP	ENST00000429205.2	hg19																																																																																				.	.		0.662	SENP3-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015670		A	7466514	C	A	7466514	2	1	254	1	0	0	0	0	0	0	0	1	14063	644	23	1		1	SENP3	17	7466514	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	96488	7466514	73728696	808	35100										
KDM6B	23135	hgsc.bcm.edu	37	chr17	7749921	7749921	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aacggaactatggagccaagCggggaggtcccccggtgaag	16	10	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:7749921C>T	ENST00000448097.2	+	8	905	c.574C>T	c.(574-576)Cgg>Tgg	p.R192W	KDM6B_ENST00000254846.5_Missense_Mutation_p.R192W			O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	192					cardiac muscle cell differentiation (GO:0055007)|cellular response to hydrogen peroxide (GO:0070301)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|mesodermal cell differentiation (GO:0048333)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|skin(5)	37						TGGAGCCAAGCGGGGAGGTCC	0.627																																					p.R192W		Atlas-SNP	.											.	KDM6B	95	.	0			c.C574T						.						67	78	74					17																	7749921		2203	4297	6500	SO:0001583	missense	23135	exon8			GCCAAGCGGGGAG	AB002344	CCDS32552.1	17p13.1	2011-07-01	2009-04-17	2009-04-17		ENSG00000132510		"Chromatin-modifying enzymes / K-demethylases"	29012	protein-coding gene	gene with protein product		611577	"jumonji domain containing 3", "jumonji domain containing 3, histone lysine demethylase"	JMJD3		10662545, 9205841	Standard	NM_001080424		Approved	KIAA0346	uc002giw.1	O15054		ENST00000448097.2:c.574C>T	chr17.hg19:g.7749921C>T	ENSP00000412513:p.Arg192Trp	73.0	0.0		63.0	26.0	NM_001080424	C9IZ40|Q96G33	Missense_Mutation	SNP	ENST00000448097.2	hg19		.	.	.	.	.	.	.	.	.	.	C	17.36	3.370768	0.61624	.	.	ENSG00000132510	ENST00000254846;ENST00000448097	T;T	0.08458	3.09;3.09	5.17	5.17	0.71159	.	0.255620	0.32055	N	0.006647	T	0.15565	0.0375	N	0.14661	0.345	0.45806	D	0.998682	D	0.89917	1.0	D	0.72338	0.977	T	0.10019	-1.0648	10	0.72032	D	0.01	-12.7822	16.5365	0.84373	0.0:1.0:0.0:0.0	.	192	O15054-1	.	W	192	ENSP00000254846:R192W;ENSP00000412513:R192W	ENSP00000254846:R192W	R	+	1	2	KDM6B	7690646	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	2.104000	0.41815	2.579000	0.87056	0.650000	0.86243	CGG	.	.		0.627	KDM6B-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440248.1	XM_043272		T	7749921	C	T	7749921	3	4	254	1	0	0	0	0	1	0	0	0	8147	759	27	1	592	1	KDM6B	17	7749921	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	283407	7749921	73445289	809	35101										
C17orf68	80169	hgsc.bcm.edu	37	chr17	8138160	8138160	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gctagaagatccagggtaggAgccaggagttgcagtcccag	15	9	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:8138160A>G	ENST00000315684.8	-	9	1531	c.1524T>C	c.(1522-1524)gcT>gcC	p.A508A	CTC1_ENST00000581671.1_5'Flank	NM_025099.5	NP_079375.3	Q2NKJ3	CTC1_HUMAN	CTS telomere maintenance complex component 1	508					bone marrow development (GO:0048539)|cellular response to DNA damage stimulus (GO:0006974)|hematopoietic stem cell proliferation (GO:0071425)|multicellular organism growth (GO:0035264)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|replicative senescence (GO:0090399)|spleen development (GO:0048536)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)|thymus development (GO:0048538)	nuclear chromosome, telomeric region (GO:0000784)|nucleus (GO:0005634)|Stn1-Ten1 complex (GO:0070188)	single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|skin(4)	29						CCAGGGTAGGAGCCAGGAGTT	0.572																																					p.A508A		Atlas-SNP	.											.	CTC1	75	.	0			c.T1524C						.						91	97	95					17																	8138160		1973	4150	6123	SO:0001819	synonymous_variant	80169	exon9			GGTAGGAGCCAGG	AL831955	CCDS42259.1	17p13.1	2011-02-21	2011-02-21	2011-02-21	ENSG00000178971	ENSG00000178971			26169	protein-coding gene	gene with protein product	"conserved telomere maintenance component 1", "alpha accessory factor 132", "conserved telomere capping protein 1"	613129	"tmp494178", "chromosome 17 open reading frame 68"	C17orf68		19854130, 19854131	Standard	NM_025099		Approved	FLJ22170, AAF132	uc002gkq.4	Q2NKJ3		ENST00000315684.8:c.1524T>C	chr17.hg19:g.8138160A>G		208.0	0.0		130.0	6.0	NM_025099	B3KR66|C9JEX5|Q1PCD1|Q2TBE3|Q8N3S6|Q9H6L0	Silent	SNP	ENST00000315684.8	hg19	CCDS42259.1																																																																																			.	.		0.572	CTC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442012.1	NM_025099		G	8138160	A	G	8138160	2	3	254	1	0	0	0	0	0	0	0	1	1878	291	11	2		2	C17orf68	17	8138160	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	388239	8138160	73057050	810	35102										
ARHGEF15	22899	hgsc.bcm.edu	37	chr17	8221748	8221748	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggggtccagccgtcaggagaAtgcccagaaggccctgggtg	17	11	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:8221748A>G	ENST00000361926.3	+	10	1858	c.1748A>G	c.(1747-1749)aAt>aGt	p.N583S	AC135178.7_ENST00000458568.1_RNA|ARHGEF15_ENST00000421050.1_Missense_Mutation_p.N583S	NM_173728.3	NP_776089.2	O94989	ARHGF_HUMAN	Rho guanine nucleotide exchange factor (GEF) 15	583	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				negative regulation of synapse maturation (GO:2000297)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|regulation of catalytic activity (GO:0050790)|retina vasculature morphogenesis in camera-type eye (GO:0061299)	cytoplasm (GO:0005737)|dendrite (GO:0030425)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(9)|large_intestine(5)|lung(11)|ovary(5)|prostate(3)|skin(2)|urinary_tract(1)	37						CGTCAGGAGAATGCCCAGAAG	0.617																																					p.N583S		Atlas-SNP	.											.	ARHGEF15	97	.	0			c.A1748G						.						78	86	83					17																	8221748		2203	4300	6503	SO:0001583	missense	22899	exon10			AGGAGAATGCCCA	AB020722	CCDS11139.1	17p13.1	2011-11-16			ENSG00000198844	ENSG00000198844		"Rho guanine nucleotide exchange factors"	15590	protein-coding gene	gene with protein product	"Rho guanine exchange factor (GEF) 15"	608504				10048485	Standard	NM_173728		Approved	KIAA0915, Vsm-RhoGEF, ARGEF15, FLJ13791, MGC44868	uc002glc.3	O94989	OTTHUMG00000108187	ENST00000361926.3:c.1748A>G	chr17.hg19:g.8221748A>G	ENSP00000355026:p.Asn583Ser	105.0	0.0		56.0	5.0	NM_025014	A8K6G1|Q8N449|Q9H8B4	Missense_Mutation	SNP	ENST00000361926.3	hg19	CCDS11139.1	.	.	.	.	.	.	.	.	.	.	a	15.03	2.713359	0.48517	.	.	ENSG00000198844	ENST00000361926;ENST00000455564;ENST00000421050	T;T	0.63417	-0.04;-0.04	5.29	5.29	0.74685	Dbl homology (DH) domain (5);	0.318671	0.31734	N	0.007150	T	0.42585	0.1209	N	0.01188	-0.97	0.32048	N	0.597275	P;P	0.48162	0.906;0.906	P;P	0.52109	0.69;0.69	T	0.53229	-0.8468	10	0.24483	T	0.36	-13.5783	11.6242	0.51136	1.0:0.0:0.0:0.0	.	583;583	D3DTR7;O94989	.;ARHGF_HUMAN	S	583;373;583	ENSP00000355026:N583S;ENSP00000412505:N583S	ENSP00000355026:N583S	N	+	2	0	ARHGEF15	8162473	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.286000	0.51724	1.999000	0.58509	0.454000	0.30748	AAT	.	.		0.617	ARHGEF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226993.2	NM_173728		G	8221748	A	G	8221748	3	3	254	1	0	0	0	0	1	0	0	0	898	101	4	2	1782	2	ARHGEF15	17	8221748	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	83588	8221748	72973462	811	35103										
NDEL1	81565	hgsc.bcm.edu	37	chr17	8347657	8347657	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgcttattggaaggaactttCcttgaagtataagcaaaggt	10	5	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:8347657C>A	ENST00000334527.7	+	2	265	c.68C>A	c.(67-69)tCc>tAc	p.S23Y	NDEL1_ENST00000380025.4_Missense_Mutation_p.S23Y|NDEL1_ENST00000585098.1_Missense_Mutation_p.S23Y|NDEL1_ENST00000402554.3_Missense_Mutation_p.S23Y|NDEL1_ENST00000583066.1_3'UTR|NDEL1_ENST00000299734.7_Missense_Mutation_p.S23Y	NM_030808.4	NP_110435.1	Q9GZM8	NDEL1_HUMAN	nudE neurodevelopment protein 1-like 1	23					activation of Cdc42 GTPase activity (GO:0032864)|central nervous system neuron axonogenesis (GO:0021955)|centrosome localization (GO:0051642)|cerebral cortex radially oriented cell migration (GO:0021799)|chromosome segregation (GO:0007059)|inner cell mass cell proliferation (GO:0001833)|mitotic cell cycle (GO:0000278)|mitotic centrosome separation (GO:0007100)|neurofilament cytoskeleton organization (GO:0060052)|neuron migration (GO:0001764)|neuron projection extension (GO:1990138)|nuclear envelope disassembly (GO:0051081)|positive regulation of axon extension (GO:0045773)|positive regulation of axon regeneration (GO:0048680)|retrograde axon cargo transport (GO:0008090)|vesicle transport along microtubule (GO:0047496)	axon hillock (GO:0043203)|cell leading edge (GO:0031252)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|neurofilament cytoskeleton (GO:0060053)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)	oligopeptidase activity (GO:0070012)			large_intestine(6)|lung(4)|skin(3)	13						AAGGAACTTTCCTTGAAGTAT	0.353																																					p.S23Y		Atlas-SNP	.											.	NDEL1	47	.	0			c.C68A						.						88	87	87					17																	8347657		2203	4300	6503	SO:0001583	missense	81565	exon2			AACTTTCCTTGAA	AF182078	CCDS11143.1, CCDS32564.1	17p13.1	2013-08-06	2013-08-06	2003-04-16	ENSG00000166579	ENSG00000166579			17620	protein-coding gene	gene with protein product		607538	"nudE nuclear distribution gene E homolog (A. nidulans)-like 1", "nudE nuclear distribution E homolog (A. nidulans)-like 1"			11163260, 11163259	Standard	NM_001025579		Approved	NUDEL, MITAP1, NDE1L1, NDE2	uc002glj.4	Q9GZM8	OTTHUMG00000108193	ENST00000334527.7:c.68C>A	chr17.hg19:g.8347657C>A	ENSP00000333982:p.Ser23Tyr	120.0	0.0		88.0	4.0	NM_001025579	B3KP93|D3DTS0|J3QT32|Q86T80|Q8TAR7|Q9UH50	Missense_Mutation	SNP	ENST00000334527.7	hg19	CCDS11143.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.169783	0.78452	.	.	ENSG00000166579	ENST00000299734;ENST00000380025;ENST00000402554;ENST00000334527	.	.	.	4.18	4.18	0.49190	.	0.126774	0.56097	D	0.000036	T	0.59810	0.2221	L	0.34521	1.04	0.80722	D	1	D;D	0.64830	0.994;0.994	P;P	0.59487	0.858;0.726	T	0.53450	-0.8437	9	0.11485	T	0.65	-1.654	16.7216	0.85411	0.0:1.0:0.0:0.0	.	23;23	Q9GZM8;A6NIZ0	NDEL1_HUMAN;.	Y	23;23;78;23	.	ENSP00000299734:S23Y	S	+	2	0	NDEL1	8288382	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.405000	0.80007	2.152000	0.67230	0.650000	0.86243	TCC	.	.		0.353	NDEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226999.2	NM_030808		A	8347657	C	A	8347657	3	1	254	1	0	0	0	0	1	0	0	0	10253	855	30	3	70	3	NDEL1	17	8347657	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	125909	8347657	72847553	812	35104										
ZNF18	7566	hgsc.bcm.edu	37	chr17	11896054	11896054	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcagggctggagagttcctcTtgaagggcagcatctgattc	13	9	3	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:11896054T>C	ENST00000322748.3	-	4	697	c.93A>G	c.(91-93)caA>caG	p.Q31Q	ZNF18_ENST00000454073.3_Silent_p.Q31Q|ZNF18_ENST00000580306.2_Silent_p.Q31Q	NM_144680.2	NP_653281.2	P17022	ZNF18_HUMAN	zinc finger protein 18	31					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)	14				Colorectal(4;3.33e-05)|COAD - Colon adenocarcinoma(4;0.000494)|READ - Rectum adenocarcinoma(10;0.233)		AGAGTTCCTCTTGAAGGGCAG	0.592																																					p.Q31Q		Atlas-SNP	.											.	ZNF18	42	.	0			c.A93G						.						76	72	73					17																	11896054		2203	4300	6503	SO:0001819	synonymous_variant	7566	exon4			TTCCTCTTGAAGG	X52342	CCDS32568.1	17p12	2013-01-09	2006-05-10		ENSG00000154957	ENSG00000154957		"Zinc fingers, C2H2-type", "-", "-", "-"	12969	protein-coding gene	gene with protein product		194524	"zinc finger protein 18 (KOX 11)"			15702252	Standard	XM_005256786		Approved	ZKSCAN6, KOX11, HDSG1, Zfp535, ZNF535, ZSCAN38	uc002gng.1	P17022	OTTHUMG00000178307	ENST00000322748.3:c.93A>G	chr17.hg19:g.11896054T>C		96.0	0.0		95.0	4.0	NM_144680	Q5QHQ3|Q8IYC4|Q8NAH6	Silent	SNP	ENST00000322748.3	hg19	CCDS32568.1																																																																																			.	.		0.592	ZNF18-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441450.2	XM_085596		C	11896054	T	C	11896054	2	2	254	1	0	0	0	0	0	0	0	1	17762	1606	56	2		2	ZNF18	17	11896054	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	3548397	11896054	69299156	813	35105										
TOM1L2	146691	hgsc.bcm.edu	37	chr17	17801962	17801962	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggttcccgttgagccgcttcTtcagggctcgaatggcatcc	12	13	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:17801962T>C	ENST00000379504.3	-	3	247	c.164A>G	c.(163-165)aAg>aGg	p.K55R	TOM1L2_ENST00000535933.1_Missense_Mutation_p.K55R|TOM1L2_ENST00000581396.1_Missense_Mutation_p.K55R|TOM1L2_ENST00000395739.4_Missense_Mutation_p.K55R|TOM1L2_ENST00000318094.10_Missense_Mutation_p.K55R|TOM1L2_ENST00000542206.1_Missense_Mutation_p.K55R|TOM1L2_ENST00000540946.1_Missense_Mutation_p.K55R	NM_001082968.1	NP_001076437.1	Q6ZVM7	TM1L2_HUMAN	target of myb1-like 2 (chicken)	55	VHS. {ECO:0000255|PROSITE- ProRule:PRU00218}.				intracellular protein transport (GO:0006886)|negative regulation of mitosis (GO:0045839)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	clathrin binding (GO:0030276)|protein kinase binding (GO:0019901)			endometrium(2)|kidney(2)|large_intestine(1)|lung(3)|prostate(2)	10	all_neural(463;0.228)					GAGCCGCTTCTTCAGGGCTCG	0.468																																					p.K55R	Melanoma(192;2505 2909 14455 25269)	Atlas-SNP	.											.	TOM1L2	54	.	0			c.A164G						.						144	115	125					17																	17801962		2203	4300	6503	SO:0001583	missense	146691	exon3			CGCTTCTTCAGGG	AJ230803	CCDS32584.1, CCDS42270.1, CCDS74000.1, CCDS74001.1, CCDS74002.1, CCDS74003.1	17p11.2	2008-07-03	2001-11-28		ENSG00000175662	ENSG00000175662			11984	protein-coding gene	gene with protein product		615519	"target of myb1 (chicken) homolog-like 1"			10036180	Standard	NM_001082968		Approved		uc002grz.4	Q6ZVM7	OTTHUMG00000059353	ENST00000379504.3:c.164A>G	chr17.hg19:g.17801962T>C	ENSP00000368818:p.Lys55Arg	314.0	1.0		295.0	119.0	NM_001033551	B7Z2L7|B7Z7F4|Q86V61|Q8TDE7|Q96M88	Missense_Mutation	SNP	ENST00000379504.3	hg19	CCDS42270.1	.	.	.	.	.	.	.	.	.	.	T	17.35	3.367733	0.61513	.	.	ENSG00000175662	ENST00000379504;ENST00000318094;ENST00000395739;ENST00000535933;ENST00000540946;ENST00000542206;ENST00000537091	T;T;T;T;T;T	0.23552	1.9;1.9;1.9;1.9;1.9;1.9	5.21	4.1	0.47936	VHS subgroup (1);ENTH/VHS (2);VHS (2);	0.089139	0.85682	D	0.000000	T	0.22936	0.0554	N	0.25647	0.755	0.24949	N	0.991804	B;B;B;B;P;B;P	0.36010	0.151;0.233;0.011;0.036;0.532;0.444;0.532	B;B;B;B;B;B;B	0.43680	0.17;0.389;0.01;0.033;0.427;0.262;0.281	T	0.12293	-1.0553	10	0.33141	T	0.24	-32.9027	11.3667	0.49677	0.0:0.0726:0.0:0.9274	.	55;55;55;55;55;55;55	B7Z8F0;B7Z2U2;F5H3S6;B7Z2L7;Q6ZVM7-3;Q6ZVM7;Q6ZVM7-2	.;.;.;.;.;TM1L2_HUMAN;.	R	55	ENSP00000368818:K55R;ENSP00000312860:K55R;ENSP00000379088:K55R;ENSP00000438621:K55R;ENSP00000437655:K55R;ENSP00000445188:K55R	ENSP00000312860:K55R	K	-	2	0	TOM1L2	17742687	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	3.315000	0.51951	2.198000	0.70561	0.533000	0.62120	AAG	.	.		0.468	TOM1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131928.1			C	17801962	T	C	17801962	3	2	254	1	0	0	0	0	1	0	0	0	16368	1609	56	2	1411	2	TOM1L2	17	17801962	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	5905908	17801962	63393248	814	35106										
ATPAF2	91647	hgsc.bcm.edu	37	chr17	17921898	17921898	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cttgtgcttgactgtggtgcTctcggagcagagatggatga	15	7	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:17921898T>C	ENST00000474627.3	-	8	989	c.835A>G	c.(835-837)Agc>Ggc	p.S279G	ATPAF2_ENST00000585101.1_Intron|ATPAF2_ENST00000469327.1_5'Flank	NM_145691.3	NP_663729.1	Q8N5M1	ATPF2_HUMAN	ATP synthase mitochondrial F1 complex assembly factor 2	279					proton-transporting ATP synthase complex assembly (GO:0043461)	mitochondrion (GO:0005739)|nuclear speck (GO:0016607)				breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|urinary_tract(1)	8	all_neural(463;0.228)					ACTGTGGTGCTCTCGGAGCAG	0.637																																					p.S279G		Atlas-SNP	.											.	ATPAF2	15	.	0			c.A835G						.						96	99	98					17																	17921898		2203	4300	6503	SO:0001583	missense	91647	exon8			TGGTGCTCTCGGA	AF052185	CCDS32585.1	17p11.2	2012-10-12			ENSG00000171953	ENSG00000171953		"Mitochondrial respiratory chain complex assembly factors"	18802	protein-coding gene	gene with protein product		608918				11410595, 11997338	Standard	NM_145691		Approved	Atp12p, ATP12, LP3663, MGC29736	uc002gse.1	Q8N5M1	OTTHUMG00000059354	ENST00000474627.3:c.835A>G	chr17.hg19:g.17921898T>C	ENSP00000417190:p.Ser279Gly	120.0	0.0		86.0	4.0	NM_145691	A6NDE5|A8K2J2|Q6XYC7	Missense_Mutation	SNP	ENST00000474627.3	hg19	CCDS32585.1	.	.	.	.	.	.	.	.	.	.	T	19.37	3.814834	0.70912	.	.	ENSG00000171953	ENST00000474627	T	0.78246	-1.16	5.16	5.16	0.70880	.	0.187046	0.64402	D	0.000002	T	0.77219	0.4098	M	0.70595	2.14	0.53005	D	0.99996	B	0.27853	0.191	B	0.26770	0.073	T	0.77370	-0.2613	10	0.62326	D	0.03	-30.7591	14.9951	0.71425	0.0:0.0:0.0:1.0	.	279	Q8N5M1	ATPF2_HUMAN	G	279	ENSP00000417190:S279G	ENSP00000417190:S279G	S	-	1	0	ATPAF2	17862623	1.000000	0.71417	0.996000	0.52242	0.974000	0.67602	7.945000	0.87732	1.947000	0.56498	0.459000	0.35465	AGC	.	.		0.637	ATPAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131934.3	NM_145691		C	17921898	T	C	17921898	3	2	254	1	0	0	0	0	1	0	0	0	1201	1551	54	2	38	2	ATPAF2	17	17921898	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	119936	17921898	63273312	815	35107										
RNF112	7732	hgsc.bcm.edu	37	chr17	19314770	19314770	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccttttgtcatcggcttggcAaacgggcaagtcttcagtcc	10	12	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:19314770A>G	ENST00000461366.1	+	1	264	c.49A>G	c.(49-51)Aaa>Gaa	p.K17E	CTB-187M2.2_ENST00000579897.1_RNA	NM_007148.4	NP_009079.2	Q9ULX5	RN112_HUMAN	ring finger protein 112	17						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|zinc ion binding (GO:0008270)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)|urinary_tract(1)	12						TCGGCTTGGCAAACGGGCAAG	0.652																																					p.K17E		Atlas-SNP	.											.	RNF112	37	.	0			c.A49G						.						39	40	40					17																	19314770		1893	4097	5990	SO:0001583	missense	7732	exon1			CTTGGCAAACGGG	AF054587	CCDS58529.1	17p11.2	2013-01-16	2008-06-13	2008-06-13	ENSG00000128482	ENSG00000128482		"RING-type (C3HC4) zinc fingers"	12968	protein-coding gene	gene with protein product		601237	"zinc finger protein 179"	ZNF179		8660987, 9806830	Standard	NM_007148		Approved	BFP	uc010vyw.2	Q9ULX5	OTTHUMG00000059601	ENST00000461366.1:c.49A>G	chr17.hg19:g.19314770A>G	ENSP00000454919:p.Lys17Glu	35.0	0.0		28.0	4.0	NM_007148	O60633|Q7Z5V9	Missense_Mutation	SNP	ENST00000461366.1	hg19	CCDS58529.1																																																																																			.	.		0.652	RNF112-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132549.4	NM_007148		G	19314770	A	G	19314770	3	3	254	1	0	0	0	0	1	0	0	0	13441	131	5	2	51	2	RNF112	17	19314770	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	1392872	19314770	61880440	816	35108										
SLC47A1	55244	hgsc.bcm.edu	37	chr17	19476161	19476161	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aattctgctctccctcaggaTccgcttcacccaggtaagat	7	14	4	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:19476161T>C	ENST00000270570.4	+	16	1559	c.1473T>C	c.(1471-1473)gaT>gaC	p.D491D	SLC47A1_ENST00000395585.1_Silent_p.D491D|SLC47A1_ENST00000457293.1_Silent_p.D491D|SLC47A1_ENST00000571335.1_Intron|SLC47A1_ENST00000575023.1_Silent_p.D189D|SLC47A1_ENST00000436810.2_Missense_Mutation_p.S437P|RP11-1113L8.1_ENST00000574267.1_RNA	NM_018242.2	NP_060712.2	Q96FL8	S47A1_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 1	491					organic cation transport (GO:0015695)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane-bounded vesicle (GO:0031988)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|monovalent cation:proton antiporter activity (GO:0005451)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(4)|lung(5)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	23	all_cancers(12;2.49e-05)|all_epithelial(12;0.00263)|Hepatocellular(7;0.00345)				Aciclovir(DB00787)|Bromodiphenhydramine(DB01237)|Cephalexin(DB00567)|Cimetidine(DB00501)|Metformin(DB00331)|Sirolimus(DB00877)	TCCCTCAGGATCCGCTTCACC	0.517																																					p.D491D		Atlas-SNP	.											.	SLC47A1	55	.	0			c.T1473C						.						111	95	100					17																	19476161		2203	4300	6503	SO:0001819	synonymous_variant	55244	exon16			TCAGGATCCGCTT		CCDS11209.1	17p11.2	2013-07-17	2013-07-17		ENSG00000142494	ENSG00000142494		"Solute carriers"	25588	protein-coding gene	gene with protein product	"multidrug and toxin extrusion 1"	609832				16330770, 16996621, 16928787	Standard	NM_018242		Approved	FLJ10847, MATE1	uc002gvy.1	Q96FL8	OTTHUMG00000059466	ENST00000270570.4:c.1473T>C	chr17.hg19:g.19476161T>C		110.0	0.0		100.0	4.0	NM_018242	Q53HF5|Q6PD77|Q86VL4|Q9NVA3	Silent	SNP	ENST00000270570.4	hg19	CCDS11209.1	.	.	.	.	.	.	.	.	.	.	T	11.94	1.787349	0.31593	.	.	ENSG00000142494	ENST00000436810	T	0.33216	1.42	5.04	-8.56	0.00904	.	.	.	.	.	T	0.16428	0.0395	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22417	-1.0217	8	0.33940	T	0.23	-9.0137	8.7303	0.34494	0.0:0.4564:0.3006:0.243	.	437	E7EX57	.	P	437	ENSP00000407155:S437P	ENSP00000407155:S437P	S	+	1	0	SLC47A1	19416753	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.713000	0.00816	-2.054000	0.00900	-1.431000	0.01090	TCC	.	.		0.517	SLC47A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132250.1	NM_018242		C	19476161	T	C	19476161	2	2	254	1	0	0	0	0	0	0	0	1	14662	1432	50	2		2	SLC47A1	17	19476161	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	161391	19476161	61719049	817	35109										
CYTSB	92521	hgsc.bcm.edu	37	chr17	20107661	20107661	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttaaggggcctttacaacaaCtaaacggacaggcattccag	9	10	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:20107661C>G	ENST00000261503.5	+	4	350	c.299C>G	c.(298-300)aCt>aGt	p.T100S	SPECC1_ENST00000584527.1_5'Flank|SPECC1_ENST00000395527.4_Missense_Mutation_p.T100S|SPECC1_ENST00000395525.3_Missense_Mutation_p.T19S|SPECC1_ENST00000536879.1_Intron|SPECC1_ENST00000395529.3_Missense_Mutation_p.T100S|SPECC1_ENST00000395522.2_Missense_Mutation_p.T19S|SPECC1_ENST00000395530.2_Missense_Mutation_p.T19S|SPECC1_ENST00000472876.1_Intron|AC004702.2_ENST00000580225.1_lincRNA	NM_001033553.2	NP_001028725.1	Q5M775	CYTSB_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1	100					cell adhesion (GO:0007155)	nucleus (GO:0005634)				breast(1)|large_intestine(3)|ovary(4)	8				KIRC - Kidney renal clear cell carcinoma(2;0.166)|Kidney(2;0.196)		TTTACAACAACTAAACGGACA	0.433																																					p.T100S		Atlas-SNP	.											.	SPECC1	100	.	0			c.C299G						.						140	153	148					17																	20107661		2203	4300	6503	SO:0001583	missense	92521	exon4			CAACAACTAAACG	AY816329, AB041533	CCDS32590.1, CCDS42280.1, CCDS42281.1, CCDS45628.1, CCDS58531.1	17p11.2	2012-11-19	2010-09-17	2010-09-17	ENSG00000128487	ENSG00000128487			30615	protein-coding gene	gene with protein product	"sperm antigen HCMOGT 1", "cytokinesis and spindle organization B", "cytospin B"	608793				15602574, 18763323, 15087372	Standard	NM_001033553		Approved	HCMOGT-1, FLJ36955, NSP, CYTSB	uc002gwq.3	Q5M775	OTTHUMG00000179808	ENST00000261503.5:c.299C>G	chr17.hg19:g.20107661C>G	ENSP00000261503:p.Thr100Ser	102.0	0.0		63.0	26.0	NM_001033553	B4DHH0|B7WNS8|Q5IBP1|Q5IBP2|Q5IBP3|Q5IBP4|Q5M772|Q5M773|Q5M774|Q86XT8|Q8N4U4|Q8WU84|Q9HCQ3	Missense_Mutation	SNP	ENST00000261503.5	hg19	CCDS32590.1	.	.	.	.	.	.	.	.	.	.	C	12.08	1.829683	0.32329	.	.	ENSG00000128487	ENST00000395530;ENST00000261503;ENST00000395529;ENST00000395522;ENST00000395527;ENST00000395525	T;T;T;T	0.62364	0.03;2.97;2.92;2.92	5.13	5.13	0.70059	.	0.379873	0.32244	N	0.006373	T	0.49423	0.1556	L	0.28115	0.83	0.80722	D	1	B;B;B;B	0.21381	0.035;0.035;0.035;0.055	B;B;B;B	0.20955	0.02;0.032;0.032;0.015	T	0.40831	-0.9542	10	0.19590	T	0.45	-6.8572	16.4284	0.83832	0.0:1.0:0.0:0.0	.	19;19;100;100	Q5M775-4;Q5M775-3;Q5M775-2;Q5M775	.;.;.;CYTSB_HUMAN	S	100;100;100;19;19;19	ENSP00000261503:T100S;ENSP00000378900:T100S;ENSP00000378893:T19S;ENSP00000378896:T19S	ENSP00000261503:T100S	T	+	2	0	SPECC1	20048253	0.011000	0.17503	0.744000	0.31058	0.874000	0.50279	0.888000	0.28268	2.558000	0.86282	0.591000	0.81541	ACT	.	.		0.433	SPECC1-018	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441206.1	NM_152904		G	20107661	C	G	20107661	3	3	254	1	0	0	0	0	1	0	0	0	4212	565	20	4	353	4	CYTSB	17	20107661	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	631500	20107661	61087549	818	35110										
SPAG5	10615	hgsc.bcm.edu	37	chr17	26907029	26907029	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aatcccagggcctttaacctTcatctgccactgctgtcaag	7	14	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:26907029T>C	ENST00000321765.5	-	16	3127	c.2795A>G	c.(2794-2796)gAa>gGa	p.E932G	ALDOC_ENST00000226253.4_5'Flank	NM_006461.3	NP_006452.3	Q96R06	SPAG5_HUMAN	sperm associated antigen 5	932					chromosome segregation (GO:0007059)|mitotic sister chromatid segregation (GO:0000070)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|microtubule plus-end (GO:0035371)|mitotic spindle (GO:0072686)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43	Lung NSC(42;0.00431)					CCTTTAACCTTCATCTGCCAC	0.542																																					p.E932G		Atlas-SNP	.											.	SPAG5	92	.	0			c.A2795G						.						78	57	64					17																	26907029		2203	4300	6503	SO:0001583	missense	10615	exon16			TAACCTTCATCTG	AF063308	CCDS32594.1	17q11.2	2008-07-18			ENSG00000076382	ENSG00000076382			13452	protein-coding gene	gene with protein product	"mitotic spindle coiled-coil related protein", "astrin", "mitotic spindle associated protein p126"	615562				11549262	Standard	NM_006461		Approved	DEEPEST, MAP126, hMAP126	uc002hbq.3	Q96R06	OTTHUMG00000166586	ENST00000321765.5:c.2795A>G	chr17.hg19:g.26907029T>C	ENSP00000323300:p.Glu932Gly	134.0	0.0		140.0	6.0	NM_006461	O95213|Q9BWE8|Q9NT17|Q9UFE6	Missense_Mutation	SNP	ENST00000321765.5	hg19	CCDS32594.1	.	.	.	.	.	.	.	.	.	.	t	17.84	3.487710	0.64074	.	.	ENSG00000076382	ENST00000321765	T	0.35973	1.28	6.04	4.78	0.61160	.	0.100234	0.43919	D	0.000504	T	0.36276	0.0961	N	0.24115	0.695	0.41174	D	0.986189	D	0.59357	0.985	P	0.56612	0.802	T	0.18618	-1.0331	10	0.62326	D	0.03	-1.4794	8.6759	0.34179	0.0:0.0954:0.0:0.9046	.	932	Q96R06	SPAG5_HUMAN	G	932	ENSP00000323300:E932G	ENSP00000323300:E932G	E	-	2	0	SPAG5	23931156	0.990000	0.36364	0.999000	0.59377	0.894000	0.52154	2.412000	0.44609	2.319000	0.78375	0.524000	0.50904	GAA	.	.		0.542	SPAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390564.2	NM_006461		C	26907029	T	C	26907029	3	2	254	1	0	0	0	0	1	0	0	0	14996	1783	62	2	822	2	SPAG5	17	26907029	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	6799368	26907029	54288181	819	35111										
SUPT6H	6830	hgsc.bcm.edu	37	chr17	27022398	27022398	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gactgttcactgccgcatcaTgaagattgacattgagaagt	10	8	2	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:27022398T>C	ENST00000314616.6	+	29	4086	c.3803T>C	c.(3802-3804)aTg>aCg	p.M1268T	SUPT6H_ENST00000347486.4_Missense_Mutation_p.M1268T	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	1268	Interaction with KDM6A. {ECO:0000250}.|S1 motif. {ECO:0000255|PROSITE- ProRule:PRU00180}.				chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					TGCCGCATCATGAAGATTGAC	0.493																																					p.M1268T		Atlas-SNP	.											.	SUPT6H	165	.	0			c.T3803C						.						121	90	100					17																	27022398		2203	4300	6503	SO:0001583	missense	6830	exon29			GCATCATGAAGAT	U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"SH2 domain containing"	11470	protein-coding gene	gene with protein product		601333	"suppressor of Ty (S.cerevisiae) 6 homolog"			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85		ENST00000314616.6:c.3803T>C	chr17.hg19:g.27022398T>C	ENSP00000319104:p.Met1268Thr	113.0	0.0		158.0	7.0	NM_003170	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Missense_Mutation	SNP	ENST00000314616.6	hg19	CCDS32596.1	.	.	.	.	.	.	.	.	.	.	T	11.72	1.723610	0.30593	.	.	ENSG00000109111	ENST00000314616	T	0.38401	1.14	5.59	5.59	0.84812	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);RNA-binding domain, S1 (1);Ribosomal protein S1, RNA-binding domain (2);	0.000000	0.85682	D	0.000000	T	0.20292	0.0488	N	0.05050	-0.12	0.80722	D	1	B	0.20887	0.049	B	0.22880	0.042	T	0.10520	-1.0626	10	0.15499	T	0.54	-19.2578	15.7706	0.78164	0.0:0.0:0.0:1.0	.	1268	Q7KZ85	SPT6H_HUMAN	T	1268	ENSP00000319104:M1268T	ENSP00000319104:M1268T	M	+	2	0	SUPT6H	24046525	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.603000	0.82811	2.123000	0.65237	0.533000	0.62120	ATG	.	.		0.493	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170		C	27022398	T	C	27022398	3	2	254	1	0	0	0	0	1	0	0	0	15415	1464	51	2	3913	2	SUPT6H	17	27022398	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	115369	27022398	54172812	820	35112										
SUPT6H	6830	hgsc.bcm.edu	37	chr17	27027431	27027431	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	atgttcagtgccattgctgcGgtgacaggccaaggacagaa	13	9	1	2	rs373264371		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:27027431G>T	ENST00000314616.6	+	35	4990	c.4707G>T	c.(4705-4707)gcG>gcT	p.A1569A	SUPT6H_ENST00000347486.4_Silent_p.A1569A	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	1569					chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					CCATTGCTGCGGTGACAGGCC	0.597																																					p.A1569A		Atlas-SNP	.											.	SUPT6H	165	.	0			c.G4707T						.						121	111	114					17																	27027431		2203	4300	6503	SO:0001819	synonymous_variant	6830	exon35			TGCTGCGGTGACA	U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"SH2 domain containing"	11470	protein-coding gene	gene with protein product		601333	"suppressor of Ty (S.cerevisiae) 6 homolog"			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85		ENST00000314616.6:c.4707G>T	chr17.hg19:g.27027431G>T		86.0	0.0		94.0	4.0	NM_003170	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Silent	SNP	ENST00000314616.6	hg19	CCDS32596.1																																																																																			.	.		0.597	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170		T	27027431	G	T	27027431	2	4	254	1	0	0	0	0	0	0	0	1	15415	1103	39	1		1	SUPT6H	17	27027431	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	5033	27027431	54167779	821	35113										
MYO18A	399687	hgsc.bcm.edu	37	chr17	27438814	27438814	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgtcctcactggcccctggcAccagagcctcctcttccaat	7	18	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:27438814A>G	ENST00000527372.1	-	16	2846	c.2666T>C	c.(2665-2667)gTg>gCg	p.V889A	MYO18A_ENST00000533112.1_Missense_Mutation_p.V889A|MYO18A_ENST00000531253.1_Missense_Mutation_p.V889A|MYO18A_ENST00000354329.4_Missense_Mutation_p.V889A	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	889	Myosin motor.				actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			GGCCCCTGGCACCAGAGCCTC	0.592											OREG0024287	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V889A	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-SNP	.											.	MYO18A	217	.	0			c.T2666C						.						40	45	44					17																	27438814		1880	4101	5981	SO:0001583	missense	399687	exon16			CCTGGCACCAGAG	D86970	CCDS45641.1, CCDS45642.1	17q11.2	2011-09-27			ENSG00000196535	ENSG00000196535		"Myosins / Myosin superfamily : Class XVIII"	31104	protein-coding gene	gene with protein product		610067				12761286	Standard	NM_078471		Approved	KIAA0216, MysPDZ	uc002hdt.1	Q92614	OTTHUMG00000166360	ENST00000527372.1:c.2666T>C	chr17.hg19:g.27438814A>G	ENSP00000437073:p.Val889Ala	81.0	0.0	794	68.0	4.0	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Missense_Mutation	SNP	ENST00000527372.1	hg19	CCDS45642.1	.	.	.	.	.	.	.	.	.	.	A	17.17	3.320411	0.60634	.	.	ENSG00000196535	ENST00000354329;ENST00000359450;ENST00000533112;ENST00000531253;ENST00000527372;ENST00000458428	T;T;T;T	0.71817	-0.6;-0.6;-0.6;-0.6	5.42	5.42	0.78866	Myosin head, motor domain (2);	0.113719	0.64402	D	0.000015	T	0.64681	0.2620	M	0.64404	1.975	0.39114	D	0.961534	B;P;B;P;P	0.36837	0.046;0.571;0.205;0.571;0.473	B;B;B;B;B	0.33846	0.015;0.085;0.078;0.085;0.171	T	0.69826	-0.5040	10	0.54805	T	0.06	.	9.1803	0.37138	0.7227:0.0:0.0:0.2773	.	558;501;889;889;889	Q92614-2;F8W6Y3;Q92614-3;Q92614-4;Q92614	.;.;.;.;MY18A_HUMAN	A	889;889;889;889;889;501	ENSP00000346291:V889A;ENSP00000435932:V889A;ENSP00000434228:V889A;ENSP00000437073:V889A	ENSP00000346291:V889A	V	-	2	0	MYO18A	24462940	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.178000	0.65037	2.052000	0.61016	0.533000	0.62120	GTG	.	.		0.592	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471		G	27438814	A	G	27438814	3	3	254	1	0	0	0	0	1	0	0	0	10074	159	6	2	3606	2	MYO18A	17	27438814	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	411383	27438814	53756396	822	35114										
CRYBA1	1411	hgsc.bcm.edu	37	chr17	27580737	27580737	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggagatctctgacgactaccCctccttgcaagccatgggct	10	14	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:27580737C>T	ENST00000225387.3	+	5	438	c.437C>T	c.(436-438)cCc>cTc	p.P146L		NM_005208.4	NP_005199.2	P05813	CRBA1_HUMAN	crystallin, beta A1	146	Beta/gamma crystallin 'Greek key' 3. {ECO:0000255|PROSITE-ProRule:PRU00028}.				lens development in camera-type eye (GO:0002088)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	structural constituent of eye lens (GO:0005212)			breast(1)|large_intestine(2)|lung(1)|prostate(1)	5			BRCA - Breast invasive adenocarcinoma(11;3.3e-05)|Colorectal(6;0.0178)|COAD - Colon adenocarcinoma(6;0.0551)			GACGACTACCCCTCCTTGCAA	0.428																																					p.P146L		Atlas-SNP	.											.	CRYBA1	15	.	0			c.C437T						.						84	83	84					17																	27580737		2203	4300	6503	SO:0001583	missense	1411	exon5			ACTACCCCTCCTT		CCDS11249.1	17q11.2-q12	2008-07-18			ENSG00000108255	ENSG00000108255			2394	protein-coding gene	gene with protein product	"eye lens structural protein"	123610		CRYB1		3745196, 3770741	Standard	NM_005208		Approved		uc002hdw.3	P05813	OTTHUMG00000132729	ENST00000225387.3:c.437C>T	chr17.hg19:g.27580737C>T	ENSP00000225387:p.Pro146Leu	123.0	0.0		162.0	27.0	NM_005208	Q13633|Q14CM9	Missense_Mutation	SNP	ENST00000225387.3	hg19	CCDS11249.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.815854	0.90790	.	.	ENSG00000108255	ENST00000225387	T	0.78126	-1.15	5.43	4.45	0.53987	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.000000	0.85682	D	0.000000	D	0.88415	0.6430	M	0.84948	2.725	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89672	0.3884	10	0.62326	D	0.03	.	14.2229	0.65839	0.0:0.9255:0.0:0.0745	.	146	P05813	CRBA1_HUMAN	L	146	ENSP00000225387:P146L	ENSP00000225387:P146L	P	+	2	0	CRYBA1	24604863	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	5.686000	0.68211	2.538000	0.85594	0.491000	0.48974	CCC	.	.		0.428	CRYBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256071.2	NM_005208		T	27580737	C	T	27580737	3	4	254	1	0	0	0	0	1	0	0	0	3909	623	22	3	455	3	CRYBA1	17	27580737	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	141923	27580737	53614473	823	35115										
ANKRD13B	124930	hgsc.bcm.edu	37	chr17	27920706	27920706	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	atccgctgcactacctcgtgTggcacaaccgccaccgcgag	10	17	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:27920706T>C	ENST00000394859.3	+	1	221	c.67T>C	c.(67-69)Tgg>Cgg	p.W23R	RP11-68I3.7_ENST00000584986.1_RNA|RP11-68I3.2_ENST00000581474.1_RNA	NM_152345.4	NP_689558.4	Q86YJ7	AN13B_HUMAN	ankyrin repeat domain 13B	23						endosome (GO:0005768)|plasma membrane (GO:0005886)				cervix(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(2)	16						CTACCTCGTGTGGCACAACCG	0.766																																					p.W23R		Atlas-SNP	.											.	ANKRD13B	39	.	0			c.T67C						.						5	6	6					17																	27920706		1909	3777	5686	SO:0001583	missense	124930	exon1			CTCGTGTGGCACA	AK092673	CCDS11251.1	17q11.2	2013-01-10			ENSG00000198720	ENSG00000198720		"Ankyrin repeat domain containing"	26363	protein-coding gene	gene with protein product		615124					Standard	NM_152345		Approved	FLJ25555	uc002hei.3	Q86YJ7	OTTHUMG00000132731	ENST00000394859.3:c.67T>C	chr17.hg19:g.27920706T>C	ENSP00000378328:p.Trp23Arg	95.0	0.0		97.0	4.0	NM_152345	Q8N7S9	Missense_Mutation	SNP	ENST00000394859.3	hg19	CCDS11251.1	.	.	.	.	.	.	.	.	.	.	T	17.07	3.296019	0.60086	.	.	ENSG00000198720	ENST00000394859	T	0.68903	-0.36	3.77	3.77	0.43336	Ankyrin repeat-containing domain (4);	0.135392	0.53938	D	0.000052	T	0.57051	0.2027	N	0.20357	0.565	0.58432	D	0.999994	P	0.35348	0.496	B	0.43728	0.429	T	0.62402	-0.6862	10	0.87932	D	0	-11.1939	10.1105	0.42559	0.0:0.0:0.0:1.0	.	23	Q86YJ7	AN13B_HUMAN	R	23	ENSP00000378328:W23R	ENSP00000378328:W23R	W	+	1	0	ANKRD13B	24944832	1.000000	0.71417	1.000000	0.80357	0.283000	0.27025	4.740000	0.62087	1.570000	0.49709	0.147000	0.16070	TGG	.	.		0.766	ANKRD13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256077.1	NM_152345		C	27920706	T	C	27920706	3	2	254	1	0	0	0	0	1	0	0	0	642	1696	59	2	69	2	ANKRD13B	17	27920706	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	339969	27920706	53274504	824	35116										
ATAD5	79915	hgsc.bcm.edu	37	chr17	29192785	29192785	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcagactgccagtgaacttaTaggaaatgagttagctataa	9	6	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:29192785T>C	ENST00000321990.4	+	11	3578	c.3200T>C	c.(3199-3201)aTa>aCa	p.I1067T	CTD-2349P21.11_ENST00000580873.1_RNA|RP13-753N3.1_ENST00000584157.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	1067					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				AGTGAACTTATAGGAAATGAG	0.303																																					p.I1067T		Atlas-SNP	.											.	ATAD5	150	.	0			c.T3200C						.						75	76	76					17																	29192785		2203	4292	6495	SO:0001583	missense	79915	exon11			AACTTATAGGAAA		CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"ATPases / AAA-type"	25752	protein-coding gene	gene with protein product	"enhanced level of genomic instability 1 homolog (S. cerevisiae)"	609534	"chromosome 17 open reading frame 41"	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.3200T>C	chr17.hg19:g.29192785T>C	ENSP00000313171:p.Ile1067Thr	279.0	0.0		229.0	68.0	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	hg19	CCDS11260.1	.	.	.	.	.	.	.	.	.	.	T	13.50	2.254797	0.39896	.	.	ENSG00000176208	ENST00000321990	T	0.20463	2.07	5.18	5.18	0.71444	.	0.292105	0.37348	N	0.002125	T	0.29588	0.0738	M	0.75615	2.305	0.40062	D	0.975905	B;B	0.30727	0.292;0.19	B;B	0.32022	0.139;0.035	T	0.17289	-1.0374	10	0.87932	D	0	.	15.1186	0.72423	0.0:0.0:0.0:1.0	.	1067;1067	Q96QE3-2;Q96QE3	.;ATAD5_HUMAN	T	1067	ENSP00000313171:I1067T	ENSP00000313171:I1067T	I	+	2	0	ATAD5	26216911	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	7.186000	0.77722	1.970000	0.57323	0.529000	0.55759	ATA	.	.		0.303	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857		C	29192785	T	C	29192785	3	2	254	1	0	0	0	0	1	0	0	0	1076	1406	49	2	3242	2	ATAD5	17	29192785	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	1272079	29192785	52002425	825	35117										
SPACA3	124912	hgsc.bcm.edu	37	chr17	31323887	31323887	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gccttgcttatttcacaagcGgtttcaacgcagctgctttg	9	11	2	0	rs548141074		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:31323887G>T	ENST00000269053.3	+	3	440	c.370G>T	c.(370-372)Ggt>Tgt	p.G124C	SPACA3_ENST00000394637.2_3'UTR|SPACA3_ENST00000394638.1_Missense_Mutation_p.G21C|SPACA3_ENST00000580599.1_Missense_Mutation_p.G55C	NM_173847.3	NP_776246.1	Q8IXA5	SACA3_HUMAN	sperm acrosome associated 3	124					cell wall macromolecule catabolic process (GO:0016998)|defense response to Gram-positive bacterium (GO:0050830)|monocyte activation (GO:0042117)|peptidoglycan catabolic process (GO:0009253)|positive regulation of macrophage activation (GO:0043032)|positive regulation of phagocytosis (GO:0050766)|response to virus (GO:0009615)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|secretory granule (GO:0030141)	lysozyme activity (GO:0003796)			breast(1)|endometrium(1)|large_intestine(3)|lung(10)|ovary(2)|urinary_tract(1)	18			BRCA - Breast invasive adenocarcinoma(9;0.193)			TTTCACAAGCGGTTTCAACGC	0.582																																					p.G124C		Atlas-SNP	.											.	SPACA3	35	.	0			c.G370T						.						105	94	98					17																	31323887		2203	4300	6503	SO:0001583	missense	124912	exon3			ACAAGCGGTTTCA	AF216311, AF099029	CCDS11275.1	17q12	2014-07-23			ENSG00000141316	ENSG00000141316			16260	protein-coding gene	gene with protein product	"cancer/testis antigen 54", "sperm lyzozyme-like acrosomal protein 1"	612749				12606493	Standard	NM_173847		Approved	ALLP17, SLLP1, LYC3, LYZL3, CT54	uc002hhs.1	Q8IXA5	OTTHUMG00000132886	ENST00000269053.3:c.370G>T	chr17.hg19:g.31323887G>T	ENSP00000269053:p.Gly124Cys	141.0	0.0		123.0	5.0	NM_173847	Q7Z4Y5	Missense_Mutation	SNP	ENST00000269053.3	hg19	CCDS11275.1	.	.	.	.	.	.	.	.	.	.	G	14.20	2.464729	0.43736	.	.	ENSG00000141316	ENST00000269053;ENST00000394638;ENST00000394637;ENST00000411740	T;T	0.78126	-1.15;-1.15	4.59	3.62	0.41486	Lysozyme-like domain (1);	0.112963	0.42821	D	0.000642	D	0.88876	0.6556	M	0.92970	3.365	0.35113	D	0.766342	D	0.89917	1.0	D	0.85130	0.997	D	0.91633	0.5320	10	0.87932	D	0	-6.5689	8.2126	0.31492	0.108:0.0:0.892:0.0	.	124	Q8IXA5	SACA3_HUMAN	C	124;21;125;32	ENSP00000269053:G124C;ENSP00000378134:G21C	ENSP00000269053:G124C	G	+	1	0	SPACA3	28348000	1.000000	0.71417	0.955000	0.39395	0.345000	0.29048	1.265000	0.33027	1.148000	0.42385	0.448000	0.29417	GGT	.	.		0.582	SPACA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256380.1	NM_173847		T	31323887	G	T	31323887	3	4	254	1	0	0	0	0	1	0	0	0	14988	1116	39	1	380	1	SPACA3	17	31323887	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	2131102	31323887	49871323	826	35118										
RAD51L3	5892	hgsc.bcm.edu	37	chr17	33445530	33445530	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	acacacaaacctgccaatgcCagtggacaggatggcagtgg	12	11	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:33445530C>A	ENST00000345365.6	-	3	508	c.253G>T	c.(253-255)Ggc>Tgc	p.G85C	RAD51D_ENST00000335858.7_Intron|RAD51D_ENST00000590016.1_Intron|RAD51D_ENST00000394589.4_Missense_Mutation_p.G85C|RAD51L3-RFFL_ENST00000593039.1_Intron|RAD51D_ENST00000360276.3_Missense_Mutation_p.G85C|RAD51D_ENST00000357906.3_Missense_Mutation_p.G85C|RAD51D_ENST00000460118.2_5'UTR|RAD51D_ENST00000590380.1_Intron	NM_002878.3	NP_002869.3	O75771	RA51D_HUMAN	RAD51 paralog D	85					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|reciprocal meiotic recombination (GO:0007131)|strand invasion (GO:0042148)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Rad51B-Rad51C-Rad51D-XRCC2 complex (GO:0033063)|replication fork (GO:0005657)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|gamma-tubulin binding (GO:0043015)|single-stranded DNA binding (GO:0003697)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|liver(1)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						CTGCCAATGCCAGTGGACAGG	0.577								Direct reversal of damage																													p.G85C		Atlas-SNP	.											.	RAD51D	53	.	0			c.G253T						.						83	86	85					17																	33445530		2203	4300	6503	SO:0001583	missense	5892	exon3			CAATGCCAGTGGA	AF034956	CCDS11287.1, CCDS11288.1, CCDS45646.1	17q11	2014-09-17	2013-07-02	2011-07-01	ENSG00000185379	ENSG00000185379			9823	protein-coding gene	gene with protein product	"recombination repair protein", "DNA repair protein RAD51 homolog 4"	602954	"RAD51 (S. cerevisiae)-like 3", "RAD51-like 3 (S. cerevisiae)", "RAD51 homolog D (S. cerevisiae)"	RAD51L3		9570954	Standard	NM_001142571		Approved	R51H3, Trad, HsTRAD	uc010ctj.2	O75771	OTTHUMG00000132930	ENST00000345365.6:c.253G>T	chr17.hg19:g.33445530C>A	ENSP00000338790:p.Gly85Cys	62.0	0.0		79.0	4.0	NM_002878	B4DJU7|E1P637|O43537|O60355|O75196|O75847|O75848|O76073|O76085|O94908|Q9UFU5	Missense_Mutation	SNP	ENST00000345365.6	hg19	CCDS11287.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.349456	0.82132	.	.	ENSG00000185379	ENST00000345365;ENST00000335858;ENST00000360276;ENST00000418935;ENST00000415064;ENST00000357906	T;T;T	0.76060	-0.11;-0.99;-0.92	4.79	4.79	0.61399	DNA recombination/repair protein RecA/RadB, ATP-binding domain (1);DNA recombination and repair protein Rad51, C-terminal (1);	0.104572	0.64402	D	0.000004	D	0.89104	0.6620	M	0.94021	3.485	0.53005	D	0.999967	D	0.89917	1.0	D	0.77557	0.99	D	0.91691	0.5366	10	0.87932	D	0	.	14.6952	0.69115	0.0:1.0:0.0:0.0	.	85	O75771	RA51D_HUMAN	C	85;85;85;85;88;85	ENSP00000338790:G85C;ENSP00000353417:G85C;ENSP00000350581:G85C	ENSP00000338408:G85C	G	-	1	0	RAD51D	30469643	1.000000	0.71417	0.512000	0.27736	0.992000	0.81027	4.690000	0.61731	2.499000	0.84300	0.555000	0.69702	GGC	.	.		0.577	RAD51D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256446.1	NM_002878		A	33445530	C	A	33445530	3	1	254	1	0	0	0	0	1	0	0	0	13005	594	21	3	948	3	RAD51L3	17	33445530	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	2121643	33445530	47749680	827	35119										
TAF15	8148	hgsc.bcm.edu	37	chr17	34171487	34171487	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tttctaccttgcagatttccGggggagaggctacggtggag	15	8	1	2	rs71381481	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:34171487G>T	ENST00000588240.1	+	15	1299	c.1184G>T	c.(1183-1185)cGg>cTg	p.R395L	TAF15_ENST00000311979.3_Missense_Mutation_p.R392L|TAF15_ENST00000592237.1_Missense_Mutation_p.R304L	NM_003487.3|NM_139215.2	NP_003478.1|NP_631961.1	Q16514	TAF12_HUMAN	TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa	33					chromatin organization (GO:0006325)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of RNA biosynthetic process (GO:2001141)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)		TAF15/NR4A3(33)	lung(1)|ovary(1)|skin(2)|stomach(1)	5		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		GCAGATTTCCGGGGGAGAGGC	0.542			T	"TEC, CHN1, ZNF384"	"extraskeletal myxoid chondrosarcomas, ALL"																																p.R395L		Atlas-SNP	.		Dom	yes		17	17q11.1-q11.2	8148	"TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa"		"L, M"	.	TAF15	46	.	0			c.G1184T						.						108	120	116					17																	34171487		2202	4299	6501	SO:0001583	missense	8148	exon15			ATTTCCGGGGGAG	U51334	CCDS32623.1, CCDS59279.1	17q11.1-q11.2	2013-02-12	2002-08-29	2001-12-07		ENSG00000270647		"RNA binding motif (RRM) containing"	11547	protein-coding gene	gene with protein product		601574	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, N, 68kD (RNA-binding protein 56)"	TAF2N		8954779, 9795213	Standard	NM_003487		Approved	hTAFII68, RBP56, Npl3	uc002hkd.4	Q92804		ENST00000588240.1:c.1184G>T	chr17.hg19:g.34171487G>T	ENSP00000466950:p.Arg395Leu	158.0	0.0		182.0	8.0	NM_139215	D3DPM5|Q15775|Q5T077	Missense_Mutation	SNP	ENST00000588240.1	hg19	CCDS32623.1	.	.	.	.	.	.	.	.	.	.	G	14.43	2.532489	0.45073	.	.	ENSG00000172660	ENST00000311979;ENST00000536077	.	.	.	4.84	3.86	0.44501	.	.	.	.	.	T	0.33059	0.0850	N	0.08118	0	0.40380	D	0.979438	P;P	0.38300	0.492;0.626	B;B	0.38712	0.145;0.28	T	0.33701	-0.9858	8	0.49607	T	0.09	-5.036	11.3543	0.49607	0.093:0.0:0.907:0.0	.	395;392	Q92804;Q92804-2	RBP56_HUMAN;.	L	395;198	.	ENSP00000309558:R395L	R	+	2	0	TAF15	31195600	1.000000	0.71417	1.000000	0.80357	0.446000	0.32137	3.369000	0.52365	2.249000	0.74217	0.591000	0.81541	CGG	.	G|0.999;A|0.001		0.542	TAF15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449134.1	NM_139215		T	34171487	G	T	34171487	3	4	254	1	0	0	0	0	1	0	0	0	15533	1116	39	1	1242	1	TAF15	17	34171487	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	725957	34171487	47023723	828	35120										
ERBB2	2064	hgsc.bcm.edu	37	chr17	37872839	37872839	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtgtcagccccagaatggctCagtgacctgttttggaccgg	13	11	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:37872839C>A	ENST00000269571.5	+	14	1877	c.1718C>A	c.(1717-1719)tCa>tAa	p.S573*	ERBB2_ENST00000406381.2_Nonsense_Mutation_p.S543*|ERBB2_ENST00000540042.1_Nonsense_Mutation_p.S543*|ERBB2_ENST00000584601.1_Nonsense_Mutation_p.S543*|ERBB2_ENST00000445658.2_Nonsense_Mutation_p.S297*|ERBB2_ENST00000578199.1_Nonsense_Mutation_p.S543*|ERBB2_ENST00000541774.1_Nonsense_Mutation_p.S558*|ERBB2_ENST00000540147.1_Nonsense_Mutation_p.S543*|ERBB2_ENST00000584450.1_Nonsense_Mutation_p.S573*			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	573					axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)	p.S573L(1)		NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	CAGAATGGCTCAGTGACCTGT	0.637		1	"A, Mis, O"		"breast, ovarian, other tumour types, NSCLC, gastric"					TCGA GBM(5;<1E-08)																											p.S573X		Atlas-SNP	.		Dom	yes		17	17q21.1	2064	"v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"		E	ERBB2,bladder,carcinoma,0,1	ERBB2	429	.	1	Substitution - Missense(1)	urinary_tract(1)	c.C1718A						.						68	58	61					17																	37872839		2203	4300	6503	SO:0001587	stop_gained	2064	exon14			ATGGCTCAGTGAC	X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"CD molecules"	3430	protein-coding gene	gene with protein product	"neuro/glioblastoma derived oncogene homolog"	164870	"v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.1718C>A	chr17.hg19:g.37872839C>A	ENSP00000269571:p.Ser573*	132.0	0.0		73.0	4.0	NM_004448	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Nonsense_Mutation	SNP	ENST00000269571.5	hg19	CCDS32642.1	.	.	.	.	.	.	.	.	.	.	C	41	8.694728	0.98918	.	.	ENSG00000141736	ENST00000406381;ENST00000541774;ENST00000445658;ENST00000269571;ENST00000540147;ENST00000540042	.	.	.	5.93	5.93	0.95920	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08179	T	0.78	.	18.9076	0.92469	0.0:1.0:0.0:0.0	.	.	.	.	X	543;558;297;573;543;543	.	ENSP00000269571:S573X	S	+	2	0	ERBB2	35126365	0.992000	0.36948	0.973000	0.42090	0.981000	0.71138	3.052000	0.49893	2.815000	0.96918	0.561000	0.74099	TCA	.	.		0.637	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2			A	37872839	C	A	37872839	4	1	254	1	0	0	0	0	0	1	0	0	5208	838	29	3	1772	3	ERBB2	17	37872839	Nonsense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	3701352	37872839	43322371	829	35121										
NR1D1	9572	hgsc.bcm.edu	37	chr17	38252091	38252091	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cctgggatatcacatcctccActgtgggctcagggcttggg	13	12	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:38252091A>G	ENST00000246672.3	-	5	1484	c.854T>C	c.(853-855)gTg>gCg	p.V285A		NM_021724.3	NP_068370.1	P20393	NR1D1_HUMAN	nuclear receptor subfamily 1, group D, member 1	285	Ligand-binding.				cell differentiation (GO:0030154)|cellular response to lipopolysaccharide (GO:0071222)|circadian regulation of gene expression (GO:0032922)|circadian temperature homeostasis (GO:0060086)|gene expression (GO:0010467)|glycogen biosynthetic process (GO:0005978)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of receptor biosynthetic process (GO:0010871)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of bile acid biosynthetic process (GO:0070859)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasomal protein catabolic process (GO:0010498)|regulation of cholesterol homeostasis (GO:2000188)|regulation of circadian rhythm (GO:0042752)|regulation of fat cell differentiation (GO:0045598)|regulation of gluconeogenesis by regulation of transcription from RNA polymerase II promoter (GO:0035947)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of lipid metabolic process (GO:0019216)|regulation of type B pancreatic cell proliferation (GO:0061469)|response to leptin (GO:0044321)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|heme binding (GO:0020037)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|steroid hormone receptor activity (GO:0003707)|transcription corepressor activity (GO:0003714)|transcription corepressor binding (GO:0001222)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(5)|lung(2)|skin(1)|upper_aerodigestive_tract(2)	11	Colorectal(19;0.000442)					CACATCCTCCACTGTGGGCTC	0.627																																					p.V285A		Atlas-SNP	.											.	NR1D1	45	.	0			c.T854C						.						52	47	48					17																	38252091		2203	4300	6503	SO:0001583	missense	9572	exon5			TCCTCCACTGTGG	X72631	CCDS11361.1	17q11.2	2013-01-16			ENSG00000126368	ENSG00000126368		"Nuclear hormone receptors"	7962	protein-coding gene	gene with protein product		602408		THRAL		1971514	Standard	NM_021724		Approved	ear-1, hRev, Rev-ErbAalpha, THRA1	uc002htz.3	P20393	OTTHUMG00000133327	ENST00000246672.3:c.854T>C	chr17.hg19:g.38252091A>G	ENSP00000246672:p.Val285Ala	115.0	0.0		97.0	4.0	NM_021724	Q0P5Z4|Q15304	Missense_Mutation	SNP	ENST00000246672.3	hg19	CCDS11361.1	.	.	.	.	.	.	.	.	.	.	A	10.69	1.420312	0.25552	.	.	ENSG00000126368	ENST00000246672	D	0.90004	-2.6	4.43	4.43	0.53597	.	0.187850	0.34879	N	0.003614	D	0.83653	0.5301	L	0.50333	1.59	0.32845	D	0.505831	B	0.18863	0.031	B	0.20184	0.028	T	0.78257	-0.2274	10	0.07813	T	0.8	.	13.1012	0.59219	1.0:0.0:0.0:0.0	.	285	P20393	NR1D1_HUMAN	A	285	ENSP00000246672:V285A	ENSP00000246672:V285A	V	-	2	0	NR1D1	35505617	0.551000	0.26497	1.000000	0.80357	0.996000	0.88848	0.996000	0.29719	1.990000	0.58119	0.533000	0.62120	GTG	.	.		0.627	NR1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257135.1			G	38252091	A	G	38252091	3	3	254	1	0	0	0	0	1	0	0	0	10624	159	6	2	1006	2	NR1D1	17	38252091	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	379252	38252091	42943119	830	35122										
KRT27	342574	hgsc.bcm.edu	37	chr17	38936687	38936687	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tccgcctccacgctctggtgAagcgctagctcgttttcaaa	9	14	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:38936687A>T	ENST00000301656.3	-	3	589	c.549T>A	c.(547-549)ctT>ctA	p.L183L	KRT27_ENST00000540723.1_5'Flank	NM_181537.3	NP_853515.2			keratin 27											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(3)|skin(1)|stomach(1)	21		Breast(137;0.000812)				CGCTCTGGTGAAGCGCTAGCT	0.458																																					p.L183L		Atlas-SNP	.											.	KRT27	41	.	0			c.T549A						.						62	56	58					17																	38936687		2203	4300	6503	SO:0001819	synonymous_variant	342574	exon3			CTGGTGAAGCGCT	AJ564206	CCDS11375.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000171446	ENSG00000171446		"-", "Intermediate filaments type I, keratins (acidic)"	30841	protein-coding gene	gene with protein product			"keratin 25C"	KRT25C		16831889	Standard	NM_181537		Approved		uc002hvg.3	Q7Z3Y8	OTTHUMG00000133371	ENST00000301656.3:c.549T>A	chr17.hg19:g.38936687A>T		123.0	0.0		82.0	4.0	NM_181537		Silent	SNP	ENST00000301656.3	hg19	CCDS11375.1																																																																																			.	.		0.458	KRT27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257216.1	NM_181537		T	38936687	A	T	38936687	2	4	254	1	0	0	0	0	0	0	0	1	8473	233	9	4		4	KRT27	17	38936687	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	684596	38936687	42258523	831	35123										
KRTAP9-9	81870	hgsc.bcm.edu	37	chr17	39411917	39411917	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggtccagctgctgtggccaaAccagctgtgggtccagctgt	14	12	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:39411917A>G	ENST00000394008.1	+	1	282	c.280A>G	c.(280-282)Acc>Gcc	p.T94A		NM_030975.2	NP_112237.2	Q9BYP9	KRA99_HUMAN	keratin associated protein 9-9	79	14 X 5 AA repeats of C-C-[RQVGE]- [SPSTNQ]-[TASL].					keratin filament (GO:0045095)				endometrium(3)|skin(2)|upper_aerodigestive_tract(1)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			CTGTGGCCAAACCAGCTGTGG	0.627																																					p.T94A		Atlas-SNP	.											.	KRTAP9-9	24	.	0			c.A280G						.						60	63	62					17																	39411917		2203	4298	6501	SO:0001583	missense	81870	exon1			GGCCAAACCAGCT	AJ406951	CCDS54127.1	17q21.2	2010-06-03			ENSG00000198083	ENSG00000198083		"Keratin associated proteins"	16773	protein-coding gene	gene with protein product			"keratin associated protein 9-5"	KRTAP9-5		11279113	Standard	NM_030975		Approved	KAP9.9, KAP9.5	uc021txh.1	Q9BYP9	OTTHUMG00000133602	ENST00000394008.1:c.280A>G	chr17.hg19:g.39411917A>G	ENSP00000377576:p.Thr94Ala	148.0	0.0		100.0	5.0	NM_030975	B5MDD6|Q9BYQ1	Missense_Mutation	SNP	ENST00000394008.1	hg19	CCDS54127.1	.	.	.	.	.	.	.	.	.	.	.	9.827	1.187478	0.21870	.	.	ENSG00000198083	ENST00000431129;ENST00000394008	T	0.01406	4.93	3.56	-2.15	0.07102	.	.	.	.	.	T	0.01523	0.0049	L	0.51422	1.61	0.09310	N	1	P	0.35033	0.481	B	0.36335	0.222	T	0.45512	-0.9256	9	0.19147	T	0.46	.	5.4575	0.16598	0.3291:0.4684:0.2025:0.0	.	79	Q9BYP9	KRA99_HUMAN	A	100;94	ENSP00000377576:T94A	ENSP00000377576:T94A	T	+	1	0	KRTAP9-9	36665443	0.366000	0.25014	0.000000	0.03702	0.007000	0.05969	0.765000	0.26546	-0.589000	0.05874	-0.501000	0.04562	ACC	.	.		0.627	KRTAP9-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257710.1	NM_030975		G	39411917	A	G	39411917	3	3	254	1	0	0	0	0	1	0	0	0	8586	43	2	2	282	2	KRTAP9-9	17	39411917	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	475230	39411917	41783293	832	35124										
KRT16	3868	hgsc.bcm.edu	37	chr17	39766790	39766790	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tggtctcctccaggctgttcTccagggatgctttctgcaag	11	12	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:39766790T>C	ENST00000301653.4	-	6	1137	c.1073A>G	c.(1072-1074)gAg>gGg	p.E358G		NM_005557.3	NP_005548.2	P08779	K1C16_HUMAN	keratin 16	358	Coil 2.|Rod.				aging (GO:0007568)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|epidermis development (GO:0008544)|hair cycle (GO:0042633)|intermediate filament cytoskeleton organization (GO:0045104)|negative regulation of cell migration (GO:0030336)	cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			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)				CAGGCTGTTCTCCAGGGATGC	0.557																																					p.E358G		Atlas-SNP	.											.	KRT16	45	.	0			c.A1073G						.						40	40	40					17																	39766790		2203	4300	6503	SO:0001583	missense	3868	exon6			CTGTTCTCCAGGG	S79867	CCDS11401.1	17q21.2	2013-01-16	2008-08-01		ENSG00000186832	ENSG00000186832		"-", "Intermediate filaments type I, keratins (acidic)"	6423	protein-coding gene	gene with protein product	"focal non-epidermolytic palmoplantar keratoderma"	148067				2451124, 16831889	Standard	NM_005557		Approved	NEPPK	uc002hxg.4	P08779	OTTHUMG00000133495	ENST00000301653.4:c.1073A>G	chr17.hg19:g.39766790T>C	ENSP00000301653:p.Glu358Gly	98.0	0.0		83.0	4.0	NM_005557	A8K488|P30654|Q16402|Q9UBG8	Missense_Mutation	SNP	ENST00000301653.4	hg19	CCDS11401.1	.	.	.	.	.	.	.	.	.	.	T	19.95	3.922437	0.73213	.	.	ENSG00000186832	ENST00000301653	D	0.91407	-2.84	4.28	4.28	0.50868	Filament (1);	0.000000	0.51477	D	0.000085	D	0.96658	0.8909	H	0.96111	3.77	0.49051	D	0.999749	D	0.89917	1.0	D	0.97110	1.0	D	0.97760	1.0220	10	0.87932	D	0	.	13.864	0.63576	0.0:0.0:0.0:1.0	.	358	P08779	K1C16_HUMAN	G	358	ENSP00000301653:E358G	ENSP00000301653:E358G	E	-	2	0	KRT16	37020316	1.000000	0.71417	0.996000	0.52242	0.985000	0.73830	7.549000	0.82163	1.929000	0.55896	0.379000	0.24179	GAG	.	.		0.557	KRT16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257408.1	NM_005557		C	39766790	T	C	39766790	3	2	254	1	0	0	0	0	1	0	0	0	8462	1551	54	2	360	2	KRT16	17	39766790	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	354873	39766790	41428420	833	35125										
KLHL10	317719	hgsc.bcm.edu	37	chr17	39998458	39998458	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	taaggatatcattgagaaagAtgagctcaatgtcaaacagg	10	5	3	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:39998458A>G	ENST00000293303.4	+	2	731	c.578A>G	c.(577-579)gAt>gGt	p.D193G		NM_152467.3	NP_689680.2	Q6JEL2	KLH10_HUMAN	kelch-like family member 10	193					cell morphogenesis (GO:0000902)|fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia morphogenesis (GO:0048808)|male gonad development (GO:0008584)|protein ubiquitination (GO:0016567)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	26		Breast(137;0.000162)				ATTGAGAAAGATGAGCTCAAT	0.398																																					p.D193G		Atlas-SNP	.											.	KLHL10	67	.	0			c.A578G						.						92	82	85					17																	39998458		1877	4122	5999	SO:0001583	missense	317719	exon2			AGAAAGATGAGCT	AK057224	CCDS42340.1	17q21.2	2013-01-30	2013-01-30		ENSG00000161594	ENSG00000161594		"Kelch-like", "BTB/POZ domain containing"	18829	protein-coding gene	gene with protein product		608778	"kelch-like 10 (Drosophila)"				Standard	NM_152467		Approved	FLJ32662	uc010cxr.3	Q6JEL2	OTTHUMG00000152510	ENST00000293303.4:c.578A>G	chr17.hg19:g.39998458A>G	ENSP00000293303:p.Asp193Gly	121.0	0.0		87.0	4.0	NM_152467	Q6NW28|Q96MC0	Missense_Mutation	SNP	ENST00000293303.4	hg19	CCDS42340.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.556300	0.86231	.	.	ENSG00000161594	ENST00000293303	T	0.75260	-0.92	5.73	5.73	0.89815	BTB/Kelch-associated (2);	0.085572	0.85682	D	0.000000	D	0.87819	0.6273	M	0.88105	2.93	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.74348	0.983;0.983	D	0.89628	0.3853	9	.	.	.	.	14.8475	0.70270	1.0:0.0:0.0:0.0	.	187;193	B4DXV2;Q6JEL2	.;KLH10_HUMAN	G	193	ENSP00000293303:D193G	.	D	+	2	0	KLHL10	37251984	1.000000	0.71417	0.998000	0.56505	0.947000	0.59692	9.027000	0.93706	2.177000	0.69029	0.533000	0.62120	GAT	.	.		0.398	KLHL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326535.1	NM_152467		G	39998458	A	G	39998458	3	3	254	1	0	0	0	0	1	0	0	0	8375	333	12	2	584	2	KLHL10	17	39998458	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	231668	39998458	41196752	834	35126										
KCNH4	23415	hgsc.bcm.edu	37	chr17	40321671	40321671	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gatgatggctgtcacgttccCgaacaccacagcgtgcatca	10	13	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:40321671C>T	ENST00000264661.3	-	9	1746	c.1414G>A	c.(1414-1416)Ggg>Agg	p.G472R	KCNH4_ENST00000607371.1_Missense_Mutation_p.G472R	NM_012285.2	NP_036417.1	Q9UQ05	KCNH4_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 4	472					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(15)|skin(2)|urinary_tract(1)	32		all_cancers(22;1.24e-06)|all_epithelial(22;4.33e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.126)		GTCACGTTCCCGAACACCACA	0.662																																					p.G472R	NSCLC(117;707 1703 2300 21308 31858)	Atlas-SNP	.											.	KCNH4	105	.	0			c.G1414A						.						78	62	68					17																	40321671		2203	4300	6503	SO:0001583	missense	23415	exon9			CGTTCCCGAACAC	AB022698	CCDS11420.1	17q21	2012-07-05				ENSG00000089558		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6253	protein-coding gene	gene with protein product		604528				10455180, 16382104	Standard	NM_012285		Approved	Kv12.3, elk1	uc002hzb.2	Q9UQ05		ENST00000264661.3:c.1414G>A	chr17.hg19:g.40321671C>T	ENSP00000264661:p.Gly472Arg	73.0	0.0		66.0	4.0	NM_012285		Missense_Mutation	SNP	ENST00000264661.3	hg19	CCDS11420.1	.	.	.	.	.	.	.	.	.	.	C	32	5.186962	0.94923	.	.	ENSG00000089558	ENST00000264661	D	0.99060	-5.38	4.36	4.36	0.52297	Ion transport (1);	0.000000	0.37219	N	0.002199	D	0.99477	0.9814	H	0.96833	3.89	0.80722	D	1	D	0.55800	0.973	P	0.60789	0.879	D	0.98087	1.0407	10	0.87932	D	0	.	17.084	0.86605	0.0:1.0:0.0:0.0	.	472	Q9UQ05	KCNH4_HUMAN	R	472	ENSP00000264661:G472R	ENSP00000264661:G472R	G	-	1	0	KCNH4	37575197	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.616000	0.83018	2.255000	0.74692	0.462000	0.41574	GGG	.	.		0.662	KCNH4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449791.2	NM_012285		T	40321671	C	T	40321671	3	4	254	1	0	0	0	0	1	0	0	0	8043	652	23	1	1671	1	KCNH4	17	40321671	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	323213	40321671	40873539	835	35127										
VPS25	84313	hgsc.bcm.edu	37	chr17	40928289	40928289	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aggagtggccagaacaactcCgtctttaccctgtatgaact	9	11	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:40928289C>A	ENST00000253794.2	+	5	409	c.369C>A	c.(367-369)tcC>tcA	p.S123S		NM_032353.2	NP_115729.1	Q9BRG1	VPS25_HUMAN	vacuolar protein sorting 25 homolog (S. cerevisiae)	123					endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)	5		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0745)		AGAACAACTCCGTCTTTACCC	0.423																																					p.S123S		Atlas-SNP	.											.	VPS25	11	.	0			c.C369A						.						91	88	89					17																	40928289		2203	4300	6503	SO:0001819	synonymous_variant	84313	exon5			CAACTCCGTCTTT	AB014763	CCDS11438.1	17q21.31	2014-02-12	2006-04-04		ENSG00000131475	ENSG00000131475			28122	protein-coding gene	gene with protein product		610907	"vacuolar protein sorting 25 (yeast)"			15511219	Standard	NM_032353		Approved	MGC10540, EAP20, DERP9	uc002ibi.3	Q9BRG1		ENST00000253794.2:c.369C>A	chr17.hg19:g.40928289C>A		174.0	0.0		121.0	5.0	NM_032353	B2R581	Silent	SNP	ENST00000253794.2	hg19	CCDS11438.1																																																																																			.	.		0.423	VPS25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452383.1	NM_032353		A	40928289	C	A	40928289	2	1	254	1	0	0	0	0	0	0	0	1	17211	639	23	1		1	VPS25	17	40928289	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	606618	40928289	40266921	836	35128										
CNTD1	124817	hgsc.bcm.edu	37	chr17	40959859	40959859	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttgcagcaagtgctttcatcCaaaaccatgagtgttggagc	10	9	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:40959859C>A	ENST00000588408.1	+	6	1075	c.799C>A	c.(799-801)Caa>Aaa	p.Q267K	CNTD1_ENST00000315066.5_3'UTR|CNTD1_ENST00000588527.1_Missense_Mutation_p.Q184K	NM_173478.2	NP_775749.2	Q8N815	CNTD1_HUMAN	cyclin N-terminal domain containing 1	267										central_nervous_system(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	10		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0749)		TGCTTTCATCCAAAACCATGA	0.408																																					p.Q267K		Atlas-SNP	.											.	CNTD1	22	.	0			c.C799A						.						127	111	116					17																	40959859		2203	4300	6503	SO:0001583	missense	124817	exon6			TTCATCCAAAACC	AK097456	CCDS11440.1	17q21.31	2014-07-03	2006-03-31	2006-03-31	ENSG00000176563	ENSG00000176563			26847	protein-coding gene	gene with protein product			"cyclin N-terminal domain containing"	CNTD		24891606	Standard	NM_173478		Approved	FLJ40137	uc002ibm.4	Q8N815		ENST00000588408.1:c.799C>A	chr17.hg19:g.40959859C>A	ENSP00000465204:p.Gln267Lys	110.0	0.0		86.0	5.0	NM_173478	Q658Q6|Q8NEP1	Missense_Mutation	SNP	ENST00000588408.1	hg19	CCDS11440.1	.	.	.	.	.	.	.	.	.	.	C	11.14	1.552239	0.27739	.	.	ENSG00000176563	ENST00000315066	.	.	.	5.92	5.92	0.95590	.	0.174500	0.49305	D	0.000148	T	0.49575	0.1565	L	0.51422	1.61	0.35743	D	0.818857	B	0.31581	0.329	B	0.25987	0.065	T	0.56263	-0.8008	9	0.27785	T	0.31	-4.1829	13.5121	0.61519	0.0:0.929:0.0:0.0709	.	267	Q8N815	CNTD1_HUMAN	K	267	.	ENSP00000316647:Q267K	Q	+	1	0	CNTD1	38213385	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.062000	0.49971	2.811000	0.96726	0.555000	0.69702	CAA	.	.		0.408	CNTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452398.1	NM_173478		A	40959859	C	A	40959859	3	1	254	1	0	0	0	0	1	0	0	0	3637	595	21	3	821	3	CNTD1	17	40959859	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	31570	40959859	40235351	837	35129										
AARSD1	80755	hgsc.bcm.edu	37	chr17	41108253	41108253	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gagattgctcacatgggtccCacagcacatgttggaatcaa	10	10	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:41108253C>T	ENST00000427569.2	-	6	666	c.631G>A	c.(631-633)Ggg>Agg	p.G211R	PTGES3L-AARSD1_ENST00000409399.1_Missense_Mutation_p.G385R|PTGES3L-AARSD1_ENST00000409103.1_Missense_Mutation_p.G294R|PTGES3L-AARSD1_ENST00000360221.4_Missense_Mutation_p.G324R|AARSD1_ENST00000416949.1_5'Flank|PTGES3L-AARSD1_ENST00000421990.2_Missense_Mutation_p.G385R	NM_001261434.1	NP_001248363.1	Q9BTE6	AASD1_HUMAN	alanyl-tRNA synthetase domain containing 1	211					alanyl-tRNA aminoacylation (GO:0006419)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	alanine-tRNA ligase activity (GO:0004813)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|Ser-tRNA(Ala) hydrolase activity (GO:0002196)			breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|skin(1)	17		Breast(137;0.00499)		BRCA - Breast invasive adenocarcinoma(366;0.161)		ACATGGGTCCCACAGCACATG	0.567																																					p.G385R		Atlas-SNP	.											AARSD1,NS,carcinoma,0,1	PTGES3L-AARSD1	15	.	0			c.G1153A						.						131	126	128					17																	41108253		2203	4300	6503	SO:0001583	missense	100885850	exon11			GGGTCCCACAGCA	BC004172	CCDS11447.1, CCDS45691.1, CCDS58552.1	17q21.31	2012-10-05			ENSG00000266967	ENSG00000266967			28417	protein-coding gene	gene with protein product		613212					Standard	NM_001261434		Approved	MGC2744		Q9BTE6	OTTHUMG00000153515	ENST00000427569.2:c.631G>A	chr17.hg19:g.41108253C>T	ENSP00000400870:p.Gly211Arg	86.0	0.0		47.0	2.0	NM_001136042	B4DI73	Missense_Mutation	SNP	ENST00000427569.2	hg19	CCDS58552.1	.	.	.	.	.	.	.	.	.	.	C	34	5.293630	0.95546	.	.	ENSG00000108825	ENST00000360221;ENST00000409399;ENST00000421990;ENST00000427569;ENST00000409103;ENST00000423601	D;D	0.90324	-2.65;-2.65	5.4	5.4	0.78164	Threonyl/alanyl tRNA synthetase, SAD (2);Alanyl-tRNA synthetase, class IIc, core domain (1);Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain (1);	0.119673	0.56097	D	0.000029	D	0.97729	0.9255	H	0.99312	4.51	0.52501	D	0.999957	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	D	0.99501	1.0953	9	0.87932	D	0	-34.1661	19.1719	0.93581	0.0:1.0:0.0:0.0	.	324;385;294;342;211	Q9BTE6-2;B4DI73;C9J5N1;B3KSP9;Q9BTE6	.;.;.;.;AASD1_HUMAN	R	324;385;385;211;294;93	ENSP00000386621:G385R;ENSP00000409924:G385R	ENSP00000353355:G324R	G	-	1	0	AARSD1	38361779	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.582000	0.82546	2.515000	0.84797	0.555000	0.69702	GGG	.	.		0.567	AARSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467729.1	NM_001261434		T	41108253	C	T	41108253	3	4	254	1	0	0	0	0	1	0	0	0	21	594	21	3	635	3	AARSD1	17	41108253	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	148394	41108253	40086957	838	35130										
MEOX1	4222	hgsc.bcm.edu	37	chr17	41720883	41720883	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcagagaggtccaggtttacCgcaatctcatatctgcggag	11	10	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:41720883C>A	ENST00000318579.4	-	2	1034	c.615G>T	c.(613-615)gcG>gcT	p.A205A	MEOX1_ENST00000549132.1_Intron|MEOX1_ENST00000329168.3_Intron|MEOX1_ENST00000393661.2_Silent_p.A90A	NM_001040002.1|NM_004527.3	NP_001035091.1|NP_004518.1	P50221	MEOX1_HUMAN	mesenchyme homeobox 1	205					multicellular organismal development (GO:0007275)|somite specification (GO:0001757)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	8		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.0753)		CCAGGTTTACCGCAATCTCAT	0.607																																					p.A205A		Atlas-SNP	.											.	MEOX1	29	.	0			c.G615T						.						62	54	56					17																	41720883		2203	4300	6503	SO:0001819	synonymous_variant	4222	exon2			GTTTACCGCAATC		CCDS11466.1, CCDS11467.1, CCDS42343.1	17q21.31	2014-07-15	2005-12-22					"Homeoboxes / ANTP class : HOXL subclass"	7013	protein-coding gene	gene with protein product		600147	"mesenchyme homeo box 1"			7987315	Standard	NM_013999		Approved	MOX1	uc002idz.3	P50221	OTTHUMG00000170513	ENST00000318579.4:c.615G>T	chr17.hg19:g.41720883C>A		114.0	0.0		87.0	4.0	NM_004527	A8K524|A8MWF9|Q15069	Silent	SNP	ENST00000318579.4	hg19	CCDS11466.1																																																																																			.	.		0.607	MEOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409452.1			A	41720883	C	A	41720883	2	1	254	1	0	0	0	0	0	0	0	1	9482	639	23	1		1	MEOX1	17	41720883	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	612630	41720883	39474327	839	35131										
CD300LG	146894	hgsc.bcm.edu	37	chr17	41924620	41924620	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctgctatggggttgcctgctGctcccaggtgagatggggag	17	9	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:41924620G>A	ENST00000317310.4	+	1	77	c.36G>A	c.(34-36)ctG>ctA	p.L12L	CD300LG_ENST00000586233.1_Silent_p.L12L|CD300LG_ENST00000588884.1_Silent_p.L12L|CD300LG_ENST00000293396.8_Silent_p.L12L|CD300LG_ENST00000539718.1_Silent_p.L12L|CD300LG_ENST00000377203.4_Silent_p.L12L	NM_145273.3	NP_660316.2	Q6UXG3	CLM9_HUMAN	CD300 molecule-like family member g	12					immune system process (GO:0002376)|immunoglobulin transcytosis in epithelial cells (GO:0002414)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(2)|lung(5)|skin(4)	19		Breast(137;0.0199)		BRCA - Breast invasive adenocarcinoma(366;0.115)		GTTGCCTGCTGCTCCCAGGTG	0.622																																					p.L12L		Atlas-SNP	.											.	CD300LG	46	.	0			c.G36A						.						90	86	87					17																	41924620		2203	4300	6503	SO:0001819	synonymous_variant	146894	exon1			CCTGCTGCTCCCA	BC025395	CCDS11470.1, CCDS54131.1, CCDS54132.1, CCDS54133.1	17q21.31	2013-01-11	2006-03-29					"Immunoglobulin superfamily / V-set domain containing"	30455	protein-coding gene	gene with protein product	"nepmucin"	610520	"CD300 antigen like family member G"			16876123, 16754720	Standard	NM_001168322		Approved	Trem4, CLM9	uc002iem.3	Q6UXG3		ENST00000317310.4:c.36G>A	chr17.hg19:g.41924620G>A		106.0	0.0		94.0	22.0	NM_001168323	B4DNY5|F5H7P9|F8W9M3|Q8IX38|Q8IX39|Q8TA95	Silent	SNP	ENST00000317310.4	hg19	CCDS11470.1																																																																																			.	.		0.622	CD300LG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457646.1	NM_145273		A	41924620	G	A	41924620	2	1	254	1	0	0	0	0	0	0	0	1	3004	1306	46	3		3	CD300LG	17	41924620	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	203737	41924620	39270590	840	35132										
TMUB2	79089	hgsc.bcm.edu	37	chr17	42266555	42266555	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agcggtagcaaccagctcctGggcgctattgtgtcagcagg	14	11	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:42266555G>A	ENST00000587989.1	+	3	354	c.201G>A	c.(199-201)ctG>ctA	p.L67L	ASB16-AS1_ENST00000588785.1_RNA|TMUB2_ENST00000357984.3_Silent_p.L47L|TMUB2_ENST00000589184.1_Intron|TMUB2_ENST00000587172.1_Silent_p.L47L|TMUB2_ENST00000538716.2_Silent_p.L67L|TMUB2_ENST00000589785.1_Silent_p.L47L|TMUB2_ENST00000446571.3_Silent_p.L47L|TMUB2_ENST00000589856.1_Silent_p.L47L|ASB16-AS1_ENST00000592897.1_RNA|TMUB2_ENST00000590235.1_Silent_p.L47L|ASB16-AS1_ENST00000591166.1_RNA|TMUB2_ENST00000319511.6_Silent_p.L47L|ASB16-AS1_ENST00000585457.1_RNA|TMUB2_ENST00000592825.1_Silent_p.L47L			Q71RG4	TMUB2_HUMAN	transmembrane and ubiquitin-like domain containing 2	67						integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(1)|lung(3)	8		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.113)		ACCAGCTCCTGGGCGCTATTG	0.607																																					p.L67L		Atlas-SNP	.											.	TMUB2	29	.	0			c.G201A						.						117	105	109					17																	42266555		2203	4300	6503	SO:0001819	synonymous_variant	79089	exon3			GCTCCTGGGCGCT		CCDS11479.1, CCDS54134.1	17q21	2006-06-27				ENSG00000168591			28459	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_177441		Approved	MGC3123	uc002ifo.3	Q71RG4		ENST00000587989.1:c.201G>A	chr17.hg19:g.42266555G>A		114.0	0.0		94.0	4.0	NM_001076674	B3KU81|Q8NDI2|Q9BPZ5|Q9HAG3	Silent	SNP	ENST00000587989.1	hg19	CCDS54134.1																																																																																			.	.		0.607	TMUB2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457711.1	NM_177441		A	42266555	G	A	42266555	2	1	254	1	0	0	0	0	0	0	0	1	16280	1335	47	3		3	TMUB2	17	42266555	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	341935	42266555	38928655	841	35133										
EFTUD2	9343	hgsc.bcm.edu	37	chr17	42937415	42937415	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agggtcggaaaatctgagccTgagatccaaagcacaaagga	12	8	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:42937415T>C	ENST00000426333.2	-	18	2017		c.e18-2		EFTUD2_ENST00000592576.1_Splice_Site|EFTUD2_ENST00000402521.3_Splice_Site|EFTUD2_ENST00000591382.1_Splice_Site	NM_001142605.1|NM_001258354.1|NM_004247.3	NP_001136077.1|NP_001245283.1|NP_004238.3	Q15029	U5S1_HUMAN	elongation factor Tu GTP binding domain containing 2						gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	32		Prostate(33;0.109)				AATCTGAGCCTGAGATCCAAA	0.493																																					.	Ovarian(10;65 485 10258 29980 30707)	Atlas-SNP	.											.	EFTUD2	85	.	0			c.1720-2A>G						.						94	88	90					17																	42937415		2203	4300	6503	SO:0001630	splice_region_variant	9343	exon19			TGAGCCTGAGATC	D21163	CCDS11489.1, CCDS45707.1, CCDS59295.1	17q21.31	2014-08-12			ENSG00000108883	ENSG00000108883			30858	protein-coding gene	gene with protein product	"U5 snRNP specific protein, 116 kD"	603892				9233818	Standard	NM_004247		Approved	U5-116KD, Snrp116, Snu114, SNRNP116	uc002ihn.2	Q15029	OTTHUMG00000179865	ENST00000426333.2:c.1720-2A>G	chr17.hg19:g.42937415T>C		145.0	0.0		116.0	5.0	NM_004247	B4DK30|B4DMC0|D3DX58|K7EJ81|Q9BUR0	Splice_Site	SNP	ENST00000426333.2	hg19	CCDS11489.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.450043	0.84101	.	.	ENSG00000108883	ENST00000426333;ENST00000262414;ENST00000402521	.	.	.	5.07	5.07	0.68467	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0055	0.71510	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	EFTUD2	40292941	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.850000	0.86915	2.135000	0.66039	0.454000	0.30748	.	.	.		0.493	EFTUD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448672.1	NM_004247	Intron	C	42937415	T	C	42937415	5	2	254	1	0	0	0	0	0	0	1	0	4963	1594	55	2	1244	2	EFTUD2	17	42937415	Splice_Site	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	670860	42937415	38257795	842	35134										
KIF18B	146909	hgsc.bcm.edu	37	chr17	43005599	43005599	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcttttgatgactgtggctgGgcaaacgcgaggggaatggc	17	7	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:43005599G>T	ENST00000593135.1	-	13	2168	c.2071C>A	c.(2071-2073)Cca>Aca	p.P691T	KIF18B_ENST00000339151.4_Missense_Mutation_p.P694T|KIF18B_ENST00000438933.2_Missense_Mutation_p.P703T|KIF18B_ENST00000590129.1_Missense_Mutation_p.P712T|KIF18B_ENST00000587309.1_Missense_Mutation_p.P703T	NM_001265577.1	NP_001252506.1	Q86Y91	KI18B_HUMAN	kinesin family member 18B	703					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|regulation of cell division (GO:0051302)	astral microtubule (GO:0000235)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule plus-end (GO:0035371)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	21		Prostate(33;0.155)				ACTGTGGCTGGGCAAACGCGA	0.642																																					p.P703T		Atlas-SNP	.											.	KIF18B	63	.	0			c.C2107A						.						28	33	31					17																	43005599		2017	4157	6174	SO:0001583	missense	146909	exon13			TGGCTGGGCAAAC		CCDS45709.1, CCDS58555.1, CCDS45709.2	17q21.31	2014-09-04			ENSG00000186185			"Kinesins"	27102	protein-coding gene	gene with protein product		614570				16084724	Standard	NM_001264573		Approved		uc010wjh.3	Q86Y91	OTTHUMG00000179867	ENST00000593135.1:c.2071C>A	chr17.hg19:g.43005599G>T	ENSP00000465992:p.Pro691Thr	127.0	0.0		79.0	4.0	NM_001264573	A6NJI2|B7ZM49|B9EGM8|D5L6I1	Missense_Mutation	SNP	ENST00000593135.1	hg19	CCDS45709.2	.	.	.	.	.	.	.	.	.	.	G	14.03	2.414533	0.42817	.	.	ENSG00000186185	ENST00000438933;ENST00000339151;ENST00000376982	T;T	0.75050	-0.88;-0.9	4.39	3.34	0.38264	.	.	.	.	.	T	0.81004	0.4733	M	0.70595	2.14	0.29974	N	0.818311	P;D;P	0.64830	0.91;0.994;0.946	P;P;P	0.60949	0.469;0.881;0.67	T	0.75297	-0.3367	9	0.66056	D	0.02	.	7.5899	0.28015	0.0991:0.0:0.7327:0.1682	.	703;700;712	Q86Y91;Q86Y91-3;Q86Y91-2	KI18B_HUMAN;.;.	T	703;694;703	ENSP00000412798:P703T;ENSP00000341466:P694T	ENSP00000341466:P694T	P	-	1	0	KIF18B	40361125	1.000000	0.71417	1.000000	0.80357	0.440000	0.31957	1.807000	0.38902	2.275000	0.75901	0.561000	0.74099	CCA	.	.		0.642	KIF18B-001	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000448724.1	NM_001080443		T	43005599	G	T	43005599	3	4	254	1	0	0	0	0	1	0	0	0	8290	1232	43	3	502	3	KIF18B	17	43005599	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	68184	43005599	38189611	843	35135										
KIF18B	146909	hgsc.bcm.edu	37	chr17	43012257	43012257	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cggggtcctcgcggatggcaAggggccccttgggctccagg	18	13	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:43012257A>G	ENST00000593135.1	-	4	615	c.518T>C	c.(517-519)cTt>cCt	p.L173P	KIF18B_ENST00000339151.4_Missense_Mutation_p.L173P|KIF18B_ENST00000438933.2_Missense_Mutation_p.L173P|KIF18B_ENST00000590129.1_Missense_Mutation_p.L182P|KIF18B_ENST00000587309.1_Missense_Mutation_p.L173P	NM_001265577.1	NP_001252506.1	Q86Y91	KI18B_HUMAN	kinesin family member 18B	182	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|regulation of cell division (GO:0051302)	astral microtubule (GO:0000235)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule plus-end (GO:0035371)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	21		Prostate(33;0.155)				GCGGATGGCAAGGGGCCCCTT	0.592																																					p.L173P		Atlas-SNP	.											.	KIF18B	63	.	0			c.T518C						.						11	13	13					17																	43012257		1821	3991	5812	SO:0001583	missense	146909	exon4			ATGGCAAGGGGCC		CCDS45709.1, CCDS58555.1, CCDS45709.2	17q21.31	2014-09-04			ENSG00000186185			"Kinesins"	27102	protein-coding gene	gene with protein product		614570				16084724	Standard	NM_001264573		Approved		uc010wjh.3	Q86Y91	OTTHUMG00000179867	ENST00000593135.1:c.518T>C	chr17.hg19:g.43012257A>G	ENSP00000465992:p.Leu173Pro	57.0	0.0		56.0	5.0	NM_001264573	A6NJI2|B7ZM49|B9EGM8|D5L6I1	Missense_Mutation	SNP	ENST00000593135.1	hg19	CCDS45709.2	.	.	.	.	.	.	.	.	.	.	A	25.2	4.615706	0.87359	.	.	ENSG00000186185	ENST00000438933;ENST00000339151;ENST00000376982	T;T	0.80033	-1.33;-1.33	5.7	5.7	0.88788	Kinesin, motor domain (4);	0.000000	0.34200	N	0.004163	D	0.92502	0.7619	H	0.94222	3.51	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.999	D	0.94443	0.7660	10	0.87932	D	0	.	15.6259	0.76855	1.0:0.0:0.0:0.0	.	182;182;182	Q86Y91;Q86Y91-3;Q86Y91-2	KI18B_HUMAN;.;.	P	173	ENSP00000412798:L173P;ENSP00000341466:L173P	ENSP00000341466:L173P	L	-	2	0	KIF18B	40367783	1.000000	0.71417	0.953000	0.39169	0.995000	0.86356	9.182000	0.94881	2.175000	0.68902	0.454000	0.30748	CTT	.	.		0.592	KIF18B-001	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000448724.1	NM_001080443		G	43012257	A	G	43012257	3	3	254	1	0	0	0	0	1	0	0	0	8290	72	3	2	2100	2	KIF18B	17	43012257	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	6658	43012257	38182953	844	35136										
FMNL1	752	hgsc.bcm.edu	37	chr17	43314685	43314685	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	catgaaccacccagcctgtgTcaatgagattgctctgagcc	9	13	2	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:43314685T>C	ENST00000331495.3	+	8	1097	c.761T>C	c.(760-762)gTc>gCc	p.V254A	FMNL1_ENST00000328118.3_Missense_Mutation_p.V254A|CTD-2020K17.3_ENST00000587534.1_RNA|FMNL1_ENST00000592006.1_3'UTR|CTD-2020K17.3_ENST00000393507.2_RNA	NM_005892.3	NP_005883	O95466	FMNL_HUMAN	formin-like 1	254	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin filament severing (GO:0051014)|cortical actin cytoskeleton organization (GO:0030866)|regulation of cell shape (GO:0008360)|substrate-dependent cell migration (GO:0006929)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|GTPase activating protein binding (GO:0032794)|Rac GTPase binding (GO:0048365)	p.V254A(1)		biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(12)|pancreas(1)|skin(1)|urinary_tract(2)	33						CCAGCCTGTGTCAATGAGATT	0.572																																					p.V254A	GBM(164;1247 1997 8702 11086 51972)	Atlas-SNP	.											FMNL1,caecum,carcinoma,0,1	FMNL1	78	.	1	Substitution - Missense(1)	large_intestine(1)	c.T761C						.						119	107	111					17																	43314685		2203	4300	6503	SO:0001583	missense	752	exon8			CCTGTGTCAATGA	AJ008112	CCDS11497.1	17q21.31	2008-05-14	2003-12-02	2003-12-03		ENSG00000184922			1212	protein-coding gene	gene with protein product		604656	"formin-like"	C17orf1B, FMNL		9799091	Standard	NM_005892		Approved	C17orf1	uc002iin.3	O95466		ENST00000331495.3:c.761T>C	chr17.hg19:g.43314685T>C	ENSP00000329219:p.Val254Ala	120.0	0.0		97.0	4.0	NM_005892	D2DGW2|Q6DKG5|Q6IBP3|Q86UH1|Q8N671|Q8TDH1|Q96H10	Missense_Mutation	SNP	ENST00000331495.3	hg19	CCDS11497.1	.	.	.	.	.	.	.	.	.	.	T	18.35	3.605830	0.66445	.	.	ENSG00000184922	ENST00000328118;ENST00000331495	D;D	0.90620	-2.7;-2.7	3.83	3.83	0.44106	GTPase-binding/formin homology 3 (1);Armadillo-type fold (1);Diaphanous GTPase-binding (1);	0.000000	0.85682	D	0.000000	D	0.95214	0.8448	M	0.87827	2.91	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.95396	0.8486	10	0.56958	D	0.05	.	12.8373	0.57780	0.0:0.0:0.0:1.0	.	254	O95466	FMNL_HUMAN	A	254	ENSP00000327442:V254A;ENSP00000329219:V254A	ENSP00000327442:V254A	V	+	2	0	FMNL1	40670468	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.868000	0.87116	1.972000	0.57404	0.379000	0.24179	GTC	.	.		0.572	FMNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450198.1	NM_005892		C	43314685	T	C	43314685	3	2	254	1	0	0	0	0	1	0	0	0	5959	1667	58	2	791	2	FMNL1	17	43314685	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	302428	43314685	37880525	845	35137										
CDC27	996	hgsc.bcm.edu	37	chr17	45249328	45249328	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	caagcaggtatttgcattgcGgtgtagtacaactgtgtcct	11	8	0	0	rs142853734		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:45249328G>A	ENST00000066544.3	-	3	299	c.206C>T	c.(205-207)cCg>cTg	p.P69L	RP5-867C24.5_ENST00000572193.1_RNA|CDC27_ENST00000446365.2_Intron|CDC27_ENST00000528748.1_5'UTR|CDC27_ENST00000531206.1_Missense_Mutation_p.P69L|CDC27_ENST00000527547.1_Missense_Mutation_p.P69L	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	69					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TTTGCATTGCGGTGTAGTACA	0.358																																					p.P69L		Atlas-SNP	.											CDC27_ENST00000531206,NS,haematopoietic_neoplasm,0,2	CDC27	337	.	0			c.C206T						.						42	42	42					17																	45249328		2202	4300	6502	SO:0001583	missense	996	exon3			CATTGCGGTGTAG	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1728	protein-coding gene	gene with protein product	"anaphase promoting complex subunit 3"	116946	"cell division cycle 27", "cell division cycle 27 homolog (S. cerevisiae)"	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.206C>T	chr17.hg19:g.45249328G>A	ENSP00000066544:p.Pro69Leu	76.0	0.0		55.0	3.0	NM_001114091	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	hg19	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.916798	0.92249	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000527547;ENST00000526866	T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07	5.69	4.7	0.59300	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.81389	0.4812	L	0.57536	1.79	0.80722	D	1	D;D;D	0.71674	0.997;0.998;0.992	P;P;P	0.57425	0.742;0.803;0.82	T	0.78183	-0.2303	10	0.19147	T	0.46	-28.2366	13.6664	0.62398	0.0:0.0:0.844:0.156	.	69;69;69	G5EA36;G3V1C4;P30260	.;.;CDC27_HUMAN	L	69	ENSP00000066544:P69L;ENSP00000434614:P69L;ENSP00000437339:P69L;ENSP00000432105:P69L	ENSP00000066544:P69L	P	-	2	0	CDC27	42604327	1.000000	0.71417	0.906000	0.35671	0.977000	0.68977	9.568000	0.98166	1.376000	0.46267	0.591000	0.81541	CCG	.	.		0.358	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2			A	45249328	G	A	45249328	3	1	254	1	0	0	0	0	1	0	0	0	3068	1116	39	1	2354	1	CDC27	17	45249328	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1934643	45249328	35945882	846	35138										
SPATA20	64847	hgsc.bcm.edu	37	chr17	48628203	48628203	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gagcctgtgttgggtgccacCgagccgctgacctcaggcca	14	14	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:48628203C>A	ENST00000356488.4	+	10	1343	c.1260C>A	c.(1258-1260)acC>acA	p.T420T	SPATA20_ENST00000393244.3_Silent_p.T376T|SPATA20_ENST00000006658.6_Silent_p.T436T|SPATA20_ENST00000511937.1_3'UTR	NM_001258372.1	NP_001245301.1	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20	420					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)	catalytic activity (GO:0003824)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;9.38e-09)			TGGGTGCCACCGAGCCGCTGA	0.642											OREG0024568	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T436T		Atlas-SNP	.											.	SPATA20	59	.	0			c.C1308A						.						68	78	74					17																	48628203		2203	4298	6501	SO:0001819	synonymous_variant	64847	exon11			TGCCACCGAGCCG		CCDS11571.1, CCDS58563.1, CCDS58564.1	17q21.33	2011-03-17			ENSG00000006282	ENSG00000006282			26125	protein-coding gene	gene with protein product	"hypothetical protein FLJ21347"	613939				12477932	Standard	NM_022827		Approved	FLJ21347, SSP411, Tisp78	uc002ird.3	Q8TB22	OTTHUMG00000162162	ENST00000356488.4:c.1260C>A	chr17.hg19:g.48628203C>A		169.0	0.0	119	125.0	5.0	NM_022827	Q2TA99|Q2XUZ6|Q6P0P1|Q8WVW3|Q9H747	Silent	SNP	ENST00000356488.4	hg19	CCDS58563.1																																																																																			.	.		0.642	SPATA20-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367651.1	NM_022827		A	48628203	C	A	48628203	2	1	254	1	0	0	0	0	0	0	0	1	15021	639	23	1		1	SPATA20	17	48628203	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	3378875	48628203	32567007	847	35139										
ABCC3	8714	hgsc.bcm.edu	37	chr17	48750986	48750986	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tctgcaactatgcccccgatGaggaccaagggcacctggag	12	13	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:48750986G>T	ENST00000285238.8	+	19	2646	c.2566G>T	c.(2566-2568)Gag>Tag	p.E856*		NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	856					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33			BRCA - Breast invasive adenocarcinoma(22;3.05e-09)		Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Doxorubicin(DB00997)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indomethacin(DB00328)|Lamivudine(DB00709)|Leucovorin(DB00650)|Methotrexate(DB00563)|Metyrapone(DB01011)|Nifedipine(DB01115)|Omeprazole(DB00338)|Phenobarbital(DB01174)|Probenecid(DB01032)|Rifampicin(DB01045)|Sulfinpyrazone(DB01138)|Verapamil(DB00661)|Vincristine(DB00541)	TGCCCCCGATGAGGACCAAGG	0.607																																					p.E856X		Atlas-SNP	.											.	ABCC3	138	.	0			c.G2566T						.						80	77	78					17																	48750986		2203	4300	6503	SO:0001587	stop_gained	8714	exon19			CCCGATGAGGACC	Y17151	CCDS32681.1, CCDS45739.1	17q21	2012-03-14			ENSG00000108846	ENSG00000108846		"ATP binding cassette transporters / subfamily C"	54	protein-coding gene	gene with protein product	"canalicular multispecific organic anion transporter 2"	604323				8894702, 9827529	Standard	NM_003786		Approved	MRP3, cMOAT2, EST90757, MLP2, MOAT-D	uc002isl.3	O15438	OTTHUMG00000162245	ENST00000285238.8:c.2566G>T	chr17.hg19:g.48750986G>T	ENSP00000285238:p.Glu856*	138.0	0.0		87.0	4.0	NM_003786	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Nonsense_Mutation	SNP	ENST00000285238.8	hg19	CCDS32681.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	29.0|29.0	4.964881|4.964881	0.92855|0.92855	.|.	.|.	ENSG00000108846|ENSG00000108846	ENST00000285238|ENST00000513745	.|.	.|.	.|.	5.05|5.05	4.08|4.08	0.47627|0.47627	.|.	0.273836|.	0.35936|.	N|.	0.002891|.	.|.	.|.	.|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.40728|.	T|.	0.16|.	-11.9696|-11.9696	14.4024|14.4024	0.67056|0.67056	0.0728:0.0:0.9272:0.0|0.0728:0.0:0.9272:0.0	.|.	.|.	.|.	.|.	X|L	856|4	.|.	ENSP00000285238:E856X|.	E|X	+|+	1|2	0|2	ABCC3|ABCC3	46105985|46105985	1.000000|1.000000	0.71417|0.71417	0.266000|0.266000	0.24541|0.24541	0.141000|0.141000	0.21300|0.21300	4.398000|4.398000	0.59697|0.59697	1.448000|1.448000	0.47680|0.47680	0.561000|0.561000	0.74099|0.74099	GAG|TGA	.	.		0.607	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038		T	48750986	G	T	48750986	4	4	254	1	0	0	0	0	0	1	0	0	54	1291	45	3	2724	3	ABCC3	17	48750986	Nonsense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	122783	48750986	32444224	848	35140										
WFIKKN2	124857	hgsc.bcm.edu	37	chr17	48913333	48913333	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtgtcgccggttctggtctcGctgggagcaggtggcagcgc	18	11	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:48913333G>A	ENST00000311378.4	+	1	563	c.35G>A	c.(34-36)cGc>cAc	p.R12H	WFIKKN2_ENST00000426127.1_Intron	NM_175575.5	NP_783165.1	Q8TEU8	WFKN2_HUMAN	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2	12					muscle fiber development (GO:0048747)|negative regulation of DNA binding (GO:0043392)|negative regulation of protein binding (GO:0032091)|palate development (GO:0060021)|skeletal system development (GO:0001501)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)	metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(13)|ovary(4)|skin(1)	29			BRCA - Breast invasive adenocarcinoma(22;1.09e-08)			TTCTGGTCTCGCTGGGAGCAG	0.706																																					p.R12H		Atlas-SNP	.											.	WFIKKN2	69	.	0			c.G35A						.						14	15	15					17																	48913333		2199	4296	6495	SO:0001583	missense	124857	exon1			GGTCTCGCTGGGA	AY358142	CCDS11575.1	17q21.33	2013-01-21			ENSG00000173714	ENSG00000173714		"Immunoglobulin superfamily / I-set domain containing", "WAP four-disulfide core domain containing"	30916	protein-coding gene	gene with protein product	"WAP four-disulfide core domain 20B"	610895				11928817, 12709070	Standard	NM_175575		Approved	WFIKKNRP, WFDC20B	uc002isv.4	Q8TEU8	OTTHUMG00000162274	ENST00000311378.4:c.35G>A	chr17.hg19:g.48913333G>A	ENSP00000311184:p.Arg12His	127.0	0.0		110.0	41.0	NM_175575	Q6UXZ9	Missense_Mutation	SNP	ENST00000311378.4	hg19	CCDS11575.1	.	.	.	.	.	.	.	.	.	.	G	10.48	1.361150	0.24684	.	.	ENSG00000173714	ENST00000311378	T	0.81415	-1.49	5.24	0.186	0.15105	.	1.186510	0.05938	N	0.636435	T	0.58652	0.2137	N	0.08118	0	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.40001	-0.9586	10	0.13853	T	0.58	.	4.3165	0.10995	0.3569:0.1618:0.4813:0.0	.	12	Q8TEU8	WFKN2_HUMAN	H	12	ENSP00000311184:R12H	ENSP00000311184:R12H	R	+	2	0	WFIKKN2	46268332	0.000000	0.05858	0.613000	0.29037	0.950000	0.60333	-0.841000	0.04359	-0.239000	0.09710	0.655000	0.94253	CGC	.	.		0.706	WFIKKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368358.1	NM_175575		A	48913333	G	A	48913333	3	1	254	1	0	0	0	0	1	0	0	0	17374	1087	38	1	37	1	WFIKKN2	17	48913333	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	162347	48913333	32281877	849	35141										
STXBP4	252983	hgsc.bcm.edu	37	chr17	53150293	53150293	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtagttgaagaaacaagagcCctgcgtagtcggattcatct	11	8	2	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:53150293C>A	ENST00000376352.2	+	13	1251	c.1044C>A	c.(1042-1044)gcC>gcA	p.A348A	STXBP4_ENST00000434978.2_Silent_p.A326A	NM_178509.5	NP_848604.3	Q6ZWJ1	STXB4_HUMAN	syntaxin binding protein 4	348					cellular response to DNA damage stimulus (GO:0006974)|glucose transport (GO:0015758)|insulin receptor signaling pathway (GO:0008286)|positive regulation of cell cycle G1/S phase transition (GO:1902808)|positive regulation of keratinocyte proliferation (GO:0010838)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(4)|ovary(1)|upper_aerodigestive_tract(2)	19						AAACAAGAGCCCTGCGTAGTC	0.378																																					p.A348A		Atlas-SNP	.											.	STXBP4	41	.	0			c.C1044A						.						79	75	76					17																	53150293		2203	4300	6503	SO:0001819	synonymous_variant	252983	exon13			AAGAGCCCTGCGT	BC041485	CCDS11584.2	17q22	2008-02-05			ENSG00000166263	ENSG00000166263			19694	protein-coding gene	gene with protein product		610415				12855681	Standard	XM_005257187		Approved	Synip, MGC50337	uc002iuf.1	Q6ZWJ1	OTTHUMG00000074043	ENST00000376352.2:c.1044C>A	chr17.hg19:g.53150293C>A		102.0	0.0		74.0	5.0	NM_178509	Q8IVZ5	Silent	SNP	ENST00000376352.2	hg19	CCDS11584.2																																																																																			.	.		0.378	STXBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157184.1	NM_178509		A	53150293	C	A	53150293	2	1	254	1	0	0	0	0	0	0	0	1	15370	610	22	3		3	STXBP4	17	53150293	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	4236960	53150293	28044917	850	35142										
LPO	4025	hgsc.bcm.edu	37	chr17	56344752	56344752	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctgtgacctctcacagccgcAgacactagaggagttgaaca	10	12	1	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:56344752A>G	ENST00000262290.4	+	12	2052	c.1736A>G	c.(1735-1737)cAg>cGg	p.Q579R	LPO_ENST00000582328.1_Missense_Mutation_p.Q496R|LPO_ENST00000543544.1_Missense_Mutation_p.Q520R|LPO_ENST00000421678.2_Missense_Mutation_p.Q496R	NM_006151.2	NP_006142.1	P22079	PERL_HUMAN	lactoperoxidase	579					defense response to bacterium (GO:0042742)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|hydrogen peroxide catabolic process (GO:0042744)|response to oxidative stress (GO:0006979)|thiocyanate metabolic process (GO:0018969)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|metal ion binding (GO:0046872)|thiocyanate peroxidase activity (GO:0036393)			breast(5)|cervix(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30						TCACAGCCGCAGACACTAGAG	0.547																																					p.Q579R		Atlas-SNP	.											.	LPO	73	.	0			c.A1736G						.						70	64	66					17																	56344752		2203	4300	6503	SO:0001583	missense	4025	exon12			AGCCGCAGACACT	M58151	CCDS32689.1, CCDS54149.1	17q23.1	2008-02-05				ENSG00000167419	1.11.1.7		6678	protein-coding gene	gene with protein product		150205				2222811, 8964511	Standard	NM_006151		Approved	SPO	uc002ivt.3	P22079		ENST00000262290.4:c.1736A>G	chr17.hg19:g.56344752A>G	ENSP00000262290:p.Gln579Arg	88.0	0.0		62.0	4.0	NM_006151	A5JUY4|E7EMJ3|Q13408|Q3KNQ2	Missense_Mutation	SNP	ENST00000262290.4	hg19	CCDS32689.1	.	.	.	.	.	.	.	.	.	.	A	0.009	-1.809130	0.00606	.	.	ENSG00000167419	ENST00000262290;ENST00000421678;ENST00000543544;ENST00000389576	T;T;T	0.68903	-0.36;-0.36;-0.36	5.11	4.01	0.46588	.	0.748721	0.13539	N	0.380388	T	0.44008	0.1273	N	0.20610	0.595	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.11329	0.001;0.006	T	0.34576	-0.9823	10	0.02654	T	1	.	6.804	0.23766	0.8069:0.0:0.1931:0.0	.	496;579	E7EMJ3;P22079	.;PERL_HUMAN	R	579;496;520;324	ENSP00000262290:Q579R;ENSP00000400245:Q496R;ENSP00000445344:Q520R	ENSP00000262290:Q579R	Q	+	2	0	LPO	53699751	0.022000	0.18835	0.073000	0.20177	0.076000	0.17211	1.540000	0.36115	0.779000	0.33543	0.455000	0.32223	CAG	.	.		0.547	LPO-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443961.1			G	56344752	A	G	56344752	3	3	254	1	0	0	0	0	1	0	0	0	8931	188	7	2	1778	2	LPO	17	56344752	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	3194459	56344752	24850458	851	35143										
TEX14	56155	hgsc.bcm.edu	37	chr17	56690838	56690838	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gatgcgctcgtacacaaggcGggttttctctaggtcctggg	14	10	1	0	rs150820263	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:56690838G>T	ENST00000240361.8	-	9	1052	c.967C>A	c.(967-969)Cgc>Agc	p.R323S	TEX14_ENST00000389934.3_Missense_Mutation_p.R317S|TEX14_ENST00000349033.5_Missense_Mutation_p.R317S			Q8IWB6	TEX14_HUMAN	testis expressed 14	323	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)			breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TACACAAGGCGGGTTTTCTCT	0.502																																					p.R323S		Atlas-SNP	.											TEX14_ENST00000240361,colon,carcinoma,0,2	TEX14	343	.	0			c.C967A						.						168	144	152					17																	56690838		2203	4300	6503	SO:0001583	missense	56155	exon9			CAAGGCGGGTTTT	AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"cancer/testis antigen 113"	605792	"testis expressed sequence 14"			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.967C>A	chr17.hg19:g.56690838G>T	ENSP00000240361:p.Arg323Ser	198.0	1.0		144.0	7.0	NM_001201457	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Missense_Mutation	SNP	ENST00000240361.8	hg19	CCDS56042.1	.	.	.	.	.	.	.	.	.	.	G	8.134	0.783782	0.16189	.	.	ENSG00000121101	ENST00000240361;ENST00000389934;ENST00000349033	T;T;T	0.40756	1.02;1.02;1.02	5.68	3.72	0.42706	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.538685	0.18620	N	0.135891	T	0.28400	0.0702	N	0.13235	0.315	0.09310	N	1	P;B;B	0.37781	0.608;0.232;0.227	B;B;B	0.41466	0.358;0.159;0.114	T	0.09509	-1.0671	10	0.40728	T	0.16	-3.5586	8.7353	0.34525	0.2317:0.0:0.7683:0.0	.	323;317;317	Q8IWB6;Q8IWB6-3;Q8IWB6-2	TEX14_HUMAN;.;.	S	323;317;317	ENSP00000240361:R323S;ENSP00000374584:R317S;ENSP00000268910:R317S	ENSP00000240361:R323S	R	-	1	0	TEX14	54045837	0.988000	0.35896	0.005000	0.12908	0.004000	0.04260	3.332000	0.52083	0.770000	0.33336	-0.254000	0.11334	CGC	.	G|1.000;A|0.000		0.502	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1			T	56690838	G	T	56690838	3	4	254	1	0	0	0	0	1	0	0	0	15793	1116	39	1	3626	1	TEX14	17	56690838	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	346086	56690838	24504372	852	35144										
DDX42	11325	hgsc.bcm.edu	37	chr17	61889542	61889542	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctttaagaaaaaggacatccCagtcctggtggccacagatg	10	10	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:61889542C>A	ENST00000578681.1	+	15	2250	c.1649C>A	c.(1648-1650)cCa>cAa	p.P550Q	DDX42_ENST00000583590.1_Missense_Mutation_p.P550Q|DDX42_ENST00000359353.5_Missense_Mutation_p.P431Q|DDX42_ENST00000457800.2_Missense_Mutation_p.P550Q|DDX42_ENST00000389924.2_Missense_Mutation_p.P550Q	NM_007372.2	NP_031398.2	Q86XP3	DDX42_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 42	550	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				protein localization (GO:0008104)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)	46						AAGGACATCCCAGTCCTGGTG	0.418																																					p.P550Q		Atlas-SNP	.											.	DDX42	86	.	0			c.C1649A						.						60	57	58					17																	61889542		2203	4300	6503	SO:0001583	missense	11325	exon14			ACATCCCAGTCCT	BC015505	CCDS32704.1	17q23	2014-02-14	2013-05-13			ENSG00000198231		"DEAD-boxes"	18676	protein-coding gene	gene with protein product	"splicing factor 3b, subunit 8"	613369	"DEAD (Asp-Glu-Ala-Asp) box polypeptide 42"			10727850, 16397294	Standard	NM_007372		Approved	RNAHP, RHELP, SF3b125, SF3B8	uc002jbv.3	Q86XP3		ENST00000578681.1:c.1649C>A	chr17.hg19:g.61889542C>A	ENSP00000464050:p.Pro550Gln	170.0	0.0		100.0	4.0	NM_203499	A6NML1|A8KA43|O75619|Q68G51|Q96BK1|Q96HR7|Q9Y3V8	Missense_Mutation	SNP	ENST00000578681.1	hg19	CCDS32704.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.668879	0.88348	.	.	ENSG00000198231	ENST00000389924;ENST00000457800;ENST00000359353	T;T	0.75260	-0.92;-0.92	5.74	5.74	0.90152	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.75184	0.3815	N	0.25031	0.7	0.80722	D	1	P;P	0.42620	0.785;0.594	P;B	0.52031	0.688;0.403	T	0.76597	-0.2901	10	0.62326	D	0.03	-8.01	19.2994	0.94138	0.0:1.0:0.0:0.0	.	96;550	B3KV84;Q86XP3	.;DDX42_HUMAN	Q	550;550;286	ENSP00000374574:P550Q;ENSP00000390121:P550Q	ENSP00000352308:P286Q	P	+	2	0	DDX42	59243274	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.082000	0.71318	2.890000	0.99128	0.650000	0.86243	CCA	.	.		0.418	DDX42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444368.1	NM_007372		A	61889542	C	A	61889542	3	1	254	1	0	0	0	0	1	0	0	0	4364	594	21	3	1699	3	DDX42	17	61889542	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	5198704	61889542	19305668	853	35145										
SCN4A	6329	hgsc.bcm.edu	37	chr17	62022891	62022891	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	atgcagtagtagaacttgccGgcaaacaggttgacacccat	10	10	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:62022891G>T	ENST00000435607.1	-	19	3625	c.3549C>A	c.(3547-3549)gcC>gcA	p.A1183A	SCN4A_ENST00000578147.1_Silent_p.A1183A	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	1183					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AGAACTTGCCGGCAAACAGGT	0.542																																					p.A1183A		Atlas-SNP	.											.	SCN4A	205	.	0			c.C3549A						.						252	252	252					17																	62022891		2200	4300	6500	SO:0001819	synonymous_variant	6329	exon19			CTTGCCGGCAAAC	U24693		17q23.3	2012-02-26	2007-01-23					"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.3549C>A	chr17.hg19:g.62022891G>T		204.0	0.0		136.0	6.0	NM_000334	Q15478|Q16447|Q7Z6B1	Silent	SNP	ENST00000435607.1	hg19	CCDS45761.1																																																																																			.	.		0.542	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334		T	62022891	G	T	62022891	2	4	254	1	0	0	0	0	0	0	0	1	13935	1103	39	1		1	SCN4A	17	62022891	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	133349	62022891	19172319	854	35146										
ABCA9	10350	hgsc.bcm.edu	37	chr17	67017907	67017907	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttcatcaatagttgattttcCttctaatttcagaaacacct	3	9	4	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:67017907C>T	ENST00000340001.4	-	18	2588	c.2377G>A	c.(2377-2379)Gga>Aga	p.G793R	ABCA9_ENST00000370732.2_Missense_Mutation_p.G793R|ABCA9_ENST00000453985.2_Missense_Mutation_p.G793R	NM_080283.3	NP_525022.2	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 9	793					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(21)|lung(35)|ovary(4)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	91	Breast(10;1.47e-12)					GTTGATTTTCCTTCTAATTTC	0.338																																					p.G793R		Atlas-SNP	.											.	ABCA9	192	.	0			c.G2377A						.						89	88	89					17																	67017907		2202	4295	6497	SO:0001583	missense	10350	exon18			ATTTTCCTTCTAA	AF423307	CCDS11681.1	17q24	2012-03-14			ENSG00000154258	ENSG00000154258		"ATP binding cassette transporters / subfamily A"	39	protein-coding gene	gene with protein product		612507					Standard	XM_005256934		Approved	EST640918	uc002jhu.3	Q8IUA7	OTTHUMG00000140371	ENST00000340001.4:c.2377G>A	chr17.hg19:g.67017907C>T	ENSP00000342216:p.Gly793Arg	62.0	0.0		57.0	4.0	NM_080283	Q6P655|Q8N2S4|Q8WWZ5|Q96MD8	Missense_Mutation	SNP	ENST00000340001.4	hg19	CCDS11681.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.031549	0.75504	.	.	ENSG00000154258	ENST00000340001;ENST00000453985;ENST00000370732;ENST00000453749	D;D	0.82619	-1.63;-1.63	5.12	4.15	0.48705	.	0.000000	0.47455	D	0.000223	D	0.89451	0.6719	M	0.70595	2.14	0.40094	D	0.97628	D;D	0.89917	1.0;0.982	D;D	0.87578	0.998;0.942	D	0.90222	0.4272	10	0.59425	D	0.04	.	12.4951	0.55923	0.0:0.9178:0.0:0.0822	.	793;793	Q8IUA7-3;Q8IUA7	.;ABCA9_HUMAN	R	793;776;793;788	ENSP00000342216:G793R;ENSP00000359767:G793R	ENSP00000342216:G793R	G	-	1	0	ABCA9	64529502	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.584000	0.60971	1.300000	0.44818	0.603000	0.83216	GGA	.	.		0.338	ABCA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277072.2	NM_172386		T	67017907	C	T	67017907	3	4	254	1	0	0	0	0	1	0	0	0	39	690	24	3	2585	3	ABCA9	17	67017907	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	4995016	67017907	14177303	855	35147										
KIF19	124602	hgsc.bcm.edu	37	chr17	72324604	72324604	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	catcagcgtggcagagctggAggaaggagctaccctcatcg	14	11	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:72324604A>G	ENST00000389916.4	+	2	218	c.80A>G	c.(79-81)gAg>gGg	p.E27G		NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	27	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						GCAGAGCTGGAGGAAGGAGCT	0.617																																					p.E27G		Atlas-SNP	.											.	KIF19	102	.	0			c.A80G						.						49	44	46					17																	72324604		2203	4299	6502	SO:0001583	missense	124602	exon2			AGCTGGAGGAAGG	AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"Kinesins"	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.80A>G	chr17.hg19:g.72324604A>G	ENSP00000374566:p.Glu27Gly	78.0	0.0		49.0	4.0	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Missense_Mutation	SNP	ENST00000389916.4	hg19	CCDS32718.2	.	.	.	.	.	.	.	.	.	.	A	16.96	3.265121	0.59431	.	.	ENSG00000196169	ENST00000551294;ENST00000389916	T;T	0.76060	-0.67;-0.99	4.96	4.96	0.65561	Kinesin, motor domain (4);	0.707634	0.11041	U	0.606080	T	0.67002	0.2847	L	0.33189	0.99	0.41417	D	0.987773	B;B;B;B	0.22604	0.056;0.072;0.016;0.016	B;B;B;B	0.27608	0.081;0.066;0.019;0.019	T	0.60234	-0.7303	10	0.38643	T	0.18	.	12.2462	0.54572	1.0:0.0:0.0:0.0	.	27;27;27;27	Q2TAC6;F8VW50;Q2TAC6-3;Q2TAC6-2	KIF19_HUMAN;.;.;.	G	27	ENSP00000449134:E27G;ENSP00000374566:E27G	ENSP00000374566:E27G	E	+	2	0	KIF19	69836199	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.295000	0.72744	1.878000	0.54408	0.529000	0.55759	GAG	.	.		0.617	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209		G	72324604	A	G	72324604	3	3	254	1	0	0	0	0	1	0	0	0	8291	304	11	2	86	2	KIF19	17	72324604	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	5306697	72324604	8870606	856	35148										
CD300C	10871	hgsc.bcm.edu	37	chr17	72537867	72537867	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcaggaagcggacattgctgAacagggagctgtggggacac	17	8	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:72537867A>G	ENST00000330793.1	-	4	896	c.536T>C	c.(535-537)tTc>tCc	p.F179S		NM_006678.3	NP_006669.1	Q08708	CLM6_HUMAN	CD300c molecule	179					cellular defense response (GO:0006968)|immune system process (GO:0002376)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)			endometrium(2)|kidney(1)|large_intestine(4)|lung(11)|skin(2)|upper_aerodigestive_tract(1)	21						GACATTGCTGAACAGGGAGCT	0.627																																					p.F179S	Esophageal Squamous(66;421 1121 20537 25337 27468)	Atlas-SNP	.											.	CD300C	41	.	0			c.T536C						.						83	65	71					17																	72537867		2203	4300	6503	SO:0001583	missense	10871	exon4			TTGCTGAACAGGG	BC022279	CCDS11701.1	17q25.2	2014-05-15	2006-03-28		ENSG00000167850	ENSG00000167850		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	19320	protein-coding gene	gene with protein product		606786	"CD300c antigen"			1349532, 10746781	Standard	NM_006678		Approved	CMRF35, LIR, CMRF-35A, CMRF35A, IGSF16	uc002jky.2	Q08708	OTTHUMG00000067608	ENST00000330793.1:c.536T>C	chr17.hg19:g.72537867A>G	ENSP00000329507:p.Phe179Ser	76.0	0.0		55.0	4.0	NM_006678		Missense_Mutation	SNP	ENST00000330793.1	hg19	CCDS11701.1	.	.	.	.	.	.	.	.	.	.	A	6.368	0.436008	0.12104	.	.	ENSG00000167850	ENST00000330793	T	0.03242	4.0	4.74	3.66	0.41972	.	0.567919	0.14416	N	0.320989	T	0.02083	0.0065	N	0.08118	0	0.09310	N	1	B	0.17465	0.022	B	0.15484	0.013	T	0.48592	-0.9022	10	0.19590	T	0.45	.	7.4927	0.27471	0.8983:0.0:0.1017:0.0	.	179	Q08708	CLM6_HUMAN	S	179	ENSP00000329507:F179S	ENSP00000329507:F179S	F	-	2	0	CD300C	70049462	0.003000	0.15002	0.072000	0.20136	0.001000	0.01503	1.620000	0.36976	0.930000	0.37217	0.477000	0.44152	TTC	.	.		0.627	CD300C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145084.1	NM_006678		G	72537867	A	G	72537867	3	3	254	1	0	0	0	0	1	0	0	0	2999	246	9	2	142	2	CD300C	17	72537867	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	213263	72537867	8657343	857	35149										
SLC16A5	9121	hgsc.bcm.edu	37	chr17	73100204	73100204	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggcaagcaggctgtcgcggcGgatgccctggagcgggatct	18	11	1	0	rs141647560	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:73100204G>C	ENST00000450736.2	+	5	1708	c.1293G>C	c.(1291-1293)gcG>gcC	p.A431A	SLC16A5_ENST00000538213.2_Silent_p.A471A|SLC16A5_ENST00000580123.1_Silent_p.A431A|SLC16A5_ENST00000329783.4_Silent_p.A431A			O15375	MOT6_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 5	431					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	22	all_lung(278;0.226)		LUSC - Lung squamous cell carcinoma(166;0.162)|Lung(188;0.235)		Pyruvic acid(DB00119)	CTGTCGCGGCGGATGCCCTGG	0.567																																					p.A431A		Atlas-SNP	.											SLC16A5_ENST00000450736,colon,carcinoma,+1,2	SLC16A5	80	.	0			c.G1293C						.						71	66	68					17																	73100204		2203	4300	6503	SO:0001819	synonymous_variant	9121	exon6			CGCGGCGGATGCC	U59299	CCDS11713.1	17q25.1	2013-07-18	2013-07-18		ENSG00000170190	ENSG00000170190		"Solute carriers"	10926	protein-coding gene	gene with protein product		603879	"solute carrier family 16 (monocarboxylic acid transporters), member 5", "solute carrier family 16, member 5 (monocarboxylic acid transporter 6)"			9425115	Standard	NM_004695		Approved	MCT5, MCT6	uc002jmr.4	O15375	OTTHUMG00000179277	ENST00000450736.2:c.1293G>C	chr17.hg19:g.73100204G>C		176.0	0.0		133.0	39.0	NM_001271765	B4E288	Silent	SNP	ENST00000450736.2	hg19	CCDS11713.1																																																																																			.	G|0.999;A|0.001		0.567	SLC16A5-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445547.1	NM_004695		C	73100204	G	C	73100204	2	2	254	1	0	0	0	0	0	0	0	1	14426	1103	39	4		4	SLC16A5	17	73100204	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	562337	73100204	8095006	858	35150										
CASKIN2	57513	hgsc.bcm.edu	37	chr17	73501024	73501024	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgggtgcggaggggaggcggGctgcagggatgcccacccgc	21	11	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:73501024G>T	ENST00000321617.3	-	11	1647	c.1061C>A	c.(1060-1062)gCc>gAc	p.A354D	CASKIN2_ENST00000433559.2_Missense_Mutation_p.A272D	NM_020753.3	NP_065804.2	Q8WXE0	CSKI2_HUMAN	CASK interacting protein 2	354						cytoplasm (GO:0005737)				endometrium(1)|kidney(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	18	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;4.57e-07)|Epithelial(20;2.92e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			GGGGAGGCGGGCTGCAGGGAT	0.682																																					p.A354D		Atlas-SNP	.											CASKIN2,NS,carcinoma,0,1	CASKIN2	66	.	0			c.C1061A						.						22	23	23					17																	73501024		2201	4294	6495	SO:0001583	missense	57513	exon11			AGGCGGGCTGCAG	AB032965	CCDS11723.1, CCDS45775.1	17q25.1	2014-09-04			ENSG00000177303	ENSG00000177303		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	18200	protein-coding gene	gene with protein product		612185				12040031	Standard	NM_020753		Approved	KIAA1139, FLJ21609, ANKS5B	uc002joc.4	Q8WXE0	OTTHUMG00000179683	ENST00000321617.3:c.1061C>A	chr17.hg19:g.73501024G>T	ENSP00000325355:p.Ala354Asp	97.0	2.0		71.0	3.0	NM_020753	B4DTT3|B7Z9H1|Q7LG69|Q9ULT1	Missense_Mutation	SNP	ENST00000321617.3	hg19	CCDS11723.1	.	.	.	.	.	.	.	.	.	.	G	11.85	1.760757	0.31137	.	.	ENSG00000177303	ENST00000321617;ENST00000433559	T;T	0.70516	-0.49;-0.3	5.07	5.07	0.68467	Src homology-3 domain (1);	0.978162	0.08318	N	0.964242	T	0.54631	0.1870	N	0.14661	0.345	0.80722	D	1	B	0.23058	0.079	B	0.20384	0.029	T	0.44019	-0.9355	10	0.33940	T	0.23	.	9.3643	0.38215	0.0943:0.0:0.9057:0.0	.	354	Q8WXE0	CSKI2_HUMAN	D	354;272	ENSP00000325355:A354D;ENSP00000406963:A272D	ENSP00000325355:A354D	A	-	2	0	CASKIN2	71012619	0.960000	0.32886	0.956000	0.39512	0.024000	0.10985	1.900000	0.39828	2.644000	0.89710	0.561000	0.74099	GCC	.	.		0.682	CASKIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447609.1	NM_020753		T	73501024	G	T	73501024	3	4	254	1	0	0	0	0	1	0	0	0	2669	1203	42	3	2587	3	CASKIN2	17	73501024	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	400820	73501024	7694186	859	35151										
LLGL2	3993	hgsc.bcm.edu	37	chr17	73570325	73570325	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggcctggtgatggagcgcgcTctgctcagtgatgagagtga	17	8	2	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:73570325T>C	ENST00000392550.3	+	23	3054	c.2937T>C	c.(2935-2937)gcT>gcC	p.A979A	LLGL2_ENST00000577200.1_Silent_p.A979A|LLGL2_ENST00000167462.5_Silent_p.A979A	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	979					cell cycle (GO:0007049)|cell division (GO:0051301)|exocytosis (GO:0006887)|regulation of establishment or maintenance of cell polarity (GO:0032878)	cytoplasm (GO:0005737)	PDZ domain binding (GO:0030165)			NS(1)|breast(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)			TGGAGCGCGCTCTGCTCAGTG	0.692																																					p.A979A		Atlas-SNP	.											.	LLGL2	155	.	0			c.T2937C						.						3	4	4					17																	73570325		1643	3154	4797	SO:0001819	synonymous_variant	3993	exon23			GCGCGCTCTGCTC	X87342	CCDS11725.1, CCDS32733.1, CCDS45776.1	17q25.1	2013-01-10	2001-11-28			ENSG00000073350		"WD repeat domain containing"	6629	protein-coding gene	gene with protein product			"lethal giant larvae (Drosophila) homolog 2"				Standard	XR_243659		Approved	HGL	uc002joh.3	Q6P1M3		ENST00000392550.3:c.2937T>C	chr17.hg19:g.73570325T>C		113.0	0.0		96.0	4.0	NM_004524	Q14521|Q9BR62	Silent	SNP	ENST00000392550.3	hg19	CCDS32733.1																																																																																			.	.		0.692	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524		C	73570325	T	C	73570325	2	2	254	1	0	0	0	0	0	0	0	1	8843	1538	54	2		2	LLGL2	17	73570325	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	69301	73570325	7624885	860	35152										
RECQL5	9400	hgsc.bcm.edu	37	chr17	73657713	73657713	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtaagccttggcgttcacacCcctgcagctgagctctatgg	11	13	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:73657713C>A	ENST00000317905.5	-	5	1006	c.847G>T	c.(847-849)Ggt>Tgt	p.G283C	RECQL5_ENST00000420326.2_Missense_Mutation_p.G283C|RECQL5_ENST00000340830.5_Missense_Mutation_p.G283C|RECQL5_ENST00000584999.1_Missense_Mutation_p.G283C|RECQL5_ENST00000423245.2_Missense_Mutation_p.G256C	NM_004259.6	NP_004250.4	O94762	RECQ5_HUMAN	RecQ protein-like 5	283	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				chromosome separation (GO:0051304)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|mitotic nuclear division (GO:0007067)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA helicase activity (GO:0003678)|nucleic acid binding (GO:0003676)|RNA polymerase II core binding (GO:0000993)			breast(1)|cervix(3)|endometrium(3)|kidney(7)|large_intestine(7)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	36	all_cancers(13;2.73e-08)|Breast(9;6.04e-09)|all_epithelial(9;6.79e-09)		all cancers(21;1.15e-06)|Epithelial(20;2.19e-06)|Lung(188;0.101)|LUSC - Lung squamous cell carcinoma(166;0.112)			GCGTTCACACCCCTGCAGCTG	0.532								Other identified genes with known or suspected DNA repair function																													p.G283C		Atlas-SNP	.											.	RECQL5	77	.	0			c.G847T						.						96	89	91					17																	73657713		2203	4300	6503	SO:0001583	missense	9400	exon5			TCACACCCCTGCA	AB006533	CCDS32735.1, CCDS42380.1, CCDS45777.1	17q25	2014-03-07	2014-03-07	2014-03-07	ENSG00000108469	ENSG00000108469			9950	protein-coding gene	gene with protein product	"RecQ protein 5"	603781				9878247	Standard	NM_004259		Approved	RecQ5, FLJ90603	uc010dgl.3	O94762		ENST00000317905.5:c.847G>T	chr17.hg19:g.73657713C>A	ENSP00000317636:p.Gly283Cys	73.0	0.0		56.0	4.0	NM_001003715	Q9H0B1|Q9P1W7|Q9UNC8	Missense_Mutation	SNP	ENST00000317905.5	hg19	CCDS42380.1	.	.	.	.	.	.	.	.	.	.	C	17.04	3.287710	0.59976	.	.	ENSG00000108469	ENST00000423245;ENST00000317905;ENST00000420326;ENST00000340830	T;T;T	0.09163	3.01;3.01;3.01	5.95	5.95	0.96441	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.53530	0.1802	H	0.98048	4.135	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.70887	-0.4750	10	0.87932	D	0	-7.074	20.3932	0.98965	0.0:1.0:0.0:0.0	.	283;256;283	O94762;Q6P4G0;O94762-3	RECQ5_HUMAN;.;.	C	283	ENSP00000317636:G283C;ENSP00000414933:G283C;ENSP00000341983:G283C	ENSP00000317636:G283C	G	-	1	0	RECQL5	71169308	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	7.677000	0.84024	2.824000	0.97209	0.655000	0.94253	GGT	.	.		0.532	RECQL5-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448207.1	NM_004259		A	73657713	C	A	73657713	3	1	254	1	0	0	0	0	1	0	0	0	13218	623	22	3	2279	3	RECQL5	17	73657713	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	87388	73657713	7537497	861	35153										
EXOC7	23265	hgsc.bcm.edu	37	chr17	74081819	74081819	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gaagatggcgctcagagctgGgtcctcgtacaccttggact	13	11	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:74081819G>T	ENST00000335146.7	-	15	1761	c.1708C>A	c.(1708-1710)Cca>Aca	p.P570T	EXOC7_ENST00000591724.1_5'Flank|EXOC7_ENST00000467929.2_Missense_Mutation_p.P491T|EXOC7_ENST00000405575.4_Missense_Mutation_p.P542T|EXOC7_ENST00000607838.1_Missense_Mutation_p.P542T|EXOC7_ENST00000589210.1_Missense_Mutation_p.P519T|EXOC7_ENST00000332065.5_Missense_Mutation_p.P488T|EXOC7_ENST00000411744.2_Missense_Mutation_p.P511T			Q9UPT5	EXOC7_HUMAN	exocyst complex component 7	570					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	centriolar satellite (GO:0034451)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)				NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	14			LUSC - Lung squamous cell carcinoma(166;0.187)			CTCAGAGCTGGGTCCTCGTAC	0.547																																					p.P570T		Atlas-SNP	.											.	EXOC7	47	.	0			c.C1708A						.						119	111	114					17																	74081819		2203	4300	6503	SO:0001583	missense	23265	exon15			GAGCTGGGTCCTC	BC029432	CCDS11741.1, CCDS32738.1, CCDS45781.1, CCDS45782.1, CCDS45784.1, CCDS74164.1	17q25.3	2013-01-22			ENSG00000182473	ENSG00000182473			23214	protein-coding gene	gene with protein product		608163				12477932	Standard	NM_001013839		Approved	EXO70, KIAA1067, YJL085W, Exo70p	uc010wsw.2	Q9UPT5	OTTHUMG00000150720	ENST00000335146.7:c.1708C>A	chr17.hg19:g.74081819G>T	ENSP00000334100:p.Pro570Thr	127.0	0.0		91.0	4.0	NM_001145297	B5MC69|B8XXP2|Q8ND93|Q8WV91|Q96FF0|Q9H8C3|Q9H9X3|Q9HA32	Missense_Mutation	SNP	ENST00000335146.7	hg19	CCDS45782.1	.	.	.	.	.	.	.	.	.	.	G	5.532	0.283140	0.10458	.	.	ENSG00000182473	ENST00000332065;ENST00000351709;ENST00000405575;ENST00000335146;ENST00000357231;ENST00000425372;ENST00000411744	.	.	.	4.06	4.06	0.47325	Cullin repeat-like-containing domain (1);	0.126283	0.53938	D	0.000051	T	0.60534	0.2276	L	0.43152	1.355	0.80722	D	1	B;B;P;B;B;B;B	0.42692	0.039;0.024;0.787;0.022;0.049;0.027;0.022	B;B;P;B;B;B;B	0.51516	0.014;0.036;0.672;0.022;0.054;0.012;0.054	T	0.56025	-0.8047	9	0.21540	T	0.41	-16.0913	16.449	0.83973	0.0:0.0:1.0:0.0	.	511;542;491;456;570;488;519	Q9UPT5-5;Q9UPT5-6;B4DJ07;F5H1P1;Q9UPT5;Q9UPT5-2;Q9UPT5-1	.;.;.;.;EXOC7_HUMAN;.;.	T	488;408;542;570;519;456;511	.	ENSP00000333806:P488T	P	-	1	0	EXOC7	71593414	1.000000	0.71417	0.994000	0.49952	0.980000	0.70556	5.981000	0.70524	2.110000	0.64415	0.585000	0.79938	CCA	.	.		0.547	EXOC7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000319768.2	NM_015219		T	74081819	G	T	74081819	3	4	254	1	0	0	0	0	1	0	0	0	5312	1232	43	3	523	3	EXOC7	17	74081819	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	424106	74081819	7113391	862	35154										
TNRC6C	57690	hgsc.bcm.edu	37	chr17	76045435	76045435	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	actccaatgctggcattaatCttaaccttaatcctaatgcc	4	12	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:76045435C>A	ENST00000588061.1	+	5	1019	c.292C>A	c.(292-294)Ctt>Att	p.L98I	TNRC6C_ENST00000588847.1_Missense_Mutation_p.L98I|TNRC6C_ENST00000541771.1_Missense_Mutation_p.L98I|TNRC6C_ENST00000301624.4_Missense_Mutation_p.L98I|TNRC6C_ENST00000544502.1_Missense_Mutation_p.L98I|TNRC6C_ENST00000335749.4_Missense_Mutation_p.L98I			Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C	98	Sufficient for interaction with argonaute family proteins.				embryonic hemopoiesis (GO:0035162)|endoderm formation (GO:0001706)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of gene silencing by miRNA (GO:0060964)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			TGGCATTAATCTTAACCTTAA	0.502																																					p.L98I		Atlas-SNP	.											.	TNRC6C	173	.	0			c.C292A						.						48	52	50					17																	76045435		2034	4184	6218	SO:0001583	missense	57690	exon4			ATTAATCTTAACC	AL834429	CCDS45798.1, CCDS45799.1	17q25.3	2012-10-04			ENSG00000078687	ENSG00000078687		"Trinucleotide (CAG) repeat containing"	29318	protein-coding gene	gene with protein product		610741					Standard	NM_018996		Approved	KIAA1582, FLJ20015	uc002juf.2	Q9HCJ0	OTTHUMG00000132642	ENST00000588061.1:c.292C>A	chr17.hg19:g.76045435C>A	ENSP00000468647:p.Leu98Ile	188.0	0.0		114.0	5.0	NM_018996	G3XAB8|Q86UE5|Q8N3D8|Q96MU9	Missense_Mutation	SNP	ENST00000588061.1	hg19	CCDS45798.1	.	.	.	.	.	.	.	.	.	.	C	13.67	2.307755	0.40795	.	.	ENSG00000078687	ENST00000455761;ENST00000395801;ENST00000335749;ENST00000301624;ENST00000541771;ENST00000544502	T;T;T;T	0.17054	2.3;2.32;2.32;2.3	4.82	4.82	0.62117	.	0.125823	0.56097	D	0.000040	T	0.37073	0.0990	L	0.47716	1.5	0.58432	D	0.999996	D;D;D	0.89917	0.998;1.0;0.997	D;D;D	0.83275	0.996;0.996;0.991	T	0.04811	-1.0925	10	0.54805	T	0.06	-10.7183	18.4841	0.90823	0.0:1.0:0.0:0.0	.	98;98;98	G3XAB8;Q9HCJ0-2;Q9HCJ0	.;.;TNR6C_HUMAN	I	98	ENSP00000336783:L98I;ENSP00000301624:L98I;ENSP00000440310:L98I;ENSP00000442421:L98I	ENSP00000301624:L98I	L	+	1	0	TNRC6C	73557030	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.361000	0.59461	2.673000	0.90976	0.655000	0.94253	CTT	.	.		0.502	TNRC6C-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395947.1	NM_018996		A	76045435	C	A	76045435	3	1	254	1	0	0	0	0	1	0	0	0	16357	913	32	3	294	3	TNRC6C	17	76045435	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1963616	76045435	5149775	863	35155										
TNRC6C	57690	hgsc.bcm.edu	37	chr17	76046560	76046560	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctaggtctgaaaggaaaaatGacaatgggacagaggcctgg	14	6	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:76046560G>A	ENST00000588061.1	+	5	2144	c.1417G>A	c.(1417-1419)Gac>Aac	p.D473N	TNRC6C_ENST00000588847.1_Missense_Mutation_p.D473N|TNRC6C_ENST00000541771.1_Missense_Mutation_p.D473N|TNRC6C_ENST00000301624.4_Missense_Mutation_p.D473N|TNRC6C_ENST00000544502.1_Missense_Mutation_p.D473N|TNRC6C_ENST00000335749.4_Missense_Mutation_p.D473N			Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C	473	Sufficient for interaction with argonaute family proteins.				embryonic hemopoiesis (GO:0035162)|endoderm formation (GO:0001706)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of gene silencing by miRNA (GO:0060964)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			AAGGAAAAATGACAATGGGAC	0.478																																					p.D473N		Atlas-SNP	.											.	TNRC6C	173	.	0			c.G1417A						.						75	76	76					17																	76046560		1883	4117	6000	SO:0001583	missense	57690	exon4			AAAAATGACAATG	AL834429	CCDS45798.1, CCDS45799.1	17q25.3	2012-10-04			ENSG00000078687	ENSG00000078687		"Trinucleotide (CAG) repeat containing"	29318	protein-coding gene	gene with protein product		610741					Standard	NM_018996		Approved	KIAA1582, FLJ20015	uc002juf.2	Q9HCJ0	OTTHUMG00000132642	ENST00000588061.1:c.1417G>A	chr17.hg19:g.76046560G>A	ENSP00000468647:p.Asp473Asn	99.0	0.0		76.0	4.0	NM_018996	G3XAB8|Q86UE5|Q8N3D8|Q96MU9	Missense_Mutation	SNP	ENST00000588061.1	hg19	CCDS45798.1	.	.	.	.	.	.	.	.	.	.	G	18.25	3.582408	0.65992	.	.	ENSG00000078687	ENST00000455761;ENST00000395801;ENST00000335749;ENST00000301624;ENST00000541771;ENST00000544502	T;T;T;T	0.23348	1.91;2.1;2.1;1.91	5.07	5.07	0.68467	.	0.268851	0.41396	D	0.000885	T	0.51143	0.1657	M	0.71036	2.16	0.46222	D	0.998935	D;D;B	0.89917	0.999;1.0;0.397	D;D;B	0.91635	0.995;0.999;0.085	T	0.40040	-0.9584	10	0.31617	T	0.26	-26.0189	18.6486	0.91421	0.0:0.0:1.0:0.0	.	473;473;473	G3XAB8;Q9HCJ0-2;Q9HCJ0	.;.;TNR6C_HUMAN	N	473	ENSP00000336783:D473N;ENSP00000301624:D473N;ENSP00000440310:D473N;ENSP00000442421:D473N	ENSP00000301624:D473N	D	+	1	0	TNRC6C	73558155	1.000000	0.71417	0.991000	0.47740	0.998000	0.95712	5.249000	0.65427	2.644000	0.89710	0.563000	0.77884	GAC	.	.		0.478	TNRC6C-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395947.1	NM_018996		A	76046560	G	A	76046560	3	1	254	1	0	0	0	0	1	0	0	0	16357	1290	45	3	1419	3	TNRC6C	17	76046560	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1125	76046560	5148650	864	35156										
EIF4A3	9775	hgsc.bcm.edu	37	chr17	78109863	78109863	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctcgatatctctgaggatgcGgatgtcgtcattctttacaa	9	9	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:78109863G>T	ENST00000269349.3	-	11	1380	c.1159C>A	c.(1159-1161)Cgc>Agc	p.R387S		NM_014740.3	NP_055555.1	P38919	IF4A3_HUMAN	eukaryotic translation initiation factor 4A3	387	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|cytokine-mediated signaling pathway (GO:0019221)|embryonic cranial skeleton morphogenesis (GO:0048701)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|mRNA binding (GO:0003729)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	10	all_neural(118;0.117)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.139)			CTGAGGATGCGGATGTCGTCA	0.428																																					p.R387S		Atlas-SNP	.											.	EIF4A3	35	.	0			c.C1159A						.						128	120	123					17																	78109863		2203	4300	6503	SO:0001583	missense	9775	exon11			GGATGCGGATGTC	BC004386	CCDS11767.1	17q25.3	2010-02-10	2010-02-10	2006-11-27		ENSG00000141543		"DEAD-boxes"	18683	protein-coding gene	gene with protein product		608546	"DEAD (Asp-Glu-Ala-Asp) box polypeptide 48", "eukaryotic translation initiation factor 4A, isoform 3"	DDX48		10623621, 14730019	Standard	NM_014740		Approved	KIAA0111, EIF4AIII	uc002jxs.3	P38919		ENST00000269349.3:c.1159C>A	chr17.hg19:g.78109863G>T	ENSP00000269349:p.Arg387Ser	81.0	0.0		58.0	4.0	NM_014740	Q15033|Q6IBQ2|Q96A18	Missense_Mutation	SNP	ENST00000269349.3	hg19	CCDS11767.1	.	.	.	.	.	.	.	.	.	.	G	9.791	1.178053	0.21787	.	.	ENSG00000141543	ENST00000269349	T	0.04551	3.6	4.18	2.12	0.27331	Helicase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.03348	0.0097	N	0.20845	0.615	0.80722	D	1	B	0.10296	0.003	B	0.12837	0.008	T	0.44605	-0.9317	10	0.72032	D	0.01	-18.3621	6.2572	0.20879	0.1016:0.0:0.7137:0.1847	.	387	P38919	IF4A3_HUMAN	S	387	ENSP00000269349:R387S	ENSP00000269349:R387S	R	-	1	0	EIF4A3	75724458	1.000000	0.71417	0.809000	0.32408	0.155000	0.21991	5.903000	0.69877	0.397000	0.25310	0.555000	0.69702	CGC	.	.		0.428	EIF4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437446.1	NM_014740		T	78109863	G	T	78109863	3	4	254	1	0	0	0	0	1	0	0	0	5028	1116	39	1	84	1	EIF4A3	17	78109863	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	2063303	78109863	3085347	865	35157										
RNF213	57674	hgsc.bcm.edu	37	chr17	78341922	78341922	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cttgccagacgaattctctcCagctgtttcccaagcgcaca	7	15	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:78341922C>A	ENST00000582970.1	+	44	12277	c.12134C>A	c.(12133-12135)cCa>cAa	p.P4045Q	RNF213_ENST00000508628.2_Missense_Mutation_p.P4094Q|CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000336301.6_Missense_Mutation_p.P2118Q|CTD-2047H16.4_ENST00000572151.1_RNA	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	4045					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			GAATTCTCTCCAGCTGTTTCC	0.468																																					p.P4045Q		Atlas-SNP	.											.	RNF213	766	.	0			c.C12134A						.						152	146	148					17																	78341922		2203	4300	6503	SO:0001583	missense	57674	exon44			TCTCTCCAGCTGT	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.12134C>A	chr17.hg19:g.78341922C>A	ENSP00000464087:p.Pro4045Gln	138.0	0.0		110.0	5.0	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	hg19	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	C	14.11	2.438437	0.43326	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301	T;T	0.24723	2.06;1.84	4.67	-5.25	0.02781	Zinc finger, RING/FYVE/PHD-type (1);	1.235290	0.05537	N	0.565002	T	0.47728	0.1461	M	0.80183	2.485	0.09310	N	1	D;P	0.61080	0.989;0.944	P;P	0.61201	0.885;0.642	T	0.58222	-0.7674	10	0.48119	T	0.1	.	13.5295	0.61613	0.0:0.278:0.0:0.722	.	4094;2118	C9JCP4;Q63HN8	.;RN213_HUMAN	Q	4045;4094;2118	ENSP00000425956:P4045Q;ENSP00000338218:P2118Q	ENSP00000338218:P2118Q	P	+	2	0	RNF213	75956517	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.289000	0.08365	-1.017000	0.03367	-0.768000	0.03414	CCA	.	.		0.468	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		A	78341922	C	A	78341922	3	1	254	1	0	0	0	0	1	0	0	0	13492	594	21	3	12623	3	RNF213	17	78341922	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	232059	78341922	2853288	866	35158										
C17orf70	80233	hgsc.bcm.edu	37	chr17	79514378	79514378	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggggtagcgtcacctcccgcCgagcaccggggccgagctgg	17	15	1	0	rs72854496	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:79514378C>A	ENST00000327787.8	-	5	1776	c.1730G>T	c.(1729-1731)cGg>cTg	p.R577L	C17orf70_ENST00000425898.2_Missense_Mutation_p.R226L|C17orf70_ENST00000537152.1_Missense_Mutation_p.R426L			Q0VG06	FP100_HUMAN	chromosome 17 open reading frame 70	577					DNA repair (GO:0006281)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	19	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0371)			CACCTCCCGCCGAGCACCGGG	0.677																																					p.R577L		Atlas-SNP	.											.	C17orf70	79	.	0			c.G1730T						.						38	38	38					17																	79514378		2202	4292	6494	SO:0001583	missense	80233	exon5			TCCCGCCGAGCAC	BC008883	CCDS32765.1, CCDS32765.2	17q25.3	2012-05-30			ENSG00000185504	ENSG00000185504			26171	protein-coding gene	gene with protein product	"Fanconi anemia-associated protein, 100kDa"	611301				17396147	Standard	NM_025161		Approved	FLJ22175, FAAP100	uc002kaq.3	Q0VG06	OTTHUMG00000167764	ENST00000327787.8:c.1730G>T	chr17.hg19:g.79514378C>A	ENSP00000333283:p.Arg577Leu	42.0	0.0		45.0	4.0	NM_025161	A6NNM1|Q8N3F7|Q9BV13|Q9H6K7|Q9H7E8	Missense_Mutation	SNP	ENST00000327787.8	hg19	CCDS32765.2	.	.	.	.	.	.	.	.	.	.	C	9.341	1.063042	0.19987	.	.	ENSG00000185504	ENST00000327787;ENST00000425898;ENST00000537152	T;T;T	0.34472	1.36;1.36;1.36	4.49	-4.3	0.03710	.	0.906018	0.09076	N	0.852135	T	0.31136	0.0787	L	0.54323	1.7	0.09310	N	1	B;P	0.35226	0.275;0.491	B;B	0.32724	0.061;0.151	T	0.34650	-0.9820	10	0.66056	D	0.02	.	12.654	0.56778	0.0:0.2074:0.0:0.7926	.	577;226	Q0VG06;E7EVV8	FP100_HUMAN;.	L	577;226;426	ENSP00000333283:R577L;ENSP00000399674:R226L;ENSP00000440151:R426L	ENSP00000333283:R577L	R	-	2	0	C17orf70	77124831	0.000000	0.05858	0.028000	0.17463	0.054000	0.15201	0.098000	0.15189	-0.676000	0.05238	-1.069000	0.02264	CGG	.	C|1.000;T|0.000		0.677	C17orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396170.1	NM_025161		A	79514378	C	A	79514378	3	1	254	1	0	0	0	0	1	0	0	0	1879	652	23	1	935	1	C17orf70	17	79514378	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1172456	79514378	1680832	867	35159										
P4HB	5034	hgsc.bcm.edu	37	chr17	79817083	79817083	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	attccttgggggaagccgtgTctccattcctgaagaacttg	11	10	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:79817083T>C	ENST00000331483.4	-	2	548	c.326A>G	c.(325-327)gAc>gGc	p.D109G	P4HB_ENST00000472244.1_5'Flank|P4HB_ENST00000439918.2_Missense_Mutation_p.D109G|P4HB_ENST00000576390.1_Intron	NM_000918.3	NP_000909.2	P07237	PDIA1_HUMAN	prolyl 4-hydroxylase, beta polypeptide	109	Thioredoxin 1. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|cellular response to hypoxia (GO:0071456)|extracellular matrix organization (GO:0030198)|lipoprotein metabolic process (GO:0042157)|peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)|protein folding (GO:0006457)|regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902175)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|procollagen-proline 4-dioxygenase complex (GO:0016222)	poly(A) RNA binding (GO:0044822)|procollagen-proline 4-dioxygenase activity (GO:0004656)|protein disulfide isomerase activity (GO:0003756)			NS(1)|breast(1)|large_intestine(2)|lung(17)|urinary_tract(1)	22	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0509)			GGAAGCCGTGTCTCCATTCCT	0.602																																					p.D109G	Colon(49;444 983 1296 7887 42561)	Atlas-SNP	.											.	P4HB	43	.	0			c.A326G						.						152	143	146					17																	79817083		2203	4298	6501	SO:0001583	missense	5034	exon2			GCCGTGTCTCCAT	J02783	CCDS11787.1	17q25	2011-10-19	2008-12-09		ENSG00000185624	ENSG00000185624	1.14.11.2, 5.3.4.1	"Protein disulfide isomerases"	8548	protein-coding gene	gene with protein product	"protein disulfide isomerase-associated 1", "protein disulfide isomerase family A, member 1", "collagen prolyl 4-hydroxylase beta"	176790	"procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), beta polypeptide (protein disulfide isomerase; thyroid hormone binding protein p55)", "procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), beta polypeptide (protein disulfide isomerase-associated 1)", "procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), beta polypeptide"	PO4DB, ERBA2L		8111381	Standard	NM_000918		Approved	PDIA1, PROHB, DSI, GIT, PDI, PO4HB, P4Hbeta	uc002kbn.1	P07237	OTTHUMG00000150269	ENST00000331483.4:c.326A>G	chr17.hg19:g.79817083T>C	ENSP00000327801:p.Asp109Gly	116.0	0.0		82.0	6.0	NM_000918	B2RDQ2|P30037|P32079|Q15205|Q6LDE5	Missense_Mutation	SNP	ENST00000331483.4	hg19	CCDS11787.1	.	.	.	.	.	.	.	.	.	.	T	14.79	2.639882	0.47153	.	.	ENSG00000185624	ENST00000331483;ENST00000537205;ENST00000436463	T	0.03242	4.0	4.59	3.49	0.39957	Thioredoxin domain (1);Thioredoxin-like fold (3);Disulphide isomerase (1);	0.173592	0.49305	D	0.000154	T	0.02455	0.0075	N	0.02120	-0.675	0.38770	D	0.954535	P	0.39964	0.697	P	0.44732	0.459	T	0.61623	-0.7025	10	0.59425	D	0.04	.	10.9514	0.47332	0.0:0.0:0.1576:0.8424	.	109	P07237	PDIA1_HUMAN	G	109;109;93	ENSP00000327801:D109G	ENSP00000327801:D109G	D	-	2	0	P4HB	77410372	1.000000	0.71417	0.864000	0.33941	0.022000	0.10575	7.768000	0.85345	0.605000	0.29947	-0.460000	0.05396	GAC	.	.		0.602	P4HB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317250.3	NM_000918		C	79817083	T	C	79817083	3	2	254	1	0	0	0	0	1	0	0	0	11368	1667	58	2	1240	2	P4HB	17	79817083	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	302705	79817083	1378127	868	35160										
FASN	2194	hgsc.bcm.edu	37	chr17	80046286	80046286	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cgatgttgtagatggcggctGagggggaacctgaaccgttg	17	7	0	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr17:80046286G>A	ENST00000306749.2	-	16	2791	c.2573C>T	c.(2572-2574)tCa>tTa	p.S858L		NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	858					acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	GATGGCGGCTGAGGGGGAACC	0.682																																					p.S858L	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.C2573T						.						28	36	33					17																	80046286		2196	4292	6488	SO:0001583	missense	2194	exon16			GCGGCTGAGGGGG	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.2573C>T	chr17.hg19:g.80046286G>A	ENSP00000304592:p.Ser858Leu	54.0	0.0		40.0	4.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	hg19	CCDS11801.1	.	.	.	.	.	.	.	.	.	.	G	13.29	2.192936	0.38707	.	.	ENSG00000169710	ENST00000306749	D	0.84800	-1.9	4.24	3.25	0.37280	.	0.145982	0.47455	D	0.000239	D	0.88771	0.6527	M	0.80616	2.505	0.20196	N	0.999921	P	0.41131	0.739	P	0.48795	0.59	T	0.82112	-0.0618	10	0.48119	T	0.1	-5.9456	14.0528	0.64749	0.0:0.1524:0.8476:0.0	.	858	P49327	FAS_HUMAN	L	858	ENSP00000304592:S858L	ENSP00000304592:S858L	S	-	2	0	FASN	77639575	0.999000	0.42202	0.002000	0.10522	0.005000	0.04900	6.083000	0.71326	0.977000	0.38444	0.462000	0.41574	TCA	.	.		0.682	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		A	80046286	G	A	80046286	3	1	254	1	0	0	0	0	1	0	0	0	5691	1294	45	3	5074	3	FASN	17	80046286	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	229203	80046286	1148924	869	35161										
EMILIN2	84034	hgsc.bcm.edu	37	chr18	2891118	2891118	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctgagagaggagctcatggaGggcatggacagaaagctggc	17	7	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:2891118G>T	ENST00000254528.3	+	4	1152	c.993G>T	c.(991-993)gaG>gaT	p.E331D		NM_032048.2	NP_114437.2	Q9BXX0	EMIL2_HUMAN	elastin microfibril interfacer 2	331					cell adhesion (GO:0007155)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix constituent conferring elasticity (GO:0030023)			breast(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(4)	48				READ - Rectum adenocarcinoma(2;0.1)		AGCTCATGGAGGGCATGGACA	0.552																																					p.E331D		Atlas-SNP	.											.	EMILIN2	97	.	0			c.G993T						.						113	116	115					18																	2891118		2203	4300	6503	SO:0001583	missense	84034	exon4			CATGGAGGGCATG	AF270513	CCDS11828.1	18p11.3	2008-02-05			ENSG00000132205	ENSG00000132205		"EMI domain containing"	19881	protein-coding gene	gene with protein product		608928					Standard	NM_032048		Approved	FLJ33200, FOAP-10	uc002kln.3	Q9BXX0	OTTHUMG00000128525	ENST00000254528.3:c.993G>T	chr18.hg19:g.2891118G>T	ENSP00000254528:p.Glu331Asp	88.0	0.0		78.0	5.0	NM_032048	B2RMY3|Q8NBH3|Q96JQ4	Missense_Mutation	SNP	ENST00000254528.3	hg19	CCDS11828.1	.	.	.	.	.	.	.	.	.	.	G	12.36	1.915026	0.33815	.	.	ENSG00000132205	ENST00000254528	T	0.32753	1.44	5.09	0.0109	0.14085	.	0.078107	0.52532	D	0.000066	T	0.24275	0.0588	M	0.61703	1.905	0.29809	N	0.831758	B	0.27882	0.192	B	0.29176	0.099	T	0.16453	-1.0402	10	0.21540	T	0.41	-40.7192	5.6585	0.17656	0.4833:0.0:0.3862:0.1306	.	331	Q9BXX0	EMIL2_HUMAN	D	331	ENSP00000254528:E331D	ENSP00000254528:E331D	E	+	3	2	EMILIN2	2881118	0.734000	0.28142	0.987000	0.45799	0.989000	0.77384	-0.068000	0.11561	0.002000	0.14630	0.557000	0.71058	GAG	.	.		0.552	EMILIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250337.2	NM_032048		T	2891118	G	T	2891118	3	4	254	1	0	0	0	0	1	0	0	0	5096	991	35	3	1007	3	EMILIN2	18	2891118	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10		2891118	75186130	870	35162										
PTPRM	5797	hgsc.bcm.edu	37	chr18	8378411	8378411	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccagattaaagaggaattccGggtaagtgatgcctaaggga	13	6	0	3	rs202020478		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:8378411G>T	ENST00000332175.8	+	25	4609	c.3572G>T	c.(3571-3573)cGg>cTg	p.R1191L	PTPRM_ENST00000580170.1_Splice_Site_p.R1204L|PTPRM_ENST00000400053.4_Splice_Site_p.R1129L|PTPRM_ENST00000444013.1_Splice_Site_p.R978L|PTPRM_ENST00000400060.4_Splice_Site_p.R1205L	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	1191	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				GAGGAATTCCGGGTAAGTGAT	0.498																																					p.R1204L		Atlas-SNP	.											.	PTPRM	185	.	0			c.G3611T						.						116	97	103					18																	8378411		2203	4300	6503	SO:0001630	splice_region_variant	5797	exon27			AATTCCGGGTAAG	X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.3573+1G>T	chr18.hg19:g.8378411G>T		156.0	0.0		87.0	4.0	NM_001105244	A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	ENST00000332175.8	hg19	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.455861	0.84209	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053;ENST00000444013	T;T;T;T	0.31510	1.49;1.49;1.49;1.49	5.7	4.82	0.62117	Protein-tyrosine phosphatase, receptor/non-receptor type (2);	0.058926	0.64402	D	0.000004	T	0.21186	0.0510	N	0.11673	0.155	0.80722	D	1	B;B;B	0.19817	0.006;0.039;0.039	B;B;B	0.22880	0.016;0.042;0.042	T	0.04203	-1.0969	10	0.72032	D	0.01	.	16.6777	0.85283	0.0:0.1298:0.8702:0.0	.	978;1204;1191	E7EVX9;A7MBN1;P28827	.;.;PTPRM_HUMAN	L	1191;1205;1129;978	ENSP00000331418:R1191L;ENSP00000382933:R1205L;ENSP00000382927:R1129L;ENSP00000387608:R978L	ENSP00000331418:R1191L	R	+	2	0	PTPRM	8368411	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	6.812000	0.75226	1.380000	0.46344	0.591000	0.81541	CGG	.	G|0.999;A|0.001		0.498	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1		Missense_Mutation	T	8378411	G	T	8378411	5	4	254	1	0	0	0	0	0	0	1	0	12821	1130	39	1	3717	1	PTPRM	18	8378411	Splice_Site	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	5487293	8378411	69698837	871	35163										
PPP4R1	9989	hgsc.bcm.edu	37	chr18	9557375	9557375	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aatgctagagttcgtcgaacTttccactgcagaaatgaaaa	8	8	0	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:9557375T>C	ENST00000400556.3	-	15	2107	c.2034A>G	c.(2032-2034)aaA>aaG	p.K678K	PPP4R1_ENST00000400555.3_Silent_p.K661K	NM_001042388.2	NP_001035847.1	Q8TF05	PP4R1_HUMAN	protein phosphatase 4, regulatory subunit 1	678					dephosphorylation (GO:0016311)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	protein phosphatase 4 complex (GO:0030289)	protein phosphatase type 4 regulator activity (GO:0030362)			large_intestine(1)|skin(2)	3						TTCGTCGAACTTTCCACTGCA	0.358																																					p.K678K	Melanoma(188;1232 2082 5061 11948 35994)	Atlas-SNP	.											.	PPP4R1	63	.	0			c.A2034G						.						109	103	105					18																	9557375		1860	4103	5963	SO:0001819	synonymous_variant	9989	exon15			TCGAACTTTCCAC	AF111106	CCDS42412.1, CCDS42413.1	18p11.22	2010-06-18			ENSG00000154845	ENSG00000154845		"Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits"	9320	protein-coding gene	gene with protein product		604908				10026142	Standard	NM_001042388		Approved	PP4R1	uc002koe.2	Q8TF05	OTTHUMG00000137466	ENST00000400556.3:c.2034A>G	chr18.hg19:g.9557375T>C		94.0	0.0		78.0	4.0	NM_001042388	Q99774|Q9UNQ7	Silent	SNP	ENST00000400556.3	hg19	CCDS42412.1																																																																																			.	.		0.358	PPP4R1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268571.1	NM_005134		C	9557375	T	C	9557375	2	2	254	1	0	0	0	0	0	0	0	1	12415	1606	56	2		2	PPP4R1	18	9557375	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	1178964	9557375	68519873	872	35164										
MC2R	4158	hgsc.bcm.edu	37	chr18	13884772	13884772	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	acatgtagcaggcgcagtagGggttacttgggcagaatgtc	15	7	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:13884772G>T	ENST00000327606.3	-	2	926	c.746C>A	c.(745-747)cCc>cAc	p.P249H		NM_000529.2	NP_000520.1	Q01718	ACTHR_HUMAN	melanocortin 2 receptor (adrenocorticotropic hormone)	249					G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|neuropeptide signaling pathway (GO:0007218)|placenta development (GO:0001890)|positive regulation of cAMP biosynthetic process (GO:0030819)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	corticotropin receptor activity (GO:0004978)|melanocortin receptor activity (GO:0004977)			breast(1)|endometrium(1)|kidney(2)|large_intestine(10)|lung(8)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30					Corticotropin(DB01285)|Cosyntropin(DB01284)	GGCGCAGTAGGGGTTACTTGG	0.537																																					p.P249H	Colon(141;1584 1782 35999 48227 48692)	Atlas-SNP	.											.	MC2R	78	.	0			c.C746A						.						88	80	82					18																	13884772		2203	4300	6503	SO:0001583	missense	4158	exon2			CAGTAGGGGTTAC		CCDS11869.1	18p11.2	2012-08-10			ENSG00000185231	ENSG00000185231		"GPCR / Class A : Melanocortin receptors"	6930	protein-coding gene	gene with protein product		607397				8390157	Standard	NM_001291911		Approved	ACTHR	uc002ksp.1	Q01718	OTTHUMG00000131721	ENST00000327606.3:c.746C>A	chr18.hg19:g.13884772G>T	ENSP00000333821:p.Pro249His	171.0	0.0		94.0	4.0	NM_000529	A8K016|Q3MI45|Q504X6	Missense_Mutation	SNP	ENST00000327606.3	hg19	CCDS11869.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.071346	0.76301	.	.	ENSG00000185231	ENST00000327606;ENST00000399821	T	0.71579	-0.58	5.18	5.18	0.71444	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.86686	0.5992	M	0.87097	2.86	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.88941	0.3380	10	0.72032	D	0.01	.	18.6835	0.91556	0.0:0.0:1.0:0.0	.	249	Q01718	ACTHR_HUMAN	H	249	ENSP00000333821:P249H	ENSP00000333821:P249H	P	-	2	0	MC2R	13874772	1.000000	0.71417	0.560000	0.28344	0.652000	0.38707	7.252000	0.78309	2.411000	0.81874	0.655000	0.94253	CCC	.	.		0.537	MC2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254639.2			T	13884772	G	T	13884772	3	4	254	1	0	0	0	0	1	0	0	0	9373	1232	43	3	151	3	MC2R	18	13884772	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	4327397	13884772	64192476	873	35165										
ZNF519	162655	hgsc.bcm.edu	37	chr18	14105088	14105088	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tacatttgaagaatttctctCcagtatggactctctgatgt	7	8	2	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:14105088C>A	ENST00000590202.1	-	3	1603	c.1451G>T	c.(1450-1452)gGa>gTa	p.G484V	RP11-411B10.3_ENST00000592926.1_RNA|ZNF519_ENST00000589203.1_Intron|ZNF519_ENST00000589498.1_Intron	NM_145287.3	NP_660330.2	Q8TB69	ZN519_HUMAN	zinc finger protein 519	484					negative regulation of transcription during meiosis (GO:0051038)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G484V(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|urinary_tract(1)	18						GAATTTCTCTCCAGTATGGAC	0.398																																					p.G484V		Atlas-SNP	.											ZNF519,NS,carcinoma,0,1	ZNF519	53	.	1	Substitution - Missense(1)	lung(1)	c.G1451T						.						59	61	61					18																	14105088		2203	4298	6501	SO:0001583	missense	162655	exon3			TTCTCTCCAGTAT	BC024227	CCDS32797.1	18p11.21	2014-06-18			ENSG00000175322	ENSG00000175322		"Zinc fingers, C2H2-type", "-"	30574	protein-coding gene	gene with protein product	"similar to Zinc finger protein 85 (Zinc finger protein HPF4) (HTF1)"					12477932	Standard	NM_145287		Approved	HsT2362, FLJ36809	uc002kst.2	Q8TB69	OTTHUMG00000182055	ENST00000590202.1:c.1451G>T	chr18.hg19:g.14105088C>A	ENSP00000464872:p.Gly484Val	78.0	0.0		75.0	3.0	NM_145287		Missense_Mutation	SNP	ENST00000590202.1	hg19	CCDS32797.1	.	.	.	.	.	.	.	.	.	.	C	13.39	2.223679	0.39300	.	.	ENSG00000175322	ENST00000309305	.	.	.	0.646	0.646	0.17789	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.67126	0.2860	M	0.66439	2.03	0.58432	D	0.999994	D	0.76494	0.999	D	0.67548	0.952	T	0.66795	-0.5833	8	0.66056	D	0.02	.	7.2226	0.25997	0.0:0.9999:0.0:1.0E-4	.	484	Q8TB69	ZN519_HUMAN	V	484	.	ENSP00000307908:G484V	G	-	2	0	ZNF519	14095088	0.370000	0.25047	0.075000	0.20258	0.293000	0.27360	2.033000	0.41136	0.661000	0.30985	0.089000	0.15464	GGA	.	.		0.398	ZNF519-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459037.1	NM_145287		A	14105088	C	A	14105088	3	1	254	1	0	0	0	0	1	0	0	0	17979	855	30	3	175	3	ZNF519	18	14105088	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	220316	14105088	63972160	874	35166										
NPC1	4864	hgsc.bcm.edu	37	chr18	21120466	21120466	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tctactttgttcaggactgcGatgctgaatgacagaacacc	9	10	2	3	rs542171272		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:21120466G>T	ENST00000269228.5	-	17	3104	c.2550C>A	c.(2548-2550)atC>atA	p.I850I	NPC1_ENST00000412552.2_Silent_p.I532I|NPC1_ENST00000540608.1_5'UTR	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	850					adult walking behavior (GO:0007628)|autophagy (GO:0006914)|bile acid metabolic process (GO:0008206)|cellular response to low-density lipoprotein particle stimulus (GO:0071404)|cellular response to steroid hormone stimulus (GO:0071383)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|establishment of protein localization to membrane (GO:0090150)|lysosomal transport (GO:0007041)|membrane raft organization (GO:0031579)|negative regulation of cell death (GO:0060548)|negative regulation of macroautophagy (GO:0016242)|protein glycosylation (GO:0006486)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|hedgehog receptor activity (GO:0008158)|receptor activity (GO:0004872)|sterol transporter activity (GO:0015248)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(10)|lung(13)|ovary(2)|stomach(1)	38	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)					TCAGGACTGCGATGCTGAATG	0.348																																					p.I850I		Atlas-SNP	.											.	NPC1	114	.	0			c.C2550A						.						96	88	90					18																	21120466		2203	4300	6503	SO:0001819	synonymous_variant	4864	exon17			GACTGCGATGCTG	AF002020	CCDS11878.1	18q11.2	2014-06-17			ENSG00000141458	ENSG00000141458			7897	protein-coding gene	gene with protein product		607623				8446622	Standard	NM_000271		Approved		uc002kum.4	O15118	OTTHUMG00000131873	ENST00000269228.5:c.2550C>A	chr18.hg19:g.21120466G>T		114.0	0.0		69.0	4.0	NM_000271	B4DET3|Q9P130	Silent	SNP	ENST00000269228.5	hg19	CCDS11878.1																																																																																			.	.		0.348	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271		T	21120466	G	T	21120466	2	4	254	1	0	0	0	0	0	0	0	1	10579	1048	37	1		1	NPC1	18	21120466	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	7015378	21120466	56956782	875	35167										
ZNF521	25925	hgsc.bcm.edu	37	chr18	22804712	22804712	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtttttggacgtgctggcccCgccctgtggtctgaactgca	13	12	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:22804712C>A	ENST00000361524.3	-	4	3318	c.3170G>T	c.(3169-3171)cGg>cTg	p.R1057L	ZNF521_ENST00000538137.2_Missense_Mutation_p.R1057L|ZNF521_ENST00000584787.1_Missense_Mutation_p.R837L|ZNF521_ENST00000579111.1_5'Flank	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	1057					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					GTGCTGGCCCCGCCCTGTGGT	0.498			T	PAX5	ALL																																p.R1057L		Atlas-SNP	.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	ZNF521,NS,carcinoma,0,1	ZNF521	269	.	0			c.G3170T						.						72	58	63					18																	22804712		2203	4300	6503	SO:0001583	missense	25925	exon4			TGGCCCCGCCCTG	AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"Zinc fingers, C2H2-type"	24605	protein-coding gene	gene with protein product	"early hematopoietic zinc finger"	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.3170G>T	chr18.hg19:g.22804712C>A	ENSP00000354794:p.Arg1057Leu	61.0	0.0		41.0	3.0	NM_015461	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Missense_Mutation	SNP	ENST00000361524.3	hg19	CCDS32806.1	.	.	.	.	.	.	.	.	.	.	C	12.14	1.847957	0.32699	.	.	ENSG00000198795	ENST00000361524;ENST00000538137;ENST00000399425	T;T	0.08720	3.06;3.07	5.98	5.98	0.97165	.	0.115877	0.64402	D	0.000008	T	0.06645	0.0170	N	0.08118	0	0.40933	D	0.984402	P	0.43094	0.799	B	0.43331	0.416	T	0.37641	-0.9697	10	0.56958	D	0.05	-26.7352	13.6254	0.62161	0.0:0.9297:0.0:0.0702	.	1057	Q96K83	ZN521_HUMAN	L	1057;1091;1057	ENSP00000354794:R1057L;ENSP00000382352:R1057L	ENSP00000354794:R1057L	R	-	2	0	ZNF521	21058710	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.785000	0.68998	2.835000	0.97688	0.650000	0.86243	CGG	.	.		0.498	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461		A	22804712	C	A	22804712	3	1	254	1	0	0	0	0	1	0	0	0	17980	652	23	1	785	1	ZNF521	18	22804712	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1684246	22804712	55272536	876	35168										
ZNF521	25925	hgsc.bcm.edu	37	chr18	22806400	22806400	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccatgagaacatcggatgtgTtcctgaagagtgttgaggtc	13	7	0	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:22806400T>C	ENST00000361524.3	-	4	1630	c.1482A>G	c.(1480-1482)gaA>gaG	p.E494E	ZNF521_ENST00000538137.2_Silent_p.E494E|ZNF521_ENST00000584787.1_Silent_p.E274E|ZNF521_ENST00000579111.1_5'Flank	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	494					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					ATCGGATGTGTTCCTGAAGAG	0.463			T	PAX5	ALL																																p.E494E		Atlas-SNP	.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	ZNF521,caecum,carcinoma,-1,1	ZNF521	269	.	0			c.A1482G						.						101	100	101					18																	22806400		2203	4300	6503	SO:0001819	synonymous_variant	25925	exon4			GATGTGTTCCTGA	AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"Zinc fingers, C2H2-type"	24605	protein-coding gene	gene with protein product	"early hematopoietic zinc finger"	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.1482A>G	chr18.hg19:g.22806400T>C		183.0	0.0		135.0	6.0	NM_015461	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Silent	SNP	ENST00000361524.3	hg19	CCDS32806.1																																																																																			.	.		0.463	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461		C	22806400	T	C	22806400	2	2	254	1	0	0	0	0	0	0	0	1	17980	1722	60	2		2	ZNF521	18	22806400	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	1688	22806400	55270848	877	35169										
CDH2	1000	hgsc.bcm.edu	37	chr18	25589802	25589802	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctggcccagttacactgtacCgcagtgaaaggtttttatct	9	10	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:25589802C>A	ENST00000269141.3	-	5	1004	c.581G>T	c.(580-582)cGg>cTg	p.R194L	CDH2_ENST00000399380.3_Missense_Mutation_p.R163L	NM_001792.3	NP_001783.2	P19022	CADH2_HUMAN	cadherin 2, type 1, N-cadherin (neuronal)	194	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|blood vessel morphogenesis (GO:0048514)|calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell-cell adhesion mediated by cadherin (GO:0044331)|cell-cell junction organization (GO:0045216)|glial cell differentiation (GO:0010001)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|neuronal stem cell maintenance (GO:0097150)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|striated muscle cell differentiation (GO:0051146)	apical plasma membrane (GO:0016324)|catenin complex (GO:0016342)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|synapse (GO:0045202)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)			NS(1)|breast(5)|cervix(2)|endometrium(7)|kidney(3)|large_intestine(22)|lung(32)|ovary(4)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						TACACTGTACCGCAGTGAAAG	0.478																																					p.R194L		Atlas-SNP	.											.	CDH2	194	.	0			c.G581T						.						93	85	88					18																	25589802		2203	4300	6503	SO:0001583	missense	1000	exon5			CTGTACCGCAGTG	S42303	CCDS11891.1	18q12.1	2010-01-26			ENSG00000170558	ENSG00000170558		"CD molecules", "Cadherins / Major cadherins"	1759	protein-coding gene	gene with protein product	"N-cadherin"	114020		NCAD		2384753, 7731968, 2216790	Standard	NM_001792		Approved	CDHN, CD325	uc002kwg.2	P19022	OTTHUMG00000059940	ENST00000269141.3:c.581G>T	chr18.hg19:g.25589802C>A	ENSP00000269141:p.Arg194Leu	85.0	0.0		61.0	4.0	NM_001792	A8MWK3|B0YIY6|Q14923|Q8N173	Missense_Mutation	SNP	ENST00000269141.3	hg19	CCDS11891.1	.	.	.	.	.	.	.	.	.	.	C	34	5.308741	0.95629	.	.	ENSG00000170558	ENST00000269141;ENST00000399380;ENST00000418492;ENST00000430882	T;T;T;T	0.61040	0.59;0.59;0.59;0.14	5.77	5.77	0.91146	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.75539	0.3863	M	0.65498	2.005	0.80722	D	1	D;D	0.89917	0.997;1.0	D;D	0.91635	0.949;0.999	T	0.69993	-0.4994	10	0.32370	T	0.25	.	20.3559	0.98840	0.0:1.0:0.0:0.0	.	163;194	A8MWK3;P19022	.;CADH2_HUMAN	L	194;163;143;109	ENSP00000269141:R194L;ENSP00000382312:R163L;ENSP00000411360:R143L;ENSP00000412120:R109L	ENSP00000269141:R194L	R	-	2	0	CDH2	23843800	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.438000	0.80431	2.890000	0.99128	0.585000	0.79938	CGG	.	.		0.478	CDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133246.3	NM_001792		A	25589802	C	A	25589802	3	1	254	1	0	0	0	0	1	0	0	0	3107	652	23	1	2187	1	CDH2	18	25589802	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	2783402	25589802	52487446	878	35170										
ASXL3	80816	hgsc.bcm.edu	37	chr18	31326158	31326158	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aagaacagttaaaagcattcGcgctaaaaagtgcagatttc	8	7	0	2	rs117661115	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:31326158G>T	ENST00000269197.5	+	12	6346	c.6346G>T	c.(6346-6348)Gcg>Tcg	p.A2116S		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	2116					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						AAAAGCATTCGCGCTAAAAAG	0.413																																					p.A2116S		Atlas-SNP	.											.	ASXL3	405	.	0			c.G6346T						.						76	78	77					18																	31326158		1860	4109	5969	SO:0001583	missense	80816	exon12			GCATTCGCGCTAA	AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"KIAA1713", "additional sex combs like 3 (Drosophila)"	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.6346G>T	chr18.hg19:g.31326158G>T	ENSP00000269197:p.Ala2116Ser	114.0	0.0		96.0	4.0	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	hg19	CCDS45847.1	.	.	.	.	.	.	.	.	.	.	G	15.03	2.712149	0.48517	.	.	ENSG00000141431	ENST00000269197	T	0.18502	2.21	6.04	6.04	0.98038	.	.	.	.	.	T	0.16214	0.0390	N	0.19112	0.55	0.37404	D	0.91298	P	0.51653	0.947	B	0.42916	0.402	T	0.01940	-1.1243	9	0.49607	T	0.09	.	20.5948	0.99439	0.0:0.0:1.0:0.0	.	2116	Q9C0F0	ASXL3_HUMAN	S	2116	ENSP00000269197:A2116S	ENSP00000269197:A2116S	A	+	1	0	ASXL3	29580156	1.000000	0.71417	0.993000	0.49108	0.933000	0.57130	3.659000	0.54489	2.873000	0.98535	0.563000	0.77884	GCG	.	G|0.998;A|0.002		0.413	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			T	31326158	G	T	31326158	3	4	254	1	0	0	0	0	1	0	0	0	1068	1087	38	1	6392	1	ASXL3	18	31326158	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	5736356	31326158	46751090	879	35171										
NOL4	8715	hgsc.bcm.edu	37	chr18	31523052	31523052	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctgtctctccagacgcatccTcttggcggcatttctactct	7	15	4	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:31523052T>C	ENST00000261592.5	-	9	1816	c.1519A>G	c.(1519-1521)Agg>Ggg	p.R507G	NOL4_ENST00000589544.1_Intron|NOL4_ENST00000535384.1_Missense_Mutation_p.R222G|NOL4_ENST00000538587.1_Missense_Mutation_p.R433G|NOL4_ENST00000269185.4_Intron|NOL4_ENST00000535475.1_Missense_Mutation_p.R288G	NM_001198546.1|NM_003787.4	NP_001185475.1|NP_003778.2	O94818	NOL4_HUMAN	nucleolar protein 4	507						nucleolus (GO:0005730)	RNA binding (GO:0003723)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	51						AGACGCATCCTCTTGGCGGCA	0.433																																					p.R507G		Atlas-SNP	.											NOL4,NS,carcinoma,0,1	NOL4	139	.	0			c.A1519G						.						105	95	98					18																	31523052		2203	4299	6502	SO:0001583	missense	8715	exon9			GCATCCTCTTGGC	AB017800	CCDS11907.2, CCDS56058.1, CCDS56059.1, CCDS59308.1	18q12	2010-05-04			ENSG00000101746	ENSG00000101746			7870	protein-coding gene	gene with protein product	"cancer/testis antigen 125"	603577				9813152	Standard	NM_003787		Approved	NOLP, HRIHFB2255, CT125	uc010dmi.3	O94818	OTTHUMG00000132291	ENST00000261592.5:c.1519A>G	chr18.hg19:g.31523052T>C	ENSP00000261592:p.Arg507Gly	89.0	0.0		65.0	4.0	NM_003787	B4DSQ0|B7Z3Z7|F5H1E3|Q6IBS2|Q9BWF1	Missense_Mutation	SNP	ENST00000261592.5	hg19	CCDS11907.2	.	.	.	.	.	.	.	.	.	.	T	18.13	3.554596	0.65425	.	.	ENSG00000101746	ENST00000261592;ENST00000399171;ENST00000535384;ENST00000535475;ENST00000538587	.	.	.	5.87	3.36	0.38483	.	0.000000	0.85682	D	0.000000	T	0.76471	0.3992	M	0.71206	2.165	0.42947	D	0.994361	D;D;D;D;D;P	0.89917	0.989;1.0;1.0;0.997;1.0;0.51	D;D;D;D;D;B	0.87578	0.985;0.998;0.998;0.971;0.998;0.419	T	0.79070	-0.1954	9	0.62326	D	0.03	-18.6544	13.3487	0.60589	0.0:0.0:0.3698:0.6302	.	192;222;433;507;222;288	F8W825;B7Z3Z7;B4DSQ0;O94818;F5H1E3;B3KRF4	.;.;.;NOL4_HUMAN;.;.	G	507;192;222;288;433	.	ENSP00000261592:R507G	R	-	1	2	NOL4	29777050	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.415000	0.52700	1.025000	0.39708	0.528000	0.53228	AGG	.	.		0.433	NOL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255386.1	NM_003787		C	31523052	T	C	31523052	3	2	254	1	0	0	0	0	1	0	0	0	10533	1550	54	2	409	2	NOL4	18	31523052	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	196894	31523052	46554196	880	35172										
MOCOS	55034	hgsc.bcm.edu	37	chr18	33775243	33775243	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctgtctatcttgaccatgcaGgtgccaccttgttctcccag	8	14	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:33775243G>T	ENST00000261326.5	+	2	187	c.166G>T	c.(166-168)Ggt>Tgt	p.G56C		NM_017947.2	NP_060417.2			molybdenum cofactor sulfurase											breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|liver(1)|lung(15)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						TGACCATGCAGGTGCCACCTT	0.388																																					p.G56C		Atlas-SNP	.											.	MOCOS	84	.	0			c.G166T						.						149	152	151					18																	33775243		2203	4300	6503	SO:0001583	missense	55034	exon2			CATGCAGGTGCCA	AK000740	CCDS11919.1	18q12	2003-12-18			ENSG00000075643	ENSG00000075643			18234	protein-coding gene	gene with protein product		613274				11302742	Standard	NM_017947		Approved	HMCS, FLJ20733, MOS	uc002kzq.4	Q96EN8	OTTHUMG00000132590	ENST00000261326.5:c.166G>T	chr18.hg19:g.33775243G>T	ENSP00000261326:p.Gly56Cys	92.0	0.0		99.0	4.0	NM_017947		Missense_Mutation	SNP	ENST00000261326.5	hg19	CCDS11919.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.457306	0.84317	.	.	ENSG00000075643	ENST00000261326	D	0.88818	-2.43	5.41	5.41	0.78517	Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	0.068985	0.64402	D	0.000014	D	0.96071	0.8720	H	0.95079	3.62	0.52501	D	0.999959	D	0.89917	1.0	D	0.97110	1.0	D	0.97014	0.9738	10	0.87932	D	0	-12.8987	14.718	0.69284	0.0:0.0:1.0:0.0	.	56	Q96EN8	MOCOS_HUMAN	C	56	ENSP00000261326:G56C	ENSP00000261326:G56C	G	+	1	0	MOCOS	32029241	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.116000	0.77119	2.538000	0.85594	0.563000	0.77884	GGT	.	.		0.388	MOCOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255801.1			T	33775243	G	T	33775243	3	4	254	1	0	0	0	0	1	0	0	0	9698	1000	35	3	172	3	MOCOS	18	33775243	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	2252191	33775243	44302005	881	35173										
ZBTB7C	201501	hgsc.bcm.edu	37	chr18	45566520	45566520	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccttgatgggtcccagaggcCcccccggcaggtcagggaac	14	15	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:45566520C>A	ENST00000588982.1	-	3	1460	c.959G>T	c.(958-960)gGg>gTg	p.G320V	ZBTB7C_ENST00000535628.2_Missense_Mutation_p.G320V|ZBTB7C_ENST00000590800.1_Missense_Mutation_p.G320V|ZBTB7C_ENST00000332053.2_Missense_Mutation_p.G320V|ZBTB7C_ENST00000586438.1_Missense_Mutation_p.G320V			A1YPR0	ZBT7C_HUMAN	zinc finger and BTB domain containing 7C	320	Pro-rich.						metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(8)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23						TCCCAGAGGCCCCCCCGGCAG	0.627																																					p.G320V		Atlas-SNP	.											.	ZBTB7C	73	.	0			c.G959T						.																																			SO:0001583	missense	201501	exon2			AGAGGCCCCCCCG	Y14591	CCDS32830.1	18q21.1	2013-01-08		2005-04-07	ENSG00000184828	ENSG00000184828		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	31700	protein-coding gene	gene with protein product			"zinc finger and BTB domain containing 36"	ZBTB36			Standard	NM_001039360		Approved	ZNF857C	uc002ldb.3	A1YPR0		ENST00000588982.1:c.959G>T	chr18.hg19:g.45566520C>A	ENSP00000468782:p.Gly320Val	58.0	0.0		57.0	4.0	NM_001039360	O73453	Missense_Mutation	SNP	ENST00000588982.1	hg19	CCDS32830.1	.	.	.	.	.	.	.	.	.	.	C	7.703	0.693455	0.15039	.	.	ENSG00000184828	ENST00000535628;ENST00000332053	T;T	0.11604	2.76;2.76	5.34	5.34	0.76211	.	0.286197	0.37261	N	0.002164	T	0.07908	0.0198	N	0.14661	0.345	0.47374	D	0.999406	B;B	0.30068	0.267;0.267	B;B	0.27380	0.079;0.079	T	0.32161	-0.9917	10	0.44086	T	0.13	.	15.6117	0.76727	0.0:0.8525:0.1475:0.0	.	320;320	B2RG49;A1YPR0	.;ZBT7C_HUMAN	V	320	ENSP00000439781:G320V;ENSP00000328732:G320V	ENSP00000328732:G320V	G	-	2	0	ZBTB7C	43820518	0.997000	0.39634	0.998000	0.56505	0.278000	0.26855	3.569000	0.53827	2.491000	0.84063	0.561000	0.74099	GGG	.	.		0.627	ZBTB7C-025	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450731.1	NM_001039360		A	45566520	C	A	45566520	3	1	254	1	0	0	0	0	1	0	0	0	17570	623	22	3	908	3	ZBTB7C	18	45566520	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	11791277	45566520	32510728	882	35174										
TCF4	6925	hgsc.bcm.edu	37	chr18	52895541	52895541	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggggaggctctgaggacaccTtctcttcctcccttcttttc	9	14	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:52895541T>C	ENST00000356073.4	-	19	2530	c.1919A>G	c.(1918-1920)aAg>aGg	p.K640R	TCF4_ENST00000566279.1_Missense_Mutation_p.K584R|TCF4_ENST00000564228.1_Missense_Mutation_p.K569R|TCF4_ENST00000543082.1_Missense_Mutation_p.K598R|TCF4_ENST00000561831.3_Missense_Mutation_p.K480R|TCF4_ENST00000544241.2_Missense_Mutation_p.K573R|TCF4_ENST00000540999.1_Missense_Mutation_p.K616R|TCF4_ENST00000537856.3_Missense_Mutation_p.K510R|TCF4_ENST00000567880.1_Missense_Mutation_p.K580R|TCF4_ENST00000568740.1_Missense_Mutation_p.K615R|TCF4_ENST00000537578.1_Missense_Mutation_p.K620R|TCF4_ENST00000568673.1_Missense_Mutation_p.K620R|TCF4_ENST00000570177.2_Missense_Mutation_p.K510R|TCF4_ENST00000566286.1_Missense_Mutation_p.K637R|TCF4_ENST00000564403.2_Missense_Mutation_p.K650R|TCF4_ENST00000457482.3_Missense_Mutation_p.K484R|TCF4_ENST00000354452.3_Missense_Mutation_p.K644R|TCF4_ENST00000561992.1_Missense_Mutation_p.K510R|TCF4_ENST00000564999.1_Missense_Mutation_p.K640R|TCF4_ENST00000570287.2_Missense_Mutation_p.K480R|TCF4_ENST00000565018.2_Missense_Mutation_p.K644R|TCF4_ENST00000398339.1_Missense_Mutation_p.K746R	NM_003199.2	NP_003190.1	P15884	ITF2_HUMAN	transcription factor 4	640	Class A specific domain.				DNA-templated transcription, initiation (GO:0006352)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein-DNA complex assembly (GO:0065004)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase recruiting transcription factor activity (GO:0001011)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TFIIB-class binding transcription factor activity (GO:0001087)|TFIIB-class transcription factor binding (GO:0001093)			breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	41				Colorectal(16;0.00108)|READ - Rectum adenocarcinoma(59;0.0649)|COAD - Colon adenocarcinoma(17;0.0718)		TGAGGACACCTTCTCTTCCTC	0.507																																					p.K746R		Atlas-SNP	.											.	TCF4	178	.	0			c.A2237G						.						130	122	125					18																	52895541		2203	4300	6503	SO:0001583	missense	6925	exon20			GACACCTTCTCTT	M74719	CCDS11960.1, CCDS42438.1, CCDS58623.1, CCDS58624.1, CCDS58625.1, CCDS58626.1, CCDS58627.1, CCDS58628.1, CCDS58629.1, CCDS58630.1, CCDS58631.1, CCDS59321.1	18q21.1	2013-05-21			ENSG00000196628	ENSG00000196628		"Basic helix-loop-helix proteins"	11634	protein-coding gene	gene with protein product		602272				9302263, 2308860	Standard	NM_001083962		Approved	SEF2-1B, ITF2, bHLHb19, E2-2	uc002lga.3	P15884	OTTHUMG00000132713	ENST00000356073.4:c.1919A>G	chr18.hg19:g.52895541T>C	ENSP00000348374:p.Lys640Arg	62.0	0.0		44.0	4.0	NM_001243226	B3KT62|B3KUC0|B4DT37|B4DUG3|B7Z5M6|B7Z6Y1|G0LNT9|G0LNU0|G0LNU1|G0LNU2|G0LNU4|G0LNU5|G0LNU8|G0LNU9|G0LNV0|G0LNV1|G0LNV2|H3BPQ1|Q08AP2|Q08AP3|Q15439|Q15440|Q15441	Missense_Mutation	SNP	ENST00000356073.4	hg19	CCDS11960.1	.	.	.	.	.	.	.	.	.	.	T	33	5.257190	0.95368	.	.	ENSG00000196628	ENST00000354452;ENST00000457482;ENST00000356073;ENST00000543082;ENST00000540999;ENST00000537578;ENST00000544241;ENST00000537856;ENST00000398339	T;T;T;T;T;T;T;T;T	0.27557	1.84;1.66;1.86;1.86;1.88;1.86;1.88;1.67;1.81	5.72	5.72	0.89469	Helix-loop-helix DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.57636	0.2067	M	0.79011	2.435	0.58432	D	0.999991	D;D;D;D;P;D;D;D;D	0.89917	1.0;1.0;1.0;0.996;0.956;0.999;0.999;0.974;0.997	D;D;D;D;P;D;D;D;D	0.91635	0.999;0.995;0.997;0.979;0.899;0.989;0.997;0.953;0.988	T	0.62671	-0.6805	10	0.87932	D	0	-16.954	14.991	0.71387	0.0:0.0:0.0:1.0	.	620;644;480;746;640;598;573;484;637	B7Z5M6;G0LNT9;G0LNV1;E9PH57;P15884;B3KUC0;B3KT62;G0LNU9;G0LNU5	.;.;.;.;ITF2_HUMAN;.;.;.;.	R	644;484;640;598;616;620;573;510;746	ENSP00000346440:K644R;ENSP00000409447:K484R;ENSP00000348374:K640R;ENSP00000439656:K598R;ENSP00000445202:K616R;ENSP00000440731:K620R;ENSP00000441562:K573R;ENSP00000439827:K510R;ENSP00000381382:K746R	ENSP00000346440:K644R	K	-	2	0	TCF4	51046539	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.997000	0.88414	2.172000	0.68678	0.528000	0.53228	AAG	.	.		0.507	TCF4-002	KNOWN	upstream_uORF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256014.1	NM_003199		C	52895541	T	C	52895541	3	2	254	1	0	0	0	0	1	0	0	0	15710	1609	56	2	88	2	TCF4	18	52895541	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	7329021	52895541	25181707	883	35175										
WDR7	23335	hgsc.bcm.edu	37	chr18	54349915	54349915	+	Frame_Shift_Del	DEL	C	C	-													0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttggcatgaatgtagttctaCcagttctctgttgggaatca							TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:54349915delC	ENST00000254442.3	+	5	562	c.351delC	c.(349-351)tacfs	p.Y117fs	WDR7_ENST00000589935.1_Intron|WDR7_ENST00000357574.3_Frame_Shift_Del_p.Y117fs	NM_015285.2	NP_056100.2	Q9Y4E6	WDR7_HUMAN	WD repeat domain 7	117					hematopoietic progenitor cell differentiation (GO:0002244)					NS(1)|breast(5)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(37)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	78				Lung(128;0.0238)|Colorectal(16;0.0296)		TGTAGTTCTACCAGTTCTCTG	0.368																																					p.Y117fs		Pindel	.											.	WDR7	166	.	0			c.350delA						.						147	135	139					18																	54349915		2203	4300	6503	SO:0001589	frameshift_variant	23335	exon5			.	AB011113	CCDS11962.1, CCDS11963.1	18q21.31	2013-01-09			ENSG00000091157	ENSG00000091157		"WD repeat domain containing"	13490	protein-coding gene	gene with protein product		613473				10828621	Standard	XM_005266674		Approved	KIAA0541, TRAG	uc002lgk.1	Q9Y4E6	OTTHUMG00000132721	ENST00000254442.3:c.351delC	chr18.hg19:g.54349915delC	ENSP00000254442:p.Tyr117fs	227.0	0.0		169.0	31.0	NM_052834	A7E2C8|Q86UX5|Q86VP2|Q96PS7	Frame_Shift_Del	DEL	ENST00000254442.3	hg19	CCDS11962.1																																																																																			.	.		0.368	WDR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256062.1			-	54349915	C	-	54349915	7	5	254	1	0	1	0	1	0	0	0	0	17335	518	18	0	365	0	WDR7	18	54349915	Frame_Shift_Del	DEL	C	TCGA-EP-A2KA-01A-11D-A183-10	1454374	54349915	23727333	884	35176										
NEDD4L	23327	hgsc.bcm.edu	37	chr18	56002763	56002763	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	actgtcacgggtggtgaggaAccaacggtaatgatccactt	12	9	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:56002763A>G	ENST00000400345.3	+	13	1402	c.1119A>G	c.(1117-1119)gaA>gaG	p.E373E	NEDD4L_ENST00000356462.6_Intron|NEDD4L_ENST00000431212.2_Silent_p.E252E|NEDD4L_ENST00000256832.7_Intron|NEDD4L_ENST00000357895.5_Silent_p.E365E|NEDD4L_ENST00000456986.1_Silent_p.E252E|NEDD4L_ENST00000456173.2_Intron|NEDD4L_ENST00000589054.1_Intron|NEDD4L_ENST00000586263.1_Intron|NEDD4L_ENST00000435432.2_Intron|NEDD4L_ENST00000256830.9_Intron|NEDD4L_ENST00000382850.4_Intron	NM_001144967.2	NP_001138439.1	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase	373					cellular sodium ion homeostasis (GO:0006883)|excretion (GO:0007588)|gene expression (GO:0010467)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of sodium ion transmembrane transport (GO:1902306)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of cation channel activity (GO:2001259)|positive regulation of caveolin-mediated endocytosis (GO:2001288)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of sodium ion transport (GO:0010765)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane depolarization (GO:0003254)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of protein catabolic process (GO:0042176)|regulation of tight junction assembly (GO:2000810)|response to metal ion (GO:0010038)|response to salt stress (GO:0009651)|sodium ion transport (GO:0006814)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|ventricular cardiac muscle cell action potential (GO:0086005)|viral life cycle (GO:0019058)|viral process (GO:0016032)|water homeostasis (GO:0030104)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ion channel binding (GO:0044325)|ligase activity (GO:0016874)|potassium channel inhibitor activity (GO:0019870)|potassium channel regulator activity (GO:0015459)|sodium channel inhibitor activity (GO:0019871)|sodium channel regulator activity (GO:0017080)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(11)|ovary(1)|prostate(4)	37						GTGGTGAGGAACCAACGGTAA	0.448																																					p.E373E		Atlas-SNP	.											.	NEDD4L	126	.	0			c.A1119G						.						121	110	113					18																	56002763		1568	3582	5150	SO:0001819	synonymous_variant	23327	exon13			TGAGGAACCAACG	AF210730	CCDS45872.1, CCDS45873.1, CCDS45874.1, CCDS45875.1, CCDS45876.1, CCDS58632.1, CCDS59323.1	18q21.31	2014-08-12	2012-02-23		ENSG00000049759				7728	protein-coding gene	gene with protein product		606384	"neural precursor cell expressed, developmentally down-regulated 4-like"			10594025, 11244092, 18322022	Standard	NM_001144965		Approved	KIAA0439, RSP5, NEDD4-2	uc002lgy.3	Q96PU5	OTTHUMG00000179875	ENST00000400345.3:c.1119A>G	chr18.hg19:g.56002763A>G		110.0	0.0		115.0	5.0	NM_001144967	O43165|Q3LSM7|Q7Z5F1|Q7Z5F2|Q7Z5N3|Q8N5A7|Q8WUU9|Q9BW58|Q9H2W4|Q9NT88	Silent	SNP	ENST00000400345.3	hg19	CCDS45872.1																																																																																			.	.		0.448	NEDD4L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448749.1			G	56002763	A	G	56002763	2	3	254	1	0	0	0	0	0	0	0	1	10320	40	2	2		2	NEDD4L	18	56002763	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	1652848	56002763	22074485	885	35177										
PMAIP1	5366	hgsc.bcm.edu	37	chr18	57569926	57569926	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcaggagatttggagacaaaCtgaacttccggcagaaactt	10	8	1	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:57569926C>T	ENST00000316660.6	+	2	336	c.106C>T	c.(106-108)Ctg>Ttg	p.L36L	PMAIP1_ENST00000269518.9_Missense_Mutation_p.T86I	NM_021127.2	NP_066950.1	Q13794	APR_HUMAN	phorbol-12-myristate-13-acetate-induced protein 1	36					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|defense response to virus (GO:0051607)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of mitochondrial membrane potential (GO:0010917)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|proteasomal protein catabolic process (GO:0010498)|reactive oxygen species metabolic process (GO:0072593)|regulation of mitochondrial membrane permeability (GO:0046902)|release of cytochrome c from mitochondria (GO:0001836)|response to dsRNA (GO:0043331)|response to UV (GO:0009411)|response to X-ray (GO:0010165)|T cell homeostasis (GO:0043029)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)	1		Colorectal(73;0.0946)				TGGAGACAAACTGAACTTCCG	0.428																																					p.L36L		Atlas-SNP	.											.	PMAIP1	1	.	0			c.C106T						.						102	103	103					18																	57569926		2203	4300	6503	SO:0001819	synonymous_variant	5366	exon2			GACAAACTGAACT	D90070	CCDS11975.1	18q21.32	2014-03-07			ENSG00000141682	ENSG00000141682			9108	protein-coding gene	gene with protein product		604959				2398525, 12879012	Standard	NM_021127		Approved	APR, NOXA	uc002lic.2	Q13794	OTTHUMG00000132765	ENST00000316660.6:c.106C>T	chr18.hg19:g.57569926C>T		82.0	0.0		79.0	4.0	NM_021127	B2R4T7|Q8N589	Silent	SNP	ENST00000316660.6	hg19	CCDS11975.1	.	.	.	.	.	.	.	.	.	.	C	10.02	1.235159	0.22626	.	.	ENSG00000141682	ENST00000269518	.	.	.	5.0	-0.0021	0.14031	.	0.495687	0.15116	N	0.279646	T	0.20901	0.0503	.	.	.	0.21984	N	0.999437	P	0.37955	0.612	B	0.35470	0.203	T	0.19679	-1.0298	8	0.87932	D	0	.	0.7495	0.00988	0.166:0.3741:0.1738:0.286	.	86	Q8N589	.	I	86	.	ENSP00000269518:T86I	T	+	2	0	PMAIP1	55720906	0.920000	0.31207	0.971000	0.41717	0.659000	0.38960	0.010000	0.13242	0.059000	0.16252	0.655000	0.94253	ACT	.	.		0.428	PMAIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256137.1	NM_021127		T	57569926	C	T	57569926	2	4	254	1	0	0	0	0	0	0	0	1	12139	564	20	3		3	PMAIP1	18	57569926	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1567163	57569926	20507322	886	35178										
KDSR	2531	hgsc.bcm.edu	37	chr18	61034244	61034244	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agcaacaggaggccactcacCaccacatgcgccccgggcag	11	17	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:61034244C>T	ENST00000406396.3	-	1	499	c.108G>A	c.(106-108)gtG>gtA	p.V36V	RP11-635N19.1_ENST00000589905.1_RNA|KDSR_ENST00000326575.5_Splice_Site_p.V36V	NM_002035.2	NP_002026.1	Q06136	KDSR_HUMAN	3-ketodihydrosphingosine reductase	36					3-keto-sphinganine metabolic process (GO:0006666)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3-dehydrosphinganine reductase activity (GO:0047560)			endometrium(2)|large_intestine(2)|lung(3)|skin(1)|stomach(1)	9						GGCCACTCACCACCACATGCG	0.701																																					p.V36V		Atlas-SNP	.											.	KDSR	17	.	0			c.G108A						.						17	21	20					18																	61034244		2191	4287	6478	SO:0001630	splice_region_variant	2531	exon1			ACTCACCACCACA		CCDS11982.1	18q21	2011-09-20	2008-02-20	2008-02-20	ENSG00000119537	ENSG00000119537	1.1.1.102	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	4021	protein-coding gene	gene with protein product	"3-dehydrosphinganine reductase", "short chain dehydrogenase/reductase family 35C, member 1"	136440	"follicular lymphoma variant translocation 1"	FVT1		8417785, 15328338, 17420465, 19027726	Standard	NM_002035		Approved	DHSR, SDR35C1	uc010dpw.3	Q06136	OTTHUMG00000132792	ENST00000406396.3:c.108+1G>A	chr18.hg19:g.61034244C>T		226.0	0.0		134.0	6.0	NM_002035	B2R5Y1|B4DMX0	Silent	SNP	ENST00000406396.3	hg19	CCDS11982.1																																																																																			.	.		0.701	KDSR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256200.2		Silent	T	61034244	C	T	61034244	5	4	254	1	0	0	0	0	0	0	1	0	8149	608	21	3	930	3	KDSR	18	61034244	Splice_Site	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	3464318	61034244	17043004	887	35179										
TSHZ1	10194	hgsc.bcm.edu	37	chr18	72999514	72999514	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	acaccccaaatggcacagagCctctcaaagcaaaggtcacc	7	15	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr18:72999514C>A	ENST00000580243.1	+	2	2500	c.2152C>A	c.(2152-2154)Cct>Act	p.P718T	TSHZ1_ENST00000322038.5_Missense_Mutation_p.P673T			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	718					anterior/posterior pattern specification (GO:0009952)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|soft palate development (GO:0060023)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(11)|liver(1)|lung(14)|ovary(1)|skin(6)|upper_aerodigestive_tract(2)	42		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		TGGCACAGAGCCTCTCAAAGC	0.577																																					p.P673T		Atlas-SNP	.											.	TSHZ1	104	.	0			c.C2017A						.						123	103	109					18																	72999514		2203	4300	6503	SO:0001583	missense	10194	exon2			ACAGAGCCTCTCA	AF039698	CCDS12009.1	18q22.3	2013-11-20	2007-07-16	2006-03-14	ENSG00000179981	ENSG00000179981		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	10669	protein-coding gene	gene with protein product		614427	"serologically defined colon cancer antigen 33", "teashirt zinc finger 1", "teashirt family zinc finger 1"	SDCCAG33		17586487	Standard	NM_005786		Approved	NY-CO-33, TSH1	uc002lly.4	Q6ZSZ6	OTTHUMG00000132859	ENST00000580243.1:c.2152C>A	chr18.hg19:g.72999514C>A	ENSP00000464391:p.Pro718Thr	85.0	0.0		64.0	4.0	NM_005786	O60534|Q4LE29|Q53EU4	Missense_Mutation	SNP	ENST00000580243.1	hg19		.	.	.	.	.	.	.	.	.	.	C	3.444	-0.113403	0.06881	.	.	ENSG00000179981	ENST00000322038	T	0.38560	1.13	5.12	4.21	0.49690	.	0.183175	0.48286	N	0.000185	T	0.33933	0.0880	L	0.54323	1.7	0.36873	D	0.88902	B	0.22346	0.068	B	0.13407	0.009	T	0.30416	-0.9979	10	0.30078	T	0.28	-11.3758	8.1816	0.31313	0.158:0.7633:0.0:0.0786	.	718	Q6ZSZ6	TSH1_HUMAN	T	673	ENSP00000323584:P673T	ENSP00000323584:P673T	P	+	1	0	TSHZ1	71128502	1.000000	0.71417	0.832000	0.32986	0.592000	0.36648	1.284000	0.33249	2.385000	0.81259	0.561000	0.74099	CCT	.	.		0.577	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786		A	72999514	C	A	72999514	3	1	254	1	0	0	0	0	1	0	0	0	16638	739	26	3	2019	3	TSHZ1	18	72999514	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	11965270	72999514	5077734	888	35180										
MEX3D	399664	hgsc.bcm.edu	37	chr19	1556545	1556545	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcgcgcgcggtccacgttctCgggcatcccagtgaccgcga	14	16	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:1556545C>T	ENST00000402693.4	-	2	972	c.973G>A	c.(973-975)Gag>Aag	p.E325K	MEX3D_ENST00000388824.6_Missense_Mutation_p.E325K|AC027307.1_ENST00000410788.1_RNA|AC027307.2_ENST00000581992.1_RNA	NM_203304.3	NP_976049.3	Q86XN8	MEX3D_HUMAN	mex-3 RNA binding family member D	325	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.				mRNA destabilization (GO:0061157)|mRNA localization resulting in posttranscriptional regulation of gene expression (GO:0010609)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	AU-rich element binding (GO:0017091)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(1)|lung(3)	4		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCCACGTTCTCGGGCATCCCA	0.697																																					p.E325K		Atlas-SNP	.											.	MEX3D	11	.	0			c.G973A						.						22	23	22					19																	1556545		2197	4296	6493	SO:0001583	missense	399664	exon2			CGTTCTCGGGCAT	AB107353	CCDS32865.2	19p13.3	2013-08-21	2013-08-21	2007-07-18	ENSG00000181588	ENSG00000181588		"RING-type (C3HC4) zinc fingers", "Mex-3 homologs"	16734	protein-coding gene	gene with protein product	"bcl-2 ARE RNA binding protein"	611009	"ring finger and KH domain containing 1", "mex-3 homolog D (C. elegans)"	RKHD1		17267406	Standard	NM_203304		Approved	Tino, KIAA2031, OK/SW-cl.4, RNF193	uc010dsn.3	Q86XN8	OTTHUMG00000150369	ENST00000402693.4:c.973G>A	chr19.hg19:g.1556545C>T	ENSP00000384398:p.Glu325Lys	75.0	0.0		89.0	4.0	NM_203304	A0PJL8|A1L023|E9PAL6|Q71M49	Missense_Mutation	SNP	ENST00000402693.4	hg19	CCDS32865.2	.	.	.	.	.	.	.	.	.	.	C	23.7	4.448362	0.84101	.	.	ENSG00000181588	ENST00000402693;ENST00000388824	T;T	0.35973	1.28;1.28	4.61	4.61	0.57282	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.000000	0.85682	D	0.000000	T	0.58736	0.2143	M	0.75264	2.295	0.80722	D	1	D	0.71674	0.998	D	0.68039	0.955	T	0.60954	-0.7160	10	0.41790	T	0.15	-28.4273	16.4135	0.83727	0.0:1.0:0.0:0.0	.	325	Q86XN8	MEX3D_HUMAN	K	325	ENSP00000384398:E325K;ENSP00000373476:E325K	ENSP00000373476:E325K	E	-	1	0	MEX3D	1507545	1.000000	0.71417	0.999000	0.59377	0.349000	0.29174	7.445000	0.80570	2.120000	0.65058	0.313000	0.20887	GAG	.	.		0.697	MEX3D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317870.2	NM_203304		T	1556545	C	T	1556545	3	4	254	1	0	0	0	0	1	0	0	0	9521	893	31	1	1049	1	MEX3D	19	1556545	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10		1556545	57572438	889	35181										
TCF3	6929	hgsc.bcm.edu	37	chr19	1611812	1611812	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	acaccttttcctcttctcgcCgtttcaaacaggctgctttg	6	14	3	0	rs538013937		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:1611812C>A	ENST00000262965.5	-	19	2203	c.1859G>T	c.(1858-1860)cGg>cTg	p.R620L	TCF3_ENST00000453954.2_Missense_Mutation_p.R532L|TCF3_ENST00000395423.3_Missense_Mutation_p.R624L|TCF3_ENST00000344749.5_Missense_Mutation_p.R617L|TCF3_ENST00000588136.1_Missense_Mutation_p.R617L	NM_003200.3	NP_003191.1	Q9HCS4	TF7L1_HUMAN	transcription factor 3	0					anterior/posterior axis specification, embryo (GO:0008595)|axial mesoderm morphogenesis (GO:0048319)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|chromatin organization (GO:0006325)|generation of neurons (GO:0048699)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	16		Acute lymphoblastic leukemia(61;5.94e-12)|all_hematologic(61;1.27e-07)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTCTTCTCGCCGTTTCAAACA	0.617			T	"PBX1, HLF, TFPT"	pre B-ALL																																p.R620L		Atlas-SNP	.		Dom	yes		19	19p13.3	6929	transcription factor 3 (E2A immunoglobulin enhancer binding factors E12/E47)		L	.	TCF3	72	.	0			c.G1859T						.						77	61	66					19																	1611812		2203	4300	6503	SO:0001583	missense	6929	exon19			TCTCGCCGTTTCA	M65214	CCDS12074.1, CCDS45899.1	19p13.3	2014-02-13	2013-02-26		ENSG00000071564	ENSG00000071564		"Basic helix-loop-helix proteins"	11633	protein-coding gene	gene with protein product	"transcription factor E2-alpha", "immunoglobulin transcription factor 1", "kappa-E2-binding factor", "E2A immunoglobulin enhancer-binding factor E12/E47", "VDR interacting repressor"	147141				2308859, 1967983	Standard	NM_003200		Approved	E2A, ITF1, MGC129647, MGC129648, bHLHb21, VDIR, E47	uc002ltt.4	P15923	OTTHUMG00000180031	ENST00000262965.5:c.1859G>T	chr19.hg19:g.1611812C>A	ENSP00000262965:p.Arg620Leu	168.0	0.0		122.0	5.0	NM_003200	Q53R97|Q6PD70|Q9NP00	Missense_Mutation	SNP	ENST00000262965.5	hg19	CCDS12074.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.307236	0.81247	.	.	ENSG00000071564	ENST00000262965;ENST00000344749;ENST00000453954;ENST00000395423	T;T;T	0.58652	1.76;1.63;0.32	4.69	4.69	0.59074	Helix-loop-helix DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.77538	0.4145	M	0.79693	2.465	0.80722	D	1	D;D;D;D	0.89917	1.0;0.997;1.0;1.0	D;D;D;D	0.91635	0.999;0.987;0.999;0.998	T	0.81658	-0.0833	10	0.87932	D	0	-13.7286	16.981	0.86327	0.0:1.0:0.0:0.0	.	617;620;624;557	P15923-2;P15923;Q2TB39;Q6PJU3	.;TFE2_HUMAN;.;.	L	620;617;617;624	ENSP00000262965:R620L;ENSP00000344375:R617L;ENSP00000378813:R624L	ENSP00000262965:R620L	R	-	2	0	TCF3	1562812	1.000000	0.71417	0.863000	0.33907	0.418000	0.31294	7.631000	0.83237	2.309000	0.77851	0.561000	0.74099	CGG	.	.		0.617	TCF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449367.1	NM_003200		A	1611812	C	A	1611812	3	1	254	1	0	0	0	0	1	0	0	0	15709	652	23	1	109	1	TCF3	19	1611812	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	55267	1611812	57517171	890	35182										
ADAT3	113179	hgsc.bcm.edu	37	chr19	1912939	1912939	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cccctacctgtgcactggctAcgacctgtacgtgacccgcg	10	17	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:1912939A>G	ENST00000602400.1	+	2	1073	c.845A>G	c.(844-846)tAc>tGc	p.Y282C	SCAMP4_ENST00000414057.2_Intron|ADAT3_ENST00000329478.2_Missense_Mutation_p.Y298C|SCAMP4_ENST00000316097.8_Intron|SCAMP4_ENST00000409472.1_Intron			Q96EY9	ADAT3_HUMAN	adenosine deaminase, tRNA-specific 3	282					tRNA processing (GO:0008033)		hydrolase activity (GO:0016787)|zinc ion binding (GO:0008270)			breast(1)|kidney(3)|pancreas(1)|skin(2)	7		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGCACTGGCTACGACCTGTAC	0.721																																					p.Y298C		Atlas-SNP	.											.	ADAT3	15	.	0			c.A893G						.						56	52	53					19																	1912939		2200	4294	6494	SO:0001583	missense	113179	exon2			CTGGCTACGACCT	BC011824	CCDS12076.1, CCDS12076.2	19p13.3	2011-05-19	2011-05-19		ENSG00000213638	ENSG00000213638			25151	protein-coding gene	gene with protein product	"tRNA-specific adenosine deaminase 3 homolog (S. cerevisiae)"	615302	"adenosine deaminase, tRNA-specific 3, TAD3 homolog (S. cerevisiae)"			12457566	Standard	NM_138422		Approved	TAD3	uc002luh.4	Q96EY9	OTTHUMG00000154591	ENST00000602400.1:c.845A>G	chr19.hg19:g.1912939A>G	ENSP00000473571:p.Tyr282Cys	53.0	0.0		87.0	4.0	NM_138422		Missense_Mutation	SNP	ENST00000602400.1	hg19		.	.	.	.	.	.	.	.	.	.	a	12.67	2.006145	0.35415	.	.	ENSG00000213638	ENST00000329478	.	.	.	5.04	5.04	0.67666	Cytidine deaminase-like (1);CMP/dCMP deaminase, zinc-binding (1);	0.138667	0.49916	D	0.000125	T	0.46502	0.1396	N	0.02368	-0.58	0.50813	D	0.999892	D	0.89917	1.0	D	0.77004	0.989	T	0.58691	-0.7592	9	0.40728	T	0.16	-22.3745	12.7244	0.57162	1.0:0.0:0.0:0.0	.	282	Q96EY9	ADAT3_HUMAN	C	282	.	ENSP00000332448:Y282C	Y	+	2	0	ADAT3	1863939	0.997000	0.39634	0.995000	0.50966	0.452000	0.32318	3.100000	0.50275	1.897000	0.54924	0.448000	0.29417	TAC	.	.		0.721	ADAT3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_138422		G	1912939	A	G	1912939	3	3	254	1	0	0	0	0	1	0	0	0	286	391	14	2	847	2	ADAT3	19	1912939	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	301127	1912939	57216044	891	35183										
MOBKL2A	126308	hgsc.bcm.edu	37	chr19	2076903	2076903	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttcacgtgggcctcggagccCatctgcgcgatgcggtcaaa	13	13	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:2076903C>T	ENST00000357066.3	-	4	910	c.531G>A	c.(529-531)atG>atA	p.M177I	MOB3A_ENST00000592280.1_Missense_Mutation_p.M177I|MOB3A_ENST00000592143.1_Intron	NM_130807.2	NP_570719.1	Q96BX8	MOB3A_HUMAN	MOB kinase activator 3A	177						intracellular (GO:0005622)	metal ion binding (GO:0046872)										CCTCGGAGCCCATCTGCGCGA	0.587																																					p.M177I		Atlas-SNP	.											.	.	.	.	0			c.G531A						.						89	74	79					19																	2076903		2203	4300	6503	SO:0001583	missense	126308	exon4			GGAGCCCATCTGC	AK095471	CCDS12081.1	19p13.3	2011-09-28	2011-09-28	2011-09-28	ENSG00000172081	ENSG00000172081		"MOB kinase activators"	29802	protein-coding gene	gene with protein product	"MOB LAK"		"MOB1, Mps One Binder kinase activator-like 2A (yeast)"	MOBKL2A		12477932	Standard	NM_130807		Approved	MOB1C, MOB-LAK, moblak	uc002luv.3	Q96BX8		ENST00000357066.3:c.531G>A	chr19.hg19:g.2076903C>T	ENSP00000349575:p.Met177Ile	99.0	0.0		147.0	6.0	NM_130807	B3KTF1|O75249|Q8TF69	Missense_Mutation	SNP	ENST00000357066.3	hg19	CCDS12081.1	.	.	.	.	.	.	.	.	.	.	C	15.73	2.918636	0.52546	.	.	ENSG00000172081	ENST00000357066	.	.	.	3.74	3.74	0.42951	.	0.131387	0.64402	D	0.000002	T	0.24851	0.0603	N	0.01277	-0.915	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.08006	-1.0743	9	0.33940	T	0.23	-37.9465	14.2648	0.66110	0.0:1.0:0.0:0.0	.	177	Q96BX8	MOB3A_HUMAN	I	177	.	ENSP00000349575:M177I	M	-	3	0	MOBKL2A	2027903	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	5.608000	0.67654	1.937000	0.56155	0.491000	0.48974	ATG	.	.		0.587	MOB3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450893.1	NM_130807		T	2076903	C	T	2076903	3	4	254	1	0	0	0	0	1	0	0	0	9693	594	21	3	130	3	MOBKL2A	19	2076903	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	163964	2076903	57052080	892	35184										
TMPRSS9	360200	hgsc.bcm.edu	37	chr19	2413833	2413833	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gagtcaccaggctacgtgacTggatcctggaggccaccacc	12	14	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:2413833T>C	ENST00000332578.3	+	9	1288	c.1288T>C	c.(1288-1290)Tgg>Cgg	p.W430R		NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	430	Peptidase S1 1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				plasminogen activation (GO:0031639)	integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCTACGTGACTGGATCCTGGA	0.672																																					p.W430R		Atlas-SNP	.											.	TMPRSS9	79	.	0			c.T1288C						.						40	42	41					19																	2413833		2203	4300	6503	SO:0001583	missense	360200	exon9			CGTGACTGGATCC	AJ488946	CCDS12088.1	19p13.3	2010-04-13						"Serine peptidases / Transmembrane"	30079	protein-coding gene	gene with protein product	"polyserase 1"	610477				12886014	Standard	NM_182973		Approved		uc010xgx.2	Q7Z410		ENST00000332578.3:c.1288T>C	chr19.hg19:g.2413833T>C	ENSP00000330264:p.Trp430Arg	116.0	0.0		96.0	4.0	NM_182973	Q6ZND6|Q7Z411	Missense_Mutation	SNP	ENST00000332578.3	hg19	CCDS12088.1	.	.	.	.	.	.	.	.	.	.	T	14.54	2.564621	0.45694	.	.	ENSG00000178297	ENST00000395264;ENST00000332578	T	0.78707	-1.2	4.04	4.04	0.47022	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.313142	0.23424	N	0.048337	D	0.92077	0.7489	H	0.98559	4.265	0.53005	D	0.999964	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.93880	0.7170	10	0.87932	D	0	.	11.8763	0.52550	0.0:0.0:0.0:1.0	.	430;464	Q7Z410;E7EMP4	TMPS9_HUMAN;.	R	464;430	ENSP00000330264:W430R	ENSP00000330264:W430R	W	+	1	0	TMPRSS9	2364833	1.000000	0.71417	0.950000	0.38849	0.070000	0.16714	7.930000	0.87610	1.493000	0.48517	0.454000	0.30748	TGG	.	.		0.672	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973		C	2413833	T	C	2413833	3	2	254	1	0	0	0	0	1	0	0	0	16268	1580	55	2	1322	2	TMPRSS9	19	2413833	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	336930	2413833	56715150	893	35185										
UBXN6	80700	hgsc.bcm.edu	37	chr19	4448329	4448329	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gctcacttggcaatggtgtcCacacccagcttcacccggtc	9	16	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:4448329C>A	ENST00000301281.6	-	5	649	c.525G>T	c.(523-525)gtG>gtT	p.V175V	MIR4746_ENST00000579802.1_RNA|CTB-50L17.7_ENST00000588798.1_RNA|UBXN6_ENST00000394765.3_Silent_p.V122V	NM_025241.2	NP_079517.1	Q9BZV1	UBXN6_HUMAN	UBX domain protein 6	175	PUB.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				NS(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	12						CAATGGTGTCCACACCCAGCT	0.637																																					p.V175V		Atlas-SNP	.											.	UBXN6	27	.	0			c.G525T						.						117	87	97					19																	4448329		2202	4299	6501	SO:0001819	synonymous_variant	80700	exon5			GGTGTCCACACCC	AF272893	CCDS12129.1, CCDS54201.1	19p13	2008-07-25	2008-07-25	2008-07-25		ENSG00000167671		"UBX domain containing"	14928	protein-coding gene	gene with protein product		611946	"UBX domain-containing 1", "UBX domain containing 1"	UBXD1		11342112	Standard	NM_025241		Approved	UBXDC2	uc002man.2	Q9BZV1		ENST00000301281.6:c.525G>T	chr19.hg19:g.4448329C>A		71.0	0.0		65.0	4.0	NM_025241	D6W626|Q96AH1|Q96IK9|Q9BZV0	Silent	SNP	ENST00000301281.6	hg19	CCDS12129.1																																																																																			.	.		0.637	UBXN6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458447.3	NM_025241		A	4448329	C	A	4448329	2	1	254	1	0	0	0	0	0	0	0	1	16932	581	21	3		3	UBXN6	19	4448329	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	2034496	4448329	54680654	894	35186										
DPP9	91039	hgsc.bcm.edu	37	chr19	4700261	4700261	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcagtctggaactcagccagTttcaaggcaatcttgggatt	10	9	5	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:4700261T>C	ENST00000598800.1	-	11	1459	c.954A>G	c.(952-954)aaA>aaG	p.K318K	DPP9_ENST00000597849.1_Silent_p.K347K|DPP9_ENST00000594671.1_Silent_p.K318K|DPP9_ENST00000262960.9_Silent_p.K347K			Q86TI2	DPP9_HUMAN	dipeptidyl-peptidase 9	318						cytoplasm (GO:0005737)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|identical protein binding (GO:0042802)|serine-type peptidase activity (GO:0008236)			cervix(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00884)		ACTCAGCCAGTTTCAAGGCAA	0.592																																					p.K347K		Atlas-SNP	.											.	DPP9	59	.	0			c.A1041G						.						41	44	43					19																	4700261		1929	4138	6067	SO:0001819	synonymous_variant	91039	exon10			AGCCAGTTTCAAG	AF452102	CCDS45928.1	19p13.3	2014-06-11	2006-01-12		ENSG00000142002	ENSG00000142002			18648	protein-coding gene	gene with protein product		608258	"dipeptidylpeptidase 9"				Standard	NM_139159		Approved		uc002mba.3	Q86TI2	OTTHUMG00000182040	ENST00000598800.1:c.954A>G	chr19.hg19:g.4700261T>C		87.0	0.0		94.0	5.0	NM_139159	O75273|O75868|Q1ZZB8|Q6AI37|Q6UAL0|Q6ZMT2|Q6ZNJ5|Q8N2J7|Q8N3F5|Q8WXD8|Q96NT8|Q9BVR3	Silent	SNP	ENST00000598800.1	hg19																																																																																				.	.		0.592	DPP9-026	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000459343.2			C	4700261	T	C	4700261	2	2	254	1	0	0	0	0	0	0	0	1	4735	1722	60	2		2	DPP9	19	4700261	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	251932	4700261	54428722	895	35187										
FEM1A	55527	hgsc.bcm.edu	37	chr19	4792961	4792961	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gagctggaggcgctgatcacCgacccggatgagatgcgcat	15	11	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:4792961C>A	ENST00000269856.3	+	1	1234	c.1095C>A	c.(1093-1095)acC>acA	p.T365T	AC005523.2_ENST00000601192.1_RNA|AC005523.3_ENST00000598782.1_lincRNA|AC005523.2_ENST00000596170.1_RNA	NM_018708.2	NP_061178.1	Q9BSK4	FEM1A_HUMAN	fem-1 homolog a (C. elegans)	365					negative regulation of inflammatory response (GO:0050728)|regulation of ubiquitin-protein transferase activity (GO:0051438)	cytoplasm (GO:0005737)	EP4 subtype prostaglandin E2 receptor binding (GO:0031867)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	17		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0139)		CGCTGATCACCGACCCGGATG	0.637																																					p.T365T		Atlas-SNP	.											.	FEM1A	41	.	0			c.C1095A						.						48	50	50					19																	4792961		2203	4300	6503	SO:0001819	synonymous_variant	55527	exon1			GATCACCGACCCG	BC004988	CCDS12135.1	19p13.3	2013-01-10	2006-11-08		ENSG00000141965	ENSG00000141965		"Ankyrin repeat domain containing"	16934	protein-coding gene	gene with protein product		613538				11441184	Standard	NM_018708		Approved		uc002mbf.3	Q9BSK4		ENST00000269856.3:c.1095C>A	chr19.hg19:g.4792961C>A		37.0	0.0		53.0	5.0	NM_018708	B2RDI3|Q711P8|Q9NPN7|Q9NPW8	Silent	SNP	ENST00000269856.3	hg19	CCDS12135.1																																																																																			.	.		0.637	FEM1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459000.1			A	4792961	C	A	4792961	2	1	254	1	0	0	0	0	0	0	0	1	5817	639	23	1		1	FEM1A	19	4792961	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	92700	4792961	54336022	896	35188										
PTPRS	5802	hgsc.bcm.edu	37	chr19	5208037	5208037	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctccagcacgatgctaagcgTgatgaagacgcccgtcctgc	11	14	0	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:5208037T>C	ENST00000587303.1	-	36	5773	c.5674A>G	c.(5674-5676)Acg>Gcg	p.T1892A	PTPRS_ENST00000588012.1_Missense_Mutation_p.T1854A|PTPRS_ENST00000357368.4_Missense_Mutation_p.T1892A|PTPRS_ENST00000348075.2_Missense_Mutation_p.T1854A|PTPRS_ENST00000592099.1_Missense_Mutation_p.T1445A|PTPRS_ENST00000353284.2_Missense_Mutation_p.T1445A|PTPRS_ENST00000588552.1_5'UTR|PTPRS_ENST00000262963.6_Missense_Mutation_p.T1872A|PTPRS_ENST00000372412.4_Missense_Mutation_p.T1893A			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	1892	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|corpus callosum development (GO:0022038)|extracellular matrix organization (GO:0030198)|hippocampus development (GO:0021766)|peptidyl-tyrosine dephosphorylation (GO:0035335)|spinal cord development (GO:0021510)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(9)|ovary(4)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)	61				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Alendronate(DB00630)|Etidronic acid(DB01077)	ATGCTAAGCGTGATGAAGACG	0.617																																					p.T1892A		Atlas-SNP	.											.	PTPRS	169	.	0			c.A5674G						.						78	59	66					19																	5208037		2203	4300	6503	SO:0001583	missense	5802	exon37			TAAGCGTGATGAA	U35234	CCDS12139.1, CCDS12140.1, CCDS45930.1, CCDS74265.1	19p13.3	2013-02-11				ENSG00000105426		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9681	protein-coding gene	gene with protein product		601576				8954782, 8524829	Standard	NM_002850		Approved		uc002mbv.3	Q13332		ENST00000587303.1:c.5674A>G	chr19.hg19:g.5208037T>C	ENSP00000467537:p.Thr1892Ala	63.0	0.0		52.0	4.0	NM_002850	O75255|O75870|Q15718|Q16341|Q2M3R7	Missense_Mutation	SNP	ENST00000587303.1	hg19	CCDS45930.1	.	.	.	.	.	.	.	.	.	.	T	14.94	2.685739	0.47991	.	.	ENSG00000105426	ENST00000536396;ENST00000372412;ENST00000357368;ENST00000355005;ENST00000356037;ENST00000262963;ENST00000348075;ENST00000355322;ENST00000544524;ENST00000353284	T;T;T;T;T	0.09630	2.96;2.96;2.96;2.96;2.96	2.78	2.78	0.32641	Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.64402	U	0.000002	T	0.08223	0.0205	N	0.00563	-1.375	0.80722	D	1	D;B;P;B;D;D	0.76494	0.999;0.05;0.882;0.384;0.995;0.995	D;B;P;B;D;D	0.87578	0.998;0.042;0.693;0.302;0.997;0.997	T	0.54609	-0.8268	10	0.66056	D	0.02	.	10.8984	0.47036	0.0:0.0:0.0:1.0	.	1474;1445;1449;1854;1892;1487	F8W800;Q13332-7;F5H2T4;Q13332-6;Q13332;Q59FX6	.;.;.;.;PTPRS_HUMAN;.	A	1487;1893;1892;1892;1883;1872;1854;1474;1449;1445	ENSP00000361489:T1893A;ENSP00000349932:T1892A;ENSP00000262963:T1872A;ENSP00000269907:T1854A;ENSP00000327313:T1445A	ENSP00000262963:T1872A	T	-	1	0	PTPRS	5159037	1.000000	0.71417	1.000000	0.80357	0.669000	0.39330	4.918000	0.63376	1.147000	0.42369	0.386000	0.25728	ACG	.	.		0.617	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2			C	5208037	T	C	5208037	3	2	254	1	0	0	0	0	1	0	0	0	12826	1696	59	2	180	2	PTPRS	19	5208037	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	415076	5208037	53920946	897	35189										
PTPRS	5802	hgsc.bcm.edu	37	chr19	5216748	5216748	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aactttcaaagtgaaaccccGgctccctgagggggctcctg	11	13	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:5216748G>A	ENST00000587303.1	-	25	4178	c.4079C>T	c.(4078-4080)cCg>cTg	p.P1360L	PTPRS_ENST00000588012.1_Intron|PTPRS_ENST00000357368.4_Missense_Mutation_p.P1360L|PTPRS_ENST00000348075.2_Intron|PTPRS_ENST00000592099.1_Intron|PTPRS_ENST00000353284.2_Intron|PTPRS_ENST00000588552.1_5'UTR|PTPRS_ENST00000262963.6_Intron|PTPRS_ENST00000372412.4_Missense_Mutation_p.P1361L			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	1360					cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|corpus callosum development (GO:0022038)|extracellular matrix organization (GO:0030198)|hippocampus development (GO:0021766)|peptidyl-tyrosine dephosphorylation (GO:0035335)|spinal cord development (GO:0021510)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(9)|ovary(4)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)	61				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Alendronate(DB00630)|Etidronic acid(DB01077)	GTGAAACCCCGGCTCCCTGAG	0.532																																					p.P1360L		Atlas-SNP	.											.	PTPRS	169	.	0			c.C4079T						.						36	44	41					19																	5216748		1851	4080	5931	SO:0001583	missense	5802	exon26			AACCCCGGCTCCC	U35234	CCDS12139.1, CCDS12140.1, CCDS45930.1, CCDS74265.1	19p13.3	2013-02-11				ENSG00000105426		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9681	protein-coding gene	gene with protein product		601576				8954782, 8524829	Standard	NM_002850		Approved		uc002mbv.3	Q13332		ENST00000587303.1:c.4079C>T	chr19.hg19:g.5216748G>A	ENSP00000467537:p.Pro1360Leu	460.0	0.0		369.0	69.0	NM_002850	O75255|O75870|Q15718|Q16341|Q2M3R7	Missense_Mutation	SNP	ENST00000587303.1	hg19	CCDS45930.1	.	.	.	.	.	.	.	.	.	.	G	12.83	2.056332	0.36277	.	.	ENSG00000105426	ENST00000536396;ENST00000372412;ENST00000357368;ENST00000355005;ENST00000356037;ENST00000355322	T;T	0.52526	0.68;0.66	3.42	3.42	0.39159	.	0.947250	0.08463	U	0.942100	T	0.25419	0.0618	N	0.14661	0.345	0.80722	D	1	P;P	0.49253	0.524;0.921	B;B	0.26517	0.029;0.07	T	0.15065	-1.0450	10	0.72032	D	0.01	.	10.6094	0.45412	0.0:0.0:0.8074:0.1926	.	1360;955	Q13332;Q59FX6	PTPRS_HUMAN;.	L	955;1361;1360;1360;1351;942	ENSP00000361489:P1361L;ENSP00000349932:P1360L	ENSP00000347106:P1360L	P	-	2	0	PTPRS	5167748	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	5.412000	0.66392	1.614000	0.50241	0.462000	0.41574	CCG	.	.		0.532	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2			A	5216748	G	A	5216748	3	1	254	1	0	0	0	0	1	0	0	0	12826	1116	39	1	1819	1	PTPRS	19	5216748	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	8711	5216748	53912235	898	35190										
MLLT1	4298	hgsc.bcm.edu	37	chr19	6222582	6222582	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttggagcttttggcctgctcAcgctccagctccttggagga	12	12	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:6222582A>G	ENST00000252674.7	-	6	823	c.660T>C	c.(658-660)cgT>cgC	p.R220R		NM_005934.3	NP_005925.2	Q03111	ENL_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 1	220					negative regulation of protein kinase activity (GO:0006469)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	DNA binding (GO:0003677)			endometrium(3)|kidney(3)|large_intestine(2)|lung(5)|prostate(2)|skin(2)	17						TGGCCTGCTCACGCTCCAGCT	0.647			T	MLL	AL																																p.R220R		Atlas-SNP	.		Dom	yes		19	19p13.3	4298	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 1 (ENL)"		L	.	MLLT1	47	.	0			c.T660C						.						42	39	40					19																	6222582		2203	4300	6503	SO:0001819	synonymous_variant	4298	exon6			CTGCTCACGCTCC		CCDS12160.1	19p13.3	2012-10-04	2001-11-28		ENSG00000130382	ENSG00000130382			7134	protein-coding gene	gene with protein product		159556	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 1"				Standard	XM_005259561		Approved	ENL, LTG19, YEATS1	uc002mek.3	Q03111	OTTHUMG00000180757	ENST00000252674.7:c.660T>C	chr19.hg19:g.6222582A>G		58.0	0.0		71.0	5.0	NM_005934	Q14768	Silent	SNP	ENST00000252674.7	hg19	CCDS12160.1																																																																																			.	.		0.647	MLLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452909.1	NM_005934		G	6222582	A	G	6222582	2	3	254	1	0	0	0	0	0	0	0	1	9634	146	6	2		2	MLLT1	19	6222582	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	1005834	6222582	52906401	899	35191										
SLC25A23	79085	hgsc.bcm.edu	37	chr19	6456473	6456473	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agcacgtcctccacattttcCagcgaatgcaacaggaagtg	9	12	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:6456473C>T	ENST00000301454.4	-	4	547	c.441G>A	c.(439-441)ctG>ctA	p.L147L	SLC25A23_ENST00000334510.5_Silent_p.L147L|SLC25A23_ENST00000414491.2_5'Flank	NM_024103.2	NP_077008.2	Q9BV35	SCMC3_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 23	147	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				adenine nucleotide transport (GO:0051503)|cellular response to calcium ion (GO:0071277)|regulation of cellular respiration (GO:0043457)|regulation of oxidative phosphorylation (GO:0002082)|regulation of sequestering of calcium ion (GO:0051282)|transmembrane transport (GO:0055085)|urea homeostasis (GO:0097274)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)			endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|pancreas(1)|skin(1)	17						CCACATTTTCCAGCGAATGCA	0.592																																					p.L147L		Atlas-SNP	.											.	SLC25A23	43	.	0			c.G441A						.						167	125	139					19																	6456473		2203	4300	6503	SO:0001819	synonymous_variant	79085	exon4			ATTTTCCAGCGAA	AJ619962	CCDS32882.1	19p13.1	2014-02-06			ENSG00000125648	ENSG00000125648		"Solute carriers", "EF-hand domain containing"	19375	protein-coding gene	gene with protein product		608746				15123600	Standard	NM_024103		Approved	FLJ30339, MGC2615, APC2	uc002mex.1	Q9BV35	OTTHUMG00000180852	ENST00000301454.4:c.441G>A	chr19.hg19:g.6456473C>T		103.0	0.0		64.0	4.0	NM_024103	B4DGB6|Q4LBC2|Q705K3|Q86Y43|Q8N2N4|Q96NQ4	Silent	SNP	ENST00000301454.4	hg19	CCDS32882.1																																																																																			.	.		0.592	SLC25A23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453325.1	NM_024103		T	6456473	C	T	6456473	2	4	254	1	0	0	0	0	0	0	0	1	14501	581	21	3		3	SLC25A23	19	6456473	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	233891	6456473	52672510	900	35192										
ZNF557	79230	hgsc.bcm.edu	37	chr19	7083073	7083073	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcataagagaatccacaatgGggagaaaccctatgaatgca	9	8	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:7083073G>T	ENST00000439035.2	+	8	830	c.590G>T	c.(589-591)gGg>gTg	p.G197V	ZNF557_ENST00000414706.1_Missense_Mutation_p.G204V|ZNF557_ENST00000252840.6_Missense_Mutation_p.G204V			Q8N988	ZN557_HUMAN	zinc finger protein 557	197					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(6)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	17				Lung(535;0.179)		ATCCACAATGGGGAGAAACCC	0.438																																					p.G204V		Atlas-SNP	.											.	ZNF557	40	.	0			c.G611T						.						62	70	67					19																	7083073		2192	4298	6490	SO:0001583	missense	79230	exon8			ACAATGGGGAGAA	AK095524	CCDS42485.1, CCDS45945.1	19p13.2	2013-09-20			ENSG00000130544	ENSG00000130544		"Zinc fingers, C2H2-type", "-"	28632	protein-coding gene	gene with protein product						12477932	Standard	NM_024341		Approved	MGC4054	uc002mgc.3	Q8N988	OTTHUMG00000181977	ENST00000439035.2:c.590G>T	chr19.hg19:g.7083073G>T	ENSP00000398965:p.Gly197Val	158.0	0.0		99.0	4.0	NM_001044387	Q6PEJ3|Q9BTZ1	Missense_Mutation	SNP	ENST00000439035.2	hg19	CCDS45945.1	.	.	.	.	.	.	.	.	.	.	G	16.66	3.186093	0.57909	.	.	ENSG00000130544	ENST00000252840;ENST00000414706;ENST00000439035	T;T;T	0.23552	1.9;1.9;1.9	0.786	0.786	0.18590	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.48857	0.1523	M	0.85299	2.745	0.54753	D	0.999985	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.51576	-0.8688	9	0.72032	D	0.01	.	7.5376	0.27719	1.0E-4:0.0:0.9999:0.0	.	197;204	Q8N988;Q8N988-2	ZN557_HUMAN;.	V	204;204;197	ENSP00000252840:G204V;ENSP00000404065:G204V;ENSP00000398965:G197V	ENSP00000252840:G204V	G	+	2	0	ZNF557	7034073	1.000000	0.71417	0.576000	0.28549	0.361000	0.29550	5.252000	0.65445	0.757000	0.33036	0.134000	0.15878	GGG	.	.		0.438	ZNF557-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458502.1	NM_024341		T	7083073	G	T	7083073	3	4	254	1	0	0	0	0	1	0	0	0	18003	1232	43	3	633	3	ZNF557	19	7083073	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	626600	7083073	52045910	901	35193										
TRAPPC5	126003	hgsc.bcm.edu	37	chr19	7747234	7747234	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cctgagcgccttcgcactgcTgttctccgagctggtacagc	11	15	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:7747234T>C	ENST00000317378.5	+	2	282	c.95T>C	c.(94-96)cTg>cCg	p.L32P	TRAPPC5_ENST00000426877.2_Missense_Mutation_p.L32P|CTD-3214H19.16_ENST00000597959.1_Missense_Mutation_p.C91R|TRAPPC5_ENST00000596148.1_Missense_Mutation_p.L32P|TRAPPC5_ENST00000595985.1_Intron	NM_174894.2	NP_777554.1	Q8IUR0	TPPC5_HUMAN	trafficking protein particle complex 5	32					vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|TRAPP complex (GO:0030008)				NS(1)|lung(2)	3						TTCGCACTGCTGTTCTCCGAG	0.751																																					p.L32P		Atlas-SNP	.											.	TRAPPC5	11	.	0			c.T95C						.						11	13	13					19																	7747234		1741	3675	5416	SO:0001583	missense	126003	exon2			CACTGCTGTTCTC	BC042161	CCDS42490.1	19p13.3	2011-10-10				ENSG00000181029		"Trafficking protein particle complex"	23067	protein-coding gene	gene with protein product							Standard	NM_001042462		Approved	MGC52424, TRS31	uc002mhj.2	Q8IUR0		ENST00000317378.5:c.95T>C	chr19.hg19:g.7747234T>C	ENSP00000316990:p.Leu32Pro	83.0	0.0		45.0	4.0	NM_001042461	A8K7I6	Missense_Mutation	SNP	ENST00000317378.5	hg19	CCDS42490.1	.	.	.	.	.	.	.	.	.	.	T	18.78	3.697840	0.68386	.	.	ENSG00000181029	ENST00000317378;ENST00000426877	T;T	0.63913	-0.07;-0.07	4.09	4.09	0.47781	NO signalling/Golgi transport  ligand-binding domain (1);	0.000000	0.64402	U	0.000007	D	0.83931	0.5361	H	0.96518	3.835	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87606	0.2500	10	0.87932	D	0	-10.4913	11.0504	0.47884	0.0:0.0:0.0:1.0	.	32	Q8IUR0	TPPC5_HUMAN	P	32	ENSP00000316990:L32P;ENSP00000399025:L32P	ENSP00000316990:L32P	L	+	2	0	TRAPPC5	7653234	1.000000	0.71417	0.996000	0.52242	0.433000	0.31745	7.354000	0.79424	1.497000	0.48584	0.454000	0.30748	CTG	.	.		0.751	TRAPPC5-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461252.1	XM_058961		C	7747234	T	C	7747234	3	2	254	1	0	0	0	0	1	0	0	0	16477	1580	55	2	97	2	TRAPPC5	19	7747234	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	664161	7747234	51381749	902	35194										
MAP2K7	5609	hgsc.bcm.edu	37	chr19	7975215	7975215	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cggcacctgcggccaggtgtGgaagatgcgcttccggaaga	16	11	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:7975215G>T	ENST00000397979.3	+	4	458	c.404G>T	c.(403-405)tGg>tTg	p.W135L	MAP2K7_ENST00000397983.3_Missense_Mutation_p.W151L|MAP2K7_ENST00000397981.3_Missense_Mutation_p.W135L|CTD-3193O13.13_ENST00000595655.1_RNA|MAP2K7_ENST00000545011.1_Missense_Mutation_p.W177L	NM_145185.2	NP_660186.1	O14733	MP2K7_HUMAN	mitogen-activated protein kinase kinase 7	135	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cellular response to sorbitol (GO:0072709)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of neuron apoptotic process (GO:0043525)|response to heat (GO:0009408)|response to osmotic stress (GO:0006970)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|magnesium ion binding (GO:0000287)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(2)|central_nervous_system(3)|endometrium(1)|large_intestine(8)|lung(4)|ovary(1)	19						GGCCAGGTGTGGAAGATGCGC	0.667																																					p.W135L		Atlas-SNP	.											.	MAP2K7	66	.	0			c.G404T						.						32	39	37					19																	7975215		2038	4183	6221	SO:0001583	missense	5609	exon4			AGGTGTGGAAGAT	AF006689	CCDS42491.1, CCDS74277.1, CCDS74278.1	19p13.3-p13.2	2011-06-09			ENSG00000076984	ENSG00000076984	2.7.12.2	"Mitogen-activated protein kinase cascade / Kinase kinases"	6847	protein-coding gene	gene with protein product		603014		PRKMK7		9312068	Standard	XM_005272489		Approved	MKK7, Jnkk2	uc002mit.3	O14733	OTTHUMG00000137368	ENST00000397979.3:c.404G>T	chr19.hg19:g.7975215G>T	ENSP00000381066:p.Trp135Leu	135.0	0.0		96.0	4.0	NM_145185	B2R9S5|D6W659|O14648|O14816|O60452|O60453|Q1PG43|Q8IY10	Missense_Mutation	SNP	ENST00000397979.3	hg19	CCDS42491.1	.	.	.	.	.	.	.	.	.	.	G	12.02	1.811931	0.32053	.	.	ENSG00000076984	ENST00000397981;ENST00000397983;ENST00000545011;ENST00000425613;ENST00000397979	T;T;T;T	0.63255	-0.03;-0.03;-0.03;-0.03	5.31	5.31	0.75309	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.122835	0.64402	D	0.000020	T	0.46776	0.1410	N	0.20574	0.59	0.48762	D	0.999704	B;B	0.13145	0.003;0.007	B;B	0.17979	0.002;0.02	T	0.39165	-0.9627	10	0.11485	T	0.65	-6.9431	16.4609	0.84044	0.0:0.0:1.0:0.0	.	135;135	O14733-4;O14733	.;MP2K7_HUMAN	L	135;151;177;151;135	ENSP00000381068:W135L;ENSP00000381070:W151L;ENSP00000443946:W177L;ENSP00000381066:W135L	ENSP00000381066:W135L	W	+	2	0	MAP2K7	7881215	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.632000	0.74281	2.502000	0.84385	0.561000	0.74099	TGG	.	.		0.667	MAP2K7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000267980.1			T	7975215	G	T	7975215	3	4	254	1	0	0	0	0	1	0	0	0	9251	1357	47	3	418	3	MAP2K7	19	7975215	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	227981	7975215	51153768	903	35195										
TIMM44	10469	hgsc.bcm.edu	37	chr19	7999080	7999080	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctgcttcctccacgccctccTtgattttccggccgagatca	7	17	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:7999080T>C	ENST00000270538.3	-	5	705	c.437A>G	c.(436-438)aAg>aGg	p.K146R	TIMM44_ENST00000598968.1_5'Flank	NM_006351.3	NP_006342.2	O43615	TIM44_HUMAN	translocase of inner mitochondrial membrane 44 homolog (yeast)	146					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|P-P-bond-hydrolysis-driven protein transmembrane transporter activity (GO:0015450)			NS(1)|endometrium(3)|kidney(3)|large_intestine(2)|liver(2)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	17						CACGCCCTCCTTGATTTTCCG	0.642																																					p.K146R		Atlas-SNP	.											.	TIMM44	47	.	0			c.A437G						.						82	88	86					19																	7999080		2203	4300	6503	SO:0001583	missense	10469	exon5			CCCTCCTTGATTT	AF026030	CCDS12192.1	19p13.3-p13.2	2008-07-04				ENSG00000104980			17316	protein-coding gene	gene with protein product		605058				10848612, 10339406	Standard	NM_006351		Approved	TIM44	uc002miz.3	O43615		ENST00000270538.3:c.437A>G	chr19.hg19:g.7999080T>C	ENSP00000270538:p.Lys146Arg	119.0	0.0		93.0	4.0	NM_006351	A8K0R9|D6W664|Q8N193	Missense_Mutation	SNP	ENST00000270538.3	hg19	CCDS12192.1	.	.	.	.	.	.	.	.	.	.	T	9.884	1.202439	0.22121	.	.	ENSG00000104980	ENST00000270538	T	0.76578	-1.03	5.52	3.33	0.38152	.	0.128073	0.64402	D	0.000001	T	0.56031	0.1958	L	0.34521	1.04	0.44685	D	0.997673	B	0.06786	0.001	B	0.08055	0.003	T	0.49370	-0.8947	10	0.02654	T	1	-42.1433	2.7702	0.05332	0.1443:0.085:0.1493:0.6214	.	146	O43615	TIM44_HUMAN	R	146	ENSP00000270538:K146R	ENSP00000270538:K146R	K	-	2	0	TIMM44	7905080	1.000000	0.71417	1.000000	0.80357	0.580000	0.36256	2.939000	0.48995	2.106000	0.64143	0.459000	0.35465	AAG	.	.		0.642	TIMM44-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461596.3			C	7999080	T	C	7999080	3	2	254	1	0	0	0	0	1	0	0	0	15927	1609	56	2	957	2	TIMM44	19	7999080	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	23865	7999080	51129903	904	35196										
ELAVL1	1994	hgsc.bcm.edu	37	chr19	8056658	8056658	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttcgttctcccgatgtcaccCctgcagtcttcggccatgtg	9	15	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:8056658C>A	ENST00000407627.2	-	2	171	c.42G>T	c.(40-42)agG>agT	p.R14S	ELAVL1_ENST00000596459.1_Missense_Mutation_p.R14S|ELAVL1_ENST00000593807.1_Missense_Mutation_p.R14S|ELAVL1_ENST00000351593.5_Missense_Mutation_p.R41S	NM_001419.2	NP_001410.2	Q15717	ELAV1_HUMAN	ELAV like RNA binding protein 1	14					3'-UTR-mediated mRNA stabilization (GO:0070935)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA stabilization (GO:0048255)|multicellular organismal development (GO:0007275)|positive regulation of translation (GO:0045727)|regulation of stem cell maintenance (GO:2000036)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|double-stranded RNA binding (GO:0003725)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA 3'-UTR binding (GO:0003730)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						CGATGTCACCCCTGCAGTCTT	0.413																																					p.R14S		Atlas-SNP	.											.	ELAVL1	44	.	0			c.G42T						.						159	138	145					19																	8056658		2203	4300	6503	SO:0001583	missense	1994	exon2			GTCACCCCTGCAG	U38175	CCDS12193.1	19p13.2	2013-10-03	2013-10-03			ENSG00000066044		"RNA binding motif (RRM) containing"	3312	protein-coding gene	gene with protein product	"embryonic lethal, abnormal vision, drosophila, homolog-like 1", "Hu antigen R"	603466	"ELAV (embryonic lethal, abnormal vision, Drosophila)-like 1 (Hu antigen R)"	HUR		8626503, 9003489	Standard	NM_001419		Approved	HuR, Hua, MelG	uc002mjb.3	Q15717		ENST00000407627.2:c.42G>T	chr19.hg19:g.8056658C>A	ENSP00000385269:p.Arg14Ser	150.0	0.0		111.0	5.0	NM_001419	B4DVB8|Q53XN6|Q9BTT1	Missense_Mutation	SNP	ENST00000407627.2	hg19	CCDS12193.1	.	.	.	.	.	.	.	.	.	.	C	12.38	1.919459	0.33908	.	.	ENSG00000066044	ENST00000407627;ENST00000351593	T;T	0.14766	2.48;2.5	5.67	4.62	0.57501	.	0.105878	0.64402	D	0.000004	T	0.05960	0.0155	N	0.03154	-0.405	0.42422	D	0.992643	B	0.06786	0.001	B	0.04013	0.001	T	0.23440	-1.0188	10	0.08837	T	0.75	.	13.6273	0.62173	0.156:0.844:0.0:0.0	.	14	Q15717	ELAV1_HUMAN	S	14;41	ENSP00000385269:R14S;ENSP00000264073:R41S	ENSP00000264073:R41S	R	-	3	2	ELAVL1	7962658	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.526000	0.35964	1.362000	0.46000	0.655000	0.94253	AGG	.	.		0.413	ELAVL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461494.3	NM_001419		A	8056658	C	A	8056658	3	1	254	1	0	0	0	0	1	0	0	0	5051	622	22	3	958	3	ELAVL1	19	8056658	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	57578	8056658	51072325	905	35197										
CD320	51293	hgsc.bcm.edu	37	chr19	8370014	8370014	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggtgcggcactggaacttggTgggtgggcacgagcctgagc	19	9	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:8370014T>A	ENST00000301458.5	-	2	233	c.169A>T	c.(169-171)Acc>Tcc	p.T57S	CD320_ENST00000596246.1_5'Flank|CD320_ENST00000537716.2_Intron	NM_016579.3	NP_057663.1	Q9NPF0	CD320_HUMAN	CD320 molecule	57	LDL-receptor class A 1. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cobalamin metabolic process (GO:0009235)|regulation of cell growth (GO:0001558)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cobalamin binding (GO:0031419)			central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)	6						TGGAACTTGGTGGGTGGGCAC	0.622																																					p.T57S		Atlas-SNP	.											.	CD320	20	.	0			c.A169T						.						59	51	53					19																	8370014		2203	4300	6503	SO:0001583	missense	51293	exon2			ACTTGGTGGGTGG	AF161254	CCDS12198.1, CCDS54210.1	19p13.3-p13.2	2008-02-05	2006-03-28			ENSG00000167775		"CD molecules"	16692	protein-coding gene	gene with protein product	"8D6 antigen"	606475	"CD320 antigen"			10727470	Standard	NM_016579		Approved	8D6, 8D6A	uc002mjj.2	Q9NPF0		ENST00000301458.5:c.169A>T	chr19.hg19:g.8370014T>A	ENSP00000301458:p.Thr57Ser	67.0	0.0		75.0	4.0	NM_016579	B2RDS5|D6W668|F5H6D3|Q53HF7	Missense_Mutation	SNP	ENST00000301458.5	hg19	CCDS12198.1	.	.	.	.	.	.	.	.	.	.	T	7.989	0.752775	0.15778	.	.	ENSG00000167775	ENST00000301458	D	0.95238	-3.65	4.87	-6.35	0.01975	.	1.638950	0.03345	N	0.195314	D	0.83294	0.5223	N	0.16266	0.395	0.09310	N	1	B	0.22346	0.068	B	0.22386	0.039	T	0.79560	-0.1753	10	0.05959	T	0.93	-3.2044	0.9076	0.01288	0.3864:0.2712:0.1187:0.2238	.	57	Q9NPF0	CD320_HUMAN	S	57	ENSP00000301458:T57S	ENSP00000301458:T57S	T	-	1	0	CD320	8276014	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.729000	0.01856	-1.522000	0.01769	-0.408000	0.06270	ACC	.	.		0.622	CD320-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461366.1	NM_016579		A	8370014	T	A	8370014	3	1	254	1	0	0	0	0	1	0	0	0	3006	1696	59	4	695	4	CD320	19	8370014	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	313356	8370014	50758969	906	35198										
FBXL12	54850	hgsc.bcm.edu	37	chr19	9922014	9922014	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aggtaccacccagcaccagcGagcgcaaggcccggaagcgc	13	16	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:9922014G>T	ENST00000247977.4	-	3	780	c.539C>A	c.(538-540)tCg>tAg	p.S180*	FBXL12_ENST00000589626.1_3'UTR|FBXL12_ENST00000588922.1_3'UTR|FBXL12_ENST00000591009.1_Nonsense_Mutation_p.S127*|FBXL12_ENST00000592067.1_3'UTR|FBXL12_ENST00000585379.1_Nonsense_Mutation_p.S127*|FBXL12_ENST00000586651.1_3'UTR	NM_017703.1	NP_060173.1	Q9NXK8	FXL12_HUMAN	F-box and leucine-rich repeat protein 12	180					protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|ubiquitin ligase complex (GO:0000151)				endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(2)	10						CAGCACCAGCGAGCGCAAGGC	0.672																																					p.S180X		Atlas-SNP	.											FBXL12,NS,carcinoma,0,1	FBXL12	17	.	0			c.C539A						.						42	42	42					19																	9922014		2202	4298	6500	SO:0001587	stop_gained	54850	exon3			ACCAGCGAGCGCA	AK000195	CCDS12218.1	19p13.2	2011-06-09				ENSG00000127452		"F-boxes / Leucine-rich repeats"	13611	protein-coding gene	gene with protein product		609079				10531037	Standard	XM_005259964		Approved	FLJ20188, Fbl12	uc002mme.3	Q9NXK8		ENST00000247977.4:c.539C>A	chr19.hg19:g.9922014G>T	ENSP00000247977:p.Ser180*	44.0	0.0		42.0	2.0	NM_017703	B3KSJ8|Q9H5K4	Nonsense_Mutation	SNP	ENST00000247977.4	hg19	CCDS12218.1	.	.	.	.	.	.	.	.	.	.	G	37	6.064635	0.97251	.	.	ENSG00000127452	ENST00000247977	.	.	.	4.76	4.76	0.60689	.	0.412737	0.24516	N	0.037847	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.1447	0.59454	0.0:0.0:1.0:0.0	.	.	.	.	X	180	.	.	S	-	2	0	FBXL12	9783014	0.980000	0.34600	0.984000	0.44739	0.817000	0.46193	1.977000	0.40589	2.474000	0.83562	0.655000	0.94253	TCG	.	.		0.672	FBXL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450265.1	NM_017703		T	9922014	G	T	9922014	4	4	254	1	0	0	0	0	0	1	0	0	5716	1059	37	1	445	1	FBXL12	19	9922014	Nonsense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1552000	9922014	49206969	907	35199										
ECSIT	51295	hgsc.bcm.edu	37	chr19	11625035	11625035	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cccgagggagccggcgagggAcctggggagggaggagaact	21	9	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:11625035A>G	ENST00000270517.7	-	3	233	c.98T>C	c.(97-99)gTc>gCc	p.V33A	RN7SL833P_ENST00000498758.2_RNA|ECSIT_ENST00000417981.2_Intron|ECSIT_ENST00000252440.7_Splice_Site_p.V33A|ECSIT_ENST00000591352.1_5'Flank|ECSIT_ENST00000592312.1_5'UTR|ECSIT_ENST00000588998.1_Intron|ECSIT_ENST00000591104.1_Splice_Site_p.V33A	NM_016581.4	NP_057665.2	Q9BQ95	ECSIT_HUMAN	ECSIT signalling integrator	33					BMP signaling pathway (GO:0030509)|innate immune response (GO:0045087)|mesoderm formation (GO:0001707)|oxidation-reduction process (GO:0055114)|regulation of oxidoreductase activity (GO:0051341)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	oxidoreductase activity, acting on NAD(P)H (GO:0016651)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	11						CCGGCGAGGGACCTGGGGAGG	0.677																																					p.V33A		Atlas-SNP	.											.	ECSIT	32	.	0			c.T98C						.						10	13	12					19																	11625035		2123	4217	6340	SO:0001630	splice_region_variant	51295	exon3			CGAGGGACCTGGG	BC005119	CCDS12262.1, CCDS45979.1, CCDS45980.1, CCDS59353.1	19p13.2	2013-05-24	2013-05-24			ENSG00000130159		"Mitochondrial respiratory chain complex assembly factors"	29548	protein-coding gene	gene with protein product	"signaling intermediate in Toll pathway evolutionarily conserved ortholog (mouse)"	608388	"ECSIT homolog (Drosophila)"			10465784, 22982022	Standard	NM_001142464		Approved	SITPEC	uc002msb.3	Q9BQ95		ENST00000270517.7:c.97-1T>C	chr19.hg19:g.11625035A>G		82.0	0.0		65.0	4.0	NM_001142464	E9PAN9|K7EMM0|Q96HQ7|Q9NYI1	Missense_Mutation	SNP	ENST00000270517.7	hg19	CCDS12262.1	.	.	.	.	.	.	.	.	.	.	a	11.39	1.624248	0.28889	.	.	ENSG00000130159	ENST00000270517;ENST00000252440	T	0.34667	1.35	5.71	-2.04	0.07343	.	0.825234	0.10603	N	0.655468	T	0.16854	0.0405	N	0.19112	0.55	0.26408	N	0.976312	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.001	T	0.21827	-1.0234	10	0.26408	T	0.33	-12.2393	1.797	0.03063	0.4283:0.2381:0.226:0.1076	.	33;33	Q9BQ95-2;Q9BQ95	.;ECSIT_HUMAN	A	33	ENSP00000270517:V33A	ENSP00000252440:V33A	V	-	2	0	ECSIT	11486035	0.017000	0.18338	0.048000	0.18961	0.025000	0.11179	0.375000	0.20518	-0.161000	0.10983	0.444000	0.29173	GTC	.	.		0.677	ECSIT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442603.2	NM_016581	Missense_Mutation	G	11625035	A	G	11625035	5	3	254	1	0	0	0	0	0	0	1	0	4902	289	10	2	1221	2	ECSIT	19	11625035	Splice_Site	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	1703021	11625035	47503948	908	35200										
MAN2B1	4125	hgsc.bcm.edu	37	chr19	12775761	12775761	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtagtgggtggctgcctcatCgttcatcacccagccaccat	10	14	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:12775761C>T	ENST00000456935.2	-	4	515	c.475G>A	c.(475-477)Gat>Aat	p.D159N	CTD-2192J16.24_ENST00000597961.1_Missense_Mutation_p.D156N|WDR83_ENST00000418543.3_5'Flank|MAN2B1_ENST00000221363.4_Missense_Mutation_p.D159N	NM_000528.3|NM_001173498.1	NP_000519.2|NP_001166969.1	O00754	MA2B1_HUMAN	mannosidase, alpha, class 2B, member 1	159			D -> N (in MANSA; results in less than 20% of wild-type enzyme activity). {ECO:0000269|PubMed:22161967}.		cellular protein modification process (GO:0006464)|mannose metabolic process (GO:0006013)|protein deglycosylation (GO:0006517)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						GCTGCCTCATCGTTCATCACC	0.622																																					p.D159N		Atlas-SNP	.											MAN2B1,NS,carcinoma,0,1	MAN2B1	91	.	0			c.G475A						.						82	58	66					19																	12775761		2203	4300	6503	SO:0001583	missense	4125	exon4			CCTCATCGTTCAT		CCDS32919.1, CCDS54224.1	19p13.2	2013-09-20			ENSG00000104774	ENSG00000104774	3.2.1.24		6826	protein-coding gene	gene with protein product		609458		MANB			Standard	NM_000528		Approved	LAMAN	uc002mub.2	O00754	OTTHUMG00000156397	ENST00000456935.2:c.475G>A	chr19.hg19:g.12775761C>T	ENSP00000395473:p.Asp159Asn	53.0	0.0		29.0	2.0	NM_001173498	G5E928|O15330|Q16680|Q93094|Q9BW13	Missense_Mutation	SNP	ENST00000456935.2	hg19	CCDS32919.1	.	.	.	.	.	.	.	.	.	.	C	36	5.789382	0.96945	.	.	ENSG00000104774	ENST00000456935;ENST00000536796;ENST00000221363	D;D	0.85773	-2.03;-2.03	5.69	5.69	0.88448	Glycoside hydrolase/deacetylase, beta/alpha-barrel (1);Glycoside hydrolase, family 38, core (2);	0.000000	0.48767	D	0.000172	D	0.95582	0.8564	H	0.98005	4.125	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97005	0.9732	10	0.87932	D	0	-50.6729	17.3077	0.87199	0.0:1.0:0.0:0.0	.	159;159	G5E928;O00754	.;MA2B1_HUMAN	N	159;98;159	ENSP00000395473:D159N;ENSP00000221363:D159N	ENSP00000221363:D159N	D	-	1	0	MAN2B1	12636761	1.000000	0.71417	0.974000	0.42286	0.898000	0.52572	7.417000	0.80156	2.688000	0.91661	0.491000	0.48974	GAT	.	.		0.622	MAN2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344062.1			T	12775761	C	T	12775761	3	4	254	1	0	0	0	0	1	0	0	0	9225	884	31	1	2644	1	MAN2B1	19	12775761	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1150726	12775761	46353222	909	35201										
GIPC1	10755	hgsc.bcm.edu	37	chr19	14589371	14589371	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtcctttcccagctccaccaTggtggccgctattgggggag	13	13	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:14589371T>C	ENST00000393033.4	-	9	1128	c.859A>G	c.(859-861)Atg>Gtg	p.M287V	GIPC1_ENST00000393029.3_Missense_Mutation_p.M190V|GIPC1_ENST00000591349.1_Missense_Mutation_p.M190V|GIPC1_ENST00000586027.1_Missense_Mutation_p.M287V|GIPC1_ENST00000393028.1_Missense_Mutation_p.M190V|GIPC1_ENST00000345425.2_Missense_Mutation_p.M287V	NM_005716.3	NP_005707.1	O14908	GIPC1_HUMAN	GIPC PDZ domain containing family, member 1	287					endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|glutamate secretion (GO:0014047)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of cytokinesis (GO:0032467)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein targeting (GO:0006605)|regulation of protein stability (GO:0031647)|regulation of synaptic plasticity (GO:0048167)|synaptic transmission (GO:0007268)	brush border (GO:0005903)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|myosin binding (GO:0017022)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			endometrium(1)|lung(4)|upper_aerodigestive_tract(1)	6						AGCTCCACCATGGTGGCCGCT	0.617																																					p.M287V	Pancreas(33;78 923 2910 41023 52850)	Atlas-SNP	.											.	GIPC1	21	.	0			c.A859G						.						43	47	46					19																	14589371		2203	4300	6503	SO:0001583	missense	10755	exon8			CCACCATGGTGGC	AF089816	CCDS12310.1, CCDS12311.1	19p13.1	2009-09-22	2005-06-28	2005-06-28					1226	protein-coding gene	gene with protein product		605072	"chromosome 19 open reading frame 3", "regulator of G-protein signalling 19 interacting protein 1"	C19orf3, RGS19IP1		9770488, 9482110	Standard	NM_005716		Approved	TIP-2, Hs.6454, GIPC, SEMCAP, GLUT1CBP, SYNECTIN, NIP	uc002myx.4	O14908		ENST00000393033.4:c.859A>G	chr19.hg19:g.14589371T>C	ENSP00000376753:p.Met287Val	149.0	0.0		107.0	6.0	NM_202468	A8K4I3|A8MZG3|Q9BTC9	Missense_Mutation	SNP	ENST00000393033.4	hg19	CCDS12310.1	.	.	.	.	.	.	.	.	.	.	t	15.53	2.861072	0.51482	.	.	ENSG00000123159	ENST00000393033;ENST00000345425;ENST00000393029;ENST00000393028;ENST00000351277	T;T;D;D	0.84944	-1.41;-1.41;-1.92;-1.92	4.28	4.28	0.50868	.	0.089037	0.85682	D	0.000000	D	0.83303	0.5225	M	0.72576	2.205	0.53005	D	0.999964	B	0.09022	0.002	B	0.14578	0.011	T	0.81254	-0.1016	10	0.54805	T	0.06	-19.0869	11.3771	0.49735	0.0:0.0:0.0:1.0	.	287	O14908	GIPC1_HUMAN	V	287;287;190;190;287	ENSP00000376753:M287V;ENSP00000340698:M287V;ENSP00000376749:M190V;ENSP00000376748:M190V	ENSP00000340698:M287V	M	-	1	0	GIPC1	14450371	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.690000	0.68241	1.586000	0.49944	0.454000	0.30748	ATG	.	.		0.617	GIPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460239.2			C	14589371	T	C	14589371	3	2	254	1	0	0	0	0	1	0	0	0	6400	1464	51	2	146	2	GIPC1	19	14589371	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	1813610	14589371	44539612	910	35202										
NOTCH3	4854	hgsc.bcm.edu	37	chr19	15281634	15281634	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	caatctccagcattactaccGagctgcagggacagcaggga	11	12	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:15281634G>T	ENST00000263388.2	-	26	4814	c.4739C>A	c.(4738-4740)tCg>tAg	p.S1580*		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	1580					forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			CATTACTACCGAGCTGCAGGG	0.617																																					p.S1580X		Atlas-SNP	.											.	NOTCH3	340	.	0			c.C4739A						.						28	25	26					19																	15281634		2203	4299	6502	SO:0001587	stop_gained	4854	exon26			ACTACCGAGCTGC	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"Ankyrin repeat domain containing"	7883	protein-coding gene	gene with protein product		600276	"Notch (Drosophila) homolog 3", "Notch homolog 3 (Drosophila)"	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.4739C>A	chr19.hg19:g.15281634G>T	ENSP00000263388:p.Ser1580*	108.0	0.0		58.0	4.0	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Nonsense_Mutation	SNP	ENST00000263388.2	hg19	CCDS12326.1	.	.	.	.	.	.	.	.	.	.	G	43	10.050665	0.99325	.	.	ENSG00000074181	ENST00000263388	.	.	.	3.92	3.92	0.45320	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.8921	0.70617	0.0:0.0:1.0:0.0	.	.	.	.	X	1580	.	ENSP00000263388:S1580X	S	-	2	0	NOTCH3	15142634	1.000000	0.71417	0.996000	0.52242	0.197000	0.23852	8.926000	0.92839	2.053000	0.61076	0.485000	0.47835	TCG	.	.		0.617	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435		T	15281634	G	T	15281634	4	4	254	1	0	0	0	0	0	1	0	0	10559	1059	37	1	2258	1	NOTCH3	19	15281634	Nonsense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	692263	15281634	43847349	911	35203										
WIZ	58525	hgsc.bcm.edu	37	chr19	15533977	15533977	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gagaagttcatctccaggatGtgccgctgtaagtgccgcac	12	11	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:15533977G>A	ENST00000389282.4	-	10	5079	c.4866C>T	c.(4864-4866)caC>caT	p.H1622H	WIZ_ENST00000599910.2_Silent_p.H939H|WIZ_ENST00000599686.3_Silent_p.H806H|WIZ_ENST00000545156.1_Silent_p.H936H|WIZ_ENST00000263381.7_Silent_p.H765H			O95785	WIZ_HUMAN	widely interspaced zinc finger motifs	1622					positive regulation of nuclear cell cycle DNA replication (GO:0010571)|protein heterotrimerization (GO:0070208)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	24						TCTCCAGGATGTGCCGCTGTA	0.622																																					p.H765H		Atlas-SNP	.											.	WIZ	152	.	0			c.C2295T						.						40	45	43					19																	15533977		1946	4144	6090	SO:0001819	synonymous_variant	58525	exon8			CAGGATGTGCCGC	AK091183	CCDS42516.1	19p13.12	2012-10-05	2007-01-18		ENSG00000011451	ENSG00000011451		"Zinc fingers, C2H2-type"	30917	protein-coding gene	gene with protein product			"WIZ zinc finger"			9795207, 12226707	Standard	NM_021241		Approved	ZNF803	uc002nbb.4	O95785		ENST00000389282.4:c.4866C>T	chr19.hg19:g.15533977G>A		72.0	0.0		55.0	4.0	NM_021241	B3KVH1|B7ZM82|M0QY21|Q4G0E0|Q6P6B0|Q6ZN24|Q7LDY6|Q7LDZ1|Q96IG5|Q96SQ6|Q9BUR8|Q9NPT1	Silent	SNP	ENST00000389282.4	hg19																																																																																				.	.		0.622	WIZ-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_021241		A	15533977	G	A	15533977	2	1	254	1	0	0	0	0	0	0	0	1	17390	1368	48	3		3	WIZ	19	15533977	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	252343	15533977	43595006	912	35204										
EPS15L1	58513	hgsc.bcm.edu	37	chr19	16488025	16488025	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aggggtcatctgagaatcctGcccctcccaaggaggaggtg	14	11	2	1	rs369284918		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:16488025G>A	ENST00000248070.6	-	22	2427	c.2288C>T	c.(2287-2289)gCa>gTa	p.A763V	EPS15L1_ENST00000455140.2_Missense_Mutation_p.A763V|EPS15L1_ENST00000535753.2_Intron|EPS15L1_ENST00000594975.1_Intron	NM_021235.2	NP_067058.1	Q9UBC2	EP15R_HUMAN	epidermal growth factor receptor pathway substrate 15-like 1	763	15 X 3 AA repeats of D-P-F.|Pro-rich.				endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)	clathrin coat of coated pit (GO:0030132)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(4)|skin(2)	30						TGAGAATCCTGCCCCTCCCAA	0.517											OREG0025332	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A763V		Atlas-SNP	.											.	EPS15L1	81	.	0			c.C2288T						.						101	108	106					19																	16488025		2203	4300	6503	SO:0001583	missense	58513	exon22			AATCCTGCCCCTC	AF110265	CCDS32944.1, CCDS58653.1, CCDS58654.1, CCDS59363.1	19p13.12	2013-01-10				ENSG00000127527		"EF-hand domain containing"	24634	protein-coding gene	gene with protein product							Standard	NM_001258374		Approved	eps15R	uc002ndx.4	Q9UBC2		ENST00000248070.6:c.2288C>T	chr19.hg19:g.16488025G>A	ENSP00000248070:p.Ala763Val	97.0	0.0	710	89.0	4.0	NM_021235	A2RRF3|A5PL29|B4DKA3	Missense_Mutation	SNP	ENST00000248070.6	hg19	CCDS32944.1	.	.	.	.	.	.	.	.	.	.	G	12.64	1.998919	0.35226	.	.	ENSG00000127527	ENST00000455140;ENST00000248070	T;T	0.22945	1.93;1.94	4.58	3.29	0.37713	.	0.607232	0.17007	N	0.190673	T	0.12347	0.0300	N	0.08118	0	0.32606	N	0.525299	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.11717	-1.0576	10	0.17369	T	0.5	.	11.6044	0.51024	0.1572:0.0:0.8428:0.0	.	763;763	Q9UBC2;G3V0H2	EP15R_HUMAN;.	V	763	ENSP00000393313:A763V;ENSP00000248070:A763V	ENSP00000248070:A763V	A	-	2	0	EPS15L1	16349025	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	1.799000	0.38824	2.093000	0.63338	0.555000	0.69702	GCA	.	.		0.517	EPS15L1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461040.1	NM_021235		A	16488025	G	A	16488025	3	1	254	1	0	0	0	0	1	0	0	0	5195	1319	46	3	314	3	EPS15L1	19	16488025	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	954048	16488025	42640958	913	35205										
UNC13A	23025	hgsc.bcm.edu	37	chr19	17785490	17785490	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgaaatcctgctcccagctgGgctggctgccccgcaccgcg	12	17	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:17785490G>T	ENST00000519716.2	-	3	127	c.128C>A	c.(127-129)cCc>cAc	p.P43H	UNC13A_ENST00000252773.7_Missense_Mutation_p.P43H|UNC13A_ENST00000428389.2_Missense_Mutation_p.P131H|UNC13A_ENST00000551649.1_Missense_Mutation_p.P43H|UNC13A_ENST00000550896.1_Missense_Mutation_p.P43H|UNC13A_ENST00000552293.1_Missense_Mutation_p.P43H	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	43	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						CTCCCAGCTGGGCTGGCTGCC	0.597																																					p.P43H		Atlas-SNP	.											.	UNC13A	299	.	0			c.C128A						.						94	96	95					19																	17785490		2110	4241	6351	SO:0001583	missense	23025	exon3			CAGCTGGGCTGGC	AB028955	CCDS46013.1, CCDS46013.2	19p13.12	2008-02-05				ENSG00000130477			23150	protein-coding gene	gene with protein product		609894					Standard	NM_001080421		Approved	KIAA1032, Munc13-1	uc031rjv.1	Q9UPW8		ENST00000519716.2:c.128C>A	chr19.hg19:g.17785490G>T	ENSP00000429562:p.Pro43His	90.0	0.0		75.0	4.0	NM_001080421	E5RHY9	Missense_Mutation	SNP	ENST00000519716.2	hg19	CCDS46013.2	.	.	.	.	.	.	.	.	.	.	G	24.4	4.523432	0.85600	.	.	ENSG00000130477	ENST00000519716;ENST00000428389;ENST00000252773;ENST00000551649;ENST00000552293;ENST00000550896	D;D;D;D;D;D	0.93133	-3.17;-3.17;-3.17;-3.17;-3.17;-3.17	4.93	4.93	0.64822	C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	U	0.000000	D	0.96577	0.8883	M	0.80183	2.485	0.51012	D	0.999904	D	0.89917	1.0	D	0.97110	1.0	D	0.97190	0.9857	10	0.87932	D	0	-18.2853	15.6143	0.76753	0.0:0.0:1.0:0.0	.	43	Q9UPW8	UN13A_HUMAN	H	43;131;43;43;43;43	ENSP00000429562:P43H;ENSP00000400409:P131H;ENSP00000252773:P43H;ENSP00000447236:P43H;ENSP00000447572:P43H;ENSP00000446831:P43H	ENSP00000252773:P43H	P	-	2	0	UNC13A	17646490	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	9.674000	0.98633	2.288000	0.76882	0.313000	0.20887	CCC	.	.		0.597	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604		T	17785490	G	T	17785490	3	4	254	1	0	0	0	0	1	0	0	0	16999	1232	43	3	5143	3	UNC13A	19	17785490	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1297465	17785490	41343493	914	35206										
UNC13A	23025	hgsc.bcm.edu	37	chr19	17785532	17785532	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tggtcgtgctcttgacattcTgcactttcagggtcacgtac	10	11	4	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:17785532T>C	ENST00000519716.2	-	3	85	c.86A>G	c.(85-87)cAg>cGg	p.Q29R	UNC13A_ENST00000252773.7_Missense_Mutation_p.Q29R|UNC13A_ENST00000428389.2_Missense_Mutation_p.Q117R|UNC13A_ENST00000551649.1_Missense_Mutation_p.Q29R|UNC13A_ENST00000550896.1_Missense_Mutation_p.Q29R|UNC13A_ENST00000552293.1_Missense_Mutation_p.Q29R	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	29	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						CTTGACATTCTGCACTTTCAG	0.587																																					p.Q29R		Atlas-SNP	.											.	UNC13A	299	.	0			c.A86G						.						133	130	131					19																	17785532		2109	4251	6360	SO:0001583	missense	23025	exon3			ACATTCTGCACTT	AB028955	CCDS46013.1, CCDS46013.2	19p13.12	2008-02-05				ENSG00000130477			23150	protein-coding gene	gene with protein product		609894					Standard	NM_001080421		Approved	KIAA1032, Munc13-1	uc031rjv.1	Q9UPW8		ENST00000519716.2:c.86A>G	chr19.hg19:g.17785532T>C	ENSP00000429562:p.Gln29Arg	131.0	0.0		87.0	4.0	NM_001080421	E5RHY9	Missense_Mutation	SNP	ENST00000519716.2	hg19	CCDS46013.2	.	.	.	.	.	.	.	.	.	.	T	19.51	3.841232	0.71488	.	.	ENSG00000130477	ENST00000519716;ENST00000428389;ENST00000252773;ENST00000551649;ENST00000552293;ENST00000550896	T;T;T;T;T;T	0.70399	-0.48;-0.48;-0.48;-0.48;-0.48;-0.48	4.93	4.93	0.64822	C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.64402	U	0.000001	T	0.80894	0.4711	M	0.65975	2.015	0.42449	D	0.992748	D	0.57257	0.979	D	0.68192	0.956	T	0.81924	-0.0710	10	0.49607	T	0.09	-18.4567	12.5081	0.55991	0.0:0.0:0.0:1.0	.	29	Q9UPW8	UN13A_HUMAN	R	29;117;29;29;29;29	ENSP00000429562:Q29R;ENSP00000400409:Q117R;ENSP00000252773:Q29R;ENSP00000447236:Q29R;ENSP00000447572:Q29R;ENSP00000446831:Q29R	ENSP00000252773:Q29R	Q	-	2	0	UNC13A	17646532	1.000000	0.71417	1.000000	0.80357	0.442000	0.32017	7.888000	0.87302	1.854000	0.53819	0.260000	0.18958	CAG	.	.		0.587	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604		C	17785532	T	C	17785532	3	2	254	1	0	0	0	0	1	0	0	0	16999	1580	55	2	5185	2	UNC13A	19	17785532	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	42	17785532	41343451	915	35207										
IL12RB1	3594	hgsc.bcm.edu	37	chr19	18183013	18183013	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gccacgttgtaggcagcaccCgagagatagggcatcttccc	12	13	1	1	rs144647048		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:18183013C>A	ENST00000600835.2	-	10	1228	c.930G>T	c.(928-930)tcG>tcT	p.S310S	IL12RB1_ENST00000322153.7_Silent_p.S310S|IL12RB1_ENST00000593993.2_Silent_p.S310S			P42701	I12R1_HUMAN	interleukin 12 receptor, beta 1	310	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-23-mediated signaling pathway (GO:0038155)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|interleukin-12 receptor complex (GO:0042022)|interleukin-23 receptor complex (GO:0072536)	cytokine receptor activity (GO:0004896)			endometrium(1)|kidney(1)|lung(3)|pancreas(1)|skin(2)	8						AGGCAGCACCCGAGAGATAGG	0.602																																					p.S310S		Atlas-SNP	.											.	IL12RB1	92	.	0			c.G930T						.						106	76	86					19																	18183013		2203	4300	6503	SO:0001819	synonymous_variant	3594	exon9			AGCACCCGAGAGA	U03187	CCDS32957.1, CCDS54232.1	19p13.1	2014-09-17						"Interleukins and interleukin receptors", "CD molecules", "Fibronectin type III domain containing"	5971	protein-coding gene	gene with protein product		601604		IL12RB		9284929	Standard	XM_005259893		Approved	CD212	uc002nhw.1	P42701		ENST00000600835.2:c.930G>T	chr19.hg19:g.18183013C>A		118.0	0.0		95.0	4.0	NM_153701	A8K308|B2RPF1|B7ZKK3|Q8N6Q7	Silent	SNP	ENST00000600835.2	hg19	CCDS54232.1																																																																																			.	C|1.000;T|0.000		0.602	IL12RB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466525.3			A	18183013	C	A	18183013	2	1	254	1	0	0	0	0	0	0	0	1	7635	639	23	1		1	IL12RB1	19	18183013	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	397481	18183013	40945970	916	35208										
ZNF90	7643	hgsc.bcm.edu	37	chr19	20228952	20228952	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cacataagaaaattcatactGgagagataacctgcaaatgt	7	7	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:20228952G>T	ENST00000418063.2	+	4	701	c.589G>T	c.(589-591)Gga>Tga	p.G197*	ZNF90_ENST00000474284.1_Intron	NM_007138.1	NP_009069.1	Q03938	ZNF90_HUMAN	zinc finger protein 90	197					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|lung(2)|ovary(1)|skin(1)	5						AATTCATACTGGAGAGATAAC	0.383																																					p.G197X		Atlas-SNP	.											.	ZNF90	93	.	0			c.G589T						.						30	29	29					19																	20228952		692	1591	2283	SO:0001587	stop_gained	7643	exon4			CATACTGGAGAGA	M61870	CCDS46028.1	19p12	2013-01-08	2006-02-01		ENSG00000213988	ENSG00000213988		"Zinc fingers, C2H2-type", "-"	13165	protein-coding gene	gene with protein product		603973	"zinc finger protein 90 (HTF9)"			8467795	Standard	NM_007138		Approved	HTF9	uc002nor.2	Q03938	OTTHUMG00000158057	ENST00000418063.2:c.589G>T	chr19.hg19:g.20228952G>T	ENSP00000410466:p.Gly197*	86.0	0.0		58.0	4.0	NM_007138	B9EH87	Nonsense_Mutation	SNP	ENST00000418063.2	hg19	CCDS46028.1	.	.	.	.	.	.	.	.	.	.	G	11.17	1.559742	0.27827	.	.	ENSG00000213988	ENST00000418063	.	.	.	1.18	-2.35	0.06684	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.8526	0.13543	0.2058:0.2191:0.5751:0.0	.	.	.	.	X	197	.	.	G	+	1	0	ZNF90	20089952	0.994000	0.37717	0.003000	0.11579	0.003000	0.03518	2.780000	0.47742	-0.850000	0.04152	-0.856000	0.03024	GGA	.	.		0.383	ZNF90-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350101.1	NM_007138		T	20228952	G	T	20228952	4	4	254	1	0	0	0	0	0	1	0	0	18214	1349	47	3	603	3	ZNF90	19	20228952	Nonsense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	2045939	20228952	38900031	917	35209										
ZNF85	7639	hgsc.bcm.edu	37	chr19	21132473	21132473	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cctttaatcatttctcacacCttactacacataagataatt	1	11	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:21132473C>A	ENST00000328178.8	+	4	1266	c.1153C>A	c.(1153-1155)Ctt>Att	p.L385I	ZNF85_ENST00000345030.6_Missense_Mutation_p.L352I|ZNF85_ENST00000601023.1_Missense_Mutation_p.L326I	NM_001256173.1|NM_003429.4	NP_001243102.1|NP_003420.2	Q03923	ZNF85_HUMAN	zinc finger protein 85	385					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)	20						TTTCTCACACCTTACTACACA	0.348																																					p.L415I		Atlas-SNP	.											.	ZNF85	72	.	0			c.C1243A						.						35	38	37					19																	21132473		2195	4295	6490	SO:0001583	missense	7639	exon5			TCACACCTTACTA	U35376	CCDS32977.1, CCDS58657.1	19p12	2013-01-08	2006-05-12			ENSG00000105750		"Zinc fingers, C2H2-type", "-"	13160	protein-coding gene	gene with protein product		603899	"zinc finger protein 85 (HPF4, HTF1)"			2505992	Standard	NM_003429		Approved	HPF4, HTF1	uc031rjx.1	Q03923		ENST00000328178.8:c.1153C>A	chr19.hg19:g.21132473C>A	ENSP00000329793:p.Leu385Ile	82.0	0.0		72.0	4.0	NM_001256171	B9ZVP4|Q6NVI0	Missense_Mutation	SNP	ENST00000328178.8	hg19	CCDS32977.1	.	.	.	.	.	.	.	.	.	.	.	11.14	1.551047	0.27739	.	.	ENSG00000105750	ENST00000328178;ENST00000345030;ENST00000421385	T;T	0.53857	0.6;0.6	1.35	1.35	0.21983	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.69691	0.3139	M	0.85542	2.76	0.09310	N	0.999997	D;P;D	0.89917	0.957;0.95;1.0	D;D;D	0.91635	0.937;0.991;0.999	T	0.55029	-0.8204	9	0.72032	D	0.01	.	4.9635	0.14078	0.0:0.79:0.0:0.2099	.	352;326;385	Q03923-2;Q49A12;Q03923	.;.;ZNF85_HUMAN	I	385;352;260	ENSP00000329793:L385I;ENSP00000342340:L352I	ENSP00000329793:L385I	L	+	1	0	ZNF85	20924313	0.068000	0.21057	0.002000	0.10522	0.002000	0.02628	0.707000	0.25704	0.681000	0.31386	0.462000	0.41574	CTT	.	.		0.348	ZNF85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463430.1	NM_003429		A	21132473	C	A	21132473	3	1	254	1	0	0	0	0	1	0	0	0	18208	681	24	3	1167	3	ZNF85	19	21132473	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	903521	21132473	37996510	918	35210										
ZNF431	170959	hgsc.bcm.edu	37	chr19	21366793	21366793	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttaaacaaaataattcatacTggagagaaactctacaaatg	5	6	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:21366793T>C	ENST00000311048.7	+	5	1831	c.1687T>C	c.(1687-1689)Tgg>Cgg	p.W563R	ZNF431_ENST00000594425.1_Intron|ZNF431_ENST00000600692.1_3'UTR	NM_133473.2	NP_597730.2	Q8TF32	ZN431_HUMAN	zinc finger protein 431	563					cell differentiation (GO:0030154)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23						TAATTCATACTGGAGAGAAAC	0.373																																					p.W563R		Atlas-SNP	.											.	ZNF431	71	.	0			c.T1687C						.						37	43	41					19																	21366793		2201	4298	6499	SO:0001583	missense	170959	exon5			TCATACTGGAGAG	AB075849	CCDS32979.1	19p12	2013-01-08				ENSG00000196705		"Zinc fingers, C2H2-type", "-"	20809	protein-coding gene	gene with protein product						11853319	Standard	NM_133473		Approved	KIAA1969	uc002npp.2	Q8TF32		ENST00000311048.7:c.1687T>C	chr19.hg19:g.21366793T>C	ENSP00000308578:p.Trp563Arg	157.0	0.0		99.0	4.0	NM_133473	A8KAK7|Q8IWC4	Missense_Mutation	SNP	ENST00000311048.7	hg19	CCDS32979.1	.	.	.	.	.	.	.	.	.	.	.	0.008	-1.899406	0.00517	.	.	ENSG00000196705	ENST00000311048	T	0.05786	3.39	1.05	1.05	0.20165	.	.	.	.	.	T	0.01940	0.0061	N	0.01048	-1.04	0.25746	N	0.985104	B	0.02656	0.0	B	0.04013	0.001	T	0.42548	-0.9445	9	0.87932	D	0	.	2.0647	0.03600	0.2853:0.0:0.2868:0.4278	.	563	Q8TF32	ZN431_HUMAN	R	563	ENSP00000308578:W563R	ENSP00000308578:W563R	W	+	1	0	ZNF431	21158633	0.008000	0.16893	0.151000	0.22473	0.141000	0.21300	-0.941000	0.03925	0.389000	0.25086	0.379000	0.24179	TGG	.	.		0.373	ZNF431-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463943.1	XM_086098		C	21366793	T	C	21366793	3	2	254	1	0	0	0	0	1	0	0	0	17920	1580	55	2	1705	2	ZNF431	19	21366793	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	234320	21366793	37762190	919	35211										
ZNF708	7562	hgsc.bcm.edu	37	chr19	21476562	21476562	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	taagtaagagttgaggacttGgtaaaggctttaccacattc	10	6	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:21476562G>T	ENST00000356929.3	-	4	1403	c.1206C>A	c.(1204-1206)acC>acA	p.T402T		NM_021269.2	NP_067092.2	P17019	ZN708_HUMAN	zinc finger protein 708	338					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K403fs*10(1)		breast(1)|central_nervous_system(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|skin(2)|stomach(1)	32						TTGAGGACTTGGTAAAGGCTT	0.368																																					p.T402T		Atlas-SNP	.											.,1	ZNF708	66	.	1	Deletion - Frameshift(1)	ovary(1)	c.C1206A						.						61	66	64					19																	21476562		2201	4296	6497	SO:0001819	synonymous_variant	7562	exon4			GGACTTGGTAAAG	X52339	CCDS32980.1	19p12	2014-02-14	2006-08-22	2005-08-16	ENSG00000182141	ENSG00000182141		"Zinc fingers, C2H2-type", "-"	12945	protein-coding gene	gene with protein product			"zinc finger protein 15-like 1 (KOX 8)", "zinc finger protein 708", "zinc finger protein 708 (KOX8)"	ZNF15, ZNF15L1		2014798	Standard	NM_021269		Approved	KOX8	uc002npq.1	P17019	OTTHUMG00000182841	ENST00000356929.3:c.1206C>A	chr19.hg19:g.21476562G>T		77.0	0.0		59.0	3.0	NM_021269	Q6ZMR0	Silent	SNP	ENST00000356929.3	hg19	CCDS32980.1																																																																																			.	.		0.368	ZNF708-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463953.1	NM_021269		T	21476562	G	T	21476562	2	4	254	1	0	0	0	0	0	0	0	1	18127	1335	47	3		3	ZNF708	19	21476562	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	109769	21476562	37652421	920	35212										
ZNF429	353088	hgsc.bcm.edu	37	chr19	21712459	21712459	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gttggtgtgtgtgtgtttcaGggaccattgacatttacaga	13	5	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:21712459G>T	ENST00000358491.4	+	2	211		c.e2-1		ZNF429_ENST00000594022.1_Splice_Site|ZNF429_ENST00000597078.1_Splice_Site	NM_001001415.2	NP_001001415.2	Q86V71	ZN429_HUMAN	zinc finger protein 429						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(13)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	34						GTGTGTTTCAGGGACCATTGA	0.403																																					.		Atlas-SNP	.											.	ZNF429	338	.	0			c.4-1G>T						.						72	79	76					19																	21712459		2200	4299	6499	SO:0001630	splice_region_variant	353088	exon2			GTTTCAGGGACCA	AY269786	CCDS42537.1	19p12	2014-02-14			ENSG00000197013	ENSG00000197013		"Zinc fingers, C2H2-type", "-"	20817	protein-coding gene	gene with protein product							Standard	NM_001001415		Approved		uc002nqd.1	Q86V71	OTTHUMG00000182848	ENST00000358491.4:c.4-1G>T	chr19.hg19:g.21712459G>T		109.0	0.0		59.0	4.0	NM_001001415	A6NLV7|Q9BZE6	Splice_Site	SNP	ENST00000358491.4	hg19	CCDS42537.1	.	.	.	.	.	.	.	.	.	.	G	3.591	-0.083509	0.07141	.	.	ENSG00000197013	ENST00000358491	.	.	.	0.926	0.926	0.19430	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.6024	0.33754	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ZNF429	21504299	0.994000	0.37717	0.179000	0.23059	0.257000	0.26127	3.033000	0.49743	0.308000	0.22923	0.313000	0.20887	.	.	.		0.403	ZNF429-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463981.1	NM_001001415	Intron	T	21712459	G	T	21712459	5	4	254	1	0	0	0	0	0	0	1	0	17917	1014	35	3	9	3	ZNF429	19	21712459	Splice_Site	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	235897	21712459	37416524	921	35213										
ZNF429	353088	hgsc.bcm.edu	37	chr19	21720450	21720450	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcaacataagaaaattcataCtggagagaaaccttacaaat	5	7	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:21720450C>G	ENST00000358491.4	+	4	1803	c.1595C>G	c.(1594-1596)aCt>aGt	p.T532S	ZNF429_ENST00000597078.1_Intron	NM_001001415.2	NP_001001415.2	Q86V71	ZN429_HUMAN	zinc finger protein 429	532					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(13)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	34						AAAATTCATACTGGAGAGAAA	0.363																																					p.T532S		Atlas-SNP	.											ZNF429,colon,carcinoma,0,2	ZNF429	338	.	0			c.C1595G						.						39	43	42					19																	21720450		2113	4256	6369	SO:0001583	missense	353088	exon4			TTCATACTGGAGA	AY269786	CCDS42537.1	19p12	2014-02-14			ENSG00000197013	ENSG00000197013		"Zinc fingers, C2H2-type", "-"	20817	protein-coding gene	gene with protein product							Standard	NM_001001415		Approved		uc002nqd.1	Q86V71	OTTHUMG00000182848	ENST00000358491.4:c.1595C>G	chr19.hg19:g.21720450C>G	ENSP00000351280:p.Thr532Ser	49.0	2.0		29.0	2.0	NM_001001415	A6NLV7|Q9BZE6	Missense_Mutation	SNP	ENST00000358491.4	hg19	CCDS42537.1	.	.	.	.	.	.	.	.	.	.	.	12.73	2.026350	0.35701	.	.	ENSG00000197013	ENST00000358491	T	0.24151	1.87	0.81	0.81	0.18732	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.23289	0.0563	N	0.05280	-0.08	0.29292	N	0.869277	D	0.65815	0.995	D	0.63703	0.917	T	0.19192	-1.0313	9	0.46703	T	0.11	.	8.393	0.32540	0.0:1.0:0.0:0.0	.	532	Q86V71	ZN429_HUMAN	S	532	ENSP00000351280:T532S	ENSP00000351280:T532S	T	+	2	0	ZNF429	21512290	0.204000	0.23447	0.477000	0.27303	0.478000	0.33099	0.600000	0.24104	0.181000	0.19994	0.184000	0.17185	ACT	.	.		0.363	ZNF429-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463981.1	NM_001001415		G	21720450	C	G	21720450	3	3	254	1	0	0	0	0	1	0	0	0	17917	565	20	4	1609	4	ZNF429	19	21720450	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	7991	21720450	37408533	922	35214										
ZNF429	353088	hgsc.bcm.edu	37	chr19	21720666	21720666	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	atgtggcaaagcttttaatcGgtcctcaagacttactcaac	7	10	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:21720666G>T	ENST00000358491.4	+	4	2019	c.1811G>T	c.(1810-1812)cGg>cTg	p.R604L	ZNF429_ENST00000597078.1_Intron	NM_001001415.2	NP_001001415.2	Q86V71	ZN429_HUMAN	zinc finger protein 429	604					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R604Q(1)		endometrium(2)|kidney(2)|large_intestine(13)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	34						GCTTTTAATCGGTCCTCAAGA	0.373																																					p.R604L		Atlas-SNP	.											ZNF429,caecum,carcinoma,+1,1	ZNF429	338	.	1	Substitution - Missense(1)	soft_tissue(1)	c.G1811T						.						57	62	60					19																	21720666		2085	4256	6341	SO:0001583	missense	353088	exon4			TTAATCGGTCCTC	AY269786	CCDS42537.1	19p12	2014-02-14			ENSG00000197013	ENSG00000197013		"Zinc fingers, C2H2-type", "-"	20817	protein-coding gene	gene with protein product							Standard	NM_001001415		Approved		uc002nqd.1	Q86V71	OTTHUMG00000182848	ENST00000358491.4:c.1811G>T	chr19.hg19:g.21720666G>T	ENSP00000351280:p.Arg604Leu	82.0	0.0		74.0	3.0	NM_001001415	A6NLV7|Q9BZE6	Missense_Mutation	SNP	ENST00000358491.4	hg19	CCDS42537.1	.	.	.	.	.	.	.	.	.	.	.	1.503	-0.551530	0.03996	.	.	ENSG00000197013	ENST00000358491	T	0.06142	3.34	1.09	-1.05	0.10036	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03827	0.0108	L	0.49513	1.565	0.09310	N	1	P	0.40032	0.699	B	0.27715	0.082	T	0.42515	-0.9447	9	0.10377	T	0.69	.	4.965	0.14085	0.7681:0.0:0.2319:0.0	.	604	Q86V71	ZN429_HUMAN	L	604	ENSP00000351280:R604L	ENSP00000351280:R604L	R	+	2	0	ZNF429	21512506	0.001000	0.12720	0.001000	0.08648	0.054000	0.15201	0.519000	0.22862	-0.272000	0.09259	0.298000	0.19748	CGG	.	.		0.373	ZNF429-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463981.1	NM_001001415		T	21720666	G	T	21720666	3	4	254	1	0	0	0	0	1	0	0	0	17917	1116	39	1	1825	1	ZNF429	19	21720666	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	216	21720666	37408317	923	35215										
ZNF208	7757	hgsc.bcm.edu	37	chr19	22155050	22155050	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tatgtttactaaagactgacAaccagctgaaggctttgcca	8	9	0	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:22155050A>G	ENST00000397126.4	-	4	2934	c.2786T>C	c.(2785-2787)tTg>tCg	p.L929S	ZNF208_ENST00000601773.1_Intron|ZNF208_ENST00000599916.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	929					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				AAAGACTGACAACCAGCTGAA	0.378																																					p.L929S		Atlas-SNP	.											.	ZNF208	817	.	0			c.T2786C						.						51	54	53					19																	22155050		2057	4205	6262	SO:0001583	missense	7757	exon4			ACTGACAACCAGC	BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"Zinc fingers, C2H2-type", "-"	12999	protein-coding gene	gene with protein product	"zinc finger protein 95"	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.2786T>C	chr19.hg19:g.22155050A>G	ENSP00000380315:p.Leu929Ser	179.0	0.0		127.0	6.0	NM_007153		Missense_Mutation	SNP	ENST00000397126.4	hg19	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	A	0.011	-1.700444	0.00725	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.07216	3.21	3.07	-5.09	0.02920	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02047	0.0064	.	.	.	0.09310	N	1	B	0.12630	0.006	B	0.06405	0.002	T	0.41305	-0.9516	8	0.02654	T	1	.	1.7227	0.02915	0.1479:0.3719:0.2861:0.1941	.	829	O43345	ZN208_HUMAN	S	929;829	ENSP00000380315:L929S	ENSP00000380315:L929S	L	-	2	0	ZNF208	21946890	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.339000	0.01102	-1.085000	0.03088	-1.661000	0.00750	TTG	.	.		0.378	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		G	22155050	A	G	22155050	3	3	254	1	0	0	0	0	1	0	0	0	17781	131	5	2	1060	2	ZNF208	19	22155050	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	434384	22155050	36973933	924	35216										
ZNF91	7644	hgsc.bcm.edu	37	chr19	23544210	23544210	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aggattgtctaaaagctttgCcacattcttcaaatttgtag	7	7	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:23544210C>T	ENST00000300619.7	-	4	1776	c.1571G>A	c.(1570-1572)gGc>gAc	p.G524D	ZNF91_ENST00000397082.2_Missense_Mutation_p.G492D|ZNF91_ENST00000599743.1_Intron|ZNF91_ENST00000596528.1_5'Flank	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	524					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				AAAAGCTTTGCCACATTCTTC	0.333																																					p.G524D		Atlas-SNP	.											.	ZNF91	349	.	0			c.G1571A						.						40	43	42					19																	23544210		2064	4235	6299	SO:0001583	missense	7644	exon4			GCTTTGCCACATT	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"Zinc fingers, C2H2-type", "-"	13166	protein-coding gene	gene with protein product		603971	"zinc finger protein 91 (HPF7, HTF10)"			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.1571G>A	chr19.hg19:g.23544210C>T	ENSP00000300619:p.Gly524Asp	77.0	0.0		89.0	4.0	NM_003430	A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	hg19	CCDS42541.1	.	.	.	.	.	.	.	.	.	.	C	12.97	2.098493	0.37048	.	.	ENSG00000167232	ENST00000300619;ENST00000397082	T;T	0.20881	2.04;2.1	1.71	0.452	0.16634	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.36853	0.0982	M	0.63169	1.94	0.26875	N	0.967662	P;D	0.89917	0.861;1.0	P;D	0.67900	0.498;0.954	T	0.14643	-1.0465	9	0.49607	T	0.09	.	8.4203	0.32696	0.0:0.7544:0.2455:0.0	.	492;524	Q05481-2;Q05481	.;ZNF91_HUMAN	D	524;492	ENSP00000300619:G524D;ENSP00000380272:G492D	ENSP00000300619:G524D	G	-	2	0	ZNF91	23336050	0.510000	0.26171	0.031000	0.17742	0.024000	0.10985	1.300000	0.33436	0.003000	0.14656	0.205000	0.17691	GGC	.	.		0.333	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430		T	23544210	C	T	23544210	3	4	254	1	0	0	0	0	1	0	0	0	18215	739	26	3	2008	3	ZNF91	19	23544210	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1389160	23544210	35584773	925	35217										
ZNF675	171392	hgsc.bcm.edu	37	chr19	23836432	23836432	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttcagtaagttttgaggatcGgttaaaagctttgccacatt	9	6	1	1	rs199957959		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:23836432G>T	ENST00000359788.4	-	4	1471	c.1303C>A	c.(1303-1305)Cga>Aga	p.R435R	ZNF675_ENST00000601935.1_Intron|ZNF675_ENST00000596211.1_Intron|ZNF675_ENST00000600313.1_Intron	NM_138330.2	NP_612203.2	Q8TD23	ZN675_HUMAN	zinc finger protein 675	435					bone resorption (GO:0045453)|cytokine-mediated signaling pathway (GO:0019221)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of interleukin-1-mediated signaling pathway (GO:2000660)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	DNA binding (GO:0003677)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				TTTGAGGATCGGTTAAAAGCT	0.378																																					p.R435R		Atlas-SNP	.											.	ZNF675	88	.	0			c.C1303A						.						52	55	54					19																	23836432		2202	4300	6502	SO:0001819	synonymous_variant	171392	exon4			AGGATCGGTTAAA		CCDS32981.1	19p12	2013-01-08						"Zinc fingers, C2H2-type", "-"	30768	protein-coding gene	gene with protein product	"TRAF6 inhibitory zinc finger"					11751921	Standard	NM_138330		Approved	TIZ, TBZF	uc002nri.3	Q8TD23		ENST00000359788.4:c.1303C>A	chr19.hg19:g.23836432G>T		54.0	0.0		33.0	4.0	NM_138330	Q8N211	Silent	SNP	ENST00000359788.4	hg19	CCDS32981.1																																																																																			.	G|0.999;A|0.001		0.378	ZNF675-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466433.1	NM_138330		T	23836432	G	T	23836432	2	4	254	1	0	0	0	0	0	0	0	1	18097	1124	39	1		1	ZNF675	19	23836432	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	292222	23836432	35292551	926	35218										
DPY19L3	147991	hgsc.bcm.edu	37	chr19	32968497	32968497	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gccggagtcaagctgtgcacGggaaggaccctaaccaacca	12	13	1	0	rs571491381		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:32968497G>T	ENST00000342179.5	+	17	1982	c.1767G>T	c.(1765-1767)acG>acT	p.T589T	DPY19L3_ENST00000586987.1_Silent_p.T589T|DPY19L3_ENST00000392250.2_Silent_p.T589T	NM_207325.2	NP_997208.2	Q6ZPD9	D19L3_HUMAN	dpy-19-like 3 (C. elegans)	589						integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(17)|ovary(4)|pancreas(1)	32	Esophageal squamous(110;0.162)					AGCTGTGCACGGGAAGGACCC	0.562																																					p.T589T		Atlas-SNP	.											.	DPY19L3	70	.	0			c.G1767T						.						131	112	119					19																	32968497		2203	4300	6503	SO:0001819	synonymous_variant	147991	exon17			GTGCACGGGAAGG		CCDS12422.1	19q13.11	2008-02-05				ENSG00000178904			27120	protein-coding gene	gene with protein product		613894					Standard	NM_207325		Approved		uc002ntg.3	Q6ZPD9		ENST00000342179.5:c.1767G>T	chr19.hg19:g.32968497G>T		120.0	0.0		80.0	5.0	NM_001172774	Q68DC7|Q6ZTB7|Q6ZTS2	Silent	SNP	ENST00000342179.5	hg19	CCDS12422.1																																																																																			.	.		0.562	DPY19L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450311.1	NM_207325		T	32968497	G	T	32968497	2	4	254	1	0	0	0	0	0	0	0	1	4744	1103	39	1		1	DPY19L3	19	32968497	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	9132065	32968497	26160486	927	35219										
WDR88	126248	hgsc.bcm.edu	37	chr19	33647426	33647426	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggccatgaaggttctgtcagTtcctgtcactttgccagaga	11	10	3	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:33647426T>C	ENST00000355868.3	+	7	1051	c.975T>C	c.(973-975)agT>agC	p.S325S	WDR88_ENST00000361680.2_Silent_p.S325S	NM_173479.3	NP_775750.3	Q6ZMY6	WDR88_HUMAN	WD repeat domain 88	325										breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	25	Esophageal squamous(110;0.137)					GTTCTGTCAGTTCCTGTCACT	0.488																																					p.S325S		Atlas-SNP	.											.	WDR88	50	.	0			c.T975C						.						88	84	85					19																	33647426		2203	4300	6503	SO:0001819	synonymous_variant	126248	exon7			TGTCAGTTCCTGT	BC031227	CCDS12429.1	19q13.11	2013-01-09	2007-04-04	2007-04-04		ENSG00000166359		"WD repeat domain containing"	26999	protein-coding gene	gene with protein product			"PQQ repeat and WD repeat domain containing"	PQWD		12477932	Standard	NM_173479		Approved		uc002nui.3	Q6ZMY6		ENST00000355868.3:c.975T>C	chr19.hg19:g.33647426T>C		93.0	0.0		100.0	4.0	NM_173479	Q8NEF8	Silent	SNP	ENST00000355868.3	hg19	CCDS12429.1																																																																																			.	.		0.488	WDR88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450840.1	NM_173479		C	33647426	T	C	33647426	2	2	254	1	0	0	0	0	0	0	0	1	17350	1722	60	2		2	WDR88	19	33647426	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	678929	33647426	25481557	928	35220										
CD22	933	hgsc.bcm.edu	37	chr19	35832318	35832318	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctctggaaactcggtcagccTccaatgtgacttctcaagca	8	13	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:35832318T>C	ENST00000085219.5	+	8	1646	c.1580T>C	c.(1579-1581)cTc>cCc	p.L527P	CD22_ENST00000594250.1_Missense_Mutation_p.L350P|CD22_ENST00000341773.6_Missense_Mutation_p.L350P|CD22_ENST00000270311.6_Missense_Mutation_p.L407P|CD22_ENST00000544992.2_Missense_Mutation_p.L527P|CD22_ENST00000536635.2_Missense_Mutation_p.L439P|CD22_ENST00000419549.2_Missense_Mutation_p.L355P	NM_001771.3	NP_001762.2	P20273	CD22_HUMAN	CD22 molecule	527	Ig-like C2-type 5.				cell adhesion (GO:0007155)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			breast(2)|endometrium(2)|kidney(3)|large_intestine(14)|lung(21)|ovary(5)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	54	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.83e-19)|OV - Ovarian serous cystadenocarcinoma(14;3.19e-18)|all cancers(14;3.41e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			TCGGTCAGCCTCCAATGTGAC	0.542																																					p.L527P	Ovarian(42;1009 1133 23674 26041)	Atlas-SNP	.											.	CD22	129	.	0			c.T1580C						.						48	48	48					19																	35832318		2203	4300	6503	SO:0001583	missense	933	exon8			TCAGCCTCCAATG	X52785	CCDS12457.1, CCDS54247.1, CCDS54248.1, CCDS54249.1, CCDS62634.1	19q13.1	2013-01-29	2006-03-28		ENSG00000012124	ENSG00000012124		"CD molecules", "Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1643	protein-coding gene	gene with protein product	"sialic acid binding Ig-like lectin 2"	107266	"CD22 antigen"			8496602, 1691828	Standard	NM_001185099		Approved	SIGLEC-2, SIGLEC2	uc010edt.3	P20273		ENST00000085219.5:c.1580T>C	chr19.hg19:g.35832318T>C	ENSP00000085219:p.Leu527Pro	33.0	0.0		64.0	4.0	NM_001185100	F5GYU4|F5H7U3|O95699|O95701|O95702|O95703|Q01665|Q32M46|Q92872|Q92873|Q9UQA6|Q9UQA7|Q9UQA8|Q9UQA9|Q9UQB0|Q9Y2A6	Missense_Mutation	SNP	ENST00000085219.5	hg19	CCDS12457.1	.	.	.	.	.	.	.	.	.	.	T	16.52	3.146397	0.57044	.	.	ENSG00000012124	ENST00000085219;ENST00000536635;ENST00000341773;ENST00000544992;ENST00000270311;ENST00000419549	D;D;D;D;D;D	0.93076	-3.16;-3.16;-3.16;-3.16;-3.16;-3.16	4.84	4.84	0.62591	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.000000	0.48767	D	0.000167	D	0.97676	0.9238	H	0.97340	3.985	0.51482	D	0.999927	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;0.999	D	0.98150	1.0441	10	0.87932	D	0	.	10.7356	0.46122	0.0:0.0:0.0:1.0	.	355;527;439;527;350	Q32M46;F5GYU4;F5H7U3;P20273;P20273-2	.;.;.;CD22_HUMAN;.	P	527;439;350;527;407;355	ENSP00000085219:L527P;ENSP00000442279:L439P;ENSP00000339349:L350P;ENSP00000441237:L527P;ENSP00000270311:L407P;ENSP00000403822:L355P	ENSP00000085219:L527P	L	+	2	0	CD22	40524158	0.818000	0.29161	0.160000	0.22671	0.040000	0.13550	3.703000	0.54808	2.031000	0.59945	0.459000	0.35465	CTC	.	.		0.542	CD22-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466099.1	NM_001771		C	35832318	T	C	35832318	3	2	254	1	0	0	0	0	1	0	0	0	2987	1551	54	2	1606	2	CD22	19	35832318	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	2184892	35832318	23296665	929	35221										
ATP4A	495	hgsc.bcm.edu	37	chr19	36051450	36051450	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccccacctttcatctccaccAggtcgcccaccaccagttgg	6	20	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:36051450A>G	ENST00000262623.3	-	6	630	c.602T>C	c.(601-603)cTg>cCg	p.L201P		NM_000704.2	NP_000695.2	P20648	ATP4A_HUMAN	ATPase, H+/K+ exchanging, alpha polypeptide	201					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|ion transmembrane transport (GO:0034220)|pH reduction (GO:0045851)|regulation of proton transport (GO:0010155)|response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|magnesium ion binding (GO:0000287)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(26)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	53	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)	CATCTCCACCAGGTCGCCCAC	0.622																																					p.L201P		Atlas-SNP	.											.	ATP4A	123	.	0			c.T602C						.						52	49	50					19																	36051450		2203	4300	6503	SO:0001583	missense	495	exon6			TCCACCAGGTCGC		CCDS12467.1	19q13.1	2010-04-20			ENSG00000105675	ENSG00000105675	3.6.3.10	"ATPases / P-type"	819	protein-coding gene	gene with protein product	"gastric H,K-ATPase alpha subunit", "H(+)-K(+)-ATPase alpha subunit", "proton pump"	137216				1330887	Standard	NM_000704		Approved	ATP6A	uc002oal.1	P20648	OTTHUMG00000048106	ENST00000262623.3:c.602T>C	chr19.hg19:g.36051450A>G	ENSP00000262623:p.Leu201Pro	65.0	0.0		48.0	4.0	NM_000704	O00738	Missense_Mutation	SNP	ENST00000262623.3	hg19	CCDS12467.1	.	.	.	.	.	.	.	.	.	.	a	19.64	3.865896	0.71949	.	.	ENSG00000105675	ENST00000262623	D	0.92397	-3.03	4.16	4.16	0.48862	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.122063	0.34802	N	0.003670	D	0.96300	0.8793	M	0.92649	3.33	0.80722	D	1	D	0.57571	0.98	D	0.65443	0.935	D	0.96764	0.9563	10	0.87932	D	0	.	11.454	0.50169	1.0:0.0:0.0:0.0	.	201	P20648	ATP4A_HUMAN	P	201	ENSP00000262623:L201P	ENSP00000262623:L201P	L	-	2	0	ATP4A	40743290	1.000000	0.71417	1.000000	0.80357	0.847000	0.48162	7.279000	0.78599	1.875000	0.54330	0.398000	0.26397	CTG	.	.		0.622	ATP4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109470.2	NM_000704		G	36051450	A	G	36051450	3	3	254	1	0	0	0	0	1	0	0	0	1145	188	7	2	2573	2	ATP4A	19	36051450	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	219132	36051450	23077533	930	35222										
MLL4	9757	hgsc.bcm.edu	37	chr19	36229093	36229093	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agaagttctacgatgggaagGtgggctcccagtggctgtgg	17	7	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:36229093G>T	ENST00000222270.7	+	36	7872		c.e36+1		KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000420124.1_Splice_Site|IGFLR1_ENST00000587101.1_5'Flank	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B						chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										CGATGGGAAGGTGGGCTCCCA	0.607																																					.		Atlas-SNP	.											.	MLL4	229	.	0			c.7872+1G>T						.						55	61	59					19																	36229093		2090	4240	6330	SO:0001630	splice_region_variant	8085	exon36			GGGAAGGTGGGCT	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"Chromatin-modifying enzymes / K-methyltransferases"	15840	protein-coding gene	gene with protein product	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.7872+1G>T	chr19.hg19:g.36229093G>T		123.0	0.0		46.0	16.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Splice_Site	SNP	ENST00000222270.7	hg19	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	G	19.36	3.812288	0.70912	.	.	ENSG00000105663	ENST00000222270;ENST00000420124	.	.	.	4.73	4.73	0.59995	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.6212	0.84931	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	AD000671.1	40920933	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	5.210000	0.65214	2.467000	0.83353	0.462000	0.41574	.	.	.		0.607	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727	Intron	T	36229093	G	T	36229093	5	4	254	1	0	0	0	0	0	0	1	0	9632	1275	44	3	8015	3	MLL4	19	36229093	Splice_Site	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	177643	36229093	22899890	931	35223										
POLR2I	5438	hgsc.bcm.edu	37	chr19	36605106	36605106	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	acgggtggtcctcggtccgcGgcaacgtggggtcctgggac	18	12	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:36605106G>T	ENST00000221859.4	-	4	725	c.236C>A	c.(235-237)cCg>cAg	p.P79Q	TBCB_ENST00000586868.1_5'Flank|TBCB_ENST00000589996.1_5'Flank|TBCB_ENST00000585746.1_5'Flank|TBCB_ENST00000221855.3_5'Flank	NM_006233.4	NP_006224.1	P36954	RPB9_HUMAN	polymerase (RNA) II (DNA directed) polypeptide I, 14.5kDa	79					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter (GO:0001193)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(1)|ovary(1)	3	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			CTCGGTCCGCGGCAACGTGGG	0.627											OREG0025437	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P79Q		Atlas-SNP	.											.	POLR2I	10	.	0			c.C236A						.						58	57	57					19																	36605106		2203	4300	6503	SO:0001583	missense	5438	exon4			GTCCGCGGCAACG		CCDS12487.1	19q13.12	2013-10-17	2002-08-29		ENSG00000105258	ENSG00000105258	2.7.7.6	"RNA polymerase subunits"	9196	protein-coding gene	gene with protein product		180662	"polymerase (RNA) II (DNA directed) polypeptide I (14.5kD)"			8034326	Standard	NM_006233		Approved	RPB9, hRPB14.5	uc002ode.3	P36954	OTTHUMG00000181749	ENST00000221859.4:c.236C>A	chr19.hg19:g.36605106G>T	ENSP00000221859:p.Pro79Gln	129.0	0.0	864	123.0	7.0	NM_006233	B2R5J2|Q6NW05	Missense_Mutation	SNP	ENST00000221859.4	hg19	CCDS12487.1	.	.	.	.	.	.	.	.	.	.	G	31	5.066869	0.93898	.	.	ENSG00000105258	ENST00000221859	T	0.46063	0.88	5.55	4.49	0.54785	.	0.000000	0.85682	D	0.000000	T	0.60971	0.2310	M	0.80847	2.515	0.80722	D	1	D	0.67145	0.996	P	0.61132	0.884	T	0.63928	-0.6526	10	0.59425	D	0.04	-33.6734	12.6656	0.56840	0.0816:0.0:0.9184:0.0	.	79	P36954	RPB9_HUMAN	Q	79	ENSP00000221859:P79Q	ENSP00000221859:P79Q	P	-	2	0	POLR2I	41296946	1.000000	0.71417	1.000000	0.80357	0.792000	0.44763	8.708000	0.91372	2.894000	0.99253	0.655000	0.94253	CCG	.	.		0.627	POLR2I-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457442.1	NM_006233		T	36605106	G	T	36605106	3	4	254	1	0	0	0	0	1	0	0	0	12231	1116	39	1	153	1	POLR2I	19	36605106	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	376013	36605106	22523877	932	35224										
ZNF565	147929	hgsc.bcm.edu	37	chr19	36685225	36685225	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gacatcaggcttagaaatggAgagtcctgtttacaggaaaa	11	6	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:36685225A>G	ENST00000355114.5	-	4	988	c.262T>C	c.(262-264)Tcc>Ccc	p.S88P	ZNF565_ENST00000304116.5_Missense_Mutation_p.S48P|ZNF565_ENST00000392173.2_Missense_Mutation_p.S48P			Q8N9K5	ZN565_HUMAN	zinc finger protein 565	88	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(4)|lung(4)|ovary(1)|skin(2)	11	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.206)			TTAGAAATGGAGAGTCCTGTT	0.488																																					p.S48P		Atlas-SNP	.											.	ZNF565	46	.	0			c.T142C						.						63	53	56					19																	36685225		2203	4300	6503	SO:0001583	missense	147929	exon4			AAATGGAGAGTCC	AK094310	CCDS12491.1	19q13.12	2013-09-20			ENSG00000196357	ENSG00000196357		"Zinc fingers, C2H2-type", "-"	26726	protein-coding gene	gene with protein product		614275					Standard	NM_001042474		Approved	FLJ36991	uc002odn.3	Q8N9K5	OTTHUMG00000180508	ENST00000355114.5:c.262T>C	chr19.hg19:g.36685225A>G	ENSP00000347234:p.Ser88Pro	104.0	0.0		73.0	4.0	NM_001042474	B3KQ35|Q6NUS2	Missense_Mutation	SNP	ENST00000355114.5	hg19		.	.	.	.	.	.	.	.	.	.	a	7.724	0.697802	0.15106	.	.	ENSG00000196357	ENST00000392173;ENST00000304116;ENST00000355114	T;T;T	0.00776	5.71;5.71;5.71	5.08	-0.579	0.11720	Krueppel-associated box (3);	0.208186	0.24386	N	0.038968	T	0.00468	0.0015	N	0.24115	0.695	0.09310	N	1	P	0.37864	0.61	B	0.29524	0.103	T	0.52961	-0.8505	10	0.17369	T	0.5	.	5.7466	0.18124	0.3113:0.5581:0.1306:0.0	.	48	Q8N9K5	ZN565_HUMAN	P	48;48;88	ENSP00000376013:S48P;ENSP00000306869:S48P;ENSP00000347234:S88P	ENSP00000306869:S48P	S	-	1	0	ZNF565	41377065	0.989000	0.36119	0.992000	0.48379	0.912000	0.54170	0.291000	0.18994	0.222000	0.20900	0.459000	0.35465	TCC	.	.		0.488	ZNF565-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000451697.1	NM_152477		G	36685225	A	G	36685225	3	3	254	1	0	0	0	0	1	0	0	0	18011	304	11	2	1365	2	ZNF565	19	36685225	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	80119	36685225	22443758	933	35225										
ZNF345	25850	hgsc.bcm.edu	37	chr19	37368101	37368101	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccttttgaatgtaaagaatgTgggaaggcctttggtagtgg	14	4	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:37368101T>C	ENST00000529555.1	+	2	1157	c.369T>C	c.(367-369)tgT>tgC	p.C123C	ZNF345_ENST00000432005.2_Intron|ZNF345_ENST00000526123.1_Intron|ZNF345_ENST00000589046.1_Silent_p.C123C|ZNF345_ENST00000420450.1_Silent_p.C123C			Q14585	ZN345_HUMAN	zinc finger protein 345	123					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(5)|ovary(2)|prostate(1)	24	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GTAAAGAATGTGGGAAGGCCT	0.423																																					p.C123C		Atlas-SNP	.											.	ZNF345	68	.	0			c.T369C						.						64	65	65					19																	37368101		2203	4300	6503	SO:0001819	synonymous_variant	25850	exon4			AGAATGTGGGAAG	X78933	CCDS12497.1	19q13.12	2013-01-08			ENSG00000251247	ENSG00000251247		"Zinc fingers, C2H2-type"	16367	protein-coding gene	gene with protein product						7865130	Standard	NM_003419		Approved	HZF10	uc002oey.4	Q14585	OTTHUMG00000048162	ENST00000529555.1:c.369T>C	chr19.hg19:g.37368101T>C		98.0	0.0		99.0	4.0	NM_001242476		Silent	SNP	ENST00000529555.1	hg19	CCDS12497.1																																																																																			.	.		0.423	ZNF345-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388258.1			C	37368101	T	C	37368101	2	2	254	1	0	0	0	0	0	0	0	1	17874	1702	59	2		2	ZNF345	19	37368101	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	682876	37368101	21760882	934	35226										
ZNF585B	92285	hgsc.bcm.edu	37	chr19	37677107	37677107	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gacttggaagtaaacaatttCccacagtgaccacatttata	6	9	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:37677107C>T	ENST00000532828.2	-	5	1583	c.1332G>A	c.(1330-1332)ggG>ggA	p.G444G	CTC-454I21.3_ENST00000585860.2_Intron|ZNF585B_ENST00000527838.1_3'UTR|ZNF585B_ENST00000312908.5_Silent_p.G32G|ZNF585B_ENST00000531805.1_Silent_p.G389G	NM_152279.3	NP_689492.3	Q52M93	Z585B_HUMAN	zinc finger protein 585B	444					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|endometrium(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TAAACAATTTCCCACAGTGAC	0.403																																					p.G444G	Melanoma(93;882 1454 18863 28917 48427)	Atlas-SNP	.											.	ZNF585B	91	.	0			c.G1332A						.						111	111	111					19																	37677107		2203	4300	6503	SO:0001819	synonymous_variant	92285	exon5			CAATTTCCCACAG	AK027834	CCDS12500.1	19q13.13	2013-01-08				ENSG00000245680		"Zinc fingers, C2H2-type", "-"	30948	protein-coding gene	gene with protein product						12477932	Standard	NM_152279		Approved	FLJ14928, SZFP41	uc002ofq.3	Q52M93		ENST00000532828.2:c.1332G>A	chr19.hg19:g.37677107C>T		243.0	0.0		198.0	61.0	NM_152279	Q8IZD3|Q96JW6	Silent	SNP	ENST00000532828.2	hg19	CCDS12500.1																																																																																			.	.		0.403	ZNF585B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388272.2	NM_152279		T	37677107	C	T	37677107	2	4	254	1	0	0	0	0	0	0	0	1	18033	842	30	3		3	ZNF585B	19	37677107	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	309006	37677107	21451876	935	35227										
RASGRP4	115727	hgsc.bcm.edu	37	chr19	38903605	38903605	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgggtgaagcccatggcaggCgaagggaaaattgcccgaga	16	8	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:38903605C>T	ENST00000587738.1	-	12	1571	c.1501G>A	c.(1501-1503)Gcc>Acc	p.A501T	RASGRP4_ENST00000293062.9_Missense_Mutation_p.A404T|RASGRP4_ENST00000587753.1_Missense_Mutation_p.A432T|RASGRP4_ENST00000426920.2_Missense_Mutation_p.A312T|RASGRP4_ENST00000433821.2_Missense_Mutation_p.A409T|RASGRP4_ENST00000586305.1_Missense_Mutation_p.A487T|RASGRP4_ENST00000454404.2_Missense_Mutation_p.A467T			Q8TDF6	GRP4_HUMAN	RAS guanyl releasing protein 4	501	EF-hand. {ECO:0000255|PROSITE- ProRule:PRU00448}.				activation of phospholipase C activity (GO:0007202)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|myeloid cell differentiation (GO:0030099)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|response to extracellular stimulus (GO:0009991)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|GTP-dependent protein binding (GO:0030742)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			cervix(1)|kidney(1)|large_intestine(4)|lung(12)|pancreas(1)|prostate(3)|skin(1)	23	all_cancers(60;4.21e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			CCATGGCAGGCGAAGGGAAAA	0.567																																					p.A501T		Atlas-SNP	.											.	RASGRP4	54	.	0			c.G1501A						.						54	59	58					19																	38903605		1928	4138	6066	SO:0001583	missense	115727	exon12			GGCAGGCGAAGGG	AY048119	CCDS46068.1, CCDS54262.1, CCDS54263.1, CCDS54264.1	19q13.1	2013-01-10						"EF-hand domain containing"	18958	protein-coding gene	gene with protein product		607320				11956218	Standard	NM_170604		Approved		uc021uub.1	Q8TDF6		ENST00000587738.1:c.1501G>A	chr19.hg19:g.38903605C>T	ENSP00000465772:p.Ala501Thr	81.0	0.0		42.0	4.0	NM_170604	A6H8M4|C0LTP2|C0LTP3|C0LTP4|C0LTP5|C0LTP7|C9J416|C9JHZ1|Q8N858|Q96QN5|Q96QN6|Q96QN7	Missense_Mutation	SNP	ENST00000587738.1	hg19	CCDS46068.1	.	.	.	.	.	.	.	.	.	.	C	19.75	3.885836	0.72410	.	.	ENSG00000171777	ENST00000433821;ENST00000293062;ENST00000426920;ENST00000405332;ENST00000454404	T;T;T	0.76709	-1.04;-0.79;-0.9	5.42	5.42	0.78866	.	0.049276	0.85682	D	0.000000	T	0.80265	0.4591	L	0.34521	1.04	0.37264	D	0.90709	D;D;D;D;D;D;D	0.89917	1.0;1.0;0.996;0.998;0.996;0.971;0.998	D;D;P;P;P;P;P	0.77557	0.943;0.99;0.557;0.67;0.557;0.742;0.67	T	0.79227	-0.1890	10	0.27082	T	0.32	-23.7961	11.764	0.51920	0.1758:0.8242:0.0:0.0	.	312;404;409;467;432;487;501	C0LTP5;C0LTP7;C0LTP2;C0LTP4;C0LTP3;Q8TDF6-2;Q8TDF6	.;.;.;.;.;.;GRP4_HUMAN	T	409;404;312;501;501	ENSP00000411878:A409T;ENSP00000293062:A404T;ENSP00000445966:A312T	ENSP00000293062:A404T	A	-	1	0	RASGRP4	43595445	0.994000	0.37717	0.273000	0.24645	0.580000	0.36256	3.070000	0.50033	2.560000	0.86352	0.650000	0.86243	GCC	.	.		0.567	RASGRP4-013	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460540.1	NM_170604		T	38903605	C	T	38903605	3	4	254	1	0	0	0	0	1	0	0	0	13092	768	27	1	544	1	RASGRP4	19	38903605	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1226498	38903605	20225378	936	35228										
RYR1	6261	hgsc.bcm.edu	37	chr19	38959769	38959769	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aacagccttccgggagattgAgattggggacggtgagggct	17	7	0	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:38959769A>G	ENST00000359596.3	+	26	3545	c.3545A>G	c.(3544-3546)gAg>gGg	p.E1182G	RYR1_ENST00000360985.3_Missense_Mutation_p.E1182G|RYR1_ENST00000355481.4_Missense_Mutation_p.E1182G			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1182	6 X approximate repeats.|B30.2/SPRY 2. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CGGGAGATTGAGATTGGGGAC	0.547																																					p.E1182G		Atlas-SNP	.											.	RYR1	708	.	0			c.A3545G						.						99	85	90					19																	38959769		2203	4300	6503	SO:0001583	missense	6261	exon26			AGATTGAGATTGG	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.3545A>G	chr19.hg19:g.38959769A>G	ENSP00000352608:p.Glu1182Gly	96.0	0.0		86.0	4.0	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	a	13.91	2.378899	0.42207	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	T;T;T	0.70399	-0.48;-0.48;-0.48	3.84	3.84	0.44239	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.168293	0.34386	U	0.004017	T	0.63768	0.2539	L	0.45228	1.405	0.44562	D	0.997521	B;B	0.24483	0.05;0.104	B;B	0.35470	0.041;0.203	T	0.60840	-0.7183	10	0.36615	T	0.2	.	8.4991	0.33148	0.9025:0.0:0.0975:0.0	.	1182;1182	P21817-2;P21817	.;RYR1_HUMAN	G	1182	ENSP00000352608:E1182G;ENSP00000347667:E1182G;ENSP00000354254:E1182G	ENSP00000347667:E1182G	E	+	2	0	RYR1	43651609	1.000000	0.71417	0.981000	0.43875	0.899000	0.52679	6.976000	0.76135	1.632000	0.50472	0.310000	0.20435	GAG	.	.		0.547	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			G	38959769	A	G	38959769	3	3	254	1	0	0	0	0	1	0	0	0	13783	304	11	2	3647	2	RYR1	19	38959769	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	56164	38959769	20169214	937	35229										
RYR1	6261	hgsc.bcm.edu	37	chr19	38976759	38976759	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgggggaggcggtgcgcgacGgtgggcagcacgctcgcgac	21	11	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:38976759G>T	ENST00000359596.3	+	34	5464	c.5464G>T	c.(5464-5466)Ggt>Tgt	p.G1822C	RYR1_ENST00000360985.3_Missense_Mutation_p.G1822C|RYR1_ENST00000355481.4_Missense_Mutation_p.G1822C			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1822	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.G1822C(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GGTGCGCGACGGTGGGCAGCA	0.701																																					p.G1822C		Atlas-SNP	.											RYR1,NS,carcinoma,0,1	RYR1	708	.	1	Substitution - Missense(1)	lung(1)	c.G5464T						.						67	66	66					19																	38976759		2202	4293	6495	SO:0001583	missense	6261	exon34			CGCGACGGTGGGC	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.5464G>T	chr19.hg19:g.38976759G>T	ENSP00000352608:p.Gly1822Cys	57.0	0.0		34.0	2.0	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	G	13.72	2.319976	0.41096	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	T;T;T	0.74106	-0.81;-0.81;-0.81	3.7	3.7	0.42460	.	0.000000	0.64402	U	0.000003	D	0.83147	0.5191	M	0.71036	2.16	0.49389	D	0.99978	D;P	0.89917	1.0;0.912	D;P	0.97110	1.0;0.706	D	0.84188	0.0443	10	0.62326	D	0.03	.	10.4488	0.44509	0.1008:0.0:0.8992:0.0	.	1822;1822	P21817-2;P21817	.;RYR1_HUMAN	C	1822	ENSP00000352608:G1822C;ENSP00000347667:G1822C;ENSP00000354254:G1822C	ENSP00000347667:G1822C	G	+	1	0	RYR1	43668599	1.000000	0.71417	0.084000	0.20598	0.774000	0.43823	5.449000	0.66619	1.886000	0.54624	0.585000	0.79938	GGT	.	.		0.701	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			T	38976759	G	T	38976759	3	4	254	1	0	0	0	0	1	0	0	0	13783	1116	39	1	5598	1	RYR1	19	38976759	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	16990	38976759	20152224	938	35230										
ACTN4	81	hgsc.bcm.edu	37	chr19	39214663	39214663	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttcaacaactggatggagagCgccatggaggacctccagga	13	10	1	1	rs527527101		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:39214663C>A	ENST00000252699.2	+	14	1714	c.1638C>A	c.(1636-1638)agC>agA	p.S546R	ACTN4_ENST00000390009.3_Missense_Mutation_p.S327R|ACTN4_ENST00000424234.2_Missense_Mutation_p.S156R	NM_004924.4	NP_004915.2	O43707	ACTN4_HUMAN	actinin, alpha 4	546					actin filament bundle assembly (GO:0051017)|blood coagulation (GO:0007596)|negative regulation of cellular component movement (GO:0051271)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cellular component movement (GO:0051272)|positive regulation of pinocytosis (GO:0048549)|positive regulation of sodium:proton antiporter activity (GO:0032417)|protein localization to tight junction (GO:1902396)|protein transport (GO:0015031)|regulation of apoptotic process (GO:0042981)|response to hypoxia (GO:0001666)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule lumen (GO:0031093)|protein complex (GO:0043234)|pseudopodium (GO:0031143)|ribonucleoprotein complex (GO:0030529)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|nucleoside binding (GO:0001882)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|urinary_tract(3)	30	all_cancers(60;1.57e-05)|Ovarian(47;0.103)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			GGATGGAGAGCGCCATGGAGG	0.607																																					p.S546R	Colon(168;199 1940 10254 46213 46384)	Atlas-SNP	.											.	ACTN4	69	.	0			c.C1638A						.						56	58	57					19																	39214663		2203	4300	6503	SO:0001583	missense	81	exon14			GGAGAGCGCCATG	D89980	CCDS12518.1	19q13	2013-01-10			ENSG00000130402	ENSG00000130402		"EF-hand domain containing"	166	protein-coding gene	gene with protein product		604638	"focal segmental glomerulosclerosis 1"	FSGS1		9461087, 10700177	Standard	NM_004924		Approved		uc002oja.2	O43707	OTTHUMG00000137382	ENST00000252699.2:c.1638C>A	chr19.hg19:g.39214663C>A	ENSP00000252699:p.Ser546Arg	145.0	0.0		94.0	4.0	NM_004924	A4K467|D6PXK4|O76048	Missense_Mutation	SNP	ENST00000252699.2	hg19	CCDS12518.1	.	.	.	.	.	.	.	.	.	.	C	12.94	2.087913	0.36855	.	.	ENSG00000130402	ENST00000252699;ENST00000424234;ENST00000390009	T;T;T	0.49432	0.78;0.78;0.78	3.75	-4.54	0.03452	.	0.209202	0.40302	N	0.001127	T	0.33731	0.0873	N	0.19112	0.55	0.45634	D	0.998568	P	0.41232	0.743	P	0.49502	0.613	T	0.23476	-1.0187	10	0.54805	T	0.06	.	6.7228	0.23340	0.1153:0.3807:0.0:0.504	.	546	O43707	ACTN4_HUMAN	R	546;156;327	ENSP00000252699:S546R;ENSP00000411187:S156R;ENSP00000439497:S327R	ENSP00000252699:S546R	S	+	3	2	ACTN4	43906503	0.000000	0.05858	0.985000	0.45067	0.978000	0.69477	-2.382000	0.01064	-0.711000	0.04995	-1.036000	0.02392	AGC	.	.		0.607	ACTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268091.1			A	39214663	C	A	39214663	3	1	254	1	0	0	0	0	1	0	0	0	207	767	27	1	1692	1	ACTN4	19	39214663	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	237904	39214663	19914320	939	35231										
HNRNPL	3191	hgsc.bcm.edu	37	chr19	39336338	39336338	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgaaaatgacaattctctggAcagggccacaaggattacag	10	8	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:39336338A>G	ENST00000221419.5	-	4	1028	c.662T>C	c.(661-663)gTc>gCc	p.V221A	HNRNPL_ENST00000600873.1_Missense_Mutation_p.V88A|AC008982.2_ENST00000600473.1_RNA	NM_001533.2	NP_001524.2	P14866	HNRPL_HUMAN	heterogeneous nuclear ribonucleoprotein L	221	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)			AATTCTCTGGACAGGGCCACA	0.498																																					p.V221A		Atlas-SNP	.											.	HNRNPL	67	.	0			c.T662C						.						85	80	82					19																	39336338		2203	4300	6503	SO:0001583	missense	3191	exon4			CTCTGGACAGGGC	X16135	CCDS33015.1, CCDS33016.1	19q13.2	2013-06-12		2007-08-16	ENSG00000104824	ENSG00000104824		"RNA binding motif (RRM) containing"	5045	protein-coding gene	gene with protein product		603083		HNRPL		2687284	Standard	NM_001533		Approved		uc021uuh.1	P14866	OTTHUMG00000182612	ENST00000221419.5:c.662T>C	chr19.hg19:g.39336338A>G	ENSP00000221419:p.Val221Ala	79.0	0.0		66.0	4.0	NM_001533	A6ND69|A6NIT8|Q9H3P3	Missense_Mutation	SNP	ENST00000221419.5	hg19	CCDS33015.1	.	.	.	.	.	.	.	.	.	.	A	31	5.072243	0.93950	.	.	ENSG00000104824	ENST00000221419;ENST00000388749;ENST00000388750;ENST00000423415;ENST00000536292	.	.	.	5.51	5.51	0.81932	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	D	0.86045	0.5839	H	0.95780	3.72	0.80722	D	1	P	0.42993	0.797	P	0.59487	0.858	D	0.89543	0.3794	9	0.87932	D	0	.	14.6052	0.68472	1.0:0.0:0.0:0.0	.	221	P14866	HNRPL_HUMAN	A	221;88;88;88;149	.	ENSP00000221419:V221A	V	-	2	0	HNRNPL	44028178	1.000000	0.71417	0.995000	0.50966	0.971000	0.66376	9.161000	0.94739	2.105000	0.64084	0.455000	0.32223	GTC	.	.		0.498	HNRNPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462670.1			G	39336338	A	G	39336338	3	3	254	1	0	0	0	0	1	0	0	0	7279	275	10	2	1147	2	HNRNPL	19	39336338	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	121675	39336338	19792645	940	35232										
PLEKHG2	64857	hgsc.bcm.edu	37	chr19	39913584	39913584	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gctgaaatgcccagcattccCtgccttaccaaaattcctga	6	14	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:39913584C>T	ENST00000409794.3	+	18	2740	c.1890C>T	c.(1888-1890)ccC>ccT	p.P630P	PLEKHG2_ENST00000409797.2_Intron|PLEKHG2_ENST00000458508.2_Silent_p.P571P|PLEKHG2_ENST00000425673.1_Silent_p.P601P|CTB-60E11.4_ENST00000601124.1_lincRNA|PLEKHG2_ENST00000378550.1_Intron	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	630					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|pancreas(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			CCAGCATTCCCTGCCTTACCA	0.547																																					p.P630P		Atlas-SNP	.											.	PLEKHG2	329	.	0			c.C1890T						.						80	77	78					19																	39913584		2203	4300	6503	SO:0001819	synonymous_variant	64857	exon18			CATTCCCTGCCTT	AK024429	CCDS33022.2	19q13.2	2013-01-11			ENSG00000090924	ENSG00000090924		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	29515	protein-coding gene	gene with protein product		611893				11839748, 18045877	Standard	NM_022835		Approved	CLG, FLJ00018, ARHGEF42	uc010xuz.2	Q9H7P9	OTTHUMG00000152570	ENST00000409794.3:c.1890C>T	chr19.hg19:g.39913584C>T		141.0	0.0		94.0	4.0	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Silent	SNP	ENST00000409794.3	hg19	CCDS33022.2	.	.	.	.	.	.	.	.	.	.	C	4.617	0.114662	0.08831	.	.	ENSG00000090924	ENST00000205135	T	0.73789	-0.78	4.96	-0.411	0.12370	.	0.170426	0.28488	N	0.015179	T	0.70815	0.3267	.	.	.	0.48288	D	0.999626	.	.	.	.	.	.	T	0.65919	-0.6051	7	0.66056	D	0.02	.	2.7681	0.05327	0.1408:0.5307:0.1378:0.1907	.	.	.	.	L	498	ENSP00000205135:P498L	ENSP00000205135:P498L	P	+	2	0	PLEKHG2	44605424	0.107000	0.21998	0.101000	0.21167	0.643000	0.38383	0.099000	0.15210	0.134000	0.18681	0.467000	0.42956	CCT	.	.		0.547	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835		T	39913584	C	T	39913584	2	4	254	1	0	0	0	0	0	0	0	1	12078	668	24	3		3	PLEKHG2	19	39913584	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	577246	39913584	19215399	941	35233										
AKT2	208	hgsc.bcm.edu	37	chr19	40743931	40743931	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agtactcaagagccgagacaAtctctgcaccataaaaccgg	8	12	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:40743931A>G	ENST00000392038.2	-	9	1074	c.776T>C	c.(775-777)aTt>aCt	p.I259T	AKT2_ENST00000579047.1_Missense_Mutation_p.I197T|AKT2_ENST00000424901.1_Missense_Mutation_p.I259T|AKT2_ENST00000311278.6_Missense_Mutation_p.I259T	NM_001243027.1|NM_001243028.1|NM_001626.4	NP_001229956.1|NP_001229957.1|NP_001617.1	P31751	AKT2_HUMAN	v-akt murine thymoma viral oncogene homolog 2	259	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of Ral GTPase activity (GO:0032859)|apoptotic process (GO:0006915)|carbohydrate transport (GO:0008643)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|fat cell differentiation (GO:0045444)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|insulin receptor signaling pathway (GO:0008286)|intracellular protein transmembrane transport (GO:0065002)|mammary gland epithelial cell differentiation (GO:0060644)|membrane organization (GO:0061024)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|peripheral nervous system myelin maintenance (GO:0032287)|positive regulation of cell motility (GO:2000147)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)|protein localization to plasma membrane (GO:0072659)|regulation of cell cycle arrest (GO:0071156)|regulation of cell migration (GO:0030334)|regulation of translation (GO:0006417)|signal transduction (GO:0007165)	cell cortex (GO:0005938)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|kidney(3)|large_intestine(9)|lung(10)|prostate(2)|skin(1)	27			Lung(22;0.000499)			AGCCGAGACAATCTCTGCACC	0.607			A		"ovarian, pancreatic "																																p.I259T		Atlas-SNP	.		Dom	yes		19	19q13.1-q13.2	208	v-akt murine thymoma viral oncogene homolog 2		E	.	AKT2	53	.	0			c.T776C						.						132	97	109					19																	40743931		2203	4300	6503	SO:0001583	missense	208	exon9			GAGACAATCTCTG	M77198	CCDS12552.1	19q13.1-q13.2	2013-01-10			ENSG00000105221	ENSG00000105221	2.7.11.1	"Pleckstrin homology (PH) domain containing"	392	protein-coding gene	gene with protein product		164731				1409633	Standard	NM_001626		Approved		uc002onf.3	P31751	OTTHUMG00000137375	ENST00000392038.2:c.776T>C	chr19.hg19:g.40743931A>G	ENSP00000375892:p.Ile259Thr	128.0	0.0		82.0	4.0	NM_001626	B2RBD8|Q05BV0|Q0VAN0|Q0VAN1|Q68GC0	Missense_Mutation	SNP	ENST00000392038.2	hg19	CCDS12552.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.511015	0.85389	.	.	ENSG00000105221	ENST00000392038;ENST00000391844;ENST00000424901;ENST00000311278;ENST00000391845	T;T;T	0.31769	1.48;1.48;1.48	4.79	4.79	0.61399	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.097802	0.64402	D	0.000002	T	0.54078	0.1836	M	0.71206	2.165	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.998;0.999	T	0.58769	-0.7578	10	0.87932	D	0	.	13.7243	0.62748	1.0:0.0:0.0:0.0	.	197;259;259	B4DG79;Q0VAN0;P31751	.;.;AKT2_HUMAN	T	259;160;259;259;79	ENSP00000375892:I259T;ENSP00000399532:I259T;ENSP00000309428:I259T	ENSP00000309428:I259T	I	-	2	0	AKT2	45435771	1.000000	0.71417	1.000000	0.80357	0.842000	0.47809	9.057000	0.93889	2.140000	0.66376	0.533000	0.62120	ATT	.	.		0.607	AKT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268029.1	NM_001626		G	40743931	A	G	40743931	3	3	254	1	0	0	0	0	1	0	0	0	480	101	4	2	693	2	AKT2	19	40743931	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	830347	40743931	18385052	942	35234										
SPTBN4	57731	hgsc.bcm.edu	37	chr19	41038617	41038617	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gctgcataagagatggctccGgcaccaggcattcatggccg	13	12	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:41038617G>A	ENST00000352632.3	+	19	4120	c.4034G>A	c.(4033-4035)cGg>cAg	p.R1345Q	SPTBN4_ENST00000392025.1_Missense_Mutation_p.R88Q|SPTBN4_ENST00000595535.1_Missense_Mutation_p.R1345Q|SPTBN4_ENST00000598249.1_Missense_Mutation_p.R1345Q|SPTBN4_ENST00000392023.1_Missense_Mutation_p.R21Q|SPTBN4_ENST00000338932.3_Missense_Mutation_p.R1345Q			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	1345					actin filament capping (GO:0051693)|adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cardiac conduction (GO:0061337)|central nervous system projection neuron axonogenesis (GO:0021952)|clustering of voltage-gated sodium channels (GO:0045162)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization to plasma membrane (GO:0090002)|fertilization (GO:0009566)|negative regulation of heart rate (GO:0010459)|positive regulation of multicellular organism growth (GO:0040018)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of sodium ion transport (GO:0002028)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|axon hillock (GO:0043203)|axon initial segment (GO:0043194)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|nuclear matrix (GO:0016363)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|PML body (GO:0016605)|spectrin (GO:0008091)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phosphatase binding (GO:0019902)|phospholipid binding (GO:0005543)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.R1345Q(1)		breast(4)|central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	73			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			AGATGGCTCCGGCACCAGGCA	0.602																																					p.R1345Q		Atlas-SNP	.											SPTBN4,NS,carcinoma,0,1	SPTBN4	213	.	1	Substitution - Missense(1)	ovary(1)	c.G4034A						.						64	53	57					19																	41038617		2203	4300	6503	SO:0001583	missense	57731	exon19			GGCTCCGGCACCA	AF082075	CCDS12559.1, CCDS42569.1	19q13.13	2013-01-10				ENSG00000160460		"Pleckstrin homology (PH) domain containing"	14896	protein-coding gene	gene with protein product		606214				11086001	Standard	NM_020971		Approved	SPTBN3, KIAA1642	uc002onz.3	Q9H254		ENST00000352632.3:c.4034G>A	chr19.hg19:g.41038617G>A	ENSP00000263373:p.Arg1345Gln	118.0	0.0		69.0	3.0	NM_020971	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Missense_Mutation	SNP	ENST00000352632.3	hg19	CCDS12559.1	.	.	.	.	.	.	.	.	.	.	G	31	5.076301	0.94000	.	.	ENSG00000160460	ENST00000428507;ENST00000352632;ENST00000338932;ENST00000392025;ENST00000392023	T;T;T;T	0.67523	0.79;0.79;-0.27;0.79	4.86	4.86	0.63082	.	0.204266	0.32175	N	0.006477	T	0.72061	0.3414	L	0.41492	1.28	0.37052	D	0.897641	D;D;D;D;D;D	0.76494	0.979;0.981;0.996;0.998;0.992;0.999	P;P;P;P;P;D	0.68943	0.788;0.535;0.709;0.905;0.709;0.961	T	0.76884	-0.2794	10	0.66056	D	0.02	.	10.4908	0.44750	0.0898:0.0:0.9102:0.0	.	1345;88;88;21;1345;1345	E9PDB1;Q9H254-3;C9JY79;E9PGQ5;Q9H254;Q71S06	.;.;.;.;SPTN4_HUMAN;.	Q	1345;1345;1345;88;21	ENSP00000263373:R1345Q;ENSP00000340345:R1345Q;ENSP00000375879:R88Q;ENSP00000375877:R21Q	ENSP00000340345:R1345Q	R	+	2	0	SPTBN4	45730457	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.304000	0.59104	2.499000	0.84300	0.561000	0.74099	CGG	.	.		0.602	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2			A	41038617	G	A	41038617	3	1	254	1	0	0	0	0	1	0	0	0	15136	1116	39	1	4104	1	SPTBN4	19	41038617	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	294686	41038617	18090366	943	35235										
ADCK4	79934	hgsc.bcm.edu	37	chr19	41206291	41206291	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccagctccatgcccagcaccCgtgtcgtgcacagctcctta	8	18	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:41206291C>A	ENST00000324464.3	-	11	1260	c.959G>T	c.(958-960)cGg>cTg	p.R320L	ADCK4_ENST00000450541.1_Missense_Mutation_p.R279L|ADCK4_ENST00000243583.6_Missense_Mutation_p.R279L	NM_024876.3	NP_079152.3	Q96D53	ADCK4_HUMAN	aarF domain containing kinase 4	320	Protein kinase.		R -> W (in NPHS9). {ECO:0000269|PubMed:24270420}.			integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(6)|stomach(2)|urinary_tract(1)	17			Lung(22;9.49e-05)|LUSC - Lung squamous cell carcinoma(20;0.000219)			GCCCAGCACCCGTGTCGTGCA	0.642																																					p.R320L		Atlas-SNP	.											.	ADCK4	92	.	0			c.G959T						.						39	39	39					19																	41206291		2203	4300	6503	SO:0001583	missense	79934	exon11			AGCACCCGTGTCG	AK022291	CCDS12562.1, CCDS46081.1	19q13.2	2008-02-05				ENSG00000123815			19041	protein-coding gene	gene with protein product		615567					Standard	NM_024876		Approved	FLJ12229, COQ8	uc002oor.2	Q96D53		ENST00000324464.3:c.959G>T	chr19.hg19:g.41206291C>A	ENSP00000315118:p.Arg320Leu	109.0	0.0		77.0	29.0	NM_024876	Q8TAJ1|Q9HA52	Missense_Mutation	SNP	ENST00000324464.3	hg19	CCDS12562.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.664953	0.88251	.	.	ENSG00000123815	ENST00000324464;ENST00000450541;ENST00000243583	T;T;T	0.52295	0.67;0.67;0.67	5.75	5.75	0.90469	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.69869	0.3159	M	0.87547	2.89	0.58432	D	0.999997	D;D	0.63046	0.978;0.992	P;D	0.66196	0.81;0.942	T	0.74312	-0.3706	10	0.66056	D	0.02	-31.0909	12.1003	0.53780	0.0:0.9204:0.0:0.0796	.	320;279	Q96D53;Q96D53-2	ADCK4_HUMAN;.	L	320;279;279	ENSP00000315118:R320L;ENSP00000412839:R279L;ENSP00000243583:R279L	ENSP00000243583:R279L	R	-	2	0	ADCK4	45898131	0.186000	0.23225	0.994000	0.49952	0.747000	0.42532	2.066000	0.41452	2.720000	0.93068	0.563000	0.77884	CGG	.	.		0.642	ADCK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462731.1	NM_024876		A	41206291	C	A	41206291	3	1	254	1	0	0	0	0	1	0	0	0	290	652	23	1	695	1	ADCK4	19	41206291	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	167674	41206291	17922692	944	35236										
EGLN2	112398	hgsc.bcm.edu	37	chr19	41306565	41306565	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agcccttggagcctgagcctGgccgggccaggatgggagtg	18	11	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:41306565G>A	ENST00000593726.1	+	1	1116	c.88G>A	c.(88-90)Ggc>Agc	p.G30S	EGLN2_ENST00000406058.2_Missense_Mutation_p.G30S|RAB4B-EGLN2_ENST00000594136.1_3'UTR|EGLN2_ENST00000303961.4_Missense_Mutation_p.G30S|EGLN2_ENST00000594140.1_5'Flank|CTC-490E21.12_ENST00000601627.1_5'Flank			Q96KS0	EGLN2_HUMAN	egl-9 family hypoxia-inducible factor 2	30					cell redox homeostasis (GO:0045454)|cellular response to hypoxia (GO:0071456)|intracellular estrogen receptor signaling pathway (GO:0030520)|peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)|positive regulation of protein catabolic process (GO:0045732)|regulation of cell growth (GO:0001558)|regulation of neuron apoptotic process (GO:0043523)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to hypoxia (GO:0001666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ferrous iron binding (GO:0008198)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|oxygen sensor activity (GO:0019826)|peptidyl-proline 4-dioxygenase activity (GO:0031545)			breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	10			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Vitamin C(DB00126)	GCCTGAGCCTGGCCGGGCCAG	0.652																																					p.G30S		Atlas-SNP	.											.	EGLN2	31	.	0			c.G88A						.						45	39	41					19																	41306565		2203	4300	6503	SO:0001583	missense	112398	exon2			GAGCCTGGCCGGG	AJ310544	CCDS12567.1	19q13.2	2013-08-21	2013-08-21		ENSG00000269858	ENSG00000269858			14660	protein-coding gene	gene with protein product	"HIF prolyl hydroxylase 1"	606424	"EGL nine (C.elegans) homolog 2", "egl nine homolog 2 (C. elegans)"				Standard	NM_080732		Approved	PHD1, HIFPH1	uc002oph.3	Q96KS0		ENST00000593726.1:c.88G>A	chr19.hg19:g.41306565G>A	ENSP00000469686:p.Gly30Ser	108.0	0.0		96.0	4.0	NM_053046	A8K5S0|Q8WWY4|Q9BV14	Missense_Mutation	SNP	ENST00000593726.1	hg19	CCDS12567.1	.	.	.	.	.	.	.	.	.	.	G	11.09	1.536840	0.27475	.	.	ENSG00000171570	ENST00000303961;ENST00000406058	T;T	0.30448	1.53;1.53	4.04	0.449	0.16619	.	0.434068	0.21393	N	0.075276	T	0.08980	0.0222	N	0.02539	-0.55	0.28523	N	0.912943	B	0.02656	0.0	B	0.04013	0.001	T	0.34850	-0.9812	10	0.08837	T	0.75	-6.1654	6.3273	0.21251	0.6573:0.0:0.3427:0.0	.	30	Q96KS0	EGLN2_HUMAN	S	30	ENSP00000307080:G30S;ENSP00000385253:G30S	ENSP00000307080:G30S	G	+	1	0	EGLN2	45998405	0.123000	0.22298	1.000000	0.80357	0.994000	0.84299	0.411000	0.21115	0.301000	0.22738	0.491000	0.48974	GGC	.	.		0.652	EGLN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463218.1			A	41306565	G	A	41306565	3	1	254	1	0	0	0	0	1	0	0	0	4971	1348	47	3	90	3	EGLN2	19	41306565	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	100274	41306565	17822418	945	35237										
BCKDHA	593	hgsc.bcm.edu	37	chr19	41916689	41916689	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	accgcgtcatggaccggcaaGgccagatcatcaaccccagc	10	16	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:41916689G>A	ENST00000269980.2	+	2	624	c.256G>A	c.(256-258)Ggc>Agc	p.G86S	CTC-435M10.3_ENST00000540732.1_Missense_Mutation_p.G120S|BCKDHA_ENST00000595085.1_Missense_Mutation_p.G120S|CTC-435M10.3_ENST00000604424.1_3'UTR|BCKDHA_ENST00000457836.2_Missense_Mutation_p.G64S	NM_000709.3|NM_001164783.1	NP_000700.1|NP_001158255.1	P12694	ODBA_HUMAN	branched chain keto acid dehydrogenase E1, alpha polypeptide	86					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity (GO:0003863)|alpha-ketoacid dehydrogenase activity (GO:0003826)|carboxy-lyase activity (GO:0016831)|metal ion binding (GO:0046872)	p.G86C(1)		central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	10						GGACCGGCAAGGCCAGATCAT	0.627																																					p.G86S		Atlas-SNP	.											BCKDHA,colon,carcinoma,0,1	BCKDHA	36	.	1	Substitution - Missense(1)	large_intestine(1)	c.G256A						.						62	64	64					19																	41916689		2203	4300	6503	SO:0001583	missense	593	exon2			CGGCAAGGCCAGA	J04474	CCDS12581.1	19q13.1-q13.2	2008-07-09	2005-11-29		ENSG00000248098	ENSG00000248098			986	protein-coding gene	gene with protein product	"maple syrup urine disease"	608348	"branched chain keto acid dehydrogenase E1, alpha polypeptide (maple syrup urine disease)", "2-oxoisovalerate dehydrogenase (lipoamide)"	OVD1A			Standard	NM_000709		Approved	MSU	uc002oqq.3	P12694	OTTHUMG00000168128	ENST00000269980.2:c.256G>A	chr19.hg19:g.41916689G>A	ENSP00000269980:p.Gly86Ser	117.0	0.0		95.0	4.0	NM_000709	B4DP47|E7EW46|Q16034|Q16472	Missense_Mutation	SNP	ENST00000269980.2	hg19	CCDS12581.1	.	.	.	.	.	.	.	.	.	.	G	35	5.554705	0.96501	.	.	ENSG00000255730;ENSG00000248098;ENSG00000248098;ENSG00000248098;ENSG00000248098	ENST00000540732;ENST00000269980;ENST00000542943;ENST00000457836;ENST00000378196	D;D;D;D	0.99167	-5.51;-5.51;-5.51;-5.51	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	D	0.99001	0.9659	L	0.54908	1.71	0.80722	D	1	D;D;D;D	0.89917	1.0;0.997;1.0;0.978	D;D;D;D	0.76575	0.988;0.975;0.985;0.932	D	0.99909	1.1192	10	0.87932	D	0	-41.0027	17.9433	0.89031	0.0:0.0:1.0:0.0	.	64;86;86;120	B4DP47;Q59EI3;P12694;F5H5P2	.;.;ODBA_HUMAN;.	S	120;86;86;64;86	ENSP00000443246:G120S;ENSP00000269980:G86S;ENSP00000440345:G86S;ENSP00000416000:G64S	ENSP00000269980:G86S	G	+	1	0	BCKDHA;CTC-435M10.3	46608529	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.316000	0.96319	2.550000	0.86006	0.643000	0.83706	GGC	.	.		0.627	BCKDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398313.3	NM_000709		A	41916689	G	A	41916689	3	1	254	1	0	0	0	0	1	0	0	0	1359	1000	35	3	262	3	BCKDHA	19	41916689	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	610124	41916689	17212294	946	35238										
PSG9	5678	hgsc.bcm.edu	37	chr19	43766182	43766182	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggctctgaccattcatccacCataggtagcttgcgtccaga	9	13	2	2	rs149244305		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:43766182C>A	ENST00000270077.3	-	3	635	c.539G>T	c.(538-540)tGg>tTg	p.W180L	PSG9_ENST00000418820.2_Intron|PSG9_ENST00000443718.3_Intron|PSG9_ENST00000244293.7_Missense_Mutation_p.W180L|PSG9_ENST00000291752.5_Intron|PSG9_ENST00000593948.1_Missense_Mutation_p.W180L|PSG9_ENST00000596730.1_Intron	NM_002784.3	NP_002775.3	Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 9	180	Ig-like C2-type 1.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.W180*(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Prostate(69;0.00682)				ATTCATCCACCATAGGTAGCT	0.517																																					p.W180L		Atlas-SNP	.											PSG9,arm,malignant_melanoma,0,1	PSG9	77	.	1	Substitution - Nonsense(1)	skin(1)	c.G539T						.						252	247	249					19																	43766182		2203	4300	6503	SO:0001583	missense	5678	exon3			ATCCACCATAGGT	M34481	CCDS12618.1	19q13.2	2013-01-29			ENSG00000183668	ENSG00000183668		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9526	protein-coding gene	gene with protein product		176398		PSG11		7806221	Standard	XM_005259076		Approved	PSGII	uc002owd.4	Q00887	OTTHUMG00000182826	ENST00000270077.3:c.539G>T	chr19.hg19:g.43766182C>A	ENSP00000270077:p.Trp180Leu	242.0	0.0		122.0	5.0	NM_002784	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Missense_Mutation	SNP	ENST00000270077.3	hg19	CCDS12618.1	.	.	.	.	.	.	.	.	.	.	N	13.06	2.125030	0.37533	.	.	ENSG00000183668	ENST00000270077;ENST00000435220;ENST00000244293	T;T	0.14022	2.54;2.54	2.12	2.12	0.27331	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.41488	0.1161	M	0.90977	3.165	0.26934	N	0.966398	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.97110	1.0;1.0;0.999	T	0.15464	-1.0436	9	0.87932	D	0	.	7.8962	0.29708	0.0:1.0:0.0:0.0	.	180;180;180	Q15227;Q6LEU7;Q00887	.;.;PSG9_HUMAN	L	180;141;180	ENSP00000270077:W180L;ENSP00000244293:W180L	ENSP00000244293:W180L	W	-	2	0	PSG9	48458022	0.024000	0.19004	0.047000	0.18901	0.005000	0.04900	0.295000	0.19065	0.860000	0.35481	0.194000	0.17425	TGG	.	.		0.517	PSG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323065.1	NM_002784		A	43766182	C	A	43766182	3	1	254	1	0	0	0	0	1	0	0	0	12674	595	21	3	757	3	PSG9	19	43766182	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1849493	43766182	15362801	947	35239										
PHLDB3	653583	hgsc.bcm.edu	37	chr19	43998856	43998856	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aggccgtgggggaggcacctGcagggagctgtggacagaaa	19	8	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:43998856G>A	ENST00000292140.5	-	9	1507	c.1147C>T	c.(1147-1149)Cag>Tag	p.Q383*		NM_198850.3	NP_942147.3	Q6NSJ2	PHLB3_HUMAN	pleckstrin homology-like domain, family B, member 3	383							enzyme binding (GO:0019899)			breast(1)|central_nervous_system(1)|lung(5)	7		Prostate(69;0.0153)				GGAGGCACCTGCAGGGAGCTG	0.602																																					p.Q383X		Atlas-SNP	.											.	PHLDB3	30	.	0			c.C1147T						.						27	32	30					19																	43998856		1968	4160	6128	SO:0001587	stop_gained	653583	exon9			GCACCTGCAGGGA		CCDS12621.2	19q13.31	2013-01-10			ENSG00000176531	ENSG00000176531		"Pleckstrin homology (PH) domain containing"	30499	protein-coding gene	gene with protein product							Standard	NM_198850		Approved	FLJ40193	uc002own.4	Q6NSJ2	OTTHUMG00000150693	ENST00000292140.5:c.1147C>T	chr19.hg19:g.43998856G>A	ENSP00000292140:p.Gln383*	157.0	0.0		96.0	4.0	NM_198850	Q8N7Z4	Nonsense_Mutation	SNP	ENST00000292140.5	hg19	CCDS12621.2	.	.	.	.	.	.	.	.	.	.	G	40	8.240158	0.98722	.	.	ENSG00000176531	ENST00000292140	.	.	.	4.6	4.6	0.57074	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	.	13.3415	0.60547	0.0:0.0:1.0:0.0	.	.	.	.	X	383	.	ENSP00000292140:Q383X	Q	-	1	0	PHLDB3	48690696	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	3.119000	0.50422	2.266000	0.75297	0.460000	0.39030	CAG	.	.		0.602	PHLDB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319643.2			A	43998856	G	A	43998856	4	1	254	1	0	0	0	0	0	1	0	0	11862	1328	46	3	807	3	PHLDB3	19	43998856	Nonsense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	232674	43998856	15130127	948	35240										
ZNF229	7772	hgsc.bcm.edu	37	chr19	44934658	44934658	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcatgaggagagctctttgtGtgaaaagaaccttaattctt	10	6	2	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:44934658G>T	ENST00000588931.1	-	6	731	c.298C>A	c.(298-300)Cac>Aac	p.H100N	ZNF229_ENST00000591289.1_Intron|CTC-512J12.4_ENST00000588655.1_RNA|ZNF229_ENST00000291187.4_Missense_Mutation_p.H94N	NM_014518.2	NP_055333.2	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	100	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|central_nervous_system(2)|endometrium(6)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	45		Prostate(69;0.0352)				AGCTCTTTGTGTGAAAAGAAC	0.398																																					p.H100N		Atlas-SNP	.											.	ZNF229	123	.	0			c.C298A						.						57	55	56					19																	44934658		1841	4091	5932	SO:0001583	missense	7772	exon6			CTTTGTGTGAAAA	AF192979	CCDS42574.1, CCDS62706.1	19q13.2	2013-01-08				ENSG00000278318		"Zinc fingers, C2H2-type", "-"	13022	protein-coding gene	gene with protein product							Standard	XM_006723372		Approved		uc002oze.1	Q9UJW7		ENST00000588931.1:c.298C>A	chr19.hg19:g.44934658G>T	ENSP00000466519:p.His100Asn	118.0	0.0		95.0	4.0	NM_014518	B2RWN3|Q59FV2|Q86WL9	Missense_Mutation	SNP	ENST00000588931.1	hg19	CCDS42574.1	.	.	.	.	.	.	.	.	.	.	G	2.312	-0.357768	0.05138	.	.	ENSG00000167383	ENST00000291187	.	.	.	2.99	0.432	0.16529	Krueppel-associated box (1);	.	.	.	.	T	0.19565	0.0470	N	0.24115	0.695	0.09310	N	1	B	0.30068	0.267	B	0.27500	0.08	T	0.20472	-1.0274	8	0.25106	T	0.35	.	5.1714	0.15112	0.1491:0.2006:0.6504:0.0	.	100	Q9UJW7	ZN229_HUMAN	N	100	.	ENSP00000291187:H100N	H	-	1	0	ZNF229	49626498	0.001000	0.12720	0.002000	0.10522	0.295000	0.27426	0.233000	0.17911	0.145000	0.18977	0.609000	0.83330	CAC	.	.		0.398	ZNF229-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460833.1	NM_014518		T	44934658	G	T	44934658	3	4	254	1	0	0	0	0	1	0	0	0	17797	1377	48	3	2183	3	ZNF229	19	44934658	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	935802	44934658	14194325	949	35241										
CLPTM1	1209	hgsc.bcm.edu	37	chr19	45489769	45489769	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cattggcaccccaacatcacCatcaacatcgtggacgacca	6	16	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:45489769C>A	ENST00000337392.5	+	7	879	c.729C>A	c.(727-729)acC>acA	p.T243T	CLPTM1_ENST00000541297.2_Silent_p.T229T|CLPTM1_ENST00000546079.1_Silent_p.T141T|CLPTM1_ENST00000589158.1_3'UTR	NM_001282175.1|NM_001282176.1|NM_001294.2	NP_001269104.1|NP_001269105.1|NP_001285.1	O96005	CLPT1_HUMAN	cleft lip and palate associated transmembrane protein 1	243					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of T cell differentiation in thymus (GO:0033081)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00354)|Epithelial(262;0.187)		CCAACATCACCATCAACATCG	0.622																																					p.T243T		Atlas-SNP	.											.	CLPTM1	109	.	0			c.C729A						.						164	125	138					19																	45489769		2203	4300	6503	SO:0001819	synonymous_variant	1209	exon7			CATCACCATCAAC	AF037339	CCDS12651.1, CCDS74394.1, CCDS74395.1	19q13.3	2008-02-05				ENSG00000104853			2087	protein-coding gene	gene with protein product		604783				9828125	Standard	NM_001294		Approved		uc002pai.3	O96005		ENST00000337392.5:c.729C>A	chr19.hg19:g.45489769C>A		93.0	0.0		72.0	4.0	NM_001294	B3KQH2|B4DDS3|B4E2X9|B7Z9X9|F5H8J3|Q53ET6|Q9BSS5	Silent	SNP	ENST00000337392.5	hg19	CCDS12651.1																																																																																			.	.		0.622	CLPTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453267.1	NM_001294		A	45489769	C	A	45489769	2	1	254	1	0	0	0	0	0	0	0	1	3556	581	21	3		3	CLPTM1	19	45489769	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	555111	45489769	13639214	950	35242										
KLC3	147700	hgsc.bcm.edu	37	chr19	45850019	45850019	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gctgcgacagtacgacccacCggcggagagccaggtgccac	14	15	0	1	rs76874841	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:45850019C>A	ENST00000391946.2	+	3	578	c.476C>A	c.(475-477)cCg>cAg	p.P159Q	KLC3_ENST00000470402.1_Missense_Mutation_p.P173Q|KLC3_ENST00000585434.1_Missense_Mutation_p.P159Q	NM_177417.2	NP_803136.2	Q6P597	KLC3_HUMAN	kinesin light chain 3	159					axon cargo transport (GO:0008088)	ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|motile cilium (GO:0031514)|neuron projection (GO:0043005)	microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	8		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		TACGACCCACCGGCGGAGAGC	0.701																																					p.P159Q		Atlas-SNP	.											.	KLC3	37	.	0			c.C476A						.						5	6	5					19																	45850019		1973	4041	6014	SO:0001583	missense	147700	exon3			ACCCACCGGCGGA	AK092481	CCDS12660.2	19q13	2013-01-10			ENSG00000104892	ENSG00000104892		"Tetratricopeptide (TTC) repeat domain containing"	20717	protein-coding gene	gene with protein product		601334					Standard	XM_005258536		Approved	KLC2L, KNS2B, KLCt	uc002pbf.1	Q6P597	OTTHUMG00000143722	ENST00000391946.2:c.476C>A	chr19.hg19:g.45850019C>A	ENSP00000375810:p.Pro159Gln	102.0	0.0		65.0	4.0	NM_177417	A0AVM3|A2RUT6|Q6GMU2|Q8NAL1|Q8WWJ9	Missense_Mutation	SNP	ENST00000391946.2	hg19	CCDS12660.2	.	.	.	.	.	.	.	.	.	.	C	11.10	1.538685	0.27475	.	.	ENSG00000104892	ENST00000391946;ENST00000470402	T;T	0.40756	1.02;1.02	4.26	3.22	0.36961	Rabaptin, GTPase-Rab5 binding (1);	0.285619	0.29537	N	0.011862	T	0.26629	0.0651	N	0.04508	-0.205	0.09310	N	1	P;P;P	0.47762	0.878;0.878;0.9	P;P;P	0.50352	0.505;0.505;0.638	T	0.04255	-1.0965	10	0.46703	T	0.11	-8.1633	7.3624	0.26754	0.0:0.8817:0.0:0.1183	.	159;173;159	Q6P597-2;Q6P597-3;Q6P597	.;.;KLC3_HUMAN	Q	159;173	ENSP00000375810:P159Q;ENSP00000436019:P173Q	ENSP00000375810:P159Q	P	+	2	0	KLC3	50541859	0.269000	0.24143	0.141000	0.22245	0.022000	0.10575	2.700000	0.47085	2.390000	0.81377	0.455000	0.32223	CCG	.	C|0.998;G|0.002		0.701	KLC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289776.1	NM_145275		A	45850019	C	A	45850019	3	1	254	1	0	0	0	0	1	0	0	0	8344	652	23	1	482	1	KLC3	19	45850019	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	360250	45850019	13278964	951	35243										
ERCC2	2068	hgsc.bcm.edu	37	chr19	45871940	45871940	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcagagccagtcccagaaacGgcagcttctcgccctcctgc	9	17	2	2	rs142462393		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:45871940G>T	ENST00000391945.4	-	5	385	c.308C>A	c.(307-309)cCg>cAg	p.P103Q	ERCC2_ENST00000221481.6_Missense_Mutation_p.P103Q|ERCC2_ENST00000391944.3_Missense_Mutation_p.P103Q|ERCC2_ENST00000485403.2_Missense_Mutation_p.P79Q|ERCC2_ENST00000391940.4_Missense_Mutation_p.P79Q	NM_000400.3	NP_000391.1	P18074	ERCC2_HUMAN	excision repair cross-complementation group 2	103	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				7-methylguanosine mRNA capping (GO:0006370)|aging (GO:0007568)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|central nervous system myelin formation (GO:0032289)|chromosome segregation (GO:0007059)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|embryonic cleavage (GO:0040016)|erythrocyte maturation (GO:0043249)|extracellular matrix organization (GO:0030198)|gene expression (GO:0010467)|hair cell differentiation (GO:0035315)|hair follicle maturation (GO:0048820)|hematopoietic stem cell differentiation (GO:0060218)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|spinal cord development (GO:0021510)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)|viral process (GO:0016032)	cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|MMXD complex (GO:0071817)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			large_intestine(4)|lung(2)|ovary(1)|pancreas(1)|stomach(1)	9		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		TCCCAGAAACGGCAGCTTCTC	0.527			"Mis, N, F, S"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.P103Q		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (D)	19	19q13.2-q13.3	2068	"excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D)"		E	.	ERCC2	78	.	0			c.C308A						.						44	44	44					19																	45871940		2203	4300	6503	SO:0001583	missense	2068	exon5	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	AGAAACGGCAGCT		CCDS33049.1, CCDS46112.1	19q13.3	2014-09-17	2014-03-07		ENSG00000104884	ENSG00000104884	3.6.4.12	"General transcription factor IIH complex subunits"	3434	protein-coding gene	gene with protein product	"excision repair cross-complementing rodent repair deficiency, complementation group 2 protein", "TFIIH basal transcription factor complex helicase XPB subunit"	126340	"xeroderma pigmentosum complementary group D", "excision repair cross-complementing rodent repair deficiency, complementation group 2"	XPD		8413672, 2184031	Standard	NM_000400		Approved	MAG, EM9, MGC102762, MGC126218, MGC126219, TFIIH	uc002pbj.2	P18074	OTTHUMG00000048190	ENST00000391945.4:c.308C>A	chr19.hg19:g.45871940G>T	ENSP00000375809:p.Pro103Gln	125.0	0.0		86.0	4.0	NM_000400	Q2TB78|Q2YDY2|Q7KZU6|Q8N721	Missense_Mutation	SNP	ENST00000391945.4	hg19	CCDS33049.1	.	.	.	.	.	.	.	.	.	.	G	8.502	0.864534	0.17250	.	.	ENSG00000104884	ENST00000391941;ENST00000391942;ENST00000391945;ENST00000391944;ENST00000391940;ENST00000221481	T;D;T;T	0.82526	-0.45;-1.62;1.0;-0.45	5.09	0.408	0.16377	DEAD2 (1);Helicase-like, DEXD box c2 type (1);Helicase, superfamily 1/2, ATP-binding domain, DinG/Rad3-type (1);	0.608859	0.17906	N	0.158018	T	0.74176	0.3682	L	0.27053	0.805	0.09310	N	1	B;P;B	0.39920	0.097;0.695;0.011	B;B;B	0.43478	0.076;0.421;0.048	T	0.63233	-0.6683	10	0.18276	T	0.48	-9.7991	13.6809	0.62484	0.0:0.0:0.3149:0.6851	.	103;79;103	E7EVE9;Q7KZU6;P18074	.;.;ERCC2_HUMAN	Q	53;79;103;103;79;103	ENSP00000375809:P103Q;ENSP00000375808:P103Q;ENSP00000375804:P79Q;ENSP00000221481:P103Q	ENSP00000221481:P103Q	P	-	2	0	ERCC2	50563780	0.191000	0.23288	0.034000	0.17996	0.553000	0.35397	0.322000	0.19576	0.033000	0.15463	-0.226000	0.12346	CCG	.	G|1.000;A|0.000		0.527	ERCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109626.2	NM_000400		T	45871940	G	T	45871940	3	4	254	1	0	0	0	0	1	0	0	0	5215	1116	39	1	2107	1	ERCC2	19	45871940	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	21921	45871940	13257043	952	35244										
ERCC1	2067	hgsc.bcm.edu	37	chr19	45920105	45920105	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcgaggatcaatgtgcagtcGgccaggatacacatcttagc	12	10	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:45920105G>T	ENST00000300853.3	-	6	1167	c.576C>A	c.(574-576)gcC>gcA	p.A192A	ERCC1_ENST00000340192.7_Silent_p.A192A|ERCC1_ENST00000591636.1_Silent_p.A192A|ERCC1_ENST00000423698.2_Silent_p.A120A|ERCC1_ENST00000588738.1_5'Flank|ERCC1_ENST00000013807.5_Silent_p.A192A|ERCC1_ENST00000589165.1_Silent_p.A192A	NM_001983.3	NP_001974.1	P07992	ERCC1_HUMAN	excision repair cross-complementation group 1	192					cell proliferation (GO:0008283)|chromosome organization (GO:0051276)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|male gonad development (GO:0008584)|mitotic recombination (GO:0006312)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|negative regulation of telomere maintenance (GO:0032205)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|nucleotide-excision repair, DNA incision, 5'-to lesion (GO:0006296)|oogenesis (GO:0048477)|post-embryonic hemopoiesis (GO:0035166)|pyrimidine dimer repair by nucleotide-excision repair (GO:0000720)|replicative cell aging (GO:0001302)|response to nutrient (GO:0007584)|response to oxidative stress (GO:0006979)|response to sucrose (GO:0009744)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)|syncytium formation (GO:0006949)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	cytoplasm (GO:0005737)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	damaged DNA binding (GO:0003684)|endonuclease activity (GO:0004519)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|single-stranded DNA binding (GO:0003697)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(2)|ovary(2)|skin(1)	15		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0247)		ATGTGCAGTCGGCCAGGATAC	0.547								Nucleotide excision repair (NER)																													p.A192A		Atlas-SNP	.											.	ERCC1	46	.	0			c.C576A						.						77	63	68					19																	45920105		2203	4300	6503	SO:0001819	synonymous_variant	2067	exon6			GCAGTCGGCCAGG		CCDS12662.1, CCDS12663.1, CCDS54279.1	19q13.32	2014-03-07	2014-03-07			ENSG00000012061			3433	protein-coding gene	gene with protein product		126380	"excision repair cross-complementing rodent repair deficiency, complementation group 1 (includes overlapping antisense sequence)"			6462228	Standard	NM_001983		Approved	RAD10	uc002pbs.2	P07992		ENST00000300853.3:c.576C>A	chr19.hg19:g.45920105G>T		111.0	0.0		77.0	4.0	NM_001983	B2RC01|B3KRR0|Q7Z7F5|Q96S40	Silent	SNP	ENST00000300853.3	hg19	CCDS12662.1																																																																																			.	.		0.547	ERCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459542.1	NM_001983		T	45920105	G	T	45920105	2	4	254	1	0	0	0	0	0	0	0	1	5214	1103	39	1		1	ERCC1	19	45920105	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	48165	45920105	13208878	953	35245										
PPM1N	147699	hgsc.bcm.edu	37	chr19	46003767	46003767	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgaacacagttttcaggactCtggcctcagaggacatccca	9	12	3	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:46003767C>A	ENST00000451287.2	+	3	1111	c.1111C>A	c.(1111-1113)Ctg>Atg	p.L371M	PPM1N_ENST00000396736.2_Missense_Mutation_p.L53M|PPM1N_ENST00000456399.2_Missense_Mutation_p.L53M|PPM1N_ENST00000396737.2_Missense_Mutation_p.L53M|PPM1N_ENST00000396735.2_Missense_Mutation_p.L53M|PPM1N_ENST00000401593.1_Missense_Mutation_p.L53M|PPM1N_ENST00000401705.1_Missense_Mutation_p.L53M|PPM1N_ENST00000324688.4_3'UTR	NM_001080401.1	NP_001073870.1	Q8N819	PPM1N_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1N (putative)	371							magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoprotein phosphatase activity (GO:0004721)			NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)	9						TTTCAGGACTCTGGCCTCAGA	0.587																																					p.L371M		Atlas-SNP	.											.	PPM1N	25	.	0			c.C1111A						.						27	27	27					19																	46003767		1909	4119	6028	SO:0001583	missense	147699	exon3			AGGACTCTGGCCT	AK097444	CCDS46115.1	19q13.32	2012-04-17			ENSG00000213889	ENSG00000213889		"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	26845	protein-coding gene	gene with protein product							Standard	NM_001080401		Approved	FLJ40125	uc002pce.3	Q8N819	OTTHUMG00000140397	ENST00000451287.2:c.1111C>A	chr19.hg19:g.46003767C>A	ENSP00000397050:p.Leu371Met	108.0	0.0		91.0	4.0	NM_001080401	Q6P662	Missense_Mutation	SNP	ENST00000451287.2	hg19	CCDS46115.1	.	.	.	.	.	.	.	.	.	.	c	14.15	2.449375	0.43531	.	.	ENSG00000213889	ENST00000401705;ENST00000456399;ENST00000396737;ENST00000451287;ENST00000396734;ENST00000396735;ENST00000401593;ENST00000402807;ENST00000396736	T	0.38240	1.15	3.55	2.5	0.30297	Protein serine/threonine phosphatase 2C, C-terminal (3);	.	.	.	.	T	0.51839	0.1698	M	0.74258	2.255	0.80722	D	1	D	0.56287	0.975	D	0.67382	0.951	T	0.49409	-0.8943	9	0.45353	T	0.12	.	6.08	0.19936	0.0:0.7676:0.0:0.2324	.	371	Q8N819	PPM1N_HUMAN	M	53;53;53;371;371;53;53;53;53	ENSP00000397050:L371M	ENSP00000379960:L371M	L	+	1	2	PPM1N	50695607	0.332000	0.24722	1.000000	0.80357	0.807000	0.45602	0.735000	0.26115	1.077000	0.40990	0.651000	0.88453	CTG	.	.		0.587	PPM1N-007	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326517.2	NM_001080401		A	46003767	C	A	46003767	3	1	254	1	0	0	0	0	1	0	0	0	12358	912	32	3	1121	3	PPM1N	19	46003767	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	83662	46003767	13125216	954	35246										
MEIS3	56917	hgsc.bcm.edu	37	chr19	47920594	47920594	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccacgatgcctgggtagtgcGgcagctcatcatactggggg	15	11	2	0	rs200901098		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:47920594G>T	ENST00000558555.1	-	2	213	c.26C>A	c.(25-27)cCg>cAg	p.P9Q	MEIS3_ENST00000559524.1_Missense_Mutation_p.P9Q|MEIS3_ENST00000561096.1_Missense_Mutation_p.P97Q|MEIS3_ENST00000441740.2_Missense_Mutation_p.P9Q|MEIS3_ENST00000331559.5_Missense_Mutation_p.P9Q|MEIS3_ENST00000561293.1_Missense_Mutation_p.P9Q			Q99687	MEIS3_HUMAN	Meis homeobox 3	9					negative regulation of apoptotic signaling pathway (GO:2001234)|positive regulation of protein kinase B signaling (GO:0051897)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)			breast(1)|large_intestine(5)|lung(11)|prostate(1)|skin(2)	20		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;0.000198)|OV - Ovarian serous cystadenocarcinoma(262;0.000439)|Epithelial(262;0.0113)|GBM - Glioblastoma multiforme(486;0.0223)		TGGGTAGTGCGGCAGCTCATC	0.662																																					p.P9Q		Atlas-SNP	.											.	MEIS3	40	.	0			c.C26A						.						30	36	34					19																	47920594		2202	4299	6501	SO:0001583	missense	56917	exon2			TAGTGCGGCAGCT	BC025404	CCDS33064.1, CCDS46132.1, CCDS74406.1	19q13.32	2012-10-02	2007-02-15		ENSG00000105419	ENSG00000105419		"Homeoboxes / TALE class"	29537	protein-coding gene	gene with protein product			"Meis1, myeloid ecotropic viral integration site 1 homolog 3 (mouse)"			8950991	Standard	NM_020160		Approved	MRG2, DKFZp547H236	uc002pgt.4	Q99687	OTTHUMG00000172280	ENST00000558555.1:c.26C>A	chr19.hg19:g.47920594G>T	ENSP00000454073:p.Pro9Gln	121.0	0.0		99.0	4.0	NM_001009813	A8K1N5|Q6NT73|Q8TC66|Q9NPW2	Missense_Mutation	SNP	ENST00000558555.1	hg19		.	.	.	.	.	.	.	.	.	.	G	14.19	2.460721	0.43736	.	.	ENSG00000105419	ENST00000331559;ENST00000441740	T;T	0.34859	1.34;1.34	3.49	2.41	0.29592	.	0.442693	0.20577	N	0.089613	T	0.35364	0.0929	L	0.52573	1.65	0.24190	N	0.995559	B;B;D	0.55385	0.286;0.144;0.971	B;B;P	0.49597	0.155;0.091;0.616	T	0.15954	-1.0419	10	0.62326	D	0.03	-12.1835	4.7832	0.13213	0.1237:0.2398:0.6365:0.0	.	9;9;9	Q99687;Q99687-3;Q99687-2	MEIS3_HUMAN;.;.	Q	9	ENSP00000333552:P9Q;ENSP00000388667:P9Q	ENSP00000333552:P9Q	P	-	2	0	MEIS3	52612406	0.994000	0.37717	0.989000	0.46669	0.890000	0.51754	1.642000	0.37207	1.008000	0.39264	0.555000	0.69702	CCG	.	G|1.000;A|0.000		0.662	MEIS3-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000417642.1	XM_085929		T	47920594	G	T	47920594	3	4	254	1	0	0	0	0	1	0	0	0	9478	1116	39	1	1283	1	MEIS3	19	47920594	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1916827	47920594	11208389	955	35247										
GLTSCR2	29997	hgsc.bcm.edu	37	chr19	48259071	48259071	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agctgacagactcgctcaggAccctgaaggtgctcactgtg	12	12	2	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:48259071A>G	ENST00000246802.5	+	10	1326	c.1288A>G	c.(1288-1290)Acc>Gcc	p.T430A	SNORD23_ENST00000408876.1_RNA|GLTSCR2_ENST00000598681.1_Intron|CTD-2571L23.6_ENST00000602048.1_RNA	NM_015710.4	NP_056525.2	Q9NZM5	GSCR2_HUMAN	glioma tumor suppressor candidate region gene 2	430						intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	15		all_cancers(25;1.47e-06)|all_lung(116;6.89e-05)|all_epithelial(76;0.000108)|Lung NSC(112;0.000117)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000301)|OV - Ovarian serous cystadenocarcinoma(262;0.00031)|Epithelial(262;0.0149)|GBM - Glioblastoma multiforme(486;0.0278)		CTCGCTCAGGACCCTGAAGGT	0.642																																					p.T430A	Colon(58;613 1041 9473 10089 15241)	Atlas-SNP	.											.	GLTSCR2	45	.	0			c.A1288G						.						62	44	50					19																	48259071		2202	4299	6501	SO:0001583	missense	29997	exon10			CTCAGGACCCTGA	AF182076	CCDS12705.1	19q13.3	2014-01-20				ENSG00000105373			4333	protein-coding gene	gene with protein product		605691				10708517, 16971513, 17657248	Standard	NM_015710		Approved	PICT-1	uc002phm.2	Q9NZM5		ENST00000246802.5:c.1288A>G	chr19.hg19:g.48259071A>G	ENSP00000246802:p.Thr430Ala	134.0	0.0		94.0	4.0	NM_015710	Q9BTC6|Q9HAX6|Q9NPP1|Q9NPR4|Q9UFI2	Missense_Mutation	SNP	ENST00000246802.5	hg19	CCDS12705.1	.	.	.	.	.	.	.	.	.	.	A	7.565	0.665510	0.14710	.	.	ENSG00000105373	ENST00000246802;ENST00000325566;ENST00000446535	T	0.45668	0.89	5.09	4.08	0.47627	.	0.420791	0.25291	N	0.031725	T	0.40297	0.1111	M	0.76328	2.33	0.29348	N	0.865573	B	0.13145	0.007	B	0.12156	0.007	T	0.37596	-0.9699	10	0.36615	T	0.2	-16.0127	7.2814	0.26314	0.9014:0.0:0.0986:0.0	.	430	Q9NZM5	GSCR2_HUMAN	A	430;424;215	ENSP00000246802:T430A	ENSP00000246802:T430A	T	+	1	0	GLTSCR2	52950883	0.808000	0.29022	0.998000	0.56505	0.675000	0.39556	1.383000	0.34385	0.960000	0.38005	0.533000	0.62120	ACC	.	.		0.642	GLTSCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464870.1	NM_015710		G	48259071	A	G	48259071	3	3	254	1	0	0	0	0	1	0	0	0	6483	275	10	2	1326	2	GLTSCR2	19	48259071	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	338477	48259071	10869912	956	35248										
PLA2G4C	8605	hgsc.bcm.edu	37	chr19	48609797	48609797	+	5'UTR	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	accttcccatggtgcactgcGgtcagaaaattctcagtcct	8	13	2	1	rs570635333		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:48609797G>T	ENST00000599921.1	-	0	347				PLA2G4C_ENST00000599111.1_Silent_p.T17T|PLA2G4C_ENST00000354276.3_5'UTR|PLA2G4C_ENST00000413144.2_5'Flank			Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC (cytosolic, calcium-independent)						arachidonic acid metabolic process (GO:0019369)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|parturition (GO:0007567)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(12)|lung(13)|ovary(2)|prostate(1)|skin(3)	38		all_cancers(25;2.84e-05)|all_lung(116;4.62e-05)|Lung NSC(112;7.61e-05)|all_epithelial(76;0.000192)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;8.09e-05)|all cancers(93;0.000517)|Epithelial(262;0.0135)|GBM - Glioblastoma multiforme(486;0.0717)		GGTGCACTGCGGTCAGAAAAT	0.517													g|||	1	0.000199681	8e-04	0	5008	,	,		18239	0		0	False		,,,				2504	0				p.T17T		Atlas-SNP	.											.	PLA2G4C	76	.	0			c.C51A						.						157	130	140					19																	48609797		2203	4300	6503	SO:0001623	5_prime_UTR_variant	8605	exon2			CACTGCGGTCAGA	AF065214	CCDS12710.1, CCDS54286.1, CCDS59403.1	19q13.3	2008-09-19					3.1.1.4		9037	protein-coding gene	gene with protein product		603602				9705332	Standard	NM_003706		Approved	cPLA2-gamma	uc002phx.3	Q9UP65		ENST00000599921.1:c.-11C>A	chr19.hg19:g.48609797G>T		200.0	0.0		121.0	5.0	NM_001159322	B2RB71|B4DI40|O75457|Q6IBI8|Q9UG68	Silent	SNP	ENST00000599921.1	hg19	CCDS12710.1																																																																																			.	.		0.517	PLA2G4C-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465551.1			T	48609797	G	T	48609797	1	4	254	0	1	0	0	0	0	0	0	0	12012	1103	39	1		1	PLA2G4C	19	48609797	5'UTR	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	350726	48609797	10519186	957	35249										
PPFIA3	8541	hgsc.bcm.edu	37	chr19	49632641	49632641	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctgccccgatccccaggtccGggagcggctgcggatggcgc	16	16	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:49632641G>T	ENST00000334186.4	+	5	861	c.512G>T	c.(511-513)cGg>cTg	p.R171L	PPFIA3_ENST00000602351.1_Missense_Mutation_p.R171L	NM_003660.2	NP_003651.1	O75145	LIPA3_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 3	171					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|presynaptic active zone (GO:0048786)				NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(16)|pancreas(1)|prostate(1)|skin(4)|urinary_tract(1)	35		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.36e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000203)|GBM - Glioblastoma multiforme(486;0.00307)|Epithelial(262;0.00677)		CCCCAGGTCCGGGAGCGGCTG	0.622																																					p.R171L		Atlas-SNP	.											.	PPFIA3	71	.	0			c.G512T						.						8	10	9					19																	49632641		2110	4138	6248	SO:0001583	missense	8541	exon5			AGGTCCGGGAGCG	AF034800	CCDS12758.1	19q13.33	2013-09-23			ENSG00000177380	ENSG00000177380		"Sterile alpha motif (SAM) domain containing"	9247	protein-coding gene	gene with protein product	"protein tyrosine phosphatase, receptor type, f polypeptide, alpha 3", "liprin-alpha 3", "liprin"	603144				9624153, 9734811	Standard	NM_003660		Approved	KIAA0654, LPNA3, MGC126567, MGC126569	uc002pmr.3	O75145	OTTHUMG00000183213	ENST00000334186.4:c.512G>T	chr19.hg19:g.49632641G>T	ENSP00000335614:p.Arg171Leu	133.0	0.0		113.0	5.0	NM_003660	A8K142|Q3MJA0|Q9H8B5|Q9UEW4	Missense_Mutation	SNP	ENST00000334186.4	hg19	CCDS12758.1	.	.	.	.	.	.	.	.	.	.	G	36	5.735724	0.96865	.	.	ENSG00000177380	ENST00000334186;ENST00000421230	T	0.55588	0.51	4.56	4.56	0.56223	.	0.000000	0.43579	D	0.000551	T	0.74045	0.3665	M	0.83312	2.635	0.80722	D	1	D;P;D	0.76494	0.982;0.865;0.999	P;P;D	0.71656	0.869;0.673;0.974	T	0.79009	-0.1978	10	0.87932	D	0	-21.0017	16.6387	0.85066	0.0:0.0:1.0:0.0	.	95;171;171	B4DEU8;O75145-2;O75145	.;.;LIPA3_HUMAN	L	171;95	ENSP00000335614:R171L	ENSP00000335614:R171L	R	+	2	0	PPFIA3	54324453	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.670000	0.74467	2.563000	0.86464	0.561000	0.74099	CGG	.	.		0.622	PPFIA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465688.1	NM_003660		T	49632641	G	T	49632641	3	4	254	1	0	0	0	0	1	0	0	0	12320	1116	39	1	526	1	PPFIA3	19	49632641	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1022844	49632641	9496342	958	35250										
RPL13A	23521	hgsc.bcm.edu	37	chr19	49994320	49994320	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aagcggatggtggttcctgcTgccctcaaggtcgtgcgtct	14	11	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:49994320T>C	ENST00000391857.4	+	6	442	c.366T>C	c.(364-366)gcT>gcC	p.A122A	SNORD32A_ENST00000364805.1_RNA|RPL13A_ENST00000477613.2_3'UTR|SNORD34_ENST00000365633.1_RNA|SNORD35A_ENST00000363389.1_RNA|SNORD33_ENST00000362761.1_RNA	NM_001270491.1|NM_012423.3	NP_001257420.1|NP_036555.1	P40429	RL13A_HUMAN	ribosomal protein L13a	122					cellular protein metabolic process (GO:0044267)|cellular response to interferon-gamma (GO:0071346)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|negative regulation of formation of translation preinitiation complex (GO:1901194)|negative regulation of translation (GO:0017148)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|focal adhesion (GO:0005925)|GAIT complex (GO:0097452)|large ribosomal subunit (GO:0015934)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			cervix(1)|endometrium(1)	2		all_lung(116;1.62e-07)|Lung NSC(112;8.47e-07)|all_neural(266;0.0381)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00154)|GBM - Glioblastoma multiforme(486;0.0246)		TGGTTCCTGCTGCCCTCAAGG	0.582																																					p.A122A		Atlas-SNP	.											.	RPL13A	13	.	0			c.T366C						.						55	52	53					19																	49994320		2203	4300	6503	SO:0001819	synonymous_variant	23521	exon6			TCCTGCTGCCCTC	X56932	CCDS12768.1, CCDS74421.1	19q13.3	2011-04-06			ENSG00000142541	ENSG00000142541		"L ribosomal proteins"	10304	protein-coding gene	gene with protein product			"tissue specific transplantation antigen 1"	TSTA1			Standard	NM_012423		Approved	L13A	uc031rlt.1	P40429	OTTHUMG00000134289	ENST00000391857.4:c.366T>C	chr19.hg19:g.49994320T>C		100.0	0.0		85.0	4.0	NM_012423	A8K505	Silent	SNP	ENST00000391857.4	hg19	CCDS12768.1																																																																																			.	.		0.582	RPL13A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258989.1			C	49994320	T	C	49994320	2	2	254	1	0	0	0	0	0	0	0	1	13575	1567	55	2		2	RPL13A	19	49994320	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	361679	49994320	9134663	959	35251										
MYH14	79784	hgsc.bcm.edu	37	chr19	50792838	50792838	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgtgcaggctctcaagactcAgcatgagcgtgacctgcagg	13	11	2	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:50792838A>G	ENST00000596571.1	+	32	4775	c.4775A>G	c.(4774-4776)cAg>cGg	p.Q1592R	MYH14_ENST00000425460.1_Missense_Mutation_p.Q1600R|MYH14_ENST00000376970.2_Missense_Mutation_p.Q1625R|MYH14_ENST00000601313.1_Missense_Mutation_p.Q1633R|MYH14_ENST00000440075.2_Missense_Mutation_p.Q1633R|MYH14_ENST00000262269.8_Missense_Mutation_p.Q1633R|MYH14_ENST00000598205.1_Missense_Mutation_p.Q1600R			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	1592					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		CTCAAGACTCAGCATGAGCGT	0.597																																					p.Q1633R		Atlas-SNP	.											.	MYH14	261	.	0			c.A4898G						.						49	60	56					19																	50792838		2194	4294	6488	SO:0001583	missense	79784	exon35			AGACTCAGCATGA	AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"Myosins / Myosin superfamily : Class II"	23212	protein-coding gene	gene with protein product		608568	"myosin, heavy polypeptide 14", "myosin, heavy chain 14"	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.4775A>G	chr19.hg19:g.50792838A>G	ENSP00000472819:p.Gln1592Arg	82.0	0.0		70.0	4.0	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Missense_Mutation	SNP	ENST00000596571.1	hg19	CCDS59411.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.070818	0.76301	.	.	ENSG00000105357	ENST00000440075;ENST00000376970;ENST00000425460;ENST00000376965;ENST00000262269	T;T;T;T	0.78481	-1.18;-1.18;-1.18;-1.18	3.95	3.95	0.45737	Myosin tail (1);	.	.	.	.	D	0.85217	0.5646	M	0.67625	2.065	0.47374	D	0.999401	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.91635	0.998;0.999;0.999	D	0.86385	0.1732	9	0.87932	D	0	.	11.0935	0.48130	1.0:0.0:0.0:0.0	.	1633;1592;1600	Q7Z406-2;Q7Z406;Q7Z406-6	.;MYH14_HUMAN;.	R	1633;1625;1600;1376;1633	ENSP00000406273:Q1633R;ENSP00000366169:Q1625R;ENSP00000407879:Q1600R;ENSP00000262269:Q1633R	ENSP00000262269:Q1633R	Q	+	2	0	MYH14	55484650	1.000000	0.71417	0.763000	0.31416	0.971000	0.66376	8.881000	0.92415	1.800000	0.52685	0.402000	0.26972	CAG	.	.		0.597	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729		G	50792838	A	G	50792838	3	3	254	1	0	0	0	0	1	0	0	0	10042	188	7	2	5032	2	MYH14	19	50792838	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	798518	50792838	8336145	960	35252										
MYH14	79784	hgsc.bcm.edu	37	chr19	50794172	50794172	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgcagaggtggagcgggatgAggagcggaagcagcgcactc	19	8	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:50794172A>G	ENST00000596571.1	+	33	4871	c.4871A>G	c.(4870-4872)gAg>gGg	p.E1624G	MYH14_ENST00000425460.1_Missense_Mutation_p.E1632G|MYH14_ENST00000376970.2_Missense_Mutation_p.E1657G|MYH14_ENST00000601313.1_Missense_Mutation_p.E1665G|MYH14_ENST00000440075.2_Missense_Mutation_p.E1665G|MYH14_ENST00000262269.8_Missense_Mutation_p.E1665G|MYH14_ENST00000598205.1_Missense_Mutation_p.E1632G			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	1624					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		GAGCGGGATGAGGAGCGGAAG	0.652																																					p.E1665G		Atlas-SNP	.											.	MYH14	261	.	0			c.A4994G						.						17	22	21					19																	50794172		2064	4191	6255	SO:0001583	missense	79784	exon36			GGGATGAGGAGCG	AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"Myosins / Myosin superfamily : Class II"	23212	protein-coding gene	gene with protein product		608568	"myosin, heavy polypeptide 14", "myosin, heavy chain 14"	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.4871A>G	chr19.hg19:g.50794172A>G	ENSP00000472819:p.Glu1624Gly	151.0	0.0		99.0	4.0	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Missense_Mutation	SNP	ENST00000596571.1	hg19	CCDS59411.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.127735	0.77549	.	.	ENSG00000105357	ENST00000440075;ENST00000376970;ENST00000425460;ENST00000376965;ENST00000262269	D;D;D;D	0.86627	-2.15;-2.15;-2.15;-2.15	4.42	4.42	0.53409	Myosin tail (1);	.	.	.	.	D	0.89962	0.6867	M	0.65975	2.015	0.47994	D	0.999561	D;P;P	0.54964	0.969;0.763;0.721	P;P;B	0.56960	0.81;0.507;0.373	D	0.89650	0.3869	9	0.45353	T	0.12	.	11.9119	0.52743	1.0:0.0:0.0:0.0	.	1665;1624;1632	Q7Z406-2;Q7Z406;Q7Z406-6	.;MYH14_HUMAN;.	G	1665;1657;1632;1408;1665	ENSP00000406273:E1665G;ENSP00000366169:E1657G;ENSP00000407879:E1632G;ENSP00000262269:E1665G	ENSP00000262269:E1665G	E	+	2	0	MYH14	55485984	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	5.644000	0.67902	1.979000	0.57680	0.402000	0.26972	GAG	.	.		0.652	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729		G	50794172	A	G	50794172	3	3	254	1	0	0	0	0	1	0	0	0	10042	304	11	2	5132	2	MYH14	19	50794172	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	1334	50794172	8334811	961	35253										
KLK7	5650	hgsc.bcm.edu	37	chr19	51485084	51485084	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gaccaggacgcctccgcagtGgagctgattgccactgagca	13	13	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:51485084G>A	ENST00000391807.1	-	3	261	c.160C>T	c.(160-162)Cac>Tac	p.H54Y	KLK7_ENST00000595820.1_Missense_Mutation_p.H54Y|KLK7_ENST00000597707.1_5'UTR|CTB-147C22.9_ENST00000594512.1_RNA|KLK7_ENST00000336317.4_Intron|KLK7_ENST00000595638.1_5'Flank	NM_139277.2	NP_644806.1	P49862	KLK7_HUMAN	kallikrein-related peptidase 7	54	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(11)|ovary(2)	19		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00382)|GBM - Glioblastoma multiforme(134;0.00895)		CCTCCGCAGTGGAGCTGATTG	0.617																																					p.H54Y		Atlas-SNP	.											.	KLK7	40	.	0			c.C160T						.						43	38	39					19																	51485084		2203	4300	6503	SO:0001583	missense	5650	exon3			CGCAGTGGAGCTG	L33404	CCDS12812.1, CCDS59414.1	19q13.33	2011-09-07	2006-10-27			ENSG00000169035		"Kallikreins", "Serine peptidases / Serine peptidases"	6368	protein-coding gene	gene with protein product		604438	"kallikrein 7 (chymotryptic, stratum corneum)"	PRSS6		8034709, 16800724, 16800723	Standard	NM_005046		Approved	SCCE	uc021uyj.1	P49862		ENST00000391807.1:c.160C>T	chr19.hg19:g.51485084G>A	ENSP00000375683:p.His54Tyr	136.0	0.0		54.0	4.0	NM_139277	A8K0U5|Q8N5N9|Q8NFV7	Missense_Mutation	SNP	ENST00000391807.1	hg19	CCDS12812.1	.	.	.	.	.	.	.	.	.	.	g	4.683	0.127019	0.08931	.	.	ENSG00000169035	ENST00000304045;ENST00000391807	D	0.88354	-2.37	4.39	2.22	0.28083	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.225297	0.22369	U	0.060966	T	0.79185	0.4403	N	0.13235	0.315	0.53688	D	0.999978	B	0.27656	0.184	B	0.32393	0.145	T	0.71477	-0.4581	10	0.54805	T	0.06	.	8.5579	0.33492	0.1963:0.0:0.8037:0.0	.	54	P49862	KLK7_HUMAN	Y	54	ENSP00000375683:H54Y	ENSP00000304791:H54Y	H	-	1	0	KLK7	56176896	0.916000	0.31088	0.007000	0.13788	0.037000	0.13140	1.203000	0.32284	0.324000	0.23333	0.552000	0.68991	CAC	.	.		0.617	KLK7-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464344.1	NM_005046		A	51485084	G	A	51485084	3	1	254	1	0	0	0	0	1	0	0	0	8418	1348	47	3	617	3	KLK7	19	51485084	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	690912	51485084	7643899	962	35254										
KLK9	284366	hgsc.bcm.edu	37	chr19	51506518	51506518	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gggggcccccagagtcacccTgtacgcgagagaagggcaga	16	12	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:51506518T>C	ENST00000594211.1	-	5	604		c.e5-2		KLK8_ENST00000391806.2_5'Flank|KLK8_ENST00000320838.5_5'Flank|KLK8_ENST00000347619.4_5'Flank|KLK8_ENST00000593490.1_5'Flank|KLK9_ENST00000376832.4_Splice_Site|KLK9_ENST00000250366.6_Splice_Site|CTB-147C22.9_ENST00000594512.1_RNA|KLK8_ENST00000291726.7_5'Flank|KLK8_ENST00000600767.1_5'Flank			Q9UKQ9	KLK9_HUMAN	kallikrein-related peptidase 9							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|skin(1)	7		all_neural(266;0.0652)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00885)		AGAGTCACCCTGTACGCGAGA	0.632																																					.		Atlas-SNP	.											KLK9,colon,carcinoma,0,1	KLK9	27	.	0			c.604-2A>G						.						36	39	38					19																	51506518		2203	4300	6503	SO:0001630	splice_region_variant	284366	exon6			TCACCCTGTACGC	AF135026	CCDS12816.1	19q13.33	2008-02-05	2006-10-27					"Kallikreins"	6370	protein-coding gene	gene with protein product		605504	"kallikrein 9"			16800724, 16800723	Standard	NM_012315		Approved	KLK-L3	uc002pux.1	Q9UKQ9		ENST00000594211.1:c.604-2A>G	chr19.hg19:g.51506518T>C		55.0	0.0		35.0	2.0	NM_012315	Q6QA55	Splice_Site	SNP	ENST00000594211.1	hg19	CCDS12816.1	.	.	.	.	.	.	.	.	.	.	T	17.51	3.408344	0.62399	.	.	ENSG00000213022	ENST00000376832;ENST00000250366	.	.	.	4.71	4.71	0.59529	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.4408	0.55623	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	KLK9	56198330	1.000000	0.71417	0.995000	0.50966	0.781000	0.44180	6.068000	0.71201	2.099000	0.63709	0.459000	0.35465	.	.	.		0.632	KLK9-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465226.1	NM_012315	Intron	C	51506518	T	C	51506518	5	2	254	1	0	0	0	0	0	0	1	0	8420	1594	55	2	154	2	KLK9	19	51506518	Splice_Site	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	21434	51506518	7622465	963	35255										
ZNF841	284371	hgsc.bcm.edu	37	chr19	52569527	52569527	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	catttgtaaggtttctctccGgtatgaattctctgatgtac	8	8	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:52569527G>T	ENST00000426391.2	-	5	1811	c.1260C>A	c.(1258-1260)acC>acA	p.T420T	ZNF841_ENST00000594295.1_Silent_p.T536T|CTC-471J1.2_ENST00000569091.1_RNA|ZNF841_ENST00000389534.4_Silent_p.T536T|ZNF841_ENST00000359973.2_Intron|ZNF432_ENST00000598446.1_Intron			Q6ZN19	ZN841_HUMAN	zinc finger protein 841	420					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(3)|lung(3)	11						GTTTCTCTCCGGTATGAATTC	0.398																																					p.T536T		Atlas-SNP	.											.	ZNF841	183	.	0			c.C1608A						.						87	81	83					19																	52569527		692	1591	2283	SO:0001819	synonymous_variant	284371	exon7			CTCTCCGGTATGA	AK131409	CCDS46161.1	19q13.41	2013-01-08			ENSG00000197608	ENSG00000197608		"Zinc fingers, C2H2-type", "-"	27611	protein-coding gene	gene with protein product							Standard	NM_001136499		Approved	LOC284371	uc010ydh.1	Q6ZN19		ENST00000426391.2:c.1260C>A	chr19.hg19:g.52569527G>T		74.0	0.0		79.0	4.0	NM_001136499	B9EG58|Q6ZN82|Q6ZP71|Q8N9U7	Silent	SNP	ENST00000426391.2	hg19																																																																																				.	.		0.398	ZNF841-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000462435.1	XM_209155		T	52569527	G	T	52569527	2	4	254	1	0	0	0	0	0	0	0	1	18204	1103	39	1		1	ZNF841	19	52569527	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1063009	52569527	6559456	964	35256										
ZNF841	284371	hgsc.bcm.edu	37	chr19	52570470	52570470	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	caggaaaaattctttgaagtGgtgaagctaaaaaacaatta	8	4	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:52570470G>T	ENST00000426391.2	-	5	868	c.317C>A	c.(316-318)cCa>cAa	p.P106Q	ZNF841_ENST00000594295.1_Missense_Mutation_p.P222Q|ZNF841_ENST00000389534.4_Missense_Mutation_p.P222Q|ZNF841_ENST00000359973.2_Missense_Mutation_p.P106Q|ZNF432_ENST00000598446.1_Intron			Q6ZN19	ZN841_HUMAN	zinc finger protein 841	106					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(3)|lung(3)	11						TCTTTGAAGTGGTGAAGCTAA	0.353																																					p.P222Q		Atlas-SNP	.											.	ZNF841	183	.	0			c.C665A						.						81	63	69					19																	52570470		692	1591	2283	SO:0001583	missense	284371	exon7			TGAAGTGGTGAAG	AK131409	CCDS46161.1	19q13.41	2013-01-08			ENSG00000197608	ENSG00000197608		"Zinc fingers, C2H2-type", "-"	27611	protein-coding gene	gene with protein product							Standard	NM_001136499		Approved	LOC284371	uc010ydh.1	Q6ZN19		ENST00000426391.2:c.317C>A	chr19.hg19:g.52570470G>T	ENSP00000415453:p.Pro106Gln	103.0	0.0		76.0	4.0	NM_001136499	B9EG58|Q6ZN82|Q6ZP71|Q8N9U7	Missense_Mutation	SNP	ENST00000426391.2	hg19		.	.	.	.	.	.	.	.	.	.	G	1.875	-0.459228	0.04508	.	.	ENSG00000197608	ENST00000389534;ENST00000426391;ENST00000359973	T;T;T	0.08370	3.51;3.33;3.1	1.74	0.511	0.16989	.	.	.	.	.	T	0.04679	0.0127	N	0.00869	-1.13	0.09310	N	1	D;P;D	0.76494	0.999;0.946;0.998	D;P;D	0.83275	0.996;0.654;0.987	T	0.29701	-1.0003	9	0.10636	T	0.68	.	1.9647	0.03393	0.2407:0.0:0.4599:0.2994	.	222;106;106	Q6ZN19-3;Q6ZN19-2;Q6ZN19	.;.;ZN841_HUMAN	Q	222;106;106	ENSP00000374185:P222Q;ENSP00000415453:P106Q;ENSP00000353060:P106Q	ENSP00000353060:P106Q	P	-	2	0	ZNF841	57262282	0.001000	0.12720	0.016000	0.15963	0.322000	0.28314	-0.184000	0.09698	0.195000	0.20347	0.313000	0.20887	CCA	.	.		0.353	ZNF841-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000462435.1	XM_209155		T	52570470	G	T	52570470	3	4	254	1	0	0	0	0	1	0	0	0	18204	1348	47	3	2113	3	ZNF841	19	52570470	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	943	52570470	6558513	965	35257										
ZNF460	10794	hgsc.bcm.edu	37	chr19	57802158	57802158	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	caggaacagctggcacagggAgtcccaagatactcctattt	10	11	0	1	rs368592252		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:57802158A>G	ENST00000360338.3	+	3	571	c.249A>G	c.(247-249)ggA>ggG	p.G83G	ZNF460_ENST00000537645.1_Silent_p.G42G	NM_006635.3	NP_006626.3	Q14592	ZN460_HUMAN	zinc finger protein 460	83	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TGGCACAGGGAGTCCCAAGAT	0.527																																					p.G83G		Atlas-SNP	.											.	ZNF460	59	.	0			c.A249G						.	A		0,4406		0,0,2203	73	69	70		249	-0.4	0	19		70	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ZNF460	NM_006635.3		0,1,6502	GG,GA,AA		0.0116,0.0,0.0077		83/563	57802158	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	10794	exon3			ACAGGGAGTCCCA	X78931	CCDS12949.1	19q13.4	2013-01-08				ENSG00000197714		"Zinc fingers, C2H2-type", "-"	21628	protein-coding gene	gene with protein product		604755	"zinc finger protein 272"	ZNF272		15004467	Standard	NM_006635		Approved	HZF8	uc002qog.2	Q14592		ENST00000360338.3:c.249A>G	chr19.hg19:g.57802158A>G		111.0	0.0		80.0	4.0	NM_006635	A4FU64|B4DNX9|Q2VPC7|Q6VSF8	Silent	SNP	ENST00000360338.3	hg19	CCDS12949.1																																																																																			.	.		0.527	ZNF460-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465727.1	NM_006635		G	57802158	A	G	57802158	2	3	254	1	0	0	0	0	0	0	0	1	17939	291	11	2		2	ZNF460	19	57802158	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	5231688	57802158	1326825	966	35258										
ZNF418	147686	hgsc.bcm.edu	37	chr19	58438656	58438656	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gatgctgaacaaggctgcccTtatgactaaaagatttccca	8	10	0	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:58438656T>C	ENST00000396147.1	-	4	1184	c.893A>G	c.(892-894)aAg>aGg	p.K298R	ZNF418_ENST00000599852.1_Missense_Mutation_p.K213R|ZNF418_ENST00000600989.1_Intron|ZNF418_ENST00000425570.3_Missense_Mutation_p.K319R|ZNF418_ENST00000599086.1_5'Flank|ZNF418_ENST00000595830.1_Missense_Mutation_p.K298R	NM_133460.1	NP_597717.1	Q8TF45	ZN418_HUMAN	zinc finger protein 418	298					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	31		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0158)		AAGGCTGCCCTTATGACTAAA	0.408																																					p.K298R		Atlas-SNP	.											.	ZNF418	76	.	0			c.A893G						.						87	92	90					19																	58438656		2195	4300	6495	SO:0001583	missense	147686	exon4			CTGCCCTTATGAC	AB075836, AY695825	CCDS42642.1	19q13.43	2013-01-08				ENSG00000196724		"Zinc fingers, C2H2-type", "-"	20647	protein-coding gene	gene with protein product						11853319	Standard	NM_133460		Approved	KIAA1956, FLJ31551	uc002qqs.1	Q8TF45		ENST00000396147.1:c.893A>G	chr19.hg19:g.58438656T>C	ENSP00000379451:p.Lys298Arg	117.0	0.0		100.0	4.0	NM_133460	Q2M1S2|Q670L5|Q96N18	Missense_Mutation	SNP	ENST00000396147.1	hg19	CCDS42642.1	.	.	.	.	.	.	.	.	.	.	.	7.945	0.743538	0.15642	.	.	ENSG00000196724	ENST00000396147;ENST00000425570;ENST00000545403	T;T	0.12879	2.64;2.64	2.47	-3.22	0.05125	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.15262	0.0368	L	0.31371	0.925	0.09310	N	1	P	0.48911	0.917	P	0.61132	0.884	T	0.13469	-1.0508	9	0.08599	T	0.76	.	8.7265	0.34471	0.0:0.485:0.0:0.515	.	298	Q8TF45	ZN418_HUMAN	R	298;319;264	ENSP00000379451:K298R;ENSP00000407039:K319R	ENSP00000379451:K298R	K	-	2	0	ZNF418	63130468	.	.	0.000000	0.03702	0.001000	0.01503	.	.	-0.711000	0.04995	0.254000	0.18369	AAG	.	.		0.408	ZNF418-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466693.1	NM_133460		C	58438656	T	C	58438656	3	2	254	1	0	0	0	0	1	0	0	0	17910	1609	56	2	1141	2	ZNF418	19	58438656	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	636498	58438656	690327	967	35259										
ZSCAN1	284312	hgsc.bcm.edu	37	chr19	58565111	58565111	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcttcacctgggtcacccacTtcatcgagcaccagaagacc	7	16	4	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:58565111T>C	ENST00000282326.1	+	6	1166	c.919T>C	c.(919-921)Ttc>Ctc	p.F307L		NM_182572.3	NP_872378.3	Q8NBB4	ZSCA1_HUMAN	zinc finger and SCAN domain containing 1	307					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)		GGTCACCCACTTCATCGAGCA	0.632																																					p.F307L		Atlas-SNP	.											ZSCAN1,right_upper_lobe,carcinoma,0,1	ZSCAN1	102	.	0			c.T919C						.						75	66	69					19																	58565111		2203	4300	6503	SO:0001583	missense	284312	exon6			ACCCACTTCATCG	AK091098	CCDS12969.1	19q13.43	2013-06-13	2004-04-21		ENSG00000152467	ENSG00000152467		"-", "Zinc fingers, C2H2-type"	23712	protein-coding gene	gene with protein product			"zinc finger with SCAN domain 1"			12477932	Standard	NM_182572		Approved	FLJ33779, ZNF915	uc002qrc.1	Q8NBB4	OTTHUMG00000183381	ENST00000282326.1:c.919T>C	chr19.hg19:g.58565111T>C	ENSP00000282326:p.Phe307Leu	88.0	0.0		73.0	3.0	NM_182572	Q3B798|Q6WLH8|Q86WS8	Missense_Mutation	SNP	ENST00000282326.1	hg19	CCDS12969.1	.	.	.	.	.	.	.	.	.	.	T	1.923	-0.447795	0.04572	.	.	ENSG00000152467	ENST00000282326	T	0.17854	2.25	1.38	-0.848	0.10727	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02230	0.0069	N	0.00121	-2.07	0.45318	D	0.998317	B	0.33883	0.43	B	0.33454	0.164	T	0.41106	-0.9527	9	0.02654	T	1	.	5.9707	0.19351	0.0:0.611:0.0:0.389	.	307	Q8NBB4	ZSCA1_HUMAN	L	307	ENSP00000282326:F307L	ENSP00000282326:F307L	F	+	1	0	ZSCAN1	63256923	0.007000	0.16637	0.004000	0.12327	0.030000	0.12068	-0.226000	0.09139	-0.363000	0.08101	-0.415000	0.06103	TTC	.	.		0.632	ZSCAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466427.1	NM_182572		C	58565111	T	C	58565111	3	2	254	1	0	0	0	0	1	0	0	0	18241	1609	56	2	933	2	ZSCAN1	19	58565111	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	126455	58565111	563872	968	35260										
ZNF132	7691	hgsc.bcm.edu	37	chr19	58945140	58945140	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	actctccagtgttcaatgagAgtggagctgtgagcaaaggc	13	8	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:58945140A>G	ENST00000254166.3	-	3	2071	c.1671T>C	c.(1669-1671)acT>acC	p.T557T	CTD-2619J13.17_ENST00000594816.1_lincRNA	NM_003433.3	NP_003424.3	P52740	ZN132_HUMAN	zinc finger protein 132	557					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(1)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0171)|Lung(386;0.182)		GTTCAATGAGAGTGGAGCTGT	0.458																																					p.T557T		Atlas-SNP	.											.	ZNF132	56	.	0			c.T1671C						.						90	90	90					19																	58945140		2203	4300	6503	SO:0001819	synonymous_variant	7691	exon3			AATGAGAGTGGAG	U09411	CCDS12980.1	19q13.4	2013-01-08	2006-06-13			ENSG00000131849		"Zinc fingers, C2H2-type", "-"	12916	protein-coding gene	gene with protein product		604074	"zinc finger protein 132 (clone pHZ-12)"			7557990	Standard	NM_003433		Approved	pHZ-12	uc002qst.4	P52740		ENST00000254166.3:c.1671T>C	chr19.hg19:g.58945140A>G		166.0	0.0		91.0	4.0	NM_003433	Q32MI9	Silent	SNP	ENST00000254166.3	hg19	CCDS12980.1																																																																																			.	.		0.458	ZNF132-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467035.1	NM_003433		G	58945140	A	G	58945140	2	3	254	1	0	0	0	0	0	0	0	1	17737	291	11	2		2	ZNF132	19	58945140	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	380029	58945140	183843	969	35261										
ZNF446	55663	hgsc.bcm.edu	37	chr19	58988926	58988926	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ccctgggcaactgttgggctGggtgagtgtggctggcatca	17	9	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr19:58988926G>T	ENST00000594369.1	+	2	722	c.341G>T	c.(340-342)tGg>tTg	p.W114L	ZNF446_ENST00000596341.1_Splice_Site_p.W114L|ZNF446_ENST00000335841.4_Splice_Site_p.W114L|CTD-2619J13.23_ENST00000598051.1_RNA	NM_017908.2	NP_060378.1	Q9NWS9	ZN446_HUMAN	zinc finger protein 446	114					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	extracellular space (GO:0005615)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	8		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)		CTGTTGGGCTGGGTGAGTGTG	0.612																																					p.W114L		Atlas-SNP	.											.	ZNF446	22	.	0			c.G341T						.						54	53	53					19																	58988926		2203	4300	6503	SO:0001630	splice_region_variant	55663	exon2			TGGGCTGGGTGAG		CCDS12982.1	19q13.43	2013-01-09				ENSG00000083838		"Zinc fingers, C2H2-type", "-", "-", "-"	21036	protein-coding gene	gene with protein product							Standard	NM_017908		Approved	ZKSCAN20, FLJ20626, ZSCAN52	uc002qsz.3	Q9NWS9		ENST00000594369.1:c.342+1G>T	chr19.hg19:g.58988926G>T		105.0	0.0		90.0	4.0	NM_017908		Missense_Mutation	SNP	ENST00000594369.1	hg19	CCDS12982.1	.	.	.	.	.	.	.	.	.	.	G	17.89	3.500718	0.64298	.	.	ENSG00000083838	ENST00000335841;ENST00000540481;ENST00000539679	T	0.05081	3.5	4.35	4.35	0.52113	Transcription regulator SCAN (1);	0.000000	0.33591	N	0.004752	T	0.13500	0.0327	L	0.27053	0.805	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.995	D;D;P	0.91635	0.999;0.961;0.791	T	0.05099	-1.0906	10	0.42905	T	0.14	-25.7239	13.0913	0.59167	0.0:0.0:1.0:0.0	.	114;114;114	F5H201;Q96AF5;Q9NWS9	.;.;ZN446_HUMAN	L	114	ENSP00000336565:W114L	ENSP00000336565:W114L	W	+	2	0	ZNF446	63680738	0.999000	0.42202	1.000000	0.80357	0.677000	0.39632	2.328000	0.43867	2.360000	0.80028	0.491000	0.48974	TGG	.	.		0.612	ZNF446-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467052.1	NM_017908	Missense_Mutation	T	58988926	G	T	58988926	5	4	254	1	0	0	0	0	0	0	1	0	17934	1362	47	3	343	3	ZNF446	19	58988926	Splice_Site	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	43786	58988926	140057	970	35262										
RBCK1	10616	hgsc.bcm.edu	37	chr20	400215	400215	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctcccaggtgggctggcagtGccccgggtgcaccttcatca	13	15	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:400215G>A	ENST00000356286.5	+	6	1301	c.596G>A	c.(595-597)tGc>tAc	p.C199Y	RBCK1_ENST00000353660.3_Missense_Mutation_p.C157Y|RBCK1_ENST00000382181.2_Missense_Mutation_p.A83T	NM_031229.2	NP_112506.2	Q9BYM8	HOIL1_HUMAN	RanBP-type and C3HC4-type zinc finger containing 1	199	Interaction with IRF3.|Interaction with TAB2.				negative regulation of necroptotic process (GO:0060546)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein linear polyubiquitination (GO:0097039)|protein polyubiquitination (GO:0000209)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	LUBAC complex (GO:0071797)	ligase activity (GO:0016874)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			kidney(1)|lung(4)	5		all_epithelial(17;0.172)|Lung NSC(37;0.191)|Breast(17;0.231)				GGCTGGCAGTGCCCCGGGTGC	0.677																																					p.C199Y		Atlas-SNP	.											.	RBCK1	38	.	0			c.G596A						.						23	22	22					20																	400215		2197	4299	6496	SO:0001583	missense	10616	exon6			GGCAGTGCCCCGG	U67322	CCDS12998.1, CCDS13000.2	20p13	2014-09-17	2006-06-28	2006-06-28	ENSG00000125826	ENSG00000125826		"RING-type (C3HC4) zinc fingers", "Zinc fingers, RAN-binding domain containing"	15864	protein-coding gene	gene with protein product	"heme-oxidized IRP2 ubiquitin ligase 1"	610924	"chromosome 20 open reading frame 18"	C20orf18			Standard	NM_031229		Approved	RBCK2, XAP4, RNF54, ZRANB4, UBCE7IP3, HOIL1	uc002wdp.4	Q9BYM8	OTTHUMG00000031634	ENST00000356286.5:c.596G>A	chr20.hg19:g.400215G>A	ENSP00000348632:p.Cys199Tyr	95.0	0.0		61.0	4.0	NM_031229	O95623|Q86SL2|Q96BS3|Q9BYM9	Missense_Mutation	SNP	ENST00000356286.5	hg19	CCDS13000.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.46|18.46	3.629185|3.629185	0.67015|0.67015	.|.	.|.	ENSG00000125826|ENSG00000125826	ENST00000382181;ENST00000414880|ENST00000356286;ENST00000353660;ENST00000400244;ENST00000400243	T|T;T	0.53423|0.73681	0.62|-0.77;-0.77	4.94|4.94	4.94|4.94	0.65067|0.65067	.|Zinc finger, RanBP2-type (3);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.85682|0.85682	0.5753|0.5753	M|M	0.76170|0.76170	2.325|2.325	0.80722|0.80722	D|D	1|1	D|D;D;D	0.76494|0.89917	0.999|1.0;1.0;1.0	P|D;D;D	0.58520|0.97110	0.84|0.999;1.0;0.999	D|D	0.87476|0.87476	0.2417|0.2417	9|10	0.62326|0.87932	D|D	0.03|0	-0.394|-0.394	16.0103|16.0103	0.80399|0.80399	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	83|189;157;199	A6PVK0|B4E0F5;Q9BYM8-3;Q9BYM8	.|.;.;HOIL1_HUMAN	T|Y	83;232|199;157;199;240	ENSP00000371616:A83T|ENSP00000348632:C199Y;ENSP00000254960:C157Y	ENSP00000371616:A83T|ENSP00000254960:C157Y	A|C	+|+	1|2	0|0	RBCK1|RBCK1	348215|348215	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	9.410000|9.410000	0.97335|0.97335	2.445000|2.445000	0.82738|0.82738	0.462000|0.462000	0.41574|0.41574	GCC|TGC	.	.		0.677	RBCK1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077461.3	NM_031229		A	400215	G	A	400215	3	1	254	1	0	0	0	0	1	0	0	0	13122	1319	46	3	637	3	RBCK1	20	400215	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10		400215	62625305	971	35263										
C20orf141	128653	hgsc.bcm.edu	37	chr20	2796266	2796266	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtgaaggtcctggacagcagGaggctctactcctgcaaatg	13	10	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:2796266G>T	ENST00000380589.4	+	2	517	c.343G>T	c.(343-345)Gag>Tag	p.E115*	TMEM239_ENST00000554164.1_Intron|TMEM239_ENST00000361033.1_5'Flank|TMEM239_ENST00000380593.4_Intron|C20orf141_ENST00000603872.1_Nonsense_Mutation_p.E115*|TMEM239_ENST00000380585.1_5'Flank	NM_080739.2	NP_542777.1	Q9NUB4	CT141_HUMAN	chromosome 20 open reading frame 141	115	Leu-rich.					integral component of membrane (GO:0016021)				endometrium(4)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)	10						TGGACAGCAGGAGGCTCTACT	0.632																																					p.E115X		Atlas-SNP	.											.	C20orf141	21	.	0			c.G343T						.						51	49	50					20																	2796266		2203	4300	6503	SO:0001587	stop_gained	128653	exon2			CAGCAGGAGGCTC		CCDS13034.1	20p13	2012-10-30			ENSG00000258713	ENSG00000258713			16134	protein-coding gene	gene with protein product							Standard	NM_001256538		Approved	dJ860F19.4	uc002wgw.3	Q9NUB4	OTTHUMG00000031707	ENST00000380589.4:c.343G>T	chr20.hg19:g.2796266G>T	ENSP00000369963:p.Glu115*	120.0	0.0		90.0	4.0	NM_080739		Nonsense_Mutation	SNP	ENST00000380589.4	hg19	CCDS13034.1	.	.	.	.	.	.	.	.	.	.	G	19.97	3.925051	0.73213	.	.	ENSG00000258713	ENST00000380589	.	.	.	4.43	3.43	0.39272	.	.	.	.	.	.	.	.	.	.	.	0.58432	D	0.99999	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	18.7417	9.8357	0.40968	0.0:0.2093:0.7907:0.0	.	.	.	.	X	115	.	ENSP00000369963:E115X	E	+	1	0	AL035460.3	2744266	0.009000	0.17119	0.035000	0.18076	0.170000	0.22686	1.817000	0.39002	1.025000	0.39708	0.655000	0.94253	GAG	.	.		0.632	C20orf141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077644.2	NM_080739		T	2796266	G	T	2796266	4	4	254	1	0	0	0	0	0	1	0	0	2091	1175	41	3	349	3	C20orf141	20	2796266	Nonsense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	2396051	2796266	60229254	972	35264										
TASP1	55617	hgsc.bcm.edu	37	chr20	13371068	13371068	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttgccacagactgtcctgccAccgcaccaggaggaagtctt	10	14	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:13371068A>G	ENST00000337743.4	-	14	1322	c.1202T>C	c.(1201-1203)gTg>gCg	p.V401A	TASP1_ENST00000539805.1_3'UTR|TASP1_ENST00000480436.1_5'UTR	NM_017714.2	NP_060184.2	Q9H6P5	TASP1_HUMAN	taspase, threonine aspartase, 1	401					positive regulation of transcription, DNA-templated (GO:0045893)		threonine-type endopeptidase activity (GO:0004298)			NS(1)|breast(1)|endometrium(2)|large_intestine(11)|liver(1)|lung(11)|stomach(2)|urinary_tract(2)	31						CTGTCCTGCCACCGCACCAGG	0.587																																					p.V401A		Atlas-SNP	.											.	TASP1	52	.	0			c.T1202C						.						73	56	61					20																	13371068		2203	4300	6503	SO:0001583	missense	55617	exon14			CCTGCCACCGCAC	AK000219	CCDS13116.1	20p12	2005-10-15	2005-10-15	2005-10-15	ENSG00000089123	ENSG00000089123	3.4.25.-		15859	protein-coding gene	gene with protein product		608270	"chromosome 20 open reading frame 13"	C20orf13		14636557	Standard	XR_430268		Approved	FLJ20212, dJ585I14.2	uc002woi.3	Q9H6P5	OTTHUMG00000031904	ENST00000337743.4:c.1202T>C	chr20.hg19:g.13371068A>G	ENSP00000338624:p.Val401Ala	77.0	0.0		65.0	4.0	NM_017714	B7Z690|B7Z963|Q5TDU9|Q9BQN0|Q9NQ08|Q9NTS6|Q9NXJ2	Missense_Mutation	SNP	ENST00000337743.4	hg19	CCDS13116.1	.	.	.	.	.	.	.	.	.	.	A	14.02	2.409482	0.42715	.	.	ENSG00000089123	ENST00000337743	D	0.92647	-3.08	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	D	0.90068	0.6898	L	0.47716	1.5	0.80722	D	1	P	0.45569	0.861	B	0.42555	0.391	D	0.90767	0.4669	10	0.59425	D	0.04	-11.4904	14.9446	0.71020	1.0:0.0:0.0:0.0	.	401	Q9H6P5	TASP1_HUMAN	A	401	ENSP00000338624:V401A	ENSP00000338624:V401A	V	-	2	0	TASP1	13319068	1.000000	0.71417	0.996000	0.52242	0.782000	0.44232	7.079000	0.76829	2.273000	0.75805	0.482000	0.46254	GTG	.	.		0.587	TASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078041.2	NM_017714		G	13371068	A	G	13371068	3	3	254	1	0	0	0	0	1	0	0	0	15604	159	6	2	64	2	TASP1	20	13371068	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	10574802	13371068	49654452	973	35265										
PCSK2	5126	hgsc.bcm.edu	37	chr20	17462588	17462588	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gctgcatggcactcagagtgCcccgtacatcgaccaggtgg	13	13	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:17462588C>T	ENST00000262545.2	+	12	2105	c.1790C>T	c.(1789-1791)gCc>gTc	p.A597V	PCSK2_ENST00000459871.1_3'UTR|PCSK2_ENST00000377899.1_Missense_Mutation_p.A578V|PCSK2_ENST00000536609.1_Missense_Mutation_p.A562V	NM_002594.3	NP_002585.2	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2	597					cellular protein metabolic process (GO:0044267)|embryo development (GO:0009790)|enkephalin processing (GO:0034230)|insulin processing (GO:0030070)|islet amyloid polypeptide processing (GO:0034231)|nervous system development (GO:0007399)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)	dendrite (GO:0030425)|extracellular space (GO:0005615)|membrane (GO:0016020)|perikaryon (GO:0043204)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|lung(17)|ovary(3)|pancreas(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	53					"""Insulin(DB00071)|Insulin Regular(DB00030)"	ACTCAGAGTGCCCCGTACATC	0.622																																					p.A597V		Atlas-SNP	.											.	PCSK2	112	.	0			c.C1790T						.						33	30	31					20																	17462588		2203	4300	6503	SO:0001583	missense	5126	exon12			AGAGTGCCCCGTA	AK312341	CCDS13125.1, CCDS56179.1, CCDS56180.1	20p11.2	2008-08-01			ENSG00000125851	ENSG00000125851			8744	protein-coding gene	gene with protein product	"neuroendocrine convertase 2", "KEX2-like endoprotease 2"	162151		NEC2		1765368	Standard	NM_001201528		Approved	PC2, SPC2	uc002wpm.3	P16519	OTTHUMG00000031941	ENST00000262545.2:c.1790C>T	chr20.hg19:g.17462588C>T	ENSP00000262545:p.Ala597Val	126.0	0.0		75.0	4.0	NM_002594	B1ANH9|B4DFQ3|Q14927|Q5JYQ1|Q8IWA8|Q9NQG3|Q9NUG1|Q9UJC6	Missense_Mutation	SNP	ENST00000262545.2	hg19	CCDS13125.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.196933	0.79015	.	.	ENSG00000125851	ENST00000377899;ENST00000262545;ENST00000536609	T;T;T	0.64260	-0.09;-0.09;-0.09	5.47	5.47	0.80525	Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	T	0.68063	0.2960	L	0.52573	1.65	0.80722	D	1	P;P;P	0.48230	0.907;0.82;0.515	P;P;B	0.51229	0.663;0.652;0.265	T	0.67043	-0.5770	10	0.44086	T	0.13	-35.8095	18.2492	0.89997	0.0:1.0:0.0:0.0	.	562;578;597	B4DFQ3;B1ANH9;P16519	.;.;NEC2_HUMAN	V	578;597;562	ENSP00000367131:A578V;ENSP00000262545:A597V;ENSP00000437458:A562V	ENSP00000262545:A597V	A	+	2	0	PCSK2	17410588	1.000000	0.71417	0.995000	0.50966	0.666000	0.39218	7.745000	0.85046	2.718000	0.92993	0.460000	0.39030	GCC	.	.		0.622	PCSK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078120.2	NM_002594		T	17462588	C	T	17462588	3	4	254	1	0	0	0	0	1	0	0	0	11610	739	26	3	1836	3	PCSK2	20	17462588	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	4091520	17462588	45562932	974	35266										
C20orf26	26074	hgsc.bcm.edu	37	chr20	20055874	20055874	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agagctgcacttcatatttcTcatcgtgccatcctacatga	6	12	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:20055874T>C	ENST00000245957.5	+	5	489	c.413T>C	c.(412-414)cTc>cCc	p.L138P	C20orf26_ENST00000389656.3_5'UTR|C20orf26_ENST00000377309.2_5'UTR|C20orf26_ENST00000377306.1_Missense_Mutation_p.L138P|C20orf26_ENST00000451767.2_Missense_Mutation_p.L138P	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN		138										NS(2)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(42)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	77				READ - Rectum adenocarcinoma(2;0.171)		TTCATATTTCTCATCGTGCCA	0.522																																					p.L138P		Atlas-SNP	.											.	C20orf26	188	.	0			c.T413C						.						175	149	158					20																	20055874		2203	4300	6503	SO:0001583	missense	26074	exon5			TATTTCTCATCGT																												ENST00000245957.5:c.413T>C	chr20.hg19:g.20055874T>C	ENSP00000245957:p.Leu138Pro	218.0	0.0		140.0	42.0	NM_015585	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Missense_Mutation	SNP	ENST00000245957.5	hg19	CCDS33447.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.265822	0.80358	.	.	ENSG00000089101	ENST00000340348;ENST00000343997;ENST00000389655;ENST00000245957;ENST00000377306;ENST00000377303;ENST00000451767;ENST00000472660	T;T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87;0.87	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.62768	0.2455	M	0.72894	2.215	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.998;1.0;0.999	T	0.66528	-0.5901	10	0.87932	D	0	.	12.3497	0.55141	0.0:0.0:0.0:1.0	.	138;138;92;138	Q8NHU2-3;F8W6K4;F8W6E2;Q8NHU2	.;.;.;CT026_HUMAN	P	92;138;138;138;138;138;138;34	ENSP00000345553:L92P;ENSP00000245957:L138P;ENSP00000366521:L138P;ENSP00000366518:L138P;ENSP00000414537:L138P;ENSP00000420498:L34P	ENSP00000245957:L138P	L	+	2	0	C20orf26	20003874	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	4.704000	0.61831	2.178000	0.69098	0.533000	0.62120	CTC	.	.		0.522	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3			C	20055874	T	C	20055874	3	2	254	1	0	0	0	0	1	0	0	0	2108	1551	54	2	427	2	C20orf26	20	20055874	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	2593286	20055874	42969646	975	35267										
GZF1	64412	hgsc.bcm.edu	37	chr20	23345335	23345335	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtacaggtggaagaagatcgGgtgcagcgaatgctggaagt	17	5	0	2	rs376361468		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:23345335G>T	ENST00000338121.5	+	2	392	c.315G>T	c.(313-315)cgG>cgT	p.R105R	GZF1_ENST00000377051.2_Silent_p.R105R|GZF1_ENST00000542987.1_Intron|GZF1_ENST00000544236.1_Intron			Q9H116	GZF1_HUMAN	GDNF-inducible zinc finger protein 1	105					branching involved in ureteric bud morphogenesis (GO:0001658)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)|sequence-specific DNA binding (GO:0043565)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|urinary_tract(2)	24	Lung NSC(19;0.0605)|Colorectal(13;0.0993)|all_lung(19;0.135)					AAGAAGATCGGGTGCAGCGAA	0.393																																					p.R105R		Atlas-SNP	.											.	GZF1	61	.	0			c.G315T						.						83	86	85					20																	23345335		2203	4300	6503	SO:0001819	synonymous_variant	64412	exon1			AGATCGGGTGCAG	AK025447	CCDS13151.1	20p11.21	2013-01-09	2006-09-19	2006-09-19	ENSG00000125812	ENSG00000125812		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	15808	protein-coding gene	gene with protein product		613842	"zinc finger protein 336"	ZNF336		14522971, 16049025	Standard	NM_022482		Approved	dJ322G13.2, ZBTB23	uc002wsz.3	Q9H116	OTTHUMG00000032069	ENST00000338121.5:c.315G>T	chr20.hg19:g.23345335G>T		123.0	0.0		93.0	4.0	NM_022482	A8K199|B2RBC3|B3KPL4|B4DF58|D3DW39|Q54A22|Q96N08|Q9BQK9|Q9H117|Q9H6W6	Silent	SNP	ENST00000338121.5	hg19	CCDS13151.1																																																																																			.	.		0.393	GZF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078333.1	NM_022482		T	23345335	G	T	23345335	2	4	254	1	0	0	0	0	0	0	0	1	6923	1219	43	3		3	GZF1	20	23345335	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	3289461	23345335	39680185	976	35268										
NINL	22981	hgsc.bcm.edu	37	chr20	25498459	25498459	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gaagacaacacagccacaaaAccttccttaaattcctcaaa	3	13	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:25498459A>G	ENST00000278886.6	-	3	280	c.207T>C	c.(205-207)ggT>ggC	p.G69G	NINL_ENST00000422516.1_Silent_p.G69G	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	69	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|microtubule (GO:0005874)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(13)|lung(25)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	57						CAGCCACAAAACCTTCCTTAA	0.408																																					p.G69G		Atlas-SNP	.											.	NINL	148	.	0			c.T207C						.						132	114	120					20																	25498459		2203	4300	6503	SO:0001819	synonymous_variant	22981	exon3			CACAAAACCTTCC		CCDS33452.1	20p11.22-p11.1	2013-01-10			ENSG00000101004	ENSG00000101004		"EF-hand domain containing"	29163	protein-coding gene	gene with protein product	"ninein-like protein"	609580				10231032	Standard	XM_005260678		Approved	KIAA0980, NLP	uc002wux.1	Q9Y2I6	OTTHUMG00000032127	ENST00000278886.6:c.207T>C	chr20.hg19:g.25498459A>G		147.0	0.0		99.0	4.0	NM_025176	A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	Silent	SNP	ENST00000278886.6	hg19	CCDS33452.1																																																																																			.	.		0.408	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078445.3	NM_025176		G	25498459	A	G	25498459	2	3	254	1	0	0	0	0	0	0	0	1	10429	30	2	2		2	NINL	20	25498459	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	2153124	25498459	37527061	977	35269										
ZNF337	26152	hgsc.bcm.edu	37	chr20	25656557	25656557	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgcacacaaaaggcttctccTctgagtgtgtgatctgatgt	10	9	3	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:25656557T>C	ENST00000376436.1	-	4	1906	c.1367A>G	c.(1366-1368)gAg>gGg	p.E456G	RP4-694B14.5_ENST00000439498.1_RNA|ZNF337_ENST00000538750.1_Missense_Mutation_p.E424G|ZNF337_ENST00000481610.1_5'Flank|RP4-694B14.5_ENST00000455791.1_RNA|RP4-694B14.5_ENST00000421829.1_RNA|RP4-694B14.5_ENST00000428254.1_RNA|ZNF337_ENST00000252979.5_Missense_Mutation_p.E456G|RP4-694B14.5_ENST00000414393.1_RNA			Q9Y3M9	ZN337_HUMAN	zinc finger protein 337	456					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						AGGCTTCTCCTCTGAGTGTGT	0.453																																					p.E456G		Atlas-SNP	.											.	ZNF337	65	.	0			c.A1367G						.						154	132	139					20																	25656557		2203	4300	6503	SO:0001583	missense	26152	exon5			TTCTCCTCTGAGT		CCDS13174.1	20p11.1	2013-09-20			ENSG00000130684	ENSG00000130684		"Zinc fingers, C2H2-type", "-"	15809	protein-coding gene	gene with protein product							Standard	XM_005260702		Approved	dJ694B14.1	uc002wuz.3	Q9Y3M9	OTTHUMG00000032131	ENST00000376436.1:c.1367A>G	chr20.hg19:g.25656557T>C	ENSP00000365619:p.Glu456Gly	136.0	0.0		96.0	4.0	NM_015655	B4DSM2|Q9Y3Y5	Missense_Mutation	SNP	ENST00000376436.1	hg19	CCDS13174.1	.	.	.	.	.	.	.	.	.	.	.	7.778	0.708927	0.15239	.	.	ENSG00000130684	ENST00000376436;ENST00000252979;ENST00000376412;ENST00000538750	T;T;T	0.11821	2.74;2.74;2.74	1.1	0.0346	0.14184	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03263	0.0095	N	0.01505	-0.83	0.26061	N	0.981343	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43702	-0.9375	9	0.02654	T	1	.	4.9952	0.14235	0.0:0.7431:0.0:0.2568	.	424;456	B4DSM2;Q9Y3M9	.;ZN337_HUMAN	G	456;456;456;424	ENSP00000365619:E456G;ENSP00000252979:E456G;ENSP00000442181:E424G	ENSP00000252979:E456G	E	-	2	0	ZNF337	25604557	0.093000	0.21703	0.024000	0.17045	0.481000	0.33189	1.428000	0.34892	0.004000	0.14682	0.248000	0.18094	GAG	.	.		0.453	ZNF337-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078454.1			C	25656557	T	C	25656557	3	2	254	1	0	0	0	0	1	0	0	0	17868	1551	54	2	892	2	ZNF337	20	25656557	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	158098	25656557	37368963	978	35270										
TTLL9	164395	hgsc.bcm.edu	37	chr20	30521650	30521650	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aaaaaacatctcccgactacCacccaaagaaggtgaggaag	8	11	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:30521650C>A	ENST00000375938.4	+	11	1049	c.796C>A	c.(796-798)Cac>Aac	p.H266N	TTLL9_ENST00000375922.4_Missense_Mutation_p.H208N|TTLL9_ENST00000375934.4_Silent_p.T233T|TTLL9_ENST00000310998.4_Missense_Mutation_p.H231N|TTLL9_ENST00000375921.2_Missense_Mutation_p.H208N|TTLL9_ENST00000535842.1_Missense_Mutation_p.H266N			Q3SXZ7	TTLL9_HUMAN	tubulin tyrosine ligase-like family, member 9	266	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)	cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)	ligase activity (GO:0016874)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			TCCCGACTACCACCCAAAGAA	0.607																																					p.H266N		Atlas-SNP	.											.	TTLL9	95	.	0			c.C796A						.						73	71	72					20																	30521650		1979	4173	6152	SO:0001583	missense	164395	exon11			GACTACCACCCAA	AL031658	CCDS42863.1	20q11	2013-02-14	2005-07-28	2005-07-28		ENSG00000131044		"Tubulin tyrosine ligase-like family"	16118	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 125"	C20orf125		15890843	Standard	NM_001008409		Approved	dJ310O13.1	uc010gdx.1	Q3SXZ7		ENST00000375938.4:c.796C>A	chr20.hg19:g.30521650C>A	ENSP00000365105:p.His266Asn	123.0	0.0		98.0	4.0	NM_001008409	A6NH06|A6NIS5|B3KSG8|Q3SXZ8|Q5JYS3|Q5JYS4	Missense_Mutation	SNP	ENST00000375938.4	hg19	CCDS42863.1	.	.	.	.	.	.	.	.	.	.	C	15.13	2.740961	0.49151	.	.	ENSG00000131044	ENST00000375938;ENST00000535842;ENST00000310998;ENST00000375921;ENST00000375935;ENST00000375922	T;T;T;T;T	0.07114	3.67;3.67;3.67;3.22;3.67	5.64	4.68	0.58851	.	0.156566	0.56097	D	0.000037	T	0.03136	0.0092	N	0.02266	-0.62	0.40990	D	0.984843	B;B	0.11235	0.003;0.004	B;B	0.15052	0.012;0.007	T	0.43130	-0.9410	10	0.08179	T	0.78	.	11.5189	0.50539	0.0:0.7283:0.2717:0.0	.	266;168	Q3SXZ7;B1ANK8	TTLL9_HUMAN;.	N	266;266;231;208;226;208	ENSP00000365105:H266N;ENSP00000442515:H266N;ENSP00000308980:H231N;ENSP00000365086:H208N;ENSP00000365088:H208N	ENSP00000308980:H231N	H	+	1	0	TTLL9	29985311	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	4.954000	0.63631	2.656000	0.90262	0.561000	0.74099	CAC	.	.		0.607	TTLL9-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001008409		A	30521650	C	A	30521650	3	1	254	1	0	0	0	0	1	0	0	0	16749	594	21	3	834	3	TTLL9	20	30521650	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	4865093	30521650	32503870	979	35271										
TM9SF4	9777	hgsc.bcm.edu	37	chr20	30734649	30734649	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	attgccaactacaacaaggaGgatgacattgtacgaggtct	10	8	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:30734649G>T	ENST00000398022.2	+	9	1180	c.945G>T	c.(943-945)gaG>gaT	p.E315D	TM9SF4_ENST00000217315.5_Missense_Mutation_p.E298D	NM_014742.3	NP_055557.2	Q92544	TM9S4_HUMAN	transmembrane 9 superfamily protein member 4	315						integral component of membrane (GO:0016021)				central_nervous_system(2)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			ACAACAAGGAGGATGACATTG	0.493																																					p.E315D		Atlas-SNP	.											.	TM9SF4	65	.	0			c.G945T						.						115	90	99					20																	30734649		2203	4300	6503	SO:0001583	missense	9777	exon9			CAAGGAGGATGAC	BC021107	CCDS13196.2	20q11.21	2004-04-19			ENSG00000101337	ENSG00000101337			30797	protein-coding gene	gene with protein product						9039502	Standard	NM_014742		Approved	KIAA0255, dJ836N17.2	uc002wxj.2	Q92544	OTTHUMG00000032206	ENST00000398022.2:c.945G>T	chr20.hg19:g.30734649G>T	ENSP00000381104:p.Glu315Asp	108.0	0.0		95.0	5.0	NM_014742	B0QYT7|Q9NUA3	Missense_Mutation	SNP	ENST00000398022.2	hg19	CCDS13196.2	.	.	.	.	.	.	.	.	.	.	G	14.89	2.669176	0.47677	.	.	ENSG00000101337	ENST00000398022;ENST00000421148;ENST00000217315	T;T	0.42513	0.97;0.97	5.61	4.66	0.58398	.	0.000000	0.85682	D	0.000000	T	0.22360	0.0539	N	0.11698	0.16	0.80722	D	1	B;B;B	0.19935	0.04;0.015;0.013	B;B;B	0.21917	0.037;0.021;0.023	T	0.06899	-1.0801	10	0.11182	T	0.66	-20.6441	9.548	0.39293	0.201:0.0:0.799:0.0	.	241;222;315	F5H3B5;B4DH88;Q92544	.;.;TM9S4_HUMAN	D	315;241;298	ENSP00000381104:E315D;ENSP00000217315:E298D	ENSP00000217315:E298D	E	+	3	2	TM9SF4	30198310	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.776000	0.38594	1.505000	0.48720	0.655000	0.94253	GAG	.	.		0.493	TM9SF4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323568.1	NM_014742		T	30734649	G	T	30734649	3	4	254	1	0	0	0	0	1	0	0	0	15995	991	35	3	979	3	TM9SF4	20	30734649	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	212999	30734649	32290871	980	35272										
DNMT3B	1789	hgsc.bcm.edu	37	chr20	31367950	31367950	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aagtcctgagcctccaagctTggtgagggggaggctatggg	17	8	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:31367950T>C	ENST00000328111.2	+	2	315				DNMT3B_ENST00000375623.4_Intron|DNMT3B_ENST00000353855.2_Intron|DNMT3B_ENST00000443239.3_Intron|DNMT3B_ENST00000348286.2_Intron|DNMT3B_ENST00000344505.4_Intron|DNMT3B_ENST00000456297.2_Intron|DNMT3B_ENST00000201963.3_Splice_Site_p.L10S	NM_006892.3	NP_008823.1	Q9UBC3	DNM3B_HUMAN	DNA (cytosine-5-)-methyltransferase 3 beta						C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation on cytosine within a CG sequence (GO:0010424)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of neuron differentiation (GO:0045666)|protein complex localization (GO:0031503)|regulation of gene expression by genetic imprinting (GO:0006349)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA-methyltransferase activity (GO:0009008)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)|unmethylated CpG binding (GO:0045322)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(16)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CCTCCAAGCTTGGTGAGGGGG	0.632																																					p.L10S		Atlas-SNP	.											.	DNMT3B	196	.	0			c.T29C						.						19	20	20					20																	31367950		2201	4299	6500	SO:0001627	intron_variant	1789	exon1			CAAGCTTGGTGAG		CCDS13204.1, CCDS13205.1, CCDS13206.1, CCDS13207.1, CCDS56183.1, CCDS56184.1	20q11.2	2014-09-17			ENSG00000088305	ENSG00000088305			2979	protein-coding gene	gene with protein product		602900				9662389, 10433969	Standard	NM_006892		Approved		uc002wyc.3	Q9UBC3	OTTHUMG00000032226	ENST00000328111.2:c.-6-174T>C	chr20.hg19:g.31367950T>C		84.0	0.0		66.0	4.0	NM_175850	A2A2E2|B4DSM8|B4DSU1|E1P5M6|E1P5M7|E7EN63|E9PBF2|Q9UBD4|Q9UJQ5|Q9UKA6|Q9UNE5|Q9Y5R9|Q9Y5S0	Missense_Mutation	SNP	ENST00000328111.2	hg19	CCDS13205.1	.	.	.	.	.	.	.	.	.	.	T	12.78	2.040099	0.35989	.	.	ENSG00000088305	ENST00000201963	D	0.97378	-4.36	4.54	3.35	0.38373	.	.	.	.	.	D	0.97402	0.9150	.	.	.	0.80722	D	1	D	0.71674	0.998	D	0.66351	0.943	D	0.96051	0.9031	8	0.37606	T	0.19	.	9.3283	0.38005	0.0:0.0:0.1794:0.8206	.	10	Q9UBC3-6	.	S	10	ENSP00000201963:L10S	ENSP00000201963:L10S	L	+	2	0	DNMT3B	30831611	0.881000	0.30235	0.986000	0.45419	0.653000	0.38743	0.728000	0.26013	2.043000	0.60533	0.459000	0.35465	TTG	.	.		0.632	DNMT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078643.2	NM_006892		C	31367950	T	C	31367950	1	2	254	0	1	0	0	0	0	0	0	0	4679	1826	63	2		2	DNMT3B	20	31367950	Intron	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	633301	31367950	31657570	981	35273										
C20orf114	92747	hgsc.bcm.edu	37	chr20	31889200	31889200	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctctctccagaagaattcatGgtcctgttggactctgtggt	10	10	3	2	rs267605886		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:31889200G>A	ENST00000253354.1	+	9	1070	c.909G>A	c.(907-909)atG>atA	p.M303I	BPIFB1_ENST00000464032.1_3'UTR	NM_033197.2	NP_149974.2	Q8TDL5	BPIB1_HUMAN	BPI fold containing family B, member 1	303					innate immune response in mucosa (GO:0002227)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)										AAGAATTCATGGTCCTGTTGG	0.547																																					p.M303I		Atlas-SNP	.											.	.	.	.	0			c.G909A						.						97	83	87					20																	31889200		2203	4300	6503	SO:0001583	missense	92747	exon9			ATTCATGGTCCTG	BC008429	CCDS13218.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000125999	ENSG00000125999		"BPI fold containing"	16108	protein-coding gene	gene with protein product	"von Ebner minor salivary gland protein"		"chromosome 20 open reading frame 114"	C20orf114		11971875, 21787333	Standard	NM_033197		Approved	dJ1187J4.1, MGC14597, bA49G10.6, LPLUNC1, VEMSGP	uc002wyw.1	Q8TDL5	OTTHUMG00000032252	ENST00000253354.1:c.909G>A	chr20.hg19:g.31889200G>A	ENSP00000253354:p.Met303Ile	75.0	0.0		58.0	4.0	NM_033197	A8K2H8|Q5QP43|Q6UWY1|Q6ZRU7|Q96HK6|Q9BQP8|Q9BWZ6|Q9H4V6	Missense_Mutation	SNP	ENST00000253354.1	hg19	CCDS13218.1	.	.	.	.	.	.	.	.	.	.	G	2.964	-0.214051	0.06101	.	.	ENSG00000125999	ENST00000253354;ENST00000375378	T	0.06371	3.31	4.81	-4.5	0.03493	.	2.143790	0.01639	N	0.023931	T	0.04497	0.0123	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35051	-0.9804	10	0.32370	T	0.25	-0.3569	2.8073	0.05431	0.4107:0.1109:0.366:0.1125	.	303	Q8TDL5	BPIB1_HUMAN	I	303;134	ENSP00000253354:M303I	ENSP00000253354:M303I	M	+	3	0	BPIFB1	31352861	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-1.736000	0.01845	-1.282000	0.02396	-1.644000	0.00765	ATG	.	.		0.547	BPIFB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106499.2	NM_033197		A	31889200	G	A	31889200	3	1	254	1	0	0	0	0	1	0	0	0	2084	1348	47	3	939	3	C20orf114	20	31889200	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	521250	31889200	31136320	982	35274										
ZNF341	84905	hgsc.bcm.edu	37	chr20	32328755	32328755	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tccagtcattattggatggcCaaggagcagtccctgatccg	11	11	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:32328755C>A	ENST00000375200.1	+	2	444	c.79C>A	c.(79-81)Caa>Aaa	p.Q27K	ZNF341_ENST00000342427.2_Missense_Mutation_p.Q27K	NM_001282933.1	NP_001269862.1	Q9BYN7	ZN341_HUMAN	zinc finger protein 341	27					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	31						ATTGGATGGCCAAGGAGCAGT	0.537																																					p.Q27K		Atlas-SNP	.											.	ZNF341	73	.	0			c.C79A						.						110	93	99					20																	32328755		2203	4300	6503	SO:0001583	missense	84905	exon2			GATGGCCAAGGAG	AK027550	CCDS13227.1, CCDS74719.1	20q11.22	2013-01-08			ENSG00000131061	ENSG00000131061		"Zinc fingers, C2H2-type"	15992	protein-coding gene	gene with protein product							Standard	NM_001282933		Approved	dJ553F4.3	uc002wzx.3	Q9BYN7	OTTHUMG00000032275	ENST00000375200.1:c.79C>A	chr20.hg19:g.32328755C>A	ENSP00000364346:p.Gln27Lys	105.0	0.0		55.0	4.0	NM_032819	A2RUF4|B2RXE5|B7ZM09|Q5JXM8|Q96ST5	Missense_Mutation	SNP	ENST00000375200.1	hg19		.	.	.	.	.	.	.	.	.	.	C	18.50	3.637217	0.67130	.	.	ENSG00000131061	ENST00000342427;ENST00000375200	T;T	0.11169	3.05;2.8	5.27	4.32	0.51571	.	0.062422	0.64402	N	0.000004	T	0.10680	0.0261	L	0.34521	1.04	0.54753	D	0.999984	B;B	0.17268	0.012;0.021	B;B	0.20184	0.012;0.028	T	0.06445	-1.0826	10	0.54805	T	0.06	-11.631	14.361	0.66771	0.1497:0.8503:0.0:0.0	.	27;27	Q9BYN7;Q9BYN7-2	ZN341_HUMAN;.	K	27	ENSP00000344308:Q27K;ENSP00000364346:Q27K	ENSP00000344308:Q27K	Q	+	1	0	ZNF341	31792416	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.378000	0.79679	1.344000	0.45657	-0.293000	0.09583	CAA	.	.		0.537	ZNF341-201	KNOWN	basic	protein_coding	protein_coding				A	32328755	C	A	32328755	3	1	254	1	0	0	0	0	1	0	0	0	17872	595	21	3	85	3	ZNF341	20	32328755	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	439555	32328755	30696765	983	35275										
UQCC	55245	hgsc.bcm.edu	37	chr20	33981955	33981955	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtaggagacacaggtatcaaTcggctgcatactggaaccca	11	10	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:33981955T>C	ENST00000374385.5	-	2	246	c.69A>G	c.(67-69)cgA>cgG	p.R23R	UQCC1_ENST00000359226.2_Silent_p.R23R|UQCC1_ENST00000491125.1_5'UTR|UQCC1_ENST00000397556.3_5'UTR|UQCC1_ENST00000374384.2_Silent_p.R23R|UQCC1_ENST00000540457.1_Intron|UQCC1_ENST00000397554.1_Silent_p.R23R|UQCC1_ENST00000374377.5_Missense_Mutation_p.I4V|UQCC1_ENST00000407996.2_Silent_p.R23R|UQCC1_ENST00000374380.2_Silent_p.R23R|UQCC1_ENST00000542501.1_Silent_p.R23R|UQCC1_ENST00000349714.5_Silent_p.R23R	NM_018244.4	NP_060714.3	Q9NVA1	UQCC1_HUMAN	ubiquinol-cytochrome c reductase complex assembly factor 1	23						cytoplasmic membrane-bounded vesicle (GO:0016023)|mitochondrion (GO:0005739)											CAGGTATCAATCGGCTGCATA	0.433																																					p.R23R		Atlas-SNP	.											.	UQCC	41	.	0			c.A69G						.						126	118	120					20																	33981955		2203	4300	6503	SO:0001819	synonymous_variant	55245	exon2			TATCAATCGGCTG	AK001712	CCDS13252.1, CCDS13253.1, CCDS13253.2, CCDS54458.1	20q11.22	2013-09-20	2013-09-20	2013-09-20	ENSG00000101019	ENSG00000101019		"Mitochondrial respiratory chain complex assembly factors"	15891	protein-coding gene	gene with protein product	"Basic FGF-repressed Zic-binding protein", "cytochrome B protein synthesis 3 homolog (S. cerevisiae)"	611797	"chromosome 20 open reading frame 44", "ubiquinol-cytochrome c reductase complex chaperone"	C20orf44, UQCC			Standard	NM_018244		Approved	FLJ10850, CBP3, BFZB	uc002xcd.3	Q9NVA1	OTTHUMG00000032335	ENST00000374385.5:c.69A>G	chr20.hg19:g.33981955T>C		132.0	0.0		98.0	4.0	NM_018244	B1AKV5|Q0VF37|Q5T348|Q5T351|Q5T353|Q86YU3|Q86YU4|Q96H66|Q9H438|Q9H452|Q9H9K8|Q9H9R5	Silent	SNP	ENST00000374385.5	hg19	CCDS13252.1	.	.	.	.	.	.	.	.	.	.	T	8.859	0.946417	0.18356	.	.	ENSG00000101019	ENST00000374377	.	.	.	5.04	1.46	0.22682	.	.	.	.	.	T	0.12944	0.0314	.	.	.	0.09310	N	0.999991	.	.	.	.	.	.	T	0.31833	-0.9929	5	0.02654	T	1	-0.1852	6.839	0.23953	0.0:0.2836:0.0:0.7164	.	.	.	.	V	4	.	ENSP00000363497:I4V	I	-	1	0	UQCC	33445369	0.239000	0.23836	0.446000	0.26920	0.870000	0.49936	0.302000	0.19192	0.404000	0.25506	0.528000	0.53228	ATT	.	.		0.433	UQCC1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078866.1	NM_018244		C	33981955	T	C	33981955	2	2	254	1	0	0	0	0	0	0	0	1	17030	1422	50	2		2	UQCC	20	33981955	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	1653200	33981955	29043565	984	35276										
TGM2	7052	hgsc.bcm.edu	37	chr20	36766769	36766769	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggttcgcccttgtgaaggccTccctctcctctgaggaccct	10	16	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:36766769T>C	ENST00000361475.2	-	10	1534	c.1361A>G	c.(1360-1362)gAg>gGg	p.E454G	TGM2_ENST00000536701.1_Missense_Mutation_p.E373G|TGM2_ENST00000536724.1_Missense_Mutation_p.E394G	NM_004613.2|NM_198951.1	NP_004604.2|NP_945189.1	P21980	TGM2_HUMAN	transglutaminase 2	454					apoptotic cell clearance (GO:0043277)|blood vessel remodeling (GO:0001974)|branching involved in salivary gland morphogenesis (GO:0060445)|isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein homooligomerization (GO:0051260)|salivary gland cavitation (GO:0060662)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			endometrium(2)|large_intestine(11)|liver(1)|lung(7)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Myeloproliferative disorder(115;0.00878)			L-Glutamine(DB00130)	TGTGAAGGCCTCCCTCTCCTC	0.587																																					p.E454G		Atlas-SNP	.											.	TGM2	88	.	0			c.A1361G						.						88	82	84					20																	36766769		2203	4300	6503	SO:0001583	missense	7052	exon10			AAGGCCTCCCTCT	M98478	CCDS13302.1	20q12	2013-05-02	2013-05-02		ENSG00000198959	ENSG00000198959	2.3.2.13	"Transglutaminases"	11778	protein-coding gene	gene with protein product	"C polypeptide, protein-glutamine-gamma-glutamyltransferase"	190196	"transglutaminase 2 (C polypeptide, protein-glutamine-gamma-glutamyltransferase)"			7912692, 11390390	Standard	NM_004613		Approved	TGC	uc002xhr.3	P21980	OTTHUMG00000032437	ENST00000361475.2:c.1361A>G	chr20.hg19:g.36766769T>C	ENSP00000355330:p.Glu454Gly	127.0	0.0		94.0	4.0	NM_198951	E1P5V9|Q16436|Q6B838|Q9BTN7|Q9UH35	Missense_Mutation	SNP	ENST00000361475.2	hg19	CCDS13302.1	.	.	.	.	.	.	.	.	.	.	T	7.361	0.624909	0.14193	.	.	ENSG00000198959	ENST00000361475;ENST00000536701;ENST00000536724	T;T;T	0.26810	1.71;1.71;1.71	4.88	2.51	0.30379	.	0.817852	0.11755	N	0.532706	T	0.28300	0.0699	M	0.75447	2.3	0.21652	N	0.99961	B;P;B;B;P	0.41188	0.404;0.602;0.404;0.282;0.741	B;B;B;B;B	0.41466	0.238;0.229;0.096;0.12;0.358	T	0.15407	-1.0438	10	0.30854	T	0.27	-9.3226	4.9211	0.13871	0.0:0.1618:0.2999:0.5383	.	394;373;454;394;454	F5H6P0;B4DIT7;P21980-2;B4DTN7;P21980	.;.;.;.;TGM2_HUMAN	G	454;373;394	ENSP00000355330:E454G;ENSP00000444701:E373G;ENSP00000437479:E394G	ENSP00000355330:E454G	E	-	2	0	TGM2	36200183	0.002000	0.14202	0.140000	0.22221	0.010000	0.07245	1.104000	0.31074	0.188000	0.20168	-0.290000	0.09829	GAG	.	.		0.587	TGM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079151.2	NM_198951		C	36766769	T	C	36766769	3	2	254	1	0	0	0	0	1	0	0	0	15845	1551	54	2	750	2	TGM2	20	36766769	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	2784814	36766769	26258751	985	35277										
LPIN3	64900	hgsc.bcm.edu	37	chr20	39986061	39986061	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gactggacacaccagggcatCaccagtctctatcacaaaat	7	13	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:39986061C>A	ENST00000373257.3	+	16	2104	c.2013C>A	c.(2011-2013)atC>atA	p.I671I		NM_022896.1	NP_075047.1	Q9BQK8	LPIN3_HUMAN	lipin 3	671	C-LIP.				fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(7)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		Myeloproliferative disorder(115;0.000739)				ACCAGGGCATCACCAGTCTCT	0.592																																					p.I671I		Atlas-SNP	.											.	LPIN3	69	.	0			c.C2013A						.						78	68	71					20																	39986061		2203	4300	6503	SO:0001819	synonymous_variant	64900	exon16			GGGCATCACCAGT	AL132654	CCDS33469.1	20q11.2-q12	2006-04-04	2002-05-23		ENSG00000132793	ENSG00000132793			14451	protein-coding gene	gene with protein product		605520	"lipin 3-like"	LIPN3L		11138012	Standard	XM_005260515		Approved	SMP2	uc002xjx.3	Q9BQK8	OTTHUMG00000033056	ENST00000373257.3:c.2013C>A	chr20.hg19:g.39986061C>A		66.0	0.0		65.0	5.0	NM_022896	B2RTT5|Q5TDB9|Q9NPY8|Q9UJE5	Silent	SNP	ENST00000373257.3	hg19	CCDS33469.1	.	.	.	.	.	.	.	.	.	.	C	9.152	1.016607	0.19355	.	.	ENSG00000132793	ENST00000445975	.	.	.	5.2	4.24	0.50183	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-12.5033	5.3388	0.15973	0.1626:0.6535:0.0:0.1839	.	.	.	.	X	161	.	.	S	+	2	0	LPIN3	39419475	0.996000	0.38824	1.000000	0.80357	0.893000	0.52053	0.453000	0.21811	1.155000	0.42497	0.563000	0.77884	TCA	.	.		0.592	LPIN3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080393.1	NM_022896		A	39986061	C	A	39986061	2	1	254	1	0	0	0	0	0	0	0	1	8929	816	29	3		3	LPIN3	20	39986061	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	3219292	39986061	23039459	986	35278										
SNX21	90203	hgsc.bcm.edu	37	chr20	44469556	44469556	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	caggacttcttcgtgctgccGgagctgcggcgggcacagag	16	12	1	1	rs533001979	byFrequency	TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:44469556G>T	ENST00000491381.1	+	4	794	c.726G>T	c.(724-726)ccG>ccT	p.P242P	SNX21_ENST00000372542.1_Silent_p.P233P|SNX21_ENST00000344780.4_3'UTR|SNX21_ENST00000462307.1_3'UTR|SNX21_ENST00000342644.5_Intron			Q969T3	SNX21_HUMAN	sorting nexin family member 21	242	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|pancreas(1)	7		Myeloproliferative disorder(115;0.0122)				TCGTGCTGCCGGAGCTGCGGC	0.662																																					p.P242P		Atlas-SNP	.											SNX21,colon,carcinoma,0,1	SNX21	23	.	0			c.G726T						.						23	26	25					20																	44469556		2202	4284	6486	SO:0001819	synonymous_variant	90203	exon4			GCTGCCGGAGCTG	AK095851	CCDS13376.1, CCDS13377.1, CCDS42883.1	20q13.12	2013-01-10	2006-07-24	2006-07-24	ENSG00000124104	ENSG00000124104		"Sorting nexins", "Tetratricopeptide (TTC) repeat domain containing"	16154	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 161"	C20orf161		12461558, 12459172	Standard	NM_152897		Approved	dJ337O18.4, SNX-L	uc002xpv.1	Q969T3	OTTHUMG00000032624	ENST00000491381.1:c.726G>T	chr20.hg19:g.44469556G>T		99.0	2.0		90.0	5.0	NM_033421	Q5JZH5|Q5JZH6|Q5JZH7|Q8WUR6|Q9BR16	Silent	SNP	ENST00000491381.1	hg19	CCDS13377.1																																																																																			.	.		0.662	SNX21-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079534.1	NM_033421		T	44469556	G	T	44469556	2	4	254	1	0	0	0	0	0	0	0	1	14908	1103	39	1		1	SNX21	20	44469556	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	4483495	44469556	18555964	987	35279										
SLC12A5	57468	hgsc.bcm.edu	37	chr20	44676618	44676618	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgatccacttcccggctcccAgggcagagaaggagtggggc	15	12	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:44676618A>G	ENST00000454036.2	+	16	2025		c.e16-1		SLC12A5_ENST00000243964.3_Splice_Site	NM_001134771.1	NP_001128243.1	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 5						cellular ion homeostasis (GO:0006873)|chloride transmembrane transport (GO:1902476)|ion transport (GO:0006811)|learning (GO:0007612)|multicellular organism growth (GO:0035264)|potassium ion transport (GO:0006813)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|thermosensory behavior (GO:0040040)|transmembrane transport (GO:0055085)|transport (GO:0006810)	dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(1)|lung(38)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	80		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)	CCCGGCTCCCAGGGCAGAGAA	0.612																																					.		Atlas-SNP	.											.	SLC12A5	181	.	0			c.1977-2A>G						.						46	41	43					20																	44676618		2203	4300	6503	SO:0001630	splice_region_variant	57468	exon16			GCTCCCAGGGCAG	AB033002	CCDS13391.1, CCDS46610.1	20q13.12	2013-05-22	2010-04-20		ENSG00000124140	ENSG00000124140		"Solute carriers"	13818	protein-coding gene	gene with protein product		606726					Standard	NM_020708		Approved	KIAA1176, KCC2	uc010zxl.1	Q9H2X9	OTTHUMG00000032638	ENST00000454036.2:c.1977-1A>G	chr20.hg19:g.44676618A>G		60.0	0.0		42.0	4.0	NM_001134771	A2RTX2|Q5VZ41|Q9H4Z0|Q9ULP4	Splice_Site	SNP	ENST00000454036.2	hg19	CCDS46610.1	.	.	.	.	.	.	.	.	.	.	A	13.44	2.237439	0.39498	.	.	ENSG00000124140	ENST00000454036;ENST00000243964	.	.	.	3.92	3.92	0.45320	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.7426	0.51801	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC12A5	44110025	1.000000	0.71417	0.995000	0.50966	0.308000	0.27856	9.067000	0.93955	1.621000	0.50320	0.374000	0.22700	.	.	.		0.612	SLC12A5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471538.1		Intron	G	44676618	A	G	44676618	5	3	254	1	0	0	0	0	0	0	1	0	14401	202	7	2	2093	2	SLC12A5	20	44676618	Splice_Site	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	207062	44676618	18348902	988	35280										
NCOA3	8202	hgsc.bcm.edu	37	chr20	46265318	46265320	+	In_Frame_Del	DEL	AAG	AAG	-													0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agcaggagcagctaagtcctAagaagaaggagaataatgca					rs149716562		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:46265318_46265320delAAG	ENST00000371998.3	+	12	2379_2381	c.2188_2190delAAG	c.(2188-2190)aagdel	p.K732del	NCOA3_ENST00000341724.6_In_Frame_Del_p.K742del|NCOA3_ENST00000372004.3_In_Frame_Del_p.K732del|NCOA3_ENST00000371997.3_In_Frame_Del_p.K742del			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	732					androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			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						GCTAAGTCCTAAGAAGAAGGAGA	0.468																																					p.739_740del		Pindel	.											.	NCOA3	156	.	0			c.2217_2219del						.																																			SO:0001651	inframe_deletion	8202	exon12			.	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7670	protein-coding gene	gene with protein product	"receptor-associated coactivator 3", "thyroid hormone receptor activator molecule 1"	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.2188_2190delAAG	chr20.hg19:g.46265324_46265326delAAG	ENSP00000361066:p.Lys732del	200.0	0.0		207.0	23.0	NM_001174088	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	In_Frame_Del	DEL	ENST00000371998.3	hg19	CCDS13407.1																																																																																			.	.		0.468	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534		-	46265320	AAG	-	46265318	7	5	254	1	0	1	0	1	0	0	0	0	10239	363	13	0	2256	0	NCOA3	20	46265318	In_Frame_Del	DEL	AAG	TCGA-EP-A2KA-01A-11D-A183-10	1588700	46265318	16760202	989	35281										
PTPN1	5770	hgsc.bcm.edu	37	chr20	49197898	49197898	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aaaggggagccgtcactgccCgagaaggacgaggaccatgc	15	11	1	1	rs150584289		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:49197898C>A	ENST00000371621.3	+	9	1359	c.1185C>A	c.(1183-1185)ccC>ccA	p.P395P	PTPN1_ENST00000541713.1_Silent_p.P322P	NM_001278618.1|NM_002827.2	NP_001265547.1|NP_002818.1	P18031	PTN1_HUMAN	protein tyrosine phosphatase, non-receptor type 1	395					actin cytoskeleton reorganization (GO:0031532)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|endoplasmic reticulum unfolded protein response (GO:0030968)|insulin receptor signaling pathway (GO:0008286)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|peptidyl-tyrosine dephosphorylation (GO:0035335)|peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity (GO:1990264)|platelet activation (GO:0030168)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|regulation of endocytosis (GO:0030100)|regulation of hepatocyte growth factor receptor signaling pathway (GO:1902202)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of signal transduction (GO:0009966)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|sorting endosome (GO:0097443)	enzyme binding (GO:0019899)|ephrin receptor binding (GO:0046875)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|skin(2)	16		Lung NSC(126;0.163)			Tiludronate(DB01133)	CGTCACTGCCCGAGAAGGACG	0.607																																					p.P395P		Atlas-SNP	.											PTPN1,NS,carcinoma,0,1	PTPN1	36	.	0			c.C1185A						.						98	69	79					20																	49197898		2203	4300	6503	SO:0001819	synonymous_variant	5770	exon9			ACTGCCCGAGAAG		CCDS13430.1, CCDS63309.1	20q13.1-q13.2	2011-06-09			ENSG00000196396	ENSG00000196396		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9642	protein-coding gene	gene with protein product		176885		PTP1B		2164224	Standard	NM_002827		Approved		uc002xvl.3	P18031	OTTHUMG00000032729	ENST00000371621.3:c.1185C>A	chr20.hg19:g.49197898C>A		142.0	0.0		68.0	3.0	NM_002827	Q5TGD8|Q9BQV9|Q9NQQ4	Silent	SNP	ENST00000371621.3	hg19	CCDS13430.1																																																																																			.	C|1.000;T|0.000		0.607	PTPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079694.2			A	49197898	C	A	49197898	2	1	254	1	0	0	0	0	0	0	0	1	12792	639	23	1		1	PTPN1	20	49197898	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	2932580	49197898	13827622	990	35282										
SYCP2	10388	hgsc.bcm.edu	37	chr20	58468228	58468228	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcttttttccgctgcctgtgAatctggtataacatcctgga	8	10	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr20:58468228A>G	ENST00000357552.3	-	22	1987	c.1762T>C	c.(1762-1764)Tca>Cca	p.S588P	SYCP2_ENST00000371001.2_Missense_Mutation_p.S588P			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	588					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			GCTGCCTGTGAATCTGGTATA	0.328																																					p.S588P		Atlas-SNP	.											.	SYCP2	204	.	0			c.T1762C						.						111	102	105					20																	58468228		2202	4299	6501	SO:0001583	missense	10388	exon21			CCTGTGAATCTGG	Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.1762T>C	chr20.hg19:g.58468228A>G	ENSP00000350162:p.Ser588Pro	87.0	0.0		84.0	4.0	NM_014258	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Missense_Mutation	SNP	ENST00000357552.3	hg19	CCDS13482.1	.	.	.	.	.	.	.	.	.	.	A	16.46	3.128301	0.56721	.	.	ENSG00000196074	ENST00000371001;ENST00000357552;ENST00000446834	T;T;T	0.26518	1.94;1.94;1.73	5.77	0.724	0.18236	.	0.362966	0.23926	N	0.043198	T	0.21062	0.0507	M	0.61703	1.905	0.09310	N	1	B	0.17038	0.02	B	0.21546	0.035	T	0.29822	-0.9999	10	0.72032	D	0.01	-0.0018	1.6469	0.02764	0.4837:0.1554:0.0809:0.28	.	588	Q9BX26	SYCP2_HUMAN	P	588	ENSP00000360040:S588P;ENSP00000350162:S588P;ENSP00000402456:S588P	ENSP00000350162:S588P	S	-	1	0	SYCP2	57901623	0.998000	0.40836	0.001000	0.08648	0.844000	0.47949	1.252000	0.32874	-0.077000	0.12752	0.477000	0.44152	TCA	.	.		0.328	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258		G	58468228	A	G	58468228	3	3	254	1	0	0	0	0	1	0	0	0	15447	246	9	2	2926	2	SYCP2	20	58468228	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	9270330	58468228	4557292	991	35283										
GRIK1	2897	hgsc.bcm.edu	37	chr21	30971254	30971254	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cccagtcaagccatcccaccGggcctgtggacaagaagaaa	10	14	1	2	rs113829116		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr21:30971254G>T	ENST00000399907.1	-	8	1513	c.1102C>A	c.(1102-1104)Cgg>Agg	p.R368R	GRIK1_ENST00000399914.1_Silent_p.R368R|GRIK1_ENST00000327783.4_Silent_p.R368R|GRIK1_ENST00000389125.3_Silent_p.R368R|GRIK1_ENST00000399913.1_Silent_p.R368R|BACH1_ENST00000462262.1_Intron|GRIK1_ENST00000389124.2_Silent_p.R368R|GRIK1_ENST00000472429.1_5'UTR|GRIK1-AS2_ENST00000333765.4_Intron|GRIK1_ENST00000399909.1_Silent_p.R368R|GRIK1_ENST00000535441.1_Silent_p.R370R|GRIK1_ENST00000309434.7_Silent_p.R370R	NM_000830.3	NP_000821.1	P39086	GRIK1_HUMAN	glutamate receptor, ionotropic, kainate 1	368					adult behavior (GO:0030534)|behavioral response to pain (GO:0048266)|central nervous system development (GO:0007417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|nervous system development (GO:0007399)|positive regulation of gamma-aminobutyric acid secretion (GO:0014054)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(18)|ovary(1)|prostate(4)|skin(1)|stomach(1)|urinary_tract(1)	45					Topiramate(DB00273)	CCATCCCACCGGGCCTGTGGA	0.383																																					p.R368R		Atlas-SNP	.											.	GRIK1	293	.	0			c.C1102A						.						78	77	77					21																	30971254		2203	4300	6503	SO:0001819	synonymous_variant	2897	exon8			CCCACCGGGCCTG		CCDS33530.1, CCDS42913.1	21q22	2012-08-29			ENSG00000171189	ENSG00000171189		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4579	protein-coding gene	gene with protein product		138245		GLUR5		8468067	Standard	XM_005260942		Approved	GluK1	uc002yno.1	P39086	OTTHUMG00000078879	ENST00000399907.1:c.1102C>A	chr21.hg19:g.30971254G>T		48.0	0.0		45.0	4.0	NM_175611	Q13001|Q86SU9	Silent	SNP	ENST00000399907.1	hg19	CCDS42913.1																																																																																			.	G|1.000;A|0.000		0.383	GRIK1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171979.1			T	30971254	G	T	30971254	2	4	254	1	0	0	0	0	0	0	0	1	6782	1115	39	1		1	GRIK1	21	30971254	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10		30971254	17158641	992	35284										
TIAM1	7074	hgsc.bcm.edu	37	chr21	32639202	32639202	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtcttgtgcgagaggcgcagGgagcgggaagtgtgcttgcg	20	7	1	1	rs139712298		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr21:32639202G>T	ENST00000286827.3	-	5	558	c.87C>A	c.(85-87)tcC>tcA	p.S29S	TIAM1_ENST00000469412.1_Intron|TIAM1_ENST00000541036.1_Silent_p.S29S	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	29					apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						AGAGGCGCAGGGAGCGGGAAG	0.582																																					p.S29S		Atlas-SNP	.											.	TIAM1	522	.	0			c.C87A						.						45	47	46					21																	32639202		2203	4300	6503	SO:0001819	synonymous_variant	7074	exon5			GCGCAGGGAGCGG		CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.87C>A	chr21.hg19:g.32639202G>T		87.0	0.0		41.0	4.0	NM_003253	B7ZLR6|F5GZ53|Q17RT7	Silent	SNP	ENST00000286827.3	hg19	CCDS13609.1																																																																																			.	G|0.999;A|0.001		0.582	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253		T	32639202	G	T	32639202	2	4	254	1	0	0	0	0	0	0	0	1	15905	1219	43	3		3	TIAM1	21	32639202	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1667948	32639202	15490693	993	35285										
SFRS15	57466	hgsc.bcm.edu	37	chr21	33068944	33068944	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcagcagcaggcacggtggcGgtgggtgcagggggtactgc	21	9	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr21:33068944G>T	ENST00000286835.7	-	8	1279	c.897C>A	c.(895-897)acC>acA	p.T299T	SCAF4_ENST00000434667.3_Silent_p.T284T|SCAF4_ENST00000399804.1_Silent_p.T299T	NM_020706.2	NP_065757.1	O95104	SFR15_HUMAN	SR-related CTD-associated factor 4	299				T -> A (in Ref. 1; AAD09327). {ECO:0000305}.		nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(11)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						GCACGGTGGCGGTGGGTGCAG	0.532																																					p.T299T		Atlas-SNP	.											.	SCAF4	142	.	0			c.C897A						.						75	77	76					21																	33068944		2203	4300	6503	SO:0001819	synonymous_variant	57466	exon8			GGTGGCGGTGGGT	AB032998	CCDS33537.1, CCDS46644.1, CCDS54482.1	21q22.1	2013-02-12	2011-01-10	2011-01-10	ENSG00000156304	ENSG00000156304		"RNA binding motif (RRM) containing"	19304	protein-coding gene	gene with protein product			"splicing factor, arginine/serine-rich 15"	SFRS15		10574461	Standard	NM_020706		Approved	KIAA1172, DKFZp434E098, SRA4	uc002ypd.2	O95104	OTTHUMG00000084903	ENST00000286835.7:c.897C>A	chr21.hg19:g.33068944G>T		147.0	0.0		114.0	5.0	NM_020706	C9JLZ0|Q0P5W8|Q6P1M5|Q8N3I8|Q9UFM1|Q9ULP8	Silent	SNP	ENST00000286835.7	hg19	CCDS33537.1																																																																																			.	.		0.532	SCAF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000192659.1	XM_047889		T	33068944	G	T	33068944	2	4	254	1	0	0	0	0	0	0	0	1	14186	1103	39	1		1	SFRS15	21	33068944	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	429742	33068944	15060951	994	35286										
SLC5A3	6526	hgsc.bcm.edu	37	chr21	35469094	35469094	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctgtaattgtgagccttctcAcaccacctcccacaaaggaa	6	14	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr21:35469094A>T	ENST00000381151.3	+	2	2109	c.1597A>T	c.(1597-1599)Aca>Tca	p.T533S	MRPS6_ENST00000399312.2_Intron|AP000320.7_ENST00000362077.4_RNA|SLC5A3_ENST00000608209.1_Missense_Mutation_p.T533S			P53794	SC5A3_HUMAN	solute carrier family 5 (sodium/myo-inositol cotransporter), member 3	533					inositol metabolic process (GO:0006020)|peripheral nervous system development (GO:0007422)|regulation of respiratory gaseous exchange (GO:0043576)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	myo-inositol:sodium symporter activity (GO:0005367)			breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	20						GAGCCTTCTCACACCACCTCC	0.468																																					p.T533S		Atlas-SNP	.											SLC5A3,rectum,NS,0,1	SLC5A3	52	.	0			c.A1597T						.						80	69	73					21																	35469094		2203	4300	6503	SO:0001583	missense	6526	exon2			CTTCTCACACCAC		CCDS33549.1	21q22.11	2013-05-22	2008-09-02		ENSG00000198743	ENSG00000198743		"Solute carriers"	11038	protein-coding gene	gene with protein product		600444	"solute carrier family 5 (inositol transporter), member 3"			7789985	Standard	NM_006933		Approved	SMIT, SMIT1	uc002yto.3	P53794	OTTHUMG00000065821	ENST00000381151.3:c.1597A>T	chr21.hg19:g.35469094A>T	ENSP00000370543:p.Thr533Ser	146.0	0.0		100.0	5.0	NM_006933	O43489	Missense_Mutation	SNP	ENST00000381151.3	hg19	CCDS33549.1	.	.	.	.	.	.	.	.	.	.	A	18.54	3.646766	0.67358	.	.	ENSG00000198743	ENST00000381151	T	0.66460	-0.21	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.77219	0.4098	L	0.53729	1.69	0.46499	D	0.999071	D	0.63880	0.993	D	0.65010	0.931	T	0.79032	-0.1969	10	0.66056	D	0.02	.	15.1328	0.72539	1.0:0.0:0.0:0.0	.	533	P53794	SC5A3_HUMAN	S	533	ENSP00000370543:T533S	ENSP00000370543:T533S	T	+	1	0	SLC5A3	34390964	1.000000	0.71417	0.993000	0.49108	0.958000	0.62258	8.930000	0.92872	2.224000	0.72417	0.533000	0.62120	ACA	.	.		0.468	SLC5A3-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000141037.1			T	35469094	A	T	35469094	3	4	254	1	0	0	0	0	1	0	0	0	14681	159	6	4	1599	4	SLC5A3	21	35469094	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	2400150	35469094	12660801	995	35287										
PSMG1	8624	hgsc.bcm.edu	37	chr21	40553799	40553799	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tttgtcttcgaaggagccgcActtccctaacacaagaaaca	7	12	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr21:40553799A>G	ENST00000331573.3	-	2	605	c.140T>C	c.(139-141)gTg>gCg	p.V47A	PSMG1_ENST00000380900.2_Missense_Mutation_p.V47A|AF129408.17_ENST00000608767.1_RNA	NM_001261824.1|NM_003720.3	NP_001248753.1|NP_003711.1	O95456	PSMG1_HUMAN	proteasome (prosome, macropain) assembly chaperone 1	47					cerebellar granule cell precursor proliferation (GO:0021930)|proteasome assembly (GO:0043248)|proteasome core complex assembly (GO:0080129)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)				autonomic_ganglia(1)|endometrium(2)|large_intestine(1)|lung(1)|skin(1)|urinary_tract(2)	8		Prostate(19;8.44e-08)				AAGGAGCCGCACTTCCCTAAC	0.328																																					p.V47A		Atlas-SNP	.											.	PSMG1	11	.	0			c.T140C						.						46	46	46					21																	40553799		2202	4299	6501	SO:0001583	missense	8624	exon2			AGCCGCACTTCCC	AJ006291	CCDS13660.1, CCDS13661.1	21q22.3	2007-10-23	2007-10-23	2007-10-23	ENSG00000183527	ENSG00000183527			3043	protein-coding gene	gene with protein product		605296	"Down syndrome critical region gene 2"	DSCR2		10872820, 17189198	Standard	NM_003720		Approved	c21-LRP, LRPC21, PAC1	uc002yxi.4	O95456	OTTHUMG00000066034	ENST00000331573.3:c.140T>C	chr21.hg19:g.40553799A>G	ENSP00000329915:p.Val47Ala	94.0	0.0		89.0	6.0	NM_203433	B5BUN2|Q6FHA3|Q6FHD3|Q6S713	Missense_Mutation	SNP	ENST00000331573.3	hg19	CCDS13660.1	.	.	.	.	.	.	.	.	.	.	A	18.01	3.526782	0.64860	.	.	ENSG00000183527	ENST00000331573;ENST00000380900	T;T	0.57436	0.4;0.4	5.46	5.46	0.80206	.	0.191307	0.44285	D	0.000475	T	0.54951	0.1890	M	0.75264	2.295	0.42482	D	0.992866	B;B	0.33940	0.433;0.433	B;B	0.34452	0.183;0.183	T	0.61317	-0.7087	10	0.66056	D	0.02	-23.2354	13.4991	0.61442	1.0:0.0:0.0:0.0	.	47;47	O95456-2;O95456	.;PSMG1_HUMAN	A	47	ENSP00000329915:V47A;ENSP00000370286:V47A	ENSP00000329915:V47A	V	-	2	0	PSMG1	39475669	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.707000	0.68370	2.069000	0.61940	0.459000	0.35465	GTG	.	.		0.328	PSMG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141404.2	NM_003720		G	40553799	A	G	40553799	3	3	254	1	0	0	0	0	1	0	0	0	12723	159	6	2	750	2	PSMG1	21	40553799	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	5084705	40553799	7576096	996	35288										
HMGN1	3150	hgsc.bcm.edu	37	chr21	40717157	40717157	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cggcctgttttccctttgctCcccttttcccttttgtttgc	6	15	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr21:40717157C>A	ENST00000380749.5	-	5	452	c.170G>T	c.(169-171)gGa>gTa	p.G57V	Y_RNA_ENST00000517106.1_RNA|snoU13_ENST00000459446.1_RNA|HMGN1_ENST00000380747.1_Missense_Mutation_p.G73V|HMGN1_ENST00000380748.1_Missense_Mutation_p.G47V|HMGN1_ENST00000361263.4_Nonsense_Mutation_p.E21*|HMGN1_ENST00000489072.1_5'UTR	NM_004965.6	NP_004956.5	P05114	HMGN1_HUMAN	high mobility group nucleosome binding domain 1	57					chromatin organization (GO:0006325)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|post-embryonic camera-type eye morphogenesis (GO:0048597)|pyrimidine dimer repair by nucleotide-excision repair (GO:0000720)|regulation of development, heterochronic (GO:0040034)|regulation of epithelial cell proliferation (GO:0050678)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to UV-B (GO:0010224)|response to UV-C (GO:0010225)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(2)|lung(1)	3		Prostate(19;8.69e-07)				TCCCTTTGCTCCCCTTTTCCC	0.383																																					p.G57V		Atlas-SNP	.											.	HMGN1	8	.	0			c.G170T						.						77	66	70					21																	40717157		2203	4297	6500	SO:0001583	missense	3150	exon5			TTTGCTCCCCTTT		CCDS33559.1	21q22.3	2011-07-01	2011-04-05	2002-08-16	ENSG00000205581	ENSG00000205581		"High-mobility group / Canonical"	4984	protein-coding gene	gene with protein product	"high-mobility group nucleosome binding 1", "nonhistone chromosomal protein HMG-14"	163920	"high-mobility group (nonhistone chromosomal) protein 14", "high-mobility group nucleosome binding domain 1"	HMG14		3782107, 2563381	Standard	NM_004965		Approved	FLJ27265, FLJ31471, MGC104230, MGC117425	uc002yxo.3	P05114	OTTHUMG00000066178	ENST00000380749.5:c.170G>T	chr21.hg19:g.40717157C>A	ENSP00000370125:p.Gly57Val	151.0	0.0		118.0	5.0	NM_004965	Q3KQR8	Missense_Mutation	SNP	ENST00000380749.5	hg19	CCDS33559.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	42|42	9.260701|9.260701	0.99117|0.99117	.|.	.|.	ENSG00000205581|ENSG00000205581	ENST00000361263|ENST00000380749;ENST00000380748;ENST00000380747	.|.	.|.	.|.	4.57|4.57	3.68|3.68	0.42216|0.42216	.|.	0.000000|.	0.34628|.	N|.	0.003812|.	.|T	.|0.59932	.|0.2230	L|L	0.49640|0.49640	1.575|1.575	0.80722|0.80722	A|A	1|1	.|P	.|0.48016	.|0.904	.|P	.|0.54629	.|0.757	.|T	.|0.71663	.|-0.4525	.|7	0.87932|0.87932	D|D	0|0	.|.	12.3827|12.3827	0.55315|0.55315	0.0:0.9177:0.0:0.0823|0.0:0.9177:0.0:0.0823	.|.	.|57	.|P05114	.|HMGN1_HUMAN	X|V	21|57;47;73	.|.	ENSP00000355293:E21X|ENSP00000370123:G73V	E|G	-|-	1|2	0|0	HMGN1|HMGN1	39639027|39639027	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	2.451000|2.451000	0.44952|0.44952	0.925000|0.925000	0.37094|0.37094	0.591000|0.591000	0.81541|0.81541	GAG|GGA	.	.		0.383	HMGN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141645.2	NM_004965		A	40717157	C	A	40717157	3	1	254	1	0	0	0	0	1	0	0	0	7243	855	30	3	140	3	HMGN1	21	40717157	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	163358	40717157	7412738	997	35289										
KRTAP10-7	386675	hgsc.bcm.edu	37	chr21	46020985	46020985	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agcttgctgcacctcctcccCctgccagcaggcctgctgtg	10	18	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr21:46020985C>A	ENST00000380102.2	+	1	489	c.464C>A	c.(463-465)cCc>cAc	p.P155H	TSPEAR_ENST00000323084.4_Intron	NM_198689.2	NP_941962.1	P60409	KR107_HUMAN	keratin associated protein 10-7	155	30 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				breast(1)|large_intestine(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8						ACCTCCTCCCCCTGCCAGCAG	0.592																																					p.P150H		Atlas-SNP	.											.	KRTAP10-7	41	.	0			c.C449A						.						62	66	65					21																	46020985		2196	4293	6489	SO:0001583	missense	386675	exon2			CCTCCCCCTGCCA	AJ566385	CCDS74803.1	21q22.3	2014-04-10			ENSG00000205441	ENSG00000272804		"Keratin associated proteins"	22970	protein-coding gene	gene with protein product				KRTAP18-7			Standard	NM_198689		Approved	KAP10.7, KAP18.7	uc002zfn.4	P60409	OTTHUMG00000188307	ENST00000380102.2:c.464C>A	chr21.hg19:g.46020985C>A	ENSP00000369445:p.Pro155His	630.0	0.0		437.0	120.0	NM_198689	Q0VDJ8|Q70LJ2	Missense_Mutation	SNP	ENST00000380102.2	hg19		.	.	.	.	.	.	.	.	.	.	N	0.395	-0.921520	0.02396	.	.	ENSG00000205441	ENST00000380102	T	0.01397	4.94	3.06	-0.735	0.11137	.	.	.	.	.	T	0.04272	0.0118	M	0.90759	3.145	0.09310	N	1	D	0.55605	0.972	P	0.45449	0.481	T	0.28554	-1.0040	9	0.34782	T	0.22	.	11.7141	0.51641	0.0:0.5698:0.4302:0.0	.	150	P60409-2	.	H	155	ENSP00000369445:P155H	ENSP00000369445:P155H	P	+	2	0	KRTAP10-7	44845413	0.000000	0.05858	0.000000	0.03702	0.103000	0.19146	-0.543000	0.06084	-0.048000	0.13401	0.460000	0.39030	CCC	.	.		0.592	KRTAP10-7-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000128038.1	NM_198689		A	46020985	C	A	46020985	3	1	254	1	0	0	0	0	1	0	0	0	8523	623	22	3	455	3	KRTAP10-7	21	46020985	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	5303828	46020985	2108910	998	35290										
LSS	4047	hgsc.bcm.edu	37	chr21	47616149	47616149	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	catcggccctctgctgccgcCgacagaactctaagccctgc	9	18	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr21:47616149C>A	ENST00000397728.3	-	18	1781	c.1703G>T	c.(1702-1704)cGg>cTg	p.R568L	LSS_ENST00000457828.2_Missense_Mutation_p.R488L|LSS_ENST00000356396.4_Missense_Mutation_p.R568L|AP001468.1_ENST00000594486.1_5'Flank|LSS_ENST00000522411.1_Missense_Mutation_p.R557L	NM_001145436.1|NM_002340.5	NP_001138908.1|NP_002331.3	P48449	ERG7_HUMAN	lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)	568					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|lipid particle (GO:0005811)|membrane (GO:0016020)	lanosterol synthase activity (GO:0000250)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|skin(1)|urinary_tract(1)	21	Breast(49;0.214)					CTGCTGCCGCCGACAGAACTC	0.557																																					p.R568L	Pancreas(114;955 2313 34923 50507)	Atlas-SNP	.											.	LSS	50	.	0			c.G1703T						.						70	67	68					21																	47616149		2203	4300	6503	SO:0001583	missense	4047	exon18			TGCCGCCGACAGA	U22526	CCDS13733.1, CCDS46654.1, CCDS54489.1	21q22.3	1998-05-07			ENSG00000160285	ENSG00000160285	5.4.99.7		6708	protein-coding gene	gene with protein product		600909				7639730, 8655142	Standard	NM_001001438		Approved	OSC	uc002zij.3	P48449	OTTHUMG00000090633	ENST00000397728.3:c.1703G>T	chr21.hg19:g.47616149C>A	ENSP00000380837:p.Arg568Leu	72.0	0.0		41.0	4.0	NM_001001438	B4DJZ9|D3DSN0|E9PEI9|G5E9Q9|Q8IYL6|Q9UEZ1	Missense_Mutation	SNP	ENST00000397728.3	hg19	CCDS13733.1	.	.	.	.	.	.	.	.	.	.	C	14.06	2.422737	0.43020	.	.	ENSG00000160285	ENST00000356396;ENST00000457828;ENST00000397728;ENST00000522411	T;T;T;T	0.16743	2.32;2.32;2.32;2.32	5.4	3.52	0.40303	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);	0.246093	0.39407	N	0.001376	T	0.12008	0.0292	N	0.26092	0.79	0.53688	D	0.999974	B;B	0.14438	0.008;0.01	B;B	0.14578	0.004;0.011	T	0.07328	-1.0778	10	0.44086	T	0.13	.	10.0437	0.42173	0.1371:0.7901:0.0:0.0728	.	557;568	E9PEI9;P48449	.;ERG7_HUMAN	L	568;488;568;557	ENSP00000348762:R568L;ENSP00000409191:R488L;ENSP00000380837:R568L;ENSP00000429133:R557L	ENSP00000348762:R568L	R	-	2	0	LSS	46440577	0.662000	0.27439	0.705000	0.30386	0.276000	0.26787	1.324000	0.33712	1.284000	0.44531	0.462000	0.41574	CGG	.	.		0.557	LSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207274.2			A	47616149	C	A	47616149	3	1	254	1	0	0	0	0	1	0	0	0	9074	652	23	1	515	1	LSS	21	47616149	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1595164	47616149	513746	999	35291										
LSS	4047	hgsc.bcm.edu	37	chr21	47647541	47647541	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctgcagccccacgtaaaatgTcatcccgttcagagccccct	7	17	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr21:47647541T>C	ENST00000397728.3	-	3	322	c.244A>G	c.(244-246)Aca>Gca	p.T82A	MCM3AP-AS1_ENST00000588753.1_RNA|LSS_ENST00000457828.2_Missense_Mutation_p.T2A|MCM3AP-AS1_ENST00000591223.1_RNA|MCM3AP-AS1_ENST00000590829.1_RNA|MCM3AP-AS1_ENST00000444998.1_RNA|MCM3AP-AS1_ENST00000414659.1_RNA|MCM3AP-AS1_ENST00000420074.1_RNA|LSS_ENST00000356396.4_Missense_Mutation_p.T82A|LSS_ENST00000464357.1_5'UTR|LSS_ENST00000522411.1_Missense_Mutation_p.T82A|MCM3AP-AS1_ENST00000455567.1_RNA|MCM3AP-AS1_ENST00000432735.1_RNA|MCM3AP-AS1_ENST00000421927.1_RNA	NM_001145436.1|NM_002340.5	NP_001138908.1|NP_002331.3	P48449	ERG7_HUMAN	lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)	82					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|lipid particle (GO:0005811)|membrane (GO:0016020)	lanosterol synthase activity (GO:0000250)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|skin(1)|urinary_tract(1)	21	Breast(49;0.214)					ACGTAAAATGTCATCCCGTTC	0.517																																					p.T82A	Pancreas(114;955 2313 34923 50507)	Atlas-SNP	.											.	LSS	50	.	0			c.A244G						.						134	123	127					21																	47647541		2203	4300	6503	SO:0001583	missense	4047	exon3			AAAATGTCATCCC	U22526	CCDS13733.1, CCDS46654.1, CCDS54489.1	21q22.3	1998-05-07			ENSG00000160285	ENSG00000160285	5.4.99.7		6708	protein-coding gene	gene with protein product		600909				7639730, 8655142	Standard	NM_001001438		Approved	OSC	uc002zij.3	P48449	OTTHUMG00000090633	ENST00000397728.3:c.244A>G	chr21.hg19:g.47647541T>C	ENSP00000380837:p.Thr82Ala	148.0	0.0		89.0	4.0	NM_001145436	B4DJZ9|D3DSN0|E9PEI9|G5E9Q9|Q8IYL6|Q9UEZ1	Missense_Mutation	SNP	ENST00000397728.3	hg19	CCDS13733.1	.	.	.	.	.	.	.	.	.	.	T	11.50	1.656718	0.29425	.	.	ENSG00000160285	ENST00000356396;ENST00000457828;ENST00000397728;ENST00000522411;ENST00000450351	T;T;T;T;T	0.18016	2.24;2.24;2.24;2.24;2.24	5.34	1.33	0.21861	.	1.211620	0.05461	N	0.551125	T	0.11836	0.0288	L	0.28556	0.865	0.09310	N	0.999993	B;B	0.06786	0.001;0.001	B;B	0.09377	0.004;0.001	T	0.34153	-0.9840	10	0.11794	T	0.64	.	6.8694	0.24113	0.0:0.0924:0.2739:0.6336	.	82;82	E9PEI9;P48449	.;ERG7_HUMAN	A	82;2;82;82;83	ENSP00000348762:T82A;ENSP00000409191:T2A;ENSP00000380837:T82A;ENSP00000429133:T82A;ENSP00000391368:T83A	ENSP00000348762:T82A	T	-	1	0	LSS	46471969	0.013000	0.17824	0.406000	0.26421	0.965000	0.64279	0.093000	0.15086	0.872000	0.35775	0.459000	0.35465	ACA	.	.		0.517	LSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207274.2			C	47647541	T	C	47647541	3	2	254	1	0	0	0	0	1	0	0	0	9074	1667	58	2	2034	2	LSS	21	47647541	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	31392	47647541	482354	1000	35292										
MCM3AP	8888	hgsc.bcm.edu	37	chr21	47680812	47680812	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttaacaccagctctctctctTgtttcaacctacagggaaga	6	12	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr21:47680812T>C	ENST00000397708.1	-	16	3730	c.3476A>G	c.(3475-3477)cAa>cGa	p.Q1159R	MCM3AP_ENST00000291688.1_Missense_Mutation_p.Q1159R|MCM3AP-AS1_ENST00000590829.1_RNA|MCM3AP_ENST00000467026.1_5'Flank			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	1159					DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					CTCTCTCTCTTGTTTCAACCT	0.483																																					p.Q1159R		Atlas-SNP	.											.	MCM3AP	146	.	0			c.A3476G						.						94	88	90					21																	47680812		2203	4300	6503	SO:0001583	missense	8888	exon15			CTCTCTTGTTTCA	AB005543	CCDS13734.1	21q22.3	2012-12-19	2007-04-04		ENSG00000160294	ENSG00000160294			6946	protein-coding gene	gene with protein product	"germinal-centre associated nuclear protein"	603294	"minichromosome maintenance deficient (S. cerevisiae) 3-associated protein", "MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein"			9712829, 16914116, 21195085	Standard	XM_005261205		Approved	Map80, KIAA0572, GANP, SAC3	uc002zir.1	O60318	OTTHUMG00000090630	ENST00000397708.1:c.3476A>G	chr21.hg19:g.47680812T>C	ENSP00000380820:p.Gln1159Arg	122.0	0.0		54.0	4.0	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Missense_Mutation	SNP	ENST00000397708.1	hg19	CCDS13734.1	.	.	.	.	.	.	.	.	.	.	T	6.224	0.409415	0.11812	.	.	ENSG00000160294	ENST00000397708;ENST00000291688	D;D	0.84660	-1.88;-1.88	5.35	1.36	0.22044	.	0.058491	0.64402	D	0.000001	T	0.71341	0.3328	L	0.29908	0.895	0.33099	D	0.538958	B	0.06786	0.001	B	0.04013	0.001	T	0.64415	-0.6413	10	0.26408	T	0.33	-12.0821	5.4631	0.16627	0.1285:0.1491:0.0:0.7224	.	1159	O60318	MCM3A_HUMAN	R	1159	ENSP00000380820:Q1159R;ENSP00000291688:Q1159R	ENSP00000291688:Q1159R	Q	-	2	0	MCM3AP	46505240	0.659000	0.27411	0.998000	0.56505	0.212000	0.24457	0.104000	0.15313	0.869000	0.35703	-0.376000	0.06991	CAA	.	.		0.483	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906		C	47680812	T	C	47680812	3	2	254	1	0	0	0	0	1	0	0	0	9397	1812	63	2	2522	2	MCM3AP	21	47680812	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	33271	47680812	449083	1001	35293										
DGCR14	8220	hgsc.bcm.edu	37	chr22	19126802	19126802	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	acagctgctcctcgtcagggAcacctggcagacgaagcaaa	11	13	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:19126802A>G	ENST00000252137.6	-	6	735	c.692T>C	c.(691-693)gTc>gCc	p.V231A		NM_022719.2	NP_073210.1	Q96DF8	DGC14_HUMAN	DiGeorge syndrome critical region gene 14	231					mRNA splicing, via spliceosome (GO:0000398)|nervous system development (GO:0007399)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)	16	Colorectal(54;0.0993)					CTCGTCAGGGACACCTGGCAG	0.587																																					p.V231A		Atlas-SNP	.											.	DGCR14	43	.	0			c.T692C						.						33	33	33					22																	19126802		2203	4300	6503	SO:0001583	missense	8220	exon6			TCAGGGACACCTG	L77566	CCDS13756.1	22q11.21	2007-02-20			ENSG00000100056	ENSG00000100056			16817	protein-coding gene	gene with protein product		601755	"DiGeorge syndrome critical region gene 13"	DGCR13		8776594, 9063747	Standard	NM_022719		Approved	DGSI, Es2el, ES2, DGS-H	uc002zou.3	Q96DF8	OTTHUMG00000150119	ENST00000252137.6:c.692T>C	chr22.hg19:g.19126802A>G	ENSP00000252137:p.Val231Ala	61.0	0.0		78.0	4.0	NM_022719	Q49AH7|Q9BTZ4	Missense_Mutation	SNP	ENST00000252137.6	hg19	CCDS13756.1	.	.	.	.	.	.	.	.	.	.	A	17.97	3.518884	0.64634	.	.	ENSG00000100056	ENST00000252137	T	0.46819	0.86	5.03	5.03	0.67393	.	0.062809	0.64402	D	0.000006	T	0.54159	0.1841	L	0.52206	1.635	0.58432	D	0.999998	D	0.55605	0.972	P	0.56563	0.801	T	0.48410	-0.9038	10	0.15066	T	0.55	-33.843	14.4069	0.67088	1.0:0.0:0.0:0.0	.	231	Q96DF8	DGC14_HUMAN	A	231	ENSP00000252137:V231A	ENSP00000252137:V231A	V	-	2	0	DGCR14	17506802	1.000000	0.71417	1.000000	0.80357	0.568000	0.35870	6.453000	0.73488	1.887000	0.54652	0.460000	0.39030	GTC	.	.		0.587	DGCR14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316432.2			G	19126802	A	G	19126802	3	3	254	1	0	0	0	0	1	0	0	0	4462	275	10	2	758	2	DGCR14	22	19126802	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10		19126802	32177764	1002	35294										
CCDC116	164592	hgsc.bcm.edu	37	chr22	21989356	21989356	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctgccgcgacggccgtcctcTgttccccaccagcttggagc	11	18	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:21989356T>C	ENST00000292779.3	+	4	1165	c.1004T>C	c.(1003-1005)cTg>cCg	p.L335P	CCDC116_ENST00000607942.1_Missense_Mutation_p.L335P	NM_152612.2	NP_689825.2	Q8IYX3	CC116_HUMAN	coiled-coil domain containing 116	335										endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(5)	22	Colorectal(54;0.105)					GGCCGTCCTCTGTTCCCCACC	0.667																																					p.L335P		Atlas-SNP	.											.	CCDC116	56	.	0			c.T1004C						.						37	39	38					22																	21989356		2203	4300	6503	SO:0001583	missense	164592	exon4			GTCCTCTGTTCCC	BC033499	CCDS13791.1	22q11.21	2006-06-27			ENSG00000161180	ENSG00000161180			26688	protein-coding gene	gene with protein product						12477932	Standard	NM_152612		Approved	FLJ36046	uc002zve.3	Q8IYX3	OTTHUMG00000150821	ENST00000292779.3:c.1004T>C	chr22.hg19:g.21989356T>C	ENSP00000292779:p.Leu335Pro	103.0	0.0		60.0	6.0	NM_152612	Q8N9Y9	Missense_Mutation	SNP	ENST00000292779.3	hg19	CCDS13791.1	.	.	.	.	.	.	.	.	.	.	T	12.40	1.925438	0.34002	.	.	ENSG00000161180	ENST00000292779	T	0.28069	1.63	4.39	3.36	0.38483	.	0.000000	0.45606	D	0.000348	T	0.42381	0.1200	L	0.47190	1.495	0.54753	D	0.999985	D;D	0.89917	1.0;0.964	D;P	0.91635	0.999;0.684	T	0.34453	-0.9828	10	0.87932	D	0	-64.7756	6.0141	0.19592	0.0:0.1146:0.0:0.8854	.	335;335	B7Z7H5;Q8IYX3-2	.;.	P	335	ENSP00000292779:L335P	ENSP00000292779:L335P	L	+	2	0	CCDC116	20319356	0.980000	0.34600	0.996000	0.52242	0.027000	0.11550	1.841000	0.39240	1.986000	0.57962	0.459000	0.35465	CTG	.	.		0.667	CCDC116-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320199.1	NM_152612		C	21989356	T	C	21989356	3	2	254	1	0	0	0	0	1	0	0	0	2755	1580	55	2	1014	2	CCDC116	22	21989356	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	2862554	21989356	29315210	1003	35295										
SDF2L1	23753	hgsc.bcm.edu	37	chr22	21998435	21998435	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcttcatcaagcctagtgtgGagccctctgcaggtcacgat	10	12	5	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:21998435G>T	ENST00000248958.4	+	3	713	c.637G>T	c.(637-639)Gag>Tag	p.E213*	KB-1440D3.14_ENST00000609038.1_lincRNA	NM_022044.2	NP_071327.2	Q9HCN8	SDF2L_HUMAN	stromal cell-derived factor 2-like 1	213						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				prostate(1)	1	Colorectal(54;0.105)					GCCTAGTGTGGAGCCCTCTGC	0.592											OREG0026342	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E213X		Atlas-SNP	.											.	SDF2L1	5	.	0			c.G637T						.						104	85	92					22																	21998435		2203	4300	6503	SO:0001587	stop_gained	23753	exon3			AGTGTGGAGCCCT		CCDS13792.1	22q11.21	2008-07-01			ENSG00000128228	ENSG00000128228			10676	protein-coding gene	gene with protein product	"dihydropyrimidinase-like 2", "PWP1-interacting protein 8"	607551				10591208, 11162531	Standard	NM_022044		Approved	AP000553.C22.4, OTTHUMT00000075032	uc002zvf.3	Q9HCN8	OTTHUMG00000150820	ENST00000248958.4:c.637G>T	chr22.hg19:g.21998435G>T	ENSP00000248958:p.Glu213*	110.0	0.0	752	87.0	4.0	NM_022044	A2RUD3|Q9BRI5	Nonsense_Mutation	SNP	ENST00000248958.4	hg19	CCDS13792.1	.	.	.	.	.	.	.	.	.	.	G	35	5.505302	0.96371	.	.	ENSG00000128228	ENST00000248958	.	.	.	4.62	4.62	0.57501	.	1.157710	0.07026	U	0.827620	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.494	12.8923	0.58078	0.0:0.0:1.0:0.0	.	.	.	.	X	213	.	ENSP00000248958:E213X	E	+	1	0	SDF2L1	20328435	1.000000	0.71417	0.469000	0.27204	0.991000	0.79684	4.782000	0.62396	2.404000	0.81709	0.479000	0.44913	GAG	.	.		0.592	SDF2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320197.1	NM_022044		T	21998435	G	T	21998435	4	4	254	1	0	0	0	0	0	1	0	0	13976	1175	41	3	647	3	SDF2L1	22	21998435	Nonsense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	9079	21998435	29306131	1004	35296										
PIWIL3	440822	hgsc.bcm.edu	37	chr22	25153957	25153957	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	actccaccaatccttctctcCtgcaagggcgctgtatgcaa	7	15	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:25153957C>A	ENST00000332271.5	-	4	689	c.273G>T	c.(271-273)caG>caT	p.Q91H	PIWIL3_ENST00000527701.1_De_novo_Start_OutOfFrame|PIWIL3_ENST00000533313.1_De_novo_Start_OutOfFrame|PIWIL3_ENST00000532537.2_5'UTR	NM_001008496.3|NM_001255975.1	NP_001008496.2|NP_001242904.1	Q7Z3Z3	PIWL3_HUMAN	piwi-like RNA-mediated gene silencing 3	91					cell differentiation (GO:0030154)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	RNA binding (GO:0003723)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(15)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50						TCCTTCTCTCCTGCAAGGGCG	0.443																																					p.Q91H		Atlas-SNP	.											.	PIWIL3	115	.	0			c.G273T						.						205	212	210					22																	25153957		2203	4300	6503	SO:0001583	missense	440822	exon4			TCTCTCCTGCAAG	AB079368	CCDS33623.1	22q11.23	2013-02-15	2013-02-15		ENSG00000184571	ENSG00000184571		"Argonaute/PIWI family"	18443	protein-coding gene	gene with protein product		610314	"piwi-like 3 (Drosophila)"			12906857	Standard	NM_001008496		Approved	HIWI3	uc003abd.2	Q7Z3Z3	OTTHUMG00000150788	ENST00000332271.5:c.273G>T	chr22.hg19:g.25153957C>A	ENSP00000330031:p.Gln91His	156.0	0.0		122.0	5.0	NM_001008496		Missense_Mutation	SNP	ENST00000332271.5	hg19	CCDS33623.1	.	.	.	.	.	.	.	.	.	.	C	3.457	-0.110792	0.06924	.	.	ENSG00000184571	ENST00000332271	T	0.04406	3.63	2.32	1.29	0.21616	.	11.182200	0.01436	U	0.014939	T	0.04318	0.0119	N	0.22421	0.69	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.38585	-0.9654	10	0.45353	T	0.12	0.251	2.9136	0.05745	0.2713:0.5712:0.0:0.1575	.	91;91	B4DYF7;Q7Z3Z3	.;PIWL3_HUMAN	H	91	ENSP00000330031:Q91H	ENSP00000330031:Q91H	Q	-	3	2	PIWIL3	23483957	.	.	0.000000	0.03702	0.007000	0.05969	.	.	0.552000	0.29026	0.455000	0.32223	CAG	.	.		0.443	PIWIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320084.2	NM_001008496		A	25153957	C	A	25153957	3	1	254	1	0	0	0	0	1	0	0	0	11968	680	24	3	2447	3	PIWIL3	22	25153957	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	3155522	25153957	26150609	1005	35297										
SGSM1	129049	hgsc.bcm.edu	37	chr22	25280066	25280066	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	accgtgagaacccacctatcAgccctggtcaatcacatgat	7	14	3	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:25280066A>G	ENST00000400359.4	+	16	1714	c.1707A>G	c.(1705-1707)tcA>tcG	p.S569S	SGSM1_ENST00000400358.4_Silent_p.S514S	NM_001039948.2|NM_133454.2	NP_001035037.1|NP_597711.1	Q2NKQ1	SGSM1_HUMAN	small G protein signaling modulator 1	569						Golgi apparatus (GO:0005794)	Rab GTPase activator activity (GO:0005097)			NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(14)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	41						CCCACCTATCAGCCCTGGTCA	0.582																																					p.S569S		Atlas-SNP	.											.	SGSM1	150	.	0			c.A1707G						.						66	66	66					22																	25280066		2048	4192	6240	SO:0001819	synonymous_variant	129049	exon16			CCTATCAGCCCTG	AB075821	CCDS46674.1, CCDS46675.1, CCDS74834.1	22q11.23	2013-07-09	2007-08-14	2007-08-14	ENSG00000167037	ENSG00000167037		"Small G protein signaling modulators"	29410	protein-coding gene	gene with protein product		611417	"RUN and TBC1 domain containing 2"	RUTBC2		11853319, 17509819, 22637480	Standard	NM_133454		Approved	KIAA1941	uc003abg.2	Q2NKQ1	OTTHUMG00000150837	ENST00000400359.4:c.1707A>G	chr22.hg19:g.25280066A>G		72.0	0.0		68.0	4.0	NM_133454	A5LGW1|A8MUT4|B0QYW0|B0QYW1|B5MEG1|B9A6J4|Q5TFL3|Q8TF60	Silent	SNP	ENST00000400359.4	hg19	CCDS46674.1																																																																																			.	.		0.582	SGSM1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320282.1	XM_059318		G	25280066	A	G	25280066	2	3	254	1	0	0	0	0	0	0	0	1	14237	175	7	2		2	SGSM1	22	25280066	Silent	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	126109	25280066	26024500	1006	35298										
ZNRF3	84133	hgsc.bcm.edu	37	chr22	29445350	29445350	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggactcccacggcaaccccgTcaccttgctgaccatggacc	9	18	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:29445350T>C	ENST00000544604.2	+	8	1356	c.1181T>C	c.(1180-1182)gTc>gCc	p.V394A	ZNRF3_ENST00000406323.3_Missense_Mutation_p.V294A|ZNRF3_ENST00000402174.1_Missense_Mutation_p.V294A|ZNRF3_ENST00000332811.4_Missense_Mutation_p.V294A	NM_001206998.1	NP_001193927.1	Q9ULT6	ZNRF3_HUMAN	zinc and ring finger 3	394					canonical Wnt signaling pathway (GO:0060070)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of non-canonical Wnt signaling pathway (GO:2000051)|protein ubiquitination (GO:0016567)|stem cell proliferation (GO:0072089)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	integral component of plasma membrane (GO:0005887)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(4)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	28						GGCAACCCCGTCACCTTGCTG	0.667																																					p.V394A		Atlas-SNP	.											.	ZNRF3	75	.	0			c.T1181C						.						56	64	61					22																	29445350		2180	4280	6460	SO:0001583	missense	84133	exon8			ACCCCGTCACCTT	AB051436	CCDS42999.1, CCDS56225.1	22q12.1	2013-01-09			ENSG00000183579	ENSG00000183579		"RING-type (C3HC4) zinc fingers"	18126	protein-coding gene	gene with protein product		612062				10574461	Standard	NM_032173		Approved	KIAA1133, BK747E2.3, FLJ22057, RNF203	uc003aeg.3	Q9ULT6	OTTHUMG00000151009	ENST00000544604.2:c.1181T>C	chr22.hg19:g.29445350T>C	ENSP00000443824:p.Val394Ala	80.0	0.0		101.0	5.0	NM_001206998	B3KU18|Q6ICH1|Q6NTF8|Q8WU18	Missense_Mutation	SNP	ENST00000544604.2	hg19	CCDS56225.1	.	.	.	.	.	.	.	.	.	.	T	10.42	1.345420	0.24426	.	.	ENSG00000183579	ENST00000544604;ENST00000332811;ENST00000462485;ENST00000402174;ENST00000406323	T;T;T;T	0.79940	-1.32;-1.32;-1.32;-1.32	5.53	4.5	0.54988	.	0.316033	0.36665	N	0.002471	T	0.67702	0.2921	L	0.44542	1.39	0.34781	D	0.734712	P	0.45531	0.86	B	0.37692	0.256	T	0.70029	-0.4984	10	0.07325	T	0.83	-5.454	10.3398	0.43870	0.0:0.0764:0.0:0.9236	.	394	Q9ULT6	ZNRF3_HUMAN	A	394;294;101;294;294	ENSP00000443824:V394A;ENSP00000328614:V294A;ENSP00000384456:V294A;ENSP00000384553:V294A	ENSP00000328614:V294A	V	+	2	0	ZNRF3	27775350	1.000000	0.71417	0.291000	0.24904	0.272000	0.26649	7.390000	0.79816	0.945000	0.37605	0.533000	0.62120	GTC	.	.		0.667	ZNRF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320943.2	XM_290972		C	29445350	T	C	29445350	3	2	254	1	0	0	0	0	1	0	0	0	18228	1667	58	2	907	2	ZNRF3	22	29445350	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	4165284	29445350	21859216	1007	35299										
GAS2L1	10633	hgsc.bcm.edu	37	chr22	29706428	29706428	+	IGR	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	accctctctctctggcctcaGgtgagggagattctgggccg	13	13	4	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:29706428G>T	ENST00000216101.6	-	0	1490				GAS2L1_ENST00000403764.1_Splice_Site|GAS2L1_ENST00000471961.1_Splice_Site|GAS2L1_ENST00000407854.1_Splice_Site|GAS2L1_ENST00000341313.6_Splice_Site|GAS2L1_ENST00000407647.2_Splice_Site|GAS2L1_ENST00000406549.3_Splice_Site|GAS2L1_ENST00000360113.2_Splice_Site	NM_006477.4	NP_006468.1	Q92737	RSLAA_HUMAN	RAS-like, family 10, member A						small GTPase mediated signal transduction (GO:0007264)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)	1						TCTGGCCTCAGGTGAGGGAGA	0.592																																					.		Atlas-SNP	.											.	GAS2L1	54	.	0			c.634-1G>T						.						68	68	68					22																	29706428		2203	4300	6503	SO:0001628	intergenic_variant	10634	exon3			GCCTCAGGTGAGG	Y07847	CCDS13854.1	22q12.2	2014-05-09			ENSG00000100276	ENSG00000100276			16954	protein-coding gene	gene with protein product		602220				8975699, 15731001	Standard	NM_006477		Approved	RRP22	uc031rxl.1	Q92737	OTTHUMG00000151106		chr22.hg19:g.29706428G>T		129.0	0.0		173.0	72.0	NM_152237	Q49AU5|Q6PI03	Splice_Site	SNP	ENST00000216101.6	hg19	CCDS13854.1	.	.	.	.	.	.	.	.	.	.	g	17.35	3.366389	0.61513	.	.	ENSG00000185340	ENST00000407647;ENST00000333679;ENST00000406549;ENST00000360113;ENST00000341313;ENST00000403764;ENST00000471961;ENST00000407854	.	.	.	4.6	4.6	0.57074	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.031	0.86461	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GAS2L1	28036428	1.000000	0.71417	1.000000	0.80357	0.606000	0.37113	9.633000	0.98432	2.104000	0.64026	0.486000	0.48141	.	.	.		0.592	RASL10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321342.1			T	29706428	G	T	29706428	1	4	254	0	1	0	0	0	0	0	0	0	6254	1014	35	3		3	GAS2L1	22	29706428	IGR	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	261078	29706428	21598138	1008	35300										
C22orf30	253143	hgsc.bcm.edu	37	chr22	32084215	32084215	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aaactccttcttctttaaccTgaaaagaaataaggaaaaaa	4	7	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:32084215T>C	ENST00000327423.6	-	8	6297		c.e8-2		PRR14L_ENST00000434485.1_Splice_Site|PRR14L_ENST00000397493.2_Splice_Site	NM_173566.2	NP_775837.2	Q5THK1	PR14L_HUMAN	proline rich 14-like											endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(5)|skin(1)|urinary_tract(2)	14						TTCTTTAACCTGAAAAGAAAT	0.363																																					.		Atlas-SNP	.											.	PRR14L	198	.	0			c.6108-2A>G						.						45	44	44					22																	32084215		2200	4297	6497	SO:0001630	splice_region_variant	253143	exon9			TTAACCTGAAAAG	BC040859	CCDS13900.2	22q12.2	2011-01-25	2011-01-25	2011-01-25	ENSG00000183530	ENSG00000183530			28738	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 30"	C22orf30		12477932	Standard	NM_173566		Approved	MGC50372	uc003alp.4	Q5THK1	OTTHUMG00000030139	ENST00000327423.6:c.6108-2A>G	chr22.hg19:g.32084215T>C		100.0	0.0		80.0	4.0	NM_173566	Q5THK4|Q6ZNN1|Q6ZWH0|Q8IW74|Q9H5T4	Splice_Site	SNP	ENST00000327423.6	hg19	CCDS13900.2	.	.	.	.	.	.	.	.	.	.	T	20.4	3.977291	0.74360	.	.	ENSG00000183530	ENST00000330495;ENST00000397493;ENST00000327423;ENST00000434485	.	.	.	5.32	5.32	0.75619	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4468	0.67356	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	PRR14L	30414215	1.000000	0.71417	0.992000	0.48379	0.942000	0.58702	6.308000	0.72820	2.005000	0.58758	0.482000	0.46254	.	.	.		0.363	PRR14L-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074993.2	NM_173566	Intron	C	32084215	T	C	32084215	5	2	254	1	0	0	0	0	0	0	1	0	2144	1594	55	2	357	2	C22orf30	22	32084215	Splice_Site	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	2377787	32084215	19220351	1009	35301										
DEPDC5	9681	hgsc.bcm.edu	37	chr22	32275652	32275652	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgcctttctcctgccctggcTgcctagccggccagcctcct	9	19	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:32275652T>C	ENST00000382112.3	+	37	3990	c.3920T>C	c.(3919-3921)cTg>cCg	p.L1307P	DEPDC5_ENST00000539165.1_Missense_Mutation_p.L133P|DEPDC5_ENST00000382105.2_Missense_Mutation_p.C1202R|DEPDC5_ENST00000266091.3_Missense_Mutation_p.L1294P|DEPDC5_ENST00000400249.2_Missense_Mutation_p.L1285P|DEPDC5_ENST00000400248.2_Missense_Mutation_p.L1285P|DEPDC5_ENST00000535622.1_Missense_Mutation_p.L1216P|DEPDC5_ENST00000382111.2_Missense_Mutation_p.L1316P|DEPDC5_ENST00000400246.1_Missense_Mutation_p.L1316P	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	1316					intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)	p.L1285P(1)		breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						CTGCCCTGGCTGCCTAGCCGG	0.582																																					p.L1316P		Atlas-SNP	.											DEPDC5,NS,carcinoma,0,1	DEPDC5	266	.	1	Substitution - Missense(1)	prostate(1)	c.T3947C						.						57	59	58					22																	32275652		2025	4196	6221	SO:0001583	missense	9681	exon38			CCTGGCTGCCTAG	AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.3920T>C	chr22.hg19:g.32275652T>C	ENSP00000371546:p.Leu1307Pro	66.0	1.0		46.0	4.0	NM_001242896	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Missense_Mutation	SNP	ENST00000382112.3	hg19	CCDS46692.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	16.75|16.75	3.210212|3.210212	0.58343|0.58343	.|.	.|.	ENSG00000100150|ENSG00000100150	ENST00000382105|ENST00000535622;ENST00000266091;ENST00000400249;ENST00000382109;ENST00000400246;ENST00000382112;ENST00000382111;ENST00000400248;ENST00000539165	T|T;T;T;T;T;T;T	0.31769|0.33865	1.48|1.39;1.81;1.81;1.76;1.82;1.76;1.81	5.72|5.72	5.72|5.72	0.89469|0.89469	.|Winged helix-turn-helix transcription repressor DNA-binding (1);	.|0.000000	.|0.64402	.|D	.|0.000003	T|T	0.53965|0.53965	0.1829|0.1829	L|L	0.47716|0.47716	1.5|1.5	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D	.|0.89917	.|0.999;1.0;1.0;1.0;0.999;0.999	.|D;D;D;D;D;D	.|0.97110	.|0.998;0.999;1.0;0.999;0.997;0.997	T|T	0.54957|0.54957	-0.8215|-0.8215	7|10	0.87932|0.62326	D|D	0|0.03	.|.	15.1862|15.1862	0.73002|0.73002	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|1316;1216;702;1294;1307;1285	.|B9EGN9;B4DH93;O75140-7;O75140-4;A8MPX9;O75140	.|.;.;.;.;.;DEPD5_HUMAN	R|P	1202|1216;1294;1285;1216;1316;1307;1316;1285;133	ENSP00000371539:C1202R|ENSP00000440210:L1216P;ENSP00000266091:L1294P;ENSP00000383108:L1285P;ENSP00000383105:L1316P;ENSP00000371546:L1307P;ENSP00000371545:L1316P;ENSP00000383107:L1285P	ENSP00000371539:C1202R|ENSP00000266091:L1294P	C|L	+|+	1|2	0|0	DEPDC5|DEPDC5	30605652|30605652	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.899000|0.899000	0.52679|0.52679	7.654000|7.654000	0.83653|0.83653	2.183000|2.183000	0.69458|0.69458	0.529000|0.529000	0.55759|0.55759	TGC|CTG	.	.		0.582	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662		C	32275652	T	C	32275652	3	2	254	1	0	0	0	0	1	0	0	0	4444	1580	55	2	4084	2	DEPDC5	22	32275652	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	191437	32275652	19028914	1010	35302										
PICK1	9463	hgsc.bcm.edu	37	chr22	38465060	38465060	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgttgaagaaagtcaagcacCggctggtggagaacatgagt	14	6	1	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:38465060C>A	ENST00000404072.3	+	6	717	c.370C>A	c.(370-372)Cgg>Agg	p.R124R	RP5-1039K5.13_ENST00000445483.1_RNA|PICK1_ENST00000356976.3_Silent_p.R124R|PICK1_ENST00000468288.1_3'UTR	NM_001039583.1|NM_001039584.1	NP_001034672.1|NP_001034673.1	Q9NRD5	PICK1_HUMAN	protein interacting with PRKCA 1	124					ATP catabolic process (GO:0006200)|cellular response to decreased oxygen levels (GO:0036294)|cellular response to glucose starvation (GO:0042149)|dendritic spine maintenance (GO:0097062)|dendritic spine organization (GO:0097061)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|glial cell development (GO:0021782)|long term synaptic depression (GO:0060292)|monoamine transport (GO:0015844)|negative regulation of Arp2/3 complex-mediated actin nucleation (GO:0034316)|neuronal ion channel clustering (GO:0045161)|positive regulation of receptor internalization (GO:0002092)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|protein targeting (GO:0006605)|receptor clustering (GO:0043113)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endocytic vesicle membrane (GO:0030666)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	actin filament binding (GO:0051015)|Arp2/3 complex binding (GO:0071933)|ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein kinase C binding (GO:0005080)|receptor binding (GO:0005102)			cervix(1)|endometrium(3)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13	Melanoma(58;0.045)					AGTCAAGCACCGGCTGGTGGA	0.632																																					p.R124R		Atlas-SNP	.											.	PICK1	30	.	0			c.C370A						.						53	45	47					22																	38465060		2203	4300	6503	SO:0001819	synonymous_variant	9463	exon6			AAGCACCGGCTGG	AL049654	CCDS13965.1	22q13.1	2006-02-14	2006-02-14	2006-02-14	ENSG00000100151	ENSG00000100151			9394	protein-coding gene	gene with protein product		605926	"protein kinase C, alpha binding protein", "protein interacting with PRKCA"	PRKCABP		10340301, 10591208	Standard	XM_006724377		Approved	dJ1039K5, MGC15204	uc003aus.3	Q9NRD5	OTTHUMG00000151159	ENST00000404072.3:c.370C>A	chr22.hg19:g.38465060C>A		111.0	0.0		92.0	4.0	NM_012407	B3KS52|O95906	Silent	SNP	ENST00000404072.3	hg19	CCDS13965.1																																																																																			.	.		0.632	PICK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321569.2	NM_012407		A	38465060	C	A	38465060	2	1	254	1	0	0	0	0	0	0	0	1	11890	643	23	1		1	PICK1	22	38465060	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	6189408	38465060	12839506	1011	35303										
PLA2G6	8398	hgsc.bcm.edu	37	chr22	38536052	38536052	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tggggcccatgatgttgcacCgagcattgcacagcagcagc	13	12	0	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:38536052C>A	ENST00000332509.3	-	5	917	c.734G>T	c.(733-735)cGg>cTg	p.R245L	PLA2G6_ENST00000335539.3_Missense_Mutation_p.R245L|PLA2G6_ENST00000402064.1_Missense_Mutation_p.R245L	NM_003560.2	NP_003551.2	O60733	PLPL9_HUMAN	phospholipase A2, group VI (cytosolic, calcium-independent)	245					cardiolipin acyl-chain remodeling (GO:0035965)|cardiolipin biosynthetic process (GO:0032049)|cell death (GO:0008219)|chemotaxis (GO:0006935)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|glycerophospholipid biosynthetic process (GO:0046474)|innate immune response (GO:0045087)|lipid catabolic process (GO:0016042)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phospholipid metabolic process (GO:0006644)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of ceramide biosynthetic process (GO:2000304)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of exocytosis (GO:0045921)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of vasodilation (GO:0045909)|regulation of store-operated calcium channel activity (GO:1901339)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|urinary bladder smooth muscle contraction (GO:0014832)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipase A2 activity (GO:0004623)			breast(2)|endometrium(6)|kidney(1)|large_intestine(4)|liver(1)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	24	Melanoma(58;0.045)				Quinacrine(DB01103)	GATGTTGCACCGAGCATTGCA	0.627																																					p.R245L		Atlas-SNP	.											.	PLA2G6	54	.	0			c.G734T						.						57	54	55					22																	38536052		2203	4300	6503	SO:0001583	missense	8398	exon5			TTGCACCGAGCAT	AF064594	CCDS13967.1, CCDS33645.1	22q13.1	2013-01-10			ENSG00000184381	ENSG00000184381	3.1.1.4	"Patatin-like phospholipase domain containing", "Parkinson disease", "Ankyrin repeat domain containing"	9039	protein-coding gene	gene with protein product	"neurodegeneration with brain iron accumulation 2"	603604				9417066, 16799181, 19029121	Standard	NM_001199562		Approved	iPLA2, PNPLA9, PARK14, iPLA2beta, NBIA2	uc003aux.1	O60733	OTTHUMG00000151246	ENST00000332509.3:c.734G>T	chr22.hg19:g.38536052C>A	ENSP00000333142:p.Arg245Leu	73.0	0.0		73.0	4.0	NM_003560	A8K597|B0QYE8|O75645|Q8N452|Q9UG29|Q9UIT0|Q9Y671	Missense_Mutation	SNP	ENST00000332509.3	hg19	CCDS13967.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.96|16.96	3.266667|3.266667	0.59540|0.59540	.|.	.|.	ENSG00000184381|ENSG00000184381	ENST00000452542|ENST00000332509;ENST00000419848;ENST00000335539;ENST00000402064;ENST00000335538;ENST00000396860	.|T;T;T	.|0.53640	.|0.61;0.61;0.61	5.69|5.69	5.69|5.69	0.88448|0.88448	.|Ankyrin repeat-containing domain (3);	.|0.104492	.|0.64402	.|D	.|0.000006	T|T	0.51261|0.51261	0.1664|0.1664	N|N	0.21324|0.21324	0.655|0.655	0.80722|0.80722	D|D	1|1	.|D;D	.|0.57257	.|0.979;0.958	.|P;P	.|0.59948	.|0.668;0.866	T|T	0.53187|0.53187	-0.8474|-0.8474	5|10	.|0.62326	.|D	.|0.03	-33.0839|-33.0839	14.0201|14.0201	0.64547|0.64547	0.0:0.928:0.0:0.072|0.0:0.928:0.0:0.072	.|.	.|245;245	.|O60733-2;O60733	.|.;PA2G6_HUMAN	C|L	76|245;106;245;245;173;245	.|ENSP00000333142:R245L;ENSP00000335149:R245L;ENSP00000386100:R245L	.|ENSP00000333142:R245L	G|R	-|-	1|2	0|0	PLA2G6|PLA2G6	36865998|36865998	0.996000|0.996000	0.38824|0.38824	0.857000|0.857000	0.33713|0.33713	0.296000|0.296000	0.27459|0.27459	3.294000|3.294000	0.51787|0.51787	2.676000|2.676000	0.91093|0.91093	0.561000|0.561000	0.74099|0.74099	GGT|CGG	.	.		0.627	PLA2G6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321860.1	NM_001004426		A	38536052	C	A	38536052	3	1	254	1	0	0	0	0	1	0	0	0	12017	652	23	1	1738	1	PLA2G6	22	38536052	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	70992	38536052	12768514	1012	35304										
DDX17	10521	hgsc.bcm.edu	37	chr22	38897259	38897259	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	taccaaatttcttcgggggaAggccaccaccacctcttgct	8	14	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:38897259A>G	ENST00000396821.3	-	2	413	c.314T>C	c.(313-315)cTt>cCt	p.L105P	DDX17_ENST00000381633.3_Missense_Mutation_p.L26P|DDX17_ENST00000432525.1_5'UTR	NM_001098504.1|NM_006386.4	NP_001091974|NP_006377.2	Q92841	DDX17_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 17	105					ATP catabolic process (GO:0006200)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of skeletal muscle cell differentiation (GO:2001014)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA helicase activity (GO:0003724)|RNA-dependent ATPase activity (GO:0008186)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(6)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	25	Melanoma(58;0.0286)					CTTCGGGGGAAGGCCACCACC	0.388																																					p.L105P	Ovarian(55;1085 1454 6392 21425)	Atlas-SNP	.											.	DDX17	73	.	0			c.T314C						.						72	73	72					22																	38897259		2203	4300	6503	SO:0001583	missense	10521	exon2			GGGGGAAGGCCAC	U59321	CCDS33646.1, CCDS46706.1	22q13.1	2012-02-23	2012-02-23		ENSG00000100201	ENSG00000100201		"DEAD-boxes"	2740	protein-coding gene	gene with protein product		608469	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 17 (72kD)", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 17"			8871553, 17226766	Standard	NM_006386		Approved	P72	uc003avy.4	Q92841	OTTHUMG00000151136	ENST00000396821.3:c.314T>C	chr22.hg19:g.38897259A>G	ENSP00000380033:p.Leu105Pro	63.0	0.0		73.0	4.0	NM_006386	B1AHM0|Q69YT1|Q6ICD6	Missense_Mutation	SNP	ENST00000396821.3	hg19	CCDS46706.1	.	.	.	.	.	.	.	.	.	.	A	14.16	2.453211	0.43531	.	.	ENSG00000100201	ENST00000396821;ENST00000381633;ENST00000403230;ENST00000404499	T;T;T	0.30182	1.54;1.54;1.54	5.58	5.58	0.84498	.	9.185410	0.00166	N	0.000000	T	0.23451	0.0567	N	0.04508	-0.205	0.80722	D	1	B;B;B	0.20988	0.001;0.05;0.008	B;B;B	0.20184	0.001;0.028;0.023	T	0.02533	-1.1145	10	0.33141	T	0.24	-14.9317	15.756	0.78025	1.0:0.0:0.0:0.0	.	26;107;105	Q92841;Q59F66;Q92841-4	DDX17_HUMAN;.;.	P	105;26;105;107	ENSP00000380033:L105P;ENSP00000371046:L26P;ENSP00000385536:L105P	ENSP00000371046:L26P	L	-	2	0	DDX17	37227205	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.645000	0.74343	2.122000	0.65172	0.482000	0.46254	CTT	.	.		0.388	DDX17-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321476.2	NM_030881		G	38897259	A	G	38897259	3	3	254	1	0	0	0	0	1	0	0	0	4346	72	3	2	1929	2	DDX17	22	38897259	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	361207	38897259	12407307	1013	35305										
CBX7	23492	hgsc.bcm.edu	37	chr22	39530449	39530449	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcaggctcccactcgccagcCgcctgcaggacgtctggggc	14	17	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:39530449C>T	ENST00000216133.5	-	5	760	c.555G>A	c.(553-555)gcG>gcA	p.A185A	CBX7_ENST00000475962.1_Intron|CBX7_ENST00000401405.3_Silent_p.A92A	NM_175709.3	NP_783640.1	O95931	CBX7_HUMAN	chromobox homolog 7	185					chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|sebaceous gland development (GO:0048733)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|single-stranded RNA binding (GO:0003727)			endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	7	Melanoma(58;0.04)					ACTCGCCAGCCGCCTGCAGGA	0.687																																					p.A185A	GBM(46;845 904 3560 9866 23971)	Atlas-SNP	.											CBX7,caecum,carcinoma,0,1	CBX7	18	.	0			c.G555A						.						13	17	16					22																	39530449		2151	4240	6391	SO:0001819	synonymous_variant	23492	exon5			GCCAGCCGCCTGC		CCDS13986.1	22q13.1	2010-07-06			ENSG00000100307	ENSG00000100307			1557	protein-coding gene	gene with protein product		608457					Standard	NM_175709		Approved		uc003axb.3	O95931	OTTHUMG00000150418	ENST00000216133.5:c.555G>A	chr22.hg19:g.39530449C>T		88.0	0.0		56.0	20.0	NM_175709	Q86T17	Silent	SNP	ENST00000216133.5	hg19	CCDS13986.1																																																																																			.	.		0.687	CBX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318020.1	NM_175709		T	39530449	C	T	39530449	2	4	254	1	0	0	0	0	0	0	0	1	2725	639	23	1		1	CBX7	22	39530449	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	633190	39530449	11774117	1014	35306										
RPL3	6122	hgsc.bcm.edu	37	chr22	39711541	39711541	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcaggtgggccttcttctggCgcagaggaagcaggcgcatc	15	11	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:39711541C>T	ENST00000216146.4	-	5	694	c.521G>A	c.(520-522)cGc>cAc	p.R174H	SNORD83A_ENST00000386747.1_RNA|SNORD83B_ENST00000386745.1_RNA|RPL3_ENST00000401609.1_Missense_Mutation_p.R122H|RPL3_ENST00000465618.1_5'UTR	NM_000967.3|NM_001033853.1	NP_000958.1|NP_001029025.1	P39023	RL3_HUMAN	ribosomal protein L3	174					cellular protein metabolic process (GO:0044267)|cellular response to interleukin-4 (GO:0071353)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			breast(1)|kidney(4)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	Melanoma(58;0.04)				Homoharringtonine(DB04865)	CTTCTTCTGGCGCAGAGGAAG	0.627																																					p.R174H		Atlas-SNP	.											RPL3,NS,carcinoma,0,1	RPL3	29	.	0			c.G521A						.						43	40	41					22																	39711541		2203	4300	6503	SO:0001583	missense	6122	exon5			TTCTGGCGCAGAG	AB007166	CCDS13988.1	22q13	2011-04-06			ENSG00000100316	ENSG00000100316		"L ribosomal proteins"	10332	protein-coding gene	gene with protein product		604163				2891103, 9582194	Standard	NM_000967		Approved	L3	uc003axi.3	P39023	OTTHUMG00000151079	ENST00000216146.4:c.521G>A	chr22.hg19:g.39711541C>T	ENSP00000346001:p.Arg174His	74.0	0.0		45.0	2.0	NM_000967	B2RDV9|Q15548|Q5I0G0	Missense_Mutation	SNP	ENST00000216146.4	hg19	CCDS13988.1	.	.	.	.	.	.	.	.	.	.	C	18.13	3.554982	0.65425	.	.	ENSG00000100316	ENST00000401609;ENST00000216146;ENST00000402527;ENST00000453303	T;T;T;T	0.23348	1.91;1.91;1.91;1.91	5.47	5.47	0.80525	Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	0.050057	0.85682	D	0.000000	T	0.31544	0.0800	L	0.58302	1.8	0.80722	D	1	B;B;B	0.17667	0.023;0.002;0.005	B;B;B	0.19391	0.025;0.004;0.008	T	0.04737	-1.0930	10	0.44086	T	0.13	.	19.3177	0.94223	0.0:1.0:0.0:0.0	.	145;122;174	Q8TBW1;G5E9G0;P39023	.;.;RL3_HUMAN	H	122;174;122;201	ENSP00000386101:R122H;ENSP00000346001:R174H;ENSP00000385762:R122H;ENSP00000415198:R201H	ENSP00000346001:R174H	R	-	2	0	RPL3	38041487	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.864000	0.62990	2.584000	0.87258	0.462000	0.41574	CGC	.	.		0.627	RPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321196.1	NM_000967		T	39711541	C	T	39711541	3	4	254	1	0	0	0	0	1	0	0	0	13594	768	27	1	714	1	RPL3	22	39711541	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	181092	39711541	11593025	1015	35307										
FAM83F	113828	hgsc.bcm.edu	37	chr22	40415332	40415332	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cctgcagctcactgacttccGgattcgggtaagttgcacca	10	13	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:40415332G>A	ENST00000333407.6	+	2	744	c.650G>A	c.(649-651)cGg>cAg	p.R217Q	FAM83F_ENST00000473717.1_Missense_Mutation_p.R49Q	NM_138435.2	NP_612444.2	Q8NEG4	FA83F_HUMAN	family with sequence similarity 83, member F	217								p.R217Q(1)		breast(1)|endometrium(2)|large_intestine(1)|lung(4)|skin(4)|urinary_tract(2)	14						ACTGACTTCCGGATTCGGGTA	0.582																																					p.R217Q		Atlas-SNP	.											FAM83F,NS,carcinoma,0,2	FAM83F	29	.	1	Substitution - Missense(1)	endometrium(1)	c.G650A						.						113	88	96					22																	40415332		2203	4300	6503	SO:0001583	missense	113828	exon2			ACTTCCGGATTCG		CCDS14000.2	22q13.1	2006-03-22			ENSG00000133477	ENSG00000133477			25148	protein-coding gene	gene with protein product						12477932	Standard	NM_138435		Approved		uc003ayk.1	Q8NEG4	OTTHUMG00000150688	ENST00000333407.6:c.650G>A	chr22.hg19:g.40415332G>A	ENSP00000330432:p.Arg217Gln	110.0	0.0		74.0	3.0	NM_138435	Q96FD6	Missense_Mutation	SNP	ENST00000333407.6	hg19	CCDS14000.2	.	.	.	.	.	.	.	.	.	.	G	9.725	1.160672	0.21538	.	.	ENSG00000133477	ENST00000333407	T	0.11169	2.8	4.94	3.93	0.45458	.	0.180528	0.49916	D	0.000135	T	0.03390	0.0098	N	0.10809	0.05	0.34242	D	0.677758	P	0.39404	0.672	B	0.25140	0.058	T	0.39901	-0.9591	10	0.23891	T	0.37	-6.1022	3.4047	0.07336	0.2311:0.0:0.5696:0.1993	.	217	Q8NEG4	FA83F_HUMAN	Q	217	ENSP00000330432:R217Q	ENSP00000330432:R217Q	R	+	2	0	FAM83F	38745278	1.000000	0.71417	0.998000	0.56505	0.590000	0.36582	4.686000	0.61700	1.310000	0.45006	0.561000	0.74099	CGG	.	.		0.582	FAM83F-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319624.3	NM_138435		A	40415332	G	A	40415332	3	1	254	1	0	0	0	0	1	0	0	0	5646	1116	39	1	656	1	FAM83F	22	40415332	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	703791	40415332	10889234	1016	35308										
SGSM3	27352	hgsc.bcm.edu	37	chr22	40803030	40803030	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tcttggtgcaggttgttcgcCgcaggacccagcggaggaag	16	10	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:40803030C>A	ENST00000248929.9	+	11	1384	c.1195C>A	c.(1195-1197)Cgc>Agc	p.R399S	SGSM3_ENST00000454798.2_Missense_Mutation_p.R332S	NM_015705.4	NP_056520.2			small G protein signaling modulator 3											cervix(1)|endometrium(4)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)|skin(6)	19						GGTTGTTCGCCGCAGGACCCA	0.612																																					p.R399S		Atlas-SNP	.											.	SGSM3	48	.	0			c.C1195A						.						45	35	39					22																	40803030		2197	4298	6495	SO:0001583	missense	27352	exon11			GTTCGCCGCAGGA	AL022238	CCDS14002.1	22q13.1-q13.2	2013-07-09	2007-08-14	2007-08-14	ENSG00000100359	ENSG00000100359		"Small G protein signaling modulators"	25228	protein-coding gene	gene with protein product	"RUN and SH3 containing 3"	610440	"RUN and TBC1 domain containing 3"	RUTBC3		11214971, 17509819	Standard	XM_005261572		Approved	DJ1042K10.2, RUSC3, RabGAP-5, RABGAP5	uc003ayu.1	Q96HU1	OTTHUMG00000151141	ENST00000248929.9:c.1195C>A	chr22.hg19:g.40803030C>A	ENSP00000248929:p.Arg399Ser	108.0	0.0		70.0	4.0	NM_015705		Missense_Mutation	SNP	ENST00000248929.9	hg19	CCDS14002.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.513408	0.85389	.	.	ENSG00000100359	ENST00000248929;ENST00000454798	T;T	0.18657	2.28;2.2	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.43055	0.1230	M	0.73962	2.25	0.80722	D	1	D;D;D;D	0.71674	0.994;0.994;0.977;0.998	P;P;P;P	0.61658	0.892;0.854;0.851;0.885	T	0.35773	-0.9775	10	0.72032	D	0.01	.	13.3361	0.60518	0.1577:0.8423:0.0:0.0	.	336;332;399;399	B4DVE3;B4DMS2;Q96HU1-2;Q96HU1	.;.;.;SGSM3_HUMAN	S	399;332	ENSP00000248929:R399S;ENSP00000390998:R332S	ENSP00000248929:R399S	R	+	1	0	SGSM3	39132976	0.993000	0.37304	0.971000	0.41717	0.949000	0.60115	3.125000	0.50469	2.578000	0.87016	0.563000	0.77884	CGC	.	.		0.612	SGSM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321504.2	NM_015705		A	40803030	C	A	40803030	3	1	254	1	0	0	0	0	1	0	0	0	14239	652	23	1	1233	1	SGSM3	22	40803030	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	387698	40803030	10501536	1017	35309										
SGSM3	27352	hgsc.bcm.edu	37	chr22	40803251	40803251	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gccaagaacatcaagcagacGgaactggtggctgacctccg	12	12	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:40803251G>T	ENST00000248929.9	+	12	1476	c.1287G>T	c.(1285-1287)acG>acT	p.T429T	SGSM3_ENST00000454798.2_Silent_p.T362T	NM_015705.4	NP_056520.2			small G protein signaling modulator 3									p.T429T(1)		cervix(1)|endometrium(4)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)|skin(6)	19						TCAAGCAGACGGAACTGGTGG	0.632																																					p.T429T		Atlas-SNP	.											SGSM3,NS,carcinoma,0,1	SGSM3	48	.	1	Substitution - coding silent(1)	endometrium(1)	c.G1287T						.						59	58	58					22																	40803251		2203	4300	6503	SO:0001819	synonymous_variant	27352	exon12			GCAGACGGAACTG	AL022238	CCDS14002.1	22q13.1-q13.2	2013-07-09	2007-08-14	2007-08-14	ENSG00000100359	ENSG00000100359		"Small G protein signaling modulators"	25228	protein-coding gene	gene with protein product	"RUN and SH3 containing 3"	610440	"RUN and TBC1 domain containing 3"	RUTBC3		11214971, 17509819	Standard	XM_005261572		Approved	DJ1042K10.2, RUSC3, RabGAP-5, RABGAP5	uc003ayu.1	Q96HU1	OTTHUMG00000151141	ENST00000248929.9:c.1287G>T	chr22.hg19:g.40803251G>T		113.0	0.0		94.0	6.0	NM_015705		Silent	SNP	ENST00000248929.9	hg19	CCDS14002.1																																																																																			.	.		0.632	SGSM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321504.2	NM_015705		T	40803251	G	T	40803251	2	4	254	1	0	0	0	0	0	0	0	1	14239	1103	39	1		1	SGSM3	22	40803251	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	221	40803251	10501315	1018	35310										
EP300	2033	hgsc.bcm.edu	37	chr22	41573037	41573037	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	accaagggttgcaaacggaaAaccaatggcgggtgccccat	12	11	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:41573037A>T	ENST00000263253.7	+	31	6541	c.5322A>T	c.(5320-5322)aaA>aaT	p.K1774N	RP1-85F18.6_ENST00000415054.1_RNA|RP1-85F18.5_ENST00000420537.1_RNA	NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	1774	Binding region for E1A adenovirus.				apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						GCAAACGGAAAACCAATGGCG	0.562			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																												p.K1774N		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	.	EP300	367	.	0			c.A5322T						.						76	67	70					22																	41573037		2203	4300	6503	SO:0001583	missense	2033	exon31	Familial Cancer Database	Broad Thumb-Hallux syndrome	ACGGAAAACCAAT	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.5322A>T	chr22.hg19:g.41573037A>T	ENSP00000263253:p.Lys1774Asn	78.0	0.0		85.0	6.0	NM_001429	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	hg19	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	A	14.61	2.586477	0.46110	.	.	ENSG00000100393	ENST00000263253	D	0.83250	-1.7	5.76	0.909	0.19332	Zinc finger, TAZ-type (5);	0.000000	0.51477	D	0.000098	D	0.90748	0.7096	M	0.88570	2.965	0.38829	D	0.955817	D	0.89917	1.0	D	0.87578	0.998	D	0.90571	0.4522	10	0.72032	D	0.01	-8.7941	10.9976	0.47585	0.6018:0.0:0.3982:0.0	.	1774	Q09472	EP300_HUMAN	N	1774	ENSP00000263253:K1774N	ENSP00000263253:K1774N	K	+	3	2	EP300	39902983	0.991000	0.36638	1.000000	0.80357	0.992000	0.81027	0.310000	0.19356	0.124000	0.18369	0.533000	0.62120	AAA	.	.		0.562	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		T	41573037	A	T	41573037	3	4	254	1	0	0	0	0	1	0	0	0	5150	11	1	4	5444	4	EP300	22	41573037	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	769786	41573037	9731529	1019	35311										
PARVB	29780	hgsc.bcm.edu	37	chr22	44564512	44564512	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cttggacctcaaatccacccTgagggttctttacaacctgt	7	13	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:44564512T>C	ENST00000338758.7	+	13	1112	c.1049T>C	c.(1048-1050)cTg>cCg	p.L350P	PARVB_ENST00000406477.3_Missense_Mutation_p.L383P|PARVB_ENST00000404989.1_Missense_Mutation_p.L313P	NM_013327.4	NP_037459.2	Q9HBI1	PARVB_HUMAN	parvin, beta	350	CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin cytoskeleton reorganization (GO:0031532)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell projection assembly (GO:0030031)|establishment or maintenance of cell polarity regulating cell shape (GO:0071963)|lamellipodium assembly (GO:0030032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(3)|large_intestine(7)|lung(8)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	25		Ovarian(80;0.0246)|all_neural(38;0.0423)				AAATCCACCCTGAGGGTTCTT	0.532																																					p.L383P		Atlas-SNP	.											.	PARVB	44	.	0			c.T1148C						.						109	99	103					22																	44564512		2203	4300	6503	SO:0001583	missense	29780	exon14			CCACCCTGAGGGT	AF151814	CCDS14056.1, CCDS46724.1, CCDS58808.1, CCDS74874.1	22q13.2-q13.33	2013-01-24			ENSG00000188677	ENSG00000188677		"Parvins"	14653	protein-coding gene	gene with protein product	"affixin"	608121				10810093, 11171322	Standard	NM_001003828		Approved	CGI-56	uc003ben.3	Q9HBI1	OTTHUMG00000150665	ENST00000338758.7:c.1049T>C	chr22.hg19:g.44564512T>C	ENSP00000342492:p.Leu350Pro	177.0	0.0		94.0	4.0	NM_001003828	B0QYM8|B0QYN1|B2R9X6|Q5TGJ5|Q86X93|Q96PN1|Q9NSP7|Q9UGT3|Q9Y368|Q9Y3L6|Q9Y3L7	Missense_Mutation	SNP	ENST00000338758.7	hg19	CCDS14056.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.187719	0.78789	.	.	ENSG00000188677	ENST00000406477;ENST00000338758;ENST00000404989	D;D;D	0.96913	-4.17;-4.17;-4.17	5.11	5.11	0.69529	Calponin homology domain (5);	0.000000	0.85682	D	0.000000	D	0.98251	0.9421	M	0.91717	3.235	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.99066	1.0832	10	0.87932	D	0	-1.6952	11.3021	0.49311	0.0:0.0:0.0:1.0	.	350;313;350;383	A6NG58;B0QYM8;Q9HBI1;Q9HBI1-2	.;.;PARVB_HUMAN;.	P	383;350;313	ENSP00000384515:L383P;ENSP00000342492:L350P;ENSP00000384353:L313P	ENSP00000342492:L350P	L	+	2	0	PARVB	42895845	1.000000	0.71417	0.987000	0.45799	0.995000	0.86356	6.125000	0.71627	1.929000	0.55896	0.533000	0.62120	CTG	.	.		0.532	PARVB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319518.2	NM_001003828		C	44564512	T	C	44564512	3	2	254	1	0	0	0	0	1	0	0	0	11478	1580	55	2	1318	2	PARVB	22	44564512	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	2991475	44564512	6740054	1020	35312										
WNT7B	7477	hgsc.bcm.edu	37	chr22	46319021	46319021	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttctgatagctgcgcagctgTttgatgcgcaggaaggtggg	16	7	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:46319021T>C	ENST00000339464.4	-	4	1139	c.765A>G	c.(763-765)aaA>aaG	p.K255K	WNT7B_ENST00000410089.1_Silent_p.K239K|WNT7B_ENST00000409496.3_Silent_p.K259K	NM_058238.2	NP_478679.1	P56706	WNT7B_HUMAN	wingless-type MMTV integration site family, member 7B	255					activation of JUN kinase activity (GO:0007257)|anatomical structure regression (GO:0060033)|apoptotic process involved in patterning of blood vessels (GO:1902262)|canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cellular metabolic process (GO:0044237)|cellular response to retinoic acid (GO:0071300)|central nervous system vasculogenesis (GO:0022009)|chorio-allantoic fusion (GO:0060710)|developmental growth involved in morphogenesis (GO:0060560)|embryonic organ development (GO:0048568)|embryonic placenta morphogenesis (GO:0060669)|establishment or maintenance of polarity of embryonic epithelium (GO:0016332)|fibroblast proliferation (GO:0048144)|forebrain regionalization (GO:0021871)|homeostatic process (GO:0042592)|in utero embryonic development (GO:0001701)|inner medullary collecting duct development (GO:0072061)|lens fiber cell development (GO:0070307)|lobar bronchus development (GO:0060482)|lung development (GO:0030324)|lung epithelium development (GO:0060428)|lung morphogenesis (GO:0060425)|lung-associated mesenchyme development (GO:0060484)|mammary gland epithelium development (GO:0061180)|metanephric collecting duct development (GO:0072205)|metanephric epithelium development (GO:0072207)|metanephric loop of Henle development (GO:0072236)|metanephros morphogenesis (GO:0003338)|negative regulation of smoothened signaling pathway (GO:0045879)|neuron differentiation (GO:0030182)|neuron projection morphogenesis (GO:0048812)|odontogenesis of dentin-containing tooth (GO:0042475)|outer medullary collecting duct development (GO:0072060)|oxygen homeostasis (GO:0032364)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JNK cascade (GO:0046330)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of cell projection size (GO:0032536)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|response to glucocorticoid (GO:0051384)|smooth muscle cell differentiation (GO:0051145)|stem cell proliferation (GO:0072089)|synapse organization (GO:0050808)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	19		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|LUAD - Lung adenocarcinoma(64;0.247)		TGCGCAGCTGTTTGATGCGCA	0.642																																					p.K255K		Atlas-SNP	.											.	WNT7B	45	.	0			c.A765G						.						58	55	56					22																	46319021		2203	4300	6503	SO:0001819	synonymous_variant	7477	exon4			CAGCTGTTTGATG	AF416743	CCDS33667.1	22q13	2013-02-28			ENSG00000188064	ENSG00000188064		"Wingless-type MMTV integration sites", "Endogenous ligands"	12787	protein-coding gene	gene with protein product		601967				8168088, 9284940, 11562755	Standard	NM_058238		Approved		uc003bgo.2	P56706	OTTHUMG00000154636	ENST00000339464.4:c.765A>G	chr22.hg19:g.46319021T>C		149.0	0.0		86.0	4.0	NM_058238	B8A596|Q96Q12	Silent	SNP	ENST00000339464.4	hg19	CCDS33667.1																																																																																			.	.		0.642	WNT7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336418.1	NM_058238		C	46319021	T	C	46319021	2	2	254	1	0	0	0	0	0	0	0	1	17410	1722	60	2		2	WNT7B	22	46319021	Silent	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	1754509	46319021	4985545	1021	35313										
GTSE1	51512	hgsc.bcm.edu	37	chr22	46704834	46704834	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agaagcatccctggggctgcGgagaaggtaaatgccacagc	14	10	0	2	rs200502529		TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:46704834G>T	ENST00000454366.1	+	4	968	c.756G>T	c.(754-756)gcG>gcT	p.A252A		NM_016426.6	NP_057510	Q9NYZ3	GTSE1_HUMAN	G-2 and S-phase expressed 1	233					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|microtubule-based process (GO:0007017)	cytoplasmic microtubule (GO:0005881)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	27		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)		CTGGGGCTGCGGAGAAGGTAA	0.622																																					p.A252A	GBM(153;542 1915 12487 29016 50495)	Atlas-SNP	.											.	GTSE1	100	.	0			c.G756T						.						33	38	36					22																	46704834		2195	4286	6481	SO:0001819	synonymous_variant	51512	exon4			GGCTGCGGAGAAG	AF223408	CCDS14074.2	22q13.2-q13.3	2008-06-10			ENSG00000075218	ENSG00000075218			13698	protein-coding gene	gene with protein product		607477				10974554, 10984615, 12750368	Standard	NM_016426		Approved	GTSE-1, B99	uc011aqy.2	Q9NYZ3	OTTHUMG00000150486	ENST00000454366.1:c.756G>T	chr22.hg19:g.46704834G>T		112.0	0.0		64.0	4.0	NM_016426	B0QYM3|Q20WK2|Q53GX5|Q5R3I6|Q6DHX4|Q9BRE0|Q9UGZ9|Q9Y557	Silent	SNP	ENST00000454366.1	hg19	CCDS14074.2																																																																																			.	G|0.999;A|0.001		0.622	GTSE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318360.2	NM_016426		T	46704834	G	T	46704834	2	4	254	1	0	0	0	0	0	0	0	1	6894	1103	39	1		1	GTSE1	22	46704834	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	385813	46704834	4599732	1022	35314										
IL17REL	400935	hgsc.bcm.edu	37	chr22	50438927	50438927	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cttccacgaggtgcctctggTccagctggaccccgcagaaa	11	15	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:50438927T>C	ENST00000389983.2	-	6	578	c.314A>G	c.(313-315)gAc>gGc	p.D105G	IL17REL_ENST00000341280.5_Missense_Mutation_p.D105G	NM_001001694.2	NP_001001694.2	Q6ZVW7	I17EL_HUMAN	interleukin 17 receptor E-like	105										endometrium(1)|large_intestine(1)|lung(3)|pancreas(1)	6		all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		GTGCCTCTGGTCCAGCTGGAC	0.647																																					p.D105G		Atlas-SNP	.											.	IL17REL	21	.	0			c.A314G						.						71	70	70					22																	50438927		2203	4300	6503	SO:0001583	missense	400935	exon6			CTCTGGTCCAGCT	AK123987	CCDS33679.1	22q13.33	2009-01-13			ENSG00000188263	ENSG00000188263			33808	protein-coding gene	gene with protein product		613414					Standard	NM_001001694		Approved	FLJ41993	uc003bje.1	Q6ZVW7	OTTHUMG00000150242	ENST00000389983.2:c.314A>G	chr22.hg19:g.50438927T>C	ENSP00000374633:p.Asp105Gly	91.0	0.0		85.0	4.0	NM_001001694	A6NCN4|A6PVC1	Missense_Mutation	SNP	ENST00000389983.2	hg19	CCDS33679.1	.	.	.	.	.	.	.	.	.	.	t	3.800	-0.041800	0.07452	.	.	ENSG00000188263	ENST00000389983;ENST00000341280	T;T	0.13657	2.57;2.57	3.99	0.135	0.14775	.	0.584334	0.15723	N	0.247831	T	0.09818	0.0241	L	0.51422	1.61	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.27123	-1.0083	10	0.27785	T	0.31	.	2.875	0.05628	0.0:0.2942:0.249:0.4568	.	105	Q6ZVW7	I17EL_HUMAN	G	105	ENSP00000374633:D105G;ENSP00000342520:D105G	ENSP00000342520:D105G	D	-	2	0	IL17REL	48781054	0.000000	0.05858	0.024000	0.17045	0.028000	0.11728	-0.252000	0.08806	0.431000	0.26258	0.529000	0.55759	GAC	.	.		0.647	IL17REL-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317011.1	NM_001001694		C	50438927	T	C	50438927	3	2	254	1	0	0	0	0	1	0	0	0	7653	1667	58	2	732	2	IL17REL	22	50438927	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	3734093	50438927	865639	1023	35315										
PLXNB2	23654	hgsc.bcm.edu	37	chr22	50720691	50720691	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcgatgaccaccatggcaaaCctctggatcaggctgaagcc	11	13	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:50720691C>T	ENST00000449103.1	-	19	3179	c.3039G>A	c.(3037-3039)agG>agA	p.R1013R	PLXNB2_ENST00000496720.1_5'Flank|PLXNB2_ENST00000359337.4_Silent_p.R1013R			O15031	PLXB2_HUMAN	plexin B2	1013	IPT/TIG 3.				brain development (GO:0007420)|neural tube closure (GO:0001843)|neuroblast proliferation (GO:0007405)|positive regulation of axonogenesis (GO:0050772)|regulation of cell shape (GO:0008360)|regulation of neuron migration (GO:2001222)|regulation of protein phosphorylation (GO:0001932)|regulation of Rho GTPase activity (GO:0032319)|semaphorin-plexin signaling pathway (GO:0071526)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	GTPase activator activity (GO:0005096)|semaphorin receptor activity (GO:0017154)			breast(2)|central_nervous_system(4)|cervix(2)|endometrium(11)|kidney(4)|large_intestine(3)|liver(1)|lung(20)|ovary(5)|prostate(6)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	66		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|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)		CCATGGCAAACCTCTGGATCA	0.682																																					p.R1013R		Atlas-SNP	.											.	PLXNB2	172	.	0			c.G3039A						.						46	50	49					22																	50720691		2087	4191	6278	SO:0001819	synonymous_variant	23654	exon19			GGCAAACCTCTGG		CCDS43035.1	22q13.33	2008-06-12			ENSG00000196576	ENSG00000196576		"Plexins"	9104	protein-coding gene	gene with protein product		604293				10520995, 12183458	Standard	NM_012401		Approved	MM1, KIAA0315, PLEXB2	uc003bkv.4	O15031	OTTHUMG00000150219	ENST00000449103.1:c.3039G>A	chr22.hg19:g.50720691C>T		122.0	0.0		90.0	20.0	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Silent	SNP	ENST00000449103.1	hg19	CCDS43035.1																																																																																			.	.		0.682	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401		T	50720691	C	T	50720691	2	4	254	1	0	0	0	0	0	0	0	1	12133	506	18	3		3	PLXNB2	22	50720691	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	281764	50720691	583875	1024	35316										
SHANK3	85358	hgsc.bcm.edu	37	chr22	51143419	51143419	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gggtgaacgtggtgaaggtcGgacacaagcaggtggtggct	19	6	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chr22:51143419G>T	ENST00000414786.2	+	16	2109	c.1882G>T	c.(1882-1884)Gga>Tga	p.G628*	SHANK3_ENST00000262795.3_Nonsense_Mutation_p.G658*|SHANK3_ENST00000445220.2_Nonsense_Mutation_p.G643*			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	642	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				adult behavior (GO:0030534)|alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|brain morphogenesis (GO:0048854)|dendritic spine morphogenesis (GO:0060997)|guanylate kinase-associated protein clustering (GO:0097117)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell volume (GO:0045794)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glutamate receptor signaling pathway (GO:1900451)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse structural plasticity (GO:0051835)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density assembly (GO:0097107)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of long term synaptic depression (GO:1900452)|regulation of long-term synaptic potentiation (GO:1900271)|social behavior (GO:0035176)|striatal medium spiny neuron differentiation (GO:0021773)|synapse assembly (GO:0007416)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)	8		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)		GGTGAAGGTCGGACACAAGCA	0.637																																					p.G628X		Atlas-SNP	.											.	SHANK3	96	.	0			c.G1882T						.						126	142	137					22																	51143419		2186	4284	6470	SO:0001587	stop_gained	85358	exon16			AAGGTCGGACACA	AB051437		22q13.3	2013-11-14			ENSG00000251322	ENSG00000251322		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	14294	protein-coding gene	gene with protein product	"proline rich synapse associated protein 2", "shank postsynaptic density protein"	606230				11258795, 11431708, 10806096, 17173049	Standard	NM_033517		Approved	SPANK-2, prosap2, KIAA1650, PSAP2	uc031ryd.1	Q9BYB0	OTTHUMG00000150169	ENST00000414786.2:c.1882G>T	chr22.hg19:g.51143419G>T	ENSP00000464552:p.Gly628*	117.0	0.0		72.0	5.0	NM_033517	D7UT47|Q8TET3	Nonsense_Mutation	SNP	ENST00000414786.2	hg19		.	.	.	.	.	.	.	.	.	.	G	40	7.936391	0.98571	.	.	ENSG00000251322	ENST00000262795;ENST00000445220	.	.	.	4.53	4.53	0.55603	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	14.7953	0.69873	0.0:0.0:1.0:0.0	.	.	.	.	X	658;643	.	ENSP00000442518:G658X	G	+	1	0	SHANK3	49490285	1.000000	0.71417	0.881000	0.34555	0.970000	0.65996	7.481000	0.81124	2.364000	0.80123	0.591000	0.81541	GGA	.	.		0.637	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420		T	51143419	G	T	51143419	4	4	254	1	0	0	0	0	0	1	0	0	14281	1117	39	1	2038	1	SHANK3	22	51143419	Nonsense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	422728	51143419	161147	1025	35317										
KAL1	3730	hgsc.bcm.edu	37	chrX	8565289	8565289	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cattcgtagctcttcttgggGaagagaggctaagtcaaaga	12	7	3	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:8565289G>T	ENST00000262648.3	-	4	476	c.327C>A	c.(325-327)ttC>ttA	p.F109L		NM_000216.2	NP_000207.2	P23352	KALM_HUMAN	Kallmann syndrome 1 sequence	109					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|liver(1)|lung(6)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(1)	32						TCTTCTTGGGGAAGAGAGGCT	0.428																																					p.F109L		Atlas-SNP	.											.	KAL1	78	.	0			c.C327A						.						39	33	35					X																	8565289		2203	4300	6503	SO:0001583	missense	3730	exon4			CTTGGGGAAGAGA		CCDS14130.1	Xp22.32	2013-02-11			ENSG00000011201	ENSG00000011201		"WAP four-disulfide core domain containing", "Fibronectin type III domain containing"	6211	protein-coding gene	gene with protein product	"anosmin-1", "WAP four-disulfide core domain 19"	300836		KAL, ADMLX		11463336	Standard	NM_000216		Approved	KALIG-1, WFDC19	uc004csf.3	P23352	OTTHUMG00000021107	ENST00000262648.3:c.327C>A	chrX.hg19:g.8565289G>T	ENSP00000262648:p.Phe109Leu	156.0	0.0		94.0	4.0	NM_000216	B2RPF8	Missense_Mutation	SNP	ENST00000262648.3	hg19	CCDS14130.1	.	.	.	.	.	.	.	.	.	.	G	11.77	1.739146	0.30774	.	.	ENSG00000011201	ENST00000262648	T	0.74947	-0.89	4.36	3.48	0.39840	.	0.000000	0.85682	D	0.000000	T	0.79417	0.4442	M	0.68952	2.095	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	T	0.77635	-0.2514	10	0.02654	T	1	.	10.1895	0.43017	0.1:0.0:0.9:0.0	.	109	P23352	KALM_HUMAN	L	109	ENSP00000262648:F109L	ENSP00000262648:F109L	F	-	3	2	KAL1	8525289	1.000000	0.71417	1.000000	0.80357	0.688000	0.40055	1.714000	0.37961	1.793000	0.52555	0.600000	0.82982	TTC	.	.		0.428	KAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055692.1	NM_000216		T	8565289	G	T	8565289	3	4	254	1	0	0	0	0	1	0	0	0	7983	1165	41	3	1759	3	KAL1	23	8565289	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10		8565289	146705271	1026	35318										
MID1	4281	hgsc.bcm.edu	37	chrX	10450648	10450648	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cagtttgcaatctgctgagcCagtttgcgaagcctcatcac	9	12	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:10450648C>A	ENST00000317552.4	-	5	1285	c.885G>T	c.(883-885)ctG>ctT	p.L295L	MID1_ENST00000380780.1_Silent_p.L295L|MID1_ENST00000380782.2_Silent_p.L295L|MID1_ENST00000453318.2_Silent_p.L295L|MID1_ENST00000380787.1_Silent_p.L295L|MID1_ENST00000380785.1_Silent_p.L295L|MID1_ENST00000380779.1_Silent_p.L295L	NM_000381.3|NM_033289.1	NP_000372.1|NP_150631.1	O15344	TRI18_HUMAN	midline 1	295			L -> P (in OGS1). {ECO:0000269|PubMed:15558842}.		microtubule cytoskeleton organization (GO:0000226)|negative regulation of microtubule depolymerization (GO:0007026)|pattern specification process (GO:0007389)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein localization to microtubule (GO:0035372)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	ligase activity (GO:0016874)|microtubule binding (GO:0008017)|phosphoprotein binding (GO:0051219)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	26						TCTGCTGAGCCAGTTTGCGAA	0.488																																					p.L346L		Atlas-SNP	.											.	MID1	72	.	0			c.G1038T						.						131	102	112					X																	10450648		2203	4300	6503	SO:0001819	synonymous_variant	4281	exon5			CTGAGCCAGTTTG	Y13667	CCDS14138.1, CCDS75952.1, CCDS75953.1	Xp22	2014-06-18	2014-06-18		ENSG00000101871	ENSG00000101871		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Fibronectin type III domain containing"	7095	protein-coding gene	gene with protein product	"Opitz/BBB syndrome"	300552				9354791, 9425238	Standard	NM_001098624		Approved	OS, FXY, TRIM18, RNF59	uc004cti.4	O15344	OTTHUMG00000021127	ENST00000317552.4:c.885G>T	chrX.hg19:g.10450648C>A		43.0	0.0		21.0	4.0	NM_001193278	B2RCG2|O75361|Q9BZX5	Silent	SNP	ENST00000317552.4	hg19	CCDS14138.1																																																																																			.	.		0.488	MID1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055738.1			A	10450648	C	A	10450648	2	1	254	1	0	0	0	0	0	0	0	1	9585	581	21	3		3	MID1	23	10450648	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1885359	10450648	144819912	1027	35319										
BMX	660	hgsc.bcm.edu	37	chrX	15534284	15534284	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aagtaccatagtgggttcttCgtggacgggaagttcctgtg	14	7	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:15534284C>T	ENST00000357607.2	+	5	563	c.375C>T	c.(373-375)ttC>ttT	p.F125F	BMX_ENST00000463891.1_3'UTR|BMX_ENST00000342014.6_Silent_p.F125F|BMX_ENST00000348343.6_Silent_p.F125F			P51813	BMX_HUMAN	BMX non-receptor tyrosine kinase	125					apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to stress (GO:0006950)|signal transduction (GO:0007165)	cytosol (GO:0005829)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|signal transducer activity (GO:0004871)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(14)|ovary(2)|urinary_tract(3)	30	Hepatocellular(33;0.183)					GTGGGTTCTTCGTGGACGGGA	0.512																																					p.F125F		Atlas-SNP	.											.	BMX	73	.	0			c.C375T						.						169	152	158					X																	15534284		2203	4300	6503	SO:0001819	synonymous_variant	660	exon5			GTTCTTCGTGGAC	AF045459	CCDS14168.1	Xp22.2	2013-05-14			ENSG00000102010	ENSG00000102010		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	1079	protein-coding gene	gene with protein product	"BTK-like on X chromosome"	300101				7970727	Standard	NM_203281		Approved	ETK, PSCTK3	uc004cwx.4	P51813	OTTHUMG00000021180	ENST00000357607.2:c.375C>T	chrX.hg19:g.15534284C>T		177.0	0.0		89.0	4.0	NM_001721	A6NIH9|O60564|Q12871	Silent	SNP	ENST00000357607.2	hg19	CCDS14168.1																																																																																			.	.		0.512	BMX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055877.1	NM_001721		T	15534284	C	T	15534284	2	4	254	1	0	0	0	0	0	0	0	1	1473	883	31	1		1	BMX	23	15534284	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	5083636	15534284	139736276	1028	35320										
CA5B	11238	hgsc.bcm.edu	37	chrX	15768181	15768181	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cagcctgagggtcattcttcAagcctctccaggcaaattgc	9	13	4	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:15768181A>G	ENST00000318636.3	+	2	171	c.35A>G	c.(34-36)cAa>cGa	p.Q12R	CA5B_ENST00000380313.1_3'UTR|CA5B_ENST00000454127.2_Missense_Mutation_p.Q12R	NM_007220.3	NP_009151.1	Q8WTZ4	CA5BL_HUMAN	carbonic anhydrase VB, mitochondrial	0						mitochondrion (GO:0005739)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|lung(3)|prostate(1)|stomach(2)	9	Hepatocellular(33;0.183)					GTCATTCTTCAAGCCTCTCCA	0.463																																					p.Q12R		Atlas-SNP	.											.	CA5B	23	.	0			c.A35G						.						117	114	115					X																	15768181		2203	4300	6503	SO:0001583	missense	11238	exon2			TTCTTCAAGCCTC	AB021660	CCDS14171.1	Xp22.1	2008-08-13			ENSG00000169239	ENSG00000169239		"Carbonic anhydrases"	1378	protein-coding gene	gene with protein product		300230				10409679	Standard	XM_005274442		Approved		uc004cxe.3	Q9Y2D0	OTTHUMG00000021183	ENST00000318636.3:c.35A>G	chrX.hg19:g.15768181A>G	ENSP00000314099:p.Gln12Arg	169.0	0.0		87.0	4.0	NM_007220	A6NEZ4	Missense_Mutation	SNP	ENST00000318636.3	hg19	CCDS14171.1	.	.	.	.	.	.	.	.	.	.	A	10.73	1.433661	0.25813	.	.	ENSG00000169239	ENST00000498004;ENST00000318636;ENST00000479740;ENST00000454127	T;T;T	0.68479	-0.33;0.16;-0.33	5.37	4.13	0.48395	.	3.866790	0.00357	N	0.000025	T	0.56077	0.1961	L	0.27053	0.805	0.09310	N	1	B	0.16603	0.018	B	0.15484	0.013	T	0.40194	-0.9576	10	0.30078	T	0.28	-6.5656	7.0154	0.24885	0.795:0.0:0.0:0.205	.	12	Q9Y2D0	CAH5B_HUMAN	R	12	ENSP00000314099:Q12R;ENSP00000417553:Q12R;ENSP00000417021:Q12R	ENSP00000314099:Q12R	Q	+	2	0	CA5B	15678102	0.894000	0.30519	0.207000	0.23584	0.621000	0.37620	1.706000	0.37878	1.800000	0.52685	0.417000	0.27973	CAA	.	.		0.463	CA5B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354933.1	NM_007220		G	15768181	A	G	15768181	3	3	254	1	0	0	0	0	1	0	0	0	2522	130	5	2	37	2	CA5B	23	15768181	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	233897	15768181	139502379	1029	35321										
DMD	1756	hgsc.bcm.edu	37	chrX	32490308	32490308	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tccccgagtctctgctccatGatttcatagtcggtgacact	8	13	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:32490308G>T	ENST00000357033.4	-	22	3128	c.2922C>A	c.(2920-2922)atC>atA	p.I974I	DMD_ENST00000378677.2_Silent_p.I970I	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	974					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				TCTGCTCCATGATTTCATAGT	0.423																																					p.I974I		Atlas-SNP	.											.	DMD	2127	.	0			c.C2922A						.						171	148	156					X																	32490308		2202	4300	6502	SO:0001819	synonymous_variant	1756	exon22			CTCCATGATTTCA	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.2922C>A	chrX.hg19:g.32490308G>T		216.0	0.0		156.0	45.0	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Silent	SNP	ENST00000357033.4	hg19	CCDS14233.1																																																																																			.	.		0.423	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		T	32490308	G	T	32490308	2	4	254	1	0	0	0	0	0	0	0	1	4582	1280	45	3		3	DMD	23	32490308	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	16722127	32490308	122780252	1030	35322										
CXorf22	170063	hgsc.bcm.edu	37	chrX	35989740	35989740	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	atgatgatacagacataggcTtagagccaggatcaggtcta	11	7	2	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:35989740T>G	ENST00000297866.5	+	12	2074	c.2008T>G	c.(2008-2010)Tta>Gta	p.L670V		NM_152632.3	NP_689845.2	Q6ZTR5	CX022_HUMAN	chromosome X open reading frame 22	670										breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(3)	44						AGACATAGGCTTAGAGCCAGG	0.373																																					p.L670V		Atlas-SNP	.											.	CXorf22	272	.	0			c.T2008G						.						23	19	20					X																	35989740		2202	4295	6497	SO:0001583	missense	170063	exon12			ATAGGCTTAGAGC	BC027936	CCDS14237.2	Xp21.1	2014-08-07			ENSG00000165164	ENSG00000165164			28546	protein-coding gene	gene with protein product						12477932	Standard	NM_152632		Approved	MGC34831	uc004ddj.3	Q6ZTR5	OTTHUMG00000021350	ENST00000297866.5:c.2008T>G	chrX.hg19:g.35989740T>G	ENSP00000297866:p.Leu670Val	131.0	0.0		78.0	25.0	NM_152632	Q5JRM8|Q8N6X8	Missense_Mutation	SNP	ENST00000297866.5	hg19	CCDS14237.2	.	.	.	.	.	.	.	.	.	.	T	15.97	2.990875	0.54041	.	.	ENSG00000165164	ENST00000297866	T	0.16597	2.33	5.72	-5.22	0.02806	.	0.529703	0.17944	N	0.156732	T	0.12518	0.0304	M	0.65975	2.015	0.09310	N	1	P	0.43287	0.802	B	0.40677	0.337	T	0.25467	-1.0131	10	0.17369	T	0.5	-3.1402	4.9309	0.13917	0.5443:0.1892:0.0:0.2665	.	670	Q6ZTR5	CX022_HUMAN	V	670	ENSP00000297866:L670V	ENSP00000297866:L670V	L	+	1	2	CXorf22	35899661	0.009000	0.17119	0.000000	0.03702	0.118000	0.20060	-0.271000	0.08572	-0.719000	0.04942	0.486000	0.48141	TTA	.	.		0.373	CXorf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056216.2	NM_152632		G	35989740	T	G	35989740	3	3	254	1	0	0	0	0	1	0	0	0	4104	1606	56	5	2054	5	CXorf22	23	35989740	Missense_Mutation	SNP	T	TCGA-EP-A2KA-01A-11D-A183-10	3499432	35989740	119280820	1031	35323										
CYBB	1536	hgsc.bcm.edu	37	chrX	37665717	37665717	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctgcaactgctggagagccaGatgcaggaaaggaacaatgc	13	9	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:37665717G>T	ENST00000378588.4	+	11	1459	c.1392G>T	c.(1390-1392)caG>caT	p.Q464H	CYBB_ENST00000545017.1_Missense_Mutation_p.Q432H|CYBB_ENST00000536160.1_Missense_Mutation_p.Q197H|TM4SF2_ENST00000465127.1_Intron	NM_000397.3	NP_000388.2	P04839	CY24B_HUMAN	cytochrome b-245, beta polypeptide	464					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|hydrogen peroxide biosynthetic process (GO:0050665)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|oxidation-reduction process (GO:0055114)|phagosome maturation (GO:0090382)|respiratory burst (GO:0045730)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|neuronal cell body (GO:0043025)|phagocytic vesicle membrane (GO:0030670)|rough endoplasmic reticulum (GO:0005791)	flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|superoxide-generating NADPH oxidase activity (GO:0016175)|voltage-gated ion channel activity (GO:0005244)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(20)|prostate(2)|skin(2)	32					Dextromethorphan(DB00514)	TGGAGAGCCAGATGCAGGAAA	0.517																																					p.Q464H		Atlas-SNP	.											.	CYBB	62	.	0			c.G1392T						.						130	103	112					X																	37665717		2202	4300	6502	SO:0001583	missense	1536	exon11			GAGCCAGATGCAG	X04011	CCDS14242.1	Xp21.1	2014-09-17	2008-07-29		ENSG00000165168	ENSG00000165168		"Cytochrome b genes"	2578	protein-coding gene	gene with protein product		300481	"chronic granulomatous disease"	CGD			Standard	NM_000397		Approved	GP91-PHOX, NOX2	uc004ddr.2	P04839	OTTHUMG00000033175	ENST00000378588.4:c.1392G>T	chrX.hg19:g.37665717G>T	ENSP00000367851:p.Gln464His	103.0	0.0		72.0	4.0	NM_000397	A8K138|Q2PP16	Missense_Mutation	SNP	ENST00000378588.4	hg19	CCDS14242.1	.	.	.	.	.	.	.	.	.	.	G	13.60	2.284215	0.40394	.	.	ENSG00000165168	ENST00000378588;ENST00000545017;ENST00000536160	D;D;D	0.94497	-3.44;-3.44;-3.44	5.61	4.63	0.57726	Ferric reductase, NAD binding (1);	0.102912	0.64402	D	0.000002	D	0.94653	0.8276	L	0.60455	1.87	0.54753	D	0.99998	D;D	0.56968	0.973;0.978	P;D	0.63703	0.847;0.917	D	0.93376	0.6739	10	0.52906	T	0.07	.	3.4369	0.07449	0.3362:0.0:0.6638:0.0	.	432;464	F5GWD2;P04839	.;CY24B_HUMAN	H	464;432;197	ENSP00000367851:Q464H;ENSP00000441896:Q432H;ENSP00000441958:Q197H	ENSP00000367851:Q464H	Q	+	3	2	CYBB	37550661	1.000000	0.71417	1.000000	0.80357	0.638000	0.38207	2.465000	0.45075	2.332000	0.79248	0.544000	0.68410	CAG	.	.		0.517	CYBB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080881.1			T	37665717	G	T	37665717	3	4	254	1	0	0	0	0	1	0	0	0	4135	933	33	3	1434	3	CYBB	23	37665717	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1675977	37665717	117604843	1032	35324										
SRPX	8406	hgsc.bcm.edu	37	chrX	38013812	38013812	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctccaccacggtgatgtgtcGaagatcaaggccacactgtg	11	12	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:38013812G>T	ENST00000378533.3	-	9	1220	c.1114C>A	c.(1114-1116)Cga>Aga	p.R372R	SRPX_ENST00000544439.1_Silent_p.R352R|SRPX_ENST00000343800.6_Silent_p.R359R|SRPX_ENST00000538295.1_Intron|SRPX_ENST00000479015.1_Intron|SRPX_ENST00000432886.2_Silent_p.R313R|TM4SF2_ENST00000465127.1_Intron	NM_006307.4	NP_006298.1	P78539	SRPX_HUMAN	sushi-repeat containing protein, X-linked	372					autophagy (GO:0006914)|cell adhesion (GO:0007155)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|phagolysosome assembly (GO:0001845)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|response to endoplasmic reticulum stress (GO:0034976)	autophagic vacuole (GO:0005776)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				autonomic_ganglia(1)|breast(2)|endometrium(5)|large_intestine(5)|lung(10)|prostate(2)	25						GTGATGTGTCGAAGATCAAGG	0.502																																					p.R372R		Atlas-SNP	.											.	SRPX	53	.	0			c.C1114A						.						92	63	73					X																	38013812		2202	4300	6502	SO:0001819	synonymous_variant	8406	exon9			TGTGTCGAAGATC	U78093	CCDS14245.1, CCDS55400.1, CCDS55401.1, CCDS55402.1	Xp21.1	2011-01-25	2011-01-25		ENSG00000101955	ENSG00000101955			11309	protein-coding gene	gene with protein product		300187	"sushi-repeat-containing protein, X chromosome", "sushi-repeat-containing protein, X-linked"			8634708, 8634709	Standard	NM_006307		Approved	ETX1	uc004ddy.2	P78539	OTTHUMG00000021362	ENST00000378533.3:c.1114C>A	chrX.hg19:g.38013812G>T		79.0	0.0		81.0	4.0	NM_006307	A8K065|B3KWP8|B4DDB8|B4DQH5|F5H4D7|G3V1L0|Q4VX66|Q99652|Q99913	Silent	SNP	ENST00000378533.3	hg19	CCDS14245.1																																																																																			.	.		0.502	SRPX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056243.1	NM_006307		T	38013812	G	T	38013812	2	4	254	1	0	0	0	0	0	0	0	1	15179	1066	37	1		1	SRPX	23	38013812	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	348095	38013812	117256748	1033	35325										
BCOR	54880	hgsc.bcm.edu	37	chrX	39934379	39934379	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ttcccggatcaggccagtgcGgtccatgctcagtgctgcca	12	14	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:39934379G>T	ENST00000378444.4	-	4	448	c.220C>A	c.(220-222)Cgc>Agc	p.R74S	BCOR_ENST00000397354.3_Missense_Mutation_p.R74S|BCOR_ENST00000378455.4_Missense_Mutation_p.R74S|BCOR_ENST00000342274.4_Missense_Mutation_p.R74S	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	74					heart development (GO:0007507)|histone H2A monoubiquitination (GO:0035518)|negative regulation of bone mineralization (GO:0030502)|negative regulation of histone H3-K36 methylation (GO:0000415)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|palate development (GO:0060021)|specification of axis polarity (GO:0065001)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	heat shock protein binding (GO:0031072)|histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.R74S(1)		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						AGGCCAGTGCGGTCCATGCTC	0.582			"F, N, S, T"	RARA	"retinoblastoma, AML, APL(translocation)"		oculo-facio-cardio-dental genetic																														p.R74S		Atlas-SNP	.		Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	BCOR	351	.	1	Substitution - Missense(1)	lung(1)	c.C220A						.						29	22	24					X																	39934379		2202	4300	6502	SO:0001583	missense	54880	exon4			CAGTGCGGTCCAT	AF317391	CCDS14250.1, CCDS48092.1, CCDS48093.1	Xp11.4	2014-09-17	2010-06-10		ENSG00000183337	ENSG00000183337		"Ankyrin repeat domain containing"	20893	protein-coding gene	gene with protein product		300485	"BCL6 co-repressor"			10898795	Standard	NM_017745		Approved	FLJ20285, KIAA1575	uc004den.4	Q6W2J9	OTTHUMG00000024100	ENST00000378444.4:c.220C>A	chrX.hg19:g.39934379G>T	ENSP00000367705:p.Arg74Ser	98.0	0.0		91.0	6.0	NM_001123385	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Missense_Mutation	SNP	ENST00000378444.4	hg19	CCDS48093.1	.	.	.	.	.	.	.	.	.	.	g	16.19	3.054336	0.55218	.	.	ENSG00000183337	ENST00000378455;ENST00000397354;ENST00000378444;ENST00000342274;ENST00000406200	T;T;T;T;T	0.69685	-0.42;-0.42;-0.42;-0.42;-0.42	5.08	4.13	0.48395	.	.	.	.	.	T	0.72439	0.3460	L	0.32530	0.975	0.44214	D	0.997042	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.85130	0.997;0.997;0.994;0.997	T	0.74225	-0.3734	9	0.52906	T	0.07	-19.8797	13.5537	0.61747	0.0:0.0:0.7808:0.2192	.	74;74;74;74	Q6W2J9-3;Q6W2J9-4;Q6W2J9;Q6W2J9-2	.;.;BCOR_HUMAN;.	S	74	ENSP00000367716:R74S;ENSP00000380512:R74S;ENSP00000367705:R74S;ENSP00000345923:R74S;ENSP00000384485:R74S	ENSP00000345923:R74S	R	-	1	0	BCOR	39819323	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.913000	0.56394	2.107000	0.64212	0.525000	0.51046	CGC	.	.		0.582	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745		T	39934379	G	T	39934379	3	4	254	1	0	0	0	0	1	0	0	0	1386	1116	39	1	5095	1	BCOR	23	39934379	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1920567	39934379	115336181	1034	35326										
CHST7	56548	hgsc.bcm.edu	37	chrX	46433646	46433646	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcaacctcagcggcgctgtcGgggaggcagtgtctcgcgag	17	12	2	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:46433646G>T	ENST00000276055.3	+	1	428	c.280G>T	c.(280-282)Ggg>Tgg	p.G94W		NM_019886.2	NP_063939.2	Q9NS84	CHST7_HUMAN	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 7	94					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|N-acetylglucosamine metabolic process (GO:0006044)|polysaccharide metabolic process (GO:0005976)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin 6-sulfotransferase activity (GO:0008459)|N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)			breast(3)|endometrium(2)|kidney(1)|lung(2)	8						CGGCGCTGTCGGGGAGGCAGT	0.692																																					p.G94W		Atlas-SNP	.											.	CHST7	23	.	0			c.G280T						.						26	21	23					X																	46433646		2203	4300	6503	SO:0001583	missense	56548	exon1			GCTGTCGGGGAGG	AB040711	CCDS14268.1	Xp11.3	2008-02-05			ENSG00000147119	ENSG00000147119		"Sulfotransferases, membrane-bound"	13817	protein-coding gene	gene with protein product		300375				10781596	Standard	NM_019886		Approved	C6ST-2, C6ST2	uc004dgt.3	Q9NS84	OTTHUMG00000021423	ENST00000276055.3:c.280G>T	chrX.hg19:g.46433646G>T	ENSP00000276055:p.Gly94Trp	100.0	0.0		62.0	5.0	NM_019886	O75667	Missense_Mutation	SNP	ENST00000276055.3	hg19	CCDS14268.1	.	.	.	.	.	.	.	.	.	.	g	10.92	1.485710	0.26686	.	.	ENSG00000147119	ENST00000276055	D	0.97688	-4.49	4.3	1.14	0.20703	.	0.483859	0.15100	N	0.280593	D	0.96719	0.8929	N	0.19112	0.55	0.30814	N	0.738525	D	0.71674	0.998	D	0.70487	0.969	D	0.94084	0.7347	10	0.66056	D	0.02	.	12.3937	0.55373	0.0:0.4722:0.5278:0.0	.	94	Q9NS84	CHST7_HUMAN	W	94	ENSP00000276055:G94W	ENSP00000276055:G94W	G	+	1	0	CHST7	46318590	1.000000	0.71417	0.770000	0.31555	0.501000	0.33797	1.088000	0.30877	0.350000	0.24002	0.509000	0.49947	GGG	.	.		0.692	CHST7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056362.1	NM_019886		T	46433646	G	T	46433646	3	4	254	1	0	0	0	0	1	0	0	0	3411	1116	39	1	282	1	CHST7	23	46433646	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	6499267	46433646	108836914	1035	35327										
GRIPAP1	56850	hgsc.bcm.edu	37	chrX	48855662	48855662	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ggaggtaccttctgagctttGctgaactccttatccaagta	9	10	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:48855662G>A	ENST00000376441.1	-	3	193	c.159C>T	c.(157-159)agC>agT	p.S53S	GRIPAP1_ENST00000376444.3_Silent_p.S53S|GRIPAP1_ENST00000376423.4_Silent_p.S53S|GRIPAP1_ENST00000376425.3_Silent_p.S53S	NM_020137.3	NP_064522.3	Q4V328	GRAP1_HUMAN	GRIP1 associated protein 1	53						blood microparticle (GO:0072562)|endosome (GO:0005768)				breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(2)	10						TCTGAGCTTTGCTGAACTCCT	0.537																																					p.S53S		Atlas-SNP	.											.	GRIPAP1	128	.	0			c.C159T						.						135	94	108					X																	48855662		2203	4300	6503	SO:0001819	synonymous_variant	56850	exon3			AGCTTTGCTGAAC	AB032993	CCDS35248.1	Xp11.23	2008-02-05			ENSG00000068400	ENSG00000068400			18706	protein-coding gene	gene with protein product		300408				10896157	Standard	NM_020137		Approved	GRASP-1, GRASP1, KIAA1167, MPMGp800B12492Q3, DKFZp434P0630	uc004dly.1	Q4V328	OTTHUMG00000033192	ENST00000376441.1:c.159C>T	chrX.hg19:g.48855662G>A		175.0	0.0		137.0	6.0	NM_020137	A6NL78|Q3MJ75|Q4V327|Q4V330|Q5HYG1|Q6N046|Q96DH8|Q9NQ43|Q9ULQ3	Silent	SNP	ENST00000376441.1	hg19	CCDS35248.1																																																																																			.	.		0.537	GRIPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080970.2	NM_207672		A	48855662	G	A	48855662	2	1	254	1	0	0	0	0	0	0	0	1	6798	1310	46	3		3	GRIPAP1	23	48855662	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	2422016	48855662	106414898	1036	35328										
CCDC22	28952	hgsc.bcm.edu	37	chrX	49105132	49105132	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	ctggcagagatccaagaactGcaccagagtgtccgggcggc	14	12	0	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:49105132G>T	ENST00000376227.3	+	12	1538	c.1368G>T	c.(1366-1368)ctG>ctT	p.L456L		NM_014008.3	NP_054727.1	O60826	CCD22_HUMAN	coiled-coil domain containing 22	456										NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(2)|skin(1)	18						TCCAAGAACTGCACCAGAGTG	0.602																																					p.L456L		Atlas-SNP	.											.	CCDC22	69	.	0			c.G1368T						.						32	33	33					X																	49105132		2197	4296	6493	SO:0001819	synonymous_variant	28952	exon12			AGAACTGCACCAG	BC000972	CCDS14322.1	Xp11.23	2008-02-05	2005-07-24	2005-07-24	ENSG00000101997	ENSG00000101997			28909	protein-coding gene	gene with protein product		300859	"chromosome X open reading frame 37"	CXorf37		12477932	Standard	NM_014008		Approved	JM1	uc004dnd.2	O60826	OTTHUMG00000024141	ENST00000376227.3:c.1368G>T	chrX.hg19:g.49105132G>T		260.0	0.0		174.0	35.0	NM_014008	A8K7G1	Silent	SNP	ENST00000376227.3	hg19	CCDS14322.1																																																																																			.	.		0.602	CCDC22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060822.1	NM_014008		T	49105132	G	T	49105132	2	4	254	1	0	0	0	0	0	0	0	1	2799	1306	46	3		3	CCDC22	23	49105132	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	249470	49105132	106165428	1037	35329										
FOXR2	139628	hgsc.bcm.edu	37	chrX	55650629	55650629	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agaagaggaggctgaggaacCagacgacaactccctccagt	12	11	0	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:55650629C>A	ENST00000339140.3	+	1	797	c.485C>A	c.(484-486)cCa>cAa	p.P162Q		NM_198451.3	NP_940853.1	Q6PJQ5	FOXR2_HUMAN	forkhead box R2	162					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|liver(1)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	19						GCTGAGGAACCAGACGACAAC	0.517																																					p.P162Q		Atlas-SNP	.											.	FOXR2	42	.	0			c.C485A						.						69	59	62					X																	55650629		2203	4300	6503	SO:0001583	missense	139628	exon1			AGGAACCAGACGA	BC012934	CCDS35308.1	Xp11	2006-12-15			ENSG00000189299	ENSG00000189299		"Forkhead boxes"	30469	protein-coding gene	gene with protein product						15202009, 15202027	Standard	NM_198451		Approved	MGC21658, FOXN6	uc004duo.3	Q6PJQ5	OTTHUMG00000021661	ENST00000339140.3:c.485C>A	chrX.hg19:g.55650629C>A	ENSP00000427329:p.Pro162Gln	154.0	0.0		86.0	5.0	NM_198451		Missense_Mutation	SNP	ENST00000339140.3	hg19	CCDS35308.1	.	.	.	.	.	.	.	.	.	.	A	0.007	-1.940364	0.00479	.	.	ENSG00000189299	ENST00000339140	D	0.93763	-3.28	3.19	0.654	0.17833	.	1.825580	0.03342	N	0.194900	T	0.68897	0.3051	N	0.00170	-1.935	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.72676	-0.4221	10	0.02654	T	1	.	0.4452	0.00492	0.4251:0.2217:0.1345:0.2187	.	162	Q6PJQ5	FOXR2_HUMAN	Q	162	ENSP00000427329:P162Q	ENSP00000427329:P162Q	P	+	2	0	FOXR2	55667354	0.017000	0.18338	0.000000	0.03702	0.007000	0.05969	0.063000	0.14410	-0.255000	0.09486	-0.314000	0.08810	CCA	.	.		0.517	FOXR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056877.2	NM_198451		A	55650629	C	A	55650629	3	1	254	1	0	0	0	0	1	0	0	0	6040	594	21	3	487	3	FOXR2	23	55650629	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	6545497	55650629	99619931	1038	35330										
FAM155B	27112	hgsc.bcm.edu	37	chrX	68725240	68725240	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aaccttgcgccgactccgagCgggcgcagcgatggcgactg	15	14	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:68725240C>A	ENST00000252338.4	+	1	157	c.115C>A	c.(115-117)Cgg>Agg	p.R39R	AL158069.1_ENST00000579664.1_RNA	NM_015686.2	NP_056501.2	O75949	F155B_HUMAN	family with sequence similarity 155, member B	39						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(2)|endometrium(4)|large_intestine(2)|lung(4)|ovary(2)|pancreas(1)	16						CGACTCCGAGCGGGCGCAGCG	0.701																																					p.R39R		Atlas-SNP	.											.	FAM155B	44	.	0			c.C115A						.						11	6	8					X																	68725240		1882	3579	5461	SO:0001819	synonymous_variant	27112	exon1			TCCGAGCGGGCGC	AF087142	CCDS35317.1	Xq13.1	2008-04-15	2008-04-15	2008-04-15	ENSG00000130054	ENSG00000130054			30701	protein-coding gene	gene with protein product			"transmembrane protein 28", "chromosome X open reading frame 63"	TMEM28, CXorf63			Standard	NM_015686		Approved	TED	uc004dxk.3	O75949	OTTHUMG00000021756	ENST00000252338.4:c.115C>A	chrX.hg19:g.68725240C>A		54.0	0.0		55.0	4.0	NM_015686	B1ALV6|B9EGK1|D3DVU1	Silent	SNP	ENST00000252338.4	hg19	CCDS35317.1																																																																																			.	.		0.701	FAM155B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057037.1	NM_015686		A	68725240	C	A	68725240	2	1	254	1	0	0	0	0	0	0	0	1	5471	759	27	1		1	FAM155B	23	68725240	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	13074611	68725240	86545320	1039	35331										
ARR3	407	hgsc.bcm.edu	37	chrX	69496000	69496000	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aagtgattggtctgacgttcCgaaaagatctgtatgtgcag	12	6	2	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:69496000C>T	ENST00000307959.8	+	6	265	c.214C>T	c.(214-216)Cga>Tga	p.R72*	ARR3_ENST00000374495.3_Nonsense_Mutation_p.R72*	NM_004312.2	NP_004303.2	P36575	ARRC_HUMAN	arrestin 3, retinal (X-arrestin)	72					endocytosis (GO:0006897)|regulation of protein phosphorylation (GO:0001932)|signal transduction (GO:0007165)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|synapse (GO:0045202)				endometrium(3)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|skin(1)	16						TCTGACGTTCCGAAAAGATCT	0.537																																					p.R72X		Atlas-SNP	.											.	ARR3	41	.	0			c.C214T						.						113	79	90					X																	69496000		2203	4300	6503	SO:0001587	stop_gained	407	exon6			ACGTTCCGAAAAG		CCDS14399.1	Xq13.1	2013-10-11			ENSG00000120500	ENSG00000120500			710	protein-coding gene	gene with protein product	"arrestin 4"	301770				8224247	Standard	NM_004312		Approved	ARRX	uc004dyb.2	P36575	OTTHUMG00000021768	ENST00000307959.8:c.214C>T	chrX.hg19:g.69496000C>T	ENSP00000311538:p.Arg72*	166.0	0.0		99.0	4.0	NM_004312	B5B0B9|Q5JT23|Q5JT24|Q6IBF5|Q96EN2	Nonsense_Mutation	SNP	ENST00000307959.8	hg19	CCDS14399.1	.	.	.	.	.	.	.	.	.	.	C	15.81	2.942918	0.53079	.	.	ENSG00000120500	ENST00000374495;ENST00000374480;ENST00000480877;ENST00000307959	.	.	.	4.23	1.43	0.22495	.	0.151709	0.56097	D	0.000039	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.2853	4.3483	0.11143	0.4395:0.3706:0.0:0.19	.	.	.	.	X	72;72;21;72	.	ENSP00000311538:R72X	R	+	1	2	ARR3	69412725	0.936000	0.31750	0.693000	0.30195	0.429000	0.31625	0.147000	0.16202	-0.047000	0.13423	-0.283000	0.09986	CGA	.	.		0.537	ARR3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057055.2	NM_004312		T	69496000	C	T	69496000	4	4	254	1	0	0	0	0	0	1	0	0	979	644	23	1	232	1	ARR3	23	69496000	Nonsense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	770760	69496000	85774560	1040	35332										
SNX12	29934	hgsc.bcm.edu	37	chrX	70282707	70282707	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agagaacaaagccataccttGctatctctctccagctcatt	5	13	3	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:70282707G>A	ENST00000374274.3	-	2	374	c.258C>T	c.(256-258)agC>agT	p.S86S	SNX12_ENST00000465030.1_5'UTR|SNX12_ENST00000276105.3_Silent_p.S82S	NM_001256185.1|NM_001256188.1|NM_013346.3	NP_001243114.1|NP_001243117.1|NP_037478.2	Q9UMY4	SNX12_HUMAN	sorting nexin 12	86	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				intracellular protein transport (GO:0006886)|negative regulation of early endosome to late endosome transport (GO:2000642)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein processing (GO:0010955)|negative regulation of protein transport (GO:0051224)|regulation of endocytosis (GO:0030100)	early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	enzyme binding (GO:0019899)|phosphatidylinositol binding (GO:0035091)			endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	8	Renal(35;0.156)					GCCATACCTTGCTATCTCTCT	0.483																																					p.S86S		Atlas-SNP	.											.	SNX12	18	.	0			c.C258T						.						105	81	89					X																	70282707		2203	4300	6503	SO:0001819	synonymous_variant	29934	exon3			TACCTTGCTATCT	AF171229	CCDS14405.1, CCDS59169.1	Xq13.1	2008-03-11			ENSG00000147164	ENSG00000147164		"Sorting nexins"	14976	protein-coding gene	gene with protein product		300883					Standard	NM_013346		Approved		uc004dyr.2	Q9UMY4	OTTHUMG00000021786	ENST00000374274.3:c.258C>T	chrX.hg19:g.70282707G>A		128.0	0.0		87.0	19.0	NM_001256185	F8W8K5|Q8WUG9	Silent	SNP	ENST00000374274.3	hg19	CCDS14405.1																																																																																			.	.		0.483	SNX12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057094.1	NM_013346		A	70282707	G	A	70282707	2	1	254	1	0	0	0	0	0	0	0	1	14898	1310	46	3		3	SNX12	23	70282707	Silent	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	786707	70282707	84987853	1041	35333										
PHKA1	5255	hgsc.bcm.edu	37	chrX	71915637	71915637	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tgtccccattgatcatcaccCactacagtggcacaggtttt	7	13	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:71915637C>T	ENST00000373542.4	-	4	534	c.375G>A	c.(373-375)gtG>gtA	p.V125V	PHKA1_ENST00000541944.1_Silent_p.V125V|PHKA1_ENST00000373539.3_Silent_p.V125V|PHKA1_ENST00000373545.3_Silent_p.V125V|PHKA1-AS1_ENST00000420998.1_RNA|PHKA1_ENST00000339490.3_Silent_p.V125V	NM_002637.3	NP_002628.2	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle)	125					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(2)|lung(18)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	52	Renal(35;0.156)					GATCATCACCCACTACAGTGG	0.458																																					p.V125V		Atlas-SNP	.											.	PHKA1	129	.	0			c.G375A						.						157	133	141					X																	71915637		2202	4280	6482	SO:0001819	synonymous_variant	5255	exon4			ATCACCCACTACA		CCDS14421.1, CCDS48137.1, CCDS55453.1	Xq12-q13	2009-07-10			ENSG00000067177	ENSG00000067177	2.7.11.19		8925	protein-coding gene	gene with protein product		311870		PHKA			Standard	NM_002637		Approved		uc004eax.4	P46020	OTTHUMG00000022696	ENST00000373542.4:c.375G>A	chrX.hg19:g.71915637C>T		1274.0	1.0		886.0	223.0	NM_001172436	B7ZL05|B7ZL07|Q2M3D7	Silent	SNP	ENST00000373542.4	hg19	CCDS14421.1																																																																																			.	.		0.458	PHKA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058896.1			T	71915637	C	T	71915637	2	4	254	1	0	0	0	0	0	0	0	1	11852	581	21	3		3	PHKA1	23	71915637	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	1632930	71915637	83354923	1042	35334										
KIAA2022	340533	hgsc.bcm.edu	37	chrX	73960460	73960460	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	aggaaggctcctgaaattccCgttggtcatcatccagaagg	11	10	2	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:73960460C>A	ENST00000055682.6	-	3	4543	c.3932G>T	c.(3931-3933)cGg>cTg	p.R1311L		NM_001008537.2	NP_001008537.1	Q5QGS0	K2022_HUMAN	KIAA2022	1311					base-excision repair, gap-filling (GO:0006287)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|nervous system development (GO:0007399)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)	delta DNA polymerase complex (GO:0043625)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|DNA-directed DNA polymerase activity (GO:0003887)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(23)|liver(1)|lung(41)|ovary(7)|pancreas(2)|prostate(4)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	109						CTGAAATTCCCGTTGGTCATC	0.532																																					p.R1311L		Atlas-SNP	.											.	KIAA2022	262	.	0			c.G3932T						.						124	115	118					X																	73960460		2203	4300	6503	SO:0001583	missense	340533	exon3			AATTCCCGTTGGT		CCDS35337.1	Xq13.3	2014-02-19			ENSG00000050030	ENSG00000050030			29433	protein-coding gene	gene with protein product	"XLMR-related protein, neurite extension"	300524				15466006, 23615299	Standard	NM_001008537		Approved	XPN, MRX98	uc004eby.3	Q5QGS0	OTTHUMG00000021860	ENST00000055682.6:c.3932G>T	chrX.hg19:g.73960460C>A	ENSP00000055682:p.Arg1311Leu	127.0	0.0		77.0	5.0	NM_001008537	A7YY87|Q5JUX9|Q8IVE9	Missense_Mutation	SNP	ENST00000055682.6	hg19	CCDS35337.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.966002	0.74131	.	.	ENSG00000050030	ENST00000373468;ENST00000055682	T;T	0.35236	1.32;1.32	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.52058	0.1711	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.55205	-0.8177	10	0.87932	D	0	-8.1691	18.525	0.90968	0.0:1.0:0.0:0.0	.	1311	Q5QGS0	K2022_HUMAN	L	1311	ENSP00000362567:R1311L;ENSP00000055682:R1311L	ENSP00000055682:R1311L	R	-	2	0	KIAA2022	73877185	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.487000	0.81328	2.317000	0.78254	0.544000	0.68410	CGG	.	.		0.532	KIAA2022-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057270.2	NM_001008537		A	73960460	C	A	73960460	3	1	254	1	0	0	0	0	1	0	0	0	8278	652	23	1	626	1	KIAA2022	23	73960460	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	2044823	73960460	81310100	1043	35335										
DRP2	1821	hgsc.bcm.edu	37	chrX	100513518	100513518	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agtcccagctgcagcgtctgAgggagcttctcctgcaggtg	14	12	2	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:100513518A>G	ENST00000395209.3	+	22	3138	c.2611A>G	c.(2611-2613)Agg>Ggg	p.R871G	DRP2_ENST00000402866.1_Missense_Mutation_p.R871G|DRP2_ENST00000538510.1_Missense_Mutation_p.R871G|DRP2_ENST00000541709.1_Missense_Mutation_p.R793G	NM_001939.2	NP_001930.2	Q13474	DRP2_HUMAN	dystrophin related protein 2	871					central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(3)|prostate(1)|skin(2)|urinary_tract(2)	31						GCAGCGTCTGAGGGAGCTTCT	0.607																																					p.R871G		Atlas-SNP	.											.	DRP2	98	.	0			c.A2611G						.						10	9	9					X																	100513518		2181	4257	6438	SO:0001583	missense	1821	exon22			CGTCTGAGGGAGC	U43519	CCDS14480.2, CCDS55465.1	Xq22	2008-02-05			ENSG00000102385	ENSG00000102385			3032	protein-coding gene	gene with protein product		300052				8640231	Standard	NM_001939		Approved		uc004egz.2	Q13474	OTTHUMG00000022020	ENST00000395209.3:c.2611A>G	chrX.hg19:g.100513518A>G	ENSP00000378635:p.Arg871Gly	92.0	0.0		97.0	4.0	NM_001939	A6ZKI5|A8K1B0|B1B1F3|B4DIZ0	Missense_Mutation	SNP	ENST00000395209.3	hg19	CCDS14480.2	.	.	.	.	.	.	.	.	.	.	A	20.9	4.069855	0.76301	.	.	ENSG00000102385	ENST00000402866;ENST00000395209;ENST00000541709;ENST00000538510	T;T;T;T	0.09723	3.02;3.02;2.95;3.02	5.39	4.15	0.48705	.	0.000000	0.85682	D	0.000000	T	0.32615	0.0835	M	0.84082	2.675	0.80722	D	1	D	0.57899	0.981	D	0.69824	0.966	T	0.09930	-1.0652	10	0.87932	D	0	-12.7117	10.4037	0.44243	0.8386:0.1614:0.0:0.0	.	871	Q13474	DRP2_HUMAN	G	871;871;793;871	ENSP00000385038:R871G;ENSP00000378635:R871G;ENSP00000444752:R793G;ENSP00000441051:R871G	ENSP00000378635:R871G	R	+	1	2	DRP2	100400174	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	3.270000	0.51600	1.798000	0.52647	0.441000	0.28932	AGG	.	.		0.607	DRP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057522.3	NM_001939		G	100513518	A	G	100513518	3	3	254	1	0	0	0	0	1	0	0	0	4766	295	11	2	2689	2	DRP2	23	100513518	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	26553058	100513518	54757042	1044	35336										
BHLHB9	80823	hgsc.bcm.edu	37	chrX	102004395	102004395	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	tggaacctgcggctggggccGattgcaaacctaggtcaggg	16	10	1	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:102004395G>T	ENST00000372735.1	+	4	1057	c.472G>T	c.(472-474)Gat>Tat	p.D158Y	BHLHB9_ENST00000447531.1_Missense_Mutation_p.D158Y|BHLHB9_ENST00000457056.1_Missense_Mutation_p.D158Y|BHLHB9_ENST00000448867.1_Missense_Mutation_p.D158Y|BHLHB9_ENST00000361229.4_Missense_Mutation_p.D158Y			Q6PI77	BHLH9_HUMAN	basic helix-loop-helix domain containing, class B, 9	158					learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of neurogenesis (GO:0050769)|positive regulation of synapse assembly (GO:0051965)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(8)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						GGCTGGGGCCGATTGCAAACC	0.483																																					p.D158Y		Atlas-SNP	.											.	BHLHB9	60	.	0			c.G472T						.						81	86	84					X																	102004395		2203	4299	6502	SO:0001583	missense	80823	exon2			GGGGCCGATTGCA	AB051488	CCDS14502.1	Xq23	2014-03-21			ENSG00000198908	ENSG00000198908		"Basic helix-loop-helix proteins", "Armadillo repeat containing"	29353	protein-coding gene	gene with protein product		300921				11214970, 15034937, 16221301	Standard	NM_030639		Approved	p60TRP, KIAA1701, GASP3	uc011mrv.2	Q6PI77	OTTHUMG00000022060	ENST00000372735.1:c.472G>T	chrX.hg19:g.102004395G>T	ENSP00000361820:p.Asp158Tyr	145.0	0.0		110.0	5.0	NM_001142530	Q9C0G2	Missense_Mutation	SNP	ENST00000372735.1	hg19	CCDS14502.1	.	.	.	.	.	.	.	.	.	.	G	1.495	-0.553643	0.03996	.	.	ENSG00000198908	ENST00000457056;ENST00000361229;ENST00000447531;ENST00000448867;ENST00000372735	T;T;T;T;T	0.12147	2.71;2.71;2.71;2.71;2.71	4.38	0.812	0.18744	.	1.046050	0.07568	N	0.918073	T	0.06096	0.0158	N	0.08118	0	0.09310	N	1	P	0.39576	0.679	B	0.35510	0.204	T	0.35226	-0.9797	9	.	.	.	-16.1094	5.6751	0.17743	0.6143:0.0:0.3857:0.0	.	158	Q6PI77	BHLH9_HUMAN	Y	158	ENSP00000403226:D158Y;ENSP00000354675:D158Y;ENSP00000405893:D158Y;ENSP00000391722:D158Y;ENSP00000361820:D158Y	.	D	+	1	0	BHLHB9	101891051	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.014000	0.13333	0.033000	0.15463	-0.395000	0.06472	GAT	.	.		0.483	BHLHB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057630.1	NM_030639		T	102004395	G	T	102004395	3	4	254	1	0	0	0	0	1	0	0	0	1420	1058	37	1	474	1	BHLHB9	23	102004395	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	1490877	102004395	53266165	1045	35337										
IRS4	8471	hgsc.bcm.edu	37	chrX	107979422	107979422	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gtggagagccacatggctccCggacaagacgacccggtccc	13	15	0	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:107979422C>A	ENST00000372129.2	-	1	229	c.153G>T	c.(151-153)ccG>ccT	p.P51P	RP6-24A23.3_ENST00000608811.1_RNA|RP6-24A23.3_ENST00000436013.1_RNA	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	51					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						ACATGGCTCCCGGACAAGACG	0.672																																					p.P51P		Atlas-SNP	.											.	IRS4	253	.	0			c.G153T						.						20	24	23					X																	107979422		2170	4211	6381	SO:0001819	synonymous_variant	8471	exon1			GGCTCCCGGACAA	AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.153G>T	chrX.hg19:g.107979422C>A		173.0	0.0		121.0	6.0	NM_003604		Silent	SNP	ENST00000372129.2	hg19	CCDS14544.1																																																																																			.	.		0.672	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604		A	107979422	C	A	107979422	2	1	254	1	0	0	0	0	0	0	0	1	7851	639	23	1		1	IRS4	23	107979422	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	5975027	107979422	47291138	1046	35338										
ALG13	79868	hgsc.bcm.edu	37	chrX	110980011	110980011	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cagctccagtcttatctaacGgtgcagcggctaatcaagct	9	12	3	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:110980011G>T	ENST00000394780.3	+	23	2611	c.2599G>T	c.(2599-2601)Ggt>Tgt	p.G867C	ALG13_ENST00000470971.1_3'UTR|ALG13_ENST00000251943.4_Missense_Mutation_p.G763C	NM_001099922.2|NM_001257231.1	NP_001093392.1|NP_001244160.1	Q9NP73	ALG13_HUMAN	ALG13, UDP-N-acetylglucosaminyltransferase subunit	867					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|lipid glycosylation (GO:0030259)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)	carbohydrate binding (GO:0030246)|cysteine-type peptidase activity (GO:0008234)|N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity (GO:0004577)|poly(A) RNA binding (GO:0044822)			endometrium(2)|lung(10)|skin(1)	13						CTTATCTAACGGTGCAGCGGC	0.453																																					p.G867C		Atlas-SNP	.											.	ALG13	230	.	0			c.G2599T						.						221	188	198					X																	110980011		1568	3582	5150	SO:0001583	missense	79868	exon23			TCTAACGGTGCAG	AF220051	CCDS14559.1, CCDS55477.1, CCDS59173.1, CCDS76011.1, CCDS76012.1, CCDS76013.1	Xq23	2014-02-24	2013-02-21	2006-11-07	ENSG00000101901	ENSG00000101901	2.4.1.141	"Tudor domain containing", "OTU domain containing"	30881	protein-coding gene	gene with protein product	"tudor domain containing 13", "N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase"	300776	"glycosyltransferase 28 domain containing 1", "chromosome X open reading frame 45", "asparagine-linked glycosylation 13 homolog (S. cerevisiae)"	GLT28D1, CXorf45		12477932	Standard	NM_018466		Approved	MDS031, YGL047W, FLJ23018, TDRD13	uc011msy.2	Q9NP73	OTTHUMG00000022209	ENST00000394780.3:c.2599G>T	chrX.hg19:g.110980011G>T	ENSP00000378260:p.Gly867Cys	262.0	0.0		166.0	7.0	NM_001099922	B1AKD6|B1AKM1|B2R5L5|B7Z6J0|B7Z804|B7Z847|B7Z9A8|B7ZAJ1|B7ZB57|Q17RC3|Q5JXY9|Q9H5U8	Missense_Mutation	SNP	ENST00000394780.3	hg19	CCDS55477.1	.	.	.	.	.	.	.	.	.	.	G	1.646	-0.515106	0.04200	.	.	ENSG00000101901	ENST00000251943;ENST00000394780;ENST00000436609	T;T	0.74106	1.59;-0.81	5.49	0.135	0.14775	.	0.517332	0.21477	N	0.073895	T	0.35480	0.0933	N	0.00436	-1.5	0.09310	N	0.999997	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.40327	-0.9569	10	0.39692	T	0.17	-0.0745	6.5785	0.22581	0.2464:0.0:0.2588:0.4948	.	789;867;763	Q9NP73-3;Q9NP73;Q9NP73-4	.;ALG13_HUMAN;.	C	763;867;500	ENSP00000251943:G763C;ENSP00000378260:G867C	ENSP00000251943:G763C	G	+	1	0	ALG13	110866667	0.155000	0.22806	0.087000	0.20705	0.066000	0.16364	0.890000	0.28295	-0.249000	0.09569	-0.328000	0.08392	GGT	.	.		0.453	ALG13-011	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272895.1	NM_018466		T	110980011	G	T	110980011	3	4	254	1	0	0	0	0	1	0	0	0	515	1116	39	1	2831	1	ALG13	23	110980011	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	3000589	110980011	44290549	1047	35339										
GLUD2	2747	hgsc.bcm.edu	37	chrX	120181981	120181981	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	gcaccgcacgccctgcaaggGaggtatccgttacagcactg	12	14	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:120181981G>A	ENST00000328078.1	+	1	520	c.443G>A	c.(442-444)gGa>gAa	p.G148E		NM_012084.3	NP_036216.2	P49448	DHE4_HUMAN	glutamate dehydrogenase 2	148					glutamate biosynthetic process (GO:0006537)|glutamate catabolic process (GO:0006538)|glutamate metabolic process (GO:0006536)|oxidation-reduction process (GO:0055114)	mitochondrion (GO:0005739)	ADP binding (GO:0043531)|glutamate dehydrogenase (NAD+) activity (GO:0004352)|glutamate dehydrogenase [NAD(P)+] activity (GO:0004353)|GTP binding (GO:0005525)|leucine binding (GO:0070728)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|urinary_tract(1)	38						CCCTGCAAGGGAGGTATCCGT	0.577																																					p.G148E		Atlas-SNP	.											.	GLUD2	89	.	0			c.G443A						.						94	67	76					X																	120181981		2203	4300	6503	SO:0001583	missense	2747	exon1			GCAAGGGAGGTAT	U08997	CCDS14603.1	Xq24-q25	2008-02-05	2003-02-24	2003-02-28	ENSG00000182890	ENSG00000182890			4336	protein-coding gene	gene with protein product		300144	"glutamate dehydrogenase pseudogene 1"	GLUDP1		8207021, 9109504	Standard	NM_012084		Approved		uc004eto.3	P49448	OTTHUMG00000022320	ENST00000328078.1:c.443G>A	chrX.hg19:g.120181981G>A	ENSP00000327589:p.Gly148Glu	246.0	0.0		147.0	38.0	NM_012084	B2R8G0|Q9UDQ4	Missense_Mutation	SNP	ENST00000328078.1	hg19	CCDS14603.1	.	.	.	.	.	.	.	.	.	.	G	17.89	3.498790	0.64298	.	.	ENSG00000182890	ENST00000328078	D	0.99685	-6.4	1.8	1.8	0.24995	Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain (1);	0.124053	0.53938	N	0.000048	D	0.99832	0.9924	H	0.99697	4.71	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97061	0.9771	10	0.87932	D	0	.	9.1461	0.36933	0.0:0.0:1.0:0.0	.	148	P49448	DHE4_HUMAN	E	148	ENSP00000327589:G148E	ENSP00000327589:G148E	G	+	2	0	GLUD2	120009662	1.000000	0.71417	0.835000	0.33067	0.842000	0.47809	6.236000	0.72339	1.228000	0.43614	0.472000	0.43445	GGA	.	.		0.577	GLUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058133.1	NM_012084		A	120181981	G	A	120181981	3	1	254	1	0	0	0	0	1	0	0	0	6485	1174	41	3	445	3	GLUD2	23	120181981	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	9201970	120181981	35088579	1048	35340										
ZIC3	7547	hgsc.bcm.edu	37	chrX	136649847	136649847	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agcccttcccatgccccttcCcgggctgcgggaagatcttt	10	16	1	1			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:136649847C>A	ENST00000287538.5	+	1	1547	c.997C>A	c.(997-999)Ccg>Acg	p.P333T	ZIC3_ENST00000370606.3_Missense_Mutation_p.P333T	NM_003413.3	NP_003404.1	O60481	ZIC3_HUMAN	Zic family member 3	333	Nuclear localization signal.				anterior/posterior pattern specification (GO:0009952)|cell differentiation (GO:0030154)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of left/right asymmetry in nervous system (GO:0035545)|determination of left/right symmetry (GO:0007368)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|heart looping (GO:0001947)|lung development (GO:0030324)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|large_intestine(3)|liver(1)|lung(18)|ovary(3)|soft_tissue(2)|urinary_tract(1)	37	Acute lymphoblastic leukemia(192;0.000127)					ATGCCCCTTCCCGGGCTGCGG	0.597																																					p.P333T		Atlas-SNP	.											.	ZIC3	93	.	0			c.C997A						.						67	73	71					X																	136649847		2202	4299	6501	SO:0001583	missense	7547	exon1			CCCTTCCCGGGCT	AF028706	CCDS14663.1	Xq24-q27.1	2013-01-08	2011-05-19		ENSG00000156925	ENSG00000156925		"Zinc fingers, C2H2-type"	12874	protein-coding gene	gene with protein product		300265	"heterotaxy 1", "Zic family member 3 (odd-paired homolog, Drosophila)"	HTX1		8298651, 7747776	Standard	NM_003413		Approved	HTX, ZNF203	uc004fak.3	O60481	OTTHUMG00000022525	ENST00000287538.5:c.997C>A	chrX.hg19:g.136649847C>A	ENSP00000287538:p.Pro333Thr	199.0	0.0		125.0	5.0	NM_003413	B2CNW4|Q14DE5|Q5JY75	Missense_Mutation	SNP	ENST00000287538.5	hg19	CCDS14663.1	.	.	.	.	.	.	.	.	.	.	C	19.29	3.798537	0.70567	.	.	ENSG00000156925	ENST00000287538;ENST00000370606	D;D	0.91124	-2.79;-2.79	4.96	4.96	0.65561	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.052480	0.85682	D	0.000000	D	0.91436	0.7297	L	0.41415	1.275	0.80722	D	1	P	0.39737	0.685	P	0.51777	0.679	D	0.92506	0.6012	10	0.87932	D	0	.	16.2665	0.82581	0.0:1.0:0.0:0.0	.	333	O60481	ZIC3_HUMAN	T	333	ENSP00000287538:P333T;ENSP00000359638:P333T	ENSP00000287538:P333T	P	+	1	0	ZIC3	136477513	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.837000	0.69381	2.299000	0.77371	0.596000	0.82720	CCG	.	.		0.597	ZIC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058526.1			A	136649847	C	A	136649847	3	1	254	1	0	0	0	0	1	0	0	0	17695	623	22	3	999	3	ZIC3	23	136649847	Missense_Mutation	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	16467866	136649847	18620713	1049	35341										
SLITRK2	84631	hgsc.bcm.edu	37	chrX	144905572	144905572	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	atcatggggctgaaagactgGacagaacatgccaattcccc	10	11	1	3			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:144905572G>T	ENST00000370490.1	+	1	5884	c.1629G>T	c.(1627-1629)tgG>tgT	p.W543C	SLITRK2_ENST00000413937.2_Missense_Mutation_p.W543C|SLITRK2_ENST00000447897.2_Missense_Mutation_p.W543C|SLITRK2_ENST00000434188.2_Missense_Mutation_p.W543C|SLITRK2_ENST00000428560.2_Missense_Mutation_p.W543C			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	543	LRRCT 2.				axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					TGAAAGACTGGACAGAACATG	0.512																																					p.W543C		Atlas-SNP	.											.	SLITRK2	221	.	0			c.G1629T						.						71	65	67					X																	144905572		2203	4300	6503	SO:0001583	missense	84631	exon5			AGACTGGACAGAA	Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"slit-like 1 (Drosophila)"	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.1629G>T	chrX.hg19:g.144905572G>T	ENSP00000359521:p.Trp543Cys	163.0	0.0		97.0	4.0	NM_001144005	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Missense_Mutation	SNP	ENST00000370490.1	hg19	CCDS14680.1	.	.	.	.	.	.	.	.	.	.	G	17.36	3.368903	0.61624	.	.	ENSG00000185985	ENST00000335565;ENST00000447897;ENST00000370490;ENST00000434188;ENST00000413937;ENST00000428560	T;T;T;T;T;T	0.56275	0.47;0.47;0.47;0.47;0.47;0.47	5.84	5.84	0.93424	Cysteine-rich flanking region, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.80053	0.4553	M	0.93678	3.445	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85242	0.1039	10	0.87932	D	0	-4.5593	16.2774	0.82651	0.0:0.0:1.0:0.0	.	543	Q9H156	SLIK2_HUMAN	C	543	ENSP00000334374:W543C;ENSP00000411681:W543C;ENSP00000359521:W543C;ENSP00000397015:W543C;ENSP00000407347:W543C;ENSP00000412010:W543C	ENSP00000334374:W543C	W	+	3	0	SLITRK2	144713264	1.000000	0.71417	1.000000	0.80357	0.761000	0.43186	9.869000	0.99810	2.448000	0.82819	0.600000	0.82982	TGG	.	.		0.512	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539		T	144905572	G	T	144905572	3	4	254	1	0	0	0	0	1	0	0	0	14758	1183	41	3	1631	3	SLITRK2	23	144905572	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	8255725	144905572	10364988	1050	35342										
AFF2	2334	hgsc.bcm.edu	37	chrX	148037651	148037651	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cctaacatccctttggctccCgagaagaagaagtacagagg	10	11	0	4			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:148037651C>A	ENST00000370460.2	+	11	2555	c.2076C>A	c.(2074-2076)ccC>ccA	p.P692P	AFF2_ENST00000286437.5_Silent_p.P333P|AFF2_ENST00000370457.5_Silent_p.P659P|AFF2_ENST00000342251.3_Silent_p.P659P	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	692					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)			breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					CTTTGGCTCCCGAGAAGAAGA	0.498																																					p.P692P		Atlas-SNP	.											.	AFF2	679	.	0			c.C2076A						.						89	93	91					X																	148037651		2203	4300	6503	SO:0001819	synonymous_variant	2334	exon11			GGCTCCCGAGAAG	U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"fragile X mental retardation 2"	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.2076C>A	chrX.hg19:g.148037651C>A		100.0	0.0		85.0	4.0	NM_002025	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Silent	SNP	ENST00000370460.2	hg19	CCDS14684.1																																																																																			.	.		0.498	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025		A	148037651	C	A	148037651	2	1	254	1	0	0	0	0	0	0	0	1	357	639	23	1		1	AFF2	23	148037651	Silent	SNP	C	TCGA-EP-A2KA-01A-11D-A183-10	3132079	148037651	7232909	1051	35343										
ZNF185	7739	hgsc.bcm.edu	37	chrX	152128427	152128427	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	agcaattcgtcagacgagagAgctgcaccagcaggtacgag	13	10	1	2			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:152128427A>G	ENST00000370268.4	+	17	1628	c.1591A>G	c.(1591-1593)Agc>Ggc	p.S531G	ZNF185_ENST00000539731.1_Missense_Mutation_p.S534G|ZNF185_ENST00000370270.2_Missense_Mutation_p.S563G|ZNF185_ENST00000535861.1_Missense_Mutation_p.S563G|ZNF185_ENST00000324823.6_Missense_Mutation_p.S299G|ZNF185_ENST00000318504.7_Missense_Mutation_p.S472G|ZNF185_ENST00000454925.1_Missense_Mutation_p.S169G|ZNF185_ENST00000318529.8_Missense_Mutation_p.S310G|ZNF185_ENST00000449285.2_Missense_Mutation_p.S532G			O15231	ZN185_HUMAN	zinc finger protein 185 (LIM domain)	531						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(3)	12	Acute lymphoblastic leukemia(192;6.56e-05)					CAGACGAGAGAGCTGCACCAG	0.572																																					p.S563G		Atlas-SNP	.											.	ZNF185	92	.	0			c.A1687G						.						37	40	39					X																	152128427		2079	4185	6264	SO:0001583	missense	7739	exon18			CGAGAGAGCTGCA	AK056517	CCDS48184.1, CCDS55528.1, CCDS55529.1, CCDS55530.1, CCDS55531.1, CCDS55532.1, CCDS69832.1	Xq28	2012-08-08			ENSG00000147394	ENSG00000147394		"Zinc fingers, C2H2-type"	12976	protein-coding gene	gene with protein product		300381				9268636	Standard	NM_001178106		Approved		uc011myg.2	O15231	OTTHUMG00000024187	ENST00000370268.4:c.1591A>G	chrX.hg19:g.152128427A>G	ENSP00000359291:p.Ser531Gly	73.0	0.0		53.0	4.0	NM_001178106	A4FTV3|A6NME5|B4DLE9|B7Z771|B8K2L9|B8K2M0|B8K2M1|B8K2M2|E9PFR6|F5GXF7|F5GZL4|F8W8V7|H0Y4M8|O00345|Q8N1R8|Q9NSD2	Missense_Mutation	SNP	ENST00000370268.4	hg19	CCDS48184.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.247|9.247	1.039815|1.039815	0.19669|0.19669	.|.	.|.	ENSG00000147394|ENSG00000147394	ENST00000426821|ENST00000535861;ENST00000539731;ENST00000449285;ENST00000318504;ENST00000535156;ENST00000324823;ENST00000370268;ENST00000318529;ENST00000370270	.|T;T;T;T;T	.|0.51071	.|0.73;0.72;0.74;0.74;0.74	4.14|4.14	-3.64|-3.64	0.04515|0.04515	.|.	.|0.566443	.|0.16697	.|N	.|0.203312	T|T	0.55577|0.55577	0.1929|0.1929	L|L	0.48642|0.48642	1.525|1.525	0.09310|0.09310	N|N	1|1	.|B;B;B;P;B;B;B;D;B	.|0.61697	.|0.161;0.161;0.002;0.907;0.28;0.161;0.037;0.99;0.162	.|B;B;B;P;B;B;B;D;B	.|0.72982	.|0.05;0.05;0.003;0.648;0.143;0.05;0.103;0.979;0.102	T|T	0.55964|0.55964	-0.8057|-0.8057	5|10	.|0.62326	.|D	.|0.03	-0.7509|-0.7509	12.7073|12.7073	0.57067|0.57067	0.246:0.0:0.754:0.0|0.246:0.0:0.754:0.0	.|.	.|532;472;502;534;563;531;169;310;294	.|O15231-3;B8K2L9;B8K2M0;F5GZL4;F5GXF7;O15231;Q8N1R8;F8W8V7;O15231-2	.|.;.;.;.;.;ZN185_HUMAN;.;.;.	G|G	316|563;534;532;472;366;299;531;310;294	.|ENSP00000440847:S563G;ENSP00000444367:S534G;ENSP00000395228:S532G;ENSP00000312782:S472G;ENSP00000359291:S531G	.|ENSP00000312782:S472G	E|S	+|+	2|1	0|0	ZNF185|ZNF185	151879083|151879083	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.013000|0.013000	0.08279|0.08279	-0.722000|-0.722000	0.04958|0.04958	-0.979000|-0.979000	0.03529|0.03529	-0.424000|-0.424000	0.05967|0.05967	GAG|AGC	.	.		0.572	ZNF185-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000377480.1	NM_007150		G	152128427	A	G	152128427	3	3	254	1	0	0	0	0	1	0	0	0	17767	304	11	2	1901	2	ZNF185	23	152128427	Missense_Mutation	SNP	A	TCGA-EP-A2KA-01A-11D-A183-10	4090776	152128427	3142133	1052	35344										
PLXNB3	5365	hgsc.bcm.edu	37	chrX	153032892	153032892	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0104761904761905	11	1	0.423087002096436	2.07697255574614	0.32579961658763	0.193528954652589	0.751940625889747	0	cggcaggggtgccacccctgGccatccgccagctggccggg	16	17	0	0			TCGA-EP-A2KA-01A-11D-A183-10	TCGA-EP-A2KA-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	484a41c8-fcaf-488d-97dc-bfe6a4b88a95	a9d75099-91a1-40aa-a8f1-e6035acd821d	g.chrX:153032892G>T	ENST00000361971.5	+	3	724	c.610G>T	c.(610-612)Gcc>Tcc	p.A204S	PLXNB3_ENST00000538543.1_Intron|U52111.14_ENST00000434284.1_RNA|PLXNB3_ENST00000538966.1_Missense_Mutation_p.A227S|U52111.14_ENST00000416854.1_RNA|PLXNB3_ENST00000538282.1_Intron|PLXNB3_ENST00000538776.1_Intron	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	204	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell chemotaxis (GO:0060326)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|negative regulation of GTPase activity (GO:0034260)|negative regulation of lamellipodium assembly (GO:0010593)|positive chemotaxis (GO:0050918)|positive regulation of endothelial cell proliferation (GO:0001938)|semaphorin-plexin signaling pathway (GO:0071526)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)			central_nervous_system(1)|endometrium(7)|large_intestine(2)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					GCCACCCCTGGCCATCCGCCA	0.711																																					p.A227S		Atlas-SNP	.											.	PLXNB3	208	.	0			c.G679T						.						10	10	10					X																	153032892		2165	4249	6414	SO:0001583	missense	5365	exon4			CCCCTGGCCATCC	AF149019	CCDS14729.1, CCDS55536.1	Xq28	2008-02-05			ENSG00000198753	ENSG00000198753		"Plexins"	9105	protein-coding gene	gene with protein product		300214		PLXN6		10520995	Standard	NM_005393		Approved	PLEXR, PLEXB3	uc010nuk.2	Q9ULL4	OTTHUMG00000024217	ENST00000361971.5:c.610G>T	chrX.hg19:g.153032892G>T	ENSP00000355378:p.Ala204Ser	50.0	0.0		66.0	10.0	NM_001163257	B7Z3E6|F5H773|Q9HDA4	Missense_Mutation	SNP	ENST00000361971.5	hg19	CCDS14729.1	.	.	.	.	.	.	.	.	.	.	G	6.317	0.426546	0.11987	.	.	ENSG00000198753	ENST00000538966;ENST00000361971	T;T	0.10668	2.85;2.85	4.79	0.894	0.19242	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	3.310250	0.01446	N	0.015302	T	0.04363	0.0120	N	0.02315	-0.6	0.19300	N	0.999976	B;B	0.14012	0.009;0.002	B;B	0.15052	0.012;0.007	T	0.37267	-0.9713	10	0.02654	T	1	.	7.8823	0.29629	0.7283:0.0:0.2717:0.0	.	227;204	F5H773;Q9ULL4	.;PLXB3_HUMAN	S	227;204	ENSP00000442736:A227S;ENSP00000355378:A204S	ENSP00000355378:A204S	A	+	1	0	PLXNB3	152686086	0.375000	0.25089	0.193000	0.23327	0.788000	0.44548	1.395000	0.34520	-0.197000	0.10350	-0.374000	0.07098	GCC	.	.		0.711	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1			T	153032892	G	T	153032892	3	4	254	1	0	0	0	0	1	0	0	0	12134	1203	42	3	734	3	PLXNB3	23	153032892	Missense_Mutation	SNP	G	TCGA-EP-A2KA-01A-11D-A183-10	904465	153032892	2237668	1053	35345										
AGRN	375790	hgsc.bcm.edu	37	chr1	981185	981185	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggggctgtgctcgtgtaagcCcggggtggctggacccaagt	18	10	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:981185C>T	ENST00000379370.2	+	15	2659	c.2609C>T	c.(2608-2610)cCc>cTc	p.P870L		NM_198576.3	NP_940978.2	O00468	AGRIN_HUMAN	agrin	870	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|clustering of voltage-gated sodium channels (GO:0045162)|extracellular matrix organization (GO:0030198)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|neuromuscular junction development (GO:0007528)|neurotransmitter receptor metabolic process (GO:0045213)|phototransduction, visible light (GO:0007603)|plasma membrane organization (GO:0007009)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of synaptic growth at neuromuscular junction (GO:0045887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor clustering (GO:0043113)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synapse organization (GO:0050808)	basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acetylcholine receptor regulator activity (GO:0030548)|calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|dystroglycan binding (GO:0002162)|heparan sulfate proteoglycan binding (GO:0043395)|laminin binding (GO:0043236)|sialic acid binding (GO:0033691)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(2)|lung(20)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	42	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00462)|Epithelial(90;5.98e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.43e-23)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000201)|Kidney(185;0.0024)|BRCA - Breast invasive adenocarcinoma(365;0.00246)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0354)|Lung(427;0.201)		TCGTGTAAGCCCGGGGTGGCT	0.672																																					p.P870L		Atlas-SNP	.											.	AGRN	110	.	0			c.C2609T						.						73	75	74					1																	981185		2203	4300	6503	SO:0001583	missense	375790	exon15			GTAAGCCCGGGGT	XM_372195	CCDS30551.1	1p36.33	2014-09-17		2007-02-16	ENSG00000188157	ENSG00000188157		"Proteoglycans / Extracellular Matrix : Other"	329	protein-coding gene	gene with protein product	"agrin proteoglycan"	103320				1851019, 12270958	Standard	NM_198576		Approved	AGRIN	uc001ack.2	O00468	OTTHUMG00000040778	ENST00000379370.2:c.2609C>T	chr1.hg19:g.981185C>T	ENSP00000368678:p.Pro870Leu	149.0	0.0		79.0	4.0	NM_198576	Q5SVA1|Q5SVA2|Q60FE1|Q7KYS8|Q8N4J5|Q96IC1|Q9BTD4	Missense_Mutation	SNP	ENST00000379370.2	hg19	CCDS30551.1	.	.	.	.	.	.	.	.	.	.	C	16.93	3.258046	0.59321	.	.	ENSG00000188157	ENST00000379370	T	0.62639	0.01	5.46	4.46	0.54185	EGF-like, laminin (3);EGF-like region, conserved site (1);	0.078972	0.48286	D	0.000187	T	0.76407	0.3983	M	0.79011	2.435	0.49389	D	0.999783	P	0.46621	0.881	P	0.56343	0.796	T	0.80183	-0.1488	10	0.72032	D	0.01	-15.6578	16.9092	0.86136	0.1369:0.8631:0.0:0.0	.	870	O00468	AGRIN_HUMAN	L	870	ENSP00000368678:P870L	ENSP00000368678:P870L	P	+	2	0	AGRN	971048	0.938000	0.31826	0.981000	0.43875	0.040000	0.13550	2.413000	0.44618	2.548000	0.85928	0.655000	0.94253	CCC	.	.		0.672	AGRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097990.2	NM_198576		T	981185	C	T	981185	3	4	255	1	0	0	0	0	1	0	0	0	397	623	22	3	2667	3	AGRN	1	981185	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10		981185	248269436	1	35346										
PIK3CD	5293	hgsc.bcm.edu	37	chr1	9781914	9781914	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccacatgaaggtgctgatgaAgcaggtgaggcccaaggccc	14	11	0	4			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:9781914A>G	ENST00000377346.4	+	16	2246	c.2051A>G	c.(2050-2052)aAg>aGg	p.K684R	PIK3CD_ENST00000543390.1_3'UTR|PIK3CD_ENST00000361110.2_Missense_Mutation_p.K708R|PIK3CD_ENST00000536656.1_Missense_Mutation_p.K708R	NM_005026.3	NP_005017.3	O00329	PK3CD_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta	684					adaptive immune response (GO:0002250)|B cell activation (GO:0042113)|B cell chemotaxis (GO:0035754)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|cytokine production (GO:0001816)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell chemotaxis (GO:0002551)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|natural killer cell activation (GO:0030101)|natural killer cell chemotaxis (GO:0035747)|natural killer cell differentiation (GO:0001779)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein phosphorylation (GO:0006468)|respiratory burst involved in defense response (GO:0002679)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|mast cell granule (GO:0042629)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(12)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31	all_lung(157;0.222)	all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0231)|Colorectal(212;7.52e-08)|COAD - Colon adenocarcinoma(227;1.78e-05)|Kidney(185;0.000322)|KIRC - Kidney renal clear cell carcinoma(229;0.00114)|BRCA - Breast invasive adenocarcinoma(304;0.0021)|STAD - Stomach adenocarcinoma(132;0.00395)|READ - Rectum adenocarcinoma(331;0.0419)	Caffeine(DB00201)	GTGCTGATGAAGCAGGTGAGG	0.711											OREG0013082	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K684R		Atlas-SNP	.											.	PIK3CD	86	.	0			c.A2051G						.						33	38	36					1																	9781914		2195	4292	6487	SO:0001583	missense	5293	exon16			TGATGAAGCAGGT		CCDS104.1	1p36.2	2014-09-17	2012-07-13		ENSG00000171608	ENSG00000171608	2.7.1.153		8977	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase, catalytic, delta polypeptide", "phosphoinositide-3-kinase C"	602839	"phosphoinositide-3-kinase, catalytic, delta polypeptide"			9113989, 9455486	Standard	NM_005026		Approved	p110D	uc001aqb.4	O00329	OTTHUMG00000001450	ENST00000377346.4:c.2051A>G	chr1.hg19:g.9781914A>G	ENSP00000366563:p.Lys684Arg	33.0	0.0	659	28.0	4.0	NM_005026	A6NCG0|G1FFP1|O15445|Q5SR49	Missense_Mutation	SNP	ENST00000377346.4	hg19	CCDS104.1	.	.	.	.	.	.	.	.	.	.	A	11.64	1.699697	0.30142	.	.	ENSG00000171608	ENST00000536656;ENST00000377346;ENST00000361110;ENST00000360563	D;D;D	0.82255	-1.59;-1.59;-1.59	5.9	4.78	0.61160	Phosphoinositide 3-kinase, accessory (PIK) domain (1);Protein kinase-like domain (1);	0.046560	0.85682	N	0.000000	T	0.69931	0.3166	N	0.16066	0.365	0.80722	D	1	P;P;B	0.36990	0.476;0.577;0.432	B;B;B	0.41619	0.361;0.191;0.344	T	0.63607	-0.6599	10	0.17832	T	0.49	-36.5769	8.3882	0.32512	0.8498:0.0:0.1502:0.0	.	683;708;684	B7ZM44;Q5SR50;O00329	.;.;PK3CD_HUMAN	R	708;684;708;708	ENSP00000446444:K708R;ENSP00000366563:K684R;ENSP00000354410:K708R	ENSP00000353766:K708R	K	+	2	0	PIK3CD	9704501	1.000000	0.71417	0.997000	0.53966	0.082000	0.17680	3.749000	0.55150	1.050000	0.40346	0.533000	0.62120	AAG	.	.		0.711	PIK3CD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004235.1	NM_005026		G	9781914	A	G	9781914	3	3	255	1	0	0	0	0	1	0	0	0	11924	72	3	2	2105	2	PIK3CD	1	9781914	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	8800729	9781914	239468707	2	35347										
PIK3CD	5293	hgsc.bcm.edu	37	chr1	9782115	9782115	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccccaagccccagaccaaggAgctgatgcacttgtgcatgc	10	15	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:9782115A>G	ENST00000377346.4	+	17	2333	c.2138A>G	c.(2137-2139)gAg>gGg	p.E713G	PIK3CD_ENST00000543390.1_3'UTR|PIK3CD_ENST00000361110.2_Missense_Mutation_p.E737G|PIK3CD_ENST00000536656.1_Missense_Mutation_p.E737G	NM_005026.3	NP_005017.3	O00329	PK3CD_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta	713					adaptive immune response (GO:0002250)|B cell activation (GO:0042113)|B cell chemotaxis (GO:0035754)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|cytokine production (GO:0001816)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell chemotaxis (GO:0002551)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|natural killer cell activation (GO:0030101)|natural killer cell chemotaxis (GO:0035747)|natural killer cell differentiation (GO:0001779)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein phosphorylation (GO:0006468)|respiratory burst involved in defense response (GO:0002679)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|mast cell granule (GO:0042629)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(12)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31	all_lung(157;0.222)	all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0231)|Colorectal(212;7.52e-08)|COAD - Colon adenocarcinoma(227;1.78e-05)|Kidney(185;0.000322)|KIRC - Kidney renal clear cell carcinoma(229;0.00114)|BRCA - Breast invasive adenocarcinoma(304;0.0021)|STAD - Stomach adenocarcinoma(132;0.00395)|READ - Rectum adenocarcinoma(331;0.0419)	Caffeine(DB00201)	CAGACCAAGGAGCTGATGCAC	0.612											OREG0013082	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E713G		Atlas-SNP	.											.	PIK3CD	86	.	0			c.A2138G						.						66	74	71					1																	9782115		2203	4300	6503	SO:0001583	missense	5293	exon17			CCAAGGAGCTGAT		CCDS104.1	1p36.2	2014-09-17	2012-07-13		ENSG00000171608	ENSG00000171608	2.7.1.153		8977	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase, catalytic, delta polypeptide", "phosphoinositide-3-kinase C"	602839	"phosphoinositide-3-kinase, catalytic, delta polypeptide"			9113989, 9455486	Standard	NM_005026		Approved	p110D	uc001aqb.4	O00329	OTTHUMG00000001450	ENST00000377346.4:c.2138A>G	chr1.hg19:g.9782115A>G	ENSP00000366563:p.Glu713Gly	147.0	0.0	659	82.0	4.0	NM_005026	A6NCG0|G1FFP1|O15445|Q5SR49	Missense_Mutation	SNP	ENST00000377346.4	hg19	CCDS104.1	.	.	.	.	.	.	.	.	.	.	A	27.0	4.795517	0.90453	.	.	ENSG00000171608	ENST00000536656;ENST00000377346;ENST00000361110;ENST00000360563	D;D;D	0.82433	-1.61;-1.61;-1.61	5.4	5.4	0.78164	Protein kinase-like domain (1);	0.107748	0.64402	D	0.000006	D	0.88016	0.6324	L	0.61218	1.895	0.80722	D	1	P;D;D	0.57571	0.57;0.98;0.975	B;P;P	0.59056	0.334;0.851;0.821	D	0.89223	0.3572	10	0.72032	D	0.01	-40.3082	14.6236	0.68605	1.0:0.0:0.0:0.0	.	712;737;713	B7ZM44;Q5SR50;O00329	.;.;PK3CD_HUMAN	G	737;713;737;737	ENSP00000446444:E737G;ENSP00000366563:E713G;ENSP00000354410:E737G	ENSP00000353766:E737G	E	+	2	0	PIK3CD	9704702	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	9.194000	0.94962	2.045000	0.60652	0.459000	0.35465	GAG	.	.		0.612	PIK3CD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004235.1	NM_005026		G	9782115	A	G	9782115	3	3	255	1	0	0	0	0	1	0	0	0	11924	304	11	2	2196	2	PIK3CD	1	9782115	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	201	9782115	239468506	3	35348										
UBE4B	10277	hgsc.bcm.edu	37	chr1	10190866	10190866	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgcagcattacttagagctcGgaagggtaagtgttcagaaa	12	6	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:10190866G>T	ENST00000253251.8	+	13	2358	c.1519G>T	c.(1519-1521)Gga>Tga	p.G507*	UBE4B_ENST00000475795.1_3'UTR|UBE4B_ENST00000343090.6_Nonsense_Mutation_p.G636*|UBE4B_ENST00000377157.3_Nonsense_Mutation_p.G391*					ubiquitination factor E4B											NS(3)|breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(14)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	48		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		CTTAGAGCTCGGAAGGGTAAG	0.423																																					p.G636X		Atlas-SNP	.											.	UBE4B	233	.	0			c.G1906T						.						100	101	100					1																	10190866		2203	4300	6503	SO:0001587	stop_gained	10277	exon14			GAGCTCGGAAGGG	AF091093	CCDS110.1, CCDS41245.1	1p36.1	2013-01-28	2011-05-19		ENSG00000130939	ENSG00000130939		"U-box domain containing"	12500	protein-coding gene	gene with protein product		613565	"ubiquitination factor E4B (homologous to yeast UFD2)", "ubiquitination factor E4B (UFD2 homolog, yeast)"			9734811, 10089879	Standard	NM_006048		Approved	UBOX3, E4, UFD2, KIAA0684	uc001aqs.4	O95155	OTTHUMG00000001797	ENST00000253251.8:c.1519G>T	chr1.hg19:g.10190866G>T	ENSP00000253251:p.Gly507*	116.0	0.0		77.0	4.0	NM_001105562		Nonsense_Mutation	SNP	ENST00000253251.8	hg19	CCDS110.1	.	.	.	.	.	.	.	.	.	.	G	48	14.290143	0.99788	.	.	ENSG00000130939	ENST00000253251;ENST00000377157;ENST00000343090	.	.	.	5.74	5.74	0.90152	.	0.049441	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.26408	T	0.33	-21.1601	19.9265	0.97104	0.0:0.0:1.0:0.0	.	.	.	.	X	507;391;636	.	ENSP00000253251:G507X	G	+	1	0	UBE4B	10113453	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	9.823000	0.99369	2.723000	0.93209	0.591000	0.81541	GGA	.	.		0.423	UBE4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005017.1	NM_006048		T	10190866	G	T	10190866	4	4	255	1	0	0	0	0	0	1	0	0	16898	1117	39	1	1960	1	UBE4B	1	10190866	Nonsense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	408751	10190866	239059755	4	35349										
VPS13D	55187	hgsc.bcm.edu	37	chr1	12389898	12389898	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cattgcaggtctgaattttcTtcagcgtgtaagaactagcc	9	9	3	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:12389898T>C	ENST00000358136.3	+	37	8340	c.8210T>C	c.(8209-8211)cTt>cCt	p.L2737P	VPS13D_ENST00000356315.4_Missense_Mutation_p.L2737P	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		CTGAATTTTCTTCAGCGTGTA	0.433																																					p.L2737P		Atlas-SNP	.											.	VPS13D	316	.	0			c.T8210C						.						96	88	91					1																	12389898		2203	4300	6503	SO:0001583	missense	55187	exon37			ATTTTCTTCAGCG	AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"vacuolar protein sorting 13D (yeast)"				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.8210T>C	chr1.hg19:g.12389898T>C	ENSP00000350854:p.Leu2737Pro	116.0	0.0		68.0	4.0	NM_015378		Missense_Mutation	SNP	ENST00000358136.3	hg19	CCDS30588.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.47|18.47	3.630866|3.630866	0.67015|0.67015	.|.	.|.	ENSG00000048707|ENSG00000048707	ENST00000011700|ENST00000356315;ENST00000358136	.|T;T	.|0.48836	.|0.8;0.8	5.67|5.67	5.67|5.67	0.87782|0.87782	.|.	.|0.062472	.|0.64402	.|D	.|0.000003	T|T	0.64091|0.64091	0.2567|0.2567	M|M	0.67953|0.67953	2.075|2.075	0.80722|0.80722	D|D	1|1	.|D;P;P	.|0.71674	.|0.998;0.49;0.488	.|D;B;B	.|0.63488	.|0.915;0.296;0.155	T|T	0.61192|0.61192	-0.7112|-0.7112	5|10	.|0.29301	.|T	.|0.29	.|.	15.8735|15.8735	0.79141|0.79141	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|644;2737;2737	.|B1AJZ2;Q5THJ4-2;Q5THJ4	.|.;.;VP13D_HUMAN	L|P	1560|2737	.|ENSP00000348666:L2737P;ENSP00000350854:L2737P	.|ENSP00000348666:L2737P	F|L	+|+	1|2	0|0	VPS13D|VPS13D	12312485|12312485	1.000000|1.000000	0.71417|0.71417	0.970000|0.970000	0.41538|0.41538	0.964000|0.964000	0.63967|0.63967	7.265000|7.265000	0.78442|0.78442	2.285000|2.285000	0.76669|0.76669	0.528000|0.528000	0.53228|0.53228	TTC|CTT	.	.		0.433	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		C	12389898	T	C	12389898	3	2	255	1	0	0	0	0	1	0	0	0	17207	1609	56	2	8352	2	VPS13D	1	12389898	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	2199032	12389898	236860723	5	35350										
AGMAT	79814	hgsc.bcm.edu	37	chr1	15901266	15901266	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	actcaccagaaagatcatacGgtggtgaaacttcgacaaga	9	9	2	4			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:15901266G>T	ENST00000375826.3	-	6	1113	c.971C>A	c.(970-972)cCg>cAg	p.P324Q	DNAJC16_ENST00000375849.1_Missense_Mutation_p.R654L|DNAJC16_ENST00000483270.1_3'UTR	NM_024758.4	NP_079034.3	Q9BSE5	SPEB_HUMAN	agmatine ureohydrolase (agmatinase)	324					agmatine biosynthetic process (GO:0097055)|cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|putrescine biosynthetic process from arginine (GO:0033388)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	agmatinase activity (GO:0008783)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(6)|lung(2)|skin(1)	12		Breast(348;0.000207)|Colorectal(325;0.000258)|Lung NSC(340;0.000359)|all_lung(284;0.000486)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.93e-07)|COAD - Colon adenocarcinoma(227;3.91e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000121)|KIRC - Kidney renal clear cell carcinoma(229;0.00257)|STAD - Stomach adenocarcinoma(313;0.00734)|READ - Rectum adenocarcinoma(331;0.0649)		AAGATCATACGGTGGTGAAAC	0.468																																					p.P324Q	NSCLC(126;1678 1780 25805 43508 49531)	Atlas-SNP	.											.	AGMAT	25	.	0			c.C971A						.						110	96	100					1																	15901266		2203	4300	6503	SO:0001583	missense	79814	exon6			TCATACGGTGGTG	AY057097	CCDS160.1	1p36.13	2009-01-05			ENSG00000116771	ENSG00000116771			18407	protein-coding gene	gene with protein product						11804860, 14648699, 11914032	Standard	NM_024758		Approved	FLJ23384	uc001awv.2	Q9BSE5	OTTHUMG00000002357	ENST00000375826.3:c.971C>A	chr1.hg19:g.15901266G>T	ENSP00000364986:p.Pro324Gln	83.0	0.0		64.0	4.0	NM_024758	Q5TDH1|Q9H5J3	Missense_Mutation	SNP	ENST00000375826.3	hg19	CCDS160.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.566|9.566	1.119660|1.119660	0.20877|0.20877	.|.	.|.	ENSG00000116771|ENSG00000116138	ENST00000375826|ENST00000375849	D|T	0.84223|0.70631	-1.82|-0.5	5.93|5.93	-4.84|-4.84	0.03151|0.03151	Ureohydrolase domain (1);|.	1.007650|.	0.07957|.	N|.	0.981860|.	T|T	0.67268|0.67268	0.2875|0.2875	L|L	0.61218|0.61218	1.895|1.895	0.09310|0.09310	N|N	1|1	B|.	0.23854|.	0.092|.	B|.	0.36808|.	0.233|.	T|T	0.62690|0.62690	-0.6801|-0.6801	10|6	0.72032|.	D|.	0.01|.	0.0126|0.0126	8.29|8.29	0.31952|0.31952	0.3792:0.0:0.5066:0.1143|0.3792:0.0:0.5066:0.1143	.|.	324|.	Q9BSE5|.	SPEB_HUMAN|.	Q|L	324|654	ENSP00000364986:P324Q|ENSP00000365009:R654L	ENSP00000364986:P324Q|.	P|R	-|+	2|2	0|0	AGMAT|DNAJC16	15773853|15773853	0.005000|0.005000	0.15991|0.15991	0.000000|0.000000	0.03702|0.03702	0.055000|0.055000	0.15305|0.15305	1.808000|1.808000	0.38912|0.38912	-0.729000|-0.729000	0.04875|0.04875	-0.332000|-0.332000	0.08345|0.08345	CCG|CGG	.	.		0.468	AGMAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006763.1	NM_024758		T	15901266	G	T	15901266	3	4	255	1	0	0	0	0	1	0	0	0	385	1116	39	1	95	1	AGMAT	1	15901266	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	3511368	15901266	233349355	6	35351										
KIF17	57576	hgsc.bcm.edu	37	chr1	21014288	21014288	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aacctgagtcttggagacatCgtcactgggcagagtgtcag	13	9	3	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:21014288C>A	ENST00000247986.2	-	8	1841	c.1531G>T	c.(1531-1533)Gat>Tat	p.D511Y	KIF17_ENST00000375044.1_Missense_Mutation_p.D411Y|KIF17_ENST00000400463.3_Missense_Mutation_p.D511Y|KIF17_ENST00000490034.1_Intron			Q9P2E2	KIF17_HUMAN	kinesin family member 17	511					ATP catabolic process (GO:0006200)|cell projection organization (GO:0030030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|neurogenesis (GO:0022008)|protein complex localization (GO:0031503)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)		TTGGAGACATCGTCACTGGGC	0.552																																					p.D511Y		Atlas-SNP	.											.	KIF17	130	.	0			c.G1531T						.						88	83	84					1																	21014288		2203	4300	6503	SO:0001583	missense	57576	exon8			AGACATCGTCACT	AB037826	CCDS213.1, CCDS44079.1, CCDS72722.1	1p36.13	2012-08-01			ENSG00000117245	ENSG00000117245		"Kinesins"	19167	protein-coding gene	gene with protein product	"kinesin-like protein KIF17", "KIF3-related motor protein", "KIF17 variant protein"	605037				10846156	Standard	XR_241202		Approved	KIAA1405, KIF3X, KIF17B, OSM-3, KLP-2	uc001bdr.4	Q9P2E2	OTTHUMG00000002863	ENST00000247986.2:c.1531G>T	chr1.hg19:g.21014288C>A	ENSP00000247986:p.Asp511Tyr	124.0	0.0		73.0	4.0	NM_001122819	A2A3Q7|A2A3Q8|O95077|Q53YS6|Q5VWA9|Q6GSA8|Q8N411	Missense_Mutation	SNP	ENST00000247986.2	hg19	CCDS213.1	.	.	.	.	.	.	.	.	.	.	C	11.34	1.608443	0.28623	.	.	ENSG00000117245	ENST00000375044;ENST00000400463;ENST00000247986	T;T;T	0.72394	-0.65;-0.53;-0.53	5.04	-0.415	0.12355	.	1.268100	0.06187	U	0.680688	T	0.58395	0.2119	L	0.39898	1.24	0.09310	N	1	P;P	0.51240	0.943;0.935	B;B	0.42851	0.4;0.3	T	0.51220	-0.8733	10	0.62326	D	0.03	.	1.369	0.02207	0.2948:0.3934:0.1435:0.1684	.	511;511	Q9P2E2-3;Q9P2E2	.;KIF17_HUMAN	Y	411;511;511	ENSP00000364184:D411Y;ENSP00000383311:D511Y;ENSP00000247986:D511Y	ENSP00000247986:D511Y	D	-	1	0	KIF17	20886875	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.066000	0.14489	-0.227000	0.09884	-0.229000	0.12294	GAT	.	.		0.552	KIF17-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276995.1	NM_020816		A	21014288	C	A	21014288	3	1	255	1	0	0	0	0	1	0	0	0	8288	884	31	1	1590	1	KIF17	1	21014288	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	5113022	21014288	228236333	7	35352										
ALPL	249	hgsc.bcm.edu	37	chr1	21894730	21894730	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cacctggaagagcttcaaacCgagatacaaggtagcctgtg	11	10	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:21894730C>A	ENST00000374840.3	+	7	1032	c.782C>A	c.(781-783)cCg>cAg	p.P261Q	ALPL_ENST00000425315.2_Missense_Mutation_p.P261Q|ALPL_ENST00000374830.1_5'Flank|ALPL_ENST00000374832.1_Missense_Mutation_p.P261Q|ALPL_ENST00000539907.1_Missense_Mutation_p.P184Q|ALPL_ENST00000540617.1_Missense_Mutation_p.P206Q	NM_000478.4	NP_000469.3	P05186	PPBT_HUMAN	alkaline phosphatase, liver/bone/kidney	261					cellular response to organic cyclic compound (GO:0071407)|cementum mineralization (GO:0071529)|developmental process involved in reproduction (GO:0003006)|endochondral ossification (GO:0001958)|osteoblast differentiation (GO:0001649)|response to antibiotic (GO:0046677)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to vitamin D (GO:0033280)|skeletal system development (GO:0001501)	anchored component of membrane (GO:0031225)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	26		all_lung(284;2.19e-05)|Lung NSC(340;2.22e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;8.7e-28)|COAD - Colon adenocarcinoma(152;1.57e-05)|GBM - Glioblastoma multiforme(114;2.66e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000177)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00856)|READ - Rectum adenocarcinoma(331;0.0623)|Lung(427;0.146)	Amifostine(DB01143)|Fospropofol(DB06716)	AGCTTCAAACCGAGATACAAG	0.567																																					p.P261Q		Atlas-SNP	.											.	ALPL	50	.	0			c.C782A						.						76	68	71					1																	21894730		2203	4300	6503	SO:0001583	missense	249	exon7			TCAAACCGAGATA	BC021289	CCDS217.1, CCDS53274.1, CCDS53275.1	1p36.12	2008-02-05			ENSG00000162551	ENSG00000162551	3.1.3.1		438	protein-coding gene	gene with protein product		171760		HOPS		3532105, 3446011	Standard	NM_001127501		Approved	TNSALP	uc001bet.3	P05186	OTTHUMG00000002949	ENST00000374840.3:c.782C>A	chr1.hg19:g.21894730C>A	ENSP00000363973:p.Pro261Gln	159.0	0.0		101.0	5.0	NM_000478	A1A4E7|B2RMP8|B7Z387|B7Z4Y6|O75090|Q2TAI7|Q59EJ7|Q5BKZ5|Q5VTG5|Q6NZI8|Q8WU32|Q9UBK0	Missense_Mutation	SNP	ENST00000374840.3	hg19	CCDS217.1	.	.	.	.	.	.	.	.	.	.	C	10.84	1.464296	0.26335	.	.	ENSG00000162551	ENST00000539907;ENST00000540617;ENST00000374840;ENST00000374832;ENST00000425315	D;D;D;D;D	0.95788	-3.81;-3.81;-3.81;-3.81;-3.81	3.97	3.97	0.46021	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.223479	0.47093	D	0.000260	D	0.95620	0.8576	L	0.33189	0.99	0.30549	N	0.765602	D;P;D	0.89917	1.0;0.932;1.0	D;P;D	0.85130	0.997;0.825;0.997	D	0.92700	0.6174	10	0.33141	T	0.24	-1.3343	15.1393	0.72599	0.0:1.0:0.0:0.0	.	184;209;261	B7Z387;B7Z1D1;P05186	.;.;PPBT_HUMAN	Q	184;206;261;261;261	ENSP00000437674:P184Q;ENSP00000442672:P206Q;ENSP00000363973:P261Q;ENSP00000363965:P261Q;ENSP00000394765:P261Q	ENSP00000363965:P261Q	P	+	2	0	ALPL	21767317	0.131000	0.22433	0.979000	0.43373	0.703000	0.40648	1.460000	0.35244	2.210000	0.71456	0.561000	0.74099	CCG	.	.		0.567	ALPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000008202.1	NM_000478		A	21894730	C	A	21894730	3	1	255	1	0	0	0	0	1	0	0	0	547	652	23	1	804	1	ALPL	1	21894730	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	880442	21894730	227355891	8	35353										
USP48	84196	hgsc.bcm.edu	37	chr1	22084236	22084236	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcctaaccaaatatgctcacCaataccaaccaagcaattcg	3	14	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:22084236C>A	ENST00000308271.9	-	2	823	c.175G>T	c.(175-177)Ggt>Tgt	p.G59C	USP48_ENST00000421625.2_Missense_Mutation_p.G59C|USP48_ENST00000400301.1_Missense_Mutation_p.G59C|USP48_ENST00000529637.1_Missense_Mutation_p.G59C	NM_032236.5	NP_115612.4	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 48	59					ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			NS(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(14)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)		ATATGCTCACCAATACCAACC	0.333																																					p.G59C		Atlas-SNP	.											USP48,colon,carcinoma,+2,1	USP48	91	.	0			c.G175T						.						108	100	103					1																	22084236		2203	4300	6503	SO:0001583	missense	84196	exon2			GCTCACCAATACC	AF502942	CCDS30623.1, CCDS44084.1	1p36.12	2008-02-05	2005-08-08	2004-04-07	ENSG00000090686	ENSG00000090686		"Ubiquitin-specific peptidases"	18533	protein-coding gene	gene with protein product			"ubiquitin specific protease 31", "ubiquitin specific protease 48"	USP31		12838346	Standard	XM_005246009		Approved	FLJ23277, FLJ11328, FLJ20103, FLJ23054, MGC14879	uc001bfb.3	Q86UV5	OTTHUMG00000007798	ENST00000308271.9:c.175G>T	chr1.hg19:g.22084236C>A	ENSP00000309262:p.Gly59Cys	104.0	0.0		78.0	5.0	NM_001032730	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Missense_Mutation	SNP	ENST00000308271.9	hg19	CCDS30623.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.906411	0.92107	.	.	ENSG00000090686	ENST00000400301;ENST00000308271;ENST00000529637;ENST00000421625	T;T;T;T	0.09538	3.0;2.97;2.97;3.24	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.36413	0.0966	M	0.73962	2.25	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;0.999;1.0;1.0;1.0;1.0	T	0.04427	-1.0952	10	0.87932	D	0	.	18.8507	0.92227	0.0:1.0:0.0:0.0	.	59;59;59;59;59;59	B7ZKS7;B7ZKS3;Q86UV5-7;Q86UV5-3;Q86UV5-2;Q86UV5	.;.;.;.;.;UBP48_HUMAN	C	59	ENSP00000383157:G59C;ENSP00000309262:G59C;ENSP00000431949:G59C;ENSP00000406256:G59C	ENSP00000309262:G59C	G	-	1	0	USP48	21956823	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.343000	0.79319	2.689000	0.91719	0.655000	0.94253	GGT	.	.		0.333	USP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021372.1	NM_032236		A	22084236	C	A	22084236	3	1	255	1	0	0	0	0	1	0	0	0	17094	594	21	3	3044	3	USP48	1	22084236	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	189506	22084236	227166385	9	35354										
HSPG2	3339	hgsc.bcm.edu	37	chr1	22180694	22180694	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctggctcctcacctggggtgTagctggggccagaatgggtg	17	10	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:22180694T>C	ENST00000374695.3	-	50	6510	c.6431A>G	c.(6430-6432)tAc>tGc	p.Y2144C	HSPG2_ENST00000430507.1_Intron	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2144	Ig-like C2-type 6.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	ACCTGGGGTGTAGCTGGGGCC	0.622																																					p.Y2144C		Atlas-SNP	.											.	HSPG2	311	.	0			c.A6431G						.						12	14	14					1																	22180694		2196	4293	6489	SO:0001583	missense	3339	exon50			GGGGTGTAGCTGG	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"Proteoglycans / Extracellular Matrix : Other", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5273	protein-coding gene	gene with protein product	"perlecan proteoglycan"	142461	"Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.6431A>G	chr1.hg19:g.22180694T>C	ENSP00000363827:p.Tyr2144Cys	109.0	0.0		58.0	4.0	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	hg19	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	T	12.66	2.005774	0.35415	.	.	ENSG00000142798	ENST00000374695	T	0.76186	-1.0	5.34	1.34	0.21922	Immunoglobulin-like (1);	1.023810	0.07853	N	0.964982	T	0.74222	0.3688	M	0.68952	2.095	0.09310	N	1	P;P	0.47106	0.86;0.89	P;B	0.44359	0.447;0.41	T	0.60954	-0.7160	10	0.40728	T	0.16	.	10.314	0.43725	0.0:0.0:0.5136:0.4864	.	84;2144	Q59EG0;P98160	.;PGBM_HUMAN	C	2144	ENSP00000363827:Y2144C	ENSP00000363827:Y2144C	Y	-	2	0	HSPG2	22053281	0.000000	0.05858	0.028000	0.17463	0.294000	0.27393	-0.282000	0.08445	0.302000	0.22762	-0.313000	0.08912	TAC	.	.		0.622	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		C	22180694	T	C	22180694	3	2	255	1	0	0	0	0	1	0	0	0	7439	1638	57	2	6936	2	HSPG2	1	22180694	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	96458	22180694	227069927	10	35355										
CDC42	998	hgsc.bcm.edu	37	chr1	22417973	22417973	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	attggctgccctggagcctcCagaaccgaagaagagccgca	12	13	0	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:22417973C>T	ENST00000344548.3	+	7	790	c.539C>T	c.(538-540)cCa>cTa	p.P180L	CDC42_ENST00000400259.1_Missense_Mutation_p.P180L|CDC42_ENST00000421089.2_Missense_Mutation_p.P222L	NM_001039802.1	NP_001034891.1	P60953	CDC42_HUMAN	cell division cycle 42	180					actin cytoskeleton organization (GO:0030036)|actin filament branching (GO:0090135)|actin filament bundle assembly (GO:0051017)|adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|canonical Wnt signaling pathway (GO:0060070)|cardiac conduction system development (GO:0003161)|cellular protein localization (GO:0034613)|dendritic cell migration (GO:0036336)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell-cell adhesion (GO:0090136)|epithelial-mesenchymal cell signaling (GO:0060684)|establishment of Golgi localization (GO:0051683)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|establishment or maintenance of cell polarity (GO:0007163)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|filopodium assembly (GO:0046847)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|heart contraction (GO:0060047)|innate immune response (GO:0045087)|keratinization (GO:0031424)|keratinocyte development (GO:0003334)|macrophage differentiation (GO:0030225)|multicellular organism growth (GO:0035264)|muscle cell differentiation (GO:0042692)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of gene expression (GO:0010629)|negative regulation of protein complex assembly (GO:0031333)|neuron fate determination (GO:0048664)|nuclear migration (GO:0007097)|nucleus localization (GO:0051647)|organelle transport along microtubule (GO:0072384)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of gene expression (GO:0010628)|positive regulation of hair follicle cell proliferation (GO:0071338)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of JNK cascade (GO:0046330)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of synapse structural plasticity (GO:0051835)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of filopodium assembly (GO:0051489)|regulation of mitosis (GO:0007088)|regulation of protein catabolic process (GO:0042176)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein kinase activity (GO:0045859)|regulation of protein stability (GO:0031647)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|sprouting angiogenesis (GO:0002040)|submandibular salivary gland formation (GO:0060661)|substantia nigra development (GO:0021762)|T cell costimulation (GO:0031295)	apical part of cell (GO:0045177)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|leading edge membrane (GO:0031256)|membrane (GO:0016020)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|spindle midzone (GO:0051233)	apolipoprotein A-I receptor binding (GO:0034191)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|protein kinase binding (GO:0019901)|thioesterase binding (GO:0031996)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(4)	12		Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;6.55e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)|Prostate(1639;0.0792)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0452)|OV - Ovarian serous cystadenocarcinoma(117;7.32e-26)|Colorectal(126;1.35e-07)|COAD - Colon adenocarcinoma(152;7.73e-06)|GBM - Glioblastoma multiforme(114;8.62e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000649)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00767)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.207)		CTGGAGCCTCCAGAACCGAAG	0.453																																					p.P180L		Atlas-SNP	.											.	CDC42	26	.	0			c.C539T						.						55	60	59					1																	22417973		2203	4300	6503	SO:0001583	missense	998	exon7			AGCCTCCAGAACC	BC018266	CCDS221.1, CCDS222.1	1p36.1	2013-01-17	2013-01-17		ENSG00000070831	ENSG00000070831			1736	protein-coding gene	gene with protein product	"GTP binding protein, 25kDa"	116952	"cell division cycle 42 (GTP-binding protein, 25kD)", "cell division cycle 42 (GTP binding protein, 25kDa)"			2124704, 2122236	Standard	NM_001039802		Approved	G25K, CDC42Hs	uc001bfr.3	P60953	OTTHUMG00000002753	ENST00000344548.3:c.539C>T	chr1.hg19:g.22417973C>T	ENSP00000341072:p.Pro180Leu	167.0	0.0		77.0	4.0	NM_001039802	P21181|P25763|Q7L8R5|Q9UDI2	Missense_Mutation	SNP	ENST00000344548.3	hg19	CCDS221.1	.	.	.	.	.	.	.	.	.	.	c	15.69	2.908707	0.52439	.	.	ENSG00000070831	ENST00000400259;ENST00000344548;ENST00000421089	T;T;T	0.67171	-0.25;-0.25;0.11	5.22	5.22	0.72569	.	0.102632	0.64402	D	0.000002	T	0.67702	0.2921	M	0.74647	2.275	0.80722	D	1	B;B;B;B	0.28178	0.202;0.009;0.202;0.003	B;B;B;B	0.21151	0.025;0.033;0.025;0.005	T	0.69774	-0.5054	10	0.66056	D	0.02	.	17.3462	0.87310	0.0:1.0:0.0:0.0	.	222;225;222;180	E7ETU3;B4E1U9;B4DMH5;P60953	.;.;.;CDC42_HUMAN	L	180;180;222	ENSP00000383118:P180L;ENSP00000341072:P180L;ENSP00000398592:P222L	ENSP00000341072:P180L	P	+	2	0	CDC42	22290560	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.426000	0.80270	2.443000	0.82685	0.455000	0.32223	CCA	.	.		0.453	CDC42-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000007787.1	NM_001791		T	22417973	C	T	22417973	3	4	255	1	0	0	0	0	1	0	0	0	3073	594	21	3	651	3	CDC42	1	22417973	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	237279	22417973	226832648	11	35356										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27106505	27106506	+	Frame_Shift_Ins	INS	-	-	T													0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aaggaggaggaacaggaccaINSaggggtgagctgcaacaaag							TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:27106505_27106506insT	ENST00000324856.7	+	20	6487_6488	c.6116_6117insT	c.(6115-6120)caagggfs	p.QG2039fs	ARID1A_ENST00000457599.2_Frame_Shift_Ins_p.QG1822fs|ARID1A_ENST00000374152.2_Frame_Shift_Ins_p.QG1656fs|ARID1A_ENST00000540690.1_Frame_Shift_Ins_p.QG367fs	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	2039					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		GAACAGGACCAAGGGGTGAGCT	0.569			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.Q2039fs		Atlas-Indel,Pindel	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.6116_6117insT						.																																			SO:0001589	frameshift_variant	8289	exon20			.	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	Exception_encountered	chr1.hg19:g.27106505_27106506insT	ENSP00000320485:p.Gln2039fs	276.0	0.0		171.0	126.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Ins	INS	ENST00000324856.7	hg19	CCDS285.1																																																																																			.	.		0.569	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		T	27106506	-	T	27106505	7	5	255	1	0	1	1	0	0	0	0	0	913	130	5	0	6194	0	ARID1A	1	27106505	Frame_Shift_Ins	INS	-	TCGA-EP-A2KB-01A-11D-A183-10	4688532	27106505	222144116	12	35357										
SYTL1	84958	hgsc.bcm.edu	37	chr1	27677307	27677307	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctccgtcccgcaggccgagcTtcagggccgcgtgctgagcc	14	17	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:27677307T>C	ENST00000543823.1	+	10	1490	c.1028T>C	c.(1027-1029)cTt>cCt	p.L343P	SYTL1_ENST00000318074.5_Missense_Mutation_p.L331P|SYTL1_ENST00000490170.1_3'UTR			Q8IYJ3	SYTL1_HUMAN	synaptotagmin-like 1	343	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)	extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|melanosome (GO:0042470)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)			NS(1)|large_intestine(4)|lung(5)|ovary(1)|urinary_tract(1)	12		Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.0115)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0908)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.5e-28)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.0013)|KIRC - Kidney renal clear cell carcinoma(1967;0.00158)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		CAGGCCGAGCTTCAGGGCCGC	0.637																																					p.L343P		Atlas-SNP	.											.	SYTL1	57	.	0			c.T1028C						.						57	53	54					1																	27677307		2203	4300	6503	SO:0001583	missense	84958	exon11			CCGAGCTTCAGGG	AK027902	CCDS298.1, CCDS53286.1	1p35.3	2008-02-05			ENSG00000142765	ENSG00000142765			15584	protein-coding gene	gene with protein product		608042				12137562	Standard	NM_032872		Approved	SLP1, JFC1, FLJ14996, exophilin-7	uc001bnw.2	Q8IYJ3	OTTHUMG00000005770	ENST00000543823.1:c.1028T>C	chr1.hg19:g.27677307T>C	ENSP00000440704:p.Leu343Pro	137.0	0.0		100.0	4.0	NM_001193308	Q5SSC9|Q96BB6|Q96GU6|Q96S89|Q96SI0	Missense_Mutation	SNP	ENST00000543823.1	hg19	CCDS53286.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.48|16.48	3.136012|3.136012	0.56936|0.56936	.|.	.|.	ENSG00000142765|ENSG00000142765	ENST00000496001|ENST00000318074;ENST00000543823;ENST00000485269	.|T;T	.|0.11930	.|2.73;2.73	4.49|4.49	4.49|4.49	0.54785|0.54785	.|C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	.|0.000000	.|0.64402	.|D	.|0.000001	T|T	0.46776|0.46776	0.1410|0.1410	M|M	0.93241|0.93241	3.395|3.395	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|1.0;1.0	T|T	0.60611|0.60611	-0.7229|-0.7229	5|10	.|0.87932	.|D	.|0	-22.0434|-22.0434	12.9621|12.9621	0.58464|0.58464	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|343;331	.|Q8IYJ3;Q8IYJ3-2	.|SYTL1_HUMAN;.	L|P	191|331;343;96	.|ENSP00000316464:L331P;ENSP00000440704:L343P	.|ENSP00000316464:L331P	F|L	+|+	1|2	0|0	SYTL1|SYTL1	27549894|27549894	1.000000|1.000000	0.71417|0.71417	0.901000|0.901000	0.35422|0.35422	0.216000|0.216000	0.24613|0.24613	4.702000|4.702000	0.61817|0.61817	1.894000|1.894000	0.54839|0.54839	0.374000|0.374000	0.22700|0.22700	TTC|CTT	.	.		0.637	SYTL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032872		C	27677307	T	C	27677307	3	2	255	1	0	0	0	0	1	0	0	0	15497	1609	56	2	1030	2	SYTL1	1	27677307	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	570802	27677307	221573314	13	35358										
MAP3K6	9064	hgsc.bcm.edu	37	chr1	27691344	27691344	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gctgaagctctcacgcacacCaaggtggtagaacagggagg	14	10	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:27691344C>T	ENST00000493901.1	-	3	639	c.400G>A	c.(400-402)Ggt>Agt	p.G134S	MAP3K6_ENST00000374040.3_Missense_Mutation_p.G134S|MAP3K6_ENST00000357582.2_Missense_Mutation_p.G134S	NM_004672.3	NP_004663.3	O95382	M3K6_HUMAN	mitogen-activated protein kinase kinase kinase 6	134					activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)			breast(4)|central_nervous_system(2)|lung(3)|ovary(1)	10		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.69e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00132)|KIRC - Kidney renal clear cell carcinoma(1967;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		TCACGCACACCAAGGTGGTAG	0.642																																					p.G134S		Atlas-SNP	.											.	MAP3K6	134	.	0			c.G400A						.						79	70	73					1																	27691344		2203	4300	6503	SO:0001583	missense	9064	exon2			GCACACCAAGGTG	AF100318	CCDS299.1, CCDS72738.1	1p36.11	2011-06-09			ENSG00000142733	ENSG00000142733		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6858	protein-coding gene	gene with protein product	"apoptosis signal regulating kinase 2"	604468				9875215	Standard	XM_005246029		Approved	MAPKKK6, ASK2, MEKK6	uc001bny.1	O95382	OTTHUMG00000004631	ENST00000493901.1:c.400G>A	chr1.hg19:g.27691344C>T	ENSP00000419591:p.Gly134Ser	165.0	0.0		123.0	5.0	NM_004672	A2ACE8|A2VDG4|A2VDG5|Q59HF4|Q5SSD4|Q75PK3|Q96B75	Missense_Mutation	SNP	ENST00000493901.1	hg19	CCDS299.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.349369	0.82132	.	.	ENSG00000142733	ENST00000374040;ENST00000493901;ENST00000357582	T;T;T	0.22539	1.95;1.95;1.95	5.4	4.48	0.54585	.	.	.	.	.	T	0.30634	0.0771	M	0.75085	2.285	0.58432	D	0.99999	B;P	0.34934	0.421;0.476	B;B	0.40101	0.213;0.319	T	0.14839	-1.0458	9	0.87932	D	0	.	12.1337	0.53957	0.0:0.9203:0.0:0.0797	.	134;134	O95382-3;O95382	.;M3K6_HUMAN	S	134	ENSP00000363152:G134S;ENSP00000419591:G134S;ENSP00000350195:G134S	ENSP00000350195:G134S	G	-	1	0	MAP3K6	27563931	0.996000	0.38824	0.064000	0.19789	0.923000	0.55619	5.057000	0.64294	1.515000	0.48885	0.655000	0.94253	GGT	.	.		0.642	MAP3K6-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000013469.2	NM_004672		T	27691344	C	T	27691344	3	4	255	1	0	0	0	0	1	0	0	0	9263	594	21	3	3578	3	MAP3K6	1	27691344	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	14037	27691344	221559277	14	35359										
STX12	23673	hgsc.bcm.edu	37	chr1	28128323	28128323	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gcaagagctggatctcgtctTtctgtaagttgattcccaaa	9	9	3	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:28128323T>C	ENST00000373943.4	+	4	548	c.423T>C	c.(421-423)ctT>ctC	p.L141L	STX12_ENST00000468761.1_3'UTR	NM_177424.2	NP_803173.1	Q86Y82	STX12_HUMAN	syntaxin 12	141					cholesterol efflux (GO:0033344)|intracellular protein transport (GO:0006886)|protein stabilization (GO:0050821)|synaptic vesicle exocytosis (GO:0016079)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|phagocytic vesicle (GO:0045335)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)			breast(1)|central_nervous_system(1)|large_intestine(3)|lung(3)	8		Colorectal(325;3.46e-05)|all_lung(284;9.43e-05)|Lung NSC(340;0.000185)|Renal(390;0.00121)|Breast(348;0.0021)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;3.96e-24)|Colorectal(126;3.46e-08)|COAD - Colon adenocarcinoma(152;1.83e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00258)|KIRC - Kidney renal clear cell carcinoma(1967;0.00302)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0649)		GATCTCGTCTTTCTGTAAGTT	0.388																																					p.L141L	Ovarian(5;5 342 2097 9488 34083)	Atlas-SNP	.											.	STX12	26	.	0			c.T423C						.						86	82	83					1																	28128323		2203	4300	6503	SO:0001819	synonymous_variant	23673	exon4			TCGTCTTTCTGTA	BC046999	CCDS310.1	1p35.3	2008-05-14			ENSG00000117758	ENSG00000117758			11430	protein-coding gene	gene with protein product		606892				9507000	Standard	NM_177424		Approved	STX13, STX14	uc001bou.4	Q86Y82	OTTHUMG00000003730	ENST00000373943.4:c.423T>C	chr1.hg19:g.28128323T>C		135.0	0.0		99.0	4.0	NM_177424	B1AJQ7|O95564	Silent	SNP	ENST00000373943.4	hg19	CCDS310.1																																																																																			.	.		0.388	STX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010519.1	NM_177424		C	28128323	T	C	28128323	2	2	255	1	0	0	0	0	0	0	0	1	15353	1828	64	2		2	STX12	1	28128323	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	436979	28128323	221122298	15	35360										
DNAJC8	22826	hgsc.bcm.edu	37	chr1	28536549	28536549	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctcttcttttgctcctgatcCagtagcaacttgtaagcttt	6	11	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:28536549C>T	ENST00000263697.4	-	5	359	c.333G>A	c.(331-333)ctG>ctA	p.L111L	DNAJC8_ENST00000489277.1_5'UTR	NM_014280.2	NP_055095.2	O75937	DNJC8_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 8	111	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	nucleoplasm (GO:0005654)				kidney(1)|large_intestine(3)|lung(2)	6		Colorectal(325;3.46e-05)|Lung NSC(340;4.08e-05)|all_lung(284;4.29e-05)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.0105)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		OV - Ovarian serous cystadenocarcinoma(117;2.81e-22)|Colorectal(126;2.99e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00275)|BRCA - Breast invasive adenocarcinoma(304;0.0059)|STAD - Stomach adenocarcinoma(196;0.00671)|READ - Rectum adenocarcinoma(331;0.0649)		GCTCCTGATCCAGTAGCAACT	0.413																																					p.L111L		Atlas-SNP	.											.	DNAJC8	13	.	0			c.G333A						.						108	93	98					1																	28536549		1854	4099	5953	SO:0001819	synonymous_variant	22826	exon5			CTGATCCAGTAGC	AF083190	CCDS41292.1	1p35	2011-09-02			ENSG00000126698	ENSG00000126698		"Heat shock proteins / DNAJ (HSP40)"	15470	protein-coding gene	gene with protein product						11147971	Standard	NM_014280		Approved	SPF31	uc001bpn.3	O75937	OTTHUMG00000003538	ENST00000263697.4:c.333G>A	chr1.hg19:g.28536549C>T		132.0	0.0		74.0	4.0	NM_014280	B4DUU4|D3DPM0|Q6IBA4|Q8N4Z5|Q9P051|Q9P067	Silent	SNP	ENST00000263697.4	hg19	CCDS41292.1																																																																																			.	.		0.413	DNAJC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009860.1	NM_014280		T	28536549	C	T	28536549	2	4	255	1	0	0	0	0	0	0	0	1	4657	581	21	3		3	DNAJC8	1	28536549	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	408226	28536549	220714072	16	35361										
HCRTR1	3061	hgsc.bcm.edu	37	chr1	32087137	32087137	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttgtcacctacctggccccaCtgggcctcatggccatggcc	10	17	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:32087137C>T	ENST00000373706.5	+	4	835	c.682C>T	c.(682-684)Ctg>Ttg	p.L228L	HCRTR1_ENST00000403528.2_Silent_p.L228L|HCRTR1_ENST00000468521.1_3'UTR|HCRTR1_ENST00000373705.1_Silent_p.L228L			O43613	OX1R_HUMAN	hypocretin (orexin) receptor 1	228					feeding behavior (GO:0007631)|neuropeptide signaling pathway (GO:0007218)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|orexin receptor activity (GO:0016499)|peptide hormone binding (GO:0017046)			breast(2)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)	7		Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.053)		CCTGGCCCCACTGGGCCTCAT	0.582																																					p.L228L		Atlas-SNP	.											.	HCRTR1	20	.	0			c.C682T						.						166	164	165					1																	32087137		2203	4300	6503	SO:0001819	synonymous_variant	3061	exon6			GCCCCACTGGGCC	AF041243	CCDS344.1	1p33	2012-08-08			ENSG00000121764	ENSG00000121764		"GPCR / Class A : Hypocretin (orexin) receptors"	4848	protein-coding gene	gene with protein product		602392				9491897	Standard	NM_001525		Approved	OX1R	uc009vtx.2	O43613	OTTHUMG00000003876	ENST00000373706.5:c.682C>T	chr1.hg19:g.32087137C>T		115.0	0.0		75.0	4.0	NM_001525	A8K3A6|Q9HBV6	Silent	SNP	ENST00000373706.5	hg19	CCDS344.1																																																																																			.	.		0.582	HCRTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011042.1	NM_001525		T	32087137	C	T	32087137	2	4	255	1	0	0	0	0	0	0	0	1	7010	564	20	3		3	HCRTR1	1	32087137	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	3550588	32087137	217163484	17	35362										
HMGB4	127540	hgsc.bcm.edu	37	chr1	34330051	34330051	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gcaagaggaagaaacggagaAagcgggatccccaggaaccc	14	10	0	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:34330051A>G	ENST00000522796.1	+	4	2164	c.259A>G	c.(259-261)Aag>Gag	p.K87E	HMGB4_ENST00000519684.1_Missense_Mutation_p.K87E|HMGB4_ENST00000425537.1_3'UTR|CSMD2_ENST00000373381.4_Intron			Q8WW32	HMGB4_HUMAN	high mobility group box 4	87						chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(1)|large_intestine(1)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	12		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				GAAACGGAGAAAGCGGGATCC	0.507																																					p.K87E		Atlas-SNP	.											.	HMGB4	27	.	0			c.A259G						.						131	148	142					1																	34330051		2203	4300	6503	SO:0001583	missense	127540	exon2			CGGAGAAAGCGGG		CCDS30668.1	1p35.1	2011-07-01	2011-04-05		ENSG00000176256	ENSG00000176256		"High-mobility group / Canonical"	24954	protein-coding gene	gene with protein product			"high-mobility group box 4"				Standard	NR_033264		Approved	FLJ40388	uc001bxp.3	Q8WW32	OTTHUMG00000013143	ENST00000522796.1:c.259A>G	chr1.hg19:g.34330051A>G	ENSP00000430919:p.Lys87Glu	178.0	0.0		94.0	4.0	NM_145205	B2R4X7|Q0QWA4	Missense_Mutation	SNP	ENST00000522796.1	hg19	CCDS30668.1	.	.	.	.	.	.	.	.	.	.	A	19.25	3.791465	0.70452	.	.	ENSG00000176256	ENST00000519684;ENST00000522796	D;D	0.94280	-3.39;-3.39	5.58	5.58	0.84498	.	0.059922	0.64402	D	0.000004	D	0.90998	0.7169	M	0.63208	1.945	0.42581	D	0.993215	P	0.49090	0.919	B	0.39465	0.3	D	0.91774	0.5430	10	0.66056	D	0.02	.	12.0666	0.53592	1.0:0.0:0.0:0.0	.	87	B2R4X7	.	E	87	ENSP00000429214:K87E;ENSP00000430919:K87E	ENSP00000429214:K87E	K	+	1	0	HMGB4	34102638	1.000000	0.71417	0.969000	0.41365	0.925000	0.55904	3.935000	0.56560	2.343000	0.79666	0.496000	0.49642	AAG	.	.		0.507	HMGB4-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375773.1	NM_145205		G	34330051	A	G	34330051	3	3	255	1	0	0	0	0	1	0	0	0	7237	15	1	2	261	2	HMGB4	1	34330051	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	2242914	34330051	214920570	18	35363										
KIAA0319L	79932	hgsc.bcm.edu	37	chr1	35928256	35928256	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	actgtagaagtggttggcaaAgagatctcctggaactgagg	14	6	1	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:35928256A>G	ENST00000325722.3	-	8	1494	c.1260T>C	c.(1258-1260)tcT>tcC	p.S420S	KIAA0319L_ENST00000485551.1_5'UTR	NM_024874.4	NP_079150.3	Q8IZA0	K319L_HUMAN	KIAA0319-like	420	PKD 2. {ECO:0000255|PROSITE- ProRule:PRU00151}.					cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(12)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	34		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TGGTTGGCAAAGAGATCTCCT	0.443																																					p.S420S		Atlas-SNP	.											.	KIAA0319L	156	.	0			c.T1260C						.						89	82	85					1																	35928256		2203	4300	6503	SO:0001819	synonymous_variant	79932	exon8			TGGCAAAGAGATC	AY163234	CCDS390.1	1p34.3	2008-10-24			ENSG00000142687	ENSG00000142687			30071	protein-coding gene	gene with protein product		613535				11347906	Standard	NM_024874		Approved	KIAA1837	uc001byx.3	Q8IZA0	OTTHUMG00000004370	ENST00000325722.3:c.1260T>C	chr1.hg19:g.35928256A>G		96.0	0.0		56.0	4.0	NM_024874	B1AN13|D3DPR8|O95010|Q6PJJ7|Q7L1C9|Q8N2B3|Q8NDA0|Q8WY39|Q8WYZ5|Q96IC3|Q96JJ0|Q9BUW6|Q9H7V0	Silent	SNP	ENST00000325722.3	hg19	CCDS390.1	.	.	.	.	.	.	.	.	.	.	A	10.43	1.348828	0.24426	.	.	ENSG00000142687	ENST00000431916	.	.	.	5.54	4.4	0.53042	.	.	.	.	.	T	0.44350	0.1289	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42172	-0.9467	4	.	.	.	-6.7581	1.2872	0.02053	0.5356:0.1665:0.1489:0.149	.	.	.	.	L	250	.	.	F	-	1	0	KIAA0319L	35700843	0.999000	0.42202	1.000000	0.80357	0.994000	0.84299	0.630000	0.24553	0.923000	0.37045	0.533000	0.62120	TTT	.	.		0.443	KIAA0319L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012684.2	NM_024874		G	35928256	A	G	35928256	2	3	255	1	0	0	0	0	0	0	0	1	8178	59	3	2		2	KIAA0319L	1	35928256	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	1598205	35928256	213322365	19	35364										
EIF2C4	192670	hgsc.bcm.edu	37	chr1	36298149	36298149	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cttgttttgcacctcagaaaCaatgtagggaagatttacta	8	7	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:36298149C>T	ENST00000373210.3	+	11	1602	c.1357C>T	c.(1357-1359)Caa>Taa	p.Q453*		NM_017629.3	NP_060099.2	Q9HCK5	AGO4_HUMAN	argonaute RISC catalytic component 4	453					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA catabolic process (GO:0006402)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|RISC complex (GO:0016442)	miRNA binding (GO:0035198)										ACCTCAGAAACAATGTAGGGA	0.398																																					p.Q453X		Atlas-SNP	.											EIF2C4,bladder,carcinoma,0,1	.	.	.	0			c.C1357T						.						122	126	124					1																	36298149		2203	4300	6503	SO:0001587	stop_gained	192670	exon11			CAGAAACAATGTA	AB046787	CCDS397.1	1p34	2013-02-15	2013-02-15	2013-02-15	ENSG00000134698	ENSG00000134698		"Argonaute/PIWI family"	18424	protein-coding gene	gene with protein product	"argonaute 4"	607356	"eukaryotic translation initiation factor 2C, 4"	EIF2C4		12906857	Standard	NM_017629		Approved	hAGO4, KIAA1567, FLJ20033	uc001bzj.2	Q9HCK5	OTTHUMG00000004243	ENST00000373210.3:c.1357C>T	chr1.hg19:g.36298149C>T	ENSP00000362306:p.Gln453*	119.0	0.0		82.0	4.0	NM_017629	A7MD27	Nonsense_Mutation	SNP	ENST00000373210.3	hg19	CCDS397.1	.	.	.	.	.	.	.	.	.	.	C	39	7.414465	0.98269	.	.	ENSG00000134698	ENST00000373210	.	.	.	5.36	5.36	0.76844	.	0.164660	0.56097	D	0.000035	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	-2.5418	19.0955	0.93249	0.0:1.0:0.0:0.0	.	.	.	.	X	453	.	ENSP00000362306:Q453X	Q	+	1	0	EIF2C4	36070736	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.511000	0.84671	0.655000	0.94253	CAA	.	.		0.398	AGO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012213.3	NM_017629		T	36298149	C	T	36298149	4	4	255	1	0	0	0	0	0	1	0	0	5010	479	17	3	1399	3	EIF2C4	1	36298149	Nonsense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	369893	36298149	212952472	20	35365										
EIF2C3	192669	hgsc.bcm.edu	37	chr1	36439085	36439085	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	atcagtctgttcggcctgccAtgtggaaaatgatgcttaat	10	8	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:36439085A>G	ENST00000373191.4	+	5	980	c.631A>G	c.(631-633)Atg>Gtg	p.M211V	AGO3_ENST00000246314.6_Intron|AGO3_ENST00000324350.5_Missense_Mutation_p.M211V|AGO3_ENST00000397828.2_Missense_Mutation_p.M211V	NM_024852.3	NP_079128.2	Q9H9G7	AGO3_HUMAN	argonaute RISC catalytic component 3	211					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA catabolic process (GO:0006402)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of stem cell proliferation (GO:0072091)	cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|RISC complex (GO:0016442)	miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)										TCGGCCTGCCATGTGGAAAAT	0.448																																					p.M211V		Atlas-SNP	.											.	.	.	.	0			c.A631G						.						202	200	201					1																	36439085		2203	4300	6503	SO:0001583	missense	192669	exon5			CCTGCCATGTGGA	AB046787	CCDS399.1, CCDS400.1	1p34	2013-06-03	2013-02-15	2013-02-15	ENSG00000126070	ENSG00000126070		"Argonaute/PIWI family"	18421	protein-coding gene	gene with protein product	"argonaute 3"	607355	"eukaryotic translation initiation factor 2C, 3"	EIF2C3		12906857	Standard	NM_024852		Approved	hAGO3, FLJ12765	uc001bzp.3	Q9H9G7	OTTHUMG00000184172	ENST00000373191.4:c.631A>G	chr1.hg19:g.36439085A>G	ENSP00000362287:p.Met211Val	236.0	0.0		139.0	6.0	NM_024852	B1ALI0|Q5TA55|Q9H1U6	Missense_Mutation	SNP	ENST00000373191.4	hg19	CCDS399.1	.	.	.	.	.	.	.	.	.	.	A	16.69	3.192029	0.58017	.	.	ENSG00000126070	ENST00000324350;ENST00000373191;ENST00000397828	T;T;T	0.09073	3.02;3.02;3.02	5.62	5.62	0.85841	Domain of unknown function DUF1785 (1);	0.000000	0.85682	D	0.000000	T	0.07954	0.0199	N	0.12502	0.225	0.80722	D	1	B;B	0.23249	0.082;0.005	B;B	0.33121	0.158;0.008	T	0.36089	-0.9762	10	0.54805	T	0.06	-32.6353	15.8286	0.78733	1.0:0.0:0.0:0.0	.	211;211	Q9H9G7;Q5TA56	AGO3_HUMAN;.	V	211	ENSP00000317425:M211V;ENSP00000362287:M211V;ENSP00000380928:M211V	ENSP00000317425:M211V	M	+	1	0	EIF2C3	36211672	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.024000	0.70857	2.141000	0.66446	0.460000	0.39030	ATG	.	.		0.448	AGO3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019831.4	NM_024852		G	36439085	A	G	36439085	3	3	255	1	0	0	0	0	1	0	0	0	5009	217	8	2	649	2	EIF2C3	1	36439085	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	140936	36439085	212811536	21	35366										
MFSD2A	84879	hgsc.bcm.edu	37	chr1	40430920	40430920	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccctggccgtcattgcctacTtcctcatctggttcgtgccc	8	17	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:40430920T>C	ENST00000372809.5	+	4	573	c.430T>C	c.(430-432)Ttc>Ctc	p.F144L	MFSD2A_ENST00000480630.1_3'UTR|MFSD2A_ENST00000420632.2_5'UTR|MFSD2A_ENST00000372811.5_Missense_Mutation_p.F131L	NM_001136493.1	NP_001129965.1	Q8NA29	NLS1_HUMAN	major facilitator superfamily domain containing 2A	144					establishment of blood-brain barrier (GO:0060856)|fatty acid transport (GO:0015908)|lipid transport across blood brain barrier (GO:1990379)|transcytosis (GO:0045056)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phospholipid transporter activity (GO:0005548)|symporter activity (GO:0015293)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	24						CATTGCCTACTTCCTCATCTG	0.582																																					p.F144L		Atlas-SNP	.											.	MFSD2A	53	.	0			c.T430C						.						165	139	148					1																	40430920		2203	4300	6503	SO:0001583	missense	84879	exon4			GCCTACTTCCTCA	AK093223	CCDS446.1, CCDS44118.1, CCDS72762.1	1p34.2	2009-09-08	2009-09-08	2009-09-08	ENSG00000168389	ENSG00000168389			25897	protein-coding gene	gene with protein product		614397	"major facilitator superfamily domain containing 2"	MFSD2		18694395	Standard	XM_005271285		Approved	FLJ14490	uc001cev.3	Q8NA29	OTTHUMG00000009293	ENST00000372809.5:c.430T>C	chr1.hg19:g.40430920T>C	ENSP00000361895:p.Phe144Leu	116.0	0.0		95.0	4.0	NM_001136493	A8K675|Q6UWU5|Q96F59|Q9BRC8	Missense_Mutation	SNP	ENST00000372809.5	hg19	CCDS44118.1	.	.	.	.	.	.	.	.	.	.	T	15.32	2.799871	0.50208	.	.	ENSG00000168389	ENST00000372811;ENST00000434861;ENST00000372809	T;D;T	0.86562	-1.17;-2.14;-1.17	5.51	5.51	0.81932	Major facilitator superfamily domain, general substrate transporter (1);	0.089074	0.85682	D	0.000000	D	0.85669	0.5750	M	0.75615	2.305	0.80722	D	1	B;B;B	0.16396	0.017;0.013;0.002	B;B;B	0.24974	0.057;0.05;0.017	T	0.81068	-0.1100	10	0.31617	T	0.26	-18.0473	9.3296	0.38014	0.0:0.0799:0.0:0.9201	.	94;144;131	B4DNN7;Q8NA29;Q8NA29-2	.;MFS2A_HUMAN;.	L	131;129;144	ENSP00000361898:F131L;ENSP00000407606:F129L;ENSP00000361895:F144L	ENSP00000361895:F144L	F	+	1	0	MFSD2A	40203507	1.000000	0.71417	1.000000	0.80357	0.782000	0.44232	2.578000	0.46051	2.085000	0.62840	0.459000	0.35465	TTC	.	.		0.582	MFSD2A-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025756.1	NM_032793		C	40430920	T	C	40430920	3	2	255	1	0	0	0	0	1	0	0	0	9539	1609	56	2	444	2	MFSD2A	1	40430920	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	3991835	40430920	208819701	22	35367										
ZNF691	51058	hgsc.bcm.edu	37	chr1	43317025	43317025	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aaccgcatccggcacgagcgGatccacctggaagagaaaca	11	13	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:43317025G>T	ENST00000372506.1	+	4	736	c.396G>T	c.(394-396)cgG>cgT	p.R132R	ZNF691_ENST00000397044.3_Silent_p.R163R|ZNF691_ENST00000372502.1_Silent_p.R154R|ZNF691_ENST00000372508.3_Silent_p.R132R|ZNF691_ENST00000372504.1_Silent_p.R154R|ZNF691_ENST00000372507.1_Silent_p.R132R	NM_001242739.1	NP_001229668.1	Q5VV52	ZN691_HUMAN	zinc finger protein 691	163						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(2)|lung(2)|ovary(2)|prostate(1)	7	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				GGCACGAGCGGATCCACCTGG	0.562																																					p.R163R		Atlas-SNP	.											.	ZNF691	30	.	0			c.G489T						.						48	47	47					1																	43317025		2203	4300	6503	SO:0001819	synonymous_variant	51058	exon4			CGAGCGGATCCAC		CCDS476.1, CCDS55595.1	1p34.2	2013-01-08			ENSG00000164011	ENSG00000164011		"Zinc fingers, C2H2-type"	28028	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_001242739		Approved	Zfp691	uc021omh.1	Q5VV52	OTTHUMG00000007623	ENST00000372506.1:c.396G>T	chr1.hg19:g.43317025G>T		74.0	0.0		48.0	4.0	NM_001242739	A8MXP6|B4DJR7|O95878|Q9NWE8	Silent	SNP	ENST00000372506.1	hg19	CCDS476.1																																																																																			.	.		0.562	ZNF691-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020192.1	NM_015911		T	43317025	G	T	43317025	2	4	255	1	0	0	0	0	0	0	0	1	18111	1161	41	3		3	ZNF691	1	43317025	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	2886105	43317025	205933596	23	35368										
KIAA0467	23334	hgsc.bcm.edu	37	chr1	43913358	43913358	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aacgagtatgccctggtgtcGgcatggcacaggtaaggctg	15	9	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:43913358G>T	ENST00000562955.1	+	66	9258	c.9258G>T	c.(9256-9258)tcG>tcT	p.S3086S	SZT2_ENST00000372442.1_Silent_p.S2244S|SZT2-AS1_ENST00000396885.2_RNA	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	3143					central nervous system development (GO:0007417)|corpus callosum morphogenesis (GO:0021540)|embryo development (GO:0009790)|pigmentation (GO:0043473)|post-embryonic development (GO:0009791)|regulation of superoxide dismutase activity (GO:1901668)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)				NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						CCCTGGTGTCGGCATGGCACA	0.572																																					p.S3086S		Atlas-SNP	.											SZT2_ENST00000562955,colon,carcinoma,0,3	SZT2	383	.	0			c.G9258T						.						45	41	42					1																	43913358		2203	4300	6503	SO:0001819	synonymous_variant	23334	exon66			GGTGTCGGCATGG	AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198			29040	protein-coding gene	gene with protein product	"seizure threshold 2 homolog A (mouse)", "seizure threshold 2 homolog B (mouse)"	615463	"chromosome 1 open reading frame 84", "KIAA0467"	C1orf84, KIAA0467		9455484	Standard	NM_015284		Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.9258G>T	chr1.hg19:g.43913358G>T		42.0	0.0		53.0	3.0	NM_015284	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Silent	SNP	ENST00000562955.1	hg19	CCDS30694.2																																																																																			.	.		0.572	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284		T	43913358	G	T	43913358	2	4	255	1	0	0	0	0	0	0	0	1	8187	1103	39	1		1	KIAA0467	1	43913358	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	596333	43913358	205337263	24	35369										
KLF17	128209	hgsc.bcm.edu	37	chr1	44595054	44595054	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aactcagcgcccatcttgaaCatgtcttcatcttctggaag	7	12	6	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:44595054C>T	ENST00000372299.3	+	2	169	c.111C>T	c.(109-111)aaC>aaT	p.N37N	KLF17_ENST00000476802.1_3'UTR	NM_173484.3	NP_775755.3	Q5JT82	KLF17_HUMAN	Kruppel-like factor 17	37					gamete generation (GO:0007276)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|central_nervous_system(1)|large_intestine(1)|lung(6)|ovary(3)|prostate(1)|skin(2)|stomach(1)	18	Acute lymphoblastic leukemia(166;0.155)					CCATCTTGAACATGTCTTCAT	0.502																																					p.N37N		Atlas-SNP	.											.	KLF17	92	.	0			c.C111T						.						124	115	118					1																	44595054		2203	4300	6503	SO:0001819	synonymous_variant	128209	exon2			CTTGAACATGTCT	BC049844	CCDS508.1	1p34.1	2011-11-15	2006-02-17	2006-02-17	ENSG00000171872	ENSG00000171872		"Zinc fingers, C2H2-type", "Kruppel-like transcription factors"	18830	protein-coding gene	gene with protein product		609602	"zinc finger protein 393"	ZNF393		16460907	Standard	NM_173484		Approved	Zfp393, FLJ40160	uc001clp.3	Q5JT82	OTTHUMG00000009664	ENST00000372299.3:c.111C>T	chr1.hg19:g.44595054C>T		144.0	0.0		84.0	4.0	NM_173484	Q86VQ7|Q8N805	Silent	SNP	ENST00000372299.3	hg19	CCDS508.1																																																																																			.	.		0.502	KLF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026646.1	NM_173484		T	44595054	C	T	44595054	2	4	255	1	0	0	0	0	0	0	0	1	8354	477	17	3		3	KLF17	1	44595054	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	681696	44595054	204655567	25	35370										
RNF220	55182	hgsc.bcm.edu	37	chr1	45092001	45092001	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tctgcttccatcaagagggaAggagagtctccaacggcatc	11	11	3	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:45092001A>G	ENST00000355387.2	+	5	1287	c.837A>G	c.(835-837)gaA>gaG	p.E279E	RNF220_ENST00000443020.2_Silent_p.E40E|RNF220_ENST00000372247.2_Silent_p.E279E|RNF220_ENST00000361799.2_Silent_p.E279E			Q5VTB9	RN220_HUMAN	ring finger protein 220	279					protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(1)|large_intestine(3)|lung(13)|ovary(2)|skin(2)|urinary_tract(2)	29						TCAAGAGGGAAGGAGAGTCTC	0.537																																					p.E279E		Atlas-SNP	.											.	RNF220	56	.	0			c.A837G						.						115	96	102					1																	45092001		2203	4300	6503	SO:0001819	synonymous_variant	55182	exon5			GAGGGAAGGAGAG	AK056424	CCDS510.1	1p34.1	2008-06-13	2008-06-13	2008-06-13	ENSG00000187147	ENSG00000187147		"RING-type (C3HC4) zinc fingers"	25552	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 164"	C1orf164		11042152	Standard	NM_018150		Approved	FLJ10597	uc001clv.1	Q5VTB9	OTTHUMG00000007697	ENST00000355387.2:c.837A>G	chr1.hg19:g.45092001A>G		109.0	0.0		64.0	4.0	NM_018150	B3KPJ3|B4DLZ9|E9PCS1|Q4KMX2|Q9NVP6	Silent	SNP	ENST00000355387.2	hg19	CCDS510.1	.	.	.	.	.	.	.	.	.	.	A	10.25	1.298112	0.23650	.	.	ENSG00000187147	ENST00000453863	.	.	.	5.32	4.2	0.49525	.	.	.	.	.	T	0.62208	0.2409	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60042	-0.7340	4	.	.	.	.	11.2096	0.48790	0.9287:0.0:0.0713:0.0	.	.	.	.	G	2	.	.	R	+	1	2	RNF220	44864588	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.349000	0.59385	1.157000	0.42530	0.519000	0.50382	AGG	.	.		0.537	RNF220-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000020683.4	NM_018150		G	45092001	A	G	45092001	2	3	255	1	0	0	0	0	0	0	0	1	13498	69	3	2		2	RNF220	1	45092001	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	496947	45092001	204158620	26	35371										
ZSWIM5	57643	hgsc.bcm.edu	37	chr1	45525908	45525908	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aatgctggccccagctgtggGgtcaggggcacctatgaaga	15	10	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:45525908G>T	ENST00000359600.5	-	3	1169	c.964C>A	c.(964-966)Ccc>Acc	p.P322T		NM_020883.1	NP_065934.1	Q9P217	ZSWM5_HUMAN	zinc finger, SWIM-type containing 5	322						extracellular space (GO:0005615)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|liver(1)|lung(13)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Acute lymphoblastic leukemia(166;0.155)					CCAGCTGTGGGGTCAGGGGCA	0.478																																					p.P322T		Atlas-SNP	.											.	ZSWIM5	72	.	0			c.C964A						.						49	45	46					1																	45525908		1884	4114	5998	SO:0001583	missense	57643	exon3			CTGTGGGGTCAGG	AB040944	CCDS41319.1	1p34.1	2010-06-16			ENSG00000162415	ENSG00000162415		"Zinc fingers, SWIM-type"	29299	protein-coding gene	gene with protein product						10819331	Standard	NM_020883		Approved	KIAA1511	uc001cnd.2	Q9P217	OTTHUMG00000008950	ENST00000359600.5:c.964C>A	chr1.hg19:g.45525908G>T	ENSP00000352614:p.Pro322Thr	123.0	0.0		85.0	4.0	NM_020883	Q5SXQ9	Missense_Mutation	SNP	ENST00000359600.5	hg19	CCDS41319.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.673196	0.88445	.	.	ENSG00000162415	ENST00000359600	T	0.21932	1.98	4.86	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.54951	0.1890	M	0.88450	2.955	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.64635	-0.6361	10	0.87932	D	0	-15.0487	18.8801	0.92352	0.0:0.0:1.0:0.0	.	322	Q9P217	ZSWM5_HUMAN	T	322	ENSP00000352614:P322T	ENSP00000352614:P322T	P	-	1	0	ZSWIM5	45298495	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.813000	0.99286	2.615000	0.88500	0.557000	0.71058	CCC	.	.		0.478	ZSWIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024823.2	XM_046581		T	45525908	G	T	45525908	3	4	255	1	0	0	0	0	1	0	0	0	18259	1232	43	3	2641	3	ZSWIM5	1	45525908	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	433907	45525908	203724713	27	35372										
MUTYH	4595	hgsc.bcm.edu	37	chr1	45800108	45800108	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	actgttgttcttagcatgctTctgcctcccttcctggctgg	9	13	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:45800108T>C	ENST00000372098.3	-	2	245	c.112A>G	c.(112-114)Aag>Gag	p.K38E	MUTYH_ENST00000488731.2_Missense_Mutation_p.K24E|MUTYH_ENST00000529984.1_Missense_Mutation_p.K24E|MUTYH_ENST00000372100.5_Missense_Mutation_p.K24E|MUTYH_ENST00000372115.3_Missense_Mutation_p.K38E|MUTYH_ENST00000528013.2_Missense_Mutation_p.K24E|MUTYH_ENST00000456914.2_Missense_Mutation_p.K24E|MUTYH_ENST00000372104.1_Missense_Mutation_p.K24E|MUTYH_ENST00000372110.3_Missense_Mutation_p.K38E|MUTYH_ENST00000354383.6_Missense_Mutation_p.K24E|MUTYH_ENST00000528332.2_Missense_Mutation_p.K38E|MUTYH_ENST00000355498.2_Missense_Mutation_p.K24E|MUTYH_ENST00000450313.1_Missense_Mutation_p.K38E|MUTYH_ENST00000448481.1_Missense_Mutation_p.K24E|MUTYH_ENST00000531105.1_Missense_Mutation_p.K24E			Q9UIF7	MUTYH_HUMAN	mutY homolog	38					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depurination (GO:0045007)|DNA repair (GO:0006281)|mismatch repair (GO:0006298)	mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|hydrolase activity, acting on glycosyl bonds (GO:0016798)|metal ion binding (GO:0046872)|MutSalpha complex binding (GO:0032407)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.155)					TTAGCATGCTTCTGCCTCCCT	0.552			Mis			colorectal		Base excision repair (BER), DNA glycosylases	MUTYH-associated polyposis																												p.K38E		Atlas-SNP	.	yes	Rec		Adenomatous polyposis coli	1	1p34.3-1p32.1	4595	mutY homolog (E. coli)		E	.	MUTYH	38	.	0			c.A112G						.						185	137	153					1																	45800108		2203	4300	6503	SO:0001583	missense	4595	exon2	Familial Cancer Database	MAP, MYH-associated polyposis	CATGCTTCTGCCT	U63329	CCDS520.1, CCDS41320.1, CCDS41321.1, CCDS41322.1, CCDS72776.1, CCDS72777.1	1p34.1	2014-09-17	2013-09-12		ENSG00000132781	ENSG00000132781			7527	protein-coding gene	gene with protein product		604933	"mutY (E. coli) homolog", "mutY homolog (E. coli)"			7823963, 10684930	Standard	NM_012222		Approved	MYH	uc009vxp.3	Q9UIF7	OTTHUMG00000007682	ENST00000372098.3:c.112A>G	chr1.hg19:g.45800108T>C	ENSP00000361170:p.Lys38Glu	133.0	0.0		79.0	4.0	NM_012222	D3DPZ4|Q15830|Q9UBP2|Q9UBS7|Q9UIF4|Q9UIF5|Q9UIF6	Missense_Mutation	SNP	ENST00000372098.3	hg19	CCDS520.1	.	.	.	.	.	.	.	.	.	.	T	11.29	1.595861	0.28445	.	.	ENSG00000132781	ENST00000529984;ENST00000528332;ENST00000372104;ENST00000448481;ENST00000456914;ENST00000354383;ENST00000355498;ENST00000372098;ENST00000372110;ENST00000372115;ENST00000488731;ENST00000450313;ENST00000372100;ENST00000531105;ENST00000435155;ENST00000528013;ENST00000483127	T;D;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.91843	2.32;-2.92;3.2;3.24;3.2;3.21;3.2;3.22;3.19;3.18;2.32;3.2;3.24;0.52;1.93;0.89;0.81	4.28	1.88	0.25563	.	0.669254	0.14006	N	0.347799	D	0.88055	0.6334	L	0.48642	1.525	0.09310	N	1	B;B;B;B;B;B	0.28291	0.206;0.085;0.137;0.085;0.172;0.085	B;B;B;B;B;B	0.31101	0.124;0.026;0.085;0.039;0.039;0.039	T	0.79543	-0.1760	10	0.54805	T	0.06	-0.3653	8.5549	0.33476	0.0:0.0:0.4386:0.5614	.	38;38;38;38;38;24	B4DEX2;E5KP25;Q9UIF7-2;Q9UIF7;E5KP27;E5KP28	.;.;.;MUTYH_HUMAN;.;.	E	24;38;24;24;24;24;24;38;38;38;24;38;24;24;24;24;30	ENSP00000437093:K24E;ENSP00000433076:K38E;ENSP00000361176:K24E;ENSP00000409718:K24E;ENSP00000407590:K24E;ENSP00000346354:K24E;ENSP00000347685:K24E;ENSP00000361170:K38E;ENSP00000361182:K38E;ENSP00000361187:K38E;ENSP00000432330:K24E;ENSP00000408176:K38E;ENSP00000361172:K24E;ENSP00000431292:K24E;ENSP00000403655:K24E;ENSP00000433130:K24E;ENSP00000436469:K30E	ENSP00000346354:K24E	K	-	1	0	MUTYH	45572695	0.000000	0.05858	0.001000	0.08648	0.013000	0.08279	0.561000	0.23515	0.405000	0.25532	0.528000	0.53228	AAG	.	.		0.552	MUTYH-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000020529.1	NM_012222		C	45800108	T	C	45800108	3	2	255	1	0	0	0	0	1	0	0	0	10002	1792	62	2	1597	2	MUTYH	1	45800108	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	274200	45800108	203450513	28	35373										
KIAA0494	9813	hgsc.bcm.edu	37	chr1	47149060	47149060	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agaaactgtgaaaattttggCaatgctgatggctttgatgt	11	4	0	4			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:47149060C>T	ENST00000371933.3	-	10	2200	c.1224G>A	c.(1222-1224)ttG>ttA	p.L408L	EFCAB14-AS1_ENST00000418985.1_RNA|EFCAB14-AS1_ENST00000442839.1_RNA|EFCAB14_ENST00000484461.1_5'Flank|EFCAB14_ENST00000544071.1_Silent_p.L344L	NM_014774.2	NP_055589.1	O75071	EFC14_HUMAN	EF-hand calcium binding domain 14	408							calcium ion binding (GO:0005509)										AAAATTTTGGCAATGCTGATG	0.353																																					p.L408L		Atlas-SNP	.											.	.	.	.	0			c.G1224A						.						112	114	113					1																	47149060		2203	4300	6503	SO:0001819	synonymous_variant	9813	exon10			TTTTGGCAATGCT	AB007963	CCDS30706.1	1p33	2013-01-10	2012-11-29	2012-11-29	ENSG00000159658	ENSG00000159658		"EF-hand domain containing"	29051	protein-coding gene	gene with protein product			"KIAA0494"	KIAA0494		9455484	Standard	NM_014774		Approved		uc001cqk.4	O75071	OTTHUMG00000007992	ENST00000371933.3:c.1224G>A	chr1.hg19:g.47149060C>T		106.0	0.0		59.0	4.0	NM_014774	D3DQ23|Q5SXB8	Silent	SNP	ENST00000371933.3	hg19	CCDS30706.1																																																																																			.	.		0.353	EFCAB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021931.1	NM_014774		T	47149060	C	T	47149060	2	4	255	1	0	0	0	0	0	0	0	1	8188	709	25	3		3	KIAA0494	1	47149060	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1348952	47149060	202101561	29	35374										
CYP4A11	1579	hgsc.bcm.edu	37	chr1	47406949	47406949	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gagccagtgggagggagggcAcgggaactgctggagggctt	21	7	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:47406949A>G	ENST00000310638.4	-	1	188	c.157T>C	c.(157-159)Tgc>Cgc	p.C53R	CYP4A11_ENST00000371904.4_Missense_Mutation_p.C53R|CYP4A11_ENST00000457840.2_5'UTR|CYP4A11_ENST00000462347.1_Missense_Mutation_p.C53R|CYP4A11_ENST00000371905.1_Missense_Mutation_p.C53R	NM_000778.3	NP_000769.2	Q02928	CP4AB_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 11	53					arachidonic acid metabolic process (GO:0019369)|cellular lipid metabolic process (GO:0044255)|epoxygenase P450 pathway (GO:0019373)|fatty acid metabolic process (GO:0006631)|leukotriene B4 catabolic process (GO:0036101)|leukotriene metabolic process (GO:0006691)|long-chain fatty acid metabolic process (GO:0001676)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|positive regulation of icosanoid secretion (GO:0032305)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)			endometrium(2)|kidney(5)|large_intestine(6)|lung(6)|ovary(5)|prostate(3)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	36					Cisplatin(DB00515)|Clofibrate(DB00636)|Dexamethasone(DB01234)|Estrone(DB00655)|Ethanol(DB00898)|Lansoprazole(DB00448)|Pegvisomant(DB00082)|Pentamidine(DB00738)|Phenobarbital(DB01174)|Rifampicin(DB01045)|Tretinoin(DB00755)	GAGGGAGGGCACGGGAACTGC	0.617																																					p.C53R		Atlas-SNP	.											.	CYP4A11	77	.	0			c.T157C						.						67	60	63					1																	47406949		2203	4300	6503	SO:0001583	missense	1579	exon1			GAGGGCACGGGAA	L04751	CCDS543.1	1p33	2008-02-05	2003-01-14		ENSG00000187048	ENSG00000187048		"Cytochrome P450s"	2642	protein-coding gene	gene with protein product		601310	"cytochrome P450, subfamily IVA, polypeptide 11"	CYP4A2		7679927	Standard	NM_000778		Approved	CYP4AII	uc001cqp.4	Q02928	OTTHUMG00000008020	ENST00000310638.4:c.157T>C	chr1.hg19:g.47406949A>G	ENSP00000311095:p.Cys53Arg	160.0	0.0		71.0	4.0	NM_000778	Q06766|Q16865|Q16866|Q5VSP8|Q86SU6|Q8IWY5	Missense_Mutation	SNP	ENST00000310638.4	hg19	CCDS543.1	.	.	.	.	.	.	.	.	.	.	-	7.618	0.676158	0.14841	.	.	ENSG00000187048	ENST00000310638;ENST00000371904;ENST00000371905	T;T;T	0.67865	-0.29;-0.29;-0.29	4.92	-0.772	0.10998	.	0.378318	0.25200	N	0.032389	T	0.56992	0.2023	L	0.43923	1.385	0.09310	N	0.999993	B	0.34255	0.445	B	0.41412	0.356	T	0.53514	-0.8428	10	0.62326	D	0.03	.	6.1817	0.20476	0.3094:0.4541:0.0:0.2365	.	53	Q02928	CP4AB_HUMAN	R	53	ENSP00000311095:C53R;ENSP00000360971:C53R;ENSP00000360972:C53R	ENSP00000311095:C53R	C	-	1	0	CYP4A11	47179536	0.002000	0.14202	0.009000	0.14445	0.031000	0.12232	1.745000	0.38278	0.068000	0.16574	-0.331000	0.08364	TGC	.	.		0.617	CYP4A11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022022.1	NM_000778		G	47406949	A	G	47406949	3	3	255	1	0	0	0	0	1	0	0	0	4185	159	6	2	1450	2	CYP4A11	1	47406949	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	257889	47406949	201843672	30	35375										
TTC39A	22996	hgsc.bcm.edu	37	chr1	51767296	51767296	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cggcgtagaagtaggacatcTtccactggcccttgtaggtg	13	10	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:51767296T>C	ENST00000447632.2	-	12	1157	c.1109A>G	c.(1108-1110)aAg>aGg	p.K370R	TTC39A_ENST00000262675.7_Missense_Mutation_p.K307R|TTC39A_ENST00000413473.2_Missense_Mutation_p.K338R|TTC39A_ENST00000371750.5_Missense_Mutation_p.K335R|TTC39A_ENST00000371747.3_Missense_Mutation_p.K369R|TTC39A_ENST00000262676.5_3'UTR|TTC39A_ENST00000451380.1_Missense_Mutation_p.K334R			Q5SRH9	TT39A_HUMAN	tetratricopeptide repeat domain 39A	370								p.0?(2)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(2)|prostate(2)|skin(3)|urinary_tract(1)	17						GTAGGACATCTTCCACTGGCC	0.582																																					p.K338R		Atlas-SNP	.											.	TTC39A	40	.	2	Whole gene deletion(2)	thyroid(1)|central_nervous_system(1)	c.A1013G						.						73	75	74					1																	51767296		2123	4237	6360	SO:0001583	missense	22996	exon12			GACATCTTCCACT	AB007921	CCDS44143.1, CCDS44144.1, CCDS72789.1, CCDS72790.1	1p32.3	2013-01-11	2008-06-23	2008-06-23	ENSG00000085831	ENSG00000085831		"Tetratricopeptide (TTC) repeat domain containing"	18657	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 34"	C1orf34		9455484, 9461476	Standard	XM_005270643		Approved	KIAA0452, DEME-6	uc010onf.2	Q5SRH9	OTTHUMG00000008193	ENST00000447632.2:c.1109A>G	chr1.hg19:g.51767296T>C	ENSP00000393952:p.Lys370Arg	100.0	0.0		44.0	4.0	NM_001144832	B7Z782|E7EQY9|G3XAF8|O43417|O75040|Q5SRH5|Q5SRH6|Q5SRH7|Q5SRH8|Q5SRI0|Q5SRI1|Q5SRI2|Q5T7S1|Q6PIU8|Q9BT24	Missense_Mutation	SNP	ENST00000447632.2	hg19		.	.	.	.	.	.	.	.	.	.	T	16.02	3.005308	0.54254	.	.	ENSG00000085831	ENST00000447632;ENST00000413473;ENST00000262675;ENST00000451380;ENST00000371750;ENST00000371747	T;T;T;T;T;T	0.64260	0.88;0.88;0.88;0.88;0.88;-0.09	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	T	0.55465	0.1922	L	0.49571	1.57	0.49687	D	0.999812	B;B;B;B;B;B	0.17667	0.002;0.002;0.005;0.023;0.006;0.019	B;B;B;B;B;B	0.21546	0.012;0.021;0.013;0.035;0.034;0.021	T	0.51371	-0.8714	10	0.19147	T	0.46	-13.2017	13.8104	0.63260	0.0:0.0:0.0:1.0	.	338;334;307;334;370;335	Q5SRH9-4;E7EQY9;D3DQ30;B7Z782;Q5SRH9;G3XAF8	.;.;.;.;TT39A_HUMAN;.	R	370;338;307;334;335;369	ENSP00000393952:K370R;ENSP00000406144:K338R;ENSP00000262675:K307R;ENSP00000397207:K334R;ENSP00000360815:K335R;ENSP00000360812:K369R	ENSP00000262675:K307R	K	-	2	0	TTC39A	51539884	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.964000	0.70379	1.925000	0.55765	0.379000	0.24179	AAG	.	.		0.582	TTC39A-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000022434.2			C	51767296	T	C	51767296	3	2	255	1	0	0	0	0	1	0	0	0	16722	1609	56	2	760	2	TTC39A	1	51767296	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	4360347	51767296	197483325	31	35376										
KTI12	112970	hgsc.bcm.edu	37	chr1	52499377	52499377	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gccagcgccacgcgcaactcTtcagcacgccggctcttgcc	10	19	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:52499377T>C	ENST00000371614.1	-	1	111	c.57A>G	c.(55-57)gaA>gaG	p.E19E	TXNDC12_ENST00000371626.4_Intron|RP11-91A18.4_ENST00000425802.1_RNA|TXNDC12_ENST00000610127.1_3'UTR	NM_138417.2	NP_612426.1	Q96EK9	KTI12_HUMAN	KTI12 homolog, chromatin associated (S. cerevisiae)	19							ATP binding (GO:0005524)			central_nervous_system(2)|endometrium(1)|kidney(1)|lung(4)|ovary(1)|stomach(2)|urinary_tract(1)	12						CGCGCAACTCTTCAGCACGCC	0.682																																					p.E19E		Atlas-SNP	.											.	KTI12	30	.	0			c.A57G						.						16	17	17					1																	52499377		2196	4289	6485	SO:0001819	synonymous_variant	112970	exon1			CAACTCTTCAGCA		CCDS562.1	1p32.3	2008-02-05			ENSG00000198841	ENSG00000198841			25160	protein-coding gene	gene with protein product						11929532	Standard	NM_138417		Approved	TOT4, MGC20419, SBBI81	uc001ctj.1	Q96EK9	OTTHUMG00000008630	ENST00000371614.1:c.57A>G	chr1.hg19:g.52499377T>C		100.0	0.0		78.0	5.0	NM_138417		Silent	SNP	ENST00000371614.1	hg19	CCDS562.1																																																																																			.	.		0.682	KTI12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023821.1	NM_138417		C	52499377	T	C	52499377	2	2	255	1	0	0	0	0	0	0	0	1	8593	1606	56	2		2	KTI12	1	52499377	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	732081	52499377	196751244	32	35377										
ZYG11B	79699	hgsc.bcm.edu	37	chr1	53237069	53237069	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgccaagattagagagcttgGatatttctaacacctcaatc	7	9	2	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:53237069G>C	ENST00000294353.6	+	3	719	c.574G>C	c.(574-576)Gat>Cat	p.D192H	ZYG11B_ENST00000443756.2_Missense_Mutation_p.D192H|ZYG11B_ENST00000545132.1_Missense_Mutation_p.D192H	NM_024646.2	NP_078922.1	Q9C0D3	ZY11B_HUMAN	zyg-11 family member B, cell cycle regulator	192										breast(1)|endometrium(1)|kidney(6)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	30						AGAGAGCTTGGATATTTCTAA	0.443																																					p.D192H		Atlas-SNP	.											.	ZYG11B	61	.	0			c.G574C						.						75	78	77					1																	53237069		2203	4300	6503	SO:0001583	missense	79699	exon3			AGCTTGGATATTT	AB051517	CCDS30717.1	1p32.3	2013-01-17	2012-12-10	2005-07-11	ENSG00000162378	ENSG00000162378		"ZYG11 cell cycle regulator family"	25820	protein-coding gene	gene with protein product			"zyg-11 homolog (C. elegans)", "zyg-11 homolog B (C. elegans)"	ZYG11		11214970	Standard	NM_024646		Approved	FLJ13456	uc001cuj.3	Q9C0D3	OTTHUMG00000008938	ENST00000294353.6:c.574G>C	chr1.hg19:g.53237069G>C	ENSP00000294353:p.Asp192His	66.0	0.0		60.0	4.0	NM_024646	Q8N2X3|Q9H8L8	Missense_Mutation	SNP	ENST00000294353.6	hg19	CCDS30717.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.354560	0.82243	.	.	ENSG00000162378	ENST00000443756;ENST00000545132;ENST00000294353	T;T;T	0.20463	2.07;2.07;2.07	5.16	5.16	0.70880	.	0.094477	0.64402	D	0.000001	T	0.49932	0.1586	M	0.78456	2.415	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.994;0.995	T	0.50841	-0.8780	10	0.59425	D	0.04	.	18.9116	0.92487	0.0:0.0:1.0:0.0	.	192;192	B4DK95;Q9C0D3	.;ZY11B_HUMAN	H	192	ENSP00000400522:D192H;ENSP00000441315:D192H;ENSP00000294353:D192H	ENSP00000294353:D192H	D	+	1	0	ZYG11B	53009657	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.711000	0.84669	2.712000	0.92718	0.650000	0.86243	GAT	.	.		0.443	ZYG11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024749.1	NM_024646		C	53237069	G	C	53237069	3	2	255	1	0	0	0	0	1	0	0	0	18268	1174	41	4	584	4	ZYG11B	1	53237069	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	737692	53237069	196013552	33	35378										
SSBP3	23648	hgsc.bcm.edu	37	chr1	54717508	54717508	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tagaattgggcagcaatggcTgtgtcccaggaactcctccc	11	12	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:54717508T>C	ENST00000371320.3	-	8	943	c.533A>G	c.(532-534)cAg>cGg	p.Q178R	SSBP3_ENST00000371319.3_Missense_Mutation_p.Q151R|SSBP3_ENST00000417664.2_Missense_Mutation_p.Q68R|SSBP3_ENST00000326956.7_5'UTR|SSBP3_ENST00000357475.4_Missense_Mutation_p.Q158R	NM_145716.2	NP_663768.1	Q9BWW4	SSBP3_HUMAN	single stranded DNA binding protein 3	178	Gly-rich.|Pro-rich.				head morphogenesis (GO:0060323)|hematopoietic progenitor cell differentiation (GO:0002244)|midbrain-hindbrain boundary initiation (GO:0021547)|positive regulation of anterior head development (GO:2000744)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prechordal plate formation (GO:0021501)|protein complex assembly (GO:0006461)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|protein complex (GO:0043234)	single-stranded DNA binding (GO:0003697)			central_nervous_system(2)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	11						CAGCAATGGCTGTGTCCCAGG	0.617																																					p.Q178R		Atlas-SNP	.											.	SSBP3	65	.	0			c.A533G						.						53	45	48					1																	54717508		2203	4300	6503	SO:0001583	missense	23648	exon8			AATGGCTGTGTCC		CCDS590.1, CCDS591.1, CCDS30726.1	1p32.3	2008-02-05	2001-11-28		ENSG00000157216	ENSG00000157216			15674	protein-coding gene	gene with protein product		607390	"single-stranded DNA-binding protein 3"			12079286	Standard	NM_145716		Approved	CSDP, SSDP, FLJ10355, SSDP1	uc001cxe.4	Q9BWW4	OTTHUMG00000008264	ENST00000371320.3:c.533A>G	chr1.hg19:g.54717508T>C	ENSP00000360371:p.Gln178Arg	233.0	0.0		111.0	5.0	NM_145716	A8K0A9|Q5T860|Q5T861|Q9BTM0|Q9BWW3	Missense_Mutation	SNP	ENST00000371320.3	hg19	CCDS591.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.445087	0.83993	.	.	ENSG00000157216	ENST00000417664;ENST00000371320;ENST00000371319;ENST00000357475;ENST00000444533;ENST00000525990	.	.	.	4.68	4.68	0.58851	.	0.266749	0.34088	U	0.004271	T	0.70727	0.3257	M	0.69523	2.12	0.58432	D	0.999997	B;P;P	0.45283	0.417;0.855;0.776	B;P;P	0.51516	0.085;0.598;0.672	T	0.72434	-0.4295	9	0.42905	T	0.14	0.0018	14.585	0.68317	0.0:0.0:0.0:1.0	.	151;158;178	Q9BWW4-2;Q9BWW4-3;Q9BWW4	.;.;SSBP3_HUMAN	R	68;178;151;158;9;41	.	ENSP00000350067:Q158R	Q	-	2	0	SSBP3	54490096	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.573000	0.67417	2.086000	0.62901	0.533000	0.62120	CAG	.	.		0.617	SSBP3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022721.1	NM_018070		C	54717508	T	C	54717508	3	2	255	1	0	0	0	0	1	0	0	0	15196	1580	55	2	677	2	SSBP3	1	54717508	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	1480439	54717508	194533113	34	35379										
ACOT11	26027	hgsc.bcm.edu	37	chr1	55050328	55050328	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgtccccacctgtaccccagGgcttggcctctgtgttctcc	9	17	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:55050328G>T	ENST00000371316.3	+	2	116	c.34G>T	c.(34-36)Ggc>Tgc	p.G12C	ACOT11_ENST00000481208.1_3'UTR|ACOT11_ENST00000343744.2_Splice_Site_p.G12C	NM_015547.3	NP_056362.1	Q8WXI4	ACO11_HUMAN	acyl-CoA thioesterase 11	12					fatty acid metabolic process (GO:0006631)|intracellular signal transduction (GO:0035556)|response to cold (GO:0009409)|response to temperature stimulus (GO:0009266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|lipid binding (GO:0008289)			NS(1)|central_nervous_system(1)|endometrium(6)|large_intestine(3)|lung(5)|ovary(1)	17						tgtaccccaGGGCTTGGCCTC	0.632																																					p.G12C	Ovarian(148;1440 1861 22015 32453 51933)	Atlas-SNP	.											.	ACOT11	105	.	0			c.G34T						.						43	44	44					1																	55050328		2203	4300	6503	SO:0001630	splice_region_variant	26027	exon2			CCCCAGGGCTTGG	AB014607	CCDS592.1, CCDS593.1	1p32.3	2011-09-13	2005-09-08	2005-09-08	ENSG00000162390	ENSG00000162390	3.1.2.-	"Acyl CoA thioesterases", "StAR-related lipid transfer (START) domain containing"	18156	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 14"	606803	"thioesterase, adipose associated"	THEA		11696000, 16103133, 16940157	Standard	NM_015547		Approved	STARD14, BFIT, KIAA0707, BFIT1, THEM1	uc001cxl.2	Q8WXI4	OTTHUMG00000009891	ENST00000371316.3:c.34-1G>T	chr1.hg19:g.55050328G>T		148.0	0.0		87.0	4.0	NM_147161	B1AQ22|D3DQ50|O75187|Q52LP1|Q53ER9|Q96DI1|Q9H883	Missense_Mutation	SNP	ENST00000371316.3	hg19	CCDS592.1	.	.	.	.	.	.	.	.	.	.	G	15.01	2.706460	0.48412	.	.	ENSG00000162390	ENST00000343744;ENST00000371316	T;T	0.14022	2.7;2.54	4.82	2.94	0.34122	.	0.459241	0.20325	N	0.094551	T	0.22399	0.0540	L	0.56769	1.78	0.38776	D	0.95466	D;P	0.64830	0.994;0.895	P;P	0.54401	0.751;0.658	T	0.02477	-1.1153	9	.	.	.	-15.2949	9.1741	0.37100	0.1677:0.0:0.8323:0.0	.	12;12	Q8WXI4;Q8WXI4-2	ACO11_HUMAN;.	C	12	ENSP00000340260:G12C;ENSP00000360366:G12C	.	G	+	1	0	ACOT11	54822916	1.000000	0.71417	0.964000	0.40570	0.274000	0.26718	0.580000	0.23803	0.579000	0.29504	0.655000	0.94253	GGC	.	.		0.632	ACOT11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027356.1	NM_015547	Missense_Mutation	T	55050328	G	T	55050328	5	4	255	1	0	0	0	0	0	0	1	0	149	1246	43	3	40	3	ACOT11	1	55050328	Splice_Site	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	332820	55050328	194200293	35	35380										
C8B	732	hgsc.bcm.edu	37	chr1	57406626	57406626	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cagggtggtgatgtgctcacTtgcccctcctcgtaccagga	12	13	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:57406626T>C	ENST00000371237.4	-	9	1360	c.1294A>G	c.(1294-1296)Agt>Ggt	p.S432G	C8B_ENST00000535057.1_Missense_Mutation_p.S370G|C8B_ENST00000543257.1_Missense_Mutation_p.S380G	NM_000066.2	NP_000057	P07358	CO8B_HUMAN	complement component 8, beta polypeptide	432	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane attack complex (GO:0005579)|vesicle (GO:0031982)				breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	52						ATGTGCTCACTTGCCCCTCCT	0.572																																					p.S432G		Atlas-SNP	.											.	C8B	107	.	0			c.A1294G						.						172	123	140					1																	57406626		2203	4300	6503	SO:0001583	missense	732	exon9			GCTCACTTGCCCC	M16973	CCDS30730.1, CCDS60151.1, CCDS60152.1	1p32.2	2014-09-17			ENSG00000021852	ENSG00000021852		"Complement system"	1353	protein-coding gene	gene with protein product		120960					Standard	NM_000066		Approved		uc001cyp.3	P07358	OTTHUMG00000008305	ENST00000371237.4:c.1294A>G	chr1.hg19:g.57406626T>C	ENSP00000360281:p.Ser432Gly	134.0	0.0		99.0	4.0	NM_000066	A1L4K7	Missense_Mutation	SNP	ENST00000371237.4	hg19	CCDS30730.1	.	.	.	.	.	.	.	.	.	.	T	29.9	5.048161	0.93740	.	.	ENSG00000021852	ENST00000371237;ENST00000543257;ENST00000535057	D;D;D	0.84370	-1.84;-1.84;-1.84	5.36	5.36	0.76844	Membrane attack complex component/perforin (MACPF) domain (3);	0.042609	0.85682	D	0.000000	D	0.92424	0.7595	M	0.84846	2.72	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.74348	0.971;0.971;0.983	D	0.91938	0.5560	10	0.33940	T	0.23	-24.8754	15.643	0.77020	0.0:0.0:0.0:1.0	.	380;370;432	F5H7G1;F5GY80;P07358	.;.;CO8B_HUMAN	G	432;380;370	ENSP00000360281:S432G;ENSP00000442548:S380G;ENSP00000440113:S370G	ENSP00000360281:S432G	S	-	1	0	C8B	57179214	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.282000	0.78630	2.143000	0.66587	0.533000	0.62120	AGT	.	.		0.572	C8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022886.2			C	57406626	T	C	57406626	3	2	255	1	0	0	0	0	1	0	0	0	2419	1609	56	2	497	2	C8B	1	57406626	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	2356298	57406626	191843995	36	35381										
C1orf87	127795	hgsc.bcm.edu	37	chr1	60503758	60503758	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgctgcactgtttaaaaaccAgagtagcttttcataattca	6	8	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:60503758A>G	ENST00000371201.3	-	6	876	c.769T>C	c.(769-771)Tgg>Cgg	p.W257R	C1orf87_ENST00000450089.2_Intron	NM_152377.2	NP_689590.1	Q8N0U7	CA087_HUMAN	chromosome 1 open reading frame 87	257							calcium ion binding (GO:0005509)			breast(2)|endometrium(2)|large_intestine(6)|lung(19)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33						TTTAAAAACCAGAGTAGCTTT	0.348																																					p.W257R	NSCLC(75;811 1386 4923 13371 51772)	Atlas-SNP	.											.	C1orf87	55	.	0			c.T769C						.						77	71	73					1																	60503758		2203	4300	6503	SO:0001583	missense	127795	exon6			AAAACCAGAGTAG	AK124828	CCDS614.1	1p32.1	2014-04-03			ENSG00000162598	ENSG00000162598			28547	protein-coding gene	gene with protein product	"carcinoma-related EF-hand protein"					12477932	Standard	NM_152377		Approved	MGC34837, CREF	uc001czs.2	Q8N0U7	OTTHUMG00000008992	ENST00000371201.3:c.769T>C	chr1.hg19:g.60503758A>G	ENSP00000360244:p.Trp257Arg	154.0	0.0		86.0	4.0	NM_152377	Q6ZU07|Q8IVS0	Missense_Mutation	SNP	ENST00000371201.3	hg19	CCDS614.1	.	.	.	.	.	.	.	.	.	.	A	1.630	-0.519349	0.04171	.	.	ENSG00000162598	ENST00000371201	T	0.39406	1.08	5.65	-0.647	0.11468	.	0.996520	0.08136	N	0.992435	T	0.24392	0.0591	L	0.29908	0.895	0.09310	N	1	B	0.14438	0.01	B	0.16289	0.015	T	0.28713	-1.0035	10	0.06625	T	0.88	8.1781	6.0477	0.19770	0.4679:0.1464:0.3858:0.0	.	257	Q8N0U7	CA087_HUMAN	R	257	ENSP00000360244:W257R	ENSP00000360244:W257R	W	-	1	0	C1orf87	60276346	0.078000	0.21339	0.251000	0.24312	0.464000	0.32679	0.515000	0.22801	-0.254000	0.09500	-0.256000	0.11100	TGG	.	.		0.348	C1orf87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024943.1	NM_152377		G	60503758	A	G	60503758	3	3	255	1	0	0	0	0	1	0	0	0	2066	188	7	2	899	2	C1orf87	1	60503758	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	3097132	60503758	188746863	37	35382										
INADL	10207	hgsc.bcm.edu	37	chr1	62626601	62626601	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gagcagctgcagatgacggcCgattaaaacgaggggatcag	15	8	1	2	rs528030209	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:62626601C>A	ENST00000371158.2	+	43	5514	c.5400C>A	c.(5398-5400)gcC>gcA	p.A1800A		NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1800					cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						AGATGACGGCCGATTAAAACG	0.413																																					p.A1800A		Atlas-SNP	.											.	INADL	179	.	0			c.C5400A						.						101	99	100					1																	62626601		1918	4122	6040	SO:0001819	synonymous_variant	10207	exon43			GACGGCCGATTAA	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.5400C>A	chr1.hg19:g.62626601C>A		85.0	0.0		51.0	4.0	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Silent	SNP	ENST00000371158.2	hg19	CCDS617.2																																																																																			.	.		0.413	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		A	62626601	C	A	62626601	2	1	255	1	0	0	0	0	0	0	0	1	7740	639	23	1		1	INADL	1	62626601	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	2122843	62626601	186624020	38	35383										
LEPR	3953	hgsc.bcm.edu	37	chr1	66067256	66067256	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gatcatgttagcaaagttacTtttttcaatctgaatgaaac	6	6	3	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:66067256T>C	ENST00000349533.6	+	9	1361	c.1176T>C	c.(1174-1176)acT>acC	p.T392T	LEPR_ENST00000371060.3_Silent_p.T392T|LEPR_ENST00000371059.3_Silent_p.T392T|LEPR_ENST00000344610.8_Silent_p.T392T|LEPR_ENST00000371058.1_Silent_p.T392T|LEPR_ENST00000462765.1_3'UTR|LEPR_ENST00000406510.3_Intron	NM_002303.5	NP_002294.2	O15243	OBRG_HUMAN	leptin receptor	0					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(22)|skin(2)	36				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		GCAAAGTTACTTTTTTCAATC	0.373																																					p.T392T		Atlas-SNP	.											.	LEPR	284	.	0			c.T1176C						.						112	109	110					1																	66067256		2203	4300	6503	SO:0001819	synonymous_variant	3953	exon9			AGTTACTTTTTTC	U43168	CCDS631.1, CCDS30740.1, CCDS30741.1, CCDS55604.1	1p31	2014-09-17			ENSG00000116678	ENSG00000116678		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6554	protein-coding gene	gene with protein product		601007				8548812, 8812446	Standard	NM_001003680		Approved	OBR, CD295	uc001dci.3	P48357	OTTHUMG00000009115	ENST00000349533.6:c.1176T>C	chr1.hg19:g.66067256T>C		166.0	0.0		90.0	4.0	NM_001003680	Q6FHL5	Silent	SNP	ENST00000349533.6	hg19	CCDS631.1																																																																																			.	.		0.373	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303		C	66067256	T	C	66067256	2	2	255	1	0	0	0	0	0	0	0	1	8737	1596	56	2		2	LEPR	1	66067256	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	3440655	66067256	183183365	39	35384										
WLS	79971	hgsc.bcm.edu	37	chr1	68610266	68610266	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	acttacctgactaacgatgaAgaagatgacagtcatggcag	10	8	1	5			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:68610266A>G	ENST00000262348.4	-	10	1601	c.1348T>C	c.(1348-1350)Ttc>Ctc	p.F450L	WLS_ENST00000540432.1_Missense_Mutation_p.F450L|WLS_ENST00000491811.1_5'UTR|WLS_ENST00000370976.3_Missense_Mutation_p.F359L|WLS_ENST00000354777.2_Missense_Mutation_p.F448L|GNG12-AS1_ENST00000420587.1_RNA|GNG12-AS1_ENST00000434072.1_RNA|GNG12-AS1_ENST00000413628.1_RNA	NM_024911.6	NP_079187.3	Q5T9L3	WLS_HUMAN	wntless Wnt ligand secretion mediator	450					anterior/posterior axis specification (GO:0009948)|mesoderm formation (GO:0001707)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|Wnt signaling pathway (GO:0016055)	cytoplasmic vesicle (GO:0031410)|early endosome membrane (GO:0031901)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(4)|prostate(3)|urinary_tract(1)	20						CTAACGATGAAGAAGATGACA	0.443																																					p.F450L		Atlas-SNP	.											.	WLS	97	.	0			c.T1348C						.						125	129	128					1																	68610266		2203	4300	6503	SO:0001583	missense	79971	exon10			CGATGAAGAAGAT	BX538320	CCDS642.1, CCDS30750.1, CCDS53331.1	1p31.2	2013-10-03	2013-10-03	2010-03-02	ENSG00000116729	ENSG00000116729			30238	protein-coding gene	gene with protein product	"wntless homolog"	611514	"chromosome 1 open reading frame 139", "G protein-coupled receptor 177", "wntless homolog (Drosophila)"	C1orf139, GPR177		12761501	Standard	NM_024911		Approved	FLJ23091, MRP, wls, EVI, mig-14	uc001dee.3	Q5T9L3	OTTHUMG00000009153	ENST00000262348.4:c.1348T>C	chr1.hg19:g.68610266A>G	ENSP00000262348:p.Phe450Leu	111.0	0.0		62.0	4.0	NM_024911	B2RNT2|Q5JRS7|Q7Z2Z9|Q8NC43	Missense_Mutation	SNP	ENST00000262348.4	hg19	CCDS642.1	.	.	.	.	.	.	.	.	.	.	A	28.0	4.884942	0.91814	.	.	ENSG00000116729	ENST00000540432;ENST00000354777;ENST00000262348;ENST00000370976	T;T;T;T	0.37584	1.19;1.19;1.19;1.19	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.49779	0.1577	M	0.69823	2.125	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.87578	0.993;0.996;0.998;0.993	T	0.46428	-0.9192	10	0.32370	T	0.25	-24.4284	15.7591	0.78063	1.0:0.0:0.0:0.0	.	450;359;450;448	F5H4K0;Q5JRS7;Q5T9L3;Q5T9L3-2	.;.;WLS_HUMAN;.	L	450;448;450;359	ENSP00000446112:F450L;ENSP00000346829:F448L;ENSP00000262348:F450L;ENSP00000360015:F359L	ENSP00000262348:F450L	F	-	1	0	WLS	68382854	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.915000	0.92740	2.123000	0.65237	0.528000	0.53228	TTC	.	.		0.443	WLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025368.1	NM_024911		G	68610266	A	G	68610266	3	3	255	1	0	0	0	0	1	0	0	0	17391	72	3	2	415	2	WLS	1	68610266	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	2543010	68610266	180640355	40	35385										
ELTD1	64123	hgsc.bcm.edu	37	chr1	79404924	79404924	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	atacagacattatctaaatgGcagtttgcattcacattttc	5	8	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:79404924G>T	ENST00000370742.3	-	4	408	c.345C>A	c.(343-345)tgC>tgA	p.C115*		NM_022159.3	NP_071442.2	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain containing 1	115					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(45)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	69				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)		TATCTAAATGGCAGTTTGCAT	0.249																																					p.C115X		Atlas-SNP	.											.	ELTD1	143	.	0			c.C345A						.						41	41	41					1																	79404924		1780	4030	5810	SO:0001587	stop_gained	64123	exon4			TAAATGGCAGTTT	AF192403	CCDS41352.1	1p33-p32	2014-08-08			ENSG00000162618	ENSG00000162618		"-", "GPCR / Class B : Orphans"	20822	protein-coding gene	gene with protein product						11050079	Standard	NM_022159		Approved	ETL	uc001diq.4	Q9HBW9	OTTHUMG00000009738	ENST00000370742.3:c.345C>A	chr1.hg19:g.79404924G>T	ENSP00000359778:p.Cys115*	450.0	1.0		278.0	219.0	NM_022159	B1AR71|Q5KU34	Nonsense_Mutation	SNP	ENST00000370742.3	hg19	CCDS41352.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.904360	0.92035	.	.	ENSG00000162618	ENST00000370742	.	.	.	6.07	1.66	0.24008	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.3662	0.44026	0.3935:0.0:0.6065:0.0	.	.	.	.	X	115	.	.	C	-	3	2	ELTD1	79177512	0.995000	0.38212	0.933000	0.37362	0.892000	0.51952	0.478000	0.22212	0.466000	0.27193	-0.237000	0.12165	TGC	.	.		0.249	ELTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026859.1	NM_022159		T	79404924	G	T	79404924	4	4	255	1	0	0	0	0	0	1	0	0	5086	1195	42	3	1775	3	ELTD1	1	79404924	Nonsense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	10794658	79404924	169845697	41	35386										
CLCA2	9635	hgsc.bcm.edu	37	chr1	86900325	86900325	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgactttcaccacagctttcCcatgaatgggactgagcttc	8	12	1	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:86900325C>T	ENST00000370565.4	+	6	1031	c.869C>T	c.(868-870)cCc>cTc	p.P290L		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	290					cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)			NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		CACAGCTTTCCCATGAATGGG	0.507																																					p.P290L	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											.	CLCA2	102	.	0			c.C869T						.						215	181	192					1																	86900325		2203	4300	6503	SO:0001583	missense	9635	exon6			GCTTTCCCATGAA		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"chloride channel, calcium activated, family member 2", "chloride channel regulator 2"				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.869C>T	chr1.hg19:g.86900325C>T	ENSP00000359596:p.Pro290Leu	131.0	0.0		89.0	4.0	NM_006536	A8K2T3|Q9Y6N2	Missense_Mutation	SNP	ENST00000370565.4	hg19	CCDS708.1	.	.	.	.	.	.	.	.	.	.	C	35	5.553198	0.96501	.	.	ENSG00000137975	ENST00000370565	T	0.03689	3.84	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.19327	0.0464	M	0.89840	3.065	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.00795	-1.1563	10	0.54805	T	0.06	-15.4545	19.4432	0.94831	0.0:1.0:0.0:0.0	.	290	Q9UQC9	CLCA2_HUMAN	L	290	ENSP00000359596:P290L	ENSP00000359596:P290L	P	+	2	0	CLCA2	86672913	0.954000	0.32549	0.272000	0.24630	0.640000	0.38277	3.925000	0.56484	2.941000	0.99782	0.655000	0.94253	CCC	.	.		0.507	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536		T	86900325	C	T	86900325	3	4	255	1	0	0	0	0	1	0	0	0	3460	623	22	3	891	3	CLCA2	1	86900325	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	7495401	86900325	162350296	42	35387										
GBP5	115362	hgsc.bcm.edu	37	chr1	89729496	89729496	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aatgaagagattatggcctcCtggcttagaataaattccct	8	8	0	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:89729496C>A	ENST00000370459.3	-	8	1412	c.1285G>T	c.(1285-1287)Gga>Tga	p.G429*	GBP5_ENST00000471171.1_5'Flank|RP4-620F22.2_ENST00000437128.1_RNA|GBP5_ENST00000343435.5_Nonsense_Mutation_p.G429*			Q96PP8	GBP5_HUMAN	guanylate binding protein 5	429						cytoplasm (GO:0005737)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			breast(1)|endometrium(1)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)	24				all cancers(265;0.00784)|Epithelial(280;0.0286)		TTATGGCCTCCTGGCTTAGAA	0.433																																					p.G429X		Atlas-SNP	.											.	GBP5	65	.	0			c.G1285T						.						173	173	173					1																	89729496		2203	4300	6503	SO:0001587	stop_gained	115362	exon9			GGCCTCCTGGCTT	AF430642	CCDS722.1	1p22.2	2008-02-05			ENSG00000154451	ENSG00000154451			19895	protein-coding gene	gene with protein product		611467					Standard	NM_052942		Approved		uc001dnd.3	Q96PP8	OTTHUMG00000010006	ENST00000370459.3:c.1285G>T	chr1.hg19:g.89729496C>A	ENSP00000359488:p.Gly429*	209.0	0.0		137.0	6.0	NM_052942	B2RCE1|Q86TM5	Nonsense_Mutation	SNP	ENST00000370459.3	hg19	CCDS722.1	.	.	.	.	.	.	.	.	.	.	C	57	29.251134	0.99975	.	.	ENSG00000154451	ENST00000343435;ENST00000370459;ENST00000443807	.	.	.	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-21.8051	16.2143	0.82195	0.0:1.0:0.0:0.0	.	.	.	.	X	429	.	ENSP00000340396:G429X	G	-	1	0	GBP5	89502084	0.983000	0.35010	0.981000	0.43875	0.823000	0.46562	4.378000	0.59568	2.762000	0.94881	0.551000	0.68910	GGA	.	.		0.433	GBP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027700.1	NM_052942		A	89729496	C	A	89729496	4	1	255	1	0	0	0	0	0	1	0	0	6285	690	24	3	491	3	GBP5	1	89729496	Nonsense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	2829171	89729496	159521125	43	35388										
GBP6	163351	hgsc.bcm.edu	37	chr1	89843997	89843997	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tatgtgacggagctcacagaActaattaaggcaaagtcctc	9	9	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:89843997A>G	ENST00000370456.4	+	5	543	c.450A>G	c.(448-450)gaA>gaG	p.E150E	GBP6_ENST00000535065.1_Silent_p.E20E	NM_198460.2	NP_940862.2	Q6ZN66	GBP6_HUMAN	guanylate binding protein family, member 6	150	GB1/RHD3-type G.|GTPase domain (Globular). {ECO:0000250}.				cellular response to interferon-gamma (GO:0071346)|defense response to bacterium (GO:0042742)|immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42		Lung NSC(277;0.0908)		all cancers(265;0.0108)|Epithelial(280;0.0398)		AGCTCACAGAACTAATTAAGG	0.403																																					p.E150E		Atlas-SNP	.											.	GBP6	87	.	0			c.A450G						.						111	119	117					1																	89843997		2203	4300	6503	SO:0001819	synonymous_variant	163351	exon5			CACAGAACTAATT	BX537949	CCDS723.1	1p22	2008-02-05			ENSG00000183347	ENSG00000183347			25395	protein-coding gene	gene with protein product		612467					Standard	NM_198460		Approved	DKFZp686G0786	uc001dnf.2	Q6ZN66	OTTHUMG00000010123	ENST00000370456.4:c.450A>G	chr1.hg19:g.89843997A>G		95.0	0.0		64.0	4.0	NM_198460	A2RRM3|Q6ZN86|Q7Z3F0	Silent	SNP	ENST00000370456.4	hg19	CCDS723.1																																																																																			.	.		0.403	GBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028001.1	NM_198460		G	89843997	A	G	89843997	2	3	255	1	0	0	0	0	0	0	0	1	6286	40	2	2		2	GBP6	1	89843997	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	114501	89843997	159406624	44	35389										
LRRC8D	55144	hgsc.bcm.edu	37	chr1	90399028	90399028	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aaagaaagagaagaaagatcCaacaggtcgaaaaacaaact	8	6	0	4			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:90399028C>A	ENST00000337338.5	+	3	808	c.401C>A	c.(400-402)cCa>cAa	p.P134Q	LRRC8D_ENST00000394593.3_Missense_Mutation_p.P134Q	NM_001134479.1	NP_001127951.1	Q7L1W4	LRC8D_HUMAN	leucine rich repeat containing 8 family, member D	134					ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(2)|skin(1)	29		all_lung(203;0.0894)|Lung NSC(277;0.227)		all cancers(265;0.0109)|Epithelial(280;0.0427)		AAGAAAGATCCAACAGGTCGA	0.418																																					p.P134Q		Atlas-SNP	.											.	LRRC8D	78	.	0			c.C401A						.						64	63	63					1																	90399028		2203	4300	6503	SO:0001583	missense	55144	exon3			AAGATCCAACAGG	AK001332	CCDS726.1	1p22.2	2008-02-05	2005-06-29	2005-06-29	ENSG00000171492	ENSG00000171492			16992	protein-coding gene	gene with protein product		612890	"leucine rich repeat containing 5"	LRRC5			Standard	NM_018103		Approved	FLJ10470	uc001dnn.3	Q7L1W4	OTTHUMG00000010583	ENST00000337338.5:c.401C>A	chr1.hg19:g.90399028C>A	ENSP00000338887:p.Pro134Gln	136.0	0.0		95.0	4.0	NM_018103	D3DT29|Q6UWB2|Q9NVW3	Missense_Mutation	SNP	ENST00000337338.5	hg19	CCDS726.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.117811	0.77323	.	.	ENSG00000171492	ENST00000337338;ENST00000394593;ENST00000527156;ENST00000441269	T;T;T	0.46063	1.49;1.49;0.88	6.07	6.07	0.98685	.	0.118552	0.56097	D	0.000022	T	0.24236	0.0587	N	0.08118	0	0.49798	D	0.999824	B	0.28378	0.209	B	0.43386	0.418	T	0.30387	-0.9980	9	.	.	.	.	20.6593	0.99626	0.0:1.0:0.0:0.0	.	134	Q7L1W4	LRC8D_HUMAN	Q	134	ENSP00000338887:P134Q;ENSP00000378093:P134Q;ENSP00000405784:P134Q	.	P	+	2	0	LRRC8D	90171616	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.074000	0.71253	2.885000	0.99019	0.655000	0.94253	CCA	.	.		0.418	LRRC8D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029203.2	NM_018103		A	90399028	C	A	90399028	3	1	255	1	0	0	0	0	1	0	0	0	9033	594	21	3	403	3	LRRC8D	1	90399028	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	555031	90399028	158851593	45	35390										
ABCA4	24	hgsc.bcm.edu	37	chr1	94517230	94517230	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	actcttgtagaagaaagtacCaaggaagtggggttccatag	12	6	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:94517230C>A	ENST00000370225.3	-	17	2698	c.2612G>T	c.(2611-2613)tGg>tTg	p.W871L	ABCA4_ENST00000535735.1_Missense_Mutation_p.W797L	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	871					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			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)		AAGAAAGTACCAAGGAAGTGG	0.413																																					p.W871L		Atlas-SNP	.											.	ABCA4	275	.	0			c.G2612T						.						74	69	71					1																	94517230		2203	4300	6503	SO:0001583	missense	24	exon17			AAGTACCAAGGAA	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.2612G>T	chr1.hg19:g.94517230C>A	ENSP00000359245:p.Trp871Leu	154.0	0.0		102.0	5.0	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	hg19	CCDS747.1	.	.	.	.	.	.	.	.	.	.	C	17.38	3.376159	0.61735	.	.	ENSG00000198691	ENST00000370225;ENST00000535735	T;T	0.76186	-1.0;-1.0	5.82	5.82	0.92795	.	0.174267	0.53938	D	0.000050	T	0.82222	0.4990	M	0.72576	2.205	0.37227	D	0.905509	D;B	0.61697	0.99;0.058	P;B	0.59546	0.859;0.049	D	0.83885	0.0281	10	0.87932	D	0	.	20.0852	0.97797	0.0:1.0:0.0:0.0	.	797;871	F5H6E5;P78363	.;ABCA4_HUMAN	L	871;797	ENSP00000359245:W871L;ENSP00000437682:W797L	ENSP00000359245:W871L	W	-	2	0	ABCA4	94289818	1.000000	0.71417	1.000000	0.80357	0.702000	0.40608	5.039000	0.64185	2.752000	0.94435	0.655000	0.94253	TGG	.	.		0.413	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		A	94517230	C	A	94517230	3	1	255	1	0	0	0	0	1	0	0	0	34	595	21	3	4345	3	ABCA4	1	94517230	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	4118202	94517230	154733391	46	35391										
AGL	178	hgsc.bcm.edu	37	chr1	100366213	100366213	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aatattattttagcatttgcGggtaccctgaggcatggtct	10	7	1	1	rs149393587	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:100366213G>T	ENST00000294724.4	+	26	3862	c.3384G>T	c.(3382-3384)gcG>gcT	p.A1128A	AGL_ENST00000361915.3_Silent_p.A1128A|AGL_ENST00000361302.3_Silent_p.A1112A|AGL_ENST00000370165.3_Silent_p.A1128A|AGL_ENST00000370163.3_Silent_p.A1128A|AGL_ENST00000370161.2_Silent_p.A1112A|AGL_ENST00000361522.4_Silent_p.A1111A	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	1128					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|inclusion body (GO:0016234)|isoamylase complex (GO:0043033)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)	4-alpha-glucanotransferase activity (GO:0004134)|amylo-alpha-1,6-glucosidase activity (GO:0004135)|glycogen debranching enzyme activity (GO:0004133)|polysaccharide binding (GO:0030247)	p.A1128A(2)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(9)|lung(35)|ovary(1)|prostate(4)|skin(3)|urinary_tract(1)	69		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		TAGCATTTGCGGGTACCCTGA	0.398																																					p.A1128A		Atlas-SNP	.											.	AGL	137	.	2	Substitution - coding silent(2)	lung(1)|kidney(1)	c.G3384T						.						213	208	210					1																	100366213		2203	4300	6503	SO:0001819	synonymous_variant	178	exon26			ATTTGCGGGTACC	BC078663	CCDS759.1, CCDS760.1, CCDS761.1	1p21	2010-04-27	2010-04-27		ENSG00000162688	ENSG00000162688	2.4.1.25, 3.2.1.33		321	protein-coding gene	gene with protein product	"glycogen debranching enzyme", "glycogen storage disease type III"	610860	"amylo-1, 6-glucosidase, 4-alpha-glucanotransferase"			1505983	Standard	NM_000028		Approved		uc001dsi.1	P35573	OTTHUMG00000010803	ENST00000294724.4:c.3384G>T	chr1.hg19:g.100366213G>T		163.0	0.0		106.0	6.0	NM_000644	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Silent	SNP	ENST00000294724.4	hg19	CCDS759.1																																																																																			.	G|0.997;A|0.003		0.398	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028		T	100366213	G	T	100366213	2	4	255	1	0	0	0	0	0	0	0	1	384	1103	39	1		1	AGL	1	100366213	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	5848983	100366213	148884408	47	35392										
CELSR2	1952	hgsc.bcm.edu	37	chr1	109794818	109794818	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggtgaatgtcaccgacgccaAcacccatcgtcctgtctttc	8	15	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:109794818A>G	ENST00000271332.3	+	1	2178	c.2117A>G	c.(2116-2118)aAc>aGc	p.N706S		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	706	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		ACCGACGCCAACACCCATCGT	0.572																																					p.N706S	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-SNP	.											.	CELSR2	228	.	0			c.A2117G						.						73	67	69					1																	109794818		2203	4300	6503	SO:0001583	missense	1952	exon1			ACGCCAACACCCA	D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3231	protein-coding gene	gene with protein product		604265	"cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.2117A>G	chr1.hg19:g.109794818A>G	ENSP00000271332:p.Asn706Ser	99.0	0.0		61.0	4.0	NM_001408	Q5T2Y7|Q92566	Missense_Mutation	SNP	ENST00000271332.3	hg19	CCDS796.1	.	.	.	.	.	.	.	.	.	.	N	18.65	3.669841	0.67814	.	.	ENSG00000143126	ENST00000271332	T	0.70749	-0.51	4.95	4.95	0.65309	Cadherin (3);Cadherin-like (1);	.	.	.	.	D	0.87212	0.6121	H	0.96142	3.775	0.58432	D	0.999993	D	0.76494	0.999	D	0.85130	0.997	D	0.91307	0.5071	9	0.87932	D	0	.	14.8253	0.70107	1.0:0.0:0.0:0.0	.	706	Q9HCU4	CELR2_HUMAN	S	706	ENSP00000271332:N706S	ENSP00000271332:N706S	N	+	2	0	CELSR2	109596341	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.709000	0.91379	2.102000	0.63906	0.529000	0.55759	AAC	.	.		0.572	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408		G	109794818	A	G	109794818	3	3	255	1	0	0	0	0	1	0	0	0	3224	43	2	2	2119	2	CELSR2	1	109794818	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	9428605	109794818	139455803	48	35393										
SLC16A4	9122	hgsc.bcm.edu	37	chr1	110918150	110918150	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agtcccaaaaacctgtttacTgtagaattcctacacagatc	5	11	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:110918150T>C	ENST00000369779.4	-	8	1515	c.1266A>G	c.(1264-1266)acA>acG	p.T422T	SLC16A4_ENST00000437429.2_Silent_p.T312T|SLC16A4_ENST00000369781.4_Silent_p.T254T|RP5-1074L1.4_ENST00000609909.1_RNA|SLC16A4_ENST00000541986.1_Silent_p.T360T|SLC16A4_ENST00000472422.2_Silent_p.T374T	NM_001201547.1|NM_004696.2	NP_001188476.1|NP_004687.1	O15374	MOT5_HUMAN	solute carrier family 16, member 4	422					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)			breast(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(2)|ovary(3)|prostate(1)|stomach(2)	16		all_cancers(81;0.000476)|all_epithelial(167;0.000401)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0251)|all cancers(265;0.0766)|Epithelial(280;0.0807)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.14)	Pyruvic acid(DB00119)	ACCTGTTTACTGTAGAATTCC	0.403																																					p.T422T		Atlas-SNP	.											.	SLC16A4	47	.	0			c.A1266G						.						81	83	82					1																	110918150		2203	4300	6503	SO:0001819	synonymous_variant	9122	exon8			GTTTACTGTAGAA	U59185	CCDS823.1, CCDS55621.1, CCDS55622.1, CCDS55623.1, CCDS55624.1	1p13.3	2013-07-18	2013-07-18		ENSG00000168679	ENSG00000168679		"Solute carriers"	10925	protein-coding gene	gene with protein product		603878	"solute carrier family 16 (monocarboxylic acid transporters), member 4", "solute carrier family 16, member 4 (monocarboxylic acid transporter 5)"			9425115	Standard	NM_004696		Approved	MCT4, MCT5	uc001dzo.2	O15374	OTTHUMG00000011285	ENST00000369779.4:c.1266A>G	chr1.hg19:g.110918150T>C		169.0	0.0		85.0	5.0	NM_004696	A8K3V5|B2R9C9|B4DJ67|B4DPX7|E7EPY8|G3V175|Q5T612|Q8WU09	Silent	SNP	ENST00000369779.4	hg19	CCDS823.1																																																																																			.	.		0.403	SLC16A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000031115.3	NM_004696		C	110918150	T	C	110918150	2	2	255	1	0	0	0	0	0	0	0	1	14425	1567	55	2		2	SLC16A4	1	110918150	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	1123332	110918150	138332471	49	35394										
CHIA	27159	hgsc.bcm.edu	37	chr1	111857937	111857937	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gagaaccgccagactttcatCacctcagtcatcaaattcct	5	14	5	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:111857937C>A	ENST00000369740.1	+	6	463	c.360C>A	c.(358-360)atC>atA	p.I120I	CHIA_ENST00000343320.6_Silent_p.I120I|CHIA_ENST00000451398.2_5'UTR|CHIA_ENST00000430615.1_Silent_p.I12I|CHIA_ENST00000353665.6_Intron|RP5-1125M8.2_ENST00000426321.1_RNA|CHIA_ENST00000483391.1_Intron	NM_001258001.1|NM_201653.3	NP_001244930.1|NP_970615.2	Q9BZP6	CHIA_HUMAN	chitinase, acidic	120					apoptotic process (GO:0006915)|cell wall chitin metabolic process (GO:0006037)|chitin catabolic process (GO:0006032)|chitin metabolic process (GO:0006030)|digestion (GO:0007586)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|positive regulation of chemokine secretion (GO:0090197)|production of molecular mediator involved in inflammatory response (GO:0002532)|response to fungus (GO:0009620)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|chitinase activity (GO:0004568)|kinase binding (GO:0019900)|lysozyme activity (GO:0003796)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		all_cancers(81;3.23e-05)|all_epithelial(167;1.2e-05)|all_lung(203;0.000154)|Lung NSC(277;0.000304)		Colorectal(144;0.0115)|Lung(183;0.0292)|COAD - Colon adenocarcinoma(174;0.0314)|all cancers(265;0.0477)|Epithelial(280;0.0918)|LUSC - Lung squamous cell carcinoma(189;0.154)		AGACTTTCATCACCTCAGTCA	0.547																																					p.I120I		Atlas-SNP	.											.	CHIA	115	.	0			c.C360A						.						128	124	125					1																	111857937		2203	4300	6503	SO:0001819	synonymous_variant	27159	exon6			TTTCATCACCTCA	AF290004	CCDS832.1, CCDS41368.1, CCDS58017.1	1p13.2	2008-05-14			ENSG00000134216	ENSG00000134216			17432	protein-coding gene	gene with protein product		606080				11085997	Standard	NM_021797		Approved	AMCase, TSA1902, CHIT2	uc001eas.4	Q9BZP6	OTTHUMG00000011165	ENST00000369740.1:c.360C>A	chr1.hg19:g.111857937C>A		138.0	0.0		96.0	4.0	NM_201653	Q32W79|Q32W80|Q3B866|Q5U5Z5|Q5VUV4|Q86UD8|Q9ULY3|Q9ULY4	Silent	SNP	ENST00000369740.1	hg19	CCDS41368.1																																																																																			.	.		0.547	CHIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030710.1			A	111857937	C	A	111857937	2	1	255	1	0	0	0	0	0	0	0	1	3344	816	29	3		3	CHIA	1	111857937	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	939787	111857937	137392684	50	35395										
SYT6	148281	hgsc.bcm.edu	37	chr1	114682411	114682411	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcagcttgtccgccatgttgCctctgaagctggggctctgg	13	12	3	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:114682411C>T	ENST00000610222.1	-	2	484	c.338G>A	c.(337-339)gGc>gAc	p.G113D	SYT6_ENST00000393296.1_Missense_Mutation_p.G113D|SYT6_ENST00000607941.1_Missense_Mutation_p.G28D|SYT6_ENST00000609117.1_Missense_Mutation_p.G28D|SYT6_ENST00000369547.1_Missense_Mutation_p.G28D			Q5T7P8	SYT6_HUMAN	synaptotagmin VI	113					acrosomal vesicle exocytosis (GO:0060478)	cell junction (GO:0030054)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|integral component of membrane (GO:0016021)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	clathrin binding (GO:0030276)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|syntaxin binding (GO:0019905)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(3)|large_intestine(10)|lung(14)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37	Lung SC(450;0.184)	all_cancers(81;4.41e-08)|all_epithelial(167;5.18e-08)|all_lung(203;1.58e-05)|Lung NSC(69;2.82e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CGCCATGTTGCCTCTGAAGCT	0.612																																					p.G28D		Atlas-SNP	.											.	SYT6	66	.	0			c.G83A						.						98	104	102					1																	114682411		2203	4300	6503	SO:0001583	missense	148281	exon2			ATGTTGCCTCTGA		CCDS871.1	1p13.1	2013-01-21			ENSG00000134207	ENSG00000134207		"Synaptotagmins"	18638	protein-coding gene	gene with protein product		607718				11543631	Standard	NM_205848		Approved		uc021orz.1	Q5T7P8	OTTHUMG00000011755	ENST00000610222.1:c.338G>A	chr1.hg19:g.114682411C>T	ENSP00000476396:p.Gly113Asp	91.0	0.0		63.0	4.0	NM_205848	B1AMB8|B3KPK1	Missense_Mutation	SNP	ENST00000610222.1	hg19		.	.	.	.	.	.	.	.	.	.	C	10.66	1.414048	0.25465	.	.	ENSG00000134207	ENST00000369547;ENST00000393296;ENST00000369546;ENST00000369545;ENST00000425037;ENST00000447981	T;T;T;T;T;T	0.56941	0.5;0.43;0.5;0.43;1.64;1.05	5.67	3.57	0.40892	.	0.617205	0.18348	N	0.143943	T	0.13457	0.0326	N	0.22421	0.69	0.32850	D	0.506496	B	0.02656	0.0	B	0.01281	0.0	T	0.10590	-1.0623	10	0.13470	T	0.59	.	4.1412	0.10194	0.0:0.5299:0.0:0.4701	.	113	Q5T7P8	SYT6_HUMAN	D	28;113;28;113;28;28	ENSP00000358560:G28D;ENSP00000376974:G113D;ENSP00000358559:G28D;ENSP00000358558:G113D;ENSP00000412443:G28D;ENSP00000389266:G28D	ENSP00000358558:G113D	G	-	2	0	SYT6	114483934	0.311000	0.24536	0.940000	0.37924	0.988000	0.76386	0.763000	0.26517	1.411000	0.46957	0.655000	0.94253	GGC	.	.		0.612	SYT6-004	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000314819.2	NM_205848		T	114682411	C	T	114682411	3	4	255	1	0	0	0	0	1	0	0	0	15493	739	26	3	1218	3	SYT6	1	114682411	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	2824474	114682411	134568210	51	35396										
CSDE1	7812	hgsc.bcm.edu	37	chr1	115282361	115282361	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	attatactgtgaacagtggaAgaaaagtctagcttgacgtt	10	5	1	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:115282361A>G	ENST00000358528.4	-	3	577	c.151T>C	c.(151-153)Ttc>Ctc	p.F51L	CSDE1_ENST00000369530.1_Missense_Mutation_p.F97L|CSDE1_ENST00000534699.1_Missense_Mutation_p.F51L|CSDE1_ENST00000261443.5_Missense_Mutation_p.F51L|CSDE1_ENST00000339438.6_Missense_Mutation_p.F51L|CSDE1_ENST00000438362.2_Missense_Mutation_p.F97L|CSDE1_ENST00000530886.1_Intron	NM_001007553.2	NP_001007554.1	O75534	CSDE1_HUMAN	cold shock domain containing E1, RNA-binding	51	CSD 1.				male gonad development (GO:0008584)|nuclear-transcribed mRNA catabolic process, no-go decay (GO:0070966)|regulation of transcription, DNA-templated (GO:0006355)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.F51L(1)		NS(1)|breast(4)|endometrium(11)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	51	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		GAACAGTGGAAGAAAAGTCTA	0.378																																					p.F97L		Atlas-SNP	.											CSDE1_ENST00000369530,NS,carcinoma,0,2	CSDE1	145	.	1	Substitution - Missense(1)	kidney(1)	c.T289C						.						209	220	216					1																	115282361		2203	4300	6503	SO:0001583	missense	7812	exon4			AGTGGAAGAAAAG		CCDS30811.1, CCDS30812.1, CCDS44197.1, CCDS55626.1	1p13.2	2011-11-02			ENSG00000009307	ENSG00000009307			29905	protein-coding gene	gene with protein product	"upstream of NRAS"	191510				2204029, 10048485	Standard	NM_007158		Approved	D1S155E, UNR	uc001efi.3	O75534	OTTHUMG00000012060	ENST00000358528.4:c.151T>C	chr1.hg19:g.115282361A>G	ENSP00000351329:p.Phe51Leu	139.0	0.0		41.0	3.0	NM_001130523	A8K281|E9PGZ0|G5E9Q2|O94961|Q5TF04|Q5TF05|Q68DF1|Q68DI9|Q9Y2S4	Missense_Mutation	SNP	ENST00000358528.4	hg19	CCDS30812.1	.	.	.	.	.	.	.	.	.	.	A	35	5.594471	0.96602	.	.	ENSG00000009307	ENST00000339438;ENST00000438362;ENST00000358528;ENST00000261443;ENST00000369530;ENST00000534699;ENST00000534389	.	.	.	5.81	5.81	0.92471	Cold shock protein (1);Nucleic acid-binding, OB-fold-like (1);Cold-shock protein, DNA-binding (1);Nucleic acid-binding, OB-fold (1);Cold-shock conserved site (1);	0.000000	0.85682	D	0.000000	T	0.69548	0.3123	L	0.50993	1.605	0.80722	D	1	D;D;P	0.64830	0.994;0.979;0.954	D;D;D	0.78314	0.991;0.973;0.916	T	0.73861	-0.3849	9	0.87932	D	0	-11.4534	16.1616	0.81721	1.0:0.0:0.0:0.0	.	97;51;97	E9PGZ0;O75534;G5E9Q2	.;CSDE1_HUMAN;.	L	51;97;51;51;97;51;51	.	ENSP00000261443:F51L	F	-	1	0	CSDE1	115083884	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.962000	0.93254	2.218000	0.71995	0.377000	0.23210	TTC	.	.		0.378	CSDE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033397.1	NM_007158		G	115282361	A	G	115282361	3	3	255	1	0	0	0	0	1	0	0	0	3931	72	3	2	2317	2	CSDE1	1	115282361	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	599950	115282361	133968260	52	35397										
TRIM45	80263	hgsc.bcm.edu	37	chr1	117661332	117661332	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	atgggcttcccaatccggctGtagcctttcaagtcttttag	9	11	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:117661332G>T	ENST00000256649.4	-	2	1072	c.546C>A	c.(544-546)taC>taA	p.Y182*	TRIM45_ENST00000369461.3_Nonsense_Mutation_p.Y125*|TRIM45_ENST00000369464.3_Nonsense_Mutation_p.Y182*	NM_025188.3	NP_079464.2	Q9H8W5	TRI45_HUMAN	tripartite motif containing 45	182					bone development (GO:0060348)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(9)|prostate(1)	23	Lung SC(450;0.225)	all_cancers(81;0.000979)|all_lung(203;7.65e-05)|all_epithelial(167;0.000134)|Lung NSC(69;0.000389)		Lung(183;0.0537)|Colorectal(144;0.172)|LUSC - Lung squamous cell carcinoma(189;0.187)		CAATCCGGCTGTAGCCTTTCA	0.517																																					p.Y182X		Atlas-SNP	.											.	TRIM45	55	.	0			c.C546A						.						88	94	92					1																	117661332		2186	4265	6451	SO:0001587	stop_gained	80263	exon2			CCGGCTGTAGCCT		CCDS893.1, CCDS44200.1	1p13.1	2011-04-20	2011-01-25		ENSG00000134253	ENSG00000134253		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19018	protein-coding gene	gene with protein product		609318	"tripartite motif-containing 45"			15351693	Standard	NM_025188		Approved	FLJ13181, RNF99	uc001egz.2	Q9H8W5	OTTHUMG00000012119	ENST00000256649.4:c.546C>A	chr1.hg19:g.117661332G>T	ENSP00000256649:p.Tyr182*	137.0	0.0		87.0	4.0	NM_001145635	Q53GN0|Q5T2K4|Q5T2K5|Q8IYV6	Nonsense_Mutation	SNP	ENST00000256649.4	hg19	CCDS893.1	.	.	.	.	.	.	.	.	.	.	G	38	6.693022	0.97768	.	.	ENSG00000134253	ENST00000256649;ENST00000369464;ENST00000369461	.	.	.	5.32	5.32	0.75619	.	0.527257	0.21274	N	0.077263	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	-16.2132	18.1728	0.89752	0.0:0.0:1.0:0.0	.	.	.	.	X	182;182;125	.	ENSP00000256649:Y182X	Y	-	3	2	TRIM45	117462855	1.000000	0.71417	1.000000	0.80357	0.306000	0.27790	3.056000	0.49923	2.771000	0.95319	0.655000	0.94253	TAC	.	.		0.517	TRIM45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033503.1	NM_025188		T	117661332	G	T	117661332	4	4	255	1	0	0	0	0	0	1	0	0	16535	1372	48	3	1216	3	TRIM45	1	117661332	Nonsense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	2378971	117661332	131589289	53	35398										
SPAG17	200162	hgsc.bcm.edu	37	chr1	118550817	118550817	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctggtgacagtccgaggaccCtcggctacaagcaaatgcaa	11	12	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:118550817C>A	ENST00000336338.5	-	31	4502	c.4437G>T	c.(4435-4437)gaG>gaT	p.E1479D		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1479						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		TCCGAGGACCCTCGGCTACAA	0.507																																					p.E1479D		Atlas-SNP	.											.	SPAG17	263	.	0			c.G4437T						.						82	71	75					1																	118550817		2203	4300	6503	SO:0001583	missense	200162	exon31			AGGACCCTCGGCT		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.4437G>T	chr1.hg19:g.118550817C>A	ENSP00000337804:p.Glu1479Asp	78.0	0.0		77.0	4.0	NM_206996	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	hg19	CCDS899.1	.	.	.	.	.	.	.	.	.	.	C	15.36	2.810801	0.50421	.	.	ENSG00000155761	ENST00000336338	T	0.19806	2.12	5.53	0.226	0.15353	.	0.547480	0.20513	N	0.090843	T	0.06690	0.0171	L	0.54323	1.7	0.09310	N	1	B	0.17268	0.021	B	0.18263	0.021	T	0.29941	-0.9995	10	0.54805	T	0.06	.	5.3301	0.15928	0.0:0.1566:0.2802:0.5631	.	1479	Q6Q759	SPG17_HUMAN	D	1479	ENSP00000337804:E1479D	ENSP00000337804:E1479D	E	-	3	2	SPAG17	118352340	0.002000	0.14202	0.000000	0.03702	0.004000	0.04260	0.045000	0.14013	0.137000	0.18759	-0.339000	0.08088	GAG	.	.		0.507	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		A	118550817	C	A	118550817	3	1	255	1	0	0	0	0	1	0	0	0	14994	680	24	3	2306	3	SPAG17	1	118550817	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	889485	118550817	130699804	54	35399										
CHD1L	9557	hgsc.bcm.edu	37	chr1	146724367	146724367	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gctgtatcctgggagatgagAtgggcctggggaagacctgc	17	8	0	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:146724367A>G	ENST00000369258.4	+	2	237	c.217A>G	c.(217-219)Atg>Gtg	p.M73V	CHD1L_ENST00000467213.1_3'UTR|CHD1L_ENST00000361293.5_Intron|CHD1L_ENST00000431239.1_Missense_Mutation_p.M73V|RP11-337C18.10_ENST00000606856.1_RNA|CHD1L_ENST00000369259.3_Intron	NM_001256336.1|NM_004284.4|NM_024568.2	NP_001243265.1|NP_004275.4|NP_078844.2	Q86WJ1	CHD1L_HUMAN	chromodomain helicase DNA binding protein 1-like	73	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|nucleotide binding (GO:0000166)			breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(923;0.0487)					GGGAGATGAGATGGGCCTGGG	0.527																																					p.M73V		Atlas-SNP	.											.	CHD1L	72	.	0			c.A217G						.						119	102	108					1																	146724367		2203	4300	6503	SO:0001583	missense	9557	exon2			GATGAGATGGGCC	AF054177	CCDS927.1, CCDS58021.1, CCDS58022.1, CCDS72882.1	1q21.1	2008-02-05			ENSG00000131778	ENSG00000131778			1916	protein-coding gene	gene with protein product		613039				9653160	Standard	NM_004284		Approved	ALC1	uc001epm.5	Q86WJ1	OTTHUMG00000150271	ENST00000369258.4:c.217A>G	chr1.hg19:g.146724367A>G	ENSP00000358262:p.Met73Val	99.0	0.0		120.0	5.0	NM_004284	A5YM64|B4DDE1|B5MDZ7|Q53EZ3|Q5VXX7|Q6DD94|Q6PK83|Q86XH3|Q96HF7|Q96SP3|Q9BVJ1|Q9NVV8	Missense_Mutation	SNP	ENST00000369258.4	hg19	CCDS927.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.194011	0.78902	.	.	ENSG00000131778	ENST00000431239;ENST00000369258;ENST00000254086	D;D	0.93659	-3.26;-3.26	5.23	5.23	0.72850	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.85682	D	0.000000	D	0.97427	0.9158	H	0.97158	3.95	0.80722	D	1	D;D	0.89917	0.982;1.0	D;D	0.87578	0.961;0.998	D	0.98358	1.0547	10	0.87932	D	0	.	11.528	0.50591	1.0:0.0:0.0:0.0	.	73;73	Q86WJ1-2;Q86WJ1	.;CHD1L_HUMAN	V	73;73;35	ENSP00000389031:M73V;ENSP00000358262:M73V	ENSP00000254086:M35V	M	+	1	0	CHD1L	145190991	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.998000	0.88491	1.975000	0.57531	0.533000	0.62120	ATG	.	.		0.527	CHD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040377.1	NM_004284		G	146724367	A	G	146724367	3	3	255	1	0	0	0	0	1	0	0	0	3326	333	12	2	223	2	CHD1L	1	146724367	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	28173550	146724367	102526254	55	35400										
DENND4B	9909	hgsc.bcm.edu	37	chr1	153906108	153906108	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aggagtgagcagctgttggaGgcgggcacccagccctcgtc	16	12	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:153906108G>A	ENST00000361217.4	-	20	3599	c.3181C>T	c.(3181-3183)Ctc>Ttc	p.L1061F	DENND4B_ENST00000474386.1_5'Flank	NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	1061					positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab protein signal transduction (GO:0032483)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	36	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			AGCTGTTGGAGGCGGGCACCC	0.711																																					p.L1061F		Atlas-SNP	.											.	DENND4B	210	.	0			c.C3181T						.						5	8	7					1																	153906108		1897	4013	5910	SO:0001583	missense	9909	exon20			GTTGGAGGCGGGC	AB007945	CCDS44228.1	1q21.3	2012-10-03	2006-01-27	2006-01-27	ENSG00000198837	ENSG00000198837		"DENN/MADD domain containing"	29044	protein-coding gene	gene with protein product			"KIAA0476"	KIAA0476		9455484, 12906859	Standard	NM_014856		Approved		uc001fdd.1	O75064	OTTHUMG00000037157	ENST00000361217.4:c.3181C>T	chr1.hg19:g.153906108G>A	ENSP00000354597:p.Leu1061Phe	220.0	0.0		379.0	219.0	NM_014856	Q5T4K0	Missense_Mutation	SNP	ENST00000361217.4	hg19	CCDS44228.1	.	.	.	.	.	.	.	.	.	.	G	14.29	2.490643	0.44249	.	.	ENSG00000198837	ENST00000361217;ENST00000368646	T;T	0.13538	2.84;2.58	5.09	4.12	0.48240	.	0.628844	0.16048	N	0.232095	T	0.04182	0.0116	L	0.27053	0.805	0.42662	D	0.993486	B	0.32968	0.392	B	0.27076	0.076	T	0.26780	-1.0093	10	0.56958	D	0.05	-18.3115	11.4825	0.50333	0.0:0.0:0.6125:0.3875	.	1061	O75064	DEN4B_HUMAN	F	1061;1072	ENSP00000354597:L1061F;ENSP00000357635:L1072F	ENSP00000354597:L1061F	L	-	1	0	DENND4B	152172732	0.997000	0.39634	1.000000	0.80357	0.940000	0.58332	1.030000	0.30153	1.191000	0.43056	0.462000	0.41574	CTC	.	.		0.711	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806		A	153906108	G	A	153906108	3	1	255	1	0	0	0	0	1	0	0	0	4436	1000	35	3	1345	3	DENND4B	1	153906108	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	7181741	153906108	95344513	56	35401										
ARHGEF11	9826	hgsc.bcm.edu	37	chr1	156908262	156908262	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggcccaggctctgactggccActctctggtagtgcagggac	14	13	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:156908262A>G	ENST00000361409.2	-	37	4762	c.4020T>C	c.(4018-4020)agT>agC	p.S1340S	ARHGEF11_ENST00000487682.1_5'UTR|ARHGEF11_ENST00000315174.8_Silent_p.S756S|MIR765_ENST00000390226.1_RNA|ARHGEF11_ENST00000368194.3_Silent_p.S1380S	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	1340					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cytokinesis (GO:0000910)|establishment of cell polarity (GO:0030010)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)|striated muscle contraction (GO:0006941)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(27)|ovary(4)|pancreas(2)|pleura(1)|prostate(4)|skin(7)|stomach(1)|urinary_tract(2)	81	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CTGACTGGCCACTCTCTGGTA	0.557																																					p.S1380S		Atlas-SNP	.											.	ARHGEF11	168	.	0			c.T4140C						.						92	82	86					1																	156908262		2203	4300	6503	SO:0001819	synonymous_variant	9826	exon38			CTGGCCACTCTCT	AB002378	CCDS1162.1, CCDS1163.1	1q21	2011-11-16			ENSG00000132694	ENSG00000132694		"Rho guanine nucleotide exchange factors"	14580	protein-coding gene	gene with protein product		605708				10526156, 9205841	Standard	NM_014784		Approved	KIAA0380, GTRAP48, PDZ-RHOGEF	uc001fqn.3	O15085	OTTHUMG00000041292	ENST00000361409.2:c.4020T>C	chr1.hg19:g.156908262A>G		106.0	0.0		117.0	6.0	NM_198236	D3DVD0|Q5VY40|Q6PFW2	Silent	SNP	ENST00000361409.2	hg19	CCDS1162.1																																																																																			.	.		0.557	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236		G	156908262	A	G	156908262	2	3	255	1	0	0	0	0	0	0	0	1	896	156	6	2		2	ARHGEF11	1	156908262	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	3002154	156908262	92342359	57	35402										
CCDC19	25790	hgsc.bcm.edu	37	chr1	159846466	159846466	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cctctgtttccatcttcttcCgcgcattttccttttccttt	3	15	3	0	rs377248471		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:159846466C>T	ENST00000368099.4	-	10	1296	c.1232G>A	c.(1231-1233)cGg>cAg	p.R411Q	CCDC19_ENST00000426543.2_Missense_Mutation_p.R326Q|CCDC19_ENST00000476696.1_5'UTR	NM_012337.2	NP_036469.2														endometrium(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	26	all_hematologic(112;0.0597)		BRCA - Breast invasive adenocarcinoma(70;0.151)			CATCTTCTTCCGCGCATTTTC	0.572																																					p.R411Q		Atlas-SNP	.											.	CCDC19	79	.	0			c.G1232A						.	T	GLN/ARG	0,4406		0,0,2203	134	105	115		1232	2.7	1	1		115	1,8599		0,1,4299	no	missense	CCDC19	NM_012337.2	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	411/552	159846466	1,13005	2203	4300	6503	SO:0001583	missense	25790	exon10			TTCTTCCGCGCAT																												ENST00000368099.4:c.1232G>A	chr1.hg19:g.159846466C>T	ENSP00000357079:p.Arg411Gln	851.0	1.0		1191.0	239.0	NM_012337		Missense_Mutation	SNP	ENST00000368099.4	hg19	CCDS30914.1	.	.	.	.	.	.	.	.	.	.	N	0.937	-0.710762	0.03230	0.0	1.16E-4	ENSG00000213085	ENST00000368099;ENST00000426543	T;T	0.09445	2.98;2.98	5.16	2.68	0.31781	.	0.524332	0.21595	N	0.072030	T	0.00845	0.0028	N	0.01297	-0.9	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48281	-0.9049	9	.	.	.	-30.5358	6.4566	0.21934	0.1391:0.0828:0.0:0.778	.	411	Q9UL16	CCD19_HUMAN	Q	411;326	ENSP00000357079:R411Q;ENSP00000403044:R326Q	.	R	-	2	0	CCDC19	158113090	0.454000	0.25728	0.985000	0.45067	0.362000	0.29581	0.222000	0.17699	0.900000	0.36469	-0.599000	0.04106	CGG	.	.		0.572	CCDC19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085979.1			T	159846466	C	T	159846466	3	4	255	1	0	0	0	0	1	0	0	0	2797	652	23	1	435	1	CCDC19	1	159846466	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	2938204	159846466	89404155	58	35403										
PIGM	93183	hgsc.bcm.edu	37	chr1	160000609	160000609	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	acgaggtctctgtaataggcGaaagacacagctgaaagcaa	11	8	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:160000609G>T	ENST00000368090.2	-	1	1174	c.921C>A	c.(919-921)ttC>ttA	p.F307L		NM_145167.2	NP_660150.1	Q9H3S5	PIGM_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class M	307					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	mannosyltransferase activity (GO:0000030)			kidney(1)|large_intestine(4)|lung(9)|ovary(2)|skin(1)	17	all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			TGTAATAGGCGAAAGACACAG	0.428																																					p.F307L		Atlas-SNP	.											.	PIGM	27	.	0			c.C921A						.						118	129	125					1																	160000609		2203	4300	6503	SO:0001583	missense	93183	exon1			ATAGGCGAAAGAC	AB028127	CCDS1192.1	1q23.2	2013-02-26	2006-06-28		ENSG00000143315	ENSG00000143315		"Dolichyl D-mannosyl phosphate dependent mannosyltransferases", "Phosphatidylinositol glycan anchor biosynthesis"	18858	protein-coding gene	gene with protein product	"GPI mannosyltransferase 1", "DPM:GlcN-(acyl-)PI mannosyltransferase", "dol-P-Man dependent GPI mannosyltransferase"	610273	"phosphatidylinositol glycan, class M"			11226175	Standard	NM_145167		Approved	GPI-MT-I	uc001fuv.1	Q9H3S5	OTTHUMG00000024081	ENST00000368090.2:c.921C>A	chr1.hg19:g.160000609G>T	ENSP00000357069:p.Phe307Leu	75.0	0.0		94.0	4.0	NM_145167		Missense_Mutation	SNP	ENST00000368090.2	hg19	CCDS1192.1	.	.	.	.	.	.	.	.	.	.	G	11.48	1.649840	0.29336	.	.	ENSG00000143315	ENST00000368090	T	0.38401	1.14	5.35	-3.78	0.04333	.	0.515563	0.20386	N	0.093346	T	0.03608	0.0103	N	0.05351	-0.065	0.22378	N	0.999154	B	0.11235	0.004	B	0.17722	0.019	T	0.36114	-0.9761	9	.	.	.	-16.7466	1.8926	0.03251	0.3216:0.3505:0.2087:0.1192	.	307	Q9H3S5	PIGM_HUMAN	L	307	ENSP00000357069:F307L	.	F	-	3	2	PIGM	158267233	0.177000	0.23109	0.298000	0.25002	0.989000	0.77384	-0.159000	0.10056	-0.272000	0.09259	0.462000	0.41574	TTC	.	.		0.428	PIGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060643.2	NM_145167		T	160000609	G	T	160000609	3	4	255	1	0	0	0	0	1	0	0	0	11901	1049	37	1	354	1	PIGM	1	160000609	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	154143	160000609	89250012	59	35404										
C1orf9	51430	hgsc.bcm.edu	37	chr1	172525148	172525148	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	atctacctcagaaatcactcCaatctcaaagcttgagtaag	5	11	4	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:172525148C>A	ENST00000263688.3	+	4	647	c.428C>A	c.(427-429)cCa>cAa	p.P143Q	SUCO_ENST00000608151.1_Missense_Mutation_p.P302Q|SUCO_ENST00000367723.4_Missense_Mutation_p.P301Q|SUCO_ENST00000610051.1_Missense_Mutation_p.P106Q	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor	143					multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)											GAAATCACTCCAATCTCAAAG	0.348																																					p.P143Q		Atlas-SNP	.											.	.	.	.	0			c.C428A						.						60	56	58					1																	172525148		2203	4299	6502	SO:0001583	missense	51430	exon4			TCACTCCAATCTC	AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"SUN-like protein 1", "osteopotentia"		"chromosome 1 open reading frame 9"	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839	ENST00000263688.3:c.428C>A	chr1.hg19:g.172525148C>A	ENSP00000263688:p.Pro143Gln	71.0	0.0		98.0	4.0	NM_014283	B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Missense_Mutation	SNP	ENST00000263688.3	hg19	CCDS1303.1	.	.	.	.	.	.	.	.	.	.	C	19.33	3.807431	0.70797	.	.	ENSG00000094975	ENST00000367723;ENST00000263688	.	.	.	5.76	4.83	0.62350	.	0.145724	0.48767	D	0.000164	T	0.39172	0.1068	L	0.32530	0.975	0.36983	D	0.894405	B;P;D;P	0.54397	0.014;0.916;0.966;0.916	B;P;P;P	0.50754	0.005;0.649;0.641;0.506	T	0.38222	-0.9671	9	0.45353	T	0.12	-5.8702	14.095	0.65016	0.1517:0.8482:0.0:0.0	.	106;143;302;143	B4DYM4;B4DZJ3;Q5H945;Q9UBS9	.;.;.;OSPT_HUMAN	Q	302;143	.	ENSP00000263688:P143Q	P	+	2	0	C1orf9	170791771	1.000000	0.71417	0.951000	0.38953	0.991000	0.79684	3.746000	0.55127	1.527000	0.49086	0.655000	0.94253	CCA	.	.		0.348	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227		A	172525148	C	A	172525148	3	1	255	1	0	0	0	0	1	0	0	0	2069	594	21	3	442	3	C1orf9	1	172525148	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	12524539	172525148	76725473	60	35405										
CEP350	9857	hgsc.bcm.edu	37	chr1	180013222	180013222	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcactctctcagagtaaagaAgggacccttgactcaaagca	8	11	4	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:180013222A>G	ENST00000367607.3	+	21	4954	c.4536A>G	c.(4534-4536)gaA>gaG	p.E1512E		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	1512	Ser-rich.				microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						AGAGTAAAGAAGGGACCCTTG	0.323																																					p.E1512E		Atlas-SNP	.											.	CEP350	418	.	0			c.A4536G						.						49	44	46					1																	180013222		2197	4283	6480	SO:0001819	synonymous_variant	9857	exon21			TAAAGAAGGGACC	AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"centrosome associated protein 350"					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.4536A>G	chr1.hg19:g.180013222A>G		70.0	0.0		96.0	5.0	NM_014810	O75068|Q8TDK3|Q8WY20	Silent	SNP	ENST00000367607.3	hg19	CCDS1336.1	.	.	.	.	.	.	.	.	.	.	A	4.179	0.031740	0.08101	.	.	ENSG00000135837	ENST00000418229	.	.	.	5.69	0.932	0.19466	.	.	.	.	.	T	0.55049	0.1896	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45352	-0.9267	4	.	.	.	.	7.9455	0.29985	0.5415:0.0:0.4585:0.0	.	.	.	.	G	121	.	.	R	+	1	2	CEP350	178279845	1.000000	0.71417	0.897000	0.35233	0.414000	0.31173	1.396000	0.34531	0.124000	0.18369	0.454000	0.30748	AGG	.	.		0.323	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810		G	180013222	A	G	180013222	2	3	255	1	0	0	0	0	0	0	0	1	3256	69	3	2		2	CEP350	1	180013222	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	7488074	180013222	69237399	61	35406										
CRB1	23418	hgsc.bcm.edu	37	chr1	197391072	197391072	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccacaggccctatgaaggccCcaactgtctgagaggtgaga	12	12	1	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:197391072C>A	ENST00000367400.3	+	6	2249	c.2114C>A	c.(2113-2115)cCc>cAc	p.P705H	CRB1_ENST00000543483.1_3'UTR|CRB1_ENST00000538660.1_Missense_Mutation_p.P705H|CRB1_ENST00000367399.2_Missense_Mutation_p.P593H|CRB1_ENST00000367397.1_Missense_Mutation_p.P86H|CRB1_ENST00000544212.1_Missense_Mutation_p.P186H|CRB1_ENST00000535699.1_Missense_Mutation_p.P636H	NM_201253.2	NP_957705.1	P82279	CRUM1_HUMAN	crumbs family member 1, photoreceptor morphogenesis associated	705	EGF-like 12. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|plasma membrane organization (GO:0007009)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(13)|kidney(4)|large_intestine(21)|lung(58)|ovary(7)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	132						TATGAAGGCCCCAACTGTCTG	0.522																																					p.P705H		Atlas-SNP	.											.	CRB1	284	.	0			c.C2114A						.						47	49	49					1																	197391072		2195	4300	6495	SO:0001583	missense	23418	exon6			AAGGCCCCAACTG		CCDS1390.1, CCDS53454.1, CCDS58052.1, CCDS58053.1	1q31-q32.1	2014-02-06	2014-02-06		ENSG00000134376	ENSG00000134376			2343	protein-coding gene	gene with protein product		604210	"crumbs (Drosophila) homolog 1", "crumbs homolog 1 (Drosophila)"	RP12		10373321, 10508521	Standard	NM_201253		Approved	LCA8	uc001gtz.3	P82279	OTTHUMG00000035663	ENST00000367400.3:c.2114C>A	chr1.hg19:g.197391072C>A	ENSP00000356370:p.Pro705His	67.0	0.0		92.0	4.0	NM_001257966	A2A308|B7Z5T2|B9EG71|Q5K3A6|Q5TC28|Q5VUT1|Q6N027|Q8WWY0|Q8WWY1	Missense_Mutation	SNP	ENST00000367400.3	hg19	CCDS1390.1	.	.	.	.	.	.	.	.	.	.	C	3.507	-0.100556	0.06967	.	.	ENSG00000134376	ENST00000535699;ENST00000538660;ENST00000367400;ENST00000367399;ENST00000544212;ENST00000367397;ENST00000367401	D;D;D;D;D;D	0.92495	-3.05;-3.05;-3.05;-3.05;-3.05;-3.05	5.65	-4.08	0.03963	Concanavalin A-like lectin/glucanase, subgroup (1);EGF (1);Epidermal growth factor-like (1);EGF-like region, conserved site (2);Epidermal growth factor-like, type 3 (1);	.	.	.	.	D	0.88149	0.6359	L	0.37750	1.13	0.09310	N	0.999997	B;P;P;B;P	0.44281	0.001;0.776;0.776;0.012;0.831	B;P;P;B;P	0.50109	0.005;0.621;0.471;0.032;0.631	T	0.80030	-0.1553	9	0.33940	T	0.23	.	6.2783	0.20993	0.105:0.4879:0.3135:0.0935	.	705;636;593;354;705	B7Z5T2;F5H0L2;P82279-3;P82279-4;P82279	.;.;.;.;CRUM1_HUMAN	H	636;705;705;593;186;86;354	ENSP00000438786:P636H;ENSP00000438091:P705H;ENSP00000356370:P705H;ENSP00000356369:P593H;ENSP00000444556:P186H;ENSP00000356367:P86H	ENSP00000356367:P86H	P	+	2	0	CRB1	195657695	0.209000	0.23505	0.001000	0.08648	0.011000	0.07611	0.739000	0.26173	-0.731000	0.04862	0.650000	0.86243	CCC	.	.		0.522	CRB1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086565.2	NM_201253		A	197391072	C	A	197391072	3	1	255	1	0	0	0	0	1	0	0	0	3850	623	22	3	2136	3	CRB1	1	197391072	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	17377850	197391072	51859549	62	35407										
CR1L	1379	hgsc.bcm.edu	37	chr1	207890960	207890960	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctcattggggagagcaccatCcgccgcacaagtgaacctca	10	14	2	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:207890960C>T	ENST00000508064.2	+	11	1626	c.1566C>T	c.(1564-1566)atC>atT	p.I522I		NM_175710.1	NP_783641.1	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like	522	Sushi 8. {ECO:0000255|PROSITE- ProRule:PRU00302}.					cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|receptor complex (GO:0043235)				endometrium(1)|kidney(1)|large_intestine(2)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						AGAGCACCATCCGCCGCACAA	0.542																																					p.I522I		Atlas-SNP	.											.	CR1L	97	.	0			c.C1566T						.						152	150	151					1																	207890960		1960	4142	6102	SO:0001819	synonymous_variant	1379	exon11			CACCATCCGCCGC	AY114160	CCDS44310.1	1q32.1	2008-02-05			ENSG00000197721	ENSG00000197721		"Complement system"	2335	protein-coding gene	gene with protein product		605886				2295627	Standard	NM_175710		Approved		uc001hga.4	Q2VPA4	OTTHUMG00000036354	ENST00000508064.2:c.1566C>T	chr1.hg19:g.207890960C>T		361.0	0.0		546.0	77.0	NM_175710	Q32MC9|Q8NEU7	Silent	SNP	ENST00000508064.2	hg19	CCDS44310.1																																																																																			.	.		0.542	CR1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390247.1	XM_114735		T	207890960	C	T	207890960	2	4	255	1	0	0	0	0	0	0	0	1	3843	845	30	3		3	CR1L	1	207890960	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	10499888	207890960	41359661	63	35408										
PLXNA2	5362	hgsc.bcm.edu	37	chr1	208202173	208202173	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctgtcctgagggtgctactgAcctctccacccagctcttgt	9	15	2	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:208202173A>G	ENST00000367033.3	-	30	6196		c.e30+1		PLXNA2_ENST00000483048.1_Splice_Site	NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2						axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		GGTGCTACTGACCTCTCCACC	0.577																																					.		Atlas-SNP	.											.	PLXNA2	178	.	0			c.5438+2T>C						.						85	80	82					1																	208202173		2203	4300	6503	SO:0001630	splice_region_variant	5362	exon31			CTACTGACCTCTC	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"Plexins"	9100	protein-coding gene	gene with protein product	"plexin 2", "plexin-A2", "semaphorin receptor OCT", "transmembrane protein OCT"	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.5438+1T>C	chr1.hg19:g.208202173A>G		81.0	0.0		84.0	4.0	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Splice_Site	SNP	ENST00000367033.3	hg19	CCDS31013.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.295700	0.81025	.	.	ENSG00000076356	ENST00000367033	.	.	.	5.36	5.36	0.76844	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3914	0.74747	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PLXNA2	206268796	1.000000	0.71417	0.993000	0.49108	0.976000	0.68499	8.999000	0.93557	2.042000	0.60477	0.533000	0.62120	.	.	.		0.577	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179	Intron	G	208202173	A	G	208202173	5	3	255	1	0	0	0	0	0	0	1	0	12129	289	10	2	256	2	PLXNA2	1	208202173	Splice_Site	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	311213	208202173	41048448	64	35409										
PROX1	5629	hgsc.bcm.edu	37	chr1	214170676	214170676	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	atctatgacagcactgattcGgaaaatgatgaagatggtaa	10	5	1	5			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:214170676G>T	ENST00000366958.4	+	2	1406	c.798G>T	c.(796-798)tcG>tcT	p.S266S	PROX1_ENST00000498508.2_Silent_p.S266S|PROX1_ENST00000261454.4_Silent_p.S266S|PROX1_ENST00000435016.1_Silent_p.S266S	NM_001270616.1	NP_001257545.1	Q92786	PROX1_HUMAN	prospero homeobox 1	266					aorta smooth muscle tissue morphogenesis (GO:0060414)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|brain development (GO:0007420)|cell fate determination (GO:0001709)|cerebellar granule cell differentiation (GO:0021707)|dentate gyrus development (GO:0021542)|dorsal spinal cord development (GO:0021516)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocardium formation (GO:0060214)|hepatocyte cell migration (GO:0002194)|hepatocyte differentiation (GO:0070365)|hepatocyte proliferation (GO:0072574)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|lens fiber cell morphogenesis (GO:0070309)|liver development (GO:0001889)|lung development (GO:0030324)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|negative regulation of bile acid biosynthetic process (GO:0070858)|negative regulation of cell proliferation (GO:0008285)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|olfactory placode formation (GO:0030910)|optic placode formation involved in camera-type eye formation (GO:0046619)|otic placode formation (GO:0043049)|pancreas development (GO:0031016)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell cycle checkpoint (GO:1901978)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of forebrain neuron differentiation (GO:2000979)|positive regulation of heart growth (GO:0060421)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of gene expression (GO:0010468)|regulation of transcription involved in lymphatic endothelial cell fate commitment (GO:0060849)|response to nutrient levels (GO:0031667)|retina morphogenesis in camera-type eye (GO:0060042)|skeletal muscle thin filament assembly (GO:0030240)|venous blood vessel morphogenesis (GO:0048845)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular cardiac myofibril assembly (GO:0055005)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DBD domain binding (GO:0050692)|DNA binding (GO:0003677)|LBD domain binding (GO:0050693)|ligand-dependent nuclear receptor binding (GO:0016922)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|prostate(2)|skin(4)	47				OV - Ovarian serous cystadenocarcinoma(81;0.0179)|all cancers(67;0.0488)|GBM - Glioblastoma multiforme(131;0.188)|Epithelial(68;0.219)		GCACTGATTCGGAAAATGATG	0.522																																					p.S266S		Atlas-SNP	.											.	PROX1	124	.	0			c.G798T						.						58	57	57					1																	214170676		2203	4300	6503	SO:0001819	synonymous_variant	5629	exon2			TGATTCGGAAAAT	U44060	CCDS31021.1	1q41	2011-06-20	2007-06-01		ENSG00000117707	ENSG00000117707		"Homeoboxes / PROS class"	9459	protein-coding gene	gene with protein product		601546	"prospero-related homeobox 1"			8812486	Standard	NM_002763		Approved		uc001hkg.2	Q92786	OTTHUMG00000036946	ENST00000366958.4:c.798G>T	chr1.hg19:g.214170676G>T		69.0	0.0		88.0	4.0	NM_001270616	A6NK29|A8K2B1|Q5SW76|Q8TB91	Silent	SNP	ENST00000366958.4	hg19	CCDS31021.1																																																																																			.	.		0.522	PROX1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089727.6	NM_002763		T	214170676	G	T	214170676	2	4	255	1	0	0	0	0	0	0	0	1	12572	1103	39	1		1	PROX1	1	214170676	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	5968503	214170676	35079945	65	35410										
TGFB2	7042	hgsc.bcm.edu	37	chr1	218520057	218520057	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttaaaaaatgcactactgtgTgctgagcgcttttctgatcc	8	9	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:218520057T>C	ENST00000366930.4	+	1	481	c.14T>C	c.(13-15)gTg>gCg	p.V5A	RP11-224O19.2_ENST00000414452.1_RNA|TGFB2_ENST00000366929.4_Missense_Mutation_p.V5A	NM_003238.3	NP_003229.1	P61812	TGFB2_HUMAN	transforming growth factor, beta 2	5					activation of protein kinase activity (GO:0032147)|angiogenesis (GO:0001525)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell proliferation (GO:0060038)|cardioblast differentiation (GO:0010002)|cartilage condensation (GO:0001502)|catagen (GO:0042637)|cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|collagen fibril organization (GO:0030199)|dopamine biosynthetic process (GO:0042416)|embryo development (GO:0009790)|embryonic digestive tract development (GO:0048566)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|face morphogenesis (GO:0060325)|generation of neurons (GO:0048699)|glial cell migration (GO:0008347)|hair follicle development (GO:0001942)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hemopoiesis (GO:0030097)|menstrual cycle phase (GO:0022601)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of immune response (GO:0050777)|negative regulation of macrophage cytokine production (GO:0010936)|neuron development (GO:0048666)|neuron fate commitment (GO:0048663)|neutrophil chemotaxis (GO:0030593)|odontogenesis (GO:0042476)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of activation-induced cell death of T cells (GO:0070237)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of catagen (GO:0051795)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of gene expression (GO:0010628)|positive regulation of heart contraction (GO:0045823)|positive regulation of immune response (GO:0050778)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of ossification (GO:0045778)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein secretion (GO:0050714)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein phosphorylation (GO:0006468)|regulation of transforming growth factor beta2 production (GO:0032909)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to progesterone (GO:0032570)|response to wounding (GO:0009611)|salivary gland morphogenesis (GO:0007435)|signal transduction by phosphorylation (GO:0023014)|SMAD protein import into nucleus (GO:0007184)|somatic stem cell division (GO:0048103)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	axon (GO:0030424)|endosome (GO:0005768)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|platelet alpha granule lumen (GO:0031093)	beta-amyloid binding (GO:0001540)|cytokine activity (GO:0005125)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta receptor binding (GO:0005160)|type II transforming growth factor beta receptor binding (GO:0005114)			breast(1)|endometrium(1)|large_intestine(11)|lung(15)|upper_aerodigestive_tract(2)|urinary_tract(1)	31				all cancers(67;0.0459)|OV - Ovarian serous cystadenocarcinoma(81;0.049)|GBM - Glioblastoma multiforme(131;0.0776)		CACTACTGTGTGCTGAGCGCT	0.408																																					p.V5A		Atlas-SNP	.											.	TGFB2	102	.	0			c.T14C						.						60	60	60					1																	218520057		2203	4300	6503	SO:0001583	missense	7042	exon1			ACTGTGTGCTGAG	M19154	CCDS1521.1, CCDS44318.1	1q41	2014-01-30			ENSG00000092969	ENSG00000092969		"Endogenous ligands"	11768	protein-coding gene	gene with protein product	"prepro-transforming growth factor beta-2"	190220					Standard	NM_003238		Approved		uc001hln.3	P61812	OTTHUMG00000039521	ENST00000366930.4:c.14T>C	chr1.hg19:g.218520057T>C	ENSP00000355897:p.Val5Ala	47.0	0.0		78.0	4.0	NM_003238	B4DKC5|P08112|Q15579|Q15581|Q4VAV9	Missense_Mutation	SNP	ENST00000366930.4	hg19	CCDS1521.1	.	.	.	.	.	.	.	.	.	.	T	17.56	3.420489	0.62622	.	.	ENSG00000092969	ENST00000366930;ENST00000366929	T;T	0.75589	-0.82;-0.95	5.8	5.8	0.92144	.	0.325329	0.32852	N	0.005570	T	0.59865	0.2225	N	0.17474	0.49	0.41815	D	0.98999	B;B;P	0.41080	0.0;0.0;0.737	B;B;B	0.39503	0.004;0.001;0.301	T	0.59931	-0.7361	10	0.13853	T	0.58	.	16.1269	0.81402	0.0:0.0:0.0:1.0	.	5;5;6	P61812-2;P61812;Q59EG9	.;TGFB2_HUMAN;.	A	5	ENSP00000355897:V5A;ENSP00000355896:V5A	ENSP00000355896:V5A	V	+	2	0	TGFB2	216586680	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.485000	0.81204	2.203000	0.70933	0.482000	0.46254	GTG	.	.		0.408	TGFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095359.2	NM_003238		C	218520057	T	C	218520057	3	2	255	1	0	0	0	0	1	0	0	0	15833	1696	59	2	16	2	TGFB2	1	218520057	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	4349381	218520057	30730564	66	35411										
EPRS	2058	hgsc.bcm.edu	37	chr1	220170686	220170686	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccttaaaaggagcagaggtcTaccaagagagaaaaccaaaa	9	8	1	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:220170686T>C	ENST00000366923.3	-	18	2451		c.e18-2			NM_004446.2	NP_004437.2	P07814	SYEP_HUMAN	glutamyl-prolyl-tRNA synthetase						cellular response to interferon-gamma (GO:0071346)|gene expression (GO:0010467)|glutamyl-tRNA aminoacylation (GO:0006424)|negative regulation of translation (GO:0017148)|prolyl-tRNA aminoacylation (GO:0006433)|protein complex assembly (GO:0006461)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|GAIT complex (GO:0097452)|membrane (GO:0016020)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|glutamate-tRNA ligase activity (GO:0004818)|proline-tRNA ligase activity (GO:0004827)|RNA stem-loop binding (GO:0035613)			breast(2)|endometrium(11)|kidney(2)|large_intestine(13)|lung(24)|ovary(1)|prostate(3)|skin(2)|stomach(2)|urinary_tract(3)	63				GBM - Glioblastoma multiforme(131;0.0735)	L-Proline(DB00172)	AGCAGAGGTCTACCAAGAGAG	0.303																																					.		Atlas-SNP	.											.	EPRS	140	.	0			c.2182-2A>G						.						46	47	46					1																	220170686		2174	4287	6461	SO:0001630	splice_region_variant	2058	exon19			GAGGTCTACCAAG	X54326	CCDS31027.1	1q41	2011-07-01			ENSG00000136628	ENSG00000136628	6.1.1.15, 6.1.1.17	"Aminoacyl tRNA synthetases / Class I", "Aminoacyl tRNA synthetases / Class II"	3418	protein-coding gene	gene with protein product	"glutamate tRNA ligase", "proline tRNA ligase"	138295		QPRS, QARS		1988429	Standard	NM_004446		Approved	EARS, PARS, GLUPRORS	uc001hly.1	P07814	OTTHUMG00000037433	ENST00000366923.3:c.2182-2A>G	chr1.hg19:g.220170686T>C		42.0	0.0		49.0	4.0	NM_004446	A0AVA9|B9EGH3|Q05BP6|Q05DF8|Q5DSM1|Q5H9S5|Q6PD57|Q86X73	Splice_Site	SNP	ENST00000366923.3	hg19	CCDS31027.1	.	.	.	.	.	.	.	.	.	.	T	13.51	2.259670	0.39995	.	.	ENSG00000136628	ENST00000366923;ENST00000536921;ENST00000435048	.	.	.	5.62	5.62	0.85841	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.41	0.67109	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	EPRS	218237309	0.960000	0.32886	0.342000	0.25602	0.123000	0.20343	2.287000	0.43505	2.150000	0.67090	0.533000	0.62120	.	.	.		0.303	EPRS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091133.2	NM_004446	Intron	C	220170686	T	C	220170686	5	2	255	1	0	0	0	0	0	0	1	0	5193	1536	53	2	2418	2	EPRS	1	220170686	Splice_Site	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	1650629	220170686	29079935	67	35412										
TMEM63A	9725	hgsc.bcm.edu	37	chr1	226059703	226059703	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	caaccagctcattttcaaagTcttgttgacctgaggaggaa	9	9	3	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:226059703T>C	ENST00000366835.3	-	5	587	c.317A>G	c.(316-318)gAc>gGc	p.D106G		NM_014698.2	NP_055513.2	O94886	CSCL1_HUMAN	transmembrane protein 63A	106					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	nucleotide binding (GO:0000166)			breast(2)|endometrium(3)|large_intestine(5)|lung(6)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24	Breast(184;0.197)					ATTTTCAAAGTCTTGTTGACC	0.458																																					p.D106G		Atlas-SNP	.											.	TMEM63A	75	.	0			c.A317G						.						117	95	102					1																	226059703		2203	4300	6503	SO:0001583	missense	9725	exon5			TCAAAGTCTTGTT		CCDS31042.1	1q42.12	2008-02-05	2005-07-25	2005-07-25	ENSG00000196187	ENSG00000196187			29118	protein-coding gene	gene with protein product			"KIAA0792"	KIAA0792		9872452, 9455484	Standard	NM_014698		Approved		uc001hpm.2	O94886	OTTHUMG00000037442	ENST00000366835.3:c.317A>G	chr1.hg19:g.226059703T>C	ENSP00000355800:p.Asp106Gly	64.0	0.0		92.0	4.0	NM_014698	Q53GI7|Q5TE96|Q8N2U2	Missense_Mutation	SNP	ENST00000366835.3	hg19	CCDS31042.1	.	.	.	.	.	.	.	.	.	.	T	16.05	3.011520	0.54468	.	.	ENSG00000196187	ENST00000366835;ENST00000436966	T	0.46063	0.88	4.97	4.97	0.65823	.	0.171002	0.47455	D	0.000237	T	0.35653	0.0939	L	0.59436	1.845	0.80722	D	1	B;P	0.34699	0.173;0.464	B;B	0.32928	0.102;0.155	T	0.12243	-1.0555	10	0.14252	T	0.57	-28.7201	11.3011	0.49306	0.0:0.0:0.0:1.0	.	106;106	B3KMR6;O94886	.;TM63A_HUMAN	G	106	ENSP00000355800:D106G	ENSP00000355800:D106G	D	-	2	0	TMEM63A	224126326	1.000000	0.71417	0.991000	0.47740	0.997000	0.91878	3.317000	0.51968	2.002000	0.58637	0.448000	0.29417	GAC	.	.		0.458	TMEM63A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091154.2	NM_014698		C	226059703	T	C	226059703	3	2	255	1	0	0	0	0	1	0	0	0	16205	1667	58	2	2186	2	TMEM63A	1	226059703	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	5889017	226059703	23190918	68	35413										
SNAP47	116841	hgsc.bcm.edu	37	chr1	227947130	227947130	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gttagaagatgcattggtgcTcagaagcgcaagaacctctt	11	8	2	4			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:227947130T>C	ENST00000366759.4	+	3	1481	c.1067T>C	c.(1066-1068)cTc>cCc	p.L356P	SNAP47_ENST00000315781.5_Missense_Mutation_p.L356P|SNAP47_ENST00000366760.1_Missense_Mutation_p.L114P	NM_053052.3	NP_444280.2	Q5SQN1	SNP47_HUMAN	synaptosomal-associated protein, 47kDa	356					long-term synaptic potentiation (GO:0060291)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|membrane (GO:0016020)|neuronal cell body (GO:0043025)				endometrium(1)|large_intestine(5)|liver(2)|lung(6)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	17						GCATTGGTGCTCAGAAGCGCA	0.502																																					p.L356P		Atlas-SNP	.											.	SNAP47	42	.	0			c.T1067C						.						137	133	134					1																	227947130		2203	4300	6503	SO:0001583	missense	116841	exon3			TGGTGCTCAGAAG	AY090635	CCDS1562.1	1q42.13	2013-10-11	2008-10-27	2008-10-27	ENSG00000143740	ENSG00000143740			30669	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 142"	C1orf142		16621800	Standard	NM_053052		Approved	SVAP1, SNAP-47	uc001hrf.2	Q5SQN1	OTTHUMG00000037697	ENST00000366759.4:c.1067T>C	chr1.hg19:g.227947130T>C	ENSP00000355721:p.Leu356Pro	22.0	0.0		64.0	4.0	NM_053052	B6EDE0|Q5HYB5|Q5TBZ3|Q8N558|Q8TB31|Q8TCW8|Q8WV46|Q96CQ3|Q96FE1|Q96I66|Q96NU3|Q9BT10|Q9BVB2	Missense_Mutation	SNP	ENST00000366759.4	hg19	CCDS1562.1	.	.	.	.	.	.	.	.	.	.	T	10.99	1.506066	0.26949	.	.	ENSG00000143740	ENST00000366760;ENST00000366759;ENST00000315781	T;T;T	0.49432	0.78;2.09;1.97	5.04	3.92	0.45320	.	0.277555	0.40469	N	0.001087	T	0.36524	0.0970	L	0.42245	1.32	0.22918	N	0.998568	B;B;B;B;B	0.22003	0.002;0.023;0.063;0.028;0.023	B;B;B;B;B	0.22601	0.005;0.023;0.04;0.018;0.023	T	0.19844	-1.0293	10	0.23302	T	0.38	-7.6889	8.8361	0.35113	0.0:0.0886:0.0:0.9114	.	114;356;168;356;114	Q5SQN1-3;Q5SQN1;Q5TBZ4;Q5SQN1-2;Q5SQN1-4	.;SNP47_HUMAN;.;.;.	P	114;356;356	ENSP00000355722:L114P;ENSP00000355721:L356P;ENSP00000314157:L356P	ENSP00000314157:L356P	L	+	2	0	SNAP47	226013753	0.113000	0.22115	0.010000	0.14722	0.074000	0.17049	1.631000	0.37092	0.957000	0.37930	0.459000	0.35465	CTC	.	.		0.502	SNAP47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091961.1	NM_053052		C	227947130	T	C	227947130	3	2	255	1	0	0	0	0	1	0	0	0	14847	1551	54	2	1077	2	SNAP47	1	227947130	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	1887427	227947130	21303491	69	35414										
PCNXL2	80003	hgsc.bcm.edu	37	chr1	233136202	233136202	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggtcgccctcgtggcagatgAccaccttcttctcgaaggac	11	14	2	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:233136202A>G	ENST00000258229.9	-	30	5411	c.5177T>C	c.(5176-5178)gTc>gCc	p.V1726A	PCNXL2_ENST00000344698.2_Missense_Mutation_p.V378A	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	1726						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				GTGGCAGATGACCACCTTCTT	0.627																																					p.V1726A		Atlas-SNP	.											.	PCNXL2	204	.	0			c.T5177C						.						64	66	66					1																	233136202		2030	4179	6209	SO:0001583	missense	80003	exon30			CAGATGACCACCT	AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749			8736	protein-coding gene	gene with protein product			"pecanex (Drosophila)-like 2"			12477932	Standard	NM_014801		Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.5177T>C	chr1.hg19:g.233136202A>G	ENSP00000258229:p.Val1726Ala	77.0	0.0		97.0	4.0	NM_014801	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Missense_Mutation	SNP	ENST00000258229.9	hg19	CCDS44335.1	.	.	.	.	.	.	.	.	.	.	A	34	5.307530	0.95629	.	.	ENSG00000135749	ENST00000344698;ENST00000258229	T;T	0.49720	0.77;0.77	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.73916	0.3648	M	0.89095	3.005	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.81914	0.99;0.995	T	0.79701	-0.1693	10	0.87932	D	0	.	16.1884	0.81971	1.0:0.0:0.0:0.0	.	1726;378	A6NKB5;A6NKB5-3	PCX2_HUMAN;.	A	378;1726	ENSP00000340759:V378A;ENSP00000258229:V1726A	ENSP00000258229:V1726A	V	-	2	0	PCNXL2	231202825	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.948000	0.93006	2.285000	0.76669	0.528000	0.53228	GTC	.	.		0.627	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092480.3	NM_014801		G	233136202	A	G	233136202	3	3	255	1	0	0	0	0	1	0	0	0	11601	275	10	2	1256	2	PCNXL2	1	233136202	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	5189072	233136202	16114419	70	35415										
FMN2	56776	hgsc.bcm.edu	37	chr1	240371184	240371184	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggcatacctcctccacccccTctacccggagcgggcatacc	8	20	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:240371184T>A	ENST00000319653.9	+	5	3302	c.3072T>A	c.(3070-3072)ccT>ccA	p.P1024P		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1024	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CTCCACCCCCTCTACCCGGAG	0.736																																					p.P1024P		Atlas-SNP	.											.	FMN2	451	.	0			c.T3072A						.						4	4	4					1																	240371184		1678	3388	5066	SO:0001819	synonymous_variant	56776	exon5			ACCCCCTCTACCC	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.3072T>A	chr1.hg19:g.240371184T>A		173.0	0.0		226.0	16.0	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	hg19	CCDS31069.2																																																																																			.	.		0.736	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		A	240371184	T	A	240371184	2	1	255	1	0	0	0	0	0	0	0	1	5958	1538	54	4		4	FMN2	1	240371184	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	7234982	240371184	8879437	71	35416										
OR2T3	343173	hgsc.bcm.edu	37	chr1	248637025	248637025	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cctcctggctgccatggcctAtgaccgatatgctgctgttt	10	13	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:248637025A>G	ENST00000359594.2	+	1	399	c.374A>G	c.(373-375)tAt>tGt	p.Y125C		NM_001005495.1	NP_001005495.1	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T, member 3	125						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(5)|lung(19)|ovary(1)|prostate(1)|skin(3)	31	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GCCATGGCCTATGACCGATAT	0.552																																					p.Y125C		Atlas-SNP	.											.	OR2T3	79	.	0			c.A374G						.						53	52	53					1																	248637025		2195	4295	6490	SO:0001583	missense	343173	exon1			TGGCCTATGACCG		CCDS31117.1	1q44	2012-08-09			ENSG00000196539	ENSG00000196539		"GPCR / Class A : Olfactory receptors"	14727	protein-coding gene	gene with protein product							Standard	NM_001005495		Approved		uc001iel.1	Q8NH03	OTTHUMG00000040452	ENST00000359594.2:c.374A>G	chr1.hg19:g.248637025A>G	ENSP00000352604:p.Tyr125Cys	545.0	0.0		787.0	209.0	NM_001005495	B2RNJ1	Missense_Mutation	SNP	ENST00000359594.2	hg19	CCDS31117.1	.	.	.	.	.	.	.	.	.	.	a	9.872	1.199201	0.22121	.	.	ENSG00000196539	ENST00000359594	T	0.01347	4.99	2.65	2.65	0.31530	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.05364	0.0142	M	0.90425	3.115	0.24293	N	0.995155	P	0.51653	0.947	P	0.47786	0.557	T	0.15578	-1.0432	9	0.62326	D	0.03	.	9.7894	0.40697	1.0:0.0:0.0:0.0	.	125	Q8NH03	OR2T3_HUMAN	C	125	ENSP00000352604:Y125C	ENSP00000352604:Y125C	Y	+	2	0	OR2T3	246703648	0.247000	0.23920	0.864000	0.33941	0.357000	0.29423	0.550000	0.23345	0.967000	0.38186	0.156000	0.16432	TAT	.	.		0.552	OR2T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097348.1	NM_001005495		G	248637025	A	G	248637025	3	3	255	1	0	0	0	0	1	0	0	0	11032	449	16	2	376	2	OR2T3	1	248637025	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	8265841	248637025	613596	72	35417										
TPO	7173	hgsc.bcm.edu	37	chr2	1440156	1440156	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cacaggagcttgcaacaacaGgtattgtttgtggattttct	10	7	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:1440156G>T	ENST00000345913.4	+	5	573	c.482G>T	c.(481-483)aGa>aTa	p.R161I	TPO_ENST00000382198.1_Splice_Site_p.R161I|TPO_ENST00000349624.3_Splice_Site_p.R161I|TPO_ENST00000337415.3_Splice_Site_p.R161I|TPO_ENST00000382201.3_Splice_Site_p.R161I|TPO_ENST00000497517.2_Intron|TPO_ENST00000539820.1_Splice_Site_p.R161I|TPO_ENST00000329066.4_Splice_Site_p.R161I|TPO_ENST00000382269.3_Splice_Site_p.R161I|TPO_ENST00000346956.3_Splice_Site_p.R161I	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	161					cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	TGCAACAACAGGTATTGTTTG	0.458																																					p.R161I		Atlas-SNP	.											.	TPO	224	.	0			c.G482T						.						115	113	114					2																	1440156		2203	4300	6503	SO:0001630	splice_region_variant	7173	exon5			ACAACAGGTATTG		CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.482+1G>T	chr2.hg19:g.1440156G>T		119.0	0.0		105.0	58.0	NM_175719	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	hg19	CCDS1643.1	.	.	.	.	.	.	.	.	.	.	G	17.74	3.464356	0.63513	.	.	ENSG00000115705	ENST00000382269;ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000539820;ENST00000329066;ENST00000382201;ENST00000423320;ENST00000382198;ENST00000422464	T;T;T;T;T;T;T;T;T;T;T	0.58797	0.45;0.31;0.31;0.31;0.31;0.45;0.31;0.31;0.31;0.31;0.31	5.07	5.07	0.68467	.	0.050880	0.85682	D	0.000000	T	0.71745	0.3376	L	0.53729	1.69	0.52099	D	0.999946	D;D;D;D;D	0.89917	0.995;0.999;1.0;0.997;0.996	D;D;D;D;D	0.91635	0.953;0.994;0.999;0.953;0.972	T	0.74444	-0.3663	10	0.72032	D	0.01	-16.0578	15.3642	0.74507	0.0:0.0:1.0:0.0	.	161;161;161;161;161	P07202-4;P07202-5;E9PFM6;P07202-2;P07202	.;.;.;.;PERT_HUMAN	I	161;161;161;161;161;161;161;161;161;161;90	ENSP00000371704:R161I;ENSP00000337263:R161I;ENSP00000318820:R161I;ENSP00000263886:R161I;ENSP00000332044:R161I;ENSP00000444840:R161I;ENSP00000329869:R161I;ENSP00000371636:R161I;ENSP00000390994:R161I;ENSP00000371633:R161I;ENSP00000405788:R90I	ENSP00000329869:R161I	R	+	2	0	TPO	1419163	1.000000	0.71417	1.000000	0.80357	0.378000	0.30076	3.983000	0.56916	2.353000	0.79882	0.313000	0.20887	AGA	.	.		0.458	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547	Missense_Mutation	T	1440156	G	T	1440156	5	4	255	1	0	0	0	0	0	0	1	0	16425	1014	35	3	496	3	TPO	2	1440156	Splice_Site	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10		1440156	241759217	73	35418										
OTOF	9381	hgsc.bcm.edu	37	chr2	26690270	26690270	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgggtttcttcttctcggggGcctcggacccctggccagag	14	13	3	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:26690270G>A	ENST00000272371.2	-	34	4316	c.4190C>T	c.(4189-4191)gCc>gTc	p.A1397V	OTOF_ENST00000402415.3_Missense_Mutation_p.A707V|OTOF_ENST00000339598.3_Missense_Mutation_p.A630V|OTOF_ENST00000338581.6_Missense_Mutation_p.A630V|OTOF_ENST00000403946.3_Missense_Mutation_p.A1397V	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	1397					membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			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)					CTTCTCGGGGGCCTCGGACCC	0.582																																					p.A1397V	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											.	OTOF	524	.	0			c.C4190T						.						53	57	56					2																	26690270		2203	4300	6503	SO:0001583	missense	9381	exon34			TCGGGGGCCTCGG	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"fer-1-like family member 2"	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.4190C>T	chr2.hg19:g.26690270G>A	ENSP00000272371:p.Ala1397Val	129.0	0.0		117.0	5.0	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Missense_Mutation	SNP	ENST00000272371.2	hg19	CCDS1725.1	.	.	.	.	.	.	.	.	.	.	G	1.494	-0.553961	0.03996	.	.	ENSG00000115155	ENST00000338581;ENST00000339598;ENST00000402415;ENST00000272371;ENST00000403946	T;T;T;T;T	0.80214	-1.11;-1.11;-1.1;-1.35;-1.35	5.44	-1.62	0.08372	.	0.974058	0.08455	N	0.943283	T	0.50650	0.1628	N	0.00926	-1.1	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.08055	0.0;0.001;0.003;0.002	T	0.38564	-0.9655	10	0.25106	T	0.35	-5.881	8.6969	0.34301	0.3889:0.1012:0.5099:0.0	.	1397;630;707;630	Q9HC10;Q9HC10-2;Q9HC10-3;Q9HC10-4	OTOF_HUMAN;.;.;.	V	630;630;707;1397;1397	ENSP00000345137:A630V;ENSP00000344521:A630V;ENSP00000383906:A707V;ENSP00000272371:A1397V;ENSP00000385255:A1397V	ENSP00000272371:A1397V	A	-	2	0	OTOF	26543774	0.980000	0.34600	0.008000	0.14137	0.016000	0.09150	0.909000	0.28558	-0.212000	0.10109	-0.742000	0.03525	GCC	.	.		0.582	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3			A	26690270	G	A	26690270	3	1	255	1	0	0	0	0	1	0	0	0	11312	1203	42	3	2040	3	OTOF	2	26690270	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	25250114	26690270	216509103	74	35419										
AGBL5	60509	hgsc.bcm.edu	37	chr2	27279548	27279548	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	attcagcccacttcgacttcCagggctgcaatttctcagag	8	13	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:27279548C>T	ENST00000360131.4	+	8	1582	c.1423C>T	c.(1423-1425)Cag>Tag	p.Q475*	AGBL5_ENST00000323064.8_Nonsense_Mutation_p.Q475*|RP11-503P10.1_ENST00000607407.1_RNA	NM_021831.5	NP_068603.4	Q8NDL9	CBPC5_HUMAN	ATP/GTP binding protein-like 5	475					protein branching point deglutamylation (GO:0035611)|protein deglutamylation (GO:0035608)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	28	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTTCGACTTCCAGGGCTGCAA	0.483																																					p.Q475X		Atlas-SNP	.											.	AGBL5	126	.	0			c.C1423T						.						109	115	113					2																	27279548		2203	4300	6503	SO:0001587	stop_gained	60509	exon8			GACTTCCAGGGCT	BC007415	CCDS1732.3, CCDS42665.1	2p23.3	2014-06-23			ENSG00000084693	ENSG00000084693			26147	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 5"	615900				24022482	Standard	NM_001035507		Approved	FLJ21839, CCP5	uc002rie.3	Q8NDL9	OTTHUMG00000128406	ENST00000360131.4:c.1423C>T	chr2.hg19:g.27279548C>T	ENSP00000353249:p.Gln475*	63.0	0.0		76.0	4.0	NM_021831	A2VDI7|B7WPG9|B7Z7I7|D6W548|Q53SW0|Q53SZ0|Q96IK8|Q9H6V0|Q9H8P8	Nonsense_Mutation	SNP	ENST00000360131.4	hg19	CCDS1732.3	.	.	.	.	.	.	.	.	.	.	C	37	6.610929	0.97705	.	.	ENSG00000084693	ENST00000323064;ENST00000360131	.	.	.	6.17	6.17	0.99709	.	0.288263	0.39759	N	0.001266	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05959	T	0.93	-16.3107	5.8667	0.18779	0.1418:0.6494:0.1365:0.0724	.	.	.	.	X	475	.	ENSP00000323681:Q475X	Q	+	1	0	AGBL5	27133052	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.666000	0.37460	2.941000	0.99782	0.655000	0.94253	CAG	.	.		0.483	AGBL5-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000309033.1	NM_021831		T	27279548	C	T	27279548	4	4	255	1	0	0	0	0	0	1	0	0	378	595	21	3	1449	3	AGBL5	2	27279548	Nonsense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	589278	27279548	215919825	75	35420										
GTF3C2	2976	hgsc.bcm.edu	37	chr2	27550059	27550059	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	actaccttatgaatagcctcCagctgcagcctgtccaggca	8	14	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:27550059C>A	ENST00000359541.2	-	18	2931	c.2502G>T	c.(2500-2502)ctG>ctT	p.L834L	GTF3C2_ENST00000264720.3_Silent_p.L834L|MPV17_ENST00000357186.6_5'Flank			Q8WUA4	TF3C2_HUMAN	general transcription factor IIIC, polypeptide 2, beta 110kDa	834					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)				central_nervous_system(4)|endometrium(6)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	38	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GAATAGCCTCCAGCTGCAGCC	0.537																																					p.N834N		Atlas-SNP	.											.	GTF3C2	73	.	0			c.C2502T						.						73	61	65					2																	27550059		2203	4300	6503	SO:0001819	synonymous_variant	2976	exon19			AGCCTCCAGCTGC	D13636	CCDS1749.1	2p23.3	2013-01-10	2002-08-29		ENSG00000115207	ENSG00000115207		"General transcription factors", "WD repeat domain containing"	4665	protein-coding gene	gene with protein product		604883	"general transcription factor IIIC, polypeptide 2 (beta subunit, 110kD)"			7729686	Standard	NM_001521		Approved	KIAA0011, TFIIIC110	uc002rjw.2	Q8WUA4	OTTHUMG00000097785	ENST00000359541.2:c.2502G>T	chr2.hg19:g.27550059C>A		64.0	0.0		44.0	4.0	NM_001521	D6W557|Q16632|Q9BWI7	Silent	SNP	ENST00000359541.2	hg19	CCDS1749.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	8.056|8.056	0.767092|0.767092	0.15983|0.15983	.|.	.|.	ENSG00000115207|ENSG00000115207	ENST00000457098|ENST00000431028;ENST00000454704;ENST00000415683	.|.	.|.	.|.	4.95|4.95	-5.06|-5.06	0.02946|0.02946	.|.	.|.	.|.	.|.	.|.	.|T	.|0.35941	.|0.0949	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.36040	.|-0.9764	.|4	.|.	.|.	.|.	-11.0966|-11.0966	1.2024|1.2024	0.01887|0.01887	0.3202:0.2795:0.2405:0.1597|0.3202:0.2795:0.2405:0.1597	.|.	.|.	.|.	.|.	X|L	128|49;343;257	.|.	.|.	G|W	-|-	1|2	0|0	GTF3C2|GTF3C2	27403563|27403563	0.946000|0.946000	0.32159|0.32159	0.897000|0.897000	0.35233|0.35233	0.975000|0.975000	0.68041|0.68041	-0.216000|-0.216000	0.09266|0.09266	-1.068000|-1.068000	0.03156|0.03156	-0.881000|-0.881000	0.02953|0.02953	GGA|TGG	.	.		0.537	GTF3C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215028.2			A	27550059	C	A	27550059	2	1	255	1	0	0	0	0	0	0	0	1	6882	581	21	3		3	GTF3C2	2	27550059	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	270511	27550059	215649314	76	35421										
C2orf16	84226	hgsc.bcm.edu	37	chr2	27803792	27803792	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tactctttccaacccagaccTcttcgactgcccaagcccac	4	19	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:27803792T>C	ENST00000408964.2	+	1	4404	c.4353T>C	c.(4351-4353)ccT>ccC	p.P1451P	RP11-158I13.2_ENST00000505973.1_RNA|ZNF512_ENST00000556601.1_5'Flank|ZNF512_ENST00000413371.2_5'Flank|ZNF512_ENST00000416005.2_5'Flank|AC074091.1_ENST00000408604.1_RNA|ZNF512_ENST00000355467.4_5'Flank|ZNF512_ENST00000379717.1_5'Flank	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1451						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					AACCCAGACCTCTTCGACTGC	0.512																																					p.P1451P		Atlas-SNP	.											.	C2orf16	357	.	0			c.T4353C						.						93	97	96					2																	27803792		1966	4152	6118	SO:0001819	synonymous_variant	84226	exon1			CAGACCTCTTCGA	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"P-S-E-R-S-H-H-S repeats containing"						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.4353T>C	chr2.hg19:g.27803792T>C		68.0	0.0		73.0	4.0	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Silent	SNP	ENST00000408964.2	hg19	CCDS42666.1																																																																																			.	.		0.512	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266		C	27803792	T	C	27803792	2	2	255	1	0	0	0	0	0	0	0	1	2159	1538	54	2		2	C2orf16	2	27803792	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	253733	27803792	215395581	77	35422										
MAP4K3	8491	hgsc.bcm.edu	37	chr2	39535144	39535144	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tccaaaaaaccatcactgtcGggctgtttagcagagaccaa	8	11	1	1	rs373302450		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:39535144G>A	ENST00000263881.3	-	15	1383	c.1059C>T	c.(1057-1059)ccC>ccT	p.P353P	MAP4K3_ENST00000341681.5_Intron|MAP4K3_ENST00000437545.1_Intron|MAP4K3_ENST00000536018.1_5'UTR	NM_003618.3	NP_003609.2	Q8IVH8	M4K3_HUMAN	mitogen-activated protein kinase kinase kinase kinase 3	353					intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)		ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			NS(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_hematologic(82;0.211)				CATCACTGTCGGGCTGTTTAG	0.368																																					p.P353P		Atlas-SNP	.											.	MAP4K3	109	.	0			c.C1059T						.	G		1,4405	2.1+/-5.4	0,1,2202	107	103	104		1059	5.8	1	2		104	0,8600		0,0,4300	no	coding-synonymous	MAP4K3	NM_003618.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		353/895	39535144	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	8491	exon15			ACTGTCGGGCTGT	AF000145	CCDS1803.1, CCDS58707.1	2p22.3	2011-06-09			ENSG00000011566	ENSG00000011566		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6865	protein-coding gene	gene with protein product		604921		RAB8IPL1		9275185	Standard	NM_003618		Approved	GLK, MAPKKKK3	uc002rro.4	Q8IVH8	OTTHUMG00000102127	ENST00000263881.3:c.1059C>T	chr2.hg19:g.39535144G>A		88.0	0.0		75.0	4.0	NM_003618	Q6IQ39|Q8IVH7|Q9UDM5|Q9Y6R5	Silent	SNP	ENST00000263881.3	hg19	CCDS1803.1																																																																																			.	.		0.368	MAP4K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219966.2	NM_003618		A	39535144	G	A	39535144	2	1	255	1	0	0	0	0	0	0	0	1	9270	1103	39	1		1	MAP4K3	2	39535144	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	11731352	39535144	203664229	78	35423										
MSH6	2956	hgsc.bcm.edu	37	chr2	48027261	48027261	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gaagaatatattcccttggaTtctgacacagtcagcactac	7	10	2	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:48027261T>C	ENST00000234420.5	+	4	2291	c.2139T>C	c.(2137-2139)gaT>gaC	p.D713D	FBXO11_ENST00000405808.1_Intron|MSH6_ENST00000540021.1_Silent_p.D583D|MSH6_ENST00000538136.1_Silent_p.D411D	NM_000179.2	NP_000170.1	P52701	MSH6_HUMAN	mutS homolog 6	713					ATP catabolic process (GO:0006200)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|response to UV (GO:0009411)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|MutSalpha complex (GO:0032301)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|guanine/thymine mispair binding (GO:0032137)|methylated histone binding (GO:0035064)|mismatched DNA binding (GO:0030983)	p.0?(2)		breast(8)|central_nervous_system(29)|cervix(1)|endometrium(32)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(75)|lung(25)|ovary(3)|prostate(3)|skin(10)|stomach(22)|thyroid(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	229		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TTCCCTTGGATTCTGACACAG	0.403			"Mis, N, F, S"		colorectal	"colorectal, endometrial, ovarian"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.D713D		Atlas-SNP	.	yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p16	2956	mutS homolog 6 (E. coli)		E	.	MSH6	341	.	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.T2139C						.						105	104	104					2																	48027261		2203	4300	6503	SO:0001819	synonymous_variant	2956	exon4	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	CTTGGATTCTGAC	U54777	CCDS1836.1, CCDS62906.1, CCDS62907.1	2p16	2014-09-17	2013-09-12		ENSG00000116062	ENSG00000116062			7329	protein-coding gene	gene with protein product		600678	"mutS (E. coli) homolog 6", "mutS homolog 6 (E. coli)"	GTBP		7604266	Standard	NM_000179		Approved		uc002rwd.4	P52701	OTTHUMG00000129129	ENST00000234420.5:c.2139T>C	chr2.hg19:g.48027261T>C		95.0	0.0		100.0	4.0	NM_000179	B4DF41|B4E3I4|F5H2F9|O43706|O43917|Q8TCX4|Q9BTB5	Silent	SNP	ENST00000234420.5	hg19	CCDS1836.1																																																																																			.	.		0.403	MSH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251180.4	NM_000179		C	48027261	T	C	48027261	2	2	255	1	0	0	0	0	0	0	0	1	9883	1490	52	2		2	MSH6	2	48027261	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	8492117	48027261	195172112	79	35424										
LHCGR	3973	hgsc.bcm.edu	37	chr2	48914978	48914978	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgtaagctgaaaaatctttcCttctataaagttcagcccga	6	9	3	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:48914978C>A	ENST00000294954.7	-	11	1979	c.1958G>T	c.(1957-1959)aGg>aTg	p.R653M	STON1-GTF2A1L_ENST00000402114.2_Intron|LHCGR_ENST00000344775.3_Missense_Mutation_p.R591M|LHCGR_ENST00000401907.1_3'UTR|LHCGR_ENST00000405626.1_Missense_Mutation_p.R626M|LHCGR_ENST00000403273.1_3'UTR	NM_000233.3	NP_000224.2	P22888	LSHR_HUMAN	luteinizing hormone/choriogonadotropin receptor	653					activation of adenylate cyclase activity (GO:0007190)|cellular response to gonadotropin stimulus (GO:0071371)|cognition (GO:0050890)|development of secondary male sexual characteristics (GO:0046544)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|ovarian follicle development (GO:0001541)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|regulation of steroid hormone biosynthetic process (GO:0090030)|seminiferous tubule development (GO:0072520)|spermatogenesis (GO:0007283)|uterus development (GO:0060065)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	choriogonadotropin hormone binding (GO:0038106)|choriogonadotropin hormone receptor activity (GO:0035472)|luteinizing hormone receptor activity (GO:0004964)			NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(3)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	56		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Buserelin(DB06719)|Cetrorelix(DB00050)|Choriogonadotropin alfa(DB00097)|Goserelin(DB00014)|Lutropin alfa(DB00044)|Menotropins(DB00032)	AAAATCTTTCCTTCTATAAAG	0.393																																					p.R653M		Atlas-SNP	.											.	LHCGR	154	.	0			c.G1958T						.						109	112	111					2																	48914978		2203	4300	6503	SO:0001583	missense	3973	exon11			TCTTTCCTTCTAT		CCDS1842.1	2p21	2012-08-10			ENSG00000138039	ENSG00000138039		"GPCR / Class A : Gonadotropin and TSH receptors"	6585	protein-coding gene	gene with protein product		152790	"hypergonadotropic hypogonadism"	HHG			Standard	NM_000233		Approved	LHR, LCGR, LGR2, ULG5	uc002rwu.4	P22888	OTTHUMG00000129257	ENST00000294954.7:c.1958G>T	chr2.hg19:g.48914978C>A	ENSP00000294954:p.Arg653Met	121.0	0.0		113.0	5.0	NM_000233	Q14751|Q15996|Q9UEW9	Missense_Mutation	SNP	ENST00000294954.7	hg19	CCDS1842.1	.	.	.	.	.	.	.	.	.	.	C	5.943	0.358092	0.11239	.	.	ENSG00000138039	ENST00000344775;ENST00000294954;ENST00000405626	T;T;T	0.78126	-1.15;-0.98;-1.05	5.92	2.91	0.33838	.	0.308493	0.36591	N	0.002519	T	0.52853	0.1760	N	0.10809	0.05	0.30632	N	0.757415	B	0.16396	0.017	B	0.10450	0.005	T	0.42832	-0.9428	9	.	.	.	.	5.1548	0.15029	0.2953:0.5304:0.0:0.1743	.	653	P22888	LSHR_HUMAN	M	591;653;626	ENSP00000344301:R591M;ENSP00000294954:R653M;ENSP00000386033:R626M	.	R	-	2	0	LHCGR	48768482	0.639000	0.27234	1.000000	0.80357	0.547000	0.35210	1.482000	0.35486	0.853000	0.35312	0.585000	0.79938	AGG	.	.		0.393	LHCGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251364.4	NM_000233.3		A	48914978	C	A	48914978	3	1	255	1	0	0	0	0	1	0	0	0	8771	681	24	3	145	3	LHCGR	2	48914978	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	887717	48914978	194284395	80	35425										
AFTPH	54812	hgsc.bcm.edu	37	chr2	64779485	64779485	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ataacaaaggagacactgatGgagaggatcaggtttgtgtt	13	4	1	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:64779485G>T	ENST00000422803.1	+	2	1191	c.877G>T	c.(877-879)Gga>Tga	p.G293*	AFTPH_ENST00000409183.1_5'Flank|AFTPH_ENST00000238855.7_Nonsense_Mutation_p.G293*|AFTPH_ENST00000409933.1_Nonsense_Mutation_p.G293*|AFTPH_ENST00000238856.4_Nonsense_Mutation_p.G293*			Q6ULP2	AFTIN_HUMAN	aftiphilin	293					protein transport (GO:0015031)	AP-1 adaptor complex (GO:0030121)|cytosol (GO:0005829)	clathrin binding (GO:0030276)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	35						AGACACTGATGGAGAGGATCA	0.373																																					p.G293X		Atlas-SNP	.											.	AFTPH	117	.	0			c.G877T						.						61	66	64					2																	64779485		2203	4300	6503	SO:0001587	stop_gained	54812	exon2			ACTGATGGAGAGG	AB073356	CCDS1878.1, CCDS46303.1	2p14	2008-02-05			ENSG00000119844	ENSG00000119844			25951	protein-coding gene	gene with protein product						14665628, 15758025, 15811338	Standard	NM_017657		Approved	MGC33965, FLJ20080, FLJ23793, Nbla10388	uc002scz.3	Q6ULP2	OTTHUMG00000129539	ENST00000422803.1:c.877G>T	chr2.hg19:g.64779485G>T	ENSP00000397726:p.Gly293*	154.0	0.0		148.0	6.0	NM_017657	D6W5E9|Q6ZM66|Q86VW3|Q8TCF3|Q9H7E3|Q9HAB9|Q9NXS4	Nonsense_Mutation	SNP	ENST00000422803.1	hg19		.	.	.	.	.	.	.	.	.	.	G	38	6.890172	0.97912	.	.	ENSG00000119844	ENST00000238856;ENST00000422803;ENST00000238855;ENST00000409933	.	.	.	5.78	1.55	0.23275	.	0.841047	0.10824	N	0.630138	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12430	T	0.62	-0.2983	5.3584	0.16073	0.4928:0.1458:0.3615:0.0	.	.	.	.	X	293	.	ENSP00000238855:G293X	G	+	1	0	AFTPH	64632989	0.996000	0.38824	0.734000	0.30879	0.983000	0.72400	0.762000	0.26503	0.390000	0.25115	0.591000	0.81541	GGA	.	.		0.373	AFTPH-202	KNOWN	basic	protein_coding	protein_coding		NM_017657		T	64779485	G	T	64779485	4	4	255	1	0	0	0	0	0	1	0	0	364	1349	47	3	879	3	AFTPH	2	64779485	Nonsense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	15864507	64779485	178419888	81	35426										
ALMS1	7840	hgsc.bcm.edu	37	chr2	73680043	73680043	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aattcctggaccagctggccAgaaaacagtattaccaacag	8	11	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:73680043A>G	ENST00000264448.6	+	8	6497	c.6386A>G	c.(6385-6387)cAg>cGg	p.Q2129R	ALMS1_ENST00000377715.1_Missense_Mutation_p.Q2129R|ALMS1_ENST00000409009.1_Missense_Mutation_p.Q2087R	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2129	34 X 47 AA approximate tandem repeat.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				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						CCAGCTGGCCAGAAAACAGTA	0.403																																					p.Q2129R		Atlas-SNP	.											.	ALMS1	384	.	0			c.A6386G						.						50	48	48					2																	73680043		1850	4102	5952	SO:0001583	missense	7840	exon8			CTGGCCAGAAAAC	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.6386A>G	chr2.hg19:g.73680043A>G	ENSP00000264448:p.Gln2129Arg	94.0	0.0		99.0	4.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	A	8.519	0.868390	0.17250	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.15834	3.28;3.28;2.39	4.08	2.9	0.33743	.	0.203527	0.24597	N	0.037173	T	0.22360	0.0539	L	0.52573	1.65	0.09310	N	1	P;D;P	0.53745	0.952;0.962;0.952	P;P;P	0.53006	0.644;0.715;0.644	T	0.04065	-1.0980	10	0.35671	T	0.21	.	7.8479	0.29437	0.7902:0.2098:0.0:0.0	.	2129;2087;2129	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	R	2087;2129;2129	ENSP00000386627:Q2087R;ENSP00000264448:Q2129R;ENSP00000366944:Q2129R	ENSP00000264448:Q2129R	Q	+	2	0	ALMS1	73533551	0.183000	0.23186	0.083000	0.20561	0.041000	0.13682	1.650000	0.37292	0.860000	0.35481	0.533000	0.62120	CAG	.	.		0.403	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		G	73680043	A	G	73680043	3	3	255	1	0	0	0	0	1	0	0	0	535	188	7	2	6416	2	ALMS1	2	73680043	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	8900558	73680043	169519330	82	35427										
CTNNA2	1496	hgsc.bcm.edu	37	chr2	80085187	80085187	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gtttgcagatgacccttgctCgtcggtaaagcgcggcacca	12	12	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:80085187C>A	ENST00000402739.4	+	3	352	c.347C>A	c.(346-348)tCg>tAg	p.S116*	CTNNA2_ENST00000541047.1_Nonsense_Mutation_p.S116*|CTNNA2_ENST00000496558.1_Nonsense_Mutation_p.S116*|CTNNA2_ENST00000361291.4_Nonsense_Mutation_p.S150*|CTNNA2_ENST00000466387.1_Nonsense_Mutation_p.S116*|CTNNA2_ENST00000540488.1_Nonsense_Mutation_p.S116*	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	116					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						GACCCTTGCTCGTCGGTAAAG	0.587																																					p.S116X		Atlas-SNP	.											.	CTNNA2	462	.	0			c.C347A						.						99	96	97					2																	80085187		2061	4193	6254	SO:0001587	stop_gained	1496	exon4			CTTGCTCGTCGGT		CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"cadherin-associated protein, related", "cancer/testis antigen 114"	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.347C>A	chr2.hg19:g.80085187C>A	ENSP00000384638:p.Ser116*	102.0	0.0		96.0	4.0	NM_001164883	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Nonsense_Mutation	SNP	ENST00000402739.4	hg19		.	.	.	.	.	.	.	.	.	.	C	37	6.135242	0.97315	.	.	ENSG00000066032	ENST00000466387;ENST00000496558;ENST00000409971;ENST00000361291;ENST00000402739;ENST00000541047;ENST00000540488	.	.	.	5.67	5.67	0.87782	.	0.070349	0.64402	D	0.000015	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.773	0.96379	0.0:1.0:0.0:0.0	.	.	.	.	X	116;116;116;150;116;116;116	.	ENSP00000355398:S150X	S	+	2	0	CTNNA2	79938695	1.000000	0.71417	0.947000	0.38551	0.965000	0.64279	7.818000	0.86416	2.677000	0.91161	0.655000	0.94253	TCG	.	.		0.587	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389		A	80085187	C	A	80085187	4	1	255	1	0	0	0	0	0	1	0	0	4015	893	31	1	357	1	CTNNA2	2	80085187	Nonsense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	6405144	80085187	163114186	83	35428										
CTNNA2	1496	hgsc.bcm.edu	37	chr2	80085274	80085274	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	catcctggcggacatggcagAtgtcatgagacttttatccc	10	11	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:80085274A>G	ENST00000402739.4	+	3	439	c.434A>G	c.(433-435)gAt>gGt	p.D145G	CTNNA2_ENST00000541047.1_Missense_Mutation_p.D145G|CTNNA2_ENST00000496558.1_Missense_Mutation_p.D145G|CTNNA2_ENST00000361291.4_Missense_Mutation_p.D179G|CTNNA2_ENST00000466387.1_Missense_Mutation_p.D145G|CTNNA2_ENST00000540488.1_Missense_Mutation_p.D145G	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	145					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						GACATGGCAGATGTCATGAGA	0.493																																					p.D145G		Atlas-SNP	.											.	CTNNA2	462	.	0			c.A434G						.						68	68	68					2																	80085274		2029	4184	6213	SO:0001583	missense	1496	exon4			TGGCAGATGTCAT		CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"cadherin-associated protein, related", "cancer/testis antigen 114"	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.434A>G	chr2.hg19:g.80085274A>G	ENSP00000384638:p.Asp145Gly	88.0	0.0		72.0	4.0	NM_001164883	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Missense_Mutation	SNP	ENST00000402739.4	hg19		.	.	.	.	.	.	.	.	.	.	A	32	5.172343	0.94807	.	.	ENSG00000066032	ENST00000466387;ENST00000496558;ENST00000361291;ENST00000402739;ENST00000541047;ENST00000540488	T;T;T;T;T;T	0.45276	0.9;0.9;0.9;0.9;0.9;0.9	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.70202	0.3197	M	0.89214	3.015	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.75283	-0.3372	10	0.51188	T	0.08	.	15.9204	0.79562	1.0:0.0:0.0:0.0	.	145;145;145	P26232;P26232-3;P26232-2	CTNA2_HUMAN;.;.	G	145;145;179;145;145;145	ENSP00000418191:D145G;ENSP00000419295:D145G;ENSP00000355398:D179G;ENSP00000384638:D145G;ENSP00000444675:D145G;ENSP00000441705:D145G	ENSP00000355398:D179G	D	+	2	0	CTNNA2	79938782	1.000000	0.71417	0.979000	0.43373	0.993000	0.82548	9.339000	0.96797	2.164000	0.68074	0.533000	0.62120	GAT	.	.		0.493	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389		G	80085274	A	G	80085274	3	3	255	1	0	0	0	0	1	0	0	0	4015	333	12	2	444	2	CTNNA2	2	80085274	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	87	80085274	163114099	84	35429										
SEMA4C	54910	hgsc.bcm.edu	37	chr2	97529483	97529483	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	acagctgcagctcctcaatcAggtgaacccagggccccagg	11	15	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:97529483A>G	ENST00000305476.5	-	12	1511	c.1379T>C	c.(1378-1380)cTg>cCg	p.L460P		NM_017789.4	NP_060259.4	Q9C0C4	SEM4C_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C	460	Dominant negative effect on myogenic differentiation. {ECO:0000250}.|Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell migration in hindbrain (GO:0021535)|cerebellum development (GO:0021549)|muscle cell differentiation (GO:0042692)|neural tube closure (GO:0001843)|positive regulation of stress-activated MAPK cascade (GO:0032874)|semaphorin-plexin signaling pathway (GO:0071526)	cell junction (GO:0030054)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synaptic vesicle membrane (GO:0030672)	receptor activity (GO:0004872)			NS(1)|kidney(1)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	17						CTCCTCAATCAGGTGAACCCA	0.607																																					p.L460P		Atlas-SNP	.											.	SEMA4C	56	.	0			c.T1379C						.						74	76	75					2																	97529483		2203	4300	6503	SO:0001583	missense	54910	exon12			TCAATCAGGTGAA	AB051526	CCDS2029.1	2q11.2	2013-01-11			ENSG00000168758	ENSG00000168758		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10731	protein-coding gene	gene with protein product	"M-Sema F"	604462		SEMAI		7656991	Standard	NM_017789		Approved	Semacl1, Semaf	uc002sxh.4	Q9C0C4	OTTHUMG00000130535	ENST00000305476.5:c.1379T>C	chr2.hg19:g.97529483A>G	ENSP00000306844:p.Leu460Pro	92.0	0.0		72.0	4.0	NM_017789	Q32MJ3|Q7Z5X0	Missense_Mutation	SNP	ENST00000305476.5	hg19	CCDS2029.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.291916	0.80914	.	.	ENSG00000168758	ENST00000305476	T	0.12569	2.67	5.26	5.26	0.73747	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.443089	0.23081	N	0.052142	T	0.32255	0.0823	M	0.67625	2.065	0.80722	D	1	P;P	0.51240	0.943;0.943	P;P	0.59171	0.853;0.853	T	0.02581	-1.1138	10	0.87932	D	0	.	14.2933	0.66295	1.0:0.0:0.0:0.0	.	460;170	Q9C0C4;Q6P5A5	SEM4C_HUMAN;.	P	460	ENSP00000306844:L460P	ENSP00000306844:L460P	L	-	2	0	SEMA4C	96893210	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.146000	0.94640	2.208000	0.71279	0.533000	0.62120	CTG	.	.		0.607	SEMA4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252957.1	NM_017789		G	97529483	A	G	97529483	3	3	255	1	0	0	0	0	1	0	0	0	14048	188	7	2	1138	2	SEMA4C	2	97529483	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	17444209	97529483	145669890	85	35430										
MAP4K4	9448	hgsc.bcm.edu	37	chr2	102486261	102486261	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cagaggacaccagagcagcgTcagtccccggtctcttttag	11	13	2	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:102486261T>C	ENST00000347699.4	+	20	2396		c.e20+2		MAP4K4_ENST00000324219.4_Splice_Site|MAP4K4_ENST00000302217.5_Splice_Site|MAP4K4_ENST00000413150.2_Splice_Site|MAP4K4_ENST00000456652.1_Splice_Site|MAP4K4_ENST00000350878.4_Splice_Site|MAP4K4_ENST00000425019.1_Splice_Site|MAP4K4_ENST00000498066.1_Splice_Site|MAP4K4_ENST00000350198.4_Splice_Site	NM_001242559.1|NM_145687.3	NP_001229488.1|NP_663720.1	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase kinase 4						intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of JNK cascade (GO:0046328)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						CAGAGCAGCGTCAGTCCCCGG	0.572																																					.		Atlas-SNP	.											.	MAP4K4	111	.	0			c.2306+2T>C						.						29	34	33					2																	102486261		2048	4187	6235	SO:0001630	splice_region_variant	9448	exon20			GCAGCGTCAGTCC	AF096300	CCDS56130.1, CCDS74546.1	2q11.2-q12	2011-06-09			ENSG00000071054	ENSG00000071054		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6866	protein-coding gene	gene with protein product	"HPK/GCK-like kinase", "hepatocyte progenitor kinase-like/germinal center kinase-like kinase"	604666				9890973, 9734811, 9135144	Standard	NM_004834		Approved	HGK, NIK, FLH21957	uc002tbf.3	O95819	OTTHUMG00000155394	ENST00000347699.4:c.2396+2T>C	chr2.hg19:g.102486261T>C		78.0	0.0		112.0	5.0	NM_145686	O75172|Q9NST7	Splice_Site	SNP	ENST00000347699.4	hg19	CCDS56130.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.190971	0.78789	.	.	ENSG00000071054	ENST00000425019;ENST00000324219;ENST00000350198;ENST00000302217;ENST00000413150;ENST00000456652;ENST00000347699;ENST00000417294;ENST00000350878;ENST00000421882	.	.	.	5.19	5.19	0.71726	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0569	0.71921	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	MAP4K4	101852693	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	7.481000	0.81124	1.960000	0.56953	0.460000	0.39030	.	.	.		0.572	MAP4K4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339839.1	NM_004834	Intron	C	102486261	T	C	102486261	5	2	255	1	0	0	0	0	0	0	1	0	9271	1681	58	2	2727	2	MAP4K4	2	102486261	Splice_Site	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	4956778	102486261	140713112	86	35431										
PTPN4	5775	hgsc.bcm.edu	37	chr2	120720202	120720202	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcaatatcaggttaaatgtcAccaatattggccagaaccca	6	10	3	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:120720202A>G	ENST00000263708.2	+	24	3062	c.2291A>G	c.(2290-2292)cAc>cGc	p.H764R	PTPN4_ENST00000544261.1_Missense_Mutation_p.H397R	NM_002830.3	NP_002821.1	P29074	PTN4_HUMAN	protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte)	764	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)			endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|urinary_tract(1)	30					Alendronate(DB00630)	GTTAAATGTCACCAATATTGG	0.308																																					p.H764R		Atlas-SNP	.											.	PTPN4	89	.	0			c.A2291G						.						44	39	41					2																	120720202		2203	4300	6503	SO:0001583	missense	5775	exon24			AATGTCACCAATA		CCDS2129.1	2q14.2	2011-06-09			ENSG00000088179	ENSG00000088179		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9656	protein-coding gene	gene with protein product		176878				1648233	Standard	NM_002830		Approved	PTPMEG	uc002tmf.2	P29074	OTTHUMG00000131436	ENST00000263708.2:c.2291A>G	chr2.hg19:g.120720202A>G	ENSP00000263708:p.His764Arg	97.0	0.0		116.0	5.0	NM_002830	B2RBV8|Q9UDA7	Missense_Mutation	SNP	ENST00000263708.2	hg19	CCDS2129.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.148096	0.78001	.	.	ENSG00000088179	ENST00000263708;ENST00000544261	D;D	0.83163	-1.69;-1.69	5.51	5.51	0.81932	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	D	0.000000	D	0.92980	0.7766	M	0.92970	3.365	0.80722	D	1	D	0.59357	0.985	D	0.74348	0.983	D	0.94565	0.7766	10	0.87932	D	0	.	15.6199	0.76799	1.0:0.0:0.0:0.0	.	764	P29074	PTN4_HUMAN	R	764;397	ENSP00000263708:H764R;ENSP00000445841:H397R	ENSP00000263708:H764R	H	+	2	0	PTPN4	120436672	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	8.976000	0.93442	2.095000	0.63458	0.377000	0.23210	CAC	.	.		0.308	PTPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254233.2			G	120720202	A	G	120720202	3	3	255	1	0	0	0	0	1	0	0	0	12805	159	6	2	2381	2	PTPN4	2	120720202	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	18233941	120720202	122479171	87	35432										
ERCC3	2071	hgsc.bcm.edu	37	chr2	128051105	128051105	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttaccacccagaggggcctgGaggtgtggtcgtccttcagc	14	12	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:128051105G>A	ENST00000285398.2	-	2	312	c.218C>T	c.(217-219)tCc>tTc	p.S73F	ERCC3_ENST00000493187.2_Missense_Mutation_p.S9F	NM_000122.1	NP_000113.1	P19447	ERCC3_HUMAN	excision repair cross-complementation group 3	73					7-methylguanosine mRNA capping (GO:0006370)|apoptotic process (GO:0006915)|DNA repair (GO:0006281)|DNA topological change (GO:0006265)|gene expression (GO:0010467)|hair cell differentiation (GO:0035315)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA duplex unwinding (GO:0000717)|nucleotide-excision repair, DNA incision (GO:0033683)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein localization (GO:0008104)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|response to UV (GO:0009411)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)|viral process (GO:0016032)	holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' DNA helicase activity (GO:0043138)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|damaged DNA binding (GO:0003684)|dATP binding (GO:0032564)|DNA binding (GO:0003677)|GTP binding (GO:0005525)|peptide binding (GO:0042277)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	31	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.073)		GAGGGGCCTGGAGGTGTGGTC	0.592			"Mis, S"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.S73F		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (B)	2	2q21	2071	"excision repair cross-complementing rodent repair deficiency, complementation group 3 (xeroderma pigmentosum group B complementing)"		E	.	ERCC3	73	.	0			c.C218T						.						77	68	71					2																	128051105		2203	4300	6503	SO:0001583	missense	2071	exon2	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	GGCCTGGAGGTGT	M31899	CCDS2144.1	2q21	2014-09-17	2014-03-07		ENSG00000163161	ENSG00000163161		"General transcription factors", "General transcription factor IIH complex subunits"	3435	protein-coding gene	gene with protein product	"xeroderma pigmentosum group B complementing"	133510	"excision repair cross-complementing rodent repair deficiency, complementation group 3"			8202161	Standard	NM_000122		Approved	XPB, BTF2, RAD25, TFIIH, GTF2H	uc002toh.1	P19447	OTTHUMG00000131530	ENST00000285398.2:c.218C>T	chr2.hg19:g.128051105G>A	ENSP00000285398:p.Ser73Phe	174.0	0.0		172.0	54.0	NM_000122	Q53QM0	Missense_Mutation	SNP	ENST00000285398.2	hg19	CCDS2144.1	.	.	.	.	.	.	.	.	.	.	G	18.90	3.721592	0.68959	.	.	ENSG00000163161	ENST00000285398;ENST00000493187	T;T	0.66995	-0.24;-0.21	4.52	4.52	0.55395	.	0.000000	0.85682	D	0.000000	T	0.64702	0.2622	L	0.54323	1.7	0.80722	D	1	B;B	0.18013	0.025;0.025	B;B	0.20767	0.031;0.031	T	0.65483	-0.6157	10	0.62326	D	0.03	-17.7841	17.448	0.87584	0.0:0.0:1.0:0.0	.	73;73	A8K359;P19447	.;ERCC3_HUMAN	F	73;9	ENSP00000285398:S73F;ENSP00000444796:S9F	ENSP00000285398:S73F	S	-	2	0	ERCC3	127767575	1.000000	0.71417	0.159000	0.22649	0.969000	0.65631	8.939000	0.92951	2.347000	0.79759	0.655000	0.94253	TCC	.	.		0.592	ERCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331028.1	NM_000122		A	128051105	G	A	128051105	3	1	255	1	0	0	0	0	1	0	0	0	5216	1174	41	3	2186	3	ERCC3	2	128051105	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	7330903	128051105	115148268	88	35433										
FAM128A	653784	hgsc.bcm.edu	37	chr2	132249809	132249809	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcggggtcgataccgccgccCgccgcctgagccagctcgta	13	17	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:132249809C>A	ENST00000309451.6	-	1	186	c.141G>T	c.(139-141)gcG>gcT	p.A47A	AC093838.4_ENST00000438378.2_RNA|MIR4784_ENST00000579560.1_RNA|MZT2A_ENST00000410036.2_Intron	NM_001085365.1	NP_001078834.1	Q6P582	MZT2A_HUMAN	mitotic spindle organizing protein 2A	47				EEMELYELAQAAGGGIDPDVFK -> LQGGGRAGRRGLTGP ASVPAR (in Ref. 2; AAI04651). {ECO:0000305}.		centrosome (GO:0005813)|gamma-tubulin ring complex (GO:0008274)|spindle (GO:0005819)				breast(1)|lung(1)	2						TACCGCCGCCCGCCGCCTGAG	0.736																																					p.A47A		Atlas-SNP	.											.	MZT2A	6	.	0			c.G141T						.						7	12	10					2																	132249809		2146	4261	6407	SO:0001819	synonymous_variant	653784	exon1			GCCGCCCGCCGCC	BC018206	CCDS42758.1	2q21.1	2013-10-11	2010-07-22	2010-07-22	ENSG00000173272	ENSG00000173272			33187	protein-coding gene	gene with protein product	"mitotic-spindle organizing protein associated with a ring of gamma-tubulin 2A"	613449	"family with sequence similarity 128, member A"	FAM128A		20360068	Standard	NM_001085365		Approved	MOZART2A	uc002tsw.4	Q6P582	OTTHUMG00000153606	ENST00000309451.6:c.141G>T	chr2.hg19:g.132249809C>A		39.0	0.0		42.0	4.0	NM_001085365	Q3SWV8|Q8WVB2	Silent	SNP	ENST00000309451.6	hg19	CCDS42758.1																																																																																			.	.		0.736	MZT2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331811.2			A	132249809	C	A	132249809	2	1	255	1	0	0	0	0	0	0	0	1	5439	639	23	1		1	FAM128A	2	132249809	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	4198704	132249809	110949564	89	35434										
TMEM163	81615	hgsc.bcm.edu	37	chr2	135308182	135308182	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgcacagcggccgcgttgctGtaacgccacaggacaatcgc	12	14	0	0	rs576374684		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:135308182G>A	ENST00000281924.6	-	4	481	c.417C>T	c.(415-417)taC>taT	p.Y139Y		NM_030923.4	NP_112185.1	Q8TC26	TM163_HUMAN	transmembrane protein 163	139						cell junction (GO:0030054)|early endosome membrane (GO:0031901)|integral component of synaptic vesicle membrane (GO:0030285)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(5)|lung(8)|stomach(1)|urinary_tract(1)	16				BRCA - Breast invasive adenocarcinoma(221;0.154)		CCGCGTTGCTGTAACGCCACA	0.522													G|||	1	0.000199681	8e-04	0	5008	,	,		21293	0		0	False		,,,				2504	0				p.Y139Y		Atlas-SNP	.											.	TMEM163	34	.	0			c.C417T						.						124	118	120					2																	135308182		2203	4300	6503	SO:0001819	synonymous_variant	81615	exon4			GTTGCTGTAACGC		CCDS2172.1	2q21.3	2008-02-05			ENSG00000152128	ENSG00000152128			25380	protein-coding gene	gene with protein product						17623043	Standard	NM_030923		Approved	DKFZP566N034, SV31	uc002ttx.3	Q8TC26	OTTHUMG00000131713	ENST00000281924.6:c.417C>T	chr2.hg19:g.135308182G>A		119.0	0.0		100.0	4.0	NM_030923	Q53QM3|Q53SV7|Q69YH3|Q9UFG3	Silent	SNP	ENST00000281924.6	hg19	CCDS2172.1																																																																																			.	.		0.522	TMEM163-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254631.2	NM_030923		A	135308182	G	A	135308182	2	1	255	1	0	0	0	0	0	0	0	1	16093	1372	48	3		3	TMEM163	2	135308182	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	3058373	135308182	107891191	90	35435										
GALNT13	114805	hgsc.bcm.edu	37	chr2	155295139	155295139	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gctgacaaagaaatccgaacCgatgacttgtgcttggatgt	11	8	0	3	rs182009673		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:155295139C>A	ENST00000392825.3	+	12	1998	c.1431C>A	c.(1429-1431)acC>acA	p.T477T	GALNT13_ENST00000487047.1_3'UTR|AC009227.2_ENST00000434635.1_RNA|GALNT13_ENST00000409237.1_Silent_p.T477T	NM_052917.2	NP_443149.2	Q8IUC8	GLT13_HUMAN	polypeptide N-acetylgalactosaminyltransferase 13	477	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(6)|lung(37)|ovary(3)|pancreas(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	65						AAATCCGAACCGATGACTTGT	0.343																																					p.T477T		Atlas-SNP	.											.	GALNT13	170	.	0			c.C1431A						.						124	123	124					2																	155295139		2203	4300	6503	SO:0001819	synonymous_variant	114805	exon12			CCGAACCGATGAC	AB067505	CCDS2199.1	2q24.1	2014-03-13	2014-03-13		ENSG00000144278	ENSG00000144278	2.4.1.41	"Glycosyltransferase family 2 domain containing"	23242	protein-coding gene	gene with protein product	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13", "polypeptide GalNAc transferase 13"	608369	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13 (GalNAc-T13)"			11572484, 12407114	Standard	XM_005246267		Approved	KIAA1918, GalNAc-T13	uc002tyr.4	Q8IUC8	OTTHUMG00000131917	ENST00000392825.3:c.1431C>A	chr2.hg19:g.155295139C>A		141.0	0.0		117.0	5.0	NM_052917	Q08ER7|Q68VI8|Q6ZWG1|Q96PX0|Q9UIE5	Silent	SNP	ENST00000392825.3	hg19	CCDS2199.1																																																																																			.	C|0.999;T|0.001		0.343	GALNT13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254870.2	NM_052917		A	155295139	C	A	155295139	2	1	255	1	0	0	0	0	0	0	0	1	6219	639	23	1		1	GALNT13	2	155295139	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	19986957	155295139	87904234	91	35436										
PKP4	8502	hgsc.bcm.edu	37	chr2	159519916	159519916	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	acccagccaccttggaaggcTctgcagggtctctccagaac	10	15	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:159519916T>C	ENST00000389759.3	+	15	2648	c.2536T>C	c.(2536-2538)Tct>Cct	p.S846P	AC005042.4_ENST00000342892.4_RNA|PKP4_ENST00000495123.1_3'UTR|PKP4_ENST00000389757.3_Missense_Mutation_p.S846P	NM_003628.3	NP_003619.2	Q99569	PKP4_HUMAN	plakophilin 4	846					cell-cell junction assembly (GO:0007043)|cell-cell signaling (GO:0007267)|positive regulation of cytokinesis (GO:0032467)|positive regulation of gene expression (GO:0010628)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell adhesion (GO:0030155)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|desmosome (GO:0030057)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)				breast(2)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(21)|ovary(6)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	61						CTTGGAAGGCTCTGCAGGGTC	0.488										HNSCC(62;0.18)																											p.S846P		Atlas-SNP	.											.	PKP4	133	.	0			c.T2536C						.						61	62	61					2																	159519916		2203	4300	6503	SO:0001583	missense	8502	exon15			GAAGGCTCTGCAG	X81889	CCDS33305.1, CCDS33306.1	2q24.1	2013-02-14			ENSG00000144283	ENSG00000144283		"Armadillo repeat containing"	9026	protein-coding gene	gene with protein product		604276				9342840, 8937994	Standard	NM_003628		Approved	p0071	uc002tzv.3	Q99569	OTTHUMG00000153969	ENST00000389759.3:c.2536T>C	chr2.hg19:g.159519916T>C	ENSP00000374409:p.Ser846Pro	126.0	0.0		118.0	5.0	NM_001005476	Q86W91	Missense_Mutation	SNP	ENST00000389759.3	hg19	CCDS33305.1	.	.	.	.	.	.	.	.	.	.	T	19.72	3.879990	0.72294	.	.	ENSG00000144283	ENST00000389757;ENST00000389759	T;T	0.52295	0.67;0.67	5.76	4.59	0.56863	Armadillo-like helical (1);Armadillo-type fold (1);	0.122752	0.56097	D	0.000027	T	0.58133	0.2101	M	0.76574	2.34	0.54753	D	0.999986	D;P;P	0.56035	0.974;0.867;0.954	P;B;P	0.50754	0.649;0.439;0.649	T	0.63637	-0.6592	10	0.87932	D	0	-10.2313	13.0322	0.58848	0.0:0.0:0.1347:0.8653	.	801;846;846	Q4W5T8;Q99569-2;Q99569	.;.;PKP4_HUMAN	P	846	ENSP00000374407:S846P;ENSP00000374409:S846P	ENSP00000374407:S846P	S	+	1	0	PKP4	159228162	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.167000	0.58209	0.978000	0.38470	0.533000	0.62120	TCT	.	.		0.488	PKP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333250.1			C	159519916	T	C	159519916	3	2	255	1	0	0	0	0	1	0	0	0	11996	1551	54	2	2590	2	PKP4	2	159519916	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	4224777	159519916	83679457	92	35437										
MARCH7	64844	hgsc.bcm.edu	37	chr2	160605076	160605076	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tctagatctcatatttttagAagagaatcaaatgaagtggt	8	4	3	4			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:160605076A>G	ENST00000259050.4	+	5	1397	c.1275A>G	c.(1273-1275)agA>agG	p.R425R	MARCH7_ENST00000539065.1_Silent_p.R369R|MARCH7_ENST00000409591.1_Silent_p.R387R|MARCH7_ENST00000409175.1_Silent_p.R425R	NM_001282805.1|NM_001282807.1|NM_022826.2	NP_001269734.1|NP_001269736.1|NP_073737.1	Q9H992	MARH7_HUMAN	membrane-associated ring finger (C3HC4) 7, E3 ubiquitin protein ligase	425					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|stomach(2)	18						ATATTTTTAGAAGAGAATCAA	0.438																																					p.R425R		Atlas-SNP	.											.	MARCH7	48	.	0			c.A1275G						.						76	80	79					2																	160605076		2203	4300	6503	SO:0001819	synonymous_variant	64844	exon5			TTTTAGAAGAGAA	AK022973	CCDS2210.1, CCDS63038.1, CCDS63039.1	2q24.2	2013-01-09	2012-02-23	2005-01-27	ENSG00000136536	ENSG00000136536		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	17393	protein-coding gene	gene with protein product		613334	"axotrophin", "membrane-associated ring finger (C3HC4) 7"	AXOT		14722266	Standard	XM_005246773		Approved	MARCH-VII, RNF177	uc002uax.3	Q9H992	OTTHUMG00000132029	ENST00000259050.4:c.1275A>G	chr2.hg19:g.160605076A>G		77.0	0.0		87.0	4.0	NM_022826	A8K9X1|B7Z7P5|D3DPB0|Q53GQ1|Q9BTR9	Silent	SNP	ENST00000259050.4	hg19	CCDS2210.1																																																																																			.	.		0.438	MARCH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255040.3	NM_022826		G	160605076	A	G	160605076	2	3	255	1	0	0	0	0	0	0	0	1	9315	243	9	2		2	MARCH7	2	160605076	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	1085160	160605076	82594297	93	35438										
SCN1A	6323	hgsc.bcm.edu	37	chr2	166900257	166900257	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gatgtaggaactgaaggtccAccaaccaaggaaaccacacc	9	12	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:166900257A>G	ENST00000303395.4	-	11	1964	c.1965T>C	c.(1963-1965)ggT>ggC	p.G655G	AC010127.3_ENST00000599041.1_RNA|AC010127.3_ENST00000595647.1_RNA|SCN1A_ENST00000409050.1_Intron|AC010127.3_ENST00000595268.1_RNA|SCN1A_ENST00000423058.2_Silent_p.G655G|SCN1A_ENST00000375405.3_Silent_p.G655G			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	655					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CTGAAGGTCCACCAACCAAGG	0.478																																					p.G655G		Atlas-SNP	.											.	SCN1A	641	.	0			c.T1965C						.						143	122	129					2																	166900257		2203	4300	6503	SO:0001819	synonymous_variant	6323	exon11			AGGTCCACCAACC	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10585	protein-coding gene	gene with protein product		182389	"febrile convulsions 3"	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.1965T>C	chr2.hg19:g.166900257A>G		142.0	0.0		115.0	5.0	NM_001165963	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Silent	SNP	ENST00000303395.4	hg19	CCDS54413.1																																																																																			.	.		0.478	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		G	166900257	A	G	166900257	2	3	255	1	0	0	0	0	0	0	0	1	13929	146	6	2		2	SCN1A	2	166900257	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	6295181	166900257	76299116	94	35439										
LRP2	4036	hgsc.bcm.edu	37	chr2	170104009	170104009	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	atggcacccagtctccagtcAgtaaaaaataaatgctctga	7	10	3	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:170104009A>G	ENST00000263816.3	-	20	3072	c.2787T>C	c.(2785-2787)acT>acC	p.T929T	LRP2_ENST00000443831.1_Silent_p.T792T	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	929					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	GTCTCCAGTCAGTAAAAAATA	0.368																																					p.T929T		Atlas-SNP	.											.	LRP2	751	.	0			c.T2787C						.						87	85	86					2																	170104009		2203	4300	6503	SO:0001819	synonymous_variant	4036	exon20			CCAGTCAGTAAAA		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.2787T>C	chr2.hg19:g.170104009A>G		77.0	0.0		86.0	4.0	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	hg19	CCDS2232.1																																																																																			.	.		0.368	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		G	170104009	A	G	170104009	2	3	255	1	0	0	0	0	0	0	0	1	8965	175	7	2		2	LRP2	2	170104009	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	3203752	170104009	73095364	95	35440										
GPR155	151556	hgsc.bcm.edu	37	chr2	175324698	175324698	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttccaggctccaccactttgTggctctgagactgatcgaaa	9	12	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:175324698T>C	ENST00000392552.2	-	10	1917	c.1679A>G	c.(1678-1680)cAc>cGc	p.H560R	GPR155_ENST00000392551.2_Missense_Mutation_p.H560R|GPR155_ENST00000295500.4_Missense_Mutation_p.H560R	NM_001267051.1|NM_152529.6	NP_001253980.1|NP_689742.4	Q7Z3F1	GP155_HUMAN	G protein-coupled receptor 155	560					cognition (GO:0050890)|intracellular signal transduction (GO:0035556)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	26						CACCACTTTGTGGCTCTGAGA	0.468																																					p.H560R		Atlas-SNP	.											.	GPR155	76	.	0			c.A1679G						.						108	97	101					2																	175324698		2203	4300	6503	SO:0001583	missense	151556	exon11			ACTTTGTGGCTCT	AY255528	CCDS2259.1, CCDS74605.1	2q31.1	2012-04-10			ENSG00000163328	ENSG00000163328			22951	protein-coding gene	gene with protein product						12679517	Standard	NM_001033045		Approved	DEPDC3, DEP.7, FLJ31819, PGR22	uc002uiu.4	Q7Z3F1	OTTHUMG00000132336	ENST00000392552.2:c.1679A>G	chr2.hg19:g.175324698T>C	ENSP00000376335:p.His560Arg	81.0	0.0		78.0	4.0	NM_001033045	B2RCI2|D3DPE2|Q4G0Y6|Q53SJ3|Q53TA8|Q69YG8|Q86SP9|Q8N261|Q8N639|Q8N8K3|Q96MV6	Missense_Mutation	SNP	ENST00000392552.2	hg19	CCDS2259.1	.	.	.	.	.	.	.	.	.	.	T	5.161	0.215270	0.09810	.	.	ENSG00000163328	ENST00000392552;ENST00000510236;ENST00000392551;ENST00000295500	T;T;T	0.40756	1.02;1.02;1.02	5.89	-0.821	0.10822	.	0.761606	0.13610	N	0.375202	T	0.16685	0.0401	N	0.08118	0	0.09310	N	0.999991	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.26608	-1.0098	10	0.12766	T	0.61	-0.024	5.368	0.16125	0.0:0.4657:0.1864:0.3479	.	40;560	F5H464;Q7Z3F1	.;GP155_HUMAN	R	560;40;560;560	ENSP00000376335:H560R;ENSP00000376334:H560R;ENSP00000295500:H560R	ENSP00000295500:H560R	H	-	2	0	GPR155	175032944	0.801000	0.28930	0.494000	0.27515	0.805000	0.45488	0.506000	0.22658	0.153000	0.19213	0.459000	0.35465	CAC	.	.		0.468	GPR155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255455.1	NM_152529		C	175324698	T	C	175324698	3	2	255	1	0	0	0	0	1	0	0	0	6668	1696	59	2	961	2	GPR155	2	175324698	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	5220689	175324698	67874675	96	35441										
OSBPL6	114880	hgsc.bcm.edu	37	chr2	179197627	179197627	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	caggactggtttgatgcatgGgtctccaaactgcgacatca	11	10	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:179197627G>T	ENST00000190611.4	+	8	892	c.516G>T	c.(514-516)tgG>tgT	p.W172C	OSBPL6_ENST00000359685.3_Missense_Mutation_p.W172C|OSBPL6_ENST00000357080.4_Missense_Mutation_p.W172C|OSBPL6_ENST00000315022.2_Missense_Mutation_p.W151C|OSBPL6_ENST00000409045.3_Missense_Mutation_p.W172C|OSBPL6_ENST00000409631.1_Missense_Mutation_p.W172C|OSBPL6_ENST00000392505.2_Missense_Mutation_p.W172C	NM_032523.3	NP_115912.1	Q9BZF3	OSBL6_HUMAN	oxysterol binding protein-like 6	172	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				lipid transport (GO:0006869)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(18)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			TTGATGCATGGGTCTCCAAAC	0.428																																					p.W172C		Atlas-SNP	.											.	OSBPL6	178	.	0			c.G516T						.						162	156	158					2																	179197627		2203	4300	6503	SO:0001583	missense	114880	exon8			TGCATGGGTCTCC	AF392448	CCDS2277.1, CCDS2278.1, CCDS56150.1, CCDS56151.1, CCDS56152.1	2q32.1	2008-05-27			ENSG00000079156	ENSG00000079156		"Oxysterol binding proteins"	16388	protein-coding gene	gene with protein product	"OSBP-related protein 6"	606734				11483621	Standard	NM_001201480		Approved	ORP6	uc002uly.3	Q9BZF3	OTTHUMG00000132579	ENST00000190611.4:c.516G>T	chr2.hg19:g.179197627G>T	ENSP00000190611:p.Trp172Cys	126.0	0.0		122.0	5.0	NM_001201482	B4DTW1|C4AMC0|C4AME4|D3DPF6|D3DPF7|Q4ZG68|Q53T68|Q59H61|Q7Z4Q1|Q86V84|Q8N9T0|Q96SR1	Missense_Mutation	SNP	ENST00000190611.4	hg19	CCDS2277.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.775178	0.90108	.	.	ENSG00000079156	ENST00000392505;ENST00000359685;ENST00000357080;ENST00000409045;ENST00000190611;ENST00000409631;ENST00000315022	T;T;T;T;T;T;T	0.58210	0.35;0.45;0.61;0.4;0.4;0.45;0.43	5.57	5.57	0.84162	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.85682	D	0.000000	D	0.83078	0.5176	H	0.96604	3.85	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;0.999;0.996;0.999;0.997;0.998	D	0.88211	0.2890	10	0.87932	D	0	-9.033	19.9215	0.97087	0.0:0.0:1.0:0.0	.	172;151;172;172;172;172	Q9BZF3-4;Q9BZF3-3;Q9BZF3-2;Q9BZF3-5;Q9BZF3;Q86V84	.;.;.;.;OSBL6_HUMAN;.	C	172;172;172;172;172;172;151	ENSP00000376293:W172C;ENSP00000352713:W172C;ENSP00000349591:W172C;ENSP00000387248:W172C;ENSP00000190611:W172C;ENSP00000386885:W172C;ENSP00000318723:W151C	ENSP00000190611:W172C	W	+	3	0	OSBPL6	178905873	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.813000	0.99286	2.785000	0.95823	0.655000	0.94253	TGG	.	.		0.428	OSBPL6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334393.2	NM_032523		T	179197627	G	T	179197627	3	4	255	1	0	0	0	0	1	0	0	0	11290	1241	43	3	581	3	OSBPL6	2	179197627	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	3872929	179197627	64001746	97	35442										
TTN	7273	hgsc.bcm.edu	37	chr2	179399454	179399454	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cccctggtttcagctgacggGcttgaccaaattctatgatt	9	11	2	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:179399454G>A	ENST00000591111.1	-	308	97189	c.96965C>T	c.(96964-96966)gCc>gTc	p.A32322V	TTN-AS1_ENST00000431259.2_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.A24898V|TTN_ENST00000589042.1_Missense_Mutation_p.A33963V|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000415561.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.A25090V|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.A25023V|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.A31395V|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000419746.1_RNA			Q8WZ42	TITIN_HUMAN	titin	32322	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CAGCTGACGGGCTTGACCAAA	0.423																																					p.A33963V		Atlas-SNP	.											.	TTN	18412	.	0			c.C101888T						.						57	56	57					2																	179399454		1873	4114	5987	SO:0001583	missense	7273	exon358			TGACGGGCTTGAC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.96965C>T	chr2.hg19:g.179399454G>A	ENSP00000465570:p.Ala32322Val	153.0	0.0		99.0	4.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	21.8	4.201966	0.79127	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.75821	-0.97;-0.97;-0.97;-0.97	6.02	6.02	0.97574	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Protein kinase, catalytic domain (1);	.	.	.	.	D	0.89312	0.6679	M	0.91972	3.26	0.58432	D	0.999994	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.65010	0.931;0.931;0.931;0.931	D	0.90503	0.4475	9	0.87932	D	0	.	20.5373	0.99239	0.0:0.0:1.0:0.0	.	24898;25023;25090;32322	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	V	31395;24898;25090;25023;24895	ENSP00000343764:A31395V;ENSP00000434586:A24898V;ENSP00000340554:A25090V;ENSP00000352154:A25023V	ENSP00000340554:A25090V	A	-	2	0	TTN	179107700	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.922000	0.87538	2.857000	0.98124	0.650000	0.86243	GCC	.	.		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179399454	G	A	179399454	3	1	255	1	0	0	0	0	1	0	0	0	16750	1203	42	3	6111	3	TTN	2	179399454	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	201827	179399454	63799919	98	35443										
TTN	7273	hgsc.bcm.edu	37	chr2	179476169	179476169	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	acaccaatagcattgactgcTctcactctcaggacatattc	5	13	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:179476169T>C	ENST00000591111.1	-	219	46088	c.45864A>G	c.(45862-45864)agA>agG	p.R15288R	TTN_ENST00000460472.2_Silent_p.R7864R|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000589042.1_Silent_p.R16929R|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342175.6_Silent_p.R8056R|TTN_ENST00000359218.5_Silent_p.R7989R|TTN_ENST00000342992.6_Silent_p.R14361R|TTN-AS1_ENST00000589234.1_RNA			Q8WZ42	TITIN_HUMAN	titin	15288	Fibronectin type-III 11. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CATTGACTGCTCTCACTCTCA	0.408																																					p.R16929R		Atlas-SNP	.											.	TTN	18412	.	0			c.A50787G						.						95	93	94					2																	179476169		2031	4192	6223	SO:0001819	synonymous_variant	7273	exon269			GACTGCTCTCACT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.45864A>G	chr2.hg19:g.179476169T>C		121.0	0.0		122.0	5.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179476169	T	C	179476169	2	2	255	1	0	0	0	0	0	0	0	1	16750	1548	54	2		2	TTN	2	179476169	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	76715	179476169	63723204	99	35444										
TTN	7273	hgsc.bcm.edu	37	chr2	179647564	179647564	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agatagcaggatgtgctgacGgttccagcctcatttacagc	11	10	1	2	rs371447978		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:179647564G>T	ENST00000591111.1	-	18	3293	c.3069C>A	c.(3067-3069)acC>acA	p.T1023T	TTN_ENST00000460472.2_Silent_p.T977T|TTN_ENST00000360870.5_Silent_p.T1023T|TTN_ENST00000589042.1_Silent_p.T1023T|RP11-88L24.4_ENST00000582038.2_RNA|TTN_ENST00000342175.6_Silent_p.T977T|TTN_ENST00000359218.5_Silent_p.T977T|TTN_ENST00000342992.6_Silent_p.T1023T			Q8WZ42	TITIN_HUMAN	titin	32576	Ig-like 3.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.T1023T(3)|p.T977T(3)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATGTGCTGACGGTTCCAGCCT	0.498																																					p.T1023T		Atlas-SNP	.											TTN_ENST00000360870,NS,carcinoma,0,11	TTN	18412	.	6	Substitution - coding silent(6)	endometrium(6)	c.C3069A						.						88	73	78					2																	179647564		2203	4300	6503	SO:0001819	synonymous_variant	7273	exon18			GCTGACGGTTCCA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.3069C>A	chr2.hg19:g.179647564G>T		120.0	0.0		97.0	4.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.498	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179647564	G	T	179647564	2	4	255	1	0	0	0	0	0	0	0	1	16750	1103	39	1		1	TTN	2	179647564	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	171395	179647564	63551809	100	35445										
ZC3H15	55854	hgsc.bcm.edu	37	chr2	187366137	187366137	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tttacattgatgcaagagatGaagaacttgaaaaaggtaat	9	3	0	5			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:187366137G>A	ENST00000337859.6	+	4	654	c.427G>A	c.(427-429)Gaa>Aaa	p.E143K	ZC3H15_ENST00000468120.1_3'UTR|ZC3H15_ENST00000544130.1_Intron	NM_018471.2	NP_060941.2	Q8WU90	ZC3HF_HUMAN	zinc finger CCCH-type containing 15	143					cytokine-mediated signaling pathway (GO:0019221)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|skin(1)	15			OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Epithelial(96;0.0922)|all cancers(119;0.233)			TGCAAGAGATGAAGAACTTGA	0.313																																					p.E143K		Atlas-SNP	.											.	ZC3H15	28	.	0			c.G427A						.						87	88	88					2																	187366137		1836	4072	5908	SO:0001583	missense	55854	exon4			AGAGATGAAGAAC		CCDS42791.1	2q32.1	2012-07-05			ENSG00000065548	ENSG00000065548		"Zinc fingers, CCCH-type domain containing"	29528	protein-coding gene	gene with protein product	"likely ortholog of mouse immediate early response, erythropoietin 4"					10880228	Standard	NM_018471		Approved	LEREPO4	uc002upo.3	Q8WU90	OTTHUMG00000154251	ENST00000337859.6:c.427G>A	chr2.hg19:g.187366137G>A	ENSP00000338788:p.Glu143Lys	78.0	0.0		125.0	5.0	NM_018471	B4DMW2|D3DPG7|Q5QTQ4|Q8WZ06|Q9NUZ3|Q9NZ37|Q9P079	Missense_Mutation	SNP	ENST00000337859.6	hg19	CCDS42791.1	.	.	.	.	.	.	.	.	.	.	G	36	5.601878	0.96614	.	.	ENSG00000065548	ENST00000337859;ENST00000536434	T	0.33438	1.41	5.94	5.94	0.96194	.	0.089037	0.85682	D	0.000000	T	0.41026	0.1141	L	0.55017	1.72	0.80722	D	1	P	0.52316	0.952	P	0.47075	0.536	T	0.10177	-1.0641	10	0.48119	T	0.1	-9.3332	20.3736	0.98901	0.0:0.0:1.0:0.0	.	143	Q8WU90	ZC3HF_HUMAN	K	143	ENSP00000338788:E143K	ENSP00000338788:E143K	E	+	1	0	ZC3H15	187074382	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.496000	0.97967	2.820000	0.97059	0.650000	0.86243	GAA	.	.		0.313	ZC3H15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334547.2	NM_018471		A	187366137	G	A	187366137	3	1	255	1	0	0	0	0	1	0	0	0	17582	1291	45	3	441	3	ZC3H15	2	187366137	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	7718573	187366137	55833236	101	35446										
SLC40A1	30061	hgsc.bcm.edu	37	chr2	190426883	190426883	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcaattacattttcttgcagCaactgtgtcacagttaaatc	5	9	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:190426883C>A	ENST00000261024.2	-	8	1863	c.1437G>T	c.(1435-1437)ttG>ttT	p.L479F		NM_014585.5	NP_055400.1	Q9NP59	S40A1_HUMAN	solute carrier family 40 (iron-regulated transporter), member 1	479					anatomical structure morphogenesis (GO:0009653)|cellular iron ion homeostasis (GO:0006879)|endothelium development (GO:0003158)|iron ion transmembrane transport (GO:0034755)|lymphocyte homeostasis (GO:0002260)|multicellular organismal iron ion homeostasis (GO:0060586)|negative regulation of apoptotic process (GO:0043066)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|spleen trabecula formation (GO:0060345)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	iron ion transmembrane transporter activity (GO:0005381)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(117;0.000917)|Epithelial(96;0.014)|all cancers(119;0.0491)			TTTCTTGCAGCAACTGTGTCA	0.313																																					p.L479F		Atlas-SNP	.											.	SLC40A1	51	.	0			c.G1437T						.						48	47	47					2																	190426883		2203	4300	6503	SO:0001583	missense	30061	exon8			TTGCAGCAACTGT	AF215636	CCDS2299.1	2q32	2014-09-17	2003-06-04	2003-06-05	ENSG00000138449	ENSG00000138449		"Solute carriers"	10909	protein-coding gene	gene with protein product	"ferroportin 1"	604653	"solute carrier family 11 (proton-coupled divalent metal ion transporters), member 3"	SLC11A3		10828623	Standard	NM_014585		Approved	MTP1, IREG1, FPN1, HFE4	uc002uqp.4	Q9NP59	OTTHUMG00000132662	ENST00000261024.2:c.1437G>T	chr2.hg19:g.190426883C>A	ENSP00000261024:p.Leu479Phe	66.0	0.0		97.0	4.0	NM_014585	Q6FI62|Q7Z4F8|Q8IVB2|Q9NRL0	Missense_Mutation	SNP	ENST00000261024.2	hg19	CCDS2299.1	.	.	.	.	.	.	.	.	.	.	C	19.46	3.832574	0.71258	.	.	ENSG00000138449	ENST00000261024	D	0.82344	-1.6	5.92	5.03	0.67393	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	D	0.90133	0.6917	M	0.83483	2.645	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.90219	0.4270	10	0.72032	D	0.01	-21.1431	9.1175	0.36766	0.0:0.7512:0.1212:0.1276	.	479	Q9NP59	S40A1_HUMAN	F	479	ENSP00000261024:L479F	ENSP00000261024:L479F	L	-	3	2	SLC40A1	190135128	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.779000	0.26746	2.814000	0.96858	0.585000	0.79938	TTG	.	.		0.313	SLC40A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255916.2			A	190426883	C	A	190426883	3	1	255	1	0	0	0	0	1	0	0	0	14643	709	25	3	282	3	SLC40A1	2	190426883	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	3060746	190426883	52772490	102	35447										
PMS1	5378	hgsc.bcm.edu	37	chr2	190656664	190656664	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gccacaagcgtagatgttaaActggtgagtgtccttgagaa	12	7	0	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:190656664A>G	ENST00000441310.2	+	2	362	c.129A>G	c.(127-129)aaA>aaG	p.K43K	PMS1_ENST00000418224.3_5'UTR|PMS1_ENST00000447232.2_Silent_p.K43K|PMS1_ENST00000409823.3_Silent_p.K43K|PMS1_ENST00000374826.4_Silent_p.K43K|PMS1_ENST00000432292.3_5'UTR|PMS1_ENST00000421722.1_3'UTR|PMS1_ENST00000409985.1_Silent_p.K43K	NM_000534.4	NP_000525.1	P54277	PMS1_HUMAN	PMS1 postmeiotic segregation increased 1 (S. cerevisiae)	43					ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)	MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|mismatched DNA binding (GO:0030983)|single-stranded DNA binding (GO:0003697)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(16)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			OV - Ovarian serous cystadenocarcinoma(117;0.0013)|Epithelial(96;0.0263)|all cancers(119;0.0751)			TAGATGTTAAACTGGTGAGTG	0.393			"Mis, N"			"colorectal, endometrial, ovarian"		Direct reversal of damage;Mismatch excision repair (MMR)																													p.K43K		Atlas-SNP	.	yes	Rec		Hereditary non-polyposis colorectal cancer	2	2q31-q33	5378	PMS1 postmeiotic segregation increased 1 (S. cerevisiae)		E	.	PMS1	78	.	0			c.A129G						.						90	82	85					2																	190656664		2203	4300	6503	SO:0001819	synonymous_variant	5378	exon2			TGTTAAACTGGTG		CCDS2302.1, CCDS46473.1, CCDS46474.1, CCDS74615.1	2q31-q33	2014-09-17	2001-11-28		ENSG00000064933	ENSG00000064933			9121	protein-coding gene	gene with protein product		600258	"postmeiotic segregation increased (S. cerevisiae) 1"	PMSL1		8072530	Standard	NM_000534		Approved		uc002urh.4	P54277	OTTHUMG00000132664	ENST00000441310.2:c.129A>G	chr2.hg19:g.190656664A>G		109.0	0.0		95.0	4.0	NM_001128143	D3DPI1|Q4VAL4|Q5FBZ3|Q5FBZ6|Q5FBZ8	Silent	SNP	ENST00000441310.2	hg19	CCDS2302.1																																																																																			.	.		0.393	PMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255918.2			G	190656664	A	G	190656664	2	3	255	1	0	0	0	0	0	0	0	1	12151	40	2	2		2	PMS1	2	190656664	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	229781	190656664	52542709	103	35448										
NAB1	4664	hgsc.bcm.edu	37	chr2	191548468	191548468	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cttatttgacccacaggatgGgtttccagatttccaggatt	9	9	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:191548468G>T	ENST00000337386.5	+	7	1471	c.1010G>T	c.(1009-1011)gGg>gTg	p.G337V	AC006460.2_ENST00000411949.1_RNA|AC006460.2_ENST00000421437.1_RNA|NAB1_ENST00000357215.5_Intron|NAB1_ENST00000484774.1_3'UTR|NAB1_ENST00000409641.1_Missense_Mutation_p.G337V|AC006460.2_ENST00000428032.1_RNA|NAB1_ENST00000409581.1_Missense_Mutation_p.G337V|NAB1_ENST00000545490.1_Intron	NM_005966.3	NP_005957.2	Q13506	NAB1_HUMAN	NGFI-A binding protein 1 (EGR1 binding protein 1)	337	Necessary for nuclear localization. {ECO:0000250}.				endochondral ossification (GO:0001958)|myelination (GO:0042552)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of epidermis development (GO:0045682)|regulation of transcription, DNA-templated (GO:0006355)|Schwann cell differentiation (GO:0014037)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				kidney(2)|large_intestine(2)|lung(1)|prostate(1)|skin(1)	7			OV - Ovarian serous cystadenocarcinoma(117;0.00318)|Epithelial(96;0.0405)|all cancers(119;0.109)			CCACAGGATGGGTTTCCAGAT	0.358																																					p.G337V		Atlas-SNP	.											.	NAB1	31	.	0			c.G1010T						.						70	72	71					2																	191548468		2203	4300	6503	SO:0001583	missense	4664	exon7			AGGATGGGTTTCC		CCDS2307.1	2q32.3-q33	2008-05-23			ENSG00000138386	ENSG00000138386			7626	protein-coding gene	gene with protein product	"EGR1 binding protein 1"	600800				7624335, 8668170, 9418898	Standard	XM_005246579		Approved		uc002usb.3	Q13506	OTTHUMG00000132689	ENST00000337386.5:c.1010G>T	chr2.hg19:g.191548468G>T	ENSP00000336894:p.Gly337Val	91.0	0.0		80.0	5.0	NM_005966	O75383|O75384|Q6GTU1|Q9UEV1	Missense_Mutation	SNP	ENST00000337386.5	hg19	CCDS2307.1	.	.	.	.	.	.	.	.	.	.	G	15.97	2.991187	0.54041	.	.	ENSG00000138386	ENST00000409581;ENST00000337386;ENST00000409641	.	.	.	5.14	5.14	0.70334	Nab1, C-terminal (1);	0.221327	0.47852	D	0.000218	T	0.56426	0.1984	L	0.27053	0.805	0.80722	D	1	P;P	0.37101	0.582;0.582	P;P	0.47299	0.543;0.543	T	0.59118	-0.7514	9	0.54805	T	0.06	-14.4149	15.9119	0.79479	0.0:0.0:1.0:0.0	.	337;337	B8ZZS2;Q13506	.;NAB1_HUMAN	V	337	.	ENSP00000336894:G337V	G	+	2	0	NAB1	191256713	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	6.179000	0.71974	2.675000	0.91044	0.650000	0.86243	GGG	.	.		0.358	NAB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255986.1	NM_005966		T	191548468	G	T	191548468	3	4	255	1	0	0	0	0	1	0	0	0	10140	1232	43	3	1024	3	NAB1	2	191548468	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	891804	191548468	51650905	104	35449										
LANCL1	10314	hgsc.bcm.edu	37	chr2	211341073	211341073	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcaaagtagccttcggccagGgatttgttataatcagcata	9	8	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:211341073G>C	ENST00000443314.1	-	1	390	c.48C>G	c.(46-48)tcC>tcG	p.S16S	LANCL1_ENST00000233714.4_Silent_p.S16S|LANCL1_ENST00000441020.3_Silent_p.S16S|CPS1_ENST00000430249.2_5'Flank|LANCL1_ENST00000431941.2_Silent_p.S16S|LANCL1_ENST00000450366.2_Silent_p.S16S			O43813	LANC1_HUMAN	LanC lantibiotic synthetase component C-like 1 (bacterial)	16					G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|G-protein coupled receptor activity (GO:0004930)|glutathione binding (GO:0043295)|low-density lipoprotein particle receptor binding (GO:0050750)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(5)|liver(1)|lung(4)|prostate(1)	12				Epithelial(149;0.00562)|Lung(261;0.0468)|LUSC - Lung squamous cell carcinoma(261;0.0495)|all cancers(144;0.0569)		CTTCGGCCAGGGATTTGTTAT	0.517																																					p.S16S		Atlas-SNP	.											.	LANCL1	23	.	0			c.C48G						.						53	51	52					2																	211341073		2203	4300	6503	SO:0001819	synonymous_variant	10314	exon2			GGCCAGGGATTTG	Y11395	CCDS2392.1	2q33-q35	2008-05-23	2001-12-04		ENSG00000115365	ENSG00000115365			6508	protein-coding gene	gene with protein product		604155	"LanC (bacterial lantibiotic synthetase component C)-like 1"	GPR69A		9512664	Standard	NM_001136574		Approved	p40	uc010zjh.2	O43813	OTTHUMG00000132991	ENST00000443314.1:c.48C>G	chr2.hg19:g.211341073G>C		374.0	0.0		322.0	163.0	NM_001136574		Silent	SNP	ENST00000443314.1	hg19	CCDS2392.1																																																																																			.	.		0.517	LANCL1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336817.1	NM_006055		C	211341073	G	C	211341073	2	2	255	1	0	0	0	0	0	0	0	1	8629	1219	43	4		4	LANCL1	2	211341073	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	19792605	211341073	31858300	105	35450										
CPS1	1373	hgsc.bcm.edu	37	chr2	211455601	211455601	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	acaggattggctgctggtgcCaaaacctacaagatgtccat	10	10	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:211455601C>T	ENST00000233072.5	+	9	1114	c.918C>T	c.(916-918)gcC>gcT	p.A306A	CPS1_ENST00000451903.2_5'Flank|CPS1_ENST00000430249.2_Silent_p.A312A	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	306	Glutamine amidotransferase type-1.				anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	CTGCTGGTGCCAAAACCTACA	0.398																																					p.A312A		Atlas-SNP	.											.	CPS1	485	.	0			c.C936T						.						85	91	89					2																	211455601		2203	4300	6503	SO:0001819	synonymous_variant	1373	exon10			TGGTGCCAAAACC	AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"carbamoyl-phosphate synthetase 1, mitochondrial"				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.918C>T	chr2.hg19:g.211455601C>T		53.0	0.0		70.0	4.0	NM_001122633	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Silent	SNP	ENST00000233072.5	hg19	CCDS2393.1																																																																																			.	.		0.398	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5			T	211455601	C	T	211455601	2	4	255	1	0	0	0	0	0	0	0	1	3825	581	21	3		3	CPS1	2	211455601	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	114528	211455601	31743772	106	35451										
ABCA12	26154	hgsc.bcm.edu	37	chr2	215797448	215797448	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcataggacttctggtctttGgcaaagttgatgaaaacctg	10	7	3	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:215797448G>T	ENST00000272895.7	-	53	7917	c.7698C>A	c.(7696-7698)gcC>gcA	p.A2566A	ABCA12_ENST00000389661.4_Silent_p.A2248A|AC072062.1_ENST00000607412.1_RNA	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	2566					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		TCTGGTCTTTGGCAAAGTTGA	0.408																																					p.A2566A	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											.	ABCA12	368	.	0			c.C7698A						.						112	107	109					2																	215797448		2203	4300	6503	SO:0001819	synonymous_variant	26154	exon53			GTCTTTGGCAAAG	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.7698C>A	chr2.hg19:g.215797448G>T		107.0	0.0		96.0	4.0	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Silent	SNP	ENST00000272895.7	hg19	CCDS33372.1																																																																																			.	.		0.408	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		T	215797448	G	T	215797448	2	4	255	1	0	0	0	0	0	0	0	1	30	1335	47	3		3	ABCA12	2	215797448	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	4341847	215797448	27401925	107	35452										
TNS1	7145	hgsc.bcm.edu	37	chr2	218712394	218712394	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctggagggctgtgggtggtcGgaaggaaggcaggcaaggag	22	5	0	0	rs567400983		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:218712394G>T	ENST00000171887.4	-	17	2923	c.2471C>A	c.(2470-2472)cCg>cAg	p.P824Q	TNS1_ENST00000419504.1_Missense_Mutation_p.P824Q|TNS1_ENST00000480665.1_5'Flank|TNS1_ENST00000430930.1_Missense_Mutation_p.P824Q	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	824					cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)	p.P824L(1)		breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		GTGGGTGGTCGGAAGGAAGGC	0.582																																					p.P824Q		Atlas-SNP	.											TNS1,NS,carcinoma,0,2	TNS1	251	.	1	Substitution - Missense(1)	endometrium(1)	c.C2471A						.						86	69	75					2																	218712394		2203	4300	6503	SO:0001583	missense	7145	exon17			GTGGTCGGAAGGA	AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	11973	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 155"	600076	"tensin", "matrix-remodelling associated 6"	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.2471C>A	chr2.hg19:g.218712394G>T	ENSP00000171887:p.Pro824Gln	103.0	0.0		92.0	4.0	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	hg19	CCDS2407.1	.	.	.	.	.	.	.	.	.	.	G	5.143	0.211988	0.09757	.	.	ENSG00000079308	ENST00000171887;ENST00000419504;ENST00000430930	D;D;D	0.91521	-2.84;-2.86;-2.85	3.77	3.77	0.43336	.	0.832278	0.10588	N	0.657099	T	0.80929	0.4718	N	0.14661	0.345	0.80722	D	1	B;B;P;P;P	0.39216	0.435;0.048;0.664;0.468;0.468	B;B;B;B;B	0.33042	0.112;0.011;0.157;0.109;0.157	T	0.75611	-0.3258	10	0.16896	T	0.51	.	13.9433	0.64069	0.0:0.0:1.0:0.0	.	824;878;824;824;824	B2RU35;A1L0S7;Q9HBL0;E9PGF5;E9PF55	.;.;TENS1_HUMAN;.;.	Q	824	ENSP00000171887:P824Q;ENSP00000408724:P824Q;ENSP00000406016:P824Q	ENSP00000171887:P824Q	P	-	2	0	TNS1	218420639	0.892000	0.30473	0.893000	0.35052	0.213000	0.24496	0.912000	0.28597	2.093000	0.63338	0.455000	0.32223	CCG	.	.		0.582	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		T	218712394	G	T	218712394	3	4	255	1	0	0	0	0	1	0	0	0	16358	1116	39	1	2804	1	TNS1	2	218712394	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	2914946	218712394	24486979	108	35453										
PLCD4	84812	hgsc.bcm.edu	37	chr2	219480768	219480768	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gcatgcacggcaggccagggGcagtgccaagcccagctgtg	16	13	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:219480768G>A	ENST00000450993.2	+	3	503	c.164G>A	c.(163-165)gGc>gAc	p.G55D	PLCD4_ENST00000432688.1_Missense_Mutation_p.G55D|PLCD4_ENST00000417849.1_Missense_Mutation_p.G55D	NM_032726.3	NP_116115.1	Q9BRC7	PLCD4_HUMAN	phospholipase C, delta 4	55	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				acrosome reaction (GO:0007340)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phosphatidylinositol metabolic process (GO:0046488)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(1)|urinary_tract(3)	23		Renal(207;0.0915)		Epithelial(149;5.11e-07)|all cancers(144;0.000104)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		CAGGCCAGGGGCAGTGCCAAG	0.582																																					p.G55D		Atlas-SNP	.											PLCD4,NS,carcinoma,0,1	PLCD4	51	.	0			c.G164A						.						37	38	37					2																	219480768		2022	4189	6211	SO:0001583	missense	84812	exon3			CCAGGGGCAGTGC	AI366170	CCDS46516.1	2q35	2013-01-10			ENSG00000115556	ENSG00000115556	3.1.4.11	"EF-hand domain containing"	9062	protein-coding gene	gene with protein product		605939				10702683, 9056492	Standard	NM_032726		Approved		uc021vwx.1	Q9BRC7	OTTHUMG00000154743	ENST00000450993.2:c.164G>A	chr2.hg19:g.219480768G>A	ENSP00000388631:p.Gly55Asp	61.0	0.0		68.0	3.0	NM_032726	Q53FS8	Missense_Mutation	SNP	ENST00000450993.2	hg19	CCDS46516.1	.	.	.	.	.	.	.	.	.	.	G	16.52	3.147017	0.57151	.	.	ENSG00000115556	ENST00000450993;ENST00000251959;ENST00000457426;ENST00000417849;ENST00000415854;ENST00000432688	T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04	5.16	4.27	0.50696	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.400623	0.27495	N	0.019116	T	0.66025	0.2748	L	0.41124	1.26	0.22066	N	0.999383	D	0.56968	0.978	D	0.63113	0.911	T	0.57734	-0.7760	10	0.10111	T	0.7	.	14.4048	0.67075	0.0:0.1487:0.8513:0.0	.	55	Q9BRC7	PLCD4_HUMAN	D	55	ENSP00000388631:G55D;ENSP00000396942:G55D;ENSP00000391850:G55D;ENSP00000396185:G55D	ENSP00000251959:G55D	G	+	2	0	PLCD4	219189012	1.000000	0.71417	0.026000	0.17262	0.839000	0.47603	5.094000	0.64523	1.380000	0.46344	0.655000	0.94253	GGC	.	.		0.582	PLCD4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336876.1			A	219480768	G	A	219480768	3	1	255	1	0	0	0	0	1	0	0	0	12042	1203	42	3	170	3	PLCD4	2	219480768	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	768374	219480768	23718605	109	35454										
SERPINE2	5270	hgsc.bcm.edu	37	chr2	224856708	224856708	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gatctggggacagcagattgTcaatcatatctgtgaagcca	11	8	4	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:224856708T>C	ENST00000258405.4	-	4	739	c.497A>G	c.(496-498)gAc>gGc	p.D166G	SERPINE2_ENST00000409304.1_Missense_Mutation_p.D166G|SERPINE2_ENST00000447280.2_Missense_Mutation_p.D178G|SERPINE2_ENST00000409840.3_Missense_Mutation_p.D166G	NM_001136528.1|NM_006216.3	NP_001130000.1|NP_006207.1	P07093	GDN_HUMAN	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2	166					blood coagulation (GO:0007596)|cerebellar granular layer morphogenesis (GO:0021683)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|innervation (GO:0060384)|long-term synaptic potentiation (GO:0060291)|mating plug formation (GO:0042628)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of plasminogen activation (GO:0010757)|negative regulation of platelet activation (GO:0010544)|negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein processing (GO:0010955)|negative regulation of proteolysis (GO:0045861)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of sodium ion transport (GO:0010766)|positive regulation of astrocyte differentiation (GO:0048711)|regulation of cell migration (GO:0030334)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of timing of cell differentiation (GO:0048505)|secretion by cell (GO:0032940)|secretory granule organization (GO:0033363)|seminal vesicle epithelium development (GO:0061108)	cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|neuromuscular junction (GO:0031594)|platelet alpha granule (GO:0031091)|vesicle (GO:0031982)	glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	17		Renal(207;0.025)|all_lung(227;0.0586)|Lung NSC(271;0.0682)|all_hematologic(139;0.0797)		Epithelial(121;5.68e-10)|all cancers(144;1.9e-07)|Lung(261;0.0088)|LUSC - Lung squamous cell carcinoma(224;0.00902)		CAGCAGATTGTCAATCATATC	0.488																																					p.D178G		Atlas-SNP	.											.	SERPINE2	103	.	0			c.A533G						.						58	51	54					2																	224856708		2203	4300	6503	SO:0001583	missense	5270	exon4			AGATTGTCAATCA	M17783	CCDS2460.1, CCDS46525.1, CCDS46526.1	2q36.1	2014-02-18	2005-08-18		ENSG00000135919	ENSG00000135919		"Serine (or cysteine) peptidase inhibitors"	8951	protein-coding gene	gene with protein product	"glial-derived nexin 1"	177010	"serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2"	PI7		7665170, 24172014	Standard	NM_006216		Approved	PN1, GDN, PNI, nexin	uc002vnu.2	P07093	OTTHUMG00000133163	ENST00000258405.4:c.497A>G	chr2.hg19:g.224856708T>C	ENSP00000258405:p.Asp166Gly	55.0	0.0		59.0	4.0	NM_001136530	B2R6A4|B4DIF2|Q53S15|Q5D0C4	Missense_Mutation	SNP	ENST00000258405.4	hg19	CCDS2460.1	.	.	.	.	.	.	.	.	.	.	T	14.21	2.468784	0.43839	.	.	ENSG00000135919	ENST00000409304;ENST00000258405;ENST00000409840;ENST00000447280;ENST00000432738	D;D;D;D;D	0.84146	-1.81;-1.81;-1.81;-1.81;-1.81	5.8	5.8	0.92144	Serpin domain (3);	0.205916	0.52532	D	0.000077	T	0.81602	0.4857	L	0.44542	1.39	0.47862	D	0.999539	P;P	0.38395	0.629;0.488	B;B	0.37731	0.257;0.257	T	0.81141	-0.1068	10	0.38643	T	0.18	.	16.1506	0.81618	0.0:0.0:0.0:1.0	.	178;166	B4DIF2;P07093	.;GDN_HUMAN	G	166;166;166;178;166	ENSP00000386412:D166G;ENSP00000258405:D166G;ENSP00000386969:D166G;ENSP00000415786:D178G;ENSP00000408452:D166G	ENSP00000258405:D166G	D	-	2	0	SERPINE2	224564952	1.000000	0.71417	0.852000	0.33557	0.932000	0.56968	5.130000	0.64745	2.206000	0.71126	0.528000	0.53228	GAC	.	.		0.488	SERPINE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256865.2	NM_006216		C	224856708	T	C	224856708	3	2	255	1	0	0	0	0	1	0	0	0	14127	1667	58	2	723	2	SERPINE2	2	224856708	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	5375940	224856708	18342665	110	35455										
DOCK10	55619	hgsc.bcm.edu	37	chr2	225652004	225652004	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	atacatactttgaagtctcgTtgtttctcaaagacagcaat	6	8	2	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:225652004T>C	ENST00000258390.7	-	49	5596	c.5529A>G	c.(5527-5529)caA>caG	p.Q1843Q	DOCK10_ENST00000409592.3_Silent_p.Q1837Q	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	1843	DHR-2.				regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		TGAAGTCTCGTTGTTTCTCAA	0.368																																					p.Q1843Q		Atlas-SNP	.											.	DOCK10	308	.	0			c.A5529G						.						137	132	134					2																	225652004		1911	4130	6041	SO:0001819	synonymous_variant	55619	exon49			GTCTCGTTGTTTC	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"Pleckstrin homology (PH) domain containing"	23479	protein-coding gene	gene with protein product	"zizimin3"	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.5529A>G	chr2.hg19:g.225652004T>C		112.0	0.0		99.0	4.0	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Silent	SNP	ENST00000258390.7	hg19	CCDS46528.1																																																																																			.	.		0.368	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1			C	225652004	T	C	225652004	2	2	255	1	0	0	0	0	0	0	0	1	4687	1722	60	2		2	DOCK10	2	225652004	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	795296	225652004	17547369	111	35456										
COL4A4	1286	hgsc.bcm.edu	37	chr2	227895215	227895215	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctttgtatcctggagggcctGgtgggccagggggacctggt	18	9	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:227895215G>A	ENST00000396625.3	-	41	4124	c.3917C>T	c.(3916-3918)cCa>cTa	p.P1306L	COL4A4_ENST00000329662.7_Missense_Mutation_p.P1306L	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	1306	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		TGGAGGGCCTGGTGGGCCAGG	0.547																																					p.P1306L		Atlas-SNP	.											.	COL4A4	215	.	0			c.C3917T						.						113	112	112					2																	227895215		1913	4107	6020	SO:0001583	missense	1286	exon41			GGGCCTGGTGGGC		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"Collagens"	2206	protein-coding gene	gene with protein product	"collagen of basement membrane, alpha-4 chain"	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.3917C>T	chr2.hg19:g.227895215G>A	ENSP00000379866:p.Pro1306Leu	77.0	0.0		72.0	4.0	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Missense_Mutation	SNP	ENST00000396625.3	hg19	CCDS42828.1	.	.	.	.	.	.	.	.	.	.	G	8.997	0.979168	0.18812	.	.	ENSG00000081052	ENST00000396625;ENST00000329662	D;D	0.95412	-3.7;-3.7	5.45	4.54	0.55810	.	.	.	.	.	D	0.96367	0.8815	M	0.72353	2.195	0.48087	D	0.999583	D	0.58620	0.983	P	0.58266	0.836	D	0.95538	0.8609	9	0.45353	T	0.12	.	11.9533	0.52966	0.0:0.1751:0.8249:0.0	.	1306	P53420	CO4A4_HUMAN	L	1306	ENSP00000379866:P1306L;ENSP00000328553:P1306L	ENSP00000328553:P1306L	P	-	2	0	COL4A4	227603459	0.963000	0.33076	0.903000	0.35520	0.304000	0.27724	0.954000	0.29175	1.255000	0.44051	0.609000	0.83330	CCA	.	.		0.547	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092		A	227895215	G	A	227895215	3	1	255	1	0	0	0	0	1	0	0	0	3695	1348	47	3	1187	3	COL4A4	2	227895215	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	2243211	227895215	15304158	112	35457										
SPHKAP	80309	hgsc.bcm.edu	37	chr2	228881550	228881550	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cacttctctgcttgcgagggAgagccaccagaaacaggctc	11	13	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:228881550A>G	ENST00000392056.3	-	7	4066	c.4020T>C	c.(4018-4020)tcT>tcC	p.S1340S	SPHKAP_ENST00000344657.5_Silent_p.S1340S	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	1340						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)			NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		CTTGCGAGGGAGAGCCACCAG	0.517																																					p.S1340S		Atlas-SNP	.											.	SPHKAP	750	.	0			c.T4020C						.						99	87	91					2																	228881550		2203	4300	6503	SO:0001819	synonymous_variant	80309	exon7			CGAGGGAGAGCCA		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"A-kinase anchor proteins"	30619	protein-coding gene	gene with protein product	"sphingosine kinase type 1-interacting protein"	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.4020T>C	chr2.hg19:g.228881550A>G		111.0	0.0		99.0	4.0	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Silent	SNP	ENST00000392056.3	hg19	CCDS46537.1																																																																																			.	.		0.517	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623		G	228881550	A	G	228881550	2	3	255	1	0	0	0	0	0	0	0	1	15063	291	11	2		2	SPHKAP	2	228881550	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	986335	228881550	14317823	113	35458										
NPPC	4880	hgsc.bcm.edu	37	chr2	232790144	232790144	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggggcgccgcactaacatccCaggccgctcatggagccgat	13	15	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:232790144C>T	ENST00000409852.1	-	2	525	c.372G>A	c.(370-372)ctG>ctA	p.L124L	NPPC_ENST00000295440.2_Silent_p.L124L	NM_024409.2	NP_077720.1	P23582	ANFC_HUMAN	natriuretic peptide C	124					cGMP biosynthetic process (GO:0006182)|growth plate cartilage chondrocyte differentiation (GO:0003418)|growth plate cartilage chondrocyte proliferation (GO:0003419)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA metabolic process (GO:0051053)|negative regulation of meiotic cell cycle (GO:0051447)|negative regulation of oocyte maturation (GO:1900194)|ossification (GO:0001503)|positive regulation of cGMP biosynthetic process (GO:0030828)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of vasodilation (GO:0045909)|post-embryonic development (GO:0009791)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood vessel size (GO:0050880)|regulation of cAMP metabolic process (GO:0030814)|regulation of cGMP metabolic process (GO:0030823)|regulation of multicellular organism growth (GO:0040014)|regulation of smooth muscle cell proliferation (GO:0048660)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|single organism reproductive process (GO:0044702)	extracellular space (GO:0005615)|secretory granule (GO:0030141)	receptor binding (GO:0005102)						all_hematologic(139;0.0123)|Acute lymphoblastic leukemia(138;0.0182)|Renal(207;0.025)		Epithelial(121;9.35e-14)|BRCA - Breast invasive adenocarcinoma(100;0.00119)|LUSC - Lung squamous cell carcinoma(224;0.00746)|Lung(119;0.00834)		ACTAACATCCCAGGCCGCTCA	0.701																																					p.L124L		Atlas-SNP	.											.	NPPC	3	.	0			c.G372A						.						30	37	34					2																	232790144		2192	4298	6490	SO:0001819	synonymous_variant	4880	exon2			ACATCCCAGGCCG		CCDS2489.1	2q37.1	2014-01-30	2010-11-09		ENSG00000163273	ENSG00000163273		"Endogenous ligands"	7941	protein-coding gene	gene with protein product		600296	"natriuretic peptide precursor C"			7698765, 8330189	Standard	NM_024409		Approved	CNP	uc002vsl.2	P23582	OTTHUMG00000133232	ENST00000409852.1:c.372G>A	chr2.hg19:g.232790144C>T		90.0	0.0		110.0	22.0	NM_024409	Q4ZG41	Silent	SNP	ENST00000409852.1	hg19	CCDS2489.1																																																																																			.	.		0.701	NPPC-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331011.1	NM_024409		T	232790144	C	T	232790144	2	4	255	1	0	0	0	0	0	0	0	1	10602	581	21	3		3	NPPC	2	232790144	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	3908594	232790144	10409229	114	35459										
C2orf54	79919	hgsc.bcm.edu	37	chr2	241826548	241826548	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgctctgcatggcagagatcCggtccttatcctggatgttg	12	10	1	1	rs373154669		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:241826548C>A	ENST00000388934.4	-	5	1441	c.1283G>T	c.(1282-1284)cGg>cTg	p.R428L	C2orf54_ENST00000307486.8_Missense_Mutation_p.R279L|C2orf54_ENST00000402775.2_Missense_Mutation_p.R260L	NM_001085437.1	NP_001078906	Q08AI8	CB054_HUMAN	chromosome 2 open reading frame 54	428										haematopoietic_and_lymphoid_tissue(1)|lung(4)|prostate(1)	6		all_epithelial(40;3.99e-16)|Breast(86;2.35e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|Lung NSC(271;0.094)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;8.14e-32)|all cancers(36;4.77e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;4.88e-06)|Lung(119;0.000452)|LUSC - Lung squamous cell carcinoma(224;0.00415)|Colorectal(34;0.021)|COAD - Colon adenocarcinoma(134;0.15)		GGCAGAGATCCGGTCCTTATC	0.597																																					p.R428L		Atlas-SNP	.											.	C2orf54	14	.	0			c.G1283T						.						89	92	91					2																	241826548		1972	4172	6144	SO:0001583	missense	79919	exon5			GAGATCCGGTCCT	AK026324, AK056601	CCDS42839.1, CCDS42840.1, CCDS63187.1	2q37.3	2011-02-23			ENSG00000172478	ENSG00000172478			26216	protein-coding gene	gene with protein product							Standard	NM_001282921		Approved	FLJ22671	uc002wae.4	Q08AI8	OTTHUMG00000151906	ENST00000388934.4:c.1283G>T	chr2.hg19:g.241826548C>A	ENSP00000373586:p.Arg428Leu	93.0	0.0		71.0	4.0	NM_001085437	B3KPP9|H7BXM3|Q08AI9|Q53QU5|Q9H622	Missense_Mutation	SNP	ENST00000388934.4	hg19	CCDS42839.1	.	.	.	.	.	.	.	.	.	.	C	17.18	3.322931	0.60634	.	.	ENSG00000172478	ENST00000402775;ENST00000307486;ENST00000388934	T;T;T	0.61040	0.14;0.67;0.67	4.55	4.55	0.56014	.	0.000000	0.47455	D	0.000224	T	0.65026	0.2652	L	0.34521	1.04	0.30073	N	0.809844	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.81914	0.989;0.992;0.995	T	0.65191	-0.6228	10	0.87932	D	0	-4.9023	12.8318	0.57750	0.0:1.0:0.0:0.0	.	428;279;260	Q08AI8;B3KU29;Q08AI8-3	CB054_HUMAN;.;.	L	260;279;428	ENSP00000385338:R260L;ENSP00000302779:R279L;ENSP00000373586:R428L	ENSP00000302779:R279L	R	-	2	0	C2orf54	241475221	0.397000	0.25270	0.142000	0.22268	0.491000	0.33493	2.692000	0.47018	2.090000	0.63153	0.467000	0.42956	CGG	.	.		0.597	C2orf54-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324353.1	NM_024861, NM_001085437		A	241826548	C	A	241826548	3	1	255	1	0	0	0	0	1	0	0	0	2177	652	23	1	64	1	C2orf54	2	241826548	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	9036404	241826548	1372825	115	35460										
FARP2	9855	hgsc.bcm.edu	37	chr2	242432429	242432429	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cgtctttaccaacttctgttTgttcttctacaaaactcatc	3	12	5	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:242432429T>C	ENST00000264042.3	+	25	3043	c.2873T>C	c.(2872-2874)tTg>tCg	p.L958S	STK25_ENST00000316586.4_3'UTR|STK25_ENST00000478403.1_5'Flank	NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	958	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton reorganization (GO:0031532)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|neuron remodeling (GO:0016322)|osteoclast differentiation (GO:0030316)|podosome assembly (GO:0071800)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of integrin activation (GO:0033623)|regulation of Rac GTPase activity (GO:0032314)|semaphorin-plexin signaling pathway (GO:0071526)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	43		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		AACTTCTGTTTGTTCTTCTAC	0.448																																					p.L958S		Atlas-SNP	.											.	FARP2	92	.	0			c.T2873C						.						127	120	122					2																	242432429		2203	4300	6503	SO:0001583	missense	9855	exon25			TCTGTTTGTTCTT	AB018336	CCDS33424.1, CCDS63197.1	2q37.3	2013-01-10			ENSG00000006607	ENSG00000006607		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	16460	protein-coding gene	gene with protein product						9872452, 12351724	Standard	NM_001282984		Approved	KIAA0793, FIR, PLEKHC3, FRG	uc002wbi.2	O94887	OTTHUMG00000151574	ENST00000264042.3:c.2873T>C	chr2.hg19:g.242432429T>C	ENSP00000264042:p.Leu958Ser	81.0	0.0		98.0	4.0	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Missense_Mutation	SNP	ENST00000264042.3	hg19	CCDS33424.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.216431	0.79352	.	.	ENSG00000006607	ENST00000264042	T	0.46819	0.86	4.88	4.88	0.63580	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.64402	D	0.000007	T	0.74176	0.3682	M	0.94063	3.49	0.80722	D	1	D	0.63880	0.993	D	0.63113	0.911	T	0.82446	-0.0453	10	0.87932	D	0	.	14.8099	0.69985	0.0:0.0:0.0:1.0	.	958	O94887	FARP2_HUMAN	S	958	ENSP00000264042:L958S	ENSP00000264042:L958S	L	+	2	0	FARP2	242081102	1.000000	0.71417	0.552000	0.28243	0.957000	0.61999	7.770000	0.85390	1.962000	0.57031	0.533000	0.62120	TTG	.	.		0.448	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1			C	242432429	T	C	242432429	3	2	255	1	0	0	0	0	1	0	0	0	5685	1821	63	2	2967	2	FARP2	2	242432429	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	605881	242432429	766944	116	35461										
NEU4	129807	hgsc.bcm.edu	37	chr2	242756144	242756144	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggcggagcaccggtccatgaAcccctgccctgtgcacgatg	13	15	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:242756144A>G	ENST00000391969.2	+	4	968	c.257A>G	c.(256-258)aAc>aGc	p.N86S	NEU4_ENST00000405370.1_Missense_Mutation_p.N86S|NEU4_ENST00000404257.1_Missense_Mutation_p.N98S|NEU4_ENST00000407683.1_Missense_Mutation_p.N86S|NEU4_ENST00000325935.6_Missense_Mutation_p.N99S	NM_001167602.1	NP_001161074.1	Q8WWR8	NEUR4_HUMAN	sialidase 4	86					ganglioside catabolic process (GO:0006689)|glycoprotein catabolic process (GO:0006516)|glycosphingolipid metabolic process (GO:0006687)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|organelle inner membrane (GO:0019866)	exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)|exo-alpha-sialidase activity (GO:0004308)			breast(1)|lung(10)|prostate(2)|skin(2)	15		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;3.84e-33)|all cancers(36;8.08e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.41e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0825)		CGGTCCATGAACCCCTGCCCT	0.677																																					p.N99S		Atlas-SNP	.											.	NEU4	39	.	0			c.A296G						.						43	42	43					2																	242756144		2203	4299	6502	SO:0001583	missense	129807	exon3			CCATGAACCCCTG	BC012899	CCDS2553.1, CCDS54441.1, CCDS54442.1	2q37.3	2008-02-05			ENSG00000204099	ENSG00000204099			21328	protein-coding gene	gene with protein product		608527					Standard	NM_001167600		Approved		uc010fzr.3	Q8WWR8	OTTHUMG00000133412	ENST00000391969.2:c.257A>G	chr2.hg19:g.242756144A>G	ENSP00000375830:p.Asn86Ser	115.0	0.0		99.0	4.0	NM_001167599	A8K056|J3KNJ5|Q96D64	Missense_Mutation	SNP	ENST00000391969.2	hg19	CCDS54442.1	.	.	.	.	.	.	.	.	.	.	A	16.96	3.267201	0.59540	.	.	ENSG00000204099	ENST00000407683;ENST00000405370;ENST00000472793;ENST00000423583;ENST00000404257;ENST00000391969;ENST00000325935;ENST00000420288;ENST00000428592	D;D;D;D;D;D;D;D	0.92397	-3.03;-3.03;-3.03;-3.03;-3.03;-3.03;-3.03;-2.0	4.24	4.24	0.50183	Neuraminidase (2);	0.099000	0.64402	U	0.000003	D	0.95449	0.8522	M	0.78049	2.395	0.43527	D	0.9958	D;D;D	0.76494	0.999;0.999;0.998	D;D;D	0.76575	0.988;0.98;0.98	D	0.95632	0.8690	10	0.62326	D	0.03	-22.5734	13.3204	0.60430	1.0:0.0:0.0:0.0	.	98;98;86	A8K211;Q8WWR8-2;Q8WWR8	.;.;NEUR4_HUMAN	S	86;86;96;86;98;86;99;86;127	ENSP00000385402:N86S;ENSP00000384804:N86S;ENSP00000397860:N86S;ENSP00000385149:N98S;ENSP00000375830:N86S;ENSP00000320318:N99S;ENSP00000388707:N86S;ENSP00000396197:N127S	ENSP00000320318:N99S	N	+	2	0	NEU4	242404817	1.000000	0.71417	0.996000	0.52242	0.567000	0.35839	6.152000	0.71812	1.546000	0.49388	0.379000	0.24179	AAC	.	.		0.677	NEU4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257270.2	NM_080741		G	242756144	A	G	242756144	3	3	255	1	0	0	0	0	1	0	0	0	10353	43	2	2	306	2	NEU4	2	242756144	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	323715	242756144	443229	117	35462										
SUMF1	285362	hgsc.bcm.edu	37	chr3	4458810	4458810	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctgcagaggtctcattactcAcaggcgcagttccttggaag	11	11	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:4458810A>G	ENST00000272902.5	-	6	876		c.e6+1		SUMF1_ENST00000534863.1_Splice_Site|SUMF1_ENST00000405420.2_Splice_Site|SUMF1_ENST00000383843.5_Splice_Site|SUMF1_ENST00000458465.2_Intron	NM_182760.3	NP_877437.2	Q8NBK3	SUMF1_HUMAN	sulfatase modifying factor 1						cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)	metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)			breast(1)|endometrium(1)|large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(3)	13		Melanoma(143;0.068)|Colorectal(144;0.233)		Epithelial(13;0.0147)|OV - Ovarian serous cystadenocarcinoma(96;0.0444)|all cancers(10;0.0549)		CTCATTACTCACAGGCGCAGT	0.547																																					.		Atlas-SNP	.											.	SUMF1	23	.	0			c.765+2T>C						.						167	148	155					3																	4458810		2203	4300	6503	SO:0001630	splice_region_variant	285362	exon6			TTACTCACAGGCG	BC017005	CCDS2564.1, CCDS54548.1, CCDS54549.1	3p26.1	2009-07-23			ENSG00000144455	ENSG00000144455			20376	protein-coding gene	gene with protein product		607939				12757705, 12757706	Standard	NM_182760		Approved	FGE, UNQ3037	uc003bpz.2	Q8NBK3	OTTHUMG00000090269	ENST00000272902.5:c.840+1T>C	chr3.hg19:g.4458810A>G		83.0	0.0		77.0	4.0	NM_001164674	B4DXK5|B7XD05|E9PGL0|G5E9B0|Q0VAC6|Q0VAC7|Q2NL78|Q53ZE4|Q6UY39|Q96AK5|Q96DK8	Splice_Site	SNP	ENST00000272902.5	hg19	CCDS2564.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.400217	0.83120	.	.	ENSG00000144455	ENST00000534982;ENST00000534863;ENST00000272902;ENST00000383843;ENST00000405420	.	.	.	5.81	5.81	0.92471	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1525	0.72713	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SUMF1	4433810	1.000000	0.71417	0.999000	0.59377	0.853000	0.48598	8.263000	0.89864	2.217000	0.71921	0.533000	0.62120	.	.	.		0.547	SUMF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206591.2	NM_182760	Intron	G	4458810	A	G	4458810	5	3	255	1	0	0	0	0	0	0	1	0	15400	173	6	2	298	2	SUMF1	3	4458810	Splice_Site	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10		4458810	193563620	118	35463										
SRGAP3	9901	hgsc.bcm.edu	37	chr3	9032408	9032408	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tttgtgggggctgctggggcAggcagcagcccggggtggtg	22	8	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:9032408A>G	ENST00000383836.3	-	21	3101	c.2674T>C	c.(2674-2676)Tgc>Cgc	p.C892R	SRGAP3_ENST00000360413.3_Missense_Mutation_p.C868R	NM_014850.3	NP_055665.1	O43295	SRGP3_HUMAN	SLIT-ROBO Rho GTPase activating protein 3	892					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)		SRGAP3/RAF1(6)	breast(1)|endometrium(2)|kidney(21)|large_intestine(7)|lung(13)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	54				OV - Ovarian serous cystadenocarcinoma(96;0.0563)		CTGCTGGGGCAGGCAGCAGCC	0.692			T	RAF1	pilocytic astrocytoma																																p.C892R		Atlas-SNP	.		Dom	yes		3	3p25.3	9901	SLIT-ROBO Rho GTPase activating protein 3		M	SRGAP3,bladder,carcinoma,+1,1	SRGAP3	146	.	0			c.T2674C						.						10	13	12					3																	9032408		2184	4272	6456	SO:0001583	missense	9901	exon21			TGGGGCAGGCAGC	AB007871	CCDS2572.1, CCDS33689.1	3p25.3	2011-07-04	2004-11-12	2004-11-12	ENSG00000196220	ENSG00000196220		"Rho GTPase activating proteins"	19744	protein-coding gene	gene with protein product		606525	"SLIT-ROBO Rho GTPase activating protein 2"	SRGAP2		12195014	Standard	NM_014850		Approved	KIAA0411, MEGAP, WRP, ARHGAP14	uc003brf.2	O43295	OTTHUMG00000090589	ENST00000383836.3:c.2674T>C	chr3.hg19:g.9032408A>G	ENSP00000373347:p.Cys892Arg	160.0	2.0		145.0	6.0	NM_014850	Q8IX13|Q8IZV8	Missense_Mutation	SNP	ENST00000383836.3	hg19	CCDS2572.1	.	.	.	.	.	.	.	.	.	.	A	11.44	1.639155	0.29157	.	.	ENSG00000196220	ENST00000383836;ENST00000360413	T;T	0.23950	1.88;2.28	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.17323	0.0416	N	0.16478	0.41	0.80722	D	1	D;P	0.53745	0.962;0.937	B;B	0.43536	0.423;0.243	T	0.05115	-1.0905	10	0.15066	T	0.55	.	14.6015	0.68445	1.0:0.0:0.0:0.0	.	868;892	O43295-2;O43295	.;SRGP2_HUMAN	R	892;868	ENSP00000373347:C892R;ENSP00000353587:C868R	ENSP00000353587:C868R	C	-	1	0	SRGAP3	9007408	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.697000	0.74603	1.938000	0.56188	0.533000	0.62120	TGC	.	.		0.692	SRGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207137.3			G	9032408	A	G	9032408	3	3	255	1	0	0	0	0	1	0	0	0	15162	188	7	2	633	2	SRGAP3	3	9032408	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	4573598	9032408	188990022	119	35464										
NUP210	23225	hgsc.bcm.edu	37	chr3	13364885	13364885	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcctggaagctggtctggatGgggtggaggtgacgggccat	19	7	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:13364885G>A	ENST00000254508.5	-	34	4774	c.4692C>T	c.(4690-4692)ccC>ccT	p.P1564P		NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	1564					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|ovary(7)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	66	all_neural(104;0.187)					TGGTCTGGATGGGGTGGAGGT	0.592																																					p.P1564P		Atlas-SNP	.											.	NUP210	182	.	0			c.C4692T						.						122	119	120					3																	13364885		2203	4300	6503	SO:0001819	synonymous_variant	23225	exon34			CTGGATGGGGTGG	AB020713	CCDS33704.1	3p25	2008-02-05			ENSG00000132182	ENSG00000132182			30052	protein-coding gene	gene with protein product		607703				2184032, 7504063	Standard	NM_024923		Approved	GP210, POM210, FLJ22389, KIAA0906	uc003bxv.1	Q8TEM1	OTTHUMG00000157268	ENST00000254508.5:c.4692C>T	chr3.hg19:g.13364885G>A		89.0	0.0		89.0	4.0	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Silent	SNP	ENST00000254508.5	hg19	CCDS33704.1																																																																																			.	.		0.592	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923		A	13364885	G	A	13364885	2	1	255	1	0	0	0	0	0	0	0	1	10769	1335	47	3		3	NUP210	3	13364885	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	4332477	13364885	184657545	120	35465										
KCNH8	131096	hgsc.bcm.edu	37	chr3	19575099	19575099	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	caaacaggcggggctgcttaTacccaagcacaactttgtag	10	11	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:19575099T>C	ENST00000328405.2	+	16	3098	c.2832T>C	c.(2830-2832)taT>taC	p.Y944Y		NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	944					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(3)|lung(37)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	77						GGGCTGCTTATACCCAAGCAC	0.552																																					p.Y944Y	NSCLC(124;1625 1765 8018 24930 42026)	Atlas-SNP	.											.	KCNH8	189	.	0			c.T2832C						.						82	80	81					3																	19575099		2203	4300	6503	SO:0001819	synonymous_variant	131096	exon16			TGCTTATACCCAA	AY053503	CCDS2632.1	3p24.3	2012-07-05			ENSG00000183960	ENSG00000183960		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18864	protein-coding gene	gene with protein product		608260				16382104	Standard	NM_144633		Approved	Kv12.1, elk3	uc003cbk.1	Q96L42	OTTHUMG00000129891	ENST00000328405.2:c.2832T>C	chr3.hg19:g.19575099T>C		125.0	0.0		120.0	5.0	NM_144633	B7Z2I7|Q59GQ6	Silent	SNP	ENST00000328405.2	hg19	CCDS2632.1																																																																																			.	.		0.552	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	NM_144633		C	19575099	T	C	19575099	2	2	255	1	0	0	0	0	0	0	0	1	8047	1413	49	2		2	KCNH8	3	19575099	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	6210214	19575099	178447331	121	35466										
UBP1	7342	hgsc.bcm.edu	37	chr3	33444345	33444345	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggaggtgaaagtgggcgctgGggaagggctgttattcacat	18	5	1	1	rs373493970		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:33444345G>T	ENST00000283629.3	-	9	1508	c.979C>A	c.(979-981)Cca>Aca	p.P327T	UBP1_ENST00000486388.1_5'UTR|UBP1_ENST00000447368.2_Missense_Mutation_p.P291T|UBP1_ENST00000283628.5_Missense_Mutation_p.P327T	NM_001128161.1|NM_014517.4	NP_001121633.1|NP_055332.3	Q9NZI7	UBIP1_HUMAN	upstream binding protein 1 (LBP-1a)	327					angiogenesis (GO:0001525)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|urinary_tract(2)	23						GTGGGCGCTGGGGAAGGGCTG	0.483																																					p.P327T		Atlas-SNP	.											.	UBP1	42	.	0			c.C979A						.	G	THR/PRO,THR/PRO,THR/PRO	0,4406		0,0,2203	84	68	73		871,979,979	-0.7	1	3		73	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	UBP1	NM_001128160.1,NM_001128161.1,NM_014517.4	38,38,38	0,1,6502	TT,TG,GG		0.0116,0.0,0.0077	benign,benign,benign	291/505,327/541,327/541	33444345	1,13005	2203	4300	6503	SO:0001583	missense	7342	exon9			GCGCTGGGGAAGG	AF198487	CCDS2659.1, CCDS46788.1	3p22.3	2004-03-02			ENSG00000153560	ENSG00000153560			12507	protein-coding gene	gene with protein product		609784				8114710	Standard	NM_014517		Approved	LBP-1a	uc010hga.3	Q9NZI7	OTTHUMG00000130749	ENST00000283629.3:c.979C>A	chr3.hg19:g.33444345G>T	ENSP00000283629:p.Pro327Thr	184.0	0.0		173.0	7.0	NM_014517	Q68CT0|Q86Y57|Q9H8V0|Q9UD76|Q9UD78	Missense_Mutation	SNP	ENST00000283629.3	hg19	CCDS2659.1	.	.	.	.	.	.	.	.	.	.	G	13.94	2.386906	0.42308	0.0	1.16E-4	ENSG00000153560	ENST00000283629;ENST00000447368;ENST00000283628	T;T;T	0.21543	2.0;2.17;2.0	6.17	-0.703	0.11261	.	0.377335	0.33327	N	0.005031	T	0.12220	0.0297	L	0.40543	1.245	0.37362	D	0.911274	B;B	0.14805	0.001;0.011	B;B	0.23852	0.002;0.049	T	0.27331	-1.0077	10	0.08599	T	0.76	0.0141	5.6838	0.17790	0.0738:0.3079:0.4747:0.1436	.	291;327	Q9NZI7-4;Q9NZI7	.;UBIP1_HUMAN	T	327;291;327	ENSP00000283629:P327T;ENSP00000395558:P291T;ENSP00000283628:P327T	ENSP00000283628:P327T	P	-	1	0	UBP1	33419349	0.998000	0.40836	0.986000	0.45419	0.961000	0.63080	0.409000	0.21082	-0.124000	0.11724	0.655000	0.94253	CCA	.	.		0.483	UBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253249.2	NM_014517		T	33444345	G	T	33444345	3	4	255	1	0	0	0	0	1	0	0	0	16910	1232	43	3	675	3	UBP1	3	33444345	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	13869246	33444345	164578085	122	35467										
DLEC1	9940	hgsc.bcm.edu	37	chr3	38150965	38150965	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcccttgtcacgtgtcaggcAtgaagaagccactggttcta	10	11	3	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:38150965A>G	ENST00000308059.6	+	22	3193	c.3172A>G	c.(3172-3174)Atg>Gtg	p.M1058V	DLEC1_ENST00000452631.2_Missense_Mutation_p.M1058V|DLEC1_ENST00000346219.3_Missense_Mutation_p.M1058V					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		CGTGTCAGGCATGAAGAAGCC	0.572																																					p.M1058V		Atlas-SNP	.											.	DLEC1	278	.	0			c.A3172G						.						102	102	102					3																	38150965		1930	4144	6074	SO:0001583	missense	9940	exon22			TCAGGCATGAAGA	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"cilia and flagella associated protein 81"	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.3172A>G	chr3.hg19:g.38150965A>G	ENSP00000308597:p.Met1058Val	95.0	0.0		91.0	4.0	NM_007337		Missense_Mutation	SNP	ENST00000308059.6	hg19	CCDS2672.2	.	.	.	.	.	.	.	.	.	.	A	18.03	3.531539	0.64972	.	.	ENSG00000008226	ENST00000308059;ENST00000346219;ENST00000452631	T;T;T	0.50548	0.74;0.74;0.74	5.2	2.79	0.32731	.	0.000000	0.85682	D	0.000000	T	0.64136	0.2571	M	0.77820	2.39	0.44380	D	0.997281	D;P;D;D	0.89917	1.0;0.955;1.0;1.0	D;P;D;D	0.87578	0.998;0.84;0.994;0.998	T	0.59773	-0.7391	10	0.34782	T	0.22	-20.4746	8.9095	0.35543	0.843:0.0:0.157:0.0	.	1058;1058;1058;1058	F8W6T4;B7ZW06;Q9Y238-3;Q9Y238	.;.;.;DLEC1_HUMAN	V	1058	ENSP00000308597:M1058V;ENSP00000315914:M1058V;ENSP00000410427:M1058V	ENSP00000308597:M1058V	M	+	1	0	DLEC1	38125969	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.002000	0.63952	0.313000	0.23062	0.533000	0.62120	ATG	.	.		0.572	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337		G	38150965	A	G	38150965	3	3	255	1	0	0	0	0	1	0	0	0	4554	217	8	2	3258	2	DLEC1	3	38150965	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	4706620	38150965	159871465	123	35468										
XIRP1	165904	hgsc.bcm.edu	37	chr3	39229651	39229651	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cctttagctcatccctctggGgggcactctgagagaagggc	13	12	3	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:39229651G>T	ENST00000340369.3	-	2	1514	c.1286C>A	c.(1285-1287)cCc>cAc	p.P429H	XIRP1_ENST00000396251.1_Missense_Mutation_p.P429H|XIRP1_ENST00000421646.1_Intron	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	429					cardiac muscle cell development (GO:0055013)|negative regulation of cell proliferation (GO:0008285)|regulation of membrane potential (GO:0042391)|sarcomere organization (GO:0045214)	fascia adherens (GO:0005916)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(14)|lung(22)|ovary(4)|pancreas(1)|prostate(2)|skin(6)	71				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		ATCCCTCTGGGGGGCACTCTG	0.562																																					p.P429H		Atlas-SNP	.											.	XIRP1	173	.	0			c.C1286A						.						147	158	154					3																	39229651		2203	4300	6503	SO:0001583	missense	165904	exon2			CTCTGGGGGGCAC	AW755250	CCDS2683.1, CCDS56245.1	3p21.33	2008-02-05	2007-06-27	2007-06-27	ENSG00000168334	ENSG00000168334			14301	protein-coding gene	gene with protein product		609777	"cardiomyopathy associated 1"	CMYA1		12203715, 15454575	Standard	NM_001198621		Approved	DKFZp451D042, Xin	uc003cjk.2	Q702N8	OTTHUMG00000131297	ENST00000340369.3:c.1286C>A	chr3.hg19:g.39229651G>T	ENSP00000343140:p.Pro429His	68.0	0.0		86.0	4.0	NM_001198621	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Missense_Mutation	SNP	ENST00000340369.3	hg19	CCDS2683.1	.	.	.	.	.	.	.	.	.	.	G	14.31	2.497610	0.44455	.	.	ENSG00000168334	ENST00000396251;ENST00000340369	T;T	0.05081	3.5;3.88	4.64	4.64	0.57946	.	0.652316	0.14310	N	0.327703	T	0.17704	0.0425	M	0.68317	2.08	0.46749	D	0.999181	D;D	0.69078	0.997;0.963	P;P	0.55667	0.781;0.735	T	0.00202	-1.1925	10	0.62326	D	0.03	.	13.2295	0.59933	0.0:0.0:1.0:0.0	.	429;429	Q702N8;Q702N8-2	XIRP1_HUMAN;.	H	429	ENSP00000379550:P429H;ENSP00000343140:P429H	ENSP00000343140:P429H	P	-	2	0	XIRP1	39204655	0.428000	0.25522	0.736000	0.30914	0.789000	0.44602	2.029000	0.41098	2.583000	0.87209	0.655000	0.94253	CCC	.	.		0.562	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522		T	39229651	G	T	39229651	3	4	255	1	0	0	0	0	1	0	0	0	17444	1232	43	3	4249	3	XIRP1	3	39229651	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	1078686	39229651	158792779	124	35469										
ULK4	54986	hgsc.bcm.edu	37	chr3	41860960	41860960	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	actgtgtatgcagccaagggAacagcccagcactctctagg	11	12	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:41860960A>G	ENST00000301831.4	-	19	2265	c.1803T>C	c.(1801-1803)gtT>gtC	p.V601V		NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	601					cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		CAGCCAAGGGAACAGCCCAGC	0.443																																					p.V601V		Atlas-SNP	.											.	ULK4	150	.	0			c.T1803C						.						109	109	109					3																	41860960		1893	4115	6008	SO:0001819	synonymous_variant	54986	exon19			CAAGGGAACAGCC	AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"unc-51-like kinase 4 (C. elegans)"			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.1803T>C	chr3.hg19:g.41860960A>G		67.0	0.0		60.0	4.0	NM_017886	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Silent	SNP	ENST00000301831.4	hg19	CCDS43071.1																																																																																			.	.		0.443	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989		G	41860960	A	G	41860960	2	3	255	1	0	0	0	0	0	0	0	1	16993	233	9	2		2	ULK4	3	41860960	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	2631309	41860960	156161470	125	35470										
ZNF35	7584	hgsc.bcm.edu	37	chr3	44700749	44700749	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aatctgactgtacatcaaaaAatccactccttagaaaaaac	3	10	2	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:44700749A>G	ENST00000396056.2	+	4	1129	c.894A>G	c.(892-894)aaA>aaG	p.K298K	ZNF35_ENST00000542250.1_Silent_p.K138K|RP11-944L7.4_ENST00000457331.1_RNA|ZNF35_ENST00000296092.3_3'UTR	NM_003420.3	NP_003411.3	P13682	ZNF35_HUMAN	zinc finger protein 35	298					cellular response to retinoic acid (GO:0071300)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cell (GO:0005623)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(3)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(1)	12		Ovarian(412;0.0228)		OV - Ovarian serous cystadenocarcinoma(275;2.49e-27)|KIRC - Kidney renal clear cell carcinoma(197;0.0475)|Kidney(197;0.0595)		TACATCAAAAAATCCACTCCT	0.403																																					p.K298K		Atlas-SNP	.											.	ZNF35	34	.	0			c.A894G						.						51	56	54					3																	44700749		2203	4300	6503	SO:0001819	synonymous_variant	7584	exon4			TCAAAAAATCCAC	X07289	CCDS2718.2	3p21.32	2013-01-08	2006-05-11		ENSG00000169981	ENSG00000169981		"Zinc fingers, C2H2-type"	13099	protein-coding gene	gene with protein product		194533	"zinc finger protein 35 (clone HF.10)"			2108922, 1572646	Standard	NM_003420		Approved	HF.10, HF10, Zfp105	uc003cnq.3	P13682	OTTHUMG00000133091	ENST00000396056.2:c.894A>G	chr3.hg19:g.44700749A>G		63.0	0.0		62.0	4.0	NM_003420	B2RBU6|Q53Y54|Q96D01	Silent	SNP	ENST00000396056.2	hg19	CCDS2718.2																																																																																			.	.		0.403	ZNF35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256749.4	NM_003420		G	44700749	A	G	44700749	2	3	255	1	0	0	0	0	0	0	0	1	17877	11	1	2		2	ZNF35	3	44700749	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	2839789	44700749	153321681	126	35471										
LIMD1	8994	hgsc.bcm.edu	37	chr3	45637017	45637017	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctagctccccggggagtgacCcaccactgcccaaaccctgc	9	19	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:45637017C>A	ENST00000273317.4	+	1	667	c.646C>A	c.(646-648)Cca>Aca	p.P216T	LIMD1_ENST00000465039.1_Intron|LIMD1_ENST00000440097.1_Missense_Mutation_p.P216T	NM_014240.2	NP_055055.1	Q9UGP4	LIMD1_HUMAN	LIM domains containing 1	216	Interaction with EGLN1/PHD2.				cell migration (GO:0016477)|cytoplasmic mRNA processing body assembly (GO:0033962)|cytoskeleton organization (GO:0007010)|gene silencing by miRNA (GO:0035195)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of hippo signaling (GO:0035331)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|phosphorylation (GO:0016310)|positive regulation of gene silencing by miRNA (GO:2000637)|regulation of cell shape (GO:0008360)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|RISC complex (GO:0016442)	transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(193;0.011)|KIRC - Kidney renal clear cell carcinoma(197;0.0264)|Kidney(197;0.0315)		GGGGAGTGACCCACCACTGCC	0.622																																					p.P216T		Atlas-SNP	.											.	LIMD1	34	.	0			c.C646A						.						65	69	68					3																	45637017		2203	4300	6503	SO:0001583	missense	8994	exon1			AGTGACCCACCAC	AJ132408	CCDS2729.1	3p21.31	2008-02-01			ENSG00000144791	ENSG00000144791			6612	protein-coding gene	gene with protein product		604543				10647888	Standard	NM_014240		Approved		uc003coq.3	Q9UGP4	OTTHUMG00000133453	ENST00000273317.4:c.646C>A	chr3.hg19:g.45637017C>A	ENSP00000273317:p.Pro216Thr	66.0	0.0		61.0	4.0	NM_014240	Q17RQ1|Q9BQQ9|Q9NQ47	Missense_Mutation	SNP	ENST00000273317.4	hg19	CCDS2729.1	.	.	.	.	.	.	.	.	.	.	C	7.101	0.574062	0.13623	.	.	ENSG00000144791	ENST00000440097;ENST00000273317	T;T	0.56611	0.45;0.65	4.12	-1.31	0.09230	.	1.773090	0.03020	N	0.150555	T	0.31040	0.0784	N	0.19112	0.55	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.04386	-1.0955	10	0.13108	T	0.6	.	1.218	0.01918	0.1341:0.3038:0.2872:0.2748	.	216	Q9UGP4	LIMD1_HUMAN	T	216	ENSP00000394537:P216T;ENSP00000273317:P216T	ENSP00000273317:P216T	P	+	1	0	LIMD1	45612021	0.000000	0.05858	0.000000	0.03702	0.327000	0.28475	0.984000	0.29565	-0.431000	0.07307	0.462000	0.41574	CCA	.	.		0.622	LIMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257327.1	NM_014240		A	45637017	C	A	45637017	3	1	255	1	0	0	0	0	1	0	0	0	8807	623	22	3	648	3	LIMD1	3	45637017	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	936268	45637017	152385413	127	35472										
SETD2	29072	hgsc.bcm.edu	37	chr3	47129614	47129614	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agtgttcacctgtatgagttCcagacaggtaagtttctgct	10	8	2	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:47129614C>T	ENST00000409792.3	-	10	5308	c.5266G>A	c.(5266-5268)Gaa>Aaa	p.E1756K	snoU13_ENST00000516129.1_RNA	NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1756					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)	p.E1253*(1)|p.E1756*(1)		breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TGTATGAGTTCCAGACAGGTA	0.378			"N, F, S, Mis"		clear cell renal carcinoma																																p.E1756K		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	SETD2_ENST00000409792,NS,carcinoma,0,2	SETD2	721	.	2	Substitution - Nonsense(2)	lung(2)	c.G5266A						.						120	125	124					3																	47129614		2203	4300	6503	SO:0001583	missense	29072	exon10			TGAGTTCCAGACA	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.5266G>A	chr3.hg19:g.47129614C>T	ENSP00000386759:p.Glu1756Lys	43.0	0.0		49.0	2.0	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	hg19	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	C	2.797	-0.249982	0.05867	.	.	ENSG00000181555	ENST00000451092;ENST00000409792	D	0.86297	-2.1	4.46	-4.26	0.03755	.	0.481780	0.18774	N	0.131531	T	0.53077	0.1774	N	0.00707	-1.245	0.20975	N	0.999818	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.60068	-0.7335	10	0.02654	T	1	.	8.4158	0.32670	0.0:0.4985:0.1305:0.3711	.	1756;1756	F2Z317;Q9BYW2	.;SETD2_HUMAN	K	1756	ENSP00000386759:E1756K	ENSP00000386759:E1756K	E	-	1	0	SETD2	47104618	0.947000	0.32204	0.005000	0.12908	0.920000	0.55202	0.827000	0.27421	-0.940000	0.03705	-0.355000	0.07637	GAA	.	.		0.378	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		T	47129614	C	T	47129614	3	4	255	1	0	0	0	0	1	0	0	0	14146	864	30	3	2476	3	SETD2	3	47129614	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1492597	47129614	150892816	128	35473										
CSPG5	10675	hgsc.bcm.edu	37	chr3	47618664	47618664	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cctcctactgcatctttgtcAtcctcctcttcctcctcctc	2	20	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:47618664A>G	ENST00000383738.2	-	2	2950	c.852T>C	c.(850-852)gaT>gaC	p.D284D	CSPG5_ENST00000465441.1_5'Flank|CSPG5_ENST00000456150.1_Silent_p.D146D|CSPG5_ENST00000264723.4_Silent_p.D284D	NM_001206943.1|NM_001206945.1	NP_001193872.1|NP_001193874.1	O95196	CSPG5_HUMAN	chondroitin sulfate proteoglycan 5 (neuroglycan C)	284	Interaction with TNC and TNR. {ECO:0000250}.				axon regeneration (GO:0031103)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|intracellular transport (GO:0046907)|nervous system development (GO:0007399)|regulation of growth (GO:0040008)|regulation of synaptic transmission (GO:0050804)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|Golgi-associated vesicle membrane (GO:0030660)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	growth factor activity (GO:0008083)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|prostate(2)	22				BRCA - Breast invasive adenocarcinoma(193;0.000266)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		catctttgtcatcctcctctt	0.507																																					p.D284D		Atlas-SNP	.											.	CSPG5	46	.	0			c.T852C						.						22	23	23					3																	47618664		2202	4300	6502	SO:0001819	synonymous_variant	10675	exon2			TTTGTCATCCTCC	AF059274	CCDS2757.1, CCDS56252.1, CCDS56253.1, CCDS74930.1	3p21.3	2008-07-18			ENSG00000114646	ENSG00000114646			2467	protein-coding gene	gene with protein product		606775				9950058	Standard	NM_006574		Approved	NGC	uc003crp.4	O95196	OTTHUMG00000133518	ENST00000383738.2:c.852T>C	chr3.hg19:g.47618664A>G		84.0	0.0		82.0	4.0	NM_006574	Q71M39|Q71M40	Silent	SNP	ENST00000383738.2	hg19	CCDS56253.1																																																																																			.	.		0.507	CSPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257489.1	NM_006574		G	47618664	A	G	47618664	2	3	255	1	0	0	0	0	0	0	0	1	3963	214	8	2		2	CSPG5	3	47618664	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	489050	47618664	150403766	129	35474										
ATRIP	84126	hgsc.bcm.edu	37	chr3	48502119	48502119	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cttctgcagcaacaggtcacCttcaagccagtgtcctgacc	8	15	3	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:48502119C>T	ENST00000320211.3	+	8	1779	c.1666C>T	c.(1666-1668)Ctt>Ttt	p.L556F	ATRIP_ENST00000357105.6_Missense_Mutation_p.L429F|ATRIP_ENST00000346691.4_Missense_Mutation_p.L556F|ATRIP_ENST00000412052.1_Missense_Mutation_p.L463F	NM_130384.2	NP_569055.1	Q8WXE1	ATRIP_HUMAN	ATR interacting protein	556					DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)	microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(2)|endometrium(1)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)	22				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		AACAGGTCACCTTCAAGCCAG	0.502								Other conserved DNA damage response genes																													p.L556F		Atlas-SNP	.											.	ATRIP	41	.	0			c.C1666T						.						77	73	74					3																	48502119		2203	4300	6503	SO:0001583	missense	84126	exon8			GGTCACCTTCAAG	AF451323	CCDS2767.1, CCDS2768.1, CCDS59449.1, CCDS59450.1	3p24.3-p22.1	2007-06-20			ENSG00000164053	ENSG00000164053			33499	protein-coding gene	gene with protein product		606605				11721054	Standard	NM_130384		Approved	FLJ12343, MGC20625, MGC21482, MGC26740	uc003ctf.2	Q8WXE1	OTTHUMG00000133532	ENST00000320211.3:c.1666C>T	chr3.hg19:g.48502119C>T	ENSP00000323099:p.Leu556Phe	105.0	0.0		87.0	5.0	NM_130384	A8K6A3|A8K714|B2RCE7|B4DU92|B5MEB7|Q69YK9|Q8NHQ2|Q8WUG7|Q96CL3|Q9HA30	Missense_Mutation	SNP	ENST00000320211.3	hg19	CCDS2768.1	.	.	.	.	.	.	.	.	.	.	C	8.183	0.794282	0.16327	.	.	ENSG00000164053	ENST00000320211;ENST00000346691;ENST00000357105;ENST00000412052	T;T;T;T	0.65916	2.64;-0.18;2.64;2.64	6.08	3.05	0.35203	.	1.010300	0.07913	N	0.974673	T	0.51092	0.1654	L	0.35723	1.085	0.09310	N	1	B;B	0.17268	0.021;0.021	B;B	0.18263	0.021;0.021	T	0.36866	-0.9730	9	.	.	.	-1.0E-4	8.1825	0.31319	0.0:0.7642:0.0:0.2358	.	556;556	Q8WXE1-2;Q8WXE1	.;ATRIP_HUMAN	F	556;556;429;463	ENSP00000323099:L556F;ENSP00000302338:L556F;ENSP00000349620:L429F;ENSP00000400930:L463F	.	L	+	1	0	ATRIP	48477123	0.323000	0.24643	0.022000	0.16811	0.968000	0.65278	0.993000	0.29680	0.329000	0.23460	0.591000	0.81541	CTT	.	.		0.502	ATRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257507.2	NM_130384		T	48502119	C	T	48502119	3	4	255	1	0	0	0	0	1	0	0	0	1205	681	24	3	1696	3	ATRIP	3	48502119	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	883455	48502119	149520311	130	35475										
COL7A1	1294	hgsc.bcm.edu	37	chr3	48625362	48625362	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggccccaggacccgggactgTtcctggccacctggggcagg	16	15	0	0	rs201566458		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:48625362T>C	ENST00000328333.8	-	21	2828	c.2721A>G	c.(2719-2721)gaA>gaG	p.E907E	COL7A1_ENST00000454817.1_Silent_p.E907E	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	907	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.|Nonhelical region (NC1).				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CCCGGGACTGTTCCTGGCCAC	0.652																																					p.E907E		Atlas-SNP	.											.	COL7A1	320	.	0			c.A2721G						.						12	14	13					3																	48625362		2193	4288	6481	SO:0001819	synonymous_variant	1294	exon21			GGACTGTTCCTGG	L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"Collagens", "Fibronectin type III domain containing"	2214	protein-coding gene	gene with protein product	"collagen VII, alpha-1 polypeptide", "LC collagen"	120120	"epidermolysis bullosa, dystrophic, dominant and recessive"	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.2721A>G	chr3.hg19:g.48625362T>C		60.0	0.0		69.0	4.0	NM_000094	Q14054|Q16507	Silent	SNP	ENST00000328333.8	hg19	CCDS2773.1																																																																																			.	.		0.652	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094		C	48625362	T	C	48625362	2	2	255	1	0	0	0	0	0	0	0	1	3706	1722	60	2		2	COL7A1	3	48625362	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	123243	48625362	149397068	131	35476										
NCKIPSD	51517	hgsc.bcm.edu	37	chr3	48720411	48720411	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgtgtacagcctcgatggccCggtcaatggcctggaggaca	14	11	1	0	rs368902568		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:48720411C>T	ENST00000294129.2	-	2	325	c.206G>A	c.(205-207)cGg>cAg	p.R69Q	NCKIPSD_ENST00000416649.2_Missense_Mutation_p.R69Q|NCKIPSD_ENST00000341520.4_Missense_Mutation_p.R69Q	NM_016453.2	NP_057537.1	Q9NZQ3	SPN90_HUMAN	NCK interacting protein with SH3 domain	69					cytoskeleton organization (GO:0007010)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|NLS-bearing protein import into nucleus (GO:0006607)|signal transduction (GO:0007165)	cytosol (GO:0005829)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	cytoskeletal protein binding (GO:0008092)			endometrium(1)|large_intestine(3)|lung(6)|prostate(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		CTCGATGGCCCGGTCAATGGC	0.632																																					p.R69Q		Atlas-SNP	.											.	NCKIPSD	52	.	0			c.G206A						.	C	GLN/ARG,GLN/ARG	0,4328		0,0,2164	77	43	55		206,206	4.9	1	3		55	1,8411		0,1,4205	no	missense,missense	NCKIPSD	NM_016453.2,NM_184231.1	43,43	0,1,6369	TT,TC,CC		0.0119,0.0,0.0078	probably-damaging,probably-damaging	69/723,69/716	48720411	1,12739	2164	4206	6370	SO:0001583	missense	51517	exon2			ATGGCCCGGTCAA	AF178432	CCDS2776.1, CCDS46827.1	3p21	2008-07-18			ENSG00000213672	ENSG00000213672			15486	protein-coding gene	gene with protein product	"dia interacting protein", "diaphanous protein interacting protein", "SH3 protein interacting with Nck, 90 kDa"	606671				10648423, 10619843	Standard	NM_016453		Approved	AF3P21, SPIN90, ORF1, WISH, WASLBP, DIP1	uc003cun.3	Q9NZQ3	OTTHUMG00000133542	ENST00000294129.2:c.206G>A	chr3.hg19:g.48720411C>T	ENSP00000294129:p.Arg69Gln	94.0	0.0		99.0	4.0	NM_184231	B4DFL5|Q6GU34|Q6SPF3|Q8TC10|Q9UGM8	Missense_Mutation	SNP	ENST00000294129.2	hg19	CCDS2776.1	.	.	.	.	.	.	.	.	.	.	C	35	5.459309	0.96240	0.0	1.19E-4	ENSG00000213672	ENST00000341520;ENST00000416649;ENST00000294129;ENST00000439518	T;T;T;T	0.52526	0.66;1.27;1.25;1.23	4.87	4.87	0.63330	.	0.000000	0.64402	U	0.000007	T	0.65709	0.2717	M	0.68952	2.095	0.58432	D	0.999997	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.994;0.997	T	0.61287	-0.7093	10	0.16896	T	0.51	.	18.0227	0.89259	0.0:1.0:0.0:0.0	.	69;69;69	C9JSC3;Q9NZQ3;Q9NZQ3-3	.;SPN90_HUMAN;.	Q	69	ENSP00000342621:R69Q;ENSP00000389059:R69Q;ENSP00000294129:R69Q;ENSP00000409675:R69Q	ENSP00000294129:R69Q	R	-	2	0	NCKIPSD	48695415	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.811000	0.86092	2.258000	0.74832	0.591000	0.81541	CGG	.	.		0.632	NCKIPSD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257520.1	NM_016453		T	48720411	C	T	48720411	3	4	255	1	0	0	0	0	1	0	0	0	10234	652	23	1	2010	1	NCKIPSD	3	48720411	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	95049	48720411	149302019	132	35477										
DALRD3	55152	hgsc.bcm.edu	37	chr3	49053492	49053492	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cagatccggaaaggggaggaTactgttgaagagcaacaacc	13	8	0	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:49053492T>C	ENST00000341949.4	-	10	1363	c.1357A>G	c.(1357-1359)Atc>Gtc	p.I453V	DALRD3_ENST00000441576.2_Splice_Site_p.Y444C|DALRD3_ENST00000440857.1_Missense_Mutation_p.I286V|DALRD3_ENST00000496568.1_5'Flank|DALRD3_ENST00000395462.4_Missense_Mutation_p.I286V|DALRD3_ENST00000313778.5_Missense_Mutation_p.I286V	NM_001009996.1	NP_001009996.1	Q5D0E6	DALD3_HUMAN	DALR anticodon binding domain containing 3	453					arginyl-tRNA aminoacylation (GO:0006420)		arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)			breast(2)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	12				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		AAGGGGAGGATACTGTTGAAG	0.592																																					p.I453V		Atlas-SNP	.											.	DALRD3	57	.	0			c.A1357G						.						58	63	61					3																	49053492		2203	4300	6503	SO:0001583	missense	55152	exon10			GGAGGATACTGTT	BC014099	CCDS2783.1, CCDS33754.1, CCDS63632.1	3p21.31	2005-01-10			ENSG00000178149	ENSG00000178149			25536	protein-coding gene	gene with protein product						12477932	Standard	NM_001009996		Approved	FLJ10496	uc003cvk.2	Q5D0E6	OTTHUMG00000156748	ENST00000341949.4:c.1357A>G	chr3.hg19:g.49053492T>C	ENSP00000344989:p.Ile453Val	93.0	0.0		88.0	4.0	NM_001009996	Q7Z5S7|Q86WY1|Q8N105|Q8NA89|Q9NVU8	Missense_Mutation	SNP	ENST00000341949.4	hg19	CCDS33754.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	2.342|2.342	-0.350941|-0.350941	0.05173|0.05173	.|.	.|.	ENSG00000178149|ENSG00000178149	ENST00000341949;ENST00000395462;ENST00000440857;ENST00000313778|ENST00000438585;ENST00000441576	T;T;T;T|T	0.77229|0.48836	-1.08;-1.08;-1.08;-1.08|0.8	5.48|5.48	-2.95|-2.95	0.05564|0.05564	Aminoacyl-tRNA synthetase, class 1a, anticodon-binding (1);DALR anticodon binding (2);|.	0.556527|.	0.19877|.	N|.	0.104049|.	T|T	0.33731|0.33731	0.0873|0.0873	L|L	0.45352|0.45352	1.415|1.415	0.09310|0.09310	N|N	0.999999|0.999999	B;B|B	0.13594|0.02656	0.008;0.004|0.0	B;B|B	0.13407|0.04013	0.007;0.009|0.001	T|T	0.28902|0.28902	-1.0029|-1.0029	10|8	0.13853|.	T|.	0.58|.	-13.1072|-13.1072	8.2195|8.2195	0.31532|0.31532	0.0:0.3099:0.1596:0.5304|0.0:0.3099:0.1596:0.5304	.|.	286;453|444	C9JJG6;Q5D0E6|Q5D0E6-2	.;DALD3_HUMAN|.	V|C	453;286;286;286|99;444	ENSP00000344989:I453V;ENSP00000378846:I286V;ENSP00000403770:I286V;ENSP00000323265:I286V|ENSP00000410623:Y444C	ENSP00000323265:I286V|.	I|Y	-|-	1|2	0|0	DALRD3|DALRD3	49028496|49028496	0.008000|0.008000	0.16893|0.16893	0.053000|0.053000	0.19242|0.19242	0.539000|0.539000	0.34962|0.34962	-0.019000|-0.019000	0.12546|0.12546	-0.208000|-0.208000	0.10171|0.10171	-0.451000|-0.451000	0.05528|0.05528	ATC|TAT	.	.		0.592	DALRD3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345581.1	NM_018114		C	49053492	T	C	49053492	3	2	255	1	0	0	0	0	1	0	0	0	4231	1406	49	2	286	2	DALRD3	3	49053492	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	333081	49053492	148968938	133	35478										
DALRD3	55152	hgsc.bcm.edu	37	chr3	49053675	49053675	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tccatactacacttgtaactCtcaaagagtgtggcaagacg	8	10	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:49053675C>A	ENST00000341949.4	-	9	1251	c.1245G>T	c.(1243-1245)gaG>gaT	p.E415D	DALRD3_ENST00000441576.2_Missense_Mutation_p.E415D|DALRD3_ENST00000440857.1_Missense_Mutation_p.E248D|DALRD3_ENST00000496568.1_5'Flank|DALRD3_ENST00000395462.4_Missense_Mutation_p.E248D|DALRD3_ENST00000313778.5_Missense_Mutation_p.E248D	NM_001009996.1	NP_001009996.1	Q5D0E6	DALD3_HUMAN	DALR anticodon binding domain containing 3	415					arginyl-tRNA aminoacylation (GO:0006420)		arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)			breast(2)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	12				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		ACTTGTAACTCTCAAAGAGTG	0.502																																					p.E415D		Atlas-SNP	.											.	DALRD3	57	.	0			c.G1245T						.						100	93	95					3																	49053675		2203	4300	6503	SO:0001583	missense	55152	exon9			GTAACTCTCAAAG	BC014099	CCDS2783.1, CCDS33754.1, CCDS63632.1	3p21.31	2005-01-10			ENSG00000178149	ENSG00000178149			25536	protein-coding gene	gene with protein product						12477932	Standard	NM_001009996		Approved	FLJ10496	uc003cvk.2	Q5D0E6	OTTHUMG00000156748	ENST00000341949.4:c.1245G>T	chr3.hg19:g.49053675C>A	ENSP00000344989:p.Glu415Asp	78.0	0.0		81.0	4.0	NM_001009996	Q7Z5S7|Q86WY1|Q8N105|Q8NA89|Q9NVU8	Missense_Mutation	SNP	ENST00000341949.4	hg19	CCDS33754.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.124|9.124	1.009636|1.009636	0.19277|0.19277	.|.	.|.	ENSG00000178149|ENSG00000178149	ENST00000441576;ENST00000341949;ENST00000395462;ENST00000440857;ENST00000313778|ENST00000438585	T;T;T;T;T|.	0.77750|.	0.9;-1.12;-1.12;-1.08;-1.12|.	5.79|5.79	0.273|0.273	0.15650|0.15650	Aminoacyl-tRNA synthetase, class 1a, anticodon-binding (1);DALR anticodon binding (2);|.	0.325026|0.325026	0.37053|0.37053	N|N	0.002265|0.002265	T|.	0.13927|.	0.0337|.	N|N	0.16368|0.16368	0.405|0.405	0.26230|0.26230	N|N	0.979024|0.979024	B;B;B;B|.	0.17852|.	0.024;0.005;0.024;0.007|.	B;B;B;B|.	0.18561|.	0.019;0.007;0.019;0.022|.	T|.	0.09185|.	-1.0686|.	10|.	0.20046|0.11794	T|T	0.44|0.64	-17.7675|-17.7675	0.7964|0.7964	0.01067|0.01067	0.3878:0.2629:0.1297:0.2196|0.3878:0.2629:0.1297:0.2196	.|.	415;248;415;415|.	B7Z727;C9JJG6;Q5D0E6-2;Q5D0E6|.	.;.;.;DALD3_HUMAN|.	D|X	415;415;248;248;248|62	ENSP00000410623:E415D;ENSP00000344989:E415D;ENSP00000378846:E248D;ENSP00000403770:E248D;ENSP00000323265:E248D|.	ENSP00000323265:E248D|ENSP00000396650:E62X	E|E	-|-	3|1	2|0	DALRD3|DALRD3	49028679|49028679	0.812000|0.812000	0.29077|0.29077	0.477000|0.477000	0.27303|0.27303	0.965000|0.965000	0.64279|0.64279	0.264000|0.264000	0.18497|0.18497	0.332000|0.332000	0.23536|0.23536	0.561000|0.561000	0.74099|0.74099	GAG|GAG	.	.		0.502	DALRD3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345581.1	NM_018114		A	49053675	C	A	49053675	3	1	255	1	0	0	0	0	1	0	0	0	4231	912	32	3	402	3	DALRD3	3	49053675	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	183	49053675	148968755	134	35479										
RNF123	63891	hgsc.bcm.edu	37	chr3	49735904	49735904	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agatacacacaactcctatgCctatgatggcaaccgcgtgc	8	13	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:49735904C>T	ENST00000327697.6	+	8	659	c.515C>T	c.(514-516)gCc>gTc	p.A172V	RNF123_ENST00000432042.1_Missense_Mutation_p.A26V	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	172	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		AACTCCTATGCCTATGATGGC	0.572																																					p.A172V		Atlas-SNP	.											.	RNF123	100	.	0			c.C515T						.						82	74	77					3																	49735904		2203	4300	6503	SO:0001583	missense	63891	exon8			CCTATGCCTATGA	AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"RING-type (C3HC4) zinc fingers"	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891	ENST00000327697.6:c.515C>T	chr3.hg19:g.49735904C>T	ENSP00000328287:p.Ala172Val	115.0	0.0		90.0	5.0	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Missense_Mutation	SNP	ENST00000327697.6	hg19	CCDS33758.1	.	.	.	.	.	.	.	.	.	.	C	36	5.628320	0.96671	.	.	ENSG00000164068	ENST00000327697;ENST00000389066;ENST00000432042	T;T	0.71103	-0.54;-0.54	4.96	4.96	0.65561	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.117675	0.56097	D	0.000030	D	0.84871	0.5568	M	0.80616	2.505	0.80722	D	1	D	0.69078	0.997	D	0.80764	0.994	D	0.86731	0.1948	10	0.87932	D	0	-25.1749	17.731	0.88377	0.0:1.0:0.0:0.0	.	172	Q5XPI4	RN123_HUMAN	V	172;172;26	ENSP00000328287:A172V;ENSP00000392443:A26V	ENSP00000328287:A172V	A	+	2	0	RNF123	49710908	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.960000	0.76036	2.735000	0.93741	0.561000	0.74099	GCC	.	.		0.572	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064		T	49735904	C	T	49735904	3	4	255	1	0	0	0	0	1	0	0	0	13448	739	26	3	541	3	RNF123	3	49735904	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	682229	49735904	148286526	135	35480										
RBM5	10181	hgsc.bcm.edu	37	chr3	50154760	50154760	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gctgcaggccatgggctggcGggaaggctctggcttgggac	19	10	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:50154760G>T	ENST00000347869.3	+	24	2445	c.2270G>T	c.(2269-2271)cGg>cTg	p.R757L	RP11-493K19.3_ENST00000437204.1_RNA|RP11-493K19.3_ENST00000425674.1_RNA	NM_005778.3	NP_005769.1	P52756	RBM5_HUMAN	RNA binding motif protein 5	757	G-patch. {ECO:0000255|PROSITE- ProRule:PRU00092}.|Required for interaction with U2AF2.				apoptotic process (GO:0006915)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(3)|large_intestine(4)|lung(6)|prostate(2)	19				BRCA - Breast invasive adenocarcinoma(193;0.000121)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		ATGGGCTGGCGGGAAGGCTCT	0.542																																					p.R757L		Atlas-SNP	.											.	RBM5	76	.	0			c.G2270T						.						164	158	160					3																	50154760		2203	4300	6503	SO:0001583	missense	10181	exon24			GCTGGCGGGAAGG	U23946	CCDS2810.1	3p21.3	2013-08-15			ENSG00000003756	ENSG00000003756		"G patch domain containing", "RNA binding motif (RRM) containing"	9902	protein-coding gene	gene with protein product		606884				10352938, 23935508	Standard	NM_005778		Approved	LUCA15, H37	uc003cyg.3	P52756	OTTHUMG00000156785	ENST00000347869.3:c.2270G>T	chr3.hg19:g.50154760G>T	ENSP00000343054:p.Arg757Leu	127.0	0.0		114.0	5.0	NM_005778	B2RA45|B4DM16|B4DMF9|B4DZ63|Q93021|Q9BU14|Q9HDA6|Q9UKY8|Q9UL24	Missense_Mutation	SNP	ENST00000347869.3	hg19	CCDS2810.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.946746	0.73672	.	.	ENSG00000003756	ENST00000347869;ENST00000543047;ENST00000544851	T	0.32272	1.46	5.48	4.6	0.57074	D111/G-patch (3);	0.247806	0.39909	N	0.001227	T	0.37348	0.1000	L	0.42581	1.335	0.80722	D	1	P;P	0.47962	0.903;0.616	P;P	0.53954	0.738;0.617	T	0.12941	-1.0528	10	0.56958	D	0.05	-14.1443	9.1131	0.36741	0.0734:0.0:0.7789:0.1477	.	447;757	Q59HE6;P52756	.;RBM5_HUMAN	L	757;756;447	ENSP00000343054:R757L	ENSP00000343054:R757L	R	+	2	0	RBM5	50129764	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	4.778000	0.62368	1.290000	0.44636	-0.188000	0.12872	CGG	.	.		0.542	RBM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345797.3	NM_005778		T	50154760	G	T	50154760	3	4	255	1	0	0	0	0	1	0	0	0	13158	1116	39	1	2360	1	RBM5	3	50154760	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	418856	50154760	147867670	136	35481										
DOCK3	1795	hgsc.bcm.edu	37	chr3	51297588	51297588	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tttctcccacacttttcaggCcttggagtaccttttcaagt	6	12	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:51297588C>A	ENST00000266037.9	+	23	2209	c.2186C>A	c.(2185-2187)gCc>gAc	p.A729D		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	729					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		ACTTTTCAGGCCTTGGAGTAC	0.443																																					p.A729D		Atlas-SNP	.											DOCK3_ENST00000266037,NS,carcinoma,0,2	DOCK3	397	.	0			c.C2186A						.						84	80	81					3																	51297588		1930	4149	6079	SO:0001630	splice_region_variant	1795	exon23			TTCAGGCCTTGGA	AB002297	CCDS46835.1	3p21	2008-02-01			ENSG00000088538	ENSG00000088538			2989	protein-coding gene	gene with protein product		603123	"dedicator of cyto-kinesis 3"			9205841	Standard	NM_004947		Approved	KIAA0299, MOCA, PBP	uc011bds.2	Q8IZD9	OTTHUMG00000156892	ENST00000266037.9:c.2185-1C>A	chr3.hg19:g.51297588C>A		193.0	0.0		182.0	8.0	NM_004947	O15017	Missense_Mutation	SNP	ENST00000266037.9	hg19	CCDS46835.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.022119	0.93462	.	.	ENSG00000088538	ENST00000266037	T	0.68624	-0.34	5.93	5.05	0.67936	.	0.046361	0.85682	D	0.000000	T	0.81941	0.4929	M	0.89287	3.02	0.80722	D	1	D	0.54047	0.964	P	0.58391	0.838	D	0.84894	0.0838	10	0.66056	D	0.02	.	15.4007	0.74838	0.0:0.9326:0.0:0.0674	.	729	Q8IZD9	DOCK3_HUMAN	D	729	ENSP00000266037:A729D	ENSP00000266037:A729D	A	+	2	0	DOCK3	51272628	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	6.082000	0.71318	2.805000	0.96524	0.655000	0.94253	GCC	.	.		0.443	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947	Missense_Mutation	A	51297588	C	A	51297588	5	1	255	1	0	0	0	0	0	0	1	0	4690	753	26	3	2276	3	DOCK3	3	51297588	Splice_Site	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1142828	51297588	146724842	137	35482										
VPRBP	9730	hgsc.bcm.edu	37	chr3	51456168	51456168	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgtgtgatggctgagttgtgAcagttatagctggcctcctc	13	8	0	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:51456168A>G	ENST00000335891.5	-	8	2061	c.2052T>C	c.(2050-2052)tgT>tgC	p.C684C				Q9Y4B6	VPRBP_HUMAN	Vpr (HIV-1) binding protein	1133					B cell differentiation (GO:0030183)|cell competition in a multicellular organism (GO:0035212)|histone H2A-T120 phosphorylation (GO:1990245)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|transcription, DNA-templated (GO:0006351)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone kinase activity (H2A-T120 specific) (GO:1990244)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(193;0.000272)|Kidney(197;0.000729)|KIRC - Kidney renal clear cell carcinoma(197;0.000875)		CTGAGTTGTGACAGTTATAGC	0.493																																					p.C1080C		Atlas-SNP	.											.	VPRBP	107	.	0			c.T3240C						.						137	139	138					3																	51456168		2034	4196	6230	SO:0001819	synonymous_variant	9730	exon15			GTTGTGACAGTTA	AB018343	CCDS74943.1, CCDS74944.1	3p21.2	2011-06-17			ENSG00000145041	ENSG00000145041		"DDB1 and CUL4 associated factors"	30911	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 1"					8195203, 11223251	Standard	NM_014703		Approved	KIAA0800, MGC102804, DCAF1	uc003dbe.2	Q9Y4B6	OTTHUMG00000156895	ENST00000335891.5:c.2052T>C	chr3.hg19:g.51456168A>G		94.0	0.0		90.0	4.0	NM_014703	Q2YD74|Q8TBD9|Q9HCA1|Q9UG37	Silent	SNP	ENST00000335891.5	hg19																																																																																				.	.		0.493	VPRBP-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014703		G	51456168	A	G	51456168	2	3	255	1	0	0	0	0	0	0	0	1	17200	273	10	2		2	VPRBP	3	51456168	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	158580	51456168	146566262	138	35483										
ERC2	26059	hgsc.bcm.edu	37	chr3	56207475	56207475	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aaaagtgcacagttcctaccTtcatttcgatgacagtctgg	8	10	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:56207475T>C	ENST00000288221.6	-	4	1403	c.1148A>G	c.(1147-1149)aAg>aGg	p.K383R		NM_015576.1	NP_056391.1	O15083	ERC2_HUMAN	ELKS/RAB6-interacting/CAST family member 2	383						cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|growth cone (GO:0030426)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)				breast(2)|endometrium(5)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|urinary_tract(1)	31				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)		AGTTCCTACCTTCATTTCGAT	0.453																																					p.K383R		Atlas-SNP	.											.	ERC2	221	.	0			c.A1148G						.						89	92	91					3																	56207475		2104	4235	6339	SO:0001630	splice_region_variant	26059	exon4			CCTACCTTCATTT	AB002376	CCDS46851.1	3p14.3	2006-08-14			ENSG00000187672	ENSG00000187672			31922	protein-coding gene	gene with protein product							Standard	NM_015576		Approved	CAST, CAST1, KIAA0378, SPBC110, Spc110, ELKSL	uc003dhr.1	O15083	OTTHUMG00000158390	ENST00000288221.6:c.1149+1A>G	chr3.hg19:g.56207475T>C		89.0	0.0		93.0	4.0	NM_015576	Q2T9F6|Q86TK4	Missense_Mutation	SNP	ENST00000288221.6	hg19	CCDS46851.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.32|18.32	3.597176|3.597176	0.66332|0.66332	.|.	.|.	ENSG00000187672|ENSG00000187672	ENST00000288221|ENST00000492584	T|.	0.56611|.	0.45|.	5.43|5.43	5.43|5.43	0.79202|0.79202	.|.	0.044301|.	0.85682|.	D|.	0.000000|.	T|T	0.77274|0.77274	0.4106|0.4106	M|M	0.81497|0.81497	2.545|2.545	0.47183|0.47183	D|D	0.999347|0.999347	D|.	0.57257|.	0.979|.	D|.	0.71414|.	0.973|.	T|T	0.79017|0.79017	-0.1975|-0.1975	10|5	0.56958|.	D|.	0.05|.	-28.8882|-28.8882	15.7711|15.7711	0.78170|0.78170	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	383|.	O15083|.	ERC2_HUMAN|.	R|G	383|22	ENSP00000288221:K383R|.	ENSP00000288221:K383R|.	K|R	-|-	2|1	0|2	ERC2|ERC2	56182515|56182515	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.945000|0.945000	0.59286|0.59286	7.553000|7.553000	0.82203|0.82203	2.182000|2.182000	0.69389|0.69389	0.455000|0.455000	0.32223|0.32223	AAG|AGG	.	.		0.453	ERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350884.2	NM_015576	Missense_Mutation	C	56207475	T	C	56207475	5	2	255	1	0	0	0	0	0	0	1	0	5213	1623	56	2	1771	2	ERC2	3	56207475	Splice_Site	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	4751307	56207475	141814955	139	35484										
C3orf63	23272	hgsc.bcm.edu	37	chr3	56658883	56658883	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aaagactatgtgtcgttgctGtatgttctgagcctgaagtc	11	7	1	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:56658883G>C	ENST00000493960.2	-	22	4301	c.4291C>G	c.(4291-4293)Cag>Gag	p.Q1431E	FAM208A_ENST00000355628.5_Missense_Mutation_p.Q1370E|FAM208A_ENST00000485156.1_Intron|FAM208A_ENST00000431842.2_Missense_Mutation_p.Q994E	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	1431							poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(11)|prostate(3)|skin(1)	32						TGTCGTTGCTGTATGTTCTGA	0.383																																					p.Q1431E		Atlas-SNP	.											.	FAM208A	113	.	0			c.C4291G						.						127	125	126					3																	56658883		2203	4300	6503	SO:0001583	missense	23272	exon22			GTTGCTGTATGTT	AF180425	CCDS2877.1, CCDS46853.1	3p14.3	2011-09-14	2011-09-14	2011-09-14	ENSG00000163946	ENSG00000163946			30314	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 63"	C3orf63		10470851, 11149944	Standard	NM_015224		Approved	se89-1, RAP140, KIAA1105	uc003die.4	Q9UK61	OTTHUMG00000158827	ENST00000493960.2:c.4291C>G	chr3.hg19:g.56658883G>C	ENSP00000417509:p.Gln1431Glu	360.0	1.0		326.0	167.0	NM_001112736	A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Missense_Mutation	SNP	ENST00000493960.2	hg19	CCDS46853.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.279138	0.80692	.	.	ENSG00000163946	ENST00000431842;ENST00000493960;ENST00000355628	T;T;T	0.53206	0.63;0.63;0.63	5.7	5.7	0.88788	.	0.000000	0.64402	D	0.000008	T	0.52613	0.1745	L	0.38838	1.175	0.47245	D	0.999367	P;B;D;B	0.61697	0.629;0.045;0.99;0.435	B;B;P;B	0.55011	0.382;0.094;0.766;0.104	T	0.54070	-0.8348	10	0.72032	D	0.01	-0.4466	14.6453	0.68756	0.0:0.0:0.8544:0.1456	.	1431;1370;994;1431	Q9UK61-3;Q9UK61-4;Q9UK61-2;Q9UK61	.;.;.;F208A_HUMAN	E	994;1431;1370	ENSP00000399410:Q994E;ENSP00000417509:Q1431E;ENSP00000347845:Q1370E	ENSP00000347845:Q1370E	Q	-	1	0	C3orf63	56633923	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.500000	0.81588	2.685000	0.91497	0.655000	0.94253	CAG	.	.		0.383	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352352.2	NM_015224		C	56658883	G	C	56658883	3	2	255	1	0	0	0	0	1	0	0	0	2241	1386	48	4	793	4	C3orf63	3	56658883	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	451408	56658883	141363547	140	35485										
CADPS	8618	hgsc.bcm.edu	37	chr3	62459862	62459862	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttttacctcttggcccatttCcatgctgcaaagttttgttg	7	10	1	0	rs368477906		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:62459862C>T	ENST00000383710.4	-	24	3812	c.3463G>A	c.(3463-3465)Gaa>Aaa	p.E1155K	CADPS_ENST00000357948.3_Missense_Mutation_p.E1076K|CADPS_ENST00000283269.9_Missense_Mutation_p.E1116K	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	1155					catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		TGGCCCATTTCCATGCTGCAA	0.353																																					p.E1155K		Atlas-SNP	.											.	CADPS	387	.	0			c.G3463A						.	C	LYS/GLU,LYS/GLU,LYS/GLU	0,4406		0,0,2203	116	116	116		3463,3226,3346	6	1	3		116	1,8599		0,1,4299	no	missense,missense,missense	CADPS	NM_003716.3,NM_183393.2,NM_183394.2	56,56,56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign	1155/1354,1076/1275,1116/1315	62459862	1,13005	2203	4300	6503	SO:0001583	missense	8618	exon24			CCATTTCCATGCT	U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"Pleckstrin homology (PH) domain containing"	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.3463G>A	chr3.hg19:g.62459862C>T	ENSP00000373215:p.Glu1155Lys	64.0	0.0		70.0	4.0	NM_003716	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Missense_Mutation	SNP	ENST00000383710.4	hg19	CCDS46858.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	18.86|18.86|18.86	3.712760|3.712760|3.712760	0.68730|0.68730|0.68730	0.0|0.0|0.0	1.16E-4|1.16E-4|1.16E-4	ENSG00000163618|ENSG00000163618|ENSG00000163618	ENST00000383709;ENST00000383710;ENST00000357948;ENST00000283269|ENST00000466621|ENST00000473635	T;T;T|.|.	0.30182|.|.	1.54;1.54;1.54|.|.	5.97|5.97|5.97	5.97|5.97|5.97	0.96955|0.96955|0.96955	.|.|.	0.095518|.|.	0.64402|.|.	D|.|.	0.000001|.|.	T|T|.	0.69187|0.69187|.	0.3083|0.3083|.	L|L|L	0.42245|0.42245|0.42245	1.32|1.32|1.32	0.80722|0.80722|0.80722	D|D|D	1|1|1	B;B;P;P|.|.	0.44521|.|.	0.016;0.449;0.799;0.837|.|.	B;B;B;P|.|.	0.47430|.|.	0.025;0.107;0.108;0.547|.|.	T|T|.	0.62358|0.62358|.	-0.6871|-0.6871|.	10|5|.	0.51188|.|.	T|.|.	0.08|.|.	.|.|.	20.428|20.428|20.428	0.99075|0.99075|0.99075	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	1076;1116;1155;1155|.|.	Q9ULU8-2;Q9ULU8-3;Q9ULU8;Q9ULU8-4|.|.	.;.;CAPS1_HUMAN;.|.|.	K|E|X	1155;1155;1076;1116|66|141	ENSP00000373215:E1155K;ENSP00000350632:E1076K;ENSP00000283269:E1116K|.|.	ENSP00000283269:E1116K|.|.	E|G|W	-|-|-	1|2|3	0|0|0	CADPS|CADPS|CADPS	62434902|62434902|62434902	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.999000|0.999000|0.999000	0.98932|0.98932|0.98932	7.818000|7.818000|7.818000	0.86416|0.86416|0.86416	2.837000|2.837000|2.837000	0.97791|0.97791|0.97791	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	GAA|GGA|TGG	.	.		0.353	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394		T	62459862	C	T	62459862	3	4	255	1	0	0	0	0	1	0	0	0	2572	864	30	3	626	3	CADPS	3	62459862	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	5800979	62459862	135562568	141	35486										
PDZRN3	23024	hgsc.bcm.edu	37	chr3	73433257	73433257	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttcagggacgggctataggtAggggtgcccacttcgggatc	16	9	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:73433257A>G	ENST00000263666.4	-	10	2574	c.2460T>C	c.(2458-2460)ccT>ccC	p.P820P	PDZRN3_ENST00000462146.2_Silent_p.P477P|PDZRN3_ENST00000466780.1_Silent_p.P477P|PDZRN3_ENST00000535920.1_Silent_p.P542P|PDZRN3_ENST00000466348.1_5'Flank|PDZRN3_ENST00000479530.1_Silent_p.P537P	NM_015009.1	NP_055824.1	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	820					neuromuscular junction development (GO:0007528)|protein ubiquitination (GO:0016567)	neuromuscular junction (GO:0031594)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(31)|ovary(4)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		GGCTATAGGTAGGGGTGCCCA	0.662																																					p.P820P		Atlas-SNP	.											.	PDZRN3	196	.	0			c.T2460C						.						52	58	56					3																	73433257		2203	4300	6503	SO:0001819	synonymous_variant	23024	exon10			ATAGGTAGGGGTG	AB029018	CCDS33789.1	3p14.1	2013-01-09	2008-08-14		ENSG00000121440	ENSG00000121440		"RING-type (C3HC4) zinc fingers"	17704	protein-coding gene	gene with protein product	"likely ortholog of mouse semaF cytoplasmic domain associated protein 3"	609729				10470851	Standard	XM_005264718		Approved	KIAA1095, SEMACAP3, LNX3	uc003dpl.1	Q9UPQ7	OTTHUMG00000158865	ENST00000263666.4:c.2460T>C	chr3.hg19:g.73433257A>G		82.0	0.0		73.0	4.0	NM_015009	A7MCZ6|Q8N2N7|Q96CC2|Q9NSQ2	Silent	SNP	ENST00000263666.4	hg19	CCDS33789.1																																																																																			.	.		0.662	PDZRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352460.1	XM_041363		G	73433257	A	G	73433257	2	3	255	1	0	0	0	0	0	0	0	1	11718	407	15	2		2	PDZRN3	3	73433257	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	10973395	73433257	124589173	142	35487										
CADM2	253559	hgsc.bcm.edu	37	chr3	85932563	85932563	+	Frame_Shift_Del	DEL	A	A	-													0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctttatttacaatgcctgtcAaaacttccaaggcatatctc							TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:85932563delA	ENST00000407528.2	+	3	396	c.334delA	c.(334-336)aaafs	p.K112fs	CADM2_ENST00000405615.2_Frame_Shift_Del_p.K114fs|CADM2_ENST00000383699.3_Frame_Shift_Del_p.K121fs	NM_001167674.1	NP_001161146.1	Q8N3J6	CADM2_HUMAN	cell adhesion molecule 2	112	Ig-like V-type.				adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|synapse (GO:0045202)				endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(1)|prostate(1)|skin(4)	38		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		AATGCCTGTCAAAACTTCCAA	0.413																																					p.V120fs		Atlas-Indel,Pindel	.											CADM2_ENST00000383699,NS,carcinoma,+2,2	CADM2	195	.	0			c.360delC						.						97	80	86					3																	85932563		2203	4300	6503	SO:0001589	frameshift_variant	253559	exon4			.	AF538973	CCDS33792.1, CCDS54613.1, CCDS54614.1	3p12.2	2013-01-11	2007-02-07	2007-02-07	ENSG00000175161	ENSG00000175161		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing"	29849	protein-coding gene	gene with protein product	"nectin-like 3"	609938	"immunoglobulin superfamily, member 4D"	IGSF4D			Standard	NM_153184		Approved	NECL3, Necl-3, SynCAM2	uc003dqj.3	Q8N3J6	OTTHUMG00000158990	ENST00000407528.2:c.334delA	chr3.hg19:g.85932563delA	ENSP00000384575:p.Lys112fs	160.0	0.0		125.0	29.0	NM_001167675	G3XHN7|G3XHN8|Q3KQY9|Q658Q7|Q8IZP8	Frame_Shift_Del	DEL	ENST00000407528.2	hg19	CCDS54614.1																																																																																			.	.		0.413	CADM2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352822.1	NM_153184		-	85932563	A	-	85932563	7	5	255	1	0	1	0	1	0	0	0	0	2569	131	5	0	415	0	CADM2	3	85932563	Frame_Shift_Del	DEL	A	TCGA-EP-A2KB-01A-11D-A183-10	12499306	85932563	112089867	143	35488	181	2								
CADM2	253559	hgsc.bcm.edu	37	chr3	85932567	85932567	+	Missense_Mutation	SNP	C	C	T													0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	atttacaatgcctgtcaaaaCttccaaggcatatctcaccg							TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:85932567C>T	ENST00000407528.2	+	3	400	c.338C>T	c.(337-339)aCt>aTt	p.T113I	CADM2_ENST00000405615.2_Missense_Mutation_p.T115I|CADM2_ENST00000383699.3_Missense_Mutation_p.T122I	NM_001167674.1	NP_001161146.1	Q8N3J6	CADM2_HUMAN	cell adhesion molecule 2	113	Ig-like V-type.				adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|synapse (GO:0045202)				endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(1)|prostate(1)|skin(4)	38		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		CCTGTCAAAACTTCCAAGGCA	0.403																																					p.T122I		Atlas-SNP	.											.	CADM2	195	.	0			c.C365T						.						97	81	87					3																	85932567		2203	4300	6503	SO:0001583	missense	253559	exon4			TCAAAACTTCCAA	AF538973	CCDS33792.1, CCDS54613.1, CCDS54614.1	3p12.2	2013-01-11	2007-02-07	2007-02-07	ENSG00000175161	ENSG00000175161		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing"	29849	protein-coding gene	gene with protein product	"nectin-like 3"	609938	"immunoglobulin superfamily, member 4D"	IGSF4D			Standard	NM_153184		Approved	NECL3, Necl-3, SynCAM2	uc003dqj.3	Q8N3J6	OTTHUMG00000158990	ENST00000407528.2:c.338C>T	chr3.hg19:g.85932567C>T	ENSP00000384575:p.Thr113Ile	157.0	0.0		121.0	31.0	NM_001167675	G3XHN7|G3XHN8|Q3KQY9|Q658Q7|Q8IZP8	Missense_Mutation	SNP	ENST00000407528.2	hg19	CCDS54614.1	.	.	.	.	.	.	.	.	.	.	C	16.04	3.009951	0.54361	.	.	ENSG00000175161	ENST00000383699;ENST00000407528;ENST00000405615	T;T;T	0.28454	1.61;1.61;1.61	5.54	5.54	0.83059	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.043673	0.85682	D	0.000000	T	0.64023	0.2561	M	0.87547	2.89	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.988;0.998;0.999	T	0.68887	-0.5290	10	0.72032	D	0.01	.	19.8568	0.96762	0.0:1.0:0.0:0.0	.	115;122;113	Q8N3J6-3;G3XHN4;Q8N3J6	.;.;CADM2_HUMAN	I	122;113;115	ENSP00000373200:T122I;ENSP00000384575:T113I;ENSP00000384193:T115I	ENSP00000373200:T122I	T	+	2	0	CADM2	86015257	1.000000	0.71417	0.952000	0.39060	0.016000	0.09150	5.721000	0.68477	2.764000	0.94973	0.650000	0.86243	ACT	.	.		0.403	CADM2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352822.1	NM_153184		T	85932567	C	T	85932567	3	4	255	1	0	0	0	0	1	0	0	0	2569	565	20	3	419	3	CADM2	3	85932567	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	4	85932567	112089863	144	35489	181	2								
OR5K4	403278	hgsc.bcm.edu	37	chr3	98073598	98073598	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcataaatgttcttaaaaaaAttatgaggaattataacatt	4	3	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:98073598A>T	ENST00000354924.2	+	1	901	c.901A>T	c.(901-903)Att>Ttt	p.I301F	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005517.1	NP_001005517.1	A6NMS3	OR5K4_HUMAN	olfactory receptor, family 5, subfamily K, member 4	301						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(13)|upper_aerodigestive_tract(1)	21						TCTTAAAAAAATTATGAGGAA	0.249																																					p.I301F		Atlas-SNP	.											.,4	OR5K4	75	.	0			c.A901T						.						80	101	94					3																	98073598		2175	4254	6429	SO:0001583	missense	403278	exon1			AAAAAAATTATGA		CCDS33802.1	3q11.2	2013-09-23			ENSG00000196098	ENSG00000196098		"GPCR / Class A : Olfactory receptors"	31291	protein-coding gene	gene with protein product							Standard	NM_001005517		Approved		uc011bgv.2	A6NMS3	OTTHUMG00000160081	ENST00000354924.2:c.901A>T	chr3.hg19:g.98073598A>T	ENSP00000347003:p.Ile301Phe	22.0	0.0		42.0	5.0	NM_001005517		Missense_Mutation	SNP	ENST00000354924.2	hg19	CCDS33802.1	.	.	.	.	.	.	.	.	.	.	A	8.782	0.928577	0.18131	.	.	ENSG00000196098	ENST00000354924	T	0.38560	1.13	4.83	-4.36	0.03645	.	1.915270	0.03787	U	0.262255	T	0.23611	0.0571	N	0.14661	0.345	0.09310	N	1	B	0.10296	0.003	B	0.10450	0.005	T	0.19257	-1.0311	10	0.49607	T	0.09	-0.152	4.4994	0.11856	0.238:0.0:0.332:0.4299	.	301	A6NMS3	OR5K4_HUMAN	F	301	ENSP00000347003:I301F	ENSP00000347003:I301F	I	+	1	0	OR5K4	99556288	0.436000	0.25586	0.001000	0.08648	0.018000	0.09664	-0.189000	0.09629	-0.889000	0.03950	-0.461000	0.05368	ATT	.	.		0.249	OR5K4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359114.1			T	98073598	A	T	98073598	3	4	255	1	0	0	0	0	1	0	0	0	11178	101	4	4	903	4	OR5K4	3	98073598	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	12141031	98073598	99948832	145	35490										
PLCXD2	257068	hgsc.bcm.edu	37	chr3	111427204	111427204	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gcagtgtggaaagtttgacgCtgcgaactctgtgggagaag	16	6	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:111427204C>A	ENST00000477665.1	+	2	919	c.595C>A	c.(595-597)Ctg>Atg	p.L199M	PLCXD2_ENST00000393934.3_Missense_Mutation_p.L199M	NM_001185106.1	NP_001172035.1	Q0VAA5	PLCX2_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 2	199	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				lipid catabolic process (GO:0016042)		phosphoric diester hydrolase activity (GO:0008081)|signal transducer activity (GO:0004871)			endometrium(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)	17						AAGTTTGACGCTGCGAACTCT	0.512																																					p.L199M		Atlas-SNP	.											.	PLCXD2	36	.	0			c.C595A						.						63	62	62					3																	111427204		2203	4300	6503	SO:0001583	missense	257068	exon2			TTGACGCTGCGAA	AK056141	CCDS2961.1, CCDS54619.1	3q13.2	2004-09-09			ENSG00000240891	ENSG00000240891			26462	protein-coding gene	gene with protein product							Standard	NM_001185106		Approved	FLJ31579	uc003dxz.3	Q0VAA5	OTTHUMG00000159279	ENST00000477665.1:c.595C>A	chr3.hg19:g.111427204C>A	ENSP00000420686:p.Leu199Met	141.0	0.0		118.0	5.0	NM_001185106	Q96N12	Missense_Mutation	SNP	ENST00000477665.1	hg19	CCDS54619.1	.	.	.	.	.	.	.	.	.	.	C	13.30	2.195817	0.38806	.	.	ENSG00000240891	ENST00000393934;ENST00000477665	.	.	.	5.73	2.93	0.34026	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);	.	.	.	.	T	0.79845	0.4516	M	0.88450	2.955	0.49915	D	0.999838	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.81673	-0.0826	8	0.87932	D	0	-9.2257	10.3159	0.43736	0.0:0.768:0.0:0.232	.	199;199	Q0VAA5;Q0VAA5-2	PLCX2_HUMAN;.	M	199	.	ENSP00000377511:L199M	L	+	1	2	PLCXD2	112909894	0.992000	0.36948	0.030000	0.17652	0.135000	0.20990	2.953000	0.49105	0.881000	0.35993	0.655000	0.94253	CTG	.	.		0.512	PLCXD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354322.1	NM_153268		A	111427204	C	A	111427204	3	1	255	1	0	0	0	0	1	0	0	0	12051	796	28	3	601	3	PLCXD2	3	111427204	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	13353606	111427204	86595226	146	35491										
SLC15A2	6565	hgsc.bcm.edu	37	chr3	121647383	121647383	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aaacaattctctgttgatagAgtccatcaaatcctttcagg	6	9	3	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:121647383A>G	ENST00000489711.1	+	15	1710	c.1322A>G	c.(1321-1323)gAg>gGg	p.E441G	SLC15A2_ENST00000295605.2_Missense_Mutation_p.E410G|SLC15A2_ENST00000465060.1_3'UTR	NM_021082.3	NP_066568.3	Q16348	S15A2_HUMAN	solute carrier family 15 (oligopeptide transporter), member 2	441					drug transport (GO:0015893)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antibiotic transporter activity (GO:0042895)|dipeptide transporter activity (GO:0042936)|high-affinity oligopeptide transporter activity (GO:0015334)|peptide:proton symporter activity (GO:0015333)			NS(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(17)|skin(6)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(114;0.0967)	Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Fosinopril(DB00492)|Glyburide(DB01016)|Moexipril(DB00691)|Nateglinide(DB00731)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Tranexamic Acid(DB00302)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	CTGTTGATAGAGTCCATCAAA	0.393																																					p.E441G		Atlas-SNP	.											.	SLC15A2	92	.	0			c.A1322G						.						168	176	173					3																	121647383		2203	4300	6503	SO:0001583	missense	6565	exon15			TGATAGAGTCCAT	BC044572	CCDS3007.1, CCDS54631.1	3q21.1	2013-07-18	2013-07-18		ENSG00000163406	ENSG00000163406		"Solute carriers"	10921	protein-coding gene	gene with protein product		602339	"solute carrier family 15 (H+/peptide transporter), member 2"			7756356	Standard	NM_021082		Approved	PEPT2	uc003eep.2	Q16348	OTTHUMG00000159423	ENST00000489711.1:c.1322A>G	chr3.hg19:g.121647383A>G	ENSP00000417085:p.Glu441Gly	126.0	0.0		100.0	6.0	NM_021082	A8K1A5|B4E2A7	Missense_Mutation	SNP	ENST00000489711.1	hg19	CCDS3007.1	.	.	.	.	.	.	.	.	.	.	A	8.753	0.921676	0.17982	.	.	ENSG00000163406	ENST00000489711;ENST00000542599;ENST00000295605	T;T	0.04454	3.62;3.62	5.65	4.48	0.54585	.	0.424514	0.28996	N	0.013477	T	0.05868	0.0153	L	0.50333	1.59	0.39041	D	0.960127	B;B	0.11235	0.004;0.0	B;B	0.16722	0.016;0.005	T	0.27020	-1.0086	10	0.30078	T	0.28	-3.7873	8.9241	0.35630	0.8349:0.0:0.0:0.165	.	410;441	B4E2A7;Q16348	.;S15A2_HUMAN	G	441;403;410	ENSP00000417085:E441G;ENSP00000295605:E410G	ENSP00000295605:E410G	E	+	2	0	SLC15A2	123130073	0.994000	0.37717	0.977000	0.42913	0.285000	0.27093	2.545000	0.45769	1.124000	0.41980	0.533000	0.62120	GAG	.	.		0.393	SLC15A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355239.1	NM_021082		G	121647383	A	G	121647383	3	3	255	1	0	0	0	0	1	0	0	0	14414	304	11	2	1380	2	SLC15A2	3	121647383	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	10220179	121647383	76375047	147	35492										
SEMA5B	54437	hgsc.bcm.edu	37	chr3	122646670	122646670	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggagttatattgggcagtgcGaagcggtggcccactgccca	15	10	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:122646670G>T	ENST00000357599.3	-	8	1203	c.817C>A	c.(817-819)Cgc>Agc	p.R273S	SEMA5B_ENST00000195173.4_Missense_Mutation_p.R273S|SEMA5B_ENST00000451055.2_Missense_Mutation_p.R327S|AC078794.1_ENST00000408284.1_RNA	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	273	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		TGGGCAGTGCGAAGCGGTGGC	0.627																																					p.R327S		Atlas-SNP	.											SEMA5B_ENST00000451055,bladder,carcinoma,0,4	SEMA5B	303	.	0			c.C979A						.						59	60	59					3																	122646670		2203	4300	6503	SO:0001583	missense	54437	exon8			CAGTGCGAAGCGG	AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"Semaphorins"	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.817C>A	chr3.hg19:g.122646670G>T	ENSP00000350215:p.Arg273Ser	54.0	0.0		75.0	3.0	NM_001256347	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Missense_Mutation	SNP	ENST00000357599.3	hg19	CCDS35491.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.039632	0.93630	.	.	ENSG00000082684	ENST00000357599;ENST00000195173;ENST00000418793;ENST00000451055;ENST00000393583	T;T;T;T	0.12774	2.65;2.65;2.65;2.65	5.53	5.53	0.82687	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.38026	0.1025	M	0.86573	2.825	0.80722	D	1	P;D;D	0.53885	0.954;0.963;0.963	P;P;P	0.58077	0.742;0.832;0.832	T	0.24297	-1.0164	10	0.87932	D	0	.	14.0515	0.64739	0.0:0.0:0.8397:0.1603	.	215;273;273	D3YTI7;B5ME80;Q9P283	.;.;SEM5B_HUMAN	S	273;273;215;327;273	ENSP00000350215:R273S;ENSP00000195173:R273S;ENSP00000389588:R327S;ENSP00000377208:R273S	ENSP00000195173:R273S	R	-	1	0	SEMA5B	124129360	1.000000	0.71417	0.984000	0.44739	0.981000	0.71138	4.148000	0.58085	2.882000	0.98803	0.655000	0.94253	CGC	.	.		0.627	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702		T	122646670	G	T	122646670	3	4	255	1	0	0	0	0	1	0	0	0	14053	1058	37	1	2702	1	SEMA5B	3	122646670	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	999287	122646670	75375760	148	35493										
RHO	6010	hgsc.bcm.edu	37	chr3	129249881	129249881	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cgcacccccactcgccggctGgtccaggtaatggcactgag	12	16	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:129249881G>A	ENST00000296271.3	+	2	618	c.524G>A	c.(523-525)tGg>tAg	p.W175*		NM_000539.3	NP_000530.1	P08100	OPSD_HUMAN	rhodopsin	175					G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction, visible light (GO:0007603)|protein phosphorylation (GO:0006468)|protein-chromophore linkage (GO:0018298)|red, far-red light phototransduction (GO:0009585)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|retinoid metabolic process (GO:0001523)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	cell-cell junction (GO:0005911)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)|photoreceptor inner segment membrane (GO:0060342)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|rough endoplasmic reticulum membrane (GO:0030867)	G-protein coupled receptor activity (GO:0004930)|metal ion binding (GO:0046872)|photoreceptor activity (GO:0009881)|retinal binding (GO:0016918)			breast(1)|endometrium(1)|large_intestine(10)|lung(6)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	22		all_neural(597;0.0227)|Myeloproliferative disorder(1037;0.0255)|Prostate(884;0.183)		GBM - Glioblastoma multiforme(114;2.58e-05)|Lung(219;0.0234)	Halothane(DB01159)	CTCGCCGGCTGGTCCAGGTAA	0.622																																					p.W175X	Esophageal Squamous(118;214 1623 30842 43234 46940)	Atlas-SNP	.											.	RHO	57	.	0			c.G524A						.						52	48	50					3																	129249881		2202	4300	6502	SO:0001587	stop_gained	6010	exon2			CCGGCTGGTCCAG	AB065668	CCDS3063.1	3q21-q24	2014-01-28	2008-04-16		ENSG00000163914	ENSG00000163914		"GPCR / Class A : Opsin receptors"	10012	protein-coding gene	gene with protein product	"opsin 2, rod pigment"	180380	"retinitis pigmentosa 4, autosomal dominant"	RP4		2016091	Standard	NM_000539		Approved	OPN2, CSNBAD1	uc003emt.3	P08100	OTTHUMG00000159542	ENST00000296271.3:c.524G>A	chr3.hg19:g.129249881G>A	ENSP00000296271:p.Trp175*	48.0	0.0		66.0	4.0	NM_000539	Q16414|Q2M249	Nonsense_Mutation	SNP	ENST00000296271.3	hg19	CCDS3063.1	.	.	.	.	.	.	.	.	.	.	G	33	5.253294	0.95336	.	.	ENSG00000163914	ENST00000296271	.	.	.	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.8606	0.92270	0.0:0.0:1.0:0.0	.	.	.	.	X	175	.	ENSP00000296271:W175X	W	+	2	0	RHO	130732571	1.000000	0.71417	1.000000	0.80357	0.525000	0.34531	9.863000	0.99569	2.448000	0.82819	0.462000	0.41574	TGG	.	.		0.622	RHO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356101.1	NM_000539		A	129249881	G	A	129249881	4	1	255	1	0	0	0	0	0	1	0	0	13345	1357	47	3	530	3	RHO	3	129249881	Nonsense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	6603211	129249881	68772549	149	35494										
ASTE1	28990	hgsc.bcm.edu	37	chr3	130735171	130735171	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcttagcaccatcttcctgcAgctcttccttacctaaataa	3	14	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:130735171A>G	ENST00000264992.3	-	5	1967	c.1526T>C	c.(1525-1527)cTg>cCg	p.L509P	ATP2C1_ENST00000504381.1_3'UTR|ATP2C1_ENST00000507488.2_3'UTR|ATP2C1_ENST00000422190.2_3'UTR|ATP2C1_ENST00000393221.4_3'UTR|ATP2C1_ENST00000359644.3_3'UTR|ATP2C1_ENST00000513801.1_3'UTR|ATP2C1_ENST00000533801.2_3'UTR|ATP2C1_ENST00000328560.8_3'UTR|ASTE1_ENST00000514044.1_Missense_Mutation_p.L509P	NM_014065.2	NP_054784.2	Q2TB18	ASTE1_HUMAN	asteroid homolog 1 (Drosophila)	509					DNA repair (GO:0006281)		nuclease activity (GO:0004518)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)	22						ATCTTCCTGCAGCTCTTCCTT	0.423																																					p.L509P		Atlas-SNP	.											.	ASTE1	67	.	0			c.T1526C						.						139	125	130					3																	130735171		2203	4300	6503	SO:0001583	missense	28990	exon5			TCCTGCAGCTCTT	AF113539	CCDS3068.1, CCDS75007.1	3q21.3	2005-11-17			ENSG00000034533	ENSG00000034533			25021	protein-coding gene	gene with protein product							Standard	NM_014065		Approved	HT001	uc003env.1	Q2TB18	OTTHUMG00000159644	ENST00000264992.3:c.1526T>C	chr3.hg19:g.130735171A>G	ENSP00000264992:p.Leu509Pro	119.0	0.0		119.0	5.0	NM_014065	B4DFL9|Q3MIB6|Q8N6G4|Q96JY1|Q9UHX6	Missense_Mutation	SNP	ENST00000264992.3	hg19	CCDS3068.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.28|10.28	1.305458|1.305458	0.23736|0.23736	.|.	.|.	ENSG00000034533|ENSG00000034533	ENST00000505290|ENST00000514044;ENST00000264992	.|.	.|.	.|.	5.86|5.86	-1.11|-1.11	0.09840|0.09840	.|.	.|0.955177	.|0.08797	.|N	.|0.892355	T|T	0.29093|0.29093	0.0723|0.0723	L|L	0.40543|0.40543	1.245|1.245	0.09310|0.09310	N|N	0.999996|0.999996	.|B;B	.|0.10296	.|0.003;0.001	.|B;B	.|0.06405	.|0.002;0.002	T|T	0.25222|0.25222	-1.0138|-1.0138	5|9	.|0.33141	.|T	.|0.24	0.6471|0.6471	4.8709|4.8709	0.13631|0.13631	0.4424:0.0:0.3353:0.2223|0.4424:0.0:0.3353:0.2223	.|.	.|509;509	.|D6RG30;Q2TB18	.|.;ASTE1_HUMAN	R|P	86|509	.|.	.|ENSP00000264992:L509P	C|L	-|-	1|2	0|0	ASTE1|ASTE1	132217861|132217861	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.052000|0.052000	0.14988|0.14988	-1.149000|-1.149000	0.03182|0.03182	-0.118000|-0.118000	0.11851|0.11851	0.533000|0.533000	0.62120|0.62120	TGC|CTG	.	.		0.423	ASTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356659.1	NM_014065		G	130735171	A	G	130735171	3	3	255	1	0	0	0	0	1	0	0	0	1062	188	7	2	521	2	ASTE1	3	130735171	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	1485290	130735171	67287259	150	35495										
PRR23A	729627	hgsc.bcm.edu	37	chr3	138725110	138725110	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gctgcggggccggctgcccaTagcctcgacggcgctcttgg	16	15	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:138725110T>C	ENST00000383163.2	-	1	0	c.1A>G	c.(1-3)Atg>Gtg	p.M1V	MRPS22_ENST00000495075.1_Intron	NM_001134659.1	NP_001128131.1	A6NEV1	PR23A_HUMAN	proline rich 23A	1										endometrium(3)|kidney(1)|lung(7)	11						CGGCTGCCCATAGCCTCGACG	0.697																																					p.M1V		Atlas-SNP	.											.	PRR23A	35	.	0			c.A1G						.						1	2	2					3																	138725110		348	1024	1372	SO:0001630	splice_region_variant	729627	exon1			TGCCCATAGCCTC		CCDS46923.1	3q22.3	2014-06-03				ENSG00000206260			37172	protein-coding gene	gene with protein product							Standard	NM_001134659		Approved		uc011bms.2	A6NEV1		ENST00000383163.2:c.1-1A>G	chr3.hg19:g.138725110T>C		19.0	0.0		12.0	8.0	NM_001134659		Missense_Mutation	SNP	ENST00000383163.2	hg19	CCDS46923.1	.	.	.	.	.	.	.	.	.	.	T	7.219	0.597077	0.13875	.	.	ENSG00000206260	ENST00000383163	.	.	.	2.52	1.36	0.22044	.	1.434950	0.04639	N	0.405053	T	0.28566	0.0707	.	.	.	0.09310	N	1	B	0.24618	0.107	B	0.23716	0.048	T	0.22382	-1.0218	8	0.36615	T	0.2	.	4.0819	0.09931	0.0:0.1761:0.0:0.8239	.	1	A6NEV1	PR23A_HUMAN	V	1	.	ENSP00000372649:M1V	M	-	1	0	PRR23A	140207800	0.000000	0.05858	0.003000	0.11579	0.209000	0.24338	-0.245000	0.08890	0.407000	0.25591	0.379000	0.24179	ATG	.	.		0.697	PRR23A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361503.1	NM_001134659	Missense_Mutation	C	138725110	T	C	138725110	5	2	255	1	0	0	0	0	0	0	1	0	12606	1420	49	2	803	2	PRR23A	3	138725110	Splice_Site	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	7989939	138725110	59297320	151	35496										
ATR	545	hgsc.bcm.edu	37	chr3	142281918	142281918	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aggagggagttgctgcaatcCgcagaagtctcgttatgatc	13	8	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:142281918C>A	ENST00000350721.4	-	4	447	c.326G>T	c.(325-327)cGg>cTg	p.R109L	ATR_ENST00000383101.3_Missense_Mutation_p.R109L	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	109					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R109L(1)		NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						TGCTGCAATCCGCAGAAGTCT	0.308								Other conserved DNA damage response genes																													p.R109L		Atlas-SNP	.											.	ATR	285	.	1	Substitution - Missense(1)	lung(1)	c.G326T						.						89	102	98					3																	142281918		2143	4277	6420	SO:0001583	missense	545	exon4			GCAATCCGCAGAA	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.326G>T	chr3.hg19:g.142281918C>A	ENSP00000343741:p.Arg109Leu	87.0	0.0		83.0	4.0	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	hg19	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	C	17.78	3.472384	0.63737	.	.	ENSG00000175054	ENST00000350721;ENST00000383101	T;T	0.40476	1.03;1.03	5.62	5.62	0.85841	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.65281	0.2676	M	0.65975	2.015	0.40605	D	0.981619	D	0.89917	1.0	D	0.81914	0.995	T	0.66532	-0.5900	10	0.59425	D	0.04	-12.9653	19.6544	0.95831	0.0:1.0:0.0:0.0	.	109	Q13535	ATR_HUMAN	L	109	ENSP00000343741:R109L;ENSP00000372581:R109L	ENSP00000343741:R109L	R	-	2	0	ATR	143764608	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.683000	0.74533	2.647000	0.89833	0.467000	0.42956	CGG	.	.		0.308	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		A	142281918	C	A	142281918	3	1	255	1	0	0	0	0	1	0	0	0	1204	652	23	1	7784	1	ATR	3	142281918	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	3556808	142281918	55740512	152	35497										
PLSCR1	5359	hgsc.bcm.edu	37	chr3	146246440	146246440	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccaggtggacagtttaatggAggctgtggcgctggcatcca	15	9	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:146246440A>G	ENST00000342435.4	-	4	683	c.273T>C	c.(271-273)ccT>ccC	p.P91P	PLSCR1_ENST00000448787.2_Intron|PLSCR1_ENST00000448205.1_Intron|PLSCR1_ENST00000487389.1_Silent_p.P84P	NM_021105.2	NP_066928.1	O15162	PLS1_HUMAN	phospholipid scramblase 1	91					acute-phase response (GO:0006953)|apoptotic process (GO:0006915)|defense response to virus (GO:0051607)|negative regulation of viral genome replication (GO:0045071)|phosphatidylserine biosynthetic process (GO:0006659)|phospholipid scrambling (GO:0017121)|platelet activation (GO:0030168)|positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity (GO:2000373)|positive regulation of gene expression (GO:0010628)|positive regulation of innate immune response (GO:0045089)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060368)|regulation of mast cell activation (GO:0033003)|response to interferon-beta (GO:0035456)	cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|CD4 receptor binding (GO:0042609)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|epidermal growth factor receptor binding (GO:0005154)|phospholipid scramblase activity (GO:0017128)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|SH3 domain binding (GO:0017124)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(1)	15						AGTTTAATGGAGGCTGTGGCG	0.443																																					p.P91P		Atlas-SNP	.											.	PLSCR1	35	.	0			c.T273C						.						101	107	105					3																	146246440		2203	4300	6503	SO:0001819	synonymous_variant	5359	exon4			TAATGGAGGCTGT	AF098642	CCDS3135.1	3q23	2004-02-27			ENSG00000188313	ENSG00000188313			9092	protein-coding gene	gene with protein product		604170				9218461	Standard	NM_021105		Approved	MMTRA1B	uc003evx.4	O15162	OTTHUMG00000159427	ENST00000342435.4:c.273T>C	chr3.hg19:g.146246440A>G		141.0	0.0		99.0	4.0	NM_021105	B2R8H8|B4DTE8	Silent	SNP	ENST00000342435.4	hg19	CCDS3135.1	.	.	.	.	.	.	.	.	.	.	A	1.765	-0.485865	0.04352	.	.	ENSG00000188313	ENST00000483300	.	.	.	4.03	2.75	0.32379	.	.	.	.	.	T	0.25568	0.0622	.	.	.	0.09310	N	0.999997	.	.	.	.	.	.	T	0.14504	-1.0470	4	.	.	.	.	4.1876	0.10405	0.6219:0.0:0.0924:0.2857	.	.	.	.	P	33	.	.	L	-	2	0	PLSCR1	147729130	0.056000	0.20664	0.115000	0.21578	0.341000	0.28922	0.487000	0.22356	1.784000	0.52394	0.402000	0.26972	CTC	.	.		0.443	PLSCR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355257.2	NM_021105		G	146246440	A	G	146246440	2	3	255	1	0	0	0	0	0	0	0	1	12118	291	11	2		2	PLSCR1	3	146246440	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	3964522	146246440	51775990	153	35498										
HPS3	84343	hgsc.bcm.edu	37	chr3	148880655	148880655	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	caccacaccattgcgaacatCggaggatctggtaagataat	9	10	1	1	rs373037058		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:148880655C>A	ENST00000296051.2	+	13	2611	c.2471C>A	c.(2470-2472)tCg>tAg	p.S824*	HPS3_ENST00000460120.1_Nonsense_Mutation_p.S659*	NM_032383.3	NP_115759.2	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3	824					organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	34			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			TTGCGAACATCGGAGGATCTG	0.363									Hermansky-Pudlak syndrome																												p.S824X		Atlas-SNP	.											.	HPS3	104	.	0			c.C2471A						.						98	96	96					3																	148880655		2203	4300	6503	SO:0001587	stop_gained	84343	exon13	Familial Cancer Database	HPS, HPS1-8	GAACATCGGAGGA	AY033141	CCDS3140.1	3q24	2014-06-18			ENSG00000163755	ENSG00000163755			15597	protein-coding gene	gene with protein product		606118				11455388	Standard	NM_032383		Approved	SUTAL	uc003ewu.1	Q969F9	OTTHUMG00000159548	ENST00000296051.2:c.2471C>A	chr3.hg19:g.148880655C>A	ENSP00000296051:p.Ser824*	74.0	0.0		79.0	4.0	NM_032383	A8K6G6|Q8WTV6|Q96AP1|Q96MR3|Q9H608	Nonsense_Mutation	SNP	ENST00000296051.2	hg19	CCDS3140.1	.	.	.	.	.	.	.	.	.	.	C	36	5.970018	0.97156	.	.	ENSG00000163755	ENST00000296051;ENST00000460120	.	.	.	5.87	5.87	0.94306	.	0.394049	0.29093	N	0.013172	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05721	T	0.95	-5.2168	20.2103	0.98287	0.0:1.0:0.0:0.0	.	.	.	.	X	824;659	.	ENSP00000296051:S824X	S	+	2	0	HPS3	150363345	0.743000	0.28239	0.116000	0.21606	0.010000	0.07245	5.958000	0.70330	2.780000	0.95670	0.563000	0.77884	TCG	.	.		0.363	HPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356151.1	NM_032383		A	148880655	C	A	148880655	4	1	255	1	0	0	0	0	0	1	0	0	7349	893	31	1	2521	1	HPS3	3	148880655	Nonsense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	2634215	148880655	49141775	154	35499										
WWTR1	25937	hgsc.bcm.edu	37	chr3	149243898	149243898	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgtcagtgctctgctccctcGaatgatatggccctctgcaa	9	13	3	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:149243898G>A	ENST00000465804.1	-	7	1176	c.920C>T	c.(919-921)tCg>tTg	p.S307L	WWTR1_ENST00000360632.3_Missense_Mutation_p.S307L|WWTR1_ENST00000467467.1_Missense_Mutation_p.S307L|RNU6-1098P_ENST00000516772.1_RNA	NM_001168278.1	NP_001161750.1	Q9GZV5	WWTR1_HUMAN	WW domain containing transcription regulator 1	307					cilium morphogenesis (GO:0060271)|gene expression (GO:0010467)|glomerulus development (GO:0032835)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast differentiation (GO:0001649)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of SMAD protein import into nucleus (GO:0060390)|regulation of transcription, DNA-templated (GO:0006355)|stem cell division (GO:0017145)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(5)|cervix(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	23			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			CTGCTCCCTCGAATGATATGG	0.453			T	CAMTA1	epitheliod hemangioendothelioma																																p.S307L		Atlas-SNP	.		Dom	yes		3	3q23-q24	607392	WW domain containing transcription regulator 1		M	WWTR1,colon,carcinoma,0,1	WWTR1	42	.	0			c.C920T						.						105	95	98					3																	149243898		2203	4300	6503	SO:0001583	missense	25937	exon7			TCCCTCGAATGAT	AK022036	CCDS3144.1	3q23-q24	2004-12-03			ENSG00000018408	ENSG00000018408			24042	protein-coding gene	gene with protein product		607392				11118213, 15096513	Standard	NM_015472		Approved	TAZ, DKFZp586I1419	uc021xfm.1	Q9GZV5	OTTHUMG00000159614	ENST00000465804.1:c.920C>T	chr3.hg19:g.149243898G>A	ENSP00000419465:p.Ser307Leu	60.0	0.0		69.0	3.0	NM_001168278	D3DNH7|Q8N3P2|Q9Y3W6	Missense_Mutation	SNP	ENST00000465804.1	hg19	CCDS3144.1	.	.	.	.	.	.	.	.	.	.	G	32	5.119092	0.94385	.	.	ENSG00000018408	ENST00000465804;ENST00000360632;ENST00000467467;ENST00000472417	T;T;T	0.51071	0.72;0.72;0.72	5.56	5.56	0.83823	.	0.061015	0.64402	D	0.000002	T	0.66587	0.2804	M	0.77103	2.36	0.80722	D	1	D	0.69078	0.997	P	0.55965	0.788	T	0.71144	-0.4678	10	0.87932	D	0	-16.6941	19.5073	0.95124	0.0:0.0:1.0:0.0	.	307	Q9GZV5	WWTR1_HUMAN	L	307;307;307;165	ENSP00000419465:S307L;ENSP00000353847:S307L;ENSP00000419234:S307L	ENSP00000353847:S307L	S	-	2	0	WWTR1	150726588	1.000000	0.71417	0.454000	0.27019	0.942000	0.58702	9.467000	0.97671	2.606000	0.88127	0.563000	0.77884	TCG	.	.		0.453	WWTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356498.1	NM_015472		A	149243898	G	A	149243898	3	1	255	1	0	0	0	0	1	0	0	0	17432	1059	37	1	290	1	WWTR1	3	149243898	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	363243	149243898	48778532	155	35500										
MED12L	116931	hgsc.bcm.edu	37	chr3	151107911	151107911	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gctttttccttcagaaccaaTctcttactccaggtatgtga	6	11	2	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:151107911T>C	ENST00000474524.1	+	36	5529	c.5491T>C	c.(5491-5493)Tct>Cct	p.S1831P	MED12L_ENST00000273432.4_Missense_Mutation_p.S1691P	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	1831						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TCAGAACCAATCTCTTACTCC	0.493																																					p.S1831P		Atlas-SNP	.											.	MED12L	271	.	0			c.T5491C						.						131	144	140					3																	151107911		2203	4300	6503	SO:0001583	missense	116931	exon36			AACCAATCTCTTA	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.5491T>C	chr3.hg19:g.151107911T>C	ENSP00000417235:p.Ser1831Pro	52.0	0.0		55.0	4.0	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Missense_Mutation	SNP	ENST00000474524.1	hg19	CCDS33876.1	.	.	.	.	.	.	.	.	.	.	T	2.556	-0.302968	0.05495	.	.	ENSG00000144893	ENST00000474524;ENST00000273432	T;T	0.58797	0.56;0.31	5.75	0.525	0.17072	Mediator complex, subunit Med12, catenin-binding (1);	0.195620	0.46145	D	0.000309	T	0.25568	0.0622	N	0.08118	0	0.22562	N	0.998985	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.25779	-1.0122	10	0.05351	T	0.99	-7.3491	5.8181	0.18512	0.0:0.1291:0.5249:0.346	.	1691;1831	F8WAE6;Q86YW9	.;MD12L_HUMAN	P	1831;1691	ENSP00000417235:S1831P;ENSP00000273432:S1691P	ENSP00000273432:S1691P	S	+	1	0	MED12L	152590601	0.210000	0.23517	0.245000	0.24217	0.971000	0.66376	0.439000	0.21575	0.074000	0.16767	0.533000	0.62120	TCT	.	.		0.493	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002		C	151107911	T	C	151107911	3	2	255	1	0	0	0	0	1	0	0	0	9438	1435	50	2	5633	2	MED12L	3	151107911	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	1864013	151107911	46914519	156	35501										
IGSF10	285313	hgsc.bcm.edu	37	chr3	151174848	151174848	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aatctgagaaggtcttgtcaGggattgtgtgaatgccattg	13	5	3	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:151174848G>A	ENST00000282466.3	-	2	289	c.290C>T	c.(289-291)cCt>cTt	p.P97L		NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	97					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			GGTCTTGTCAGGGATTGTGTG	0.468																																					p.P97L		Atlas-SNP	.											.	IGSF10	279	.	0			c.C290T						.						124	109	114					3																	151174848		2203	4300	6503	SO:0001583	missense	285313	exon2			TTGTCAGGGATTG	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"Immunoglobulin superfamily / I-set domain containing"	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.290C>T	chr3.hg19:g.151174848G>A	ENSP00000282466:p.Pro97Leu	88.0	0.0		91.0	4.0	NM_178822	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	hg19	CCDS3160.1	.	.	.	.	.	.	.	.	.	.	G	14.62	2.589048	0.46110	.	.	ENSG00000152580	ENST00000282466	T	0.60920	0.15	5.87	4.05	0.47172	.	0.670883	0.12960	N	0.425111	T	0.52322	0.1727	L	0.58428	1.81	0.37437	D	0.914269	P	0.39352	0.669	B	0.39904	0.313	T	0.57382	-0.7821	10	0.72032	D	0.01	.	4.9421	0.13971	0.0708:0.1336:0.5389:0.2567	.	97	Q6WRI0	IGS10_HUMAN	L	97	ENSP00000282466:P97L	ENSP00000282466:P97L	P	-	2	0	IGSF10	152657538	0.286000	0.24305	0.081000	0.20488	0.896000	0.52359	1.305000	0.33493	0.796000	0.33947	0.655000	0.94253	CCT	.	.		0.468	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822		A	151174848	G	A	151174848	3	1	255	1	0	0	0	0	1	0	0	0	7606	1000	35	3	7649	3	IGSF10	3	151174848	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	66937	151174848	46847582	157	35502										
GFM1	85476	hgsc.bcm.edu	37	chr3	158364696	158364696	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cttttattaacaaattggacCgaatgggctccaacccagcc	7	12	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:158364696C>A	ENST00000486715.1	+	4	889	c.532C>A	c.(532-534)Cga>Aga	p.R178R	GFM1_ENST00000264263.5_Silent_p.R178R|GFM1_ENST00000478576.1_Silent_p.R178R	NM_024996.5	NP_079272.4			G elongation factor, mitochondrial 1											breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|urinary_tract(2)	22			Lung(72;0.00309)|LUSC - Lung squamous cell carcinoma(72;0.0043)			CAAATTGGACCGAATGGGCTC	0.463																																					p.R178R		Atlas-SNP	.											.	GFM1	83	.	0			c.C532A						.						83	80	81					3																	158364696		2203	4300	6503	SO:0001819	synonymous_variant	85476	exon4			TTGGACCGAATGG	AF309777	CCDS33885.1	3q25	2008-02-05			ENSG00000168827	ENSG00000168827			13780	protein-coding gene	gene with protein product		606639	"G translation elongation factor, mitochondrial"			11374907, 11735030	Standard	NM_024996		Approved	EFGM, GFM, EGF1	uc003fce.3	Q96RP9	OTTHUMG00000158804	ENST00000486715.1:c.532C>A	chr3.hg19:g.158364696C>A		93.0	0.0		92.0	4.0	NM_024996		Silent	SNP	ENST00000486715.1	hg19	CCDS33885.1																																																																																			.	.		0.463	GFM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352271.1	NM_024996		A	158364696	C	A	158364696	2	1	255	1	0	0	0	0	0	0	0	1	6349	644	23	1		1	GFM1	3	158364696	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	7189848	158364696	39657734	158	35503										
OTOL1	131149	hgsc.bcm.edu	37	chr3	161221475	161221475	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	acatatgttttttcctaccaTattacggtgagggggcgacc	10	9	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:161221475T>C	ENST00000327928.4	+	4	1179	c.1179T>C	c.(1177-1179)caT>caC	p.H393H		NM_001080440.1	NP_001073909.1	A6NHN0	OTOL1_HUMAN	otolin 1	393	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.					collagen trimer (GO:0005581)|extracellular region (GO:0005576)				central_nervous_system(2)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)	27						TTTCCTACCATATTACGGTGA	0.438																																					p.H393H		Atlas-SNP	.											.	OTOL1	63	.	0			c.T1179C						.						63	56	59					3																	161221475		1925	4126	6051	SO:0001819	synonymous_variant	131149	exon4			CTACCATATTACG		CCDS46948.1	3q26.1	2011-05-19	2011-05-19			ENSG00000182447			34071	protein-coding gene	gene with protein product	"C1q and tumor necrosis factor related protein 15"		"otolin 1 homolog (zebrafish)"			17544811, 15905077	Standard	NM_001080440		Approved	C1QTNF15	uc011bpb.2	A6NHN0		ENST00000327928.4:c.1179T>C	chr3.hg19:g.161221475T>C		71.0	0.0		72.0	4.0	NM_001080440		Silent	SNP	ENST00000327928.4	hg19	CCDS46948.1																																																																																			.	.		0.438	OTOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353184.1	NM_001080440		C	161221475	T	C	161221475	2	2	255	1	0	0	0	0	0	0	0	1	11313	1403	49	2		2	OTOL1	3	161221475	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	2856779	161221475	36800955	159	35504										
LRRIQ4	344657	hgsc.bcm.edu	37	chr3	169546665	169546665	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tttagagaaattatacattgGgcaagaccagggattcaaac	9	6	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:169546665G>T	ENST00000340806.6	+	2	1139	c.1139G>T	c.(1138-1140)gGg>gTg	p.G380V		NM_001080460.1	NP_001073929.1	A6NIV6	LRIQ4_HUMAN	leucine-rich repeats and IQ motif containing 4	380										breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	30						TTATACATTGGGCAAGACCAG	0.438																																					p.G380V		Atlas-SNP	.											.	LRRIQ4	68	.	0			c.G1139T						.						124	120	121					3																	169546665		1854	4100	5954	SO:0001583	missense	344657	exon2			ACATTGGGCAAGA		CCDS46951.1	3q26.2	2008-08-08	2008-06-12	2008-06-12	ENSG00000188306	ENSG00000188306			34298	protein-coding gene	gene with protein product	"leucine rich repeat containing 64"						Standard	NM_001080460		Approved	LRRC64	uc003fgb.3	A6NIV6	OTTHUMG00000164420	ENST00000340806.6:c.1139G>T	chr3.hg19:g.169546665G>T	ENSP00000342188:p.Gly380Val	69.0	0.0		88.0	4.0	NM_001080460		Missense_Mutation	SNP	ENST00000340806.6	hg19	CCDS46951.1	.	.	.	.	.	.	.	.	.	.	G	13.28	2.189830	0.38707	.	.	ENSG00000188306	ENST00000340806	T	0.17054	2.3	5.77	4.89	0.63831	.	0.000000	0.64402	D	0.000002	T	0.38054	0.1026	L	0.60012	1.86	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.08106	-1.0738	10	0.39692	T	0.17	.	15.8421	0.78857	0.0:0.0:0.863:0.137	.	380	A6NIV6	LRIQ4_HUMAN	V	380	ENSP00000342188:G380V	ENSP00000342188:G380V	G	+	2	0	LRRIQ4	171029359	1.000000	0.71417	0.982000	0.44146	0.036000	0.12997	6.502000	0.73695	1.419000	0.47118	-0.182000	0.12963	GGG	.	.		0.438	LRRIQ4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378698.1	NM_001080460		T	169546665	G	T	169546665	3	4	255	1	0	0	0	0	1	0	0	0	9040	1232	43	3	1145	3	LRRIQ4	3	169546665	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	8325190	169546665	28475765	160	35505										
MAP3K13	9175	hgsc.bcm.edu	37	chr3	185198180	185198180	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tggcagagaagctagacgacCtgctgtcccagacgccagag	13	12	0	4			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:185198180C>A	ENST00000265026.3	+	13	2996	c.2662C>A	c.(2662-2664)Ctg>Atg	p.L888M	TMEM41A_ENST00000475480.1_5'UTR|MAP3K13_ENST00000446828.1_Missense_Mutation_p.L681M|MAP3K13_ENST00000535426.1_Missense_Mutation_p.L744M|MAP3K13_ENST00000443863.1_Missense_Mutation_p.L744M|MAP3K13_ENST00000424227.1_Missense_Mutation_p.L888M	NM_004721.4	NP_004712.1			mitogen-activated protein kinase kinase kinase 13											NS(1)|biliary_tract(1)|breast(3)|endometrium(3)|kidney(1)|large_intestine(13)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54	all_cancers(143;7.21e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)			GCTAGACGACCTGCTGTCCCA	0.517																																					p.L888M		Atlas-SNP	.											.	MAP3K13	209	.	0			c.C2662A						.						114	102	106					3																	185198180		2203	4300	6503	SO:0001583	missense	9175	exon13			GACGACCTGCTGT	BC031677	CCDS3270.1, CCDS56298.1	3q27	2011-06-09			ENSG00000073803	ENSG00000073803		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6852	protein-coding gene	gene with protein product	"leucine zipper-bearing kinase"	604915				9353328	Standard	NM_004721		Approved	LZK, MEKK13	uc003fpi.3	O43283	OTTHUMG00000156673	ENST00000265026.3:c.2662C>A	chr3.hg19:g.185198180C>A	ENSP00000265026:p.Leu888Met	134.0	0.0		73.0	4.0	NM_004721		Missense_Mutation	SNP	ENST00000265026.3	hg19	CCDS3270.1	.	.	.	.	.	.	.	.	.	.	C	11.64	1.697519	0.30142	.	.	ENSG00000073803	ENST00000446828;ENST00000424227;ENST00000443863;ENST00000535426;ENST00000265026	T;T;T;T;T	0.78246	-1.16;-1.11;-1.04;-1.04;-1.11	5.86	4.94	0.65067	.	0.086755	0.49305	D	0.000144	T	0.59959	0.2232	N	0.16656	0.425	0.80722	D	1	B;P;P	0.38195	0.204;0.622;0.488	B;B;B	0.34180	0.082;0.177;0.086	T	0.59311	-0.7478	10	0.13470	T	0.59	.	14.2652	0.66113	0.2188:0.7812:0.0:0.0	.	744;681;888	O43283-4;O43283-5;O43283	.;.;M3K13_HUMAN	M	681;888;744;744;888	ENSP00000411483:L681M;ENSP00000399910:L888M;ENSP00000409325:L744M;ENSP00000439257:L744M;ENSP00000265026:L888M	ENSP00000265026:L888M	L	+	1	2	MAP3K13	186680874	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.613000	0.46351	2.773000	0.95371	0.655000	0.94253	CTG	.	.		0.517	MAP3K13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345268.1	NM_004721		A	185198180	C	A	185198180	3	1	255	1	0	0	0	0	1	0	0	0	9256	680	24	3	2708	3	MAP3K13	3	185198180	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	15651515	185198180	12824250	161	35506										
LIPH	200879	hgsc.bcm.edu	37	chr3	185236957	185236957	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gggacaggactctttttgtgAcgtgccgcagctgacacact	12	11	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:185236957A>G	ENST00000296252.4	-	6	1000	c.859T>C	c.(859-861)Tca>Cca	p.S287P	LIPH_ENST00000424591.2_Missense_Mutation_p.S253P	NM_139248.2	NP_640341.1	Q8WWY8	LIPH_HUMAN	lipase, member H	287					lipid catabolic process (GO:0016042)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(2)	20	all_cancers(143;8.87e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;1.31e-21)			TCTTTTTGTGACGTGCCGCAG	0.478																																					p.S287P		Atlas-SNP	.											.	LIPH	56	.	0			c.T859C						.						132	132	132					3																	185236957		2203	4300	6503	SO:0001583	missense	200879	exon6			TTTGTGACGTGCC	AY093498	CCDS3272.1	3q27	2012-07-31			ENSG00000163898	ENSG00000163898			18483	protein-coding gene	gene with protein product		607365				12213196, 12063250	Standard	XM_006713529		Approved	mPA-PLA1, PLA1B, mPA-PLA1alpha, LPDLR	uc003fpm.3	Q8WWY8	OTTHUMG00000156657	ENST00000296252.4:c.859T>C	chr3.hg19:g.185236957A>G	ENSP00000296252:p.Ser287Pro	117.0	0.0		99.0	4.0	NM_139248	A2IBA7|Q8TEC7	Missense_Mutation	SNP	ENST00000296252.4	hg19	CCDS3272.1	.	.	.	.	.	.	.	.	.	.	A	10.59	1.392802	0.25118	.	.	ENSG00000163898	ENST00000296252;ENST00000424591	D;D	0.90844	-2.74;-2.74	5.01	-10.0	0.00425	Lipase, N-terminal (1);	1.076220	0.07157	N	0.850046	T	0.66944	0.2841	N	0.01417	-0.88	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.12837	0.003;0.008	T	0.59467	-0.7449	10	0.33141	T	0.24	2.0167	5.2024	0.15273	0.3999:0.4034:0.114:0.0826	.	253;287	A2IBA6;Q8WWY8	.;LIPH_HUMAN	P	287;253	ENSP00000296252:S287P;ENSP00000396384:S253P	ENSP00000296252:S287P	S	-	1	0	LIPH	186719651	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.081000	0.11321	-1.587000	0.01630	-0.474000	0.04947	TCA	.	.		0.478	LIPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345153.1			G	185236957	A	G	185236957	3	3	255	1	0	0	0	0	1	0	0	0	8833	275	10	2	516	2	LIPH	3	185236957	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	38777	185236957	12785473	162	35507										
FETUB	26998	hgsc.bcm.edu	37	chr3	186358341	186358341	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggccctcaacccctcggctcTgctctcccggggctgcaatg	11	18	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:186358341T>C	ENST00000265029.3	+	1	193	c.92T>C	c.(91-93)cTg>cCg	p.L31P	FETUB_ENST00000382136.3_Missense_Mutation_p.L31P|FETUB_ENST00000450521.1_Missense_Mutation_p.L31P|FETUB_ENST00000382134.3_Missense_Mutation_p.L31P|FETUB_ENST00000539949.1_Intron|FETUB_ENST00000488561.1_3'UTR|RP11-134F2.2_ENST00000428501.1_RNA|RP11-134F2.2_ENST00000455926.1_RNA	NM_014375.2	NP_055190.2	Q9UGM5	FETUB_HUMAN	fetuin B	31	Cystatin fetuin-B-type 1. {ECO:0000255|PROSITE-ProRule:PRU00862}.				binding of sperm to zona pellucida (GO:0007339)|negative regulation of endopeptidase activity (GO:0010951)|single fertilization (GO:0007338)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|metalloendopeptidase inhibitor activity (GO:0008191)			endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)	20	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0479)		CCCTCGGCTCTGCTCTCCCGG	0.582																																					p.L31P		Atlas-SNP	.											.	FETUB	53	.	0			c.T92C						.						159	165	163					3																	186358341		2203	4300	6503	SO:0001583	missense	26998	exon1			CGGCTCTGCTCTC	AJ242928	CCDS3279.1	3q27.3	2008-05-15			ENSG00000090512	ENSG00000090512			3658	protein-coding gene	gene with protein product		605954				10947975	Standard	XM_005247350		Approved		uc003fqn.3	Q9UGM5	OTTHUMG00000156586	ENST00000265029.3:c.92T>C	chr3.hg19:g.186358341T>C	ENSP00000265029:p.Leu31Pro	174.0	0.0		129.0	6.0	NM_014375	B2RCW6|E9PG06|Q1RMZ0|Q5J876|Q6DK58|Q6GRB6|Q9Y6Z0	Missense_Mutation	SNP	ENST00000265029.3	hg19	CCDS3279.1	.	.	.	.	.	.	.	.	.	.	T	11.07	1.531121	0.27387	.	.	ENSG00000090512	ENST00000450521;ENST00000265029;ENST00000382134;ENST00000382136	T;T;T;T	0.17213	2.69;2.69;2.9;2.29	4.17	0.513	0.17000	Proteinase inhibitor I25, cystatin (1);	1.282600	0.05444	N	0.548118	T	0.24661	0.0598	M	0.75447	2.3	0.09310	N	1	B;B;B	0.29481	0.105;0.005;0.245	B;B;B	0.35039	0.042;0.008;0.194	T	0.40739	-0.9547	10	0.87932	D	0	-0.575	6.0607	0.19837	0.0:0.3217:0.0:0.6783	.	31;31;31	E9PG06;E9PG08;Q9UGM5	.;.;FETUB_HUMAN	P	31	ENSP00000404288:L31P;ENSP00000265029:L31P;ENSP00000371569:L31P;ENSP00000371571:L31P	ENSP00000265029:L31P	L	+	2	0	FETUB	187841035	0.004000	0.15560	0.000000	0.03702	0.011000	0.07611	1.566000	0.36396	0.087000	0.17167	0.533000	0.62120	CTG	.	.		0.582	FETUB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344679.1	NM_014375		C	186358341	T	C	186358341	3	2	255	1	0	0	0	0	1	0	0	0	5829	1580	55	2	94	2	FETUB	3	186358341	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	1121384	186358341	11664089	163	35508										
LRRC15	131578	hgsc.bcm.edu	37	chr3	194080638	194080638	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gaagatattccctgggagctGtctgaggcggttgttctgca	14	8	2	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:194080638G>A	ENST00000347624.3	-	2	1220	c.1135C>T	c.(1135-1137)Cag>Tag	p.Q379*	LRRC15_ENST00000439944.2_Nonsense_Mutation_p.Q385*|LRRC15_ENST00000428839.1_Nonsense_Mutation_p.Q385*	NM_130830.4	NP_570843.2	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15	379					negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|positive regulation of cell migration (GO:0030335)|receptor-mediated virion attachment to host cell (GO:0046813)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	collagen binding (GO:0005518)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)			biliary_tract(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(20)|ovary(4)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.94e-05)		CCTGGGAGCTGTCTGAGGCGG	0.582																																					p.Q385X		Atlas-SNP	.											.	LRRC15	137	.	0			c.C1153T						.						59	58	58					3																	194080638		2203	4300	6503	SO:0001587	stop_gained	131578	exon3			GGAGCTGTCTGAG	AB071037	CCDS3306.1, CCDS46984.1	3q29	2008-02-05			ENSG00000172061	ENSG00000172061			20818	protein-coding gene	gene with protein product						12923058	Standard	NM_001135057		Approved	LIB	uc003ftu.3	Q8TF66	OTTHUMG00000156048	ENST00000347624.3:c.1135C>T	chr3.hg19:g.194080638G>A	ENSP00000306276:p.Gln379*	117.0	0.0		91.0	4.0	NM_001135057	Q495Q6|Q7RTN7	Nonsense_Mutation	SNP	ENST00000347624.3	hg19	CCDS3306.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.643587	0.87859	.	.	ENSG00000172061	ENST00000347624;ENST00000439944;ENST00000428839	.	.	.	5.2	2.19	0.27852	.	1.169430	0.06219	N	0.686472	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	.	2.6203	0.04914	0.1546:0.4506:0.24:0.1548	.	.	.	.	X	379;385;385	.	ENSP00000306276:Q379X	Q	-	1	0	LRRC15	195561933	.	.	0.887000	0.34795	0.979000	0.70002	.	.	1.318000	0.45170	0.655000	0.94253	CAG	.	.		0.582	LRRC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342858.2			A	194080638	G	A	194080638	4	1	255	1	0	0	0	0	0	1	0	0	8979	1386	48	3	614	3	LRRC15	3	194080638	Nonsense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	7722297	194080638	3941792	164	35509										
TMEM175	84286	hgsc.bcm.edu	37	chr4	951958	951958	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agctggccatgtggaccacgGcgctgctgcaccaggcggag	16	13	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:951958G>A	ENST00000264771.4	+	11	1374	c.1189G>A	c.(1189-1191)Gcg>Acg	p.A397T	TMEM175_ENST00000508204.1_Missense_Mutation_p.A315T|TMEM175_ENST00000515740.1_Missense_Mutation_p.A281T	NM_032326.2	NP_115702.1	Q9BSA9	TM175_HUMAN	transmembrane protein 175	397						integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)				NS(1)|endometrium(1)|large_intestine(2)|lung(6)|pancreas(1)|upper_aerodigestive_tract(3)	14			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GTGGACCACGGCGCTGCTGCA	0.677																																					p.A397T		Atlas-SNP	.											.	TMEM175	44	.	0			c.G1189A						.						30	30	30					4																	951958		2198	4295	6493	SO:0001583	missense	84286	exon11			ACCACGGCGCTGC	BC005158	CCDS3341.1, CCDS75087.1, CCDS75088.1	4p16.3	2008-02-05			ENSG00000127419	ENSG00000127419			28709	protein-coding gene	gene with protein product						12477932	Standard	XM_005272301		Approved	MGC4618	uc003gbq.3	Q9BSA9	OTTHUMG00000118996	ENST00000264771.4:c.1189G>A	chr4.hg19:g.951958G>A	ENSP00000264771:p.Ala397Thr	112.0	0.0		91.0	4.0	NM_032326	D3DVN4|Q8ND13	Missense_Mutation	SNP	ENST00000264771.4	hg19	CCDS3341.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.39|15.39	2.819061|2.819061	0.50633|0.50633	.|.	.|.	ENSG00000127419|ENSG00000127419	ENST00000264771;ENST00000515740;ENST00000508204|ENST00000505148	T;T;T|.	0.53206|.	1.14;1.21;0.63|.	4.65|4.65	3.81|3.81	0.43845|0.43845	.|.	0.064516|.	0.64402|.	N|.	0.000009|.	T|T	0.65354|0.65354	0.2683|0.2683	M|M	0.70275|0.70275	2.135|2.135	0.47737|0.47737	D|D	0.999509|0.999509	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.83275|.	0.996;0.996|.	T|T	0.63844|0.63844	-0.6545|-0.6545	10|5	0.72032|.	D|.	0.01|.	-8.2942|-8.2942	10.4562|10.4562	0.44553|0.44553	0.0973:0.0:0.9027:0.0|0.0973:0.0:0.9027:0.0	.|.	315;397|.	D3DVN5;Q9BSA9|.	.;TM175_HUMAN|.	T|D	397;281;315|233	ENSP00000264771:A397T;ENSP00000427039:A281T;ENSP00000423669:A315T|.	ENSP00000264771:A397T|.	A|G	+|+	1|2	0|0	TMEM175|TMEM175	941958|941958	1.000000|1.000000	0.71417|0.71417	0.690000|0.690000	0.30148|0.30148	0.002000|0.002000	0.02628|0.02628	8.944000|8.944000	0.92980|0.92980	0.954000|0.954000	0.37851|0.37851	-0.339000|-0.339000	0.08088|0.08088	GCG|GGC	.	.		0.677	TMEM175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239193.2	NM_032326		A	951958	G	A	951958	3	1	255	1	0	0	0	0	1	0	0	0	16106	1203	42	3	1227	3	TMEM175	4	951958	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10		951958	190202318	165	35510										
TACC3	10460	hgsc.bcm.edu	37	chr4	1725265	1725265	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcgtctgttcttcgtgtgtcAcagaaagaaaatgtgccacc	9	10	3	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:1725265A>G	ENST00000313288.4	+	2	223	c.117A>G	c.(115-117)tcA>tcG	p.S39S	TMEM129_ENST00000382936.3_5'Flank|TMEM129_ENST00000303277.2_5'Flank|TMEM129_ENST00000536901.1_5'Flank	NM_006342.2	NP_006333.1	Q9Y6A5	TACC3_HUMAN	transforming, acidic coiled-coil containing protein 3	39					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|cytoplasmic sequestering of transcription factor (GO:0042994)|hemopoiesis (GO:0030097)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of cell cycle (GO:0051726)|regulation of microtubule-based process (GO:0032886)|response to hypoxia (GO:0001666)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				central_nervous_system(1)|endometrium(4)|large_intestine(1)|lung(10)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	25		Breast(71;0.212)|all_epithelial(65;0.241)	OV - Ovarian serous cystadenocarcinoma(23;0.00765)|Epithelial(3;0.0126)			TTCGTGTGTCACAGAAAGAAA	0.463																																					p.S39S	Ovarian(120;482 2294 11894 35824)	Atlas-SNP	.											.	TACC3	69	.	0			c.A117G						.						64	64	64					4																	1725265		2203	4298	6501	SO:0001819	synonymous_variant	10460	exon2			TGTGTCACAGAAA	AF093543	CCDS3352.1	4p16.3	2008-07-29			ENSG00000013810	ENSG00000013810			11524	protein-coding gene	gene with protein product		605303				17675670	Standard	NM_006342		Approved	ERIC1	uc003gdo.3	Q9Y6A5	OTTHUMG00000089535	ENST00000313288.4:c.117A>G	chr4.hg19:g.1725265A>G		155.0	0.0		99.0	4.0	NM_006342	Q2NKK4|Q3KQS5|Q9UMQ1	Silent	SNP	ENST00000313288.4	hg19	CCDS3352.1																																																																																			.	.		0.463	TACC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000203730.2			G	1725265	A	G	1725265	2	3	255	1	0	0	0	0	0	0	0	1	15518	146	6	2		2	TACC3	4	1725265	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	773307	1725265	189429011	166	35511										
JAKMIP1	152789	hgsc.bcm.edu	37	chr4	6087187	6087187	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccatgtccccgatcccgggcGggagctctctctttggacta	11	15	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:6087187G>T	ENST00000282924.5	-	4	1279	c.794C>A	c.(793-795)cCg>cAg	p.P265Q	JAKMIP1_ENST00000409831.1_Missense_Mutation_p.P265Q|JAKMIP1_ENST00000410077.2_Missense_Mutation_p.P100Q|JAKMIP1_ENST00000457227.2_5'UTR|JAKMIP1_ENST00000409021.3_Missense_Mutation_p.P265Q|JAKMIP1_ENST00000409371.3_Missense_Mutation_p.P100Q	NM_144720.3	NP_653321.1	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein 1	265	Mediates association with microtubules.				cognition (GO:0050890)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|microtubule (GO:0005874)|ribonucleoprotein complex (GO:0030529)	GABA receptor binding (GO:0050811)|RNA binding (GO:0003723)			NS(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						GATCCCGGGCGGGAGCTCTCT	0.612																																					p.P265Q		Atlas-SNP	.											.	JAKMIP1	250	.	0			c.C794A						.						50	52	52					4																	6087187		2203	4300	6503	SO:0001583	missense	152789	exon4			CCGGGCGGGAGCT	AK056126	CCDS3385.1, CCDS47005.1	4p16.1	2013-10-11	2009-08-13		ENSG00000152969	ENSG00000152969			26460	protein-coding gene	gene with protein product		611195				18941173	Standard	NM_144720		Approved	MARLIN1, JAMIP1, Gababrbp, FLJ31564	uc010idb.1	Q96N16	OTTHUMG00000125491	ENST00000282924.5:c.794C>A	chr4.hg19:g.6087187G>T	ENSP00000282924:p.Pro265Gln	95.0	0.0		63.0	4.0	NM_001099433	A6H2J2|A6H2J3|A6H2J4|A6H2J5|A8MTK6|B4DHZ8|B8ZZR7|D3DVT0|Q86Y69|Q8N7G3	Missense_Mutation	SNP	ENST00000282924.5	hg19	CCDS3385.1	.	.	.	.	.	.	.	.	.	.	G	14.90	2.672284	0.47781	.	.	ENSG00000152969	ENST00000409021;ENST00000409371;ENST00000418227;ENST00000425341;ENST00000429819;ENST00000282924;ENST00000409831;ENST00000410077	T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5	4.29	4.29	0.51040	.	0.000000	0.64402	D	0.000007	T	0.51449	0.1675	M	0.73217	2.22	0.39418	D	0.966877	D;D;D;D;D	0.63880	0.993;0.983;0.98;0.98;0.983	P;P;P;P;P	0.61132	0.774;0.884;0.838;0.838;0.884	T	0.60193	-0.7311	10	0.72032	D	0.01	.	15.9279	0.79635	0.0:0.0:1.0:0.0	.	100;265;100;265;265	B4DHZ8;F2Z2K5;Q96N16-5;Q96N16-2;Q96N16	.;.;.;.;JKIP1_HUMAN	Q	265;100;265;265;157;265;265;100	ENSP00000386711:P265Q;ENSP00000387042:P100Q;ENSP00000282924:P265Q;ENSP00000386925:P265Q;ENSP00000386745:P100Q	ENSP00000282924:P265Q	P	-	2	0	JAKMIP1	6138088	1.000000	0.71417	0.902000	0.35471	0.201000	0.24016	5.460000	0.66691	2.239000	0.73571	0.655000	0.94253	CCG	.	.		0.612	JAKMIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246816.2	NM_144720		T	6087187	G	T	6087187	3	4	255	1	0	0	0	0	1	0	0	0	7949	1116	39	1	1848	1	JAKMIP1	4	6087187	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	4361922	6087187	185067089	167	35512										
KIAA0232	9778	hgsc.bcm.edu	37	chr4	6882546	6882546	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tatgaagcaagatgtacaggAgagagagattctggagcaaa	13	4	1	4			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:6882546A>G	ENST00000307659.5	+	10	4496	c.4041A>G	c.(4039-4041)ggA>ggG	p.G1347G	KIAA0232_ENST00000425103.1_Silent_p.G1347G	NM_014743.2	NP_055558.2	Q92628	K0232_HUMAN	KIAA0232	1347							ATP binding (GO:0005524)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(12)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	41						GATGTACAGGAGAGAGAGATT	0.458																																					p.G1347G		Atlas-SNP	.											.	KIAA0232	102	.	0			c.A4041G						.						78	79	79					4																	6882546		1895	4125	6020	SO:0001819	synonymous_variant	9778	exon10			TACAGGAGAGAGA	D86985	CCDS43209.1	4p16.1	2012-11-29			ENSG00000170871	ENSG00000170871			28992	protein-coding gene	gene with protein product						9039502	Standard	NM_014743		Approved		uc003gjq.4	Q92628	OTTHUMG00000160072	ENST00000307659.5:c.4041A>G	chr4.hg19:g.6882546A>G		89.0	0.0		78.0	4.0	NM_014743	A7E2D2	Silent	SNP	ENST00000307659.5	hg19	CCDS43209.1																																																																																			.	.		0.458	KIAA0232-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359102.2	NM_014743		G	6882546	A	G	6882546	2	3	255	1	0	0	0	0	0	0	0	1	8172	291	11	2		2	KIAA0232	4	6882546	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	795359	6882546	184271730	168	35513										
SORCS2	57537	hgsc.bcm.edu	37	chr4	7719906	7719906	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cctgtttgtggtgcggcaggAgcaggtgagtgagcacctcc	16	10	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:7719906A>G	ENST00000507866.2	+	18	2529	c.2420A>G	c.(2419-2421)gAg>gGg	p.E807G	SORCS2_ENST00000329016.9_Missense_Mutation_p.E635G	NM_020777.2	NP_065828.2	Q96PQ0	SORC2_HUMAN	sortilin-related VPS10 domain containing receptor 2	807	PKD. {ECO:0000255|PROSITE- ProRule:PRU00151}.				neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(8)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	42						GTGCGGCAGGAGCAGGTGAGT	0.697																																					p.E807G		Atlas-SNP	.											SORCS2,colon,carcinoma,0,1	SORCS2	98	.	0			c.A2420G						.						21	25	24					4																	7719906		2095	4200	6295	SO:0001583	missense	57537	exon18			GGCAGGAGCAGGT	AB037750	CCDS47008.1	4p16.1	2008-02-05			ENSG00000184985	ENSG00000184985			16698	protein-coding gene	gene with protein product		606284				11499680	Standard	NM_020777		Approved	KIAA1329	uc003gkb.4	Q96PQ0	OTTHUMG00000159981	ENST00000507866.2:c.2420A>G	chr4.hg19:g.7719906A>G	ENSP00000422185:p.Glu807Gly	153.0	2.0		82.0	5.0	NM_020777	Q9P2L7	Missense_Mutation	SNP	ENST00000507866.2	hg19	CCDS47008.1	.	.	.	.	.	.	.	.	.	.	A	19.72	3.880370	0.72294	.	.	ENSG00000184985	ENST00000507866;ENST00000329016	T;T	0.65916	-0.18;-0.18	4.41	4.41	0.53225	PKD/Chitinase domain (1);PKD domain (3);	0.229367	0.35040	N	0.003495	T	0.73079	0.3541	M	0.62723	1.935	0.80722	D	1	P;P	0.43314	0.803;0.803	P;P	0.56865	0.755;0.808	T	0.76386	-0.2978	10	0.72032	D	0.01	.	13.8152	0.63287	1.0:0.0:0.0:0.0	.	635;807	B5MED8;Q96PQ0	.;SORC2_HUMAN	G	807;635	ENSP00000422185:E807G;ENSP00000329124:E635G	ENSP00000329124:E635G	E	+	2	0	SORCS2	7770806	1.000000	0.71417	1.000000	0.80357	0.424000	0.31475	7.762000	0.85270	1.852000	0.53769	0.533000	0.62120	GAG	.	.		0.697	SORCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358685.4	NM_020777		G	7719906	A	G	7719906	3	3	255	1	0	0	0	0	1	0	0	0	14946	304	11	2	2490	2	SORCS2	4	7719906	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	837360	7719906	183434370	169	35514										
BOD1L	259282	hgsc.bcm.edu	37	chr4	13602619	13602619	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	acaacctcctggaactggtgTcacttcatcctttcctgaga	7	13	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:13602619T>C	ENST00000040738.5	-	10	6040	c.5905A>G	c.(5905-5907)Aca>Gca	p.T1969A		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	1969						nucleus (GO:0005634)	DNA binding (GO:0003677)										GGAACTGGTGTCACTTCATCC	0.463																																					p.T1969A		Atlas-SNP	.											.	.	.	.	0			c.A5905G						.						147	141	143					4																	13602619		2203	4300	6503	SO:0001583	missense	259282	exon10			CTGGTGTCACTTC	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.5905A>G	chr4.hg19:g.13602619T>C	ENSP00000040738:p.Thr1969Ala	99.0	0.0		63.0	4.0	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	hg19	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	T	0.007	-1.957397	0.00465	.	.	ENSG00000038219	ENST00000040738	T	0.05580	3.42	5.28	2.29	0.28610	.	0.728860	0.12720	N	0.444822	T	0.01800	0.0057	N	0.01576	-0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46679	-0.9174	10	0.02654	T	1	-0.033	5.1288	0.14899	0.0:0.4699:0.2731:0.257	.	1969	Q8NFC6	BOD1L_HUMAN	A	1969	ENSP00000040738:T1969A	ENSP00000040738:T1969A	T	-	1	0	BOD1L	13211717	0.000000	0.05858	0.003000	0.11579	0.476000	0.33039	0.733000	0.26087	0.105000	0.17753	0.379000	0.24179	ACA	.	.		0.463	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		C	13602619	T	C	13602619	3	2	255	1	0	0	0	0	1	0	0	0	1483	1667	58	2	3318	2	BOD1L	4	13602619	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	5882713	13602619	177551657	170	35515										
CPEB2	132864	hgsc.bcm.edu	37	chr4	15005655	15005655	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gaacggcttctaccccgggcTgccgtcgtccatgaacccgg	12	16	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:15005655T>C	ENST00000507071.1	+	1	134	c.47T>C	c.(46-48)cTg>cCg	p.L16P	CPEB2_ENST00000382401.3_Missense_Mutation_p.L16P|CPEB2_ENST00000345451.3_Missense_Mutation_p.L16P|CPEB2_ENST00000541112.1_Missense_Mutation_p.L453P|CPEB2_ENST00000442003.2_Missense_Mutation_p.L453P|CPEB2_ENST00000382395.3_Missense_Mutation_p.L16P|RP11-665G4.1_ENST00000513384.1_RNA|RP11-665G4.1_ENST00000502344.1_RNA|CPEB2_ENST00000538197.1_Missense_Mutation_p.L453P|CPEB2_ENST00000259997.5_Missense_Mutation_p.L16P			Q7Z5Q1	CPEB2_HUMAN	cytoplasmic polyadenylation element binding protein 2	16	Pro-rich.				cellular response to arsenic-containing substance (GO:0071243)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|cellular response to oxidative stress (GO:0034599)|negative regulation of cytoplasmic translation (GO:2000766)|negative regulation of cytoplasmic translational elongation (GO:1900248)|negative regulation of GTPase activity (GO:0034260)	cytoplasm (GO:0005737)|messenger ribonucleoprotein complex (GO:1990124)|nucleus (GO:0005634)	GTPase inhibitor activity (GO:0005095)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ribosomal large subunit binding (GO:0043023)|ribosomal small subunit binding (GO:0043024)|ribosome binding (GO:0043022)|translation repressor activity, nucleic acid binding (GO:0000900)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|skin(3)	14						TACCCCGGGCTGCCGTCGTCC	0.751																																					p.L453P		Atlas-SNP	.											.	CPEB2	77	.	0			c.T1358C						.						11	11	11					4																	15005655		1756	3492	5248	SO:0001583	missense	132864	exon1			CCGGGCTGCCGTC	AY247744	CCDS56325.1, CCDS56326.1	4p15.33	2013-02-12			ENSG00000137449	ENSG00000137449		"RNA binding motif (RRM) containing"	21745	protein-coding gene	gene with protein product		610605				12672660	Standard	NM_182485		Approved		uc003gnk.2	Q7Z5Q1	OTTHUMG00000090669	ENST00000507071.1:c.47T>C	chr4.hg19:g.15005655T>C	ENSP00000424084:p.Leu16Pro	119.0	0.0		79.0	5.0	NM_001177381	E7EPM3|F5H160|Q3B8N6|Q3MI89|Q3MI90|Q3MI92|Q7Z5Q0	Missense_Mutation	SNP	ENST00000507071.1	hg19		.	.	.	.	.	.	.	.	.	.	t	17.12	3.308889	0.60305	.	.	ENSG00000137449	ENST00000538197;ENST00000541112;ENST00000442003;ENST00000507071;ENST00000345451;ENST00000382395;ENST00000382401;ENST00000259997;ENST00000382391	T;T;T;T;T;T;T;T	0.52983	0.68;0.68;0.64;0.83;0.77;0.77;0.78;0.82	1.96	0.266	0.15617	.	0.352702	0.23680	U	0.045626	T	0.24890	0.0604	N	0.22421	0.69	0.53005	D	0.999962	B;B;B;B;B;B	0.33637	0.289;0.289;0.191;0.42;0.289;0.296	B;B;B;B;B;B	0.26614	0.045;0.045;0.02;0.071;0.045;0.032	T	0.05869	-1.0859	10	0.59425	D	0.04	.	4.7864	0.13227	0.2749:0.0:0.0:0.7251	.	16;16;453;453;16;16	Q7Z5Q1-4;Q7Z5Q1-6;E7EPM3;F5H160;Q7Z5Q1-5;Q7Z5Q1	.;.;.;.;.;CPEB2_HUMAN	P	453;453;453;16;16;16;16;16;16	ENSP00000443985:L453P;ENSP00000437884:L453P;ENSP00000414270:L453P;ENSP00000424084:L16P;ENSP00000334058:L16P;ENSP00000371832:L16P;ENSP00000371838:L16P;ENSP00000259997:L16P	ENSP00000259997:L16P	L	+	2	0	CPEB2	14614753	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	2.610000	0.46325	0.610000	0.30035	0.333000	0.21579	CTG	.	.		0.751	CPEB2-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000207349.2	XM_059607		C	15005655	T	C	15005655	3	2	255	1	0	0	0	0	1	0	0	0	3803	1580	55	2	1360	2	CPEB2	4	15005655	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	1403036	15005655	176148621	171	35516										
SLIT2	9353	hgsc.bcm.edu	37	chr4	20618726	20618726	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgtgcccatggcacatgccaGcccagcagccaggcaggctt	12	15	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:20618726G>T	ENST00000504154.1	+	35	4293	c.4041G>T	c.(4039-4041)caG>caT	p.Q1347H	SLIT2_ENST00000503823.1_Missense_Mutation_p.Q1339H|SLIT2_ENST00000503837.1_Missense_Mutation_p.Q1343H|SLIT2_ENST00000273739.5_Missense_Mutation_p.Q1360H	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	1347	EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00076}.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)			NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						GCACATGCCAGCCCAGCAGCC	0.577																																					p.Q1347H		Atlas-SNP	.											.	SLIT2	290	.	0			c.G4041T						.						56	55	55					4																	20618726		2203	4300	6503	SO:0001583	missense	9353	exon35			ATGCCAGCCCAGC	AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"slit (Drosophila) homolog 2"	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.4041G>T	chr4.hg19:g.20618726G>T	ENSP00000422591:p.Gln1347His	100.0	0.0		79.0	4.0	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Missense_Mutation	SNP	ENST00000504154.1	hg19	CCDS3426.1	.	.	.	.	.	.	.	.	.	.	G	12.38	1.921298	0.33908	.	.	ENSG00000145147	ENST00000503823;ENST00000504154;ENST00000273739;ENST00000382173;ENST00000503837	T;T;T;T	0.80824	-1.4;-1.42;-1.33;-1.38	5.94	3.07	0.35406	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.321839	0.36555	N	0.002537	T	0.61553	0.2356	N	0.12920	0.275	0.34239	D	0.677448	B;B	0.06786	0.001;0.0	B;B	0.10450	0.005;0.001	T	0.61564	-0.7037	10	0.30078	T	0.28	.	6.7824	0.23654	0.0689:0.2964:0.5169:0.1178	.	1339;1347	O94813-3;O94813	.;SLIT2_HUMAN	H	1339;1347;1360;1343;1343	ENSP00000427548:Q1339H;ENSP00000422591:Q1347H;ENSP00000273739:Q1360H;ENSP00000422261:Q1343H	ENSP00000273739:Q1360H	Q	+	3	2	SLIT2	20227824	0.990000	0.36364	1.000000	0.80357	0.993000	0.82548	0.278000	0.18753	1.512000	0.48834	0.650000	0.86243	CAG	.	.		0.577	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2			T	20618726	G	T	20618726	3	4	255	1	0	0	0	0	1	0	0	0	14755	962	34	3	4179	3	SLIT2	4	20618726	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	5613071	20618726	170535550	172	35517										
SLC34A2	10568	hgsc.bcm.edu	37	chr4	25664190	25664190	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gtacctcgaaggggccgcagGtcagcagcccactgcccctg	13	16	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:25664190G>A	ENST00000382051.3	+	2	118	c.68G>A	c.(67-69)gGt>gAt	p.G23D	SLC34A2_ENST00000503434.1_Missense_Mutation_p.G23D|SLC34A2_ENST00000504570.1_Missense_Mutation_p.G23D	NM_001177998.1|NM_006424.2	NP_001171469.1|NP_006415	O95436	NPT2B_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 2	23					aging (GO:0007568)|cellular phosphate ion homeostasis (GO:0030643)|in utero embryonic development (GO:0001701)|ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|response to fructose (GO:0009750)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	phosphate ion binding (GO:0042301)|sodium ion binding (GO:0031402)|sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|sodium:phosphate symporter activity (GO:0005436)		SLC34A2/ROS1(14)	breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|skin(4)	41		Breast(46;0.0503)				GGGGCCGCAGGTCAGCAGCCC	0.547			T	ROS1	NSCLC																																p.G23D		Atlas-SNP	.		Dom	yes		4	4p15.2	10568	"solute carrier family 34 (sodium phosphate), member 2"		E	.	SLC34A2	93	.	0			c.G68A						.						69	70	70					4																	25664190		2203	4300	6503	SO:0001583	missense	10568	exon2			CCGCAGGTCAGCA	AF111856	CCDS3435.1, CCDS54750.1	4p15.2	2013-07-17	2013-07-17		ENSG00000157765	ENSG00000157765		"Solute carriers"	11020	protein-coding gene	gene with protein product		604217	"solute carrier family 34 (sodium phosphate), member 2"			10329428, 10610722	Standard	NM_006424		Approved	NAPI-3B	uc003grr.3	O95436	OTTHUMG00000097757	ENST00000382051.3:c.68G>A	chr4.hg19:g.25664190G>A	ENSP00000371483:p.Gly23Asp	124.0	0.0		90.0	4.0	NM_001177998	A5PL17|Q8N2K2|Q8WYA9|Q9P0V7	Missense_Mutation	SNP	ENST00000382051.3	hg19	CCDS3435.1	.	.	.	.	.	.	.	.	.	.	G	6.559	0.471493	0.12461	.	.	ENSG00000157765	ENST00000513204;ENST00000504570;ENST00000382051;ENST00000503434;ENST00000507530	T;T;T;T;T	0.54071	0.59;2.0;2.0;2.0;0.59	5.25	-2.44	0.06502	.	2.205720	0.01628	N	0.023400	T	0.43919	0.1269	L	0.44542	1.39	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.22836	-1.0205	10	0.35671	T	0.21	1.0696	7.1731	0.25728	0.3183:0.3219:0.3598:0.0	.	23;23	O95436-2;O95436	.;NPT2B_HUMAN	D	23	ENSP00000423038:G23D;ENSP00000425501:G23D;ENSP00000371483:G23D;ENSP00000423021:G23D;ENSP00000424266:G23D	ENSP00000371483:G23D	G	+	2	0	SLC34A2	25273288	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.130000	0.10498	-0.372000	0.07992	-0.165000	0.13383	GGT	.	.		0.547	SLC34A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214990.1	NM_006424		A	25664190	G	A	25664190	3	1	255	1	0	0	0	0	1	0	0	0	14583	1261	44	3	70	3	SLC34A2	4	25664190	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	5045464	25664190	165490086	173	35518										
SEL1L3	23231	hgsc.bcm.edu	37	chr4	25849271	25849271	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttccacctttttttgtacacGggaatgctacttctgaactc	6	11	1	1	rs200467510	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:25849271G>T	ENST00000399878.3	-	2	500	c.378C>A	c.(376-378)ccC>ccA	p.P126P	SEL1L3_ENST00000513364.1_Intron|SEL1L3_ENST00000502949.1_5'UTR|SEL1L3_ENST00000264868.5_Silent_p.P91P	NM_015187.3	NP_056002.2	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3 (C. elegans)	126						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(2)	14						TTTTGTACACGGGAATGCTAC	0.393																																					p.P126P		Atlas-SNP	.											.	SEL1L3	62	.	0			c.C378A						.						109	100	103					4																	25849271		1878	4117	5995	SO:0001819	synonymous_variant	23231	exon2			GTACACGGGAATG	BC009945	CCDS47037.1, CCDS75113.1	4p15.2	2009-09-24			ENSG00000091490	ENSG00000091490			29108	protein-coding gene	gene with protein product	"KIAA0746 protein"					9872452	Standard	XM_005248143		Approved	KIAA0746	uc003gru.4	Q68CR1	OTTHUMG00000160331	ENST00000399878.3:c.378C>A	chr4.hg19:g.25849271G>T		172.0	0.0		97.0	4.0	NM_015187	A0PJH6|A8K0X2|O94847|Q6P999|Q96G59	Silent	SNP	ENST00000399878.3	hg19	CCDS47037.1																																																																																			.	G|0.996;A|0.004		0.393	SEL1L3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360261.1	NM_015187		T	25849271	G	T	25849271	2	4	255	1	0	0	0	0	0	0	0	1	14027	1103	39	1		1	SEL1L3	4	25849271	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	185081	25849271	165305005	174	35519										
PDS5A	23244	hgsc.bcm.edu	37	chr4	39910134	39910134	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	atgacgaatagcttcttctgGatcatgtgatctaaccttta	7	8	4	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:39910134G>T	ENST00000303538.8	-	11	1653	c.1114C>A	c.(1114-1116)Cca>Aca	p.P372T	PDS5A_ENST00000503396.1_Missense_Mutation_p.P372T	NM_001100399.1	NP_001093869.1			PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae)											breast(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(14)|prostate(3)|skin(1)|urinary_tract(1)	39						GCTTCTTCTGGATCATGTGAT	0.358																																					p.P372T		Atlas-SNP	.											.	PDS5A	114	.	0			c.C1114A						.						118	109	111					4																	39910134		1838	4087	5925	SO:0001583	missense	23244	exon11			CTTCTGGATCATG	AF294791	CCDS47045.1, CCDS54759.1	4p14	2007-06-20			ENSG00000121892	ENSG00000121892			29088	protein-coding gene	gene with protein product		613200				11076961, 15855230	Standard	NM_001100399		Approved	KIAA0648, PIG54, SCC-112	uc003guv.4	Q29RF7	OTTHUMG00000160582	ENST00000303538.8:c.1114C>A	chr4.hg19:g.39910134G>T	ENSP00000303427:p.Pro372Thr	92.0	0.0		68.0	4.0	NM_001100399		Missense_Mutation	SNP	ENST00000303538.8	hg19	CCDS47045.1	.	.	.	.	.	.	.	.	.	.	G	10.80	1.451583	0.26074	.	.	ENSG00000121892	ENST00000303538;ENST00000503396	T;T	0.68331	-0.13;-0.32	4.93	4.93	0.64822	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.77329	0.4114	L	0.46741	1.465	0.80722	D	1	B;D	0.89917	0.328;1.0	B;D	0.97110	0.155;1.0	T	0.76083	-0.3089	9	.	.	.	-8.9094	18.1354	0.89617	0.0:0.0:1.0:0.0	.	372;372	Q29RF7-3;Q29RF7	.;PDS5A_HUMAN	T	372	ENSP00000303427:P372T;ENSP00000426749:P372T	.	P	-	1	0	PDS5A	39586529	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.843000	0.99491	2.285000	0.76669	0.557000	0.71058	CCA	.	.		0.358	PDS5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361287.1	NM_015200		T	39910134	G	T	39910134	3	4	255	1	0	0	0	0	1	0	0	0	11700	1174	41	3	3024	3	PDS5A	4	39910134	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	14060863	39910134	151244142	175	35520										
RBM47	54502	hgsc.bcm.edu	37	chr4	40439926	40439926	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gccgccgcccctggctgcctTctggtagcgcgagtactgct	13	16	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:40439926T>C	ENST00000381793.2	-	3	1381	c.985A>G	c.(985-987)Aag>Gag	p.K329E	RBM47_ENST00000319592.4_Missense_Mutation_p.K329E|RBM47_ENST00000514014.1_Missense_Mutation_p.K291E|RBM47_ENST00000295971.7_Missense_Mutation_p.K329E|RBM47_ENST00000515809.1_Intron|RBM47_ENST00000381795.6_Missense_Mutation_p.K329E			A0AV96	RBM47_HUMAN	RNA binding motif protein 47	329					hematopoietic progenitor cell differentiation (GO:0002244)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(5)|endometrium(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	29						CTGGCTGCCTTCTGGTAGCGC	0.652																																					p.K329E		Atlas-SNP	.											.	RBM47	146	.	0			c.A985G						.						41	39	40					4																	40439926		2203	4300	6503	SO:0001583	missense	54502	exon4			CTGCCTTCTGGTA	AK000280	CCDS3460.1, CCDS43223.1	4p14	2013-02-12			ENSG00000163694	ENSG00000163694		"RNA binding motif (RRM) containing"	30358	protein-coding gene	gene with protein product							Standard	NM_019027		Approved	FLJ20273, NET18	uc003gvc.2	A0AV96	OTTHUMG00000128598	ENST00000381793.2:c.985A>G	chr4.hg19:g.40439926T>C	ENSP00000371212:p.Lys329Glu	135.0	0.0		97.0	4.0	NM_001098634	A0PJK2|B5MED4|Q8NI52|Q8NI53|Q9NXG3	Missense_Mutation	SNP	ENST00000381793.2	hg19	CCDS43223.1	.	.	.	.	.	.	.	.	.	.	T	16.86	3.239228	0.58995	.	.	ENSG00000163694	ENST00000319592;ENST00000381793;ENST00000381795;ENST00000295971;ENST00000514014	T;T;T;T;T	0.74315	-0.83;-0.83;-0.83;-0.83;-0.83	5.58	5.58	0.84498	Nucleotide-binding, alpha-beta plait (1);	0.096829	0.64402	D	0.000001	T	0.72374	0.3452	M	0.62723	1.935	0.80722	D	1	P;B	0.47106	0.89;0.142	P;B	0.45881	0.496;0.103	T	0.71833	-0.4473	10	0.05351	T	0.99	-29.902	15.7506	0.77983	0.0:0.0:0.0:1.0	.	329;329	A0AV96-2;A0AV96	.;RBM47_HUMAN	E	329;329;329;329;291	ENSP00000320108:K329E;ENSP00000371212:K329E;ENSP00000371214:K329E;ENSP00000295971:K329E;ENSP00000423243:K291E	ENSP00000295971:K329E	K	-	1	0	RBM47	40134683	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	5.916000	0.69981	2.125000	0.65367	0.379000	0.24179	AAG	.	.		0.652	RBM47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250456.2	NM_019027		C	40439926	T	C	40439926	3	2	255	1	0	0	0	0	1	0	0	0	13156	1792	62	2	812	2	RBM47	4	40439926	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	529792	40439926	150714350	176	35521										
RBM47	54502	hgsc.bcm.edu	37	chr4	40440443	40440443	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttcttcatcttggggatcccGccgatgaagaggcggcagtt	13	10	3	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:40440443G>A	ENST00000381793.2	-	3	864	c.468C>T	c.(466-468)ggC>ggT	p.G156G	RBM47_ENST00000319592.4_Silent_p.G156G|RBM47_ENST00000514014.1_Silent_p.G118G|RBM47_ENST00000295971.7_Silent_p.G156G|RBM47_ENST00000515809.1_Intron|RBM47_ENST00000381795.6_Silent_p.G156G			A0AV96	RBM47_HUMAN	RNA binding motif protein 47	156	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				hematopoietic progenitor cell differentiation (GO:0002244)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(5)|endometrium(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	29						TGGGGATCCCGCCGATGAAGA	0.647																																					p.G156G		Atlas-SNP	.											RBM47_ENST00000381793,NS,carcinoma,0,3	RBM47	146	.	0			c.C468T						.						45	42	43					4																	40440443		2201	4292	6493	SO:0001819	synonymous_variant	54502	exon4			GATCCCGCCGATG	AK000280	CCDS3460.1, CCDS43223.1	4p14	2013-02-12			ENSG00000163694	ENSG00000163694		"RNA binding motif (RRM) containing"	30358	protein-coding gene	gene with protein product							Standard	NM_019027		Approved	FLJ20273, NET18	uc003gvc.2	A0AV96	OTTHUMG00000128598	ENST00000381793.2:c.468C>T	chr4.hg19:g.40440443G>A		52.0	0.0		40.0	2.0	NM_001098634	A0PJK2|B5MED4|Q8NI52|Q8NI53|Q9NXG3	Silent	SNP	ENST00000381793.2	hg19	CCDS43223.1																																																																																			.	.		0.647	RBM47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250456.2	NM_019027		A	40440443	G	A	40440443	2	1	255	1	0	0	0	0	0	0	0	1	13156	1074	38	1		1	RBM47	4	40440443	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	517	40440443	150713833	177	35522										
NSUN7	79730	hgsc.bcm.edu	37	chr4	40762502	40762502	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cagctgtatcttcccaagtaCcacaatagtaagtagataag	7	9	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:40762502C>T	ENST00000381782.2	+	3	845	c.350C>T	c.(349-351)aCc>aTc	p.T117I	NSUN7_ENST00000316607.5_Missense_Mutation_p.T117I	NM_024677.4	NP_078953	Q8NE18	NSUN7_HUMAN	NOP2/Sun domain family, member 7	117							methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|cervix(1)|large_intestine(1)|lung(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	12						TTCCCAAGTACCACAATAGTA	0.313																																					p.T117I		Atlas-SNP	.											.	NSUN7	70	.	0			c.C350T						.						104	103	103					4																	40762502		2203	4300	6503	SO:0001583	missense	79730	exon3			CAAGTACCACAAT	BC036568	CCDS3461.2	4p14	2013-10-11	2009-11-23		ENSG00000179299	ENSG00000179299		"NOP2/Sun domain containing"	25857	protein-coding gene	gene with protein product			"NOL1/NOP2/Sun domain family, member 7"			17442852	Standard	NM_024677		Approved	FLJ14001	uc003gvj.4	Q8NE18	OTTHUMG00000128597	ENST00000381782.2:c.350C>T	chr4.hg19:g.40762502C>T	ENSP00000371201:p.Thr117Ile	124.0	0.0		94.0	4.0	NM_024677	C9JI19|Q8N9K8|Q9H815	Missense_Mutation	SNP	ENST00000381782.2	hg19	CCDS3461.2	.	.	.	.	.	.	.	.	.	.	C	10.78	1.447320	0.25987	.	.	ENSG00000179299	ENST00000381782;ENST00000316607	T;T	0.38560	1.13;1.13	5.68	4.61	0.57282	.	0.564882	0.19101	N	0.122720	T	0.32823	0.0842	M	0.65975	2.015	0.28396	N	0.91885	P;P;P	0.36086	0.536;0.529;0.529	B;B;B	0.29077	0.045;0.098;0.098	T	0.30357	-0.9981	10	0.32370	T	0.25	-7.528	4.7215	0.12920	0.2082:0.6638:0.0:0.128	.	117;117;117	Q8NE18;Q8NE18-2;Q8NE18-3	NSUN7_HUMAN;.;.	I	117	ENSP00000371201:T117I;ENSP00000319127:T117I	ENSP00000319127:T117I	T	+	2	0	NSUN7	40457259	0.938000	0.31826	1.000000	0.80357	0.977000	0.68977	1.526000	0.35964	2.835000	0.97688	0.650000	0.86243	ACC	.	.		0.313	NSUN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250454.2	NM_024677		T	40762502	C	T	40762502	3	4	255	1	0	0	0	0	1	0	0	0	10692	507	18	3	356	3	NSUN7	4	40762502	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	322059	40762502	150391774	178	35523										
BEND4	389206	hgsc.bcm.edu	37	chr4	42127600	42127600	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cctttttaccagagacctacCtctgtcggctggtcagctgg	10	13	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:42127600C>T	ENST00000502486.1	-	4	1725	c.1146G>A	c.(1144-1146)gaG>gaA	p.E382E	BEND4_ENST00000504360.1_Splice_Site_p.E378E	NM_207406.3	NP_997289.2	Q6ZU67	BEND4_HUMAN	BEN domain containing 4	382										NS(2)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(15)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	26						AGAGACCTACCTCTGTCGGCT	0.453																																					p.E382E		Atlas-SNP	.											.	BEND4	67	.	0			c.G1146A						.						101	105	104					4																	42127600		1933	4128	6061	SO:0001630	splice_region_variant	389206	exon4			ACCTACCTCTGTC	AK092951	CCDS47048.1	4p13	2012-11-22	2008-10-03	2008-10-03	ENSG00000188848	ENSG00000188848		"BEN domain containing"	23815	protein-coding gene	gene with protein product			"coiled-coil domain containing 4"	CCDC4			Standard	NM_207406		Approved	FLJ35632, FLJ43965	uc003gwn.3	Q6ZU67	OTTHUMG00000160531	ENST00000502486.1:c.1146+1G>A	chr4.hg19:g.42127600C>T		137.0	0.0		78.0	4.0	NM_001159547	A1A5D6|A1A5D7|C9JQZ5|Q58A26|Q58A27	Silent	SNP	ENST00000502486.1	hg19	CCDS47048.1																																																																																			.	.		0.453	BEND4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360975.2	NM_207406	Silent	T	42127600	C	T	42127600	5	4	255	1	0	0	0	0	0	0	1	0	1400	695	24	3	470	3	BEND4	4	42127600	Splice_Site	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1365098	42127600	149026676	179	35524										
DCUN1D4	23142	hgsc.bcm.edu	37	chr4	52740446	52740446	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttgttttgtaggaagtctgcGgtcttgcagttcttcagact	11	7	4	1	rs142966675		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:52740446G>T	ENST00000334635.5	+	4	326	c.146G>T	c.(145-147)cGg>cTg	p.R49L	DCUN1D4_ENST00000451288.2_Missense_Mutation_p.R93L|DCUN1D4_ENST00000381437.4_5'UTR|DCUN1D4_ENST00000381441.3_Missense_Mutation_p.R49L|DCUN1D4_ENST00000513800.1_3'UTR	NM_001040402.1	NP_001035492.1	Q92564	DCNL4_HUMAN	DCN1, defective in cullin neddylation 1, domain containing 4	49						nucleus (GO:0005634)		p.R49P(1)		endometrium(2)|large_intestine(2)|lung(2)|ovary(2)|skin(1)	9			GBM - Glioblastoma multiforme(4;1.93e-11)|LUSC - Lung squamous cell carcinoma(32;0.00654)			GGAAGTCTGCGGTCTTGCAGT	0.383													G|||	1	0.000199681	8e-04	0	5008	,	,		17024	0		0	False		,,,				2504	0				p.R49L		Atlas-SNP	.											DCUN1D4,NS,carcinoma,0,1	DCUN1D4	26	.	1	Substitution - Missense(1)	ovary(1)	c.G146T						.	G	LEU/ARG,LEU/ARG	1,4405	2.1+/-5.4	0,1,2202	125	122	123		146,146	4.3	1	4	dbSNP_134	123	0,8600		0,0,4300	no	missense,missense	DCUN1D4	NM_001040402.1,NM_015115.2	102,102	0,1,6502	TT,TG,GG		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	49/293,49/258	52740446	1,13005	2203	4300	6503	SO:0001583	missense	23142	exon4			GTCTGCGGTCTTG	D87466	CCDS3487.2, CCDS33982.1, CCDS75123.1	4q11	2013-06-10	2013-06-10		ENSG00000109184	ENSG00000109184			28998	protein-coding gene	gene with protein product		612977	"DCN1, defective in cullin neddylation 1, domain containing 4 (S. cerevisiae)"			15988528	Standard	XM_005265731		Approved	KIAA0276	uc003gze.3	Q92564	OTTHUMG00000128700	ENST00000334635.5:c.146G>T	chr4.hg19:g.52740446G>T	ENSP00000334625:p.Arg49Leu	39.0	0.0		32.0	4.0	NM_015115	B4DH25|Q7Z3F3|Q7Z6B8	Missense_Mutation	SNP	ENST00000334635.5	hg19	CCDS33982.1	.	.	.	.	.	.	.	.	.	.	g	21.0	4.077896	0.76528	2.27E-4	0.0	ENSG00000109184	ENST00000334635;ENST00000381441;ENST00000505403;ENST00000451288	.	.	.	5.18	4.34	0.51931	.	0.394763	0.26971	N	0.021575	T	0.40743	0.1129	N	0.22421	0.69	0.80722	D	1	P;P;P	0.42785	0.499;0.79;0.473	B;B;B	0.43838	0.072;0.433;0.122	T	0.13899	-1.0492	9	0.25751	T	0.34	-8.7843	11.2283	0.48897	0.0843:0.0:0.9157:0.0	.	93;49;49	B4DH25;Q92564-2;Q92564	.;.;DCNL4_HUMAN	L	49;49;93;93	.	ENSP00000334625:R49L	R	+	2	0	DCUN1D4	52435203	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.188000	0.77739	1.194000	0.43101	0.651000	0.88453	CGG	.	G|1.000;T|0.000		0.383	DCUN1D4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250599.2	NM_015115		T	52740446	G	T	52740446	3	4	255	1	0	0	0	0	1	0	0	0	4318	1116	39	1	160	1	DCUN1D4	4	52740446	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	10612846	52740446	138413830	180	35525										
SPATA18	132671	hgsc.bcm.edu	37	chr4	52917894	52917894	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gcggaaaacctgaaaagactGgtctcaaacgaaactttacg	9	9	1	2	rs151044158		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:52917894G>A	ENST00000295213.4	+	1	398	c.24G>A	c.(22-24)ctG>ctA	p.L8L	SPATA18_ENST00000506829.1_3'UTR|SPATA18_ENST00000419395.2_Silent_p.L8L	NM_145263.2	NP_660306.1	Q8TC71	MIEAP_HUMAN	spermatogenesis associated 18	8					cellular response to DNA damage stimulus (GO:0006974)|mitochondrial protein catabolic process (GO:0035694)|mitochondrion degradation by induced vacuole formation (GO:0035695)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial outer membrane (GO:0005741)				breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(4;1.77e-13)|LUSC - Lung squamous cell carcinoma(32;0.00204)			TGAAAAGACTGGTCTCAAACG	0.582																																					p.L8L		Atlas-SNP	.											SPATA18_ENST00000295213,NS,carcinoma,0,2	SPATA18	222	.	0			c.G24A						.						132	127	129					4																	52917894		2203	4300	6503	SO:0001819	synonymous_variant	132671	exon1			AAGACTGGTCTCA	BC025396	CCDS3489.1, CCDS75124.1	4q11	2012-01-23	2012-01-23		ENSG00000163071	ENSG00000163071			29579	protein-coding gene	gene with protein product		612814	"spermatogenesis associated 18 homolog (rat)"			21300779	Standard	XR_245253		Approved	FLJ32906	uc003gzl.3	Q8TC71	OTTHUMG00000128698	ENST00000295213.4:c.24G>A	chr4.hg19:g.52917894G>A		60.0	0.0		41.0	2.0	NM_145263	B4E2R0|E5RLK1|Q8IY48|Q8N7D7	Silent	SNP	ENST00000295213.4	hg19	CCDS3489.1																																																																																			.	G|1.000;C|0.000		0.582	SPATA18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250597.2	NM_145263		A	52917894	G	A	52917894	2	1	255	1	0	0	0	0	0	0	0	1	15018	1335	47	3		3	SPATA18	4	52917894	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	177448	52917894	138236382	181	35526										
UBA6	55236	hgsc.bcm.edu	37	chr4	68534270	68534270	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ataaaacacattgacttaccCgttatttgttgtatagatcc	5	8	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:68534270C>A	ENST00000322244.5	-	9	851	c.792G>T	c.(790-792)acG>acT	p.T264T	UBA6_ENST00000420827.2_Splice_Site_p.T264T	NM_018227.5	NP_060697.4	A0AVT1	UBA6_HUMAN	ubiquitin-like modifier activating enzyme 6	264					protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|FAT10 activating enzyme activity (GO:0019780)|ligase activity (GO:0016874)			central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(6)|liver(1)|lung(23)|skin(2)|upper_aerodigestive_tract(2)	44						TTGACTTACCCGTTATTTGTT	0.338																																					p.T264T		Atlas-SNP	.											.	UBA6	98	.	0			c.G792T						.						114	111	112					4																	68534270		2202	4300	6502	SO:0001630	splice_region_variant	55236	exon9			CTTACCCGTTATT	AK094164	CCDS3516.1	4q13.2	2008-02-05	2007-11-30	2007-11-30	ENSG00000033178	ENSG00000033178		"Ubiquitin-like modifier activating enzymes"	25581	protein-coding gene	gene with protein product	"UBA6, ubiquitin-activating enzyme E1"	611361	"ubiquitin-activating enzyme E1-like 2"	UBE1L2		17580310	Standard	NM_018227		Approved	FLJ10808	uc003hdg.4	A0AVT1	OTTHUMG00000129299	ENST00000322244.5:c.793+1G>T	chr4.hg19:g.68534270C>A		153.0	0.0		114.0	5.0	NM_018227	A6N8M7|B2RAV3|Q4W5K0|Q6UV21|Q86T78|Q86TC7|Q8N5T3|Q8N9E4|Q9H3T7|Q9NVC9	Silent	SNP	ENST00000322244.5	hg19	CCDS3516.1																																																																																			.	.		0.338	UBA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251429.2	NM_018227	Silent	A	68534270	C	A	68534270	5	1	255	1	0	0	0	0	0	0	1	0	16847	666	23	1	2466	1	UBA6	4	68534270	Splice_Site	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	15616376	68534270	122620006	182	35527										
UGT2A2	10941	hgsc.bcm.edu	37	chr4	70504773	70504773	+	Intron	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tacataggagactggtgctgGgattttcccacagtgtctct	11	9	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:70504773G>T	ENST00000503640.1	-	1	771				UGT2A1_ENST00000512704.1_Intron|UGT2A1_ENST00000286604.4_Intron|UGT2A1_ENST00000514019.1_Missense_Mutation_p.P397T|UGT2A2_ENST00000457664.2_Missense_Mutation_p.P196T	NM_006798.3	NP_006789.2	Q9Y4X1	UD2A1_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide A1, complex locus						cellular glucuronidation (GO:0052695)|detection of chemical stimulus (GO:0009593)|metabolic process (GO:0008152)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(1)|skin(2)	30						ACTGGTGCTGGGATTTTCCCA	0.428																																					p.P397T		Atlas-SNP	.											.	UGT2A1	131	.	0			c.C1189A						.						54	56	56					4																	70504773		1971	4172	6143	SO:0001627	intron_variant	10941	exon3			GTGCTGGGATTTT	AJ006054	CCDS3529.1, CCDS58901.1, CCDS58902.1	4q13	2013-03-28	2010-12-02					"UDP glucuronosyltransferases"	12542	protein-coding gene	gene with protein product		604716	"UDP glycosyltransferase 2 family, polypeptide A1", "UDP glucuronosyltransferase 2 family, polypeptide A1"			10359671	Standard	NM_001252274		Approved		uc011caq.2	Q9Y4X1	OTTHUMG00000184942	ENST00000503640.1:c.715+7874C>A	chr4.hg19:g.70504773G>T		195.0	0.0		100.0	4.0	NM_001252274	B4E2F4|D3GER1|D3GER2|E9PDM7|J3KNA3	Missense_Mutation	SNP	ENST00000503640.1	hg19	CCDS3529.1	.	.	.	.	.	.	.	.	.	.	G	17.94	3.510468	0.64522	.	.	ENSG00000173610	ENST00000457664;ENST00000514019	T;T	0.65364	-0.15;-0.15	5.98	5.98	0.97165	.	.	.	.	.	D	0.83501	0.5268	M	0.90759	3.145	.	.	.	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.85693	0.1308	8	0.66056	D	0.02	.	17.9458	0.89038	0.0:0.0:1.0:0.0	.	397;196	E9PDM7;Q9Y4X1-2	.;.	T	196;397	ENSP00000387888:P196T;ENSP00000425497:P397T	ENSP00000387888:P196T	P	-	1	0	UGT2A1	70539362	1.000000	0.71417	0.993000	0.49108	0.558000	0.35554	9.004000	0.93583	2.838000	0.97847	0.591000	0.81541	CCA	.	.		0.428	UGT2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251554.3	NM_006798		T	70504773	G	T	70504773	1	4	255	0	1	0	0	0	0	0	0	0	16969	1232	43	3		3	UGT2A2	4	70504773	Intron	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	1970503	70504773	120649503	183	35528										
ADAMTS3	9508	hgsc.bcm.edu	37	chr4	73179418	73179418	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gattattgcactggcgtgttCtgaaacgaacaccagttcca	9	10	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:73179418C>A	ENST00000286657.4	-	12	1757	c.1721G>T	c.(1720-1722)aGa>aTa	p.R574I		NM_014243.2	NP_055058.2	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 3	574	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|protein processing (GO:0016485)|vascular endothelial growth factor production (GO:0010573)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.R574K(1)		NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(33)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	76			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CTGGCGTGTTCTGAAACGAAC	0.388																																					p.R574I	NSCLC(168;1941 2048 2918 13048 43078)	Atlas-SNP	.											ADAMTS3,NS,carcinoma,0,1	ADAMTS3	164	.	1	Substitution - Missense(1)	endometrium(1)	c.G1721T						.						115	90	98					4																	73179418		2203	4300	6503	SO:0001583	missense	9508	exon12			CGTGTTCTGAAAC	AB002364	CCDS3553.1	4q21	2008-07-29	2005-08-19		ENSG00000156140	ENSG00000156140	3.4.24.-	"ADAM metallopeptidases with thrombospondin type 1 motif"	219	protein-coding gene	gene with protein product		605011	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3"			10094461	Standard	NM_014243		Approved	KIAA0366, ADAMTS-4	uc003hgk.2	O15072	OTTHUMG00000129912	ENST00000286657.4:c.1721G>T	chr4.hg19:g.73179418C>A	ENSP00000286657:p.Arg574Ile	117.0	0.0		68.0	3.0	NM_014243	A1L3U9|Q9BXZ8	Missense_Mutation	SNP	ENST00000286657.4	hg19	CCDS3553.1	.	.	.	.	.	.	.	.	.	.	C	34	5.379997	0.95945	.	.	ENSG00000156140	ENST00000286657	T	0.80909	-1.43	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	D	0.94272	0.8160	H	0.98133	4.155	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95070	0.8203	10	0.56958	D	0.05	.	20.5373	0.99239	0.0:1.0:0.0:0.0	.	574	O15072	ATS3_HUMAN	I	574	ENSP00000286657:R574I	ENSP00000286657:R574I	R	-	2	0	ADAMTS3	73398282	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.857000	0.98124	0.650000	0.86243	AGA	.	.		0.388	ADAMTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252164.2			A	73179418	C	A	73179418	3	1	255	1	0	0	0	0	1	0	0	0	267	913	32	3	1940	3	ADAMTS3	4	73179418	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	2674645	73179418	117974858	184	35529										
CCDC158	339965	hgsc.bcm.edu	37	chr4	77255317	77255317	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cagtgtgttagcttttgtagAgtgctgagttaaaacaattt	10	4	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:77255317A>G	ENST00000388914.3	-	18	2820	c.2668T>C	c.(2668-2670)Tct>Cct	p.S890P		NM_001042784.1	NP_001036249.1	Q5M9N0	CD158_HUMAN	coiled-coil domain containing 158	890										breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(1)	56						GCTTTTGTAGAGTGCTGAGTT	0.373																																					p.S890P		Atlas-SNP	.											.	CCDC158	114	.	0			c.T2668C						.						153	145	148					4																	77255317		1891	4122	6013	SO:0001583	missense	339965	exon18			TTGTAGAGTGCTG	BC035224	CCDS43242.1	4q21.1	2009-04-06			ENSG00000163749	ENSG00000163749			26374	protein-coding gene	gene with protein product						12477932	Standard	NM_001042784		Approved	FLJ25770	uc003hkb.4	Q5M9N0	OTTHUMG00000160916	ENST00000388914.3:c.2668T>C	chr4.hg19:g.77255317A>G	ENSP00000373566:p.Ser890Pro	174.0	0.0		124.0	5.0	NM_001042784	Q8IYQ1|Q8N7D4|Q8N7E3	Missense_Mutation	SNP	ENST00000388914.3	hg19	CCDS43242.1	.	.	.	.	.	.	.	.	.	.	A	6.993	0.553351	0.13374	.	.	ENSG00000163749	ENST00000388914	T	0.33216	1.42	5.19	4.01	0.46588	.	0.308471	0.23670	N	0.045733	T	0.13628	0.0330	N	0.08118	0	0.80722	D	1	B	0.14805	0.011	B	0.13407	0.009	T	0.10497	-1.0627	10	0.26408	T	0.33	.	6.204	0.20591	0.8875:0.0:0.1125:0.0	.	890	Q5M9N0	CD158_HUMAN	P	890	ENSP00000373566:S890P	ENSP00000373566:S890P	S	-	1	0	CCDC158	77474341	0.998000	0.40836	0.982000	0.44146	0.035000	0.12851	1.977000	0.40589	2.188000	0.69820	0.533000	0.62120	TCT	.	.		0.373	CCDC158-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362694.2	NM_001042784		G	77255317	A	G	77255317	3	3	255	1	0	0	0	0	1	0	0	0	2792	304	11	2	701	2	CCDC158	4	77255317	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	4075899	77255317	113898959	185	35530										
SHROOM3	57619	hgsc.bcm.edu	37	chr4	77660862	77660862	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggagcatgcaacaagatggcTaccattgatgagaatgggaa	13	6	0	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:77660862T>C	ENST00000296043.6	+	5	2489	c.1536T>C	c.(1534-1536)gcT>gcC	p.A512A		NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	512					actin cytoskeleton organization (GO:0030036)|apical protein localization (GO:0045176)|cell morphogenesis (GO:0000902)|cellular pigment accumulation (GO:0043482)|columnar/cuboidal epithelial cell development (GO:0002066)|neural tube closure (GO:0001843)|pattern specification process (GO:0007389)|regulation of cell shape (GO:0008360)	adherens junction (GO:0005912)|apical junction complex (GO:0043296)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)				NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(29)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	60			Lung(101;0.0903)			ACAAGATGGCTACCATTGATG	0.537																																					p.A512A		Atlas-SNP	.											.	SHROOM3	134	.	0			c.T1536C						.						119	120	119					4																	77660862		2203	4300	6503	SO:0001819	synonymous_variant	57619	exon5			GATGGCTACCATT	AB055660	CCDS3579.2	4q21.1	2009-11-25			ENSG00000138771	ENSG00000138771			30422	protein-coding gene	gene with protein product		604570				10589677, 16615870	Standard	NM_020859		Approved	ShrmL, SHRM, KIAA1481, APXL3	uc011cbx.2	Q8TF72	OTTHUMG00000157075	ENST00000296043.6:c.1536T>C	chr4.hg19:g.77660862T>C		93.0	0.0		54.0	4.0	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Silent	SNP	ENST00000296043.6	hg19	CCDS3579.2																																																																																			.	.		0.537	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859		C	77660862	T	C	77660862	2	2	255	1	0	0	0	0	0	0	0	1	14310	1509	53	2		2	SHROOM3	4	77660862	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	405545	77660862	113493414	186	35531										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79284759	79284759	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	atgcccactacctgctgctcGgggaccactgtgttcctgac	10	15	0	1	rs199918192		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:79284759G>T	ENST00000325942.6	+	21	2955	c.2515G>T	c.(2515-2517)Ggg>Tgg	p.G839W	FRAS1_ENST00000264895.6_Missense_Mutation_p.G839W	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	839					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						CCTGCTGCTCGGGGACCACTG	0.572																																					p.G839W		Atlas-SNP	.											.	FRAS1	779	.	0			c.G2515T						.						43	43	43					4																	79284759		2074	4209	6283	SO:0001583	missense	80144	exon21			CTGCTCGGGGACC	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.2515G>T	chr4.hg19:g.79284759G>T	ENSP00000326330:p.Gly839Trp	134.0	0.0		77.0	4.0	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000325942.6	hg19	CCDS54772.1	.	.	.	.	.	.	.	.	.	.	G	16.48	3.134900	0.56828	.	.	ENSG00000138759	ENST00000325942;ENST00000264895	T;T	0.32988	1.43;2.5	5.12	4.27	0.50696	.	0.000000	0.85682	D	0.000000	T	0.66557	0.2801	H	0.96633	3.855	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.75260	-0.3380	10	0.72032	D	0.01	.	10.6501	0.45642	0.1542:0.0:0.8458:0.0	.	839;839	E9PHH6;A2RRR8	.;.	W	839	ENSP00000326330:G839W;ENSP00000264895:G839W	ENSP00000264895:G839W	G	+	1	0	FRAS1	79503783	1.000000	0.71417	0.378000	0.26068	0.725000	0.41563	4.170000	0.58229	1.163000	0.42636	0.585000	0.79938	GGG	.	.		0.572	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2			T	79284759	G	T	79284759	3	4	255	1	0	0	0	0	1	0	0	0	6050	1116	39	1	2597	1	FRAS1	4	79284759	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	1623897	79284759	111869517	187	35532										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79455681	79455681	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cttaacactgaatttcagctCtgcaataatgagaaggtgtt	8	7	2	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:79455681C>A	ENST00000264895.6	+	71	11444	c.11004C>A	c.(11002-11004)ctC>ctA	p.L3668L		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3664					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						AATTTCAGCTCTGCAATAATG	0.418																																					p.L3668L		Atlas-SNP	.											.	FRAS1	779	.	0			c.C11004A						.						169	153	158					4																	79455681		1907	4119	6026	SO:0001819	synonymous_variant	80144	exon71			TCAGCTCTGCAAT	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.11004C>A	chr4.hg19:g.79455681C>A		140.0	0.0		79.0	4.0	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000264895.6	hg19	CCDS54771.1	.	.	.	.	.	.	.	.	.	.	C	8.382	0.837726	0.16891	.	.	ENSG00000138759	ENST00000512123	T	0.66995	-0.24	5.29	1.07	0.20283	.	0.000000	0.64402	D	0.000003	T	0.69744	0.3145	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.69339	-0.5171	7	0.87932	D	0	.	7.3831	0.26868	0.1098:0.4326:0.3864:0.0711	.	.	.	.	M	1897	ENSP00000422834:L1897M	ENSP00000422834:L1897M	L	+	1	2	FRAS1	79674705	0.945000	0.32115	1.000000	0.80357	0.995000	0.86356	0.050000	0.14120	0.542000	0.28846	0.591000	0.81541	CTG	.	.		0.418	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	79455681	C	A	79455681	2	1	255	1	0	0	0	0	0	0	0	1	6050	900	32	3		3	FRAS1	4	79455681	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	170922	79455681	111698595	188	35533										
CDS1	1040	hgsc.bcm.edu	37	chr4	85562071	85562071	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gtaaactccttcgtgacagaAtgtgagccctcagaactttt	8	10	1	4			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:85562071A>G	ENST00000295887.5	+	10	1383	c.960A>G	c.(958-960)gaA>gaG	p.E320E		NM_001263.3	NP_001254.2	O96017	CHK2_HUMAN	CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 1	0	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|liver(2)|lung(5)|ovary(1)	20		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.00101)		TCGTGACAGAATGTGAGCCCT	0.413																																					p.E320E		Atlas-SNP	.											.	CDS1	58	.	0			c.A960G						.						161	149	153					4																	85562071		2203	4300	6503	SO:0001819	synonymous_variant	1040	exon10			GACAGAATGTGAG	U65887	CCDS3608.1	4q21	2008-02-05			ENSG00000163624	ENSG00000163624	2.7.7.41		1800	protein-coding gene	gene with protein product		603548				9806839, 9115637	Standard	NM_001263		Approved		uc011ccv.2	Q92903	OTTHUMG00000130428	ENST00000295887.5:c.960A>G	chr4.hg19:g.85562071A>G		167.0	0.0		98.0	4.0	NM_001263	A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Silent	SNP	ENST00000295887.5	hg19	CCDS3608.1																																																																																			.	.		0.413	CDS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252817.2			G	85562071	A	G	85562071	2	3	255	1	0	0	0	0	0	0	0	1	3179	98	4	2		2	CDS1	4	85562071	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	6106390	85562071	105592205	189	35534										
KLHL8	57563	hgsc.bcm.edu	37	chr4	88098001	88098001	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgttcatttccatcatgtccAcctactgcatacactttacc	3	14	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:88098001A>G	ENST00000273963.5	-	6	1457	c.1116T>C	c.(1114-1116)ggT>ggC	p.G372G	KLHL8_ENST00000512111.1_Silent_p.G372G|KLHL8_ENST00000498875.2_Silent_p.G296G|KLHL8_ENST00000425278.2_Silent_p.G189G|KLHL8_ENST00000545252.1_Silent_p.G21G	NM_020803.3	NP_065854.3	Q9P2G9	KLHL8_HUMAN	kelch-like family member 8	372					protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	Cul3-RING ubiquitin ligase complex (GO:0031463)|nucleus (GO:0005634)				breast(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|stomach(1)|upper_aerodigestive_tract(1)	17		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)		CATCATGTCCACCTACTGCAT	0.313																																					p.G372G		Atlas-SNP	.											.	KLHL8	51	.	0			c.T1116C						.						203	183	190					4																	88098001		2203	4300	6503	SO:0001819	synonymous_variant	57563	exon6			ATGTCCACCTACT	AB037799	CCDS3617.1, CCDS75163.1	4q21.3	2013-01-30	2013-01-30		ENSG00000145332	ENSG00000145332		"Kelch-like", "BTB/POZ domain containing"	18644	protein-coding gene	gene with protein product		611967	"kelch-like 8 (Drosophila)"				Standard	XM_005263153		Approved	KIAA1378	uc003hql.1	Q9P2G9	OTTHUMG00000130593	ENST00000273963.5:c.1116T>C	chr4.hg19:g.88098001A>G		156.0	0.0		97.0	4.0	NM_020803	Q53XA3|Q6N018	Silent	SNP	ENST00000273963.5	hg19	CCDS3617.1																																																																																			.	.		0.313	KLHL8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253040.1			G	88098001	A	G	88098001	2	3	255	1	0	0	0	0	0	0	0	1	8404	146	6	2		2	KLHL8	4	88098001	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	2535930	88098001	103056275	190	35535										
HERC3	8916	hgsc.bcm.edu	37	chr4	89591124	89591124	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cattcttaattcccgtactgTttaacaattatatcacagca	3	10	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:89591124T>C	ENST00000402738.1	+	15	1986	c.1747T>C	c.(1747-1749)Ttt>Ctt	p.F583L	HERC3_ENST00000543130.1_Missense_Mutation_p.F27L|HERC3_ENST00000264345.3_Missense_Mutation_p.F583L	NM_001271602.1|NM_014606.1	NP_001258531.1|NP_055421.1	Q15034	HERC3_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 3	583					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|prostate(2)|skin(2)	45				OV - Ovarian serous cystadenocarcinoma(123;0.000319)		TCCCGTACTGTTTAACAATTA	0.418																																					p.F583L		Atlas-SNP	.											.	HERC3	82	.	0			c.T1747C						.						115	116	116					4																	89591124		2203	4300	6503	SO:0001583	missense	8916	exon15			GTACTGTTTAACA	D25215	CCDS34028.1	4q21	2012-02-23	2012-02-23		ENSG00000138641	ENSG00000138641			4876	protein-coding gene	gene with protein product		605200	"hect domain and RLD 3"			10702688	Standard	NM_014606		Approved	KIAA0032	uc003hrw.2	Q15034	OTTHUMG00000150436	ENST00000402738.1:c.1747T>C	chr4.hg19:g.89591124T>C	ENSP00000385684:p.Phe583Leu	136.0	0.0		81.0	4.0	NM_014606	A8K1S5|Q8IXX3	Missense_Mutation	SNP	ENST00000402738.1	hg19	CCDS34028.1	.	.	.	.	.	.	.	.	.	.	T	15.85	2.956114	0.53293	.	.	ENSG00000138641	ENST00000402738;ENST00000264345;ENST00000543130	T;T;T	0.38401	1.14;1.14;1.36	5.08	5.08	0.68730	.	0.111220	0.64402	D	0.000005	T	0.24198	0.0586	N	0.19112	0.55	0.43471	D	0.995686	B	0.14805	0.011	B	0.17979	0.02	T	0.06826	-1.0805	10	0.12103	T	0.63	.	15.313	0.74048	0.0:0.0:0.0:1.0	.	583	Q15034	HERC3_HUMAN	L	583;583;27	ENSP00000385684:F583L;ENSP00000264345:F583L;ENSP00000441703:F27L	ENSP00000264345:F583L	F	+	1	0	HERC3	89810147	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.509000	0.45459	2.261000	0.74972	0.533000	0.62120	TTT	.	.		0.418	HERC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318081.2	NM_014606		C	89591124	T	C	89591124	3	2	255	1	0	0	0	0	1	0	0	0	7068	1725	60	2	1797	2	HERC3	4	89591124	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	1493123	89591124	101563152	191	35536										
NAP1L5	266812	hgsc.bcm.edu	37	chr4	89618533	89618533	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgcacacccctccatctcgcCggtgagctcttggatcttgg	10	15	3	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:89618533C>T	ENST00000323061.5	-	1	853	c.373G>A	c.(373-375)Ggc>Agc	p.G125S	HERC3_ENST00000543130.1_Intron|HERC3_ENST00000402738.1_Intron|HERC3_ENST00000264345.3_Intron	NM_153757.2	NP_715638.1	Q96NT1	NP1L5_HUMAN	nucleosome assembly protein 1-like 5	125	Glu-rich.				nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				endometrium(2)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(123;0.000181)		TCCATCTCGCCGGTGAGCTCT	0.517																																					p.G125S		Atlas-SNP	.											.	NAP1L5	23	.	0			c.G373A						.						64	67	66					4																	89618533		2203	4300	6503	SO:0001583	missense	266812	exon1			TCTCGCCGGTGAG	NM_153757	CCDS3632.1	4q21-q22	2006-04-12			ENSG00000177432	ENSG00000177432			19968	protein-coding gene	gene with protein product		612203				12383514	Standard	NM_153757		Approved	DRLM	uc003hrx.3	Q96NT1	OTTHUMG00000130950	ENST00000323061.5:c.373G>A	chr4.hg19:g.89618533C>T	ENSP00000320488:p.Gly125Ser	173.0	0.0		100.0	4.0	NM_153757		Missense_Mutation	SNP	ENST00000323061.5	hg19	CCDS3632.1	.	.	.	.	.	.	.	.	.	.	C	14.23	2.474854	0.43942	.	.	ENSG00000177432	ENST00000323061;ENST00000539293	T	0.23147	1.92	3.61	1.12	0.20585	.	.	.	.	.	T	0.23410	0.0566	M	0.85197	2.74	0.22317	N	0.999202	P	0.42757	0.789	B	0.29440	0.102	T	0.20107	-1.0285	9	0.33141	T	0.24	-8.3765	5.2981	0.15764	0.0:0.6275:0.0:0.3725	.	125	Q96NT1	NP1L5_HUMAN	S	125	ENSP00000320488:G125S	ENSP00000320488:G125S	G	-	1	0	NAP1L5	89837556	0.740000	0.28207	0.921000	0.36526	0.994000	0.84299	0.735000	0.26115	0.328000	0.23435	0.446000	0.29264	GGC	.	.		0.517	NAP1L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253551.1	NM_153757		T	89618533	C	T	89618533	3	4	255	1	0	0	0	0	1	0	0	0	10169	652	23	1	179	1	NAP1L5	4	89618533	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	27409	89618533	101535743	192	35537										
FAM190A	401145	hgsc.bcm.edu	37	chr4	91230222	91230222	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	caccttcagaatttttagccTtgactgaagattctgtgtct	7	9	3	4			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:91230222T>C	ENST00000509176.1	+	2	1075	c.787T>C	c.(787-789)Ttg>Ctg	p.L263L	CCSER1_ENST00000333691.8_Silent_p.L263L|CCSER1_ENST00000432775.2_Silent_p.L263L	NM_001145065.1	NP_001138537.1	Q9C0I3	CCSE1_HUMAN	coiled-coil serine-rich protein 1	263																	ATTTTTAGCCTTGACTGAAGA	0.433																																					p.L263L		Atlas-SNP	.											.	.	.	.	0			c.T787C						.						151	140	143					4																	91230222		1859	4119	5978	SO:0001819	synonymous_variant	401145	exon2			TTAGCCTTGACTG		CCDS47099.1, CCDS47100.1	4q22.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184305	ENSG00000184305			29349	protein-coding gene	gene with protein product			"family with sequence similarity 190, member A"	FAM190A		11214970	Standard	NM_001145065		Approved	KIAA1680	uc003hsv.4	Q9C0I3	OTTHUMG00000160950	ENST00000509176.1:c.787T>C	chr4.hg19:g.91230222T>C		46.0	0.0		31.0	4.0	NM_001145065	Q4W5M0|Q86V57	Silent	SNP	ENST00000509176.1	hg19	CCDS47099.1																																																																																			.	.		0.433	CCSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363109.3	NM_001145065		C	91230222	T	C	91230222	2	2	255	1	0	0	0	0	0	0	0	1	5526	1606	56	2		2	FAM190A	4	91230222	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	1611689	91230222	99924054	193	35538										
TSPAN5	10098	hgsc.bcm.edu	37	chr4	99408000	99408000	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	caaactgggtcaaagccgccGagatcggtgatggaagagat	14	8	1	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:99408000G>T	ENST00000305798.3	-	3	570	c.168C>A	c.(166-168)ctC>ctA	p.L56L	TSPAN5_ENST00000505184.1_5'UTR|TSPAN5_ENST00000509168.1_5'UTR	NM_005723.3	NP_005714.2	P62079	TSN5_HUMAN	tetraspanin 5	56					establishment of protein localization to plasma membrane (GO:0090002)|positive regulation of Notch signaling pathway (GO:0045747)|protein maturation (GO:0051604)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)	p.L56L(1)		kidney(2)|large_intestine(6)|lung(5)|upper_aerodigestive_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(123;1.89e-07)		CAAAGCCGCCGAGATCGGTGA	0.512																																					p.L56L		Atlas-SNP	.											TSPAN5,NS,carcinoma,0,1	TSPAN5	32	.	1	Substitution - coding silent(1)	lung(1)	c.C168A						.						142	139	140					4																	99408000		2203	4300	6503	SO:0001819	synonymous_variant	10098	exon3			GCCGCCGAGATCG		CCDS3646.1	4q22.3	2013-02-14	2005-03-21	2005-03-21	ENSG00000168785	ENSG00000168785		"Tetraspanins"	17753	protein-coding gene	gene with protein product		613136	"transmembrane 4 superfamily member 9"	TM4SF9			Standard	NM_005723		Approved	Tspan-5, NET-4	uc003hub.3	P62079	OTTHUMG00000131008	ENST00000305798.3:c.168C>A	chr4.hg19:g.99408000G>T		122.0	0.0		92.0	4.0	NM_005723	B2RDY2|O60628|O60746|Q6FHE5|Q9JLY1	Silent	SNP	ENST00000305798.3	hg19	CCDS3646.1																																																																																			.	.		0.512	TSPAN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253641.2	NM_005723		T	99408000	G	T	99408000	2	4	255	1	0	0	0	0	0	0	0	1	16665	1045	37	1		1	TSPAN5	4	99408000	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	8177778	99408000	91746276	194	35539										
DAPP1	27071	hgsc.bcm.edu	37	chr4	100756811	100756811	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gcaacctcacacgccatgctGctgaagctcttctcctctca	6	17	4	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:100756811G>T	ENST00000512369.1	+	2	201	c.133G>T	c.(133-135)Gct>Tct	p.A45S	DAPP1_ENST00000296414.7_Missense_Mutation_p.A45S	NM_014395.2	NP_055210.2	Q9UN19	DAPP1_HUMAN	dual adaptor of phosphotyrosine and 3-phosphoinositides	45	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phospholipid binding (GO:0005543)			endometrium(1)|kidney(1)|lung(4)	6				OV - Ovarian serous cystadenocarcinoma(123;7.04e-09)		ACGCCATGCTGCTGAAGCTCT	0.552																																					p.A45S		Atlas-SNP	.											.	DAPP1	47	.	0			c.G133T						.						147	146	146					4																	100756811		2096	4222	6318	SO:0001583	missense	27071	exon2			CATGCTGCTGAAG	AF186022	CCDS47112.1	4q25-q27	2013-02-14			ENSG00000070190	ENSG00000070190		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	16500	protein-coding gene	gene with protein product		605768				10432293	Standard	NM_014395		Approved	BAM32	uc003hvf.4	Q9UN19	OTTHUMG00000160974	ENST00000512369.1:c.133G>T	chr4.hg19:g.100756811G>T	ENSP00000423602:p.Ala45Ser	124.0	0.0		100.0	5.0	NM_014395	Q8TCK5|Q9UHF2	Missense_Mutation	SNP	ENST00000512369.1	hg19	CCDS47112.1	.	.	.	.	.	.	.	.	.	.	G	17.48	3.399565	0.62177	.	.	ENSG00000070190	ENST00000296414;ENST00000512369	D;D	0.92099	-2.97;-2.97	5.9	5.9	0.94986	SH2 motif (5);	0.051911	0.85682	D	0.000000	D	0.95059	0.8400	L	0.59967	1.855	0.80722	D	1	P;D;D	0.76494	0.905;0.999;0.991	P;D;P	0.65443	0.751;0.935;0.876	D	0.93983	0.7260	10	0.44086	T	0.13	-0.2833	19.8893	0.96923	0.0:0.0:1.0:0.0	.	45;45;45	B4DW38;Q9UN19-2;Q9UN19	.;.;DAPP1_HUMAN	S	45	ENSP00000296414:A45S;ENSP00000423602:A45S	ENSP00000296414:A45S	A	+	1	0	DAPP1	100975834	1.000000	0.71417	0.060000	0.19600	0.017000	0.09413	8.816000	0.91979	2.788000	0.95919	0.650000	0.86243	GCT	.	.		0.552	DAPP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363215.1			T	100756811	G	T	100756811	3	4	255	1	0	0	0	0	1	0	0	0	4241	1319	46	3	139	3	DAPP1	4	100756811	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	1348811	100756811	90397465	195	35540										
TBCK	93627	hgsc.bcm.edu	37	chr4	107154107	107154107	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aaagttaccttgccaatacaCaagatcaggatgagacacta	7	9	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:107154107C>T	ENST00000273980.5	-	18	2074	c.1627G>A	c.(1627-1629)Gtg>Atg	p.V543M	TBCK_ENST00000361687.4_Missense_Mutation_p.V480M|TBCK_ENST00000394706.3_Missense_Mutation_p.V504M|TBCK_ENST00000394708.2_Missense_Mutation_p.V543M|TBCK_ENST00000432496.2_Missense_Mutation_p.V543M					TBC1 domain containing kinase											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	25						TGCCAATACACAAGATCAGGA	0.353																																					p.V543M		Atlas-SNP	.											.	TBCK	89	.	0			c.G1627A						.						117	113	115					4																	107154107		2203	4300	6503	SO:0001583	missense	93627	exon17			AATACACAAGATC		CCDS3673.1, CCDS54788.1, CCDS54789.1	4q24	2014-09-17			ENSG00000145348	ENSG00000145348			28261	protein-coding gene	gene with protein product						12471243	Standard	XR_427553		Approved	MGC16169, HSPC302	uc010ilv.2	Q8TEA7	OTTHUMG00000131214	ENST00000273980.5:c.1627G>A	chr4.hg19:g.107154107C>T	ENSP00000273980:p.Val543Met	195.0	0.0		87.0	4.0	NM_001163436		Missense_Mutation	SNP	ENST00000273980.5	hg19	CCDS54788.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.953603	0.92660	.	.	ENSG00000145348	ENST00000273980;ENST00000432496;ENST00000361687;ENST00000394706;ENST00000394708	T;T;T;T;T	0.04156	3.69;3.69;3.69;3.69;3.69	5.46	5.46	0.80206	Rab-GAP/TBC domain (4);	0.000000	0.85682	D	0.000000	T	0.29321	0.0730	M	0.88241	2.94	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.997;0.986;0.998	T	0.10245	-1.0638	10	0.87932	D	0	.	19.3032	0.94151	0.0:1.0:0.0:0.0	.	543;504;480	Q8TEA7;Q8TEA7-2;Q8TEA7-3	TBCK_HUMAN;.;.	M	543;543;480;504;543	ENSP00000273980:V543M;ENSP00000405847:V543M;ENSP00000355338:V480M;ENSP00000378196:V504M;ENSP00000378198:V543M	ENSP00000273980:V543M	V	-	1	0	TBCK	107373556	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.656000	0.83736	2.563000	0.86464	0.655000	0.94253	GTG	.	.		0.353	TBCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253953.4	NM_033115		T	107154107	C	T	107154107	3	4	255	1	0	0	0	0	1	0	0	0	15651	478	17	3	1094	3	TBCK	4	107154107	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	6397296	107154107	84000169	196	35541										
PAPSS1	9061	hgsc.bcm.edu	37	chr4	108576006	108576006	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gccgtccagcctctctttatCttcatgagtcgcagtcagaa	8	13	4	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:108576006C>T	ENST00000265174.4	-	8	1218	c.946G>A	c.(946-948)Gat>Aat	p.D316N	PAPSS1_ENST00000511304.1_5'UTR	NM_005443.4	NP_005434.4	O43252	PAPS1_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase 1	316					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sulfate assimilation (GO:0000103)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	adenylylsulfate kinase activity (GO:0004020)|ATP binding (GO:0005524)|nucleotidyltransferase activity (GO:0016779)|sulfate adenylyltransferase (ATP) activity (GO:0004781)			NS(1)|endometrium(2)|kidney(5)|large_intestine(2)|lung(5)|ovary(1)	16		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.49e-05)		CTCTCTTTATCTTCATGAGTC	0.468																																					p.D316N		Atlas-SNP	.											.	PAPSS1	57	.	0			c.G946A						.						98	101	100					4																	108576006		2203	4300	6503	SO:0001583	missense	9061	exon8			CTTTATCTTCATG	Y10387	CCDS3676.1	4q24	2012-07-13			ENSG00000138801	ENSG00000138801	2.7.7.4, 2.7.1.25		8603	protein-coding gene	gene with protein product		603262				9576487, 9771708	Standard	NM_005443		Approved	ATPSK1, PAPSS	uc003hyk.3	O43252	OTTHUMG00000131210	ENST00000265174.4:c.946G>A	chr4.hg19:g.108576006C>T	ENSP00000265174:p.Asp316Asn	151.0	0.0		95.0	4.0	NM_005443	O43841|O75332|Q96FB1|Q96TF4|Q9P1P9|Q9UE98	Missense_Mutation	SNP	ENST00000265174.4	hg19	CCDS3676.1	.	.	.	.	.	.	.	.	.	.	C	13.91	2.377210	0.42105	.	.	ENSG00000138801	ENST00000265174	T	0.24151	1.87	5.72	5.72	0.89469	Sulphate adenylyltransferase (2);PUA-like domain (1);	0.130031	0.64402	D	0.000002	T	0.33177	0.0854	L	0.58583	1.82	0.80722	D	1	B	0.21309	0.054	B	0.26864	0.074	T	0.05954	-1.0854	10	0.51188	T	0.08	-19.2517	19.8968	0.96969	0.0:1.0:0.0:0.0	.	316	O43252	PAPS1_HUMAN	N	316	ENSP00000265174:D316N	ENSP00000265174:D316N	D	-	1	0	PAPSS1	108795455	1.000000	0.71417	0.734000	0.30879	0.071000	0.16799	3.445000	0.52921	2.691000	0.91804	0.655000	0.94253	GAT	.	.		0.468	PAPSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253946.2			T	108576006	C	T	108576006	3	4	255	1	0	0	0	0	1	0	0	0	11443	913	32	3	948	3	PAPSS1	4	108576006	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1421899	108576006	82578270	197	35542										
SEC24B	10427	hgsc.bcm.edu	37	chr4	110384380	110384380	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cgagtgcctcccaaccatacTcctcttttgtgaatcactac	5	15	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:110384380T>C	ENST00000265175.5	+	2	512	c.457T>C	c.(457-459)Tcc>Ccc	p.S153P	SEC24B_ENST00000504968.2_Missense_Mutation_p.S184P|SEC24B_ENST00000399100.2_Missense_Mutation_p.S153P	NM_006323.2	NP_006314.2	O95487	SC24B_HUMAN	SEC24 family member B	153					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|aorta morphogenesis (GO:0035909)|auditory receptor cell stereocilium organization (GO:0060088)|cellular protein metabolic process (GO:0044267)|cochlear nucleus development (GO:0021747)|COPII vesicle coating (GO:0048208)|coronary artery morphogenesis (GO:0060982)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|lung lobe morphogenesis (GO:0060463)|membrane organization (GO:0061024)|neural tube closure (GO:0001843)|outflow tract morphogenesis (GO:0003151)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|pulmonary artery morphogenesis (GO:0061156)|regulation of cargo loading into COPII-coated vesicle (GO:1901301)|regulation of establishment of planar polarity involved in neural tube closure (GO:0090178)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|membrane (GO:0016020)	transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)		CCAACCATACTCCTCTTTTGT	0.498																																					p.S153P		Atlas-SNP	.											.	SEC24B	186	.	0			c.T457C						.						267	257	260					4																	110384380		2045	4185	6230	SO:0001583	missense	10427	exon2			CCATACTCCTCTT	AJ131245	CCDS43260.1, CCDS47124.1, CCDS75179.1	4q25	2013-10-21	2013-10-21		ENSG00000138802	ENSG00000138802			10704	protein-coding gene	gene with protein product		607184	"SEC24 (S. cerevisiae) related gene family, member B", "SEC24 family, member B (S. cerevisiae)"			10075675, 10329445	Standard	XM_005262688		Approved		uc003hzk.3	O95487	OTTHUMG00000161372	ENST00000265175.5:c.457T>C	chr4.hg19:g.110384380T>C	ENSP00000265175:p.Ser153Pro	140.0	0.0		103.0	5.0	NM_006323	B7ZKM8|B7ZKN4|Q0VG08	Missense_Mutation	SNP	ENST00000265175.5	hg19	CCDS47124.1	.	.	.	.	.	.	.	.	.	.	T	13.36	2.213861	0.39102	.	.	ENSG00000138802	ENST00000504968;ENST00000399100;ENST00000265175	T;D;T	0.82619	-1.18;-1.63;-1.38	4.5	0.453	0.16639	.	0.891618	0.09768	N	0.758401	T	0.67411	0.2890	N	0.24115	0.695	0.41022	D	0.985088	B;B;B;B	0.15141	0.001;0.012;0.002;0.007	B;B;B;B	0.09377	0.002;0.004;0.004;0.004	T	0.55860	-0.8074	10	0.30854	T	0.27	-3.8125	3.5609	0.07882	0.163:0.1809:0.0:0.656	.	103;184;153;153	B4DTM6;B7ZKM8;O95487-2;O95487	.;.;.;SC24B_HUMAN	P	184;153;153	ENSP00000428564:S184P;ENSP00000382051:S153P;ENSP00000265175:S153P	ENSP00000265175:S153P	S	+	1	0	SEC24B	110603829	0.954000	0.32549	0.988000	0.46212	0.993000	0.82548	0.162000	0.16501	0.163000	0.19507	0.260000	0.18958	TCC	.	.		0.498	SEC24B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364693.2			C	110384380	T	C	110384380	3	2	255	1	0	0	0	0	1	0	0	0	14010	1551	54	2	463	2	SEC24B	4	110384380	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	1808374	110384380	80769896	198	35543										
SEC24B	10427	hgsc.bcm.edu	37	chr4	110453794	110453794	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	attctctctttttcttttcaGggtgcagtacatgttaatga	7	7	4	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:110453794G>T	ENST00000265175.5	+	21	3445		c.e21-1		SEC24B_ENST00000504968.2_Splice_Site|SEC24B_ENST00000399100.2_Splice_Site	NM_006323.2	NP_006314.2	O95487	SC24B_HUMAN	SEC24 family member B						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|aorta morphogenesis (GO:0035909)|auditory receptor cell stereocilium organization (GO:0060088)|cellular protein metabolic process (GO:0044267)|cochlear nucleus development (GO:0021747)|COPII vesicle coating (GO:0048208)|coronary artery morphogenesis (GO:0060982)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|lung lobe morphogenesis (GO:0060463)|membrane organization (GO:0061024)|neural tube closure (GO:0001843)|outflow tract morphogenesis (GO:0003151)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|pulmonary artery morphogenesis (GO:0061156)|regulation of cargo loading into COPII-coated vesicle (GO:1901301)|regulation of establishment of planar polarity involved in neural tube closure (GO:0090178)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|membrane (GO:0016020)	transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)		TTTCTTTTCAGGGTGCAGTAC	0.398																																					.		Atlas-SNP	.											.	SEC24B	186	.	0			c.3391-1G>T						.						111	102	105					4																	110453794		1892	4113	6005	SO:0001630	splice_region_variant	10427	exon21			TTTTCAGGGTGCA	AJ131245	CCDS43260.1, CCDS47124.1, CCDS75179.1	4q25	2013-10-21	2013-10-21		ENSG00000138802	ENSG00000138802			10704	protein-coding gene	gene with protein product		607184	"SEC24 (S. cerevisiae) related gene family, member B", "SEC24 family, member B (S. cerevisiae)"			10075675, 10329445	Standard	XM_005262688		Approved		uc003hzk.3	O95487	OTTHUMG00000161372	ENST00000265175.5:c.3391-1G>T	chr4.hg19:g.110453794G>T		85.0	0.0		49.0	4.0	NM_006323	B7ZKM8|B7ZKN4|Q0VG08	Splice_Site	SNP	ENST00000265175.5	hg19	CCDS47124.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.323452	0.81580	.	.	ENSG00000138802	ENST00000504968;ENST00000399100;ENST00000265175	.	.	.	5.62	5.62	0.85841	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.6544	0.95831	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SEC24B	110673243	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	9.244000	0.95423	2.647000	0.89833	0.467000	0.42956	.	.	.		0.398	SEC24B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364693.2		Intron	T	110453794	G	T	110453794	5	4	255	1	0	0	0	0	0	0	1	0	14010	1014	35	3	3472	3	SEC24B	4	110453794	Splice_Site	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	69414	110453794	80700482	199	35544										
AP1AR	55435	hgsc.bcm.edu	37	chr4	113174413	113174413	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gtgagcacttaacaatagagGtaagtagtccttaatttgat	9	5	0	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:113174413G>A	ENST00000274000.5	+	2	487		c.e2+1		AP1AR_ENST00000309703.6_Splice_Site	NM_018569.4	NP_061039.3	Q63HQ0	AP1AR_HUMAN	adaptor-related protein complex 1 associated regulatory protein						cellular protein localization (GO:0034613)|negative regulation of cell motility (GO:2000146)|negative regulation of receptor recycling (GO:0001920)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|protein transport (GO:0015031)|regulation of Arp2/3 complex-mediated actin nucleation (GO:0034315)|vesicle targeting, trans-Golgi to endosome (GO:0048203)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|transport vesicle (GO:0030133)	AP-1 adaptor complex binding (GO:0035650)|kinesin binding (GO:0019894)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)	9						AACAATAGAGGTAAGTAGTCC	0.353																																					.		Atlas-SNP	.											.	AP1AR	25	.	0			c.132+1G>A						.						62	64	63					4																	113174413		2203	4299	6502	SO:0001630	splice_region_variant	55435	exon2			ATAGAGGTAAGTA	AL136628	CCDS3696.1, CCDS47125.1	4q25	2009-09-28	2009-09-25	2009-09-25	ENSG00000138660	ENSG00000138660			28808	protein-coding gene	gene with protein product	"gamma1-adaptin brefeldin A resistance"	610851	"chromosome 4 open reading frame 16"	C4orf16		15775984	Standard	NM_018569		Approved	PRO0971, 2C18, gamma-BAR	uc003iaj.4	Q63HQ0	OTTHUMG00000132849	ENST00000274000.5:c.132+1G>A	chr4.hg19:g.113174413G>A		126.0	0.0		83.0	5.0	NM_001128426	B2RCV7|Q96GG6|Q9H0V0|Q9P1L4	Splice_Site	SNP	ENST00000274000.5	hg19	CCDS3696.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.416841	0.83449	.	.	ENSG00000138660	ENST00000274000;ENST00000309703	.	.	.	5.26	5.26	0.73747	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.2417	0.93887	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	AP1AR	113393862	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.582000	0.82546	2.619000	0.88677	0.650000	0.86243	.	.	.		0.353	AP1AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256323.2	NM_018569	Intron	A	113174413	G	A	113174413	5	1	255	1	0	0	0	0	0	0	1	0	730	1275	44	3	139	3	AP1AR	4	113174413	Splice_Site	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	2720619	113174413	77979863	200	35545										
ALPK1	80216	hgsc.bcm.edu	37	chr4	113360847	113360847	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	attgctatttttcagattttAgaggacaagacaataaaggg	9	4	1	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:113360847A>G	ENST00000458497.1	+	14	3636	c.3357A>G	c.(3355-3357)ttA>ttG	p.L1119L	ALPK1_ENST00000177648.9_Silent_p.L1119L|ALPK1_ENST00000504176.2_Silent_p.L1041L	NM_001102406.1|NM_025144.3	NP_001095876.1|NP_079420.3	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	1119	Alpha-type protein kinase. {ECO:0000255|PROSITE-ProRule:PRU00501}.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(20)|ovary(6)|prostate(2)|urinary_tract(1)	53		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		TTCAGATTTTAGAGGACAAGA	0.373																																					p.L1119L		Atlas-SNP	.											.	ALPK1	125	.	0			c.A3357G						.						92	82	86					4																	113360847		2202	4300	6502	SO:0001819	synonymous_variant	80216	exon14			GATTTTAGAGGAC	AY044164	CCDS3697.1, CCDS58923.1	4q26	2008-02-05			ENSG00000073331	ENSG00000073331			20917	protein-coding gene	gene with protein product	"lymphocyte alpha-kinase"	607347				10021370, 10819331	Standard	NM_025144		Approved	Lak, FLJ22670, KIAA1527	uc003ian.4	Q96QP1	OTTHUMG00000132911	ENST00000458497.1:c.3357A>G	chr4.hg19:g.113360847A>G		148.0	0.0		89.0	4.0	NM_001102406	B4E3G1|F5H138|Q68CI9|Q6P9F9|Q6ZNK4|Q9P201	Silent	SNP	ENST00000458497.1	hg19	CCDS3697.1																																																																																			.	.		0.373	ALPK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256421.2	NM_025144		G	113360847	A	G	113360847	2	3	255	1	0	0	0	0	0	0	0	1	544	417	15	2		2	ALPK1	4	113360847	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	186434	113360847	77793429	201	35546										
ANK2	287	hgsc.bcm.edu	37	chr4	114095576	114095576	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tttatttttctcgcagtctgAcagcaatgcaagcttcctcc	6	12	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:114095576A>G	ENST00000357077.4	+	2	142	c.89A>G	c.(88-90)gAc>gGc	p.D30G	ANK2_ENST00000506722.1_Missense_Mutation_p.D9G|ANK2_ENST00000264366.6_Missense_Mutation_p.D30G|ANK2_ENST00000394537.3_Missense_Mutation_p.D30G	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	30					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		TCGCAGTCTGACAGCAATGCA	0.408																																					p.D30G		Atlas-SNP	.											.	ANK2	576	.	0			c.A89G						.						59	54	56					4																	114095576		2203	4300	6503	SO:0001583	missense	287	exon2			AGTCTGACAGCAA	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.89A>G	chr4.hg19:g.114095576A>G	ENSP00000349588:p.Asp30Gly	200.0	0.0		95.0	4.0	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	hg19	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.502551	0.85176	.	.	ENSG00000145362	ENST00000503271;ENST00000503423;ENST00000506722;ENST00000504454;ENST00000394537;ENST00000357077;ENST00000264366;ENST00000508613;ENST00000511380;ENST00000343056	T;T;T;T;T;T;T;T;T	0.69685	1.82;-0.13;-0.38;-0.32;-0.38;-0.41;-0.42;-0.38;-0.38	5.54	5.54	0.83059	Ankyrin repeat-containing domain (2);	0.000000	0.53938	D	0.000052	T	0.81004	0.4733	M	0.70275	2.135	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;0.996	D;D;D;D;D	0.91635	0.998;0.999;0.999;0.998;0.987	T	0.83334	-0.0011	10	0.87932	D	0	.	15.3587	0.74453	1.0:0.0:0.0:0.0	.	30;30;30;9;9	Q01484;Q01484-2;Q01484-4;Q01484-5;F8WEF9	ANK2_HUMAN;.;.;.;.	G	9;9;9;45;30;30;30;45;47;9	ENSP00000423799:D9G;ENSP00000421011:D9G;ENSP00000421067:D9G;ENSP00000424722:D45G;ENSP00000378044:D30G;ENSP00000349588:D30G;ENSP00000264366:D30G;ENSP00000422900:D45G;ENSP00000425775:D47G	ENSP00000264366:D30G	D	+	2	0	ANK2	114315025	1.000000	0.71417	1.000000	0.80357	0.842000	0.47809	9.067000	0.93955	2.098000	0.63641	0.533000	0.62120	GAC	.	.		0.408	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		G	114095576	A	G	114095576	3	3	255	1	0	0	0	0	1	0	0	0	621	275	10	2	120	2	ANK2	4	114095576	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	734729	114095576	77058700	202	35547										
ANK2	287	hgsc.bcm.edu	37	chr4	114279607	114279607	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgattctcccgattcttcccCagaagaacagaaatcagtaa	6	11	3	4			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:114279607C>A	ENST00000357077.4	+	38	9886	c.9833C>A	c.(9832-9834)cCa>cAa	p.P3278Q	ANK2_ENST00000509550.1_Intron|ANK2_ENST00000506722.1_Intron|ANK2_ENST00000264366.6_Missense_Mutation_p.P3245Q|ANK2_ENST00000394537.3_Intron|ANK2_ENST00000510275.2_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	3278					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		GATTCTTCCCCAGAAGAACAG	0.443																																					p.P3278Q		Atlas-SNP	.											.	ANK2	576	.	0			c.C9833A						.						101	98	99					4																	114279607		2203	4300	6503	SO:0001583	missense	287	exon38			CTTCCCCAGAAGA	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.9833C>A	chr4.hg19:g.114279607C>A	ENSP00000349588:p.Pro3278Gln	146.0	0.0		116.0	6.0	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	hg19	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.980398	0.74474	.	.	ENSG00000145362	ENST00000357077;ENST00000264366;ENST00000505342	T;T;D	0.96265	-0.33;-0.34;-3.96	5.71	5.71	0.89125	.	0.000000	0.56097	D	0.000024	D	0.97854	0.9295	M	0.71581	2.175	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.96981	0.9715	10	0.32370	T	0.25	.	19.8625	0.96789	0.0:1.0:0.0:0.0	.	3245;3278	Q01484;Q01484-4	ANK2_HUMAN;.	Q	3278;3245;288	ENSP00000349588:P3278Q;ENSP00000264366:P3245Q;ENSP00000422498:P288Q	ENSP00000264366:P3245Q	P	+	2	0	ANK2	114499056	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	7.487000	0.81328	2.689000	0.91719	0.655000	0.94253	CCA	.	.		0.443	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		A	114279607	C	A	114279607	3	1	255	1	0	0	0	0	1	0	0	0	621	594	21	3	10048	3	ANK2	4	114279607	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	184031	114279607	76874669	203	35548										
PRSS12	8492	hgsc.bcm.edu	37	chr4	119203115	119203115	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agtttggtgacactttttatCcaaggtacaaaggctgagac	10	7	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:119203115C>A	ENST00000296498.3	-	13	2886	c.2604G>T	c.(2602-2604)tgG>tgT	p.W868C	PRSS12_ENST00000510903.1_5'Flank|SNHG8_ENST00000384096.1_lincRNA	NM_003619.3	NP_003610.2	P56730	NETR_HUMAN	protease, serine, 12 (neurotrypsin, motopsin)	868	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				exocytosis (GO:0006887)|zymogen activation (GO:0031638)	axon (GO:0030424)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)|terminal bouton (GO:0043195)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(3)|kidney(1)|large_intestine(9)|lung(11)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	29						CACTTTTTATCCAAGGTACAA	0.448																																					p.W868C		Atlas-SNP	.											.	PRSS12	71	.	0			c.G2604T						.						94	96	96					4																	119203115		2203	4300	6503	SO:0001583	missense	8492	exon13			TTTTATCCAAGGT	AJ001531	CCDS3709.1	4q25-q26	2010-05-07			ENSG00000164099	ENSG00000164099		"Serine peptidases / Serine peptidases"	9477	protein-coding gene	gene with protein product		606709				9540828, 9245503	Standard	NM_003619		Approved	BSSP-3, MRT1	uc003ica.2	P56730	OTTHUMG00000161166	ENST00000296498.3:c.2604G>T	chr4.hg19:g.119203115C>A	ENSP00000296498:p.Trp868Cys	81.0	0.0		64.0	4.0	NM_003619	Q9UP16	Missense_Mutation	SNP	ENST00000296498.3	hg19	CCDS3709.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.676123	0.88445	.	.	ENSG00000164099	ENST00000296498	D	0.99121	-5.45	6.17	6.17	0.99709	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.85682	D	0.000000	D	0.99616	0.9860	H	0.97186	3.955	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97998	1.0358	10	0.87932	D	0	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	868	P56730	NETR_HUMAN	C	868	ENSP00000296498:W868C	ENSP00000296498:W868C	W	-	3	0	PRSS12	119422563	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.456000	0.80751	2.941000	0.99782	0.655000	0.94253	TGG	.	.		0.448	PRSS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256516.2			A	119203115	C	A	119203115	3	1	255	1	0	0	0	0	1	0	0	0	12627	856	30	3	27	3	PRSS12	4	119203115	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	4923508	119203115	71951161	204	35549										
SEC24D	9871	hgsc.bcm.edu	37	chr4	119666159	119666159	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tttttgagcttccctggtgcTtcagcagttggcaaggaaga	12	8	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:119666159T>C	ENST00000280551.6	-	14	2002	c.1764A>G	c.(1762-1764)gaA>gaG	p.E588E	SEC24D_ENST00000511481.1_Silent_p.E219E|SEC24D_ENST00000429811.2_Silent_p.E144E|SEC24D_ENST00000505134.1_5'UTR|SEC24D_ENST00000419654.2_Silent_p.E144E|SEC24D_ENST00000379735.5_Silent_p.E589E			O94855	SC24D_HUMAN	SEC24 family member D	588					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(13)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37						TCCCTGGTGCTTCAGCAGTTG	0.388																																					p.E588E		Atlas-SNP	.											.	SEC24D	96	.	0			c.A1764G						.						124	130	128					4																	119666159		2203	4300	6503	SO:0001819	synonymous_variant	9871	exon14			TGGTGCTTCAGCA	AB018298	CCDS3710.1	4q26	2013-10-21	2013-10-21		ENSG00000150961	ENSG00000150961			10706	protein-coding gene	gene with protein product		607186	"SEC24 (S. cerevisiae) related gene family, member D", "SEC24 family, member D (S. cerevisiae)"			9872452, 10075675	Standard	NM_014822		Approved	KIAA0755	uc003ici.4	O94855	OTTHUMG00000132957	ENST00000280551.6:c.1764A>G	chr4.hg19:g.119666159T>C		252.0	0.0		170.0	7.0	NM_014822	Q8IYI7	Silent	SNP	ENST00000280551.6	hg19	CCDS3710.1																																																																																			.	.		0.388	SEC24D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256514.4			C	119666159	T	C	119666159	2	2	255	1	0	0	0	0	0	0	0	1	14012	1606	56	2		2	SEC24D	4	119666159	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	463044	119666159	71488117	205	35550										
MYOZ2	51778	hgsc.bcm.edu	37	chr4	120079175	120079175	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gtttacttttgattaaatacAgcacagtattgctatgcaga	7	6	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:120079175A>G	ENST00000307128.5	+	4	459		c.e4-1			NM_016599.4	NP_057683.1			myozenin 2											endometrium(1)|large_intestine(6)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	16						GATTAAATACAGCACAGTATT	0.378																																					.		Atlas-SNP	.											.	MYOZ2	34	.	0			c.247-2A>G						.						101	102	102					4																	120079175		2203	4300	6503	SO:0001630	splice_region_variant	51778	exon4			AAATACAGCACAG	AF249873	CCDS3711.1	4q26-q27	2014-09-17	2002-01-07	2002-01-11	ENSG00000172399	ENSG00000172399			1330	protein-coding gene	gene with protein product		605602	"chromosome 4 open reading frame 5"	C4orf5		8619474, 9110174	Standard	NM_016599		Approved	CS-1	uc003icp.4	Q9NPC6	OTTHUMG00000132968	ENST00000307128.5:c.247-1A>G	chr4.hg19:g.120079175A>G		146.0	0.0		75.0	4.0	NM_016599		Splice_Site	SNP	ENST00000307128.5	hg19	CCDS3711.1	.	.	.	.	.	.	.	.	.	.	A	18.29	3.592099	0.66219	.	.	ENSG00000172399	ENST00000307128	.	.	.	5.7	5.7	0.88788	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9541	0.79871	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MYOZ2	120298623	1.000000	0.71417	0.997000	0.53966	0.806000	0.45545	5.215000	0.65241	2.163000	0.67991	0.533000	0.62120	.	.	.		0.378	MYOZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256526.2		Intron	G	120079175	A	G	120079175	5	3	255	1	0	0	0	0	0	0	1	0	10105	202	7	2	255	2	MYOZ2	4	120079175	Splice_Site	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	413016	120079175	71075101	206	35551										
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123280777	123280777	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gtccaattattatacatgacGacaattcctctgataaagat	5	8	1	3	rs368229897		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:123280777G>T	ENST00000264501.4	+	85	15074	c.14701G>T	c.(14701-14703)Gac>Tac	p.D4901Y	KIAA1109_ENST00000388738.3_Missense_Mutation_p.D4901Y			Q2LD37	K1109_HUMAN	KIAA1109	4901					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						TATACATGACGACAATTCCTC	0.348																																					p.D4901Y		Atlas-SNP	.											KIAA1109,colon,carcinoma,0,1	KIAA1109	424	.	0			c.G14701T						.	G	TYR/ASP	0,3686		0,0,1843	127	113	118		14701	5.9	1	4		118	1,8177		0,1,4088	no	missense	KIAA1109	NM_015312.3	160	0,1,5931	TT,TG,GG		0.0122,0.0,0.0084	possibly-damaging	4901/5006	123280777	1,11863	1843	4089	5932	SO:0001583	missense	84162	exon83			CATGACGACAATT	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.14701G>T	chr4.hg19:g.123280777G>T	ENSP00000264501:p.Asp4901Tyr	136.0	0.0		70.0	3.0	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.443890	0.83993	0.0	1.22E-4	ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000438707;ENST00000431755	T;T;T	0.48836	0.8;0.8;0.8	5.94	5.94	0.96194	Fragile site-associated protein, C-terminal (1);	0.334301	0.34879	N	0.003608	T	0.49949	0.1587	N	0.19112	0.55	0.80722	D	1	P;P	0.46512	0.693;0.879	P;P	0.52267	0.47;0.694	T	0.49799	-0.8901	10	0.56958	D	0.05	.	20.3731	0.98895	0.0:0.0:1.0:0.0	.	4900;4901	Q2LD37-4;Q2LD37	.;K1109_HUMAN	Y	4901;4901;1570;502	ENSP00000264501:D4901Y;ENSP00000373390:D4901Y;ENSP00000410874:D1570Y	ENSP00000264501:D4901Y	D	+	1	0	KIAA1109	123500227	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.271000	0.72569	2.829000	0.97493	0.650000	0.86243	GAC	.	.		0.348	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		T	123280777	G	T	123280777	3	4	255	1	0	0	0	0	1	0	0	0	8217	1058	37	1	15031	1	KIAA1109	4	123280777	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	3201602	123280777	67873499	207	35552										
FAT4	79633	hgsc.bcm.edu	37	chr4	126328107	126328107	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttcgcatcgacccagaatccGgagatctgatagcaaccagg	10	12	1	3	rs200789529		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:126328107G>T	ENST00000394329.3	+	3	5393	c.5380G>T	c.(5380-5382)Gga>Tga	p.G1794*	FAT4_ENST00000335110.5_Nonsense_Mutation_p.G92*	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	1794	Cadherin 17. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						CCCAGAATCCGGAGATCTGAT	0.473																																					p.G1794X		Atlas-SNP	.											FAT4_ENST00000394329,caecum,carcinoma,0,2	FAT4	1752	.	0			c.G5380T						.						130	123	125					4																	126328107		2203	4300	6503	SO:0001587	stop_gained	79633	exon3			GAATCCGGAGATC	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.5380G>T	chr4.hg19:g.126328107G>T	ENSP00000377862:p.Gly1794*	164.0	1.0		94.0	4.0	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Nonsense_Mutation	SNP	ENST00000394329.3	hg19	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	46	12.534214	0.99675	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	.	.	.	5.28	5.28	0.74379	.	0.000000	0.33610	U	0.004730	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	19.2767	0.94034	0.0:0.0:1.0:0.0	.	.	.	.	X	1794;92	.	ENSP00000335169:G92X	G	+	1	0	FAT4	126547557	1.000000	0.71417	0.990000	0.47175	0.597000	0.36814	9.365000	0.97139	2.622000	0.88805	0.585000	0.79938	GGA	.	.		0.473	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		T	126328107	G	T	126328107	4	4	255	1	0	0	0	0	0	1	0	0	5700	1117	39	1	5390	1	FAT4	4	126328107	Nonsense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	3047330	126328107	64826169	208	35553										
ELF2	1998	hgsc.bcm.edu	37	chr4	139981781	139981781	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tatccttgaactgatatacaAgcctctgtccttcaaccttt	4	12	2	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:139981781A>G	ENST00000394235.2	-	9	1320	c.818T>C	c.(817-819)cTt>cCt	p.L273P	ELF2_ENST00000265495.4_Missense_Mutation_p.L273P|ELF2_ENST00000515489.1_5'Flank|ELF2_ENST00000510408.1_Missense_Mutation_p.L213P|ELF2_ENST00000358635.3_Missense_Mutation_p.L225P|ELF2_ENST00000379550.1_Missense_Mutation_p.L285P|ELF2_ENST00000379549.2_Missense_Mutation_p.L196P	NM_001276458.1	NP_001263387.1			E74-like factor 2 (ets domain transcription factor)											endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	19	all_hematologic(180;0.162)					CTGATATACAAGCCTCTGTCC	0.368																																					p.H225P		Atlas-SNP	.											.	ELF2	43	.	0			c.A674C						.						105	106	105					4																	139981781		2203	4300	6503	SO:0001583	missense	1998	exon6			TATACAAGCCTCT	AF256222	CCDS3744.1, CCDS3745.1, CCDS64062.1, CCDS64063.1	4q28	2008-02-05			ENSG00000109381	ENSG00000109381			3317	protein-coding gene	gene with protein product						8756667	Standard	NM_201999		Approved	EU32, NERF, NERF-2, NERF-1A, NERF-1B	uc003ihm.2	Q15723	OTTHUMG00000133383	ENST00000394235.2:c.818T>C	chr4.hg19:g.139981781A>G	ENSP00000377782:p.Leu273Pro	154.0	0.0		96.0	4.0	NM_006874		Missense_Mutation	SNP	ENST00000394235.2	hg19	CCDS3744.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.707552	0.89018	.	.	ENSG00000109381	ENST00000358635;ENST00000394235;ENST00000379550;ENST00000265495;ENST00000379549;ENST00000540754;ENST00000510408;ENST00000420916;ENST00000512627	T;T;T;T;T;T;T;T	0.26957	1.7;1.7;1.7;1.7;1.7;1.7;1.7;1.7	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.60715	0.2290	M	0.91972	3.26	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.992;1.0;0.999;0.992	D;D;D;D;D	0.91635	0.995;0.945;0.994;0.999;0.945	T	0.70378	-0.4888	9	.	.	.	.	16.0102	0.80396	1.0:0.0:0.0:0.0	.	88;273;196;213;225	B7Z8R4;Q15723-1;E9PCX3;B7Z720;Q15723-3	.;.;.;.;.	P	225;273;285;273;196;88;213;196;184	ENSP00000351458:L225P;ENSP00000377782:L273P;ENSP00000368868:L285P;ENSP00000265495:L273P;ENSP00000368867:L196P;ENSP00000426997:L213P;ENSP00000397796:L196P;ENSP00000426087:L184P	.	L	-	2	0	ELF2	140201231	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.336000	0.96533	2.190000	0.69967	0.533000	0.62120	CTT	.	.		0.368	ELF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257233.2	NM_006874		G	139981781	A	G	139981781	3	3	255	1	0	0	0	0	1	0	0	0	5056	72	3	2	935	2	ELF2	4	139981781	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	13653674	139981781	51172495	209	35554										
USP38	84640	hgsc.bcm.edu	37	chr4	144135131	144135131	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	atccaacaacagctgccttcAtctgtgactcacttgtgaat	6	12	3	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:144135131A>G	ENST00000307017.4	+	9	2508	c.2002A>G	c.(2002-2004)Atc>Gtc	p.I668V	USP38_ENST00000510377.1_Missense_Mutation_p.I668V	NM_032557.5	NP_115946.2	Q8NB14	UBP38_HUMAN	ubiquitin specific peptidase 38	668	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	33	all_hematologic(180;0.158)					AGCTGCCTTCATCTGTGACTC	0.418																																					p.I668V		Atlas-SNP	.											USP38,NS,carcinoma,0,1	USP38	92	.	0			c.A2002G						.						141	154	150					4																	144135131		2203	4299	6502	SO:0001583	missense	84640	exon9			GCCTTCATCTGTG	AF211481	CCDS3758.1	4q31.1	2008-02-05	2005-08-08		ENSG00000170185	ENSG00000170185		"Ubiquitin-specific peptidases"	20067	protein-coding gene	gene with protein product			"ubiquitin specific protease 38"			12838346	Standard	NM_032557		Approved	KIAA1891, HP43.8KD	uc003ijb.3	Q8NB14	OTTHUMG00000161420	ENST00000307017.4:c.2002A>G	chr4.hg19:g.144135131A>G	ENSP00000303434:p.Ile668Val	92.0	1.0		66.0	3.0	NM_032557	B3KX93|Q3ZCV1|Q8NDF5|Q96DK6|Q96PZ6|Q9BY55	Missense_Mutation	SNP	ENST00000307017.4	hg19	CCDS3758.1	.	.	.	.	.	.	.	.	.	.	A	3.162	-0.171904	0.06421	.	.	ENSG00000170185	ENST00000510377;ENST00000307017	T;T	0.07567	3.18;3.19	5.52	3.71	0.42584	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.432949	0.23521	N	0.047300	T	0.02230	0.0069	N	0.00621	-1.32	0.20403	N	0.999903	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42716	-0.9435	10	0.27785	T	0.31	-8.4565	6.1744	0.20434	0.1693:0.0:0.6825:0.1482	.	668;668	Q8NB14;Q3ZCV1	UBP38_HUMAN;.	V	668	ENSP00000427647:I668V;ENSP00000303434:I668V	ENSP00000303434:I668V	I	+	1	0	USP38	144354581	1.000000	0.71417	0.998000	0.56505	0.960000	0.62799	3.018000	0.49625	0.602000	0.29896	0.477000	0.44152	ATC	.	.		0.418	USP38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364869.1	NM_032557		G	144135131	A	G	144135131	3	3	255	1	0	0	0	0	1	0	0	0	17084	217	8	2	2036	2	USP38	4	144135131	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	4153350	144135131	47019145	210	35555										
MMAA	166785	hgsc.bcm.edu	37	chr4	146575291	146575291	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	acgttcacaagtctggaaacCaaaggtaagcttgcttgcat	9	9	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:146575291C>A	ENST00000281317.5	+	6	2175	c.965C>A	c.(964-966)cCa>cAa	p.P322Q	MMAA_ENST00000541599.1_Missense_Mutation_p.P41Q	NM_172250.2	NP_758454.1	Q8IVH4	MMAA_HUMAN	methylmalonic aciduria (cobalamin deficiency) cblA type	322					cellular lipid metabolic process (GO:0044255)|cobalamin biosynthetic process (GO:0009236)|cobalamin metabolic process (GO:0009235)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	mitochondrial matrix (GO:0005759)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)	17	all_hematologic(180;0.151)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GTCTGGAAACCAAAGGTAAGC	0.398																																					p.P322Q		Atlas-SNP	.											.	MMAA	46	.	0			c.C965A						.						125	116	119					4																	146575291		2203	4300	6503	SO:0001583	missense	166785	exon6			GGAAACCAAAGGT	AF524841	CCDS3766.1	4q31.1	2011-05-12	2005-07-11			ENSG00000151611			18871	protein-coding gene	gene with protein product		607481	"methylmalonic aciduria (cobalamin deficiency) type A"			12438653	Standard	NM_172250		Approved	cblA	uc003ikh.4	Q8IVH4		ENST00000281317.5:c.965C>A	chr4.hg19:g.146575291C>A	ENSP00000281317:p.Pro322Gln	94.0	0.0		76.0	4.0	NM_172250	B3KX40|Q495G7	Missense_Mutation	SNP	ENST00000281317.5	hg19	CCDS3766.1	.	.	.	.	.	.	.	.	.	.	C	32	5.176237	0.94846	.	.	ENSG00000151611	ENST00000281317;ENST00000537246;ENST00000541599	D;D	0.92805	-3.11;-3.11	5.49	5.49	0.81192	.	0.050420	0.85682	D	0.000000	D	0.97195	0.9083	M	0.92412	3.305	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97864	1.0282	10	0.87932	D	0	-14.0752	19.3608	0.94436	0.0:1.0:0.0:0.0	.	322	Q8IVH4	MMAA_HUMAN	Q	322;322;41	ENSP00000281317:P322Q;ENSP00000442284:P41Q	ENSP00000281317:P322Q	P	+	2	0	MMAA	146794741	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.456000	0.80751	2.572000	0.86782	0.650000	0.86243	CCA	.	.		0.398	MMAA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364668.2			A	146575291	C	A	146575291	3	1	255	1	0	0	0	0	1	0	0	0	9648	594	21	3	983	3	MMAA	4	146575291	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	2440160	146575291	44578985	211	35556										
ZNF827	152485	hgsc.bcm.edu	37	chr4	146744660	146744660	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	atggtgattgtctaaatgtgTcttctgaaaagaaagggctg	12	4	3	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:146744660T>C	ENST00000508784.1	-	8	2524	c.2297A>G	c.(2296-2298)gAc>gGc	p.D766G	ZNF827_ENST00000379448.4_Missense_Mutation_p.D766G|ZNF827_ENST00000513320.1_Missense_Mutation_p.D416G			Q17R98	ZN827_HUMAN	zinc finger protein 827	766					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	all_hematologic(180;0.151)					TCTAAATGTGTCTTCTGAAAA	0.443																																					p.D766G		Atlas-SNP	.											.	ZNF827	102	.	0			c.A2297G						.						128	131	130					4																	146744660		2203	4300	6503	SO:0001583	missense	152485	exon8			AATGTGTCTTCTG	AK091130	CCDS34072.1	4q31.22	2013-01-08			ENSG00000151612	ENSG00000151612		"Zinc fingers, C2H2-type"	27193	protein-coding gene	gene with protein product						12477932	Standard	NM_178835		Approved		uc003ikm.3	Q17R98	OTTHUMG00000161362	ENST00000508784.1:c.2297A>G	chr4.hg19:g.146744660T>C	ENSP00000421863:p.Asp766Gly	99.0	0.0		83.0	4.0	NM_178835	B7ZL52|Q7Z4S7|Q8N279	Missense_Mutation	SNP	ENST00000508784.1	hg19		.	.	.	.	.	.	.	.	.	.	T	17.27	3.346311	0.61073	.	.	ENSG00000151612	ENST00000508784;ENST00000513320;ENST00000379448;ENST00000281318;ENST00000440280	T;T;T	0.08008	3.18;3.14;3.22	5.52	5.52	0.82312	.	0.135755	0.64402	D	0.000003	T	0.16128	0.0388	N	0.24115	0.695	0.47819	D	0.999528	P;D;P	0.63880	0.906;0.993;0.906	B;D;P	0.68192	0.418;0.956;0.52	T	0.02232	-1.1191	10	0.72032	D	0.01	-20.9382	13.1743	0.59617	0.0:0.0:0.0:1.0	.	416;766;766	G5E9Z1;Q17R98;Q17R98-2	.;ZN827_HUMAN;.	G	766;416;766;765;416	ENSP00000421863:D766G;ENSP00000423130:D416G;ENSP00000368761:D766G	ENSP00000281318:D765G	D	-	2	0	ZNF827	146964110	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	4.529000	0.60588	2.096000	0.63516	0.397000	0.26171	GAC	.	.		0.443	ZNF827-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000364654.2	NM_178835		C	146744660	T	C	146744660	3	2	255	1	0	0	0	0	1	0	0	0	18195	1667	58	2	960	2	ZNF827	4	146744660	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	169369	146744660	44409616	212	35557										
PET112L	5188	hgsc.bcm.edu	37	chr4	152679945	152679945	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggcaaagttccaggtagagaTgcatcaaaaaaagaaaccaa	9	7	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:152679945T>C	ENST00000515812.1	-	2	322	c.306A>G	c.(304-306)gcA>gcG	p.A102A	PET112_ENST00000263985.6_Silent_p.A102A|PET112_ENST00000512306.1_Silent_p.A102A|PET112_ENST00000508611.1_Silent_p.A102A																breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	23						CAGGTAGAGATGCATCAAAAA	0.323																																					p.A102A		Atlas-SNP	.											.	PET112	43	.	0			c.A306G						.						89	95	93					4																	152679945		2203	4300	6503	SO:0001819	synonymous_variant	5188	exon2			TAGAGATGCATCA																												ENST00000515812.1:c.306A>G	chr4.hg19:g.152679945T>C		100.0	0.0		89.0	4.0	NM_004564		Silent	SNP	ENST00000515812.1	hg19																																																																																				.	.		0.323	PET112-002	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365672.1			C	152679945	T	C	152679945	2	2	255	1	0	0	0	0	0	0	0	1	11743	1451	51	2		2	PET112L	4	152679945	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	5935285	152679945	38474331	213	35558										
KIAA0922	23240	hgsc.bcm.edu	37	chr4	154524546	154524546	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	caagacagaggcaaaatgctAgctcctcttcacagcaaaac	7	12	2	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:154524546A>G	ENST00000409663.3	+	24	2780	c.2728A>G	c.(2728-2730)Agc>Ggc	p.S910G	KIAA0922_ENST00000440693.1_Missense_Mutation_p.S827G|KIAA0922_ENST00000409959.3_Missense_Mutation_p.S911G	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	910	Poly-Ser.					integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(16)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	63	all_hematologic(180;0.093)	Renal(120;0.118)				GCAAAATGCTAGCTCCTCTTC	0.438																																					p.S911G		Atlas-SNP	.											.	KIAA0922	214	.	0			c.A2731G						.						168	154	159					4																	154524546		2203	4300	6503	SO:0001583	missense	23240	exon24			AATGCTAGCTCCT	AK096538	CCDS3783.2, CCDS47148.1	4q31.3	2008-02-05			ENSG00000121210	ENSG00000121210			29146	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_015196		Approved	DKFZp586H1322, TMEM131L	uc010ipp.3	A2VDJ0	OTTHUMG00000153244	ENST00000409663.3:c.2728A>G	chr4.hg19:g.154524546A>G	ENSP00000386574:p.Ser910Gly	247.0	0.0		171.0	147.0	NM_001131007	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Missense_Mutation	SNP	ENST00000409663.3	hg19	CCDS3783.2	.	.	.	.	.	.	.	.	.	.	A	10.73	1.433805	0.25813	.	.	ENSG00000121210	ENST00000409663;ENST00000440693;ENST00000409959;ENST00000240487	T;T;T;T	0.19250	2.42;2.16;2.42;2.16	6.17	0.976	0.19727	.	0.397804	0.34853	N	0.003640	T	0.13072	0.0317	L	0.36672	1.1	0.09310	N	1	B;B;B	0.15719	0.014;0.002;0.001	B;B;B	0.12837	0.008;0.006;0.002	T	0.24012	-1.0172	10	0.26408	T	0.33	-3.2992	5.69	0.17825	0.6965:0.0:0.1887:0.1148	.	827;911;910	A2VDJ0-3;A2VDJ0-5;A2VDJ0	.;.;T131L_HUMAN	G	910;827;911;688	ENSP00000386574:S910G;ENSP00000409663:S827G;ENSP00000386787:S911G;ENSP00000240487:S688G	ENSP00000240487:S688G	S	+	1	0	KIAA0922	154743996	0.986000	0.35501	0.018000	0.16275	0.871000	0.50021	2.084000	0.41625	-0.033000	0.13736	0.533000	0.62120	AGC	.	.		0.438	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196		G	154524546	A	G	154524546	3	3	255	1	0	0	0	0	1	0	0	0	8210	420	15	2	2825	2	KIAA0922	4	154524546	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	1844601	154524546	36629730	214	35559										
KLHL2	11275	hgsc.bcm.edu	37	chr4	166226800	166226800	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccaagcaccaaaggctatccGgagtgtggaatgctatgact	11	10	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:166226800G>T	ENST00000226725.6	+	9	1221	c.962G>T	c.(961-963)cGg>cTg	p.R321L	KLHL2_ENST00000514860.1_Missense_Mutation_p.R325L|KLHL2_ENST00000421009.2_Missense_Mutation_p.R224L|KLHL2_ENST00000509028.1_Intron|KLHL2_ENST00000506761.1_Missense_Mutation_p.R155L|KLHL2_ENST00000538127.1_Missense_Mutation_p.R233L	NM_007246.3	NP_009177.3	O95198	KLHL2_HUMAN	kelch-like family member 2	321					protein ubiquitination (GO:0016567)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)	actin binding (GO:0003779)			endometrium(3)|large_intestine(5)|lung(4)|prostate(1)|urinary_tract(1)	14	all_hematologic(180;0.221)			GBM - Glioblastoma multiforme(119;2.94e-27)|COAD - Colon adenocarcinoma(41;1.4e-05)|Kidney(143;4.95e-05)|KIRC - Kidney renal clear cell carcinoma(143;0.000927)		AAGGCTATCCGGAGTGTGGAA	0.458																																					p.R325L		Atlas-SNP	.											.	KLHL2	42	.	0			c.G974T						.						173	166	168					4																	166226800		2203	4300	6503	SO:0001583	missense	11275	exon9			CTATCCGGAGTGT	AF059569	CCDS34094.1, CCDS54815.1, CCDS54816.1	4q21.2	2013-01-30	2013-01-30		ENSG00000109466	ENSG00000109466		"Kelch-like", "BTB/POZ domain containing"	6353	protein-coding gene	gene with protein product	"mayven"	605774	"kelch (Drosophila)-like 2 (Mayven)", "kelch-like 2, Mayven (Drosophila)"			10397770, 16035103	Standard	NM_007246		Approved	MAV	uc011cjm.2	O95198	OTTHUMG00000161294	ENST00000226725.6:c.962G>T	chr4.hg19:g.166226800G>T	ENSP00000226725:p.Arg321Leu	152.0	0.0		99.0	4.0	NM_001161521	A6NCM7|B2RD18|B4DFH7|F5H6M3|Q8N484|Q8TBH5	Missense_Mutation	SNP	ENST00000226725.6	hg19	CCDS34094.1	.	.	.	.	.	.	.	.	.	.	G	34	5.294774	0.95546	.	.	ENSG00000109466	ENST00000226725;ENST00000514860;ENST00000538127;ENST00000421009;ENST00000506761	T;T;T;T;T	0.78481	-1.18;-1.18;-1.18;-1.18;-1.18	5.6	5.6	0.85130	Galactose oxidase, beta-propeller (1);	0.058050	0.64402	D	0.000001	D	0.83774	0.5327	M	0.68317	2.08	0.80722	D	1	D;D	0.54601	0.967;0.967	P;P	0.52793	0.709;0.709	D	0.83359	0.0001	10	0.44086	T	0.13	.	19.6107	0.95606	0.0:0.0:1.0:0.0	.	325;321	B4DFH7;O95198	.;KLHL2_HUMAN	L	321;325;233;224;155	ENSP00000226725:R321L;ENSP00000424198:R325L;ENSP00000437526:R233L;ENSP00000408974:R224L;ENSP00000424108:R155L	ENSP00000226725:R321L	R	+	2	0	KLHL2	166446250	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.869000	0.99810	2.648000	0.89879	0.655000	0.94253	CGG	.	.		0.458	KLHL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364439.1			T	166226800	G	T	166226800	3	4	255	1	0	0	0	0	1	0	0	0	8383	1116	39	1	1038	1	KLHL2	4	166226800	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	11702254	166226800	24927476	215	35560										
AADAT	51166	hgsc.bcm.edu	37	chr4	170999725	170999725	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	atctccaggattaatgatcaTttcaaacacctaacaaaaga	4	9	3	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:170999725T>C	ENST00000337664.4	-	4	655	c.379A>G	c.(379-381)Atg>Gtg	p.M127V	AADAT_ENST00000353187.2_Missense_Mutation_p.M127V|AADAT_ENST00000509167.1_Missense_Mutation_p.M131V|AADAT_ENST00000515480.1_Missense_Mutation_p.M127V	NM_016228.3	NP_057312.1	Q8N5Z0	AADAT_HUMAN	aminoadipate aminotransferase	127					2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|kynurenine metabolic process (GO:0070189)|L-kynurenine metabolic process (GO:0097052)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)|tryptophan catabolic process to kynurenine (GO:0019441)	mitochondrial matrix (GO:0005759)	2-aminoadipate transaminase activity (GO:0047536)|kynurenine-oxoglutarate transaminase activity (GO:0016212)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|pancreas(1)|stomach(1)	11		Prostate(90;0.00601)|Renal(120;0.0183)|all_neural(102;0.122)|Melanoma(52;0.17)		GBM - Glioblastoma multiforme(119;0.0355)|LUSC - Lung squamous cell carcinoma(193;0.118)		TTAATGATCATTTCAAACACC	0.373																																					p.M127V		Atlas-SNP	.											.	AADAT	28	.	0			c.A379G						.						105	102	103					4																	170999725		2203	4300	6503	SO:0001583	missense	51166	exon5			TGATCATTTCAAA	AF097994	CCDS3814.1, CCDS75209.1	4q33	2010-12-09			ENSG00000109576	ENSG00000109576	2.6.1.39		17929	protein-coding gene	gene with protein product	"kynurenine aminotransferase II", "L kynurenine/alpha aminoadipate aminotransferase"	611754				12126930, 10441733	Standard	NM_182662		Approved	KATII, KAT2	uc003isr.3	Q8N5Z0	OTTHUMG00000160912	ENST00000337664.4:c.379A>G	chr4.hg19:g.170999725T>C	ENSP00000336808:p.Met127Val	102.0	0.0		67.0	4.0	NM_182662	B3KP84|Q9UL02	Missense_Mutation	SNP	ENST00000337664.4	hg19	CCDS3814.1	.	.	.	.	.	.	.	.	.	.	T	16.91	3.254043	0.59212	.	.	ENSG00000109576	ENST00000337664;ENST00000515480;ENST00000509167;ENST00000353187;ENST00000510340;ENST00000507375;ENST00000502392	D;D;D;D;D;D;D	0.89875	-2.58;-2.58;-2.58;-2.58;-2.58;-2.58;-2.58	5.42	5.42	0.78866	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.84678	0.5525	L	0.42744	1.35	0.58432	D	0.999998	P;P	0.47302	0.554;0.893	B;B	0.42593	0.272;0.392	T	0.82583	-0.0385	10	0.10636	T	0.68	-26.7196	15.7937	0.78388	0.0:0.0:0.0:1.0	.	131;127	Q8N5Z0-2;Q8N5Z0	.;AADAT_HUMAN	V	127;127;131;127;118;127;127	ENSP00000336808:M127V;ENSP00000423341:M127V;ENSP00000423190:M131V;ENSP00000226840:M127V;ENSP00000425067:M118V;ENSP00000421389:M127V;ENSP00000423843:M127V	ENSP00000336808:M127V	M	-	1	0	AADAT	171236300	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	7.211000	0.77933	2.188000	0.69820	0.528000	0.53228	ATG	.	.		0.373	AADAT-004	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000362952.1	NM_016228		C	170999725	T	C	170999725	3	2	255	1	0	0	0	0	1	0	0	0	14	1493	52	2	938	2	AADAT	4	170999725	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	4772925	170999725	20154551	216	35561										
HPGD	3248	hgsc.bcm.edu	37	chr4	175443106	175443106	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctgtcttacctctcagttgtTgctggtcagccacatcgcac	8	14	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:175443106T>C	ENST00000296522.6	-	2	652	c.206A>G	c.(205-207)cAa>cGa	p.Q69R	HPGD_ENST00000422112.2_Missense_Mutation_p.Q69R|HPGD_ENST00000541923.1_5'UTR|RP11-440I14.2_ENST00000515178.1_lincRNA|HPGD_ENST00000296521.7_Missense_Mutation_p.Q69R|HPGD_ENST00000542498.1_Missense_Mutation_p.Q69R|HPGD_ENST00000510901.1_5'UTR|HPGD_ENST00000504433.1_Missense_Mutation_p.Q69R	NM_000860.5|NM_001145816.2|NM_001256301.1|NM_001256307.1	NP_000851.2|NP_001139288.1|NP_001243230.1|NP_001243236.1	P15428	PGDH_HUMAN	hydroxyprostaglandin dehydrogenase 15-(NAD)	69					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|ductus arteriosus closure (GO:0097070)|female pregnancy (GO:0007565)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|negative regulation of cell cycle (GO:0045786)|ovulation (GO:0030728)|parturition (GO:0007567)|prostaglandin metabolic process (GO:0006693)|small molecule metabolic process (GO:0044281)|thrombin receptor signaling pathway (GO:0070493)|transforming growth factor beta receptor signaling pathway (GO:0007179)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	15-hydroxyprostaglandin dehydrogenase (NAD+) activity (GO:0016404)|catalytic activity (GO:0003824)|NAD binding (GO:0051287)|NAD+ binding (GO:0070403)|prostaglandin E receptor activity (GO:0004957)|protein homodimerization activity (GO:0042803)			kidney(1)|lung(3)|prostate(3)	7		Prostate(90;0.00763)|Melanoma(52;0.0179)|Renal(120;0.0376)|Breast(14;0.0991)|all_hematologic(60;0.124)|all_neural(102;0.196)		all cancers(43;2.6e-18)|Epithelial(43;4.19e-16)|OV - Ovarian serous cystadenocarcinoma(60;5.23e-09)|GBM - Glioblastoma multiforme(59;0.00176)|STAD - Stomach adenocarcinoma(60;0.00299)|LUSC - Lung squamous cell carcinoma(193;0.0253)		TCTCAGTTGTTGCTGGTCAGC	0.537																																					p.Q69R		Atlas-SNP	.											.	HPGD	19	.	0			c.A206G						.						175	175	175					4																	175443106		2203	4300	6503	SO:0001583	missense	3248	exon2			AGTTGTTGCTGGT		CCDS3821.1, CCDS54821.1, CCDS58933.1, CCDS58934.1, CCDS58935.1	4q34-q35	2011-09-14			ENSG00000164120	ENSG00000164120	1.1.1.141	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	5154	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 36C, member 1"	601688				19027726	Standard	NM_000860		Approved	SDR36C1	uc003itu.3	P15428	OTTHUMG00000160772	ENST00000296522.6:c.206A>G	chr4.hg19:g.175443106T>C	ENSP00000296522:p.Gln69Arg	85.0	0.0		57.0	4.0	NM_000860	B4DTA4|B4DU74|B4DV57|D3DP43|E7EV11|O00749|Q06F08|Q12998	Missense_Mutation	SNP	ENST00000296522.6	hg19	CCDS3821.1	.	.	.	.	.	.	.	.	.	.	T	12.99	2.103285	0.37145	.	.	ENSG00000164120	ENST00000296522;ENST00000296521;ENST00000422112;ENST00000542498;ENST00000504433	T;D;T;D;D	0.87729	-1.35;-1.76;-1.35;-2.29;-2.29	5.39	2.86	0.33363	NAD(P)-binding domain (1);	0.454373	0.27744	N	0.018032	T	0.74619	0.3740	N	0.16233	0.39	0.26141	N	0.980274	B;B;B;B;B;B	0.13145	0.001;0.0;0.007;0.0;0.0;0.0	B;B;B;B;B;B	0.11329	0.006;0.0;0.005;0.0;0.0;0.001	T	0.62163	-0.6912	10	0.40728	T	0.16	.	7.3943	0.26927	0.0:0.077:0.144:0.779	.	69;69;69;69;69;69	E7EV11;O00749;E9PBZ2;Q12998;B4DV57;P15428	.;.;.;.;.;PGDH_HUMAN	R	69	ENSP00000296522:Q69R;ENSP00000296521:Q69R;ENSP00000398720:Q69R;ENSP00000443644:Q69R;ENSP00000420892:Q69R	ENSP00000296521:Q69R	Q	-	2	0	HPGD	175679681	0.997000	0.39634	0.811000	0.32455	0.891000	0.51852	3.014000	0.49590	0.326000	0.23384	0.379000	0.24179	CAA	.	.		0.537	HPGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362228.3			C	175443106	T	C	175443106	3	2	255	1	0	0	0	0	1	0	0	0	7343	1812	63	2	618	2	HPGD	4	175443106	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	4443381	175443106	15711170	217	35562										
SLC12A7	10723	hgsc.bcm.edu	37	chr5	1088466	1088466	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cgcactcatggaaatggcggTcagcattgtctgcaaaaaga	11	9	3	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:1088466T>C	ENST00000264930.5	-	5	542	c.499A>G	c.(499-501)Acc>Gcc	p.T167A		NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	167					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	GAAATGGCGGTCAGCATTGTC	0.582																																					p.T167A		Atlas-SNP	.											.	SLC12A7	97	.	0			c.A499G						.						58	51	54					5																	1088466		2183	4290	6473	SO:0001583	missense	10723	exon5			TGGCGGTCAGCAT	AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504		"Solute carriers"	10915	protein-coding gene	gene with protein product		604879				10347194	Standard	NM_006598		Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.499A>G	chr5.hg19:g.1088466T>C	ENSP00000264930:p.Thr167Ala	100.0	0.0		122.0	5.0	NM_006598	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Missense_Mutation	SNP	ENST00000264930.5	hg19	CCDS34129.1	.	.	.	.	.	.	.	.	.	.	T	16.03	3.005794	0.54254	.	.	ENSG00000113504	ENST00000264930;ENST00000343658	D	0.98807	-5.15	3.48	3.48	0.39840	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.99251	0.9739	H	0.94658	3.565	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.99110	1.0846	10	0.87932	D	0	.	11.0972	0.48152	0.0:0.0:0.0:1.0	.	167	Q9Y666	S12A7_HUMAN	A	167	ENSP00000264930:T167A	ENSP00000264930:T167A	T	-	1	0	SLC12A7	1141466	1.000000	0.71417	0.955000	0.39395	0.238000	0.25445	7.198000	0.77823	1.363000	0.46019	0.379000	0.24179	ACC	.	.		0.582	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598		C	1088466	T	C	1088466	3	2	255	1	0	0	0	0	1	0	0	0	14403	1667	58	2	2832	2	SLC12A7	5	1088466	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10		1088466	179826794	218	35563										
KIAA0947	23379	hgsc.bcm.edu	37	chr5	5489287	5489287	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccatggggtatacagttagcAgccgtgtatgctctttgtga	12	8	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:5489287A>G	ENST00000296564.7	+	19	6867	c.6645A>G	c.(6643-6645)gcA>gcG	p.A2215A		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		2215					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						TACAGTTAGCAGCCGTGTATG	0.413																																					p.A2215A		Atlas-SNP	.											.	KIAA0947	301	.	0			c.A6645G						.						53	53	53					5																	5489287		1857	4108	5965	SO:0001819	synonymous_variant	23379	exon19			GTTAGCAGCCGTG																												ENST00000296564.7:c.6645A>G	chr5.hg19:g.5489287A>G		76.0	0.0		83.0	4.0	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Silent	SNP	ENST00000296564.7	hg19	CCDS47187.1																																																																																			.	.		0.413	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1			G	5489287	A	G	5489287	2	3	255	1	0	0	0	0	0	0	0	1	8211	175	7	2		2	KIAA0947	5	5489287	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	4400821	5489287	175425973	219	35564										
RICTOR	253260	hgsc.bcm.edu	37	chr5	38950476	38950476	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cccataaatgaagtctctaaTtgtaatgttttctgtacagt	6	7	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:38950476T>A	ENST00000357387.3	-	31	3504	c.3474A>T	c.(3472-3474)caA>caT	p.Q1158H	RICTOR_ENST00000296782.5_Missense_Mutation_p.Q1158H	NM_152756.3	NP_689969.2			RPTOR independent companion of MTOR, complex 2											NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|prostate(3)|skin(5)	75	all_lung(31;0.000396)					AAGTCTCTAATTGTAATGTTT	0.373																																					p.Q1158H		Atlas-SNP	.											.	RICTOR	182	.	0			c.A3474T						.						168	171	170					5																	38950476		2203	4300	6503	SO:0001583	missense	253260	exon31			CTCTAATTGTAAT		CCDS34148.1, CCDS68861.1	5p13.1	2009-07-09			ENSG00000164327	ENSG00000164327			28611	protein-coding gene	gene with protein product	"rapamycin-insensitive companion of mTOR", "pianissimo"	609022				12477932	Standard	XM_005248278		Approved	MGC39830, AVO3, PIA, KIAA1999	uc003jlp.2	Q6R327	OTTHUMG00000162037	ENST00000357387.3:c.3474A>T	chr5.hg19:g.38950476T>A	ENSP00000349959:p.Gln1158His	309.0	1.0		427.0	190.0	NM_152756		Missense_Mutation	SNP	ENST00000357387.3	hg19	CCDS34148.1	.	.	.	.	.	.	.	.	.	.	T	11.42	1.634307	0.29068	.	.	ENSG00000164327	ENST00000357387;ENST00000296782	T;T	0.44881	0.91;0.91	5.86	-0.886	0.10590	.	0.193901	0.53938	D	0.000058	T	0.19725	0.0474	N	0.08118	0	0.22684	N	0.99886	B;B	0.28584	0.216;0.216	B;B	0.31337	0.128;0.128	T	0.17440	-1.0369	10	0.87932	D	0	-15.0279	6.2372	0.20770	0.0:0.3467:0.2363:0.417	.	1158;1158	Q6R327;Q6R327-3	RICTR_HUMAN;.	H	1158	ENSP00000349959:Q1158H;ENSP00000296782:Q1158H	ENSP00000296782:Q1158H	Q	-	3	2	RICTOR	38986233	0.995000	0.38212	0.994000	0.49952	0.994000	0.84299	0.143000	0.16115	-0.010000	0.14271	0.528000	0.53228	CAA	.	.		0.373	RICTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366985.1	NM_152756		A	38950476	T	A	38950476	3	1	255	1	0	0	0	0	1	0	0	0	13373	1490	52	4	1684	4	RICTOR	5	38950476	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	33461189	38950476	141964784	220	35565										
ITGA2	3673	hgsc.bcm.edu	37	chr5	52376343	52376343	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	attttattctctacataggtAacaacaggaagtgttccagt	7	7	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:52376343A>G	ENST00000296585.5	+	25	3074	c.2931A>G	c.(2929-2931)gtA>gtG	p.V977V		NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	977					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular response to hormone stimulus (GO:0032870)|collagen-activated signaling pathway (GO:0038065)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|hepatocyte differentiation (GO:0070365)|hypotonic response (GO:0006971)|integrin-mediated signaling pathway (GO:0007229)|mammary gland development (GO:0030879)|mesodermal cell differentiation (GO:0048333)|organ morphogenesis (GO:0009887)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell projection organization (GO:0031346)|positive regulation of collagen binding (GO:0033343)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA binding (GO:0043388)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|response to amine (GO:0014075)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to muscle activity (GO:0014850)|response to organic cyclic compound (GO:0014070)|skin morphogenesis (GO:0043589)|substrate-dependent cell migration (GO:0006929)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	axon terminus (GO:0043679)|basal part of cell (GO:0045178)|cell outer membrane (GO:0009279)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin alpha2-beta1 complex (GO:0034666)|integrin complex (GO:0008305)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)			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)				CTACATAGGTAACAACAGGAA	0.438																																					p.V977V		Atlas-SNP	.											.	ITGA2	211	.	0			c.A2931G						.						145	135	139					5																	52376343		2203	4300	6503	SO:0001819	synonymous_variant	3673	exon25			ATAGGTAACAACA		CCDS3957.1	5q11.2	2010-03-23			ENSG00000164171	ENSG00000164171		"CD molecules", "Integrins"	6137	protein-coding gene	gene with protein product		192974		CD49B			Standard	NM_002203		Approved	CD49b	uc003joy.3	P17301	OTTHUMG00000131165	ENST00000296585.5:c.2931A>G	chr5.hg19:g.52376343A>G		92.0	0.0		99.0	4.0	NM_002203	Q14595	Silent	SNP	ENST00000296585.5	hg19	CCDS3957.1																																																																																			.	.		0.438	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203		G	52376343	A	G	52376343	2	3	255	1	0	0	0	0	0	0	0	1	7884	349	13	2		2	ITGA2	5	52376343	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	13425867	52376343	128538917	221	35566										
IL31RA	133396	hgsc.bcm.edu	37	chr5	55164685	55164685	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gaaaaatttaacctgcacttGgagtccaggaaaggaaacca	9	8	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:55164685G>A	ENST00000447346.2	+	3	286	c.221G>A	c.(220-222)tGg>tAg	p.W74*	IL31RA_ENST00000359040.5_Nonsense_Mutation_p.W74*|IL31RA_ENST00000297015.3_Intron|IL31RA_ENST00000396836.2_Nonsense_Mutation_p.W74*|IL31RA_ENST00000354961.4_Nonsense_Mutation_p.W55*|IL31RA_ENST00000396834.1_Nonsense_Mutation_p.W55*|IL31RA_ENST00000490985.1_5'UTR	NM_001242636.1|NM_139017.5	NP_001229565.1|NP_620586.3	Q8NI17	IL31R_HUMAN	interleukin 31 receptor A	42	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|homeostatic process (GO:0042592)|JAK-STAT cascade (GO:0007259)|macrophage differentiation (GO:0030225)|MAPK cascade (GO:0000165)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of macrophage activation (GO:0043031)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cytokine binding (GO:0019955)|cytokine receptor activity (GO:0004896)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)	21		Lung NSC(810;6.93e-05)|Prostate(74;0.00741)|Breast(144;0.0544)|Ovarian(174;0.223)				ACCTGCACTTGGAGTCCAGGA	0.418																																					p.W74X		Atlas-SNP	.											.	IL31RA	84	.	0			c.G221A						.						104	108	106					5																	55164685		2203	4300	6503	SO:0001587	stop_gained	133396	exon3			GCACTTGGAGTCC	AY499339	CCDS3970.2, CCDS56365.1, CCDS56366.1, CCDS56367.1, CCDS75244.1, CCDS75245.1	5q11.2	2013-02-11			ENSG00000164509	ENSG00000164509		"Interleukins and interleukin receptors", "Fibronectin type III domain containing"	18969	protein-coding gene	gene with protein product		609510				15184896, 11877449	Standard	NM_139017		Approved	CRL3, GLM-R, CRL, Glmr, IL-31RA	uc003jql.3	Q8NI17	OTTHUMG00000097045	ENST00000447346.2:c.221G>A	chr5.hg19:g.55164685G>A	ENSP00000415900:p.Trp74*	66.0	0.0		81.0	4.0	NM_001242637	A6NIF8|Q2TBA1|Q6EBC3|Q6EBC4|Q6EBC5|Q6EBC6|Q6UWL8|Q8WYJ0	Nonsense_Mutation	SNP	ENST00000447346.2	hg19	CCDS3970.2	.	.	.	.	.	.	.	.	.	.	G	22.5	4.304348	0.81136	.	.	ENSG00000164509	ENST00000396836;ENST00000396834;ENST00000447346;ENST00000359040;ENST00000354961	.	.	.	3.95	3.95	0.45737	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.8596	11.6914	0.51519	0.0:0.0:1.0:0.0	.	.	.	.	X	74;55;74;74;55	.	ENSP00000347047:W55X	W	+	2	0	IL31RA	55200442	1.000000	0.71417	1.000000	0.80357	0.845000	0.48019	4.519000	0.60517	2.201000	0.70794	0.655000	0.94253	TGG	.	.		0.418	IL31RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214148.1	NM_139017		A	55164685	G	A	55164685	4	1	255	1	0	0	0	0	0	1	0	0	7700	1357	47	3	231	3	IL31RA	5	55164685	Nonsense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	2788342	55164685	125750575	222	35567										
MAP1B	4131	hgsc.bcm.edu	37	chr5	71492350	71492350	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gacaaggctgcagaggctggTggtgccgaggagcagtatgg	19	7	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:71492350T>C	ENST00000296755.7	+	5	3466	c.3168T>C	c.(3166-3168)ggT>ggC	p.G1056G		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1056					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		CAGAGGCTGGTGGTGCCGAGG	0.517																																					p.G1056G	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.T3168C						.						111	114	113					5																	71492350		2203	4300	6503	SO:0001819	synonymous_variant	4131	exon5			GGCTGGTGGTGCC	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.3168T>C	chr5.hg19:g.71492350T>C		100.0	0.0		78.0	4.0	NM_005909	A2BDK5	Silent	SNP	ENST00000296755.7	hg19	CCDS4012.1																																																																																			.	.		0.517	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		C	71492350	T	C	71492350	2	2	255	1	0	0	0	0	0	0	0	1	9237	1683	59	2		2	MAP1B	5	71492350	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	16327665	71492350	109422910	223	35568										
RGNEF	64283	hgsc.bcm.edu	37	chr5	73163834	73163834	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tccagaagtgttccaggcacCaccttggaaaggtaaggctg	12	10	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:73163834C>T	ENST00000426542.2	+	18	2306	c.2286C>T	c.(2284-2286)acC>acT	p.T762T	ARHGEF28_ENST00000545377.1_Silent_p.T762T|ARHGEF28_ENST00000287898.5_Silent_p.T762T|ARHGEF28_ENST00000296794.6_Silent_p.T762T|ARHGEF28_ENST00000296799.4_Silent_p.T449T|ARHGEF28_ENST00000437974.1_Silent_p.T762T|ARHGEF28_ENST00000513042.2_Silent_p.T762T			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	762					central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)										TTCCAGGCACCACCTTGGAAA	0.537																																					p.T762T		Atlas-SNP	.											.	.	.	.	0			c.C2286T						.						96	92	93					5																	73163834		1957	4142	6099	SO:0001819	synonymous_variant	64283	exon19			AGGCACCACCTTG		CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.2286C>T	chr5.hg19:g.73163834C>T		103.0	0.0		93.0	4.0	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Silent	SNP	ENST00000426542.2	hg19	CCDS54870.1																																																																																			.	.		0.537	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1			T	73163834	C	T	73163834	2	4	255	1	0	0	0	0	0	0	0	1	13298	581	21	3		3	RGNEF	5	73163834	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1671484	73163834	107751426	224	35569										
PAPD4	167153	hgsc.bcm.edu	37	chr5	78938677	78938677	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tttttttcaggtaaatcagaAgactgaagcacggcatatac	8	7	2	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:78938677A>G	ENST00000296783.3	+	8	994	c.695A>G	c.(694-696)aAg>aGg	p.K232R	PAPD4_ENST00000428308.2_Missense_Mutation_p.K232R|PAPD4_ENST00000504233.1_Missense_Mutation_p.K232R|PAPD4_ENST00000423041.2_Missense_Mutation_p.K228R|PAPD4_ENST00000453514.1_Missense_Mutation_p.K232R			Q6PIY7	GLD2_HUMAN	PAP associated domain containing 4	232					hematopoietic progenitor cell differentiation (GO:0002244)|histone mRNA catabolic process (GO:0071044)|mRNA processing (GO:0006397)|RNA polyadenylation (GO:0043631)	cytoplasm (GO:0005737)|nuclear RNA-directed RNA polymerase complex (GO:0031380)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)			biliary_tract(1)|breast(2)|endometrium(4)|kidney(3)|large_intestine(9)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Lung NSC(167;0.00293)|all_lung(232;0.00323)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;8.61e-47)|Epithelial(54;1.32e-41)|all cancers(79;2.45e-36)		GTAAATCAGAAGACTGAAGCA	0.323																																					p.K232R		Atlas-SNP	.											.	PAPD4	51	.	0			c.A695G						.						97	87	90					5																	78938677		2203	4300	6503	SO:0001583	missense	167153	exon8			ATCAGAAGACTGA	AL833136	CCDS4048.1, CCDS75265.1, CCDS75266.1	5q14.1	2014-03-21			ENSG00000164329	ENSG00000164329			26776	protein-coding gene	gene with protein product	"TUTase2"	614121				12477932	Standard	NM_173797		Approved	FLJ38499, GLD2, TUT2	uc003kgb.2	Q6PIY7	OTTHUMG00000108163	ENST00000296783.3:c.695A>G	chr5.hg19:g.78938677A>G	ENSP00000296783:p.Lys232Arg	121.0	0.0		125.0	5.0	NM_173797	Q86WZ2|Q8N927	Missense_Mutation	SNP	ENST00000296783.3	hg19	CCDS4048.1	.	.	.	.	.	.	.	.	.	.	A	9.732	1.162472	0.21538	.	.	ENSG00000164329	ENST00000453514;ENST00000423041;ENST00000504233;ENST00000428308;ENST00000296783	T;T;T;T	0.56103	0.48;0.95;0.48;0.48	5.88	5.88	0.94601	.	0.230281	0.52532	D	0.000076	T	0.32585	0.0834	N	0.13003	0.285	0.45295	D	0.998291	B;B;B	0.25719	0.007;0.027;0.132	B;B;B	0.18871	0.01;0.023;0.017	T	0.25398	-1.0133	10	0.02654	T	1	-10.5102	16.275	0.82640	1.0:0.0:0.0:0.0	.	232;228;232	Q6PIY7;Q6PIY7-2;D6RAF2	GLD2_HUMAN;.;.	R	232;228;232;232;232	ENSP00000397563:K232R;ENSP00000393412:K228R;ENSP00000396861:K232R;ENSP00000296783:K232R	ENSP00000296783:K232R	K	+	2	0	PAPD4	78974433	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.706000	0.61845	2.248000	0.74166	0.477000	0.44152	AAG	.	.		0.323	PAPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226967.1	NM_173797		G	78938677	A	G	78938677	3	3	255	1	0	0	0	0	1	0	0	0	11433	72	3	2	717	2	PAPD4	5	78938677	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	5774843	78938677	101976583	225	35570										
VCAN	1462	hgsc.bcm.edu	37	chr5	82849183	82849183	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcctgcctgtttcttctcagAtaccgagacatgtgactatg	8	11	2	3	rs13184139		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:82849183A>G	ENST00000265077.3	+	11	10059	c.9494A>G	c.(9493-9495)gAt>gGt	p.D3165G	VCAN_ENST00000513016.1_3'UTR|VCAN-AS1_ENST00000513899.1_RNA|VCAN_ENST00000343200.5_Splice_Site_p.D2178G|VCAN_ENST00000512590.2_Splice_Site_p.D1363G|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000502527.2_Splice_Site_p.D424G|VCAN_ENST00000342785.4_Splice_Site_p.D1411G	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	3165					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	TTCTTCTCAGATACCGAGACA	0.493																																					p.D3165G		Atlas-SNP	.											.	VCAN	498	.	0			c.A9494G						.						105	93	97					5																	82849183		2203	4300	6503	SO:0001630	splice_region_variant	1462	exon11			TCTCAGATACCGA	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.9494-1A>G	chr5.hg19:g.82849183A>G		52.0	0.0		59.0	4.0	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	hg19	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.018909	0.75275	.	.	ENSG00000038427	ENST00000265077;ENST00000343200;ENST00000342785;ENST00000512590;ENST00000502527	T;T;T;T;T	0.16897	2.31;2.31;2.31;2.31;2.31	6.06	6.06	0.98353	C-type lectin-like (1);	0.000000	0.64402	D	0.000007	T	0.38241	0.1033	L	0.49256	1.55	0.58432	D	0.999998	D;D;B;D	0.89917	1.0;1.0;0.318;1.0	D;D;P;D	0.91635	0.999;0.998;0.64;0.999	T	0.05451	-1.0884	10	0.62326	D	0.03	.	16.6093	0.84858	1.0:0.0:0.0:0.0	.	1411;424;2178;3165	P13611-3;P13611-4;P13611-2;P13611	.;.;.;CSPG2_HUMAN	G	3165;2178;1411;1363;424	ENSP00000265077:D3165G;ENSP00000340062:D2178G;ENSP00000342768:D1411G;ENSP00000425959:D1363G;ENSP00000421362:D424G	ENSP00000265077:D3165G	D	+	2	0	VCAN	82884939	1.000000	0.71417	1.000000	0.80357	0.297000	0.27493	9.339000	0.96797	2.324000	0.78689	0.533000	0.62120	GAT	.	A|1.000;|0.000		0.493	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	Missense_Mutation	G	82849183	A	G	82849183	5	3	255	1	0	0	0	0	0	0	1	0	17153	347	12	2	9532	2	VCAN	5	82849183	Splice_Site	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	3910506	82849183	98066077	226	35571										
PAM	5066	hgsc.bcm.edu	37	chr5	102237061	102237061	+	Splice_Site	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttaatcttttttttaatagtCcgatacatacttctgcatgt	4	7	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:102237061C>A	ENST00000438793.3	+	3	682	c.212C>A	c.(211-213)tCc>tAc	p.S71Y	PAM_ENST00000304400.7_Splice_Site_p.S71Y|PAM_ENST00000274392.9_Intron|PAM_ENST00000346918.2_Splice_Site_p.S71Y|PAM_ENST00000379787.4_5'UTR|PAM_ENST00000348126.2_Splice_Site_p.S71Y|PAM_ENST00000455264.2_Splice_Site_p.S71Y	NM_000919.3|NM_001177306.1|NM_138766.2	NP_000910.2|NP_001170777.1|NP_620121.1	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase	71	Peptidylglycine alpha-hydroxylating monooxygenase. {ECO:0000250}.				central nervous system development (GO:0007417)|heart development (GO:0007507)|lactation (GO:0007595)|limb development (GO:0060173)|long-chain fatty acid metabolic process (GO:0001676)|maternal process involved in female pregnancy (GO:0060135)|odontogenesis (GO:0042476)|ovulation cycle process (GO:0022602)|peptide amidation (GO:0001519)|protein amidation (GO:0018032)|protein homooligomerization (GO:0051260)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of protein secretion (GO:0050708)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to pH (GO:0009268)|toxin metabolic process (GO:0009404)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)|trans-Golgi network (GO:0005802)	calcium ion binding (GO:0005509)|copper ion binding (GO:0005507)|L-ascorbic acid binding (GO:0031418)|peptidylamidoglycolate lyase activity (GO:0004598)|peptidylglycine monooxygenase activity (GO:0004504)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	25		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)	TTTTAATAGTCCGATACATAC	0.353																																					p.S71Y		Atlas-SNP	.											.	PAM	180	.	0			c.C212A						.						98	100	99					5																	102237061		2203	4300	6503	SO:0001630	splice_region_variant	5066	exon3			AATAGTCCGATAC	AB095007	CCDS4092.1, CCDS4093.1, CCDS4094.1, CCDS43348.1, CCDS54885.1	5q	2008-02-05			ENSG00000145730	ENSG00000145730	1.14.17.3		8596	protein-coding gene	gene with protein product	"peptidyl-alpha-hydroxyglycine alpha-amidating lyase", "peptidylglycine alpha-hydroxylating monooxygenase"	170270				2357221	Standard	NM_000919		Approved	PAL, PHM	uc003knt.3	P19021	OTTHUMG00000128729	ENST00000438793.3:c.211-1C>A	chr5.hg19:g.102237061C>A		380.0	1.0		382.0	137.0	NM_138822	A6NMR0|A8K293|O43211|O95080|Q16252|Q16253|Q54A45|Q86U53|Q8WVC7|Q9UCG0	Missense_Mutation	SNP	ENST00000438793.3	hg19	CCDS54885.1	.	.	.	.	.	.	.	.	.	.	C	18.29	3.592299	0.66219	.	.	ENSG00000145730	ENST00000438793;ENST00000346918;ENST00000348126;ENST00000304400;ENST00000455264	T;T;T;T;T	0.36340	1.26;1.26;1.26;1.26;1.26	5.39	5.39	0.77823	Copper type II, ascorbate-dependent monooxygenase, N-terminal (2);PHM/PNGase F domain (1);	0.000000	0.85682	D	0.000000	T	0.61362	0.2341	M	0.65975	2.015	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;0.998;1.0;0.998	D;D;P;D;D	0.91635	0.999;0.998;0.892;0.998;0.943	T	0.63001	-0.6734	10	0.72032	D	0.01	.	19.5261	0.95208	0.0:1.0:0.0:0.0	.	71;71;71;71;71	P19021;P19021-4;P19021-3;P19021-5;P19021-2	AMD_HUMAN;.;.;.;.	Y	71	ENSP00000396493:S71Y;ENSP00000282992:S71Y;ENSP00000314638:S71Y;ENSP00000306100:S71Y;ENSP00000403461:S71Y	ENSP00000306100:S71Y	S	+	2	0	PAM	102264960	1.000000	0.71417	1.000000	0.80357	0.696000	0.40369	5.307000	0.65762	2.668000	0.90789	0.650000	0.86243	TCC	.	.		0.353	PAM-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250640.2	NM_000919	Missense_Mutation	A	102237061	C	A	102237061	5	1	255	1	0	0	0	0	0	0	1	0	11421	869	30	3	222	3	PAM	5	102237061	Splice_Site	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	19387878	102237061	78678199	227	35572										
SEMA6A	57556	hgsc.bcm.edu	37	chr5	115823894	115823894	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gcttgaacaaagtatggttcTgtagacaaacaggcacttta	9	7	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:115823894T>C	ENST00000343348.6	-	9	1443		c.e9-2		SEMA6A_ENST00000510263.1_Splice_Site|SEMA6A_ENST00000257414.8_Splice_Site|CTB-118N6.3_ENST00000514214.1_RNA|CTB-118N6.3_ENST00000508640.1_RNA|SEMA6A_ENST00000503962.1_5'Flank|CTB-118N6.3_ENST00000510682.1_RNA	NM_020796.3	NP_065847	Q9H2E6	SEM6A_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A						apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|centrosome localization (GO:0051642)|cytoskeleton organization (GO:0007010)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|positive regulation of neuron migration (GO:2001224)|semaphorin-plexin signaling pathway (GO:0071526)	axon (GO:0030424)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31		all_cancers(142;0.00316)|all_epithelial(76;5.71e-05)|Prostate(80;0.00845)|Ovarian(225;0.0796)|Lung NSC(810;0.171)|all_lung(232;0.203)		OV - Ovarian serous cystadenocarcinoma(64;1.59e-08)|Epithelial(69;2e-08)|all cancers(49;5.7e-08)|COAD - Colon adenocarcinoma(49;0.151)		AGTATGGTTCTGTAGACAAAC	0.383																																					.		Atlas-SNP	.											.	SEMA6A	93	.	0			c.656-2A>G						.						77	70	72					5																	115823894		1863	4111	5974	SO:0001630	splice_region_variant	57556	exon10			TGGTTCTGTAGAC	AB037789	CCDS47256.1, CCDS75288.1	5q23.1	2014-07-29			ENSG00000092421			"Semaphorins"	10738	protein-coding gene	gene with protein product	"sema VIa"	605885		SEMAQ		9204478, 10993894	Standard	XM_006714663		Approved	KIAA1368, SEMA6A1, SEMA, HT018	uc010jck.3	Q9H2E6	OTTHUMG00000162987	ENST00000343348.6:c.656-2A>G	chr5.hg19:g.115823894T>C		126.0	0.0		139.0	6.0	NM_020796	Q9P2H9	Splice_Site	SNP	ENST00000343348.6	hg19	CCDS47256.1	.	.	.	.	.	.	.	.	.	.	T	14.69	2.609553	0.46527	.	.	ENSG00000092421	ENST00000343348;ENST00000257414;ENST00000510263	.	.	.	5.86	5.86	0.93980	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.2215	0.82262	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	SEMA6A	115851793	1.000000	0.71417	0.999000	0.59377	0.446000	0.32137	7.997000	0.88414	2.367000	0.80283	0.528000	0.53228	.	.	.		0.383	SEMA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371270.1	NM_020796	Intron	C	115823894	T	C	115823894	5	2	255	1	0	0	0	0	0	0	1	0	14054	1594	55	2	2482	2	SEMA6A	5	115823894	Splice_Site	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	13586833	115823894	65091366	228	35573										
SRFBP1	153443	hgsc.bcm.edu	37	chr5	121309963	121309963	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aacttgtcaggagtgttggcCgactgaagtcaaaaaagtta	11	6	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:121309963C>A	ENST00000339397.4	+	2	181	c.109C>A	c.(109-111)Cga>Aga	p.R37R		NM_152546.2	NP_689759.2			serum response factor binding protein 1											central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|skin(1)	15		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000227)|Epithelial(69;0.000365)|all cancers(49;0.00517)		GAGTGTTGGCCGACTGAAGTC	0.313																																					p.R37R		Atlas-SNP	.											.	SRFBP1	47	.	0			c.C109A						.						70	65	67					5																	121309963		1816	4073	5889	SO:0001819	synonymous_variant	153443	exon2			GTTGGCCGACTGA	AK058015	CCDS43354.1	5q23.1	2006-12-21				ENSG00000151304			26333	protein-coding gene	gene with protein product	"BUD22 homolog (S. cerevisiae)"	610479				15492011	Standard	NM_152546		Approved	FLJ25286, p49, STRAP, BUD22, Rlb1	uc003kst.1	Q8NEF9		ENST00000339397.4:c.109C>A	chr5.hg19:g.121309963C>A		135.0	0.0		115.0	5.0	NM_152546		Silent	SNP	ENST00000339397.4	hg19	CCDS43354.1																																																																																			.	.		0.313	SRFBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371200.1	NM_152546		A	121309963	C	A	121309963	2	1	255	1	0	0	0	0	0	0	0	1	15159	644	23	1		1	SRFBP1	5	121309963	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	5486069	121309963	59605297	229	35574										
FBN2	2201	hgsc.bcm.edu	37	chr5	127704892	127704892	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tacctgaattttttgcagggCatggctggcagggttctcca	12	9	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:127704892C>T	ENST00000508053.1	-	22	3205	c.2231G>A	c.(2230-2232)tGc>tAc	p.C744Y	FBN2_ENST00000508989.1_Missense_Mutation_p.C711Y|FBN2_ENST00000262464.4_Missense_Mutation_p.C744Y|Y_RNA_ENST00000384560.1_RNA|FBN2_ENST00000511489.1_5'UTR			P35556	FBN2_HUMAN	fibrillin 2	744	TB 3.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		TTTTGCAGGGCATGGCTGGCA	0.463																																					p.C744Y		Atlas-SNP	.											.	FBN2	858	.	0			c.G2231A						.						108	101	103					5																	127704892		2203	4300	6503	SO:0001583	missense	2201	exon16			GCAGGGCATGGCT	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.2231G>A	chr5.hg19:g.127704892C>T	ENSP00000424571:p.Cys744Tyr	42.0	0.0		39.0	15.0	NM_001999	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	hg19	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.466836	0.84425	.	.	ENSG00000138829	ENST00000262464;ENST00000508053;ENST00000508989	D;D;D	0.99875	-7.4;-7.4;-7.4	4.57	4.57	0.56435	Matrix fibril-associated (3);TGF-beta binding (1);	0.000000	0.64402	D	0.000001	D	0.99880	0.9943	M	0.90252	3.1	0.80722	D	1	D;D	0.89917	1.0;0.997	D;D	0.91635	0.999;0.996	D	0.96462	0.9342	10	0.72032	D	0.01	.	18.667	0.91493	0.0:1.0:0.0:0.0	.	711;744	D6RJI3;P35556	.;FBN2_HUMAN	Y	744;744;711	ENSP00000262464:C744Y;ENSP00000424571:C744Y;ENSP00000425596:C711Y	ENSP00000262464:C744Y	C	-	2	0	FBN2	127732791	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	7.609000	0.82925	2.824000	0.97209	0.655000	0.94253	TGC	.	.		0.463	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		T	127704892	C	T	127704892	3	4	255	1	0	0	0	0	1	0	0	0	5711	710	25	3	6707	3	FBN2	5	127704892	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	6394929	127704892	53210368	230	35575										
PCDHB11	56125	hgsc.bcm.edu	37	chr5	140579924	140579924	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cagacaataggaaataccccGagttagttctggacaaggcg	11	9	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:140579924G>T	ENST00000354757.3	+	1	577	c.577G>T	c.(577-579)Gag>Tag	p.E193*	PCDHB11_ENST00000536699.1_Intron	NM_018931.2	NP_061754.1	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11	193	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.E193Q(1)		NS(2)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GAAATACCCCGAGTTAGTTCT	0.463																																					p.E193X		Atlas-SNP	.											PCDHB11,NS,NS,0,1	PCDHB11	162	.	1	Substitution - Missense(1)	NS(1)	c.G577T						.						62	65	64					5																	140579924		2203	4300	6503	SO:0001587	stop_gained	56125	exon1			TACCCCGAGTTAG	AF152490	CCDS4253.1	5q31	2010-01-26			ENSG00000197479	ENSG00000197479		"Cadherins / Protocadherins : Clustered"	8682	other	protocadherin	"cadherin ME2"	606337				10380929	Standard	NM_018931		Approved	PCDH-BETA11, ME2	uc003liy.3	Q9Y5F2	OTTHUMG00000129618	ENST00000354757.3:c.577G>T	chr5.hg19:g.140579924G>T	ENSP00000346802:p.Glu193*	196.0	0.0		262.0	123.0	NM_018931	B4DSF7|Q2M223	Nonsense_Mutation	SNP	ENST00000354757.3	hg19	CCDS4253.1	.	.	.	.	.	.	.	.	.	.	G	34	5.355734	0.95854	.	.	ENSG00000197479	ENST00000354757	.	.	.	2.7	2.7	0.31948	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	13.3974	0.60861	0.0:0.0:1.0:0.0	.	.	.	.	X	193	.	ENSP00000346802:E193X	E	+	1	0	PCDHB11	140560108	1.000000	0.71417	0.739000	0.30968	0.889000	0.51656	9.162000	0.94745	1.496000	0.48567	0.467000	0.42956	GAG	.	.		0.463	PCDHB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251813.1	NM_018931		T	140579924	G	T	140579924	4	4	255	1	0	0	0	0	0	1	0	0	11545	1059	37	1	579	1	PCDHB11	5	140579924	Nonsense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	12875032	140579924	40335336	231	35576										
PCDHB15	56121	hgsc.bcm.edu	37	chr5	140626597	140626597	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cagagactcgggcaccaacgCccaggtcacctactcgctgc	10	17	1	1	rs532029427		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:140626597C>G	ENST00000231173.3	+	1	1451	c.1451C>G	c.(1450-1452)gCc>gGc	p.A484G		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	484	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(8)|kidney(3)|large_intestine(14)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	61			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGCACCAACGCCCAGGTCACC	0.647																																					p.A484G		Atlas-SNP	.											.	PCDHB15	138	.	0			c.C1451G						.						61	73	68					5																	140626597		2203	4296	6499	SO:0001583	missense	56121	exon1			CCAACGCCCAGGT	AF152494	CCDS4257.1	5q31	2011-06-07			ENSG00000113248	ENSG00000113248		"Cadherins / Protocadherins : Clustered"	8686	other	protocadherin		606341				10380929	Standard	NM_018935		Approved	PCDH-BETA15	uc003lje.3	Q9Y5E8	OTTHUMG00000129609	ENST00000231173.3:c.1451C>G	chr5.hg19:g.140626597C>G	ENSP00000231173:p.Ala484Gly	240.0	0.0		277.0	125.0	NM_018935	Q8IUX5	Missense_Mutation	SNP	ENST00000231173.3	hg19	CCDS4257.1	.	.	.	.	.	.	.	.	.	.	C	17.10	3.304160	0.60305	.	.	ENSG00000113248	ENST00000231173	T	0.51574	0.7	4.52	4.52	0.55395	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.41903	0.1179	N	0.17800	0.525	0.38899	D	0.957276	P	0.36125	0.538	B	0.43838	0.433	T	0.52034	-0.8629	9	0.72032	D	0.01	.	14.1287	0.65238	0.0:0.8486:0.1514:0.0	.	484	Q9Y5E8	PCDBF_HUMAN	G	484	ENSP00000231173:A484G	ENSP00000231173:A484G	A	+	2	0	PCDHB15	140606781	0.398000	0.25279	1.000000	0.80357	0.980000	0.70556	0.978000	0.29488	2.251000	0.74343	0.485000	0.47835	GCC	.	.		0.647	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935		G	140626597	C	G	140626597	3	3	255	1	0	0	0	0	1	0	0	0	11549	739	26	4	1453	4	PCDHB15	5	140626597	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	46673	140626597	40288663	232	35577										
PCDHGA4	56111	hgsc.bcm.edu	37	chr5	140735864	140735864	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttcttccccgggtacagtaaTtgcacttttcaacgtgcatg	8	11	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:140735864T>C	ENST00000571252.1	+	1	1097	c.1097T>C	c.(1096-1098)aTt>aCt	p.I366T	PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018917.2	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4	366	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTACAGTAATTGCACTTTTC	0.453																																					p.I366T		Atlas-SNP	.											.	PCDHGA4	150	.	0			c.T1097C						.						30	29	30					5																	140735864		1968	4109	6077	SO:0001583	missense	56111	exon1			CAGTAATTGCACT	AF152511	CCDS58979.1, CCDS58979.2, CCDS75331.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8702	other	protocadherin		606291				10380929	Standard	NM_018917		Approved	PCDH-GAMMA-A4		Q9Y5G9		ENST00000571252.1:c.1097T>C	chr5.hg19:g.140735864T>C	ENSP00000458570:p.Ile366Thr	91.0	0.0		114.0	45.0	NM_018917	Q9Y5D3	Missense_Mutation	SNP	ENST00000571252.1	hg19	CCDS58979.1																																																																																			.	.		0.453	PCDHGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437959.1	NM_018917		C	140735864	T	C	140735864	3	2	255	1	0	0	0	0	1	0	0	0	11565	1493	52	2	1099	2	PCDHGA4	5	140735864	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	109267	140735864	40179396	233	35578										
ARHGEF37	389337	hgsc.bcm.edu	37	chr5	148980735	148980735	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tatcatcaaagtgaacagcaGattcctccatgatctgcagg	8	10	3	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:148980735G>T	ENST00000333677.6	+	3	414	c.251G>T	c.(250-252)aGa>aTa	p.R84I		NM_001001669.2	NP_001001669.2	A1IGU5	ARH37_HUMAN	Rho guanine nucleotide exchange factor (GEF) 37	84	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.					cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(5)|lung(6)|ovary(1)|prostate(2)|stomach(3)	17						GTGAACAGCAGATTCCTCCAT	0.468																																					p.R84I		Atlas-SNP	.											.	ARHGEF37	45	.	0			c.G251T						.						106	107	107					5																	148980735		1971	4174	6145	SO:0001583	missense	389337	exon3			ACAGCAGATTCCT	BC041325	CCDS43385.1	5q33.1	2012-07-24			ENSG00000183111	ENSG00000183111		"Rho guanine nucleotide exchange factors"	34430	protein-coding gene	gene with protein product							Standard	XM_005268448		Approved	FLJ41603	uc003lra.1	A1IGU5	OTTHUMG00000163491	ENST00000333677.6:c.251G>T	chr5.hg19:g.148980735G>T	ENSP00000328083:p.Arg84Ile	85.0	0.0		89.0	4.0	NM_001001669	Q6ZW51	Missense_Mutation	SNP	ENST00000333677.6	hg19	CCDS43385.1	.	.	.	.	.	.	.	.	.	.	G	16.70	3.196217	0.58126	.	.	ENSG00000183111	ENST00000505810;ENST00000333677	T;T	0.64803	-0.12;-0.12	5.4	1.71	0.24356	Dbl homology (DH) domain (5);	0.132397	0.30742	U	0.008966	T	0.57110	0.2031	L	0.41906	1.305	0.48185	D	0.999602	P	0.47106	0.89	P	0.50490	0.642	T	0.51787	-0.8661	10	0.46703	T	0.11	.	7.4622	0.27302	0.3404:0.0:0.6596:0.0	.	84	A1IGU5	ARH37_HUMAN	I	84	ENSP00000425621:R84I;ENSP00000328083:R84I	ENSP00000328083:R84I	R	+	2	0	ARHGEF37	148960928	0.998000	0.40836	0.986000	0.45419	0.556000	0.35491	0.781000	0.26774	0.134000	0.18681	0.561000	0.74099	AGA	.	.		0.468	ARHGEF37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373763.1	NM_001001669		T	148980735	G	T	148980735	3	4	255	1	0	0	0	0	1	0	0	0	906	942	33	3	257	3	ARHGEF37	5	148980735	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	8244871	148980735	31934525	234	35579										
MYOZ3	91977	hgsc.bcm.edu	37	chr5	150056368	150056368	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agtggcttggaactcctccgTctcagacccagcttcaacag	9	14	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:150056368T>C	ENST00000520112.1	+	2	546	c.436T>C	c.(436-438)Tct>Cct	p.S146P	MYOZ3_ENST00000297130.4_Silent_p.R229R|MYOZ3_ENST00000456566.2_3'UTR|MYOZ3_ENST00000517768.1_Silent_p.R229R					myozenin 3											large_intestine(2)|lung(1)|skin(2)	5		Medulloblastoma(196;0.134)|all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AACTCCTCCGTCTCAGACCCA	0.637																																					p.R229R		Atlas-SNP	.											.	MYOZ3	21	.	0			c.T687C						.						60	68	65					5																	150056368		2203	4300	6503	SO:0001583	missense	91977	exon7			CCTCCGTCTCAGA	AF480443	CCDS4309.1	5q33.2	2008-07-18			ENSG00000164591	ENSG00000164591			18565	protein-coding gene	gene with protein product	"calsarcin 3", "FATZ related protein 3"	610735				11842093	Standard	NM_001122853		Approved	CS-3, CS3, FRP3	uc003lsr.3	Q8TDC0	OTTHUMG00000130077	ENST00000520112.1:c.436T>C	chr5.hg19:g.150056368T>C	ENSP00000429439:p.Ser146Pro	77.0	0.0		82.0	4.0	NM_001122853		Silent	SNP	ENST00000520112.1	hg19		.	.	.	.	.	.	.	.	.	.	T	11.96	1.794993	0.31777	.	.	ENSG00000164591	ENST00000520112	.	.	.	5.2	-0.127	0.13510	.	.	.	.	.	T	0.55689	0.1936	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54820	-0.8236	5	0.87932	D	0	-26.3218	3.1134	0.06366	0.3182:0.4096:0.0:0.2722	.	.	.	.	P	146	.	ENSP00000429439:S146P	S	+	1	0	MYOZ3	150036561	0.041000	0.20044	0.994000	0.49952	0.976000	0.68499	-0.244000	0.08903	-0.040000	0.13580	-0.132000	0.14878	TCT	.	.		0.637	MYOZ3-007	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000374429.1	NM_001122853		C	150056368	T	C	150056368	3	2	255	1	0	0	0	0	1	0	0	0	10106	1654	58	2	709	2	MYOZ3	5	150056368	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	1075633	150056368	30858892	235	35580										
RARS	5917	hgsc.bcm.edu	37	chr5	167945066	167945066	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gtggagaaagatagacagacTggtgagtgtctttttttttt	12	3	1	5			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:167945066T>C	ENST00000231572.3	+	14	1926	c.1872T>C	c.(1870-1872)acT>acC	p.T624T	RARS_ENST00000538719.1_Splice_Site_p.T418T	NM_002887.3	NP_002878.2	P54136	SYRC_HUMAN	arginyl-tRNA synthetase	624					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	arginine binding (GO:0034618)|arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|tRNA binding (GO:0000049)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|stomach(1)	22	Renal(175;0.000159)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0208)|all_neural(177;0.0227)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0693)|Epithelial(171;0.131)|OV - Ovarian serous cystadenocarcinoma(192;0.156)		ATAGACAGACTGGTGAGTGTC	0.403																																					p.T624T		Atlas-SNP	.											.	RARS	58	.	0			c.T1872C						.						36	36	36					5																	167945066		2203	4300	6503	SO:0001630	splice_region_variant	5917	exon14			ACAGACTGGTGAG	BC000528	CCDS4367.1	5q35.1	2011-07-01			ENSG00000113643	ENSG00000113643	6.1.1.19	"Aminoacyl tRNA synthetases / Class I"	9870	protein-coding gene	gene with protein product	"arginine tRNA ligase 1, cytoplasmic"	107820				7590355	Standard	NM_002887		Approved	DALRD1	uc003lzx.3	P54136	OTTHUMG00000130411	ENST00000231572.3:c.1873+1T>C	chr5.hg19:g.167945066T>C		69.0	0.0		84.0	5.0	NM_002887	B2RBS9|Q53GY4|Q9BWA1	Silent	SNP	ENST00000231572.3	hg19	CCDS4367.1																																																																																			.	.		0.403	RARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252794.2	NM_002887	Silent	C	167945066	T	C	167945066	5	2	255	1	0	0	0	0	0	0	1	0	13073	1594	55	2	1926	2	RARS	5	167945066	Splice_Site	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	17888698	167945066	12970194	236	35581										
NPM1	4869	hgsc.bcm.edu	37	chr5	170827199	170827199	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gatgaggaagctgaagaaaaAgcgccagtgaagaaagtgag	15	4	0	6			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:170827199A>G	ENST00000296930.5	+	7	868	c.567A>G	c.(565-567)aaA>aaG	p.K189K	NPM1_ENST00000517671.1_Silent_p.K189K|NPM1_ENST00000351986.6_Silent_p.K189K|NPM1_ENST00000393820.2_Silent_p.K189K	NM_002520.6	NP_002511.1	P06748	NPM_HUMAN	nucleophosmin (nucleolar phosphoprotein B23, numatrin)	189					cell aging (GO:0007569)|CENP-A containing nucleosome assembly (GO:0034080)|centrosome cycle (GO:0007098)|DNA repair (GO:0006281)|intracellular protein transport (GO:0006886)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of centrosome duplication (GO:0010826)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|nucleocytoplasmic transport (GO:0006913)|nucleosome assembly (GO:0006334)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of translation (GO:0045727)|protein localization (GO:0008104)|protein oligomerization (GO:0051259)|regulation of centriole replication (GO:0046599)|regulation of eIF2 alpha phosphorylation by dsRNA (GO:0060735)|regulation of endodeoxyribonuclease activity (GO:0032071)|regulation of endoribonuclease activity (GO:0060699)|response to stress (GO:0006950)|ribosome assembly (GO:0042255)|signal transduction (GO:0007165)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle pole centrosome (GO:0031616)	histone binding (GO:0042393)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)|ribosomal large subunit binding (GO:0043023)|ribosomal small subunit binding (GO:0043024)|RNA binding (GO:0003723)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|unfolded protein binding (GO:0051082)		NPM1/ALK(632)	central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4261)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	4269	Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			ctgaagaAAAAGCGCCAGTGA	0.333			"T, F "	"ALK, RARA, MLF1"	"NHL, APL, AML"																																p.K189K		Atlas-SNP	.		Dom	yes		5	5q35	4869	"nucleophosmin (nucleolar phosphoprotein B23, numatrin)"		L	.	NPM1	5003	.	0			c.A567G						.						110	103	106					5																	170827199		2203	4300	6503	SO:0001819	synonymous_variant	4869	exon7			AGAAAAAGCGCCA	M26697	CCDS4376.1, CCDS4377.1, CCDS43399.1	5q35.1	2014-09-17			ENSG00000181163	ENSG00000181163			7910	protein-coding gene	gene with protein product	"nucleolar phosphoprotein B23", "numatrin", "nucleophosmin/nucleoplasmin family, member 1"	164040				8471164, 8122112	Standard	NM_002520		Approved	B23, NPM	uc003mbi.3	P06748	OTTHUMG00000130465	ENST00000296930.5:c.567A>G	chr5.hg19:g.170827199A>G		137.0	0.0		125.0	5.0	NM_199185	A8K3N7|B5BU00|D3DQL6|P08693|Q12826|Q13440|Q13441|Q14115|Q5EU94|Q5EU95|Q5EU96|Q5EU97|Q5EU98|Q5EU99|Q6V962|Q8WTW5|Q96AT6|Q96DC4|Q96EA5|Q9BYG9|Q9UDJ7	Silent	SNP	ENST00000296930.5	hg19	CCDS4376.1																																																																																			.	.		0.333	NPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252858.2	NM_002520		G	170827199	A	G	170827199	2	3	255	1	0	0	0	0	0	0	0	1	10596	69	3	2		2	NPM1	5	170827199	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	2882133	170827199	10088061	237	35582										
C6orf146	222826	hgsc.bcm.edu	37	chr6	4070154	4070154	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	actgaagattttttgaattcCctttaaaaaataatttaatt	3	4	0	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:4070154C>A	ENST00000274673.3	-	7	706	c.303G>T	c.(301-303)agG>agT	p.R101S	FAM217A_ENST00000380188.2_5'UTR	NM_173563.2	NP_775834.2	Q8IXS0	F217A_HUMAN	family with sequence similarity 217, member A	101																	TTTTGAATTCCCtttaaaaaa	0.284																																					p.R101S		Atlas-SNP	.											.	.	.	.	0			c.G303T						.						18	19	19					6																	4070154		2192	4267	6459	SO:0001630	splice_region_variant	222826	exon7			GAATTCCCTTTAA	BC039349	CCDS4489.1	6p25.1	2012-02-07	2012-02-07	2012-02-07	ENSG00000145975	ENSG00000145975			21362	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 146"	C6orf146			Standard	NM_173563		Approved	MGC43581	uc003mvx.3	Q8IXS0	OTTHUMG00000014159	ENST00000274673.3:c.303-1G>T	chr6.hg19:g.4070154C>A		68.0	0.0		100.0	4.0	NM_173563	Q5JYK1	Missense_Mutation	SNP	ENST00000274673.3	hg19	CCDS4489.1	.	.	.	.	.	.	.	.	.	.	C	14.44	2.535360	0.45176	.	.	ENSG00000145975	ENST00000274673;ENST00000470599;ENST00000498677	T	0.18016	2.24	5.54	4.66	0.58398	.	0.153207	0.43919	D	0.000515	T	0.05090	0.0136	N	0.24115	0.695	0.33064	D	0.534462	B	0.31931	0.347	B	0.31751	0.135	T	0.14504	-1.0470	10	0.87932	D	0	.	9.3285	0.38008	0.0:0.9029:0.0:0.0971	.	101	Q8IXS0	CF146_HUMAN	S	101;229;38	ENSP00000274673:R101S	ENSP00000274673:R101S	R	-	3	2	C6orf146	4015153	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.640000	0.37186	1.546000	0.49388	0.650000	0.86243	AGG	.	.		0.284	FAM217A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352577.2	NM_173563	Missense_Mutation	A	4070154	C	A	4070154	5	1	255	1	0	0	0	0	0	0	1	0	2337	637	22	3	1227	3	C6orf146	6	4070154	Splice_Site	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10		4070154	167044913	238	35583										
JARID2	3720	hgsc.bcm.edu	37	chr6	15497298	15497298	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gtcacgcagattcagcacatCcacaagctgggccggcgctg	12	14	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:15497298C>T	ENST00000341776.2	+	7	2086	c.1842C>T	c.(1840-1842)atC>atT	p.I614I	JARID2_ENST00000541660.1_Silent_p.I576I|JARID2_ENST00000397311.3_Silent_p.I442I	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	614					central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	59	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				TTCAGCACATCCACAAGCTGG	0.622																																					p.I614I		Atlas-SNP	.											.	JARID2	135	.	0			c.C1842T						.						29	24	25					6																	15497298		2203	4298	6501	SO:0001819	synonymous_variant	3720	exon7			GCACATCCACAAG	U57592	CCDS4533.1, CCDS58996.1	6p24-p23	2008-02-05	2006-10-06	2004-01-30	ENSG00000008083	ENSG00000008083			6196	protein-coding gene	gene with protein product		601594	"jumonji (mouse) homolog", "Jumonji, AT rich interactive domain 2"	JMJ		8894700	Standard	NM_001267040		Approved		uc003nbj.4	Q92833	OTTHUMG00000014293	ENST00000341776.2:c.1842C>T	chr6.hg19:g.15497298C>T		155.0	0.0		156.0	67.0	NM_004973	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Silent	SNP	ENST00000341776.2	hg19	CCDS4533.1																																																																																			.	.		0.622	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973		T	15497298	C	T	15497298	2	4	255	1	0	0	0	0	0	0	0	1	7954	845	30	3		3	JARID2	6	15497298	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	11427144	15497298	155617769	239	35584										
LRRC16A	55604	hgsc.bcm.edu	37	chr6	25529110	25529110	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agcagggtattgtcaccagcAccacccagcaggtaagcgag	12	12	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:25529110A>G	ENST00000329474.6	+	24	2424	c.2056A>G	c.(2056-2058)Acc>Gcc	p.T686A		NM_001173977.1|NM_017640.5	NP_001167448.1|NP_060110.4	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	686					actin filament organization (GO:0007015)|barbed-end actin filament uncapping (GO:0051638)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|lamellipodium assembly (GO:0030032)|negative regulation of barbed-end actin filament capping (GO:2000813)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of lamellipodium organization (GO:1902745)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|ruffle organization (GO:0031529)|urate metabolic process (GO:0046415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|lamellipodium (GO:0030027)|nucleus (GO:0005634)	protein complex binding (GO:0032403)	p.T686P(1)		breast(4)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	50						TGTCACCAGCACCACCCAGCA	0.473																																					p.T686A		Atlas-SNP	.											LRRC16A,colon,carcinoma,0,1	LRRC16A	168	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2056G						.						22	26	25					6																	25529110		1971	4163	6134	SO:0001583	missense	55604	exon24			ACCAGCACCACCC	AK000055	CCDS54973.1	6p22.1	2010-09-10	2008-02-12	2008-02-12	ENSG00000079691	ENSG00000079691			21581	protein-coding gene	gene with protein product	"capping protein, Arp2/3, and Myosin-I Linker homolog 1 (Dictyostelium)"	609593	"leucine rich repeat containing 16"	LRRC16		19846667	Standard	NM_017640		Approved	dJ501N12.1, FLJ20048, CARMIL, CARMIL1	uc011djw.2	Q5VZK9	OTTHUMG00000014393	ENST00000329474.6:c.2056A>G	chr6.hg19:g.25529110A>G	ENSP00000331983:p.Thr686Ala	60.0	0.0		30.0	3.0	NM_001173977	B8X1J0|Q6ZUH5|Q6ZW07|Q9NXU7	Missense_Mutation	SNP	ENST00000329474.6	hg19	CCDS54973.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.561053	0.86335	.	.	ENSG00000079691	ENST00000329474;ENST00000399313	T	0.46063	0.88	5.69	5.69	0.88448	.	0.045312	0.85682	D	0.000000	T	0.44644	0.1303	L	0.32530	0.975	0.80722	D	1	D;D;D;D	0.89917	0.998;1.0;0.999;0.998	D;D;D;D	0.85130	0.993;0.996;0.997;0.993	T	0.42599	-0.9442	10	0.44086	T	0.13	.	15.6029	0.76639	1.0:0.0:0.0:0.0	.	686;686;686;686	Q5VZK9;B2RTQ5;Q5VZK9-2;B8X1J0	LR16A_HUMAN;.;.;.	A	686	ENSP00000331983:T686A	ENSP00000331983:T686A	T	+	1	0	LRRC16A	25637089	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.554000	0.90689	2.157000	0.67596	0.533000	0.62120	ACC	.	.		0.473	LRRC16A-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040045.2	NM_017640		G	25529110	A	G	25529110	3	3	255	1	0	0	0	0	1	0	0	0	8980	159	6	2	2150	2	LRRC16A	6	25529110	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	10031812	25529110	145585957	240	35585										
ZNF311	282890	hgsc.bcm.edu	37	chr6	28967374	28967374	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgaagttcacagctacatccTcaaatgtcactgactcctga	6	12	3	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:28967374T>C	ENST00000377179.3	-	5	712	c.200A>G	c.(199-201)gAg>gGg	p.E67G	ZNF311_ENST00000483450.1_5'UTR	NM_001010877.2	NP_001010877.2	Q5JNZ3	ZN311_HUMAN	zinc finger protein 311	67	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|skin(3)|upper_aerodigestive_tract(2)	28						AGCTACATCCTCAAATGTCAC	0.438																																					p.E67G		Atlas-SNP	.											.	ZNF311	59	.	0			c.A200G						.						137	99	112					6																	28967374		1511	2709	4220	SO:0001583	missense	282890	exon5			ACATCCTCAAATG	AL833166	CCDS34357.1	6p21.33	2013-01-08			ENSG00000197935	ENSG00000197935		"Zinc fingers, C2H2-type", "-"	13847	protein-coding gene	gene with protein product							Standard	XM_006715067		Approved		uc003nlu.2	Q5JNZ3	OTTHUMG00000031292	ENST00000377179.3:c.200A>G	chr6.hg19:g.28967374T>C	ENSP00000366384:p.Glu67Gly	84.0	0.0		91.0	4.0	NM_001010877	A2BFK5|B0S7Y4|Q92971	Missense_Mutation	SNP	ENST00000377179.3	hg19	CCDS34357.1	.	.	.	.	.	.	.	.	.	.	T	15.52	2.858953	0.51376	.	.	ENSG00000197935	ENST00000377179	T	0.02216	4.39	3.48	2.34	0.29019	Krueppel-associated box (4);	.	.	.	.	T	0.03434	0.0099	M	0.63169	1.94	0.25543	N	0.987162	D	0.69078	0.997	D	0.67900	0.954	T	0.41052	-0.9530	9	0.72032	D	0.01	-19.7298	6.3444	0.21341	0.0:0.125:0.0:0.875	.	67	Q5JNZ3	ZN311_HUMAN	G	67	ENSP00000366384:E67G	ENSP00000366384:E67G	E	-	2	0	ZNF311	29075353	0.874000	0.30092	0.995000	0.50966	0.597000	0.36814	1.099000	0.31013	1.532000	0.49169	0.477000	0.44152	GAG	.	.		0.438	ZNF311-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076631.3	XM_212581		C	28967374	T	C	28967374	3	2	255	1	0	0	0	0	1	0	0	0	17849	1551	54	2	1812	2	ZNF311	6	28967374	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	3438264	28967374	142147693	241	35586										
OR2B3	442184	hgsc.bcm.edu	37	chr6	29054566	29054566	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agactgcagcactgagttgcCgaaaccaatgagccatgaga	11	10	0	4	rs369975513		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:29054566C>A	ENST00000377173.2	-	1	524	c.460G>T	c.(460-462)Ggc>Tgc	p.G154C		NM_001005226.2	NP_001005226.1	O76000	OR2B3_HUMAN	olfactory receptor, family 2, subfamily B, member 3	154						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|kidney(2)|lung(17)|prostate(1)|skin(2)	24						ACTGAGTTGCCGAAACCAATG	0.488																																					p.G154C		Atlas-SNP	.											.	OR2B3	44	.	0			c.G460T						.						63	58	60					6																	29054566		2203	4300	6503	SO:0001583	missense	442184	exon1			AGTTGCCGAAACC		CCDS34358.1	6p22.2-p21.31	2012-08-09	2008-10-22	2008-10-22	ENSG00000204703	ENSG00000204703		"GPCR / Class A : Olfactory receptors"	8238	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily B, member 3 pseudogene"	OR2B3P			Standard	NM_001005226		Approved	OR6-4	uc003nlx.3	O76000	OTTHUMG00000031226	ENST00000377173.2:c.460G>T	chr6.hg19:g.29054566C>A	ENSP00000366378:p.Gly154Cys	72.0	0.0		102.0	5.0	NM_001005226	B0UYQ1|Q5ST41|Q96R13	Missense_Mutation	SNP	ENST00000377173.2	hg19	CCDS34358.1	.	.	.	.	.	.	.	.	.	.	C	6.722	0.501960	0.12822	.	.	ENSG00000204703	ENST00000377173	T	0.37411	1.2	3.83	-0.243	0.13035	GPCR, rhodopsin-like superfamily (1);	0.341386	0.21456	U	0.074252	T	0.18087	0.0434	N	0.16368	0.405	0.09310	N	1	D	0.57899	0.981	D	0.63877	0.919	T	0.09952	-1.0651	10	0.62326	D	0.03	.	5.5456	0.17061	0.0:0.39:0.2112:0.3988	.	154	O76000	OR2B3_HUMAN	C	154	ENSP00000366378:G154C	ENSP00000366378:G154C	G	-	1	0	OR2B3	29162545	0.000000	0.05858	0.001000	0.08648	0.118000	0.20060	-3.800000	0.00363	-0.342000	0.08363	-0.409000	0.06214	GGC	.	.		0.488	OR2B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076469.2			A	29054566	C	A	29054566	3	1	255	1	0	0	0	0	1	0	0	0	10999	652	23	1	485	1	OR2B3	6	29054566	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	87192	29054566	142060501	242	35587										
TRIM10	10107	hgsc.bcm.edu	37	chr6	30121749	30121749	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	taggtaactgctccttctcaGgagctcagggagaaactgga	12	9	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:30121749G>T	ENST00000449742.2	-	7	1518	c.1443C>A	c.(1441-1443)tcC>tcA	p.S481S	TRIM10_ENST00000376704.3_Intron	NM_006778.3	NP_006769.2	Q9UDY6	TRI10_HUMAN	tripartite motif containing 10	481	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				erythrocyte differentiation (GO:0030218)|innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			ovary(1)	1						CTCCTTCTCAGGAGCTCAGGG	0.532																																					p.S481S		Atlas-SNP	.											.	TRIM10	65	.	0			c.C1443A						.						90	98	95					6																	30121749		1509	2708	4217	SO:0001819	synonymous_variant	10107	exon7			TTCTCAGGAGCTC	Y07829	CCDS4676.1, CCDS34375.1	6p21.3	2013-01-09	2011-01-25	2001-11-23	ENSG00000204613	ENSG00000204613		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	10072	protein-coding gene	gene with protein product		605701	"tripartite motif-containing 10"	RNF9		9271628, 10207104	Standard	NM_052828		Approved	RFB30, HERF1	uc003npo.3	Q9UDY6	OTTHUMG00000031295	ENST00000449742.2:c.1443C>A	chr6.hg19:g.30121749G>T		96.0	0.0		95.0	4.0	NM_006778	A6NF84|Q5SRJ5|Q5SRK8|Q86Z08|Q96QB6|Q9C023|Q9C024	Silent	SNP	ENST00000449742.2	hg19	CCDS34375.1																																																																																			.	.		0.532	TRIM10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076634.1			T	30121749	G	T	30121749	2	4	255	1	0	0	0	0	0	0	0	1	16501	987	35	3		3	TRIM10	6	30121749	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	1067183	30121749	140993318	243	35588										
TRIM10	10107	hgsc.bcm.edu	37	chr6	30121896	30121896	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	acctcatagtcaagagacacCctcacctgccggggctgctc	9	16	3	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:30121896C>A	ENST00000449742.2	-	7	1371	c.1296G>T	c.(1294-1296)agG>agT	p.R432S	TRIM10_ENST00000376704.3_Intron	NM_006778.3	NP_006769.2	Q9UDY6	TRI10_HUMAN	tripartite motif containing 10	432	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				erythrocyte differentiation (GO:0030218)|innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			ovary(1)	1						CAAGAGACACCCTCACCTGCC	0.622																																					p.R432S		Atlas-SNP	.											.	TRIM10	65	.	0			c.G1296T						.						48	43	45					6																	30121896		1510	2708	4218	SO:0001583	missense	10107	exon7			AGACACCCTCACC	Y07829	CCDS4676.1, CCDS34375.1	6p21.3	2013-01-09	2011-01-25	2001-11-23	ENSG00000204613	ENSG00000204613		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	10072	protein-coding gene	gene with protein product		605701	"tripartite motif-containing 10"	RNF9		9271628, 10207104	Standard	NM_052828		Approved	RFB30, HERF1	uc003npo.3	Q9UDY6	OTTHUMG00000031295	ENST00000449742.2:c.1296G>T	chr6.hg19:g.30121896C>A	ENSP00000397073:p.Arg432Ser	72.0	0.0		93.0	4.0	NM_006778	A6NF84|Q5SRJ5|Q5SRK8|Q86Z08|Q96QB6|Q9C023|Q9C024	Missense_Mutation	SNP	ENST00000449742.2	hg19	CCDS34375.1	.	.	.	.	.	.	.	.	.	.	C	10.89	1.478151	0.26511	.	.	ENSG00000204613	ENST00000449742;ENST00000376706	T	0.68765	-0.35	6.01	0.57	0.17347	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.122378	0.37012	N	0.002293	T	0.55386	0.1917	M	0.79475	2.455	0.80722	D	1	P	0.40000	0.698	P	0.48368	0.575	T	0.56727	-0.7931	10	0.54805	T	0.06	.	2.8201	0.05469	0.349:0.4022:0.1057:0.1431	.	432	Q9UDY6	TRI10_HUMAN	S	432	ENSP00000397073:R432S	ENSP00000365896:R432S	R	-	3	2	TRIM10	30229875	0.000000	0.05858	0.998000	0.56505	0.959000	0.62525	-1.892000	0.01610	0.132000	0.18615	0.643000	0.83706	AGG	.	.		0.622	TRIM10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076634.1			A	30121896	C	A	30121896	3	1	255	1	0	0	0	0	1	0	0	0	16501	622	22	3	241	3	TRIM10	6	30121896	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	147	30121896	140993171	244	35589										
DDR1	780	hgsc.bcm.edu	37	chr6	30862315	30862315	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gtgttggaagaggagctgacGgttcacctctctgtccctgg	14	10	2	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:30862315G>T	ENST00000324771.8	+	13	1928	c.1380G>T	c.(1378-1380)acG>acT	p.T460T	DDR1_ENST00000513240.1_Silent_p.T460T|DDR1_ENST00000452441.1_Silent_p.T460T|DDR1_ENST00000376575.3_Silent_p.T460T|DDR1_ENST00000446312.1_3'UTR|DDR1_ENST00000361741.4_Intron|DDR1_ENST00000376568.3_Silent_p.T460T|DDR1_ENST00000454612.2_Silent_p.T460T|DDR1_ENST00000376569.3_Silent_p.T460T|DDR1_ENST00000508312.1_Silent_p.T478T|DDR1_ENST00000418800.2_Silent_p.T460T|DDR1_ENST00000376567.2_Silent_p.T460T|DDR1_ENST00000376570.4_Silent_p.T460T			Q08345	DDR1_HUMAN	discoidin domain receptor tyrosine kinase 1	460					branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|ear development (GO:0043583)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine autophosphorylation (GO:0038083)|protein autophosphorylation (GO:0046777)|regulation of cell growth (GO:0001558)|regulation of cell-matrix adhesion (GO:0001952)|regulation of extracellular matrix disassembly (GO:0010715)|smooth muscle cell migration (GO:0014909)|smooth muscle cell-matrix adhesion (GO:0061302)|wound healing, spreading of cells (GO:0044319)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.T460T(2)|p.T459T(1)		central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(1)|prostate(1)|skin(1)	29					Imatinib(DB00619)	AGGAGCTGACGGTTCACCTCT	0.627																																					p.T478T		Atlas-SNP	.											DDR1_ENST00000376575,NS,carcinoma,0,6	DDR1	213	.	3	Substitution - coding silent(3)	lung(3)	c.G1434T						.						142	124	130					6																	30862315		2203	4300	6503	SO:0001819	synonymous_variant	780	exon11			GCTGACGGTTCAC	X99031	CCDS4690.1, CCDS34385.1, CCDS47396.1, CCDS56411.1, CCDS75419.1	6p21.33	2010-02-17	2008-01-23		ENSG00000204580	ENSG00000204580	2.7.10.1	"CD molecules"	2730	protein-coding gene	gene with protein product		600408	"discoidin domain receptor family, member 1"	NTRK4, PTK3A, NEP, CAK, EDDR1		7789998	Standard	NM_001954		Approved	RTK6, CD167	uc003nrv.3	Q08345	OTTHUMG00000031236	ENST00000324771.8:c.1380G>T	chr6.hg19:g.30862315G>T		57.0	0.0		64.0	3.0	NM_001202523	B5A975|B5A976|B7Z2K0|Q14196|Q16562|Q2L6H3|Q4LE50|Q5ST11|Q5ST12|Q6NSK4|Q9UD35|Q9UD36|Q9UD37|Q9UD86|Q9UDL2	Silent	SNP	ENST00000324771.8	hg19	CCDS34385.1																																																																																			.	.		0.627	DDR1-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076494.3	NM_013994		T	30862315	G	T	30862315	2	4	255	1	0	0	0	0	0	0	0	1	4338	1103	39	1		1	DDR1	6	30862315	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	740419	30862315	140252752	245	35590										
BAT3	7917	hgsc.bcm.edu	37	chr6	31608658	31608658	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	taccacctgaagcctcagtcCcatcatagtggtcagccagc	8	15	3	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:31608658C>T	ENST00000375964.6	-	20	3068	c.2755G>A	c.(2755-2757)Gga>Aga	p.G919R	BAG6_ENST00000375976.4_Missense_Mutation_p.G913R|BAG6_ENST00000211379.5_Missense_Mutation_p.G913R|BAG6_ENST00000362049.6_Missense_Mutation_p.G913R|BAG6_ENST00000404765.2_Missense_Mutation_p.G949R|BAG6_ENST00000470875.1_5'Flank|BAG6_ENST00000439687.2_Missense_Mutation_p.G787R	NM_004639.3|NM_080703.2	NP_004630.3|NP_542434.1	P46379	BAG6_HUMAN	BCL2-associated athanogene 6	919					brain development (GO:0007420)|cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|embryo development (GO:0009790)|immune system process (GO:0002376)|internal peptidyl-lysine acetylation (GO:0018393)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|kidney development (GO:0001822)|lung development (GO:0030324)|negative regulation of apoptotic process (GO:0043066)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of proteolysis (GO:0045861)|protein stabilization (GO:0050821)|regulation of cell proliferation (GO:0042127)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)|tail-anchored membrane protein insertion into ER membrane (GO:0071816)|transport (GO:0006810)|ubiquitin-dependent protein catabolic process (GO:0006511)	BAT3 complex (GO:0071818)|cytosol (GO:0005829)|nucleus (GO:0005634)	polyubiquitin binding (GO:0031593)|proteasome binding (GO:0070628)|ribosome binding (GO:0043022)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(2)|pancreas(2)|skin(3)|urinary_tract(2)	36						AGCCTCAGTCCCATCATAGTG	0.547																																					p.G919R		Atlas-SNP	.											.	BAG6	73	.	0			c.G2755A						.						83	66	72					6																	31608658		1511	2709	4220	SO:0001583	missense	7917	exon20			TCAGTCCCATCAT	M31294	CCDS4709.1, CCDS47403.1, CCDS56414.1, CCDS56415.1	6p21.3	2011-06-14	2010-12-09	2010-12-09	ENSG00000204463	ENSG00000204463			13919	protein-coding gene	gene with protein product		142590	"HLA-B associated transcript 3"	BAT3		2156268	Standard	NM_004639		Approved	G3, D6S52E	uc003nvf.4	P46379	OTTHUMG00000031171	ENST00000375964.6:c.2755G>A	chr6.hg19:g.31608658C>T	ENSP00000365131:p.Gly919Arg	61.0	0.0		83.0	4.0	NM_004639	A2ADJ7|A3KQ42|A3KQ44|A6NGY6|A6PWF7|B0UX84|B4DZ12|B4E3V4|E7EMZ4|F8VXY4|O95874|Q5HYL9|Q5SQ35|Q5SQ36|Q5SQ37|Q5SQ41|Q5SRP8|Q5SRP9|Q5STC1|Q5STX1|Q5STX3|Q96SA6|Q9BCN4	Missense_Mutation	SNP	ENST00000375964.6	hg19	CCDS47403.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.33|16.33	3.092130|3.092130	0.55968|0.55968	.|.	.|.	ENSG00000204463|ENSG00000204463	ENST00000375976;ENST00000375964;ENST00000211379;ENST00000404765;ENST00000439687;ENST00000362049|ENST00000422948;ENST00000441793	T;T;T;T;T;T|.	0.45668|.	1.55;1.55;1.55;1.56;0.89;1.55|.	4.96|4.96	4.96|4.96	0.65561|0.65561	.|.	0.168112|.	0.51477|.	D|.	0.000086|.	T|.	0.21307|.	0.0513|.	N|N	0.22421|0.22421	0.69|0.69	0.34548|0.34548	D|D	0.711047|0.711047	D;D;D;D|.	0.76494|.	0.967;0.999;0.999;0.999|.	P;D;D;D|.	0.76071|.	0.71;0.951;0.973;0.987|.	T|.	0.07309|.	-1.0779|.	10|.	0.25106|.	T|.	0.35|.	.|.	6.615|6.615	0.22773|0.22773	0.1798:0.7312:0.0:0.0889|0.1798:0.7312:0.0:0.0889	.|.	787;913;919;913|.	E7EMZ4;F8VXY4;P46379;P46379-2|.	.;.;BAG6_HUMAN;.|.	R|X	913;919;913;949;787;913|19;61	ENSP00000365143:G913R;ENSP00000365131:G919R;ENSP00000211379:G913R;ENSP00000384494:G949R;ENSP00000402856:G787R;ENSP00000354875:G913R|.	ENSP00000211379:G913R|.	G|W	-|-	1|3	0|0	BAG6|BAG6	31716637|31716637	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.169000|1.169000	0.31871|0.31871	2.753000|2.753000	0.94483|0.94483	0.650000|0.650000	0.86243|0.86243	GGA|TGG	.	.		0.547	BAG6-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_080703		T	31608658	C	T	31608658	3	4	255	1	0	0	0	0	1	0	0	0	1322	632	22	3	667	3	BAT3	6	31608658	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	746343	31608658	139506409	246	35591										
ANKS1A	23294	hgsc.bcm.edu	37	chr6	35047653	35047653	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	catcatcgcctccctcgcagAcagaccgtacgaggagccgc	10	17	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:35047653A>G	ENST00000360359.3	+	16	2630	c.2492A>G	c.(2491-2493)gAc>gGc	p.D831G	ANKS1A_ENST00000535627.1_Intron|ANKS1A_ENST00000470698.1_3'UTR	NM_015245.2	NP_056060.2	Q92625	ANS1A_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1A	831	SAM 2. {ECO:0000255|PROSITE- ProRule:PRU00184}.				ephrin receptor signaling pathway (GO:0048013)|neuron remodeling (GO:0016322)|substrate-dependent cell migration (GO:0006929)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleus (GO:0005634)				cervix(2)|endometrium(3)|large_intestine(4)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						TCCCTCGCAGACAGACCGTAC	0.602																																					p.D831G		Atlas-SNP	.											.	ANKS1A	123	.	0			c.A2492G						.						24	23	23					6																	35047653		2194	4287	6481	SO:0001583	missense	23294	exon16			TCGCAGACAGACC	D86982	CCDS4798.1	6p21.31	2013-01-10	2006-02-17	2006-02-17	ENSG00000064999	ENSG00000064999		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	20961	protein-coding gene	gene with protein product		608994	"ankyrin repeat and SAM domain containing 1", "ankyrin repeat and sterile alpha motif domain containing 1"	ANKS1		9039502	Standard	NM_015245		Approved	KIAA0229	uc003ojx.4	Q92625	OTTHUMG00000014559	ENST00000360359.3:c.2492A>G	chr6.hg19:g.35047653A>G	ENSP00000353518:p.Asp831Gly	71.0	0.0		91.0	4.0	NM_015245	A2RUC1|B4DQW8|Q5JYI9|Q5SYR2|Q86WQ7	Missense_Mutation	SNP	ENST00000360359.3	hg19	CCDS4798.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.620170	0.87460	.	.	ENSG00000064999	ENST00000360359;ENST00000373990	T	0.06449	3.3	5.66	5.66	0.87406	Sterile alpha motif domain (1);Sterile alpha motif/pointed domain (2);	0.000000	0.51477	D	0.000083	T	0.09069	0.0224	L	0.31420	0.93	0.80722	D	1	B;B;P	0.49635	0.212;0.004;0.926	P;B;D	0.63381	0.7;0.102;0.914	T	0.10543	-1.0625	10	0.72032	D	0.01	-11.983	15.8895	0.79286	1.0:0.0:0.0:0.0	.	157;157;831	Q49AR9;E7EM84;Q92625	.;.;ANS1A_HUMAN	G	831;157	ENSP00000353518:D831G	ENSP00000353518:D831G	D	+	2	0	ANKS1A	35155631	1.000000	0.71417	0.953000	0.39169	0.842000	0.47809	9.315000	0.96313	2.153000	0.67306	0.459000	0.35465	GAC	.	.		0.602	ANKS1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040262.1	XM_166478		G	35047653	A	G	35047653	3	3	255	1	0	0	0	0	1	0	0	0	688	275	10	2	2554	2	ANKS1A	6	35047653	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	3438995	35047653	136067414	247	35592										
PNPLA1	285848	hgsc.bcm.edu	37	chr6	36270243	36270243	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aactaggccaagaacagcccCaaggtatggacccttctggc	10	13	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:36270243C>T	ENST00000394571.2	+	6	1381	c.1381C>T	c.(1381-1383)Caa>Taa	p.Q461*	PNPLA1_ENST00000388715.3_Nonsense_Mutation_p.Q366*|PNPLA1_ENST00000312917.5_Nonsense_Mutation_p.Q375*	NM_001145717.1	NP_001139189.2	Q8N8W4	PLPL1_HUMAN	patatin-like phospholipase domain containing 1	461					lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)			breast(1)|kidney(1)|large_intestine(4)|lung(9)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	22						AGAACAGCCCCAAGGTATGGA	0.572											OREG0017382	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q461X		Atlas-SNP	.											.	PNPLA1	92	.	0			c.C1381T						.						104	109	107					6																	36270243		2203	4300	6503	SO:0001587	stop_gained	285848	exon6			CAGCCCCAAGGTA		CCDS34438.1, CCDS47416.1, CCDS54997.1	6p21.31	2009-01-12			ENSG00000180316	ENSG00000180316		"Patatin-like phospholipase domain containing"	21246	protein-coding gene	gene with protein product		612121				16799181, 19029121	Standard	NM_001145717		Approved	FLJ38755, dJ50J22.1	uc010jwf.2	Q8N8W4	OTTHUMG00000014590	ENST00000394571.2:c.1381C>T	chr6.hg19:g.36270243C>T	ENSP00000378072:p.Gln461*	57.0	0.0	861	79.0	4.0	NM_001145717	A3RMU3|J3JS20|Q2A6N1|Q3SY95|Q3SY96|Q5R3L2	Nonsense_Mutation	SNP	ENST00000394571.2	hg19	CCDS54997.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.078915	0.76528	.	.	ENSG00000180316	ENST00000388715;ENST00000312917;ENST00000457797;ENST00000394571	.	.	.	4.35	2.53	0.30540	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	0.7404	5.2586	0.15561	0.2022:0.6918:0.0:0.106	.	.	.	.	X	366;375;462;461	.	ENSP00000321116:Q375X	Q	+	1	0	PNPLA1	36378221	0.009000	0.17119	0.080000	0.20451	0.193000	0.23685	0.665000	0.25083	0.563000	0.29222	0.650000	0.86243	CAA	.	.		0.572	PNPLA1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_173676		T	36270243	C	T	36270243	4	4	255	1	0	0	0	0	0	1	0	0	12173	595	21	3	1430	3	PNPLA1	6	36270243	Nonsense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1222590	36270243	134844824	248	35593										
TSPO2	222642	hgsc.bcm.edu	37	chr6	41011697	41011697	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aggccctgctgcacctgctgCtgctgtatgggctggtggtg	16	11	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:41011697C>T	ENST00000373161.1	+	4	579	c.334C>T	c.(334-336)Ctg>Ttg	p.L112L	TSPO2_ENST00000470917.1_Silent_p.L112L|TSPO2_ENST00000373158.2_Silent_p.C64C	NM_001010873.2	NP_001010873.1	Q5TGU0	TSPO2_HUMAN	translocator protein 2	112					transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cholesterol binding (GO:0015485)			breast(1)|endometrium(2)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						GCACCTGCTGCTGCTGTATGG	0.627																																					p.L112L		Atlas-SNP	.											.	TSPO2	26	.	0			c.C334T						.						78	57	64					6																	41011697		2203	4300	6503	SO:0001819	synonymous_variant	222642	exon4			CTGCTGCTGCTGT		CCDS34444.1	6p21.1	2009-09-18	2009-09-04	2009-09-04	ENSG00000112212	ENSG00000112212			21256	protein-coding gene	gene with protein product	"similar to RIKEN cDNA 2510027D20"		"benzodiazapine receptor (peripheral)-like 1"	BZRPL1		19729679	Standard	NM_001010873		Approved	dJ34B21.2	uc003opj.3	Q5TGU0	OTTHUMG00000014666	ENST00000373161.1:c.334C>T	chr6.hg19:g.41011697C>T		89.0	0.0		68.0	4.0	NM_001010873	B2RPR2|B7ZMN8|Q3SX82	Silent	SNP	ENST00000373161.1	hg19	CCDS34444.1																																																																																			.	.		0.627	TSPO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040493.1	NM_001010873.2		T	41011697	C	T	41011697	2	4	255	1	0	0	0	0	0	0	0	1	16671	796	28	3		3	TSPO2	6	41011697	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	4741454	41011697	130103370	249	35594										
UBR2	23304	hgsc.bcm.edu	37	chr6	42573470	42573470	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	atcacacagagagaagagtgAcacctactattgcatgctgt	9	9	1	4			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:42573470A>G	ENST00000372899.1	+	6	932	c.674A>G	c.(673-675)gAc>gGc	p.D225G	UBR2_ENST00000372903.2_Missense_Mutation_p.D225G|UBR2_ENST00000372901.1_Missense_Mutation_p.D225G	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	225					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			GAGAAGAGTGACACCTACTAT	0.328																																					p.D225G		Atlas-SNP	.											.	UBR2	134	.	0			c.A674G						.						102	102	102					6																	42573470		2203	4299	6502	SO:0001583	missense	23304	exon6			AGAGTGACACCTA	BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"Ubiquitin protein ligase E3 component n-recognins"	21289	protein-coding gene	gene with protein product		609134	"chromosome 6 open reading frame 133"	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.674A>G	chr6.hg19:g.42573470A>G	ENSP00000361990:p.Asp225Gly	94.0	0.0		98.0	4.0	NM_001184801	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Missense_Mutation	SNP	ENST00000372899.1	hg19	CCDS4870.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.210388	0.79240	.	.	ENSG00000024048	ENST00000372903;ENST00000372899;ENST00000372901	T;T;T	0.74526	-0.85;0.08;0.08	5.22	5.22	0.72569	Adaptor protein ClpS, core (1);Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like (2);	0.000000	0.85682	D	0.000000	T	0.59473	0.2196	L	0.42245	1.32	0.80722	D	1	B;P	0.39847	0.385;0.691	B;B	0.40038	0.178;0.317	T	0.65578	-0.6134	10	0.46703	T	0.11	-12.8997	15.1076	0.72332	1.0:0.0:0.0:0.0	.	225;225	Q8IWV8;Q8IWV8-2	UBR2_HUMAN;.	G	225	ENSP00000361994:D225G;ENSP00000361990:D225G;ENSP00000361992:D225G	ENSP00000361990:D225G	D	+	2	0	UBR2	42681448	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.299000	0.78831	1.980000	0.57719	0.455000	0.32223	GAC	.	.		0.328	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255		G	42573470	A	G	42573470	3	3	255	1	0	0	0	0	1	0	0	0	16917	275	10	2	696	2	UBR2	6	42573470	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	1561773	42573470	128541597	250	35595										
CUL7	9820	hgsc.bcm.edu	37	chr6	43010877	43010877	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gatgctgcttggaaggccccGggtagccaaggagctccagt	15	11	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:43010877G>T	ENST00000265348.3	-	18	3482	c.3397C>A	c.(3397-3399)Cgg>Agg	p.R1133R	CUL7_ENST00000535468.1_Silent_p.R1217R|CUL7_ENST00000478630.1_5'Flank			Q14999	CUL7_HUMAN	cullin 7	1133					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|epithelial to mesenchymal transition (GO:0001837)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|mitotic cytokinesis (GO:0000281)|placenta development (GO:0001890)|positive regulation of dendrite morphogenesis (GO:0050775)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	3M complex (GO:1990393)|anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|Cul7-RING ubiquitin ligase complex (GO:0031467)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(8)|liver(1)|lung(11)|ovary(3)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	49			all cancers(41;0.00231)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			GGAAGGCCCCGGGTAGCCAAG	0.622																																					p.R1217R		Atlas-SNP	.											.	CUL7	133	.	0			c.C3649A						.						53	52	52					6																	43010877		2203	4300	6503	SO:0001819	synonymous_variant	9820	exon18			GGCCCCGGGTAGC	BC033647	CCDS4881.1, CCDS55003.1	6p21.1	2011-05-24	2004-03-22	2004-03-22	ENSG00000044090	ENSG00000044090			21024	protein-coding gene	gene with protein product		609577	"KIAA0076"	KIAA0076		12481031, 12904573	Standard	NM_014780		Approved	dJ20C7.5	uc011dvb.2	Q14999	OTTHUMG00000014718	ENST00000265348.3:c.3397C>A	chr6.hg19:g.43010877G>T		47.0	0.0		59.0	4.0	NM_001168370	B4DYZ0|F5H0L1|Q5T654	Silent	SNP	ENST00000265348.3	hg19	CCDS4881.1																																																																																			.	.		0.622	CUL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040575.1	NM_014780		T	43010877	G	T	43010877	2	4	255	1	0	0	0	0	0	0	0	1	4062	1115	39	1		1	CUL7	6	43010877	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	437407	43010877	128104190	251	35596										
XPO5	57510	hgsc.bcm.edu	37	chr6	43515423	43515423	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gtacccacatacgcaatgaaAgcatcaacatctgacagcac	6	13	2	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:43515423A>G	ENST00000265351.7	-	19	2292	c.2082T>C	c.(2080-2082)gcT>gcC	p.A694A		NM_020750.2	NP_065801.1	Q9HAV4	XPO5_HUMAN	exportin 5	694					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(4)|lung(10)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	34	all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243)		all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524)			ACGCAATGAAAGCATCAACAT	0.478																																					p.A694A		Atlas-SNP	.											.	XPO5	79	.	0			c.T2082C						.						100	96	97					6																	43515423		1969	4163	6132	SO:0001819	synonymous_variant	57510	exon19			AATGAAAGCATCA	AB033117	CCDS47430.1	6p21.1	2011-04-13			ENSG00000124571	ENSG00000124571		"Exportins"	17675	protein-coding gene	gene with protein product		607845				11777942, 12426392	Standard	NM_020750		Approved	KIAA1291	uc003ovp.3	Q9HAV4	OTTHUMG00000014742	ENST00000265351.7:c.2082T>C	chr6.hg19:g.43515423A>G		85.0	0.0		103.0	5.0	NM_020750	Q5JTE6|Q96G48|Q96HN3|Q9BWM6|Q9BZV5|Q9H9M4|Q9NT89|Q9NW39|Q9ULC9	Silent	SNP	ENST00000265351.7	hg19	CCDS47430.1																																																																																			.	.		0.478	XPO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040657.2	NM_020750		G	43515423	A	G	43515423	2	3	255	1	0	0	0	0	0	0	0	1	17462	59	3	2		2	XPO5	6	43515423	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	504546	43515423	127599644	252	35597										
TFAP2D	83741	hgsc.bcm.edu	37	chr6	50740456	50740456	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gaactacttggaaaaacacaCtactcacaagaacggcggag	9	10	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:50740456C>T	ENST00000008391.3	+	8	1466	c.1238C>T	c.(1237-1239)aCt>aTt	p.T413I		NM_172238.3	NP_758438.2			transcription factor AP-2 delta (activating enhancer binding protein 2 delta)											NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(26)|ovary(6)|pancreas(1)|prostate(5)|stomach(1)	60	Lung NSC(77;0.0334)					GAAAAACACACTACTCACAAG	0.512																																					p.T413I		Atlas-SNP	.											.	TFAP2D	144	.	0			c.C1238T						.						66	65	65					6																	50740456		2203	4300	6503	SO:0001583	missense	83741	exon8			AACACACTACTCA	AY028376	CCDS4933.1	6p12.3	2008-02-05	2004-10-26	2004-10-27		ENSG00000008197			15581	protein-coding gene	gene with protein product		610161	"transcription factor AP-2 beta (activating enhancer-binding protein 2 beta)-like 1"	TFAP2BL1		11733187	Standard	NM_172238		Approved		uc003paf.3	Q7Z6R9		ENST00000008391.3:c.1238C>T	chr6.hg19:g.50740456C>T	ENSP00000008391:p.Thr413Ile	85.0	0.0		120.0	43.0	NM_172238		Missense_Mutation	SNP	ENST00000008391.3	hg19	CCDS4933.1	.	.	.	.	.	.	.	.	.	.	C	11.60	1.688160	0.29962	.	.	ENSG00000008197	ENST00000008391	D	0.96885	-4.16	5.31	4.45	0.53987	Transcription factor AP-2, C-terminal (1);	0.155858	0.43579	D	0.000551	D	0.89132	0.6628	N	0.08118	0	0.44149	D	0.996941	B	0.19583	0.037	B	0.34346	0.18	D	0.85696	0.1310	10	0.66056	D	0.02	-8.3512	16.1801	0.81892	0.0:0.8665:0.1335:0.0	.	413	Q7Z6R9	AP2D_HUMAN	I	413	ENSP00000008391:T413I	ENSP00000008391:T413I	T	+	2	0	TFAP2D	50848415	1.000000	0.71417	0.987000	0.45799	0.690000	0.40134	7.487000	0.81328	1.258000	0.44101	-0.355000	0.07637	ACT	.	.		0.512	TFAP2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040881.1	NM_172238		T	50740456	C	T	50740456	3	4	255	1	0	0	0	0	1	0	0	0	15805	565	20	3	1268	3	TFAP2D	6	50740456	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	7225033	50740456	120374611	253	35598										
DST	667	hgsc.bcm.edu	37	chr6	56346864	56346864	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcactttatgctgatcaatgAgagtccggagagcatcctca	9	10	3	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:56346864A>G	ENST00000361203.3	-	85	20562	c.20555T>C	c.(20554-20556)cTc>cCc	p.L6852P	DST_ENST00000370769.4_Missense_Mutation_p.L6963P|DST_ENST00000370754.5_Missense_Mutation_p.L7141P|DST_ENST00000244364.6_Missense_Mutation_p.L4549P|DST_ENST00000421834.2_Missense_Mutation_p.L4875P|DST_ENST00000370788.2_Missense_Mutation_p.L4766P|DST_ENST00000446842.2_Missense_Mutation_p.L6637P|DST_ENST00000312431.6_3'UTR			Q03001	DYST_HUMAN	dystonin	6853					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			CTGATCAATGAGAGTCCGGAG	0.453																																					p.L4549P		Atlas-SNP	.											.	DST	1427	.	0			c.T13646C						.						40	42	41					6																	56346864		1944	4136	6080	SO:0001583	missense	667	exon71			TCAATGAGAGTCC	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.20555T>C	chr6.hg19:g.56346864A>G	ENSP00000354508:p.Leu6852Pro	30.0	0.0		71.0	4.0	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	hg19		.	.	.	.	.	.	.	.	.	.	A	16.38	3.107436	0.56291	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T	0.61742	0.08;0.08;0.08;0.08;0.08;0.08;0.08	5.86	5.86	0.93980	.	0.000000	0.48286	D	0.000184	T	0.71204	0.3312	M	0.74881	2.28	0.35649	D	0.811618	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.996	D;D;D;D;D	0.97110	1.0;1.0;0.999;0.982;0.946	T	0.73404	-0.3993	9	0.52906	T	0.07	.	16.5602	0.84551	1.0:0.0:0.0:0.0	.	4875;6963;7141;6961;4549	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	P	4549;7141;6963;4875;6637;4766;6852	ENSP00000244364:L4549P;ENSP00000359790:L7141P;ENSP00000359805:L6963P;ENSP00000400883:L4875P;ENSP00000393645:L6637P;ENSP00000359824:L4766P;ENSP00000354508:L6852P	ENSP00000244364:L4549P	L	-	2	0	DST	56454823	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	7.412000	0.80091	2.367000	0.80283	0.528000	0.53228	CTC	.	.		0.453	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		G	56346864	A	G	56346864	3	3	255	1	0	0	0	0	1	0	0	0	4785	304	11	2	1925	2	DST	6	56346864	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	5606408	56346864	114768203	254	35599										
DST	667	hgsc.bcm.edu	37	chr6	56358808	56358808	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	atattaatcaaagcacatacTttcctttcattgagtttggt	5	7	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:56358808T>C	ENST00000361203.3	-	78	19441	c.19434A>G	c.(19432-19434)aaA>aaG	p.K6478K	DST_ENST00000370769.4_Splice_Site_p.K6589K|DST_ENST00000370754.5_Splice_Site_p.K6767K|DST_ENST00000244364.6_Splice_Site_p.K4175K|DST_ENST00000421834.2_Splice_Site_p.K4501K|DST_ENST00000370788.2_Splice_Site_p.K4392K|DST_ENST00000446842.2_Splice_Site_p.K6263K|DST_ENST00000312431.6_3'UTR|DST_ENST00000340834.4_5'Flank			Q03001	DYST_HUMAN	dystonin	6478					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			AAGCACATACTTTCCTTTCAT	0.348																																					p.K4175K		Atlas-SNP	.											.	DST	1427	.	0			c.A12525G						.						136	119	124					6																	56358808		1823	4087	5910	SO:0001630	splice_region_variant	667	exon64			ACATACTTTCCTT	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.19434+1A>G	chr6.hg19:g.56358808T>C		121.0	0.0		138.0	6.0	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000361203.3	hg19																																																																																				.	.		0.348	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	Silent	C	56358808	T	C	56358808	5	2	255	1	0	0	0	0	0	0	1	0	4785	1623	56	2	3074	2	DST	6	56358808	Splice_Site	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	11944	56358808	114756259	255	35600										
DST	667	hgsc.bcm.edu	37	chr6	56436957	56436957	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gacaaattatttgttttttcAaggaccaaagccttatcact	5	8	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:56436957A>G	ENST00000361203.3	-	49	13036	c.13029T>C	c.(13027-13029)ctT>ctC	p.L4343L	DST_ENST00000370769.4_Silent_p.L4345L|DST_ENST00000370754.5_Silent_p.L4523L|DST_ENST00000244364.6_Silent_p.L1931L|DST_ENST00000421834.2_Silent_p.L2257L|DST_ENST00000370788.2_Silent_p.L2257L|DST_ENST00000446842.2_Silent_p.L4019L|DST_ENST00000312431.6_3'UTR			Q03001	DYST_HUMAN	dystonin	4343					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TTGTTTTTTCAAGGACCAAAG	0.303																																					p.L1931L		Atlas-SNP	.											.	DST	1427	.	0			c.T5793C						.						47	42	44					6																	56436957		1798	4055	5853	SO:0001819	synonymous_variant	667	exon34			TTTTTCAAGGACC	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.13029T>C	chr6.hg19:g.56436957A>G		40.0	0.0		54.0	4.0	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000361203.3	hg19																																																																																				.	.		0.303	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		G	56436957	A	G	56436957	2	3	255	1	0	0	0	0	0	0	0	1	4785	117	5	2		2	DST	6	56436957	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	78149	56436957	114678110	256	35601										
KIAA1586	57691	hgsc.bcm.edu	37	chr6	56917800	56917800	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	taaggattgttcagcagttcGgcatttgggatcgaaagcag	13	6	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:56917800G>T	ENST00000370733.4	+	4	710	c.503G>T	c.(502-504)cGg>cTg	p.R168L	KIAA1586_ENST00000488682.1_3'UTR|KIAA1586_ENST00000545356.1_Missense_Mutation_p.R141L	NM_020931.2	NP_065982.1	Q9HCI6	K1586_HUMAN	KIAA1586	168							nucleic acid binding (GO:0003676)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|skin(1)	18	Lung NSC(77;0.0969)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			TCAGCAGTTCGGCATTTGGGA	0.363																																					p.R168L		Atlas-SNP	.											.	KIAA1586	59	.	0			c.G503T						.						92	88	89					6																	56917800		2203	4300	6503	SO:0001583	missense	57691	exon4			CAGTTCGGCATTT	AB046806	CCDS34480.1, CCDS69138.1	6p12.1	2014-03-27			ENSG00000168116	ENSG00000168116			21360	protein-coding gene	gene with protein product						10997877	Standard	NM_001286274		Approved		uc003pdj.3	Q9HCI6	OTTHUMG00000014915	ENST00000370733.4:c.503G>T	chr6.hg19:g.56917800G>T	ENSP00000359768:p.Arg168Leu	75.0	0.0		97.0	4.0	NM_020931	A8K4M3|Q8IW25	Missense_Mutation	SNP	ENST00000370733.4	hg19	CCDS34480.1	.	.	.	.	.	.	.	.	.	.	g	10.92	1.487165	0.26686	.	.	ENSG00000168116	ENST00000370733;ENST00000545356	T;T	0.32023	1.47;1.47	3.7	-1.16	0.09678	.	.	.	.	.	T	0.03827	0.0108	N	0.08118	0	0.20074	N	0.999935	B;B	0.26483	0.15;0.15	B;B	0.23018	0.043;0.043	T	0.39840	-0.9594	9	0.32370	T	0.25	.	3.7093	0.08413	0.4506:0.1941:0.3553:0.0	.	141;168	F5H2N6;Q9HCI6	.;K1586_HUMAN	L	168;141	ENSP00000359768:R168L;ENSP00000445507:R141L	ENSP00000359768:R168L	R	+	2	0	KIAA1586	57025759	0.044000	0.20184	0.755000	0.31263	0.980000	0.70556	-0.274000	0.08537	-0.113000	0.11958	0.467000	0.42956	CGG	.	.		0.363	KIAA1586-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041033.1	NM_020931		T	56917800	G	T	56917800	3	4	255	1	0	0	0	0	1	0	0	0	8254	1116	39	1	517	1	KIAA1586	6	56917800	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	480843	56917800	114197267	257	35602										
BAI3	577	hgsc.bcm.edu	37	chr6	69684659	69684659	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttgtttaaaattgcagcaccTtatgaaatatgccctgagga	8	7	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:69684659T>C	ENST00000370598.1	+	9	2351	c.1530T>C	c.(1528-1530)ccT>ccC	p.P510P		NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	510					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				TTGCAGCACCTTATGAAATAT	0.413																																					p.P510P		Atlas-SNP	.											.	BAI3	451	.	0			c.T1530C						.						100	96	97					6																	69684659		2203	4300	6503	SO:0001819	synonymous_variant	577	exon9			AGCACCTTATGAA	AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"-", "GPCR / Class B : Orphans"	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.1530T>C	chr6.hg19:g.69684659T>C		112.0	0.0		147.0	6.0	NM_001704	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Silent	SNP	ENST00000370598.1	hg19	CCDS4968.1																																																																																			.	.		0.413	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			C	69684659	T	C	69684659	2	2	255	1	0	0	0	0	0	0	0	1	1300	1596	56	2		2	BAI3	6	69684659	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	12766859	69684659	101430408	258	35603										
PRSS35	167681	hgsc.bcm.edu	37	chr6	84234261	84234261	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aattggaagcgcaaaatcatTgcggtctactcagggcacca	10	10	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:84234261T>C	ENST00000369700.3	+	2	1278	c.1101T>C	c.(1099-1101)atT>atC	p.I367I	PRSS35_ENST00000536636.1_Silent_p.I367I	NM_153362.2	NP_699193.2	Q8N3Z0	PRS35_HUMAN	protease, serine, 35	367	Peptidase S1.					extracellular region (GO:0005576)|mitochondrion (GO:0005739)	serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(2)|large_intestine(12)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	32		all_cancers(76;0.000113)|Acute lymphoblastic leukemia(125;1.09e-08)|all_hematologic(105;3.12e-05)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0768)		GCAAAATCATTGCGGTCTACT	0.522																																					p.I367I		Atlas-SNP	.											.	PRSS35	60	.	0			c.T1101C						.						76	71	73					6																	84234261		2203	4300	6503	SO:0001819	synonymous_variant	167681	exon2			AATCATTGCGGTC	BC037170	CCDS4999.1	6q14.2	2010-05-12	2004-07-09	2004-07-09	ENSG00000146250	ENSG00000146250		"Serine peptidases / Serine peptidases"	21387	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 158"	C6orf158			Standard	NM_153362		Approved	MGC46520, dJ223E3.1	uc003pjz.3	Q8N3Z0	OTTHUMG00000015113	ENST00000369700.3:c.1101T>C	chr6.hg19:g.84234261T>C		59.0	0.0		87.0	4.0	NM_153362	A8K7B3|Q9BQP6	Silent	SNP	ENST00000369700.3	hg19	CCDS4999.1																																																																																			.	.		0.522	PRSS35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041352.1	NM_153362		C	84234261	T	C	84234261	2	2	255	1	0	0	0	0	0	0	0	1	12636	1800	63	2		2	PRSS35	6	84234261	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	14549602	84234261	86880806	259	35604										
SPACA1	81833	hgsc.bcm.edu	37	chr6	88768538	88768538	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggaaacttctaagacaagacCaagtgagtaatgaatggata	10	5	1	4			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:88768538C>A	ENST00000237201.1	+	4	589	c.472C>A	c.(472-474)Caa>Aaa	p.Q158K		NM_030960.2	NP_112222.1	Q9HBV2	SACA1_HUMAN	sperm acrosome associated 1	158					acrosome assembly (GO:0001675)	acrosomal membrane (GO:0002080)|integral component of membrane (GO:0016021)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(12)|skin(1)|upper_aerodigestive_tract(2)	20		all_cancers(76;8.24e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;4.11e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.00011)		BRCA - Breast invasive adenocarcinoma(108;0.11)		AAGACAAGACCAAGTGAGTAA	0.333																																					p.Q158K		Atlas-SNP	.											.	SPACA1	49	.	0			c.C472A						.						69	69	69					6																	88768538		2203	4300	6503	SO:0001583	missense	81833	exon4			CAAGACCAAGTGA	AF203447	CCDS5014.1	6q15	2012-09-20			ENSG00000118434	ENSG00000118434			14967	protein-coding gene	gene with protein product		612739					Standard	NM_030960		Approved	SAMP32	uc003pmn.3	Q9HBV2	OTTHUMG00000015183	ENST00000237201.1:c.472C>A	chr6.hg19:g.88768538C>A	ENSP00000237201:p.Gln158Lys	91.0	0.0		89.0	5.0	NM_030960		Missense_Mutation	SNP	ENST00000237201.1	hg19	CCDS5014.1	.	.	.	.	.	.	.	.	.	.	C	16.52	3.146618	0.57044	.	.	ENSG00000118434	ENST00000237201	T	0.23147	1.92	5.77	5.77	0.91146	.	0.088226	0.49916	D	0.000136	T	0.21921	0.0528	L	0.55103	1.725	0.33206	D	0.552773	P	0.40970	0.734	P	0.46510	0.519	T	0.04579	-1.0941	10	0.44086	T	0.13	-16.1234	13.8419	0.63444	0.1525:0.8475:0.0:0.0	.	158	Q9HBV2	SACA1_HUMAN	K	158	ENSP00000237201:Q158K	ENSP00000237201:Q158K	Q	+	1	0	SPACA1	88825257	0.996000	0.38824	0.991000	0.47740	0.643000	0.38383	2.284000	0.43478	2.733000	0.93635	0.585000	0.79938	CAA	.	.		0.333	SPACA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041459.1			A	88768538	C	A	88768538	3	1	255	1	0	0	0	0	1	0	0	0	14987	595	21	3	486	3	SPACA1	6	88768538	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	4534277	88768538	82346529	260	35605										
MDN1	23195	hgsc.bcm.edu	37	chr6	90368429	90368429	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gctgctgctcctcagagtgtTcttcaggatgctgagcagca	12	11	3	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:90368429T>G	ENST00000369393.3	-	89	15036	c.14921A>C	c.(14920-14922)gAa>gCa	p.E4974A	MDN1_ENST00000428876.1_Missense_Mutation_p.E4974A			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	4974					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		CTCAGAGTGTTCTTCAGGATG	0.542																																					p.E4974A		Atlas-SNP	.											.	MDN1	478	.	0			c.A14921C						.						294	256	269					6																	90368429		2203	4300	6503	SO:0001583	missense	23195	exon89			GAGTGTTCTTCAG	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.14921A>C	chr6.hg19:g.90368429T>G	ENSP00000358400:p.Glu4974Ala	319.0	1.0		314.0	149.0	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	hg19	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	T	10.95	1.495882	0.26774	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.03889	3.77;3.77	5.09	3.93	0.45458	.	0.395777	0.24470	N	0.038257	T	0.01222	0.0040	N	0.16478	0.41	0.33461	D	0.584991	B	0.10296	0.003	B	0.11329	0.006	T	0.46748	-0.9169	10	0.35671	T	0.21	.	9.9126	0.41415	0.0:0.0818:0.0:0.9182	.	4974	Q9NU22	MDN1_HUMAN	A	4974	ENSP00000358400:E4974A;ENSP00000413970:E4974A	ENSP00000358400:E4974A	E	-	2	0	MDN1	90425150	1.000000	0.71417	0.514000	0.27761	0.007000	0.05969	4.247000	0.58750	0.897000	0.36392	0.454000	0.30748	GAA	.	.		0.542	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			G	90368429	T	G	90368429	3	3	255	1	0	0	0	0	1	0	0	0	9424	1783	62	5	1925	5	MDN1	6	90368429	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	1599891	90368429	80746638	261	35606										
MDN1	23195	hgsc.bcm.edu	37	chr6	90428309	90428309	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cccttacagttccctccaccTtctctagcagcctcctccaa	3	20	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:90428309T>C	ENST00000369393.3	-	43	6474	c.6359A>G	c.(6358-6360)aAg>aGg	p.K2120R	MDN1_ENST00000428876.1_Missense_Mutation_p.K2120R			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	2120					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		TCCCTCCACCTTCTCTAGCAG	0.463																																					p.K2120R		Atlas-SNP	.											.	MDN1	478	.	0			c.A6359G						.						110	100	104					6																	90428309		2203	4300	6503	SO:0001583	missense	23195	exon43			TCCACCTTCTCTA	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.6359A>G	chr6.hg19:g.90428309T>C	ENSP00000358400:p.Lys2120Arg	71.0	0.0		78.0	4.0	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	hg19	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	T	7.537	0.659870	0.14645	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.03272	3.99;3.99	5.91	4.75	0.60458	ATPase, AAA+ type, core (1);	0.159044	0.56097	D	0.000038	T	0.00936	0.0031	N	0.13235	0.315	0.32896	D	0.512502	B	0.06786	0.001	B	0.17979	0.02	T	0.49652	-0.8917	10	0.22109	T	0.4	.	11.7235	0.51696	0.0:0.0685:0.0:0.9315	.	2120	Q9NU22	MDN1_HUMAN	R	2120	ENSP00000358400:K2120R;ENSP00000413970:K2120R	ENSP00000358400:K2120R	K	-	2	0	MDN1	90485030	1.000000	0.71417	1.000000	0.80357	0.303000	0.27691	2.403000	0.44530	1.067000	0.40740	0.528000	0.53228	AAG	.	.		0.463	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			C	90428309	T	C	90428309	3	2	255	1	0	0	0	0	1	0	0	0	9424	1609	56	2	10671	2	MDN1	6	90428309	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	59880	90428309	80686758	262	35607										
SIM1	6492	hgsc.bcm.edu	37	chr6	100898180	100898180	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggactgaggctgtctctgagAtgtacatgatcttcccatct	10	10	3	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:100898180A>G	ENST00000369208.3	-	4	1093	c.311T>C	c.(310-312)aTc>aCc	p.I104T	SIM1_ENST00000262901.4_Missense_Mutation_p.I104T			P81133	SIM1_HUMAN	single-minded family bHLH transcription factor 1	104	PAS 1. {ECO:0000255|PROSITE- ProRule:PRU00140}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(4)|endometrium(5)|kidney(1)|large_intestine(15)|lung(34)|ovary(4)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	79		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0774)		TGTCTCTGAGATGTACATGAT	0.537																																					p.I104T		Atlas-SNP	.											.	SIM1	173	.	0			c.T311C						.						178	161	167					6																	100898180		2203	4300	6503	SO:0001583	missense	6492	exon3			TCTGAGATGTACA	U70212	CCDS5045.1	6q16.3	2013-10-17	2013-10-17		ENSG00000112246	ENSG00000112246		"Basic helix-loop-helix proteins"	10882	protein-coding gene	gene with protein product		603128	"single-minded (Drosophila) homolog 1", "single-minded homolog 1 (Drosophila)"			9199934, 11448938	Standard	NM_005068		Approved	bHLHe14	uc003pqj.4	P81133	OTTHUMG00000015275	ENST00000369208.3:c.311T>C	chr6.hg19:g.100898180A>G	ENSP00000358210:p.Ile104Thr	57.0	0.0		90.0	4.0	NM_005068	Q5TDP7	Missense_Mutation	SNP	ENST00000369208.3	hg19	CCDS5045.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.493368	0.84962	.	.	ENSG00000112246	ENST00000369208;ENST00000262901	T;T	0.18502	2.21;2.21	4.99	4.99	0.66335	PAS (2);PAS fold (1);	0.000000	0.85682	D	0.000000	T	0.34337	0.0894	M	0.79011	2.435	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.28364	-1.0046	10	0.87932	D	0	.	14.6886	0.69068	1.0:0.0:0.0:0.0	.	104	P81133	SIM1_HUMAN	T	104	ENSP00000358210:I104T;ENSP00000262901:I104T	ENSP00000262901:I104T	I	-	2	0	SIM1	101004901	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	8.932000	0.92897	1.885000	0.54596	0.459000	0.35465	ATC	.	.		0.537	SIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041628.3	NM_005068		G	100898180	A	G	100898180	3	3	255	1	0	0	0	0	1	0	0	0	14338	333	12	2	2025	2	SIM1	6	100898180	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	10469871	100898180	70216887	263	35608										
SMPD2	6610	hgsc.bcm.edu	37	chr6	109764241	109764241	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cgtcagccagcaggagctgaAgccatttccctttggtgtcc	11	13	1	1	rs145532915	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:109764241A>G	ENST00000258052.3	+	8	1045	c.686A>G	c.(685-687)aAg>aGg	p.K229R	PPIL6_ENST00000424445.2_5'Flank|PPIL6_ENST00000521072.2_5'Flank|PPIL6_ENST00000440797.2_5'Flank	NM_003080.2	NP_003071.2	O60906	NSMA_HUMAN	sphingomyelin phosphodiesterase 2, neutral membrane (neutral sphingomyelinase)	229					apoptotic signaling pathway (GO:0097190)|ceramide biosynthetic process (GO:0046513)|glycosphingolipid metabolic process (GO:0006687)|neurotrophin TRK receptor signaling pathway (GO:0048011)|response to mechanical stimulus (GO:0009612)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin metabolic process (GO:0006684)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)			endometrium(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(2)	8		all_cancers(87;1.1e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000144)|all_lung(197;0.0221)|Colorectal(196;0.0488)|Lung SC(18;0.0548)		Epithelial(106;0.0137)|all cancers(137;0.0188)|OV - Ovarian serous cystadenocarcinoma(136;0.0228)|BRCA - Breast invasive adenocarcinoma(108;0.0566)		CAGGAGCTGAAGCCATTTCCC	0.502																																					p.K229R		Atlas-SNP	.											.	SMPD2	25	.	0			c.A686G						.						96	88	91					6																	109764241		2203	4300	6503	SO:0001583	missense	6610	exon8			AGCTGAAGCCATT	AJ222801	CCDS5075.1	6q21	2009-10-23			ENSG00000135587	ENSG00000135587	3.1.4.12		11121	protein-coding gene	gene with protein product		603498				9520418	Standard	XM_005267109		Approved	nSMase, ISC1	uc003pti.3	O60906	OTTHUMG00000015348	ENST00000258052.3:c.686A>G	chr6.hg19:g.109764241A>G	ENSP00000258052:p.Lys229Arg	105.0	0.0		124.0	6.0	NM_003080	Q5TED1|Q9BWR3	Missense_Mutation	SNP	ENST00000258052.3	hg19	CCDS5075.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	1.731|1.731	-0.494046|-0.494046	0.04322|0.04322	.|.	.|.	ENSG00000135587|ENSG00000135587	ENST00000258052|ENST00000458487	T|.	0.32272|.	1.46|.	5.95|5.95	0.512|0.512	0.16994|0.16994	Endonuclease/exonuclease/phosphatase (2);|.	1.230960|.	0.05155|.	N|.	0.496721|.	T|T	0.12263|0.12263	0.0298|0.0298	N|N	0.21282|0.21282	0.65|0.65	0.09310|0.09310	N|N	1|1	B|.	0.21821|.	0.061|.	B|.	0.22152|.	0.038|.	T|T	0.33240|0.33240	-0.9876|-0.9876	10|5	0.13470|.	T|.	0.59|.	-0.2032|-0.2032	8.7389|8.7389	0.34545|0.34545	0.5746:0.0:0.4254:0.0|0.5746:0.0:0.4254:0.0	.|.	229|.	O60906|.	NSMA_HUMAN|.	R|G	229|126	ENSP00000258052:K229R|.	ENSP00000258052:K229R|.	K|S	+|+	2|1	0|0	SMPD2|SMPD2	109870934|109870934	0.030000|0.030000	0.19436|0.19436	0.001000|0.001000	0.08648|0.08648	0.147000|0.147000	0.21601|0.21601	0.364000|0.364000	0.20325|0.20325	0.077000|0.077000	0.16863|0.16863	0.533000|0.533000	0.62120|0.62120	AAG|AGC	.	A|0.999;T|0.001		0.502	SMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041755.1			G	109764241	A	G	109764241	3	3	255	1	0	0	0	0	1	0	0	0	14820	72	3	2	716	2	SMPD2	6	109764241	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	8866061	109764241	61350826	264	35609										
LAMA2	3908	hgsc.bcm.edu	37	chr6	129722435	129722435	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctttaaaagagggcaatgacAtactcgatgaagccaaccgt	9	9	0	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:129722435A>G	ENST00000421865.2	+	38	5561	c.5512A>G	c.(5512-5514)Ata>Gta	p.I1838V		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	1838	Domain II and I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		GGGCAATGACATACTCGATGA	0.388																																					p.I1838V		Atlas-SNP	.											.	LAMA2	481	.	0			c.A5512G						.						141	137	139					6																	129722435		2203	4300	6503	SO:0001583	missense	3908	exon38			AATGACATACTCG	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"Laminins"	6482	protein-coding gene	gene with protein product	"merosin", "congenital muscular dystrophy"	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.5512A>G	chr6.hg19:g.129722435A>G	ENSP00000400365:p.Ile1838Val	111.0	0.0		97.0	4.0	NM_000426	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	hg19	CCDS5138.1	.	.	.	.	.	.	.	.	.	.	A	10.54	1.378577	0.24944	.	.	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865	T	0.09723	2.95	5.28	1.41	0.22369	Laminin I (1);	0.261499	0.38492	N	0.001671	T	0.01627	0.0052	L	0.29908	0.895	0.30704	N	0.75001	B;B	0.11235	0.004;0.004	B;B	0.20184	0.026;0.028	T	0.47674	-0.9099	10	0.06891	T	0.86	.	6.3007	0.21111	0.6158:0.2486:0.1356:0.0	.	1838;1838	A6NF00;P24043	.;LAMA2_HUMAN	V	1838	ENSP00000400365:I1838V	ENSP00000346769:I1838V	I	+	1	0	LAMA2	129764128	1.000000	0.71417	0.933000	0.37362	0.848000	0.48234	1.173000	0.31920	0.059000	0.16252	0.533000	0.62120	ATA	.	.		0.388	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			G	129722435	A	G	129722435	3	3	255	1	0	0	0	0	1	0	0	0	8615	217	8	2	5662	2	LAMA2	6	129722435	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	19958194	129722435	41392632	265	35610										
ECT2L	345930	hgsc.bcm.edu	37	chr6	139135640	139135640	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccttatagctctttcaggaaAgagtggctcttataagtcat	8	8	4	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:139135640A>G	ENST00000423192.1	+	3	240	c.79A>G	c.(79-81)Aga>Gga	p.R27G	ECT2L_ENST00000541398.1_5'Flank|ECT2L_ENST00000367682.2_Missense_Mutation_p.R27G			Q008S8	ECT2L_HUMAN	epithelial cell transforming 2 like	27							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			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						CTTTCAGGAAAGAGTGGCTCT	0.378			"N, Splice, Mis"		ETP ALL																																p.R27G		Atlas-SNP	.		Rec	yes		6	6q24.1	345930	epithelial cell transforming sequence 2 oncogene-like		L	.	ECT2L	75	.	0			c.A79G						.						72	70	71					6																	139135640		1844	4092	5936	SO:0001583	missense	345930	exon3			CAGGAAAGAGTGG		CCDS43508.1	6q24.1	2014-03-11	2014-03-11		ENSG00000203734	ENSG00000203734		"Rho guanine nucleotide exchange factors", "F-boxes /  "other""	21118	protein-coding gene	gene with protein product	"lung specific F-box and DH domain containing protein", "F-box protein 49"		"chromosome 6 open reading frame 91", "epithelial cell transforming sequence 2 oncogene-like"	C6orf91			Standard	NM_001077706		Approved	ARHGEF32, FBXO49, LFDH	uc021zfx.1	Q008S8	OTTHUMG00000015679	ENST00000423192.1:c.79A>G	chr6.hg19:g.139135640A>G	ENSP00000387388:p.Arg27Gly	66.0	0.0		65.0	4.0	NM_001195037	B2RUV6|Q5JWK2|Q5JWK3|Q5JWK4	Missense_Mutation	SNP	ENST00000423192.1	hg19	CCDS43508.1	.	.	.	.	.	.	.	.	.	.	A	19.22	3.784984	0.70222	.	.	ENSG00000203734	ENST00000423192;ENST00000401414;ENST00000367682	T;T;T	0.69175	-0.18;-0.38;-0.18	5.43	4.22	0.49857	.	.	.	.	.	T	0.71643	0.3364	M	0.62723	1.935	0.80722	D	1	D	0.71674	0.998	D	0.78314	0.991	T	0.75525	-0.3287	9	0.87932	D	0	.	10.4461	0.44495	0.8373:0.1627:0.0:0.0	.	27	Q008S8	ECT2L_HUMAN	G	27	ENSP00000387388:R27G;ENSP00000385187:R27G;ENSP00000356655:R27G	ENSP00000356655:R27G	R	+	1	2	ECT2L	139177333	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.000000	0.57039	2.066000	0.61787	0.533000	0.62120	AGA	.	.		0.378	ECT2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042441.3	NM_001077706		G	139135640	A	G	139135640	3	3	255	1	0	0	0	0	1	0	0	0	4904	64	3	2	85	2	ECT2L	6	139135640	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	9413205	139135640	31979427	266	35611										
PLAGL1	5325	hgsc.bcm.edu	37	chr6	144263706	144263706	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cattttgttggggtcgtgggTctggaggtggtttttcaggt	17	4	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:144263706T>C	ENST00000360537.2	-	5	2160	c.247A>G	c.(247-249)Acc>Gcc	p.T83A	PLAGL1_ENST00000437412.1_Missense_Mutation_p.T31A|PLAGL1_ENST00000354765.2_Missense_Mutation_p.T83A|PLAGL1_ENST00000429150.1_Missense_Mutation_p.T83A|PLAGL1_ENST00000392307.1_Missense_Mutation_p.T31A|PLAGL1_ENST00000367571.1_Missense_Mutation_p.T83A|PLAGL1_ENST00000416623.1_Missense_Mutation_p.T83A|PLAGL1_ENST00000367572.1_Missense_Mutation_p.T31A|PLAGL1_ENST00000444202.1_Missense_Mutation_p.T83A|PLAGL1_ENST00000392309.1_Missense_Mutation_p.T83A			Q9UM63	PLAL1_HUMAN	pleiomorphic adenoma gene-like 1	83					apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			endometrium(1)|large_intestine(4)|lung(2)|prostate(1)|skin(3)|stomach(2)	13				OV - Ovarian serous cystadenocarcinoma(155;5.74e-07)|GBM - Glioblastoma multiforme(68;0.0885)		GGGTCGTGGGTCTGGAGGTGG	0.542											OREG0017707	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T83A		Atlas-SNP	.											.	PLAGL1	33	.	0			c.A247G						.						124	114	118					6																	144263706		2203	4300	6503	SO:0001583	missense	5325	exon7			CGTGGGTCTGGAG	U81992	CCDS5202.1, CCDS5203.1	6q24-q25	2013-01-08			ENSG00000118495	ENSG00000118495		"Zinc fingers, C2H2-type"	9046	protein-coding gene	gene with protein product		603044				9722527, 9671765	Standard	NM_006718		Approved	ZAC, LOT1	uc003qkf.3	Q9UM63	OTTHUMG00000015738	ENST00000360537.2:c.247A>G	chr6.hg19:g.144263706T>C	ENSP00000353734:p.Thr83Ala	43.0	0.0	1685	55.0	4.0	NM_001080953	B2RBA4|B2RCM8|E1P595|E1P597|O76019|Q7Z3V8|Q92981|Q96JR9|Q9UIZ0	Missense_Mutation	SNP	ENST00000360537.2	hg19	CCDS5202.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.021705	0.75275	.	.	ENSG00000118495	ENST00000360537;ENST00000354765;ENST00000444202;ENST00000429150;ENST00000392309;ENST00000416623;ENST00000437412;ENST00000392307;ENST00000367572;ENST00000367571;ENST00000417959	T;T;T;T;T;T;T;T;T;T;T	0.29917	1.55;1.55;1.55;1.55;1.55;1.55;2.73;2.73;2.73;1.55;2.73	6.16	3.75	0.43078	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.082393	0.52532	N	0.000071	T	0.27454	0.0674	L	0.45285	1.41	0.40727	D	0.982711	D	0.65815	0.995	P	0.62184	0.899	T	0.08411	-1.0723	10	0.72032	D	0.01	-23.0055	7.8278	0.29326	0.1236:0.0665:0.0:0.8099	.	83	Q9UM63	PLAL1_HUMAN	A	83;83;83;83;83;83;31;31;31;83;31	ENSP00000353734:T83A;ENSP00000346810:T83A;ENSP00000400929:T83A;ENSP00000398409:T83A;ENSP00000376125:T83A;ENSP00000400060:T83A;ENSP00000392418:T31A;ENSP00000376124:T31A;ENSP00000356544:T31A;ENSP00000356543:T83A;ENSP00000395960:T31A	ENSP00000346810:T83A	T	-	1	0	PLAGL1	144305399	1.000000	0.71417	0.754000	0.31244	0.990000	0.78478	7.977000	0.88081	0.547000	0.28938	0.528000	0.53228	ACC	.	.		0.542	PLAGL1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042541.1			C	144263706	T	C	144263706	3	2	255	1	0	0	0	0	1	0	0	0	12028	1667	58	2	1148	2	PLAGL1	6	144263706	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	5128066	144263706	26851361	267	35612										
TCP10	6953	hgsc.bcm.edu	37	chr6	167789461	167789461	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cgaccctgctcaccagctccTctggctgctgccgtctgctc	9	19	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:167789461T>C	ENST00000397829.4	-	6	848	c.681A>G	c.(679-681)agA>agG	p.R227R	TCP10_ENST00000366827.2_Silent_p.R227R	NM_004610.3	NP_004601.3	Q12799	TCP10_HUMAN	t-complex 10	254						cytosol (GO:0005829)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(2)|lung(6)	18		Breast(66;1.53e-05)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;4.05e-20)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)|GBM - Glioblastoma multiforme(31;0.0386)		CACCAGCTCCTCTGGCTGCTG	0.572																																					p.R227R		Atlas-SNP	.											.	TCP10	35	.	0			c.A681G						.						20	24	22					6																	167789461		1985	4167	6152	SO:0001819	synonymous_variant	6953	exon6			AGCTCCTCTGGCT	U03399	CCDS43527.1	6q27	2012-09-20	2012-09-20		ENSG00000203690	ENSG00000203690			11656	protein-coding gene	gene with protein product		187020	"t-complex 10 (a murine tcp homolog)", "t-complex 10 (mouse)", "t-complex 10 homolog (mouse)"			8111376	Standard	NM_004610		Approved		uc003qvv.1	Q12799	OTTHUMG00000016026	ENST00000397829.4:c.681A>G	chr6.hg19:g.167789461T>C		113.0	0.0		120.0	5.0	NM_004610	Q5JR60|Q6P4F4	Silent	SNP	ENST00000397829.4	hg19	CCDS43527.1																																																																																			.	.		0.572	TCP10-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365570.1	NM_004610		C	167789461	T	C	167789461	2	2	255	1	0	0	0	0	0	0	0	1	15725	1548	54	2		2	TCP10	6	167789461	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	23525755	167789461	3325606	268	35613										
TBP	6908	hgsc.bcm.edu	37	chr6	170871004	170871004	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gagcaacaaaggcagcagcaGcaacaacaacagcagcagca	10	12	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:170871004G>A	ENST00000392092.2	+	3	459	c.180G>A	c.(178-180)caG>caA	p.Q60Q	TBP_ENST00000540980.1_Silent_p.Q40Q|TBP_ENST00000230354.6_Silent_p.Q60Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	60	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		Ggcagcagcagcaacaacaac	0.542																																					p.Q60Q		Atlas-SNP	.											.	TBP	58	.	0			c.G180A						.						43	45	44					6																	170871004		2203	4300	6503	SO:0001819	synonymous_variant	6908	exon3			GCAGCAGCAACAA	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"General transcription factors"	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.180G>A	chr6.hg19:g.170871004G>A		58.0	0.0		73.0	4.0	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	hg19	CCDS5315.1																																																																																			.	.		0.542	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194		A	170871004	G	A	170871004	2	1	255	1	0	0	0	0	0	0	0	1	15659	962	34	3		3	TBP	6	170871004	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	3081543	170871004	244063	269	35614										
TNRC18	84629	hgsc.bcm.edu	37	chr7	5427683	5427683	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cccgggcaaagctgccactgTactttataaggctctgcatg	10	12	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:5427683T>A	ENST00000430969.1	-	5	2120	c.1772A>T	c.(1771-1773)tAc>tTc	p.Y591F	TNRC18_ENST00000399537.4_Missense_Mutation_p.Y591F	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	591							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		GCTGCCACTGTACTTTATAAG	0.682																																					p.Y591F		Atlas-SNP	.											.	TNRC18	311	.	0			c.A1772T						.						6	8	7					7																	5427683		1928	4082	6010	SO:0001583	missense	84629	exon5			CCACTGTACTTTA	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"Trinucleotide (CAG) repeat containing"	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.1772A>T	chr7.hg19:g.5427683T>A	ENSP00000395538:p.Tyr591Phe	70.0	0.0		55.0	4.0	NM_001080495	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	hg19	CCDS47534.1	.	.	.	.	.	.	.	.	.	.	t	15.00	2.703990	0.48412	.	.	ENSG00000182095	ENST00000399537;ENST00000430969	T;T	0.33216	1.43;1.42	4.83	4.83	0.62350	.	.	.	.	.	T	0.52191	0.1719	M	0.63843	1.955	0.40329	D	0.978904	D	0.76494	0.999	D	0.78314	0.991	T	0.56998	-0.7886	9	0.62326	D	0.03	.	14.419	0.67171	0.0:0.0:0.0:1.0	.	591	O15417	TNC18_HUMAN	F	591	ENSP00000382452:Y591F;ENSP00000395538:Y591F	ENSP00000382452:Y591F	Y	-	2	0	TNRC18	5394209	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	5.390000	0.66261	1.804000	0.52760	0.454000	0.30748	TAC	.	.		0.682	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				A	5427683	T	A	5427683	3	1	255	1	0	0	0	0	1	0	0	0	16354	1638	57	4	7238	4	TNRC18	7	5427683	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10		5427683	153710980	270	35615										
MPP6	51678	hgsc.bcm.edu	37	chr7	24690104	24690104	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctgtttcttatttttcatagGgtgtgacatttagggttgaa	10	4	2	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:24690104G>T	ENST00000222644.5	+	5	674	c.424G>T	c.(424-426)Ggt>Tgt	p.G142C	MPP6_ENST00000409761.1_Splice_Site_p.G30C|MPP6_ENST00000396475.2_Splice_Site_p.G142C			Q99547	MPH6_HUMAN	membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6)	0					maturation of 5.8S rRNA (GO:0000460)	cytoplasm (GO:0005737)|exosome (RNase complex) (GO:0000178)|nucleolus (GO:0005730)|nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|pancreas(1)|skin(2)	20						TTTTTCATAGGGTGTGACATT	0.323																																					p.G142C		Atlas-SNP	.											.	MPP6	62	.	0			c.G424T						.						50	53	52					7																	24690104		2202	4299	6501	SO:0001630	splice_region_variant	51678	exon6			TCATAGGGTGTGA	AF162130	CCDS5388.1	7p15	2007-08-01			ENSG00000105926	ENSG00000105926			18167	protein-coding gene	gene with protein product		606959				10753959, 11311936	Standard	NM_016447		Approved	PALS2, VAM-1, p55T	uc003swx.3	Q9NZW5	OTTHUMG00000023507	ENST00000222644.5:c.424-1G>T	chr7.hg19:g.24690104G>T		108.0	0.0		84.0	5.0	NM_016447	B2RAF0	Missense_Mutation	SNP	ENST00000222644.5	hg19	CCDS5388.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.354341	0.82243	.	.	ENSG00000105926	ENST00000432190;ENST00000222644;ENST00000409761;ENST00000396475;ENST00000430180	D;D;D;D;D	0.84944	-1.92;-1.92;-1.92;-1.92;-1.92	6.06	6.06	0.98353	PDZ/DHR/GLGF (4);	0.000000	0.64402	D	0.000018	D	0.95604	0.8571	H	0.97611	4.04	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96542	0.9401	9	.	.	.	.	18.8014	0.92018	0.0:0.0:1.0:0.0	.	142	Q9NZW5	MPP6_HUMAN	C	142;142;30;142;142	ENSP00000395859:G142C;ENSP00000222644:G142C;ENSP00000386262:G30C;ENSP00000379737:G142C;ENSP00000391020:G142C	.	G	+	1	0	MPP6	24656629	1.000000	0.71417	1.000000	0.80357	0.725000	0.41563	9.130000	0.94437	2.882000	0.98803	0.655000	0.94253	GGT	.	.		0.323	MPP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250272.4		Missense_Mutation	T	24690104	G	T	24690104	5	4	255	1	0	0	0	0	0	0	1	0	9747	1246	43	3	438	3	MPP6	7	24690104	Splice_Site	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	19262421	24690104	134448559	271	35616										
OSBPL3	26031	hgsc.bcm.edu	37	chr7	24870476	24870476	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aaatggcttgcttccagctcGgtagtagctagatgcatacg	11	9	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:24870476G>T	ENST00000313367.2	-	16	2246	c.1795C>A	c.(1795-1797)Cga>Aga	p.R599R	OSBPL3_ENST00000396431.1_Silent_p.R568R|OSBPL3_ENST00000431825.2_Silent_p.R532R|OSBPL3_ENST00000352860.1_Silent_p.R568R|OSBPL3_ENST00000396429.1_Silent_p.R563R|OSBPL3_ENST00000353930.1_Silent_p.R563R|OSBPL3_ENST00000409069.1_Silent_p.R532R	NM_015550.2	NP_056365.1	Q9H4L5	OSBL3_HUMAN	oxysterol binding protein-like 3	599					lipid transport (GO:0006869)	cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(19)|prostate(1)|skin(3)|urinary_tract(1)	43						CTTCCAGCTCGGTAGTAGCTA	0.428																																					p.R599R		Atlas-SNP	.											.	OSBPL3	100	.	0			c.C1795A						.						124	130	128					7																	24870476		2203	4300	6503	SO:0001819	synonymous_variant	26031	exon16			CAGCTCGGTAGTA	AB014604	CCDS5390.1, CCDS5391.1, CCDS5392.1, CCDS47564.1	7p15.3	2013-01-10			ENSG00000070882	ENSG00000070882		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16370	protein-coding gene	gene with protein product		606732		OSBP3		9734811	Standard	XM_005249698		Approved	ORP-3, ORP3, KIAA0704	uc003sxf.3	Q9H4L5	OTTHUMG00000023277	ENST00000313367.2:c.1795C>A	chr7.hg19:g.24870476G>T		119.0	0.0		80.0	4.0	NM_015550	A4D167|A4D168|A4D169|A4D170|A4D171|A4D172|B8ZZ79|B8ZZP0|O14591|O43357|O43358|Q8N702|Q8N703|Q8N704|Q8NFH0|Q8NFH1|Q8NI12|Q8NI13|Q9BZF4|Q9UED6	Silent	SNP	ENST00000313367.2	hg19	CCDS5390.1																																																																																			.	.		0.428	OSBPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214085.2			T	24870476	G	T	24870476	2	4	255	1	0	0	0	0	0	0	0	1	11288	1124	39	1		1	OSBPL3	7	24870476	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	180372	24870476	134268187	272	35617										
HOXA11	3207	hgsc.bcm.edu	37	chr7	27222608	27222608	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccagctctcggatctggtacTtggtataggggcagcgcttt	13	10	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:27222608T>C	ENST00000006015.3	-	2	820	c.749A>G	c.(748-750)aAg>aGg	p.K250R	HOXA11-AS_ENST00000520360.1_RNA|HOXA11-AS_ENST00000522863.1_RNA|HOXA11-AS_ENST00000522674.1_RNA|HOXA10_ENST00000396344.4_5'Flank|HOXA11-AS_ENST00000520395.1_RNA|RP1-170O19.20_ENST00000470747.4_5'Flank	NM_005523.5	NP_005514.1	P31270	HXA11_HUMAN	homeobox A11	250					anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|developmental growth (GO:0048589)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal joint morphogenesis (GO:0060272)|male gonad development (GO:0008584)|mesodermal cell fate specification (GO:0007501)|metanephros development (GO:0001656)|multicellular organismal development (GO:0007275)|organ induction (GO:0001759)|positive regulation of cell development (GO:0010720)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)|uterus development (GO:0060065)	nucleus (GO:0005634)|protein complex (GO:0043234)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(8)|ovary(1)|skin(2)	16						GATCTGGTACTTGGTATAGGG	0.572			T	NUP98	CML																																p.K250R		Atlas-SNP	.		Dom	yes		7	7p15-p14.2	3207	homeo box A11		L	.	HOXA11	29	.	0			c.A749G						.						89	86	87					7																	27222608		2203	4300	6503	SO:0001583	missense	3207	exon2			TGGTACTTGGTAT		CCDS5411.1	7p15.2	2014-09-17	2005-12-22		ENSG00000005073	ENSG00000005073		"Homeoboxes / ANTP class : HOXL subclass"	5101	protein-coding gene	gene with protein product		142958	"homeo box A11"	HOX1I, HOX1		1973146, 1358459	Standard	NM_005523		Approved		uc003syx.3	P31270	OTTHUMG00000023437	ENST00000006015.3:c.749A>G	chr7.hg19:g.27222608T>C	ENSP00000006015:p.Lys250Arg	102.0	0.0		72.0	4.0	NM_005523	A4D190	Missense_Mutation	SNP	ENST00000006015.3	hg19	CCDS5411.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	28.7|28.7	4.946108|4.946108	0.92593|0.92593	.|.	.|.	ENSG00000005073|ENSG00000005073	ENST00000006015|ENST00000517402	D|.	0.96334|.	-3.98|.	5.91|5.91	5.91|5.91	0.95273|0.95273	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.60779|0.60779	0.2295|0.2295	L|L	0.39245|0.39245	1.2|1.2	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.80764|.	0.994|.	T|T	0.56739|0.56739	-0.7929|-0.7929	10|5	0.87932|.	D|.	0|.	.|.	16.3512|16.3512	0.83208|0.83208	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	250|.	P31270|.	HXA11_HUMAN|.	R|G	250|220	ENSP00000006015:K250R|.	ENSP00000006015:K250R|.	K|S	-|-	2|1	0|0	HOXA11|HOXA11	27189133|27189133	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	8.040000|8.040000	0.89188|0.89188	2.266000|2.266000	0.75297|0.75297	0.533000|0.533000	0.62120|0.62120	AAG|AGT	.	.		0.572	HOXA11-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358754.1			C	27222608	T	C	27222608	3	2	255	1	0	0	0	0	1	0	0	0	7299	1609	56	2	196	2	HOXA11	7	27222608	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	2352132	27222608	131916055	273	35618										
C7orf36	57002	hgsc.bcm.edu	37	chr7	39610225	39610225	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gacgactccgaggaacattgAggtaatttttaaagtctaaa	9	6	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:39610225A>G	ENST00000223273.2	+	2	293	c.250A>G	c.(250-252)Agt>Ggt	p.S84G	YAE1D1_ENST00000432096.2_Splice_Site_p.R84G|YAE1D1_ENST00000448268.1_Splice_Site_p.S84G	NM_020192.3	NP_064577.1	Q9NRH1	YAED1_HUMAN	Yae1 domain containing 1	84																	AGGAACATTGAGGTAATTTTT	0.358																																					p.S84G		Atlas-SNP	.											.	YAE1D1	2	.	0			c.A250G						.						103	106	105					7																	39610225		2203	4300	6503	SO:0001630	splice_region_variant	57002	exon2			ACATTGAGGTAAT	AF226046	CCDS5459.1, CCDS64630.1	7p14.1	2011-11-24	2011-11-24	2011-11-24	ENSG00000241127	ENSG00000241127			24857	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 36"	C7orf36		12477932	Standard	NM_020192		Approved	GK003	uc003thc.4	Q9NRH1	OTTHUMG00000128689	ENST00000223273.2:c.251+1A>G	chr7.hg19:g.39610225A>G		102.0	0.0		75.0	4.0	NM_020192	A4D1W4|B4DE83|Q6IAF7|Q8WVZ5	Missense_Mutation	SNP	ENST00000223273.2	hg19	CCDS5459.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.73|14.73	2.622666|2.622666	0.46840|0.46840	.|.	.|.	ENSG00000241127|ENSG00000241127	ENST00000432096|ENST00000223273;ENST00000448268	T|T;T	0.46819|0.53857	0.86|0.6;0.68	6.02|6.02	6.02|6.02	0.97574|0.97574	.|.	.|0.078660	.|0.85682	.|D	.|0.000000	T|T	0.69620|0.69620	0.3131|0.3131	M|M	0.74467|0.74467	2.265|2.265	0.22511|0.22511	N|N	0.999035|0.999035	.|D	.|0.76494	.|0.999	.|P	.|0.61070	.|0.883	T|T	0.66705|0.66705	-0.5856|-0.5856	6|10	.|0.66056	.|D	.|0.02	-12.0254|-12.0254	15.1131|15.1131	0.72375|0.72375	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|84	.|Q9NRH1	.|CG036_HUMAN	G|G	84|84	ENSP00000395777:R84G|ENSP00000223273:S84G;ENSP00000400511:S84G	.|ENSP00000223273:S84G	R|S	+|+	1|1	2|0	C7orf36|C7orf36	39576750|39576750	1.000000|1.000000	0.71417|0.71417	0.970000|0.970000	0.41538|0.41538	0.390000|0.390000	0.30446|0.30446	6.415000|6.415000	0.73328|0.73328	2.304000|2.304000	0.77564|0.77564	0.528000|0.528000	0.53228|0.53228	AGG|AGT	.	.		0.358	YAE1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250586.1	NM_020192	Missense_Mutation	G	39610225	A	G	39610225	5	3	255	1	0	0	0	0	0	0	1	0	2392	318	11	2	256	2	C7orf36	7	39610225	Splice_Site	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	12387617	39610225	119528438	274	35619										
YKT6	10652	hgsc.bcm.edu	37	chr7	44250697	44250697	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccaaatccgaggtgctgggaAcacagtctaaagccttctat	9	11	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:44250697A>G	ENST00000223369.2	+	6	622	c.535A>G	c.(535-537)Aca>Gca	p.T179A	YKT6_ENST00000447123.1_3'UTR|YKT6_ENST00000496112.1_Intron	NM_006555.3	NP_006546.1	O15498	YKT6_HUMAN	YKT6 v-SNARE homolog (S. cerevisiae)	179	v-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00290}.				ER to Golgi vesicle-mediated transport (GO:0006888)|metabolic process (GO:0008152)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)|vesicle docking involved in exocytosis (GO:0006904)|vesicle targeting (GO:0006903)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|SNARE complex (GO:0031201)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|SNAP receptor activity (GO:0005484)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(1)	7						GGTGCTGGGAACACAGTCTAA	0.502																																					p.T179A		Atlas-SNP	.											.	YKT6	12	.	0			c.A535G						.						94	91	92					7																	44250697		2203	4300	6503	SO:0001583	missense	10652	exon6			CTGGGAACACAGT	BC007319	CCDS5482.1	7p13	2006-07-07			ENSG00000106636	ENSG00000106636			16959	protein-coding gene	gene with protein product	"R-SNARE"	606209				15479160, 15544955	Standard	NM_006555		Approved		uc003tkm.3	O15498	OTTHUMG00000129089	ENST00000223369.2:c.535A>G	chr7.hg19:g.44250697A>G	ENSP00000223369:p.Thr179Ala	146.0	0.0		99.0	4.0	NM_006555	B4DR94|Q53F01|Q6FGU9|Q6IB15	Missense_Mutation	SNP	ENST00000223369.2	hg19	CCDS5482.1	.	.	.	.	.	.	.	.	.	.	A	2.683	-0.274933	0.05679	.	.	ENSG00000106636	ENST00000223369	T	0.39787	1.06	5.27	1.61	0.23674	Synaptobrevin (2);	0.653853	0.16508	N	0.211353	T	0.14270	0.0345	N	0.02865	-0.47	0.23893	N	0.996549	B	0.02656	0.0	B	0.01281	0.0	T	0.32929	-0.9888	10	0.02654	T	1	-0.7788	7.4757	0.27374	0.7474:0.0:0.2526:0.0	.	179	O15498	YKT6_HUMAN	A	179	ENSP00000223369:T179A	ENSP00000223369:T179A	T	+	1	0	YKT6	44217222	0.103000	0.21917	0.025000	0.17156	0.979000	0.70002	2.011000	0.40922	0.040000	0.15660	0.533000	0.62120	ACA	.	.		0.502	YKT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251125.2	NM_006555		G	44250697	A	G	44250697	3	3	255	1	0	0	0	0	1	0	0	0	17500	43	2	2	557	2	YKT6	7	44250697	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	4640472	44250697	114887966	275	35620										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48312768	48312768	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctcaattatttaagtttgacAtgaatgttttcacatctctt	4	7	3	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:48312768A>G	ENST00000435803.1	+	17	3529	c.3505A>G	c.(3505-3507)Atg>Gtg	p.M1169V		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1169					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						TAAGTTTGACATGAATGTTTT	0.383																																					p.M1169V		Atlas-SNP	.											.	ABCA13	1192	.	0			c.A3505G						.						95	91	92					7																	48312768		1843	4092	5935	SO:0001583	missense	154664	exon17			TTTGACATGAATG	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.3505A>G	chr7.hg19:g.48312768A>G	ENSP00000411096:p.Met1169Val	113.0	0.0		97.0	5.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	A	1.760	-0.487001	0.04352	.	.	ENSG00000179869	ENST00000435803	D	0.84442	-1.85	5.64	-7.85	0.01192	.	1.722330	0.03242	N	0.180484	T	0.73273	0.3566	L	0.44542	1.39	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.55560	-0.8122	9	.	.	.	.	1.7537	0.02977	0.2465:0.1869:0.3627:0.2039	.	1169	Q86UQ4	ABCAD_HUMAN	V	1169	ENSP00000411096:M1169V	.	M	+	1	0	ABCA13	48283314	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-1.146000	0.03191	-1.461000	0.01909	-1.783000	0.00646	ATG	.	.		0.383	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		G	48312768	A	G	48312768	3	3	255	1	0	0	0	0	1	0	0	0	31	217	8	2	3400	2	ABCA13	7	48312768	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	4062071	48312768	110825895	276	35621										
ZPBP	11055	hgsc.bcm.edu	37	chr7	50070900	50070900	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gataataataatgaggctcaCgataagctgtaaaaaattaa	7	4	1	1	rs368593046	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:50070900C>T	ENST00000046087.2	-	5	563	c.494G>A	c.(493-495)cGt>cAt	p.R165H	ZPBP_ENST00000491129.1_Intron|ZPBP_ENST00000419417.1_Missense_Mutation_p.R164H	NM_001159878.1|NM_007009.2	NP_001153350.1|NP_008940.2	Q9BS86	ZPBP1_HUMAN	zona pellucida binding protein	165					acrosome assembly (GO:0001675)|binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|extracellular region (GO:0005576)|nucleus (GO:0005634)|zona pellucida receptor complex (GO:0002199)				NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(3)	29	Glioma(55;0.08)|all_neural(89;0.245)					ATGAGGCTCACGATAAGCTGT	0.279													C|||	3	0.000599042	0	0	5008	,	,		16839	0.003		0	False		,,,				2504	0				p.R165H		Atlas-SNP	.											ZPBP,caecum,carcinoma,0,1	ZPBP	65	.	0			c.G494A						.	C	HIS/ARG,HIS/ARG	0,4404		0,0,2202	22	23	23		491,494	3.3	1	7		23	1,8591		0,1,4295	no	missense,missense	ZPBP	NM_001159878.1,NM_007009.2	29,29	0,1,6497	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	164/351,165/352	50070900	1,12995	2202	4296	6498	SO:0001583	missense	11055	exon5			GGCTCACGATAAG	D17570	CCDS5509.1, CCDS55110.1	7p14.3	2013-01-11			ENSG00000042813	ENSG00000042813		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15662	protein-coding gene	gene with protein product		608498				9378618	Standard	NM_007009		Approved	SP38, ZPBP1	uc003tou.3	Q9BS86	OTTHUMG00000023528	ENST00000046087.2:c.494G>A	chr7.hg19:g.50070900C>T	ENSP00000046087:p.Arg165His	35.0	0.0		35.0	2.0	NM_007009	A4D253|C9JPU1|Q15941|Q75KX9|Q75MI3	Missense_Mutation	SNP	ENST00000046087.2	hg19	CCDS5509.1	.	.	.	.	.	.	.	.	.	.	C	14.23	2.472613	0.43942	0.0	1.16E-4	ENSG00000042813	ENST00000046087;ENST00000419417	T;T	0.57752	0.38;0.38	5.25	3.33	0.38152	.	0.539928	0.18189	N	0.148884	T	0.45074	0.1324	M	0.69823	2.125	0.30181	N	0.800381	P;P	0.35944	0.529;0.529	B;B	0.29785	0.107;0.107	T	0.50499	-0.8821	9	.	.	.	-19.0611	8.0263	0.30438	0.1451:0.5656:0.2893:0.0	.	164;165	C9JPU1;Q9BS86	.;ZPBP1_HUMAN	H	165;164	ENSP00000046087:R165H;ENSP00000402071:R164H	.	R	-	2	0	ZPBP	50041446	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.170000	0.31883	2.604000	0.88044	0.655000	0.94253	CGT	.	.		0.279	ZPBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251374.1	NM_007009		T	50070900	C	T	50070900	3	4	255	1	0	0	0	0	1	0	0	0	18234	536	19	1	577	1	ZPBP	7	50070900	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1758132	50070900	109067763	277	35622										
EGFR	1956	hgsc.bcm.edu	37	chr7	55224338	55224338	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggcgatctccacatcctgccGgtggcatttagggggtgagt	15	10	1	1	rs2302536	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:55224338G>T	ENST00000275493.2	+	9	1296	c.1119G>T	c.(1117-1119)ccG>ccT	p.P373P	EGFR_ENST00000342916.3_Silent_p.P373P|EGFR_ENST00000344576.2_Silent_p.P373P|EGFR_ENST00000420316.2_Silent_p.P373P|EGFR_ENST00000442591.1_Silent_p.P373P|EGFR_ENST00000454757.2_Silent_p.P320P|EGFR_ENST00000455089.1_Silent_p.P328P	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	373					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)	p.P373P(2)		NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	ACATCCTGCCGGTGGCATTTA	0.408		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																											p.P373P		Atlas-SNP	.	yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"		"E, O"	EGFR_ENST00000344576,colon,carcinoma,0,2	EGFR	20426	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G1119T						.						80	82	82					7																	55224338		2203	4300	6503	SO:0001819	synonymous_variant	1956	exon9	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	CCTGCCGGTGGCA		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"	131550	"epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.1119G>T	chr7.hg19:g.55224338G>T		162.0	0.0		120.0	5.0	NM_201283	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	hg19	CCDS5514.1																																																																																			.	G|0.997;A|0.003		0.408	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		T	55224338	G	T	55224338	2	4	255	1	0	0	0	0	0	0	0	1	4969	1103	39	1		1	EGFR	7	55224338	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	5153438	55224338	103914325	278	35623										
EGFR	1956	hgsc.bcm.edu	37	chr7	55272980	55272980	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cagtccgttcccaaaaggccCgctggctctgtgcagaatcc	10	15	1	1	rs55796214	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:55272980C>A	ENST00000275493.2	+	28	3480	c.3303C>A	c.(3301-3303)ccC>ccA	p.P1101P	EGFR_ENST00000442591.1_Intron|EGFR_ENST00000454757.2_Silent_p.P1048P	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	1101					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	CCAAAAGGCCCGCTGGCTCTG	0.542		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																											p.P1101P		Atlas-SNP	.	yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"		"E, O"	EGFR,colon,carcinoma,0,1	EGFR	20426	.	0			c.C3303A						.						68	65	66					7																	55272980		2203	4300	6503	SO:0001819	synonymous_variant	1956	exon28	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	AAGGCCCGCTGGC		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"	131550	"epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.3303C>A	chr7.hg19:g.55272980C>A		92.0	0.0		55.0	3.0	NM_005228	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	hg19	CCDS5514.1																																																																																			.	C|1.000;G|0.000		0.542	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		A	55272980	C	A	55272980	2	1	255	1	0	0	0	0	0	0	0	1	4969	639	23	1		1	EGFR	7	55272980	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	48642	55272980	103865683	279	35624										
GUSB	2990	hgsc.bcm.edu	37	chr7	65429376	65429376	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cacgtattttctgcgtttttGatccagacccagatggtact	8	10	1	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:65429376G>T	ENST00000304895.4	-	11	1853	c.1723C>A	c.(1723-1725)Caa>Aaa	p.Q575K	GUSB_ENST00000421103.1_Missense_Mutation_p.Q429K|GUSB_ENST00000345660.6_Missense_Mutation_p.Q524K	NM_000181.3	NP_000172.2	P08236	BGLR_HUMAN	glucuronidase, beta	575					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-glucuronidase activity (GO:0004566)	p.Q575*(1)		breast(1)|cervix(2)|kidney(2)|large_intestine(4)|lung(10)|skin(1)	20						CTGCGTTTTTGATCCAGACCC	0.443																																					p.Q575K		Atlas-SNP	.											GUSB,NS,carcinoma,0,1	GUSB	52	.	1	Substitution - Nonsense(1)	lung(1)	c.C1723A						.						84	70	75					7																	65429376		2203	4297	6500	SO:0001583	missense	2990	exon11			GTTTTTGATCCAG	M15182	CCDS5530.1, CCDS64665.1	7q11.21	2012-10-02			ENSG00000169919	ENSG00000169919	3.2.1.31		4696	protein-coding gene	gene with protein product		611499				3468507	Standard	NM_000181		Approved		uc003tun.3	P08236	OTTHUMG00000023735	ENST00000304895.4:c.1723C>A	chr7.hg19:g.65429376G>T	ENSP00000302728:p.Gln575Lys	99.0	0.0		42.0	2.0	NM_000181	B4E1F6|E9PCV0|Q549U0|Q96CL9	Missense_Mutation	SNP	ENST00000304895.4	hg19	CCDS5530.1	.	.	.	.	.	.	.	.	.	.	G	14.09	2.432249	0.43122	.	.	ENSG00000169919	ENST00000304895;ENST00000421103;ENST00000345660	D;D;D	0.95137	-3.62;-3.62;-3.62	5.39	1.37	0.22104	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycoside hydrolase, family 2, TIM barrel (1);	0.364416	0.35124	N	0.003433	D	0.86628	0.5978	N	0.20685	0.6	0.39059	D	0.960485	B;B	0.12630	0.006;0.002	B;B	0.17433	0.018;0.004	T	0.74783	-0.3548	10	0.15499	T	0.54	.	9.5261	0.39165	0.0:0.2243:0.3974:0.3783	.	429;575	E9PCV0;P08236	.;BGLR_HUMAN	K	575;429;524	ENSP00000302728:Q575K;ENSP00000391390:Q429K;ENSP00000340734:Q524K	ENSP00000302728:Q575K	Q	-	1	0	GUSB	65066811	1.000000	0.71417	0.119000	0.21687	0.227000	0.25037	1.842000	0.39250	0.067000	0.16545	-0.188000	0.12872	CAA	.	.		0.443	GUSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251637.3	NM_000181		T	65429376	G	T	65429376	3	4	255	1	0	0	0	0	1	0	0	0	6911	1299	45	3	240	3	GUSB	7	65429376	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	10156396	65429376	93709287	280	35625										
KCTD7	154881	hgsc.bcm.edu	37	chr7	66098342	66098342	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctgcggtgctacgaagacacCatgttggcagccatgttcag	12	11	1	1	rs150589535		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:66098342C>T	ENST00000275532.3	+	2	409	c.225C>T	c.(223-225)acC>acT	p.T75T	KCTD7_ENST00000443322.1_Silent_p.T75T	NM_001167961.2|NM_153033.4	NP_001161433.1|NP_694578.1	Q96MP8	KCTD7_HUMAN	potassium channel tetramerization domain containing 7	75	BTB.				cell death (GO:0008219)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|urinary_tract(1)	16						ACGAAGACACCATGTTGGCAG	0.562																																					p.T75T		Atlas-SNP	.											.	KCTD7	26	.	0			c.C225T						.						131	97	108					7																	66098342		2203	4300	6503	SO:0001819	synonymous_variant	154881	exon2			AGACACCATGTTG	AK056631	CCDS5534.1, CCDS55117.1	7q11.21	2014-09-17	2013-06-20		ENSG00000243335	ENSG00000243335			21957	protein-coding gene	gene with protein product		611725	"potassium channel tetramerisation domain containing 7"			12477932	Standard	NM_001167961		Approved	FLJ32069, EPM3, CLN14	uc003tve.3	Q96MP8	OTTHUMG00000129543	ENST00000275532.3:c.225C>T	chr7.hg19:g.66098342C>T		116.0	0.0		75.0	4.0	NM_001167961	A4D2M4|Q8IVR0	Silent	SNP	ENST00000275532.3	hg19	CCDS5534.1																																																																																			.	C|1.000;G|0.000		0.562	KCTD7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251733.2	NM_153033		T	66098342	C	T	66098342	2	4	255	1	0	0	0	0	0	0	0	1	8123	581	21	3		3	KCTD7	7	66098342	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	668966	66098342	93040321	281	35626										
SEMA3C	10512	hgsc.bcm.edu	37	chr7	80433423	80433423	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gaacagcattaatacttacaGgacatattcgagcaatcatg	7	8	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:80433423G>T	ENST00000265361.3	-	8	1361	c.800C>A	c.(799-801)cCt>cAt	p.P267H	SEMA3C_ENST00000419255.2_Splice_Site_p.P267H|SEMA3C_ENST00000536800.1_Splice_Site_p.P119H|SEMA3C_ENST00000544525.1_Splice_Site_p.P285H	NM_006379.3	NP_006370.1	Q99985	SEM3C_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	267	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|blood vessel remodeling (GO:0001974)|cardiac right ventricle morphogenesis (GO:0003215)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|immune response (GO:0006955)|limb bud formation (GO:0060174)|neural crest cell migration (GO:0001755)|neural tube development (GO:0021915)|outflow tract morphogenesis (GO:0003151)|post-embryonic development (GO:0009791)|pulmonary myocardium development (GO:0003350)|response to drug (GO:0042493)|somitogenesis (GO:0001756)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						AATACTTACAGGACATATTCG	0.328																																					p.P267H		Atlas-SNP	.											.	SEMA3C	106	.	0			c.C800A						.						143	135	138					7																	80433423		2203	4300	6503	SO:0001630	splice_region_variant	10512	exon8			CTTACAGGACATA	AB000220	CCDS5596.1	7q21-q31	2013-01-11			ENSG00000075223	ENSG00000075223		"Semaphorins", "Immunoglobulin superfamily / I-set domain containing"	10725	protein-coding gene	gene with protein product		602645		SEMAE		7748561, 9168980	Standard	NM_006379		Approved	SemE	uc003uhj.3	Q99985	OTTHUMG00000023447	ENST00000265361.3:c.801+1C>A	chr7.hg19:g.80433423G>T		154.0	0.0		120.0	5.0	NM_006379	B4DRL8	Missense_Mutation	SNP	ENST00000265361.3	hg19	CCDS5596.1	.	.	.	.	.	.	.	.	.	.	G	19.11	3.763294	0.69763	.	.	ENSG00000075223	ENST00000265361;ENST00000419255;ENST00000544525;ENST00000536800	T;T;T;T	0.21734	1.99;1.99;1.99;1.99	5.62	4.71	0.59529	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.097572	0.64402	D	0.000001	T	0.41026	0.1141	L	0.51422	1.61	0.80722	D	1	D;D;D	0.89917	0.992;1.0;1.0	P;D;D	0.74674	0.871;0.973;0.984	T	0.15809	-1.0424	10	0.59425	D	0.04	.	16.6279	0.84984	0.0:0.1295:0.8705:0.0	.	119;285;267	B4DRL8;F5H1Z7;Q99985	.;.;SEM3C_HUMAN	H	267;267;285;119	ENSP00000265361:P267H;ENSP00000411193:P267H;ENSP00000445649:P285H;ENSP00000438258:P119H	ENSP00000265361:P267H	P	-	2	0	SEMA3C	80271359	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	6.783000	0.75078	2.637000	0.89404	0.585000	0.79938	CCT	.	.		0.328	SEMA3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253279.1	NM_006379	Missense_Mutation	T	80433423	G	T	80433423	5	4	255	1	0	0	0	0	0	0	1	0	14041	1014	35	3	1499	3	SEMA3C	7	80433423	Splice_Site	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	14335081	80433423	78705240	282	35627										
GRM3	2913	hgsc.bcm.edu	37	chr7	86415661	86415661	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcagtgataagtcgcgctatGattactttgccaggaccgtg	11	9	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:86415661G>C	ENST00000361669.2	+	3	1652	c.553G>C	c.(553-555)Gat>Cat	p.D185H	AC005009.2_ENST00000418031.1_RNA|GRM3_ENST00000536043.1_Missense_Mutation_p.D57H|GRM3_ENST00000546348.1_Intron|GRM3_ENST00000394720.2_Missense_Mutation_p.D183H|AC005009.2_ENST00000452471.1_RNA|GRM3_ENST00000439827.1_Missense_Mutation_p.D185H	NM_000840.2	NP_000831.2	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3	185					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of adenylate cyclase activity (GO:0007194)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|axon (GO:0030424)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group II metabotropic glutamate receptor activity (GO:0001641)			NS(2)|breast(6)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(43)|ovary(3)|pancreas(2)|prostate(4)|skin(25)|upper_aerodigestive_tract(5)	109	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)					GTCGCGCTATGATTACTTTGC	0.567																																					p.D185H	GBM(52;969 1098 3139 52280)	Atlas-SNP	.											.	GRM3	237	.	0			c.G553C						.						132	126	128					7																	86415661		2203	4300	6503	SO:0001583	missense	2913	exon3			CGCTATGATTACT		CCDS5600.1	7q21.1-q21.2	2012-08-29			ENSG00000198822	ENSG00000198822		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4595	protein-coding gene	gene with protein product		601115				8824806	Standard	NM_000840		Approved	GPRC1C, mGlu3, MGLUR3	uc003uid.3	Q14832	OTTHUMG00000022884	ENST00000361669.2:c.553G>C	chr7.hg19:g.86415661G>C	ENSP00000355316:p.Asp185His	294.0	0.0		224.0	89.0	NM_000840	Q2PNZ6|Q75MV4|Q75N17|Q86YG6|Q8TBH9	Missense_Mutation	SNP	ENST00000361669.2	hg19	CCDS5600.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.565840	0.86439	.	.	ENSG00000198822	ENST00000361669;ENST00000454217;ENST00000536043;ENST00000439827;ENST00000394720	D;D;D;D;D	0.86769	-2.17;-2.17;-2.17;-2.17;-2.17	5.83	5.83	0.93111	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.93993	0.8076	M	0.80422	2.495	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.998;0.999	D	0.94127	0.7385	10	0.87932	D	0	.	19.122	0.93367	0.0:0.0:1.0:0.0	.	57;185;185	F5GYZ2;G5E9K2;Q14832	.;.;GRM3_HUMAN	H	185;57;57;185;183	ENSP00000355316:D185H;ENSP00000405427:D57H;ENSP00000441407:D57H;ENSP00000398767:D185H;ENSP00000378209:D183H	ENSP00000355316:D185H	D	+	1	0	GRM3	86253597	1.000000	0.71417	0.994000	0.49952	0.968000	0.65278	9.756000	0.98918	2.770000	0.95276	0.655000	0.94253	GAT	.	.		0.567	GRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253362.2			C	86415661	G	C	86415661	3	2	255	1	0	0	0	0	1	0	0	0	6807	1290	45	4	559	4	GRM3	7	86415661	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	5982238	86415661	72723002	283	35628										
CDK14	5218	hgsc.bcm.edu	37	chr7	90747440	90747440	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agaagctggagaaagcatgcGggcctttgggaaaaacaata	13	6	0	2	rs74839397	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:90747440G>T	ENST00000380050.3	+	14	1486	c.1355G>T	c.(1354-1356)cGg>cTg	p.R452L	CDK14_ENST00000265741.3_Missense_Mutation_p.R434L|CDK14_ENST00000436577.2_Missense_Mutation_p.R323L|CDK14_ENST00000406263.1_Missense_Mutation_p.R406L			O94921	CDK14_HUMAN	cyclin-dependent kinase 14	452					cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of cell cycle (GO:0051726)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoplasmic cyclin-dependent protein kinase holoenzyme complex (GO:0000308)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			breast(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|liver(1)|lung(12)|ovary(1)|skin(4)	32						GAAAGCATGCGGGCCTTTGGG	0.403																																					p.R434L	GBM(83;1228 1256 8311 16577 31299)	Atlas-SNP	.											.	CDK14	153	.	0			c.G1301T						.						84	85	85					7																	90747440		2203	4300	6503	SO:0001583	missense	5218	exon13			GCATGCGGGCCTT		CCDS5619.1, CCDS75626.1, CCDS75627.1, CCDS75628.1	7q21-q22	2011-11-08	2009-12-16	2009-12-16	ENSG00000058091	ENSG00000058091		"Cyclin-dependent kinases"	8883	protein-coding gene	gene with protein product		610679	"PFTAIRE protein kinase 1"	PFTK1		9202329, 11313143, 19884882	Standard	XM_005250436		Approved	PFTAIRE1	uc003ukz.1	O94921	OTTHUMG00000023649	ENST00000380050.3:c.1355G>T	chr7.hg19:g.90747440G>T	ENSP00000369390:p.Arg452Leu	115.0	0.0		93.0	4.0	NM_012395	A4D1E6|A6NK51|A8WFP6|B4DHG5|B4DNM2|Q75N06|Q75N22|Q8N764|Q9H3D7|Q9UDR0	Missense_Mutation	SNP	ENST00000380050.3	hg19		.	.	.	.	.	.	.	.	.	.	G	12.57	1.976929	0.34848	.	.	ENSG00000058091	ENST00000380050;ENST00000265741;ENST00000406263;ENST00000436577	T;T;T;T	0.71934	-0.5;-0.52;-0.5;-0.61	5.87	5.87	0.94306	.	0.063724	0.64402	D	0.000009	T	0.56934	0.2019	L	0.29908	0.895	0.42726	D	0.993693	B;P;B	0.41748	0.18;0.761;0.18	B;B;B	0.35278	0.03;0.199;0.018	T	0.57985	-0.7716	10	0.31617	T	0.26	-12.2164	14.7159	0.69269	0.069:0.0:0.931:0.0	.	323;434;452	E7EUK8;O94921-2;O94921	.;.;CDK14_HUMAN	L	452;434;406;323	ENSP00000369390:R452L;ENSP00000265741:R434L;ENSP00000385034:R406L;ENSP00000398936:R323L	ENSP00000265741:R434L	R	+	2	0	CDK14	90585376	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.148000	0.64857	2.941000	0.99782	0.655000	0.94253	CGG	.	G|0.999;A|0.001		0.403	CDK14-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000059970.5	NM_012395		T	90747440	G	T	90747440	3	4	255	1	0	0	0	0	1	0	0	0	3132	1116	39	1	1351	1	CDK14	7	90747440	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	4331779	90747440	68391223	284	35629										
AKAP9	10142	hgsc.bcm.edu	37	chr7	91712764	91712764	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tttacagagtgaatgttcctCagaagaagttactgaaataa	8	5	1	5			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:91712764C>A	ENST00000359028.2	+	34	8702	c.8477C>A	c.(8476-8478)tCa>tAa	p.S2826*	AKAP9_ENST00000356239.3_Nonsense_Mutation_p.S2814*|AKAP9_ENST00000358100.2_Nonsense_Mutation_p.S2826*			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	2826					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			GAATGTTCCTCAGAAGAAGTT	0.353			T	BRAF	papillary thyroid																																p.S2814X		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.C8441A						.						45	46	46					7																	91712764		2202	4300	6502	SO:0001587	stop_gained	10142	exon33			GTTCCTCAGAAGA	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	379	protein-coding gene	gene with protein product	"A-kinase anchoring protein 450", "AKAP9-BRAF fusion protein", "AKAP120-like protein", "centrosome- and golgi-localized protein kinase N-associated protein", "protein kinase A anchoring protein 9", "A-kinase anchor protein, 350kDa", "protein phosphatase 1, regulatory subunit 45", "yotiao"	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.8477C>A	chr7.hg19:g.91712764C>A	ENSP00000351922:p.Ser2826*	118.0	0.0		73.0	4.0	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Nonsense_Mutation	SNP	ENST00000359028.2	hg19		.	.	.	.	.	.	.	.	.	.	C	51	17.537519	0.99888	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394534	.	.	.	4.47	3.56	0.40772	.	0.893166	0.09107	N	0.847544	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.4215	0.61001	0.1633:0.8367:0.0:0.0	.	.	.	.	X	2814;2826;2826;2818;660	.	ENSP00000348573:S2814X	S	+	2	0	AKAP9	91550700	0.985000	0.35326	0.784000	0.31847	0.948000	0.59901	3.785000	0.55424	1.046000	0.40249	0.591000	0.81541	TCA	.	.		0.353	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751		A	91712764	C	A	91712764	4	1	255	1	0	0	0	0	0	1	0	0	459	838	29	3	8571	3	AKAP9	7	91712764	Nonsense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	965324	91712764	67425899	285	35630										
COL1A2	1278	hgsc.bcm.edu	37	chr7	94043018	94043018	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttagggtgctccaggtcctgAtggaaacaatggtgctcagg	14	8	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:94043018A>G	ENST00000297268.6	+	27	2045	c.1574A>G	c.(1573-1575)gAt>gGt	p.D525G		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	525					blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	CCAGGTCCTGATGGAAACAAT	0.458										HNSCC(75;0.22)																											p.D525G		Atlas-SNP	.											.	COL1A2	240	.	0			c.A1574G						.						109	103	105					7																	94043018		2203	4300	6503	SO:0001583	missense	1278	exon27			GTCCTGATGGAAA	Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"Collagens"	2198	protein-coding gene	gene with protein product	"alpha 2(I)-collagen", "alpha-2 collagen type I", "type I procollagen", "collagen I, alpha-2 polypeptide", "collagen of skin, tendon and bone, alpha-2 chain"	120160	"osteogenesis imperfecta type IV"	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.1574A>G	chr7.hg19:g.94043018A>G	ENSP00000297268:p.Asp525Gly	119.0	0.0		59.0	4.0	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Missense_Mutation	SNP	ENST00000297268.6	hg19	CCDS34682.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.962792	0.74016	.	.	ENSG00000164692	ENST00000297268;ENST00000545487	D	0.93189	-3.18	5.4	5.4	0.78164	.	0.054395	0.64402	D	0.000001	D	0.94676	0.8283	L	0.46819	1.47	0.80722	D	1	P	0.47253	0.892	P	0.58820	0.846	D	0.95208	0.8323	10	0.72032	D	0.01	.	15.7429	0.77914	1.0:0.0:0.0:0.0	.	525	P08123	CO1A2_HUMAN	G	525;526	ENSP00000297268:D525G	ENSP00000297268:D525G	D	+	2	0	COL1A2	93880954	1.000000	0.71417	0.998000	0.56505	0.969000	0.65631	9.292000	0.96076	2.181000	0.69327	0.533000	0.62120	GAT	.	.		0.458	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089		G	94043018	A	G	94043018	3	3	255	1	0	0	0	0	1	0	0	0	3680	333	12	2	1680	2	COL1A2	7	94043018	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	2330254	94043018	65095645	286	35631										
PPP1R9A	55607	hgsc.bcm.edu	37	chr7	94540701	94540701	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctgagcaggatgaggaggaaGatagtgatgagaacagttac	15	4	0	5			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:94540701G>T	ENST00000433881.1	+	2	1808	c.1276G>T	c.(1276-1278)Gat>Tat	p.D426Y	PPP1R9A_ENST00000424654.1_Missense_Mutation_p.D426Y|PPP1R9A_ENST00000433360.1_Missense_Mutation_p.D426Y|PPP1R9A_ENST00000340694.4_Missense_Mutation_p.D426Y|PPP1R9A_ENST00000456331.2_Missense_Mutation_p.D426Y|PPP1R9A_ENST00000289495.5_Missense_Mutation_p.D426Y			Q9ULJ8	NEB1_HUMAN	protein phosphatase 1, regulatory subunit 9A	426	Interacts with protein phosphatase 1. {ECO:0000250}.				actin filament organization (GO:0007015)|calcium-mediated signaling (GO:0019722)|neuron projection development (GO:0031175)	cell junction (GO:0030054)|cortical actin cytoskeleton (GO:0030864)|dendritic spine (GO:0043197)|filopodium (GO:0030175)|growth cone (GO:0030426)|synapse (GO:0045202)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(11)|liver(2)|lung(22)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(8)|urinary_tract(5)	71	all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09)		STAD - Stomach adenocarcinoma(171;0.0031)			TGAGGAGGAAGATAGTGATGA	0.423										HNSCC(28;0.073)																											p.D426Y		Atlas-SNP	.											.	PPP1R9A	264	.	0			c.G1276T						.						73	66	68					7																	94540701		2203	4300	6503	SO:0001583	missense	55607	exon2			GAGGAAGATAGTG	AB033048	CCDS34683.1, CCDS55127.1, CCDS55128.1	7q21.3	2013-01-10	2011-10-04		ENSG00000158528	ENSG00000158528		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Sterile alpha motif (SAM) domain containing"	14946	protein-coding gene	gene with protein product		602468	"protein phosphatase 1, regulatory (inhibitor) subunit 9A"			10574462	Standard	NM_001166160		Approved	Neurabin-I, KIAA1222, FLJ20068	uc010lfj.3	Q9ULJ8	OTTHUMG00000155566	ENST00000433881.1:c.1276G>T	chr7.hg19:g.94540701G>T	ENSP00000398870:p.Asp426Tyr	127.0	0.0		92.0	4.0	NM_017650	A1L494|B2RWQ1|E9PCA0|E9PCK6|E9PDX1|F8W7J9|O76059|Q9NXT2	Missense_Mutation	SNP	ENST00000433881.1	hg19	CCDS34683.1	.	.	.	.	.	.	.	.	.	.	G	17.18	3.324299	0.60634	.	.	ENSG00000158528	ENST00000433360;ENST00000340694;ENST00000424654;ENST00000433881;ENST00000289495;ENST00000456331	T;T;T;T;T;T	0.17854	2.25;2.3;2.29;2.3;2.29;2.29	5.55	5.55	0.83447	.	0.188618	0.45867	D	0.000331	T	0.42131	0.1189	M	0.63428	1.95	0.53688	D	0.999978	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.85130	0.981;0.995;0.997;0.98;0.972	T	0.03249	-1.1056	9	.	.	.	.	19.8905	0.96928	0.0:0.0:1.0:0.0	.	426;426;426;426;426	B7ZLX4;F8W7J9;E9PDX1;E9PCK6;Q9ULJ8	.;.;.;.;NEB1_HUMAN	Y	426	ENSP00000405514:D426Y;ENSP00000344524:D426Y;ENSP00000411342:D426Y;ENSP00000398870:D426Y;ENSP00000289495:D426Y;ENSP00000402893:D426Y	.	D	+	1	0	PPP1R9A	94378637	1.000000	0.71417	1.000000	0.80357	0.798000	0.45092	7.964000	0.87933	2.789000	0.95967	0.655000	0.94253	GAT	.	.		0.423	PPP1R9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340662.1	NM_001166160		T	94540701	G	T	94540701	3	4	255	1	0	0	0	0	1	0	0	0	12390	942	33	3	1278	3	PPP1R9A	7	94540701	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	497683	94540701	64597962	287	35632										
SLC25A13	10165	hgsc.bcm.edu	37	chr7	95820553	95820553	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttgatgggatgtggtacctcCagcagcctcaaataaattga	10	8	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:95820553C>A	ENST00000265631.5	-	7	758	c.622G>T	c.(622-624)Gga>Tga	p.G208*	SLC25A13_ENST00000416240.2_Nonsense_Mutation_p.G208*|SLC25A13_ENST00000542654.1_Nonsense_Mutation_p.G100*			Q9UJS0	CMC2_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 13	208					aspartate transport (GO:0015810)|ATP biosynthetic process (GO:0006754)|carbohydrate metabolic process (GO:0005975)|cellular respiration (GO:0045333)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|transporter activity (GO:0005215)			breast(4)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|prostate(1)|skin(4)	42	all_cancers(62;7.75e-08)|all_epithelial(64;1.16e-07)		STAD - Stomach adenocarcinoma(171;0.194)		L-Aspartic Acid(DB00128)	GTGGTACCTCCAGCAGCCTCA	0.323																																					p.G208X		Atlas-SNP	.											.	SLC25A13	131	.	0			c.G622T						.						72	72	72					7																	95820553		2203	4300	6503	SO:0001587	stop_gained	10165	exon7			TACCTCCAGCAGC	AF118838	CCDS5645.1, CCDS55130.1	7q21.3	2013-05-22	2012-03-29		ENSG00000004864	ENSG00000004864		"Solute carriers", "EF-hand domain containing"	10983	protein-coding gene	gene with protein product	"mitochondrial aspartate glutamate carrier 2"	603859	"solute carrier family 25, member 13 (citrin)"	CTLN2		10369257	Standard	NM_014251		Approved	CITRIN, ARALAR2	uc003uog.4	Q9UJS0	OTTHUMG00000023074	ENST00000265631.5:c.622G>T	chr7.hg19:g.95820553C>A	ENSP00000265631:p.Gly208*	91.0	0.0		74.0	4.0	NM_001160210	O14566|O14575|Q546F9|Q9NZW1|Q9UNI7	Nonsense_Mutation	SNP	ENST00000265631.5	hg19	CCDS5645.1	.	.	.	.	.	.	.	.	.	.	C	37	6.412669	0.97546	.	.	ENSG00000004864	ENST00000265631;ENST00000416240;ENST00000542654	.	.	.	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	-17.1499	19.2746	0.94026	0.0:1.0:0.0:0.0	.	.	.	.	X	208;208;100	.	ENSP00000265631:G208X	G	-	1	0	SLC25A13	95658489	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.879000	0.69690	2.868000	0.98415	0.557000	0.71058	GGA	.	.		0.323	SLC25A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059395.2	NM_014251		A	95820553	C	A	95820553	4	1	255	1	0	0	0	0	0	1	0	0	14490	603	21	3	1456	3	SLC25A13	7	95820553	Nonsense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1279852	95820553	63318110	288	35633										
BHLHA15	168620	hgsc.bcm.edu	37	chr7	97842082	97842082	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	caagctctaccagcactaccAgcagcagcagcaggtggctg	11	14	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:97842082A>G	ENST00000609256.1	+	2	587	c.461A>G	c.(460-462)cAg>cGg	p.Q154R	BHLHA15_ENST00000314018.2_Missense_Mutation_p.Q154R			Q7RTS1	BHA15_HUMAN	basic helix-loop-helix family, member a15	154					calcium-mediated signaling (GO:0019722)|cell maturation (GO:0048469)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|Golgi organization (GO:0007030)|intracellular distribution of mitochondria (GO:0048312)|mitochondrial calcium ion transport (GO:0006851)	nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)										CAGCACTACCAGCAGCAGCAG	0.662																																					p.Q154R		Atlas-SNP	.											.	BHLHA15	11	.	0			c.A461G						.						9	9	9					7																	97842082		2125	4180	6305	SO:0001583	missense	168620	exon1			ACTACCAGCAGCA	BK000276	CCDS5655.1	7q21.3	2009-01-12	2009-01-12	2009-01-12	ENSG00000180535	ENSG00000180535		"Basic helix-loop-helix proteins"	22265	protein-coding gene	gene with protein product		608606	"basic helix-loop-helix domain containing, class B, 8"	BHLHB8		14516699, 18557763	Standard	NM_177455		Approved	MIST1, bHLHa15	uc003upf.1	Q7RTS1	OTTHUMG00000154289	ENST00000609256.1:c.461A>G	chr7.hg19:g.97842082A>G	ENSP00000476312:p.Gln154Arg	100.0	0.0		73.0	4.0	NM_177455	A4D271|Q14DE4	Missense_Mutation	SNP	ENST00000609256.1	hg19	CCDS5655.1	.	.	.	.	.	.	.	.	.	.	A	17.37	3.373778	0.61624	.	.	ENSG00000180535	ENST00000314018	D	0.93763	-3.28	3.33	3.33	0.38152	Helix-loop-helix DNA-binding (1);	0.499336	0.18937	U	0.127043	D	0.92427	0.7596	L	0.27053	0.805	0.58432	D	0.999997	D	0.71674	0.998	D	0.75484	0.986	D	0.88226	0.2900	10	0.14252	T	0.57	-9.3665	11.1497	0.48451	1.0:0.0:0.0:0.0	.	154	Q7RTS1	BHA15_HUMAN	R	154	ENSP00000326391:Q154R	ENSP00000326391:Q154R	Q	+	2	0	BHLHA15	97680018	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	5.744000	0.68664	1.270000	0.44297	0.402000	0.26972	CAG	.	.		0.662	BHLHA15-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472733.1	NM_177455		G	97842082	A	G	97842082	3	3	255	1	0	0	0	0	1	0	0	0	1419	188	7	2	463	2	BHLHA15	7	97842082	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	2021529	97842082	61296581	289	35634										
TRRAP	8295	hgsc.bcm.edu	37	chr7	98545947	98545947	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggttgtcatgaaaacggagcGggcgatgctgatcgaggtaa	16	6	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:98545947G>T	ENST00000359863.4	+	33	4840	c.4631G>T	c.(4630-4632)cGg>cTg	p.R1544L	TRRAP_ENST00000446306.3_Missense_Mutation_p.R1525L|TRRAP_ENST00000355540.3_Missense_Mutation_p.R1526L	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	1544					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			AAAACGGAGCGGGCGATGCTG	0.498																																					p.R1544L		Atlas-SNP	.											.	TRRAP	863	.	0			c.G4631T						.						85	77	80					7																	98545947		2203	4300	6503	SO:0001583	missense	8295	exon33			CGGAGCGGGCGAT	AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.4631G>T	chr7.hg19:g.98545947G>T	ENSP00000352925:p.Arg1544Leu	112.0	0.0		99.0	4.0	NM_001244580	A4D265|O75218|Q9Y631|Q9Y6H4	Missense_Mutation	SNP	ENST00000359863.4	hg19	CCDS59066.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.2|21.2	4.108936|4.108936	0.77096|0.77096	.|.	.|.	ENSG00000196367|ENSG00000196367	ENST00000456197|ENST00000359863;ENST00000355540;ENST00000446306	.|T;T	.|0.66995	.|-0.24;-0.24	5.74|5.74	5.74|5.74	0.90152|0.90152	.|Armadillo-like helical (1);Armadillo-type fold (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.65123|0.65123	0.2661|0.2661	L|L	0.36672|0.36672	1.1|1.1	0.80722|0.80722	D|D	1|1	.|P;P;P	.|0.48911	.|0.917;0.65;0.79	.|P;B;B	.|0.45406	.|0.479;0.147;0.306	T|T	0.65557|0.65557	-0.6139|-0.6139	5|10	.|0.48119	.|T	.|0.1	.|.	20.2825|20.2825	0.98528|0.98528	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1526;1265;1544	.|Q9Y4A5-2;Q59FH1;Q9Y4A5	.|.;.;TRRAP_HUMAN	W|L	1266|1544;1526;1524	.|ENSP00000352925:R1544L;ENSP00000347733:R1526L	.|ENSP00000347733:R1526L	G|R	+|+	1|2	0|0	TRRAP|TRRAP	98383883|98383883	1.000000|1.000000	0.71417|0.71417	0.727000|0.727000	0.30756|0.30756	0.205000|0.205000	0.24178|0.24178	9.420000|9.420000	0.97426|0.97426	2.873000|2.873000	0.98535|0.98535	0.561000|0.561000	0.74099|0.74099	GGG|CGG	.	.		0.498	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496		T	98545947	G	T	98545947	3	4	255	1	0	0	0	0	1	0	0	0	16616	1116	39	1	4699	1	TRRAP	7	98545947	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	703865	98545947	60592716	290	35635										
SMURF1	57154	hgsc.bcm.edu	37	chr7	98645414	98645414	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cttctggactagatctctttCgtatctctgggcaggaagct	10	10	3	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:98645414C>T	ENST00000361125.1	-	11	1442	c.1123G>A	c.(1123-1125)Gaa>Aaa	p.E375K	AC004893.11_ENST00000482799.2_RNA|SMURF1_ENST00000361368.2_Missense_Mutation_p.E349K|AC004893.11_ENST00000468960.2_RNA	NM_020429.2	NP_065162.1	Q9HCE7	SMUF1_HUMAN	SMAD specific E3 ubiquitin protein ligase 1	375					BMP signaling pathway (GO:0030509)|cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of ossification (GO:0030279)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein export from nucleus (GO:0006611)|protein localization to cell surface (GO:0034394)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	activin binding (GO:0048185)|I-SMAD binding (GO:0070411)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|urinary_tract(1)	25	all_cancers(62;1.05e-08)|all_epithelial(64;4.34e-09)|Lung NSC(181;0.00902)|all_lung(186;0.0145)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)|Lung(104;0.224)			AGATCTCTTTCGTATCTCTGG	0.562																																					p.E375K		Atlas-SNP	.											SMURF1,colon,carcinoma,0,3	SMURF1	58	.	0			c.G1123A						.						150	148	148					7																	98645414		2203	4300	6503	SO:0001583	missense	57154	exon11			CTCTTTCGTATCT	AB046845	CCDS34689.1, CCDS34690.1	7q21.1-q31.1	2004-07-29			ENSG00000198742	ENSG00000198742			16807	protein-coding gene	gene with protein product		605568				10458166	Standard	NM_020429		Approved	KIAA1625	uc003upu.2	Q9HCE7	OTTHUMG00000150272	ENST00000361125.1:c.1123G>A	chr7.hg19:g.98645414C>T	ENSP00000354621:p.Glu375Lys	67.0	0.0		67.0	3.0	NM_020429	A4D279|B7ZMB6|B9EGV3|O75853|Q547Q3|Q9UJT8	Missense_Mutation	SNP	ENST00000361125.1	hg19	CCDS34690.1	.	.	.	.	.	.	.	.	.	.	C	15.11	2.735783	0.49045	.	.	ENSG00000198742	ENST00000361368;ENST00000361125	T;T	0.40756	1.33;1.02	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.15825	0.0381	N	0.00746	-1.225	0.80722	D	1	B;B;B	0.12630	0.006;0.003;0.003	B;B;B	0.09377	0.002;0.004;0.001	T	0.33471	-0.9867	10	0.02654	T	1	.	19.2699	0.94004	0.0:1.0:0.0:0.0	.	349;375;349	Q9HCE7-2;Q9HCE7;B9EGV3	.;SMUF1_HUMAN;.	K	349;375	ENSP00000355326:E349K;ENSP00000354621:E375K	ENSP00000354621:E375K	E	-	1	0	SMURF1	98483350	0.999000	0.42202	0.284000	0.24805	0.965000	0.64279	4.069000	0.57541	2.527000	0.85204	0.563000	0.77884	GAA	.	.		0.562	SMURF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000335001.2	NM_020429		T	98645414	C	T	98645414	3	4	255	1	0	0	0	0	1	0	0	0	14834	893	31	1	1186	1	SMURF1	7	98645414	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	99467	98645414	60493249	291	35636										
PTCD1	26024	hgsc.bcm.edu	37	chr7	99032620	99032620	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aaactctcctcctcctcctcGtcttcttcctgcgtggccgt	6	18	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:99032620G>A	ENST00000292478.4	-	2	496	c.246C>T	c.(244-246)gaC>gaT	p.D82D	ATP5J2-PTCD1_ENST00000437572.1_5'Flank|PTCD1_ENST00000555673.1_Silent_p.D131D|ATP5J2-PTCD1_ENST00000413834.1_Silent_p.D131D|PTCD1_ENST00000485746.1_5'UTR	NM_015545.3	NP_056360.2	O75127	PTCD1_HUMAN	pentatricopeptide repeat domain 1	82					tRNA 3'-end processing (GO:0042780)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|tRNA binding (GO:0000049)			endometrium(5)|large_intestine(3)|lung(16)|ovary(2)|skin(1)	27	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			CCTCCTCCTCGTCTTCTTCCT	0.612																																					p.D131D		Atlas-SNP	.											PTCD1,colon,carcinoma,0,1	.	.	.	0			c.C393T						.						63	67	66					7																	99032620		2203	4300	6503	SO:0001819	synonymous_variant	100526740	exon3			CTCCTCGTCTTCT	AB014532	CCDS34691.1	7q22.1	2006-01-27				ENSG00000106246			22198	protein-coding gene	gene with protein product		614774					Standard	NM_015545		Approved	KIAA0632		O75127		ENST00000292478.4:c.246C>T	chr7.hg19:g.99032620G>A		114.0	0.0		83.0	4.0	NM_001198879	Q3ZB78|Q66K60|Q9UDV2	Silent	SNP	ENST00000292478.4	hg19	CCDS34691.1																																																																																			.	.		0.612	PTCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336391.1	NM_015545		A	99032620	G	A	99032620	2	1	255	1	0	0	0	0	0	0	0	1	12739	1136	40	1		1	PTCD1	7	99032620	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	387206	99032620	60106043	292	35637										
ZNF655	79027	hgsc.bcm.edu	37	chr7	99170201	99170201	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcttagaatacagaataccgAtgacaatgataagtatgaca	7	6	1	5			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:99170201A>G	ENST00000394163.2	+	3	653	c.470A>G	c.(469-471)gAt>gGt	p.D157G	ZNF655_ENST00000425063.1_3'UTR|ZNF655_ENST00000419215.2_3'UTR|GS1-259H13.10_ENST00000455905.1_Intron|ZNF655_ENST00000252713.4_Missense_Mutation_p.D157G|ZNF655_ENST00000493277.1_Missense_Mutation_p.D192G|GS1-259H13.10_ENST00000486324.1_Intron|ZNF655_ENST00000424881.1_Missense_Mutation_p.D192G	NM_001009960.1|NM_138494.2	NP_001009960.1|NP_612503.1	Q8N720	ZN655_HUMAN	zinc finger protein 655	157					negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	16	all_epithelial(64;3.19e-09)|Lung NSC(181;0.0066)|all_lung(186;0.011)|Esophageal squamous(72;0.0166)					CAGAATACCGATGACAATGAT	0.378																																					p.D192G		Atlas-SNP	.											.	ZNF655	75	.	0			c.A575G						.						65	65	65					7																	99170201		2203	4300	6503	SO:0001583	missense	79027	exon4			ATACCGATGACAA	AY099353	CCDS5669.1, CCDS5670.1, CCDS34695.1, CCDS47655.1	7q22.1	2013-01-08			ENSG00000197343	ENSG00000197343		"Zinc fingers, C2H2-type", "-"	30899	protein-coding gene	gene with protein product						11179890, 15558030	Standard	NM_001083956		Approved	VIK-1, VIK	uc010lgc.3	Q8N720	OTTHUMG00000156637	ENST00000394163.2:c.470A>G	chr7.hg19:g.99170201A>G	ENSP00000377718:p.Asp157Gly	60.0	0.0		44.0	5.0	NM_001085368	A4D291|A6NGD3|B4E3M4|B7Z9Q9|D6W5T4|Q8IV00|Q8TA89|Q96EZ3|Q9BQ85	Missense_Mutation	SNP	ENST00000394163.2	hg19	CCDS5669.1	.	.	.	.	.	.	.	.	.	.	A	4.079	0.012634	0.07912	.	.	ENSG00000197343	ENST00000252713;ENST00000493277;ENST00000424881;ENST00000394163	T;T;T;T	0.06294	3.39;3.32;3.32;3.39	4.56	4.56	0.56223	.	0.000000	0.46145	D	0.000320	T	0.17023	0.0409	L	0.47716	1.5	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.992	T	0.00205	-1.1922	10	0.87932	D	0	-7.711	10.6033	0.45379	1.0:0.0:0.0:0.0	.	192;157	Q8N720-3;Q8N720	.;ZN655_HUMAN	G	157;192;192;157	ENSP00000252713:D157G;ENSP00000419135:D192G;ENSP00000393876:D192G;ENSP00000377718:D157G	ENSP00000252713:D157G	D	+	2	0	ZNF655	99008137	0.026000	0.19158	0.985000	0.45067	0.077000	0.17291	2.941000	0.49011	2.275000	0.75901	0.528000	0.53228	GAT	.	.		0.378	ZNF655-009	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000344929.1	NM_138494		G	99170201	A	G	99170201	3	3	255	1	0	0	0	0	1	0	0	0	18083	333	12	2	1007	2	ZNF655	7	99170201	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	137581	99170201	59968462	293	35638										
MCM7	4176	hgsc.bcm.edu	37	chr7	99691801	99691801	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aatttgggcacttaccagagCagtggaaaggcgcaggatag	14	7	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:99691801C>T	ENST00000303887.5	-	13	2488	c.1843G>A	c.(1843-1845)Gct>Act	p.A615T	MIR106B_ENST00000385301.1_RNA|MIR93_ENST00000385024.1_RNA|MCM7_ENST00000343023.6_Intron|MIR25_ENST00000384816.1_RNA|MCM7_ENST00000354230.3_Missense_Mutation_p.A439T	NM_005916.3	NP_005907.3	P33993	MCM7_HUMAN	minichromosome maintenance complex component 7	615	Interaction with ATRIP.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to epidermal growth factor stimulus (GO:0071364)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of phosphorylation (GO:0042325)|response to drug (GO:0042493)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|single-stranded DNA binding (GO:0003697)			endometrium(1)|kidney(5)|large_intestine(5)|lung(4)|ovary(1)|stomach(1)	17	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CTTACCAGAGCAGTGGAAAGG	0.582																																					p.A615T		Atlas-SNP	.											.	MCM7	136	.	0			c.G1843A						.						99	96	97					7																	99691801		2203	4300	6503	SO:0001583	missense	4176	exon13			CCAGAGCAGTGGA		CCDS5683.1, CCDS5684.1	7q21.3-q22.1	2014-06-12	2007-04-04		ENSG00000166508	ENSG00000166508			6950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 104"	600592	"minichromosome maintenance deficient (S. cerevisiae) 7", "MCM7 minichromosome maintenance deficient 7 (S. cerevisiae)"	MCM2		7842741	Standard	NM_005916		Approved	CDC47, PPP1R104	uc003usw.1	P33993	OTTHUMG00000154671	ENST00000303887.5:c.1843G>A	chr7.hg19:g.99691801C>T	ENSP00000307288:p.Ala615Thr	91.0	0.0		75.0	4.0	NM_005916	A4D2A1|A4D2A2|E9PGN9|Q15076|Q96D34|Q96GL1	Missense_Mutation	SNP	ENST00000303887.5	hg19	CCDS5683.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.679838	0.88542	.	.	ENSG00000166508	ENST00000303887;ENST00000542483;ENST00000362082;ENST00000354230	T;T	0.18338	2.22;2.22	5.21	5.21	0.72293	.	0.060985	0.64402	D	0.000004	T	0.59838	0.2223	H	0.98507	4.25	0.80722	D	1	D	0.71674	0.998	D	0.72075	0.976	T	0.76252	-0.3027	10	0.87932	D	0	-17.0029	16.289	0.82738	0.0:1.0:0.0:0.0	.	615	P33993	MCM7_HUMAN	T	615;552;508;439	ENSP00000307288:A615T;ENSP00000346171:A439T	ENSP00000307288:A615T	A	-	1	0	MCM7	99529737	1.000000	0.71417	1.000000	0.80357	0.699000	0.40488	7.227000	0.78070	2.716000	0.92895	0.561000	0.74099	GCT	.	.		0.582	MCM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336534.3			T	99691801	C	T	99691801	3	4	255	1	0	0	0	0	1	0	0	0	9401	710	25	3	328	3	MCM7	7	99691801	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	521600	99691801	59446862	294	35639										
AP4M1	9179	hgsc.bcm.edu	37	chr7	99701748	99701748	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aagtttttttggatgtggtcGagagattgtctgtactgata	12	3	1	2	rs387906838		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:99701748G>T	ENST00000359593.4	+	7	735	c.577G>T	c.(577-579)Gag>Tag	p.E193*	AP4M1_ENST00000429084.1_Nonsense_Mutation_p.E200*|MCM7_ENST00000303887.5_5'Flank|MCM7_ENST00000343023.6_5'Flank|AP4M1_ENST00000422582.1_Nonsense_Mutation_p.E65*|AP4M1_ENST00000421755.1_Nonsense_Mutation_p.E193*	NM_004722.3	NP_004713.2	O00189	AP4M1_HUMAN	adaptor-related protein complex 4, mu 1 subunit	193	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				Golgi to endosome transport (GO:0006895)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|Golgi trans cisterna (GO:0000138)|trans-Golgi network (GO:0005802)	transporter activity (GO:0005215)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)	17	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GGATGTGGTCGAGAGATTGTC	0.453																																					p.E193X	Pancreas(174;1182 2812 29595 49511)	Atlas-SNP	.											.	AP4M1	39	.	0			c.G577T						.						127	112	117					7																	99701748		2203	4300	6503	SO:0001587	stop_gained	9179	exon7			GTGGTCGAGAGAT	Y08387	CCDS5685.1	7q22.1	2012-06-29			ENSG00000221838	ENSG00000221838			574	protein-coding gene	gene with protein product	"mu-adaptin-related protein-2", "mu subunit of AP-4", "AP-4 adapter complex mu subunit", "adaptor-related protein complex AP-4 mu4 subunit"	602296				9013859, 10066790, 21620353	Standard	NM_004722		Approved	MU-ARP2, MU-4, SPG50	uc003utb.4	O00189	OTTHUMG00000154722	ENST00000359593.4:c.577G>T	chr7.hg19:g.99701748G>T	ENSP00000352603:p.Glu193*	121.0	0.0		84.0	4.0	NM_004722	D6W5U1|Q8WV65|Q9UHK9	Nonsense_Mutation	SNP	ENST00000359593.4	hg19	CCDS5685.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.746250	0.89663	.	.	ENSG00000221838	ENST00000438383;ENST00000429084;ENST00000359593;ENST00000439416;ENST00000421755;ENST00000422582	.	.	.	4.75	4.75	0.60458	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-9.649	15.2786	0.73764	0.0:0.0:1.0:0.0	.	.	.	.	X	125;200;193;149;193;65	.	ENSP00000352603:E193X	E	+	1	0	AP4M1	99539684	1.000000	0.71417	0.884000	0.34674	0.971000	0.66376	7.136000	0.77285	2.455000	0.83008	0.561000	0.74099	GAG	.	.		0.453	AP4M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336772.4	NM_004722		T	99701748	G	T	99701748	4	4	255	1	0	0	0	0	0	1	0	0	753	1059	37	1	603	1	AP4M1	7	99701748	Nonsense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	9947	99701748	59436915	295	35640										
PILRA	29992	hgsc.bcm.edu	37	chr7	99971978	99971978	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	accagtctgtgtatttctgcCgagttgagctggacacacgg	12	10	2	1	rs141936238		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:99971978C>A	ENST00000198536.2	+	2	588	c.376C>A	c.(376-378)Cga>Aga	p.R126R	PILRA_ENST00000350573.2_Silent_p.R126R|PILRA_ENST00000394000.2_Silent_p.R126R|PILRA_ENST00000474013.1_3'UTR|PILRA_ENST00000453419.1_Silent_p.R126R	NM_013439.2	NP_038467.2	Q9UKJ1	PILRA_HUMAN	paired immunoglobin-like type 2 receptor alpha	126	Ig-like V-type.				signal transduction (GO:0007165)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|pancreas(1)|skin(1)|urinary_tract(1)	15	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GTATTTCTGCCGAGTTGAGCT	0.577																																					p.R126R		Atlas-SNP	.											.	PILRA	28	.	0			c.C376A						.						103	104	103					7																	99971978		2203	4300	6503	SO:0001819	synonymous_variant	29992	exon2			TTCTGCCGAGTTG	AF161080	CCDS5691.1, CCDS5692.1, CCDS47660.1	7q22.1	2013-01-11			ENSG00000085514	ENSG00000085514		"Immunoglobulin superfamily / V-set domain containing"	20396	protein-coding gene	gene with protein product		605341				10660620	Standard	NM_178272		Approved	FDF03	uc003uuo.1	Q9UKJ1	OTTHUMG00000155248	ENST00000198536.2:c.376C>A	chr7.hg19:g.99971978C>A		98.0	0.0		89.0	4.0	NM_013439	Q8NHI1	Silent	SNP	ENST00000198536.2	hg19	CCDS5691.1																																																																																			.	C|1.000;G|0.000		0.577	PILRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339016.1	NM_013439		A	99971978	C	A	99971978	2	1	255	1	0	0	0	0	0	0	0	1	11934	644	23	1		1	PILRA	7	99971978	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	270230	99971978	59166685	296	35641										
TFR2	7036	hgsc.bcm.edu	37	chr7	100226878	100226878	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccctggccctgaccttaccgTtgctcaccatggaggaaaag	10	14	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:100226878T>C	ENST00000462107.1	-	11	1675	c.1388A>G	c.(1387-1389)aAc>aGc	p.N463S	TFR2_ENST00000223051.3_Missense_Mutation_p.N463S|TFR2_ENST00000431692.1_3'UTR|TFR2_ENST00000544242.1_Missense_Mutation_p.N4S			Q9UP52	TFR2_HUMAN	transferrin receptor 2	463					cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)|receptor-mediated endocytosis (GO:0006898)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transferrin receptor activity (GO:0004998)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	23	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)				Gallium nitrate(DB05260)	GACCTTACCGTTGCTCACCAT	0.662																																					p.N463S		Atlas-SNP	.											.	TFR2	53	.	0			c.A1388G						.						95	89	91					7																	100226878		2203	4300	6503	SO:0001583	missense	7036	exon10			TTACCGTTGCTCA	AF053356	CCDS34707.1	7q22	2003-01-27			ENSG00000106327	ENSG00000106327			11762	protein-coding gene	gene with protein product		604720				9799793, 12130528	Standard	NM_003227		Approved	HFE3, TFRC2	uc003uvv.1	Q9UP52	OTTHUMG00000159598	ENST00000462107.1:c.1388A>G	chr7.hg19:g.100226878T>C	ENSP00000420525:p.Asn463Ser	62.0	0.0		30.0	4.0	NM_003227	A6NGM7|O75422|Q1HE13|Q9HA99|Q9NX67	Missense_Mutation	SNP	ENST00000462107.1	hg19	CCDS34707.1	.	.	.	.	.	.	.	.	.	.	T	14.76	2.631235	0.46944	.	.	ENSG00000106327	ENST00000223051;ENST00000462107;ENST00000544242	T;T;T	0.46819	0.86;0.86;0.86	4.54	3.35	0.38373	Peptidase M28 (1);	0.273448	0.38837	N	0.001546	T	0.28466	0.0704	N	0.17922	0.545	0.80722	D	1	B	0.22800	0.075	B	0.23018	0.043	T	0.05131	-1.0904	10	0.25751	T	0.34	-26.323	6.9773	0.24683	0.0:0.1054:0.0:0.8946	.	463	Q9UP52	TFR2_HUMAN	S	463;463;4	ENSP00000223051:N463S;ENSP00000420525:N463S;ENSP00000443656:N4S	ENSP00000223051:N463S	N	-	2	0	TFR2	100064814	0.999000	0.42202	0.994000	0.49952	0.916000	0.54674	3.319000	0.51983	0.736000	0.32559	0.459000	0.35465	AAC	.	.		0.662	TFR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356392.3	NM_003227		C	100226878	T	C	100226878	3	2	255	1	0	0	0	0	1	0	0	0	15826	1725	60	2	1053	2	TFR2	7	100226878	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	254900	100226878	58911785	297	35642										
LRRC17	10234	hgsc.bcm.edu	37	chr7	102584705	102584705	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agaattagatttatcaaacaAcagtctgcaaaactttgact	5	7	2	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:102584705A>G	ENST00000339431.4	+	4	1272	c.977A>G	c.(976-978)aAc>aGc	p.N326S	FBXL13_ENST00000379308.3_Intron|FBXL13_ENST00000313221.4_Intron|FBXL13_ENST00000456695.1_Intron|FBXL13_ENST00000455112.2_Intron|FBXL13_ENST00000436908.1_Intron|FBXL13_ENST00000379306.3_Intron|FBXL13_ENST00000393772.2_Intron|FBXL13_ENST00000379305.3_Intron|LRRC17_ENST00000485478.1_3'UTR|LRRC17_ENST00000249377.4_3'UTR	NM_001031692.2	NP_001026862.1	Q8N6Y2	LRC17_HUMAN	leucine rich repeat containing 17	326					bone marrow development (GO:0048539)|negative regulation of osteoclast differentiation (GO:0045671)|ossification (GO:0001503)	extracellular space (GO:0005615)				NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	17						TTATCAAACAACAGTCTGCAA	0.353																																					p.N326S		Atlas-SNP	.											.	LRRC17	45	.	0			c.A977G						.						98	105	103					7																	102584705		2203	4299	6502	SO:0001583	missense	10234	exon4			CAAACAACAGTCT	U32907	CCDS5727.1, CCDS34721.1	7q22.1	2009-05-26			ENSG00000128606	ENSG00000128606			16895	protein-coding gene	gene with protein product						8982252, 19336404	Standard	NM_005824		Approved	P37NB, H_RG318M05.3	uc003vau.3	Q8N6Y2	OTTHUMG00000157210	ENST00000339431.4:c.977A>G	chr7.hg19:g.102584705A>G	ENSP00000344242:p.Asn326Ser	110.0	0.0		78.0	33.0	NM_001031692	Q13288|Q6UWA7|Q75MG5	Missense_Mutation	SNP	ENST00000339431.4	hg19	CCDS34721.1	.	.	.	.	.	.	.	.	.	.	A	27.1	4.800116	0.90538	.	.	ENSG00000128606	ENST00000339431	T	0.68025	-0.3	5.93	5.93	0.95920	.	0.000000	0.64402	D	0.000004	D	0.87018	0.6073	H	0.94385	3.53	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.90545	0.4505	10	0.87932	D	0	-37.8037	16.3943	0.83563	1.0:0.0:0.0:0.0	.	326	Q8N6Y2	LRC17_HUMAN	S	326	ENSP00000344242:N326S	ENSP00000344242:N326S	N	+	2	0	LRRC17	102371941	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.339000	0.96797	2.281000	0.76405	0.533000	0.62120	AAC	.	.		0.353	LRRC17-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347930.1	NM_005824		G	102584705	A	G	102584705	3	3	255	1	0	0	0	0	1	0	0	0	8982	43	2	2	1005	2	LRRC17	7	102584705	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	2357827	102584705	56553958	298	35643										
ORC5L	5001	hgsc.bcm.edu	37	chr7	103808900	103808900	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agaagtatctccggtaactgTctcaatacttcctctgatac	6	11	3	2	rs34022264		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:103808900T>C	ENST00000297431.4	-	9	1020				ORC5_ENST00000545943.1_Intron|ORC5_ENST00000447452.2_Missense_Mutation_p.T300A	NM_002553.3	NP_002544.1	O43913	ORC5_HUMAN	origin recognition complex, subunit 5						DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)	ATP binding (GO:0005524)|DNA replication origin binding (GO:0003688)|nucleotide binding (GO:0000166)			kidney(1)|large_intestine(2)|lung(9)|pancreas(1)|upper_aerodigestive_tract(1)	14						CCGGTAACTGTCTCAATACTT	0.353																																					p.T300A		Atlas-SNP	.											.	ORC5	48	.	0			c.A898G						.						116	112	113					7																	103808900		2203	4300	6503	SO:0001627	intron_variant	5001	exon9			TAACTGTCTCAAT		CCDS5734.1, CCDS47681.1	7q22.1	2014-06-13	2010-10-12	2010-10-12	ENSG00000164815	ENSG00000164815			8491	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 117"	602331	"origin recognition complex, subunit 5 (yeast homolog)-like", "origin recognition complex, subunit 5-like (yeast)", "origin recognition complex, subunit 5 homolog (yeast)"	ORC5L		9417919, 9829972	Standard	NM_002553		Approved	Orc5p, ORC5T, PPP1R117	uc003vcb.3	O43913	OTTHUMG00000157275	ENST00000297431.4:c.877+20A>G	chr7.hg19:g.103808900T>C		112.0	0.0		80.0	4.0	NM_181747	A4D0P8|O60590|O95268	Missense_Mutation	SNP	ENST00000297431.4	hg19	CCDS5734.1	.	.	.	.	.	.	.	.	.	.	T	6.855	0.527054	0.13066	.	.	ENSG00000164815	ENST00000447452	T	0.22539	1.95	5.64	0.546	0.17196	.	.	.	.	.	T	0.07007	0.0178	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.39901	-0.9591	8	0.06365	T	0.9	.	3.8006	0.08757	0.2442:0.2226:0.0:0.5332	.	300	O43913-2	.	A	300	ENSP00000395747:T300A	ENSP00000395747:T300A	T	-	1	0	ORC5	103596136	0.002000	0.14202	0.064000	0.19789	0.170000	0.22686	0.412000	0.21131	0.105000	0.17753	-1.304000	0.01323	ACA	.	.		0.353	ORC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348286.1	NM_002553		C	103808900	T	C	103808900	1	2	255	0	1	0	0	0	0	0	0	0	11274	1667	58	2		2	ORC5L	7	103808900	Intron	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	1224195	103808900	55329763	299	35644										
CDHR3	222256	hgsc.bcm.edu	37	chr7	105621574	105621574	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcagtttcaaggcaacttggCagaaggtaggatacaccagg	12	8	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:105621574C>A	ENST00000317716.9	+	3	490	c.410C>A	c.(409-411)gCa>gAa	p.A137E	CDHR3_ENST00000343407.5_5'UTR|CDHR3_ENST00000478080.1_Missense_Mutation_p.A49E|CDHR3_ENST00000470188.1_3'UTR|CDHR3_ENST00000542731.1_Missense_Mutation_p.A137E|CDHR3_ENST00000541203.1_Missense_Mutation_p.A137E	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	137	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						GGCAACTTGGCAGAAGGTAGG	0.502																																					p.A137E		Atlas-SNP	.											.	CDHR3	153	.	0			c.C410A						.						69	63	65					7																	105621574		2020	4176	6196	SO:0001583	missense	222256	exon3			ACTTGGCAGAAGG	AK126338	CCDS47684.1, CCDS75651.1	7q22.2	2011-07-01			ENSG00000128536	ENSG00000128536		"Cadherins / Cadherin-related"	26308	protein-coding gene	gene with protein product		615610					Standard	NM_152750		Approved	FLJ44366, FLJ23834, CDH28	uc003vdl.4	Q6ZTQ4	OTTHUMG00000157520	ENST00000317716.9:c.410C>A	chr7.hg19:g.105621574C>A	ENSP00000325954:p.Ala137Glu	128.0	0.0		83.0	4.0	NM_152750	Q8TCI7	Missense_Mutation	SNP	ENST00000317716.9	hg19	CCDS47684.1	.	.	.	.	.	.	.	.	.	.	C	17.00	3.277273	0.59758	.	.	ENSG00000128536	ENST00000542731;ENST00000317716;ENST00000478080;ENST00000541203	T;T;T;T	0.57107	0.44;0.44;0.42;1.0	5.02	4.12	0.48240	Cadherin (1);	0.078618	0.52532	D	0.000061	T	0.67832	0.2935	M	0.69823	2.125	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.989;0.997	T	0.65734	-0.6096	10	0.13470	T	0.59	-12.075	14.5236	0.67870	0.0:0.8518:0.1482:0.0	.	124;137	B3KYA0;Q6ZTQ4	.;CDHR3_HUMAN	E	137;137;49;137	ENSP00000439766:A137E;ENSP00000325954:A137E;ENSP00000417771:A49E;ENSP00000443733:A137E	ENSP00000325954:A137E	A	+	2	0	CDHR3	105408810	0.991000	0.36638	0.881000	0.34555	0.540000	0.34992	2.119000	0.41958	1.442000	0.47568	0.561000	0.74099	GCA	.	.		0.502	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	NM_152750		A	105621574	C	A	105621574	3	1	255	1	0	0	0	0	1	0	0	0	3122	710	25	3	420	3	CDHR3	7	105621574	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1812674	105621574	53517089	300	35645										
MDFIC	29969	hgsc.bcm.edu	37	chr7	114619590	114619590	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agcgcttgcctcagcttcagActtcagcccaggtgccaagt	10	14	3	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:114619590A>G	ENST00000393486.1	+	4	837	c.247A>G	c.(247-249)Act>Gct	p.T83A	MDFIC_ENST00000257724.3_Missense_Mutation_p.T192A	NM_001166345.1|NM_199072.4	NP_001159817.1|NP_951038.1			MyoD family inhibitor domain containing											breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	8						TCAGCTTCAGACTTCAGCCCA	0.423																																					p.T192A		Atlas-SNP	.											.	MDFIC	30	.	0			c.A574G						.						65	64	64					7																	114619590		2203	4300	6503	SO:0001583	missense	29969	exon4			CTTCAGACTTCAG	AF054589	CCDS34737.1, CCDS55155.1	7q31.1-q31.2	2006-01-11			ENSG00000135272	ENSG00000135272			28870	protein-coding gene	gene with protein product		614511				10671520	Standard	NM_199072		Approved	HIC	uc003vhf.3	Q9P1T7	OTTHUMG00000023647	ENST00000393486.1:c.247A>G	chr7.hg19:g.114619590A>G	ENSP00000377126:p.Thr83Ala	140.0	0.0		87.0	4.0	NM_199072		Missense_Mutation	SNP	ENST00000393486.1	hg19	CCDS55155.1	.	.	.	.	.	.	.	.	.	.	A	13.78	2.338646	0.41398	.	.	ENSG00000135272	ENST00000257724;ENST00000393486;ENST00000427207;ENST00000498196	.	.	.	5.98	0.822	0.18806	.	0.572336	0.18522	N	0.138727	T	0.42810	0.1219	M	0.66506	2.035	0.33700	D	0.61444	B	0.10296	0.003	B	0.08055	0.003	T	0.39981	-0.9587	9	0.17832	T	0.49	0.0133	5.9591	0.19289	0.5295:0.2302:0.2403:0.0	.	83	Q9P1T7	MDFIC_HUMAN	A	192;83;69;28	.	ENSP00000257724:T192A	T	+	1	0	MDFIC	114406826	0.937000	0.31787	0.005000	0.12908	0.893000	0.52053	0.472000	0.22116	-0.078000	0.12730	0.482000	0.46254	ACT	.	.		0.423	MDFIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059968.4	NM_199072		G	114619590	A	G	114619590	3	3	255	1	0	0	0	0	1	0	0	0	9414	275	10	2	630	2	MDFIC	7	114619590	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	8998016	114619590	44519073	301	35646										
ST7	7982	hgsc.bcm.edu	37	chr7	116759658	116759658	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	caaatacggaacttcattcaTtgaacaagtctcagtaagcc	6	10	3	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:116759658T>C	ENST00000393446.2	+	3	581	c.278T>C	c.(277-279)aTt>aCt	p.I93T	ST7-AS2_ENST00000434993.1_RNA|ST7-AS2_ENST00000442719.1_RNA|ST7_ENST00000465133.1_Missense_Mutation_p.I50T|ST7_ENST00000393449.1_Missense_Mutation_p.I93T|ST7-AS2_ENST00000432541.1_RNA|ST7_ENST00000323984.3_Missense_Mutation_p.I93T|ST7_ENST00000422922.1_Missense_Mutation_p.I47T|ST7_ENST00000432298.1_Missense_Mutation_p.I47T|ST7_ENST00000393451.3_Missense_Mutation_p.I93T|ST7_ENST00000393444.3_Missense_Mutation_p.I50T|ST7_ENST00000487459.1_3'UTR|ST7_ENST00000393447.4_Missense_Mutation_p.I50T|ST7_ENST00000393443.1_Missense_Mutation_p.I43T|ST7_ENST00000265437.5_Missense_Mutation_p.I93T			Q9Y561	LRP12_HUMAN	suppression of tumorigenicity 7	0	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(1)	21	all_cancers(3;3.88e-07)|all_epithelial(6;3.42e-07)|Lung NSC(10;0.00072)|all_lung(10;0.000847)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		ACTTCATTCATTGAACAAGTC	0.408																																					p.I93T		Atlas-SNP	.											.	ST7	64	.	0			c.T278C						.						127	121	123					7																	116759658		2203	4300	6503	SO:0001583	missense	7982	exon3			CATTCATTGAACA	AJ277291	CCDS5769.1, CCDS5770.1	7q31.2	2008-06-06			ENSG00000004866	ENSG00000004866			11351	protein-coding gene	gene with protein product		600833		FAM4A1		8105370, 8938430	Standard	NM_021908		Approved	TSG7, SEN4, ETS7q, HELG, RAY1, FAM4A	uc003vin.3	Q9NRC1	OTTHUMG00000023888	ENST00000393446.2:c.278T>C	chr7.hg19:g.116759658T>C	ENSP00000377092:p.Ile93Thr	133.0	0.0		100.0	4.0	NM_018412	A8K137|B4DRQ2	Missense_Mutation	SNP	ENST00000393446.2	hg19		.	.	.	.	.	.	.	.	.	.	T	27.0	4.787341	0.90367	.	.	ENSG00000004866	ENST00000393446;ENST00000265437;ENST00000393451;ENST00000323984;ENST00000393449;ENST00000417919;ENST00000446490;ENST00000421345;ENST00000432298;ENST00000422922;ENST00000449366;ENST00000393443;ENST00000465133;ENST00000477742;ENST00000393447;ENST00000393444;ENST00000420755;ENST00000490039	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.24723	1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.56202	0.1969	M	0.83603	2.65	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.987;1.0;0.987;1.0;1.0;0.984;1.0	D;D;D;D;D;D;D	0.97110	0.979;1.0;0.979;0.999;0.999;0.964;0.999	T	0.61753	-0.6998	10	0.87932	D	0	-13.1569	16.2903	0.82747	0.0:0.0:0.0:1.0	.	41;50;93;43;47;93;93	C9JU30;B7Z4L1;B7Z573;Q9NRC1-6;B7Z4U3;Q9NRC1-2;Q9NRC1	.;.;.;.;.;.;ST7_HUMAN	T	93;93;93;93;93;43;93;41;47;47;43;43;50;41;50;50;41;41	ENSP00000377092:I93T;ENSP00000265437:I93T;ENSP00000377097:I93T;ENSP00000325673:I93T;ENSP00000377095:I93T;ENSP00000391444:I43T;ENSP00000402934:I93T;ENSP00000416858:I41T;ENSP00000411118:I47T;ENSP00000414031:I47T;ENSP00000413601:I43T;ENSP00000377089:I43T;ENSP00000420052:I50T;ENSP00000419715:I41T;ENSP00000377093:I50T;ENSP00000377090:I50T;ENSP00000388698:I41T;ENSP00000419516:I41T	ENSP00000265437:I93T	I	+	2	0	ST7	116546894	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.698000	0.84413	2.326000	0.78906	0.533000	0.62120	ATT	.	.		0.408	ST7-013	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000319687.1	NM_021908		C	116759658	T	C	116759658	3	2	255	1	0	0	0	0	1	0	0	0	15244	1493	52	2	288	2	ST7	7	116759658	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	2140068	116759658	42379005	302	35647										
FLNC	2318	hgsc.bcm.edu	37	chr7	128477572	128477572	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctgttcgatccaagcagctgAaccccaagaaagccatcgcc	8	15	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:128477572A>G	ENST00000325888.8	+	4	1081	c.820A>G	c.(820-822)Aac>Gac	p.N274D	FLNC_ENST00000346177.6_Missense_Mutation_p.N274D	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	274					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						CAAGCAGCTGAACCCCAAGAA	0.597																																					p.N274D		Atlas-SNP	.											.	FLNC	339	.	0			c.A820G						.						115	126	122					7																	128477572		2155	4282	6437	SO:0001583	missense	2318	exon4			CAGCTGAACCCCA	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"actin binding protein 280"	102565	"filamin C, gamma (actin binding protein 280)"	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.820A>G	chr7.hg19:g.128477572A>G	ENSP00000327145:p.Asn274Asp	121.0	0.0		69.0	4.0	NM_001127487	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Missense_Mutation	SNP	ENST00000325888.8	hg19	CCDS43644.1	.	.	.	.	.	.	.	.	.	.	A	19.45	3.830803	0.71258	.	.	ENSG00000128591	ENST00000325888;ENST00000346177	T;T	0.58506	0.33;0.33	5.03	3.86	0.44501	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.235147	0.41396	D	0.000886	T	0.36826	0.0981	N	0.13098	0.295	0.31065	N	0.713702	B;B	0.28636	0.218;0.0	B;B	0.28305	0.088;0.023	T	0.39078	-0.9631	10	0.54805	T	0.06	.	6.7381	0.23421	0.6885:0.1591:0.0:0.1523	.	274;274	Q14315-2;Q14315	.;FLNC_HUMAN	D	274	ENSP00000327145:N274D;ENSP00000344002:N274D	ENSP00000327145:N274D	N	+	1	0	FLNC	128264808	0.988000	0.35896	1.000000	0.80357	0.997000	0.91878	0.692000	0.25482	0.745000	0.32763	0.533000	0.62120	AAC	.	.		0.597	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3			G	128477572	A	G	128477572	3	3	255	1	0	0	0	0	1	0	0	0	5943	246	9	2	834	2	FLNC	7	128477572	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	11717914	128477572	30661091	303	35648										
LRGUK	136332	hgsc.bcm.edu	37	chr7	133876488	133876488	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	atctctcaagacgtttttgaTgaaatggtgaacatggtaag	10	5	2	4			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:133876488T>C	ENST00000285928.2	+	12	1485	c.1416T>C	c.(1414-1416)gaT>gaC	p.D472D		NM_144648.1	NP_653249.1	Q96M69	LRGUK_HUMAN	leucine-rich repeats and guanylate kinase domain containing	472	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)			breast(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(23)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	49						ACGTTTTTGATGAAATGGTGA	0.338																																					p.D472D		Atlas-SNP	.											.	LRGUK	113	.	0			c.T1416C						.						130	121	124					7																	133876488		2203	4300	6503	SO:0001819	synonymous_variant	136332	exon12			TTTTGATGAAATG	AK057348	CCDS5830.1	7q33	2006-10-27			ENSG00000155530	ENSG00000155530			21964	protein-coding gene	gene with protein product							Standard	NM_144648		Approved	FLJ32786	uc003vrm.1	Q96M69	OTTHUMG00000155320	ENST00000285928.2:c.1416T>C	chr7.hg19:g.133876488T>C		154.0	0.0		87.0	4.0	NM_144648	Q2M3I1	Silent	SNP	ENST00000285928.2	hg19	CCDS5830.1																																																																																			.	.		0.338	LRGUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339442.1	NM_144648		C	133876488	T	C	133876488	2	2	255	1	0	0	0	0	0	0	0	1	8952	1461	51	2		2	LRGUK	7	133876488	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	5398916	133876488	25262175	304	35649										
ZC3HAV1L	92092	hgsc.bcm.edu	37	chr7	138719329	138719329	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cattctgcaaaagcaggatcCgaagctggttttcattgaga	10	8	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:138719329C>A	ENST00000275766.1	-	2	472	c.461G>T	c.(460-462)cGg>cTg	p.R154L		NM_080660.3	NP_542391.2	Q96H79	ZCCHL_HUMAN	zinc finger CCCH-type, antiviral 1-like	154										NS(2)|endometrium(2)|large_intestine(1)|lung(4)|skin(1)	10						AAGCAGGATCCGAAGCTGGTT	0.453																																					p.R154L		Atlas-SNP	.											.	ZC3HAV1L	15	.	0			c.G461T						.						112	109	110					7																	138719329		2203	4300	6503	SO:0001583	missense	92092	exon2			AGGATCCGAAGCT	BC008842	CCDS5850.1	7q34	2006-07-03	2006-07-03	2006-07-03	ENSG00000146858	ENSG00000146858			22423	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 39"	C7orf39			Standard	NM_080660		Approved	MGC14289	uc003vum.1	Q96H79	OTTHUMG00000157229	ENST00000275766.1:c.461G>T	chr7.hg19:g.138719329C>A	ENSP00000275766:p.Arg154Leu	93.0	0.0		80.0	4.0	NM_080660	Q8WUD9	Missense_Mutation	SNP	ENST00000275766.1	hg19	CCDS5850.1	.	.	.	.	.	.	.	.	.	.	C	15.54	2.862521	0.51482	.	.	ENSG00000146858	ENST00000275766	T	0.38560	1.13	5.86	1.96	0.26148	.	0.356873	0.20743	N	0.086485	T	0.30355	0.0762	L	0.52573	1.65	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.17137	-1.0379	10	0.33940	T	0.23	.	3.2547	0.06827	0.1435:0.56:0.1392:0.1573	.	154	Q96H79	ZCCHL_HUMAN	L	154	ENSP00000275766:R154L	ENSP00000275766:R154L	R	-	2	0	ZC3HAV1L	138369869	0.024000	0.19004	0.009000	0.14445	0.941000	0.58515	0.569000	0.23638	0.461000	0.27071	0.650000	0.86243	CGG	.	.		0.453	ZC3HAV1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348090.1	NM_080660		A	138719329	C	A	138719329	3	1	255	1	0	0	0	0	1	0	0	0	17591	652	23	1	457	1	ZC3HAV1L	7	138719329	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	4842841	138719329	20419334	305	35650										
SLC37A3	84255	hgsc.bcm.edu	37	chr7	140069457	140069457	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gagtcgctttctctgcactgGggaacaaatggttgctgctc	12	10	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:140069457G>T	ENST00000326232.9	-	4	427	c.224C>A	c.(223-225)cCc>cAc	p.P75H	SLC37A3_ENST00000340308.3_Missense_Mutation_p.P75H|RNA5SP247_ENST00000411181.1_RNA|SLC37A3_ENST00000461089.1_5'UTR|SLC37A3_ENST00000447932.2_Missense_Mutation_p.P75H|SLC37A3_ENST00000429996.2_Missense_Mutation_p.P75H	NM_207113.1	NP_996996.1	Q8NCC5	SPX3_HUMAN	solute carrier family 37, member 3	75					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|stomach(3)	24	Melanoma(164;0.0142)					CTCTGCACTGGGGAACAAATG	0.483																																					p.P75H	Esophageal Squamous(133;211 1716 4665 11387 37873)	Atlas-SNP	.											.	SLC37A3	80	.	0			c.C224A						.						99	87	91					7																	140069457		2203	4300	6503	SO:0001583	missense	84255	exon4			GCACTGGGGAACA	AK074823	CCDS5858.1, CCDS5859.1, CCDS75669.1	7q34	2013-07-17	2013-07-17		ENSG00000157800	ENSG00000157800		"Solute carriers"	20651	protein-coding gene	gene with protein product							Standard	NM_001287498		Approved	DKFZp761N0624	uc003vvo.3	Q8NCC5	OTTHUMG00000157343	ENST00000326232.9:c.224C>A	chr7.hg19:g.140069457G>T	ENSP00000321498:p.Pro75His	44.0	0.0		47.0	4.0	NM_207113	Q6PIU7|Q86SS4|Q9BQG7	Missense_Mutation	SNP	ENST00000326232.9	hg19	CCDS5859.1	.	.	.	.	.	.	.	.	.	.	G	15.32	2.798989	0.50208	.	.	ENSG00000157800	ENST00000340308;ENST00000447932;ENST00000326232;ENST00000429996;ENST00000539816;ENST00000469193	T;T;T;T;T	0.47869	2.15;2.45;2.45;0.83;0.85	5.2	5.2	0.72013	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.335918	0.31199	N	0.008065	T	0.60599	0.2281	M	0.63843	1.955	0.46416	D	0.999031	P;P;P;P;P	0.43578	0.743;0.708;0.565;0.811;0.619	P;P;B;P;P	0.53401	0.683;0.554;0.43;0.725;0.566	T	0.61048	-0.7141	10	0.49607	T	0.09	-24.2852	16.5098	0.84281	0.0:0.0:1.0:0.0	.	75;75;75;75;75	B4DKF5;F5H743;Q8NCC5-2;Q8NCC5-3;Q8NCC5	.;.;.;.;SPX3_HUMAN	H	75	ENSP00000343358:P75H;ENSP00000397481:P75H;ENSP00000321498:P75H;ENSP00000412208:P75H;ENSP00000419024:P75H	ENSP00000321498:P75H	P	-	2	0	SLC37A3	139715926	1.000000	0.71417	0.643000	0.29450	0.204000	0.24138	3.508000	0.53378	2.435000	0.82474	0.591000	0.81541	CCC	.	.		0.483	SLC37A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348492.1	NM_032295		T	140069457	G	T	140069457	3	4	255	1	0	0	0	0	1	0	0	0	14614	1232	43	3	1457	3	SLC37A3	7	140069457	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	1350128	140069457	19069206	306	35651										
ADCK2	90956	hgsc.bcm.edu	37	chr7	140373468	140373468	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gttggtgaaattcttcccccTcctactcctctaccccctca	4	18	3	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:140373468T>C	ENST00000072869.4	+	1	516	c.338T>C	c.(337-339)cTc>cCc	p.L113P	ADCK2_ENST00000476491.1_Missense_Mutation_p.L113P	NM_052853.3	NP_443085.2	Q7Z695	ADCK2_HUMAN	aarF domain containing kinase 2	113						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|kidney(2)|large_intestine(2)|lung(5)|prostate(1)|skin(4)	15	Melanoma(164;0.00956)					TTCTTCCCCCTCCTACTCCTC	0.657																																					p.L113P		Atlas-SNP	.											.	ADCK2	37	.	0			c.T338C						.						82	92	89					7																	140373468		2203	4300	6503	SO:0001583	missense	90956	exon1			TCCCCCTCCTACT	AF131745	CCDS5861.1	7q34	2003-07-21			ENSG00000133597	ENSG00000133597			19039	protein-coding gene	gene with protein product							Standard	NM_052853		Approved	MGC20727	uc003vvy.1	Q7Z695	OTTHUMG00000157409	ENST00000072869.4:c.338T>C	chr7.hg19:g.140373468T>C	ENSP00000072869:p.Leu113Pro	83.0	0.0		68.0	4.0	NM_052853	Q96CN6|Q9Y6T5	Missense_Mutation	SNP	ENST00000072869.4	hg19	CCDS5861.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.446707	0.84101	.	.	ENSG00000133597	ENST00000072869;ENST00000476491	T;T	0.55413	0.52;0.52	4.63	4.63	0.57726	.	0.000000	0.64402	D	0.000002	T	0.66376	0.2783	L	0.49778	1.585	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76575	0.988;0.988	T	0.70040	-0.4981	10	0.87932	D	0	0.0817	14.0644	0.64819	0.0:0.0:0.0:1.0	.	113;113	C9JE15;Q7Z695	.;ADCK2_HUMAN	P	113	ENSP00000072869:L113P;ENSP00000420512:L113P	ENSP00000072869:L113P	L	+	2	0	ADCK2	140019937	1.000000	0.71417	0.806000	0.32338	0.806000	0.45545	5.782000	0.68973	1.736000	0.51660	0.459000	0.35465	CTC	.	.		0.657	ADCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348734.1	NM_052853		C	140373468	T	C	140373468	3	2	255	1	0	0	0	0	1	0	0	0	289	1551	54	2	340	2	ADCK2	7	140373468	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	304011	140373468	18765195	307	35652										
WEE2	494551	hgsc.bcm.edu	37	chr7	141414139	141414139	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tctggtcaatattaatccctTcactccagagtcctataaaa	4	11	3	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:141414139T>C	ENST00000397541.2	+	2	879	c.473T>C	c.(472-474)tTc>tCc	p.F158S	WEE2-AS1_ENST00000462383.1_RNA|WEE2-AS1_ENST00000495800.1_RNA|WEE2-AS1_ENST00000478332.1_RNA|WEE2-AS1_ENST00000488785.1_RNA|WEE2-AS1_ENST00000471512.1_RNA|WEE2-AS1_ENST00000459753.1_RNA|WEE2-AS1_ENST00000465110.1_RNA	NM_001105558.1	NP_001099028.1	P0C1S8	WEE2_HUMAN	WEE1 homolog 2 (S. pombe)	158					female meiotic division (GO:0007143)|female pronucleus assembly (GO:0035038)|mitotic nuclear division (GO:0007067)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of oocyte maturation (GO:1900194)|regulation of meiosis I (GO:0060631)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(2)|stomach(1)	31	Melanoma(164;0.0171)					ATTAATCCCTTCACTCCAGAG	0.423																																					p.F158S		Atlas-SNP	.											.	WEE2	59	.	0			c.T473C						.						80	75	76					7																	141414139		1839	4097	5936	SO:0001583	missense	494551	exon2			ATCCCTTCACTCC	AK131218	CCDS43660.1	7q32	2008-07-02			ENSG00000214102	ENSG00000214102			19684	protein-coding gene	gene with protein product		614084					Standard	NM_001105558		Approved	FLJ16107	uc003vwn.2	P0C1S8	OTTHUMG00000157536	ENST00000397541.2:c.473T>C	chr7.hg19:g.141414139T>C	ENSP00000380675:p.Phe158Ser	83.0	0.0		43.0	4.0	NM_001105558		Missense_Mutation	SNP	ENST00000397541.2	hg19	CCDS43660.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.179199	0.78564	.	.	ENSG00000214102	ENST00000397541	T	0.48201	0.82	5.03	3.87	0.44632	.	0.000000	0.64402	U	0.000001	T	0.67468	0.2896	M	0.82323	2.585	0.58432	D	0.999992	D	0.76494	0.999	D	0.69307	0.963	T	0.71059	-0.4702	10	0.87932	D	0	.	10.802	0.46493	0.0:0.0747:0.0:0.9252	.	158	P0C1S8	WEE2_HUMAN	S	158	ENSP00000380675:F158S	ENSP00000380675:F158S	F	+	2	0	WEE2	141060608	1.000000	0.71417	0.989000	0.46669	0.979000	0.70002	6.539000	0.73856	0.932000	0.37266	0.477000	0.44152	TTC	.	.		0.423	WEE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349091.1	NM_001105558		C	141414139	T	C	141414139	3	2	255	1	0	0	0	0	1	0	0	0	17360	1783	62	2	479	2	WEE2	7	141414139	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	1040671	141414139	17724524	308	35653										
CLCN1	1180	hgsc.bcm.edu	37	chr7	143016896	143016896	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cagacagggagcaggacataGggatgcccaagaagacaggc	15	9	0	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:143016896G>A	ENST00000343257.2	+	2	316	c.229G>A	c.(229-231)Ggg>Agg	p.G77R		NM_000083.2	NP_000074	P35523	CLCN1_HUMAN	chloride channel, voltage-sensitive 1	77					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|neuronal action potential propagation (GO:0019227)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	adenyl nucleotide binding (GO:0030554)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(4)|central_nervous_system(1)|endometrium(1)|large_intestine(11)|lung(26)|ovary(3)|prostate(2)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	58	Melanoma(164;0.205)					GCAGGACATAGGGATGCCCAA	0.443																																					p.G77R		Atlas-SNP	.											.	CLCN1	141	.	0			c.G229A						.						192	160	171					7																	143016896		2203	4300	6503	SO:0001583	missense	1180	exon2			GACATAGGGATGC	Z25884	CCDS5881.1	7q12	2012-09-26	2012-02-23		ENSG00000188037	ENSG00000188037		"Ion channels / Chloride channels : Voltage-sensitive"	2019	protein-coding gene	gene with protein product	"Thomsen disease, autosomal dominant"	118425	"chloride channel 1, skeletal muscle"			1379744	Standard	NM_000083		Approved	CLC1, ClC-1	uc003wcr.1	P35523	OTTHUMG00000152695	ENST00000343257.2:c.229G>A	chr7.hg19:g.143016896G>A	ENSP00000339867:p.Gly77Arg	91.0	0.0		88.0	39.0	NM_000083	A4D2H5|Q2M202	Missense_Mutation	SNP	ENST00000343257.2	hg19	CCDS5881.1	.	.	.	.	.	.	.	.	.	.	.	7.643	0.681360	0.14907	.	.	ENSG00000188037	ENST00000343257	D	0.84800	-1.9	5.45	3.66	0.41972	.	0.651527	0.15301	N	0.269603	T	0.77212	0.4097	L	0.47716	1.5	0.09310	N	1	B	0.12013	0.005	B	0.08055	0.003	T	0.59337	-0.7473	10	0.16420	T	0.52	.	7.5381	0.27723	0.2616:0.0:0.7384:0.0	.	77	P35523	CLCN1_HUMAN	R	77	ENSP00000339867:G77R	ENSP00000339867:G77R	G	+	1	0	CLCN1	142727018	0.000000	0.05858	0.162000	0.22713	0.249000	0.25844	0.554000	0.23407	0.705000	0.31890	0.650000	0.86243	GGG	.	.		0.443	CLCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327420.1	NM_000083		A	143016896	G	A	143016896	3	1	255	1	0	0	0	0	1	0	0	0	3464	1000	35	3	235	3	CLCN1	7	143016896	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	1602757	143016896	16121767	309	35654										
NOBOX	135935	hgsc.bcm.edu	37	chr7	144096261	144096261	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gtctggtcagaagtcagcagCatggggggctctaggaacag	16	8	4	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:144096261C>T	ENST00000467773.1	-	8	1250	c.1251G>A	c.(1249-1251)atG>atA	p.M417I	NOBOX_ENST00000223140.5_Missense_Mutation_p.M300I|NOBOX_ENST00000483238.1_Missense_Mutation_p.M385I	NM_001080413.3	NP_001073882.3	O60393	NOBOX_HUMAN	NOBOX oogenesis homeobox	417	Pro-rich.				oogenesis (GO:0048477)|ovarian follicle development (GO:0001541)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)	26	Melanoma(164;0.14)					AAGTCAGCAGCATGGGGGGCT	0.592																																					p.M417I		Atlas-SNP	.											.	NOBOX	130	.	0			c.G1251A						.						14	15	14					7																	144096261		1965	4106	6071	SO:0001583	missense	135935	exon8			CAGCAGCATGGGG			7q35	2011-06-20			ENSG00000106410	ENSG00000106410		"Homeoboxes / PRD class"	22448	protein-coding gene	gene with protein product	"newborn ovary homeobox-encoding gene"	610934				11804785, 16597639	Standard	NM_001080413		Approved	OG2, Og2x	uc022aoj.1	O60393	OTTHUMG00000158051	ENST00000467773.1:c.1251G>A	chr7.hg19:g.144096261C>T	ENSP00000419457:p.Met417Ile	99.0	0.0		61.0	4.0	NM_001080413	A6NCD3|A8MZN5	Missense_Mutation	SNP	ENST00000467773.1	hg19		.	.	.	.	.	.	.	.	.	.	C	10.76	1.441820	0.25900	.	.	ENSG00000106410	ENST00000483238;ENST00000467773;ENST00000223140	D;D;D	0.93189	-2.85;-3.18;-2.86	4.92	0.389	0.16269	.	1.413510	0.03906	N	0.281122	D	0.87458	0.6182	L	0.40543	1.245	0.19945	N	0.999947	B	0.20671	0.047	B	0.15870	0.014	T	0.70651	-0.4813	10	0.18276	T	0.48	-2.8092	1.6801	0.02830	0.1449:0.4316:0.142:0.2816	.	417	O60393	NOBOX_HUMAN	I	385;417;300	ENSP00000419565:M385I;ENSP00000419457:M417I;ENSP00000223140:M300I	ENSP00000223140:M300I	M	-	3	0	NOBOX	143727194	0.404000	0.25328	0.950000	0.38849	0.982000	0.71751	0.294000	0.19047	0.133000	0.18654	0.561000	0.74099	ATG	.	.		0.592	NOBOX-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000350095.1	XM_001134420		T	144096261	C	T	144096261	3	4	255	1	0	0	0	0	1	0	0	0	10521	710	25	3	836	3	NOBOX	7	144096261	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1079365	144096261	15042402	310	35655										
GIMAP8	155038	hgsc.bcm.edu	37	chr7	150171349	150171349	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggacatctcatctttaaagaAcattgactcagaagttagaa	7	7	3	4			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:150171349A>G	ENST00000307271.3	+	4	1506	c.932A>G	c.(931-933)aAc>aGc	p.N311S		NM_175571.2	NP_783161.1	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	311	AIG1-type G 2.					cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(26)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)		TCTTTAAAGAACATTGACTCA	0.458																																					p.N311S		Atlas-SNP	.											.	GIMAP8	136	.	0			c.A932G						.						73	80	77					7																	150171349		2203	4300	6503	SO:0001583	missense	155038	exon4			TAAAGAACATTGA	AL834361	CCDS34777.1	7q36.1	2014-04-04			ENSG00000171115	ENSG00000171115		"GTPases, IMAP"	21792	protein-coding gene	gene with protein product	"immune-associated nucleotide-binding protein 9"					15474311	Standard	XM_005249951		Approved	DKFZp667I133, hIAN6, IAN9	uc003whj.3	Q8ND71	OTTHUMG00000158327	ENST00000307271.3:c.932A>G	chr7.hg19:g.150171349A>G	ENSP00000305107:p.Asn311Ser	85.0	0.0		94.0	4.0	NM_175571		Missense_Mutation	SNP	ENST00000307271.3	hg19	CCDS34777.1	.	.	.	.	.	.	.	.	.	.	A	7.642	0.681042	0.14907	.	.	ENSG00000171115	ENST00000307271	T	0.60920	0.15	4.47	-4.25	0.03766	AIG1 (1);	1.311810	0.05394	N	0.539498	T	0.29028	0.0721	N	0.11064	0.09	0.09310	N	1	B	0.18610	0.029	B	0.15870	0.014	T	0.09100	-1.0690	10	0.16896	T	0.51	.	2.0799	0.03632	0.2938:0.1806:0.3872:0.1384	.	311	Q8ND71	GIMA8_HUMAN	S	311	ENSP00000305107:N311S	ENSP00000305107:N311S	N	+	2	0	GIMAP8	149802282	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.199000	0.03032	-0.661000	0.05345	0.528000	0.53228	AAC	.	.		0.458	GIMAP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350701.1	NM_175571		G	150171349	A	G	150171349	3	3	255	1	0	0	0	0	1	0	0	0	6393	43	2	2	942	2	GIMAP8	7	150171349	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	6075088	150171349	8967314	311	35656										
ACCN3	9311	hgsc.bcm.edu	37	chr7	150747908	150747908	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctctgaaccccaactatgagCcagagccctctgatccccta	6	17	2	4			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:150747908C>G	ENST00000349064.5	+	4	1075	c.877C>G	c.(877-879)Cca>Gca	p.P293A	ASIC3_ENST00000357922.4_Missense_Mutation_p.P293A|ASIC3_ENST00000297512.8_Missense_Mutation_p.P293A	NM_004769.3|NM_020321.3	NP_004760.1|NP_064717.1	Q9UHC3	ASIC3_HUMAN	acid-sensing (proton-gated) ion channel 3	293					cation transmembrane transport (GO:0098655)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ion transmembrane transport (GO:0034220)|response to acid chemical (GO:0001101)|response to acidic pH (GO:0010447)|response to heat (GO:0009408)|sensory perception (GO:0007600)|sensory perception of sour taste (GO:0050915)|signal transduction (GO:0007165)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cation channel activity (GO:0005261)|enterobactin transporter activity (GO:0042931)|ligand-gated sodium channel activity (GO:0015280)|sodium channel activity (GO:0005272)										CAACTATGAGCCAGAGCCCTC	0.647																																					p.P293A		Atlas-SNP	.											.	.	.	.	0			c.C877G						.						29	33	32					7																	150747908		2203	4300	6503	SO:0001583	missense	9311	exon4			TATGAGCCAGAGC	AB010575	CCDS5914.1, CCDS5915.1, CCDS5916.1	7q35	2012-02-23	2012-02-22	2012-02-22	ENSG00000213199	ENSG00000213199		"Ion channels / Acid-sensing (proton-gated) ion channels"	101	protein-coding gene	gene with protein product	"testis sodium channel 1"	611741	"amiloride-sensitive cation channel 3, testis", "amiloride-sensitive cation channel 3"	ACCN3		9571199, 9744806	Standard	NM_004769		Approved	TNaC1, DRASIC	uc003wio.3	Q9UHC3	OTTHUMG00000158685	ENST00000349064.5:c.877C>G	chr7.hg19:g.150747908C>G	ENSP00000344838:p.Pro293Ala	64.0	0.0		66.0	15.0	NM_020322	B2R9V0|O60263|O75906|Q59FN9|Q9UER8|Q9UHC4	Missense_Mutation	SNP	ENST00000349064.5	hg19	CCDS5916.1	.	.	.	.	.	.	.	.	.	.	C	0.305	-0.971659	0.02215	.	.	ENSG00000213199	ENST00000357922;ENST00000349064;ENST00000297512	T;T;T	0.61859	0.07;0.07;0.07	4.84	0.71	0.18157	.	972.779000	0.00855	N	0.001860	T	0.47875	0.1469	L	0.54323	1.7	0.09310	N	1	B;B;B	0.28128	0.114;0.039;0.201	B;B;B	0.24701	0.053;0.023;0.055	T	0.05616	-1.0874	10	0.15952	T	0.53	-1.1147	1.8255	0.03119	0.139:0.4629:0.1363:0.2617	.	293;293;293	Q9UHC3-2;Q9UHC3-3;Q9UHC3	.;.;ACCN3_HUMAN	A	293	ENSP00000350600:P293A;ENSP00000344838:P293A;ENSP00000297512:P293A	ENSP00000297512:P293A	P	+	1	0	ACCN3	150378841	0.068000	0.21057	0.014000	0.15608	0.027000	0.11550	0.424000	0.21330	0.201000	0.20466	0.650000	0.86243	CCA	.	.		0.647	ASIC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351725.1	NM_004769		G	150747908	C	G	150747908	3	3	255	1	0	0	0	0	1	0	0	0	130	739	26	4	891	4	ACCN3	7	150747908	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	576559	150747908	8390755	312	35657										
CSMD1	64478	hgsc.bcm.edu	37	chr8	2949044	2949044	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cctcatttacttacctgcatAgcgaatcttgaatcctttct	4	12	3	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:2949044A>G	ENST00000520002.1	-	49	7837	c.7282T>C	c.(7282-7284)Tat>Cat	p.Y2428H	CSMD1_ENST00000602723.1_Missense_Mutation_p.Y2428H|CSMD1_ENST00000400186.3_Missense_Mutation_p.Y2428H|CSMD1_ENST00000542608.1_Missense_Mutation_p.Y2427H|CSMD1_ENST00000602557.1_Missense_Mutation_p.Y2428H|CSMD1_ENST00000537824.1_Missense_Mutation_p.Y2427H			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	2428	CUB 14. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		TTACCTGCATAGCGAATCTTG	0.303																																					p.Y2427H		Atlas-SNP	.											.	CSMD1	1469	.	0			c.T7279C						.						110	103	105					8																	2949044		1831	4081	5912	SO:0001583	missense	64478	exon48			CTGCATAGCGAAT			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.7282T>C	chr8.hg19:g.2949044A>G	ENSP00000430733:p.Tyr2428His	92.0	0.0		76.0	4.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.7|22.7	4.321693|4.321693	0.81580|0.81580	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000335551|ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608	.|T;T;T;T	.|0.57107	.|0.42;0.42;0.42;0.42	5.78|5.78	5.78|5.78	0.91487|0.91487	.|CUB (5);	.|0.000000	.|0.64402	.|D	.|0.000001	T|T	0.78020|0.78020	0.4218|0.4218	M|M	0.92649|0.92649	3.33|3.33	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.97110	.|0.999;1.0;0.999	T|T	0.79524|0.79524	-0.1768|-0.1768	5|10	.|0.24483	.|T	.|0.36	.|.	16.0976|16.0976	0.81139|0.81139	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|2428;2428;2427	.|E5RIG2;Q96PZ7;F5H2I8	.|.;CSMD1_HUMAN;.	P|H	1844|2428;2428;2289;2427;2427	.|ENSP00000383047:Y2428H;ENSP00000430733:Y2428H;ENSP00000441462:Y2427H;ENSP00000446243:Y2427H	.|ENSP00000320445:Y2289H	L|Y	-|-	2|1	0|0	CSMD1|CSMD1	2936451|2936451	1.000000|1.000000	0.71417|0.71417	0.093000|0.093000	0.20910|0.20910	0.878000|0.878000	0.50629|0.50629	9.011000|9.011000	0.93618|0.93618	2.198000|2.198000	0.70561|0.70561	0.443000|0.443000	0.29094|0.29094	CTA|TAT	.	.		0.303	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		G	2949044	A	G	2949044	3	3	255	1	0	0	0	0	1	0	0	0	3946	420	15	2	3507	2	CSMD1	8	2949044	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10		2949044	143414978	313	35658										
TNKS	8658	hgsc.bcm.edu	37	chr8	9623750	9623750	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tctgtcttcgtatttctaggTtctcctttcattaatgccat	5	10	5	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:9623750T>C	ENST00000310430.6	+	25	3581	c.3555T>C	c.(3553-3555)ggT>ggC	p.G1185G	TNKS_ENST00000518281.1_Splice_Site_p.G948G	NM_003747.2	NP_003738.2	O95271	TNKS1_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	1185	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|mRNA transport (GO:0051028)|negative regulation of DNA binding (GO:0043392)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein poly-ADP-ribosylation (GO:0070212)|protein polyubiquitination (GO:0000209)|protein transport (GO:0015031)|regulation of telomere maintenance via telomerase (GO:0032210)|spindle assembly (GO:0051225)|Wnt signaling pathway (GO:0016055)	chromosome, centromeric region (GO:0000775)|chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nuclear chromosome, telomeric region (GO:0000784)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	NAD+ ADP-ribosyltransferase activity (GO:0003950)|zinc ion binding (GO:0008270)			NS(1)|endometrium(10)|kidney(6)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	49				COAD - Colon adenocarcinoma(149;0.0467)		TATTTCTAGGTTCTCCTTTCA	0.378																																					p.G1185G		Atlas-SNP	.											.	TNKS	198	.	0			c.T3555C						.						75	76	76					8																	9623750		2203	4300	6503	SO:0001630	splice_region_variant	8658	exon25			TCTAGGTTCTCCT	AF082556	CCDS5974.1	8p23.1	2013-01-10			ENSG00000173273	ENSG00000173273		"Poly (ADP-ribose) polymerases", "Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	11941	protein-coding gene	gene with protein product		603303				9822378, 10198177	Standard	XM_006716263		Approved	TIN1, TINF1, TNKS1, PARP-5a, PARP5A, pART5	uc003wss.3	O95271	OTTHUMG00000090481	ENST00000310430.6:c.3554-1T>C	chr8.hg19:g.9623750T>C		61.0	0.0		71.0	4.0	NM_003747	O95272|Q4G0F2	Silent	SNP	ENST00000310430.6	hg19	CCDS5974.1																																																																																			.	.		0.378	TNKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206935.1	NM_003747	Silent	C	9623750	T	C	9623750	5	2	255	1	0	0	0	0	0	0	1	0	16334	1739	60	2	3653	2	TNKS	8	9623750	Splice_Site	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	6674706	9623750	136740272	314	35659										
RP1L1	94137	hgsc.bcm.edu	37	chr8	10469337	10469337	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cctgcccacccggcagagggAgcgttgtgcggggagactcc	16	14	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:10469337A>G	ENST00000382483.3	-	4	2494	c.2271T>C	c.(2269-2271)gcT>gcC	p.A757A		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	757					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		CGGCAGAGGGAGCGTTGTGCG	0.642																																					p.A757A		Atlas-SNP	.											.	RP1L1	453	.	0			c.T2271C						.						47	54	52					8																	10469337		1976	4157	6133	SO:0001819	synonymous_variant	94137	exon4			AGAGGGAGCGTTG	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.2271T>C	chr8.hg19:g.10469337A>G		105.0	0.0		125.0	5.0	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	hg19	CCDS43708.1																																																																																			.	.		0.642	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			G	10469337	A	G	10469337	2	3	255	1	0	0	0	0	0	0	0	1	13548	291	11	2		2	RP1L1	8	10469337	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	845587	10469337	135894685	315	35660										
WHSC1L1	54904	hgsc.bcm.edu	37	chr8	38173035	38173035	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgcatctgcagtagctgaagGgctatctacttgctttccaa	9	10	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:38173035G>T	ENST00000317025.8	-	11	2531	c.2014C>A	c.(2014-2016)Cct>Act	p.P672T	WHSC1L1_ENST00000525081.1_5'Flank|WHSC1L1_ENST00000433384.2_Missense_Mutation_p.P672T|WHSC1L1_ENST00000527502.1_Missense_Mutation_p.P672T	NM_023034.1	NP_075447.1	Q9BZ95	NSD3_HUMAN	Wolf-Hirschhorn syndrome candidate 1-like 1	672					histone lysine methylation (GO:0034968)|histone methylation (GO:0016571)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)			GTAGCTGAAGGGCTATCTACT	0.393			T	NUP98	AML																																p.P672T		Atlas-SNP	.		Dom	yes		8	8p12	54904	Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3)		L	.	WHSC1L1	137	.	0			c.C2014A						.						139	127	131					8																	38173035		1892	4119	6011	SO:0001583	missense	54904	exon11			CTGAAGGGCTATC	AF332469	CCDS6105.1, CCDS43729.1	8p11.2	2013-05-20			ENSG00000147548	ENSG00000147548			12767	protein-coding gene	gene with protein product		607083				10802047, 23269674	Standard	NM_023034		Approved	FLJ20353, NSD3	uc003xli.3	Q9BZ95		ENST00000317025.8:c.2014C>A	chr8.hg19:g.38173035G>T	ENSP00000313983:p.Pro672Thr	83.0	0.0		95.0	4.0	NM_023034	B7ZL11|D3DSX1|Q1RMD3|Q3B796|Q6ZSA5|Q9BYU8|Q9BYU9|Q9H2M8|Q9H9W9|Q9NXA6	Missense_Mutation	SNP	ENST00000317025.8	hg19	CCDS43729.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.626784	0.87560	.	.	ENSG00000147548	ENST00000433384;ENST00000317025;ENST00000446459;ENST00000527502	D;D;D	0.96104	-3.91;-3.91;-3.91	6.01	6.01	0.97437	Zinc finger, FYVE/PHD-type (1);	0.000000	0.48286	U	0.000194	D	0.97542	0.9195	M	0.69358	2.11	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.997	D	0.97609	1.0128	10	0.87932	D	0	.	20.5211	0.99222	0.0:0.0:1.0:0.0	.	672;672;672	B7ZL11;Q9BZ95-2;Q9BZ95	.;.;NSD3_HUMAN	T	672;672;609;672	ENSP00000393284:P672T;ENSP00000313983:P672T;ENSP00000434730:P672T	ENSP00000313983:P672T	P	-	1	0	WHSC1L1	38292192	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.476000	0.97823	2.861000	0.98227	0.650000	0.86243	CCT	.	.		0.393	WHSC1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381924.3	NM_023034		T	38173035	G	T	38173035	3	4	255	1	0	0	0	0	1	0	0	0	17378	1232	43	3	2355	3	WHSC1L1	8	38173035	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	27703698	38173035	108190987	316	35661										
ADAM18	8749	hgsc.bcm.edu	37	chr8	39495084	39495084	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccagttcaaattgactgttaTactgtcttccttggaattgt	7	8	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:39495084T>C	ENST00000265707.5	+	9	734	c.689T>C	c.(688-690)aTa>aCa	p.I230T	ADAM18_ENST00000541111.1_5'UTR|ADAM18_ENST00000379866.1_Missense_Mutation_p.I206T	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	230	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(31)|ovary(1)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)	71		all_cancers(7;1.32e-05)|all_epithelial(6;3.08e-10)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00769)|Breast(189;0.0112)	LUSC - Lung squamous cell carcinoma(45;0.000199)			TTGACTGTTATACTGTCTTCC	0.303																																					p.I230T		Atlas-SNP	.											.	ADAM18	169	.	0			c.T689C						.						84	80	81					8																	39495084		2203	4299	6502	SO:0001583	missense	8749	exon9			CTGTTATACTGTC	AJ133004	CCDS6113.1, CCDS55225.1	8p11.22	2008-08-07	2005-08-18		ENSG00000168619	ENSG00000168619		"ADAM metallopeptidase domain containing"	196	protein-coding gene	gene with protein product			"a disintegrin and metalloproteinase domain 18"			12200459	Standard	NM_014237		Approved	tMDCIII, ADAM27	uc003xni.3	Q9Y3Q7	OTTHUMG00000164040	ENST00000265707.5:c.689T>C	chr8.hg19:g.39495084T>C	ENSP00000265707:p.Ile230Thr	173.0	0.0		182.0	81.0	NM_014237	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Missense_Mutation	SNP	ENST00000265707.5	hg19	CCDS6113.1	.	.	.	.	.	.	.	.	.	.	T	8.687	0.906443	0.17833	.	.	ENSG00000168619	ENST00000265707;ENST00000379866;ENST00000522198	T;T	0.63096	-0.02;-0.02	5.18	-0.21	0.13176	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	1.402720	0.04412	N	0.366199	T	0.50051	0.1593	L	0.35487	1.065	0.09310	N	1	B;B	0.26445	0.149;0.087	B;B	0.30572	0.111;0.117	T	0.39099	-0.9630	10	0.49607	T	0.09	.	3.0133	0.06051	0.304:0.1712:0.0:0.5247	.	206;230	Q9Y3Q7-2;Q9Y3Q7	.;ADA18_HUMAN	T	230;206;162	ENSP00000265707:I230T;ENSP00000369195:I206T	ENSP00000265707:I230T	I	+	2	0	ADAM18	39614241	0.051000	0.20477	0.001000	0.08648	0.842000	0.47809	0.209000	0.17435	-0.154000	0.11118	-0.256000	0.11100	ATA	.	.		0.303	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237		C	39495084	T	C	39495084	3	2	255	1	0	0	0	0	1	0	0	0	239	1406	49	2	723	2	ADAM18	8	39495084	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	1322049	39495084	106868938	317	35662										
HOOK3	84376	hgsc.bcm.edu	37	chr8	42819578	42819578	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aggaagaaggcatttgcagcTccagactcaattagaacagc	10	9	1	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:42819578T>C	ENST00000307602.4	+	9	940	c.740T>C	c.(739-741)cTc>cCc	p.L247P		NM_032410.3	NP_115786.1	Q86VS8	HOOK3_HUMAN	hook microtubule-tethering protein 3	247					cytoplasmic microtubule organization (GO:0031122)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|Golgi localization (GO:0051645)|interkinetic nuclear migration (GO:0022027)|lysosome organization (GO:0007040)|microtubule anchoring at centrosome (GO:0034454)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|protein localization to centrosome (GO:0071539)|protein transport (GO:0015031)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|FHF complex (GO:0070695)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule organizing center (GO:0005815)|pericentriolar material (GO:0000242)	identical protein binding (GO:0042802)|microtubule binding (GO:0008017)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	31	Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.000105)|Lung NSC(58;0.000419)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)			CATTTGCAGCTCCAGACTCAA	0.348			T	RET	papillary thyroid																																p.L247P		Atlas-SNP	.		Dom	yes		8	8p11.21	84376	hook homolog 3		E	.	HOOK3	71	.	0			c.T740C						.						87	86	86					8																	42819578		2203	4300	6503	SO:0001583	missense	84376	exon9			TGCAGCTCCAGAC	AK090540	CCDS6139.1	8p11.21	2013-08-21	2013-08-21		ENSG00000168172	ENSG00000168172			23576	protein-coding gene	gene with protein product		607825	"hook homolog 3 (Drosophila)"			9927460	Standard	NM_032410		Approved	HK3	uc003xpr.3	Q86VS8	OTTHUMG00000165278	ENST00000307602.4:c.740T>C	chr8.hg19:g.42819578T>C	ENSP00000305699:p.Leu247Pro	86.0	0.0		91.0	4.0	NM_032410	D3DSY8|Q8NBH0|Q9BY13	Missense_Mutation	SNP	ENST00000307602.4	hg19	CCDS6139.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.477781	0.84640	.	.	ENSG00000168172	ENST00000307602	T	0.26810	1.71	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.55657	0.1934	M	0.82323	2.585	0.80722	D	1	D;D	0.71674	0.998;0.992	D;D	0.78314	0.991;0.951	T	0.61598	-0.7030	10	0.72032	D	0.01	-0.4757	16.2274	0.82306	0.0:0.0:0.0:1.0	.	247;247	Q2VJ45;Q86VS8	.;HOOK3_HUMAN	P	247	ENSP00000305699:L247P	ENSP00000305699:L247P	L	+	2	0	HOOK3	42938735	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.642000	0.83385	2.229000	0.72834	0.528000	0.53228	CTC	.	.		0.348	HOOK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383172.2	NM_032410		C	42819578	T	C	42819578	3	2	255	1	0	0	0	0	1	0	0	0	7293	1551	54	2	774	2	HOOK3	8	42819578	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	3324494	42819578	103544444	318	35663										
HGSNAT	138050	hgsc.bcm.edu	37	chr8	43054663	43054663	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cgtcgccactgccctctgggTgctcattgcctacatcctct	8	17	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:43054663T>C	ENST00000458501.2	+	18	1943	c.1943T>C	c.(1942-1944)gTg>gCg	p.V648A	HGSNAT_ENST00000297798.7_Missense_Mutation_p.V352A|HGSNAT_ENST00000379644.4_Missense_Mutation_p.V620A|HGSNAT_ENST00000521576.1_Missense_Mutation_p.V337A			Q68CP4	HGNAT_HUMAN	heparan-alpha-glucosaminide N-acetyltransferase	648					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lysosomal transport (GO:0007041)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	heparan-alpha-glucosaminide N-acetyltransferase activity (GO:0015019)|transferase activity, transferring acyl groups (GO:0016746)			cervix(1)|endometrium(2)|large_intestine(4)|lung(6)	13	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)			GCCCTCTGGGTGCTCATTGCC	0.507																																					p.V620A		Atlas-SNP	.											.	HGSNAT	85	.	0			c.T1859C						.						50	52	51					8																	43054663		2200	4299	6499	SO:0001583	missense	138050	exon18			TCTGGGTGCTCAT		CCDS47852.1	8p11.1	2011-11-16	2006-09-05	2006-08-16	ENSG00000165102	ENSG00000165102	2.3.1.78		26527	protein-coding gene	gene with protein product		610453	"transmembrane protein 76"	TMEM76		17033958, 16960811	Standard	NM_152419		Approved	FLJ32731, HGNAT	uc003xpx.4	Q68CP4	OTTHUMG00000164102	ENST00000458501.2:c.1943T>C	chr8.hg19:g.43054663T>C	ENSP00000389524:p.Val648Ala	70.0	0.0		87.0	4.0	NM_152419	B4E2V0	Missense_Mutation	SNP	ENST00000458501.2	hg19		.	.	.	.	.	.	.	.	.	.	T	17.27	3.347366	0.61183	.	.	ENSG00000165102	ENST00000458501;ENST00000379644;ENST00000521576;ENST00000297798	T;T;T;T	0.77620	-1.11;-1.11;-1.11;-1.11	5.29	5.29	0.74685	.	0.309598	0.29239	N	0.012723	T	0.75027	0.3794	M	0.75150	2.29	0.50039	D	0.999842	B	0.28439	0.212	B	0.25987	0.065	T	0.70934	-0.4737	10	0.17369	T	0.5	-11.1733	13.1833	0.59668	0.0:0.0:0.0:1.0	.	648	Q68CP4	HGNAT_HUMAN	A	648;620;337;352	ENSP00000389524:V648A;ENSP00000368965:V620A;ENSP00000429029:V337A;ENSP00000297798:V352A	ENSP00000297798:V352A	V	+	2	0	HGSNAT	43173820	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.525000	0.81892	1.988000	0.58038	0.460000	0.39030	GTG	.	.		0.507	HGSNAT-202	KNOWN	basic	protein_coding	protein_coding		XM_372038		C	43054663	T	C	43054663	3	2	255	1	0	0	0	0	1	0	0	0	7097	1696	59	2	1929	2	HGSNAT	8	43054663	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	235085	43054663	103309359	319	35664										
PXDNL	137902	hgsc.bcm.edu	37	chr8	52359722	52359722	+	Splice_Site	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cttccacagggagctgccctCctgcaaaaagaggtaaagaa	10	11	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:52359722C>A	ENST00000356297.4	-	12	1467	c.1367G>T	c.(1366-1368)gGa>gTa	p.G456V	PXDNL_ENST00000543296.1_Splice_Site_p.G456V	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	456	Ig-like C2-type 3.				hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				GAGCTGCCCTCCTGCAAAAAG	0.512																																					p.G456V		Atlas-SNP	.											PXDNL_ENST00000356297,NS,carcinoma,0,1	PXDNL	414	.	0			c.G1367T						.						88	87	87					8																	52359722		2012	4179	6191	SO:0001630	splice_region_variant	137902	exon12			TGCCCTCCTGCAA		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"Immunoglobulin superfamily / I-set domain containing"	26359	protein-coding gene	gene with protein product	"polysomal ribonuclease 1 homolog (Xenopus)"	615904	"peroxidasin homolog-like (Drosophila)"			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.1367-1G>T	chr8.hg19:g.52359722C>A		62.0	0.0		68.0	3.0	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	hg19	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	C	15.43	2.830139	0.50845	.	.	ENSG00000147485	ENST00000356297;ENST00000543296	D;D	0.86694	-2.16;-2.16	3.84	3.84	0.44239	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.94411	0.8202	M	0.93375	3.41	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	D	0.95047	0.8183	9	0.87932	D	0	.	11.2432	0.48980	0.0:1.0:0.0:0.0	.	456	A1KZ92	PXDNL_HUMAN	V	456	ENSP00000348645:G456V;ENSP00000444865:G456V	ENSP00000348645:G456V	G	-	2	0	PXDNL	52522275	1.000000	0.71417	0.731000	0.30826	0.436000	0.31835	5.882000	0.69714	1.677000	0.50941	0.467000	0.42956	GGA	.	.		0.512	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	Missense_Mutation	A	52359722	C	A	52359722	5	1	255	1	0	0	0	0	0	0	1	0	12863	869	30	3	3072	3	PXDNL	8	52359722	Splice_Site	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	9305059	52359722	94004300	320	35665										
CHD7	55636	hgsc.bcm.edu	37	chr8	61757431	61757431	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tttgctttgcagttggggacGgtggacagacattctttccc	12	9	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:61757431G>T	ENST00000423902.2	+	22	5338	c.4859G>T	c.(4858-4860)cGg>cTg	p.R1620L	CHD7_ENST00000524602.1_Intron	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	1620					adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			AGTTGGGGACGGTGGACAGAC	0.468																																					p.R1620L		Atlas-SNP	.											.	CHD7	534	.	0			c.G4859T						.						65	61	63					8																	61757431		1951	4151	6102	SO:0001583	missense	55636	exon22			GGGGACGGTGGAC	AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"CHARGE association"	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.4859G>T	chr8.hg19:g.61757431G>T	ENSP00000392028:p.Arg1620Leu	70.0	0.0		110.0	5.0	NM_017780	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Missense_Mutation	SNP	ENST00000423902.2	hg19	CCDS47865.1	.	.	.	.	.	.	.	.	.	.	G	35	5.421990	0.96111	.	.	ENSG00000171316	ENST00000307121;ENST00000423902	T	0.74632	-0.86	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	D	0.88680	0.6502	M	0.88775	2.98	0.80722	D	1	D	0.60575	0.988	D	0.66979	0.948	D	0.89906	0.4048	10	0.87932	D	0	-18.7363	20.054	0.97641	0.0:0.0:1.0:0.0	.	1620	Q9P2D1	CHD7_HUMAN	L	1620	ENSP00000392028:R1620L	ENSP00000307304:R1620L	R	+	2	0	CHD7	61919985	1.000000	0.71417	0.936000	0.37596	0.991000	0.79684	9.869000	0.99810	2.808000	0.96608	0.655000	0.94253	CGG	.	.		0.468	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762		T	61757431	G	T	61757431	3	4	255	1	0	0	0	0	1	0	0	0	3332	1116	39	1	4941	1	CHD7	8	61757431	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	9397709	61757431	84606591	321	35666										
CHD7	55636	hgsc.bcm.edu	37	chr8	61765453	61765453	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gagcctctcgaactctgtacCgcattgagctgctacggaag	11	12	2	1	rs192260844		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:61765453C>A	ENST00000423902.2	+	31	6648	c.6169C>A	c.(6169-6171)Cgc>Agc	p.R2057S	CHD7_ENST00000524602.1_Intron	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	2057					adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			AACTCTGTACCGCATTGAGCT	0.562																																					p.R2057S		Atlas-SNP	.											.	CHD7	534	.	0			c.C6169A						.						116	119	118					8																	61765453		1944	4154	6098	SO:0001583	missense	55636	exon31			CTGTACCGCATTG	AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"CHARGE association"	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.6169C>A	chr8.hg19:g.61765453C>A	ENSP00000392028:p.Arg2057Ser	57.0	0.0		72.0	4.0	NM_017780	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Missense_Mutation	SNP	ENST00000423902.2	hg19	CCDS47865.1	.	.	.	.	.	.	.	.	.	.	C	32	5.127115	0.94429	.	.	ENSG00000171316	ENST00000307121;ENST00000423902	D	0.83163	-1.69	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	D	0.91452	0.7302	M	0.78916	2.43	0.80722	D	1	D	0.76494	0.999	D	0.76575	0.988	D	0.92212	0.5777	10	0.87932	D	0	-12.4264	19.215	0.93772	0.0:1.0:0.0:0.0	.	2057	Q9P2D1	CHD7_HUMAN	S	2057	ENSP00000392028:R2057S	ENSP00000307304:R2057S	R	+	1	0	CHD7	61928007	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	6.062000	0.71155	2.539000	0.85634	0.655000	0.94253	CGC	.	C|1.000;T|0.000		0.562	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762		A	61765453	C	A	61765453	3	1	255	1	0	0	0	0	1	0	0	0	3332	652	23	1	6287	1	CHD7	8	61765453	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	8022	61765453	84598569	322	35667										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77618142	77618142	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	caccagggcctggaggagacGgctcaccgggcagtggcatc	16	13	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:77618142G>T	ENST00000521891.2	+	2	2267	c.1819G>T	c.(1819-1821)Ggc>Tgc	p.G607C	ZFHX4_ENST00000517683.1_Intron|ZFHX4_ENST00000050961.6_Missense_Mutation_p.G607C|ZFHX4_ENST00000455469.2_Missense_Mutation_p.G607C|ZFHX4_ENST00000518282.1_Missense_Mutation_p.G607C	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	607					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			TGGAGGAGACGGCTCACCGGG	0.572										HNSCC(33;0.089)																											p.G607C		Atlas-SNP	.											.	ZFHX4	878	.	0			c.G1819T						.						72	79	76					8																	77618142		2098	4202	6300	SO:0001583	missense	79776	exon2			GGAGACGGCTCAC		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.1819G>T	chr8.hg19:g.77618142G>T	ENSP00000430497:p.Gly607Cys	51.0	0.0		78.0	4.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	hg19	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	G	18.87	3.715909	0.68844	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.55234	0.53;0.57;0.53;0.53	5.65	5.65	0.86999	.	0.000000	0.45361	U	0.000367	T	0.65026	0.2652	L	0.45581	1.43	0.80722	D	1	D;D;D;B	0.61697	0.983;0.99;0.99;0.262	P;P;P;B	0.61397	0.775;0.888;0.888;0.108	T	0.56884	-0.7905	10	0.30854	T	0.27	.	19.9142	0.97043	0.0:0.0:1.0:0.0	.	607;607;607;607	Q86UP3;Q86UP3-4;G3V138;Q86UP3-3	ZFHX4_HUMAN;.;.;.	C	607	ENSP00000430497:G607C;ENSP00000399605:G607C;ENSP00000050961:G607C;ENSP00000430848:G607C	ENSP00000050961:G607C	G	+	1	0	ZFHX4	77780697	1.000000	0.71417	0.982000	0.44146	0.944000	0.59088	7.411000	0.80078	2.941000	0.99782	0.655000	0.94253	GGC	.	.		0.572	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		T	77618142	G	T	77618142	3	4	255	1	0	0	0	0	1	0	0	0	17650	1116	39	1	1821	1	ZFHX4	8	77618142	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	15852689	77618142	68745880	323	35668										
WWP1	11059	hgsc.bcm.edu	37	chr8	87479044	87479044	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tttaatcgcttggatctaccAccatataagagttatgaaca	6	8	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:87479044A>G	ENST00000517970.1	+	25	2998	c.2691A>G	c.(2689-2691)ccA>ccG	p.P897P	WWP1_ENST00000349423.2_Silent_p.P679P|WWP1_ENST00000341922.2_Silent_p.P767P|WWP1_ENST00000265428.4_Silent_p.P897P	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	897	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				central nervous system development (GO:0007417)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(9)|liver(4)|lung(10)|prostate(2)|urinary_tract(1)	31						TGGATCTACCACCATATAAGA	0.308																																					p.P897P		Atlas-SNP	.											.	WWP1	97	.	0			c.A2691G						.						88	95	93					8																	87479044		2203	4300	6503	SO:0001819	synonymous_variant	11059	exon25			TCTACCACCATAT	AY043361	CCDS6242.1	8q21.3	2013-07-22			ENSG00000123124	ENSG00000123124			17004	protein-coding gene	gene with protein product		602307				9169421, 9647693	Standard	NM_007013		Approved	AIP5, DKFZP434D2111	uc003ydt.3	Q9H0M0	OTTHUMG00000163690	ENST00000517970.1:c.2691A>G	chr8.hg19:g.87479044A>G		90.0	0.0		83.0	4.0	NM_007013	O00307|Q5YLC1|Q96BP4	Silent	SNP	ENST00000517970.1	hg19	CCDS6242.1																																																																																			.	.		0.308	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374755.1	NM_007013		G	87479044	A	G	87479044	2	3	255	1	0	0	0	0	0	0	0	1	17430	146	6	2		2	WWP1	8	87479044	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	9860902	87479044	58884978	324	35669										
VPS13B	157680	hgsc.bcm.edu	37	chr8	100654256	100654256	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tctaaattttattccctttgAcatatttattactgcaagta	3	7	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:100654256A>G	ENST00000358544.2	+	34	5624	c.5513A>G	c.(5512-5514)gAc>gGc	p.D1838G	VPS13B_ENST00000357162.2_Missense_Mutation_p.D1813G|VPS13B_ENST00000395996.1_3'UTR	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	1838					protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			ATTCCCTTTGACATATTTATT	0.383																																					p.D1838G	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											.	VPS13B	811	.	0			c.A5513G						.						74	75	74					8																	100654256		2203	4300	6503	SO:0001583	missense	157680	exon34			CCTTTGACATATT	AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.5513A>G	chr8.hg19:g.100654256A>G	ENSP00000351346:p.Asp1838Gly	51.0	0.0		64.0	4.0	NM_017890	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	hg19	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	A	26.4	4.737823	0.89573	.	.	ENSG00000132549	ENST00000357162;ENST00000358544	T;T	0.74106	-0.81;-0.79	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.80904	0.4713	L	0.34521	1.04	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	T	0.82991	-0.0182	10	0.87932	D	0	.	16.3943	0.83563	1.0:0.0:0.0:0.0	.	1813;1838	Q7Z7G8-2;Q7Z7G8	.;VP13B_HUMAN	G	1813;1838	ENSP00000349685:D1813G;ENSP00000351346:D1838G	ENSP00000349685:D1813G	D	+	2	0	VPS13B	100723432	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.019000	0.93662	2.281000	0.76405	0.533000	0.62120	GAC	.	.		0.383	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		G	100654256	A	G	100654256	3	3	255	1	0	0	0	0	1	0	0	0	17205	275	10	2	5837	2	VPS13B	8	100654256	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	13175212	100654256	45709766	325	35670										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113331157	113331157	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	actaaagtaaatcctggaagAcactgatacctaataatatc	5	8	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:113331157A>G	ENST00000297405.5	-	47	7513	c.7269T>C	c.(7267-7269)tgT>tgC	p.C2423C	CSMD3_ENST00000343508.3_Silent_p.C2383C|CSMD3_ENST00000455883.2_Silent_p.C2319C|CSMD3_ENST00000352409.3_Silent_p.C2353C	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2423	Sushi 13. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						ATCCTGGAAGACACTGATACC	0.363										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.C2423C		Atlas-SNP	.											CSMD3_ENST00000343508,NS,carcinoma,0,2	CSMD3	2325	.	0			c.T7269C						.						95	87	90					8																	113331157		2203	4300	6503	SO:0001819	synonymous_variant	114788	exon47			TGGAAGACACTGA	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.7269T>C	chr8.hg19:g.113331157A>G		80.0	0.0		74.0	3.0	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	hg19	CCDS6315.1																																																																																			.	.		0.363	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		G	113331157	A	G	113331157	2	3	255	1	0	0	0	0	0	0	0	1	3948	273	10	2		2	CSMD3	8	113331157	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	12676901	113331157	33032865	326	35671										
TAF2	6873	hgsc.bcm.edu	37	chr8	120793297	120793297	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agaaagtaaactgtaccttcTgtagaaaatagctttgaaag	8	5	1	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:120793297T>C	ENST00000378164.2	-	17	2547	c.2249A>G	c.(2248-2250)cAg>cGg	p.Q750R		NM_003184.3	NP_003175	Q6P1X5	TAF2_HUMAN	TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa	750					G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to organic cyclic compound (GO:0014070)|transcription initiation from RNA polymerase II promoter (GO:0006367)	transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	metallopeptidase activity (GO:0008237)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(21)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	49	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			CTGTACCTTCTGTAGAAAATA	0.323																																					p.Q750R		Atlas-SNP	.											.	TAF2	204	.	0			c.A2249G						.						59	66	63					8																	120793297		2203	4300	6503	SO:0001583	missense	6873	exon17			ACCTTCTGTAGAA	AF040701	CCDS34937.1	8q24	2012-07-18	2002-08-29	2001-12-07	ENSG00000064313	ENSG00000064313			11536	protein-coding gene	gene with protein product		604912	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, B, 150kD"	TAF2B		9774672, 9418870	Standard	NM_003184		Approved	TAFII150, CIF150	uc003you.3	Q6P1X5	OTTHUMG00000165009	ENST00000378164.2:c.2249A>G	chr8.hg19:g.120793297T>C	ENSP00000367406:p.Gln750Arg	123.0	0.0		119.0	5.0	NM_003184	B2RE82|O43487|O43604|O60668|Q86WW7|Q8IWK4	Missense_Mutation	SNP	ENST00000378164.2	hg19	CCDS34937.1	.	.	.	.	.	.	.	.	.	.	T	19.79	3.892076	0.72524	.	.	ENSG00000064313	ENST00000378164	T	0.47528	0.84	5.65	5.65	0.86999	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.55178	0.1904	M	0.67953	2.075	0.80722	D	1	P	0.46621	0.881	P	0.46796	0.527	T	0.57929	-0.7726	10	0.48119	T	0.1	-25.2293	16.1864	0.81955	0.0:0.0:0.0:1.0	.	750	Q6P1X5	TAF2_HUMAN	R	750	ENSP00000367406:Q750R	ENSP00000367406:Q750R	Q	-	2	0	TAF2	120862478	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	6.099000	0.71466	2.281000	0.76405	0.528000	0.53228	CAG	.	.		0.323	TAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381436.1	NM_003184		C	120793297	T	C	120793297	3	2	255	1	0	0	0	0	1	0	0	0	15539	1580	55	2	1390	2	TAF2	8	120793297	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	7462140	120793297	25570725	327	35672										
DEPDC6	64798	hgsc.bcm.edu	37	chr8	120977517	120977517	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctgcagcccagggaggaggaAggggtcaagtatgagcgcac	17	9	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:120977517A>G	ENST00000286234.5	+	4	601	c.471A>G	c.(469-471)gaA>gaG	p.E157E	DEPTOR_ENST00000523492.1_Silent_p.E56E	NM_022783.2	NP_073620.2	Q8TB45	DPTOR_HUMAN	DEP domain containing MTOR-interacting protein	157	DEP 2. {ECO:0000255|PROSITE- ProRule:PRU00066}.				intracellular signal transduction (GO:0035556)|negative regulation of cell size (GO:0045792)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of TOR signaling (GO:0032007)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)	intracellular (GO:0005622)				endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	18						GGGAGGAGGAAGGGGTCAAGT	0.517																																					p.E157E		Atlas-SNP	.											.	DEPTOR	41	.	0			c.A471G						.						106	94	98					8																	120977517		2203	4300	6503	SO:0001819	synonymous_variant	64798	exon4			GGAGGAAGGGGTC		CCDS6331.1, CCDS64960.1	8q24.12	2011-12-13	2010-12-08	2010-12-08	ENSG00000155792	ENSG00000155792			22953	protein-coding gene	gene with protein product		612974	"DEP domain containing 6"	DEPDC6		19446321	Standard	NM_022783		Approved	DEP.6, FLJ12428	uc003yow.4	Q8TB45	OTTHUMG00000165052	ENST00000286234.5:c.471A>G	chr8.hg19:g.120977517A>G		72.0	0.0		86.0	4.0	NM_022783	B2RCL9|B4DN97|E7EV87|Q96EQ1|Q9H0R7|Q9H894|Q9HA07	Silent	SNP	ENST00000286234.5	hg19	CCDS6331.1																																																																																			.	.		0.517	DEPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381601.1	NM_022783		G	120977517	A	G	120977517	2	3	255	1	0	0	0	0	0	0	0	1	4445	69	3	2		2	DEPDC6	8	120977517	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	184220	120977517	25386505	328	35673										
MTBP	27085	hgsc.bcm.edu	37	chr8	121528368	121528368	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agttttacaaaatgaacttcGaactgaagtatcccgattga	7	7	0	3	rs574546258		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:121528368G>T	ENST00000305949.1	+	18	2228	c.2183G>T	c.(2182-2184)cGa>cTa	p.R728L		NM_022045.4	NP_071328.2	Q96DY7	MTBP_HUMAN	MDM2 binding protein	728	Interaction with MDM2. {ECO:0000250}.				cell cycle arrest (GO:0007050)|mitotic spindle checkpoint (GO:0071174)|negative regulation of cell proliferation (GO:0008285)|protein localization to kinetochore (GO:0034501)|traversing start control point of mitotic cell cycle (GO:0007089)	chromatin (GO:0000785)|kinetochore (GO:0000776)		p.R728Q(1)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	Lung NSC(37;5.68e-08)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)			AATGAACTTCGAACTGAAGTA	0.398																																					p.R728L		Atlas-SNP	.											MTBP,caecum,carcinoma,0,1	MTBP	77	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2183T						.						65	63	64					8																	121528368		2203	4299	6502	SO:0001583	missense	27085	exon18			AACTTCGAACTGA		CCDS6333.1	8q24.1-q24.2	2014-03-03	2014-03-03		ENSG00000172167	ENSG00000172167			7417	protein-coding gene	gene with protein product		605927	"MDM2 (mouse double minute 2)-binding protein, 104kD", "Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse) binding protein, 104kDa"			10906133, 11060448	Standard	NM_022045		Approved		uc003ypc.2	Q96DY7	OTTHUMG00000165040	ENST00000305949.1:c.2183G>T	chr8.hg19:g.121528368G>T	ENSP00000303398:p.Arg728Leu	106.0	0.0		100.0	4.0	NM_022045	B4DUR5|Q9HA89	Missense_Mutation	SNP	ENST00000305949.1	hg19	CCDS6333.1	.	.	.	.	.	.	.	.	.	.	G	16.30	3.085033	0.55861	.	.	ENSG00000172167	ENST00000305949	.	.	.	5.98	4.18	0.49190	.	0.140607	0.44688	D	0.000424	T	0.50274	0.1606	M	0.71581	2.175	0.09310	N	1	B	0.28439	0.212	B	0.36418	0.224	T	0.51834	-0.8655	9	0.72032	D	0.01	-3.0102	9.6219	0.39727	0.1027:0.2372:0.6601:0.0	.	728	Q96DY7	MTBP_HUMAN	L	728	.	ENSP00000303398:R728L	R	+	2	0	MTBP	121597549	0.002000	0.14202	0.007000	0.13788	0.010000	0.07245	1.024000	0.30077	0.848000	0.35191	-0.226000	0.12346	CGA	.	.		0.398	MTBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381530.1	NM_022045		T	121528368	G	T	121528368	3	4	255	1	0	0	0	0	1	0	0	0	9921	1058	37	1	2253	1	MTBP	8	121528368	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	550851	121528368	24835654	329	35674										
ANXA13	312	hgsc.bcm.edu	37	chr8	124693533	124693533	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gtccccggaggtatctgagcGaaccatgtcagagagagact	13	10	2	3	rs201212750		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:124693533G>T	ENST00000419625.1	-	11	970	c.898C>A	c.(898-900)Cgc>Agc	p.R300S	ANXA13_ENST00000262219.6_Missense_Mutation_p.R341S	NM_004306.2	NP_004297.2	P27216	ANX13_HUMAN	annexin A13	300					cell differentiation (GO:0030154)|negative regulation of Golgi to plasma membrane protein transport (GO:0042997)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|exocytic vesicle (GO:0070382)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylglycerol binding (GO:1901611)|phosphatidylserine binding (GO:0001786)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	25	Lung NSC(37;2.06e-11)|Ovarian(258;0.00579)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00288)			GTATCTGAGCGAACCATGTCA	0.493																																					p.R341S		Atlas-SNP	.											.	ANXA13	38	.	0			c.C1021A						.						212	220	217					8																	124693533		2203	4300	6503	SO:0001583	missense	312	exon12			CTGAGCGAACCAT	Z11502	CCDS34939.1, CCDS47917.1	8q24.13	2005-11-09			ENSG00000104537	ENSG00000104537		"Annexins"	536	protein-coding gene	gene with protein product		602573		ANX13		9503022	Standard	NM_004306		Approved		uc003yqt.3	P27216	OTTHUMG00000164987	ENST00000419625.1:c.898C>A	chr8.hg19:g.124693533G>T	ENSP00000390809:p.Arg300Ser	153.0	0.0		124.0	5.0	NM_001003954	Q9BQR5	Missense_Mutation	SNP	ENST00000419625.1	hg19	CCDS47917.1	.	.	.	.	.	.	.	.	.	.	G	0.913	-0.718427	0.03182	.	.	ENSG00000104537	ENST00000262219;ENST00000419625	T;T	0.03152	4.03;4.03	5.71	3.83	0.44106	Annexin repeat, conserved site (1);	0.766484	0.13479	N	0.384821	T	0.01905	0.0060	N	0.10685	0.025	0.24403	N	0.994693	B;B	0.10296	0.003;0.002	B;B	0.12837	0.008;0.005	T	0.45760	-0.9239	10	0.02654	T	1	.	8.6176	0.33842	0.0:0.1495:0.5417:0.3088	.	300;341	P27216;P27216-2	ANX13_HUMAN;.	S	341;300	ENSP00000262219:R341S;ENSP00000390809:R300S	ENSP00000262219:R341S	R	-	1	0	ANXA13	124762714	0.627000	0.27129	0.983000	0.44433	0.595000	0.36748	0.298000	0.19120	0.677000	0.31305	0.655000	0.94253	CGC	.	G|1.000;A|0.000		0.493	ANXA13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381308.1	NM_004306		T	124693533	G	T	124693533	3	4	255	1	0	0	0	0	1	0	0	0	717	1058	37	1	56	1	ANXA13	8	124693533	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	3165165	124693533	21670489	330	35675										
FER1L6	654463	hgsc.bcm.edu	37	chr8	124989814	124989814	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggcaacccatttcattgaccTgaagaaaatctccaacgaac	6	12	2	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:124989814T>C	ENST00000522917.1	+	10	1234	c.1028T>C	c.(1027-1029)cTg>cCg	p.L343P	FER1L6_ENST00000399018.1_Missense_Mutation_p.L343P	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	343	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.					integral component of membrane (GO:0016021)				NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			TTCATTGACCTGAAGAAAATC	0.453																																					p.L343P		Atlas-SNP	.											.	FER1L6	268	.	0			c.T1028C						.						99	100	100					8																	124989814		1957	4153	6110	SO:0001583	missense	654463	exon10			TTGACCTGAAGAA	AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"fer-1-like 6 (C. elegans)"				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.1028T>C	chr8.hg19:g.124989814T>C	ENSP00000428280:p.Leu343Pro	143.0	0.0		124.0	5.0	NM_001039112		Missense_Mutation	SNP	ENST00000522917.1	hg19	CCDS43767.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.440800	0.83993	.	.	ENSG00000214814	ENST00000522917;ENST00000399018	T;T	0.15603	2.41;2.41	5.53	5.53	0.82687	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.52532	U	0.000062	T	0.48390	0.1497	M	0.88704	2.975	0.80722	D	1	D	0.76494	0.999	D	0.68621	0.959	T	0.58463	-0.7632	10	0.87932	D	0	.	15.6745	0.77303	0.0:0.0:0.0:1.0	.	343	Q2WGJ9	FR1L6_HUMAN	P	343	ENSP00000428280:L343P;ENSP00000381982:L343P	ENSP00000381982:L343P	L	+	2	0	FER1L6	125058995	1.000000	0.71417	0.985000	0.45067	0.985000	0.73830	7.997000	0.88414	2.109000	0.64355	0.459000	0.35465	CTG	.	.		0.453	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112		C	124989814	T	C	124989814	3	2	255	1	0	0	0	0	1	0	0	0	5823	1580	55	2	1062	2	FER1L6	8	124989814	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	296281	124989814	21374208	331	35676										
KIAA0196	9897	hgsc.bcm.edu	37	chr8	126040930	126040930	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggcacccacaacatctgcagGaatttcaggtatcttctggc	9	12	4	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:126040930G>T	ENST00000318410.7	-	28	3704	c.3355C>A	c.(3355-3357)Cct>Act	p.P1119T	KIAA0196_ENST00000517845.1_Missense_Mutation_p.P971T	NM_014846.3	NP_055661.3	Q12768	STRUM_HUMAN	KIAA0196	1119					cell death (GO:0008219)|endosomal transport (GO:0016197)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|WASH complex (GO:0071203)				NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	42	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)			ACATCTGCAGGAATTTCAGGT	0.398																																					p.P1119T		Atlas-SNP	.											.	KIAA0196	90	.	0			c.C3355A						.						115	108	110					8																	126040930		2203	4300	6503	SO:0001583	missense	9897	exon28			CTGCAGGAATTTC		CCDS6355.1	8q24.13	2014-05-09			ENSG00000164961	ENSG00000164961			28984	protein-coding gene	gene with protein product	"strumpellin"	610657	"spastic paraplegia 8 (autosomal dominant)"	SPG8		9973294, 17160902, 23085491	Standard	NM_014846		Approved		uc003yrt.3	Q12768	OTTHUMG00000164991	ENST00000318410.7:c.3355C>A	chr8.hg19:g.126040930G>T	ENSP00000318016:p.Pro1119Thr	61.0	0.0		99.0	4.0	NM_014846	A8K4R7|Q3KQX5|Q8TBQ2	Missense_Mutation	SNP	ENST00000318410.7	hg19	CCDS6355.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.45|13.45	2.239469|2.239469	0.39598|0.39598	.|.	.|.	ENSG00000164961|ENSG00000164961	ENST00000318410;ENST00000517845|ENST00000523273	D;D|.	0.86097|.	-2.07;-2.07|.	5.63|5.63	5.63|5.63	0.86233|0.86233	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72028|0.72028	0.3410|0.3410	L|L	0.54323|0.54323	1.7|1.7	0.80722|0.80722	D|D	1|1	D|.	0.71674|.	0.998|.	D|.	0.76071|.	0.987|.	T|T	0.67848|0.67848	-0.5564|-0.5564	10|5	0.42905|.	T|.	0.14|.	-16.0633|-16.0633	19.7005|19.7005	0.96050|0.96050	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1119|.	Q12768|.	STRUM_HUMAN|.	T|Y	1119;971|684	ENSP00000318016:P1119T;ENSP00000429676:P971T|.	ENSP00000318016:P1119T|.	P|S	-|-	1|2	0|0	KIAA0196|KIAA0196	126110112|126110112	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.940000|0.940000	0.58332|0.58332	9.869000|9.869000	0.99810|0.99810	2.657000|2.657000	0.90304|0.90304	0.555000|0.555000	0.69702|0.69702	CCT|TCC	.	.		0.398	KIAA0196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381369.1	NM_014846		T	126040930	G	T	126040930	3	4	255	1	0	0	0	0	1	0	0	0	8170	1174	41	3	132	3	KIAA0196	8	126040930	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	1051116	126040930	20323092	332	35677										
TRAPPC9	83696	hgsc.bcm.edu	37	chr8	141449296	141449296	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tggcaccgcttcttgtaatgTctagaaaatacatgaaaatg	8	7	2	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:141449296T>C	ENST00000438773.2	-	3	718	c.585A>G	c.(583-585)agA>agG	p.R195R	TRAPPC9_ENST00000389328.4_Splice_Site_p.R293R|TRAPPC9_ENST00000389327.3_Splice_Site_p.R195R	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	195					cell differentiation (GO:0030154)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	47						TCTTGTAATGTCTAGAAAATA	0.468																																					p.R293R		Atlas-SNP	.											.	TRAPPC9	114	.	0			c.A879G						.						59	58	59					8																	141449296		2203	4300	6503	SO:0001630	splice_region_variant	83696	exon3			GTAATGTCTAGAA	BC006206	CCDS34946.1, CCDS55278.1	8q24.3	2010-10-22			ENSG00000167632	ENSG00000167632		"Trafficking protein particle complex"	30832	protein-coding gene	gene with protein product	"TRAPP 120 kDa subunit", "tularik gene 1"	611966				11572484	Standard	NM_031466		Approved	IKBKBBP, NIBP, KIAA1882, T1, TRS120, MRT13	uc003yvh.2	Q96Q05	OTTHUMG00000164187	ENST00000438773.2:c.585-1A>G	chr8.hg19:g.141449296T>C		57.0	0.0		93.0	4.0	NM_031466	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Silent	SNP	ENST00000438773.2	hg19	CCDS55278.1	.	.	.	.	.	.	.	.	.	.	T	12.52	1.963289	0.34659	.	.	ENSG00000167632	ENST00000520857	.	.	.	5.8	2.08	0.27032	.	.	.	.	.	T	0.58708	0.2141	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50955	-0.8766	4	.	.	.	.	9.8245	0.40903	0.0:0.3333:0.0:0.6667	.	.	.	.	A	48	.	.	T	-	1	0	TRAPPC9	141518478	1.000000	0.71417	0.978000	0.43139	0.726000	0.41606	0.762000	0.26503	0.117000	0.18138	0.528000	0.53228	ACA	.	.		0.468	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466	Silent	C	141449296	T	C	141449296	5	2	255	1	0	0	0	0	0	0	1	0	16480	1681	58	2	2945	2	TRAPPC9	8	141449296	Splice_Site	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	15408366	141449296	4914726	333	35678										
EIF2C2	27161	hgsc.bcm.edu	37	chr8	141542567	141542567	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggcccggaaggccaccaggtGagcgtagtatgctggcgctg	17	11	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:141542567G>T	ENST00000220592.5	-	18	2531	c.2419C>A	c.(2419-2421)Cac>Aac	p.H807N	AGO2_ENST00000519980.1_Missense_Mutation_p.H773N|CASC7_ENST00000560295.1_lincRNA	NM_012154.3	NP_036286.2	Q9UKV8	AGO2_HUMAN	argonaute RISC catalytic component 2	807	Interaction with guide RNA.|Piwi. {ECO:0000255|HAMAP-Rule:MF_03031}.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|negative regulation of translational initiation (GO:0045947)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|regulation of transcription, DNA-templated (GO:0006355)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|mRNA cap binding complex (GO:0005845)|nucleus (GO:0005634)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|RISC complex (GO:0016442)	endoribonuclease activity (GO:0004521)|endoribonuclease activity, cleaving siRNA-paired mRNA (GO:0070551)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA 7-methylguanosine cap binding (GO:0000340)|siRNA binding (GO:0035197)|translation initiation factor activity (GO:0003743)										GCCACCAGGTGAGCGTAGTAT	0.587																																					p.H807N		Atlas-SNP	.											.	.	.	.	0			c.C2419A						.						79	62	68					8																	141542567		2203	4300	6503	SO:0001583	missense	27161	exon18			CCAGGTGAGCGTA	AF121255	CCDS6380.1, CCDS55279.1	8q24.3	2013-02-15	2013-02-15	2013-02-15	ENSG00000123908	ENSG00000123908		"Argonaute/PIWI family"	3263	protein-coding gene	gene with protein product	"argonaute 2"	606229	"eukaryotic translation initiation factor 2C, 2"	EIF2C2		10534406, 12906857	Standard	NM_012154		Approved	hAGO2, Q10	uc003yvn.3	Q9UKV8	OTTHUMG00000164232	ENST00000220592.5:c.2419C>A	chr8.hg19:g.141542567G>T	ENSP00000220592:p.His807Asn	72.0	0.0		95.0	4.0	NM_012154	Q8TCZ5|Q8WV58|Q96ID1	Missense_Mutation	SNP	ENST00000220592.5	hg19	CCDS6380.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.503296	0.85176	.	.	ENSG00000123908	ENST00000220592;ENST00000519980	T;T	0.31510	1.49;1.49	5.96	5.96	0.96718	Stem cell self-renewal protein Piwi (3);Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.70806	0.3266	H	0.95365	3.66	0.80722	D	1	P;P	0.48694	0.894;0.914	D;D	0.72075	0.945;0.976	T	0.77872	-0.2426	10	0.87932	D	0	1.7967	20.422	0.99049	0.0:0.0:1.0:0.0	.	773;807	Q9UKV8-2;Q9UKV8	.;AGO2_HUMAN	N	807;773	ENSP00000220592:H807N;ENSP00000430176:H773N	ENSP00000220592:H807N	H	-	1	0	EIF2C2	141611749	1.000000	0.71417	0.996000	0.52242	0.964000	0.63967	7.877000	0.87225	2.832000	0.97577	0.655000	0.94253	CAC	.	.		0.587	AGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377866.4			T	141542567	G	T	141542567	3	4	255	1	0	0	0	0	1	0	0	0	5008	1290	45	3	168	3	EIF2C2	8	141542567	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	93271	141542567	4821455	334	35679										
SLC45A4	57210	hgsc.bcm.edu	37	chr8	142228278	142228278	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	accgtggtctcgccctccccCtcctcactctcggtgtcccc	7	22	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:142228278C>A	ENST00000024061.3	-	4	1615	c.1308G>T	c.(1306-1308)gaG>gaT	p.E436D	SLC45A4_ENST00000517878.1_Missense_Mutation_p.E487D|SLC45A4_ENST00000519067.1_Missense_Mutation_p.E436D|SLC45A4_ENST00000433583.2_Missense_Mutation_p.E429D	NM_001080431.1	NP_001073900.1	Q5BKX6	S45A4_HUMAN	solute carrier family 45, member 4						transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31	all_cancers(97;1.52e-15)|all_epithelial(106;2.92e-14)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)			CGCCCTCCCCCTCCTCACTCT	0.672																																					p.E436D		Atlas-SNP	.											.	SLC45A4	71	.	0			c.G1308T						.						63	55	58					8																	142228278		2203	4300	6503	SO:0001583	missense	57210	exon4			CTCCCCCTCCTCA	AB032952	CCDS34948.1, CCDS69550.1, CCDS75795.1	8q24.3	2013-05-22						"Solute carriers"	29196	protein-coding gene	gene with protein product							Standard	NM_001080431		Approved	KIAA1126	uc003ywd.1	Q5BKX6		ENST00000024061.3:c.1308G>T	chr8.hg19:g.142228278C>A	ENSP00000024061:p.Glu436Asp	71.0	0.0		85.0	33.0	NM_001080431	Q6ZRI2|Q9ULU3	Missense_Mutation	SNP	ENST00000024061.3	hg19	CCDS34948.1	.	.	.	.	.	.	.	.	.	.	C	11.22	1.575869	0.28092	.	.	ENSG00000022567	ENST00000519067;ENST00000517878;ENST00000433583;ENST00000024061	D;D;D;D	0.95482	-3.72;-3.72;-3.72;-3.72	5.07	4.18	0.49190	.	0.000000	0.85682	D	0.000000	D	0.90321	0.6972	N	0.25647	0.755	0.45194	D	0.998207	B;B;B	0.21452	0.034;0.056;0.056	B;B;B	0.21360	0.012;0.034;0.027	D	0.86630	0.1885	10	0.38643	T	0.18	-35.5141	10.8078	0.46529	0.0:0.8493:0.0:0.1507	.	487;436;436	E7EV90;Q5BKX6-3;Q5BKX6-2	.;.;.	D	436;487;429;436	ENSP00000429059:E436D;ENSP00000428137:E487D;ENSP00000400799:E429D;ENSP00000024061:E436D	ENSP00000024061:E436D	E	-	3	2	SLC45A4	142297460	0.986000	0.35501	1.000000	0.80357	0.169000	0.22640	0.211000	0.17474	2.535000	0.85469	0.561000	0.74099	GAG	.	.		0.672	SLC45A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378571.3	XM_050325		A	142228278	C	A	142228278	3	1	255	1	0	0	0	0	1	0	0	0	14658	680	24	3	1108	3	SLC45A4	8	142228278	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	685711	142228278	4135744	335	35680										
GPIHBP1	338328	hgsc.bcm.edu	37	chr8	144296897	144296897	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cttgtccccagtgctgctgcGgtgctacacctgcaagtccc	10	16	0	0	rs578073937		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:144296897G>T	ENST00000330824.2	+	3	266	c.191G>T	c.(190-192)cGg>cTg	p.R64L		NM_178172.3	NP_835466.1	Q8IV16	HDBP1_HUMAN	glycosylphosphatidylinositol anchored high density lipoprotein binding protein 1	64	UPAR/Ly6.				cholesterol homeostasis (GO:0042632)|intracellular protein transport (GO:0006886)|positive regulation of chylomicron remnant clearance (GO:0090321)|positive regulation of lipoprotein lipase activity (GO:0051006)|protein import (GO:0017038)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|protein transmembrane transport (GO:0071806)|response to heparin (GO:0071503)|transcytosis (GO:0045056)|triglyceride homeostasis (GO:0070328)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|external side of plasma membrane (GO:0009897)|high-density lipoprotein particle (GO:0034364)	chylomicron binding (GO:0035478)|lipase binding (GO:0035473)|lipid binding (GO:0008289)|lipoprotein particle binding (GO:0071813)|protein transmembrane transporter activity (GO:0008320)			lung(2)	2	all_cancers(97;6.49e-11)|all_epithelial(106;2.77e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					GTGCTGCTGCGGTGCTACACC	0.672																																					p.R64L		Atlas-SNP	.											.	GPIHBP1	12	.	0			c.G191T						.						42	31	35					8																	144296897		2183	4269	6452	SO:0001583	missense	338328	exon3			TGCTGCGGTGCTA	AF088057	CCDS34954.1	8q24.3	2014-07-14	2008-02-07						24945	protein-coding gene	gene with protein product	"endothelial cell LPL transporter"	612757	"GPI anchored high density lipoprotein binding protein 1"			12496272, 17883852, 17620854, 17403372	Standard	NM_178172		Approved	LOC338328, GPI-HBP1	uc003yxu.2	Q8IV16		ENST00000330824.2:c.191G>T	chr8.hg19:g.144296897G>T	ENSP00000329266:p.Arg64Leu	94.0	0.0		122.0	6.0	NM_178172	Q6P3T2|Q86W15	Missense_Mutation	SNP	ENST00000330824.2	hg19	CCDS34954.1	.	.	.	.	.	.	.	.	.	.	g	11.57	1.679548	0.29783	.	.	ENSG00000182851	ENST00000330824	T	0.77098	-1.07	3.95	-6.09	0.02145	Ly-6 antigen / uPA receptor -like (1);	1.872550	0.03244	N	0.180936	T	0.67173	0.2865	L	0.51422	1.61	0.09310	N	1	B	0.14438	0.01	B	0.08055	0.003	T	0.51309	-0.8722	10	0.59425	D	0.04	-16.5311	3.1887	0.06609	0.5921:0.1332:0.141:0.1337	.	64	Q8IV16	HDBP1_HUMAN	L	64	ENSP00000329266:R64L	ENSP00000329266:R64L	R	+	2	0	GPIHBP1	144368272	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-1.697000	0.01910	-1.253000	0.02488	0.450000	0.29827	CGG	.	.		0.672	GPIHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381113.1	NM_178172		T	144296897	G	T	144296897	3	4	255	1	0	0	0	0	1	0	0	0	6620	1116	39	1	201	1	GPIHBP1	8	144296897	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	2068619	144296897	2067125	336	35681										
DOCK8	81704	hgsc.bcm.edu	37	chr9	304685	304685	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgagtcggaaaccttggagtGcagtgaacccgctgctcagg	14	10	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:304685G>A	ENST00000453981.1	+	5	621	c.509G>A	c.(508-510)tGc>tAc	p.C170Y	DOCK8_ENST00000432829.2_Missense_Mutation_p.C102Y|DOCK8_ENST00000469391.1_Missense_Mutation_p.C102Y			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	170					blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		ACCTTGGAGTGCAGTGAACCC	0.458																																					p.C170Y		Atlas-SNP	.											.	DOCK8	401	.	0			c.G509A						.						118	122	121					9																	304685		2203	4300	6503	SO:0001583	missense	81704	exon5			TGGAGTGCAGTGA	AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.509G>A	chr9.hg19:g.304685G>A	ENSP00000408464:p.Cys170Tyr	62.0	0.0		81.0	4.0	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Missense_Mutation	SNP	ENST00000453981.1	hg19	CCDS6440.2	.	.	.	.	.	.	.	.	.	.	G	11.54	1.668349	0.29604	.	.	ENSG00000107099	ENST00000453981;ENST00000287364;ENST00000432829;ENST00000487230;ENST00000469391	T;T;T;T	0.30182	2.67;2.67;1.54;2.67	6.02	-1.91	0.07641	.	1.513220	0.03048	N	0.154177	T	0.22589	0.0545	L	0.34521	1.04	0.09310	N	1	B;B;B	0.12013	0.0;0.005;0.0	B;B;B	0.06405	0.0;0.002;0.0	T	0.16748	-1.0392	10	0.27082	T	0.32	.	6.8557	0.24040	0.4355:0.3584:0.2061:0.0	.	102;170;170	E9PH09;A2A349;Q8NF50	.;.;DOCK8_HUMAN	Y	170;170;102;102;102	ENSP00000408464:C170Y;ENSP00000394888:C102Y;ENSP00000418318:C102Y;ENSP00000419438:C102Y	ENSP00000287364:C170Y	C	+	2	0	DOCK8	294685	0.000000	0.05858	0.000000	0.03702	0.963000	0.63663	-0.198000	0.09505	-0.390000	0.07774	0.655000	0.94253	TGC	.	.		0.458	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307		A	304685	G	A	304685	3	1	255	1	0	0	0	0	1	0	0	0	4695	1319	46	3	527	3	DOCK8	9	304685	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10		304685	140908746	337	35682										
KIAA0020	9933	hgsc.bcm.edu	37	chr9	2807906	2807906	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agtgtttttgcaaaacaaccTgtaaaatatactgaagctta	6	6	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:2807906T>C	ENST00000397885.2	-	17	1930		c.e17-2			NM_014878.4	NP_055693.4	Q15397	K0020_HUMAN	KIAA0020							endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(50;0.0319)		CAAAACAACCTGTAAAATATA	0.353																																					.		Atlas-SNP	.											.	KIAA0020	56	.	0			c.1724-2A>G						.						74	70	71					9																	2807906		2203	4300	6503	SO:0001630	splice_region_variant	9933	exon18			ACAACCTGTAAAA	AL832239	CCDS6448.2	9p24.2	2012-11-29			ENSG00000080608	ENSG00000080608			29676	protein-coding gene	gene with protein product	"penguin homolog (Drosophila)", "minor histocompatibility antigen HA-8"	609960				7584026, 7584028, 21266351	Standard	NM_014878		Approved	XTP5, PEN, PUF6, hPUF-A, HA-8	uc003zhp.1	Q15397	OTTHUMG00000019450	ENST00000397885.2:c.1724-2A>G	chr9.hg19:g.2807906T>C		42.0	0.0		73.0	4.0	NM_014878	A8K804|Q547G7|Q5SZY9|Q6IB47|Q96B27|Q96L78|Q96L79|Q96L80	Splice_Site	SNP	ENST00000397885.2	hg19	CCDS6448.2	.	.	.	.	.	.	.	.	.	.	T	17.26	3.345515	0.61073	.	.	ENSG00000080608	ENST00000397885	.	.	.	5.87	5.87	0.94306	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.9	0.70672	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	KIAA0020	2797906	1.000000	0.71417	0.994000	0.49952	0.835000	0.47333	6.124000	0.71620	2.258000	0.74832	0.529000	0.55759	.	.	.		0.353	KIAA0020-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051529.3	NM_014878	Intron	C	2807906	T	C	2807906	5	2	255	1	0	0	0	0	0	0	1	0	8161	1594	55	2	232	2	KIAA0020	9	2807906	Splice_Site	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	2503221	2807906	138405525	338	35683										
DNAI1	27019	hgsc.bcm.edu	37	chr9	34506838	34506838	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gccctccttctgcagctcagCcaagtctggcaagcactcag	9	16	4	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:34506838C>T	ENST00000242317.4	+	13	1448	c.1277C>T	c.(1276-1278)gCc>gTc	p.A426V		NM_001281428.1|NM_012144.2	NP_001268357.1|NP_036276.1	Q9UI46	DNAI1_HUMAN	dynein, axonemal, intermediate chain 1	426					cell projection organization (GO:0030030)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	motor activity (GO:0003774)			autonomic_ganglia(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(13)|prostate(1)|skin(2)|urinary_tract(1)	34	all_epithelial(49;0.244)		LUSC - Lung squamous cell carcinoma(29;0.0107)|STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.0222)		TGCAGCTCAGCCAAGTCTGGC	0.627									Kartagener syndrome																												p.A426V		Atlas-SNP	.											.	DNAI1	72	.	0			c.C1277T						.						55	46	49					9																	34506838		2203	4300	6503	SO:0001583	missense	27019	exon13	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GCTCAGCCAAGTC	AF091619	CCDS6557.1, CCDS75829.1	9p13.3	2013-02-19	2006-09-04		ENSG00000122735	ENSG00000122735		"Axonemal dyneins", "WD repeat domain containing"	2954	protein-coding gene	gene with protein product		604366	"dynein, axonemal, intermediate polypeptide 1"			10577904, 21953912	Standard	NM_012144		Approved	DIC1, PCD, CILD1	uc003zum.3	Q9UI46	OTTHUMG00000019825	ENST00000242317.4:c.1277C>T	chr9.hg19:g.34506838C>T	ENSP00000242317:p.Ala426Val	73.0	0.0		95.0	4.0	NM_012144	B7Z7U1|Q5T8G7|Q8NHQ7|Q9UEZ8	Missense_Mutation	SNP	ENST00000242317.4	hg19	CCDS6557.1	.	.	.	.	.	.	.	.	.	.	C	2.468	-0.322458	0.05350	.	.	ENSG00000122735	ENST00000242317	D	0.85861	-2.04	5.16	5.16	0.70880	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.336395	0.30320	N	0.009891	T	0.81211	0.4775	L	0.49455	1.56	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.75777	-0.3198	10	0.21540	T	0.41	.	15.8168	0.78608	0.0:1.0:0.0:0.0	.	426	Q9UI46	DNAI1_HUMAN	V	426	ENSP00000242317:A426V	ENSP00000242317:A426V	A	+	2	0	DNAI1	34496838	1.000000	0.71417	0.938000	0.37757	0.015000	0.08874	5.579000	0.67457	2.390000	0.81377	0.563000	0.77884	GCC	.	.		0.627	DNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052192.1			T	34506838	C	T	34506838	3	4	255	1	0	0	0	0	1	0	0	0	4611	739	26	3	1327	3	DNAI1	9	34506838	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	31698932	34506838	106706593	339	35684										
DNAJB5	25822	hgsc.bcm.edu	37	chr9	34990809	34990809	+	5'UTR	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gaatgggtttgtaaagtttcGgtaagtccctccggagaagg	14	6	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:34990809G>T	ENST00000541010.1	+	0	591				DNAJB5_ENST00000545841.1_Intron|DNAJB5_ENST00000453597.3_Splice_Site_p.R103L|DNAJB5_ENST00000312316.5_Intron|DNAJB5_ENST00000335998.3_Splice_Site_p.R23L|DNAJB5_ENST00000454002.2_Splice_Site_p.R61L			O75953	DNJB5_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 5						negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein folding (GO:0006457)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|nucleus (GO:0005634)	chaperone binding (GO:0051087)			kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(32;0.00575)			GTAAAGTTTCGGTAAGTCCCT	0.527																																					p.R103L		Atlas-SNP	.											.	DNAJB5	69	.	0			c.G308T						.						42	40	40					9																	34990809		692	1591	2283	SO:0001623	5_prime_UTR_variant	25822	exon2			AGTTTCGGTAAGT	AF088982	CCDS35007.1, CCDS47959.1, CCDS47960.1, CCDS47960.2	9p	2011-09-02			ENSG00000137094	ENSG00000137094		"Heat shock proteins / DNAJ (HSP40)"	14887	protein-coding gene	gene with protein product		611328				10570961, 11147971	Standard	NM_001135004		Approved	Hsc40	uc003zvs.4	O75953	OTTHUMG00000019840	ENST00000541010.1:c.-2422G>T	chr9.hg19:g.34990809G>T		69.0	0.0		59.0	4.0	NM_001135004	B3KN14|B4DSA6|J3KQM9|J3KR08|Q5T656|Q8TDR7|Q96EM4	Missense_Mutation	SNP	ENST00000541010.1	hg19	CCDS35007.1	.	.	.	.	.	.	.	.	.	.	G	16.14	3.039055	0.55003	.	.	ENSG00000137094	ENST00000453597;ENST00000335998;ENST00000454002	T;T;T	0.57107	0.42;0.53;0.46	4.59	4.59	0.56863	.	.	.	.	.	T	0.45915	0.1366	N	0.08118	0	0.80722	D	1	D	0.53745	0.962	P	0.53450	0.726	T	0.57283	-0.7838	9	0.87932	D	0	.	14.5683	0.68194	0.0:0.0:1.0:0.0	.	61	B4DSA6	.	L	103;23;61	ENSP00000404079:R103L;ENSP00000337626:R23L;ENSP00000413684:R61L	ENSP00000337626:R23L	R	+	2	0	DNAJB5	34980809	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.954000	0.70298	2.102000	0.63906	0.561000	0.74099	CGA	.	.		0.527	DNAJB5-008	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401397.1			T	34990809	G	T	34990809	1	4	255	0	1	0	0	0	0	0	0	0	4625	1130	39	1		1	DNAJB5	9	34990809	5'UTR	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	483971	34990809	106222622	340	35685										
CCIN	881	hgsc.bcm.edu	37	chr9	36170794	36170794	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tctgtacattgtcactggacGgtgcttggtgaaaggttata	12	6	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:36170794G>T	ENST00000335119.2	+	1	1406	c.1295G>T	c.(1294-1296)cGg>cTg	p.R432L		NM_005893.2	NP_005884.2	Q13939	CALI_HUMAN	calicin	432					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				breast(3)|endometrium(2)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(4)	21			STAD - Stomach adenocarcinoma(86;0.228)			GTCACTGGACGGTGCTTGGTG	0.552																																					p.R432L		Atlas-SNP	.											.	CCIN	56	.	0			c.G1295T						.						141	107	119					9																	36170794		2203	4300	6503	SO:0001583	missense	881	exon1			CTGGACGGTGCTT	Z46967	CCDS6599.1	9p13.1	2013-10-02			ENSG00000185972	ENSG00000185972		"BTB/POZ domain containing"	1568	protein-coding gene	gene with protein product		603960				7641791	Standard	NM_005893		Approved	KBTBD14, BTBD20	uc003zzb.4	Q13939	OTTHUMG00000019901	ENST00000335119.2:c.1295G>T	chr9.hg19:g.36170794G>T	ENSP00000334996:p.Arg432Leu	86.0	0.0		92.0	5.0	NM_005893	Q9BXG7	Missense_Mutation	SNP	ENST00000335119.2	hg19	CCDS6599.1	.	.	.	.	.	.	.	.	.	.	G	17.06	3.291280	0.59976	.	.	ENSG00000185972	ENST00000335119	T	0.66099	-0.19	5.73	5.73	0.89815	Kelch-type beta propeller (1);	0.000000	0.51477	D	0.000095	T	0.65729	0.2719	L	0.27053	0.805	0.37591	D	0.920177	D	0.60160	0.987	D	0.67725	0.953	T	0.62586	-0.6823	10	0.18276	T	0.48	.	15.3816	0.74661	0.0:0.0:1.0:0.0	.	432	Q13939	CALI_HUMAN	L	432	ENSP00000334996:R432L	ENSP00000334996:R432L	R	+	2	0	CCIN	36160794	1.000000	0.71417	0.992000	0.48379	0.989000	0.77384	5.491000	0.66887	2.699000	0.92147	0.491000	0.48974	CGG	.	.		0.552	CCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052418.1	NM_005893		T	36170794	G	T	36170794	3	4	255	1	0	0	0	0	1	0	0	0	2880	1116	39	1	1297	1	CCIN	9	36170794	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	1179985	36170794	105042637	341	35686										
FAM75A1	647060	hgsc.bcm.edu	37	chr9	39361559	39361559	+	Frame_Shift_Del	DEL	C	C	-													0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cagaatactgagctatgcagCcagcagtcaacaagccactc							TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:39361559delC	ENST00000377647.3	+	4	3826	c.3797delC	c.(3796-3798)gccfs	p.A1266fs		NM_001085452.1	NP_001078921.1	Q5TZJ5	S31A1_HUMAN	SPATA31 subfamily A, member 1	1266					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											AGCTATGCAGCCAGCAGTCAA	0.502																																					p.A1266fs		Atlas-INDEL	.											.	.	.	.	0			c.3796delG						.						0	1	1					9																	39361559		0	1	1	SO:0001589	frameshift_variant	647060	exon4			.		CCDS43808.1	9p12	2012-10-15	2012-10-12	2012-10-12	ENSG00000204849	ENSG00000204849			23394	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 36", "family with sequence similarity 75, member A1"	C9orf36, FAM75A1		20850414	Standard	XM_006716851		Approved	DKFZP434B204, C9orf36A, OTTHUMG00000013156		Q5TZJ5	OTTHUMG00000013156	ENST00000377647.3:c.3797delC	chr9.hg19:g.39361559delC	ENSP00000366875:p.Ala1266fs	36.0	0.0		38.0	14.0	NM_001085452		Frame_Shift_Del	DEL	ENST00000377647.3	hg19	CCDS43808.1																																																																																			.	.		0.502	SPATA31A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036910.1	NM_001085452		-	39361559	C	-	39361559	7	5	255	1	0	1	0	1	0	0	0	0	5627	739	26	0	3811	0	FAM75A1	9	39361559	Frame_Shift_Del	DEL	C	TCGA-EP-A2KB-01A-11D-A183-10	3190765	39361559	101851872	342	35687										
FAM75A1	642265	hgsc.bcm.edu	37	chr9	39890810	39890810	+	Frame_Shift_Del	DEL	C	C	-													0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cagaatactgagctatgcagCcagcagtcaacaagccactc							TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:39890810delC	ENST00000456183.2	+	4	3826	c.3797delC	c.(3796-3798)gccfs	p.A1266fs		NM_001040065.1	NP_001035154.1	Q5RGS2	S31A2_HUMAN	SPATA31 subfamily A, member 2	1266					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											AGCTATGCAGCCAGCAGTCAA	0.502																																					p.A1266fs		Atlas-INDEL	.											.	.	.	.	0			c.3796delG						.																																			SO:0001589	frameshift_variant	647060	exon4			.			9p13.1	2012-10-15	2012-10-12	2012-10-12	ENSG00000204848				32002	protein-coding gene	gene with protein product			"family with sequence similarity 75, member A2"	FAM75A2		20850414	Standard			Approved	OTTHUMG00000013563	uc004abm.3	Q5RGS2	OTTHUMG00000013563	ENST00000456183.2:c.3797delC	chr9.hg19:g.39890810delC	ENSP00000406957:p.Ala1266fs	19.0	0.0		65.0	21.0	NM_001085452		Frame_Shift_Del	DEL	ENST00000456183.2	hg19	CCDS43809.1																																																																																			.	.		0.502	SPATA31A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037739.1	NM_001040065		-	39890810	C	-	39890810	7	5	255	1	0	1	0	1	0	0	0	0	5627	739	26	0	7871	0	FAM75A1	9	39890810	Frame_Shift_Del	DEL	C	TCGA-EP-A2KB-01A-11D-A183-10	529251	39890810	101322621	343	35688										
MAMDC2	256691	hgsc.bcm.edu	37	chr9	72659502	72659502	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctcgctttgtgcccgcagccCtgcagctcgccggtgccctc	11	19	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:72659502C>T	ENST00000377182.4	+	2	654	c.37C>T	c.(37-39)Ctg>Ttg	p.L13L		NM_153267.4	NP_694999.3	Q7Z304	MAMC2_HUMAN	MAM domain containing 2	13					peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)	endoplasmic reticulum (GO:0005783)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	glycosaminoglycan binding (GO:0005539)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)	14						GCCCGCAGCCCTGCAGCTCGC	0.622																																					p.L13L		Atlas-SNP	.											.	MAMDC2	55	.	0			c.C37T						.						40	36	37					9																	72659502		1976	3820	5796	SO:0001819	synonymous_variant	256691	exon2			GCAGCCCTGCAGC	BC040299	CCDS6631.1	9q21.2	2008-02-05			ENSG00000165072	ENSG00000165072			23673	protein-coding gene	gene with protein product		612879					Standard	NM_153267		Approved	MGC21981	uc004ahm.2	Q7Z304	OTTHUMG00000019990	ENST00000377182.4:c.37C>T	chr9.hg19:g.72659502C>T		86.0	0.0		99.0	4.0	NM_153267	Q5VW47|Q8WX43|Q96BM4	Silent	SNP	ENST00000377182.4	hg19	CCDS6631.1																																																																																			.	.		0.622	MAMDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052600.1	NM_153267		T	72659502	C	T	72659502	2	4	255	1	0	0	0	0	0	0	0	1	9212	680	24	3		3	MAMDC2	9	72659502	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	32768692	72659502	68553929	344	35689										
TRPM3	80036	hgsc.bcm.edu	37	chr9	73235023	73235023	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	attcagctcctgggaaatgtCgtcaaccatgtcgttctcag	9	11	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:73235023C>A	ENST00000377111.2	-	15	2305	c.2062G>T	c.(2062-2064)Gac>Tac	p.D688Y	TRPM3_ENST00000396292.4_Missense_Mutation_p.D560Y|TRPM3_ENST00000423814.3_Missense_Mutation_p.D715Y|TRPM3_ENST00000377105.1_Missense_Mutation_p.D547Y|TRPM3_ENST00000377110.3_Missense_Mutation_p.D688Y|TRPM3_ENST00000377106.1_Missense_Mutation_p.D560Y|TRPM3_ENST00000396280.5_Missense_Mutation_p.D537Y|TRPM3_ENST00000357533.2_Missense_Mutation_p.D692Y|TRPM3_ENST00000396285.1_Missense_Mutation_p.D535Y|TRPM3_ENST00000358082.3_Missense_Mutation_p.D550Y|TRPM3_ENST00000408909.2_Missense_Mutation_p.D547Y|TRPM3_ENST00000360823.2_Missense_Mutation_p.D550Y	NM_001007471.2	NP_001007472.2	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	713					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)	p.D560N(1)|p.D692N(1)		NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						TGGGAAATGTCGTCAACCATG	0.602																																					p.D688Y		Atlas-SNP	.											TRPM3_ENST00000423814,NS,carcinoma,0,2	TRPM3	700	.	2	Substitution - Missense(2)	lung(2)	c.G2062T						.						73	69	71					9																	73235023		2203	4300	6503	SO:0001583	missense	80036	exon15			AAATGTCGTCAAC	AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"Voltage-gated ion channels / Transient receptor potential cation channels"	17992	protein-coding gene	gene with protein product	"melastatin 2"	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377111.2:c.2062G>T	chr9.hg19:g.73235023C>A	ENSP00000366315:p.Asp688Tyr	73.0	0.0		82.0	4.0	NM_001007471	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Missense_Mutation	SNP	ENST00000377111.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.3|25.3	4.620384|4.620384	0.87460|0.87460	.|.	.|.	ENSG00000083067|ENSG00000083067	ENST00000377111;ENST00000377110;ENST00000377106;ENST00000360823;ENST00000377105;ENST00000357533;ENST00000408909;ENST00000396285;ENST00000396292;ENST00000358082;ENST00000423814|ENST00000396280	T;T;T;T;T;T;T;T;T;T;T|.	0.63580|.	-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05|.	6.07|6.07	6.07|6.07	0.98685|0.98685	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.82637|0.82637	0.5080|0.5080	M|M	0.81802|0.81802	2.56|2.56	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D;D|.	0.89917|.	1.0;0.998;1.0;0.995;1.0;1.0;0.999;0.999|.	D;D;D;D;D;D;D;D|.	0.97110|.	0.992;0.97;1.0;0.981;0.987;0.997;0.986;0.971|.	T|T	0.81455|0.81455	-0.0925|-0.0925	10|5	0.87932|.	D|.	0|.	-30.4518|-30.4518	20.6439|20.6439	0.99570|0.99570	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	688;688;678;692;550;547;660;535|.	Q9HCF6-2;Q9HCF6-10;Q9HCF6-4;A2A3F7;A2A3F4;G5E9G1;Q9HCF6-8;A2A3F3|.	.;.;.;.;.;.;.;.|.	Y|L	688;688;560;550;547;692;547;535;560;550;715|536	ENSP00000366315:D688Y;ENSP00000366314:D688Y;ENSP00000366310:D560Y;ENSP00000354066:D550Y;ENSP00000366309:D547Y;ENSP00000350140:D692Y;ENSP00000386127:D547Y;ENSP00000379581:D535Y;ENSP00000379587:D560Y;ENSP00000350791:D550Y;ENSP00000389542:D715Y|.	ENSP00000350140:D692Y|.	D|R	-|-	1|2	0|0	TRPM3|TRPM3	72424843|72424843	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.800000|0.800000	0.45204|0.45204	7.818000|7.818000	0.86416|0.86416	2.890000|2.890000	0.99128|0.99128	0.650000|0.650000	0.86243|0.86243	GAC|CGA	.	.		0.602	TRPM3-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000214157.5	NM_206945		A	73235023	C	A	73235023	3	1	255	1	0	0	0	0	1	0	0	0	16602	884	31	1	3105	1	TRPM3	9	73235023	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	575521	73235023	67978408	345	35690										
C9orf79	286234	hgsc.bcm.edu	37	chr9	90500432	90500432	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aggcttccttctggggagacCccacacccaagcacatggag	11	14	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:90500432C>T	ENST00000325643.5	+	4	1096	c.1030C>T	c.(1030-1032)Ccc>Tcc	p.P344S		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	344					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CTGGGGAGACCCCACACCCAA	0.597																																					p.P344S		Atlas-SNP	.											.	.	.	.	0			c.C1030T						.						58	59	59					9																	90500432		2203	4300	6503	SO:0001583	missense	286234	exon4			GGAGACCCCACAC	AK093185	CCDS6676.1	9q22.1-q22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000177992	ENSG00000177992			26672	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 79", "family with sequence similarity 75, member E1"	C9orf79, FAM75E1			Standard	NM_178828		Approved	FLJ35866	uc004app.4	Q6ZUB1	OTTHUMG00000020157	ENST00000325643.5:c.1030C>T	chr9.hg19:g.90500432C>T	ENSP00000322640:p.Pro344Ser	76.0	0.0		94.0	4.0	NM_178828	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Missense_Mutation	SNP	ENST00000325643.5	hg19	CCDS6676.1	.	.	.	.	.	.	.	.	.	.	.	9.083	0.999705	0.19121	.	.	ENSG00000177992	ENST00000325643	T	0.03386	3.95	3.37	0.169	0.15017	.	.	.	.	.	T	0.02848	0.0085	L	0.35542	1.07	0.09310	N	1	B	0.33637	0.42	B	0.32928	0.155	T	0.46665	-0.9175	9	0.26408	T	0.33	.	4.9674	0.14098	0.0:0.4366:0.4329:0.1305	.	344	Q6ZUB1	CI079_HUMAN	S	344	ENSP00000322640:P344S	ENSP00000322640:P344S	P	+	1	0	C9orf79	89690252	0.000000	0.05858	0.001000	0.08648	0.110000	0.19582	-0.559000	0.05971	0.197000	0.20387	0.557000	0.71058	CCC	.	.		0.597	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828		T	90500432	C	T	90500432	3	4	255	1	0	0	0	0	1	0	0	0	2499	623	22	3	1044	3	C9orf79	9	90500432	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	17265409	90500432	50712999	346	35691										
PHF2	5253	hgsc.bcm.edu	37	chr9	96428080	96428080	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	atgagtacgtgtcggatgacGgtgagctcaagatcgacgag	15	7	1	4			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:96428080G>T	ENST00000359246.4	+	15	2417	c.2050G>T	c.(2050-2052)Ggt>Tgt	p.G684C	PHF2_ENST00000375376.4_Intron	NM_005392.3	NP_005383.3	O75151	PHF2_HUMAN	PHD finger protein 2	684					liver development (GO:0001889)|negative regulation of chromatin silencing at rDNA (GO:0061188)|protein demethylation (GO:0006482)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K9 specific) (GO:0032454)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)		GTCGGATGACGGTGAGCTCAA	0.597																																					p.G684C		Atlas-SNP	.											.	PHF2	113	.	0			c.G2050T						.						123	131	129					9																	96428080		2203	4300	6503	SO:0001583	missense	5253	exon15			GATGACGGTGAGC	AF043725	CCDS35069.1	9q22	2013-01-28			ENSG00000197724	ENSG00000197724		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	8920	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 1E", "centromere protein 35"	604351				10051327, 20129925	Standard	NM_005392		Approved	KIAA0662, JHDM1E, CENP-35	uc004aub.3	O75151	OTTHUMG00000020253	ENST00000359246.4:c.2050G>T	chr9.hg19:g.96428080G>T	ENSP00000352185:p.Gly684Cys	98.0	0.0		106.0	5.0	NM_005392	Q4VXG0|Q8N3K2|Q9Y6N4	Missense_Mutation	SNP	ENST00000359246.4	hg19	CCDS35069.1	.	.	.	.	.	.	.	.	.	.	G	17.59	3.427605	0.62733	.	.	ENSG00000197724	ENST00000359246	T	0.20881	2.04	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	T	0.42404	0.1201	L	0.46157	1.445	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.30966	-0.9960	10	0.72032	D	0.01	-30.6856	18.5484	0.91055	0.0:0.0:1.0:0.0	.	102;684	Q8N359;O75151	.;PHF2_HUMAN	C	684	ENSP00000352185:G684C	ENSP00000352185:G684C	G	+	1	0	PHF2	95467901	1.000000	0.71417	0.729000	0.30791	0.070000	0.16714	9.246000	0.95438	2.375000	0.81037	0.591000	0.81541	GGT	.	.		0.597	PHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053162.1	NM_005392		T	96428080	G	T	96428080	3	4	255	1	0	0	0	0	1	0	0	0	11839	1116	39	1	2108	1	PHF2	9	96428080	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	5927648	96428080	44785351	347	35692										
TMEFF1	8577	hgsc.bcm.edu	37	chr9	103312401	103312401	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agatgacactagtttgttggGaaagaaagatgatggactac	12	4	0	5			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:103312401G>A	ENST00000374879.4	+	7	1166	c.734G>A	c.(733-735)gGa>gAa	p.G245E	TMEFF1_ENST00000334943.6_Missense_Mutation_p.G206E|MSANTD3-TMEFF1_ENST00000502978.1_Silent_p.G208G	NM_003692.4	NP_003683.2	Q8IYR6	TEFF1_HUMAN	transmembrane protein with EGF-like and two follistatin-like domains 1	245					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|kidney(1)|large_intestine(7)|lung(9)|stomach(1)	19		Acute lymphoblastic leukemia(62;0.0452)				AGTTTGTTGGGAAAGAAAGAT	0.363																																					p.G319E		Atlas-SNP	.											.	.	.	.	0			c.G956A						.						127	119	122					9																	103312401		2203	4300	6503	SO:0001583	missense	100526694	exon7			TGTTGGGAAAGAA	U19878	CCDS6750.1	9q31	2010-05-04			ENSG00000241697	ENSG00000241697			11866	protein-coding gene	gene with protein product	"tomoregulin-1", "cancer/testis antigen family 120, member 1"	603421		C9orf2		9730596	Standard	NM_003692		Approved	H7365, CT120.1		Q8IYR6	OTTHUMG00000020367	ENST00000374879.4:c.734G>A	chr9.hg19:g.103312401G>A	ENSP00000364013:p.Gly245Glu	65.0	0.0		63.0	4.0	NM_001198812	Q13086|Q8N3T8	Missense_Mutation	SNP	ENST00000374879.4	hg19	CCDS6750.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.099068	0.76983	.	.	ENSG00000241697	ENST00000334943;ENST00000374879	T;T	0.57273	0.44;0.41	5.74	5.74	0.90152	.	0.109197	0.64402	D	0.000006	T	0.53867	0.1823	N	0.14661	0.345	0.80722	D	1	P;D	0.76494	0.893;0.999	P;D	0.71656	0.706;0.974	T	0.45906	-0.9229	10	0.11182	T	0.66	-35.667	17.4089	0.87480	0.0:0.0:1.0:0.0	.	245;206	Q8IYR6;Q8IYR6-2	TEFF1_HUMAN;.	E	206;245	ENSP00000334447:G206E;ENSP00000364013:G245E	ENSP00000334447:G206E	G	+	2	0	TMEFF1	102352222	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.774000	0.75012	2.702000	0.92279	0.585000	0.79938	GGA	.	.		0.363	TMEFF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053418.1	NM_003692		A	103312401	G	A	103312401	3	1	255	1	0	0	0	0	1	0	0	0	16028	1174	41	3	760	3	TMEFF1	9	103312401	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	6884321	103312401	37901030	348	35693										
LPPR1	54886	hgsc.bcm.edu	37	chr9	104079680	104079680	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttcataactttaaaggaacgCaaggatctccttccaaaccc	5	12	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:104079680C>T	ENST00000374874.3	+	7	1286	c.847C>T	c.(847-849)Caa>Taa	p.Q283*	LPPR1_ENST00000395056.2_Nonsense_Mutation_p.Q283*	NM_207299.1	NP_997182.1	Q8TBJ4	LPPR1_HUMAN		283					nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)										TAAAGGAACGCAAGGATCTCC	0.512																																					p.Q283X		Atlas-SNP	.											.	.	.	.	0			c.C847T						.						159	163	161					9																	104079680		2203	4300	6503	SO:0001587	stop_gained	0	exon7			GGAACGCAAGGAT																												ENST00000374874.3:c.847C>T	chr9.hg19:g.104079680C>T	ENSP00000364008:p.Gln283*	97.0	0.0		68.0	4.0	NM_207299	Q5VX23|Q9NXE2	Nonsense_Mutation	SNP	ENST00000374874.3	hg19	CCDS6751.1	.	.	.	.	.	.	.	.	.	.	C	38	7.188050	0.98121	.	.	ENSG00000148123	ENST00000374874;ENST00000374871;ENST00000395056	.	.	.	5.79	5.79	0.91817	.	0.563221	0.18337	N	0.144320	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08381	T	0.77	-6.635	12.34	0.55089	0.0:0.9238:0.0:0.0762	.	.	.	.	X	283	.	ENSP00000364005:Q283X	Q	+	1	0	RP11-35N6.1	103119501	1.000000	0.71417	0.987000	0.45799	0.997000	0.91878	4.587000	0.60991	2.746000	0.94184	0.655000	0.94253	CAA	.	.		0.512	LPPR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053425.1			T	104079680	C	T	104079680	4	4	255	1	0	0	0	0	0	1	0	0	8933	711	25	3	869	3	LPPR1	9	104079680	Nonsense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	767279	104079680	37133751	349	35694										
BAAT	570	hgsc.bcm.edu	37	chr9	104130448	104130448	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cagcctcctcaaaatattccAaatctgttacttctggtttg	5	11	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:104130448A>G	ENST00000395051.3	-	2	693	c.623T>C	c.(622-624)tTg>tCg	p.L208S	BAAT_ENST00000259407.2_Missense_Mutation_p.L208S			Q14032	BAAT_HUMAN	bile acid CoA:amino acid N-acyltransferase	208					acyl-CoA metabolic process (GO:0006637)|bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid conjugation (GO:0002152)|bile acid metabolic process (GO:0008206)|fatty acid metabolic process (GO:0006631)|glycine metabolic process (GO:0006544)|liver development (GO:0001889)|organ regeneration (GO:0031100)|small molecule metabolic process (GO:0044281)|taurine metabolic process (GO:0019530)	cytosol (GO:0005829)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carboxylic ester hydrolase activity (GO:0052689)|glycine N-choloyltransferase activity (GO:0047963)|long-chain acyl-CoA hydrolase activity (GO:0052816)|medium-chain acyl-CoA hydrolase activity (GO:0052815)|N-acyltransferase activity (GO:0016410)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)|very long chain acyl-CoA hydrolase activity (GO:0052817)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		Acute lymphoblastic leukemia(62;0.0559)			Glycine(DB00145)	AAAATATTCCAAATCTGTTAC	0.468																																					p.L208S		Atlas-SNP	.											.	BAAT	52	.	0			c.T623C						.						74	80	78					9																	104130448		2203	4300	6503	SO:0001583	missense	570	exon3			TATTCCAAATCTG	L34081	CCDS6752.1	9q22.3	2014-06-24	2014-06-24		ENSG00000136881	ENSG00000136881	2.3.1.65		932	protein-coding gene	gene with protein product	"glycine N-choloyltransferase"	602938	"bile acid Coenzyme A:amino acid N-acyltransferase (glycine N-choloyltransferase)", "bile acid CoA: amino acid N-acyltransferase (glycine N-choloyltransferase)"				Standard	NM_001701		Approved	BAT	uc010mtd.3	Q14032	OTTHUMG00000020377	ENST00000395051.3:c.623T>C	chr9.hg19:g.104130448A>G	ENSP00000378491:p.Leu208Ser	118.0	0.0		142.0	65.0	NM_001127610	Q3B7W9|Q96L31	Missense_Mutation	SNP	ENST00000395051.3	hg19	CCDS6752.1	.	.	.	.	.	.	.	.	.	.	A	18.26	3.583815	0.65992	.	.	ENSG00000136881	ENST00000259407;ENST00000395051	T;T	0.38722	1.12;1.12	4.38	4.38	0.52667	BAAT/Acyl-CoA thioester hydrolase C-terminal (1);	0.155821	0.25575	N	0.029736	T	0.65176	0.2666	M	0.82517	2.595	0.26564	N	0.973674	D	0.89917	1.0	D	0.83275	0.996	T	0.60772	-0.7197	10	0.87932	D	0	-15.8757	11.6118	0.51064	1.0:0.0:0.0:0.0	.	208	Q14032	BAAT_HUMAN	S	208	ENSP00000259407:L208S;ENSP00000378491:L208S	ENSP00000259407:L208S	L	-	2	0	BAAT	103170269	1.000000	0.71417	0.268000	0.24571	0.880000	0.50808	8.507000	0.90522	1.850000	0.53721	0.459000	0.35465	TTG	.	.		0.468	BAAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053433.1			G	104130448	A	G	104130448	3	3	255	1	0	0	0	0	1	0	0	0	1280	131	5	2	641	2	BAAT	9	104130448	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	50768	104130448	37082983	350	35695										
ZNF462	58499	hgsc.bcm.edu	37	chr9	109689751	109689751	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agctctgagagagatggcccTcctgtggagaatgagatgtt	14	7	1	4			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:109689751T>C	ENST00000277225.5	+	3	3847	c.3558T>C	c.(3556-3558)ccT>ccC	p.P1186P	ZNF462_ENST00000441147.2_Silent_p.P31P|ZNF462_ENST00000457913.1_Silent_p.P1186P			Q96JM2	ZN462_HUMAN	zinc finger protein 462	1186					chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						GAGATGGCCCTCCTGTGGAGA	0.557																																					p.P1186P		Atlas-SNP	.											.	ZNF462	322	.	0			c.T3558C						.						198	201	200					9																	109689751		2203	4300	6503	SO:0001819	synonymous_variant	58499	exon3			TGGCCCTCCTGTG	AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"Zinc fingers, C2H2-type"	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.3558T>C	chr9.hg19:g.109689751T>C		55.0	0.0		85.0	4.0	NM_021224	Q5T0T4|Q8N408	Silent	SNP	ENST00000277225.5	hg19	CCDS35096.1																																																																																			.	.		0.557	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224		C	109689751	T	C	109689751	2	2	255	1	0	0	0	0	0	0	0	1	17941	1538	54	2		2	ZNF462	9	109689751	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	5559303	109689751	31523680	351	35696										
AKAP2	11217	hgsc.bcm.edu	37	chr9	112900259	112900259	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gcagaatgccattcaacaagCcatagccgagcaggtggata	11	10	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:112900259C>A	ENST00000259318.7	+	2	1949	c.1742C>A	c.(1741-1743)gCc>gAc	p.A581D	AKAP2_ENST00000555236.1_Missense_Mutation_p.A812D|AKAP2_ENST00000510514.5_Missense_Mutation_p.A812D|PALM2-AKAP2_ENST00000302798.7_Missense_Mutation_p.A812D|PALM2-AKAP2_ENST00000374530.3_Missense_Mutation_p.A812D|AKAP2_ENST00000434623.2_Missense_Mutation_p.A670D|AKAP2_ENST00000374525.1_Missense_Mutation_p.A670D	NM_001136562.2	NP_001130034.1	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2	581										breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	33						ATTCAACAAGCCATAGCCGAG	0.562																																					p.A812D		Atlas-SNP	.											.	PALM2-AKAP2	117	.	0			c.C2435A						.						37	39	38					9																	112900259		2203	4300	6503	SO:0001583	missense	445815	exon8			AACAAGCCATAGC	AB023137	CCDS43861.1, CCDS48003.1, CCDS56581.1	9q31.3	2009-10-16			ENSG00000241978	ENSG00000241978		"A-kinase anchor proteins"	372	protein-coding gene	gene with protein product	"protein kinase A2"	604582		PRKA2		10231032	Standard	NM_001136562		Approved	AKAP-KL, KIAA0920, DKFZp564L0716		Q9Y2D5	OTTHUMG00000156811	ENST00000259318.7:c.1742C>A	chr9.hg19:g.112900259C>A	ENSP00000259318:p.Ala581Asp	73.0	0.0		90.0	4.0	NM_007203	B1ALX9|B2RTU4|B3KQ00|B4DTZ2|B7ZW07|B9EJB5|Q9UG26	Missense_Mutation	SNP	ENST00000259318.7	hg19	CCDS48003.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.323456	0.81580	.	.	ENSG00000157654;ENSG00000157654;ENSG00000241978;ENSG00000241978;ENSG00000241978;ENSG00000241978;ENSG00000241978;ENSG00000241978	ENST00000374530;ENST00000302798;ENST00000555236;ENST00000510514;ENST00000434623;ENST00000374525;ENST00000480388;ENST00000259318	T;T;T;T;T;T;T;T	0.60040	1.55;1.58;1.55;1.58;0.79;0.24;0.22;0.87	6.06	6.06	0.98353	RII binding domain (1);	0.000000	0.85682	D	0.000000	T	0.76969	0.4062	M	0.70275	2.135	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.97110	0.997;0.999;0.999;0.999;1.0;0.999;0.999;0.999	T	0.76022	-0.3111	10	0.56958	D	0.05	-29.3009	19.6279	0.95687	0.0:1.0:0.0:0.0	.	581;670;664;670;671;812;812;630	Q9Y2D5;Q9Y2D5-7;B4E2K2;Q9Y2D5-5;B1ALY1;Q9Y2D5-6;Q9Y2D5-4;C9JVY5	AKAP2_HUMAN;.;.;.;.;.;.;.	D	812;812;812;812;670;670;630;581	ENSP00000363654:A812D;ENSP00000305861:A812D;ENSP00000451476:A812D;ENSP00000421522:A812D;ENSP00000404782:A670D;ENSP00000363649:A670D;ENSP00000419268:A630D;ENSP00000259318:A581D	ENSP00000259318:A581D	A	+	2	0	PALM2-AKAP2;AKAP2	111940080	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.076000	0.57591	2.880000	0.98712	0.650000	0.86243	GCC	.	.		0.562	AKAP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346067.3	NM_001004065		A	112900259	C	A	112900259	3	1	255	1	0	0	0	0	1	0	0	0	451	739	26	3	2015	3	AKAP2	9	112900259	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	3210508	112900259	28313172	352	35697										
SVEP1	79987	hgsc.bcm.edu	37	chr9	113169106	113169106	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gacaggtgagttttggagcaCcgtgcaagatgtagccctcg	14	9	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:113169106C>T	ENST00000401783.2	-	38	9110	c.8774G>A	c.(8773-8775)gGt>gAt	p.G2925D	SVEP1_ENST00000297826.5_Missense_Mutation_p.G851D|SVEP1_ENST00000374469.1_Missense_Mutation_p.G2902D	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2925	Sushi 25. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						TTTTGGAGCACCGTGCAAGAT	0.537																																					p.G2925D		Atlas-SNP	.											.	SVEP1	326	.	0			c.G8774A						.						148	149	149					9																	113169106		2064	4209	6273	SO:0001583	missense	79987	exon38			GGAGCACCGTGCA	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.8774G>A	chr9.hg19:g.113169106C>T	ENSP00000384917:p.Gly2925Asp	70.0	0.0		81.0	4.0	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	hg19	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	C	16.70	3.195395	0.58126	.	.	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826	T;T;T	0.72725	-0.68;-0.68;-0.68	5.41	5.41	0.78517	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.85682	D	0.000000	D	0.89037	0.6601	H	0.94698	3.57	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91255	0.5032	10	0.56958	D	0.05	.	19.1906	0.93664	0.0:1.0:0.0:0.0	.	2925	Q4LDE5	SVEP1_HUMAN	D	2925;2902;851	ENSP00000384917:G2925D;ENSP00000363593:G2902D;ENSP00000297826:G851D	ENSP00000297826:G851D	G	-	2	0	SVEP1	112208927	1.000000	0.71417	0.197000	0.23402	0.142000	0.21351	7.582000	0.82546	2.548000	0.85928	0.591000	0.81541	GGT	.	.		0.537	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	113169106	C	T	113169106	3	4	255	1	0	0	0	0	1	0	0	0	15435	507	18	3	1985	3	SVEP1	9	113169106	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	268847	113169106	28044325	353	35698										
TNC	3371	hgsc.bcm.edu	37	chr9	117853209	117853209	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccccactctgtcgcttgtgcCggatgactttcttgaggacc	10	14	2	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:117853209C>A	ENST00000350763.4	-	2	500	c.89G>T	c.(88-90)cGg>cTg	p.R30L	TNC_ENST00000423613.2_Missense_Mutation_p.R30L|TNC_ENST00000345230.3_Missense_Mutation_p.R30L|TNC_ENST00000346706.3_Missense_Mutation_p.R30L|TNC_ENST00000537320.1_Missense_Mutation_p.R30L|TNC_ENST00000340094.3_Missense_Mutation_p.R30L|TNC_ENST00000542877.1_Missense_Mutation_p.R30L|TNC_ENST00000535648.1_Missense_Mutation_p.R30L|TNC_ENST00000341037.4_Missense_Mutation_p.R30L	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	30					bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)			NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						TCGCTTGTGCCGGATGACTTT	0.572																																					p.R30L		Atlas-SNP	.											.	TNC	282	.	0			c.G89T						.						72	71	71					9																	117853209		2203	4300	6503	SO:0001583	missense	3371	exon2			TTGTGCCGGATGA		CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	5318	protein-coding gene	gene with protein product	"hexabrachion (tenascin)"	187380	"hexabrachion (tenascin C, cytotactin)", "deafness, autosomal dominant 56"	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.89G>T	chr9.hg19:g.117853209C>A	ENSP00000265131:p.Arg30Leu	71.0	0.0		94.0	4.0	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	ENST00000350763.4	hg19	CCDS6811.1	.	.	.	.	.	.	.	.	.	.	C	33	5.244959	0.95272	.	.	ENSG00000041982	ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000442945;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877;ENST00000534839	T;T;T;T;T;T;T;T;T;T	0.37915	1.17;1.17;1.17;1.17;1.17;1.17;1.17;1.17;1.17;1.17	5.58	5.58	0.84498	.	0.056725	0.64402	D	0.000003	T	0.62889	0.2465	M	0.73962	2.25	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.65717	-0.6100	10	0.87932	D	0	.	18.5353	0.91008	0.0:1.0:0.0:0.0	.	30;30	E9PC84;P24821	.;TENA_HUMAN	L	30	ENSP00000344400:R30L;ENSP00000438152:R30L;ENSP00000344555:R30L;ENSP00000345861:R30L;ENSP00000265131:R30L;ENSP00000339553:R30L;ENSP00000411406:R30L;ENSP00000443478:R30L;ENSP00000442242:R30L;ENSP00000443469:R30L	ENSP00000344400:R30L	R	-	2	0	TNC	116893030	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	5.640000	0.67875	2.609000	0.88269	0.462000	0.41574	CGG	.	.		0.572	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160		A	117853209	C	A	117853209	3	1	255	1	0	0	0	0	1	0	0	0	16285	652	23	1	6624	1	TNC	9	117853209	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	4684103	117853209	23360222	354	35699										
OR1K1	392392	hgsc.bcm.edu	37	chr9	125562726	125562726	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgtacttcttctttgccctgGgggtaactgatagctgtctt	10	9	3	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:125562726G>T	ENST00000277309.2	+	1	357	c.325G>T	c.(325-327)Ggg>Tgg	p.G109W		NM_080859.1	NP_543135.1	Q8NGR3	OR1K1_HUMAN	olfactory receptor, family 1, subfamily K, member 1	109						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(8)|lung(2)|ovary(1)|skin(4)|stomach(1)	17						CTTTGCCCTGGGGGTAACTGA	0.597																																					p.G109W		Atlas-SNP	.											.	OR1K1	34	.	0			c.G325T						.						107	91	96					9																	125562726		2203	4300	6503	SO:0001583	missense	392392	exon1			GCCCTGGGGGTAA	AL359512	CCDS35132.1	9q33	2013-09-20			ENSG00000165204	ENSG00000165204		"GPCR / Class A : Olfactory receptors"	8212	protein-coding gene	gene with protein product							Standard	NM_080859		Approved	hg99, MNAB	uc011lze.2	Q8NGR3	OTTHUMG00000020625	ENST00000277309.2:c.325G>T	chr9.hg19:g.125562726G>T	ENSP00000277309:p.Gly109Trp	51.0	0.0		64.0	4.0	NM_080859	B9EH41|Q4VXB7|Q96R23	Missense_Mutation	SNP	ENST00000277309.2	hg19	CCDS35132.1	.	.	.	.	.	.	.	.	.	.	G	8.813	0.935697	0.18206	.	.	ENSG00000165204	ENST00000277309	T	0.01369	4.97	4.37	0.299	0.15771	GPCR, rhodopsin-like superfamily (1);	0.456308	0.16047	U	0.232155	T	0.09379	0.0231	H	0.94582	3.555	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.07673	-1.0760	10	0.87932	D	0	.	4.7794	0.13195	0.2576:0.2983:0.444:0.0	.	109	Q8NGR3	OR1K1_HUMAN	W	109	ENSP00000277309:G109W	ENSP00000277309:G109W	G	+	1	0	OR1K1	124602547	0.010000	0.17322	0.006000	0.13384	0.073000	0.16967	1.649000	0.37281	-0.120000	0.11809	0.655000	0.94253	GGG	.	.		0.597	OR1K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053958.1			T	125562726	G	T	125562726	3	4	255	1	0	0	0	0	1	0	0	0	10971	1232	43	3	327	3	OR1K1	9	125562726	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	7709517	125562726	15650705	355	35700										
CRB2	286204	hgsc.bcm.edu	37	chr9	126133645	126133645	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctgaccagctgcaggacctgGggcagcacgtgcacgtgggt	16	12	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:126133645G>T	ENST00000373631.3	+	8	2225	c.2224G>T	c.(2224-2226)Ggg>Tgg	p.G742W	CRB2_ENST00000359999.3_Missense_Mutation_p.G742W|CRB2_ENST00000373629.2_Missense_Mutation_p.G410W	NM_173689.5	NP_775960.4	Q5IJ48	CRUM2_HUMAN	crumbs family member 2	742	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cardiovascular system development (GO:0072358)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|mesoderm formation (GO:0001707)|negative regulation of endopeptidase activity (GO:0010951)|notochord formation (GO:0014028)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|somitogenesis (GO:0001756)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)			NS(2)|breast(1)|cervix(1)|endometrium(2)|lung(11)|ovary(1)|prostate(2)|skin(3)	23						GCAGGACCTGGGGCAGCACGT	0.692																																					p.G742W		Atlas-SNP	.											.	CRB2	86	.	0			c.G2224T						.						69	72	71					9																	126133645		2203	4299	6502	SO:0001583	missense	286204	exon8			GACCTGGGGCAGC	AK095783	CCDS6852.2	9q33.2	2014-02-06	2014-02-06		ENSG00000148204	ENSG00000148204			18688	protein-coding gene	gene with protein product		609720	"crumbs homolog 2 (Drosophila)"			14767562	Standard	XM_005251934		Approved	FLJ38464, FLJ16786	uc004bnx.1	Q5IJ48	OTTHUMG00000020638	ENST00000373631.3:c.2224G>T	chr9.hg19:g.126133645G>T	ENSP00000362734:p.Gly742Trp	124.0	0.0		143.0	6.0	NM_173689	A2A3N4|Q0QD46|Q5JS41|Q5JS43|Q6ZTA9|Q6ZWI6	Missense_Mutation	SNP	ENST00000373631.3	hg19	CCDS6852.2	.	.	.	.	.	.	.	.	.	.	.	18.97	3.735415	0.69189	.	.	ENSG00000148204	ENST00000359999;ENST00000373631;ENST00000373629	T;T;T	0.79940	-1.32;-1.32;-1.32	4.92	3.81	0.43845	Concanavalin A-like lectin/glucanase (1);Laminin G domain (1);	0.341780	0.21813	N	0.068728	D	0.90501	0.7024	M	0.89414	3.03	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.993;0.998	D	0.92209	0.5774	10	0.87932	D	0	.	14.1206	0.65184	0.0866:0.0:0.9134:0.0	.	742;742	Q5IJ48;Q5IJ48-2	CRUM2_HUMAN;.	W	742;742;410	ENSP00000353092:G742W;ENSP00000362734:G742W;ENSP00000362732:G410W	ENSP00000353092:G742W	G	+	1	0	CRB2	125173466	0.998000	0.40836	0.994000	0.49952	0.959000	0.62525	2.542000	0.45744	2.276000	0.75962	0.563000	0.77884	GGG	.	.		0.692	CRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053990.3	NM_173689		T	126133645	G	T	126133645	3	4	255	1	0	0	0	0	1	0	0	0	3851	1232	43	3	2254	3	CRB2	9	126133645	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	570919	126133645	15079786	356	35701										
WDR38	401551	hgsc.bcm.edu	37	chr9	127619818	127619818	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccacacctgtgccttcacccCagatgggaaaatcttagtgt	8	13	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:127619818C>A	ENST00000373574.1	+	9	910	c.854C>A	c.(853-855)cCa>cAa	p.P285Q		NM_001045476.1|NM_001276374.1	NP_001038941.1|NP_001263303.1	Q5JTN6	WDR38_HUMAN	WD repeat domain 38	285					hematopoietic progenitor cell differentiation (GO:0002244)					breast(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	8						GCCTTCACCCCAGATGGGAAA	0.552																																					p.P286Q		Atlas-SNP	.											.	WDR38	21	.	0			c.C857A						.						82	91	88					9																	127619818		1999	4170	6169	SO:0001583	missense	401551	exon9			TCACCCCAGATGG		CCDS43876.1, CCDS75898.1, CCDS75899.1	9q33.3	2013-01-09			ENSG00000136918	ENSG00000136918		"WD repeat domain containing"	23745	protein-coding gene	gene with protein product							Standard	NM_001276375		Approved		uc011lzo.3	Q5JTN6	OTTHUMG00000020664	ENST00000373574.1:c.854C>A	chr9.hg19:g.127619818C>A	ENSP00000362677:p.Pro285Gln	125.0	0.0		108.0	5.0	NM_001276374	A0PK24	Missense_Mutation	SNP	ENST00000373574.1	hg19	CCDS43876.1	.	.	.	.	.	.	.	.	.	.	C	14.23	2.474754	0.43942	.	.	ENSG00000136918	ENST00000373574	D	0.84944	-1.92	5.01	2.12	0.27331	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.419228	0.21641	N	0.071336	D	0.89336	0.6686	M	0.81239	2.535	0.31405	N	0.676203	P;P;P;P	0.52577	0.954;0.906;0.906;0.954	P;P;P;P	0.57720	0.826;0.546;0.546;0.826	D	0.87407	0.2373	10	0.66056	D	0.02	.	8.6557	0.34062	0.0:0.6297:0.2894:0.0809	.	285;286;275;285	B9EK65;B7ZW23;B7ZW24;Q5JTN6	.;.;.;WDR38_HUMAN	Q	285	ENSP00000362677:P285Q	ENSP00000362677:P285Q	P	+	2	0	WDR38	126659639	0.082000	0.21442	0.468000	0.27192	0.506000	0.33950	1.737000	0.38197	0.377000	0.24735	-0.165000	0.13383	CCA	.	.		0.552	WDR38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054048.1	NM_001045476		A	127619818	C	A	127619818	3	1	255	1	0	0	0	0	1	0	0	0	17307	594	21	3	888	3	WDR38	9	127619818	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1486173	127619818	13593613	357	35702										
CIZ1	25792	hgsc.bcm.edu	37	chr9	130947925	130947925	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttcatggggaccccaacaggAggaggtcccagcaaggactg	14	11	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:130947925A>G	ENST00000393608.1	-	5	691	c.489T>C	c.(487-489)ccT>ccC	p.P163P	CIZ1_ENST00000541172.1_Silent_p.P62P|CIZ1_ENST00000372954.1_Silent_p.P139P|CIZ1_ENST00000325721.8_Silent_p.P139P|CIZ1_ENST00000476727.2_5'UTR|CIZ1_ENST00000372948.3_Silent_p.P163P|CIZ1_ENST00000538431.1_Silent_p.P163P|CIZ1_ENST00000357558.5_Silent_p.P163P|CIZ1_ENST00000277465.4_Silent_p.P163P|CIZ1_ENST00000372938.5_Silent_p.P163P	NM_012127.2	NP_036259.2	Q9ULV3	CIZ1_HUMAN	CDKN1A interacting zinc finger protein 1	163					maintenance of protein location in nucleus (GO:0051457)|positive regulation of DNA-dependent DNA replication initiation (GO:0032298)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|liver(1)|lung(9)|ovary(3)|prostate(2)|urinary_tract(2)	35						CCCCAACAGGAGGAGGTCCCA	0.612																																					p.P193P		Atlas-SNP	.											.	CIZ1	75	.	0			c.T579C						.						65	65	65					9																	130947925		2203	4300	6503	SO:0001819	synonymous_variant	25792	exon5			AACAGGAGGAGGT	AB030835	CCDS6894.1, CCDS48033.1, CCDS48034.1, CCDS75910.1	9q34.1	2012-10-05			ENSG00000148337	ENSG00000148337			16744	protein-coding gene	gene with protein product		611420				10529385	Standard	NM_001131015		Approved	LSFR1, ZNF356	uc011mas.2	Q9ULV3	OTTHUMG00000020735	ENST00000393608.1:c.489T>C	chr9.hg19:g.130947925A>G		125.0	0.0		119.0	5.0	NM_001257975	A8K9J8|B4E131|B7ZAS8|Q5SYW3|Q5SYW5|Q8WU72|Q9H868|Q9NYM8|Q9UHK4|Q9Y3F9|Q9Y3G0	Silent	SNP	ENST00000393608.1	hg19	CCDS6894.1																																																																																			.	.		0.612	CIZ1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054399.1	NM_012127		G	130947925	A	G	130947925	2	3	255	1	0	0	0	0	0	0	0	1	3443	291	11	2		2	CIZ1	9	130947925	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	3328107	130947925	10265506	358	35703										
GLE1	2733	hgsc.bcm.edu	37	chr9	131277857	131277857	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tatggtacttcagtcctcacGggggatcaaagtggaaggct	13	8	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:131277857G>T	ENST00000309971.4	+	3	477	c.371G>T	c.(370-372)cGg>cTg	p.R124L	GLE1_ENST00000539582.1_5'UTR|GLE1_ENST00000372770.4_Missense_Mutation_p.R124L	NM_001003722.1	NP_001003722.1	Q53GS7	GLE1_HUMAN	GLE1 RNA export mediator	124					mRNA export from nucleus (GO:0006406)|poly(A)+ mRNA export from nucleus (GO:0016973)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)|nuclear pore (GO:0005643)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	16						CAGTCCTCACGGGGGATCAAA	0.428																																					p.R124L		Atlas-SNP	.											.	GLE1	42	.	0			c.G371T						.						68	58	61					9																	131277857		2203	4300	6503	SO:0001583	missense	2733	exon3			CCTCACGGGGGAT	AF058922	CCDS6904.1, CCDS35154.1	9q34.13	2014-09-17	2013-06-18	2007-10-04	ENSG00000119392	ENSG00000119392			4315	protein-coding gene	gene with protein product		603371	"GLE1 (yeast homolog)-like, RNA export mediator", "GLE1 RNA export mediator-like (yeast)", "GLE1 RNA export mediator (yeast)", "lethal congenital contracture syndrome 1", "GLE1 RNA export mediator homolog (yeast)"	GLE1L, LCCS1		9618489, 18204449	Standard	NM_001499		Approved	hGLE1	uc004bvj.3	Q53GS7	OTTHUMG00000020749	ENST00000309971.4:c.371G>T	chr9.hg19:g.131277857G>T	ENSP00000308622:p.Arg124Leu	93.0	0.0		51.0	4.0	NM_001499	O75458|Q53GT9|Q5VVU1|Q8NCP6|Q9UFL6	Missense_Mutation	SNP	ENST00000309971.4	hg19	CCDS35154.1	.	.	.	.	.	.	.	.	.	.	G	18.00	3.524413	0.64747	.	.	ENSG00000119392	ENST00000309971;ENST00000372770	T;T	0.68903	-0.36;0.05	5.16	4.26	0.50523	.	0.178384	0.47455	D	0.000240	T	0.62853	0.2462	L	0.58101	1.795	0.58432	D	0.999999	P;P	0.44627	0.752;0.839	B;P	0.45276	0.283;0.475	T	0.59500	-0.7443	10	0.29301	T	0.29	-10.662	8.2898	0.31950	0.1817:0.0:0.8183:0.0	.	124;124	Q53GS7;Q53GS7-2	GLE1_HUMAN;.	L	124	ENSP00000308622:R124L;ENSP00000361856:R124L	ENSP00000308622:R124L	R	+	2	0	GLE1	130317678	1.000000	0.71417	0.904000	0.35570	0.879000	0.50718	2.922000	0.48860	1.185000	0.42971	0.313000	0.20887	CGG	.	.		0.428	GLE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054456.1	NM_001003722		T	131277857	G	T	131277857	3	4	255	1	0	0	0	0	1	0	0	0	6443	1116	39	1	381	1	GLE1	9	131277857	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	329932	131277857	9935574	359	35704										
GPR107	57720	hgsc.bcm.edu	37	chr9	132897357	132897357	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gaaagtcaagaaggtgaccaAcggctccgtggagccccagg	14	11	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:132897357A>G	ENST00000372406.1	+	20	2267	c.1760A>G	c.(1759-1761)aAc>aGc	p.N587S	GPR107_ENST00000372410.3_Missense_Mutation_p.N558S|GPR107_ENST00000347136.6_Missense_Mutation_p.N539S	NM_001136557.1	NP_001130029.1	Q5VW38	GP107_HUMAN	G protein-coupled receptor 107	587						integral component of membrane (GO:0016021)				endometrium(2)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	11		Ovarian(14;0.000531)				AAGGTGACCAACGGCTCCGTG	0.493																																					p.N587S		Atlas-SNP	.											.	GPR107	30	.	0			c.A1760G						.						91	81	85					9																	132897357		2203	4300	6503	SO:0001583	missense	57720	exon20			TGACCAACGGCTC	AF376725	CCDS35162.1, CCDS48041.1, CCDS48042.1	9q34.2	2014-01-30			ENSG00000148358	ENSG00000148358		"GPCR / Unclassified : 7TM orphan receptors"	17830	protein-coding gene	gene with protein product							Standard	NM_020960		Approved	KIAA1624, RP11-88G17, FLJ20998, LUSTR1	uc004bzd.2	Q5VW38	OTTHUMG00000020804	ENST00000372406.1:c.1760A>G	chr9.hg19:g.132897357A>G	ENSP00000361483:p.Asn587Ser	46.0	0.0		71.0	5.0	NM_001136557	A6NJ53|Q2TB81|Q5JPA3|Q5VW39|Q96T26|Q9H658|Q9HCE8	Missense_Mutation	SNP	ENST00000372406.1	hg19	CCDS48041.1	.	.	.	.	.	.	.	.	.	.	A	17.23	3.336884	0.60963	.	.	ENSG00000148358	ENST00000372406;ENST00000347136;ENST00000372410	T;T;T	0.29917	1.79;1.55;1.75	5.34	4.18	0.49190	.	0.062767	0.64402	D	0.000011	T	0.44705	0.1306	L	0.50333	1.59	0.46279	D	0.998964	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.83275	0.996;0.994;0.994	T	0.19353	-1.0308	10	0.27785	T	0.31	-31.4048	9.323	0.37975	0.84:0.0:0.0:0.16	.	558;587;539	G5E994;Q5VW38;Q5VW38-2	.;GP107_HUMAN;.	S	587;539;558	ENSP00000361483:N587S;ENSP00000336988:N539S;ENSP00000361487:N558S	ENSP00000336988:N539S	N	+	2	0	GPR107	131937178	1.000000	0.71417	0.845000	0.33349	0.985000	0.73830	6.669000	0.74462	0.832000	0.34804	0.379000	0.24179	AAC	.	.		0.493	GPR107-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054643.2			G	132897357	A	G	132897357	3	3	255	1	0	0	0	0	1	0	0	0	6631	43	2	2	1838	2	GPR107	9	132897357	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	1619500	132897357	8316074	360	35705										
TTF1	7270	hgsc.bcm.edu	37	chr9	135277238	135277238	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgtttttataagcaggtgctGgtattcctgcagtttcacca	9	8	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:135277238G>T	ENST00000334270.2	-	2	1010	c.971C>A	c.(970-972)cCa>cAa	p.P324Q		NM_001205296.1|NM_007344.3	NP_001192225.1|NP_031370.2	Q15361	TTF1_HUMAN	transcription termination factor, RNA polymerase I	324					chromatin remodeling (GO:0006338)|DNA-templated transcription, termination (GO:0006353)|gene expression (GO:0010467)|negative regulation of DNA replication (GO:0008156)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(2)|pancreas(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;4.25e-06)|Epithelial(140;9.09e-05)		AGCAGGTGCTGGTATTCCTGC	0.502																																					p.P324Q		Atlas-SNP	.											.	TTF1	82	.	0			c.C971A						.						102	101	101					9																	135277238		2203	4300	6503	SO:0001583	missense	7270	exon2			GGTGCTGGTATTC	BC050734	CCDS6948.1, CCDS75925.1	9q34.3	2008-02-05			ENSG00000125482	ENSG00000125482			12397	protein-coding gene	gene with protein product		600777				7597036	Standard	NM_007344		Approved		uc004cbl.3	Q15361	OTTHUMG00000020836	ENST00000334270.2:c.971C>A	chr9.hg19:g.135277238G>T	ENSP00000333920:p.Pro324Gln	69.0	0.0		98.0	4.0	NM_007344	A1L160|Q4VXF3|Q58EY2|Q6P5T5	Missense_Mutation	SNP	ENST00000334270.2	hg19	CCDS6948.1	.	.	.	.	.	.	.	.	.	.	G	8.526	0.869911	0.17322	.	.	ENSG00000125482	ENST00000334270;ENST00000245588	T	0.09911	2.93	2.64	1.56	0.23342	.	.	.	.	.	T	0.07683	0.0193	L	0.36672	1.1	0.09310	N	1	P	0.48694	0.914	B	0.37731	0.257	T	0.29701	-1.0003	9	0.72032	D	0.01	.	5.9584	0.19286	0.0:0.0:0.6921:0.3079	.	324	Q15361	TTF1_HUMAN	Q	324	ENSP00000333920:P324Q	ENSP00000245588:P324Q	P	-	2	0	TTF1	134267059	0.000000	0.05858	0.005000	0.12908	0.010000	0.07245	0.192000	0.17096	1.158000	0.42547	0.467000	0.42956	CCA	.	.		0.502	TTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054784.2	NM_007344		T	135277238	G	T	135277238	3	4	255	1	0	0	0	0	1	0	0	0	16733	1348	47	3	1786	3	TTF1	9	135277238	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	2379881	135277238	5936193	361	35706										
KCNT1	402381	hgsc.bcm.edu	37	chr9	138594134	138594134	+	5'Flank	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cctgacggggcgcggaccccGgggggcgtctgccgggaggc	21	14	1	1	rs139034501	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:138594134G>T	ENST00000298466.5	-	0	0				SOHLH1_ENST00000425225.1_5'Flank|KCNT1_ENST00000487664.1_Silent_p.P10P|KCNT1_ENST00000371757.2_Silent_p.P10P|KCNT1_ENST00000298480.5_Silent_p.P10P	NM_001012415.2	NP_001012415	Q5JUK2	SOLH1_HUMAN	spermatogenesis and oogenesis specific basic helix-loop-helix 1						oogenesis (GO:0048477)|ovarian follicle development (GO:0001541)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(5)|prostate(1)	12		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.66e-07)|Epithelial(140;1.11e-06)|all cancers(34;6.45e-05)		cgcggaccccggggggcgtct	0.726																																					p.P10P		Atlas-SNP	.											.	KCNT1	139	.	0			c.G30T						.						11	15	14					9																	138594134		2150	4219	6369	SO:0001631	upstream_gene_variant	57582	exon1			GACCCCGGGGGGC	BC031861	CCDS35174.1, CCDS48054.1	9q34.3	2013-05-21	2006-03-16	2006-03-16	ENSG00000165643	ENSG00000165643		"Basic helix-loop-helix proteins"	27845	protein-coding gene	gene with protein product	"spermatogenesis associated 27"	610224	"chromosome 9 open reading frame 157"	C9orf157		12477932	Standard	NM_001012415		Approved	NOHLH, TEB2, bA100C15.3, bHLHe80, SPATA27	uc010nbe.3	Q5JUK2	OTTHUMG00000020915		chr9.hg19:g.138594134G>T	Exception_encountered	96.0	0.0		95.0	4.0	NM_001272003	C9JG81|Q5EE14|Q5EGC2|Q8NEE3	Silent	SNP	ENST00000298466.5	hg19	CCDS35174.1																																																																																			.	G|0.996;A|0.004		0.726	SOHLH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055018.2	NM_001012415		T	138594134	G	T	138594134	1	4	255	0	1	0	0	0	0	0	0	0	8100	1103	39	1		1	KCNT1	9	138594134	5'Flank	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	3316896	138594134	2619297	362	35707										
FBXW5	54461	hgsc.bcm.edu	37	chr9	139836076	139836076	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cgaagaaggcatcggagcccCggccctcacccagcacgggc	13	17	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:139836076C>A	ENST00000325285.3	-	7	1236	c.1157G>T	c.(1156-1158)cGg>cTg	p.R386L	FBXW5_ENST00000483559.1_5'UTR	NM_018998.3	NP_061871.1	Q969U6	FBXW5_HUMAN	F-box and WD repeat domain containing 5	386					centrosome duplication (GO:0051298)|mitotic nuclear division (GO:0007067)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	protein kinase binding (GO:0019901)			breast(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	12	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.19)	OV - Ovarian serous cystadenocarcinoma(145;7.8e-06)|Epithelial(140;0.000106)		ATCGGAGCCCCGGCCCTCACC	0.647																																					p.R386L		Atlas-SNP	.											.	FBXW5	36	.	0			c.G1157T						.						66	54	58					9																	139836076		2187	4289	6476	SO:0001583	missense	54461	exon7			GAGCCCCGGCCCT	BC014130	CCDS7014.1	9q34.3	2013-01-09	2007-02-08		ENSG00000159069	ENSG00000159069		"F-boxes / WD-40 domains", "WD repeat domain containing"	13613	protein-coding gene	gene with protein product		609072	"F-box and WD-40 domain protein 5"				Standard	NM_018998		Approved	DKFZP434B205, MGC20962, Fbw5	uc004cjx.3	Q969U6	OTTHUMG00000020967	ENST00000325285.3:c.1157G>T	chr9.hg19:g.139836076C>A	ENSP00000313034:p.Arg386Leu	97.0	0.0		124.0	5.0	NM_018998	B2RDZ6|Q59ET5|Q5SPZ8|Q5SPZ9|Q5SQ00|Q5SQ02|Q5SQ03|Q5SQ04|Q8WY79|Q96GJ6|Q9BSU8|Q9H6A8|Q9HBQ6|Q9NSZ3	Missense_Mutation	SNP	ENST00000325285.3	hg19	CCDS7014.1	.	.	.	.	.	.	.	.	.	.	C	15.66	2.898965	0.52227	.	.	ENSG00000159069	ENST00000325285;ENST00000433269	T;T	0.78707	-1.2;1.48	4.61	3.64	0.41730	Soluble quinoprotein glucose/sorbosone dehydrogenase (1);	0.058160	0.64402	D	0.000003	T	0.78027	0.4219	L	0.60455	1.87	0.53688	D	0.999977	D;P	0.57899	0.981;0.945	P;P	0.54815	0.761;0.55	T	0.73968	-0.3815	10	0.25106	T	0.35	-5.1164	7.9241	0.29863	0.0:0.7183:0.1497:0.132	.	251;386	Q59ET5;Q969U6	.;FBXW5_HUMAN	L	386;221	ENSP00000313034:R386L;ENSP00000409102:R221L	ENSP00000313034:R386L	R	-	2	0	FBXW5	138955897	0.989000	0.36119	1.000000	0.80357	0.466000	0.32739	2.646000	0.46630	2.286000	0.76751	0.561000	0.74099	CGG	.	.		0.647	FBXW5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055227.1	NM_018998		A	139836076	C	A	139836076	3	1	255	1	0	0	0	0	1	0	0	0	5776	652	23	1	555	1	FBXW5	9	139836076	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1241942	139836076	1377355	363	35708										
NDOR1	27158	hgsc.bcm.edu	37	chr9	140109380	140109380	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgtctatccctccatgagctGgagcgggagaagctgctgga	14	10	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:140109380G>A	ENST00000344894.5	+	8	1058	c.975G>A	c.(973-975)ctG>ctA	p.L325L	NDOR1_ENST00000371521.4_Silent_p.L325L|NDOR1_ENST00000427047.2_Silent_p.L291L|NDOR1_ENST00000458322.2_Silent_p.L325L	NM_001144028.1|NM_014434.2	NP_001137500.1|NP_055249.1			NADPH dependent diflavin oxidoreductase 1											breast(1)|endometrium(5)|large_intestine(1)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	15	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		TCCATGAGCTGGAGCGGGAGA	0.622																																					p.L325L		Atlas-SNP	.											.	NDOR1	71	.	0			c.G975A						.						44	48	47					9																	140109380		2203	4300	6503	SO:0001819	synonymous_variant	27158	exon8			TGAGCTGGAGCGG	BC015735	CCDS7036.1, CCDS48061.1, CCDS48062.1, CCDS48063.1	9q34.3	2008-02-05			ENSG00000188566	ENSG00000188566			29838	protein-coding gene	gene with protein product	"NADPH dependent FMN and FAD containing oxidoreductase"	606073				10625700, 12631275	Standard	XM_005266066		Approved	NR1, bA350O14.9	uc004clx.3	Q9UHB4	OTTHUMG00000020986	ENST00000344894.5:c.975G>A	chr9.hg19:g.140109380G>A		56.0	0.0		98.0	4.0	NM_001144026		Silent	SNP	ENST00000344894.5	hg19	CCDS7036.1																																																																																			.	.		0.622	NDOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254704.1	NM_014434		A	140109380	G	A	140109380	2	1	255	1	0	0	0	0	0	0	0	1	10258	1335	47	3		3	NDOR1	9	140109380	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	273304	140109380	1104051	364	35709										
C9orf167	54863	hgsc.bcm.edu	37	chr9	140173890	140173890	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggcgcggcgcgtggccgacgTggtggcgcgggccgaagcgg	23	12	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:140173890T>C	ENST00000357503.2	+	2	945	c.749T>C	c.(748-750)gTg>gCg	p.V250A		NM_017723.2	NP_060193.2	Q9NXH8	TOR4A_HUMAN	torsin family 4, member A	250					chaperone mediated protein folding requiring cofactor (GO:0051085)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)										GTGGCCGACGTGGTGGCGCGG	0.726																																					p.V250A		Atlas-SNP	.											.	.	.	.	0			c.T749C						.						6	7	6					9																	140173890		1995	3865	5860	SO:0001583	missense	54863	exon2			CCGACGTGGTGGC	AK023361	CCDS7041.1	9q34.3	2012-04-03	2012-04-03	2012-04-03	ENSG00000198113	ENSG00000198113			25981	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 167"	C9orf167			Standard	NM_017723		Approved	FLJ20245	uc004cmn.3	Q9NXH8	OTTHUMG00000131779	ENST00000357503.2:c.749T>C	chr9.hg19:g.140173890T>C	ENSP00000350102:p.Val250Ala	50.0	0.0		62.0	4.0	NM_017723	A2BFA4	Missense_Mutation	SNP	ENST00000357503.2	hg19	CCDS7041.1	.	.	.	.	.	.	.	.	.	.	T	13.50	2.254599	0.39896	.	.	ENSG00000198113	ENST00000357503	T	0.48201	0.82	4.95	4.95	0.65309	ATPase, AAA+ type, core (1);	0.139529	0.64402	D	0.000009	T	0.48804	0.1520	L	0.56769	1.78	0.36011	D	0.838041	P	0.48162	0.906	P	0.49085	0.6	T	0.53899	-0.8373	10	0.07990	T	0.79	-15.8208	13.4891	0.61384	0.0:0.0:0.0:1.0	.	250	Q9NXH8	CI167_HUMAN	A	250	ENSP00000350102:V250A	ENSP00000350102:V250A	V	+	2	0	C9orf167	139293711	0.983000	0.35010	0.884000	0.34674	0.005000	0.04900	2.128000	0.42045	1.841000	0.53522	0.529000	0.55759	GTG	.	.		0.726	TOR4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254711.1	NM_017723		C	140173890	T	C	140173890	3	2	255	1	0	0	0	0	1	0	0	0	2470	1696	59	2	751	2	C9orf167	9	140173890	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	64510	140173890	1039541	365	35710										
PITRM1	10531	hgsc.bcm.edu	37	chr10	3208566	3208566	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tccatgggagtagtacggaaCtgcacgctagggaaggagaa	15	7	0	1	rs33996077|rs114690446		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:3208566C>T	ENST00000224949.4	-	4	307	c.273G>A	c.(271-273)caG>caA	p.Q91Q	PITRM1-AS1_ENST00000598280.1_RNA|PITRM1-AS1_ENST00000601046.1_RNA|PITRM1_ENST00000380989.2_Silent_p.Q91Q|PITRM1_ENST00000451104.2_Silent_p.Q59Q			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	91					positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						TAGTACGGAACTGCACGCTAG	0.493																																					p.Q91Q		Atlas-SNP	.											PITRM1,colon,carcinoma,-1,3	PITRM1	109	.	0			c.G273A						.						104	104	104					10																	3208566		2070	4185	6255	SO:0001819	synonymous_variant	10531	exon4			ACGGAACTGCACG	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"PreP peptidasome"		"pitrilysin metalloproteinase 1"			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.273G>A	chr10.hg19:g.3208566C>T		26.0	1.0		54.0	6.0	NM_014889	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Silent	SNP	ENST00000224949.4	hg19	CCDS59208.1																																																																																			.	.		0.493	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2			T	3208566	C	T	3208566	2	4	255	1	0	0	0	0	0	0	0	1	11962	564	20	3		3	PITRM1	10	3208566	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10		3208566	132326181	366	35711										
FAM188A	80013	hgsc.bcm.edu	37	chr10	15883432	15883432	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aaatatatcttacaagaatgTtccacttggcaactagactc	5	9	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:15883432T>C	ENST00000277632.3	-	4	622	c.402A>G	c.(400-402)gaA>gaG	p.E134E	FAM188A_ENST00000477891.1_5'UTR	NM_024948.2	NP_079224.1	Q9H8M7	F188A_HUMAN	family with sequence similarity 188, member A	134					apoptotic process (GO:0006915)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(2)|endometrium(5)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	22						TACAAGAATGTTCCACTTGGC	0.318																																					p.E134E	Pancreas(159;946 1953 2111 4475 22008)	Atlas-SNP	.											.	FAM188A	44	.	0			c.A402G						.						68	66	67					10																	15883432		2203	4300	6503	SO:0001819	synonymous_variant	80013	exon4			AGAATGTTCCACT	AK023459	CCDS7110.1	10p13	2009-07-14	2009-07-14	2009-07-14	ENSG00000148481	ENSG00000148481			23578	protein-coding gene	gene with protein product	"caspase recruitment domain containing pro-apoptotic protein", "CARD-containing protein"	611649	"chromosome 10 open reading frame 97"	C10orf97		12054670, 17652099	Standard	XM_005252600		Approved	FLJ13397, CARP, my042, DERP5	uc001iod.1	Q9H8M7	OTTHUMG00000017734	ENST00000277632.3:c.402A>G	chr10.hg19:g.15883432T>C		71.0	0.0		90.0	6.0	NM_024948	Q5SZ68|Q5SZ69|Q5SZ70|Q6IA40|Q6P7P0|Q7Z2S1|Q8WUF1|Q9H3I4	Silent	SNP	ENST00000277632.3	hg19	CCDS7110.1																																																																																			.	.		0.318	FAM188A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046990.2	NM_024948		C	15883432	T	C	15883432	2	2	255	1	0	0	0	0	0	0	0	1	5519	1722	60	2		2	FAM188A	10	15883432	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	12674866	15883432	119651315	367	35712										
CUBN	8029	hgsc.bcm.edu	37	chr10	17142090	17142090	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gaaaatagagagcattgtcaCtgctgaggagttcatgaggg	14	5	2	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:17142090C>G	ENST00000377833.4	-	14	1744	c.1679G>C	c.(1678-1680)aGt>aCt	p.S560T		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	560	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	AGCATTGTCACTGCTGAGGAG	0.428																																					p.S560T		Atlas-SNP	.											CUBN,NS,carcinoma,0,1	CUBN	515	.	0			c.G1679C						.						115	115	115					10																	17142090		2203	4300	6503	SO:0001583	missense	8029	exon14			TTGTCACTGCTGA	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.1679G>C	chr10.hg19:g.17142090C>G	ENSP00000367064:p.Ser560Thr	205.0	0.0		264.0	116.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	C	17.35	3.366420	0.61513	.	.	ENSG00000107611	ENST00000377833	T	0.60672	0.17	5.51	5.51	0.81932	CUB (5);	0.000000	0.50627	D	0.000111	T	0.57651	0.2068	L	0.41961	1.31	0.80722	D	1	P	0.38827	0.649	P	0.46940	0.532	T	0.50398	-0.8833	10	0.19590	T	0.45	.	14.894	0.70630	0.0:0.7463:0.2537:0.0	.	560	O60494	CUBN_HUMAN	T	560	ENSP00000367064:S560T	ENSP00000367064:S560T	S	-	2	0	CUBN	17182096	1.000000	0.71417	1.000000	0.80357	0.755000	0.42902	3.996000	0.57009	2.586000	0.87340	0.650000	0.86243	AGT	.	.		0.428	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		G	17142090	C	G	17142090	3	3	255	1	0	0	0	0	1	0	0	0	4053	565	20	4	9408	4	CUBN	10	17142090	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1258658	17142090	118392657	368	35713										
CAMK2G	818	hgsc.bcm.edu	37	chr10	75607747	75607747	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccggctctctggtccttacaTcataggctccagccttgatc	8	15	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:75607747T>C	ENST00000351293.3	-	9	752	c.695A>G	c.(694-696)gAt>gGt	p.D232G	CAMK2G_ENST00000423381.1_Splice_Site_p.D232G|CAMK2G_ENST00000372765.1_Splice_Site_p.D232G|CAMK2G_ENST00000444854.2_Intron|CAMK2G_ENST00000394762.2_Splice_Site_p.D232G|RP11-574K11.8_ENST00000446730.2_RNA|CAMK2G_ENST00000322635.3_Splice_Site_p.D232G|CAMK2G_ENST00000322680.3_Splice_Site_p.D232G|CAMK2G_ENST00000472912.1_5'UTR|CAMK2G_ENST00000305762.7_Splice_Site_p.D232G	NM_001222.3|NM_172173.2	NP_001213.2|NP_751913.1	Q13555	KCC2G_HUMAN	calcium/calmodulin-dependent protein kinase II gamma	232	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				calcium ion transport (GO:0006816)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|dephosphorylation (GO:0016311)|G1/S transition of mitotic cell cycle (GO:0000082)|insulin secretion (GO:0030073)|interferon-gamma-mediated signaling pathway (GO:0060333)|nervous system development (GO:0007399)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of calcium ion transport (GO:0051924)|regulation of relaxation of cardiac muscle (GO:1901897)|regulation of skeletal muscle adaptation (GO:0014733)|synaptic transmission (GO:0007268)	calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-dependent protein serine/threonine phosphatase activity (GO:0004723)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|protein homodimerization activity (GO:0042803)			kidney(2)|large_intestine(2)|lung(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	15	Prostate(51;0.0112)				Bosutinib(DB06616)	GGTCCTTACATCATAGGCTCC	0.567																																					p.D232G		Atlas-SNP	.											.	CAMK2G	79	.	0			c.A695G						.						97	90	92					10																	75607747		2203	4300	6503	SO:0001630	splice_region_variant	818	exon9			CTTACATCATAGG	U81554	CCDS7336.1, CCDS7337.1, CCDS7338.1, CCDS73153.1	10q22	2008-10-30	2008-10-30		ENSG00000148660	ENSG00000148660			1463	protein-coding gene	gene with protein product		602123	"calcium/calmodulin-dependent protein kinase (CaM kinase) II gamma"	CAMKG		8287681	Standard	NM_001204492		Approved		uc001jvm.2	Q13555	OTTHUMG00000018492	ENST00000351293.3:c.696+1A>G	chr10.hg19:g.75607747T>C		70.0	0.0		102.0	5.0	NM_172170	O00561|O15378|Q13279|Q13282|Q13556|Q5SQZ3|Q5SQZ4|Q5SWX4|Q7KYX5|Q8N4I3|Q8NIA4	Missense_Mutation	SNP	ENST00000351293.3	hg19	CCDS7336.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.90|17.90	3.502198|3.502198	0.64298|0.64298	.|.	.|.	ENSG00000148660|ENSG00000148660	ENST00000351293;ENST00000322635;ENST00000423381;ENST00000394763;ENST00000322680;ENST00000394762;ENST00000433289;ENST00000305762;ENST00000372765|ENST00000441192	T;T;T;T;T;T;T;T|.	0.65916|.	-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18|.	5.62|5.62	5.62|5.62	0.85841|0.85841	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.063315|.	0.64402|.	D|.	0.000009|.	T|.	0.54062|.	0.1835|.	N|N	0.25380|0.25380	0.74|0.74	0.80722|0.80722	D|D	1|1	B;B;B;B;B;B;B;B|.	0.32188|.	0.035;0.022;0.028;0.007;0.011;0.001;0.359;0.002|.	B;B;B;B;B;B;B;B|.	0.39258|.	0.203;0.105;0.129;0.01;0.071;0.013;0.295;0.043|.	T|.	0.50825|.	-0.8782|.	10|.	0.87932|.	D|.	0|.	.|.	15.8199|15.8199	0.78631|0.78631	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	224;232;232;232;232;232;232;232|.	B3KY86;Q13555-4;Q13555-6;Q13555-10;A8K6N9;Q13555;Q13555-5;Q13555-8|.	.;.;.;.;.;KCC2G_HUMAN;.;.|.	G|W	232;232;232;232;232;232;167;232;232|10	ENSP00000277853:D232G;ENSP00000315599:D232G;ENSP00000410298:D232G;ENSP00000319060:D232G;ENSP00000378243:D232G;ENSP00000393784:D167G;ENSP00000307082:D232G;ENSP00000361851:D232G|.	ENSP00000307082:D232G|.	D|X	-|-	2|3	0|0	CAMK2G|CAMK2G	75277753|75277753	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	8.040000|8.040000	0.89188|0.89188	2.133000|2.133000	0.65898|0.65898	0.533000|0.533000	0.62120|0.62120	GAT|TGA	.	.		0.567	CAMK2G-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048715.1	NM_172169	Missense_Mutation	C	75607747	T	C	75607747	5	2	255	1	0	0	0	0	0	0	1	0	2604	1449	50	2	1127	2	CAMK2G	10	75607747	Splice_Site	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	58465657	75607747	59927000	369	35714										
MYST4	23522	hgsc.bcm.edu	37	chr10	76790465	76790465	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cctgcacggactttaacgatGcaaagaggcatgaacatgag	11	9	0	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:76790465G>A	ENST00000287239.4	+	18	6372	c.5883G>A	c.(5881-5883)atG>atA	p.M1961I	KAT6B_ENST00000372714.1_Missense_Mutation_p.M1669I|KAT6B_ENST00000372724.1_Missense_Mutation_p.M1669I|KAT6B_ENST00000372711.1_Missense_Mutation_p.M1778I|KAT6B_ENST00000372725.1_Missense_Mutation_p.M1669I	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	1961	Interaction with RUNX1 and RUNX2.|Met-rich.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										CTTTAACGATGCAAAGAGGCA	0.527																																					p.M1961I		Atlas-SNP	.											.	.	.	.	0			c.G5883A						.						150	142	145					10																	76790465		2203	4300	6503	SO:0001583	missense	23522	exon18			AACGATGCAAAGA	AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	17582	protein-coding gene	gene with protein product	"MOZ-related factor"	605880	"MYST histone acetyltransferase (monocytic leukemia) 4"	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.5883G>A	chr10.hg19:g.76790465G>A	ENSP00000287239:p.Met1961Ile	48.0	0.0		84.0	4.0	NM_012330	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Missense_Mutation	SNP	ENST00000287239.4	hg19	CCDS7345.1	.	.	.	.	.	.	.	.	.	.	G	12.54	1.969524	0.34754	.	.	ENSG00000156650	ENST00000372725;ENST00000372724;ENST00000287239;ENST00000372714;ENST00000372711	T;T;T;T;T	0.75938	-0.97;-0.97;-0.98;-0.97;-0.97	5.69	5.69	0.88448	.	0.000000	0.64402	D	0.000009	T	0.72326	0.3446	N	0.14661	0.345	0.48571	D	0.99967	P;P;B	0.44281	0.831;0.794;0.447	P;B;B	0.54664	0.758;0.406;0.212	T	0.75961	-0.3133	10	0.62326	D	0.03	-10.6573	15.3019	0.73958	0.0:0.1395:0.8605:0.0	.	1778;1669;1961	Q8WYB5-2;Q8WYB5-3;Q8WYB5	.;.;KAT6B_HUMAN	I	1669;1669;1961;1669;1778	ENSP00000361810:M1669I;ENSP00000361809:M1669I;ENSP00000287239:M1961I;ENSP00000361799:M1669I;ENSP00000361796:M1778I	ENSP00000287239:M1961I	M	+	3	0	KAT6B	76460471	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.328000	0.79160	2.682000	0.91365	0.563000	0.77884	ATG	.	.		0.527	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330		A	76790465	G	A	76790465	3	1	255	1	0	0	0	0	1	0	0	0	10114	1319	46	3	5945	3	MYST4	10	76790465	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	1182718	76790465	58744282	370	35715										
COMTD1	118881	hgsc.bcm.edu	37	chr10	76995129	76995129	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cctgcggctgctccagggtcAgctgcgtgaaaggagagggt	17	10	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:76995129A>G	ENST00000372538.3	-	3	306	c.224T>C	c.(223-225)cTg>cCg	p.L75P	COMTD1_ENST00000460899.1_5'UTR	NM_144589.2	NP_653190.2	Q86VU5	CMTD1_HUMAN	catechol-O-methyltransferase domain containing 1	75						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	O-methyltransferase activity (GO:0008171)			central_nervous_system(1)|large_intestine(1)|lung(1)	3	all_cancers(46;0.0642)|all_epithelial(25;0.00604)|Prostate(51;0.0112)|Ovarian(15;0.183)					CTCCAGGGTCAGCTGCGTGAA	0.687																																					p.L75P	Colon(106;1192 2596 47278)	Atlas-SNP	.											.	COMTD1	6	.	0			c.T224C						.						7	9	8					10																	76995129		2130	4233	6363	SO:0001630	splice_region_variant	118881	exon3			AGGGTCAGCTGCG		CCDS7349.1	10q22.2	2013-09-20			ENSG00000165644	ENSG00000165644			26309	protein-coding gene	gene with protein product						12975309	Standard	NM_144589		Approved	FLJ23841	uc001jxb.3	Q86VU5	OTTHUMG00000018518	ENST00000372538.3:c.223-1T>C	chr10.hg19:g.76995129A>G		28.0	0.0		38.0	4.0	NM_144589	Q8TE79	Missense_Mutation	SNP	ENST00000372538.3	hg19	CCDS7349.1	.	.	.	.	.	.	.	.	.	.	A	19.79	3.893335	0.72524	.	.	ENSG00000165644	ENST00000536650;ENST00000372538	T	0.23552	1.9	5.18	5.18	0.71444	.	0.081681	0.49305	D	0.000149	T	0.44787	0.1310	M	0.73962	2.25	0.80722	D	1	D	0.64830	0.994	P	0.60682	0.878	T	0.35822	-0.9773	10	0.33141	T	0.24	-16.9948	11.4178	0.49962	1.0:0.0:0.0:0.0	.	75	Q86VU5	CMTD1_HUMAN	P	75	ENSP00000361616:L75P	ENSP00000361616:L75P	L	-	2	0	COMTD1	76665135	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	3.145000	0.50623	1.942000	0.56320	0.379000	0.24179	CTG	.	.		0.687	COMTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048802.1	NM_144589	Missense_Mutation	G	76995129	A	G	76995129	5	3	255	1	0	0	0	0	0	0	1	0	3728	202	7	2	584	2	COMTD1	10	76995129	Splice_Site	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	204664	76995129	58539618	371	35716										
DLG5	9231	hgsc.bcm.edu	37	chr10	79614037	79614037	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	acacctcttcaaggcgttggTgtgctggttctgcaggctct	12	11	4	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:79614037T>C	ENST00000372391.2	-	4	633	c.628A>G	c.(628-630)Acc>Gcc	p.T210A	DLG5_ENST00000372388.2_Missense_Mutation_p.T210A	NM_004747.3	NP_004738.3	Q8TDM6	DLG5_HUMAN	discs, large homolog 5 (Drosophila)	210					apical protein localization (GO:0045176)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|intracellular signal transduction (GO:0035556)|metanephric collecting duct development (GO:0072205)|midbrain development (GO:0030901)|negative regulation of cell proliferation (GO:0008285)|polarized epithelial cell differentiation (GO:0030859)|protein complex assembly (GO:0006461)|protein localization to adherens junction (GO:0071896)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|zonula adherens assembly (GO:0045186)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cytoskeletal protein binding (GO:0008092)|receptor signaling complex scaffold activity (GO:0030159)			breast(9)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(17)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	60	all_cancers(46;0.0316)|all_epithelial(25;0.00147)|Breast(12;0.0015)|Prostate(51;0.0146)		Epithelial(14;0.00105)|OV - Ovarian serous cystadenocarcinoma(4;0.00151)|all cancers(16;0.00446)			AAGGCGTTGGTGTGCTGGTTC	0.602																																					p.T210A		Atlas-SNP	.											.	DLG5	154	.	0			c.A628G						.						106	78	88					10																	79614037		2203	4300	6503	SO:0001583	missense	9231	exon4			CGTTGGTGTGCTG	U61843	CCDS7353.2	10q23	2008-07-09	2001-11-28		ENSG00000151208	ENSG00000151208			2904	protein-coding gene	gene with protein product		604090	"discs, large (Drosophila) homolog 5"			9738934	Standard	XM_005270276		Approved	P-dlg, KIAA0583	uc001jzk.3	Q8TDM6	OTTHUMG00000018548	ENST00000372391.2:c.628A>G	chr10.hg19:g.79614037T>C	ENSP00000361467:p.Thr210Ala	71.0	0.0		98.0	4.0	NM_004747	A6H8Y3|Q149N1|Q5T1H7|Q5T1H8|Q6DKG3|Q86WC0|Q8TDM7|Q9UE73|Q9Y4E3	Missense_Mutation	SNP	ENST00000372391.2	hg19	CCDS7353.2	.	.	.	.	.	.	.	.	.	.	T	17.58	3.425876	0.62733	.	.	ENSG00000151208	ENST00000372391;ENST00000372388	T;T	0.44482	0.92;0.92	5.55	5.55	0.83447	.	0.000000	0.38164	N	0.001794	T	0.27489	0.0675	L	0.31294	0.92	0.32367	N	0.556406	P	0.34977	0.478	B	0.31390	0.129	T	0.35773	-0.9775	10	0.19590	T	0.45	.	10.105	0.42528	0.0:0.0747:0.0:0.9253	.	210	Q8TDM6	DLG5_HUMAN	A	210	ENSP00000361467:T210A;ENSP00000361464:T210A	ENSP00000361464:T210A	T	-	1	0	DLG5	79284043	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.994000	0.56994	2.111000	0.64477	0.533000	0.62120	ACC	.	.		0.602	DLG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048900.2			C	79614037	T	C	79614037	3	2	255	1	0	0	0	0	1	0	0	0	4560	1696	59	2	5247	2	DLG5	10	79614037	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	2618908	79614037	55920710	372	35717										
LIPA	3988	hgsc.bcm.edu	37	chr10	90974647	90974647	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cctccaaggggcatccaggcCccaaatgaagtcaagatgct	10	13	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:90974647C>A	ENST00000336233.5	-	10	1460	c.1138G>T	c.(1138-1140)Ggc>Tgc	p.G380C	LIPA_ENST00000371837.1_Missense_Mutation_p.G324C|LIPA_ENST00000456827.1_Missense_Mutation_p.G380C			P38571	LICH_HUMAN	lipase A, lysosomal acid, cholesterol esterase	380					cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cytokine production (GO:0001816)|homeostasis of number of cells within a tissue (GO:0048873)|inflammatory response (GO:0006954)|lipid catabolic process (GO:0016042)|lung development (GO:0030324)|tissue remodeling (GO:0048771)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	lipase activity (GO:0016298)|sterol esterase activity (GO:0004771)			endometrium(1)|large_intestine(2)|lung(3)	6		Colorectal(252;0.0162)		GBM - Glioblastoma multiforme(2;0.00406)		GCATCCAGGCCCCAAATGAAG	0.428																																					p.G380C		Atlas-SNP	.											.	LIPA	29	.	0			c.G1138T						.						56	55	56					10																	90974647		2203	4300	6503	SO:0001583	missense	3988	exon10			CCAGGCCCCAAAT	M74775	CCDS7401.1, CCDS73160.1	10q23.2-q23.3	2012-07-13	2008-08-01		ENSG00000107798	ENSG00000107798	3.1.1.13		6617	protein-coding gene	gene with protein product	"Wolman disease"	613497				8432549	Standard	NM_000235		Approved	LAL, CESD	uc009xtq.3	P38571	OTTHUMG00000018716	ENST00000336233.5:c.1138G>T	chr10.hg19:g.90974647C>A	ENSP00000337354:p.Gly380Cys	57.0	0.0		95.0	4.0	NM_000235	B2RBH5|D3DR29|Q16529|Q53H21|Q5T074|Q5T771|Q96EJ0	Missense_Mutation	SNP	ENST00000336233.5	hg19	CCDS7401.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.323546	0.81580	.	.	ENSG00000107798	ENST00000336233;ENST00000371837;ENST00000371829;ENST00000541980;ENST00000354621;ENST00000456827;ENST00000425287	T;T;T	0.72615	-0.67;-0.67;-0.67	5.08	5.08	0.68730	Alpha/beta hydrolase fold-1 (1);	0.000000	0.85682	D	0.000000	D	0.90376	0.6988	H	0.97983	4.12	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.93551	0.6886	10	0.87932	D	0	-25.2992	18.018	0.89247	0.0:1.0:0.0:0.0	.	382;324;380	E7EUT7;P38571-2;P38571	.;.;LICH_HUMAN	C	380;324;380;380;338;380;382	ENSP00000337354:G380C;ENSP00000360903:G324C;ENSP00000413019:G380C	ENSP00000337354:G380C	G	-	1	0	LIPA	90964627	1.000000	0.71417	1.000000	0.80357	0.761000	0.43186	6.929000	0.75852	2.802000	0.96397	0.563000	0.77884	GGC	.	.		0.428	LIPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049308.1	NM_000235		A	90974647	C	A	90974647	3	1	255	1	0	0	0	0	1	0	0	0	8828	623	22	3	65	3	LIPA	10	90974647	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	11360610	90974647	44560100	373	35718										
CEP55	55165	hgsc.bcm.edu	37	chr10	95275260	95275260	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tttgagttggaaaagaaaacGgaaacagctgctcattcact	9	7	2	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:95275260G>T	ENST00000371485.3	+	5	931	c.627G>T	c.(625-627)acG>acT	p.T209T		NM_001127182.1|NM_018131.4	NP_001120654|NP_060601	Q53EZ4	CEP55_HUMAN	centrosomal protein 55kDa	209	Interaction with PDCD6IP.|Interaction with TSG101.				establishment of protein localization (GO:0045184)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|midbody (GO:0030496)				kidney(1)|large_intestine(5)|lung(6)|stomach(1)	13		Colorectal(252;0.207)				AAAAGAAAACGGAAACAGCTG	0.428																																					p.T209T		Atlas-SNP	.											.	CEP55	35	.	0			c.G627T						.						90	97	95					10																	95275260		2203	4300	6503	SO:0001819	synonymous_variant	55165	exon5			GAAAACGGAAACA	AK001402	CCDS7428.1	10q24.1	2014-02-20	2005-12-01	2005-12-01	ENSG00000138180	ENSG00000138180			1161	protein-coding gene	gene with protein product	"cancer/testis antigen 111"	610000	"chromosome 10 open reading frame 3"	C10orf3		16198290	Standard	NM_018131		Approved	FLJ10540, CT111	uc009xug.3	Q53EZ4	OTTHUMG00000018774	ENST00000371485.3:c.627G>T	chr10.hg19:g.95275260G>T		111.0	0.0		148.0	6.0	NM_018131	B2RDG8|Q32WF5|Q3MV20|Q5VY28|Q6N034|Q96H32|Q9NVS7	Silent	SNP	ENST00000371485.3	hg19	CCDS7428.1	.	.	.	.	.	.	.	.	.	.	G	6.531	0.466146	0.12402	.	.	ENSG00000138180	ENST00000445435	.	.	.	5.15	-1.78	0.07957	.	.	.	.	.	T	0.58495	0.2126	.	.	.	0.42839	D	0.994042	.	.	.	.	.	.	T	0.57528	-0.7796	4	.	.	.	0.731	12.3702	0.55250	0.7186:0.0:0.2814:0.0	.	.	.	.	L	49	.	.	R	+	2	0	CEP55	95265250	0.001000	0.12720	0.816000	0.32577	0.858000	0.48976	-0.134000	0.10436	-0.200000	0.10300	0.655000	0.94253	CGG	.	.		0.428	CEP55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049434.1	NM_018131		T	95275260	G	T	95275260	2	4	255	1	0	0	0	0	0	0	0	1	3257	1103	39	1		1	CEP55	10	95275260	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	4300613	95275260	40259487	374	35719										
C10orf12	26148	hgsc.bcm.edu	37	chr10	98741962	98741962	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cgaggaaggaggtggagacgTttcacctcgaaaagaacctc	13	9	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:98741962T>C	ENST00000286067.2	+	1	922	c.815T>C	c.(814-816)gTt>gCt	p.V272A		NM_015652.2	NP_056467.2	Q8N655	CJ012_HUMAN	chromosome 10 open reading frame 12	272										NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(3)|prostate(2)|skin(2)|stomach(4)	45		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		GGTGGAGACGTTTCACCTCGA	0.532																																					p.V272A		Atlas-SNP	.											.	C10orf12	94	.	0			c.T815C						.						85	87	86					10																	98741962		2203	4300	6503	SO:0001583	missense	26148	exon1			GAGACGTTTCACC	BC024315	CCDS7452.1	10q24.2	2014-03-11			ENSG00000155640	ENSG00000155640			23420	protein-coding gene	gene with protein product						24550272	Standard	NM_015652		Approved	DKFZP564P1916, FLJ13022	uc001kmv.3	Q8N655	OTTHUMG00000018840	ENST00000286067.2:c.815T>C	chr10.hg19:g.98741962T>C	ENSP00000286067:p.Val272Ala	86.0	0.0		108.0	6.0	NM_015652	Q9H945|Q9Y457	Missense_Mutation	SNP	ENST00000286067.2	hg19	CCDS7452.1	.	.	.	.	.	.	.	.	.	.	T	0.012	-1.684454	0.00745	.	.	ENSG00000155640	ENST00000286067;ENST00000539886	T	0.06142	3.34	6.05	2.0	0.26442	.	1.252050	0.05965	N	0.641308	T	0.02418	0.0074	N	0.04508	-0.205	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.42413	-0.9453	10	0.02654	T	1	0.2746	1.7815	0.03032	0.1436:0.4815:0.1393:0.2357	.	106;272	A0PJI9;Q8N655	.;CJ012_HUMAN	A	272;106	ENSP00000286067:V272A	ENSP00000286067:V272A	V	+	2	0	C10orf12	98731952	0.000000	0.05858	0.000000	0.03702	0.088000	0.18126	-0.470000	0.06639	0.102000	0.17638	0.533000	0.62120	GTT	.	.		0.532	C10orf12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049627.1	NM_015652		C	98741962	T	C	98741962	3	2	255	1	0	0	0	0	1	0	0	0	1591	1725	60	2	817	2	C10orf12	10	98741962	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	3466702	98741962	36792785	375	35720										
RRP12	23223	hgsc.bcm.edu	37	chr10	99150246	99150246	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgaagggtcacggggtagccCcaggcctccaggtcttgctt	14	12	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:99150246C>A	ENST00000370992.4	-	6	798	c.687G>T	c.(685-687)tgG>tgT	p.W229C	RRP12_ENST00000315563.6_Intron|RRP12_ENST00000414986.1_Missense_Mutation_p.W168C|RRP12_ENST00000536831.1_Missense_Mutation_p.W35C	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	229						integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		CGGGGTAGCCCCAGGCCTCCA	0.607																																					p.W229C		Atlas-SNP	.											.	RRP12	97	.	0			c.G687T						.						52	51	52					10																	99150246		2203	4300	6503	SO:0001583	missense	23223	exon6			GTAGCCCCAGGCC		CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"KIAA0690"	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.687G>T	chr10.hg19:g.99150246C>A	ENSP00000360031:p.Trp229Cys	52.0	0.0		57.0	4.0	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Missense_Mutation	SNP	ENST00000370992.4	hg19	CCDS7457.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.131751	0.77662	.	.	ENSG00000052749	ENST00000370992;ENST00000414986;ENST00000536831	T;T;T	0.69435	-0.15;-0.15;-0.4	5.5	5.5	0.81552	Armadillo-like helical (1);Armadillo-type fold (1);	0.054484	0.85682	D	0.000000	D	0.84588	0.5505	M	0.85197	2.74	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	D	0.86643	0.1893	10	0.87932	D	0	-13.0765	19.4752	0.94985	0.0:1.0:0.0:0.0	.	168;35;229	E9PCK7;F5H456;Q5JTH9	.;.;RRP12_HUMAN	C	229;168;35	ENSP00000360031:W229C;ENSP00000414863:W168C;ENSP00000446184:W35C	ENSP00000360031:W229C	W	-	3	0	RRP12	99140236	1.000000	0.71417	1.000000	0.80357	0.743000	0.42351	7.729000	0.84864	2.596000	0.87737	0.650000	0.86243	TGG	.	.		0.607	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179		A	99150246	C	A	99150246	3	1	255	1	0	0	0	0	1	0	0	0	13701	624	22	3	3322	3	RRP12	10	99150246	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	408284	99150246	36384501	376	35721										
SCD	6319	hgsc.bcm.edu	37	chr10	102112216	102112216	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	caaagctcggctgcccctacGgctctttctgatcattgcca	8	15	3	1	rs145182376		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:102112216G>T	ENST00000370355.2	+	3	785	c.404G>T	c.(403-405)cGg>cTg	p.R135L		NM_005063.4	NP_005054.3	O00767	ACOD_HUMAN	stearoyl-CoA desaturase (delta-9-desaturase)	135					fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	iron ion binding (GO:0005506)|stearoyl-CoA 9-desaturase activity (GO:0004768)			endometrium(1)|large_intestine(3)|lung(5)	9		Colorectal(252;0.0323)		Epithelial(162;1.97e-10)|all cancers(201;1.73e-08)		CTGCCCCTACGGCTCTTTCTG	0.512																																					p.R135L	Colon(67;260 1459 9574 11663)	Atlas-SNP	.											.	SCD	25	.	0			c.G404T						.						144	139	140					10																	102112216		2203	4300	6503	SO:0001583	missense	6319	exon3			CCCTACGGCTCTT	AF097514	CCDS7493.1	10q23-q24	2013-01-25			ENSG00000099194	ENSG00000099194	1.14.19.1	"Fatty acid desaturases"	10571	protein-coding gene	gene with protein product	"acyl-CoA desaturase", "fatty acid desaturase", "delta-9-desaturase"	604031	"stearoyl-CoA desaturase opposite strand"	SCDOS		7909540, 10229681	Standard	NM_005063		Approved	FADS5	uc001kqy.3	O00767	OTTHUMG00000018906	ENST00000370355.2:c.404G>T	chr10.hg19:g.102112216G>T	ENSP00000359380:p.Arg135Leu	68.0	0.0		97.0	4.0	NM_005063	B2R5U0|D3DR68|Q16150|Q53GR9|Q5W037|Q5W038|Q6GSS4|Q96KF6|Q9BS07|Q9Y695	Missense_Mutation	SNP	ENST00000370355.2	hg19	CCDS7493.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.099752	0.76983	.	.	ENSG00000099194	ENST00000423840;ENST00000370355	T	0.16743	2.32	5.24	5.24	0.73138	Fatty acid desaturase, type 1 (1);	0.000000	0.56097	D	0.000022	T	0.59662	0.2210	H	0.97365	3.99	0.58432	D	0.999993	D	0.65815	0.995	D	0.74023	0.982	T	0.76135	-0.3070	10	0.87932	D	0	-26.3907	18.8237	0.92108	0.0:0.0:1.0:0.0	.	135	O00767	ACOD_HUMAN	L	135	ENSP00000359380:R135L	ENSP00000359380:R135L	R	+	2	0	SCD	102102206	0.928000	0.31464	0.615000	0.29064	0.233000	0.25261	4.858000	0.62947	2.469000	0.83416	0.561000	0.74099	CGG	.	G|1.000;A|0.000		0.512	SCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049857.2	NM_005063		T	102112216	G	T	102112216	3	4	255	1	0	0	0	0	1	0	0	0	13901	1116	39	1	414	1	SCD	10	102112216	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	2961970	102112216	33422531	377	35722										
BTRC	8945	hgsc.bcm.edu	37	chr10	103281409	103281409	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tctacagacaaaacttgccaAtggcacttccagtatgattg	7	10	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:103281409A>T	ENST00000370187.3	+	5	456	c.338A>T	c.(337-339)aAt>aTt	p.N113I	BTRC_ENST00000393441.4_Missense_Mutation_p.N72I|BTRC_ENST00000408038.2_Missense_Mutation_p.N77I	NM_033637.3	NP_378663.1	Q9Y297	FBW1A_HUMAN	beta-transducin repeat containing E3 ubiquitin protein ligase	113					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cellular response to organic cyclic compound (GO:0071407)|G2/M transition of mitotic cell cycle (GO:0000086)|mammary gland epithelial cell proliferation (GO:0033598)|mitotic cell cycle (GO:0000278)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of proteolysis (GO:0045862)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein dephosphorylation (GO:0006470)|protein destabilization (GO:0031648)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|rhythmic process (GO:0048511)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(4)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|stomach(1)|urinary_tract(1)	27		Colorectal(252;0.234)		Epithelial(162;1.05e-08)|all cancers(201;6.59e-07)		AAACTTGCCAATGGCACTTCC	0.378																																					p.N113I		Atlas-SNP	.											.	BTRC	64	.	0			c.A338T						.						72	68	69					10																	103281409		2203	4300	6503	SO:0001583	missense	8945	exon5			TTGCCAATGGCAC	Y14153	CCDS7511.1, CCDS7512.1, CCDS73183.1	10q24.32	2013-01-10	2012-02-23		ENSG00000166167	ENSG00000166167		"F-boxes / WD-40 domains", "WD repeat domain containing"	1144	protein-coding gene	gene with protein product		603482	"beta-transducin repeat containing"			9660940, 10331953, 18354483	Standard	NM_033637		Approved	bTrCP, betaTrCP, FBXW1A, Fwd1, beta-TrCP1, bTrCP1	uc001kta.4	Q9Y297	OTTHUMG00000018932	ENST00000370187.3:c.338A>T	chr10.hg19:g.103281409A>T	ENSP00000359206:p.Asn113Ile	100.0	0.0		148.0	53.0	NM_033637	B5MD49|Q5W141|Q5W142|Q9Y213	Missense_Mutation	SNP	ENST00000370187.3	hg19	CCDS7512.1	.	.	.	.	.	.	.	.	.	.	A	15.17	2.752726	0.49362	.	.	ENSG00000166167	ENST00000370187;ENST00000393441;ENST00000408038;ENST00000370183	T;T;T	0.60920	0.3;0.29;0.15	5.6	5.6	0.85130	.	0.137255	0.50627	D	0.000112	T	0.48660	0.1512	L	0.29908	0.895	0.38130	D	0.938118	B;B;B	0.16396	0.001;0.0;0.017	B;B;B	0.12156	0.005;0.003;0.007	T	0.50355	-0.8838	10	0.62326	D	0.03	-17.033	16.1249	0.81386	1.0:0.0:0.0:0.0	.	87;77;113	B7Z3H4;Q9Y297-2;Q9Y297	.;.;FBW1A_HUMAN	I	113;72;77;95	ENSP00000359206:N113I;ENSP00000377088:N72I;ENSP00000385339:N77I	ENSP00000359202:N95I	N	+	2	0	BTRC	103271399	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.547000	0.90665	2.262000	0.75019	0.529000	0.55759	AAT	.	.		0.378	BTRC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049936.1	NM_033637		T	103281409	A	T	103281409	3	4	255	1	0	0	0	0	1	0	0	0	1571	101	4	4	356	4	BTRC	10	103281409	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	1169193	103281409	32253338	378	35723										
CYP17A1	1586	hgsc.bcm.edu	37	chr10	104590471	104590471	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tacagcctttaggtgctaccCtcagcctgggcttccctcca	8	16	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:104590471C>A	ENST00000369887.3	-	8	1686	c.1515G>T	c.(1513-1515)gaG>gaT	p.E505D	CYP17A1-AS1_ENST00000369884.4_RNA|CYP17A1_ENST00000489268.1_5'Flank	NM_000102.3	NP_000093.1	P05093	CP17A_HUMAN	cytochrome P450, family 17, subfamily A, polypeptide 1	505					adrenal gland development (GO:0030325)|androgen biosynthetic process (GO:0006702)|biphenyl metabolic process (GO:0018879)|cellular response to antibiotic (GO:0071236)|cellular response to gonadotropin stimulus (GO:0071371)|cellular response to lipopolysaccharide (GO:0071222)|dibenzo-p-dioxin metabolic process (GO:0018894)|glucocorticoid biosynthetic process (GO:0006704)|hippocampus development (GO:0021766)|hormone biosynthetic process (GO:0042446)|Leydig cell differentiation (GO:0033327)|ovulation (GO:0030728)|phenol-containing compound metabolic process (GO:0018958)|phthalate metabolic process (GO:0018963)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|progesterone metabolic process (GO:0042448)|response to acetate (GO:0010034)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to fungicide (GO:0060992)|response to herbicide (GO:0009635)|response to insecticide (GO:0017085)|response to ionizing radiation (GO:0010212)|response to methylmercury (GO:0051597)|response to nutrient levels (GO:0031667)|response to retinoic acid (GO:0032526)|response to steroid hormone (GO:0048545)|sex differentiation (GO:0007548)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	axon (GO:0030424)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)	17-alpha-hydroxyprogesterone aldolase activity (GO:0047442)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|steroid 17-alpha-monooxygenase activity (GO:0004508)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.122)|all_hematologic(284;0.152)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)	Abiraterone(DB05812)|Aminophenazone(DB01424)|Dexamethasone(DB01234)|Metoclopramide(DB01233)|Progesterone(DB00396)	AGGTGCTACCCTCAGCCTGGG	0.562																																					p.E505D		Atlas-SNP	.											.	CYP17A1	48	.	0			c.G1515T						.						25	26	26					10																	104590471		2203	4300	6503	SO:0001583	missense	1586	exon8			GCTACCCTCAGCC	M19489	CCDS7541.1	10q24.3	2010-05-04	2003-02-14	2003-02-28	ENSG00000148795	ENSG00000148795	1.14.99.9	"Cytochrome P450s"	2593	protein-coding gene	gene with protein product	"Steroid 17-alpha-monooxygenase"	609300	"cytochrome P450, subfamily XVII (steroid 17-alpha-hydroxylase), adrenal hyperplasia"	CYP17		1347802	Standard	NM_000102		Approved	P450C17, CPT7, S17AH	uc001kwg.3	P05093	OTTHUMG00000018969	ENST00000369887.3:c.1515G>T	chr10.hg19:g.104590471C>A	ENSP00000358903:p.Glu505Asp	73.0	0.0		92.0	4.0	NM_000102	Q5TZV7	Missense_Mutation	SNP	ENST00000369887.3	hg19	CCDS7541.1	.	.	.	.	.	.	.	.	.	.	C	15.22	2.767519	0.49574	.	.	ENSG00000148795	ENST00000369887	T	0.69306	-0.39	5.31	2.36	0.29203	.	0.832824	0.11132	N	0.596157	T	0.42314	0.1197	N	0.08118	0	0.09310	N	1	B	0.30511	0.282	B	0.24394	0.053	T	0.28996	-1.0026	10	0.51188	T	0.08	.	7.1653	0.25687	0.0:0.5752:0.3354:0.0894	.	505	P05093	CP17A_HUMAN	D	505	ENSP00000358903:E505D	ENSP00000358903:E505D	E	-	3	2	CYP17A1	104580461	0.077000	0.21312	0.137000	0.22149	0.571000	0.35966	0.510000	0.22723	0.711000	0.32018	-0.225000	0.12378	GAG	.	.		0.562	CYP17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050101.1	NM_000102		A	104590471	C	A	104590471	3	1	255	1	0	0	0	0	1	0	0	0	4149	680	24	3	15	3	CYP17A1	10	104590471	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1309062	104590471	30944276	379	35724										
GFRA1	2674	hgsc.bcm.edu	37	chr10	117853332	117853332	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tactggagtctatgtagttgGgggtcatgactgtgcctaaa	13	6	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:117853332G>T	ENST00000355422.6	-	8	1446	c.896C>A	c.(895-897)cCc>cAc	p.P299H	GFRA1_ENST00000369236.1_Missense_Mutation_p.P294H|GFRA1_ENST00000439649.3_Missense_Mutation_p.P294H|GFRA1_ENST00000544592.1_Missense_Mutation_p.P178H	NM_005264.4	NP_005255.1	P56159	GFRA1_HUMAN	GDNF family receptor alpha 1	299					axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	glial cell-derived neurotrophic factor receptor activity (GO:0016167)|receptor binding (GO:0005102)			endometrium(2)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)	26		Lung NSC(174;0.21)		all cancers(201;0.0337)		TATGTAGTTGGGGGTCATGAC	0.423																																					p.P299H	Ovarian(128;329 1725 45498 46808 50759)	Atlas-SNP	.											.	GFRA1	107	.	0			c.C896A						.						80	77	78					10																	117853332		2203	4300	6503	SO:0001583	missense	2674	exon8			TAGTTGGGGGTCA	AF038421	CCDS7593.1, CCDS44481.1	10q25-q26	2011-01-25			ENSG00000151892	ENSG00000151892			4243	protein-coding gene	gene with protein product		601496		GDNFRA		9465905, 9545641	Standard	NM_005264		Approved	RETL1, GDNFR, GFR-ALPHA-1, RET1L, TRNR1	uc001lcj.3	P56159	OTTHUMG00000019097	ENST00000355422.6:c.896C>A	chr10.hg19:g.117853332G>T	ENSP00000347591:p.Pro299His	101.0	0.0		123.0	5.0	NM_005264	A8KA21|O15507|O43912	Missense_Mutation	SNP	ENST00000355422.6	hg19	CCDS44481.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.719313	0.89205	.	.	ENSG00000151892	ENST00000439649;ENST00000369236;ENST00000355422;ENST00000544592;ENST00000369234	T;T	0.65916	-0.18;-0.18	5.98	5.98	0.97165	GDNF/GAS1 (2);	0.000000	0.85682	D	0.000000	D	0.83344	0.5234	M	0.87758	2.905	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.84862	0.0820	10	0.87932	D	0	-27.5613	20.4366	0.99092	0.0:0.0:1.0:0.0	.	299;294	P56159;P56159-2	GFRA1_HUMAN;.	H	299;294;294;178;294	ENSP00000358239:P294H;ENSP00000442179:P178H	ENSP00000347591:P294H	P	-	2	0	GFRA1	117843322	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	9.033000	0.93741	2.837000	0.97791	0.591000	0.81541	CCC	.	.		0.423	GFRA1-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050512.2	NM_145793		T	117853332	G	T	117853332	3	4	255	1	0	0	0	0	1	0	0	0	6355	1232	43	3	517	3	GFRA1	10	117853332	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	13262861	117853332	17681415	380	35725										
C10orf119	79892	hgsc.bcm.edu	37	chr10	121608999	121608999	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	attcaaatcaaaaggagaagAcaagttcagagagttcagct	9	6	4	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:121608999A>G	ENST00000360003.3	-	7	833	c.664T>C	c.(664-666)Tct>Cct	p.S222P	MCMBP_ENST00000466047.1_5'UTR|MCMBP_ENST00000369077.3_Missense_Mutation_p.S222P	NM_001256378.1|NM_001256379.1|NM_024834.3	NP_001243307.1|NP_001243308.1|NP_079110.1	Q9BTE3	MCMBP_HUMAN	minichromosome maintenance complex binding protein	222					DNA-dependent DNA replication (GO:0006261)|mitotic nuclear division (GO:0007067)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(2)|skin(2)	21						AAAGGAGAAGACAAGTTCAGA	0.423																																					p.S222P		Atlas-SNP	.											.	MCMBP	49	.	0			c.T664C						.						122	110	114					10																	121608999		2203	4300	6503	SO:0001583	missense	79892	exon7			GAGAAGACAAGTT	BC007219	CCDS7617.1, CCDS58099.1	10q26.13	2013-10-11	2011-01-05	2011-01-05	ENSG00000197771	ENSG00000197771			25782	protein-coding gene	gene with protein product		610909	"chromosome 10 open reading frame 119"	C10orf119		17296731	Standard	NM_024834		Approved	FLJ13081, MCM-BP	uc001ler.3	Q9BTE3	OTTHUMG00000019159	ENST00000360003.3:c.664T>C	chr10.hg19:g.121608999A>G	ENSP00000353098:p.Ser222Pro	51.0	0.0		94.0	4.0	NM_024834	B3KSP7|Q6IA56|Q9BVT9|Q9H916	Missense_Mutation	SNP	ENST00000360003.3	hg19	CCDS7617.1	.	.	.	.	.	.	.	.	.	.	A	15.01	2.707718	0.48412	.	.	ENSG00000197771	ENST00000360003;ENST00000369077	T;T	0.53857	0.6;0.6	5.52	4.32	0.51571	.	0.135013	0.51477	D	0.000083	T	0.41880	0.1178	L	0.42245	1.32	0.47009	D	0.999282	P;P	0.46220	0.874;0.8	B;B	0.38616	0.277;0.143	T	0.33240	-0.9876	10	0.30854	T	0.27	-4.2227	12.3622	0.55209	0.8739:0.0:0.0:0.126	.	222;222	Q9BTE3-2;Q9BTE3	.;MCMBP_HUMAN	P	222	ENSP00000353098:S222P;ENSP00000358073:S222P	ENSP00000353098:S222P	S	-	1	0	MCMBP	121598989	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	4.001000	0.57046	2.228000	0.72767	0.533000	0.62120	TCT	.	.		0.423	MCMBP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050684.1	NM_024834		G	121608999	A	G	121608999	3	3	255	1	0	0	0	0	1	0	0	0	1590	275	10	2	1304	2	C10orf119	10	121608999	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	3755667	121608999	13925748	381	35726										
TACC2	10579	hgsc.bcm.edu	37	chr10	123845759	123845759	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agtgctgcccagagaggagcAgaagacagtggagtgaaagc	16	7	0	4			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:123845759A>G	ENST00000369005.1	+	4	4084	c.3744A>G	c.(3742-3744)gcA>gcG	p.A1248A	TACC2_ENST00000358010.1_Intron|TACC2_ENST00000515603.1_Silent_p.A1248A|TACC2_ENST00000453444.2_Silent_p.A1248A|TACC2_ENST00000515273.1_Silent_p.A1248A|TACC2_ENST00000334433.3_Silent_p.A1248A|TACC2_ENST00000513429.1_Intron	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	1248					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				AGAGAGGAGCAGAAGACAGTG	0.597																																					p.A1248A		Atlas-SNP	.											.	TACC2	271	.	0			c.A3744G						.						84	92	89					10																	123845759		2203	4300	6503	SO:0001819	synonymous_variant	10579	exon4			AGGAGCAGAAGAC	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.3744A>G	chr10.hg19:g.123845759A>G		64.0	0.0		84.0	4.0	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Silent	SNP	ENST00000369005.1	hg19	CCDS7626.1																																																																																			.	.		0.597	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1			G	123845759	A	G	123845759	2	3	255	1	0	0	0	0	0	0	0	1	15517	175	7	2		2	TACC2	10	123845759	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	2236760	123845759	11688988	382	35727										
TACC2	10579	hgsc.bcm.edu	37	chr10	123848021	123848021	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccaggcctggcccatccatgTtaccttcggttcctaagaag	9	14	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:123848021T>C	ENST00000369005.1	+	5	5828	c.5488T>C	c.(5488-5490)Tta>Cta	p.L1830L	TACC2_ENST00000358010.1_Intron|TACC2_ENST00000515603.1_Silent_p.L1830L|TACC2_ENST00000453444.2_Silent_p.L1830L|TACC2_ENST00000515273.1_Silent_p.L1830L|TACC2_ENST00000334433.3_Silent_p.L1830L|TACC2_ENST00000513429.1_Intron	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	1830					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				CCCATCCATGTTACCTTCGGT	0.438																																					p.L1830L		Atlas-SNP	.											.	TACC2	271	.	0			c.T5488C						.						59	52	54					10																	123848021		2203	4300	6503	SO:0001819	synonymous_variant	10579	exon5			TCCATGTTACCTT	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.5488T>C	chr10.hg19:g.123848021T>C		100.0	0.0		143.0	6.0	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Silent	SNP	ENST00000369005.1	hg19	CCDS7626.1																																																																																			.	.		0.438	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1			C	123848021	T	C	123848021	2	2	255	1	0	0	0	0	0	0	0	1	15517	1722	60	2		2	TACC2	10	123848021	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	2262	123848021	11686726	383	35728										
TACC2	10579	hgsc.bcm.edu	37	chr10	123996925	123996925	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cacagagagaggctgctcacCcaacagacgtctccatctcc	8	16	3	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:123996925C>A	ENST00000369005.1	+	17	8483	c.8143C>A	c.(8143-8145)Cca>Aca	p.P2715T	TACC2_ENST00000369001.1_Missense_Mutation_p.P342T|TACC2_ENST00000358010.1_Missense_Mutation_p.P861T|TACC2_ENST00000260733.3_Missense_Mutation_p.P793T|TACC2_ENST00000515603.1_Missense_Mutation_p.P2593T|TACC2_ENST00000453444.2_Missense_Mutation_p.P2642T|TACC2_ENST00000515273.1_Missense_Mutation_p.P2642T|TACC2_ENST00000369000.1_Missense_Mutation_p.P338T|TACC2_ENST00000334433.3_Missense_Mutation_p.P2715T|TACC2_ENST00000513429.1_Missense_Mutation_p.P861T|TACC2_ENST00000369004.3_Missense_Mutation_p.P775T|TACC2_ENST00000368999.1_Missense_Mutation_p.P805T|TACC2_ENST00000360561.3_Missense_Mutation_p.P763T	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	2715					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				GGCTGCTCACCCAACAGACGT	0.488																																					p.P2715T		Atlas-SNP	.											.	TACC2	271	.	0			c.C8143A						.						42	43	43					10																	123996925		2203	4300	6503	SO:0001583	missense	10579	exon17			GCTCACCCAACAG	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.8143C>A	chr10.hg19:g.123996925C>A	ENSP00000358001:p.Pro2715Thr	52.0	0.0		87.0	4.0	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	hg19	CCDS7626.1	.	.	.	.	.	.	.	.	.	.	C	17.56	3.418832	0.62622	.	.	ENSG00000138162	ENST00000369005;ENST00000513429;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000358010;ENST00000453444;ENST00000340076;ENST00000369001;ENST00000369000;ENST00000360561;ENST00000368999;ENST00000369004;ENST00000260733;ENST00000496913	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.22539	3.81;3.48;3.85;3.79;3.81;3.48;3.85;1.96;1.95;3.34;3.35;3.34;3.35;2.01	4.93	4.93	0.64822	.	0.000000	0.34777	N	0.003693	T	0.29158	0.0725	L	0.29908	0.895	0.40157	D	0.977016	D;P;D;D;P;P;P;P;D	0.56521	0.976;0.848;0.976;0.976;0.746;0.746;0.941;0.894;0.976	P;P;P;D;P;P;P;P;D	0.64506	0.877;0.521;0.877;0.926;0.487;0.557;0.761;0.688;0.909	T	0.01791	-1.1273	10	0.30078	T	0.28	-8.7553	11.2233	0.48869	0.0:0.9147:0.0:0.0853	.	2642;775;2593;2642;763;793;338;861;2715	E9PBC6;D6RAA5;E7EMZ9;B7ZMJ9;O95359-6;O95359-1;O95359-2;O95359-5;O95359	.;.;.;.;.;.;.;.;TACC2_HUMAN	T	2715;861;2642;2593;2715;861;2642;2628;342;338;763;805;775;793;373	ENSP00000358001:P2715T;ENSP00000425062:P861T;ENSP00000424467:P2642T;ENSP00000427618:P2593T;ENSP00000334280:P2715T;ENSP00000350701:P861T;ENSP00000395048:P2642T;ENSP00000357997:P342T;ENSP00000357996:P338T;ENSP00000353763:P763T;ENSP00000357995:P805T;ENSP00000422815:P775T;ENSP00000260733:P793T;ENSP00000422725:P373T	ENSP00000260733:P793T	P	+	1	0	TACC2	123986915	1.000000	0.71417	0.999000	0.59377	0.950000	0.60333	1.815000	0.38981	2.431000	0.82371	0.655000	0.94253	CCA	.	.		0.488	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1			A	123996925	C	A	123996925	3	1	255	1	0	0	0	0	1	0	0	0	15517	623	22	3	8277	3	TACC2	10	123996925	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	148904	123996925	11537822	384	35729										
KNDC1	85442	hgsc.bcm.edu	37	chr10	135025267	135025267	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gggccgagggcaaccctcgcGgcacagacctggagaacccc	14	16	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:135025267G>T	ENST00000304613.3	+	23	4162	c.4141G>T	c.(4141-4143)Ggc>Tgc	p.G1381C	KNDC1_ENST00000368572.2_Missense_Mutation_p.G1383C			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	1381					cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)	p.G1381C(1)		NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		CAACCCTCGCGGCACAGACCT	0.662																																					p.G1381C		Atlas-SNP	.											KNDC1,NS,carcinoma,0,1	KNDC1	155	.	1	Substitution - Missense(1)	lung(1)	c.G4141T						.						39	39	39					10																	135025267		2202	4299	6501	SO:0001583	missense	85442	exon23			CCTCGCGGCACAG	AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"RasGEF domain family, member 2"	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.4141G>T	chr10.hg19:g.135025267G>T	ENSP00000304437:p.Gly1381Cys	44.0	0.0		89.0	4.0	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	hg19	CCDS7674.1	.	.	.	.	.	.	.	.	.	.	G	0.834	-0.744189	0.03065	.	.	ENSG00000171798	ENST00000304613;ENST00000368572	T;T	0.30981	1.51;1.51	3.34	-2.44	0.06502	Ras guanine nucleotide exchange factor, domain (1);	1.176820	0.06429	U	0.723675	T	0.19208	0.0461	N	0.14661	0.345	0.09310	N	1	B	0.25609	0.13	B	0.22386	0.039	T	0.25916	-1.0118	10	0.37606	T	0.19	-10.3462	12.5612	0.56281	0.1245:0.0:0.8755:0.0	.	1381	Q76NI1	VKIND_HUMAN	C	1381;1383	ENSP00000304437:G1381C;ENSP00000357561:G1383C	ENSP00000304437:G1381C	G	+	1	0	KNDC1	134875257	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.307000	0.08167	-1.014000	0.03379	-2.027000	0.00425	GGC	.	.		0.662	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643		T	135025267	G	T	135025267	3	4	255	1	0	0	0	0	1	0	0	0	8435	1116	39	1	4231	1	KNDC1	10	135025267	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	11028342	135025267	509480	385	35730										
ATHL1	80162	hgsc.bcm.edu	37	chr11	292027	292027	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tccacccagaagccgccaggGccatcctggagtaccgcatc	10	17	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:292027G>A	ENST00000409548.2	+	5	1073	c.958G>A	c.(958-960)Gcc>Acc	p.A320T	ATHL1_ENST00000409479.1_Missense_Mutation_p.A320T|ATHL1_ENST00000409655.1_Missense_Mutation_p.A143T	NM_025092.4	NP_079368.3	Q32M88	ATHL1_HUMAN	ATH1, acid trehalase-like 1 (yeast)	320					carbohydrate metabolic process (GO:0005975)		hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(7)|prostate(1)|skin(3)	17		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;5.38e-28)|Epithelial(43;3.25e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		AGCCGCCAGGGCCATCCTGGA	0.667																																					p.A320T		Atlas-SNP	.											.	ATHL1	88	.	0			c.G958A						.						56	46	49					11																	292027		2202	4297	6499	SO:0001583	missense	80162	exon5			GCCAGGGCCATCC	AK090428	CCDS31322.2	11p15.5	2005-10-27			ENSG00000142102	ENSG00000142102			26210	protein-coding gene	gene with protein product							Standard	NM_025092		Approved	FLJ22635	uc010qvu.2	Q32M88	OTTHUMG00000153218	ENST00000409548.2:c.958G>A	chr11.hg19:g.292027G>A	ENSP00000387185:p.Ala320Thr	78.0	0.0		55.0	4.0	NM_025092	Q658X8|Q8TEG9|Q9H635	Missense_Mutation	SNP	ENST00000409548.2	hg19	CCDS31322.2	.	.	.	.	.	.	.	.	.	.	g	16.03	3.005962	0.54361	.	.	ENSG00000142102	ENST00000409548;ENST00000409655;ENST00000409479	.	.	.	4.45	3.29	0.37713	Glycoside hydrolase, family 65, central catalytic (1);Six-hairpin glycosidase (1);Six-hairpin glycosidase-like (1);	0.353127	0.28230	N	0.016106	T	0.47525	0.1450	L	0.45470	1.425	0.31428	N	0.673523	P;P;B	0.46064	0.774;0.872;0.232	P;P;B	0.52031	0.688;0.593;0.172	T	0.49899	-0.8890	9	0.30078	T	0.28	.	8.2845	0.31920	0.1031:0.1623:0.7346:0.0	.	320;320;143	Q32M88;E7EMA9;B8ZZ60	ATHL1_HUMAN;.;.	T	320;143;320	.	ENSP00000387099:A320T	A	+	1	0	ATHL1	282027	0.571000	0.26659	1.000000	0.80357	0.721000	0.41392	2.193000	0.42658	2.031000	0.59945	0.457000	0.33378	GCC	.	.		0.667	ATHL1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330164.3	NM_025092		A	292027	G	A	292027	3	1	255	1	0	0	0	0	1	0	0	0	1104	1203	42	3	972	3	ATHL1	11	292027	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10		292027	134714489	386	35731										
B4GALNT4	338707	hgsc.bcm.edu	37	chr11	377296	377296	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccgtggacgtgaccgctcagTacatggagcggctgaacgcg	15	12	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:377296T>C	ENST00000329962.6	+	14	2173	c.2173T>C	c.(2173-2175)Tac>Cac	p.Y725H		NM_178537.4	NP_848632.2	Q76KP1	B4GN4_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 4	725					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			endometrium(2)|kidney(4)|large_intestine(1)|liver(2)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	24		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GACCGCTCAGTACATGGAGCG	0.701																																					p.Y725H		Atlas-SNP	.											.	B4GALNT4	83	.	0			c.T2173C						.						14	9	11					11																	377296		2045	4051	6096	SO:0001583	missense	338707	exon14			GCTCAGTACATGG	AB089939	CCDS7694.1	11p15.5	2013-02-19			ENSG00000182272	ENSG00000182272	2.4.1.-	"Beta 4-glycosyltransferases"	26315	protein-coding gene	gene with protein product						15044014	Standard	NM_178537		Approved	FLJ25045, NGalNAc-T1	uc001lpb.3	Q76KP1	OTTHUMG00000119075	ENST00000329962.6:c.2173T>C	chr11.hg19:g.377296T>C	ENSP00000328277:p.Tyr725His	79.0	0.0		91.0	4.0	NM_178537	Q96LV2	Missense_Mutation	SNP	ENST00000329962.6	hg19	CCDS7694.1	.	.	.	.	.	.	.	.	.	.	t	16.11	3.031147	0.54790	.	.	ENSG00000182272	ENST00000329962	T	0.15139	2.45	3.28	3.28	0.37604	.	0.081321	0.51477	D	0.000094	T	0.37183	0.0994	M	0.68952	2.095	0.47659	D	0.99948	D	0.69078	0.997	D	0.79784	0.993	T	0.19844	-1.0293	10	0.59425	D	0.04	-27.5924	12.0889	0.53713	0.0:0.0:0.0:1.0	.	725	Q76KP1	B4GN4_HUMAN	H	725	ENSP00000328277:Y725H	ENSP00000328277:Y725H	Y	+	1	0	B4GALNT4	367296	1.000000	0.71417	1.000000	0.80357	0.083000	0.17756	7.329000	0.79170	1.508000	0.48769	0.172000	0.16884	TAC	.	.		0.701	B4GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239289.2	NM_178537		C	377296	T	C	377296	3	2	255	1	0	0	0	0	1	0	0	0	1269	1638	57	2	2227	2	B4GALNT4	11	377296	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	85269	377296	134629220	387	35732										
SIGIRR	59307	hgsc.bcm.edu	37	chr11	407512	407512	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctttaggatgaagttcacgaActtgcggtcctcggggcagt	13	9	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:407512A>G	ENST00000431843.2	-	6	844	c.538T>C	c.(538-540)Ttc>Ctc	p.F180L	SIGIRR_ENST00000397632.3_Missense_Mutation_p.F180L|SIGIRR_ENST00000531205.1_Missense_Mutation_p.F180L|SIGIRR_ENST00000382520.2_Missense_Mutation_p.F180L|SIGIRR_ENST00000529486.1_5'UTR|SIGIRR_ENST00000332725.3_Missense_Mutation_p.F180L	NM_001135054.1	NP_001128526.1	Q6IA17	SIGIR_HUMAN	single immunoglobulin and toll-interleukin 1 receptor (TIR) domain	180	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				acute-phase response (GO:0006953)|negative regulation of chemokine biosynthetic process (GO:0045079)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				cervix(2)|endometrium(1)|liver(1)|lung(5)|prostate(2)|skin(1)|urinary_tract(1)	13		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AAGTTCACGAACTTGCGGTCC	0.677																																					p.F180L		Atlas-SNP	.											.	SIGIRR	22	.	0			c.T538C						.						26	26	26					11																	407512		2188	4289	6477	SO:0001583	missense	59307	exon6			TCACGAACTTGCG		CCDS31325.1	11p15.5	2013-01-11	2005-10-10					"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	30575	protein-coding gene	gene with protein product	"single immunoglobulin domain IL1R1 related"	605478				10346978	Standard	NM_021805		Approved	TIR8	uc001lpe.1	Q6IA17		ENST00000431843.2:c.538T>C	chr11.hg19:g.407512A>G	ENSP00000403104:p.Phe180Leu	132.0	0.0		167.0	7.0	NM_001135053	Q3KQY2|Q6UXI3|Q9H733	Missense_Mutation	SNP	ENST00000431843.2	hg19	CCDS31325.1	.	.	.	.	.	.	.	.	.	.	a	16.69	3.193513	0.58017	.	.	ENSG00000185187	ENST00000431843;ENST00000397632;ENST00000332725;ENST00000531205;ENST00000382520;ENST00000528209;ENST00000530494	T;T;T;T;T;T	0.23147	1.92;1.92;1.92;1.92;1.92;1.92	2.75	2.75	0.32379	Toll/interleukin-1 receptor homology (TIR) domain (3);	0.063235	0.64402	D	0.000004	T	0.28928	0.0718	M	0.78344	2.41	0.80722	D	1	P;B	0.42296	0.775;0.362	B;B	0.39660	0.306;0.166	T	0.15178	-1.0446	10	0.40728	T	0.16	.	10.2759	0.43510	1.0:0.0:0.0:0.0	.	180;180	C9JFX4;Q6IA17	.;SIGIR_HUMAN	L	180;180;180;180;180;76;124	ENSP00000403104:F180L;ENSP00000380756:F180L;ENSP00000333656:F180L;ENSP00000433022:F180L;ENSP00000371960:F180L;ENSP00000435135:F76L	ENSP00000333656:F180L	F	-	1	0	SIGIRR	397512	1.000000	0.71417	1.000000	0.80357	0.226000	0.24999	5.558000	0.67319	1.525000	0.49052	0.240000	0.17902	TTC	.	.		0.677	SIGIRR-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383884.3	NM_021805		G	407512	A	G	407512	3	3	255	1	0	0	0	0	1	0	0	0	14319	43	2	2	714	2	SIGIRR	11	407512	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	30216	407512	134599004	388	35733										
LRRC56	115399	hgsc.bcm.edu	37	chr11	540775	540775	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gctggcaaggcctgcacaacCcctgcccacagagcaagggc	12	16	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:540775C>T	ENST00000270115.7	+	4	591	c.91C>T	c.(91-93)Ccc>Tcc	p.P31S		NM_198075.3	NP_932341.1	Q8IYG6	LRC56_HUMAN	leucine rich repeat containing 56	31										kidney(1)|lung(4)|skin(1)	6		all_cancers(49;2.16e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CCTGCACAACCCCTGCCCACA	0.662																																					p.P31S		Atlas-SNP	.											.	LRRC56	23	.	0			c.C91T						.						50	46	47					11																	540775		2200	4299	6499	SO:0001583	missense	115399	exon4			CACAACCCCTGCC		CCDS7700.1	11p15.5	2005-10-18			ENSG00000161328	ENSG00000161328			25430	protein-coding gene	gene with protein product						12477932	Standard	NM_198075		Approved	FLJ00101, DKFZp761L1518	uc010qvz.2	Q8IYG6	OTTHUMG00000132003	ENST00000270115.7:c.91C>T	chr11.hg19:g.540775C>T	ENSP00000270115:p.Pro31Ser	67.0	0.0		69.0	4.0	NM_198075	Q8N3Q4	Missense_Mutation	SNP	ENST00000270115.7	hg19	CCDS7700.1	.	.	.	.	.	.	.	.	.	.	c	23.1	4.372993	0.82573	.	.	ENSG00000161328	ENST00000270115	T	0.41065	1.01	4.88	4.88	0.63580	.	0.000000	0.64402	D	0.000001	T	0.63768	0.2539	M	0.70275	2.135	0.38924	D	0.957805	D	0.89917	1.0	D	0.91635	0.999	T	0.69075	-0.5241	10	0.59425	D	0.04	-11.9051	15.5375	0.76016	0.0:1.0:0.0:0.0	.	31	Q8IYG6	LRC56_HUMAN	S	31	ENSP00000270115:P31S	ENSP00000270115:P31S	P	+	1	0	LRRC56	530775	0.697000	0.27767	1.000000	0.80357	0.940000	0.58332	1.652000	0.37313	2.287000	0.76781	0.556000	0.70494	CCC	.	.		0.662	LRRC56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254969.1	NM_198075		T	540775	C	T	540775	3	4	255	1	0	0	0	0	1	0	0	0	9021	623	22	3	93	3	LRRC56	11	540775	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	133263	540775	134465741	389	35734										
TH	7054	hgsc.bcm.edu	37	chr11	2190970	2190970	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	acggccttcccctccttctcCtcaaaggccacagcctccag	6	20	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:2190970C>T	ENST00000381178.1	-	3	333	c.315G>A	c.(313-315)gaG>gaA	p.E105E	TH_ENST00000333684.5_Silent_p.E78E|TH_ENST00000352909.3_Silent_p.E74E|TH_ENST00000381175.1_Silent_p.E101E	NM_199292.2	NP_954986.2	P07101	TY3H_HUMAN	tyrosine hydroxylase	105					anatomical structure morphogenesis (GO:0009653)|catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|cellular response to growth factor stimulus (GO:0071363)|cellular response to manganese ion (GO:0071287)|cellular response to nicotine (GO:0071316)|cerebral cortex development (GO:0021987)|circadian sleep/wake cycle (GO:0042745)|dopamine biosynthetic process (GO:0042416)|dopamine biosynthetic process from tyrosine (GO:0006585)|eating behavior (GO:0042755)|embryonic camera-type eye morphogenesis (GO:0048596)|epinephrine biosynthetic process (GO:0042418)|eye photoreceptor cell development (GO:0042462)|fatty acid metabolic process (GO:0006631)|glycoside metabolic process (GO:0016137)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|isoquinoline alkaloid metabolic process (GO:0033076)|learning (GO:0007612)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|memory (GO:0007613)|multicellular organismal aging (GO:0010259)|neurotransmitter biosynthetic process (GO:0042136)|norepinephrine biosynthetic process (GO:0042421)|organ morphogenesis (GO:0009887)|phthalate metabolic process (GO:0018963)|phytoalexin metabolic process (GO:0052314)|pigmentation (GO:0043473)|regulation of heart contraction (GO:0008016)|response to activity (GO:0014823)|response to amphetamine (GO:0001975)|response to corticosterone (GO:0051412)|response to electrical stimulus (GO:0051602)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to ether (GO:0045472)|response to herbicide (GO:0009635)|response to hypoxia (GO:0001666)|response to light stimulus (GO:0009416)|response to lipopolysaccharide (GO:0032496)|response to nutrient levels (GO:0031667)|response to peptide hormone (GO:0043434)|response to pyrethroid (GO:0046684)|response to salt stress (GO:0009651)|response to water deprivation (GO:0009414)|response to zinc ion (GO:0010043)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|sphingolipid metabolic process (GO:0006665)|synaptic transmission, dopaminergic (GO:0001963)|synaptic vesicle amine transport (GO:0015842)|terpene metabolic process (GO:0042214)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|melanosome membrane (GO:0033162)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perikaryon (GO:0043204)|smooth endoplasmic reticulum (GO:0005790)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	amino acid binding (GO:0016597)|dopamine binding (GO:0035240)|enzyme binding (GO:0019899)|ferric iron binding (GO:0008199)|ferrous iron binding (GO:0008198)|oxygen binding (GO:0019825)|tetrahydrobiopterin binding (GO:0034617)|tyrosine 3-monooxygenase activity (GO:0004511)			NS(1)|endometrium(1)|large_intestine(1)|lung(7)|skin(1)	11		all_epithelial(84;1.46e-23)|Lung NSC(207;4.44e-11)|all_lung(207;1.11e-09)|Ovarian(85;1.78e-06)|Breast(177;1.78e-05)|Medulloblastoma(188;0.0208)|all_neural(188;0.0416)	Colorectal(5;0.00245)|COAD - Colon adenocarcinoma(6;0.0239)	BRCA - Breast invasive adenocarcinoma(625;8.45e-09)|Lung(200;0.000152)|LUSC - Lung squamous cell carcinoma(625;0.00154)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)|Metyrosine(DB00765)|Tetrahydrobiopterin(DB00360)	CCTCCTTCTCCTCAAAGGCCA	0.687																																					p.E105E		Atlas-SNP	.											.	TH	43	.	0			c.G315A						.						41	42	42					11																	2190970		2202	4299	6501	SO:0001819	synonymous_variant	7054	exon3			CTTCTCCTCAAAG	X05290	CCDS7730.1, CCDS7731.1, CCDS31338.1	11p15.5	2013-06-03			ENSG00000180176	ENSG00000180176	1.14.16.2		11782	protein-coding gene	gene with protein product	"tyrosine 3-monooxygenase"	191290					Standard	NM_199292		Approved	DYT5b	uc001lvq.3	P07101	OTTHUMG00000009559	ENST00000381178.1:c.315G>A	chr11.hg19:g.2190970C>T		197.0	0.0		155.0	86.0	NM_199292	B7ZL70|B7ZL73|Q0PWM2|Q0PWM3|Q15585|Q15588|Q15589|Q2M3B4	Silent	SNP	ENST00000381178.1	hg19	CCDS7731.1																																																																																			.	.		0.687	TH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026597.1	NM_000360		T	2190970	C	T	2190970	2	4	255	1	0	0	0	0	0	0	0	1	15853	680	24	3		3	TH	11	2190970	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1650195	2190970	132815546	390	35735										
ART1	417	hgsc.bcm.edu	37	chr11	3681383	3681383	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgaagcatgttgcagcccagCagtttggtgaggacaccttc	12	10	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:3681383C>T	ENST00000250693.1	+	3	735	c.634C>T	c.(634-636)Cag>Tag	p.Q212*		NM_004314.2	NP_004305.2	P52961	NAR1_HUMAN	ADP-ribosyltransferase 1	212					innate immune response (GO:0045087)|protein ADP-ribosylation (GO:0006471)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			endometrium(1)|large_intestine(2)|liver(1)|lung(3)|skin(1)	8		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0351)|LUSC - Lung squamous cell carcinoma(625;0.195)		TGCAGCCCAGCAGTTTGGTGA	0.652																																					p.Q212X		Atlas-SNP	.											.	ART1	21	.	0			c.C634T						.						41	38	39					11																	3681383		2201	4298	6499	SO:0001587	stop_gained	417	exon3			GCCCAGCAGTTTG	S74683	CCDS7744.1	11p15	2006-02-23			ENSG00000129744	ENSG00000129744		"CD molecules"	723	protein-coding gene	gene with protein product		601625				8812442	Standard	NM_004314		Approved	ART2, CD296	uc001lye.1	P52961	OTTHUMG00000011845	ENST00000250693.1:c.634C>T	chr11.hg19:g.3681383C>T	ENSP00000250693:p.Gln212*	124.0	0.0		138.0	6.0	NM_004314	Q6NTD2|Q96KT9	Nonsense_Mutation	SNP	ENST00000250693.1	hg19	CCDS7744.1	.	.	.	.	.	.	.	.	.	.	C	16.94	3.261029	0.59431	.	.	ENSG00000129744	ENST00000250693	.	.	.	5.28	0.88	0.19161	.	1.067370	0.07168	N	0.851914	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.5498	0.27790	0.5685:0.3517:0.0:0.0798	.	.	.	.	X	212	.	.	Q	+	1	0	ART1	3637959	0.000000	0.05858	0.392000	0.26245	0.713000	0.41058	-1.075000	0.03423	-0.094000	0.12374	0.467000	0.42956	CAG	.	.		0.652	ART1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032765.1	NM_004314		T	3681383	C	T	3681383	4	4	255	1	0	0	0	0	0	1	0	0	997	711	25	3	640	3	ART1	11	3681383	Nonsense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1490413	3681383	131325133	391	35736										
NUP98	4928	hgsc.bcm.edu	37	chr11	3716712	3716712	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aacagagcaaagatgcgcagTctctcatcctggatgaagga	11	9	2	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:3716712T>C	ENST00000324932.7	-	26	4554	c.4134A>G	c.(4132-4134)agA>agG	p.R1378R	NUP98_ENST00000355260.3_Silent_p.R1378R|NUP98_ENST00000488828.1_5'UTR|NUP98_ENST00000359171.4_Silent_p.R1378R	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	1395					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|DNA replication (GO:0006260)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore organization (GO:0006999)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nuclear pore outer ring (GO:0031080)|nucleoplasm (GO:0005654)	peptide binding (GO:0042277)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		AGATGCGCAGTCTCTCATCCT	0.468			T	"HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"	AML																																p.R1378R		Atlas-SNP	.		Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	.	NUP98	149	.	0			c.A4134G						.						199	202	201					11																	3716712		2201	4298	6499	SO:0001819	synonymous_variant	4928	exon26			GCGCAGTCTCTCA	AF071076, AF231130, BC012906, BG773331	CCDS7746.1, CCDS31347.1, CCDS41605.1, CCDS41606.1	11p15	2008-02-26	2002-08-29		ENSG00000110713	ENSG00000110713			8068	protein-coding gene	gene with protein product		601021	"nucleoporin 98kD"			9166830	Standard	NM_139131		Approved	NUP96	uc001lyh.3	P52948	OTTHUMG00000011846	ENST00000324932.7:c.4134A>G	chr11.hg19:g.3716712T>C		57.0	0.0		71.0	4.0	NM_016320	Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Silent	SNP	ENST00000324932.7	hg19	CCDS7746.1	.	.	.	.	.	.	.	.	.	.	T	7.320	0.616757	0.14129	.	.	ENSG00000110713	ENST00000429801	.	.	.	5.05	2.63	0.31362	.	.	.	.	.	T	0.53367	0.1792	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42172	-0.9467	4	.	.	.	-8.7075	5.0929	0.14718	0.0:0.314:0.1488:0.5372	.	.	.	.	A	331	.	.	T	-	1	0	NUP98	3673288	0.833000	0.29383	0.992000	0.48379	0.590000	0.36582	-0.014000	0.12656	0.319000	0.23209	0.456000	0.33151	ACT	.	.		0.468	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	NM_016320		C	3716712	T	C	3716712	2	2	255	1	0	0	0	0	0	0	0	1	10782	1664	58	2		2	NUP98	11	3716712	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	35329	3716712	131289804	392	35737										
UBQLN3	50613	hgsc.bcm.edu	37	chr11	5530073	5530073	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tctccaagttactgagcaccCggtcctggctacgtatcatc	8	14	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:5530073C>G	ENST00000311659.4	-	2	863	c.716G>C	c.(715-717)cGg>cCg	p.R239P	HBG2_ENST00000380259.2_Intron	NM_017481.2	NP_059509.1	Q9H347	UBQL3_HUMAN	ubiquilin 3	239								p.R239L(1)		NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|prostate(1)|skin(2)	39		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ACTGAGCACCCGGTCCTGGCT	0.483																																					p.R239P	Ovarian(72;684 1260 12332 41642 52180)	Atlas-SNP	.											UBQLN3,right_lower_lobe,carcinoma,+1,1	UBQLN3	107	.	1	Substitution - Missense(1)	lung(1)	c.G716C						.						91	86	87					11																	5530073		2201	4297	6498	SO:0001583	missense	50613	exon2			AGCACCCGGTCCT	AF230481	CCDS7758.1	11p15	2013-02-12			ENSG00000175520	ENSG00000175520		"Ubiquilin family"	12510	protein-coding gene	gene with protein product		605473				10831842	Standard	NM_017481		Approved	TUP-1	uc001may.1	Q9H347	OTTHUMG00000066886	ENST00000311659.4:c.716G>C	chr11.hg19:g.5530073C>G	ENSP00000347997:p.Arg239Pro	122.0	1.0		98.0	4.0	NM_017481	Q9NRE0	Missense_Mutation	SNP	ENST00000311659.4	hg19	CCDS7758.1	.	.	.	.	.	.	.	.	.	.	C	19.60	3.857233	0.71834	.	.	ENSG00000175520	ENST00000311659	T	0.46819	0.86	5.53	5.53	0.82687	.	0.000000	0.41294	D	0.000906	T	0.57917	0.2086	M	0.67517	2.055	0.45946	D	0.998773	P	0.38300	0.626	P	0.45681	0.49	T	0.61232	-0.7104	10	0.87932	D	0	-29.1404	17.3163	0.87225	0.0:1.0:0.0:0.0	.	239	Q9H347	UBQL3_HUMAN	P	239	ENSP00000347997:R239P	ENSP00000347997:R239P	R	-	2	0	UBQLN3	5486649	0.999000	0.42202	0.998000	0.56505	0.989000	0.77384	3.839000	0.55835	2.750000	0.94351	0.591000	0.81541	CGG	.	.		0.483	UBQLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143348.1	NM_017481		G	5530073	C	G	5530073	3	3	255	1	0	0	0	0	1	0	0	0	16913	652	23	4	1255	4	UBQLN3	11	5530073	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1813361	5530073	129476443	393	35738										
DNHD1	144132	hgsc.bcm.edu	37	chr11	6591490	6591490	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcttcagcttcagttttctaCgggggtcctctgggggacac	12	11	5	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:6591490C>A	ENST00000527990.2	+	39	12969	c.12969C>A	c.(12967-12969)taC>taA	p.Y4323*	DNHD1_ENST00000254579.6_Nonsense_Mutation_p.Y4323*			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	4323					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		CAGTTTTCTACGGGGGTCCTC	0.562																																					p.Y4323X		Atlas-SNP	.											.	DNHD1	198	.	0			c.C12969A						.						26	29	28					11																	6591490		1884	4107	5991	SO:0001587	stop_gained	144132	exon41			TTTCTACGGGGGT	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 47", "dynein heavy chain domain 1-like", "coiled-coil domain containing 35"	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.12969C>A	chr11.hg19:g.6591490C>A	ENSP00000436180:p.Tyr4323*	96.0	0.0		97.0	4.0	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Nonsense_Mutation	SNP	ENST00000527990.2	hg19	CCDS44532.1	.	.	.	.	.	.	.	.	.	.	C	56	25.934574	0.99967	.	.	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000530197	.	.	.	5.43	0.343	0.16001	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.3498	7.5916	0.28025	0.0:0.4312:0.0:0.5688	.	.	.	.	X	4323;4323;591	.	ENSP00000254579:Y4323X	Y	+	3	2	DNHD1	6548066	1.000000	0.71417	0.999000	0.59377	0.969000	0.65631	0.324000	0.19610	0.022000	0.15160	-0.302000	0.09304	TAC	.	.		0.562	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666		A	6591490	C	A	6591490	4	1	255	1	0	0	0	0	0	1	0	0	4670	547	19	1	13132	1	DNHD1	11	6591490	Nonsense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1061417	6591490	128415026	394	35739										
PLEKHA7	144100	hgsc.bcm.edu	37	chr11	16838667	16838667	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctgccacacggtgccatcccGgtgcgcccggcgctcttcac	11	19	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:16838667G>T	ENST00000355661.3	-	11	1556	c.1546C>A	c.(1546-1548)Cgg>Agg	p.R516R	PLEKHA7_ENST00000532079.1_Intron|PLEKHA7_ENST00000448080.2_Silent_p.R516R|PLEKHA7_ENST00000531066.1_Silent_p.R516R			Q6IQ23	PKHA7_HUMAN	pleckstrin homology domain containing, family A member 7	516					epithelial cell-cell adhesion (GO:0090136)|zonula adherens maintenance (GO:0045218)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|zonula adherens (GO:0005915)	delta-catenin binding (GO:0070097)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(1)|prostate(2)|skin(7)|urinary_tract(1)	37						GTGCCATCCCGGTGCGCCCGG	0.662																																					p.R516R		Atlas-SNP	.											.	PLEKHA7	120	.	0			c.C1546A						.						49	53	51					11																	16838667		2199	4294	6493	SO:0001819	synonymous_variant	144100	exon11			CATCCCGGTGCGC	BC033239	CCDS31434.1	11p15	2013-01-10			ENSG00000166689	ENSG00000166689		"Pleckstrin homology (PH) domain containing"	27049	protein-coding gene	gene with protein product		612686				12477932	Standard	NM_175058		Approved	DKFZp686M22243	uc001mmo.3	Q6IQ23	OTTHUMG00000165954	ENST00000355661.3:c.1546C>A	chr11.hg19:g.16838667G>T		77.0	0.0		100.0	4.0	NM_175058	B4DK33|B4DWC3|Q86VZ7	Silent	SNP	ENST00000355661.3	hg19	CCDS31434.1																																																																																			.	.		0.662	PLEKHA7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000387242.2	NM_175058		T	16838667	G	T	16838667	2	4	255	1	0	0	0	0	0	0	0	1	12070	1115	39	1		1	PLEKHA7	11	16838667	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	10247177	16838667	118167849	395	35740										
ABCC8	6833	hgsc.bcm.edu	37	chr11	17428527	17428527	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gtcgatggccaccaggaccaTgtgcttgagcagctgtgaga	14	10	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:17428527T>C	ENST00000389817.3	-	25	3138	c.3070A>G	c.(3070-3072)Atg>Gtg	p.M1024V	ABCC8_ENST00000302539.4_Missense_Mutation_p.M1025V			Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 8	1024	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium ion transmembrane transporter activity (GO:0015079)|sulfonylurea receptor activity (GO:0008281)			NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(38)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	67				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Chlorpropamide(DB00672)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Gliquidone(DB01251)|Glyburide(DB01016)|Glycodiazine(DB01382)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)|Tolbutamide(DB01124)	ACCAGGACCATGTGCTTGAGC	0.637																																					p.M1024V		Atlas-SNP	.											.	ABCC8	170	.	0			c.A3070G						.						93	89	91					11																	17428527		2200	4293	6493	SO:0001583	missense	6833	exon25			GGACCATGTGCTT	L78207	CCDS31437.1, CCDS73264.1	11p15.1	2014-09-17			ENSG00000006071	ENSG00000006071		"ATP binding cassette transporters / subfamily C"	59	protein-coding gene	gene with protein product	"sulfonylurea receptor (hyperinsulinemia)"	600509		SUR, HRINS		7920639, 7716548	Standard	NM_000352		Approved	HI, PHHI, SUR1, MRP8, ABC36, HHF1, TNDM2	uc001mnc.3	Q09428	OTTHUMG00000166316	ENST00000389817.3:c.3070A>G	chr11.hg19:g.17428527T>C	ENSP00000374467:p.Met1024Val	151.0	0.0		95.0	4.0	NM_000352	A6NMX8|E3UYX6|O75948|Q16583	Missense_Mutation	SNP	ENST00000389817.3	hg19	CCDS31437.1	.	.	.	.	.	.	.	.	.	.	T	7.030	0.560413	0.13498	.	.	ENSG00000006071	ENST00000389817;ENST00000302539	D;D	0.87412	-2.25;-2.25	5.97	5.97	0.96955	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.096709	0.64402	D	0.000001	T	0.69726	0.3143	N	0.02345	-0.59	0.32596	N	0.526506	B	0.02656	0.0	B	0.01281	0.0	T	0.70193	-0.4939	10	0.33141	T	0.24	.	10.2347	0.43275	0.2549:0.0:0.0:0.7451	.	1024	Q09428	ABCC8_HUMAN	V	1024;1025	ENSP00000374467:M1024V;ENSP00000303960:M1025V	ENSP00000303960:M1025V	M	-	1	0	ABCC8	17385103	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.932000	0.40143	2.275000	0.75901	0.533000	0.62120	ATG	.	.		0.637	ABCC8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389093.1	NM_000352		C	17428527	T	C	17428527	3	2	255	1	0	0	0	0	1	0	0	0	58	1464	51	2	1735	2	ABCC8	11	17428527	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	589860	17428527	117577989	396	35741										
FANCF	2188	hgsc.bcm.edu	37	chr11	22646564	22646564	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agacagcgctgggtggcggcTagtcactaaagtcaaaagcc	13	10	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:22646564T>C	ENST00000327470.3	-	1	823	c.793A>G	c.(793-795)Agc>Ggc	p.S265G	AC103801.2_ENST00000428556.2_5'Flank	NM_022725.3	NP_073562.1	Q9NPI8	FANCF_HUMAN	Fanconi anemia, complementation group F	265					DNA repair (GO:0006281)|ovarian follicle development (GO:0001541)|spermatogenesis (GO:0007283)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)	ubiquitin-protein transferase activity (GO:0004842)			kidney(3)|large_intestine(3)|lung(6)|skin(1)	13						GGGTGGCGGCTAGTCACTAAA	0.547			"N, F"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia		OREG0020844	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S265G		Atlas-SNP	.	yes	Rec		Fanconi anaemia F	11	11p15	2188	"Fanconi anemia, complementation group F"		L	.	FANCF	24	.	0			c.A793G						.						51	61	57					11																	22646564		2203	4300	6503	SO:0001583	missense	2188	exon1	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GGCGGCTAGTCAC		CCDS7857.1	11p15	2014-09-17				ENSG00000183161		"Fanconi anemia, complementation groups"	3587	protein-coding gene	gene with protein product		613897				9382107	Standard	NM_022725		Approved	FAF	uc001mql.1	Q9NPI8		ENST00000327470.3:c.793A>G	chr11.hg19:g.22646564T>C	ENSP00000330875:p.Ser265Gly	103.0	0.0	757	79.0	4.0	NM_022725	Q52LM0	Missense_Mutation	SNP	ENST00000327470.3	hg19	CCDS7857.1	.	.	.	.	.	.	.	.	.	.	T	2.373	-0.343870	0.05208	.	.	ENSG00000183161	ENST00000327470	T	0.31247	1.5	5.34	-0.254	0.12992	.	0.618762	0.16096	N	0.229836	T	0.05227	0.0139	N	0.00483	-1.445	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.33879	-0.9851	10	0.02654	T	1	-2.4823	1.633	0.02736	0.131:0.4128:0.1282:0.328	.	265	Q9NPI8	FANCF_HUMAN	G	265	ENSP00000330875:S265G	ENSP00000330875:S265G	S	-	1	0	FANCF	22603140	0.000000	0.05858	0.000000	0.03702	0.052000	0.14988	0.260000	0.18424	0.034000	0.15491	0.459000	0.35465	AGC	.	.		0.547	FANCF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387712.2	NM_022725		C	22646564	T	C	22646564	3	2	255	1	0	0	0	0	1	0	0	0	5675	1522	53	2	335	2	FANCF	11	22646564	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	5218037	22646564	112359952	397	35742										
LIN7C	55327	hgsc.bcm.edu	37	chr11	27523454	27523454	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agtttttccaataattcaatTgctctacaaatatctagagt	4	7	3	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:27523454T>C	ENST00000278193.2	-	2	71	c.51A>G	c.(49-51)gcA>gcG	p.A17A	LIN7C_ENST00000524596.1_Silent_p.A17A	NM_018362.3	NP_060832.1	Q9NUP9	LIN7C_HUMAN	lin-7 homolog C (C. elegans)	17	L27. {ECO:0000255|PROSITE- ProRule:PRU00365}.				exocytosis (GO:0006887)|morphogenesis of an epithelial sheet (GO:0002011)|neurotransmitter secretion (GO:0007269)|protein transport (GO:0015031)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|MPP7-DLG1-LIN7 complex (GO:0097025)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	cytoskeletal protein binding (GO:0008092)|L27 domain binding (GO:0097016)|protein domain specific binding (GO:0019904)			endometrium(2)|lung(2)|upper_aerodigestive_tract(1)	5						ATAATTCAATTGCTCTACAAA	0.388																																					p.A17A		Atlas-SNP	.											LIN7C,NS,carcinoma,0,1	LIN7C	24	.	0			c.A51G						.						81	79	79					11																	27523454		2201	4298	6499	SO:0001819	synonymous_variant	55327	exon2			TTCAATTGCTCTA	AK002077	CCDS7864.1	11p14	2008-07-18				ENSG00000148943			17789	protein-coding gene	gene with protein product	"LIN-7 protein 3"	612332				10341223	Standard	NM_018362		Approved	MALS-3, Lin7c, LIN-7C, LIN-7-C, VELI3, FLJ11215	uc001mrl.3	Q9NUP9		ENST00000278193.2:c.51A>G	chr11.hg19:g.27523454T>C		94.0	0.0		87.0	28.0	NM_018362		Silent	SNP	ENST00000278193.2	hg19	CCDS7864.1																																																																																			.	.		0.388	LIN7C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388311.2	NM_018362		C	27523454	T	C	27523454	2	2	255	1	0	0	0	0	0	0	0	1	8821	1799	63	2		2	LIN7C	11	27523454	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	4876890	27523454	107483062	398	35743										
RCN1	5954	hgsc.bcm.edu	37	chr11	32125951	32125951	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggaaatattggagaactggaAcatgtttgtcggaagccaag	13	5	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:32125951A>G	ENST00000054950.3	+	6	1222	c.929A>G	c.(928-930)aAc>aGc	p.N310S	RP1-65P5.3_ENST00000533009.1_RNA|RCN1_ENST00000532942.1_Missense_Mutation_p.N259S	NM_002901.2	NP_002892.1	Q15293	RCN1_HUMAN	reticulocalbin 1, EF-hand calcium binding domain	310	EF-hand 6. {ECO:0000255|PROSITE- ProRule:PRU00448}.				camera-type eye development (GO:0043010)|in utero embryonic development (GO:0001701)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)	calcium ion binding (GO:0005509)			breast(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(6)	17	Lung SC(675;0.225)					GAGAACTGGAACATGTTTGTC	0.403																																					p.N310S		Atlas-SNP	.											.	RCN1	37	.	0			c.A929G						.						97	82	87					11																	32125951		2202	4299	6501	SO:0001583	missense	5954	exon6			ACTGGAACATGTT	D42073	CCDS7876.1	11p13	2013-01-10			ENSG00000049449	ENSG00000049449		"EF-hand domain containing"	9934	protein-coding gene	gene with protein product	"proliferation-inducing gene 20"	602735		RCN		9192846, 8586628	Standard	NM_002901		Approved	Rcal, PIG20, FLJ37041	uc010reb.2	Q15293		ENST00000054950.3:c.929A>G	chr11.hg19:g.32125951A>G	ENSP00000054950:p.Asn310Ser	139.0	0.0		115.0	5.0	NM_002901	B7Z1M1|D3DR00	Missense_Mutation	SNP	ENST00000054950.3	hg19	CCDS7876.1	.	.	.	.	.	.	.	.	.	.	a	13.79	2.340836	0.41498	.	.	ENSG00000049449	ENST00000532942;ENST00000054950;ENST00000528630	T;T	0.53423	0.62;0.84	5.82	4.7	0.59300	EF-hand-like domain (1);	0.077381	0.85682	N	0.000000	T	0.46405	0.1391	M	0.62154	1.92	0.80722	D	1	B;B	0.23854	0.024;0.092	B;B	0.25884	0.036;0.064	T	0.42783	-0.9431	10	0.59425	D	0.04	-30.5925	11.5839	0.50908	0.9307:0.0:0.0693:0.0	.	310;259	Q15293;B7Z1M1	RCN1_HUMAN;.	S	259;310;7	ENSP00000436422:N259S;ENSP00000054950:N310S	ENSP00000054950:N310S	N	+	2	0	RCN1	32082527	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	6.312000	0.72840	1.045000	0.40225	0.533000	0.62120	AAC	.	.		0.403	RCN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388510.1	NM_002901		G	32125951	A	G	32125951	3	3	255	1	0	0	0	0	1	0	0	0	13194	43	2	2	951	2	RCN1	11	32125951	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	4602497	32125951	102880565	399	35744										
C11orf41	25758	hgsc.bcm.edu	37	chr11	33573676	33573676	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctgcagtttgtgagccaagcGgacaacatacagtcctgcaa	10	11	0	1	rs372452571		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:33573676G>T	ENST00000321505.4	+	5	3033	c.2853G>T	c.(2851-2853)gcG>gcT	p.A951A	KIAA1549L_ENST00000389726.3_Silent_p.A957A|KIAA1549L_ENST00000265654.5_Silent_p.A957A			Q6ZVL6	K154L_HUMAN	KIAA1549-like	951						integral component of membrane (GO:0016021)											TGAGCCAAGCGGACAACATAC	0.453																																					p.A951A		Atlas-SNP	.											C11orf41_ENST00000321505,NS,carcinoma,0,2	.	.	.	0			c.G2853T						.						69	68	68					11																	33573676		1929	4140	6069	SO:0001819	synonymous_variant	25758	exon5			CCAAGCGGACAAC	U10991	CCDS44565.1, CCDS44565.2	11p13	2012-08-09	2012-08-09	2012-08-09	ENSG00000110427	ENSG00000110427			24836	protein-coding gene	gene with protein product		612297	"chromosome 11 open reading frame 69", "chromosome 11 open reading frame 41"	C11orf69, C11orf41			Standard	NM_012194		Approved	G2, MGC34830	uc021qfs.1	Q6ZVL6	OTTHUMG00000150410	ENST00000321505.4:c.2853G>T	chr11.hg19:g.33573676G>T		103.0	0.0		75.0	4.0	NM_012194	B0QYU0	Silent	SNP	ENST00000321505.4	hg19	CCDS44565.2	.	.	.	.	.	.	.	.	.	.	G	5.776	0.327476	0.10956	.	.	ENSG00000110427	ENST00000526400	.	.	.	6.08	-12.2	0.00006	.	.	.	.	.	T	0.31295	0.0792	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	T	0.47586	-0.9106	4	.	.	.	-5.2645	1.6363	0.02743	0.1523:0.2863:0.297:0.2645	.	.	.	.	L	349	.	.	R	+	2	0	C11orf41	33530252	0.000000	0.05858	0.000000	0.03702	0.659000	0.38960	-4.800000	0.00184	-3.665000	0.00124	-2.047000	0.00414	CGG	.	.		0.453	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194		T	33573676	G	T	33573676	2	4	255	1	0	0	0	0	0	0	0	1	1642	1103	39	1		1	C11orf41	11	33573676	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	1447725	33573676	101432840	400	35745										
LMO2	4005	hgsc.bcm.edu	37	chr11	33890910	33890910	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	actctgaagggtccaggctcTtcctttcgatggccgaggac	12	12	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:33890910T>C	ENST00000395833.3	-	1	452	c.23A>G	c.(22-24)aAg>aGg	p.K8R	LMO2_ENST00000493667.1_5'Flank|LMO2_ENST00000257818.2_Missense_Mutation_p.K77R	NM_001142315.1|NM_001142316.1	NP_001135787.1|NP_001135788.1	P25791	RBTN2_HUMAN	LIM domain only 2 (rhombotin-like 1)	8					cellular response to thyroid hormone stimulus (GO:0097067)|embryonic hemopoiesis (GO:0035162)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|multicellular organismal development (GO:0007275)|negative regulation of erythrocyte differentiation (GO:0045647)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|chromatin binding (GO:0003682)|cofactor binding (GO:0048037)|E-box binding (GO:0070888)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|large_intestine(1)|lung(7)|prostate(1)|stomach(1)|urinary_tract(1)	14						GTCCAGGCTCTTCCTTTCGAT	0.771			T	TRD@	T-ALL																																p.K77R		Atlas-SNP	.		Dom	yes		11	11p13	4005	LIM domain only 2 (rhombotin-like 1) (RBTN2)		L	.	LMO2	21	.	0			c.A230G						.						6	5	5					11																	33890910		1480	2776	4256	SO:0001583	missense	4005	exon4			AGGCTCTTCCTTT	X61118	CCDS7888.2, CCDS44567.1	11p13	2008-07-18			ENSG00000135363	ENSG00000135363			6642	protein-coding gene	gene with protein product	"T-cell translocation gene 2", "rhombotin-like 1"	180385		RBTNL1		2034676	Standard	NM_005574		Approved	TTG2, RHOM2, RBTN2	uc010rem.2	P25791	OTTHUMG00000157176	ENST00000395833.3:c.23A>G	chr11.hg19:g.33890910T>C	ENSP00000379175:p.Lys8Arg	41.0	0.0		45.0	4.0	NM_005574	Q9HD58	Missense_Mutation	SNP	ENST00000395833.3	hg19	CCDS44567.1	.	.	.	.	.	.	.	.	.	.	T	15.47	2.844132	0.51164	.	.	ENSG00000135363	ENST00000395833;ENST00000257818	T;T	0.60672	0.17;0.56	4.38	4.38	0.52667	.	0.125963	0.49916	U	0.000126	T	0.44008	0.1273	L	0.46157	1.445	0.45580	D	0.998524	P;B	0.40144	0.704;0.011	B;B	0.29716	0.106;0.003	T	0.38499	-0.9658	10	0.20046	T	0.44	.	13.2524	0.60060	0.0:0.0:0.0:1.0	.	77;8	P25791-3;P25791	.;RBTN2_HUMAN	R	8;77	ENSP00000379175:K8R;ENSP00000257818:K77R	ENSP00000257818:K77R	K	-	2	0	LMO2	33847486	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.515000	0.67049	1.609000	0.50190	0.377000	0.23210	AAG	.	.		0.771	LMO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347777.1	NM_005574		C	33890910	T	C	33890910	3	2	255	1	0	0	0	0	1	0	0	0	8861	1609	56	2	465	2	LMO2	11	33890910	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	317234	33890910	101115606	401	35746										
EHF	26298	hgsc.bcm.edu	37	chr11	34673334	34673334	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctcagatctccatgacaaccAccagtcaccttcctgttggt	6	15	3	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:34673334A>G	ENST00000533754.1	+	6	743	c.526A>G	c.(526-528)Acc>Gcc	p.T176A	EHF_ENST00000530286.1_Missense_Mutation_p.T176A|EHF_ENST00000531794.1_Missense_Mutation_p.T198A|EHF_ENST00000450654.2_Intron|EHF_ENST00000257831.3_Missense_Mutation_p.T176A					ets homologous factor										NFIA/EHF(2)	autonomic_ganglia(1)|cervix(1)|endometrium(3)|kidney(3)|lung(8)|upper_aerodigestive_tract(1)	17		all_hematologic(20;0.117)	Epithelial(1;0.055)|all cancers(1;0.137)|STAD - Stomach adenocarcinoma(6;0.235)			CATGACAACCACCAGTCACCT	0.488																																					p.T198A		Atlas-SNP	.											.	EHF	38	.	0			c.A592G						.						124	114	117					11																	34673334		2202	4298	6500	SO:0001583	missense	26298	exon6			ACAACCACCAGTC	AF170583	CCDS7894.1, CCDS55752.1, CCDS55753.1	11p12	2008-07-18				ENSG00000135373			3246	protein-coding gene	gene with protein product	"epithelium-specific ets factor 3", "ESE3 transcription factor"	605439				10527851	Standard	NM_012153		Approved	ESE3, ESEJ	uc021qfu.1	Q9NZC4		ENST00000533754.1:c.526A>G	chr11.hg19:g.34673334A>G	ENSP00000435837:p.Thr176Ala	85.0	0.0		57.0	4.0	NM_001206616		Missense_Mutation	SNP	ENST00000533754.1	hg19	CCDS7894.1	.	.	.	.	.	.	.	.	.	.	A	5.794	0.330767	0.10956	.	.	ENSG00000135373	ENST00000257831;ENST00000530286;ENST00000533754;ENST00000531794	T;T;T;T	0.06687	3.29;3.29;3.29;3.27	6.17	-0.36	0.12568	.	0.378824	0.22635	N	0.057538	T	0.02304	0.0071	N	0.03608	-0.345	0.24015	N	0.996169	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40136	-0.9579	10	0.17369	T	0.5	.	0.6405	0.00810	0.3025:0.1157:0.263:0.3188	.	198;176	E9PSB2;Q9NZC4	.;EHF_HUMAN	A	176;176;176;198	ENSP00000257831:T176A;ENSP00000433508:T176A;ENSP00000435837:T176A;ENSP00000435835:T198A	ENSP00000257831:T176A	T	+	1	0	EHF	34629910	0.006000	0.16342	0.270000	0.24601	0.969000	0.65631	0.044000	0.13992	-0.052000	0.13311	0.533000	0.62120	ACC	.	.		0.488	EHF-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000389855.1	NM_012153		G	34673334	A	G	34673334	3	3	255	1	0	0	0	0	1	0	0	0	4983	159	6	2	544	2	EHF	11	34673334	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	782424	34673334	100333182	402	35747										
PHF21A	51317	hgsc.bcm.edu	37	chr11	46098351	46098351	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tggcttggagttcatgaagcTgtttctttaagtcagcattc	10	7	3	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:46098351T>C	ENST00000418153.2	-	5	306	c.107A>G	c.(106-108)cAg>cGg	p.Q36R	PHF21A_ENST00000257821.4_Missense_Mutation_p.Q36R|PHF21A_ENST00000323180.6_Missense_Mutation_p.Q36R			Q96BD5	PF21A_HUMAN	PHD finger protein 21A	36	Gln-rich.				blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|suckling behavior (GO:0001967)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(10)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	29						TTCATGAAGCTGTTTCTTTAA	0.373																																					p.Q36R		Atlas-SNP	.											.	PHF21A	107	.	0			c.A107G						.						132	123	126					11																	46098351		2202	4299	6501	SO:0001583	missense	51317	exon5			TGAAGCTGTTTCT	AL359593	CCDS31474.1, CCDS44578.1	11p11.2	2013-01-28			ENSG00000135365	ENSG00000135365		"Zinc fingers, PHD-type"	24156	protein-coding gene	gene with protein product		608325				11214970, 12032298	Standard	NM_001101802		Approved	BHC80, KIAA1696, BM-006	uc001ncc.4	Q96BD5	OTTHUMG00000167038	ENST00000418153.2:c.107A>G	chr11.hg19:g.46098351T>C	ENSP00000398824:p.Gln36Arg	105.0	0.0		89.0	4.0	NM_016621	D3DQP5|Q6AWA2|Q9C0G7|Q9H8V9|Q9HAK6|Q9NZE9	Missense_Mutation	SNP	ENST00000418153.2	hg19	CCDS44578.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.949696	0.73787	.	.	ENSG00000135365	ENST00000257821;ENST00000323180;ENST00000418153;ENST00000524497;ENST00000531959;ENST00000529734;ENST00000529782;ENST00000533757	T;T;T;T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.82	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.55273	0.1910	N	0.24115	0.695	0.46317	D	0.998986	D;D	0.60160	0.987;0.981	D;D	0.70487	0.953;0.969	T	0.56257	-0.8009	10	0.44086	T	0.13	-4.1686	16.3786	0.83431	0.0:0.0:0.0:1.0	.	36;36	Q96BD5;Q96BD5-2	PF21A_HUMAN;.	R	36;36;36;43;43;36;13;36	ENSP00000257821:Q36R;ENSP00000323152:Q36R;ENSP00000398824:Q36R;ENSP00000431273:Q43R;ENSP00000432916:Q43R;ENSP00000436157:Q36R;ENSP00000435121:Q13R;ENSP00000432406:Q36R	ENSP00000257821:Q36R	Q	-	2	0	PHF21A	46054927	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.676000	0.74498	2.323000	0.78572	0.528000	0.53228	CAG	.	.		0.373	PHF21A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392583.1	NM_016621		C	46098351	T	C	46098351	3	2	255	1	0	0	0	0	1	0	0	0	11842	1580	55	2	2021	2	PHF21A	11	46098351	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	11425017	46098351	88908165	403	35748										
OR10AG1	282770	hgsc.bcm.edu	37	chr11	55735603	55735603	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cttacaaatagccacgtagcGgtcataggccatcactgtca	8	12	3	0	rs150679428		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:55735603G>T	ENST00000312345.2	-	1	387	c.337C>A	c.(337-339)Cgc>Agc	p.R113S		NM_001005491.1	NP_001005491.1	Q8NH19	O10AG_HUMAN	olfactory receptor, family 10, subfamily AG, member 1	113						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R113C(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(24)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	40	Esophageal squamous(21;0.0137)					GCCACGTAGCGGTCATAGGCC	0.428																																					p.R113S		Atlas-SNP	.											OR10AG1,NS,carcinoma,+1,2	OR10AG1	100	.	1	Substitution - Missense(1)	large_intestine(1)	c.C337A						.						88	86	86					11																	55735603		2201	4296	6497	SO:0001583	missense	282770	exon1			CGTAGCGGTCATA	AB065594	CCDS31514.1	11q11	2012-08-09			ENSG00000174970	ENSG00000174970		"GPCR / Class A : Olfactory receptors"	19607	protein-coding gene	gene with protein product							Standard	NM_001005491		Approved		uc010rit.2	Q8NH19	OTTHUMG00000166824	ENST00000312345.2:c.337C>A	chr11.hg19:g.55735603G>T	ENSP00000311477:p.Arg113Ser	92.0	1.0		88.0	4.0	NM_001005491	B2RNH4|Q6IEU3	Missense_Mutation	SNP	ENST00000312345.2	hg19	CCDS31514.1	.	.	.	.	.	.	.	.	.	.	G	13.26	2.184166	0.38609	.	.	ENSG00000174970	ENST00000312345	T	0.77620	-1.11	5.47	4.56	0.56223	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49305	D	0.000159	D	0.90532	0.7033	H	0.97540	4.025	0.29222	N	0.873839	D	0.67145	0.996	D	0.69824	0.966	D	0.86697	0.1927	10	0.87932	D	0	.	7.4436	0.27198	0.0851:0.0:0.7504:0.1645	.	113	Q8NH19	O10AG_HUMAN	S	113	ENSP00000311477:R113S	ENSP00000311477:R113S	R	-	1	0	OR10AG1	55492179	0.972000	0.33761	0.961000	0.40146	0.030000	0.12068	1.405000	0.34635	1.357000	0.45904	0.477000	0.44152	CGC	.	G|1.000;A|0.000		0.428	OR10AG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391531.1	NM_001005491		T	55735603	G	T	55735603	3	4	255	1	0	0	0	0	1	0	0	0	10906	1116	39	1	571	1	OR10AG1	11	55735603	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	9637252	55735603	79270913	404	35749										
OR9G4	283189	hgsc.bcm.edu	37	chr11	56511197	56511197	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctgggaatctgctgagaaacCcaacaagatgaattcagtca	9	9	3	3	rs367701319		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:56511197C>A	ENST00000302957.3	-	1	90	c.91G>T	c.(91-93)Ggt>Tgt	p.G31C		NM_001005284.1	NP_001005284.1	Q8NGQ1	OR9G4_HUMAN	olfactory receptor, family 9, subfamily G, member 4	31						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G31S(1)		NS(1)|autonomic_ganglia(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	34						GCTGAGAAACCCAACAAGATG	0.428																																					p.G31C		Atlas-SNP	.											OR9G4,NS,carcinoma,0,1	OR9G4	73	.	1	Substitution - Missense(1)	prostate(1)	c.G91T						.	C	CYS/GLY	1,4401	2.1+/-5.4	0,1,2200	84	77	79		91	4.9	1	11		79	0,8592		0,0,4296	no	missense	OR9G4	NM_001005284.1	159	0,1,6496	AA,AC,CC		0.0,0.0227,0.0077	probably-damaging	31/328	56511197	1,12993	2201	4296	6497	SO:0001583	missense	283189	exon1			AGAAACCCAACAA	BK004400	CCDS31537.1	11q11	2012-08-09			ENSG00000172457	ENSG00000172457		"GPCR / Class A : Olfactory receptors"	15322	protein-coding gene	gene with protein product							Standard	NM_001005284		Approved		uc010rjo.2	Q8NGQ1	OTTHUMG00000166932	ENST00000302957.3:c.91G>T	chr11.hg19:g.56511197C>A	ENSP00000307515:p.Gly31Cys	138.0	0.0		95.0	4.0	NM_001005284	Q6IF62|Q96RA9	Missense_Mutation	SNP	ENST00000302957.3	hg19	CCDS31537.1	.	.	.	.	.	.	.	.	.	.	C	15.09	2.729180	0.48833	2.27E-4	0.0	ENSG00000172457	ENST00000302957	T	0.00662	5.93	4.9	4.9	0.64082	.	0.000000	0.40385	N	0.001118	T	0.03136	0.0092	H	0.94734	3.575	0.48830	D	0.999713	B	0.23735	0.09	B	0.25506	0.061	T	0.06144	-1.0843	10	0.87932	D	0	-13.0418	16.802	0.85617	0.0:1.0:0.0:0.0	.	31	Q8NGQ1	OR9G4_HUMAN	C	31	ENSP00000307515:G31C	ENSP00000307515:G31C	G	-	1	0	OR9G4	56267773	0.985000	0.35326	0.984000	0.44739	0.716000	0.41182	3.940000	0.56599	2.546000	0.85860	0.549000	0.68633	GGT	.	.		0.428	OR9G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391945.1	NM_001005284		A	56511197	C	A	56511197	3	1	255	1	0	0	0	0	1	0	0	0	11260	623	22	3	895	3	OR9G4	11	56511197	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	775594	56511197	78495319	405	35750										
YPEL4	219539	hgsc.bcm.edu	37	chr11	57413467	57413467	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gagcccctcagtcccagccgTtgtccttcaccatgtgtgac	9	16	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:57413467T>C	ENST00000524669.1	-	5	3093	c.371A>G	c.(370-372)aAc>aGc	p.N124S	AP000662.4_ENST00000530595.1_RNA|YPEL4_ENST00000544993.1_Missense_Mutation_p.N124S|YPEL4_ENST00000534711.1_Missense_Mutation_p.N124S|YPEL4_ENST00000531442.1_5'Flank|YPEL4_ENST00000300022.3_Missense_Mutation_p.N124S			Q96NS1	YPEL4_HUMAN	yippee-like 4 (Drosophila)	124						nucleus (GO:0005634)				lung(2)|skin(1)	3						GTCCCAGCCGTTGTCCTTCAC	0.552																																					p.N124S		Atlas-SNP	.											.	YPEL4	5	.	0			c.A371G						.						173	130	145					11																	57413467		2201	4296	6497	SO:0001583	missense	219539	exon5			CAGCCGTTGTCCT	AK054775	CCDS7963.1	11q12	2008-02-05				ENSG00000166793			18328	protein-coding gene	gene with protein product		609725					Standard	NM_145008		Approved	FLJ30213	uc001nkv.4	Q96NS1		ENST00000524669.1:c.371A>G	chr11.hg19:g.57413467T>C	ENSP00000432648:p.Asn124Ser	64.0	0.0		75.0	4.0	NM_145008	B3KW92|Q2M3U7|Q65Z98	Missense_Mutation	SNP	ENST00000524669.1	hg19	CCDS7963.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.309891	0.81247	.	.	ENSG00000166793	ENST00000524669;ENST00000300022;ENST00000544993;ENST00000534711	.	.	.	5.42	5.42	0.78866	.	0.000000	0.64402	D	0.000001	T	0.51415	0.1673	L	0.45285	1.41	0.80722	D	1	P	0.37612	0.602	B	0.38803	0.282	T	0.48127	-0.9062	9	0.24483	T	0.36	-7.3639	15.1263	0.72486	0.0:0.0:0.0:1.0	.	124	Q96NS1	YPEL4_HUMAN	S	124	.	ENSP00000300022:N124S	N	-	2	0	YPEL4	57170043	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.775000	0.85489	2.057000	0.61298	0.459000	0.35465	AAC	.	.		0.552	YPEL4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393370.1	NM_145008		C	57413467	T	C	57413467	3	2	255	1	0	0	0	0	1	0	0	0	17507	1725	60	2	16	2	YPEL4	11	57413467	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	902270	57413467	77593049	406	35751										
FAM111B	374393	hgsc.bcm.edu	37	chr11	58877115	58877115	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	catcatgaattccatgaagaCtgaagaaaacaagtcattta	6	7	2	5			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:58877115C>A	ENST00000343597.3	+	3	208	c.17C>A	c.(16-18)aCt>aAt	p.T6N	FAM111B_ENST00000529618.1_Intron|FAM111B_ENST00000411426.1_Intron	NM_198947.3	NP_945185.1	Q6SJ93	F111B_HUMAN	family with sequence similarity 111, member B	6							catalytic activity (GO:0003824)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(12)|ovary(3)|pancreas(1)|skin(1)	40						TCCATGAAGACTGAAGAAAAC	0.368																																					p.T6N		Atlas-SNP	.											.	FAM111B	84	.	0			c.C17A						.						97	88	91					11																	58877115		2201	4295	6496	SO:0001583	missense	374393	exon3			TGAAGACTGAAGA	BC062456	CCDS7972.1, CCDS44611.1	11q12.1	2014-03-13			ENSG00000189057	ENSG00000189057			24200	protein-coding gene	gene with protein product		615584				24268661	Standard	NM_198947		Approved	CANP	uc001nnl.3	Q6SJ93	OTTHUMG00000167279	ENST00000343597.3:c.17C>A	chr11.hg19:g.58877115C>A	ENSP00000341565:p.Thr6Asn	61.0	0.0		64.0	4.0	NM_198947	B4E2G2|Q6P661	Missense_Mutation	SNP	ENST00000343597.3	hg19	CCDS7972.1	.	.	.	.	.	.	.	.	.	.	C	0.627	-0.818934	0.02776	.	.	ENSG00000189057	ENST00000343597	T	0.31769	1.48	1.65	-0.869	0.10649	.	.	.	.	.	T	0.14917	0.0360	N	0.22421	0.69	0.09310	N	1	B	0.27594	0.182	B	0.15870	0.014	T	0.18209	-1.0344	9	0.37606	T	0.19	.	2.8272	0.05488	0.0:0.4:0.3498:0.2503	.	6	Q6SJ93	F111B_HUMAN	N	6	ENSP00000341565:T6N	ENSP00000341565:T6N	T	+	2	0	FAM111B	58633691	0.039000	0.19947	0.011000	0.14972	0.005000	0.04900	-0.073000	0.11468	-0.208000	0.10171	-0.378000	0.06908	ACT	.	.		0.368	FAM111B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393974.1	NM_198947		A	58877115	C	A	58877115	3	1	255	1	0	0	0	0	1	0	0	0	5405	565	20	3	19	3	FAM111B	11	58877115	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1463648	58877115	76129401	407	35752										
PATL1	219988	hgsc.bcm.edu	37	chr11	59406813	59406813	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cagggtctgaactctgtaggTcttcaccacggctcaggagg	13	11	5	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:59406813T>C	ENST00000300146.9	-	17	2177	c.2093A>G	c.(2092-2094)gAc>gGc	p.D698G	AP000442.1_ENST00000531311.1_RNA|AP000442.1_ENST00000531108.1_RNA	NM_152716.2	NP_689929.2	Q86TB9	PATL1_HUMAN	protein associated with topoisomerase II homolog 1 (yeast)	698	Involved in nuclear spleckles localization.|Region C.				cytoplasmic mRNA processing body assembly (GO:0033962)|deadenylation-dependent decapping of nuclear-transcribed mRNA (GO:0000290)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(2)|lung(5)|ovary(1)|prostate(2)	11						ACTCTGTAGGTCTTCACCACG	0.438																																					p.D698G		Atlas-SNP	.											.	PATL1	92	.	0			c.A2093G						.																																			SO:0001583	missense	219988	exon17			TGTAGGTCTTCAC	AK094193	CCDS44613.1	11q12.1	2012-06-07	2007-10-18		ENSG00000166889	ENSG00000166889			26721	protein-coding gene	gene with protein product		614660				17936923	Standard	NM_152716		Approved	FLJ36874, Pat1b	uc001noe.4	Q86TB9	OTTHUMG00000167423	ENST00000300146.9:c.2093A>G	chr11.hg19:g.59406813T>C	ENSP00000300146:p.Asp698Gly	109.0	0.0		91.0	4.0	NM_152716	B3KXT9|Q2TA86|Q6P166|Q8N9M6|Q8NI63	Missense_Mutation	SNP	ENST00000300146.9	hg19	CCDS44613.1	.	.	.	.	.	.	.	.	.	.	T	17.03	3.284592	0.59867	.	.	ENSG00000166889	ENST00000300146	T	0.42513	0.97	5.67	5.67	0.87782	.	0.195541	0.53938	D	0.000056	T	0.26810	0.0656	N	0.11427	0.14	0.44042	D	0.996777	B	0.27316	0.175	B	0.29267	0.1	T	0.11060	-1.0603	10	0.20046	T	0.44	-15.7101	15.5908	0.76526	0.0:0.0:0.0:1.0	.	698	Q86TB9	PATL1_HUMAN	G	698	ENSP00000300146:D698G	ENSP00000300146:D698G	D	-	2	0	PATL1	59163389	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.072000	0.57563	2.170000	0.68504	0.533000	0.62120	GAC	.	.		0.438	PATL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394559.1	NM_152716		C	59406813	T	C	59406813	3	2	255	1	0	0	0	0	1	0	0	0	11484	1667	58	2	231	2	PATL1	11	59406813	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	529698	59406813	75599703	408	35753										
EML3	256364	hgsc.bcm.edu	37	chr11	62370651	62370651	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aaagcccagcacacaggtgtAggtagcccattcccggtctc	10	14	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:62370651A>G	ENST00000394773.2	-	20	2633	c.2326T>C	c.(2326-2328)Tac>Cac	p.Y776H	RP11-831H9.3_ENST00000532626.1_RNA|EML3_ENST00000494176.2_Missense_Mutation_p.Y748H|EML3_ENST00000278845.4_Missense_Mutation_p.Y777H|EML3_ENST00000531557.1_Missense_Mutation_p.Y559H|EML3_ENST00000438258.1_5'Flank|MTA2_ENST00000527204.1_5'Flank|MTA2_ENST00000278823.2_5'Flank|EML3_ENST00000529309.1_Missense_Mutation_p.Y776H	NM_153265.2	NP_694997.2	Q32P44	EMAL3_HUMAN	echinoderm microtubule associated protein like 3	776						cytoplasm (GO:0005737)|microtubule (GO:0005874)				biliary_tract(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						ACACAGGTGTAGGTAGCCCAT	0.632																																					p.Y776H		Atlas-SNP	.											.	EML3	61	.	0			c.T2326C						.						120	114	116					11																	62370651		2202	4299	6501	SO:0001583	missense	256364	exon20			AGGTGTAGGTAGC	AK093146	CCDS8023.2	11q12.3	2013-01-10			ENSG00000149499	ENSG00000149499		"WD repeat domain containing"	26666	protein-coding gene	gene with protein product						15225882, 14744259	Standard	NM_153265		Approved	FLJ35827, ELP95	uc001ntu.1	Q32P44	OTTHUMG00000149817	ENST00000394773.2:c.2326T>C	chr11.hg19:g.62370651A>G	ENSP00000378254:p.Tyr776His	51.0	0.0		62.0	4.0	NM_153265	Q6ZQW7|Q8NA55	Missense_Mutation	SNP	ENST00000394773.2	hg19	CCDS8023.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.72|17.72	3.458939|3.458939	0.63401|0.63401	.|.	.|.	ENSG00000149499|ENSG00000149499	ENST00000394776|ENST00000439994;ENST00000394773;ENST00000278845;ENST00000531557;ENST00000494176;ENST00000529309	.|T;T;T;T;T	.|0.29917	.|1.71;1.67;1.55;1.69;1.62	4.78|4.78	4.78|4.78	0.61160|0.61160	.|WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);	.|0.071188	.|0.64402	.|D	.|0.000020	T|T	0.44993|0.44993	0.1320|0.1320	L|L	0.43152|0.43152	1.355|1.355	0.47276|0.47276	D|D	0.999371|0.999371	.|D;D;B;D;D	.|0.89917	.|1.0;0.999;0.02;0.999;1.0	.|D;D;B;D;D	.|0.91635	.|0.999;0.979;0.039;0.994;0.974	T|T	0.23726|0.23726	-1.0180|-1.0180	5|10	.|0.32370	.|T	.|0.25	-28.4302|-28.4302	12.2654|12.2654	0.54674|0.54674	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|776;776;559;777;748	.|Q32P44-2;Q32P44;G3V195;B7WPE2;G3V1D0	.|.;EMAL3_HUMAN;.;.;.	P|H	770|27;776;777;559;748;776	.|ENSP00000378254:Y776H;ENSP00000278845:Y777H;ENSP00000433417:Y559H;ENSP00000435064:Y748H;ENSP00000434513:Y776H	.|ENSP00000278845:Y777H	L|Y	-|-	2|1	0|0	EML3|EML3	62127227|62127227	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	5.696000|5.696000	0.68287|0.68287	1.787000|1.787000	0.52448|0.52448	0.459000|0.459000	0.35465|0.35465	CTA|TAC	.	.		0.632	EML3-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313432.1	NM_153265		G	62370651	A	G	62370651	3	3	255	1	0	0	0	0	1	0	0	0	5100	420	15	2	376	2	EML3	11	62370651	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	2963838	62370651	72635865	409	35754										
EML3	256364	hgsc.bcm.edu	37	chr11	62375157	62375157	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccccaaagacaccctgtttcCgggtaagggtcccattccca	8	16	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:62375157C>A	ENST00000394773.2	-	11	1650	c.1343G>T	c.(1342-1344)cGg>cTg	p.R448L	RP11-831H9.3_ENST00000532626.1_RNA|EML3_ENST00000494176.2_Missense_Mutation_p.R420L|EML3_ENST00000278845.4_Missense_Mutation_p.R449L|EML3_ENST00000531557.1_Missense_Mutation_p.R231L|EML3_ENST00000438258.1_Intron|EML3_ENST00000529309.1_Missense_Mutation_p.R448L	NM_153265.2	NP_694997.2	Q32P44	EMAL3_HUMAN	echinoderm microtubule associated protein like 3	448						cytoplasm (GO:0005737)|microtubule (GO:0005874)				biliary_tract(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						ACCCTGTTTCCGGGTAAGGGT	0.567																																					p.R448L		Atlas-SNP	.											.	EML3	61	.	0			c.G1343T						.						110	101	104					11																	62375157		2202	4299	6501	SO:0001583	missense	256364	exon11			TGTTTCCGGGTAA	AK093146	CCDS8023.2	11q12.3	2013-01-10			ENSG00000149499	ENSG00000149499		"WD repeat domain containing"	26666	protein-coding gene	gene with protein product						15225882, 14744259	Standard	NM_153265		Approved	FLJ35827, ELP95	uc001ntu.1	Q32P44	OTTHUMG00000149817	ENST00000394773.2:c.1343G>T	chr11.hg19:g.62375157C>A	ENSP00000378254:p.Arg448Leu	102.0	0.0		90.0	4.0	NM_153265	Q6ZQW7|Q8NA55	Missense_Mutation	SNP	ENST00000394773.2	hg19	CCDS8023.2	.	.	.	.	.	.	.	.	.	.	C	18.21	3.572935	0.65765	.	.	ENSG00000149499	ENST00000394773;ENST00000278845;ENST00000531557;ENST00000494176;ENST00000529309	T;T;T;T;T	0.41065	1.01;1.01;1.57;1.57;1.57	5.2	5.2	0.72013	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.140261	0.47093	D	0.000260	T	0.52058	0.1711	L	0.54323	1.7	0.37064	D	0.898224	P;P;B;B;D	0.61697	0.768;0.658;0.035;0.36;0.99	P;B;B;B;P	0.58454	0.573;0.369;0.042;0.044;0.839	T	0.61282	-0.7094	10	0.87932	D	0	-2.1889	9.855	0.41079	0.0:0.9067:0.0:0.0933	.	448;448;231;449;420	Q32P44-2;Q32P44;G3V195;B7WPE2;G3V1D0	.;EMAL3_HUMAN;.;.;.	L	448;449;231;420;448	ENSP00000378254:R448L;ENSP00000278845:R449L;ENSP00000433417:R231L;ENSP00000435064:R420L;ENSP00000434513:R448L	ENSP00000278845:R449L	R	-	2	0	EML3	62131733	1.000000	0.71417	0.977000	0.42913	0.919000	0.55068	2.977000	0.49297	2.446000	0.82766	0.460000	0.39030	CGG	.	.		0.567	EML3-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313432.1	NM_153265		A	62375157	C	A	62375157	3	1	255	1	0	0	0	0	1	0	0	0	5100	652	23	1	1395	1	EML3	11	62375157	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	4506	62375157	72631359	410	35755										
MARK2	2011	hgsc.bcm.edu	37	chr11	63666539	63666539	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttcagatagtgtctgctgtgCagtactgtcaccagaagttt	10	8	3	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:63666539C>T	ENST00000509502.2	+	7	854	c.391C>T	c.(391-393)Cag>Tag	p.Q131*	MARK2_ENST00000502399.3_Nonsense_Mutation_p.Q164*|MARK2_ENST00000402010.2_Nonsense_Mutation_p.Q164*|MARK2_ENST00000377809.4_Nonsense_Mutation_p.Q164*|MARK2_ENST00000350490.7_Nonsense_Mutation_p.Q164*|MARK2_ENST00000425897.2_Nonsense_Mutation_p.Q131*|MARK2_ENST00000513765.2_Nonsense_Mutation_p.Q131*|MARK2_ENST00000508192.1_Nonsense_Mutation_p.Q164*|MARK2_ENST00000413835.2_Nonsense_Mutation_p.Q164*|MARK2_ENST00000361128.5_Nonsense_Mutation_p.Q164*|MARK2_ENST00000408948.3_Nonsense_Mutation_p.Q131*|MARK2_ENST00000315032.8_Nonsense_Mutation_p.Q164*|MARK2_ENST00000377810.3_Nonsense_Mutation_p.Q131*	NM_017490.3	NP_059672.2			MAP/microtubule affinity-regulating kinase 2											autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33						GTCTGCTGTGCAGTACTGTCA	0.517																																					p.Q164X		Atlas-SNP	.											.	MARK2	91	.	0			c.C490T						.						209	198	202					11																	63666539		2201	4297	6498	SO:0001587	stop_gained	2011	exon7			GCTGTGCAGTACT	BC008771	CCDS8051.1, CCDS41665.1, CCDS8051.2, CCDS53649.1, CCDS53650.1, CCDS53651.1	11q13.1	2013-06-27	2002-07-26	2002-08-01	ENSG00000072518	ENSG00000072518			3332	protein-coding gene	gene with protein product	"ELKL motif kinase 1", "serine/threonine kinase", "protein-serine/threonine kinase", "Ser/Thr protein kinase PAR-1B"	600526	"ELKL motif kinase"	EMK1		9730619, 10516437	Standard	NM_017490		Approved	PAR-1, Par1b, PAR-1B	uc001nxw.3	Q7KZI7	OTTHUMG00000160504	ENST00000509502.2:c.391C>T	chr11.hg19:g.63666539C>T	ENSP00000423974:p.Gln131*	93.0	0.0		103.0	5.0	NM_001163296		Nonsense_Mutation	SNP	ENST00000509502.2	hg19	CCDS41665.1	.	.	.	.	.	.	.	.	.	.	c	40	8.234273	0.98719	.	.	ENSG00000072518	ENST00000402010;ENST00000315032;ENST00000377809;ENST00000413835;ENST00000377810;ENST00000508192;ENST00000361128;ENST00000350490;ENST00000502399;ENST00000543220;ENST00000509502;ENST00000513765;ENST00000408948;ENST00000425897	.	.	.	4.98	4.98	0.66077	.	0.124939	0.56097	D	0.000035	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	17.1794	0.86851	0.0:1.0:0.0:0.0	.	.	.	.	X	164;164;164;164;131;164;164;164;164;131;131;131;131;131	.	ENSP00000326632:Q164X	Q	+	1	0	MARK2	63423115	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.648000	0.83479	2.583000	0.87209	0.558000	0.71614	CAG	.	.		0.517	MARK2-003	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000360862.2	NM_017490		T	63666539	C	T	63666539	4	4	255	1	0	0	0	0	0	1	0	0	9322	711	25	3	516	3	MARK2	11	63666539	Nonsense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1291382	63666539	71339977	411	35756										
SNX15	29907	hgsc.bcm.edu	37	chr11	64802421	64802421	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	caacaacagcccccagctcaAggagttcttccgggtatgtg	10	13	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:64802421A>G	ENST00000377244.3	+	4	489	c.359A>G	c.(358-360)aAg>aGg	p.K120R	SNX15_ENST00000352068.5_Missense_Mutation_p.K120R|RP11-399J13.3_ENST00000301886.3_3'UTR	NM_013306.4|NM_147777.3	NP_037438.2|NP_680086.2	Q9NRS6	SNX15_HUMAN	sorting nexin 15	120	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				intracellular protein transport (GO:0006886)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	14						CCCCAGCTCAAGGAGTTCTTC	0.572																																					p.K120R	Esophageal Squamous(56;269 1304 3324 8253)	Atlas-SNP	.											.	SNX15	35	.	0			c.A359G						.						64	58	60					11																	64802421		2201	4297	6498	SO:0001583	missense	29907	exon4			AGCTCAAGGAGTT	AF175267	CCDS8089.1, CCDS8090.1	11q12	2008-05-22			ENSG00000110025	ENSG00000110025		"Sorting nexins"	14978	protein-coding gene	gene with protein product		605964				11208079	Standard	NM_013306		Approved			Q9NRS6	OTTHUMG00000037387	ENST00000377244.3:c.359A>G	chr11.hg19:g.64802421A>G	ENSP00000366452:p.Lys120Arg	89.0	0.0		105.0	5.0	NM_147777	E5KQS6|Q9NRS5	Missense_Mutation	SNP	ENST00000377244.3	hg19	CCDS8089.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.245899	0.80024	.	.	ENSG00000110025	ENST00000377244;ENST00000534637;ENST00000524831;ENST00000352068	T;T;T;T	0.39406	1.08;1.08;1.08;1.08	5.38	5.38	0.77491	Phox homologous domain (5);	0.000000	0.85682	D	0.000000	T	0.46870	0.1415	N	0.25245	0.725	0.80722	D	1	D;P;D	0.89917	1.0;0.92;1.0	D;P;D	0.87578	0.998;0.491;0.998	T	0.31806	-0.9930	10	0.13470	T	0.59	-6.2292	13.33	0.60480	1.0:0.0:0.0:0.0	.	120;120;120	E5KQS5;E5KQS6;Q9NRS6	.;.;SNX15_HUMAN	R	120;116;108;120	ENSP00000366452:K120R;ENSP00000437277:K116R;ENSP00000431690:K108R;ENSP00000316410:K120R	ENSP00000316410:K120R	K	+	2	0	SNX15	64558997	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	8.529000	0.90602	2.046000	0.60703	0.455000	0.32223	AAG	.	.		0.572	SNX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091004.3			G	64802421	A	G	64802421	3	3	255	1	0	0	0	0	1	0	0	0	14901	72	3	2	373	2	SNX15	11	64802421	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	1135882	64802421	70204095	412	35757										
SCYL1	57410	hgsc.bcm.edu	37	chr11	65299085	65299085	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gctgaggagtatcagcagaaGatcatccctgtggtggtcaa	13	8	3	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:65299085G>T	ENST00000270176.5	+	8	1124	c.1047G>T	c.(1045-1047)aaG>aaT	p.K349N	SCYL1_ENST00000527009.1_Missense_Mutation_p.K206N|SCYL1_ENST00000420247.2_Missense_Mutation_p.K349N|SCYL1_ENST00000533862.1_Missense_Mutation_p.K349N|SCYL1_ENST00000279270.6_Missense_Mutation_p.K349N|SCYL1_ENST00000525364.1_Missense_Mutation_p.K349N|SCYL1_ENST00000524944.1_Missense_Mutation_p.K349N	NM_020680.3	NP_065731.3	Q96KG9	NTKL_HUMAN	SCY1-like 1 (S. cerevisiae)	349					peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|transcription, DNA-templated (GO:0006351)	cis-Golgi network (GO:0005801)|COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|protein tyrosine kinase activity (GO:0004713)			ovary(1)|skin(1)	2						ATCAGCAGAAGATCATCCCTG	0.567																																					p.K349N		Atlas-SNP	.											.	SCYL1	76	.	0			c.G1047T						.						90	92	91					11																	65299085		2141	4246	6387	SO:0001583	missense	57410	exon8			GCAGAAGATCATC	AF225424	CCDS41672.1, CCDS44646.1	11q11-q12	2008-07-21	2002-11-26	2002-11-29	ENSG00000142186	ENSG00000142186			14372	protein-coding gene	gene with protein product	"teratoma-associated tyrosine kinase", "telomerase transcriptional elements-interacting factor", "telomerase regulation-associated protein"	607982	"N-terminal kinase-like"	NTKL		11118629	Standard	NM_020680		Approved	HT019, P105, GKLP, NKTL, TAPK, TRAP, TEIF, MGC78454	uc001oea.1	Q96KG9	OTTHUMG00000166325	ENST00000270176.5:c.1047G>T	chr11.hg19:g.65299085G>T	ENSP00000270176:p.Lys349Asn	69.0	0.0		89.0	4.0	NM_020680	A6NJF1|Q96G50|Q96KG8|Q96KH1|Q9HAW5|Q9HBL3|Q9NR53	Missense_Mutation	SNP	ENST00000270176.5	hg19	CCDS41672.1	.	.	.	.	.	.	.	.	.	.	G	15.43	2.830629	0.50845	.	.	ENSG00000142186	ENST00000270176;ENST00000525364;ENST00000420247;ENST00000533862;ENST00000527630;ENST00000349495;ENST00000279270;ENST00000524944;ENST00000527009	T;T;T;T;T;T;T;T	0.33654	1.4;1.4;1.4;1.4;1.4;1.4;1.4;1.4	5.17	4.24	0.50183	Armadillo-like helical (1);Armadillo-type fold (1);	0.220459	0.45867	D	0.000338	T	0.36386	0.0965	M	0.67953	2.075	0.48830	D	0.999717	B;B;B;B	0.29716	0.004;0.109;0.018;0.255	B;B;B;B	0.32624	0.027;0.149;0.047;0.07	T	0.37820	-0.9689	10	0.72032	D	0.01	-32.2004	8.5896	0.33679	0.1756:0.0:0.8244:0.0	.	349;349;349;349	E9PS17;Q96KG9-6;Q96KG9-2;Q96KG9	.;.;.;NTKL_HUMAN	N	349;349;349;349;349;349;349;349;206	ENSP00000270176:K349N;ENSP00000431635:K349N;ENSP00000408192:K349N;ENSP00000437254:K349N;ENSP00000433450:K349N;ENSP00000279270:K349N;ENSP00000432175:K349N;ENSP00000436993:K206N	ENSP00000270176:K349N	K	+	3	2	SCYL1	65055661	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.452000	0.35156	2.609000	0.88269	0.650000	0.86243	AAG	.	.		0.567	SCYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389159.2	NM_020680		T	65299085	G	T	65299085	3	4	255	1	0	0	0	0	1	0	0	0	13962	933	33	3	1077	3	SCYL1	11	65299085	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	496664	65299085	69707431	413	35758										
TMEM151A	256472	hgsc.bcm.edu	37	chr11	66062755	66062755	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	acagtggacttcactgagctCgagtggcacatctgctccaa	10	12	2	1	rs377003155		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:66062755C>A	ENST00000327259.4	+	2	1182	c.1038C>A	c.(1036-1038)ctC>ctA	p.L346L		NM_153266.3	NP_694998.1	Q8N4L1	T151A_HUMAN	transmembrane protein 151A	346						integral component of membrane (GO:0016021)				central_nervous_system(1)|kidney(4)|lung(6)	11						TCACTGAGCTCGAGTGGCACA	0.716																																					p.L346L		Atlas-SNP	.											.	TMEM151A	39	.	0			c.C1038A						.						8	8	8					11																	66062755		2151	4199	6350	SO:0001819	synonymous_variant	256472	exon2			TGAGCTCGAGTGG	BC033898	CCDS8133.1	11q13.2	2007-10-25	2007-10-25	2007-10-25	ENSG00000179292	ENSG00000179292			28497	protein-coding gene	gene with protein product			"transmembrane protein 151"	TMEM151		12477932	Standard	NM_153266		Approved	MGC33486	uc001ohl.3	Q8N4L1	OTTHUMG00000166920	ENST00000327259.4:c.1038C>A	chr11.hg19:g.66062755C>A		76.0	0.0		65.0	4.0	NM_153266	Q8ND14	Silent	SNP	ENST00000327259.4	hg19	CCDS8133.1																																																																																			.	.		0.716	TMEM151A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391897.1	NM_153266		A	66062755	C	A	66062755	2	1	255	1	0	0	0	0	0	0	0	1	16085	871	31	1		1	TMEM151A	11	66062755	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	763670	66062755	68943761	414	35759										
SPTBN2	6712	hgsc.bcm.edu	37	chr11	66468660	66468660	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttctctctcatccaggcctgGgtctccgtgcactctaagtg	9	14	4	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:66468660G>T	ENST00000533211.1	-	17	3241	c.2910C>A	c.(2908-2910)acC>acA	p.T970T	SPTBN2_ENST00000529997.1_Silent_p.T970T|SPTBN2_ENST00000309996.2_Silent_p.T970T			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	970					actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						TCCAGGCCTGGGTCTCCGTGC	0.617																																					p.T970T		Atlas-SNP	.											.	SPTBN2	188	.	0			c.C2910A						.						51	48	49					11																	66468660		2199	4295	6494	SO:0001819	synonymous_variant	6712	exon16			GGCCTGGGTCTCC	AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"Pleckstrin homology (PH) domain containing"	11276	protein-coding gene	gene with protein product		604985	"spinocerebellar ataxia 5"	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.2910C>A	chr11.hg19:g.66468660G>T		112.0	0.0		119.0	6.0	NM_006946	O14872|O14873	Silent	SNP	ENST00000533211.1	hg19	CCDS8150.1																																																																																			.	.		0.617	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946		T	66468660	G	T	66468660	2	4	255	1	0	0	0	0	0	0	0	1	15135	1219	43	3		3	SPTBN2	11	66468660	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	405905	66468660	68537856	415	35760										
PC	5091	hgsc.bcm.edu	37	chr11	66639169	66639169	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgggctcaccttggccacctTgatgatgtctgggatgtgca	13	10	2	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:66639169T>C	ENST00000393958.2	-	4	403	c.310A>G	c.(310-312)Aag>Gag	p.K104E	PC_ENST00000393960.1_Missense_Mutation_p.K104E|PC_ENST00000355677.3_Missense_Mutation_p.K104E|PC_ENST00000393955.2_Missense_Mutation_p.K104E|PC_ENST00000524491.1_Missense_Mutation_p.K64E	NM_000920.3	NP_000911.2	P11498	PYC_HUMAN	pyruvate carboxylase	104	Biotin carboxylation.				biotin metabolic process (GO:0006768)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|oxaloacetate metabolic process (GO:0006107)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|pyruvate carboxylase activity (GO:0004736)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Melanoma(852;0.0525)		Lung(977;0.153)|LUSC - Lung squamous cell carcinoma(976;0.227)	Biotin(DB00121)|Pyruvic acid(DB00119)	TTGGCCACCTTGATGATGTCT	0.657																																					p.K104E		Atlas-SNP	.											.	PC	116	.	0			c.A310G						.						21	21	21					11																	66639169		2175	4281	6456	SO:0001583	missense	5091	exon4			CCACCTTGATGAT	U04641	CCDS8152.1	11q13.4-q13.5	2012-07-11			ENSG00000173599	ENSG00000173599	6.4.1.1		8636	protein-coding gene	gene with protein product		608786				6548474	Standard	NM_022172		Approved	PCB	uc001ojn.1	P11498	OTTHUMG00000167099	ENST00000393958.2:c.310A>G	chr11.hg19:g.66639169T>C	ENSP00000377530:p.Lys104Glu	86.0	0.0		88.0	4.0	NM_000920	B4DN00|Q16705	Missense_Mutation	SNP	ENST00000393958.2	hg19	CCDS8152.1	.	.	.	.	.	.	.	.	.	.	T	10.02	1.236804	0.22711	.	.	ENSG00000173599	ENST00000393955;ENST00000393958;ENST00000393960;ENST00000524491;ENST00000355677	D;D;D;D;D	0.97328	-4.34;-4.34;-4.34;-4.34;-4.34	4.45	4.45	0.53987	Pre-ATP-grasp fold (1);PreATP-grasp-like fold (1);Biotin carboxylation domain (1);Carbamoyl-phosphate synthase, large subunit, N-terminal (1);	0.062464	0.64402	D	0.000010	D	0.88247	0.6385	N	0.01515	-0.825	0.46849	D	0.999229	B	0.10296	0.003	B	0.19666	0.026	D	0.84399	0.0559	10	0.10902	T	0.67	-30.511	11.7276	0.51718	0.0:0.0:0.0:1.0	.	104	P11498	PYC_HUMAN	E	104;104;104;64;104	ENSP00000377527:K104E;ENSP00000377530:K104E;ENSP00000377532:K104E;ENSP00000434192:K64E;ENSP00000347900:K104E	ENSP00000347900:K104E	K	-	1	0	PC	66395745	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.069000	0.50026	1.874000	0.54306	0.533000	0.62120	AAG	.	.		0.657	PC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393115.1	NM_001040716		C	66639169	T	C	66639169	3	2	255	1	0	0	0	0	1	0	0	0	11506	1821	63	2	3302	2	PC	11	66639169	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	170509	66639169	68367347	416	35761										
PC	5091	hgsc.bcm.edu	37	chr11	66639568	66639568	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tttggggaggcagcgggggcGgtggaggttcggcggattcc	22	7	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:66639568G>T	ENST00000393958.2	-	3	156	c.63C>A	c.(61-63)acC>acA	p.T21T	PC_ENST00000393960.1_Silent_p.T21T|PC_ENST00000355677.3_Silent_p.T21T|PC_ENST00000393955.2_Silent_p.T21T|PC_ENST00000524491.1_5'UTR	NM_000920.3	NP_000911.2	P11498	PYC_HUMAN	pyruvate carboxylase	21					biotin metabolic process (GO:0006768)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|oxaloacetate metabolic process (GO:0006107)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|pyruvate carboxylase activity (GO:0004736)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Melanoma(852;0.0525)		Lung(977;0.153)|LUSC - Lung squamous cell carcinoma(976;0.227)	Biotin(DB00121)|Pyruvic acid(DB00119)	CAGCGGGGGCGGTGGAGGTTC	0.622																																					p.T21T		Atlas-SNP	.											.	PC	116	.	0			c.C63A						.						23	19	21					11																	66639568		2186	4277	6463	SO:0001819	synonymous_variant	5091	exon3			GGGGGCGGTGGAG	U04641	CCDS8152.1	11q13.4-q13.5	2012-07-11			ENSG00000173599	ENSG00000173599	6.4.1.1		8636	protein-coding gene	gene with protein product		608786				6548474	Standard	NM_022172		Approved	PCB	uc001ojn.1	P11498	OTTHUMG00000167099	ENST00000393958.2:c.63C>A	chr11.hg19:g.66639568G>T		89.0	0.0		89.0	4.0	NM_000920	B4DN00|Q16705	Silent	SNP	ENST00000393958.2	hg19	CCDS8152.1																																																																																			.	.		0.622	PC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393115.1	NM_001040716		T	66639568	G	T	66639568	2	4	255	1	0	0	0	0	0	0	0	1	11506	1103	39	1		1	PC	11	66639568	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	399	66639568	68366948	417	35762										
CORO1B	57175	hgsc.bcm.edu	37	chr11	67210003	67210003	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggtgctgtcccaggtaacacGggacacgcgaatgtcctcat	12	12	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:67210003G>T	ENST00000341356.5	-	2	207	c.97C>A	c.(97-99)Cgt>Agt	p.R33S	CORO1B_ENST00000393893.1_Missense_Mutation_p.R33S|CORO1B_ENST00000539724.1_5'Flank|CORO1B_ENST00000453768.2_Missense_Mutation_p.R33S|CORO1B_ENST00000545016.1_Missense_Mutation_p.R33S	NM_020441.2	NP_065174.1	Q9BR76	COR1B_HUMAN	coronin, actin binding protein, 1B	33					actin cytoskeleton organization (GO:0030036)|actin filament branching (GO:0090135)|actin filament bundle assembly (GO:0051017)|cell migration (GO:0016477)|endothelial cell chemotaxis (GO:0035767)|negative regulation of Arp2/3 complex-mediated actin nucleation (GO:0034316)|positive regulation of lamellipodium morphogenesis (GO:2000394)|protein localization to cell leading edge (GO:1902463)|ruffle organization (GO:0031529)|wound healing (GO:0042060)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)|Arp2/3 complex binding (GO:0071933)|identical protein binding (GO:0042802)	p.R33C(1)		cervix(1)|endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	13			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)			CAGGTAACACGGGACACGCGA	0.597																																					p.R33S		Atlas-SNP	.											CORO1B,NS,carcinoma,0,1	CORO1B	30	.	1	Substitution - Missense(1)	ovary(1)	c.C97A						.						129	94	106					11																	67210003		2199	4295	6494	SO:0001583	missense	57175	exon2			TAACACGGGACAC	AK000860	CCDS8164.1	11q13.1	2013-01-10	2001-11-28		ENSG00000172725	ENSG00000172725		"Coronins", "WD repeat domain containing"	2253	protein-coding gene	gene with protein product		609849	"coronin, actin-binding protein, 1B"			9778037	Standard	NM_001018070		Approved	coronin-2	uc001olk.1	Q9BR76	OTTHUMG00000167775	ENST00000341356.5:c.97C>A	chr11.hg19:g.67210003G>T	ENSP00000340211:p.Arg33Ser	123.0	1.0		149.0	6.0	NM_020441	B2RD45	Missense_Mutation	SNP	ENST00000341356.5	hg19	CCDS8164.1	.	.	.	.	.	.	.	.	.	.	G	28.6	4.932938	0.92458	.	.	ENSG00000172725	ENST00000393893;ENST00000341356;ENST00000393886;ENST00000453768;ENST00000545016	T;T;T;T	0.76316	0.15;0.15;1.84;-1.01	4.31	3.39	0.38822	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);Domain of unknown function DUF1899 (1);	0.000000	0.44285	D	0.000474	T	0.81936	0.4928	M	0.71581	2.175	0.58432	D	0.999991	B;P;P	0.51057	0.064;0.535;0.941	B;B;P	0.53593	0.111;0.325;0.73	T	0.81703	-0.0812	10	0.41790	T	0.15	-13.6447	12.3892	0.55348	0.0839:0.0:0.9161:0.0	.	33;33;33	E7EW44;F5H0D2;Q9BR76	.;.;COR1B_HUMAN	S	33;33;60;33;33	ENSP00000377471:R33S;ENSP00000340211:R33S;ENSP00000416006:R33S;ENSP00000438056:R33S	ENSP00000340211:R33S	R	-	1	0	CORO1B	66966579	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.577000	0.46042	1.145000	0.42336	0.563000	0.77884	CGT	.	.		0.597	CORO1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396220.1	NM_020441		T	67210003	G	T	67210003	3	4	255	1	0	0	0	0	1	0	0	0	3756	1116	39	1	1412	1	CORO1B	11	67210003	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	570435	67210003	67796513	418	35763										
SHANK2	22941	hgsc.bcm.edu	37	chr11	70336441	70336441	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cagaaacggggcttttgggcTcccaggaacagtgggcgtca	15	10	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:70336441T>C	ENST00000423696.2	-	13	1390	c.1354A>G	c.(1354-1356)Agc>Ggc	p.S452G	SHANK2_ENST00000449116.2_Missense_Mutation_p.S233G|SHANK2_ENST00000409161.1_Missense_Mutation_p.S235G|SHANK2_ENST00000409530.1_Missense_Mutation_p.S242G|SHANK2_ENST00000338508.4_Missense_Mutation_p.S832G|SHANK2_ENST00000357171.3_Missense_Mutation_p.S243G|SHANK2_ENST00000449833.2_Missense_Mutation_p.S236G			Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2	452					adult behavior (GO:0030534)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|ionotropic glutamate receptor binding (GO:0035255)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(30)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			GCTTTTGGGCTCCCAGGAACA	0.597																																					p.S243G		Atlas-SNP	.											.	SHANK2	340	.	0			c.A727G						.						121	114	116					11																	70336441		2200	4294	6494	SO:0001583	missense	22941	exon8			TTGGGCTCCCAGG	AF141901		11q13.2	2013-01-10			ENSG00000162105	ENSG00000162105		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	14295	protein-coding gene	gene with protein product		603290	"cortactin binding protein 1"	CORTBP1		10506216	Standard	XM_005277930		Approved	CTTNBP1, ProSAP1, SHANK, SPANK-3	uc001oqc.3	Q9UPX8	OTTHUMG00000154615	ENST00000423696.2:c.1354A>G	chr11.hg19:g.70336441T>C	ENSP00000394536:p.Ser452Gly	99.0	0.0		102.0	5.0	NM_133266	C0SPG8|C0SPG9|Q3Y8G9|Q52LK2|Q9UKP1	Missense_Mutation	SNP	ENST00000423696.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.65|13.65	2.300054|2.300054	0.40694|0.40694	.|.	.|.	ENSG00000162105|ENSG00000162105	ENST00000412252|ENST00000449833;ENST00000409161;ENST00000424924;ENST00000338508;ENST00000423696;ENST00000433693;ENST00000294018;ENST00000409530;ENST00000449116;ENST00000357171	.|T;T;T;T;T;T;T;T;T	.|0.57752	.|2.25;2.25;3.02;0.98;2.4;2.39;0.78;0.38;0.79	4.63|4.63	4.63|4.63	0.57726|0.57726	.|.	.|0.068309	.|0.53938	.|D	.|0.000056	T|T	0.55847|0.55847	0.1946|0.1946	M|M	0.74881|0.74881	2.28|2.28	0.47476|0.47476	D|D	0.999434|0.999434	.|B;B;B;B	.|0.30179	.|0.002;0.271;0.198;0.132	.|B;B;B;B	.|0.35727	.|0.004;0.066;0.157;0.209	T|T	0.55153|0.55153	-0.8185|-0.8185	5|10	.|0.27785	.|T	.|0.31	.|.	14.06|14.06	0.64793|0.64793	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|233;452;831;236	.|B7ZKU9;Q9UPX8;Q9UPX8-3;Q9UPX8-4	.|.;SHAN2_HUMAN;.;.	G|G	241|236;235;110;832;452;470;455;242;233;243	.|ENSP00000399423:S236G;ENSP00000386491:S235G;ENSP00000402944:S110G;ENSP00000345193:S832G;ENSP00000394536:S452G;ENSP00000294018:S455G;ENSP00000387324:S242G;ENSP00000394939:S233G;ENSP00000349694:S243G	.|ENSP00000294018:S455G	E|S	-|-	2|1	0|0	SHANK2|SHANK2	70014089|70014089	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.915000|0.915000	0.54546|0.54546	4.315000|4.315000	0.59172|0.59172	1.715000|1.715000	0.51383|0.51383	0.379000|0.379000	0.24179|0.24179	GAG|AGC	.	.		0.597	SHANK2-203	KNOWN	basic	protein_coding	protein_coding		NM_012309		C	70336441	T	C	70336441	3	2	255	1	0	0	0	0	1	0	0	0	14280	1551	54	2	3074	2	SHANK2	11	70336441	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	3126438	70336441	64670075	419	35764										
PDE2A	5138	hgsc.bcm.edu	37	chr11	72292016	72292016	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	caaggcaaagatctcgatgtCcctggttgagaggcagaaag	13	8	1	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:72292016C>T	ENST00000334456.5	-	24	2292	c.2047G>A	c.(2047-2049)Gac>Aac	p.D683N	PDE2A_ENST00000418754.2_Splice_Site_p.D568N|PDE2A_ENST00000540345.1_Splice_Site_p.D674N|PDE2A_ENST00000376450.3_Splice_Site_p.D427N|PDE2A_ENST00000544570.1_Splice_Site_p.D676N|PDE2A_ENST00000444035.2_Splice_Site_p.D674N	NM_002599.4	NP_002590.1	O00408	PDE2A_HUMAN	phosphodiesterase 2A, cGMP-stimulated	683	Catalytic. {ECO:0000250}.				blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to drug (GO:0035690)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to mechanical stimulus (GO:0071260)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP catabolic process (GO:0046069)|cGMP-mediated signaling (GO:0019934)|establishment of endothelial barrier (GO:0061028)|metabolic process (GO:0008152)|monocyte differentiation (GO:0030224)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vascular permeability (GO:0043116)|positive regulation of inflammatory response (GO:0050729)|positive regulation of vascular permeability (GO:0043117)|protein targeting to mitochondrion (GO:0006626)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	calcium channel activity (GO:0005262)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|drug binding (GO:0008144)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|TPR domain binding (GO:0030911)			breast(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(21)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	36			BRCA - Breast invasive adenocarcinoma(5;3.55e-05)		Caffeine(DB00201)|Tofisopam(DB08811)	ATCTCGATGTCCCTGGTTGAG	0.522																																					p.D683N		Atlas-SNP	.											.	PDE2A	156	.	0			c.G2047A						.						109	92	98					11																	72292016		2200	4293	6493	SO:0001630	splice_region_variant	5138	exon24			CGATGTCCCTGGT	U67733	CCDS8216.1, CCDS44670.1, CCDS53678.1, CCDS73345.1	11q13.1-q14.1	2008-05-14			ENSG00000186642	ENSG00000186642	3.1.4.17	"Phosphodiesterases"	8777	protein-coding gene	gene with protein product		602658				9210593	Standard	NM_002599		Approved		uc010rrc.2	O00408	OTTHUMG00000102045	ENST00000334456.5:c.2046-1G>A	chr11.hg19:g.72292016C>T		89.0	0.0		71.0	4.0	NM_002599	B2R646|B3KRV5|E9PGI1|F6W5Z0|Q5J791|Q5J792|Q5J793|Q6ZMR1	Missense_Mutation	SNP	ENST00000334456.5	hg19	CCDS8216.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.831249	0.91036	.	.	ENSG00000186642	ENST00000334456;ENST00000376450;ENST00000444035;ENST00000429363;ENST00000544570;ENST00000418754;ENST00000540345;ENST00000420501;ENST00000441209;ENST00000542223	D;D;D;D;D;D;D;D;D	0.83837	-1.77;-1.77;-1.77;-1.77;-1.77;-1.77;-1.77;-1.77;-1.77	5.36	5.36	0.76844	Metal-dependent phosphohydrolase, HD domain (1);5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.133385	0.48767	D	0.000161	D	0.88477	0.6447	M	0.74258	2.255	0.49798	D	0.999824	D;P;D;P;P;P	0.59767	0.986;0.867;0.958;0.903;0.926;0.851	P;P;P;P;P;P	0.58780	0.476;0.714;0.805;0.667;0.845;0.644	D	0.89579	0.3819	10	0.87932	D	0	.	12.7673	0.57399	0.1639:0.8361:0.0:0.0	.	568;683;674;676;683;427	E9PEF1;O00408;E9PGI1;F6W5Z0;B2R646;Q6ZMR1	.;PDE2A_HUMAN;.;.;.;.	N	683;427;674;752;676;568;674;62;224;114	ENSP00000334910:D683N;ENSP00000365633:D427N;ENSP00000411657:D674N;ENSP00000442256:D676N;ENSP00000410310:D568N;ENSP00000446399:D674N;ENSP00000388997:D62N;ENSP00000392457:D224N;ENSP00000440834:D114N	ENSP00000334910:D683N	D	-	1	0	PDE2A	71969664	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.308000	0.65768	2.523000	0.85059	0.655000	0.94253	GAC	.	.		0.522	PDE2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219839.2	NM_002599	Missense_Mutation	T	72292016	C	T	72292016	5	4	255	1	0	0	0	0	0	0	1	0	11645	869	30	3	810	3	PDE2A	11	72292016	Splice_Site	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1955575	72292016	62714500	420	35765										
ODZ4	26011	hgsc.bcm.edu	37	chr11	78437179	78437179	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctccatcctccaagcttggaCgcgtcaatttcatagccctg	7	15	2	0	rs369844183		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:78437179C>A	ENST00000278550.7	-	23	3957	c.3495G>T	c.(3493-3495)gcG>gcT	p.A1165A		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	1165					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										CAAGCTTGGACGCGTCAATTT	0.458																																					p.A1165A		Atlas-SNP	.											ODZ4_ENST00000278550,NS,carcinoma,0,2	.	.	.	0			c.G3495T						.						320	310	313					11																	78437179		1943	4136	6079	SO:0001819	synonymous_variant	26011	exon23			CTTGGACGCGTCA	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"odz, odd Oz/ten-m homolog 4 (Drosophila)"	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.3495G>T	chr11.hg19:g.78437179C>A		432.0	0.0		372.0	138.0	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Silent	SNP	ENST00000278550.7	hg19	CCDS44688.1																																																																																			.	.		0.458	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			A	78437179	C	A	78437179	2	1	255	1	0	0	0	0	0	0	0	1	10846	523	19	1		1	ODZ4	11	78437179	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	6145163	78437179	56569337	421	35766										
FAT3	120114	hgsc.bcm.edu	37	chr11	92087868	92087868	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	acaaagacttaggttctaatGgtgaagtgacttactcagtc	9	7	2	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:92087868G>T	ENST00000298047.6	+	1	2607	c.2590G>T	c.(2590-2592)Ggt>Tgt	p.G864C	FAT3_ENST00000409404.2_Missense_Mutation_p.G864C|FAT3_ENST00000525166.1_Missense_Mutation_p.G714C|FAT3_ENST00000541502.1_Missense_Mutation_p.G864C			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	864	Cadherin 8. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				AGGTTCTAATGGTGAAGTGAC	0.408										TCGA Ovarian(4;0.039)																											p.G864C		Atlas-SNP	.											.	FAT3	1822	.	0			c.G2590T						.						94	91	92					11																	92087868		1948	4145	6093	SO:0001583	missense	120114	exon1			TCTAATGGTGAAG	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.2590G>T	chr11.hg19:g.92087868G>T	ENSP00000298047:p.Gly864Cys	73.0	0.0		98.0	4.0	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	hg19		.	.	.	.	.	.	.	.	.	.	G	17.59	3.426755	0.62733	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000541502;ENST00000525166	T;T;T;T	0.54675	4.62;4.62;0.56;4.62	5.71	5.71	0.89125	.	.	.	.	.	D	0.82825	0.5121	H	0.96805	3.885	0.58432	D	0.999997	D	0.89917	1.0	D	0.97110	1.0	D	0.88238	0.2908	9	0.87932	D	0	.	18.8459	0.92205	0.0:0.0:1.0:0.0	.	864	Q8TDW7-3	.	C	864;864;864;714	ENSP00000298047:G864C;ENSP00000387040:G864C;ENSP00000443786:G864C;ENSP00000432586:G714C	ENSP00000298047:G864C	G	+	1	0	FAT3	91727516	1.000000	0.71417	0.843000	0.33291	0.978000	0.69477	9.787000	0.99055	2.700000	0.92200	0.467000	0.42956	GGT	.	.		0.408	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		T	92087868	G	T	92087868	3	4	255	1	0	0	0	0	1	0	0	0	5699	1348	47	3	2592	3	FAT3	11	92087868	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	13650689	92087868	42918648	422	35767										
CNTN5	53942	hgsc.bcm.edu	37	chr11	100061877	100061877	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gaatagctattcttccagacGggagtctacggatcctaaat	9	9	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:100061877G>T	ENST00000524871.1	+	14	1890	c.1600G>T	c.(1600-1602)Ggg>Tgg	p.G534W	CNTN5_ENST00000528682.1_Missense_Mutation_p.G534W|CNTN5_ENST00000279463.3_Missense_Mutation_p.G534W|CNTN5_ENST00000418526.2_Missense_Mutation_p.G460W|CNTN5_ENST00000527185.1_Missense_Mutation_p.G534W	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	534	Ig-like C2-type 5.				cell adhesion (GO:0007155)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)		p.G534W(2)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(12)|lung(38)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	81		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		TCTTCCAGACGGGAGTCTACG	0.368																																					p.G534W		Atlas-SNP	.											CNTN5_ENST00000524871,right_upper_lobe,carcinoma,0,2	CNTN5	324	.	2	Substitution - Missense(2)	lung(2)	c.G1600T						.						61	60	60					11																	100061877		1816	4070	5886	SO:0001583	missense	53942	exon13			CCAGACGGGAGTC	AB013802	CCDS53696.1, CCDS53697.1, CCDS58168.1	11q22.1	2013-02-11			ENSG00000149972	ENSG00000149972		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2175	protein-coding gene	gene with protein product		607219					Standard	NM_014361		Approved	NB-2, hNB-2	uc021qpb.1	O94779	OTTHUMG00000167579	ENST00000524871.1:c.1600G>T	chr11.hg19:g.100061877G>T	ENSP00000435637:p.Gly534Trp	39.0	0.0		47.0	3.0	NM_001243270	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Missense_Mutation	SNP	ENST00000524871.1	hg19	CCDS53696.1	.	.	.	.	.	.	.	.	.	.	G	16.42	3.118768	0.56505	.	.	ENSG00000149972	ENST00000527185;ENST00000528682;ENST00000524871;ENST00000418526;ENST00000279463	T;T;T;T;T	0.37058	1.22;1.22;1.22;1.22;1.22	5.52	4.59	0.56863	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.142130	0.64402	D	0.000003	T	0.71048	0.3294	H	0.95780	3.72	0.46654	D	0.999149	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.76575	0.988;0.957;0.975	T	0.81867	-0.0735	10	0.87932	D	0	.	15.7452	0.77936	0.0:0.1369:0.8631:0.0	.	534;460;534	E9PKE8;O94779-2;O94779	.;.;CNTN5_HUMAN	W	534;534;534;460;534	ENSP00000433575:G534W;ENSP00000436185:G534W;ENSP00000435637:G534W;ENSP00000393229:G460W;ENSP00000279463:G534W	ENSP00000279463:G534W	G	+	1	0	CNTN5	99567087	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.309000	0.59135	1.439000	0.47511	0.650000	0.86243	GGG	.	.		0.368	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361		T	100061877	G	T	100061877	3	4	255	1	0	0	0	0	1	0	0	0	3646	1116	39	1	1646	1	CNTN5	11	100061877	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	7974009	100061877	34944639	423	35768										
BIRC3	330	hgsc.bcm.edu	37	chr11	102206786	102206786	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tggatagtctactaactgccGgaattattaatgaacaagaa	8	6	1	2	rs145025961		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:102206786G>T	ENST00000263464.3	+	7	4164	c.1414G>T	c.(1414-1416)Gga>Tga	p.G472*	BIRC3_ENST00000532808.1_Nonsense_Mutation_p.G472*	NM_001165.4	NP_001156.1	Q13489	BIRC3_HUMAN	baculoviral IAP repeat containing 3	472	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				apoptotic process (GO:0006915)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of necroptotic process (GO:0060546)|negative regulation of phosphorylation (GO:0042326)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein ubiquitination (GO:0031398)|protein heterooligomerization (GO:0051291)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cysteine-type endopeptidase activity (GO:2000116)|regulation of inflammatory response (GO:0050727)|regulation of innate immune response (GO:0045088)|regulation of necroptotic process (GO:0060544)|regulation of nucleotide-binding oligomerization domain containing signaling pathway (GO:0070424)|regulation of RIG-I signaling pathway (GO:0039535)|regulation of toll-like receptor signaling pathway (GO:0034121)|spermatogenesis (GO:0007283)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane raft (GO:0045121)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.G472R(1)		endometrium(3)|kidney(2)|large_intestine(7)|lung(5)|ovary(3)|skin(1)	21	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0146)		ACTAACTGCCGGAATTATTAA	0.303			T	MALT1	MALT																																p.G472X		Atlas-SNP	.		Dom	yes		11	11q22-q23	330	baculoviral IAP repeat-containing 3		L	BIRC3,colon,carcinoma,0,1	BIRC3	56	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1414T						.						92	96	94					11																	102206786		2203	4298	6501	SO:0001587	stop_gained	330	exon7			ACTGCCGGAATTA	L49432	CCDS8315.1	11q22	2011-01-25	2011-01-25			ENSG00000023445		"Baculoviral IAP repeat containing", "RING-type (C3HC4) zinc fingers"	591	protein-coding gene	gene with protein product	"apoptosis inhibitor 2", "TNFR2-TRAF signaling complex protein", "mammalian IAP homolog C", "inhibitor of apoptosis protein 1"	601721	"baculoviral IAP repeat-containing 3"	API2		8552191, 8548810	Standard	NM_001165		Approved	cIAP2, hiap-1, MIHC, RNF49, MALT2, c-IAP2	uc001pgx.3	Q13489		ENST00000263464.3:c.1414G>T	chr11.hg19:g.102206786G>T	ENSP00000263464:p.Gly472*	115.0	0.0		127.0	7.0	NM_001165	Q16628|Q9HC27|Q9UP46	Nonsense_Mutation	SNP	ENST00000263464.3	hg19	CCDS8315.1	.	.	.	.	.	.	.	.	.	.	G	19.03	3.748137	0.69533	.	.	ENSG00000023445	ENST00000263464;ENST00000532808;ENST00000532609	.	.	.	5.28	0.32	0.15878	.	0.466068	0.27631	N	0.018503	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10377	T	0.69	.	9.1626	0.37032	0.7035:0.0:0.2965:0.0	.	.	.	.	X	472;472;240	.	ENSP00000263464:G472X	G	+	1	0	BIRC3	101711996	0.005000	0.15991	0.001000	0.08648	0.074000	0.17049	0.374000	0.20501	-0.101000	0.12219	-0.294000	0.09567	GGA	.	G|1.000;A|0.000		0.303	BIRC3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394159.1	NM_001165		T	102206786	G	T	102206786	4	4	255	1	0	0	0	0	0	1	0	0	1436	1117	39	1	1436	1	BIRC3	11	102206786	Nonsense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	2144909	102206786	32799730	424	35769										
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	103152947	103152947	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gtgtggttgttggagacatgTtacggaaagctgtaagttaa	14	3	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:103152947T>C	ENST00000375735.2	+	72	10945	c.10801T>C	c.(10801-10803)Tta>Cta	p.L3601L	DYNC2H1_ENST00000398093.3_Silent_p.L3608L|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3601					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		TGGAGACATGTTACGGAAAGC	0.299																																					p.L3608L		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.T10822C						.						90	89	89					11																	103152947		1800	4054	5854	SO:0001819	synonymous_variant	79659	exon73			GACATGTTACGGA	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.10801T>C	chr11.hg19:g.103152947T>C		106.0	0.0		76.0	4.0	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Silent	SNP	ENST00000375735.2	hg19	CCDS53701.1																																																																																			.	.		0.299	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		C	103152947	T	C	103152947	2	2	255	1	0	0	0	0	0	0	0	1	4848	1722	60	2		2	DYNC2H1	11	103152947	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	946161	103152947	31853569	425	35770										
ZC3H12C	85463	hgsc.bcm.edu	37	chr11	110035709	110035709	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agcagtgaagggagcatgagCtgtgggagcagtgactccta	16	7	0	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:110035709C>T	ENST00000278590.3	+	6	1950	c.1899C>T	c.(1897-1899)agC>agT	p.S633S	ZC3H12C_ENST00000453089.2_Silent_p.S602S|ZC3H12C_ENST00000528673.1_Silent_p.S634S	NM_033390.1	NP_203748.1	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	633							endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.72e-06)|BRCA - Breast invasive adenocarcinoma(274;1.17e-05)|all cancers(92;9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0279)		GGAGCATGAGCTGTGGGAGCA	0.522																																					p.S633S		Atlas-SNP	.											.	ZC3H12C	83	.	0			c.C1899T						.						57	60	59					11																	110035709		2053	4209	6262	SO:0001819	synonymous_variant	85463	exon6			CATGAGCTGTGGG		CCDS44727.1	11q22.3	2012-07-05			ENSG00000149289	ENSG00000149289		"Zinc fingers, CCCH-type domain containing"	29362	protein-coding gene	gene with protein product	"MCP induced protein 3"	615001				11214970, 18178554	Standard	NM_033390		Approved	KIAA1726, MCPIP3	uc009yxw.3	Q9C0D7	OTTHUMG00000166572	ENST00000278590.3:c.1899C>T	chr11.hg19:g.110035709C>T		74.0	0.0		55.0	4.0	NM_033390	B4DI65|B4DR47	Silent	SNP	ENST00000278590.3	hg19	CCDS44727.1																																																																																			.	.		0.522	ZC3H12C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390491.1	NM_033390		T	110035709	C	T	110035709	2	4	255	1	0	0	0	0	0	0	0	1	17578	796	28	3		3	ZC3H12C	11	110035709	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	6882762	110035709	24970807	426	35771										
ARHGAP20	57569	hgsc.bcm.edu	37	chr11	110479748	110479748	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcttctttgccagaattgacCcacaactggtaatctctctc	5	13	4	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:110479748C>A	ENST00000260283.4	-	9	1019	c.735G>T	c.(733-735)tgG>tgT	p.W245C	ARHGAP20_ENST00000528829.1_Missense_Mutation_p.W209C|ARHGAP20_ENST00000524756.1_Missense_Mutation_p.W222C|ARHGAP20_ENST00000533353.1_Missense_Mutation_p.W219C|ARHGAP20_ENST00000357139.3_Missense_Mutation_p.W219C|ARHGAP20_ENST00000527598.1_Missense_Mutation_p.W209C	NM_020809.3	NP_065860.2	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20	245	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(18)|lung(13)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	60		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;3.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|all cancers(92;0.000147)|OV - Ovarian serous cystadenocarcinoma(223;0.0475)		CAGAATTGACCCACAACTGGT	0.333																																					p.W245C		Atlas-SNP	.											.	ARHGAP20	150	.	0			c.G735T						.						118	129	125					11																	110479748		2201	4298	6499	SO:0001583	missense	57569	exon9			ATTGACCCACAAC	AB037812	CCDS31673.1, CCDS58175.1, CCDS58176.1, CCDS58177.1	11q23.2	2011-06-29			ENSG00000137727	ENSG00000137727		"Rho GTPase activating proteins"	18357	protein-coding gene	gene with protein product		609568				14532992	Standard	NM_020809		Approved	KIAA1391	uc001pkz.2	Q9P2F6	OTTHUMG00000166590	ENST00000260283.4:c.735G>T	chr11.hg19:g.110479748C>A	ENSP00000260283:p.Trp245Cys	124.0	0.0		102.0	5.0	NM_020809	A8K8C5|B0YIW7|B0YIW8|Q6RJU1|Q6RJU2|Q6RJU3|Q6RJU5|Q8IXS1	Missense_Mutation	SNP	ENST00000260283.4	hg19	CCDS31673.1	.	.	.	.	.	.	.	.	.	.	C	14.28	2.489791	0.44249	.	.	ENSG00000137727	ENST00000260283;ENST00000357139;ENST00000524756;ENST00000528829;ENST00000533353;ENST00000527598	T;T;T;T;T;T	0.16743	2.32;2.32;2.32;2.32;2.32;2.32	5.76	5.76	0.90799	Ras-association (2);	0.000000	0.85682	D	0.000000	T	0.47154	0.1430	M	0.79011	2.435	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.40683	-0.9550	10	0.87932	D	0	.	19.9345	0.97131	0.0:1.0:0.0:0.0	.	245;222	Q9P2F6;Q9P2F6-3	RHG20_HUMAN;.	C	245;219;222;209;219;209	ENSP00000260283:W245C;ENSP00000349660:W219C;ENSP00000432076:W222C;ENSP00000436319:W209C;ENSP00000436522:W219C;ENSP00000431399:W209C	ENSP00000260283:W245C	W	-	3	0	ARHGAP20	109984958	1.000000	0.71417	1.000000	0.80357	0.036000	0.12997	6.588000	0.74076	2.882000	0.98803	0.655000	0.94253	TGG	.	.		0.333	ARHGAP20-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390628.1	NM_020809		A	110479748	C	A	110479748	3	1	255	1	0	0	0	0	1	0	0	0	870	624	22	3	2872	3	ARHGAP20	11	110479748	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	444039	110479748	24526768	427	35772										
SIK2	23235	hgsc.bcm.edu	37	chr11	111594228	111594228	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttaccaatttaggctccagcAgaagcgactctttcttcaga	7	11	3	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:111594228A>G	ENST00000304987.3	+	15	2329	c.2156A>G	c.(2155-2157)cAg>cGg	p.Q719R		NM_015191.1	NP_056006.1	Q9H0K1	SIK2_HUMAN	salt-inducible kinase 2	719					insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of insulin receptor signaling pathway (GO:0046626)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	30						AGGCTCCAGCAGAAGCGACTC	0.423																																					p.Q719R		Atlas-SNP	.											.	SIK2	89	.	0			c.A2156G						.						49	57	54					11																	111594228		2201	4297	6498	SO:0001583	missense	23235	exon15			TCCAGCAGAAGCG	AB018324	CCDS8347.1	11q23.1	2008-12-23	2008-12-23	2008-12-23	ENSG00000170145	ENSG00000170145			21680	protein-coding gene	gene with protein product		608973	"SNF1-like kinase 2"	SNF1LK2		15067358	Standard	NM_015191		Approved	KIAA0781, QIK, DKFZp434K1115, LOH11CR1I	uc001plt.3	Q9H0K1	OTTHUMG00000150644	ENST00000304987.3:c.2156A>G	chr11.hg19:g.111594228A>G	ENSP00000305976:p.Gln719Arg	87.0	0.0		88.0	4.0	NM_015191	A8K5B8|B0YJ94|O94878|Q17RV0|Q6AZE2|Q76N03|Q8NCV7|Q96CZ8	Missense_Mutation	SNP	ENST00000304987.3	hg19	CCDS8347.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.180288	0.78677	.	.	ENSG00000170145	ENST00000304987	D	0.83914	-1.78	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	D	0.89536	0.6743	M	0.61703	1.905	0.58432	D	0.999999	D	0.63880	0.993	D	0.70227	0.968	D	0.90303	0.4331	10	0.66056	D	0.02	.	15.7606	0.78076	1.0:0.0:0.0:0.0	.	719	Q9H0K1	SIK2_HUMAN	R	719	ENSP00000305976:Q719R	ENSP00000305976:Q719R	Q	+	2	0	SIK2	111099438	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.783000	0.91813	2.202000	0.70862	0.533000	0.62120	CAG	.	.		0.423	SIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319352.3	NM_015191		G	111594228	A	G	111594228	3	3	255	1	0	0	0	0	1	0	0	0	14333	188	7	2	2214	2	SIK2	11	111594228	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	1114480	111594228	23412288	428	35773										
PTS	5805	hgsc.bcm.edu	37	chr11	112097190	112097190	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agcacggaaggtggtggccgTcgctgccaggcacaagtgtc	16	11	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:112097190T>C	ENST00000280362.3	+	1	103	c.24T>C	c.(22-24)cgT>cgC	p.R8R	PTS_ENST00000525803.1_Silent_p.R8R|PTS_ENST00000524931.1_5'Flank	NM_000317.2	NP_000308.1	Q03393	PTPS_HUMAN	6-pyruvoyltetrahydropterin synthase	8					cellular amino acid metabolic process (GO:0006520)|central nervous system development (GO:0007417)|nitric oxide metabolic process (GO:0046209)|regulation of nitric-oxide synthase activity (GO:0050999)|small molecule metabolic process (GO:0044281)|tetrahydrobiopterin biosynthetic process (GO:0006729)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)	6-pyruvoyltetrahydropterin synthase activity (GO:0003874)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			breast(1)|large_intestine(1)	2		all_cancers(61;2.51e-14)|all_epithelial(67;1.64e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;1.27e-06)|BRCA - Breast invasive adenocarcinoma(274;1.43e-06)|all cancers(92;2.1e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0519)		GTGGTGGCCGTCGCTGCCAGG	0.721																																					p.R8R		Atlas-SNP	.											.	PTS	7	.	0			c.T24C						.						24	20	21					11																	112097190		2168	4246	6414	SO:0001819	synonymous_variant	5805	exon1			TGGCCGTCGCTGC	U63382	CCDS8359.1	11q22.3	2014-04-01				ENSG00000150787	4.2.3.12		9689	protein-coding gene	gene with protein product		612719				8188266	Standard	NM_000317		Approved	PTPS	uc001pnj.4	Q03393		ENST00000280362.3:c.24T>C	chr11.hg19:g.112097190T>C		77.0	0.0		76.0	4.0	NM_000317	B0YJ87|Q8WVG8	Silent	SNP	ENST00000280362.3	hg19	CCDS8359.1																																																																																			.	.		0.721	PTS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393541.1	NM_000317		C	112097190	T	C	112097190	2	2	255	1	0	0	0	0	0	0	0	1	12833	1654	58	2		2	PTS	11	112097190	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	502962	112097190	22909326	429	35774										
ANKK1	255239	hgsc.bcm.edu	37	chr11	113266922	113266922	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cgctgctgggaccaggacccCaagaagaggccatgctttct	12	13	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:113266922C>A	ENST00000303941.3	+	5	910	c.816C>A	c.(814-816)ccC>ccA	p.P272P		NM_178510.1	NP_848605.1	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1	272	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|stomach(1)	29		all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194)		BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238)		ACCAGGACCCCAAGAAGAGGC	0.642																																					p.P272P		Atlas-SNP	.											.	ANKK1	83	.	0			c.C816A						.						90	95	93					11																	113266922		1967	4134	6101	SO:0001819	synonymous_variant	255239	exon5			GGACCCCAAGAAG	AJ541797	CCDS44734.1	11q23.2	2013-01-10			ENSG00000170209	ENSG00000170209		"Ankyrin repeat domain containing"	21027	protein-coding gene	gene with protein product		608774				15146457	Standard	NM_178510		Approved	X-kinase	uc001pny.3	Q8NFD2	OTTHUMG00000167715	ENST00000303941.3:c.816C>A	chr11.hg19:g.113266922C>A		121.0	0.0		104.0	5.0	NM_178510		Silent	SNP	ENST00000303941.3	hg19	CCDS44734.1																																																																																			.	.		0.642	ANKK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395830.1	NM_178510		A	113266922	C	A	113266922	2	1	255	1	0	0	0	0	0	0	0	1	631	581	21	3		3	ANKK1	11	113266922	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1169732	113266922	21739594	430	35775										
FXYD6	53826	hgsc.bcm.edu	37	chr11	117712509	117712509	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	caaaagaacaaacttacttaGgataaggaggatcccaaccg	8	9	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:117712509G>T	ENST00000526014.1	-	4	764	c.169C>A	c.(169-171)Cta>Ata	p.L57I	FXYD6_ENST00000527717.1_Missense_Mutation_p.L57I|FXYD6_ENST00000524656.1_Missense_Mutation_p.L57I|FXYD6_ENST00000530956.1_Missense_Mutation_p.L57I|FXYD6_ENST00000540359.1_Missense_Mutation_p.L57I|FXYD6_ENST00000527429.1_Missense_Mutation_p.L57I|FXYD6-FXYD2_ENST00000532984.1_Missense_Mutation_p.L57I|FXYD6_ENST00000260282.4_Missense_Mutation_p.L57I|FXYD6_ENST00000584394.1_Missense_Mutation_p.L57I|FXYD6_ENST00000539526.1_Missense_Mutation_p.L57I|RP11-728F11.4_ENST00000581173.2_RNA|FXYD6_ENST00000583233.1_5'UTR|FXYD6_ENST00000529335.2_Missense_Mutation_p.L56I|FXYD6_ENST00000584230.1_Missense_Mutation_p.L57I	NM_022003.3	NP_071286.1	Q9H0Q3	FXYD6_HUMAN	FXYD domain containing ion transport regulator 6	57					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ion channel activity (GO:0005216)			central_nervous_system(1)|large_intestine(5)|lung(1)|skin(1)	8	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|Breast(348;0.111)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.89e-05)|Epithelial(105;0.00122)		AACTTACTTAGGATAAGGAGG	0.527																																					p.L57I		Atlas-SNP	.											.	.	.	.	0			c.C169A						.						106	100	102					11																	117712509		2201	4296	6497	SO:0001583	missense	100533181	exon4			TACTTAGGATAAG	BC093040	CCDS8387.1	11q23.3	2010-04-14	2002-01-14		ENSG00000137726	ENSG00000137726			4030	protein-coding gene	gene with protein product	"phosphohippolin"	606683	"FXYD domain-containing ion transport regulator 6"			10950925	Standard	NM_022003		Approved			Q9H0Q3		ENST00000526014.1:c.169C>A	chr11.hg19:g.117712509G>T	ENSP00000433312:p.Leu57Ile	112.0	0.0		87.0	5.0	NM_001243598	A8K0R4|J3QLD2|Q6FIG9|Q6UW52	Missense_Mutation	SNP	ENST00000526014.1	hg19	CCDS8387.1	.	.	.	.	.	.	.	.	.	.	G	16.91	3.253512	0.59212	.	.	ENSG00000137726	ENST00000540359;ENST00000539526;ENST00000260282;ENST00000527717;ENST00000526014;ENST00000524656;ENST00000529335	T;T;T;T;T;T;T	0.72051	-0.62;-0.62;-0.62;-0.62;-0.62;-0.62;-0.62	5.42	4.51	0.55191	.	.	.	.	.	D	0.82360	0.5020	.	.	.	0.51767	D	0.999933	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.83361	0.0002	8	0.62326	D	0.03	.	10.4055	0.44254	0.0904:0.0:0.9096:0.0	.	57;57	E9PJ02;Q9H0Q3	.;FXYD6_HUMAN	I	57;57;57;57;57;57;56	ENSP00000444243:L57I;ENSP00000442756:L57I;ENSP00000260282:L57I;ENSP00000431446:L57I;ENSP00000433312:L57I;ENSP00000431427:L57I;ENSP00000436629:L56I	ENSP00000260282:L57I	L	-	1	2	FXYD6	117217719	1.000000	0.71417	0.933000	0.37362	0.483000	0.33249	4.120000	0.57897	1.282000	0.44496	-0.126000	0.14955	CTA	.	.		0.527	FXYD6-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392307.1	NM_022003		T	117712509	G	T	117712509	3	4	255	1	0	0	0	0	1	0	0	0	6130	991	35	3	134	3	FXYD6	11	117712509	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	4445587	117712509	17294007	431	35776										
OR8D2	283160	hgsc.bcm.edu	37	chr11	124189725	124189725	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agtgggcgacagatagcaacAtaacggtcatattccatggc	11	9	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:124189725A>G	ENST00000357438.2	-	1	459	c.369T>C	c.(367-369)taT>taC	p.Y123Y		NM_001002918.1	NP_001002918.1	Q9GZM6	OR8D2_HUMAN	olfactory receptor, family 8, subfamily D, member 2	123						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	25		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0525)		AGATAGCAACATAACGGTCAT	0.418																																					p.Y123Y		Atlas-SNP	.											OR8D2,right_upper_lobe,carcinoma,0,1	OR8D2	65	.	0			c.T369C						.						94	89	91					11																	124189725		2201	4299	6500	SO:0001819	synonymous_variant	283160	exon1			AGCAACATAACGG	AF162668	CCDS31707.1	11q24.1	2012-08-09			ENSG00000197263	ENSG00000197263		"GPCR / Class A : Olfactory receptors"	8482	protein-coding gene	gene with protein product							Standard	NM_001002918		Approved		uc010sah.2	Q9GZM6	OTTHUMG00000165978	ENST00000357438.2:c.369T>C	chr11.hg19:g.124189725A>G		56.0	0.0		50.0	2.0	NM_001002918	B9EH49|Q6IFR0	Silent	SNP	ENST00000357438.2	hg19	CCDS31707.1																																																																																			.	.		0.418	OR8D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387286.1	NM_001002918		G	124189725	A	G	124189725	2	3	255	1	0	0	0	0	0	0	0	1	11241	224	8	2		2	OR8D2	11	124189725	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	6477216	124189725	10816791	432	35777										
OR8A1	390275	hgsc.bcm.edu	37	chr11	124440852	124440852	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gcctctgtgttctacaccacGgtaatccccatgttgaatcc	7	14	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:124440852G>T	ENST00000284287.3	+	1	960	c.888G>T	c.(886-888)acG>acT	p.T296T		NM_001005194.1	NP_001005194.1	Q8NGG7	OR8A1_HUMAN	olfactory receptor, family 8, subfamily A, member 1	296					axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			haematopoietic_and_lymphoid_tissue(1)|lung(16)|ovary(2)|prostate(1)|skin(2)	22		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0214)		TCTACACCACGGTAATCCCCA	0.468																																					p.T296T		Atlas-SNP	.											.	OR8A1	61	.	0			c.G888T						.						79	70	73					11																	124440852		2201	4299	6500	SO:0001819	synonymous_variant	390275	exon1			CACCACGGTAATC	BK004495	CCDS31712.1	11q24.2	2012-08-09			ENSG00000196119	ENSG00000196119		"GPCR / Class A : Olfactory receptors"	8469	protein-coding gene	gene with protein product							Standard	NM_001005194		Approved	OST025	uc010san.2	Q8NGG7	OTTHUMG00000165923	ENST00000284287.3:c.888G>T	chr11.hg19:g.124440852G>T		180.0	0.0		154.0	8.0	NM_001005194	Q6IEW7|Q96RC6	Silent	SNP	ENST00000284287.3	hg19	CCDS31712.1																																																																																			.	.		0.468	OR8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387062.1	NM_001005194		T	124440852	G	T	124440852	2	4	255	1	0	0	0	0	0	0	0	1	11234	1103	39	1		1	OR8A1	11	124440852	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	251127	124440852	10565664	433	35778										
SPATA19	219938	hgsc.bcm.edu	37	chr11	133714476	133714476	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gacatcttctcccttacaccCtgggaagggtggttgatgga	12	10	2	1	rs138068697		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:133714476C>G	ENST00000299140.3	-	3	249	c.195G>C	c.(193-195)caG>caC	p.Q65H	SPATA19_ENST00000532889.1_Missense_Mutation_p.Q65H	NM_174927.1	NP_777587.1	Q7Z5L4	SPT19_HUMAN	spermatogenesis associated 19	65					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	mitochondrial outer membrane (GO:0005741)				cervix(1)|endometrium(2)|large_intestine(2)|lung(5)|prostate(1)	11	all_hematologic(175;0.127)	all_cancers(12;5.59e-17)|all_epithelial(12;2.65e-12)|all_lung(97;0.00045)|Lung NSC(97;0.000861)|Breast(109;0.000873)|Medulloblastoma(222;0.0425)|Esophageal squamous(93;0.0844)|all_neural(223;0.117)		Epithelial(10;4.36e-10)|all cancers(11;7.1e-09)|BRCA - Breast invasive adenocarcinoma(10;8.45e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00286)|Lung(977;0.207)		CCCTTACACCCTGGGAAGGGT	0.512																																					p.Q65H		Atlas-SNP	.											.	SPATA19	36	.	0			c.G195C						.						136	131	132					11																	133714476		2201	4297	6498	SO:0001583	missense	219938	exon3			TACACCCTGGGAA	AK098717	CCDS8493.1	11q25	2010-04-23				ENSG00000166118			30614	protein-coding gene	gene with protein product	"spergen 1", "cancer/testis antigen 132"	609805				12477932	Standard	XM_005271448		Approved	FLJ25851, spergen1, SPAS1, CT132	uc001qgv.1	Q7Z5L4		ENST00000299140.3:c.195G>C	chr11.hg19:g.133714476C>G	ENSP00000299140:p.Gln65His	225.0	0.0		178.0	110.0	NM_174927	Q8N7A9	Missense_Mutation	SNP	ENST00000299140.3	hg19	CCDS8493.1	.	.	.	.	.	.	.	.	.	.	C	8.443	0.851238	0.17034	.	.	ENSG00000166118	ENST00000299140;ENST00000532889	T;T	0.46451	0.87;0.87	1.33	1.33	0.21861	.	.	.	.	.	T	0.36193	0.0958	N	0.08118	0	0.09310	N	1	D	0.54397	0.966	P	0.61592	0.891	T	0.16070	-1.0415	9	0.87932	D	0	.	6.4121	0.21696	0.0:1.0:0.0:0.0	.	65	Q7Z5L4	SPT19_HUMAN	H	65	ENSP00000299140:Q65H;ENSP00000435248:Q65H	ENSP00000299140:Q65H	Q	-	3	2	SPATA19	133219686	0.038000	0.19896	0.010000	0.14722	0.010000	0.07245	0.441000	0.21611	0.585000	0.29608	0.591000	0.81541	CAG	.	C|1.000;T|0.000		0.512	SPATA19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393281.1	NM_174927		G	133714476	C	G	133714476	3	3	255	1	0	0	0	0	1	0	0	0	15019	680	24	4	324	4	SPATA19	11	133714476	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	9273624	133714476	1292040	434	35779										
PLEKHG6	55200	hgsc.bcm.edu	37	chr12	6436814	6436814	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tggaaacactccacagggccCggcttcggggccagcttccc	12	16	0	0	rs149885168		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:6436814C>A	ENST00000396988.3	+	15	2295	c.2065C>A	c.(2065-2067)Cgg>Agg	p.R689R	PLEKHG6_ENST00000449001.2_Silent_p.R657R|PLEKHG6_ENST00000304581.8_Silent_p.R219R|PLEKHG6_ENST00000011684.7_Silent_p.R689R	NM_001144856.1	NP_001138328.1	Q3KR16	PKHG6_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 6	689						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|skin(4)	23						CCACAGGGCCCGGCTTCGGGG	0.637																																					p.R689R		Atlas-SNP	.											PLEKHG6,NS,carcinoma,0,1	PLEKHG6	62	.	0			c.C2065A						.						12	15	14					12																	6436814		2189	4277	6466	SO:0001819	synonymous_variant	55200	exon15			AGGGCCCGGCTTC	AK001527	CCDS8541.1, CCDS44808.1	12p13.31	2013-01-11			ENSG00000008323	ENSG00000008323		"Pleckstrin homology (PH) domain containing"	25562	protein-coding gene	gene with protein product		611743					Standard	NM_018173		Approved	FLJ10665	uc001qnr.3	Q3KR16	OTTHUMG00000168266	ENST00000396988.3:c.2065C>A	chr12.hg19:g.6436814C>A		43.0	0.0		48.0	2.0	NM_001144856	Q3SWR1|Q8N1P1|Q8WYY1|Q9H8F4|Q9NVK9	Silent	SNP	ENST00000396988.3	hg19	CCDS8541.1																																																																																			.	C|1.000;G|0.000		0.637	PLEKHG6-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399031.1	NM_018173		A	6436814	C	A	6436814	2	1	255	1	0	0	0	0	0	0	0	1	12083	643	23	1		1	PLEKHG6	12	6436814	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10		6436814	127415081	435	35780										
CLEC1A	51267	hgsc.bcm.edu	37	chr12	10224077	10224077	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggatggccacacagtctctgCttcttgggctggtgacatct	12	11	3	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:10224077C>T	ENST00000315330.4	-	6	760	c.698G>A	c.(697-699)aGc>aAc	p.S233N	CLEC1A_ENST00000420265.2_Missense_Mutation_p.S141N|CLEC1A_ENST00000457018.2_Missense_Mutation_p.S200N	NM_016511.2	NP_057595.2	Q8NC01	CLC1A_HUMAN	C-type lectin domain family 1, member A	233	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)	p.S233N(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	23						ACAGTCTCTGCTTCTTGGGCT	0.383																																					p.S233N		Atlas-SNP	.											CLEC1A,NS,carcinoma,0,1	CLEC1A	48	.	1	Substitution - Missense(1)	lung(1)	c.G698A						.						169	157	161					12																	10224077		2203	4300	6503	SO:0001583	missense	51267	exon6			TCTCTGCTTCTTG	AY358587	CCDS8612.1, CCDS73443.1	12p13.31	2005-02-09				ENSG00000150048		"C-type lectin domain containing"	24355	protein-coding gene	gene with protein product		606782				10671229, 11745369	Standard	XM_005253383		Approved	CLEC1, MGC34328	uc001qxb.3	Q8NC01		ENST00000315330.4:c.698G>A	chr12.hg19:g.10224077C>T	ENSP00000326407:p.Ser233Asn	72.0	0.0		63.0	3.0	NM_016511	Q8IUW7|Q9NZH3	Missense_Mutation	SNP	ENST00000315330.4	hg19	CCDS8612.1	.	.	.	.	.	.	.	.	.	.	C	0.146	-1.096261	0.01843	.	.	ENSG00000150048	ENST00000315330;ENST00000457018;ENST00000420265	T;T;T	0.16597	2.33;2.33;2.33	5.42	-0.634	0.11516	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.724899	0.13080	N	0.415351	T	0.09730	0.0239	L	0.28344	0.845	0.21020	N	0.999804	B;B;B	0.20164	0.042;0.018;0.001	B;B;B	0.22601	0.04;0.028;0.012	T	0.43196	-0.9406	10	0.08381	T	0.77	.	9.157	0.36998	0.0:0.5607:0.0:0.4393	.	141;200;233	E7ESV9;E9PFB4;Q8NC01	.;.;CLC1A_HUMAN	N	233;200;141	ENSP00000326407:S233N;ENSP00000415048:S200N;ENSP00000417010:S141N	ENSP00000326407:S233N	S	-	2	0	CLEC1A	10115344	0.157000	0.22836	0.034000	0.17996	0.578000	0.36192	-0.765000	0.04730	-0.459000	0.07013	-0.253000	0.11424	AGC	.	.		0.383	CLEC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399924.1	NM_016511		T	10224077	C	T	10224077	3	4	255	1	0	0	0	0	1	0	0	0	3507	797	28	3	148	3	CLEC1A	12	10224077	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	3787263	10224077	123627818	436	35781										
TAS2R42	353164	hgsc.bcm.edu	37	chr12	11338858	11338858	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccattttcatggccctcctaTgggcctctgtgctggagtct	10	13	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:11338858T>C	ENST00000334266.1	-	1	685	c.686A>G	c.(685-687)cAt>cGt	p.H229R		NM_181429.1	NP_852094.1	Q7RTR8	T2R42_HUMAN	taste receptor, type 2, member 42	229					sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|kidney(2)|lung(4)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(49;0.0455)			GGCCCTCCTATGGGCCTCTGT	0.413																																					p.H229R	Melanoma(15;352 722 10077 19546 48810)	Atlas-SNP	.											.	TAS2R42	30	.	0			c.A686G						.						74	77	76					12																	11338858		2203	4300	6503	SO:0001583	missense	353164	exon1			CTCCTATGGGCCT	AX097739, AB199241	CCDS31747.1	12p13	2012-08-22			ENSG00000186136	ENSG00000186136		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	18888	protein-coding gene	gene with protein product		613966				12679530	Standard	NM_181429		Approved	T2R24, T2R55, hT2R55, TAS2R55	uc001qzr.1	Q7RTR8	OTTHUMG00000168567	ENST00000334266.1:c.686A>G	chr12.hg19:g.11338858T>C	ENSP00000334050:p.His229Arg	81.0	0.0		87.0	4.0	NM_181429	A2RRP4|Q645X0	Missense_Mutation	SNP	ENST00000334266.1	hg19	CCDS31747.1	.	.	.	.	.	.	.	.	.	.	T	9.369	1.070082	0.20147	.	.	ENSG00000186136	ENST00000334266	T	0.00958	5.5	3.6	3.6	0.41247	GPCR, rhodopsin-like superfamily (1);	0.076157	0.52532	D	0.000072	T	0.07279	0.0184	H	0.94886	3.595	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.05289	-1.0894	10	0.87932	D	0	.	8.7846	0.34811	0.0:0.0:0.0:1.0	.	229	Q7RTR8	T2R42_HUMAN	R	229	ENSP00000334050:H229R	ENSP00000334050:H229R	H	-	2	0	TAS2R42	11230125	0.807000	0.29009	0.144000	0.22314	0.003000	0.03518	2.142000	0.42177	1.669000	0.50854	0.533000	0.62120	CAT	.	.		0.413	TAS2R42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400243.1	NM_181429		C	11338858	T	C	11338858	3	2	255	1	0	0	0	0	1	0	0	0	15595	1464	51	2	262	2	TAS2R42	12	11338858	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	1114781	11338858	122513037	437	35782										
SYT10	341359	hgsc.bcm.edu	37	chr12	33579155	33579155	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttttaaagcagtttggacttCtgctgggatgtcaggggaag	14	5	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:33579155C>T	ENST00000228567.3	-	2	723	c.427G>A	c.(427-429)Gaa>Aaa	p.E143K	SYT10_ENST00000567656.1_5'Flank|SYT10_ENST00000535526.1_5'UTR	NM_198992.3	NP_945343.1	Q6XYQ8	SYT10_HUMAN	synaptotagmin X	143					regulation of calcium ion-dependent exocytosis (GO:0017158)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(3)|skin(4)|urinary_tract(1)	42	Lung NSC(5;8.37e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0334)					GTTTGGACTTCTGCTGGGATG	0.383																																					p.E143K		Atlas-SNP	.											.	SYT10	109	.	0			c.G427A						.						186	193	191					12																	33579155		2203	4300	6503	SO:0001583	missense	341359	exon2			GGACTTCTGCTGG	AY198413	CCDS8732.1	12p11	2013-01-21			ENSG00000110975	ENSG00000110975		"Synaptotagmins"	19266	protein-coding gene	gene with protein product							Standard	NM_198992		Approved		uc001rll.1	Q6XYQ8	OTTHUMG00000169269	ENST00000228567.3:c.427G>A	chr12.hg19:g.33579155C>T	ENSP00000228567:p.Glu143Lys	675.0	2.0		621.0	235.0	NM_198992	Q495U2	Missense_Mutation	SNP	ENST00000228567.3	hg19	CCDS8732.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.782972	0.90282	.	.	ENSG00000110975	ENST00000228567	T	0.56103	0.48	3.78	3.78	0.43462	.	0.000000	0.41938	U	0.000791	T	0.53449	0.1797	M	0.71036	2.16	0.80722	D	1	P	0.38711	0.643	B	0.38327	0.271	T	0.60352	-0.7280	10	0.40728	T	0.16	.	15.8987	0.79356	0.0:1.0:0.0:0.0	.	143	Q6XYQ8	SYT10_HUMAN	K	143	ENSP00000228567:E143K	ENSP00000228567:E143K	E	-	1	0	SYT10	33470422	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.798000	0.75155	2.390000	0.81377	0.655000	0.94253	GAA	.	.		0.383	SYT10-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403222.1	NM_198992		T	33579155	C	T	33579155	3	4	255	1	0	0	0	0	1	0	0	0	15481	922	32	3	1168	3	SYT10	12	33579155	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	22240297	33579155	100272740	438	35783										
PDZRN4	29951	hgsc.bcm.edu	37	chr12	41946515	41946515	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgggcctgacagtctgttacCgaacagatgatgaagaagac	12	8	1	6			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:41946515C>A	ENST00000402685.2	+	6	1269	c.1261C>A	c.(1261-1263)Cga>Aga	p.R421R	PDZRN4_ENST00000298919.7_Silent_p.R161R|PDZRN4_ENST00000539469.2_Silent_p.R163R	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	421	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.						ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R163R(1)|p.R421R(1)		breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				AGTCTGTTACCGAACAGATGA	0.473																																					p.R421R		Atlas-SNP	.											.	PDZRN4	346	.	2	Substitution - coding silent(2)	lung(2)	c.C1261A						.						149	132	138					12																	41946515		2203	4300	6503	SO:0001819	synonymous_variant	29951	exon6			TGTTACCGAACAG	AK094690	CCDS8739.1, CCDS53777.1	12q12	2008-08-14	2008-08-14			ENSG00000165966		"RING-type (C3HC4) zinc fingers"	30552	protein-coding gene	gene with protein product	"similar to semaF cytoplasmic domain associated protein 3"	609730				11230166, 15010864	Standard	NM_013377		Approved	DKFZp434B0417, LNX4, FLJ33777, IMAGE5767589	uc010skn.2	Q6ZMN7		ENST00000402685.2:c.1261C>A	chr12.hg19:g.41946515C>A		122.0	0.0		96.0	4.0	NM_001164595	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Silent	SNP	ENST00000402685.2	hg19	CCDS53777.1																																																																																			.	.		0.473	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377		A	41946515	C	A	41946515	2	1	255	1	0	0	0	0	0	0	0	1	11719	644	23	1		1	PDZRN4	12	41946515	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	8367360	41946515	91905380	439	35784										
PRPH	5630	hgsc.bcm.edu	37	chr12	49690226	49690226	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccctcgaaggacgtggacgaTgccactctgtcccgcctgga	12	15	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:49690226T>C	ENST00000257860.4	+	3	2117	c.618T>C	c.(616-618)gaT>gaC	p.D206D	RP11-161H23.9_ENST00000553259.1_RNA	NM_006262.3	NP_006253.2	P23942	PRPH2_HUMAN	peripherin	0					cell adhesion (GO:0007155)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(8)|skin(1)	12						ACGTGGACGATGCCACTCTGT	0.577																																					p.D206D		Atlas-SNP	.											.	PRPH	26	.	0			c.T618C						.						84	76	78					12																	49690226		2203	4300	6503	SO:0001819	synonymous_variant	5630	exon3			GGACGATGCCACT		CCDS8783.1	12q12-q13	2013-01-16						"Intermediate filaments type III"	9461	protein-coding gene	gene with protein product		170710		NEF4		1378416	Standard	XM_005269025		Approved	PRPH1	uc001rtu.3	P41219		ENST00000257860.4:c.618T>C	chr12.hg19:g.49690226T>C		74.0	0.0		77.0	4.0	NM_006262	Q5TFH5|Q6DK65	Silent	SNP	ENST00000257860.4	hg19	CCDS8783.1																																																																																			.	.		0.577	PRPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393381.1	NM_006262		C	49690226	T	C	49690226	2	2	255	1	0	0	0	0	0	0	0	1	12588	1461	51	2		2	PRPH	12	49690226	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	7743711	49690226	84161669	440	35785										
TROAP	10024	hgsc.bcm.edu	37	chr12	49725141	49725141	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccctccctcaggccccacccGggtctgcaccaaccctgtgg	9	21	2	0	rs200487146	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:49725141G>T	ENST00000257909.3	+	14	2319	c.2243G>T	c.(2242-2244)cGg>cTg	p.R748L	TROAP_ENST00000551245.1_Missense_Mutation_p.R838L|TROAP_ENST00000547923.1_Missense_Mutation_p.R427L	NM_005480.3	NP_005471.3	Q12815	TROAP_HUMAN	trophinin associated protein	748					cell adhesion (GO:0007155)	cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	32						GGCCCCACCCGGGTCTGCACC	0.602											OREG0021792	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R748L		Atlas-SNP	.											.	TROAP	80	.	0			c.G2243T						.						52	50	51					12																	49725141		2203	4300	6503	SO:0001583	missense	10024	exon14			CCACCCGGGTCTG	U04810	CCDS8784.1, CCDS41779.1, CCDS61117.1	12q13.12	2012-10-17	2012-10-17		ENSG00000135451	ENSG00000135451			12327	protein-coding gene	gene with protein product	"tastin"	603872				7758945	Standard	NM_005480		Approved	TASTIN	uc001rtx.4	Q12815	OTTHUMG00000169486	ENST00000257909.3:c.2243G>T	chr12.hg19:g.49725141G>T	ENSP00000257909:p.Arg748Leu	97.0	0.0	964	123.0	5.0	NM_005480	F8VSF9|Q6PJU7|Q8N5B2	Missense_Mutation	SNP	ENST00000257909.3	hg19	CCDS8784.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.612630	0.87258	.	.	ENSG00000135451	ENST00000551245;ENST00000257909;ENST00000547923	.	.	.	5.93	5.93	0.95920	.	0.000000	0.53938	D	0.000058	T	0.70806	0.3266	L	0.47190	1.495	0.34673	D	0.72388	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.78033	-0.2362	9	0.87932	D	0	-20.8276	15.8438	0.78871	0.0:0.0:1.0:0.0	.	838;427;748	F8W130;F8W1U0;Q12815	.;.;TROAP_HUMAN	L	838;748;427	.	ENSP00000257909:R748L	R	+	2	0	TROAP	48011408	0.985000	0.35326	0.892000	0.35008	0.967000	0.64934	3.669000	0.54561	2.815000	0.96918	0.561000	0.74099	CGG	.	G|0.999;A|0.001		0.602	TROAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404300.1	NM_005480		T	49725141	G	T	49725141	3	4	255	1	0	0	0	0	1	0	0	0	16590	1116	39	1	2395	1	TROAP	12	49725141	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	34915	49725141	84126754	441	35786										
KRT2	3849	hgsc.bcm.edu	37	chr12	53040547	53040547	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cactcctcgccctccagcagTttgcggtaggtggcgatctc	11	15	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:53040547T>C	ENST00000309680.3	-	7	1467	c.1446A>G	c.(1444-1446)aaA>aaG	p.K482K		NM_000423.2	NP_000414.2	P35908	K22E_HUMAN	keratin 2	482	Coil 2.|Rod.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte activation (GO:0032980)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(18)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32				BRCA - Breast invasive adenocarcinoma(357;0.19)		CCTCCAGCAGTTTGCGGTAGG	0.627																																					p.K482K		Atlas-SNP	.											.	KRT2	94	.	0			c.A1446G						.						96	86	89					12																	53040547		2203	4300	6503	SO:0001819	synonymous_variant	3849	exon7			CAGCAGTTTGCGG		CCDS8835.1	12q13.13	2013-01-16	2008-08-01	2006-07-17	ENSG00000172867	ENSG00000172867		"-", "Intermediate filaments type II, keratins (basic)"	6439	protein-coding gene	gene with protein product	"epidermal ichthyosis bullosa of Siemens"	600194	"keratin 2A (epidermal ichthyosis bullosa of Siemens)"	KRT2A		7524919, 16831889	Standard	NM_000423		Approved	KRTE	uc001sat.3	P35908	OTTHUMG00000169748	ENST00000309680.3:c.1446A>G	chr12.hg19:g.53040547T>C		66.0	0.0		67.0	4.0	NM_000423	Q4VAQ2	Silent	SNP	ENST00000309680.3	hg19	CCDS8835.1																																																																																			.	.		0.627	KRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405704.1	NM_000423		C	53040547	T	C	53040547	2	2	255	1	0	0	0	0	0	0	0	1	8466	1722	60	2		2	KRT2	12	53040547	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	3315406	53040547	80811348	442	35787										
KRT1	3848	hgsc.bcm.edu	37	chr12	53069530	53069530	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggcacattctccagacatccTgtaggagaaaataagaaaat	8	8	1	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:53069530T>C	ENST00000252244.3	-	8	1534		c.e8-2			NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1						complement activation, lectin pathway (GO:0001867)|establishment of skin barrier (GO:0061436)|fibrinolysis (GO:0042730)|negative regulation of inflammatory response (GO:0050728)|regulation of angiogenesis (GO:0045765)|response to oxidative stress (GO:0006979)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(7)|skin(3)	39						CCAGACATCCTGTAGGAGAAA	0.517																																					.		Atlas-SNP	.											.	KRT1	110	.	0			c.1476-2A>G						.						87	81	83					12																	53069530		2203	4300	6503	SO:0001630	splice_region_variant	3848	exon9			ACATCCTGTAGGA	X69725	CCDS8836.1	12q13.13	2014-06-05	2008-08-01		ENSG00000167768	ENSG00000167768		"-", "Intermediate filaments type II, keratins (basic)"	6412	protein-coding gene	gene with protein product		139350	"epidermolytic hyperkeratosis 1"	EHK1		2461420, 2470667, 16831889	Standard	NM_006121		Approved	KRT1A	uc001sau.1	P04264	OTTHUMG00000169749	ENST00000252244.3:c.1476-2A>G	chr12.hg19:g.53069530T>C		153.0	0.0		139.0	6.0	NM_006121	B2RA01|P85925|P86104|Q14720|Q6GSJ0|Q9H298	Splice_Site	SNP	ENST00000252244.3	hg19	CCDS8836.1	.	.	.	.	.	.	.	.	.	.	T	11.10	1.540002	0.27563	.	.	ENSG00000167768	ENST00000252244	.	.	.	4.55	4.55	0.56014	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.244	0.37513	0.0:0.0951:0.0:0.9049	.	.	.	.	.	-1	.	.	.	-	.	.	KRT1	51355797	0.997000	0.39634	0.953000	0.39169	0.419000	0.31324	2.849000	0.48286	1.812000	0.52913	0.379000	0.24179	.	.	.		0.517	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1	NM_006121	Intron	C	53069530	T	C	53069530	5	2	255	1	0	0	0	0	0	0	1	0	8456	1594	55	2	468	2	KRT1	12	53069530	Splice_Site	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	28983	53069530	80782365	443	35788										
KRT77	374454	hgsc.bcm.edu	37	chr12	53086273	53086273	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tccagggacagcttgaccccCagcatggcctggtagtcacg	12	14	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:53086273C>T	ENST00000341809.3	-	7	1387	c.1359G>A	c.(1357-1359)ctG>ctA	p.L453L	KRT77_ENST00000537195.1_Silent_p.L220L|RP11-641A6.3_ENST00000547533.1_RNA	NM_175078.2	NP_778253.2	Q7Z794	K2C1B_HUMAN	keratin 77	453	Coil 2.|Rod.					cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(2)|endometrium(2)|large_intestine(3)|lung(11)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25						GCTTGACCCCCAGCATGGCCT	0.657																																					p.L453L		Atlas-SNP	.											.	KRT77	58	.	0			c.G1359A						.						54	49	51					12																	53086273		2203	4300	6503	SO:0001819	synonymous_variant	374454	exon7			GACCCCCAGCATG	BK000975	CCDS8837.1	12q13.13	2013-06-25	2006-07-17	2006-07-17	ENSG00000189182	ENSG00000189182		"-", "Intermediate filaments type II, keratins (basic)"	20411	protein-coding gene	gene with protein product		611158	"keratin 1B"	KRT1B		11683385, 16831889	Standard	NM_175078		Approved		uc001saw.3	Q7Z794	OTTHUMG00000169450	ENST00000341809.3:c.1359G>A	chr12.hg19:g.53086273C>T		102.0	0.0		100.0	5.0	NM_175078	Q7RTS8	Silent	SNP	ENST00000341809.3	hg19	CCDS8837.1																																																																																			.	.		0.657	KRT77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404111.1	NM_175078		T	53086273	C	T	53086273	2	4	255	1	0	0	0	0	0	0	0	1	8499	581	21	3		3	KRT77	12	53086273	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	16743	53086273	80765622	444	35789										
TARBP2	8620	hgsc.bcm.edu	37	chr12	53899518	53899518	+	IGR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aaattcagtaggagagaagaTcctgtccctccgcagttgct	10	10	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:53899518T>C	ENST00000267017.3	-	0	592				TARBP2_ENST00000456234.2_Missense_Mutation_p.I255T|TARBP2_ENST00000552857.1_Silent_p.D142D|TARBP2_ENST00000394357.2_Missense_Mutation_p.I255T|TARBP2_ENST00000266987.2_Missense_Mutation_p.I276T	NM_003717.2	NP_003708.1	O15130	NPFF_HUMAN	neuropeptide FF-amide peptide precursor						acute inflammatory response to antigenic stimulus (GO:0002438)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of appetite (GO:0032099)|negative regulation of heart rate (GO:0010459)|negative regulation of insulin secretion (GO:0046676)|neuropeptide signaling pathway (GO:0007218)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of membrane depolarization (GO:0003254)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|response to morphine (GO:0043278)|somatostatin secretion (GO:0070253)|spinal cord development (GO:0021510)|synaptic transmission (GO:0007268)|vasopressin secretion (GO:0030103)	axon terminus (GO:0043679)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|perikaryon (GO:0043204)|vesicle (GO:0031982)	receptor binding (GO:0005102)			haematopoietic_and_lymphoid_tissue(1)|prostate(1)|urinary_tract(1)	3						GGAGAGAAGATCCTGTCCCTC	0.617																																					p.I276T		Atlas-SNP	.											.	TARBP2	35	.	0			c.T827C						.						104	107	106					12																	53899518		2203	4300	6503	SO:0001628	intergenic_variant	6895	exon8			AGAAGATCCTGTC	AF005271	CCDS8862.1	12q13.13	2013-02-26			ENSG00000139574	ENSG00000139574		"Endogenous ligands"	7901	protein-coding gene	gene with protein product		604643				9224703	Standard	NM_003717		Approved	FMRFAL	uc001sdw.1	O15130	OTTHUMG00000169856		chr12.hg19:g.53899518T>C		46.0	0.0		61.0	4.0	NM_134323	Q3SXL4	Missense_Mutation	SNP	ENST00000267017.3	hg19	CCDS8862.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.701358	0.88924	.	.	ENSG00000139546	ENST00000266987;ENST00000456234;ENST00000394357	T;T;T	0.65364	-0.15;-0.14;-0.14	4.98	4.98	0.66077	.	0.050187	0.85682	D	0.000000	T	0.59569	0.2203	L	0.59436	1.845	0.80722	D	1	P	0.34522	0.455	B	0.34991	0.193	T	0.63888	-0.6535	10	0.54805	T	0.06	-8.0569	14.0884	0.64973	0.0:0.0:0.0:1.0	.	276	Q15633	TRBP2_HUMAN	T	276;255;255	ENSP00000266987:I276T;ENSP00000416077:I255T;ENSP00000377885:I255T	ENSP00000266987:I276T	I	+	2	0	TARBP2	52185785	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.690000	0.61731	2.227000	0.72691	0.459000	0.35465	ATC	.	.		0.617	NPFF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406301.1	NM_003717		C	53899518	T	C	53899518	1	2	255	0	1	0	0	0	0	0	0	0	15571	1435	50	2		2	TARBP2	12	53899518	IGR	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	813245	53899518	79952377	445	35790										
GTSF1	121355	hgsc.bcm.edu	37	chr12	54858950	54858950	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttctcagggtccagggagtcGgctgaaagacagaagtgttt	14	7	1	3	rs146835334		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:54858950G>T	ENST00000552397.1	-	3	914	c.18C>A	c.(16-18)acC>acA	p.T6T	GTSF1_ENST00000305879.5_Splice_Site_p.T6T|RP11-753H16.3_ENST00000550474.1_RNA|GTSF1_ENST00000552395.1_Intron|RP11-753H16.5_ENST00000552785.1_RNA			Q8WW33	GTSF1_HUMAN	gametocyte specific factor 1	6						cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	5		Myeloproliferative disorder(1001;0.00452)				CCAGGGAGTCGGCTGAAAGAC	0.428																																					p.T6T		Atlas-SNP	.											.	GTSF1	15	.	0			c.C18A						.						103	97	99					12																	54858950		2203	4300	6503	SO:0001630	splice_region_variant	121355	exon3			GGAGTCGGCTGAA	AK098819	CCDS8881.1	12q13.2	2008-02-04	2007-11-27	2007-11-27		ENSG00000170627			26565	protein-coding gene	gene with protein product			"family with sequence similarity 112, member B"	FAM112B		12477932	Standard	NM_144594		Approved	FLJ32942	uc001sgb.3	Q8WW33		ENST00000552397.1:c.17-1C>A	chr12.hg19:g.54858950G>T		82.0	0.0		87.0	4.0	NM_144594	B3KQ60|Q0VGM4|Q8N778	Silent	SNP	ENST00000552397.1	hg19	CCDS8881.1																																																																																			.	G|1.000;A|0.000		0.428	GTSF1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406187.1	NM_144594	Silent	T	54858950	G	T	54858950	5	4	255	1	0	0	0	0	0	0	1	0	6895	1130	39	1	509	1	GTSF1	12	54858950	Splice_Site	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	959432	54858950	78992945	446	35791										
MMP19	4327	hgsc.bcm.edu	37	chr12	56234938	56234938	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gttgaagggatcctctaggcCacaacgaggctgcctcatgc	12	12	2	1	rs202159629		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:56234938C>A	ENST00000322569.4	-	3	347	c.256G>T	c.(256-258)Ggc>Tgc	p.G86C	MMP19_ENST00000394182.1_5'Flank|MMP19_ENST00000409200.3_Missense_Mutation_p.G86C|MMP19_ENST00000547487.1_5'UTR|MMP19_ENST00000548629.1_Missense_Mutation_p.G86C	NM_002429.4	NP_002420.1	Q99542	MMP19_HUMAN	matrix metallopeptidase 19	86					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|luteolysis (GO:0001554)|ovarian follicle development (GO:0001541)|ovulation from ovarian follicle (GO:0001542)|proteolysis (GO:0006508)|response to cAMP (GO:0051591)|response to hormone (GO:0009725)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(2)|skin(2)	26					Marimastat(DB00786)	TCCTCTAGGCCACAACGAGGC	0.547																																					p.G86C		Atlas-SNP	.											.	MMP19	61	.	0			c.G256T						.						96	98	97					12																	56234938		2203	4300	6503	SO:0001583	missense	4327	exon3			CTAGGCCACAACG	X92521	CCDS8895.1, CCDS61146.1	12q14	2005-08-08	2005-08-08			ENSG00000123342			7165	protein-coding gene	gene with protein product		601807	"matrix metalloproteinase 19"	MMP18		9232430	Standard	NM_002429		Approved	RASI-1	uc001sib.4	Q99542	OTTHUMG00000170216	ENST00000322569.4:c.256G>T	chr12.hg19:g.56234938C>A	ENSP00000313437:p.Gly86Cys	35.0	0.0		45.0	4.0	NM_001272101	B4E030|O15278|O95606|Q99580	Missense_Mutation	SNP	ENST00000322569.4	hg19	CCDS8895.1	.	.	.	.	.	.	.	.	.	.	C	32	5.106959	0.94292	.	.	ENSG00000123342	ENST00000322569;ENST00000548629;ENST00000409200	T;T;T	0.67171	-0.25;-0.25;-0.25	5.8	5.8	0.92144	Peptidoglycan binding-like (1);Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.87116	0.6097	M	0.93939	3.475	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.89741	0.3933	10	0.87932	D	0	.	18.8323	0.92145	0.0:1.0:0.0:0.0	.	86;86	B4E030;Q99542	.;MMP19_HUMAN	C	86	ENSP00000313437:G86C;ENSP00000446979:G86C;ENSP00000386625:G86C	ENSP00000313437:G86C	G	-	1	0	MMP19	54521205	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.860000	0.75473	2.755000	0.94549	0.655000	0.94253	GGC	.	C|0.999;T|0.001		0.547	MMP19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408023.1	NM_002429		A	56234938	C	A	56234938	3	1	255	1	0	0	0	0	1	0	0	0	9666	594	21	3	1298	3	MMP19	12	56234938	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1375988	56234938	77616957	447	35792										
ESYT1	23344	hgsc.bcm.edu	37	chr12	56530663	56530663	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	caaactccagactctatatgAaactagtcatgagggtatgg	9	8	2	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:56530663A>G	ENST00000394048.5	+	16	2032	c.1768A>G	c.(1768-1770)Aaa>Gaa	p.K590E	ESYT1_ENST00000541590.1_Missense_Mutation_p.K600E|ESYT1_ENST00000267113.4_Missense_Mutation_p.K600E	NM_001184796.1|NM_015292.2	NP_001171725.1|NP_056107.1	Q9BSJ8	ESYT1_HUMAN	extended synaptotagmin-like protein 1	590					lipid transport (GO:0006869)	integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|large_intestine(4)|lung(10)|ovary(5)|prostate(1)|skin(3)|urinary_tract(1)	28						ACTCTATATGAAACTAGTCAT	0.527																																					p.K600E		Atlas-SNP	.											.	ESYT1	84	.	0			c.A1798G						.						69	70	69					12																	56530663		2203	4300	6503	SO:0001583	missense	23344	exon16			TATATGAAACTAG	AK074368	CCDS8904.1, CCDS53801.1	12q13.2	2014-07-02	2009-06-23	2009-06-23		ENSG00000139641		"Synaptotagmins"	29534	protein-coding gene	gene with protein product			"family with sequence similarity 62 (C2 domain containing), member A"	FAM62A		9872452, 10350628, 17672888	Standard	NM_015292		Approved	MBC2, KIAA0747	uc001sjr.3	Q9BSJ8		ENST00000394048.5:c.1768A>G	chr12.hg19:g.56530663A>G	ENSP00000377612:p.Lys590Glu	88.0	0.0		77.0	4.0	NM_001184796	A0FGR7|A8K2S2|O94848|Q6PJN4|Q9H6J1|Q9H6W2|Q9Y416	Missense_Mutation	SNP	ENST00000394048.5	hg19	CCDS8904.1	.	.	.	.	.	.	.	.	.	.	A	18.27	3.587028	0.66105	.	.	ENSG00000139641	ENST00000394048;ENST00000402331;ENST00000267113;ENST00000541590	T;T;T	0.69685	-0.42;-0.42;-0.42	4.95	4.95	0.65309	C2 calcium/lipid-binding domain, CaLB (1);	0.094256	0.64402	D	0.000001	T	0.71567	0.3355	M	0.78456	2.415	0.51767	D	0.999936	P;B	0.38129	0.619;0.307	P;B	0.44359	0.447;0.138	T	0.70306	-0.4908	10	0.25751	T	0.34	-12.5496	13.8923	0.63747	1.0:0.0:0.0:0.0	.	600;590	Q9BSJ8-2;Q9BSJ8	.;ESYT1_HUMAN	E	590;544;600;600	ENSP00000377612:K590E;ENSP00000267113:K600E;ENSP00000445952:K600E	ENSP00000267113:K600E	K	+	1	0	ESYT1	54816930	1.000000	0.71417	1.000000	0.80357	0.846000	0.48090	8.098000	0.89540	1.991000	0.58162	0.533000	0.62120	AAA	.	.		0.527	ESYT1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000407906.1	NM_015292		G	56530663	A	G	56530663	3	3	255	1	0	0	0	0	1	0	0	0	5266	247	9	2	1860	2	ESYT1	12	56530663	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	295725	56530663	77321232	448	35793										
SMARCC2	6601	hgsc.bcm.edu	37	chr12	56580987	56580987	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcaccggcagtttagtgagcGgtgcattgctgacatgtttg	13	8	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:56580987G>T	ENST00000267064.4	-	2	301	c.215C>A	c.(214-216)cCg>cAg	p.P72Q	SMARCC2_ENST00000550859.1_5'UTR|SMARCC2_ENST00000394023.3_Missense_Mutation_p.P72Q|SMARCC2_ENST00000347471.4_Missense_Mutation_p.P72Q|SMARCC2_ENST00000550164.1_Missense_Mutation_p.P72Q|RP11-977G19.5_ENST00000553176.1_RNA	NM_003075.3	NP_003066.2	Q8TAQ2	SMRC2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	72					ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome disassembly (GO:0006337)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)	p.P72L(2)		breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(3)|lung(20)|ovary(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(18;0.123)			TTTAGTGAGCGGTGCATTGCT	0.463																																					p.P72Q		Atlas-SNP	.											SMARCC2_ENST00000267064,NS,carcinoma,0,2	SMARCC2	212	.	2	Substitution - Missense(2)	lung(2)	c.C215A						.						95	95	95					12																	56580987		2203	4300	6503	SO:0001583	missense	6601	exon2			GTGAGCGGTGCAT	U66616	CCDS8907.1, CCDS8908.1, CCDS55835.1	12q13.2	2008-05-14				ENSG00000139613			11105	protein-coding gene	gene with protein product		601734				8804307, 9693044	Standard	NM_001130420		Approved	BAF170, Rsc8, CRACC2	uc001skb.3	Q8TAQ2	OTTHUMG00000170288	ENST00000267064.4:c.215C>A	chr12.hg19:g.56580987G>T	ENSP00000267064:p.Pro72Gln	89.0	0.0		71.0	4.0	NM_139067	F8VTJ5|Q59GV3|Q92923|Q96E12|Q96GY4	Missense_Mutation	SNP	ENST00000267064.4	hg19	CCDS8907.1	.	.	.	.	.	.	.	.	.	.	G	19.51	3.841509	0.71488	.	.	ENSG00000139613	ENST00000394023;ENST00000550164;ENST00000347471;ENST00000267064	T;T;T	0.49139	0.79;0.81;0.79	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.66436	0.2789	M	0.71036	2.16	0.58432	D	0.999997	D;D;D;D	0.71674	0.993;0.988;0.998;0.993	D;P;P;D	0.63877	0.919;0.832;0.881;0.919	T	0.65742	-0.6094	10	0.46703	T	0.11	-12.5461	17.8735	0.88818	0.0:0.0:1.0:0.0	.	72;77;72;72	F8VTJ5;Q59G16;Q8TAQ2;Q8TAQ2-2	.;.;SMRC2_HUMAN;.	Q	72	ENSP00000449396:P72Q;ENSP00000302919:P72Q;ENSP00000267064:P72Q	ENSP00000267064:P72Q	P	-	2	0	SMARCC2	54867254	1.000000	0.71417	0.993000	0.49108	0.974000	0.67602	9.196000	0.94978	2.836000	0.97738	0.655000	0.94253	CCG	.	.		0.463	SMARCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408370.1			T	56580987	G	T	56580987	3	4	255	1	0	0	0	0	1	0	0	0	14791	1116	39	1	3634	1	SMARCC2	12	56580987	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	50324	56580987	77270908	449	35794										
RBMS2	5939	hgsc.bcm.edu	37	chr12	56982115	56982115	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agctatgcaaggagcttacaTctcccagtacacccctgtgc	8	14	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:56982115T>C	ENST00000262031.5	+	12	1195	c.1100T>C	c.(1099-1101)aTc>aCc	p.I367T	RNU6-343P_ENST00000364709.1_RNA|RBMS2_ENST00000542360.1_Missense_Mutation_p.I222T|RBMS2_ENST00000550726.1_Missense_Mutation_p.I242T|RBMS2_ENST00000552247.2_Missense_Mutation_p.I304T	NM_002898.3	NP_002889.1	Q15434	RBMS2_HUMAN	RNA binding motif, single stranded interacting protein 2	367					RNA processing (GO:0006396)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.I367T(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(8)|prostate(3)|skin(2)|urinary_tract(1)	18						GGAGCTTACATCTCCCAGTAC	0.453																																					p.I367T		Atlas-SNP	.											RBMS2,NS,carcinoma,0,1	RBMS2	29	.	1	Substitution - Missense(1)	endometrium(1)	c.T1100C						.						158	139	146					12																	56982115		2203	4300	6503	SO:0001583	missense	5939	exon12			CTTACATCTCCCA	D28483	CCDS8923.1	12q13.13	2013-02-12			ENSG00000076067	ENSG00000076067		"RNA binding motif (RRM) containing"	9909	protein-coding gene	gene with protein product		602387				8041632	Standard	NM_002898		Approved	SCR3	uc001sln.2	Q15434	OTTHUMG00000170488	ENST00000262031.5:c.1100T>C	chr12.hg19:g.56982115T>C	ENSP00000262031:p.Ile367Thr	102.0	1.0		122.0	5.0	NM_002898		Missense_Mutation	SNP	ENST00000262031.5	hg19	CCDS8923.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.152326	0.78001	.	.	ENSG00000076067	ENST00000262031;ENST00000552247;ENST00000550726;ENST00000542360	T;T;T	0.27256	2.53;2.49;1.68	4.8	4.8	0.61643	.	0.156720	0.53938	D	0.000048	T	0.41949	0.1181	M	0.61703	1.905	0.80722	D	1	P;D	0.62365	0.95;0.991	P;P	0.61477	0.635;0.889	T	0.15636	-1.0430	10	0.20046	T	0.44	.	13.7659	0.62995	0.0:0.0:0.0:1.0	.	222;367	F5H5C8;Q15434	.;RBMS2_HUMAN	T	367;304;242;222	ENSP00000262031:I367T;ENSP00000447426:I304T;ENSP00000449678:I242T	ENSP00000262031:I367T	I	+	2	0	RBMS2	55268382	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.234000	0.78134	2.155000	0.67459	0.482000	0.46254	ATC	.	.		0.453	RBMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409366.2	NM_002898		C	56982115	T	C	56982115	3	2	255	1	0	0	0	0	1	0	0	0	13164	1435	50	2	1146	2	RBMS2	12	56982115	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	401128	56982115	76869780	450	35795										
BAZ2A	11176	hgsc.bcm.edu	37	chr12	56992704	56992704	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aaaatccataggatttttgaTgatgcgccggtacccactca	8	10	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:56992704T>C	ENST00000551812.1	-	28	5693	c.5500A>G	c.(5500-5502)Atc>Gtc	p.I1834V	BAZ2A_ENST00000379441.3_Missense_Mutation_p.I1804V|BAZ2A_ENST00000179765.5_Missense_Mutation_p.I1802V|BAZ2A_ENST00000553222.1_5'Flank|BAZ2A_ENST00000549884.1_Missense_Mutation_p.I1832V	NM_013449.3	NP_038477.2	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	1834	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.				chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA methylation (GO:0006306)|heterochromatin assembly involved in chromatin silencing (GO:0070869)|histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|histone H4 deacetylation (GO:0070933)|histone H4-K20 methylation (GO:0034770)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|nucleolus (GO:0005730)|rDNA heterochromatin (GO:0033553)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|lysine-acetylated histone binding (GO:0070577)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(15)|urinary_tract(1)	31						GGATTTTTGATGATGCGCCGG	0.532																																					p.I1834V		Atlas-SNP	.											.	BAZ2A	263	.	0			c.A5500G						.						28	29	29					12																	56992704		1889	4119	6008	SO:0001583	missense	11176	exon28			TTTTGATGATGCG	AB032254	CCDS44924.1, CCDS73483.1	12q13.3	2013-01-28				ENSG00000076108		"Zinc fingers, PHD-type"	962	protein-coding gene	gene with protein product	"TTF-I interacting peptide 5"	605682				10662543, 11532953	Standard	XM_005268596		Approved	KIAA0314, TIP5, WALp3	uc001slq.1	Q9UIF9	OTTHUMG00000170332	ENST00000551812.1:c.5500A>G	chr12.hg19:g.56992704T>C	ENSP00000446880:p.Ile1834Val	64.0	0.0		65.0	4.0	NM_013449	B3KN66|O00536|O15030|Q68DI8|Q96H26	Missense_Mutation	SNP	ENST00000551812.1	hg19	CCDS44924.1	.	.	.	.	.	.	.	.	.	.	T	16.50	3.140015	0.56936	.	.	ENSG00000076108	ENST00000379441;ENST00000179765;ENST00000551812;ENST00000549787;ENST00000549884	T;T;T;T;T	0.32753	1.44;1.44;1.44;1.44;1.44	5.81	4.66	0.58398	Bromodomain (6);Bromodomain, conserved site (1);	0.127834	0.51477	D	0.000096	T	0.52484	0.1737	M	0.73598	2.24	0.47698	D	0.999492	B;P;P;B	0.36378	0.094;0.495;0.55;0.0	B;P;P;B	0.56042	0.387;0.686;0.79;0.007	T	0.53078	-0.8489	10	0.59425	D	0.04	-11.7719	11.3801	0.49752	0.0:0.0721:0.0:0.9279	.	1832;1830;1834;1807	F8VU39;Q9UIF9-3;Q9UIF9;Q9UIF9-2	.;.;BAZ2A_HUMAN;.	V	1804;1802;1834;766;1832	ENSP00000368754:I1804V;ENSP00000179765:I1802V;ENSP00000446880:I1834V;ENSP00000448760:I766V;ENSP00000447941:I1832V	ENSP00000179765:I1802V	I	-	1	0	BAZ2A	55278971	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	2.886000	0.48578	1.141000	0.42275	0.529000	0.55759	ATC	.	.		0.532	BAZ2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408561.1	NM_013449		C	56992704	T	C	56992704	3	2	255	1	0	0	0	0	1	0	0	0	1331	1464	51	2	225	2	BAZ2A	12	56992704	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	10589	56992704	76859191	451	35796										
TMEM194A	23306	hgsc.bcm.edu	37	chr12	57472459	57472459	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tagccgcactgtcccaccgcCcccgactcccgagccccagg	9	22	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:57472459C>T	ENST00000300128.4	-	1	93	c.70G>A	c.(70-72)Ggc>Agc	p.G24S	TMEM194A_ENST00000553654.1_Intron|TMEM194A_ENST00000379391.3_Missense_Mutation_p.G24S	NM_001130963.1	NP_001124435.1	O14524	T194A_HUMAN	transmembrane protein 194A	24						integral component of membrane (GO:0016021)				endometrium(3)|large_intestine(3)|lung(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						GTCCCACCGCCCCCGACTCCC	0.692																																					p.G24S		Atlas-SNP	.											.	TMEM194A	64	.	0			c.G70A						.						46	60	55					12																	57472459		2200	4296	6496	SO:0001583	missense	23306	exon1			CACCGCCCCCGAC	AB006624	CCDS31841.1, CCDS44927.1	12q13.3	2008-06-10	2008-06-10	2008-06-10		ENSG00000166881			29001	protein-coding gene	gene with protein product			"transmembrane protein 194"	TMEM194			Standard	NM_015257		Approved	KIAA0286	uc001smy.3	O14524		ENST00000300128.4:c.70G>A	chr12.hg19:g.57472459C>T	ENSP00000300128:p.Gly24Ser	124.0	0.0		104.0	5.0	NM_015257	Q17R72|Q68DH0|Q6IQ25	Missense_Mutation	SNP	ENST00000300128.4	hg19	CCDS44927.1	.	.	.	.	.	.	.	.	.	.	C	12.68	2.010282	0.35511	.	.	ENSG00000166881	ENST00000379391;ENST00000300128	T;T	0.53206	0.63;0.85	3.82	3.82	0.43975	.	0.531789	0.17932	N	0.157122	T	0.42787	0.1218	L	0.51422	1.61	0.19575	N	0.999969	P;P	0.37330	0.455;0.59	B;B	0.37888	0.133;0.26	T	0.41805	-0.9488	10	0.52906	T	0.07	-0.1012	11.5069	0.50472	0.0:1.0:0.0:0.0	.	24;24	O14524;O14524-2	T194A_HUMAN;.	S	24	ENSP00000368701:G24S;ENSP00000300128:G24S	ENSP00000300128:G24S	G	-	1	0	TMEM194A	55758726	0.037000	0.19845	0.288000	0.24862	0.047000	0.14425	2.059000	0.41384	2.415000	0.81967	0.655000	0.94253	GGC	.	.		0.692	TMEM194A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411272.1	NM_015257		T	57472459	C	T	57472459	3	4	255	1	0	0	0	0	1	0	0	0	16131	623	22	3	1300	3	TMEM194A	12	57472459	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	479755	57472459	76379436	452	35797										
LRP1	4035	hgsc.bcm.edu	37	chr12	57539101	57539101	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gcccaggtgtctaccatcacAcctacgagcacgcggcagac	10	16	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:57539101A>G	ENST00000243077.3	+	6	1135	c.669A>G	c.(667-669)acA>acG	p.T223T	LRP1_ENST00000338962.4_Silent_p.T223T|LRP1_ENST00000554174.1_Silent_p.T223T|RP11-545N8.3_ENST00000554476.1_RNA|LRP1_ENST00000553277.1_Silent_p.T223T|RP11-545N8.3_ENST00000555461.1_RNA	NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	223					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	CTACCATCACACCTACGAGCA	0.592																																					p.T223T		Atlas-SNP	.											.	LRP1	428	.	0			c.A669G						.						106	64	78					12																	57539101		2203	4300	6503	SO:0001819	synonymous_variant	4035	exon6			CATCACACCTACG	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"CD molecules", "Low density lipoprotein receptors"	6692	protein-coding gene	gene with protein product		107770	"alpha-2-macroglobulin receptor"	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.669A>G	chr12.hg19:g.57539101A>G		84.0	0.0		87.0	4.0	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	hg19	CCDS8932.1																																																																																			.	.		0.592	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		G	57539101	A	G	57539101	2	3	255	1	0	0	0	0	0	0	0	1	8960	146	6	2		2	LRP1	12	57539101	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	66642	57539101	76312794	453	35798										
LRP1	4035	hgsc.bcm.edu	37	chr12	57599189	57599189	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	atctgtggggacgaggcacgCtgcgtgcgcaccgagaaagc	16	11	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:57599189C>A	ENST00000243077.3	+	74	11857	c.11391C>A	c.(11389-11391)cgC>cgA	p.R3797R		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	3797	EGF-like 14. {ECO:0000255|PROSITE- ProRule:PRU00076}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	ACGAGGCACGCTGCGTGCGCA	0.677																																					p.R3797R		Atlas-SNP	.											.	LRP1	428	.	0			c.C11391A						.						35	36	36					12																	57599189		2200	4299	6499	SO:0001819	synonymous_variant	4035	exon74			GGCACGCTGCGTG	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"CD molecules", "Low density lipoprotein receptors"	6692	protein-coding gene	gene with protein product		107770	"alpha-2-macroglobulin receptor"	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.11391C>A	chr12.hg19:g.57599189C>A		66.0	0.0		93.0	4.0	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	hg19	CCDS8932.1																																																																																			.	.		0.677	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		A	57599189	C	A	57599189	2	1	255	1	0	0	0	0	0	0	0	1	8960	784	28	3		3	LRP1	12	57599189	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	60088	57599189	76252706	454	35799										
GLI1	2735	hgsc.bcm.edu	37	chr12	57864991	57864991	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agaacaggggtgcccagtggGgtctgactccacaggactgg	16	10	1	2	rs149553839	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:57864991G>T	ENST00000228682.2	+	12	2559	c.2468G>T	c.(2467-2469)gGg>gTg	p.G823V	GLI1_ENST00000546141.1_Missense_Mutation_p.G782V|GLI1_ENST00000543426.1_Missense_Mutation_p.G695V	NM_005269.2	NP_005260.1	P08151	GLI1_HUMAN	GLI family zinc finger 1	823					cerebellar cortex morphogenesis (GO:0021696)|digestive tract morphogenesis (GO:0048546)|dorsal/ventral pattern formation (GO:0009953)|epidermal cell differentiation (GO:0009913)|lung development (GO:0030324)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|notochord regression (GO:0060032)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|regulation of smoothened signaling pathway (GO:0008589)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|spermatogenesis (GO:0007283)|ventral midline development (GO:0007418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|primary cilium (GO:0072372)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription regulatory region DNA binding (GO:0044212)			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)			TGCCCAGTGGGGTCTGACTCC	0.597																																					p.G823V	Pancreas(157;841 1936 10503 41495 50368)	Atlas-SNP	.											.	GLI1	141	.	0			c.G2468T						.						69	75	73					12																	57864991		2203	4300	6503	SO:0001583	missense	2735	exon12			CAGTGGGGTCTGA		CCDS8940.1, CCDS53806.1, CCDS53807.1	12q13.2-q13.3	2013-01-25	2009-03-05	2005-01-14		ENSG00000111087		"Zinc fingers, C2H2-type"	4317	protein-coding gene	gene with protein product		165220	"glioma-associated oncogene homolog 1 (zinc finger protein)", "glioma-associated oncogene family zinc finger 1"	GLI		2850480	Standard	NM_005269		Approved		uc001snx.3	P08151		ENST00000228682.2:c.2468G>T	chr12.hg19:g.57864991G>T	ENSP00000228682:p.Gly823Val	69.0	0.0		84.0	4.0	NM_005269	D0EUY3|E9PQQ9|F5H6H8|Q8TDN9	Missense_Mutation	SNP	ENST00000228682.2	hg19	CCDS8940.1	.	.	.	.	.	.	.	.	.	.	G	16.70	3.194657	0.58017	.	.	ENSG00000111087	ENST00000543426;ENST00000228682;ENST00000546141;ENST00000528467	T;T;T;T	0.13196	2.72;2.61;2.69;2.69	4.62	3.72	0.42706	.	0.000000	0.43110	D	0.000603	T	0.18257	0.0438	N	0.22421	0.69	0.80722	D	1	D	0.71674	0.998	P	0.58721	0.844	T	0.01056	-1.1466	10	0.59425	D	0.04	.	12.4531	0.55688	0.0884:0.0:0.9116:0.0	.	823	P08151	GLI1_HUMAN	V	695;823;782;782	ENSP00000437607:G695V;ENSP00000228682:G823V;ENSP00000441006:G782V;ENSP00000434408:G782V	ENSP00000228682:G823V	G	+	2	0	GLI1	56151258	0.998000	0.40836	1.000000	0.80357	0.888000	0.51559	4.325000	0.59234	2.566000	0.86566	0.484000	0.47621	GGG	.	G|0.999;A|0.001		0.597	GLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394197.1	NM_005269		T	57864991	G	T	57864991	3	4	255	1	0	0	0	0	1	0	0	0	6445	1232	43	3	2510	3	GLI1	12	57864991	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	265802	57864991	75986904	455	35800										
MARS	4141	hgsc.bcm.edu	37	chr12	57910119	57910119	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gatggatgaagtgacaaaacAagtatgaagcttaagccctg	11	6	0	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:57910119A>C	ENST00000262027.5	+	20	2689	c.2555A>C	c.(2554-2556)cAa>cCa	p.Q852P	MIR616_ENST00000385293.1_RNA|RN7SL312P_ENST00000582079.1_RNA	NM_004990.3	NP_004981.2	P56192	SYMC_HUMAN	methionyl-tRNA synthetase	852	WHEP-TRS.				gene expression (GO:0010467)|methionyl-tRNA aminoacylation (GO:0006431)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|methionine-tRNA ligase activity (GO:0004825)|tRNA binding (GO:0000049)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	33			GBM - Glioblastoma multiforme(3;4.27e-41)		L-Methionine(DB00134)	GTGACAAAACAAGTATGAAGC	0.483																																					p.Q852P		Atlas-SNP	.											.	MARS	84	.	0			c.A2555C						.						75	65	69					12																	57910119		2203	4300	6503	SO:0001630	splice_region_variant	4141	exon20			CAAAACAAGTATG	X94754	CCDS8942.1	12q13.3	2014-05-06	2007-02-26		ENSG00000166986	ENSG00000166986	6.1.1.10	"Aminoacyl tRNA synthetases / Class I"	6898	protein-coding gene	gene with protein product	"methionine tRNA ligase 1, cytoplasmic"	156560				10448063, 24482476	Standard	NM_004990		Approved	MetRS, SPG70	uc001sog.3	P56192	OTTHUMG00000169996	ENST00000262027.5:c.2556+1A>C	chr12.hg19:g.57910119A>C		163.0	0.0		156.0	69.0	NM_004990	B3KVK7|Q14895|Q53H14|Q96A15|Q96BZ0|Q9NSE0	Missense_Mutation	SNP	ENST00000262027.5	hg19	CCDS8942.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.230007	0.79688	.	.	ENSG00000166986	ENST00000262027;ENST00000552914	T;T	0.67865	-0.29;-0.29	5.47	5.47	0.80525	WHEP-TRS (3);S15/NS1, RNA-binding (2);	0.000000	0.85682	D	0.000000	D	0.85159	0.5633	M	0.92219	3.285	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.87925	0.2706	10	0.54805	T	0.06	-16.7991	13.806	0.63233	1.0:0.0:0.0:0.0	.	852	P56192	SYMC_HUMAN	P	852;171	ENSP00000262027:Q852P;ENSP00000449787:Q171P	ENSP00000262027:Q852P	Q	+	2	0	MARS	56196386	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	5.696000	0.68287	2.216000	0.71823	0.459000	0.35465	CAA	.	.		0.483	MARS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407014.1	NM_004990	Missense_Mutation	C	57910119	A	C	57910119	5	2	255	1	0	0	0	0	0	0	1	0	9325	144	5	5	2633	5	MARS	12	57910119	Splice_Site	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	45128	57910119	75941776	456	35801										
CAND1	55832	hgsc.bcm.edu	37	chr12	67699020	67699020	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	caggctttggttcctccagtGgtggcttgtgttggagaccc	14	10	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:67699020G>T	ENST00000545606.1	+	10	2009	c.1572G>T	c.(1570-1572)gtG>gtT	p.V524V		NM_018448.3	NP_060918.2	Q86VP6	CAND1_HUMAN	cullin-associated and neddylation-dissociated 1	524					cell differentiation (GO:0030154)|negative regulation of catalytic activity (GO:0043086)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|protein ubiquitination (GO:0016567)|SCF complex assembly (GO:0010265)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				NS(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)	35			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)		TTCCTCCAGTGGTGGCTTGTG	0.423																																					p.V524V		Atlas-SNP	.											.	CAND1	100	.	0			c.G1572T						.						202	176	185					12																	67699020		2203	4300	6503	SO:0001819	synonymous_variant	55832	exon10			TCCAGTGGTGGCT		CCDS8977.1	12q14	2008-02-05			ENSG00000111530	ENSG00000111530			30688	protein-coding gene	gene with protein product	"TBP interacting protein"	607727				10048485, 8954946	Standard	NM_018448		Approved	TIP120A, DKFZp434M1414, KIAA0829, TIP120	uc001stn.2	Q86VP6	OTTHUMG00000169060	ENST00000545606.1:c.1572G>T	chr12.hg19:g.67699020G>T		163.0	0.0		173.0	7.0	NM_018448	B2RAU3|O94918|Q6PIY4|Q8NDJ4|Q96JZ9|Q96T19|Q9BTC4|Q9H0G2|Q9P0H7|Q9UF85	Silent	SNP	ENST00000545606.1	hg19	CCDS8977.1																																																																																			.	.		0.423	CAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402105.1	NM_018448		T	67699020	G	T	67699020	2	4	255	1	0	0	0	0	0	0	0	1	2617	1335	47	3		3	CAND1	12	67699020	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	9788901	67699020	66152875	457	35802										
IFNG	3458	hgsc.bcm.edu	37	chr12	68551870	68551870	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctctgcattatttttctgtcActctccttggaaggaaagag	8	9	4	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:68551870A>T	ENST00000229135.3	-	3	320	c.189T>A	c.(187-189)agT>agA	p.S63R	IFNG-AS1_ENST00000536914.1_RNA	NM_000619.2	NP_000610.2	P01579	IFNG_HUMAN	interferon, gamma	63					adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|apoptotic process (GO:0006915)|CD8-positive, alpha-beta T cell differentiation involved in immune response (GO:0002302)|cell cycle arrest (GO:0007050)|cell surface receptor signaling pathway (GO:0007166)|cellular component movement (GO:0006928)|cellular response to interleukin-18 (GO:0071351)|cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endoplasmic reticulum unfolded protein response (GO:0030968)|extrinsic apoptotic signaling pathway (GO:0097191)|humoral immune response (GO:0006959)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003340)|negative regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072308)|negative regulation of myelination (GO:0031642)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neutrophil apoptotic process (GO:0001781)|neutrophil chemotaxis (GO:0030593)|positive regulation of calcidiol 1-monooxygenase activity (GO:0060559)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of fructose 1,6-bisphosphate 1-phosphatase activity (GO:0060550)|positive regulation of fructose 1,6-bisphosphate metabolic process (GO:0060552)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-23 production (GO:0032747)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000309)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of vitamin D biosynthetic process (GO:0060557)|protein import into nucleus, translocation (GO:0000060)|regulation of insulin secretion (GO:0050796)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of the force of heart contraction (GO:0002026)|response to drug (GO:0042493)|response to virus (GO:0009615)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|interferon-gamma receptor binding (GO:0005133)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)	12			Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000829)	Glucosamine(DB01296)|Olsalazine(DB01250)	TTTTTCTGTCACTCTCCTTGG	0.373																																					p.S63R		Atlas-SNP	.											.	IFNG	38	.	0			c.T189A						.						87	87	87					12																	68551870		2203	4300	6503	SO:0001583	missense	3458	exon3			TCTGTCACTCTCC		CCDS8980.1	12q14	2007-10-17			ENSG00000111537	ENSG00000111537		"Interferons"	5438	protein-coding gene	gene with protein product		147570					Standard	NM_000619		Approved		uc001stw.1	P01579	OTTHUMG00000169113	ENST00000229135.3:c.189T>A	chr12.hg19:g.68551870A>T	ENSP00000229135:p.Ser63Arg	93.0	0.0		112.0	37.0	NM_000619	B5BU88|Q53ZV4	Missense_Mutation	SNP	ENST00000229135.3	hg19	CCDS8980.1	.	.	.	.	.	.	.	.	.	.	A	15.10	2.733736	0.48939	.	.	ENSG00000111537	ENST00000229135	T	0.53423	0.62	5.38	3.05	0.35203	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.570944	0.19887	N	0.103839	T	0.57975	0.2090	M	0.71581	2.175	0.29060	N	0.883959	P	0.51240	0.943	P	0.57846	0.828	T	0.54180	-0.8332	9	.	.	.	-1.2533	6.9182	0.24371	0.8183:0.0:0.1817:0.0	.	63	P01579	IFNG_HUMAN	R	63	ENSP00000229135:S63R	.	S	-	3	2	IFNG	66838137	0.985000	0.35326	0.986000	0.45419	0.551000	0.35334	1.381000	0.34362	0.458000	0.26988	-0.250000	0.11733	AGT	.	.		0.373	IFNG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402301.1			T	68551870	A	T	68551870	3	4	255	1	0	0	0	0	1	0	0	0	7557	156	6	4	319	4	IFNG	12	68551870	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	852850	68551870	65300025	458	35803										
CSRP2	1466	hgsc.bcm.edu	37	chr12	77253334	77253334	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aaatgaattttacctttacaAtagatttcaccttctttttc	2	8	2	2	rs202057442	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:77253334A>G	ENST00000311083.5	-	5	621	c.498T>C	c.(496-498)taT>taC	p.Y166Y	CSRP2_ENST00000547435.1_Silent_p.Y166Y|CSRP2_ENST00000552330.1_Silent_p.Y216Y|CSRP2_ENST00000546966.1_Silent_p.Y166Y	NM_001321.1	NP_001312.1	Q16527	CSRP2_HUMAN	cysteine and glycine-rich protein 2	166	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)	focal adhesion (GO:0005925)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			kidney(1)|large_intestine(4)|ovary(1)|prostate(1)|skin(1)	8						TACCTTTACAATAGATTTCAC	0.353													A|||	4	0.000798722	0	0	5008	,	,		20252	0		0	False		,,,				2504	0.0041				p.Y166Y		Atlas-SNP	.											.	CSRP2	22	.	0			c.T498C						.						76	70	72					12																	77253334		2203	4300	6503	SO:0001819	synonymous_variant	1466	exon5			TTTACAATAGATT	BC000992	CCDS9015.1	12q21.1	2005-10-30				ENSG00000175183			2470	protein-coding gene	gene with protein product		601871				7499425, 9286703	Standard	XM_006719258		Approved	SmLIM, CRP2, LMO5	uc001syl.1	Q16527		ENST00000311083.5:c.498T>C	chr12.hg19:g.77253334A>G		333.0	1.0		332.0	161.0	NM_001321	Q93030	Silent	SNP	ENST00000311083.5	hg19	CCDS9015.1																																																																																			.	A|0.999;G|0.001		0.353	CSRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406572.1	NM_001321		G	77253334	A	G	77253334	2	3	255	1	0	0	0	0	0	0	0	1	3969	108	4	2		2	CSRP2	12	77253334	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	8701464	77253334	56598561	459	35804										
RASSF9	9182	hgsc.bcm.edu	37	chr12	86198974	86198974	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tattcggtaatatttcagtcGttcttccagctgttcaattc	6	9	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:86198974G>A	ENST00000361228.3	-	2	1182	c.814C>T	c.(814-816)Cga>Tga	p.R272*		NM_005447.3	NP_005438.2	O75901	RASF9_HUMAN	Ras association (RalGDS/AF-6) domain family (N-terminal) member 9	272					endosomal transport (GO:0016197)|protein targeting (GO:0006605)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|trans-Golgi network transport vesicle membrane (GO:0012510)	transporter activity (GO:0005215)	p.R272*(2)		endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TATTTCAGTCGTTCTTCCAGC	0.398																																					p.R272X		Atlas-SNP	.											RASSF9_ENST00000361228,rectum,carcinoma,0,2	RASSF9	100	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C814T						.						113	108	110					12																	86198974		1886	4108	5994	SO:0001587	stop_gained	9182	exon2			TCAGTCGTTCTTC		CCDS44950.1	12q21.31	2008-02-22	2008-02-22	2008-02-22		ENSG00000198774			15739	protein-coding gene	gene with protein product		610383	"peptidylglycine alpha-amidating monooxygenase COOH-terminal interactor"	PAMCI		9837933, 18272789	Standard	NM_005447		Approved	P-CIP1	uc001taf.1	O75901	OTTHUMG00000169831	ENST00000361228.3:c.814C>T	chr12.hg19:g.86198974G>A	ENSP00000354884:p.Arg272*	141.0	0.0		109.0	35.0	NM_005447	B3KMQ4|Q8N5U8	Nonsense_Mutation	SNP	ENST00000361228.3	hg19	CCDS44950.1	.	.	.	.	.	.	.	.	.	.	G	18.72	3.685307	0.68157	.	.	ENSG00000198774	ENST00000361228	.	.	.	4.9	1.88	0.25563	.	0.581472	0.16373	U	0.217227	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06891	T	0.86	-15.3805	10.6117	0.45425	0.0:0.1108:0.2861:0.6031	.	.	.	.	X	272	.	ENSP00000354884:R272X	R	-	1	2	RASSF9	84723105	0.009000	0.17119	0.003000	0.11579	0.198000	0.23893	0.492000	0.22435	0.148000	0.19059	-0.188000	0.12872	CGA	.	.		0.398	RASSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406109.1			A	86198974	G	A	86198974	4	1	255	1	0	0	0	0	0	1	0	0	13108	1153	40	1	497	1	RASSF9	12	86198974	Nonsense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	8945640	86198974	47652921	460	35805										
C12orf50	160419	hgsc.bcm.edu	37	chr12	88376940	88376940	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aggaattcgttttcgccaggCtgaatcattatatgatgttg	10	6	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:88376940C>T	ENST00000298699.2	-	12	1339	c.1159G>A	c.(1159-1161)Gcc>Acc	p.A387T	C12orf50_ENST00000550553.1_Missense_Mutation_p.A348T	NM_152589.1	NP_689802.1	Q8NA57	CL050_HUMAN	chromosome 12 open reading frame 50	387										NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|urinary_tract(2)	34						TTTCGCCAGGCTGAATCATTA	0.279																																					p.A387T		Atlas-SNP	.											.	C12orf50	70	.	0			c.G1159A						.						83	88	86					12																	88376940		2202	4291	6493	SO:0001583	missense	160419	exon12			GCCAGGCTGAATC	AK093140	CCDS9031.1	12q21.32	2006-02-03				ENSG00000165805			26665	protein-coding gene	gene with protein product						12477932	Standard	NM_152589		Approved	FLJ35821	uc001tam.1	Q8NA57	OTTHUMG00000169869	ENST00000298699.2:c.1159G>A	chr12.hg19:g.88376940C>T	ENSP00000298699:p.Ala387Thr	94.0	0.0		82.0	4.0	NM_152589	Q6P674	Missense_Mutation	SNP	ENST00000298699.2	hg19	CCDS9031.1	.	.	.	.	.	.	.	.	.	.	c	10.18	1.279964	0.23392	.	.	ENSG00000165805	ENST00000298699;ENST00000550553	T;T	0.31510	1.5;1.49	5.67	1.84	0.25277	.	0.490245	0.20530	N	0.090524	T	0.19685	0.0473	L	0.35288	1.05	0.80722	D	1	B	0.12630	0.006	B	0.16289	0.015	T	0.06232	-1.0838	10	0.20519	T	0.43	.	8.2739	0.31860	0.0:0.6665:0.0:0.3335	.	387	Q8NA57	CL050_HUMAN	T	387;348	ENSP00000298699:A387T;ENSP00000448344:A348T	ENSP00000298699:A387T	A	-	1	0	C12orf50	86901071	0.991000	0.36638	1.000000	0.80357	0.883000	0.51084	0.671000	0.25172	0.450000	0.26774	-0.726000	0.03593	GCC	.	.		0.279	C12orf50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406328.1	NM_152589		T	88376940	C	T	88376940	3	4	255	1	0	0	0	0	1	0	0	0	1697	797	28	3	93	3	C12orf50	12	88376940	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	2177966	88376940	45474955	461	35806										
UHRF1BP1L	23074	hgsc.bcm.edu	37	chr12	100441351	100441351	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcacttctctctaccacaagAtgatcaatatgtacagttac	4	11	4	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:100441351A>G	ENST00000279907.7	-	19	4250	c.4038T>C	c.(4036-4038)caT>caC	p.H1346H	UHRF1BP1L_ENST00000545232.2_Silent_p.H996H	NM_015054.1	NP_055869.1	A0JNW5	UH1BL_HUMAN	UHRF1 binding protein 1-like	1346										breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(21)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	50						CTACCACAAGATGATCAATAT	0.368																																					p.H1346H		Atlas-SNP	.											.	UHRF1BP1L	144	.	0			c.T4038C						.						134	131	132					12																	100441351		2203	4300	6503	SO:0001819	synonymous_variant	23074	exon19			CACAAGATGATCA		CCDS31882.1, CCDS31883.1	12q23.1	2011-04-15	2008-08-15		ENSG00000111647	ENSG00000111647			29102	protein-coding gene	gene with protein product							Standard	XM_005268737		Approved	KIAA0701	uc001tgq.3	A0JNW5	OTTHUMG00000170195	ENST00000279907.7:c.4038T>C	chr12.hg19:g.100441351A>G		87.0	0.0		87.0	4.0	NM_015054	A0PJE5|O75183|Q8NDL1|Q96C30|Q9BTS5|Q9H0F1	Silent	SNP	ENST00000279907.7	hg19	CCDS31882.1	.	.	.	.	.	.	.	.	.	.	A	9.313	1.056189	0.19907	.	.	ENSG00000111647	ENST00000548712	.	.	.	5.53	0.757	0.18427	.	.	.	.	.	T	0.51160	0.1658	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40001	-0.9586	4	.	.	.	-2.7127	4.9898	0.14209	0.5483:0.0:0.2921:0.1596	.	.	.	.	T	107	.	.	I	-	2	0	UHRF1BP1L	98965482	0.955000	0.32602	0.998000	0.56505	0.980000	0.70556	0.035000	0.13797	0.409000	0.25649	0.379000	0.24179	ATC	.	.		0.368	UHRF1BP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407875.1	NM_001006947		G	100441351	A	G	100441351	2	3	255	1	0	0	0	0	0	0	0	1	16984	330	12	2		2	UHRF1BP1L	12	100441351	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	12064411	100441351	33410544	462	35807										
UTP20	27340	hgsc.bcm.edu	37	chr12	101736358	101736358	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcaagaaaattgctttgtacGgtttttgaggtctgtactat	9	5	2	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:101736358G>T	ENST00000261637.4	+	33	4410	c.4236G>T	c.(4234-4236)acG>acT	p.T1412T		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	1412					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						TGCTTTGTACGGTTTTTGAGG	0.343																																					p.T1412T		Atlas-SNP	.											.	UTP20	222	.	0			c.G4236T						.						54	55	54					12																	101736358		2202	4299	6501	SO:0001819	synonymous_variant	27340	exon33			TTGTACGGTTTTT	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"down regulated in metastasis"	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.4236G>T	chr12.hg19:g.101736358G>T		97.0	0.0		92.0	4.0	NM_014503	Q9H3H4	Silent	SNP	ENST00000261637.4	hg19	CCDS9081.1																																																																																			.	.		0.343	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		T	101736358	G	T	101736358	2	4	255	1	0	0	0	0	0	0	0	1	17114	1103	39	1		1	UTP20	12	101736358	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	1295007	101736358	32115537	463	35808										
HCFC2	29915	hgsc.bcm.edu	37	chr12	104495757	104495757	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	acattttaggtaggaaatgcAgatgtacctgactacagctt	9	7	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:104495757A>G	ENST00000229330.4	+	14	1994	c.1890A>G	c.(1888-1890)gcA>gcG	p.A630A	HCFC2_ENST00000550335.1_3'UTR	NM_013320.2	NP_037452.1	Q9Y5Z7	HCFC2_HUMAN	host cell factor C2	630	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	35						TAGGAAATGCAGATGTACCTG	0.318																																					p.A630A	Esophageal Squamous(184;1814 2036 4771 6974 15702)	Atlas-SNP	.											.	HCFC2	94	.	0			c.A1890G						.						109	98	102					12																	104495757		2203	4300	6503	SO:0001819	synonymous_variant	29915	exon14			AAATGCAGATGTA	AF117210	CCDS9097.1	12q23.3	2011-03-30			ENSG00000111727	ENSG00000111727			24972	protein-coding gene	gene with protein product		607926				10196288	Standard	NM_013320		Approved	HCF-2	uc001tkj.4	Q9Y5Z7	OTTHUMG00000170175	ENST00000229330.4:c.1890A>G	chr12.hg19:g.104495757A>G		91.0	0.0		95.0	4.0	NM_013320	B2R8Q5|C0H5X3	Silent	SNP	ENST00000229330.4	hg19	CCDS9097.1																																																																																			.	.		0.318	HCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407780.1	NM_013320		G	104495757	A	G	104495757	2	3	255	1	0	0	0	0	0	0	0	1	7002	175	7	2		2	HCFC2	12	104495757	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	2759399	104495757	29356138	464	35809										
TCP11L2	255394	hgsc.bcm.edu	37	chr12	106740125	106740125	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccaagccctcaaaaatgcatGcctcctatgccaggaggcct	8	15	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:106740125G>A	ENST00000299045.3	+	10	1551	c.1377G>A	c.(1375-1377)atG>atA	p.M459I		NM_152772.1	NP_689985.1	Q8N4U5	T11L2_HUMAN	t-complex 11, testis-specific-like 2	459										endometrium(2)|kidney(2)|large_intestine(5)|ovary(3)|prostate(1)|urinary_tract(2)	15						AAAAATGCATGCCTCCTATGC	0.413																																					p.M459I		Atlas-SNP	.											.	TCP11L2	59	.	0			c.G1377A						.						64	58	60					12																	106740125		2203	4300	6503	SO:0001583	missense	255394	exon10			ATGCATGCCTCCT	BC033617	CCDS9104.1, CCDS66456.1	12q23.3	2014-08-12	2012-09-20		ENSG00000166046	ENSG00000166046			28627	protein-coding gene	gene with protein product			"t-complex 11 (mouse) like 2", "t-complex 11 (mouse)-like 2"				Standard	XM_005268769		Approved	MGC40368	uc001tln.3	Q8N4U5	OTTHUMG00000170087	ENST00000299045.3:c.1377G>A	chr12.hg19:g.106740125G>A	ENSP00000299045:p.Met459Ile	127.0	0.0		108.0	42.0	NM_152772	B2RA65|G3V1Y9	Missense_Mutation	SNP	ENST00000299045.3	hg19	CCDS9104.1	.	.	.	.	.	.	.	.	.	.	G	14.74	2.625977	0.46840	.	.	ENSG00000166046	ENST00000299045	T	0.10960	2.82	5.69	5.69	0.88448	.	0.588706	0.19966	N	0.102109	T	0.08980	0.0222	N	0.21142	0.635	0.80722	D	1	B	0.11235	0.004	B	0.16722	0.016	T	0.21895	-1.0232	10	0.34782	T	0.22	-3.3243	13.0662	0.59034	0.0733:0.0:0.9267:0.0	.	459	Q8N4U5	T11L2_HUMAN	I	459	ENSP00000299045:M459I	ENSP00000299045:M459I	M	+	3	0	TCP11L2	105264255	1.000000	0.71417	0.988000	0.46212	0.984000	0.73092	3.394000	0.52551	2.685000	0.91497	0.655000	0.94253	ATG	.	.		0.413	TCP11L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407206.1	NM_152772		A	106740125	G	A	106740125	3	1	255	1	0	0	0	0	1	0	0	0	15730	1319	46	3	1411	3	TCP11L2	12	106740125	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	2244368	106740125	27111770	465	35810										
POLR3B	55703	hgsc.bcm.edu	37	chr12	106824192	106824192	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cgagaaaagtgagtggtcctCgctccctccagccatctcag	10	14	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:106824192C>T	ENST00000228347.4	+	14	1627	c.1405C>T	c.(1405-1407)Cgc>Tgc	p.R469C	POLR3B_ENST00000539066.1_Missense_Mutation_p.R411C	NM_018082.5	NP_060552.4	Q9NW08	RPC2_HUMAN	polymerase (RNA) III (DNA directed) polypeptide B	469					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(22)|ovary(1)|prostate(3)|skin(3)|urinary_tract(2)	57						GAGTGGTCCTCGCTCCCTCCA	0.493																																					p.R469C		Atlas-SNP	.											.	POLR3B	123	.	0			c.C1405T						.						114	105	108					12																	106824192		2203	4300	6503	SO:0001583	missense	55703	exon14			GGTCCTCGCTCCC	AY092084	CCDS9105.1, CCDS53824.1	12q23.3	2014-08-12			ENSG00000013503	ENSG00000013503		"RNA polymerase subunits"	30348	protein-coding gene	gene with protein product		614366				12391170	Standard	NM_018082		Approved	RPC2, FLJ10388	uc001tlp.3	Q9NW08	OTTHUMG00000170077	ENST00000228347.4:c.1405C>T	chr12.hg19:g.106824192C>T	ENSP00000228347:p.Arg469Cys	115.0	0.0		91.0	4.0	NM_018082	A8K6H0|B3KV73|F5H1E6|Q9NW59	Missense_Mutation	SNP	ENST00000228347.4	hg19	CCDS9105.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.737375	0.89482	.	.	ENSG00000013503	ENST00000228347;ENST00000551370;ENST00000539066	D;D	0.97553	-4.43;-4.43	5.56	4.66	0.58398	RNA polymerase Rpb2, domain 3 (1);	0.000000	0.85682	D	0.000000	D	0.99124	0.9698	H	0.98559	4.265	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98855	1.0760	10	0.87932	D	0	-12.6298	15.7308	0.77804	0.1378:0.8622:0.0:0.0	.	469	Q9NW08	RPC2_HUMAN	C	469;469;411	ENSP00000228347:R469C;ENSP00000445721:R411C	ENSP00000228347:R469C	R	+	1	0	POLR3B	105348322	1.000000	0.71417	0.996000	0.52242	0.997000	0.91878	7.452000	0.80683	1.301000	0.44836	0.655000	0.94253	CGC	.	.		0.493	POLR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407166.1	NM_018082		T	106824192	C	T	106824192	3	4	255	1	0	0	0	0	1	0	0	0	12238	884	31	1	1459	1	POLR3B	12	106824192	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	84067	106824192	27027703	466	35811										
GIT2	9815	hgsc.bcm.edu	37	chr12	110390999	110390999	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttgtcttgactctcaacgctGtgctggttattgatggtttt	10	7	2	2	rs369471977		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:110390999G>A	ENST00000355312.3	-	13	1139	c.1140C>T	c.(1138-1140)caC>caT	p.H380H	GIT2_ENST00000547815.1_Silent_p.H380H|GIT2_ENST00000553118.1_Silent_p.H380H|GIT2_ENST00000457474.2_Silent_p.H382H|GIT2_ENST00000338373.5_Silent_p.H380H|GIT2_ENST00000356259.4_Silent_p.H380H|GIT2_ENST00000360185.4_Silent_p.H380H|GIT2_ENST00000551209.1_Silent_p.H379H|TCHP_ENST00000550780.1_Intron|GIT2_ENST00000361006.5_Silent_p.H380H|GIT2_ENST00000343646.5_Intron|GIT2_ENST00000320063.9_Silent_p.H380H|GIT2_ENST00000354574.4_Silent_p.H382H	NM_057169.3	NP_476510.1	Q14161	GIT2_HUMAN	G protein-coupled receptor kinase interacting ArfGAP 2	380					behavioral response to pain (GO:0048266)|regulation of ARF GTPase activity (GO:0032312)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(8)|skin(4)	27						TCTCAACGCTGTGCTGGTTAT	0.418																																					p.H382H		Atlas-SNP	.											.	GIT2	81	.	0			c.C1146T						.	G	,,,,,	0,4406		0,0,2203	244	207	220		1146,1140,1140,1140,1140,1140	5.2	1	12		220	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GIT2	NM_001135213.1,NM_001135214.1,NM_014776.3,NM_057169.3,NM_057170.3,NM_139201.2	,,,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,,,	382/682,380/730,380/680,380/760,380/632,380/472	110390999	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9815	exon14			AACGCTGTGCTGG	AF124491	CCDS9138.1, CCDS9139.1, CCDS44968.1, CCDS44969.1, CCDS55884.1	12q24.1	2013-01-10	2008-09-05			ENSG00000139436		"ADP-ribosylation factor GTPase activating proteins", "Ankyrin repeat domain containing"	4273	protein-coding gene	gene with protein product		608564	"G protein-coupled receptor kinase interactor 2"			9826657, 10896954	Standard	NM_139201		Approved	KIAA0148	uc001tps.2	Q14161	OTTHUMG00000169313	ENST00000355312.3:c.1140C>T	chr12.hg19:g.110390999G>A		448.0	0.0		467.0	195.0	NM_001135213	Q86U59|Q96CI2|Q9BV91|Q9Y5V2	Silent	SNP	ENST00000355312.3	hg19	CCDS9138.1																																																																																			.	.		0.418	GIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403407.1	NM_057169		A	110390999	G	A	110390999	2	1	255	1	0	0	0	0	0	0	0	1	6405	1368	48	3		3	GIT2	12	110390999	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	3566807	110390999	23460896	467	35812										
ATP2A2	488	hgsc.bcm.edu	37	chr12	110729905	110729905	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	attttactcatattagtagcCaatgcaattgtgggtgtatg	9	5	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:110729905C>A	ENST00000539276.2	+	4	409	c.300C>A	c.(298-300)gcC>gcA	p.A100A	ATP2A2_ENST00000552636.1_5'UTR|ATP2A2_ENST00000395494.2_Silent_p.A100A|ATP2A2_ENST00000308664.6_Silent_p.A100A			P16615	AT2A2_HUMAN	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	100					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|epidermis development (GO:0008544)|ER-nucleus signaling pathway (GO:0006984)|ion transmembrane transport (GO:0034220)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart rate (GO:0010460)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|calcium-transporting ATPase activity involved in regulation of cardiac muscle cell membrane potential (GO:0086039)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|S100 protein binding (GO:0044548)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(10)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	38						TATTAGTAGCCAATGCAATTG	0.348																																					p.A100A		Atlas-SNP	.											.	ATP2A2	78	.	0			c.C300A						.						114	111	112					12																	110729905		2203	4300	6503	SO:0001819	synonymous_variant	488	exon4			AGTAGCCAATGCA		CCDS9143.1, CCDS9144.1	12q24.11	2012-10-22			ENSG00000174437	ENSG00000174437	3.6.3.8	"ATPases / P-type"	812	protein-coding gene	gene with protein product	"sarcoplasmic/endoplasmic reticulum calcium ATPase 2", "calcium pump 2"	108740		ATP2B, DAR		10080178	Standard	NM_170665		Approved	SERCA2	uc001tqk.4	P16615	OTTHUMG00000169327	ENST00000539276.2:c.300C>A	chr12.hg19:g.110729905C>A		217.0	0.0		199.0	8.0	NM_001681	A6NDN7|B4DF05|P16614|Q86VJ2	Silent	SNP	ENST00000539276.2	hg19	CCDS9144.1	.	.	.	.	.	.	.	.	.	.	C	10.23	1.292457	0.23564	.	.	ENSG00000174437	ENST00000548169	.	.	.	5.33	4.44	0.53790	.	.	.	.	.	T	0.68952	0.3057	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.67726	-0.5596	4	.	.	.	.	13.1455	0.59459	0.2912:0.7088:0.0:0.0	.	.	.	.	K	18	.	.	Q	+	1	0	ATP2A2	109214288	0.999000	0.42202	1.000000	0.80357	0.998000	0.95712	0.750000	0.26334	1.228000	0.43614	0.563000	0.77884	CAA	.	.		0.348	ATP2A2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403539.1	NM_001681		A	110729905	C	A	110729905	2	1	255	1	0	0	0	0	0	0	0	1	1137	581	21	3		3	ATP2A2	12	110729905	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	338906	110729905	23121990	468	35813										
ALDH2	217	hgsc.bcm.edu	37	chr12	112204899	112204899	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gcccgaggtcttctgcaaccAggtgagcccaccggccgggc	14	16	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:112204899A>G	ENST00000261733.2	+	1	174	c.113A>G	c.(112-114)cAg>cGg	p.Q38R	ALDH2_ENST00000416293.3_Splice_Site_p.Q38R|RP11-162P23.2_ENST00000546840.2_Intron	NM_000690.3	NP_000681.2	P05091	ALDH2_HUMAN	aldehyde dehydrogenase 2 family (mitochondrial)	38					alcohol metabolic process (GO:0006066)|carbohydrate metabolic process (GO:0005975)|ethanol catabolic process (GO:0006068)|ethanol oxidation (GO:0006069)|neurotransmitter biosynthetic process (GO:0042136)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)|electron carrier activity (GO:0009055)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(6)|ovary(2)|prostate(1)|skin(2)|stomach(1)	22					Amyl Nitrite(DB01612)|Benzyl alcohol(DB06770)|Disulfiram(DB00822)|Guanidine(DB00536)|Nitric Oxide(DB00435)|Nitroglycerin(DB00727)	TTCTGCAACCAGGTGAGCCCA	0.741			T	HMGA2	leiomyoma																																p.Q38R		Atlas-SNP	.		Dom	yes		12	12q24.2	217	aldehyde dehydrogenase 2 family (mitochondrial)		M	.	ALDH2	91	.	0			c.A113G						.						3	4	3					12																	112204899		1828	3711	5539	SO:0001630	splice_region_variant	217	exon1			GCAACCAGGTGAG	M26760	CCDS9155.1, CCDS55885.1	12q24.12	2007-12-14				ENSG00000111275	1.2.1.3	"Aldehyde dehydrogenases"	404	protein-coding gene	gene with protein product		100650				4015823, 2987944	Standard	NM_000690		Approved		uc001tst.3	P05091	OTTHUMG00000169603	ENST00000261733.2:c.114+1A>G	chr12.hg19:g.112204899A>G		5.0	0.0		14.0	5.0	NM_001204889	B4DW54|E7EUE5|Q03639|Q6IB13|Q6IV71	Missense_Mutation	SNP	ENST00000261733.2	hg19	CCDS9155.1	.	.	.	.	.	.	.	.	.	.	a	13.52	2.260407	0.39995	.	.	ENSG00000111275	ENST00000416293;ENST00000261733;ENST00000553044	T;T	0.15834	2.39;2.39	4.62	4.62	0.57501	Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.305652	0.35739	N	0.003008	T	0.10895	0.0266	N	0.14661	0.345	0.80722	D	1	B;B;B	0.17667	0.001;0.023;0.005	B;B;B	0.18561	0.005;0.022;0.004	T	0.10337	-1.0634	10	0.40728	T	0.16	.	11.8849	0.52596	1.0:0.0:0.0:0.0	.	38;38;38	E7EUE5;F8VXI5;P05091	.;.;ALDH2_HUMAN	R	38	ENSP00000403349:Q38R;ENSP00000261733:Q38R	ENSP00000261733:Q38R	Q	+	2	0	ALDH2	110689282	1.000000	0.71417	0.987000	0.45799	0.004000	0.04260	2.620000	0.46410	1.846000	0.53633	0.529000	0.55759	CAG	.	.		0.741	ALDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405008.1	NM_000690	Missense_Mutation	G	112204899	A	G	112204899	5	3	255	1	0	0	0	0	0	0	1	0	496	202	7	2	115	2	ALDH2	12	112204899	Splice_Site	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	1474994	112204899	21646996	469	35814										
C12orf51	283450	hgsc.bcm.edu	37	chr12	112622466	112622466	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tggtgtcttcttcctgcagcGggatgtagatctcgtctttg	12	9	4	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:112622466G>A	ENST00000430131.2	-	60	10183	c.9038C>T	c.(9037-9039)cCg>cTg	p.P3013L	HECTD4_ENST00000550722.1_Missense_Mutation_p.P3289L|HECTD4_ENST00000377560.5_Missense_Mutation_p.P3263L			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	3013					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.P3263Q(1)|p.P3013Q(1)									TTCCTGCAGCGGGATGTAGAT	0.632																																					p.P3301L		Atlas-SNP	.											.	.	.	.	2	Substitution - Missense(2)	kidney(2)	c.C9902T						.						102	123	116					12																	112622466		2119	4237	6356	SO:0001583	missense	283450	exon61			TGCAGCGGGATGT	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 51"	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.9038C>T	chr12.hg19:g.112622466G>A	ENSP00000404379:p.Pro3013Leu	94.0	0.0		88.0	4.0	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Missense_Mutation	SNP	ENST00000430131.2	hg19		.	.	.	.	.	.	.	.	.	.	G	15.56	2.868299	0.51588	.	.	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722	T;T;T	0.69040	-0.36;-0.33;-0.37	5.52	4.63	0.57726	.	.	.	.	.	T	0.55800	0.1943	L	0.29908	0.895	0.80722	D	1	B	0.18310	0.027	B	0.08055	0.003	T	0.55108	-0.8192	9	0.87932	D	0	.	14.0839	0.64942	0.0724:0.0:0.9276:0.0	.	3013	Q9Y4D8	K0614_HUMAN	L	3263;3013;3289	ENSP00000366783:P3263L;ENSP00000404379:P3013L;ENSP00000449784:P3289L	ENSP00000366783:P3263L	P	-	2	0	C12orf51	111106849	1.000000	0.71417	0.984000	0.44739	0.046000	0.14306	8.972000	0.93424	1.338000	0.45544	0.591000	0.81541	CCG	.	.		0.632	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		A	112622466	G	A	112622466	3	1	255	1	0	0	0	0	1	0	0	0	1698	1116	39	1	3016	1	C12orf51	12	112622466	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	417567	112622466	21229429	470	35815										
OAS2	4939	hgsc.bcm.edu	37	chr12	113444238	113444238	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gtcagctgagttctggctccAcacccagccccgaggtttat	10	14	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:113444238A>G	ENST00000342315.4	+	8	1703	c.1489A>G	c.(1489-1491)Aca>Gca	p.T497A	RP1-71H24.1_ENST00000552784.1_RNA|OAS2_ENST00000392583.2_Missense_Mutation_p.T497A	NM_016817.2	NP_058197.2	P29728	OAS2_HUMAN	2'-5'-oligoadenylate synthetase 2, 69/71kDa	497	OAS domain 2.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|nucleobase-containing compound metabolic process (GO:0006139)|protein glycosylation (GO:0006486)|protein myristoylation (GO:0018377)|purine nucleotide biosynthetic process (GO:0006164)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						TTCTGGCTCCACACCCAGCCC	0.463																																					p.T497A	Pancreas(199;709 2232 18410 33584 35052)	Atlas-SNP	.											.	OAS2	86	.	0			c.A1489G						.						66	65	65					12																	113444238		2203	4300	6503	SO:0001583	missense	4939	exon8			GGCTCCACACCCA	M87284	CCDS31906.1, CCDS41839.1, CCDS44982.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111335			8087	protein-coding gene	gene with protein product		603350	"2'-5'-oligoadenylate synthetase 2 (69-71 kD)"			9790745	Standard	NM_002535		Approved		uc001tuj.3	P29728	OTTHUMG00000169802	ENST00000342315.4:c.1489A>G	chr12.hg19:g.113444238A>G	ENSP00000342278:p.Thr497Ala	131.0	0.0		98.0	4.0	NM_002535	A8K9T1|Q6PJ33|Q86XX8	Missense_Mutation	SNP	ENST00000342315.4	hg19	CCDS31906.1	.	.	.	.	.	.	.	.	.	.	.	10.07	1.249420	0.22880	.	.	ENSG00000111335	ENST00000342315;ENST00000392583	T;T	0.08546	3.08;3.08	4.51	-4.63	0.03359	-oligoadenylate synthetase 1, domain 2/C-terminal (2);-5&apos (2);2&apos (2);	1.183370	0.06544	N	0.743700	T	0.04003	0.0112	N	0.13043	0.29	0.09310	N	1	B;B	0.14805	0.011;0.005	B;B	0.18561	0.022;0.022	T	0.42275	-0.9461	10	0.44086	T	0.13	-18.8292	1.0937	0.01668	0.3049:0.2906:0.2632:0.1412	.	497;497	P29728;P29728-2	OAS2_HUMAN;.	A	497	ENSP00000342278:T497A;ENSP00000376362:T497A	ENSP00000342278:T497A	T	+	1	0	OAS2	111928621	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.022000	0.13511	-1.146000	0.02854	-0.290000	0.09829	ACA	.	.		0.463	OAS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405937.1			G	113444238	A	G	113444238	3	3	255	1	0	0	0	0	1	0	0	0	10809	159	6	2	1590	2	OAS2	12	113444238	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	821772	113444238	20407657	471	35816										
TBX3	6926	hgsc.bcm.edu	37	chr12	115114249	115114249	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgtgtctttcatcaaacaccCtcatggactgcagggtgagc	10	11	4	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:115114249C>A	ENST00000257566.3	-	6	1357	c.968G>T	c.(967-969)aGg>aTg	p.R323M	TBX3_ENST00000349155.2_Missense_Mutation_p.R303M	NM_016569.3	NP_057653.3	O15119	TBX3_HUMAN	T-box 3	323					anterior/posterior axis specification, embryo (GO:0008595)|atrioventricular bundle cell differentiation (GO:0003167)|blood vessel development (GO:0001568)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cardiac muscle cell fate commitment (GO:0060923)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|female genitalia development (GO:0030540)|follicle-stimulating hormone secretion (GO:0046884)|forelimb morphogenesis (GO:0035136)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|limbic system development (GO:0021761)|luteinizing hormone secretion (GO:0032275)|male genitalia development (GO:0030539)|mammary gland development (GO:0030879)|mammary placode formation (GO:0060596)|mesoderm morphogenesis (GO:0048332)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sinoatrial node cell development (GO:0060931)|skeletal system development (GO:0001501)|specification of organ position (GO:0010159)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum morphogenesis (GO:0060412)	nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			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)		ATCAAACACCCTCATGGACTG	0.493																																					p.R323M		Atlas-SNP	.											.	TBX3	106	.	0			c.G968T						.						132	120	124					12																	115114249		2203	4300	6503	SO:0001583	missense	6926	exon6			AACACCCTCATGG	BC025258	CCDS9175.1, CCDS9176.1	12q24.21	2013-09-05	2008-07-31		ENSG00000135111	ENSG00000135111		"T-boxes"	11602	protein-coding gene	gene with protein product		601621	"ulnar mammary syndrome"	UMS		8988164	Standard	NM_005996		Approved	TBX3-ISO, XHL	uc001tvt.1	O15119	OTTHUMG00000169586	ENST00000257566.3:c.968G>T	chr12.hg19:g.115114249C>A	ENSP00000257566:p.Arg323Met	126.0	0.0		108.0	5.0	NM_016569	Q8TB20|Q9UKF8	Missense_Mutation	SNP	ENST00000257566.3	hg19	CCDS9176.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.804866	0.90623	.	.	ENSG00000135111	ENST00000349155;ENST00000257566;ENST00000361100	D;D	0.89270	-2.49;-2.47	5.11	5.11	0.69529	Transcription factor, T-box, region of unknown function (1);	0.114431	0.31612	N	0.007357	D	0.93213	0.7838	L	0.59436	1.845	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.87578	0.987;0.998	D	0.93164	0.6560	10	0.49607	T	0.09	.	17.516	0.87773	0.0:1.0:0.0:0.0	.	303;323	O15119-2;O15119	.;TBX3_HUMAN	M	303;323;323	ENSP00000257567:R303M;ENSP00000257566:R323M	ENSP00000257566:R323M	R	-	2	0	TBX3	113598632	1.000000	0.71417	0.990000	0.47175	0.997000	0.91878	7.260000	0.78391	2.363000	0.80096	0.655000	0.94253	AGG	.	.		0.493	TBX3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404947.2	NM_016569, NM_005996		A	115114249	C	A	115114249	3	1	255	1	0	0	0	0	1	0	0	0	15674	681	24	3	1275	3	TBX3	12	115114249	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1670011	115114249	18737646	472	35817										
NOS1	4842	hgsc.bcm.edu	37	chr12	117653120	117653120	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gcaagagggtccagttaggaGctgaaaaccctgtggaaaga	14	7	0	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:117653120G>T	ENST00000338101.4	-	29	4405	c.4401C>A	c.(4399-4401)agC>agA	p.S1467R	NOS1_ENST00000344089.3_3'UTR|NOS1_ENST00000317775.6_Missense_Mutation_p.S1433R			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		CCAGTTAGGAGCTGAAAACCC	0.582																																					p.S1467R	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											.	NOS1	240	.	0			c.C4401A						.						70	76	74					12																	117653120		1888	4104	5992	SO:0001583	missense	4842	exon30			TTAGGAGCTGAAA		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.4401C>A	chr12.hg19:g.117653120G>T	ENSP00000337459:p.Ser1467Arg	92.0	0.0		86.0	4.0	NM_001204218		Missense_Mutation	SNP	ENST00000338101.4	hg19	CCDS55890.1	.	.	.	.	.	.	.	.	.	.	G	15.42	2.829256	0.50845	.	.	ENSG00000089250	ENST00000317775;ENST00000338101	T;T	0.01347	4.99;5.01	4.95	2.94	0.34122	.	0.164696	0.53938	D	0.000043	T	0.00815	0.0027	N	0.02011	-0.69	0.80722	D	1	B	0.27498	0.18	B	0.27076	0.076	T	0.66180	-0.5988	10	0.62326	D	0.03	-27.6639	10.5436	0.45047	0.0:0.1445:0.7059:0.1497	.	1433	P29475	NOS1_HUMAN	R	1433;1467	ENSP00000320758:S1433R;ENSP00000337459:S1467R	ENSP00000320758:S1433R	S	-	3	2	NOS1	116137503	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.337000	0.52120	1.185000	0.42971	0.655000	0.94253	AGC	.	.		0.582	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1			T	117653120	G	T	117653120	3	4	255	1	0	0	0	0	1	0	0	0	10550	962	34	3	9	3	NOS1	12	117653120	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	2538871	117653120	16198775	473	35818										
KNTC1	9735	hgsc.bcm.edu	37	chr12	123055607	123055607	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aatggacttcaattggcagaGatattttttacagcagaaaa	8	5	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:123055607G>C	ENST00000333479.7	+	24	2130	c.1953G>C	c.(1951-1953)gaG>gaC	p.E651D	KNTC1_ENST00000450485.2_Missense_Mutation_p.E614D	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	651					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|protein complex assembly (GO:0006461)|regulation of exit from mitosis (GO:0007096)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)		p.E651D(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(8)|large_intestine(12)|lung(20)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	72	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)		AATTGGCAGAGATATTTTTTA	0.363																																					p.E651D		Atlas-SNP	.											KNTC1,NS,carcinoma,0,2	KNTC1	182	.	1	Substitution - Missense(1)	endometrium(1)	c.G1953C						.						91	88	89					12																	123055607		1815	4076	5891	SO:0001583	missense	9735	exon24			GGCAGAGATATTT		CCDS45002.1	12q24.31	2013-01-17			ENSG00000184445	ENSG00000184445			17255	protein-coding gene	gene with protein product	"rough deal homolog (Drosophila)"	607363				11146660, 11590237	Standard	NM_014708		Approved	KIAA0166, ROD	uc001ucv.3	P50748	OTTHUMG00000168861	ENST00000333479.7:c.1953G>C	chr12.hg19:g.123055607G>C	ENSP00000328236:p.Glu651Asp	254.0	0.0		232.0	15.0	NM_014708	A7E2C4|B3KSG2	Missense_Mutation	SNP	ENST00000333479.7	hg19	CCDS45002.1	.	.	.	.	.	.	.	.	.	.	G	11.62	1.692717	0.30052	.	.	ENSG00000184445	ENST00000450485;ENST00000333479	T;T	0.24350	1.86;2.4	5.49	2.17	0.27698	.	0.157403	0.44483	D	0.000453	T	0.18718	0.0449	L	0.51422	1.61	0.80722	D	1	P;B	0.36282	0.546;0.361	B;B	0.29353	0.101;0.075	T	0.04454	-1.0950	10	0.51188	T	0.08	-16.2422	8.0109	0.30353	0.4138:0.0:0.5862:0.0	.	614;651	E7ES84;P50748	.;KNTC1_HUMAN	D	614;651	ENSP00000397992:E614D;ENSP00000328236:E651D	ENSP00000328236:E651D	E	+	3	2	KNTC1	121621560	0.998000	0.40836	0.936000	0.37596	0.798000	0.45092	1.472000	0.35376	0.800000	0.34041	0.643000	0.83706	GAG	.	.		0.363	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2			C	123055607	G	C	123055607	3	2	255	1	0	0	0	0	1	0	0	0	8437	933	33	4	2043	4	KNTC1	12	123055607	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	5402487	123055607	10796288	474	35819										
SBNO1	55206	hgsc.bcm.edu	37	chr12	123798234	123798234	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gaatccaagtttacaatggaTttcatgacaatttctaaagc	6	7	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:123798234T>C	ENST00000602398.1	-	24	3280	c.3153A>G	c.(3151-3153)aaA>aaG	p.K1051K	SBNO1_ENST00000267176.4_Silent_p.K1050K|SBNO1_ENST00000602750.1_Silent_p.K1050K|SBNO1_ENST00000420886.2_Silent_p.K1051K			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	1051					regulation of transcription, DNA-templated (GO:0006355)					NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		TTACAATGGATTTCATGACAA	0.333																																					p.K1051K		Atlas-SNP	.											.	SBNO1	138	.	0			c.A3153G						.						73	74	73					12																	123798234		2203	4300	6503	SO:0001819	synonymous_variant	55206	exon23			AATGGATTTCATG	AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"sno, strawberry notch homolog 1 (Drosophila)"				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.3153A>G	chr12.hg19:g.123798234T>C		66.0	0.0		68.0	4.0	NM_001167856	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Silent	SNP	ENST00000602398.1	hg19	CCDS53844.1																																																																																			.	.		0.333	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183		C	123798234	T	C	123798234	2	2	255	1	0	0	0	0	0	0	0	1	13877	1490	52	2		2	SBNO1	12	123798234	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	742627	123798234	10053661	475	35820										
TCTN2	79867	hgsc.bcm.edu	37	chr12	124189191	124189191	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctcatctcggatgctggcgcGgtggaagggattactcagca	14	10	3	0	rs145483549		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:124189191G>T	ENST00000303372.5	+	15	1853	c.1725G>T	c.(1723-1725)gcG>gcT	p.A575A	RP11-338K17.8_ENST00000538837.1_lincRNA|TCTN2_ENST00000426174.2_Silent_p.A574A	NM_001143850.2|NM_024809.4	NP_001137322.1|NP_079085.2	Q96GX1	TECT2_HUMAN	tectonic family member 2	575					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)		p.A575A(1)		breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000163)|Epithelial(86;0.000502)|all cancers(50;0.00451)		ATGCTGGCGCGGTGGAAGGGA	0.532																																					p.A575A		Atlas-SNP	.											TCTN2,NS,carcinoma,0,2	TCTN2	50	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1725T						.						92	74	80					12																	124189191		2203	4300	6503	SO:0001819	synonymous_variant	79867	exon15			TGGCGCGGTGGAA	AK056924	CCDS9253.1, CCDS45007.1	12q24.31	2011-04-12	2007-08-20	2007-08-20	ENSG00000168778	ENSG00000168778		"Tectonic proteins"	25774	protein-coding gene	gene with protein product	"Meckel syndrome, type 8"	613846	"chromosome 12 open reading frame 38"	C12orf38		21462283	Standard	NM_024809		Approved	FLJ12975, TECT2, MKS8	uc001ufp.3	Q96GX1	OTTHUMG00000168700	ENST00000303372.5:c.1725G>T	chr12.hg19:g.124189191G>T		95.0	0.0		65.0	3.0	NM_024809	A8K7Y8|B3KPW5|Q9H966	Silent	SNP	ENST00000303372.5	hg19	CCDS9253.1																																																																																			.	G|1.000;A|0.000		0.532	TCTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400652.1	NM_024809		T	124189191	G	T	124189191	2	4	255	1	0	0	0	0	0	0	0	1	15738	1103	39	1		1	TCTN2	12	124189191	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	390957	124189191	9662704	476	35821										
NCOR2	9612	hgsc.bcm.edu	37	chr12	124824721	124824721	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gctgctgctgcccccaccccCgccgctgctgccgctgctct	10	22	1	0	rs61519723|rs112797765|rs143952466	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:124824721C>T	ENST00000405201.1	-	37	5518	c.5518G>A	c.(5518-5520)Ggg>Agg	p.G1840R	NCOR2_ENST00000356219.3_Missense_Mutation_p.G1847R|NCOR2_ENST00000404121.2_Missense_Mutation_p.G1401R|NCOR2_ENST00000397355.1_Missense_Mutation_p.G1831R|NCOR2_ENST00000404621.1_Missense_Mutation_p.G1830R|NCOR2_ENST00000429285.2_Missense_Mutation_p.G1830R			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1851					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		cccccacccccgccgctgctg	0.711																																					p.G1840R		Atlas-SNP	.											.,32	NCOR2	475	.	0			c.G5518A						.						14	20	18					12																	124824721		1941	4120	6061	SO:0001583	missense	9612	exon39			CACCCCCGCCGCT	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"nuclear receptor co-repressor 2"			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.5518G>A	chr12.hg19:g.124824721C>T	ENSP00000384018:p.Gly1840Arg	68.0	1.0		79.0	5.0	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	hg19	CCDS41858.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.12|12.12	1.844110|1.844110	0.32606|0.32606	.|.	.|.	ENSG00000196498|ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000429285|ENST00000440187;ENST00000453428	T;T;T;T;T;T|.	0.21191|.	2.03;2.29;2.02;2.29;2.04;2.29|.	2.64|2.64	2.64|2.64	0.31445|0.31445	.|.	0.074331|.	0.53938|.	U|.	0.000049|.	T|T	0.32704|0.32704	0.0838|0.0838	L|L	0.29908|0.29908	0.895|0.895	0.23855|0.23855	N|N	0.996651|0.996651	D;P|.	0.71674|.	0.998;0.929|.	P;B|.	0.51297|.	0.665;0.088|.	T|T	0.18650|0.18650	-1.0330|-1.0330	10|5	0.13470|.	T|.	0.59|.	.|.	8.4775|8.4775	0.33023|0.33023	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1831;1840|.	C9J239;C9JFD3|.	.;.|.	R|Q	1840;1830;1847;1831;1839;1401;1830|74;169	ENSP00000384018:G1840R;ENSP00000384202:G1830R;ENSP00000348551:G1847R;ENSP00000380513:G1831R;ENSP00000385618:G1401R;ENSP00000400281:G1830R|.	ENSP00000348551:G1847R|.	G|R	-|-	1|2	0|0	NCOR2|NCOR2	123390674|123390674	0.931000|0.931000	0.31567|0.31567	0.959000|0.959000	0.39883|0.39883	0.993000|0.993000	0.82548|0.82548	-0.026000|-0.026000	0.12392|0.12392	1.307000|1.307000	0.44944|0.44944	0.491000|0.491000	0.48974|0.48974	GGG|CGG	.	.		0.711	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312		T	124824721	C	T	124824721	3	4	255	1	0	0	0	0	1	0	0	0	10245	652	23	1	2070	1	NCOR2	12	124824721	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	635530	124824721	9027174	477	35822										
DDX51	317781	hgsc.bcm.edu	37	chr12	132626881	132626881	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gcctgttggggcagaaacacAgaggtcgctaggccggtagc	16	10	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:132626881A>G	ENST00000397333.3	-	4	795	c.757T>C	c.(757-759)Tgt>Cgt	p.C253R	NOC4L_ENST00000330579.1_5'Flank	NM_175066.3	NP_778236.2	Q8N8A6	DDX51_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 51	253	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			endometrium(1)|lung(5)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.59e-08)|Epithelial(86;3.62e-07)|all cancers(50;2.13e-05)		GCAGAAACACAGAGGTCGCTA	0.607																																					p.C253R		Atlas-SNP	.											.	DDX51	33	.	0			c.T757C						.						63	74	70					12																	132626881		2071	4202	6273	SO:0001583	missense	317781	exon4			AAACACAGAGGTC	BC040185	CCDS41865.1	12q24.33	2005-10-12				ENSG00000185163		"DEAD-boxes"	20082	protein-coding gene	gene with protein product							Standard	NM_175066		Approved		uc001ujy.4	Q8N8A6		ENST00000397333.3:c.757T>C	chr12.hg19:g.132626881A>G	ENSP00000380495:p.Cys253Arg	33.0	0.0		49.0	4.0	NM_175066	A8MPT9|Q5CZ71|Q8IXK5|Q96ED1	Missense_Mutation	SNP	ENST00000397333.3	hg19	CCDS41865.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.051028	0.75960	.	.	ENSG00000185163	ENST00000397333	T	0.15139	2.45	4.71	4.71	0.59529	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.34395	0.0896	L	0.51914	1.62	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	T	0.07028	-1.0794	10	0.87932	D	0	-8.5514	12.1532	0.54062	1.0:0.0:0.0:0.0	.	253	Q8N8A6	DDX51_HUMAN	R	253	ENSP00000380495:C253R	ENSP00000380495:C253R	C	-	1	0	DDX51	131192834	1.000000	0.71417	0.985000	0.45067	0.988000	0.76386	8.427000	0.90275	1.756000	0.51951	0.402000	0.26972	TGT	.	.		0.607	DDX51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398978.1	NM_175066		G	132626881	A	G	132626881	3	3	255	1	0	0	0	0	1	0	0	0	4371	188	7	2	1291	2	DDX51	12	132626881	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	7802160	132626881	1225014	478	35823										
ANKLE2	23141	hgsc.bcm.edu	37	chr12	133313525	133313525	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aggctctcagggtcagtaccGggtctctggggctgcctcca	14	13	3	0	rs201586661		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:133313525G>T	ENST00000357997.5	-	8	1636	c.1547C>A	c.(1546-1548)cCg>cAg	p.P516Q	ANKLE2_ENST00000337516.5_Missense_Mutation_p.P516Q|ANKLE2_ENST00000542374.1_5'Flank|ANKLE2_ENST00000539605.1_Missense_Mutation_p.P454Q	NM_015114.1	NP_055929.1	Q86XL3	ANKL2_HUMAN	ankyrin repeat and LEM domain containing 2	516					mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope reassembly (GO:0007084)|negative regulation of phosphorylation (GO:0042326)|positive regulation of protein dephosphorylation (GO:0035307)|regulation of catalytic activity (GO:0050790)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	protein phosphatase 2A binding (GO:0051721)|protein phosphatase type 2A regulator activity (GO:0008601)			NS(2)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|lung(20)|ovary(1)|urinary_tract(2)	45	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.3e-08)|Epithelial(86;1.56e-07)|all cancers(50;4.94e-06)		GGTCAGTACCGGGTCTCTGGG	0.622																																					p.P516Q		Atlas-SNP	.											ANKLE2,NS,carcinoma,0,1	ANKLE2	76	.	0			c.C1547A						.						65	78	74					12																	133313525		1982	4154	6136	SO:0001583	missense	23141	exon8			AGTACCGGGTCTC	AB014592	CCDS41869.1	12q24.33	2013-01-11	2008-03-25	2008-03-25	ENSG00000176915	ENSG00000176915		"Ankyrin repeat domain containing"	29101	protein-coding gene	gene with protein product	"LEM domain containing 7"		"KIAA0692"	KIAA0692		9734811	Standard	XM_005266159		Approved	LEMD7, Lem4	uc001ukx.2	Q86XL3	OTTHUMG00000168046	ENST00000357997.5:c.1547C>A	chr12.hg19:g.133313525G>T	ENSP00000350686:p.Pro516Gln	64.0	0.0		76.0	4.0	NM_015114	A8KAG3|B3KN97|B3KSF8|O75176|Q6P6A5|Q8TAZ9|Q96DH4	Missense_Mutation	SNP	ENST00000357997.5	hg19	CCDS41869.1	.	.	.	.	.	.	.	.	.	.	g	21.1	4.102404	0.76983	.	.	ENSG00000176915	ENST00000539605;ENST00000357997;ENST00000337516;ENST00000535036	T;T;T;T	0.53857	0.6;0.6;0.6;0.6	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.75287	0.3829	M	0.77616	2.38	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.77161	-0.2689	10	0.87932	D	0	-19.8516	19.9201	0.97084	0.0:0.0:1.0:0.0	.	516;516	Q86XL3-2;Q86XL3	.;ANKL2_HUMAN	Q	454;516;516;79	ENSP00000446268:P454Q;ENSP00000350686:P516Q;ENSP00000337651:P516Q;ENSP00000437585:P79Q	ENSP00000337651:P516Q	P	-	2	0	ANKLE2	131823598	1.000000	0.71417	0.913000	0.36048	0.294000	0.27393	9.005000	0.93587	2.785000	0.95823	0.650000	0.86243	CCG	.	.		0.622	ANKLE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397712.1			T	133313525	G	T	133313525	3	4	255	1	0	0	0	0	1	0	0	0	633	1116	39	1	1293	1	ANKLE2	12	133313525	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	686644	133313525	538370	479	35824										
ZNF10	7556	hgsc.bcm.edu	37	chr12	133727625	133727625	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	atgttgtagacactggtgacCttcaaggatgtatttgtgga	12	5	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:133727625C>G	ENST00000248211.6	+	3	267	c.45C>G	c.(43-45)acC>acG	p.T15T	ZNF10_ENST00000540927.1_Intron|ZNF10_ENST00000402932.2_Silent_p.T15T|ZNF268_ENST00000416488.1_Silent_p.T15T|CTD-2140B24.4_ENST00000540096.2_Silent_p.T15T|ZNF10_ENST00000426665.2_Silent_p.T15T	NM_015394.4	NP_056209.2	P21506	ZNF10_HUMAN	zinc finger protein 10	15	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|prostate(1)|skin(5)|urinary_tract(1)	26	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;1.28e-06)|all_epithelial(31;0.0051)|Lung NSC(355;0.00948)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		CACTGGTGACCTTCAAGGATG	0.453																																					p.T15T		Atlas-SNP	.											.	ZNF10	58	.	0			c.C45G						.						279	245	257					12																	133727625		2203	4300	6503	SO:0001819	synonymous_variant	7556	exon3			GGTGACCTTCAAG	X52332, BC024182	CCDS9283.1	12q24.33	2013-01-08	2005-05-22		ENSG00000256223	ENSG00000256223		"Zinc fingers, C2H2-type", "-"	12879	protein-coding gene	gene with protein product		194538	"zinc finger protein 10 (KOX 1)"			7865130, 8262519	Standard	NM_015394		Approved	KOX1	uc001ulq.3	P21506	OTTHUMG00000167944	ENST00000248211.6:c.45C>G	chr12.hg19:g.133727625C>G		206.0	0.0		208.0	84.0	NM_015394	B2RBS1|Q8TC91	Silent	SNP	ENST00000248211.6	hg19	CCDS9283.1																																																																																			.	.		0.453	ZNF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397182.1	NM_015394		G	133727625	C	G	133727625	2	3	255	1	0	0	0	0	0	0	0	1	17727	668	24	4		4	ZNF10	12	133727625	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	414100	133727625	124270	480	35825										
ZMYM2	7750	hgsc.bcm.edu	37	chr13	20659971	20659971	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cgcctccaaagtccacagaaTcttaatcagaggatggatgt	9	10	2	2	rs374447547		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:20659971T>C	ENST00000382874.2	+	26	4141	c.3951T>C	c.(3949-3951)aaT>aaC	p.N1317N	ZMYM2_ENST00000382869.3_Silent_p.N1317N|ZMYM2_ENST00000382871.2_Silent_p.N1317N	NM_001190964.1	NP_001177893.1	Q9UBW7	ZMYM2_HUMAN	zinc finger, MYM-type 2	1317					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|PML body (GO:0016605)	ubiquitin conjugating enzyme binding (GO:0031624)|zinc ion binding (GO:0008270)			large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	10		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)		GTCCACAGAATCTTAATCAGA	0.378																																					p.N1317N		Atlas-SNP	.											.	ZMYM2	191	.	0			c.T3951C						.	T	,,,	0,3638		0,0,1819	70	64	66		3951,3951,3951,3951	0	1	13		66	1,8149		0,1,4074	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZMYM2	NM_001190964.1,NM_001190965.1,NM_003453.3,NM_197968.2	,,,	0,1,5893	CC,CT,TT		0.0123,0.0,0.0085	,,,	1317/1378,1317/1378,1317/1378,1317/1378	20659971	1,11787	1819	4075	5894	SO:0001819	synonymous_variant	7750	exon26			ACAGAATCTTAAT	AF012126	CCDS45016.1	13q11-q12	2013-01-08	2006-07-13	2006-07-13	ENSG00000121741	ENSG00000121741		"Zinc fingers, MYM type"	12989	protein-coding gene	gene with protein product		602221	"zinc finger protein 198"	ZNF198		9499416, 9425908	Standard	XM_005266517		Approved	RAMP, FIM, MYM	uc001ums.3	Q9UBW7	OTTHUMG00000016507	ENST00000382874.2:c.3951T>C	chr13.hg19:g.20659971T>C		108.0	0.0		85.0	4.0	NM_001190964	A6NDG0|A6NI02|O43212|O43434|O60898|Q5W0Q4|Q5W0T3|Q63HP0|Q8NE39|Q9H0V5|Q9H538|Q9UEU2	Silent	SNP	ENST00000382874.2	hg19	CCDS45016.1																																																																																			.	.		0.378	ZMYM2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044051.2	NM_003453		C	20659971	T	C	20659971	2	2	255	1	0	0	0	0	0	0	0	1	17715	1432	50	2		2	ZMYM2	13	20659971	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10		20659971	94509907	481	35826										
LATS2	26524	hgsc.bcm.edu	37	chr13	21555762	21555762	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcccagaggtcgctgggctcCatgctgtcctgtctgacatg	12	13	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:21555762C>A	ENST00000382592.4	-	6	2913	c.2508G>T	c.(2506-2508)atG>atT	p.M836I	LATS2_ENST00000542899.1_Missense_Mutation_p.M836I	NM_014572.2	NP_055387.2			large tumor suppressor kinase 2											breast(4)|central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(2)	45		all_cancers(29;4.74e-22)|all_epithelial(30;1.45e-18)|all_lung(29;4.69e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000781)|Epithelial(112;0.00144)|OV - Ovarian serous cystadenocarcinoma(117;0.0183)|Lung(94;0.0375)|LUSC - Lung squamous cell carcinoma(192;0.104)		CGCTGGGCTCCATGCTGTCCT	0.512																																					p.M836I		Atlas-SNP	.											.	LATS2	176	.	0			c.G2508T						.						53	49	50					13																	21555762		2203	4300	6503	SO:0001583	missense	26524	exon6			GGGCTCCATGCTG	AB028019	CCDS9294.1	13q11-q12	2013-04-25	2013-04-25		ENSG00000150457	ENSG00000150457			6515	protein-coding gene	gene with protein product		604861	"LATS (large tumor suppressor, Drosophila) homolog 2", "LATS, large tumor suppressor, homolog 2 (Drosophila)"			10673337	Standard	NM_014572		Approved		uc001unr.4	Q9NRM7	OTTHUMG00000016531	ENST00000382592.4:c.2508G>T	chr13.hg19:g.21555762C>A	ENSP00000372035:p.Met836Ile	64.0	0.0		90.0	4.0	NM_014572		Missense_Mutation	SNP	ENST00000382592.4	hg19	CCDS9294.1	.	.	.	.	.	.	.	.	.	.	C	19.24	3.789402	0.70337	.	.	ENSG00000150457	ENST00000382592;ENST00000542899	T;T	0.60171	0.21;0.21	5.69	5.69	0.88448	Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.49695	0.1572	N	0.21324	0.655	0.80722	D	1	B	0.28998	0.23	B	0.30646	0.118	T	0.49312	-0.8953	10	0.59425	D	0.04	.	19.8632	0.96793	0.0:1.0:0.0:0.0	.	836	Q9NRM7	LATS2_HUMAN	I	836	ENSP00000372035:M836I;ENSP00000441817:M836I	ENSP00000372035:M836I	M	-	3	0	LATS2	20453762	1.000000	0.71417	1.000000	0.80357	0.744000	0.42396	7.770000	0.85390	2.713000	0.92767	0.644000	0.83932	ATG	.	.		0.512	LATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044102.1			A	21555762	C	A	21555762	3	1	255	1	0	0	0	0	1	0	0	0	8656	594	21	3	770	3	LATS2	13	21555762	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	895791	21555762	93614116	482	35827										
ATP12A	479	hgsc.bcm.edu	37	chr13	25276160	25276160	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cagccaacagtgaaacagtgGaagacattgcacatcgcctc	9	12	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:25276160G>T	ENST00000381946.3	+	14	2136	c.1969G>T	c.(1969-1971)Gaa>Taa	p.E657*	ATP12A_ENST00000218548.6_Nonsense_Mutation_p.E663*|RNY1P7_ENST00000384743.1_RNA			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	657					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		TGAAACAGTGGAAGACATTGC	0.458																																					p.E663X	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-SNP	.											.	ATP12A	172	.	0			c.G1987T						.						227	185	199					13																	25276160		2203	4300	6503	SO:0001587	stop_gained	479	exon14			ACAGTGGAAGACA	L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"ATPases / P-type"	13816	protein-coding gene	gene with protein product	"ATPase, Na+K+ transporting, alpha-1 polypeptide-like", "potassium-transporting ATPase alpha chain 2", "proton pump", "non-gastric H(+)/K(+) ATPase alpha subunit", "sodium/potassium ATPase, alpha polypeptide-like"	182360	"ATPase, Na+/K+ transporting, alpha polypeptide-like 1"	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.1969G>T	chr13.hg19:g.25276160G>T	ENSP00000371372:p.Glu657*	112.0	0.0		107.0	5.0	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Nonsense_Mutation	SNP	ENST00000381946.3	hg19	CCDS31948.1	.	.	.	.	.	.	.	.	.	.	G	41	9.131705	0.99077	.	.	ENSG00000075673	ENST00000218548;ENST00000381946	.	.	.	5.4	5.4	0.78164	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	17.0213	0.86434	0.0:0.0:1.0:0.0	.	.	.	.	X	663;657	.	ENSP00000218548:E663X	E	+	1	0	ATP12A	24174160	1.000000	0.71417	1.000000	0.80357	0.552000	0.35366	9.695000	0.98691	2.692000	0.91855	0.467000	0.42956	GAA	.	.		0.458	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676		T	25276160	G	T	25276160	4	4	255	1	0	0	0	0	0	1	0	0	1122	1175	41	3	2041	3	ATP12A	13	25276160	Nonsense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	3720398	25276160	89893718	483	35828										
ATP8A2	51761	hgsc.bcm.edu	37	chr13	26273474	26273474	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	actctcgtgcaaagcggtcaTatgctgcaggtaggaacctg	12	10	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:26273474T>C	ENST00000381655.2	+	25	2517	c.2375T>C	c.(2374-2376)aTa>aCa	p.I792T	ATP8A2_ENST00000255283.8_Missense_Mutation_p.I752T|ATP8A2_ENST00000491840.1_3'UTR	NM_016529.4	NP_057613.4	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8A, member 2	752					aging (GO:0007568)|axonogenesis (GO:0007409)|detection of light stimulus involved in visual perception (GO:0050908)|eating behavior (GO:0042755)|inner ear morphogenesis (GO:0042472)|involuntary skeletal muscle contraction (GO:0003011)|negative regulation of cell proliferation (GO:0008285)|neurofilament cytoskeleton organization (GO:0060052)|neuromuscular process controlling posture (GO:0050884)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phospholipid translocation (GO:0061092)|response to auditory stimulus (GO:0010996)|retina layer formation (GO:0010842)|skin development (GO:0043588)	cell projection (GO:0042995)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(17)|lung(31)|ovary(4)|skin(3)|stomach(1)|urinary_tract(1)	72		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		AAAGCGGTCATATGCTGCAGG	0.532																																					p.I792T		Atlas-SNP	.											.	ATP8A2	181	.	0			c.T2375C						.						63	62	63					13																	26273474		1946	4136	6082	SO:0001583	missense	51761	exon25			CGGTCATATGCTG	AL137256	CCDS41873.1	13q12	2010-04-20	2010-03-31		ENSG00000132932	ENSG00000132932	3.6.3.1	"ATPases / P-type"	13533	protein-coding gene	gene with protein product		605870	"ATPase, aminophospholipid transporter-like, Class I, type 8A, member 2", "ATPase, aminophospholipid transporter-like, class I, type 8A, member 2"			11015572, 19778899	Standard	NM_016529		Approved	ATPIB, ML-1	uc001uqk.3	Q9NTI2	OTTHUMG00000016611	ENST00000381655.2:c.2375T>C	chr13.hg19:g.26273474T>C	ENSP00000371070:p.Ile792Thr	91.0	0.0		90.0	48.0	NM_016529	Q9H527|Q9NPU6|Q9NTL2|Q9NYM3	Missense_Mutation	SNP	ENST00000381655.2	hg19	CCDS41873.1	.	.	.	.	.	.	.	.	.	.	T	19.00	3.741347	0.69304	.	.	ENSG00000132932	ENST00000381655;ENST00000255283;ENST00000544544	D;D	0.82803	-1.65;-1.65	5.88	5.88	0.94601	HAD-like domain (2);	0.049064	0.85682	D	0.000000	D	0.94627	0.8268	H	0.98111	4.15	0.80722	D	1	D;D;D	0.62365	0.991;0.989;0.991	D;D;D	0.72625	0.978;0.962;0.967	D	0.96526	0.9389	10	0.87932	D	0	.	16.2824	0.82697	0.0:0.0:0.0:1.0	.	752;572;752	B7Z880;F5GZN5;Q9NTI2	.;.;AT8A2_HUMAN	T	792;752;572	ENSP00000371070:I792T;ENSP00000255283:I752T	ENSP00000255283:I752T	I	+	2	0	ATP8A2	25171474	1.000000	0.71417	0.498000	0.27564	0.450000	0.32258	8.035000	0.88872	2.250000	0.74265	0.533000	0.62120	ATA	.	.		0.532	ATP8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044236.2	NM_016529		C	26273474	T	C	26273474	3	2	255	1	0	0	0	0	1	0	0	0	1193	1406	49	2	2473	2	ATP8A2	13	26273474	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	997314	26273474	88896404	484	35829										
SLC46A3	283537	hgsc.bcm.edu	37	chr13	29287117	29287117	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gagcaaaaatcgtctcttacCagaagcattcttaaaaagca	6	9	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:29287117C>A	ENST00000266943.6	-	3	1129	c.760G>T	c.(760-762)Ggt>Tgt	p.G254C	SLC46A3_ENST00000380814.4_Missense_Mutation_p.G254C	NM_001135919.1|NM_181785.3	NP_001129391.1|NP_861450.1	Q7Z3Q1	S46A3_HUMAN	solute carrier family 46, member 3	254					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(2)|prostate(1)|skin(1)	15		Lung SC(185;0.0367)		all cancers(112;0.159)		CGTCTCTTACCAGAAGCATTC	0.333																																					p.G254C		Atlas-SNP	.											.	SLC46A3	86	.	0			c.G760T						.						45	45	45					13																	29287117		2203	4299	6502	SO:0001583	missense	283537	exon3			TCTTACCAGAAGC		CCDS9332.1, CCDS45021.1	13q12.3	2013-05-22	2007-03-29		ENSG00000139508	ENSG00000139508		"Solute carriers"	27501	protein-coding gene	gene with protein product							Standard	NM_001135919		Approved	DKFZp686A1775, FLJ42613	uc001usj.3	Q7Z3Q1	OTTHUMG00000016650	ENST00000266943.6:c.760G>T	chr13.hg19:g.29287117C>A	ENSP00000266943:p.Gly254Cys	89.0	0.0		95.0	4.0	NM_181785	Q3ZCV8|Q6NUK5|Q6P9B3|Q6ZVG5|Q96QA1	Missense_Mutation	SNP	ENST00000266943.6	hg19	CCDS9332.1	.	.	.	.	.	.	.	.	.	.	C	0.612	-0.824657	0.02755	.	.	ENSG00000139508	ENST00000266943;ENST00000380814	T;T	0.51817	0.69;0.69	5.63	-6.26	0.02033	Major facilitator superfamily domain, general substrate transporter (1);	0.966988	0.08658	N	0.912940	T	0.24547	0.0595	N	0.21448	0.665	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.10450	0.003;0.003;0.005	T	0.15838	-1.0423	10	0.33141	T	0.24	-1.1839	2.8164	0.05457	0.2368:0.2601:0.0692:0.434	.	179;254;254	B5MEH0;Q7Z3Q1-2;Q7Z3Q1	.;.;S46A3_HUMAN	C	254	ENSP00000266943:G254C;ENSP00000370192:G254C	ENSP00000266943:G254C	G	-	1	0	SLC46A3	28185117	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-0.202000	0.09451	-1.350000	0.02199	-0.797000	0.03246	GGT	.	.		0.333	SLC46A3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276111.1	NM_181785		A	29287117	C	A	29287117	3	1	255	1	0	0	0	0	1	0	0	0	14661	594	21	3	655	3	SLC46A3	13	29287117	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	3013643	29287117	85882761	485	35830										
FRY	10129	hgsc.bcm.edu	37	chr13	32776658	32776658	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctgagctcacactccccctcTtctcaggtaccaggcaatag	7	16	3	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:32776658T>C	ENST00000380250.3	+	31	4508	c.4012T>C	c.(4012-4014)Ttc>Ctc	p.F1338L		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	1338						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		ACTCCCCCTCTTCTCAGGTAC	0.463																																					p.F1338L		Atlas-SNP	.											.	FRY	312	.	0			c.T4012C						.						67	65	66					13																	32776658		1957	4151	6108	SO:0001583	missense	10129	exon31			CCCCTCTTCTCAG	AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"chromosome 13 open reading frame 14"	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.4012T>C	chr13.hg19:g.32776658T>C	ENSP00000369600:p.Phe1338Leu	72.0	0.0		84.0	5.0	NM_023037	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	hg19	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	T	28.1	4.893649	0.91889	.	.	ENSG00000073910	ENST00000380250;ENST00000380257	T	0.34667	1.35	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	T	0.58906	0.2155	M	0.73962	2.25	0.80722	D	1	D	0.55605	0.972	D	0.68621	0.959	T	0.57969	-0.7719	10	0.33940	T	0.23	.	15.405	0.74871	0.0:0.0:0.0:1.0	.	1338	Q5TBA9	FRY_HUMAN	L	1338;177	ENSP00000369600:F1338L	ENSP00000369600:F1338L	F	+	1	0	FRY	31674658	1.000000	0.71417	1.000000	0.80357	0.835000	0.47333	7.640000	0.83355	2.060000	0.61445	0.374000	0.22700	TTC	.	.		0.463	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037		C	32776658	T	C	32776658	3	2	255	1	0	0	0	0	1	0	0	0	6071	1609	56	2	4134	2	FRY	13	32776658	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	3489541	32776658	82393220	486	35831										
BRCA2	675	hgsc.bcm.edu	37	chr13	32950834	32950834	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aacaaaaccatatttaccatCacgtgcactaacaagacagc	4	12	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:32950834C>T	ENST00000380152.3	+	21	8893	c.8660C>T	c.(8659-8661)tCa>tTa	p.S2887L	BRCA2_ENST00000544455.1_Missense_Mutation_p.S2887L			P51587	BRCA2_HUMAN	breast cancer 2, early onset	2887					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TATTTACCATCACGTGCACTA	0.373			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											p.S2887L	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	.	BRCA2	812	.	0			c.C8660T						.						96	89	92					13																	32950834		2203	4300	6503	SO:0001583	missense	675	exon21	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	TACCATCACGTGC	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.8660C>T	chr13.hg19:g.32950834C>T	ENSP00000369497:p.Ser2887Leu	89.0	0.0		89.0	4.0	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	hg19	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.266028	0.80358	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.59224	0.28;0.28	5.32	5.32	0.75619	Nucleic acid-binding, OB-fold-like (1);	0.262114	0.32488	N	0.006038	T	0.65322	0.2680	L	0.55834	1.745	0.09310	N	1	D	0.59767	0.986	P	0.53266	0.722	T	0.60905	-0.7170	10	0.45353	T	0.12	.	17.1817	0.86857	0.0:1.0:0.0:0.0	.	2887	P51587	BRCA2_HUMAN	L	2887	ENSP00000369497:S2887L;ENSP00000439902:S2887L	ENSP00000369497:S2887L	S	+	2	0	BRCA2	31848834	0.144000	0.22641	0.009000	0.14445	0.551000	0.35334	3.051000	0.49885	2.469000	0.83416	0.655000	0.94253	TCA	.	.		0.373	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		T	32950834	C	T	32950834	3	4	255	1	0	0	0	0	1	0	0	0	1501	838	29	3	8738	3	BRCA2	13	32950834	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	174176	32950834	82219044	487	35832										
KL	9365	hgsc.bcm.edu	37	chr13	33635814	33635814	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aagttcaagtacggagacctCcccatgtacataatatccaa	6	11	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:33635814C>T	ENST00000380099.3	+	4	2606	c.2598C>T	c.(2596-2598)ctC>ctT	p.L866L	KL_ENST00000487852.1_3'UTR	NM_004795.3	NP_004786.2	Q9UEF7	KLOT_HUMAN	klotho	866	Glycosyl hydrolase-1 2.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|calcium ion homeostasis (GO:0055074)|carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-glucosidase activity (GO:0008422)|beta-glucuronidase activity (GO:0004566)|fibroblast growth factor binding (GO:0017134)|signal transducer activity (GO:0004871)|vitamin D binding (GO:0005499)			breast(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|skin(5)	41	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		ACGGAGACCTCCCCATGTACA	0.522																																					p.L866L		Atlas-SNP	.											.	KL	106	.	0			c.C2598T						.						116	114	115					13																	33635814		2203	4300	6503	SO:0001819	synonymous_variant	9365	exon4			AGACCTCCCCATG	AB005142	CCDS9347.1	13q12	2008-02-05			ENSG00000133116	ENSG00000133116			6344	protein-coding gene	gene with protein product		604824				9464267	Standard	NM_004795		Approved		uc001uus.3	Q9UEF7	OTTHUMG00000017408	ENST00000380099.3:c.2598C>T	chr13.hg19:g.33635814C>T		88.0	0.0		83.0	4.0	NM_004795	Q5VZ95|Q96KV5|Q96KW5|Q9UEI9|Q9Y4F0	Silent	SNP	ENST00000380099.3	hg19	CCDS9347.1																																																																																			.	.		0.522	KL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045987.1			T	33635814	C	T	33635814	2	4	255	1	0	0	0	0	0	0	0	1	8340	842	30	3		3	KL	13	33635814	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	684980	33635814	81534064	488	35833										
NBEA	26960	hgsc.bcm.edu	37	chr13	35517180	35517180	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gcaacatccggatgaaattcGcagtgttgattggactcata	10	8	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:35517180G>T	ENST00000400445.3	+	1	757	c.223G>T	c.(223-225)Gca>Tca	p.A75S	NBEA_ENST00000379939.2_Missense_Mutation_p.A75S|NBEA_ENST00000310336.4_Missense_Mutation_p.A75S|NBEA_ENST00000540320.1_Missense_Mutation_p.A75S	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	75					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		GATGAAATTCGCAGTGTTGAT	0.587																																					p.A75S		Atlas-SNP	.											.	NBEA	340	.	0			c.G223T						.						118	130	126					13																	35517180		2088	4211	6299	SO:0001583	missense	26960	exon1			AAATTCGCAGTGT	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.223G>T	chr13.hg19:g.35517180G>T	ENSP00000383295:p.Ala75Ser	165.0	0.0		116.0	5.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.592953	0.86953	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336	T;T;T;T	0.56611	0.45;0.45;0.45;0.45	4.49	4.49	0.54785	.	0.186397	0.31542	N	0.007462	T	0.66607	0.2806	M	0.64567	1.98	0.80722	D	1	D	0.69078	0.997	D	0.74023	0.982	T	0.62676	-0.6804	10	0.13853	T	0.58	.	16.1514	0.81624	0.0:0.0:1.0:0.0	.	75	Q5T321	.	S	75	ENSP00000440951:A75S;ENSP00000383295:A75S;ENSP00000369271:A75S;ENSP00000308534:A75S	ENSP00000308534:A75S	A	+	1	0	NBEA	34415180	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.950000	0.93019	2.068000	0.61886	0.561000	0.74099	GCA	.	.		0.587	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		T	35517180	G	T	35517180	3	4	255	1	0	0	0	0	1	0	0	0	10196	1087	38	1	225	1	NBEA	13	35517180	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	1881366	35517180	79652698	489	35834										
NHLRC3	387921	hgsc.bcm.edu	37	chr13	39613731	39613731	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	acatcccaaagatattagtgTtcacagaggatggatatttc	8	7	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:39613731T>C	ENST00000379600.3	+	3	590	c.268T>C	c.(268-270)Ttc>Ctc	p.F90L	PROSER1_ENST00000350125.3_5'Flank|PROSER1_ENST00000352251.3_5'Flank|NHLRC3_ENST00000379599.2_Missense_Mutation_p.F90L|NHLRC3_ENST00000470258.1_5'UTR	NM_001012754.3	NP_001012772.1	Q5JS37	NHLC3_HUMAN	NHL repeat containing 3	90						extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|large_intestine(3)|lung(4)|skin(2)	11		Lung NSC(96;6.01e-07)|Breast(139;0.00394)|Prostate(109;0.00676)|Lung SC(185;0.0548)|Hepatocellular(188;0.114)		all cancers(112;2.37e-08)|Epithelial(112;3.14e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00101)|BRCA - Breast invasive adenocarcinoma(63;0.00335)|GBM - Glioblastoma multiforme(144;0.0128)		GATATTAGTGTTCACAGAGGA	0.388																																					p.F90L		Atlas-SNP	.											.	NHLRC3	35	.	0			c.T268C						.						69	68	69					13																	39613731		2203	4300	6503	SO:0001583	missense	387921	exon3			TTAGTGTTCACAG		CCDS31961.1, CCDS31962.1	13q13.3	2007-12-18			ENSG00000188811	ENSG00000188811			33751	protein-coding gene	gene with protein product							Standard	NM_001017370		Approved		uc001uxc.4	Q5JS37	OTTHUMG00000016765	ENST00000379600.3:c.268T>C	chr13.hg19:g.39613731T>C	ENSP00000368920:p.Phe90Leu	81.0	0.0		85.0	4.0	NM_001012754	B2RTZ2|B4DTL0|Q69YI9	Missense_Mutation	SNP	ENST00000379600.3	hg19	CCDS31961.1	.	.	.	.	.	.	.	.	.	.	T	33	5.206169	0.95033	.	.	ENSG00000188811	ENST00000379600;ENST00000379599;ENST00000537150	D;D	0.89939	-2.54;-2.59	5.39	5.39	0.77823	Six-bladed beta-propeller, TolB-like (1);	0.046859	0.85682	N	0.000000	D	0.90283	0.6961	L	0.54908	1.71	0.51767	D	0.999937	D;D;B;B	0.59767	0.982;0.986;0.058;0.197	P;P;B;B	0.53649	0.661;0.731;0.028;0.083	D	0.89720	0.3918	9	.	.	.	-14.8357	14.8927	0.70620	0.0:0.0:0.0:1.0	.	90;90;90;90	B4DTL0;Q5JS37;B4DRC8;F5GZB5	.;NHLC3_HUMAN;.;.	L	90	ENSP00000368920:F90L;ENSP00000368919:F90L	.	F	+	1	0	NHLRC3	38511731	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.899000	0.87370	2.162000	0.67917	0.460000	0.39030	TTC	.	.		0.388	NHLRC3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044616.2	NM_001012754		C	39613731	T	C	39613731	3	2	255	1	0	0	0	0	1	0	0	0	10416	1725	60	2	278	2	NHLRC3	13	39613731	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	4096551	39613731	75556147	490	35835										
NAA16	79612	hgsc.bcm.edu	37	chr13	41892974	41892974	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgaaaggattaacactgaacTgtttaggaaaaaaagaagaa	9	3	0	4			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:41892974T>C	ENST00000379406.3	+	3	496	c.172T>C	c.(172-174)Tgt>Cgt	p.C58R	NAA16_ENST00000379367.3_Missense_Mutation_p.C58R|NAA16_ENST00000403412.3_Missense_Mutation_p.C58R	NM_024561.4	NP_078837.3	Q6N069	NAA16_HUMAN	N(alpha)-acetyltransferase 16, NatA auxiliary subunit	58					N-terminal protein amino acid acetylation (GO:0006474)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NatA complex (GO:0031415)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ribosome binding (GO:0043022)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|urinary_tract(2)	31						AACACTGAACTGTTTAGGAAA	0.294																																					p.C58R		Atlas-SNP	.											.	NAA16	74	.	0			c.T172C						.						88	89	89					13																	41892974		2202	4294	6496	SO:0001583	missense	79612	exon3			CTGAACTGTTTAG	AL833341	CCDS9379.1, CCDS45044.1	13q14.11	2013-01-10	2010-01-14	2010-01-14	ENSG00000172766	ENSG00000172766		"N(alpha)-acetyltransferase subunits", "Tetratricopeptide (TTC) repeat domain containing"	26164	protein-coding gene	gene with protein product			"NMDA receptor regulated 1-like"	NARG1L		11483580, 19660095	Standard	NM_024561		Approved	FLJ22054, MGC40612, PRO2435	uc001uyf.2	Q6N069	OTTHUMG00000016791	ENST00000379406.3:c.172T>C	chr13.hg19:g.41892974T>C	ENSP00000368716:p.Cys58Arg	84.0	0.0		82.0	4.0	NM_001110798	B0QZ59|Q5VSP9|Q6P2D5|Q8N5J3|Q8N870	Missense_Mutation	SNP	ENST00000379406.3	hg19	CCDS9379.1	.	.	.	.	.	.	.	.	.	.	T	19.92	3.916345	0.73098	.	.	ENSG00000172766	ENST00000379367;ENST00000379406;ENST00000403412	T;T;T	0.72394	0.74;0.74;-0.65	4.23	4.23	0.50019	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.64402	D	0.000002	D	0.84437	0.5472	M	0.88570	2.965	0.80722	D	1	D;D;P	0.89917	0.97;1.0;0.906	P;D;P	0.97110	0.665;1.0;0.57	D	0.84033	0.0360	10	0.21014	T	0.42	-10.8295	13.7888	0.63126	0.0:0.0:0.0:1.0	.	58;58;58	Q6N069;Q6N069-4;Q6N069-5	NAA16_HUMAN;.;.	R	58	ENSP00000368674:C58R;ENSP00000368716:C58R;ENSP00000386103:C58R	ENSP00000368674:C58R	C	+	1	0	NAA16	40790974	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.355000	0.79434	1.897000	0.54924	0.533000	0.62120	TGT	.	.		0.294	NAA16-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044672.2	NM_018527		C	41892974	T	C	41892974	3	2	255	1	0	0	0	0	1	0	0	0	10128	1580	55	2	182	2	NAA16	13	41892974	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	2279243	41892974	73276904	491	35836										
NAA16	79612	hgsc.bcm.edu	37	chr13	41897285	41897285	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	atttgctgaaagattatgatAtggccctaaaactgttggaa	9	5	0	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:41897285A>G	ENST00000379406.3	+	5	820	c.496A>G	c.(496-498)Atg>Gtg	p.M166V	NAA16_ENST00000379367.3_Missense_Mutation_p.M166V|NAA16_ENST00000403412.3_Missense_Mutation_p.M166V	NM_024561.4	NP_078837.3	Q6N069	NAA16_HUMAN	N(alpha)-acetyltransferase 16, NatA auxiliary subunit	166					N-terminal protein amino acid acetylation (GO:0006474)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NatA complex (GO:0031415)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ribosome binding (GO:0043022)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|urinary_tract(2)	31						AGATTATGATATGGCCCTAAA	0.383																																					p.M166V		Atlas-SNP	.											.	NAA16	74	.	0			c.A496G						.						152	149	150					13																	41897285		2203	4300	6503	SO:0001583	missense	79612	exon5			TATGATATGGCCC	AL833341	CCDS9379.1, CCDS45044.1	13q14.11	2013-01-10	2010-01-14	2010-01-14	ENSG00000172766	ENSG00000172766		"N(alpha)-acetyltransferase subunits", "Tetratricopeptide (TTC) repeat domain containing"	26164	protein-coding gene	gene with protein product			"NMDA receptor regulated 1-like"	NARG1L		11483580, 19660095	Standard	NM_024561		Approved	FLJ22054, MGC40612, PRO2435	uc001uyf.2	Q6N069	OTTHUMG00000016791	ENST00000379406.3:c.496A>G	chr13.hg19:g.41897285A>G	ENSP00000368716:p.Met166Val	97.0	0.0		94.0	4.0	NM_001110798	B0QZ59|Q5VSP9|Q6P2D5|Q8N5J3|Q8N870	Missense_Mutation	SNP	ENST00000379406.3	hg19	CCDS9379.1	.	.	.	.	.	.	.	.	.	.	A	15.08	2.726646	0.48833	.	.	ENSG00000172766	ENST00000379367;ENST00000379406;ENST00000403412	T;T;T	0.73575	0.67;0.67;-0.76	5.74	5.74	0.90152	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.059999	0.64402	D	0.000002	T	0.74465	0.3720	L	0.56769	1.78	0.50813	D	0.99989	B;B;B	0.18610	0.005;0.029;0.004	B;B;B	0.31946	0.017;0.138;0.021	T	0.69789	-0.5050	10	0.33141	T	0.24	-6.42	16.0153	0.80434	1.0:0.0:0.0:0.0	.	166;166;166	Q6N069;Q6N069-4;Q6N069-5	NAA16_HUMAN;.;.	V	166	ENSP00000368674:M166V;ENSP00000368716:M166V;ENSP00000386103:M166V	ENSP00000368674:M166V	M	+	1	0	NAA16	40795285	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.637000	0.91014	2.187000	0.69744	0.528000	0.53228	ATG	.	.		0.383	NAA16-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044672.2	NM_018527		G	41897285	A	G	41897285	3	3	255	1	0	0	0	0	1	0	0	0	10128	449	16	2	514	2	NAA16	13	41897285	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	4311	41897285	73272593	492	35837										
NUDT15	55270	hgsc.bcm.edu	37	chr13	48611895	48611895	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cgcgcgctatgacggccagcGcacagccgcgcgggcggcgg	18	16	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:48611895G>A	ENST00000258662.2	+	1	193	c.13G>A	c.(13-15)Gca>Aca	p.A5T	SUCLA2_ENST00000543413.1_5'UTR	NM_018283.1	NP_060753.1	Q9NV35	NUD15_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 15	5					dGTP catabolic process (GO:0006203)|GTP catabolic process (GO:0006184)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity (GO:0035539)|8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity (GO:0008413)|metal ion binding (GO:0046872)			endometrium(1)|kidney(3)|large_intestine(2)|lung(1)	7		all_cancers(8;3.75e-25)|all_epithelial(8;1.78e-13)|all_lung(13;2.85e-06)|Breast(56;0.000141)|all_hematologic(8;0.000219)|Lung NSC(96;0.000226)|Prostate(109;0.00132)|Acute lymphoblastic leukemia(8;0.0167)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;4.83e-07)		GACGGCCAGCGCACAGCCGCG	0.716											OREG0022405	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A5T		Atlas-SNP	.											.	NUDT15	12	.	0			c.G13A						.																																			SO:0001583	missense	55270	exon1			GCCAGCGCACAGC		CCDS9407.1	13q14.12	2006-04-12			ENSG00000136159	ENSG00000136159		"Nudix motif containing"	23063	protein-coding gene	gene with protein product		615792				12767940	Standard	NM_018283		Approved	MTH2, FLJ10956	uc001vbw.1	Q9NV35	OTTHUMG00000016890	ENST00000258662.2:c.13G>A	chr13.hg19:g.48611895G>A	ENSP00000258662:p.Ala5Thr	74.0	0.0	955	61.0	4.0	NM_018283	A2RUR6|Q32Q27|Q6P2C9	Missense_Mutation	SNP	ENST00000258662.2	hg19	CCDS9407.1	.	.	.	.	.	.	.	.	.	.	G	12.13	1.846455	0.32606	.	.	ENSG00000136159	ENST00000258662	T	0.34859	1.34	4.72	2.97	0.34412	NUDIX hydrolase domain-like (1);	0.727696	0.13528	N	0.381185	T	0.26304	0.0642	L	0.40543	1.245	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.19321	-1.0309	10	0.26408	T	0.33	-5.0166	6.6964	0.23201	0.0964:0.1793:0.7243:0.0	.	5	Q9NV35	NUD15_HUMAN	T	5	ENSP00000258662:A5T	ENSP00000258662:A5T	A	+	1	0	NUDT15	47509896	0.009000	0.17119	0.001000	0.08648	0.000000	0.00434	1.572000	0.36461	0.718000	0.32166	-0.140000	0.14226	GCA	.	.		0.716	NUDT15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044862.3	NM_018283		A	48611895	G	A	48611895	3	1	255	1	0	0	0	0	1	0	0	0	10740	1087	38	1	15	1	NUDT15	13	48611895	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	6714610	48611895	66557983	493	35838										
FNDC3A	22862	hgsc.bcm.edu	37	chr13	49781309	49781309	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgtgccattcgccagtgccaAgactctctgggacaccagga	11	13	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:49781309A>G	ENST00000492622.2	+	26	3680	c.3375A>G	c.(3373-3375)caA>caG	p.Q1125Q	FNDC3A_ENST00000541916.1_Silent_p.Q1125Q|FNDC3A_ENST00000398316.3_Silent_p.Q1069Q	NM_001079673.1	NP_001073141.1	Q9Y2H6	FND3A_HUMAN	fibronectin type III domain containing 3A	1125	Fibronectin type-III 9. {ECO:0000255|PROSITE-ProRule:PRU00316}.				fertilization (GO:0009566)|Sertoli cell development (GO:0060009)|single organismal cell-cell adhesion (GO:0016337)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|prostate(5)|skin(2)|urinary_tract(1)	41		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)		GCCAGTGCCAAGACTCTCTGG	0.527																																					p.Q1125Q		Atlas-SNP	.											.	FNDC3A	93	.	0			c.A3375G						.						116	103	107					13																	49781309		2203	4300	6503	SO:0001819	synonymous_variant	22862	exon26			GTGCCAAGACTCT	AB023187	CCDS9413.2, CCDS41886.1	13q14.12	2013-02-11	2005-01-20	2005-01-22	ENSG00000102531	ENSG00000102531		"Fibronectin type III domain containing"	20296	protein-coding gene	gene with protein product		615794	"fibronectin type III domain containing 3"	FNDC3			Standard	NM_001079673		Approved	bA203I16.5, KIAA0970	uc001vcm.3	Q9Y2H6	OTTHUMG00000016911	ENST00000492622.2:c.3375A>G	chr13.hg19:g.49781309A>G		77.0	0.0		85.0	4.0	NM_001079673	B4DYG1|Q5HYC9|Q5JVF8|Q5JVF9|Q6EVH3|Q6EVH4|Q6N020|Q6P9D5|Q6ZME4|Q9H1W1	Silent	SNP	ENST00000492622.2	hg19	CCDS41886.1																																																																																			.	.		0.527	FNDC3A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354845.2	NM_014923		G	49781309	A	G	49781309	2	3	255	1	0	0	0	0	0	0	0	1	5977	69	3	2		2	FNDC3A	13	49781309	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	1169414	49781309	65388569	494	35839										
COMMD6	170622	hgsc.bcm.edu	37	chr13	76104273	76104273	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aaactgtggaatcgtcatttCaaagcacttggtctttactt	7	8	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:76104273C>T	ENST00000377615.3	-	4	348	c.184G>A	c.(184-186)Gaa>Aaa	p.E62K	COMMD6_ENST00000460675.1_5'UTR|COMMD6_ENST00000377619.5_Missense_Mutation_p.E77K|COMMD6_ENST00000355801.4_Missense_Mutation_p.E62K|COMMD6_ENST00000406936.3_Missense_Mutation_p.E62K			Q7Z4G1	COMD6_HUMAN	COMM domain containing 6	62	COMM. {ECO:0000255|PROSITE- ProRule:PRU00602}.				negative regulation of NF-kappaB transcription factor activity (GO:0032088)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	NF-kappaB binding (GO:0051059)			breast(1)|lung(1)|urinary_tract(1)	3		Breast(118;0.0979)|Prostate(6;0.122)		GBM - Glioblastoma multiforme(99;0.0104)		ATCGTCATTTCAAAGCACTTG	0.383																																					p.E62K		Atlas-SNP	.											.	COMMD6	4	.	0			c.G184A						.						148	132	138					13																	76104273		2203	4300	6503	SO:0001583	missense	170622	exon3			TCATTTCAAAGCA	AY542161	CCDS9451.1, CCDS9452.1	13q22	2004-02-18			ENSG00000188243	ENSG00000188243			24015	protein-coding gene	gene with protein product		612377				15799966	Standard	NM_203497		Approved	Acrg	uc001vjn.1	Q7Z4G1	OTTHUMG00000017089	ENST00000377615.3:c.184G>A	chr13.hg19:g.76104273C>T	ENSP00000366841:p.Glu62Lys	81.0	0.0		79.0	5.0	NM_203495	A6NF28|B7ZLN0|Q5TBK4	Missense_Mutation	SNP	ENST00000377615.3	hg19	CCDS9451.1	.	.	.	.	.	.	.	.	.	.	C	36	5.637347	0.96693	.	.	ENSG00000188243	ENST00000406936;ENST00000377615;ENST00000377619;ENST00000355801	T;T;T;T	0.15834	2.39;2.39;2.39;2.39	5.23	5.23	0.72850	COMM domain (1);	0.000000	0.85682	D	0.000000	T	0.46092	0.1375	.	.	.	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.83275	0.996;0.994	T	0.46219	-0.9207	9	0.72032	D	0.01	.	18.7681	0.91881	0.0:1.0:0.0:0.0	.	62;62	Q7Z4G1;Q7Z4G1-2	COMD6_HUMAN;.	K	62;62;77;62	ENSP00000385660:E62K;ENSP00000366841:E62K;ENSP00000366845:E77K;ENSP00000348054:E62K	ENSP00000348054:E62K	E	-	1	0	COMMD6	75002274	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.313000	0.78978	2.613000	0.88420	0.655000	0.94253	GAA	.	.		0.383	COMMD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045288.4	XM_085023		T	76104273	C	T	76104273	3	4	255	1	0	0	0	0	1	0	0	0	3722	835	29	3	124	3	COMMD6	13	76104273	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	26322964	76104273	39065605	495	35840										
SCEL	8796	hgsc.bcm.edu	37	chr13	78130761	78130761	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	caccactcagggaaccacacGgaagcagcaggattttcacg	10	13	2	0	rs200836262		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:78130761G>T	ENST00000349847.3	+	3	158	c.74G>T	c.(73-75)cGg>cTg	p.R25L	SCEL_ENST00000535157.1_Missense_Mutation_p.R25L|SCEL_ENST00000377246.3_Missense_Mutation_p.R25L	NM_144777.2	NP_659001.2	O95171	SCEL_HUMAN	sciellin	25					embryo development (GO:0009790)|epidermis development (GO:0008544)|keratinocyte differentiation (GO:0030216)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	zinc ion binding (GO:0008270)	p.R25L(1)		breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(18)|ovary(5)|prostate(1)|stomach(1)|urinary_tract(1)	40		Acute lymphoblastic leukemia(28;0.0282)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0233)		GGAACCACACGGAAGCAGCAG	0.433																																					p.R25L		Atlas-SNP	.											.	SCEL	85	.	1	Substitution - Missense(1)	lung(1)	c.G74T						.						182	187	186					13																	78130761		2203	4300	6503	SO:0001583	missense	8796	exon3			CCACACGGAAGCA	AF045941	CCDS9458.1, CCDS9459.1, CCDS53877.1	13q22	2008-07-18			ENSG00000136155	ENSG00000136155			10573	protein-coding gene	gene with protein product		604112				9813070	Standard	NM_003843		Approved	FLJ21667, MGC22531	uc001vki.3	O95171	OTTHUMG00000017107	ENST00000349847.3:c.74G>T	chr13.hg19:g.78130761G>T	ENSP00000302579:p.Arg25Leu	84.0	0.0		92.0	4.0	NM_003843	B7Z797|F5H651|Q53H61|Q5W0S8|Q5W0S9|Q86X00	Missense_Mutation	SNP	ENST00000349847.3	hg19	CCDS9459.1	.	.	.	.	.	.	.	.	.	.	g	0.005	-2.196575	0.00299	.	.	ENSG00000136155	ENST00000348770;ENST00000535157;ENST00000377246;ENST00000349847	T;T;T	0.21734	1.99;1.99;1.99	5.16	-2.02	0.07388	.	0.552403	0.15231	N	0.273429	T	0.04048	0.0113	N	0.00583	-1.355	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.31475	-0.9942	10	0.30854	T	0.27	1.2565	2.1981	0.03916	0.3887:0.0711:0.2974:0.2428	.	25;25;25	F5H651;O95171-2;O95171	.;.;SCEL_HUMAN	L	25	ENSP00000437895:R25L;ENSP00000366454:R25L;ENSP00000302579:R25L	ENSP00000315127:R25L	R	+	2	0	SCEL	77028762	0.020000	0.18652	0.001000	0.08648	0.000000	0.00434	-0.378000	0.07446	-0.882000	0.03987	-3.487000	0.00034	CGG	.	.		0.433	SCEL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045339.2	NM_144777		T	78130761	G	T	78130761	3	4	255	1	0	0	0	0	1	0	0	0	13903	1116	39	1	80	1	SCEL	13	78130761	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	2026488	78130761	37039117	496	35841										
DZIP1	22873	hgsc.bcm.edu	37	chr13	96293971	96293971	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctccagccgcggcctgaactGgaagaagggcaggggccccg	16	14	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:96293971G>A	ENST00000376829.2	-	5	1026	c.175C>T	c.(175-177)Cag>Tag	p.Q59*	DZIP1_ENST00000361396.2_Nonsense_Mutation_p.Q59*|DZIP1_ENST00000347108.3_Nonsense_Mutation_p.Q59*|DZIP1_ENST00000466027.1_5'UTR|DZIP1_ENST00000361156.3_Nonsense_Mutation_p.Q59*	NM_198968.3	NP_945319.1	Q86YF9	DZIP1_HUMAN	DAZ interacting zinc finger protein 1	59					cilium assembly (GO:0042384)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(20)|lung(11)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	38	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.141)			GGCCTGAACTGGAAGAAGGGC	0.741																																					p.Q59X		Atlas-SNP	.											.	DZIP1	195	.	0			c.C175T						.						31	35	34					13																	96293971		2188	4258	6446	SO:0001587	stop_gained	22873	exon5			TGAACTGGAAGAA	AB023213	CCDS9477.1, CCDS9478.1	13q32.1	2013-05-22	2013-05-22		ENSG00000134874	ENSG00000134874		"Zinc fingers, C2H2-type"	20908	protein-coding gene	gene with protein product		608671	"DAZ interacting protein 1"				Standard	NM_014934		Approved	KIAA0996, DZIP	uc001vmk.4	Q86YF9	OTTHUMG00000017224	ENST00000376829.2:c.175C>T	chr13.hg19:g.96293971G>A	ENSP00000366025:p.Gln59*	13.0	0.0		18.0	5.0	NM_014934	Q5W078|Q5W079|Q8WY45|Q8WY46|Q9UGA5|Q9Y2K0	Nonsense_Mutation	SNP	ENST00000376829.2	hg19	CCDS9478.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.959865	0.74016	.	.	ENSG00000134874	ENST00000347108;ENST00000361156;ENST00000361396;ENST00000376829	.	.	.	4.78	4.78	0.61160	.	0.109676	0.64402	D	0.000012	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.9704	12.888	0.58055	0.0:0.0:0.8374:0.1626	.	.	.	.	X	59	.	ENSP00000257312:Q59X	Q	-	1	0	DZIP1	95091972	1.000000	0.71417	1.000000	0.80357	0.252000	0.25951	2.342000	0.43992	2.212000	0.71576	0.551000	0.68910	CAG	.	.		0.741	DZIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045496.3	NM_014934		A	96293971	G	A	96293971	4	1	255	1	0	0	0	0	0	1	0	0	4865	1357	47	3	2504	3	DZIP1	13	96293971	Nonsense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	18163210	96293971	18875907	497	35842										
SLC10A2	6555	hgsc.bcm.edu	37	chr13	103703608	103703608	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gatttactaaatgccataccTgtaccagggtagaccagcaa	8	10	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:103703608T>C	ENST00000245312.3	-	4	1356	c.760A>G	c.(760-762)Agg>Ggg	p.R254G		NM_000452.2	NP_000443	Q12908	NTCP2_HUMAN	solute carrier family 10 (sodium/bile acid cotransporter), member 2	254					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteasome complex (GO:0000502)	bile acid:sodium symporter activity (GO:0008508)			breast(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_neural(89;0.0662)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)				Aciclovir(DB00787)|Cyclosporine(DB00091)|Ursodeoxycholic acid(DB01586)|Valaciclovir(DB00577)	ATGCCATACCTGTACCAGGGT	0.428																																					p.R254G		Atlas-SNP	.											.	SLC10A2	67	.	0			c.A760G						.						68	70	70					13																	103703608		2203	4300	6503	SO:0001630	splice_region_variant	6555	exon4			CATACCTGTACCA	U10417	CCDS9506.1	13q33	2013-07-18	2013-07-18		ENSG00000125255	ENSG00000125255		"Solute carriers"	10906	protein-coding gene	gene with protein product		601295		ASBT, ISBT		8661017	Standard	NM_000452		Approved		uc001vpy.4	Q12908	OTTHUMG00000017313	ENST00000245312.3:c.761+1A>G	chr13.hg19:g.103703608T>C		46.0	0.0		54.0	4.0	NM_000452	A1L4F4|Q13839	Missense_Mutation	SNP	ENST00000245312.3	hg19	CCDS9506.1	.	.	.	.	.	.	.	.	.	.	T	16.98	3.270568	0.59540	.	.	ENSG00000125255	ENST00000245312	T	0.78707	-1.2	5.46	5.46	0.80206	.	0.042424	0.85682	D	0.000000	T	0.77974	0.4211	M	0.76433	2.335	0.53688	D	0.99997	B	0.24920	0.114	B	0.21917	0.037	T	0.76061	-0.3097	10	0.48119	T	0.1	-14.0415	15.5257	0.75901	0.0:0.0:0.0:1.0	.	254	Q12908	NTCP2_HUMAN	G	254	ENSP00000245312:R254G	ENSP00000245312:R254G	R	-	1	2	SLC10A2	102501609	1.000000	0.71417	1.000000	0.80357	0.091000	0.18340	7.818000	0.86416	2.082000	0.62665	0.377000	0.23210	AGG	.	.		0.428	SLC10A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045716.1		Missense_Mutation	C	103703608	T	C	103703608	5	2	255	1	0	0	0	0	0	0	1	0	14389	1594	55	2	298	2	SLC10A2	13	103703608	Splice_Site	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	7409637	103703608	11466270	498	35843										
MYO16	23026	hgsc.bcm.edu	37	chr13	109318307	109318307	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgcttgctagagtcccttccCcttggccaacggcagcgtct	10	15	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:109318307C>A	ENST00000357550.2	+	1	77	c.36C>A	c.(34-36)ccC>ccA	p.P12P	MYO16_ENST00000356711.2_Silent_p.P12P|MYO16_ENST00000251041.5_Silent_p.P12P	NM_001198950.1	NP_001185879.1			myosin XVI											NS(3)|breast(4)|central_nervous_system(2)|endometrium(10)|kidney(8)|large_intestine(27)|lung(51)|ovary(9)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	121	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			AGTCCCTTCCCCTTGGCCAAC	0.517																																					p.P34P		Atlas-SNP	.											.	MYO16	285	.	0			c.C102A						.						84	75	78					13																	109318307		2203	4300	6503	SO:0001819	synonymous_variant	23026	exon2			CCTTCCCCTTGGC		CCDS32008.1, CCDS73598.1	13q33.3	2014-06-12			ENSG00000041515	ENSG00000041515		"Myosins / Myosin superfamily : Class XVI", "Ankyrin repeat domain containing"	29822	protein-coding gene	gene with protein product	"neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 3", "protein phosphatase 1, regulatory subunit 107"	615479				11588169, 17029291, 21946561	Standard	NM_001198950		Approved	MYR8, KIAA0865, Myo16b, NYAP3, PPP1R107	uc001vqt.1	Q9Y6X6	OTTHUMG00000017333	ENST00000357550.2:c.36C>A	chr13.hg19:g.109318307C>A		50.0	0.0		63.0	4.0	NM_001198950		Silent	SNP	ENST00000357550.2	hg19	CCDS32008.1																																																																																			.	.		0.517	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011		A	109318307	C	A	109318307	2	1	255	1	0	0	0	0	0	0	0	1	10073	610	22	3		3	MYO16	13	109318307	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	5614699	109318307	5851571	499	35844										
RNASE4	6038	hgsc.bcm.edu	37	chr14	21167714	21167714	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgatgatgcaaagacggaagAtgactttgtatcactgcaag	11	6	1	5			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:21167714A>G	ENST00000555835.1	+	2	860	c.184A>G	c.(184-186)Atg>Gtg	p.M62V	AL163636.6_ENST00000553909.1_3'UTR|RP11-903H12.3_ENST00000554286.1_RNA|RNASE4_ENST00000397995.2_Missense_Mutation_p.M62V|RNASE4_ENST00000555597.1_Missense_Mutation_p.M62V|RNASE4_ENST00000304704.4_Missense_Mutation_p.M62V	NM_002937.3	NP_002928.1	P34096	RNAS4_HUMAN	ribonuclease, RNase A family, 4	62					cellular response to starvation (GO:0009267)|mRNA cleavage (GO:0006379)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	nucleic acid binding (GO:0003676)|pancreatic ribonuclease activity (GO:0004522)			central_nervous_system(1)|large_intestine(1)|lung(3)|skin(1)	6	all_cancers(95;0.00304)		Epithelial(56;5.13e-07)|all cancers(55;4.73e-06)	GBM - Glioblastoma multiforme(265;0.0133)		AAGACGGAAGATGACTTTGTA	0.498																																					p.M62V	Esophageal Squamous(59;1059 1362 26290 51151)	Atlas-SNP	.											.	RNASE4	18	.	0			c.A184G						.						154	125	135					14																	21167714		2203	4300	6503	SO:0001583	missense	6038	exon2			CGGAAGATGACTT	U36775	CCDS9555.1	14q11	2014-07-16			ENSG00000258818	ENSG00000258818		"Ribonucleases, RNase A"	10047	protein-coding gene	gene with protein product		601030				7501448	Standard	NM_002937		Approved		uc001vxy.4	P34096	OTTHUMG00000029575	ENST00000555835.1:c.184A>G	chr14.hg19:g.21167714A>G	ENSP00000452245:p.Met62Val	89.0	0.0		55.0	4.0	NM_002937		Missense_Mutation	SNP	ENST00000555835.1	hg19	CCDS9555.1	.	.	.	.	.	.	.	.	.	.	A	18.60	3.659341	0.67586	.	.	ENSG00000258818;ENSG00000258818;ENSG00000258818;ENSG00000181784;ENSG00000181784;ENSG00000181784	ENST00000555835;ENST00000397995;ENST00000555597;ENST00000398001;ENST00000304704;ENST00000397999	T;T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02;1.02	5.81	5.81	0.92471	Ribonuclease A, domain (4);	0.112323	0.64402	D	0.000004	T	0.67608	0.2911	M	0.89715	3.055	0.35604	D	0.808104	D	0.67145	0.996	D	0.63283	0.913	T	0.80627	-0.1298	10	0.72032	D	0.01	-32.3892	12.8374	0.57782	1.0:0.0:0.0:0.0	.	62	P34096	RNAS4_HUMAN	V	62	ENSP00000452245:M62V;ENSP00000381081:M62V;ENSP00000451624:M62V;ENSP00000381087:M62V;ENSP00000307096:M62V;ENSP00000381085:M62V	ENSP00000307096:M62V	M	+	1	0	AL163636.2;RNASE4	20237554	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	3.185000	0.50934	2.343000	0.79666	0.533000	0.62120	ATG	.	.		0.498	RNASE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073729.3			G	21167714	A	G	21167714	3	3	255	1	0	0	0	0	1	0	0	0	13421	333	12	2	186	2	RNASE4	14	21167714	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10		21167714	86181826	500	35845										
PABPN1	8106	hgsc.bcm.edu	37	chr14	23794468	23794468	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcttccaggggccgggctagAgcgacatcatggtattcccc	12	13	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:23794468A>G	ENST00000216727.4	+	7	1075	c.894A>G	c.(892-894)agA>agG	p.R298R	BCL2L2-PABPN1_ENST00000553781.1_Silent_p.R325R|PABPN1_ENST00000397276.2_3'UTR|AL049829.1_ENST00000594872.1_5'Flank|PABPN1_ENST00000556821.1_Silent_p.R170R|BCL2L2-PABPN1_ENST00000557008.1_Silent_p.R325R	NM_004643.3	NP_004634.1	Q86U42	PABP2_HUMAN	poly(A) binding protein, nuclear 1	298	Interacts with PAPOLA. {ECO:0000250}.|Necessary for homooligomerization.				gene expression (GO:0010467)|modification by virus of host mRNA processing (GO:0046778)|modulation by virus of host morphology or physiology (GO:0019048)|modulation by virus of host process (GO:0019054)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|muscle contraction (GO:0006936)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)|viral life cycle (GO:0019058)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			large_intestine(1)|lung(1)|ovary(2)	4	all_cancers(95;6.69e-06)			GBM - Glioblastoma multiforme(265;0.00643)		GCCGGGCTAGAGCGACATCAT	0.428																																					p.R325R		Atlas-SNP	.											.	.	.	.	0			c.A975G						.						109	108	108					14																	23794468		2203	4300	6503	SO:0001819	synonymous_variant	100529063	exon9			GGCTAGAGCGACA	AF026029	CCDS9592.1	14q11.2	2013-02-12	2001-11-28		ENSG00000100836	ENSG00000100836		"RNA binding motif (RRM) containing"	8565	protein-coding gene	gene with protein product		602279	"poly(A)-binding protein, nuclear 1"	OPMD, PABP2		7795598	Standard	NM_004643		Approved	PAB2		Q86U42	OTTHUMG00000028739	ENST00000216727.4:c.894A>G	chr14.hg19:g.23794468A>G		201.0	0.0		109.0	5.0	NM_001199864	D3DS49|O43484	Silent	SNP	ENST00000216727.4	hg19	CCDS9592.1																																																																																			.	.		0.428	PABPN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071767.4	NM_004643		G	23794468	A	G	23794468	2	3	255	1	0	0	0	0	0	0	0	1	11377	301	11	2		2	PABPN1	14	23794468	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	2626754	23794468	83555072	501	35846										
LRRC16B	90668	hgsc.bcm.edu	37	chr14	24523712	24523712	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gccctgtccaaggtctgcccTggccctgggtgagtggcaaa	14	13	1	1	rs561201986		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:24523712T>C	ENST00000342740.5	+	5	508	c.354T>C	c.(352-354)ccT>ccC	p.P118P	LRRC16B_ENST00000334420.7_5'UTR	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	118						cytoplasm (GO:0005737)				breast(3)|central_nervous_system(2)|cervix(3)|endometrium(7)|kidney(1)|large_intestine(9)|liver(1)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	52				GBM - Glioblastoma multiforme(265;0.019)		AGGTCTGCCCTGGCCCTGGGT	0.582																																					p.P118P		Atlas-SNP	.											.	LRRC16B	120	.	0			c.T354C						.						71	62	65					14																	24523712		2203	4300	6503	SO:0001819	synonymous_variant	90668	exon5			CTGCCCTGGCCCT	AI017934	CCDS32054.1	14q11.2-q12	2010-09-10	2008-02-12	2008-02-12					20272	protein-coding gene	gene with protein product		614716	"chromosome 14 open reading frame 121"	C14orf121		19846667	Standard	NM_138360		Approved	BC008134, crml-1, CARMIL3	uc001wlj.2	Q8ND23		ENST00000342740.5:c.354T>C	chr14.hg19:g.24523712T>C		79.0	0.0		71.0	4.0	NM_138360	Q8TEF7|Q96HS9	Silent	SNP	ENST00000342740.5	hg19	CCDS32054.1																																																																																			.	.		0.582	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360		C	24523712	T	C	24523712	2	2	255	1	0	0	0	0	0	0	0	1	8981	1567	55	2		2	LRRC16B	14	24523712	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	729244	24523712	82825828	502	35847										
RNF31	55072	hgsc.bcm.edu	37	chr14	24621043	24621043	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	acgcactccccagctggggcCgggcagagctggcactgtca	14	15	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:24621043C>A	ENST00000324103.6	+	11	2292	c.1972C>A	c.(1972-1974)Cgg>Agg	p.R658R	RP11-468E2.4_ENST00000558468.1_Silent_p.R133R|RNF31_ENST00000382687.3_Silent_p.R507R|RNF31_ENST00000559275.1_Silent_p.R507R	NM_017999.4	NP_060469.4	Q96EP0	RNF31_HUMAN	ring finger protein 31	658					CD40 signaling pathway (GO:0023035)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein linear polyubiquitination (GO:0097039)|protein polyubiquitination (GO:0000209)|T cell receptor signaling pathway (GO:0050852)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|LUBAC complex (GO:0071797)	ligase activity (GO:0016874)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|prostate(4)|skin(2)|soft_tissue(1)	39				GBM - Glioblastoma multiforme(265;0.00861)		CAGCTGGGGCCGGGCAGAGCT	0.617																																					p.R658R		Atlas-SNP	.											RNF31,NS,carcinoma,0,1	RNF31	95	.	0			c.C1972A						.						63	70	68					14																	24621043		1971	4157	6128	SO:0001819	synonymous_variant	55072	exon11			TGGGGCCGGGCAG	AK000973	CCDS41931.1	14q11.2	2012-09-20			ENSG00000092098	ENSG00000092098		"RING-type (C3HC4) zinc fingers"	16031	protein-coding gene	gene with protein product	"HOIL-1-interacting protein"	612487				10422847	Standard	NM_017999		Approved	ZIBRA, FLJ10111, FLJ23501, HOIP	uc001wmn.1	Q96EP0	OTTHUMG00000028798	ENST00000324103.6:c.1972C>A	chr14.hg19:g.24621043C>A		50.0	0.0		28.0	2.0	NM_017999	A0A962|Q86VI2|Q8TEI0|Q96GB4|Q96NF1|Q9H5F1|Q9NWD2	Silent	SNP	ENST00000324103.6	hg19	CCDS41931.1																																																																																			.	.		0.617	RNF31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071921.3	NM_017999		A	24621043	C	A	24621043	2	1	255	1	0	0	0	0	0	0	0	1	13502	643	23	1		1	RNF31	14	24621043	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	97331	24621043	82728497	503	35848										
C14orf166	51637	hgsc.bcm.edu	37	chr14	52471128	52471128	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tctgcgattgctgcacatagAggagctcagagagctacaga	12	9	2	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:52471128A>G	ENST00000261700.3	+	8	794	c.629A>G	c.(628-630)gAg>gGg	p.E210G	C14orf166_ENST00000556760.1_3'UTR	NM_016039.2	NP_057123.1	Q9Y224	CN166_HUMAN	chromosome 14 open reading frame 166	210					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|RNA transport (GO:0050658)|transcription, DNA-templated (GO:0006351)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|tRNA-splicing ligase complex (GO:0072669)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA polymerase II core binding (GO:0000993)			endometrium(1)|large_intestine(3)|lung(2)	6	Breast(41;0.0639)|all_epithelial(31;0.101)					CTGCACATAGAGGAGCTCAGA	0.393																																					p.E210G		Atlas-SNP	.											.	C14orf166	23	.	0			c.A629G						.						66	69	68					14																	52471128		2203	4300	6503	SO:0001583	missense	51637	exon8			ACATAGAGGAGCT	AF151857	CCDS9705.1	14q22.1	2014-05-29			ENSG00000087302	ENSG00000087302			23169	protein-coding gene	gene with protein product	"RLL motif containing 1"	610858				10810093, 24608264	Standard	NM_016039		Approved	CGI-99, RLLM1, CLE, CLE7, LCRP369	uc010aod.3	Q9Y224	OTTHUMG00000152332	ENST00000261700.3:c.629A>G	chr14.hg19:g.52471128A>G	ENSP00000261700:p.Glu210Gly	144.0	0.0		96.0	5.0	NM_016039		Missense_Mutation	SNP	ENST00000261700.3	hg19	CCDS9705.1	.	.	.	.	.	.	.	.	.	.	A	17.42	3.385530	0.61956	.	.	ENSG00000087302	ENST00000261700	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.65883	0.2734	M	0.64404	1.975	0.80722	D	1	B;B	0.10296	0.003;0.003	B;B	0.12156	0.007;0.007	T	0.60255	-0.7299	9	0.33141	T	0.24	-13.0206	16.8222	0.85835	1.0:0.0:0.0:0.0	.	210;210	Q9Y224;Q549M8	CN166_HUMAN;.	G	210	.	ENSP00000261700:E210G	E	+	2	0	C14orf166	51540878	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.105000	0.94246	2.371000	0.80710	0.533000	0.62120	GAG	.	.		0.393	C14orf166-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276887.1	NM_016039		G	52471128	A	G	52471128	3	3	255	1	0	0	0	0	1	0	0	0	1758	304	11	2	659	2	C14orf166	14	52471128	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	27850085	52471128	54878412	504	35849										
PTGER2	5732	hgsc.bcm.edu	37	chr14	52781586	52781586	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggcactggcgcccgagagccGcgcgtgcacctacttcgctt	13	16	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:52781586G>T	ENST00000245457.5	+	1	474	c.320G>T	c.(319-321)cGc>cTc	p.R107L	PTGER2_ENST00000557436.1_Intron	NM_000956.3	NP_000947.2	P43116	PE2R2_HUMAN	prostaglandin E receptor 2 (subtype EP2), 53kDa	107					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|cellular response to prostaglandin E stimulus (GO:0071380)|G-protein coupled receptor signaling pathway (GO:0007186)|regulation of cell proliferation (GO:0042127)|response to lipopolysaccharide (GO:0032496)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	prostaglandin E receptor activity (GO:0004957)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15	Breast(41;0.0639)|all_epithelial(31;0.0729)				Alprostadil(DB00770)|Dinoprostone(DB00917)|Misoprostol(DB00929)	CCCGAGAGCCGCGCGTGCACC	0.647																																					p.R107L		Atlas-SNP	.											.	PTGER2	27	.	0			c.G320T						.						43	39	41					14																	52781586		2191	4277	6468	SO:0001583	missense	5732	exon1			AGAGCCGCGCGTG		CCDS9708.1	14q22	2012-08-08	2002-08-29		ENSG00000125384	ENSG00000125384		"GPCR / Class A : Prostanoid receptors"	9594	protein-coding gene	gene with protein product		176804	"prostaglandin E receptor 2 (subtype EP2), 53kD"			8250933, 7759114	Standard	NM_000956		Approved	EP2	uc001wzr.3	P43116	OTTHUMG00000140300	ENST00000245457.5:c.320G>T	chr14.hg19:g.52781586G>T	ENSP00000245457:p.Arg107Leu	128.0	0.0		91.0	4.0	NM_000956	D3DSC0|Q52LG8	Missense_Mutation	SNP	ENST00000245457.5	hg19	CCDS9708.1	.	.	.	.	.	.	.	.	.	.	G	9.490	1.100330	0.20552	.	.	ENSG00000125384	ENST00000245457	T	0.70045	-0.45	5.09	3.24	0.37175	GPCR, rhodopsin-like superfamily (1);	0.662303	0.15967	N	0.235991	T	0.48003	0.1476	L	0.32530	0.975	0.09310	N	1	B	0.14438	0.01	B	0.18871	0.023	T	0.29579	-1.0007	10	0.10377	T	0.69	-7.4094	5.3613	0.16089	0.1739:0.0:0.6661:0.1599	.	107	P43116	PE2R2_HUMAN	L	107	ENSP00000245457:R107L	ENSP00000245457:R107L	R	+	2	0	PTGER2	51851336	0.000000	0.05858	0.674000	0.29902	0.967000	0.64934	0.187000	0.16998	0.631000	0.30412	0.563000	0.77884	CGC	.	.		0.647	PTGER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276890.1			T	52781586	G	T	52781586	3	4	255	1	0	0	0	0	1	0	0	0	12756	1087	38	1	322	1	PTGER2	14	52781586	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	310458	52781586	54567954	505	35850										
OTX2	5015	hgsc.bcm.edu	37	chr14	57271044	57271044	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gtcgtcctctcccggcgctgTttccggggggtggctgcggg	18	13	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:57271044T>C	ENST00000555006.1	-	3	519	c.111A>G	c.(109-111)aaA>aaG	p.K37K	OTX2_ENST00000554788.1_Intron|OTX2_ENST00000554559.1_Intron|OTX2_ENST00000339475.5_Silent_p.K45K|OTX2_ENST00000408990.3_Silent_p.K37K			P32243	OTX2_HUMAN	orthodenticle homeobox 2	37					axon guidance (GO:0007411)|cell fate specification (GO:0001708)|diencephalon morphogenesis (GO:0048852)|dorsal/ventral pattern formation (GO:0009953)|endoderm development (GO:0007492)|eye photoreceptor cell fate commitment (GO:0042706)|forebrain development (GO:0030900)|inner ear morphogenesis (GO:0042472)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|neuron fate determination (GO:0048664)|positive regulation of embryonic development (GO:0040019)|positive regulation of gastrulation (GO:2000543)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|primitive streak formation (GO:0090009)|protein complex assembly (GO:0006461)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of smoothened signaling pathway (GO:0008589)|somite rostral/caudal axis specification (GO:0032525)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|nucleus (GO:0005634)|protein complex (GO:0043234)	eukaryotic initiation factor 4E binding (GO:0008190)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	19	Medulloblastoma(1;0.00184)|all_neural(1;0.00414)					CCCGGCGCTGTTTCCGGGGGG	0.632																																					p.K45K		Atlas-SNP	.											.	OTX2	47	.	0			c.A135G						.						40	39	40					14																	57271044		2203	4300	6503	SO:0001819	synonymous_variant	5015	exon2			GCGCTGTTTCCGG	AF298117	CCDS9728.1, CCDS41960.1	14q22.3	2014-09-17	2007-02-15		ENSG00000165588	ENSG00000165588		"Homeoboxes / PRD class"	8522	protein-coding gene	gene with protein product		600037	"orthodenticle homolog 2 (Drosophila)"			7959790	Standard	NM_021728		Approved		uc031qor.1	P32243	OTTHUMG00000152338	ENST00000555006.1:c.111A>G	chr14.hg19:g.57271044T>C		127.0	0.0		89.0	4.0	NM_001270525	B2RAN5|Q6GTV3|Q9HAW3|Q9P2R1	Silent	SNP	ENST00000555006.1	hg19	CCDS41960.1																																																																																			.	.		0.632	OTX2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411522.1	NM_021728.		C	57271044	T	C	57271044	2	2	255	1	0	0	0	0	0	0	0	1	11330	1722	60	2		2	OTX2	14	57271044	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	4489458	57271044	50078496	506	35851										
DACT1	51339	hgsc.bcm.edu	37	chr14	59112097	59112097	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gtcattgcagatgtgaatccCaagtaccagtgtgatctggt	11	8	2	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:59112097C>A	ENST00000335867.4	+	4	780	c.756C>A	c.(754-756)ccC>ccA	p.P252P	DACT1_ENST00000541264.2_5'UTR|DACT1_ENST00000395153.3_Silent_p.P215P|DACT1_ENST00000555845.1_3'UTR|DACT1_ENST00000556859.1_5'UTR			Q9NYF0	DACT1_HUMAN	dishevelled-binding antagonist of beta-catenin 1	252					dendrite morphogenesis (GO:0048813)|embryonic hindgut morphogenesis (GO:0048619)|gastrulation with mouth forming second (GO:0001702)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of catenin import into nucleus (GO:0035412)|regulation of protein stability (GO:0031647)|regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000095)|synapse organization (GO:0050808)|Wnt signaling pathway (GO:0016055)	beta-catenin destruction complex (GO:0030877)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|protein kinase A binding (GO:0051018)|protein kinase C binding (GO:0005080)			endometrium(7)|kidney(3)|large_intestine(11)|lung(27)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	53						ATGTGAATCCCAAGTACCAGT	0.478																																					p.P252P		Atlas-SNP	.											.	DACT1	119	.	0			c.C756A						.						164	151	155					14																	59112097		2203	4300	6503	SO:0001819	synonymous_variant	51339	exon4			GAATCCCAAGTAC	AF251079	CCDS9736.1, CCDS41961.1	14q22.3	2013-05-15	2013-05-15		ENSG00000165617	ENSG00000165617			17748	protein-coding gene	gene with protein product		607861	"dapper homolog 1, antagonist of beta-catenin (xenopus)", "dapper, antagonist of beta-catenin, homolog 1 (Xenopus laevis)"			11970895	Standard	NM_001079520		Approved	DAPPER1, THYEX3, HDPR1, DAPPER, FRODO	uc001xdw.3	Q9NYF0	OTTHUMG00000140324	ENST00000335867.4:c.756C>A	chr14.hg19:g.59112097C>A		151.0	0.0		106.0	5.0	NM_016651	A8MYJ2|Q86TY0	Silent	SNP	ENST00000335867.4	hg19	CCDS9736.1																																																																																			.	.		0.478	DACT1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325515.1	NM_016651		A	59112097	C	A	59112097	2	1	255	1	0	0	0	0	0	0	0	1	4224	581	21	3		3	DACT1	14	59112097	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1841053	59112097	48237443	507	35852										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64492096	64492096	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccttatggttttgaattcatCcgaaggcaaaatgccacttg	8	9	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:64492096C>A	ENST00000344113.4	+	41	6421	c.6209C>A	c.(6208-6210)tCc>tAc	p.S2070Y	SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000554584.1_Missense_Mutation_p.S2070Y|SYNE2_ENST00000358025.3_Missense_Mutation_p.S2070Y	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	2070					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		TTGAATTCATCCGAAGGCAAA	0.348																																					p.S2070Y		Atlas-SNP	.											SYNE2,NS,carcinoma,0,1	SYNE2	577	.	0			c.C6209A						.						65	61	62					14																	64492096		1815	4081	5896	SO:0001583	missense	23224	exon41			ATTCATCCGAAGG	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.6209C>A	chr14.hg19:g.64492096C>A	ENSP00000341781:p.Ser2070Tyr	110.0	0.0		56.0	3.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	hg19	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	C	13.90	2.376495	0.42105	.	.	ENSG00000054654	ENST00000358025;ENST00000344113;ENST00000554584;ENST00000261678	T;T;T	0.57107	0.78;0.78;0.42	5.9	5.9	0.94986	.	0.464601	0.20763	N	0.086123	T	0.52008	0.1708	N	0.24115	0.695	0.80722	D	1	D;D	0.59767	0.976;0.986	P;P	0.56700	0.642;0.804	T	0.43814	-0.9368	10	0.33141	T	0.24	.	13.0004	0.58672	0.2011:0.7989:0.0:0.0	.	2070;2070	Q8WXH0;Q8WXH0-2	SYNE2_HUMAN;.	Y	2070	ENSP00000350719:S2070Y;ENSP00000341781:S2070Y;ENSP00000452570:S2070Y	ENSP00000261678:S2070Y	S	+	2	0	SYNE2	63561849	0.894000	0.30519	0.999000	0.59377	0.961000	0.63080	1.321000	0.33678	2.800000	0.96347	0.455000	0.32223	TCC	.	.		0.348	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		A	64492096	C	A	64492096	3	1	255	1	0	0	0	0	1	0	0	0	15461	855	30	3	6367	3	SYNE2	14	64492096	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	5379999	64492096	42857444	508	35853										
C14orf50	145376	hgsc.bcm.edu	37	chr14	65054066	65054066	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggaatcaggaggggaaaagaAacgcatgacttttgttcagt	13	5	2	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:65054066A>G	ENST00000298705.1	+	10	962	c.866A>G	c.(865-867)aAa>aGa	p.K289R	RP11-973N13.3_ENST00000554454.1_RNA|RP11-973N13.3_ENST00000556634.1_RNA	NM_172365.1	NP_758953.1	Q96LQ0	PPR36_HUMAN	protein phosphatase 1, regulatory subunit 36	289					negative regulation of phosphatase activity (GO:0010923)		phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										GGGGAAAAGAAACGCATGACT	0.408																																					p.K289R		Atlas-SNP	.											.	.	.	.	0			c.A866G						.						108	110	109					14																	65054066		2203	4300	6503	SO:0001583	missense	145376	exon10			AAAAGAAACGCAT		CCDS9767.1	14q23.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000165807	ENSG00000165807		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	20097	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 50"	C14orf50			Standard	NM_172365		Approved		uc001xhl.1	Q96LQ0	OTTHUMG00000141316	ENST00000298705.1:c.866A>G	chr14.hg19:g.65054066A>G	ENSP00000298705:p.Lys289Arg	92.0	0.0		78.0	4.0	NM_172365	Q6NTH6	Missense_Mutation	SNP	ENST00000298705.1	hg19	CCDS9767.1	.	.	.	.	.	.	.	.	.	.	A	10.42	1.346610	0.24426	.	.	ENSG00000165807	ENST00000298705	T	0.31769	1.48	5.55	3.23	0.37069	.	0.260360	0.33290	N	0.005062	T	0.20618	0.0496	L	0.41710	1.295	0.30347	N	0.785176	B	0.20671	0.047	B	0.18263	0.021	T	0.10337	-1.0634	10	0.31617	T	0.26	-21.223	4.8722	0.13639	0.7216:0.0:0.2784:0.0	.	289	Q96LQ0	PPR36_HUMAN	R	289	ENSP00000298705:K289R	ENSP00000298705:K289R	K	+	2	0	C14orf50	64123819	0.989000	0.36119	0.995000	0.50966	0.994000	0.84299	1.872000	0.39549	0.940000	0.37473	0.533000	0.62120	AAA	.	.		0.408	PPP1R36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280667.1	NM_172365		G	65054066	A	G	65054066	3	3	255	1	0	0	0	0	1	0	0	0	1779	14	1	2	904	2	C14orf50	14	65054066	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	561970	65054066	42295474	509	35854										
SPTB	6710	hgsc.bcm.edu	37	chr14	65252316	65252316	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctctcagtaggacagaggccTcctgggccttctcgttgttc	11	13	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:65252316T>C	ENST00000389721.5	-	17	3826	c.3794A>G	c.(3793-3795)gAg>gGg	p.E1265G	SPTB_ENST00000542895.1_Missense_Mutation_p.E1265G|SPTB_ENST00000389720.3_Missense_Mutation_p.E1265G|SPTB_ENST00000556626.1_Missense_Mutation_p.E1265G|SPTB_ENST00000389722.3_Missense_Mutation_p.E1265G	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	1265					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		GACAGAGGCCTCCTGGGCCTT	0.557																																					p.E1265G		Atlas-SNP	.											.	SPTB	378	.	0			c.A3794G						.						71	62	65					14																	65252316		2203	4300	6503	SO:0001583	missense	6710	exon17			GAGGCCTCCTGGG		CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"Pleckstrin homology (PH) domain containing"	11274	protein-coding gene	gene with protein product	"spherocytosis, clinical type I"	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.3794A>G	chr14.hg19:g.65252316T>C	ENSP00000374371:p.Glu1265Gly	56.0	0.0		62.0	4.0	NM_001024858	Q15510|Q15519	Missense_Mutation	SNP	ENST00000389721.5	hg19	CCDS32100.1	.	.	.	.	.	.	.	.	.	.	T	14.28	2.487581	0.44249	.	.	ENSG00000070182	ENST00000389723;ENST00000389722;ENST00000335612;ENST00000556626;ENST00000389721;ENST00000542895;ENST00000389720	T;T;T;T;T	0.38401	1.14;1.14;1.14;1.14;1.14	5.18	5.18	0.71444	.	0.054164	0.64402	D	0.000001	T	0.50990	0.1648	M	0.78637	2.42	0.80722	D	1	B;P	0.43314	0.085;0.803	B;P	0.48795	0.126;0.59	T	0.57219	-0.7849	10	0.66056	D	0.02	.	14.2976	0.66325	0.0:0.0:0.0:1.0	.	1265;1269	P11277;Q59FP5	SPTB1_HUMAN;.	G	1269;1265;49;1265;1265;1265;1265	ENSP00000374372:E1265G;ENSP00000451752:E1265G;ENSP00000374371:E1265G;ENSP00000443882:E1265G;ENSP00000374370:E1265G	ENSP00000334218:E49G	E	-	2	0	SPTB	64322069	1.000000	0.71417	0.999000	0.59377	0.104000	0.19210	7.981000	0.88123	2.080000	0.62538	0.443000	0.29094	GAG	.	.		0.557	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1			C	65252316	T	C	65252316	3	2	255	1	0	0	0	0	1	0	0	0	15133	1551	54	2	3337	2	SPTB	14	65252316	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	198250	65252316	42097224	510	35855										
SLC39A9	55334	hgsc.bcm.edu	37	chr14	69922540	69922540	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cttgctggtctttgcattggCagcaccagttatgtccatgg	11	10	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:69922540C>T	ENST00000336643.5	+	6	1328	c.650C>T	c.(649-651)gCa>gTa	p.A217V	SLC39A9_ENST00000555245.1_3'UTR|SLC39A9_ENST00000031146.4_Missense_Mutation_p.A151V|SLC39A9_ENST00000556605.1_Missense_Mutation_p.A217V|SLC39A9_ENST00000557046.1_Missense_Mutation_p.A194V	NM_018375.4	NP_060845.2	Q9NUM3	S39A9_HUMAN	solute carrier family 39, member 9	217					zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)			breast(1)|endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|skin(1)|stomach(1)	14				all cancers(60;0.00299)|BRCA - Breast invasive adenocarcinoma(234;0.0145)|OV - Ovarian serous cystadenocarcinoma(108;0.0373)		TTTGCATTGGCAGCACCAGTT	0.438																																					p.A217V		Atlas-SNP	.											.	SLC39A9	27	.	0			c.C650T						.						141	128	132					14																	69922540		2203	4300	6503	SO:0001583	missense	55334	exon6			CATTGGCAGCACC		CCDS9795.1, CCDS58327.1, CCDS58328.1	14q24.1	2013-07-17	2013-07-17			ENSG00000029364		"Solute carriers"	20182	protein-coding gene	gene with protein product							Standard	NM_018375		Approved	FLJ11274	uc001xle.3	Q9NUM3		ENST00000336643.5:c.650C>T	chr14.hg19:g.69922540C>T	ENSP00000336887:p.Ala217Val	179.0	0.0		92.0	4.0	NM_001252150	G3V5J8|Q53HN3|Q5MJQ0|Q6P2Q1|Q86WY2	Missense_Mutation	SNP	ENST00000336643.5	hg19	CCDS9795.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.062484	0.76187	.	.	ENSG00000029364	ENST00000556605;ENST00000336643;ENST00000557046	T;T;T	0.47869	0.83;0.83;0.83	5.19	5.19	0.71726	.	0.094168	0.64402	D	0.000001	T	0.67401	0.2889	M	0.65320	2	0.80722	D	1	D;D;D	0.89917	0.998;1.0;0.993	D;D;D	0.74674	0.984;0.951;0.934	T	0.69331	-0.5173	10	0.72032	D	0.01	-12.7867	18.8944	0.92417	0.0:1.0:0.0:0.0	.	194;217;217	Q9NUM3-2;G3V5J8;Q9NUM3	.;.;S39A9_HUMAN	V	217;217;194	ENSP00000452385:A217V;ENSP00000336887:A217V;ENSP00000451833:A194V	ENSP00000031146:A217V	A	+	2	0	SLC39A9	68992293	1.000000	0.71417	1.000000	0.80357	0.110000	0.19582	7.649000	0.83500	2.696000	0.92011	0.467000	0.42956	GCA	.	.		0.438	SLC39A9-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412446.1	NM_018375		T	69922540	C	T	69922540	3	4	255	1	0	0	0	0	1	0	0	0	14640	710	25	3	672	3	SLC39A9	14	69922540	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	4670224	69922540	37427000	511	35856										
ADAM20	8748	hgsc.bcm.edu	37	chr14	70989894	70989894	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	atttcttggtagcaactctgAgatgcactccttgcatcttg	8	10	3	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:70989894A>G	ENST00000256389.3	-	2	1975	c.1731T>C	c.(1729-1731)tcT>tcC	p.S577S	RP11-486O13.4_ENST00000556646.1_lincRNA	NM_003814.4	NP_003805.3	O43506	ADA20_HUMAN	ADAM metallopeptidase domain 20	527	Cys-rich.				binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(2)	27			KIRC - Kidney renal clear cell carcinoma(12;0.133)|Kidney(31;0.188)	all cancers(60;0.00294)|BRCA - Breast invasive adenocarcinoma(234;0.00668)|OV - Ovarian serous cystadenocarcinoma(108;0.0344)		AGCAACTCTGAGATGCACTCC	0.408																																					p.S577S		Atlas-SNP	.											.	ADAM20	59	.	0			c.T1731C						.						197	142	161					14																	70989894		2203	4300	6503	SO:0001819	synonymous_variant	8748	exon2			ACTCTGAGATGCA	AF029899	CCDS32111.1	14q24.2	2012-04-30	2005-08-18		ENSG00000134007	ENSG00000134007		"ADAM metallopeptidase domain containing"	199	protein-coding gene	gene with protein product		603712	"a disintegrin and metalloproteinase domain 20"			9469942	Standard	NM_003814		Approved		uc001xme.3	O43506	OTTHUMG00000167548	ENST00000256389.3:c.1731T>C	chr14.hg19:g.70989894A>G		125.0	0.0		85.0	5.0	NM_003814	Q6GTZ1|Q9UKJ9	Silent	SNP	ENST00000256389.3	hg19	CCDS32111.1																																																																																			.	.		0.408	ADAM20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395004.2			G	70989894	A	G	70989894	2	3	255	1	0	0	0	0	0	0	0	1	242	291	11	2		2	ADAM20	14	70989894	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	1067354	70989894	36359646	512	35857										
PCNX	22990	hgsc.bcm.edu	37	chr14	71517418	71517418	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgtgtatacctatattgcccCatggcagatcacatggggtt	10	9	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:71517418C>T	ENST00000304743.2	+	23	4834	c.4388C>T	c.(4387-4389)cCa>cTa	p.P1463L	PCNX_ENST00000439984.3_Missense_Mutation_p.P1352L|PCNX_ENST00000238570.5_Missense_Mutation_p.P1463L	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	1463						integral component of membrane (GO:0016021)				NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		TATATTGCCCCATGGCAGATC	0.378																																					p.P1463L		Atlas-SNP	.											.	PCNX	198	.	0			c.C4388T						.						147	149	148					14																	71517418		2203	4300	6503	SO:0001583	missense	22990	exon23			TTGCCCCATGGCA	AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"pecanex-like 1 (Drosophila)"	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.4388C>T	chr14.hg19:g.71517418C>T	ENSP00000304192:p.Pro1463Leu	152.0	0.0		97.0	4.0	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Missense_Mutation	SNP	ENST00000304743.2	hg19	CCDS9806.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.2|21.2	4.110140|4.110140	0.77210|0.77210	.|.	.|.	ENSG00000100731|ENSG00000100731	ENST00000554691|ENST00000304743;ENST00000238570;ENST00000439984	.|T;T;T	.|0.14391	.|2.84;2.53;2.51	5.61|5.61	5.61|5.61	0.85477|0.85477	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.47488|0.47488	0.1448|0.1448	M|M	0.89478|0.89478	3.035|3.035	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.91635	.|0.999;0.999;0.997	T|T	0.54788|0.54788	-0.8241|-0.8241	5|10	.|0.87932	.|D	.|0	.|.	19.6512|19.6512	0.95812|0.95812	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1463;1352;1463	.|Q96RV3-3;B2RTR6;Q96RV3	.|.;.;PCX1_HUMAN	Y|L	522|1463;1463;1352	.|ENSP00000304192:P1463L;ENSP00000238570:P1463L;ENSP00000396617:P1352L	.|ENSP00000238570:P1463L	H|P	+|+	1|2	0|0	PCNX|PCNX	70587171|70587171	1.000000|1.000000	0.71417|0.71417	0.969000|0.969000	0.41365|0.41365	0.744000|0.744000	0.42396|0.42396	7.776000|7.776000	0.85560|0.85560	2.646000|2.646000	0.89796|0.89796	0.563000|0.563000	0.77884|0.77884	CAT|CCA	.	.		0.378	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982		T	71517418	C	T	71517418	3	4	255	1	0	0	0	0	1	0	0	0	11600	594	21	3	4478	3	PCNX	14	71517418	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	527524	71517418	35832122	513	35858										
PAPLN	89932	hgsc.bcm.edu	37	chr14	73719406	73719406	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	atcgaccatgaggcctacccCgaccacatgtgccagcgcca	9	17	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:73719406C>A	ENST00000554301.1	+	10	1180	c.1017C>A	c.(1015-1017)ccC>ccA	p.P339P	PAPLN_ENST00000381166.3_Silent_p.P339P|PAPLN_ENST00000427855.1_Silent_p.P339P|PAPLN_ENST00000340738.5_Silent_p.P312P|PAPLN_ENST00000555445.1_Silent_p.P339P			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	339	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.					basement membrane (GO:0005604)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(3)	42				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)		AGGCCTACCCCGACCACATGT	0.647																																					p.P312P		Atlas-SNP	.											.	PAPLN	180	.	0			c.C936A						.						75	75	75					14																	73719406		2203	4299	6502	SO:0001819	synonymous_variant	89932	exon10			CTACCCCGACCAC	BC042057	CCDS32114.1	14q24.2	2013-01-11				ENSG00000100767		"Immunoglobulin superfamily / I-set domain containing"	19262	protein-coding gene	gene with protein product						11076767, 19734141	Standard	NM_173462		Approved	MGC50452	uc001xnw.4	O95428		ENST00000554301.1:c.1017C>A	chr14.hg19:g.73719406C>A		117.0	0.0		60.0	4.0	NM_173462	B4DES8|B4DGE6|Q659F2|Q6UXJ4|Q6ZNM1|Q6ZUJ0|Q7Z681|Q8IVU0	Silent	SNP	ENST00000554301.1	hg19																																																																																				.	.		0.647	PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	NM_173462		A	73719406	C	A	73719406	2	1	255	1	0	0	0	0	0	0	0	1	11437	639	23	1		1	PAPLN	14	73719406	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	2201988	73719406	33630134	514	35859										
PTGR2	145482	hgsc.bcm.edu	37	chr14	74350824	74350824	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctgcattccagtccatgatgAcaggaggtaacattggaaag	11	8	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:74350824A>G	ENST00000555661.1	+	10	1145	c.1000A>G	c.(1000-1002)Aca>Gca	p.T334A	ZNF410_ENST00000324593.6_5'Flank|ZNF410_ENST00000555044.1_5'Flank|PTGR2_ENST00000267568.4_Missense_Mutation_p.T334A|ZNF410_ENST00000540593.1_5'Flank|ZNF410_ENST00000442160.3_5'Flank|RP5-1021I20.4_ENST00000556551.2_Missense_Mutation_p.T264A|PTGR2_ENST00000553813.1_Missense_Mutation_p.T200A|PTGR2_ENST00000555228.1_Missense_Mutation_p.T334A			Q8N8N7	PTGR2_HUMAN	prostaglandin reductase 2	334					prostaglandin metabolic process (GO:0006693)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	13-prostaglandin reductase activity (GO:0036132)|15-oxoprostaglandin 13-oxidase activity (GO:0047522)			NS(1)|large_intestine(3)|lung(2)|prostate(1)|skin(2)	9					Indomethacin(DB00328)	GTCCATGATGACAGGAGGTAA	0.333																																					p.T334A	Esophageal Squamous(98;1155 1417 16452 47043 47872)	Atlas-SNP	.											.	PTGR2	21	.	0			c.A1000G						.						122	106	111					14																	74350824		2203	4298	6501	SO:0001583	missense	145482	exon10			ATGATGACAGGAG	AK096410	CCDS9820.1	14q24.1-q24.2	2008-06-04	2008-06-02	2008-06-03		ENSG00000140043			20149	protein-coding gene	gene with protein product		608642	"zinc binding alcohol dehydrogenase domain containing 1"	ZADH1		17449869	Standard	NM_152444		Approved	FLJ39091	uc001xow.3	Q8N8N7		ENST00000555661.1:c.1000A>G	chr14.hg19:g.74350824A>G	ENSP00000452280:p.Thr334Ala	106.0	0.0		91.0	4.0	NM_152444	Q3L8A4|Q6MZH8	Missense_Mutation	SNP	ENST00000555661.1	hg19	CCDS9820.1	.	.	.	.	.	.	.	.	.	.	A	15.73	2.919849	0.52653	.	.	ENSG00000140043;ENSG00000140043;ENSG00000140043;ENSG00000258653	ENST00000555228;ENST00000555661;ENST00000267568;ENST00000553813	T;T;T;T	0.75367	-0.93;-0.93;-0.93;-0.93	5.7	5.7	0.88788	GroES-like (1);	0.249108	0.45606	D	0.000359	T	0.58075	0.2097	L	0.28054	0.825	0.39287	D	0.964665	B	0.06786	0.001	B	0.06405	0.002	T	0.56492	-0.7970	10	0.32370	T	0.25	-14.5219	6.2839	0.21023	0.7847:0.0:0.0735:0.1418	.	334	Q8N8N7	PTGR2_HUMAN	A	334;334;334;200	ENSP00000450975:T334A;ENSP00000452280:T334A;ENSP00000267568:T334A;ENSP00000450824:T200A	ENSP00000267568:T334A	T	+	1	0	RP5-1021I20.4;PTGR2	73420577	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.446000	0.44908	2.175000	0.68902	0.533000	0.62120	ACA	.	.		0.333	PTGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412575.1			G	74350824	A	G	74350824	3	3	255	1	0	0	0	0	1	0	0	0	12767	275	10	2	1034	2	PTGR2	14	74350824	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	631418	74350824	32998716	515	35860										
C14orf4	64207	hgsc.bcm.edu	37	chr14	77491917	77491917	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tactctctctagagcaagggAagcaaaatttgtggctgggg	13	7	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:77491917A>G	ENST00000238647.3	-	1	3117	c.2219T>C	c.(2218-2220)tTc>tCc	p.F740S		NM_024496.3	NP_078772.1	Q9H1B7	I2BPL_HUMAN	interferon regulatory factor 2 binding protein-like	740					development of secondary female sexual characteristics (GO:0046543)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	extracellular space (GO:0005615)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	11						AGAGCAAGGGAAGCAAAATTT	0.577																																					p.F740S		Atlas-SNP	.											.	IRF2BPL	40	.	0			c.T2219C						.						62	57	59					14																	77491917		2203	4300	6503	SO:0001583	missense	64207	exon1			CAAGGGAAGCAAA	AJ277365	CCDS9854.1	14q24.3	2011-02-23	2011-02-23	2011-02-23	ENSG00000119669	ENSG00000119669			14282	protein-coding gene	gene with protein product	"enhanced at puberty 1"	611720	"chromosome 14 open reading frame 4"	C14orf4		11095982, 17627301	Standard	NM_024496		Approved	EAP1, KIAA1865	uc001xsy.4	Q9H1B7		ENST00000238647.3:c.2219T>C	chr14.hg19:g.77491917A>G	ENSP00000238647:p.Phe740Ser	115.0	0.0		79.0	4.0	NM_024496	Q8NDQ2|Q96JG2|Q9H3I7	Missense_Mutation	SNP	ENST00000238647.3	hg19	CCDS9854.1	.	.	.	.	.	.	.	.	.	.	A	19.42	3.823779	0.71143	.	.	ENSG00000119669	ENST00000238647	T	0.77877	-1.13	4.64	4.64	0.57946	Zinc finger, RING/FYVE/PHD-type (1);	0.000000	0.85682	U	0.000000	D	0.86653	0.5984	M	0.84326	2.69	0.80722	D	1	D	0.60160	0.987	P	0.60682	0.878	D	0.88885	0.3342	10	0.87932	D	0	.	13.3656	0.60682	1.0:0.0:0.0:0.0	.	740	Q9H1B7	I2BPL_HUMAN	S	740	ENSP00000238647:F740S	ENSP00000238647:F740S	F	-	2	0	IRF2BPL	76561670	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.097000	0.94193	1.948000	0.56530	0.379000	0.24179	TTC	.	.		0.577	IRF2BPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414298.1	NM_024496		G	77491917	A	G	77491917	3	3	255	1	0	0	0	0	1	0	0	0	1775	246	9	2	175	2	C14orf4	14	77491917	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	3141093	77491917	29857623	516	35861										
SPATA7	55812	hgsc.bcm.edu	37	chr14	88892683	88892683	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcagagagactacacctaagTctacataaatccagtaaagt	6	9	2	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:88892683T>C	ENST00000393545.4	+	6	769	c.480T>C	c.(478-480)agT>agC	p.S160S	SPATA7_ENST00000356583.5_Silent_p.S128S|SPATA7_ENST00000556553.1_Silent_p.S128S|SPATA7_ENST00000045347.7_Silent_p.S160S	NM_018418.4	NP_060888.2	Q9P0W8	SPAT7_HUMAN	spermatogenesis associated 7	160					response to stimulus (GO:0050896)|visual perception (GO:0007601)					cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)	18						TACACCTAAGTCTACATAAAT	0.458																																					p.S160S		Atlas-SNP	.											.	SPATA7	58	.	0			c.T480C						.						80	71	74					14																	88892683		2203	4300	6503	SO:0001819	synonymous_variant	55812	exon6			CCTAAGTCTACAT	AF144487	CCDS9883.1, CCDS32132.1	14q31.3	2011-02-17				ENSG00000042317			20423	protein-coding gene	gene with protein product		609868	"Leber congenital amaurosis 3"	LCA3		9799089, 19268277	Standard	NM_018418		Approved	HSD3	uc001xwq.3	Q9P0W8		ENST00000393545.4:c.480T>C	chr14.hg19:g.88892683T>C		92.0	0.0		76.0	4.0	NM_018418	Q5BKY5|Q8WX30|Q96HF3|Q9H0X0|Q9P0W7	Silent	SNP	ENST00000393545.4	hg19	CCDS9883.1																																																																																			.	.		0.458	SPATA7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410172.1			C	88892683	T	C	88892683	2	2	255	1	0	0	0	0	0	0	0	1	15029	1664	58	2		2	SPATA7	14	88892683	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	11400766	88892683	18456857	517	35862										
TTC8	123016	hgsc.bcm.edu	37	chr14	89338781	89338781	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gctgtgctggagatgcggaaGggccacgttgaacaggtcag	17	8	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:89338781G>T	ENST00000345383.5	+	12	1386	c.1302G>T	c.(1300-1302)aaG>aaT	p.K434N	TTC8_ENST00000354441.6_Missense_Mutation_p.K179N|TTC8_ENST00000346301.4_Missense_Mutation_p.K404N|TTC8_ENST00000338104.6_Missense_Mutation_p.K460N|TTC8_ENST00000536576.1_Missense_Mutation_p.K205N|TTC8_ENST00000380656.2_Missense_Mutation_p.K444N|TTC8_ENST00000358622.5_Missense_Mutation_p.K246N	NM_198309.2	NP_938051.1	Q8TAM2	TTC8_HUMAN	tetratricopeptide repeat domain 8	470					axon guidance (GO:0007411)|camera-type eye photoreceptor cell differentiation (GO:0060219)|cilium assembly (GO:0042384)|establishment of anatomical structure orientation (GO:0048560)|fat cell differentiation (GO:0045444)|multicellular organism growth (GO:0035264)|nonmotile primary cilium assembly (GO:0035058)|olfactory bulb development (GO:0021772)|protein transport (GO:0015031)|regulation of protein localization (GO:0032880)|renal tubule development (GO:0061326)|sensory perception of smell (GO:0007608)|sensory processing (GO:0050893)	BBSome (GO:0034464)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)			endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|prostate(1)	15						AGATGCGGAAGGGCCACGTTG	0.527																																					p.K444N		Atlas-SNP	.											TTC8,colon,carcinoma,0,1	TTC8	42	.	0			c.G1332T						.						135	113	120					14																	89338781		2203	4300	6503	SO:0001583	missense	123016	exon13			GCGGAAGGGCCAC	AK093891	CCDS9885.1, CCDS9886.1, CCDS32137.1, CCDS73674.1, CCDS73675.1	14q31.3	2013-02-14				ENSG00000165533		"Tetratricopeptide (TTC) repeat domain containing"	20087	protein-coding gene	gene with protein product		608132				14520415, 20451172	Standard	NM_144596		Approved	BBS8, RP51	uc001xxi.3	Q8TAM2		ENST00000345383.5:c.1302G>T	chr14.hg19:g.89338781G>T	ENSP00000339486:p.Lys434Asn	89.0	0.0		48.0	3.0	NM_144596	A6NFG2|B3KWA5|Q67B97|Q86SY0|Q86TV9|Q86U26|Q8NDH9|Q96DG8	Missense_Mutation	SNP	ENST00000345383.5	hg19	CCDS9885.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	15.20|15.20|15.20	2.764018|2.764018|2.764018	0.49574|0.49574|0.49574	.|.|.	.|.|.	ENSG00000165533|ENSG00000165533|ENSG00000165533	ENST00000557580|ENST00000345383;ENST00000536576;ENST00000346301;ENST00000338104;ENST00000354441;ENST00000380656;ENST00000358622|ENST00000554686	.|T;T;T;T;T;T;T|.	.|0.59638|.	.|0.25;0.25;0.25;0.25;0.25;0.25;0.25|.	5.59|5.59|5.59	5.59|5.59|5.59	0.84812|0.84812|0.84812	.|Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);|.	.|0.091515|.	.|0.64402|.	.|D|.	.|0.000001|.	T|T|T	0.67382|0.67382|0.67382	0.2887|0.2887|0.2887	M|M|M	0.77820|0.77820|0.77820	2.39|2.39|2.39	0.58432|0.58432|0.58432	D|D|D	0.999997|0.999997|0.999997	.|B;B;B;B;B|.	.|0.32467|.	.|0.372;0.007;0.22;0.002;0.005|.	.|B;B;B;B;B|.	.|0.30716|.	.|0.065;0.031;0.119;0.012;0.018|.	T|T|T	0.68655|0.68655|0.68655	-0.5351|-0.5351|-0.5351	5|10|5	.|0.23302|.	.|T|.	.|0.38|.	-13.9832|-13.9832|-13.9832	7.6284|7.6284|7.6284	0.28226|0.28226|0.28226	0.1954:0.0:0.8046:0.0|0.1954:0.0:0.8046:0.0|0.1954:0.0:0.8046:0.0	.|.|.	.|179;205;470;414;444|.	.|Q8TAM2-2;B3KSL8;Q8TAM2;Q8TAM2-3;Q8TAM2-4|.	.|.;.;TTC8_HUMAN;.;.|.	W|N|M	233|434;205;404;460;179;444;246|394	.|ENSP00000339486:K434N;ENSP00000445067:K205N;ENSP00000298324:K404N;ENSP00000337653:K460N;ENSP00000346427:K179N;ENSP00000370031:K444N;ENSP00000351439:K246N|.	.|ENSP00000337653:K460N|.	G|K|R	+|+|+	1|3|2	0|2|0	TTC8|TTC8|TTC8	88408534|88408534|88408534	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.993000|0.993000|0.993000	0.82548|0.82548|0.82548	2.383000|2.383000|2.383000	0.44354|0.44354|0.44354	2.793000|2.793000|2.793000	0.96121|0.96121|0.96121	0.561000|0.561000|0.561000	0.74099|0.74099|0.74099	GGG|AAG|AGG	.	.		0.527	TTC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410861.1	NM_144596		T	89338781	G	T	89338781	3	4	255	1	0	0	0	0	1	0	0	0	16729	991	35	3	1382	3	TTC8	14	89338781	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	446098	89338781	18010759	518	35863										
TTC7B	145567	hgsc.bcm.edu	37	chr14	91142948	91142948	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	acagatgcactctgcagactGatgaggcggtcactcttgtg	12	10	3	4			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:91142948G>T	ENST00000328459.6	-	9	1192	c.1071C>A	c.(1069-1071)atC>atA	p.I357I	RP11-661G16.1_ENST00000554967.1_RNA|TTC7B_ENST00000357056.2_Silent_p.I357I	NM_001010854.1	NP_001010854.1	Q86TV6	TTC7B_HUMAN	tetratricopeptide repeat domain 7B	357										NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	36		Melanoma(154;0.222)				TCTGCAGACTGATGAGGCGGT	0.507																																					p.I357I		Atlas-SNP	.											.	TTC7B	93	.	0			c.C1071A						.						178	138	151					14																	91142948		2203	4300	6503	SO:0001819	synonymous_variant	145567	exon9			CAGACTGATGAGG	BC035865	CCDS32140.1	14q32.12	2013-01-11	2004-06-02	2004-06-04		ENSG00000165914		"Tetratricopeptide (TTC) repeat domain containing"	19858	protein-coding gene	gene with protein product			"tetratricopeptide repeat domain 7 like 1"	TTC7L1			Standard	XM_005267367		Approved		uc001xyp.3	Q86TV6		ENST00000328459.6:c.1071C>A	chr14.hg19:g.91142948G>T		129.0	0.0		75.0	4.0	NM_001010854	Q86U24|Q86VT3	Silent	SNP	ENST00000328459.6	hg19	CCDS32140.1	.	.	.	.	.	.	.	.	.	.	G	7.902	0.734532	0.15574	.	.	ENSG00000165914	ENST00000554462	.	.	.	5.15	4.25	0.50352	.	.	.	.	.	T	0.55986	0.1955	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52771	-0.8531	4	.	.	.	-18.8632	6.6615	0.23016	0.1513:0.1511:0.6975:0.0	.	.	.	.	K	27	.	.	Q	-	1	0	TTC7B	90212701	1.000000	0.71417	1.000000	0.80357	0.671000	0.39405	3.417000	0.52714	1.153000	0.42468	0.563000	0.77884	CAG	.	.		0.507	TTC7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411364.2			T	91142948	G	T	91142948	2	4	255	1	0	0	0	0	0	0	0	1	16728	1280	45	3		3	TTC7B	14	91142948	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	1804167	91142948	16206592	519	35864										
C14orf159	80017	hgsc.bcm.edu	37	chr14	91655256	91655256	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctatttttgtcatttcagggAaccgggggattgggcacctg	13	8	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:91655256A>G	ENST00000523771.1	+	9	1525	c.922A>G	c.(922-924)Aac>Gac	p.N308D	C14orf159_ENST00000428926.2_Missense_Mutation_p.N308D|C14orf159_ENST00000521077.2_Missense_Mutation_p.N313D|C14orf159_ENST00000523816.1_Missense_Mutation_p.N308D|C14orf159_ENST00000520328.1_Missense_Mutation_p.N296D|C14orf159_ENST00000412671.2_Missense_Mutation_p.N313D|C14orf159_ENST00000518868.1_Missense_Mutation_p.N313D|C14orf159_ENST00000256324.10_Missense_Mutation_p.N313D|C14orf159_ENST00000525393.2_Missense_Mutation_p.N184D|C14orf159_ENST00000522322.1_Missense_Mutation_p.N308D			Q7Z3D6	CN159_HUMAN	chromosome 14 open reading frame 159	308						mitochondrion (GO:0005739)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	21		all_cancers(154;0.0191)|all_epithelial(191;0.241)		Epithelial(152;0.141)|OV - Ovarian serous cystadenocarcinoma(161;0.207)		CATTTCAGGGAACCGGGGGAT	0.418																																					p.N313D		Atlas-SNP	.											.	C14orf159	57	.	0			c.A937G						.						34	31	32					14																	91655256		2203	4300	6503	SO:0001583	missense	80017	exon9			TCAGGGAACCGGG	AK097294	CCDS32141.1, CCDS41979.1, CCDS45150.1, CCDS66693.1, CCDS73677.1	14q32.11	2012-09-26			ENSG00000133943	ENSG00000133943			20498	protein-coding gene	gene with protein product							Standard	NM_001102367		Approved	FLJ39975	uc001xze.2	Q7Z3D6	OTTHUMG00000164980	ENST00000523771.1:c.922A>G	chr14.hg19:g.91655256A>G	ENSP00000429655:p.Asn308Asp	68.0	0.0		45.0	4.0	NM_001102368	B3KUI7|Q86SW3|Q86SX8|Q86SX9|Q86T08|Q86TV5|Q96GW5|Q9H7G0|Q9H8Y9|Q9H9W6	Missense_Mutation	SNP	ENST00000523771.1	hg19	CCDS32141.1	.	.	.	.	.	.	.	.	.	.	A	9.641	1.139046	0.21205	.	.	ENSG00000133943	ENST00000520328;ENST00000256324;ENST00000521077;ENST00000518868;ENST00000523816;ENST00000517518;ENST00000525393;ENST00000428926;ENST00000522322;ENST00000523771;ENST00000412671	T;T;T;T;T;T;T;T;T;T;T	0.18810	2.19;2.19;2.19;2.19;2.19;2.19;2.19;2.19;2.19;2.19;2.19	4.45	3.29	0.37713	.	0.397550	0.27991	N	0.017036	T	0.28267	0.0698	M	0.77103	2.36	0.09310	N	1	P;P;P;P;P;P	0.47484	0.77;0.58;0.896;0.728;0.728;0.728	B;B;P;B;B;B	0.46510	0.422;0.272;0.519;0.297;0.297;0.297	T	0.12268	-1.0554	10	0.39692	T	0.17	.	7.1423	0.25562	0.7619:0.1566:0.0815:0.0	.	308;184;313;296;313;313	Q7Z3D6;Q8NB88;B3KVU6;Q7Z3D6-5;Q7Z3D6-2;Q7Z3D6-3	CN159_HUMAN;.;.;.;.;.	D	296;313;313;313;308;313;184;308;308;308;313	ENSP00000429453:N296D;ENSP00000256324:N313D;ENSP00000430137:N313D;ENSP00000428263:N313D;ENSP00000428974:N308D;ENSP00000428652:N313D;ENSP00000435459:N184D;ENSP00000404343:N308D;ENSP00000427953:N308D;ENSP00000429655:N308D;ENSP00000404196:N313D	ENSP00000256324:N313D	N	+	1	0	C14orf159	90725009	0.002000	0.14202	0.004000	0.12327	0.022000	0.10575	0.554000	0.23407	0.562000	0.29204	0.533000	0.62120	AAC	.	.		0.418	C14orf159-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381273.1	NM_024952		G	91655256	A	G	91655256	3	3	255	1	0	0	0	0	1	0	0	0	1757	246	9	2	963	2	C14orf159	14	91655256	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	512308	91655256	15694284	520	35865										
GPR68	8111	hgsc.bcm.edu	37	chr14	91700731	91700731	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccgctggatctggtccttgcGgctcttctgggtgccgtggc	15	13	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:91700731G>A	ENST00000531499.2	-	2	1003	c.664C>T	c.(664-666)Cgc>Tgc	p.R222C	GPR68_ENST00000535815.1_Missense_Mutation_p.R222C|GPR68_ENST00000238699.3_Missense_Mutation_p.R232C|GPR68_ENST00000529300.1_5'Flank			Q15743	OGR1_HUMAN	G protein-coupled receptor 68	222					cellular response to pH (GO:0071467)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of osteoclast development (GO:2001206)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(2)|endometrium(1)|kidney(1)|lung(2)|skin(1)|urinary_tract(1)	8		all_cancers(154;0.0555)		COAD - Colon adenocarcinoma(157;0.21)		TGGTCCTTGCGGCTCTTCTGG	0.672																																					p.R222C		Atlas-SNP	.											GPR68,colon,carcinoma,0,1	GPR68	32	.	0			c.C664T						.						33	19	24					14																	91700731		2194	4286	6480	SO:0001583	missense	8111	exon2			CCTTGCGGCTCTT	U48405	CCDS9894.1, CCDS9894.2	14q31	2012-08-21				ENSG00000119714		"GPCR / Class A : Orphans"	4519	protein-coding gene	gene with protein product		601404				8661159	Standard	NM_001177676		Approved	OGR1	uc001xzg.3	Q15743		ENST00000531499.2:c.664C>T	chr14.hg19:g.91700731G>A	ENSP00000434045:p.Arg222Cys	55.0	0.0		27.0	2.0	NM_001177676	Q13334|Q4VBB4|Q6IX34	Missense_Mutation	SNP	ENST00000531499.2	hg19	CCDS9894.2	.	.	.	.	.	.	.	.	.	.	G	20.3	3.966791	0.74131	.	.	ENSG00000119714	ENST00000531499;ENST00000238699;ENST00000535815;ENST00000529102	T;T;T;T	0.73469	-0.75;-0.75;-0.75;-0.75	5.22	4.25	0.50352	GPCR, rhodopsin-like superfamily (1);	0.138533	0.46442	D	0.000295	T	0.77498	0.4139	L	0.38175	1.15	0.48236	D	0.999615	D;D	0.89917	1.0;1.0	D;D	0.66847	0.947;0.947	T	0.78753	-0.2081	10	0.72032	D	0.01	.	10.6504	0.45645	0.0:0.0:0.5656:0.4344	.	222;222	Q6NWR5;Q15743	.;OGR1_HUMAN	C	222;232;222;222	ENSP00000434045:R222C;ENSP00000238699:R232C;ENSP00000440797:R222C;ENSP00000432740:R222C	ENSP00000238699:R232C	R	-	1	0	GPR68	90770484	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.819000	0.62664	2.453000	0.82957	0.549000	0.68633	CGC	.	.		0.672	GPR68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395245.2			A	91700731	G	A	91700731	3	1	255	1	0	0	0	0	1	0	0	0	6715	1116	39	1	437	1	GPR68	14	91700731	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	45475	91700731	15648809	521	35866										
SMEK1	55671	hgsc.bcm.edu	37	chr14	91937188	91937188	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttctaacacttacataatgcCaagaaagcatgcttcgaggc	7	10	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:91937188C>A	ENST00000554943.1	-	10	1768	c.1653G>T	c.(1651-1653)ttG>ttT	p.L551F	SMEK1_ENST00000554684.1_Missense_Mutation_p.L538F|SMEK1_ENST00000555462.1_Missense_Mutation_p.L312F|SMEK1_ENST00000337238.4_Missense_Mutation_p.L538F|SMEK1_ENST00000428424.2_Missense_Mutation_p.L312F			Q6IN85	P4R3A_HUMAN	SMEK homolog 1, suppressor of mek1 (Dictyostelium)	551					positive regulation of gluconeogenesis (GO:0045722)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)				NS(1)|endometrium(1)|kidney(1)|liver(1)|lung(1)|stomach(1)	6		all_cancers(154;0.0691)|all_epithelial(191;0.219)		COAD - Colon adenocarcinoma(157;0.221)		TACATAATGCCAAGAAAGCAT	0.353																																					p.L538F		Atlas-SNP	.											.	SMEK1	94	.	0			c.G1614T						.						110	112	111					14																	91937188		2203	4300	6503	SO:0001583	missense	55671	exon11			TAATGCCAAGAAA	AK000714	CCDS9895.1, CCDS61532.1	14q32.12	2008-09-15	2006-10-12	2006-10-12		ENSG00000100796			20219	protein-coding gene	gene with protein product		610351	"KIAA2010"	KIAA2010		16085932, 18487071	Standard	XM_005267842		Approved	FLJ20707, MSTP033, FLFL1, smk-1, smk1	uc001xzm.3	Q6IN85		ENST00000554943.1:c.1653G>T	chr14.hg19:g.91937188C>A	ENSP00000450883:p.Leu551Phe	142.0	0.0		93.0	4.0	NM_032560	Q69YK6|Q86U23|Q86YI7|Q8IVG1|Q9H3F1|Q9H7U8|Q9NV01|Q9NWP1	Missense_Mutation	SNP	ENST00000554943.1	hg19		.	.	.	.	.	.	.	.	.	.	C	17.44	3.389892	0.61956	.	.	ENSG00000100796	ENST00000554684;ENST00000337238;ENST00000428424;ENST00000554943;ENST00000555462;ENST00000554390	T;T;T;T;T;T	0.58358	0.34;0.34;0.34;0.34;0.34;0.34	5.8	3.92	0.45320	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.72342	0.3448	M	0.89601	3.045	0.80722	D	1	D;D;D	0.89917	0.997;1.0;1.0	D;D;D	0.87578	0.986;0.99;0.998	T	0.71948	-0.4438	10	0.72032	D	0.01	-9.0136	4.8908	0.13726	0.1475:0.6134:0.0:0.2391	.	312;551;538	Q6IN85-4;Q6IN85;Q6IN85-2	.;P4R3A_HUMAN;.	F	538;538;312;551;312;538	ENSP00000450864:L538F;ENSP00000337125:L538F;ENSP00000392704:L312F;ENSP00000450883:L551F;ENSP00000450891:L312F;ENSP00000452596:L538F	ENSP00000337125:L538F	L	-	3	2	SMEK1	91006941	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	0.843000	0.27640	0.729000	0.32403	0.650000	0.86243	TTG	.	.		0.353	SMEK1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000411665.1	NM_032560		A	91937188	C	A	91937188	3	1	255	1	0	0	0	0	1	0	0	0	14808	593	21	3	872	3	SMEK1	14	91937188	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	236457	91937188	15412352	522	35867										
TC2N	123036	hgsc.bcm.edu	37	chr14	92258866	92258866	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agtttgtagattttgaagttTaatagcaaatacaaacgttt	7	3	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:92258866T>A	ENST00000435962.2	-	9	1215	c.892A>T	c.(892-894)Aaa>Taa	p.K298*	TC2N_ENST00000340892.5_Nonsense_Mutation_p.K298*|TC2N_ENST00000360594.5_Nonsense_Mutation_p.K298*|TC2N_ENST00000556018.1_Intron	NM_001128596.1	NP_001122068	Q8N9U0	TAC2N_HUMAN	tandem C2 domains, nuclear	298					regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(5)|skin(1)|upper_aerodigestive_tract(2)	18				COAD - Colon adenocarcinoma(157;0.218)		TTTTGAAGTTTAATAGCAAAT	0.294																																					p.K298X		Atlas-SNP	.											.	TC2N	49	.	0			c.A892T						.						87	86	86					14																	92258866		2203	4300	6503	SO:0001587	stop_gained	123036	exon9			GAAGTTTAATAGC	AA243837	CCDS9897.1, CCDS73679.1	14q32.12	2007-10-17	2007-08-17	2007-08-17		ENSG00000165929			19859	protein-coding gene	gene with protein product	"C2 calcium-dependent domain containing 1"		"chromosome 14 open reading frame 47", "membrane targeting (tandem) C2 domain containing 1"	C14orf47, MTAC2D1		11526914	Standard	NM_001128596		Approved	FLJ36557, Tac2-N, C2CD1	uc001xzt.4	Q8N9U0		ENST00000435962.2:c.892A>T	chr14.hg19:g.92258866T>A	ENSP00000387882:p.Lys298*	108.0	0.0		81.0	4.0	NM_001128596		Nonsense_Mutation	SNP	ENST00000435962.2	hg19	CCDS9897.1	.	.	.	.	.	.	.	.	.	.	T	34	5.397552	0.96009	.	.	ENSG00000165929	ENST00000435962;ENST00000340892;ENST00000360594;ENST00000556590	.	.	.	5.65	5.65	0.86999	.	0.194116	0.53938	D	0.000054	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-28.4697	15.87	0.79108	0.0:0.0:0.0:1.0	.	.	.	.	X	298;298;298;50	.	ENSP00000343199:K298X	K	-	1	0	TC2N	91328619	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	6.360000	0.73064	2.137000	0.66172	0.455000	0.32223	AAA	.	.		0.294	TC2N-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411778.1	NM_152332		A	92258866	T	A	92258866	4	1	255	1	0	0	0	0	0	1	0	0	15680	1763	61	4	596	4	TC2N	14	92258866	Nonsense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	321678	92258866	15090674	523	35868										
KIAA1409	57578	hgsc.bcm.edu	37	chr14	94088153	94088153	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	taggaagtcgtgcatagatcGgtgtgacatagagaagcctc	13	7	0	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:94088153G>T	ENST00000393151.2	+	30	4574	c.4574G>T	c.(4573-4575)cGg>cTg	p.R1525L	UNC79_ENST00000555664.1_Missense_Mutation_p.R1525L|UNC79_ENST00000256339.4_Missense_Mutation_p.R1348L|UNC79_ENST00000553484.1_Missense_Mutation_p.R1547L			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	1525					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						TGCATAGATCGGTGTGACATA	0.453																																					p.R1348L		Atlas-SNP	.											UNC79,NS,carcinoma,+1,2	UNC79	366	.	0			c.G4043T						.						95	89	91					14																	94088153		2203	4300	6503	SO:0001583	missense	57578	exon30			TAGATCGGTGTGA	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"KIAA1409"	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.4574G>T	chr14.hg19:g.94088153G>T	ENSP00000376858:p.Arg1525Leu	139.0	0.0		75.0	3.0	NM_020818	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	hg19		.	.	.	.	.	.	.	.	.	.	G	15.70	2.912066	0.52439	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.24538	1.88;1.85;1.88;1.88	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	T	0.22205	0.0535	L	0.32530	0.975	0.49915	D	0.999838	P	0.40302	0.712	B	0.37731	0.257	T	0.01290	-1.1394	10	0.54805	T	0.06	-20.337	14.5913	0.68368	0.0694:0.0:0.9306:0.0	.	1547	C9JQL1	.	L	1348;1525;1547;1525;1547	ENSP00000256339:R1348L;ENSP00000450868:R1525L;ENSP00000451360:R1547L;ENSP00000376858:R1525L	ENSP00000256339:R1348L	R	+	2	0	KIAA1409	93157906	1.000000	0.71417	0.991000	0.47740	0.849000	0.48306	6.424000	0.73366	2.847000	0.97988	0.591000	0.81541	CGG	.	.		0.453	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		T	94088153	G	T	94088153	3	4	255	1	0	0	0	0	1	0	0	0	8239	1116	39	1	4149	1	KIAA1409	14	94088153	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	1829287	94088153	13261387	524	35869										
IFI27L1	122509	hgsc.bcm.edu	37	chr14	94568841	94568841	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aggggcagctggactctctgTgacatctaaagttatcgggg	14	8	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:94568841T>C	ENST00000555523.1	+	5	461	c.242T>C	c.(241-243)gTg>gCg	p.V81A	IFI27L1_ENST00000554562.1_3'UTR|IFI27L1_ENST00000556381.1_3'UTR|IFI27L1_ENST00000557218.1_Missense_Mutation_p.V27A|IFI27L1_ENST00000557066.1_Missense_Mutation_p.V27A|IFI27L1_ENST00000554544.1_Missense_Mutation_p.V16A|IFI27L1_ENST00000393115.3_Missense_Mutation_p.V81A|IFI27L1_ENST00000553664.1_Silent_p.C103C|IFI27L1_ENST00000553350.1_Intron	NM_206949.2	NP_996832.1	Q96BM0	I27L1_HUMAN	interferon, alpha-inducible protein 27-like 1	81						integral component of membrane (GO:0016021)				lung(2)	2						GGACTCTCTGTGACATCTAAA	0.612																																					p.V81A		Atlas-SNP	.											.	IFI27L1	11	.	0			c.T242C						.						62	58	60					14																	94568841		2203	4300	6503	SO:0001583	missense	122509	exon5			TCTCTGTGACATC	BC015423	CCDS9919.1	14q32.13	2008-10-08	2008-10-08	2008-10-08		ENSG00000165948			19754	protein-coding gene	gene with protein product		611320	"family with sequence similarity 14, member B"	FAM14B			Standard	NM_145249		Approved		uc001yck.3	Q96BM0		ENST00000555523.1:c.242T>C	chr14.hg19:g.94568841T>C	ENSP00000451851:p.Val81Ala	136.0	0.0		83.0	4.0	NM_145249		Missense_Mutation	SNP	ENST00000555523.1	hg19	CCDS9919.1	.	.	.	.	.	.	.	.	.	.	t	8.223	0.802934	0.16397	.	.	ENSG00000165948	ENST00000555523;ENST00000393115;ENST00000554166;ENST00000555341;ENST00000557218;ENST00000554544;ENST00000557066	T;T;T;T	0.28454	1.61;1.61;1.61;1.61	3.27	-3.93	0.04143	.	1.300780	0.06118	U	0.668363	T	0.18341	0.0440	N	0.17474	0.49	0.09310	N	1	B	0.11235	0.004	B	0.09377	0.004	T	0.29336	-1.0015	10	0.32370	T	0.25	.	10.7815	0.46379	0.0:0.6969:0.0:0.3031	.	81	Q96BM0	I27L1_HUMAN	A	81;81;80;80;27;16;27	ENSP00000451851:V81A;ENSP00000376824:V81A;ENSP00000452226:V80A;ENSP00000451608:V80A	ENSP00000376824:V81A	V	+	2	0	IFI27L1	93638594	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.504000	0.00449	-0.877000	0.04012	-0.332000	0.08345	GTG	.	.		0.612	IFI27L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412868.1	NM_206949		C	94568841	T	C	94568841	3	2	255	1	0	0	0	0	1	0	0	0	7522	1696	59	2	256	2	IFI27L1	14	94568841	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	480688	94568841	12780699	525	35870										
ATG2B	55102	hgsc.bcm.edu	37	chr14	96781572	96781572	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cctacggcaatgagaaattcCtatacagaacaagacaaaga	7	9	0	4			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:96781572C>A	ENST00000359933.4	-	23	4455		c.e23-1			NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B						autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		TGAGAAATTCCTATACAGAAC	0.368																																					.		Atlas-SNP	.											.	ATG2B	169	.	0			c.3562-1G>T						.						32	31	31					14																	96781572		2203	4300	6503	SO:0001630	splice_region_variant	55102	exon24			AAATTCCTATACA	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 103", "ATG2 autophagy related 2 homolog B (S. cerevisiae)"	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.3562-1G>T	chr14.hg19:g.96781572C>A		205.0	0.0		98.0	4.0	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Splice_Site	SNP	ENST00000359933.4	hg19	CCDS9944.2	.	.	.	.	.	.	.	.	.	.	C	21.3	4.127594	0.77549	.	.	ENSG00000066739	ENST00000359933	.	.	.	5.46	5.46	0.80206	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.6732	0.95918	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ATG2B	95851325	1.000000	0.71417	0.997000	0.53966	0.773000	0.43773	6.915000	0.75770	2.730000	0.93505	0.591000	0.81541	.	.	.		0.368	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036	Intron	A	96781572	C	A	96781572	5	1	255	1	0	0	0	0	0	0	1	0	1094	695	24	3	2755	3	ATG2B	14	96781572	Splice_Site	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	2212731	96781572	10567968	526	35871										
SETD3	84193	hgsc.bcm.edu	37	chr14	99927679	99927679	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcaaaagtaacggacagaccTatattaatccacgttttaga	6	8	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:99927679T>C	ENST00000331768.5	-	4	356		c.e4-2		SETD3_ENST00000329331.3_Splice_Site|SETD3_ENST00000453938.1_Intron|SETD3_ENST00000436070.2_Splice_Site	NM_032233.2	NP_115609.2	Q86TU7	SETD3_HUMAN	SET domain containing 3						histone H3-K36 methylation (GO:0010452)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)|peptidyl-lysine trimethylation (GO:0018023)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(1)|skin(1)	25		all_cancers(154;0.224)|all_epithelial(191;0.0644)|Melanoma(154;0.0866)				CGGACAGACCTATATTAATCC	0.373																																					.		Atlas-SNP	.											.	SETD3	56	.	0			c.197-2A>G						.						77	78	78					14																	99927679		2203	4299	6502	SO:0001630	splice_region_variant	84193	exon5			CAGACCTATATTA	AK026680	CCDS9951.1, CCDS9952.1	14q32.2	2006-02-15	2006-02-15	2006-02-15	ENSG00000183576	ENSG00000183576			20493	protein-coding gene	gene with protein product		615671	"chromosome 14 open reading frame 154"	C14orf154			Standard	NM_032233		Approved	FLJ23027	uc001ygc.3	Q86TU7	OTTHUMG00000028970	ENST00000331768.5:c.197-2A>G	chr14.hg19:g.99927679T>C		73.0	0.0		49.0	4.0	NM_032233	A0PJU3|A5PLP0|B4DZE8|Q0VAQ2|Q659C0|Q86TU8|Q96GY9|Q9H5U5	Splice_Site	SNP	ENST00000331768.5	hg19	CCDS9951.1	.	.	.	.	.	.	.	.	.	.	T	17.69	3.451830	0.63290	.	.	ENSG00000183576	ENST00000331768;ENST00000329331;ENST00000436070	.	.	.	5.45	5.45	0.79879	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.8249	0.78690	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	SETD3	98997432	1.000000	0.71417	0.945000	0.38365	0.664000	0.39144	7.965000	0.87945	2.194000	0.70268	0.533000	0.62120	.	.	.		0.373	SETD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072339.3	NM_032233	Intron	C	99927679	T	C	99927679	5	2	255	1	0	0	0	0	0	0	1	0	14147	1536	53	2	1675	2	SETD3	14	99927679	Splice_Site	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	3146107	99927679	7421861	527	35872										
RTL1	388015	hgsc.bcm.edu	37	chr14	101351053	101351053	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gttggatgagccctcggaggActccatttgttttgatgatg	13	7	0	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:101351053A>G	ENST00000534062.1	-	1	131	c.73T>C	c.(73-75)Tcc>Ccc	p.S25P	MIR127_ENST00000384876.1_RNA|MIR433_ENST00000384837.1_RNA|MIR136_ENST00000385207.1_RNA|MIR432_ENST00000606207.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	25					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)				breast(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(5)|pancreas(1)|prostate(2)|skin(2)	21						CCCTCGGAGGACTCCATTTGT	0.552																																					p.S25P		Atlas-SNP	.											.	RTL1	120	.	0			c.T73C						.						35	34	34					14																	101351053		1568	3582	5150	SO:0001583	missense	388015	exon1			CGGAGGACTCCAT		CCDS53910.1	14q32.2	2012-04-18			ENSG00000254656	ENSG00000254656			14665	protein-coding gene	gene with protein product		611896				16155747, 15854907, 12796779	Standard	NM_001134888		Approved	PEG11, MART1, Mar1	uc010txj.1	A6NKG5	OTTHUMG00000167573	ENST00000534062.1:c.73T>C	chr14.hg19:g.101351053A>G	ENSP00000435342:p.Ser25Pro	76.0	0.0		68.0	4.0	NM_001134888	E9PKS8	Missense_Mutation	SNP	ENST00000534062.1	hg19	CCDS53910.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.947356	0.73672	.	.	ENSG00000254656	ENST00000534062	T	0.34072	1.38	3.48	3.48	0.39840	.	.	.	.	.	T	0.42630	0.1211	N	0.24115	0.695	0.27226	N	0.959524	D	0.71674	0.998	D	0.77557	0.99	T	0.15896	-1.0421	9	0.66056	D	0.02	.	8.659	0.34081	1.0:0.0:0.0:0.0	.	25	E9PKS8	.	P	25	ENSP00000435342:S25P	ENSP00000435342:S25P	S	-	1	0	RTL1	100420806	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.308000	0.43690	1.819000	0.53055	0.459000	0.35465	TCC	.	.		0.552	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888		G	101351053	A	G	101351053	3	3	255	1	0	0	0	0	1	0	0	0	13739	275	10	2	4007	2	RTL1	14	101351053	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	1423374	101351053	5998487	528	35873										
TUBGCP5	114791	hgsc.bcm.edu	37	chr15	22846911	22846911	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttgtatgttccagatgacagGgttttggttactgagactca	11	6	1	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:22846911G>T	ENST00000283645.4	+	8	916	c.786G>T	c.(784-786)agG>agT	p.R262S	TUBGCP5_ENST00000453949.2_Missense_Mutation_p.R262S	NM_052903.4	NP_443135.3	Q96RT8	GCP5_HUMAN	tubulin, gamma complex associated protein 5	262					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gamma-tubulin ring complex (GO:0008274)|microtubule (GO:0005874)|nucleus (GO:0005634)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)	p.R262S(1)		breast(5)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(23)|prostate(1)|skin(2)|urinary_tract(1)	46		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.86e-06)|Epithelial(43;2.63e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000949)		CAGATGACAGGGTTTTGGTTA	0.353																																					p.R262S		Atlas-SNP	.											TUBGCP5,NS,carcinoma,0,1	TUBGCP5	82	.	1	Substitution - Missense(1)	kidney(1)	c.G786T						.						145	125	132					15																	22846911		2203	4300	6503	SO:0001583	missense	114791	exon8			TGACAGGGTTTTG	AB067486	CCDS73697.1, CCDS73698.1	15q11.1	2014-04-17			ENSG00000153575	ENSG00000275835			18600	protein-coding gene	gene with protein product	"gamma-tubulin complex component GCP5"	608147				11694571	Standard	NM_052903		Approved	GCP5, KIAA1899	uc001yur.4	Q96RT8	OTTHUMG00000188371	ENST00000283645.4:c.786G>T	chr15.hg19:g.22846911G>T	ENSP00000283645:p.Arg262Ser	127.0	0.0		99.0	4.0	NM_052903	E9PB12|Q6IQ52|Q96PY8	Missense_Mutation	SNP	ENST00000283645.4	hg19	CCDS10008.1	.	.	.	.	.	.	.	.	.	.	.	11.95	1.791713	0.31685	.	.	ENSG00000153575	ENST00000283645;ENST00000453949	T;T	0.23754	1.89;1.89	4.93	-6.3	0.02007	.	0.108809	0.64402	N	0.000009	T	0.09992	0.0245	L	0.27053	0.805	0.23391	N	0.99777	B;B	0.33583	0.418;0.418	B;B	0.21151	0.033;0.033	T	0.32508	-0.9904	10	0.14656	T	0.56	-14.6251	10.5009	0.44804	0.5496:0.087:0.3634:0.0	.	262;262	Q96RT8;E9PB12	GCP5_HUMAN;.	S	262	ENSP00000283645:R262S;ENSP00000409217:R262S	ENSP00000283645:R262S	R	+	3	2	TUBGCP5	20398352	0.994000	0.37717	0.052000	0.19188	0.967000	0.64934	0.506000	0.22658	-1.218000	0.02601	-0.880000	0.02959	AGG	.	.		0.353	TUBGCP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250998.2	NM_052903		T	22846911	G	T	22846911	3	4	255	1	0	0	0	0	1	0	0	0	16784	1223	43	3	816	3	TUBGCP5	15	22846911	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10		22846911	79684481	529	35874										
RYR3	6263	hgsc.bcm.edu	37	chr15	33855061	33855061	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctcaaggagaaattagactcCagtcacaagcgagacataga	9	9	2	4			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:33855061C>A	ENST00000389232.4	+	11	1066	c.996C>A	c.(994-996)tcC>tcA	p.S332S	RYR3_ENST00000415757.3_Silent_p.S332S	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	332	MIR 4. {ECO:0000255|PROSITE- ProRule:PRU00131}.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			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)		AATTAGACTCCAGTCACAAGC	0.403																																					p.S332S		Atlas-SNP	.											.	RYR3	760	.	0			c.C996A						.						69	68	68					15																	33855061		1867	4108	5975	SO:0001819	synonymous_variant	6263	exon11			AGACTCCAGTCAC		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.996C>A	chr15.hg19:g.33855061C>A		127.0	0.0		100.0	4.0	NM_001243996	O15175|Q15412	Silent	SNP	ENST00000389232.4	hg19	CCDS45210.1																																																																																			.	.		0.403	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			A	33855061	C	A	33855061	2	1	255	1	0	0	0	0	0	0	0	1	13785	581	21	3		3	RYR3	15	33855061	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	11008150	33855061	68676331	530	35875										
SLC12A6	9990	hgsc.bcm.edu	37	chr15	34547524	34547524	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	caaatgtggtaccaagataaAagcagaggccaacagcccca	9	11	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:34547524A>G	ENST00000354181.3	-	8	1307	c.815T>C	c.(814-816)tTt>tCt	p.F272S	SLC12A6_ENST00000560164.1_Missense_Mutation_p.F84S|SLC12A6_ENST00000558589.1_Missense_Mutation_p.F263S|SLC12A6_ENST00000558667.1_Missense_Mutation_p.F272S|RP11-1084A12.2_ENST00000559867.1_RNA|SLC12A6_ENST00000290209.5_Missense_Mutation_p.F221S|SLC12A6_ENST00000397702.2_Missense_Mutation_p.F213S|SLC12A6_ENST00000560611.1_Missense_Mutation_p.F272S|SLC12A6_ENST00000458406.2_Missense_Mutation_p.F213S|SLC12A6_ENST00000451844.2_Missense_Mutation_p.F84S|SLC12A6_ENST00000397707.2_Missense_Mutation_p.F257S			Q9UHW9	S12A6_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 6	272					angiogenesis (GO:0001525)|cellular hypotonic response (GO:0071476)|cellular hypotonic salinity response (GO:0071477)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|rubidium ion transport (GO:0035826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium ion transmembrane transporter activity (GO:0015079)|potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)|rubidium ion transmembrane transporter activity (GO:0035827)			central_nervous_system(5)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|skin(3)	45		all_lung(180;2.78e-08)		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	Potassium Chloride(DB00761)	ACCAAGATAAAAGCAGAGGCC	0.438																																					p.F272S		Atlas-SNP	.											.	SLC12A6	205	.	0			c.T815C						.						90	93	92					15																	34547524		2201	4298	6499	SO:0001583	missense	9990	exon7			AGATAAAAGCAGA	AF108831	CCDS10036.1, CCDS42010.1, CCDS42011.1, CCDS42012.1, CCDS58352.1	15q13	2014-09-17	2013-07-18		ENSG00000140199	ENSG00000140199		"Solute carriers"	10914	protein-coding gene	gene with protein product		604878	"agenesis of corpus callosum and peripheral neuropathy (Andermann syndrome)"	KCC3, ACCPN		10187864, 10347194	Standard	NM_133647		Approved		uc001zhw.3	Q9UHW9	OTTHUMG00000129441	ENST00000354181.3:c.815T>C	chr15.hg19:g.34547524A>G	ENSP00000346112:p.Phe272Ser	91.0	0.0		69.0	5.0	NM_133647	A0AV76|Q2VI00|Q7Z2E7|Q7Z4G5|Q8TDD4|Q9UFR2|Q9Y642|Q9Y665	Missense_Mutation	SNP	ENST00000354181.3	hg19	CCDS58352.1	.	.	.	.	.	.	.	.	.	.	A	27.3	4.822965	0.90873	.	.	ENSG00000140199	ENST00000290209;ENST00000397707;ENST00000354181;ENST00000397702;ENST00000458406;ENST00000451844	D;D;D;D;D	0.88975	-2.42;-2.45;-2.44;-2.44;-1.98	5.43	5.43	0.79202	Amino acid permease domain (1);	0.114524	0.64402	D	0.000015	D	0.96750	0.8939	H	0.98333	4.205	0.80722	D	1	D;D;D;D	0.89917	0.997;1.0;1.0;1.0	D;D;D;D	0.87578	0.928;0.998;0.973;0.995	D	0.98152	1.0442	10	0.87932	D	0	.	14.5986	0.68424	1.0:0.0:0.0:0.0	.	257;272;221;84	Q9UHW9-3;Q9UHW9;A0AV76;B3KXX3	.;S12A6_HUMAN;.;.	S	221;257;263;213;213;84	ENSP00000290209:F221S;ENSP00000380819:F257S;ENSP00000380814:F213S;ENSP00000387725:F213S;ENSP00000390199:F84S	ENSP00000290209:F221S	F	-	2	0	SLC12A6	32334816	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.139000	0.94554	2.279000	0.76181	0.533000	0.62120	TTT	.	.		0.438	SLC12A6-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000417991.1	NM_005135		G	34547524	A	G	34547524	3	3	255	1	0	0	0	0	1	0	0	0	14402	14	1	2	2713	2	SLC12A6	15	34547524	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	692463	34547524	67983868	531	35876										
THBS1	7057	hgsc.bcm.edu	37	chr15	39886569	39886569	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tctatgataaaacctatgctGgtggtagactagggttgttt	11	5	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:39886569G>T	ENST00000260356.5	+	21	3598	c.3433G>T	c.(3433-3435)Ggt>Tgt	p.G1145C	CTD-2033D15.1_ENST00000560769.1_RNA	NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	1145	TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		AACCTATGCTGGTGGTAGACT	0.403																																					p.G1145C		Atlas-SNP	.											.	THBS1	106	.	0			c.G3433T						.						154	145	148					15																	39886569		2200	4297	6497	SO:0001583	missense	7057	exon21			TATGCTGGTGGTA		CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"thrombospondin-1p180"	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.3433G>T	chr15.hg19:g.39886569G>T	ENSP00000260356:p.Gly1145Cys	106.0	0.0		98.0	4.0	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Missense_Mutation	SNP	ENST00000260356.5	hg19	CCDS32194.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.986764	0.93106	.	.	ENSG00000137801	ENST00000260356	D	0.98060	-4.69	5.44	5.44	0.79542	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Thrombospondin, C-terminal (2);	0.000000	0.35320	N	0.003294	D	0.98953	0.9644	M	0.89214	3.015	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99659	1.0993	10	0.87932	D	0	-23.7926	19.6125	0.95613	0.0:0.0:1.0:0.0	.	1060;1145	B4E3J7;P07996	.;TSP1_HUMAN	C	1145	ENSP00000260356:G1145C	ENSP00000260356:G1145C	G	+	1	0	THBS1	37673861	1.000000	0.71417	0.989000	0.46669	0.985000	0.73830	9.813000	0.99286	2.698000	0.92095	0.591000	0.81541	GGT	.	.		0.403	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246		T	39886569	G	T	39886569	3	4	255	1	0	0	0	0	1	0	0	0	15868	1348	47	3	3511	3	THBS1	15	39886569	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	5339045	39886569	62644823	532	35877										
PLCB2	5330	hgsc.bcm.edu	37	chr15	40588496	40588496	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aagttactcatgctaacttaCgggcagagaactcaaaggag	10	8	2	1	rs377366618		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:40588496C>T	ENST00000260402.3	-	16	1946		c.e16+1		PLCB2_ENST00000456256.2_Splice_Site|PLCB2_ENST00000557821.1_Splice_Site	NM_001284297.1|NM_004573.2	NP_001271226.1|NP_004564.2	Q00722	PLCB2_HUMAN	phospholipase C, beta 2						activation of phospholipase C activity (GO:0007202)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|sensory perception of bitter taste (GO:0050913)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)	p.?(2)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(3)	39		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0508)		TGCTAACTTACGGGCAGAGAA	0.537																																					.		Atlas-SNP	.											PLCB2_ENST00000260402,NS,carcinoma,0,2	PLCB2	177	.	2	Unknown(2)	lung(2)	c.1696+1G>A						.	C		0,3848		0,0,1924	49	49	49			4.2	1	15		49	1,8259		0,1,4129	no	splice-5	PLCB2	NM_004573.2		0,1,6053	TT,TC,CC		0.0121,0.0,0.0083			40588496	1,12107	1924	4130	6054	SO:0001630	splice_region_variant	5330	exon17			AACTTACGGGCAG		CCDS42020.1, CCDS61591.1, CCDS61592.1, CCDS73704.1	15q15.1	2012-01-23			ENSG00000137841	ENSG00000137841	3.1.4.11		9055	protein-coding gene	gene with protein product		604114				1644792, 9925923	Standard	XM_005254448		Approved	FLJ38135	uc001zld.3	Q00722	OTTHUMG00000172412	ENST00000260402.3:c.1696+1G>A	chr15.hg19:g.40588496C>T		69.0	0.0		41.0	2.0	NM_004573	A8K6J2|B9EGH5	Splice_Site	SNP	ENST00000260402.3	hg19	CCDS42020.1	.	.	.	.	.	.	.	.	.	.	C	16.31	3.087138	0.55968	0.0	1.21E-4	ENSG00000137841	ENST00000260402;ENST00000456256	.	.	.	4.25	4.25	0.50352	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.8043	0.46507	0.0:0.9123:0.0:0.0877	.	.	.	.	.	-1	.	.	.	-	.	.	PLCB2	38375788	1.000000	0.71417	0.997000	0.53966	0.769000	0.43574	6.525000	0.73795	2.379000	0.81126	0.561000	0.74099	.	.	.		0.537	PLCB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418430.1		Intron	T	40588496	C	T	40588496	5	4	255	1	0	0	0	0	0	0	1	0	12037	550	19	1	1928	1	PLCB2	15	40588496	Splice_Site	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	701927	40588496	61942896	533	35878										
NDUFAF1	51103	hgsc.bcm.edu	37	chr15	41689120	41689120	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctctgtgaggaggctttgccAggagaagccactggtttctg	14	9	2	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:41689120A>G	ENST00000260361.4	-	2	519	c.138T>C	c.(136-138)ccT>ccC	p.P46P		NM_016013.3	NP_057097.2	Q9Y375	CIA30_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 1	46					mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|mitochondrial respiratory chain complex I (GO:0005747)	unfolded protein binding (GO:0051082)			endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	12		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;8e-17)|GBM - Glioblastoma multiforme(113;1.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.114)		AGGCTTTGCCAGGAGAAGCCA	0.443																																					p.P46P		Atlas-SNP	.											.	NDUFAF1	39	.	0			c.T138C						.						60	63	62					15																	41689120		2203	4300	6503	SO:0001819	synonymous_variant	51103	exon2			TTTGCCAGGAGAA	AF151823	CCDS10075.1	15q11.2-q21.3	2012-10-12	2012-05-08		ENSG00000137806	ENSG00000137806		"Mitochondrial respiratory chain complex assembly factors"	18828	protein-coding gene	gene with protein product		606934				11935339, 10810093	Standard	NM_016013		Approved	CIA30, CGI-65	uc001znx.3	Q9Y375	OTTHUMG00000130340	ENST00000260361.4:c.138T>C	chr15.hg19:g.41689120A>G		188.0	0.0		100.0	4.0	NM_016013	Q9BVZ5	Silent	SNP	ENST00000260361.4	hg19	CCDS10075.1																																																																																			.	.		0.443	NDUFAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252692.2	NM_016013		G	41689120	A	G	41689120	2	3	255	1	0	0	0	0	0	0	0	1	10283	175	7	2		2	NDUFAF1	15	41689120	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	1100624	41689120	60842272	534	35879										
PLA2G4D	283748	hgsc.bcm.edu	37	chr15	42364008	42364008	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccggggctccgggatcctccTcatcagccgtcccatgaaga	11	16	2	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:42364008T>C	ENST00000290472.3	-	15	1631	c.1537A>G	c.(1537-1539)Agg>Ggg	p.R513G		NM_178034.3	NP_828848.3	Q86XP0	PA24D_HUMAN	phospholipase A2, group IVD (cytosolic)	513	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)	p.R513G(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(7)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(109;6.37e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.019)|Ovarian(310;0.143)|Colorectal(260;0.245)		OV - Ovarian serous cystadenocarcinoma(18;4.9e-17)|GBM - Glioblastoma multiforme(94;1.02e-06)		GGGATCCTCCTCATCAGCCGT	0.617																																					p.R513G		Atlas-SNP	.											PLA2G4D,caecum,carcinoma,0,1	PLA2G4D	72	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1537G						.						49	53	52					15																	42364008		2203	4299	6502	SO:0001583	missense	283748	exon15			TCCTCCTCATCAG	AB090876	CCDS32203.1	15q14	2008-09-19				ENSG00000159337	3.1.1.4		30038	protein-coding gene	gene with protein product		612864				14709560	Standard	NM_178034		Approved	cPLA2delta	uc001zox.3	Q86XP0		ENST00000290472.3:c.1537A>G	chr15.hg19:g.42364008T>C	ENSP00000290472:p.Arg513Gly	117.0	1.0		88.0	4.0	NM_178034	Q8N176	Missense_Mutation	SNP	ENST00000290472.3	hg19	CCDS32203.1	.	.	.	.	.	.	.	.	.	.	T	16.91	3.252913	0.59212	.	.	ENSG00000159337	ENST00000290472	T	0.04194	3.68	4.79	4.79	0.61399	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	0.374808	0.23768	N	0.044741	T	0.07188	0.0182	L	0.34521	1.04	0.36349	D	0.859993	P	0.47484	0.896	P	0.46172	0.506	T	0.31641	-0.9936	10	0.59425	D	0.04	-7.4413	14.0078	0.64475	0.0:0.0:0.0:1.0	.	513	Q86XP0	PA24D_HUMAN	G	513	ENSP00000290472:R513G	ENSP00000290472:R513G	R	-	1	2	PLA2G4D	40151300	1.000000	0.71417	0.950000	0.38849	0.231000	0.25187	2.538000	0.45710	1.798000	0.52647	0.459000	0.35465	AGG	.	.		0.617	PLA2G4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419317.1	NM_178034		C	42364008	T	C	42364008	3	2	255	1	0	0	0	0	1	0	0	0	12013	1550	54	2	943	2	PLA2G4D	15	42364008	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	674888	42364008	60167384	535	35880										
TRIM69	140691	hgsc.bcm.edu	37	chr15	45051022	45051022	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gtgagcattcaggcaaagacGgaacaacagaactccttcga	10	10	1	3	rs148920822		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:45051022G>T	ENST00000559390.1	+	5	1711	c.783G>T	c.(781-783)acG>acT	p.T261T	TRIM69_ENST00000560442.1_Silent_p.T57T|TRIM69_ENST00000338264.4_Silent_p.T102T|TRIM69_ENST00000558173.1_Silent_p.T57T|TRIM69_ENST00000558329.1_Intron|TRIM69_ENST00000561043.1_Intron|TRIM69_ENST00000329464.4_Silent_p.T261T			Q86WT6	TRI69_HUMAN	tripartite motif containing 69	261					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.T261T(1)		cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(9)|skin(1)	20		all_cancers(109;2.47e-13)|all_epithelial(112;2.84e-11)|Lung NSC(122;2.23e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;5.5e-19)|GBM - Glioblastoma multiforme(94;1.07e-06)|Colorectal(105;0.138)|COAD - Colon adenocarcinoma(120;0.141)		AGGCAAAGACGGAACAACAGA	0.463																																					p.T261T	Pancreas(84;519 1450 1802 20427 34706)	Atlas-SNP	.											TRIM69,NS,carcinoma,0,1	TRIM69	47	.	1	Substitution - coding silent(1)	endometrium(1)	c.G783T						.						71	60	63					15																	45051022		2198	4298	6496	SO:0001819	synonymous_variant	140691	exon4			AAAGACGGAACAA	AF302088	CCDS10114.1, CCDS32220.1, CCDS73719.1	15q15-q21	2013-01-09	2011-01-25	2006-09-26	ENSG00000185880	ENSG00000185880		"RING-type (C3HC4) zinc fingers", "Tripartite motif containing / Tripartite motif containing"	17857	protein-coding gene	gene with protein product			"ring finger protein 36", "tripartite motif-containing 69"	RNF36			Standard	XM_005254162		Approved	Trif, TRIMLESS	uc001zug.1	Q86WT6	OTTHUMG00000131246	ENST00000559390.1:c.783G>T	chr15.hg19:g.45051022G>T		118.0	0.0		86.0	4.0	NM_182985	A8MX03|Q309B0|Q4G1A5|Q6W897|Q8IYY3|Q8WY16|Q8WY17	Silent	SNP	ENST00000559390.1	hg19	CCDS32220.1																																																																																			.	G|0.999;A|0.001		0.463	TRIM69-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416171.1			T	45051022	G	T	45051022	2	4	255	1	0	0	0	0	0	0	0	1	16557	1103	39	1		1	TRIM69	15	45051022	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	2687014	45051022	57480370	536	35881										
SHF	90525	hgsc.bcm.edu	37	chr15	45490991	45490991	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gggcgaggttccagcctgtcCctgagtctgataatgcgcag	14	11	1	2	rs545098594		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:45490991C>T	ENST00000290894.8	-	2	776	c.282G>A	c.(280-282)agG>agA	p.R94R	CTD-2651B20.6_ENST00000563103.1_RNA|RP11-519G16.2_ENST00000560034.1_RNA|CTD-2651B20.7_ENST00000568314.1_RNA|SHF_ENST00000318390.6_Silent_p.R151R	NM_138356.2	NP_612365			Src homology 2 domain containing F									p.R94R(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(2)	12		all_cancers(109;8.13e-11)|all_epithelial(112;6.29e-09)|Lung NSC(122;3.57e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;4.1e-16)|GBM - Glioblastoma multiforme(94;5.98e-06)		CCAGCCTGTCCCTGAGTCTGA	0.532											OREG0023105	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R94R		Atlas-SNP	.											SHF,NS,carcinoma,0,1	SHF	27	.	1	Substitution - coding silent(1)	endometrium(1)	c.G282A						.						155	157	157					15																	45490991		1978	4151	6129	SO:0001819	synonymous_variant	90525	exon2			CCTGTCCCTGAGT	BC007586	CCDS10120.2, CCDS73721.1	15q21.1	2013-02-14			ENSG00000138606	ENSG00000138606		"SH2 domain containing"	25116	protein-coding gene	gene with protein product						11095946	Standard	NM_138356		Approved		uc001zuy.3	Q7M4L6	OTTHUMG00000131353	ENST00000290894.8:c.282G>A	chr15.hg19:g.45490991C>T		47.0	0.0	932	51.0	3.0	NM_138356		Silent	SNP	ENST00000290894.8	hg19	CCDS10120.2																																																																																			.	.		0.532	SHF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254141.2	NM_138356		T	45490991	C	T	45490991	2	4	255	1	0	0	0	0	0	0	0	1	14292	622	22	3		3	SHF	15	45490991	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	439969	45490991	57040401	537	35882										
SLC12A1	6557	hgsc.bcm.edu	37	chr15	48593518	48593518	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aatgttgcccacagagttacCgccaagttcgactgaatgaa	9	10	0	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:48593518C>A	ENST00000558405.1	+	25	3117	c.3103C>A	c.(3103-3105)Cgc>Agc	p.R1035S	SLC12A1_ENST00000396577.3_Missense_Mutation_p.R1035S|SLC12A1_ENST00000380993.3_Missense_Mutation_p.R1035S			Q13621	S12A1_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 1	1035					cell death (GO:0008219)|chemical homeostasis (GO:0048878)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|kidney development (GO:0001822)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:potassium:chloride symporter activity (GO:0008511)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|prostate(2)|skin(1)	59		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Potassium Chloride(DB00761)|Quinethazone(DB01325)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	ACAGAGTTACCGCCAAGTTCG	0.363																																					p.R1035S		Atlas-SNP	.											SLC12A1_ENST00000396577,NS,carcinoma,-1,2	SLC12A1	243	.	0			c.C3103A						.						83	67	72					15																	48593518		2198	4297	6495	SO:0001583	missense	6557	exon26			AGTTACCGCCAAG		CCDS10129.2, CCDS53940.1	15q15-q21	2013-07-18	2013-07-18		ENSG00000074803	ENSG00000074803		"Solute carriers"	10910	protein-coding gene	gene with protein product		600839				8640224	Standard	NM_000338		Approved	NKCC2	uc010bem.3	Q13621	OTTHUMG00000131495	ENST00000558405.1:c.3103C>A	chr15.hg19:g.48593518C>A	ENSP00000453409:p.Arg1035Ser	104.0	1.0		72.0	3.0	NM_001184832	A8JYA2|E9PDW4	Missense_Mutation	SNP	ENST00000558405.1	hg19	CCDS10129.2	.	.	.	.	.	.	.	.	.	.	c	25.7	4.662565	0.88251	.	.	ENSG00000074803	ENST00000380993;ENST00000396577	D;D	0.85702	-2.02;-2.02	5.14	5.14	0.70334	.	0.066635	0.64402	D	0.000007	D	0.91449	0.7301	M	0.78801	2.425	0.80722	D	1	D;D	0.67145	0.996;0.979	P;P	0.59487	0.724;0.858	D	0.92638	0.6122	10	0.87932	D	0	.	18.588	0.91197	0.0:1.0:0.0:0.0	.	1035;1035	E9PDW4;Q13621	.;S12A1_HUMAN	S	1035	ENSP00000370381:R1035S;ENSP00000379822:R1035S	ENSP00000370381:R1035S	R	+	1	0	SLC12A1	46380810	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.574000	0.82434	2.385000	0.81259	0.650000	0.86243	CGC	.	.		0.363	SLC12A1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417131.1			A	48593518	C	A	48593518	3	1	255	1	0	0	0	0	1	0	0	0	14397	652	23	1	3301	1	SLC12A1	15	48593518	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	3102527	48593518	53937874	538	35883										
CYP19A1	1588	hgsc.bcm.edu	37	chr15	51504537	51504537	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	attctttgcaaaattttcaaGagtaaattcattgggtttgg	8	4	3	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:51504537G>T	ENST00000396402.1	-	9	1396	c.1243C>A	c.(1243-1245)Ctt>Att	p.L415I	CYP19A1_ENST00000396404.4_Missense_Mutation_p.L415I|RP11-108K3.1_ENST00000559909.1_lincRNA|CYP19A1_ENST00000559878.1_Missense_Mutation_p.L415I|CYP19A1_ENST00000260433.2_Missense_Mutation_p.L415I	NM_000103.3	NP_000094.2	P11511	CP19A_HUMAN	cytochrome P450, family 19, subfamily A, polypeptide 1	415					androgen metabolic process (GO:0008209)|estrogen biosynthetic process (GO:0006703)|prostate gland growth (GO:0060736)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)	aromatase activity (GO:0070330)|electron carrier activity (GO:0009055)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)			endometrium(1)|kidney(4)|large_intestine(9)|lung(11)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	33				all cancers(107;0.000372)|GBM - Glioblastoma multiforme(94;0.0128)	Aminoglutethimide(DB00357)|Anastrozole(DB01217)|Betamethasone(DB00443)|Bifonazole(DB04794)|Buserelin(DB06719)|Carbimazole(DB00389)|Chlorphenesin(DB00856)|Clomifene(DB00882)|Clotrimazole(DB00257)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Dexamethasone(DB01234)|Diethylstilbestrol(DB00255)|Dinoprostone(DB00917)|Drostanolone(DB00858)|Econazole(DB01127)|Edetic Acid(DB00974)|Etomidate(DB00292)|Exemestane(DB00990)|Ketoconazole(DB01026)|Letrozole(DB01006)|Levomethadyl Acetate(DB01227)|Levonorgestrel(DB00367)|Mefloquine(DB00358)|Melatonin(DB01065)|Methadone(DB00333)|Methyltestosterone(DB06710)|Miconazole(DB01110)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nicotine(DB00184)|Paclitaxel(DB01229)|Raloxifene(DB00481)|Sulfathiazole(DB06147)|Tamoxifen(DB00675)|Terbinafine(DB00857)|Testolactone(DB00894)|Testosterone(DB00624)|Tioconazole(DB01007)|Trastuzumab(DB00072)	AAATTTTCAAGAGTAAATTCA	0.393																																					p.L415I	Melanoma(142;1016 1807 39614 48966 51721)	Atlas-SNP	.											.	CYP19A1	75	.	0			c.C1243A						.						88	91	90					15																	51504537		2196	4293	6489	SO:0001583	missense	1588	exon10			TTTCAAGAGTAAA	D14473	CCDS10139.1	15q21	2009-01-26	2003-02-14	2003-02-28	ENSG00000137869	ENSG00000137869		"Cytochrome P450s"	2594	protein-coding gene	gene with protein product		107910	"cytochrome P450, subfamily XIX (aromatization of androgens)"	CYP19		8477708	Standard	NM_031226		Approved	ARO, P-450AROM, CPV1, ARO1, CYAR, aromatase	uc001zza.4	P11511	OTTHUMG00000131747	ENST00000396402.1:c.1243C>A	chr15.hg19:g.51504537G>T	ENSP00000379683:p.Leu415Ile	195.0	0.0		107.0	6.0	NM_031226	Q16731|Q3B764|Q58FA0|Q8IYJ7	Missense_Mutation	SNP	ENST00000396402.1	hg19	CCDS10139.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.256347	0.80246	.	.	ENSG00000137869	ENST00000396402;ENST00000260433;ENST00000396404	T;T;T	0.68025	-0.3;-0.3;-0.3	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	D	0.82756	0.5106	M	0.86740	2.835	0.80722	D	1	P	0.48162	0.906	D	0.66602	0.945	D	0.83981	0.0332	10	0.54805	T	0.06	-21.5947	13.3083	0.60365	0.0718:0.0:0.9282:0.0	.	415	P11511	CP19A_HUMAN	I	415	ENSP00000379683:L415I;ENSP00000260433:L415I;ENSP00000379685:L415I	ENSP00000260433:L415I	L	-	1	0	CYP19A1	49291829	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.606000	0.82863	2.767000	0.95098	0.655000	0.94253	CTT	.	.		0.393	CYP19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254669.1			T	51504537	G	T	51504537	3	4	255	1	0	0	0	0	1	0	0	0	4150	942	33	3	276	3	CYP19A1	15	51504537	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	2911019	51504537	51026855	539	35884										
MYO5C	55930	hgsc.bcm.edu	37	chr15	52532010	52532010	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gaatcgtcggatactctggaAtctgcgtctggccagccacg	12	12	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:52532010A>G	ENST00000261839.7	-	21	2784	c.2623T>C	c.(2623-2625)Ttc>Ctc	p.F875L	MYO5C_ENST00000443683.2_Intron	NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	875	IQ 5. {ECO:0000255|PROSITE- ProRule:PRU00116}.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(7)|large_intestine(15)|lung(12)|ovary(7)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66				all cancers(107;0.0137)		ATACTCTGGAATCTGCGTCTG	0.453																																					p.F875L		Atlas-SNP	.											.	MYO5C	162	.	0			c.T2623C						.						69	69	69					15																	52532010		1977	4161	6138	SO:0001583	missense	55930	exon21			TCTGGAATCTGCG	AF272390	CCDS42036.1	15q21	2011-09-27				ENSG00000128833		"Myosins / Myosin superfamily : Class V"	7604	protein-coding gene	gene with protein product	"myosin 5C"	610022				11870218	Standard	NM_018728		Approved	MGC74969	uc010bff.3	Q9NQX4		ENST00000261839.7:c.2623T>C	chr15.hg19:g.52532010A>G	ENSP00000261839:p.Phe875Leu	130.0	0.0		100.0	4.0	NM_018728	Q6P1W8	Missense_Mutation	SNP	ENST00000261839.7	hg19	CCDS42036.1	.	.	.	.	.	.	.	.	.	.	A	28.9	4.957245	0.92726	.	.	ENSG00000128833	ENST00000261839	T	0.28454	1.61	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.48822	0.1521	L	0.59967	1.855	0.80722	D	1	D	0.55800	0.973	P	0.60789	0.879	T	0.46133	-0.9213	10	0.51188	T	0.08	.	15.1608	0.72782	1.0:0.0:0.0:0.0	.	875	Q9NQX4	MYO5C_HUMAN	L	875	ENSP00000261839:F875L	ENSP00000261839:F875L	F	-	1	0	MYO5C	50319302	1.000000	0.71417	0.999000	0.59377	0.970000	0.65996	7.168000	0.77570	2.058000	0.61347	0.528000	0.53228	TTC	.	.		0.453	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728		G	52532010	A	G	52532010	3	3	255	1	0	0	0	0	1	0	0	0	10089	101	4	2	2689	2	MYO5C	15	52532010	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	1027473	52532010	49999382	540	35885										
RAB27A	5873	hgsc.bcm.edu	37	chr15	55520885	55520885	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aaaacccatagcatctctgaAgaacgctgtcgttaagctac	7	11	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:55520885A>G	ENST00000396307.2	-	4	516	c.265T>C	c.(265-267)Ttc>Ctc	p.F89L	RAB27A_ENST00000336787.1_Missense_Mutation_p.F89L|RAB27A_ENST00000569493.1_Missense_Mutation_p.F89L|RAB27A_ENST00000564609.1_Missense_Mutation_p.F89L	NM_004580.4	NP_004571.2	P51159	RB27A_HUMAN	RAB27A, member RAS oncogene family	89					antigen processing and presentation (GO:0019882)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cytotoxic T cell degranulation (GO:0043316)|exocytosis (GO:0006887)|exosomal secretion (GO:1990182)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|multivesicular body organization (GO:0036257)|multivesicular body sorting pathway (GO:0071985)|natural killer cell degranulation (GO:0043320)|positive regulation of exocytosis (GO:0045921)|positive regulation of gene expression (GO:0010628)|protein targeting (GO:0006605)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle transport (GO:0048489)	apical plasma membrane (GO:0016324)|dendrite (GO:0030425)|exocytic vesicle (GO:0070382)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|melanosome (GO:0042470)|multivesicular body membrane (GO:0032585)|photoreceptor outer segment (GO:0001750)|secretory granule membrane (GO:0030667)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(2)|liver(1)|lung(3)|ovary(1)|skin(1)	9				all cancers(107;0.0273)|GBM - Glioblastoma multiforme(80;0.0993)		GCATCTCTGAAGAACGCTGTC	0.398																																					p.F89L		Atlas-SNP	.											.	RAB27A	18	.	0			c.T265C						.						110	103	106					15																	55520885		2193	4292	6485	SO:0001583	missense	5873	exon5			CTCTGAAGAACGC	U38654	CCDS10153.1	15q15-q21.1	2014-09-17			ENSG00000069974	ENSG00000069974		"RAB, member RAS oncogene"	9766	protein-coding gene	gene with protein product		603868				7592656	Standard	NM_183235		Approved	RAB27, RAM, GS2, HsT18676	uc002acq.3	P51159	OTTHUMG00000131959	ENST00000396307.2:c.265T>C	chr15.hg19:g.55520885A>G	ENSP00000379601:p.Phe89Leu	127.0	0.0		94.0	4.0	NM_183235	O00195|Q6FI40|Q9UIR9|Q9Y5U3	Missense_Mutation	SNP	ENST00000396307.2	hg19	CCDS10153.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.570844	0.86542	.	.	ENSG00000069974	ENST00000396307;ENST00000396304;ENST00000336787	T;T	0.75704	-0.96;-0.96	5.92	5.92	0.95590	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.64227	0.2579	N	0.16098	0.37	0.80722	D	1	P	0.41159	0.74	B	0.42138	0.377	T	0.70842	-0.4762	10	0.87932	D	0	-13.5705	15.5447	0.76090	1.0:0.0:0.0:0.0	.	89	P51159	RB27A_HUMAN	L	89	ENSP00000379601:F89L;ENSP00000337761:F89L	ENSP00000337761:F89L	F	-	1	0	RAB27A	53308177	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	9.228000	0.95250	2.267000	0.75376	0.528000	0.53228	TTC	.	.		0.398	RAB27A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254918.1	NM_004580, NM_183236		G	55520885	A	G	55520885	3	3	255	1	0	0	0	0	1	0	0	0	12929	72	3	2	412	2	RAB27A	15	55520885	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	2988875	55520885	47010507	541	35886										
HERC1	8925	hgsc.bcm.edu	37	chr15	63916007	63916007	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cagcttaaccttccacgctcGggaaggcaggcggaggtctg	14	12	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:63916007G>T	ENST00000443617.2	-	73	13615	c.13528C>A	c.(13528-13530)Cga>Aga	p.R4510R		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	4510	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						TTCCACGCTCGGGAAGGCAGG	0.483																																					p.R4510R		Atlas-SNP	.											.	HERC1	624	.	0			c.C13528A						.						95	96	96					15																	63916007		2024	4174	6198	SO:0001819	synonymous_variant	8925	exon73			ACGCTCGGGAAGG	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.13528C>A	chr15.hg19:g.63916007G>T		75.0	0.0		50.0	4.0	NM_003922	Q8IW65	Silent	SNP	ENST00000443617.2	hg19	CCDS45277.1																																																																																			.	.		0.483	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		T	63916007	G	T	63916007	2	4	255	1	0	0	0	0	0	0	0	1	7066	1124	39	1		1	HERC1	15	63916007	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	8395122	63916007	38615385	542	35887										
HERC1	8925	hgsc.bcm.edu	37	chr15	63918224	63918224	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcagcagtctccaggatgagTacatgaggtcagagaagtgg	14	7	3	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:63918224T>A	ENST00000443617.2	-	71	13322	c.13235A>T	c.(13234-13236)tAc>tTc	p.Y4412F		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	4412					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						CCAGGATGAGTACATGAGGTC	0.592																																					p.Y4412F		Atlas-SNP	.											.	HERC1	624	.	0			c.A13235T						.						68	70	69					15																	63918224		2061	4206	6267	SO:0001583	missense	8925	exon71			GATGAGTACATGA	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.13235A>T	chr15.hg19:g.63918224T>A	ENSP00000390158:p.Tyr4412Phe	97.0	0.0		60.0	4.0	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	hg19	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	T	14.34	2.504984	0.44558	.	.	ENSG00000103657	ENST00000443617	T	0.25912	1.77	5.51	5.51	0.81932	.	0.078149	0.52532	D	0.000065	T	0.24198	0.0586	L	0.38531	1.155	0.58432	D	0.999999	P	0.41232	0.743	B	0.39617	0.305	T	0.01966	-1.1238	10	0.46703	T	0.11	.	15.924	0.79597	0.0:0.0:0.0:1.0	.	4412	Q15751	HERC1_HUMAN	F	4412	ENSP00000390158:Y4412F	ENSP00000390158:Y4412F	Y	-	2	0	HERC1	61705277	1.000000	0.71417	1.000000	0.80357	0.421000	0.31385	7.997000	0.88414	2.217000	0.71921	0.533000	0.62120	TAC	.	.		0.592	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		A	63918224	T	A	63918224	3	1	255	1	0	0	0	0	1	0	0	0	7066	1638	57	4	1382	4	HERC1	15	63918224	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	2217	63918224	38613168	543	35888										
SPG21	51324	hgsc.bcm.edu	37	chr15	65261628	65261628	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggtatgtcccgaattttatgAggttccacataagaattttg	9	6	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:65261628A>G	ENST00000204566.2	-	7	928	c.633T>C	c.(631-633)ccT>ccC	p.P211P	SPG21_ENST00000416889.2_Silent_p.P184P|SPG21_ENST00000559199.1_Silent_p.P57P|SPG21_ENST00000433215.2_Silent_p.P211P	NM_016630.3	NP_057714.1	Q9NZD8	SPG21_HUMAN	spastic paraplegia 21 (autosomal recessive, Mast syndrome)	211					antigen receptor-mediated signaling pathway (GO:0050851)|cell death (GO:0008219)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network transport vesicle (GO:0030140)	CD4 receptor binding (GO:0042609)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|urinary_tract(1)	10						GAATTTTATGAGGTTCCACAT	0.348																																					p.P211P		Atlas-SNP	.											.	SPG21	29	.	0			c.T633C						.						105	109	108					15																	65261628		2202	4299	6501	SO:0001819	synonymous_variant	51324	exon7			TTTATGAGGTTCC	AF208861	CCDS10198.1, CCDS45279.1	15q21-q22	2008-02-05	2007-04-23		ENSG00000090487	ENSG00000090487			20373	protein-coding gene	gene with protein product	"maspardin"	608181				11113139, 14564668	Standard	XM_006720564		Approved	ACP33, GL010, BM-019, MAST	uc002aoe.3	Q9NZD8	OTTHUMG00000133098	ENST00000204566.2:c.633T>C	chr15.hg19:g.65261628A>G		85.0	0.0		71.0	4.0	NM_001127889	B4DW44|Q6ZMB6	Silent	SNP	ENST00000204566.2	hg19	CCDS10198.1																																																																																			.	.		0.348	SPG21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256758.3	NM_016630		G	65261628	A	G	65261628	2	3	255	1	0	0	0	0	0	0	0	1	15058	291	11	2		2	SPG21	15	65261628	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	1343404	65261628	37269764	544	35889										
KBTBD13	390594	hgsc.bcm.edu	37	chr15	65370197	65370197	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tatggccactgcatggtggcCcaccgcgacagcctctatgt	11	14	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:65370197C>A	ENST00000432196.2	+	1	1044	c.1044C>A	c.(1042-1044)gcC>gcA	p.A348A	RASL12_ENST00000434605.2_5'Flank	NM_001101362.2	NP_001094832.1	C9JR72	KBTBD_HUMAN	kelch repeat and BTB (POZ) domain containing 13	348					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				lung(1)|prostate(1)|skin(1)	3						GCATGGTGGCCCACCGCGACA	0.687																																					p.A348A		Atlas-SNP	.											.	KBTBD13	9	.	0			c.C1044A						.						16	17	17					15																	65370197		1774	3679	5453	SO:0001819	synonymous_variant	390594	exon1			GGTGGCCCACCGC		CCDS45281.1	15q22.31	2014-09-17			ENSG00000234438	ENSG00000234438		"BTB/POZ domain containing"	37227	protein-coding gene	gene with protein product	"nemaline myopathy type 6"	613727				21109227, 22542517	Standard	NM_001101362		Approved	hCG_1645727, NEM6	uc010uis.2	C9JR72		ENST00000432196.2:c.1044C>A	chr15.hg19:g.65370197C>A		103.0	0.0		85.0	4.0	NM_001101362		Silent	SNP	ENST00000432196.2	hg19	CCDS45281.1																																																																																			.	.		0.687	KBTBD13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418468.2	NM_001101362		A	65370197	C	A	65370197	2	1	255	1	0	0	0	0	0	0	0	1	8001	610	22	3		3	KBTBD13	15	65370197	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	108569	65370197	37161195	545	35890										
ITGA11	22801	hgsc.bcm.edu	37	chr15	68631922	68631922	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aatgaccttcccggcactcgTctcctttagcacagctccat	6	16	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:68631922T>C	ENST00000315757.7	-	11	1278	c.1192A>G	c.(1192-1194)Acg>Gcg	p.T398A	ITGA11_ENST00000423218.2_Missense_Mutation_p.T398A	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	398					cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|collagen-activated signaling pathway (GO:0038065)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|osteoblast differentiation (GO:0001649)|substrate-dependent cell migration (GO:0006929)	focal adhesion (GO:0005925)|integrin alpha11-beta1 complex (GO:0034681)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(6)|lung(22)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	52						CCGGCACTCGTCTCCTTTAGC	0.582																																					p.T398A		Atlas-SNP	.											.	ITGA11	110	.	0			c.A1192G						.						70	76	74					15																	68631922		2022	4175	6197	SO:0001583	missense	22801	exon11			CACTCGTCTCCTT	AF109681	CCDS45291.1	15q22.3-q23	2010-03-23				ENSG00000137809		"Integrins"	6136	protein-coding gene	gene with protein product		604789				10486209	Standard	NM_001004439		Approved	HsT18964	uc002ari.3	Q9UKX5		ENST00000315757.7:c.1192A>G	chr15.hg19:g.68631922T>C	ENSP00000327290:p.Thr398Ala	85.0	0.0		58.0	5.0	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Missense_Mutation	SNP	ENST00000315757.7	hg19	CCDS45291.1	.	.	.	.	.	.	.	.	.	.	T	12.01	1.810639	0.32053	.	.	ENSG00000137809	ENST00000315757;ENST00000423218;ENST00000535491;ENST00000537153	T;T	0.71817	-0.6;-0.6	5.09	5.09	0.68999	.	0.094573	0.64402	D	0.000001	T	0.65821	0.2728	L	0.55481	1.735	0.43039	D	0.994626	B;P	0.38767	0.068;0.646	B;B	0.40825	0.097;0.341	T	0.62987	-0.6737	10	0.10377	T	0.69	.	14.1169	0.65159	0.0:0.0:0.0:1.0	.	398;398	A8K8T0;Q9UKX5	.;ITA11_HUMAN	A	398;398;33;398	ENSP00000327290:T398A;ENSP00000403392:T398A	ENSP00000327290:T398A	T	-	1	0	ITGA11	66418976	1.000000	0.71417	0.743000	0.31040	0.163000	0.22366	6.289000	0.72696	1.938000	0.56188	0.454000	0.30748	ACG	.	.		0.582	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211		C	68631922	T	C	68631922	3	2	255	1	0	0	0	0	1	0	0	0	7883	1667	58	2	2454	2	ITGA11	15	68631922	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	3261725	68631922	33899470	546	35891										
SPESP1	246777	hgsc.bcm.edu	37	chr15	69238897	69238897	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aaaatatgtgtagatcaaggAgagtcacagccttattaaaa	8	5	2	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:69238897A>G	ENST00000310673.3	+	2	1178	c.1024A>G	c.(1024-1026)Aga>Gga	p.R342G	NOX5_ENST00000448182.3_Intron|NOX5_ENST00000455873.3_Intron|RP11-809H16.2_ENST00000557966.1_RNA|NOX5_ENST00000260364.5_Intron	NM_145658.3	NP_663633.1	Q6UW49	SPESP_HUMAN	sperm equatorial segment protein 1	342					acrosome reaction (GO:0007340)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organismal development (GO:0007275)	acrosomal vesicle (GO:0001669)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|prostate(1)|skin(1)|urinary_tract(1)	19						TAGATCAAGGAGAGTCACAGC	0.264																																					p.R342G		Atlas-SNP	.											.	SPESP1	39	.	0			c.A1024G						.						31	33	32					15																	69238897		1940	4083	6023	SO:0001583	missense	246777	exon2			TCAAGGAGAGTCA	AF275321	CCDS10230.1	15q22.31	2011-04-15				ENSG00000258484			15570	protein-coding gene	gene with protein product		609399				12773409	Standard	NM_145658		Approved	SP-ESP	uc002arn.2	Q6UW49		ENST00000310673.3:c.1024A>G	chr15.hg19:g.69238897A>G	ENSP00000312284:p.Arg342Gly	41.0	0.0		38.0	4.0	NM_145658	Q8NG22|Q8WVH8	Missense_Mutation	SNP	ENST00000310673.3	hg19	CCDS10230.1	.	.	.	.	.	.	.	.	.	.	A	3.487	-0.104586	0.06967	.	.	ENSG00000258484	ENST00000310673	T	0.27720	1.65	5.19	1.62	0.23740	.	0.617328	0.14594	N	0.310099	T	0.14442	0.0349	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.31668	-0.9935	10	0.13853	T	0.58	-0.7094	6.5665	0.22515	0.716:0.0:0.284:0.0	.	342	Q6UW49	SPESP_HUMAN	G	342	ENSP00000312284:R342G	ENSP00000312284:R342G	R	+	1	2	SPESP1	67025951	0.004000	0.15560	0.023000	0.16930	0.022000	0.10575	-0.118000	0.10692	0.386000	0.24997	-0.274000	0.10170	AGA	.	.		0.264	SPESP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257125.1	NM_145658		G	69238897	A	G	69238897	3	3	255	1	0	0	0	0	1	0	0	0	15055	296	11	2	1030	2	SPESP1	15	69238897	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	606975	69238897	33292495	547	35892										
MYO9A	4649	hgsc.bcm.edu	37	chr15	72196317	72196317	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgattggcgaattcgaactgTttccagcatcccggtgtatc	10	10	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:72196317T>C	ENST00000356056.5	-	21	3302	c.2830A>G	c.(2830-2832)Aca>Gca	p.T944A	MYO9A_ENST00000424560.1_Missense_Mutation_p.T944A|MYO9A_ENST00000566885.1_Missense_Mutation_p.T564A|MYO9A_ENST00000444904.1_Missense_Mutation_p.T925A|MYO9A_ENST00000564571.1_Missense_Mutation_p.T944A|MYO9A_ENST00000563542.1_5'UTR	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	944	Myosin motor.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)			NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						ATTCGAACTGTTTCCAGCATC	0.378																																					p.T944A		Atlas-SNP	.											.	MYO9A	203	.	0			c.A2830G						.						94	86	88					15																	72196317		2199	4297	6496	SO:0001583	missense	4649	exon21			GAACTGTTTCCAG	AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"Myosins / Myosin superfamily : Class IX"	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.2830A>G	chr15.hg19:g.72196317T>C	ENSP00000348349:p.Thr944Ala	125.0	0.0		91.0	4.0	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	hg19	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	T	29.5	5.013916	0.93404	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904;ENST00000261864	D;D;D	0.87491	-2.26;-2.26;-2.26	5.24	5.24	0.73138	Myosin head, motor domain (2);	.	.	.	.	D	0.90978	0.7163	L	0.50333	1.59	0.80722	D	1	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.87578	0.998;0.978;0.992	D	0.89742	0.3934	9	0.33141	T	0.24	.	15.3061	0.73992	0.0:0.0:0.0:1.0	.	925;925;944	B2RTY4-2;B7WP69;B2RTY4	.;.;MYO9A_HUMAN	A	944;944;925;925	ENSP00000348349:T944A;ENSP00000399162:T944A;ENSP00000398250:T925A	ENSP00000261864:T925A	T	-	1	0	MYO9A	69983371	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.499000	0.81566	2.203000	0.70933	0.533000	0.62120	ACA	.	.		0.378	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901		C	72196317	T	C	72196317	3	2	255	1	0	0	0	0	1	0	0	0	10093	1725	60	2	4904	2	MYO9A	15	72196317	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	2957420	72196317	30335075	548	35893										
PARP6	56965	hgsc.bcm.edu	37	chr15	72552968	72552968	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	catgaggcgcccaacccgaaGctctggtacacctagtttgc	10	14	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:72552968G>T	ENST00000569795.1	-	10	1294	c.607C>A	c.(607-609)Ctt>Att	p.L203I	PARP6_ENST00000287196.9_Missense_Mutation_p.L203I|PARP6_ENST00000260376.7_Missense_Mutation_p.L203I|PARP6_ENST00000413097.2_5'UTR			Q2NL67	PARP6_HUMAN	poly (ADP-ribose) polymerase family, member 6	203							NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(8)|skin(1)|urinary_tract(1)	18						CCAACCCGAAGCTCTGGTACA	0.532																																					p.L203I		Atlas-SNP	.											.	PARP6	44	.	0			c.C607A						.						371	360	363					15																	72552968		1894	4124	6018	SO:0001583	missense	56965	exon9			CCCGAAGCTCTGG	AL390093	CCDS10241.2	15q22	2010-02-16			ENSG00000137817	ENSG00000137817		"Poly (ADP-ribose) polymerases"	26921	protein-coding gene	gene with protein product						15273990	Standard	XM_005254557		Approved	pART17	uc002auc.3	Q2NL67	OTTHUMG00000133443	ENST00000569795.1:c.607C>A	chr15.hg19:g.72552968G>T	ENSP00000456348:p.Leu203Ile	109.0	0.0		67.0	4.0	NM_020214	Q9H7C5|Q9H9X6|Q9HAF3|Q9NPS6|Q9UFG4	Missense_Mutation	SNP	ENST00000569795.1	hg19	CCDS10241.2	.	.	.	.	.	.	.	.	.	.	G	13.21	2.169618	0.38315	.	.	ENSG00000137817	ENST00000419739;ENST00000287196;ENST00000260376;ENST00000413097;ENST00000544520;ENST00000336471	.	.	.	4.93	4.93	0.64822	.	0.073354	0.56097	D	0.000033	T	0.47544	0.1451	L	0.50333	1.59	0.32288	N	0.566733	B;B;B	0.17038	0.002;0.004;0.02	B;B;B	0.13407	0.007;0.005;0.009	T	0.54768	-0.8244	9	0.35671	T	0.21	-8.8612	14.4766	0.67551	0.0:0.1474:0.8526:0.0	.	203;203;155	Q0VDG0;Q2NL67;A0PJ50	.;PARP6_HUMAN;.	I	203;203;203;68;68;203	.	ENSP00000260376:L203I	L	-	1	0	PARP6	70340022	1.000000	0.71417	1.000000	0.80357	0.331000	0.28603	5.178000	0.65037	2.277000	0.76020	0.585000	0.79938	CTT	.	.		0.532	PARP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257315.2	NM_020214		T	72552968	G	T	72552968	3	4	255	1	0	0	0	0	1	0	0	0	11473	971	34	3	1345	3	PARP6	15	72552968	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	356651	72552968	29978424	549	35894										
MPI	4351	hgsc.bcm.edu	37	chr15	75182887	75182887	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gtattcccactttcctgtgcGgtgcagcagtatgcctgggg	13	11	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:75182887G>T	ENST00000352410.4	+	2	103	c.36G>T	c.(34-36)gcG>gcT	p.A12A	MPI_ENST00000563786.1_5'UTR|MPI_ENST00000535694.1_Intron|MPI_ENST00000566377.1_Silent_p.A12A|MPI_ENST00000564003.1_Intron|MPI_ENST00000563422.1_Silent_p.A12A|MPI_ENST00000565576.1_Silent_p.A12A|MPI_ENST00000562606.1_Intron|MPI_ENST00000323744.6_Silent_p.A12A			P34949	MPI_HUMAN	mannose phosphate isomerase	12					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	mannose-6-phosphate isomerase activity (GO:0004476)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|upper_aerodigestive_tract(1)	9						TTTCCTGTGCGGTGCAGCAGT	0.617																																					p.A12A		Atlas-SNP	.											.	MPI	32	.	0			c.G36T						.						82	69	74					15																	75182887		2197	4295	6492	SO:0001819	synonymous_variant	4351	exon2			CTGTGCGGTGCAG		CCDS10272.1, CCDS73756.1, CCDS73757.1, CCDS73758.1	15q24.1	2013-09-19			ENSG00000178802	ENSG00000178802	5.3.1.8		7216	protein-coding gene	gene with protein product	"mannose-6-phosphate isomerase"	154550					Standard	NM_002435		Approved		uc002azc.1	P34949	OTTHUMG00000142826	ENST00000352410.4:c.36G>T	chr15.hg19:g.75182887G>T		108.0	0.0		66.0	4.0	NM_002435	A8K8K9|Q96AB0	Silent	SNP	ENST00000352410.4	hg19	CCDS10272.1																																																																																			.	.		0.617	MPI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286418.4			T	75182887	G	T	75182887	2	4	255	1	0	0	0	0	0	0	0	1	9738	1103	39	1		1	MPI	15	75182887	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	2629919	75182887	27348505	550	35895										
COX5A	9377	hgsc.bcm.edu	37	chr15	75221502	75221502	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	atctggcttgttgaagtatgTtacccagcgagcatcaaact	9	9	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:75221502T>C	ENST00000322347.6	-	2	325	c.172A>G	c.(172-174)Aca>Gca	p.T58A	COX5A_ENST00000568517.1_5'UTR|COX5A_ENST00000568783.1_Missense_Mutation_p.T58A|COX5A_ENST00000562233.1_Missense_Mutation_p.T58A|COX5A_ENST00000564811.1_Missense_Mutation_p.T58A|COX5A_ENST00000567270.1_Intron	NM_004255.3	NP_004246.2	P20674	COX5A_HUMAN	cytochrome c oxidase subunit Va	58					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)	cytochrome-c oxidase activity (GO:0004129)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|pancreas(1)	3						TTGAAGTATGTTACCCAGCGA	0.398																																					p.T58A		Atlas-SNP	.											.	COX5A	9	.	0			c.A172G						.						155	141	146					15																	75221502		2197	4295	6492	SO:0001583	missense	9377	exon2			AGTATGTTACCCA	M22760	CCDS10273.1	15q25	2011-07-04			ENSG00000178741	ENSG00000178741	1.9.3.1	"Mitochondrial respiratory chain complex / Complex IV"	2267	protein-coding gene	gene with protein product		603773				10072584, 2853101	Standard	NM_004255		Approved		uc002azi.4	P20674	OTTHUMG00000142825	ENST00000322347.6:c.172A>G	chr15.hg19:g.75221502T>C	ENSP00000317780:p.Thr58Ala	183.0	0.0		121.0	39.0	NM_004255	P30045|Q8TB65	Missense_Mutation	SNP	ENST00000322347.6	hg19	CCDS10273.1	.	.	.	.	.	.	.	.	.	.	T	18.46	3.628961	0.67015	.	.	ENSG00000178741	ENST00000322347	.	.	.	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.35393	0.0930	N	0.05467	-0.045	0.58432	D	0.999997	B	0.09022	0.002	B	0.19666	0.026	T	0.26849	-1.0091	9	0.06625	T	0.88	-10.27	14.6722	0.68953	0.0:0.0:0.0:1.0	.	58	P20674	COX5A_HUMAN	A	58	.	ENSP00000317780:T58A	T	-	1	0	COX5A	73008555	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	7.454000	0.80714	2.150000	0.67090	0.528000	0.53228	ACA	.	.		0.398	COX5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286417.1	NM_004255		C	75221502	T	C	75221502	3	2	255	1	0	0	0	0	1	0	0	0	3774	1725	60	2	292	2	COX5A	15	75221502	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	38615	75221502	27309890	551	35896										
MAN2C1	4123	hgsc.bcm.edu	37	chr15	75649212	75649212	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gggccagcccaaagccgtgtTctgacagatccatccagcga	11	14	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:75649212T>C	ENST00000267978.5	-	22	2625	c.2579A>G	c.(2578-2580)gAa>gGa	p.E860G	RP11-817O13.6_ENST00000563660.1_lincRNA|MAN2C1_ENST00000569482.1_Missense_Mutation_p.E860G|MAN2C1_ENST00000565683.1_Missense_Mutation_p.E877G|MAN2C1_ENST00000563622.1_Missense_Mutation_p.E761G	NM_006715.3	NP_006706.2	Q9NTJ4	MA2C1_HUMAN	mannosidase, alpha, class 2C, member 1	860					mannose metabolic process (GO:0006013)		alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(4)|kidney(6)|large_intestine(6)|lung(20)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	44						AAAGCCGTGTTCTGACAGATC	0.622																																					p.E877G		Atlas-SNP	.											.	MAN2C1	76	.	0			c.A2630G						.						84	70	75					15																	75649212		2197	4294	6491	SO:0001583	missense	4123	exon22			CCGTGTTCTGACA	AF044414	CCDS32298.1, CCDS58389.1, CCDS58390.1, CCDS58391.1	15q24.2	2013-09-19			ENSG00000140400	ENSG00000140400	3.2.1.24		6827	protein-coding gene	gene with protein product		154580		MANA1, MANA		1757461, 752528	Standard	NM_006715		Approved		uc002bah.4	Q9NTJ4	OTTHUMG00000172698	ENST00000267978.5:c.2579A>G	chr15.hg19:g.75649212T>C	ENSP00000267978:p.Glu860Gly	115.0	0.0		86.0	4.0	NM_001256494	H3BMX2|H3BQY8|H3BUT6|Q13358|Q68EM8|Q9UL64	Missense_Mutation	SNP	ENST00000267978.5	hg19	CCDS32298.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.826047	0.90955	.	.	ENSG00000140400	ENST00000267978	T	0.20598	2.06	5.09	5.09	0.68999	Glycosyl hydrolases 38, C-terminal (1);Glycoside hydrolase-type carbohydrate-binding (1);	0.000000	0.85682	D	0.000000	T	0.53351	0.1791	M	0.90759	3.145	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.993	T	0.64198	-0.6464	10	0.87932	D	0	-30.0163	14.0368	0.64649	0.0:0.0:0.0:1.0	.	860;860	Q68EM8;Q9NTJ4	.;MA2C1_HUMAN	G	860	ENSP00000267978:E860G	ENSP00000267978:E860G	E	-	2	0	MAN2C1	73436265	1.000000	0.71417	0.900000	0.35374	0.920000	0.55202	5.946000	0.70234	1.932000	0.55993	0.459000	0.35465	GAA	.	.		0.622	MAN2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419965.1			C	75649212	T	C	75649212	3	2	255	1	0	0	0	0	1	0	0	0	9227	1783	62	2	563	2	MAN2C1	15	75649212	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	427710	75649212	26882180	552	35897										
PTPN9	5780	hgsc.bcm.edu	37	chr15	75761250	75761250	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cctctgggtcctcatgcgtgAcaccgtctggaacacattaa	9	13	3	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:75761250A>G	ENST00000306726.2	-	13	2154	c.1642T>C	c.(1642-1644)Tca>Cca	p.S548P		NM_002833.2	NP_002824.1	P43378	PTN9_HUMAN	protein tyrosine phosphatase, non-receptor type 9	548	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|protein tyrosine phosphatase activity (GO:0004725)			central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CTCATGCGTGACACCGTCTGG	0.542																																					p.S548P		Atlas-SNP	.											.	PTPN9	53	.	0			c.T1642C						.						98	80	86					15																	75761250		2197	4294	6491	SO:0001583	missense	5780	exon13			TGCGTGACACCGT		CCDS10280.1	15q23	2011-06-09			ENSG00000169410	ENSG00000169410		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9661	protein-coding gene	gene with protein product		600768				1557404	Standard	NM_002833		Approved	MEG2	uc002bal.3	P43378	OTTHUMG00000142838	ENST00000306726.2:c.1642T>C	chr15.hg19:g.75761250A>G	ENSP00000303554:p.Ser548Pro	100.0	0.0		67.0	4.0	NM_002833	Q53XR9	Missense_Mutation	SNP	ENST00000306726.2	hg19	CCDS10280.1	.	.	.	.	.	.	.	.	.	.	A	17.86	3.492680	0.64074	.	.	ENSG00000169410	ENST00000306726;ENST00000544966	D	0.84070	-1.8	6.17	4.99	0.66335	Protein-tyrosine phosphatase, receptor/non-receptor type (4);Protein-tyrosine/Dual-specificity phosphatase (1);	0.326738	0.32987	N	0.005418	T	0.75693	0.3884	M	0.66439	2.03	0.40294	D	0.978539	P	0.45240	0.854	B	0.36534	0.227	T	0.77680	-0.2497	10	0.51188	T	0.08	.	4.2373	0.10632	0.6653:0.1864:0.1483:0.0	.	548	P43378	PTN9_HUMAN	P	548;538	ENSP00000303554:S548P	ENSP00000303554:S548P	S	-	1	0	PTPN9	73548303	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.971000	0.49248	2.371000	0.80710	0.533000	0.62120	TCA	.	.		0.542	PTPN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286474.1			G	75761250	A	G	75761250	3	3	255	1	0	0	0	0	1	0	0	0	12809	275	10	2	143	2	PTPN9	15	75761250	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	112038	75761250	26770142	553	35898										
CSPG4	1464	hgsc.bcm.edu	37	chr15	75982391	75982391	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctctggtgtcaggcccaggcGgtgttcctggaggtgacgag	17	10	2	1	rs200187536		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:75982391G>T	ENST00000308508.5	-	3	1107	c.1015C>A	c.(1015-1017)Cgc>Agc	p.R339S		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	339	Globular or compact configuration stabilized by disulfide bonds.|Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						AGGCCCAGGCGGTGTTCCTGG	0.642																																					p.R339S		Atlas-SNP	.											.	CSPG4	175	.	0			c.C1015A						.						17	15	16					15																	75982391		2192	4283	6475	SO:0001583	missense	1464	exon3			CCAGGCGGTGTTC	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"Proteoglycans / Cell surface : Other"	2466	protein-coding gene	gene with protein product	"melanoma-associated chondroitin sulfate proteoglycan"	601172	"chondroitin sulfate proteoglycan 4 (melanoma-associated)"			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.1015C>A	chr15.hg19:g.75982391G>T	ENSP00000312506:p.Arg339Ser	63.0	0.0		62.0	4.0	NM_001897	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	hg19	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	.	14.64	2.596974	0.46318	.	.	ENSG00000173546	ENST00000308508	T	0.18502	2.21	5.26	4.26	0.50523	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.181054	0.36815	N	0.002398	T	0.19167	0.0460	L	0.29908	0.895	0.32592	N	0.527029	P	0.52170	0.951	P	0.50934	0.654	T	0.05146	-1.0903	10	0.19590	T	0.45	.	15.6861	0.77411	0.0:0.0:0.8538:0.1462	.	339	Q6UVK1	CSPG4_HUMAN	S	339	ENSP00000312506:R339S	ENSP00000312506:R339S	R	-	1	0	CSPG4	73769446	0.996000	0.38824	1.000000	0.80357	0.667000	0.39255	2.026000	0.41069	2.463000	0.83235	0.555000	0.69702	CGC	.	G|0.999;A|0.001		0.642	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897		T	75982391	G	T	75982391	3	4	255	1	0	0	0	0	1	0	0	0	3962	1116	39	1	5985	1	CSPG4	15	75982391	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	221141	75982391	26549001	554	35899										
RASGRF1	5923	hgsc.bcm.edu	37	chr15	79254552	79254552	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctttcttcatccattacaaaAgattggtccagtaaatattg	5	8	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:79254552A>G	ENST00000419573.3	-	28	4030	c.3756T>C	c.(3754-3756)tcT>tcC	p.S1252S	RASGRF1_ENST00000394745.3_Silent_p.S468S|RASGRF1_ENST00000558480.2_Silent_p.S1236S	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	1252	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						CCATTACAAAAGATTGGTCCA	0.478																																					p.S1252S		Atlas-SNP	.											.	RASGRF1	168	.	0			c.T3756C						.						67	65	66					15																	79254552		2196	4292	6488	SO:0001819	synonymous_variant	5923	exon28			TACAAAAGATTGG	M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.3756T>C	chr15.hg19:g.79254552A>G		92.0	0.0		54.0	4.0	NM_002891	F8VPA5|H0YKF2|J3KQP9|Q16027	Silent	SNP	ENST00000419573.3	hg19	CCDS10309.1																																																																																			.	.		0.478	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891		G	79254552	A	G	79254552	2	3	255	1	0	0	0	0	0	0	0	1	13087	59	3	2		2	RASGRF1	15	79254552	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	3272161	79254552	23276840	555	35900										
IL16	3603	hgsc.bcm.edu	37	chr15	81592606	81592606	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gtcctgtgagacgaagctacTtgacgaaaagaccagcaaac	10	10	0	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:81592606T>C	ENST00000302987.4	+	13	2939	c.2939T>C	c.(2938-2940)cTt>cCt	p.L980P	IL16_ENST00000394652.2_Missense_Mutation_p.L279P|IL16_ENST00000394660.2_Missense_Mutation_p.L980P|RP11-761I4.4_ENST00000607019.1_RNA			Q14005	IL16_HUMAN	interleukin 16	980					immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						ACGAAGCTACTTGACGAAAAG	0.537																																					p.L980P		Atlas-SNP	.											.	IL16	254	.	0			c.T2939C						.						99	85	89					15																	81592606		2203	4300	6503	SO:0001583	missense	3603	exon14			AGCTACTTGACGA	U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"Interleukins and interleukin receptors"	5980	protein-coding gene	gene with protein product	"prointerleukin 16", "lymphocyte chemoattractant factor"	603035	"interleukin 16 (lymphocyte chemoattractant factor)"			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.2939T>C	chr15.hg19:g.81592606T>C	ENSP00000302935:p.Leu980Pro	133.0	0.0		98.0	4.0	NM_001172128	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Missense_Mutation	SNP	ENST00000302987.4	hg19	CCDS42069.1	.	.	.	.	.	.	.	.	.	.	T	9.145	1.014763	0.19355	.	.	ENSG00000172349	ENST00000394660;ENST00000355368;ENST00000302987;ENST00000329842;ENST00000394653;ENST00000394652;ENST00000394656	T;T;T	0.12147	2.72;2.71;3.32	4.91	-0.636	0.11508	.	1.216530	0.06243	N	0.690824	T	0.20251	0.0487	L	0.56769	1.78	0.09310	N	0.999998	P;D;D;P;P;P	0.62365	0.875;0.991;0.971;0.93;0.898;0.938	P;P;P;P;B;P	0.53861	0.549;0.736;0.691;0.564;0.352;0.555	T	0.19192	-1.0313	10	0.36615	T	0.2	.	2.7427	0.05258	0.1132:0.3187:0.1154:0.4526	.	812;473;517;370;980;980	F8W7Z5;Q6ZTT5;B7Z8M3;B3KY62;Q14005;Q14005-2	.;.;.;.;IL16_HUMAN;.	P	980;812;980;517;370;279;279	ENSP00000378155:L980P;ENSP00000302935:L980P;ENSP00000378147:L279P	ENSP00000302935:L980P	L	+	2	0	IL16	79379661	0.000000	0.05858	0.000000	0.03702	0.089000	0.18198	-0.668000	0.05268	-0.031000	0.13781	0.482000	0.46254	CTT	.	.		0.537	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217		C	81592606	T	C	81592606	3	2	255	1	0	0	0	0	1	0	0	0	7642	1609	56	2	2989	2	IL16	15	81592606	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	2338054	81592606	20938786	556	35901										
MEX3B	84206	hgsc.bcm.edu	37	chr15	82335547	82335547	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgaccgcggtgtggcagaccGggcactcgggctcgctcttc	15	14	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:82335547G>T	ENST00000329713.4	-	2	2099	c.1664C>A	c.(1663-1665)cCg>cAg	p.P555Q	AC026956.1_ENST00000410589.1_RNA|MEX3B_ENST00000558133.1_3'UTR	NM_032246.4	NP_115622.2	Q6ZN04	MEX3B_HUMAN	mex-3 RNA binding family member B	555					protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.P555L(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|upper_aerodigestive_tract(1)	19						GTGGCAGACCGGGCACTCGGG	0.637																																					p.P555Q		Atlas-SNP	.											MEX3B,caecum,carcinoma,+1,1	MEX3B	50	.	1	Substitution - Missense(1)	breast(1)	c.C1664A						.						47	47	47					15																	82335547		2203	4300	6503	SO:0001583	missense	84206	exon2			CAGACCGGGCACT	AK131424	CCDS10319.1	15q25.1	2013-08-21	2013-08-21	2007-07-18	ENSG00000183496	ENSG00000183496		"RING-type (C3HC4) zinc fingers", "Mex-3 homologs"	25297	protein-coding gene	gene with protein product		611008	"ring finger and KH domain containing 3", "mex-3 homolog B (C. elegans)"	RKHD3		11230166, 17267406	Standard	NM_032246		Approved	DKFZp434J0617, RNF195	uc002bgq.2	Q6ZN04	OTTHUMG00000147356	ENST00000329713.4:c.1664C>A	chr15.hg19:g.82335547G>T	ENSP00000329918:p.Pro555Gln	89.0	0.0		59.0	3.0	NM_032246	Q4G0W1|Q8IVG2|Q9H0J0	Missense_Mutation	SNP	ENST00000329713.4	hg19	CCDS10319.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.016541	0.75161	.	.	ENSG00000183496	ENST00000329713	D	0.94613	-3.47	4.3	4.3	0.51218	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.142695	0.47093	D	0.000260	D	0.98460	0.9487	H	0.98388	4.22	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99761	1.1021	10	0.87932	D	0	-26.3696	17.2971	0.87173	0.0:0.0:1.0:0.0	.	555	Q6ZN04	MEX3B_HUMAN	Q	555	ENSP00000329918:P555Q	ENSP00000329918:P555Q	P	-	2	0	MEX3B	80122602	1.000000	0.71417	0.992000	0.48379	0.998000	0.95712	9.191000	0.94940	2.381000	0.81170	0.561000	0.74099	CCG	.	.		0.637	MEX3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304000.1	XM_290645		T	82335547	G	T	82335547	3	4	255	1	0	0	0	0	1	0	0	0	9519	1116	39	1	49	1	MEX3B	15	82335547	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	742941	82335547	20195845	557	35902										
ZNF592	9640	hgsc.bcm.edu	37	chr15	85327163	85327163	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gccattgcagaggcccccagCgagatgccaggggatgaggt	16	11	0	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:85327163C>A	ENST00000560079.2	+	4	1545	c.1257C>A	c.(1255-1257)agC>agA	p.S419R	ZNF592_ENST00000299927.3_Missense_Mutation_p.S419R	NM_014630.2	NP_055445.2	Q92610	ZN592_HUMAN	zinc finger protein 592	419					cell death (GO:0008219)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|kidney(1)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(143;0.0587)			AGGCCCCCAGCGAGATGCCAG	0.582																																					p.S419R		Atlas-SNP	.											.	ZNF592	95	.	0			c.C1257A						.						49	55	53					15																	85327163		2203	4299	6502	SO:0001583	missense	9640	exon4			CCCCAGCGAGATG	D86966	CCDS32317.1	15q25.2	2011-03-15				ENSG00000166716		"Zinc fingers, C2H2-type"	28986	protein-coding gene	gene with protein product		613624	"spinocerebellar ataxia, autosomal recessive 5"	SCAR5		9039502, 12030328, 20531441	Standard	NM_014630		Approved	KIAA0211, CAMOS	uc002bld.3	Q92610		ENST00000560079.2:c.1257C>A	chr15.hg19:g.85327163C>A	ENSP00000452877:p.Ser419Arg	80.0	0.0		100.0	4.0	NM_014630	Q2M1T2|Q504Y9	Missense_Mutation	SNP	ENST00000560079.2	hg19	CCDS32317.1	.	.	.	.	.	.	.	.	.	.	C	1.893	-0.455094	0.04540	.	.	ENSG00000166716	ENST00000299927	T	0.00620	6.17	5.65	-7.46	0.01369	.	0.491158	0.25425	N	0.030768	T	0.00384	0.0012	N	0.08118	0	0.09310	N	1	B	0.16603	0.018	B	0.15052	0.012	T	0.47661	-0.9100	10	0.45353	T	0.12	-1.8687	10.4445	0.44486	0.0:0.2587:0.1042:0.6372	.	419	Q92610	ZN592_HUMAN	R	419	ENSP00000299927:S419R	ENSP00000299927:S419R	S	+	3	2	ZNF592	83128167	0.000000	0.05858	0.007000	0.13788	0.015000	0.08874	-1.787000	0.01764	-1.212000	0.02620	-0.812000	0.03155	AGC	.	.		0.582	ZNF592-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418779.2	NM_014630		A	85327163	C	A	85327163	3	1	255	1	0	0	0	0	1	0	0	0	18037	767	27	1	1259	1	ZNF592	15	85327163	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	2991616	85327163	17204229	558	35903										
AKAP13	11214	hgsc.bcm.edu	37	chr15	86286858	86286858	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tttcagtgtccccaaaaaggAacagcatctctcggacacac	7	13	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:86286858A>G	ENST00000394518.2	+	36	8289	c.8194A>G	c.(8194-8196)Aac>Gac	p.N2732D	RP11-158M2.3_ENST00000558375.1_RNA|AKAP13_ENST00000560579.1_3'UTR|AKAP13_ENST00000394510.2_Missense_Mutation_p.N977D|AKAP13_ENST00000361243.2_Missense_Mutation_p.N2736D	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	2732	Interaction with ESR1.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						CCCAAAAAGGAACAGCATCTC	0.532																																					p.N2736D	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.A8206G						.						159	162	161					15																	86286858		2202	4299	6501	SO:0001583	missense	11214	exon36			AAAAGGAACAGCA	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"A-kinase anchor proteins", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	371	protein-coding gene	gene with protein product		604686	"lymphoid blast crisis oncogene"	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.8194A>G	chr15.hg19:g.86286858A>G	ENSP00000378026:p.Asn2732Asp	129.0	0.0		78.0	4.0	NM_006738	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	hg19	CCDS32319.1	.	.	.	.	.	.	.	.	.	.	A	13.26	2.183948	0.38609	.	.	ENSG00000170776	ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540;ENST00000394510	T;T;T	0.49139	0.79;0.79;0.79	5.72	4.6	0.57074	.	.	.	.	.	T	0.41236	0.1150	M	0.63843	1.955	0.38449	D	0.94691	P;P	0.41524	0.639;0.753	B;B	0.37091	0.122;0.241	T	0.38845	-0.9642	9	0.35671	T	0.21	.	8.371	0.32415	0.8496:0.0:0.1504:0.0	.	2732;2736	Q12802;Q12802-2	AKP13_HUMAN;.	D	2736;2732;2735;2711;977	ENSP00000354718:N2736D;ENSP00000378026:N2732D;ENSP00000378018:N977D	ENSP00000354718:N2736D	N	+	1	0	AKAP13	84087862	1.000000	0.71417	1.000000	0.80357	0.025000	0.11179	4.156000	0.58138	1.001000	0.39076	-0.297000	0.09499	AAC	.	.		0.532	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200		G	86286858	A	G	86286858	3	3	255	1	0	0	0	0	1	0	0	0	449	246	9	2	8402	2	AKAP13	15	86286858	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	959695	86286858	16244534	559	35904										
ACAN	176	hgsc.bcm.edu	37	chr15	89398363	89398363	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	acaccttcaccccccgtgccCagctggactgagctgcccag	9	19	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:89398363C>T	ENST00000561243.1	+	11	2547	c.2547C>T	c.(2545-2547)ccC>ccT	p.P849P	ACAN_ENST00000352105.7_Silent_p.P849P|ACAN_ENST00000439576.2_Silent_p.P849P|ACAN_ENST00000559004.1_Silent_p.P849P			P16112	PGCA_HUMAN	aggrecan	848					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			CCCCCGTGCCCAGCTGGACTG	0.597																																					p.P849P		Atlas-SNP	.											.	ACAN	220	.	0			c.C2547T						.						37	42	40					15																	89398363		1970	4150	6120	SO:0001819	synonymous_variant	176	exon12			CGTGCCCAGCTGG	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	319	protein-coding gene	gene with protein product	"aggrecan proteoglycan"	155760	"chondroitin sulfate proteoglycan 1", "aggrecan 1"	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.2547C>T	chr15.hg19:g.89398363C>T		142.0	0.0		110.0	5.0	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Silent	SNP	ENST00000561243.1	hg19	CCDS53970.1																																																																																			.	.		0.597	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135		T	89398363	C	T	89398363	2	4	255	1	0	0	0	0	0	0	0	1	117	581	21	3		3	ACAN	15	89398363	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	3111505	89398363	13133029	560	35905										
RLBP1	6017	hgsc.bcm.edu	37	chr15	89753607	89753607	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgggcagcgtgcccccgaagTcagagggcaggatgttctca	15	11	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:89753607T>C	ENST00000268125.5	-	9	1302	c.863A>G	c.(862-864)gAc>gGc	p.D288G		NM_000326.4	NP_000317.1	P12271	RLBP1_HUMAN	retinaldehyde binding protein 1	288	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	cell body (GO:0044297)|cytosol (GO:0005829)	11-cis retinal binding (GO:0005502)|retinol binding (GO:0019841)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(1)|prostate(1)|skin(1)	18	Lung NSC(78;0.0472)|all_lung(78;0.089)				Vitamin A(DB00162)	GCCCCCGAAGTCAGAGGGCAG	0.562																																					p.D288G		Atlas-SNP	.											.	RLBP1	34	.	0			c.A863G						.						79	76	77					15																	89753607		2200	4299	6499	SO:0001583	missense	6017	exon9			CCGAAGTCAGAGG	BC004199	CCDS32324.1	15q26.1	2007-07-16	2001-11-28			ENSG00000140522			10024	protein-coding gene	gene with protein product		180090	"retinaldehyde-binding protein 1"			1733864, 9326942	Standard	NM_000326		Approved	CRALBP	uc002bnl.3	P12271		ENST00000268125.5:c.863A>G	chr15.hg19:g.89753607T>C	ENSP00000268125:p.Asp288Gly	70.0	0.0		94.0	4.0	NM_000326	B2R667	Missense_Mutation	SNP	ENST00000268125.5	hg19	CCDS32324.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.651773	0.88056	.	.	ENSG00000140522	ENST00000268125	T	0.75260	-0.92	5.21	5.21	0.72293	Cellular retinaldehyde-binding/triple function, C-terminal (5);	0.047924	0.85682	D	0.000000	D	0.83459	0.5259	M	0.66939	2.045	0.80722	D	1	D	0.57257	0.979	D	0.62955	0.909	D	0.85519	0.1202	10	0.72032	D	0.01	-15.3192	15.084	0.72135	0.0:0.0:0.0:1.0	.	288	P12271	RLBP1_HUMAN	G	288	ENSP00000268125:D288G	ENSP00000268125:D288G	D	-	2	0	RLBP1	87554611	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	7.668000	0.83897	1.974000	0.57490	0.454000	0.30748	GAC	.	.		0.562	RLBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421135.1	NM_000326		C	89753607	T	C	89753607	3	2	255	1	0	0	0	0	1	0	0	0	13403	1667	58	2	94	2	RLBP1	15	89753607	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	355244	89753607	12777785	561	35906										
POLG	5428	hgsc.bcm.edu	37	chr15	89876764	89876764	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctcgagagcatctggatgtcCaatgggttgtgccgcagctg	14	10	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:89876764C>A	ENST00000268124.5	-	2	555	c.222G>T	c.(220-222)ttG>ttT	p.L74F	POLG_ENST00000442287.2_Missense_Mutation_p.L74F|RP11-217B1.2_ENST00000569473.1_RNA|RP11-217B1.2_ENST00000562356.1_RNA|POLG_ENST00000525806.1_5'Flank	NM_001126131.1|NM_002693.2	NP_001119603.1|NP_002684.1	P54098	DPOG1_HUMAN	polymerase (DNA directed), gamma	74					aging (GO:0007568)|base-excision repair, gap-filling (GO:0006287)|cell death (GO:0008219)|DNA metabolic process (GO:0006259)|DNA-dependent DNA replication (GO:0006261)|mitochondrial DNA replication (GO:0006264)	extracellular vesicular exosome (GO:0070062)|gamma DNA polymerase complex (GO:0005760)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|exonuclease activity (GO:0004527)|protease binding (GO:0002020)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(3)|urinary_tract(2)	33	Lung NSC(78;0.0472)|all_lung(78;0.089)		STAD - Stomach adenocarcinoma(125;0.165)			TCTGGATGTCCAATGGGTTGT	0.672								DNA polymerases (catalytic subunits)																													p.L74F	Colon(73;648 1203 11348 18386 27782)	Atlas-SNP	.											.	POLG	75	.	0			c.G222T						.						42	37	38					15																	89876764		2200	4299	6499	SO:0001583	missense	5428	exon2			GATGTCCAATGGG	X98093	CCDS10350.1	15q24	2014-09-17			ENSG00000140521	ENSG00000140521		"DNA polymerases"	9179	protein-coding gene	gene with protein product		174763				9465903	Standard	NM_002693		Approved	POLG1, POLGA	uc002bnr.4	P54098	OTTHUMG00000149646	ENST00000268124.5:c.222G>T	chr15.hg19:g.89876764C>A	ENSP00000268124:p.Leu74Phe	85.0	0.0		70.0	4.0	NM_002693	Q8NFM2|Q92515	Missense_Mutation	SNP	ENST00000268124.5	hg19	CCDS10350.1	.	.	.	.	.	.	.	.	.	.	C	17.18	3.324251	0.60634	.	.	ENSG00000140521	ENST00000268124;ENST00000442287	D;D	0.96885	-4.16;-4.16	5.07	5.07	0.68467	.	0.066963	0.64402	D	0.000018	D	0.97148	0.9068	M	0.65975	2.015	0.48830	D	0.999712	D	0.76494	0.999	D	0.85130	0.997	D	0.96671	0.9496	10	0.56958	D	0.05	-13.0334	8.5579	0.33492	0.2756:0.583:0.1414:0.0	.	74	P54098	DPOG1_HUMAN	F	74	ENSP00000268124:L74F;ENSP00000399851:L74F	ENSP00000268124:L74F	L	-	3	2	POLG	87677768	1.000000	0.71417	0.968000	0.41197	0.801000	0.45260	1.317000	0.33631	2.359000	0.80004	0.561000	0.74099	TTG	.	.		0.672	POLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000312854.2	NM_002693		A	89876764	C	A	89876764	3	1	255	1	0	0	0	0	1	0	0	0	12209	593	21	3	3585	3	POLG	15	89876764	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	123157	89876764	12654628	562	35907										
PLIN1	5346	hgsc.bcm.edu	37	chr15	90210232	90210232	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cttcagggcatctgatagggAcatggccctccccttggttg	12	12	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:90210232A>G	ENST00000300055.5	-	8	1309	c.1144T>C	c.(1144-1146)Tcc>Ccc	p.S382P	PLIN1_ENST00000430628.2_Missense_Mutation_p.S382P	NM_002666.4	NP_002657.3	O60240	PLIN1_HUMAN	perilipin 1	382					lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|lipid particle (GO:0005811)	lipid binding (GO:0008289)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|skin(2)	13						TCTGATAGGGACATGGCCCTC	0.607																																					p.S382P		Atlas-SNP	.											.	PLIN1	36	.	0			c.T1144C						.						71	57	62					15																	90210232		2200	4299	6499	SO:0001583	missense	5346	exon8			ATAGGGACATGGC	AB005293	CCDS10353.1	15q26	2009-08-12	2009-08-12	2009-08-12	ENSG00000166819	ENSG00000166819		"Perilipins"	9076	protein-coding gene	gene with protein product		170290	"perilipin"	PLIN		9521880, 19638644	Standard	NM_002666		Approved		uc010upx.1	O60240	OTTHUMG00000149813	ENST00000300055.5:c.1144T>C	chr15.hg19:g.90210232A>G	ENSP00000300055:p.Ser382Pro	120.0	0.0		87.0	4.0	NM_001145311	Q8N5Y6	Missense_Mutation	SNP	ENST00000300055.5	hg19	CCDS10353.1	.	.	.	.	.	.	.	.	.	.	A	14.43	2.534171	0.45073	.	.	ENSG00000166819	ENST00000300055;ENST00000430628	T;T	0.06068	3.35;3.35	5.13	5.13	0.70059	.	1.710450	0.03407	N	0.204264	T	0.25827	0.0629	M	0.68317	2.08	0.32269	N	0.569184	D	0.76494	0.999	D	0.72338	0.977	T	0.00318	-1.1821	10	0.52906	T	0.07	-29.9343	9.4675	0.38822	0.806:0.194:0.0:0.0	.	382	O60240	PLIN1_HUMAN	P	382	ENSP00000300055:S382P;ENSP00000402167:S382P	ENSP00000300055:S382P	S	-	1	0	PLIN1	88011236	1.000000	0.71417	0.999000	0.59377	0.156000	0.22039	2.497000	0.45354	1.933000	0.56026	0.459000	0.35465	TCC	.	.		0.607	PLIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313424.2	NM_002666		G	90210232	A	G	90210232	3	3	255	1	0	0	0	0	1	0	0	0	12098	275	10	2	432	2	PLIN1	15	90210232	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	333468	90210232	12321160	563	35908										
ANPEP	290	hgsc.bcm.edu	37	chr15	90346884	90346884	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggagcgggctgcaccttgctGtaggagatggcgtcaaacag	16	9	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:90346884G>T	ENST00000300060.6	-	8	1744	c.1431C>A	c.(1429-1431)taC>taA	p.Y477*	ANPEP_ENST00000558177.1_5'Flank	NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase	477	Metalloprotease.	Transition state stabilizer.			angiogenesis (GO:0001525)|angiotensin maturation (GO:0002003)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|viral process (GO:0016032)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|receptor activity (GO:0004872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	57	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)|Icatibant(DB06196)	GCACCTTGCTGTAGGAGATGG	0.667																																					p.Y477X	NSCLC(30;827 977 2459 19669 26125)	Atlas-SNP	.											.	ANPEP	124	.	0			c.C1431A						.						72	68	69					15																	90346884		2200	4298	6498	SO:0001587	stop_gained	290	exon8			CTTGCTGTAGGAG	M22324	CCDS10356.1	15q25-q26	2008-07-31	2008-07-31		ENSG00000166825	ENSG00000166825	3.4.11.2	"CD molecules"	500	protein-coding gene	gene with protein product	"aminopeptidase N", "aminopeptidase M", "microsomal aminopeptidase"	151530		CD13, PEPN		2428842, 1977688	Standard	NM_001150		Approved	LAP1, gp150, p150	uc002bop.4	P15144	OTTHUMG00000149814	ENST00000300060.6:c.1431C>A	chr15.hg19:g.90346884G>T	ENSP00000300060:p.Tyr477*	111.0	0.0		96.0	4.0	NM_001150	Q16728|Q6GT90|Q8IUK3|Q8IVH3|Q9UCE0	Nonsense_Mutation	SNP	ENST00000300060.6	hg19	CCDS10356.1	.	.	.	.	.	.	.	.	.	.	G	39	7.620069	0.98393	.	.	ENSG00000166825	ENST00000300060	.	.	.	4.58	2.68	0.31781	.	0.124363	0.56097	D	0.000029	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.0156	0.30379	0.2021:0.0:0.7978:0.0	.	.	.	.	X	477	.	ENSP00000300060:Y477X	Y	-	3	2	ANPEP	88147888	1.000000	0.71417	1.000000	0.80357	0.485000	0.33311	3.527000	0.53517	0.922000	0.37019	0.305000	0.20034	TAC	.	.		0.667	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313425.1			T	90346884	G	T	90346884	4	4	255	1	0	0	0	0	0	1	0	0	710	1372	48	3	1528	3	ANPEP	15	90346884	Nonsense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	136652	90346884	12184508	564	35909										
ZNF710	374655	hgsc.bcm.edu	37	chr15	90610374	90610374	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agctagccgtcacgggatggAgggcttcatggactcaggga	16	9	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:90610374A>G	ENST00000268154.4	+	2	256	c.5A>G	c.(4-6)gAg>gGg	p.E2G		NM_198526.2	NP_940928.2	Q8N1W2	ZN710_HUMAN	zinc finger protein 710	2					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(1)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	19	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.00769)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.129)			CACGGGATGGAGGGCTTCATG	0.587																																					p.E2G		Atlas-SNP	.											.	ZNF710	50	.	0			c.A5G						.						53	36	42					15																	90610374		2200	4298	6498	SO:0001583	missense	374655	exon2			GGATGGAGGGCTT	AK094712	CCDS10358.1	15q26.1	2013-01-08			ENSG00000140548	ENSG00000140548		"Zinc fingers, C2H2-type"	25352	protein-coding gene	gene with protein product							Standard	XM_005254905		Approved	DKFZp547K1113, FLJ37393, FLJ00306	uc002bov.2	Q8N1W2	OTTHUMG00000149812	ENST00000268154.4:c.5A>G	chr15.hg19:g.90610374A>G	ENSP00000268154:p.Glu2Gly	104.0	0.0		86.0	42.0	NM_198526	A0AVS3|Q6ZMK9|Q8NDU0	Missense_Mutation	SNP	ENST00000268154.4	hg19	CCDS10358.1	.	.	.	.	.	.	.	.	.	.	A	14.66	2.601097	0.46423	.	.	ENSG00000140548	ENST00000268154	T	0.12569	2.67	5.28	5.28	0.74379	.	0.000000	0.39274	N	0.001419	T	0.11281	0.0275	L	0.27053	0.805	0.49687	D	0.999815	P	0.46987	0.888	B	0.39465	0.3	T	0.03148	-1.1067	10	0.87932	D	0	-26.3241	14.2008	0.65703	1.0:0.0:0.0:0.0	.	2	Q8N1W2	ZN710_HUMAN	G	2	ENSP00000268154:E2G	ENSP00000268154:E2G	E	+	2	0	ZNF710	88411378	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.966000	0.63715	2.217000	0.71921	0.533000	0.62120	GAG	.	.		0.587	ZNF710-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313423.1	NM_198526		G	90610374	A	G	90610374	3	3	255	1	0	0	0	0	1	0	0	0	18130	304	11	2	7	2	ZNF710	15	90610374	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	263490	90610374	11921018	565	35910										
BLM	641	hgsc.bcm.edu	37	chr15	91304196	91304196	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctcacaagcactgctgtgaaAgatcagaataaacatactgc	7	10	2	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:91304196A>G	ENST00000355112.3	+	7	1711	c.1593A>G	c.(1591-1593)aaA>aaG	p.K531K	BLM_ENST00000560509.1_Silent_p.K531K	NM_000057.2	NP_000048.1	P54132	BLM_HUMAN	Bloom syndrome, RecQ helicase-like	531	Necessary for interaction with SPIDR.				alpha-beta T cell differentiation (GO:0046632)|ATP catabolic process (GO:0006200)|cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA strand renaturation (GO:0000733)|double-strand break repair via homologous recombination (GO:0000724)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell division (GO:0051782)|negative regulation of DNA recombination (GO:0045910)|negative regulation of mitotic recombination (GO:0045950)|negative regulation of thymocyte apoptotic process (GO:0070244)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of transcription, DNA-templated (GO:0045893)|protein oligomerization (GO:0051259)|regulation of binding (GO:0051098)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to X-ray (GO:0010165)|telomere maintenance (GO:0000723)	cytoplasm (GO:0005737)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nuclear chromosome (GO:0000228)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|pronucleus (GO:0045120)|replication fork (GO:0005657)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent helicase activity (GO:0008026)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|p53 binding (GO:0002039)|single-stranded DNA binding (GO:0003697)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(11)|liver(4)|lung(9)|ovary(6)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)			CTGCTGTGAAAGATCAGAATA	0.353			"Mis, N, F"			"leukemia, lymphoma, skin squamous cell , other cancers"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Bloom syndrome																												p.K531K		Atlas-SNP	.	yes	Rec		Bloom Syndrome	15	15q26.1	641	Bloom Syndrome		"L, E"	.	BLM	122	.	0			c.A1593G						.						60	62	61					15																	91304196		2198	4298	6496	SO:0001819	synonymous_variant	641	exon7	Familial Cancer Database		TGTGAAAGATCAG	U39817	CCDS10363.1, CCDS73782.1	15q26.1	2014-09-17	2009-03-19		ENSG00000197299	ENSG00000197299			1058	protein-coding gene	gene with protein product		604610	"Bloom syndrome"			9388193	Standard	NM_000057		Approved	BS, RECQL3, RECQ2	uc002bpr.3	P54132	OTTHUMG00000149834	ENST00000355112.3:c.1593A>G	chr15.hg19:g.91304196A>G		112.0	0.0		93.0	4.0	NM_000057	Q52M96	Silent	SNP	ENST00000355112.3	hg19	CCDS10363.1																																																																																			.	.		0.353	BLM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313495.1			G	91304196	A	G	91304196	2	3	255	1	0	0	0	0	0	0	0	1	1445	69	3	2		2	BLM	15	91304196	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	693822	91304196	11227196	566	35911										
FURIN	5045	hgsc.bcm.edu	37	chr15	91423173	91423173	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cagaattggaccacagtggcCccccagcggaagtgcatcat	11	13	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:91423173C>A	ENST00000268171.3	+	12	1614	c.1335C>A	c.(1333-1335)gcC>gcA	p.A445A		NM_002569.2	NP_002560.1	P09958	FURIN_HUMAN	furin (paired basic amino acid cleaving enzyme)	445					cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of low-density lipoprotein particle receptor catabolic process (GO:0032804)|negative regulation of transforming growth factor beta1 production (GO:0032911)|nerve growth factor processing (GO:0032455)|nerve growth factor production (GO:0032902)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|post-translational protein modification (GO:0043687)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)|regulation of protein catabolic process (GO:0042176)|secretion by cell (GO:0032940)|signal peptide processing (GO:0006465)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|nerve growth factor binding (GO:0048406)|peptidase activity (GO:0008233)|peptide binding (GO:0042277)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(4)|endometrium(4)|large_intestine(3)|liver(2)|lung(13)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	36	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			CCACAGTGGCCCCCCAGCGGA	0.652																																					p.A445A		Atlas-SNP	.											.	FURIN	85	.	0			c.C1335A						.						28	30	30					15																	91423173		2198	4298	6496	SO:0001819	synonymous_variant	5045	exon12			AGTGGCCCCCCAG	X17094	CCDS10364.1	15q26.1	2007-01-24	2002-12-04	2002-12-06	ENSG00000140564	ENSG00000140564			8568	protein-coding gene	gene with protein product		136950	"paired basic amino acid cleaving enzyme (furin, membrane associated receptor protein)"	PCSK3, FUR, PACE		2251280, 1741956	Standard	NM_002569		Approved	SPC1	uc002bpu.1	P09958	OTTHUMG00000149831	ENST00000268171.3:c.1335C>A	chr15.hg19:g.91423173C>A		117.0	0.0		68.0	4.0	NM_002569	Q14336|Q6LBS3|Q9UCZ5	Silent	SNP	ENST00000268171.3	hg19	CCDS10364.1	.	.	.	.	.	.	.	.	.	.	C	7.250	0.603082	0.13939	.	.	ENSG00000140564	ENST00000535252	.	.	.	4.65	4.65	0.58169	.	.	.	.	.	T	0.58750	0.2144	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.64326	-0.6434	5	0.87932	D	0	-4.0563	3.3192	0.07044	0.2843:0.4838:0.1457:0.0861	.	.	.	.	H	44	.	ENSP00000439549:P44H	P	+	2	0	FURIN	89224177	0.651000	0.27340	1.000000	0.80357	0.734000	0.41952	-0.153000	0.10144	2.410000	0.81850	0.485000	0.47835	CCC	.	.		0.652	FURIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313492.1	NM_002569		A	91423173	C	A	91423173	2	1	255	1	0	0	0	0	0	0	0	1	6107	610	22	3		3	FURIN	15	91423173	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	118977	91423173	11108219	567	35912										
CHD2	1106	hgsc.bcm.edu	37	chr15	93498741	93498741	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgagatcctcttgaaagataAggtgtgtaattaatatctaa	8	4	2	3	rs397514739		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:93498741A>G	ENST00000394196.4	+	15	2876	c.1808A>G	c.(1807-1809)aAg>aGg	p.K603R	CHD2_ENST00000557381.1_Splice_Site_p.K603R	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	603	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			TTGAAAGATAAGGTGTGTAAT	0.348																																					p.K603R		Atlas-SNP	.											.	CHD2	280	.	0			c.A1808G						.						50	45	47					15																	93498741		2196	4294	6490	SO:0001630	splice_region_variant	1106	exon15			AAGATAAGGTGTG	AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.1809+1A>G	chr15.hg19:g.93498741A>G		147.0	0.0		98.0	4.0	NM_001271	C6G482|Q96IP5	Missense_Mutation	SNP	ENST00000394196.4	hg19	CCDS10374.2	.	.	.	.	.	.	.	.	.	.	A	29.4	5.002609	0.93227	.	.	ENSG00000173575	ENST00000394196;ENST00000557381	D;D	0.93426	-3.22;-3.22	5.16	5.16	0.70880	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.35677	U	0.003046	D	0.88869	0.6554	N	0.04636	-0.2	0.80722	D	1	P;P	0.49358	0.923;0.753	P;B	0.51055	0.657;0.288	D	0.91058	0.4883	10	0.51188	T	0.08	-21.7144	14.9865	0.71351	1.0:0.0:0.0:0.0	.	603;603	O14647;O14647-2	CHD2_HUMAN;.	R	603	ENSP00000377747:K603R;ENSP00000451366:K603R	ENSP00000377747:K603R	K	+	2	0	CHD2	91299745	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	9.331000	0.96430	1.926000	0.55796	0.528000	0.53228	AAG	.	.		0.348	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271	Missense_Mutation	G	93498741	A	G	93498741	5	3	255	1	0	0	0	0	0	0	1	0	3327	86	3	2	1866	2	CHD2	15	93498741	Splice_Site	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	2075568	93498741	9032651	568	35913										
CHSY1	22856	hgsc.bcm.edu	37	chr15	101718547	101718547	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcttgtgcatccagctcctcAtgctccacaaactggatttt	6	13	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:101718547A>G	ENST00000254190.3	-	3	1930	c.1455T>C	c.(1453-1455)caT>caC	p.H485H	CHSY1_ENST00000543813.1_5'UTR	NM_014918.4	NP_055733.2	Q86X52	CHSS1_HUMAN	chondroitin sulfate synthase 1	485					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|negative regulation of ossification (GO:0030279)|response to nutrient levels (GO:0031667)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(5)|skin(1)	24	Lung NSC(78;0.00217)|all_lung(78;0.00271)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			CCAGCTCCTCATGCTCCACAA	0.478																																					p.H485H		Atlas-SNP	.											.	CHSY1	60	.	0			c.T1455C						.						51	51	51					15																	101718547		2203	4300	6503	SO:0001819	synonymous_variant	22856	exon3			CTCCTCATGCTCC	AB023207	CCDS10390.1	15q26.3	2013-02-19	2008-01-24	2008-01-24	ENSG00000131873	ENSG00000131873	2.4.1.175, 2.4.1.226	"Beta 3-glycosyltransferases", "Beta 4-glycosyltransferases"	17198	protein-coding gene	gene with protein product		608183	"carbohydrate (chondroitin) synthase 1"			11514575	Standard	NM_014918		Approved	KIAA0990, CSS1	uc021sxt.1	Q86X52	OTTHUMG00000149873	ENST00000254190.3:c.1455T>C	chr15.hg19:g.101718547A>G		93.0	0.0		81.0	4.0	NM_014918	Q6UX38|Q7LFU5|Q9Y2J5	Silent	SNP	ENST00000254190.3	hg19	CCDS10390.1																																																																																			.	.		0.478	CHSY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313624.1	NM_014918		G	101718547	A	G	101718547	2	3	255	1	0	0	0	0	0	0	0	1	3414	214	8	2		2	CHSY1	15	101718547	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	8219806	101718547	812845	569	35914										
ITFG3	83986	hgsc.bcm.edu	37	chr16	312091	312091	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgtcatcctgtgtcattgcaGgttagtggccacctctactc	9	12	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:312091G>T	ENST00000399932.3	+	7	1159		c.e7-1		ITFG3_ENST00000600536.1_Splice_Site|ITFG3_ENST00000301679.2_Splice_Site|ITFG3_ENST00000450082.2_Splice_Site|ITFG3_ENST00000442458.2_Splice_Site|ITFG3_ENST00000301678.3_Splice_Site	NM_001284497.1	NP_001271426.1	Q9H0X4	ITFG3_HUMAN	integrin alpha FG-GAP repeat containing 3							cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(3)|endometrium(2)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	16		all_cancers(16;0.000129)|all_epithelial(16;0.000206)|Hepatocellular(16;0.00264)|Lung NSC(18;0.0626)|all_lung(18;0.13)				TGTCATTGCAGGTTAGTGGCC	0.607																																					.		Atlas-SNP	.											.	ITFG3	42	.	0			c.709-1G>T						.						55	59	58					16																	312091		2171	4282	6453	SO:0001630	splice_region_variant	83986	exon7			ATTGCAGGTTAGT	AL136542	CCDS10402.1	16p13.3	2006-03-31	2006-03-31	2006-03-31	ENSG00000167930	ENSG00000167930			14163	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 9"	C16orf9			Standard	XM_005255622		Approved	DKFZP761D0211, FLJ32603	uc002cgf.3	Q9H0X4	OTTHUMG00000060728	ENST00000399932.3:c.709-1G>T	chr16.hg19:g.312091G>T		243.0	0.0		113.0	5.0	NM_032039	D3DU45|Q7L416|Q96FR1|Q96MC7|Q96S30	Splice_Site	SNP	ENST00000399932.3	hg19	CCDS10402.1	.	.	.	.	.	.	.	.	.	.	G	12.71	2.020735	0.35606	.	.	ENSG00000167930	ENST00000399932;ENST00000301679;ENST00000442458;ENST00000449945;ENST00000301678;ENST00000450082	.	.	.	4.87	4.87	0.63330	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.8952	0.63766	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ITFG3	252092	1.000000	0.71417	0.964000	0.40570	0.085000	0.17905	4.929000	0.63455	2.434000	0.82447	0.462000	0.41574	.	.	.		0.607	ITFG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134227.2	NM_032039	Intron	T	312091	G	T	312091	5	4	255	1	0	0	0	0	0	0	1	0	7880	1014	35	3	726	3	ITFG3	16	312091	Splice_Site	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10		312091	90042662	570	35915										
DECR2	26063	hgsc.bcm.edu	37	chr16	461574	461574	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cgcatccttctctgctaagcTctaggtgaggtactgctccc	9	14	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:461574T>C	ENST00000219481.5	+	8	1013	c.875T>C	c.(874-876)cTc>cCc	p.L292P	DECR2_ENST00000424398.2_Missense_Mutation_p.L280P|DECR2_ENST00000461947.1_Intron	NM_020664.3	NP_065715.1	Q9NUI1	DECR2_HUMAN	2,4-dienoyl CoA reductase 2, peroxisomal	292					unsaturated fatty acid biosynthetic process (GO:0006636)	peroxisomal membrane (GO:0005778)	2,4-dienoyl-CoA reductase (NADPH) activity (GO:0008670)|receptor binding (GO:0005102)|trans-2-enoyl-CoA reductase (NADPH) activity (GO:0019166)			central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)	9		Hepatocellular(16;0.00015)				TCTGCTAAGCTCTAGGTGAGG	0.627																																					p.L292P		Atlas-SNP	.											.	DECR2	47	.	0			c.T875C						.						120	97	105					16																	461574		2202	4300	6502	SO:0001583	missense	26063	exon8			CTAAGCTCTAGGT	AJ293009	CCDS10409.1	16p13.3	2011-09-14			ENSG00000242612	ENSG00000242612	1.3.1.34	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	2754	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 17C, member 1"	615839				11514237, 19027726	Standard	NM_020664		Approved	PDCR, SDR17C1	uc002chb.3	Q9NUI1	OTTHUMG00000047846	ENST00000219481.5:c.875T>C	chr16.hg19:g.461574T>C	ENSP00000219481:p.Leu292Pro	158.0	0.0		98.0	4.0	NM_020664	Q6ZRS7|Q96ET0	Missense_Mutation	SNP	ENST00000219481.5	hg19	CCDS10409.1	.	.	.	.	.	.	.	.	.	.	T	17.96	3.516322	0.64634	.	.	ENSG00000242612	ENST00000219481;ENST00000424398	D;T	0.82526	-1.62;-1.26	5.34	5.34	0.76211	.	0.514511	0.19597	N	0.110489	D	0.86707	0.5997	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.87882	0.2678	10	0.87932	D	0	.	14.4897	0.67642	0.0:0.0:0.0:1.0	.	292	Q9NUI1	DECR2_HUMAN	P	292;280	ENSP00000219481:L292P;ENSP00000400374:L280P	ENSP00000219481:L292P	L	+	2	0	DECR2	401575	1.000000	0.71417	1.000000	0.80357	0.751000	0.42716	7.524000	0.81866	2.030000	0.59900	0.459000	0.35465	CTC	.	.		0.627	DECR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109069.4	NM_020664		C	461574	T	C	461574	3	2	255	1	0	0	0	0	1	0	0	0	4385	1551	54	2	905	2	DECR2	16	461574	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	149483	461574	89893179	571	35916										
ATP6V0C	527	hgsc.bcm.edu	37	chr16	2564163	2564163	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tttcgccgtcatgggcgcctCggccgccatggtcttcagcg	13	15	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:2564163C>A	ENST00000330398.4	+	1	293	c.59C>A	c.(58-60)tCg>tAg	p.S20*	ATP6V0C_ENST00000565223.1_5'Flank|ATP6C_ENST00000569317.1_Nonsense_Mutation_p.S20*|RP11-20I23.1_ENST00000564543.1_Intron|ATP6V0C_ENST00000568562.1_Intron	NM_001198569.1|NM_001694.3	NP_001185498.1|NP_001685.1	P27449	VATL_HUMAN	ATPase, H+ transporting, lysosomal 16kDa, V0 subunit c	20					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of Wnt signaling pathway (GO:0030177)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|phagocytic vesicle membrane (GO:0030670)|proton-transporting V-type ATPase, V0 domain (GO:0033179)	proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|ubiquitin protein ligase binding (GO:0031625)			endometrium(1)|lung(1)|ovary(1)	3		Ovarian(90;0.17)				ATGGGCGCCTCGGCCGCCATG	0.731																																					p.S20X		Atlas-SNP	.											.	ATP6V0C	10	.	0			c.C59A						.						13	13	13					16																	2564163		2187	4284	6471	SO:0001587	stop_gained	527	exon2			GCGCCTCGGCCGC	M62762	CCDS10470.1	16p13.3	2010-04-21	2002-08-29	2002-05-10	ENSG00000185883	ENSG00000185883	3.6.3.14	"ATPases / V-type"	855	protein-coding gene	gene with protein product		108745	"ATPase, H+ transporting, lysosomal (vacuolar proton pump) 16kD"	ATPL, ATP6C, ATP6L		1709739, 8250920	Standard	NM_001694		Approved	VATL, Vma3	uc021tav.1	P27449	OTTHUMG00000128865	ENST00000330398.4:c.59C>A	chr16.hg19:g.2564163C>A	ENSP00000329757:p.Ser20*	98.0	0.0		88.0	5.0	NM_001198569	Q6FH26	Nonsense_Mutation	SNP	ENST00000330398.4	hg19	CCDS10470.1	.	.	.	.	.	.	.	.	.	.	C	40	8.243972	0.98722	.	.	ENSG00000185883	ENST00000330398	.	.	.	3.66	3.66	0.41972	.	0.000000	0.85682	U	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	-13.4529	12.9649	0.58478	0.0:1.0:0.0:0.0	.	.	.	.	X	20	.	ENSP00000329757:S20X	S	+	2	0	ATP6V0C	2504164	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.136000	0.71703	1.892000	0.54788	0.543000	0.68304	TCG	.	.		0.731	ATP6V0C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250810.1	NM_001694		A	2564163	C	A	2564163	4	1	255	1	0	0	0	0	0	1	0	0	1172	893	31	1	61	1	ATP6V0C	16	2564163	Nonsense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	2102589	2564163	87790590	572	35917										
SRRM2	23524	hgsc.bcm.edu	37	chr16	2818026	2818026	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	atgctctctgtccctgccccTggggtgccccactctgatgt	10	16	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:2818026T>C	ENST00000301740.8	+	11	8046	c.7497T>C	c.(7495-7497)ccT>ccC	p.P2499P	AC092117.2_ENST00000581119.1_RNA|SRRM2_ENST00000574593.1_3'UTR	NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	2499	Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						TCCCTGCCCCTGGGGTGCCCC	0.642																																					p.P2499P		Atlas-SNP	.											.	SRRM2	263	.	0			c.T7497C						.						68	65	66					16																	2818026		2198	4300	6498	SO:0001819	synonymous_variant	23524	exon11			TGCCCCTGGGGTG	AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.7497T>C	chr16.hg19:g.2818026T>C		121.0	0.0		80.0	4.0	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Silent	SNP	ENST00000301740.8	hg19	CCDS32373.1																																																																																			.	.		0.642	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			C	2818026	T	C	2818026	2	2	255	1	0	0	0	0	0	0	0	1	15184	1567	55	2		2	SRRM2	16	2818026	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	253863	2818026	87536727	573	35918										
THOC6	79228	hgsc.bcm.edu	37	chr16	3076554	3076554	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggctgggggagactgtcagtTgcacactatggaccttgaaa	14	8	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:3076554T>C	ENST00000326266.8	+	7	745	c.449T>C	c.(448-450)tTg>tCg	p.L150S	HCFC1R1_ENST00000248089.3_5'Flank|HCFC1R1_ENST00000396916.1_5'Flank|HCFC1R1_ENST00000574980.1_5'Flank|HCFC1R1_ENST00000572355.1_5'Flank|HCFC1R1_ENST00000574151.1_5'Flank|THOC6_ENST00000253952.9_Missense_Mutation_p.L150S|THOC6_ENST00000575576.1_Missense_Mutation_p.L126S|THOC6_ENST00000574549.1_Missense_Mutation_p.L126S|HCFC1R1_ENST00000354679.3_5'Flank	NM_024339.3	NP_077315.2	Q86W42	THOC6_HUMAN	THO complex 6 homolog (Drosophila)	150					apoptotic process (GO:0006915)|central nervous system development (GO:0007417)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	13						GACTGTCAGTTGCACACTATG	0.547																																					p.L150S		Atlas-SNP	.											.	THOC6	40	.	0			c.T449C						.						86	78	81					16																	3076554		2198	4300	6498	SO:0001583	missense	79228	exon7			GTCAGTTGCACAC	BC050674	CCDS10491.1, CCDS45392.1	16p13.3	2013-02-11	2006-03-02	2006-03-02		ENSG00000131652		"WD repeat domain containing", "THO complex subunits"	28369	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 35"	615403	"WD repeat domain 58"	WDR58		12477932	Standard	NM_024339		Approved	MGC2655, fSAP35	uc002ctb.2	Q86W42		ENST00000326266.8:c.449T>C	chr16.hg19:g.3076554T>C	ENSP00000326531:p.Leu150Ser	95.0	0.0		88.0	4.0	NM_001142350	B2RA85|Q8NBR1|Q9BTV9	Missense_Mutation	SNP	ENST00000326266.8	hg19	CCDS10491.1	.	.	.	.	.	.	.	.	.	.	T	14.56	2.570538	0.45798	.	.	ENSG00000131652	ENST00000326266;ENST00000253952	T;T	0.35421	1.31;1.31	5.7	5.7	0.88788	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.127145	0.50627	D	0.000113	T	0.33702	0.0872	L	0.34521	1.04	0.42318	D	0.992244	P;P	0.49961	0.763;0.93	B;P	0.44860	0.293;0.462	T	0.19484	-1.0304	10	0.87932	D	0	-29.3651	13.9169	0.63905	0.0:0.0:0.0:1.0	.	150;150	Q86W42-3;Q86W42	.;THOC6_HUMAN	S	150	ENSP00000326531:L150S;ENSP00000253952:L150S	ENSP00000253952:L150S	L	+	2	0	THOC6	3016555	1.000000	0.71417	0.290000	0.24890	0.989000	0.77384	6.624000	0.74243	2.178000	0.69098	0.459000	0.35465	TTG	.	.		0.547	THOC6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436981.1	NM_024339		C	3076554	T	C	3076554	3	2	255	1	0	0	0	0	1	0	0	0	15884	1821	63	2	475	2	THOC6	16	3076554	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	258528	3076554	87278199	574	35919										
MEFV	4210	hgsc.bcm.edu	37	chr16	3306411	3306411	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gcgtactcttccccatagtaGgtgaccagcagagtggccat	11	12	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:3306411G>T	ENST00000219596.1	-	1	216	c.177C>A	c.(175-177)acC>acA	p.T59T	MEFV_ENST00000541159.1_Silent_p.T59T|MEFV_ENST00000339854.4_Silent_p.T59T|MEFV_ENST00000536379.1_Silent_p.T59T	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	59	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						CCCCATAGTAGGTGACCAGCA	0.632																																					p.T59T		Atlas-SNP	.											.	MEFV	170	.	0			c.C177A						.						81	79	79					16																	3306411		2197	4300	6497	SO:0001819	synonymous_variant	4210	exon1			ATAGTAGGTGACC	AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"Tripartite motif containing / Tripartite motif containing"	6998	protein-coding gene	gene with protein product	"pyrin"	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.177C>A	chr16.hg19:g.3306411G>T		136.0	0.0		87.0	4.0	NM_000243	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Silent	SNP	ENST00000219596.1	hg19	CCDS10498.1																																																																																			.	.		0.632	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243		T	3306411	G	T	3306411	2	4	255	1	0	0	0	0	0	0	0	1	9468	987	35	3		3	MEFV	16	3306411	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	229857	3306411	87048342	575	35920										
ZNF263	10127	hgsc.bcm.edu	37	chr16	3334126	3334126	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gatccagagcagggtgcaggAgctgcatccggagagcggcg	18	10	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:3334126A>G	ENST00000219069.5	+	1	1184	c.308A>G	c.(307-309)gAg>gGg	p.E103G	ZNF263_ENST00000573578.1_Missense_Mutation_p.E103G|ZNF263_ENST00000574253.1_Missense_Mutation_p.E103G|ZNF263_ENST00000538765.1_Intron	NM_005741.4	NP_005732.2	O14978	ZN263_HUMAN	zinc finger protein 263	103	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)|skin(4)|urinary_tract(3)	20						AGGGTGCAGGAGCTGCATCCG	0.582																																					p.E103G		Atlas-SNP	.											.	ZNF263	58	.	0			c.A308G						.						74	77	76					16																	3334126		2197	4300	6497	SO:0001583	missense	10127	exon1			TGCAGGAGCTGCA	AC004232	CCDS10499.1	16p13.3	2013-01-09			ENSG00000006194	ENSG00000006194		"Zinc fingers, C2H2-type", "-", "-", "-"	13056	protein-coding gene	gene with protein product		604191				9256059	Standard	NM_005741		Approved	FPM315, ZKSCAN12, ZSCAN44	uc002cuq.3	O14978	OTTHUMG00000129323	ENST00000219069.5:c.308A>G	chr16.hg19:g.3334126A>G	ENSP00000219069:p.Glu103Gly	134.0	0.0		125.0	5.0	NM_005741	B2R634|O43387|Q96H95	Missense_Mutation	SNP	ENST00000219069.5	hg19	CCDS10499.1	.	.	.	.	.	.	.	.	.	.	A	15.57	2.874040	0.51695	.	.	ENSG00000006194	ENST00000219069	T	0.05081	3.5	5.06	5.06	0.68205	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	0.000000	0.53938	D	0.000046	T	0.09730	0.0239	N	0.25647	0.755	0.35551	D	0.803839	P;P	0.52577	0.954;0.954	P;P	0.54706	0.759;0.741	T	0.31888	-0.9927	10	0.34782	T	0.22	.	11.3814	0.49759	1.0:0.0:0.0:0.0	.	103;103	O14978;D3DUC1	ZN263_HUMAN;.	G	103	ENSP00000219069:E103G	ENSP00000219069:E103G	E	+	2	0	ZNF263	3274127	0.994000	0.37717	1.000000	0.80357	0.997000	0.91878	0.634000	0.24614	2.251000	0.74343	0.533000	0.62120	GAG	.	.		0.582	ZNF263-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251463.2			G	3334126	A	G	3334126	3	3	255	1	0	0	0	0	1	0	0	0	17818	304	11	2	310	2	ZNF263	16	3334126	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	27715	3334126	87020627	576	35921										
DNASE1	1773	hgsc.bcm.edu	37	chr16	3705477	3705477	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcaacatccagacatttgggGagaccaagatgtccaatgcc	9	11	1	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:3705477G>A	ENST00000246949.5	+	2	3312	c.103G>A	c.(103-105)Gag>Aag	p.E35K	DNASE1_ENST00000407479.1_Missense_Mutation_p.E35K|DNASE1_ENST00000414110.2_5'UTR	NM_005223.3	NP_005214.2	P24855	DNAS1_HUMAN	deoxyribonuclease I	35					apoptotic process (GO:0006915)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	deoxyribonuclease I activity (GO:0004530)			lung(1)	1		Ovarian(90;0.0261)		Kidney(780;0.0556)		GACATTTGGGGAGACCAAGAT	0.627																																					p.E35K		Atlas-SNP	.											.	DNASE1	16	.	0			c.G103A						.						79	66	71					16																	3705477		2197	4300	6497	SO:0001583	missense	1773	exon2			TTTGGGGAGACCA		CCDS10507.1	16p13.3	2008-02-05			ENSG00000213918	ENSG00000213918	3.1.21.1		2956	protein-coding gene	gene with protein product		125505		DNL1		2349940	Standard	XM_005255148		Approved		uc002cvr.3	P24855	OTTHUMG00000129426	ENST00000246949.5:c.103G>A	chr16.hg19:g.3705477G>A	ENSP00000246949:p.Glu35Lys	139.0	0.0		82.0	4.0	NM_005223	B4DV35|Q14UU9|Q14UV0	Missense_Mutation	SNP	ENST00000246949.5	hg19	CCDS10507.1	.	.	.	.	.	.	.	.	.	.	G	33	5.211441	0.95069	.	.	ENSG00000213918	ENST00000407479;ENST00000246949	T;T	0.59083	0.29;0.29	5.39	5.39	0.77823	Endonuclease/exonuclease/phosphatase (2);	0.284400	0.39475	N	0.001348	T	0.64843	0.2635	L	0.58669	1.825	0.80722	D	1	P	0.50066	0.931	P	0.52424	0.698	T	0.60826	-0.7186	10	0.27082	T	0.32	-26.2267	16.3008	0.82811	0.0:0.0:1.0:0.0	.	35	P24855	DNAS1_HUMAN	K	35	ENSP00000385905:E35K;ENSP00000246949:E35K	ENSP00000246949:E35K	E	+	1	0	DNASE1	3645478	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.992000	0.56980	2.543000	0.85770	0.561000	0.74099	GAG	.	.		0.627	DNASE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251585.2			A	3705477	G	A	3705477	3	1	255	1	0	0	0	0	1	0	0	0	4662	1175	41	3	105	3	DNASE1	16	3705477	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	371351	3705477	86649276	577	35922										
MGRN1	23295	hgsc.bcm.edu	37	chr16	4715144	4715144	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cccacgtgctcttggctgccTttgaaaaggtaagtgccatc	10	12	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:4715144T>C	ENST00000399577.5	+	7	763	c.670T>C	c.(670-672)Ttt>Ctt	p.F224L	MGRN1_ENST00000262370.7_Missense_Mutation_p.F224L|MGRN1_ENST00000586183.1_Missense_Mutation_p.F224L|MGRN1_ENST00000588994.1_Missense_Mutation_p.F224L|MGRN1_ENST00000415496.1_Missense_Mutation_p.F225L	NM_001142290.2	NP_001135762.1	O60291	MGRN1_HUMAN	mahogunin ring finger 1, E3 ubiquitin protein ligase	224					endosome to lysosome transport (GO:0008333)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18						CTTGGCTGCCTTTGAAAAGGT	0.642																																					p.F224L		Atlas-SNP	.											.	MGRN1	66	.	0			c.T670C						.						54	60	58					16																	4715144		2056	4193	6249	SO:0001583	missense	23295	exon7			GCTGCCTTTGAAA	AB011116	CCDS42115.1, CCDS45401.1, CCDS45402.1, CCDS45401.2, CCDS59256.1	16p13	2012-02-23	2012-02-23					"RING-type (C3HC4) zinc fingers"	20254	protein-coding gene	gene with protein product		607559	"mahogunin, ring finger 1"			9628581	Standard	NM_015246		Approved	KIAA0544, RNF156	uc002cxa.3	O60291		ENST00000399577.5:c.670T>C	chr16.hg19:g.4715144T>C	ENSP00000382487:p.Phe224Leu	154.0	0.0		61.0	4.0	NM_001142291	A4URL3|A4URL4|Q86W76	Missense_Mutation	SNP	ENST00000399577.5	hg19	CCDS45402.1	.	.	.	.	.	.	.	.	.	.	t	19.62	3.862379	0.71949	.	.	ENSG00000102858	ENST00000262370;ENST00000399577;ENST00000415496;ENST00000536343	T;T;T;T	0.27256	1.68;1.68;1.68;1.68	4.99	3.9	0.45041	.	0.047367	0.85682	N	0.000000	T	0.36413	0.0966	L	0.41356	1.27	0.58432	D	0.999994	D;D;D;D;P;D	0.76494	0.998;0.999;0.999;0.999;0.815;0.997	D;D;D;D;P;D	0.87578	0.998;0.99;0.97;0.978;0.646;0.995	T	0.04870	-1.0921	10	0.29301	T	0.29	-6.8499	8.5715	0.33572	0.0:0.088:0.0:0.912	.	224;224;224;225;224;224	O60291-4;O60291-3;B4DR12;E9PB19;O60291-2;O60291	.;.;.;.;.;MGRN1_HUMAN	L	224;224;225;224	ENSP00000262370:F224L;ENSP00000382487:F224L;ENSP00000393311:F225L;ENSP00000443810:F224L	ENSP00000262370:F224L	F	+	1	0	MGRN1	4655145	1.000000	0.71417	1.000000	0.80357	0.582000	0.36321	5.766000	0.68843	0.941000	0.37499	-0.259000	0.10710	TTT	.	.		0.642	MGRN1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000432060.2			C	4715144	T	C	4715144	3	2	255	1	0	0	0	0	1	0	0	0	9568	1609	56	2	699	2	MGRN1	16	4715144	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	1009667	4715144	85639609	578	35923										
GRIN2A	2903	hgsc.bcm.edu	37	chr16	9857312	9857312	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gagtggaggaaagggttatcGgaggtgtggtctggcaagag	20	3	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:9857312G>T	ENST00000396573.2	-	14	4398	c.4089C>A	c.(4087-4089)tcC>tcA	p.S1363S	GRIN2A_ENST00000396575.2_Silent_p.S1363S|GRIN2A_ENST00000562109.1_Intron|GRIN2A_ENST00000535259.1_Intron|GRIN2A_ENST00000404927.2_Intron|GRIN2A_ENST00000330684.3_Silent_p.S1363S	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	1363					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)	p.S1363S(1)		NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	AAGGGTTATCGGAGGTGTGGT	0.557																																					p.S1363S		Atlas-SNP	.											GRIN2A,NS,carcinoma,0,1	GRIN2A	366	.	1	Substitution - coding silent(1)	lung(1)	c.C4089A						.						72	68	69					16																	9857312		2197	4300	6497	SO:0001819	synonymous_variant	2903	exon14			GTTATCGGAGGTG		CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.4089C>A	chr16.hg19:g.9857312G>T		120.0	0.0		63.0	4.0	NM_000833	O00669|Q17RZ6	Silent	SNP	ENST00000396573.2	hg19	CCDS10539.1																																																																																			.	.		0.557	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			T	9857312	G	T	9857312	2	4	255	1	0	0	0	0	0	0	0	1	6788	1103	39	1		1	GRIN2A	16	9857312	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	5142168	9857312	80497441	579	35924										
GRIN2A	2903	hgsc.bcm.edu	37	chr16	9862782	9862782	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gaagcgcagcttccagtagaAgaggtgctcccagatgaagg	14	9	0	4			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:9862782A>G	ENST00000396573.2	-	13	2830	c.2521T>C	c.(2521-2523)Ttc>Ctc	p.F841L	GRIN2A_ENST00000396575.2_Missense_Mutation_p.F841L|GRIN2A_ENST00000562109.1_Missense_Mutation_p.F841L|GRIN2A_ENST00000535259.1_Missense_Mutation_p.F684L|GRIN2A_ENST00000404927.2_Missense_Mutation_p.F841L|GRIN2A_ENST00000330684.3_Missense_Mutation_p.F841L	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	841					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	TTCCAGTAGAAGAGGTGCTCC	0.582																																					p.F841L		Atlas-SNP	.											.	GRIN2A	366	.	0			c.T2521C						.						93	81	85					16																	9862782		2197	4300	6497	SO:0001583	missense	2903	exon13			AGTAGAAGAGGTG		CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.2521T>C	chr16.hg19:g.9862782A>G	ENSP00000379818:p.Phe841Leu	77.0	0.0		55.0	5.0	NM_000833	O00669|Q17RZ6	Missense_Mutation	SNP	ENST00000396573.2	hg19	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	A	27.8	4.862599	0.91511	.	.	ENSG00000183454	ENST00000396573;ENST00000404927;ENST00000535259;ENST00000330684;ENST00000396575	T;T;T;T;T	0.38722	1.12;1.12;1.12;1.12;1.12	4.3	4.3	0.51218	Glutamate [NMDA] receptor, epsilon subunit, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.64170	0.2574	M	0.80746	2.51	0.80722	D	1	D;D;D	0.64830	0.992;0.994;0.979	D;D;D	0.73708	0.968;0.981;0.973	T	0.67971	-0.5532	9	.	.	.	.	12.9416	0.58348	1.0:0.0:0.0:0.0	.	684;841;841	F5GZ52;Q17RZ6;Q12879	.;.;NMDE1_HUMAN	L	841;841;684;841;841	ENSP00000379818:F841L;ENSP00000385872:F841L;ENSP00000441572:F684L;ENSP00000332549:F841L;ENSP00000379820:F841L	.	F	-	1	0	GRIN2A	9770283	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.176000	0.94839	1.692000	0.51112	0.460000	0.39030	TTC	.	.		0.582	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			G	9862782	A	G	9862782	3	3	255	1	0	0	0	0	1	0	0	0	6788	72	3	2	1881	2	GRIN2A	16	9862782	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	5470	9862782	80491971	580	35925										
GRIN2A	2903	hgsc.bcm.edu	37	chr16	9943750	9943750	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttgtcatccggctcacagtcGgagaaggacttgtacctggg	13	10	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:9943750G>T	ENST00000396573.2	-	6	1500	c.1191C>A	c.(1189-1191)tcC>tcA	p.S397S	GRIN2A_ENST00000396575.2_Silent_p.S397S|GRIN2A_ENST00000562109.1_Silent_p.S397S|GRIN2A_ENST00000535259.1_Silent_p.S240S|GRIN2A_ENST00000404927.2_Silent_p.S397S|GRIN2A_ENST00000330684.3_Silent_p.S397S	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	397					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GCTCACAGTCGGAGAAGGACT	0.582																																					p.S397S		Atlas-SNP	.											.	GRIN2A	366	.	0			c.C1191A						.						135	111	119					16																	9943750		2197	4300	6497	SO:0001819	synonymous_variant	2903	exon6			ACAGTCGGAGAAG		CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.1191C>A	chr16.hg19:g.9943750G>T		120.0	0.0		62.0	4.0	NM_000833	O00669|Q17RZ6	Silent	SNP	ENST00000396573.2	hg19	CCDS10539.1																																																																																			.	.		0.582	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			T	9943750	G	T	9943750	2	4	255	1	0	0	0	0	0	0	0	1	6788	1103	39	1		1	GRIN2A	16	9943750	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	80968	9943750	80411003	581	35926										
RSL1D1	26156	hgsc.bcm.edu	37	chr16	11935611	11935611	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	atcccaattgctgacaaacgAggaaaagatgggaagtgcag	12	7	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:11935611A>G	ENST00000571133.1	-	7	868	c.796T>C	c.(796-798)Tcg>Ccg	p.S266P	RSL1D1_ENST00000542106.1_Missense_Mutation_p.S46P	NM_015659.2	NP_056474.2	O76021	RL1D1_HUMAN	ribosomal L1 domain containing 1	266					osteoblast differentiation (GO:0001649)|regulation of apoptotic process (GO:0042981)|regulation of cellular senescence (GO:2000772)|regulation of protein localization (GO:0032880)	membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|stomach(2)|urinary_tract(2)	15						CTGACAAACGAGGAAAAGATG	0.363																																					p.S266P		Atlas-SNP	.											.	RSL1D1	40	.	0			c.T796C						.						73	74	73					16																	11935611		2197	4300	6497	SO:0001583	missense	26156	exon7			CAAACGAGGAAAA	AY154473	CCDS10551.1	16p13.13	2011-08-12			ENSG00000171490	ENSG00000171490			24534	protein-coding gene	gene with protein product		615874				15334068, 9859858	Standard	NM_015659		Approved	PBK1, L12, DKFZP564M182, CSIG, UTP30	uc002dbp.1	O76021	OTTHUMG00000129824	ENST00000571133.1:c.796T>C	chr16.hg19:g.11935611A>G	ENSP00000460871:p.Ser266Pro	135.0	0.0		122.0	5.0	NM_015659	B4DJ58|D3DUG7|Q2M1T7|Q6PL22|Q8IWS7|Q8WUZ1|Q9HDA9|Q9Y3Z9	Missense_Mutation	SNP	ENST00000571133.1	hg19	CCDS10551.1	.	.	.	.	.	.	.	.	.	.	A	13.96	2.393795	0.42410	.	.	ENSG00000171490	ENST00000355674;ENST00000396503;ENST00000542106	T	0.51817	0.69	4.91	4.91	0.64330	.	0.072138	0.56097	D	0.000021	T	0.65407	0.2688	M	0.78456	2.415	0.46927	D	0.999259	D;D	0.76494	0.999;0.999	D;D	0.70227	0.949;0.968	T	0.68938	-0.5277	10	0.66056	D	0.02	-7.6655	9.1436	0.36919	0.8164:0.1836:0.0:0.0	.	266;266	Q32Q62;O76021	.;RL1D1_HUMAN	P	265;266;46	ENSP00000347897:S265P	ENSP00000347897:S265P	S	-	1	0	RSL1D1	11843112	1.000000	0.71417	0.876000	0.34364	0.081000	0.17604	4.390000	0.59646	1.975000	0.57531	0.397000	0.26171	TCG	.	.		0.363	RSL1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252059.2	NM_015659		G	11935611	A	G	11935611	3	3	255	1	0	0	0	0	1	0	0	0	13715	304	11	2	688	2	RSL1D1	16	11935611	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	1991861	11935611	78419142	582	35927										
SMG1	23049	hgsc.bcm.edu	37	chr16	18863750	18863750	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gacaggtgatacaactgtccCaaaatgaagtcaggttctcc	9	10	2	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:18863750C>A	ENST00000446231.2	-	32	5215	c.4803G>T	c.(4801-4803)ttG>ttT	p.L1601F	SMG1_ENST00000389467.3_Missense_Mutation_p.L1601F			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	1601	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.|Interaction with SMG8 and SMG9.				DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.L1601F(1)|p.L1597F(1)		NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						ACAACTGTCCCAAAATGAAGT	0.418																																					p.L1601F		Atlas-SNP	.											.	SMG1	401	.	2	Substitution - Missense(2)	lung(2)	c.G4803T						.						50	46	47					16																	18863750		1922	4146	6068	SO:0001583	missense	23049	exon32			CTGTCCCAAAATG	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase-related kinase"	607032	"smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.4803G>T	chr16.hg19:g.18863750C>A	ENSP00000402515:p.Leu1601Phe	109.0	0.0		88.0	4.0	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	ENST00000446231.2	hg19	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	C	17.33	3.361432	0.61403	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	T;T	0.01178	5.22;5.23	5.07	5.07	0.68467	PIK-related kinase (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.46758	D	0.000267	T	0.01523	0.0049	L	0.34521	1.04	0.44012	D	0.996726	P	0.41313	0.745	B	0.35413	0.202	T	0.69716	-0.5070	10	0.59425	D	0.04	.	18.8053	0.92034	0.0:1.0:0.0:0.0	.	1601	Q96Q15	SMG1_HUMAN	F	1601	ENSP00000402515:L1601F;ENSP00000374118:L1601F	ENSP00000374118:L1601F	L	-	3	2	SMG1	18771251	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.979000	0.49313	2.513000	0.84729	0.462000	0.41574	TTG	.	.		0.418	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		A	18863750	C	A	18863750	3	1	255	1	0	0	0	0	1	0	0	0	14810	593	21	3	6310	3	SMG1	16	18863750	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	6928139	18863750	71491003	583	35928										
GTF3C1	2975	hgsc.bcm.edu	37	chr16	27506736	27506736	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggcagggtgcccgtagatgaGgtaccacagaaacatgtgga	15	8	0	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:27506736G>T	ENST00000356183.4	-	15	2443	c.2428C>A	c.(2428-2430)Ctc>Atc	p.L810I	GTF3C1_ENST00000561623.1_Missense_Mutation_p.L810I	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	810					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						CCGTAGATGAGGTACCACAGA	0.587																																					p.L810I		Atlas-SNP	.											.	GTF3C1	210	.	0			c.C2428A						.						45	39	41					16																	27506736		2197	4300	6497	SO:0001583	missense	2975	exon15			AGATGAGGTACCA	U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"General transcription factors"	4664	protein-coding gene	gene with protein product		603246	"general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.2428C>A	chr16.hg19:g.27506736G>T	ENSP00000348510:p.Leu810Ile	134.0	0.0		88.0	4.0	NM_001520	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Missense_Mutation	SNP	ENST00000356183.4	hg19	CCDS32414.1	.	.	.	.	.	.	.	.	.	.	G	18.11	3.549773	0.65311	.	.	ENSG00000077235	ENST00000356183;ENST00000388971	T	0.35973	1.28	5.55	4.4	0.53042	.	0.086693	0.48286	D	0.000186	T	0.32704	0.0838	L	0.48877	1.53	0.41008	D	0.98498	D;P	0.54397	0.966;0.886	P;P	0.45794	0.493;0.491	T	0.07790	-1.0754	10	0.48119	T	0.1	-20.3752	7.9264	0.29876	0.1224:0.0:0.7202:0.1574	.	810;810	Q12789;Q12789-3	TF3C1_HUMAN;.	I	810;808	ENSP00000348510:L810I	ENSP00000348510:L810I	L	-	1	0	GTF3C1	27414237	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	0.951000	0.29135	2.603000	0.88011	0.655000	0.94253	CTC	.	.		0.587	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520		T	27506736	G	T	27506736	3	4	255	1	0	0	0	0	1	0	0	0	6881	1000	35	3	3993	3	GTF3C1	16	27506736	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	8642986	27506736	62848017	584	35929										
SH2B1	25970	hgsc.bcm.edu	37	chr16	28884047	28884047	+	Intron	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gtgagcagagcaggtctgcaGgggaggaggtgcccgtgcac	19	9	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:28884047G>T	ENST00000322610.8	+	10	2336				SH2B1_ENST00000395532.4_Intron|SH2B1_ENST00000545570.1_Missense_Mutation_p.G330W|SH2B1_ENST00000563674.1_Intron|SH2B1_ENST00000337120.5_Intron|SH2B1_ENST00000538342.1_Intron|SH2B1_ENST00000359285.5_Missense_Mutation_p.G640W			Q9NRF2	SH2B1_HUMAN	SH2B adaptor protein 1						blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|intracellular signal transduction (GO:0035556)|lamellipodium assembly (GO:0030032)|positive regulation of mitosis (GO:0045840)|regulation of DNA biosynthetic process (GO:2000278)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25						CAGGTCTGCAGGGGAGGAGGT	0.607																																					p.G640W		Atlas-SNP	.											.	SH2B1	160	.	0			c.G1918T						.						49	42	45					16																	28884047		2197	4300	6497	SO:0001627	intron_variant	25970	exon8			TCTGCAGGGGAGG	AK055104	CCDS32424.1, CCDS53996.1, CCDS53997.1	16p11.2	2013-02-14						"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	30417	protein-coding gene	gene with protein product	"SH2-B homolog"	608937				11827956, 10594240	Standard	NM_001145812		Approved	FLJ30542, SH2B	uc002drl.3	Q9NRF2		ENST00000322610.8:c.1897+21G>T	chr16.hg19:g.28884047G>T		181.0	0.0		96.0	4.0	NM_001145797	A8K2R7|Q96FK3|Q96SX3|Q9NRF1|Q9NRF3|Q9P2P7|Q9Y3Y3	Missense_Mutation	SNP	ENST00000322610.8	hg19	CCDS53996.1	.	.	.	.	.	.	.	.	.	.	g	16.30	3.083218	0.55861	.	.	ENSG00000178188	ENST00000545570;ENST00000359285	T;T	0.46063	1.57;0.88	5.1	5.1	0.69264	.	.	.	.	.	T	0.46367	0.1389	N	0.14661	0.345	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	T	0.45381	-0.9265	9	0.37606	T	0.19	.	14.0194	0.64545	0.0:0.0:1.0:0.0	.	330;640	F5GXU7;Q9NRF2-3	.;.	W	330;640	ENSP00000440354:G330W;ENSP00000352232:G640W	ENSP00000352232:G640W	G	+	1	0	SH2B1	28791548	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.294000	0.51787	2.363000	0.80096	0.558000	0.71614	GGG	.	.		0.607	SH2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000432666.1	NM_015503		T	28884047	G	T	28884047	1	4	255	0	1	0	0	0	0	0	0	0	14242	1000	35	3		3	SH2B1	16	28884047	Intron	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	1377311	28884047	61470706	585	35930										
ATP2A1	487	hgsc.bcm.edu	37	chr16	28914131	28914131	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cagtgcaccgaggacaacacCcactttgagggcatagactg	11	12	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:28914131C>A	ENST00000357084.3	+	19	2910	c.2643C>A	c.(2641-2643)acC>acA	p.T881T	ATP2A1_ENST00000395503.4_Silent_p.T881T|ATP2A1_ENST00000536376.1_Silent_p.T756T	NM_173201.3	NP_775293.1	O14983	AT2A1_HUMAN	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	881					apoptotic mitochondrial changes (GO:0008637)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|ion transmembrane transport (GO:0034220)|maintenance of mitochondrion location (GO:0051659)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|negative regulation of striated muscle contraction (GO:0045988)|positive regulation of endoplasmic reticulum calcium ion concentration (GO:0032470)|positive regulation of fast-twitch skeletal muscle fiber contraction (GO:0031448)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|regulation of striated muscle contraction (GO:0006942)|relaxation of skeletal muscle (GO:0090076)|response to endoplasmic reticulum stress (GO:0034976)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|H zone (GO:0031673)|I band (GO:0031674)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-transporting ATPase activity (GO:0005388)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(2)	38						AGGACAACACCCACTTTGAGG	0.602																																					p.T881T		Atlas-SNP	.											.	ATP2A1	116	.	0			c.C2643A						.						91	78	82					16																	28914131		2197	4300	6497	SO:0001819	synonymous_variant	487	exon19			CAACACCCACTTT		CCDS10643.1, CCDS42139.1, CCDS66997.1	16p12.1	2012-10-22			ENSG00000196296	ENSG00000196296	3.6.3.8	"ATPases / P-type"	811	protein-coding gene	gene with protein product	"sarcoplasmic/endoplasmic reticulum calcium ATPase 1", "calcium pump 1"	108730		ATP2A			Standard	NM_004320		Approved	SERCA1	uc002dro.1	O14983	OTTHUMG00000131760	ENST00000357084.3:c.2643C>A	chr16.hg19:g.28914131C>A		160.0	0.0		121.0	5.0	NM_004320	A8K5J9|B3KY17|O14984	Silent	SNP	ENST00000357084.3	hg19	CCDS10643.1																																																																																			.	.		0.602	ATP2A1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254686.2	NM_004320		A	28914131	C	A	28914131	2	1	255	1	0	0	0	0	0	0	0	1	1136	610	22	3		3	ATP2A1	16	28914131	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	30084	28914131	61440622	586	35931										
CORO1A	11151	hgsc.bcm.edu	37	chr16	30196584	30196584	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cgccacgtgtttggacagccGgccaaggccgaccagtgcta	13	14	0	0	rs61736363		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:30196584G>T	ENST00000219150.5	+	2	359	c.54G>T	c.(52-54)ccG>ccT	p.P18P	RP11-455F5.5_ENST00000566144.1_RNA|CORO1A_ENST00000570045.1_Silent_p.P18P|CORO1A_ENST00000565497.1_Silent_p.P18P|RP11-455F5.5_ENST00000568506.1_RNA|CORO1A_ENST00000566619.1_3'UTR|RP11-455F5.5_ENST00000567153.1_RNA	NM_001193333.2|NM_007074.3	NP_001180262.1|NP_009005.1	P31146	COR1A_HUMAN	coronin, actin binding protein, 1A	18					actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|calcium ion transport (GO:0006816)|cell-substrate adhesion (GO:0031589)|cellular component movement (GO:0006928)|cellular response to interleukin-4 (GO:0071353)|homeostasis of number of cells within a tissue (GO:0048873)|innate immune response (GO:0045087)|leukocyte chemotaxis (GO:0030595)|negative regulation of actin nucleation (GO:0051126)|phagocytosis (GO:0006909)|phagolysosome assembly (GO:0001845)|positive chemotaxis (GO:0050918)|positive regulation of cell migration (GO:0030335)|positive regulation of T cell proliferation (GO:0042102)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|T cell homeostasis (GO:0043029)|uropod organization (GO:0032796)	actin filament (GO:0005884)|cell-cell junction (GO:0005911)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|lamellipodium (GO:0030027)|membrane (GO:0016020)|phagocytic cup (GO:0001891)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	actin filament binding (GO:0051015)|cytoskeletal protein binding (GO:0008092)|phosphatidylinositol 3-kinase binding (GO:0043548)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	9						TTGGACAGCCGGCCAAGGCCG	0.577																																					p.P18P		Atlas-SNP	.											.	CORO1A	36	.	0			c.G54T						.						95	83	87					16																	30196584		2197	4300	6497	SO:0001819	synonymous_variant	11151	exon2			ACAGCCGGCCAAG	X89109	CCDS10673.1	16p11.2	2014-09-17	2001-11-28		ENSG00000102879	ENSG00000102879		"Coronins", "WD repeat domain containing"	2252	protein-coding gene	gene with protein product	"Clabp TACO"	605000	"coronin, actin-binding protein, 1A"			9778037	Standard	NM_007074		Approved	HCORO1, p57, coronin-1	uc002dww.3	P31146	OTTHUMG00000132148	ENST00000219150.5:c.54G>T	chr16.hg19:g.30196584G>T		127.0	0.0		93.0	4.0	NM_007074	B2RBL1|Q2YD73	Silent	SNP	ENST00000219150.5	hg19	CCDS10673.1																																																																																			.	G|0.986;C|0.014		0.577	CORO1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255195.2	NM_007074		T	30196584	G	T	30196584	2	4	255	1	0	0	0	0	0	0	0	1	3755	1103	39	1		1	CORO1A	16	30196584	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	1282453	30196584	60158169	587	35932										
ZNF629	23361	hgsc.bcm.edu	37	chr16	30795164	30795164	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggtgccgcagcagcttggacCactggctgaagctcttgccg	14	13	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:30795164C>T	ENST00000262525.4	-	3	692	c.485G>A	c.(484-486)tGg>tAg	p.W162*		NM_001080417.1	NP_001073886.1	Q9UEG4	ZN629_HUMAN	zinc finger protein 629	162					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(3)|urinary_tract(1)	22			Colorectal(24;0.198)			CAGCTTGGACCACTGGCTGAA	0.692																																					p.W162X		Atlas-SNP	.											.	ZNF629	44	.	0			c.G485A						.						31	33	33					16																	30795164		2197	4299	6496	SO:0001587	stop_gained	23361	exon3			TTGGACCACTGGC	AB002324	CCDS45463.1	16p11.2	2013-01-08				ENSG00000102870		"Zinc fingers, C2H2-type"	29008	protein-coding gene	gene with protein product			"zinc finger protein 65"	ZNF65		9205841	Standard	NM_001080417		Approved	KIAA0326	uc002dzs.1	Q9UEG4		ENST00000262525.4:c.485G>A	chr16.hg19:g.30795164C>T	ENSP00000262525:p.Trp162*	153.0	0.0		99.0	4.0	NM_001080417	Q15938	Nonsense_Mutation	SNP	ENST00000262525.4	hg19	CCDS45463.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.746570	0.89663	.	.	ENSG00000102870	ENST00000262525	.	.	.	4.89	4.89	0.63831	.	0.000000	0.42682	D	0.000674	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	-19.9411	10.8269	0.46638	0.0:0.9108:0.0:0.0892	.	.	.	.	X	162	.	ENSP00000262525:W162X	W	-	2	0	ZNF629	30702665	0.000000	0.05858	1.000000	0.80357	0.997000	0.91878	0.009000	0.13219	2.416000	0.81992	0.561000	0.74099	TGG	.	.		0.692	ZNF629-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434291.1	NM_015309		T	30795164	C	T	30795164	4	4	255	1	0	0	0	0	0	1	0	0	18068	595	21	3	2128	3	ZNF629	16	30795164	Nonsense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	598580	30795164	59559589	588	35933										
ZNF646	9726	hgsc.bcm.edu	37	chr16	31088245	31088245	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gccagagcccctcctctcccCatcccagccagcagccttct	6	22	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:31088245C>T	ENST00000394979.2	+	1	1023	c.600C>T	c.(598-600)ccC>ccT	p.P200P	ZNF646_ENST00000300850.5_Silent_p.P200P|ZNF668_ENST00000300849.4_5'Flank|ZNF668_ENST00000564456.1_5'Flank			O15015	ZN646_HUMAN	zinc finger protein 646	200					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(1)|lung(21)|ovary(1)|prostate(4)|skin(3)	49						CTCCTCTCCCCATCCCAGCCA	0.602																																					p.P200P		Atlas-SNP	.											.	ZNF646	133	.	0			c.C600T						.						45	50	48					16																	31088245		2196	4300	6496	SO:0001819	synonymous_variant	9726	exon2			TCTCCCCATCCCA	AB002294	CCDS10702.1	16p11.2	2013-01-08			ENSG00000167395	ENSG00000167395		"Zinc fingers, C2H2-type"	29004	protein-coding gene	gene with protein product							Standard	NM_014699		Approved	KIAA0296	uc002eap.3	O15015	OTTHUMG00000047355	ENST00000394979.2:c.600C>T	chr16.hg19:g.31088245C>T		91.0	0.0		71.0	6.0	NM_014699	Q8IVD8	Silent	SNP	ENST00000394979.2	hg19																																																																																				.	.		0.602	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699		T	31088245	C	T	31088245	2	4	255	1	0	0	0	0	0	0	0	1	18077	581	21	3		3	ZNF646	16	31088245	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	293081	31088245	59266508	589	35934										
SLC5A2	6524	hgsc.bcm.edu	37	chr16	31499986	31499986	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gtcatgctggccgcgctcatGtcctcgctggcctccatctt	10	16	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:31499986G>T	ENST00000330498.3	+	10	1192	c.1173G>T	c.(1171-1173)atG>atT	p.M391I	AC026471.6_ENST00000565137.1_RNA	NM_003041.3	NP_003032.1	P31639	SC5A2_HUMAN	solute carrier family 5 (sodium/glucose cotransporter), member 2	391					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	low-affinity glucose:sodium symporter activity (GO:0005362)			endometrium(2)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	25					Canagliflozin(DB08907)|Dapagliflozin(DB06292)	CCGCGCTCATGTCCTCGCTGG	0.706																																					p.M391I		Atlas-SNP	.											.	SLC5A2	58	.	0			c.G1173T						.						28	25	26					16																	31499986		2196	4299	6495	SO:0001583	missense	6524	exon10			GCTCATGTCCTCG		CCDS10714.1	16p11.2	2013-05-22			ENSG00000140675	ENSG00000140675		"Solute carriers"	11037	protein-coding gene	gene with protein product		182381		SGLT2		8244402	Standard	NM_003041		Approved		uc002ecf.4	P31639	OTTHUMG00000176620	ENST00000330498.3:c.1173G>T	chr16.hg19:g.31499986G>T	ENSP00000327943:p.Met391Ile	113.0	0.0		56.0	4.0	NM_003041	A2RRD2	Missense_Mutation	SNP	ENST00000330498.3	hg19	CCDS10714.1	.	.	.	.	.	.	.	.	.	.	G	32	5.107688	0.94292	.	.	ENSG00000140675	ENST00000330498	D	0.90955	-2.76	4.7	4.7	0.59300	.	0.000000	0.85682	D	0.000000	D	0.93350	0.7880	L	0.49455	1.56	0.80722	D	1	D	0.59357	0.985	D	0.72338	0.977	D	0.93607	0.6935	10	0.59425	D	0.04	.	15.2095	0.73209	0.0:0.0:1.0:0.0	.	391	P31639	SC5A2_HUMAN	I	391	ENSP00000327943:M391I	ENSP00000327943:M391I	M	+	3	0	SLC5A2	31407487	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.651000	0.98493	2.453000	0.82957	0.561000	0.74099	ATG	.	.		0.706	SLC5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255627.2			T	31499986	G	T	31499986	3	4	255	1	0	0	0	0	1	0	0	0	14680	1377	48	3	1211	3	SLC5A2	16	31499986	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	411741	31499986	58854767	590	35935										
PHKB	5257	hgsc.bcm.edu	37	chr16	47545621	47545621	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gcccaacaacatgtcttcacTctgttttcaatgtgcataca	5	12	4	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:47545621T>C	ENST00000323584.5	+	5	475	c.451T>C	c.(451-453)Tct>Cct	p.S151P	PHKB_ENST00000566044.1_Missense_Mutation_p.S144P|PHKB_ENST00000455779.1_Missense_Mutation_p.S144P|PHKB_ENST00000299167.8_Missense_Mutation_p.S151P|PHKB_ENST00000567402.1_3'UTR	NM_000293.2	NP_000284.1	Q93100	KPBB_HUMAN	phosphorylase kinase, beta	151					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|liver(1)|lung(18)|ovary(1)|skin(1)	41		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				ATGTCTTCACTCTGTTTTCAA	0.333																																					p.S151P		Atlas-SNP	.											.	PHKB	298	.	0			c.T451C						.						144	125	132					16																	47545621		2201	4300	6501	SO:0001583	missense	5257	exon5			CTTCACTCTGTTT		CCDS10729.1, CCDS42161.1	16q12-q13	2009-07-10			ENSG00000102893	ENSG00000102893	2.7.11.19		8927	protein-coding gene	gene with protein product		172490					Standard	NM_000293		Approved		uc002eev.4	Q93100	OTTHUMG00000133102	ENST00000323584.5:c.451T>C	chr16.hg19:g.47545621T>C	ENSP00000313504:p.Ser151Pro	138.0	0.0		86.0	4.0	NM_000293	Q8N4T5	Missense_Mutation	SNP	ENST00000323584.5	hg19	CCDS10729.1	.	.	.	.	.	.	.	.	.	.	T	33	5.237119	0.95240	.	.	ENSG00000102893	ENST00000299167;ENST00000455779;ENST00000323584	D;D	0.91631	-2.88;-2.88	5.87	5.87	0.94306	Six-hairpin glycosidase-like (1);Glycoside hydrolase 15-related (1);	0.000000	0.85682	D	0.000000	D	0.96147	0.8744	M	0.81942	2.565	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.91635	0.999;0.99;0.982	D	0.96562	0.9416	10	0.87932	D	0	-24.1279	16.5764	0.84681	0.0:0.0:0.0:1.0	.	144;151;144	B4DQ16;Q93100;Q93100-4	.;KPBB_HUMAN;.	P	144;144;151	ENSP00000414345:S144P;ENSP00000313504:S151P	ENSP00000299167:S144P	S	+	1	0	PHKB	46103122	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	7.795000	0.85887	2.371000	0.80710	0.533000	0.62120	TCT	.	.		0.333	PHKB-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000430413.1			C	47545621	T	C	47545621	3	2	255	1	0	0	0	0	1	0	0	0	11854	1551	54	2	528	2	PHKB	16	47545621	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	16045635	47545621	42809132	591	35936										
CBLN1	869	hgsc.bcm.edu	37	chr16	49313350	49313350	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	caggaatccggagaaggtcgAgtacttccagccccccatca	10	14	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:49313350A>G	ENST00000219197.6	-	3	912	c.547T>C	c.(547-549)Tcg>Ccg	p.S183P	CBLN1_ENST00000536749.1_Missense_Mutation_p.S183P	NM_004352.3	NP_004343.1	P23435	CBLN1_HUMAN	cerebellin 1 precursor	183	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.|Necessary for interaction with CBLN3, and homotrimerization. {ECO:0000250}.				cerebellar granule cell differentiation (GO:0021707)|heterophilic cell-cell adhesion (GO:0007157)|nervous system development (GO:0007399)|positive regulation of synapse assembly (GO:0051965)|protein secretion (GO:0009306)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|extracellular region (GO:0005576)|postsynaptic membrane (GO:0045211)				breast(1)|kidney(3)|large_intestine(2)|lung(3)	9		all_cancers(37;0.0766)|all_lung(18;0.24)				GAGAAGGTCGAGTACTTCCAG	0.602																																					p.S183P		Atlas-SNP	.											.	CBLN1	26	.	0			c.T547C						.						109	103	105					16																	49313350		2200	4300	6500	SO:0001583	missense	869	exon3			AGGTCGAGTACTT	M58583	CCDS10736.1	16q12.1	2008-02-05			ENSG00000102924	ENSG00000102924			1543	protein-coding gene	gene with protein product		600432				7877445, 1704129	Standard	NM_004352		Approved		uc002efq.3	P23435	OTTHUMG00000133148	ENST00000219197.6:c.547T>C	chr16.hg19:g.49313350A>G	ENSP00000219197:p.Ser183Pro	214.0	0.0		133.0	6.0	NM_004352	B2RAN9|P02682|Q52M09	Missense_Mutation	SNP	ENST00000219197.6	hg19	CCDS10736.1	.	.	.	.	.	.	.	.	.	.	A	19.83	3.900943	0.72754	.	.	ENSG00000102924	ENST00000219197;ENST00000536749	T;T	0.44881	0.91;0.91	5.49	5.49	0.81192	Tumour necrosis factor-like (2);Complement C1q protein (4);	0.064023	0.64402	D	0.000004	T	0.55226	0.1907	M	0.86805	2.84	0.58432	D	0.999999	B	0.20052	0.041	B	0.30716	0.119	T	0.59506	-0.7442	10	0.72032	D	0.01	-6.1619	15.88	0.79197	1.0:0.0:0.0:0.0	.	183	P23435	CBLN1_HUMAN	P	183	ENSP00000219197:S183P;ENSP00000444651:S183P	ENSP00000219197:S183P	S	-	1	0	CBLN1	47870851	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.183000	0.94887	2.193000	0.70182	0.533000	0.62120	TCG	.	.		0.602	CBLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256845.4	NM_004352		G	49313350	A	G	49313350	3	3	255	1	0	0	0	0	1	0	0	0	2706	304	11	2	38	2	CBLN1	16	49313350	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	1767729	49313350	41041403	592	35937										
ZNF423	23090	hgsc.bcm.edu	37	chr16	49670350	49670350	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gatattgtggtcccgcagccGgtgattctgcagcagcacct	12	12	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:49670350G>T	ENST00000561648.1	-	4	2766	c.2713C>A	c.(2713-2715)Cgg>Agg	p.R905R	ZNF423_ENST00000563137.2_Silent_p.R845R|ZNF423_ENST00000562871.1_Silent_p.R845R|ZNF423_ENST00000535559.1_Silent_p.R788R|ZNF423_ENST00000262383.2_Silent_p.R905R|ZNF423_ENST00000562520.1_Silent_p.R845R|ZNF423_ENST00000567169.1_Silent_p.R788R	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	905					cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				TCCCGCAGCCGGTGATTCTGC	0.602																																					p.R905R		Atlas-SNP	.											.	ZNF423	463	.	0			c.C2713A						.						64	61	62					16																	49670350		2198	4300	6498	SO:0001819	synonymous_variant	23090	exon4			GCAGCCGGTGATT	AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"Zinc fingers, C2H2-type"	16762	protein-coding gene	gene with protein product	"OLF-1/EBF associated zinc finger gene", " Smad- and Olf-interacting zinc finger protein", "early B-cell factor associated zinc finger protein"	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.2713C>A	chr16.hg19:g.49670350G>T		95.0	0.0		81.0	4.0	NM_015069	O94860|Q76N04|Q9NZ13	Silent	SNP	ENST00000561648.1	hg19	CCDS32445.1																																																																																			.	.		0.602	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069		T	49670350	G	T	49670350	2	4	255	1	0	0	0	0	0	0	0	1	17913	1115	39	1		1	ZNF423	16	49670350	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	357000	49670350	40684403	593	35938										
NKD1	85407	hgsc.bcm.edu	37	chr16	50667325	50667325	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	caagcactttgtgaggtcccCcaaggcccagggcaagagtg	13	12	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:50667325C>T	ENST00000268459.3	+	10	1270	c.1046C>T	c.(1045-1047)cCc>cTc	p.P349L		NM_033119.4	NP_149110.1	Q969G9	NKD1_HUMAN	naked cuticle homolog 1 (Drosophila)	349					eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of convergent extension involved in axis elongation (GO:1901233)|positive regulation of non-canonical Wnt signaling pathway via JNK cascade (GO:1901231)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(9)|prostate(1)|urinary_tract(2)	23		all_cancers(37;0.229)		GBM - Glioblastoma multiforme(240;0.243)		GTGAGGTCCCCCAAGGCCCAG	0.667																																					p.P349L		Atlas-SNP	.											.	NKD1	43	.	0			c.C1046T						.						47	55	52					16																	50667325		2198	4300	6498	SO:0001583	missense	85407	exon10			GGTCCCCCAAGGC	AF358135	CCDS10743.1	16q12.1	2013-01-10			ENSG00000140807	ENSG00000140807		"EF-hand domain containing"	17045	protein-coding gene	gene with protein product		607851				11356022	Standard	NM_033119		Approved		uc002egg.2	Q969G9	OTTHUMG00000133169	ENST00000268459.3:c.1046C>T	chr16.hg19:g.50667325C>T	ENSP00000268459:p.Pro349Leu	275.0	0.0		149.0	7.0	NM_033119	B2RC39|Q8WZ08	Missense_Mutation	SNP	ENST00000268459.3	hg19	CCDS10743.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.364808	0.82463	.	.	ENSG00000140807	ENST00000268459	T	0.80994	-1.44	4.18	4.18	0.49190	.	0.000000	0.85682	D	0.000000	T	0.81283	0.4790	M	0.65975	2.015	0.80722	D	1	P	0.39250	0.665	B	0.43728	0.429	T	0.80781	-0.1229	10	0.33141	T	0.24	-24.5648	14.8623	0.70389	0.0:1.0:0.0:0.0	.	349	Q969G9	NKD1_HUMAN	L	349	ENSP00000268459:P349L	ENSP00000268459:P349L	P	+	2	0	NKD1	49224826	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.057000	0.76669	2.162000	0.67917	0.460000	0.39030	CCC	.	.		0.667	NKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256873.1			T	50667325	C	T	50667325	3	4	255	1	0	0	0	0	1	0	0	0	10450	623	22	3	1084	3	NKD1	16	50667325	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	996975	50667325	39687428	594	35939										
CHD9	80205	hgsc.bcm.edu	37	chr16	53358168	53358168	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctacaaaacttgcagtcactGcaagtaactgctgggttgat	9	9	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:53358168G>A	ENST00000398510.3	+	38	8142	c.8055G>A	c.(8053-8055)ctG>ctA	p.L2685L	CHD9_ENST00000447540.1_Silent_p.L2670L|CHD9_ENST00000564845.1_Silent_p.L2669L|CHD9_ENST00000566029.1_Silent_p.L2669L			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	2685					cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				TGCAGTCACTGCAAGTAACTG	0.483																																					p.L2669L		Atlas-SNP	.											.	CHD9	203	.	0			c.G8007A						.						78	77	77					16																	53358168		1894	4124	6018	SO:0001819	synonymous_variant	80205	exon39			GTCACTGCAAGTA	AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.8055G>A	chr16.hg19:g.53358168G>A		124.0	0.0		96.0	5.0	NM_025134	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Silent	SNP	ENST00000398510.3	hg19																																																																																				.	.		0.483	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134		A	53358168	G	A	53358168	2	1	255	1	0	0	0	0	0	0	0	1	3334	1306	46	3		3	CHD9	16	53358168	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	2690843	53358168	36996585	595	35940										
LPCAT2	54947	hgsc.bcm.edu	37	chr16	55543151	55543151	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cagtgccaggtgccggcgtcGggaacgtggggctgcggccg	20	12	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:55543151G>T	ENST00000262134.5	+	1	242	c.58G>T	c.(58-60)Ggg>Tgg	p.G20W		NM_017839.4	NP_060309.2	Q7L5N7	PCAT2_HUMAN	lysophosphatidylcholine acyltransferase 2	20					glycerophospholipid biosynthetic process (GO:0046474)|membrane organization (GO:0061024)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)|1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)|1-alkylglycerophosphocholine O-acetyltransferase activity (GO:0047192)|calcium ion binding (GO:0005509)	p.G20W(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	12						TGCCGGCGTCGGGAACGTGGG	0.726																																					p.G20W		Atlas-SNP	.											LPCAT2,NS,carcinoma,0,1	LPCAT2	35	.	1	Substitution - Missense(1)	lung(1)	c.G58T						.						4	6	5					16																	55543151		1880	3891	5771	SO:0001583	missense	54947	exon1			GGCGTCGGGAACG	AK000488	CCDS10753.1	16q12.2	2013-01-10	2007-12-17	2007-12-17	ENSG00000087253	ENSG00000087253		"EF-hand domain containing"	26032	protein-coding gene	gene with protein product		612040	"acyltransferase like 1"	AYTL1		16704971	Standard	NM_017839		Approved	FLJ20481	uc002eie.4	Q7L5N7	OTTHUMG00000133238	ENST00000262134.5:c.58G>T	chr16.hg19:g.55543151G>T	ENSP00000262134:p.Gly20Trp	91.0	0.0		36.0	2.0	NM_017839	A3KBM1|Q6MZJ6|Q9NX23	Missense_Mutation	SNP	ENST00000262134.5	hg19	CCDS10753.1	.	.	.	.	.	.	.	.	.	.	G	13.76	2.333120	0.41297	.	.	ENSG00000087253	ENST00000262134	T	0.74842	-0.88	4.69	3.66	0.41972	.	0.470628	0.22804	N	0.055437	T	0.78767	0.4335	L	0.54323	1.7	0.09310	N	0.999999	D	0.64830	0.994	D	0.64506	0.926	T	0.67624	-0.5623	10	0.72032	D	0.01	-9.5442	6.9664	0.24625	0.1269:0.0:0.8731:0.0	.	20	Q7L5N7	PCAT2_HUMAN	W	20	ENSP00000262134:G20W	ENSP00000262134:G20W	G	+	1	0	LPCAT2	54100652	0.708000	0.27876	0.080000	0.20451	0.010000	0.07245	0.837000	0.27558	2.436000	0.82500	0.643000	0.83706	GGG	.	.		0.726	LPCAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256977.2	NM_017839		T	55543151	G	T	55543151	3	4	255	1	0	0	0	0	1	0	0	0	8920	1116	39	1	60	1	LPCAT2	16	55543151	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	2184983	55543151	34811602	596	35941										
CETP	1071	hgsc.bcm.edu	37	chr16	57007309	57007309	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccttctcgcccacactgctgGgggactcccgcatgctgtac	10	17	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:57007309G>T	ENST00000566128.1	+	9	889	c.622G>T	c.(622-624)Ggg>Tgg	p.G208W	CETP_ENST00000200676.3_Missense_Mutation_p.G273W|CETP_ENST00000379780.2_Intron					cholesteryl ester transfer protein, plasma											NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(4)|skin(3)	23						CACACTGCTGGGGGACTCCCG	0.602																																					p.G273W		Atlas-SNP	.											.	CETP	50	.	0			c.G817T						.						79	75	76					16																	57007309		2198	4300	6498	SO:0001583	missense	1071	exon9			CTGCTGGGGGACT	M30185	CCDS10772.1, CCDS67032.1	16q13	2012-10-02			ENSG00000087237	ENSG00000087237		"BPI fold containing"	1869	protein-coding gene	gene with protein product	"BPI fold containing family F"	118470				3600759, 2334701	Standard	NM_000078		Approved	BPIFF	uc002eki.2	P11597	OTTHUMG00000133279	ENST00000566128.1:c.622G>T	chr16.hg19:g.57007309G>T	ENSP00000456276:p.Gly208Trp	109.0	0.0		91.0	4.0	NM_000078		Missense_Mutation	SNP	ENST00000566128.1	hg19		.	.	.	.	.	.	.	.	.	.	G	13.03	2.115257	0.37339	.	.	ENSG00000087237	ENST00000200676	T	0.08282	3.11	3.68	-1.51	0.08664	Lipid-binding serum glycoprotein, C-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	0.356298	0.25233	U	0.032142	T	0.05960	0.0155	L	0.27053	0.805	0.20764	N	0.999851	P	0.40230	0.708	P	0.45538	0.484	T	0.24476	-1.0159	10	0.72032	D	0.01	-2.0762	1.2121	0.01907	0.216:0.311:0.3149:0.1581	.	273	P11597	CETP_HUMAN	W	273	ENSP00000200676:G273W	ENSP00000200676:G273W	G	+	1	0	CETP	55564810	0.995000	0.38212	0.853000	0.33588	0.611000	0.37282	0.167000	0.16602	0.072000	0.16694	0.313000	0.20887	GGG	.	.		0.602	CETP-003	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000432305.1	NM_000078		T	57007309	G	T	57007309	3	4	255	1	0	0	0	0	1	0	0	0	3279	1232	43	3	851	3	CETP	16	57007309	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	1464158	57007309	33347444	597	35942										
TK2	7084	hgsc.bcm.edu	37	chr16	66575828	66575828	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	attccaggcatgtcgtcttcCcacttgcaatattgccctcg	7	14	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:66575828C>A	ENST00000451102.2	-	3	535	c.185G>T	c.(184-186)gGg>gTg	p.G62V	TK2_ENST00000563369.2_5'UTR|TK2_ENST00000544898.1_Missense_Mutation_p.G13V|TK2_ENST00000417693.3_Missense_Mutation_p.G62V|TK2_ENST00000527800.1_5'UTR|TK2_ENST00000545043.2_Intron|TK2_ENST00000299697.7_Missense_Mutation_p.G104V|TK2_ENST00000525974.1_5'UTR|TK2_ENST00000564917.1_Missense_Mutation_p.G62V|TK2_ENST00000527284.1_Missense_Mutation_p.G31V			O00142	KITM_HUMAN	thymidine kinase 2, mitochondrial	62					deoxyribonucleoside monophosphate biosynthetic process (GO:0009157)|DNA replication (GO:0006260)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|thymidine kinase activity (GO:0004797)			large_intestine(1)|lung(2)|urinary_tract(1)	4		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0736)|Epithelial(162;0.237)		TGTCGTCTTCCCACTTGCAAT	0.488																																					p.G62V		Atlas-SNP	.											.	TK2	17	.	0			c.G185T						.						137	109	118					16																	66575828		2201	4300	6501	SO:0001583	missense	7084	exon3			GTCTTCCCACTTG		CCDS10805.1, CCDS10805.2, CCDS54016.1, CCDS54017.1, CCDS54018.1, CCDS61955.1	16q22-q23.1	2012-10-02			ENSG00000166548	ENSG00000166548	2.7.1.21		11831	protein-coding gene	gene with protein product		188250					Standard	NM_004614		Approved		uc002eos.3	O00142	OTTHUMG00000137499	ENST00000451102.2:c.185G>T	chr16.hg19:g.66575828C>A	ENSP00000414334:p.Gly62Val	84.0	0.0		53.0	4.0	NM_001172645	B4DGJ7|B4DZK7|B7ZAB1|E9PH08|O15238	Missense_Mutation	SNP	ENST00000451102.2	hg19	CCDS10805.2	.	.	.	.	.	.	.	.	.	.	C	25.7	4.661623	0.88154	.	.	ENSG00000166548	ENST00000299697;ENST00000417693;ENST00000451102;ENST00000527284;ENST00000544898	D;D;D;D;D	0.99931	-8.18;-8.18;-8.18;-8.18;-8.18	6.06	6.06	0.98353	.	0.097274	0.64402	D	0.000001	D	0.99941	0.9974	H	0.96175	3.78	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.999;0.998;1.0;1.0	D	0.96319	0.9235	10	0.87932	D	0	-40.5018	16.1399	0.81515	0.0:1.0:0.0:0.0	.	62;13;26;104;31	O00142;F5GYK4;A4IF54;E5KNQ5;O00142-2	KITM_HUMAN;.;.;.;.	V	104;62;62;31;13	ENSP00000299697:G104V;ENSP00000407469:G62V;ENSP00000414334:G62V;ENSP00000435312:G31V;ENSP00000440898:G13V	ENSP00000299697:G104V	G	-	2	0	TK2	65133329	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.121000	0.64691	2.880000	0.98712	0.650000	0.86243	GGG	.	.		0.488	TK2-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268806.4			A	66575828	C	A	66575828	3	1	255	1	0	0	0	0	1	0	0	0	15948	623	22	3	644	3	TK2	16	66575828	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	9568519	66575828	23778925	598	35943										
RLTPR	146206	hgsc.bcm.edu	37	chr16	67685847	67685847	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	catgcggctatcaatcacggGgaccttggcagagagcattg	13	10	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:67685847G>T	ENST00000334583.6	+	26	2940	c.2612G>T	c.(2611-2613)gGg>gTg	p.G871V	RLTPR_ENST00000545661.1_Missense_Mutation_p.G835V	NM_001013838.1	NP_001013860.1	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing	871					cell migration (GO:0016477)|establishment of protein localization (GO:0045184)|homeostasis of number of cells (GO:0048872)|maintenance of cell polarity (GO:0030011)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma secretion (GO:1902715)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|F-actin capping protein complex (GO:0008290)|immunological synapse (GO:0001772)|membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(4)|kidney(1)|lung(9)|urinary_tract(2)	18		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)		TCAATCACGGGGACCTTGGCA	0.602																																					p.G871V		Atlas-SNP	.											.	RLTPR	124	.	0			c.G2612T						.						131	137	135					16																	67685847		2130	4237	6367	SO:0001583	missense	146206	exon26			TCACGGGGACCTT	AB113647	CCDS45513.1	16q22.1	2010-09-10				ENSG00000159753			27089	protein-coding gene	gene with protein product	"RGD, leucine-rich repeat, tropomodulin and proline-rich containing protein", "leucine rich repeat containing 16C"	610859				15588584, 19846667	Standard	XM_005255807		Approved	LRRC16C, CARMIL2	uc002etn.3	Q6F5E8		ENST00000334583.6:c.2612G>T	chr16.hg19:g.67685847G>T	ENSP00000334958:p.Gly871Val	78.0	0.0		62.0	4.0	NM_001013838	B8X2Z3	Missense_Mutation	SNP	ENST00000334583.6	hg19	CCDS45513.1	.	.	.	.	.	.	.	.	.	.	G	8.766	0.924689	0.18056	.	.	ENSG00000159753	ENST00000334583;ENST00000545661	T;T	0.12984	2.63;2.63	4.85	2.78	0.32641	.	0.534882	0.17245	N	0.181361	T	0.13756	0.0333	L	0.57536	1.79	0.24410	N	0.994663	B;B	0.27559	0.181;0.022	B;B	0.29267	0.1;0.006	T	0.14587	-1.0467	10	0.51188	T	0.08	-12.016	6.1459	0.20285	0.1038:0.2032:0.693:0.0	.	835;871	B8X2Z3;Q6F5E8	.;LR16C_HUMAN	V	871;835	ENSP00000334958:G871V;ENSP00000441481:G835V	ENSP00000334958:G871V	G	+	2	0	RLTPR	66243348	0.856000	0.29760	0.841000	0.33234	0.549000	0.35272	2.433000	0.44793	1.256000	0.44068	0.655000	0.94253	GGG	.	.		0.602	RLTPR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467858.1	NM_001013838		T	67685847	G	T	67685847	3	4	255	1	0	0	0	0	1	0	0	0	13409	1232	43	3	2714	3	RLTPR	16	67685847	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	1110019	67685847	22668906	599	35944										
THAP11	57215	hgsc.bcm.edu	37	chr16	67876832	67876832	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cagcagcagcaacagcagcaGcagcagcagcagcagcagca	12	14	0	0	rs141903290		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:67876832G>A	ENST00000303596.1	+	1	620	c.375G>A	c.(373-375)caG>caA	p.Q125Q	CENPT_ENST00000562787.1_Intron	NM_020457.2	NP_065190.2	Q96EK4	THA11_HUMAN	THAP domain containing 11	125	Gln-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|urinary_tract(1)	8		Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00412)|Epithelial(162;0.018)|all cancers(182;0.118)		aacagcagcagcagcagcagc	0.677																																					p.Q125Q		Atlas-SNP	.											THAP11,NS,carcinoma,0,1	THAP11	27	.	0			c.G375A						.						33	39	37					16																	67876832		2053	4030	6083	SO:0001819	synonymous_variant	57215	exon1			GCAGCAGCAGCAG	AB015338	CCDS10847.1	16q22.1	2013-01-25			ENSG00000168286	ENSG00000168286		"THAP (C2CH-type zinc finger) domain containing"	23194	protein-coding gene	gene with protein product		609119				12575992, 8325628	Standard	NM_020457		Approved	HRIHFB2206, CTG-B45d, CTG-B43a	uc002euo.3	Q96EK4	OTTHUMG00000137546	ENST00000303596.1:c.375G>A	chr16.hg19:g.67876832G>A		49.0	1.0		29.0	2.0	NM_020457	A4UCT5|A8K002|O94795	Silent	SNP	ENST00000303596.1	hg19	CCDS10847.1																																																																																			.	G|0.998;A|0.002		0.677	THAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268879.1	NM_020457		A	67876832	G	A	67876832	2	1	255	1	0	0	0	0	0	0	0	1	15858	962	34	3		3	THAP11	16	67876832	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	190985	67876832	22477921	600	35945										
ESRP2	80004	hgsc.bcm.edu	37	chr16	68265144	68265144	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggtgccccccatcagcactcGgctcatctcctctgtggaac	9	17	4	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:68265144G>T	ENST00000565858.1	-	12	1764	c.1678C>A	c.(1678-1680)Cga>Aga	p.R560R	ESRP2_ENST00000473183.2_Silent_p.R550R|RP11-96D1.11_ENST00000571197.1_RNA	NM_024939.2	NP_079215.2	Q9H6T0	ESRP2_HUMAN	epithelial splicing regulatory protein 2	560					mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)	16						ATCAGCACTCGGCTCATCTCC	0.632																																					p.R550R		Atlas-SNP	.											.	ESRP2	118	.	0			c.C1648A						.						89	71	77					16																	68265144		2198	4300	6498	SO:0001819	synonymous_variant	80004	exon12			GCACTCGGCTCAT	AK025571	CCDS10863.1	16q22.1	2013-02-12	2009-03-10	2009-03-10	ENSG00000103067	ENSG00000103067		"RNA binding motif (RRM) containing"	26152	protein-coding gene	gene with protein product		612960	"RNA binding motif protein 35B"	RBM35B		12477932	Standard	NM_024939		Approved	FLJ21918	uc002evq.1	Q9H6T0	OTTHUMG00000137557	ENST00000565858.1:c.1678C>A	chr16.hg19:g.68265144G>T		110.0	0.0		98.0	4.0	NM_024939	Q8N6H8|Q8WZ15|Q9H6I4	Silent	SNP	ENST00000565858.1	hg19																																																																																				.	.		0.632	ESRP2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000433083.1	NM_024939		T	68265144	G	T	68265144	2	4	255	1	0	0	0	0	0	0	0	1	5261	1124	39	1		1	ESRP2	16	68265144	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	388312	68265144	22089609	601	35946										
COG4	25839	hgsc.bcm.edu	37	chr16	70546324	70546324	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cagcaatttcaggttggcatCaatcatgctccctgctcaac	7	13	4	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:70546324C>T	ENST00000323786.5	-	5	577	c.556G>A	c.(556-558)Gat>Aat	p.D186N	COG4_ENST00000393612.4_Missense_Mutation_p.D182N|COG4_ENST00000564653.1_Intron	NM_001195139.1|NM_015386.2	NP_001182068.1|NP_056201.2	Q9H9E3	COG4_HUMAN	component of oligomeric golgi complex 4	182					Golgi organization (GO:0007030)|Golgi vesicle prefusion complex stabilization (GO:0048213)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|pancreas(1)|prostate(2)	33		Ovarian(137;0.0694)				AGGTTGGCATCAATCATGCTC	0.463																																					p.D186N		Atlas-SNP	.											.	COG4	64	.	0			c.G556A						.						68	58	61					16																	70546324		2198	4300	6498	SO:0001583	missense	25839	exon5			TGGCATCAATCAT	AL050101	CCDS10892.2, CCDS73909.1	16q22.1	2013-09-20			ENSG00000103051	ENSG00000103051		"Components of oligomeric golgi complex"	18620	protein-coding gene	gene with protein product		606976				11980916	Standard	NM_015386		Approved	COD1, DKFZP586E1519	uc002ezc.3	Q9H9E3	OTTHUMG00000128515	ENST00000323786.5:c.556G>A	chr16.hg19:g.70546324C>T	ENSP00000315775:p.Asp186Asn	83.0	0.0		57.0	4.0	NM_015386	B4DMN8|C9JS23|Q96D40|Q9BRF0|Q9BVZ2|Q9H5Y4|Q9Y3W3	Missense_Mutation	SNP	ENST00000323786.5	hg19	CCDS10892.2	.	.	.	.	.	.	.	.	.	.	C	22.8	4.341999	0.81911	.	.	ENSG00000103051	ENST00000323786;ENST00000338984;ENST00000393612;ENST00000534772	T;T;T	0.49139	0.98;0.98;0.79	5.53	5.53	0.82687	.	0.089049	0.85682	D	0.000000	T	0.44540	0.1298	L	0.43152	1.355	0.80722	D	1	B;B	0.20671	0.021;0.047	B;B	0.17098	0.008;0.017	T	0.22556	-1.0213	10	0.34782	T	0.22	-15.4266	19.466	0.94939	0.0:1.0:0.0:0.0	.	181;182	Q6PIW8;Q9H9E3	.;COG4_HUMAN	N	186;182;182;109	ENSP00000315775:D186N;ENSP00000377236:D182N;ENSP00000461912:D109N	ENSP00000315775:D186N	D	-	1	0	COG4	69103825	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.550000	0.82173	2.607000	0.88179	0.655000	0.94253	GAT	.	.		0.463	COG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250326.3			T	70546324	C	T	70546324	3	4	255	1	0	0	0	0	1	0	0	0	3662	826	29	3	1873	3	COG4	16	70546324	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	2281180	70546324	19808429	602	35947										
ZFHX3	463	hgsc.bcm.edu	37	chr16	72992020	72992020	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tacttatagtgccagttgcaCttggggcacttgagtgtctt	11	8	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:72992020C>T	ENST00000268489.5	-	2	2697	c.2025G>A	c.(2023-2025)aaG>aaA	p.K675K	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	675					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				GCCAGTTGCACTTGGGGCACT	0.602																																					p.K675K		Atlas-SNP	.											.	ZFHX3	404	.	0			c.G2025A						.						45	49	48					16																	72992020		2198	4300	6498	SO:0001819	synonymous_variant	463	exon2			GTTGCACTTGGGG	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	777	protein-coding gene	gene with protein product		104155	"AT-binding transcription factor 1"	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.2025G>A	chr16.hg19:g.72992020C>T		41.0	0.0		39.0	4.0	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	hg19	CCDS10908.1																																																																																			.	.		0.602	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		T	72992020	C	T	72992020	2	4	255	1	0	0	0	0	0	0	0	1	17649	564	20	3		3	ZFHX3	16	72992020	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	2445696	72992020	17362733	603	35948										
LDHD	197257	hgsc.bcm.edu	37	chr16	75149474	75149474	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cgactcatcgcgcccgtgctGctctcggaccaccgcggcag	12	18	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:75149474G>T	ENST00000450168.2	-	2	207	c.157C>A	c.(157-159)Cag>Aag	p.Q53K	LDHD_ENST00000300051.4_Missense_Mutation_p.Q53K	NM_194436.2	NP_919417.1			lactate dehydrogenase D											endometrium(1)|large_intestine(2)|lung(12)|upper_aerodigestive_tract(1)	16						CGCCCGTGCTGCTCTCGGACC	0.647																																					p.Q53K		Atlas-SNP	.											.	LDHD	34	.	0			c.C157A						.						27	32	30					16																	75149474		2197	4300	6497	SO:0001583	missense	197257	exon2			CGTGCTGCTCTCG	AY092767	CCDS10913.1, CCDS45529.1	16q22.3	2011-01-27			ENSG00000166816	ENSG00000166816			19708	protein-coding gene	gene with protein product		607490				12127981	Standard	NM_153486		Approved		uc002fdm.3	Q86WU2	OTTHUMG00000137605	ENST00000450168.2:c.157C>A	chr16.hg19:g.75149474G>T	ENSP00000417011:p.Gln53Lys	153.0	0.0		101.0	5.0	NM_194436		Missense_Mutation	SNP	ENST00000450168.2	hg19	CCDS45529.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.337595	0.81911	.	.	ENSG00000166816	ENST00000450168;ENST00000300051	T;T	0.41400	1.0;1.0	5.06	5.06	0.68205	FAD-binding, type 2, subdomain 1 (1);FAD-binding, type 2 (1);	0.261864	0.38548	N	0.001647	T	0.46151	0.1378	L	0.53617	1.68	0.80722	D	1	P;P	0.48503	0.911;0.857	P;B	0.44359	0.447;0.333	T	0.51834	-0.8655	10	0.62326	D	0.03	-7.672	18.0365	0.89305	0.0:0.0:1.0:0.0	.	53;53	Q86WU2-2;Q86WU2	.;LDHD_HUMAN	K	53	ENSP00000417011:Q53K;ENSP00000300051:Q53K	ENSP00000300051:Q53K	Q	-	1	0	LDHD	73706975	1.000000	0.71417	0.355000	0.25773	0.535000	0.34838	8.832000	0.92079	2.371000	0.80710	0.561000	0.74099	CAG	.	.		0.647	LDHD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434651.1	NM_153486		T	75149474	G	T	75149474	3	4	255	1	0	0	0	0	1	0	0	0	8712	1328	46	3	1406	3	LDHD	16	75149474	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	2157454	75149474	15205279	604	35949										
CHST6	4166	hgsc.bcm.edu	37	chr16	75513666	75513666	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggaaaccagaaagaggaggaGgaaggtctgcgccaggagga	18	6	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:75513666G>A	ENST00000332272.4	-	3	240	c.61C>T	c.(61-63)Ctc>Ttc	p.L21F	RP11-77K12.4_ENST00000530512.3_RNA|CHST6_ENST00000390664.2_Missense_Mutation_p.L21F	NM_021615.4	NP_067628.1	Q9GZX3	CHST6_HUMAN	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 6	21					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|N-acetylglucosamine metabolic process (GO:0006044)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)			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						AAGAGGAGGAGGAAGGTCTGC	0.697																																					p.L21F		Atlas-SNP	.											CHST6,colon,carcinoma,0,1	CHST6	57	.	0			c.C61T						.						13	15	15					16																	75513666		2183	4291	6474	SO:0001583	missense	4166	exon3			GGAGGAGGAAGGT	AF280086	CCDS10918.1	16q22	2008-02-05			ENSG00000183196	ENSG00000183196		"Sulfotransferases, membrane-bound"	6938	protein-coding gene	gene with protein product		605294		MCDC1		8644739, 11017086	Standard	NM_021615		Approved		uc002fef.3	Q9GZX3	OTTHUMG00000137612	ENST00000332272.4:c.61C>T	chr16.hg19:g.75513666G>A	ENSP00000328983:p.Leu21Phe	54.0	0.0		45.0	3.0	NM_021615	D3DUK3	Missense_Mutation	SNP	ENST00000332272.4	hg19	CCDS10918.1	.	.	.	.	.	.	.	.	.	.	G	5.371	0.253730	0.10185	.	.	ENSG00000183196	ENST00000332272;ENST00000390664	D;D	0.96856	-4.15;-4.15	5.01	1.82	0.25136	.	1.375640	0.04765	N	0.427071	D	0.89976	0.6871	N	0.17082	0.46	0.24533	N	0.994109	B	0.02656	0.0	B	0.04013	0.001	T	0.80759	-0.1239	10	0.10902	T	0.67	.	3.6852	0.08326	0.1772:0.0:0.4082:0.4146	.	21	Q9GZX3	CHST6_HUMAN	F	21	ENSP00000328983:L21F;ENSP00000375079:L21F	ENSP00000328983:L21F	L	-	1	0	CHST6	74071167	0.843000	0.29541	0.757000	0.31301	0.732000	0.41865	1.006000	0.29847	0.422000	0.26005	0.591000	0.81541	CTC	.	.		0.697	CHST6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435478.1	NM_021615		A	75513666	G	A	75513666	3	1	255	1	0	0	0	0	1	0	0	0	3410	1000	35	3	1130	3	CHST6	16	75513666	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	364192	75513666	14841087	605	35950										
PLCG2	5336	hgsc.bcm.edu	37	chr16	81972412	81972412	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctttggtgtcccaggttctcGgtgctcgccatctccccaaa	9	15	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:81972412G>A	ENST00000359376.3	+	29	3419	c.3205G>A	c.(3205-3207)Ggt>Agt	p.G1069S		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	1069	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)	p.G1069S(2)		NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						CCAGGTTCTCGGTGCTCGCCA	0.542																																					p.G1069S		Atlas-SNP	.											PLCG2_ENST00000359376,NS,carcinoma,0,4	PLCG2	276	.	2	Substitution - Missense(2)	endometrium(2)	c.G3205A						.						88	84	86					16																	81972412		1943	4138	6081	SO:0001583	missense	5336	exon29			GTTCTCGGTGCTC		CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"SH2 domain containing"	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.3205G>A	chr16.hg19:g.81972412G>A	ENSP00000352336:p.Gly1069Ser	152.0	0.0		99.0	4.0	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Missense_Mutation	SNP	ENST00000359376.3	hg19	CCDS42204.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.033268	0.93575	.	.	ENSG00000197943	ENST00000359376	T	0.66638	-0.22	5.39	5.39	0.77823	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.048118	0.85682	D	0.000000	T	0.64702	0.2622	N	0.05608	-0.01	0.80722	D	1	D	0.69078	0.997	P	0.59424	0.857	T	0.70163	-0.4947	10	0.42905	T	0.14	.	19.1452	0.93463	0.0:0.0:1.0:0.0	.	1069	P16885	PLCG2_HUMAN	S	1069	ENSP00000352336:G1069S	ENSP00000352336:G1069S	G	+	1	0	PLCG2	80529913	1.000000	0.71417	0.901000	0.35422	0.690000	0.40134	9.444000	0.97578	2.517000	0.84864	0.561000	0.74099	GGT	.	.		0.542	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1			A	81972412	G	A	81972412	3	1	255	1	0	0	0	0	1	0	0	0	12045	1116	39	1	3315	1	PLCG2	16	81972412	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	6458746	81972412	8382341	606	35951										
IRF8	3394	hgsc.bcm.edu	37	chr16	85946744	85946744	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cctgactgtgcagccttctgTggacgattacatggggatga	13	9	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:85946744T>C	ENST00000268638.5	+	5	877	c.455T>C	c.(454-456)gTg>gCg	p.V152A	IRF8_ENST00000562492.1_5'Flank	NM_002163.2	NP_002154.1	Q02556	IRF8_HUMAN	interferon regulatory factor 8	152					cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phagocytosis (GO:0006909)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	24		Prostate(104;0.0771)				CAGCCTTCTGTGGACGATTAC	0.577																																					p.V152A		Atlas-SNP	.											.	IRF8	65	.	0			c.T455C						.						111	117	115					16																	85946744		2198	4300	6498	SO:0001583	missense	3394	exon5			CTTCTGTGGACGA	M91196	CCDS10956.1	16q24.1	2014-09-17	2004-11-12	2004-11-12	ENSG00000140968	ENSG00000140968			5358	protein-coding gene	gene with protein product		601565	"interferon consensus sequence binding protein 1"	ICSBP1		1460054, 11997525	Standard	NM_002163		Approved	IRF-8, ICSBP	uc002fjh.3	Q02556	OTTHUMG00000137648	ENST00000268638.5:c.455T>C	chr16.hg19:g.85946744T>C	ENSP00000268638:p.Val152Ala	132.0	0.0		68.0	4.0	NM_002163	A0AV82	Missense_Mutation	SNP	ENST00000268638.5	hg19	CCDS10956.1	.	.	.	.	.	.	.	.	.	.	T	12.04	1.818382	0.32145	.	.	ENSG00000140968	ENST00000268638	D	0.96967	-4.19	4.86	3.75	0.43078	.	0.655707	0.15813	N	0.243361	D	0.91945	0.7449	L	0.48642	1.525	0.80722	D	1	B	0.06786	0.001	B	0.12156	0.007	T	0.83257	-0.0050	10	0.08179	T	0.78	-21.0783	6.6795	0.23113	0.0:0.0779:0.1554:0.7667	.	152	Q02556	IRF8_HUMAN	A	152	ENSP00000268638:V152A	ENSP00000268638:V152A	V	+	2	0	IRF8	84504245	0.998000	0.40836	0.901000	0.35422	0.968000	0.65278	1.156000	0.31712	0.798000	0.33994	0.459000	0.35465	GTG	.	.		0.577	IRF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269100.2	NM_002163		C	85946744	T	C	85946744	3	2	255	1	0	0	0	0	1	0	0	0	7845	1696	59	2	469	2	IRF8	16	85946744	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	3974332	85946744	4408009	607	35952										
SLC7A5	8140	hgsc.bcm.edu	37	chr16	87871523	87871523	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aggatggagggcaggtggccTtcccgggaccccacgaagaa	16	11	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:87871523T>C	ENST00000261622.4	-	7	1133	c.1068A>G	c.(1066-1068)gaA>gaG	p.E356E	RP4-536B24.2_ENST00000563687.1_RNA|SLC7A5_ENST00000565644.1_Silent_p.E90E	NM_003486.5	NP_003477.4	Q01650	LAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, L system), member 5	356					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|nervous system development (GO:0007399)|neutral amino acid transport (GO:0015804)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-amino acid transmembrane transporter activity (GO:0015179)|neutral amino acid transmembrane transporter activity (GO:0015175)|peptide antigen binding (GO:0042605)			endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(80;0.049)	Dextrothyroxine(DB00509)|L-DOPA(DB01235)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Melphalan(DB01042)	GCAGGTGGCCTTCCCGGGACC	0.657																																					p.E356E		Atlas-SNP	.											.	SLC7A5	28	.	0			c.A1068G						.						114	92	99					16																	87871523		2198	4298	6496	SO:0001819	synonymous_variant	8140	exon7			GTGGCCTTCCCGG	AF077866	CCDS10964.1	16q24.3	2013-05-22	2011-07-12		ENSG00000103257	ENSG00000103257		"CD molecules", "Solute carriers"	11063	protein-coding gene	gene with protein product		600182				9751058, 7829099	Standard	XM_006721286		Approved	LAT1, E16, D16S469E, MPE16, CD98	uc002fkm.3	Q01650	OTTHUMG00000137658	ENST00000261622.4:c.1068A>G	chr16.hg19:g.87871523T>C		130.0	0.0		90.0	4.0	NM_003486	Q8IV97|Q9UBN8|Q9UP15|Q9UQC0	Silent	SNP	ENST00000261622.4	hg19	CCDS10964.1																																																																																			.	.		0.657	SLC7A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269110.2	NM_003486		C	87871523	T	C	87871523	2	2	255	1	0	0	0	0	0	0	0	1	14715	1606	56	2		2	SLC7A5	16	87871523	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	1924779	87871523	2483230	608	35953										
PABPN1L	390748	hgsc.bcm.edu	37	chr16	88932215	88932215	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctgtgcccttggttcctaccCacggtctcagggctcagcag	11	15	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:88932215C>T	ENST00000419291.2	-	2	401	c.390G>A	c.(388-390)gtG>gtA	p.V130V	PABPN1L_ENST00000411789.2_Splice_Site_p.V130V|PABPN1L_ENST00000378358.4_Splice_Site_p.V130V|PABPN1L_ENST00000427766.1_Splice_Site_p.V130V	NM_001080487.2	NP_001073956.2	A6NDY0	EPAB2_HUMAN	poly(A) binding protein, nuclear 1-like (cytoplasmic)	130						cytoplasm (GO:0005737)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			kidney(1)	1						GGTTCCTACCCACGGTCTCAG	0.667																																					p.V130V		Atlas-SNP	.											.	PABPN1L	25	.	0			c.G390A						.						23	28	26					16																	88932215		1991	4153	6144	SO:0001630	splice_region_variant	390748	exon2			CCTACCCACGGTC		CCDS45547.1, CCDS45547.2, CCDS73925.1	16q24.3	2013-02-12	2009-12-17		ENSG00000205022	ENSG00000205022		"RNA binding motif (RRM) containing"	37237	protein-coding gene	gene with protein product	"embryonic poly(A) binding protein 2"					18483763	Standard	NM_001080487		Approved	ePABP2	uc010vpe.2	A6NDY0		ENST00000419291.2:c.391+1G>A	chr16.hg19:g.88932215C>T		198.0	0.0		124.0	5.0	NM_001080487	A1L3B3|A2VDI2	Silent	SNP	ENST00000419291.2	hg19	CCDS45547.2																																																																																			.	.		0.667	PABPN1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407502.1	NM_001080487	Silent	T	88932215	C	T	88932215	5	4	255	1	0	0	0	0	0	0	1	0	11378	608	21	3	502	3	PABPN1L	16	88932215	Splice_Site	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1060692	88932215	1422538	609	35954										
SPG7	6687	hgsc.bcm.edu	37	chr16	89616941	89616941	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gatcctgtccaaggaagaacAgaaagtggttgcgtttcatg	12	7	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:89616941A>G	ENST00000268704.2	+	13	1718	c.1703A>G	c.(1702-1704)cAg>cGg	p.Q568R		NM_003119.2	NP_003110.1	Q9UQ90	SPG7_HUMAN	spastic paraplegia 7 (pure and complicated autosomal recessive)	568					anterograde axon cargo transport (GO:0008089)|cell death (GO:0008219)|mitochondrion organization (GO:0007005)|nervous system development (GO:0007399)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metalloendopeptidase activity (GO:0004222)|peptidase activity (GO:0008233)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|urinary_tract(1)	20		all_hematologic(23;0.00824)|Colorectal(91;0.102)		all cancers(4;1.39e-07)|OV - Ovarian serous cystadenocarcinoma(4;5.64e-06)|BRCA - Breast invasive adenocarcinoma(80;0.015)		AAGGAAGAACAGAAAGTGGTT	0.592																																					p.Q568R		Atlas-SNP	.											.	SPG7	75	.	0			c.A1703G						.						116	107	110					16																	89616941		2198	4300	6498	SO:0001583	missense	6687	exon13			AAGAACAGAAAGT	Y16610	CCDS10977.1, CCDS10978.1	16q24.3	2010-04-21	2007-04-23		ENSG00000197912	ENSG00000197912		"ATPases / AAA-type"	11237	protein-coding gene	gene with protein product	"paraplegin"	602783	"cell matrix adhesion regulator"	CMAR		9635427, 9634528	Standard	XM_006721264		Approved	CAR, SPG5C	uc002fnj.3	Q9UQ90	OTTHUMG00000138046	ENST00000268704.2:c.1703A>G	chr16.hg19:g.89616941A>G	ENSP00000268704:p.Gln568Arg	100.0	0.0		78.0	4.0	NM_003119	O75756|Q2TB70|Q58F00|Q96IB0	Missense_Mutation	SNP	ENST00000268704.2	hg19	CCDS10977.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	1.222|1.222	-0.626757|-0.626757	0.03610|0.03610	.|.	.|.	ENSG00000197912|ENSG00000197912	ENST00000268704|ENST00000312613	T|.	0.80909|.	-1.43|.	5.84|5.84	3.53|3.53	0.40419|0.40419	Peptidase M41 (1);Peptidase M41, FtsH (2);|.	0.160396|.	0.56097|.	N|.	0.000027|.	T|T	0.07279|0.07279	0.0184|0.0184	N|N	0.00034|0.00034	-2.565|-2.565	0.80722|0.80722	D|D	1|1	B|.	0.06786|.	0.001|.	B|.	0.06405|.	0.002|.	T|T	0.10706|0.10706	-1.0618|-1.0618	10|6	0.06757|0.87932	T|D	0.87|0	.|.	3.2925|3.2925	0.06954|0.06954	0.5682:0.0:0.2664:0.1654|0.5682:0.0:0.2664:0.1654	.|.	568|.	Q9UQ90|.	SPG7_HUMAN|.	R|G	568|160	ENSP00000268704:Q568R|.	ENSP00000268704:Q568R|ENSP00000310320:R160G	Q|R	+|+	2|1	0|2	SPG7|SPG7	88144442|88144442	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.310000|0.310000	0.27922|0.27922	3.457000|3.457000	0.53007|0.53007	1.052000|1.052000	0.40392|0.40392	0.459000|0.459000	0.35465|0.35465	CAG|AGA	.	.		0.592	SPG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269921.2	NM_003119		G	89616941	A	G	89616941	3	3	255	1	0	0	0	0	1	0	0	0	15059	188	7	2	1903	2	SPG7	16	89616941	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	684726	89616941	737812	610	35955										
DEF8	54849	hgsc.bcm.edu	37	chr16	90023996	90023996	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	caggtgattctggagctgccCgagcagtcggagaagcagaa	15	9	1	3	rs377269615		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:90023996C>A	ENST00000268676.7	+	5	572	c.483C>A	c.(481-483)ccC>ccA	p.P161P	DEF8_ENST00000418391.2_Silent_p.P100P|DEF8_ENST00000563594.1_Silent_p.P100P|DEF8_ENST00000569453.1_Silent_p.P100P|DEF8_ENST00000570182.1_Silent_p.P90P|DEF8_ENST00000563795.1_Silent_p.P100P|DEF8_ENST00000567874.1_Silent_p.P40P	NM_207514.2	NP_997397.1	Q6ZN54	DEFI8_HUMAN	differentially expressed in FDCP 8 homolog (mouse)	161					intracellular signal transduction (GO:0035556)		zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12		all_cancers(9;7.59e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.0019)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0274)		TGGAGCTGCCCGAGCAGTCGG	0.682																																					p.P161P		Atlas-SNP	.											.	DEF8	28	.	0			c.C483A						.						33	29	31					16																	90023996		2188	4291	6479	SO:0001819	synonymous_variant	54849	exon5			GCTGCCCGAGCAG	AK131370	CCDS10989.1, CCDS45555.1, CCDS58493.1, CCDS58494.1, CCDS58495.1, CCDS58496.1	16q24.3	2011-01-31			ENSG00000140995	ENSG00000140995			25969	protein-coding gene	gene with protein product						12477932	Standard	NM_207514		Approved	FLJ20186	uc002fpn.2	Q6ZN54	OTTHUMG00000138989	ENST00000268676.7:c.483C>A	chr16.hg19:g.90023996C>A		421.0	0.0		273.0	232.0	NM_207514	B3KT65|B4DK62|B4E0S9|B7Z3H6|H3BUG7|Q8N8N3|Q9NXL0	Silent	SNP	ENST00000268676.7	hg19	CCDS10989.1																																																																																			.	.		0.682	DEF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000272878.1	NM_207514		A	90023996	C	A	90023996	2	1	255	1	0	0	0	0	0	0	0	1	4389	639	23	1		1	DEF8	16	90023996	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	407055	90023996	330757	611	35956										
INPP5K	51763	hgsc.bcm.edu	37	chr17	1399994	1399994	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tccagtcccacgggctgctgGggaagtccgaggttgaagag	16	10	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:1399994G>T	ENST00000421807.2	-	9	1455	c.1067C>A	c.(1066-1068)cCc>cAc	p.P356H	INPP5K_ENST00000320345.6_Missense_Mutation_p.P280H|INPP5K_ENST00000397335.3_Missense_Mutation_p.P264H|INPP5K_ENST00000542125.1_Missense_Mutation_p.P260H|INPP5K_ENST00000406424.4_Missense_Mutation_p.P280H	NM_016532.3	NP_057616.2	Q9BT40	INP5K_HUMAN	inositol polyphosphate-5-phosphatase K	356	Required for ruffle localization.				actin cytoskeleton organization (GO:0030036)|cellular response to cAMP (GO:0071320)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to hormone stimulus (GO:0032870)|cellular response to insulin stimulus (GO:0032869)|cellular response to tumor necrosis factor (GO:0071356)|dephosphorylation (GO:0016311)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inositol phosphate dephosphorylation (GO:0046855)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of dephosphorylation (GO:0035305)|negative regulation of glucose transport (GO:0010829)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of stress fiber assembly (GO:0051497)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of renal water transport (GO:2001153)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of urine volume (GO:0035810)|protein targeting to plasma membrane (GO:0072661)|regulation of glycogen biosynthetic process (GO:0005979)|ruffle assembly (GO:0097178)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	inositol bisphosphate phosphatase activity (GO:0016312)|inositol trisphosphate phosphatase activity (GO:0046030)|inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity (GO:0052659)|inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|inositol-polyphosphate 5-phosphatase activity (GO:0004445)|lipid phosphatase activity (GO:0042577)|phosphatidylinositol phosphate 5-phosphatase activity (GO:0034595)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity (GO:0034485)|vasopressin receptor activity (GO:0005000)			endometrium(1)|large_intestine(7)|lung(3)|skin(1)	12						CGGGCTGCTGGGGAAGTCCGA	0.582																																					p.P356H		Atlas-SNP	.											.	INPP5K	30	.	0			c.C1067A						.						132	108	116					17																	1399994		2203	4300	6503	SO:0001583	missense	51763	exon9			CTGCTGGGGAAGT		CCDS11004.1, CCDS11005.1	17p13.3	2008-09-09			ENSG00000132376	ENSG00000132376			33882	protein-coding gene	gene with protein product	"skeletal muscle and kidney enriched inositol phosphatase"	607875				10753883, 12536145	Standard	NM_016532		Approved	SKIP	uc002fsr.3	Q9BT40	OTTHUMG00000150648	ENST00000421807.2:c.1067C>A	chr17.hg19:g.1399994G>T	ENSP00000413937:p.Pro356His	165.0	0.0		145.0	6.0	NM_016532	B2R6I2|B2R750|D3DTH8|Q15733|Q9NPJ5|Q9P2R5	Missense_Mutation	SNP	ENST00000421807.2	hg19	CCDS11004.1	.	.	.	.	.	.	.	.	.	.	G	13.03	2.116506	0.37339	.	.	ENSG00000132376	ENST00000421807;ENST00000406424;ENST00000350761;ENST00000320345;ENST00000397335;ENST00000542125	D;D;D;D	0.97906	-4.6;-4.6;-4.54;-4.49	5.85	-1.1	0.09872	.	1.048160	0.07457	N	0.899909	D	0.93514	0.7930	L	0.31926	0.97	0.26738	N	0.970452	B;B	0.14438	0.01;0.003	B;B	0.10450	0.004;0.005	D	0.85590	0.1245	10	0.41790	T	0.15	-2.9489	3.4814	0.07603	0.3146:0.0:0.279:0.4063	.	260;356	F5GXZ0;Q9BT40	.;INP5K_HUMAN	H	280;280;356;280;264;260	ENSP00000385177:P280H;ENSP00000318476:P280H;ENSP00000380496:P264H;ENSP00000440147:P260H	ENSP00000318476:P280H	P	-	2	0	INPP5K	1346744	0.991000	0.36638	0.996000	0.52242	0.891000	0.51852	0.109000	0.15417	-0.125000	0.11703	0.650000	0.86243	CCC	.	.		0.582	INPP5K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319381.4			T	1399994	G	T	1399994	3	4	255	1	0	0	0	0	1	0	0	0	7769	1232	43	3	295	3	INPP5K	17	1399994	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10		1399994	79795216	612	35957										
DPH1	1801	hgsc.bcm.edu	37	chr17	1943643	1943643	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tattctgggcactttgggccGccagggcagtcctaagatcc	12	12	1	1	rs201983229		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:1943643G>A	ENST00000263083.6	+	8	941	c.896G>A	c.(895-897)cGc>cAc	p.R299H	OVCA2_ENST00000572195.1_5'Flank|DPH1_ENST00000570477.1_Missense_Mutation_p.R219H|RP11-667K14.4_ENST00000572404.1_RNA	NM_001383.3	NP_001374.3	Q9BZG8	DPH1_HUMAN	diphthamide biosynthesis 1	299					cell proliferation (GO:0008283)|peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)|translation (GO:0006412)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(3)|large_intestine(2)|lung(6)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	17						ACTTTGGGCCGCCAGGGCAGT	0.602																																					p.R299H		Atlas-SNP	.											.	DPH1	32	.	0			c.G896A						.	G	HIS/ARG	2,3900		0,2,1949	49	50	49		896	5.1	1	17		49	0,8312		0,0,4156	yes	missense	DPH1	NM_001383.3	29	0,2,6105	AA,AG,GG		0.0,0.0513,0.0164	probably-damaging	299/444	1943643	2,12212	1951	4156	6107	SO:0001583	missense	1801	exon8			TGGGCCGCCAGGG	S81752	CCDS42228.1	17p13.3	2013-05-02	2013-05-02	2005-06-03	ENSG00000108963	ENSG00000108963			3003	protein-coding gene	gene with protein product	"ovarian tumor suppressor candidate 1"	603527	"diptheria toxin resistance protein required for diphthamide biosynthesis-like 1 (S. cerevisiae)", "DPH-like 1 (S. cerevisiae)", "DPH1 homolog (S. cerevisiae)"	DPH2L, DPH2L1		8603384, 15485916, 22869748	Standard	NM_001383		Approved	OVCA1	uc002fts.3	Q9BZG8	OTTHUMG00000177724	ENST00000263083.6:c.896G>A	chr17.hg19:g.1943643G>A	ENSP00000263083:p.Arg299His	76.0	0.0		86.0	4.0	NM_001383	D3DTI3|Q16439|Q4VBA2|Q9BTW7|Q9UCY0	Missense_Mutation	SNP	ENST00000263083.6	hg19	CCDS42228.1	.	.	.	.	.	.	.	.	.	.	G	32	5.139864	0.94560	5.13E-4	0.0	ENSG00000108963	ENST00000263083	T	0.50548	0.74	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.71476	0.3344	M	0.89785	3.06	0.80722	D	1	D;D;D	0.67145	0.996;0.996;0.992	P;P;P	0.58928	0.848;0.848;0.848	T	0.79160	-0.1918	10	0.72032	D	0.01	-16.2111	17.1373	0.86743	0.0:0.0:1.0:0.0	.	309;309;299	E7ENH3;B4DNK0;Q9BZG8	.;.;DPH1_HUMAN	H	299	ENSP00000263083:R299H	ENSP00000263083:R299H	R	+	2	0	DPH1	1890393	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.384000	0.79751	2.380000	0.81148	0.491000	0.48974	CGC	.	.		0.602	DPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438660.1	NM_001383		A	1943643	G	A	1943643	3	1	255	1	0	0	0	0	1	0	0	0	4721	1087	38	1	926	1	DPH1	17	1943643	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	543649	1943643	79251567	613	35958										
ZFP3	124961	hgsc.bcm.edu	37	chr17	4995559	4995559	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	atactggagagaaaccatatGaatgtaatgaatgtgggaag	12	3	0	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:4995559G>T	ENST00000318833.3	+	2	1096	c.760G>T	c.(760-762)Gaa>Taa	p.E254*		NM_153018.2	NP_694563.1	Q96NJ6	ZFP3_HUMAN	ZFP3 zinc finger protein	254					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(3)|prostate(1)	20						GAAACCATATGAATGTAATGA	0.393																																					p.E254X		Atlas-SNP	.											.	ZFP3	54	.	0			c.G760T						.						64	65	65					17																	4995559		2203	4300	6503	SO:0001587	stop_gained	124961	exon2			CCATATGAATGTA	BX647638	CCDS11067.1	17p13.2	2013-01-08	2012-11-27		ENSG00000180787	ENSG00000180787		"Zinc fingers, C2H2-type"	12861	protein-coding gene	gene with protein product		194480	"zinc finger protein homologous to Zfp-3 in mouse", "zinc finger protein 3 homolog (mouse)"				Standard	NM_153018		Approved	FLJ30726, ZNF752	uc002gaq.3	Q96NJ6		ENST00000318833.3:c.760G>T	chr17.hg19:g.4995559G>T	ENSP00000320347:p.Glu254*	54.0	0.0		69.0	4.0	NM_153018	A5PLL4	Nonsense_Mutation	SNP	ENST00000318833.3	hg19	CCDS11067.1	.	.	.	.	.	.	.	.	.	.	G	35	5.530654	0.96446	.	.	ENSG00000180787	ENST00000318833	.	.	.	3.93	2.96	0.34315	.	0.000000	0.37437	N	0.002089	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.15499	T	0.54	-15.6006	6.2313	0.20736	0.2204:0.0:0.7796:0.0	.	.	.	.	X	254	.	ENSP00000320347:E254X	E	+	1	0	ZFP3	4936283	0.000000	0.05858	0.771000	0.31576	0.971000	0.66376	-1.015000	0.03637	1.247000	0.43917	0.563000	0.77884	GAA	.	.		0.393	ZFP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438979.1	NM_153018		T	4995559	G	T	4995559	4	4	255	1	0	0	0	0	0	1	0	0	17658	1291	45	3	762	3	ZFP3	17	4995559	Nonsense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	3051916	4995559	76199651	614	35959										
SLC13A5	284111	hgsc.bcm.edu	37	chr17	6597477	6597477	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gaaggcacaatgaatagcagGgtggccacaaagatggccac	13	9	0	2	rs139660928		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:6597477G>T	ENST00000433363.2	-	8	1328	c.1095C>A	c.(1093-1095)acC>acA	p.T365T	SLC13A5_ENST00000293800.6_Silent_p.T348T|SLC13A5_ENST00000381074.4_Silent_p.T322T|SLC13A5_ENST00000573648.1_Silent_p.T365T	NM_001284510.1|NM_177550.3	NP_001271439.1|NP_808218.1	Q86YT5	S13A5_HUMAN	solute carrier family 13 (sodium-dependent citrate transporter), member 5	365					transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	citrate transmembrane transporter activity (GO:0015137)|sodium:dicarboxylate symporter activity (GO:0017153)|succinate transmembrane transporter activity (GO:0015141)	p.T365T(1)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|prostate(5)|skin(3)|urinary_tract(1)	26						TGAATAGCAGGGTGGCCACAA	0.522																																					p.T365T		Atlas-SNP	.											SLC13A5,NS,carcinoma,0,1	SLC13A5	57	.	1	Substitution - coding silent(1)	prostate(1)	c.C1095A						.						86	72	77					17																	6597477		2203	4300	6503	SO:0001819	synonymous_variant	284111	exon8			TAGCAGGGTGGCC	AJ489980	CCDS11079.1, CCDS45593.1, CCDS67136.1, CCDS67137.1	17p13.1	2013-05-22			ENSG00000141485	ENSG00000141485		"Solute carriers"	23089	protein-coding gene	gene with protein product		608305				12445824	Standard	NM_001284510		Approved	NACT	uc002gdj.3	Q86YT5	OTTHUMG00000102052	ENST00000433363.2:c.1095C>A	chr17.hg19:g.6597477G>T		65.0	0.0		80.0	4.0	NM_001143838	B3KXR0|B7Z4P2|B7ZLB4|F8W7N2|Q6ZMG1	Silent	SNP	ENST00000433363.2	hg19	CCDS11079.1																																																																																			.	G|1.000;C|0.000		0.522	SLC13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219853.2	NM_177550		T	6597477	G	T	6597477	2	4	255	1	0	0	0	0	0	0	0	1	14410	1219	43	3		3	SLC13A5	17	6597477	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	1601918	6597477	74597733	615	35960										
DLG4	1742	hgsc.bcm.edu	37	chr17	7097797	7097797	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agccgcagtccttggtcttgTcgtaatcaaacagggccctg	11	12	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:7097797T>C	ENST00000399506.2	-	12	1510	c.1319A>G	c.(1318-1320)gAc>gGc	p.D440G	DLG4_ENST00000302955.6_Missense_Mutation_p.D437G|DLG4_ENST00000399510.2_Missense_Mutation_p.D483G			P78352	DLG4_HUMAN	discs, large homolog 4 (Drosophila)	440	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|axon guidance (GO:0007411)|dendritic spine morphogenesis (GO:0060997)|establishment of protein localization (GO:0045184)|learning (GO:0007612)|locomotory exploration behavior (GO:0035641)|negative regulation of receptor internalization (GO:0002091)|nervous system development (GO:0007399)|neuromuscular process controlling balance (GO:0050885)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synaptic transmission (GO:0050806)|protein complex assembly (GO:0006461)|protein localization to synapse (GO:0035418)|receptor localization to synapse (GO:0097120)|regulation of grooming behavior (GO:2000821)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|signal transduction (GO:0007165)|social behavior (GO:0035176)|synaptic transmission (GO:0007268)|synaptic vesicle maturation (GO:0016188)|vocalization behavior (GO:0071625)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|cerebellar mossy fiber (GO:0044300)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|dendrite cytoplasm (GO:0032839)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|juxtaparanode region of axon (GO:0044224)|neuron projection terminus (GO:0044306)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	acetylcholine receptor binding (GO:0033130)|beta-1 adrenergic receptor binding (GO:0031697)|D1 dopamine receptor binding (GO:0031748)|ionotropic glutamate receptor binding (GO:0035255)|P2Y1 nucleotide receptor binding (GO:0031812)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein phosphatase binding (GO:0019903)|scaffold protein binding (GO:0097110)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)	18					Guanidine(DB00536)	CTTGGTCTTGTCGTAATCAAA	0.602																																					p.D483G		Atlas-SNP	.											.	DLG4	110	.	0			c.A1448G						.						32	37	36					17																	7097797		2067	4218	6285	SO:0001583	missense	1742	exon14			GTCTTGTCGTAAT	U83192	CCDS45599.1, CCDS45600.1	17p13.1	2008-12-15	2001-12-04		ENSG00000132535	ENSG00000132535			2903	protein-coding gene	gene with protein product		602887				9286702	Standard	NM_001128827		Approved	PSD-95, PSD95, SAP90, SAP-90	uc010cly.3	P78352	OTTHUMG00000134327	ENST00000399506.2:c.1319A>G	chr17.hg19:g.7097797T>C	ENSP00000382425:p.Asp440Gly	56.0	0.0		56.0	4.0	NM_001365	B7Z1S1|G5E939|Q92941|Q9UKK8	Missense_Mutation	SNP	ENST00000399506.2	hg19		.	.	.	.	.	.	.	.	.	.	T	27.3	4.815425	0.90790	.	.	ENSG00000132535	ENST00000399506;ENST00000302955;ENST00000399510;ENST00000293813;ENST00000380912;ENST00000539674	T;T;T	0.50813	0.73;0.73;0.73	5.3	5.3	0.74995	Src homology-3 domain (4);	.	.	.	.	T	0.73984	0.3657	M	0.91561	3.22	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;0.989	D;D;D;D	0.91635	0.994;0.98;0.999;0.995	T	0.79964	-0.1581	9	0.66056	D	0.02	.	13.2525	0.60060	0.0:0.0:0.0:1.0	.	480;440;437;483	B9EGL1;P78352;G5E939;P78352-2	.;DLG4_HUMAN;.;.	G	440;437;483;483;380;483	ENSP00000382425:D440G;ENSP00000307471:D437G;ENSP00000382428:D483G	ENSP00000293813:D483G	D	-	2	0	DLG4	7038521	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	6.077000	0.71275	2.235000	0.73313	0.533000	0.62120	GAC	.	.		0.602	DLG4-002	KNOWN	non_canonical_TEC|not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000259419.2	NM_001365		C	7097797	T	C	7097797	3	2	255	1	0	0	0	0	1	0	0	0	4559	1667	58	2	891	2	DLG4	17	7097797	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	500320	7097797	74097413	616	35961										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11661007	11661007	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgcctagacacactcagaacCaggtaggccaagaaacaagg	10	11	1	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:11661007C>T	ENST00000262442.4	+	35	7061	c.6993C>T	c.(6991-6993)acC>acT	p.T2331T	DNAH9_ENST00000454412.2_Silent_p.T2331T	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2331	AAA 2. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		CACTCAGAACCAGGTAGGCCA	0.463																																					p.T2331T		Atlas-SNP	.											.	DNAH9	695	.	0			c.C6993T						.						84	72	77					17																	11661007		2203	4300	6503	SO:0001819	synonymous_variant	1770	exon35			CAGAACCAGGTAG	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.6993C>T	chr17.hg19:g.11661007C>T		148.0	0.0		143.0	6.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	hg19	CCDS11160.1																																																																																			.	.		0.463	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		T	11661007	C	T	11661007	2	4	255	1	0	0	0	0	0	0	0	1	4610	581	21	3		3	DNAH9	17	11661007	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	4563210	11661007	69534203	617	35962										
ELAC2	60528	hgsc.bcm.edu	37	chr17	12899257	12899257	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccatcaagtgccacacttacCaaggcgcgttctctctgcag	8	15	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:12899257C>A	ENST00000338034.4	-	18	1937	c.1698G>T	c.(1696-1698)ttG>ttT	p.L566F	ELAC2_ENST00000426905.3_Splice_Site_p.L526F|ELAC2_ENST00000395962.2_Splice_Site_p.L547F	NM_018127.6|NM_173717.1	NP_060597.4|NP_776065.1	Q9BQ52	RNZ2_HUMAN	elaC ribonuclease Z 2	566					mitochondrial tRNA 3'-trailer cleavage, endonucleolytic (GO:0072684)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|skin(1)	23						CCACACTTACCAAGGCGCGTT	0.557																																					p.L566F		Atlas-SNP	.											.	ELAC2	48	.	0			c.G1698T						.						89	67	75					17																	12899257		2203	4299	6502	SO:0001630	splice_region_variant	60528	exon18			ACTTACCAAGGCG	AF304370	CCDS11164.1, CCDS54093.1	17p11.2	2013-05-24	2013-05-24		ENSG00000006744	ENSG00000006744	3.1.26.11		14198	protein-coding gene	gene with protein product	"tRNase Z (long form)"	605367	"elaC (E. coli) homolog 2", "elaC homolog 2 (E. coli)"			10986046, 16636667, 21559454	Standard	NM_018127		Approved	FLJ10530, HPC2	uc010vvr.2	Q9BQ52	OTTHUMG00000058764	ENST00000338034.4:c.1698+1G>T	chr17.hg19:g.12899257C>A		74.0	0.0		80.0	4.0	NM_018127	B4DPL9|Q6IA94|Q9HAS8|Q9HAS9|Q9NVT1	Missense_Mutation	SNP	ENST00000338034.4	hg19	CCDS11164.1	.	.	.	.	.	.	.	.	.	.	C	11.50	1.657201	0.29425	.	.	ENSG00000006744	ENST00000426905;ENST00000338034;ENST00000395962;ENST00000457438	T;T;T	0.76578	-1.03;-1.03;-1.03	5.17	5.17	0.71159	Beta-lactamase-like (1);	0.067543	0.64402	D	0.000010	T	0.71600	0.3359	L	0.29908	0.895	0.80722	D	1	B;B;B;B;B;B;B;B	0.31625	0.107;0.012;0.284;0.012;0.107;0.332;0.031;0.019	B;B;B;B;B;B;B;B	0.38954	0.152;0.034;0.188;0.021;0.152;0.286;0.092;0.037	T	0.67082	-0.5760	9	.	.	.	-19.2864	16.2022	0.82088	0.0:1.0:0.0:0.0	.	526;549;547;364;566;326;551;194	B4DPL9;E9PGJ0;G5E9D5;E7ES68;Q9BQ52;B3KSU9;B4DT15;Q9BQ52-3	.;.;.;.;RNZ2_HUMAN;.;.;.	F	526;566;547;244	ENSP00000405223:L526F;ENSP00000337445:L566F;ENSP00000379291:L547F	.	L	-	3	2	ELAC2	12839982	1.000000	0.71417	0.997000	0.53966	0.178000	0.23041	3.229000	0.51278	2.688000	0.91661	0.591000	0.81541	TTG	.	.		0.557	ELAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129934.5		Missense_Mutation	A	12899257	C	A	12899257	5	1	255	1	0	0	0	0	0	0	1	0	5049	608	21	3	810	3	ELAC2	17	12899257	Splice_Site	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1238250	12899257	68295953	618	35963										
CDRT15	146822	hgsc.bcm.edu	37	chr17	14139241	14139241	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccagctgtggacccgcatccAtgcctggaggaggaggttgc	15	12	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:14139241A>G	ENST00000420162.2	-	3	514	c.499T>C	c.(499-501)Tgg>Cgg	p.W167R	CDRT15_ENST00000431716.2_Missense_Mutation_p.W101R	NM_001007530.1	NP_001007531.1	Q96T59	CDRTF_HUMAN	CMT1A duplicated region transcript 15	167										endometrium(2)|large_intestine(1)|lung(2)|prostate(1)	6				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		ACCCGCATCCATGCCTGGAGG	0.612																																					p.W167R		Atlas-SNP	.											.	CDRT15	20	.	0			c.T499C						.						12	12	12					17																	14139241		1993	3893	5886	SO:0001583	missense	146822	exon3			GCATCCATGCCTG	AF355097	CCDS32569.1	17p12	2012-11-19			ENSG00000223510	ENSG00000223510			14395	protein-coding gene	gene with protein product						11381029	Standard	NM_001007530		Approved		uc010vvu.2	Q96T59	OTTHUMG00000179686	ENST00000420162.2:c.499T>C	chr17.hg19:g.14139241A>G	ENSP00000402355:p.Trp167Arg	311.0	0.0		357.0	81.0	NM_001007530	B2RUU5	Missense_Mutation	SNP	ENST00000420162.2	hg19	CCDS32569.1	.	.	.	.	.	.	.	.	.	.	A	0.007	-1.962593	0.00461	.	.	ENSG00000223510	ENST00000431716;ENST00000420162	T	0.57907	0.37	.	.	.	.	.	.	.	.	T	0.42200	0.1192	N	0.14661	0.345	0.09310	N	1	D	0.54397	0.966	P	0.55667	0.781	T	0.32052	-0.9921	7	0.24483	T	0.36	.	.	.	.	.	167	Q96T59	CDRTF_HUMAN	R	101;167	ENSP00000402355:W167R	ENSP00000402355:W167R	W	-	1	0	CDRT15	14079966	0.019000	0.18553	0.011000	0.14972	0.011000	0.07611	0.140000	0.16056	0.103000	0.17682	0.102000	0.15555	TGG	.	.		0.612	CDRT15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252853.1	NM_001007530		G	14139241	A	G	14139241	3	3	255	1	0	0	0	0	1	0	0	0	3177	217	8	2	69	2	CDRT15	17	14139241	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	1239984	14139241	67055969	619	35964										
FAM83G	644815	hgsc.bcm.edu	37	chr17	18881095	18881095	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tctgagtggcgcctccggagAgggactgagtgctctctcac	14	12	3	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:18881095A>G	ENST00000388995.6	-	5	2107	c.1884T>C	c.(1882-1884)ccT>ccC	p.P628P	SLC5A10_ENST00000395642.1_Intron|SLC5A10_ENST00000417251.2_Intron|FAM83G_ENST00000345041.4_Silent_p.P628P|SLC5A10_ENST00000395647.2_Intron|SLC5A10_ENST00000395645.3_Intron|SLC5A10_ENST00000317977.6_Intron|SLC5A10_ENST00000395643.2_Intron|FAM83G_ENST00000585154.2_Silent_p.P628P			A6ND36	FA83G_HUMAN	family with sequence similarity 83, member G	628					BMP signaling pathway (GO:0030509)	cytosol (GO:0005829)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(3)|stomach(1)	22						GCCTCCGGAGAGGGACTGAGT	0.667																																					p.P628P		Atlas-SNP	.											.	FAM83G	51	.	0			c.T1884C						.						32	38	36					17																	18881095		2022	4180	6202	SO:0001819	synonymous_variant	644815	exon5			CCGGAGAGGGACT	AK123558	CCDS42276.1	17p11.2	2014-05-01	2006-03-22		ENSG00000188522	ENSG00000188522			32554	protein-coding gene	gene with protein product	"protein associated with SMAD1"	615886				24554596	Standard	NM_001039999		Approved	FLJ41564, PAWS1	uc002guw.3	A6ND36	OTTHUMG00000059411	ENST00000388995.6:c.1884T>C	chr17.hg19:g.18881095A>G		65.0	0.0		86.0	4.0	NM_001039999	Q3KQZ4|Q6ZW60	Silent	SNP	ENST00000388995.6	hg19	CCDS42276.1																																																																																			.	.		0.667	FAM83G-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253108.4			G	18881095	A	G	18881095	2	3	255	1	0	0	0	0	0	0	0	1	5647	291	11	2		2	FAM83G	17	18881095	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	4741854	18881095	62314115	620	35965										
SEZ6	124925	hgsc.bcm.edu	37	chr17	27286199	27286199	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccgggccgtcaggtcatcccCatcatagaaggtaagcacat	10	13	3	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:27286199C>T	ENST00000317338.12	-	10	2379	c.1951G>A	c.(1951-1953)Ggg>Agg	p.G651R	SEZ6_ENST00000442608.3_Missense_Mutation_p.G651R|SEZ6_ENST00000360295.9_Missense_Mutation_p.G651R|PIPOX_ENST00000583215.1_Intron|SEZ6_ENST00000335960.6_Intron			Q53EL9	SEZ6_HUMAN	seizure related 6 homolog (mouse)	651	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|negative regulation of dendrite development (GO:2000171)|positive regulation of dendrite development (GO:1900006)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	apical dendrite (GO:0097440)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(4)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	29	Lung NSC(42;0.0137)		Epithelial(11;4.73e-06)|all cancers(11;2.91e-05)|BRCA - Breast invasive adenocarcinoma(11;8.06e-05)|OV - Ovarian serous cystadenocarcinoma(11;0.111)			AGGTCATCCCCATCATAGAAG	0.612																																					p.G651R		Atlas-SNP	.											.	SEZ6	61	.	0			c.G1951A						.						39	44	42					17																	27286199		1946	4142	6088	SO:0001583	missense	124925	exon10			CATCCCCATCATA	AY038048	CCDS45638.1, CCDS45639.1	17q11.2	2008-03-06	2001-11-28		ENSG00000063015	ENSG00000063015			15955	protein-coding gene	gene with protein product			"seizure related gene 6 (mouse) homolog"			17086543	Standard	NM_178860		Approved		uc002hdp.2	Q53EL9	OTTHUMG00000168010	ENST00000317338.12:c.1951G>A	chr17.hg19:g.27286199C>T	ENSP00000312942:p.Gly651Arg	76.0	0.0		97.0	4.0	NM_001098635	B6ZDN1|Q8N701|Q8NB57|Q8ND50|Q8TD25|Q96NI5|Q96NQ3	Missense_Mutation	SNP	ENST00000317338.12	hg19	CCDS45639.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.627003	0.87560	.	.	ENSG00000063015	ENST00000442608;ENST00000360295;ENST00000317338;ENST00000541381	T;T	0.26957	1.7;1.7	4.82	4.82	0.62117	CUB (5);	0.000000	0.85682	D	0.000000	T	0.58495	0.2126	M	0.90369	3.11	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.79784	0.982;0.993	T	0.67364	-0.5689	10	0.87932	D	0	.	15.8044	0.78481	0.0:1.0:0.0:0.0	.	651;651	Q53EL9-3;Q53EL9	.;SEZ6_HUMAN	R	651;651;526;651	ENSP00000403784:G651R;ENSP00000353440:G651R	ENSP00000312942:G526R	G	-	1	0	SEZ6	24310325	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.651000	0.83577	2.680000	0.91292	0.655000	0.94253	GGG	.	.		0.612	SEZ6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397475.3			T	27286199	C	T	27286199	3	4	255	1	0	0	0	0	1	0	0	0	14157	594	21	3	1078	3	SEZ6	17	27286199	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	8405104	27286199	53909011	621	35966										
TP53I13	90313	hgsc.bcm.edu	37	chr17	27896100	27896100	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gagcctgtggcctctgcctcCgcaggtaggagccctggagg	16	13	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:27896100C>T	ENST00000301057.7	+	2	252	c.137C>T	c.(136-138)cCg>cTg	p.P46L	RP11-68I3.4_ENST00000579050.1_RNA|RP11-68I3.2_ENST00000581474.1_RNA|ABHD15_ENST00000307201.4_5'Flank	NM_138349.2	NP_612358.3	Q8NBR0	P5I13_HUMAN	tumor protein p53 inducible protein 13	46						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|kidney(1)|lung(1)|urinary_tract(1)	4				READ - Rectum adenocarcinoma(3;0.236)		CCTCTGCCTCCGCAGGTAGGA	0.662																																					p.P46L		Atlas-SNP	.											.	TP53I13	17	.	0			c.C137T						.						10	14	13					17																	27896100		1982	4152	6134	SO:0001583	missense	90313	exon2			TGCCTCCGCAGGT	AK075341	CCDS42289.1	17q11.2	2006-01-16				ENSG00000167543			25102	protein-coding gene	gene with protein product						14767535	Standard	NM_138349		Approved	DSCP1	uc002hee.3	Q8NBR0		ENST00000301057.7:c.137C>T	chr17.hg19:g.27896100C>T	ENSP00000301057:p.Pro46Leu	27.0	0.0		80.0	4.0	NM_138349	Q7L5U3	Missense_Mutation	SNP	ENST00000301057.7	hg19	CCDS42289.1	.	.	.	.	.	.	.	.	.	.	C	12.89	2.074611	0.36566	.	.	ENSG00000167543	ENST00000301057	.	.	.	5.1	1.35	0.21983	.	0.576450	0.16267	N	0.221980	T	0.59088	0.2168	M	0.65975	2.015	0.46241	D	0.998941	D	0.57899	0.981	P	0.48063	0.565	T	0.63668	-0.6585	9	0.66056	D	0.02	-1.4311	10.6249	0.45502	0.5919:0.4081:0.0:0.0	.	46	Q8NBR0	P5I13_HUMAN	L	46	.	ENSP00000301057:P46L	P	+	2	0	TP53I13	24920226	0.004000	0.15560	1.000000	0.80357	0.599000	0.36880	0.057000	0.14279	0.630000	0.30394	0.456000	0.33151	CCG	.	.		0.662	TP53I13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447804.2	NM_138349		T	27896100	C	T	27896100	3	4	255	1	0	0	0	0	1	0	0	0	16401	652	23	1	143	1	TP53I13	17	27896100	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	609901	27896100	53299110	622	35967										
NF1	4763	hgsc.bcm.edu	37	chr17	29676237	29676237	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cagaaattgtgacaaatttgAagtgaatacacagagcgtgg	11	5	0	5			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:29676237A>G	ENST00000358273.4	+	49	7672	c.7289A>G	c.(7288-7290)gAa>gGa	p.E2430G	NF1_ENST00000444181.2_Missense_Mutation_p.E223G|NF1_ENST00000417592.2_Missense_Mutation_p.E143G|NF1_ENST00000356175.3_Missense_Mutation_p.E2409G	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	2430					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(3)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		GACAAATTTGAAGTGAATACA	0.353			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																											p.E2430G		Atlas-SNP	.	yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	.	NF1	1586	.	11	Whole gene deletion(8)|Unknown(3)	soft_tissue(7)|autonomic_ganglia(2)|lung(1)|central_nervous_system(1)	c.A7289G						.						89	81	84					17																	29676237		2203	4300	6503	SO:0001583	missense	4763	exon49	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	AATTTGAAGTGAA		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.7289A>G	chr17.hg19:g.29676237A>G	ENSP00000351015:p.Glu2430Gly	66.0	0.0		72.0	5.0	NM_001042492	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	hg19	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	A	27.3	4.822818	0.90873	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735;ENST00000444181;ENST00000417592	T;T;T;T	0.66815	2.97;3.12;2.8;-0.23	5.78	5.78	0.91487	Armadillo-type fold (1);	0.114676	0.64402	D	0.000020	T	0.81024	0.4737	M	0.73962	2.25	0.58432	D	0.999999	D;D	0.63046	0.989;0.992	D;P	0.72982	0.979;0.864	T	0.80480	-0.1364	10	0.38643	T	0.18	.	16.1138	0.81283	1.0:0.0:0.0:0.0	.	2409;2430	P21359-2;P21359	.;NF1_HUMAN	G	2430;2409;2075;223;143	ENSP00000351015:E2430G;ENSP00000348498:E2409G;ENSP00000389907:E2075G;ENSP00000396481:E223G	ENSP00000348498:E2409G	E	+	2	0	NF1	26700363	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.564000	0.90726	2.220000	0.72140	0.533000	0.62120	GAA	.	.		0.353	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		G	29676237	A	G	29676237	3	3	255	1	0	0	0	0	1	0	0	0	10365	246	9	2	7544	2	NF1	17	29676237	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	1780137	29676237	51518973	623	35968										
C17orf75	64149	hgsc.bcm.edu	37	chr17	30666839	30666839	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	attttgcacttactttagctCcacagatgcaacattaccca	4	12	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:30666839C>A	ENST00000577809.1	-	3	389	c.340G>T	c.(340-342)Gag>Tag	p.E114*	RP11-227G15.3_ENST00000581915.1_RNA|C17orf75_ENST00000225805.4_Nonsense_Mutation_p.E114*	NM_022344.3	NP_071739.2	Q9HAS0	NJMU_HUMAN	chromosome 17 open reading frame 75	114										ovary(1)	1		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)			TACTTTAGCTCCACAGATGCA	0.433																																					p.E114X		Atlas-SNP	.											.	C17orf75	23	.	0			c.G340T						.						149	145	146					17																	30666839		1933	4139	6072	SO:0001587	stop_gained	64149	exon3			TTAGCTCCACAGA	AB062437	CCDS58537.1	17q11.2	2013-01-21			ENSG00000108666	ENSG00000108666			30173	protein-coding gene	gene with protein product							Standard	NM_022344		Approved	NJMU-R1	uc002hhg.3	Q9HAS0		ENST00000577809.1:c.340G>T	chr17.hg19:g.30666839C>A	ENSP00000464275:p.Glu114*	82.0	0.0		88.0	4.0	NM_022344	Q7Z2H4	Nonsense_Mutation	SNP	ENST00000577809.1	hg19	CCDS58537.1	.	.	.	.	.	.	.	.	.	.	C	34	5.381196	0.95945	.	.	ENSG00000108666	ENST00000225805	.	.	.	5.68	4.71	0.59529	.	0.098652	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-27.107	14.5631	0.68153	0.0:0.9298:0.0:0.0702	.	.	.	.	X	114	.	ENSP00000225805:E114X	E	-	1	0	C17orf75	27690952	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.265000	0.78442	1.396000	0.46663	0.650000	0.86243	GAG	.	.		0.433	C17orf75-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447204.1	NM_022344		A	30666839	C	A	30666839	4	1	255	1	0	0	0	0	0	1	0	0	1882	864	30	3	882	3	C17orf75	17	30666839	Nonsense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	990602	30666839	50528371	624	35969										
LIG3	3980	hgsc.bcm.edu	37	chr17	33319691	33319691	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gcgtccaggcctcgctgatgAcacctgtgcagcccatgttg	12	14	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:33319691A>G	ENST00000378526.4	+	8	1568	c.1435A>G	c.(1435-1437)Aca>Gca	p.T479A	LIG3_ENST00000262327.5_Missense_Mutation_p.T479A	NM_013975.3	NP_039269.2	P49916	DNLI3_HUMAN	ligase III, DNA, ATP-dependent	479					base-excision repair (GO:0006284)|base-excision repair, DNA ligation (GO:0006288)|DNA biosynthetic process (GO:0071897)|DNA repair (GO:0006281)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitochondrial DNA repair (GO:0043504)|negative regulation of DNA recombination (GO:0045910)|nucleotide-excision repair (GO:0006289)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(8)|lung(9)|ovary(3)|pancreas(2)|prostate(1)|skin(3)|stomach(1)	31		Ovarian(249;0.17)			Bleomycin(DB00290)	CTCGCTGATGACACCTGTGCA	0.607								Other BER factors																													p.T479A		Atlas-SNP	.											.	LIG3	164	.	0			c.A1435G						.						52	43	46					17																	33319691		2203	4300	6503	SO:0001583	missense	3980	exon8			CTGATGACACCTG		CCDS11284.2, CCDS11285.2	17q11.2-q12	2008-10-29			ENSG00000005156	ENSG00000005156			6600	protein-coding gene	gene with protein product		600940	"ligase II, DNA, ATP-dependent"	LIG2		7760816	Standard	NM_002311		Approved		uc002hik.2	P49916	OTTHUMG00000128519	ENST00000378526.4:c.1435A>G	chr17.hg19:g.33319691A>G	ENSP00000367787:p.Thr479Ala	89.0	0.0		95.0	4.0	NM_013975	Q16714|Q6NVK3	Missense_Mutation	SNP	ENST00000378526.4	hg19	CCDS11284.2	.	.	.	.	.	.	.	.	.	.	A	28.8	4.953740	0.92660	.	.	ENSG00000005156	ENST00000378526;ENST00000262327	T;T	0.18810	2.19;2.19	5.5	5.5	0.81552	DNA ligase, ATP-dependent, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.38799	0.1054	M	0.73962	2.25	0.80722	D	1	P;P;P	0.45283	0.855;0.855;0.855	P;P;P	0.51355	0.667;0.667;0.667	T	0.18461	-1.0336	10	0.54805	T	0.06	-20.6633	14.9457	0.71029	1.0:0.0:0.0:0.0	.	479;479;479	E5KLB5;P49916;E5KLB6	.;DNLI3_HUMAN;.	A	479	ENSP00000367787:T479A;ENSP00000262327:T479A	ENSP00000262327:T479A	T	+	1	0	LIG3	30343804	1.000000	0.71417	0.978000	0.43139	0.955000	0.61496	8.914000	0.92735	2.308000	0.77769	0.533000	0.62120	ACA	.	.		0.607	LIG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250330.3	NM_013975		G	33319691	A	G	33319691	3	3	255	1	0	0	0	0	1	0	0	0	8791	275	10	2	1461	2	LIG3	17	33319691	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	2652852	33319691	47875519	625	35970										
GAS2L2	246176	hgsc.bcm.edu	37	chr17	34074044	34074044	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cttccccatacctcaggaatGgtgccatctctctggaggcc	9	15	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:34074044G>T	ENST00000254466.6	-	5	1103	c.1076C>A	c.(1075-1077)cCa>cAa	p.P359Q	GAS2L2_ENST00000587565.1_Missense_Mutation_p.P343Q	NM_139285.3	NP_644814.1	Q8NHY3	GA2L2_HUMAN	growth arrest-specific 2 like 2	359					cell cycle arrest (GO:0007050)|microtubule bundle formation (GO:0001578)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	actin filament binding (GO:0051015)|cytoskeletal adaptor activity (GO:0008093)|microtubule binding (GO:0008017)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CCTCAGGAATGGTGCCATCTC	0.587																																					p.P359Q		Atlas-SNP	.											.	GAS2L2	94	.	0			c.C1076A						.						46	50	49					17																	34074044		2203	4300	6503	SO:0001583	missense	246176	exon5			AGGAATGGTGCCA	AF508784	CCDS11298.1	17q21	2014-05-06			ENSG00000132139	ENSG00000270765			24846	protein-coding gene	gene with protein product		611398				12584248	Standard	NM_139285		Approved	GAR17	uc002hjv.2	Q8NHY3	OTTHUMG00000188386	ENST00000254466.6:c.1076C>A	chr17.hg19:g.34074044G>T	ENSP00000254466:p.Pro359Gln	86.0	0.0		80.0	5.0	NM_139285	Q8NHY4	Missense_Mutation	SNP	ENST00000254466.6	hg19	CCDS11298.1	.	.	.	.	.	.	.	.	.	.	G	12.97	2.098403	0.37048	.	.	ENSG00000132139	ENST00000254466	T	0.19938	2.11	4.54	3.57	0.40892	.	0.492528	0.18269	N	0.146396	T	0.22704	0.0548	L	0.56769	1.78	0.09310	N	1	P	0.44578	0.838	B	0.42422	0.387	T	0.11397	-1.0589	10	0.66056	D	0.02	-0.9574	8.404	0.32603	0.1065:0.0:0.8935:0.0	.	359	Q8NHY3	GA2L2_HUMAN	Q	359	ENSP00000254466:P359Q	ENSP00000254466:P359Q	P	-	2	0	GAS2L2	31098157	0.031000	0.19500	0.001000	0.08648	0.259000	0.26198	2.704000	0.47118	1.264000	0.44198	0.313000	0.20887	CCA	.	.		0.587	GAS2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256497.1	NM_139285		T	34074044	G	T	34074044	3	4	255	1	0	0	0	0	1	0	0	0	6255	1348	47	3	1574	3	GAS2L2	17	34074044	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	754353	34074044	47121166	626	35971										
LHX1	3975	hgsc.bcm.edu	37	chr17	35300345	35300345	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcggacccagcccgcccttcTcgtcgctgtcggtcaacggt	11	17	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:35300345T>C	ENST00000254457.5	+	5	2549	c.1138T>C	c.(1138-1140)Tcg>Ccg	p.S380P	RP11-445F12.2_ENST00000607336.1_RNA	NM_005568.3	NP_005559.2	P48742	LHX1_HUMAN	LIM homeobox 1	380					anatomical structure formation involved in morphogenesis (GO:0048646)|anatomical structure morphogenesis (GO:0009653)|anterior/posterior axis specification (GO:0009948)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell-cell signaling (GO:0007267)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation (GO:0021937)|cerebellum development (GO:0021549)|cervix development (GO:0060067)|comma-shaped body morphogenesis (GO:0072049)|dorsal/ventral pattern formation (GO:0009953)|ectoderm formation (GO:0001705)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|embryonic viscerocranium morphogenesis (GO:0048703)|endoderm formation (GO:0001706)|epithelium development (GO:0060429)|forebrain regionalization (GO:0021871)|gastrulation with mouth forming second (GO:0001702)|head development (GO:0060322)|horizontal cell localization (GO:0035852)|kidney development (GO:0001822)|lateral motor column neuron migration (GO:0097477)|mesonephric duct development (GO:0072177)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric glomerulus development (GO:0072224)|metanephric part of ureteric bud development (GO:0035502)|metanephric renal vesicle morphogenesis (GO:0072283)|metanephric S-shaped body morphogenesis (GO:0072284)|motor neuron axon guidance (GO:0008045)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct elongation (GO:0035849)|nephric duct morphogenesis (GO:0072178)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|oviduct development (GO:0060066)|oviduct epithelium development (GO:0035846)|paramesonephric duct development (GO:0061205)|pattern specification process (GO:0007389)|positive regulation of anterior head development (GO:2000744)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of embryonic development (GO:0040019)|positive regulation of gastrulation (GO:2000543)|positive regulation of nephron tubule epithelial cell differentiation (GO:2000768)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|primitive streak formation (GO:0090009)|pronephros development (GO:0048793)|regulation of gene expression (GO:0010468)|renal vesicle morphogenesis (GO:0072077)|retina layer formation (GO:0010842)|S-shaped body morphogenesis (GO:0072050)|somite rostral/caudal axis specification (GO:0032525)|spinal cord association neuron differentiation (GO:0021527)|telencephalon development (GO:0021537)|transcription from RNA polymerase II promoter (GO:0006366)|ureteric bud development (GO:0001657)|urogenital system development (GO:0001655)|uterine epithelium development (GO:0035847)|uterus development (GO:0060065)|vagina development (GO:0060068)|ventral spinal cord development (GO:0021517)	nucleus (GO:0005634)|protein complex (GO:0043234)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	16		Breast(25;0.00607)				CCCGCCCTTCTCGTCGCTGTC	0.716																																					p.S380P		Atlas-SNP	.											.	LHX1	48	.	0			c.T1138C						.						14	16	15					17																	35300345		2183	4260	6443	SO:0001583	missense	3975	exon5			CCCTTCTCGTCGC	U14755	CCDS11316.1	17q12	2014-04-11			ENSG00000132130	ENSG00000273706		"Homeoboxes / LIM class"	6593	protein-coding gene	gene with protein product		601999				9212161	Standard	NM_005568		Approved	LIM-1, LIM1	uc002hnh.2	P48742	OTTHUMG00000188456	ENST00000254457.5:c.1138T>C	chr17.hg19:g.35300345T>C	ENSP00000254457:p.Ser380Pro	68.0	0.0		82.0	5.0	NM_005568	Q3MIW0	Missense_Mutation	SNP	ENST00000254457.5	hg19	CCDS11316.1	.	.	.	.	.	.	.	.	.	.	T	13.02	2.110911	0.37242	.	.	ENSG00000132130	ENST00000254457	D	0.90676	-2.71	4.73	4.73	0.59995	.	0.075094	0.53938	D	0.000052	D	0.84106	0.5399	L	0.27053	0.805	0.44142	D	0.996931	B	0.06786	0.001	B	0.06405	0.002	T	0.79427	-0.1808	10	0.27785	T	0.31	.	14.3888	0.66963	0.0:0.0:0.0:1.0	.	380	P48742	LHX1_HUMAN	P	380	ENSP00000254457:S380P	ENSP00000254457:S380P	S	+	1	0	LHX1	32374458	1.000000	0.71417	0.991000	0.47740	0.933000	0.57130	4.015000	0.57152	1.988000	0.58038	0.459000	0.35465	TCG	.	.		0.716	LHX1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256704.3	NM_005568		C	35300345	T	C	35300345	3	2	255	1	0	0	0	0	1	0	0	0	8779	1551	54	2	1156	2	LHX1	17	35300345	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	1226301	35300345	45894865	627	35972										
HNF1B	6928	hgsc.bcm.edu	37	chr17	36070598	36070598	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	accgactggctggtcaccatGgcgctgttgccatggtgact	13	12	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:36070598G>T	ENST00000225893.4	-	5	1480	c.1119C>A	c.(1117-1119)gcC>gcA	p.A373A	HNF1B_ENST00000561193.1_Silent_p.A347A|HNF1B_ENST00000427275.2_Silent_p.A347A|HNF1B_ENST00000560016.1_Silent_p.A373A	NM_000458.2|NM_001165923.1	NP_000449.1|NP_001159395.1	P35680	HNF1B_HUMAN	HNF1 homeobox B	373					anterior/posterior pattern specification (GO:0009952)|branching morphogenesis of an epithelial tube (GO:0048754)|embryonic digestive tract morphogenesis (GO:0048557)|endocrine pancreas development (GO:0031018)|endodermal cell fate specification (GO:0001714)|epithelial cell proliferation (GO:0050673)|genitalia development (GO:0048806)|hepatoblast differentiation (GO:0061017)|hindbrain development (GO:0030902)|inner cell mass cell differentiation (GO:0001826)|insulin secretion (GO:0030073)|kidney development (GO:0001822)|mesonephric duct formation (GO:0072181)|negative regulation of mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis (GO:0061296)|negative regulation of mesenchymal cell apoptotic process involved in metanephros development (GO:1900212)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephric nephron tubule development (GO:0039020)|pronephros development (GO:0048793)|regulation of branch elongation involved in ureteric bud branching (GO:0072095)|regulation of endodermal cell fate specification (GO:0042663)|regulation of pronephros size (GO:0035565)|regulation of Wnt signaling pathway (GO:0030111)|response to glucose (GO:0009749)|ureteric bud elongation (GO:0060677)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(6)|kidney(3)|large_intestine(2)|liver(1)|lung(3)|ovary(3)|prostate(1)|skin(2)	28		Breast(25;0.00765)|Ovarian(249;0.15)	STAD - Stomach adenocarcinoma(1;0.0142)			TGGTCACCATGGCGCTGTTGC	0.537																																					p.A373A	Colon(71;102 1179 9001 27917 43397)	Atlas-SNP	.											.	HNF1B	61	.	0			c.C1119A						.						79	71	74					17																	36070598		2203	4300	6503	SO:0001819	synonymous_variant	6928	exon5			CACCATGGCGCTG	BC017714	CCDS11324.1, CCDS58538.1	17q12	2014-05-06	2007-08-24	2007-08-24	ENSG00000108753	ENSG00000275410		"Homeoboxes / HNF class"	11630	protein-coding gene	gene with protein product		189907	"transcription factor 2, hepatic; LF-B3; variant hepatic nuclear factor"	TCF2		1677179, 10484768	Standard	NM_000458		Approved	LFB3, VHNF1, HNF1beta, MODY5	uc002hok.4	P35680	OTTHUMG00000188478	ENST00000225893.4:c.1119C>A	chr17.hg19:g.36070598G>T		102.0	0.0		96.0	4.0	NM_000458	B4DKM3|E0YMJ9	Silent	SNP	ENST00000225893.4	hg19	CCDS11324.1																																																																																			.	.		0.537	HNF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256807.3	NM_000458		T	36070598	G	T	36070598	2	4	255	1	0	0	0	0	0	0	0	1	7261	1335	47	3		3	HNF1B	17	36070598	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	770253	36070598	45124612	628	35973										
HNF1B	6928	hgsc.bcm.edu	37	chr17	36091619	36091619	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tggaggagaggagctgggctGgtggtggggggagccgtggg	26	4	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:36091619G>A	ENST00000225893.4	-	4	1373	c.1012C>T	c.(1012-1014)Cag>Tag	p.Q338*	HNF1B_ENST00000561193.1_Nonsense_Mutation_p.Q312*|HNF1B_ENST00000427275.2_Nonsense_Mutation_p.Q312*|HNF1B_ENST00000560016.1_Nonsense_Mutation_p.Q338*	NM_000458.2|NM_001165923.1	NP_000449.1|NP_001159395.1	P35680	HNF1B_HUMAN	HNF1 homeobox B	338					anterior/posterior pattern specification (GO:0009952)|branching morphogenesis of an epithelial tube (GO:0048754)|embryonic digestive tract morphogenesis (GO:0048557)|endocrine pancreas development (GO:0031018)|endodermal cell fate specification (GO:0001714)|epithelial cell proliferation (GO:0050673)|genitalia development (GO:0048806)|hepatoblast differentiation (GO:0061017)|hindbrain development (GO:0030902)|inner cell mass cell differentiation (GO:0001826)|insulin secretion (GO:0030073)|kidney development (GO:0001822)|mesonephric duct formation (GO:0072181)|negative regulation of mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis (GO:0061296)|negative regulation of mesenchymal cell apoptotic process involved in metanephros development (GO:1900212)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephric nephron tubule development (GO:0039020)|pronephros development (GO:0048793)|regulation of branch elongation involved in ureteric bud branching (GO:0072095)|regulation of endodermal cell fate specification (GO:0042663)|regulation of pronephros size (GO:0035565)|regulation of Wnt signaling pathway (GO:0030111)|response to glucose (GO:0009749)|ureteric bud elongation (GO:0060677)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(6)|kidney(3)|large_intestine(2)|liver(1)|lung(3)|ovary(3)|prostate(1)|skin(2)	28		Breast(25;0.00765)|Ovarian(249;0.15)	STAD - Stomach adenocarcinoma(1;0.0142)			GAGCTGGGCTGGTGGTGGGGG	0.592																																					p.Q338X	Colon(71;102 1179 9001 27917 43397)	Atlas-SNP	.											.	HNF1B	61	.	0			c.C1012T						.						78	60	66					17																	36091619		2203	4300	6503	SO:0001587	stop_gained	6928	exon4			TGGGCTGGTGGTG	BC017714	CCDS11324.1, CCDS58538.1	17q12	2014-05-06	2007-08-24	2007-08-24	ENSG00000108753	ENSG00000275410		"Homeoboxes / HNF class"	11630	protein-coding gene	gene with protein product		189907	"transcription factor 2, hepatic; LF-B3; variant hepatic nuclear factor"	TCF2		1677179, 10484768	Standard	NM_000458		Approved	LFB3, VHNF1, HNF1beta, MODY5	uc002hok.4	P35680	OTTHUMG00000188478	ENST00000225893.4:c.1012C>T	chr17.hg19:g.36091619G>A	ENSP00000225893:p.Gln338*	421.0	0.0		431.0	174.0	NM_000458	B4DKM3|E0YMJ9	Nonsense_Mutation	SNP	ENST00000225893.4	hg19	CCDS11324.1	.	.	.	.	.	.	.	.	.	.	G	38	7.176410	0.98114	.	.	ENSG00000108753	ENST00000225893;ENST00000427275;ENST00000544593;ENST00000539087	.	.	.	5.2	5.2	0.72013	.	0.163295	0.56097	D	0.000039	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25751	T	0.34	-1.8848	17.4606	0.87619	0.0:0.0:1.0:0.0	.	.	.	.	X	338;312;338;226	.	ENSP00000225893:Q338X	Q	-	1	0	HNF1B	33165732	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	9.155000	0.94700	2.713000	0.92767	0.650000	0.86243	CAG	.	.		0.592	HNF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256807.3	NM_000458		A	36091619	G	A	36091619	4	1	255	1	0	0	0	0	0	1	0	0	7261	1357	47	3	685	3	HNF1B	17	36091619	Nonsense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	21021	36091619	45103591	629	35974										
PIP4K2B	8396	hgsc.bcm.edu	37	chr17	36935671	36935671	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gcgatgcacagtgagccgatGgctgaacacgttcctggtaa	13	10	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:36935671G>A	ENST00000269554.3	-	5	1099	c.619C>T	c.(619-621)Cat>Tat	p.H207Y	PIP4K2B_ENST00000311500.6_5'UTR	NM_003559.4	NP_003550.1	P78356	PI42B_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, beta	207	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				cell surface receptor signaling pathway (GO:0007166)|intracellular signal transduction (GO:0035556)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|1-phosphatidylinositol-5-phosphate 4-kinase activity (GO:0016309)|ATP binding (GO:0005524)|receptor signaling protein activity (GO:0005057)			endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(8)|ovary(1)	19						GTGAGCCGATGGCTGAACACG	0.567																																					p.H207Y		Atlas-SNP	.											.	PIP4K2B	35	.	0			c.C619T						.						183	139	154					17																	36935671		2203	4300	6503	SO:0001583	missense	8396	exon5			GCCGATGGCTGAA	U85245	CCDS11329.1	17q21.2	2007-08-14	2007-08-14	2007-08-14		ENSG00000276293	2.7.1.149		8998	protein-coding gene	gene with protein product		603261	"phosphatidylinositol-4-phosphate 5-kinase, type II, beta"	PIP5K2B		9038203, 14691457, 9367159	Standard	NM_003559		Approved	PIP5KIIB, PIP5KIIbeta	uc002hqs.3	P78356		ENST00000269554.3:c.619C>T	chr17.hg19:g.36935671G>A	ENSP00000269554:p.His207Tyr	74.0	0.0		98.0	4.0	NM_003559	Q5U0E8|Q8TBP2	Missense_Mutation	SNP	ENST00000269554.3	hg19	CCDS11329.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.092795	0.76756	.	.	ENSG00000141720	ENST00000269554;ENST00000311500	T	0.30182	1.54	4.92	4.92	0.64577	Phosphatidylinositol-4-phosphate 5-kinase, core (2);Phosphatidylinositol-4-phosphate 5-kinase, core, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.60143	0.2246	M	0.87180	2.865	0.80722	D	1	D;D;D	0.69078	0.997;0.997;0.988	D;D;P	0.67382	0.951;0.918;0.871	T	0.66352	-0.5945	10	0.54805	T	0.06	-14.8159	16.8353	0.85955	0.0:0.0:1.0:0.0	.	207;207;207	C9JMM2;P78356-2;P78356	.;.;PI42B_HUMAN	Y	207	ENSP00000269554:H207Y	ENSP00000269554:H207Y	H	-	1	0	PIP4K2B	34189197	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.259000	0.95561	2.546000	0.85860	0.655000	0.94253	CAT	.	.		0.567	PIP4K2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256791.1	NM_003559		A	36935671	G	A	36935671	3	1	255	1	0	0	0	0	1	0	0	0	11946	1348	47	3	655	3	PIP4K2B	17	36935671	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	844052	36935671	44259539	630	35975										
TOP2A	7153	hgsc.bcm.edu	37	chr17	38561112	38561112	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gttaaccattcctttcgatcAtctatctgttttttgctaaa	4	9	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:38561112A>G	ENST00000423485.1	-	17	2135	c.1977T>C	c.(1975-1977)gaT>gaC	p.D659D		NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	659					apoptotic chromosome condensation (GO:0030263)|ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA ligation (GO:0006266)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|embryonic cleavage (GO:0040016)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|positive regulation of apoptotic process (GO:0043065)|positive regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral genome replication (GO:0045070)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|DNA-dependent ATPase activity (GO:0008094)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(9)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	39		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	CCTTTCGATCATCTATCTGTT	0.343																																					p.D659D		Atlas-SNP	.											.	TOP2A	124	.	0			c.T1977C						.						82	73	76					17																	38561112		1811	4077	5888	SO:0001819	synonymous_variant	7153	exon17			TCGATCATCTATC		CCDS45672.1	17q21-q22	2008-08-06	2002-08-29		ENSG00000131747	ENSG00000131747	5.99.1.2		11989	protein-coding gene	gene with protein product		126430	"topoisomerase (DNA) II alpha (170kD)"	TOP2			Standard	NM_001067		Approved		uc002huq.3	P11388	OTTHUMG00000155008	ENST00000423485.1:c.1977T>C	chr17.hg19:g.38561112A>G		68.0	0.0		68.0	4.0	NM_001067	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Silent	SNP	ENST00000423485.1	hg19	CCDS45672.1																																																																																			.	.		0.343	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1			G	38561112	A	G	38561112	2	3	255	1	0	0	0	0	0	0	0	1	16380	214	8	2		2	TOP2A	17	38561112	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	1625441	38561112	42634098	631	35976										
KRTAP4-12	83755	hgsc.bcm.edu	37	chr17	39279994	39279994	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	acagactggcagcactggggTctgcagcagctggacacaca	13	12	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:39279994T>C	ENST00000394014.1	-	1	425	c.381A>G	c.(379-381)agA>agG	p.R127R		NM_031854.2	NP_114060.1	Q9BQ66	KR412_HUMAN	keratin associated protein 4-12	127	31 X 5 AA repeats of C-C-[GRQVIL]-[SPTR]- [VSTQPC].		Missing (in allele KAP4.12-v1). {ECO:0000269|PubMed:15955084}.			keratin filament (GO:0045095)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	13		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			agcactggggtctgcagcagc	0.667																																					p.R127R		Atlas-SNP	.											KRTAP4-12,NS,carcinoma,0,1	KRTAP4-12	32	.	0			c.A381G						.						19	26	23					17																	39279994		2126	4172	6298	SO:0001819	synonymous_variant	83755	exon1			CTGGGGTCTGCAG	AJ406943	CCDS32649.1	17q21.2	2013-06-25			ENSG00000213416	ENSG00000213416		"Keratin associated proteins"	16776	protein-coding gene	gene with protein product						11279113	Standard	NM_031854		Approved	KAP4.12	uc002hwa.3	Q9BQ66	OTTHUMG00000133632	ENST00000394014.1:c.381A>G	chr17.hg19:g.39279994T>C		84.0	2.0		121.0	5.0	NM_031854	A3KMC5|Q495I0	Silent	SNP	ENST00000394014.1	hg19	CCDS32649.1																																																																																			.	.		0.667	KRTAP4-12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257777.1			C	39279994	T	C	39279994	2	2	255	1	0	0	0	0	0	0	0	1	8559	1664	58	2		2	KRTAP4-12	17	39279994	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	718882	39279994	41915216	632	35977										
DHX58	79132	hgsc.bcm.edu	37	chr17	40255722	40255722	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgcagttgatgcagagtagcTgcacgtgctccactgggaac	13	10	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:40255722T>C	ENST00000251642.3	-	12	1880	c.1658A>G	c.(1657-1659)cAg>cGg	p.Q553R		NM_024119.2	NP_077024.2	Q96C10	DHX58_HUMAN	DEXH (Asp-Glu-X-His) box polypeptide 58	553	Repressor domain.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of innate immune response (GO:0045824)|negative regulation of MDA-5 signaling pathway (GO:0039534)|negative regulation of RIG-I signaling pathway (GO:0039536)|negative regulation of type I interferon production (GO:0032480)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of RIG-I signaling pathway (GO:1900246)|positive regulation of type I interferon production (GO:0032481)|regulation of innate immune response (GO:0045088)|response to virus (GO:0009615)|viral process (GO:0016032)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		all_cancers(22;9.73e-07)|all_epithelial(22;3.58e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.126)		GCAGAGTAGCTGCACGTGCTC	0.642																																					p.Q553R		Atlas-SNP	.											.	DHX58	39	.	0			c.A1658G						.						72	59	64					17																	40255722		2203	4300	6503	SO:0001583	missense	79132	exon12			AGTAGCTGCACGT	BC014949	CCDS11416.1	17q21.2	2008-02-05			ENSG00000108771	ENSG00000108771			29517	protein-coding gene	gene with protein product	"RNA helicase LGP2"	608588				11735219	Standard	NM_024119		Approved	LGP2, D11LGP2	uc002hyw.3	Q96C10	OTTHUMG00000133493	ENST00000251642.3:c.1658A>G	chr17.hg19:g.40255722T>C	ENSP00000251642:p.Gln553Arg	54.0	0.0		81.0	4.0	NM_024119	Q9HAM6	Missense_Mutation	SNP	ENST00000251642.3	hg19	CCDS11416.1	.	.	.	.	.	.	.	.	.	.	T	11.39	1.624609	0.28889	.	.	ENSG00000108771	ENST00000251642	T	0.40225	1.04	5.72	-0.744	0.11101	C-terminal domain of RIG-I (1);	0.398185	0.25903	N	0.027544	T	0.27027	0.0662	L	0.36672	1.1	0.09310	N	0.999999	B;B	0.11235	0.004;0.001	B;B	0.09377	0.004;0.004	T	0.25293	-1.0136	10	0.15499	T	0.54	.	10.7752	0.46346	0.0:0.5459:0.0:0.4541	.	546;553	B7Z455;Q96C10	.;DHX58_HUMAN	R	553	ENSP00000251642:Q553R	ENSP00000251642:Q553R	Q	-	2	0	DHX58	37509248	0.215000	0.23574	0.277000	0.24703	0.788000	0.44548	0.035000	0.13797	-0.102000	0.12197	0.454000	0.30748	CAG	.	.		0.642	DHX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257396.1	NM_024119		C	40255722	T	C	40255722	3	2	255	1	0	0	0	0	1	0	0	0	4516	1580	55	2	390	2	DHX58	17	40255722	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	975728	40255722	40939488	633	35978										
STAT5A	6776	hgsc.bcm.edu	37	chr17	40460208	40460208	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tttcacagcggaacgcaaccTgtggaacctgaaaccattca	8	12	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:40460208T>C	ENST00000345506.4	+	17	2561	c.1919T>C	c.(1918-1920)cTg>cCg	p.L640P	STAT5A_ENST00000452307.2_Missense_Mutation_p.L637P|STAT5A_ENST00000588868.1_Missense_Mutation_p.L609P|STAT5A_ENST00000590949.1_Missense_Mutation_p.L640P|STAT5A_ENST00000546010.2_Missense_Mutation_p.L610P|STAT5A_ENST00000587646.1_Missense_Mutation_p.L128P	NM_003152.3	NP_003143.2	P42229	STA5A_HUMAN	signal transducer and activator of transcription 5A	640	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				2-oxoglutarate metabolic process (GO:0006103)|allantoin metabolic process (GO:0000255)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|citrate metabolic process (GO:0006101)|creatine metabolic process (GO:0006600)|creatinine metabolic process (GO:0046449)|development of secondary female sexual characteristics (GO:0046543)|development of secondary male sexual characteristics (GO:0046544)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|fatty acid metabolic process (GO:0006631)|female pregnancy (GO:0007565)|isoleucine metabolic process (GO:0006549)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|lipid storage (GO:0019915)|luteinization (GO:0001553)|mammary gland epithelium development (GO:0061180)|natural killer cell differentiation (GO:0001779)|negative regulation of erythrocyte differentiation (GO:0045647)|negative regulation of mast cell apoptotic process (GO:0033026)|oxaloacetate metabolic process (GO:0006107)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch development (GO:0048541)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of mast cell differentiation (GO:0060376)|positive regulation of mast cell proliferation (GO:0070668)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prolactin signaling pathway (GO:0038161)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of cell adhesion (GO:0030155)|regulation of epithelial cell differentiation (GO:0030856)|regulation of multicellular organism growth (GO:0040014)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|succinate metabolic process (GO:0006105)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|taurine metabolic process (GO:0019530)|transcription, DNA-templated (GO:0006351)|valine metabolic process (GO:0006573)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	calcium ion binding (GO:0005509)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	14		all_cancers(22;1.56e-06)|all_epithelial(22;3.17e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.128)		GAACGCAACCTGTGGAACCTG	0.547																																					p.L640P		Atlas-SNP	.											.	STAT5A	49	.	0			c.T1919C						.						79	71	74					17																	40460208		2203	4300	6503	SO:0001583	missense	6776	exon17			GCAACCTGTGGAA	U43185	CCDS11424.1, CCDS74066.1, CCDS74067.1	17q11.2	2013-02-14			ENSG00000126561	ENSG00000126561		"SH2 domain containing"	11366	protein-coding gene	gene with protein product		601511		STAT5		7719937, 8631883	Standard	NM_003152		Approved	MGF	uc002hzj.2	P42229	OTTHUMG00000150725	ENST00000345506.4:c.1919T>C	chr17.hg19:g.40460208T>C	ENSP00000341208:p.Leu640Pro	144.0	0.0		149.0	6.0	NM_003152	Q1KLZ6	Missense_Mutation	SNP	ENST00000345506.4	hg19	CCDS11424.1	.	.	.	.	.	.	.	.	.	.	T	18.85	3.710982	0.68730	.	.	ENSG00000126561	ENST00000345506;ENST00000546010;ENST00000540577;ENST00000452307	D;D;D	0.88664	-2.41;-2.41;-2.41	5.06	5.06	0.68205	SH2 motif (4);	0.147903	0.46145	D	0.000306	D	0.88108	0.6348	N	0.11064	0.09	0.80722	D	1	D;D;D;P;D	0.69078	0.997;0.997;0.997;0.529;0.997	D;D;D;P;D	0.69142	0.938;0.958;0.938;0.489;0.962	D	0.90804	0.4696	10	0.87932	D	0	-19.3234	14.4833	0.67597	0.0:0.0:0.0:1.0	.	640;637;610;611;640	A8K6I5;Q8WWS9;Q1KLZ6;Q59GY7;P42229	.;.;.;.;STA5A_HUMAN	P	640;610;611;637	ENSP00000341208:L640P;ENSP00000443107:L610P;ENSP00000400320:L637P	ENSP00000341208:L640P	L	+	2	0	STAT5A	37713734	1.000000	0.71417	1.000000	0.80357	0.587000	0.36485	6.927000	0.75840	1.919000	0.55581	0.459000	0.35465	CTG	.	.		0.547	STAT5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319804.1	NM_003152		C	40460208	T	C	40460208	3	2	255	1	0	0	0	0	1	0	0	0	15283	1580	55	2	1977	2	STAT5A	17	40460208	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	204486	40460208	40735002	634	35979										
HSD17B1	3292	hgsc.bcm.edu	37	chr17	40706435	40706435	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gccagcagcttgagcctgatCgagtgcggcccagtgcacac	13	14	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:40706435C>T	ENST00000585807.1	+	5	4272	c.552C>T	c.(550-552)atC>atT	p.I184I	RP11-400F19.8_ENST00000585572.1_RNA|HSD17B1_ENST00000225929.5_Silent_p.I185I|RP11-400F19.6_ENST00000590513.1_RNA	NM_000413.2	NP_000404.2	P14061	DHB1_HUMAN	hydroxysteroid (17-beta) dehydrogenase 1	184					bone development (GO:0060348)|cellular response to metal ion (GO:0071248)|estrogen biosynthetic process (GO:0006703)|estrogen metabolic process (GO:0008210)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|estradiol 17-beta-dehydrogenase activity (GO:0004303)			NS(1)|endometrium(1)|kidney(1)|lung(2)	5		all_cancers(22;5.59e-08)|all_epithelial(22;7e-07)|Ovarian(249;0.0261)		BRCA - Breast invasive adenocarcinoma(366;0.129)	Equilin(DB02187)	TGAGCCTGATCGAGTGCGGCC	0.677																																					p.I184I		Atlas-SNP	.											.	HSD17B1	24	.	0			c.C552T						.						29	26	27					17																	40706435		2203	4299	6502	SO:0001819	synonymous_variant	3292	exon5			CCTGATCGAGTGC		CCDS11428.1	17q11-q21	2011-09-14					1.1.1.62	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	5210	protein-coding gene	gene with protein product	"Estradiol 17-beta-dehydrogenase-1", "short chain dehydrogenase/reductase family 28CE, member 1"	109684		EDHB17, EDH17B2		2330005, 19027726	Standard	NM_000413		Approved	HSD17, MGC138140, SDR28C1	uc002hzw.3	P14061		ENST00000585807.1:c.552C>T	chr17.hg19:g.40706435C>T		39.0	0.0		60.0	4.0	NM_000413	B3KXS1|Q2M2L8	Silent	SNP	ENST00000585807.1	hg19	CCDS11428.1																																																																																			.	.		0.677	HSD17B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450392.1	NM_000413		T	40706435	C	T	40706435	2	4	255	1	0	0	0	0	0	0	0	1	7387	874	31	1		1	HSD17B1	17	40706435	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	246227	40706435	40488775	635	35980										
PLEKHH3	79990	hgsc.bcm.edu	37	chr17	40823547	40823547	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgaagcgcgcatattccgccAgttccgagtccgggagtgcc	13	13	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:40823547A>G	ENST00000591022.1	-	8	1493	c.1106T>C	c.(1105-1107)cTg>cCg	p.L369P	PLEKHH3_ENST00000293349.6_Missense_Mutation_p.L369P|PLEKHH3_ENST00000412503.1_Missense_Mutation_p.L369P|PLEKHH3_ENST00000456950.2_5'UTR	NM_024927.4	NP_079203	Q7Z736	PKHH3_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 3	369	MyTH4. {ECO:0000255|PROSITE- ProRule:PRU00359}.				signal transduction (GO:0007165)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)				endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)|skin(2)	13		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.14)		ATATTCCGCCAGTTCCGAGTC	0.637																																					p.L369P		Atlas-SNP	.											.	PLEKHH3	49	.	0			c.T1106C						.						17	19	18					17																	40823547		2203	4300	6503	SO:0001583	missense	79990	exon8			TCCGCCAGTTCCG	BC052978	CCDS11434.1	17q21.2	2013-01-11				ENSG00000068137		"Pleckstrin homology (PH) domain containing"	26105	protein-coding gene	gene with protein product						12477932	Standard	NM_024927		Approved	FLJ21019	uc002iau.3	Q7Z736		ENST00000591022.1:c.1106T>C	chr17.hg19:g.40823547A>G	ENSP00000468678:p.Leu369Pro	74.0	0.0		77.0	4.0	NM_024927	C9JQ76|Q59H20|Q96B28|Q9H7D6|Q9NT18	Missense_Mutation	SNP	ENST00000591022.1	hg19	CCDS11434.1	.	.	.	.	.	.	.	.	.	.	A	27.3	4.817898	0.90790	.	.	ENSG00000068137	ENST00000456950;ENST00000293349;ENST00000412503	D;D	0.92495	-3.05;-3.05	4.7	4.7	0.59300	MyTH4 domain (2);	0.000000	0.34156	N	0.004212	D	0.88500	0.6453	N	0.02539	-0.55	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.71656	0.974;0.972	D	0.89265	0.3600	10	0.31617	T	0.26	-4.1834	13.8699	0.63612	1.0:0.0:0.0:0.0	.	369;369	Q7Z736-2;Q7Z736	.;PKHH3_HUMAN	P	31;369;369	ENSP00000293349:L369P;ENSP00000411885:L369P	ENSP00000293349:L369P	L	-	2	0	PLEKHH3	38077073	1.000000	0.71417	0.995000	0.50966	0.956000	0.61745	9.287000	0.95975	1.760000	0.52011	0.459000	0.35465	CTG	.	.		0.637	PLEKHH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452332.1	NM_024927		G	40823547	A	G	40823547	3	3	255	1	0	0	0	0	1	0	0	0	12087	188	7	2	1299	2	PLEKHH3	17	40823547	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	117112	40823547	40371663	636	35981										
C17orf104	284071	hgsc.bcm.edu	37	chr17	42744141	42744141	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aagaatcaggagttgatatcTaccattatggaagagacaga	10	5	2	4			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:42744141T>C	ENST00000409122.2	+	5	1004	c.862T>C	c.(862-864)Tac>Cac	p.Y288H	C17orf104_ENST00000359945.3_Missense_Mutation_p.Y288H|C17orf104_ENST00000409464.1_Missense_Mutation_p.Y122H	NM_001145080.2	NP_001138552.2	A2RUB1	CQ104_HUMAN	chromosome 17 open reading frame 104	288										autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|pancreas(1)|skin(1)	24						AGTTGATATCTACCATTATGG	0.353																																					p.Y288H		Atlas-SNP	.											.	C17orf104	75	.	0			c.T862C						.						38	37	37					17																	42744141		2203	4299	6502	SO:0001583	missense	284071	exon5			GATATCTACCATT		CCDS45703.1, CCDS45703.2	17q21.31	2009-09-08			ENSG00000180336	ENSG00000180336			26670	protein-coding gene	gene with protein product							Standard	NM_001145080		Approved	FLJ35848	uc002iha.3	A2RUB1	OTTHUMG00000153039	ENST00000409122.2:c.862T>C	chr17.hg19:g.42744141T>C	ENSP00000386452:p.Tyr288His	74.0	0.0		100.0	4.0	NM_001145080	B4DXJ2|B5MD93|B9EGQ6|C4AM97|Q4G0Y1|Q8IVZ7|Q8NA45	Missense_Mutation	SNP	ENST00000409122.2	hg19	CCDS45703.2	.	.	.	.	.	.	.	.	.	.	T	4.722	0.134328	0.09032	.	.	ENSG00000180336	ENST00000359945;ENST00000409122;ENST00000432494;ENST00000456912;ENST00000409464	T;T;T;T	0.49432	0.8;0.78;0.97;0.79	5.37	4.28	0.50868	.	0.090041	0.48286	D	0.000195	T	0.33527	0.0866	L	0.27053	0.805	0.34532	D	0.709362	B;B;P	0.34639	0.166;0.166;0.461	B;B;B	0.34873	0.191;0.191;0.191	T	0.50915	-0.8771	10	0.49607	T	0.09	-9.9905	9.589	0.39534	0.0:0.0798:0.0:0.9202	.	288;288;122	A2RUB1-5;A2RUB1;A2RUB1-1	.;CQ104_HUMAN;.	H	288;288;122;122;122	ENSP00000353028:Y288H;ENSP00000386452:Y288H;ENSP00000399809:Y122H;ENSP00000386586:Y122H	ENSP00000353028:Y288H	Y	+	1	0	C17orf104	40099667	1.000000	0.71417	0.985000	0.45067	0.503000	0.33858	3.577000	0.53885	2.149000	0.67028	0.377000	0.23210	TAC	.	.		0.353	C17orf104-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329171.2	NM_001145080		C	42744141	T	C	42744141	3	2	255	1	0	0	0	0	1	0	0	0	1853	1522	53	2	880	2	C17orf104	17	42744141	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	1920594	42744141	38451069	637	35982										
ITGB3	3690	hgsc.bcm.edu	37	chr17	45368371	45368371	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gtgacctccctgaagagttgTctctatccttcaatgccacc	7	14	2	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:45368371T>C	ENST00000559488.1	+	9	1193	c.1177T>C	c.(1177-1179)Tct>Cct	p.S393P	ITGB3_ENST00000435993.2_Missense_Mutation_p.S346P|ITGB3_ENST00000571680.1_Missense_Mutation_p.S393P|ITGB3_ENST00000560629.1_Missense_Mutation_p.V381A	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	393					activation of protein kinase activity (GO:0032147)|angiogenesis involved in wound healing (GO:0060055)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|mesodermal cell differentiation (GO:0048333)|negative chemotaxis (GO:0050919)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein folding (GO:0006457)|regulation of bone resorption (GO:0045124)|smooth muscle cell migration (GO:0014909)|substrate adhesion-dependent cell spreading (GO:0034446)|tube development (GO:0035295)|viral entry into host cell (GO:0046718)|wound healing (GO:0042060)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|melanosome (GO:0042470)|microvillus membrane (GO:0031528)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|receptor complex (GO:0043235)|ruffle membrane (GO:0032587)	cell adhesion molecule binding (GO:0050839)|extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|identical protein binding (GO:0042802)|platelet-derived growth factor receptor binding (GO:0005161)|protease binding (GO:0002020)|protein disulfide isomerase activity (GO:0003756)|receptor activity (GO:0004872)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	39					Abciximab(DB00054)|Antithymocyte globulin(DB00098)|Eptifibatide(DB00063)|Tirofiban(DB00775)	TGAAGAGTTGTCTCTATCCTT	0.493																																					p.S393P		Atlas-SNP	.											.	ITGB3	157	.	0			c.T1177C						.						142	121	129					17																	45368371		2203	4300	6503	SO:0001583	missense	3690	exon9			GAGTTGTCTCTAT		CCDS11511.1	17q21.32	2014-09-17			ENSG00000259207	ENSG00000259207		"CD molecules", "Integrins"	6156	protein-coding gene	gene with protein product	"platelet glycoprotein IIIa"	173470		GP3A		2454952	Standard	NM_000212		Approved	CD61, GPIIIa	uc002ilj.3	P05106	OTTHUMG00000171956	ENST00000559488.1:c.1177T>C	chr17.hg19:g.45368371T>C	ENSP00000452786:p.Ser393Pro	92.0	0.0		113.0	5.0	NM_000212	A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Missense_Mutation	SNP	ENST00000559488.1	hg19	CCDS11511.1	.	.	.	.	.	.	.	.	.	.	T	16.31	3.086976	0.55861	.	.	ENSG00000178852	ENST00000262017;ENST00000435993	T	0.67171	-0.25	5.33	5.33	0.75918	Integrin beta subunit, N-terminal (2);von Willebrand factor, type A (1);	0.293457	0.38663	N	0.001615	T	0.79782	0.4505	M	0.73962	2.25	0.53688	D	0.999978	D;D	0.65815	0.995;0.99	D;P	0.64042	0.921;0.82	T	0.82454	-0.0449	10	0.72032	D	0.01	.	14.26	0.66078	0.0:0.0:0.0:1.0	.	393;393	P05106;Q2YFE1	ITB3_HUMAN;.	P	393;346	ENSP00000407801:S346P	ENSP00000262017:S393P	S	+	1	0	C17orf57	42723370	1.000000	0.71417	0.983000	0.44433	0.630000	0.37929	1.750000	0.38329	2.013000	0.59113	0.374000	0.22700	TCT	.	.		0.493	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3	NM_000212		C	45368371	T	C	45368371	3	2	255	1	0	0	0	0	1	0	0	0	7904	1667	58	2	1211	2	ITGB3	17	45368371	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	2624230	45368371	35826839	638	35983										
SP6	80320	hgsc.bcm.edu	37	chr17	45925602	45925602	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cccctggcagctcatagcccTgcgagaagtccacctccggg	11	17	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:45925602T>C	ENST00000536300.1	-	2	525	c.194A>G	c.(193-195)cAg>cGg	p.Q65R	SP6_ENST00000342234.2_Missense_Mutation_p.Q65R	NM_001258248.1	NP_001245177.1	Q3SY56	SP6_HUMAN	Sp6 transcription factor	65					positive regulation of cell proliferation (GO:0008284)|regulation of odontogenesis (GO:0042481)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(1)|lung(5)|prostate(1)|skin(1)	8						CTCATAGCCCTGCGAGAAGTC	0.697																																					p.Q65R		Atlas-SNP	.											SP6,NS,carcinoma,0,1	SP6	26	.	0			c.A194G						.						14	17	16					17																	45925602		2187	4289	6476	SO:0001583	missense	80320	exon2			TAGCCCTGCGAGA		CCDS11520.1	17q21.32	2013-01-08			ENSG00000189120	ENSG00000189120		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	14530	protein-coding gene	gene with protein product	"epiprofin"	608613				11087666, 14551215	Standard	NM_001258248		Approved	KLF14, Epfn	uc002img.2	Q3SY56	OTTHUMG00000132067	ENST00000536300.1:c.194A>G	chr17.hg19:g.45925602T>C	ENSP00000438209:p.Gln65Arg	33.0	0.0		69.0	3.0	NM_001258248	B3KXS4	Missense_Mutation	SNP	ENST00000536300.1	hg19	CCDS11520.1	.	.	.	.	.	.	.	.	.	.	T	15.41	2.825497	0.50739	.	.	ENSG00000189120	ENST00000342234;ENST00000536300	T;T	0.07444	3.19;3.19	4.29	4.29	0.51040	.	0.000000	0.41194	D	0.000924	T	0.04815	0.0130	N	0.08118	0	0.35986	D	0.836369	P	0.41232	0.743	B	0.38056	0.264	T	0.50065	-0.8871	10	0.38643	T	0.18	.	12.5416	0.56174	0.0:0.0:0.0:1.0	.	65	Q3SY56	SP6_HUMAN	R	65	ENSP00000340799:Q65R;ENSP00000438209:Q65R	ENSP00000340799:Q65R	Q	-	2	0	SP6	43280601	1.000000	0.71417	0.956000	0.39512	0.862000	0.49288	3.150000	0.50662	1.799000	0.52666	0.379000	0.24179	CAG	.	.		0.697	SP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441395.1	NM_199262		C	45925602	T	C	45925602	3	2	255	1	0	0	0	0	1	0	0	0	14983	1580	55	2	940	2	SP6	17	45925602	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	557231	45925602	35269608	639	35984										
ITGA3	3675	hgsc.bcm.edu	37	chr17	48166578	48166578	+	3'UTR	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cctccagggagcaccctgccCaccaagaagcactgggtgac	11	16	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:48166578C>A	ENST00000320031.8	+	0	3622				ITGA3_ENST00000007722.7_Silent_p.P1050P	NM_002204.2|NM_005501.2	NP_002195.1|NP_005492.1	P26006	ITA3_HUMAN	integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3 receptor)						blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|lung development (GO:0030324)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|negative regulation of cell projection organization (GO:0031345)|nephron development (GO:0072006)|neuron migration (GO:0001764)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|regulation of BMP signaling pathway (GO:0030510)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of Wnt signaling pathway (GO:0030111)|renal filtration (GO:0097205)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|skin development (GO:0043588)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integrin alpha3-beta1 complex (GO:0034667)|integrin complex (GO:0008305)|invadopodium membrane (GO:0071438)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	glycoprotein binding (GO:0001948)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)			endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)	31						GCACCCTGCCCACCAAGAAGC	0.602																																					p.P1050P		Atlas-SNP	.											.	ITGA3	128	.	0			c.C3150A						.						130	114	119					17																	48166578		2203	4300	6503	SO:0001624	3_prime_UTR_variant	3675	exon25			CCTGCCCACCAAG	M59911	CCDS11557.1, CCDS11558.1	17q21.33	2010-03-23	2003-10-13		ENSG00000005884	ENSG00000005884		"CD molecules", "Integrins"	6139	protein-coding gene	gene with protein product		605025	"antigen identified by monoclonal antibody J143"	MSK18		1655803, 9704023	Standard	NM_005501		Approved	CD49c, VLA3a, VCA-2, GAP-B3	uc010dbm.3	P26006	OTTHUMG00000161890	ENST00000320031.8:c.*136C>A	chr17.hg19:g.48166578C>A		110.0	0.0		87.0	4.0	NM_005501	A7E246|B7ZM80|B9EGQ1|D3DTX4|D3DTX5	Silent	SNP	ENST00000320031.8	hg19	CCDS11558.1																																																																																			.	.		0.602	ITGA3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000366298.1	NM_005501		A	48166578	C	A	48166578	1	1	255	0	1	0	0	0	0	0	0	0	7886	581	21	3		3	ITGA3	17	48166578	3'UTR	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	2240976	48166578	33028632	640	35985										
MPO	4353	hgsc.bcm.edu	37	chr17	56355209	56355209	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgccaggaagcaggggatgcGcgctgagcggttggtgagga	20	7	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:56355209G>A	ENST00000225275.3	-	7	1359	c.1183C>T	c.(1183-1185)Cgc>Tgc	p.R395C	MPO_ENST00000578493.1_5'UTR|MPO_ENST00000340482.3_Missense_Mutation_p.R427C	NM_000250.1	NP_000241.1	P05164	PERM_HUMAN	myeloperoxidase	395					aging (GO:0007568)|defense response (GO:0006952)|defense response to fungus (GO:0050832)|hydrogen peroxide catabolic process (GO:0042744)|hypochlorous acid biosynthetic process (GO:0002149)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of apoptotic process (GO:0043066)|negative regulation of growth of symbiont in host (GO:0044130)|oxidation-reduction process (GO:0055114)|removal of superoxide radicals (GO:0019430)|respiratory burst involved in defense response (GO:0002679)|response to food (GO:0032094)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|response to oxidative stress (GO:0006979)|response to yeast (GO:0001878)	azurophil granule (GO:0042582)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|secretory granule (GO:0030141)	chromatin binding (GO:0003682)|heme binding (GO:0020037)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(13)|ovary(2)|pancreas(1)|skin(4)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	46					Aminosalicylic Acid(DB00233)|Bivalirudin(DB00006)|Calcipotriol(DB02300)|Carboplatin(DB00958)|Cefaclor(DB00833)|Cefdinir(DB00535)|Cisplatin(DB00515)|Cysteamine(DB00847)|Dapsone(DB00250)|Enoxaparin(DB01225)|Human Serum Albumin(DB00062)|L-Carnitine(DB00583)|Melatonin(DB01065)|Mesalazine(DB00244)|Nabumetone(DB00461)|Octreotide(DB00104)|Oxaliplatin(DB00526)|Propylthiouracil(DB00550)|Ticlopidine(DB00208)|Tolmetin(DB00500)	CAGGGGATGCGCGCTGAGCGG	0.622																																					p.R395C		Atlas-SNP	.											.	MPO	114	.	0			c.C1183T						.						58	60	59					17																	56355209		2203	4300	6503	SO:0001583	missense	4353	exon7			GGATGCGCGCTGA		CCDS11604.1	17q21.3-q23	2014-09-17				ENSG00000005381	1.11.1.7		7218	protein-coding gene	gene with protein product		606989					Standard	NM_000250		Approved		uc002ivu.1	P05164		ENST00000225275.3:c.1183C>T	chr17.hg19:g.56355209G>A	ENSP00000225275:p.Arg395Cys	38.0	0.0		37.0	15.0	NM_000250	A1L4B8|Q14862|Q4PJH5|Q9UCL7	Missense_Mutation	SNP	ENST00000225275.3	hg19	CCDS11604.1	.	.	.	.	.	.	.	.	.	.	G	4.434	0.080249	0.08533	.	.	ENSG00000005381	ENST00000340482;ENST00000225275	T;T	0.73363	-0.74;-0.74	4.8	-0.804	0.10882	.	1.422290	0.03913	N	0.282206	T	0.71082	0.3298	L	0.56340	1.77	0.09310	N	1	B	0.16396	0.017	B	0.13407	0.009	T	0.59118	-0.7514	10	0.66056	D	0.02	-2.9074	10.6686	0.45745	0.0:0.3017:0.3917:0.3066	.	395	P05164	PERM_HUMAN	C	427;395	ENSP00000344419:R427C;ENSP00000225275:R395C	ENSP00000225275:R395C	R	-	1	0	MPO	53710208	0.000000	0.05858	0.037000	0.18230	0.157000	0.22087	-0.360000	0.07622	-0.244000	0.09639	-3.360000	0.00041	CGC	.	.		0.622	MPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443971.1			A	56355209	G	A	56355209	3	1	255	1	0	0	0	0	1	0	0	0	9741	1087	38	1	1078	1	MPO	17	56355209	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	8188631	56355209	24840001	641	35986										
PPM1E	4591	hgsc.bcm.edu	37	chr17	57058078	57058078	+	IGR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgtctcctgtctgttcagggTtggaaaatgaacagttcaaa	10	7	4	1	rs267604972		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:57058078T>C	ENST00000393066.3	-	0	3622				PPM1E_ENST00000308249.2_Silent_p.L652L	NM_001005207.2	NP_001005207.1	O94972	TRI37_HUMAN	tripartite motif containing 37						aggresome assembly (GO:0070842)|negative regulation of centriole replication (GO:0046600)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autoubiquitination (GO:0051865)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|peroxisome (GO:0005777)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(13)|ovary(1)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					CTGTTCAGGGTTGGAAAATGA	0.453									Mulibrey Nanism				T|||	1	0.000199681	8e-04	0	5008	,	,		19193	0		0	False		,,,				2504	0				p.L652L		Atlas-SNP	.											.	PPM1E	97	.	0			c.T1954C						.						161	170	167					17																	57058078		2203	4300	6503	SO:0001628	intergenic_variant	22843	exon7	Familial Cancer Database	Perheentupa syndrome	TCAGGGTTGGAAA	AB020705	CCDS32694.1, CCDS45746.1	17q	2014-02-17	2011-01-25	2001-11-30		ENSG00000108395		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	7523	protein-coding gene	gene with protein product	"RING-B-box-coiled-coil protein"	605073	"tripartite motif-containing 37"	MUL		9106536, 10888877	Standard	NM_015294		Approved	KIAA0898, POB1, TEF3	uc002iwy.4	O94972			chr17.hg19:g.57058078T>C		92.0	0.0		100.0	4.0	NM_014906	Q7Z3E6|Q8IYF7|Q8WYF7	Silent	SNP	ENST00000393066.3	hg19	CCDS45746.1																																																																																			.	.		0.453	TRIM37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445928.1	NM_015294		C	57058078	T	C	57058078	1	2	255	0	1	0	0	0	0	0	0	0	12350	1722	60	2		2	PPM1E	17	57058078	IGR	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	702869	57058078	24137132	642	35987										
BCAS3	54828	hgsc.bcm.edu	37	chr17	59024696	59024696	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	atctgtatactcttcacaggGgagaaactgaagccaaagta	9	8	3	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:59024696G>T	ENST00000390652.5	+	14	1235	c.1204G>T	c.(1204-1206)Gga>Tga	p.G402*	BCAS3_ENST00000588462.1_Nonsense_Mutation_p.G402*|BCAS3_ENST00000588874.1_Nonsense_Mutation_p.G173*|BCAS3_ENST00000585744.1_Nonsense_Mutation_p.G173*|BCAS3_ENST00000408905.3_Nonsense_Mutation_p.G402*|BCAS3_ENST00000589222.1_Nonsense_Mutation_p.G402*|BCAS3_ENST00000407086.3_Nonsense_Mutation_p.G402*	NM_001099432.1	NP_001092902.1			breast carcinoma amplified sequence 3									p.G402*(1)		NS(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(24)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)			TCTTCACAGGGGAGAAACTGA	0.413																																					p.G402X		Atlas-SNP	.											BCAS3,NS,carcinoma,0,1	BCAS3	90	.	1	Substitution - Nonsense(1)	lung(1)	c.G1204T						.						176	162	167					17																	59024696		1895	4127	6022	SO:0001587	stop_gained	54828	exon14			CACAGGGGAGAAA	AF361219	CCDS11626.1, CCDS45749.1	17q23.2	2013-06-25			ENSG00000141376	ENSG00000141376		"WD repeat domain containing"	14347	protein-coding gene	gene with protein product		607470				12378525	Standard	NM_017679		Approved	FLJ20128	uc002iyv.4	Q9H6U6	OTTHUMG00000180064	ENST00000390652.5:c.1204G>T	chr17.hg19:g.59024696G>T	ENSP00000375067:p.Gly402*	78.0	0.0		65.0	4.0	NM_001099432		Nonsense_Mutation	SNP	ENST00000390652.5	hg19	CCDS45749.1	.	.	.	.	.	.	.	.	.	.	G	40	7.913706	0.98557	.	.	ENSG00000141376	ENST00000390652;ENST00000407086;ENST00000405070;ENST00000408905;ENST00000360207;ENST00000405217	.	.	.	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	20.0192	0.97489	0.0:0.0:1.0:0.0	.	.	.	.	X	402;402;402;402;194;207	.	ENSP00000353336:G194X	G	+	1	0	BCAS3	56379478	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.463000	0.97652	2.722000	0.93159	0.591000	0.81541	GGA	.	.		0.413	BCAS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449578.1	NM_017679		T	59024696	G	T	59024696	4	4	255	1	0	0	0	0	0	1	0	0	1352	1233	43	3	1254	3	BCAS3	17	59024696	Nonsense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	1966618	59024696	22170514	643	35988										
ACE	1636	hgsc.bcm.edu	37	chr17	61561702	61561702	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gcccaccaggaaggtgctgcAggctggctcctccaggccct	13	16	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:61561702A>G	ENST00000290866.4	+	12	1745	c.1721A>G	c.(1720-1722)cAg>cGg	p.Q574R	ACE_ENST00000490216.2_5'Flank|ACE_ENST00000428043.1_Missense_Mutation_p.Q574R|ACE_ENST00000577647.1_5'Flank|ACE_ENST00000413513.3_5'Flank|ACE_ENST00000290863.6_5'Flank|ACE_ENST00000421982.2_5'Flank	NM_000789.3	NP_000780.1	P12821	ACE_HUMAN	angiotensin I converting enzyme	574	Peptidase M2 1.				angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|arachidonic acid secretion (GO:0050482)|blood vessel remodeling (GO:0001974)|cellular protein metabolic process (GO:0044267)|hematopoietic stem cell differentiation (GO:0060218)|hormone catabolic process (GO:0042447)|kidney development (GO:0001822)|mononuclear cell proliferation (GO:0032943)|peptide catabolic process (GO:0043171)|regulation of blood pressure (GO:0008217)|regulation of renal output by angiotensin (GO:0002019)|regulation of smooth muscle cell migration (GO:0014910)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|bradykinin receptor binding (GO:0031711)|carboxypeptidase activity (GO:0004180)|chloride ion binding (GO:0031404)|drug binding (GO:0008144)|endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|peptidyl-dipeptidase activity (GO:0008241)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(3)|lung(22)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	51					Benazepril(DB00542)|Candoxatril(DB00616)|Captopril(DB01197)|Cilazapril(DB01340)|Enalapril(DB00584)|Fosinopril(DB00492)|Lisinopril(DB00722)|Moexipril(DB00691)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Rescinnamine(DB01180)|Spirapril(DB01348)|Trandolapril(DB00519)	AAGGTGCTGCAGGCTGGCTCC	0.657																																					p.Q574R		Atlas-SNP	.											.	ACE	187	.	0			c.A1721G						.						28	22	24					17																	61561702		2200	4292	6492	SO:0001583	missense	1636	exon12			TGCTGCAGGCTGG	J04144	CCDS11637.1, CCDS45755.1, CCDS54155.1	17q23.3	2013-06-12	2013-06-12		ENSG00000159640	ENSG00000159640	3.4.15.1	"CD molecules"	2707	protein-coding gene	gene with protein product	"peptidyl-dipeptidase A"	106180	"angiotensin I converting enzyme (peptidyl-dipeptidase A) 1"	DCP1		2554286, 10319862	Standard	NM_001178057		Approved	ACE1, CD143	uc002jau.2	P12821	OTTHUMG00000154927	ENST00000290866.4:c.1721A>G	chr17.hg19:g.61561702A>G	ENSP00000290866:p.Gln574Arg	97.0	0.0		78.0	4.0	NM_000789	B0LPF0|B4DXI3|E7EU16|P22966|Q53YX9|Q59GY8|Q7M4L4	Missense_Mutation	SNP	ENST00000290866.4	hg19	CCDS11637.1	.	.	.	.	.	.	.	.	.	.	A	2.670	-0.277821	0.05679	.	.	ENSG00000159640	ENST00000290866;ENST00000428043	T;T	0.34072	1.38;1.38	4.97	1.49	0.22878	.	0.625902	0.18067	N	0.152745	T	0.23014	0.0556	L	0.28694	0.88	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.003	T	0.06058	-1.0848	10	0.23302	T	0.38	-10.2723	8.8603	0.35253	0.5885:0.0:0.4115:0.0	.	574;574	P12821-2;P12821	.;ACE_HUMAN	R	574	ENSP00000290866:Q574R;ENSP00000397593:Q574R	ENSP00000290866:Q574R	Q	+	2	0	ACE	58915434	0.830000	0.29337	0.307000	0.25127	0.023000	0.10783	1.317000	0.33631	0.064000	0.16427	0.379000	0.24179	CAG	.	.		0.657	ACE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337675.2			G	61561702	A	G	61561702	3	3	255	1	0	0	0	0	1	0	0	0	136	188	7	2	1767	2	ACE	17	61561702	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	2537006	61561702	19633508	644	35989										
DCAF7	10238	hgsc.bcm.edu	37	chr17	61666468	61666468	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gagatcaacaatgtgcagtgGgcatcaactcagcccgactg	11	11	3	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:61666468G>T	ENST00000310827.4	+	8	1180	c.963G>T	c.(961-963)tgG>tgT	p.W321C	DCAF7_ENST00000415273.2_Missense_Mutation_p.W121C|DCAF7_ENST00000431926.1_Intron|DCAF7_ENST00000577702.1_3'UTR	NM_005828.3	NP_005819.3	P61962	DCAF7_HUMAN	DDB1 and CUL4 associated factor 7	321					multicellular organismal development (GO:0007275)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|protein complex (GO:0043234)				endometrium(6)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)	18						ATGTGCAGTGGGCATCAACTC	0.567																																					p.W321C		Atlas-SNP	.											.	DCAF7	36	.	0			c.G963T						.						107	104	105					17																	61666468		2063	4198	6261	SO:0001583	missense	10238	exon8			GCAGTGGGCATCA	U94747	CCDS74127.1	17q23.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000136485		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	30915	protein-coding gene	gene with protein product	"seven-WD-repeat protein of the AN11 family-1", "human anthocyanin"	605973	"WD repeat domain 68"	WDR68		9192870, 20940704	Standard	NM_005828		Approved	HAN11, SWAN-1	uc002jbc.4	P61962		ENST00000310827.4:c.963G>T	chr17.hg19:g.61666468G>T	ENSP00000308344:p.Trp321Cys	107.0	0.0		124.0	5.0	NM_005828	B4E039|D3DU14|O15491|Q9DAE4	Missense_Mutation	SNP	ENST00000310827.4	hg19		.	.	.	.	.	.	.	.	.	.	G	21.7	4.182068	0.78677	.	.	ENSG00000136485	ENST00000310827;ENST00000415273	T;T	0.61510	0.1;1.4	5.31	5.31	0.75309	WD40/YVTN repeat-like-containing domain (1);	0.113458	0.64402	D	0.000004	T	0.78610	0.4310	.	.	.	0.80722	D	1	D;D	0.89917	1.0;0.984	D;D	0.91635	0.999;0.929	T	0.80670	-0.1279	9	0.72032	D	0.01	-17.8074	19.1619	0.93537	0.0:0.0:1.0:0.0	.	121;321	B4E039;P61962	.;DCAF7_HUMAN	C	321;121	ENSP00000308344:W321C;ENSP00000403920:W121C	ENSP00000308344:W321C	W	+	3	0	DCAF7	59020200	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.657000	0.98554	2.758000	0.94735	0.563000	0.77884	TGG	.	.		0.567	DCAF7-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_005828		T	61666468	G	T	61666468	3	4	255	1	0	0	0	0	1	0	0	0	4277	1241	43	3	990	3	DCAF7	17	61666468	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	104766	61666468	19528742	645	35990										
SSTR2	6752	hgsc.bcm.edu	37	chr17	71166524	71166524	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggctgaatgagaccacggagAcccagaggaccctcctcaat	11	13	1	4			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:71166524A>G	ENST00000357585.2	+	2	1435	c.1066A>G	c.(1066-1068)Acc>Gcc	p.T356A	RP11-143K11.5_ENST00000580671.1_RNA|SSTR2_ENST00000315332.2_Intron	NM_001050.2	NP_001041.1	P30874	SSR2_HUMAN	somatostatin receptor 2	356				T -> A (in Ref. 5; BAG36594). {ECO:0000305}.	adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cell-cell signaling (GO:0007267)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucocorticoid stimulus (GO:0071385)|cerebellum development (GO:0021549)|digestion (GO:0007586)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cell proliferation (GO:0008285)|peristalsis (GO:0030432)|regulation of muscle contraction (GO:0006937)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|somatostatin receptor activity (GO:0004994)			endometrium(2)|large_intestine(5)|lung(2)|prostate(2)	11			LUSC - Lung squamous cell carcinoma(166;0.197)		Octreotide(DB00104)|Pasireotide(DB06663)|Vapreotide(DB04894)	GACCACGGAGACCCAGAGGAC	0.557																																					p.T356A		Atlas-SNP	.											.	SSTR2	27	.	0			c.A1066G						.						55	51	52					17																	71166524		2203	4300	6503	SO:0001583	missense	6752	exon2			ACGGAGACCCAGA		CCDS11691.1	17q24	2012-08-08				ENSG00000180616		"GPCR / Class A : Somatostatin receptors"	11331	protein-coding gene	gene with protein product		182452				8449518	Standard	NM_001050		Approved		uc002jje.3	P30874		ENST00000357585.2:c.1066A>G	chr17.hg19:g.71166524A>G	ENSP00000350198:p.Thr356Ala	73.0	0.0		86.0	5.0	NM_001050	A8K3Y0|B2R9P7|Q4VBP0|Q96GE0|Q96TF2|Q9BWH1	Missense_Mutation	SNP	ENST00000357585.2	hg19	CCDS11691.1	.	.	.	.	.	.	.	.	.	.	A	11.41	1.630056	0.28978	.	.	ENSG00000180616	ENST00000357585	T	0.72394	-0.65	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	T	0.62429	0.2427	L	0.43152	1.355	0.80722	D	1	B	0.14805	0.011	B	0.16289	0.015	T	0.57705	-0.7765	10	0.18710	T	0.47	.	15.0092	0.71536	1.0:0.0:0.0:0.0	.	356	P30874	SSR2_HUMAN	A	356	ENSP00000350198:T356A	ENSP00000350198:T356A	T	+	1	0	SSTR2	68678119	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.905000	0.92613	2.084000	0.62774	0.533000	0.62120	ACC	.	.		0.557	SSTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441633.1			G	71166524	A	G	71166524	3	3	255	1	0	0	0	0	1	0	0	0	15213	275	10	2	1068	2	SSTR2	17	71166524	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	9500056	71166524	10028686	646	35991										
TMEM104	54868	hgsc.bcm.edu	37	chr17	72815910	72815910	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cgatcttcactctcctcctcGgaccgttcaccttctttgac	5	17	5	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:72815910G>T	ENST00000335464.5	+	9	820	c.658G>T	c.(658-660)Gga>Tga	p.G220*	TMEM104_ENST00000417024.2_Nonsense_Mutation_p.G233*|TMEM104_ENST00000582330.1_Nonsense_Mutation_p.G220*|TMEM104_ENST00000582773.1_Nonsense_Mutation_p.G220*	NM_017728.3	NP_060198.3	Q8NE00	TM104_HUMAN	transmembrane protein 104	220						integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(5)|ovary(1)	19	all_lung(278;0.23)					TCTCCTCCTCGGACCGTTCAC	0.562																																					p.G220X		Atlas-SNP	.											.	TMEM104	49	.	0			c.G658T						.						203	163	177					17																	72815910		2203	4300	6503	SO:0001587	stop_gained	54868	exon9			CTCCTCGGACCGT	AK074029	CCDS32723.1	17q25.1	2005-12-19				ENSG00000109066			25984	protein-coding gene	gene with protein product							Standard	NM_017728		Approved	FLJ20255, FLJ00021	uc002jls.4	Q8NE00		ENST00000335464.5:c.658G>T	chr17.hg19:g.72815910G>T	ENSP00000334849:p.Gly220*	163.0	0.0		148.0	6.0	NM_017728	Q8TEU1|Q9NT56|Q9NXH1	Nonsense_Mutation	SNP	ENST00000335464.5	hg19	CCDS32723.1	.	.	.	.	.	.	.	.	.	.	G	38	6.859352	0.97893	.	.	ENSG00000109066	ENST00000335464;ENST00000417024	.	.	.	5.06	5.06	0.68205	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	-5.8226	17.5725	0.87939	0.0:0.0:1.0:0.0	.	.	.	.	X	220;233	.	ENSP00000334849:G220X	G	+	1	0	TMEM104	70327505	1.000000	0.71417	0.829000	0.32907	0.946000	0.59487	8.796000	0.91877	2.506000	0.84524	0.561000	0.74099	GGA	.	.		0.562	TMEM104-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444442.1	NM_017728		T	72815910	G	T	72815910	4	4	255	1	0	0	0	0	0	1	0	0	16033	1117	39	1	688	1	TMEM104	17	72815910	Nonsense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	1649386	72815910	8379300	647	35992										
C17orf28	283987	hgsc.bcm.edu	37	chr17	72955014	72955014	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aggctggcccaccttgttgaAgtcgcagagcttccagaaga	12	11	0	4			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:72955014A>G	ENST00000425042.2	-	9	1218	c.1141T>C	c.(1141-1143)Ttc>Ctc	p.F381L		NM_030630.2	NP_085133.1	Q8IV36	HID1_HUMAN	HID1 domain containing	381					intracellular protein transport (GO:0006886)|response to brefeldin A (GO:0031001)	cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi medial cisterna (GO:0005797)|Golgi trans cisterna (GO:0000138)											ACCTTGTTGAAGTCGCAGAGC	0.617											OREG0024721	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F381L		Atlas-SNP	.											.	.	.	.	0			c.T1141C						.						56	44	48					17																	72955014		2203	4300	6503	SO:0001583	missense	283987	exon9			TGTTGAAGTCGCA		CCDS32726.1	17q25.1	2012-10-10	2012-10-10	2012-10-10	ENSG00000167861	ENSG00000167861			15736	protein-coding gene	gene with protein product	"downregulated in multiple cancer 1"	605752	"chromosome 17 open reading frame 28"	C17orf28		11281419, 21337012	Standard	NM_030630		Approved	DMC1, HID-1	uc002jmj.4	Q8IV36	OTTHUMG00000166490	ENST00000425042.2:c.1141T>C	chr17.hg19:g.72955014A>G	ENSP00000413520:p.Phe381Leu	103.0	0.0	1141	120.0	5.0	NM_030630	Q8N5L6|Q8TE83|Q9NT34	Missense_Mutation	SNP	ENST00000425042.2	hg19	CCDS32726.1	.	.	.	.	.	.	.	.	.	.	A	11.26	1.585401	0.28268	.	.	ENSG00000167861	ENST00000525426;ENST00000425042;ENST00000318565	.	.	.	4.97	3.87	0.44632	.	0.112112	0.64402	D	0.000009	T	0.29158	0.0725	N	0.05441	-0.05	0.37945	D	0.932478	B;B	0.09022	0.002;0.0	B;B	0.10450	0.005;0.004	T	0.10109	-1.0644	9	0.13108	T	0.6	-18.5177	11.0934	0.48130	0.8611:0.0:0.0:0.1389	.	380;381	Q8IV36-2;Q8IV36	.;CQ028_HUMAN	L	153;381;153	.	ENSP00000317795:F153L	F	-	1	0	C17orf28	70466609	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.643000	0.67895	0.725000	0.32318	0.369000	0.22263	TTC	.	.		0.617	HID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390011.2	NM_030630		G	72955014	A	G	72955014	3	3	255	1	0	0	0	0	1	0	0	0	1855	72	3	2	1269	2	C17orf28	17	72955014	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	139104	72955014	8240196	648	35993										
KCTD2	23510	hgsc.bcm.edu	37	chr17	73059137	73059137	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttcaggagagaggatcgcggAtgtaaactaagaccccgaaa	12	8	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:73059137A>G	ENST00000322444.6	+	6	793	c.787A>G	c.(787-789)Atg>Gtg	p.M263V	KCTD2_ENST00000581589.1_Missense_Mutation_p.M64V	NM_015353.1	NP_056168.1	Q14681	KCTD2_HUMAN	potassium channel tetramerization domain containing 2	263					protein homooligomerization (GO:0051260)		protein complex binding (GO:0032403)			kidney(1)|lung(2)	3	all_lung(278;0.226)					AGGATCGCGGATGTAAACTAA	0.547																																					p.M263V		Atlas-SNP	.											.	KCTD2	15	.	0			c.A787G						.						74	63	67					17																	73059137		2203	4300	6503	SO:0001583	missense	23510	exon6			TCGCGGATGTAAA	BC033329	CCDS32728.1	17q25.2	2013-06-20	2013-06-20			ENSG00000180901			21294	protein-coding gene	gene with protein product		613422	"potassium channel tetramerisation domain containing 2"			12620391	Standard	XR_248405		Approved	KIAA0176	uc002jmp.3	Q14681		ENST00000322444.6:c.787A>G	chr17.hg19:g.73059137A>G	ENSP00000312814:p.Met263Val	64.0	0.0		125.0	5.0	NM_015353		Missense_Mutation	SNP	ENST00000322444.6	hg19	CCDS32728.1	.	.	.	.	.	.	.	.	.	.	A	15.68	2.903938	0.52333	.	.	ENSG00000180901	ENST00000322444;ENST00000375286	T	0.55234	0.53	4.73	4.73	0.59995	.	0.224065	0.52532	D	0.000076	T	0.42449	0.1203	L	0.31294	0.92	0.50039	D	0.999845	B	0.24721	0.11	B	0.24974	0.057	T	0.43376	-0.9395	10	0.72032	D	0.01	.	13.2495	0.60043	1.0:0.0:0.0:0.0	.	263	Q14681	KCTD2_HUMAN	V	263;245	ENSP00000312814:M263V	ENSP00000312814:M263V	M	+	1	0	KCTD2	70570732	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	8.458000	0.90364	2.108000	0.64289	0.533000	0.62120	ATG	.	.		0.547	KCTD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445538.1			G	73059137	A	G	73059137	3	3	255	1	0	0	0	0	1	0	0	0	8116	333	12	2	809	2	KCTD2	17	73059137	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	104123	73059137	8136073	649	35994										
TSEN54	283989	hgsc.bcm.edu	37	chr17	73518036	73518036	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agaacggagtcacgggagccGgtaagcggcgctggaacttc	16	10	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:73518036G>T	ENST00000333213.6	+	8	910	c.874G>T	c.(874-876)Ggt>Tgt	p.G292C		NM_207346.2	NP_997229.2	Q7Z6J9	SEN54_HUMAN	TSEN54 tRNA splicing endonuclease subunit	292					mRNA processing (GO:0006397)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(5)|ovary(2)	13	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;4.57e-07)|Epithelial(20;2.92e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			CACGGGAGCCGGTAAGCGGCG	0.697																																					p.G292C		Atlas-SNP	.											.	TSEN54	27	.	0			c.G874T						.						16	19	18					17																	73518036		2195	4295	6490	SO:0001583	missense	283989	exon8			GGAGCCGGTAAGC	AK097583	CCDS11724.1	17q25.1	2013-08-06	2013-08-06		ENSG00000182173	ENSG00000182173		"tRNA splicing endonuclease subunits"	27561	protein-coding gene	gene with protein product		608755	"tRNA splicing endonuclease 54 homolog (SEN54, S. cerevisiae)", "tRNA splicing endonuclease 54 homolog (S. cerevisiae)"			15109492	Standard	NM_207346		Approved	SEN54, SEN54L	uc002jof.1	Q7Z6J9		ENST00000333213.6:c.874G>T	chr17.hg19:g.73518036G>T	ENSP00000327487:p.Gly292Cys	82.0	0.0		72.0	4.0	NM_207346	Q86WV3|Q86XE4|Q8N9H2	Missense_Mutation	SNP	ENST00000333213.6	hg19	CCDS11724.1	.	.	.	.	.	.	.	.	.	.	G	1.918	-0.449054	0.04572	.	.	ENSG00000182173	ENST00000333213	T	0.56776	0.44	4.96	-9.92	0.00455	.	1.215030	0.05564	N	0.569760	T	0.23133	0.0559	N	0.03115	-0.41	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.43426	-0.9392	10	0.52906	T	0.07	16.6892	6.2324	0.20742	0.073:0.3457:0.3986:0.1826	.	292	Q7Z6J9	SEN54_HUMAN	C	292	ENSP00000327487:G292C	ENSP00000327487:G292C	G	+	1	0	TSEN54	71029631	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.717000	0.01876	-3.844000	0.00100	-0.333000	0.08304	GGT	.	.		0.697	TSEN54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447618.1	NM_207346		T	73518036	G	T	73518036	3	4	255	1	0	0	0	0	1	0	0	0	16629	1116	39	1	904	1	TSEN54	17	73518036	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	458899	73518036	7677174	650	35995										
LLGL2	3993	hgsc.bcm.edu	37	chr17	73566143	73566143	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agggctaccgctggaaggggCacgagcgcctggcagcccgc	17	14	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:73566143C>A	ENST00000392550.3	+	15	1798	c.1681C>A	c.(1681-1683)Cac>Aac	p.H561N	LLGL2_ENST00000167462.5_Missense_Mutation_p.H561N|LLGL2_ENST00000577200.1_Missense_Mutation_p.H561N	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	561					cell cycle (GO:0007049)|cell division (GO:0051301)|exocytosis (GO:0006887)|regulation of establishment or maintenance of cell polarity (GO:0032878)	cytoplasm (GO:0005737)	PDZ domain binding (GO:0030165)			NS(1)|breast(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)			CTGGAAGGGGCACGAGCGCCT	0.662																																					p.H561N		Atlas-SNP	.											.	LLGL2	155	.	0			c.C1681A						.						30	29	29					17																	73566143		2202	4298	6500	SO:0001583	missense	3993	exon15			AAGGGGCACGAGC	X87342	CCDS11725.1, CCDS32733.1, CCDS45776.1	17q25.1	2013-01-10	2001-11-28			ENSG00000073350		"WD repeat domain containing"	6629	protein-coding gene	gene with protein product			"lethal giant larvae (Drosophila) homolog 2"				Standard	XR_243659		Approved	HGL	uc002joh.3	Q6P1M3		ENST00000392550.3:c.1681C>A	chr17.hg19:g.73566143C>A	ENSP00000376333:p.His561Asn	83.0	0.0		88.0	4.0	NM_004524	Q14521|Q9BR62	Missense_Mutation	SNP	ENST00000392550.3	hg19	CCDS32733.1	.	.	.	.	.	.	.	.	.	.	C	16.33	3.091673	0.55968	.	.	ENSG00000073350	ENST00000167462;ENST00000392550;ENST00000545227	T;T	0.50813	0.73;0.73	5.19	5.19	0.71726	.	0.049489	0.85682	D	0.000000	T	0.69788	0.3150	M	0.83312	2.635	0.58432	D	0.999997	P;P;P;P;D	0.69078	0.859;0.872;0.921;0.92;0.997	B;B;P;P;P	0.60949	0.406;0.396;0.601;0.73;0.881	T	0.75190	-0.3405	10	0.66056	D	0.02	0.2915	18.7672	0.91878	0.0:1.0:0.0:0.0	.	188;550;550;561;561	B4DVR9;B3KX47;G3V1I9;Q6P1M3-2;Q6P1M3	.;.;.;.;L2GL2_HUMAN	N	561;561;550	ENSP00000167462:H561N;ENSP00000376333:H561N	ENSP00000167462:H561N	H	+	1	0	LLGL2	71077738	1.000000	0.71417	0.936000	0.37596	0.899000	0.52679	7.620000	0.83070	2.431000	0.82371	0.549000	0.68633	CAC	.	.		0.662	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524		A	73566143	C	A	73566143	3	1	255	1	0	0	0	0	1	0	0	0	8843	710	25	3	1770	3	LLGL2	17	73566143	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	48107	73566143	7629067	651	35996										
UNK	85451	hgsc.bcm.edu	37	chr17	73811297	73811297	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	atgcagcagtcgggcagctgTccccgaggacccttctgcgc	13	15	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:73811297T>C	ENST00000589666.1	+	7	1034	c.924T>C	c.(922-924)tgT>tgC	p.C308C	UNK_ENST00000293218.3_Silent_p.C384C	NM_001080419.2	NP_001073888.2	Q9C0B0	UNK_HUMAN	unkempt family zinc finger	308							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			cervix(3)|endometrium(8)|kidney(2)|large_intestine(5)|lung(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	25			all cancers(21;2.61e-06)|Epithelial(20;7.39e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|LUSC - Lung squamous cell carcinoma(166;0.154)			CGGGCAGCTGTCCCCGAGGAC	0.647																																					p.C308C		Atlas-SNP	.											.	UNK	87	.	0			c.T924C						.						147	158	154					17																	73811297		2095	4206	6301	SO:0001819	synonymous_variant	85451	exon7			CAGCTGTCCCCGA	AB051540	CCDS45778.1, CCDS45778.2	17q25.3	2013-10-17	2013-10-17	2007-02-06		ENSG00000132478		"Zinc fingers, CCCH-type domain containing"	29369	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 5", "zinc finger CCCH-type containing 5", "unkempt homolog (Drosophila)"	ZC3HDC5, ZC3H5		11214970	Standard	NM_001080419		Approved	KIAA1753	uc021udd.2	Q9C0B0		ENST00000589666.1:c.924T>C	chr17.hg19:g.73811297T>C		116.0	0.0		97.0	4.0	NM_001080419		Silent	SNP	ENST00000589666.1	hg19	CCDS45778.2																																																																																			.	.		0.647	UNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448835.1	NM_001080419		C	73811297	T	C	73811297	2	2	255	1	0	0	0	0	0	0	0	1	17015	1673	58	2		2	UNK	17	73811297	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	245154	73811297	7383913	652	35997										
FBF1	85302	hgsc.bcm.edu	37	chr17	73916127	73916127	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gctccaggtctgcctggtgcTgctgctgcagactccccagc	12	16	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:73916127T>C	ENST00000586717.1	-	18	2123	c.1850A>G	c.(1849-1851)cAg>cGg	p.Q617R	FBF1_ENST00000389570.4_Missense_Mutation_p.Q617R|FBF1_ENST00000319129.5_Missense_Mutation_p.Q616R			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	617					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	4						TGCCTGGTGCTGCTGCTGCAG	0.652																																					p.Q616R		Atlas-SNP	.											.	FBF1	48	.	0			c.A1847G						.						23	27	25					17																	73916127		1982	4165	6147	SO:0001583	missense	85302	exon18			TGGTGCTGCTGCT	AK074045	CCDS45779.1	17q25.3	2011-04-21			ENSG00000188878	ENSG00000188878			24674	protein-coding gene	gene with protein product	"albatross"					11347906	Standard	NM_001080542		Approved	FLJ00103, FBF-1, KIAA1863, ALB	uc002jqc.3	Q8TES7		ENST00000586717.1:c.1850A>G	chr17.hg19:g.73916127T>C	ENSP00000465132:p.Gln617Arg	96.0	0.0		115.0	5.0	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000586717.1	hg19		.	.	.	.	.	.	.	.	.	.	T	0.008	-1.929620	0.00488	.	.	ENSG00000188878	ENST00000337792;ENST00000389570;ENST00000319129;ENST00000427433	T;T	0.15487	2.42;2.43	5.15	0.435	0.16544	.	.	.	.	.	T	0.04770	0.0129	N	0.01454	-0.855	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.0;0.001;0.002	T	0.41251	-0.9519	9	0.02654	T	1	-5.5969	9.2857	0.37755	0.0:0.6645:0.0:0.3355	.	631;617;616	Q8TES7-6;Q8TES7;A6NLR5	.;FBF1_HUMAN;.	R	617;617;616;630	ENSP00000374221:Q617R;ENSP00000324292:Q616R	ENSP00000324292:Q616R	Q	-	2	0	FBF1	71427722	0.033000	0.19621	0.393000	0.26258	0.099000	0.18886	0.456000	0.21859	0.104000	0.17725	-0.408000	0.06270	CAG	.	.		0.652	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542		C	73916127	T	C	73916127	3	2	255	1	0	0	0	0	1	0	0	0	5703	1580	55	2	1602	2	FBF1	17	73916127	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	104830	73916127	7279083	653	35998										
SFRS2	6427	hgsc.bcm.edu	37	chr17	74732955	74732955	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cggcggctgtggtgtgagtcCggggggcggccgtagcgcgc	22	11	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:74732955C>T	ENST00000392485.2	-	1	460	c.288G>A	c.(286-288)ccG>ccA	p.P96P	MFSD11_ENST00000586622.1_5'UTR|MFSD11_ENST00000590514.1_5'Flank|MIR636_ENST00000384825.1_RNA|MFSD11_ENST00000336509.4_5'Flank|MFSD11_ENST00000591864.1_5'UTR|MFSD11_ENST00000355954.3_5'Flank|SRSF2_ENST00000508921.3_Silent_p.P96P|SRSF2_ENST00000359995.5_Silent_p.P96P|MFSD11_ENST00000590393.1_5'Flank|MFSD11_ENST00000593181.1_5'Flank|RP11-318A15.7_ENST00000587459.1_Intron|MFSD11_ENST00000588460.1_5'UTR	NM_003016.4	NP_003007.2	Q01130	SRSF2_HUMAN	serine/arginine-rich splicing factor 2	96					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA biosynthetic process (GO:2001141)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	extracellular vesicular exosome (GO:0070062)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|transcription corepressor activity (GO:0003714)	p.P95_R102del(21)|p.P95_D97del(2)		haematopoietic_and_lymphoid_tissue(320)|kidney(2)|large_intestine(1)|lung(4)|prostate(2)	329						GGTGTGAGTCCGGGGGGCGGC	0.741			Mis		"MDS, CLL"																																p.P96P		Atlas-SNP	.		Dom	yes		17	17q25	6427	serine/arginine-rich splicing factor 2		L	.	SRSF2	544	.	23	Deletion - In frame(23)	haematopoietic_and_lymphoid_tissue(23)	c.G288A						.						14	17	16					17																	74732955		2126	4192	6318	SO:0001819	synonymous_variant	6427	exon1			TGAGTCCGGGGGG	M90104	CCDS11749.1	17q25.2	2014-09-17	2010-06-22	2010-06-22	ENSG00000161547	ENSG00000161547		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10783	protein-coding gene	gene with protein product	"SR splicing factor 2"	600813	"splicing factor, arginine/serine-rich 2"	SFRS2		8530103, 20516191	Standard	NM_003016		Approved	SC-35, SC35, PR264, SFRS2A	uc002jsv.3	Q01130		ENST00000392485.2:c.288G>A	chr17.hg19:g.74732955C>T		33.0	0.0		38.0	4.0	NM_001195427	B3KWD5|B4DN89|H0YG49	Silent	SNP	ENST00000392485.2	hg19	CCDS11749.1																																																																																			.	.		0.741	SRSF2-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437489.1	NM_003016		T	74732955	C	T	74732955	2	4	255	1	0	0	0	0	0	0	0	1	14190	639	23	1		1	SFRS2	17	74732955	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	816828	74732955	6462255	654	35999										
DNAH17	8632	hgsc.bcm.edu	37	chr17	76456313	76456313	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gctttggccaggtctgtttcAcaggccttttgcttctcagt	10	11	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:76456313A>G	ENST00000585328.1	-	59	9475	c.9351T>C	c.(9349-9351)tgT>tgC	p.C3117C	DNAH17_ENST00000389840.5_Silent_p.C3108C|DNAH17_ENST00000586052.1_5'UTR	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	3108	Stalk. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			GGTCTGTTTCACAGGCCTTTT	0.572																																					p.C3122C		Atlas-SNP	.											.	DNAH17	347	.	0			c.T9366C						.						65	58	60					17																	76456313		2203	4300	6503	SO:0001819	synonymous_variant	8632	exon59			TGTTTCACAGGCC	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"Axonemal dyneins"	2946	protein-coding gene	gene with protein product		610063	"dynein, axonemal, heavy polypeptide 17", "dynein, axonemal, heavy chain like 1", "dynein, axonemal, heavy like 1"	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.9351T>C	chr17.hg19:g.76456313A>G		96.0	0.0		116.0	5.0	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	hg19																																																																																				.	.		0.572	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		G	76456313	A	G	76456313	2	3	255	1	0	0	0	0	0	0	0	1	4603	157	6	2		2	DNAH17	17	76456313	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	1723358	76456313	4738897	655	36000										
USP36	57602	hgsc.bcm.edu	37	chr17	76810529	76810529	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	atagtgcccggcatggcagcTgtagcccgagtgcaccagga	14	12	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:76810529T>C	ENST00000542802.3	-	11	1572	c.1129A>G	c.(1129-1131)Agc>Ggc	p.S377G	USP36_ENST00000588467.1_5'UTR|USP36_ENST00000449938.2_Missense_Mutation_p.S77G|USP36_ENST00000312010.6_Missense_Mutation_p.S377G			Q9P275	UBP36_HUMAN	ubiquitin specific peptidase 36	377	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	34			BRCA - Breast invasive adenocarcinoma(99;0.000842)|OV - Ovarian serous cystadenocarcinoma(97;0.151)			GCATGGCAGCTGTAGCCCGAG	0.527																																					p.S377G		Atlas-SNP	.											.	USP36	243	.	0			c.A1129G						.						92	68	76					17																	76810529		2203	4300	6503	SO:0001583	missense	57602	exon11			GGCAGCTGTAGCC	AB040886	CCDS32755.1	17q25.3	2008-02-05	2005-08-08			ENSG00000055483		"Ubiquitin-specific peptidases"	20062	protein-coding gene	gene with protein product		612543	"ubiquitin specific protease 36"			12838346	Standard	NM_025090		Approved	KIAA1453, FLJ12851	uc002jvz.1	Q9P275		ENST00000542802.3:c.1129A>G	chr17.hg19:g.76810529T>C	ENSP00000441214:p.Ser377Gly	83.0	0.0		96.0	4.0	NM_025090	Q05C98|Q05DD0|Q6IQ38|Q8NDM8|Q9NVC8	Missense_Mutation	SNP	ENST00000542802.3	hg19	CCDS32755.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.411169	0.83340	.	.	ENSG00000055483	ENST00000312010;ENST00000449938;ENST00000542802;ENST00000432878	T;T;T	0.06687	3.27;3.27;3.27	5.16	5.16	0.70880	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site (1);Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.077885	0.85682	D	0.000000	T	0.24509	0.0594	L	0.53561	1.675	0.58432	D	0.999996	D;D	0.76494	0.999;0.999	D;D	0.76071	0.987;0.978	T	0.00565	-1.1668	10	0.87932	D	0	-32.9359	14.672	0.68951	0.0:0.0:0.0:1.0	.	377;377	Q9P275;Q9P275-2	UBP36_HUMAN;.	G	377;77;377;377	ENSP00000310590:S377G;ENSP00000401119:S77G;ENSP00000441214:S377G	ENSP00000310590:S377G	S	-	1	0	USP36	74322124	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.123000	0.57917	1.936000	0.56123	0.533000	0.62120	AGC	.	.		0.527	USP36-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437472.3	NM_025090		C	76810529	T	C	76810529	3	2	255	1	0	0	0	0	1	0	0	0	17082	1580	55	2	2282	2	USP36	17	76810529	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	354216	76810529	4384681	656	36001										
ENGASE	64772	hgsc.bcm.edu	37	chr17	77073755	77073755	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctcggaccagttagatattaTgacaaggacaccaccaaacc	7	12	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:77073755T>C	ENST00000579016.1	+	3	225	c.225T>C	c.(223-225)taT>taC	p.Y75Y	ENGASE_ENST00000539857.2_5'UTR	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	75						cytoplasm (GO:0005737)	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925)			breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						TTAGATATTATGACAAGGACA	0.433																																					p.Y75Y		Atlas-SNP	.											.	ENGASE	55	.	0			c.T225C						.						120	122	121					17																	77073755		1927	4129	6056	SO:0001819	synonymous_variant	64772	exon3			ATATTATGACAAG	AF512564	CCDS42394.1	17q25.3	2009-03-03			ENSG00000167280	ENSG00000167280	3.2.1.96		24622	protein-coding gene	gene with protein product	"Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase", "Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase"	611898				12114544, 18586680	Standard	NM_001042573		Approved	FLJ21865	uc002jwv.4	Q8NFI3	OTTHUMG00000167714	ENST00000579016.1:c.225T>C	chr17.hg19:g.77073755T>C		61.0	0.0		78.0	4.0	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Silent	SNP	ENST00000579016.1	hg19	CCDS42394.1																																																																																			.	.		0.433	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759		C	77073755	T	C	77073755	2	2	255	1	0	0	0	0	0	0	0	1	5120	1471	51	2		2	ENGASE	17	77073755	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	263226	77073755	4121455	657	36002										
NPTX1	4884	hgsc.bcm.edu	37	chr17	78445639	78445639	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctggtaggcctcccagacccCgtcccgggtggtccaggtga	14	15	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:78445639C>A	ENST00000306773.4	-	4	1127	c.970G>T	c.(970-972)Ggg>Tgg	p.G324W	NPTX1_ENST00000575212.1_5'Flank	NM_002522.3	NP_002513.2	Q15818	NPTX1_HUMAN	neuronal pentraxin I	324	Pentaxin.				axonogenesis involved in innervation (GO:0060385)|cellular response to glucose stimulus (GO:0071333)|cellular response to potassium ion (GO:0035865)|central nervous system development (GO:0007417)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial transport (GO:0006839)|synaptic transmission (GO:0007268)|transport (GO:0006810)	cytoplasmic vesicle (GO:0031410)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			kidney(1)|large_intestine(2)|liver(1)|lung(4)|prostate(2)|upper_aerodigestive_tract(1)	11	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0487)			TCCCAGACCCCGTCCCGGGTG	0.622																																					p.G324W		Atlas-SNP	.											.	NPTX1	28	.	0			c.G970T						.						56	45	49					17																	78445639		2203	4300	6503	SO:0001583	missense	4884	exon4			AGACCCCGTCCCG	U61849	CCDS32762.1	17q25.3	2008-05-14				ENSG00000171246			7952	protein-coding gene	gene with protein product		602367				8884281	Standard	NM_002522		Approved		uc002jyp.1	Q15818		ENST00000306773.4:c.970G>T	chr17.hg19:g.78445639C>A	ENSP00000307549:p.Gly324Trp	74.0	0.0		84.0	4.0	NM_002522	B3KXH3|Q5FWE6	Missense_Mutation	SNP	ENST00000306773.4	hg19	CCDS32762.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.889179	0.91889	.	.	ENSG00000171246	ENST00000306773;ENST00000535681	T	0.23348	1.91	5.02	5.02	0.67125	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.68412	0.2998	H	0.97940	4.11	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.81699	-0.0814	10	0.87932	D	0	-31.6303	18.1318	0.89604	0.0:1.0:0.0:0.0	.	324	Q15818	NPTX1_HUMAN	W	324;86	ENSP00000307549:G324W	ENSP00000307549:G324W	G	-	1	0	NPTX1	76060234	1.000000	0.71417	0.996000	0.52242	0.965000	0.64279	7.582000	0.82546	2.607000	0.88179	0.561000	0.74099	GGG	.	.		0.622	NPTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438051.1			A	78445639	C	A	78445639	3	1	255	1	0	0	0	0	1	0	0	0	10611	652	23	1	336	1	NPTX1	17	78445639	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1371884	78445639	2749571	658	36003										
PYCR1	5831	hgsc.bcm.edu	37	chr17	79892336	79892336	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttgagctggcctgggtgctgTtctgagtgcagcagcatctt	14	9	2	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:79892336T>C	ENST00000329875.8	-	6	727	c.663A>G	c.(661-663)gaA>gaG	p.E221E	PYCR1_ENST00000577756.1_Intron|PYCR1_ENST00000402252.2_Silent_p.E248E|PYCR1_ENST00000403172.4_Silent_p.E190E|PYCR1_ENST00000337943.5_Silent_p.E221E|RP11-498C9.13_ENST00000583521.1_RNA	NM_001282280.1|NM_001282281.1|NM_006907.2	NP_001269209.1|NP_001269210.1|NP_008838.2	P32322	P5CR1_HUMAN	pyrroline-5-carboxylate reductase 1	221					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to oxidative stress (GO:0034599)|L-proline biosynthetic process (GO:0055129)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|proline biosynthetic process (GO:0006561)|regulation of mitochondrial membrane potential (GO:0051881)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	identical protein binding (GO:0042802)|pyrroline-5-carboxylate reductase activity (GO:0004735)			endometrium(2)|kidney(1)|lung(1)|prostate(1)	5	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.0165)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)		L-Proline(DB00172)	CTGGGTGCTGTTCTGAGTGCA	0.647																																					p.E221E		Atlas-SNP	.											.	PYCR1	44	.	0			c.A663G						.						48	35	39					17																	79892336		2200	4296	6496	SO:0001819	synonymous_variant	5831	exon6			GTGCTGTTCTGAG		CCDS11794.1, CCDS11795.1, CCDS62365.1, CCDS62366.1	17q25.3	2013-09-23			ENSG00000183010	ENSG00000183010	1.5.1.2		9721	protein-coding gene	gene with protein product		179035				1730675	Standard	XM_005256381		Approved	P5C	uc002kcr.1	P32322	OTTHUMG00000178436	ENST00000329875.8:c.663A>G	chr17.hg19:g.79892336T>C		59.0	0.0		58.0	4.0	NM_153824	A6NFM2|B4DMU0|Q6FHI4|Q96DI6|Q9HBQ4	Silent	SNP	ENST00000329875.8	hg19	CCDS11795.1	.	.	.	.	.	.	.	.	.	.	T	7.318	0.616408	0.14129	.	.	ENSG00000183010	ENST00000403172	.	.	.	3.47	-1.76	0.08006	.	.	.	.	.	T	0.67382	0.2887	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68965	-0.5270	5	0.72032	D	0.01	.	10.5871	0.45288	0.0:0.6585:0.0:0.3415	.	.	.	.	A	222	.	ENSP00000385483:T222A	T	-	1	0	PYCR1	77485627	0.737000	0.28175	0.851000	0.33527	0.749000	0.42624	-0.089000	0.11180	-0.293000	0.08986	0.459000	0.35465	ACA	.	.		0.647	PYCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441953.1			C	79892336	T	C	79892336	2	2	255	1	0	0	0	0	0	0	0	1	12870	1722	60	2		2	PYCR1	17	79892336	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	1446697	79892336	1302874	659	36004										
FASN	2194	hgsc.bcm.edu	37	chr17	80038328	80038328	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gggctgggctctgctgggccTgcagctgggagcacatttca	16	11	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:80038328T>C	ENST00000306749.2	-	40	7183	c.6965A>G	c.(6964-6966)cAg>cGg	p.Q2322R	FASN_ENST00000579758.1_Intron	NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	2322	Thioesterase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	CTGCTGGGCCTGCAGCTGGGA	0.662																																					p.Q2322R	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.A6965G						.						18	18	18					17																	80038328		2177	4290	6467	SO:0001583	missense	2194	exon40			TGGGCCTGCAGCT	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.6965A>G	chr17.hg19:g.80038328T>C	ENSP00000304592:p.Gln2322Arg	74.0	0.0		110.0	5.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	hg19	CCDS11801.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.844098	0.91197	.	.	ENSG00000169710	ENST00000306749	T	0.27104	1.69	4.63	4.63	0.57726	Thioesterase (1);	0.068460	0.64402	D	0.000014	T	0.46014	0.1371	L	0.52905	1.665	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.46470	-0.9189	10	0.87932	D	0	-29.5622	14.1766	0.65546	0.0:0.0:0.0:1.0	.	2322	P49327	FAS_HUMAN	R	2322	ENSP00000304592:Q2322R	ENSP00000304592:Q2322R	Q	-	2	0	FASN	77631617	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.681000	0.84073	1.955000	0.56771	0.482000	0.46254	CAG	.	.		0.662	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		C	80038328	T	C	80038328	3	2	255	1	0	0	0	0	1	0	0	0	5691	1580	55	2	586	2	FASN	17	80038328	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	145992	80038328	1156882	660	36005										
TBCD	6904	hgsc.bcm.edu	37	chr17	80897247	80897247	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgcatccctgtcccagatccGgaagaccacggccagccagg	11	16	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:80897247G>A	ENST00000355528.4	+	37	3504	c.3374G>A	c.(3373-3375)cGg>cAg	p.R1125Q	TBCD_ENST00000576691.1_3'UTR|TBCD_ENST00000539345.2_Missense_Mutation_p.R1163Q	NM_005993.4	NP_005984.3	Q9BTW9	TBCD_HUMAN	tubulin folding cofactor D	1125					'de novo' posttranslational protein folding (GO:0051084)|adherens junction assembly (GO:0034333)|cellular protein metabolic process (GO:0044267)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of microtubule polymerization (GO:0031115)|positive regulation of GTPase activity (GO:0043547)|post-chaperonin tubulin folding pathway (GO:0007023)|protein folding (GO:0006457)|tight junction assembly (GO:0070830)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|tight junction (GO:0005923)	beta-tubulin binding (GO:0048487)|chaperone binding (GO:0051087)|GTPase activator activity (GO:0005096)					Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)			TCCCAGATCCGGAAGACCACG	0.642																																					p.R1125Q		Atlas-SNP	.											.	TBCD	94	.	0			c.G3374A						.						86	92	90					17																	80897247		2203	4298	6501	SO:0001583	missense	6904	exon37			AGATCCGGAAGAC	BC003094	CCDS45818.1	17q25.3	2006-11-21	2006-11-21			ENSG00000141556			11581	protein-coding gene	gene with protein product		604649	"tubulin-specific chaperone d"				Standard	NM_005993		Approved		uc002kfz.3	Q9BTW9		ENST00000355528.4:c.3374G>A	chr17.hg19:g.80897247G>A	ENSP00000347719:p.Arg1125Gln	75.0	0.0		70.0	4.0	NM_005993	O95458|Q7L8K1|Q8IXP6|Q8NAX0|Q8WYH4|Q96E74|Q9UF82|Q9UG46|Q9Y2J3	Missense_Mutation	SNP	ENST00000355528.4	hg19	CCDS45818.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.335358	0.81801	.	.	ENSG00000141556	ENST00000355528;ENST00000334614;ENST00000539345	T	0.59364	0.27	5.38	5.38	0.77491	Armadillo-like helical (1);	0.000000	0.85682	D	0.000000	T	0.81230	0.4779	M	0.91510	3.215	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.85190	0.1009	9	.	.	.	.	16.6114	0.84884	0.0:0.0:1.0:0.0	.	914;1125;1163	F8WC00;Q9BTW9;Q9BTW9-4	.;TBCD_HUMAN;.	Q	1125;914;117	ENSP00000347719:R1125Q	.	R	+	2	0	TBCD	78490536	1.000000	0.71417	1.000000	0.80357	0.185000	0.23345	8.798000	0.91888	2.526000	0.85167	0.313000	0.20887	CGG	.	.		0.642	TBCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439415.1	NM_005993		A	80897247	G	A	80897247	3	1	255	1	0	0	0	0	1	0	0	0	15648	1116	39	1	3520	1	TBCD	17	80897247	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	858919	80897247	297963	661	36006										
MYOM1	8736	hgsc.bcm.edu	37	chr18	3071875	3071875	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cgtctgggagacctcccaacAcccgggcacgatctgcaagc	11	16	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr18:3071875A>G	ENST00000356443.4	-	37	5054	c.4721T>C	c.(4720-4722)gTg>gCg	p.V1574A	MYOM1_ENST00000400569.3_Missense_Mutation_p.V1574A|MYOM1_ENST00000261606.7_Missense_Mutation_p.V1478A	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	1574	Ig-like C2-type 5.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						ACCTCCCAACACCCGGGCACG	0.547																																					p.V1574A		Atlas-SNP	.											.	MYOM1	192	.	0			c.T4721C						.						64	69	68					18																	3071875		2016	4196	6212	SO:0001583	missense	8736	exon37			CCCAACACCCGGG	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7613	protein-coding gene	gene with protein product	"skelemin"	603508	"myomesin 1 (skelemin) (185kD)", "myomesin 1 (skelemin) 185kDa", "myomesin 1, 185kDa"			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.4721T>C	chr18.hg19:g.3071875A>G	ENSP00000348821:p.Val1574Ala	86.0	0.0		95.0	4.0	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	hg19	CCDS45824.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.185271	0.78677	.	.	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.53423	0.73;0.74;0.62	4.88	4.88	0.63580	.	0.000000	0.85682	D	0.000000	T	0.73249	0.3563	M	0.90595	3.13	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.77477	-0.2573	10	0.42905	T	0.14	.	14.9381	0.70973	1.0:0.0:0.0:0.0	.	1478;1574	P52179-2;P52179	.;MYOM1_HUMAN	A	1574;1574;1478	ENSP00000348821:V1574A;ENSP00000383413:V1574A;ENSP00000261606:V1478A	ENSP00000261606:V1478A	V	-	2	0	MYOM1	3061875	1.000000	0.71417	0.931000	0.37212	0.673000	0.39480	9.087000	0.94110	2.165000	0.68154	0.460000	0.39030	GTG	.	.		0.547	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803		G	3071875	A	G	3071875	3	3	255	1	0	0	0	0	1	0	0	0	10100	159	6	2	344	2	MYOM1	18	3071875	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10		3071875	75005373	662	36007										
MYOM1	8736	hgsc.bcm.edu	37	chr18	3187546	3187546	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	acattctccttctcccaaacCgtgtgggagcgaggtttaat	9	11	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr18:3187546C>A	ENST00000356443.4	-	5	1194	c.861G>T	c.(859-861)acG>acT	p.T287T	MYOM1_ENST00000400569.3_Silent_p.T287T|MYOM1_ENST00000261606.7_Silent_p.T287T|RP13-270P17.2_ENST00000580139.1_RNA	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	287	Ig-like C2-type 1.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						TCTCCCAAACCGTGTGGGAGC	0.428																																					p.T287T		Atlas-SNP	.											.	MYOM1	192	.	0			c.G861T						.						138	132	134					18																	3187546		1972	4149	6121	SO:0001819	synonymous_variant	8736	exon5			CCAAACCGTGTGG	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7613	protein-coding gene	gene with protein product	"skelemin"	603508	"myomesin 1 (skelemin) (185kD)", "myomesin 1 (skelemin) 185kDa", "myomesin 1, 185kDa"			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.861G>T	chr18.hg19:g.3187546C>A		115.0	0.0		89.0	4.0	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Silent	SNP	ENST00000356443.4	hg19	CCDS45824.1																																																																																			.	.		0.428	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803		A	3187546	C	A	3187546	2	1	255	1	0	0	0	0	0	0	0	1	10100	639	23	1		1	MYOM1	18	3187546	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	115671	3187546	74889702	663	36008										
MYOM1	8736	hgsc.bcm.edu	37	chr18	3215059	3215059	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gaaggcctcggactcccggcGgtgcgcggcggaggagcggc	20	13	0	0	rs371866822		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr18:3215059G>T	ENST00000356443.4	-	2	496	c.163C>A	c.(163-165)Cgc>Agc	p.R55S	MYOM1_ENST00000400569.3_Missense_Mutation_p.R55S|MYOM1_ENST00000261606.7_Missense_Mutation_p.R55S|RP13-270P17.2_ENST00000580139.1_RNA	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	55					muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						GACTCCCGGCGGTGCGCGGCG	0.701																																					p.R55S		Atlas-SNP	.											MYOM1,NS,carcinoma,+1,1	MYOM1	192	.	0			c.C163A						.	G	SER/ARG,SER/ARG	1,4041		0,1,2020	26	33	30		163,163	5.7	1	18		30	0,8350		0,0,4175	no	missense,missense	MYOM1	NM_003803.3,NM_019856.1	110,110	0,1,6195	TT,TG,GG		0.0,0.0247,0.0081	probably-damaging,probably-damaging	55/1686,55/1590	3215059	1,12391	2021	4175	6196	SO:0001583	missense	8736	exon2			CCCGGCGGTGCGC	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7613	protein-coding gene	gene with protein product	"skelemin"	603508	"myomesin 1 (skelemin) (185kD)", "myomesin 1 (skelemin) 185kDa", "myomesin 1, 185kDa"			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.163C>A	chr18.hg19:g.3215059G>T	ENSP00000348821:p.Arg55Ser	83.0	1.0		60.0	4.0	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	hg19	CCDS45824.1	.	.	.	.	.	.	.	.	.	.	G	16.87	3.242192	0.58995	2.47E-4	0.0	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.58652	0.51;0.51;0.32	5.67	5.67	0.87782	.	0.396008	0.25316	N	0.031556	T	0.54415	0.1857	N	0.24115	0.695	0.43503	D	0.995752	D;P	0.61697	0.99;0.465	P;B	0.49665	0.618;0.095	T	0.59553	-0.7433	10	0.72032	D	0.01	.	16.7016	0.85350	0.0:0.0:1.0:0.0	.	55;55	P52179-2;P52179	.;MYOM1_HUMAN	S	55	ENSP00000348821:R55S;ENSP00000383413:R55S;ENSP00000261606:R55S	ENSP00000261606:R55S	R	-	1	0	MYOM1	3205059	1.000000	0.71417	1.000000	0.80357	0.760000	0.43138	5.850000	0.69473	2.673000	0.90976	0.655000	0.94253	CGC	.	.		0.701	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803		T	3215059	G	T	3215059	3	4	255	1	0	0	0	0	1	0	0	0	10100	1116	39	1	5042	1	MYOM1	18	3215059	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	27513	3215059	74862189	664	36009										
ZFP161	7541	hgsc.bcm.edu	37	chr18	5291320	5291320	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgtccgccgtgtggagtttcTcatgcttcctcaatctgcct	9	13	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr18:5291320T>C	ENST00000357006.4	-	4	1225	c.887A>G	c.(886-888)gAg>gGg	p.E296G	ZBTB14_ENST00000400143.3_Missense_Mutation_p.E296G	NM_001143823.2|NM_001243704.1	NP_001137295.1|NP_001230633.1	O43829	ZBT14_HUMAN	zinc finger and BTB domain containing 14	296					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)										GTGGAGTTTCTCATGCTTCCT	0.478																																					p.E296G		Atlas-SNP	.											ZFP161,right_lower_lobe,carcinoma,0,1	.	.	.	0			c.A887G						.						100	91	94					18																	5291320		2203	4300	6503	SO:0001583	missense	7541	exon4			AGTTTCTCATGCT	D89859	CCDS11837.1	18p11.31	2013-09-19	2013-01-08	2013-01-08	ENSG00000198081	ENSG00000198081		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	12860	protein-coding gene	gene with protein product		602126	"zinc finger protein 161 homolog (mouse)", "zinc finger protein 161", "ZFP161 zinc finger protein"	ZFP161		9244432	Standard	NM_001243702		Approved	ZNF478	uc010dkp.3	O43829	OTTHUMG00000131563	ENST00000357006.4:c.887A>G	chr18.hg19:g.5291320T>C	ENSP00000349503:p.Glu296Gly	76.0	0.0		95.0	4.0	NM_001243702	O00403|Q2TB80	Missense_Mutation	SNP	ENST00000357006.4	hg19	CCDS11837.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.287205	0.80803	.	.	ENSG00000198081	ENST00000357006;ENST00000400143	T;T	0.18657	2.2;2.2	5.8	5.8	0.92144	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.110120	0.64402	D	0.000015	T	0.41696	0.1170	L	0.54323	1.7	0.80722	D	1	D	0.69078	0.997	D	0.68765	0.96	T	0.12016	-1.0564	10	0.46703	T	0.11	-20.0105	16.143	0.81539	0.0:0.0:0.0:1.0	.	296	O43829	ZF161_HUMAN	G	296	ENSP00000349503:E296G;ENSP00000383009:E296G	ENSP00000349503:E296G	E	-	2	0	ZFP161	5281320	1.000000	0.71417	0.522000	0.27862	0.974000	0.67602	7.919000	0.87513	2.206000	0.71126	0.528000	0.53228	GAG	.	.		0.478	ZBTB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254425.1	NM_003409		C	5291320	T	C	5291320	3	2	255	1	0	0	0	0	1	0	0	0	17655	1551	54	2	466	2	ZFP161	18	5291320	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	2076261	5291320	72785928	665	36010										
TWSG1	57045	hgsc.bcm.edu	37	chr18	9337333	9337333	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cactctgtgctagtgatgtgAgcaaatgcctcattcaggta	10	9	3	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr18:9337333A>G	ENST00000262120.5	+	2	297	c.106A>G	c.(106-108)Agc>Ggc	p.S36G	TWSG1_ENST00000581641.1_Missense_Mutation_p.S36G|RP11-888D10.3_ENST00000584509.1_lincRNA	NM_020648.5	NP_065699.1	Q9GZX9	TWSG1_HUMAN	twisted gastrulation BMP signaling modulator 1	36	Cys-rich.				BMP signaling pathway (GO:0030509)|camera-type eye development (GO:0043010)|cell differentiation (GO:0030154)|forebrain development (GO:0030900)|hemopoiesis (GO:0030097)|mesoderm formation (GO:0001707)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of osteoblast differentiation (GO:0045668)|ossification (GO:0001503)|positive regulation of BMP signaling pathway (GO:0030513)|salivary gland morphogenesis (GO:0007435)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|pancreas(2)	10						TAGTGATGTGAGCAAATGCCT	0.373																																					p.S36G		Atlas-SNP	.											.	TWSG1	23	.	0			c.A106G						.						141	124	129					18																	9337333		2203	4300	6503	SO:0001583	missense	57045	exon2			GATGTGAGCAAAT	AA486291	CCDS11844.1	18p11.3	2013-10-03	2013-10-03		ENSG00000128791	ENSG00000128791			12429	protein-coding gene	gene with protein product		605049	"twisted gastrulation homolog 1 (Drosophila)"			11260715	Standard	NM_020648		Approved	TSG	uc002knz.3	Q9GZX9	OTTHUMG00000131597	ENST00000262120.5:c.106A>G	chr18.hg19:g.9337333A>G	ENSP00000262120:p.Ser36Gly	35.0	0.0		44.0	4.0	NM_020648	B2RE08|D3DUH9|Q8NBI7|Q96K46	Missense_Mutation	SNP	ENST00000262120.5	hg19	CCDS11844.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.146938	0.77888	.	.	ENSG00000128791	ENST00000262120	.	.	.	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	T	0.67373	0.2886	M	0.74467	2.265	0.53688	D	0.99997	D	0.57899	0.981	P	0.51806	0.68	T	0.72600	-0.4244	9	0.87932	D	0	-27.5754	12.6797	0.56914	1.0:0.0:0.0:0.0	.	36	Q9GZX9	TWSG1_HUMAN	G	36	.	ENSP00000262120:S36G	S	+	1	0	TWSG1	9327333	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.345000	0.72995	2.242000	0.73789	0.533000	0.62120	AGC	.	.		0.373	TWSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254480.2			G	9337333	A	G	9337333	3	3	255	1	0	0	0	0	1	0	0	0	16800	304	11	2	108	2	TWSG1	18	9337333	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	4046013	9337333	68739915	666	36011										
CEP192	55125	hgsc.bcm.edu	37	chr18	13015339	13015339	+	5'UTR	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcttatagattgttgtgcttGatgctggaaaacattttgaa	9	4	1	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr18:13015339G>T	ENST00000325971.8	+	0	612				CEP192_ENST00000506447.1_Missense_Mutation_p.D178Y			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa						centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						TGTTGTGCTTGATGCTGGAAA	0.378																																					p.D178Y		Atlas-SNP	.											.	CEP192	340	.	0			c.G532T						.						192	141	156					18																	13015339		692	1591	2283	SO:0001623	5_prime_UTR_variant	55125	exon6			GTGCTTGATGCTG	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	25515	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 62"					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.-982G>T	chr18.hg19:g.13015339G>T		89.0	0.0		89.0	4.0	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	hg19		.	.	.	.	.	.	.	.	.	.	G	9.907	1.208592	0.22205	.	.	ENSG00000101639	ENST00000506447	T	0.07444	3.19	4.37	3.49	0.39957	.	.	.	.	.	T	0.09113	0.0225	L	0.27053	0.805	0.22266	N	0.999246	P	0.48016	0.904	P	0.46253	0.509	T	0.18335	-1.0340	9	0.66056	D	0.02	.	10.2776	0.43519	0.0:0.2188:0.7812:0.0	.	178	E9PF99	.	Y	178	ENSP00000427550:D178Y	ENSP00000427550:D178Y	D	+	1	0	CEP192	13005339	0.047000	0.20315	0.002000	0.10522	0.015000	0.08874	2.120000	0.41968	1.184000	0.42957	0.563000	0.77884	GAT	.	.		0.378	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142		T	13015339	G	T	13015339	1	4	255	0	1	0	0	0	0	0	0	0	3253	1290	45	3		3	CEP192	18	13015339	5'UTR	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	3678006	13015339	65061909	667	36012										
MIB1	57534	hgsc.bcm.edu	37	chr18	19383906	19383906	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggccacacagctatgcaagcTgctagtcagaatggacatgt	11	10	1	1	rs144652547		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr18:19383906T>C	ENST00000261537.6	+	10	1674	c.1410T>C	c.(1408-1410)gcT>gcC	p.A470A	MIB1_ENST00000578646.1_3'UTR	NM_020774.2	NP_065825.1	Q86YT6	MIB1_HUMAN	mindbomb E3 ubiquitin protein ligase 1	470					blood vessel development (GO:0001568)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|negative regulation of neuron differentiation (GO:0045665)|neural tube formation (GO:0001841)|Notch signaling pathway (GO:0007219)|positive regulation of endocytosis (GO:0045807)|somitogenesis (GO:0001756)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(13)|ovary(5)	27			STAD - Stomach adenocarcinoma(5;0.212)			CTATGCAAGCTGCTAGTCAGA	0.333																																					p.A470A		Atlas-SNP	.											.	MIB1	87	.	0			c.T1410C						.	T		1,4405	2.1+/-5.4	0,1,2202	99	91	94		1410	3.3	1	18	dbSNP_134	94	0,8600		0,0,4300	no	coding-synonymous	MIB1	NM_020774.2		0,1,6502	CC,CT,TT		0.0,0.0227,0.0077		470/1007	19383906	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	57534	exon10			GCAAGCTGCTAGT	AB037744	CCDS11871.1	18q11.2	2014-09-17	2012-02-23		ENSG00000101752	ENSG00000101752		"Zinc fingers, ZZ-type", "Ankyrin repeat domain containing"	21086	protein-coding gene	gene with protein product		608677	"mindbomb homolog 1 (Drosophila)"				Standard	NM_020774		Approved	DIP-1, MIB, KIAA1323, ZZANK2, ZZZ6	uc002ktq.3	Q86YT6	OTTHUMG00000131753	ENST00000261537.6:c.1410T>C	chr18.hg19:g.19383906T>C		66.0	0.0		88.0	4.0	NM_020774	B0YJ38|Q2TB37|Q68D01|Q6YI51|Q8NBY0|Q8TCB5|Q8TCL7|Q9P2M3	Silent	SNP	ENST00000261537.6	hg19	CCDS11871.1																																																																																			.	T|1.000;C|0.000		0.333	MIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254675.1	NM_020774		C	19383906	T	C	19383906	2	2	255	1	0	0	0	0	0	0	0	1	9575	1567	55	2		2	MIB1	18	19383906	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	6368567	19383906	58693342	668	36013										
LAMA3	3909	hgsc.bcm.edu	37	chr18	21355846	21355846	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tttccacggagacaactgtgAgaagtgtgcaattggatact	11	7	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr18:21355846A>G	ENST00000313654.9	+	10	1605	c.1364A>G	c.(1363-1365)gAg>gGg	p.E455G	LAMA3_ENST00000399516.3_Missense_Mutation_p.E455G	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	455	Domain V.|Laminin EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00460}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					GACAACTGTGAGAAGTGTGCA	0.498																																					p.E455G		Atlas-SNP	.											.	LAMA3	397	.	0			c.A1364G						.						83	79	81					18																	21355846		1963	4157	6120	SO:0001583	missense	3909	exon10			ACTGTGAGAAGTG	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"Laminins"	6483	protein-coding gene	gene with protein product		600805	"laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.1364A>G	chr18.hg19:g.21355846A>G	ENSP00000324532:p.Glu455Gly	122.0	0.0		101.0	5.0	NM_001127717	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	hg19	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.117370	0.77323	.	.	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000416669;ENST00000538801	T;T	0.64618	-0.11;-0.11	4.92	4.92	0.64577	EGF-like, laminin (4);	.	.	.	.	T	0.78464	0.4287	M	0.79258	2.445	0.80722	D	1	D;D;D	0.89917	0.99;1.0;0.999	P;D;D	0.77557	0.894;0.986;0.99	T	0.81695	-0.0816	9	0.87932	D	0	.	13.6779	0.62465	1.0:0.0:0.0:0.0	.	455;455;455	F5H8G3;Q6VU67;Q16787	.;.;LAMA3_HUMAN	G	455;455;453;455	ENSP00000324532:E455G;ENSP00000382432:E455G	ENSP00000324532:E455G	E	+	2	0	LAMA3	19609844	1.000000	0.71417	0.999000	0.59377	0.756000	0.42949	7.578000	0.82498	2.072000	0.62099	0.482000	0.46254	GAG	.	.		0.498	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		G	21355846	A	G	21355846	3	3	255	1	0	0	0	0	1	0	0	0	8616	304	11	2	1402	2	LAMA3	18	21355846	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	1971940	21355846	56721402	669	36014										
TTC39C	125488	hgsc.bcm.edu	37	chr18	21660556	21660556	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cttctctttttagcttatatCaaaggtgggtggatccttag	9	7	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr18:21660556C>T	ENST00000317571.3	+	5	704	c.468C>T	c.(466-468)atC>atT	p.I156I	RP11-403A21.3_ENST00000578443.1_RNA|TTC39C_ENST00000578150.1_3'UTR|TTC39C_ENST00000304621.6_Silent_p.I95I	NM_001135993.1	NP_001129465.1	Q8N584	TT39C_HUMAN	tetratricopeptide repeat domain 39C	156										breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)	19						TAGCTTATATCAAAGGTGGGT	0.348																																					p.I156I		Atlas-SNP	.											.	TTC39C	83	.	0			c.C468T						.						48	48	48					18																	21660556		2203	4300	6503	SO:0001819	synonymous_variant	125488	exon5			TTATATCAAAGGT	AK091080	CCDS32804.1, CCDS45839.1, CCDS58616.1	18q11.2	2014-02-07	2008-06-23	2008-06-23	ENSG00000168234	ENSG00000168234		"Tetratricopeptide (TTC) repeat domain containing"	26595	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 17"	C18orf17		14702039	Standard	NM_153211		Approved	FLJ33761, HsT2697	uc002kuw.3	Q8N584	OTTHUMG00000179403	ENST00000317571.3:c.468C>T	chr18.hg19:g.21660556C>T		75.0	0.0		83.0	4.0	NM_001135993	B7WP63|J3QRR1|Q0VAJ2|Q8N284	Silent	SNP	ENST00000317571.3	hg19	CCDS45839.1																																																																																			.	.		0.348	TTC39C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446107.1	NM_153211		T	21660556	C	T	21660556	2	4	255	1	0	0	0	0	0	0	0	1	16724	816	29	3		3	TTC39C	18	21660556	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	304710	21660556	56416692	670	36015										
SLC14A1	6563	hgsc.bcm.edu	37	chr18	43310402	43310402	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aaagctcttggctatgtcacCggtgacatgaaagaacttgc	10	9	2	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr18:43310402C>A	ENST00000321925.4	+	3	349	c.117C>A	c.(115-117)acC>acA	p.T39T	SLC14A1_ENST00000402943.2_Intron|SLC14A1_ENST00000502059.2_Intron|SLC14A1_ENST00000535474.1_Intron|SLC14A1_ENST00000591943.1_3'UTR|RP11-116O18.3_ENST00000589510.1_RNA|SLC14A1_ENST00000586142.1_Silent_p.T39T|RP11-116O18.3_ENST00000586213.1_RNA|SLC14A1_ENST00000589700.1_Silent_p.T39T|SLC14A1_ENST00000415427.3_Silent_p.T95T|SLC14A1_ENST00000436407.3_Silent_p.T95T	NM_001128588.3|NM_001146036.2|NM_015865.6	NP_001122060.3|NP_001139508.2|NP_056949.4	Q13336	UT1_HUMAN	solute carrier family 14 (urea transporter), member 1 (Kidd blood group)	39					transmembrane transport (GO:0055085)|urea transmembrane transport (GO:0071918)|urea transport (GO:0015840)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	urea channel activity (GO:0015265)|urea transmembrane transporter activity (GO:0015204)|water transmembrane transporter activity (GO:0005372)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(11)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	21						GCTATGTCACCGGTGACATGA	0.478																																					p.T95T		Atlas-SNP	.											.	SLC14A1	84	.	0			c.C285A						.						117	105	109					18																	43310402		2203	4300	6503	SO:0001819	synonymous_variant	6563	exon2			TGTCACCGGTGAC	BC040128	CCDS11925.1, CCDS45860.1	18q11-q12	2014-07-19	2014-01-02		ENSG00000141469	ENSG00000141469		"Blood group antigens", "Solute carriers"	10918	protein-coding gene	gene with protein product		613868	"Kidd blood group", "solute carrier family 14 (urea transporter), member 1"	JK		7797558	Standard	NM_001146037		Approved	HsT1341, RACH1, RACH2	uc010dnk.3	Q13336	OTTHUMG00000132617	ENST00000321925.4:c.117C>A	chr18.hg19:g.43310402C>A		99.0	0.0		97.0	5.0	NM_001146037	A8K0P3|B3KR62|B3KVX3|C9EHF2|Q86VM5	Silent	SNP	ENST00000321925.4	hg19	CCDS11925.1																																																																																			.	.		0.478	SLC14A1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255860.2	NM_015865		A	43310402	C	A	43310402	2	1	255	1	0	0	0	0	0	0	0	1	14411	639	23	1		1	SLC14A1	18	43310402	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	21649846	43310402	34766846	671	36016										
MAPK4	5596	hgsc.bcm.edu	37	chr18	48255833	48255833	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctcggagcccaagctcatccTggacctgtcgcactggaagc	11	15	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr18:48255833T>C	ENST00000400384.2	+	6	2409	c.1373T>C	c.(1372-1374)cTg>cCg	p.L458P	MAPK4_ENST00000592595.1_3'UTR|MAPK4_ENST00000540640.1_Missense_Mutation_p.L247P	NM_002747.3	NP_002738.2	P31152	MK04_HUMAN	mitogen-activated protein kinase 4	458					cell cycle (GO:0007049)|MAPK cascade (GO:0000165)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)			lung(4)|skin(3)|upper_aerodigestive_tract(1)	8		Colorectal(6;0.0297)		Colorectal(21;0.156)		AAGCTCATCCTGGACCTGTCG	0.716																																					p.L458P		Atlas-SNP	.											.	MAPK4	75	.	0			c.T1373C						.						6	8	7					18																	48255833		1977	4100	6077	SO:0001583	missense	5596	exon6			TCATCCTGGACCT	X59727	CCDS42437.1	18q21.1	2012-10-02			ENSG00000141639	ENSG00000141639		"Mitogen-activated protein kinase cascade / Kinases"	6878	protein-coding gene	gene with protein product		176949		PRKM4		8290275	Standard	XM_005258299		Approved	Erk3-related, Erk4	uc002lev.3	P31152	OTTHUMG00000179853	ENST00000400384.2:c.1373T>C	chr18.hg19:g.48255833T>C	ENSP00000383234:p.Leu458Pro	63.0	0.0		66.0	4.0	NM_002747	A1A4C4|Q0VG04	Missense_Mutation	SNP	ENST00000400384.2	hg19	CCDS42437.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.623861	0.87460	.	.	ENSG00000141639	ENST00000400384;ENST00000540640	T;T	0.77489	-1.1;0.86	5.36	5.36	0.76844	.	0.300400	0.23000	N	0.053089	T	0.78285	0.4259	N	0.24115	0.695	0.80722	D	1	D	0.63880	0.993	P	0.59056	0.851	T	0.81424	-0.0939	10	0.87932	D	0	-28.2539	14.3448	0.66654	0.0:0.0:0.0:1.0	.	458	P31152	MK04_HUMAN	P	458;247	ENSP00000383234:L458P;ENSP00000439231:L247P	ENSP00000383234:L458P	L	+	2	0	MAPK4	46509831	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.865000	0.87049	2.010000	0.58986	0.459000	0.35465	CTG	.	.		0.716	MAPK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448631.2	NM_002747		C	48255833	T	C	48255833	3	2	255	1	0	0	0	0	1	0	0	0	9289	1580	55	2	1391	2	MAPK4	18	48255833	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	4945431	48255833	29821415	672	36017										
ZNF532	55205	hgsc.bcm.edu	37	chr18	56586800	56586800	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agggcgcctctccagtctgcGgtcgtgaccaatgcagtttc	12	13	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr18:56586800G>T	ENST00000336078.4	+	4	2057	c.1281G>T	c.(1279-1281)gcG>gcT	p.A427A	ZNF532_ENST00000591808.1_Silent_p.A427A|ZNF532_ENST00000591230.1_Silent_p.A427A|ZNF532_ENST00000591083.1_Silent_p.A427A|ZNF532_ENST00000589288.1_Silent_p.A427A	NM_018181.4	NP_060651.2	Q9HCE3	ZN532_HUMAN	zinc finger protein 532	427					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(14)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(4)|urinary_tract(1)	52						TCCAGTCTGCGGTCGTGACCA	0.602																																					p.A427A		Atlas-SNP	.											ZNF532,caecum,carcinoma,0,1	ZNF532	108	.	0			c.G1281T						.						36	32	33					18																	56586800		2203	4300	6503	SO:0001819	synonymous_variant	55205	exon4			GTCTGCGGTCGTG	AB046849	CCDS11969.1	18q21.32	2005-08-22			ENSG00000074657	ENSG00000074657		"Zinc fingers, C2H2-type"	30940	protein-coding gene	gene with protein product						10997877	Standard	XM_005266723		Approved	FLJ10697	uc002lho.3	Q9HCE3	OTTHUMG00000132759	ENST00000336078.4:c.1281G>T	chr18.hg19:g.56586800G>T		103.0	0.0		97.0	4.0	NM_018181	Q4G0V6|Q7L7Z7|Q96QR7|Q9NVJ6	Silent	SNP	ENST00000336078.4	hg19	CCDS11969.1																																																																																			.	.		0.602	ZNF532-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256130.1	NM_018181		T	56586800	G	T	56586800	2	4	255	1	0	0	0	0	0	0	0	1	17987	1103	39	1		1	ZNF532	18	56586800	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	8330967	56586800	21490448	673	36018										
FAM69C	125704	hgsc.bcm.edu	37	chr18	72114420	72114420	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gcctgcagcaccttcttgccTctgttgtagtgcaggcagcg	12	13	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr18:72114420T>C	ENST00000343998.6	-	2	305	c.297A>G	c.(295-297)agA>agG	p.R99R	FAM69C_ENST00000400291.2_Intron	NM_001044369.2	NP_001037834.2	Q0P6D2	FA69C_HUMAN	family with sequence similarity 69, member C	99						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	transferase activity, transferring phosphorus-containing groups (GO:0016772)			breast(1)|large_intestine(2)|ovary(2)	5						CCTTCTTGCCTCTGTTGTAGT	0.667																																					p.R99R		Atlas-SNP	.											.	FAM69C	45	.	0			c.A297G						.						12	13	13					18																	72114420		689	1591	2280	SO:0001819	synonymous_variant	125704	exon2			CTTGCCTCTGTTG	BC019628	CCDS42445.2	18q22.3	2012-08-03	2009-07-23	2009-07-23	ENSG00000187773	ENSG00000187773			31729	protein-coding gene	gene with protein product		614544	"chromosome 18 open reading frame 51"	C18orf51		21334309	Standard	NM_001044369		Approved		uc002llk.3	Q0P6D2	OTTHUMG00000156984	ENST00000343998.6:c.297A>G	chr18.hg19:g.72114420T>C		50.0	0.0		55.0	4.0	NM_001044369		Silent	SNP	ENST00000343998.6	hg19	CCDS42445.2																																																																																			.	.		0.667	FAM69C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346971.2	XM_058931		C	72114420	T	C	72114420	2	2	255	1	0	0	0	0	0	0	0	1	5612	1548	54	2		2	FAM69C	18	72114420	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	15527620	72114420	5962828	674	36019										
CTDP1	9150	hgsc.bcm.edu	37	chr18	77488935	77488935	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cgccaccccagccgcagatgTttggtgaagagctgcctgac	12	14	0	4			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr18:77488935T>C	ENST00000299543.7	+	11	2593	c.2446T>C	c.(2446-2448)Ttt>Ctt	p.F816L	CTDP1_ENST00000075430.7_Intron	NM_001202504.1|NM_004715.4	NP_001189433.1|NP_004706.3	Q9Y5B0	CTDP1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1	816					exit from mitosis (GO:0010458)|gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|protein dephosphorylation (GO:0006470)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	CTD phosphatase activity (GO:0008420)|DNA-directed RNA polymerase activity (GO:0003899)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(2)|urinary_tract(1)	35		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)		GCCGCAGATGTTTGGTGAAGA	0.547																																					p.F816L		Atlas-SNP	.											.	CTDP1	67	.	0			c.T2446C						.						183	201	195					18																	77488935		2203	4300	6503	SO:0001583	missense	9150	exon11			CAGATGTTTGGTG	AF081287	CCDS12017.1, CCDS12018.1, CCDS74239.1	18q23	2014-09-17			ENSG00000060069	ENSG00000060069		"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	2498	protein-coding gene	gene with protein product		604927				9405607, 9765293	Standard	NM_004715		Approved	FCP1	uc002lnh.2	Q9Y5B0	OTTHUMG00000132920	ENST00000299543.7:c.2446T>C	chr18.hg19:g.77488935T>C	ENSP00000299543:p.Phe816Leu	63.0	0.0		73.0	4.0	NM_004715	A8MY97|Q7Z644|Q96BZ1|Q9Y6F5	Missense_Mutation	SNP	ENST00000299543.7	hg19	CCDS12017.1	.	.	.	.	.	.	.	.	.	.	T	10.21	1.286684	0.23478	.	.	ENSG00000060069	ENST00000299543	T	0.53423	0.62	5.26	2.75	0.32379	FCP1-like phosphatase, C-terminal (1);	0.764123	0.12984	N	0.423034	T	0.40694	0.1127	L	0.60455	1.87	0.80722	D	1	B;B	0.20550	0.01;0.046	B;B	0.22601	0.006;0.04	T	0.09292	-1.0681	10	0.21014	T	0.42	-2.5086	7.2897	0.26360	0.0:0.0794:0.1441:0.7765	.	697;816	Q9Y5B0-3;Q9Y5B0	.;CTDP1_HUMAN	L	816	ENSP00000299543:F816L	ENSP00000299543:F816L	F	+	1	0	CTDP1	75589923	1.000000	0.71417	0.969000	0.41365	0.033000	0.12548	2.202000	0.42743	0.280000	0.22209	0.496000	0.49642	TTT	.	.		0.547	CTDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256432.1	NM_004715		C	77488935	T	C	77488935	3	2	255	1	0	0	0	0	1	0	0	0	4004	1725	60	2	2488	2	CTDP1	18	77488935	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	5374515	77488935	588313	675	36020										
SHC2	25759	hgsc.bcm.edu	37	chr19	422413	422413	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggggctgctgtcacgcctgcCgccactgagcactcatgcaa	12	15	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:422413C>A	ENST00000264554.6	-	11	1352	c.1353G>T	c.(1351-1353)gcG>gcT	p.A451A		NM_012435.2	NP_036567.2	P98077	SHC2_HUMAN	SHC (Src homology 2 domain containing) transforming protein 2	451	CH1.				activation of MAPK activity (GO:0000187)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)	cytosol (GO:0005829)				endometrium(2)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	21		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCACGCCTGCCGCCACTGAGC	0.687																																					p.A451A		Atlas-SNP	.											.	SHC2	47	.	0			c.G1353T						.																																			SO:0001819	synonymous_variant	25759	exon11			GCCTGCCGCCACT	AB001451	CCDS45891.1	19p13.3	2013-02-14				ENSG00000129946		"SH2 domain containing"	29869	protein-coding gene	gene with protein product	"neuronal Shc adaptor homolog"	605217				7527937, 9507002	Standard	NM_012435		Approved	SLI, SCK, SHCB	uc002loq.4	P98077		ENST00000264554.6:c.1353G>T	chr19.hg19:g.422413C>A		88.0	0.0		98.0	4.0	NM_012435	O60230|Q9NPL5|Q9UCX4	Silent	SNP	ENST00000264554.6	hg19	CCDS45891.1																																																																																			.	.		0.687	SHC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451840.3			A	422413	C	A	422413	2	1	255	1	0	0	0	0	0	0	0	1	14286	639	23	1		1	SHC2	19	422413	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10		422413	58706570	676	36021										
AP3D1	8943	hgsc.bcm.edu	37	chr19	2138617	2138617	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tggccactgggaggcacttaCatacgtcagcttgcagaccg	12	12	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:2138617C>T	ENST00000345016.5	-	2	424		c.e2+1		AP3D1_ENST00000356926.4_Splice_Site|AP3D1_ENST00000350812.6_Splice_Site|AP3D1_ENST00000355272.6_Splice_Site	NM_003938.6	NP_003929.4	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1 subunit						anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|endosome to melanosome transport (GO:0035646)|eye pigment biosynthetic process (GO:0006726)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein localization to membrane (GO:0072657)|protein localization to organelle (GO:0033365)|regulation of sequestering of zinc ion (GO:0061088)|synaptic vesicle membrane organization (GO:0048499)	endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane coat (GO:0030117)|terminal bouton (GO:0043195)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(23)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GAGGCACTTACATACGTCAGC	0.537																																					.		Atlas-SNP	.											.	AP3D1	81	.	0			c.192+1G>A						.						104	110	108					19																	2138617		2179	4260	6439	SO:0001630	splice_region_variant	8943	exon3			CACTTACATACGT	U91930	CCDS42459.1, CCDS58638.1	19p13.3	2014-09-04			ENSG00000065000	ENSG00000065000			568	protein-coding gene	gene with protein product		607246				9151686, 9303295	Standard	NM_003938		Approved	ADTD	uc002lva.4	O14617	OTTHUMG00000180354	ENST00000345016.5:c.192+1G>A	chr19.hg19:g.2138617C>T		72.0	0.0		101.0	7.0	NM_003938	O00202|O75262|Q59HF5|Q96G11|Q9H3C6	Splice_Site	SNP	ENST00000345016.5	hg19	CCDS42459.1	.	.	.	.	.	.	.	.	.	.	C	18.67	3.673503	0.67928	.	.	ENSG00000065000	ENST00000356926;ENST00000345016;ENST00000355272;ENST00000343722;ENST00000350812	.	.	.	5.3	5.3	0.74995	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.2978	0.90153	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	AP3D1	2089617	1.000000	0.71417	0.110000	0.21437	0.587000	0.36485	7.379000	0.79691	2.633000	0.89246	0.563000	0.77884	.	.	.		0.537	AP3D1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450912.1		Intron	T	2138617	C	T	2138617	5	4	255	1	0	0	0	0	0	0	1	0	746	492	17	3	3542	3	AP3D1	19	2138617	Splice_Site	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1716204	2138617	56990366	677	36022										
C19orf29	58509	hgsc.bcm.edu	37	chr19	3626642	3626642	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgcgccgtccctcgtcctccCggcgccgtcggtttcgccgc	12	20	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:3626642C>T	ENST00000429344.2	-	1	171	c.119G>A	c.(118-120)cGg>cAg	p.R40Q	CACTIN_ENST00000221899.3_5'UTR|CACTIN_ENST00000248420.5_Missense_Mutation_p.R40Q	NM_001080543.1	NP_001074012.1	Q8WUQ7	CATIN_HUMAN	cactin, spliceosome C complex subunit	40					cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|multicellular organismal development (GO:0007275)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)										CTCGTCCTCCCGGCGCCGTCG	0.761																																					p.R40Q		Atlas-SNP	.											.	.	.	.	0			c.G119A						.						4	6	5					19																	3626642		1821	3910	5731	SO:0001583	missense	58509	exon1			TCCTCCCGGCGCC	BC019848	CCDS45920.1	19p13.3	2012-06-08	2012-06-08	2012-06-08	ENSG00000105298	ENSG00000105298			29938	protein-coding gene	gene with protein product	"NY REN 24 antigen", "functional spliceosome-associated protein c", "cactin homolog (Drosophila)"		"chromosome 19 open reading frame 29"	C19orf29		8619474, 9110174, 21429463, 20829348	Standard	NM_001080543		Approved	NY-REN-24, fSAPc, cactin	uc002lyh.3	Q8WUQ7		ENST00000429344.2:c.119G>A	chr19.hg19:g.3626642C>T	ENSP00000415078:p.Arg40Gln	29.0	0.0		35.0	5.0	NM_021231	A6NNA9|A9UL12|O75229|Q7LE08|Q9BTA6|Q9Y5A4	Missense_Mutation	SNP	ENST00000429344.2	hg19	CCDS45920.1	.	.	.	.	.	.	.	.	.	.	C	15.81	2.943503	0.53079	.	.	ENSG00000105298	ENST00000429344;ENST00000248420	.	.	.	4.74	3.68	0.42216	.	.	.	.	.	T	0.15478	0.0373	N	0.08118	0	0.26132	N	0.980404	B	0.32731	0.382	B	0.23018	0.043	T	0.06180	-1.0841	8	0.15499	T	0.54	.	9.4039	0.38449	0.0:0.8936:0.0:0.1064	.	40	Q8WUQ7	CS029_HUMAN	Q	40	.	ENSP00000248420:R40Q	R	-	2	0	C19orf29	3577642	0.999000	0.42202	1.000000	0.80357	0.935000	0.57460	2.971000	0.49248	2.352000	0.79861	0.555000	0.69702	CGG	.	.		0.761	CACTIN-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457370.2			T	3626642	C	T	3626642	3	4	255	1	0	0	0	0	1	0	0	0	1920	652	23	1	2197	1	C19orf29	19	3626642	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1488025	3626642	55502341	678	36023										
SIRT6	51548	hgsc.bcm.edu	37	chr19	4179153	4179153	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cacgttctggctgaccaggaAgcggaggaggcccacgcgct	15	13	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:4179153A>G	ENST00000337491.2	-	3	389	c.325T>C	c.(325-327)Ttc>Ctc	p.F109L	SIRT6_ENST00000305232.6_Missense_Mutation_p.F109L|SIRT6_ENST00000381935.3_Missense_Mutation_p.F37L|SIRT6_ENST00000601488.1_Intron|SIRT6_ENST00000594279.1_Missense_Mutation_p.F37L	NM_016539.2	NP_057623.2	Q8N6T7	SIR6_HUMAN	sirtuin 6	109	Deacetylase sirtuin-type. {ECO:0000255|PROSITE-ProRule:PRU00236}.				histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|protein ADP-ribosylation (GO:0006471)|regulation of double-strand break repair via homologous recombination (GO:0010569)	nuclear telomeric heterochromatin (GO:0005724)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (GO:0017136)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(1)|lung(4)|ovary(1)|skin(1)	8		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.023)|STAD - Stomach adenocarcinoma(1328;0.18)		CTGACCAGGAAGCGGAGGAGG	0.677																																					p.F109L		Atlas-SNP	.											.	SIRT6	16	.	0			c.T325C						.						25	23	23					19																	4179153		2203	4300	6503	SO:0001583	missense	51548	exon3			CCAGGAAGCGGAG	AF233396	CCDS12122.1, CCDS54199.1	19p13.3	2010-06-25	2010-06-25			ENSG00000077463			14934	protein-coding gene	gene with protein product		606211	"sirtuin (silent mating type information regulation 2, S. cerevisiae, homolog) 6", "sirtuin (silent mating type information regulation 2 homolog) 6 (S. cerevisiae)"			10873683	Standard	NM_016539		Approved		uc002lzo.3	Q8N6T7		ENST00000337491.2:c.325T>C	chr19.hg19:g.4179153A>G	ENSP00000337332:p.Phe109Leu	67.0	0.0		93.0	5.0	NM_016539	B2RCD0|O75291|Q6IAF5|Q6PK99|Q8NCD2|Q9BSI5|Q9BWP3|Q9NRC7|Q9UQD1	Missense_Mutation	SNP	ENST00000337491.2	hg19	CCDS12122.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.587910	0.86851	.	.	ENSG00000077463	ENST00000337491;ENST00000305232;ENST00000381935	T;T;T	0.17370	2.28;2.28;2.28	4.97	4.97	0.65823	.	0.170832	0.53938	D	0.000060	T	0.27349	0.0671	L	0.41824	1.3	0.51767	D	0.999936	P;D;D	0.71674	0.882;0.991;0.998	P;P;D	0.65443	0.722;0.848;0.935	T	0.03443	-1.1036	10	0.11485	T	0.65	-27.9351	13.4809	0.61334	1.0:0.0:0.0:0.0	.	109;109;37	Q8N6T7-2;Q8N6T7;B7Z5U1	.;SIRT6_HUMAN;.	L	109;109;37	ENSP00000337332:F109L;ENSP00000305310:F109L;ENSP00000371360:F37L	ENSP00000305310:F109L	F	-	1	0	SIRT6	4130153	1.000000	0.71417	0.961000	0.40146	0.724000	0.41520	6.898000	0.75676	1.877000	0.54381	0.454000	0.30748	TTC	.	.		0.677	SIRT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457931.2			G	4179153	A	G	4179153	3	3	255	1	0	0	0	0	1	0	0	0	14357	72	3	2	766	2	SIRT6	19	4179153	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	552511	4179153	54949830	679	36024										
PRR22	163154	hgsc.bcm.edu	37	chr19	5783322	5783322	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccactgctgtcaggcagggcCggcccagggacctcgcacag	14	16	1	0	rs188791439	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:5783322C>A	ENST00000419421.2	-	3	1040	c.936G>T	c.(934-936)ccG>ccT	p.P312P		NM_001134316.1	NP_001127788.1	Q8IZ63	PRR22_HUMAN	proline rich 22	312										endometrium(2)|large_intestine(1)|prostate(1)|urinary_tract(1)	5						CAGGCAGGGCCGGCCCAGGGA	0.642																																					p.P312P		Atlas-SNP	.											.	PRR22	25	.	0			c.G936T						.						38	42	41					19																	5783322		2203	4297	6500	SO:0001819	synonymous_variant	163154	exon3			CAGGGCCGGCCCA	BC023278	CCDS45933.1	19p13.3	2012-12-20			ENSG00000212123	ENSG00000212123			28354	protein-coding gene	gene with protein product						12477932	Standard	NM_001134316		Approved	MGC24975	uc010xiv.1	Q8IZ63	OTTHUMG00000180553	ENST00000419421.2:c.936G>T	chr19.hg19:g.5783322C>A		66.0	0.0		85.0	4.0	NM_001134316	E9PB31	Silent	SNP	ENST00000419421.2	hg19	CCDS45933.1																																																																																			.	C|0.997;T|0.003		0.642	PRR22-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368523.1	NM_153359		A	5783322	C	A	5783322	2	1	255	1	0	0	0	0	0	0	0	1	12605	639	23	1		1	PRR22	19	5783322	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1604169	5783322	53345661	680	36025										
XAB2	56949	hgsc.bcm.edu	37	chr19	7691045	7691045	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gtagttggacttgccggcctTagacacgaaacgctcgtcgt	12	11	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:7691045T>C	ENST00000358368.4	-	5	671	c.634A>G	c.(634-636)Aag>Gag	p.K212E	XAB2_ENST00000534844.1_Missense_Mutation_p.K209E	NM_020196.2	NP_064581.2	Q9HCS7	SYF1_HUMAN	XPA binding protein 2	212					blastocyst development (GO:0001824)|DNA repair (GO:0006281)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	26						TTGCCGGCCTTAGACACGAAA	0.642								Direct reversal of damage;Nucleotide excision repair (NER)																													p.K212E		Atlas-SNP	.											.	XAB2	69	.	0			c.A634G						.						71	77	75					19																	7691045		2203	4299	6502	SO:0001583	missense	56949	exon5			CGGCCTTAGACAC	AB026111	CCDS32892.1	19p13.3	2013-08-21				ENSG00000076924			14089	protein-coding gene	gene with protein product	"SYF1 homolog, RNA splicing factor (S. cerevisiae)", "SYF1 pre-mRNA-splicing factor"	610850				10944529	Standard	NM_020196		Approved	HCNP, HCRN, SYF1, NTC90	uc002mgx.3	Q9HCS7		ENST00000358368.4:c.634A>G	chr19.hg19:g.7691045T>C	ENSP00000351137:p.Lys212Glu	90.0	0.0		101.0	41.0	NM_020196	Q8TET6|Q96HB0|Q96IW0|Q9NRG6|Q9ULP3	Missense_Mutation	SNP	ENST00000358368.4	hg19	CCDS32892.1	.	.	.	.	.	.	.	.	.	.	T	8.852	0.944764	0.18356	.	.	ENSG00000076924	ENST00000358368;ENST00000534844	T;T	0.62941	-0.01;-0.01	4.96	3.95	0.45737	.	0.000000	0.85682	D	0.000000	T	0.54565	0.1866	M	0.63169	1.94	0.49299	D	0.999776	B	0.20780	0.048	B	0.13407	0.009	T	0.47736	-0.9094	10	0.28530	T	0.3	-47.5253	8.3945	0.32548	0.0:0.0911:0.0:0.9089	.	212	Q9HCS7	SYF1_HUMAN	E	212;209	ENSP00000351137:K212E;ENSP00000438225:K209E	ENSP00000351137:K212E	K	-	1	0	XAB2	7597045	1.000000	0.71417	0.993000	0.49108	0.025000	0.11179	7.454000	0.80714	0.756000	0.33013	-0.388000	0.06559	AAG	.	.		0.642	XAB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461021.1	NM_020196		C	7691045	T	C	7691045	3	2	255	1	0	0	0	0	1	0	0	0	17433	1763	61	2	1993	2	XAB2	19	7691045	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	1907723	7691045	51437938	681	36026										
COL5A3	50509	hgsc.bcm.edu	37	chr19	10106242	10106242	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gacctagctgtcactcaccaTcttgcccactcggccagggg	10	16	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:10106242T>C	ENST00000264828.3	-	16	1670	c.1585A>G	c.(1585-1587)Atg>Gtg	p.M529V	CTD-2553C6.1_ENST00000592332.1_RNA	NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	529	Collagen-like 2.|Triple-helical region.				axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			TCACTCACCATCTTGCCCACT	0.552																																					p.M529V		Atlas-SNP	.											.	COL5A3	243	.	0			c.A1585G						.						75	59	64					19																	10106242		2203	4300	6503	SO:0001583	missense	50509	exon16			TCACCATCTTGCC	AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573		"Collagens"	14864	protein-coding gene	gene with protein product		120216				10722718	Standard	NM_015719		Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.1585A>G	chr19.hg19:g.10106242T>C	ENSP00000264828:p.Met529Val	55.0	0.0		80.0	4.0	NM_015719	Q9NZQ6	Missense_Mutation	SNP	ENST00000264828.3	hg19	CCDS12222.1	.	.	.	.	.	.	.	.	.	.	T	13.23	2.174270	0.38413	.	.	ENSG00000080573	ENST00000264828	D	0.89617	-2.54	5.06	3.93	0.45458	.	0.370933	0.26069	N	0.026526	T	0.78457	0.4286	N	0.16166	0.38	0.21675	N	0.999594	B	0.27013	0.166	B	0.28916	0.096	T	0.69359	-0.5166	10	0.48119	T	0.1	.	8.2267	0.31572	0.0:0.0:0.2636:0.7364	.	529	P25940	CO5A3_HUMAN	V	529	ENSP00000264828:M529V	ENSP00000264828:M529V	M	-	1	0	COL5A3	9967242	0.989000	0.36119	1.000000	0.80357	0.933000	0.57130	1.365000	0.34182	2.038000	0.60285	0.533000	0.62120	ATG	.	.		0.552	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719		C	10106242	T	C	10106242	3	2	255	1	0	0	0	0	1	0	0	0	3700	1435	50	2	3860	2	COL5A3	19	10106242	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	2415197	10106242	49022741	682	36027										
RDH8	50700	hgsc.bcm.edu	37	chr19	10131464	10131464	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agcctcgctatccagctgctGcagttcaacatcttgtgagg	10	12	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:10131464G>A	ENST00000171214.1	+	4	771	c.522G>A	c.(520-522)ctG>ctA	p.L174L	RDH8_ENST00000591589.1_Silent_p.L194L	NM_015725.2	NP_056540.2	Q9NYR8	RDH8_HUMAN	retinol dehydrogenase 8 (all-trans)	174					estrogen biosynthetic process (GO:0006703)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|steroid biosynthetic process (GO:0006694)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|NADP-retinol dehydrogenase activity (GO:0052650)|retinol dehydrogenase activity (GO:0004745)			endometrium(3)|large_intestine(3)|lung(10)|ovary(3)|pancreas(1)|prostate(1)	21			Epithelial(33;4.24e-05)		Vitamin A(DB00162)	TCCAGCTGCTGCAGTTCAACA	0.567																																					p.L194L		Atlas-SNP	.											.	RDH8	51	.	0			c.G582A						.						67	54	58					19																	10131464		2203	4300	6503	SO:0001819	synonymous_variant	50700	exon4			GCTGCTGCAGTTC	AF229845	CCDS12223.1, CCDS12223.2	19p13.2	2011-09-14				ENSG00000080511	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	14423	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 28C, member 2"	608575				10753906, 19027726	Standard	NM_015725		Approved	PRRDH, SDR28C2	uc002mmr.4	Q9NYR8		ENST00000171214.1:c.522G>A	chr19.hg19:g.10131464G>A		101.0	0.0		80.0	4.0	NM_015725	Q9H838	Silent	SNP	ENST00000171214.1	hg19																																																																																				.	.		0.567	RDH8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				A	10131464	G	A	10131464	2	1	255	1	0	0	0	0	0	0	0	1	13211	1306	46	3		3	RDH8	19	10131464	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	25222	10131464	48997519	683	36028										
TYK2	7297	hgsc.bcm.edu	37	chr19	10476357	10476357	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctccccctcggcctgggccaGcagcctcaggtggcacacgg	13	18	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:10476357G>A	ENST00000525621.1	-	7	1328	c.847C>T	c.(847-849)Ctg>Ttg	p.L283L	TYK2_ENST00000524462.1_Silent_p.L98L|TYK2_ENST00000529370.1_Silent_p.L283L|TYK2_ENST00000264818.6_Silent_p.L283L	NM_003331.4	NP_003322.3	P29597	TYK2_HUMAN	tyrosine kinase 2	283	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cytokine-mediated signaling pathway (GO:0019221)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(11)|kidney(6)|large_intestine(3)|lung(19)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64			OV - Ovarian serous cystadenocarcinoma(20;1.77e-09)|Epithelial(33;3.92e-06)|all cancers(31;8.95e-06)			GCCTGGGCCAGCAGCCTCAGG	0.672																																					p.L283L		Atlas-SNP	.											.	TYK2	126	.	0			c.C847T						.						19	22	21					19																	10476357		2201	4296	6497	SO:0001819	synonymous_variant	7297	exon7			GGGCCAGCAGCCT		CCDS12236.1	19p13.2	2014-09-17			ENSG00000105397	ENSG00000105397	2.7.10.1		12440	protein-coding gene	gene with protein product		176941				2156206	Standard	NM_003331		Approved	JTK1	uc002moc.4	P29597	OTTHUMG00000166373	ENST00000525621.1:c.847C>T	chr19.hg19:g.10476357G>A		93.0	0.0		93.0	45.0	NM_003331	Q6QB10|Q96CH0	Silent	SNP	ENST00000525621.1	hg19	CCDS12236.1																																																																																			.	.		0.672	TYK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389443.1			A	10476357	G	A	10476357	2	1	255	1	0	0	0	0	0	0	0	1	16825	962	34	3		3	TYK2	19	10476357	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	344893	10476357	48652626	684	36029										
ILF3	3609	hgsc.bcm.edu	37	chr19	10793837	10793837	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggccgatcctgacaaagcacGgcaagaacccagtcatggag	12	12	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:10793837G>T	ENST00000590261.1	+	13	1573	c.1573G>T	c.(1573-1575)Ggc>Tgc	p.G525C	ILF3_ENST00000250241.8_Missense_Mutation_p.G525C|ILF3_ENST00000589998.1_Missense_Mutation_p.G525C|ILF3_ENST00000449870.1_Missense_Mutation_p.G529C|ILF3_ENST00000407004.3_Missense_Mutation_p.G529C|ILF3_ENST00000592763.1_Missense_Mutation_p.G529C|ILF3_ENST00000420083.1_Missense_Mutation_p.G525C|ILF3_ENST00000588657.1_Missense_Mutation_p.G529C|ILF3_ENST00000318511.3_Missense_Mutation_p.G525C			Q12906	ILF3_HUMAN	interleukin enhancer binding factor 3, 90kDa	525	DRBM 2. {ECO:0000255|PROSITE- ProRule:PRU00266}.				defense response to virus (GO:0051607)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|negative regulation of viral genome replication (GO:0045071)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31			Epithelial(33;6.86e-06)|all cancers(31;1.65e-05)			GACAAAGCACGGCAAGAACCC	0.552																																					p.G529C		Atlas-SNP	.											.	ILF3	99	.	0			c.G1585T						.						95	98	97					19																	10793837		2203	4300	6503	SO:0001583	missense	3609	exon14			AAGCACGGCAAGA	U10324	CCDS12246.1, CCDS12247.1, CCDS45965.1, CCDS45966.1, CCDS45967.1	19p13.2	2012-08-10	2002-08-29		ENSG00000129351	ENSG00000129351			6038	protein-coding gene	gene with protein product	"M-phase phosphoprotein 4"	603182	"interleukin enhancer binding factor 3, 90kD"			7519613, 8885239	Standard	NM_012218		Approved	NF90, MPHOSPH4, MPP4, DRBP76, NFAR-1	uc002mpo.3	Q12906		ENST00000590261.1:c.1573G>T	chr19.hg19:g.10793837G>T	ENSP00000468156:p.Gly525Cys	84.0	0.0		99.0	4.0	NM_017620	A8K6F2|G5E9M5|O43409|Q6P1X1|Q86XY7|Q99544|Q99545|Q9BZH4|Q9BZH5|Q9NQ95|Q9NQ96|Q9NQ97|Q9NQ98|Q9NQ99|Q9NQA0|Q9NQA1|Q9NQA2|Q9NRN2|Q9NRN3|Q9NRN4|Q9UMZ9|Q9UN00|Q9UN84|Q9UNA2	Missense_Mutation	SNP	ENST00000590261.1	hg19	CCDS12246.1	.	.	.	.	.	.	.	.	.	.	G	33	5.284864	0.95517	.	.	ENSG00000129351	ENST00000336059;ENST00000449870;ENST00000318511;ENST00000420083;ENST00000407004;ENST00000250241	T;T;T;T;T	0.19250	2.18;2.16;2.18;2.21;2.18	5.83	5.83	0.93111	Double-stranded RNA-binding (2);Double-stranded RNA-binding-like (1);	0.113792	0.64402	D	0.000011	T	0.54951	0.1890	M	0.87180	2.865	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.999;1.0	D;D;D;D;D;D	0.97110	1.0;0.995;0.995;0.994;0.973;0.987	T	0.60403	-0.7270	10	0.87932	D	0	.	18.8865	0.92379	0.0:0.0:1.0:0.0	.	529;529;525;529;525;525	Q12906-4;G5E9M5;Q12906;Q12906-6;Q12906-2;Q12906-5	.;.;ILF3_HUMAN;.;.;.	C	525;529;525;525;529;525	ENSP00000404121:G529C;ENSP00000315205:G525C;ENSP00000405436:G525C;ENSP00000384660:G529C;ENSP00000250241:G525C	ENSP00000250241:G525C	G	+	1	0	ILF3	10654837	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	9.771000	0.98977	2.761000	0.94854	0.650000	0.86243	GGC	.	.		0.552	ILF3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452074.1			T	10793837	G	T	10793837	3	4	255	1	0	0	0	0	1	0	0	0	7721	1116	39	1	1635	1	ILF3	19	10793837	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	317480	10793837	48335146	685	36030										
ZNF20	7568	hgsc.bcm.edu	37	chr19	12243683	12243683	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agtgtgtgtcctttcatgtaTatgcaaggaagagaaatacc	10	6	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:12243683T>C	ENST00000334213.5	-	4	1542	c.1318A>G	c.(1318-1320)Ata>Gta	p.I440V	ZNF20_ENST00000485451.1_5'Flank|ZNF625-ZNF20_ENST00000430024.1_3'UTR|ZNF20_ENST00000600335.1_Intron	NM_001203250.1|NM_021143.3	NP_001190179.1|NP_066966.2	P17024	ZNF20_HUMAN	zinc finger protein 20	440					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|lung(6)	8						CTTTCATGTATATGCAAGGAA	0.418																																					p.I440V		Atlas-SNP	.											.	ZNF20	86	.	0			c.A1318G						.						93	98	96					19																	12243683		2187	4295	6482	SO:0001583	missense	7568	exon4			CATGTATATGCAA	X52344	CCDS45986.1	19p13.2	2013-01-08	2006-05-10		ENSG00000132010	ENSG00000132010		"Zinc fingers, C2H2-type", "-"	12992	protein-coding gene	gene with protein product		194557	"zinc finger protein 20 (KOX 13)"				Standard	NM_021143		Approved	KOX13	uc002mtf.2	P17024	OTTHUMG00000156409	ENST00000334213.5:c.1318A>G	chr19.hg19:g.12243683T>C	ENSP00000335437:p.Ile440Val	75.0	0.0		89.0	4.0	NM_021143	Q8N457|Q9UG41	Missense_Mutation	SNP	ENST00000334213.5	hg19	CCDS45986.1	.	.	.	.	.	.	.	.	.	.	T	4.502	0.093141	0.08632	.	.	ENSG00000132010	ENST00000334213;ENST00000292241	T	0.07327	3.2	0.94	-0.317	0.12736	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03136	0.0092	N	0.04320	-0.23	0.09310	N	1	B	0.18461	0.028	B	0.20767	0.031	T	0.47560	-0.9108	9	0.19147	T	0.46	.	4.1968	0.10447	0.3019:0.0:0.0:0.6981	.	440	P17024	ZNF20_HUMAN	V	440	ENSP00000335437:I440V	ENSP00000292241:I440V	I	-	1	0	ZNF20	12104683	0.000000	0.05858	0.001000	0.08648	0.918000	0.54935	-7.956000	0.00027	-0.189000	0.10482	0.260000	0.18958	ATA	.	.		0.418	ZNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344101.1	NM_021143		C	12243683	T	C	12243683	3	2	255	1	0	0	0	0	1	0	0	0	17776	1406	49	2	284	2	ZNF20	19	12243683	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	1449846	12243683	46885300	686	36031										
LPHN1	22859	hgsc.bcm.edu	37	chr19	14273762	14273762	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcagctggctcaccaccagcCgcccgttgttgccctcagtg	10	17	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:14273762C>A	ENST00000340736.6	-	6	1163	c.866G>T	c.(865-867)cGg>cTg	p.R289L	CTB-55O6.12_ENST00000592086.1_RNA|CTB-55O6.12_ENST00000588387.1_RNA|LPHN1_ENST00000361434.3_Missense_Mutation_p.R284L|LPHN1_ENST00000591528.1_5'UTR	NM_001008701.2	NP_001008701.1	O94910	LPHN1_HUMAN	latrophilin 1	289	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|heterophilic cell-cell adhesion (GO:0007157)|neuropeptide signaling pathway (GO:0007218)|positive regulation of synapse maturation (GO:0090129)	axon (GO:0030424)|cell junction (GO:0030054)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)			central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						CACCACCAGCCGCCCGTTGTT	0.632																																					p.R289L		Atlas-SNP	.											.	LPHN1	107	.	0			c.G866T						.						88	63	71					19																	14273762		2203	4300	6503	SO:0001583	missense	22859	exon6			ACCAGCCGCCCGT	AB020628	CCDS12307.1, CCDS32928.1	19p13.2	2014-08-08				ENSG00000072071		"-", "GPCR / Class B : Orphans"	20973	protein-coding gene	gene with protein product						10994649	Standard	NM_014921		Approved	KIAA0821, CIRL1, LEC2	uc010xnn.2	O94910		ENST00000340736.6:c.866G>T	chr19.hg19:g.14273762C>A	ENSP00000340688:p.Arg289Leu	62.0	0.0		89.0	4.0	NM_001008701	Q96IE7|Q9BU07|Q9HAR3	Missense_Mutation	SNP	ENST00000340736.6	hg19	CCDS32928.1	.	.	.	.	.	.	.	.	.	.	C	33	5.194948	0.94960	.	.	ENSG00000072071	ENST00000340736;ENST00000361434	D;D	0.89050	-2.46;-2.46	5.27	5.27	0.74061	Olfactomedin-like (3);	0.000000	0.64402	D	0.000001	D	0.92067	0.7486	M	0.62016	1.91	0.80722	D	1	P;D	0.57571	0.888;0.98	P;P	0.56823	0.614;0.807	D	0.92831	0.6280	10	0.72032	D	0.01	.	16.3786	0.83431	0.0:1.0:0.0:0.0	.	284;289	O94910-2;O94910	.;LPHN1_HUMAN	L	289;284	ENSP00000340688:R289L;ENSP00000355328:R284L	ENSP00000340688:R289L	R	-	2	0	LPHN1	14134762	0.902000	0.30710	1.000000	0.80357	0.996000	0.88848	2.133000	0.42093	2.450000	0.82876	0.655000	0.94253	CGG	.	.		0.632	LPHN1-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459696.1	NM_014921		A	14273762	C	A	14273762	3	1	255	1	0	0	0	0	1	0	0	0	8924	652	23	1	3634	1	LPHN1	19	14273762	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	2030079	14273762	44855221	687	36032										
EMR3	84658	hgsc.bcm.edu	37	chr19	14765979	14765979	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgtccacaatcttttgcagcTttgaagacataaagaatttt	6	7	1	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:14765979T>A	ENST00000253673.5	-	6	494		c.e6-2		EMR3_ENST00000344373.4_Splice_Site|EMR3_ENST00000443157.2_Intron|EMR3_ENST00000599900.1_Intron	NM_032571.3	NP_115960.2	Q9BY15	EMR3_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 3						G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(14)|ovary(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	50						CTTTTGCAGCTTTGAAGACAT	0.378																																					.		Atlas-SNP	.											.	EMR3	99	.	0			c.394-2A>T						.						80	78	79					19																	14765979		2202	4299	6501	SO:0001630	splice_region_variant	84658	exon7			TGCAGCTTTGAAG	AF239764	CCDS12315.1, CCDS74296.1, CCDS74297.1	19p13.1	2014-08-08				ENSG00000131355		"-", "GPCR / Class B : Orphans"	23647	protein-coding gene	gene with protein product		606101				11279179, 12975309	Standard	XM_005260118		Approved		uc002mzi.4	Q9BY15		ENST00000253673.5:c.394-2A>T	chr19.hg19:g.14765979T>A		259.0	1.0		309.0	135.0	NM_032571		Splice_Site	SNP	ENST00000253673.5	hg19	CCDS12315.1	.	.	.	.	.	.	.	.	.	.	T	14.57	2.574356	0.45902	.	.	ENSG00000131355	ENST00000253673;ENST00000344373	.	.	.	2.99	2.99	0.34606	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.835	0.29365	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	EMR3	14626979	1.000000	0.71417	0.880000	0.34516	0.430000	0.31655	2.085000	0.41634	1.623000	0.50342	0.533000	0.62120	.	.	.		0.378	EMR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466488.1	NM_032571	Intron	A	14765979	T	A	14765979	5	1	255	1	0	0	0	0	0	0	1	0	5108	1623	56	4	1610	4	EMR3	19	14765979	Splice_Site	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	492217	14765979	44363004	688	36033										
ZNF333	84449	hgsc.bcm.edu	37	chr19	14815924	14815924	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	catagaagagagggagacacCattgactcgagaggaccggc	14	9	0	5			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:14815924C>T	ENST00000292530.6	+	6	456	c.365C>T	c.(364-366)cCa>cTa	p.P122L	ZNF333_ENST00000601134.1_Silent_p.T62T|ZNF333_ENST00000536363.1_Missense_Mutation_p.P13L|ZNF333_ENST00000540689.2_Missense_Mutation_p.P122L	NM_032433.2	NP_115809.1	Q96JL9	ZN333_HUMAN	zinc finger protein 333	122					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|pancreas(1)|prostate(1)	21						AGGGAGACACCATTGACTCGA	0.607																																					p.P122L	NSCLC(60;75 1281 16985 25154 29885)	Atlas-SNP	.											.	ZNF333	76	.	0			c.C365T						.						56	50	52					19																	14815924		2203	4300	6503	SO:0001583	missense	84449	exon6			AGACACCATTGAC		CCDS12316.1, CCDS74298.1	19p13	2013-01-08				ENSG00000160961		"Zinc fingers, C2H2-type", "-"	15624	protein-coding gene	gene with protein product		611811				12151103	Standard	XM_005260098		Approved	KIAA1806	uc002mzn.3	Q96JL9		ENST00000292530.6:c.365C>T	chr19.hg19:g.14815924C>T	ENSP00000292530:p.Pro122Leu	90.0	0.0		72.0	4.0	NM_032433	Q6P2E6|Q86WS6|Q8TDL0	Missense_Mutation	SNP	ENST00000292530.6	hg19	CCDS12316.1	.	.	.	.	.	.	.	.	.	.	C	13.01	2.108868	0.37242	.	.	ENSG00000160961	ENST00000392987;ENST00000536363;ENST00000540689;ENST00000292530	T;T;T	0.05855	3.38;5.9;3.42	1.94	-1.49	0.08718	.	.	.	.	.	T	0.03348	0.0097	N	0.24115	0.695	0.09310	N	1	B;B	0.10296	0.002;0.003	B;B	0.10450	0.003;0.005	T	0.48352	-0.9043	9	0.08179	T	0.78	.	5.0306	0.14407	0.0:0.4861:0.0:0.5139	.	122;122	Q96JL9;Q6P2E6	ZN333_HUMAN;.	L	122;13;122;122	ENSP00000439749:P13L;ENSP00000438130:P122L;ENSP00000292530:P122L	ENSP00000292530:P122L	P	+	2	0	ZNF333	14676924	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.162000	0.10012	-0.288000	0.09051	-0.929000	0.02709	CCA	.	.		0.607	ZNF333-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466496.1	NM_032433		T	14815924	C	T	14815924	3	4	255	1	0	0	0	0	1	0	0	0	17865	594	21	3	383	3	ZNF333	19	14815924	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	49945	14815924	44313059	689	36034										
FCHO1	23149	hgsc.bcm.edu	37	chr19	17892040	17892040	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctctttgtactcgctcctagAcctgatgcctgcacctgctg	8	15	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:17892040A>G	ENST00000596536.1	+	21	1911	c.1628A>G	c.(1627-1629)gAc>gGc	p.D543G	FCHO1_ENST00000389133.4_Splice_Site_p.D543G|FCHO1_ENST00000597512.1_Splice_Site_p.D550G|FCHO1_ENST00000252771.7_Splice_Site_p.D543G|FCHO1_ENST00000600676.1_Splice_Site_p.D543G|FCHO1_ENST00000539407.1_Splice_Site_p.D543G|FCHO1_ENST00000596951.1_Splice_Site_p.D543G|FCHO1_ENST00000594202.1_Splice_Site_p.D543G|FCHO1_ENST00000595033.1_Splice_Site_p.D493G	NM_015122.2	NP_055937.1	O14526	FCHO1_HUMAN	FCH domain only 1	543	Pro-rich.				clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)	coated pit (GO:0005905)|plasma membrane (GO:0005886)	AP-2 adaptor complex binding (GO:0035612)			NS(2)|breast(1)|large_intestine(6)|liver(1)|lung(12)	22						TCGCTCCTAGACCTGATGCCT	0.627																																					p.D543G		Atlas-SNP	.											.	FCHO1	69	.	0			c.A1628G						.						65	69	68					19																	17892040		2203	4300	6503	SO:0001630	splice_region_variant	23149	exon20			TCCTAGACCTGAT	AB006628	CCDS32955.1, CCDS59365.1, CCDS59366.1	19p13.12	2008-02-05				ENSG00000130475			29002	protein-coding gene	gene with protein product		613437				12477932	Standard	NM_001161357		Approved	KIAA0290	uc002nhg.3	O14526		ENST00000596536.1:c.1628-1A>G	chr19.hg19:g.17892040A>G		49.0	0.0		74.0	4.0	NM_001161358	A6NHE6|A8K5U5|B4E120|Q05C93|Q8IW22	Missense_Mutation	SNP	ENST00000596536.1	hg19	CCDS32955.1	.	.	.	.	.	.	.	.	.	.	A	10.12	1.262610	0.23051	.	.	ENSG00000130475	ENST00000252771;ENST00000389133;ENST00000539407	T;T;T	0.34667	1.35;1.35;1.35	4.68	4.68	0.58851	.	2.071930	0.02799	U	0.122929	T	0.36082	0.0954	L	0.44542	1.39	0.09310	N	0.999997	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.21999	-1.0229	9	.	.	.	.	10.4931	0.44762	1.0:0.0:0.0:0.0	.	543;543	O14526;O14526-2	FCHO1_HUMAN;.	G	543	ENSP00000252771:D543G;ENSP00000373785:D543G;ENSP00000437978:D543G	.	D	+	2	0	FCHO1	17753040	0.678000	0.27586	0.085000	0.20634	0.217000	0.24651	1.511000	0.35801	1.741000	0.51731	0.402000	0.26972	GAC	.	.		0.627	FCHO1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466946.2	NM_015122	Missense_Mutation	G	17892040	A	G	17892040	5	3	255	1	0	0	0	0	0	0	1	0	5795	289	10	2	1698	2	FCHO1	19	17892040	Splice_Site	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	3076116	17892040	41236943	690	36035										
SLC5A5	6528	hgsc.bcm.edu	37	chr19	17988895	17988895	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cctggggcgcatctctgcccCagaccaggtgagtcccaccc	11	18	1	2	rs149570759		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:17988895C>A	ENST00000222248.3	+	7	1309	c.962C>A	c.(961-963)cCa>cAa	p.P321Q		NM_000453.2	NP_000444.1	Q92911	SC5A5_HUMAN	solute carrier family 5 (sodium/iodide cotransporter), member 5	321					cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|iodide transport (GO:0015705)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	iodide transmembrane transporter activity (GO:0015111)|sodium:iodide symporter activity (GO:0008507)	p.P321L(1)		NS(2)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|skin(3)	31						ATCTCTGCCCCAGACCAGGTG	0.602																																					p.P321Q	Melanoma(65;1008 1708 7910 46650)	Atlas-SNP	.											SLC5A5,arm,malignant_melanoma,0,1	SLC5A5	67	.	1	Substitution - Missense(1)	skin(1)	c.C962A						.						64	52	56					19																	17988895		2203	4300	6503	SO:0001583	missense	6528	exon7			CTGCCCCAGACCA		CCDS12368.1	19p13.11	2013-07-19	2013-07-19		ENSG00000105641	ENSG00000105641		"Solute carriers"	11040	protein-coding gene	gene with protein product		601843	"solute carrier family 5 (sodium iodide symporter), member 5"			9231811	Standard	NM_000453		Approved	NIS	uc002nhr.4	Q92911		ENST00000222248.3:c.962C>A	chr19.hg19:g.17988895C>A	ENSP00000222248:p.Pro321Gln	36.0	0.0		35.0	4.0	NM_000453	O43702|Q2M335|Q9NYB6	Missense_Mutation	SNP	ENST00000222248.3	hg19	CCDS12368.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.344851	0.61073	.	.	ENSG00000105641	ENST00000222248	D	0.88124	-2.34	4.87	4.87	0.63330	.	0.172230	0.50627	D	0.000101	D	0.92309	0.7560	M	0.87097	2.86	0.80722	D	1	P	0.42078	0.77	P	0.52031	0.688	D	0.92576	0.6070	10	0.48119	T	0.1	.	15.607	0.76682	0.0:1.0:0.0:0.0	.	321	Q92911	SC5A5_HUMAN	Q	321	ENSP00000222248:P321Q	ENSP00000222248:P321Q	P	+	2	0	SLC5A5	17849895	0.988000	0.35896	0.983000	0.44433	0.145000	0.21501	5.721000	0.68477	2.557000	0.86248	0.555000	0.69702	CCA	.	.		0.602	SLC5A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466690.1			A	17988895	C	A	17988895	3	1	255	1	0	0	0	0	1	0	0	0	14683	594	21	3	988	3	SLC5A5	19	17988895	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	96855	17988895	41140088	691	36036										
UPF1	5976	hgsc.bcm.edu	37	chr19	18963017	18963017	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gccgcagcatgtcctcctgcGgtacgaggacgcctaccagt	12	15	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:18963017G>T	ENST00000599848.1	+	6	1093	c.884G>T	c.(883-885)cGg>cTg	p.R295L	UPF1_ENST00000262803.5_Missense_Mutation_p.R295L|UPF1_ENST00000600310.1_3'UTR			Q92900	RENT1_HUMAN	UPF1 regulator of nonsense transcripts homolog (yeast)	295	Sufficient for interaction with RENT2.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|dosage compensation by inactivation of X chromosome (GO:0009048)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translational termination (GO:0006449)|RNA metabolic process (GO:0016070)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	40						GTCCTCCTGCGGTACGAGGAC	0.607																																					p.R295L		Atlas-SNP	.											.	UPF1	88	.	0			c.G884T						.						88	77	81					19																	18963017		2203	4300	6503	SO:0001583	missense	5976	exon6			TCCTGCGGTACGA	AF074016	CCDS12386.1, CCDS74315.1	19p13.2-p13.11	2012-02-29	2006-02-07	2006-02-07	ENSG00000005007	ENSG00000005007			9962	protein-coding gene	gene with protein product	"UP Frameshift 1", "smg-2 homolog, nonsense mediated mRNA decay factor (C. elegans)"	601430	"regulator of nonsense transcripts 1"	RENT1		8855285, 9064659	Standard	XM_005260015		Approved	HUPF1, KIAA0221, NORF1, pNORF1, smg-2	uc002nkf.3	Q92900		ENST00000599848.1:c.884G>T	chr19.hg19:g.18963017G>T	ENSP00000470142:p.Arg295Leu	121.0	0.0		117.0	5.0	NM_002911	O00239|O43343|Q86Z25|Q92842	Missense_Mutation	SNP	ENST00000599848.1	hg19		.	.	.	.	.	.	.	.	.	.	G	23.6	4.432643	0.83776	.	.	ENSG00000005007	ENST00000262803	D	0.90324	-2.65	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	D	0.93400	0.7895	M	0.90425	3.115	0.80722	D	1	P;P	0.42871	0.689;0.792	B;B	0.43413	0.24;0.419	D	0.94873	0.8032	10	0.87932	D	0	-37.4037	17.4668	0.87634	0.0:0.0:1.0:0.0	.	295;295	Q92900;Q92900-2	RENT1_HUMAN;.	L	295	ENSP00000262803:R295L	ENSP00000262803:R295L	R	+	2	0	UPF1	18824017	1.000000	0.71417	0.822000	0.32727	0.390000	0.30446	9.429000	0.97481	2.362000	0.80069	0.561000	0.74099	CGG	.	.		0.607	UPF1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000464684.1	NM_002911		T	18963017	G	T	18963017	3	4	255	1	0	0	0	0	1	0	0	0	17018	1116	39	1	906	1	UPF1	19	18963017	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	974122	18963017	40165966	692	36037										
NCAN	1463	hgsc.bcm.edu	37	chr19	19359573	19359573	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggtgcccgcaaggccaagtaCaatgtccatgccactgtaag	11	12	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:19359573C>A	ENST00000252575.6	+	14	3801	c.3702C>A	c.(3700-3702)taC>taA	p.Y1234*	NCAN_ENST00000538881.1_Nonsense_Mutation_p.Y685*	NM_004386.2	NP_004377.2	O14594	NCAN_HUMAN	neurocan	1234	Sushi. {ECO:0000255|PROSITE- ProRule:PRU00302}.			Y -> N (in Ref. 1; AAC80576). {ECO:0000305}.	axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|regulation of synapse structural plasticity (GO:0051823)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(32)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64			Epithelial(12;0.00544)		Hyaluronan(DB08818)	AGGCCAAGTACAATGTCCATG	0.577																																					p.Y1234X		Atlas-SNP	.											.	NCAN	277	.	0			c.C3702A						.						130	90	104					19																	19359573		2203	4300	6503	SO:0001587	stop_gained	1463	exon14			CAAGTACAATGTC	AF026547	CCDS12397.1	19p12	2014-01-30	2007-02-15	2007-02-15	ENSG00000130287	ENSG00000130287		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans", "Endogenous ligands"	2465	protein-coding gene	gene with protein product	"neurocan proteoglycan"	600826	"chondroitin sulfate proteoglycan 3"	CSPG3		1326557, 21353194	Standard	NM_004386		Approved		uc002nlz.3	O14594		ENST00000252575.6:c.3702C>A	chr19.hg19:g.19359573C>A	ENSP00000252575:p.Tyr1234*	129.0	0.0		126.0	60.0	NM_004386	Q9UPK6	Nonsense_Mutation	SNP	ENST00000252575.6	hg19	CCDS12397.1	.	.	.	.	.	.	.	.	.	.	C	36	5.830964	0.97003	.	.	ENSG00000130287	ENST00000539499;ENST00000252575;ENST00000538881	.	.	.	4.54	0.94	0.19513	.	0.273768	0.19634	N	0.109617	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.0681	0.25164	0.0:0.6342:0.0:0.3658	.	.	.	.	X	1248;1234;685	.	ENSP00000252575:Y1234X	Y	+	3	2	NCAN	19220573	0.974000	0.33945	0.989000	0.46669	0.867000	0.49689	0.350000	0.20079	0.056000	0.16144	-0.293000	0.09583	TAC	.	.		0.577	NCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460111.2	NM_004386		A	19359573	C	A	19359573	4	1	255	1	0	0	0	0	0	1	0	0	10213	489	17	3	3752	3	NCAN	19	19359573	Nonsense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	396556	19359573	39769410	693	36038										
ZNF737	100129842	hgsc.bcm.edu	37	chr19	20727871	20727871	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgtagtaaggtgtgaggaccAgttgaaggctttgccacatt	13	6	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:20727871A>G	ENST00000427401.4	-	4	1232	c.1138T>C	c.(1138-1140)Tgg>Cgg	p.W380R		NM_001159293.1	NP_001152765.1	O75373	ZN737_HUMAN	zinc finger protein 737	380					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|kidney(1)|lung(7)|ovary(1)|stomach(1)|urinary_tract(1)	13						TGTGAGGACCAGTTGAAGGCT	0.418																																					p.W380R		Atlas-SNP	.											ZNF737,NS,carcinoma,+1,1	ZNF737	50	.	0			c.T1138C						.						44	42	43					19																	20727871		692	1591	2283	SO:0001583	missense	100129842	exon4			AGGACCAGTTGAA	BC015765	CCDS54238.1	19p12	2013-01-08						"Zinc fingers, C2H2-type", "-"	32468	protein-coding gene	gene with protein product		603984					Standard	NM_001159293		Approved	ZNF102	uc002npa.3	O75373		ENST00000427401.4:c.1138T>C	chr19.hg19:g.20727871A>G	ENSP00000395733:p.Trp380Arg	49.0	0.0		50.0	2.0	NM_001159293	C9JHM3	Missense_Mutation	SNP	ENST00000427401.4	hg19	CCDS54238.1	.	.	.	.	.	.	.	.	.	.	N	0.003	-2.411008	0.00191	.	.	ENSG00000237440	ENST00000427401	T	0.07327	3.2	0.801	0.801	0.18679	.	.	.	.	.	T	0.01523	0.0049	N	0.00155	-1.965	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.47071	-0.9145	9	0.13108	T	0.6	.	5.4149	0.16368	1.0:0.0:0.0:0.0	.	380	C9JHM3	.	R	380	ENSP00000395733:W380R	ENSP00000395733:W380R	W	-	1	0	ZNF737	20519711	0.000000	0.05858	0.789000	0.31954	0.791000	0.44710	-4.572000	0.00214	0.147000	0.19030	0.145000	0.16022	TGG	.	.		0.418	ZNF737-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447844.2	NM_145289		G	20727871	A	G	20727871	3	3	255	1	0	0	0	0	1	0	0	0	18141	188	7	2	476	2	ZNF737	19	20727871	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	1368298	20727871	38401112	694	36039										
ZNF99	7652	hgsc.bcm.edu	37	chr19	22940398	22940398	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tttctaagggctgagaaatgCttaaaagctttgccacattc	8	8	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:22940398C>T	ENST00000596209.1	-	4	2403	c.2313G>A	c.(2311-2313)aaG>aaA	p.K771K	CTC-451A6.4_ENST00000442497.2_lincRNA|ZNF99_ENST00000397104.3_Silent_p.K680K	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	771					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				CTGAGAAATGCTTAAAAGCTT	0.358																																					p.K771K		Atlas-SNP	.											ZNF99,NS,carcinoma,0,1	ZNF99	273	.	0			c.G2313A						.						30	32	32					19																	22940398		1951	4133	6084	SO:0001819	synonymous_variant	7652	exon4			GAAATGCTTAAAA	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"Zinc fingers, C2H2-type", "-"	13175	protein-coding gene	gene with protein product		603981	"zinc finger protein 99 (F8281)", "chromosome 19 open reading frame 9"	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.2313G>A	chr19.hg19:g.22940398C>T		32.0	0.0		44.0	3.0	NM_001080409	M0R335	Silent	SNP	ENST00000596209.1	hg19	CCDS59369.1																																																																																			.	.		0.358	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124		T	22940398	C	T	22940398	2	4	255	1	0	0	0	0	0	0	0	1	18219	796	28	3		3	ZNF99	19	22940398	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	2212527	22940398	36188585	695	36040										
ANKRD27	84079	hgsc.bcm.edu	37	chr19	33140643	33140643	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gtatcaaaatgtaggactcaAactgacaagtagactggatg	10	6	2	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:33140643A>G	ENST00000306065.4	-	3	316	c.158T>C	c.(157-159)tTt>tCt	p.F53S	ANKRD27_ENST00000587352.1_Missense_Mutation_p.F53S	NM_032139.2	NP_115515.2	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)	53					early endosome to late endosome transport (GO:0045022)|positive regulation of GTPase activity (GO:0043547)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|lysosome (GO:0005764)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			breast(3)|endometrium(7)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	42	Esophageal squamous(110;0.137)					GTAGGACTCAAACTGACAAGT	0.448																																					p.F53S		Atlas-SNP	.											.	ANKRD27	86	.	0			c.T158C						.						163	167	165					19																	33140643		2203	4300	6503	SO:0001583	missense	84079	exon3			GACTCAAACTGAC	AK054561	CCDS32986.1	19q13.12	2013-01-10				ENSG00000105186		"Ankyrin repeat domain containing"	25310	protein-coding gene	gene with protein product	"Vps9 domain and ankyrin-repeat-containing protein"					11230166, 16525121	Standard	NM_032139		Approved	FLJ00040, DKFZp434L0718, VARP	uc002ntn.1	Q96NW4		ENST00000306065.4:c.158T>C	chr19.hg19:g.33140643A>G	ENSP00000304292:p.Phe53Ser	72.0	0.0		99.0	4.0	NM_032139	Q71MF5|Q86UC3|Q8ND80|Q9H0I4	Missense_Mutation	SNP	ENST00000306065.4	hg19	CCDS32986.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.030480	0.75504	.	.	ENSG00000105186	ENST00000306065	T	0.69926	-0.44	6.16	6.16	0.99307	.	0.000000	0.64402	D	0.000018	T	0.81654	0.4868	M	0.70275	2.135	0.48511	D	0.999661	D	0.89917	1.0	D	0.87578	0.998	T	0.83295	-0.0031	10	0.87932	D	0	-26.6583	16.8061	0.85666	1.0:0.0:0.0:0.0	.	53	Q96NW4	ANR27_HUMAN	S	53	ENSP00000304292:F53S	ENSP00000304292:F53S	F	-	2	0	ANKRD27	37832483	1.000000	0.71417	1.000000	0.80357	0.432000	0.31715	6.248000	0.72418	2.367000	0.80283	0.528000	0.53228	TTT	.	.		0.448	ANKRD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450329.1	NM_032139		G	33140643	A	G	33140643	3	3	255	1	0	0	0	0	1	0	0	0	655	14	1	2	3102	2	ANKRD27	19	33140643	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	10200245	33140643	25988340	696	36041										
RHPN2	85415	hgsc.bcm.edu	37	chr19	33498926	33498926	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tggaggagacatacctgcggCtctctgaaaggcatctatgg	13	9	2	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:33498926C>A	ENST00000254260.3	-	7	789	c.754G>T	c.(754-756)Gcc>Tcc	p.A252S	RHPN2_ENST00000400226.4_Missense_Mutation_p.A101S	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	252	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(5)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(3)|skin(3)|urinary_tract(1)	44	Esophageal squamous(110;0.137)					ATACCTGCGGCTCTCTGAAAG	0.622																																					p.A252S		Atlas-SNP	.											.	RHPN2	107	.	0			c.G754T						.						30	26	27					19																	33498926		2203	4299	6502	SO:0001583	missense	85415	exon7			CTGCGGCTCTCTG	AF268032	CCDS12427.1	19q13.12	2008-02-05				ENSG00000131941			19974	protein-coding gene	gene with protein product						12221077	Standard	NM_033103		Approved		uc002nuf.3	Q8IUC4		ENST00000254260.3:c.754G>T	chr19.hg19:g.33498926C>A	ENSP00000254260:p.Ala252Ser	118.0	0.0		159.0	60.0	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	hg19	CCDS12427.1	.	.	.	.	.	.	.	.	.	.	C	12.69	2.013648	0.35511	.	.	ENSG00000131941	ENST00000254260;ENST00000400226	T;T	0.32023	1.47;1.47	4.21	4.21	0.49690	BRO1 domain (3);	0.163049	0.53938	D	0.000056	T	0.29976	0.0750	L	0.48362	1.52	0.53688	D	0.99997	P	0.36577	0.558	B	0.37267	0.245	T	0.08269	-1.0730	10	0.28530	T	0.3	-15.1431	16.9558	0.86259	0.0:1.0:0.0:0.0	.	252	Q8IUC4	RHPN2_HUMAN	S	252;101	ENSP00000254260:A252S;ENSP00000402244:A101S	ENSP00000254260:A252S	A	-	1	0	RHPN2	38190766	1.000000	0.71417	1.000000	0.80357	0.337000	0.28794	4.743000	0.62110	2.079000	0.62486	0.455000	0.32223	GCC	.	.		0.622	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103		A	33498926	C	A	33498926	3	1	255	1	0	0	0	0	1	0	0	0	13366	797	28	3	1342	3	RHPN2	19	33498926	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	358283	33498926	25630057	697	36042										
LSR	51599	hgsc.bcm.edu	37	chr19	35757273	35757273	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcctcacagtgtatgccgccGgcaaagcagccacctcaggt	10	15	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:35757273G>T	ENST00000361790.3	+	6	1093	c.934G>T	c.(934-936)Ggc>Tgc	p.G312C	LSR_ENST00000347609.4_Missense_Mutation_p.G275C|LSR_ENST00000354900.3_Missense_Mutation_p.G293C|USF2_ENST00000379134.3_5'Flank|USF2_ENST00000222305.3_5'Flank|LSR_ENST00000602122.1_Missense_Mutation_p.G293C|LSR_ENST00000360798.3_Missense_Mutation_p.G244C|USF2_ENST00000595068.1_5'Flank|AD000684.2_ENST00000602262.1_RNA|LSR_ENST00000427250.1_Missense_Mutation_p.G156C|USF2_ENST00000594064.1_5'Flank|USF2_ENST00000343550.5_5'Flank	NM_205834.3	NP_991403.1	Q86X29	LSR_HUMAN	lipolysis stimulated lipoprotein receptor	312					embryo development (GO:0009790)|liver development (GO:0001889)	chylomicron (GO:0042627)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|low-density lipoprotein particle (GO:0034362)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	13	all_lung(56;3.91e-09)|Lung NSC(56;5.64e-09)|Esophageal squamous(110;0.162)		Epithelial(14;1.33e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.29e-18)|all cancers(14;7.11e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			GTATGCCGCCGGCAAAGCAGC	0.617																																					p.G312C		Atlas-SNP	.											.	LSR	60	.	0			c.G934T						.						85	86	85					19																	35757273		2203	4300	6503	SO:0001583	missense	51599	exon6			GCCGCCGGCAAAG	AF130366	CCDS12449.1, CCDS12450.1, CCDS12451.1, CCDS59376.1	19q13.12	2013-01-11			ENSG00000105699	ENSG00000105699		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29572	protein-coding gene	gene with protein product	"lipolysis-stimulated remnant", "immunoglobulin-like domain containing receptor 3"					10224102	Standard	NM_015925		Approved	LISCH7, ILDR3	uc002nyl.3	Q86X29		ENST00000361790.3:c.934G>T	chr19.hg19:g.35757273G>T	ENSP00000354575:p.Gly312Cys	105.0	0.0		98.0	4.0	NM_205834	A6NDW3|B4DKL4|E9PHD4|O00112|O00426|Q6ZT80|Q8NBM0|Q9BT33|Q9UQL3	Missense_Mutation	SNP	ENST00000361790.3	hg19	CCDS12450.1	.	.	.	.	.	.	.	.	.	.	G	18.79	3.698566	0.68386	.	.	ENSG00000105699	ENST00000361790;ENST00000354900;ENST00000360798;ENST00000347609;ENST00000427250	T;T;T;T;T	0.73681	-0.04;0.05;-0.51;0.07;-0.77	3.99	3.99	0.46301	.	0.000000	0.85682	D	0.000000	D	0.82337	0.5015	L	0.53249	1.67	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;0.996	D	0.84456	0.0591	10	0.87932	D	0	-27.9253	13.6187	0.62123	0.0:0.0:1.0:0.0	.	250;275;293;244;293;312	Q9BT33;Q86X29-2;Q86X29-3;A6NDW3;E9PHD4;Q86X29	.;.;.;.;.;LSR_HUMAN	C	312;293;244;275;156	ENSP00000354575:G312C;ENSP00000346976:G293C;ENSP00000354034:G244C;ENSP00000262627:G275C;ENSP00000394479:G156C	ENSP00000262627:G275C	G	+	1	0	LSR	40449113	1.000000	0.71417	0.937000	0.37676	0.716000	0.41182	7.524000	0.81866	2.025000	0.59659	0.462000	0.41574	GGC	.	.		0.617	LSR-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465513.2	NM_015925		T	35757273	G	T	35757273	3	4	255	1	0	0	0	0	1	0	0	0	9073	1116	39	1	956	1	LSR	19	35757273	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	2258347	35757273	23371710	698	36043										
GAPDHS	26330	hgsc.bcm.edu	37	chr19	36033226	36033226	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gccacttccccacagcaaagAgcccaaacagatcccctgga	7	17	0	2	rs148474705	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:36033226A>G	ENST00000222286.4	+	5	571	c.455A>G	c.(454-456)gAg>gGg	p.E152G	AD000090.2_ENST00000590717.1_RNA|AD000090.2_ENST00000588286.1_RNA|AD000090.2_ENST00000590125.1_RNA|AD000090.2_ENST00000444728.1_RNA|AD000090.2_ENST00000589137.1_RNA	NM_014364.4	NP_055179.1	O14556	G3PT_HUMAN	glyceraldehyde-3-phosphate dehydrogenase, spermatogenic	152					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|positive regulation of glycolytic process (GO:0045821)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	cytosol (GO:0005829)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity (GO:0004365)|NAD binding (GO:0051287)|NADP binding (GO:0050661)			endometrium(1)|kidney(1)|large_intestine(1)|lung(8)	11	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			CACAGCAAAGAGCCCAAACAG	0.597																																					p.E152G		Atlas-SNP	.											.	GAPDHS	34	.	0			c.A455G						.						47	46	46					19																	36033226		2203	4300	6503	SO:0001583	missense	26330	exon5			GCAAAGAGCCCAA	AJ005371	CCDS12465.1	19q13.1	2008-02-05		2005-05-06		ENSG00000105679			24864	protein-coding gene	gene with protein product		609169		GAPDS		10714828	Standard	NM_014364		Approved	GAPDH-2, GAPD2	uc002oaf.1	O14556		ENST00000222286.4:c.455A>G	chr19.hg19:g.36033226A>G	ENSP00000222286:p.Glu152Gly	82.0	0.0		121.0	5.0	NM_014364	B2RC82|O60823|Q6JTT9|Q9HCU6	Missense_Mutation	SNP	ENST00000222286.4	hg19	CCDS12465.1	.	.	.	.	.	.	.	.	.	.	A	10.11	1.260585	0.23051	.	.	ENSG00000105679	ENST00000222286	T	0.39997	1.05	4.47	2.27	0.28462	Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain (2);NAD(P)-binding domain (1);	0.565559	0.18952	N	0.126644	T	0.32010	0.0815	L	0.39633	1.23	0.25093	N	0.990842	B	0.29212	0.237	B	0.33042	0.157	T	0.29792	-1.0000	10	0.87932	D	0	-4.4196	5.0327	0.14419	0.6245:0.1917:0.0:0.1838	.	152	O14556	G3PT_HUMAN	G	152	ENSP00000222286:E152G	ENSP00000222286:E152G	E	+	2	0	GAPDHS	40725066	0.997000	0.39634	0.965000	0.40720	0.028000	0.11728	4.661000	0.61518	0.294000	0.22547	-0.648000	0.03929	GAG	.	A|0.999;C|0.001		0.597	GAPDHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460423.1	NM_014364		G	36033226	A	G	36033226	3	3	255	1	0	0	0	0	1	0	0	0	6245	304	11	2	473	2	GAPDHS	19	36033226	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	275953	36033226	23095757	699	36044										
ZFP82	284406	hgsc.bcm.edu	37	chr19	36884281	36884281	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tactctaagaccagagccacAcaaaaaggccttcccacatt	5	14	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:36884281A>G	ENST00000392161.3	-	5	1203	c.961T>C	c.(961-963)Tgt>Cgt	p.C321R	ZFP82_ENST00000392171.1_Missense_Mutation_p.C321R	NM_133466.2	NP_597723.1	Q8N141	ZFP82_HUMAN	ZFP82 zinc finger protein	321					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						CCAGAGCCACACAAAAAGGCC	0.453																																					p.C321R		Atlas-SNP	.											.	ZFP82	71	.	0			c.T961C						.						116	116	116					19																	36884281		2203	4300	6503	SO:0001583	missense	284406	exon5			AGCCACACAAAAA	AL834267	CCDS12493.1	19q13.13	2013-01-08	2012-11-27	2008-07-01		ENSG00000181007		"Zinc fingers, C2H2-type", "-"	28682	protein-coding gene	gene with protein product			"zinc finger protein 545", "zinc finger protein 82 homolog (mouse)", "zinc finger protein 82"	ZNF545		11853319	Standard	NM_133466		Approved	MGC45380, KIAA1948	uc002ody.1	Q8N141		ENST00000392161.3:c.961T>C	chr19.hg19:g.36884281A>G	ENSP00000431265:p.Cys321Arg	92.0	0.0		117.0	5.0	NM_133466	Q8NC63|Q8TF53	Missense_Mutation	SNP	ENST00000392161.3	hg19	CCDS12493.1	.	.	.	.	.	.	.	.	.	.	A	9.204	1.029132	0.19512	.	.	ENSG00000181007	ENST00000392161;ENST00000392171	T;T	0.07216	3.21;3.21	4.38	4.38	0.52667	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.45361	D	0.000370	T	0.03095	0.0091	N	0.01009	-1.055	0.20873	N	0.99984	B	0.32324	0.364	B	0.37943	0.261	T	0.45644	-0.9247	10	0.22109	T	0.4	.	8.5849	0.33653	0.8282:0.0:0.0:0.1718	.	321	Q8N141	ZFP82_HUMAN	R	321	ENSP00000431265:C321R;ENSP00000446080:C321R	ENSP00000431265:C321R	C	-	1	0	ZFP82	41576121	0.000000	0.05858	1.000000	0.80357	0.988000	0.76386	-0.554000	0.06006	1.977000	0.57605	0.533000	0.62120	TGT	.	.		0.453	ZFP82-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109552.2	NM_133466		G	36884281	A	G	36884281	3	3	255	1	0	0	0	0	1	0	0	0	17668	159	6	2	641	2	ZFP82	19	36884281	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	851055	36884281	22244702	700	36045										
FAM98C	147965	hgsc.bcm.edu	37	chr19	38897603	38897603	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccaattcgagaggttctgacCccagaatcggacatctccat	8	13	2	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:38897603C>A	ENST00000252530.5	+	7	823	c.804C>A	c.(802-804)acC>acA	p.T268T	FAM98C_ENST00000343358.7_Intron|FAM98C_ENST00000588262.1_Missense_Mutation_p.P135T	NM_174905.3	NP_777565.3	Q17RN3	FA98C_HUMAN	family with sequence similarity 98, member C	268										endometrium(2)|large_intestine(3)|lung(6)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	15	all_cancers(60;3.95e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			AGGTTCTGACCCCAGAATCGG	0.617																																					p.T268T		Atlas-SNP	.											.	FAM98C	39	.	0			c.C804A						.						116	119	118					19																	38897603		2025	4178	6203	SO:0001819	synonymous_variant	147965	exon7			TCTGACCCCAGAA		CCDS42562.1	19q13.2	2008-02-05				ENSG00000130244			27119	protein-coding gene	gene with protein product						12477932	Standard	NM_174905		Approved	FLJ44669	uc002oin.1	Q17RN3		ENST00000252530.5:c.804C>A	chr19.hg19:g.38897603C>A		80.0	0.0		96.0	5.0	NM_174905	A6NMW3|Q66K45	Silent	SNP	ENST00000252530.5	hg19	CCDS42562.1																																																																																			.	.		0.617	FAM98C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459222.1	NM_174905		A	38897603	C	A	38897603	2	1	255	1	0	0	0	0	0	0	0	1	5666	610	22	3		3	FAM98C	19	38897603	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	2013322	38897603	20231380	701	36046										
RYR1	6261	hgsc.bcm.edu	37	chr19	38948829	38948829	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cgggtgggctgggccctcacCgagggctacaccccctaccc	13	18	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:38948829C>A	ENST00000359596.3	+	18	2064	c.2064C>A	c.(2062-2064)acC>acA	p.T688T	RYR1_ENST00000360985.3_Silent_p.T688T|RYR1_ENST00000355481.4_Silent_p.T688T			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	688	B30.2/SPRY 1. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.T688T(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GGGCCCTCACCGAGGGCTACA	0.627																																					p.T688T		Atlas-SNP	.											RYR1,right_upper_lobe,carcinoma,0,2	RYR1	708	.	1	Substitution - coding silent(1)	lung(1)	c.C2064A						.						56	52	53					19																	38948829		2203	4300	6503	SO:0001819	synonymous_variant	6261	exon18			CCTCACCGAGGGC	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.2064C>A	chr19.hg19:g.38948829C>A		31.0	0.0		43.0	2.0	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	hg19	CCDS33011.1																																																																																			.	.		0.627	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			A	38948829	C	A	38948829	2	1	255	1	0	0	0	0	0	0	0	1	13783	639	23	1		1	RYR1	19	38948829	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	51226	38948829	20180154	702	36047										
PLEKHG2	64857	hgsc.bcm.edu	37	chr19	39907025	39907025	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tggagaacagcagcagcgccGggggtattgccgagtgcttc	16	10	0	1	rs138517241		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:39907025G>T	ENST00000409794.3	+	5	1367	c.517G>T	c.(517-519)Ggg>Tgg	p.G173W	PLEKHG2_ENST00000409797.2_Missense_Mutation_p.G173W|PLEKHG2_ENST00000378550.1_Missense_Mutation_p.G173W|PLEKHG2_ENST00000425673.1_Missense_Mutation_p.G173W|PLEKHG2_ENST00000458508.2_Missense_Mutation_p.G114W	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	173	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|pancreas(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			CAGCAGCGCCGGGGGTATTGC	0.667																																					p.G173W		Atlas-SNP	.											.	PLEKHG2	329	.	0			c.G517T						.	G	TRP/GLY	0,4406		0,0,2203	67	76	73		517	3.6	0.9	19	dbSNP_134	73	3,8597	3.0+/-9.4	0,3,4297	yes	missense	PLEKHG2	NM_022835.2	184	0,3,6500	TT,TG,GG		0.0349,0.0,0.0231	probably-damaging	173/1387	39907025	3,13003	2203	4300	6503	SO:0001583	missense	64857	exon5			AGCGCCGGGGGTA	AK024429	CCDS33022.2	19q13.2	2013-01-11			ENSG00000090924	ENSG00000090924		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	29515	protein-coding gene	gene with protein product		611893				11839748, 18045877	Standard	NM_022835		Approved	CLG, FLJ00018, ARHGEF42	uc010xuz.2	Q9H7P9	OTTHUMG00000152570	ENST00000409794.3:c.517G>T	chr19.hg19:g.39907025G>T	ENSP00000386733:p.Gly173Trp	125.0	0.0		100.0	4.0	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Missense_Mutation	SNP	ENST00000409794.3	hg19	CCDS33022.2	.	.	.	.	.	.	.	.	.	.	G	19.01	3.742926	0.69418	0.0	3.49E-4	ENSG00000090924	ENST00000409794;ENST00000425673;ENST00000378550;ENST00000458508;ENST00000409797;ENST00000451354	T;T;T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05;-0.05;1.67	4.68	3.59	0.41128	Dbl homology (DH) domain (5);	0.224873	0.29106	N	0.013135	T	0.72415	0.3457	L	0.58354	1.805	0.39894	D	0.9738	D;D;D	0.76494	0.999;0.997;0.964	D;D;P	0.76071	0.986;0.987;0.883	T	0.73202	-0.4057	10	0.46703	T	0.11	.	11.1867	0.48660	0.0:0.3533:0.6467:0.0	.	173;114;173	Q9H7P9;E7ESZ3;Q9H7P9-2	PKHG2_HUMAN;.;.	W	173;173;173;114;173;174	ENSP00000386733:G173W;ENSP00000392906:G173W;ENSP00000367812:G173W;ENSP00000408857:G114W;ENSP00000386492:G173W;ENSP00000412818:G174W	ENSP00000367812:G173W	G	+	1	0	PLEKHG2	44598865	0.979000	0.34478	0.948000	0.38648	0.814000	0.46013	3.584000	0.53936	2.452000	0.82932	0.491000	0.48974	GGG	.	G|1.000;T|0.000		0.667	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835		T	39907025	G	T	39907025	3	4	255	1	0	0	0	0	1	0	0	0	12078	1116	39	1	531	1	PLEKHG2	19	39907025	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	958196	39907025	19221958	703	36048										
PLEKHG2	64857	hgsc.bcm.edu	37	chr19	39907052	39907052	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttgccgagtgcttcgtgcagAgggtgagtggaggggtgggg	22	5	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:39907052A>G	ENST00000409794.3	+	5	1394	c.544A>G	c.(544-546)Agg>Ggg	p.R182G	PLEKHG2_ENST00000409797.2_Missense_Mutation_p.R182G|PLEKHG2_ENST00000378550.1_Missense_Mutation_p.R182G|PLEKHG2_ENST00000425673.1_Missense_Mutation_p.R182G|PLEKHG2_ENST00000458508.2_Missense_Mutation_p.R123G	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	182	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|pancreas(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			CTTCGTGCAGAGGGTGAGTGG	0.672																																					p.R182G		Atlas-SNP	.											.	PLEKHG2	329	.	0			c.A544G						.						51	59	56					19																	39907052		2203	4299	6502	SO:0001583	missense	64857	exon5			GTGCAGAGGGTGA	AK024429	CCDS33022.2	19q13.2	2013-01-11			ENSG00000090924	ENSG00000090924		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	29515	protein-coding gene	gene with protein product		611893				11839748, 18045877	Standard	NM_022835		Approved	CLG, FLJ00018, ARHGEF42	uc010xuz.2	Q9H7P9	OTTHUMG00000152570	ENST00000409794.3:c.544A>G	chr19.hg19:g.39907052A>G	ENSP00000386733:p.Arg182Gly	83.0	0.0		97.0	4.0	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Missense_Mutation	SNP	ENST00000409794.3	hg19	CCDS33022.2	.	.	.	.	.	.	.	.	.	.	A	20.4	3.987110	0.74589	.	.	ENSG00000090924	ENST00000409794;ENST00000425673;ENST00000378550;ENST00000458508;ENST00000409797;ENST00000451354	T;T;T;T;T;T	0.68624	-0.34;-0.34;-0.34;-0.34;-0.34;1.52	4.68	2.53	0.30540	Dbl homology (DH) domain (5);	0.000000	0.64402	D	0.000008	T	0.79953	0.4535	M	0.80028	2.48	0.36209	D	0.851219	D;P;P	0.71674	0.998;0.953;0.942	D;D;P	0.80764	0.994;0.945;0.693	T	0.83170	-0.0094	10	0.72032	D	0.01	.	10.7161	0.46013	0.6954:0.3046:0.0:0.0	.	182;123;182	Q9H7P9;E7ESZ3;Q9H7P9-2	PKHG2_HUMAN;.;.	G	182;182;182;123;182;183	ENSP00000386733:R182G;ENSP00000392906:R182G;ENSP00000367812:R182G;ENSP00000408857:R123G;ENSP00000386492:R182G;ENSP00000412818:R183G	ENSP00000367812:R182G	R	+	1	2	PLEKHG2	44598892	0.996000	0.38824	1.000000	0.80357	0.956000	0.61745	2.022000	0.41030	0.282000	0.22254	-0.680000	0.03767	AGG	.	.		0.672	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835		G	39907052	A	G	39907052	3	3	255	1	0	0	0	0	1	0	0	0	12078	295	11	2	558	2	PLEKHG2	19	39907052	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	27	39907052	19221931	704	36049										
CYP2B6	1555	hgsc.bcm.edu	37	chr19	41518302	41518302	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cacagaggcagtcatctatgAgattcagagattttccgacc	9	10	3	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:41518302A>G	ENST00000324071.4	+	7	1071	c.1064A>G	c.(1063-1065)gAg>gGg	p.E355G	CYP2B6_ENST00000330446.5_Missense_Mutation_p.E155G|CYP2B6_ENST00000593831.1_Missense_Mutation_p.E119G	NM_000767.4	NP_000758.1	P20813	CP2B6_HUMAN	cytochrome P450, family 2, subfamily B, polypeptide 6	355					cellular ketone metabolic process (GO:0042180)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			NS(1)|breast(1)|endometrium(5)|kidney(1)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	28			LUSC - Lung squamous cell carcinoma(20;0.00322)		Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Antipyrine(DB01435)|Artemether(DB06697)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzphetamine(DB00865)|Benzyl alcohol(DB06770)|Bifonazole(DB04794)|Brompheniramine(DB00835)|Bupropion(DB01156)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Cholecalciferol(DB00169)|Cinnarizine(DB00568)|Cisapride(DB00604)|Cisplatin(DB00515)|Citalopram(DB00215)|Clobazam(DB00349)|Clofibrate(DB00636)|Clopidogrel(DB00758)|Clotiazepam(DB01559)|Clotrimazole(DB00257)|Colchicine(DB01394)|Cyclophosphamide(DB00531)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diphenhydramine(DB01075)|Domperidone(DB01184)|Doxorubicin(DB00997)|Efavirenz(DB00625)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erythromycin(DB00199)|Estrone(DB00655)|Ethanol(DB00898)|Ethylmorphine(DB01466)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluoxetine(DB00472)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Fosphenytoin(DB01320)|Halothane(DB01159)|Ifosfamide(DB01181)|Imipramine(DB00458)|Irinotecan(DB00762)|Isoflurane(DB00753)|Itraconazole(DB01167)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Lidocaine(DB00281)|Loperamide(DB00836)|Lopinavir(DB01601)|Lorcaserin(DB04871)|Malathion(DB00772)|Memantine(DB01043)|Methadone(DB00333)|Methimazole(DB00763)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyltestosterone(DB06710)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midazolam(DB00683)|Modafinil(DB00745)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitric Oxide(DB00435)|Orphenadrine(DB01173)|Ospemifene(DB04938)|Paroxetine(DB00715)|Perhexiline(DB01074)|Permethrin(DB04930)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Prasugrel(DB06209)|Primidone(DB00794)|Promethazine(DB01069)|Propofol(DB00818)|Quinidine(DB00908)|Raloxifene(DB00481)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Ropivacaine(DB00296)|Roxithromycin(DB00778)|Selegiline(DB01037)|Sertraline(DB01104)|Sevoflurane(DB01236)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfaphenazole(DB06729)|Sulfinpyrazone(DB01138)|Tamoxifen(DB00675)|Temazepam(DB00231)|Testosterone(DB00624)|Thiotepa(DB04572)|Ticlopidine(DB00208)|Tramadol(DB00193)|Tretinoin(DB00755)|Valproic Acid(DB00313)|Venlafaxine(DB00285)|Verapamil(DB00661)	GTCATCTATGAGATTCAGAGA	0.532																																					p.E355G		Atlas-SNP	.											.	CYP2B6	79	.	0			c.A1064G						.						121	96	104					19																	41518302		2203	4300	6503	SO:0001583	missense	1555	exon7			TCTATGAGATTCA	AF182277	CCDS12570.1	19q13.2	2013-07-25	2003-01-14		ENSG00000197408	ENSG00000197408		"Cytochrome P450s"	2615	protein-coding gene	gene with protein product		123930	"cytochrome P450, subfamily IIB (phenobarbital-inducible), polypeptide 6", "cytochrome P450, family 2, subfamily B", "cytochrome P450, subfamily IIB (phenobarbital-inducible)"	CYP2B		7668294, 15128046	Standard	NM_000767		Approved	CPB6, CYPIIB6	uc002opr.1	P20813	OTTHUMG00000182714	ENST00000324071.4:c.1064A>G	chr19.hg19:g.41518302A>G	ENSP00000324648:p.Glu355Gly	93.0	0.0		97.0	4.0	NM_000767	B4DWP3|Q2V565|Q9UK46	Missense_Mutation	SNP	ENST00000324071.4	hg19	CCDS12570.1	.	.	.	.	.	.	.	.	.	.	.	16.78	3.217813	0.58560	.	.	ENSG00000197408	ENST00000324071;ENST00000330446	D;D	0.97114	-4.25;-4.25	4.3	4.3	0.51218	.	0.000000	0.85682	D	0.000000	D	0.98852	0.9612	H	0.96996	3.92	0.48975	D	0.999733	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.99167	1.0863	10	0.87932	D	0	.	11.4609	0.50211	1.0:0.0:0.0:0.0	.	155;355	B4DWP3;P20813	.;CP2B6_HUMAN	G	355;155	ENSP00000324648:E355G;ENSP00000330650:E155G	ENSP00000324648:E355G	E	+	2	0	CYP2B6	46210142	1.000000	0.71417	0.981000	0.43875	0.303000	0.27691	8.505000	0.90515	1.800000	0.52685	0.248000	0.18094	GAG	.	.		0.532	CYP2B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463260.1	NM_000767		G	41518302	A	G	41518302	3	3	255	1	0	0	0	0	1	0	0	0	4166	304	11	2	1090	2	CYP2B6	19	41518302	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	1611250	41518302	17610681	705	36050										
ZNF221	7638	hgsc.bcm.edu	37	chr19	44471269	44471269	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agctatacaaatgtgagcagTgtgagaaggggtacaacagt	13	5	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:44471269T>C	ENST00000251269.5	+	6	1943	c.1615T>C	c.(1615-1617)Tgt>Cgt	p.C539R	ZNF221_ENST00000592350.1_Missense_Mutation_p.C539R|ZNF221_ENST00000587682.1_Missense_Mutation_p.C539R	NM_013359.2	NP_037491	Q9UK13	ZN221_HUMAN	zinc finger protein 221	539					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(11)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	30		Prostate(69;0.0352)				ATGTGAGCAGTGTGAGAAGGG	0.428																																					p.C539R		Atlas-SNP	.											.	ZNF221	59	.	0			c.T1615C						.						97	90	92					19																	44471269		2203	4300	6503	SO:0001583	missense	7638	exon6			GAGCAGTGTGAGA	AF187987	CCDS12633.1	19q13.31	2013-01-08				ENSG00000159905		"Zinc fingers, C2H2-type", "-"	13014	protein-coding gene	gene with protein product							Standard	NM_013359		Approved		uc002oxx.2	Q9UK13		ENST00000251269.5:c.1615T>C	chr19.hg19:g.44471269T>C	ENSP00000251269:p.Cys539Arg	87.0	0.0		91.0	4.0	NM_013359	B2RAI6|Q2M2H2|Q9P1U8	Missense_Mutation	SNP	ENST00000251269.5	hg19	CCDS12633.1	.	.	.	.	.	.	.	.	.	.	t	17.52	3.409350	0.62399	.	.	ENSG00000159905	ENST00000251269	T	0.29655	1.56	2.81	2.81	0.32909	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.58906	0.2155	M	0.90595	3.13	0.53688	D	0.999971	D	0.89917	1.0	D	0.91635	0.999	T	0.65853	-0.6067	9	0.87932	D	0	.	10.1779	0.42950	0.0:0.0:0.0:1.0	.	539	Q9UK13	ZN221_HUMAN	R	539	ENSP00000251269:C539R	ENSP00000251269:C539R	C	+	1	0	ZNF221	49163109	1.000000	0.71417	0.155000	0.22561	0.235000	0.25334	7.212000	0.77941	1.271000	0.44313	0.379000	0.24179	TGT	.	.		0.428	ZNF221-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460068.1			C	44471269	T	C	44471269	3	2	255	1	0	0	0	0	1	0	0	0	17790	1696	59	2	1629	2	ZNF221	19	44471269	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	2952967	44471269	14657714	706	36051										
ZNF223	7766	hgsc.bcm.edu	37	chr19	44570978	44570978	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttcgtaggctggatttgtgtAagcatcagacgatccacaca	10	9	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:44570978A>T	ENST00000434772.3	+	5	1252	c.997A>T	c.(997-999)Aag>Tag	p.K333*	ZNF223_ENST00000591793.1_Nonsense_Mutation_p.K443*	NM_013361.4	NP_037493.3	Q9UK11	ZN223_HUMAN	zinc finger protein 223	333					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18		Prostate(69;0.0352)				GGATTTGTGTAAGCATCAGAC	0.443																																					p.K333X		Atlas-SNP	.											.	ZNF223	61	.	0			c.A997T						.						109	107	108					19																	44570978		2203	4300	6503	SO:0001587	stop_gained	7766	exon5			TTGTGTAAGCATC	AF187989	CCDS12635.1	19q13.2	2013-01-08				ENSG00000178386		"Zinc fingers, C2H2-type", "-"	13016	protein-coding gene	gene with protein product							Standard	XM_006723365		Approved		uc002oyf.1	Q9UK11		ENST00000434772.3:c.997A>T	chr19.hg19:g.44570978A>T	ENSP00000401947:p.Lys333*	103.0	0.0		135.0	52.0	NM_013361	Q15736|Q8TBJ3|Q9HCA9	Nonsense_Mutation	SNP	ENST00000434772.3	hg19	CCDS12635.1	.	.	.	.	.	.	.	.	.	.	A	37	6.246649	0.97408	.	.	ENSG00000178386	ENST00000434772	.	.	.	2.46	0.269	0.15631	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.6982	0.17867	0.5965:0.0:0.4035:0.0	.	.	.	.	X	333	.	ENSP00000401947:K333X	K	+	1	0	ZNF223	49262818	0.000000	0.05858	0.001000	0.08648	0.825000	0.46686	-1.667000	0.01961	0.188000	0.20168	0.260000	0.18958	AAG	.	.		0.443	ZNF223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460469.2			T	44570978	A	T	44570978	4	4	255	1	0	0	0	0	0	1	0	0	17792	363	13	4	1011	4	ZNF223	19	44570978	Nonsense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	99709	44570978	14558005	707	36052										
ZNF225	7768	hgsc.bcm.edu	37	chr19	44635250	44635250	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aagtcctttagtgatgtctcCgtccttgatcttcatcaaca	6	11	4	2	rs201221735		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:44635250C>A	ENST00000262894.6	+	5	763	c.483C>A	c.(481-483)tcC>tcA	p.S161S	ZNF225_ENST00000590612.1_Silent_p.S161S|ZNF225_ENST00000592780.1_3'UTR	NM_013362.2	NP_037494.2	Q9UK10	ZN225_HUMAN	zinc finger protein 225	161					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|skin(1)|stomach(1)	16		Prostate(69;0.0352)|all_neural(266;0.202)				GTGATGTCTCCGTCCTTGATC	0.413																																					p.S161S		Atlas-SNP	.											.	ZNF225	41	.	0			c.C483A						.						110	110	110					19																	44635250		2032	4213	6245	SO:0001819	synonymous_variant	7768	exon5			TGTCTCCGTCCTT	AF187991	CCDS46100.1	19q13.31	2013-01-08				ENSG00000256294		"Zinc fingers, C2H2-type", "-"	13018	protein-coding gene	gene with protein product							Standard	NM_013362		Approved		uc002oyj.1	Q9UK10		ENST00000262894.6:c.483C>A	chr19.hg19:g.44635250C>A		103.0	0.0		121.0	5.0	NM_013362	A8K8S2|Q53F12|Q9NS46|Q9UID8	Silent	SNP	ENST00000262894.6	hg19	CCDS46100.1																																																																																			.	C|1.000;T|0.000		0.413	ZNF225-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460581.1			A	44635250	C	A	44635250	2	1	255	1	0	0	0	0	0	0	0	1	17794	639	23	1		1	ZNF225	19	44635250	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	64272	44635250	14493733	708	36053										
MARK4	57787	hgsc.bcm.edu	37	chr19	45801087	45801087	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cgggcagggggtgggggtggTgggggtgtgcagaatgggcc	26	5	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:45801087T>C	ENST00000262891.4	+	15	2083	c.1752T>C	c.(1750-1752)ggT>ggC	p.G584G	MARK4_ENST00000300843.4_Silent_p.G584G	NM_001199867.1	NP_001186796.1	Q96L34	MARK4_HUMAN	MAP/microtubule affinity-regulating kinase 4	584					microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|nervous system development (GO:0007399)|positive regulation of programmed cell death (GO:0043068)|protein phosphorylation (GO:0006468)	centrosome (GO:0005813)|microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|gamma-tubulin binding (GO:0043015)|microtubule binding (GO:0008017)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)|ubiquitin binding (GO:0043130)			NS(1)|biliary_tract(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	31		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0102)		GTGGGGGTGGTGGGGGTGTGC	0.731																																					p.G584G		Atlas-SNP	.											.	MARK4	132	.	0			c.T1752C						.						2	3	3					19																	45801087		1796	3555	5351	SO:0001819	synonymous_variant	57787	exon15			GGGTGGTGGGGGT	AB049127	CCDS12658.1, CCDS56097.1	19q13.32	2014-04-07	2002-06-12	2002-06-14	ENSG00000007047	ENSG00000007047	2.7.11.1		13538	protein-coding gene	gene with protein product		606495	"MAP/microtubule affinity-regulating kinase like 1"	MARKL1		23400999, 11326310, 9108484	Standard	NM_001199867		Approved	Nbla00650, FLJ90097, KIAA1860, PAR-1D	uc002paz.2	Q96L34	OTTHUMG00000181769	ENST00000262891.4:c.1752T>C	chr19.hg19:g.45801087T>C		46.0	0.0		88.0	7.0	NM_001199867	Q8NG37|Q96JG7|Q96SQ2|Q9BYD8	Silent	SNP	ENST00000262891.4	hg19	CCDS56097.1																																																																																			.	.		0.731	MARK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457537.1	NM_031417		C	45801087	T	C	45801087	2	2	255	1	0	0	0	0	0	0	0	1	9324	1683	59	2		2	MARK4	19	45801087	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	1165837	45801087	13327896	709	36054										
RSPH6A	81492	hgsc.bcm.edu	37	chr19	46307718	46307718	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agatgcgggctatctgggccCgcaggtagttggcctcgttg	16	10	1	1	rs139803225		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:46307718C>A	ENST00000221538.3	-	3	1587	c.1445G>T	c.(1444-1446)cGg>cTg	p.R482L	RSPH6A_ENST00000600188.1_Missense_Mutation_p.R218L|RSPH6A_ENST00000597055.1_Missense_Mutation_p.R482L	NM_030785.3	NP_110412.1	Q9H0K4	RSH6A_HUMAN	radial spoke head 6 homolog A (Chlamydomonas)	482						intracellular (GO:0005622)		p.R482P(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	32						TATCTGGGCCCGCAGGTAGTT	0.622																																					p.R482L		Atlas-SNP	.											RSPH6A,NS,carcinoma,0,1	RSPH6A	70	.	1	Substitution - Missense(1)	lung(1)	c.G1445T						.						55	50	52					19																	46307718		2203	4300	6503	SO:0001583	missense	81492	exon3			TGGGCCCGCAGGT	AL136761	CCDS12675.1	19q13.3	2010-02-17	2009-11-18	2009-11-18	ENSG00000104941	ENSG00000104941			14241	protein-coding gene	gene with protein product		607548	"radial spokehead-like 1"	RSHL1		11237735	Standard	NM_030785		Approved	RSP4, RSP6, RSPH4B	uc002pdm.3	Q9H0K4		ENST00000221538.3:c.1445G>T	chr19.hg19:g.46307718C>A	ENSP00000221538:p.Arg482Leu	113.0	0.0		113.0	6.0	NM_030785	Q53FE2|Q6PEZ9	Missense_Mutation	SNP	ENST00000221538.3	hg19	CCDS12675.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.150863	0.78001	.	.	ENSG00000104941	ENST00000221538	T	0.34072	1.38	3.8	3.8	0.43715	.	0.000000	0.85682	D	0.000000	T	0.66346	0.2780	M	0.91818	3.245	0.48135	D	0.99959	D	0.89917	1.0	D	0.91635	0.999	T	0.75249	-0.3384	10	0.87932	D	0	-5.2906	14.008	0.64478	0.0:1.0:0.0:0.0	.	482	Q9H0K4	RSH6A_HUMAN	L	482	ENSP00000221538:R482L	ENSP00000221538:R482L	R	-	2	0	RSPH6A	50999558	1.000000	0.71417	0.988000	0.46212	0.658000	0.38924	7.298000	0.78815	2.428000	0.82296	0.456000	0.33151	CGG	.	C|1.000;G|0.000		0.622	RSPH6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461657.1			A	46307718	C	A	46307718	3	1	255	1	0	0	0	0	1	0	0	0	13722	652	23	1	724	1	RSPH6A	19	46307718	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	506631	46307718	12821265	710	36055										
CCDC9	26093	hgsc.bcm.edu	37	chr19	47764057	47764057	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cgaggttcacctcacctctcTggagctggagacacctcaat	9	14	4	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:47764057T>C	ENST00000221922.6	+	5	645	c.423T>C	c.(421-423)tcT>tcC	p.S141S		NM_015603.2	NP_056418.1	Q9Y3X0	CCDC9_HUMAN	coiled-coil domain containing 9	141	Gly-rich.						poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|urinary_tract(1)	12		all_cancers(25;0.0432)|all_epithelial(76;0.00812)|Medulloblastoma(540;0.0208)|all_neural(266;0.0416)|Hepatocellular(1079;0.114)		OV - Ovarian serous cystadenocarcinoma(262;8.51e-95)|Epithelial(262;1.15e-92)|all cancers(93;7.67e-84)|GBM - Glioblastoma multiforme(486;0.024)|STAD - Stomach adenocarcinoma(1328;0.183)		CTCACCTCTCTGGAGCTGGAG	0.642																																					p.S141S		Atlas-SNP	.											.	CCDC9	37	.	0			c.T423C						.						36	37	37					19																	47764057		2203	4297	6500	SO:0001819	synonymous_variant	26093	exon5			CCTCTCTGGAGCT	AL050284	CCDS12698.1	19q13.33	2008-02-05				ENSG00000105321			24560	protein-coding gene	gene with protein product						11230166	Standard	NM_015603		Approved	DKFZP586M1019	uc010xym.2	Q9Y3X0		ENST00000221922.6:c.423T>C	chr19.hg19:g.47764057T>C		146.0	0.0		143.0	6.0	NM_015603		Silent	SNP	ENST00000221922.6	hg19	CCDS12698.1																																																																																			.	.		0.642	CCDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466917.1	NM_015603		C	47764057	T	C	47764057	2	2	255	1	0	0	0	0	0	0	0	1	2869	1567	55	2		2	CCDC9	19	47764057	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	1456339	47764057	11364926	711	36056										
LIG1	3978	hgsc.bcm.edu	37	chr19	48630537	48630537	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aggaagctggaactcacctcTccattgaggtagatgaggtc	12	9	2	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:48630537T>C	ENST00000263274.7	-	21	2420	c.2001A>G	c.(1999-2001)ggA>ggG	p.G667G	LIG1_ENST00000536218.1_Silent_p.G599G|CTC-453G23.5_ENST00000596839.1_RNA|LIG1_ENST00000427526.2_Silent_p.G636G|CTC-453G23.5_ENST00000596563.1_RNA	NM_000234.1	NP_000225.1	P18858	DNLI1_HUMAN	ligase I, DNA, ATP-dependent	667					anatomical structure morphogenesis (GO:0009653)|base-excision repair (GO:0006284)|cell division (GO:0051301)|DNA biosynthetic process (GO:0071897)|DNA ligation involved in DNA repair (GO:0051103)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|response to hydrogen peroxide (GO:0042542)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(22)|prostate(2)|skin(1)	44		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)	AACTCACCTCTCCATTGAGGT	0.602								Nucleotide excision repair (NER)																													p.G667G		Atlas-SNP	.											.	LIG1	151	.	0			c.A2001G						.						175	128	144					19																	48630537		2203	4300	6503	SO:0001819	synonymous_variant	3978	exon21			CACCTCTCCATTG		CCDS12711.1, CCDS74409.1, CCDS74410.1	19q13.2-q13.3	2014-09-17				ENSG00000105486	6.5.1.1		6598	protein-coding gene	gene with protein product		126391					Standard	XM_005258934		Approved		uc002pia.1	P18858		ENST00000263274.7:c.2001A>G	chr19.hg19:g.48630537T>C		89.0	0.0		98.0	4.0	NM_000234	B2RAI8|Q2TB12|Q32P23	Silent	SNP	ENST00000263274.7	hg19	CCDS12711.1																																																																																			.	.		0.602	LIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465575.1	NM_000234		C	48630537	T	C	48630537	2	2	255	1	0	0	0	0	0	0	0	1	8790	1538	54	2		2	LIG1	19	48630537	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	866480	48630537	10498446	712	36057										
FUT1	2523	hgsc.bcm.edu	37	chr19	49253770	49253770	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gttgctggtgaccacgaaaaCgggggcttcgtgccgtgccc	15	12	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:49253770C>T	ENST00000310160.3	-	4	1743	c.769G>A	c.(769-771)Gtt>Att	p.V257I	FUT1_ENST00000601931.1_5'Flank	NM_000148.3	NP_000139.1	P19526	FUT1_HUMAN	fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase, H blood group)	257					carbohydrate metabolic process (GO:0005975)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	fucosyltransferase activity (GO:0008417)|galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(3)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	17		all_lung(116;1.7e-06)|all_epithelial(76;3.52e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000135)|all cancers(93;0.000354)|Epithelial(262;0.0191)|GBM - Glioblastoma multiforme(486;0.0222)		ACCACGAAAACGGGGGCTTCG	0.612																																					p.V257I		Atlas-SNP	.											FUT1,caecum,carcinoma,0,1	FUT1	44	.	0			c.G769A						.						108	96	100					19																	49253770		2203	4300	6503	SO:0001583	missense	2523	exon4			CGAAAACGGGGGC		CCDS12733.1	19q13.33	2014-07-19	2006-01-19		ENSG00000174951	ENSG00000174951	2.4.1.69	"Blood group antigens", "Fucosyltransferases"	4012	protein-coding gene	gene with protein product		211100	"fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase, Bombay phenotype included)", "fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase)"	H, HSC			Standard	NM_000148		Approved		uc002pkk.3	P19526		ENST00000310160.3:c.769G>A	chr19.hg19:g.49253770C>T	ENSP00000312021:p.Val257Ile	41.0	0.0		48.0	2.0	NM_000148	O14505|O14506|O14507	Missense_Mutation	SNP	ENST00000310160.3	hg19	CCDS12733.1	.	.	.	.	.	.	.	.	.	.	C	4.015	0.000199	0.07819	.	.	ENSG00000174951	ENST00000310160;ENST00000539428	D	0.96587	-4.06	4.46	0.0669	0.14363	.	0.649436	0.13918	N	0.353746	D	0.88187	0.6369	N	0.08118	0	0.24263	N	0.995272	B	0.13594	0.008	B	0.12156	0.007	T	0.77864	-0.2429	10	0.22109	T	0.4	-2.9453	8.1744	0.31272	0.0:0.5508:0.0:0.4492	.	257	P19526	FUT1_HUMAN	I	257;247	ENSP00000312021:V257I	ENSP00000312021:V257I	V	-	1	0	FUT1	53945582	0.000000	0.05858	0.861000	0.33841	0.006000	0.05464	-1.446000	0.02398	0.056000	0.16144	-0.484000	0.04775	GTT	.	.		0.612	FUT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466194.1	NM_000148		T	49253770	C	T	49253770	3	4	255	1	0	0	0	0	1	0	0	0	6109	536	19	1	332	1	FUT1	19	49253770	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	623233	49253770	9875213	713	36058										
TULP2	7288	hgsc.bcm.edu	37	chr19	49401098	49401098	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctgtttccctactcactctcTcatcaatgtgtcattatcct	3	14	5	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:49401098T>C	ENST00000221399.3	-	2	172	c.28A>G	c.(28-30)Aga>Gga	p.R10G	NUCB1_ENST00000405315.4_5'Flank|NUCB1_ENST00000407032.1_5'Flank|NUCB1_ENST00000263273.5_5'Flank	NM_003323.2	NP_003314.2	O00295	TULP2_HUMAN	tubby like protein 2	10					visual perception (GO:0007601)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	protein complex binding (GO:0032403)			NS(1)|breast(2)|central_nervous_system(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	22		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000259)|all cancers(93;0.000435)|Epithelial(262;0.0221)|GBM - Glioblastoma multiforme(486;0.0234)		ACTCACTCTCTCATCAATGTG	0.522																																					p.R10G		Atlas-SNP	.											.	TULP2	60	.	0			c.A28G						.						188	149	162					19																	49401098		2203	4300	6503	SO:0001583	missense	7288	exon2			ACTCTCTCATCAA	U82469	CCDS12739.1	19q13.1	2009-08-06			ENSG00000104804	ENSG00000104804			12424	protein-coding gene	gene with protein product	"cancer/testis antigen 65"	602309				9096357	Standard	NM_003323		Approved	TUBL2, CT65	uc002pkz.2	O00295	OTTHUMG00000164406	ENST00000221399.3:c.28A>G	chr19.hg19:g.49401098T>C	ENSP00000221399:p.Arg10Gly	63.0	0.0		83.0	4.0	NM_003323	Q8TC50	Missense_Mutation	SNP	ENST00000221399.3	hg19	CCDS12739.1	.	.	.	.	.	.	.	.	.	.	T	8.126	0.782051	0.16189	.	.	ENSG00000104804	ENST00000221399;ENST00000518572;ENST00000522945	D;T;T	0.82893	-1.66;2.23;1.46	4.03	4.03	0.46877	.	0.819393	0.10887	N	0.623123	T	0.68952	0.3057	N	0.19112	0.55	0.21105	N	0.999787	B	0.23650	0.089	B	0.17098	0.017	T	0.53005	-0.8499	10	0.13108	T	0.6	.	9.64	0.39833	0.0:0.0:0.0:1.0	.	10	O00295	TULP2_HUMAN	G	10	ENSP00000221399:R10G;ENSP00000428420:R10G;ENSP00000430040:R10G	ENSP00000221399:R10G	R	-	1	2	TULP2	54092910	0.232000	0.23762	0.390000	0.26220	0.004000	0.04260	2.132000	0.42083	2.063000	0.61619	0.448000	0.29417	AGA	.	.		0.522	TULP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378633.1	NM_003323		C	49401098	T	C	49401098	3	2	255	1	0	0	0	0	1	0	0	0	16789	1559	54	2	1582	2	TULP2	19	49401098	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	147328	49401098	9727885	714	36059										
PPFIA3	8541	hgsc.bcm.edu	37	chr19	49640052	49640052	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gaactggacggctccgatgaGgaggaggcagaggggatgtt	19	6	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:49640052G>T	ENST00000334186.4	+	15	2086	c.1737G>T	c.(1735-1737)gaG>gaT	p.E579D	PPFIA3_ENST00000602351.1_Missense_Mutation_p.E579D	NM_003660.2	NP_003651.1	O75145	LIPA3_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 3	579					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|presynaptic active zone (GO:0048786)				NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(16)|pancreas(1)|prostate(1)|skin(4)|urinary_tract(1)	35		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.36e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000203)|GBM - Glioblastoma multiforme(486;0.00307)|Epithelial(262;0.00677)		GCTCCGATGAGGAGGAGGCAG	0.647																																					p.E579D		Atlas-SNP	.											.	PPFIA3	71	.	0			c.G1737T						.						38	33	35					19																	49640052		2198	4300	6498	SO:0001583	missense	8541	exon15			CGATGAGGAGGAG	AF034800	CCDS12758.1	19q13.33	2013-09-23			ENSG00000177380	ENSG00000177380		"Sterile alpha motif (SAM) domain containing"	9247	protein-coding gene	gene with protein product	"protein tyrosine phosphatase, receptor type, f polypeptide, alpha 3", "liprin-alpha 3", "liprin"	603144				9624153, 9734811	Standard	NM_003660		Approved	KIAA0654, LPNA3, MGC126567, MGC126569	uc002pmr.3	O75145	OTTHUMG00000183213	ENST00000334186.4:c.1737G>T	chr19.hg19:g.49640052G>T	ENSP00000335614:p.Glu579Asp	75.0	0.0		109.0	5.0	NM_003660	A8K142|Q3MJA0|Q9H8B5|Q9UEW4	Missense_Mutation	SNP	ENST00000334186.4	hg19	CCDS12758.1	.	.	.	.	.	.	.	.	.	.	G	8.109	0.778381	0.16120	.	.	ENSG00000177380	ENST00000334186;ENST00000421230	T	0.52983	0.64	3.31	-0.258	0.12975	.	0.000000	0.47455	U	0.000236	T	0.32882	0.0844	L	0.47078	1.49	0.42488	D	0.992888	B;B;B	0.20261	0.043;0.0;0.0	B;B;B	0.24006	0.05;0.005;0.0	T	0.08249	-1.0731	10	0.13853	T	0.58	-17.3817	6.9779	0.24686	0.5916:0.0:0.4084:0.0	.	503;579;579	B4DEU8;O75145-2;O75145	.;.;LIPA3_HUMAN	D	579;503	ENSP00000335614:E579D	ENSP00000335614:E579D	E	+	3	2	PPFIA3	54331864	0.902000	0.30710	0.998000	0.56505	0.795000	0.44927	-0.020000	0.12525	0.042000	0.15717	0.542000	0.68232	GAG	.	.		0.647	PPFIA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465688.1	NM_003660		T	49640052	G	T	49640052	3	4	255	1	0	0	0	0	1	0	0	0	12320	991	35	3	1791	3	PPFIA3	19	49640052	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	238954	49640052	9488931	715	36060										
CD37	951	hgsc.bcm.edu	37	chr19	49842011	49842011	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggttccaagtcctcatcctgAgaggtaacgggtcggaggcg	15	10	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:49842011A>G	ENST00000323906.4	+	6	643	c.502A>G	c.(502-504)Aga>Gga	p.R168G	CD37_ENST00000426897.2_Missense_Mutation_p.R100G|CD37_ENST00000598095.1_Missense_Mutation_p.R100G|CTC-301O7.4_ENST00000358234.4_lincRNA|CD37_ENST00000535669.2_Missense_Mutation_p.R168G	NM_001774.2	NP_001765.1	P11049	CD37_HUMAN	CD37 molecule	168					defense response to protozoan (GO:0042832)|negative regulation of cell proliferation (GO:0008285)|negative regulation of myeloid dendritic cell activation (GO:0030886)|positive regulation of immunoglobulin production (GO:0002639)|regulation of defense response to virus (GO:0050688)|regulation of humoral immune response (GO:0002920)	extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|endometrium(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(1)	11		all_lung(116;2.81e-06)|Lung NSC(112;5.89e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00088)|GBM - Glioblastoma multiforme(486;0.0443)		CCTCATCCTGAGAGGTAACGG	0.607																																					p.R168G		Atlas-SNP	.											.	CD37	33	.	0			c.A502G						.						74	64	67					19																	49842011		2203	4300	6503	SO:0001583	missense	951	exon6			ATCCTGAGAGGTA		CCDS12760.1, CCDS46139.1	19p13-q13.4	2013-02-14	2006-03-28			ENSG00000104894		"CD molecules", "Tetraspanins"	1666	protein-coding gene	gene with protein product		151523	"CD37 antigen"			8436422	Standard	XM_005259435		Approved	TSPAN26	uc002pnd.3	P11049		ENST00000323906.4:c.502A>G	chr19.hg19:g.49842011A>G	ENSP00000325708:p.Arg168Gly	76.0	0.0		85.0	4.0	NM_001774	B4DVC1|Q3KPF9	Missense_Mutation	SNP	ENST00000323906.4	hg19	CCDS12760.1	.	.	.	.	.	.	.	.	.	.	A	13.37	2.217901	0.39201	.	.	ENSG00000104894	ENST00000323906;ENST00000426897;ENST00000535669	T;T;T	0.79247	-1.25;-1.25;-1.25	3.95	2.83	0.33086	Tetraspanin, EC2 domain (1);	1.119980	0.06880	N	0.802384	T	0.71264	0.3319	L	0.50333	1.59	0.09310	N	1	P;B;B;B	0.37276	0.589;0.27;0.27;0.072	B;B;B;B	0.36030	0.216;0.136;0.136;0.067	T	0.61048	-0.7141	10	0.41790	T	0.15	.	6.874	0.24137	0.7627:0.2373:0.0:0.0	.	100;168;168;168	B4DVC1;B7ZAN3;B4DW15;P11049	.;.;.;CD37_HUMAN	G	168;100;168	ENSP00000325708:R168G;ENSP00000413151:R100G;ENSP00000441037:R168G	ENSP00000325708:R168G	R	+	1	2	CD37	54533823	0.074000	0.21230	0.246000	0.24233	0.107000	0.19398	0.809000	0.27168	1.561000	0.49584	0.402000	0.26972	AGA	.	.		0.607	CD37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465532.1			G	49842011	A	G	49842011	3	3	255	1	0	0	0	0	1	0	0	0	3010	296	11	2	524	2	CD37	19	49842011	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	201959	49842011	9286972	716	36061										
MYH14	79784	hgsc.bcm.edu	37	chr19	50775107	50775107	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	atcccactccacccctcaggAgcggaagctgctggaagatc	10	15	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:50775107A>G	ENST00000596571.1	+	23	3050	c.3050A>G	c.(3049-3051)gAg>gGg	p.E1017G	MYH14_ENST00000262269.8_Splice_Site_p.E1058G|MYH14_ENST00000440075.2_Splice_Site_p.E1058G|MYH14_ENST00000376970.2_Splice_Site_p.E1050G|MYH14_ENST00000425460.1_Splice_Site_p.E1025G|MYH14_ENST00000601313.1_Splice_Site_p.E1058G|MYH14_ENST00000598205.1_Splice_Site_p.E1025G			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	1017					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		ACCCCTCAGGAGCGGAAGCTG	0.562																																					p.E1058G		Atlas-SNP	.											.	MYH14	261	.	0			c.A3173G						.						30	33	32					19																	50775107		1997	4159	6156	SO:0001630	splice_region_variant	79784	exon26			CTCAGGAGCGGAA	AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"Myosins / Myosin superfamily : Class II"	23212	protein-coding gene	gene with protein product		608568	"myosin, heavy polypeptide 14", "myosin, heavy chain 14"	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.3049-1A>G	chr19.hg19:g.50775107A>G		73.0	0.0		90.0	4.0	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Missense_Mutation	SNP	ENST00000596571.1	hg19	CCDS59411.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.65|19.65	3.866778|3.866778	0.72065|0.72065	.|.	.|.	ENSG00000105357|ENSG00000105357	ENST00000440075;ENST00000376970;ENST00000425460;ENST00000262269|ENST00000301415;ENST00000376965	D;D;D;D|.	0.86694|.	-2.16;-2.16;-2.16;-2.16|.	3.14|3.14	3.14|3.14	0.36123|0.36123	.|.	.|.	.|.	.|.	.|.	T|T	0.78729|0.78729	0.4329|0.4329	M|M	0.90977|0.90977	3.165|3.165	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.81914|.	0.992;0.989;0.995|.	T|T	0.81890|0.81890	-0.0725|-0.0725	9|5	0.87932|.	D|.	0|.	.|.	10.0111|10.0111	0.41986|0.41986	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	1058;1017;1025|.	Q7Z406-2;Q7Z406;Q7Z406-6|.	.;MYH14_HUMAN;.|.	G|G	1058;1050;1025;1058|1017	ENSP00000406273:E1058G;ENSP00000366169:E1050G;ENSP00000407879:E1025G;ENSP00000262269:E1058G|.	ENSP00000262269:E1058G|.	E|S	+|+	2|1	0|0	MYH14|MYH14	55466919|55466919	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.836000|0.836000	0.47400|0.47400	8.595000|8.595000	0.90840|0.90840	1.674000|1.674000	0.50907|0.50907	0.482000|0.482000	0.46254|0.46254	GAG|AGC	.	.		0.562	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729	Missense_Mutation	G	50775107	A	G	50775107	5	3	255	1	0	0	0	0	0	0	1	0	10042	318	11	2	3271	2	MYH14	19	50775107	Splice_Site	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	933096	50775107	8353876	717	36062										
FAM71E1	112703	hgsc.bcm.edu	37	chr19	50971076	50971076	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aaagagctggacgaacttcaAggggaacagcctgggtggga	16	7	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:50971076A>G	ENST00000600100.1	-	4	914	c.550T>C	c.(550-552)Ttg>Ctg	p.L184L	FAM71E1_ENST00000595790.1_Silent_p.L168L			Q6IPT2	F71E1_HUMAN	family with sequence similarity 71, member E1	184										breast(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.0077)|GBM - Glioblastoma multiforme(134;0.026)		ACGAACTTCAAGGGGAACAGC	0.637																																					p.L168L		Atlas-SNP	.											.	FAM71E1	21	.	0			c.T502C						.						25	24	24					19																	50971076		2203	4300	6503	SO:0001819	synonymous_variant	112703	exon4			ACTTCAAGGGGAA		CCDS33081.1	19q13.33	2007-11-20				ENSG00000142530			25107	protein-coding gene	gene with protein product							Standard	XM_005258472		Approved		uc002psg.3	Q6IPT2		ENST00000600100.1:c.550T>C	chr19.hg19:g.50971076A>G		61.0	0.0		77.0	4.0	NM_138411	Q96EJ5|Q9BSM9	Silent	SNP	ENST00000600100.1	hg19																																																																																				.	.		0.637	FAM71E1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000464754.2			G	50971076	A	G	50971076	2	3	255	1	0	0	0	0	0	0	0	1	5619	69	3	2		2	FAM71E1	19	50971076	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	195969	50971076	8157907	718	36063										
ZNF610	162963	hgsc.bcm.edu	37	chr19	52856964	52856964	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	acattcatggacgtggccatCgaattctctcaggaggagtg	12	9	3	0	rs375754279		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:52856964C>T	ENST00000403906.3	+	4	549	c.93C>T	c.(91-93)atC>atT	p.I31I	ZNF610_ENST00000601151.1_Silent_p.I31I|ZNF610_ENST00000327920.8_Silent_p.I31I|ZNF610_ENST00000321287.8_Silent_p.I31I	NM_001161425.1	NP_001154897.1	Q8N9Z0	ZN610_HUMAN	zinc finger protein 610	31	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.I31I(1)		NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(8)|liver(2)|lung(9)|ovary(2)|stomach(2)|upper_aerodigestive_tract(2)	34				OV - Ovarian serous cystadenocarcinoma(262;0.00396)|GBM - Glioblastoma multiforme(134;0.00434)		ACGTGGCCATCGAATTCTCTC	0.438																																					p.I31I		Atlas-SNP	.											ZNF610,NS,carcinoma,0,1	ZNF610	84	.	1	Substitution - coding silent(1)	ovary(1)	c.C93T						.	C	,,,	1,4405	2.1+/-5.4	0,1,2202	98	98	98		93,93,93,93	-2.9	0.9	19		98	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZNF610	NM_001161425.1,NM_001161426.1,NM_001161427.1,NM_173530.2	,,,	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	,,,	31/463,31/463,31/420,31/463	52856964	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	162963	exon4			GGCCATCGAATTC	AK093359	CCDS12851.1, CCDS54309.1	19q13.41	2013-01-08			ENSG00000167554	ENSG00000167554		"Zinc fingers, C2H2-type", "-"	26687	protein-coding gene	gene with protein product						12477932	Standard	NM_001161425		Approved	FLJ36040	uc002pyx.4	Q8N9Z0		ENST00000403906.3:c.93C>T	chr19.hg19:g.52856964C>T		66.0	0.0		73.0	4.0	NM_001161427	A8K4C3|Q86YH8|Q8NDS9	Silent	SNP	ENST00000403906.3	hg19	CCDS12851.1																																																																																			.	.		0.438	ZNF610-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462880.1	NM_173530		T	52856964	C	T	52856964	2	4	255	1	0	0	0	0	0	0	0	1	18051	874	31	1		1	ZNF610	19	52856964	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1885888	52856964	6272019	719	36064										
ZNF845	91664	hgsc.bcm.edu	37	chr19	53856000	53856000	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcatactggagagaaaccttAcaagtgtaatgagtgtggca	11	6	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:53856000A>G	ENST00000595091.1	+	5	2291	c.2072A>G	c.(2071-2073)tAc>tGc	p.Y691C	ZNF845_ENST00000458035.1_Missense_Mutation_p.Y691C			Q96IR2	ZN845_HUMAN	zinc finger protein 845	691				Missing (in Ref. 1; BAG58121). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						GAGAAACCTTACAAGTGTAAT	0.418																																					p.Y691C		Atlas-SNP	.											.	ZNF845	101	.	0			c.A2072G						.						67	69	68					19																	53856000		692	1591	2283	SO:0001583	missense	91664	exon4			AACCTTACAAGTG	BC007307	CCDS46170.1	19q13.42	2013-01-08			ENSG00000213799	ENSG00000213799		"Zinc fingers, C2H2-type", "-"	25112	protein-coding gene	gene with protein product							Standard	NM_138374		Approved		uc010ydv.1	Q96IR2		ENST00000595091.1:c.2072A>G	chr19.hg19:g.53856000A>G	ENSP00000470005:p.Tyr691Cys	77.0	0.0		94.0	4.0	NM_138374		Missense_Mutation	SNP	ENST00000595091.1	hg19	CCDS46170.1	.	.	.	.	.	.	.	.	.	.	A	10.92	1.486382	0.26686	.	.	ENSG00000213799	ENST00000458035	T	0.25414	1.8	2.07	2.07	0.26955	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.36496	0.0969	M	0.64676	1.99	0.09310	N	1	D	0.55172	0.97	P	0.56788	0.806	T	0.12477	-1.0546	9	0.66056	D	0.02	.	4.8789	0.13670	0.5432:0.0:0.0:0.4568	.	691	Q96IR2	ZN845_HUMAN	C	691	ENSP00000388311:Y691C	ENSP00000388311:Y691C	Y	+	2	0	ZNF845	58547812	0.000000	0.05858	0.001000	0.08648	0.052000	0.14988	-0.258000	0.08733	0.956000	0.37904	0.378000	0.23410	TAC	.	.		0.418	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908		G	53856000	A	G	53856000	3	3	255	1	0	0	0	0	1	0	0	0	18206	391	14	2	2082	2	ZNF845	19	53856000	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	999036	53856000	5272983	720	36065										
TMC4	147798	hgsc.bcm.edu	37	chr19	54664261	54664261	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccgtaggagttagccagagcCacagtgtacgccatcaggat	12	11	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:54664261C>A	ENST00000376591.4	-	14	2144	c.2013G>T	c.(2011-2013)gtG>gtT	p.V671V	LENG1_ENST00000222224.3_5'Flank|TMC4_ENST00000416963.1_Silent_p.V253V|TMC4_ENST00000301187.4_Silent_p.V665V	NM_001145303.1|NM_144686.2	NP_001138775|NP_653287.2	Q7Z404	TMC4_HUMAN	transmembrane channel-like 4	671					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(7)|large_intestine(4)|lung(6)|pancreas(1)|skin(1)|urinary_tract(1)	22	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					tagccagAGCCACAGTGTACG	0.582																																					p.V671V		Atlas-SNP	.											.	TMC4	89	.	0			c.G2013T						.						60	57	58					19																	54664261		2203	4300	6503	SO:0001819	synonymous_variant	147798	exon14			CAGAGCCACAGTG	AY236492	CCDS12882.1, CCDS46174.1	19q13.42	2008-02-05			ENSG00000167608	ENSG00000167608			22998	protein-coding gene	gene with protein product						12812529, 12906855	Standard	XM_005277069		Approved		uc010erf.3	Q7Z404	OTTHUMG00000066485	ENST00000376591.4:c.2013G>T	chr19.hg19:g.54664261C>A		88.0	0.0		100.0	4.0	NM_001145303	Q7Z5M3|Q8N5E4|Q8TBS7	Silent	SNP	ENST00000376591.4	hg19	CCDS46174.1																																																																																			.	.		0.582	TMC4-011	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000156164.2			A	54664261	C	A	54664261	2	1	255	1	0	0	0	0	0	0	0	1	16002	581	21	3		3	TMC4	19	54664261	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	808261	54664261	4464722	721	36066										
LILRA5	353514	hgsc.bcm.edu	37	chr19	54822783	54822783	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	catccacctgtggctgggggTcacagggcccacagggaaca	14	13	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:54822783T>C	ENST00000301219.3	-	5	732	c.613A>G	c.(613-615)Acc>Gcc	p.T205A	LILRA5_ENST00000446712.3_Missense_Mutation_p.T193A|LILRA5_ENST00000346508.3_Missense_Mutation_p.T193A|AC008984.2_ENST00000507363.1_RNA|LILRA5_ENST00000432233.3_Missense_Mutation_p.T205A	NM_021250.2	NP_067073.1	A6NI73	LIRA5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 5	205	Ig-like C2-type 2.				innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	20	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TGGCTGGGGGTCACAGGGCCC	0.597																																					p.T205A		Atlas-SNP	.											.	LILRA5	49	.	0			c.A613G						.						56	58	57					19																	54822783		2203	4300	6503	SO:0001583	missense	353514	exon5			TGGGGGTCACAGG	AF212842	CCDS12888.1, CCDS12889.1	19q13.4	2013-01-11	2005-05-13	2005-05-13	ENSG00000187116	ENSG00000187116		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	16309	protein-coding gene	gene with protein product		606047		LILRB7		10941842	Standard	NM_181986		Approved	ILT11, LIR9, CD85, CD85f	uc002qfe.3	A6NI73	OTTHUMG00000065357	ENST00000301219.3:c.613A>G	chr19.hg19:g.54822783T>C	ENSP00000301219:p.Thr205Ala	157.0	0.0		132.0	6.0	NM_181879	A6NHI3	Missense_Mutation	SNP	ENST00000301219.3	hg19	CCDS12888.1	.	.	.	.	.	.	.	.	.	.	T	12.55	1.971507	0.34754	.	.	ENSG00000187116	ENST00000301219;ENST00000346508;ENST00000446712;ENST00000432233	T;T;T;T	0.03635	3.86;3.86;3.86;3.86	3.14	0.665	0.17896	Immunoglobulin-like fold (1);	1.446230	0.05063	U	0.480129	T	0.12050	0.0293	M	0.90542	3.125	0.09310	N	1	B;P;B;P	0.40931	0.408;0.733;0.199;0.705	B;B;B;P	0.46110	0.138;0.27;0.155;0.504	T	0.25433	-1.0132	10	0.72032	D	0.01	.	3.0226	0.06080	0.0:0.1505:0.2548:0.5948	.	193;205;193;205	A6NI73-4;A6NI73-3;A6NI73-2;A6NI73	.;.;.;LIRA5_HUMAN	A	205;193;193;205	ENSP00000301219:T205A;ENSP00000302948:T193A;ENSP00000389499:T193A;ENSP00000404236:T205A	ENSP00000301219:T205A	T	-	1	0	LILRA5	59514595	0.000000	0.05858	0.001000	0.08648	0.494000	0.33585	-0.073000	0.11468	0.260000	0.21731	0.172000	0.16884	ACC	.	.		0.597	LILRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140231.1	NM_181985		C	54822783	T	C	54822783	3	2	255	1	0	0	0	0	1	0	0	0	8797	1667	58	2	384	2	LILRA5	19	54822783	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	158522	54822783	4306200	722	36067										
NLRP9	338321	hgsc.bcm.edu	37	chr19	56244026	56244026	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agcacacaggctttttagtcGggctctgttcaccttaggtg	11	10	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:56244026G>T	ENST00000332836.2	-	2	1198	c.1171C>A	c.(1171-1173)Cga>Aga	p.R391R		NM_176820.2	NP_789790.2	Q7RTR0	NALP9_HUMAN	NLR family, pyrin domain containing 9	391	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.					cytoplasm (GO:0005737)	ATP binding (GO:0005524)			NS(2)|breast(5)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(15)|lung(21)|ovary(2)|prostate(3)|skin(7)|urinary_tract(3)	74		Colorectal(82;0.000133)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.123)		CTTTTTAGTCGGGCTCTGTTC	0.418																																					p.R391R		Atlas-SNP	.											.	NLRP9	163	.	0			c.C1171A						.						88	89	89					19																	56244026		2203	4298	6501	SO:0001819	synonymous_variant	338321	exon2			TTAGTCGGGCTCT	AY154464	CCDS12934.1	19q13.43	2006-12-08	2006-12-08	2006-12-08				"Nucleotide-binding domain and leucine rich repeat containing"	22941	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 9"	609663	"NACHT, leucine rich repeat and PYD containing 9"	NALP9		12563287	Standard	NM_176820		Approved	NOD6, PAN12, CLR19.1	uc002qly.3	Q7RTR0		ENST00000332836.2:c.1171C>A	chr19.hg19:g.56244026G>T		62.0	0.0		90.0	4.0	NM_176820	B2RN12|Q86W27	Silent	SNP	ENST00000332836.2	hg19	CCDS12934.1																																																																																			.	.		0.418	NLRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453653.1	NM_176820		T	56244026	G	T	56244026	2	4	255	1	0	0	0	0	0	0	0	1	10493	1124	39	1		1	NLRP9	19	56244026	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	1421243	56244026	2884957	723	36068										
TRIB3	57761	hgsc.bcm.edu	37	chr20	376998	376998	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gcagccgatgtctggagcctGggcgtggcgctcttcaccat	14	13	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr20:376998G>T	ENST00000217233.3	+	4	1294	c.741G>T	c.(739-741)ctG>ctT	p.L247L	TRIB3_ENST00000422053.2_Silent_p.L274L	NM_021158.3	NP_066981.2	Q96RU7	TRIB3_HUMAN	tribbles pseudokinase 3	247	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular lipid metabolic process (GO:0044255)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of protein binding (GO:0032092)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein phosphorylation (GO:0006468)|regulation of glucose transport (GO:0010827)|regulation of MAP kinase activity (GO:0043405)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)|transcription corepressor activity (GO:0003714)|transferase activity, transferring phosphorus-containing groups (GO:0016772)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase regulator activity (GO:0055106)			breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(3)|lung(9)|ovary(2)|skin(1)	21		all_epithelial(17;0.165)|Lung NSC(37;0.191)|Breast(17;0.231)		Colorectal(46;0.101)|COAD - Colon adenocarcinoma(99;0.112)		TCTGGAGCCTGGGCGTGGCGC	0.657																																					p.L247L	Melanoma(101;421 2374 19538)	Atlas-SNP	.											.	TRIB3	50	.	0			c.G741T						.						40	37	38					20																	376998		2203	4299	6502	SO:0001819	synonymous_variant	57761	exon4			GAGCCTGGGCGTG	AF250311	CCDS12997.1	20p13-p12.2	2013-10-03	2013-10-03	2004-05-04	ENSG00000101255	ENSG00000101255			16228	protein-coding gene	gene with protein product		607898	"chromosome 20 open reading frame 97", "tribbles homolog 3 (Drosophila)"	C20orf97		12791994, 16715410	Standard	XM_005260773		Approved	dJ1103G7.3, TRB3	uc002wdm.3	Q96RU7	OTTHUMG00000031627	ENST00000217233.3:c.741G>T	chr20.hg19:g.376998G>T		98.0	0.0		96.0	4.0	NM_021158	Q53GU4|Q53ZW7|Q6I9Y9|Q8TAI6|Q9H5M8|Q9NUD2	Silent	SNP	ENST00000217233.3	hg19	CCDS12997.1																																																																																			.	.		0.657	TRIB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077441.2	NM_021158		T	376998	G	T	376998	2	4	255	1	0	0	0	0	0	0	0	1	16499	1335	47	3		3	TRIB3	20	376998	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10		376998	62648522	724	36069										
ADAM33	80332	hgsc.bcm.edu	37	chr20	3655209	3655209	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctttgttcccaggatccctgTggccacaggttcctttccag	9	14	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr20:3655209T>C	ENST00000356518.2	-	6	783	c.542A>G	c.(541-543)cAc>cGc	p.H181R	ADAM33_ENST00000350009.2_Missense_Mutation_p.H181R|ADAM33_ENST00000379861.4_Missense_Mutation_p.H181R|ADAM33_ENST00000466620.1_5'Flank	NM_025220.2	NP_079496.1	Q9BZ11	ADA33_HUMAN	ADAM metallopeptidase domain 33	181					proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|skin(3)	29						AGGATCCCTGTGGCCACAGGT	0.592																																					p.H181R		Atlas-SNP	.											.	ADAM33	76	.	0			c.A542G						.						76	81	79					20																	3655209		2203	4300	6503	SO:0001583	missense	80332	exon6			TCCCTGTGGCCAC	AL117415, AB055891	CCDS13058.1, CCDS63219.1	20p13	2010-04-06	2005-08-18		ENSG00000149451	ENSG00000149451		"ADAM metallopeptidase domain containing"	15478	protein-coding gene	gene with protein product		607114	"a disintegrin and metalloproteinase domain 33", "chromosome 20 open reading frame 153"	C20orf153		11814695	Standard	XM_005260843		Approved	DKFZp434K0521, dJ964F7.1	uc002wit.3	Q9BZ11	OTTHUMG00000031758	ENST00000356518.2:c.542A>G	chr20.hg19:g.3655209T>C	ENSP00000348912:p.His181Arg	48.0	0.0		57.0	4.0	NM_025220	A0A1K6|Q5JT75|Q5JT76|Q8N0W6	Missense_Mutation	SNP	ENST00000356518.2	hg19	CCDS13058.1	.	.	.	.	.	.	.	.	.	.	T	12.85	2.062992	0.36373	.	.	ENSG00000149451	ENST00000356518;ENST00000379861;ENST00000350009;ENST00000439201	T;T;T	0.01538	4.79;4.8;4.83	4.77	4.77	0.60923	.	.	.	.	.	T	0.04318	0.0119	L	0.32530	0.975	0.37575	D	0.919572	D;D;D;D;D	0.67145	0.996;0.984;0.985;0.975;0.975	P;P;P;P;P	0.61070	0.883;0.575;0.756;0.575;0.575	T	0.63175	-0.6696	9	0.25751	T	0.34	.	13.5427	0.61684	0.0:0.0:0.0:1.0	.	181;193;181;181;181	B4DTZ3;B4E1Y6;Q9BZ11-2;Q9BZ11;A2A2L3	.;.;.;ADA33_HUMAN;.	R	181	ENSP00000348912:H181R;ENSP00000369190:H181R;ENSP00000322550:H181R	ENSP00000322550:H181R	H	-	2	0	ADAM33	3603209	0.731000	0.28111	0.267000	0.24556	0.096000	0.18686	2.444000	0.44890	2.137000	0.66172	0.533000	0.62120	CAC	.	.		0.592	ADAM33-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077763.2	NM_025220		C	3655209	T	C	3655209	3	2	255	1	0	0	0	0	1	0	0	0	250	1696	59	2	1967	2	ADAM33	20	3655209	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	3278211	3655209	59370311	725	36070										
SIGLEC1	6614	hgsc.bcm.edu	37	chr20	3670895	3670895	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tccacgaagaccatcatggtGggcgtcttgggagggtctgt	15	9	3	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr20:3670895G>T	ENST00000344754.4	-	18	4607	c.4608C>A	c.(4606-4608)ccC>ccA	p.P1536P	SIGLEC1_ENST00000202578.4_Silent_p.P1536P	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	1536	Ig-like C2-type 16.				cell-matrix adhesion (GO:0007160)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of T cell apoptotic process (GO:0070234)|single organismal cell-cell adhesion (GO:0016337)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|liver(2)|lung(24)|ovary(3)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)	70						CCATCATGGTGGGCGTCTTGG	0.602																																					p.P1536P		Atlas-SNP	.											.	SIGLEC1	210	.	0			c.C4608A						.						9	6	7					20																	3670895		2111	4144	6255	SO:0001819	synonymous_variant	6614	exon18			CATGGTGGGCGTC	AF230073	CCDS13060.1	20p13	2013-01-29	2006-01-19	2006-01-19	ENSG00000088827	ENSG00000088827		"CD molecules", "Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	11127	protein-coding gene	gene with protein product		600751	"sialoadhesin"	SN		8530048	Standard	XM_006723610		Approved	SIGLEC-1, CD169, FLJ00051, FLJ00055, FLJ00073, FLJ32150, dJ1009E24.1, sialoadhesin	uc002wja.3	Q9BZZ2	OTTHUMG00000031757	ENST00000344754.4:c.4608C>A	chr20.hg19:g.3670895G>T		46.0	0.0		47.0	4.0	NM_023068	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Silent	SNP	ENST00000344754.4	hg19	CCDS13060.1	.	.	.	.	.	.	.	.	.	.	G	4.313	0.057463	0.08339	.	.	ENSG00000088827	ENST00000419548	.	.	.	5.48	-0.652	0.11450	.	.	.	.	.	T	0.43897	0.1268	.	.	.	0.58432	D	0.999997	.	.	.	.	.	.	T	0.30119	-0.9989	4	.	.	.	.	4.1016	0.10015	0.4441:0.1778:0.3781:0.0	.	.	.	.	N	350	.	.	H	-	1	0	SIGLEC1	3618895	0.011000	0.17503	0.956000	0.39512	0.527000	0.34593	-0.145000	0.10265	0.290000	0.22444	0.561000	0.74099	CAC	.	.		0.602	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068		T	3670895	G	T	3670895	2	4	255	1	0	0	0	0	0	0	0	1	14320	1335	47	3		3	SIGLEC1	20	3670895	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	15686	3670895	59354625	726	36071										
KIF16B	55614	hgsc.bcm.edu	37	chr20	16492142	16492142	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gacttccgccgaagtagatcTctcacacgttcgttataaat	7	11	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr20:16492142T>C	ENST00000354981.2	-	6	634	c.477A>G	c.(475-477)agA>agG	p.R159R	KIF16B_ENST00000408042.1_Silent_p.R159R|KIF16B_ENST00000378003.2_5'UTR|KIF16B_ENST00000355755.3_Silent_p.R159R	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	159	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|early endosome to late endosome transport (GO:0045022)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|formation of primary germ layer (GO:0001704)|Golgi to endosome transport (GO:0006895)|microtubule-based movement (GO:0007018)|receptor catabolic process (GO:0032801)|regulation of receptor recycling (GO:0001919)	early endosome (GO:0005769)|endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(24)|ovary(1)|prostate(15)|skin(3)|upper_aerodigestive_tract(2)	74						GAAGTAGATCTCTCACACGTT	0.338																																					p.R159R		Atlas-SNP	.											.	KIF16B	305	.	0			c.A477G						.						70	69	69					20																	16492142		2203	4300	6503	SO:0001819	synonymous_variant	55614	exon6			TAGATCTCTCACA	AK000142	CCDS13122.1, CCDS56178.1	20p11.23	2008-03-03	2008-03-03	2008-03-03	ENSG00000089177	ENSG00000089177		"Kinesins"	15869	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 23"	C20orf23		16084724, 16782399	Standard	NM_024704		Approved	FLJ20135, dJ971B4.1, SNX23	uc010gci.2	Q96L93	OTTHUMG00000031927	ENST00000354981.2:c.477A>G	chr20.hg19:g.16492142T>C		106.0	0.0		94.0	4.0	NM_001199865	A6NKJ9|A7E2A8|B1AKG3|B1AKT7|C9JDN5|C9JI52|C9JSM8|C9JWJ7|Q2TBF5|Q5HYC0|Q5HYK1|Q5JWW3|Q5TFK5|Q86VL9|Q86YS5|Q8IYU0|Q9BQJ8|Q9BQM0|Q9BQM1|Q9BQM5|Q9H5U0|Q9HCI2|Q9NXN9	Silent	SNP	ENST00000354981.2	hg19	CCDS13122.1																																																																																			.	.		0.338	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683		C	16492142	T	C	16492142	2	2	255	1	0	0	0	0	0	0	0	1	8287	1548	54	2		2	KIF16B	20	16492142	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	12821247	16492142	46533378	727	36072										
MYLK2	85366	hgsc.bcm.edu	37	chr20	30419870	30419870	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aacaacctggcggagaaagcCaaacgctgtaaccgacgcct	10	13	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr20:30419870C>A	ENST00000375994.2	+	11	1914	c.1641C>A	c.(1639-1641)gcC>gcA	p.A547A	MYLK2_ENST00000375985.4_Silent_p.A547A|MYLK2_ENST00000468730.1_3'UTR			Q9H1R3	MYLK2_HUMAN	myosin light chain kinase 2	547					cardiac muscle contraction (GO:0060048)|cardiac muscle tissue morphogenesis (GO:0055008)|neuromuscular synaptic transmission (GO:0007274)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of gene expression (GO:0010628)|protein autophosphorylation (GO:0046777)|regulation of muscle filament sliding (GO:0032971)|skeletal muscle cell differentiation (GO:0035914)|skeletal muscle satellite cell differentiation (GO:0014816)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|myosin light chain kinase activity (GO:0004687)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			CGGAGAAAGCCAAACGCTGTA	0.602																																					p.A547A		Atlas-SNP	.											.	MYLK2	76	.	0			c.C1641A						.						46	36	40					20																	30419870		2203	4300	6503	SO:0001819	synonymous_variant	85366	exon12			GAAAGCCAAACGC	AF325549	CCDS13191.1	20q13.31	2014-09-17	2008-01-23		ENSG00000101306	ENSG00000101306	2.7.11.18		16243	protein-coding gene	gene with protein product	"skeletal muscle myosin light chain kinase"	606566	"myosin light chain kinase 2, skeletal muscle"				Standard	NM_033118		Approved	skMLCK, KMLC, MLCK2	uc002wwq.2	Q9H1R3	OTTHUMG00000032194	ENST00000375994.2:c.1641C>A	chr20.hg19:g.30419870C>A		77.0	0.0		98.0	6.0	NM_033118	Q569L1|Q96I84	Silent	SNP	ENST00000375994.2	hg19	CCDS13191.1																																																																																			.	.		0.602	MYLK2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078583.2	NM_033118		A	30419870	C	A	30419870	2	1	255	1	0	0	0	0	0	0	0	1	10066	581	21	3		3	MYLK2	20	30419870	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	13927728	30419870	32605650	728	36073										
CEP250	11190	hgsc.bcm.edu	37	chr20	34067549	34067549	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	atagaggtcaccaaggggcaGctggaggtccagattcaaac	13	9	2	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr20:34067549G>T	ENST00000397527.1	+	19	3087	c.2367G>T	c.(2365-2367)caG>caT	p.Q789H	RP3-477O4.14_ENST00000444933.1_RNA|CEP250_ENST00000342580.4_Missense_Mutation_p.Q789H|RP3-477O4.14_ENST00000416260.1_RNA|RP3-477O4.14_ENST00000453914.1_RNA	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	789	Gln/Glu-rich.				centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of centriole-centriole cohesion (GO:0030997)	centriole (GO:0005814)|centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)|spindle pole centrosome (GO:0031616)	protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			CCAAGGGGCAGCTGGAGGTCC	0.488																																					p.Q789H		Atlas-SNP	.											.	CEP250	141	.	0			c.G2367T						.						104	103	104					20																	34067549		2203	4300	6503	SO:0001583	missense	11190	exon19			GGGGCAGCTGGAG	AF022655	CCDS13255.1	20q11.22	2014-02-20	2006-01-11	2006-01-11	ENSG00000126001	ENSG00000126001			1859	protein-coding gene	gene with protein product		609689	"centrosomal protein 2"	CEP2		9506584, 9647649	Standard	NM_007186		Approved	C-NAP1	uc021wco.1	Q9BV73	OTTHUMG00000032343	ENST00000397527.1:c.2367G>T	chr20.hg19:g.34067549G>T	ENSP00000380661:p.Gln789His	170.0	0.0		127.0	41.0	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Missense_Mutation	SNP	ENST00000397527.1	hg19	CCDS13255.1	.	.	.	.	.	.	.	.	.	.	G	17.50	3.404417	0.62288	.	.	ENSG00000126001	ENST00000397527;ENST00000342580	T;T	0.16597	2.33;2.33	5.15	0.996	0.19844	.	0.000000	0.56097	D	0.000035	T	0.38374	0.1038	M	0.87180	2.865	0.33820	D	0.628968	D	0.89917	1.0	D	0.87578	0.998	T	0.46816	-0.9164	10	0.45353	T	0.12	.	5.1638	0.15075	0.3723:0.0:0.4954:0.1323	.	789	Q9BV73	CP250_HUMAN	H	789	ENSP00000380661:Q789H;ENSP00000341541:Q789H	ENSP00000341541:Q789H	Q	+	3	2	CEP250	33530963	0.985000	0.35326	1.000000	0.80357	0.997000	0.91878	0.006000	0.13152	0.354000	0.24105	0.655000	0.94253	CAG	.	.		0.488	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186		T	34067549	G	T	34067549	3	4	255	1	0	0	0	0	1	0	0	0	3254	962	34	3	2429	3	CEP250	20	34067549	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	3647679	34067549	28957971	729	36074										
CEP250	11190	hgsc.bcm.edu	37	chr20	34086433	34086433	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cattttttcagaccagaatgGagctaggagcctctttaaga	9	8	2	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr20:34086433G>T	ENST00000397527.1	+	27	4385	c.3665G>T	c.(3664-3666)gGa>gTa	p.G1222V	CEP250_ENST00000342580.4_Missense_Mutation_p.G1166V	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	1222	Gln/Glu-rich.				centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of centriole-centriole cohesion (GO:0030997)	centriole (GO:0005814)|centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)|spindle pole centrosome (GO:0031616)	protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			GACCAGAATGGAGCTAGGAGC	0.527																																					p.G1222V		Atlas-SNP	.											.	CEP250	141	.	0			c.G3665T						.						75	80	78					20																	34086433		2203	4300	6503	SO:0001583	missense	11190	exon27			AGAATGGAGCTAG	AF022655	CCDS13255.1	20q11.22	2014-02-20	2006-01-11	2006-01-11	ENSG00000126001	ENSG00000126001			1859	protein-coding gene	gene with protein product		609689	"centrosomal protein 2"	CEP2		9506584, 9647649	Standard	NM_007186		Approved	C-NAP1	uc021wco.1	Q9BV73	OTTHUMG00000032343	ENST00000397527.1:c.3665G>T	chr20.hg19:g.34086433G>T	ENSP00000380661:p.Gly1222Val	42.0	0.0		54.0	4.0	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Missense_Mutation	SNP	ENST00000397527.1	hg19	CCDS13255.1	.	.	.	.	.	.	.	.	.	.	G	15.57	2.872338	0.51695	.	.	ENSG00000126001	ENST00000397527;ENST00000342580	T;T	0.10860	2.86;2.83	4.18	2.05	0.26809	.	0.625363	0.15036	N	0.284178	T	0.12732	0.0309	M	0.65975	2.015	0.39236	D	0.963764	P	0.39480	0.675	B	0.41813	0.367	T	0.11690	-1.0577	10	0.30854	T	0.27	.	4.7449	0.13033	0.3708:0.0:0.6292:0.0	.	1222	Q9BV73	CP250_HUMAN	V	1222;1166	ENSP00000380661:G1222V;ENSP00000341541:G1166V	ENSP00000341541:G1166V	G	+	2	0	CEP250	33549847	0.029000	0.19370	0.536000	0.28039	0.848000	0.48234	0.483000	0.22292	0.455000	0.26910	0.455000	0.32223	GGA	.	.		0.527	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186		T	34086433	G	T	34086433	3	4	255	1	0	0	0	0	1	0	0	0	3254	1174	41	3	3759	3	CEP250	20	34086433	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	18884	34086433	28939087	730	36075										
KIAA1755	85449	hgsc.bcm.edu	37	chr20	36851952	36851952	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aggctcacctgcatccccccAggggggtcggccttctcgaa	12	16	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr20:36851952A>G	ENST00000279024.4	-	9	2527	c.2256T>C	c.(2254-2256)ccT>ccC	p.P752P		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	752										breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				GCATCCCCCCAGGGGGGTCGG	0.617																																					p.P752P		Atlas-SNP	.											.	KIAA1755	145	.	0			c.T2256C						.						37	35	36					20																	36851952		2203	4300	6503	SO:0001819	synonymous_variant	85449	exon9			CCCCCCAGGGGGG	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.2256T>C	chr20.hg19:g.36851952A>G		66.0	0.0		79.0	4.0	NM_001029864	Q9C0A8	Silent	SNP	ENST00000279024.4	hg19	CCDS33467.1																																																																																			.	.		0.617	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864		G	36851952	A	G	36851952	2	3	255	1	0	0	0	0	0	0	0	1	8266	175	7	2		2	KIAA1755	20	36851952	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	2765519	36851952	26173568	731	36076										
SNAI1	6615	hgsc.bcm.edu	37	chr20	48600493	48600493	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggcgccccaagcccagccaaTtgcctgggcctcccttcggc	11	19	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr20:48600493T>C	ENST00000244050.2	+	2	276	c.215T>C	c.(214-216)aTt>aCt	p.I72T		NM_005985.3	NP_005976.2	O95863	SNAI1_HUMAN	snail family zinc finger 1	72					cartilage morphogenesis (GO:0060536)|cell migration (GO:0016477)|epithelial to mesenchymal transition (GO:0001837)|hair follicle morphogenesis (GO:0031069)|left/right pattern formation (GO:0060972)|mesoderm formation (GO:0001707)|negative regulation of cell differentiation involved in embryonic placenta development (GO:0060806)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|Notch signaling involved in heart development (GO:0061314)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of tight junction assembly (GO:2000810)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	kinase binding (GO:0019900)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)	17			BRCA - Breast invasive adenocarcinoma(9;4.03e-06)			GCCCAGCCAATTGCCTGGGCC	0.662																																					p.I72T		Atlas-SNP	.											.	SNAI1	28	.	0			c.T215C						.						44	50	48					20																	48600493		2203	4300	6503	SO:0001583	missense	6615	exon2			AGCCAATTGCCTG	AF125377	CCDS13423.1	20q13.2	2013-05-23	2013-05-23		ENSG00000124216	ENSG00000124216		"Snail homologs", "Zinc fingers, C2H2-type"	11128	protein-coding gene	gene with protein product		604238	"snail 1 (drosophila homolog), zinc finger protein", "snail homolog 1 (Drosophila)"			10585766	Standard	NM_005985		Approved	SNA, SLUGH2, SNAH, SNAIL1, SNAIL	uc002xuz.3	O95863	OTTHUMG00000033048	ENST00000244050.2:c.215T>C	chr20.hg19:g.48600493T>C	ENSP00000244050:p.Ile72Thr	72.0	0.0		86.0	5.0	NM_005985	B2R842|Q9P113|Q9UBP7|Q9UHH7	Missense_Mutation	SNP	ENST00000244050.2	hg19	CCDS13423.1	.	.	.	.	.	.	.	.	.	.	T	1.677	-0.507608	0.04231	.	.	ENSG00000124216	ENST00000244050	T	0.21734	1.99	4.09	1.77	0.24775	.	1.733090	0.02986	N	0.146262	T	0.13243	0.0321	N	0.17474	0.49	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.24728	-1.0152	10	0.15066	T	0.55	1.2354	5.9026	0.18976	0.0:0.16:0.1486:0.6914	.	72	O95863	SNAI1_HUMAN	T	72	ENSP00000244050:I72T	ENSP00000244050:I72T	I	+	2	0	SNAI1	48033900	0.000000	0.05858	0.000000	0.03702	0.651000	0.38670	0.378000	0.20569	0.234000	0.21139	-0.410000	0.06199	ATT	.	.		0.662	SNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080350.1			C	48600493	T	C	48600493	3	2	255	1	0	0	0	0	1	0	0	0	14841	1493	52	2	221	2	SNAI1	20	48600493	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	11748541	48600493	14425027	732	36077										
SLC2A4RG	56731	hgsc.bcm.edu	37	chr20	62373570	62373570	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cgatgcagagacacatccgcCtggtgcacctggggtgcggc	15	13	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr20:62373570C>T	ENST00000266077.2	+	5	719	c.667C>T	c.(667-669)Ctg>Ttg	p.L223L	RP4-583P15.10_ENST00000447343.2_RNA|SLC2A4RG_ENST00000493772.1_3'UTR	NM_020062.3	NP_064446.2	Q9NR83	S2A4R_HUMAN	SLC2A4 regulator	223					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|kidney(1)|lung(2)|prostate(2)|skin(1)	7	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					ACACATCCGCCTGGTGCACCT	0.706																																					p.L223L		Atlas-SNP	.											.	SLC2A4RG	20	.	0			c.C667T						.						16	20	18					20																	62373570		2171	4269	6440	SO:0001819	synonymous_variant	56731	exon5			ATCCGCCTGGTGC	AF249267	CCDS13537.1	20q13.33	2010-03-11			ENSG00000125520	ENSG00000125520			15930	protein-coding gene	gene with protein product	"GLUT4 enhancer factor", "Huntington's disease gene regulatory region-binding protein 1"	609493				10825161	Standard	NM_020062		Approved	GEF, HDBP1, Si-1-2, Si-1-2-19	uc002ygq.3	Q9NR83	OTTHUMG00000032997	ENST00000266077.2:c.667C>T	chr20.hg19:g.62373570C>T		126.0	0.0		137.0	62.0	NM_020062	Q2PHL5|Q6F6I6|Q6F6I7|Q6GTK5|Q8TAH5|Q8WVW7|Q96QD3|Q9BV85	Silent	SNP	ENST00000266077.2	hg19	CCDS13537.1																																																																																			.	.		0.706	SLC2A4RG-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080202.1	NM_020062		T	62373570	C	T	62373570	2	4	255	1	0	0	0	0	0	0	0	1	14562	680	24	3		3	SLC2A4RG	20	62373570	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	13773077	62373570	651950	733	36078										
CXADR	1525	hgsc.bcm.edu	37	chr21	18919456	18919456	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tagtcccgaagaccagggacCgctggacatcgagtggctga	14	11	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr21:18919456C>A	ENST00000284878.7	+	2	903	c.155C>A	c.(154-156)cCg>cAg	p.P52Q	CXADR_ENST00000400169.1_Missense_Mutation_p.P52Q|CXADR_ENST00000306618.10_Missense_Mutation_p.P52Q|CXADR_ENST00000400166.1_Missense_Mutation_p.P52Q|CXADR_ENST00000356275.6_Missense_Mutation_p.P52Q|CXADR_ENST00000400165.1_Missense_Mutation_p.P52Q	NM_001338.4	NP_001329.1	P78310	CXAR_HUMAN	coxsackie virus and adenovirus receptor	52	Ig-like C2-type 1.				actin cytoskeleton reorganization (GO:0031532)|AV node cell to bundle of His cell communication (GO:0086067)|blood coagulation (GO:0007596)|cardiac muscle fiber development (GO:0048739)|cell-cell junction organization (GO:0045216)|defense response to virus (GO:0051607)|epithelial structure maintenance (GO:0010669)|gamma-delta T cell activation (GO:0046629)|germ cell migration (GO:0008354)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|homotypic cell-cell adhesion (GO:0034109)|leukocyte migration (GO:0050900)|mitochondrion organization (GO:0007005)|neutrophil chemotaxis (GO:0030593)|regulation of immune response (GO:0050776)|transepithelial transport (GO:0070633)|viral process (GO:0016032)	acrosomal vesicle (GO:0001669)|adherens junction (GO:0005912)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell body (GO:0044297)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|filopodium (GO:0030175)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|cell adhesion molecule binding (GO:0050839)|connexin binding (GO:0071253)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|PDZ domain binding (GO:0030165)|receptor binding (GO:0005102)|virus receptor activity (GO:0001618)			endometrium(2)|large_intestine(5)|lung(1)|ovary(1)|prostate(2)	11				Epithelial(23;0.000206)|all cancers(11;0.000302)|OV - Ovarian serous cystadenocarcinoma(11;0.0194)|Lung(58;0.0233)|COAD - Colon adenocarcinoma(22;0.0389)|Colorectal(24;0.0483)|LUSC - Lung squamous cell carcinoma(23;0.0782)		GACCAGGGACCGCTGGACATC	0.468																																					p.P52Q		Atlas-SNP	.											.	CXADR	44	.	0			c.C155A						.						91	77	82					21																	18919456		2203	4300	6503	SO:0001583	missense	1525	exon2			AGGGACCGCTGGA	Y07593	CCDS33519.1, CCDS56204.1, CCDS56205.1, CCDS56206.1, CCDS56207.1	21q21.1	2013-01-29			ENSG00000154639	ENSG00000154639		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	2559	protein-coding gene	gene with protein product		602621				9036860, 9096397	Standard	NM_001338		Approved	CAR	uc002yki.3	P78310	OTTHUMG00000074508	ENST00000284878.7:c.155C>A	chr21.hg19:g.18919456C>A	ENSP00000284878:p.Pro52Gln	67.0	0.0		57.0	4.0	NM_001207065	B2R8V8|B7WPI3|D3YHP0|O00694|Q8WWT6|Q8WWT7|Q8WWT8|Q9UKV4	Missense_Mutation	SNP	ENST00000284878.7	hg19	CCDS33519.1	.	.	.	.	.	.	.	.	.	.	C	16.55	3.153859	0.57259	.	.	ENSG00000154639	ENST00000284878;ENST00000400166;ENST00000356275;ENST00000400169;ENST00000400165;ENST00000306618	T;T;T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19;-1.19;-1.19	5.11	4.21	0.49690	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.145075	0.64402	D	0.000006	D	0.84960	0.5588	M	0.72894	2.215	0.54753	D	0.999982	D;D;D;D;D	0.89917	0.974;1.0;0.998;0.989;1.0	P;D;D;P;D	0.75020	0.768;0.978;0.977;0.905;0.985	T	0.82470	-0.0441	10	0.13853	T	0.58	.	14.7428	0.69469	0.1461:0.8539:0.0:0.0	.	52;52;52;52;52	P78310-3;P78310-4;B7WPI3;P78310;P78310-5	.;.;.;CXAR_HUMAN;.	Q	52	ENSP00000284878:P52Q;ENSP00000383030:P52Q;ENSP00000348620:P52Q;ENSP00000383033:P52Q;ENSP00000383029:P52Q;ENSP00000303395:P52Q	ENSP00000284878:P52Q	P	+	2	0	CXADR	17841327	0.998000	0.40836	0.635000	0.29338	0.466000	0.32739	6.588000	0.74076	1.449000	0.47699	0.655000	0.94253	CCG	.	.		0.468	CXADR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000158209.1			A	18919456	C	A	18919456	3	1	255	1	0	0	0	0	1	0	0	0	4078	652	23	1	161	1	CXADR	21	18919456	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10		18919456	29210439	734	36079										
ADAMTS5	11096	hgsc.bcm.edu	37	chr21	28296553	28296553	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gcggctgcgaagtgtgtgatCccactttattgctgccatga	12	10	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr21:28296553C>A	ENST00000284987.5	-	8	2733	c.2612G>T	c.(2611-2613)gGa>gTa	p.G871V	AP001601.2_ENST00000426771.1_RNA	NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 5	871	Spacer.				defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	72						AGTGTGTGATCCCACTTTATT	0.522																																					p.G871V	Esophageal Squamous(53;683 1080 10100 14424 45938)	Atlas-SNP	.											.	ADAMTS5	184	.	0			c.G2612T						.						108	103	105					21																	28296553		2203	4300	6503	SO:0001583	missense	11096	exon8			TGTGATCCCACTT	AF142099	CCDS13579.1	21q21.3	2008-07-31	2008-07-31		ENSG00000154736	ENSG00000154736		"ADAM metallopeptidases with thrombospondin type 1 motif"	221	protein-coding gene	gene with protein product	"aggrecanase-2"	605007	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"			10438522	Standard	NM_007038		Approved	ADMP-2, ADAMTS11	uc002ymg.3	Q9UNA0	OTTHUMG00000078686	ENST00000284987.5:c.2612G>T	chr21.hg19:g.28296553C>A	ENSP00000284987:p.Gly871Val	104.0	0.0		133.0	51.0	NM_007038	Q52LV4|Q9UKP2	Missense_Mutation	SNP	ENST00000284987.5	hg19	CCDS13579.1	.	.	.	.	.	.	.	.	.	.	C	0.265	-0.996879	0.02145	.	.	ENSG00000154736	ENST00000284987	T	0.63096	-0.02	5.54	2.69	0.31865	.	0.846026	0.10799	N	0.632875	T	0.34629	0.0904	N	0.04203	-0.255	0.34851	D	0.741686	B	0.02656	0.0	B	0.04013	0.001	T	0.30208	-0.9986	10	0.30078	T	0.28	.	3.8348	0.08889	0.3709:0.392:0.1617:0.0755	.	871	Q9UNA0	ATS5_HUMAN	V	871	ENSP00000284987:G871V	ENSP00000284987:G871V	G	-	2	0	ADAMTS5	27218424	0.343000	0.24818	0.416000	0.26546	0.125000	0.20455	1.929000	0.40114	0.401000	0.25424	-0.274000	0.10170	GGA	.	.		0.522	ADAMTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171648.1			A	28296553	C	A	28296553	3	1	255	1	0	0	0	0	1	0	0	0	269	855	30	3	184	3	ADAMTS5	21	28296553	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	9377097	28296553	19833342	735	36080										
SLC37A1	54020	hgsc.bcm.edu	37	chr21	43979198	43979198	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cacaggggccttgaaaattcCagtaagtaaacgtgcccagg	11	10	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr21:43979198C>A	ENST00000352133.2	+	11	1962	c.980C>A	c.(979-981)cCa>cAa	p.P327Q	AP001625.6_ENST00000442605.1_RNA|SLC37A1_ENST00000398341.3_Splice_Site_p.P327Q			P57057	GLPT_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 1	327					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	transporter activity (GO:0005215)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|liver(2)|lung(3)	15						TTGAAAATTCCAGTAAGTAAA	0.557																																					p.P327Q		Atlas-SNP	.											.	SLC37A1	48	.	0			c.C980A						.						38	40	39					21																	43979198		2203	4300	6503	SO:0001630	splice_region_variant	54020	exon12			AAATTCCAGTAAG	AJ269529	CCDS13689.1	21q22.3	2013-07-17	2013-07-17		ENSG00000160190	ENSG00000160190		"Solute carriers"	11024	protein-coding gene	gene with protein product		608094	"solute carrier family 37 (glycerol-3-phosphate transporter), member 1"			11112347	Standard	NM_018964		Approved		uc002zbi.3	P57057	OTTHUMG00000086803	ENST00000352133.2:c.981+1C>A	chr21.hg19:g.43979198C>A		37.0	0.0		51.0	5.0	NM_018964	D3DSJ7|Q9HAQ1	Missense_Mutation	SNP	ENST00000352133.2	hg19	CCDS13689.1	.	.	.	.	.	.	.	.	.	.	C	17.34	3.365300	0.61513	.	.	ENSG00000160190	ENST00000398341;ENST00000352133	T;T	0.63096	-0.02;-0.02	5.7	5.7	0.88788	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.80618	0.4657	M	0.82193	2.58	0.80722	D	1	D	0.76494	0.999	D	0.71414	0.973	T	0.82659	-0.0348	10	0.66056	D	0.02	-17.2009	16.7639	0.85519	0.0:1.0:0.0:0.0	.	327	P57057	GLPT_HUMAN	Q	327	ENSP00000381383:P327Q;ENSP00000344648:P327Q	ENSP00000344648:P327Q	P	+	2	0	SLC37A1	42852267	0.997000	0.39634	0.652000	0.29579	0.003000	0.03518	5.609000	0.67661	2.688000	0.91661	0.655000	0.94253	CCA	.	.		0.557	SLC37A1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195377.1		Missense_Mutation	A	43979198	C	A	43979198	5	1	255	1	0	0	0	0	0	0	1	0	14612	608	21	3	1018	3	SLC37A1	21	43979198	Splice_Site	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	15682645	43979198	4150697	736	36081										
WDR4	10785	hgsc.bcm.edu	37	chr21	44274711	44274711	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cgcagttctcctggcaccagAatgcaatcctggacgcggca	11	14	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr21:44274711A>G	ENST00000398208.2	-	8	811	c.752T>C	c.(751-753)tTc>tCc	p.F251S	WDR4_ENST00000492742.1_5'UTR|WDR4_ENST00000330317.2_Missense_Mutation_p.F251S	NM_001260474.1|NM_001260475.1|NM_001260476.1|NM_018669.5	NP_001247403.1|NP_001247404.1|NP_001247405.1|NP_061139.2			WD repeat domain 4											haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|ovary(2)	11				Colorectal(79;0.0165)|Lung(125;0.0484)|STAD - Stomach adenocarcinoma(101;0.0624)|COAD - Colon adenocarcinoma(84;0.128)|LUSC - Lung squamous cell carcinoma(216;0.244)		CTGGCACCAGAATGCAATCCT	0.607																																					p.F251S		Atlas-SNP	.											.	WDR4	35	.	0			c.T752C						.						36	36	36					21																	44274711		2203	4300	6503	SO:0001583	missense	10785	exon8			CACCAGAATGCAA	AJ243912	CCDS13691.1	21q22.3	2013-01-09			ENSG00000160193	ENSG00000160193		"WD repeat domain containing"	12756	protein-coding gene	gene with protein product	"TRM82 tRNA methyltransferase 82 homolog (S. cerevisiae)"	605924				12403464	Standard	NM_018669		Approved	TRM82, TRMT82	uc002zci.4	P57081	OTTHUMG00000086826	ENST00000398208.2:c.752T>C	chr21.hg19:g.44274711A>G	ENSP00000381266:p.Phe251Ser	51.0	0.0		55.0	4.0	NM_018669		Missense_Mutation	SNP	ENST00000398208.2	hg19	CCDS13691.1	.	.	.	.	.	.	.	.	.	.	A	5.960	0.361096	0.11296	.	.	ENSG00000160193	ENST00000330317;ENST00000398208	T;T	0.36878	1.23;1.23	3.46	2.28	0.28536	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.321965	0.29791	N	0.011181	T	0.22360	0.0539	L	0.29908	0.895	0.29659	N	0.843374	B;B	0.15141	0.012;0.009	B;B	0.16289	0.015;0.006	T	0.10567	-1.0624	10	0.44086	T	0.13	-19.9255	5.1598	0.15054	0.406:0.0:0.0:0.594	.	250;251	P57081-2;P57081	.;WDR4_HUMAN	S	251	ENSP00000328671:F251S;ENSP00000381266:F251S	ENSP00000328671:F251S	F	-	2	0	WDR4	43147780	0.996000	0.38824	0.432000	0.26747	0.382000	0.30200	1.487000	0.35540	0.508000	0.28173	0.482000	0.46254	TTC	.	.		0.607	WDR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195479.1			G	44274711	A	G	44274711	3	3	255	1	0	0	0	0	1	0	0	0	17308	246	9	2	502	2	WDR4	21	44274711	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	295513	44274711	3855184	737	36082										
C21orf29	54084	hgsc.bcm.edu	37	chr21	45953608	45953608	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gtccgtggtgagggagaagaCgcctgcggacacagccagga	17	10	0	3	rs370848096	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr21:45953608C>T	ENST00000323084.4	-	3	567	c.502G>A	c.(502-504)Gtc>Atc	p.V168I	TSPEAR_ENST00000397916.1_Missense_Mutation_p.V100I	NM_001272037.1|NM_144991.2	NP_001258966.1|NP_659428.2	Q8WU66	TSEAR_HUMAN	thrombospondin-type laminin G domain and EAR repeats	168	Laminin G-like.				sensory perception of sound (GO:0007605)	cell surface (GO:0009986)|ciliary membrane (GO:0060170)|extracellular region (GO:0005576)|stereocilium (GO:0032420)				breast(1)|central_nervous_system(6)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	37						AGGGAGAAGACGCCTGCGGAC	0.697													C|||	2	0.000399361	0	0	5008	,	,		12838	0		0	False		,,,				2504	0.002				p.V168I		Atlas-SNP	.											.	TSPEAR	110	.	0			c.G502A						.						25	25	25					21																	45953608		2192	4291	6483	SO:0001583	missense	54084	exon3			AGAAGACGCCTGC	AJ487962	CCDS13712.1, CCDS74801.1	21q22.3	2012-10-30	2011-01-25	2011-01-25	ENSG00000175894	ENSG00000175894			1268	protein-coding gene	gene with protein product		612920	"chromosome 21 open reading frame 29", "deafness, autosomal recessive 98"	C21orf29, DFNB98		12095917, 22678063	Standard	NM_144991		Approved	MGC11251, TSP-EAR	uc002zfe.1	Q8WU66	OTTHUMG00000041215	ENST00000323084.4:c.502G>A	chr21.hg19:g.45953608C>T	ENSP00000321987:p.Val168Ile	124.0	0.0		188.0	74.0	NM_144991		Missense_Mutation	SNP	ENST00000323084.4	hg19	CCDS13712.1	.	.	.	.	.	.	.	.	.	.	c	1.389	-0.581309	0.03854	.	.	ENSG00000175894	ENST00000323084;ENST00000397916;ENST00000341581	T;T	0.43688	0.94;0.94	4.99	-0.667	0.11395	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);Laminin G, thrombospondin-type, N-terminal (1);	0.779066	0.12485	N	0.464779	T	0.15912	0.0383	N	0.03608	-0.345	0.09310	N	1	B	0.18741	0.03	B	0.09377	0.004	T	0.26155	-1.0111	10	0.16896	T	0.51	3.2862	6.7678	0.23576	0.4228:0.2357:0.0:0.3415	.	168	Q8WU66	TSEAR_HUMAN	I	168;100;168	ENSP00000321987:V168I;ENSP00000381012:V100I	ENSP00000321987:V168I	V	-	1	0	TSPEAR	44778036	0.995000	0.38212	0.012000	0.15200	0.000000	0.00434	3.040000	0.49799	-0.754000	0.04715	-2.269000	0.00276	GTC	.	.		0.697	TSPEAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098761.1	NM_144991		T	45953608	C	T	45953608	3	4	255	1	0	0	0	0	1	0	0	0	2126	536	19	1	1547	1	C21orf29	21	45953608	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1678897	45953608	2176287	738	36083										
ITGB2	3689	hgsc.bcm.edu	37	chr21	46321640	46321640	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cacggtcttgtccacgaaggAcccgaagcctgcagggcaca	12	14	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr21:46321640A>G	ENST00000397850.2	-	7	960	c.508T>C	c.(508-510)Tcc>Ccc	p.S170P	ITGB2_ENST00000397854.3_Missense_Mutation_p.S113P|ITGB2_ENST00000355153.4_Missense_Mutation_p.S170P|ITGB2_ENST00000397857.1_Missense_Mutation_p.S170P|ITGB2_ENST00000397852.1_Missense_Mutation_p.S170P|ITGB2_ENST00000302347.5_Missense_Mutation_p.S170P			P05107	ITB2_HUMAN	integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)	170	VWFA.				apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|neutrophil chemotaxis (GO:0030593)|receptor clustering (GO:0043113)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|vesicle (GO:0031982)	cell adhesion molecule binding (GO:0050839)|glycoprotein binding (GO:0001948)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(4)|skin(3)	35				Colorectal(79;0.0669)	Simvastatin(DB00641)	TCCACGAAGGACCCGAAGCCT	0.637																																					p.S170P		Atlas-SNP	.											.	ITGB2	107	.	0			c.T508C						.						60	54	56					21																	46321640		2203	4300	6503	SO:0001583	missense	3689	exon6			CGAAGGACCCGAA	AK222505	CCDS13716.1	21q22.3	2014-09-17	2006-03-02		ENSG00000160255	ENSG00000160255		"CD molecules", "Complement system", "Integrins"	6155	protein-coding gene	gene with protein product		600065	"integrin, beta 2 (antigen CD18 (p95), lymphocyte function-associated antigen 1; macrophage antigen 1 (mac-1) beta subunit)"	CD18, MFI7			Standard	NM_000211		Approved	LFA-1, MAC-1	uc002zgf.3	P05107	OTTHUMG00000090257	ENST00000397850.2:c.508T>C	chr21.hg19:g.46321640A>G	ENSP00000380948:p.Ser170Pro	63.0	0.0		67.0	5.0	NM_000211	B3KTS8|D3DSM1|Q16418|Q53HS5|Q9UD72	Missense_Mutation	SNP	ENST00000397850.2	hg19	CCDS13716.1	.	.	.	.	.	.	.	.	.	.	A	16.07	3.017791	0.54576	.	.	ENSG00000160255	ENST00000397852;ENST00000397857;ENST00000397854;ENST00000355153;ENST00000397850;ENST00000302347;ENST00000545414;ENST00000320216	D;D;D;D;D;D;D	0.94758	-3.51;-3.51;-3.51;-3.51;-3.51;-3.51;-3.51	4.14	4.14	0.48551	Integrin beta subunit, N-terminal (2);von Willebrand factor, type A (1);	.	.	.	.	D	0.97751	0.9262	H	0.95470	3.675	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.78314	0.991;0.991	D	0.98047	1.0385	9	0.62326	D	0.03	.	11.1595	0.48507	1.0:0.0:0.0:0.0	.	113;170	A8MYE6;P05107	.;ITB2_HUMAN	P	170;170;113;170;170;170;113;161	ENSP00000380950:S170P;ENSP00000380955:S170P;ENSP00000380952:S113P;ENSP00000347279:S170P;ENSP00000380948:S170P;ENSP00000303242:S170P;ENSP00000317697:S161P	ENSP00000303242:S170P	S	-	1	0	ITGB2	45146068	1.000000	0.71417	0.977000	0.42913	0.053000	0.15095	5.377000	0.66184	1.750000	0.51863	0.454000	0.30748	TCC	.	.		0.637	ITGB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206566.2	NM_000211		G	46321640	A	G	46321640	3	3	255	1	0	0	0	0	1	0	0	0	7903	275	10	2	1845	2	ITGB2	21	46321640	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	368032	46321640	1808255	739	36084										
ITGB2	3689	hgsc.bcm.edu	37	chr21	46330223	46330223	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttctggcaccaggtgcagccGggccccgactcgatgcattc	12	15	1	0	rs375907746		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr21:46330223G>T	ENST00000397850.2	-	4	575	c.123C>A	c.(121-123)ccC>ccA	p.P41P	ITGB2_ENST00000397854.3_Silent_p.P41P|ITGB2_ENST00000355153.4_Silent_p.P41P|ITGB2_ENST00000397857.1_Silent_p.P41P|ITGB2_ENST00000397852.1_Silent_p.P41P|ITGB2_ENST00000397846.3_Silent_p.P41P|ITGB2_ENST00000302347.5_Silent_p.P41P|ITGB2_ENST00000523126.1_5'UTR			P05107	ITB2_HUMAN	integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)	41					apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|neutrophil chemotaxis (GO:0030593)|receptor clustering (GO:0043113)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|vesicle (GO:0031982)	cell adhesion molecule binding (GO:0050839)|glycoprotein binding (GO:0001948)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(4)|skin(3)	35				Colorectal(79;0.0669)	Simvastatin(DB00641)	AGGTGCAGCCGGGCCCCGACT	0.662																																					p.P41P		Atlas-SNP	.											.	ITGB2	107	.	0			c.C123A						.						47	44	45					21																	46330223		2203	4300	6503	SO:0001819	synonymous_variant	3689	exon3			GCAGCCGGGCCCC	AK222505	CCDS13716.1	21q22.3	2014-09-17	2006-03-02		ENSG00000160255	ENSG00000160255		"CD molecules", "Complement system", "Integrins"	6155	protein-coding gene	gene with protein product		600065	"integrin, beta 2 (antigen CD18 (p95), lymphocyte function-associated antigen 1; macrophage antigen 1 (mac-1) beta subunit)"	CD18, MFI7			Standard	NM_000211		Approved	LFA-1, MAC-1	uc002zgf.3	P05107	OTTHUMG00000090257	ENST00000397850.2:c.123C>A	chr21.hg19:g.46330223G>T		104.0	0.0		143.0	6.0	NM_000211	B3KTS8|D3DSM1|Q16418|Q53HS5|Q9UD72	Silent	SNP	ENST00000397850.2	hg19	CCDS13716.1																																																																																			.	.		0.662	ITGB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206566.2	NM_000211		T	46330223	G	T	46330223	2	4	255	1	0	0	0	0	0	0	0	1	7903	1103	39	1		1	ITGB2	21	46330223	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	8583	46330223	1799672	740	36085										
CCT8L2	150160	hgsc.bcm.edu	37	chr22	17072001	17072001	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tttattatcccttcagttccCacacccattaggaggttccc	5	14	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:17072001C>A	ENST00000359963.3	-	1	1699	c.1440G>T	c.(1438-1440)gtG>gtT	p.V480V		NM_014406.4	NP_055221.1	Q96SF2	TCPQM_HUMAN	chaperonin containing TCP1, subunit 8 (theta)-like 2	480					anion transport (GO:0006820)|cellular protein metabolic process (GO:0044267)|potassium ion transmembrane transport (GO:0071805)|transport (GO:0006810)	cytoplasm (GO:0005737)	anion channel activity (GO:0005253)|ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)			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)				CTTCAGTTCCCACACCCATTA	0.512																																					p.V480V		Atlas-SNP	.											CCT8L2,bladder,carcinoma,0,1	CCT8L2	150	.	0			c.G1440T						.						145	141	143					22																	17072001		2203	4300	6503	SO:0001819	synonymous_variant	150160	exon1			AGTTCCCACACCC	AP003553	CCDS13738.1	22q11.1	2011-09-01			ENSG00000198445	ENSG00000198445			15553	protein-coding gene	gene with protein product							Standard	NM_014406		Approved	CESK1	uc002zlp.1	Q96SF2	OTTHUMG00000141302	ENST00000359963.3:c.1440G>T	chr22.hg19:g.17072001C>A		285.0	0.0		155.0	113.0	NM_014406	A4QPH3|Q9UJS3	Silent	SNP	ENST00000359963.3	hg19	CCDS13738.1																																																																																			.	.		0.512	CCT8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280580.1			A	17072001	C	A	17072001	2	1	255	1	0	0	0	0	0	0	0	1	2963	581	21	3		3	CCT8L2	22	17072001	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10		17072001	34232565	741	36086										
CLTCL1	8218	hgsc.bcm.edu	37	chr22	19222036	19222036	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	attcaaggtttatcacctttGgtgcagacgctgcaactttg	9	9	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:19222036G>T	ENST00000263200.10	-	7	1235	c.1163C>A	c.(1162-1164)cCa>cAa	p.P388Q	CLTCL1_ENST00000353891.5_Missense_Mutation_p.P388Q|CLTCL1_ENST00000427926.1_Missense_Mutation_p.P388Q	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	388	Globular terminal domain.				anatomical structure morphogenesis (GO:0009653)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|positive regulation of glucose import (GO:0046326)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|spindle (GO:0005819)|trans-Golgi network (GO:0005802)	signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					TATCACCTTTGGTGCAGACGC	0.428			T	?	ALCL																																p.P388Q		Atlas-SNP	.		Dom	yes		22	22q11.21	8218	"clathrin, heavy polypeptide-like 1"		L	.	CLTCL1	115	.	0			c.C1163A						.						38	37	38					22																	19222036		1884	4117	6001	SO:0001583	missense	8218	exon7			ACCTTTGGTGCAG		CCDS46662.1, CCDS54497.1, CCDS46662.2, CCDS54497.2	22q11.2	2008-06-10	2006-09-29		ENSG00000070371	ENSG00000070371			2093	protein-coding gene	gene with protein product		601273	"clathrin, heavy polypeptide-like 1"	CLTCL		8844170, 15133132	Standard	NM_007098		Approved	CLTD, CLH22, CHC22	uc021wle.1	P53675	OTTHUMG00000150109	ENST00000263200.10:c.1163C>A	chr22.hg19:g.19222036G>T	ENSP00000445677:p.Pro388Gln	138.0	0.0		83.0	4.0	NM_001835	B7Z7U5|Q14017|Q15808|Q15809	Missense_Mutation	SNP	ENST00000263200.10	hg19	CCDS46662.1	.	.	.	.	.	.	.	.	.	.	G	19.68	3.873517	0.72180	.	.	ENSG00000070371	ENST00000353891;ENST00000263200;ENST00000427926	T;T;T	0.52754	0.65;0.65;0.65	3.29	3.29	0.37713	Armadillo-type fold (1);	0.000000	0.64402	D	0.000002	T	0.72269	0.3439	M	0.88842	2.985	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.997;1.0	T	0.79971	-0.1578	10	0.66056	D	0.02	-6.0763	15.0953	0.72229	0.0:0.0:1.0:0.0	.	388;388	P53675-2;P53675	.;CLH2_HUMAN	Q	388	ENSP00000439662:P388Q;ENSP00000445677:P388Q;ENSP00000441158:P388Q	ENSP00000445677:P388Q	P	-	2	0	CLTCL1	17602036	1.000000	0.71417	1.000000	0.80357	0.814000	0.46013	8.619000	0.90938	1.847000	0.53656	0.460000	0.39030	CCA	.	.		0.428	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098		T	19222036	G	T	19222036	3	4	255	1	0	0	0	0	1	0	0	0	3569	1348	47	3	3863	3	CLTCL1	22	19222036	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	2150035	19222036	32082530	742	36087										
C22orf29	79680	hgsc.bcm.edu	37	chr22	19839039	19839039	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cgaacagagcacttctagatAcagagttggacccagacaca	9	11	1	4			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:19839039A>G	ENST00000405640.1	-	2	1414	c.746T>C	c.(745-747)gTa>gCa	p.V249A	GNB1L_ENST00000329517.6_Intron|C22orf29_ENST00000328554.4_Missense_Mutation_p.V249A|C22orf29_ENST00000407472.1_Missense_Mutation_p.V249A|GNB1L_ENST00000403325.1_Intron|GNB1L_ENST00000405009.1_Intron|GNB1L_ENST00000460402.1_Intron|C22orf29_ENST00000484072.1_Intron			Q7L3V2	BOP_HUMAN	chromosome 22 open reading frame 29	249					mitochondrial outer membrane permeabilization (GO:0097345)|regulation of mitochondrial membrane potential (GO:0051881)	mitochondrion (GO:0005739)				NS(1)|large_intestine(1)|lung(3)|prostate(1)|urinary_tract(1)	7	Colorectal(54;0.0993)					ACTTCTAGATACAGAGTTGGA	0.592																																					p.V249A		Atlas-SNP	.											.	C22orf29	23	.	0			c.T746C						.						66	70	69					22																	19839039		2203	4300	6503	SO:0001583	missense	79680	exon3			CTAGATACAGAGT	BX640998	CCDS13769.1	22q11.21	2006-07-05			ENSG00000215012	ENSG00000215012			26112	protein-coding gene	gene with protein product						12477932	Standard	NM_024627		Approved	FLJ21125	uc002zqh.3	Q7L3V2	OTTHUMG00000030314	ENST00000405640.1:c.746T>C	chr22.hg19:g.19839039A>G	ENSP00000384924:p.Val249Ala	102.0	0.0		88.0	4.0	NM_024627	A8K5E7|D3DX21|Q6MZM8|Q6N000|Q9H7A0	Missense_Mutation	SNP	ENST00000405640.1	hg19	CCDS13769.1	.	.	.	.	.	.	.	.	.	.	A	6.930	0.541218	0.13250	.	.	ENSG00000215012	ENST00000407472;ENST00000328554;ENST00000405640	T;T;T	0.26957	1.7;1.7;1.7	3.72	-7.43	0.01383	.	7.488640	0.01795	N	0.032529	T	0.10337	0.0253	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.15350	-1.0440	10	0.21540	T	0.41	.	3.99	0.09533	0.5967:0.1215:0.1589:0.1228	.	249	Q7L3V2	CV029_HUMAN	A	249	ENSP00000386111:V249A;ENSP00000330596:V249A;ENSP00000384924:V249A	ENSP00000330596:V249A	V	-	2	0	C22orf29	18219039	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.175000	0.03102	-1.792000	0.01259	-1.338000	0.01255	GTA	.	.		0.592	C22orf29-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317290.2	NM_024627		G	19839039	A	G	19839039	3	3	255	1	0	0	0	0	1	0	0	0	2143	391	14	2	352	2	C22orf29	22	19839039	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	617003	19839039	31465527	743	36088										
SNAP29	9342	hgsc.bcm.edu	37	chr22	21235375	21235375	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tacaagtaaagaacaggaagCaaagtaccaggccagccacc	9	11	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:21235375C>T	ENST00000215730.7	+	3	601	c.473C>T	c.(472-474)gCa>gTa	p.A158V		NM_004782.3	NP_004773.1	O95721	SNP29_HUMAN	synaptosomal-associated protein, 29kDa	158					autophagic vacuole fusion (GO:0000046)|exocytosis (GO:0006887)|membrane fusion (GO:0061025)|protein transport (GO:0015031)|vesicle targeting (GO:0006903)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|SNARE complex (GO:0031201)|synapse (GO:0045202)	SNAP receptor activity (GO:0005484)			breast(1)|endometrium(1)|large_intestine(5)|lung(1)|upper_aerodigestive_tract(1)	9	all_cancers(11;2.77e-25)|all_epithelial(7;8.92e-24)|Lung NSC(8;1.49e-15)|all_lung(8;2.54e-14)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000592)|Lung(15;0.0117)			GAACAGGAAGCAAAGTACCAG	0.403																																					p.A158V		Atlas-SNP	.											.	SNAP29	22	.	0			c.C473T						.						84	73	76					22																	21235375		2203	4300	6503	SO:0001583	missense	9342	exon3			AGGAAGCAAAGTA	AF115436	CCDS13784.1	22q11.21	2008-06-10	2002-08-29		ENSG00000099940	ENSG00000099940			11133	protein-coding gene	gene with protein product	"soluble 29 kDa NSF attachment protein"	604202	"synaptosomal-associated protein, 29kD"			9852078, 10591208	Standard	NM_004782		Approved	SNAP-29, CEDNIK	uc011ahw.2	O95721	OTTHUMG00000150765	ENST00000215730.7:c.473C>T	chr22.hg19:g.21235375C>T	ENSP00000215730:p.Ala158Val	209.0	1.0		153.0	107.0	NM_004782		Missense_Mutation	SNP	ENST00000215730.7	hg19	CCDS13784.1	.	.	.	.	.	.	.	.	.	.	C	11.80	1.748021	0.30955	.	.	ENSG00000099940	ENST00000215730;ENST00000439214	.	.	.	4.79	-0.269	0.12930	SNAP-25 (1);	0.768768	0.12064	N	0.502901	T	0.26593	0.0650	N	0.22421	0.69	0.09310	N	1	B	0.30068	0.267	B	0.29942	0.109	T	0.19386	-1.0307	9	0.30078	T	0.28	-0.6118	10.2209	0.43196	0.4547:0.4386:0.1067:0.0	.	158	O95721	SNP29_HUMAN	V	158;65	.	ENSP00000215730:A158V	A	+	2	0	SNAP29	19565375	0.156000	0.22821	0.309000	0.25155	0.988000	0.76386	0.979000	0.29500	0.201000	0.20466	0.491000	0.48974	GCA	.	.		0.403	SNAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320000.4	NM_004782		T	21235375	C	T	21235375	3	4	255	1	0	0	0	0	1	0	0	0	14846	710	25	3	483	3	SNAP29	22	21235375	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1396336	21235375	30069191	744	36089										
AIFM3	150209	hgsc.bcm.edu	37	chr22	21329042	21329042	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctgcggcaggagggcttctcCgaccggatcgtcctgtgcac	14	14	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:21329042C>A	ENST00000399167.2	+	8	897	c.657C>A	c.(655-657)tcC>tcA	p.S219S	AIFM3_ENST00000399163.2_Silent_p.S219S|AIFM3_ENST00000465606.1_3'UTR|AIFM3_ENST00000333607.6_Silent_p.S219S|AIFM3_ENST00000405089.1_Silent_p.S225S|AIFM3_ENST00000440238.2_Silent_p.S219S|AIFM3_ENST00000335375.5_Silent_p.S207S	NM_144704.2	NP_653305.1	Q96NN9	AIFM3_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 3	219					cell redox homeostasis (GO:0045454)|execution phase of apoptosis (GO:0097194)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	21	all_cancers(11;3.71e-26)|all_epithelial(7;1.59e-23)|Lung NSC(8;3.06e-15)|all_lung(8;5.05e-14)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0367)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)			AGGGCTTCTCCGACCGGATCG	0.642																																					p.S225S		Atlas-SNP	.											AIFM3,colon,carcinoma,0,1	AIFM3	49	.	0			c.C675A						.						68	63	64					22																	21329042		2203	4300	6503	SO:0001819	synonymous_variant	150209	exon8			CTTCTCCGACCGG	AK094844	CCDS13786.1, CCDS33605.1, CCDS54503.1	22q11.21	2007-05-03			ENSG00000183773	ENSG00000183773			26398	protein-coding gene	gene with protein product						15764604	Standard	NM_144704		Approved	AIFL, FLJ30473		Q96NN9	OTTHUMG00000150804	ENST00000399167.2:c.657C>A	chr22.hg19:g.21329042C>A		115.0	1.0		67.0	3.0	NM_001146288	B7WP37|D3DX37|D3DX38|Q6ZT44|Q8N1V3|Q8N5E0	Silent	SNP	ENST00000399167.2	hg19	CCDS13786.1																																																																																			.	.		0.642	AIFM3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320150.1	NM_144704		A	21329042	C	A	21329042	2	1	255	1	0	0	0	0	0	0	0	1	428	639	23	1		1	AIFM3	22	21329042	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	93667	21329042	29975524	745	36090										
EWSR1	2130	hgsc.bcm.edu	37	chr22	29692342	29692342	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccacccactgccaaggctgcCgtggaatggtttgatggtga	13	11	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:29692342C>A	ENST00000397938.2	+	12	1597	c.1278C>A	c.(1276-1278)gcC>gcA	p.A426A	EWSR1_ENST00000332050.6_Silent_p.A353A|EWSR1_ENST00000406548.1_Silent_p.A425A|EWSR1_ENST00000332035.6_Silent_p.A370A|EWSR1_ENST00000331029.7_Silent_p.A388A|EWSR1_ENST00000414183.2_Silent_p.A431A	NM_001163285.1|NM_001163286.1|NM_005243.3|NM_013986.3	NP_001156757.1|NP_001156758.1|NP_005234.1|NP_053733.2	Q01844	EWS_HUMAN	EWS RNA-binding protein 1	426	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		EWSR1/ATF1(347)|EWSR1/POU5F1(10)|EWSR1/PBX1(3)|EWSR1/DDIT3(45)|EWSR1/FEV(11)|EWSR1/CREB1(44)|EWSR1/SMARCA5(2)|EWSR1/ETV4(6)|EWSR1/ERG(178)|EWSR1/ZNF384(4)|EWSR1/ETV1(7)|EWSR1/FLI1(2569)|EWSR1/NR4A3(146)|EWSR1/SP3(3)|EWSR1/PATZ1(2)|EWSR1/WT1(234)|EWSR1/NFATC2(9)	breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|liver(1)|lung(6)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						CCAAGGCTGCCGTGGAATGGT	0.502			T	"FLI1, ERG, ZNF278, NR4A3, FEV, ATF1, ETV1, ETV4, WT1, ZNF384, CREB1, POU5F1,  PBX1"	"Ewing sarcoma,  desmoplastic small round cell tumor , ALL, clear cell sarcoma, sarcoma, myoepithelioma"																																p.A431A		Atlas-SNP	.		Dom	yes		22	22q12	2130	Ewing sarcoma breakpoint region 1 (EWS)		"L, M"	.	EWSR1	104	.	0			c.C1293A						.						114	91	99					22																	29692342		2203	4300	6503	SO:0001819	synonymous_variant	2130	exon13			GGCTGCCGTGGAA		CCDS13851.1, CCDS13852.1, CCDS13852.2, CCDS54512.1, CCDS54513.1, CCDS54514.1	22q12.2	2013-05-24	2013-05-24		ENSG00000182944	ENSG00000182944		"RNA binding motif (RRM) containing"	3508	protein-coding gene	gene with protein product		133450	"Ewing sarcoma breakpoint region 1"			1522903	Standard	NM_005243		Approved	EWS	uc003aev.3	Q01844	OTTHUMG00000151107	ENST00000397938.2:c.1278C>A	chr22.hg19:g.29692342C>A		102.0	0.0		82.0	4.0	NM_013986	B0QYK1|Q5THL0|Q92635|Q96FE8|Q96MN4|Q96MX4|Q9BWA2	Silent	SNP	ENST00000397938.2	hg19	CCDS13851.1	.	.	.	.	.	.	.	.	.	.	C	5.371	0.253678	0.10185	.	.	ENSG00000182944	ENST00000360091	.	.	.	5.52	-11.0	0.00169	.	.	.	.	.	T	0.58221	0.2107	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.71020	-0.4713	4	.	.	.	.	14.8813	0.70534	0.0782:0.2555:0.0:0.6663	.	.	.	.	S	82	.	.	R	+	1	0	EWSR1	28022342	0.000000	0.05858	0.081000	0.20488	0.814000	0.46013	-4.087000	0.00297	-2.355000	0.00614	-1.578000	0.00866	CGT	.	.		0.502	EWSR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321345.1	NM_005243		A	29692342	C	A	29692342	2	1	255	1	0	0	0	0	0	0	0	1	5298	639	23	1		1	EWSR1	22	29692342	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	8363300	29692342	21612224	746	36091										
MORC2	22880	hgsc.bcm.edu	37	chr22	31333570	31333570	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggtccaaccacccaactcacCgcactggatggtggtgggga	13	13	1	0	rs201852637		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:31333570C>T	ENST00000397641.3	-	15	1906	c.1498G>A	c.(1498-1500)Gat>Aat	p.D500N	MORC2_ENST00000469915.1_Intron|MORC2_ENST00000215862.4_Splice_Site_p.D438N			Q9Y6X9	MORC2_HUMAN	MORC family CW-type zinc finger 2	500						cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	21						CCCAACTCACCGCACTGGATG	0.552																																					p.D438N		Atlas-SNP	.											MORC2,caecum,carcinoma,0,1	MORC2	78	.	0			c.G1312A						.						68	70	69					22																	31333570		2203	4300	6503	SO:0001630	splice_region_variant	22880	exon16			ACTCACCGCACTG	AB020659	CCDS33636.1	22q12.2	2005-06-15	2005-06-15	2005-06-15	ENSG00000133422	ENSG00000133422			23573	protein-coding gene	gene with protein product			"zinc finger, CW-type with coiled-coil domain 1", "zinc finger, CW type with coiled-coil domain 1"	ZCWCC1		14607086	Standard	XM_005261391		Approved	ZCW3, KIAA0852, AC004542.C22.1	uc003aje.1	Q9Y6X9	OTTHUMG00000151193	ENST00000397641.3:c.1498+1G>A	chr22.hg19:g.31333570C>T		55.0	0.0		28.0	2.0	NM_014941	B2RNB1|Q9UF28|Q9Y6V2	Missense_Mutation	SNP	ENST00000397641.3	hg19		.	.	.	.	.	.	.	.	.	.	C	29.5	5.011379	0.93346	.	.	ENSG00000133422	ENST00000397641;ENST00000215862	T;T	0.15139	2.46;2.45	5.4	5.4	0.78164	Zinc finger, CW-type (2);	0.000000	0.85682	D	0.000000	T	0.50222	0.1603	M	0.87269	2.87	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.54649	-0.8262	9	.	.	.	.	19.5178	0.95171	0.0:1.0:0.0:0.0	.	500	Q9Y6X9	MORC2_HUMAN	N	500;438	ENSP00000380763:D500N;ENSP00000215862:D438N	.	D	-	1	0	MORC2	29663570	1.000000	0.71417	1.000000	0.80357	0.464000	0.32679	7.442000	0.80503	2.681000	0.91329	0.555000	0.69702	GAT	.	C|0.999;T|0.001		0.552	MORC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000321710.2	NM_014941	Missense_Mutation	T	31333570	C	T	31333570	5	4	255	1	0	0	0	0	0	0	1	0	9711	666	23	1	1648	1	MORC2	22	31333570	Splice_Site	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1641228	31333570	19970996	747	36092										
PATZ1	23598	hgsc.bcm.edu	37	chr22	31724792	31724792	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cctttgttgccataggtcctGgcgcagtggaacgctgctcc	12	13	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:31724792G>A	ENST00000266269.5	-	4	2255	c.1626C>T	c.(1624-1626)gcC>gcT	p.A542A	PATZ1_ENST00000351933.4_Intron|PATZ1_ENST00000405309.3_Nonsense_Mutation_p.Q521*|RP3-400N23.6_ENST00000440456.1_RNA	NM_014323.2	NP_055138.2	Q9HBE1	PATZ1_HUMAN	POZ (BTB) and AT hook containing zinc finger 1	542					male gonad development (GO:0008584)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)		EWSR1/PATZ1(2)	NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(2)	12						CATAGGTCCTGGCGCAGTGGA	0.617																																					p.Q521X		Atlas-SNP	.											.	PATZ1	24	.	0			c.C1561T						.						70	58	62					22																	31724792		2203	4300	6503	SO:0001819	synonymous_variant	23598	exon4			GGTCCTGGCGCAG	AL096880	CCDS13894.1, CCDS13895.1, CCDS13896.1, CCDS46691.1	22q12.2	2013-01-09	2006-09-19	2006-09-19	ENSG00000100105	ENSG00000100105		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	13071	protein-coding gene	gene with protein product		605165	"zinc finger protein 278"	ZNF278		10591208, 18241078, 18401526	Standard	NM_014323		Approved	MAZR, dJ400N23, ZBTB19, ZSG, RIAZ, PATZ	uc003akq.3	Q9HBE1	OTTHUMG00000151254	ENST00000266269.5:c.1626C>T	chr22.hg19:g.31724792G>A		105.0	0.0		73.0	4.0	NM_032052	Q9HBE2|Q9HBE3|Q9P1A9|Q9UDU0|Q9Y529	Nonsense_Mutation	SNP	ENST00000266269.5	hg19	CCDS13894.1	.	.	.	.	.	.	.	.	.	.	G	43	10.223038	0.99362	.	.	ENSG00000100105	ENST00000405309	.	.	.	4.91	4.91	0.64330	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	0.1094	17.4491	0.87587	0.0:0.0:1.0:0.0	.	.	.	.	X	521	.	ENSP00000384173:Q521X	Q	-	1	0	PATZ1	30054792	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.130000	0.89598	2.447000	0.82792	0.462000	0.41574	CAG	.	.		0.617	PATZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321932.1	NM_032052		A	31724792	G	A	31724792	2	1	255	1	0	0	0	0	0	0	0	1	11485	1357	47	3		3	PATZ1	22	31724792	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	391222	31724792	19579774	748	36093										
SFI1	9814	hgsc.bcm.edu	37	chr22	31969140	31969140	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	atcagcactggcaaaaacggAgatttctaaaggcctggctt	10	9	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:31969140A>G	ENST00000400288.2	+	9	967	c.862A>G	c.(862-864)Aga>Gga	p.R288G	SFI1_ENST00000540643.1_Missense_Mutation_p.R264G|SFI1_ENST00000443326.1_Missense_Mutation_p.R206G|SFI1_ENST00000400289.1_Missense_Mutation_p.R206G|SFI1_ENST00000443011.1_Missense_Mutation_p.R135G|SFI1_ENST00000414585.1_Missense_Mutation_p.R135G|SFI1_ENST00000432498.1_Missense_Mutation_p.R288G	NM_001007467.2	NP_001007468.1	A8K8P3	SFI1_HUMAN	Sfi1 homolog, spindle assembly associated (yeast)	288					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(2)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)	38						GCAAAAACGGAGATTTCTAAA	0.502											OREG0003525	type=REGULATORY REGION|Gene=SFI1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.R288G		Atlas-SNP	.											.	SFI1	78	.	0			c.A862G						.						81	81	81					22																	31969140		1903	4134	6037	SO:0001583	missense	9814	exon9			AAACGGAGATTTC	AB011114	CCDS43004.1, CCDS43005.1, CCDS58803.1, CCDS58804.1	22q12.2	2014-06-13			ENSG00000198089	ENSG00000198089			29064	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 139"	612765				14504268	Standard	NM_001007467		Approved	KIAA0542, PISD, PPP1R139	uc003ale.4	A8K8P3	OTTHUMG00000030249	ENST00000400288.2:c.862A>G	chr22.hg19:g.31969140A>G	ENSP00000383145:p.Arg288Gly	51.0	0.0	828	53.0	4.0	NM_001007467	A1L373|A1L387|A2A2L2|B1AKL9|B5MDB7|B7Z1V6|B7Z8G3|B7ZBE2|B7ZBE3|O60289|Q2TAN8|Q5W1B5|Q86TK0|Q8N4U8|Q8N8C1|Q8WU14	Missense_Mutation	SNP	ENST00000400288.2	hg19	CCDS43004.1	.	.	.	.	.	.	.	.	.	.	A	11.18	1.562377	0.27915	.	.	ENSG00000198089	ENST00000432498;ENST00000540643;ENST00000443326;ENST00000421060;ENST00000414585;ENST00000443011;ENST00000400289;ENST00000400288	T;T;T;T;T;T;T	0.37058	1.22;1.22;1.22;2.73;2.71;1.22;1.22	5.87	3.62	0.41486	.	0.712062	0.14740	N	0.301244	T	0.35451	0.0932	N	0.08118	0	0.09310	N	1	P;P;D;P;P;D	0.76494	0.835;0.835;0.999;0.95;0.897;0.967	B;B;D;P;P;P	0.71414	0.311;0.311;0.973;0.487;0.465;0.74	T	0.18840	-1.0324	10	0.31617	T	0.26	.	10.2417	0.43316	0.6827:0.3173:0.0:0.0	.	264;206;206;288;288;264	A8K8P3-9;A8K8P3-10;A8K8P3-3;A8K8P3-2;A8K8P3;A8K8P3-5	.;.;.;.;SFI1_HUMAN;.	G	288;264;206;264;135;135;206;288	ENSP00000402679:R288G;ENSP00000443025:R264G;ENSP00000416469:R206G;ENSP00000397148:R135G;ENSP00000401199:R135G;ENSP00000383146:R206G;ENSP00000383145:R288G	ENSP00000383145:R288G	R	+	1	2	SFI1	30299140	0.004000	0.15560	0.002000	0.10522	0.005000	0.04900	1.848000	0.39309	1.008000	0.39264	0.533000	0.62120	AGA	.	.		0.502	SFI1-023	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337180.3	NM_014775		G	31969140	A	G	31969140	3	3	255	1	0	0	0	0	1	0	0	0	14171	296	11	2	892	2	SFI1	22	31969140	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	244348	31969140	19335426	749	36094										
DEPDC5	9681	hgsc.bcm.edu	37	chr22	32217607	32217607	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	agctgctggagttagcatatCatgaagctgctggaaggtga	14	6	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:32217607C>T	ENST00000382112.3	+	22	2060	c.1990C>T	c.(1990-1992)Cat>Tat	p.H664Y	DEPDC5_ENST00000400248.2_Missense_Mutation_p.H664Y|DEPDC5_ENST00000266091.3_Missense_Mutation_p.H664Y|DEPDC5_ENST00000400249.2_Missense_Mutation_p.H664Y|DEPDC5_ENST00000382111.2_Missense_Mutation_p.H664Y|DEPDC5_ENST00000400246.1_Missense_Mutation_p.H664Y|DEPDC5_ENST00000536766.1_Intron|DEPDC5_ENST00000382105.2_Intron|DEPDC5_ENST00000535622.1_Intron	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	664					intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						GTTAGCATATCATGAAGCTGC	0.542																																					p.H664Y		Atlas-SNP	.											.	DEPDC5	266	.	0			c.C1990T						.						128	135	133					22																	32217607		2116	4242	6358	SO:0001583	missense	9681	exon22			GCATATCATGAAG	AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.1990C>T	chr22.hg19:g.32217607C>T	ENSP00000371546:p.His664Tyr	88.0	0.0		74.0	4.0	NM_001136029	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Missense_Mutation	SNP	ENST00000382112.3	hg19	CCDS46692.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.18|19.18	3.777990|3.777990	0.70107|0.70107	.|.	.|.	ENSG00000100150|ENSG00000100150	ENST00000266091;ENST00000400249;ENST00000400246;ENST00000382112;ENST00000382111;ENST00000400248|ENST00000433147	T;T;T;T;T;T|.	0.24151|.	1.89;1.91;1.87;1.91;1.87;1.91|.	5.91|5.91	4.83|4.83	0.62350|0.62350	.|.	0.151077|.	0.64402|.	D|.	0.000018|.	T|T	0.69646|0.69646	0.3134|0.3134	L|L	0.56769|0.56769	1.78|1.78	0.80722|0.80722	D|D	1|1	P;P;B;P|.	0.47604|.	0.867;0.898;0.031;0.837|.	B;B;B;B|.	0.43867|.	0.317;0.434;0.01;0.335|.	T|T	0.66858|0.66858	-0.5817|-0.5817	10|5	0.40728|.	T|.	0.16|.	.|.	14.9866|14.9866	0.71353|0.71353	0.143:0.857:0.0:0.0|0.143:0.857:0.0:0.0	.|.	664;664;664;664|.	B9EGN9;O75140-4;A8MPX9;O75140|.	.;.;.;DEPD5_HUMAN|.	Y|L	664|61	ENSP00000266091:H664Y;ENSP00000383108:H664Y;ENSP00000383105:H664Y;ENSP00000371546:H664Y;ENSP00000371545:H664Y;ENSP00000383107:H664Y|.	ENSP00000266091:H664Y|.	H|S	+|+	1|2	0|0	DEPDC5|DEPDC5	30547607|30547607	1.000000|1.000000	0.71417|0.71417	0.916000|0.916000	0.36221|0.36221	0.997000|0.997000	0.91878|0.91878	5.554000|5.554000	0.67294|0.67294	2.801000|2.801000	0.96364|0.96364	0.655000|0.655000	0.94253|0.94253	CAT|TCA	.	.		0.542	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662		T	32217607	C	T	32217607	3	4	255	1	0	0	0	0	1	0	0	0	4444	826	29	3	2094	3	DEPDC5	22	32217607	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	248467	32217607	19086959	750	36095										
SSTR3	6753	hgsc.bcm.edu	37	chr22	37602782	37602782	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tctcctccccatcctcctccTcctcatcctcctcctcagtc	1	24	3	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:37602782T>C	ENST00000328544.3	-	2	1594	c.1061A>G	c.(1060-1062)gAg>gGg	p.E354G	SSTR3_ENST00000402501.1_Missense_Mutation_p.E354G	NM_001051.3	NP_001042.1	P32745	SSR3_HUMAN	somatostatin receptor 3	354	Glu-rich (acidic).				cell-cell signaling (GO:0007267)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucocorticoid stimulus (GO:0071385)|cerebellum development (GO:0021549)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|hormone-mediated apoptotic signaling pathway (GO:0008628)|negative regulation of cell proliferation (GO:0008285)|response to starvation (GO:0042594)|somatostatin signaling pathway (GO:0038170)|spermatogenesis (GO:0007283)	ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)	14					Pasireotide(DB06663)	atcctcctcctcctcatcctc	0.701																																					p.E354G		Atlas-SNP	.											.	SSTR3	42	.	0			c.A1061G						.						30	31	30					22																	37602782		2203	4300	6503	SO:0001583	missense	6753	exon2			TCCTCCTCCTCAT		CCDS13944.1	22q13.1	2012-08-08			ENSG00000183473	ENSG00000278195		"GPCR / Class A : Somatostatin receptors"	11332	protein-coding gene	gene with protein product		182453				8449518	Standard	XM_006724311		Approved		uc003arb.3	P32745	OTTHUMG00000150537	ENST00000328544.3:c.1061A>G	chr22.hg19:g.37602782T>C	ENSP00000330138:p.Glu354Gly	41.0	0.0		44.0	4.0	NM_001051	A8K550|Q53ZR7	Missense_Mutation	SNP	ENST00000328544.3	hg19	CCDS13944.1	.	.	.	.	.	.	.	.	.	.	T	9.129	1.010998	0.19277	.	.	ENSG00000183473	ENST00000328544;ENST00000402501	T;T	0.73047	-0.71;-0.71	5.17	5.17	0.71159	.	1.685100	0.02858	N	0.129966	T	0.70868	0.3273	L	0.50333	1.59	0.50467	D	0.999873	B	0.02656	0.0	B	0.06405	0.002	T	0.27054	-1.0085	10	0.25751	T	0.34	.	14.9968	0.71439	0.0:0.0:0.0:1.0	.	354	P32745	SSR3_HUMAN	G	354	ENSP00000330138:E354G;ENSP00000384904:E354G	ENSP00000330138:E354G	E	-	2	0	SSTR3	35932728	0.823000	0.29233	0.300000	0.25030	0.021000	0.10359	2.080000	0.41586	1.942000	0.56320	0.459000	0.35465	GAG	.	.		0.701	SSTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318802.1			C	37602782	T	C	37602782	3	2	255	1	0	0	0	0	1	0	0	0	15214	1551	54	2	199	2	SSTR3	22	37602782	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	5385175	37602782	13701784	751	36096										
TOMM22	56993	hgsc.bcm.edu	37	chr22	39078943	39078943	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tatgatcctggttcttcccgTtgtctttgagacggagaagt	11	8	2	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:39078943T>C	ENST00000216034.4	+	3	327	c.296T>C	c.(295-297)gTt>gCt	p.V99A	RP3-508I15.9_ENST00000412067.1_RNA|RP3-508I15.9_ENST00000444381.1_RNA|RP3-508I15.9_ENST00000431924.2_RNA	NM_020243.4	NP_064628.1	Q9NS69	TOM22_HUMAN	translocase of outer mitochondrial membrane 22 homolog (yeast)	99	TMD; necessary for mitochondrion outer membrane localization and integration in the TOM complex. {ECO:0000250}.				cellular protein metabolic process (GO:0044267)|protein import into mitochondrial outer membrane (GO:0045040)|protein targeting to mitochondrion (GO:0006626)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane translocase complex (GO:0005742)|mitochondrion (GO:0005739)	protein transmembrane transporter activity (GO:0008320)			large_intestine(1)|lung(2)	3	Melanoma(58;0.04)					GTTCTTCCCGTTGTCTTTGAG	0.542																																					p.V99A		Atlas-SNP	.											.	TOMM22	10	.	0			c.T296C						.						143	130	135					22																	39078943		2203	4300	6503	SO:0001583	missense	56993	exon3			TTCCCGTTGTCTT	AB040119	CCDS13975.1	22q12-q13	2010-07-29			ENSG00000100216	ENSG00000100216			18002	protein-coding gene	gene with protein product		607046				10982837, 10900208	Standard	NM_020243		Approved	TOM22	uc003awe.3	Q9NS69	OTTHUMG00000150991	ENST00000216034.4:c.296T>C	chr22.hg19:g.39078943T>C	ENSP00000216034:p.Val99Ala	130.0	0.0		95.0	4.0	NM_020243		Missense_Mutation	SNP	ENST00000216034.4	hg19	CCDS13975.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.562765	0.86335	.	.	ENSG00000100216	ENST00000216034	.	.	.	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.80497	0.4634	M	0.86864	2.845	0.80722	D	1	D	0.63046	0.992	D	0.63488	0.915	D	0.84407	0.0563	9	0.72032	D	0.01	-22.5999	15.351	0.74384	0.0:0.0:0.0:1.0	.	99	Q9NS69	TOM22_HUMAN	A	99	.	ENSP00000216034:V99A	V	+	2	0	TOMM22	37408889	1.000000	0.71417	0.999000	0.59377	0.717000	0.41224	7.501000	0.81600	2.024000	0.59613	0.460000	0.39030	GTT	.	.		0.542	TOMM22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320842.1			C	39078943	T	C	39078943	3	2	255	1	0	0	0	0	1	0	0	0	16371	1725	60	2	306	2	TOMM22	22	39078943	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	1476161	39078943	12225623	752	36097										
SUN2	25777	hgsc.bcm.edu	37	chr22	39147022	39147022	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cacccgtgcctctcctcctcCgcacccgcaggtcctcacct	6	23	2	0	rs373600095		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:39147022C>A	ENST00000405510.1	-	5	663	c.305G>T	c.(304-306)cGg>cTg	p.R102L	SUN2_ENST00000216064.4_Missense_Mutation_p.R102L|RP3-508I15.14_ENST00000416406.1_RNA|SUN2_ENST00000405018.1_Missense_Mutation_p.R102L|SUN2_ENST00000411587.2_Intron|SUN2_ENST00000406622.1_Missense_Mutation_p.R102L	NM_001199580.1	NP_001186509.1	Q9UH99	SUN2_HUMAN	Sad1 and UNC84 domain containing 2	102	LMNA-binding. {ECO:0000250}.|Poly-Arg.|Ser-rich.				centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|mitotic spindle organization (GO:0007052)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)	condensed nuclear chromosome (GO:0000794)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nuclear inner membrane (GO:0005637)|nuclear membrane (GO:0031965)|SUN-KASH complex (GO:0034993)	identical protein binding (GO:0042802)|lamin binding (GO:0005521)|microtubule binding (GO:0008017)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(2)|stomach(1)	15						TCTCCTCCTCCGCACCCGCAG	0.657																																					p.R102L		Atlas-SNP	.											.	SUN2	59	.	0			c.G305T						.						30	28	29					22																	39147022		2203	4300	6503	SO:0001583	missense	25777	exon5			CTCCTCCGCACCC	AF202723	CCDS13978.1, CCDS56231.1	22q12-q13	2010-05-18	2010-05-18	2010-01-27	ENSG00000100242	ENSG00000100242			14210	protein-coding gene	gene with protein product		613569	"unc-84 homolog B (C. elegans)"	UNC84B		10508607, 10375507	Standard	NM_015374		Approved		uc010gxq.2	Q9UH99	OTTHUMG00000151031	ENST00000405510.1:c.305G>T	chr22.hg19:g.39147022C>A	ENSP00000385740:p.Arg102Leu	52.0	0.0		53.0	4.0	NM_001199580	B0QY62|O75156|Q2NKN8|Q2T9F7|Q504T5|Q6B4H1|Q7Z3E3	Missense_Mutation	SNP	ENST00000405510.1	hg19	CCDS13978.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.5|20.5	3.995441|3.995441	0.74703|0.74703	.|.	.|.	ENSG00000100242|ENSG00000100242	ENST00000417332|ENST00000405510;ENST00000216064;ENST00000405018;ENST00000406622;ENST00000456894;ENST00000452294;ENST00000433561	.|T;T;T;T;T;T;T	.|0.43688	.|2.57;2.57;2.23;2.57;0.94;0.98;1.1	4.97|4.97	4.97|4.97	0.65823|0.65823	.|.	.|0.126644	.|0.42420	.|D	.|0.000713	.|T	.|0.51618	.|0.1685	L|L	0.27053|0.27053	0.805|0.805	0.39641|0.39641	D|D	0.970326|0.970326	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0	.|D;D;D;D	.|0.81914	.|0.995;0.995;0.995;0.995	.|T	.|0.53975	.|-0.8362	.|10	0.87932|0.42905	D|T	0|0.14	-25.0041|-25.0041	16.4198|16.4198	0.83754|0.83754	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|137;102;102;102	.|B4E2A6;Q2T9F7;B0QY62;Q9UH99	.|.;.;.;SUN2_HUMAN	X|L	122|102	.|ENSP00000385740:R102L;ENSP00000216064:R102L;ENSP00000385616:R102L;ENSP00000383992:R102L;ENSP00000415588:R102L;ENSP00000414950:R102L;ENSP00000411615:R102L	ENSP00000412928:G122X|ENSP00000216064:R102L	G|R	-|-	1|2	0|0	SUN2|SUN2	37476968|37476968	0.963000|0.963000	0.33076|0.33076	0.998000|0.998000	0.56505|0.56505	0.595000|0.595000	0.36748|0.36748	4.507000|4.507000	0.60434|0.60434	2.299000|2.299000	0.77371|0.77371	0.563000|0.563000	0.77884|0.77884	GGA|CGG	.	.		0.657	SUN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321057.1	XM_039332		A	39147022	C	A	39147022	3	1	255	1	0	0	0	0	1	0	0	0	15407	652	23	1	1908	1	SUN2	22	39147022	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	68079	39147022	12157544	753	36098										
CACNA1I	8911	hgsc.bcm.edu	37	chr22	39994207	39994207	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ctgctgaactgcgtgacactTggcatgtaccagccgtgcga	12	12	0	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:39994207T>C	ENST00000402142.3	+	2	288	c.288T>C	c.(286-288)ctT>ctC	p.L96L	CACNA1I_ENST00000401624.1_Silent_p.L96L|CACNA1I_ENST00000407673.1_Silent_p.L96L|CACNA1I_ENST00000400164.3_Silent_p.L96L|CACNA1I_ENST00000404898.1_Silent_p.L96L|CACNA1I_ENST00000336649.4_Silent_p.L96L	NM_021096.3	NP_066919.2	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type, alpha 1I subunit	96					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|signal transduction (GO:0007165)|sleep (GO:0030431)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(2)|lung(27)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Melanoma(58;0.0749)				Cinnarizine(DB00568)|Flunarizine(DB04841)|Paramethadione(DB00617)|Spironolactone(DB00421)|Verapamil(DB00661)|Zonisamide(DB00909)	GCGTGACACTTGGCATGTACC	0.642																																					p.L96L		Atlas-SNP	.											.	CACNA1I	264	.	0			c.T288C						.						74	80	78					22																	39994207		2163	4255	6418	SO:0001819	synonymous_variant	8911	exon2			GACACTTGGCATG	AF129133	CCDS46710.1, CCDS46711.1	22q13.1	2012-03-07	2007-02-16		ENSG00000100346	ENSG00000100346		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1396	protein-coding gene	gene with protein product		608230				10454147, 16382099	Standard	NM_021096		Approved	Cav3.3	uc003ayd.3	Q9P0X4	OTTHUMG00000151096	ENST00000402142.3:c.288T>C	chr22.hg19:g.39994207T>C		140.0	0.0		98.0	4.0	NM_001003406	B0QY12|B0QY13|B0QY14|O95504|Q5JZ88|Q7Z6S9|Q8NFX6|Q9NZC8|Q9UH15|Q9UH30|Q9ULU9|Q9UNE6	Silent	SNP	ENST00000402142.3	hg19	CCDS46710.1																																																																																			.	.		0.642	CACNA1I-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321290.1	NM_001003406		C	39994207	T	C	39994207	2	2	255	1	0	0	0	0	0	0	0	1	2548	1799	63	2		2	CACNA1I	22	39994207	Silent	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	847185	39994207	11310359	754	36099										
EP300	2033	hgsc.bcm.edu	37	chr22	41572904	41572904	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cacccagagcccaggcgattCtcgccgcctgagtatccagc	10	17	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:41572904C>A	ENST00000263253.7	+	31	6408	c.5189C>A	c.(5188-5190)tCt>tAt	p.S1730Y	RP1-85F18.6_ENST00000415054.1_RNA|RP1-85F18.5_ENST00000420537.1_RNA	NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	1730	Binding region for E1A adenovirus.				apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)	p.S1730F(1)		NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						CCAGGCGATTCTCGCCGCCTG	0.542			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																												p.S1730Y		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	EP300,NS,carcinoma,0,1	EP300	367	.	1	Substitution - Missense(1)	lung(1)	c.C5189A						.						77	71	73					22																	41572904		2203	4300	6503	SO:0001583	missense	2033	exon31	Familial Cancer Database	Broad Thumb-Hallux syndrome	GCGATTCTCGCCG	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.5189C>A	chr22.hg19:g.41572904C>A	ENSP00000263253:p.Ser1730Tyr	95.0	0.0		92.0	4.0	NM_001429	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	hg19	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	C	17.55	3.418313	0.62622	.	.	ENSG00000100393	ENST00000263253	D	0.85013	-1.93	5.75	5.75	0.90469	Zinc finger, TAZ-type (4);	0.000000	0.48286	D	0.000194	D	0.92782	0.7705	M	0.77103	2.36	0.58432	D	0.999999	D	0.71674	0.998	D	0.80764	0.994	D	0.92983	0.6408	10	0.87932	D	0	-8.2686	19.9469	0.97185	0.0:1.0:0.0:0.0	.	1730	Q09472	EP300_HUMAN	Y	1730	ENSP00000263253:S1730Y	ENSP00000263253:S1730Y	S	+	2	0	EP300	39902850	1.000000	0.71417	0.995000	0.50966	0.805000	0.45488	4.851000	0.62896	2.714000	0.92807	0.650000	0.86243	TCT	.	.		0.542	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		A	41572904	C	A	41572904	3	1	255	1	0	0	0	0	1	0	0	0	5150	913	32	3	5311	3	EP300	22	41572904	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1578697	41572904	9731662	755	36100										
CCDC134	79879	hgsc.bcm.edu	37	chr22	42205910	42205910	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gatgtttgaggtgaagcggcGggagcagctgttggcactga	18	6	0	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:42205910G>T	ENST00000255784.5	+	3	235	c.131G>T	c.(130-132)cGg>cTg	p.R44L	CCDC134_ENST00000402061.3_Missense_Mutation_p.R44L	NM_024821.2	NP_079097.1	Q9H6E4	CC134_HUMAN	coiled-coil domain containing 134	44						extracellular region (GO:0005576)|membrane (GO:0016020)				large_intestine(1)|lung(2)|ovary(2)|skin(1)	6						GTGAAGCGGCGGGAGCAGCTG	0.522																																					p.R44L		Atlas-SNP	.											.	CCDC134	19	.	0			c.G131T						.						66	59	62					22																	42205910		2203	4300	6503	SO:0001583	missense	79879	exon3			AGCGGCGGGAGCA	AL021453	CCDS33654.1	22q13.2	2010-12-24			ENSG00000100147	ENSG00000100147			26185	protein-coding gene	gene with protein product						18087676	Standard	NM_024821		Approved	FLJ22349	uc003bbh.1	Q9H6E4	OTTHUMG00000151262	ENST00000255784.5:c.131G>T	chr22.hg19:g.42205910G>T	ENSP00000255784:p.Arg44Leu	131.0	0.0		95.0	4.0	NM_024821		Missense_Mutation	SNP	ENST00000255784.5	hg19	CCDS33654.1	.	.	.	.	.	.	.	.	.	.	G	18.36	3.607388	0.66558	.	.	ENSG00000100147	ENST00000402061;ENST00000255784;ENST00000429249	.	.	.	4.84	3.82	0.43975	.	0.057402	0.64402	D	0.000003	T	0.35885	0.0947	L	0.38175	1.15	0.43326	D	0.995359	P;P	0.47191	0.761;0.891	B;B	0.43950	0.437;0.331	T	0.21724	-1.0237	9	0.66056	D	0.02	-23.4126	4.5115	0.11914	0.2863:0.0:0.7137:0.0	.	44;44	B0QY51;Q9H6E4	.;CC134_HUMAN	L	44	.	ENSP00000255784:R44L	R	+	2	0	CCDC134	40535856	1.000000	0.71417	0.673000	0.29887	0.468000	0.32798	6.717000	0.74707	2.683000	0.91414	0.655000	0.94253	CGG	.	.		0.522	CCDC134-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000321964.1	NM_024821		T	42205910	G	T	42205910	3	4	255	1	0	0	0	0	1	0	0	0	2770	1116	39	1	137	1	CCDC134	22	42205910	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	633006	42205910	9098656	756	36101										
SEPT3	55964	hgsc.bcm.edu	37	chr22	42377812	42377812	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cgcaagaagaccatgaagacCggtttcgacttcaacatcat	8	11	2	4			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:42377812C>A	ENST00000396426.3	+	2	429	c.174C>A	c.(172-174)acC>acA	p.T58T	SEPT3_ENST00000396425.3_Silent_p.T58T|SEPT3_ENST00000291236.11_Intron|CTA-250D10.19_ENST00000424613.1_RNA|SEPT3_ENST00000328414.8_Silent_p.T58T|SEPT3_ENST00000406029.1_Intron	NM_145733.2	NP_663786.2	Q9UH03	SEPT3_HUMAN	septin 3	58	Septin-type G.				cell cycle (GO:0007049)|cell division (GO:0051301)	cell junction (GO:0030054)|septin complex (GO:0031105)|synapse (GO:0045202)	GTP binding (GO:0005525)			breast(1)|kidney(3)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	17						CCATGAAGACCGGTTTCGACT	0.572																																					p.T58T		Atlas-SNP	.											.	SEPT3	53	.	0			c.C174A						.						126	99	109					22																	42377812		2203	4300	6503	SO:0001819	synonymous_variant	55964	exon2			GAAGACCGGTTTC	AF285107	CCDS14026.2, CCDS14027.2	22q13.2	2013-01-21			ENSG00000100167	ENSG00000100167		"Septins"	10750	protein-coding gene	gene with protein product		608314		SEP3			Standard	NM_019106		Approved		uc003bbr.4	Q9UH03	OTTHUMG00000030494	ENST00000396426.3:c.174C>A	chr22.hg19:g.42377812C>A		83.0	0.0		72.0	6.0	NM_019106	B1AHR0|Q2NKJ7|Q59GF7|Q6IBZ6|Q8N3P3|Q9HD35	Silent	SNP	ENST00000396426.3	hg19	CCDS14026.2																																																																																			.	.		0.572	SEPT3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322051.1	NM_145734		A	42377812	C	A	42377812	2	1	255	1	0	0	0	0	0	0	0	1	14080	639	23	1		1	SEPT3	22	42377812	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	171902	42377812	8926754	757	36102										
TCF20	6942	hgsc.bcm.edu	37	chr22	42607070	42607070	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tttgctggactgactaggtcCgaagccacctcaccttttct	8	13	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:42607070C>A	ENST00000359486.3	-	1	4378	c.4242G>T	c.(4240-4242)tcG>tcT	p.S1414S	TCF20_ENST00000404876.1_5'Flank|TCF20_ENST00000335626.4_Silent_p.S1414S	NM_005650.1	NP_005641.1	Q9UGU0	TCF20_HUMAN	transcription factor 20 (AR1)	1414					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(13)|lung(22)|ovary(5)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(5)	66						TGACTAGGTCCGAAGCCACCT	0.502																																					p.S1414S		Atlas-SNP	.											.	TCF20	164	.	0			c.G4242T						.						121	119	120					22																	42607070		2203	4300	6503	SO:0001819	synonymous_variant	6942	exon1			TAGGTCCGAAGCC	U19345	CCDS14032.1, CCDS14033.1	22q13.3	2011-02-08			ENSG00000100207	ENSG00000100207			11631	protein-coding gene	gene with protein product	"stromelysin-1 platelet-derived growth factor-responsive element binding protein"	603107				9730594, 10995766	Standard	NM_005650		Approved	AR1, SPBP	uc003bcj.1	Q9UGU0	OTTHUMG00000150920	ENST00000359486.3:c.4242G>T	chr22.hg19:g.42607070C>A		112.0	0.0		82.0	4.0	NM_181492	A9JX12|O14528|Q13078|Q4V353|Q9H4M0	Silent	SNP	ENST00000359486.3	hg19	CCDS14033.1																																																																																			.	.		0.502	TCF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320531.1	NM_181492		A	42607070	C	A	42607070	2	1	255	1	0	0	0	0	0	0	0	1	15705	639	23	1		1	TCF20	22	42607070	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	229258	42607070	8697496	758	36103										
LDOC1L	84247	hgsc.bcm.edu	37	chr22	44893427	44893427	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttcagctttggacgtctgcgGctgcaccatgctggccagag	13	12	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:44893427G>A	ENST00000341255.3	-	2	519	c.10C>T	c.(10-12)Ccg>Tcg	p.P4S		NM_032287.2	NP_115663.2	Q6ICC9	LDOCL_HUMAN	leucine zipper, down-regulated in cancer 1-like	4										breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(3)|prostate(2)	11		Ovarian(80;0.024)|all_neural(38;0.0416)		LUAD - Lung adenocarcinoma(64;0.0161)		GACGTCTGCGGCTGCACCATG	0.617																																					p.P4S		Atlas-SNP	.											.	LDOC1L	24	.	0			c.C10T						.						37	26	30					22																	44893427		2202	4296	6498	SO:0001583	missense	84247	exon2			TCTGCGGCTGCAC	CR456439	CCDS33662.1	22q13.3	2006-09-06			ENSG00000188636	ENSG00000188636			13343	protein-coding gene	gene with protein product						15716091, 16093683	Standard	NM_032287		Approved	dJ1033E15.2, DKFZp761O17121, Mart6, Mar6	uc003beu.1	Q6ICC9	OTTHUMG00000150465	ENST00000341255.3:c.10C>T	chr22.hg19:g.44893427G>A	ENSP00000340434:p.Pro4Ser	119.0	0.0		66.0	4.0	NM_032287	Q6ZTR1	Missense_Mutation	SNP	ENST00000341255.3	hg19	CCDS33662.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.429699	0.83776	.	.	ENSG00000188636	ENST00000341255	T	0.28666	1.6	2.95	2.95	0.34219	.	.	.	.	.	T	0.30262	0.0759	N	0.08118	0	0.33260	D	0.559666	D	0.60575	0.988	D	0.65140	0.932	T	0.43458	-0.9390	9	0.87932	D	0	-17.9232	9.6217	0.39725	0.0:0.0:1.0:0.0	.	4	Q6ICC9	LDOCL_HUMAN	S	4	ENSP00000340434:P4S	ENSP00000340434:P4S	P	-	1	0	LDOC1L	43272091	1.000000	0.71417	0.991000	0.47740	0.987000	0.75469	4.044000	0.57361	1.969000	0.57287	0.467000	0.42956	CCG	.	.		0.617	LDOC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318222.1	NM_032287		A	44893427	G	A	44893427	3	1	255	1	0	0	0	0	1	0	0	0	8719	1203	42	3	713	3	LDOC1L	22	44893427	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	2286357	44893427	6411139	759	36104										
PHF21B	112885	hgsc.bcm.edu	37	chr22	45291935	45291935	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccaaatgttccgtggtaaccAggcctagcgctaccatgaag	10	12	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:45291935A>G	ENST00000313237.5	-	6	1010	c.860T>C	c.(859-861)cTg>cCg	p.L287P	PHF21B_ENST00000403565.1_Missense_Mutation_p.L83P|PHF21B_ENST00000447824.3_Missense_Mutation_p.L233P|PHF21B_ENST00000396103.3_Missense_Mutation_p.L245P|PHF21B_ENST00000404079.2_Missense_Mutation_p.L233P	NM_138415.4	NP_612424.1	Q96EK2	PF21B_HUMAN	PHD finger protein 21B	287							zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(14)|ovary(2)|prostate(1)|skin(2)	25		all_neural(38;0.00802)|Glioma(61;0.0353)|Ovarian(80;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0203)		CGTGGTAACCAGGCCTAGCGC	0.522																																					p.L287P		Atlas-SNP	.											.	PHF21B	61	.	0			c.T860C						.						215	186	196					22																	45291935		2203	4300	6503	SO:0001583	missense	112885	exon6			GTAACCAGGCCTA	AK091480	CCDS14061.1, CCDS56234.1, CCDS63504.1	22q13.31	2013-01-28			ENSG00000056487	ENSG00000056487		"Zinc fingers, PHD-type"	25161	protein-coding gene	gene with protein product			"PHD finger protein 4"	PHF4		12477932	Standard	NM_138415		Approved	BHC80L, FLJ34161	uc011aql.2	Q96EK2	OTTHUMG00000151199	ENST00000313237.5:c.860T>C	chr22.hg19:g.45291935A>G	ENSP00000324403:p.Leu287Pro	139.0	0.0		98.0	67.0	NM_138415	B0QYW3|B0QYW4|B3KRU4|B7Z4F8|Q5TFL2|Q6ICC0	Missense_Mutation	SNP	ENST00000313237.5	hg19	CCDS14061.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.254463	0.80135	.	.	ENSG00000056487	ENST00000403565;ENST00000313237;ENST00000396103;ENST00000404079;ENST00000447824;ENST00000414269	T;T;T;T;T;T	0.62639	0.01;0.01;0.01;0.01;0.01;0.01	5.23	5.23	0.72850	.	0.000000	0.52532	D	0.000062	T	0.75466	0.3853	L	0.57536	1.79	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;1.0;0.999;0.999;0.999	T	0.77846	-0.2436	10	0.66056	D	0.02	-21.6784	14.1049	0.65083	1.0:0.0:0.0:0.0	.	233;245;233;287;83	B7Z657;Q96EK2-3;B7Z4F8;Q96EK2;B1AHC5	.;.;.;PF21B_HUMAN;.	P	83;287;245;233;233;83	ENSP00000385053:L83P;ENSP00000324403:L287P;ENSP00000379410:L245P;ENSP00000385105:L233P;ENSP00000388619:L233P;ENSP00000401091:L83P	ENSP00000324403:L287P	L	-	2	0	PHF21B	43670599	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.799000	0.85936	1.954000	0.56735	0.460000	0.39030	CTG	.	.		0.522	PHF21B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321731.2	NM_138415		G	45291935	A	G	45291935	3	3	255	1	0	0	0	0	1	0	0	0	11843	188	7	2	767	2	PHF21B	22	45291935	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	398508	45291935	6012631	760	36105										
FBLN1	2192	hgsc.bcm.edu	37	chr22	45943008	45943008	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccctgtagccaggagtgtgcCaacgtctacggctcctacca	10	15	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:45943008C>T	ENST00000327858.6	+	12	1460	c.1365C>T	c.(1363-1365)gcC>gcT	p.A455A	FBLN1_ENST00000348697.2_Silent_p.A455A|FBLN1_ENST00000402984.3_Silent_p.A493A|FBLN1_ENST00000476366.1_3'UTR|FBLN1_ENST00000262722.7_Silent_p.A455A|FBLN1_ENST00000340923.5_Silent_p.A455A|FBLN1_ENST00000442170.2_Silent_p.A455A	NM_006486.2	NP_006477	P23142	FBLN1_HUMAN	fibulin 1	455	EGF-like 7; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|viral process (GO:0016032)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)|peptidase activator activity (GO:0016504)			biliary_tract(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)	30		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		AGGAGTGTGCCAACGTCTACG	0.587																																					p.A455A		Atlas-SNP	.											.	FBLN1	143	.	0			c.C1365T						.						102	82	89					22																	45943008		2203	4300	6503	SO:0001819	synonymous_variant	2192	exon12			GTGTGCCAACGTC		CCDS14067.1, CCDS14068.1, CCDS14069.1, CCDS43028.1	22q13.31	2010-06-15			ENSG00000077942	ENSG00000077942		"Fibulins"	3600	protein-coding gene	gene with protein product		135820				2269669, 1400330	Standard	NM_006485		Approved	FBLN	uc003bgj.1	P23142	OTTHUMG00000151340	ENST00000327858.6:c.1365C>T	chr22.hg19:g.45943008C>T		80.0	0.0		45.0	33.0	NM_006487	B0QY42|B1AHL4|P23143|P23144|P37888|Q5TIC4|Q8TBH8|Q9HBQ5|Q9UC21|Q9UGR4|Q9UH41	Silent	SNP	ENST00000327858.6	hg19	CCDS14067.1																																																																																			.	.		0.587	FBLN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322287.1	NM_006486		T	45943008	C	T	45943008	2	4	255	1	0	0	0	0	0	0	0	1	5706	581	21	3		3	FBLN1	22	45943008	Silent	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	651073	45943008	5361558	761	36106										
MLC1	23209	hgsc.bcm.edu	37	chr22	50515343	50515343	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cgctgtcagacatggagcccTacgaagaaacagaactgtca	10	11	2	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:50515343T>C	ENST00000311597.5	-	7	1132		c.e7-2		MLC1_ENST00000431262.2_Splice_Site|MLC1_ENST00000395876.2_Splice_Site|MLC1_ENST00000450140.2_Splice_Site|MLC1_ENST00000538737.1_Splice_Site|MLC1_ENST00000535444.1_Splice_Site	NM_015166.3	NP_055981.1	Q15049	MLC1_HUMAN	megalencephalic leukoencephalopathy with subcortical cysts 1						caveolin-mediated endocytosis (GO:0072584)|cellular response to cholesterol (GO:0071397)|ion transport (GO:0006811)|positive regulation of intracellular transport (GO:0032388)|protein oligomerization (GO:0051259)|regulation of response to osmotic stress (GO:0047484)|transport (GO:0006810)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	protein complex binding (GO:0032403)|protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|pancreas(1)|prostate(3)	18		all_cancers(38;7.69e-11)|all_epithelial(38;9.52e-10)|all_lung(38;3.67e-05)|Breast(42;0.000776)|Lung NSC(38;0.000946)|Ovarian(80;0.0365)|Lung SC(80;0.113)		READ - Rectum adenocarcinoma(2;0.000669)|Colorectal(2;0.00242)|LUAD - Lung adenocarcinoma(64;0.0695)|BRCA - Breast invasive adenocarcinoma(115;0.216)		CATGGAGCCCTACGAAGAAAC	0.577																																					.		Atlas-SNP	.											.	MLC1	48	.	0			c.526-2A>G						.						92	93	93					22																	50515343		2203	4300	6503	SO:0001630	splice_region_variant	23209	exon8			GAGCCCTACGAAG	D25217	CCDS14083.1	22q13.33	2007-03-20			ENSG00000100427	ENSG00000100427			17082	protein-coding gene	gene with protein product		605908				7584026, 7584028	Standard	XR_430476		Approved	MLC, KIAA0027, LVM, VL	uc003bjg.1	Q15049	OTTHUMG00000150236	ENST00000311597.5:c.526-2A>G	chr22.hg19:g.50515343T>C		134.0	0.0		99.0	4.0	NM_139202	B3KW61|B7Z659|Q5JZ83|Q8TAG4|Q96RP5|Q9UGY8	Splice_Site	SNP	ENST00000311597.5	hg19	CCDS14083.1	.	.	.	.	.	.	.	.	.	.	T	13.24	2.178820	0.38511	.	.	ENSG00000100427	ENST00000395876;ENST00000311597;ENST00000538737;ENST00000431262;ENST00000535444;ENST00000450140;ENST00000442311	.	.	.	4.86	4.86	0.63082	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.9803	0.53115	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	MLC1	48857470	0.997000	0.39634	0.031000	0.17742	0.007000	0.05969	4.190000	0.58365	1.793000	0.52555	0.533000	0.62120	.	.	.		0.577	MLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316979.2	NM_015166	Intron	C	50515343	T	C	50515343	5	2	255	1	0	0	0	0	0	0	1	0	9621	1536	53	2	633	2	MLC1	22	50515343	Splice_Site	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	4572335	50515343	789223	762	36107										
PANX2	56666	hgsc.bcm.edu	37	chr22	50609290	50609290	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ggccgcgctgcttctgcagcTgaagctggagctgccgttcg	15	13	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:50609290T>C	ENST00000395842.2	+	1	131	c.131T>C	c.(130-132)cTg>cCg	p.L44P	PANX2_ENST00000159647.5_Missense_Mutation_p.L44P	NM_052839.3	NP_443071.2	Q96RD6	PANX2_HUMAN	pannexin 2	44					ion transport (GO:0006811)|protein hexamerization (GO:0034214)|response to ischemia (GO:0002931)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gap junction hemi-channel activity (GO:0055077)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(1)|skin(1)	7		all_cancers(38;1.14e-10)|all_epithelial(38;2.12e-09)|all_lung(38;7.01e-05)|Breast(42;0.000523)|Lung NSC(38;0.0018)|Ovarian(80;0.0365)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.105)		CTTCTGCAGCTGAAGCTGGAG	0.682																																					p.L44P		Atlas-SNP	.											.	PANX2	69	.	0			c.T131C						.						8	8	8					22																	50609290		2143	4196	6339	SO:0001583	missense	56666	exon1			TGCAGCTGAAGCT		CCDS14085.2, CCDS54544.1	22q13.33	2011-12-05			ENSG00000073150	ENSG00000073150		"Ion channels / Pannexins"	8600	protein-coding gene	gene with protein product		608421				14702039, 14597722	Standard	NM_052839		Approved	hPANX2, PX2	uc003bjn.4	Q96RD6	OTTHUMG00000044649	ENST00000395842.2:c.131T>C	chr22.hg19:g.50609290T>C	ENSP00000379183:p.Leu44Pro	88.0	0.0		55.0	4.0	NM_052839	B7Z684|Q96RD5|Q9UGX8	Missense_Mutation	SNP	ENST00000395842.2	hg19	CCDS14085.2	.	.	.	.	.	.	.	.	.	.	T	12.53	1.965566	0.34659	.	.	ENSG00000073150	ENST00000159647;ENST00000395842	T;T	0.33438	1.41;1.41	3.42	3.42	0.39159	.	0.000000	0.64402	U	0.000011	T	0.38692	0.1050	N	0.24115	0.695	0.80722	D	1	D;D	0.71674	0.998;0.997	D;D	0.74023	0.982;0.979	T	0.32693	-0.9897	10	0.87932	D	0	-6.376	11.9315	0.52849	0.0:0.0:0.0:1.0	.	44;44	Q96RD6-1;Q96RD6	.;PANX2_HUMAN	P	44	ENSP00000159647:L44P;ENSP00000379183:L44P	ENSP00000159647:L44P	L	+	2	0	PANX2	48951417	1.000000	0.71417	0.997000	0.53966	0.923000	0.55619	6.904000	0.75708	1.205000	0.43262	0.248000	0.18094	CTG	.	.		0.682	PANX2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075010.3	NM_052839		C	50609290	T	C	50609290	3	2	255	1	0	0	0	0	1	0	0	0	11430	1580	55	2	133	2	PANX2	22	50609290	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	93947	50609290	695276	763	36108										
CPT1B	1375	hgsc.bcm.edu	37	chr22	51008052	51008052	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gatgtggaagaagatcgtgtTctcgcctgcaatcatgtagg	13	7	2	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:51008052T>C	ENST00000360719.2	-	18	2325	c.2188A>G	c.(2188-2190)Aac>Gac	p.N730D	CPT1B_ENST00000395650.2_Missense_Mutation_p.N730D|CPT1B_ENST00000457250.1_Missense_Mutation_p.N696D|CPT1B_ENST00000405237.3_Missense_Mutation_p.N730D|CPT1B_ENST00000440709.1_Missense_Mutation_p.N649D|CPT1B_ENST00000312108.7_Missense_Mutation_p.N730D|CHKB-CPT1B_ENST00000453634.1_3'UTR|CPT1B_ENST00000434492.2_Missense_Mutation_p.N525D	NM_001145135.1|NM_152245.2	NP_001138607.1|NP_689451.1	Q92523	CPT1B_HUMAN	carnitine palmitoyltransferase 1B (muscle)	730					carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	carnitine O-palmitoyltransferase activity (GO:0004095)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22		all_cancers(38;8.8e-15)|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)		all cancers(3;3.56e-77)|OV - Ovarian serous cystadenocarcinoma(4;5.39e-74)|Epithelial(4;5.58e-70)|GBM - Glioblastoma multiforme(4;5.59e-08)|LUAD - Lung adenocarcinoma(64;0.0016)|Lung(4;0.00942)|BRCA - Breast invasive adenocarcinoma(115;0.207)		AAGATCGTGTTCTCGCCTGCA	0.517																																					p.N730D	Esophageal Squamous(170;988 1933 25577 30295 48163)	Atlas-SNP	.											.	CPT1B	61	.	0			c.A2188G						.						146	124	132					22																	51008052		2203	4300	6503	SO:0001583	missense	1375	exon18			TCGTGTTCTCGCC	U62733	CCDS14098.1, CCDS46734.1	22q13.33	2007-07-26			ENSG00000205560	ENSG00000205560			2329	protein-coding gene	gene with protein product		601987				9070950	Standard	NM_152245		Approved	M-CPT1, CPT1-M	uc003bmm.3	Q92523	OTTHUMG00000137390	ENST00000360719.2:c.2188A>G	chr22.hg19:g.51008052T>C	ENSP00000353945:p.Asn730Asp	138.0	0.0		97.0	4.0	NM_001145135	B7Z4U4|B7Z5T8|E9PCP2|Q13389|Q99655|Q9BY90	Missense_Mutation	SNP	ENST00000360719.2	hg19	CCDS14098.1	.	.	.	.	.	.	.	.	.	.	T	10.32	1.318010	0.23994	.	.	ENSG00000205560	ENST00000405237;ENST00000312108;ENST00000360719;ENST00000457250;ENST00000440709;ENST00000434492;ENST00000395650	T;T;T;T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13;-1.13;-1.13;-1.13	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.65091	0.2658	N	0.17872	0.535	0.80722	D	1	P;B;B;B	0.43938	0.822;0.011;0.018;0.049	B;B;B;B	0.42625	0.393;0.023;0.06;0.101	T	0.63060	-0.6721	10	0.18276	T	0.48	-33.1143	13.0547	0.58973	0.0:0.0:0.0:1.0	.	649;696;525;730	E9PCP2;B7Z4U4;A2RRE8;Q92523	.;.;.;CPT1B_HUMAN	D	730;730;730;696;649;525;730	ENSP00000385486:N730D;ENSP00000312189:N730D;ENSP00000353945:N730D;ENSP00000409342:N696D;ENSP00000414713:N649D;ENSP00000410966:N525D;ENSP00000379011:N730D	ENSP00000312189:N730D	N	-	1	0	CPT1B	49354918	1.000000	0.71417	0.947000	0.38551	0.395000	0.30598	3.095000	0.50235	1.963000	0.57068	0.459000	0.35465	AAC	.	.		0.517	CPT1B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317264.5	NM_152246		C	51008052	T	C	51008052	3	2	255	1	0	0	0	0	1	0	0	0	3834	1783	62	2	138	2	CPT1B	22	51008052	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	398762	51008052	296514	764	36109										
GYG2	8908	hgsc.bcm.edu	37	chrX	2774545	2774545	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgctcattatgtaggggcagAccaaggcttactgaatagtt	11	7	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:2774545A>G	ENST00000381163.3	+	7	869	c.587A>G	c.(586-588)gAc>gGc	p.D196G	GYG2_ENST00000542787.1_Missense_Mutation_p.D196G|GYG2_ENST00000381161.1_3'UTR|GYG2-AS1_ENST00000445107.1_RNA|GYG2_ENST00000398806.3_Missense_Mutation_p.D165G|GYG2_ENST00000338623.5_Missense_Mutation_p.D196G	NM_001079855.1|NM_001184702.1|NM_003918.2	NP_001073324.1|NP_001171631.1|NP_003909.2	O15488	GLYG2_HUMAN	glycogenin 2	196					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	glycogenin glucosyltransferase activity (GO:0008466)			endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)	13		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GTAGGGGCAGACCAAGGCTTA	0.448																																					p.D196G		Atlas-SNP	.											.	GYG2	39	.	0			c.A587G						.						114	93	100					X																	2774545		2203	4299	6502	SO:0001583	missense	8908	exon7			GGGCAGACCAAGG	U94361	CCDS14121.1, CCDS48074.1	Xp22.3	2013-02-22			ENSG00000056998	ENSG00000056998	2.4.1.186	"Glycosyltransferase family 8 domain containing"	4700	protein-coding gene	gene with protein product	"glycogenin glucosyltransferase"	300198				9857012	Standard	NM_001079855		Approved	GN-2	uc004cqs.1	O15488	OTTHUMG00000021079	ENST00000381163.3:c.587A>G	chrX.hg19:g.2774545A>G	ENSP00000370555:p.Asp196Gly	108.0	0.0		80.0	4.0	NM_003918	B7WNN6|O15485|O15486|O15487|O15489|O15490	Missense_Mutation	SNP	ENST00000381163.3	hg19	CCDS14121.1	.	.	.	.	.	.	.	.	.	.	A	13.33	2.204566	0.38905	.	.	ENSG00000056998	ENST00000398806;ENST00000381163;ENST00000338623;ENST00000542787	T;T;T;T	0.81330	-1.48;-1.48;-1.48;-1.48	3.34	3.34	0.38264	.	0.000000	0.64402	D	0.000020	D	0.92974	0.7764	H	0.98629	4.285	0.51482	D	0.999926	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0	D	0.94089	0.7351	10	0.87932	D	0	.	11.4252	0.50007	1.0:0.0:0.0:0.0	.	196;196;156;165;165;196	O15488-6;O15488-4;O15488-3;A8K8Y1;O15488-2;O15488	.;.;.;.;.;GLYG2_HUMAN	G	165;196;196;196	ENSP00000381786:D165G;ENSP00000370555:D196G;ENSP00000341273:D196G;ENSP00000446092:D196G	ENSP00000341273:D196G	D	+	2	0	GYG2	2784545	1.000000	0.71417	0.145000	0.22337	0.006000	0.05464	7.242000	0.78210	1.191000	0.43056	0.425000	0.28330	GAC	.	.		0.448	GYG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055645.1	NM_003918		G	2774545	A	G	2774545	3	3	255	1	0	0	0	0	1	0	0	0	6915	275	10	2	609	2	GYG2	23	2774545	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10		2774545	152496015	765	36110										
RPGR	6103	hgsc.bcm.edu	37	chrX	38145015	38145015	+	Intron	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttgtactcctctccatcctgCctttcattctcttcttcgcc	3	17	4	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:38145015C>A	ENST00000339363.3	-	14	2688				RPGR_ENST00000318842.7_Intron|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000309513.3_Intron|RPGR_ENST00000378505.2_Missense_Mutation_p.R1079S|RPGR_ENST00000342811.3_Intron|RPGR_ENST00000338898.3_Intron			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator						cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						CTCCATCCTGCCTTTCATTCT	0.423																																					p.R1079S		Atlas-SNP	.											.	RPGR	175	.	0			c.G3237T						.						408	328	355					X																	38145015		2202	4300	6502	SO:0001627	intron_variant	6103	exon15			ATCCTGCCTTTCA	U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"retinitis pigmentosa 15", "cone dystrophy 1 (X-linked)"	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.2520+1331G>T	chrX.hg19:g.38145015C>A		832.0	1.0		745.0	365.0	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	Missense_Mutation	SNP	ENST00000339363.3	hg19		.	.	.	.	.	.	.	.	.	.	c	9.446	1.089200	0.20390	.	.	ENSG00000156313	ENST00000378505	T	0.02197	4.4	2.56	1.49	0.22878	.	1.292120	0.05640	U	0.583284	T	0.02304	0.0071	L	0.48642	1.525	0.40039	D	0.975626	P	0.37233	0.588	B	0.20955	0.032	T	0.50939	-0.8768	10	0.87932	D	0	.	5.1985	0.15250	0.3421:0.6579:0.0:0.0	.	1079	E9PE28	.	S	1079	ENSP00000367766:R1079S	ENSP00000367766:R1079S	R	-	3	2	RPGR	38029959	0.000000	0.05858	0.035000	0.18076	0.523000	0.34469	-0.557000	0.05985	1.252000	0.44001	0.339000	0.21740	AGG	.	.		0.423	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328		A	38145015	C	A	38145015	1	1	255	0	1	0	0	0	0	0	0	0	13563	738	26	3		3	RPGR	23	38145015	Intron	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	35370470	38145015	117125545	766	36111										
ARAF	369	hgsc.bcm.edu	37	chrX	47430811	47430811	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttgcaccgcacccaggccgaTgagttgcctgcctgcctact	10	16	0	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:47430811T>A	ENST00000377045.4	+	16	1970	c.1776T>A	c.(1774-1776)gaT>gaA	p.D592E	ARAF_ENST00000470206.1_Intron	NM_001256196.1|NM_001654.4	NP_001243125.1|NP_001645.1	P10398	ARAF_HUMAN	A-Raf proto-oncogene, serine/threonine kinase	592					cellular protein modification process (GO:0006464)|negative regulation of apoptotic process (GO:0043066)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|regulation of TOR signaling (GO:0032006)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)			biliary_tract(1)|endometrium(4)|large_intestine(7)|liver(2)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	29					Adenosine triphosphate(DB00171)	CCCAGGCCGATGAGTTGCCTG	0.647																																					p.D595E		Atlas-SNP	.											.	ARAF	67	.	0			c.T1785A						.						57	39	45					X																	47430811		2203	4300	6503	SO:0001583	missense	369	exon16			GGCCGATGAGTTG	X04790	CCDS35232.1, CCDS59164.1, CCDS75970.1	Xp11.3-p11.23	2014-06-26	2014-06-26	2005-01-19	ENSG00000078061	ENSG00000078061			646	protein-coding gene	gene with protein product		311010	"v-raf murine sarcoma 3611 viral oncogene homolog 1"	ARAF1			Standard	NM_001654		Approved		uc004dic.2	P10398	OTTHUMG00000021446	ENST00000377045.4:c.1776T>A	chrX.hg19:g.47430811T>A	ENSP00000366244:p.Asp592Glu	137.0	0.0		146.0	73.0	NM_001256196	P07557|Q5H9B2|Q5H9B3	Missense_Mutation	SNP	ENST00000377045.4	hg19	CCDS35232.1	.	.	.	.	.	.	.	.	.	.	t	3.051	-0.195418	0.06259	.	.	ENSG00000078061	ENST00000377045	T	0.72942	-0.7	5.26	-6.7	0.01766	.	0.059749	0.64402	D	0.000004	T	0.27384	0.0672	N	0.02011	-0.69	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.41142	-0.9525	10	0.02654	T	1	.	5.3103	0.15828	0.1124:0.5063:0.1977:0.1836	.	592	P10398	ARAF_HUMAN	E	592	ENSP00000366244:D592E	ENSP00000366244:D592E	D	+	3	2	ARAF	47315755	0.969000	0.33509	0.946000	0.38457	0.994000	0.84299	0.003000	0.13083	-1.053000	0.03218	0.427000	0.28365	GAT	.	.		0.647	ARAF-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056418.1			A	47430811	T	A	47430811	3	1	255	1	0	0	0	0	1	0	0	0	837	1461	51	4	1834	4	ARAF	23	47430811	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	9285796	47430811	107839749	767	36112										
WDR13	64743	hgsc.bcm.edu	37	chrX	48458757	48458757	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gacaccgcctggcctgctgcTcactcgacggcagcatctcc	10	18	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:48458757T>C	ENST00000218056.5	+	5	1079	c.574T>C	c.(574-576)Tca>Cca	p.S192P	WDR13_ENST00000376729.5_Missense_Mutation_p.S192P	NM_001166426.1|NM_017883.4	NP_001159898.1|NP_060353	Q9H1Z4	WDR13_HUMAN	WD repeat domain 13	192						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|large_intestine(4)|lung(4)|ovary(2)	11						GGCCTGCTGCTCACTCGACGG	0.632																																					p.S192P		Atlas-SNP	.											.	WDR13	96	.	0			c.T574C						.						88	61	70					X																	48458757		2203	4300	6503	SO:0001583	missense	64743	exon5			TGCTGCTCACTCG	AF329819	CCDS14302.1	Xp11.23	2013-01-09			ENSG00000101940	ENSG00000101940		"WD repeat domain containing"	14352	protein-coding gene	gene with protein product		300512					Standard	NM_017883		Approved		uc004dkj.2	Q9H1Z4	OTTHUMG00000024119	ENST00000218056.5:c.574T>C	chrX.hg19:g.48458757T>C	ENSP00000218056:p.Ser192Pro	69.0	0.0		61.0	4.0	NM_017883	Q06DW8|Q06DX0|Q06DX1|Q9BUL7|Q9NWW4	Missense_Mutation	SNP	ENST00000218056.5	hg19	CCDS14302.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.684538	0.88639	.	.	ENSG00000101940	ENST00000376729;ENST00000218056	T;T	0.71103	-0.54;-0.54	4.93	4.93	0.64822	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.82416	0.5032	M	0.75615	2.305	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.993	D	0.84370	0.0543	10	0.87932	D	0	.	11.6068	0.51037	0.0:0.0:0.0:1.0	.	70;192	B4DVQ7;Q9H1Z4	.;WDR13_HUMAN	P	192	ENSP00000365919:S192P;ENSP00000218056:S192P	ENSP00000218056:S192P	S	+	1	0	WDR13	48343701	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	7.034000	0.76511	1.641000	0.50575	0.356000	0.21956	TCA	.	.		0.632	WDR13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060743.2			C	48458757	T	C	48458757	3	2	255	1	0	0	0	0	1	0	0	0	17290	1551	54	2	592	2	WDR13	23	48458757	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	1027946	48458757	106811803	768	36113										
IQSEC2	23096	hgsc.bcm.edu	37	chrX	53277936	53277936	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tgttgaactgcttctgccggTtccctaggaattcccctatc	8	13	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:53277936T>C	ENST00000375368.5	-	5	2596	c.2396A>G	c.(2395-2397)aAc>aGc	p.N799S	IQSEC2_ENST00000375365.2_Missense_Mutation_p.N604S|IQSEC2_ENST00000396435.3_Missense_Mutation_p.N809S			Q5JU85	IQEC2_HUMAN	IQ motif and Sec7 domain 2	799	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(10)|ovary(4)|skin(1)	29						CTTCTGCCGGTTCCCTAGGAA	0.597																																					p.N809S		Atlas-SNP	.											.	IQSEC2	195	.	0			c.A2426G						.						100	75	83					X																	53277936		2203	4300	6503	SO:0001583	missense	23096	exon6			TGCCGGTTCCCTA	AB011094	CCDS35298.1, CCDS48130.1	Xp11.23	2014-01-31			ENSG00000124313	ENSG00000124313			29059	protein-coding gene	gene with protein product		300522	"mental retardation, X-linked 1 (non-dysmorphic)"	MRX1		9628581, 20473311	Standard	NM_001243197		Approved	KIAA0522	uc004dsd.3	Q5JU85	OTTHUMG00000021608	ENST00000375368.5:c.2396A>G	chrX.hg19:g.53277936T>C	ENSP00000364517:p.Asn799Ser	111.0	0.0		95.0	4.0	NM_001111125	B3KT97|C7SDG1|O60275|Q5JUX1	Missense_Mutation	SNP	ENST00000375368.5	hg19		.	.	.	.	.	.	.	.	.	.	T	16.77	3.215009	0.58452	.	.	ENSG00000124313	ENST00000396435;ENST00000375368;ENST00000375365	T;T;T	0.53423	0.62;0.62;0.62	5.6	5.6	0.85130	.	0.193919	0.53938	D	0.000056	T	0.41213	0.1149	L	0.38175	1.15	0.58432	D	0.999998	B;P	0.40970	0.229;0.734	B;B	0.39531	0.159;0.302	T	0.42498	-0.9448	10	0.72032	D	0.01	.	13.7602	0.62961	0.0:0.0:0.0:1.0	.	809;604	Q5JU85-2;Q5JU85-3	.;.	S	809;799;604	ENSP00000379712:N809S;ENSP00000364517:N799S;ENSP00000364514:N604S	ENSP00000364514:N604S	N	-	2	0	IQSEC2	53294661	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.040000	0.89188	1.893000	0.54813	0.430000	0.28490	AAC	.	.		0.597	IQSEC2-201	KNOWN	basic	protein_coding	protein_coding		XM_291345		C	53277936	T	C	53277936	3	2	255	1	0	0	0	0	1	0	0	0	7827	1725	60	2	2080	2	IQSEC2	23	53277936	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	4819179	53277936	101992624	769	36114										
WNK3	65267	hgsc.bcm.edu	37	chrX	54335737	54335737	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ttggtttcatgactttaaatCgttttaagtacctatacaaa	5	6	1	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:54335737C>A	ENST00000375159.2	-	3	721	c.722G>T	c.(721-723)cGa>cTa	p.R241L	WNK3_ENST00000375169.3_Missense_Mutation_p.R241L|WNK3_ENST00000354646.2_Missense_Mutation_p.R241L			Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	241	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of ion transmembrane transporter activity (GO:0032414)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of rubidium ion transmembrane transporter activity (GO:2000688)|positive regulation of rubidium ion transport (GO:2000682)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(24)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						GACTTTAAATCGTTTTAAGTA	0.358																																					p.R241L		Atlas-SNP	.											.	WNK3	218	.	0			c.G722T						.						49	42	44					X																	54335737		2203	4300	6503	SO:0001583	missense	65267	exon4			TTAAATCGTTTTA	AJ409088	CCDS14357.1, CCDS35302.1	Xp11.22	2008-05-14	2005-01-19	2005-01-22	ENSG00000196632	ENSG00000196632			14543	protein-coding gene	gene with protein product		300358	"protein kinase, lysine deficient 3"	PRKWNK3			Standard	NM_020922		Approved		uc004dtc.2	Q9BYP7	OTTHUMG00000021626	ENST00000375159.2:c.722G>T	chrX.hg19:g.54335737C>A	ENSP00000364301:p.Arg241Leu	78.0	0.0		60.0	4.0	NM_001002838	B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	Missense_Mutation	SNP	ENST00000375159.2	hg19	CCDS14357.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.586794	0.86851	.	.	ENSG00000196632	ENST00000375169;ENST00000354646;ENST00000375159	T;T;T	0.66995	-0.24;-0.24;-0.24	4.93	4.93	0.64822	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.40469	N	0.001090	T	0.79919	0.4529	M	0.64170	1.965	0.51012	D	0.999902	D;D	0.89917	0.999;1.0	D;D	0.85130	0.99;0.997	T	0.82436	-0.0458	10	0.87932	D	0	-7.7154	16.24	0.82402	0.0:1.0:0.0:0.0	.	241;241	Q9BYP7-3;Q9BYP7	.;WNK3_HUMAN	L	241	ENSP00000364312:R241L;ENSP00000346667:R241L;ENSP00000364301:R241L	ENSP00000346667:R241L	R	-	2	0	WNK3	54352462	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.688000	0.84153	2.175000	0.68902	0.422000	0.28245	CGA	.	.		0.358	WNK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056799.2	NM_020922		A	54335737	C	A	54335737	3	1	255	1	0	0	0	0	1	0	0	0	17394	884	31	1	4764	1	WNK3	23	54335737	Missense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1057801	54335737	100934823	770	36115										
ITIH5L	347365	hgsc.bcm.edu	37	chrX	54784888	54784888	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	caaaggccttctggctgttgTtggtggccccttcactgtgg	13	11	2	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:54784888T>C	ENST00000218436.6	-	8	1648	c.1619A>G	c.(1618-1620)aAc>aGc	p.N540S		NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	540					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)										CTGGCTGTTGTTGGTGGCCCC	0.627																																					p.N540S		Atlas-SNP	.											.	.	.	.	0			c.A1619G						.						15	15	15					X																	54784888		2200	4290	6490	SO:0001583	missense	347365	exon8			CTGTTGTTGGTGG	AY358170	CCDS14361.1	Xp11.22-p11.21	2011-10-26	2011-10-26	2011-10-26	ENSG00000102313	ENSG00000102313			28907	protein-coding gene	gene with protein product			"inter-alpha (globulin) inhibitor H5-like"	ITIH5L		12975309	Standard	NM_198510		Approved	UNQ6369	uc004dtj.2	Q6UXX5	OTTHUMG00000021634	ENST00000218436.6:c.1619A>G	chrX.hg19:g.54784888T>C	ENSP00000218436:p.Asn540Ser	77.0	0.0		98.0	4.0	NM_198510	A6NN03	Missense_Mutation	SNP	ENST00000218436.6	hg19	CCDS14361.1	.	.	.	.	.	.	.	.	.	.	T	9.673	1.147282	0.21288	.	.	ENSG00000102313	ENST00000218436	T	0.10763	2.84	3.7	2.22	0.28083	.	1.294390	0.05575	U	0.571857	T	0.13286	0.0322	M	0.67953	2.075	0.29653	N	0.843819	B	0.17852	0.024	B	0.21546	0.035	T	0.47898	-0.9081	10	0.09084	T	0.74	.	7.9866	0.30216	0.0:0.1363:0.0:0.8637	.	540	Q6UXX5	ITH5L_HUMAN	S	540	ENSP00000218436:N540S	ENSP00000218436:N540S	N	-	2	0	ITIH5L	54801613	0.000000	0.05858	0.996000	0.52242	0.206000	0.24218	0.061000	0.14366	1.162000	0.42619	0.483000	0.47432	AAC	.	.		0.627	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056814.2	NM_198510		C	54784888	T	C	54784888	3	2	255	1	0	0	0	0	1	0	0	0	7917	1725	60	2	2346	2	ITIH5L	23	54784888	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	449151	54784888	100485672	771	36116										
AR	367	hgsc.bcm.edu	37	chrX	66766306	66766306	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	catcctggcacactctcttcAcagccgaagaaggccagttg	9	14	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:66766306A>G	ENST00000374690.3	+	1	1842	c.1318A>G	c.(1318-1320)Aca>Gca	p.T440A	AR_ENST00000504326.1_Missense_Mutation_p.T440A|AR_ENST00000513847.1_3'UTR|AR_ENST00000396044.3_Missense_Mutation_p.T440A	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	438	Modulating.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	CACTCTCTTCACAGCCGAAGA	0.746									Androgen Insensitivity Syndrome																												p.T440A		Atlas-SNP	.											.	AR	249	.	0			c.A1318G						.						4	4	4					X																	66766306		1370	2920	4290	SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	CTCTTCACAGCCG	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.1318A>G	chrX.hg19:g.66766306A>G	ENSP00000363822:p.Thr440Ala	45.0	0.0		43.0	4.0	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	hg19	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	a	13.33	2.205347	0.39003	.	.	ENSG00000169083	ENST00000544984;ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	D;D;D	0.95035	-3.59;-3.59;-3.59	5.06	2.67	0.31697	.	0.840433	0.10974	N	0.613442	D	0.92545	0.7632	M	0.74881	2.28	0.27541	N	0.9508	B;B;P	0.43701	0.01;0.005;0.815	B;B;B	0.42214	0.074;0.042;0.38	D	0.84511	0.0622	10	0.29301	T	0.29	.	4.8744	0.13650	0.6413:0.0:0.3587:0.0	.	440;440;438	E7EVX6;D3YPQ2;P10275	.;.;ANDR_HUMAN	A	250;440;440;440;432	ENSP00000363822:T440A;ENSP00000421155:T440A;ENSP00000379359:T440A	ENSP00000363822:T440A	T	+	1	0	AR	66683031	0.991000	0.36638	0.950000	0.38849	0.951000	0.60555	0.992000	0.29667	0.759000	0.33084	0.414000	0.27820	ACA	.	.		0.746	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		G	66766306	A	G	66766306	3	3	255	1	0	0	0	0	1	0	0	0	836	159	6	2	1320	2	AR	23	66766306	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	11981418	66766306	88504254	772	36117										
PJA1	64219	hgsc.bcm.edu	37	chrX	68381880	68381880	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tagcctgtggaggttcccgcTcttctttccccggcagagtc	11	14	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:68381880T>C	ENST00000361478.1	-	2	1579	c.1202A>G	c.(1201-1203)gAg>gGg	p.E401G	PJA1_ENST00000477231.1_5'Flank|PJA1_ENST00000374571.4_Missense_Mutation_p.E346G|PJA1_ENST00000374583.1_Missense_Mutation_p.E401G|PJA1_ENST00000374584.3_Missense_Mutation_p.E213G	NM_001032396.2|NM_022368.4|NM_145119.3	NP_001027568.1|NP_071763.2|NP_660095.1	Q8NG27	PJA1_HUMAN	praja ring finger 1, E3 ubiquitin protein ligase	401					protein catabolic process (GO:0030163)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(5)|lung(12)|ovary(1)	21						AGGTTCCCGCTCTTCTTTCCC	0.642																																					p.E401G		Atlas-SNP	.											.	PJA1	106	.	0			c.A1202G						.						28	30	29					X																	68381880		2203	4300	6503	SO:0001583	missense	64219	exon2			TCCCGCTCTTCTT	AK021892	CCDS14392.1, CCDS14393.1, CCDS35316.1	Xq13.1	2013-01-09	2012-02-23		ENSG00000181191	ENSG00000181191		"RING-type (C3HC4) zinc fingers"	16648	protein-coding gene	gene with protein product		300420	"praja 1", "praja ring finger 1"			12036302	Standard	NM_001032396		Approved	FLJ11830, RNF70	uc004dxh.3	Q8NG27	OTTHUMG00000021753	ENST00000361478.1:c.1202A>G	chrX.hg19:g.68381880T>C	ENSP00000355014:p.Glu401Gly	74.0	0.0		93.0	4.0	NM_145119	A2A322|Q5JUT8|Q5JUT9|Q8NG28|Q9HAC1	Missense_Mutation	SNP	ENST00000361478.1	hg19	CCDS14393.1	.	.	.	.	.	.	.	.	.	.	t	18.46	3.627998	0.66901	.	.	ENSG00000181191	ENST00000396010;ENST00000374584;ENST00000374583;ENST00000361478;ENST00000374571	T;T;T;T	0.06294	3.32;3.32;3.32;3.32	3.59	3.59	0.41128	.	0.000000	0.53938	U	0.000056	T	0.17280	0.0415	L	0.61218	1.895	0.42671	D	0.993515	D;D	0.63046	0.97;0.992	P;P	0.62740	0.749;0.906	T	0.00520	-1.1692	10	0.87932	D	0	-12.4008	9.8043	0.40783	0.0:0.0:0.0:1.0	.	401;213	Q8NG27;Q8NG27-2	PJA1_HUMAN;.	G	316;213;401;401;346	ENSP00000363712:E213G;ENSP00000363711:E401G;ENSP00000355014:E401G;ENSP00000363699:E346G	ENSP00000355014:E401G	E	-	2	0	PJA1	68298605	1.000000	0.71417	0.068000	0.19968	0.023000	0.10783	5.616000	0.67709	1.672000	0.50884	0.438000	0.28831	GAG	.	.		0.642	PJA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057031.2	NM_145119		C	68381880	T	C	68381880	3	2	255	1	0	0	0	0	1	0	0	0	11970	1551	54	2	733	2	PJA1	23	68381880	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	1615574	68381880	86888680	773	36118										
ZMYM3	9203	hgsc.bcm.edu	37	chrX	70465850	70465850	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	actcaccgggataggcatcgAgaaaggcaccgggactttct	12	11	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:70465850A>G	ENST00000353904.2	-	16	2858	c.2671T>C	c.(2671-2673)Tcg>Ccg	p.S891P	ZMYM3_ENST00000373988.1_Missense_Mutation_p.S893P|ZMYM3_ENST00000373984.3_Missense_Mutation_p.S893P|ZMYM3_ENST00000314425.5_Missense_Mutation_p.S891P|ZMYM3_ENST00000489332.1_5'UTR|ZMYM3_ENST00000373998.1_Missense_Mutation_p.S879P	NM_005096.3	NP_005087.1	Q14202	ZMYM3_HUMAN	zinc finger, MYM-type 3	891					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(7)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(12)|lung(17)|ovary(1)|prostate(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(35;0.156)					ATAGGCATCGAGAAAGGCACC	0.572																																					p.S891P		Atlas-SNP	.											.	ZMYM3	137	.	0			c.T2671C						.						122	99	107					X																	70465850		2203	4300	6503	SO:0001583	missense	9203	exon16			GCATCGAGAAAGG	AB002383	CCDS14409.1, CCDS55443.1, CCDS55444.1	Xq13.1	2013-01-08	2005-12-19	2005-12-19	ENSG00000147130	ENSG00000147130		"Zinc fingers, MYM type"	13054	protein-coding gene	gene with protein product		300061	"zinc finger protein 261"	ZNF261		10486218	Standard	NM_201599		Approved	ZNF198L2, DXS6673E, KIAA0385, MYM	uc004dzh.2	Q14202	OTTHUMG00000021799	ENST00000353904.2:c.2671T>C	chrX.hg19:g.70465850A>G	ENSP00000343909:p.Ser891Pro	96.0	0.0		89.0	4.0	NM_005096	D3DVV3|O15089|Q96E26	Missense_Mutation	SNP	ENST00000353904.2	hg19	CCDS14409.1	.	.	.	.	.	.	.	.	.	.	a	15.19	2.760658	0.49468	.	.	ENSG00000147130	ENST00000314425;ENST00000373998;ENST00000353904;ENST00000373984;ENST00000373988	T;T;T;T;T	0.41400	1.61;1.0;1.61;1.61;1.61	5.12	5.12	0.69794	.	0.000000	0.64402	D	0.000008	T	0.42449	0.1203	N	0.15975	0.35	0.41935	D	0.990581	D;D	0.67145	0.996;0.994	D;P	0.65010	0.931;0.854	T	0.27706	-1.0066	10	0.15952	T	0.53	-7.3014	14.089	0.64977	1.0:0.0:0.0:0.0	.	879;891	Q14202-2;Q14202	.;ZMYM3_HUMAN	P	891;879;891;893;893	ENSP00000322845:S891P;ENSP00000363110:S879P;ENSP00000343909:S891P;ENSP00000363096:S893P;ENSP00000363100:S893P	ENSP00000322845:S891P	S	-	1	0	ZMYM3	70382575	1.000000	0.71417	0.997000	0.53966	0.943000	0.58893	2.833000	0.48159	1.902000	0.55061	0.427000	0.28365	TCG	.	.		0.572	ZMYM3-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057154.1	NM_201599		G	70465850	A	G	70465850	3	3	255	1	0	0	0	0	1	0	0	0	17716	304	11	2	1481	2	ZMYM3	23	70465850	Missense_Mutation	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	2083970	70465850	84804710	774	36119										
DACH2	117154	hgsc.bcm.edu	37	chrX	85404070	85404070	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	ccgctgcaaactcatcaccaGgaaagacttcgaaactttgt	7	12	2	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:85404070G>T	ENST00000373125.4	+	1	446	c.446G>T	c.(445-447)aGg>aTg	p.R149M	DACH2_ENST00000373131.1_Missense_Mutation_p.R149M	NM_053281.3	NP_444511.1	Q96NX9	DACH2_HUMAN	dachshund family transcription factor 2	149	DACHbox-N.				development of primary female sexual characteristics (GO:0046545)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(14)|lung(28)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	71						CTCATCACCAGGAAAGACTTC	0.557																																					p.R149M		Atlas-SNP	.											.	DACH2	263	.	0			c.G446T						.						46	47	46					X																	85404070		2203	4300	6503	SO:0001583	missense	117154	exon1			TCACCAGGAAAGA	AF428101	CCDS14455.1, CCDS48140.1, CCDS55457.1	Xq21.3	2014-02-03	2014-02-03		ENSG00000126733	ENSG00000126733			16814	protein-coding gene	gene with protein product		300608	"dachshund homolog 2 (Drosophila)"				Standard	NM_053281		Approved		uc004eew.2	Q96NX9	OTTHUMG00000021944	ENST00000373125.4:c.446G>T	chrX.hg19:g.85404070G>T	ENSP00000362217:p.Arg149Met	61.0	0.0		59.0	4.0	NM_001139514	B1AJV3|B4DQG3|Q8NAY3|Q8ND17|Q96N55	Missense_Mutation	SNP	ENST00000373125.4	hg19	CCDS14455.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.958200	0.73902	.	.	ENSG00000126733	ENST00000344497;ENST00000373131;ENST00000373125	D;D	0.84370	-1.84;-1.84	4.5	4.5	0.54988	DNA binding domain, putative (1);Transforming protein Ski (2);	0.000000	0.56097	D	0.000037	D	0.92166	0.7516	M	0.81497	2.545	0.80722	D	1	D;D	0.76494	0.991;0.999	D;D	0.77557	0.984;0.99	D	0.92951	0.6380	10	0.54805	T	0.06	.	16.1211	0.81357	0.0:0.0:1.0:0.0	.	149;149	Q96NX9-2;Q96NX9	.;DACH2_HUMAN	M	149	ENSP00000362223:R149M;ENSP00000362217:R149M	ENSP00000345134:R149M	R	+	2	0	DACH2	85290726	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.806000	0.91930	2.071000	0.62044	0.544000	0.68410	AGG	.	.		0.557	DACH2-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359266.1	NM_053281		T	85404070	G	T	85404070	3	4	255	1	0	0	0	0	1	0	0	0	4223	1000	35	3	448	3	DACH2	23	85404070	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	14938220	85404070	69866490	775	36120										
MUM1L1	139221	hgsc.bcm.edu	37	chrX	105450466	105450466	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cagagactggattttgaagaActtgaggaagaaggtcaagc	13	5	1	5			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:105450466A>G	ENST00000357175.2	+	4	1690	c.1041A>G	c.(1039-1041)gaA>gaG	p.E347E	MUM1L1_ENST00000337685.2_Silent_p.E347E|MUM1L1_ENST00000372552.1_Silent_p.E347E	NM_001171020.1	NP_001164491.1	Q5H9M0	MUML1_HUMAN	melanoma associated antigen (mutated) 1-like 1	347						extracellular vesicular exosome (GO:0070062)				autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31						ATTTTGAAGAACTTGAGGAAG	0.408																																					p.E347E		Atlas-SNP	.											.	MUM1L1	166	.	0			c.A1041G						.						23	21	21					X																	105450466		1849	4080	5929	SO:0001819	synonymous_variant	139221	exon5			TGAAGAACTTGAG	AK090835	CCDS55469.1	Xq22.3	2008-02-05			ENSG00000157502	ENSG00000157502			26583	protein-coding gene	gene with protein product							Standard	NM_152423		Approved	FLJ33516	uc004emf.2	Q5H9M0	OTTHUMG00000022146	ENST00000357175.2:c.1041A>G	chrX.hg19:g.105450466A>G		104.0	0.0		100.0	4.0	NM_152423	D3DUX2|Q49AS5|Q8N2C0|Q96MT6	Silent	SNP	ENST00000357175.2	hg19	CCDS55469.1																																																																																			.	.		0.408	MUM1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057795.1	NM_152423		G	105450466	A	G	105450466	2	3	255	1	0	0	0	0	0	0	0	1	9995	40	2	2		2	MUM1L1	23	105450466	Silent	SNP	A	TCGA-EP-A2KB-01A-11D-A183-10	20046396	105450466	49820094	776	36121										
RNF128	79589	hgsc.bcm.edu	37	chrX	105970375	105970375	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	acggccaggactcgccgctgGagcctgtggctggggtcctg	17	13	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:105970375G>T	ENST00000255499.2	+	1	482	c.232G>T	c.(232-234)Gag>Tag	p.E78*	RNF128_ENST00000324342.3_Intron	NM_194463.1	NP_919445.1	Q8TEB7	RN128_HUMAN	ring finger protein 128, E3 ubiquitin protein ligase	78	PA.				negative regulation of cytokine biosynthetic process (GO:0042036)	cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(6)|ovary(1)	11						CTCGCCGCTGGAGCCTGTGGC	0.677																																					p.E78X		Atlas-SNP	.											.	RNF128	74	.	0			c.G232T						.						15	13	14					X																	105970375		2146	4174	6320	SO:0001587	stop_gained	79589	exon1			CCGCTGGAGCCTG	AK027169	CCDS14520.1, CCDS14521.1	Xq22.3	2013-01-09	2012-02-23		ENSG00000133135	ENSG00000133135		"RING-type (C3HC4) zinc fingers"	21153	protein-coding gene	gene with protein product		300439	"ring finger protein 128"				Standard	NM_024539		Approved	FLJ23516, GRAIL	uc004eml.3	Q8TEB7	OTTHUMG00000022151	ENST00000255499.2:c.232G>T	chrX.hg19:g.105970375G>T	ENSP00000255499:p.Glu78*	192.0	0.0		208.0	75.0	NM_194463	A0PJI4|Q6PH80|Q6ZTJ8|Q96RF3|Q9H5E4	Nonsense_Mutation	SNP	ENST00000255499.2	hg19	CCDS14521.1	.	.	.	.	.	.	.	.	.	.	g	40	8.078396	0.98643	.	.	ENSG00000133135	ENST00000255499	.	.	.	4.7	4.7	0.59300	.	0.763681	0.12066	N	0.502641	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10377	T	0.69	.	10.5584	0.45131	0.0:0.1912:0.8088:0.0	.	.	.	.	X	78	.	ENSP00000255499:E78X	E	+	1	0	RNF128	105857031	0.996000	0.38824	0.985000	0.45067	0.975000	0.68041	1.794000	0.38774	2.082000	0.62665	0.509000	0.49947	GAG	.	.		0.677	RNF128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057804.1	NM_024539		T	105970375	G	T	105970375	4	4	255	1	0	0	0	0	0	1	0	0	13451	1175	41	3	644	3	RNF128	23	105970375	Nonsense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	519909	105970375	49300185	777	36122										
MID2	11043	hgsc.bcm.edu	37	chrX	107097839	107097839	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cataccctctgcgatgacagCaaactctggagatgaacctc	8	13	2	3			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:107097839C>T	ENST00000262843.6	+	3	1269	c.721C>T	c.(721-723)Caa>Taa	p.Q241*	MID2_ENST00000443968.2_Splice_Site_p.Q241*	NM_012216.3|NM_052817.2	NP_036348.2|NP_438112.2	Q9UJV3	TRIM1_HUMAN	midline 2	241					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein localization to microtubule (GO:0035372)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	ligase activity (GO:0016874)|microtubule binding (GO:0008017)|phosphoprotein binding (GO:0051219)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)|ovary(1)|prostate(2)	19						GCGATGACAGCAAACTCTGGA	0.463																																					p.Q241X		Atlas-SNP	.											.	MID2	122	.	0			c.C721T						.						129	106	114					X																	107097839		2203	4300	6503	SO:0001630	splice_region_variant	11043	exon3			TGACAGCAAACTC		CCDS14532.2, CCDS14533.2	Xq22.1-q22.2	2013-02-11			ENSG00000080561	ENSG00000080561		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Fibronectin type III domain containing"	7096	protein-coding gene	gene with protein product		300204				10400986	Standard	NM_012216		Approved	FXY2, TRIM1, RNF60	uc004enl.3	Q9UJV3	OTTHUMG00000022171	ENST00000262843.6:c.721-1C>T	chrX.hg19:g.107097839C>T		106.0	0.0		101.0	5.0	NM_012216	A6NEL8|A6PVI5|Q5JYF5|Q8WWK1|Q9UJR9	Nonsense_Mutation	SNP	ENST00000262843.6	hg19	CCDS14532.2	.	.	.	.	.	.	.	.	.	.	C	43	10.251219	0.99368	.	.	ENSG00000080561	ENST00000262843;ENST00000443968	.	.	.	5.17	5.17	0.71159	.	0.059879	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8595	0.70369	0.0:1.0:0.0:0.0	.	.	.	.	X	241	.	.	Q	+	1	0	MID2	106984495	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.021000	0.76425	2.388000	0.81334	0.600000	0.82982	CAA	.	.		0.463	MID2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057852.2	NM_012216	Nonsense_Mutation	T	107097839	C	T	107097839	5	4	255	1	0	0	0	0	0	0	1	0	9587	724	25	3	731	3	MID2	23	107097839	Splice_Site	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	1127464	107097839	48172721	778	36123										
DOCK11	139818	hgsc.bcm.edu	37	chrX	117744275	117744275	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	tcccgagacatatcatcatgTcttacattcactgcttcttg	5	12	5	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:117744275T>C	ENST00000276202.7	+	28	3053	c.2990T>C	c.(2989-2991)gTc>gCc	p.V997A	DOCK11_ENST00000276204.6_Missense_Mutation_p.V997A	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	997					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(4)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(17)|liver(1)|lung(35)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	84						TATCATCATGTCTTACATTCA	0.423																																					p.V997A		Atlas-SNP	.											.	DOCK11	185	.	0			c.T2990C						.						153	121	132					X																	117744275		2203	4300	6503	SO:0001583	missense	139818	exon28			ATCATGTCTTACA	AK125641	CCDS35373.1	Xq24	2013-10-25			ENSG00000147251	ENSG00000147251		"Pleckstrin homology (PH) domain containing"	23483	protein-coding gene	gene with protein product	"zizimin2"	300681				12432077, 16968698	Standard	NM_144658		Approved	FLJ32122, FLJ43653, ZIZ2, ACG	uc004eqp.2	Q5JSL3	OTTHUMG00000022256	ENST00000276202.7:c.2990T>C	chrX.hg19:g.117744275T>C	ENSP00000276202:p.Val997Ala	88.0	0.0		99.0	4.0	NM_144658	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Missense_Mutation	SNP	ENST00000276202.7	hg19	CCDS35373.1	.	.	.	.	.	.	.	.	.	.	T	4.159	0.028049	0.08054	.	.	ENSG00000147251	ENST00000276204;ENST00000276202	T;T	0.03580	3.88;3.88	5.14	5.14	0.70334	.	0.174630	0.49916	D	0.000134	T	0.01592	0.0051	N	0.03608	-0.345	0.29348	N	0.865558	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.40961	-0.9535	10	0.07482	T	0.82	-7.7299	7.1266	0.25475	0.0:0.1496:0.0:0.8504	.	997;997	A6NIW2;Q5JSL3	.;DOC11_HUMAN	A	997	ENSP00000276204:V997A;ENSP00000276202:V997A	ENSP00000276202:V997A	V	+	2	0	DOCK11	117628303	0.953000	0.32496	1.000000	0.80357	0.812000	0.45895	1.804000	0.38873	1.817000	0.53016	0.481000	0.45027	GTC	.	.		0.423	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658		C	117744275	T	C	117744275	3	2	255	1	0	0	0	0	1	0	0	0	4688	1667	58	2	3100	2	DOCK11	23	117744275	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	10646436	117744275	37526285	779	36124										
ZNF75D	7626	hgsc.bcm.edu	37	chrX	134426381	134426381	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	caagagcactgcctcctttcCcagctcatgggctgtgacct	9	15	1	2			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:134426381C>A	ENST00000370766.3	-	4	3139	c.430G>T	c.(430-432)Gga>Tga	p.G144*	ZNF75D_ENST00000370764.1_Intron|ZNF75D_ENST00000494295.1_Intron	NM_007131.3	NP_009062.2	P51815	ZN75D_HUMAN	zinc finger protein 75D	144					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(14)|upper_aerodigestive_tract(1)|urinary_tract(2)	31						GCCTCCTTTCCCAGCTCATGG	0.522																																					p.G144X		Atlas-SNP	.											.	ZNF75D	65	.	0			c.G430T						.						74	67	70					X																	134426381		2203	4300	6503	SO:0001587	stop_gained	7626	exon3			CCTTTCCCAGCTC	S43109	CCDS14648.1, CCDS55503.1	Xq26	2013-01-09	2008-06-11	2008-06-11	ENSG00000186376	ENSG00000186376		"Zinc fingers, C2H2-type", "-", "-", "-"	13145	protein-coding gene	gene with protein product		314997	"zinc finger protein 75 (D8C6)"	ZNF82, ZNF75		1505955	Standard	XM_005262469		Approved	ZKSCAN24, D8C6, ZSCAN28	uc004eyo.3	P51815	OTTHUMG00000022482	ENST00000370766.3:c.430G>T	chrX.hg19:g.134426381C>A	ENSP00000359802:p.Gly144*	90.0	0.0		82.0	4.0	NM_007131	A6NK62|B3KRI7|Q5JPG0|Q6LDE0	Nonsense_Mutation	SNP	ENST00000370766.3	hg19	CCDS14648.1	.	.	.	.	.	.	.	.	.	.	C	54	22.293001	0.99947	.	.	ENSG00000186376	ENST00000370766	.	.	.	2.3	-0.642	0.11486	.	.	.	.	.	.	.	.	.	.	.	0.19775	N	0.999954	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	.	2.7469	0.05270	0.0:0.4105:0.2511:0.3384	.	.	.	.	X	144	.	ENSP00000359802:G144X	G	-	1	0	ZNF75D	134254047	0.362000	0.24980	0.059000	0.19551	0.570000	0.35934	-0.047000	0.11963	-0.314000	0.08716	-0.355000	0.07637	GGA	.	.		0.522	ZNF75D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058415.1	NM_007131		A	134426381	C	A	134426381	4	1	255	1	0	0	0	0	0	1	0	0	18149	632	22	3	1118	3	ZNF75D	23	134426381	Nonsense_Mutation	SNP	C	TCGA-EP-A2KB-01A-11D-A183-10	16682106	134426381	20844179	780	36125										
MMGT1	93380	hgsc.bcm.edu	37	chrX	135053250	135053250	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	gattcatcttctttttctgtTaatcgcatataagaacgatc	5	8	4	1			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:135053250T>A	ENST00000305963.2	-	2	486	c.99A>T	c.(97-99)ttA>ttT	p.L33F	MMGT1_ENST00000433339.2_Missense_Mutation_p.L98F	NM_173470.1	NP_775741.1	Q8N4V1	MMGT1_HUMAN	membrane magnesium transporter 1	33					magnesium ion transport (GO:0015693)	early endosome (GO:0005769)|ER membrane protein complex (GO:0072546)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	magnesium ion transmembrane transporter activity (GO:0015095)			cervix(1)|endometrium(1)|kidney(1)	3						CTTTTTCTGTTAATCGCATAT	0.294																																					p.L33F		Atlas-SNP	.											.	MMGT1	14	.	0			c.A99T						.						161	153	156					X																	135053250		2203	4300	6503	SO:0001583	missense	93380	exon2			TTCTGTTAATCGC	AL157477	CCDS14653.1	Xq26.3	2012-05-23	2008-11-21	2008-11-21	ENSG00000169446	ENSG00000169446			28100	protein-coding gene	gene with protein product	"ER membrane protein complex subunit 5"		"transmembrane protein 32"	TMEM32		18057121, 22119785	Standard	NM_173470		Approved	EMC5	uc004ezi.1	Q8N4V1	OTTHUMG00000022499	ENST00000305963.2:c.99A>T	chrX.hg19:g.135053250T>A	ENSP00000306220:p.Leu33Phe	578.0	0.0		484.0	245.0	NM_173470	B2R625|B4DIY3|D3DWG7|Q5JPP7	Missense_Mutation	SNP	ENST00000305963.2	hg19	CCDS14653.1	.	.	.	.	.	.	.	.	.	.	T	17.61	3.431485	0.62844	.	.	ENSG00000169446	ENST00000305963;ENST00000433339	.	.	.	5.17	5.17	0.71159	.	0.000000	0.64402	D	0.000001	T	0.69878	0.3160	M	0.62266	1.93	0.58432	D	0.999997	D;D	0.89917	1.0;0.958	D;P	0.91635	0.999;0.815	T	0.71276	-0.4641	9	0.52906	T	0.07	.	8.5328	0.33344	0.0:0.0932:0.0:0.9068	.	98;33	Q8N4V1-2;Q8N4V1	.;MMGT1_HUMAN	F	33;98	.	ENSP00000306220:L33F	L	-	3	2	MMGT1	134880916	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.536000	0.36072	1.832000	0.53329	0.481000	0.45027	TTA	.	.		0.294	MMGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058453.3	NM_173470		A	135053250	T	A	135053250	3	1	255	1	0	0	0	0	1	0	0	0	9656	1751	61	4	308	4	MMGT1	23	135053250	Missense_Mutation	SNP	T	TCGA-EP-A2KB-01A-11D-A183-10	626869	135053250	20217310	781	36126										
SOX3	6658	hgsc.bcm.edu	37	chrX	139587141	139587141	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	cagcgagtccggcgggaaggGtaggcttatcaaaatgctcc	14	10	1	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:139587141G>T	ENST00000370536.2	-	1	84	c.85C>A	c.(85-87)Ccc>Acc	p.P29T		NM_005634.2	NP_005625.2	P41225	SOX3_HUMAN	SRY (sex determining region Y)-box 3	29					central nervous system development (GO:0007417)|face development (GO:0060324)|hypothalamus development (GO:0021854)|negative regulation of neuron differentiation (GO:0045665)|neuron development (GO:0048666)|organ morphogenesis (GO:0009887)|pituitary gland development (GO:0021983)|sensory organ development (GO:0007423)|Sertoli cell development (GO:0060009)|sex determination (GO:0007530)|spermatid differentiation (GO:0048515)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|pancreas(1)|skin(1)	10	Acute lymphoblastic leukemia(192;7.65e-05)					GGCGGGAAGGGTAGGCTTATC	0.652																																					p.P29T		Atlas-SNP	.											.	SOX3	44	.	0			c.C85A						.						10	10	10					X																	139587141		2193	4281	6474	SO:0001583	missense	6658	exon1			GGAAGGGTAGGCT		CCDS14669.1	Xq27.1	2013-10-17			ENSG00000134595	ENSG00000134595		"SRY (sex determining region Y)-boxes"	11199	protein-coding gene	gene with protein product		313430	"panhypopituitarism"	PHP		15800844	Standard	NM_005634		Approved		uc004fbd.1	P41225	OTTHUMG00000022544	ENST00000370536.2:c.85C>A	chrX.hg19:g.139587141G>T	ENSP00000359567:p.Pro29Thr	126.0	0.0		125.0	31.0	NM_005634	P35714|Q5JWI3|Q9NP49	Missense_Mutation	SNP	ENST00000370536.2	hg19	CCDS14669.1	.	.	.	.	.	.	.	.	.	.	g	11.55	1.672375	0.29693	.	.	ENSG00000134595	ENST00000370536	D	0.98493	-4.96	3.67	1.8	0.24995	.	.	.	.	.	D	0.93455	0.7912	N	0.19112	0.55	0.23879	N	0.996589	B	0.24186	0.099	B	0.22753	0.041	D	0.86525	0.1818	8	.	.	.	.	5.0479	0.14494	0.1311:0.2109:0.658:0.0	.	29	P41225	SOX3_HUMAN	T	29	ENSP00000359567:P29T	.	P	-	1	0	SOX3	139414807	0.050000	0.20438	0.229000	0.23960	0.689000	0.40095	0.143000	0.16115	0.179000	0.19938	0.525000	0.51046	CCC	.	.		0.652	SOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058577.1			T	139587141	G	T	139587141	3	4	255	1	0	0	0	0	1	0	0	0	14966	1261	44	3	1259	3	SOX3	23	139587141	Missense_Mutation	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	4533891	139587141	15683419	782	36127										
GPR50	9248	hgsc.bcm.edu	37	chrX	150345211	150345211	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0127877237851662	10	1	0.504942147711443	1.36793418198191	0.436152927588434	0.0737549409645707	0.539423391760488	0	aacatggggcccaccctagcGgttcccaccccctatggctg	10	17	0	0			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:150345211G>T	ENST00000218316.3	+	1	87	c.18G>T	c.(16-18)gcG>gcT	p.A6A	GPR50-AS1_ENST00000454196.1_RNA	NM_004224.3	NP_004215.2	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	6					cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|identical protein binding (GO:0042802)|melatonin receptor activity (GO:0008502)			breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	38	Acute lymphoblastic leukemia(192;6.56e-05)					CCACCCTAGCGGTTCCCACCC	0.557																																					p.A6A		Atlas-SNP	.											.	GPR50	195	.	0			c.G18T						.						67	70	69					X																	150345211		1931	4111	6042	SO:0001819	synonymous_variant	9248	exon1			CCTAGCGGTTCCC	U52219	CCDS44012.1	Xq28	2012-08-21			ENSG00000102195	ENSG00000102195		"GPCR / Class A : Orphans"	4506	protein-coding gene	gene with protein product		300207				9933574, 18400093	Standard	NM_004224		Approved	H9, Mel1c	uc010ntg.2	Q13585	OTTHUMG00000024166	ENST00000218316.3:c.18G>T	chrX.hg19:g.150345211G>T		104.0	0.0		98.0	4.0	NM_004224	Q0VGG3|Q3ZAR0	Silent	SNP	ENST00000218316.3	hg19	CCDS44012.1																																																																																			.	.		0.557	GPR50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060874.1	NM_004224		T	150345211	G	T	150345211	2	4	255	1	0	0	0	0	0	0	0	1	6705	1103	39	1		1	GPR50	23	150345211	Silent	SNP	G	TCGA-EP-A2KB-01A-11D-A183-10	10758070	150345211	4925349	783	36128										
MTOR	2475	hgsc.bcm.edu	37	chr1	11316988	11316988	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	gctcctccctgtagacactcAcagctgcatgtctccggccc	8	18	2	1			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr1:11316988A>T	ENST00000361445.4	-	4	581		c.e4+1			NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)						cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	GTAGACACTCACAGCTGCATG	0.557																																					.		Atlas-SNP	.											.	MTOR	327	.	0			c.504+2T>A						.						37	32	34					1																	11316988		2203	4300	6503	SO:0001630	splice_region_variant	2475	exon5			ACACTCACAGCTG	L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"FK506 binding protein 12-rapamycin associated protein 2", "rapamycin target protein", "FKBP12-rapamycin complex-associated protein 1", "FKBP-rapamycin associated protein", "rapamycin associated protein FRAP2", "dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)", "rapamycin and FKBP12 target 1", "mammalian target of rapamycin"	601231	"FK506 binding protein 12-rapamycin associated protein 1"	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.504+1T>A	chr1.hg19:g.11316988A>T		79.0	0.0		28.0	19.0	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Splice_Site	SNP	ENST00000361445.4	hg19	CCDS127.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.563445	0.86335	.	.	ENSG00000198793	ENST00000361445;ENST00000539766	.	.	.	5.42	5.42	0.78866	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.5192	0.75851	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MTOR	11239575	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	8.888000	0.92464	2.068000	0.61886	0.451000	0.29950	.	.	.		0.557	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958	Intron	T	11316988	A	T	11316988	5	4	256	1	0	0	0	0	0	0	1	0	9963	173	6	4	7363	4	MTOR	1	11316988	Splice_Site	SNP	A	TCGA-EP-A2KC-01A-11D-A20W-10		11316988	237933633	1	36129										
RNF220	55182	hgsc.bcm.edu	37	chr1	45111114	45111114	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	ccagcaatggtgaaagcagcAagcaggaggccatgcagaag	14	9	0	2			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr1:45111114A>T	ENST00000355387.2	+	12	1849	c.1399A>T	c.(1399-1401)Aag>Tag	p.K467*	RNF220_ENST00000443020.2_Nonsense_Mutation_p.K254*|RNF220_ENST00000372247.2_Nonsense_Mutation_p.K467*|TMEM53_ENST00000372244.3_Silent_p.L28L|TMEM53_ENST00000372242.3_Nonsense_Mutation_p.L159*|RNF220_ENST00000480686.1_3'UTR|RNF220_ENST00000361799.2_Nonsense_Mutation_p.K467*|TMEM53_ENST00000372243.3_Nonsense_Mutation_p.L69*			Q5VTB9	RN220_HUMAN	ring finger protein 220	467					protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(1)|large_intestine(3)|lung(13)|ovary(2)|skin(2)|urinary_tract(2)	29						TGAAAGCAGCAAGCAGGAGGC	0.592																																					p.K467X		Atlas-SNP	.											.	RNF220	56	.	0			c.A1399T						.						108	91	96					1																	45111114		2203	4300	6503	SO:0001587	stop_gained	55182	exon12			AGCAGCAAGCAGG	AK056424	CCDS510.1	1p34.1	2008-06-13	2008-06-13	2008-06-13	ENSG00000187147	ENSG00000187147		"RING-type (C3HC4) zinc fingers"	25552	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 164"	C1orf164		11042152	Standard	NM_018150		Approved	FLJ10597	uc001clv.1	Q5VTB9	OTTHUMG00000007697	ENST00000355387.2:c.1399A>T	chr1.hg19:g.45111114A>T	ENSP00000347548:p.Lys467*	148.0	0.0		29.0	14.0	NM_018150	B3KPJ3|B4DLZ9|E9PCS1|Q4KMX2|Q9NVP6	Nonsense_Mutation	SNP	ENST00000355387.2	hg19	CCDS510.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	39|39	7.302589|7.302589	0.98196|0.98196	.|.	.|.	ENSG00000187147|ENSG00000126106	ENST00000355387;ENST00000361799;ENST00000453887;ENST00000372247;ENST00000443020;ENST00000440132;ENST00000335497;ENST00000372248|ENST00000372243;ENST00000372242	.|.	.|.	.|.	5.74|5.74	5.74|5.74	0.90152|0.90152	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|.	.|.	.|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.87932|0.02654	D|T	0|1	.|.	16.0229|16.0229	0.80512|0.80512	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|.	.|.	.|.	X|X	467;467;467;467;254;183;209;210|69;159	.|.	ENSP00000335580:K209X|ENSP00000361316:L159X	K|L	+|-	1|2	0|0	RNF220|TMEM53	44883701|44883701	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	8.527000|8.527000	0.90594|0.90594	2.189000|2.189000	0.69895|0.69895	0.459000|0.459000	0.35465|0.35465	AAG|TTG	.	.		0.592	RNF220-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000020683.4	NM_018150		T	45111114	A	T	45111114	4	4	256	1	0	0	0	0	0	1	0	0	13498	131	5	4	1441	4	RNF220	1	45111114	Nonsense_Mutation	SNP	A	TCGA-EP-A2KC-01A-11D-A20W-10	33794126	45111114	204139507	2	36130										
DOCK7	85440	hgsc.bcm.edu	37	chr1	62971484	62971484	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	tttggattccgttacagaaaCggtctgcaatttaaaaataa	7	6	1	1			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr1:62971484C>T	ENST00000340370.5	-	35	4404	c.4387G>A	c.(4387-4389)Gtt>Att	p.V1463I	DOCK7_ENST00000251157.5_Missense_Mutation_p.V1485I	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	1494					activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						GTTACAGAAACGGTCTGCAAT	0.383																																					p.V1485I		Atlas-SNP	.											.	DOCK7	184	.	0			c.G4453A						.						90	74	80					1																	62971484		2203	4300	6503	SO:0001583	missense	85440	exon36			CAGAAACGGTCTG		CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.4387G>A	chr1.hg19:g.62971484C>T	ENSP00000340742:p.Val1463Ile	69.0	0.0		20.0	6.0	NM_001271999	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Missense_Mutation	SNP	ENST00000340370.5	hg19	CCDS30734.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.5|23.5	4.420760|4.420760	0.83559|0.83559	.|.	.|.	ENSG00000116641|ENSG00000116641	ENST00000454575|ENST00000371140;ENST00000251157;ENST00000340370;ENST00000395441	.|T;T	.|0.52057	.|0.68;0.68	5.06|5.06	5.06|5.06	0.68205|0.68205	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.68284|0.68284	0.2984|0.2984	M|M	0.72894|0.72894	2.215|2.215	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D	.|0.89917	.|0.999;0.999;0.999;1.0;0.994;0.988	.|D;P;D;D;P;P	.|0.83275	.|0.993;0.847;0.996;0.996;0.819;0.859	T|T	0.66874|0.66874	-0.5813|-0.5813	5|10	.|0.34782	.|T	.|0.22	.|.	18.4148|18.4148	0.90565|0.90565	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1494;1485;1463;1454;1454;1485	.|Q96N67;Q96N67-2;Q96N67-5;Q96N67-4;Q96N67-3;Q96N67-6	.|DOCK7_HUMAN;.;.;.;.;.	H|I	656|1494;1485;1463;224	.|ENSP00000251157:V1485I;ENSP00000340742:V1463I	.|ENSP00000251157:V1485I	R|V	-|-	2|1	0|0	DOCK7|DOCK7	62744072|62744072	1.000000|1.000000	0.71417|0.71417	0.990000|0.990000	0.47175|0.47175	0.510000|0.510000	0.34073|0.34073	7.818000|7.818000	0.86416|0.86416	2.339000|2.339000	0.79563|0.79563	0.591000|0.591000	0.81541|0.81541	CGT|GTT	.	.		0.383	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407		T	62971484	C	T	62971484	3	4	256	1	0	0	0	0	1	0	0	0	4694	536	19	1	2002	1	DOCK7	1	62971484	Missense_Mutation	SNP	C	TCGA-EP-A2KC-01A-11D-A20W-10	17860370	62971484	186279137	3	36131										
DNAJB4	11080	hgsc.bcm.edu	37	chr1	78481825	78481825	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	tgggctgccatttccaaaaaAtcctgaccaacgtggtgacc	9	12	0	2			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr1:78481825A>G	ENST00000370763.5	+	3	1165	c.908A>G	c.(907-909)aAt>aGt	p.N303S	DNAJB4_ENST00000487931.1_3'UTR|GIPC2_ENST00000476882.1_Intron	NM_007034.3	NP_008965.2	Q9UDY4	DNJB4_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 4	303					protein folding (GO:0006457)|response to heat (GO:0009408)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chaperone binding (GO:0051087)|unfolded protein binding (GO:0051082)			endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	10						TTTCCAAAAAATCCTGACCAA	0.403																																					p.N303S		Atlas-SNP	.											.	DNAJB4	30	.	0			c.A908G						.						120	120	120					1																	78481825		2203	4300	6503	SO:0001583	missense	11080	exon3			CAAAAAATCCTGA	U40992	CCDS684.1	1p31.1	2011-09-02			ENSG00000162616	ENSG00000162616		"Heat shock proteins / DNAJ (HSP40)"	14886	protein-coding gene	gene with protein product		611327				9546042, 11147971	Standard	NM_007034		Approved	HLJ1	uc001dij.3	Q9UDY4	OTTHUMG00000040905	ENST00000370763.5:c.908A>G	chr1.hg19:g.78481825A>G	ENSP00000359799:p.Asn303Ser	94.0	0.0		42.0	12.0	NM_007034	B2R824|Q13431	Missense_Mutation	SNP	ENST00000370763.5	hg19	CCDS684.1	.	.	.	.	.	.	.	.	.	.	A	10.57	1.387982	0.25118	.	.	ENSG00000162616	ENST00000370763	T	0.43688	0.94	5.96	5.96	0.96718	Chaperone DnaJ, C-terminal (1);HSP40/DnaJ peptide-binding (1);	0.000000	0.85682	D	0.000000	T	0.16557	0.0398	N	0.16790	0.44	0.80722	D	1	B	0.12013	0.005	B	0.17098	0.017	T	0.05582	-1.0876	10	0.28530	T	0.3	.	16.4484	0.83959	1.0:0.0:0.0:0.0	.	303	Q9UDY4	DNJB4_HUMAN	S	303	ENSP00000359799:N303S	ENSP00000359799:N303S	N	+	2	0	DNAJB4	78254413	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.833000	0.48159	2.285000	0.76669	0.533000	0.62120	AAT	.	.		0.403	DNAJB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098248.3			G	78481825	A	G	78481825	3	3	256	1	0	0	0	0	1	0	0	0	4624	101	4	2	918	2	DNAJB4	1	78481825	Missense_Mutation	SNP	A	TCGA-EP-A2KC-01A-11D-A20W-10	15510341	78481825	170768796	4	36132										
CD5L	922	hgsc.bcm.edu	37	chr1	157805798	157805798	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	taggggttccgctggcagctCcacagcccagctcccggcac	12	17	0	0			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr1:157805798C>A	ENST00000368174.4	-	3	299	c.203G>T	c.(202-204)gGa>gTa	p.G68V	CD5L_ENST00000484609.1_5'UTR	NM_005894.2	NP_005885.1	O43866	CD5L_HUMAN	CD5 molecule-like	68	SRCR 1. {ECO:0000255|PROSITE- ProRule:PRU00196}.				apoptotic process (GO:0006915)|cellular defense response (GO:0006968)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	scavenger receptor activity (GO:0005044)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	52	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			GCTGGCAGCTCCACAGCCCAG	0.562																																					p.G68V		Atlas-SNP	.											.	CD5L	112	.	0			c.G203T						.						151	155	154					1																	157805798		2203	4300	6503	SO:0001583	missense	922	exon3			GCAGCTCCACAGC	U82812	CCDS1171.1	1q21-q23	2008-02-05	2006-03-28		ENSG00000073754	ENSG00000073754			1690	protein-coding gene	gene with protein product		602592	"apoptosis inhibitor 6", "CD5 antigen-like (scavenger receptor cysteine rich family)"	API6		9045627	Standard	NM_005894		Approved	Spalpha	uc001frk.4	O43866	OTTHUMG00000022440	ENST00000368174.4:c.203G>T	chr1.hg19:g.157805798C>A	ENSP00000357156:p.Gly68Val	244.0	1.0		82.0	49.0	NM_005894	A8K7M5|Q6UX63	Missense_Mutation	SNP	ENST00000368174.4	hg19	CCDS1171.1	.	.	.	.	.	.	.	.	.	.	C	18.87	3.715138	0.68844	.	.	ENSG00000073754	ENST00000368174	T	0.38887	1.11	4.85	4.85	0.62838	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.312596	0.23017	N	0.052895	T	0.62829	0.2460	M	0.85859	2.78	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.69079	-0.5240	10	0.87932	D	0	.	15.5102	0.75776	0.0:1.0:0.0:0.0	.	68	O43866	CD5L_HUMAN	V	68	ENSP00000357156:G68V	ENSP00000357156:G68V	G	-	2	0	CD5L	156072422	1.000000	0.71417	0.732000	0.30844	0.323000	0.28346	5.528000	0.67129	2.503000	0.84419	0.563000	0.77884	GGA	.	.		0.562	CD5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058346.1	NM_005894		A	157805798	C	A	157805798	3	1	256	1	0	0	0	0	1	0	0	0	3029	855	30	3	856	3	CD5L	1	157805798	Missense_Mutation	SNP	C	TCGA-EP-A2KC-01A-11D-A20W-10	79323973	157805798	91444823	5	36133										
C1orf125	126859	hgsc.bcm.edu	37	chr1	179339142	179339142	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	cgccttgtagaccatgtctgGcatcaccctgttcgaaggaa	10	12	2	1			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr1:179339142G>T	ENST00000367618.3	+	4	690	c.303G>T	c.(301-303)tgG>tgT	p.W101C	AXDND1_ENST00000461179.2_3'UTR|AXDND1_ENST00000457238.2_Missense_Mutation_p.W101C	NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	101										NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(27)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	59						ACCATGTCTGGCATCACCCTG	0.433																																					p.W101C		Atlas-SNP	.											.	AXDND1	142	.	0			c.G303T						.						81	73	76					1																	179339142		2203	4300	6503	SO:0001583	missense	126859	exon4			TGTCTGGCATCAC	BX647935	CCDS30948.1	1q25.2	2011-02-18	2011-02-18	2011-02-18	ENSG00000162779	ENSG00000162779			26564	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 125"	C1orf125		14702039	Standard	NM_144696		Approved	FLJ32940	uc001gmo.3	Q5T1B0	OTTHUMG00000035266	ENST00000367618.3:c.303G>T	chr1.hg19:g.179339142G>T	ENSP00000356590:p.Trp101Cys	129.0	0.0		69.0	50.0	NM_144696	Q6AWB2|Q96LJ3|Q96M01	Missense_Mutation	SNP	ENST00000367618.3	hg19	CCDS30948.1	.	.	.	.	.	.	.	.	.	.	G	18.53	3.643924	0.67244	.	.	ENSG00000162779	ENST00000509175;ENST00000367618;ENST00000360322;ENST00000507383;ENST00000457238;ENST00000508285;ENST00000511889;ENST00000434088	T;T;T	0.79352	-0.39;-1.26;-0.02	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	D	0.86435	0.5932	M	0.65498	2.005	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.87667	0.2538	10	0.87932	D	0	-16.8437	14.4325	0.67259	0.0:0.0:1.0:0.0	.	59;101	E9PCJ4;Q5T1B0	.;AXDN1_HUMAN	C	59;101;59;59;101;101;59;35	ENSP00000356590:W101C;ENSP00000416712:W101C;ENSP00000391716:W35C	ENSP00000353471:W59C	W	+	3	0	AXDND1	177605765	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.636000	0.67848	2.464000	0.83262	0.579000	0.79373	TGG	.	.		0.433	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	NM_144696		T	179339142	G	T	179339142	3	4	256	1	0	0	0	0	1	0	0	0	1995	1212	42	3	313	3	C1orf125	1	179339142	Missense_Mutation	SNP	G	TCGA-EP-A2KC-01A-11D-A20W-10	21533344	179339142	69911479	6	36134										
KIDINS220	57498	hgsc.bcm.edu	37	chr2	8934018	8934018	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	agtctcgcctgctttgttggGcctataaagtaatcgcccat	9	11	1	0			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr2:8934018G>A	ENST00000256707.3	-	12	1379	c.1198C>T	c.(1198-1200)Ccc>Tcc	p.P400S	KIDINS220_ENST00000427284.1_Missense_Mutation_p.P400S|KIDINS220_ENST00000418530.1_Missense_Mutation_p.P358S|KIDINS220_ENST00000473731.1_Missense_Mutation_p.P400S|KIDINS220_ENST00000319688.5_Missense_Mutation_p.P401S	NM_020738.2	NP_065789.1	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate, 220kDa	400					activation of MAPKK activity (GO:0000186)|cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|dendrite morphogenesis (GO:0048813)|in utero embryonic development (GO:0001701)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of neuron projection development (GO:0010976)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|protein complex (GO:0043234)	PDZ domain binding (GO:0030165)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(25)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	60	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					GCTTTGTTGGGCCTATAAAGT	0.413																																					p.P400S		Atlas-SNP	.											.	KIDINS220	136	.	0			c.C1198T						.						87	80	82					2																	8934018		1817	4078	5895	SO:0001583	missense	57498	exon12			TGTTGGGCCTATA	AK025528	CCDS42650.1	2p24	2013-01-10			ENSG00000134313	ENSG00000134313		"Ankyrin repeat domain containing"	29508	protein-coding gene	gene with protein product	"ankyrin repeat-rich membrane-spanning protein"	615759				10998417, 10574462	Standard	NM_020738		Approved	ARMS	uc002qzc.2	Q9ULH0	OTTHUMG00000151658	ENST00000256707.3:c.1198C>T	chr2.hg19:g.8934018G>A	ENSP00000256707:p.Pro400Ser	62.0	0.0		24.0	12.0	NM_020738	A1L4N4|Q4VC08|Q6MZU2|Q9H889|Q9H9E4|Q9NT37|Q9UF42	Missense_Mutation	SNP	ENST00000256707.3	hg19	CCDS42650.1	.	.	.	.	.	.	.	.	.	.	g	18.56	3.650018	0.67472	.	.	ENSG00000134313	ENST00000496383;ENST00000541927;ENST00000256707;ENST00000427284;ENST00000418530;ENST00000473731;ENST00000489024;ENST00000319688	T;T;T;T;T;T;T	0.52983	0.64;2.48;2.48;2.48;2.48;2.48;2.48	5.83	5.83	0.93111	Ankyrin repeat-containing domain (2);	0.000000	0.85682	D	0.000000	T	0.62405	0.2425	L	0.35854	1.095	0.80722	D	1	D;D;D;D	0.89917	1.0;0.974;1.0;1.0	D;P;D;D	0.91635	0.996;0.829;0.999;0.999	T	0.59716	-0.7402	10	0.48119	T	0.1	.	20.1862	0.98216	0.0:0.0:1.0:0.0	.	401;401;358;400	B4DK94;E9PH70;Q9ULH0-2;Q9ULH0	.;.;.;KDIS_HUMAN	S	147;84;400;400;358;400;401;401	ENSP00000420364:P147S;ENSP00000256707:P400S;ENSP00000411849:P400S;ENSP00000414923:P358S;ENSP00000418974:P400S;ENSP00000419964:P401S;ENSP00000319947:P401S	ENSP00000256707:P400S	P	-	1	0	KIDINS220	8851469	1.000000	0.71417	0.999000	0.59377	0.211000	0.24417	9.390000	0.97246	2.775000	0.95449	0.632000	0.83419	CCC	.	.		0.413	KIDINS220-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323408.2	NM_020738		A	8934018	G	A	8934018	3	1	256	1	0	0	0	0	1	0	0	0	8280	1203	42	3	4193	3	KIDINS220	2	8934018	Missense_Mutation	SNP	G	TCGA-EP-A2KC-01A-11D-A20W-10		8934018	234265355	7	36135										
BIRC6	57448	hgsc.bcm.edu	37	chr2	32724674	32724675	+	Silent	DNP	TC	TC	AT													0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	gtgaagctcttagaattcacTctggagcagaattttgaagt							TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr2:32724674_32724675TC>AT	ENST00000421745.2	+	46	8663_8664	c.8529_8530TC>AT	c.(8527-8532)acTCtg>acATtg	p.2843_2844TL>TL		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	2843					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					TAGAATTCACTCTGGAGCAGAA	0.446																																					p.T2843T|p.L2844L	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.|BIRC6_ENST00000421745,NS,carcinoma,0,2	BIRC6	838	.	0			c.T8529A|c.C8530T						.																																			SO:0001819	synonymous_variant	57448	exon46			ATTCACTCTGGAG|TTCACTCTGGAGC	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	Exception_encountered	chr2.hg19:g.32724674_32724675delinsAT		87.0	0.0		26.0|25.0	9.0|8.0	NM_016252	Q9ULD1	Silent	SNP	ENST00000421745.2	hg19	CCDS33175.2																																																																																			.	.		0.446	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		AT	32724675	TC	AT	32724674	2	1	256	1	0	0	0	0	0	0	0	1	1438	1538	54	4		4	BIRC6	2	32724674	Silent	DNP	TC	TCGA-EP-A2KC-01A-11D-A20W-10	23790656	32724674	210474699	8	36136										
KCNK12	56660	hgsc.bcm.edu	37	chr2	47748598	47748598	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	aaggtgacgaagcagaagtaGagcgagtccacgtagtccca	13	9	0	3			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr2:47748598G>C	ENST00000327876.4	-	2	1348	c.741C>G	c.(739-741)ctC>ctG	p.L247L	MSH2_ENST00000461394.1_Intron	NM_022055.1	NP_071338.1	Q9HB15	KCNKC_HUMAN	potassium channel, subfamily K, member 12	247						integral component of membrane (GO:0016021)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)	p.0?(2)|p.?(2)		NS(1)|endometrium(1)|lung(3)|ovary(1)	6		all_hematologic(82;0.0495)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AGCAGAAGTAGAGCGAGTCCA	0.652																																					p.L247L		Atlas-SNP	.											.	KCNK12	11	.	4	Whole gene deletion(2)|Unknown(2)	haematopoietic_and_lymphoid_tissue(3)|prostate(1)	c.C741G						.						47	46	46					2																	47748598		2203	4299	6502	SO:0001819	synonymous_variant	56660	exon2			GAAGTAGAGCGAG	AF287302	CCDS1835.1	2p16.3	2012-03-07			ENSG00000184261	ENSG00000184261		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6274	protein-coding gene	gene with protein product		607366				11060316	Standard	NM_022055		Approved	THIK-2, THIK2, K2p12.1	uc002rwb.3	Q9HB15	OTTHUMG00000129131	ENST00000327876.4:c.741C>G	chr2.hg19:g.47748598G>C		110.0	0.0		31.0	11.0	NM_022055		Silent	SNP	ENST00000327876.4	hg19	CCDS1835.1																																																																																			.	.		0.652	KCNK12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251182.2	NM_022055		C	47748598	G	C	47748598	2	2	256	1	0	0	0	0	0	0	0	1	8069	929	33	4		4	KCNK12	2	47748598	Silent	SNP	G	TCGA-EP-A2KC-01A-11D-A20W-10	15023924	47748598	195450775	9	36137										
LRP2	4036	hgsc.bcm.edu	37	chr2	170147487	170147487	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	ttctcttggggaacatttatGaacatcatgaggaccgcttt	9	8	2	2			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr2:170147487G>A	ENST00000263816.3	-	8	1075	c.790C>T	c.(790-792)Cat>Tat	p.H264Y	LRP2_ENST00000443831.1_Missense_Mutation_p.H264Y	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	264	LDL-receptor class A 7. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	GAACATTTATGAACATCATGA	0.458																																					p.H264Y		Atlas-SNP	.											.	LRP2	751	.	0			c.C790T						.						111	109	109					2																	170147487		2203	4300	6503	SO:0001583	missense	4036	exon8			ATTTATGAACATC		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.790C>T	chr2.hg19:g.170147487G>A	ENSP00000263816:p.His264Tyr	186.0	0.0		51.0	14.0	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	hg19	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	G	0.013	-1.639858	0.00799	.	.	ENSG00000081479	ENST00000263816;ENST00000443831	T;T	0.58506	0.33;0.33	4.1	0.0961	0.14488	.	0.421230	0.24072	N	0.041806	T	0.44052	0.1275	L	0.54323	1.7	0.09310	N	1	B;B	0.23316	0.083;0.044	B;B	0.30495	0.116;0.112	T	0.26744	-1.0094	9	.	.	.	.	0.8316	0.01132	0.2232:0.1846:0.4028:0.1894	.	264;264	E9PC35;P98164	.;LRP2_HUMAN	Y	264	ENSP00000263816:H264Y;ENSP00000409813:H264Y	.	H	-	1	0	LRP2	169855733	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	1.195000	0.32186	0.006000	0.14734	-0.941000	0.02677	CAT	.	.		0.458	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		A	170147487	G	A	170147487	3	1	256	1	0	0	0	0	1	0	0	0	8965	1290	45	3	13465	3	LRP2	2	170147487	Missense_Mutation	SNP	G	TCGA-EP-A2KC-01A-11D-A20W-10	122398889	170147487	73051886	10	36138										
MFSD6	54842	hgsc.bcm.edu	37	chr2	191301480	191301501	+	Frame_Shift_Del	DEL	TGAACTCAAGCACAGCAACCCC	TGAACTCAAGCACAGCAACCCC	-													0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	ccgtatgatggacttgacttTgaactcaagcacagcaaccc					rs201082615|rs147259731|rs184975766	byFrequency	TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	TGAACTCAAGCACAGCAACCCC	TGAACTCAAGCACAGCAACCCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr2:191301480_191301501delTGAACTCAAGCACAGCAACCCC	ENST00000392328.1	+	3	1049_1070	c.725_746delTGAACTCAAGCACAGCAACCCC	c.(724-747)ttgaactcaagcacagcaacccctfs	p.LNSSTATP242fs	MFSD6_ENST00000281416.7_Frame_Shift_Del_p.LNSSTATP242fs	NM_017694.3	NP_060164.3	Q6ZSS7	MFSD6_HUMAN	major facilitator superfamily domain containing 6	242					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(3)|stomach(1)	23						GACTTGACTTTGAACTCAAGCACAGCAACCCCTGTCTCCCCA	0.459																																					p.242_249del		Pindel	.											.	MFSD6	58	.	0			c.724_745del						.																																			SO:0001589	frameshift_variant	54842	exon3			.		CCDS2306.1	2q32.2	2008-10-29			ENSG00000151690	ENSG00000151690			24711	protein-coding gene	gene with protein product		613476					Standard	NM_017694		Approved	FLJ20160	uc002urz.2	Q6ZSS7	OTTHUMG00000132671	ENST00000392328.1:c.725_746delTGAACTCAAGCACAGCAACCCC	chr2.hg19:g.191301480_191301501delTGAACTCAAGCACAGCAACCCC	ENSP00000376141:p.Leu242fs	0.0	0.0		12.0	12.0	NM_017694	D3KSZ4|Q86TH2|Q9NXM3	Frame_Shift_Del	DEL	ENST00000392328.1	hg19	CCDS2306.1																																																																																			.	.		0.459	MFSD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255931.1			-	191301501	TGAACTCAAGCACAGCAACCCC	-	191301480	7	5	256	1	0	1	0	1	0	0	0	0	9544	1821	63	0	727	0	MFSD6	2	191301480	Frame_Shift_Del	DEL	TGAACTCAAGCACAGCAACCCC	TCGA-EP-A2KC-01A-11D-A20W-10	21153993	191301480	51897893	11	36139										
SPHKAP	80309	hgsc.bcm.edu	37	chr2	228883534	228883534	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	tgtggtgaacttcatcaatgGaatgcctcaggataacattg	10	7	3	1			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr2:228883534G>A	ENST00000392056.3	-	7	2082	c.2036C>T	c.(2035-2037)tCc>tTc	p.S679F	SPHKAP_ENST00000344657.5_Missense_Mutation_p.S679F	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	679						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)			NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		TTCATCAATGGAATGCCTCAG	0.413																																					p.S679F		Atlas-SNP	.											.	SPHKAP	750	.	0			c.C2036T						.						257	235	242					2																	228883534		2203	4300	6503	SO:0001583	missense	80309	exon7			TCAATGGAATGCC		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"A-kinase anchor proteins"	30619	protein-coding gene	gene with protein product	"sphingosine kinase type 1-interacting protein"	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.2036C>T	chr2.hg19:g.228883534G>A	ENSP00000375909:p.Ser679Phe	194.0	0.0		63.0	22.0	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	hg19	CCDS46537.1	.	.	.	.	.	.	.	.	.	.	G	14.63	2.591492	0.46214	.	.	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.53640	0.61;0.61	5.62	3.77	0.43336	.	0.211818	0.49916	D	0.000127	T	0.66268	0.2772	M	0.68593	2.085	0.49130	D	0.999751	D;D	0.89917	0.994;1.0	P;D	0.74023	0.819;0.982	T	0.70414	-0.4878	10	0.87932	D	0	.	15.5583	0.76216	0.0:0.2613:0.7387:0.0	.	679;679	Q2M3C7;Q2M3C7-2	SPKAP_HUMAN;.	F	679	ENSP00000375909:S679F;ENSP00000339886:S679F	ENSP00000339886:S679F	S	-	2	0	SPHKAP	228591778	1.000000	0.71417	0.993000	0.49108	0.407000	0.30961	2.855000	0.48333	0.788000	0.33755	0.655000	0.94253	TCC	.	.		0.413	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623		A	228883534	G	A	228883534	3	1	256	1	0	0	0	0	1	0	0	0	15063	1174	41	3	3090	3	SPHKAP	2	228883534	Missense_Mutation	SNP	G	TCGA-EP-A2KC-01A-11D-A20W-10	37582054	228883534	14315839	12	36140										
TRIP12	9320	hgsc.bcm.edu	37	chr2	230723949	230723949	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	tctctgtcctttttcttttcTgactccgtgaaccgccagtg	7	13	3	2			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr2:230723949T>A	ENST00000283943.5	-	3	618	c.440A>T	c.(439-441)cAg>cTg	p.Q147L	TRIP12_ENST00000409677.1_Missense_Mutation_p.Q189L|TRIP12_ENST00000543084.1_Missense_Mutation_p.Q189L|TRIP12_ENST00000389044.4_Missense_Mutation_p.Q189L|TRIP12_ENST00000389045.3_Intron	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	147					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		TTTTCTTTTCTGACTCCGTGA	0.488																																					p.Q147L		Atlas-SNP	.											.	TRIP12	207	.	0			c.A440T						.						111	114	113					2																	230723949		2203	4300	6503	SO:0001583	missense	9320	exon3			CTTTTCTGACTCC	L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.440A>T	chr2.hg19:g.230723949T>A	ENSP00000283943:p.Gln147Leu	101.0	0.0		50.0	21.0	NM_004238	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Missense_Mutation	SNP	ENST00000283943.5	hg19	CCDS33391.1	.	.	.	.	.	.	.	.	.	.	T	17.94	3.511511	0.64522	.	.	ENSG00000153827	ENST00000283943;ENST00000389044;ENST00000543084;ENST00000409677;ENST00000453485;ENST00000435716;ENST00000428959;ENST00000430954	T;T	0.50001	0.76;0.76	5.71	4.54	0.55810	.	0.055337	0.85682	N	0.000000	T	0.31040	0.0784	N	0.19112	0.55	0.58432	D	0.999991	B;B;B	0.19817	0.0;0.039;0.0	B;B;B	0.18871	0.0;0.023;0.0	T	0.08310	-1.0728	10	0.48119	T	0.1	.	8.1668	0.31230	0.1338:0.0:0.1402:0.726	.	147;189;147	D4HL82;Q14CA3;Q14669	.;.;TRIPC_HUMAN	L	147;189;189;189;17;147;147;189	ENSP00000283943:Q147L;ENSP00000373696:Q189L	ENSP00000283943:Q147L	Q	-	2	0	TRIP12	230432193	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	3.628000	0.54259	0.969000	0.38237	0.455000	0.32223	CAG	.	.		0.488	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238		A	230723949	T	A	230723949	3	1	256	1	0	0	0	0	1	0	0	0	16571	1580	55	4	5694	4	TRIP12	2	230723949	Missense_Mutation	SNP	T	TCGA-EP-A2KC-01A-11D-A20W-10	1840415	230723949	12475424	13	36141										
ALPP	250	hgsc.bcm.edu	37	chr2	233245689	233245690	+	Frame_Shift_Ins	INS	-	-	T													0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	gcctcgtcactgccgaccacINStcccacgtcttctccttcgg							TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr2:233245689_233245690insT	ENST00000392027.2	+	9	1409_1410	c.1140_1141insT	c.(1141-1143)tccfs	p.S381fs	AC068134.8_ENST00000441266.1_RNA|AC068134.8_ENST00000439072.1_RNA	NM_001632.3	NP_001623.3	P05187	PPB1_HUMAN	alkaline phosphatase, placental	381					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|endometrium(1)|kidney(4)|large_intestine(2)|liver(1)|lung(10)|ovary(2)	22		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)		CTGCCGACCACTCCCACGTCTT	0.629																																					p.H380fs		Atlas-INDEL	.											.	ALPP	53	.	0			c.1140_1141insT						.																																			SO:0001589	frameshift_variant	250	exon9			.	M14169	CCDS2490.1	2q37.1	2010-06-24	2010-06-24		ENSG00000163283	ENSG00000163283	3.1.3.1		439	protein-coding gene	gene with protein product	"Regan isozyme"	171800	"alkaline phosphatase, placental (Regan isozyme)"			3001717, 3461452	Standard	XM_005246439		Approved		uc002vsq.3	P05187	OTTHUMG00000133255	ENST00000392027.2:c.1141dupT	chr2.hg19:g.233245690_233245690dupT	ENSP00000375881:p.Ser381fs	261.0	0.0		67.0	14.0	NM_001632	P05188|P06861|Q53S78|Q96DB7	Frame_Shift_Ins	INS	ENST00000392027.2	hg19	CCDS2490.1																																																																																			.	.		0.629	ALPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257032.3	NM_001632		T	233245690	-	T	233245689	7	5	256	1	0	1	1	0	0	0	0	0	548	564	20	0	1174	0	ALPP	2	233245689	Frame_Shift_Ins	INS	-	TCGA-EP-A2KC-01A-11D-A20W-10	2521740	233245689	9953684	14	36142										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266098	41266098	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	gcagcaacagtcttacctggActctggaatccattctggtg	10	11	3	0	rs121913396|rs121913416		TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr3:41266098A>G	ENST00000349496.5	+	3	375	c.95A>G	c.(94-96)gAc>gGc	p.D32G	CTNNB1_ENST00000453024.1_Missense_Mutation_p.D25G|CTNNB1_ENST00000396183.3_Missense_Mutation_p.D32G|CTNNB1_ENST00000405570.1_Missense_Mutation_p.D32G|CTNNB1_ENST00000396185.3_Missense_Mutation_p.D32G	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	32			D -> A (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|D -> G (in PTR and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629}.|D -> Y (in PTR, hepatoblastoma and hepatocellular carcinoma; dbSNP:rs28931588). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:11703283, ECO:0000269|PubMed:9927029}.|Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.D32G(65)|p.A5_A80del(53)|p.D32V(33)|p.D32A(16)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.WQQQSYLD25?(5)|p.W25_D32del(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.S29_H36del(1)|p.D32del(1)|p.M14_S45del(1)|p.Q28_D32>H(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.D32fs*9(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TCTTACCTGGACTCTGGAATC	0.483	D32V(HEC265_ENDOMETRIUM)|D32V(HEC6_ENDOMETRIUM)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.D32G	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,+1,128	CTNNB1	4904	.	260	Deletion - In frame(120)|Substitution - Missense(114)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(154)|large_intestine(24)|pancreas(19)|central_nervous_system(16)|stomach(14)|endometrium(7)|skin(7)|ovary(4)|prostate(3)|pituitary(3)|small_intestine(2)|NS(2)|adrenal_gland(1)|soft_tissue(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)	c.A95G						.						92	77	82					3																	41266098		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	ACCTGGACTCTGG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.95A>G	chr3.hg19:g.41266098A>G	ENSP00000344456:p.Asp32Gly	347.0	2.0		117.0	18.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.308122	0.81247	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.50001	0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.69788	0.3150	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.74137	-0.3762	10	0.87932	D	0	0.3843	16.0676	0.80897	1.0:0.0:0.0:0.0	.	32	P35222	CTNB1_HUMAN	G	25;32;32;32;32;25;32;32;32	ENSP00000400508:D25G;ENSP00000385604:D32G;ENSP00000412219:D32G;ENSP00000379486:D32G;ENSP00000344456:D32G;ENSP00000411226:D25G;ENSP00000379488:D32G;ENSP00000409302:D32G;ENSP00000401599:D32G	ENSP00000344456:D32G	D	+	2	0	CTNNB1	41241102	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.201000	0.70794	0.533000	0.62120	GAC	.	.		0.483	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266098	A	G	41266098	3	3	256	1	0	0	0	0	1	0	0	0	4018	275	10	2	101	2	CTNNB1	3	41266098	Missense_Mutation	SNP	A	TCGA-EP-A2KC-01A-11D-A20W-10		41266098	156756332	15	36143										
DNAH1	25981	hgsc.bcm.edu	37	chr3	52428551	52428551	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	gaatccggcaccggactggcTgtcagaccgggcttggcgag	16	12	1	1			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr3:52428551T>C	ENST00000420323.2	+	67	10958	c.10697T>C	c.(10696-10698)cTg>cCg	p.L3566P		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	3631					cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		CCGGACTGGCTGTCAGACCGG	0.592																																					p.L3566P		Atlas-SNP	.											.	DNAH1	534	.	0			c.T10697C						.						79	89	85					3																	52428551		2059	4197	6256	SO:0001583	missense	25981	exon67			ACTGGCTGTCAGA	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.10697T>C	chr3.hg19:g.52428551T>C	ENSP00000401514:p.Leu3566Pro	228.0	0.0		86.0	28.0	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	hg19	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.586845	0.86851	.	.	ENSG00000114841	ENST00000420323;ENST00000273600	T	0.11821	2.74	5.27	5.27	0.74061	.	0.000000	0.52532	D	0.000064	T	0.54598	0.1868	H	0.98199	4.17	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	T	0.73487	-0.3967	10	0.87932	D	0	.	15.2198	0.73303	0.0:0.0:0.0:1.0	.	3566;3631	C9JXH6;Q9P2D7-2	.;.	P	3566;319	ENSP00000401514:L3566P	ENSP00000273600:L319P	L	+	2	0	DNAH1	52403591	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.170000	0.77587	2.005000	0.58758	0.533000	0.62120	CTG	.	.		0.592	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		C	52428551	T	C	52428551	3	2	256	1	0	0	0	0	1	0	0	0	4599	1580	55	2	10959	2	DNAH1	3	52428551	Missense_Mutation	SNP	T	TCGA-EP-A2KC-01A-11D-A20W-10	11162453	52428551	145593879	16	36144										
EPHB3	2049	hgsc.bcm.edu	37	chr3	184290761	184290761	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	gtgtgcatccaccaccgcagGcttcgcactcttccccgaga	9	17	1	1			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr3:184290761G>T	ENST00000330394.2	+	3	1105	c.653G>T	c.(652-654)gGc>gTc	p.G218V	EIF2B5_ENST00000444495.1_Intron	NM_004443.3	NP_004434.2	P54753	EPHB3_HUMAN	EPH receptor B3	218	Cys-rich.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell migration (GO:0016477)|central nervous system projection neuron axonogenesis (GO:0021952)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|digestive tract morphogenesis (GO:0048546)|ephrin receptor signaling pathway (GO:0048013)|palate development (GO:0060021)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of axonogenesis (GO:0050770)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell-cell adhesion (GO:0022407)|regulation of Rac GTPase activity (GO:0032314)|retinal ganglion cell axon guidance (GO:0031290)|substrate adhesion-dependent cell spreading (GO:0034446)|thymus development (GO:0048538)|urogenital system development (GO:0001655)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|ephrin receptor activity (GO:0005003)			breast(5)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_cancers(143;1.89e-10)|Ovarian(172;0.0339)		Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22)			ACCACCGCAGGCTTCGCACTC	0.642																																					p.G218V		Atlas-SNP	.											.	EPHB3	114	.	0			c.G653T						.						56	59	58					3																	184290761		2203	4300	6503	SO:0001583	missense	2049	exon3			CCGCAGGCTTCGC	X75208	CCDS3268.1	3q27.1	2013-09-19	2004-10-28		ENSG00000182580	ENSG00000182580		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3394	protein-coding gene	gene with protein product		601839	"EphB3"	ETK2		8397371	Standard	NM_004443		Approved	Hek2, Tyro6	uc003foz.3	P54753	OTTHUMG00000156710	ENST00000330394.2:c.653G>T	chr3.hg19:g.184290761G>T	ENSP00000332118:p.Gly218Val	93.0	0.0		34.0	16.0	NM_004443	Q7Z740	Missense_Mutation	SNP	ENST00000330394.2	hg19	CCDS3268.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.951178	0.73787	.	.	ENSG00000182580	ENST00000330394	T	0.73152	-0.72	5.27	5.27	0.74061	.	0.110493	0.64402	D	0.000009	T	0.73225	0.3560	L	0.52905	1.665	0.80722	D	1	P	0.48089	0.905	P	0.46796	0.527	T	0.77507	-0.2562	10	0.87932	D	0	.	17.8822	0.88843	0.0:0.0:1.0:0.0	.	218	P54753	EPHB3_HUMAN	V	218	ENSP00000332118:G218V	ENSP00000332118:G218V	G	+	2	0	EPHB3	185773455	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.290000	0.78711	2.445000	0.82738	0.561000	0.74099	GGC	.	.		0.642	EPHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345413.1	NM_004443		T	184290761	G	T	184290761	3	4	256	1	0	0	0	0	1	0	0	0	5178	1203	42	3	663	3	EPHB3	3	184290761	Missense_Mutation	SNP	G	TCGA-EP-A2KC-01A-11D-A20W-10	131862210	184290761	13731669	17	36145										
BCL6	604	hgsc.bcm.edu	37	chr3	187447378	187447378	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	cagccacactgtagtgcataTcacttcgtgcctcttctggg	9	13	3	0			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr3:187447378T>A	ENST00000406870.2	-	5	1181	c.815A>T	c.(814-816)gAt>gTt	p.D272V	BCL6_ENST00000450123.2_Missense_Mutation_p.D272V|RP11-211G3.3_ENST00000437407.1_Intron|RP11-211G3.3_ENST00000449623.1_Intron|BCL6_ENST00000232014.4_Missense_Mutation_p.D272V	NM_001706.4	NP_001697.2	P41182	BCL6_HUMAN	B-cell CLL/lymphoma 6	272					actin cytoskeleton organization (GO:0030036)|B cell differentiation (GO:0030183)|cell morphogenesis (GO:0000902)|cellular response to DNA damage stimulus (GO:0006974)|erythrocyte development (GO:0048821)|germinal center formation (GO:0002467)|inflammatory response (GO:0006954)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of isotype switching to IgE isotypes (GO:0048294)|negative regulation of mast cell cytokine production (GO:0032764)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cellular component movement (GO:0051272)|protein import into nucleus, translocation (GO:0000060)|regulation of germinal center formation (GO:0002634)|regulation of immune response (GO:0050776)|regulation of inflammatory response (GO:0050727)|regulation of memory T cell differentiation (GO:0043380)|regulation of Rho GTPase activity (GO:0032319)|Rho protein signal transduction (GO:0007266)|spermatogenesis (GO:0007283)|type 2 immune response (GO:0042092)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|metal ion binding (GO:0046872)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(9)|lung(10)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	40	all_cancers(143;9.45e-12)|Ovarian(172;0.0418)		OV - Ovarian serous cystadenocarcinoma(80;1.76e-18)	GBM - Glioblastoma multiforme(93;0.0141)		GTAGTGCATATCACTTCGTGC	0.547			"T, Mis"	"IG loci, ZNFN1A1, LCP1, PIM1, TFRC, CIITA, NACA, HSPCB, HSPCA, HIST1H4I, IL21R,  POU2AF1, ARHH, EIF4A2, SFRS3"	"NHL, CLL"																																p.D272V		Atlas-SNP	.		Dom	yes		3	3q27	604	B-cell CLL/lymphoma 6		L	.	BCL6	107	.	0			c.A815T						.						83	87	86					3																	187447378		2203	4300	6503	SO:0001583	missense	604	exon4			TGCATATCACTTC		CCDS3289.1, CCDS46975.1	3q27	2013-01-09	2008-08-01		ENSG00000113916	ENSG00000113916		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	1001	protein-coding gene	gene with protein product		109565	"zinc finger protein 51"	ZNF51			Standard	NM_001130845		Approved	ZBTB27, LAZ3, BCL5, BCL6A	uc003frq.2	P41182	OTTHUMG00000156441	ENST00000406870.2:c.815A>T	chr3.hg19:g.187447378T>A	ENSP00000384371:p.Asp272Val	121.0	0.0		37.0	10.0	NM_001134738	A7E241|B8PSA7|D3DNV5	Missense_Mutation	SNP	ENST00000406870.2	hg19	CCDS3289.1	.	.	.	.	.	.	.	.	.	.	T	16.33	3.093098	0.56075	.	.	ENSG00000113916	ENST00000406870;ENST00000232014;ENST00000450123	T;T;T	0.08720	3.06;3.06;3.08	5.46	5.46	0.80206	.	0.132239	0.64402	D	0.000002	T	0.09992	0.0245	L	0.40543	1.245	0.80722	D	1	P;P	0.48911	0.917;0.808	B;B	0.41860	0.368;0.368	T	0.03413	-1.1039	10	0.56958	D	0.05	.	15.0324	0.71717	0.0:0.0:0.0:1.0	.	272;272	B8PSA7;P41182	.;BCL6_HUMAN	V	272	ENSP00000384371:D272V;ENSP00000232014:D272V;ENSP00000413122:D272V	ENSP00000232014:D272V	D	-	2	0	BCL6	188930072	1.000000	0.71417	0.980000	0.43619	0.942000	0.58702	5.412000	0.66392	2.203000	0.70933	0.459000	0.35465	GAT	.	.		0.547	BCL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344202.1	NM_138931		A	187447378	T	A	187447378	3	1	256	1	0	0	0	0	1	0	0	0	1376	1435	50	4	1329	4	BCL6	3	187447378	Missense_Mutation	SNP	T	TCGA-EP-A2KC-01A-11D-A20W-10	3156617	187447378	10575052	18	36146			1	46		2	2	15	T		2.849096e-05
BCL6	604	hgsc.bcm.edu	37	chr3	187447392	187447392	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	tgcatatcacttcgtgcctcTtctgggattgtttccttggg	10	10	3	0			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr3:187447392T>C	ENST00000406870.2	-	5	1167	c.801A>G	c.(799-801)gaA>gaG	p.E267E	BCL6_ENST00000450123.2_Silent_p.E267E|RP11-211G3.3_ENST00000437407.1_Intron|RP11-211G3.3_ENST00000449623.1_Intron|BCL6_ENST00000232014.4_Silent_p.E267E	NM_001706.4	NP_001697.2	P41182	BCL6_HUMAN	B-cell CLL/lymphoma 6	267					actin cytoskeleton organization (GO:0030036)|B cell differentiation (GO:0030183)|cell morphogenesis (GO:0000902)|cellular response to DNA damage stimulus (GO:0006974)|erythrocyte development (GO:0048821)|germinal center formation (GO:0002467)|inflammatory response (GO:0006954)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of isotype switching to IgE isotypes (GO:0048294)|negative regulation of mast cell cytokine production (GO:0032764)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cellular component movement (GO:0051272)|protein import into nucleus, translocation (GO:0000060)|regulation of germinal center formation (GO:0002634)|regulation of immune response (GO:0050776)|regulation of inflammatory response (GO:0050727)|regulation of memory T cell differentiation (GO:0043380)|regulation of Rho GTPase activity (GO:0032319)|Rho protein signal transduction (GO:0007266)|spermatogenesis (GO:0007283)|type 2 immune response (GO:0042092)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|metal ion binding (GO:0046872)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(9)|lung(10)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	40	all_cancers(143;9.45e-12)|Ovarian(172;0.0418)		OV - Ovarian serous cystadenocarcinoma(80;1.76e-18)	GBM - Glioblastoma multiforme(93;0.0141)		TTCGTGCCTCTTCTGGGATTG	0.572			"T, Mis"	"IG loci, ZNFN1A1, LCP1, PIM1, TFRC, CIITA, NACA, HSPCB, HSPCA, HIST1H4I, IL21R,  POU2AF1, ARHH, EIF4A2, SFRS3"	"NHL, CLL"																																p.E267E		Atlas-SNP	.		Dom	yes		3	3q27	604	B-cell CLL/lymphoma 6		L	.	BCL6	107	.	0			c.A801G						.						77	80	79					3																	187447392		2203	4300	6503	SO:0001819	synonymous_variant	604	exon4			TGCCTCTTCTGGG		CCDS3289.1, CCDS46975.1	3q27	2013-01-09	2008-08-01		ENSG00000113916	ENSG00000113916		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	1001	protein-coding gene	gene with protein product		109565	"zinc finger protein 51"	ZNF51			Standard	NM_001130845		Approved	ZBTB27, LAZ3, BCL5, BCL6A	uc003frq.2	P41182	OTTHUMG00000156441	ENST00000406870.2:c.801A>G	chr3.hg19:g.187447392T>C		121.0	0.0		41.0	11.0	NM_001134738	A7E241|B8PSA7|D3DNV5	Silent	SNP	ENST00000406870.2	hg19	CCDS3289.1																																																																																			.	.		0.572	BCL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344202.1	NM_138931		C	187447392	T	C	187447392	2	2	256	1	0	0	0	0	0	0	0	1	1376	1606	56	2		2	BCL6	3	187447392	Silent	SNP	T	TCGA-EP-A2KC-01A-11D-A20W-10	14	187447392	10575038	19	36147			1	46		2	2	15	T		2.849096e-05
ATP13A4	84239	hgsc.bcm.edu	37	chr3	193174846	193174846	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	tgcacctttcatgaatgccaGtcggtcacctcccatctctt	6	15	3	1			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr3:193174846G>T	ENST00000342695.4	-	16	2180	c.1858C>A	c.(1858-1860)Ctg>Atg	p.L620M	ATP13A4_ENST00000392443.3_Missense_Mutation_p.L601M	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	620						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(27)|ovary(2)|prostate(3)|skin(11)|upper_aerodigestive_tract(2)	71	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		ATGAATGCCAGTCGGTCACCT	0.502																																					p.L620M		Atlas-SNP	.											.	ATP13A4	154	.	0			c.C1858A						.						105	90	95					3																	193174846		2203	4300	6503	SO:0001583	missense	84239	exon16			ATGCCAGTCGGTC	AK095277	CCDS3304.2	3q29	2010-04-20			ENSG00000127249	ENSG00000127249		"ATPases / P-type"	25422	protein-coding gene	gene with protein product		609556				14702039, 12975309	Standard	XM_005247829		Approved	DKFZp761I1011, FLJ37958	uc003ftd.3	Q4VNC1	OTTHUMG00000074067	ENST00000342695.4:c.1858C>A	chr3.hg19:g.193174846G>T	ENSP00000339182:p.Leu620Met	168.0	0.0		62.0	22.0	NM_032279	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	Missense_Mutation	SNP	ENST00000342695.4	hg19	CCDS3304.2	.	.	.	.	.	.	.	.	.	.	G	0.412	-0.912741	0.02415	.	.	ENSG00000127249	ENST00000392443;ENST00000342695	T;T	0.71817	-0.6;-0.6	6.08	0.395	0.16304	ATPase, cation-transporting, domain N (1);ATPase, P-type, cytoplasmic domain N (1);	2.312790	0.01449	N	0.015389	T	0.54598	0.1868	N	0.20328	0.56	0.09310	N	0.999998	B;B;B	0.14438	0.003;0.01;0.003	B;B;B	0.21360	0.01;0.034;0.01	T	0.35176	-0.9799	10	0.11794	T	0.64	-23.6273	6.8172	0.23837	0.0624:0.0941:0.4278:0.4158	.	601;620;620	B7WPN9;Q4VNC1-2;Q4VNC1	.;.;AT134_HUMAN	M	601;620	ENSP00000376238:L601M;ENSP00000339182:L620M	ENSP00000339182:L620M	L	-	1	2	ATP13A4	194657540	0.007000	0.16637	0.745000	0.31077	0.845000	0.48019	0.405000	0.21015	0.119000	0.18210	0.655000	0.94253	CTG	.	.		0.502	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157244.4	NM_032279		T	193174846	G	T	193174846	3	4	256	1	0	0	0	0	1	0	0	0	1126	1020	36	3	1792	3	ATP13A4	3	193174846	Missense_Mutation	SNP	G	TCGA-EP-A2KC-01A-11D-A20W-10	5727454	193174846	4847584	20	36148										
WNT8A	7478	hgsc.bcm.edu	37	chr5	137426639	137426639	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	aaaactgaggtcataagcagCtgtaactgcaaattccagtg	9	8	1	1			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr5:137426639C>T	ENST00000398754.1	+	6	938	c.933C>T	c.(931-933)agC>agT	p.S311S	WNT8A_ENST00000506684.1_Silent_p.S329S	NM_058244.2	NP_490645.1	Q9H1J5	WNT8A_HUMAN	wingless-type MMTV integration site family, member 8A	311					canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:0061317)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|endoderm development (GO:0007492)|establishment of organ orientation (GO:0048561)|neural crest cell fate commitment (GO:0014034)|neuron differentiation (GO:0030182)|palate development (GO:0060021)|polarity specification of anterior/posterior axis (GO:0009949)|polarity specification of proximal/distal axis (GO:0010085)|regulation of protein localization (GO:0032880)|regulation of transcription involved in anterior/posterior axis specification (GO:0044324)|response to retinoic acid (GO:0032526)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|skin(2)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TCATAAGCAGCTGTAACTGCA	0.562																																					p.S311S		Atlas-SNP	.											.	WNT8A	36	.	0			c.C933T						.						124	131	129					5																	137426639		2128	4247	6375	SO:0001819	synonymous_variant	7478	exon6			AAGCAGCTGTAAC	AB057725	CCDS43368.1, CCDS75311.1	5q31	2008-07-18			ENSG00000061492	ENSG00000061492		"Wingless-type MMTV integration sites"	12788	protein-coding gene	gene with protein product		606360				11408932	Standard	XM_005272076		Approved	WNT8D	uc003lcd.1	Q9H1J5	OTTHUMG00000129196	ENST00000398754.1:c.933C>T	chr5.hg19:g.137426639C>T		121.0	0.0		49.0	25.0	NM_058244	Q96S51	Silent	SNP	ENST00000398754.1	hg19	CCDS43368.1																																																																																			.	.		0.562	WNT8A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280395.1	NM_058244		T	137426639	C	T	137426639	2	4	256	1	0	0	0	0	0	0	0	1	17411	796	28	3		3	WNT8A	5	137426639	Silent	SNP	C	TCGA-EP-A2KC-01A-11D-A20W-10		137426639	43488621	21	36149										
PCDHA7	56141	hgsc.bcm.edu	37	chr5	140215321	140215321	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	gtggccgacgtgaacgacaaCgccccggcgttcgcgcagcc	14	16	0	1			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr5:140215321C>T	ENST00000525929.1	+	1	1353	c.1353C>T	c.(1351-1353)aaC>aaT	p.N451N	PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA7_ENST00000378125.3_Silent_p.N451N|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA3_ENST00000522353.2_Intron	NM_018910.2	NP_061733.1	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7	451	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|biliary_tract(1)|breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGAACGACAACGCCCCGGCGT	0.677																																					p.N451N	NSCLC(160;258 2013 5070 22440 28951)	Atlas-SNP	.											.	PCDHA7	367	.	0			c.C1353T						.						65	69	68					5																	140215321		2203	4298	6501	SO:0001819	synonymous_variant	56141	exon1			CGACAACGCCCCG	AF152485	CCDS54918.1	5q31	2010-11-26				ENSG00000204963		"Cadherins / Protocadherins : Clustered"	8673	other	complex locus constituent	"KIAA0345-like 7", "ortholog to mouse CNR4"	606313		CNRS4		10380929, 10662547	Standard	NM_018910		Approved	CNR4, CRNR4		Q9UN72		ENST00000525929.1:c.1353C>T	chr5.hg19:g.140215321C>T		379.0	0.0		113.0	55.0	NM_031852	O75282	Silent	SNP	ENST00000525929.1	hg19	CCDS54918.1																																																																																			.	.		0.677	PCDHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372887.2	NM_018910		T	140215321	C	T	140215321	2	4	256	1	0	0	0	0	0	0	0	1	11538	535	19	1		1	PCDHA7	5	140215321	Silent	SNP	C	TCGA-EP-A2KC-01A-11D-A20W-10	2788682	140215321	40699939	22	36150										
TAP1	6890	hgsc.bcm.edu	37	chr6	32816536	32816536	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	cagaccactgggtgggcagcGaggggtgcggtccaggtact	18	10	0	1			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr6:32816536G>A	ENST00000354258.4	-	7	1800	c.1639C>T	c.(1639-1641)Cgc>Tgc	p.R547C	TAPSAR1_ENST00000453426.1_lincRNA|TAP1_ENST00000425148.2_Missense_Mutation_p.R286C|PSMB9_ENST00000395330.1_Intron	NM_000593.5	NP_000584.2	Q03518	TAP1_HUMAN	transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)	547	Involved in peptide-binding site.				antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytosol to ER transport (GO:0046967)|defense response (GO:0006952)|intracellular transport of viral protein in host cell (GO:0019060)|peptide transport (GO:0015833)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)|TAP complex (GO:0042825)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|MHC class Ib protein binding (GO:0023029)|peptide antigen binding (GO:0042605)|peptide transporter activity (GO:0015197)|protein homodimerization activity (GO:0042803)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(4)|prostate(1)|skin(1)	21					Lapatinib(DB01259)	GGTGGGCAGCGAGGGGTGCGG	0.532																																					p.R547C		Atlas-SNP	.											.	TAP1	39	.	0			c.C1639T						.						130	132	131					6																	32816536		2203	4300	6503	SO:0001583	missense	6890	exon7			GGCAGCGAGGGGT		CCDS4758.1	6p21.3	2014-09-17			ENSG00000168394	ENSG00000168394		"ATP binding cassette transporters / subfamily B"	43	protein-coding gene	gene with protein product		170260		ABCB2		1529427, 1946428	Standard	NM_000593		Approved	PSF1, RING4, D6S114E	uc003ocg.3	Q03518	OTTHUMG00000031067	ENST00000354258.4:c.1639C>T	chr6.hg19:g.32816536G>A	ENSP00000346206:p.Arg547Cys	94.0	0.0		37.0	8.0	NM_000593	Q16149|Q96CP4	Missense_Mutation	SNP	ENST00000354258.4	hg19	CCDS4758.1	.	.	.	.	.	.	.	.	.	.	G	8.083	0.772865	0.16051	.	.	ENSG00000168394	ENST00000354258;ENST00000425148	D;D	0.87334	-2.22;-2.24	5.02	-1.79	0.07932	.	1.376040	0.04789	N	0.431351	T	0.66046	0.2750	L	0.47190	1.495	0.09310	N	0.999999	B	0.13145	0.007	B	0.08055	0.003	T	0.51624	-0.8682	10	0.37606	T	0.19	6.0E-4	5.1321	0.14915	0.4823:0.0:0.3802:0.1375	.	547	Q03518	TAP1_HUMAN	C	547;286	ENSP00000346206:R547C;ENSP00000401919:R286C	ENSP00000346206:R547C	R	-	1	0	TAP1	32924514	0.002000	0.14202	0.028000	0.17463	0.681000	0.39784	-0.198000	0.09505	-0.630000	0.05567	0.643000	0.83706	CGC	.	.		0.532	TAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076087.2	NM_000593		A	32816536	G	A	32816536	3	1	256	1	0	0	0	0	1	0	0	0	15565	1058	37	1	807	1	TAP1	6	32816536	Missense_Mutation	SNP	G	TCGA-EP-A2KC-01A-11D-A20W-10		32816536	138298531	23	36151										
ECT2L	345930	hgsc.bcm.edu	37	chr6	139202242	139202242	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	agcattgtcatcaaacagagCgattctgagtgctgccaata	9	9	3	2	rs368116476		TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr6:139202242C>T	ENST00000423192.1	+	14	1975	c.1814C>T	c.(1813-1815)gCg>gTg	p.A605V	ECT2L_ENST00000367682.2_Missense_Mutation_p.A605V|ECT2L_ENST00000541398.1_Missense_Mutation_p.A536V|RP3-509I19.6_ENST00000572284.1_RNA			Q008S8	ECT2L_HUMAN	epithelial cell transforming 2 like	605	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)			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						TCAAACAGAGCGATTCTGAGT	0.368			"N, Splice, Mis"		ETP ALL																																p.A605V		Atlas-SNP	.		Rec	yes		6	6q24.1	345930	epithelial cell transforming sequence 2 oncogene-like		L	.	ECT2L	75	.	0			c.C1814T						.						114	108	110					6																	139202242		1959	4162	6121	SO:0001583	missense	345930	exon14			ACAGAGCGATTCT		CCDS43508.1	6q24.1	2014-03-11	2014-03-11		ENSG00000203734	ENSG00000203734		"Rho guanine nucleotide exchange factors", "F-boxes /  "other""	21118	protein-coding gene	gene with protein product	"lung specific F-box and DH domain containing protein", "F-box protein 49"		"chromosome 6 open reading frame 91", "epithelial cell transforming sequence 2 oncogene-like"	C6orf91			Standard	NM_001077706		Approved	ARHGEF32, FBXO49, LFDH	uc021zfx.1	Q008S8	OTTHUMG00000015679	ENST00000423192.1:c.1814C>T	chr6.hg19:g.139202242C>T	ENSP00000387388:p.Ala605Val	106.0	0.0		62.0	17.0	NM_001195037	B2RUV6|Q5JWK2|Q5JWK3|Q5JWK4	Missense_Mutation	SNP	ENST00000423192.1	hg19	CCDS43508.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.024108	0.93462	.	.	ENSG00000203734	ENST00000423192;ENST00000367682;ENST00000541398	T;T;T	0.64085	-0.08;-0.08;1.52	5.53	5.53	0.82687	Dbl homology (DH) domain (5);	0.135350	0.27773	U	0.017910	T	0.72244	0.3436	M	0.61703	1.905	0.42102	D	0.991345	D;D	0.89917	1.0;1.0	D;D	0.79108	0.99;0.992	T	0.73871	-0.3846	10	0.59425	D	0.04	-4.1812	16.3823	0.83472	0.0:1.0:0.0:0.0	.	536;605	F5H7S9;Q008S8	.;ECT2L_HUMAN	V	605;605;536	ENSP00000387388:A605V;ENSP00000356655:A605V;ENSP00000442307:A536V	ENSP00000356655:A605V	A	+	2	0	ECT2L	139243935	1.000000	0.71417	0.966000	0.40874	0.989000	0.77384	5.783000	0.68982	2.609000	0.88269	0.655000	0.94253	GCG	.	.		0.368	ECT2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042441.3	NM_001077706		T	139202242	C	T	139202242	3	4	256	1	0	0	0	0	1	0	0	0	4904	768	27	1	1864	1	ECT2L	6	139202242	Missense_Mutation	SNP	C	TCGA-EP-A2KC-01A-11D-A20W-10	106385706	139202242	31912825	24	36152										
NOX3	50508	hgsc.bcm.edu	37	chr6	155776225	155776225	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	tcttcataccagtagaacgtGtcaataaacagataaaaatt	5	7	3	2			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr6:155776225G>T	ENST00000159060.2	-	2	189	c.87C>A	c.(85-87)gaC>gaA	p.D29E		NM_015718.2	NP_056533.1	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	29					detection of gravity (GO:0009590)|otolith development (GO:0048840)|superoxide anion generation (GO:0042554)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NADPH oxidase complex (GO:0043020)	superoxide-generating NADPH oxidase activity (GO:0016175)			cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	45		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)		AGTAGAACGTGTCAATAAACA	0.328																																					p.D29E		Atlas-SNP	.											.	NOX3	93	.	0			c.C87A						.						62	60	61					6																	155776225		2203	4300	6503	SO:0001583	missense	50508	exon2			GAACGTGTCAATA	AF190122	CCDS5250.1	6q25.3	2008-05-15			ENSG00000074771	ENSG00000074771			7890	protein-coding gene	gene with protein product		607105				11376945	Standard	NM_015718		Approved	GP91-3	uc003qqm.3	Q9HBY0	OTTHUMG00000015883	ENST00000159060.2:c.87C>A	chr6.hg19:g.155776225G>T	ENSP00000159060:p.Asp29Glu	199.0	0.0		101.0	52.0	NM_015718	Q9HBJ9	Missense_Mutation	SNP	ENST00000159060.2	hg19	CCDS5250.1	.	.	.	.	.	.	.	.	.	.	G	10.66	1.413843	0.25465	.	.	ENSG00000074771	ENST00000159060	D	0.94966	-3.57	5.61	3.83	0.44106	.	0.158387	0.44483	D	0.000443	D	0.84079	0.5393	L	0.50333	1.59	0.33157	D	0.546529	P	0.36282	0.546	B	0.30401	0.115	T	0.77405	-0.2600	10	0.29301	T	0.29	-17.4884	8.9582	0.35832	0.2475:0.0:0.7525:0.0	.	29	Q9HBY0	NOX3_HUMAN	E	29	ENSP00000159060:D29E	ENSP00000159060:D29E	D	-	3	2	NOX3	155817917	1.000000	0.71417	0.811000	0.32455	0.895000	0.52256	1.267000	0.33050	0.843000	0.35070	0.650000	0.86243	GAC	.	.		0.328	NOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042819.1			T	155776225	G	T	155776225	3	4	256	1	0	0	0	0	1	0	0	0	10566	1368	48	3	1667	3	NOX3	6	155776225	Missense_Mutation	SNP	G	TCGA-EP-A2KC-01A-11D-A20W-10	16573983	155776225	15338842	25	36153										
PCLO	27445	hgsc.bcm.edu	37	chr7	82581541	82581541	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	agtagactcatccattgttaCgactgttctgtgagacttgg	10	8	2	2	rs547500251		TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr7:82581541C>T	ENST00000333891.9	-	5	9065	c.8728G>A	c.(8728-8730)Gta>Ata	p.V2910I	PCLO_ENST00000423517.2_Missense_Mutation_p.V2910I|PCLO_ENST00000437081.1_5'Flank	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TCCATTGTTACGACTGTTCTG	0.443																																					p.V2910I		Atlas-SNP	.											Q9Y6V0-3,NS,carcinoma,0,3	PCLO	1506	.	0			c.G8728A						.						205	194	198					7																	82581541		1964	4149	6113	SO:0001583	missense	27445	exon5			TTGTTACGACTGT	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.8728G>A	chr7.hg19:g.82581541C>T	ENSP00000334319:p.Val2910Ile	81.0	0.0		37.0	24.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	C	12.27	1.888821	0.33348	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.56444	0.49;0.46	5.68	4.8	0.61643	.	.	.	.	.	T	0.52289	0.1725	M	0.66939	2.045	0.80722	D	1	P;P	0.37061	0.58;0.58	B;B	0.35240	0.198;0.198	T	0.58940	-0.7547	9	0.87932	D	0	.	14.4892	0.67639	0.0:0.9296:0.0:0.0704	.	2910;2910	Q9Y6V0-5;Q9Y6V0-6	.;.	I	2841;2910;2910	ENSP00000334319:V2910I;ENSP00000388393:V2910I	ENSP00000334319:V2910I	V	-	1	0	PCLO	82419477	1.000000	0.71417	0.996000	0.52242	0.865000	0.49528	6.064000	0.71169	1.396000	0.46663	0.563000	0.77884	GTA	.	.		0.443	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		T	82581541	C	T	82581541	3	4	256	1	0	0	0	0	1	0	0	0	11592	536	19	1	6801	1	PCLO	7	82581541	Missense_Mutation	SNP	C	TCGA-EP-A2KC-01A-11D-A20W-10		82581541	76557122	26	36154										
PCLO	27445	hgsc.bcm.edu	37	chr7	82784846	82784846	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	cccagtctgctgagctggagGcttagcaggaccaagaggct	14	11	1	2			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr7:82784846G>T	ENST00000333891.9	-	2	1448	c.1111C>A	c.(1111-1113)Cct>Act	p.P371T	PCLO_ENST00000423517.2_Missense_Mutation_p.P371T	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TGAGCTGGAGGCTTAGCAGGA	0.567																																					p.P371T		Atlas-SNP	.											.	PCLO	1506	.	0			c.C1111A						.						51	53	52					7																	82784846		1976	4166	6142	SO:0001583	missense	27445	exon2			CTGGAGGCTTAGC	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.1111C>A	chr7.hg19:g.82784846G>T	ENSP00000334319:p.Pro371Thr	251.0	0.0		117.0	16.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	G	0.035	-1.310297	0.01342	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.18016	2.24;2.25	4.07	-1.37	0.09056	.	.	.	.	.	T	0.12433	0.0302	L	0.42245	1.32	0.09310	N	0.999997	B;B	0.15141	0.005;0.012	B;B	0.15870	0.005;0.014	T	0.31558	-0.9939	9	0.87932	D	0	.	2.9002	0.05703	0.2141:0.2269:0.45:0.109	.	371;371	Q9Y6V0-5;Q9Y6V0-6	.;.	T	371	ENSP00000334319:P371T;ENSP00000388393:P371T	ENSP00000334319:P371T	P	-	1	0	PCLO	82622782	0.054000	0.20591	0.000000	0.03702	0.268000	0.26511	-0.022000	0.12480	-0.994000	0.03463	-0.797000	0.03246	CCT	.	.		0.567	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		T	82784846	G	T	82784846	3	4	256	1	0	0	0	0	1	0	0	0	11592	1203	42	3	14430	3	PCLO	7	82784846	Missense_Mutation	SNP	G	TCGA-EP-A2KC-01A-11D-A20W-10	203305	82784846	76353817	27	36155										
ZNF804B	219578	hgsc.bcm.edu	37	chr7	88964537	88964537	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	tgcttccataaaagagaacaCcactcagttgaaaggcacaa	7	10	1	2			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr7:88964537C>T	ENST00000333190.4	+	4	2850	c.2241C>T	c.(2239-2241)caC>caT	p.H747H		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	747							metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			AAAGAGAACACCACTCAGTTG	0.413										HNSCC(36;0.09)																											p.H747H		Atlas-SNP	.											.	ZNF804B	322	.	0			c.C2241T						.						86	79	81					7																	88964537		2203	4300	6503	SO:0001819	synonymous_variant	219578	exon4			AGAACACCACTCA	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"zinc finger 804B"				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.2241C>T	chr7.hg19:g.88964537C>T		131.0	0.0		58.0	6.0	NM_181646	B2RTV2|Q7Z714|Q96MN7	Silent	SNP	ENST00000333190.4	hg19	CCDS5613.1																																																																																			.	.		0.413	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646		T	88964537	C	T	88964537	2	4	256	1	0	0	0	0	0	0	0	1	18186	506	18	3		3	ZNF804B	7	88964537	Silent	SNP	C	TCGA-EP-A2KC-01A-11D-A20W-10	6179691	88964537	70174126	28	36156										
PTCD1	26024	hgsc.bcm.edu	37	chr7	99021404	99021404	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	cttggggcacacacccggtcAaaggtgggagggtactgggc	17	10	1	0			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr7:99021404A>G	ENST00000292478.4	-	7	2164	c.1914T>C	c.(1912-1914)ttT>ttC	p.F638F	ATP5J2-PTCD1_ENST00000413834.1_Silent_p.F687F|PTCD1_ENST00000555673.1_Silent_p.F687F	NM_015545.3	NP_056360.2	O75127	PTCD1_HUMAN	pentatricopeptide repeat domain 1	638					tRNA 3'-end processing (GO:0042780)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|tRNA binding (GO:0000049)			endometrium(5)|large_intestine(3)|lung(16)|ovary(2)|skin(1)	27	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			ACACCCGGTCAAAGGTGGGAG	0.582																																					p.F687F		Atlas-SNP	.											.	.	.	.	0			c.T2061C						.						158	141	147					7																	99021404		2203	4300	6503	SO:0001819	synonymous_variant	100526740	exon8			CCGGTCAAAGGTG	AB014532	CCDS34691.1	7q22.1	2006-01-27				ENSG00000106246			22198	protein-coding gene	gene with protein product		614774					Standard	NM_015545		Approved	KIAA0632		O75127		ENST00000292478.4:c.1914T>C	chr7.hg19:g.99021404A>G		132.0	0.0		66.0	25.0	NM_001198879	Q3ZB78|Q66K60|Q9UDV2	Silent	SNP	ENST00000292478.4	hg19	CCDS34691.1																																																																																			.	.		0.582	PTCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336391.1	NM_015545		G	99021404	A	G	99021404	2	3	256	1	0	0	0	0	0	0	0	1	12739	127	5	2		2	PTCD1	7	99021404	Silent	SNP	A	TCGA-EP-A2KC-01A-11D-A20W-10	10056867	99021404	60117259	29	36157										
NAPEPLD	222236	hgsc.bcm.edu	37	chr7	102760530	102760530	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	gagctaaagatgggatccgtGagaaatatgagctcatccat	11	7	1	3			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr7:102760530G>A	ENST00000417955.1	-	3	589	c.435C>T	c.(433-435)ctC>ctT	p.L145L	NAPEPLD_ENST00000341533.4_Silent_p.L145L|NAPEPLD_ENST00000455523.2_Silent_p.L218L|NAPEPLD_ENST00000427257.1_Silent_p.L145L|NAPEPLD_ENST00000465647.1_Silent_p.L145L			Q6IQ20	NAPEP_HUMAN	N-acyl phosphatidylethanolamine phospholipase D	145					phospholipid catabolic process (GO:0009395)	extracellular vesicular exosome (GO:0070062)|photoreceptor outer segment membrane (GO:0042622)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						TGGGATCCGTGAGAAATATGA	0.502																																					p.L145L		Atlas-SNP	.											.	NAPEPLD	49	.	0			c.C435T						.						161	124	136					7																	102760530		2203	4300	6503	SO:0001819	synonymous_variant	222236	exon3			ATCCGTGAGAAAT	BC037350, AY357337	CCDS5729.1	7q22.1	2014-03-14			ENSG00000161048	ENSG00000161048	3.1.4.54		21683	protein-coding gene	gene with protein product	"chromosome 7 open reading frame 18, N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D"	612334				14634025, 15820312, 18067139	Standard	NM_198990		Approved	FMP30, C7orf18, NAPE-PLD	uc003vbd.2	Q6IQ20	OTTHUMG00000157204	ENST00000417955.1:c.435C>T	chr7.hg19:g.102760530G>A		169.0	0.0		56.0	35.0	NM_001122838	Q5CZ87|Q769K1	Silent	SNP	ENST00000417955.1	hg19	CCDS5729.1																																																																																			.	.		0.502	NAPEPLD-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347904.1	NM_198990		A	102760530	G	A	102760530	2	1	256	1	0	0	0	0	0	0	0	1	10172	1277	45	3		3	NAPEPLD	7	102760530	Silent	SNP	G	TCGA-EP-A2KC-01A-11D-A20W-10	3739126	102760530	56378133	30	36158										
PPP1R3A	5506	hgsc.bcm.edu	37	chr7	113519408	113519408	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	tccttggtgaatgagacacaTctgctgtgattgcccgggtg	13	9	1	3			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr7:113519408T>C	ENST00000284601.3	-	4	1807	c.1739A>G	c.(1738-1740)gAt>gGt	p.D580G		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	580					glycogen metabolic process (GO:0005977)	integral component of membrane (GO:0016021)		p.D580V(1)		NS(2)|breast(8)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|liver(1)|lung(43)|ovary(10)|pancreas(7)|prostate(3)|skin(15)|stomach(1)|upper_aerodigestive_tract(2)	121						ATGAGACACATCTGCTGTGAT	0.483																																					p.D580G		Atlas-SNP	.											PPP1R3A,colon,carcinoma,+1,2	PPP1R3A	317	.	1	Substitution - Missense(1)	ovary(1)	c.A1739G						.						116	111	113					7																	113519408		2203	4300	6503	SO:0001583	missense	5506	exon4			GACACATCTGCTG	AF024578	CCDS5759.1	7q31.1	2012-04-17	2011-10-04	2001-07-02	ENSG00000154415	ENSG00000154415	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9291	protein-coding gene	gene with protein product	"glycogen-associated regulatory subunit of protein phosphatase-1", "protein phosphatase 1 regulatory subunit GM"	600917	"protein phosphatase 1, regulatory (inhibitor) subunit 3A (glycogen and sarcoplasmic reticulum binding subunit, skeletal muscle)", "protein phosphatase 1, regulatory (inhibitor) subunit 3A"	PPP1R3		7926294	Standard	NM_002711		Approved	GM	uc010ljy.1	Q16821	OTTHUMG00000156944	ENST00000284601.3:c.1739A>G	chr7.hg19:g.113519408T>C	ENSP00000284601:p.Asp580Gly	228.0	0.0		83.0	48.0	NM_002711	A0AVQ2|A4D0T6|O43476|Q75LN8|Q7KYM8|Q86UI6	Missense_Mutation	SNP	ENST00000284601.3	hg19	CCDS5759.1	.	.	.	.	.	.	.	.	.	.	T	13.20	2.167400	0.38315	.	.	ENSG00000154415	ENST00000284601	T	0.18960	2.18	5.89	2.34	0.29019	.	0.367658	0.26407	N	0.024551	T	0.21427	0.0516	M	0.69823	2.125	0.09310	N	1	B	0.19200	0.034	B	0.12156	0.007	T	0.17410	-1.0370	10	0.44086	T	0.13	-0.3165	7.6128	0.28139	0.0:0.2351:0.0:0.7649	.	580	Q16821	PPR3A_HUMAN	G	580	ENSP00000284601:D580G	ENSP00000284601:D580G	D	-	2	0	PPP1R3A	113306644	0.000000	0.05858	0.004000	0.12327	0.062000	0.15995	0.087000	0.14958	0.505000	0.28104	0.460000	0.39030	GAT	.	.		0.483	PPP1R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346724.1	NM_002711		C	113519408	T	C	113519408	3	2	256	1	0	0	0	0	1	0	0	0	12383	1435	50	2	1633	2	PPP1R3A	7	113519408	Missense_Mutation	SNP	T	TCGA-EP-A2KC-01A-11D-A20W-10	10758878	113519408	45619255	31	36159										
ZNF398	57541	hgsc.bcm.edu	37	chr7	148863347	148863347	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	actttacaagaatatcatgaAgggcaactacgagtctctca	7	9	3	2			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr7:148863347A>G	ENST00000475153.1	+	3	785	c.518A>G	c.(517-519)aAg>aGg	p.K173R	ZNF398_ENST00000420008.2_Missense_Mutation_p.K2R|ZNF398_ENST00000540950.1_Missense_Mutation_p.K178R|ZNF398_ENST00000483892.1_Missense_Mutation_p.K2R|ZNF398_ENST00000426851.2_Missense_Mutation_p.K2R|ZNF398_ENST00000491174.1_Missense_Mutation_p.K2R|ZNF398_ENST00000335901.4_Missense_Mutation_p.K2R			Q8TD17	ZN398_HUMAN	zinc finger protein 398	173	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(14)|ovary(1)	25	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00143)			AATATCATGAAGGGCAACTAC	0.453																																					p.K173R		Atlas-SNP	.											.	ZNF398	54	.	0			c.A518G						.						139	134	136					7																	148863347		2203	4300	6503	SO:0001583	missense	57541	exon3			TCATGAAGGGCAA	AB037760	CCDS5894.1, CCDS47739.1	7q35	2013-01-08			ENSG00000197024	ENSG00000197024		"Zinc fingers, C2H2-type", "-"	18373	protein-coding gene	gene with protein product						11779858	Standard	NM_170686		Approved	ZER6, KIAA1339, P51, P71	uc003wfl.3	Q8TD17	OTTHUMG00000158970	ENST00000475153.1:c.518A>G	chr7.hg19:g.148863347A>G	ENSP00000420418:p.Lys173Arg	145.0	0.0		62.0	25.0	NM_170686	A8K384|B4E377|Q8TD18|Q9P2K7|Q9UDV8	Missense_Mutation	SNP	ENST00000475153.1	hg19	CCDS5894.1	.	.	.	.	.	.	.	.	.	.	A	17.08	3.299033	0.60195	.	.	ENSG00000197024	ENST00000426851;ENST00000420008;ENST00000475153;ENST00000483892;ENST00000491174;ENST00000540950;ENST00000335901	T;T;T;T;T;T;T	0.05717	3.4;3.4;4.72;3.4;3.4;4.72;3.4	5.24	5.24	0.73138	Krueppel-associated box (4);	0.000000	0.48767	D	0.000177	T	0.07324	0.0185	N	0.01352	-0.895	0.33048	D	0.532414	D;P	0.69078	0.997;0.543	D;B	0.79108	0.992;0.306	T	0.49952	-0.8884	10	0.62326	D	0.03	-23.2364	13.1015	0.59222	1.0:0.0:0.0:0.0	.	178;173	B4DXA9;Q8TD17	.;ZN398_HUMAN	R	2;2;173;2;2;178;2	ENSP00000389972:K2R;ENSP00000416751:K2R;ENSP00000420418:K173R;ENSP00000418564:K2R;ENSP00000419391:K2R;ENSP00000439340:K178R;ENSP00000338984:K2R	ENSP00000338984:K2R	K	+	2	0	ZNF398	148494280	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	2.923000	0.48868	1.979000	0.57680	0.460000	0.39030	AAG	.	.		0.453	ZNF398-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352722.2			G	148863347	A	G	148863347	3	3	256	1	0	0	0	0	1	0	0	0	17900	72	3	2	528	2	ZNF398	7	148863347	Missense_Mutation	SNP	A	TCGA-EP-A2KC-01A-11D-A20W-10	35343939	148863347	10275316	32	36160										
KCNB2	9312	hgsc.bcm.edu	37	chr8	73480262	73480262	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	gcatccaggagccttcacttCcattttaaatttctaccgga	6	12	2	0			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr8:73480262C>A	ENST00000523207.1	+	2	881	c.293C>A	c.(292-294)tCc>tAc	p.S98Y		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	98					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	GCCTTCACTTCCATTTTAAAT	0.463																																					p.S98Y		Atlas-SNP	.											.	KCNB2	228	.	0			c.C293A						.						78	80	79					8																	73480262		2203	4300	6503	SO:0001583	missense	9312	exon2			TCACTTCCATTTT	U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.293C>A	chr8.hg19:g.73480262C>A	ENSP00000430846:p.Ser98Tyr	114.0	0.0		63.0	8.0	NM_004770	Q7Z7D0|Q9BXD3	Missense_Mutation	SNP	ENST00000523207.1	hg19	CCDS6209.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.040219	0.75732	.	.	ENSG00000182674	ENST00000523207	T	0.76578	-1.03	5.93	5.93	0.95920	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.000000	0.31577	U	0.007412	T	0.81749	0.4888	N	0.21448	0.665	0.80722	D	1	D	0.71674	0.998	D	0.77557	0.99	T	0.79415	-0.1813	10	0.32370	T	0.25	.	19.9643	0.97261	0.0:1.0:0.0:0.0	.	98	Q92953	KCNB2_HUMAN	Y	98	ENSP00000430846:S98Y	ENSP00000430846:S98Y	S	+	2	0	KCNB2	73642816	1.000000	0.71417	0.983000	0.44433	0.974000	0.67602	7.818000	0.86416	2.826000	0.97356	0.655000	0.94253	TCC	.	.		0.463	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770		A	73480262	C	A	73480262	3	1	256	1	0	0	0	0	1	0	0	0	8022	855	30	3	295	3	KCNB2	8	73480262	Missense_Mutation	SNP	C	TCGA-EP-A2KC-01A-11D-A20W-10		73480262	72883760	33	36161										
TMEM67	91147	hgsc.bcm.edu	37	chr8	94800156	94800156	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	agtgacattgatatcaaagaTgccaacagccagtctgtgaa	9	8	2	4			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr8:94800156T>C	ENST00000453321.3	+	14	1555	c.1497T>C	c.(1495-1497)gaT>gaC	p.D499D	TMEM67_ENST00000409623.3_Silent_p.D418D	NM_153704.5	NP_714915.3	Q5HYA8	MKS3_HUMAN	transmembrane protein 67	499					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of centrosome duplication (GO:0010826)	centrosome (GO:0005813)|ciliary membrane (GO:0060170)|cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)	filamin binding (GO:0031005)|unfolded protein binding (GO:0051082)			breast(3)|endometrium(8)|kidney(5)|large_intestine(4)|liver(2)|lung(15)|ovary(2)|skin(1)|urinary_tract(1)	41	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.00896)			ATATCAAAGATGCCAACAGCC	0.363																																					p.D499D		Atlas-SNP	.											.	TMEM67	187	.	0			c.T1497C						.						157	140	146					8																	94800156		2203	4300	6503	SO:0001819	synonymous_variant	91147	exon14			CAAAGATGCCAAC	BX648768	CCDS6258.2, CCDS47893.1	8q22.1	2014-09-17			ENSG00000164953	ENSG00000164953			28396	protein-coding gene	gene with protein product	"Meckelin"	609884	"Meckel syndrome, type 3"	MKS3		12384791, 16415887, 19508969	Standard	NM_153704		Approved	MGC26979, JBTS6, NPHP11	uc011lgk.2	Q5HYA8	OTTHUMG00000153119	ENST00000453321.3:c.1497T>C	chr8.hg19:g.94800156T>C		147.0	0.0		95.0	31.0	NM_153704	B3KRU5|B3KT47|G5E9H2|Q3ZCX3|Q7Z5T8|Q8IZ06	Silent	SNP	ENST00000453321.3	hg19	CCDS6258.2	.	.	.	.	.	.	.	.	.	.	T	0.012	-1.648910	0.00785	.	.	ENSG00000164953	ENST00000520680	.	.	.	5.94	-3.95	0.04118	.	.	.	.	.	T	0.54046	0.1834	.	.	.	0.51767	D	0.999932	.	.	.	.	.	.	T	0.50792	-0.8786	4	.	.	.	-9.9885	10.5332	0.44988	0.0:0.3893:0.089:0.5217	.	.	.	.	R	107	.	.	C	+	1	0	TMEM67	94869332	0.981000	0.34729	0.006000	0.13384	0.013000	0.08279	0.212000	0.17497	-1.420000	0.02009	-2.549000	0.00178	TGC	.	.		0.363	TMEM67-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329641.2	NM_153704		C	94800156	T	C	94800156	2	2	256	1	0	0	0	0	0	0	0	1	16211	1461	51	2		2	TMEM67	8	94800156	Silent	SNP	T	TCGA-EP-A2KC-01A-11D-A20W-10	21319894	94800156	51563866	34	36162										
PRPF4	9128	hgsc.bcm.edu	37	chr9	116049016	116049016	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	aatgtaggagcaattgtattCcatcccaaatccactgtctc	6	11	1	0			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr9:116049016C>T	ENST00000374198.4	+	9	945	c.843C>T	c.(841-843)ttC>ttT	p.F281F	PRPF4_ENST00000374199.4_Silent_p.F280F	NM_001244926.1|NM_004697.4	NP_001231855.1|NP_004688.2	O43172	PRP4_HUMAN	pre-mRNA processing factor 4	281				NVGAIVFH -> KKEQLHSI (in Ref. 3; AAC02261). {ECO:0000305}.	gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U4/U6 snRNP (GO:0071001)				NS(1)|breast(2)|endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|prostate(2)	23						CAATTGTATTCCATCCCAAAT	0.443																																					p.F281F		Atlas-SNP	.											.	PRPF4	56	.	0			c.C843T						.						299	292	294					9																	116049016		2203	4300	6503	SO:0001819	synonymous_variant	9128	exon9			TGTATTCCATCCC	AF001687	CCDS6791.1, CCDS59142.1	9q31-q33	2013-10-03	2013-10-03		ENSG00000136875	ENSG00000136875		"WD repeat domain containing"	17349	protein-coding gene	gene with protein product	"PRP4/STK/WD splicing factor", "U4/U6 small nuclear ribonucleoprotein Prp4"	607795	"PRP4 pre-mRNA processing factor 4 homolog (yeast)"			9257651, 9404889	Standard	NM_004697		Approved	Prp4p, HPRP4, HPRP4P, PRP4, SNRNP60	uc004bgx.3	O43172	OTTHUMG00000020517	ENST00000374198.4:c.843C>T	chr9.hg19:g.116049016C>T		145.0	0.0		37.0	10.0	NM_004697	O43445|O43864|Q5T1M8|Q96DG2|Q96IK4	Silent	SNP	ENST00000374198.4	hg19	CCDS6791.1																																																																																			.	.		0.443	PRPF4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053708.2	NM_004697		T	116049016	C	T	116049016	2	4	256	1	0	0	0	0	0	0	0	1	12582	854	30	3		3	PRPF4	9	116049016	Silent	SNP	C	TCGA-EP-A2KC-01A-11D-A20W-10		116049016	25164415	35	36163										
YME1L1	10730	hgsc.bcm.edu	37	chr10	27436456	27436456	+	Frame_Shift_Del	DEL	G	G	-													0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	gagggagaagggttctggacGgatgtgccagttatcggttg					rs369706082		TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr10:27436456delG	ENST00000326799.3	-	3	458	c.310delC	c.(310-312)cgtfs	p.R104fs	YME1L1_ENST00000477432.1_Frame_Shift_Del_p.R104fs|YME1L1_ENST00000376016.3_Intron|YME1L1_ENST00000375972.3_Intron	NM_139312.2	NP_647473.1	Q96TA2	YMEL1_HUMAN	YME1-like 1 ATPase	104					cell proliferation (GO:0008283)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|mitochondrion organization (GO:0007005)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	23						GGTTCTGGACGGAtgtgccag	0.448																																					p.R104fs		Atlas-Indel,Pindel	.											.	YME1L1	71	.	0			c.311delG						.						221	176	191					10																	27436456		2203	4300	6503	SO:0001589	frameshift_variant	10730	exon3			.	AJ132637	CCDS7151.1, CCDS7152.1, CCDS58072.1	10p14	2013-06-10	2013-06-10		ENSG00000136758	ENSG00000136758		"ATPases / AAA-type"	12843	protein-coding gene	gene with protein product		607472	"YME1 (S.cerevisiae)-like 1", "YME1-like 1 (S. cerevisiae)"			22262461	Standard	NM_139312		Approved		uc001itj.3	Q96TA2	OTTHUMG00000017853	ENST00000326799.3:c.310delC	chr10.hg19:g.27436456delG	ENSP00000318480:p.Arg104fs	283.0	0.0		90.0	43.0	NM_139312	B4DNM1|D3DRV8|D3DRV9|Q5T8D9|Q9H1Q0|Q9UMR9	Frame_Shift_Del	DEL	ENST00000326799.3	hg19	CCDS7152.1																																																																																			.	.		0.448	YME1L1-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047306.1	NM_139312		-	27436456	G	-	27436456	7	5	256	1	0	1	0	1	0	0	0	0	17502	1116	39	0	2083	0	YME1L1	10	27436456	Frame_Shift_Del	DEL	G	TCGA-EP-A2KC-01A-11D-A20W-10		27436456	108098291	36	36164										
NRG3	10718	hgsc.bcm.edu	37	chr10	84498384	84498384	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	gatcaatttctgccgaaaacTgattccatcttatcggatcc	6	11	3	1			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr10:84498384T>C	ENST00000404547.1	+	3	1005	c.1005T>C	c.(1003-1005)acT>acC	p.T335T	NRG3_ENST00000556918.1_Silent_p.T165T|NRG3_ENST00000372142.2_Silent_p.T114T|NRG3_ENST00000372141.2_Silent_p.T335T|NRG3_ENST00000404576.2_Silent_p.T139T			P56975	NRG3_HUMAN	neuregulin 3	335					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|intracellular signal transduction (GO:0035556)|mammary placode formation (GO:0060596)|pattern specification process (GO:0007389)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	growth factor activity (GO:0008083)|receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(41)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	69				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		TGCCGAAAACTGATTCCATCT	0.413																																					p.T335T		Atlas-SNP	.											NRG3_ENST00000372142,NS,carcinoma,0,2	NRG3	301	.	0			c.T1005C						.						157	139	146					10																	84498384		2203	4300	6503	SO:0001819	synonymous_variant	10718	exon3			GAAAACTGATTCC	AK098823	CCDS31233.1, CCDS53547.1	10q22-q23	2003-09-09			ENSG00000185737	ENSG00000185737			7999	protein-coding gene	gene with protein product		605533				9275162	Standard	NM_001010848		Approved		uc001kco.2	P56975	OTTHUMG00000018626	ENST00000404547.1:c.1005T>C	chr10.hg19:g.84498384T>C		158.0	0.0		68.0	21.0	NM_001165972	A4D7U1|Q0PEH2|Q5VYH3	Silent	SNP	ENST00000404547.1	hg19	CCDS31233.1																																																																																			.	.		0.413	NRG3-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412262.1	XM_166086		C	84498384	T	C	84498384	2	2	256	1	0	0	0	0	0	0	0	1	10658	1567	55	2		2	NRG3	10	84498384	Silent	SNP	T	TCGA-EP-A2KC-01A-11D-A20W-10	57061928	84498384	51036363	37	36165										
FRA10AC1	118924	hgsc.bcm.edu	37	chr10	95436450	95436450	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	ttctttgaagatgaatgtccTgaaaaggaaacatcattgat	8	5	2	5			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr10:95436450T>C	ENST00000359204.4	-	12	985		c.e12-2		FRA10AC1_ENST00000536233.1_Splice_Site|FRA10AC1_ENST00000371430.2_Splice_Site|FRA10AC1_ENST00000394100.2_Splice_Site|FRA10AC1_ENST00000460752.1_5'Flank	NM_145246.4	NP_660289.2	Q70Z53	F10C1_HUMAN	fragile site, folic acid type, rare, fra(10)(q23.3) or fra(10)(q24.2) candidate 1							nucleus (GO:0005634)				NS(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(4)|urinary_tract(1)	14						ATGAATGTCCTGAAAAGGAAA	0.269																																					.		Atlas-SNP	.											.	FRA10AC1	68	.	0			c.788-2A>G						.						33	36	35					10																	95436450		2192	4268	6460	SO:0001630	splice_region_variant	118924	exon13			ATGTCCTGAAAAG	AK090955	CCDS7430.1	10q23.33	2014-01-28	2010-05-25	2010-05-25	ENSG00000148690	ENSG00000148690			1162	protein-coding gene	gene with protein product		608866	"chromosome 10 open reading frame 4"	C10orf4		15203205	Standard	NM_145246		Approved		uc001kiz.2	Q70Z53	OTTHUMG00000018776	ENST00000359204.4:c.788-2A>G	chr10.hg19:g.95436450T>C		237.0	1.0		87.0	45.0	NM_145246	C9JCR4|C9JCR5|C9JMY4|Q70Z49|Q70Z50|Q70Z51|Q70Z52|Q8N293|Q8WVH5|Q96JQ8	Splice_Site	SNP	ENST00000359204.4	hg19	CCDS7430.1	.	.	.	.	.	.	.	.	.	.	T	12.09	1.832343	0.32421	.	.	ENSG00000148690	ENST00000359204;ENST00000536233;ENST00000371426;ENST00000371430;ENST00000394100	.	.	.	4.9	4.9	0.64082	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.1899	0.48679	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	FRA10AC1	95426440	1.000000	0.71417	0.869000	0.34112	0.379000	0.30106	3.557000	0.53741	1.953000	0.56701	0.460000	0.39030	.	.	.		0.269	FRA10AC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049439.1	NM_145246	Intron	C	95436450	T	C	95436450	5	2	256	1	0	0	0	0	0	0	1	0	6049	1594	55	2	173	2	FRA10AC1	10	95436450	Splice_Site	SNP	T	TCGA-EP-A2KC-01A-11D-A20W-10	10938066	95436450	40098297	38	36166										
CYP2C8	1558	hgsc.bcm.edu	37	chr10	96802834	96802834	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	caatctcttcctggactttaGctgacaagacacaagaaaga	7	10	1	4			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr10:96802834G>C	ENST00000371270.3	-	7	1056	c.962C>G	c.(961-963)gCt>gGt	p.A321G	CYP2C8_ENST00000535898.1_Splice_Site_p.A219G|CYP2C8_ENST00000539050.1_Splice_Site_p.A235G	NM_000770.3|NM_001198853.1|NM_001198855.1	NP_000761.3|NP_001185782.1|NP_001185784.1	P10632	CP2C8_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 8	321					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|omega-hydroxylase P450 pathway (GO:0097267)|organic acid metabolic process (GO:0006082)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|caffeine oxidase activity (GO:0034875)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)			breast(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|skin(3)	21		Colorectal(252;0.0397)		all cancers(201;6.21e-05)	Abiraterone(DB05812)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Almotriptan(DB00918)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amprenavir(DB00701)|Antipyrine(DB01435)|Apixaban(DB06605)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bezafibrate(DB01393)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Buprenorphine(DB00921)|Bupropion(DB01156)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Candesartan(DB00796)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Cisapride(DB00604)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Colchicine(DB01394)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dapsone(DB00250)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Diltiazem(DB00343)|Domperidone(DB01184)|Eltrombopag(DB06210)|Enzalutamide(DB08899)|Erlotinib(DB00530)|Estradiol(DB00783)|Eszopiclone(DB00402)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Felodipine(DB01023)|Fenofibrate(DB01039)|Fluorouracil(DB00544)|Fluvastatin(DB01095)|Fosphenytoin(DB01320)|Gemfibrozil(DB01241)|Halofantrine(DB01218)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Ifosfamide(DB01181)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Liotrix(DB01583)|Loperamide(DB00836)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Medroxyprogesterone Acetate(DB00603)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Methadone(DB00333)|Metronidazole(DB00916)|Mirtazapine(DB00370)|Mometasone(DB00764)|Montelukast(DB00471)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Naloxone(DB01183)|Naproxen(DB00788)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Omeprazole(DB00338)|Oxybutynin(DB01062)|Paclitaxel(DB01229)|Paramethadione(DB00617)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Perphenazine(DB00850)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenprocoumon(DB00946)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Propafenone(DB01182)|Propofol(DB00818)|Pyrimethamine(DB00205)|Quinidine(DB00908)|Quinine(DB00468)|Raloxifene(DB00481)|Regorafenib(DB08896)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rifapentine(DB01201)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Salmeterol(DB00938)|Saquinavir(DB01232)|Secobarbital(DB00418)|Selegiline(DB01037)|Simvastatin(DB00641)|Sitagliptin(DB01261)|Sorafenib(DB00398)|Spironolactone(DB00421)|Sulfadiazine(DB00359)|Sulfamethoxazole(DB01015)|Sulfaphenazole(DB06729)|Sulfinpyrazone(DB01138)|Tamoxifen(DB00675)|Tazarotene(DB00799)|Temazepam(DB00231)|Terbinafine(DB00857)|Testosterone(DB00624)|Theophylline(DB00277)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tolbutamide(DB01124)|Torasemide(DB00214)|Trametinib(DB08911)|Tretinoin(DB00755)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Verapamil(DB00661)|Vismodegib(DB08828)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zidovudine(DB00495)|Zopiclone(DB01198)	CTGGACTTTAGCTGACAAGAC	0.433																																					p.A321G		Atlas-SNP	.											CYP2C8,NS,carcinoma,0,1	CYP2C8	73	.	0			c.C962G						.						134	110	118					10																	96802834		2203	4300	6503	SO:0001630	splice_region_variant	1558	exon7			ACTTTAGCTGACA	M17397	CCDS7438.1, CCDS55721.1, CCDS73166.1	10q24.1	2007-12-14	2003-01-14		ENSG00000138115	ENSG00000138115		"Cytochrome P450s"	2622	protein-coding gene	gene with protein product		601129	"cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 8"			7841444	Standard	NM_001198853		Approved	CPC8	uc001kkb.3	P10632	OTTHUMG00000018804	ENST00000371270.3:c.962-1C>G	chr10.hg19:g.96802834G>C		163.0	0.0		38.0	14.0	NM_000770	A8K9N8|B0AZN2|B7Z1F6|Q5VX93|Q8WWB1|Q9UCZ9	Missense_Mutation	SNP	ENST00000371270.3	hg19	CCDS7438.1	.	.	.	.	.	.	.	.	.	.	G	12.59	1.983095	0.34942	.	.	ENSG00000138115	ENST00000371270;ENST00000535868;ENST00000535898;ENST00000539050	T;T;T	0.13901	2.55;2.55;2.55	4.49	-1.05	0.10036	.	0.235594	0.33854	U	0.004496	T	0.09202	0.0227	L	0.46947	1.48	0.36495	D	0.868631	B;B;B;B	0.13594	0.001;0.003;0.008;0.004	B;B;B;B	0.15052	0.006;0.005;0.01;0.012	T	0.12993	-1.0526	10	0.59425	D	0.04	.	1.8674	0.03201	0.1746:0.1298:0.432:0.2636	.	235;219;289;321	F5H7Q9;B7Z1F6;B7Z8S1;P10632	.;.;.;CP2C8_HUMAN	G	321;288;219;235	ENSP00000360317:A321G;ENSP00000445062:A219G;ENSP00000442343:A235G	ENSP00000360317:A321G	A	-	2	0	CYP2C8	96792824	0.993000	0.37304	0.947000	0.38551	0.903000	0.53119	0.750000	0.26334	0.140000	0.18849	0.585000	0.79938	GCT	.	.		0.433	CYP2C8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049499.2	NM_000770	Missense_Mutation	C	96802834	G	C	96802834	5	2	256	1	0	0	0	0	0	0	1	0	4169	985	34	4	522	4	CYP2C8	10	96802834	Splice_Site	SNP	G	TCGA-EP-A2KC-01A-11D-A20W-10	1366384	96802834	38731913	39	36167										
OAT	4942	hgsc.bcm.edu	37	chr10	126092375	126092375	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	taacgtgacaacctggtgccTggtgcagagctctcgcactc	11	13	1	2			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr10:126092375T>A	ENST00000368845.5	-	6	855	c.763A>T	c.(763-765)Agg>Tgg	p.R255W	OAT_ENST00000467675.1_5'UTR|OAT_ENST00000539214.1_Missense_Mutation_p.R117W	NM_000274.3	NP_000265.1	P04181	OAT_HUMAN	ornithine aminotransferase	255					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-proline biosynthetic process (GO:0055129)|protein hexamerization (GO:0034214)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ornithine-oxo-acid transaminase activity (GO:0004587)|pyridoxal phosphate binding (GO:0030170)			endometrium(2)|large_intestine(1)|lung(2)	5		all_lung(145;0.0271)|Lung NSC(174;0.0436)|Colorectal(57;0.102)|all_neural(114;0.116)			L-Ornithine(DB00129)	ACCTGGTGCCTGGTGCAGAGC	0.512											OREG0020605	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R255W		Atlas-SNP	.											.	OAT	25	.	0			c.A763T						.						117	88	98					10																	126092375		2203	4300	6503	SO:0001583	missense	4942	exon6			GGTGCCTGGTGCA	BC016928	CCDS7639.1, CCDS53586.1	10q26	2014-09-17	2010-01-20		ENSG00000065154	ENSG00000065154	2.6.1.13		8091	protein-coding gene	gene with protein product	"Ornithine aminotransferase", "ornithine aminotransferase precursor", "gyrate atrophy"	613349				1682785	Standard	NM_000274		Approved	HOGA	uc001lhp.3	P04181	OTTHUMG00000019213	ENST00000368845.5:c.763A>T	chr10.hg19:g.126092375T>A	ENSP00000357838:p.Arg255Trp	152.0	0.0	1547	41.0	12.0	NM_000274	D3DRF0|Q16068|Q16069|Q68CS0|Q6IAV9|Q9UD03	Missense_Mutation	SNP	ENST00000368845.5	hg19	CCDS7639.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.575067	0.86542	.	.	ENSG00000065154	ENST00000539214;ENST00000368845	D;D	0.99060	-5.38;-5.38	4.82	-2.36	0.06663	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.382419	0.31963	N	0.006790	D	0.98648	0.9547	M	0.86953	2.85	0.37842	D	0.929079	P	0.50272	0.933	P	0.53006	0.715	D	0.98327	1.0531	10	0.87932	D	0	-9.3808	10.8424	0.46724	0.0:0.0703:0.3237:0.606	.	255	P04181	OAT_HUMAN	W	117;255	ENSP00000439042:R117W;ENSP00000357838:R255W	ENSP00000357838:R255W	R	-	1	2	OAT	126082365	0.993000	0.37304	0.967000	0.41034	0.996000	0.88848	1.347000	0.33975	-0.390000	0.07774	0.533000	0.62120	AGG	.	.		0.512	OAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050863.1	NM_000274		A	126092375	T	A	126092375	3	1	256	1	0	0	0	0	1	0	0	0	10812	1579	55	4	576	4	OAT	10	126092375	Missense_Mutation	SNP	T	TCGA-EP-A2KC-01A-11D-A20W-10	29289541	126092375	9442372	40	36168										
BRSK2	9024	hgsc.bcm.edu	37	chr11	1466531	1466531	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	cctgtgtccacagagggggcAagaatgagcccgaaccagag	14	11	0	4			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr11:1466531A>G	ENST00000528841.1	+	10	1204	c.820A>G	c.(820-822)Aag>Gag	p.K274E	BRSK2_ENST00000531197.1_Missense_Mutation_p.K274E|BRSK2_ENST00000526678.1_Missense_Mutation_p.K274E|BRSK2_ENST00000528710.1_Missense_Mutation_p.K214E|BRSK2_ENST00000382179.1_Missense_Mutation_p.K320E|BRSK2_ENST00000308219.9_Missense_Mutation_p.K274E|BRSK2_ENST00000308230.5_Missense_Mutation_p.K274E|BRSK2_ENST00000544817.1_5'UTR			Q8IWQ3	BRSK2_HUMAN	BR serine/threonine kinase 2	274					actin cytoskeleton reorganization (GO:0031532)|axonogenesis (GO:0007409)|establishment of cell polarity (GO:0030010)|exocytosis (GO:0006887)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mitotic nuclear division (GO:0007067)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			endometrium(4)|large_intestine(1)|lung(5)	10		all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00144)|Lung(200;0.0713)|LUSC - Lung squamous cell carcinoma(625;0.0842)		CAGAGGGGGCAAGAATGAGCC	0.692																																					p.K320E		Atlas-SNP	.											.	BRSK2	97	.	0			c.A958G						.						31	39	36					11																	1466531		2127	4227	6354	SO:0001583	missense	9024	exon10			GGGGGCAAGAATG	AF020089	CCDS41590.1, CCDS58106.1, CCDS58107.1, CCDS58108.1, CCDS60696.1	11p15.5	2008-02-05	2003-09-11	2005-01-27	ENSG00000174672	ENSG00000174672			11405	protein-coding gene	gene with protein product	"serine/threonine kinase 29"	609236	"chromsosome 11 open reading frame 7"	C11orf7, STK29		9852686, 9929968	Standard	NM_001256629		Approved	PEN11B	uc001ltm.4	Q8IWQ3	OTTHUMG00000167089	ENST00000528841.1:c.820A>G	chr11.hg19:g.1466531A>G	ENSP00000432000:p.Lys274Glu	137.0	0.0		33.0	19.0	NM_001256630	B3KVE9|E9PLM7|O60843|O95099|Q5J5B4|Q6ZMQ4|Q8TB60	Missense_Mutation	SNP	ENST00000528841.1	hg19	CCDS58107.1	.	.	.	.	.	.	.	.	.	.	A	13.69	2.312984	0.40895	.	.	ENSG00000174672	ENST00000308219;ENST00000531197;ENST00000308230;ENST00000528841;ENST00000526678;ENST00000528710;ENST00000382179	T;T;T;T;T;T;T	0.72942	-0.69;-0.69;-0.7;-0.7;-0.7;-0.51;-0.53	3.72	3.72	0.42706	Protein kinase-like domain (1);	0.058569	0.64402	U	0.000003	T	0.76097	0.3940	L	0.54323	1.7	0.80722	D	1	P;D;P;B;B	0.71674	0.913;0.998;0.913;0.354;0.138	P;P;P;B;B	0.60541	0.702;0.876;0.615;0.101;0.06	T	0.74312	-0.3706	10	0.31617	T	0.26	.	12.5717	0.56341	1.0:0.0:0.0:0.0	.	274;320;274;274;274	Q8IWQ3-4;Q8IWQ3-5;Q8IWQ3-3;Q8IWQ3;Q8IWQ3-2	.;.;.;BRSK2_HUMAN;.	E	274;274;274;274;274;214;320	ENSP00000310697:K274E;ENSP00000431152:K274E;ENSP00000310805:K274E;ENSP00000432000:K274E;ENSP00000433370:K274E;ENSP00000433235:K214E;ENSP00000371614:K320E	ENSP00000310697:K274E	K	+	1	0	BRSK2	1423107	1.000000	0.71417	1.000000	0.80357	0.046000	0.14306	5.442000	0.66575	1.569000	0.49696	0.260000	0.18958	AAG	.	.		0.692	BRSK2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393033.1	NM_003957		G	1466531	A	G	1466531	3	3	256	1	0	0	0	0	1	0	0	0	1526	131	5	2	858	2	BRSK2	11	1466531	Missense_Mutation	SNP	A	TCGA-EP-A2KC-01A-11D-A20W-10		1466531	133539985	41	36169										
ACCSL	390110	hgsc.bcm.edu	37	chr11	44072129	44072129	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	aaagtgacatgaactgcattGaggacaccttgcttcagtac	9	9	1	3			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr11:44072129G>T	ENST00000378832.1	+	3	648	c.592G>T	c.(592-594)Gag>Tag	p.E198*		NM_001031854.2	NP_001027025.2	Q4AC99	1A1L2_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)-like	198					biosynthetic process (GO:0009058)		catalytic activity (GO:0003824)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(14)|ovary(5)|pancreas(1)|skin(2)	34						GAACTGCATTGAGGACACCTT	0.468																																					p.E198X		Atlas-SNP	.											.	ACCSL	57	.	0			c.G592T						.						205	205	205					11																	44072129		1989	4179	6168	SO:0001587	stop_gained	390110	exon3			TGCATTGAGGACA		CCDS41636.1	11p11.2	2008-11-26			ENSG00000205126	ENSG00000205126			34391	protein-coding gene	gene with protein product							Standard	NM_001031854		Approved		uc001mxw.1	Q4AC99	OTTHUMG00000166426	ENST00000378832.1:c.592G>T	chr11.hg19:g.44072129G>T	ENSP00000368109:p.Glu198*	217.0	0.0		63.0	27.0	NM_001031854		Nonsense_Mutation	SNP	ENST00000378832.1	hg19	CCDS41636.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.881766	0.91740	.	.	ENSG00000205126	ENST00000378832	.	.	.	5.08	5.08	0.68730	.	0.456429	0.26220	N	0.025640	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	-3.6168	16.0109	0.80402	0.0:0.0:1.0:0.0	.	.	.	.	X	198	.	ENSP00000368109:E198X	E	+	1	0	ACCSL	44028705	1.000000	0.71417	0.067000	0.19924	0.003000	0.03518	5.434000	0.66526	2.642000	0.89623	0.655000	0.94253	GAG	.	.		0.468	ACCSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389717.1	NM_001031854		T	44072129	G	T	44072129	4	4	256	1	0	0	0	0	0	1	0	0	134	1291	45	3	602	3	ACCSL	11	44072129	Nonsense_Mutation	SNP	G	TCGA-EP-A2KC-01A-11D-A20W-10	42605598	44072129	90934387	42	36170										
TCN1	6947	hgsc.bcm.edu	37	chr11	59620709	59620709	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	ttcgcctccactcagaagttCccagtaggttctgtcattat	7	12	3	1			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr11:59620709C>A	ENST00000257264.3	-	8	1311	c.1207G>T	c.(1207-1209)Gaa>Taa	p.E403*	TCN1_ENST00000532419.1_5'Flank	NM_001062.3	NP_001053.2	P20061	TCO1_HUMAN	transcobalamin I (vitamin B12 binding protein, R binder family)	403	Cobalamin binding.|Globular C-terminal beta domain.				cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|cobalt ion transport (GO:0006824)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cobalamin binding (GO:0031419)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29		all_epithelial(135;0.198)			Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CTCAGAAGTTCCCAGTAGGTT	0.512																																					p.E403X		Atlas-SNP	.											.	TCN1	64	.	0			c.G1207T						.						202	196	198					11																	59620709		2201	4295	6496	SO:0001587	stop_gained	6947	exon8			GAAGTTCCCAGTA	J05068	CCDS7978.1	11q11-q12	2008-07-21			ENSG00000134827	ENSG00000134827			11652	protein-coding gene	gene with protein product	"haptocorin", "haptocorrin"	189905					Standard	NM_001062		Approved	TCI, TC1	uc001noj.2	P20061	OTTHUMG00000167400	ENST00000257264.3:c.1207G>T	chr11.hg19:g.59620709C>A	ENSP00000257264:p.Glu403*	198.0	0.0		70.0	8.0	NM_001062	A8KAC5|Q8WV77	Nonsense_Mutation	SNP	ENST00000257264.3	hg19	CCDS7978.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.804790	0.90623	.	.	ENSG00000134827	ENST00000257264	.	.	.	5.21	-3.96	0.04106	.	1.180030	0.06487	N	0.733900	.	.	.	.	.	.	0.54753	D	0.999989	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.7525	11.2238	0.48871	0.0:0.1833:0.6546:0.1622	.	.	.	.	X	403	.	ENSP00000257264:E403X	E	-	1	0	TCN1	59377285	0.915000	0.31059	0.279000	0.24732	0.856000	0.48823	-0.314000	0.08092	-0.622000	0.05626	-0.182000	0.12963	GAA	.	.		0.512	TCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394503.1	NM_001062		A	59620709	C	A	59620709	4	1	256	1	0	0	0	0	0	1	0	0	15721	864	30	3	102	3	TCN1	11	59620709	Nonsense_Mutation	SNP	C	TCGA-EP-A2KC-01A-11D-A20W-10	15548580	59620709	75385807	43	36171										
NXF1	10482	hgsc.bcm.edu	37	chr11	62560160	62560160	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	tctggtgtagtcccagttgtTgtcctgaaggcacctggagt	13	9	1	1			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr11:62560160T>A	ENST00000532297.1	-	21	2403	c.1774A>T	c.(1774-1776)Aac>Tac	p.N592Y	TMEM223_ENST00000307366.7_5'Flank|TMEM223_ENST00000525631.1_5'Flank|TMEM223_ENST00000527073.1_5'Flank|NXF1_ENST00000294172.2_Missense_Mutation_p.N592Y|NXF1_ENST00000533048.1_5'UTR|NXF1_ENST00000531709.2_3'UTR			Q9UBU9	NXF1_HUMAN	nuclear RNA export factor 1	592	TAP-C. {ECO:0000255|PROSITE- ProRule:PRU00611}.				gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|poly(A)+ mRNA export from nucleus (GO:0016973)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear inclusion body (GO:0042405)|nuclear pore (GO:0005643)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)	mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(9)|lung(13)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TCCCAGTTGTTGTCCTGAAGG	0.502																																					p.N592Y		Atlas-SNP	.											.	NXF1	67	.	0			c.A1774T						.						128	114	118					11																	62560160		2201	4299	6500	SO:0001583	missense	10482	exon20			AGTTGTTGTCCTG	AF112880	CCDS8037.1, CCDS44629.1	11q12-q13	2008-07-21			ENSG00000162231	ENSG00000162231			8071	protein-coding gene	gene with protein product	"tip associating protein"	602647				9175835, 9660949	Standard	NM_001081491		Approved	TAP, Mex67, DKFZp667O0311	uc001nvf.1	Q9UBU9	OTTHUMG00000167612	ENST00000532297.1:c.1774A>T	chr11.hg19:g.62560160T>A	ENSP00000436679:p.Asn592Tyr	177.0	0.0		53.0	16.0	NM_006362	B4E269|Q99799|Q9UQL2	Missense_Mutation	SNP	ENST00000532297.1	hg19	CCDS8037.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.396992	0.83120	.	.	ENSG00000162231	ENST00000294172;ENST00000532297	T;T	0.52983	0.64;0.64	5.06	5.06	0.68205	TAP, C-terminal (3);UBA-like (1);	0.000000	0.85682	D	0.000000	T	0.71022	0.3291	M	0.86953	2.85	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.74968	-0.3483	10	0.48119	T	0.1	-29.245	12.7796	0.57469	0.0:0.0:0.0:1.0	.	592	Q9UBU9	NXF1_HUMAN	Y	592	ENSP00000294172:N592Y;ENSP00000436679:N592Y	ENSP00000294172:N592Y	N	-	1	0	NXF1	62316736	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.355000	0.79434	1.921000	0.55644	0.374000	0.22700	AAC	.	.		0.502	NXF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395365.2	NM_006362		A	62560160	T	A	62560160	3	1	256	1	0	0	0	0	1	0	0	0	10791	1812	63	4	93	4	NXF1	11	62560160	Missense_Mutation	SNP	T	TCGA-EP-A2KC-01A-11D-A20W-10	2939451	62560160	72446356	44	36172										
OR8D2	283160	hgsc.bcm.edu	37	chr11	124189177	124189177	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	gtcaggatgactgccttcccCtagtcatcttcttcagtgca	8	13	5	1			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr11:124189177C>A	ENST00000357438.2	-	1	1007	c.917G>T	c.(916-918)aGg>aTg	p.R306M		NM_001002918.1	NP_001002918.1	Q9GZM6	OR8D2_HUMAN	olfactory receptor, family 8, subfamily D, member 2	306						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	25		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0525)		CTGCCTTCCCCTAGTCATCTT	0.398																																					p.R306M		Atlas-SNP	.											OR8D2,NS,carcinoma,+1,2	OR8D2	65	.	0			c.G917T						.						98	98	98					11																	124189177		2201	4299	6500	SO:0001583	missense	283160	exon1			CTTCCCCTAGTCA	AF162668	CCDS31707.1	11q24.1	2012-08-09			ENSG00000197263	ENSG00000197263		"GPCR / Class A : Olfactory receptors"	8482	protein-coding gene	gene with protein product							Standard	NM_001002918		Approved		uc010sah.2	Q9GZM6	OTTHUMG00000165978	ENST00000357438.2:c.917G>T	chr11.hg19:g.124189177C>A	ENSP00000350022:p.Arg306Met	70.0	0.0		34.0	9.0	NM_001002918	B9EH49|Q6IFR0	Missense_Mutation	SNP	ENST00000357438.2	hg19	CCDS31707.1	.	.	.	.	.	.	.	.	.	.	c	7.982	0.751422	0.15778	.	.	ENSG00000197263	ENST00000357438	T	0.39229	1.09	2.97	0.878	0.19150	.	0.323087	0.22065	N	0.065119	T	0.35278	0.0926	L	0.59967	1.855	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.31475	-0.9942	10	0.51188	T	0.08	.	8.5416	0.33395	0.6119:0.388:0.0:0.0	.	306	Q9GZM6	OR8D2_HUMAN	M	306	ENSP00000350022:R306M	ENSP00000350022:R306M	R	-	2	0	OR8D2	123694387	0.000000	0.05858	0.003000	0.11579	0.007000	0.05969	-0.222000	0.09190	0.247000	0.21414	0.590000	0.80494	AGG	.	.		0.398	OR8D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387286.1	NM_001002918		A	124189177	C	A	124189177	3	1	256	1	0	0	0	0	1	0	0	0	11241	681	24	3	21	3	OR8D2	11	124189177	Missense_Mutation	SNP	C	TCGA-EP-A2KC-01A-11D-A20W-10	61629017	124189177	10817339	45	36173										
FKBP11	51303	hgsc.bcm.edu	37	chr12	49317594	49317594	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	atggtggaaatccccgttttCcataggccaagtgagaagga	12	8	0	1			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr12:49317594C>T	ENST00000550765.1	-	5	757	c.359G>A	c.(358-360)gGa>gAa	p.G120E	CCDC65_ENST00000266984.5_Intron|AC073610.5_ENST00000537495.1_Intron|FKBP11_ENST00000453172.2_Missense_Mutation_p.G120E|FKBP11_ENST00000444214.2_Missense_Mutation_p.G18E|RP11-302B13.5_ENST00000398092.4_Intron|FKBP11_ENST00000552878.1_Missense_Mutation_p.G120E	NM_016594.2	NP_057678.1	Q9NYL4	FKB11_HUMAN	FK506 binding protein 11, 19 kDa	120	PPIase FKBP-type. {ECO:0000255|PROSITE- ProRule:PRU00277}.				chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			kidney(1)|large_intestine(3)|lung(1)	5						TCCCCGTTTTCCATAGGCCAA	0.507																																					p.G120E		Atlas-SNP	.											.	FKBP11	12	.	0			c.G359A						.						164	141	149					12																	49317594		2203	4300	6503	SO:0001583	missense	51303	exon5			CGTTTTCCATAGG	AF238079	CCDS8773.1, CCDS44870.1, CCDS44871.1	12q13.12	2008-08-04	2002-08-29			ENSG00000134285			18624	protein-coding gene	gene with protein product		610571	"FK506 binding protein 11 (19 kDa)"			12036304, 16596453	Standard	NM_016594		Approved	FKBP19	uc001rsp.3	Q9NYL4		ENST00000550765.1:c.359G>A	chr12.hg19:g.49317594C>T	ENSP00000449751:p.Gly120Glu	196.0	0.0		65.0	13.0	NM_016594	B4DWB7	Missense_Mutation	SNP	ENST00000550765.1	hg19	CCDS8773.1	.	.	.	.	.	.	.	.	.	.	C	18.23	3.577281	0.65878	.	.	ENSG00000134285	ENST00000444214;ENST00000550765;ENST00000552878;ENST00000453172	T;T;T;T	0.68479	-0.33;-0.33;-0.33;-0.33	5.16	5.16	0.70880	Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain (2);	0.000000	0.85682	D	0.000000	D	0.88959	0.6579	H	0.98155	4.16	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92981	0.6406	10	0.87932	D	0	-8.3201	17.8082	0.88608	0.0:1.0:0.0:0.0	.	120;120	B4DWB7;Q9NYL4	.;FKB11_HUMAN	E	18;120;120;120	ENSP00000412403:G18E;ENSP00000449751:G120E;ENSP00000447911:G120E;ENSP00000396874:G120E	ENSP00000412403:G18E	G	-	2	0	FKBP11	47603861	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.373000	0.73128	2.574000	0.86865	0.650000	0.86243	GGA	.	.		0.507	FKBP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408927.1	NM_016594		T	49317594	C	T	49317594	3	4	256	1	0	0	0	0	1	0	0	0	5911	855	30	3	311	3	FKBP11	12	49317594	Missense_Mutation	SNP	C	TCGA-EP-A2KC-01A-11D-A20W-10		49317594	84534301	46	36174										
TPH2	121278	hgsc.bcm.edu	37	chr12	72388234	72388234	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	gtcagagacacatgccatgaActcttgggacatgttccact	9	11	2	2			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr12:72388234A>G	ENST00000333850.3	+	8	1098	c.957A>G	c.(955-957)gaA>gaG	p.E319E		NM_173353.3	NP_775489.2	Q8IWU9	TPH2_HUMAN	tryptophan hydroxylase 2	319					aromatic amino acid family metabolic process (GO:0009072)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to lithium ion (GO:0071285)|circadian rhythm (GO:0007623)|indolalkylamine biosynthetic process (GO:0046219)|response to activity (GO:0014823)|response to calcium ion (GO:0051592)|response to estrogen (GO:0043627)|response to glucocorticoid (GO:0051384)|response to nutrient levels (GO:0031667)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|neuron projection (GO:0043005)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|tryptophan 5-monooxygenase activity (GO:0004510)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	41					L-Tryptophan(DB00150)	CATGCCATGAACTCTTGGGAC	0.393																																					p.E319E		Atlas-SNP	.											.	TPH2	81	.	0			c.A957G						.						156	152	153					12																	72388234		2203	4300	6503	SO:0001819	synonymous_variant	121278	exon8			CCATGAACTCTTG	AY098914	CCDS31859.1	12q15	2008-02-07				ENSG00000139287	1.14.16.4		20692	protein-coding gene	gene with protein product		607478				12511643	Standard	NM_173353		Approved	NTPH, FLJ37295	uc009zrw.1	Q8IWU9		ENST00000333850.3:c.957A>G	chr12.hg19:g.72388234A>G		142.0	0.0		41.0	13.0	NM_173353	A6NGA4|Q14CB0	Silent	SNP	ENST00000333850.3	hg19	CCDS31859.1																																																																																			.	.		0.393	TPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405234.1	NM_173353		G	72388234	A	G	72388234	2	3	256	1	0	0	0	0	0	0	0	1	16417	40	2	2		2	TPH2	12	72388234	Silent	SNP	A	TCGA-EP-A2KC-01A-11D-A20W-10	23070640	72388234	61463661	47	36175										
FBN1	2200	hgsc.bcm.edu	37	chr15	48802359	48802359	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	cggccattctgtaaacactcAtcaatgtctaaaatcaaagt	5	10	5	0			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr15:48802359A>C	ENST00000316623.5	-	14	2051	c.1596T>G	c.(1594-1596)gaT>gaG	p.D532E		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	532	EGF-like 8; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		GTAAACACTCATCAATGTCTA	0.383																																					p.D532E		Atlas-SNP	.											.	FBN1	310	.	0			c.T1596G						.						74	67	70					15																	48802359		2197	4296	6493	SO:0001583	missense	2200	exon14			ACACTCATCAATG	X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.1596T>G	chr15.hg19:g.48802359A>C	ENSP00000325527:p.Asp532Glu	167.0	0.0		52.0	21.0	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	hg19	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	A	16.39	3.110957	0.56398	.	.	ENSG00000166147	ENST00000316623	D	0.95307	-3.67	5.5	0.665	0.17896	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.97539	0.9194	H	0.96489	3.83	0.80722	D	1	D	0.63046	0.992	D	0.79108	0.992	D	0.96179	0.9129	10	0.87932	D	0	.	8.7594	0.34665	0.696:0.0:0.304:0.0	.	532	P35555	FBN1_HUMAN	E	532	ENSP00000325527:D532E	ENSP00000325527:D532E	D	-	3	2	FBN1	46589651	0.499000	0.26083	1.000000	0.80357	0.357000	0.29423	-0.007000	0.12810	0.137000	0.18759	-0.326000	0.08463	GAT	.	.		0.383	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			C	48802359	A	C	48802359	3	2	256	1	0	0	0	0	1	0	0	0	5710	214	8	5	7231	5	FBN1	15	48802359	Missense_Mutation	SNP	A	TCGA-EP-A2KC-01A-11D-A20W-10		48802359	53729033	48	36176										
RPS2	6187	hgsc.bcm.edu	37	chr16	2013233	2013233	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	atccttgagagaggcccccaGgaagaaatcaatgatctctg	10	10	2	4	rs377086871		TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr16:2013233G>A	ENST00000343262.4	-	4	348	c.292C>T	c.(292-294)Ctg>Ttg	p.L98L	RPS2_ENST00000530225.1_Silent_p.L98L|RPS2_ENST00000529806.1_Silent_p.L68L|RPS2_ENST00000526522.1_Silent_p.L98L|SNHG9_ENST00000459373.1_lincRNA|SNORA64_ENST00000384674.1_RNA|SNORA10_ENST00000384084.1_RNA	NM_002952.3	NP_002943.2	P15880	RS2_HUMAN	ribosomal protein S2	98					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of transferase activity (GO:0051347)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|urinary_tract(2)	7						GAGGCCCCCAGGAAGAAATCA	0.448													G|||	1	0.000199681	8e-04	0	5008	,	,		18340	0		0	False		,,,				2504	0				p.L98L		Atlas-SNP	.											.	RPS2	18	.	0			c.C292T						.	G		2,4360		0,2,2179	8	8	8		292	-2.3	0.9	16		8	0,8546		0,0,4273	no	coding-synonymous	RPS2	NM_002952.3		0,2,6452	AA,AG,GG		0.0,0.0459,0.0155		98/294	2013233	2,12906	2181	4273	6454	SO:0001819	synonymous_variant	6187	exon4			CCCCCAGGAAGAA	AB007147	CCDS10452.1	16p13.3	2011-04-05			ENSG00000140988	ENSG00000140988		"S ribosomal proteins"	10404	protein-coding gene	gene with protein product		603624				9582194	Standard	NM_002952		Approved	LLREP3, S2	uc002cno.2	P15880	OTTHUMG00000128708	ENST00000343262.4:c.292C>T	chr16.hg19:g.2013233G>A		129.0	0.0		34.0	14.0	NM_002952	B2R5G0|D3DU82|Q3MIB1	Silent	SNP	ENST00000343262.4	hg19	CCDS10452.1																																																																																			.	.		0.448	RPS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250613.2	NM_002952		A	2013233	G	A	2013233	2	1	256	1	0	0	0	0	0	0	0	1	13646	991	35	3		3	RPS2	16	2013233	Silent	SNP	G	TCGA-EP-A2KC-01A-11D-A20W-10		2013233	88341520	49	36177										
SPAG5	10615	hgsc.bcm.edu	37	chr17	26912926	26912926	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	ttcctctctgtgccttgcctCctccctttctgctttgaggc	7	16	2	1			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr17:26912926C>A	ENST00000321765.5	-	7	2028	c.1696G>T	c.(1696-1698)Gag>Tag	p.E566*		NM_006461.3	NP_006452.3	Q96R06	SPAG5_HUMAN	sperm associated antigen 5	566	Interaction with KNSTRN.				chromosome segregation (GO:0007059)|mitotic sister chromatid segregation (GO:0000070)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|microtubule plus-end (GO:0035371)|mitotic spindle (GO:0072686)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43	Lung NSC(42;0.00431)					TGCCTTGCCTCCTCCCTTTCT	0.498																																					p.E566X		Atlas-SNP	.											.	SPAG5	92	.	0			c.G1696T						.						225	197	207					17																	26912926		2203	4300	6503	SO:0001587	stop_gained	10615	exon7			TTGCCTCCTCCCT	AF063308	CCDS32594.1	17q11.2	2008-07-18			ENSG00000076382	ENSG00000076382			13452	protein-coding gene	gene with protein product	"mitotic spindle coiled-coil related protein", "astrin", "mitotic spindle associated protein p126"	615562				11549262	Standard	NM_006461		Approved	DEEPEST, MAP126, hMAP126	uc002hbq.3	Q96R06	OTTHUMG00000166586	ENST00000321765.5:c.1696G>T	chr17.hg19:g.26912926C>A	ENSP00000323300:p.Glu566*	206.0	0.0		71.0	19.0	NM_006461	O95213|Q9BWE8|Q9NT17|Q9UFE6	Nonsense_Mutation	SNP	ENST00000321765.5	hg19	CCDS32594.1	.	.	.	.	.	.	.	.	.	.	C	41	8.745863	0.98937	.	.	ENSG00000076382	ENST00000321765;ENST00000536674	.	.	.	5.79	3.63	0.41609	.	0.205973	0.34178	N	0.004186	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	-6.2652	11.993	0.53186	0.0:0.6638:0.3362:0.0	.	.	.	.	X	566;63	.	ENSP00000323300:E566X	E	-	1	0	SPAG5	23937053	1.000000	0.71417	0.910000	0.35882	0.997000	0.91878	1.684000	0.37649	1.399000	0.46721	0.655000	0.94253	GAG	.	.		0.498	SPAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390564.2	NM_006461		A	26912926	C	A	26912926	4	1	256	1	0	0	0	0	0	1	0	0	14996	864	30	3	1957	3	SPAG5	17	26912926	Nonsense_Mutation	SNP	C	TCGA-EP-A2KC-01A-11D-A20W-10		26912926	54282284	50	36178										
EVI2B	2124	hgsc.bcm.edu	37	chr17	29632211	29632211	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	aaagtatagacaaatgacttTggtggttgtgtggtagaagt	13	2	0	3			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr17:29632211T>C	ENST00000330927.4	-	2	571	c.417A>G	c.(415-417)ccA>ccG	p.P139P	EVI2B_ENST00000544462.1_Silent_p.P154P|NF1_ENST00000358273.4_Intron|NF1_ENST00000356175.3_Intron|EVI2B_ENST00000577894.1_Silent_p.P139P	NM_006495.3	NP_006486.3	P34910	EVI2B_HUMAN	ecotropic viral integration site 2B	139						integral component of plasma membrane (GO:0005887)		p.0?(8)|p.?(3)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|urinary_tract(1)	12		all_cancers(10;6.97e-11)|all_epithelial(10;0.0051)|all_hematologic(16;0.0149)|Breast(31;0.0155)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|all_lung(9;0.0468)|Lung NSC(157;0.094)		UCEC - Uterine corpus endometrioid carcinoma (4;6.64e-05)|all cancers(4;6.88e-13)|Epithelial(4;8.95e-12)|OV - Ovarian serous cystadenocarcinoma(4;1.01e-11)|GBM - Glioblastoma multiforme(4;0.184)		CAAATGACTTTGGTGGTTGTG	0.438																																					p.P139P		Atlas-SNP	.											.	EVI2B	33	.	11	Whole gene deletion(8)|Unknown(3)	soft_tissue(7)|autonomic_ganglia(2)|lung(1)|central_nervous_system(1)	c.A417G						.						418	347	371					17																	29632211		2203	4300	6503	SO:0001819	synonymous_variant	2124	exon2			TGACTTTGGTGGT		CCDS11266.1	17q11.2	2011-08-11			ENSG00000185862	ENSG00000185862		"CD molecules"	3500	protein-coding gene	gene with protein product		158381				1903357	Standard	NM_006495		Approved	D17S376, EVDB, CD361	uc002hgk.2	P34910	OTTHUMG00000132869	ENST00000330927.4:c.417A>G	chr17.hg19:g.29632211T>C		617.0	0.0		292.0	23.0	NM_006495	B7Z4A7	Silent	SNP	ENST00000330927.4	hg19	CCDS11266.1																																																																																			.	.		0.438	EVI2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256349.2	NM_006495		C	29632211	T	C	29632211	2	2	256	1	0	0	0	0	0	0	0	1	5290	1799	63	2		2	EVI2B	17	29632211	Silent	SNP	T	TCGA-EP-A2KC-01A-11D-A20W-10	2719285	29632211	51562999	51	36179										
AANAT	15	hgsc.bcm.edu	37	chr17	74465363	74465363	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	gttcgaggagggctgccttgTggccttcatcatcggctcgc	14	12	2	0			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr17:74465363T>A	ENST00000392492.3	+	3	506	c.272T>A	c.(271-273)gTg>gAg	p.V91E	AANAT_ENST00000250615.3_Missense_Mutation_p.V136E	NM_001088.2	NP_001079.1	Q16613	SNAT_HUMAN	aralkylamine N-acetyltransferase	91	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|circadian rhythm (GO:0007623)|indolalkylamine biosynthetic process (GO:0046219)|melatonin biosynthetic process (GO:0030187)|N-terminal protein amino acid acetylation (GO:0006474)|response to calcium ion (GO:0051592)|response to copper ion (GO:0046688)|response to corticosterone (GO:0051412)|response to cytokine (GO:0034097)|response to insulin (GO:0032868)|response to light stimulus (GO:0009416)|response to prostaglandin E (GO:0034695)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)	aralkylamine N-acetyltransferase activity (GO:0004059)|arylamine N-acetyltransferase activity (GO:0004060)			lung(1)	1						GGCTGCCTTGTGGCCTTCATC	0.627																																					p.V136E		Atlas-SNP	.											.	AANAT	7	.	0			c.T407A						.						133	134	134					17																	74465363		2203	4300	6503	SO:0001583	missense	15	exon6			GCCTTGTGGCCTT	U40347	CCDS11745.1, CCDS54169.1	17q25.1	2013-10-15	2010-05-07		ENSG00000129673	ENSG00000129673	2.3.1.87		19	protein-coding gene	gene with protein product	"serotonin N-acetyltransferase"	600950	"arylalkylamine N-acetyltransferase"			8661026	Standard	NM_001088		Approved	SNAT	uc002jro.3	Q16613	OTTHUMG00000180179	ENST00000392492.3:c.272T>A	chr17.hg19:g.74465363T>A	ENSP00000376282:p.Val91Glu	133.0	0.0		50.0	19.0	NM_001166579	A0AVF2|J3KMZ5|Q562F4	Missense_Mutation	SNP	ENST00000392492.3	hg19	CCDS11745.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.293262	0.80914	.	.	ENSG00000129673	ENST00000250615;ENST00000392492	T;T	0.32023	1.47;1.47	4.98	3.9	0.45041	GCN5-related N-acetyltransferase (GNAT) domain (2);Acyl-CoA N-acyltransferase (2);	0.056648	0.64402	D	0.000001	T	0.58609	0.2134	M	0.88450	2.955	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	T	0.63395	-0.6647	10	0.87932	D	0	-13.3083	10.3711	0.44055	0.0:0.0777:0.0:0.9223	.	91	Q16613	SNAT_HUMAN	E	136;91	ENSP00000250615:V136E;ENSP00000376282:V91E	ENSP00000250615:V136E	V	+	2	0	AANAT	71976958	1.000000	0.71417	0.867000	0.34043	0.868000	0.49771	4.741000	0.62095	0.755000	0.32990	0.379000	0.24179	GTG	.	.		0.627	AANAT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450130.1	NM_001088		A	74465363	T	A	74465363	3	1	256	1	0	0	0	0	1	0	0	0	18	1696	59	4	417	4	AANAT	17	74465363	Missense_Mutation	SNP	T	TCGA-EP-A2KC-01A-11D-A20W-10	44833152	74465363	6729847	52	36180										
RNF213	57674	hgsc.bcm.edu	37	chr17	78328357	78328357	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	cctgcaaccaggacgctctcCaggaggcgggcacattcagg	13	14	2	0			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr17:78328357C>A	ENST00000582970.1	+	36	10986	c.10843C>A	c.(10843-10845)Cag>Aag	p.Q3615K	CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000508628.2_Missense_Mutation_p.Q3664K|RNF213_ENST00000336301.6_Missense_Mutation_p.Q1688K|CTD-2047H16.4_ENST00000572151.1_RNA	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	3615					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			GGACGCTCTCCAGGAGGCGGG	0.552																																					p.Q3615K		Atlas-SNP	.											.	RNF213	766	.	0			c.C10843A						.						52	49	50					17																	78328357		2203	4300	6503	SO:0001583	missense	57674	exon36			GCTCTCCAGGAGG	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.10843C>A	chr17.hg19:g.78328357C>A	ENSP00000464087:p.Gln3615Lys	73.0	0.0		41.0	9.0	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	hg19	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	C	14.13	2.442249	0.43326	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301	T	0.27402	1.67	4.93	4.93	0.64822	.	0.061356	0.64402	D	0.000002	T	0.60676	0.2287	M	0.82323	2.585	0.40522	D	0.980849	D;D	0.89917	1.0;0.998	D;P	0.87578	0.998;0.872	T	0.67795	-0.5578	10	0.59425	D	0.04	.	18.1568	0.89694	0.0:1.0:0.0:0.0	.	3664;1688	C9JCP4;Q63HN8	.;RN213_HUMAN	K	3615;3664;1688	ENSP00000338218:Q1688K	ENSP00000338218:Q1688K	Q	+	1	0	RNF213	75942952	1.000000	0.71417	0.933000	0.37362	0.689000	0.40095	6.771000	0.74996	2.288000	0.76882	0.650000	0.86243	CAG	.	.		0.552	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		A	78328357	C	A	78328357	3	1	256	1	0	0	0	0	1	0	0	0	13492	595	21	3	11300	3	RNF213	17	78328357	Missense_Mutation	SNP	C	TCGA-EP-A2KC-01A-11D-A20W-10	3862994	78328357	2866853	53	36181										
LAMA1	284217	hgsc.bcm.edu	37	chr18	7017348	7017348	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	cccggtctcaagatggcacaCggcagaatgggagcctttca	12	12	2	2			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr18:7017348C>A	ENST00000389658.3	-	20	2830	c.2737G>T	c.(2737-2739)Gtg>Ttg	p.V913L		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	913	Laminin EGF-like 9. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				AGATGGCACACGGCAGAATGG	0.478																																					p.V913L		Atlas-SNP	.											.	LAMA1	458	.	0			c.G2737T						.						159	122	134					18																	7017348		2203	4300	6503	SO:0001583	missense	284217	exon20			GGCACACGGCAGA	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.2737G>T	chr18.hg19:g.7017348C>A	ENSP00000374309:p.Val913Leu	91.0	0.0		21.0	11.0	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	hg19	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	C	7.105	0.574830	0.13623	.	.	ENSG00000101680	ENST00000389658	T	0.61392	0.11	5.5	-0.263	0.12954	EGF-like, laminin (3);	0.569558	0.17079	N	0.187875	T	0.39064	0.1064	L	0.38531	1.155	0.09310	N	1	B	0.17465	0.022	B	0.20577	0.03	T	0.19095	-1.0316	10	0.18276	T	0.48	.	5.8486	0.18679	0.0:0.3242:0.1401:0.5357	.	913	P25391	LAMA1_HUMAN	L	913	ENSP00000374309:V913L	ENSP00000374309:V913L	V	-	1	0	LAMA1	7007348	0.000000	0.05858	0.065000	0.19835	0.225000	0.24961	-0.794000	0.04584	0.023000	0.15187	-0.158000	0.13435	GTG	.	.		0.478	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		A	7017348	C	A	7017348	3	1	256	1	0	0	0	0	1	0	0	0	8614	536	19	1	6666	1	LAMA1	18	7017348	Missense_Mutation	SNP	C	TCGA-EP-A2KC-01A-11D-A20W-10		7017348	71059900	54	36182										
PSG1	5669	hgsc.bcm.edu	37	chr19	43382065	43382065	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	gatcatgtggaatcacttacGgtgtaaggtgaaggtgaaac	13	5	2	2	rs545006367		TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr19:43382065G>A	ENST00000436291.2	-	2	546	c.430C>T	c.(430-432)Ctg>Ttg	p.L144L	PSG1_ENST00000244296.2_Splice_Site_p.L144L|PSG1_ENST00000601073.1_5'UTR|PSG1_ENST00000595124.1_Splice_Site_p.P144S|PSG1_ENST00000403380.3_Splice_Site_p.P144S|PSG1_ENST00000312439.6_Splice_Site_p.L144L|PSG1_ENST00000595356.1_Splice_Site_p.L144L	NM_001184825.1|NM_001184826.1	NP_001171754.1|NP_001171755.1	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	144	Ig-like V-type.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30		Prostate(69;0.00682)				AATCACTTACGGTGTAAGGTG	0.522													.|||	1	0.000199681	0	0	5008	,	,		19792	0		0	False		,,,				2504	0.001				p.L144L		Atlas-SNP	.											.	PSG1	196	.	0			c.C430T						.						278	246	257					19																	43382065		2201	4299	6500	SO:0001630	splice_region_variant	5669	exon2			ACTTACGGTGTAA		CCDS12612.1, CCDS54275.1, CCDS59392.1, CCDS74380.1	19q13.2	2013-01-29			ENSG00000231924	ENSG00000231924		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9514	protein-coding gene	gene with protein product		176390		PSBG1			Standard	NM_006905		Approved	PSGGA, CD66f, PBG1		P11464	OTTHUMG00000151123	ENST00000436291.2:c.430+1C>T	chr19.hg19:g.43382065G>A		182.0	0.0		46.0	10.0	NM_001184826	O75236|P11462|P11463|Q15231|Q15241|Q15243|Q16660|Q6ICR4|Q9P1W5|Q9UQ79	Silent	SNP	ENST00000436291.2	hg19	CCDS54275.1	.	.	.	.	.	.	.	.	.	.	N	1.997	-0.430475	0.04669	.	.	ENSG00000231924	ENST00000403380	T	0.00808	5.67	1.64	-3.28	0.05033	.	.	.	.	.	T	0.00608	0.0020	.	.	.	0.80722	D	1	B;B	0.09022	0.002;0.0	B;B	0.11329	0.006;0.004	T	0.51608	-0.8684	7	.	.	.	.	4.5493	0.12105	0.1581:0.4279:0.414:0.0	.	144;144	G5E9F7;Q8NBY8	.;.	S	144	ENSP00000385386:P144S	.	P	-	1	0	PSG1	48073905	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	-0.768000	0.04715	-0.682000	0.05197	-2.968000	0.00081	CCG	.	.		0.522	PSG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321426.1		Silent	A	43382065	G	A	43382065	5	1	256	1	0	0	0	0	0	0	1	0	12665	1130	39	1	902	1	PSG1	19	43382065	Splice_Site	SNP	G	TCGA-EP-A2KC-01A-11D-A20W-10		43382065	15746918	55	36183										
ZNF667	63934	hgsc.bcm.edu	37	chr19	56952618	56952618	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	ccacatttactacattcataGggtttctctgaagaatgact	6	9	2	3			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr19:56952618G>A	ENST00000504904.3	-	7	2465	c.1746C>T	c.(1744-1746)ccC>ccT	p.P582P	ZNF667_ENST00000292069.6_Silent_p.P582P|ZNF667_ENST00000591790.1_3'UTR|ZNF667_ENST00000342634.3_Silent_p.P710P			Q5HYK9	ZN667_HUMAN	zinc finger protein 667	582					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	38		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0615)		TACATTCATAGGGTTTCTCTG	0.393																																					p.P582P		Atlas-SNP	.											.	ZNF667	95	.	0			c.C1746T						.						119	115	116					19																	56952618		2203	4300	6503	SO:0001819	synonymous_variant	63934	exon5			TTCATAGGGTTTC		CCDS12944.1	19q13.43	2013-01-08				ENSG00000198046		"Zinc fingers, C2H2-type", "-"	28854	protein-coding gene	gene with protein product		611024					Standard	NM_022103		Approved	FLJ14011	uc002qnd.3	Q5HYK9		ENST00000504904.3:c.1746C>T	chr19.hg19:g.56952618G>A		95.0	0.0		29.0	11.0	NM_022103	B2RMS6|B9EK36|Q6B093|Q9H807	Silent	SNP	ENST00000504904.3	hg19	CCDS12944.1																																																																																			.	.		0.393	ZNF667-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458394.1	NM_022103		A	56952618	G	A	56952618	2	1	256	1	0	0	0	0	0	0	0	1	18089	987	35	3		3	ZNF667	19	56952618	Silent	SNP	G	TCGA-EP-A2KC-01A-11D-A20W-10	13570553	56952618	2176365	56	36184										
FAM113A	64773	hgsc.bcm.edu	37	chr20	2819099	2819099	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	tcccttcaaccacatcccgcCgcagggagcctgccaggggc	11	18	1	0			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr20:2819099C>A	ENST00000360652.2	-	6	1122	c.620G>T	c.(619-621)cGg>cTg	p.R207L	VPS16_ENST00000380445.3_5'Flank|VPS16_ENST00000380469.3_5'Flank|PCED1A_ENST00000356872.3_Missense_Mutation_p.R156L	NM_022760.4	NP_073597.2	Q9H1Q7	PED1A_HUMAN	PC-esterase domain containing 1A	207																	CACATCCCGCCGCAGGGAGCC	0.572																																					p.R207L		Atlas-SNP	.											.	.	.	.	0			c.G620T						.						57	61	59					20																	2819099		2203	4300	6503	SO:0001583	missense	64773	exon6			TCCCGCCGCAGGG	AK026029	CCDS13035.1, CCDS59442.1	20p13	2012-06-11	2012-06-11	2012-06-11	ENSG00000132635	ENSG00000132635			16212	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 81", "family with sequence similarity 113, member A"	C20orf81, FAM113A		20056006	Standard	NM_022760		Approved	bA12M19.1, FLJ22376	uc002wgz.2	Q9H1Q7	OTTHUMG00000031716	ENST00000360652.2:c.620G>T	chr20.hg19:g.2819099C>A	ENSP00000353868:p.Arg207Leu	78.0	0.0		23.0	11.0	NM_022760	Q5JUA5|Q5JUA6|Q6PK19|Q86WF5|Q96CG7|Q9H1Q6|Q9H6D1	Missense_Mutation	SNP	ENST00000360652.2	hg19	CCDS13035.1	.	.	.	.	.	.	.	.	.	.	C	14.11	2.436922	0.43224	.	.	ENSG00000132635	ENST00000356872;ENST00000360652;ENST00000448755;ENST00000439542	T;T;T;T	0.16897	2.31;2.31;2.31;2.31	4.14	3.19	0.36642	Esterase, SGNH hydrolase-type (1);Esterase, SGNH hydrolase-type, subgroup (1);	0.075463	0.52532	D	0.000063	T	0.35278	0.0926	L	0.61387	1.9	0.58432	D	0.999995	D;D;D;D	0.89917	0.974;1.0;0.999;0.99	P;D;D;D	0.91635	0.643;0.999;0.997;0.909	T	0.08249	-1.0731	10	0.87932	D	0	-12.4744	9.7095	0.40236	0.0:0.896:0.0:0.104	.	156;203;54;207	Q9H1Q7-2;D3DVX4;B4DEI2;Q9H1Q7	.;.;.;F113A_HUMAN	L	156;207;156;207	ENSP00000349334:R156L;ENSP00000353868:R207L;ENSP00000388935:R156L;ENSP00000401711:R207L	ENSP00000349334:R156L	R	-	2	0	FAM113A	2767099	0.991000	0.36638	1.000000	0.80357	0.994000	0.84299	2.953000	0.49105	1.090000	0.41315	0.563000	0.77884	CGG	.	.		0.572	PCED1A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077676.2	NM_022760		A	2819099	C	A	2819099	3	1	256	1	0	0	0	0	1	0	0	0	5406	652	23	1	756	1	FAM113A	20	2819099	Missense_Mutation	SNP	C	TCGA-EP-A2KC-01A-11D-A20W-10		2819099	60206421	57	36185										
PAK7	57144	hgsc.bcm.edu	37	chr20	9546904	9546904	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	ctttgtggtacccagacgggTactggtgactgcttgaggaa	14	8	0	3			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr20:9546904T>A	ENST00000378429.3	-	6	1664	c.1118A>T	c.(1117-1119)tAc>tTc	p.Y373F	PAK7_ENST00000353224.5_Missense_Mutation_p.Y373F|PAK7_ENST00000378423.1_Missense_Mutation_p.Y373F	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	373	Linker.				apoptotic process (GO:0006915)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|learning (GO:0007612)|locomotory behavior (GO:0007626)|memory (GO:0007613)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(44)|ovary(2)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)	81			COAD - Colon adenocarcinoma(9;0.194)			CCCAGACGGGTACTGGTGACT	0.577																																					p.Y373F		Atlas-SNP	.											.	PAK7	194	.	0			c.A1118T						.						184	178	180					20																	9546904		2203	4300	6503	SO:0001583	missense	57144	exon5			GACGGGTACTGGT	AB033090	CCDS13107.1	20p12	2008-06-17	2008-06-17		ENSG00000101349	ENSG00000101349			15916	protein-coding gene	gene with protein product		608038	"p21(CDKN1A)-activated kinase 7"			11756552, 10574462	Standard	NM_020341		Approved	KIAA1264, PAK5	uc002wnk.2	Q9P286	OTTHUMG00000031857	ENST00000378429.3:c.1118A>T	chr20.hg19:g.9546904T>A	ENSP00000367686:p.Tyr373Phe	52.0	0.0		20.0	9.0	NM_177990	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Missense_Mutation	SNP	ENST00000378429.3	hg19	CCDS13107.1	.	.	.	.	.	.	.	.	.	.	T	10.92	1.485918	0.26686	.	.	ENSG00000101349	ENST00000378429;ENST00000353224;ENST00000378423;ENST00000439520	T;T;T	0.29142	1.58;1.58;1.58	5.94	4.81	0.61882	.	0.105803	0.64402	D	0.000002	T	0.37265	0.0997	L	0.43152	1.355	0.46203	D	0.99892	D;B	0.63880	0.993;0.0	P;B	0.52957	0.714;0.001	T	0.05099	-1.0906	9	.	.	.	.	13.154	0.59505	0.0:0.0:0.1335:0.8665	.	373;373	B0AZM9;Q9P286	.;PAK7_HUMAN	F	373;373;373;321	ENSP00000367686:Y373F;ENSP00000322957:Y373F;ENSP00000367679:Y373F	.	Y	-	2	0	PAK7	9494904	1.000000	0.71417	0.993000	0.49108	0.918000	0.54935	2.468000	0.45102	1.031000	0.39867	0.482000	0.46254	TAC	.	.		0.577	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1			A	9546904	T	A	9546904	3	1	256	1	0	0	0	0	1	0	0	0	11414	1638	57	4	1065	4	PAK7	20	9546904	Missense_Mutation	SNP	T	TCGA-EP-A2KC-01A-11D-A20W-10	6727805	9546904	53478616	58	36186										
SLC2A10	81031	hgsc.bcm.edu	37	chr20	45354541	45354541	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	agctaccctgaccgccatggGgctggtggaccgtgcaggcc	15	14	0	1			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr20:45354541G>A	ENST00000359271.2	+	2	1116	c.866G>A	c.(865-867)gGg>gAg	p.G289E		NM_030777.3	NP_110404.1	O95528	GTR10_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 10	289					glucose transport (GO:0015758)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sugar:proton symporter activity (GO:0005351)			central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|liver(2)|lung(13)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	34		Myeloproliferative disorder(115;0.0122)				ACCGCCATGGGGCTGGTGGAC	0.652																																					p.G289E		Atlas-SNP	.											.	SLC2A10	75	.	0			c.G866A						.						91	87	89					20																	45354541		2203	4300	6503	SO:0001583	missense	81031	exon2			CCATGGGGCTGGT	AL137188	CCDS13402.1	20q13.12	2013-05-22			ENSG00000197496	ENSG00000197496		"Solute carriers"	13444	protein-coding gene	gene with protein product		606145				11247674	Standard	NM_030777		Approved	GLUT10	uc002xsl.3	O95528	OTTHUMG00000032657	ENST00000359271.2:c.866G>A	chr20.hg19:g.45354541G>A	ENSP00000352216:p.Gly289Glu	118.0	0.0		25.0	12.0	NM_030777	A8K4J6|Q3MIX5|Q9H4I6	Missense_Mutation	SNP	ENST00000359271.2	hg19	CCDS13402.1	.	.	.	.	.	.	.	.	.	.	G	11.75	1.730922	0.30684	.	.	ENSG00000197496	ENST00000359271	T	0.74106	-0.81	5.76	3.8	0.43715	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);Sugar transporter, conserved site (1);	0.408064	0.28021	N	0.016918	T	0.70254	0.3203	M	0.67397	2.05	0.34626	D	0.719087	B	0.14012	0.009	B	0.17433	0.018	T	0.70633	-0.4818	10	0.33141	T	0.24	-11.7486	11.0217	0.47722	0.071:0.2991:0.6299:0.0	.	289	O95528	GTR10_HUMAN	E	289	ENSP00000352216:G289E	ENSP00000352216:G289E	G	+	2	0	SLC2A10	44787948	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	1.920000	0.40025	0.775000	0.33450	0.655000	0.94253	GGG	.	.		0.652	SLC2A10-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079578.2			A	45354541	G	A	45354541	3	1	256	1	0	0	0	0	1	0	0	0	14554	1232	43	3	872	3	SLC2A10	20	45354541	Missense_Mutation	SNP	G	TCGA-EP-A2KC-01A-11D-A20W-10	35807637	45354541	17670979	59	36187										
ZNF70	7621	hgsc.bcm.edu	37	chr22	24086004	24086004	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	tttctatagcttctccccagAatgaatcttctgatggcgaa	7	10	4	3			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chr22:24086004A>T	ENST00000341976.3	-	2	1784	c.1324T>A	c.(1324-1326)Tct>Act	p.S442T		NM_021916.2	NP_068735.1	Q9UC06	ZNF70_HUMAN	zinc finger protein 70	442					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|urinary_tract(1)	21						TTCTCCCCAGAATGAATCTTC	0.537																																					p.S442T		Atlas-SNP	.											.	ZNF70	49	.	0			c.T1324A						.						105	111	109					22																	24086004		2203	4300	6503	SO:0001583	missense	7621	exon2			CCCCAGAATGAAT	X60077	CCDS13812.1	22q11.23	2013-01-08	2006-05-12		ENSG00000187792	ENSG00000187792		"Zinc fingers, C2H2-type"	13140	protein-coding gene	gene with protein product		194544	"zinc finger protein 70 (Cos17)"			1639391	Standard	NM_021916		Approved	Cos17, MGC48959	uc002zxs.3	Q9UC06	OTTHUMG00000150739	ENST00000341976.3:c.1324T>A	chr22.hg19:g.24086004A>T	ENSP00000339314:p.Ser442Thr	166.0	0.0		40.0	23.0	NM_021916		Missense_Mutation	SNP	ENST00000341976.3	hg19	CCDS13812.1	.	.	.	.	.	.	.	.	.	.	A	0.018	-1.471305	0.01044	.	.	ENSG00000187792	ENST00000341976	T	0.07688	3.17	3.55	2.53	0.30540	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02193	0.0068	N	0.01529	-0.815	0.22142	N	0.999333	B	0.02656	0.0	B	0.01281	0.0	T	0.45731	-0.9241	9	0.02654	T	1	.	4.3065	0.10949	0.2421:0.6393:0.0:0.1186	.	442	Q9UC06	ZNF70_HUMAN	T	442	ENSP00000339314:S442T	ENSP00000339314:S442T	S	-	1	0	ZNF70	22416004	0.000000	0.05858	0.482000	0.27366	0.419000	0.31324	-1.198000	0.03035	1.068000	0.40764	-0.406000	0.06334	TCT	.	.		0.537	ZNF70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319881.1	NM_021916		T	24086004	A	T	24086004	3	4	256	1	0	0	0	0	1	0	0	0	18118	246	9	4	20	4	ZNF70	22	24086004	Missense_Mutation	SNP	A	TCGA-EP-A2KC-01A-11D-A20W-10		24086004	27218562	60	36188										
MID1IP1	58526	hgsc.bcm.edu	37	chrX	38664209	38664209	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	gcgcggccaccatgatgcaaAtctgcgacacctacaaccag	9	15	1	1			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chrX:38664209A>G	ENST00000336949.6	+	2	955	c.10A>G	c.(10-12)Atc>Gtc	p.I4V	MID1IP1-AS1_ENST00000436893.1_RNA|MID1IP1_ENST00000457894.1_Missense_Mutation_p.I4V|MID1IP1_ENST00000378474.3_Missense_Mutation_p.I4V	NM_021242.4	NP_067065.1	Q9NPA3	M1IP1_HUMAN	MID1 interacting protein 1	4					lipid metabolic process (GO:0006629)|negative regulation of microtubule depolymerization (GO:0007026)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of ligase activity (GO:0051351)|protein polymerization (GO:0051258)|regulation of lipid biosynthetic process (GO:0046890)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)				kidney(1)|large_intestine(3)|lung(2)|prostate(1)	7						CATGATGCAAATCTGCGACAC	0.617																																					p.I4V		Atlas-SNP	.											.	MID1IP1	12	.	0			c.A10G						.						102	71	81					X																	38664209		2202	4300	6502	SO:0001583	missense	58526	exon2			ATGCAAATCTGCG		CCDS14249.1	Xp11.4	2012-02-23	2012-02-23		ENSG00000165175	ENSG00000165175			20715	protein-coding gene	gene with protein product	"gastrulation specific G12 homolog (zebrafish)"		"MID1 interacting protein 1 (gastrulation specific G12-like (zebrafish))"				Standard	NM_001098790		Approved	STRAIT11499, FLJ10386, MIG12, THRSPL, G12-like	uc010ngz.3	Q9NPA3	OTTHUMG00000024092	ENST00000336949.6:c.10A>G	chrX.hg19:g.38664209A>G	ENSP00000338706:p.Ile4Val	183.0	0.0		49.0	39.0	NM_021242	D3DWB2	Missense_Mutation	SNP	ENST00000336949.6	hg19	CCDS14249.1	.	.	.	.	.	.	.	.	.	.	A	16.06	3.015428	0.54468	.	.	ENSG00000165175	ENST00000457894;ENST00000378474;ENST00000336949	.	.	.	4.57	3.4	0.38934	.	0.270105	0.31370	N	0.007779	T	0.40448	0.1117	L	0.34521	1.04	0.42072	D	0.991211	P	0.39094	0.659	B	0.38921	0.285	T	0.31696	-0.9934	9	0.72032	D	0.01	0.3579	8.5973	0.33723	0.9052:0.0:0.0948:0.0	.	4	Q9NPA3	M1IP1_HUMAN	V	4	.	ENSP00000338706:I4V	I	+	1	0	MID1IP1	38549153	1.000000	0.71417	0.996000	0.52242	0.992000	0.81027	2.989000	0.49393	0.608000	0.30000	0.430000	0.28490	ATC	.	.		0.617	MID1IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060655.1			G	38664209	A	G	38664209	3	3	256	1	0	0	0	0	1	0	0	0	9586	101	4	2	12	2	MID1IP1	23	38664209	Missense_Mutation	SNP	A	TCGA-EP-A2KC-01A-11D-A20W-10		38664209	116606351	61	36189										
RGAG1	57529	hgsc.bcm.edu	37	chrX	109695030	109695030	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	ccagtgagagcaacagcctcTggggtgatgtctgcaccacc	12	13	2	2			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chrX:109695030T>A	ENST00000465301.2	+	3	1431	c.1185T>A	c.(1183-1185)tcT>tcA	p.S395S	RGAG1_ENST00000540313.1_Silent_p.S395S	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	395										NS(1)|autonomic_ganglia(1)|breast(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	73						CAACAGCCTCTGGGGTGATGT	0.512																																					p.S395S		Atlas-SNP	.											.	RGAG1	168	.	0			c.T1185A						.						187	196	193					X																	109695030		2203	4300	6503	SO:0001819	synonymous_variant	57529	exon3			AGCCTCTGGGGTG	AY121804	CCDS14552.1	Xq23	2008-02-05			ENSG00000243978	ENSG00000243978			29245	protein-coding gene	gene with protein product						10718198, 15716091, 16093683	Standard	NM_020769		Approved	KIAA1318, Mart9, Mar9	uc004eor.2	Q8NET4	OTTHUMG00000022196	ENST00000465301.2:c.1185T>A	chrX.hg19:g.109695030T>A		57.0	0.0		17.0	12.0	NM_020769	Q9P2M8	Silent	SNP	ENST00000465301.2	hg19	CCDS14552.1																																																																																			.	.		0.512	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	NM_020769		A	109695030	T	A	109695030	2	1	256	1	0	0	0	0	0	0	0	1	13289	1567	55	4		4	RGAG1	23	109695030	Silent	SNP	T	TCGA-EP-A2KC-01A-11D-A20W-10	71030821	109695030	45575530	62	36190										
ZNF185	7739	hgsc.bcm.edu	37	chrX	152106689	152106689	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	3	1	0.977368421052632	3.25789473684211	0.723976608187134	1	1	0	cacagcagcccaggaggatgCaaaggcagacccaaaggggt	14	11	0	1			TCGA-EP-A2KC-01A-11D-A20W-10	TCGA-EP-A2KC-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0fa04a7-a506-4a22-b41f-ee8b13a9d83c	da91c6e7-c91e-4c80-bb15-8e0cd4881866	g.chrX:152106689C>T	ENST00000370268.4	+	15	1227	c.1190C>T	c.(1189-1191)gCa>gTa	p.A397V	ZNF185_ENST00000449285.2_Missense_Mutation_p.A398V|ZNF185_ENST00000324823.6_Missense_Mutation_p.A165V|ZNF185_ENST00000370270.2_Missense_Mutation_p.A429V|ZNF185_ENST00000539731.1_Missense_Mutation_p.A400V|ZNF185_ENST00000318529.8_Missense_Mutation_p.A176V|ZNF185_ENST00000318504.7_Missense_Mutation_p.A338V|ZNF185_ENST00000535861.1_Missense_Mutation_p.A429V			O15231	ZN185_HUMAN	zinc finger protein 185 (LIM domain)	397						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(3)	12	Acute lymphoblastic leukemia(192;6.56e-05)					CAGGAGGATGCAAAGGCAGAC	0.572																																					p.A429V		Atlas-SNP	.											.	ZNF185	92	.	0			c.C1286T						.						54	55	55					X																	152106689		2105	4186	6291	SO:0001583	missense	7739	exon16			AGGATGCAAAGGC	AK056517	CCDS48184.1, CCDS55528.1, CCDS55529.1, CCDS55530.1, CCDS55531.1, CCDS55532.1, CCDS69832.1	Xq28	2012-08-08			ENSG00000147394	ENSG00000147394		"Zinc fingers, C2H2-type"	12976	protein-coding gene	gene with protein product		300381				9268636	Standard	NM_001178106		Approved		uc011myg.2	O15231	OTTHUMG00000024187	ENST00000370268.4:c.1190C>T	chrX.hg19:g.152106689C>T	ENSP00000359291:p.Ala397Val	102.0	0.0		33.0	26.0	NM_001178106	A4FTV3|A6NME5|B4DLE9|B7Z771|B8K2L9|B8K2M0|B8K2M1|B8K2M2|E9PFR6|F5GXF7|F5GZL4|F8W8V7|H0Y4M8|O00345|Q8N1R8|Q9NSD2	Missense_Mutation	SNP	ENST00000370268.4	hg19	CCDS48184.1	.	.	.	.	.	.	.	.	.	.	C	4.286	0.052232	0.08291	.	.	ENSG00000147394	ENST00000535861;ENST00000539731;ENST00000449285;ENST00000318504;ENST00000535156;ENST00000324823;ENST00000433245;ENST00000370268;ENST00000318529;ENST00000370270;ENST00000436731	T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87	3.52	-4.25	0.03766	.	2.230900	0.02245	N	0.066102	T	0.25419	0.0618	L	0.40543	1.245	0.09310	N	1	B;B;B;B;B;B;B;B	0.17667	0.004;0.023;0.001;0.002;0.004;0.004;0.003;0.017	B;B;B;B;B;B;B;B	0.15484	0.004;0.013;0.002;0.004;0.004;0.004;0.007;0.005	T	0.24870	-1.0148	10	0.02654	T	1	4.8009	2.39	0.04376	0.1413:0.497:0.1392:0.2226	.	398;338;368;400;429;397;176;160	O15231-3;B8K2L9;B8K2M0;F5GZL4;F5GXF7;O15231;F8W8V7;O15231-2	.;.;.;.;.;ZN185_HUMAN;.;.	V	429;400;398;338;232;165;263;397;176;160;102	ENSP00000440847:A429V;ENSP00000444367:A400V;ENSP00000395228:A398V;ENSP00000312782:A338V;ENSP00000359291:A397V	ENSP00000312782:A338V	A	+	2	0	ZNF185	151857345	0.000000	0.05858	0.000000	0.03702	0.049000	0.14656	-1.805000	0.01737	-1.312000	0.02306	0.600000	0.82982	GCA	.	.		0.572	ZNF185-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000377480.1	NM_007150		T	152106689	C	T	152106689	3	4	256	1	0	0	0	0	1	0	0	0	17767	710	25	3	1366	3	ZNF185	23	152106689	Missense_Mutation	SNP	C	TCGA-EP-A2KC-01A-11D-A20W-10	42411659	152106689	3163871	63	36191										
PRDM16	63976	hgsc.bcm.edu	37	chr1	3322119	3322120	+	Frame_Shift_Ins	INS	-	-	C													0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	gcagcacgtgggcgctcgggINScccacgcctgccccgactgc					rs200562747		TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr1:3322119_3322120insC	ENST00000270722.5	+	8	1142_1143	c.1093_1094insC	c.(1093-1095)gccfs	p.A365fs	PRDM16_ENST00000378391.2_Frame_Shift_Ins_p.A365fs|PRDM16_ENST00000442529.2_Frame_Shift_Ins_p.A365fs|PRDM16_ENST00000511072.1_Frame_Shift_Ins_p.A366fs|PRDM16_ENST00000514189.1_Frame_Shift_Ins_p.A366fs|PRDM16_ENST00000441472.2_Frame_Shift_Ins_p.A365fs|PRDM16_ENST00000512462.1_3'UTR|PRDM16_ENST00000378398.3_Frame_Shift_Ins_p.A366fs			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	365					brown fat cell differentiation (GO:0050873)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurogenesis (GO:0022008)|palate development (GO:0060021)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular respiration (GO:0043457)|somatic stem cell maintenance (GO:0035019)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(3)	59	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		GGGCGCTCGGGCCCACGCCTGC	0.658			T	EVI1	"MDS, AML"																																p.A365fs		Atlas-INDEL	.		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	.	PRDM16	147	.	0			c.1093_1094insC						.																																			SO:0001589	frameshift_variant	63976	exon8			.	AF294278	CCDS41236.1, CCDS44048.1, CCDS41236.2, CCDS44048.2	1p36.23-p33	2013-01-08			ENSG00000142611	ENSG00000142611		"Zinc fingers, C2H2-type"	14000	protein-coding gene	gene with protein product	"MDS1/EVI1-like", "PR-domain zinc finger protein 16", "transcription factor MEL1"	605557				11050005	Standard	NM_199454		Approved	MEL1, PFM13, KIAA1675, MGC166915	uc001akf.3	Q9HAZ2	OTTHUMG00000000581	ENST00000270722.5:c.1096dupC	chr1.hg19:g.3322122_3322122dupC	ENSP00000270722:p.Ala365fs	39.0	0.0		84.0	11.0	NM_022114	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Frame_Shift_Ins	INS	ENST00000270722.5	hg19	CCDS41236.2																																																																																			.	.		0.658	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114		C	3322120	-	C	3322119	7	5	257	1	0	1	1	0	0	0	0	0	12469	1203	42	0	1123	0	PRDM16	1	3322119	Frame_Shift_Ins	INS	-	TCGA-EP-A3JL-01A-11D-A20W-10		3322119	245928502	1	36192										
CROCC	9696	hgsc.bcm.edu	37	chr1	17256975	17256975	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	ctccgagaacagctggaccaGgcaggctcggccaaccaggc	13	15	0	1			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr1:17256975G>T	ENST00000375541.5	+	7	804	c.735G>T	c.(733-735)caG>caT	p.Q245H	CROCC_ENST00000467938.1_3'UTR	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		AGCTGGACCAGGCAGGCTCGG	0.647																																					p.Q245H		Atlas-SNP	.											.	CROCC	185	.	0			c.G735T						.						41	36	38					1																	17256975		2199	4292	6491	SO:0001583	missense	9696	exon7			GGACCAGGCAGGC	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"rootletin, ciliary rootlet protein"	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.735G>T	chr1.hg19:g.17256975G>T	ENSP00000364691:p.Gln245His	150.0	0.0		123.0	25.0	NM_014675		Missense_Mutation	SNP	ENST00000375541.5	hg19	CCDS30616.1	.	.	.	.	.	.	.	.	.	.	G	13.45	2.239464	0.39598	.	.	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.12361	2.69	5.21	4.3	0.51218	.	.	.	.	.	T	0.22704	0.0548	L	0.38175	1.15	0.47341	D	0.999391	D;D	0.65815	0.974;0.995	P;P	0.60415	0.827;0.874	T	0.00773	-1.1572	9	0.49607	T	0.09	.	12.2477	0.54581	0.0837:0.0:0.9163:0.0	.	108;245	A1L0S8;Q5TZA2	.;CROCC_HUMAN	H	245;126	ENSP00000364691:Q245H	ENSP00000364691:Q245H	Q	+	3	2	CROCC	17129562	1.000000	0.71417	0.995000	0.50966	0.975000	0.68041	2.345000	0.44018	1.187000	0.43000	0.555000	0.69702	CAG	.	.		0.647	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675		T	17256975	G	T	17256975	3	4	257	1	0	0	0	0	1	0	0	0	3895	991	35	3	761	3	CROCC	1	17256975	Missense_Mutation	SNP	G	TCGA-EP-A3JL-01A-11D-A20W-10	13934856	17256975	231993646	2	36193										
SLC44A5	204962	hgsc.bcm.edu	37	chr1	75684996	75684996	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	tgcccccctggagctatgacTttgtatacaggtacccccga	9	14	0	1			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr1:75684996T>A	ENST00000370855.5	-	16	1325	c.1212A>T	c.(1210-1212)aaA>aaT	p.K404N	SLC44A5_ENST00000370859.3_Missense_Mutation_p.K404N|SLC44A5_ENST00000535611.1_Missense_Mutation_p.K274N	NM_152697.4	NP_689910.2	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5	404					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				kidney(1)|large_intestine(13)|lung(35)|ovary(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61						GAGCTATGACTTTGTATACAG	0.373																																					p.K404N		Atlas-SNP	.											.	SLC44A5	231	.	0			c.A1212T						.						104	96	99					1																	75684996		2203	4300	6503	SO:0001583	missense	204962	exon16			TATGACTTTGTAT	BC034580	CCDS667.1, CCDS44164.1	1p31.1	2013-05-22			ENSG00000137968	ENSG00000137968		"Solute carriers"	28524	protein-coding gene	gene with protein product						15715662	Standard	NM_152697		Approved	MGC34032, CTL5	uc001dgu.3	Q8NCS7	OTTHUMG00000009721	ENST00000370855.5:c.1212A>T	chr1.hg19:g.75684996T>A	ENSP00000359892:p.Lys404Asn	87.0	0.0		51.0	20.0	NM_152697	B5MCU3|Q4G0K0|Q8NA44|Q8NB86	Missense_Mutation	SNP	ENST00000370855.5	hg19	CCDS667.1	.	.	.	.	.	.	.	.	.	.	T	13.60	2.286165	0.40394	.	.	ENSG00000137968	ENST00000370859;ENST00000536707;ENST00000370855;ENST00000535611;ENST00000535790	T;T;T	0.23348	1.91;1.91;1.91	5.04	5.04	0.67666	.	0.149246	0.64402	D	0.000013	T	0.33990	0.0882	M	0.81614	2.55	0.58432	D	0.999997	P;B;P;P;P	0.48764	0.915;0.389;0.853;0.896;0.896	P;B;P;P;P	0.57720	0.826;0.285;0.826;0.726;0.802	T	0.25606	-1.0127	10	0.14252	T	0.57	-9.9512	15.0851	0.72145	0.0:0.0:0.0:1.0	.	398;443;404;404;443	B7Z5Y4;B7Z470;Q8NCS7;Q8NCS7-2;F5GYS0	.;.;CTL5_HUMAN;.;.	N	404;443;404;274;397	ENSP00000359896:K404N;ENSP00000359892:K404N;ENSP00000443090:K274N	ENSP00000359892:K404N	K	-	3	2	SLC44A5	75457584	1.000000	0.71417	0.503000	0.27626	0.043000	0.13939	4.298000	0.59067	2.025000	0.59659	0.533000	0.62120	AAA	.	.		0.373	SLC44A5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026921.1	NM_152697		A	75684996	T	A	75684996	3	1	257	1	0	0	0	0	1	0	0	0	14654	1606	56	4	1094	4	SLC44A5	1	75684996	Missense_Mutation	SNP	T	TCGA-EP-A3JL-01A-11D-A20W-10	58428021	75684996	173565625	3	36194										
CD2	914	hgsc.bcm.edu	37	chr1	117311336	117311336	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	cagaaaggcccgcccctcccCagacctcgagttcagccaaa	8	18	1	2			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr1:117311336C>A	ENST00000369478.3	+	5	1095	c.987C>A	c.(985-987)ccC>ccA	p.P329P		NM_001767.3	NP_001758.2	P06729	CD2_HUMAN	CD2 molecule	329	Pro-rich.				apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|heterotypic cell-cell adhesion (GO:0034113)|leukocyte migration (GO:0050900)|membrane raft polarization (GO:0001766)|natural killer cell activation (GO:0030101)|positive regulation of interferon-gamma secretion (GO:1902715)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of myeloid dendritic cell activation (GO:0030887)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of T cell differentiation (GO:0045580)|single organismal cell-cell adhesion (GO:0016337)|T cell activation (GO:0042110)	anchored component of plasma membrane (GO:0046658)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)			NS(1)|breast(2)|large_intestine(3)|liver(1)|lung(8)|skin(2)|stomach(1)	18	Lung SC(450;0.225)	all_cancers(81;3.15e-06)|Acute lymphoblastic leukemia(138;1.7e-08)|all_epithelial(167;8.38e-07)|all_lung(203;3.37e-06)|Lung NSC(69;2.31e-05)		Epithelial(280;6.71e-26)|OV - Ovarian serous cystadenocarcinoma(397;4.74e-24)|all cancers(265;1.93e-22)|Lung(183;0.0543)|Kidney(133;0.0813)|Colorectal(144;0.174)|KIRC - Kidney renal clear cell carcinoma(1967;0.176)|LUSC - Lung squamous cell carcinoma(189;0.189)|BRCA - Breast invasive adenocarcinoma(282;0.201)	Alefacept(DB00092)	CGCCCCTCCCCAGACCTCGAG	0.537																																					p.P329P	NSCLC(14;263 555 26380 43512 51332)	Atlas-SNP	.											.	CD2	43	.	0			c.C987A						.						74	82	79					1																	117311336		2203	4300	6503	SO:0001819	synonymous_variant	914	exon5			CCTCCCCAGACCT	BC033583	CCDS889.1	1p13	2013-01-11	2006-03-28		ENSG00000116824	ENSG00000116824		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing"	1639	protein-coding gene	gene with protein product		186990	"CD2 antigen (p50), sheep red blood cell receptor"	SRBC		2437578	Standard	NM_001767		Approved		uc001egu.4	P06729	OTTHUMG00000022750	ENST00000369478.3:c.987C>A	chr1.hg19:g.117311336C>A		148.0	0.0		109.0	35.0	NM_001767	Q96TE5	Silent	SNP	ENST00000369478.3	hg19	CCDS889.1																																																																																			.	.		0.537	CD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059039.2	NM_001767		A	117311336	C	A	117311336	2	1	257	1	0	0	0	0	0	0	0	1	2981	581	21	3		3	CD2	1	117311336	Silent	SNP	C	TCGA-EP-A3JL-01A-11D-A20W-10	41626340	117311336	131939285	4	36195										
SHC1	6464	hgsc.bcm.edu	37	chr1	154941042	154941042	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	agtgattggcattccagcaaAtttcaggttactcctcccca	7	12	1	1			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr1:154941042A>C	ENST00000368445.5	-	4	893	c.679T>G	c.(679-681)Ttt>Gtt	p.F227V	SHC1_ENST00000368450.1_Missense_Mutation_p.F117V|SHC1_ENST00000448116.2_Missense_Mutation_p.F227V|SHC1_ENST00000368453.4_Missense_Mutation_p.F117V|SHC1_ENST00000490667.1_5'Flank|SHC1_ENST00000606391.1_Missense_Mutation_p.F28V|SHC1_ENST00000368449.4_5'UTR	NM_183001.4	NP_892113.4	P29353	SHC1_HUMAN	SHC (Src homology 2 domain containing) transforming protein 1	227	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|Ras protein signal transduction (GO:0007265)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of growth (GO:0040008)|single organismal cell-cell adhesion (GO:0016337)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|Shc-EGFR complex (GO:0070435)	ephrin receptor binding (GO:0046875)|epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phospholipid binding (GO:0005543)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)			breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	20	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			ATTCCAGCAAATTTCAGGTTA	0.582																																					p.F227V	NSCLC(4;32 234 1864 2492 3259 13747 17376)	Atlas-SNP	.											.	SHC1	91	.	0			c.T679G						.						139	143	141					1																	154941042		2203	4300	6503	SO:0001583	missense	6464	exon4			CAGCAAATTTCAG	U73377	CCDS1076.1, CCDS30881.1, CCDS44233.1, CCDS44234.1	1q21	2013-02-14	2002-01-14		ENSG00000160691	ENSG00000160691		"SH2 domain containing"	10840	protein-coding gene	gene with protein product		600560	"SHC (Src homology 2 domain-containing) transforming protein 1"	SHC		1623525	Standard	NM_003029		Approved	p66	uc001ffw.3	P29353	OTTHUMG00000037295	ENST00000368445.5:c.679T>G	chr1.hg19:g.154941042A>C	ENSP00000357430:p.Phe227Val	156.0	0.0		146.0	64.0	NM_183001	B5BU19|D3DV78|O15290|Q5T180|Q5T183|Q5T184|Q5T185|Q5T186|Q8N4K5|Q96CL1	Missense_Mutation	SNP	ENST00000368445.5	hg19	CCDS30881.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.414936	0.83449	.	.	ENSG00000160691	ENST00000368445;ENST00000448116;ENST00000368449;ENST00000368453;ENST00000368450;ENST00000368443;ENST00000412170;ENST00000366442	T;T;T;T;T;T;T	0.19250	2.16;2.16;2.16;2.16;2.16;2.16;2.16	4.92	4.92	0.64577	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	T	0.35451	0.0932	M	0.71206	2.165	0.80722	D	1	D;D	0.58620	0.983;0.964	D;D	0.73708	0.981;0.973	T	0.10870	-1.0611	10	0.48119	T	0.1	.	14.7303	0.69377	1.0:0.0:0.0:0.0	.	227;227	P29353-6;P29353	.;SHC1_HUMAN	V	227;227;28;117;117;163;117;117	ENSP00000357430:F227V;ENSP00000401303:F227V;ENSP00000357434:F28V;ENSP00000357438:F117V;ENSP00000357435:F117V;ENSP00000398441:F117V;ENSP00000396162:F117V	ENSP00000396162:F117V	F	-	1	0	SHC1	153207666	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.761000	0.91691	2.066000	0.61787	0.383000	0.25322	TTT	.	.		0.582	SHC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090781.2	NM_183001		C	154941042	A	C	154941042	3	2	257	1	0	0	0	0	1	0	0	0	14285	101	4	5	1111	5	SHC1	1	154941042	Missense_Mutation	SNP	A	TCGA-EP-A3JL-01A-11D-A20W-10	37629706	154941042	94309579	5	36196										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158612680	158612680	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	tgatccattcttccagctccTcaaggtctcggtagaattgt	8	11	3	2			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr1:158612680T>C	ENST00000368147.4	-	32	4709	c.4529A>G	c.(4528-4530)gAg>gGg	p.E1510G		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1510					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TTCCAGCTCCTCAAGGTCTCG	0.478																																					p.E1510G		Atlas-SNP	.											.	SPTA1	720	.	0			c.A4529G						.						172	163	166					1																	158612680		1995	4166	6161	SO:0001583	missense	6708	exon32			AGCTCCTCAAGGT	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.4529A>G	chr1.hg19:g.158612680T>C	ENSP00000357129:p.Glu1510Gly	276.0	0.0		292.0	13.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.106445	0.77096	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.37584	1.19;1.19	5.2	5.2	0.72013	.	0.256644	0.20373	N	0.093604	T	0.31918	0.0812	M	0.62209	1.925	0.46654	D	0.99914	P	0.36599	0.56	B	0.42625	0.393	T	0.24799	-1.0150	10	0.66056	D	0.02	.	14.0466	0.64708	0.0:0.0:0.0:1.0	.	1510	P02549	SPTA1_HUMAN	G	1510	ENSP00000357130:E1510G;ENSP00000357129:E1510G	ENSP00000357129:E1510G	E	-	2	0	SPTA1	156879304	1.000000	0.71417	0.675000	0.29917	0.638000	0.38207	7.330000	0.79181	2.189000	0.69895	0.533000	0.62120	GAG	.	.		0.478	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		C	158612680	T	C	158612680	3	2	257	1	0	0	0	0	1	0	0	0	15131	1551	54	2	2814	2	SPTA1	1	158612680	Missense_Mutation	SNP	T	TCGA-EP-A3JL-01A-11D-A20W-10	3671638	158612680	90637941	6	36197										
PIGM	93183	hgsc.bcm.edu	37	chr1	160001525	160001525	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	cgccccagtgcttggtggagCccatgatctgaccgtgcgac	13	14	1	2			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr1:160001525C>G	ENST00000368090.2	-	1	258	c.5G>C	c.(4-6)gGc>gCc	p.G2A		NM_145167.2	NP_660150.1	Q9H3S5	PIGM_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class M	2					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	mannosyltransferase activity (GO:0000030)			kidney(1)|large_intestine(4)|lung(9)|ovary(2)|skin(1)	17	all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			CTTGGTGGAGCCCATGATCTG	0.582																																					p.G2A		Atlas-SNP	.											.	PIGM	27	.	0			c.G5C						.						42	48	45					1																	160001525		2203	4300	6503	SO:0001583	missense	93183	exon1			GTGGAGCCCATGA	AB028127	CCDS1192.1	1q23.2	2013-02-26	2006-06-28		ENSG00000143315	ENSG00000143315		"Dolichyl D-mannosyl phosphate dependent mannosyltransferases", "Phosphatidylinositol glycan anchor biosynthesis"	18858	protein-coding gene	gene with protein product	"GPI mannosyltransferase 1", "DPM:GlcN-(acyl-)PI mannosyltransferase", "dol-P-Man dependent GPI mannosyltransferase"	610273	"phosphatidylinositol glycan, class M"			11226175	Standard	NM_145167		Approved	GPI-MT-I	uc001fuv.1	Q9H3S5	OTTHUMG00000024081	ENST00000368090.2:c.5G>C	chr1.hg19:g.160001525C>G	ENSP00000357069:p.Gly2Ala	105.0	0.0		104.0	17.0	NM_145167		Missense_Mutation	SNP	ENST00000368090.2	hg19	CCDS1192.1	.	.	.	.	.	.	.	.	.	.	C	12.10	1.836149	0.32421	.	.	ENSG00000143315	ENST00000368090	T	0.39997	1.05	4.63	-4.04	0.04010	.	1.050460	0.07514	N	0.909476	T	0.04679	0.0127	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.27468	-1.0073	9	.	.	.	-4.1484	1.1246	0.01732	0.1368:0.2197:0.2694:0.3741	.	2	Q9H3S5	PIGM_HUMAN	A	2	ENSP00000357069:G2A	.	G	-	2	0	PIGM	158268149	0.000000	0.05858	0.001000	0.08648	0.345000	0.29048	-0.514000	0.06298	-1.179000	0.02737	0.561000	0.74099	GGC	.	.		0.582	PIGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060643.2	NM_145167		G	160001525	C	G	160001525	3	3	257	1	0	0	0	0	1	0	0	0	11901	739	26	4	1270	4	PIGM	1	160001525	Missense_Mutation	SNP	C	TCGA-EP-A3JL-01A-11D-A20W-10	1388845	160001525	89249096	7	36198										
PRG4	10216	hgsc.bcm.edu	37	chr1	186277360	186277383	+	In_Frame_Del	DEL	ACTACCCCCAAGAAGCCTGCTCCA	ACTACCCCCAAGAAGCCTGCTCCA	-													0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	cccccaaggagcctgcacccActacccccaagaagcctgct					rs148222256|rs146935964		TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	ACTACCCCCAAGAAGCCTGCTCCA	ACTACCCCCAAGAAGCCTGCTCCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr1:186277360_186277383delACTACCCCCAAGAAGCCTGCTCCA	ENST00000445192.2	+	7	2554_2577	c.2509_2532delACTACCCCCAAGAAGCCTGCTCCA	c.(2509-2532)actacccccaagaagcctgctccadel	p.TTPKKPAP837del	PRG4_ENST00000367483.4_In_Frame_Del_p.TTPKKPAP796del|PRG4_ENST00000367484.3_In_Frame_Del_p.TTPKKPAP366del|PRG4_ENST00000367486.3_In_Frame_Del_p.TTPKKPAP794del|PRG4_ENST00000367485.4_In_Frame_Del_p.TTPKKPAP744del	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	837	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)	p.P842P(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						GCCTGCACCCACTACCCCCAAGAAGCCTGCTCCAACTACTCCTG	0.558																																					p.836_844del		Pindel	.											.	PRG4	259	.	1	Substitution - coding silent(1)	lung(1)	c.2508_2531del						.																																			SO:0001651	inframe_deletion	10216	exon7			.	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"lubricin", "megakaryocyte stimulating factor", "articular superficial zone protein", "Jacobs camptodactyly-arthropathy-pericarditis syndrome", "camptodactyly, arthropathy, coxa vara, pericarditis syndrome", "bG174L6.2 (MSF: megakaryocyte stimulating factor )"	604283	"proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.2509_2532delACTACCCCCAAGAAGCCTGCTCCA	chr1.hg19:g.186277360_186277383delACTACCCCCAAGAAGCCTGCTCCA	ENSP00000399679:p.Thr837_Pro844del	272.0	0.0		262.0	16.0	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	In_Frame_Del	DEL	ENST00000445192.2	hg19	CCDS1369.1																																																																																			.	.		0.558	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807		-	186277383	ACTACCCCCAAGAAGCCTGCTCCA	-	186277360	7	5	257	1	0	1	0	1	0	0	0	0	12493	159	6	0	2531	0	PRG4	1	186277360	In_Frame_Del	DEL	ACTACCCCCAAGAAGCCTGCTCCA	TCGA-EP-A3JL-01A-11D-A20W-10	26275835	186277360	62973261	8	36199			1	47		3	2	24	N	T_ACTACCCCCAAGAAGCCTGCTCCA_A	5.943603e-05
PRG4	10216	hgsc.bcm.edu	37	chr1	186277380	186277380	+	Silent	SNP	T	T	A													0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	actacccccaagaagcctgcTccaactactcctgagacacc							TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr1:186277380T>A	ENST00000445192.2	+	7	2574	c.2529T>A	c.(2527-2529)gcT>gcA	p.A843A	PRG4_ENST00000367483.4_Silent_p.A802A|PRG4_ENST00000367484.3_Silent_p.A372A|PRG4_ENST00000367486.3_Silent_p.A800A|PRG4_ENST00000367485.4_Silent_p.A750A	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	843	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						AGAAGCCTGCTCCAACTACTC	0.542																																					p.A843A		Atlas-SNP	.											.	PRG4	259	.	0			c.T2529A						.						195	226	215					1																	186277380		2203	4300	6503	SO:0001819	synonymous_variant	10216	exon7			GCCTGCTCCAACT	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"lubricin", "megakaryocyte stimulating factor", "articular superficial zone protein", "Jacobs camptodactyly-arthropathy-pericarditis syndrome", "camptodactyly, arthropathy, coxa vara, pericarditis syndrome", "bG174L6.2 (MSF: megakaryocyte stimulating factor )"	604283	"proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.2529T>A	chr1.hg19:g.186277380T>A		277.0	0.0		261.0	23.0	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Silent	SNP	ENST00000445192.2	hg19	CCDS1369.1																																																																																			.	.		0.542	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807		A	186277380	T	A	186277380	2	1	257	1	0	0	0	0	0	0	0	1	12493	1538	54	4		4	PRG4	1	186277380	Silent	SNP	T	TCGA-EP-A3JL-01A-11D-A20W-10	20	186277380	62973241	9	36200	182	2	1	47		3	2	24	N	T_ACTACCCCCAAGAAGCCTGCTCCA_A	5.943603e-05
PRG4	10216	hgsc.bcm.edu	37	chr1	186277383	186277383	+	Silent	SNP	A	A	C													0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	acccccaagaagcctgctccAactactcctgagacacctcc							TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr1:186277383A>C	ENST00000445192.2	+	7	2577	c.2532A>C	c.(2530-2532)ccA>ccC	p.P844P	PRG4_ENST00000367483.4_Silent_p.P803P|PRG4_ENST00000367484.3_Silent_p.P373P|PRG4_ENST00000367486.3_Silent_p.P801P|PRG4_ENST00000367485.4_Silent_p.P751P	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	844	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						AGCCTGCTCCAACTACTCCTG	0.542																																					p.P844P		Atlas-SNP	.											.	PRG4	259	.	0			c.A2532C						.						194	224	214					1																	186277383		2203	4300	6503	SO:0001819	synonymous_variant	10216	exon7			TGCTCCAACTACT	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"lubricin", "megakaryocyte stimulating factor", "articular superficial zone protein", "Jacobs camptodactyly-arthropathy-pericarditis syndrome", "camptodactyly, arthropathy, coxa vara, pericarditis syndrome", "bG174L6.2 (MSF: megakaryocyte stimulating factor )"	604283	"proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.2532A>C	chr1.hg19:g.186277383A>C		275.0	0.0		266.0	29.0	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Silent	SNP	ENST00000445192.2	hg19	CCDS1369.1																																																																																			.	.		0.542	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807		C	186277383	A	C	186277383	2	2	257	1	0	0	0	0	0	0	0	1	12493	117	5	5		5	PRG4	1	186277383	Silent	SNP	A	TCGA-EP-A3JL-01A-11D-A20W-10	3	186277383	62973238	10	36201	182	2	1	47		3	2	24	N	T_ACTACCCCCAAGAAGCCTGCTCCA_A	5.943603e-05
RYR2	6262	hgsc.bcm.edu	37	chr1	237802427	237802427	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	aatgggcttcttgcagcaatGgaagaagccatcaaaatcgc	10	9	2	1			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr1:237802427G>A	ENST00000366574.2	+	46	7358	c.7041G>A	c.(7039-7041)atG>atA	p.M2347I	RYR2_ENST00000542537.1_Missense_Mutation_p.M2331I|RYR2_ENST00000360064.6_Missense_Mutation_p.M2345I	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	2347	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TTGCAGCAATGGAAGAAGCCA	0.493																																					p.M2347I		Atlas-SNP	.											.	RYR2	1273	.	0			c.G7041A						.						113	116	115					1																	237802427		1929	4122	6051	SO:0001583	missense	6262	exon46			AGCAATGGAAGAA	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.7041G>A	chr1.hg19:g.237802427G>A	ENSP00000355533:p.Met2347Ile	199.0	0.0		201.0	93.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	G	12.00	1.805433	0.31961	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.97752	-4.52;-4.52;-4.52	5.05	4.14	0.48551	.	0.000000	0.85682	D	0.000000	D	0.92515	0.7623	N	0.25890	0.77	0.80722	D	1	B	0.19817	0.039	B	0.19666	0.026	D	0.86251	0.1649	10	0.02654	T	1	.	8.7322	0.34505	0.0766:0.0:0.7738:0.1496	.	2347	Q92736	RYR2_HUMAN	I	2347;2345;2331	ENSP00000355533:M2347I;ENSP00000353174:M2345I;ENSP00000443798:M2331I	ENSP00000353174:M2345I	M	+	3	0	RYR2	235869050	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.546000	0.60705	1.256000	0.44068	0.561000	0.74099	ATG	.	.		0.493	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		A	237802427	G	A	237802427	3	1	257	1	0	0	0	0	1	0	0	0	13784	1348	47	3	7223	3	RYR2	1	237802427	Missense_Mutation	SNP	G	TCGA-EP-A3JL-01A-11D-A20W-10	51525044	237802427	11448194	11	36202										
POMC	5443	hgsc.bcm.edu	37	chr2	25384548	25384548	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	tccgggggttctcggtcagaGgctgctcgtcgccatttccc	13	14	2	1			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr2:25384548G>C	ENST00000405623.1	-	3	661	c.206C>G	c.(205-207)cCt>cGt	p.P69R	RP11-509E16.1_ENST00000567599.1_lincRNA|POMC_ENST00000380794.1_Missense_Mutation_p.P69R|POMC_ENST00000395826.2_Missense_Mutation_p.P69R|POMC_ENST00000264708.3_Missense_Mutation_p.P69R			P01189	COLI_HUMAN	proopiomelanocortin	69					cell-cell signaling (GO:0007267)|cellular pigmentation (GO:0033059)|cellular protein metabolic process (GO:0044267)|generation of precursor metabolites and energy (GO:0006091)|glucose homeostasis (GO:0042593)|negative regulation of tumor necrosis factor production (GO:0032720)|neuropeptide signaling pathway (GO:0007218)|peptide hormone processing (GO:0016486)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of appetite (GO:0032098)|regulation of blood pressure (GO:0008217)|regulation of corticosterone secretion (GO:2000852)|regulation of glycogen metabolic process (GO:0070873)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|peroxisomal matrix (GO:0005782)|secretory granule (GO:0030141)|secretory granule lumen (GO:0034774)	G-protein coupled receptor binding (GO:0001664)|hormone activity (GO:0005179)|receptor binding (GO:0005102)|type 1 melanocortin receptor binding (GO:0070996)|type 3 melanocortin receptor binding (GO:0031781)|type 4 melanocortin receptor binding (GO:0031782)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(5)|ovary(1)	12	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Loperamide(DB00836)	CTCGGTCAGAGGCTGCTCGTC	0.687																																					p.P69R	Colon(110;1515 1566 8452 10082 43216)	Atlas-SNP	.											.	POMC	33	.	0			c.C206G	GRCh37	CD064616	POMC	D		.						13	10	11					2																	25384548		2017	3975	5992	SO:0001583	missense	5443	exon4			GTCAGAGGCTGCT		CCDS1717.1	2p23	2013-02-25	2008-07-31		ENSG00000115138	ENSG00000115138		"Endogenous ligands"	9201	protein-coding gene	gene with protein product	"adrenocorticotropin", "beta-lipotropin", "alpha-melanocyte stimulating hormone", "beta-melanocyte stimulating hormone", "beta-endorphin", "adrenocorticotropic hormone", "opiomelanocortin prepropeptide"	176830				6254047, 9620771	Standard	NM_001035256		Approved	MSH, POC, CLIP, ACTH, NPP, LPH	uc002rfz.1	P01189	OTTHUMG00000094764	ENST00000405623.1:c.206C>G	chr2.hg19:g.25384548G>C	ENSP00000384092:p.Pro69Arg	113.0	0.0		80.0	19.0	NM_001035256	P78442|Q53T23|Q9UD39|Q9UD40	Missense_Mutation	SNP	ENST00000405623.1	hg19	CCDS1717.1	.	.	.	.	.	.	.	.	.	.	G	13.02	2.112128	0.37242	.	.	ENSG00000115138	ENST00000380794;ENST00000405623;ENST00000264708;ENST00000395826;ENST00000449220	D;D;D;D;D	0.83591	-1.74;-1.74;-1.74;-1.74;-1.74	5.19	3.27	0.37495	Pro-opiomelanocortin N-terminal (1);	0.114016	0.64402	D	0.000010	D	0.87414	0.6171	M	0.72118	2.19	0.54753	D	0.999982	D	0.58970	0.984	P	0.59889	0.865	D	0.86808	0.1996	10	0.87932	D	0	-17.9688	10.087	0.42423	0.1787:0.0:0.8213:0.0	.	69	P01189	COLI_HUMAN	R	69	ENSP00000370171:P69R;ENSP00000384092:P69R;ENSP00000264708:P69R;ENSP00000379170:P69R;ENSP00000387993:P69R	ENSP00000264708:P69R	P	-	2	0	POMC	25238052	1.000000	0.71417	0.709000	0.30452	0.083000	0.17756	3.390000	0.52523	0.595000	0.29777	-0.224000	0.12420	CCT	.	.		0.687	POMC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211573.3	NM_001035256		C	25384548	G	C	25384548	3	2	257	1	0	0	0	0	1	0	0	0	12251	1000	35	4	601	4	POMC	2	25384548	Missense_Mutation	SNP	G	TCGA-EP-A3JL-01A-11D-A20W-10		25384548	217814825	12	36203										
NXPH2	11249	hgsc.bcm.edu	37	chr2	139428887	139428887	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	tccatttccatggtcaacaaTtttccctgtgatgaggagat	8	9	1	3			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr2:139428887T>C	ENST00000272641.3	-	2	506	c.400A>G	c.(400-402)Att>Gtt	p.I134V		NM_007226.2	NP_009157.1	O95156	NXPH2_HUMAN	neurexophilin 2	134	III.				neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)				endometrium(1)|large_intestine(3)|lung(6)|ovary(3)|prostate(3)|skin(3)|urinary_tract(3)	22				BRCA - Breast invasive adenocarcinoma(221;0.101)		TGGTCAACAATTTTCCCTGTG	0.408																																					p.I134V		Atlas-SNP	.											.	NXPH2	63	.	0			c.A400G						.						58	52	54					2																	139428887		1868	4116	5984	SO:0001583	missense	11249	exon2			CAACAATTTTCCC	AF043467	CCDS46421.1	2q22.1	2008-05-15			ENSG00000144227	ENSG00000144227			8076	protein-coding gene	gene with protein product		604635				9570794	Standard	NM_007226		Approved	NPH2	uc002tvi.3	O95156	OTTHUMG00000153636	ENST00000272641.3:c.400A>G	chr2.hg19:g.139428887T>C	ENSP00000272641:p.Ile134Val	191.0	0.0		113.0	30.0	NM_007226	B7WP24|Q494R1|Q75QC3	Missense_Mutation	SNP	ENST00000272641.3	hg19	CCDS46421.1	.	.	.	.	.	.	.	.	.	.	T	17.18	3.322995	0.60634	.	.	ENSG00000144227	ENST00000272641	.	.	.	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.68256	0.2981	L	0.41824	1.3	0.58432	D	0.999999	D	0.63046	0.992	D	0.80764	0.994	T	0.66208	-0.5981	8	.	.	.	-21.3489	16.2026	0.82095	0.0:0.0:0.0:1.0	.	134	O95156	NXPH2_HUMAN	V	134	.	.	I	-	1	0	NXPH2	139145357	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.997000	0.88414	2.285000	0.76669	0.533000	0.62120	ATT	.	.		0.408	NXPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331901.1			C	139428887	T	C	139428887	3	2	257	1	0	0	0	0	1	0	0	0	10800	1493	52	2	398	2	NXPH2	2	139428887	Missense_Mutation	SNP	T	TCGA-EP-A3JL-01A-11D-A20W-10	114044339	139428887	103770486	13	36204										
SF3B1	23451	hgsc.bcm.edu	37	chr2	198267752	198267752	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	tcaatagcggttcaatgaccAcgaggatctgaaaaagagaa	10	7	3	3			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr2:198267752A>G	ENST00000335508.6	-	13	1818	c.1727T>C	c.(1726-1728)gTg>gCg	p.V576A	SNORA4_ENST00000365564.1_RNA|SF3B1_ENST00000462613.1_5'Flank	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	576					anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)			NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			TTCAATGACCACGAGGATCTG	0.333			Mis		myelodysplastic syndrome																																p.V576A		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	.	SF3B1	1038	.	0			c.T1727C						.						54	52	53					2																	198267752		2203	4298	6501	SO:0001583	missense	23451	exon13			ATGACCACGAGGA	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"splicing factor 3b, subunit 1, 155kD"			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.1727T>C	chr2.hg19:g.198267752A>G	ENSP00000335321:p.Val576Ala	149.0	0.0		90.0	23.0	NM_012433	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	hg19	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.262632	0.80358	.	.	ENSG00000115524	ENST00000335508	T	0.63744	-0.06	5.55	5.55	0.83447	Armadillo-like helical (1);Armadillo-type fold (1);	0.063724	0.64402	D	0.000008	T	0.74496	0.3724	M	0.82923	2.615	0.80722	D	1	P	0.41524	0.753	P	0.48770	0.589	T	0.78807	-0.2059	10	0.72032	D	0.01	.	15.71	0.77620	1.0:0.0:0.0:0.0	.	576	O75533	SF3B1_HUMAN	A	576	ENSP00000335321:V576A	ENSP00000335321:V576A	V	-	2	0	SF3B1	197975997	1.000000	0.71417	1.000000	0.80357	0.606000	0.37113	9.227000	0.95236	2.105000	0.64084	0.533000	0.62120	GTG	.	.		0.333	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			G	198267752	A	G	198267752	3	3	257	1	0	0	0	0	1	0	0	0	14164	159	6	2	2239	2	SF3B1	2	198267752	Missense_Mutation	SNP	A	TCGA-EP-A3JL-01A-11D-A20W-10	58838865	198267752	44931621	14	36205										
ERBB4	2066	hgsc.bcm.edu	37	chr2	212543852	212543852	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	acgacagacattggtctggcCcaggtccccaacagccatca	9	15	2	1			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr2:212543852C>A	ENST00000342788.4	-	13	1857	c.1547G>T	c.(1546-1548)gGg>gTg	p.G516V	ERBB4_ENST00000436443.1_Missense_Mutation_p.G516V|ERBB4_ENST00000402597.1_Missense_Mutation_p.G516V	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	516	Cys-rich.				cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	TTGGTCTGGCCCAGGTCCCCA	0.488										TSP Lung(8;0.080)																											p.G516V		Atlas-SNP	.											.	ERBB4	480	.	0			c.G1547T						.						86	76	80					2																	212543852		2203	4300	6503	SO:0001583	missense	2066	exon13			TCTGGCCCAGGTC	L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.1547G>T	chr2.hg19:g.212543852C>A	ENSP00000342235:p.Gly516Val	256.0	0.0		172.0	43.0	NM_001042599	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	hg19	CCDS2394.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.7|20.7	4.027090|4.027090	0.75390|0.75390	.|.	.|.	ENSG00000178568|ENSG00000178568	ENST00000260943|ENST00000342788;ENST00000436443;ENST00000402597	T|T;T;T	0.50813|0.52057	0.73|0.68;0.68;0.68	5.33|5.33	4.46|4.46	0.54185|0.54185	.|Growth factor, receptor (1);	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.76807|0.76807	0.4039|0.4039	H|H	0.95043|0.95043	3.615|3.615	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D	.|0.97110	.|1.0;0.999;0.999;1.0;1.0	D|D	0.83648|0.83648	0.0154|0.0154	8|10	0.87932|0.87932	D|D	0|0	.|.	13.2211|13.2211	0.59887|0.59887	0.0:0.921:0.0:0.079|0.0:0.921:0.0:0.079	.|.	.|516;516;375;516;516	.|Q15303-4;Q15303-2;Q53QS8;Q15303-3;Q15303	.|.;.;.;.;ERBB4_HUMAN	C|V	516|516	ENSP00000260943:G516C|ENSP00000342235:G516V;ENSP00000403204:G516V;ENSP00000385565:G516V	ENSP00000260943:G516C|ENSP00000342235:G516V	G|G	-|-	1|2	0|0	ERBB4|ERBB4	212252097|212252097	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.876000|0.876000	0.50452|0.50452	5.482000|5.482000	0.66833|0.66833	1.247000|1.247000	0.43917|0.43917	0.591000|0.591000	0.81541|0.81541	GGC|GGG	.	.		0.488	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		A	212543852	C	A	212543852	3	1	257	1	0	0	0	0	1	0	0	0	5211	623	22	3	2443	3	ERBB4	2	212543852	Missense_Mutation	SNP	C	TCGA-EP-A3JL-01A-11D-A20W-10	14276100	212543852	30655521	15	36206										
TTLL4	9654	hgsc.bcm.edu	37	chr2	219619007	219619007	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	agcaaagagcccagcctttcTacccagacgttacctgtgat	8	13	1	3			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr2:219619007T>C	ENST00000392102.1	+	20	3835	c.3495T>C	c.(3493-3495)tcT>tcC	p.S1165S	TTLL4_ENST00000442769.1_Silent_p.S1101S|TTLL4_ENST00000258398.4_Silent_p.S1165S|TTLL4_ENST00000457313.1_Missense_Mutation_p.L968P	NM_014640.4	NP_055455.3	Q14679	TTLL4_HUMAN	tubulin tyrosine ligase-like family, member 4	1165					protein polyglutamylation (GO:0018095)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)|tubulin binding (GO:0015631)			endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	39		Renal(207;0.0915)		Epithelial(149;5.03e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0101)		CCAGCCTTTCTACCCAGACGT	0.532																																					p.S1165S	GBM(172;1818 2053 15407 20943 49753)	Atlas-SNP	.											.	TTLL4	96	.	0			c.T3495C						.						135	132	133					2																	219619007		2203	4300	6503	SO:0001819	synonymous_variant	9654	exon20			CCTTTCTACCCAG		CCDS2422.1	2p24.3-p24.1	2013-02-14			ENSG00000135912	ENSG00000135912		"Tubulin tyrosine ligase-like family"	28976	protein-coding gene	gene with protein product						11054573	Standard	NM_014640		Approved	KIAA0173	uc002viy.3	Q14679	OTTHUMG00000133081	ENST00000392102.1:c.3495T>C	chr2.hg19:g.219619007T>C		190.0	0.0		136.0	29.0	NM_014640	A8K6V5|Q8WW29	Silent	SNP	ENST00000392102.1	hg19	CCDS2422.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.237|0.237	-1.016493|-1.016493	0.02078|0.02078	.|.	.|.	ENSG00000135912|ENSG00000135912	ENST00000457313|ENST00000417855	T|.	0.03920|.	3.76|.	4.76|4.76	-8.26|-8.26	0.01021|0.01021	.|.	.|.	.|.	.|.	.|.	T|T	0.39226|0.39226	0.1070|0.1070	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.42085|0.42085	-0.9472|-0.9472	8|4	0.27082|.	T|.	0.32|.	.|.	15.1222|15.1222	0.72453|0.72453	0.0:0.2323:0.0:0.7677|0.0:0.2323:0.0:0.7677	.|.	968|.	E9PH58|.	.|.	P|H	968|157	ENSP00000393332:L968P|.	ENSP00000393332:L968P|.	L|Y	+|+	2|1	0|0	TTLL4|TTLL4	219327251|219327251	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.003000|0.003000	0.03518|0.03518	-1.139000|-1.139000	0.03213|0.03213	-1.893000|-1.893000	0.01106|0.01106	-1.601000|-1.601000	0.00813|0.00813	CTA|TAC	.	.		0.532	TTLL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256726.1	NM_014640		C	219619007	T	C	219619007	2	2	257	1	0	0	0	0	0	0	0	1	16744	1509	53	2		2	TTLL4	2	219619007	Silent	SNP	T	TCGA-EP-A3JL-01A-11D-A20W-10	7075155	219619007	23580366	16	36207										
SGPP2	130367	hgsc.bcm.edu	37	chr2	223423159	223423159	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	gcctggactcggccagccccCtcttccccgtgtgtgtcata	10	17	2	0			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr2:223423159C>T	ENST00000321276.7	+	5	828	c.742C>T	c.(742-744)Ctc>Ttc	p.L248F		NM_152386.2	NP_689599.2	Q8IWX5	SGPP2_HUMAN	sphingosine-1-phosphate phosphatase 2	248					dephosphorylation (GO:0016311)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	sphingosine-1-phosphate phosphatase activity (GO:0042392)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	18		Renal(207;0.0376)		Epithelial(121;2.08e-09)|all cancers(144;9.25e-07)|LUSC - Lung squamous cell carcinoma(224;0.011)|Lung(261;0.0143)		GGCCAGCCCCCTCTTCCCCGT	0.572																																					p.L248F		Atlas-SNP	.											.	SGPP2	39	.	0			c.C742T						.						145	129	134					2																	223423159		2203	4300	6503	SO:0001583	missense	130367	exon5			AGCCCCCTCTTCC	AF542512	CCDS2453.1	2q36.3	2010-05-26	2010-05-26		ENSG00000163082	ENSG00000163082			19953	protein-coding gene	gene with protein product		612827				12411432	Standard	NM_152386		Approved	SPP2, FLJ39004	uc010zlo.2	Q8IWX5	OTTHUMG00000133156	ENST00000321276.7:c.742C>T	chr2.hg19:g.223423159C>T	ENSP00000315137:p.Leu248Phe	356.0	0.0		211.0	55.0	NM_152386	A3KPB4|Q8N8Q6	Missense_Mutation	SNP	ENST00000321276.7	hg19	CCDS2453.1	.	.	.	.	.	.	.	.	.	.	C	12.14	1.848654	0.32699	.	.	ENSG00000163082	ENST00000321276	.	.	.	5.19	5.19	0.71726	.	0.154766	0.44902	D	0.000413	T	0.39682	0.1087	L	0.28115	0.83	0.47214	D	0.999355	B	0.24920	0.114	B	0.21360	0.034	T	0.24119	-1.0169	9	0.13470	T	0.59	-29.0954	9.9835	0.41828	0.0:0.8747:0.0:0.1253	.	248	Q8IWX5	SGPP2_HUMAN	F	248	.	ENSP00000315137:L248F	L	+	1	0	SGPP2	223131403	0.711000	0.27906	1.000000	0.80357	0.931000	0.56810	1.247000	0.32815	2.402000	0.81655	0.655000	0.94253	CTC	.	.		0.572	SGPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256856.2			T	223423159	C	T	223423159	3	4	257	1	0	0	0	0	1	0	0	0	14235	681	24	3	760	3	SGPP2	2	223423159	Missense_Mutation	SNP	C	TCGA-EP-A3JL-01A-11D-A20W-10	3804152	223423159	19776214	17	36208										
GADL1	339896	hgsc.bcm.edu	37	chr3	30827899	30827899	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	tgatttcatctactaggtacCtaaaattaaaagtcacaata	4	7	3	1			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr3:30827899C>T	ENST00000282538.5	-	13	1401		c.e13-1			NM_207359.2	NP_997242.2	Q6ZQY3	GADL1_HUMAN	glutamate decarboxylase-like 1						carboxylic acid metabolic process (GO:0019752)		aspartate 1-decarboxylase activity (GO:0004068)|pyridoxal phosphate binding (GO:0030170)|sulfinoalanine decarboxylase activity (GO:0004782)			breast(2)|endometrium(3)|kidney(2)|lung(17)|upper_aerodigestive_tract(1)	25						TACTAGGTACCTAAAATTAAA	0.323																																					.		Atlas-SNP	.											.	GADL1	91	.	0			c.1251-1G>A						.						104	96	99					3																	30827899		2194	4297	6491	SO:0001630	splice_region_variant	339896	exon14			AGGTACCTAAAAT	AK128643	CCDS2649.2	3p23-p22	2009-01-14			ENSG00000144644	ENSG00000144644			27949	protein-coding gene	gene with protein product		615601					Standard	NM_207359		Approved		uc003cep.2	Q6ZQY3	OTTHUMG00000130621	ENST00000282538.5:c.1251-1G>A	chr3.hg19:g.30827899C>T		105.0	0.0		52.0	16.0	NM_207359		Splice_Site	SNP	ENST00000282538.5	hg19	CCDS2649.2	.	.	.	.	.	.	.	.	.	.	C	20.8	4.056184	0.76074	.	.	ENSG00000144644	ENST00000282538	.	.	.	5.96	5.96	0.96718	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.1922	0.89810	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	GADL1	30802903	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	5.187000	0.65087	2.831000	0.97527	0.650000	0.86243	.	.	.		0.323	GADL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253106.2	NM_207359	Intron	T	30827899	C	T	30827899	5	4	257	1	0	0	0	0	0	0	1	0	6193	695	24	3	327	3	GADL1	3	30827899	Splice_Site	SNP	C	TCGA-EP-A3JL-01A-11D-A20W-10		30827899	167194531	18	36209										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41274911	41274911	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	tgtctttggactctcaggaaTctttcagatgctgcaactaa	8	9	4	1			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr3:41274911T>A	ENST00000349496.5	+	8	1441	c.1161T>A	c.(1159-1161)aaT>aaA	p.N387K	CTNNB1_ENST00000396183.3_Missense_Mutation_p.N387K|CTNNB1_ENST00000396185.3_Missense_Mutation_p.N387K|CTNNB1_ENST00000453024.1_Missense_Mutation_p.N380K|CTNNB1_ENST00000405570.1_Missense_Mutation_p.N387K	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	387					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.N387K(4)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CTCTCAGGAATCTTTCAGATG	0.393		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.N387K	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,carcinoma,0,5	CTNNB1	4904	.	4	Substitution - Missense(4)	large_intestine(1)|prostate(1)|liver(1)|kidney(1)	c.T1161A						.						102	93	96					3																	41274911		2203	4300	6503	SO:0001583	missense	1499	exon8	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	CAGGAATCTTTCA	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.1161T>A	chr3.hg19:g.41274911T>A	ENSP00000344456:p.Asn387Lys	162.0	0.0		100.0	22.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	19.46	3.832364	0.71258	.	.	ENSG00000168036	ENST00000405570;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185	D;D;D;D;D	0.83992	-1.79;-1.79;-1.79;-1.79;-1.79	5.72	1.33	0.21861	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.90263	0.6955	M	0.89478	3.035	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	D	0.88091	0.2813	10	0.54805	T	0.06	-10.1444	8.463	0.32938	0.0:0.3714:0.0:0.6286	.	315;387	B4DSW9;P35222	.;CTNB1_HUMAN	K	387;387;387;380;387	ENSP00000385604:N387K;ENSP00000379486:N387K;ENSP00000344456:N387K;ENSP00000411226:N380K;ENSP00000379488:N387K	ENSP00000344456:N387K	N	+	3	2	CTNNB1	41249915	0.995000	0.38212	0.998000	0.56505	0.998000	0.95712	0.358000	0.20216	0.227000	0.20999	0.533000	0.62120	AAT	.	.		0.393	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		A	41274911	T	A	41274911	3	1	257	1	0	0	0	0	1	0	0	0	4018	1432	50	4	1187	4	CTNNB1	3	41274911	Missense_Mutation	SNP	T	TCGA-EP-A3JL-01A-11D-A20W-10	10447012	41274911	156747519	19	36210										
CCDC36	339834	hgsc.bcm.edu	37	chr3	49294178	49294178	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	aaatatcaagcccaaagtatGtttttgtgtgacccacgtga	8	8	1	2			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr3:49294178G>A	ENST00000438782.1	+	8	1484	c.1248G>A	c.(1246-1248)atG>atA	p.M416I	CCDC36_ENST00000296449.5_Missense_Mutation_p.M416I|CCDC36_ENST00000452691.2_Missense_Mutation_p.M416I			Q8IYA8	CCD36_HUMAN	coiled-coil domain containing 36	416										endometrium(1)|kidney(2)|large_intestine(3)|liver(1)|lung(3)|ovary(1)|urinary_tract(3)	14				BRCA - Breast invasive adenocarcinoma(193;9.11e-05)|Kidney(197;0.00248)|KIRC - Kidney renal clear cell carcinoma(197;0.00262)		CCCAAAGTATGTTTTTGTGTG	0.463																																					p.M416I		Atlas-SNP	.											.	CCDC36	77	.	0			c.G1248A						.						102	105	104					3																	49294178		2203	4300	6503	SO:0001583	missense	339834	exon8			AAGTATGTTTTTG	AK058049	CCDS33755.2	3p21.31	2009-08-06			ENSG00000173421	ENSG00000173421			27945	protein-coding gene	gene with protein product	"cancer/testis antigen 74"						Standard	NM_178173		Approved	FLJ25320, CT74	uc011bck.1	Q8IYA8	OTTHUMG00000155920	ENST00000438782.1:c.1248G>A	chr3.hg19:g.49294178G>A	ENSP00000391788:p.Met416Ile	145.0	0.0		81.0	17.0	NM_001135197	C9JJL0|Q05DG9|Q96LP7	Missense_Mutation	SNP	ENST00000438782.1	hg19	CCDS33755.2	.	.	.	.	.	.	.	.	.	.	G	14.33	2.503317	0.44558	.	.	ENSG00000173421	ENST00000296449;ENST00000438782;ENST00000452691;ENST00000309062	T;T;T	0.41065	1.01;1.01;1.01	5.14	0.046	0.14232	.	1.023130	0.07771	N	0.951799	T	0.24122	0.0584	N	0.19112	0.55	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.22661	-1.0210	10	0.28530	T	0.3	3.69	4.2145	0.10528	0.3871:0.1664:0.4465:0.0	.	416	Q8IYA8	CCD36_HUMAN	I	416;416;416;396	ENSP00000296449:M416I;ENSP00000391788:M416I;ENSP00000407837:M416I	ENSP00000296449:M416I	M	+	3	0	CCDC36	49269182	0.000000	0.05858	0.000000	0.03702	0.974000	0.67602	-0.161000	0.10026	0.092000	0.17331	0.655000	0.94253	ATG	.	.		0.463	CCDC36-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342332.1	NM_178173		A	49294178	G	A	49294178	3	1	257	1	0	0	0	0	1	0	0	0	2810	1377	48	3	1274	3	CCDC36	3	49294178	Missense_Mutation	SNP	G	TCGA-EP-A3JL-01A-11D-A20W-10	8019267	49294178	148728252	20	36211										
TMF1	7110	hgsc.bcm.edu	37	chr3	69084238	69084238	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	tggcagccgcttgttctgtaCgctgcaatgcaagcctaagg	12	11	1	0			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr3:69084238C>A	ENST00000398559.2	-	9	2396	c.2180G>T	c.(2179-2181)cGt>cTt	p.R727L	CTD-2013N24.2_ENST00000601735.1_RNA|CTD-2013N24.2_ENST00000596732.1_RNA|CTD-2013N24.2_ENST00000598783.1_RNA|CTD-2013N24.2_ENST00000596523.1_RNA|CTD-2013N24.2_ENST00000482368.2_RNA|CTD-2013N24.2_ENST00000596274.1_RNA|CTD-2013N24.2_ENST00000595925.1_RNA|CTD-2013N24.2_ENST00000601511.1_RNA|CTD-2013N24.2_ENST00000599467.1_RNA|TMF1_ENST00000543976.1_Missense_Mutation_p.R730L|CTD-2013N24.2_ENST00000597950.1_RNA			P82094	TMF1_HUMAN	TATA element modulatory factor 1	727					acrosome assembly (GO:0001675)|cellular response to organic cyclic compound (GO:0071407)|defense response to bacterium (GO:0042742)|Leydig cell differentiation (GO:0033327)|luteinizing hormone secretion (GO:0032275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|positive regulation of cytokine production (GO:0001819)|positive regulation of testosterone secretion (GO:2000845)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of transcription, DNA-templated (GO:0006355)|sperm motility (GO:0030317)|spermatid nucleus differentiation (GO:0007289)|transcription from RNA polymerase II promoter (GO:0006366)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription cofactor activity (GO:0003712)			cervix(1)|kidney(1)|large_intestine(4)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;4.48e-05)|Epithelial(33;0.000274)|LUSC - Lung squamous cell carcinoma(21;0.0123)|KIRC - Kidney renal clear cell carcinoma(39;0.211)|Kidney(39;0.247)		TTGTTCTGTACGCTGCAATGC	0.433																																					p.R727L		Atlas-SNP	.											.	TMF1	77	.	0			c.G2180T						.						194	194	194					3																	69084238		1952	4145	6097	SO:0001583	missense	7110	exon9			TCTGTACGCTGCA		CCDS43105.1	3p21-p12	2009-02-11			ENSG00000144747	ENSG00000144747			11870	protein-coding gene	gene with protein product		601126				1409643	Standard	NM_007114		Approved	ARA160, TMF	uc003dnn.3	P82094	OTTHUMG00000158771	ENST00000398559.2:c.2180G>T	chr3.hg19:g.69084238C>A	ENSP00000381567:p.Arg727Leu	183.0	0.0		122.0	41.0	NM_007114	B7ZLJ2|Q17R87|Q59GK0	Missense_Mutation	SNP	ENST00000398559.2	hg19	CCDS43105.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.669977	0.88348	.	.	ENSG00000144747	ENST00000398559;ENST00000543976;ENST00000356248	T;T	0.24538	1.85;1.85	5.03	5.03	0.67393	.	0.049125	0.85682	D	0.000000	T	0.49423	0.1556	L	0.59912	1.85	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.46119	-0.9214	10	0.52906	T	0.07	-10.6806	18.7275	0.91720	0.0:1.0:0.0:0.0	.	730;727	P82094-2;P82094	.;TMF1_HUMAN	L	727;730;643	ENSP00000381567:R727L;ENSP00000438706:R730L	ENSP00000348582:R643L	R	-	2	0	TMF1	69166928	1.000000	0.71417	1.000000	0.80357	0.552000	0.35366	7.776000	0.85560	2.486000	0.83907	0.655000	0.94253	CGT	.	.		0.433	TMF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352106.1	NM_007114		A	69084238	C	A	69084238	3	1	257	1	0	0	0	0	1	0	0	0	16243	536	19	1	1137	1	TMF1	3	69084238	Missense_Mutation	SNP	C	TCGA-EP-A3JL-01A-11D-A20W-10	19790060	69084238	128938192	21	36212										
MYH15	22989	hgsc.bcm.edu	37	chr3	108220704	108220704	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	cctcctttatgctcagactcTgcagagagaagaaaaatata	7	9	2	4			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr3:108220704T>C	ENST00000273353.3	-	4	312		c.e4-2			NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15							cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						GCTCAGACTCTGCAGAGAGAA	0.378																																					.		Atlas-SNP	.											.	MYH15	223	.	0			c.256-2A>G						.						135	130	132					3																	108220704		1890	4120	6010	SO:0001630	splice_region_variant	22989	exon5			AGACTCTGCAGAG	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"Myosins / Myosin superfamily : Class II"	31073	protein-coding gene	gene with protein product		609929	"myosin, heavy polypeptide 15"			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.256-2A>G	chr3.hg19:g.108220704T>C		148.0	0.0		77.0	19.0	NM_014981		Splice_Site	SNP	ENST00000273353.3	hg19	CCDS43127.1	.	.	.	.	.	.	.	.	.	.	T	15.79	2.938203	0.52972	.	.	ENSG00000144821	ENST00000273353	.	.	.	5.58	4.42	0.53409	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.2051	0.48765	0.0:0.073:0.0:0.927	.	.	.	.	.	-1	.	.	.	-	.	.	MYH15	109703394	1.000000	0.71417	0.237000	0.24090	0.191000	0.23601	5.616000	0.67709	0.941000	0.37499	0.482000	0.46254	.	.	.		0.378	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988	Intron	C	108220704	T	C	108220704	5	2	257	1	0	0	0	0	0	0	1	0	10043	1594	55	2	5742	2	MYH15	3	108220704	Splice_Site	SNP	T	TCGA-EP-A3JL-01A-11D-A20W-10	39136466	108220704	89801726	22	36213										
CD200R1L	344807	hgsc.bcm.edu	37	chr3	112548190	112548190	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	tgcaaaaattgttgaatagtTctgtgtcatctgctttccac	7	8	3	1			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr3:112548190T>C	ENST00000398214.1	-	2	313	c.88A>G	c.(88-90)Aac>Gac	p.N30D	CD200R1L_ENST00000448932.1_Missense_Mutation_p.N9D|CD200R1L_ENST00000488794.1_Missense_Mutation_p.N9D	NM_001008784.2	NP_001008784.2	Q6Q8B3	MO2R2_HUMAN	CD200 receptor 1-like	30						integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|urinary_tract(2)	19						GTTGAATAGTTCTGTGTCATC	0.388																																					p.N30D		Atlas-SNP	.											.	CD200R1L	47	.	0			c.A88G						.						145	139	141					3																	112548190		2148	4279	6427	SO:0001583	missense	344807	exon2			AATAGTTCTGTGT	AY284976	CCDS43131.1, CCDS56267.1	3q13.2	2014-05-15	2008-10-08		ENSG00000206531	ENSG00000206531		"Immunoglobulin superfamily / C2-set domain containing"	24665	protein-coding gene	gene with protein product	"CD200 receptor 2"						Standard	NM_001008784		Approved	CD200RLa, CD200R2	uc003dzi.1	Q6Q8B3	OTTHUMG00000159283	ENST00000398214.1:c.88A>G	chr3.hg19:g.112548190T>C	ENSP00000381272:p.Asn30Asp	231.0	0.0		157.0	34.0	NM_001008784	Q6WHB7	Missense_Mutation	SNP	ENST00000398214.1	hg19	CCDS43131.1	.	.	.	.	.	.	.	.	.	.	T	12.25	1.880352	0.33162	.	.	ENSG00000206531	ENST00000398214;ENST00000488794;ENST00000448932	T;T;T	0.19250	2.16;2.2;2.2	1.71	0.348	0.16026	.	0.868493	0.09575	N	0.783729	T	0.22859	0.0552	L	0.55834	1.745	0.09310	N	1	D	0.57257	0.979	P	0.49999	0.628	T	0.17684	-1.0361	10	0.24483	T	0.36	.	3.8221	0.08839	0.0:0.2132:0.0:0.7868	.	30	Q6Q8B3	MO2R2_HUMAN	D	30;9;9	ENSP00000381272:N30D;ENSP00000418413:N9D;ENSP00000415132:N9D	ENSP00000381272:N30D	N	-	1	0	CD200R1L	114030880	0.000000	0.05858	0.002000	0.10522	0.066000	0.16364	-0.236000	0.09003	0.076000	0.16826	0.379000	0.24179	AAC	.	.		0.388	CD200R1L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354365.1	NM_001008784		C	112548190	T	C	112548190	3	2	257	1	0	0	0	0	1	0	0	0	2984	1783	62	2	747	2	CD200R1L	3	112548190	Missense_Mutation	SNP	T	TCGA-EP-A3JL-01A-11D-A20W-10	4327486	112548190	85474240	23	36214										
KIAA1407	57577	hgsc.bcm.edu	37	chr3	113720527	113720527	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	ttttctgacgttcctcctctTgggcctttaactgggcctga	9	12	2	2			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr3:113720527T>C	ENST00000295878.3	-	13	2224	c.2078A>G	c.(2077-2079)cAa>cGa	p.Q693R	KIAA1407_ENST00000545063.1_3'UTR	NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	693										endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						TTCCTCCTCTTGGGCCTTTAA	0.408																																					p.Q693R		Atlas-SNP	.											.	KIAA1407	80	.	0			c.A2078G						.						213	209	210					3																	113720527		2203	4300	6503	SO:0001583	missense	57577	exon13			TCCTCTTGGGCCT	AF509494	CCDS2977.1	3q13.31	2005-01-10			ENSG00000163617	ENSG00000163617			29272	protein-coding gene	gene with protein product						10718198	Standard	NM_020817		Approved		uc003eax.3	Q8NCU4	OTTHUMG00000159337	ENST00000295878.3:c.2078A>G	chr3.hg19:g.113720527T>C	ENSP00000295878:p.Gln693Arg	319.0	0.0		211.0	63.0	NM_020817	B4DYL1|Q9P2E0	Missense_Mutation	SNP	ENST00000295878.3	hg19	CCDS2977.1	.	.	.	.	.	.	.	.	.	.	T	12.73	2.027008	0.35797	.	.	ENSG00000163617	ENST00000295878	T	0.29655	1.56	5.19	4.0	0.46444	.	0.250949	0.41194	D	0.000933	T	0.36441	0.0967	L	0.59912	1.85	0.80722	D	1	P	0.50272	0.933	P	0.51582	0.674	T	0.08953	-1.0697	10	0.21014	T	0.42	.	9.4002	0.38428	0.159:0.0:0.0:0.841	.	693	Q8NCU4	K1407_HUMAN	R	693	ENSP00000295878:Q693R	ENSP00000295878:Q693R	Q	-	2	0	KIAA1407	115203217	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.265000	0.43311	1.059000	0.40554	0.528000	0.53228	CAA	.	.		0.408	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817		C	113720527	T	C	113720527	3	2	257	1	0	0	0	0	1	0	0	0	8238	1812	63	2	752	2	KIAA1407	3	113720527	Missense_Mutation	SNP	T	TCGA-EP-A3JL-01A-11D-A20W-10	1172337	113720527	84301903	24	36215										
ENAM	10117	hgsc.bcm.edu	37	chr4	71508497	71508497	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	aacaaataatagttcctacaAagaatccaaccagcccctgg	5	12	0	1			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr4:71508497A>G	ENST00000396073.3	+	9	1635	c.1354A>G	c.(1354-1356)Aag>Gag	p.K452E	ENAM_ENST00000472903.1_Intron	NM_031889.2	NP_114095.2	Q9NRM1	ENAM_HUMAN	enamelin	452					amelogenesis (GO:0097186)|biomineral tissue development (GO:0031214)	proteinaceous extracellular matrix (GO:0005578)				haematopoietic_and_lymphoid_tissue(1)|ovary(3)|upper_aerodigestive_tract(2)	6			Lung(101;0.235)			AGTTCCTACAAAGAATCCAAC	0.423																																					p.K452E		Atlas-SNP	.											.	ENAM	140	.	0			c.A1354G						.						34	36	35					4																	71508497		2191	4300	6491	SO:0001583	missense	10117	exon9			CCTACAAAGAATC	AF125373	CCDS3544.2	4q13.3	2008-02-05			ENSG00000132464	ENSG00000132464			3344	protein-coding gene	gene with protein product		606585	"amelogenesis imperfecta 2, hypocalcification (autosomal dominant)"	AIH2		11978766	Standard	NM_031889		Approved		uc011caw.1	Q9NRM1	OTTHUMG00000129914	ENST00000396073.3:c.1354A>G	chr4.hg19:g.71508497A>G	ENSP00000379383:p.Lys452Glu	92.0	0.0		46.0	12.0	NM_031889	Q17RI5|Q9H3D1	Missense_Mutation	SNP	ENST00000396073.3	hg19	CCDS3544.2	.	.	.	.	.	.	.	.	.	.	A	11.19	1.564318	0.27915	.	.	ENSG00000132464	ENST00000396073	T	0.35421	1.31	5.93	3.32	0.38043	.	0.091579	0.48286	D	0.000190	T	0.32224	0.0822	L	0.53249	1.67	0.23430	N	0.997698	P	0.40553	0.721	B	0.38755	0.281	T	0.19484	-1.0304	10	0.54805	T	0.06	-7.7204	9.6873	0.40107	0.6596:0.3404:0.0:0.0	.	452	Q9NRM1	ENAM_HUMAN	E	452	ENSP00000379383:K452E	ENSP00000379383:K452E	K	+	1	0	ENAM	71727361	0.853000	0.29707	0.771000	0.31576	0.104000	0.19210	1.436000	0.34980	1.044000	0.40200	0.533000	0.62120	AAG	.	.		0.423	ENAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252166.3	NM_031889		G	71508497	A	G	71508497	3	3	257	1	0	0	0	0	1	0	0	0	5114	15	1	2	1384	2	ENAM	4	71508497	Missense_Mutation	SNP	A	TCGA-EP-A3JL-01A-11D-A20W-10		71508497	119645779	25	36216										
ALB	213	hgsc.bcm.edu	37	chr4	74274387	74274388	+	Frame_Shift_Ins	INS	-	-	A													0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	gaaatggctgactgctgtgcINSaaaacaagaacctgagagaa							TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr4:74274387_74274388insA	ENST00000295897.4	+	4	436_437	c.347_348insA	c.(346-351)gcaaaafs	p.AK116fs	ALB_ENST00000503124.1_Intron|ALB_ENST00000415165.2_Intron|ALB_ENST00000505649.1_3'UTR|ALB_ENST00000401494.3_Intron|ALB_ENST00000509063.1_Frame_Shift_Ins_p.AK116fs	NM_000477.5	NP_000468.1	Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GACTGCTGTGCAAAACAAGAAC	0.441																																					p.A116fs		Atlas-INDEL	.											.	ALB	132	.	0			c.347_348insA						.																																			SO:0001589	frameshift_variant	213	exon4			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000295897.4:c.351dupA	chr4.hg19:g.74274391_74274391dupA	ENSP00000295897:p.Ala116fs	141.0	0.0		78.0	20.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Frame_Shift_Ins	INS	ENST00000295897.4	hg19	CCDS3555.1																																																																																			.	.		0.441	ALB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252173.3	NM_000477		A	74274388	-	A	74274387	7	5	257	1	0	1	1	0	0	0	0	0	486	710	25	0	361	0	ALB	4	74274387	Frame_Shift_Ins	INS	-	TCGA-EP-A3JL-01A-11D-A20W-10	2765890	74274387	116879889	26	36217										
MMRN1	22915	hgsc.bcm.edu	37	chr4	90856345	90856345	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	aagcattctgtattatgaatCcctcaataaaactctttcta	3	9	4	1			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr4:90856345C>A	ENST00000394980.1	+	7	1833	c.1514C>A	c.(1513-1515)tCc>tAc	p.S505Y	MMRN1_ENST00000508372.1_Missense_Mutation_p.S247Y|MMRN1_ENST00000264790.2_Missense_Mutation_p.S505Y|MMRN1_ENST00000394981.1_Intron			Q13201	MMRN1_HUMAN	multimerin 1	505					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)				breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|liver(2)|lung(34)|ovary(5)|prostate(1)|skin(6)|stomach(1)|urinary_tract(2)	72		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)		TATTATGAATCCCTCAATAAA	0.383																																					p.S505Y		Atlas-SNP	.											.	MMRN1	174	.	0			c.C1514A						.						92	90	91					4																	90856345		2203	4300	6503	SO:0001583	missense	22915	exon6			ATGAATCCCTCAA	U27109	CCDS3635.1	4q22	2008-02-05	2004-03-02	2004-03-02	ENSG00000138722	ENSG00000138722		"EMI domain containing"	7178	protein-coding gene	gene with protein product	"glycoprotein Ia*"	601456	"multimerin"	MMRN		7629143, 10828608	Standard	NM_007351		Approved	ECM, EMILIN4, GPIa*	uc003hst.3	Q13201	OTTHUMG00000130947	ENST00000394980.1:c.1514C>A	chr4.hg19:g.90856345C>A	ENSP00000378431:p.Ser505Tyr	216.0	0.0		134.0	26.0	NM_007351	Q4W5L1|Q6P3T8|Q6ZUL9	Missense_Mutation	SNP	ENST00000394980.1	hg19	CCDS3635.1	.	.	.	.	.	.	.	.	.	.	C	10.71	1.426915	0.25726	.	.	ENSG00000138722	ENST00000394980;ENST00000264790;ENST00000508372	T;T;T	0.74632	-0.56;-0.56;-0.86	5.12	5.12	0.69794	.	0.082304	0.52532	D	0.000078	D	0.84415	0.5467	M	0.68952	2.095	0.80722	D	1	D	0.76494	0.999	D	0.62955	0.909	D	0.85271	0.1056	10	0.62326	D	0.03	.	19.4343	0.94785	0.0:1.0:0.0:0.0	.	505	Q13201	MMRN1_HUMAN	Y	505;505;247	ENSP00000378431:S505Y;ENSP00000264790:S505Y;ENSP00000426461:S247Y	ENSP00000264790:S505Y	S	+	2	0	MMRN1	91075368	1.000000	0.71417	0.958000	0.39756	0.022000	0.10575	2.521000	0.45563	2.751000	0.94390	0.591000	0.81541	TCC	.	.		0.383	MMRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253546.2	NM_007351		A	90856345	C	A	90856345	3	1	257	1	0	0	0	0	1	0	0	0	9679	855	30	3	1536	3	MMRN1	4	90856345	Missense_Mutation	SNP	C	TCGA-EP-A3JL-01A-11D-A20W-10	16581958	90856345	100297931	27	36218										
SMARCAD1	56916	hgsc.bcm.edu	37	chr4	95198291	95198291	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	tagcaccagtgaaatacgaaGaatgttttcctctaagacag	8	8	1	3			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr4:95198291G>T	ENST00000354268.4	+	16	2136	c.2063G>T	c.(2062-2064)aGa>aTa	p.R688I	SMARCAD1_ENST00000457823.2_Missense_Mutation_p.R688I|SMARCAD1_ENST00000509418.1_Missense_Mutation_p.R258I			Q9H4L7	SMRCD_HUMAN	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	688					ATP-dependent chromatin remodeling (GO:0043044)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|chromosome separation (GO:0051304)|DNA double-strand break processing (GO:0000729)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|nucleotide metabolic process (GO:0009117)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|regulation of DNA recombination (GO:0000018)	heterochromatin (GO:0000792)|nuclear matrix (GO:0016363)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|liver(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44				OV - Ovarian serous cystadenocarcinoma(123;4.33e-08)		GAAATACGAAGAATGTTTTCC	0.373																																					p.R688I		Atlas-SNP	.											.	SMARCAD1	97	.	0			c.G2063T						.						165	161	162					4																	95198291		2203	4300	6503	SO:0001583	missense	56916	exon16			TACGAAGAATGTT	AB032948	CCDS3639.1, CCDS47101.1, CCDS58914.1	4q22-q23	2008-02-05			ENSG00000163104	ENSG00000163104			18398	protein-coding gene	gene with protein product		612761				11031099	Standard	NM_001128430		Approved	ETL1, DKFZP762K2015, KIAA1122, DKFZp762K2015	uc003htb.4	Q9H4L7	OTTHUMG00000130971	ENST00000354268.4:c.2063G>T	chr4.hg19:g.95198291G>T	ENSP00000346217:p.Arg688Ile	125.0	0.0		84.0	19.0	NM_001128429	B7Z799|Q05D56|Q96SX1|Q9H017|Q9H860|Q9NPU9|Q9ULU7	Missense_Mutation	SNP	ENST00000354268.4	hg19	CCDS3639.1	.	.	.	.	.	.	.	.	.	.	G	17.16	3.319756	0.60524	.	.	ENSG00000163104	ENST00000359052;ENST00000457823;ENST00000354268;ENST00000509418	D;D;D;D	0.93811	-3.24;-3.24;-3.24;-3.29	5.52	5.52	0.82312	SNF2-related (1);	0.000000	0.51477	D	0.000086	D	0.92951	0.7757	L	0.45744	1.44	0.80722	D	1	B;B	0.26602	0.154;0.127	B;B	0.38755	0.281;0.185	D	0.89850	0.4009	10	0.33141	T	0.24	-21.537	19.4533	0.94876	0.0:0.0:1.0:0.0	.	688;688	Q9H4L7;Q9H4L7-2	SMRCD_HUMAN;.	I	688;688;688;258	ENSP00000351947:R688I;ENSP00000415576:R688I;ENSP00000346217:R688I;ENSP00000423286:R258I	ENSP00000346217:R688I	R	+	2	0	SMARCAD1	95417314	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.475000	0.81041	2.604000	0.88044	0.555000	0.69702	AGA	.	.		0.373	SMARCAD1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253583.1	NM_020159		T	95198291	G	T	95198291	3	4	257	1	0	0	0	0	1	0	0	0	14787	942	33	3	2121	3	SMARCAD1	4	95198291	Missense_Mutation	SNP	G	TCGA-EP-A3JL-01A-11D-A20W-10	4341946	95198291	95955985	28	36219										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13794081	13794081	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	ttgattattggcatattcacAtcatcaataaaaacagtcat	4	7	4	1			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr5:13794081A>G	ENST00000265104.4	-	48	8078	c.7974T>C	c.(7972-7974)gaT>gaC	p.D2658D		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2658	AAA 3. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					GCATATTCACATCATCAATAA	0.348									Kartagener syndrome																												p.D2658D		Atlas-SNP	.											.	DNAH5	868	.	0			c.T7974C						.						110	101	104					5																	13794081		2203	4300	6503	SO:0001819	synonymous_variant	1767	exon48	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	ATTCACATCATCA	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.7974T>C	chr5.hg19:g.13794081A>G		243.0	0.0		225.0	118.0	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	hg19	CCDS3882.1																																																																																			.	.		0.348	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		G	13794081	A	G	13794081	2	3	257	1	0	0	0	0	0	0	0	1	4606	214	8	2		2	DNAH5	5	13794081	Silent	SNP	A	TCGA-EP-A3JL-01A-11D-A20W-10		13794081	167121179	29	36220										
CDH18	1016	hgsc.bcm.edu	37	chr5	19483500	19483500	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	ggcttctgcatggcaggtccGcacacgcccatctctctcgc	10	17	3	0			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr5:19483500G>A	ENST00000507958.1	-	14	2782	c.1792C>T	c.(1792-1794)Cgg>Tgg	p.R598W	CDH18_ENST00000502796.1_Silent_p.C561C|CDH18_ENST00000274170.4_Missense_Mutation_p.R598W|CDH18_ENST00000506372.1_Silent_p.C562C|CDH18_ENST00000382275.1_Missense_Mutation_p.R598W			Q13634	CAD18_HUMAN	cadherin 18, type 2	598	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					TGGCAGGTCCGCACACGCCCA	0.522																																					p.R598W		Atlas-SNP	.											CDH18_ENST00000507958,colon,carcinoma,0,4	CDH18	561	.	0			c.C1792T						.						78	69	72					5																	19483500		2203	4300	6503	SO:0001583	missense	1016	exon12			AGGTCCGCACACG	U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"Cadherins / Major cadherins"	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.1792C>T	chr5.hg19:g.19483500G>A	ENSP00000425093:p.Arg598Trp	234.0	0.0		322.0	61.0	NM_004934	A8K0I2|B4DHG6|Q8N5Z2	Missense_Mutation	SNP	ENST00000507958.1	hg19	CCDS3889.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.350073	0.82132	.	.	ENSG00000145526	ENST00000382275;ENST00000507958;ENST00000542864;ENST00000274170	T;T;T	0.60299	0.2;0.2;0.2	5.54	5.54	0.83059	Cadherin (1);	0.120662	0.53938	D	0.000054	T	0.64034	0.2562	L	0.50333	1.59	0.47778	D	0.999513	D	0.69078	0.997	P	0.57468	0.821	T	0.62224	-0.6899	9	.	.	.	.	11.9208	0.52791	0.0:0.0:0.7291:0.2709	.	598	Q13634	CAD18_HUMAN	W	598	ENSP00000371710:R598W;ENSP00000425093:R598W;ENSP00000274170:R598W	.	R	-	1	2	CDH18	19519257	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.741000	0.47426	2.615000	0.88500	0.655000	0.94253	CGG	.	.		0.522	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934		A	19483500	G	A	19483500	3	1	257	1	0	0	0	0	1	0	0	0	3105	1088	38	1	588	1	CDH18	5	19483500	Missense_Mutation	SNP	G	TCGA-EP-A3JL-01A-11D-A20W-10	5689419	19483500	161431760	30	36221										
RAD1	5810	hgsc.bcm.edu	37	chr5	34914840	34914840	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	gcacacactttgcattttccActgttactttgataccattt	4	11	0	1			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr5:34914840A>G	ENST00000382038.2	-	2	1577	c.158T>C	c.(157-159)gTg>gCg	p.V53A	RAD1_ENST00000341754.4_Missense_Mutation_p.V53A|BRIX1_ENST00000336767.5_5'Flank	NM_002853.3	NP_002844.1	O60671	RAD1_HUMAN	RAD1 checkpoint DNA exonuclease	53					cellular response to DNA damage stimulus (GO:0006974)|cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|meiotic recombination checkpoint (GO:0051598)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|substantia nigra development (GO:0021762)	chromosome (GO:0005694)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|damaged DNA binding (GO:0003684)|exodeoxyribonuclease III activity (GO:0008853)			endometrium(3)|large_intestine(1)|lung(5)|urinary_tract(1)	10	all_lung(31;0.000107)	Lung NSC(810;5.19e-05)|Ovarian(839;0.0448)|Breast(839;0.198)	COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)			TGCATTTTCCACTGTTACTTT	0.383								Other conserved DNA damage response genes																													p.V53A		Atlas-SNP	.											.	RAD1	17	.	0			c.T158C						.						175	162	167					5																	34914840		2203	4300	6503	SO:0001583	missense	5810	exon2			TTTTCCACTGTTA	AF074717	CCDS3905.1	5p13	2014-08-08	2014-08-08		ENSG00000113456	ENSG00000113456	3.1.11.2		9806	protein-coding gene	gene with protein product	"exonuclease homolog RAD1", "checkpoint control protein HRAD1", "cell cycle checkpoint protein Hrad1", "Rad1-like DNA damage checkpoint", "DNA repair exonuclease REC1"	603153	"RAD1 (S. pombe) homolog", "RAD1 homolog (S. pombe)"			9716408, 9828137	Standard	NR_026591		Approved	HRAD1, REC1	uc003jix.3	O60671	OTTHUMG00000090783	ENST00000382038.2:c.158T>C	chr5.hg19:g.34914840A>G	ENSP00000371469:p.Val53Ala	179.0	1.0		185.0	116.0	NM_002853	O75572|O95304|Q1W161|Q5KSM0|Q5KSM1|Q9UEP1	Missense_Mutation	SNP	ENST00000382038.2	hg19	CCDS3905.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.050769	0.75960	.	.	ENSG00000113456	ENST00000382038;ENST00000341754;ENST00000542494	T;T	0.10005	2.92;2.92	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.23965	0.0580	L	0.47078	1.49	0.80722	D	1	P	0.38129	0.619	P	0.53224	0.721	T	0.00451	-1.1731	10	0.52906	T	0.07	.	16.0193	0.80468	1.0:0.0:0.0:0.0	.	53	O60671	RAD1_HUMAN	A	53	ENSP00000371469:V53A;ENSP00000340879:V53A	ENSP00000313467:V53A	V	-	2	0	RAD1	34950597	1.000000	0.71417	0.997000	0.53966	0.686000	0.39977	8.574000	0.90763	2.190000	0.69967	0.533000	0.62120	GTG	.	.		0.383	RAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207567.1	NM_002853		G	34914840	A	G	34914840	3	3	257	1	0	0	0	0	1	0	0	0	12993	159	6	2	710	2	RAD1	5	34914840	Missense_Mutation	SNP	A	TCGA-EP-A3JL-01A-11D-A20W-10	15431340	34914840	146000420	31	36222										
C5orf42	65250	hgsc.bcm.edu	37	chr5	37226698	37226698	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	agtcagcaaaagttttacagTatttgaggtcagctttatca	8	6	3	1			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr5:37226698T>A	ENST00000508244.1	-	11	2092	c.1999A>T	c.(1999-2001)Act>Tct	p.T667S	C5orf42_ENST00000425232.2_Missense_Mutation_p.T667S|C5orf42_ENST00000274258.7_5'UTR			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	667						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			AGTTTTACAGTATTTGAGGTC	0.318																																					p.T667S		Atlas-SNP	.											.	C5orf42	422	.	0			c.A1999T						.						37	30	32					5																	37226698		692	1591	2283	SO:0001583	missense	65250	exon12			TTACAGTATTTGA		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.1999A>T	chr5.hg19:g.37226698T>A	ENSP00000421690:p.Thr667Ser	142.0	0.0		184.0	42.0	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	hg19	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	T	16.45	3.125779	0.56721	.	.	ENSG00000197603	ENST00000508244;ENST00000425232	D;D	0.98381	-4.9;-4.9	5.22	4.06	0.47325	.	0.158419	0.41712	U	0.000829	D	0.98333	0.9447	M	0.73598	2.24	0.80722	D	1	D	0.61697	0.99	P	0.61722	0.893	D	0.97907	1.0306	10	0.54805	T	0.06	-8.2488	10.8567	0.46802	0.0:0.0745:0.0:0.9255	.	667	E9PH94	.	S	667	ENSP00000421690:T667S;ENSP00000389014:T667S	ENSP00000389014:T667S	T	-	1	0	C5orf42	37262455	1.000000	0.71417	0.575000	0.28536	0.957000	0.61999	3.508000	0.53378	0.831000	0.34780	0.482000	0.46254	ACT	.	.		0.318	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		A	37226698	T	A	37226698	3	1	257	1	0	0	0	0	1	0	0	0	2303	1638	57	4	7758	4	C5orf42	5	37226698	Missense_Mutation	SNP	T	TCGA-EP-A3JL-01A-11D-A20W-10	2311858	37226698	143688562	32	36223										
MAP1B	4131	hgsc.bcm.edu	37	chr5	71489897	71489897	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	atctctcagaatcagtggaaGtcccatctccctttgacatc	6	13	4	2			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr5:71489897G>A	ENST00000296755.7	+	5	1013	c.715G>A	c.(715-717)Gtc>Atc	p.V239I		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	239					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		ATCAGTGGAAGTCCCATCTCC	0.453																																					p.V239I	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.G715A						.						109	104	106					5																	71489897		2203	4300	6503	SO:0001583	missense	4131	exon5			GTGGAAGTCCCAT	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.715G>A	chr5.hg19:g.71489897G>A	ENSP00000296755:p.Val239Ile	144.0	0.0		83.0	13.0	NM_005909	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	hg19	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	G	9.782	1.175522	0.21704	.	.	ENSG00000131711	ENST00000296755;ENST00000511641;ENST00000504492	T;T;T	0.21932	1.98;1.98;1.98	6.08	6.08	0.98989	.	0.000000	0.64402	D	0.000013	T	0.16471	0.0396	L	0.33485	1.01	0.37405	D	0.913005	B;B	0.31077	0.307;0.307	B;B	0.20767	0.031;0.031	T	0.05649	-1.0872	10	0.48119	T	0.1	-18.972	13.8168	0.63297	0.0695:0.0:0.9305:0.0	.	113;239	A2BDK6;P46821	.;MAP1B_HUMAN	I	239;256;113	ENSP00000296755:V239I;ENSP00000423444:V256I;ENSP00000423416:V113I	ENSP00000296755:V239I	V	+	1	0	MAP1B	71525653	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	6.233000	0.72320	2.894000	0.99253	0.591000	0.81541	GTC	.	.		0.453	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		A	71489897	G	A	71489897	3	1	257	1	0	0	0	0	1	0	0	0	9237	1029	36	3	733	3	MAP1B	5	71489897	Missense_Mutation	SNP	G	TCGA-EP-A3JL-01A-11D-A20W-10	34263199	71489897	109425363	33	36224										
GPR98	84059	hgsc.bcm.edu	37	chr5	89989829	89989829	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	atctccaattcaaggggtgcCtgacccactttggagaactt	9	11	2	2			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr5:89989829C>A	ENST00000405460.2	+	33	7352	c.7256C>A	c.(7255-7257)cCt>cAt	p.P2419H		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	2419					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		CAAGGGGTGCCTGACCCACTT	0.483																																					p.P2419H		Atlas-SNP	.											.	GPR98	605	.	0			c.C7256A						.						81	78	79					5																	89989829		1907	4120	6027	SO:0001583	missense	84059	exon33			GGGTGCCTGACCC	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.7256C>A	chr5.hg19:g.89989829C>A	ENSP00000384582:p.Pro2419His	169.0	0.0		109.0	31.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	C	17.02	3.281408	0.59758	.	.	ENSG00000164199	ENST00000405460;ENST00000296619	T	0.29142	1.58	5.97	5.97	0.96955	.	0.045090	0.85682	D	0.000000	T	0.57961	0.2089	M	0.67953	2.075	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.56860	-0.7909	10	0.87932	D	0	.	20.4135	0.99023	0.0:1.0:0.0:0.0	.	2419;2419	E7ETI5;Q8WXG9	.;GPR98_HUMAN	H	2419	ENSP00000384582:P2419H	ENSP00000296619:P2419H	P	+	2	0	GPR98	90025585	0.997000	0.39634	1.000000	0.80357	0.036000	0.12997	5.910000	0.69931	2.835000	0.97688	0.591000	0.81541	CCT	.	.		0.483	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		A	89989829	C	A	89989829	3	1	257	1	0	0	0	0	1	0	0	0	6730	681	24	3	7386	3	GPR98	5	89989829	Missense_Mutation	SNP	C	TCGA-EP-A3JL-01A-11D-A20W-10	18499932	89989829	90925431	34	36225										
GRIA1	2890	hgsc.bcm.edu	37	chr5	153149817	153149817	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	cggaccacagaggaggggatGattcgagtgaggaaatccaa	15	7	0	3			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr5:153149817G>A	ENST00000285900.5	+	13	2455	c.2112G>A	c.(2110-2112)atG>atA	p.M704I	GRIA1_ENST00000448073.4_Missense_Mutation_p.M714I|GRIA1_ENST00000518142.1_Missense_Mutation_p.M624I|GRIA1_ENST00000340592.5_Missense_Mutation_p.M704I|GRIA1_ENST00000521843.2_Missense_Mutation_p.M635I|GRIA1_ENST00000518783.1_Missense_Mutation_p.M714I	NM_000827.3|NM_001258019.1	NP_000818.2|NP_001244948.1	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1	704					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|axonal spine (GO:0044308)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|neuron spine (GO:0044309)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|PDZ domain binding (GO:0030165)			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)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Perampanel(DB08883)|Sevoflurane(DB01236)	AGGAGGGGATGATTCGAGTGA	0.488																																					p.M714I		Atlas-SNP	.											GRIA1_ENST00000544403,NS,malignant_melanoma,0,2	GRIA1	321	.	0			c.G2142A						.						139	125	130					5																	153149817		2203	4300	6503	SO:0001583	missense	2890	exon13			GGGGATGATTCGA		CCDS4322.1, CCDS47318.1, CCDS58986.1, CCDS58987.1, CCDS58988.1, CCDS58989.1	5q33	2012-08-29			ENSG00000155511	ENSG00000155511		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4571	protein-coding gene	gene with protein product		138248		GLUR1		1652753, 1319477	Standard	NM_000827		Approved	GluA1, GLURA	uc011dcy.2	P42261	OTTHUMG00000130148	ENST00000285900.5:c.2112G>A	chr5.hg19:g.153149817G>A	ENSP00000285900:p.Met704Ile	181.0	0.0		122.0	63.0	NM_001258021	B7Z2S0|B7Z2W8|B7Z3F6|B7Z9G9|D3DQI4|E7ESV8|Q2NKM6	Missense_Mutation	SNP	ENST00000285900.5	hg19	CCDS4322.1	.	.	.	.	.	.	.	.	.	.	G	2.259	-0.369632	0.05069	.	.	ENSG00000155511	ENST00000285900;ENST00000544403;ENST00000518142;ENST00000537037;ENST00000340592;ENST00000521843;ENST00000544794;ENST00000518783;ENST00000448073	T;T;T;T;T;T;T	0.36157	1.82;1.82;1.27;1.82;1.82;1.82;1.27	5.41	5.41	0.78517	Ionotropic glutamate receptor (2);	0.039962	0.85682	D	0.000000	T	0.08891	0.0220	N	0.00039	-2.51	0.47547	D	0.999458	B;B;B;B;B	0.23249	0.082;0.082;0.002;0.066;0.004	B;B;B;B;B	0.24006	0.05;0.05;0.002;0.03;0.007	T	0.41645	-0.9497	10	0.17369	T	0.5	.	18.1724	0.89751	0.0:0.0:1.0:0.0	.	714;714;624;704;704	E7ESV8;B7Z9G9;B7Z3F6;P42261-2;P42261	.;.;.;.;GRIA1_HUMAN	I	704;704;624;658;704;637;635;714;714	ENSP00000285900:M704I;ENSP00000427920:M624I;ENSP00000339343:M704I;ENSP00000427864:M637I;ENSP00000442108:M635I;ENSP00000428994:M714I;ENSP00000415569:M714I	ENSP00000285900:M704I	M	+	3	0	GRIA1	153130010	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	1.553000	0.36255	2.525000	0.85131	0.655000	0.94253	ATG	.	.		0.488	GRIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252456.3			A	153149817	G	A	153149817	3	1	257	1	0	0	0	0	1	0	0	0	6776	1290	45	3	2162	3	GRIA1	5	153149817	Missense_Mutation	SNP	G	TCGA-EP-A3JL-01A-11D-A20W-10	63159988	153149817	27765443	35	36226										
ARG1	383	hgsc.bcm.edu	37	chr6	131904974	131904974	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	cagtgaacacagcagttgcaAtaaccttggcttgtttcgga	10	9	0	1			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr6:131904974A>G	ENST00000368087.3	+	8	1034	c.895A>G	c.(895-897)Ata>Gta	p.I299V	MED23_ENST00000479213.1_5'Flank|ARG1_ENST00000356962.2_Missense_Mutation_p.I307V|MED23_ENST00000354577.4_Intron			P05089	ARGI1_HUMAN	arginase 1	299					arginine catabolic process (GO:0006527)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to glucagon stimulus (GO:0071377)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interleukin-4 (GO:0071353)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen biosynthetic process (GO:0032964)|liver development (GO:0001889)|lung development (GO:0030324)|mammary gland involution (GO:0060056)|maternal process involved in female pregnancy (GO:0060135)|positive regulation of endothelial cell proliferation (GO:0001938)|protein homotrimerization (GO:0070207)|regulation of L-arginine import (GO:0010963)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to axon injury (GO:0048678)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to herbicide (GO:0009635)|response to manganese ion (GO:0010042)|response to methylmercury (GO:0051597)|response to selenium ion (GO:0010269)|response to vitamin A (GO:0033189)|response to vitamin E (GO:0033197)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	arginase activity (GO:0004053)|manganese ion binding (GO:0030145)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(1)|skin(3)	14	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0106)|OV - Ovarian serous cystadenocarcinoma(155;0.0713)	L-Ornithine(DB00129)	AGCAGTTGCAATAACCTTGGC	0.443																																					p.I307V		Atlas-SNP	.											.	ARG1	33	.	0			c.A919G						.						149	129	136					6																	131904974		2203	4300	6503	SO:0001583	missense	383	exon8			GTTGCAATAACCT		CCDS5145.1, CCDS59038.1	6q23	2013-05-01	2013-05-01		ENSG00000118520	ENSG00000118520	3.5.3.1		663	protein-coding gene	gene with protein product		608313	"arginase, liver"			22959135	Standard	NM_000045		Approved		uc003qcp.2	P05089	OTTHUMG00000015566	ENST00000368087.3:c.895A>G	chr6.hg19:g.131904974A>G	ENSP00000357066:p.Ile299Val	85.0	0.0		78.0	44.0	NM_001244438	A6NEA0|Q5JWT5|Q5JWT6|Q8TE72|Q9BS50	Missense_Mutation	SNP	ENST00000368087.3	hg19	CCDS5145.1	.	.	.	.	.	.	.	.	.	.	A	0.286	-0.983316	0.02180	.	.	ENSG00000118520	ENST00000368087;ENST00000356962;ENST00000476845	D;D;D	0.87029	-1.79;-1.79;-2.2	6.01	-12.0	0.00017	Ureohydrolase domain (1);	0.478827	0.24642	N	0.036796	T	0.29288	0.0729	N	0.01515	-0.825	0.58432	D	0.999999	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.60525	-0.7246	10	0.13470	T	0.59	-0.439	4.1367	0.10174	0.2305:0.1302:0.4215:0.2178	.	307;299	P05089-2;P05089	.;ARGI1_HUMAN	V	299;307;213	ENSP00000357066:I299V;ENSP00000349446:I307V;ENSP00000417694:I213V	ENSP00000349446:I307V	I	+	1	0	ARG1	131946667	0.000000	0.05858	0.000000	0.03702	0.813000	0.45954	-2.288000	0.01150	-3.324000	0.00187	-0.911000	0.02809	ATA	.	.		0.443	ARG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042223.1			G	131904974	A	G	131904974	3	3	257	1	0	0	0	0	1	0	0	0	857	101	4	2	925	2	ARG1	6	131904974	Missense_Mutation	SNP	A	TCGA-EP-A3JL-01A-11D-A20W-10		131904974	39210093	36	36227										
PDK4	5166	hgsc.bcm.edu	37	chr7	95222151	95222151	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	tattgaagattttgattggtGactgggtcaactgtacaggc	12	5	1	4			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr7:95222151G>A	ENST00000005178.5	-	4	647	c.450C>T	c.(448-450)gtC>gtT	p.V150V		NM_002612.3	NP_002603.1	Q16654	PDK4_HUMAN	pyruvate dehydrogenase kinase, isozyme 4	150	Histidine kinase. {ECO:0000255|PROSITE- ProRule:PRU00107}.				cellular metabolic process (GO:0044237)|cellular response to fatty acid (GO:0071398)|cellular response to starvation (GO:0009267)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|negative regulation of anoikis (GO:2000811)|protein phosphorylation (GO:0006468)|pyruvate metabolic process (GO:0006090)|reactive oxygen species metabolic process (GO:0072593)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of bone resorption (GO:0045124)|regulation of cellular ketone metabolic process (GO:0010565)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of fatty acid oxidation (GO:0046320)|regulation of glucose metabolic process (GO:0010906)|regulation of pH (GO:0006885)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	15	all_cancers(62;1.06e-10)|all_epithelial(64;1.04e-09)|Lung NSC(181;0.128)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0151)			TTTGATTGGTGACTGGGTCAA	0.383																																					p.V150V		Atlas-SNP	.											.	PDK4	42	.	0			c.C450T						.						161	155	157					7																	95222151		2203	4300	6503	SO:0001819	synonymous_variant	5166	exon4			ATTGGTGACTGGG	U54617	CCDS5643.1	7q21.3-q22.1	2008-07-18	2005-11-16		ENSG00000004799	ENSG00000004799			8812	protein-coding gene	gene with protein product		602527	"pyruvate dehydrogenase kinase, isoenzyme 4"			7499431	Standard	NM_002612		Approved		uc003uoa.3	Q16654	OTTHUMG00000153977	ENST00000005178.5:c.450C>T	chr7.hg19:g.95222151G>A		189.0	0.0		129.0	35.0	NM_002612		Silent	SNP	ENST00000005178.5	hg19	CCDS5643.1																																																																																			.	.		0.383	PDK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333298.1	NM_002612		A	95222151	G	A	95222151	2	1	257	1	0	0	0	0	0	0	0	1	11687	1277	45	3		3	PDK4	7	95222151	Silent	SNP	G	TCGA-EP-A3JL-01A-11D-A20W-10		95222151	63916512	37	36228										
ZBTB10	65986	hgsc.bcm.edu	37	chr8	81412172	81412172	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	agcattaaatcagaagctccAgagtctgtagttgtggacta	10	7	2	2			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr8:81412172A>G	ENST00000430430.1	+	3	2195	c.1416A>G	c.(1414-1416)ccA>ccG	p.P472P	ZBTB10_ENST00000426744.2_Silent_p.P472P|ZBTB10_ENST00000455036.3_Silent_p.P472P|ZBTB10_ENST00000379091.4_Silent_p.P180P	NM_001277145.1	NP_001264074.1	Q96DT7	ZBT10_HUMAN	zinc finger and BTB domain containing 10	472					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(4)	20	all_cancers(3;1.68e-09)|all_epithelial(4;5.13e-11)|Lung NSC(7;1.75e-07)|all_lung(9;7.38e-07)|Breast(3;2.96e-06)		BRCA - Breast invasive adenocarcinoma(6;0.000434)|Epithelial(68;0.00486)|all cancers(69;0.0296)			CAGAAGCTCCAGAGTCTGTAG	0.373																																					p.P472P		Atlas-SNP	.											.	ZBTB10	51	.	0			c.A1416G						.						85	86	86					8																	81412172		1806	4074	5880	SO:0001819	synonymous_variant	65986	exon2			AGCTCCAGAGTCT	AK022814	CCDS47880.1, CCDS64920.1	8q13-q21.1	2013-01-09			ENSG00000205189	ENSG00000205189		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	30953	protein-coding gene	gene with protein product						12477932	Standard	NM_001105539		Approved	RINZF, FLJ12752	uc003ybx.5	Q96DT7	OTTHUMG00000155016	ENST00000430430.1:c.1416A>G	chr8.hg19:g.81412172A>G		68.0	0.0		77.0	16.0	NM_023929	A4FVD0|Q86W96|Q8IXI9|Q96MH9	Silent	SNP	ENST00000430430.1	hg19	CCDS47880.1																																																																																			.	.		0.373	ZBTB10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338055.2	NM_023929		G	81412172	A	G	81412172	2	3	257	1	0	0	0	0	0	0	0	1	17538	175	7	2		2	ZBTB10	8	81412172	Silent	SNP	A	TCGA-EP-A3JL-01A-11D-A20W-10		81412172	64951850	38	36229										
SLC39A4	55630	hgsc.bcm.edu	37	chr8	145641255	145641255	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	gcagcagccagctcaggcccGgggtcagggccttggggctc	17	14	2	0			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr8:145641255G>A	ENST00000301305.3	-	2	518	c.413C>T	c.(412-414)cCg>cTg	p.P138L	SLC39A4_ENST00000276833.5_Missense_Mutation_p.P113L|SLC39A4_ENST00000531013.1_5'Flank	NM_130849.2	NP_570901	Q6P5W5	S39A4_HUMAN	solute carrier family 39 (zinc transporter), member 4	138					cellular response to zinc ion starvation (GO:0034224)|cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	14	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;1.12e-40)|all cancers(56;8.17e-36)|BRCA - Breast invasive adenocarcinoma(115;0.0407)|Colorectal(110;0.055)			GCTCAGGCCCGGGGTCAGGGC	0.706																																					p.P138L		Atlas-SNP	.											.	SLC39A4	54	.	0			c.C413T						.						10	12	11					8																	145641255		2166	4252	6418	SO:0001583	missense	55630	exon2			AGGCCCGGGGTCA	AK025537	CCDS6424.1, CCDS43782.1	8q24.3	2013-05-22			ENSG00000147804	ENSG00000147804		"Solute carriers"	17129	protein-coding gene	gene with protein product		607059	"acrodermatitis enteropathica, zinc-deficiency type"	AEZ		12801924, 12659941, 14709598	Standard	NM_017767		Approved	ZIP4, AWMS2	uc003zcq.3	Q6P5W5		ENST00000301305.3:c.413C>T	chr8.hg19:g.145641255G>A	ENSP00000301305:p.Pro138Leu	19.0	0.0		111.0	7.0	NM_130849	Q7L5S5|Q9H6T8|Q9NXC4	Missense_Mutation	SNP	ENST00000301305.3	hg19	CCDS6424.1	.	.	.	.	.	.	.	.	.	.	G	3.253	-0.152854	0.06585	.	.	ENSG00000147804	ENST00000276833;ENST00000301305	T;T	0.52526	0.66;0.66	4.4	-5.19	0.02832	.	9.789490	0.00628	N	0.000469	T	0.24044	0.0582	N	0.08118	0	0.20821	N	0.999843	B;B	0.10296	0.0;0.003	B;B	0.06405	0.001;0.002	T	0.10359	-1.0633	10	0.21540	T	0.41	-2.7766	5.8431	0.18645	0.5706:0.0:0.2018:0.2275	.	138;113	Q6P5W5;A6NDY5	S39A4_HUMAN;.	L	113;138	ENSP00000276833:P113L;ENSP00000301305:P138L	ENSP00000276833:P113L	P	-	2	0	SLC39A4	145612063	0.000000	0.05858	0.079000	0.20413	0.008000	0.06430	-1.143000	0.03200	-1.080000	0.03109	-0.683000	0.03753	CCG	.	.		0.706	SLC39A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382688.1			A	145641255	G	A	145641255	3	1	257	1	0	0	0	0	1	0	0	0	14635	1116	39	1	1574	1	SLC39A4	8	145641255	Missense_Mutation	SNP	G	TCGA-EP-A3JL-01A-11D-A20W-10	64229083	145641255	722767	39	36230										
ZCCHC7	84186	hgsc.bcm.edu	37	chr9	37302184	37302184	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	aataatttatttgttttgtaGgagaagatggtataaactgg	10	1	0	2			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr9:37302184G>A	ENST00000336755.5	+	3	716		c.e3-1		ZCCHC7_ENST00000461038.1_Splice_Site|ZCCHC7_ENST00000534928.1_Splice_Site	NM_032226.2	NP_115602.2	Q8N3Z6	ZCHC7_HUMAN	zinc finger, CCHC domain containing 7							cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	30				GBM - Glioblastoma multiforme(29;0.0137)		TTGTTTTGTAGGAGAAGATGG	0.294																																					.		Atlas-SNP	.											.	ZCCHC7	56	.	0			c.611-1G>A						.						93	99	97					9																	37302184		2203	4297	6500	SO:0001630	splice_region_variant	84186	exon3			TTTGTAGGAGAAG	AK026264	CCDS6608.2	9p13.1	2008-05-02			ENSG00000147905	ENSG00000147905		"Zinc fingers, CCHC domain containing"	26209	protein-coding gene	gene with protein product							Standard	NM_032226		Approved	FLJ22611, AIR1	uc003zzq.3	Q8N3Z6	OTTHUMG00000019915	ENST00000336755.5:c.611-1G>A	chr9.hg19:g.37302184G>A		75.0	0.0		38.0	7.0	NM_032226	B2RCI4|D3DRQ0|Q5T0Q8|Q5T0Q9|Q5T0R0|Q8N2M1|Q8N4J2|Q8TBK8|Q9H648|Q9P0F0	Splice_Site	SNP	ENST00000336755.5	hg19	CCDS6608.2	.	.	.	.	.	.	.	.	.	.	G	21.0	4.082142	0.76528	.	.	ENSG00000147905	ENST00000336755	.	.	.	5.87	5.87	0.94306	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.9706	0.92713	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ZCCHC7	37292184	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	5.747000	0.68689	2.775000	0.95449	0.650000	0.86243	.	.	.		0.294	ZCCHC7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052453.2	NM_032226	Intron	A	37302184	G	A	37302184	5	1	257	1	0	0	0	0	0	0	1	0	17608	1014	35	3	616	3	ZCCHC7	9	37302184	Splice_Site	SNP	G	TCGA-EP-A3JL-01A-11D-A20W-10		37302184	103911247	40	36231										
FAM120A	23196	hgsc.bcm.edu	37	chr9	96318785	96318785	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	ctgggaacactgttgtccttGgatgtattttgatgggaagc	13	6	0	1			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr9:96318785G>T	ENST00000277165.6	+	13	2590	c.2396G>T	c.(2395-2397)tGg>tTg	p.W799L	FAM120A_ENST00000333936.5_Missense_Mutation_p.W827L|FAM120A_ENST00000340893.4_Missense_Mutation_p.W799L	NM_014612.3	NP_055427.2	Q9NZB2	F120A_HUMAN	family with sequence similarity 120A	799						cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(3)|large_intestine(8)|lung(12)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						TGTTGTCCTTGGATGTATTTT	0.502																																					p.W799L		Atlas-SNP	.											.	FAM120A	105	.	0			c.G2396T						.						188	186	187					9																	96318785		2203	4300	6503	SO:0001583	missense	23196	exon13			GTCCTTGGATGTA	AF214737	CCDS6706.1, CCDS75859.1	9q22.31	2013-03-08	2006-07-04	2006-07-04	ENSG00000048828	ENSG00000048828			13247	protein-coding gene	gene with protein product	"DNA polymerase-transactivated protein 1", "oxidative stess-associated Src activator"	612265	"chromosome 9 open reading frame 10"	C9orf10		14585507	Standard	NM_001286722		Approved	KIAA0183, DNAPTP1, OSSA	uc004atw.3	Q9NZB2	OTTHUMG00000020252	ENST00000277165.6:c.2396G>T	chr9.hg19:g.96318785G>T	ENSP00000277165:p.Trp799Leu	180.0	0.0		132.0	34.0	NM_014612	A6NGU0|C4AMC6|O60649|Q14688|Q4VXF4|Q4VXF5|Q4VXG2|Q86V69|Q96I21|Q9NZB1	Missense_Mutation	SNP	ENST00000277165.6	hg19	CCDS6706.1	.	.	.	.	.	.	.	.	.	.	G	34	5.291703	0.95546	.	.	ENSG00000048828	ENST00000277165;ENST00000333936;ENST00000340893;ENST00000427765	T;T;T;T	0.52057	0.68;0.68;0.68;0.68	5.92	5.92	0.95590	.	0.000000	0.64402	D	0.000001	T	0.70710	0.3255	M	0.69823	2.125	0.80722	D	1	D;D;D	0.89917	0.998;1.0;1.0	D;D;D	0.87578	0.994;0.998;0.994	T	0.71517	-0.4569	10	0.87932	D	0	-8.7224	20.3214	0.98679	0.0:0.0:1.0:0.0	.	799;827;799	Q9NZB2-4;Q9NZB2-6;Q9NZB2	.;.;F120A_HUMAN	L	799;827;799;221	ENSP00000277165:W799L;ENSP00000334918:W827L;ENSP00000344698:W799L;ENSP00000412440:W221L	ENSP00000277165:W799L	W	+	2	0	FAM120A	95358606	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.837000	0.99465	2.804000	0.96469	0.655000	0.94253	TGG	.	.		0.502	FAM120A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053160.2	NM_014612		T	96318785	G	T	96318785	3	4	257	1	0	0	0	0	1	0	0	0	5420	1357	47	3	2446	3	FAM120A	9	96318785	Missense_Mutation	SNP	G	TCGA-EP-A3JL-01A-11D-A20W-10	59016601	96318785	44894646	41	36232										
ZNF169	169841	hgsc.bcm.edu	37	chr9	97063227	97063227	+	Missense_Mutation	SNP	T	T	C													0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	agccctacctgtgccctgatTgtgggcgtggctttggtcag							TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr9:97063227T>C	ENST00000395395.2	+	5	1477	c.1387T>C	c.(1387-1389)Tgt>Cgt	p.C463R	ZNF169_ENST00000340911.4_3'UTR	NM_194320.2	NP_919301.2	Q14929	ZN169_HUMAN	zinc finger protein 169	463					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	24		Acute lymphoblastic leukemia(62;0.136)				GTGCCCTGATTGTGGGCGTGG	0.582																																					p.C463R		Atlas-SNP	.											.	ZNF169	60	.	0			c.T1387C						.						68	64	65					9																	97063227		2203	4300	6503	SO:0001583	missense	169841	exon5			CCTGATTGTGGGC	U28322	CCDS6709.2	9q22.32	2014-07-30			ENSG00000175787	ENSG00000175787		"Zinc fingers, C2H2-type", "-"	12957	protein-coding gene	gene with protein product		603404				9186526, 9071574	Standard	NM_001301275		Approved	MGC51961	uc004aum.1	Q14929	OTTHUMG00000020264	ENST00000395395.2:c.1387T>C	chr9.hg19:g.97063227T>C	ENSP00000378792:p.Cys463Arg	99.0	0.0		77.0	17.0	NM_194320	A2AGP5|A8K127|Q6PI28	Missense_Mutation	SNP	ENST00000395395.2	hg19	CCDS6709.2	.	.	.	.	.	.	.	.	.	.	T	17.05	3.289253	0.59976	.	.	ENSG00000175787	ENST00000395395;ENST00000340911	D	0.85955	-2.05	2.83	2.83	0.33086	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.93733	0.7997	H	0.96398	3.815	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93853	0.7147	9	0.87932	D	0	.	9.4444	0.38688	0.0:0.0:0.0:1.0	.	463	Q14929	ZN169_HUMAN	R	463;272	ENSP00000378792:C463R	ENSP00000340711:C272R	C	+	1	0	ZNF169	96103048	1.000000	0.71417	0.981000	0.43875	0.880000	0.50808	6.388000	0.73195	1.556000	0.49512	0.491000	0.48974	TGT	.	.		0.582	ZNF169-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253714.1	NM_194320		C	97063227	T	C	97063227	3	2	257	1	0	0	0	0	1	0	0	0	17757	1812	63	2	1401	2	ZNF169	9	97063227	Missense_Mutation	SNP	T	TCGA-EP-A3JL-01A-11D-A20W-10	744442	97063227	44150204	42	36233	183	2								
ZNF169	169841	hgsc.bcm.edu	37	chr9	97063234	97063234	+	Missense_Mutation	SNP	G	G	C													0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	cctgtgccctgattgtgggcGtggctttggtcagaaggtca							TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr9:97063234G>C	ENST00000395395.2	+	5	1484	c.1394G>C	c.(1393-1395)cGt>cCt	p.R465P	ZNF169_ENST00000340911.4_3'UTR	NM_194320.2	NP_919301.2	Q14929	ZN169_HUMAN	zinc finger protein 169	465					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	24		Acute lymphoblastic leukemia(62;0.136)				GATTGTGGGCGTGGCTTTGGT	0.577																																					p.R465P		Atlas-SNP	.											.	ZNF169	60	.	0			c.G1394C						.						72	65	67					9																	97063234		2203	4300	6503	SO:0001583	missense	169841	exon5			GTGGGCGTGGCTT	U28322	CCDS6709.2	9q22.32	2014-07-30			ENSG00000175787	ENSG00000175787		"Zinc fingers, C2H2-type", "-"	12957	protein-coding gene	gene with protein product		603404				9186526, 9071574	Standard	NM_001301275		Approved	MGC51961	uc004aum.1	Q14929	OTTHUMG00000020264	ENST00000395395.2:c.1394G>C	chr9.hg19:g.97063234G>C	ENSP00000378792:p.Arg465Pro	114.0	0.0		82.0	16.0	NM_194320	A2AGP5|A8K127|Q6PI28	Missense_Mutation	SNP	ENST00000395395.2	hg19	CCDS6709.2	.	.	.	.	.	.	.	.	.	.	G	14.94	2.686586	0.47991	.	.	ENSG00000175787	ENST00000395395;ENST00000340911	T	0.19806	2.12	2.83	1.9	0.25705	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.41743	0.1172	M	0.76170	2.325	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.32508	-0.9904	9	0.87932	D	0	.	9.1112	0.36730	0.0:0.0:0.7796:0.2204	.	465	Q14929	ZN169_HUMAN	P	465;274	ENSP00000378792:R465P	ENSP00000340711:R274P	R	+	2	0	ZNF169	96103055	0.900000	0.30661	0.995000	0.50966	0.938000	0.57974	2.159000	0.42339	0.750000	0.32877	-0.251000	0.11542	CGT	.	.		0.577	ZNF169-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253714.1	NM_194320		C	97063234	G	C	97063234	3	2	257	1	0	0	0	0	1	0	0	0	17757	1145	40	4	1408	4	ZNF169	9	97063234	Missense_Mutation	SNP	G	TCGA-EP-A3JL-01A-11D-A20W-10	7	97063234	44150197	43	36234	183	2								
SFMBT2	57713	hgsc.bcm.edu	37	chr10	7327859	7327860	+	Missense_Mutation	DNP	GA	GA	TT													0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	ggttggcgggtgctgtcctcGaaccagtcaagtcacgtatg							TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr10:7327859_7327860GA>TT	ENST00000361972.4	-	5	583_584	c.493_494TC>AA	c.(493-495)TCg>AAg	p.S165K	SFMBT2_ENST00000379713.3_Missense_Mutation_p.S165K|SFMBT2_ENST00000397167.1_Missense_Mutation_p.S165K	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	165					negative regulation of gene expression (GO:0010629)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	histone binding (GO:0042393)	p.S165L(1)		NS(2)|breast(3)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(26)|lung(34)|ovary(5)|pancreas(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	99						TGCTGTCCTCGAACCAGTCAAG	0.426																																					p.S165X|p.S165T		Atlas-SNP	.											SFMBT2,NS,malignant_melanoma,0,1|.	SFMBT2	209	.	1	Substitution - Missense(1)	NS(1)	c.C494A|c.T493A						.																																			SO:0001583	missense	57713	exon5			GTCCTCGAACCAG|TCCTCGAACCAGT	AB046837	CCDS31138.1	10p15.1	2013-01-10	2003-11-14		ENSG00000198879	ENSG00000198879		"Sterile alpha motif (SAM) domain containing"	20256	protein-coding gene	gene with protein product		615392	"Scm-related gene containing four mbt domains 2"			10997877	Standard	NM_001029880		Approved	KIAA1617	uc009xio.2	Q5VUG0	OTTHUMG00000017630	ENST00000361972.4:c.493_494delinsTT	chr10.hg19:g.7327859_7327860delinsTT	ENSP00000355109:p.Ser165Lys	233.0	0.0		179.0	31.0	NM_001029880	A7MD09|Q9HCF5	Nonsense_Mutation|Missense_Mutation	SNP	ENST00000361972.4	hg19	CCDS31138.1																																																																																			.	.		0.426	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046673.1	NM_001029880		TT	7327860	GA	TT	7327859	3	4	257	1	0	0	0	0	1	0	0	0	14173	1059	37	1	2258	1	SFMBT2	10	7327859	Missense_Mutation	DNP	GA	TCGA-EP-A3JL-01A-11D-A20W-10		7327859	128206888	44	36235										
ALOX5	240	hgsc.bcm.edu	37	chr10	45939709	45939709	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	gcatctgggtgcagtgtgggCgctgagccagttccaggaaa	16	9	1	1			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr10:45939709C>T	ENST00000374391.2	+	13	1873	c.1820C>T	c.(1819-1821)gCg>gTg	p.A607V	ALOX5_ENST00000542434.1_Intron|RP11-67C2.2_ENST00000435635.1_RNA	NM_000698.3|NM_001256153.1	NP_000689.1|NP_001243082.1	P09917	LOX5_HUMAN	arachidonate 5-lipoxygenase	607	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				arachidonic acid metabolic process (GO:0019369)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|leukotriene production involved in inflammatory response (GO:0002540)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular space (GO:0005615)|nuclear envelope (GO:0005635)|nuclear envelope lumen (GO:0005641)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)	arachidonate 5-lipoxygenase activity (GO:0004051)|iron ion binding (GO:0005506)			breast(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|pancreas(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		Lung SC(717;0.0257)			Aminosalicylic Acid(DB00233)|Balsalazide(DB01014)|Diclofenac(DB00586)|Diethylcarbamazine(DB00711)|Masoprocol(DB00179)|Meclofenamic acid(DB00939)|Mesalazine(DB00244)|Minocycline(DB01017)|Montelukast(DB00471)|Sulfasalazine(DB00795)|Vitamin E(DB00163)|Zileuton(DB00744)	GCAGTGTGGGCGCTGAGCCAG	0.667																																					p.A607V		Atlas-SNP	.											.	ALOX5	88	.	0			c.C1820T						.						14	14	14					10																	45939709		2144	4213	6357	SO:0001583	missense	240	exon13			TGTGGGCGCTGAG	J03571	CCDS7212.1, CCDS58078.1	10q11.2	2008-03-18			ENSG00000012779	ENSG00000012779	1.13.11.34	"Arachidonate lipoxygenases"	435	protein-coding gene	gene with protein product		152390				2565035	Standard	NM_001256153		Approved	5-LOX	uc001jce.4	P09917	OTTHUMG00000018081	ENST00000374391.2:c.1820C>T	chr10.hg19:g.45939709C>T	ENSP00000363512:p.Ala607Val	102.0	0.0		118.0	11.0	NM_000698	B7ZLS0|E5FPY5|E5FPY7|E5FPY8|Q5JQ14	Missense_Mutation	SNP	ENST00000374391.2	hg19	CCDS7212.1	.	.	.	.	.	.	.	.	.	.	C	16.36	3.102526	0.56183	.	.	ENSG00000012779	ENST00000374391	D	0.89196	-2.48	4.91	4.91	0.64330	Lipoxygenase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.89392	0.6702	L	0.35249	1.045	0.80722	D	1	D;D	0.89917	0.999;1.0	P;P	0.60236	0.846;0.871	D	0.87271	0.2286	10	0.27082	T	0.32	-34.4302	15.6441	0.77033	0.0:1.0:0.0:0.0	.	575;607	E5FPY8;P09917	.;LOX5_HUMAN	V	607	ENSP00000363512:A607V	ENSP00000363512:A607V	A	+	2	0	ALOX5	45259715	1.000000	0.71417	0.972000	0.41901	0.990000	0.78478	7.651000	0.83577	2.559000	0.86315	0.650000	0.86243	GCG	.	.		0.667	ALOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047780.1			T	45939709	C	T	45939709	3	4	257	1	0	0	0	0	1	0	0	0	540	768	27	1	1870	1	ALOX5	10	45939709	Missense_Mutation	SNP	C	TCGA-EP-A3JL-01A-11D-A20W-10	38611850	45939709	89595038	45	36236										
ACTR1A	10121	hgsc.bcm.edu	37	chr10	104247919	104247919	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	atcctcacctcctctgagaaAgtctgcagctggtccttaga	8	13	3	2			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr10:104247919A>C	ENST00000369905.4	-	4	366	c.303T>G	c.(301-303)acT>acG	p.T101T	ACTR1A_ENST00000446605.2_Silent_p.T54T|ACTR1A_ENST00000545684.1_Silent_p.T27T|ACTR1A_ENST00000487599.1_Silent_p.T101T	NM_005736.3	NP_005727.1	P61163	ACTZ_HUMAN	ARP1 actin-related protein 1 homolog A, centractin alpha (yeast)	101					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|vesicle-mediated transport (GO:0016192)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|extracellular vesicular exosome (GO:0070062)|microtubule associated complex (GO:0005875)	ATP binding (GO:0005524)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)	13		Colorectal(252;0.122)		Epithelial(162;5.34e-09)|all cancers(201;1.43e-07)|BRCA - Breast invasive adenocarcinoma(275;0.222)		CCTCTGAGAAAGTCTGCAGCT	0.493																																					p.T101T		Atlas-SNP	.											.	ACTR1A	26	.	0			c.T303G						.						145	120	129					10																	104247919		2203	4300	6503	SO:0001819	synonymous_variant	10121	exon4			TGAGAAAGTCTGC	X82206	CCDS7536.1	10q24	2008-07-08	2001-11-28		ENSG00000138107	ENSG00000138107			167	protein-coding gene	gene with protein product		605143	"ARP1 (actin-related protein 1, yeast) homolog A (centractin alpha)"			1528266	Standard	NM_005736		Approved	ARP1	uc001kvv.3	P61163	OTTHUMG00000018956	ENST00000369905.4:c.303T>G	chr10.hg19:g.104247919A>C		129.0	0.0		73.0	17.0	NM_005736	B2R6B0|P42024	Silent	SNP	ENST00000369905.4	hg19	CCDS7536.1																																																																																			.	.		0.493	ACTR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050053.1			C	104247919	A	C	104247919	2	2	257	1	0	0	0	0	0	0	0	1	209	59	3	5		5	ACTR1A	10	104247919	Silent	SNP	A	TCGA-EP-A3JL-01A-11D-A20W-10	58308210	104247919	31286828	46	36237										
ADD3	120	hgsc.bcm.edu	37	chr10	111883814	111883814	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	cttacaggcatcctctcattCgagagaagcctaggcacaag	9	12	1	1			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr10:111883814C>G	ENST00000356080.4	+	10	1550	c.1183C>G	c.(1183-1185)Cga>Gga	p.R395G	ADD3_ENST00000277900.8_Missense_Mutation_p.R395G|ADD3_ENST00000360162.3_Missense_Mutation_p.R395G	NM_016824.3	NP_058432.1	Q9UEY8	ADDG_HUMAN	adducin 3 (gamma)	395						cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	29		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;4.15e-05)|all cancers(201;0.000587)|BRCA - Breast invasive adenocarcinoma(275;0.0742)		TCCTCTCATTCGAGAGAAGCC	0.448																																					p.R395G		Atlas-SNP	.											.	ADD3	89	.	0			c.C1183G						.						110	96	101					10																	111883814		2203	4300	6503	SO:0001583	missense	120	exon10			CTCATTCGAGAGA	U37122	CCDS7561.1, CCDS7562.1	10q25.2	2005-11-08			ENSG00000148700	ENSG00000148700			245	protein-coding gene	gene with protein product		601568		ADDL		8893809	Standard	XM_005269529		Approved		uc001kyv.3	Q9UEY8	OTTHUMG00000019032	ENST00000356080.4:c.1183C>G	chr10.hg19:g.111883814C>G	ENSP00000348381:p.Arg395Gly	75.0	0.0		72.0	22.0	NM_001121	D3DRA8|O43243|Q5VU09|Q92773|Q9UEY7	Missense_Mutation	SNP	ENST00000356080.4	hg19	CCDS7561.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.126136	0.77549	.	.	ENSG00000148700	ENST00000360162;ENST00000356080;ENST00000277900	T;T;T	0.25250	1.81;1.81;1.81	6.03	5.07	0.68467	.	0.000000	0.85682	D	0.000000	T	0.52175	0.1718	M	0.80982	2.52	0.80722	D	1	D;D	0.71674	0.998;0.994	D;D	0.71870	0.975;0.954	T	0.55276	-0.8166	10	0.87932	D	0	-8.6307	14.5785	0.68268	0.2131:0.7869:0.0:0.0	.	395;395	Q9UEY8;Q9UEY8-2	ADDG_HUMAN;.	G	395	ENSP00000353286:R395G;ENSP00000348381:R395G;ENSP00000277900:R395G	ENSP00000277900:R395G	R	+	1	2	ADD3	111873804	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.951000	0.56684	2.861000	0.98227	0.655000	0.94253	CGA	.	.		0.448	ADD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050289.1	NM_019903		G	111883814	C	G	111883814	3	3	257	1	0	0	0	0	1	0	0	0	306	876	31	4	1217	4	ADD3	10	111883814	Missense_Mutation	SNP	C	TCGA-EP-A3JL-01A-11D-A20W-10	7635895	111883814	23650933	47	36238										
USP47	55031	hgsc.bcm.edu	37	chr11	11963990	11963990	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	caatcagattatttgttttgCtacctgaacaatccccagta	5	10	1	2			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr11:11963990C>G	ENST00000399455.2	+	21	2602	c.2482C>G	c.(2482-2484)Cta>Gta	p.L828V	USP47_ENST00000527733.1_Missense_Mutation_p.L808V|USP47_ENST00000539466.1_5'UTR|USP47_ENST00000339865.5_Missense_Mutation_p.L740V	NM_001282659.1	NP_001269588.1	Q96K76	UBP47_HUMAN	ubiquitin specific peptidase 47	828					base-excision repair (GO:0006284)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of G2/M transition of mitotic cell cycle (GO:0010972)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell growth (GO:0030307)|response to drug (GO:0042493)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	ubiquitin-specific protease activity (GO:0004843)|WD40-repeat domain binding (GO:0071987)			breast(4)|endometrium(7)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46				Epithelial(150;0.000339)		ATTTGTTTTGCTACCTGAACA	0.428																																					p.L740V		Atlas-SNP	.											.	USP47	91	.	0			c.C2218G						.						109	100	103					11																	11963990		1860	4095	5955	SO:0001583	missense	55031	exon19			GTTTTGCTACCTG	AK027362	CCDS41619.1, CCDS60725.1	11p15.2	2008-02-05	2005-08-08		ENSG00000170242	ENSG00000170242		"Ubiquitin-specific peptidases"	20076	protein-coding gene	gene with protein product		614460	"Trf (TATA binding protein-related factor)-proximal homolog (Drosophila)", "ubiquitin specific protease 47"			12838346	Standard	XM_005252997		Approved		uc001mjr.3	Q96K76	OTTHUMG00000165685	ENST00000399455.2:c.2482C>G	chr11.hg19:g.11963990C>G	ENSP00000382382:p.Leu828Val	113.0	0.0		67.0	14.0	NM_017944	B3KXF5|E9PM46|Q658U0|Q86Y73|Q8TEP6|Q9BWI0|Q9NWN1	Missense_Mutation	SNP	ENST00000399455.2	hg19		.	.	.	.	.	.	.	.	.	.	C	15.52	2.856656	0.51376	.	.	ENSG00000170242	ENST00000339865;ENST00000527733;ENST00000399455;ENST00000540365	T;T;T	0.11604	2.78;2.77;2.76	5.81	2.59	0.31030	.	0.066887	0.64402	D	0.000010	T	0.16896	0.0406	L	0.29908	0.895	0.80722	D	1	D;D;D	0.76494	0.999;0.997;0.998	D;D;D	0.68039	0.934;0.91;0.955	T	0.01114	-1.1447	10	0.56958	D	0.05	.	8.0802	0.30739	0.0:0.5189:0.0:0.4811	.	828;808;740	Q96K76;E9PM46;Q96K76-2	UBP47_HUMAN;.;.	V	740;808;828;25	ENSP00000339957:L740V;ENSP00000433146:L808V;ENSP00000382382:L828V	ENSP00000339957:L740V	L	+	1	2	USP47	11920566	0.999000	0.42202	1.000000	0.80357	0.997000	0.91878	1.148000	0.31614	0.267000	0.21916	0.591000	0.81541	CTA	.	.		0.428	USP47-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000385853.2	NM_017944		G	11963990	C	G	11963990	3	3	257	1	0	0	0	0	1	0	0	0	17093	796	28	4	2292	4	USP47	11	11963990	Missense_Mutation	SNP	C	TCGA-EP-A3JL-01A-11D-A20W-10		11963990	123042526	48	36239										
OR10Q1	219960	hgsc.bcm.edu	37	chr11	57995759	57995759	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	gacagcctggtgcacgcggaTgtcagcgcaggccaggcgca	16	13	1	0			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr11:57995759T>A	ENST00000316770.2	-	1	631	c.589A>T	c.(589-591)Atc>Ttc	p.I197F		NM_001004471.2	NP_001004471.1	Q8NGQ4	O10Q1_HUMAN	olfactory receptor, family 10, subfamily Q, member 1	197						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)	35		Breast(21;0.0589)				TGCACGCGGATGTCAGCGCAG	0.597																																					p.I197F		Atlas-SNP	.											.	OR10Q1	79	.	0			c.A589T						.						77	65	69					11																	57995759		2201	4295	6496	SO:0001583	missense	219960	exon1			CGCGGATGTCAGC	AB065735	CCDS31547.1	11q12.1	2012-08-09			ENSG00000180475	ENSG00000180475		"GPCR / Class A : Olfactory receptors"	15134	protein-coding gene	gene with protein product							Standard	NM_001004471		Approved		uc010rkd.2	Q8NGQ4	OTTHUMG00000167542	ENST00000316770.2:c.589A>T	chr11.hg19:g.57995759T>A	ENSP00000314324:p.Ile197Phe	172.0	0.0		114.0	42.0	NM_001004471	Q6IFG4	Missense_Mutation	SNP	ENST00000316770.2	hg19	CCDS31547.1	.	.	.	.	.	.	.	.	.	.	T	10.90	1.480804	0.26598	.	.	ENSG00000180475	ENST00000316770	T	0.00130	8.69	4.47	3.32	0.38043	GPCR, rhodopsin-like superfamily (1);	0.332026	0.21704	N	0.070378	T	0.00328	0.0010	M	0.72576	2.205	0.24380	N	0.994799	P	0.50066	0.931	P	0.58077	0.832	T	0.37126	-0.9719	10	0.87932	D	0	.	9.3326	0.38032	0.1608:0.0:0.0:0.8392	.	197	Q8NGQ4	O10Q1_HUMAN	F	197	ENSP00000314324:I197F	ENSP00000314324:I197F	I	-	1	0	OR10Q1	57752335	0.782000	0.28689	0.294000	0.24946	0.016000	0.09150	1.131000	0.31406	0.726000	0.32339	-0.481000	0.04817	ATC	.	.		0.597	OR10Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394706.1	NM_001004471		A	57995759	T	A	57995759	3	1	257	1	0	0	0	0	1	0	0	0	10925	1464	51	4	374	4	OR10Q1	11	57995759	Missense_Mutation	SNP	T	TCGA-EP-A3JL-01A-11D-A20W-10	46031769	57995759	77010757	49	36240										
MS4A15	219995	hgsc.bcm.edu	37	chr11	60543106	60543106	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	cttcctgccaaacgccttcaGcgcagacttcaacatcccca	5	18	2	1			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr11:60543106G>A	ENST00000405633.3	+	7	720	c.641G>A	c.(640-642)aGc>aAc	p.S214N	MS4A15_ENST00000337911.4_Missense_Mutation_p.S121N|MS4A15_ENST00000528170.1_Missense_Mutation_p.S173N	NM_001098835.1	NP_001092305.1	Q8N5U1	M4A15_HUMAN	membrane-spanning 4-domains, subfamily A, member 15	214						integral component of membrane (GO:0016021)				breast(1)|large_intestine(2)|lung(3)	6						AACGCCTTCAGCGCAGACTTC	0.577											OREG0020991	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S214N		Atlas-SNP	.											.	MS4A15	37	.	0			c.G641A						.						144	147	146					11																	60543106		2203	4300	6503	SO:0001583	missense	219995	exon7			CCTTCAGCGCAGA	AY584608	CCDS7991.1, CCDS44617.1, CCDS60802.1	11q12.2	2008-03-25							28573	protein-coding gene	gene with protein product							Standard	NM_001098835		Approved		uc009ynf.1	Q8N5U1		ENST00000405633.3:c.641G>A	chr11.hg19:g.60543106G>A	ENSP00000386022:p.Ser214Asn	99.0	0.0	1046	45.0	17.0	NM_001098835	A9UJY6|A9UJY7|F2Z2J5	Missense_Mutation	SNP	ENST00000405633.3	hg19	CCDS44617.1	.	.	.	.	.	.	.	.	.	.	G	7.611	0.674789	0.14841	.	.	ENSG00000166961	ENST00000528170;ENST00000337911;ENST00000405633	T;T;T	0.14766	2.48;2.52;2.94	5.25	4.34	0.51931	.	0.648678	0.16274	N	0.221645	T	0.12475	0.0303	L	0.57536	1.79	0.20703	N	0.999865	B;B	0.31383	0.321;0.115	B;B	0.23275	0.045;0.045	T	0.21008	-1.0258	10	0.17369	T	0.5	-20.6529	9.7942	0.40724	0.0954:0.0:0.9046:0.0	.	173;214	F2Z2J5;Q8N5U1	.;M4A15_HUMAN	N	173;121;214	ENSP00000434165:S173N;ENSP00000338692:S121N;ENSP00000386022:S214N	ENSP00000338692:S121N	S	+	2	0	MS4A15	60299682	0.972000	0.33761	0.996000	0.52242	0.260000	0.26232	2.068000	0.41471	1.206000	0.43276	-0.148000	0.13756	AGC	.	.		0.577	MS4A15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395618.1			A	60543106	G	A	60543106	3	1	257	1	0	0	0	0	1	0	0	0	9868	971	34	3	663	3	MS4A15	11	60543106	Missense_Mutation	SNP	G	TCGA-EP-A3JL-01A-11D-A20W-10	2547347	60543106	74463410	50	36241										
TECTA	7007	hgsc.bcm.edu	37	chr11	120989400	120989400	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	aatggctacaagattctcatCcccaaaggaagctatggaag	9	9	1	1			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr11:120989400C>T	ENST00000392793.1	+	7	1447	c.1176C>T	c.(1174-1176)atC>atT	p.I392I	TECTA_ENST00000264037.2_Silent_p.I392I			O75443	TECTA_HUMAN	tectorin alpha	392	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)			TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		AGATTCTCATCCCCAAAGGAA	0.522																																					p.I392I		Atlas-SNP	.											.	TECTA	329	.	0			c.C1176T						.						66	70	69					11																	120989400		2203	4299	6502	SO:0001819	synonymous_variant	7007	exon6			TCTCATCCCCAAA	AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.1176C>T	chr11.hg19:g.120989400C>T		89.0	0.0		54.0	12.0	NM_005422		Silent	SNP	ENST00000392793.1	hg19	CCDS8434.1																																																																																			.	.		0.522	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422		T	120989400	C	T	120989400	2	4	257	1	0	0	0	0	0	0	0	1	15762	845	30	3		3	TECTA	11	120989400	Silent	SNP	C	TCGA-EP-A3JL-01A-11D-A20W-10	60446294	120989400	14017116	51	36242										
UBE2N	7334	hgsc.bcm.edu	37	chr12	93835640	93835640	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	tgggcggttaccttgatgatCctgcggggcagcccggccat	15	12	0	2			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr12:93835640C>A	ENST00000318066.2	-	1	398	c.21G>T	c.(19-21)agG>agT	p.R7S	UBE2N_ENST00000550657.1_Missense_Mutation_p.R7S|UBE2N_ENST00000549833.1_5'Flank|UBE2N_ENST00000552442.1_Missense_Mutation_p.R7S	NM_003348.3	NP_003339.1	P61088	UBE2N_HUMAN	ubiquitin-conjugating enzyme E2N	7					cellular protein modification process (GO:0006464)|cytokine-mediated signaling pathway (GO:0019221)|DNA double-strand break processing (GO:0000729)|double-strand break repair via homologous recombination (GO:0000724)|Fc-epsilon receptor signaling pathway (GO:0038095)|histone ubiquitination (GO:0016574)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of DNA repair (GO:0045739)|positive regulation of histone modification (GO:0031058)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|postreplication repair (GO:0006301)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of DNA repair (GO:0006282)|regulation of histone ubiquitination (GO:0033182)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|protein complex (GO:0043234)|UBC13-MMS2 complex (GO:0031372)|UBC13-UEV1A complex (GO:0035370)|ubiquitin ligase complex (GO:0000151)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)	p.R7S(1)		endometrium(3)|liver(2)|lung(5)	10						CCTTGATGATCCTGCGGGGCA	0.692								Direct reversal of damage;Rad6 pathway																													p.R7S	Pancreas(197;738 2228 30225 32034 33454)	Atlas-SNP	.											UBE2N,NS,carcinoma,0,1	UBE2N	20	.	1	Substitution - Missense(1)	lung(1)	c.G21T						.						32	35	34					12																	93835640		2203	4300	6503	SO:0001583	missense	7334	exon1			GATGATCCTGCGG	D83004	CCDS31875.1	12q22	2011-05-19	2011-05-19			ENSG00000177889		"Ubiquitin-conjugating enzymes E2"	12492	protein-coding gene	gene with protein product		603679	"ubiquitin-conjugating enzyme E2N (homologous to yeast UBC13)", "ubiquitin-conjugating enzyme E2N (UBC13 homolog, yeast)"			8902611	Standard	NM_003348		Approved	UbcH-ben, UBC13, MGC8489	uc001tcp.3	P61088	OTTHUMG00000170156	ENST00000318066.2:c.21G>T	chr12.hg19:g.93835640C>A	ENSP00000316176:p.Arg7Ser	258.0	0.0		199.0	55.0	NM_003348	Q16781|Q53Y81	Missense_Mutation	SNP	ENST00000318066.2	hg19	CCDS31875.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.047672	0.75846	.	.	ENSG00000177889	ENST00000318066;ENST00000550657;ENST00000552442	T;T;T	0.79454	-1.27;-1.27;-1.27	4.68	4.68	0.58851	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.000000	0.47852	U	0.000205	D	0.92391	0.7585	H	0.98664	4.295	0.58432	D	0.999995	D	0.71674	0.998	D	0.74348	0.983	D	0.94877	0.8035	10	0.87932	D	0	0.6113	14.9532	0.71091	0.0:1.0:0.0:0.0	.	7	P61088	UBE2N_HUMAN	S	7	ENSP00000316176:R7S;ENSP00000449352:R7S;ENSP00000448352:R7S	ENSP00000316176:R7S	R	-	3	2	UBE2N	92359771	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	4.501000	0.60393	2.581000	0.87130	0.557000	0.71058	AGG	.	.		0.692	UBE2N-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407710.1	NM_003348		A	93835640	C	A	93835640	3	1	257	1	0	0	0	0	1	0	0	0	16881	854	30	3	453	3	UBE2N	12	93835640	Missense_Mutation	SNP	C	TCGA-EP-A3JL-01A-11D-A20W-10		93835640	40016255	52	36243										
DHX37	57647	hgsc.bcm.edu	37	chr12	125451669	125451669	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	ggtcggggcgtcctctttacCttgtggccgggctctggagg	17	11	2	0			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr12:125451669C>T	ENST00000308736.2	-	11	1602	c.1504G>A	c.(1504-1506)Gaa>Aaa	p.E502K	DHX37_ENST00000544745.1_Splice_Site_p.E289K	NM_032656.3	NP_116045.2	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	502	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.						ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(5)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|liver(1)|lung(27)|ovary(1)|prostate(2)|skin(3)	65	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)		TCCTCTTTACCTTGTGGCCGG	0.667																																					p.E502K		Atlas-SNP	.											.	DHX37	114	.	0			c.G1504A						.						45	35	38					12																	125451669		2203	4300	6503	SO:0001630	splice_region_variant	57647	exon11			CTTTACCTTGTGG	AB040950	CCDS9261.1	12q24.31	2004-03-25	2003-06-13	2003-06-20		ENSG00000150990		"DEAH-boxes"	17210	protein-coding gene	gene with protein product			"DEAD/DEAH box helicase DDX37"	DDX37		10819331	Standard	NM_032656		Approved	KIAA1517, MGC4322, MGC2695	uc001ugy.3	Q8IY37		ENST00000308736.2:c.1504+1G>A	chr12.hg19:g.125451669C>T		103.0	0.0		87.0	7.0	NM_032656	Q9BUI7|Q9P211	Missense_Mutation	SNP	ENST00000308736.2	hg19	CCDS9261.1	.	.	.	.	.	.	.	.	.	.	C	13.12	2.142791	0.37825	.	.	ENSG00000150990	ENST00000308736;ENST00000544745	T;T	0.13307	2.6;2.6	4.96	4.96	0.65561	Helicase, C-terminal (1);	0.512553	0.15366	U	0.266111	T	0.09512	0.0234	N	0.13272	0.32	0.53688	D	0.999971	B	0.02656	0.0	B	0.04013	0.001	T	0.25012	-1.0144	9	.	.	.	-9.1	15.9979	0.80265	0.0:1.0:0.0:0.0	.	502	Q8IY37	DHX37_HUMAN	K	502;289	ENSP00000311135:E502K;ENSP00000439009:E289K	.	E	-	1	0	DHX37	124017622	1.000000	0.71417	0.959000	0.39883	0.063000	0.16089	3.301000	0.51842	2.308000	0.77769	0.655000	0.94253	GAA	.	.		0.667	DHX37-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032656	Missense_Mutation	T	125451669	C	T	125451669	5	4	257	1	0	0	0	0	0	0	1	0	4512	695	24	3	2037	3	DHX37	12	125451669	Splice_Site	SNP	C	TCGA-EP-A3JL-01A-11D-A20W-10	31616029	125451669	8400226	53	36244										
PGAM5	192111	hgsc.bcm.edu	37	chr12	133291565	133291565	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	ggcacatcttcctcatcaggCattcccagtaccacgtggat	8	14	3	0			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr12:133291565C>T	ENST00000498926.2	+	2	371	c.313C>T	c.(313-315)Cat>Tat	p.H105Y	PXMP2_ENST00000545677.1_Missense_Mutation_p.A144V|PGAM5_ENST00000317555.2_Missense_Mutation_p.H105Y|PGAM5_ENST00000543955.1_5'UTR|PGAM5_ENST00000454808.2_5'UTR	NM_001170543.1|NM_001170544.1	NP_001164014.1|NP_001164015.1	Q96HS1	PGAM5_HUMAN	phosphoglycerate mutase family member 5	105					dephosphorylation (GO:0016311)|necroptotic process (GO:0070266)|positive regulation of GTPase activity (GO:0043547)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|phosphatase activity (GO:0016791)|phosphoprotein phosphatase activity (GO:0004721)|protein complex binding (GO:0032403)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	5	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.89e-08)|Epithelial(86;1.14e-07)|all cancers(50;3.57e-06)		CCTCATCAGGCATTCCCAGTA	0.587																																					p.H105Y		Atlas-SNP	.											.	PGAM5	18	.	0			c.C313T						.						130	86	101					12																	133291565		2202	4300	6502	SO:0001583	missense	192111	exon2			ATCAGGCATTCCC	BC008196	CCDS9280.1, CCDS53845.1	12q24.33	2011-07-28			ENSG00000247077	ENSG00000247077			28763	protein-coding gene	gene with protein product		614939				11283018	Standard	NM_001170543		Approved	MGC5352, BXLBv68	uc009zyv.3	Q96HS1	OTTHUMG00000168021	ENST00000498926.2:c.313C>T	chr12.hg19:g.133291565C>T	ENSP00000438465:p.His105Tyr	185.0	0.0		112.0	25.0	NM_138575	A9LN06|C9IZY7|Q96JB0	Missense_Mutation	SNP	ENST00000498926.2	hg19	CCDS53845.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	26.7|26.7	4.758363|4.758363	0.89843|0.89843	.|.	.|.	ENSG00000176894|ENSG00000247077	ENST00000545677|ENST00000317555;ENST00000498926	.|T;D	.|0.90261	.|-0.65;-2.64	4.64|4.64	4.64|4.64	0.57946|0.57946	.|Histidine phosphatase superfamily, clade-1 (2);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.97492|0.97492	0.9179|0.9179	H|H	0.99026|0.99026	4.405|4.405	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.91635	.|0.994;0.999	D|D	0.99806|0.99806	1.1038|1.1038	6|10	0.87932|0.87932	D|D	0|0	-2.6454|-2.6454	17.5103|17.5103	0.87758|0.87758	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|105;105	.|Q96HS1;Q96HS1-2	.|PGAM5_HUMAN;.	V|Y	144|105	.|ENSP00000321503:H105Y;ENSP00000438465:H105Y	ENSP00000444697:A144V|ENSP00000321503:H105Y	A|H	+|+	2|1	0|0	PXMP2|PGAM5	131801638|131801638	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.942000|0.942000	0.58702|0.58702	7.448000|7.448000	0.80631|0.80631	2.136000|2.136000	0.66102|0.66102	0.462000|0.462000	0.41574|0.41574	GCA|CAT	.	.		0.587	PGAM5-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397562.1	NM_138575		T	133291565	C	T	133291565	3	4	257	1	0	0	0	0	1	0	0	0	11785	710	25	3	319	3	PGAM5	12	133291565	Missense_Mutation	SNP	C	TCGA-EP-A3JL-01A-11D-A20W-10	7839896	133291565	560330	54	36245										
ZMYM5	9205	hgsc.bcm.edu	37	chr13	20411886	20411886	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	tcacagggagacaaacaagaTgtactataaaattcttggaa	8	6	2	2			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr13:20411886T>C	ENST00000337963.4	-	6	1212	c.948A>G	c.(946-948)acA>acG	p.T316T	ZMYM5_ENST00000382907.4_3'UTR|ZMYM5_ENST00000382905.4_Silent_p.T316T	NM_001142684.1	NP_001136156.1	Q9UJ78	ZMYM5_HUMAN	zinc finger, MYM-type 5	316						nucleus (GO:0005634)	zinc ion binding (GO:0008270)			kidney(1)|large_intestine(5)|lung(9)	15		all_cancers(29;2.96e-22)|all_epithelial(30;3.76e-20)|all_lung(29;4.38e-20)|Lung NSC(5;5.8e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.61e-05)|Epithelial(112;4.89e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00171)|Lung(94;0.00942)|LUSC - Lung squamous cell carcinoma(192;0.0431)		ACAAACAAGATGTACTATAAA	0.338																																					p.T316T		Atlas-SNP	.											.	ZMYM5	73	.	0			c.A948G						.						55	57	56					13																	20411886		2203	4293	6496	SO:0001819	synonymous_variant	9205	exon6			ACAAGATGTACTA	AF161535	CCDS31942.1, CCDS31943.1	13q12	2013-01-08	2005-09-12	2005-09-12	ENSG00000132950	ENSG00000132950		"Zinc fingers, MYM type"	13029	protein-coding gene	gene with protein product			"zinc finger protein 237"	ZNF237			Standard	NM_001039650		Approved	ZNF198L1, MYM	uc010tcn.1	Q9UJ78	OTTHUMG00000016504	ENST00000337963.4:c.948A>G	chr13.hg19:g.20411886T>C		168.0	0.0		76.0	12.0	NM_001039650	B2R6V1|Q5T6E1|Q5T6E2|Q5T6E4|Q96IY6|Q9NZY5|Q9UBW0|Q9UJ77	Silent	SNP	ENST00000337963.4	hg19																																																																																				.	.		0.338	ZMYM5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014242		C	20411886	T	C	20411886	2	2	257	1	0	0	0	0	0	0	0	1	17718	1451	51	2		2	ZMYM5	13	20411886	Silent	SNP	T	TCGA-EP-A3JL-01A-11D-A20W-10		20411886	94757992	55	36246										
STARD13	90627	hgsc.bcm.edu	37	chr13	33703451	33703451	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	attgtcatagatactgactcGgctggctctgtggcaggacg	13	9	2	2			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr13:33703451G>C	ENST00000336934.5	-	5	1479	c.1363C>G	c.(1363-1365)Cga>Gga	p.R455G	STARD13_ENST00000399365.3_Missense_Mutation_p.R337G|STARD13_ENST00000255486.4_Missense_Mutation_p.R447G	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	455					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	40	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		ATACTGACTCGGCTGGCTCTG	0.562																																					p.R455G		Atlas-SNP	.											STARD13,NS,carcinoma,0,1	STARD13	100	.	0			c.C1363G						.						59	59	59					13																	33703451		2203	4300	6503	SO:0001583	missense	90627	exon5			TGACTCGGCTGGC	AL049801	CCDS9348.1, CCDS9349.1, CCDS9350.1	13q13.1	2013-08-13	2007-08-16		ENSG00000133121	ENSG00000133121		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	19164	protein-coding gene	gene with protein product		609866	"START domain containing 13", "long intergenic non-protein coding RNA 464"	LINC00464		8812419	Standard	NM_178006		Approved	GT650, DLC2, ARHGAP37	uc001uuw.3	Q9Y3M8	OTTHUMG00000016708	ENST00000336934.5:c.1363C>G	chr13.hg19:g.33703451G>C	ENSP00000338785:p.Arg455Gly	122.0	1.0		66.0	20.0	NM_178006	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Missense_Mutation	SNP	ENST00000336934.5	hg19	CCDS9348.1	.	.	.	.	.	.	.	.	.	.	G	16.38	3.106770	0.56291	.	.	ENSG00000133121	ENST00000399365;ENST00000255486;ENST00000336934;ENST00000399364	T;T;T	0.10005	2.92;2.95;2.95	5.82	0.185	0.15096	.	0.050408	0.85682	D	0.000000	T	0.34774	0.0909	M	0.83603	2.65	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.998;0.989;0.998	T	0.44065	-0.9352	10	0.56958	D	0.05	.	17.1869	0.86868	0.0:0.0:0.3381:0.6619	.	447;420;455;447	Q9Y3M8-5;Q9Y3M8-4;Q9Y3M8;Q9Y3M8-2	.;.;STA13_HUMAN;.	G	337;447;455;447	ENSP00000382300:R337G;ENSP00000255486:R447G;ENSP00000338785:R455G	ENSP00000255486:R447G	R	-	1	2	STARD13	32601451	1.000000	0.71417	0.053000	0.19242	0.981000	0.71138	1.444000	0.35068	0.050000	0.15949	0.655000	0.94253	CGA	.	.		0.562	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2	NM_001243466		C	33703451	G	C	33703451	3	2	257	1	0	0	0	0	1	0	0	0	15271	1124	39	4	2018	4	STARD13	13	33703451	Missense_Mutation	SNP	G	TCGA-EP-A3JL-01A-11D-A20W-10	13291565	33703451	81466427	56	36247										
TRPC4	7223	hgsc.bcm.edu	37	chr13	38211433	38211433	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	tgttttgatcgtctatgaaaTaacccaaagtttttgatatc	6	6	1	3			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr13:38211433T>C	ENST00000379705.3	-	11	3398	c.2541A>G	c.(2539-2541)ttA>ttG	p.L847L	TRPC4_ENST00000379673.2_Intron|TRPC4_ENST00000447043.1_Intron|TRPC4_ENST00000379679.1_Silent_p.L674L|TRPC4_ENST00000358477.2_Intron|TRPC4_ENST00000355779.2_Intron|TRPC4_ENST00000338947.5_Silent_p.L674L|TRPC4_ENST00000426868.2_Intron|TRPC4_ENST00000379681.3_Silent_p.L852L			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	847	Binds to ITPR1, ITPR2 and ITPR3.				axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|gamma-aminobutyric acid secretion (GO:0014051)|ion transmembrane transport (GO:0034220)|oligodendrocyte differentiation (GO:0048709)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|calcium channel complex (GO:0034704)|caveola (GO:0005901)|cell surface (GO:0009986)|cortical cytoskeleton (GO:0030863)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			NS(2)|breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(26)|lung(30)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	83				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		GTCTATGAAATAACCCAAAGT	0.443																																					p.L852L		Atlas-SNP	.											.	TRPC4	389	.	0			c.A2556G						.						75	76	75					13																	38211433		2203	4300	6503	SO:0001819	synonymous_variant	7223	exon11			ATGAAATAACCCA	U40983	CCDS9365.1, CCDS45035.1, CCDS45036.1, CCDS45038.1, CCDS45039.1	13q13.3	2013-01-10			ENSG00000133107	ENSG00000133107		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	12336	protein-coding gene	gene with protein product		603651				8646775, 16382100	Standard	NM_016179		Approved	HTRP4, TRP4	uc010abx.3	Q9UBN4	OTTHUMG00000016752	ENST00000379705.3:c.2541A>G	chr13.hg19:g.38211433T>C		141.0	0.0		72.0	26.0	NM_003306	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Silent	SNP	ENST00000379705.3	hg19	CCDS9365.1																																																																																			.	.		0.443	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306		C	38211433	T	C	38211433	2	2	257	1	0	0	0	0	0	0	0	1	16595	1403	49	2		2	TRPC4	13	38211433	Silent	SNP	T	TCGA-EP-A3JL-01A-11D-A20W-10	4507982	38211433	76958445	57	36248										
FREM2	341640	hgsc.bcm.edu	37	chr13	39261907	39261907	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	gtgcgctactctcacctgggCgcgcgcagcccgtctcggga	14	16	2	0			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr13:39261907C>A	ENST00000280481.7	+	1	642	c.426C>A	c.(424-426)ggC>ggA	p.G142G		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	142					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		CTCACCTGGGCGCGCGCAGCC	0.687																																					p.G142G		Atlas-SNP	.											.	FREM2	385	.	0			c.C426A						.						29	29	29					13																	39261907		2196	4297	6493	SO:0001819	synonymous_variant	341640	exon1			CCTGGGCGCGCGC	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.426C>A	chr13.hg19:g.39261907C>A		12.0	0.0		42.0	17.0	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	hg19	CCDS31960.1																																																																																			.	.		0.687	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		A	39261907	C	A	39261907	2	1	257	1	0	0	0	0	0	0	0	1	6053	755	27	1		1	FREM2	13	39261907	Silent	SNP	C	TCGA-EP-A3JL-01A-11D-A20W-10	1050474	39261907	75907971	58	36249										
EFNB2	1948	hgsc.bcm.edu	37	chr13	107164993	107164993	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	gtttggcacagttgaggagaGgggtattttccttcttaata	12	5	1	2			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr13:107164993G>A	ENST00000245323.4	-	2	439	c.290C>T	c.(289-291)cCt>cTt	p.P97L		NM_004093.3	NP_004084.1	P52799	EFNB2_HUMAN	ephrin-B2	97	Ephrin RBD. {ECO:0000255|PROSITE- ProRule:PRU00884}.				anatomical structure morphogenesis (GO:0009653)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell signaling (GO:0007267)|ephrin receptor signaling pathway (GO:0048013)|lymph vessel development (GO:0001945)|negative regulation of keratinocyte proliferation (GO:0010839)|organ morphogenesis (GO:0009887)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|regulation of chemotaxis (GO:0050920)|viral process (GO:0016032)	focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ephrin receptor binding (GO:0046875)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	13	Lung NSC(43;0.015)|all_neural(89;0.0741)|Lung SC(71;0.14)|Medulloblastoma(90;0.169)					GTTGAGGAGAGGGGTATTTTC	0.378																																					p.P97L		Atlas-SNP	.											.	EFNB2	39	.	0			c.C290T						.						169	170	170					13																	107164993		2203	4300	6503	SO:0001583	missense	1948	exon2			AGGAGAGGGGTAT	L38734	CCDS9507.1	13q33	2011-03-09			ENSG00000125266	ENSG00000125266		"Ephrins"	3227	protein-coding gene	gene with protein product	"HTK ligand", "ligand of eph-related kinase 5", "eph-related receptor tyrosine kinase ligand 5"	600527		EPLG5		7833926	Standard	NM_004093		Approved	LERK5, Htk-L, HTKL, MGC126226, MGC126227, MGC126228	uc001vqi.3	P52799	OTTHUMG00000017324	ENST00000245323.4:c.290C>T	chr13.hg19:g.107164993G>A	ENSP00000245323:p.Pro97Leu	225.0	0.0		123.0	36.0	NM_004093	Q5JV56	Missense_Mutation	SNP	ENST00000245323.4	hg19	CCDS9507.1	.	.	.	.	.	.	.	.	.	.	G	6.077	0.382471	0.11524	.	.	ENSG00000125266	ENST00000245323	D	0.92699	-3.09	5.41	5.41	0.78517	Cupredoxin (2);	0.048352	0.85682	D	0.000000	T	0.79913	0.4528	N	0.01529	-0.815	0.80722	D	1	B	0.10296	0.003	B	0.17979	0.02	T	0.76013	-0.3114	10	0.08179	T	0.78	.	19.571	0.95419	0.0:0.0:1.0:0.0	.	97	P52799	EFNB2_HUMAN	L	97	ENSP00000245323:P97L	ENSP00000245323:P97L	P	-	2	0	EFNB2	105962994	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.379000	0.73154	2.709000	0.92574	0.655000	0.94253	CCT	.	.		0.378	EFNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045733.4	NM_004093		A	107164993	G	A	107164993	3	1	257	1	0	0	0	0	1	0	0	0	4958	1000	35	3	727	3	EFNB2	13	107164993	Missense_Mutation	SNP	G	TCGA-EP-A3JL-01A-11D-A20W-10	67903086	107164993	8004885	59	36250										
NFKBIA	4792	hgsc.bcm.edu	37	chr14	35871997	35872005	+	In_Frame_Del	DEL	CCAAGGACA	CCAAGGACA	-													0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	ctgagcattgacatcagcacCcaaggacaccaaaagctcca							TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	CCAAGGACA	CCAAGGACA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr14:35871997_35872005delCCAAGGACA	ENST00000216797.5	-	4	709_717	c.608_616delTGTCCTTGG	c.(607-618)gtgtccttgggt>ggt	p.VSL203del	NFKBIA_ENST00000557100.1_Intron|NFKBIA_ENST00000557389.1_In_Frame_Del_p.VSL113del|NFKBIA_ENST00000557140.1_In_Frame_Del_p.VSL203del	NM_020529.2	NP_065390.1	P25963	IKBA_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha	203					apoptotic process (GO:0006915)|cellular response to cold (GO:0070417)|cytoplasmic sequestering of NF-kappaB (GO:0007253)|cytoplasmic sequestering of transcription factor (GO:0042994)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA binding (GO:0043392)|negative regulation of lipid storage (GO:0010888)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of Notch signaling pathway (GO:0045746)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070427)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein import into nucleus, translocation (GO:0000060)|regulation of cell proliferation (GO:0042127)|regulation of NF-kappaB import into nucleus (GO:0042345)|response to exogenous dsRNA (GO:0043330)|response to muramyl dipeptide (GO:0032495)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I-kappaB/NF-kappaB complex (GO:0033256)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|nuclear localization sequence binding (GO:0008139)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(1)|large_intestine(2)|liver(1)	7	Breast(36;0.0484)|Hepatocellular(127;0.158)		Lung(238;9.25e-06)|LUAD - Lung adenocarcinoma(48;1.53e-05)|Epithelial(34;0.00314)|all cancers(34;0.00891)	GBM - Glioblastoma multiforme(112;0.0222)	Acetylsalicylic acid(DB00945)	ACATCAGCACCCAAGGACACCAAAAGCTC	0.502																																					p.203_206del		Atlas-INDEL	.											.	NFKBIA	28	.	0			c.609_617del						.																																			SO:0001651	inframe_deletion	4792	exon4			.		CCDS9656.1	14q13	2014-09-17			ENSG00000100906	ENSG00000100906		"Ankyrin repeat domain containing"	7797	protein-coding gene	gene with protein product		164008		NFKBI		1829648	Standard	NM_020529		Approved	IKBA, MAD-3, IkappaBalpha	uc001wtf.4	P25963	OTTHUMG00000140220	ENST00000216797.5:c.608_616delTGTCCTTGG	chr14.hg19:g.35871997_35872005delCCAAGGACA	ENSP00000216797:p.Val203_Leu205del	110.0	0.0		76.0	12.0	NM_020529	B2R8L6	In_Frame_Del	DEL	ENST00000216797.5	hg19	CCDS9656.1																																																																																			.	.		0.502	NFKBIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276683.1	NM_020529		-	35872005	CCAAGGACA	-	35871997	7	5	257	1	0	1	0	1	0	0	0	0	10386	623	22	0	349	0	NFKBIA	14	35871997	In_Frame_Del	DEL	CCAAGGACA	TCGA-EP-A3JL-01A-11D-A20W-10		35871997	71477543	60	36251										
MNS1	55329	hgsc.bcm.edu	37	chr15	56748716	56748716	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	tttcaatctcttgttttcttCtgcctgaacgaaaaatttaa	4	8	4	1			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr15:56748716C>G	ENST00000260453.3	-	3	393	c.229G>C	c.(229-231)Gaa>Caa	p.E77Q		NM_018365.2	NP_060835.1	Q8NEH6	MNS1_HUMAN	meiosis-specific nuclear structural 1	77	Glu-rich.				cilium organization (GO:0044782)|left/right axis specification (GO:0070986)|meiotic nuclear division (GO:0007126)	axoneme (GO:0005930)|intermediate filament (GO:0005882)|nuclear envelope (GO:0005635)|sperm flagellum (GO:0036126)	identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(4)|ovary(2)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	20				all cancers(107;0.0196)|GBM - Glioblastoma multiforme(80;0.101)		TTGTTTTCTTCTGCCTGAACG	0.328																																					p.E77Q		Atlas-SNP	.											.	MNS1	39	.	0			c.G229C						.						146	133	137					15																	56748716		2191	4292	6483	SO:0001583	missense	55329	exon3			TTTCTTCTGCCTG	AK002084	CCDS10158.1	15q21.3	2013-01-16			ENSG00000138587	ENSG00000138587			29636	protein-coding gene	gene with protein product	"spermatogenesis associated 40"	610766				7625268, 8032679	Standard	NM_018365		Approved	FLJ11222, SPATA40	uc002adr.2	Q8NEH6	OTTHUMG00000132034	ENST00000260453.3:c.229G>C	chr15.hg19:g.56748716C>G	ENSP00000260453:p.Glu77Gln	279.0	0.0		104.0	32.0	NM_018365	Q8IYT6|Q9NUP4	Missense_Mutation	SNP	ENST00000260453.3	hg19	CCDS10158.1	.	.	.	.	.	.	.	.	.	.	C	14.80	2.643694	0.47258	.	.	ENSG00000138587	ENST00000260453	T	0.15952	2.38	5.87	4.91	0.64330	.	0.043082	0.85682	D	0.000000	T	0.13756	0.0333	L	0.38175	1.15	0.58432	D	0.999997	B	0.32653	0.379	B	0.27380	0.079	T	0.06499	-1.0823	10	0.23302	T	0.38	-24.5181	15.5183	0.75842	0.0:0.8612:0.1388:0.0	.	77	Q8NEH6	MNS1_HUMAN	Q	77	ENSP00000260453:E77Q	ENSP00000260453:E77Q	E	-	1	0	MNS1	54536008	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.044000	0.49830	2.941000	0.99782	0.655000	0.94253	GAA	.	.		0.328	MNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255047.2	NM_018365		G	56748716	C	G	56748716	3	3	257	1	0	0	0	0	1	0	0	0	9686	922	32	4	1290	4	MNS1	15	56748716	Missense_Mutation	SNP	C	TCGA-EP-A3JL-01A-11D-A20W-10		56748716	45782676	61	36252										
SPESP1	246777	hgsc.bcm.edu	37	chr15	69238762	69238762	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	gtaataaaattgatgacatcGaaactgttattaacatgctg	7	5	0	2	rs543376040		TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr15:69238762G>C	ENST00000310673.3	+	2	1043	c.889G>C	c.(889-891)Gaa>Caa	p.E297Q	NOX5_ENST00000260364.5_Intron|RP11-809H16.2_ENST00000557966.1_RNA|NOX5_ENST00000448182.3_Intron|NOX5_ENST00000455873.3_Intron	NM_145658.3	NP_663633.1	Q6UW49	SPESP_HUMAN	sperm equatorial segment protein 1	297				E -> V (in Ref. 1; AAM69364). {ECO:0000305}.	acrosome reaction (GO:0007340)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organismal development (GO:0007275)	acrosomal vesicle (GO:0001669)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|prostate(1)|skin(1)|urinary_tract(1)	19						TGATGACATCGAAACTGTTAT	0.343																																					p.E297Q		Atlas-SNP	.											.	SPESP1	39	.	0			c.G889C						.																																			SO:0001583	missense	246777	exon2			GACATCGAAACTG	AF275321	CCDS10230.1	15q22.31	2011-04-15				ENSG00000258484			15570	protein-coding gene	gene with protein product		609399				12773409	Standard	NM_145658		Approved	SP-ESP	uc002arn.2	Q6UW49		ENST00000310673.3:c.889G>C	chr15.hg19:g.69238762G>C	ENSP00000312284:p.Glu297Gln	127.0	0.0		51.0	12.0	NM_145658	Q8NG22|Q8WVH8	Missense_Mutation	SNP	ENST00000310673.3	hg19	CCDS10230.1	.	.	.	.	.	.	.	.	.	.	G	11.70	1.716215	0.30413	.	.	ENSG00000258484	ENST00000310673	T	0.24538	1.85	5.33	1.36	0.22044	.	0.848427	0.10122	N	0.713266	T	0.29945	0.0749	L	0.32530	0.975	0.09310	N	1	D	0.59767	0.986	P	0.57101	0.813	T	0.15378	-1.0439	10	0.49607	T	0.09	-3.5278	6.813	0.23814	0.3748:0.0:0.6252:0.0	.	297	Q6UW49	SPESP_HUMAN	Q	297	ENSP00000312284:E297Q	ENSP00000312284:E297Q	E	+	1	0	SPESP1	67025816	0.071000	0.21146	0.027000	0.17364	0.352000	0.29268	0.380000	0.20602	0.339000	0.23719	0.655000	0.94253	GAA	.	.		0.343	SPESP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257125.1	NM_145658		C	69238762	G	C	69238762	3	2	257	1	0	0	0	0	1	0	0	0	15055	1059	37	4	895	4	SPESP1	15	69238762	Missense_Mutation	SNP	G	TCGA-EP-A3JL-01A-11D-A20W-10	12490046	69238762	33292630	62	36253										
TBC1D21	161514	hgsc.bcm.edu	37	chr15	74177139	74177139	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	tagcacgtgacattcagaaaAtctatgacaaagatcccctg	7	10	2	4			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr15:74177139A>C	ENST00000300504.2	+	5	468	c.385A>C	c.(385-387)Atc>Ctc	p.I129L	TBC1D21_ENST00000562056.1_Intron|TBC1D21_ENST00000535547.2_Missense_Mutation_p.I93L	NM_153356.1	NP_699187.1	Q8IYX1	TBC21_HUMAN	TBC1 domain family, member 21	129	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.					acrosomal vesicle (GO:0001669)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(2)|large_intestine(2)|lung(6)|ovary(3)|skin(1)|stomach(1)|urinary_tract(1)	17						CATTCAGAAAATCTATGACAA	0.522																																					p.I129L		Atlas-SNP	.											.	TBC1D21	38	.	0			c.A385C						.						98	79	85					15																	74177139		2198	4297	6495	SO:0001583	missense	161514	exon5			CAGAAAATCTATG	BC033516	CCDS10252.1, CCDS66822.1	15q24	2013-07-09			ENSG00000167139	ENSG00000167139			28536	protein-coding gene	gene with protein product	"male germ cell-specific expressed, containing a RabGAP domain"					21128978	Standard	XR_243080		Approved	MGC34741, MgcRabGAP	uc002avz.3	Q8IYX1	OTTHUMG00000137594	ENST00000300504.2:c.385A>C	chr15.hg19:g.74177139A>C	ENSP00000300504:p.Ile129Leu	109.0	0.0		88.0	33.0	NM_153356	B9A6M2	Missense_Mutation	SNP	ENST00000300504.2	hg19	CCDS10252.1	.	.	.	.	.	.	.	.	.	.	A	3.053	-0.194900	0.06259	.	.	ENSG00000167139	ENST00000300504;ENST00000535547	T;T	0.10860	2.83;2.83	5.45	4.54	0.55810	Rab-GAP/TBC domain (4);	0.130000	0.35349	N	0.003272	T	0.03564	0.0102	N	0.01352	-0.895	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39375	-0.9617	10	0.11794	T	0.64	.	11.8283	0.52280	0.1757:0.8243:0.0:0.0	.	93;129	B9A6M2;Q8IYX1	.;TBC21_HUMAN	L	129;93	ENSP00000300504:I129L;ENSP00000439325:I93L	ENSP00000300504:I129L	I	+	1	0	TBC1D21	71964192	0.999000	0.42202	0.982000	0.44146	0.751000	0.42716	2.548000	0.45794	1.304000	0.44892	-0.233000	0.12211	ATC	.	.		0.522	TBC1D21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268994.1	NM_153356		C	74177139	A	C	74177139	3	2	257	1	0	0	0	0	1	0	0	0	15625	101	4	5	403	5	TBC1D21	15	74177139	Missense_Mutation	SNP	A	TCGA-EP-A3JL-01A-11D-A20W-10	4938377	74177139	28354253	63	36254										
WDR24	84219	hgsc.bcm.edu	37	chr16	735892	735892	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	cattggtgatgagtgtggccGaggagtcgagcagaactgtg	17	6	0	3			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr16:735892G>A	ENST00000248142.6	-	9	1939	c.1940C>T	c.(1939-1941)tCg>tTg	p.S647L	JMJD8_ENST00000454700.1_5'Flank|WDR24_ENST00000293883.4_Missense_Mutation_p.S517L|JMJD8_ENST00000562111.1_5'Flank|JMJD8_ENST00000609261.1_5'Flank|JMJD8_ENST00000562824.1_5'Flank|JMJD8_ENST00000293882.4_5'Flank|JMJD8_ENST00000412368.2_5'Flank			Q96S15	WDR24_HUMAN	WD repeat domain 24	647										breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|urinary_tract(3)	19		Hepatocellular(780;0.0218)				GAGTGTGGCCGAGGAGTCGAG	0.622																																					p.S517L		Atlas-SNP	.											.	WDR24	111	.	0			c.C1550T						.						125	123	123					16																	735892		2201	4300	6501	SO:0001583	missense	84219	exon5			GTGGCCGAGGAGT	AL136863	CCDS10420.1	16p13.3	2013-01-09			ENSG00000127580	ENSG00000127580		"WD repeat domain containing"	20852	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 21"	C16orf21		11230166	Standard	NM_032259		Approved	DKFZp434F054, JFP7	uc002ciz.1	Q96S15	OTTHUMG00000090421	ENST00000248142.6:c.1940C>T	chr16.hg19:g.735892G>A	ENSP00000248142:p.Ser647Leu	132.0	0.0		93.0	30.0	NM_032259	A2IDB8|D3DU59|Q96GC7|Q9H0B7	Missense_Mutation	SNP	ENST00000248142.6	hg19		.	.	.	.	.	.	.	.	.	.	G	12.35	1.911432	0.33721	.	.	ENSG00000127580	ENST00000248142;ENST00000293883	T;T	0.78595	-1.19;0.23	4.66	4.66	0.58398	.	0.278573	0.29660	N	0.011521	T	0.60495	0.2273	N	0.14661	0.345	0.39880	D	0.973628	B	0.33022	0.394	B	0.22880	0.042	T	0.63065	-0.6720	10	0.30854	T	0.27	-10.1837	16.2618	0.82550	0.0:0.0:1.0:0.0	.	517	Q96S15-2	.	L	647;517	ENSP00000248142:S647L;ENSP00000293883:S517L	ENSP00000248142:S647L	S	-	2	0	WDR24	675893	1.000000	0.71417	0.962000	0.40283	0.206000	0.24218	5.741000	0.68638	2.423000	0.82170	0.561000	0.74099	TCG	.	.		0.622	WDR24-201	KNOWN	basic	protein_coding	protein_coding		NM_032259		A	735892	G	A	735892	3	1	257	1	0	0	0	0	1	0	0	0	17296	1059	37	1	842	1	WDR24	16	735892	Missense_Mutation	SNP	G	TCGA-EP-A3JL-01A-11D-A20W-10		735892	89618861	64	36255										
VWA3A	146177	hgsc.bcm.edu	37	chr16	22162149	22162150	+	Nonsense_Mutation	DNP	CC	CC	AA													0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	tgtgaaagtgcacaccatttCcttgaactgctcagacaggt							TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr16:22162149_22162150CC>AA	ENST00000389398.5	+	30	3359_3360	c.3263_3264CC>AA	c.(3262-3264)tCC>tAA	p.S1088*	VWA3A_ENST00000389397.4_Nonsense_Mutation_p.S190*|VWA3A_ENST00000563755.1_Nonsense_Mutation_p.S190*	NM_173615.3	NP_775886.3	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	1088	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.					extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7				GBM - Glioblastoma multiforme(48;0.0439)		CACACCATTTCCTTGAACTGCT	0.48																																					p.S1088Y|p.S1088S		Atlas-SNP	.											.	VWA3A	115	.	0			c.C3263A|c.C3264A						.																																			SO:0001587	stop_gained	146177	exon30			CCATTTCCTTGAA|CATTTCCTTGAAC	AK128606, AK098260	CCDS45441.1	16p12.1	2008-02-05				ENSG00000175267			27088	protein-coding gene	gene with protein product						12477932	Standard	XM_006721021		Approved	FLJ46765, FLJ40941	uc010vbq.2	A6NCI4		Exception_encountered	chr16.hg19:g.22162149_22162150delinsAA	ENSP00000374049:p.Ser1088*	108.0	0.0		70.0	17.0|15.0	NM_173615	A4QMU8|A6NNC0|Q6UTX4|Q6ZQZ9|Q8IUY6|Q8N9W1	Missense_Mutation|Silent	SNP	ENST00000389398.5	hg19	CCDS45441.1																																																																																			.	.		0.48	VWA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430052.1			AA	22162150	CC	AA	22162149	4	1	257	1	0	0	0	0	0	1	0	0	17255	855	30	3	3381	3	VWA3A	16	22162149	Nonsense_Mutation	DNP	CC	TCGA-EP-A3JL-01A-11D-A20W-10	21426257	22162149	68192604	65	36256										
SF3B3	23450	hgsc.bcm.edu	37	chr16	70595533	70595533	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	ggttttttttttcccctcagGtattggccatgtcaagccgc	9	11	2	0			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr16:70595533G>A	ENST00000302516.5	+	17	2345	c.2134G>A	c.(2134-2136)Gta>Ata	p.V712I		NM_012426.4	NP_036558.3	Q15393	SF3B3_HUMAN	splicing factor 3b, subunit 3, 130kDa	712					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|protein complex assembly (GO:0006461)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	nucleic acid binding (GO:0003676)			breast(2)|endometrium(8)|kidney(2)|large_intestine(8)|liver(3)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	53		Ovarian(137;0.0694)				TTCCCCTCAGGTATTGGCCAT	0.443																																					p.V712I		Atlas-SNP	.											.	SF3B3	99	.	0			c.G2134A						.						107	105	106					16																	70595533		2198	4300	6498	SO:0001630	splice_region_variant	23450	exon17			CCTCAGGTATTGG	AJ001443	CCDS10894.1	16q22	2008-08-01	2002-08-29		ENSG00000189091	ENSG00000189091			10770	protein-coding gene	gene with protein product		605592	"splicing factor 3b, subunit 3, 130kD"			10490618	Standard	NM_012426		Approved	SAP130, SF3b130, RSE1, KIAA0017	uc002ezf.3	Q15393	OTTHUMG00000137582	ENST00000302516.5:c.2134-1G>A	chr16.hg19:g.70595533G>A		79.0	0.0		46.0	8.0	NM_012426	Q6NTI8|Q96GC0|Q9BPY2|Q9UFX7|Q9UJ29	Missense_Mutation	SNP	ENST00000302516.5	hg19	CCDS10894.1	.	.	.	.	.	.	.	.	.	.	G	17.62	3.434964	0.62955	.	.	ENSG00000189091	ENST00000302516	T	0.37058	1.22	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	T	0.36826	0.0981	L	0.46741	1.465	0.80722	D	1	B	0.22346	0.068	B	0.24006	0.05	T	0.08269	-1.0730	9	.	.	.	.	20.282	0.98514	0.0:0.0:1.0:0.0	.	712	Q15393	SF3B3_HUMAN	I	712	ENSP00000305790:V712I	.	V	+	1	0	SF3B3	69153034	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	9.807000	0.99171	2.786000	0.95864	0.563000	0.77884	GTA	.	.		0.443	SF3B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268972.1	NM_012426	Missense_Mutation	A	70595533	G	A	70595533	5	1	257	1	0	0	0	0	0	0	1	0	14167	1275	44	3	2196	3	SF3B3	16	70595533	Splice_Site	SNP	G	TCGA-EP-A3JL-01A-11D-A20W-10	48433384	70595533	19759220	66	36257										
PER1	5187	hgsc.bcm.edu	37	chr17	8051980	8051980	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	accttcgtaacccgaatggaTgcgctctgcaatcagcaggc	10	13	2	0			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr17:8051980T>C	ENST00000317276.4	-	8	1267	c.1030A>G	c.(1030-1032)Atc>Gtc	p.I344V	PER1_ENST00000581082.1_Missense_Mutation_p.I324V|PER1_ENST00000354903.5_Missense_Mutation_p.I328V|PER1_ENST00000578089.1_5'Flank	NM_002616.2	NP_002607.2	O15534	PER1_HUMAN	period circadian clock 1	344					circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|entrainment of circadian clock by photoperiod (GO:0043153)|histone H3 acetylation (GO:0043966)|histone H3 deacetylation (GO:0070932)|histone H4 acetylation (GO:0043967)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of circadian rhythm (GO:0042752)|regulation of cytokine production involved in inflammatory response (GO:1900015)|regulation of hair cycle (GO:0042634)|regulation of p38MAPK cascade (GO:1900744)|regulation of sodium ion transport (GO:0002028)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|E-box binding (GO:0070888)|kinase binding (GO:0019900)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|signal transducer activity (GO:0004871)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(15)|ovary(4)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						CCCGAATGGATGCGCTCTGCA	0.617			T	ETV6	"AML, CMML"			Other conserved DNA damage response genes																													p.I344V		Atlas-SNP	.		Dom	yes		17	17p13.1-17p12	5187	period homolog 1 (Drosophila)		L	.	PER1	104	.	0			c.A1030G						.						80	80	80					17																	8051980		2203	4300	6503	SO:0001583	missense	5187	exon8			AATGGATGCGCTC	AB002107	CCDS11131.1	17p13.1	2012-12-13	2012-12-13			ENSG00000179094			8845	protein-coding gene	gene with protein product		602260	"period (Drosophila) homolog 1", "period homolog 1 (Drosophila)"	PER		9323128	Standard	NM_002616		Approved	RIGUI	uc002gkd.3	O15534		ENST00000317276.4:c.1030A>G	chr17.hg19:g.8051980T>C	ENSP00000314420:p.Ile344Val	64.0	0.0		72.0	19.0	NM_002616	B2RPA8|B4DI49|D3DTR3	Missense_Mutation	SNP	ENST00000317276.4	hg19	CCDS11131.1	.	.	.	.	.	.	.	.	.	.	T	8.750	0.921047	0.17982	.	.	ENSG00000179094	ENST00000317276;ENST00000354903	T;T	0.34667	2.79;1.35	4.83	1.35	0.21983	.	0.170445	0.51477	N	0.000087	T	0.18087	0.0434	N	0.02830	-0.485	0.38959	D	0.958516	B;P	0.40970	0.063;0.734	B;P	0.50825	0.054;0.651	T	0.24476	-1.0159	10	0.02654	T	1	-9.7898	7.3697	0.26794	0.0:0.2772:0.0:0.7228	.	328;344	B4DI49;O15534	.;PER1_HUMAN	V	344;328	ENSP00000314420:I344V;ENSP00000346979:I328V	ENSP00000314420:I344V	I	-	1	0	PER1	7992705	0.249000	0.23941	0.986000	0.45419	0.922000	0.55478	0.693000	0.25497	0.295000	0.22570	0.460000	0.39030	ATC	.	.		0.617	PER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441481.2			C	8051980	T	C	8051980	3	2	257	1	0	0	0	0	1	0	0	0	11738	1464	51	2	2906	2	PER1	17	8051980	Missense_Mutation	SNP	T	TCGA-EP-A3JL-01A-11D-A20W-10		8051980	73143230	67	36258										
CD300C	10871	hgsc.bcm.edu	37	chr17	72539019	72539020	+	Nonsense_Mutation	DNP	CG	CG	AT													0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	cccagggtgtgggctgggttCggggctgtcctttctggtca					rs147705680		TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	C|G	C|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr17:72539019_72539020CG>AT	ENST00000330793.1	-	3	867_868	c.507_508CG>AT	c.(505-510)ccCGaa>ccATaa	p.E170*		NM_006678.3	NP_006669.1	Q08708	CLM6_HUMAN	CD300c molecule	170	Pro-rich.				cellular defense response (GO:0006968)|immune system process (GO:0002376)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)			endometrium(2)|kidney(1)|large_intestine(4)|lung(11)|skin(2)|upper_aerodigestive_tract(1)	21						GGGCTGGGTTCGGGGCTGTCCT	0.663																																					p.E170X|p.P169P	Esophageal Squamous(66;421 1121 20537 25337 27468)	Atlas-SNP	.											.	CD300C	41	.	0			c.G508T|c.C507A						.																																			SO:0001587	stop_gained	10871	exon3			TGGGTTCGGGGCT|GGGTTCGGGGCTG	BC022279	CCDS11701.1	17q25.2	2014-05-15	2006-03-28		ENSG00000167850	ENSG00000167850		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	19320	protein-coding gene	gene with protein product		606786	"CD300c antigen"			1349532, 10746781	Standard	NM_006678		Approved	CMRF35, LIR, CMRF-35A, CMRF35A, IGSF16	uc002jky.2	Q08708	OTTHUMG00000067608	ENST00000330793.1:c.507_508delinsAT	chr17.hg19:g.72539019_72539020delinsAT	ENSP00000329507:p.Glu170*	144.0|145.0	0.0		118.0|121.0	37.0	NM_006678		Nonsense_Mutation|Silent	SNP	ENST00000330793.1	hg19	CCDS11701.1																																																																																			.	.|G|1.000;A|0.000		0.663	CD300C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145084.1	NM_006678		AT	72539020	CG	AT	72539019	4	1	257	1	0	0	0	0	0	1	0	0	2999	893	31	1	174	1	CD300C	17	72539019	Nonsense_Mutation	DNP	CG	TCGA-EP-A3JL-01A-11D-A20W-10	64487039	72539019	8656191	68	36259										
C17orf101	79701	hgsc.bcm.edu	37	chr17	80373361	80373361	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	ctcgccacggcgggccaggaCctctgcgaccccgtcgtcgg	14	18	1	0			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr17:80373361C>T	ENST00000313056.5	-	2	368	c.217G>A	c.(217-219)Gtc>Atc	p.V73I	Y_RNA_ENST00000364369.1_RNA|HEXDC_ENST00000337014.6_5'Flank|OGFOD3_ENST00000329197.5_Missense_Mutation_p.V73I	NM_024648.2|NM_175902.4	NP_078924.1|NP_787098.3	Q6PK18	OGFD3_HUMAN	2-oxoglutarate and iron-dependent oxygenase domain containing 3	73						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)										CGGGCCAGGACCTCTGCGACC	0.662																																					p.V73I		Atlas-SNP	.											.	.	.	.	0			c.G217A						.						74	75	75					17																	80373361		2202	4299	6501	SO:0001583	missense	79701	exon2			CCAGGACCTCTGC	BC023602	CCDS11811.1, CCDS11812.1	17q25.3	2012-10-23	2012-10-23	2012-10-23	ENSG00000181396	ENSG00000181396			26174	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 101"	C17orf101		12477932	Standard	NM_175902		Approved	FLJ22222	uc002keu.2	Q6PK18		ENST00000313056.5:c.217G>A	chr17.hg19:g.80373361C>T	ENSP00000320116:p.Val73Ile	74.0	0.0		77.0	25.0	NM_175902	C9JDC8|Q8IZ37|Q9H6J2	Missense_Mutation	SNP	ENST00000313056.5	hg19	CCDS11811.1	.	.	.	.	.	.	.	.	.	.	C	15.56	2.869700	0.51588	.	.	ENSG00000181396	ENST00000313056;ENST00000329197	T;T	0.33654	1.86;1.4	5.0	5.0	0.66597	.	0.154165	0.43919	D	0.000506	T	0.44371	0.1290	L	0.50333	1.59	0.41997	D	0.990875	P;D	0.60575	0.893;0.988	B;P	0.52386	0.446;0.697	T	0.25257	-1.0137	10	0.28530	T	0.3	-40.5448	15.8258	0.78706	0.0:1.0:0.0:0.0	.	73;73	Q6PK18;Q6PK18-2	CQ101_HUMAN;.	I	73	ENSP00000320116:V73I;ENSP00000330075:V73I	ENSP00000320116:V73I	V	-	1	0	C17orf101	77966650	1.000000	0.71417	0.983000	0.44433	0.024000	0.10985	3.342000	0.52159	2.299000	0.77371	0.655000	0.94253	GTC	.	.		0.662	OGFOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442895.1	NM_175902		T	80373361	C	T	80373361	3	4	257	1	0	0	0	0	1	0	0	0	1850	507	18	3	951	3	C17orf101	17	80373361	Missense_Mutation	SNP	C	TCGA-EP-A3JL-01A-11D-A20W-10	7834342	80373361	821849	69	36260										
DCC	1630	hgsc.bcm.edu	37	chr18	50918256	50918256	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	ttctgcaagtgcaaaatacaAggtgaagttctaattgatag	9	5	2	2			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr18:50918256A>G	ENST00000442544.2	+	17	3303	c.2687A>G	c.(2686-2688)aAg>aGg	p.K896R	DCC_ENST00000581580.1_Splice_Site_p.K531R|DCC_ENST00000412726.1_Splice_Site_p.K724R	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	896	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		GCAAAATACAAGGTGAAGTTC	0.423																																					p.K896R		Atlas-SNP	.											.	DCC	360	.	0			c.A2687G						.						64	63	63					18																	50918256		2203	4300	6503	SO:0001630	splice_region_variant	1630	exon17			AATACAAGGTGAA	X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2701	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 1"	120470	"deleted in colorectal carcinoma"			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.2688+1A>G	chr18.hg19:g.50918256A>G		52.0	0.0		49.0	20.0	NM_005215		Missense_Mutation	SNP	ENST00000442544.2	hg19	CCDS11952.1	.	.	.	.	.	.	.	.	.	.	A	14.28	2.489428	0.44249	.	.	ENSG00000187323	ENST00000442544;ENST00000412726	T;T	0.56611	0.45;0.45	5.24	5.24	0.73138	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.51719	0.1691	L	0.39692	1.235	0.52099	D	0.999949	B;B;P	0.38167	0.145;0.145;0.621	B;B;P	0.47251	0.093;0.093;0.542	T	0.42515	-0.9447	10	0.15066	T	0.55	.	14.1331	0.65268	1.0:0.0:0.0:0.0	.	724;724;896	E7EQM8;B4DYX2;P43146	.;.;DCC_HUMAN	R	896;724	ENSP00000389140:K896R;ENSP00000397322:K724R	ENSP00000397322:K724R	K	+	2	0	DCC	49172254	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.164000	0.94755	1.981000	0.57761	0.377000	0.23210	AAG	.	.		0.423	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215	Missense_Mutation	G	50918256	A	G	50918256	5	3	257	1	0	0	0	0	0	0	1	0	4284	86	3	2	2753	2	DCC	18	50918256	Splice_Site	SNP	A	TCGA-EP-A3JL-01A-11D-A20W-10		50918256	27158992	70	36261										
ANKRD24	170961	hgsc.bcm.edu	37	chr19	4224480	4224480	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	ccagattctgcagatgcagaGactccaggctcagggccgct	12	13	2	3			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr19:4224480G>C	ENST00000600132.1	+	22	3695	c.3419G>C	c.(3418-3420)aGa>aCa	p.R1140T	ANKRD24_ENST00000318934.4_Missense_Mutation_p.R1140T|ANKRD24_ENST00000262970.5_Missense_Mutation_p.R1230T	NM_133475.1	NP_597732.1	Q8TF21	ANR24_HUMAN	ankyrin repeat domain 24	1140										endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)	21				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0233)|STAD - Stomach adenocarcinoma(1328;0.181)		CAGATGCAGAGACTCCAGGCT	0.617																																					p.R1140T		Atlas-SNP	.											.	ANKRD24	180	.	0			c.G3419C						.						45	52	50					19																	4224480		2105	4240	6345	SO:0001583	missense	170961	exon22			TGCAGAGACTCCA	AB075861	CCDS45925.1	19p13.3	2013-01-10				ENSG00000089847		"Ankyrin repeat domain containing"	29424	protein-coding gene	gene with protein product						11853319	Standard	NM_133475		Approved	KIAA1981	uc010dtt.1	Q8TF21		ENST00000600132.1:c.3419G>C	chr19.hg19:g.4224480G>C	ENSP00000471252:p.Arg1140Thr	84.0	0.0		48.0	15.0	NM_133475	O75268|O95781	Missense_Mutation	SNP	ENST00000600132.1	hg19	CCDS45925.1	.	.	.	.	.	.	.	.	.	.	G	18.54	3.645540	0.67358	.	.	ENSG00000089847	ENST00000318934;ENST00000262970	T;T	0.36340	1.28;1.26	5.39	5.39	0.77823	.	.	.	.	.	T	0.47229	0.1434	L	0.44542	1.39	0.09310	N	1	D	0.53885	0.963	P	0.55749	0.783	T	0.39078	-0.9631	9	0.66056	D	0.02	.	14.6299	0.68647	0.0:0.0:1.0:0.0	.	1140	Q8TF21	ANR24_HUMAN	T	1140;1230	ENSP00000321731:R1140T;ENSP00000262970:R1230T	ENSP00000262970:R1230T	R	+	2	0	ANKRD24	4175480	0.199000	0.23386	0.008000	0.14137	0.957000	0.61999	3.193000	0.50997	2.542000	0.85734	0.484000	0.47621	AGA	.	.		0.617	ANKRD24-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458188.1	XM_114000		C	4224480	G	C	4224480	3	2	257	1	0	0	0	0	1	0	0	0	653	942	33	4	3501	4	ANKRD24	19	4224480	Missense_Mutation	SNP	G	TCGA-EP-A3JL-01A-11D-A20W-10		4224480	54904503	71	36262										
MUC16	94025	hgsc.bcm.edu	37	chr19	8994178	8994178	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	tgcagccagagtacagagggCcaacactggtgttcttgaac	12	10	1	3			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr19:8994178C>A	ENST00000397910.4	-	65	41710	c.41507G>T	c.(41506-41508)gGc>gTc	p.G13836V	MUC16_ENST00000380951.5_Missense_Mutation_p.G477V	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13839	SEA 12. {ECO:0000255|PROSITE- ProRule:PRU00188}.			Missing (in Ref. 3; AAK74120). {ECO:0000305}.	cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTACAGAGGGCCAACACTGGT	0.527																																					p.G13836V		Atlas-SNP	.											.	MUC16	4315	.	0			c.G41507T						.						114	101	105					19																	8994178		2000	4175	6175	SO:0001583	missense	94025	exon65			AGAGGGCCAACAC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.41507G>T	chr19.hg19:g.8994178C>A	ENSP00000381008:p.Gly13836Val	123.0	0.0		93.0	22.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	14.26|14.26	2.483391|2.483391	0.44147|0.44147	.|.	.|.	ENSG00000181143|ENSG00000181143	ENST00000542240|ENST00000397910;ENST00000380951	.|T;T	.|0.39056	.|1.1;1.1	3.74|3.74	2.67|2.67	0.31697|0.31697	.|SEA (1);	.|0.203527	.|0.24523	.|N	.|0.037787	T|T	0.65048|0.65048	0.2654|0.2654	M|M	0.87547|0.87547	2.89|2.89	.|.	.|.	.|.	.|D;D	.|0.89917	.|0.994;1.0	.|D;D	.|0.87578	.|0.936;0.998	T|T	0.75752|0.75752	-0.3207|-0.3207	4|9	.|0.87932	.|D	.|0	.|.	9.4867|9.4867	0.38933|0.38933	0.0:0.7852:0.2148:0.0|0.0:0.7852:0.2148:0.0	.|.	.|21481;13836	.|Q8WXI7;B5ME49	.|MUC16_HUMAN;.	S|V	676|13836;477	.|ENSP00000381008:G13836V;ENSP00000370338:G477V	.|ENSP00000370338:G477V	A|G	-|-	1|2	0|0	MUC16|MUC16	8855178|8855178	0.005000|0.005000	0.15991|0.15991	0.001000|0.001000	0.08648|0.08648	0.212000|0.212000	0.24457|0.24457	0.338000|0.338000	0.19858|0.19858	0.905000|0.905000	0.36596|0.36596	0.650000|0.650000	0.86243|0.86243	GCC|GGC	.	.		0.527	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	8994178	C	A	8994178	3	1	257	1	0	0	0	0	1	0	0	0	9982	739	26	3	2096	3	MUC16	19	8994178	Missense_Mutation	SNP	C	TCGA-EP-A3JL-01A-11D-A20W-10	4769698	8994178	50134805	72	36263										
KLK8	11202	hgsc.bcm.edu	37	chr19	51503826	51503826	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	cccagcaccttgtcctcctgTgccctggagtgtcctgcagc	10	17	0	0			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr19:51503826T>A	ENST00000600767.1	-	4	573	c.84A>T	c.(82-84)gcA>gcT	p.A28A	KLK8_ENST00000347619.4_Intron|KLK8_ENST00000391806.2_Silent_p.A73A|KLK8_ENST00000593490.1_Intron|CTB-147C22.9_ENST00000594512.1_RNA|KLK8_ENST00000291726.7_Silent_p.A28A|KLK8_ENST00000598195.1_5'Flank|KLK9_ENST00000250366.6_3'UTR|KLK8_ENST00000320838.5_Intron|KLK9_ENST00000376832.4_3'UTR			O60259	KLK8_HUMAN	kallikrein-related peptidase 8	28					cell death (GO:0008219)|keratinocyte proliferation (GO:0043616)|memory (GO:0007613)|negative regulation of axon regeneration (GO:0048681)|negative regulation of myelination (GO:0031642)|neuron projection morphogenesis (GO:0048812)|regulation of synapse organization (GO:0050807)|response to wounding (GO:0009611)|synapse organization (GO:0050808)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(8)|prostate(1)	15		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.0033)|GBM - Glioblastoma multiforme(134;0.00888)		TGTCCTCCTGTGCCCTGGAGT	0.642																																					p.A73A		Atlas-SNP	.											.	KLK8	46	.	0			c.A219T						.						65	58	60					19																	51503826		2203	4300	6503	SO:0001819	synonymous_variant	11202	exon3			CTCCTGTGCCCTG	AB008390	CCDS12813.1, CCDS12814.1, CCDS12815.1, CCDS42600.1, CCDS74433.1	19q13	2011-09-07	2006-10-27			ENSG00000129455		"Kallikreins", "Serine peptidases / Serine peptidases"	6369	protein-coding gene	gene with protein product		605644	"kallikrein 8 (neuropsin/ovasin)"	PRSS19		10102990, 9714609, 16800724, 16800723	Standard	NM_144505		Approved	HNP, TADG14, neuropsin, ovasin	uc002pur.1	O60259		ENST00000600767.1:c.84A>T	chr19.hg19:g.51503826T>A		101.0	0.0		74.0	28.0	NM_144505	Q5V9X1|Q5V9X2|Q8IW69|Q9HCB3|Q9NR68|Q9NR69|Q9UIL9|Q9UQ47	Silent	SNP	ENST00000600767.1	hg19	CCDS12813.1																																																																																			.	.		0.642	KLK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465032.2	NM_007196		A	51503826	T	A	51503826	2	1	257	1	0	0	0	0	0	0	0	1	8419	1683	59	4		4	KLK8	19	51503826	Silent	SNP	T	TCGA-EP-A3JL-01A-11D-A20W-10	42509648	51503826	7625157	73	36264										
LILRA6	79168	hgsc.bcm.edu	37	chr19	54746124	54746124	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	cccctgacaccagatggtcaCggggctcccccagctgatca	10	17	2	3			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr19:54746124C>T	ENST00000396365.2	-	3	172	c.133G>A	c.(133-135)Gtg>Atg	p.V45M	LILRA6_ENST00000419410.2_Missense_Mutation_p.V45M|LILRB3_ENST00000407860.2_Missense_Mutation_p.V45M|LILRA6_ENST00000391735.3_Missense_Mutation_p.V45M|LILRA6_ENST00000270464.5_Missense_Mutation_p.V45M|LILRA6_ENST00000440558.2_Missense_Mutation_p.V45M|LILRA6_ENST00000245621.5_Missense_Mutation_p.V45M	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	45					immune system process (GO:0002376)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CAGATGGTCACGGGGCTCCCC	0.597																																					p.V45M		Atlas-SNP	.											.	LILRA6	75	.	0			c.G133A						.						123	129	127					19																	54746124		2203	4300	6503	SO:0001583	missense	79168	exon3			TGGTCACGGGGCT	AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15495	protein-coding gene	gene with protein product			"leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6"	LILRB6		10941842	Standard	NM_024318		Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.133G>A	chr19.hg19:g.54746124C>T	ENSP00000379651:p.Val45Met	601.0	0.0		379.0	57.0	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	hg19	CCDS42610.1	.	.	.	.	.	.	.	.	.	.	C	12.77	2.036077	0.35893	.	.	ENSG00000204577;ENSG00000244482;ENSG00000244482;ENSG00000244482;ENSG00000244482;ENSG00000244482;ENSG00000244482;ENSG00000244482	ENST00000407860;ENST00000440558;ENST00000270464;ENST00000419410;ENST00000391735;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T;T;T;T	0.16897	2.31;2.31;2.31;2.31;2.31;2.31;2.31	3.93	0.456	0.16655	Immunoglobulin-like fold (1);	0.129146	0.35124	N	0.003429	T	0.35364	0.0929	M	0.79805	2.47	0.09310	N	0.999999	D;D;D;D;D;D;D;D;D;D	0.89917	1.0;0.998;0.995;0.998;1.0;1.0;1.0;1.0;1.0;1.0	D;P;P;P;D;D;D;D;D;D	0.87578	0.916;0.814;0.773;0.846;0.991;0.918;0.919;0.963;0.998;0.98	T	0.08994	-1.0695	10	0.38643	T	0.18	.	6.3692	0.21471	0.0:0.6643:0.0:0.3357	.	45;45;45;45;45;45;45;45;45;45	C9JFH3;Q6PI73-2;B5MCX0;B5ME96;Q6PI73;F8WCY4;F8WD89;D3YTC4;F8W6G6;O75022-2	.;.;.;.;LIRA6_HUMAN;.;.;.;.;.	M	45	ENSP00000384274:V45M;ENSP00000390120:V45M;ENSP00000270464:V45M;ENSP00000411227:V45M;ENSP00000375615:V45M;ENSP00000379651:V45M;ENSP00000245621:V45M	ENSP00000245621:V45M	V	-	1	0	LILRB3;LILRA6	59437936	0.000000	0.05858	0.079000	0.20413	0.013000	0.08279	-0.719000	0.04974	-0.013000	0.14199	0.184000	0.17185	GTG	.	.		0.597	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318		T	54746124	C	T	54746124	3	4	257	1	0	0	0	0	1	0	0	0	8798	536	19	1	1336	1	LILRA6	19	54746124	Missense_Mutation	SNP	C	TCGA-EP-A3JL-01A-11D-A20W-10	3242298	54746124	4382859	74	36265										
LILRB4	11006	hgsc.bcm.edu	37	chr19	55176617	55176617	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	gcccctcatgcctacagggtCagtcccccacagtggtgagt	11	15	2	1			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr19:55176617C>T	ENST00000391736.1	+	8	1058	c.743C>T	c.(742-744)tCa>tTa	p.S248L	LILRB4_ENST00000391733.3_Missense_Mutation_p.S248L|LILRB4_ENST00000391734.3_Missense_Mutation_p.S248L|LILRB4_ENST00000430952.2_Missense_Mutation_p.S248L|LILRB4_ENST00000270452.2_Missense_Mutation_p.S248L	NM_001278426.2|NM_001278428.2|NM_001278429.2|NM_001278430.2	NP_001265355.1|NP_001265357.1|NP_001265358.1|NP_001265359.1	Q8NHJ6	LIRB4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4	248					immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(20)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	39				GBM - Glioblastoma multiforme(193;0.035)		CCTACAGGGTCAGTCCCCCAC	0.647																																					p.S248L		Atlas-SNP	.											.	LILRB4	86	.	0			c.C743T						.						43	37	39					19																	55176617		2203	4300	6503	SO:0001583	missense	11006	exon6			CAGGGTCAGTCCC	U82979	CCDS12902.1, CCDS42618.1	19q13.4	2013-01-11				ENSG00000186818		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6608	protein-coding gene	gene with protein product		604821				9151699, 9079806	Standard	XM_005277050		Approved	LIR-5, ILT3, HM18, LIR5, CD85k	uc002qgp.3	Q8NHJ6		ENST00000391736.1:c.743C>T	chr19.hg19:g.55176617C>T	ENSP00000375616:p.Ser248Leu	225.0	0.0		162.0	38.0	NM_006847	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Missense_Mutation	SNP	ENST00000391736.1	hg19	CCDS12902.1	.	.	.	.	.	.	.	.	.	.	C	4.788	0.146516	0.09134	.	.	ENSG00000186818	ENST00000391736;ENST00000270452;ENST00000430952;ENST00000391734;ENST00000391733;ENST00000434286	T;T;T;T;T;T	0.00493	7.08;7.08;7.08;7.04;7.1;7.0	1.26	1.26	0.21427	.	.	.	.	.	T	0.00524	0.0017	L	0.55213	1.73	0.09310	N	1	B;B;B;B;P	0.48230	0.068;0.141;0.22;0.274;0.907	B;B;B;B;B	0.44224	0.012;0.012;0.061;0.084;0.444	T	0.53464	-0.8435	9	0.41790	T	0.15	.	5.8815	0.18858	0.0:1.0:0.0:0.0	.	248;247;248;248;248	A8MUE1;C9JST2;Q8NHJ6-3;Q8NHJ6-2;Q8NHJ6	.;.;.;.;LIRB4_HUMAN	L	248;248;248;248;248;247	ENSP00000375616:S248L;ENSP00000270452:S248L;ENSP00000408995:S248L;ENSP00000375614:S248L;ENSP00000375613:S248L;ENSP00000401962:S247L	ENSP00000270452:S248L	S	+	2	0	LILRB4	59868429	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.326000	0.07965	0.969000	0.38237	0.407000	0.27541	TCA	.	.		0.647	LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3			T	55176617	C	T	55176617	3	4	257	1	0	0	0	0	1	0	0	0	8802	838	29	3	765	3	LILRB4	19	55176617	Missense_Mutation	SNP	C	TCGA-EP-A3JL-01A-11D-A20W-10	430493	55176617	3952366	75	36266										
NLRP8	126205	hgsc.bcm.edu	37	chr19	56473481	56473482	+	Frame_Shift_Del	DEL	TG	TG	-													0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	tggtggcaagacttatgctcTgtgtttgcaacgaatgataa							TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr19:56473481_56473482delTG	ENST00000291971.3	+	4	2162_2163	c.2091_2092delTG	c.(2089-2094)tctgtgfs	p.V698fs	NLRP8_ENST00000590542.1_Frame_Shift_Del_p.V698fs	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	698					neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		ACTTATGCTCTGTGTTTGCAAC	0.5																																					p.697_697del		Atlas-Indel,Pindel	.											.	NLRP8	225	.	0			c.2090_2091del						.																																			SO:0001589	frameshift_variant	126205	exon4			.	AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"Nucleotide-binding domain and leucine rich repeat containing"	22940	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"	609659	"NACHT, leucine rich repeat and PYD containing 8"	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.2091_2092delTG	chr19.hg19:g.56473483_56473484delTG	ENSP00000291971:p.Val698fs	173.0	0.0		142.0	15.0	NM_176811	Q7RTR4	Frame_Shift_Del	DEL	ENST00000291971.3	hg19	CCDS12937.1																																																																																			.	.		0.5	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811		-	56473482	TG	-	56473481	7	5	257	1	0	1	0	1	0	0	0	0	10492	1567	55	0	2105	0	NLRP8	19	56473481	Frame_Shift_Del	DEL	TG	TCGA-EP-A3JL-01A-11D-A20W-10	1296864	56473481	2655502	76	36267										
CHRNA4	1137	hgsc.bcm.edu	37	chr20	61978128	61978128	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	ccagggcggcaggaagaggcCcaccgtccccagcaggcaga	15	15	0	2			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr20:61978128C>A	ENST00000370263.4	-	6	2067	c.1846G>T	c.(1846-1848)Ggc>Tgc	p.G616C	CHRNA4_ENST00000463705.1_5'UTR	NM_000744.6|NM_001256573.1	NP_000735.1|NP_001243502.1	P43681	ACHA4_HUMAN	cholinergic receptor, nicotinic, alpha 4 (neuronal)	616					action potential (GO:0001508)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cognition (GO:0050890)|DNA repair (GO:0006281)|exploration behavior (GO:0035640)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|neurological system process (GO:0050877)|regulation of dopamine secretion (GO:0014059)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of membrane potential (GO:0042391)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(19)|prostate(3)|skin(3)|soft_tissue(1)	33	all_cancers(38;1.71e-10)				Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273)	AGGAAGAGGCCCACCGTCCCC	0.647																																					p.G616C		Atlas-SNP	.											.	CHRNA4	98	.	0			c.G1846T						.						101	63	76					20																	61978128		2202	4298	6500	SO:0001583	missense	1137	exon6			AGAGGCCCACCGT		CCDS13517.1	20q13.33	2013-09-20	2012-02-07		ENSG00000101204	ENSG00000101204		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1958	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 4 (neuronal)"	118504	"cholinergic receptor, nicotinic, alpha polypeptide 4"	EBN, EBN1		1505988	Standard	NM_000744		Approved	BFNC	uc002yes.3	P43681	OTTHUMG00000033080	ENST00000370263.4:c.1846G>T	chr20.hg19:g.61978128C>A	ENSP00000359285:p.Gly616Cys	57.0	0.0		72.0	29.0	NM_000744	Q4JGR7|Q4VAQ5|Q4VAQ6	Missense_Mutation	SNP	ENST00000370263.4	hg19	CCDS13517.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.846034	0.91277	.	.	ENSG00000101204	ENST00000370258;ENST00000370263;ENST00000539366	D	0.86769	-2.17	4.43	4.43	0.53597	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.152326	0.64402	D	0.000015	D	0.93566	0.7946	M	0.79805	2.47	0.80722	D	1	D;D	0.89917	0.985;1.0	D;D	0.97110	0.964;1.0	D	0.94674	0.7859	10	0.87932	D	0	.	17.3789	0.87399	0.0:1.0:0.0:0.0	.	545;616	Q4VAQ5;P43681	.;ACHA4_HUMAN	C	522;616;545	ENSP00000359285:G616C	ENSP00000359280:G522C	G	-	1	0	CHRNA4	61448572	1.000000	0.71417	0.995000	0.50966	0.877000	0.50540	7.574000	0.82434	2.177000	0.69029	0.511000	0.50034	GGC	.	.		0.647	CHRNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080508.3			A	61978128	C	A	61978128	3	1	257	1	0	0	0	0	1	0	0	0	3387	623	22	3	41	3	CHRNA4	20	61978128	Missense_Mutation	SNP	C	TCGA-EP-A3JL-01A-11D-A20W-10		61978128	1047392	77	36268										
SAMSN1	64092	hgsc.bcm.edu	37	chr21	15873032	15873032	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	catccccattggtgttttgcAaataatgtctatgatgtctc	7	9	2	1			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr21:15873032A>G	ENST00000400566.1	-	6	667	c.586T>C	c.(586-588)Tgc>Cgc	p.C196R	SAMSN1_ENST00000400564.1_Missense_Mutation_p.C28R|SAMSN1_ENST00000285670.2_Missense_Mutation_p.C264R|SAMSN1_ENST00000463807.1_5'Flank	NM_022136.4	NP_071419.3	Q9NSI8	SAMN1_HUMAN	SAM domain, SH3 domain and nuclear localization signals 1	196	SH3.				negative regulation of adaptive immune response (GO:0002820)|negative regulation of B cell activation (GO:0050869)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)	cell projection (GO:0042995)|cytosol (GO:0005829)|nucleus (GO:0005634)	phosphotyrosine binding (GO:0001784)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	24				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.00118)|Colorectal(24;0.00961)|Lung(58;0.164)		GGTGTTTTGCAAATAATGTCT	0.373																																					p.C264R		Atlas-SNP	.											.	SAMSN1	112	.	0			c.T790C						.						187	165	172					21																	15873032		1847	4101	5948	SO:0001583	missense	64092	exon7			TTTTGCAAATAAT	AF222927	CCDS42906.1, CCDS58786.1, CCDS74774.1	21q11	2013-01-10	2006-12-13		ENSG00000155307	ENSG00000155307		"SAM and SH3 domain containing", "Sterile alpha motif (SAM) domain containing"	10528	protein-coding gene	gene with protein product	"nuclear localization signals, SAM and SH3 domain containing 1", "SAM and SH3 domain containing 2", "hematopoietic adapter-containing SH3 and sterile &#945;-motif (SAM) domains 1", "Src homology domain 3 (SH3)-containing adapter protein SH3 lymphocyte protein 2"	607978				11536050, 11594764	Standard	NM_022136		Approved	NASH1, SASH2, SH3D6B, HACS1, SLy2	uc002yjv.1	Q9NSI8	OTTHUMG00000074317	ENST00000400566.1:c.586T>C	chr21.hg19:g.15873032A>G	ENSP00000383411:p.Cys196Arg	180.0	0.0		98.0	12.0	NM_001256370	B3KWJ3|F8WAA1|Q8NFF7|Q9C041	Missense_Mutation	SNP	ENST00000400566.1	hg19	CCDS42906.1	.	.	.	.	.	.	.	.	.	.	A	16.34	3.094882	0.56075	.	.	ENSG00000155307	ENST00000285670;ENST00000400566;ENST00000400564	T;T;T	0.26518	3.34;3.34;1.73	5.77	3.34	0.38264	Src homology-3 domain (2);Variant SH3 (1);	0.174005	0.64402	D	0.000006	T	0.13243	0.0321	N	0.00300	-1.685	0.58432	D	0.999997	D;D;P	0.64830	0.994;0.96;0.955	P;P;P	0.59221	0.854;0.788;0.632	T	0.44892	-0.9298	10	0.33940	T	0.23	-6.0622	11.0838	0.48074	0.7523:0.0:0.0:0.2476	.	28;264;196	Q9NSI8-2;F8WAA1;Q9NSI8	.;.;SAMN1_HUMAN	R	264;196;28	ENSP00000285670:C264R;ENSP00000383411:C196R;ENSP00000383409:C28R	ENSP00000285670:C264R	C	-	1	0	SAMSN1	14794903	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	4.293000	0.59037	0.409000	0.25649	0.528000	0.53228	TGC	.	.		0.373	SAMSN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157914.1			G	15873032	A	G	15873032	3	3	257	1	0	0	0	0	1	0	0	0	13845	130	5	2	547	2	SAMSN1	21	15873032	Missense_Mutation	SNP	A	TCGA-EP-A3JL-01A-11D-A20W-10		15873032	32256863	78	36269										
DYRK1A	1859	hgsc.bcm.edu	37	chr21	38865436	38865436	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	ttttggttgaaatgcacactGgagaacctctgttcagtggt	11	7	2	2			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr21:38865436G>T	ENST00000398960.2	+	7	1144	c.1069G>T	c.(1069-1071)Gga>Tga	p.G357*	DYRK1A_ENST00000451934.1_Nonsense_Mutation_p.G357*|DYRK1A_ENST00000455387.2_Nonsense_Mutation_p.G129*|DYRK1A_ENST00000339659.4_Nonsense_Mutation_p.G348*|DYRK1A_ENST00000398956.2_Nonsense_Mutation_p.G357*|DYRK1A_ENST00000321219.8_Nonsense_Mutation_p.G357*|DYRK1A_ENST00000338785.3_Nonsense_Mutation_p.G357*	NM_001396.3|NM_130438.2	NP_001387.2|NP_569122.1	Q13627	DYR1A_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A	357	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.			G -> R (in Ref. 6; CAA05059). {ECO:0000305}.	circadian rhythm (GO:0007623)|mitotic cell cycle (GO:0000278)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|nervous system development (GO:0007399)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of protein deacetylation (GO:0090312)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|tau protein binding (GO:0048156)			breast(4)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						AATGCACACTGGAGAACCTCT	0.413																																					p.G357X	Melanoma(114;464 1602 31203 43785 45765)	Atlas-SNP	.											.	DYRK1A	85	.	0			c.G1069T						.						169	153	159					21																	38865436		2203	4300	6503	SO:0001587	stop_gained	1859	exon7			CACACTGGAGAAC	U52373	CCDS13653.1, CCDS13654.1, CCDS42925.1, CCDS42926.1	21q22.13	2010-04-21			ENSG00000157540	ENSG00000157540			3091	protein-coding gene	gene with protein product		600855		DYRK1, DYRK, MNBH		9284911	Standard	NM_130436		Approved		uc002ywk.3	Q13627	OTTHUMG00000086657	ENST00000398960.2:c.1069G>T	chr21.hg19:g.38865436G>T	ENSP00000381932:p.Gly357*	132.0	0.0		73.0	16.0	NM_001396	O60769|Q92582|Q92810|Q9UNM5	Nonsense_Mutation	SNP	ENST00000398960.2	hg19	CCDS42925.1	.	.	.	.	.	.	.	.	.	.	G	51	17.496504	0.99887	.	.	ENSG00000157540	ENST00000338785;ENST00000339659;ENST00000321219;ENST00000451934;ENST00000398960;ENST00000398956;ENST00000455387	.	.	.	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	20.3431	0.98773	0.0:0.0:1.0:0.0	.	.	.	.	X	357;348;357;357;357;357;129	.	ENSP00000319032:G357X	G	+	1	0	DYRK1A	37787306	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.813000	0.99286	2.880000	0.98712	0.650000	0.86243	GGA	.	.		0.413	DYRK1A-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194804.1	NM_001396		T	38865436	G	T	38865436	4	4	257	1	0	0	0	0	0	1	0	0	4856	1349	47	3	1095	3	DYRK1A	21	38865436	Nonsense_Mutation	SNP	G	TCGA-EP-A3JL-01A-11D-A20W-10	22992404	38865436	9264459	79	36270										
GAB4	128954	hgsc.bcm.edu	37	chr22	17450871	17450871	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	agcctgtgaggctgcctctgGtgtggccatgggaggccagg	18	10	1	1			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr22:17450871G>T	ENST00000400588.1	-	4	1006	c.899C>A	c.(898-900)aCc>aAc	p.T300N	GAB4_ENST00000523144.1_Intron	NM_001037814.1	NP_001032903.1	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member 4	300										breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(24)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44		all_epithelial(15;0.112)|Lung NSC(13;0.248)				GCTGCCTCTGGTGTGGCCATG	0.597																																					p.T300N		Atlas-SNP	.											.	GAB4	95	.	0			c.C899A						.						75	84	81					22																	17450871		2184	4293	6477	SO:0001583	missense	128954	exon4			CCTCTGGTGTGGC	AK057252	CCDS42976.1	22q11.2	2013-01-10			ENSG00000215568	ENSG00000215568		"Pleckstrin homology (PH) domain containing"	18325	protein-coding gene	gene with protein product							Standard	NM_001037814		Approved		uc002zlw.3	Q2WGN9	OTTHUMG00000149992	ENST00000400588.1:c.899C>A	chr22.hg19:g.17450871G>T	ENSP00000383431:p.Thr300Asn	152.0	0.0		77.0	29.0	NM_001037814		Missense_Mutation	SNP	ENST00000400588.1	hg19	CCDS42976.1	.	.	.	.	.	.	.	.	.	.	G	7.774	0.708157	0.15239	.	.	ENSG00000215568	ENST00000400588	T	0.42131	0.98	1.97	1.97	0.26223	.	0.408932	0.25503	N	0.030225	T	0.29491	0.0735	L	0.38175	1.15	0.28401	N	0.918643	P	0.47409	0.895	B	0.43838	0.433	T	0.14008	-1.0488	10	0.09590	T	0.72	.	9.9586	0.41682	0.0:0.0:1.0:0.0	.	300	Q2WGN9	GAB4_HUMAN	N	300	ENSP00000383431:T300N	ENSP00000383431:T300N	T	-	2	0	GAB4	15830871	1.000000	0.71417	0.999000	0.59377	0.058000	0.15608	8.431000	0.90285	1.398000	0.46701	0.411000	0.27672	ACC	.	.		0.597	GAB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315426.1	XM_372882		T	17450871	G	T	17450871	3	4	257	1	0	0	0	0	1	0	0	0	6159	1261	44	3	853	3	GAB4	22	17450871	Missense_Mutation	SNP	G	TCGA-EP-A3JL-01A-11D-A20W-10		17450871	33853695	80	36271										
RASD2	23551	hgsc.bcm.edu	37	chr22	35947948	35947948	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	tctgcatgcgccgcgtcaagGagatggacgcctatggcatg	14	11	2	1			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chr22:35947948G>A	ENST00000216127.4	+	3	1312	c.670G>A	c.(670-672)Gag>Aag	p.E224K		NM_014310.3	NP_055125.2	Q96D21	RHES_HUMAN	RASD family, member 2	224	Interaction with GNB1, GNB2 and GNB3.				locomotory behavior (GO:0007626)|negative regulation of protein ubiquitination (GO:0031397)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein sumoylation (GO:0033235)|regulation of cAMP-mediated signaling (GO:0043949)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission, dopaminergic (GO:0001963)	plasma membrane (GO:0005886)	G-protein beta-subunit binding (GO:0031681)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(2)|large_intestine(1)|lung(8)|prostate(1)|skin(1)	13						CCGCGTCAAGGAGATGGACGC	0.642																																					p.E224K		Atlas-SNP	.											.	RASD2	34	.	0			c.G670A						.						96	80	85					22																	35947948		2203	4300	6503	SO:0001583	missense	23551	exon3			GTCAAGGAGATGG	AF279143	CCDS13916.1	22q13.1	2014-05-09			ENSG00000100302	ENSG00000100302			18229	protein-coding gene	gene with protein product	"tumor endothelial marker 2", "Ras homolog enriched in striatum"	612842				10947988, 10467249, 14724584	Standard	NM_014310		Approved	TEM2, Rhes, MGC:4834	uc003anx.3	Q96D21	OTTHUMG00000150607	ENST00000216127.4:c.670G>A	chr22.hg19:g.35947948G>A	ENSP00000216127:p.Glu224Lys	74.0	0.0		54.0	15.0	NM_014310	O95520|Q5THY8	Missense_Mutation	SNP	ENST00000216127.4	hg19	CCDS13916.1	.	.	.	.	.	.	.	.	.	.	G	12.12	1.843199	0.32606	.	.	ENSG00000100302	ENST00000216127	T	0.70631	-0.5	5.68	5.68	0.88126	.	0.479994	0.25294	N	0.031720	T	0.60612	0.2282	N	0.22421	0.69	0.42256	D	0.991998	B	0.02656	0.0	B	0.04013	0.001	T	0.53194	-0.8473	10	0.27785	T	0.31	.	19.8575	0.96767	0.0:0.0:1.0:0.0	.	224	Q96D21	RHES_HUMAN	K	224	ENSP00000216127:E224K	ENSP00000216127:E224K	E	+	1	0	RASD2	34277894	1.000000	0.71417	0.992000	0.48379	0.913000	0.54294	7.935000	0.87658	2.705000	0.92388	0.556000	0.70494	GAG	.	.		0.642	RASD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319063.1	NM_014310		A	35947948	G	A	35947948	3	1	257	1	0	0	0	0	1	0	0	0	13082	1175	41	3	676	3	RASD2	22	35947948	Missense_Mutation	SNP	G	TCGA-EP-A3JL-01A-11D-A20W-10	18497077	35947948	15356618	81	36272										
PCDH11Y	83259	hgsc.bcm.edu	37	chrY	4968507	4968507	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	5	1	1.09817351598174	1.6472602739726	0.898505603985056	1	1	0	acctactactttcaagcctgAcagccctgatttggcccgac	7	15	1	2			TCGA-EP-A3JL-01A-11D-A20W-10	TCGA-EP-A3JL-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3c3e9b90-d106-48ce-a6d4-999adc5870e0	87055f49-edc2-4751-a7c5-8715fea95a43	g.chrY:4968507A>G	ENST00000333703.4	+	5	3368	c.2855A>G	c.(2854-2856)gAc>gGc	p.D952G	PCDH11Y_ENST00000215473.6_Missense_Mutation_p.D963G|PCDH11Y_ENST00000362095.5_Missense_Mutation_p.D963G	NM_001278619.1|NM_032971.2	NP_001265548.1|NP_116753.1	Q9BZA8	PC11Y_HUMAN	protocadherin 11 Y-linked	963					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|kidney(2)|large_intestine(7)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						TTCAAGCCTGACAGCCCTGAT	0.458																																					p.D963G		Atlas-SNP	.											.	PCDH11Y	163	.	0			c.A2888G						.																																			SO:0001583	missense	83259	exon2			AGCCTGACAGCCC	AF332217	CCDS14776.1, CCDS14777.1, CCDS76066.1	Yp11.2	2010-01-26	2002-05-22	2002-05-24	ENSG00000099715	ENSG00000099715		"Cadherins / Protocadherins : Non-clustered"	15813	protein-coding gene	gene with protein product		400022	"protocadherin 22"	PCDH22		10644456, 11003707	Standard	NM_032971		Approved	PCDHY	uc004fqo.3	Q9BZA8	OTTHUMG00000035105	ENST00000333703.4:c.2855A>G	chrY.hg19:g.4968507A>G	ENSP00000330552:p.Asp952Gly	59.0	0.0		46.0	21.0	NM_032972	Q70LR6|Q70LR8|Q70LS0|Q70LS1|Q70LS2|Q70LS3|Q70LS4|Q70LS5|Q8WY34|Q9BZA9|Q9H4E1	Missense_Mutation	SNP	ENST00000333703.4	hg19	CCDS14776.1																																																																																			.	.		0.458	PCDH11Y-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084979.2	NM_032973		G	4968507	A	G	4968507	3	3	257	1	0	0	0	0	1	0	0	0	11518	275	10	2	2930	2	PCDH11Y	24	4968507	Missense_Mutation	SNP	A	TCGA-EP-A3JL-01A-11D-A20W-10		4968507	54405059	82	36273										
GLIS1	148979	hgsc.bcm.edu	37	chr1	53974802	53974802	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	gcagggctcacctgtggcagGcaagggcgtgctgaggctgt	18	10	1	1	rs540910687		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr1:53974802G>A	ENST00000312233.2	-	9	2262	c.1696C>T	c.(1696-1698)Cct>Tct	p.P566S		NM_147193.2	NP_671726.2			GLIS family zinc finger 1											endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|skin(3)|urinary_tract(4)	24						CCTGTGGCAGGCAAGGGCGTG	0.667																																					p.P566S		Atlas-SNP	.											.	GLIS1	52	.	0			c.C1696T						.						33	28	30					1																	53974802		2193	4286	6479	SO:0001583	missense	148979	exon9			TGGCAGGCAAGGG	AK093474	CCDS582.1	1p32.3	2008-02-05			ENSG00000174332	ENSG00000174332		"Zinc fingers, C2H2-type"	29525	protein-coding gene	gene with protein product		610378				12042312, 14500813	Standard	NM_147193		Approved	FLJ36155	uc001cvr.1	Q8NBF1	OTTHUMG00000008079	ENST00000312233.2:c.1696C>T	chr1.hg19:g.53974802G>A	ENSP00000309653:p.Pro566Ser	39.0	0.0		56.0	9.0	NM_147193		Missense_Mutation	SNP	ENST00000312233.2	hg19	CCDS582.1	.	.	.	.	.	.	.	.	.	.	G	9.829	1.187991	0.21954	.	.	ENSG00000174332	ENST00000312233	T	0.09630	2.96	3.94	2.01	0.26516	.	0.423149	0.20122	N	0.098788	T	0.04003	0.0112	N	0.12746	0.255	0.24107	N	0.99586	B	0.10296	0.003	B	0.06405	0.002	T	0.43702	-0.9375	10	0.06494	T	0.89	.	3.8607	0.08994	0.234:0.2024:0.5637:0.0	.	566	Q8NBF1	GLIS1_HUMAN	S	566	ENSP00000309653:P566S	ENSP00000309653:P566S	P	-	1	0	GLIS1	53747390	0.996000	0.38824	0.997000	0.53966	0.679000	0.39708	0.547000	0.23299	0.422000	0.26005	0.561000	0.74099	CCT	.	.		0.667	GLIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022109.1	NM_147193		A	53974802	G	A	53974802	3	1	258	1	0	0	0	0	1	0	0	0	6453	1203	42	3	174	3	GLIS1	1	53974802	Missense_Mutation	SNP	G	TCGA-EP-A3RK-01A-11D-A22F-10		53974802	195275819	1	36274										
PALMD	54873	hgsc.bcm.edu	37	chr1	100154970	100154970	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	atctgaacaccagaattcttCacccacttgtcaggaggacg	8	12	4	2			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr1:100154970C>G	ENST00000263174.4	+	7	1529	c.1154C>G	c.(1153-1155)tCa>tGa	p.S385*	PALMD_ENST00000605497.1_Nonsense_Mutation_p.S385*	NM_017734.4	NP_060204.1	Q9NP74	PALMD_HUMAN	palmdelphin	385				S -> L (in Ref. 4; CAC01335). {ECO:0000305}.	regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|membrane (GO:0016020)				central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(8)|ovary(6)|pancreas(1)|prostate(2)	31		all_epithelial(167;0.000813)|all_lung(203;0.0214)|Lung NSC(277;0.0216)		Epithelial(280;0.067)|all cancers(265;0.117)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)		CAGAATTCTTCACCCACTTGT	0.448																																					p.S385X		Atlas-SNP	.											.	PALMD	64	.	0			c.C1154G						.						54	46	49					1																	100154970		2203	4300	6503	SO:0001587	stop_gained	54873	exon7			ATTCTTCACCCAC	AJ312214	CCDS758.1	1p22-p21	2008-07-18			ENSG00000099260	ENSG00000099260			15846	protein-coding gene	gene with protein product		610182		C1orf11		11478809	Standard	NM_017734		Approved	FLJ20271, PALML	uc001dsg.3	Q9NP74	OTTHUMG00000010764	ENST00000263174.4:c.1154C>G	chr1.hg19:g.100154970C>G	ENSP00000263174:p.Ser385*	88.0	0.0		77.0	19.0	NM_017734	Q9H7E6|Q9NPM5|Q9NPM6|Q9NPS0	Nonsense_Mutation	SNP	ENST00000263174.4	hg19	CCDS758.1	.	.	.	.	.	.	.	.	.	.	C	33	5.274693	0.95459	.	.	ENSG00000099260	ENST00000263174	.	.	.	5.68	3.77	0.43336	.	0.813719	0.11449	N	0.562931	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-0.221	6.9823	0.24709	0.1311:0.6738:0.1265:0.0687	.	.	.	.	X	385	.	ENSP00000263174:S385X	S	+	2	0	PALMD	99927558	0.001000	0.12720	0.013000	0.15412	0.042000	0.13812	0.996000	0.29719	0.702000	0.31825	-0.253000	0.11424	TCA	.	.		0.448	PALMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029672.1	NM_017734		G	100154970	C	G	100154970	4	3	258	1	0	0	0	0	0	1	0	0	11420	838	29	4	1180	4	PALMD	1	100154970	Nonsense_Mutation	SNP	C	TCGA-EP-A3RK-01A-11D-A22F-10	46180168	100154970	149095651	2	36275										
PLA2G4A	5321	hgsc.bcm.edu	37	chr1	186880477	186880477	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	taagggagagcatgaagaaaCtcttgggtccaaagaatagt	12	5	1	4			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr1:186880477C>T	ENST00000367466.3	+	7	666	c.514C>T	c.(514-516)Ctc>Ttc	p.L172F	PLA2G4A_ENST00000442353.2_Intron|PLA2G4A_ENST00000466600.1_3'UTR	NM_024420.2	NP_077734	P47712	PA24A_HUMAN	phospholipase A2, group IVA (cytosolic, calcium-dependent)	172	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.|Phospholipid binding. {ECO:0000305}.				arachidonic acid metabolic process (GO:0019369)|arachidonic acid secretion (GO:0050482)|blood coagulation (GO:0007596)|cardiolipin acyl-chain remodeling (GO:0035965)|cellular response to antibiotic (GO:0071236)|glycerophospholipid biosynthetic process (GO:0046474)|icosanoid biosynthetic process (GO:0046456)|icosanoid metabolic process (GO:0006690)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|platelet activation (GO:0030168)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|calcium-dependent phospholipid binding (GO:0005544)|lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|prostate(3)|skin(4)|stomach(1)	53					Aldesleukin(DB00041)|Carbachol(DB00411)|Carbenicillin(DB00578)|Epirubicin(DB00445)|Fluocinolone Acetonide(DB00591)|Fluticasone Propionate(DB00588)|Niflumic Acid(DB04552)|Orlistat(DB01083)|Quinacrine(DB01103)|Streptokinase(DB00086)|Suramin(DB04786)	CATGAAGAAACTCTTGGGTCC	0.393																																					p.L172F		Atlas-SNP	.											.	PLA2G4A	125	.	0			c.C514T						.						132	136	135					1																	186880477		2203	4300	6503	SO:0001583	missense	5321	exon7			AAGAAACTCTTGG	M72393	CCDS1372.1	1q25	2014-09-17			ENSG00000116711	ENSG00000116711	3.1.1.4, 3.1.1.5		9035	protein-coding gene	gene with protein product		600522		PLA2G4		8175726	Standard	NM_024420		Approved	cPLA2-alpha	uc001gsc.3	P47712	OTTHUMG00000035512	ENST00000367466.3:c.514C>T	chr1.hg19:g.186880477C>T	ENSP00000356436:p.Leu172Phe	124.0	0.0		133.0	24.0	NM_024420	B1AKG4|Q29R80	Missense_Mutation	SNP	ENST00000367466.3	hg19	CCDS1372.1	.	.	.	.	.	.	.	.	.	.	C	12.26	1.884991	0.33255	.	.	ENSG00000116711	ENST00000367466	T	0.04360	3.64	4.94	4.03	0.46877	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (2);	0.119689	0.56097	N	0.000023	T	0.04452	0.0122	N	0.25825	0.765	0.80722	D	1	B	0.12013	0.005	B	0.10450	0.005	T	0.40794	-0.9544	10	0.42905	T	0.14	-11.2159	11.5527	0.50729	0.0:0.9108:0.0:0.0892	.	172	P47712	PA24A_HUMAN	F	172	ENSP00000356436:L172F	ENSP00000356436:L172F	L	+	1	0	PLA2G4A	185147100	1.000000	0.71417	1.000000	0.80357	0.684000	0.39900	1.416000	0.34759	1.200000	0.43188	-0.157000	0.13467	CTC	.	.		0.393	PLA2G4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086236.1	NM_024420		T	186880477	C	T	186880477	3	4	258	1	0	0	0	0	1	0	0	0	12010	565	20	3	536	3	PLA2G4A	1	186880477	Missense_Mutation	SNP	C	TCGA-EP-A3RK-01A-11D-A22F-10	86725507	186880477	62370144	3	36276										
ASPM	259266	hgsc.bcm.edu	37	chr1	197094016	197094016	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	atacctgaaaagcaaacgctAttttccaaagcaacctgaga	6	10	0	2			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr1:197094016A>G	ENST00000367409.4	-	12	3408	c.3152T>C	c.(3151-3153)aTa>aCa	p.I1051T	ASPM_ENST00000367408.1_Missense_Mutation_p.I301T|ASPM_ENST00000294732.7_Missense_Mutation_p.I1051T	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	1051	CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						AGCAAACGCTATTTTCCAAAG	0.274																																					p.I1051T		Atlas-SNP	.											.	ASPM	444	.	0			c.T3152C						.						145	155	152					1																	197094016		2203	4299	6502	SO:0001583	missense	259266	exon12			AACGCTATTTTCC	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"microcephaly, primary autosomal recessive 5", "asp (abnormal spindle)-like, microcephaly associated (Drosophila)"	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.3152T>C	chr1.hg19:g.197094016A>G	ENSP00000356379:p.Ile1051Thr	127.0	0.0		201.0	15.0	NM_001206846	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	hg19	CCDS1389.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.107128	0.77096	.	.	ENSG00000066279	ENST00000367409;ENST00000294732;ENST00000367408	T;T;T	0.66099	-0.19;-0.19;-0.19	5.54	5.54	0.83059	Calponin homology domain (4);	0.000000	0.85682	D	0.000000	T	0.81795	0.4898	M	0.87758	2.905	0.80722	D	1	D;D	0.89917	0.986;1.0	P;D	0.79108	0.655;0.992	D	0.85328	0.1088	10	0.87932	D	0	.	15.9651	0.79966	1.0:0.0:0.0:0.0	.	1051;1051	Q4G1H1;Q8IZT6	.;ASPM_HUMAN	T	1051;1051;301	ENSP00000356379:I1051T;ENSP00000294732:I1051T;ENSP00000356378:I301T	ENSP00000294732:I1051T	I	-	2	0	ASPM	195360639	1.000000	0.71417	0.973000	0.42090	0.913000	0.54294	8.405000	0.90213	2.230000	0.72887	0.455000	0.32223	ATA	.	.		0.274	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136		G	197094016	A	G	197094016	3	3	258	1	0	0	0	0	1	0	0	0	1056	449	16	2	7349	2	ASPM	1	197094016	Missense_Mutation	SNP	A	TCGA-EP-A3RK-01A-11D-A22F-10	10213539	197094016	52156605	4	36277										
GREB1	9687	hgsc.bcm.edu	37	chr2	11738862	11738862	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	tgacgaagcagagggtggaaCagtatgttctgaagctagac	14	6	1	4			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr2:11738862C>G	ENST00000381486.2	+	15	2509	c.2209C>G	c.(2209-2211)Cag>Gag	p.Q737E	GREB1_ENST00000234142.5_Missense_Mutation_p.Q737E	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	737						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		GAGGGTGGAACAGTATGTTCT	0.453																																					p.Q737E	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											.	GREB1	308	.	0			c.C2209G						.						200	203	202					2																	11738862		1986	4174	6160	SO:0001583	missense	9687	exon15			GTGGAACAGTATG		CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"gene regulated by estrogen in breast cancer"	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.2209C>G	chr2.hg19:g.11738862C>G	ENSP00000370896:p.Gln737Glu	85.0	0.0		87.0	25.0	NM_014668	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	hg19	CCDS42655.1	.	.	.	.	.	.	.	.	.	.	C	11.97	1.798630	0.31777	.	.	ENSG00000196208	ENST00000381486;ENST00000234142;ENST00000432985	T;T;T	0.46451	3.2;3.2;0.87	5.16	5.16	0.70880	.	0.332987	0.29908	N	0.010887	T	0.40909	0.1136	L	0.56769	1.78	0.58432	D	0.999998	P;P	0.41131	0.739;0.604	B;B	0.33454	0.164;0.164	T	0.50206	-0.8855	10	0.66056	D	0.02	-12.7435	18.6712	0.91512	0.0:1.0:0.0:0.0	.	371;737	C9JIG0;Q4ZG55	.;GREB1_HUMAN	E	737;737;371	ENSP00000370896:Q737E;ENSP00000234142:Q737E;ENSP00000403886:Q371E	ENSP00000234142:Q737E	Q	+	1	0	GREB1	11656313	1.000000	0.71417	0.019000	0.16419	0.006000	0.05464	5.547000	0.67249	2.413000	0.81919	0.655000	0.94253	CAG	.	.		0.453	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668		G	11738862	C	G	11738862	3	3	258	1	0	0	0	0	1	0	0	0	6769	479	17	4	2371	4	GREB1	2	11738862	Missense_Mutation	SNP	C	TCGA-EP-A3RK-01A-11D-A22F-10		11738862	231460511	5	36278										
ATAD2B	54454	hgsc.bcm.edu	37	chr2	23980355	23980355	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	tctaacttctcattattgctAcattccagtgcctctagttt	4	11	3	0			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr2:23980355A>G	ENST00000238789.5	-	25	4354	c.4011T>C	c.(4009-4011)tgT>tgC	p.C1337C	ATAD2B_ENST00000474583.1_5'UTR	NM_001242338.1|NM_017552.2	NP_001229267.1|NP_060022.1	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B	1337						nucleus (GO:0005634)	ATP binding (GO:0005524)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CATTATTGCTACATTCCAGTG	0.383																																					p.C1337C		Atlas-SNP	.											.	ATAD2B	110	.	0			c.T4011C						.						168	159	162					2																	23980355		1838	4098	5936	SO:0001819	synonymous_variant	54454	exon25			ATTGCTACATTCC	AB033066	CCDS46227.1	2p24.1-p23.3	2010-04-21		2007-02-08	ENSG00000119778	ENSG00000119778		"ATPases / AAA-type"	29230	protein-coding gene	gene with protein product		615347					Standard	XM_005264372		Approved	KIAA1240	uc002rek.4	Q9ULI0	OTTHUMG00000151902	ENST00000238789.5:c.4011T>C	chr2.hg19:g.23980355A>G		167.0	0.0		160.0	39.0	NM_017552	B9ZVQ5|Q6ZNA6|Q8N9E7	Silent	SNP	ENST00000238789.5	hg19	CCDS46227.1	.	.	.	.	.	.	.	.	.	.	A	8.117	0.780074	0.16120	.	.	ENSG00000119778	ENST00000381024	.	.	.	5.27	-1.28	0.09318	.	.	.	.	.	T	0.55878	0.1948	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52102	-0.8620	4	.	.	.	.	10.4273	0.44387	0.4544:0.0:0.5456:0.0	.	.	.	.	A	613	.	.	V	-	2	0	ATAD2B	23833859	0.984000	0.35163	0.994000	0.49952	0.966000	0.64601	0.847000	0.27696	-0.131000	0.11578	-0.371000	0.07208	GTA	.	.		0.383	ATAD2B-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324333.1	NM_017552		G	23980355	A	G	23980355	2	3	258	1	0	0	0	0	0	0	0	1	1072	389	14	2		2	ATAD2B	2	23980355	Silent	SNP	A	TCGA-EP-A3RK-01A-11D-A22F-10	12241493	23980355	219219018	6	36279										
DGUOK	1716	hgsc.bcm.edu	37	chr2	74185303	74185303	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	gaggctctgatgaacattccAgtgctggtgttggatgtcaa	13	7	2	2			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr2:74185303A>G	ENST00000264093.4	+	6	823	c.738A>G	c.(736-738)ccA>ccG	p.P246P	DGUOK-AS1_ENST00000453103.1_RNA|DGUOK_ENST00000356837.6_Silent_p.P224P|DGUOK_ENST00000348222.1_Silent_p.P158P|DGUOK_ENST00000462685.1_3'UTR|DGUOK-AS1_ENST00000413452.1_RNA|DGUOK-AS1_ENST00000439192.1_RNA	NM_080916.2	NP_550438.1	Q16854	DGUOK_HUMAN	deoxyguanosine kinase	246					deoxyribonucleoside monophosphate biosynthetic process (GO:0009157)|dGTP metabolic process (GO:0046070)|guanosine metabolic process (GO:0008617)|negative regulation of neuron projection development (GO:0010977)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide biosynthetic process (GO:0009165)|protein phosphorylation (GO:0006468)|purine deoxyribonucleoside metabolic process (GO:0046122)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|deoxyguanosine kinase activity (GO:0004138)|nucleoside kinase activity (GO:0019206)			endometrium(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	8					Nelarabine(DB01280)	TGAACATTCCAGTGCTGGTGT	0.423																																					p.P246P		Atlas-SNP	.											.	DGUOK	16	.	0			c.A738G						.						126	121	123					2																	74185303		2203	4300	6503	SO:0001819	synonymous_variant	1716	exon6			CATTCCAGTGCTG	U41668	CCDS1931.1, CCDS1932.1	2p13	2008-02-05			ENSG00000114956	ENSG00000114956	2.7.1.113		2858	protein-coding gene	gene with protein product		601465					Standard	NM_080916		Approved	dGK	uc002sjx.3	Q16854	OTTHUMG00000129819	ENST00000264093.4:c.738A>G	chr2.hg19:g.74185303A>G		147.0	0.0		174.0	36.0	NM_080916	P78532|Q16759|Q4ZG09|Q7L1W9|Q96BC1	Silent	SNP	ENST00000264093.4	hg19	CCDS1931.1																																																																																			.	.		0.423	DGUOK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252050.1			G	74185303	A	G	74185303	2	3	258	1	0	0	0	0	0	0	0	1	4477	175	7	2		2	DGUOK	2	74185303	Silent	SNP	A	TCGA-EP-A3RK-01A-11D-A22F-10	50204948	74185303	169014070	7	36280										
SPEG	10290	hgsc.bcm.edu	37	chr2	220326612	220326612	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	gtctctctccaggtgggtctAcatcccctttcagcagcccc	8	17	4	0			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr2:220326612A>G	ENST00000312358.7	+	7	2581	c.2449A>G	c.(2449-2451)Aca>Gca	p.T817A	SPEG_ENST00000396686.1_5'UTR|SPEG_ENST00000396689.2_5'UTR|SPEG_ENST00000396695.2_Missense_Mutation_p.T25A|SPEG_ENST00000396688.1_5'UTR|SPEG_ENST00000396698.1_Missense_Mutation_p.T713A|SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	817					cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		AGGTGGGTCTACATCCCCTTT	0.632																																					p.T817A		Atlas-SNP	.											.	SPEG	272	.	0			c.A2449G						.						73	82	79					2																	220326612		2013	4189	6202	SO:0001583	missense	10290	exon7			GGGTCTACATCCC	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"Immunoglobulin superfamily / I-set domain containing"	16901	protein-coding gene	gene with protein product		615950	"aortic preferentially expressed gene 1"	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.2449A>G	chr2.hg19:g.220326612A>G	ENSP00000311684:p.Thr817Ala	76.0	0.0		75.0	15.0	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	hg19	CCDS42824.1	.	.	.	.	.	.	.	.	.	.	A	6.684	0.494829	0.12702	.	.	ENSG00000072195	ENST00000312358;ENST00000265327;ENST00000396698;ENST00000396695	T;T;T	0.64618	-0.11;0.26;0.71	5.3	-2.07	0.07276	.	0.769546	0.11051	N	0.605041	T	0.35128	0.0921	N	0.14661	0.345	0.09310	N	1	B;B;B	0.14012	0.0;0.006;0.009	B;B;B	0.11329	0.0;0.001;0.006	T	0.16689	-1.0394	10	0.16896	T	0.51	.	4.0769	0.09908	0.3991:0.0:0.2018:0.3991	.	817;25;713	Q15772;Q15772-3;B9ZVR7	SPEG_HUMAN;.;.	A	817;817;713;25	ENSP00000311684:T817A;ENSP00000379926:T713A;ENSP00000379923:T25A	ENSP00000265327:T817A	T	+	1	0	SPEG	220034856	0.014000	0.17966	0.812000	0.32479	0.055000	0.15305	0.191000	0.17076	-0.721000	0.04929	-2.877000	0.00098	ACA	.	.		0.632	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		G	220326612	A	G	220326612	3	3	258	1	0	0	0	0	1	0	0	0	15051	391	14	2	2475	2	SPEG	2	220326612	Missense_Mutation	SNP	A	TCGA-EP-A3RK-01A-11D-A22F-10	146141309	220326612	22872761	8	36281										
PER2	8864	hgsc.bcm.edu	37	chr2	239161713	239161713	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	gctgcaggggcgagctgctgCgggactgaaagagcggtggg	21	8	0	2			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr2:239161713C>A	ENST00000254657.3	-	19	3230	c.2951G>T	c.(2950-2952)cGc>cTc	p.R984L	AC096574.4_ENST00000456601.1_RNA|PER2_ENST00000254658.3_3'UTR	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN	period circadian clock 2	984	Interaction with PPARG. {ECO:0000250|UniProtKB:O54943}.				circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|fatty acid metabolic process (GO:0006631)|gluconeogenesis (GO:0006094)|glycogen biosynthetic process (GO:0005978)|histone H3 deacetylation (GO:0070932)|lactate biosynthetic process (GO:0019249)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of DNA-templated transcription, termination (GO:0060567)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of glutamate uptake involved in transmission of nerve impulse (GO:0051946)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of vasoconstriction (GO:0019229)|response to ischemia (GO:0002931)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	pre-mRNA binding (GO:0036002)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|ubiquitin binding (GO:0043130)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)		CGAGCTGCTGCGGGACTGAAA	0.677																																					p.R984L		Atlas-SNP	.											PER2,NS,carcinoma,0,1	PER2	85	.	0			c.G2951T						.						35	38	37					2																	239161713		2203	4299	6502	SO:0001583	missense	8864	exon19			CTGCTGCGGGACT	AB002345	CCDS2528.1	2q37.3	2012-12-13	2012-12-13		ENSG00000132326	ENSG00000132326			8846	protein-coding gene	gene with protein product		603426	"period (Drosophila) homolog 2", "period homolog 2 (Drosophila)"			9427249, 17218255	Standard	NM_022817		Approved	KIAA0347	uc002vyc.3	O15055	OTTHUMG00000152884	ENST00000254657.3:c.2951G>T	chr2.hg19:g.239161713C>A	ENSP00000254657:p.Arg984Leu	61.0	0.0		56.0	14.0	NM_022817	A2I2P7|Q4ZG49|Q6DT41|Q9UQ45	Missense_Mutation	SNP	ENST00000254657.3	hg19	CCDS2528.1	.	.	.	.	.	.	.	.	.	.	C	17.99	3.522094	0.64747	.	.	ENSG00000132326	ENST00000254657	T	0.29917	1.55	4.64	4.64	0.57946	.	0.055536	0.64402	N	0.000001	T	0.60907	0.2305	M	0.86864	2.845	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.69003	-0.5260	10	0.72032	D	0.01	-18.9691	15.3952	0.74787	0.0:1.0:0.0:0.0	.	984;984	B4DH14;O15055	.;PER2_HUMAN	L	984	ENSP00000254657:R984L	ENSP00000254657:R984L	R	-	2	0	PER2	238826452	1.000000	0.71417	0.915000	0.36163	0.075000	0.17131	5.419000	0.66435	2.290000	0.77057	0.655000	0.94253	CGC	.	.		0.677	PER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257167.1	NM_022817		A	239161713	C	A	239161713	3	1	258	1	0	0	0	0	1	0	0	0	11739	768	27	1	836	1	PER2	2	239161713	Missense_Mutation	SNP	C	TCGA-EP-A3RK-01A-11D-A22F-10	18835101	239161713	4037660	9	36282										
BRPF1	7862	hgsc.bcm.edu	37	chr3	9776140	9776140	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	tggaggtggacttgcatggcCgcgtccaccgcatcagcatc	13	13	1	0			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr3:9776140C>T	ENST00000457855.1	+	1	327	c.316C>T	c.(316-318)Cgc>Tgc	p.R106C	BRPF1_ENST00000302054.3_Missense_Mutation_p.R106C|BRPF1_ENST00000383829.2_Missense_Mutation_p.R106C|BRPF1_ENST00000424362.1_Missense_Mutation_p.R106C|BRPF1_ENST00000433861.2_Missense_Mutation_p.R106C			P55201	BRPF1_HUMAN	bromodomain and PHD finger containing, 1	106	Interaction with KAT6A and KAT6B.				chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	49	Medulloblastoma(99;0.227)					CTTGCATGGCCGCGTCCACCG	0.602																																					p.R106C		Atlas-SNP	.											.	BRPF1	104	.	0			c.C316T						.						106	111	109					3																	9776140		2203	4300	6503	SO:0001583	missense	7862	exon2			CATGGCCGCGTCC	M91585	CCDS2575.1, CCDS33692.1	3p26-p25	2008-07-18			ENSG00000156983	ENSG00000156983			14255	protein-coding gene	gene with protein product	"peregrin", "bromodomain-containing protein, 140kD"	602410				8946209, 7906940	Standard	NM_001003694		Approved	BR140	uc003bsf.3	P55201	OTTHUMG00000097033	ENST00000457855.1:c.316C>T	chr3.hg19:g.9776140C>T	ENSP00000410210:p.Arg106Cys	59.0	0.0		68.0	7.0	NM_001003694	B4DEZ6|Q7Z6E0|Q8TCM6|Q9UHI0	Missense_Mutation	SNP	ENST00000457855.1	hg19	CCDS2575.1	.	.	.	.	.	.	.	.	.	.	C	32	5.159886	0.94727	.	.	ENSG00000156983	ENST00000433861;ENST00000424362;ENST00000383829;ENST00000302054;ENST00000457855	T;T;T;T;T	0.55234	0.53;0.53;0.53;0.53;0.53	5.73	5.73	0.89815	Enhancer of polycomb-like, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.75199	0.3817	M	0.78049	2.395	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.997;0.992;0.992;0.997	T	0.77225	-0.2666	10	0.87932	D	0	.	19.4877	0.95037	0.0:1.0:0.0:0.0	.	106;106;106;106	P55201-4;P55201-3;P55201-2;P55201	.;.;.;BRPF1_HUMAN	C	106	ENSP00000402485:R106C;ENSP00000398863:R106C;ENSP00000373340:R106C;ENSP00000306297:R106C;ENSP00000410210:R106C	ENSP00000306297:R106C	R	+	1	0	BRPF1	9751140	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.446000	0.60014	2.709000	0.92574	0.563000	0.77884	CGC	.	.		0.602	BRPF1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338485.1	NM_001003694		T	9776140	C	T	9776140	3	4	258	1	0	0	0	0	1	0	0	0	1522	652	23	1	318	1	BRPF1	3	9776140	Missense_Mutation	SNP	C	TCGA-EP-A3RK-01A-11D-A22F-10		9776140	188246290	10	36283										
SCN5A	6331	hgsc.bcm.edu	37	chr3	38597244	38597244	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	ctgtcatgaagatgtcctggCcccctaagtgcaaagagaag	11	10	1	3			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr3:38597244C>A	ENST00000333535.4	-	26	4594	c.4445G>T	c.(4444-4446)gGc>gTc	p.G1482V	SCN5A_ENST00000464652.1_5'Flank|SCN5A_ENST00000449557.2_Missense_Mutation_p.G1428V|SCN5A_ENST00000451551.2_Missense_Mutation_p.G1428V|SCN5A_ENST00000423572.2_Missense_Mutation_p.G1481V|SCN5A_ENST00000413689.1_Missense_Mutation_p.G1482V|SCN5A_ENST00000414099.2_Missense_Mutation_p.G1464V|SCN5A_ENST00000455624.2_Missense_Mutation_p.G1481V|SCN5A_ENST00000443581.1_Missense_Mutation_p.G1481V|SCN5A_ENST00000450102.2_Missense_Mutation_p.G1428V|SCN5A_ENST00000425664.1_Missense_Mutation_p.G1464V			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit	1482					AV node cell to bundle of His cell communication (GO:0086067)|brainstem development (GO:0003360)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|cardiac ventricle development (GO:0003231)|cellular response to calcium ion (GO:0071277)|cerebellum development (GO:0021549)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane depolarization during SA node cell action potential (GO:0086046)|neuronal action potential (GO:0019228)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of action potential (GO:0045760)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of sodium ion transport (GO:0010765)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|telencephalon development (GO:0021537)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	ankyrin binding (GO:0030506)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)			NS(3)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|lung(27)|ovary(6)|pancreas(3)|prostate(10)|skin(9)|upper_aerodigestive_tract(4)	107	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Ajmaline(DB01426)|Aprindine(DB01429)|Benzonatate(DB00868)|Carbamazepine(DB00564)|Cinchocaine(DB00527)|Cocaine(DB00907)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lidocaine(DB00281)|Mexiletine(DB00379)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)|Ranolazine(DB00243)|Riluzole(DB00740)|Tocainide(DB01056)|Valproic Acid(DB00313)|Verapamil(DB00661)|Zonisamide(DB00909)	GATGTCCTGGCCCCCTAAGTG	0.567																																					p.G1482V		Atlas-SNP	.											.	SCN5A	634	.	0			c.G4445T						.						85	92	89					3																	38597244		2203	4300	6503	SO:0001583	missense	6331	exon26			TCCTGGCCCCCTA	AJ310893	CCDS46796.1, CCDS46797.1, CCDS46798.1, CCDS46799.1, CCDS54569.1, CCDS54570.1	3p21	2014-09-17	2007-01-23		ENSG00000183873	ENSG00000183873		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10593	protein-coding gene	gene with protein product	"long QT syndrome 3"	600163	"sodium channel, voltage-gated, type V, alpha (long QT syndrome 3)"	CMD1E		7842012, 15466643, 16382098	Standard	NM_198056		Approved	Nav1.5, LQT3, HB1, HBBD, PFHB1, IVF, HB2, HH1, SSS1, CDCD2, CMPD2, ICCD	uc021wvl.1	Q14524	OTTHUMG00000156166	ENST00000333535.4:c.4445G>T	chr3.hg19:g.38597244C>A	ENSP00000328968:p.Gly1482Val	122.0	0.0		116.0	14.0	NM_198056	A5H1P8|A6N922|A6N923|B2RTU0|E7ET19|E9PEF3|E9PEK2|E9PFW7|Q59H93|Q75RX9|Q75RY0|Q86UR3|Q8IZC9|Q96J69	Missense_Mutation	SNP	ENST00000333535.4	hg19	CCDS46796.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.942477	0.73672	.	.	ENSG00000183873	ENST00000414099;ENST00000423572;ENST00000413689;ENST00000451551;ENST00000443581;ENST00000425664;ENST00000333535;ENST00000455624;ENST00000450102;ENST00000449557	D;D;D;D;D;D;D;D;D;D	0.96967	-4.04;-4.05;-4.05;-4.08;-4.05;-4.04;-4.05;-4.19;-4.08;-4.08	4.47	3.6	0.41247	.	0.048825	0.85682	D	0.000000	D	0.98460	0.9487	H	0.94264	3.515	0.80722	D	1	D;D;D;D;D;B	0.89917	1.0;1.0;1.0;0.998;1.0;0.388	D;D;D;D;D;B	0.97110	0.995;0.999;0.998;0.972;1.0;0.203	D	0.99094	1.0841	10	0.87932	D	0	.	12.7104	0.57086	0.0:0.9199:0.0:0.0801	.	1428;1481;1464;1482;1481;1482	E9PEF3;E9PHB6;E9PG18;Q14524;Q14524-2;E9PEK2	.;.;.;SCN5A_HUMAN;.;.	V	1464;1481;1482;1428;1481;1464;1482;1481;1428;1428	ENSP00000398962:G1464V;ENSP00000398266:G1481V;ENSP00000410257:G1482V;ENSP00000388797:G1428V;ENSP00000397915:G1481V;ENSP00000416634:G1464V;ENSP00000328968:G1482V;ENSP00000399524:G1481V;ENSP00000403355:G1428V;ENSP00000413996:G1428V	ENSP00000328968:G1482V	G	-	2	0	SCN5A	38572248	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.606000	0.82863	1.112000	0.41740	0.644000	0.83932	GGC	.	.		0.567	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	NM_198056		A	38597244	C	A	38597244	3	1	258	1	0	0	0	0	1	0	0	0	13937	739	26	3	1617	3	SCN5A	3	38597244	Missense_Mutation	SNP	C	TCGA-EP-A3RK-01A-11D-A22F-10	28821104	38597244	159425186	11	36284										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266104	41266104	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	acagtcttacctggactctgGaatccattctggtgccacta	8	12	3	0	rs28931589|rs121913416		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr3:41266104G>A	ENST00000349496.5	+	3	381	c.101G>A	c.(100-102)gGa>gAa	p.G34E	CTNNB1_ENST00000396183.3_Missense_Mutation_p.G34E|CTNNB1_ENST00000396185.3_Missense_Mutation_p.G34E|CTNNB1_ENST00000453024.1_Missense_Mutation_p.G27E|CTNNB1_ENST00000405570.1_Missense_Mutation_p.G34E	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	34			G -> E (in PTR). {ECO:0000269|PubMed:10192393}.|G -> R (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|G -> V (in hepatoblastoma; dbSNP:rs28931589). {ECO:0000269|PubMed:9927029}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.G34E(73)|p.G34V(72)|p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.D32_H36>D(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.D32fs*9(1)|p.A5_T40del(1)|p.S29_H36del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.GIHS34?(1)|p.A5_I35del(1)|p.D32_H36del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CTGGACTCTGGAATCCATTCT	0.488	G34E(AGS_STOMACH)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.G34E	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,0,161	CTNNB1	4904	.	276	Substitution - Missense(145)|Deletion - In frame(105)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(146)|endometrium(30)|large_intestine(27)|stomach(21)|central_nervous_system(20)|skin(8)|pancreas(8)|ovary(6)|small_intestine(2)|lung(2)|adrenal_gland(1)|haematopoietic_and_lymphoid_tissue(1)|biliary_tract(1)|pituitary(1)|prostate(1)|bone(1)	c.G101A						.						93	78	83					3																	41266104		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	ACTCTGGAATCCA	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.101G>A	chr3.hg19:g.41266104G>A	ENSP00000344456:p.Gly34Glu	192.0	0.0		174.0	30.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.678424	0.88542	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.50548	0.74;0.74;0.74;0.74;0.74;0.74;0.74;0.74;0.74	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.72053	0.3413	M	0.79258	2.445	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74188	-0.3746	10	0.87932	D	0	-31.2232	19.9596	0.97236	0.0:0.0:1.0:0.0	.	34	P35222	CTNB1_HUMAN	E	27;34;34;34;34;27;34;34;34	ENSP00000400508:G27E;ENSP00000385604:G34E;ENSP00000412219:G34E;ENSP00000379486:G34E;ENSP00000344456:G34E;ENSP00000411226:G27E;ENSP00000379488:G34E;ENSP00000409302:G34E;ENSP00000401599:G34E	ENSP00000344456:G34E	G	+	2	0	CTNNB1	41241108	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.726000	0.93360	0.655000	0.94253	GGA	.	.		0.488	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		A	41266104	G	A	41266104	3	1	258	1	0	0	0	0	1	0	0	0	4018	1174	41	3	107	3	CTNNB1	3	41266104	Missense_Mutation	SNP	G	TCGA-EP-A3RK-01A-11D-A22F-10	2668860	41266104	156756326	12	36285										
TBCCD1	55171	hgsc.bcm.edu	37	chr3	186269064	186269064	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	tacctggaactgcttcctttGatccctaaaattgcgattat	6	10	0	1			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr3:186269064G>T	ENST00000424280.1	-	7	2028	c.1549C>A	c.(1549-1551)Caa>Aaa	p.Q517K	TBCCD1_ENST00000479590.1_5'Flank|TBCCD1_ENST00000338733.5_Missense_Mutation_p.Q517K|TBCCD1_ENST00000446782.1_Missense_Mutation_p.Q421K	NM_001134415.1	NP_001127887.1	Q9NVR7	TBCC1_HUMAN	TBCC domain containing 1	517					cell morphogenesis (GO:0000902)|cytoskeleton organization (GO:0007010)|maintenance of centrosome location (GO:0051661)|maintenance of Golgi location (GO:0051684)|regulation of cell migration (GO:0030334)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|spindle pole centrosome (GO:0031616)				breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|skin(1)	17	all_cancers(143;3.75e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.3e-21)	GBM - Glioblastoma multiforme(93;0.0474)		TGCTTCCTTTGATCCCTAAAA	0.348																																					p.Q517K		Atlas-SNP	.											.	TBCCD1	42	.	0			c.C1549A						.						91	80	84					3																	186269064		2203	4300	6503	SO:0001583	missense	55171	exon7			TCCTTTGATCCCT	BC025748	CCDS3276.1, CCDS75061.1	3q27.3	2006-03-09			ENSG00000113838	ENSG00000113838			25546	protein-coding gene	gene with protein product						12477932	Standard	NM_001134415		Approved	FLJ10560	uc003fqg.3	Q9NVR7	OTTHUMG00000156613	ENST00000424280.1:c.1549C>A	chr3.hg19:g.186269064G>T	ENSP00000411253:p.Gln517Lys	94.0	0.0		108.0	19.0	NM_001134415	B3KW69|D3DNU6|G5E9J4	Missense_Mutation	SNP	ENST00000424280.1	hg19	CCDS3276.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.713053	0.89112	.	.	ENSG00000113838	ENST00000424280;ENST00000338733;ENST00000446782	D;D;D	0.83591	-1.74;-1.74;-1.74	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	D	0.88851	0.6549	M	0.71296	2.17	0.58432	D	0.999997	D;D	0.62365	0.981;0.991	P;P	0.58331	0.829;0.837	D	0.89917	0.4056	10	0.66056	D	0.02	-10.6982	16.3537	0.83227	0.0:0.0:1.0:0.0	.	421;517	G5E9J4;Q9NVR7	.;TBCC1_HUMAN	K	517;517;421	ENSP00000411253:Q517K;ENSP00000341652:Q517K;ENSP00000397091:Q421K	ENSP00000341652:Q517K	Q	-	1	0	TBCCD1	187751758	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	9.031000	0.93731	2.460000	0.83146	0.557000	0.71058	CAA	.	.		0.348	TBCCD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344774.1	NM_018138		T	186269064	G	T	186269064	3	4	258	1	0	0	0	0	1	0	0	0	15647	1299	45	3	128	3	TBCCD1	3	186269064	Missense_Mutation	SNP	G	TCGA-EP-A3RK-01A-11D-A22F-10	145002960	186269064	11753366	13	36286										
ARAP2	116984	hgsc.bcm.edu	37	chr4	36230363	36230363	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	catttacaatcatttctcctTgaaacttaaagaatggggat	6	7	2	2			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr4:36230363T>C	ENST00000303965.4	-	2	1235	c.746A>G	c.(745-747)cAa>cGa	p.Q249R		NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	249					regulation of ARF GTPase activity (GO:0032312)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(32)|ovary(2)|pancreas(1)|prostate(3)|skin(7)|urinary_tract(1)	82						CATTTCTCCTTGAAACTTAAA	0.388																																					p.Q249R		Atlas-SNP	.											.	ARAP2	210	.	0			c.A746G						.						145	141	143					4																	36230363		2203	4300	6503	SO:0001583	missense	116984	exon2			TCTCCTTGAAACT	AF411982	CCDS3441.1	4p15.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000047365	ENSG00000047365		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16924	protein-coding gene	gene with protein product		606645	"centaurin, delta 1"	CENTD1			Standard	NM_015230		Approved	PARX	uc003gsq.2	Q8WZ64	OTTHUMG00000097811	ENST00000303965.4:c.746A>G	chr4.hg19:g.36230363T>C	ENSP00000302895:p.Gln249Arg	170.0	0.0		193.0	39.0	NM_015230	Q4W5D2|Q7Z2L5|Q96L70|Q96P49|Q9Y4E4	Missense_Mutation	SNP	ENST00000303965.4	hg19	CCDS3441.1	.	.	.	.	.	.	.	.	.	.	T	15.74	2.923499	0.52653	.	.	ENSG00000047365	ENST00000303965	T	0.09163	3.01	5.98	4.76	0.60689	.	0.085474	0.50627	D	0.000119	T	0.08088	0.0202	L	0.29908	0.895	0.27303	N	0.957524	P;P	0.35077	0.483;0.483	B;B	0.30943	0.122;0.122	T	0.23762	-1.0179	10	0.30854	T	0.27	.	12.256	0.54625	0.0:0.0:0.1409:0.8591	.	179;249	A7E2A5;Q8WZ64	.;ARAP2_HUMAN	R	249	ENSP00000302895:Q249R	ENSP00000302895:Q249R	Q	-	2	0	ARAP2	35906758	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	2.547000	0.45786	2.307000	0.77673	0.529000	0.55759	CAA	.	.		0.388	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215074.2	NM_015230		C	36230363	T	C	36230363	3	2	258	1	0	0	0	0	1	0	0	0	839	1812	63	2	4496	2	ARAP2	4	36230363	Missense_Mutation	SNP	T	TCGA-EP-A3RK-01A-11D-A22F-10		36230363	154923913	14	36287										
TMED7	51014	hgsc.bcm.edu	37	chr5	114952130	114952130	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	agcttcgtgaattgaaacacAggcagattccatctgcagag	10	9	1	4			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr5:114952130A>G	ENST00000456936.3	-	3	831	c.451T>C	c.(451-453)Tgt>Cgt	p.C151R	TMED7-TICAM2_ENST00000282382.4_Missense_Mutation_p.C151R|TMED7_ENST00000503010.1_5'UTR|TICAM2_ENST00000408996.4_Missense_Mutation_p.C151R|AC010226.4_ENST00000515570.1_RNA|TMED7-TICAM2_ENST00000333314.3_Missense_Mutation_p.C151R|AC010226.4_ENST00000508517.1_RNA	NM_181836.5	NP_861974.1	Q9Y3B3	TMED7_HUMAN	transmembrane emp24 protein transport domain containing 7	151					protein transport (GO:0015031)	COPI vesicle coat (GO:0030126)|COPII vesicle coat (GO:0030127)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|liver(1)|lung(1)|urinary_tract(1)	6		all_cancers(142;0.0223)|all_epithelial(76;0.000869)|Prostate(80;0.0115)|Ovarian(225;0.156)		OV - Ovarian serous cystadenocarcinoma(64;3.34e-07)|Epithelial(69;1.08e-06)|all cancers(49;4.56e-05)		ATTGAAACACAGGCAGATTCC	0.388																																					p.C151R	Pancreas(167;237 2002 3207 14549 49356)	Atlas-SNP	.											.	.	.	.	0			c.T451C						.						60	60	60					5																	114952130		2202	4300	6502	SO:0001583	missense	100302736	exon3			AAACACAGGCAGA	AK074962	CCDS4120.1	5q22.3	2011-04-19			ENSG00000134970	ENSG00000134970			24253	protein-coding gene	gene with protein product						10810093	Standard	NM_181836		Approved	CGI-109, FLJ90481		Q9Y3B3	OTTHUMG00000132013	ENST00000456936.3:c.451T>C	chr5.hg19:g.114952130A>G	ENSP00000405926:p.Cys151Arg	87.0	0.0		121.0	25.0	NM_001164468	Q8NBU8|Q8WUU6|Q96K51	Missense_Mutation	SNP	ENST00000456936.3	hg19	CCDS4120.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.288538	0.80914	.	.	ENSG00000243414;ENSG00000251201;ENSG00000251201;ENSG00000134970	ENST00000408996;ENST00000282382;ENST00000333314;ENST00000456936	T;T;T;T	0.16743	2.32;2.32;2.32;2.32	5.95	5.95	0.96441	GOLD (1);	0.221872	0.51477	D	0.000083	T	0.46678	0.1405	M	0.83852	2.665	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.91635	0.989;0.999	T	0.50575	-0.8812	10	0.72032	D	0.01	-17.7955	15.3926	0.74758	1.0:0.0:0.0:0.0	.	151;151	Q9Y3B3;Q6JUT2	TMED7_HUMAN;.	R	151	ENSP00000386341:C151R;ENSP00000282382:C151R;ENSP00000333650:C151R;ENSP00000405926:C151R	ENSP00000405926:C151R	C	-	1	0	TMED7;TICAM2;TMED7-TICAM2	114980029	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.339000	0.96797	2.280000	0.76307	0.460000	0.39030	TGT	.	.		0.388	TMED7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254990.4	NM_181836		G	114952130	A	G	114952130	3	3	258	1	0	0	0	0	1	0	0	0	16024	188	7	2	227	2	TMED7	5	114952130	Missense_Mutation	SNP	A	TCGA-EP-A3RK-01A-11D-A22F-10		114952130	65963130	15	36288										
DDX46	9879	hgsc.bcm.edu	37	chr5	134152221	134152221	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	gctccaactgcaggaaatgcTgagaaattagaaattgctaa	9	7	0	2			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr5:134152221T>A	ENST00000354283.4	+	19	2673	c.2538T>A	c.(2536-2538)gcT>gcA	p.A846A	DDX46_ENST00000452510.2_Silent_p.A846A			Q7L014	DDX46_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	846					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CAGGAAATGCTGAGAAATTAG	0.393																																					p.A846A	Colon(13;391 453 4901 21675 24897)	Atlas-SNP	.											.	DDX46	77	.	0			c.T2538A						.						56	60	59					5																	134152221		2203	4300	6503	SO:0001819	synonymous_variant	9879	exon19			AAATGCTGAGAAA		CCDS34240.1, CCDS75306.1	5q31.1	2010-01-25			ENSG00000145833	ENSG00000145833		"DEAD-boxes"	18681	protein-coding gene	gene with protein product							Standard	XM_005272142		Approved	KIAA0801, FLJ25329, PRPF5, Prp5	uc003kzw.3	Q7L014	OTTHUMG00000163072	ENST00000354283.4:c.2538T>A	chr5.hg19:g.134152221T>A		69.0	0.0		67.0	12.0	NM_014829	O94894|Q96EI0|Q9Y658	Silent	SNP	ENST00000354283.4	hg19	CCDS34240.1																																																																																			.	.		0.393	DDX46-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371584.1	NM_014829		A	134152221	T	A	134152221	2	1	258	1	0	0	0	0	0	0	0	1	4366	1567	55	4		4	DDX46	5	134152221	Silent	SNP	T	TCGA-EP-A3RK-01A-11D-A22F-10	19200091	134152221	46763039	16	36289										
PDE6A	5145	hgsc.bcm.edu	37	chr5	149324082	149324082	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	cgctctcctccatgctgctcGgggagtggtagttgctgaag	14	11	1	1			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr5:149324082G>A	ENST00000255266.5	-	1	274	c.155C>T	c.(154-156)cCg>cTg	p.P52L		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	52					cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	44			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Caffeine(DB00201)	CATGCTGCTCGGGGAGTGGTA	0.517																																					p.P52L		Atlas-SNP	.											.	PDE6A	98	.	0			c.C155T						.						62	60	61					5																	149324082		2203	4300	6503	SO:0001583	missense	5145	exon1			CTGCTCGGGGAGT		CCDS4299.1	5q31.2-q34	2013-02-14			ENSG00000132915	ENSG00000132915	3.1.4.17	"Phosphodiesterases"	8785	protein-coding gene	gene with protein product		180071		PDEA		2155175	Standard	NM_000440		Approved	RP43	uc003lrg.4	P16499	OTTHUMG00000130047	ENST00000255266.5:c.155C>T	chr5.hg19:g.149324082G>A	ENSP00000255266:p.Pro52Leu	59.0	0.0		48.0	9.0	NM_000440	Q0P638	Missense_Mutation	SNP	ENST00000255266.5	hg19	CCDS4299.1	.	.	.	.	.	.	.	.	.	.	G	0.004	-2.262729	0.00262	.	.	ENSG00000132915	ENST00000255266	T	0.57907	0.37	5.47	2.87	0.33458	.	1.746250	0.03262	N	0.183402	T	0.16685	0.0401	N	0.00179	-1.91	0.09310	N	0.999995	B	0.02656	0.0	B	0.01281	0.0	T	0.45308	-0.9270	10	0.02654	T	1	.	7.1312	0.25502	0.7419:0.0:0.2581:0.0	.	52	P16499	PDE6A_HUMAN	L	52	ENSP00000255266:P52L	ENSP00000255266:P52L	P	-	2	0	PDE6A	149304275	1.000000	0.71417	0.287000	0.24848	0.191000	0.23601	4.943000	0.63554	0.366000	0.24427	-1.069000	0.02264	CCG	.	.		0.517	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2			A	149324082	G	A	149324082	3	1	258	1	0	0	0	0	1	0	0	0	11654	1116	39	1	2515	1	PDE6A	5	149324082	Missense_Mutation	SNP	G	TCGA-EP-A3RK-01A-11D-A22F-10	15171861	149324082	31591178	17	36290										
UBR2	23304	hgsc.bcm.edu	37	chr6	42612241	42612241	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	agcagaacaatactctaataGaagaaatgctatacctcatt	5	8	2	3			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr6:42612241G>A	ENST00000372899.1	+	20	2509	c.2251G>A	c.(2251-2253)Gaa>Aaa	p.E751K	UBR2_ENST00000372883.3_Missense_Mutation_p.E255K|UBR2_ENST00000372901.1_Missense_Mutation_p.E751K	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	751					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			TACTCTAATAGAAGAAATGCT	0.308																																					p.E751K		Atlas-SNP	.											.	UBR2	134	.	0			c.G2251A						.						95	98	97					6																	42612241		2203	4299	6502	SO:0001583	missense	23304	exon20			CTAATAGAAGAAA	BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"Ubiquitin protein ligase E3 component n-recognins"	21289	protein-coding gene	gene with protein product		609134	"chromosome 6 open reading frame 133"	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.2251G>A	chr6.hg19:g.42612241G>A	ENSP00000361990:p.Glu751Lys	64.0	0.0		96.0	22.0	NM_015255	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Missense_Mutation	SNP	ENST00000372899.1	hg19	CCDS4870.1	.	.	.	.	.	.	.	.	.	.	G	36	5.616641	0.96649	.	.	ENSG00000024048	ENST00000372899;ENST00000372901;ENST00000372883	T;T;T	0.57436	0.4;0.4;0.4	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	T	0.73552	0.3601	M	0.82193	2.58	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.85130	0.997;0.978	T	0.74565	-0.3623	10	0.66056	D	0.02	-26.7082	20.5632	0.99335	0.0:0.0:1.0:0.0	.	751;751	Q8IWV8-4;Q8IWV8	.;UBR2_HUMAN	K	751;751;255	ENSP00000361990:E751K;ENSP00000361992:E751K;ENSP00000361974:E255K	ENSP00000361974:E255K	E	+	1	0	UBR2	42720219	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.268000	0.78473	2.937000	0.99478	0.650000	0.86243	GAA	.	.		0.308	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255		A	42612241	G	A	42612241	3	1	258	1	0	0	0	0	1	0	0	0	16917	943	33	3	2475	3	UBR2	6	42612241	Missense_Mutation	SNP	G	TCGA-EP-A3RK-01A-11D-A22F-10		42612241	128502826	18	36291										
L3MBTL3	84456	hgsc.bcm.edu	37	chr6	130455007	130455007	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	ggtgtcagaatttatacagaGcttacctgggtgtgaagaac	12	6	1	4			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr6:130455007G>C	ENST00000529410.1	+	24	2635	c.2156G>C	c.(2155-2157)aGc>aCc	p.S719T	L3MBTL3_ENST00000361794.2_Missense_Mutation_p.S719T|RP11-73O6.3_ENST00000609978.1_RNA|L3MBTL3_ENST00000526019.1_Missense_Mutation_p.S694T|L3MBTL3_ENST00000533560.1_Missense_Mutation_p.S694T|L3MBTL3_ENST00000368139.2_Missense_Mutation_p.S694T|RP11-73O6.3_ENST00000415964.1_RNA|RP11-73O6.3_ENST00000591297.1_RNA|L3MBTL3_ENST00000368136.2_Missense_Mutation_p.S719T			Q96JM7	LMBL3_HUMAN	l(3)mbt-like 3 (Drosophila)	719	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				chromatin modification (GO:0016568)|erythrocyte maturation (GO:0043249)|granulocyte differentiation (GO:0030851)|macrophage differentiation (GO:0030225)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				cervix(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|skin(4)|stomach(1)|urinary_tract(1)	43				GBM - Glioblastoma multiforme(226;0.0266)|OV - Ovarian serous cystadenocarcinoma(155;0.154)		TTTATACAGAGCTTACCTGGG	0.338																																					p.S719T		Atlas-SNP	.											.	L3MBTL3	99	.	0			c.G2156C						.						114	108	110					6																	130455007		2203	4300	6503	SO:0001583	missense	84456	exon22			TACAGAGCTTACC	AB058701	CCDS34537.1, CCDS34538.1	6q23	2013-01-10			ENSG00000198945	ENSG00000198945		"Sterile alpha motif (SAM) domain containing"	23035	protein-coding gene	gene with protein product							Standard	NM_032438		Approved	KIAA1798	uc003qbt.3	Q96JM7	OTTHUMG00000015554	ENST00000529410.1:c.2156G>C	chr6.hg19:g.130455007G>C	ENSP00000431962:p.Ser719Thr	62.0	0.0		30.0	6.0	NM_032438	Q4VXE1|Q5VUM9|Q6P9B5	Missense_Mutation	SNP	ENST00000529410.1	hg19	CCDS34537.1	.	.	.	.	.	.	.	.	.	.	G	9.528	1.109998	0.20714	.	.	ENSG00000198945	ENST00000529410;ENST00000533560;ENST00000361794;ENST00000368139;ENST00000526019;ENST00000368136	T;T;T;T;T;T	0.56444	0.46;0.46;0.46;0.46;0.46;0.46	5.37	4.48	0.54585	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.537613	0.21802	N	0.068903	T	0.22205	0.0535	N	0.20986	0.625	0.28057	N	0.933143	P;B	0.45474	0.859;0.379	P;B	0.44394	0.448;0.241	T	0.12863	-1.0531	10	0.10902	T	0.67	.	14.1835	0.65590	0.0:0.15:0.85:0.0	.	694;719	Q96JM7-2;Q96JM7	.;LMBL3_HUMAN	T	719;694;719;694;694;719	ENSP00000431962:S719T;ENSP00000437185:S694T;ENSP00000354526:S719T;ENSP00000357121:S694T;ENSP00000436706:S694T;ENSP00000357118:S719T	ENSP00000354526:S719T	S	+	2	0	L3MBTL3	130496700	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.591000	0.46163	1.357000	0.45904	0.561000	0.74099	AGC	.	.		0.338	L3MBTL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042195.2	XM_027074		C	130455007	G	C	130455007	3	2	258	1	0	0	0	0	1	0	0	0	8602	971	34	4	2234	4	L3MBTL3	6	130455007	Missense_Mutation	SNP	G	TCGA-EP-A3RK-01A-11D-A22F-10	87842766	130455007	40660060	19	36292										
MRPS24	64951	hgsc.bcm.edu	37	chr7	43906467	43906467	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	tctccaactggttaccccggCgctttaaaaccagctggtca	8	14	2	0			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr7:43906467C>T	ENST00000317534.5	-	4	396	c.335G>A	c.(334-336)cGc>cAc	p.R112H	URGCP-MRPS24_ENST00000603700.1_3'UTR|MRPS24_ENST00000467084.1_5'UTR	NM_032014.2	NP_114403.1	Q96EL2	RT24_HUMAN	mitochondrial ribosomal protein S24	112					translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrial small ribosomal subunit (GO:0005763)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	5						GTTACCCCGGCGCTTTAAAAC	0.557																																					p.R112H		Atlas-SNP	.											.	MRPS24	9	.	0			c.G335A						.						66	62	63					7																	43906467		2203	4300	6503	SO:0001583	missense	64951	exon4			CCCCGGCGCTTTA	AB061207	CCDS5473.1	7p14	2012-09-13			ENSG00000062582	ENSG00000062582		"Mitochondrial ribosomal proteins / small subunits"	14510	protein-coding gene	gene with protein product		611986				8127713, 11279123	Standard	NM_032014		Approved	MRP-S24, HSPC335	uc003tit.1	Q96EL2	OTTHUMG00000023175	ENST00000317534.5:c.335G>A	chr7.hg19:g.43906467C>T	ENSP00000318158:p.Arg112His	41.0	0.0		52.0	11.0	NM_032014	A4D1U9|P82668|Q96Q23|Q9P047	Missense_Mutation	SNP	ENST00000317534.5	hg19	CCDS5473.1	.	.	.	.	.	.	.	.	.	.	C	19.03	3.747046	0.69418	.	.	ENSG00000062582	ENST00000317534	T	0.63417	-0.04	5.0	4.12	0.48240	.	0.000000	0.85682	D	0.000000	T	0.79381	0.4436	M	0.89601	3.045	0.80722	D	1	D	0.76494	0.999	P	0.62014	0.897	T	0.82723	-0.0316	10	0.87932	D	0	-12.1142	11.1372	0.48381	0.0:0.9091:0.0:0.0909	.	112	Q96EL2	RT24_HUMAN	H	112	ENSP00000318158:R112H	ENSP00000318158:R112H	R	-	2	0	MRPS24	43872992	1.000000	0.71417	1.000000	0.80357	0.456000	0.32438	7.099000	0.76981	1.110000	0.41699	-0.136000	0.14681	CGC	.	.		0.557	MRPS24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250949.1	NM_032014		T	43906467	C	T	43906467	3	4	258	1	0	0	0	0	1	0	0	0	9844	768	27	1	172	1	MRPS24	7	43906467	Missense_Mutation	SNP	C	TCGA-EP-A3RK-01A-11D-A22F-10		43906467	115232196	20	36293										
COBL	23242	hgsc.bcm.edu	37	chr7	51287547	51287547	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	aaccaagttctgctgcgaccCgagggccccatcgtgggggg	15	13	1	0	rs566661748		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr7:51287547C>T	ENST00000265136.7	-	2	301	c.136G>A	c.(136-138)Ggg>Agg	p.G46R	COBL_ENST00000441453.1_Missense_Mutation_p.G46R|COBL_ENST00000395540.2_Missense_Mutation_p.G46R|COBL_ENST00000395542.2_Missense_Mutation_p.G46R	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	46					actin filament network formation (GO:0051639)|actin filament polymerization (GO:0030041)|collateral sprouting in absence of injury (GO:0048669)|digestive tract development (GO:0048565)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|liver development (GO:0001889)|neural tube closure (GO:0001843)|notochord development (GO:0030903)|positive regulation of dendrite development (GO:1900006)|somite specification (GO:0001757)	actin filament (GO:0005884)|axon (GO:0030424)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic growth cone (GO:0044294)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)			NS(2)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(26)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Glioma(55;0.08)					TGCTGCGACCCGAGGGCCCCA	0.622													C|||	1	0.000199681	8e-04	0	5008	,	,		16046	0		0	False		,,,				2504	0				p.G46R	NSCLC(189;2119 2138 12223 30818 34679)	Atlas-SNP	.											.	COBL	167	.	0			c.G136A						.						50	50	50					7																	51287547		2203	4300	6503	SO:0001583	missense	23242	exon2			GCGACCCGAGGGC	AB014533	CCDS34637.1, CCDS75601.1, CCDS75602.1	7p12.2-p12.1	2012-12-07	2012-12-07		ENSG00000106078	ENSG00000106078			22199	protein-coding gene	gene with protein product		610317	"cordon-bleu homolog (mouse)"				Standard	NM_015198		Approved	KIAA0633	uc003tpr.4	O75128	OTTHUMG00000155999	ENST00000265136.7:c.136G>A	chr7.hg19:g.51287547C>T	ENSP00000265136:p.Gly46Arg	74.0	0.0		62.0	10.0	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Missense_Mutation	SNP	ENST00000265136.7	hg19	CCDS34637.1	.	.	.	.	.	.	.	.	.	.	C	7.362	0.625104	0.14257	.	.	ENSG00000106078	ENST00000265136;ENST00000395542;ENST00000395540;ENST00000441453;ENST00000449281	T;T	0.11712	2.76;2.75	5.73	-2.45	0.06481	Cordon-bleu domain (1);	0.565367	0.14832	N	0.295802	T	0.05502	0.0145	L	0.47716	1.5	0.09310	N	1	P;B;P;P	0.48350	0.621;0.055;0.909;0.803	B;B;B;B	0.33196	0.12;0.011;0.159;0.129	T	0.45571	-0.9252	10	0.13108	T	0.6	.	6.1535	0.20324	0.0:0.2549:0.1786:0.5664	.	46;46;46;46	O75128-3;O75128-5;O75128-7;O75128	.;.;.;COBL_HUMAN	R	46;46;46;46;30	ENSP00000265136:G46R;ENSP00000378912:G46R	ENSP00000265136:G46R	G	-	1	0	COBL	51255041	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.685000	0.05167	-0.180000	0.10637	-0.345000	0.07892	GGG	.	.		0.622	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198		T	51287547	C	T	51287547	3	4	258	1	0	0	0	0	1	0	0	0	3655	652	23	1	3697	1	COBL	7	51287547	Missense_Mutation	SNP	C	TCGA-EP-A3RK-01A-11D-A22F-10	7381080	51287547	107851116	21	36294										
SEMA3A	10371	hgsc.bcm.edu	37	chr7	83592651	83592651	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	ttctctcttcagggctgtggCcatggtgattatctggccag	12	10	4	1			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr7:83592651C>T	ENST00000265362.4	-	16	2044	c.1730G>A	c.(1729-1731)gGc>gAc	p.G577D	SEMA3A_ENST00000436949.1_Missense_Mutation_p.G577D	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	577					apoptotic process (GO:0006915)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|dendrite morphogenesis (GO:0048813)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of epithelial cell migration (GO:0010633)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neural crest cell migration involved in sympathetic nervous system development (GO:1903045)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of male gonad development (GO:2000020)|positive regulation of neuron migration (GO:2001224)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of heart rate (GO:0002027)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sensory system development (GO:0048880)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular region (GO:0005576)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|neuropilin binding (GO:0038191)|receptor activity (GO:0004872)			breast(3)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						AGGGCTGTGGCCATGGTGATT	0.398																																					p.G577D		Atlas-SNP	.											SEMA3A,NS,carcinoma,0,1	SEMA3A	121	.	0			c.G1730A						.						96	92	93					7																	83592651		2203	4300	6503	SO:0001583	missense	10371	exon16			CTGTGGCCATGGT	L26081	CCDS5599.1	7p12.1	2013-01-11			ENSG00000075213	ENSG00000075213		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10723	protein-coding gene	gene with protein product	"sema III"	603961		SEMAD		8269517, 7748561	Standard	NM_006080		Approved	SEMA1, SemD, coll-1, Hsema-I	uc003uhz.3	Q14563	OTTHUMG00000023443	ENST00000265362.4:c.1730G>A	chr7.hg19:g.83592651C>T	ENSP00000265362:p.Gly577Asp	75.0	0.0		62.0	10.0	NM_006080		Missense_Mutation	SNP	ENST00000265362.4	hg19	CCDS5599.1	.	.	.	.	.	.	.	.	.	.	C	8.717	0.913383	0.17907	.	.	ENSG00000075213	ENST00000265362;ENST00000436949	T;T	0.27890	1.64;1.64	5.96	3.18	0.36537	.	0.763914	0.12855	N	0.433563	T	0.24275	0.0588	L	0.50333	1.59	0.45806	D	0.998687	B	0.26512	0.151	B	0.27715	0.082	T	0.03017	-1.1082	10	0.12103	T	0.63	.	6.308	0.21149	0.1325:0.6786:0.0:0.1888	.	577	Q14563	SEM3A_HUMAN	D	577	ENSP00000265362:G577D;ENSP00000415260:G577D	ENSP00000265362:G577D	G	-	2	0	SEMA3A	83430587	0.992000	0.36948	0.984000	0.44739	0.833000	0.47200	3.027000	0.49697	0.417000	0.25871	0.585000	0.79938	GGC	.	.		0.398	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080		T	83592651	C	T	83592651	3	4	258	1	0	0	0	0	1	0	0	0	14039	739	26	3	593	3	SEMA3A	7	83592651	Missense_Mutation	SNP	C	TCGA-EP-A3RK-01A-11D-A22F-10	32305104	83592651	75546012	22	36295										
RB1CC1	9821	hgsc.bcm.edu	37	chr8	53536345	53536345	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	ttaattttgtccataagttaTactttcttattccatgatac	3	7	1	1	rs145350535		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr8:53536345T>C	ENST00000025008.5	-	24	5305	c.4782A>G	c.(4780-4782)gtA>gtG	p.V1594V	RB1CC1_ENST00000521611.1_Intron|RB1CC1_ENST00000435644.2_Silent_p.V1591V|RB1CC1_ENST00000539297.1_Silent_p.V1591V	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1	1594					autophagic vacuole assembly (GO:0000045)|cell cycle (GO:0007049)|heart development (GO:0007507)|JNK cascade (GO:0007254)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell size (GO:0045793)|positive regulation of protein phosphorylation (GO:0001934)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)				NS(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(19)|ovary(8)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	60		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				CCATAAGTTATACTTTCTTAT	0.348																																					p.V1594V	GBM(180;1701 2102 13475 42023 52570)	Atlas-SNP	.											.	RB1CC1	163	.	0			c.A4782G						.	C	,	1,4405	2.1+/-5.4	0,1,2202	70	70	70		4773,4782	2.8	1	8	dbSNP_134	70	0,8596		0,0,4298	no	coding-synonymous,coding-synonymous	RB1CC1	NM_001083617.1,NM_014781.4	,	0,1,6500	CC,CT,TT		0.0,0.0227,0.0077	,	1591/1592,1594/1595	53536345	1,13001	2203	4298	6501	SO:0001819	synonymous_variant	9821	exon24			AAGTTATACTTTC	AB059622	CCDS34892.1, CCDS47856.1	8q11	2014-06-13				ENSG00000023287			15574	protein-coding gene	gene with protein product	"200 kDa FAK family kinase-interacting protein", "phosphatase 1, regulatory subunit 131"	606837				11850849, 7724523, 18443221	Standard	NM_014781		Approved	KIAA0203, Cc1, DRAGOU14, FIP200, ATG17, PPP1R131	uc003xre.4	Q8TDY2		ENST00000025008.5:c.4782A>G	chr8.hg19:g.53536345T>C		72.0	0.0		99.0	19.0	NM_014781	Q86YR4|Q8WVU9|Q92601	Silent	SNP	ENST00000025008.5	hg19	CCDS34892.1																																																																																			.	T|1.000;C|0.000		0.348	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378011.1	NM_014781		C	53536345	T	C	53536345	2	2	258	1	0	0	0	0	0	0	0	1	13114	1393	49	2		2	RB1CC1	8	53536345	Silent	SNP	T	TCGA-EP-A3RK-01A-11D-A22F-10		53536345	92827677	23	36296										
HEY1	23462	hgsc.bcm.edu	37	chr8	80679323	80679323	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	ggtctcgtcggcgcttctcaAttatctgcagaaggcaagca	11	11	3	1			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr8:80679323A>C	ENST00000354724.3	-	3	369	c.170T>G	c.(169-171)aTt>aGt	p.I57S	RP11-27N21.3_ENST00000607172.1_lincRNA|HEY1_ENST00000523976.1_5'Flank|HEY1_ENST00000337919.5_Missense_Mutation_p.I57S|RP11-26J3.1_ENST00000502766.2_lincRNA|HEY1_ENST00000435063.2_5'Flank	NM_012258.3	NP_036390.3	Q9Y5J3	HEY1_HUMAN	hes-related family bHLH transcription factor with YRPW motif 1	57	Transcriptional repression and interaction with NCOR1 and SIN3A. {ECO:0000250}.|bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				angiogenesis (GO:0001525)|anterior/posterior axis specification (GO:0009948)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular valve formation (GO:0003190)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac septum morphogenesis (GO:0060411)|cardiac ventricle morphogenesis (GO:0003208)|cellular response to glucocorticoid stimulus (GO:0071385)|dorsal aorta morphogenesis (GO:0035912)|endocardial cushion morphogenesis (GO:0003203)|endocardial cushion to mesenchymal transition involved in heart valve formation (GO:0003199)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|heart trabecula formation (GO:0060347)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000820)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|osteoblast development (GO:0002076)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary valve morphogenesis (GO:0003184)|regulation of vasculogenesis (GO:2001212)|transcription from RNA polymerase II promoter (GO:0006366)|umbilical cord morphogenesis (GO:0036304)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	microsatellite binding (GO:0035939)|protein binding transcription factor activity (GO:0000988)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)		HEY1/NCOA2(10)	cervix(1)|kidney(2)|large_intestine(5)|lung(14)	22	all_lung(9;5.1e-05)		Epithelial(68;0.076)|all cancers(69;0.179)			GCGCTTCTCAATTATCTGCAG	0.408			T	NCOA2	mesenchymal chondrosarcoma																																p.I57S		Atlas-SNP	.		Dom	yes		8	8q21	23462	hairy/enhancer-of-split related with YRPW motif 1		M	.	HEY1	51	.	0			c.T170G						.						79	81	80					8																	80679323		2203	4300	6503	SO:0001583	missense	23462	exon3			TTCTCAATTATCT	AF151522	CCDS6225.1, CCDS43749.1, CCDS64915.1	8q21	2013-10-17	2013-10-17					"Basic helix-loop-helix proteins"	4880	protein-coding gene	gene with protein product		602953	"hairy/enhancer-of-split related with YRPW motif 1"			10415358, 10403790	Standard	NM_001040708		Approved	HESR-1, CHF2, HESR1, HRT-1, CHF-2, HERP2, BHLHb31	uc003ybl.3	Q9Y5J3		ENST00000354724.3:c.170T>G	chr8.hg19:g.80679323A>C	ENSP00000346761:p.Ile57Ser	74.0	0.0		79.0	16.0	NM_012258	B2R883|Q5TZS3|Q8NAM2|Q9NYP4	Missense_Mutation	SNP	ENST00000354724.3	hg19	CCDS6225.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.145600	0.77888	.	.	ENSG00000164683	ENST00000354724;ENST00000542205;ENST00000337919;ENST00000518733	D;D;D	0.98135	-4.74;-4.74;-4.74	4.67	4.67	0.58626	Helix-loop-helix DNA-binding (5);	0.093833	0.64402	D	0.000001	D	0.98210	0.9408	L	0.61218	1.895	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.99353	1.0915	10	0.87932	D	0	-13.5869	14.1195	0.65177	1.0:0.0:0.0:0.0	.	57;57	Q9Y5J3;Q9Y5J3-2	HEY1_HUMAN;.	S	57;57;57;19	ENSP00000346761:I57S;ENSP00000338272:I57S;ENSP00000429705:I19S	ENSP00000338272:I57S	I	-	2	0	HEY1	80841878	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	8.924000	0.92827	1.740000	0.51718	0.459000	0.35465	ATT	.	.		0.408	HEY1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000379516.1	NM_012258		C	80679323	A	C	80679323	3	2	258	1	0	0	0	0	1	0	0	0	7087	101	4	5	768	5	HEY1	8	80679323	Missense_Mutation	SNP	A	TCGA-EP-A3RK-01A-11D-A22F-10	27142978	80679323	65684699	24	36297										
C9orf64	84267	hgsc.bcm.edu	37	chr9	86571248	86571248	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	gcctcgtcggccgccctgggGttcagctcatgaagggcttt	14	13	2	1	rs560017514		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr9:86571248G>A	ENST00000376344.3	-	1	384	c.168C>T	c.(166-168)aaC>aaT	p.N56N	C9orf64_ENST00000314700.1_Intron|C9orf64_ENST00000376340.2_5'Flank	NM_032307.3	NP_115683.3	Q5T6V5	CI064_HUMAN	chromosome 9 open reading frame 64	56										central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	15						CCGCCCTGGGGTTCAGCTCAT	0.647													G|||	1	0.000199681	8e-04	0	5008	,	,		16276	0		0	False		,,,				2504	0				p.N56N		Atlas-SNP	.											.	C9orf64	28	.	0			c.C168T						.						58	59	59					9																	86571248		1992	4158	6150	SO:0001819	synonymous_variant	84267	exon1			CCTGGGGTTCAGC	AK090882	CCDS6666.2	9q22.1	2014-06-11			ENSG00000165118	ENSG00000165118			28144	protein-coding gene	gene with protein product		611342				24911101	Standard	NM_032307		Approved	MGC10999	uc004anb.3	Q5T6V5	OTTHUMG00000020111	ENST00000376344.3:c.168C>T	chr9.hg19:g.86571248G>A		54.0	0.0		55.0	8.0	NM_032307	B2RPI6|Q8N2B1|Q9BT18	Silent	SNP	ENST00000376344.3	hg19	CCDS6666.2																																																																																			.	.		0.647	C9orf64-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052865.1	NM_032307		A	86571248	G	A	86571248	2	1	258	1	0	0	0	0	0	0	0	1	2491	1252	44	3		3	C9orf64	9	86571248	Silent	SNP	G	TCGA-EP-A3RK-01A-11D-A22F-10		86571248	54642183	25	36298										
ATRNL1	26033	hgsc.bcm.edu	37	chr10	117075032	117075032	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	tgttcctgtcacgcagctcaAaattgttctggattgagaac	9	9	3	1			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr10:117075032A>T	ENST00000355044.3	+	18	2949	c.2823A>T	c.(2821-2823)caA>caT	p.Q941H	ATRNL1_ENST00000423111.2_Missense_Mutation_p.Q38H|ATRNL1_ENST00000303745.7_5'UTR	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	941					G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(11)|liver(2)|lung(44)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		ACGCAGCTCAAAATTGTTCTG	0.363																																					p.Q941H		Atlas-SNP	.											.	ATRNL1	219	.	0			c.A2823T						.						128	116	120					10																	117075032		2203	4300	6503	SO:0001583	missense	26033	exon18			AGCTCAAAATTGT	AB011106	CCDS7592.1, CCDS73204.1	10q26	2004-03-04			ENSG00000107518	ENSG00000107518			29063	protein-coding gene	gene with protein product		612869				9628581	Standard	NM_001276282		Approved	KIAA0534, FLJ45344, ALP	uc001lcg.3	Q5VV63	OTTHUMG00000019096	ENST00000355044.3:c.2823A>T	chr10.hg19:g.117075032A>T	ENSP00000347152:p.Gln941His	63.0	0.0		71.0	14.0	NM_207303	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Missense_Mutation	SNP	ENST00000355044.3	hg19	CCDS7592.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.49|16.49	3.138174|3.138174	0.56936|0.56936	.|.	.|.	ENSG00000107518|ENSG00000107518	ENST00000526373|ENST00000355044;ENST00000423111	.|T;D	.|0.84730	.|2.48;-1.89	5.47|5.47	0.417|0.417	0.16421|0.16421	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	.|D	.|0.88085	.|0.6342	M|M	0.67953|0.67953	2.075|2.075	0.80722|0.80722	D|D	1|1	.|D;D	.|0.67145	.|0.996;0.996	.|D;D	.|0.75484	.|0.986;0.986	.|D	.|0.83462	.|0.0054	.|10	.|0.15952	.|T	.|0.53	-11.9019|-11.9019	9.6941|9.6941	0.40147|0.40147	0.5711:0.0:0.4289:0.0|0.5711:0.0:0.4289:0.0	.|.	.|38;941	.|B4DH41;Q5VV63	.|.;ATRN1_HUMAN	X|H	71|941;38	.|ENSP00000347152:Q941H;ENSP00000409624:Q38H	.|ENSP00000347152:Q941H	K|Q	+|+	1|3	0|2	ATRNL1|ATRNL1	117065022|117065022	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.990000|0.990000	0.78478|0.78478	1.004000|1.004000	0.29822|0.29822	0.077000|0.077000	0.16863|0.16863	0.454000|0.454000	0.30748|0.30748	AAA|CAA	.	.		0.363	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349		T	117075032	A	T	117075032	3	4	258	1	0	0	0	0	1	0	0	0	1207	11	1	4	2893	4	ATRNL1	10	117075032	Missense_Mutation	SNP	A	TCGA-EP-A3RK-01A-11D-A22F-10		117075032	18459715	26	36299										
BSCL2	26580	hgsc.bcm.edu	37	chr11	62458597	62458597	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	cttccttccgggaattgtctCtttttcggatgttaacctgt	8	10	1	0	rs144725547		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr11:62458597C>T	ENST00000403550.1	-	8	1253	c.830G>A	c.(829-831)aGa>aAa	p.R277K	BSCL2_ENST00000421906.1_Missense_Mutation_p.R277K|LRRN4CL_ENST00000317449.4_5'Flank|HNRNPUL2-BSCL2_ENST00000403734.2_3'UTR|BSCL2_ENST00000407022.3_Missense_Mutation_p.R277K|BSCL2_ENST00000360796.5_Missense_Mutation_p.R341K|BSCL2_ENST00000433053.1_Missense_Mutation_p.R341K|BSCL2_ENST00000405837.1_Missense_Mutation_p.R341K|BSCL2_ENST00000278893.7_Missense_Mutation_p.E230K			Q96G97	BSCL2_HUMAN	Berardinelli-Seip congenital lipodystrophy 2 (seipin)	277					cell death (GO:0008219)|fat cell differentiation (GO:0045444)|lipid catabolic process (GO:0016042)|lipid particle organization (GO:0034389)|lipid storage (GO:0019915)|negative regulation of lipid catabolic process (GO:0050995)	integral component of endoplasmic reticulum membrane (GO:0030176)				endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	12						GGAATTGTCTCTTTTTCGGAT	0.517																																					p.R341K		Atlas-SNP	.											.	BSCL2	35	.	0			c.G1022A						.	C	LYS/ARG,LYS/GLU,LYS/ARG	0,4404		0,0,2202	99	86	90		830,688,1022	3.9	0	11	dbSNP_134	90	1,8597	1.2+/-3.3	0,1,4298	no	missense,missense,missense	BSCL2	NM_032667.6,NM_001130702.2,NM_001122955.3	26,56,26	0,1,6500	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign	277/399,230/288,341/463	62458597	1,13001	2202	4299	6501	SO:0001583	missense	26580	exon8			TTGTCTCTTTTTC		CCDS8031.1, CCDS44627.1, CCDS55769.1	11q13	2014-09-17	2009-07-30		ENSG00000168000	ENSG00000168000			15832	protein-coding gene	gene with protein product		606158	"spastic paraplegia 17 (Silver syndrome)"	GNG3LG, SPG17		11479539, 14981520	Standard	NM_001122955		Approved		uc001nur.4	Q96G97	OTTHUMG00000150624	ENST00000403550.1:c.830G>A	chr11.hg19:g.62458597C>T	ENSP00000385561:p.Arg277Lys	100.0	0.0		76.0	16.0	NM_001122955	G3XAE4|Q567S1|Q96SV1|Q9BSQ0	Missense_Mutation	SNP	ENST00000403550.1	hg19	CCDS8031.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.46|12.46	1.945135|1.945135	0.34283|0.34283	0.0|0.0	1.16E-4|1.16E-4	ENSG00000168000|ENSG00000168000	ENST00000278893|ENST00000449636;ENST00000405837;ENST00000433053;ENST00000360796;ENST00000403550;ENST00000407022;ENST00000421906	D|D;D;D;D;D;D	0.88664|0.88975	-2.41|-2.45;-2.43;-2.43;-2.41;-2.41;-2.41	5.01|5.01	3.88|3.88	0.44766|0.44766	.|.	.|0.561612	.|0.16354	.|U	.|0.218064	T|T	0.79329|0.79329	0.4427|0.4427	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	B|B;B;B	0.02656|0.09022	0.0|0.0;0.002;0.0	B|B;B;B	0.04013|0.06405	0.001|0.001;0.002;0.001	T|T	0.63116|0.63116	-0.6709|-0.6709	8|8	0.72032|.	D|.	0.01|.	-0.0196|-0.0196	9.231|9.231	0.37437|0.37437	0.0:0.8823:0.0:0.1177|0.0:0.8823:0.0:0.1177	.|.	230|277;341;277	Q96G97-3|Q53EN3;G3XAE4;Q96G97	.|.;.;BSCL2_HUMAN	K|K	230|26;341;341;341;277;277;277	ENSP00000278893:E230K|ENSP00000385332:R341K;ENSP00000414002:R341K;ENSP00000354032:R341K;ENSP00000385561:R277K;ENSP00000384080:R277K;ENSP00000413209:R277K	ENSP00000278893:E230K|.	E|R	-|-	1|2	0|0	BSCL2|BSCL2	62215173|62215173	0.001000|0.001000	0.12720|0.12720	0.013000|0.013000	0.15412|0.15412	0.609000|0.609000	0.37215|0.37215	1.139000|1.139000	0.31504|0.31504	2.331000|2.331000	0.79229|0.79229	0.491000|0.491000	0.48974|0.48974	GAG|AGA	.	C|1.000;T|0.000		0.517	BSCL2-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000319185.1	NM_032667		T	62458597	C	T	62458597	3	4	258	1	0	0	0	0	1	0	0	0	1529	913	32	3	382	3	BSCL2	11	62458597	Missense_Mutation	SNP	C	TCGA-EP-A3RK-01A-11D-A22F-10		62458597	72547919	27	36300										
PYGM	5837	hgsc.bcm.edu	37	chr11	64522286	64522286	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	cgaaatactcctgcttcagcCgcagctccttcccttcgaag	7	16	1	0			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr11:64522286C>T	ENST00000164139.3	-	8	1276	c.878G>A	c.(877-879)cGg>cAg	p.R293Q	PYGM_ENST00000462303.1_5'Flank|PYGM_ENST00000377432.3_Missense_Mutation_p.R205Q	NM_005609.2	NP_005600.1	P11217	PYGM_HUMAN	phosphorylase, glycogen, muscle	293					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glycogen phosphorylase activity (GO:0008184)|nucleotide binding (GO:0000166)|pyridoxal phosphate binding (GO:0030170)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CTGCTTCAGCCGCAGCTCCTT	0.622																																					p.R293Q		Atlas-SNP	.											.	PYGM	77	.	0			c.G878A						.						72	58	63					11																	64522286		2201	4297	6498	SO:0001583	missense	5837	exon8			TTCAGCCGCAGCT		CCDS8079.1, CCDS53659.1	11q12-q13.2	2013-03-01	2008-07-31		ENSG00000068976	ENSG00000068976	2.4.1.1	"Glycogen phosphorylases"	9726	protein-coding gene	gene with protein product	"McArdle syndrome", "glycogen storage disease type V", "glycogen phosphorylase, muscle form"	608455	"phosphorylase, glycogen; muscle"				Standard	NM_005609		Approved		uc001oax.4	P11217	OTTHUMG00000066835	ENST00000164139.3:c.878G>A	chr11.hg19:g.64522286C>T	ENSP00000164139:p.Arg293Gln	38.0	0.0		29.0	8.0	NM_005609	A0AVK1|A6NDY6	Missense_Mutation	SNP	ENST00000164139.3	hg19	CCDS8079.1	.	.	.	.	.	.	.	.	.	.	C	37	6.060709	0.97246	.	.	ENSG00000068976	ENST00000377432;ENST00000164139;ENST00000540450	D;D	0.98028	-3.89;-4.67	4.89	4.89	0.63831	.	0.000000	0.49305	D	0.000149	D	0.99074	0.9682	H	0.97587	4.035	0.80722	D	1	D;D	0.76494	0.998;0.999	P;P	0.61477	0.889;0.844	D	0.99116	1.0848	10	0.87932	D	0	-29.6636	15.5838	0.76465	0.0:1.0:0.0:0.0	.	205;293	A6NDY6;P11217	.;PYGM_HUMAN	Q	205;293;274	ENSP00000366650:R205Q;ENSP00000164139:R293Q	ENSP00000164139:R293Q	R	-	2	0	PYGM	64278862	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.651000	0.83577	2.551000	0.86045	0.561000	0.74099	CGG	.	.		0.622	PYGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143254.2	NM_005609		T	64522286	C	T	64522286	3	4	258	1	0	0	0	0	1	0	0	0	12877	652	23	1	1702	1	PYGM	11	64522286	Missense_Mutation	SNP	C	TCGA-EP-A3RK-01A-11D-A22F-10	2063689	64522286	70484230	28	36301										
BATF2	116071	hgsc.bcm.edu	37	chr11	64757247	64757247	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	gcagggactggatctccttcCgcagggcgaggttgtctttt	14	10	2	0	rs374070737		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr11:64757247C>A	ENST00000301887.4	-	3	309	c.179G>T	c.(178-180)cGg>cTg	p.R60L	BATF2_ENST00000435842.2_5'UTR|BATF2_ENST00000527716.1_Missense_Mutation_p.R36L	NM_138456.3	NP_612465.3	Q8N1L9	BATF2_HUMAN	basic leucine zipper transcription factor, ATF-like 2	60	Leucine-zipper. {ECO:0000255|PROSITE- ProRule:PRU00978}.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				defense response to protozoan (GO:0042832)|myeloid dendritic cell differentiation (GO:0043011)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(1)|ovary(1)|skin(1)	9						GATCTCCTTCCGCAGGGCGAG	0.652																																					p.R60L		Atlas-SNP	.											.	BATF2	20	.	0			c.G179T						.						37	37	37					11																	64757247		2201	4297	6498	SO:0001583	missense	116071	exon3			TCCTTCCGCAGGG	AK092453	CCDS8087.1, CCDS73317.1	11q13.1	2013-01-10			ENSG00000168062	ENSG00000168062		"basic leucine zipper proteins"	25163	protein-coding gene	gene with protein product		614983					Standard	NM_138456		Approved	MGC20410	uc001ocf.1	Q8N1L9	OTTHUMG00000165633	ENST00000301887.4:c.179G>T	chr11.hg19:g.64757247C>A	ENSP00000301887:p.Arg60Leu	61.0	0.0		59.0	10.0	NM_138456	D9IC56|Q8NAF4|Q8NAL8|Q96EH4	Missense_Mutation	SNP	ENST00000301887.4	hg19	CCDS8087.1	.	.	.	.	.	.	.	.	.	.	C	14.04	2.417424	0.42918	.	.	ENSG00000168062	ENST00000301887;ENST00000527716;ENST00000534177	T;T	0.57907	0.37;0.37	3.62	0.625	0.17665	Basic-leucine zipper (bZIP) transcription factor (2);bZIP transcription factor, bZIP-1 (1);	0.382732	0.18429	N	0.141495	T	0.65739	0.2720	M	0.80183	2.485	0.32888	D	0.511487	D	0.89917	1.0	D	0.87578	0.998	T	0.67860	-0.5561	10	0.87932	D	0	-29.101	2.8463	0.05545	0.2207:0.536:0.0:0.2434	.	60	Q8N1L9	BATF2_HUMAN	L	60;36;59	ENSP00000301887:R60L;ENSP00000435640:R59L	ENSP00000301887:R60L	R	-	2	0	BATF2	64513823	0.987000	0.35691	0.967000	0.41034	0.119000	0.20118	0.196000	0.17176	0.337000	0.23665	-0.347000	0.07816	CGG	.	.		0.652	BATF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385478.2	NM_138456		A	64757247	C	A	64757247	3	1	258	1	0	0	0	0	1	0	0	0	1326	652	23	1	649	1	BATF2	11	64757247	Missense_Mutation	SNP	C	TCGA-EP-A3RK-01A-11D-A22F-10	234961	64757247	70249269	29	36302										
NLRX1	79671	hgsc.bcm.edu	37	chr11	119044251	119044251	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	ccggctgcccagggaggagcGccagtttggcccaacctttg	14	14	0	0	rs548995927		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr11:119044251G>A	ENST00000409109.1	+	5	880	c.293G>A	c.(292-294)cGc>cAc	p.R98H	NLRX1_ENST00000474751.2_3'UTR|NLRX1_ENST00000525863.1_Missense_Mutation_p.R98H|NLRX1_ENST00000409991.1_Missense_Mutation_p.R98H|NLRX1_ENST00000409265.4_Missense_Mutation_p.R98H|NLRX1_ENST00000292199.2_Missense_Mutation_p.R98H	NM_001282144.1	NP_001269073.1	Q86UT6	NLRX1_HUMAN	NLR family member X1	98	Required for interaction with MAVS.				innate immune response (GO:0045087)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of RIG-I signaling pathway (GO:0039536)|negative regulation of type I interferon production (GO:0032480)|viral process (GO:0016032)	mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)			cervix(1)|endometrium(2)|kidney(2)|lung(10)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	22	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		AGGGAGGAGCGCCAGTTTGGC	0.617																																					p.R98H		Atlas-SNP	.											NLRX1_ENST00000409265,NS,carcinoma,0,2	NLRX1	128	.	0			c.G293A						.						59	59	59					11																	119044251		2200	4295	6495	SO:0001583	missense	79671	exon5			AGGAGCGCCAGTT	AB094095	CCDS8416.1	11q23.3	2007-02-07			ENSG00000160703	ENSG00000160703		"Nucleotide-binding domain and leucine rich repeat containing"	29890	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat containing X1", "NOD-like receptor X1", "NLR family, X1"	611947				12766759	Standard	XM_005271669		Approved	NOD9, CLR11.3	uc001pvw.3	Q86UT6	OTTHUMG00000154476	ENST00000409109.1:c.293G>A	chr11.hg19:g.119044251G>A	ENSP00000387334:p.Arg98His	41.0	0.0		40.0	9.0	NM_024618	A8K6Q1|B3KPK2|B3KTA2|Q7RTR3|Q96D51|Q9H724	Missense_Mutation	SNP	ENST00000409109.1	hg19	CCDS8416.1	.	.	.	.	.	.	.	.	.	.	G	16.48	3.135233	0.56828	.	.	ENSG00000160703	ENST00000454811;ENST00000449394;ENST00000422249;ENST00000409991;ENST00000292199;ENST00000409265;ENST00000409109;ENST00000525863	T;T;T;T;T;T;T;T	0.71817	1.09;1.09;1.1;-0.51;-0.51;-0.6;-0.51;-0.6	5.6	5.6	0.85130	.	0.000000	0.64402	D	0.000007	T	0.62913	0.2467	L	0.32530	0.975	0.47476	D	0.999432	B;B	0.25667	0.131;0.042	B;B	0.22880	0.042;0.013	T	0.60697	-0.7212	10	0.52906	T	0.07	.	17.3764	0.87392	0.0:0.0:1.0:0.0	.	98;98	Q86UT6-2;Q86UT6	.;NLRX1_HUMAN	H	98	ENSP00000400268:R98H;ENSP00000402801:R98H;ENSP00000402381:R98H;ENSP00000386851:R98H;ENSP00000292199:R98H;ENSP00000386858:R98H;ENSP00000387334:R98H;ENSP00000433442:R98H	ENSP00000292199:R98H	R	+	2	0	NLRX1	118549461	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.818000	0.62657	2.637000	0.89404	0.561000	0.74099	CGC	.	.		0.617	NLRX1-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335403.1	NM_170722		A	119044251	G	A	119044251	3	1	258	1	0	0	0	0	1	0	0	0	10494	1087	38	1	307	1	NLRX1	11	119044251	Missense_Mutation	SNP	G	TCGA-EP-A3RK-01A-11D-A22F-10	54287004	119044251	15962265	30	36303										
SDS	10993	hgsc.bcm.edu	37	chr12	113834987	113834988	+	Frame_Shift_Ins	INS	-	-	T													0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	acctggtgatcttgggcaggINSgagacaagtttgcctgcggt							TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr12:113834987_113834988insT	ENST00000257549.4	-	6	757_758	c.635_636insA	c.(634-636)tccfs	p.S212fs		NM_006843.2	NP_006834.2	P20132	SDHL_HUMAN	serine dehydratase	212					gluconeogenesis (GO:0006094)|L-serine catabolic process (GO:0006565)|pyruvate biosynthetic process (GO:0042866)|response to amino acid (GO:0043200)|response to cobalamin (GO:0033590)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	L-serine ammonia-lyase activity (GO:0003941)|L-threonine ammonia-lyase activity (GO:0004794)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)			large_intestine(2)|lung(6)|pancreas(1)|prostate(1)|urinary_tract(1)	11					L-Serine(DB00133)	TCTTGGGCAGGGAGACAAGTTT	0.629																																					p.S212fs		Atlas-INDEL	.											.	SDS	35	.	0			c.636_637insA						.																																			SO:0001589	frameshift_variant	10993	exon6			.	J05037	CCDS9169.1	12q24.13	2014-06-24			ENSG00000135094	ENSG00000135094	4.3.1.17		10691	protein-coding gene	gene with protein product	"L-serine ammonia-lyase"	182128				2674117	Standard	NM_006843		Approved	SDH	uc001tvg.3	P20132	OTTHUMG00000169554	ENST00000257549.4:c.635_636insA	chr12.hg19:g.113834987_113834988insT	ENSP00000257549:p.Ser212fs	84.0	0.0		69.0	13.0	NM_006843	A8K9P5	Frame_Shift_Ins	INS	ENST00000257549.4	hg19	CCDS9169.1																																																																																			.	.		0.629	SDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404790.1	NM_006843		T	113834988	-	T	113834987	7	5	258	1	0	1	1	0	0	0	0	0	13990	1219	43	0	362	0	SDS	12	113834987	Frame_Shift_Ins	INS	-	TCGA-EP-A3RK-01A-11D-A22F-10		113834987	20016908	31	36304										
SPATA13	221178	hgsc.bcm.edu	37	chr13	24798144	24798144	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	gcacacagccggctgcatgaCgactactcccgccgcgtctc	10	18	1	1			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr13:24798144C>T	ENST00000382095.4	+	2	185				SPATA13_ENST00000382108.3_Silent_p.D359D|SPATA13_ENST00000424834.2_Silent_p.D359D|RP11-307N16.6_ENST00000382141.4_Silent_p.D359D	NM_153023.2	NP_694568.1	Q96N96	SPT13_HUMAN	spermatogenesis associated 13						cell migration (GO:0016477)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell migration (GO:0030334)	cytoplasm (GO:0005737)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			breast(4)|endometrium(2)|large_intestine(9)|lung(4)|ovary(1)|prostate(1)|skin(2)	23		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)		GGCTGCATGACGACTACTCCC	0.672																																					p.D359D		Atlas-SNP	.											.	SPATA13	92	.	0			c.C1077T						.						14	20	18					13																	24798144		692	1590	2282	SO:0001627	intron_variant	221178	exon2			GCATGACGACTAC	AK055770	CCDS9305.1, CCDS53857.1, CCDS66517.1, CCDS66518.1, CCDS73553.1	13q12.13	2013-01-10			ENSG00000182957	ENSG00000182957		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	23222	protein-coding gene	gene with protein product		613324					Standard	NM_001286795		Approved	FLJ31208, ARHGEF29	uc021rhg.1	Q96N96	OTTHUMG00000016578	ENST00000382095.4:c.-222-25471C>T	chr13.hg19:g.24798144C>T		29.0	0.0		34.0	11.0	NM_001166271	A2VEA9|A6NF85|B4DQB1|B4DSZ0|B4DVM8|J3KPJ7|J3KQH2|Q5VX68|Q6ZML1|Q8N873|Q8TEK6	Silent	SNP	ENST00000382095.4	hg19	CCDS9305.1	.	.	.	.	.	.	.	.	.	.	C	2.779	-0.253857	0.05829	.	.	ENSG00000182957	ENST00000424834	.	.	.	4.68	-0.709	0.11237	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.9277	0.41503	0.0:0.4233:0.0:0.5767	.	.	.	.	X	397	.	.	R	+	1	2	SPATA13	23696144	0.013000	0.17824	0.800000	0.32199	0.175000	0.22909	-1.432000	0.02430	-0.589000	0.05874	-0.361000	0.07541	CGA	.	.		0.672	SPATA13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044180.2	NM_153023		T	24798144	C	T	24798144	1	4	258	0	1	0	0	0	0	0	0	0	15015	535	19	1		1	SPATA13	13	24798144	Intron	SNP	C	TCGA-EP-A3RK-01A-11D-A22F-10		24798144	90371734	32	36305										
FANCI	55215	hgsc.bcm.edu	37	chr15	89844660	89844660	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	tttgtccaagttactggagcCctcctctcctcaggtactag	8	13	2	0			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr15:89844660C>T	ENST00000310775.7	+	27	3079	c.2993C>T	c.(2992-2994)cCc>cTc	p.P998L	FANCI_ENST00000300027.8_Missense_Mutation_p.P938L	NM_001113378.1	NP_001106849.1	Q9NVI1	FANCI_HUMAN	Fanconi anemia, complementation group I	998					cell cycle (GO:0007049)|DNA repair (GO:0006281)|positive regulation of protein ubiquitination (GO:0031398)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA polymerase binding (GO:0070182)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	Lung NSC(78;0.0472)|all_lung(78;0.089)					TTACTGGAGCCCTCCTCTCCT	0.413								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.P998L		Atlas-SNP	.											.	FANCI	129	.	0			c.C2993T						.						145	132	136					15																	89844660		2200	4299	6499	SO:0001583	missense	55215	exon27	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TGGAGCCCTCCTC	BC004277	CCDS10349.2, CCDS45346.1	15q26.1	2014-09-17	2007-05-03	2007-05-03	ENSG00000140525	ENSG00000140525		"Fanconi anemia, complementation groups"	25568	protein-coding gene	gene with protein product		611360	"KIAA1794"	KIAA1794		14630800, 17460694, 17412408	Standard	NM_001113378		Approved	FLJ10719	uc010bnp.1	Q9NVI1	OTTHUMG00000132993	ENST00000310775.7:c.2993C>T	chr15.hg19:g.89844660C>T	ENSP00000310842:p.Pro998Leu	88.0	0.0		94.0	27.0	NM_001113378	A4ZVE4|A5YMH4|A6NJZ0|Q96JN1|Q96ST0|Q9BT96	Missense_Mutation	SNP	ENST00000310775.7	hg19	CCDS45346.1	.	.	.	.	.	.	.	.	.	.	C	31	5.073351	0.94000	.	.	ENSG00000140525	ENST00000300027;ENST00000310775;ENST00000447611	T;T;T	0.70869	-0.52;-0.49;0.18	5.4	5.4	0.78164	.	0.054186	0.85682	D	0.000000	D	0.82522	0.5055	L	0.61036	1.89	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77004	0.984;0.989;0.989	T	0.80605	-0.1308	10	0.36615	T	0.2	-13.2025	19.1729	0.93588	0.0:1.0:0.0:0.0	.	998;938;938	Q9NVI1;Q9NVI1-2;Q9NVI1-1	FANCI_HUMAN;.;.	L	938;998;938	ENSP00000300027:P938L;ENSP00000310842:P998L;ENSP00000413249:P938L	ENSP00000300027:P938L	P	+	2	0	FANCI	87645664	1.000000	0.71417	0.988000	0.46212	0.984000	0.73092	7.278000	0.78587	2.541000	0.85698	0.655000	0.94253	CCC	.	.		0.413	FANCI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421140.1	NM_018193		T	89844660	C	T	89844660	3	4	258	1	0	0	0	0	1	0	0	0	5677	623	22	3	3095	3	FANCI	15	89844660	Missense_Mutation	SNP	C	TCGA-EP-A3RK-01A-11D-A22F-10		89844660	12686732	33	36306										
MMP2	4313	hgsc.bcm.edu	37	chr16	55517934	55517934	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	tctaccacctccaggatcatTggctacacacctgatctgga	7	14	3	1			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr16:55517934T>A	ENST00000219070.4	+	3	896	c.387T>A	c.(385-387)atT>atA	p.I129I	MMP2_ENST00000570308.1_Silent_p.I53I|MMP2_ENST00000543485.1_Silent_p.I53I|MMP2_ENST00000437642.2_Silent_p.I79I	NM_004530.4	NP_004521.1	P08253	MMP2_HUMAN	matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)	129	Collagenase-like 1.				angiogenesis (GO:0001525)|blood vessel maturation (GO:0001955)|bone trabecula formation (GO:0060346)|cellular protein metabolic process (GO:0044267)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|positive regulation of innate immune response (GO:0045089)|proteolysis (GO:0006508)|response to hypoxia (GO:0001666)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|sarcomere (GO:0030017)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|liver(2)|lung(23)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	58		Renal(780;0.00183)|Breast(268;0.00354)|Hepatocellular(780;0.00826)|all_neural(199;0.0189)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0185)|all cancers(182;7.16e-45)|Epithelial(162;5.26e-37)|GBM - Glioblastoma multiforme(240;9e-08)|Kidney(780;0.00227)|BRCA - Breast invasive adenocarcinoma(181;0.00786)	Captopril(DB01197)|Marimastat(DB00786)	CCAGGATCATTGGCTACACAC	0.478																																					p.I129I		Atlas-SNP	.											.	MMP2	119	.	0			c.T387A						.						197	151	166					16																	55517934		2198	4300	6498	SO:0001819	synonymous_variant	4313	exon3			GATCATTGGCTAC		CCDS10752.1, CCDS45487.1	16q13-q21	2008-02-05	2005-08-08		ENSG00000087245	ENSG00000087245	3.4.24.24		7166	protein-coding gene	gene with protein product		120360	"matrix metalloproteinase 2 (gelatinase A, 72kD gelatinase, 72kD type IV collagenase)", "matrix metalloproteinase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)"	CLG4, CLG4A			Standard	NM_004530		Approved	TBE-1	uc002ehz.4	P08253	OTTHUMG00000133202	ENST00000219070.4:c.387T>A	chr16.hg19:g.55517934T>A		72.0	0.0		80.0	21.0	NM_004530	B2R6U1|B4DWH3|E9PE45|Q9UCJ8	Silent	SNP	ENST00000219070.4	hg19	CCDS10752.1																																																																																			.	.		0.478	MMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256913.3			A	55517934	T	A	55517934	2	1	258	1	0	0	0	0	0	0	0	1	9667	1800	63	4		4	MMP2	16	55517934	Silent	SNP	T	TCGA-EP-A3RK-01A-11D-A22F-10		55517934	34836819	34	36307										
ANKFY1	51479	hgsc.bcm.edu	37	chr17	4098292	4098292	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	cctgtcgccgtgtcaggtgcGtctgtgtggctgccgcgctg	16	13	2	0			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr17:4098292G>A	ENST00000341657.4	-	10	1388	c.1353C>T	c.(1351-1353)gaC>gaT	p.D451D	ANKFY1_ENST00000574367.1_Silent_p.D451D|ANKFY1_ENST00000570535.1_Silent_p.D493D|ANKFY1_ENST00000433651.1_Silent_p.D451D|Y_RNA_ENST00000384660.1_RNA	NM_016376.3	NP_057460.3	Q9P2R3	ANFY1_HUMAN	ankyrin repeat and FYVE domain containing 1	451					endosomal vesicle fusion (GO:0034058)|endosome localization (GO:0032439)|Golgi to lysosome transport (GO:0090160)|positive regulation of pinocytosis (GO:0048549)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|macropinosome (GO:0044354)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphatidylinositol phosphate binding (GO:1901981)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|liver(1)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						TGTCAGGTGCGTCTGTGTGGC	0.572																																					p.D493D		Atlas-SNP	.											.	ANKFY1	81	.	0			c.C1479T						.						42	45	44					17																	4098292		2097	4233	6330	SO:0001819	synonymous_variant	51479	exon10			AGGTGCGTCTGTG	AB033081	CCDS42236.1, CCDS58502.1	17p13.3	2013-01-10			ENSG00000185722	ENSG00000185722		"Zinc fingers, FYVE domain containing", "BTB/POZ domain containing", "Ankyrin repeat domain containing"	20763	protein-coding gene	gene with protein product		607927				10940552, 17273843	Standard	NM_016376		Approved	ANKHZN, KIAA1255, ZFYVE14, BTBD23	uc002fxn.3	Q9P2R3	OTTHUMG00000177727	ENST00000341657.4:c.1353C>T	chr17.hg19:g.4098292G>A		51.0	0.0		60.0	11.0	NM_001257999	A8KA65|Q5RKV4|Q9ULG5	Silent	SNP	ENST00000341657.4	hg19																																																																																				.	.		0.572	ANKFY1-008	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000438702.1	NM_016376		A	4098292	G	A	4098292	2	1	258	1	0	0	0	0	0	0	0	1	626	1136	40	1		1	ANKFY1	17	4098292	Silent	SNP	G	TCGA-EP-A3RK-01A-11D-A22F-10		4098292	77096918	35	36308										
ALPK2	115701	hgsc.bcm.edu	37	chr18	56247067	56247067	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	cctcggtgtaggttagggttAtctctgggcaaagttcatag	13	7	2	0			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr18:56247067A>G	ENST00000361673.3	-	4	1154	c.941T>C	c.(940-942)aTa>aCa	p.I314T	ALPK2_ENST00000587399.1_5'Flank	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	314						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						GGTTAGGGTTATCTCTGGGCA	0.473											OREG0025011	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I314T		Atlas-SNP	.											.	ALPK2	487	.	0			c.T941C						.						121	119	120					18																	56247067		2203	4300	6503	SO:0001583	missense	115701	exon4			AGGGTTATCTCTG	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"Immunoglobulin superfamily / I-set domain containing"	20565	protein-coding gene	gene with protein product	"heart alpha-kinase"					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.941T>C	chr18.hg19:g.56247067A>G	ENSP00000354991:p.Ile314Thr	139.0	0.0	1014	171.0	28.0	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	hg19	CCDS11966.2	.	.	.	.	.	.	.	.	.	.	A	16.75	3.210392	0.58343	.	.	ENSG00000198796	ENST00000361673	T	0.57595	0.39	6.17	5.03	0.67393	.	0.361375	0.20142	N	0.098359	T	0.36276	0.0961	L	0.46157	1.445	0.26363	N	0.977016	P	0.43431	0.807	B	0.31016	0.123	T	0.39683	-0.9602	10	0.34782	T	0.22	-14.5358	6.9803	0.24700	0.7737:0.151:0.0753:0.0	.	314	Q86TB3	ALPK2_HUMAN	T	314	ENSP00000354991:I314T	ENSP00000354991:I314T	I	-	2	0	ALPK2	54398047	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.122000	0.31295	2.371000	0.80710	0.533000	0.62120	ATA	.	.		0.473	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947		G	56247067	A	G	56247067	3	3	258	1	0	0	0	0	1	0	0	0	545	449	16	2	5611	2	ALPK2	18	56247067	Missense_Mutation	SNP	A	TCGA-EP-A3RK-01A-11D-A22F-10		56247067	21830181	36	36309										
GMIP	51291	hgsc.bcm.edu	37	chr19	19745495	19745495	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	gcgtcgtagaggtggaagggGatcacgggctcggtgagctg	20	7	1	2			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr19:19745495G>C	ENST00000203556.4	-	18	2042	c.1905C>G	c.(1903-1905)atC>atG	p.I635M	GMIP_ENST00000587238.1_Missense_Mutation_p.I609M|GMIP_ENST00000586269.1_Intron|GMIP_ENST00000445806.2_Missense_Mutation_p.I606M	NM_016573.2	NP_057657.2	Q9P107	GMIP_HUMAN	GEM interacting protein	635	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				intracellular signal transduction (GO:0035556)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|Rho GTPase activator activity (GO:0005100)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24						GGTGGAAGGGGATCACGGGCT	0.662																																					p.I635M		Atlas-SNP	.											.	GMIP	55	.	0			c.C1905G						.						125	127	126					19																	19745495		2203	4300	6503	SO:0001583	missense	51291	exon18			GAAGGGGATCACG	AF132541	CCDS12408.1, CCDS74318.1	19p13.11	2011-09-07				ENSG00000089639		"Rho GTPase activating proteins"	24852	protein-coding gene	gene with protein product		609694				12093360, 16086184	Standard	XM_005259927		Approved	ARHGAP46	uc002nnd.3	Q9P107		ENST00000203556.4:c.1905C>G	chr19.hg19:g.19745495G>C	ENSP00000203556:p.Ile635Met	81.0	0.0		79.0	8.0	NM_016573	A0AVN9|B7ZLZ0	Missense_Mutation	SNP	ENST00000203556.4	hg19	CCDS12408.1	.	.	.	.	.	.	.	.	.	.	G	11.40	1.627043	0.28978	.	.	ENSG00000089639	ENST00000203556;ENST00000445806	T;T	0.22134	1.97;1.97	4.85	2.66	0.31614	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.413090	0.17679	N	0.165690	T	0.15262	0.0368	L	0.35542	1.07	0.25262	N	0.989587	P;B;P	0.35155	0.487;0.028;0.487	B;B;B	0.37047	0.24;0.065;0.24	T	0.14476	-1.0471	10	0.32370	T	0.25	-13.9627	7.3109	0.26473	0.0911:0.0:0.7409:0.168	.	606;609;635	E7ERB7;B7ZLZ0;Q9P107	.;.;GMIP_HUMAN	M	635;606	ENSP00000203556:I635M;ENSP00000397075:I606M	ENSP00000203556:I635M	I	-	3	3	GMIP	19606495	0.201000	0.23410	1.000000	0.80357	0.993000	0.82548	0.025000	0.13577	0.439000	0.26476	0.561000	0.74099	ATC	.	.		0.662	GMIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460551.1	NM_016573		C	19745495	G	C	19745495	3	2	258	1	0	0	0	0	1	0	0	0	6499	1164	41	4	1023	4	GMIP	19	19745495	Missense_Mutation	SNP	G	TCGA-EP-A3RK-01A-11D-A22F-10		19745495	39383488	37	36310										
PPP5C	5536	hgsc.bcm.edu	37	chr19	46890688	46890688	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	gacatccggaaaattgagcgGaatcgacaacccccagattc	9	12	0	2			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr19:46890688G>A	ENST00000012443.4	+	9	1216	c.1113G>A	c.(1111-1113)cgG>cgA	p.R371R	PPP5C_ENST00000391919.1_Silent_p.R243R	NM_006247.3	NP_006238.1	P53041	PPP5_HUMAN	protein phosphatase 5, catalytic subunit	371	Catalytic.				cell death (GO:0008219)|DNA repair (GO:0006281)|mitotic nuclear division (GO:0007067)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein dephosphorylation (GO:0006470)|protein heterooligomerization (GO:0051291)|response to morphine (GO:0043278)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|RNA binding (GO:0003723)|signal transducer activity (GO:0004871)			endometrium(4)|kidney(1)|large_intestine(5)|liver(2)|lung(4)|ovary(1)|pancreas(1)	18		Ovarian(192;0.0731)|all_neural(266;0.196)		OV - Ovarian serous cystadenocarcinoma(262;0.000196)|all cancers(93;0.00192)|GBM - Glioblastoma multiforme(486;0.0499)|Epithelial(262;0.0504)		AAATTGAGCGGAATCGACAAC	0.622																																					p.R371R		Atlas-SNP	.											.	PPP5C	44	.	0			c.G1113A						.						76	62	67					19																	46890688		2203	4300	6503	SO:0001819	synonymous_variant	5536	exon9			TGAGCGGAATCGA		CCDS12684.1	19q13.3	2013-01-10			ENSG00000011485	ENSG00000011485	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits", "Tetratricopeptide (TTC) repeat domain containing"	9322	protein-coding gene	gene with protein product		600658		PPP5		8666404	Standard	NM_006247		Approved	PP5	uc002pem.3	P53041	OTTHUMG00000134287	ENST00000012443.4:c.1113G>A	chr19.hg19:g.46890688G>A		44.0	0.0		47.0	13.0	NM_006247	Q16722|Q53XV2	Silent	SNP	ENST00000012443.4	hg19	CCDS12684.1																																																																																			.	.		0.622	PPP5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258969.2	NM_006247		A	46890688	G	A	46890688	2	1	258	1	0	0	0	0	0	0	0	1	12418	1161	41	3		3	PPP5C	19	46890688	Silent	SNP	G	TCGA-EP-A3RK-01A-11D-A22F-10	27145193	46890688	12238295	38	36311										
ZNF665	79788	hgsc.bcm.edu	37	chr19	53669326	53669326	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	tgaaagcttactccaagctgAttttcaatatgcctgtttcc	6	10	1	2			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr19:53669326A>G	ENST00000600412.1	-	2	337	c.222T>C	c.(220-222)aaT>aaC	p.N74N	ZNF665_ENST00000396424.3_Silent_p.N139N|CTD-2245F17.2_ENST00000600257.1_RNA			Q9H7R5	ZN665_HUMAN	zinc finger protein 665	74					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	35				GBM - Glioblastoma multiforme(134;0.0196)		CTCCAAGCTGATTTTCAATAT	0.373																																					p.N139N		Atlas-SNP	.											.	ZNF665	136	.	0			c.T417C						.						119	125	123					19																	53669326		2145	4278	6423	SO:0001819	synonymous_variant	79788	exon4			AAGCTGATTTTCA		CCDS46169.1	19q13.42	2013-01-08				ENSG00000197497		"Zinc fingers, C2H2-type", "-"	25885	protein-coding gene	gene with protein product							Standard	NM_024733		Approved	FLJ14345	uc010eqm.1	Q9H7R5		ENST00000600412.1:c.222T>C	chr19.hg19:g.53669326A>G		138.0	0.0		162.0	42.0	NM_024733	A8K5T8	Silent	SNP	ENST00000600412.1	hg19																																																																																				.	.		0.373	ZNF665-002	PUTATIVE	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000464179.1	NM_024733		G	53669326	A	G	53669326	2	3	258	1	0	0	0	0	0	0	0	1	18088	330	12	2		2	ZNF665	19	53669326	Silent	SNP	A	TCGA-EP-A3RK-01A-11D-A22F-10	6778638	53669326	5459657	39	36312										
ZNF677	342926	hgsc.bcm.edu	37	chr19	53747007	53747007	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	gggtggttaccatcttctggAgggatgttatcctcatcgag	13	8	3	0			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr19:53747007A>T	ENST00000598513.1	-	4	309	c.159T>A	c.(157-159)ccT>ccA	p.P53P	ZNF677_ENST00000601828.1_Silent_p.P53P|CTD-2245F17.6_ENST00000596041.1_RNA|ZNF677_ENST00000601413.1_Silent_p.P53P|ZNF677_ENST00000599012.1_Silent_p.P53P|ZNF677_ENST00000594681.1_Silent_p.P53P|ZNF677_ENST00000598806.1_Silent_p.P53P|ZNF677_ENST00000333952.4_Silent_p.P53P	NM_182609.2	NP_872415.1	Q86XU0	ZN677_HUMAN	zinc finger protein 677	53	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(13)|lung(6)|ovary(1)|pancreas(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				GBM - Glioblastoma multiforme(134;0.00352)		CATCTTCTGGAGGGATGTTAT	0.502																																					p.P53P		Atlas-SNP	.											.	ZNF677	94	.	0			c.T159A						.						115	106	109					19																	53747007		2203	4300	6503	SO:0001819	synonymous_variant	342926	exon4			TTCTGGAGGGATG	BC050038	CCDS12861.1	19q13.42	2013-01-08				ENSG00000197928		"Zinc fingers, C2H2-type", "-"	28730	protein-coding gene	gene with protein product	"hypothetical protein MGC48625"					12477932	Standard	NM_182609		Approved	MGC48625	uc002qbg.1	Q86XU0		ENST00000598513.1:c.159T>A	chr19.hg19:g.53747007A>T		71.0	0.0		82.0	21.0	NM_182609		Silent	SNP	ENST00000598513.1	hg19	CCDS12861.1																																																																																			.	.		0.502	ZNF677-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464189.1	NM_182609		T	53747007	A	T	53747007	2	4	258	1	0	0	0	0	0	0	0	1	18099	291	11	4		4	ZNF677	19	53747007	Silent	SNP	A	TCGA-EP-A3RK-01A-11D-A22F-10	77681	53747007	5381976	40	36313										
PTPRT	11122	hgsc.bcm.edu	37	chr20	40944364	40944364	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	tccatgtggccatacttactCcattggctttgctgagtgcc	9	12	0	1			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr20:40944364C>T	ENST00000373187.1	-	12	2137	c.2138G>A	c.(2137-2139)gGa>gAa	p.G713E	PTPRT_ENST00000373201.1_Splice_Site_p.G713E|PTPRT_ENST00000373198.4_Splice_Site_p.G713E|PTPRT_ENST00000373193.3_Splice_Site_p.G713E|PTPRT_ENST00000356100.2_Splice_Site_p.G713E|PTPRT_ENST00000373184.1_Splice_Site_p.G713E|PTPRT_ENST00000373190.1_Splice_Site_p.G713E			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	713	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)			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)				CATACTTACTCCATTGGCTTT	0.458																																					p.G713E		Atlas-SNP	.											.	PTPRT	372	.	0			c.G2138A						.						70	67	68					20																	40944364		1943	4139	6082	SO:0001630	splice_region_variant	11122	exon12			CTTACTCCATTGG	AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.2139+1G>A	chr20.hg19:g.40944364C>T		110.0	0.0		86.0	13.0	NM_007050	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Missense_Mutation	SNP	ENST00000373187.1	hg19	CCDS42874.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.162735	0.78226	.	.	ENSG00000196090	ENST00000373190;ENST00000373187;ENST00000373193;ENST00000356100;ENST00000373198;ENST00000373184;ENST00000373201	T;T;T;T;T;T;T	0.35421	1.33;1.32;1.32;1.33;1.31;1.36;1.35	5.82	4.87	0.63330	.	0.000000	0.85682	D	0.000000	T	0.64046	0.2563	M	0.84326	2.69	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.77557	0.99;0.967	T	0.71354	-0.4618	10	0.87932	D	0	.	16.3453	0.83126	0.1331:0.8669:0.0:0.0	.	713;713	O14522-1;O14522	.;PTPRT_HUMAN	E	713	ENSP00000362286:G713E;ENSP00000362283:G713E;ENSP00000362289:G713E;ENSP00000348408:G713E;ENSP00000362294:G713E;ENSP00000362280:G713E;ENSP00000362297:G713E	ENSP00000348408:G713E	G	-	2	0	PTPRT	40377778	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.060000	0.71141	1.440000	0.47531	0.655000	0.94253	GGA	.	.		0.458	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1		Missense_Mutation	T	40944364	C	T	40944364	5	4	258	1	0	0	0	0	0	0	1	0	12827	869	30	3	2328	3	PTPRT	20	40944364	Splice_Site	SNP	C	TCGA-EP-A3RK-01A-11D-A22F-10		40944364	22081156	41	36314										
PREX1	57580	hgsc.bcm.edu	37	chr20	47307560	47307560	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	tgccgtcttggccatgcagaCaaaccacttattcttggccg	9	13	2	1			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr20:47307560C>A	ENST00000371941.3	-	9	1133	c.1111G>T	c.(1111-1113)Gtc>Ttc	p.V371F	PREX1_ENST00000396220.1_Missense_Mutation_p.V371F	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	371	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			GCCATGCAGACAAACCACTTA	0.592																																					p.V371F		Atlas-SNP	.											.	PREX1	441	.	0			c.G1111T						.						181	137	152					20																	47307560		2203	4300	6503	SO:0001583	missense	57580	exon9			TGCAGACAAACCA	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.1111G>T	chr20.hg19:g.47307560C>A	ENSP00000361009:p.Val371Phe	131.0	0.0		132.0	30.0	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	hg19	CCDS13410.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.402320	0.83230	.	.	ENSG00000124126	ENST00000371941;ENST00000396220	D;D	0.88277	-2.36;-2.36	5.32	5.32	0.75619	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.48767	U	0.000165	D	0.94016	0.8083	M	0.67625	2.065	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94449	0.7665	10	0.87932	D	0	.	19.0098	0.92868	0.0:1.0:0.0:0.0	.	371	Q8TCU6	PREX1_HUMAN	F	371	ENSP00000361009:V371F;ENSP00000379522:V371F	ENSP00000361009:V371F	V	-	1	0	PREX1	46740967	1.000000	0.71417	0.988000	0.46212	0.374000	0.29953	7.818000	0.86416	2.491000	0.84063	0.655000	0.94253	GTC	.	.		0.592	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		A	47307560	C	A	47307560	3	1	258	1	0	0	0	0	1	0	0	0	12488	478	17	3	3996	3	PREX1	20	47307560	Missense_Mutation	SNP	C	TCGA-EP-A3RK-01A-11D-A22F-10	6363196	47307560	15717960	42	36315										
BCR	613	hgsc.bcm.edu	37	chr22	23656199	23656199	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	agagctgcatgctcaacctgCtgctgtccctgccggaggcc	12	15	1	1	rs200185744		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr22:23656199C>G	ENST00000305877.8	+	21	4253	c.3502C>G	c.(3502-3504)Ctg>Gtg	p.L1168V	BCR_ENST00000436990.2_3'UTR|BCR_ENST00000359540.3_Missense_Mutation_p.L1124V	NM_004327.3	NP_004318.3	P11274	BCR_HUMAN	breakpoint cluster region	1168	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				actin cytoskeleton organization (GO:0030036)|brain development (GO:0007420)|inner ear morphogenesis (GO:0042472)|negative regulation of cell migration (GO:0030336)|negative regulation of inflammatory response (GO:0050728)|negative regulation of neutrophil degranulation (GO:0043314)|neuromuscular process controlling balance (GO:0050885)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of phagocytosis (GO:0050766)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|kinase activity (GO:0016301)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)|Rac GTPase activator activity (GO:0030675)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)		BCR/JAK2(6)	central_nervous_system(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	35					Bosutinib(DB06616)|Ponatinib(DB08901)	GCTCAACCTGCTGCTGTCCCT	0.607			T	"ABL1,  FGFR1, JAK2 "	"CML, ALL, AML"																																p.L1168V		Atlas-SNP	.		Dom	yes		22	22q11.21	613	breakpoint cluster region		L	.	BCR	74	.	0			c.C3502G						.						148	134	139					22																	23656199		2203	4300	6503	SO:0001583	missense	613	exon21			AACCTGCTGCTGT		CCDS13806.1, CCDS13807.1	22q11	2013-01-10			ENSG00000186716	ENSG00000186716		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	1014	protein-coding gene	gene with protein product		151410		D22S11, BCR1		1657398, 18070886	Standard	NM_004327		Approved	D22S662, CML, PHL, ALL	uc002zww.3	P11274	OTTHUMG00000150655	ENST00000305877.8:c.3502C>G	chr22.hg19:g.23656199C>G	ENSP00000303507:p.Leu1168Val	36.0	0.0		25.0	7.0	NM_004327	P78501|Q12842|Q4LE80|Q6NZI3	Missense_Mutation	SNP	ENST00000305877.8	hg19	CCDS13806.1	.	.	.	.	.	.	.	.	.	.	.	17.65	3.441507	0.63067	.	.	ENSG00000186716	ENST00000305877;ENST00000359540;ENST00000334149	T;T	0.21361	2.01;2.01	4.51	4.51	0.55191	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.64402	D	0.000001	T	0.26846	0.0657	N	0.21142	0.635	0.80722	D	1	D;P;P	0.55605	0.972;0.83;0.927	P;P;P	0.61940	0.896;0.821;0.842	T	0.01648	-1.1304	10	0.49607	T	0.09	.	10.2946	0.43616	0.0:0.896:0.0:0.104	.	757;1124;1168	B4E065;P11274-2;P11274	.;.;BCR_HUMAN	V	1168;1124;833	ENSP00000303507:L1168V;ENSP00000352535:L1124V	ENSP00000303507:L1168V	L	+	1	2	BCR	21986199	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	2.897000	0.48664	2.255000	0.74692	0.455000	0.32223	CTG	.	C|1.000;T|0.000		0.607	BCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075819.1	NM_004327		G	23656199	C	G	23656199	3	3	258	1	0	0	0	0	1	0	0	0	1388	796	28	4	3584	4	BCR	22	23656199	Missense_Mutation	SNP	C	TCGA-EP-A3RK-01A-11D-A22F-10		23656199	27648367	43	36316										
CACNG2	10369	hgsc.bcm.edu	37	chr22	37098516	37098516	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	ggtcttgcaaacccctctggAgtagagccaatagtcggttc	11	11	2	1			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr22:37098516A>T	ENST00000300105.6	-	1	1087	c.106T>A	c.(106-108)Tcc>Acc	p.S36T	RP1-293L6.1_ENST00000430281.1_RNA	NM_006078.3	NP_006069.1	Q9Y698	CCG2_HUMAN	calcium channel, voltage-dependent, gamma subunit 2	36					membrane depolarization (GO:0051899)|membrane hyperpolarization (GO:0060081)|neuromuscular junction development (GO:0007528)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	18						ACCCCTCTGGAGTAGAGCCAA	0.483																																					p.S36T		Atlas-SNP	.											.	CACNG2	43	.	0			c.T106A						.						232	205	214					22																	37098516		2203	4300	6503	SO:0001583	missense	10369	exon1			CTCTGGAGTAGAG	AF096322	CCDS13931.1	22q13.1	2006-08-01			ENSG00000166862	ENSG00000166862		"Calcium channel subunits"	1406	protein-coding gene	gene with protein product		602911					Standard	NM_006078		Approved	stargazin, MGC138502, MGC138504	uc003aps.2	Q9Y698	OTTHUMG00000030612	ENST00000300105.6:c.106T>A	chr22.hg19:g.37098516A>T	ENSP00000300105:p.Ser36Thr	174.0	0.0		162.0	32.0	NM_006078	Q2M1M1|Q5TGT3|Q9UGZ7	Missense_Mutation	SNP	ENST00000300105.6	hg19	CCDS13931.1	.	.	.	.	.	.	.	.	.	.	a	17.39	3.377764	0.61735	.	.	ENSG00000166862	ENST00000300105	D	0.90444	-2.67	4.77	4.77	0.60923	.	0.000000	0.85682	D	0.000000	D	0.89660	0.6779	N	0.25789	0.76	0.58432	D	0.999993	D	0.53885	0.963	D	0.67231	0.95	D	0.85636	0.1273	10	0.05525	T	0.97	-16.2417	14.3496	0.66691	1.0:0.0:0.0:0.0	.	36	Q9Y698	CCG2_HUMAN	T	36	ENSP00000300105:S36T	ENSP00000300105:S36T	S	-	1	0	CACNG2	35428462	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.764000	0.91719	1.778000	0.52293	0.446000	0.29264	TCC	.	.		0.483	CACNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075500.2			T	37098516	A	T	37098516	3	4	258	1	0	0	0	0	1	0	0	0	2559	304	11	4	881	4	CACNG2	22	37098516	Missense_Mutation	SNP	A	TCGA-EP-A3RK-01A-11D-A22F-10	13442317	37098516	14206050	44	36317										
IL2RB	3560	hgsc.bcm.edu	37	chr22	37524431	37524431	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0666666666666667	3	1	0.94	1.504	0.791578947368421	1	1	0	cttgcaaagaagggggcatcCtctcttcaccggccccactg	10	15	2	1			TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	g.chr22:37524431C>T	ENST00000216223.5	-	10	1559	c.1361G>A	c.(1360-1362)aGg>aAg	p.R454K		NM_000878.3	NP_000869.1	P14784	IL2RB_HUMAN	interleukin 2 receptor, beta	454					cytokine-mediated signaling pathway (GO:0019221)|interleukin-2-mediated signaling pathway (GO:0038110)|negative regulation of apoptotic process (GO:0043066)|protein complex assembly (GO:0006461)|signal transduction (GO:0007165)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	interleukin-2 binding (GO:0019976)|interleukin-2 receptor activity (GO:0004911)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(5)	23					Aldesleukin(DB00041)|Basiliximab(DB00074)|Daclizumab(DB00111)|Denileukin diftitox(DB00004)	AGGGGGCATCCTCTCTTCACC	0.662																																					p.R454K		Atlas-SNP	.											.	IL2RB	44	.	0			c.G1361A						.						11	13	13					22																	37524431		2081	4116	6197	SO:0001583	missense	3560	exon10			GGCATCCTCTCTT	M26062	CCDS13942.1	22q13	2011-02-15			ENSG00000100385	ENSG00000100385		"Interleukins and interleukin receptors", "CD molecules"	6009	protein-coding gene	gene with protein product		146710	"interleukin 15 receptor, beta"	IL15RB			Standard	NM_000878		Approved	CD122	uc003aqv.1	P14784	OTTHUMG00000150534	ENST00000216223.5:c.1361G>A	chr22.hg19:g.37524431C>T	ENSP00000216223:p.Arg454Lys	25.0	0.0		32.0	8.0	NM_000878	B2R765	Missense_Mutation	SNP	ENST00000216223.5	hg19	CCDS13942.1	.	.	.	.	.	.	.	.	.	.	C	8.146	0.786378	0.16189	.	.	ENSG00000100385	ENST00000216223	T	0.08193	3.12	4.55	-1.13	0.09775	.	6.192590	0.00974	N	0.003289	T	0.03651	0.0104	N	0.05510	-0.035	0.09310	N	1	B	0.11235	0.004	B	0.12156	0.007	T	0.33445	-0.9868	10	0.11794	T	0.64	-13.4104	0.3876	0.00405	0.1871:0.2786:0.1844:0.3498	.	454	P14784	IL2RB_HUMAN	K	454	ENSP00000216223:R454K	ENSP00000216223:R454K	R	-	2	0	IL2RB	35854377	0.000000	0.05858	0.025000	0.17156	0.078000	0.17371	-0.316000	0.08071	0.226000	0.20979	0.655000	0.94253	AGG	.	.		0.662	IL2RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318792.1			T	37524431	C	T	37524431	3	4	258	1	0	0	0	0	1	0	0	0	7696	681	24	3	298	3	IL2RB	22	37524431	Missense_Mutation	SNP	C	TCGA-EP-A3RK-01A-11D-A22F-10	425915	37524431	13780135	45	36318										
KLHL17	339451	hgsc.bcm.edu	37	chr1	899359	899359	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cgtcgctgccatgagcacccGgaggcgctatgtgcgagtgg	16	12	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:899359G>T	ENST00000338591.3	+	9	1522	c.1415G>T	c.(1414-1416)cGg>cTg	p.R472L	PLEKHN1_ENST00000379410.3_5'Flank|PLEKHN1_ENST00000379407.3_5'Flank|PLEKHN1_ENST00000379409.2_5'Flank	NM_198317.2	NP_938073.1	Q6TDP4	KLH17_HUMAN	kelch-like family member 17	472	Interaction with F-actin. {ECO:0000250}.				actin cytoskeleton organization (GO:0030036)|brain development (GO:0007420)|protein ubiquitination (GO:0016567)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|dendrite cytoplasm (GO:0032839)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	protein complex scaffold (GO:0032947)			central_nervous_system(1)|kidney(2)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.52e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.59e-23)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.000469)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		ATGAGCACCCGGAGGCGCTAT	0.682																																					p.R472L		Atlas-SNP	.											.	KLHL17	31	.	0			c.G1415T						.						83	89	87					1																	899359		2203	4298	6501	SO:0001583	missense	339451	exon9			GCACCCGGAGGCG	AY423763	CCDS30550.1	1p36	2013-01-30	2013-01-30		ENSG00000187961	ENSG00000187961		"Kelch-like", "BTB/POZ domain containing"	24023	protein-coding gene	gene with protein product	"actinfilin"		"kelch-like 17 (Drosophila)"			12063253	Standard	NM_198317		Approved		uc001aca.2	Q6TDP4	OTTHUMG00000040721	ENST00000338591.3:c.1415G>T	chr1.hg19:g.899359G>T	ENSP00000343930:p.Arg472Leu	109.0	0.0		36.0	4.0	NM_198317	Q5SV94	Missense_Mutation	SNP	ENST00000338591.3	hg19	CCDS30550.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.140149	0.77775	.	.	ENSG00000187961	ENST00000338591;ENST00000455747;ENST00000540863	T	0.78816	-1.21	5.5	4.6	0.57074	Galactose oxidase, beta-propeller (1);	0.000000	0.85682	D	0.000000	T	0.79986	0.4541	M	0.78801	2.425	0.80722	D	1	P	0.43169	0.8	B	0.42593	0.392	T	0.82633	-0.0361	10	0.66056	D	0.02	.	14.59	0.68356	0.0705:0.0:0.9295:0.0	.	472	Q6TDP4	KLH17_HUMAN	L	472;348;195	ENSP00000343930:R472L	ENSP00000343930:R472L	R	+	2	0	KLHL17	889222	1.000000	0.71417	1.000000	0.80357	0.484000	0.33280	3.778000	0.55371	1.338000	0.45544	-0.369000	0.07265	CGG	.	.		0.682	KLHL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097875.3	NM_198317		T	899359	G	T	899359	3	4	259	1	0	0	0	0	1	0	0	0	8381	1116	39	1	1449	1	KLHL17	1	899359	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10		899359	248351262	1	36319										
TAS1R1	80835	hgsc.bcm.edu	37	chr1	6630972	6630972	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	actggctttctccacaggtcTtgtagcttcaatgagcatgg	10	10	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:6630972T>C	ENST00000333172.6	+	2	388	c.195T>C	c.(193-195)tcT>tcC	p.S65S	TAS1R1_ENST00000351136.3_Silent_p.S65S|TAS1R1_ENST00000328191.4_Silent_p.S65S	NM_138697.3	NP_619642.2	Q7RTX1	TS1R1_HUMAN	taste receptor, type 1, member 1	65					detection of chemical stimulus involved in sensory perception of taste (GO:0050912)|sensory perception of umami taste (GO:0050917)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(13)|ovary(1)|skin(1)|urinary_tract(2)	29	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;8.73e-34)|all_epithelial(116;9.26e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Breast(487;0.000353)|Renal(390;0.0007)|Colorectal(325;0.00104)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443)		Colorectal(212;1.29e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00108)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0642)		TCCACAGGTCTTGTAGCTTCA	0.557																																					p.S65S		Atlas-SNP	.											.	TAS1R1	76	.	0			c.T195C						.						106	96	99					1																	6630972		2203	4300	6503	SO:0001819	synonymous_variant	80835	exon2			CAGGTCTTGTAGC		CCDS81.1, CCDS82.1	1p36.23	2012-08-22	2003-03-24		ENSG00000173662	ENSG00000173662		"Taste receptors / Type 1", "GPCR / Unclassified : Taste receptors"	14448	protein-coding gene	gene with protein product		606225	"G protein-coupled receptor 70"	GPR70			Standard	NM_138697		Approved	T1R1, TR1	uc001ant.3	Q7RTX1	OTTHUMG00000001441	ENST00000333172.6:c.195T>C	chr1.hg19:g.6630972T>C		85.0	0.0		66.0	4.0	NM_177540	B2RMX0|Q5SY22|Q5SY24|Q8NGZ7|Q8TDJ7|Q8TDJ8|Q8TDJ9|Q8TDK0	Silent	SNP	ENST00000333172.6	hg19	CCDS81.1																																																																																			.	.		0.557	TAS1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004211.1			C	6630972	T	C	6630972	2	2	259	1	0	0	0	0	0	0	0	1	15577	1596	56	2		2	TAS1R1	1	6630972	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	5731613	6630972	242619649	2	36320										
THAP3	90326	hgsc.bcm.edu	37	chr1	6692465	6692465	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tcccaggtcctccctgaggcGggggccggagaggacagtcc	16	14	0	2	rs146637042	byFrequency	TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:6692465G>T	ENST00000054650.4	+	5	506	c.348G>T	c.(346-348)gcG>gcT	p.A116A	THAP3_ENST00000377627.3_Silent_p.A123A|THAP3_ENST00000307896.6_Silent_p.A115A|DNAJC11_ENST00000465508.1_5'Flank	NM_001195753.1	NP_001182682.1	Q8WTV1	THAP3_HUMAN	THAP domain containing, apoptosis associated protein 3	116							DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|large_intestine(1)|prostate(1)	4	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;7.39e-28)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;1.29e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000513)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0642)		TCCCTGAGGCGGGGGCCGGAG	0.597																																					p.A123A		Atlas-SNP	.											.	THAP3	43	.	0			c.G369T						.						45	44	44					1																	6692465		2203	4300	6503	SO:0001819	synonymous_variant	90326	exon4			TGAGGCGGGGGCC	BC022081	CCDS86.1, CCDS55572.1, CCDS55573.1	1p36.1	2013-01-25			ENSG00000041988	ENSG00000041988		"THAP (C2CH-type zinc finger) domain containing"	20855	protein-coding gene	gene with protein product		612532				12575992	Standard	NM_138350		Approved		uc001aod.3	Q8WTV1	OTTHUMG00000001440	ENST00000054650.4:c.348G>T	chr1.hg19:g.6692465G>T		122.0	0.0		95.0	4.0	NM_138350	Q569K1|Q5TH66|Q5TH67|Q8N8T6|Q9BSC7|Q9Y3H2|Q9Y3H3	Silent	SNP	ENST00000054650.4	hg19	CCDS55572.1																																																																																			.	G|1.000;A|0.000		0.597	THAP3-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004203.1	NM_138350		T	6692465	G	T	6692465	2	4	259	1	0	0	0	0	0	0	0	1	15860	1103	39	1		1	THAP3	1	6692465	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	61493	6692465	242558156	3	36321										
NMNAT1	64802	hgsc.bcm.edu	37	chr1	10042608	10042608	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cacaaaaatccggagagcccTcagaaggggccagagcattc	11	12	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:10042608T>C	ENST00000377205.1	+	5	833	c.689T>C	c.(688-690)cTc>cCc	p.L230P	RP11-807G9.2_ENST00000413148.1_RNA	NM_022787.3	NP_073624.2	Q9HAN9	NMNA1_HUMAN	nicotinamide nucleotide adenylyltransferase 1	230					NAD biosynthetic process (GO:0009435)|NAD metabolic process (GO:0019674)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nicotinamide-nucleotide adenylyltransferase activity (GO:0000309)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)			large_intestine(2)|lung(2)|stomach(1)	5		all_lung(284;0.000407)|Renal(390;0.000469)|Lung NSC(185;0.000577)|Colorectal(325;0.0062)|Breast(348;0.00686)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.31e-08)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(185;0.00028)|BRCA - Breast invasive adenocarcinoma(304;0.00032)|KIRC - Kidney renal clear cell carcinoma(229;0.00101)|STAD - Stomach adenocarcinoma(132;0.00908)|READ - Rectum adenocarcinoma(331;0.0419)		CGGAGAGCCCTCAGAAGGGGC	0.453																																					p.L230P		Atlas-SNP	.											.	NMNAT1	18	.	0			c.T689C						.						73	72	72					1																	10042608		2203	4300	6503	SO:0001583	missense	64802	exon5			GAGCCCTCAGAAG	AF312734	CCDS108.1, CCDS72698.1	1p36.22	2014-01-28	2003-04-30	2003-05-02	ENSG00000173614	ENSG00000173614	2.7.7.1		17877	protein-coding gene	gene with protein product		608700	"nicotinamide nucleotide adenylyltransferase", "Leber congenital amaurosis 9", "Leber's congenital amaurosis 9"	LCA9		11248244, 11027696, 22842227	Standard	XR_244792		Approved	NMNAT, PNAT1	uc001aqp.3	Q9HAN9	OTTHUMG00000001799	ENST00000377205.1:c.689T>C	chr1.hg19:g.10042608T>C	ENSP00000366410:p.Leu230Pro	159.0	0.0		97.0	4.0	NM_022787	B1AN63|Q8TAE9|Q9H247|Q9H6B6	Missense_Mutation	SNP	ENST00000377205.1	hg19	CCDS108.1	.	.	.	.	.	.	.	.	.	.	T	19.66	3.869628	0.72065	.	.	ENSG00000173614	ENST00000377205	D	0.98455	-4.94	5.01	5.01	0.66863	Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.64402	D	0.000001	D	0.99239	0.9735	H	0.95504	3.68	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	D	0.98968	1.0800	10	0.87932	D	0	1.1088	15.0172	0.71594	0.0:0.0:0.0:1.0	.	230	Q9HAN9	NMNA1_HUMAN	P	230	ENSP00000366410:L230P	ENSP00000366410:L230P	L	+	2	0	NMNAT1	9965195	1.000000	0.71417	0.561000	0.28357	0.996000	0.88848	5.942000	0.70203	2.005000	0.58758	0.379000	0.24179	CTC	.	.		0.453	NMNAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005029.1			C	10042608	T	C	10042608	3	2	259	1	0	0	0	0	1	0	0	0	10507	1551	54	2	703	2	NMNAT1	1	10042608	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	3350143	10042608	239208013	4	36322										
UBE4B	10277	hgsc.bcm.edu	37	chr1	10205093	10205093	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gaagcgctgtaaaactcagcTtaaggtttgtatagctaagt	10	6	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:10205093T>A	ENST00000253251.8	+	17	2911	c.2072T>A	c.(2071-2073)cTt>cAt	p.L691H	UBE4B_ENST00000343090.6_Missense_Mutation_p.L820H|UBE4B_ENST00000377157.3_Missense_Mutation_p.L575H					ubiquitination factor E4B											NS(3)|breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(14)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	48		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		AAAACTCAGCTTAAGGTTTGT	0.393																																					p.L820H		Atlas-SNP	.											.	UBE4B	233	.	0			c.T2459A						.						63	62	62					1																	10205093		2203	4300	6503	SO:0001583	missense	10277	exon18			CTCAGCTTAAGGT	AF091093	CCDS110.1, CCDS41245.1	1p36.1	2013-01-28	2011-05-19		ENSG00000130939	ENSG00000130939		"U-box domain containing"	12500	protein-coding gene	gene with protein product		613565	"ubiquitination factor E4B (homologous to yeast UFD2)", "ubiquitination factor E4B (UFD2 homolog, yeast)"			9734811, 10089879	Standard	NM_006048		Approved	UBOX3, E4, UFD2, KIAA0684	uc001aqs.4	O95155	OTTHUMG00000001797	ENST00000253251.8:c.2072T>A	chr1.hg19:g.10205093T>A	ENSP00000253251:p.Leu691His	150.0	0.0		93.0	4.0	NM_001105562		Missense_Mutation	SNP	ENST00000253251.8	hg19	CCDS110.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.219400	0.79464	.	.	ENSG00000130939	ENST00000253251;ENST00000377157;ENST00000343090	T;T;T	0.52057	0.68;0.68;0.68	5.83	5.83	0.93111	Ubiquitin conjugation factor E4, core (1);	0.000000	0.85682	D	0.000000	T	0.56572	0.1994	M	0.82517	2.595	0.80722	D	1	B;B;B	0.33637	0.42;0.42;0.366	B;B;B	0.36186	0.188;0.219;0.118	T	0.61222	-0.7106	10	0.56958	D	0.05	-18.9981	16.1846	0.81942	0.0:0.0:0.0:1.0	.	691;820;691	A8K8S9;O95155;O95155-2	.;UBE4B_HUMAN;.	H	691;575;820	ENSP00000253251:L691H;ENSP00000366362:L575H;ENSP00000343001:L820H	ENSP00000253251:L691H	L	+	2	0	UBE4B	10127680	1.000000	0.71417	0.997000	0.53966	0.975000	0.68041	7.462000	0.80851	2.229000	0.72834	0.533000	0.62120	CTT	.	.		0.393	UBE4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005017.1	NM_006048		A	10205093	T	A	10205093	3	1	259	1	0	0	0	0	1	0	0	0	16898	1609	56	4	2529	4	UBE4B	1	10205093	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	162485	10205093	239045528	5	36323										
KAZ	23254	hgsc.bcm.edu	37	chr1	15430640	15430640	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cagtgggaagcacatcctccGgagacacctggcagaggaga	14	11	0	3	rs147449416		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:15430640G>A	ENST00000376030.2	+	13	2297	c.2003G>A	c.(2002-2004)cGg>cAg	p.R668Q		NM_201628.2	NP_963922.2	Q674X7	KAZRN_HUMAN	kazrin, periplakin interacting protein	668	SAM 3. {ECO:0000255|PROSITE- ProRule:PRU00184}.				keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(1)|prostate(2)	25						CACATCCTCCGGAGACACCTG	0.632																																					p.R668Q		Atlas-SNP	.											.	KAZN	57	.	0			c.G2003A						.	G	GLN/ARG	0,4406		0,0,2203	47	37	40		2003	5.7	1	1	dbSNP_134	40	1,8599		0,1,4299	no	missense	KAZN	NM_201628.2	43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	668/776	15430640	1,13005	2203	4300	6503	SO:0001583	missense	23254	exon13			TCCTCCGGAGACA	AY505119	CCDS30604.1, CCDS41267.1, CCDS152.2, CCDS41268.1	1p36.21	2014-02-12	2011-01-31		ENSG00000189337	ENSG00000189337		"Sterile alpha motif (SAM) domain containing"	29173	protein-coding gene	gene with protein product						15337775, 18840647	Standard	NM_015209		Approved	KIAA1026, KAZRIN, FLJ43806	uc001avm.4	Q674X7	OTTHUMG00000002042	ENST00000376030.2:c.2003G>A	chr1.hg19:g.15430640G>A	ENSP00000365198:p.Arg668Gln	118.0	0.0		73.0	4.0	NM_201628	B0QYQ0|B1AK78|Q5TGF1|Q674X4|Q674X6|Q6ZUD1|Q8IYN7|Q8N409|Q9UIL2|Q9UPX4	Missense_Mutation	SNP	ENST00000376030.2	hg19	CCDS152.2	.	.	.	.	.	.	.	.	.	.	G	32	5.130480	0.94473	0.0	1.16E-4	ENSG00000189337	ENST00000376030	T	0.38887	1.11	5.67	5.67	0.87782	Sterile alpha motif domain (1);Sterile alpha motif/pointed domain (1);	0.195189	0.32819	N	0.005614	T	0.63640	0.2528	M	0.87269	2.87	0.80722	D	1	D	0.69078	0.997	P	0.55785	0.784	T	0.70766	-0.4783	10	0.87932	D	0	-33.8907	15.2647	0.73651	0.0:0.0:1.0:0.0	.	668	Q674X7	KAZRN_HUMAN	Q	668	ENSP00000365198:R668Q	ENSP00000365198:R668Q	R	+	2	0	KAZN	15303227	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	4.598000	0.61069	2.671000	0.90904	0.585000	0.79938	CGG	.	G|1.000;A|0.000		0.632	KAZN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005690.2	NM_001017999		A	15430640	G	A	15430640	3	1	259	1	0	0	0	0	1	0	0	0	7997	1116	39	1	2309	1	KAZ	1	15430640	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	5225547	15430640	233819981	6	36324										
SPEN	23013	hgsc.bcm.edu	37	chr1	16261624	16261624	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aacaagaagcttgctgacccCgtcacccttaaaatcgagac	7	13	1	3	rs151181793		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:16261624C>A	ENST00000375759.3	+	11	9093	c.8889C>A	c.(8887-8889)ccC>ccA	p.P2963P		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	2963					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		TTGCTGACCCCGTCACCCTTA	0.592																																					p.P2963P		Atlas-SNP	.											SPEN,caecum,carcinoma,0,1	SPEN	374	.	0			c.C8889A						.						60	64	63					1																	16261624		2203	4300	6503	SO:0001819	synonymous_variant	23013	exon11			TGACCCCGTCACC		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"RNA binding motif (RRM) containing"	17575	protein-coding gene	gene with protein product		613484	"SPEN homolog, transcriptional regulator (Drosophila)", "spen homolog, transcriptional regulator (Drosophila)"			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.8889C>A	chr1.hg19:g.16261624C>A		196.0	0.0		80.0	4.0	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Silent	SNP	ENST00000375759.3	hg19	CCDS164.1																																																																																			.	C|0.998;T|0.002		0.592	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		A	16261624	C	A	16261624	2	1	259	1	0	0	0	0	0	0	0	1	15053	639	23	1		1	SPEN	1	16261624	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	830984	16261624	232988997	7	36325										
CLCNKA	1187	hgsc.bcm.edu	37	chr1	16351303	16351303	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tggggacagccacctgctccGgtatctttcctggactgtgt	12	12	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:16351303G>T	ENST00000331433.4	+	4	294	c.275G>T	c.(274-276)cGg>cTg	p.R92L	CLCNKA_ENST00000375692.1_Missense_Mutation_p.R92L|CLCNKA_ENST00000420078.1_Missense_Mutation_p.R92L|CLCNKA_ENST00000439316.2_Intron|CLCNKA_ENST00000464764.1_Intron			P51800	CLCKA_HUMAN	chloride channel, voltage-sensitive Ka	92					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|metal ion binding (GO:0046872)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(1)	19		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	Niflumic Acid(DB04552)	CACCTGCTCCGGTATCTTTCC	0.637																																					p.R92L		Atlas-SNP	.											.	CLCNKA	56	.	0			c.G275T						.						134	101	112					1																	16351303		2203	4300	6503	SO:0001583	missense	1187	exon4			TGCTCCGGTATCT		CCDS167.1, CCDS41269.1, CCDS57973.1	1p36	2012-09-26	2012-02-23		ENSG00000186510	ENSG00000186510		"Ion channels / Chloride channels : Voltage-sensitive"	2026	protein-coding gene	gene with protein product		602024	"chloride channel Ka"			8544406	Standard	NM_004070		Approved	hClC-Ka	uc001axu.3	P51800	OTTHUMG00000009529	ENST00000331433.4:c.275G>T	chr1.hg19:g.16351303G>T	ENSP00000332771:p.Arg92Leu	241.0	0.0		124.0	6.0	NM_004070	B4DPD3|E7EPH6|Q5T5P8|Q5T5Q4|Q7Z6D1|Q86VT1	Missense_Mutation	SNP	ENST00000331433.4	hg19	CCDS167.1	.	.	.	.	.	.	.	.	.	.	G	17.13	3.311349	0.60414	.	.	ENSG00000186510	ENST00000375692;ENST00000420078;ENST00000331433	D;D;D	0.92752	-3.1;-3.1;-3.1	4.0	4.0	0.46444	Chloride channel, core (2);	0.131851	0.51477	D	0.000085	D	0.91389	0.7283	M	0.75447	2.3	0.80722	D	1	B;B	0.28512	0.214;0.214	B;B	0.37304	0.198;0.246	D	0.90447	0.4436	10	0.66056	D	0.02	.	7.7785	0.29051	0.1153:0.0:0.8847:0.0	.	92;92	Q5T5Q4;P51800	.;CLCKA_HUMAN	L	92	ENSP00000364844:R92L;ENSP00000410353:R92L;ENSP00000332771:R92L	ENSP00000332771:R92L	R	+	2	0	CLCNKA	16223890	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.392000	0.66272	2.220000	0.72140	0.462000	0.41574	CGG	.	.		0.637	CLCNKA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026326.1			T	16351303	G	T	16351303	3	4	259	1	0	0	0	0	1	0	0	0	3471	1116	39	1	285	1	CLCNKA	1	16351303	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	89679	16351303	232899318	8	36326										
ACTL8	81569	hgsc.bcm.edu	37	chr1	18152877	18152877	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgatgggggatcacgtctccTccaccaaggccacagtctgg	12	13	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:18152877T>C	ENST00000375406.1	+	3	1180	c.964T>C	c.(964-966)Tcc>Ccc	p.S322P		NM_030812.2	NP_110439.2	Q9H568	ACTL8_HUMAN	actin-like 8	322					epithelial cell differentiation (GO:0030855)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(10)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	28		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00186)|all_lung(284;0.0054)|Lung NSC(340;0.00566)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;6.43e-06)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.00652)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)		TCACGTCTCCTCCACCAAGGC	0.592											OREG0013157	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S322P		Atlas-SNP	.											.	ACTL8	58	.	0			c.T964C						.						75	81	79					1																	18152877		2203	4300	6503	SO:0001583	missense	81569	exon3			GTCTCCTCCACCA	AK057339	CCDS183.1	1p36.2-p35	2009-03-25			ENSG00000117148	ENSG00000117148			24018	protein-coding gene	gene with protein product	"cancer/testis antigen 57"						Standard	NM_030812		Approved	CT57	uc001bat.3	Q9H568	OTTHUMG00000002512	ENST00000375406.1:c.964T>C	chr1.hg19:g.18152877T>C	ENSP00000364555:p.Ser322Pro	199.0	0.0	723	100.0	4.0	NM_030812	Q13104|Q96M75	Missense_Mutation	SNP	ENST00000375406.1	hg19	CCDS183.1	.	.	.	.	.	.	.	.	.	.	T	11.90	1.777503	0.31411	.	.	ENSG00000117148	ENST00000375406	D	0.94862	-3.54	4.88	-8.75	0.00834	.	0.749624	0.11425	N	0.565373	D	0.87462	0.6183	L	0.48362	1.52	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.73714	-0.3896	10	0.87932	D	0	-4.8049	3.4932	0.07645	0.2065:0.4713:0.1381:0.1841	.	322	Q9H568	ACTL8_HUMAN	P	322	ENSP00000364555:S322P	ENSP00000364555:S322P	S	+	1	0	ACTL8	18025464	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-0.004000	0.12878	-1.235000	0.02545	0.533000	0.62120	TCC	.	.		0.592	ACTL8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007143.1	NM_030812		C	18152877	T	C	18152877	3	2	259	1	0	0	0	0	1	0	0	0	202	1551	54	2	970	2	ACTL8	1	18152877	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1801574	18152877	231097744	9	36327										
ZNF436	80818	hgsc.bcm.edu	37	chr1	23688528	23688528	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctgaaactcttctcacattcGgtacattcataaggtttctc	5	11	4	1	rs144729139		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:23688528G>T	ENST00000314011.4	-	4	1483	c.1347C>A	c.(1345-1347)acC>acA	p.T449T	ZNF436_ENST00000374608.3_Silent_p.T449T	NM_001077195.1	NP_001070663.1	Q9C0F3	ZN436_HUMAN	zinc finger protein 436	449					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T449T(1)		breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	19		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;5.97e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000977)|KIRC - Kidney renal clear cell carcinoma(1967;0.00336)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		TCTCACATTCGGTACATTCAT	0.433																																					p.T449T		Atlas-SNP	.											.	ZNF436	49	.	1	Substitution - coding silent(1)	lung(1)	c.C1347A						.						89	93	91					1																	23688528		2203	4300	6503	SO:0001819	synonymous_variant	80818	exon4			ACATTCGGTACAT	AB051497	CCDS233.1	1p36	2013-01-08			ENSG00000125945	ENSG00000125945		"Zinc fingers, C2H2-type", "-"	20814	protein-coding gene	gene with protein product		611703				11214970	Standard	NM_001077195		Approved	KIAA1710, Zfp46	uc001bgt.3	Q9C0F3	OTTHUMG00000003232	ENST00000314011.4:c.1347C>A	chr1.hg19:g.23688528G>T		173.0	0.0		88.0	4.0	NM_001077195	Q658I9	Silent	SNP	ENST00000314011.4	hg19	CCDS233.1																																																																																			.	G|1.000;A|0.000		0.433	ZNF436-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008908.1	NM_030634		T	23688528	G	T	23688528	2	4	259	1	0	0	0	0	0	0	0	1	17924	1103	39	1		1	ZNF436	1	23688528	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	5535651	23688528	225562093	10	36328										
ASAP3	55616	hgsc.bcm.edu	37	chr1	23762411	23762411	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	caaaggcctccagtaccgacAggaggtccctgttgcaaatg	11	12	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:23762411A>G	ENST00000336689.3	-	17	1726	c.1682T>C	c.(1681-1683)cTg>cCg	p.L561P	ASAP3_ENST00000437606.2_Missense_Mutation_p.L552P|ASAP3_ENST00000495646.1_Missense_Mutation_p.L65P	NM_017707.3	NP_060177.2	Q8TDY4	ASAP3_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 3	561					cell migration (GO:0016477)|positive regulation of ARF GTPase activity (GO:0032850)|regulation of stress fiber assembly (GO:0051492)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	24						CAGTACCGACAGGAGGTCCCT	0.577																																					p.L561P		Atlas-SNP	.											.	ASAP3	65	.	0			c.T1682C						.						110	112	112					1																	23762411		2203	4300	6503	SO:0001583	missense	55616	exon17			ACCGACAGGAGGT	AK000206	CCDS235.1, CCDS44087.1	1p36.13	2013-01-10	2008-10-09	2008-09-22	ENSG00000088280	ENSG00000088280		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	14987	protein-coding gene	gene with protein product	"centaurin, beta 6"		"development and differentiation enhancing factor-like 1"	DDEFL1		14654939	Standard	NM_017707		Approved	FLJ20199, UPLC1, CENTB6	uc001bha.2	Q8TDY4	OTTHUMG00000003234	ENST00000336689.3:c.1682T>C	chr1.hg19:g.23762411A>G	ENSP00000338769:p.Leu561Pro	159.0	0.0		79.0	4.0	NM_017707	B3KRW0|B4DHH4|Q6P9F4|Q86UY1|Q9NXK2	Missense_Mutation	SNP	ENST00000336689.3	hg19	CCDS235.1	.	.	.	.	.	.	.	.	.	.	A	9.001	0.980135	0.18812	.	.	ENSG00000088280	ENST00000538685;ENST00000495646;ENST00000336689;ENST00000437606	T;T;T	0.54279	1.93;0.59;0.58	3.88	2.76	0.32466	Ankyrin repeat-containing domain (1);	0.302991	0.27168	N	0.020605	T	0.31949	0.0813	N	0.14661	0.345	0.21861	N	0.999509	B;B;B;B	0.24823	0.059;0.112;0.006;0.033	B;B;B;B	0.28305	0.018;0.056;0.088;0.021	T	0.17471	-1.0368	10	0.51188	T	0.08	.	6.1593	0.20356	0.7955:0.0:0.2045:0.0	.	552;430;84;561	Q8TDY4-3;B4DRP2;Q9NXH7;Q8TDY4	.;.;.;ASAP3_HUMAN	P	84;65;561;552	ENSP00000436150:L65P;ENSP00000338769:L561P;ENSP00000408826:L552P	ENSP00000338769:L561P	L	-	2	0	ASAP3	23634998	0.922000	0.31269	0.925000	0.36789	0.716000	0.41182	3.953000	0.56699	1.759000	0.51996	0.363000	0.22086	CTG	.	.		0.577	ASAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008916.2	NM_017707		G	23762411	A	G	23762411	3	3	259	1	0	0	0	0	1	0	0	0	1012	188	7	2	1065	2	ASAP3	1	23762411	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	73883	23762411	225488210	11	36329										
RPL11	6135	hgsc.bcm.edu	37	chr1	24022327	24022327	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tcagcatcgcagacaagaagCgcaggacaggctgcattggg	14	10	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:24022327C>T	ENST00000374550.3	+	5	481	c.436C>T	c.(436-438)Cgc>Tgc	p.R146C	RPL11_ENST00000482370.1_3'UTR	NM_000975.3|NM_001199802.1	NP_000966.2|NP_001186731.1	P62913	RL11_HUMAN	ribosomal protein L11	146					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein localization to nucleus (GO:0034504)|protein targeting (GO:0006605)|ribosomal large subunit biogenesis (GO:0042273)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(2)	6		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.13e-24)|Colorectal(126;5.06e-08)|COAD - Colon adenocarcinoma(152;2.92e-06)|GBM - Glioblastoma multiforme(114;4.4e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|KIRC - Kidney renal clear cell carcinoma(1967;0.00322)|STAD - Stomach adenocarcinoma(196;0.0124)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0837)|LUSC - Lung squamous cell carcinoma(448;0.185)		AGACAAGAAGCGCAGGACAGG	0.527																																					p.R146C		Atlas-SNP	.											RPL11,NS,carcinoma,-1,1	RPL11	21	.	0			c.C436T						.						70	61	64					1																	24022327		2202	4299	6501	SO:0001583	missense	6135	exon5			AAGAAGCGCAGGA	L05092	CCDS238.1	1p36.1-p35	2011-04-06			ENSG00000142676	ENSG00000142676		"L ribosomal proteins"	10301	protein-coding gene	gene with protein product		604175				9582194, 10343117	Standard	NM_000975		Approved	L11	uc001bhk.3	P62913	OTTHUMG00000002926	ENST00000374550.3:c.436C>T	chr1.hg19:g.24022327C>T	ENSP00000363676:p.Arg146Cys	121.0	0.0		73.0	3.0	NM_000975	P25121|P39026|Q8TDH2|Q9Y674	Missense_Mutation	SNP	ENST00000374550.3	hg19	CCDS238.1	.	.	.	.	.	.	.	.	.	.	C	19.55	3.848686	0.71603	.	.	ENSG00000142676	ENST00000374550;ENST00000458455	T;T	0.78481	-1.18;-1.18	5.7	5.7	0.88788	Ribosomal protein L5 domain (2);	0.000000	0.85682	D	0.000000	D	0.84969	0.5590	M	0.91920	3.255	0.80722	D	1	B;B	0.17667	0.023;0.018	B;B	0.26969	0.072;0.075	T	0.83316	-0.0020	10	0.87932	D	0	-6.3587	19.819	0.96583	0.0:1.0:0.0:0.0	.	145;146	P62913-2;P62913	.;RL11_HUMAN	C	146;144	ENSP00000363676:R146C;ENSP00000398888:R144C	ENSP00000363676:R146C	R	+	1	0	RPL11	23894914	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	4.542000	0.60677	2.688000	0.91661	0.591000	0.81541	CGC	.	.		0.527	RPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008168.1	NM_000975		T	24022327	C	T	24022327	3	4	259	1	0	0	0	0	1	0	0	0	13572	768	27	1	454	1	RPL11	1	24022327	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	259916	24022327	225228294	12	36330										
PDIK1L	149420	hgsc.bcm.edu	37	chr1	26448825	26448825	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acattcatagacacagagacAaagaaggaactcttggggag	11	7	2	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:26448825A>G	ENST00000374271.4	+	4	1070	c.783A>G	c.(781-783)acA>acG	p.T261T	PDIK1L_ENST00000374269.1_Silent_p.T261T	NM_001243532.1|NM_001243533.1|NM_152835.4	NP_001230461.1|NP_001230462.1|NP_690048.1	Q8N165	PDK1L_HUMAN	PDLIM1 interacting kinase 1 like	261	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	7		Colorectal(325;0.000147)|Renal(390;0.00211)|Lung NSC(340;0.00239)|all_lung(284;0.00366)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;7.32e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000735)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.015)|READ - Rectum adenocarcinoma(331;0.0649)		ACACAGAGACAAAGAAGGAAC	0.438																																					p.T261T		Atlas-SNP	.											.	PDIK1L	19	.	0			c.A783G						.						97	100	99					1																	26448825		2203	4300	6503	SO:0001819	synonymous_variant	149420	exon3			AGAGACAAAGAAG	AF411102	CCDS274.1	1p35.1	2008-02-05			ENSG00000175087	ENSG00000175087			18981	protein-coding gene	gene with protein product		610785				14631099	Standard	NM_152835		Approved	CLIK1L	uc009vsb.3	Q8N165	OTTHUMG00000007511	ENST00000374271.4:c.783A>G	chr1.hg19:g.26448825A>G		168.0	0.0		92.0	4.0	NM_001243532	B2R777|D3DPK2|Q5T2I0|Q8NDB3	Silent	SNP	ENST00000374271.4	hg19	CCDS274.1																																																																																			.	.		0.438	PDIK1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019752.1	NM_152835		G	26448825	A	G	26448825	2	3	259	1	0	0	0	0	0	0	0	1	11682	117	5	2		2	PDIK1L	1	26448825	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2426498	26448825	222801796	13	36331										
GPATCH3	63906	hgsc.bcm.edu	37	chr1	27219162	27219162	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gggcacagtgctaactcaccTtggtgtggcgctcaaaggtg	14	10	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:27219162T>C	ENST00000361720.5	-	5	1255	c.1232A>G	c.(1231-1233)aAg>aGg	p.K411R	GPN2_ENST00000374135.4_5'Flank	NM_022078.2	NP_071361.2	Q96I76	GPTC3_HUMAN	G patch domain containing 3	411	G-patch. {ECO:0000255|PROSITE- ProRule:PRU00092}.						nucleic acid binding (GO:0003676)			endometrium(2)|large_intestine(1)|lung(11)|skin(1)	15		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;3.97e-51)|OV - Ovarian serous cystadenocarcinoma(117;9.55e-30)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000513)|STAD - Stomach adenocarcinoma(196;0.000595)|KIRC - Kidney renal clear cell carcinoma(1967;0.00072)|READ - Rectum adenocarcinoma(331;0.0419)		CTAACTCACCTTGGTGTGGCG	0.562																																					p.K411R		Atlas-SNP	.											.	GPATCH3	30	.	0			c.A1232G						.						159	152	154					1																	27219162		2203	4300	6503	SO:0001630	splice_region_variant	63906	exon5			CTCACCTTGGTGT	BC007767	CCDS290.1	1p35.3-p35.1	2013-01-28		2006-12-13	ENSG00000198746	ENSG00000198746		"G patch domain containing"	25720	protein-coding gene	gene with protein product				GPATC3			Standard	NM_022078		Approved	FLJ12455	uc001bne.3	Q96I76	OTTHUMG00000004229	ENST00000361720.5:c.1233+1A>G	chr1.hg19:g.27219162T>C		163.0	0.0		94.0	4.0	NM_022078	Q5JYH2|Q8NDJ2|Q9H9Z3	Missense_Mutation	SNP	ENST00000361720.5	hg19	CCDS290.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	21.5|21.5	4.154835|4.154835	0.78114|0.78114	.|.	.|.	ENSG00000198746|ENSG00000198746	ENST00000361720;ENST00000536641;ENST00000374122;ENST00000450844|ENST00000445019	T;T|.	0.32753|.	1.44;1.44|.	5.18|5.18	5.18|5.18	0.71444|0.71444	D111/G-patch (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.54902|0.54902	0.1887|0.1887	L|L	0.28400|0.28400	0.85|0.85	0.80722|0.80722	D|D	1|1	D|.	0.62365|.	0.991|.	P|.	0.62649|.	0.905|.	T|T	0.51505|0.51505	-0.8697|-0.8697	10|5	0.35671|.	T|.	0.21|.	-32.4964|-32.4964	15.1942|15.1942	0.73071|0.73071	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	411|.	Q96I76|.	GPTC3_HUMAN|.	R|G	411;393;222;29|61	ENSP00000354645:K411R;ENSP00000399036:K29R|.	ENSP00000354645:K411R|.	K|R	-|-	2|1	0|2	GPATCH3|GPATCH3	27091749|27091749	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.895000|0.895000	0.52256|0.52256	6.886000|6.886000	0.75611|0.75611	2.172000|2.172000	0.68678|0.68678	0.533000|0.533000	0.62120|0.62120	AAG|AGG	.	.		0.562	GPATCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012181.1	NM_022078	Missense_Mutation	C	27219162	T	C	27219162	5	2	259	1	0	0	0	0	0	0	1	0	6600	1623	56	2	357	2	GPATCH3	1	27219162	Splice_Site	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	770337	27219162	222031459	14	36332										
GPATCH3	63906	hgsc.bcm.edu	37	chr1	27226824	27226824	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agccaccgccgcgctcttctCggaactggctaaaatagctc	9	15	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:27226824C>A	ENST00000361720.5	-	1	133	c.110G>T	c.(109-111)cGa>cTa	p.R37L		NM_022078.2	NP_071361.2	Q96I76	GPTC3_HUMAN	G patch domain containing 3	37							nucleic acid binding (GO:0003676)			endometrium(2)|large_intestine(1)|lung(11)|skin(1)	15		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;3.97e-51)|OV - Ovarian serous cystadenocarcinoma(117;9.55e-30)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000513)|STAD - Stomach adenocarcinoma(196;0.000595)|KIRC - Kidney renal clear cell carcinoma(1967;0.00072)|READ - Rectum adenocarcinoma(331;0.0419)		GCGCTCTTCTCGGAACTGGCT	0.632																																					p.R37L		Atlas-SNP	.											.	GPATCH3	30	.	0			c.G110T						.						33	34	33					1																	27226824		2203	4300	6503	SO:0001583	missense	63906	exon1			TCTTCTCGGAACT	BC007767	CCDS290.1	1p35.3-p35.1	2013-01-28		2006-12-13	ENSG00000198746	ENSG00000198746		"G patch domain containing"	25720	protein-coding gene	gene with protein product				GPATC3			Standard	NM_022078		Approved	FLJ12455	uc001bne.3	Q96I76	OTTHUMG00000004229	ENST00000361720.5:c.110G>T	chr1.hg19:g.27226824C>A	ENSP00000354645:p.Arg37Leu	129.0	0.0		46.0	4.0	NM_022078	Q5JYH2|Q8NDJ2|Q9H9Z3	Missense_Mutation	SNP	ENST00000361720.5	hg19	CCDS290.1	.	.	.	.	.	.	.	.	.	.	C	15.39	2.818395	0.50633	.	.	ENSG00000198746	ENST00000361720;ENST00000536641	T	0.27402	1.67	5.5	5.5	0.81552	.	0.193744	0.45361	D	0.000371	T	0.20820	0.0501	L	0.28274	0.84	0.80722	D	1	B	0.10296	0.003	B	0.06405	0.002	T	0.05971	-1.0853	10	0.19590	T	0.45	-17.9273	11.8439	0.52371	0.2156:0.7844:0.0:0.0	.	37	Q96I76	GPTC3_HUMAN	L	37	ENSP00000354645:R37L	ENSP00000354645:R37L	R	-	2	0	GPATCH3	27099411	1.000000	0.71417	0.995000	0.50966	0.879000	0.50718	3.382000	0.52463	2.854000	0.98071	0.655000	0.94253	CGA	.	.		0.632	GPATCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012181.1	NM_022078		A	27226824	C	A	27226824	3	1	259	1	0	0	0	0	1	0	0	0	6600	884	31	1	1495	1	GPATCH3	1	27226824	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	7662	27226824	222023797	15	36333										
PTPRU	10076	hgsc.bcm.edu	37	chr1	29638034	29638034	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggagcactgttccagcatcgTcatgatcaccaagctggtcg	11	12	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:29638034T>C	ENST00000345512.3	+	21	3083	c.2954T>C	c.(2953-2955)gTc>gCc	p.V985A	PTPRU_ENST00000428026.2_Missense_Mutation_p.V975A|PTPRU_ENST00000373779.3_Missense_Mutation_p.V975A|PTPRU_ENST00000460170.2_Missense_Mutation_p.V981A|PTPRU_ENST00000356870.3_Missense_Mutation_p.V981A|PTPRU_ENST00000415600.2_3'UTR|PTPRU_ENST00000323874.8_Missense_Mutation_p.V981A	NM_005704.4	NP_005695.3	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	985	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|homotypic cell-cell adhesion (GO:0034109)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|organ regeneration (GO:0031100)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|response to glucocorticoid (GO:0051384)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(26)|ovary(1)|prostate(3)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	79		Colorectal(325;0.000399)|Lung NSC(340;0.00953)|all_lung(284;0.0112)|Breast(348;0.0126)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;6.99e-07)|COAD - Colon adenocarcinoma(152;3.18e-05)|STAD - Stomach adenocarcinoma(196;0.0234)|READ - Rectum adenocarcinoma(331;0.0686)|BRCA - Breast invasive adenocarcinoma(304;0.0871)		TCCAGCATCGTCATGATCACC	0.637																																					p.V985A		Atlas-SNP	.											.	PTPRU	374	.	0			c.T2954C						.						117	101	106					1																	29638034		2203	4300	6503	SO:0001583	missense	10076	exon21			GCATCGTCATGAT	U71075	CCDS334.1, CCDS335.1, CCDS44098.1, CCDS44098.2, CCDS53290.1	1p35.3	2013-02-11			ENSG00000060656	ENSG00000060656		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9683	protein-coding gene	gene with protein product	"pi R-PTP-Psi"	602454				8700514, 9434160	Standard	NM_133178		Approved	PTPRO, hPTP-J, PCP-2, FMI, PTP	uc001bru.3	Q92729	OTTHUMG00000003699	ENST00000345512.3:c.2954T>C	chr1.hg19:g.29638034T>C	ENSP00000334941:p.Val985Ala	178.0	0.0		89.0	4.0	NM_005704	A6H8L1|O00197|P78399|Q59HA4|Q5SYU4|Q5SYU5|Q92735|Q92850	Missense_Mutation	SNP	ENST00000345512.3	hg19	CCDS334.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.592865	0.86953	.	.	ENSG00000060656	ENST00000345512;ENST00000373779;ENST00000356870;ENST00000323874;ENST00000428026;ENST00000460170	T;T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79;0.79	4.76	4.76	0.60689	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.64402	D	0.000001	T	0.65821	0.2728	M	0.90145	3.09	0.80722	D	1	P;P;P;P;P	0.42010	0.725;0.725;0.725;0.768;0.768	B;P;B;P;P	0.49853	0.26;0.49;0.404;0.624;0.624	T	0.72320	-0.4329	9	.	.	.	.	13.9164	0.63899	0.0:0.0:0.0:1.0	.	975;981;975;981;985	Q92729-3;Q92729-4;Q92729-2;E9PH42;Q92729	.;.;.;.;PTPRU_HUMAN	A	985;975;981;981;975;981	ENSP00000334941:V985A;ENSP00000362884:V975A;ENSP00000349333:V981A;ENSP00000314987:V981A;ENSP00000392332:V975A;ENSP00000432906:V981A	.	V	+	2	0	PTPRU	29510621	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.864000	0.87037	2.133000	0.65898	0.533000	0.62120	GTC	.	.		0.637	PTPRU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010447.1			C	29638034	T	C	29638034	3	2	259	1	0	0	0	0	1	0	0	0	12828	1667	58	2	3058	2	PTPRU	1	29638034	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	2411210	29638034	219612587	16	36334										
IQCC	55721	hgsc.bcm.edu	37	chr1	32672950	32672950	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctgtgagagggaccagtcacAaccaagcgcaccactggagg	13	12	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:32672950A>G	ENST00000291358.6	+	5	689	c.668A>G	c.(667-669)cAa>cGa	p.Q223R	DCDC2B_ENST00000409358.1_5'Flank|IQCC_ENST00000537469.1_Missense_Mutation_p.Q303R|RP4-622L5.7_ENST00000373604.4_RNA|RP4-622L5.7_ENST00000421616.1_RNA	NM_018134.2	NP_060604.2	Q4KMZ1	IQCC_HUMAN	IQ motif containing C	223										endometrium(4)|large_intestine(1)|lung(3)|ovary(4)|skin(2)|urinary_tract(1)	15		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				GACCAGTCACAACCAAGCGCA	0.567																																					p.Q303R		Atlas-SNP	.											.	IQCC	46	.	0			c.A908G						.						74	71	72					1																	32672950		2203	4300	6503	SO:0001583	missense	55721	exon5			AGTCACAACCAAG	AL049795	CCDS355.1, CCDS53293.1	1p36.11-p34.2	2008-02-05			ENSG00000160051	ENSG00000160051			25545	protein-coding gene	gene with protein product							Standard	NM_018134		Approved	FLJ10547	uc001bum.2	Q4KMZ1	OTTHUMG00000005739	ENST00000291358.6:c.668A>G	chr1.hg19:g.32672950A>G	ENSP00000291358:p.Gln223Arg	185.0	0.0		110.0	5.0	NM_001160042	F5H7T8|Q4KMS3|Q4KMZ5|Q53FL2|Q5TFJ8|Q9NVS3	Missense_Mutation	SNP	ENST00000291358.6	hg19	CCDS355.1	.	.	.	.	.	.	.	.	.	.	A	11.38	1.622522	0.28889	.	.	ENSG00000160051	ENST00000537469;ENST00000291358	T;T	0.25250	1.81;1.81	3.64	2.5	0.30297	.	0.737321	0.11771	N	0.531108	T	0.18635	0.0447	L	0.32530	0.975	0.09310	N	1	B;B	0.21225	0.053;0.053	B;B	0.20767	0.031;0.018	T	0.22347	-1.0219	10	0.62326	D	0.03	0.0351	5.9218	0.19086	0.8796:0.0:0.1204:0.0	.	303;223	F5H7T8;Q4KMZ1	.;IQCC_HUMAN	R	303;223	ENSP00000442291:Q303R;ENSP00000291358:Q223R	ENSP00000291358:Q223R	Q	+	2	0	IQCC	32445537	0.026000	0.19158	0.032000	0.17829	0.013000	0.08279	1.489000	0.35562	0.752000	0.32923	0.459000	0.35465	CAA	.	.		0.567	IQCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015731.3	NM_018134		G	32672950	A	G	32672950	3	3	259	1	0	0	0	0	1	0	0	0	7813	130	5	2	926	2	IQCC	1	32672950	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	3034916	32672950	216577671	17	36335										
BSDC1	55108	hgsc.bcm.edu	37	chr1	32834115	32834115	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cagtcatgtccaagtcaaagTctttctcccagtcctcactg	6	14	5	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:32834115T>C	ENST00000455895.2	-	10	1226	c.1193A>G	c.(1192-1194)gAc>gGc	p.D398G	BSDC1_ENST00000419121.2_Missense_Mutation_p.D342G|BSDC1_ENST00000413080.1_Missense_Mutation_p.D337G|BSDC1_ENST00000341071.7_Missense_Mutation_p.D415G|BSDC1_ENST00000463967.1_5'UTR|BSDC1_ENST00000526031.1_Missense_Mutation_p.D303G|BSDC1_ENST00000446293.2_Missense_Mutation_p.D415G	NM_001143888.1|NM_018045.6	NP_001137360.1|NP_060515.3	Q9NW68	BSDC1_HUMAN	BSD domain containing 1	398										breast(1)|central_nervous_system(2)|kidney(1)|lung(6)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	17		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				CAAGTCAAAGTCTTTCTCCCA	0.582																																					p.D415G		Atlas-SNP	.											.	BSDC1	52	.	0			c.A1244G						.						116	102	107					1																	32834115		2203	4300	6503	SO:0001583	missense	55108	exon10			TCAAAGTCTTTCT	BX641056	CCDS363.2, CCDS44101.1, CCDS44102.1, CCDS44103.1, CCDS72752.1	1p35.1	2008-02-05			ENSG00000160058	ENSG00000160058			25501	protein-coding gene	gene with protein product						12477932	Standard	XM_005270985		Approved	FLJ10276, RP4-811H24.7	uc010ohg.2	Q9NW68	OTTHUMG00000007588	ENST00000455895.2:c.1193A>G	chr1.hg19:g.32834115T>C	ENSP00000412173:p.Asp398Gly	151.0	0.0		94.0	4.0	NM_001143888	B4DMS7|B4DTI7|B4DTP7|B4E2X8|Q49AT8|Q68DY6|Q6IAA3|Q6MZK1|Q6UXS1|Q9HAL9	Missense_Mutation	SNP	ENST00000455895.2	hg19	CCDS363.2	.	.	.	.	.	.	.	.	.	.	T	29.9	5.041911	0.93685	.	.	ENSG00000160058	ENST00000455895;ENST00000413080;ENST00000341071;ENST00000526031;ENST00000419121;ENST00000446293	.	.	.	5.45	5.45	0.79879	.	0.041854	0.85682	D	0.000000	T	0.69566	0.3125	L	0.55481	1.735	0.80722	D	1	D;D;D;D;D	0.65815	0.995;0.968;0.983;0.99;0.97	P;P;P;P;P	0.62560	0.904;0.732;0.864;0.864;0.543	T	0.72858	-0.4165	9	0.87932	D	0	-14.8468	15.0267	0.71674	0.0:0.0:0.0:1.0	.	303;342;415;415;398	Q9NW68-9;Q9NW68-8;Q9NW68-7;Q9NW68-3;Q9NW68	.;.;.;.;BSDC1_HUMAN	G	398;337;415;303;342;415	.	ENSP00000344816:D415G	D	-	2	0	BSDC1	32606702	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.964000	0.87933	2.205000	0.71048	0.533000	0.62120	GAC	.	.		0.582	BSDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020056.3	NM_018045		C	32834115	T	C	32834115	3	2	259	1	0	0	0	0	1	0	0	0	1530	1667	58	2	107	2	BSDC1	1	32834115	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	161165	32834115	216416506	18	36336										
KIAA1522	57648	hgsc.bcm.edu	37	chr1	33238480	33238480	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccccagactcacagaaagagCtggcctgaccaccaggcacc	9	17	1	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:33238480C>T	ENST00000373480.1	+	7	3203	c.3100C>T	c.(3100-3102)Ctg>Ttg	p.L1034L	YARS_ENST00000469100.1_5'Flank|KIAA1522_ENST00000373481.3_Silent_p.L1045L|KIAA1522_ENST00000401073.2_Silent_p.L1093L|KIAA1522_ENST00000294521.3_Silent_p.L142L	NM_001198972.1	NP_001185901.1	Q9P206	K1522_HUMAN	KIAA1522	1034										breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(2)|lung(5)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				ACAGAAAGAGCTGGCCTGACC	0.562											OREG0013333	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L1093L		Atlas-SNP	.											.	KIAA1522	68	.	0			c.C3277T						.						75	76	76					1																	33238480		1986	4165	6151	SO:0001819	synonymous_variant	57648	exon7			AAAGAGCTGGCCT	AL713671	CCDS41298.1, CCDS55588.1, CCDS55589.1	1p35.1	2009-02-18			ENSG00000162522	ENSG00000162522			29301	protein-coding gene	gene with protein product						10819331	Standard	NM_020888		Approved		uc001bvu.1	Q9P206	OTTHUMG00000008088	ENST00000373480.1:c.3100C>T	chr1.hg19:g.33238480C>T		152.0	0.0	838	82.0	4.0	NM_020888	B4DQU8|B5MDY0|C9JH84|Q8TCQ0	Silent	SNP	ENST00000373480.1	hg19	CCDS55588.1																																																																																			.	.		0.562	KIAA1522-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022130.1			T	33238480	C	T	33238480	2	4	259	1	0	0	0	0	0	0	0	1	8247	796	28	3		3	KIAA1522	1	33238480	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	404365	33238480	216012141	19	36337										
ZMYM1	79830	hgsc.bcm.edu	37	chr1	35579987	35579987	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttgagtcatttgctgacattGgtttccaaatttgaatttgt	8	5	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:35579987G>T	ENST00000373330.1	+	11	2730	c.2556G>T	c.(2554-2556)ttG>ttT	p.L852F	ZMYM1_ENST00000359858.4_Missense_Mutation_p.L852F|ZMYM1_ENST00000373329.1_3'UTR			Q5SVZ6	ZMYM1_HUMAN	zinc finger, MYM-type 1	852						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(8)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TGCTGACATTGGTTTCCAAAT	0.348																																					p.L852F		Atlas-SNP	.											.	ZMYM1	86	.	0			c.G2556T						.						82	69	73					1																	35579987		1831	4084	5915	SO:0001583	missense	79830	exon10			GACATTGGTTTCC	AK096206	CCDS41302.1	1p34.3	2008-05-02	2005-09-12		ENSG00000197056	ENSG00000197056		"Zinc fingers, MYM type"	26253	protein-coding gene	gene with protein product			"zinc finger, MYM domain containing 1"			12477932	Standard	XM_005271216		Approved	FLJ23151, MYM	uc001bym.3	Q5SVZ6	OTTHUMG00000004374	ENST00000373330.1:c.2556G>T	chr1.hg19:g.35579987G>T	ENSP00000362427:p.Leu852Phe	173.0	0.0		119.0	5.0	NM_024772	D3DPR7|Q7Z3Q4	Missense_Mutation	SNP	ENST00000373330.1	hg19	CCDS41302.1	.	.	.	.	.	.	.	.	.	.	G	0.823	-0.747979	0.03065	.	.	ENSG00000197056	ENST00000359858;ENST00000373329;ENST00000373330	T;T;T	0.25579	1.79;1.79;1.79	3.91	0.451	0.16629	Ribonuclease H-like (1);	1.200770	0.06331	N	0.706201	T	0.14485	0.0350	L	0.29908	0.895	0.18873	N	0.999986	P;P	0.42409	0.779;0.578	B;B	0.33690	0.168;0.12	T	0.19549	-1.0302	9	.	.	.	1.379	3.8662	0.09018	0.2631:0.0:0.5556:0.1813	.	833;852	B4DSJ9;Q5SVZ6	.;ZMYM1_HUMAN	F	852;777;852	ENSP00000352920:L852F;ENSP00000362426:L777F;ENSP00000362427:L852F	.	L	+	3	2	ZMYM1	35352574	0.006000	0.16342	0.189000	0.23252	0.064000	0.16182	0.003000	0.13083	0.093000	0.17368	0.455000	0.32223	TTG	.	.		0.348	ZMYM1-001	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012705.1	NM_024772		T	35579987	G	T	35579987	3	4	259	1	0	0	0	0	1	0	0	0	17714	1339	47	3	2590	3	ZMYM1	1	35579987	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	2341507	35579987	213670634	20	36338										
GNL2	29889	hgsc.bcm.edu	37	chr1	38048471	38048471	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	caggtaagtttcaatgtgagGggaacgagtacccattggat	13	6	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:38048471G>T	ENST00000373062.3	-	7	801	c.703C>A	c.(703-705)Cct>Act	p.P235T		NM_013285.2	NP_037417.1	Q13823	NOG2_HUMAN	guanine nucleotide binding protein-like 2 (nucleolar)	235	CP-type G. {ECO:0000255|PROSITE- ProRule:PRU01058}.				GTP catabolic process (GO:0006184)|ribosome biogenesis (GO:0042254)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	30		Myeloproliferative disorder(586;0.0393)				TCAATGTGAGGGGAACGAGTA	0.393																																					p.P235T		Atlas-SNP	.											.	GNL2	58	.	0			c.C703A						.						171	159	163					1																	38048471		2203	4300	6503	SO:0001583	missense	29889	exon7			TGTGAGGGGAACG	L05425	CCDS421.1	1p34	2008-02-05			ENSG00000134697	ENSG00000134697			29925	protein-coding gene	gene with protein product		609365				8822211	Standard	NM_013285		Approved	Ngp-1, HUMAUANTIG	uc001cbk.3	Q13823	OTTHUMG00000004322	ENST00000373062.3:c.703C>A	chr1.hg19:g.38048471G>T	ENSP00000362153:p.Pro235Thr	122.0	0.0		85.0	5.0	NM_013285	Q9BWN7	Missense_Mutation	SNP	ENST00000373062.3	hg19	CCDS421.1	.	.	.	.	.	.	.	.	.	.	G	13.85	2.359782	0.41801	.	.	ENSG00000134697	ENST00000373062;ENST00000545489	T	0.14516	2.5	5.87	3.94	0.45596	.	0.329365	0.37053	N	0.002278	T	0.13628	0.0330	L	0.49640	1.575	0.44937	D	0.997951	B	0.27068	0.167	B	0.29598	0.104	T	0.05484	-1.0882	10	0.18276	T	0.48	-8.6586	11.9514	0.52956	0.0664:0.1223:0.8113:0.0	.	235	Q13823	NOG2_HUMAN	T	235;76	ENSP00000362153:P235T	ENSP00000362153:P235T	P	-	1	0	GNL2	37821058	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.276000	0.65580	0.768000	0.33290	0.591000	0.81541	CCT	.	.		0.393	GNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012478.1	NM_013285		T	38048471	G	T	38048471	3	4	259	1	0	0	0	0	1	0	0	0	6544	1232	43	3	1532	3	GNL2	1	38048471	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	2468484	38048471	211202150	21	36339										
MACF1	23499	hgsc.bcm.edu	37	chr1	39816575	39816575	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acgtgagttgacagctcttcGggaaaagcttcatcaggcta	11	9	3	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:39816575G>T	ENST00000372915.3	+	42	11186	c.11099G>T	c.(11098-11100)cGg>cTg	p.R3700L	MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000317713.7_Missense_Mutation_p.R1633L|MACF1_ENST00000567887.1_Missense_Mutation_p.R3732L|MACF1_ENST00000289893.4_Missense_Mutation_p.R2135L|MACF1_ENST00000361689.2_Missense_Mutation_p.R1633L|MACF1_ENST00000545844.1_Missense_Mutation_p.R1633L|MACF1_ENST00000564288.1_Missense_Mutation_p.R3695L|MACF1_ENST00000539005.1_Missense_Mutation_p.R1633L			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	3700					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			ACAGCTCTTCGGGAAAAGCTT	0.532																																					p.R1633L		Atlas-SNP	.											.	MACF1	909	.	0			c.G4898T						.						87	83	84					1																	39816575		2203	4300	6503	SO:0001583	missense	23499	exon39			CTCTTCGGGAAAA	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.11099G>T	chr1.hg19:g.39816575G>T	ENSP00000362006:p.Arg3700Leu	90.0	0.0		51.0	5.0	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	hg19		.	.	.	.	.	.	.	.	.	.	G	15.29	2.789068	0.49997	.	.	ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000530262;ENST00000289893	T;T;T;T;T;T;T	0.62105	1.28;0.05;1.28;1.28;1.28;1.28;1.1	6.06	-6.09	0.02145	.	0.634882	0.14357	N	0.324734	T	0.59459	0.2195	L	0.51422	1.61	0.38205	D	0.940317	P;P;P;B	0.49862	0.474;0.862;0.929;0.009	B;P;B;B	0.49451	0.166;0.611;0.411;0.021	T	0.66810	-0.5829	10	0.23302	T	0.38	.	17.7482	0.88427	0.7216:0.0:0.2784:0.0	.	3700;1633;1633;1598	Q9UPN3;F8W8Q1;Q9UPN3-2;Q9UPN3-3	MACF1_HUMAN;.;.;.	L	1633;3700;1633;1633;1633;1782;2135	ENSP00000439537:R1633L;ENSP00000362006:R3700L;ENSP00000354573:R1633L;ENSP00000313438:R1633L;ENSP00000444364:R1633L;ENSP00000437059:R1782L;ENSP00000289893:R2135L	ENSP00000289893:R2135L	R	+	2	0	MACF1	39589162	0.240000	0.23847	0.129000	0.21949	0.899000	0.52679	0.087000	0.14958	-1.783000	0.01274	-0.781000	0.03364	CGG	.	.		0.532	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		T	39816575	G	T	39816575	3	4	259	1	0	0	0	0	1	0	0	0	9153	1116	39	1	11199	1	MACF1	1	39816575	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1768104	39816575	209434046	22	36340										
PPIE	10450	hgsc.bcm.edu	37	chr1	40218983	40218983	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agggcagcaaggacgggaagCcaaagcagaaggtgatcatc	15	8	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:40218983C>T	ENST00000324379.5	+	10	881	c.862C>T	c.(862-864)Cca>Tca	p.P288S	PPIE_ENST00000372830.1_Intron|PPIE_ENST00000356511.2_Intron	NM_006112.3	NP_006103.1	Q9UNP9	PPIE_HUMAN	peptidylprolyl isomerase E (cyclophilin E)	288	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				mRNA splicing, via spliceosome (GO:0000398)|positive regulation of viral genome replication (GO:0045070)|protein folding (GO:0006457)|regulation of transcription, DNA-templated (GO:0006355)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	cyclosporin A binding (GO:0016018)|nucleotide binding (GO:0000166)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			kidney(3)|large_intestine(2)|lung(2)|prostate(1)|urinary_tract(1)	9	all_cancers(7;1.63e-13)|all_lung(5;2.27e-16)|all_epithelial(6;1.35e-15)|Lung NSC(20;1.49e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.87e-18)|Epithelial(16;2.7e-17)|all cancers(16;5.5e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			GGACGGGAAGCCAAAGCAGAA	0.582																																					p.P288S		Atlas-SNP	.											.	PPIE	33	.	0			c.C862T						.						133	105	115					1																	40218983		2203	4300	6503	SO:0001583	missense	10450	exon10			GGGAAGCCAAAGC	AF042385	CCDS442.1, CCDS443.1, CCDS53299.1	1p32	2013-02-12			ENSG00000084072	ENSG00000084072		"RNA binding motif (RRM) containing"	9258	protein-coding gene	gene with protein product	"peptidyl-prolyl cis-trans isomerase E", "cyclophilin 33", "cyclophilin E", "PPIase E", "rotamase E", "peptidylprolyl isomerase E, isoform 1"	602435				9747881	Standard	NM_203456		Approved	CyP-33, MGC3736, MGC111222	uc001cdw.3	Q9UNP9	OTTHUMG00000009248	ENST00000324379.5:c.862C>T	chr1.hg19:g.40218983C>T	ENSP00000312769:p.Pro288Ser	128.0	0.0		43.0	4.0	NM_006112	B2R971|O43634|O43635|Q32Q72|Q3S611|Q5TGA0|Q5TGA2|Q5TGA3|Q9UIZ5	Missense_Mutation	SNP	ENST00000324379.5	hg19	CCDS443.1	.	.	.	.	.	.	.	.	.	.	C	17.32	3.358716	0.61403	.	.	ENSG00000084072	ENST00000324379;ENST00000372835	T;T	0.58797	0.31;0.31	4.35	4.35	0.52113	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (3);Cyclophilin-like (1);	.	.	.	.	T	0.76983	0.4064	H	0.96833	3.89	0.80722	D	1	P;P	0.42248	0.774;0.571	P;B	0.46253	0.509;0.232	D	0.85144	0.0982	9	0.56958	D	0.05	.	17.0155	0.86418	0.0:1.0:0.0:0.0	.	209;288	B4E3F2;Q9UNP9	.;PPIE_HUMAN	S	288;237	ENSP00000312769:P288S;ENSP00000361925:P237S	ENSP00000312769:P288S	P	+	1	0	PPIE	39991570	0.994000	0.37717	0.995000	0.50966	0.996000	0.88848	2.789000	0.47813	2.422000	0.82143	0.563000	0.77884	CCA	.	.		0.582	PPIE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025642.2	NM_006112		T	40218983	C	T	40218983	3	4	259	1	0	0	0	0	1	0	0	0	12334	739	26	3	900	3	PPIE	1	40218983	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	402408	40218983	209031638	23	36341										
RLF	6018	hgsc.bcm.edu	37	chr1	40703878	40703878	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttaaccatgttccaacatcgGtattccccatttcagtgtca	5	12	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:40703878G>C	ENST00000372771.4	+	8	3531	c.3504G>C	c.(3502-3504)cgG>cgC	p.R1168R		NM_012421.3	NP_036553.2	Q13129	RLF_HUMAN	rearranged L-myc fusion	1168					chromosome organization (GO:0051276)|DNA integration (GO:0015074)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(18)|lung(18)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(4)|urinary_tract(2)	68	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)			TCCAACATCGGTATTCCCCAT	0.328																																					p.R1168R		Atlas-SNP	.											.	RLF	152	.	0			c.G3504C						.						79	84	83					1																	40703878		2203	4300	6503	SO:0001819	synonymous_variant	6018	exon8			ACATCGGTATTCC		CCDS448.1	1p32	2010-05-07	2005-08-16		ENSG00000117000	ENSG00000117000		"Zinc fingers, C2H2-type"	10025	protein-coding gene	gene with protein product		180610	"rearranged L-myc fusion sequence"			1649386	Standard	NM_012421		Approved	ZNF292L, Zn-15L	uc001cfc.4	Q13129	OTTHUMG00000005763	ENST00000372771.4:c.3504G>C	chr1.hg19:g.40703878G>C		94.0	0.0		68.0	4.0	NM_012421	Q14CQ1|Q9NU60	Silent	SNP	ENST00000372771.4	hg19	CCDS448.1																																																																																			.	.		0.328	RLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015767.1	NM_012421		C	40703878	G	C	40703878	2	2	259	1	0	0	0	0	0	0	0	1	13404	1248	44	4		4	RLF	1	40703878	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	484895	40703878	208546743	24	36342										
SMAP2	64744	hgsc.bcm.edu	37	chr1	40881972	40881972	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gctctctaaagactccattcTttcactgtatggatcccaga	6	12	3	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:40881972T>C	ENST00000539317.1	+	8	759	c.566T>C	c.(565-567)cTt>cCt	p.L189P		NM_001198980.1	NP_001185909.1	Q8WU79	SMAP2_HUMAN	small ArfGAP2	269	Interaction with clathrin heavy chains. {ECO:0000250}.				regulation of ARF GTPase activity (GO:0032312)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			central_nervous_system(3)|kidney(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(2)|upper_aerodigestive_tract(1)	24	Lung NSC(20;1.56e-05)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;1.04e-17)			GACTCCATTCTTTCACTGTAT	0.498																																					p.L269P		Atlas-SNP	.											.	SMAP2	48	.	0			c.T806C						.						127	124	125					1																	40881972		2203	4300	6503	SO:0001583	missense	64744	exon8			CCATTCTTTCACT	AL137764	CCDS451.1, CCDS55592.1, CCDS55593.1, CCDS72763.1	1p35.3-p34.1	2008-09-22	2008-09-05	2008-01-09	ENSG00000084070	ENSG00000084070		"ADP-ribosylation factor GTPase activating proteins"	25082	protein-coding gene	gene with protein product			"stromal membrane-associated protein 1-like", "stromal membrane-associated GTPase-activating protein 2"	SMAP1L		16571680	Standard	NM_001198978		Approved		uc001cfj.3	Q8WU79	OTTHUMG00000007301	ENST00000539317.1:c.566T>C	chr1.hg19:g.40881972T>C	ENSP00000442835:p.Leu189Pro	106.0	0.0		65.0	4.0	NM_022733	B2R7T1|B7Z5B5|B7Z8V2|D3DPV2|Q5QPL2|Q96C93|Q9NST2|Q9UJL8	Missense_Mutation	SNP	ENST00000539317.1	hg19	CCDS55593.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.566921	0.86439	.	.	ENSG00000084070	ENST00000372718;ENST00000372708;ENST00000539317	T;T;T	0.65549	0.58;0.47;-0.16	6.17	6.17	0.99709	.	0.000000	0.64402	D	0.000003	T	0.79003	0.4373	M	0.76170	2.325	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.998	D;D;D	0.91635	0.999;0.997;0.995	T	0.81215	-0.1034	10	0.87932	D	0	-18.1823	14.7743	0.69713	0.0:0.0:0.0:1.0	.	189;239;269	B7Z5B5;Q8WU79-2;Q8WU79	.;.;SMAP2_HUMAN	P	269;239;189	ENSP00000361803:L269P;ENSP00000361793:L239P;ENSP00000442835:L189P	ENSP00000361793:L239P	L	+	2	0	SMAP2	40654559	1.000000	0.71417	0.981000	0.43875	0.979000	0.70002	7.274000	0.78538	2.371000	0.80710	0.533000	0.62120	CTT	.	.		0.498	SMAP2-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022733		C	40881972	T	C	40881972	3	2	259	1	0	0	0	0	1	0	0	0	14782	1609	56	2	836	2	SMAP2	1	40881972	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	178094	40881972	208368649	25	36343										
WDR65	149465	hgsc.bcm.edu	37	chr1	43664184	43664184	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atttaaggaataccaagaagAggcatattccatcagccttc	7	9	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:43664184A>G	ENST00000372492.4	+	8	1619	c.1295A>G	c.(1294-1296)gAg>gGg	p.E432G	RNA5SP46_ENST00000362370.1_RNA|WDR65_ENST00000528956.1_Missense_Mutation_p.E432G	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		432										NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				TACCAAGAAGAGGCATATTCC	0.393																																					p.E432G		Atlas-SNP	.											.	WDR65	76	.	0			c.A1295G						.						92	83	86					1																	43664184		2203	4300	6503	SO:0001583	missense	149465	exon8			AAGAAGAGGCATA																												ENST00000372492.4:c.1295A>G	chr1.hg19:g.43664184A>G	ENSP00000361570:p.Glu432Gly	93.0	0.0		73.0	4.0	NM_152498	A6NKQ3|Q17RI9|Q5TAI0	Missense_Mutation	SNP	ENST00000372492.4	hg19		.	.	.	.	.	.	.	.	.	.	A	24.3	4.513918	0.85389	.	.	ENSG00000243710	ENST00000372492;ENST00000528956	T;T	0.09911	2.93;2.93	5.09	5.09	0.68999	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);	0.000000	0.85682	D	0.000000	T	0.40791	0.1131	M	0.91768	3.24	0.53688	D	0.999976	D;D	0.71674	0.992;0.998	D;D	0.75484	0.923;0.986	T	0.49293	-0.8955	10	0.42905	T	0.14	.	14.8451	0.70254	1.0:0.0:0.0:0.0	.	432;432	Q96MR6;Q96MR6-2	WDR65_HUMAN;.	G	432	ENSP00000361570:E432G;ENSP00000435310:E432G	ENSP00000361570:E432G	E	+	2	0	WDR65	43436771	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	8.495000	0.90481	1.916000	0.55485	0.379000	0.24179	GAG	.	.		0.393	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1			G	43664184	A	G	43664184	3	3	259	1	0	0	0	0	1	0	0	0	17331	304	11	2	1321	2	WDR65	1	43664184	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2782212	43664184	205586437	26	36344										
ARTN	9048	hgsc.bcm.edu	37	chr1	44401362	44401362	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttggaggcctctccacgctgTcccactgcccctggcctagg	11	17	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:44401362T>C	ENST00000372359.5	+	3	816	c.34T>C	c.(34-36)Tcc>Ccc	p.S12P	ARTN_ENST00000372354.3_Missense_Mutation_p.S12P|ARTN_ENST00000414809.3_Missense_Mutation_p.S12P|ARTN_ENST00000472435.1_Missense_Mutation_p.S12P|ARTN_ENST00000498139.2_Missense_Mutation_p.S12P|ARTN_ENST00000479128.1_Missense_Mutation_p.S12P|ARTN_ENST00000438616.3_5'Flank	NM_057091.2	NP_476432.2	Q5T4W7	ARTN_HUMAN	artemin	12					axon guidance (GO:0007411)|induction of positive chemotaxis (GO:0050930)|lymphocyte migration into lymphoid organs (GO:0097021)|neuroblast proliferation (GO:0007405)|peripheral nervous system development (GO:0007422)|Peyer's patch morphogenesis (GO:0061146)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	receptor binding (GO:0005102)					Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)				CTCCACGCTGTCCCACTGCCC	0.597																																					p.S12P		Atlas-SNP	.											.	ARTN	6	.	0			c.T34C						.						91	64	73					1																	44401362		2203	4300	6503	SO:0001583	missense	9048	exon2			ACGCTGTCCCACT	AF109401	CCDS501.1, CCDS502.1	1p33-p32	2014-01-30			ENSG00000117407	ENSG00000117407		"Endogenous ligands"	727	protein-coding gene	gene with protein product	"neublastin", "neurotrophic factor"	603886				9883723	Standard	NM_057090		Approved	NBN, EVN, ENOVIN	uc001ckt.3	Q5T4W7	OTTHUMG00000007705	ENST00000372359.5:c.34T>C	chr1.hg19:g.44401362T>C	ENSP00000361434:p.Ser12Pro	192.0	0.0		103.0	5.0	NM_001136215	D3DPY1|D3DPY3|O95441|O96030|Q6P6A3	Missense_Mutation	SNP	ENST00000372359.5	hg19	CCDS501.1	.	.	.	.	.	.	.	.	.	.	T	12.62	1.993505	0.35131	.	.	ENSG00000117407	ENST00000372359;ENST00000414809;ENST00000477048;ENST00000471394;ENST00000498139;ENST00000491846;ENST00000479128;ENST00000472435;ENST00000474592;ENST00000372354	D;D;T;T;D;T;T;T;T;D	0.84146	-1.81;-1.81;0.62;0.62;-1.81;0.65;0.62;0.62;0.65;-1.81	3.77	0.451	0.16629	.	1.699210	0.03814	N	0.266359	T	0.70439	0.3224	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.57277	-0.7839	10	0.33940	T	0.23	.	5.4568	0.16594	0.0:0.5345:0.0:0.4655	.	12;12	Q5T4W7-3;Q5T4W7	.;ARTN_HUMAN	P	12	ENSP00000361434:S12P;ENSP00000387435:S12P;ENSP00000434784:S12P;ENSP00000435804:S12P;ENSP00000436727:S12P;ENSP00000436149:S12P;ENSP00000434071:S12P;ENSP00000435140:S12P;ENSP00000434856:S12P;ENSP00000361429:S12P	ENSP00000361429:S12P	S	+	1	0	ARTN	44173949	0.767000	0.28508	0.002000	0.10522	0.075000	0.17131	0.732000	0.26072	0.088000	0.17205	0.533000	0.62120	TCC	.	.		0.597	ARTN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000020713.2	NM_057090		C	44401362	T	C	44401362	3	2	259	1	0	0	0	0	1	0	0	0	1001	1667	58	2	36	2	ARTN	1	44401362	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	737178	44401362	204849259	27	36345										
SLC6A9	6536	hgsc.bcm.edu	37	chr1	44468248	44468248	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgatgccgtcaaaggctcccTccagggtcactccgcggaca	11	15	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:44468248T>C	ENST00000360584.2	-	7	1204	c.1013A>G	c.(1012-1014)gAg>gGg	p.E338G	SLC6A9_ENST00000357730.2_Missense_Mutation_p.E284G|SLC6A9_ENST00000537678.1_Missense_Mutation_p.E200G|SLC6A9_ENST00000372307.3_Missense_Mutation_p.E200G|SLC6A9_ENST00000475075.2_Missense_Mutation_p.E154G|SLC6A9_ENST00000372310.3_Missense_Mutation_p.E265G|SLC6A9_ENST00000372306.3_Missense_Mutation_p.E265G	NM_201649.3	NP_964012.2	P48067	SC6A9_HUMAN	solute carrier family 6 (neurotransmitter transporter, glycine), member 9	338					transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycine:sodium symporter activity (GO:0015375)|neurotransmitter:sodium symporter activity (GO:0005328)			endometrium(3)|large_intestine(8)|lung(7)|ovary(1)|skin(1)|urinary_tract(2)	22	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)			Glycine(DB00145)	AAAGGCTCCCTCCAGGGTCAC	0.597																																					p.E338G		Atlas-SNP	.											.	SLC6A9	109	.	0			c.A1013G						.						115	115	115					1																	44468248		2203	4300	6503	SO:0001583	missense	6536	exon7			GCTCCCTCCAGGG	S70609	CCDS30695.1, CCDS41316.1, CCDS41317.1	1p33	2013-05-22			ENSG00000196517	ENSG00000196517		"Solute carriers"	11056	protein-coding gene	gene with protein product		601019				8183239, 7587377	Standard	NM_006934		Approved	GLYT1	uc001cll.4	P48067	OTTHUMG00000008294	ENST00000360584.2:c.1013A>G	chr1.hg19:g.44468248T>C	ENSP00000353791:p.Glu338Gly	140.0	0.0		73.0	4.0	NM_201649	A6NDH1|A6NII2|A6NNZ8|Q5TAB8|Q5TAB9|Q5TAC0	Missense_Mutation	SNP	ENST00000360584.2	hg19	CCDS41317.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.357665	0.82243	.	.	ENSG00000196517	ENST00000372307;ENST00000372306;ENST00000372310;ENST00000475075;ENST00000360584;ENST00000357730;ENST00000537678	T;T;T;T;T;T;T	0.74526	-0.85;-0.85;-0.85;-0.85;-0.85;-0.85;-0.85	4.51	4.51	0.55191	.	0.321665	0.36972	N	0.002311	D	0.86339	0.5909	M	0.88241	2.94	0.48571	D	0.999678	P;D;D;P;P;P	0.52996	0.837;0.957;0.957;0.905;0.947;0.565	P;P;P;P;P;B	0.60473	0.52;0.836;0.875;0.586;0.667;0.324	D	0.89187	0.3548	10	0.72032	D	0.01	.	14.2805	0.66208	0.0:0.0:0.0:1.0	.	269;265;200;265;284;338	B7Z3W8;B7Z8W5;B7Z3A9;P48067-2;P48067-3;P48067	.;.;.;.;.;SC6A9_HUMAN	G	200;265;265;154;338;284;200	ENSP00000361381:E200G;ENSP00000361380:E265G;ENSP00000361384:E265G;ENSP00000434460:E154G;ENSP00000353791:E338G;ENSP00000350362:E284G;ENSP00000442523:E200G	ENSP00000350362:E284G	E	-	2	0	SLC6A9	44240835	1.000000	0.71417	0.986000	0.45419	0.974000	0.67602	5.927000	0.70080	2.006000	0.58801	0.459000	0.35465	GAG	.	.		0.597	SLC6A9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000022825.2	NM_201649		C	44468248	T	C	44468248	3	2	259	1	0	0	0	0	1	0	0	0	14706	1551	54	2	1139	2	SLC6A9	1	44468248	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	66886	44468248	204782373	28	36346										
PLK3	1263	hgsc.bcm.edu	37	chr1	45266606	45266606	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gagccgcgtcgccaagccgcAtcagcgcgagaaggtgggtc	16	13	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:45266606A>G	ENST00000372201.4	+	2	544	c.305A>G	c.(304-306)cAt>cGt	p.H102R	PLK3_ENST00000465443.1_3'UTR	NM_004073.2	NP_004064.2	Q9H4B4	PLK3_HUMAN	polo-like kinase 3	102	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cytoplasmic microtubule organization (GO:0031122)|endomitotic cell cycle (GO:0007113)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|Golgi disassembly (GO:0090166)|mitotic cell cycle checkpoint (GO:0007093)|mitotic G1/S transition checkpoint (GO:0044819)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process involved in cellular response to hypoxia (GO:2000777)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|regulation of cell division (GO:0051302)|regulation of cytokinesis (GO:0032465)|response to osmotic stress (GO:0006970)|response to radiation (GO:0009314)|response to reactive oxygen species (GO:0000302)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|Golgi stack (GO:0005795)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)			endometrium(4)|large_intestine(2)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.155)					GCCAAGCCGCATCAGCGCGAG	0.672																																					p.H102R		Atlas-SNP	.											.	PLK3	41	.	0			c.A305G						.						26	30	29					1																	45266606		2202	4298	6500	SO:0001583	missense	1263	exon2			AGCCGCATCAGCG	AJ293866	CCDS515.1	1p34.1	2013-01-18	2010-06-24	2004-01-28	ENSG00000173846	ENSG00000173846			2154	protein-coding gene	gene with protein product		602913	"cytokine-inducible kinase", "polo-like kinase 3 (Drosophila)"	CNK		8702627	Standard	NM_004073		Approved	FNK, PRK	uc001cmn.3	Q9H4B4	OTTHUMG00000008491	ENST00000372201.4:c.305A>G	chr1.hg19:g.45266606A>G	ENSP00000361275:p.His102Arg	155.0	0.0		74.0	4.0	NM_004073	Q15767|Q5JR99|Q96CV1	Missense_Mutation	SNP	ENST00000372201.4	hg19	CCDS515.1	.	.	.	.	.	.	.	.	.	.	a	23.9	4.474547	0.84640	.	.	ENSG00000173846	ENST00000372201;ENST00000543983	T	0.23147	1.92	4.67	4.67	0.58626	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.14098	0.0341	N	0.04686	-0.185	0.80722	D	1	B	0.21753	0.06	B	0.17433	0.018	T	0.06972	-1.0797	9	0.45353	T	0.12	-9.7578	13.3485	0.60589	1.0:0.0:0.0:0.0	.	102	Q9H4B4	PLK3_HUMAN	R	102;77	ENSP00000361275:H102R	ENSP00000361275:H102R	H	+	2	0	PLK3	45039193	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.959000	0.93110	1.760000	0.52011	0.449000	0.29647	CAT	.	.		0.672	PLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023429.1	NM_004073		G	45266606	A	G	45266606	3	3	259	1	0	0	0	0	1	0	0	0	12106	217	8	2	311	2	PLK3	1	45266606	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	798358	45266606	203984015	29	36347										
ZSWIM5	57643	hgsc.bcm.edu	37	chr1	45484490	45484490	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tggcacagtgcacactcttcAccaccagggggatgagagct	12	12	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:45484490A>G	ENST00000359600.5	-	14	3399	c.3194T>C	c.(3193-3195)gTg>gCg	p.V1065A		NM_020883.1	NP_065934.1	Q9P217	ZSWM5_HUMAN	zinc finger, SWIM-type containing 5	1065						extracellular space (GO:0005615)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|liver(1)|lung(13)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Acute lymphoblastic leukemia(166;0.155)					CACACTCTTCACCACCAGGGG	0.587											OREG0013450	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V1065A		Atlas-SNP	.											.	ZSWIM5	72	.	0			c.T3194C						.						68	64	66					1																	45484490		2047	4200	6247	SO:0001583	missense	57643	exon14			CTCTTCACCACCA	AB040944	CCDS41319.1	1p34.1	2010-06-16			ENSG00000162415	ENSG00000162415		"Zinc fingers, SWIM-type"	29299	protein-coding gene	gene with protein product						10819331	Standard	NM_020883		Approved	KIAA1511	uc001cnd.2	Q9P217	OTTHUMG00000008950	ENST00000359600.5:c.3194T>C	chr1.hg19:g.45484490A>G	ENSP00000352614:p.Val1065Ala	195.0	0.0	932	121.0	6.0	NM_020883	Q5SXQ9	Missense_Mutation	SNP	ENST00000359600.5	hg19	CCDS41319.1	.	.	.	.	.	.	.	.	.	.	A	17.18	3.323778	0.60634	.	.	ENSG00000162415	ENST00000359600	T	0.55413	0.52	4.84	3.69	0.42338	.	0.000000	0.85682	D	0.000000	T	0.62024	0.2394	M	0.75264	2.295	0.58432	D	0.999996	P	0.45474	0.859	P	0.51415	0.669	T	0.62859	-0.6765	10	0.45353	T	0.12	-8.8877	11.509	0.50483	0.8654:0.0:0.0:0.1346	.	1065	Q9P217	ZSWM5_HUMAN	A	1065	ENSP00000352614:V1065A	ENSP00000352614:V1065A	V	-	2	0	ZSWIM5	45257077	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.910000	0.92685	0.919000	0.36945	0.459000	0.35465	GTG	.	.		0.587	ZSWIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024823.2	XM_046581		G	45484490	A	G	45484490	3	3	259	1	0	0	0	0	1	0	0	0	18259	159	6	2	367	2	ZSWIM5	1	45484490	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	217884	45484490	203766131	30	36348										
MUTYH	4595	hgsc.bcm.edu	37	chr1	45799158	45799158	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tccctcggaaggctgtgactTcagctacgtctctgaataga	10	11	2	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:45799158T>C	ENST00000372098.3	-	3	399	c.266A>G	c.(265-267)gAa>gGa	p.E89G	MUTYH_ENST00000488731.2_Intron|MUTYH_ENST00000372100.5_Missense_Mutation_p.E75G|MUTYH_ENST00000528332.2_Intron|MUTYH_ENST00000450313.1_Missense_Mutation_p.E92G|MUTYH_ENST00000372115.3_Missense_Mutation_p.E78G|MUTYH_ENST00000456914.2_Missense_Mutation_p.E64G|MUTYH_ENST00000529984.1_Intron|MUTYH_ENST00000372110.3_Missense_Mutation_p.E79G|MUTYH_ENST00000372104.1_Missense_Mutation_p.E64G|MUTYH_ENST00000528013.2_Missense_Mutation_p.E78G|MUTYH_ENST00000531105.1_Intron|MUTYH_ENST00000448481.1_Missense_Mutation_p.E75G|MUTYH_ENST00000354383.6_Missense_Mutation_p.E65G|MUTYH_ENST00000355498.2_Missense_Mutation_p.E64G			Q9UIF7	MUTYH_HUMAN	mutY homolog	89					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depurination (GO:0045007)|DNA repair (GO:0006281)|mismatch repair (GO:0006298)	mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|hydrolase activity, acting on glycosyl bonds (GO:0016798)|metal ion binding (GO:0046872)|MutSalpha complex binding (GO:0032407)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.155)					GGCTGTGACTTCAGCTACGTC	0.602			Mis			colorectal		Base excision repair (BER), DNA glycosylases	MUTYH-associated polyposis																												p.E92G		Atlas-SNP	.	yes	Rec		Adenomatous polyposis coli	1	1p34.3-1p32.1	4595	mutY homolog (E. coli)		E	.	MUTYH	38	.	0			c.A275G						.						95	82	86					1																	45799158		2203	4300	6503	SO:0001583	missense	4595	exon3	Familial Cancer Database	MAP, MYH-associated polyposis	GTGACTTCAGCTA	U63329	CCDS520.1, CCDS41320.1, CCDS41321.1, CCDS41322.1, CCDS72776.1, CCDS72777.1	1p34.1	2014-09-17	2013-09-12		ENSG00000132781	ENSG00000132781			7527	protein-coding gene	gene with protein product		604933	"mutY (E. coli) homolog", "mutY homolog (E. coli)"			7823963, 10684930	Standard	NM_012222		Approved	MYH	uc009vxp.3	Q9UIF7	OTTHUMG00000007682	ENST00000372098.3:c.266A>G	chr1.hg19:g.45799158T>C	ENSP00000361170:p.Glu89Gly	160.0	0.0		92.0	4.0	NM_001128425	D3DPZ4|Q15830|Q9UBP2|Q9UBS7|Q9UIF4|Q9UIF5|Q9UIF6	Missense_Mutation	SNP	ENST00000372098.3	hg19	CCDS520.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.248113	0.80024	.	.	ENSG00000132781	ENST00000372104;ENST00000448481;ENST00000456914;ENST00000354383;ENST00000355498;ENST00000372098;ENST00000372110;ENST00000372115;ENST00000450313;ENST00000372100;ENST00000435155;ENST00000528013;ENST00000483127	T;T;T;T;T;T;T;T;T;T;T;T;T	0.51817	3.08;3.09;3.08;3.09;3.08;3.08;3.08;3.08;3.08;3.09;1.82;0.79;0.69	5.86	5.86	0.93980	DNA glycosylase (1);	0.150359	0.64402	D	0.000015	T	0.60779	0.2295	M	0.64997	1.995	0.52501	D	0.99995	D;D;P;D;D	0.57899	0.967;0.981;0.894;0.967;0.967	P;P;B;P;P	0.55999	0.497;0.789;0.393;0.497;0.619	T	0.64368	-0.6424	10	0.72032	D	0.01	-14.7918	14.8146	0.70024	0.0:0.0:0.0:1.0	.	92;79;89;78;65	E5KP25;Q9UIF7-2;Q9UIF7;E5KP27;E5KP28	.;.;MUTYH_HUMAN;.;.	G	64;75;64;65;64;89;79;78;92;75;75;78;70	ENSP00000361176:E64G;ENSP00000409718:E75G;ENSP00000407590:E64G;ENSP00000346354:E65G;ENSP00000347685:E64G;ENSP00000361170:E89G;ENSP00000361182:E79G;ENSP00000361187:E78G;ENSP00000408176:E92G;ENSP00000361172:E75G;ENSP00000403655:E75G;ENSP00000433130:E78G;ENSP00000436469:E70G	ENSP00000346354:E65G	E	-	2	0	MUTYH	45571745	1.000000	0.71417	0.967000	0.41034	0.535000	0.34838	3.796000	0.55507	2.232000	0.73038	0.533000	0.62120	GAA	.	.		0.602	MUTYH-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000020529.1	NM_012222		C	45799158	T	C	45799158	3	2	259	1	0	0	0	0	1	0	0	0	10002	1783	62	2	1430	2	MUTYH	1	45799158	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	314668	45799158	203451463	31	36349										
ELAVL4	1996	hgsc.bcm.edu	37	chr1	50610679	50610679	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aatggtccgacatccaatacAagcaatggaccctccagcaa	7	13	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:50610679A>G	ENST00000371823.4	+	2	284	c.60A>G	c.(58-60)acA>acG	p.T20T	ELAVL4_ENST00000371821.1_Silent_p.T25T|ELAVL4_ENST00000371824.1_Silent_p.T20T|ELAVL4_ENST00000448907.2_Silent_p.T23T|ELAVL4_ENST00000492299.1_3'UTR|ELAVL4_ENST00000371819.1_Silent_p.T25T|ELAVL4_ENST00000357083.4_Silent_p.T37T|ELAVL4_ENST00000371827.1_Silent_p.T20T	NM_001144774.1|NM_021952.3	NP_001138246.1|NP_068771.2	P26378	ELAV4_HUMAN	ELAV like neuron-specific RNA binding protein 4	20					mRNA processing (GO:0006397)|RNA processing (GO:0006396)		AU-rich element binding (GO:0017091)|mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(2)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	32						CATCCAATACAAGCAATGGAC	0.413																																					p.T37T		Atlas-SNP	.											.	ELAVL4	124	.	0			c.A111G						.						89	77	81					1																	50610679		2203	4300	6503	SO:0001819	synonymous_variant	1996	exon2			CAATACAAGCAAT	AY033998	CCDS553.1, CCDS44138.1, CCDS44139.1, CCDS44140.1, CCDS53315.1, CCDS72788.1	1p34	2013-10-03	2013-10-03		ENSG00000162374	ENSG00000162374		"RNA binding motif (RRM) containing"	3315	protein-coding gene	gene with protein product	"Hu antigen D"	168360	"ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)", "ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4"	HUD		8222755	Standard	XM_005270581		Approved	PNEM	uc001csb.2	P26378	OTTHUMG00000007877	ENST00000371823.4:c.60A>G	chr1.hg19:g.50610679A>G		132.0	0.0		79.0	5.0	NM_001144775	B1APY6|B1APY7|B7Z4G7|Q8IYD4|Q96J74|Q96J75|Q9UD24	Silent	SNP	ENST00000371823.4	hg19	CCDS553.1																																																																																			.	.		0.413	ELAVL4-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000021712.1	NM_021952		G	50610679	A	G	50610679	2	3	259	1	0	0	0	0	0	0	0	1	5054	117	5	2		2	ELAVL4	1	50610679	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	4811521	50610679	198639942	32	36350										
LDLRAD1	388633	hgsc.bcm.edu	37	chr1	54474774	54474774	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggttgaaggacagcgccaccAcccagggccgcagggtgggc	17	13	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:54474774A>G	ENST00000371360.1	-	6	516	c.499T>C	c.(499-501)Tgg>Cgg	p.W167R	LDLRAD1_ENST00000371362.3_Missense_Mutation_p.W78R|LDLRAD1_ENST00000545928.1_Missense_Mutation_p.W124R|LDLRAD1_ENST00000420619.1_Missense_Mutation_p.W128R	NM_001010978.2	NP_001010978.2	Q5T700	LRAD1_HUMAN	low density lipoprotein receptor class A domain containing 1	167	LDL-receptor class A 3; atypical. {ECO:0000255|PROSITE-ProRule:PRU00124}.					integral component of membrane (GO:0016021)				large_intestine(3)|prostate(1)|skin(3)	7						CAGCGCCACCACCCAGGGCCG	0.592																																					p.W167R		Atlas-SNP	.											.	LDLRAD1	22	.	0			c.T499C						.						101	97	98					1																	54474774		2203	4300	6503	SO:0001583	missense	388633	exon6			GCCACCACCCAGG		CCDS30725.1, CCDS60145.1, CCDS60146.1, CCDS60147.1	1p32.3	2008-02-05	2005-10-07		ENSG00000203985	ENSG00000203985			32069	protein-coding gene	gene with protein product			"low density lipoprotein receptor A domain containing 1"				Standard	NM_001010978		Approved		uc001cwm.2	Q5T700	OTTHUMG00000008433	ENST00000371360.1:c.499T>C	chr1.hg19:g.54474774A>G	ENSP00000360411:p.Trp167Arg	206.0	0.0		95.0	5.0	NM_001010978	A0PJY0|B7ZME3|Q5T6Z9	Missense_Mutation	SNP	ENST00000371360.1	hg19	CCDS30725.1	.	.	.	.	.	.	.	.	.	.	A	15.56	2.871021	0.51695	.	.	ENSG00000203985	ENST00000371362;ENST00000371360;ENST00000545928;ENST00000420619	D;D;D;D	0.87103	-2.21;-2.21;-2.21;-2.21	4.5	3.31	0.37934	.	0.000000	0.52532	D	0.000074	D	0.90566	0.7043	M	0.67953	2.075	0.42889	D	0.994199	D;D	0.89917	0.996;1.0	P;D	0.76575	0.731;0.988	D	0.88188	0.2875	10	0.25106	T	0.35	-20.3964	10.4302	0.44403	0.837:0.163:0.0:0.0	.	124;167	B7ZME3;Q5T700	.;LRAD1_HUMAN	R	78;167;124;128	ENSP00000360413:W78R;ENSP00000360411:W167R;ENSP00000445871:W124R;ENSP00000411017:W128R	ENSP00000360411:W167R	W	-	1	0	LDLRAD1	54247362	0.998000	0.40836	0.994000	0.49952	0.607000	0.37147	4.376000	0.59556	1.905000	0.55150	0.533000	0.62120	TGG	.	.		0.592	LDLRAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023243.1	NM_001010978		G	54474774	A	G	54474774	3	3	259	1	0	0	0	0	1	0	0	0	8714	159	6	2	122	2	LDLRAD1	1	54474774	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	3864095	54474774	194775847	33	36351										
CDCP2	200008	hgsc.bcm.edu	37	chr1	54618517	54618517	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tctgtcccaagagtgcctacCttccatggcttgggcctgga	11	13	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:54618517C>T	ENST00000371330.1	-	1	926	c.79G>A	c.(79-81)Ggt>Agt	p.G27S	RP11-446E24.4_ENST00000525949.1_Intron|RP11-446E24.4_ENST00000311841.7_3'UTR	NM_201546.2	NP_963840.2	Q5VXM1	CDCP2_HUMAN	CUB domain containing protein 2	27						extracellular region (GO:0005576)				kidney(1)|large_intestine(6)|lung(13)|ovary(1)|prostate(2)|stomach(1)	24						GAGTGCCTACCTTCCATGGCT	0.627																																					p.G27S		Atlas-SNP	.											.	CDCP2	52	.	0			c.G79A						.						81	85	84					1																	54618517		2203	4300	6503	SO:0001630	splice_region_variant	200008	exon1			GCCTACCTTCCAT		CCDS588.2	1p32.3	2011-02-10			ENSG00000157211	ENSG00000157211			27297	protein-coding gene	gene with protein product		612320				12477932	Standard	NM_201546		Approved		uc001cwv.2	Q5VXM1	OTTHUMG00000155307	ENST00000371330.1:c.79+1G>A	chr1.hg19:g.54618517C>T		216.0	0.0		125.0	26.0	NM_201546	Q6ZWJ3	Missense_Mutation	SNP	ENST00000371330.1	hg19	CCDS588.2	.	.	.	.	.	.	.	.	.	.	C	21.0	4.080918	0.76528	.	.	ENSG00000157211	ENST00000371330	T	0.26957	1.7	4.96	4.96	0.65561	.	0.000000	0.85682	D	0.000000	T	0.27384	0.0672	N	0.17901	0.54	0.51767	D	0.999933	D	0.57899	0.981	P	0.53490	0.727	T	0.01591	-1.1317	9	.	.	.	-6.7344	15.5363	0.76004	0.0:1.0:0.0:0.0	.	27	Q5VXM1	CDCP2_HUMAN	S	27	ENSP00000360381:G27S	.	G	-	1	0	CDCP2	54391105	0.975000	0.34042	1.000000	0.80357	0.588000	0.36517	1.350000	0.34010	2.574000	0.86865	0.650000	0.86243	GGT	.	.		0.627	CDCP2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000022209.2	NM_201546	Missense_Mutation	T	54618517	C	T	54618517	5	4	259	1	0	0	0	0	0	0	1	0	3096	695	24	3	1286	3	CDCP2	1	54618517	Splice_Site	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	143743	54618517	194632104	34	36352										
USP24	23358	hgsc.bcm.edu	37	chr1	55537593	55537593	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aagctgtggcatacgctaacGtgtcctgcagaagattcaaa	10	9	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:55537593G>T	ENST00000294383.6	-	67	7693	c.7694C>A	c.(7693-7695)aCg>aAg	p.T2565K	USP24_ENST00000484447.1_5'UTR|USP24_ENST00000407756.1_Missense_Mutation_p.T2405K	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	2565					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						ATACGCTAACGTGTCCTGCAG	0.493											OREG0013507	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T2565K		Atlas-SNP	.											.	USP24	323	.	0			c.C7694A						.						67	64	65					1																	55537593		2062	4209	6271	SO:0001583	missense	23358	exon67			GCTAACGTGTCCT	AB028980	CCDS44154.1, CCDS44154.2	1p32.3	2008-04-11	2005-08-08		ENSG00000162402	ENSG00000162402		"Ubiquitin-specific peptidases"	12623	protein-coding gene	gene with protein product		610569	"ubiquitin specific protease 24"			12838346	Standard	NM_015306		Approved	KIAA1057	uc021onw.1	Q9UPU5	OTTHUMG00000008135	ENST00000294383.6:c.7694C>A	chr1.hg19:g.55537593G>T	ENSP00000294383:p.Thr2565Lys	137.0	0.0	1008	66.0	4.0	NM_015306	Q6ZSY2|Q8N2Y4|Q9NXD1	Missense_Mutation	SNP	ENST00000294383.6	hg19	CCDS44154.2	.	.	.	.	.	.	.	.	.	.	G	25.4	4.633083	0.87660	.	.	ENSG00000162402	ENST00000294383;ENST00000407756	T;T	0.04406	3.63;3.67	4.56	4.56	0.56223	.	0.000000	0.64402	D	0.000001	T	0.19725	0.0474	M	0.62723	1.935	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.00473	-1.1718	10	0.62326	D	0.03	.	17.5474	0.87866	0.0:0.0:1.0:0.0	.	2405	B7WPF4	.	K	2565;2405	ENSP00000294383:T2565K;ENSP00000385700:T2405K	ENSP00000294383:T2565K	T	-	2	0	USP24	55310181	1.000000	0.71417	0.991000	0.47740	0.817000	0.46193	9.024000	0.93689	2.374000	0.81015	0.655000	0.94253	ACG	.	.		0.493	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2			T	55537593	G	T	55537593	3	4	259	1	0	0	0	0	1	0	0	0	17070	1145	40	1	176	1	USP24	1	55537593	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	919076	55537593	193713028	35	36353										
FGGY	55277	hgsc.bcm.edu	37	chr1	60019838	60019838	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agggcacggcctcatctgtgAggggcagccagtgacgtcac	15	12	3	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:60019838A>G	ENST00000303721.7	+	8	1016	c.842A>G	c.(841-843)gAg>gGg	p.E281G	FGGY_ENST00000371218.4_Missense_Mutation_p.E281G|FGGY_ENST00000474476.1_3'UTR|FGGY_ENST00000371210.1_5'UTR|FGGY_ENST00000371212.1_Missense_Mutation_p.E193G	NM_018291.3	NP_060761.3	Q96C11	FGGY_HUMAN	FGGY carbohydrate kinase domain containing	281					carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|neuron cellular homeostasis (GO:0070050)		kinase activity (GO:0016301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	22	all_cancers(7;7.36e-05)					CTCATCTGTGAGGGGCAGCCA	0.517																																					p.E281G		Atlas-SNP	.											.	FGGY	99	.	0			c.A842G						.						74	57	63					1																	60019838		2203	4300	6503	SO:0001583	missense	55277	exon8			TCTGTGAGGGGCA		CCDS611.2, CCDS44155.1, CCDS58003.1, CCDS60155.1	1p32.1	2008-10-23			ENSG00000172456	ENSG00000172456			25610	protein-coding gene	gene with protein product		611370				17671248	Standard	NM_018291		Approved	FLJ10986	uc009wac.3	Q96C11	OTTHUMG00000008424	ENST00000303721.7:c.842A>G	chr1.hg19:g.60019838A>G	ENSP00000305922:p.Glu281Gly	153.0	0.0		93.0	5.0	NM_001113411	B1AK92|B1AK93|B1AK94|B2RDR8|D3DQ56|Q9HA63|Q9NV20	Missense_Mutation	SNP	ENST00000303721.7	hg19	CCDS611.2	.	.	.	.	.	.	.	.	.	.	A	16.73	3.203046	0.58234	.	.	ENSG00000172456	ENST00000371218;ENST00000303721;ENST00000371212	T;T;T	0.25250	2.82;2.82;1.81	5.28	5.28	0.74379	.	0.049083	0.85682	D	0.000000	T	0.25938	0.0632	L	0.52364	1.645	0.80722	D	1	B;B;B;B	0.15141	0.004;0.012;0.002;0.004	B;B;B;B	0.17722	0.019;0.009;0.002;0.005	T	0.03706	-1.1011	9	.	.	.	-23.3108	15.3844	0.74684	1.0:0.0:0.0:0.0	.	281;193;281;281	Q96C11-3;B1AK94;F2Z2V1;Q96C11	.;.;.;FGGY_HUMAN	G	281;281;193	ENSP00000360262:E281G;ENSP00000305922:E281G;ENSP00000360256:E193G	.	E	+	2	0	FGGY	59792426	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	7.233000	0.78125	2.210000	0.71456	0.533000	0.62120	GAG	.	.		0.517	FGGY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023210.2	NM_001113411		G	60019838	A	G	60019838	3	3	259	1	0	0	0	0	1	0	0	0	5879	304	11	2	868	2	FGGY	1	60019838	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	4482245	60019838	189230783	36	36354										
INADL	10207	hgsc.bcm.edu	37	chr1	62330060	62330060	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgactcctagattgcaggaaAtggatgaagaaagagaaatt	11	4	0	5			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:62330060A>G	ENST00000371158.2	+	20	2704	c.2590A>G	c.(2590-2592)Atg>Gtg	p.M864V	INADL_ENST00000316485.6_Missense_Mutation_p.M864V	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	864					cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						ATTGCAGGAAATGGATGAAGA	0.418																																					p.M864V		Atlas-SNP	.											.	INADL	179	.	0			c.A2590G						.						114	111	112					1																	62330060		2203	4300	6503	SO:0001583	missense	10207	exon20			CAGGAAATGGATG	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.2590A>G	chr1.hg19:g.62330060A>G	ENSP00000360200:p.Met864Val	170.0	0.0		100.0	4.0	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	hg19	CCDS617.2	.	.	.	.	.	.	.	.	.	.	A	0.282	-0.985589	0.02180	.	.	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000255202	T;T	0.10960	2.94;2.82	5.48	-1.59	0.08453	.	0.326888	0.28809	N	0.014075	T	0.06188	0.0160	L	0.42245	1.32	0.20764	N	0.999857	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.35919	-0.9769	10	0.16896	T	0.51	.	2.3489	0.04279	0.1658:0.3049:0.3789:0.1504	.	864;864;864	F8W8T2;Q8NI35;Q8NI35-4	.;INADL_HUMAN;.	V	864	ENSP00000360200:M864V;ENSP00000326199:M864V	ENSP00000255202:M864V	M	+	1	0	INADL	62102648	0.000000	0.05858	0.032000	0.17829	0.673000	0.39480	-0.584000	0.05800	-0.202000	0.10268	0.454000	0.30748	ATG	.	.		0.418	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		G	62330060	A	G	62330060	3	3	259	1	0	0	0	0	1	0	0	0	7740	101	4	2	2664	2	INADL	1	62330060	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2310222	62330060	186920561	37	36355										
INADL	10207	hgsc.bcm.edu	37	chr1	62582321	62582321	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggggaggacatgagaaatgcCtcacaggagacagtggccac	15	9	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:62582321C>A	ENST00000371158.2	+	36	4887	c.4773C>A	c.(4771-4773)gcC>gcA	p.A1591A	INADL_ENST00000543708.1_Silent_p.A405A	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1591	PDZ 9. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						TGAGAAATGCCTCACAGGAGA	0.507																																					p.A1591A		Atlas-SNP	.											.	INADL	179	.	0			c.C4773A						.						73	76	75					1																	62582321		1984	4156	6140	SO:0001819	synonymous_variant	10207	exon36			AAATGCCTCACAG	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.4773C>A	chr1.hg19:g.62582321C>A		95.0	0.0		51.0	4.0	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Silent	SNP	ENST00000371158.2	hg19	CCDS617.2																																																																																			.	.		0.507	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		A	62582321	C	A	62582321	2	1	259	1	0	0	0	0	0	0	0	1	7740	668	24	3		3	INADL	1	62582321	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	252261	62582321	186668300	38	36356										
DOCK7	85440	hgsc.bcm.edu	37	chr1	63099217	63099217	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atatatggttctgcacactcTccaatgtctccttgctgtag	7	11	3	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:63099217T>C	ENST00000340370.5	-	10	1085	c.1068A>G	c.(1066-1068)ggA>ggG	p.G356G	DOCK7_ENST00000404627.2_Silent_p.G356G|DOCK7_ENST00000251157.5_Silent_p.G356G	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	356					activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						CTGCACACTCTCCAATGTCTC	0.368																																					p.G356G		Atlas-SNP	.											.	DOCK7	184	.	0			c.A1068G						.						253	247	249					1																	63099217		2203	4300	6503	SO:0001819	synonymous_variant	85440	exon10			ACACTCTCCAATG		CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.1068A>G	chr1.hg19:g.63099217T>C		161.0	0.0		95.0	4.0	NM_001271999	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Silent	SNP	ENST00000340370.5	hg19	CCDS30734.1																																																																																			.	.		0.368	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407		C	63099217	T	C	63099217	2	2	259	1	0	0	0	0	0	0	0	1	4694	1538	54	2		2	DOCK7	1	63099217	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	516896	63099217	186151404	39	36357										
DNAJC6	9829	hgsc.bcm.edu	37	chr1	65867511	65867511	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tcctcgcatggtactcccacCcatcaaagcaaaccccagac	5	18	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:65867511C>A	ENST00000395325.3	+	15	2161	c.2004C>A	c.(2002-2004)acC>acA	p.T668T	DNAJC6_ENST00000371069.4_Silent_p.T725T|DNAJC6_ENST00000263441.7_Silent_p.T655T	NM_014787.3	NP_055602.1	O75061	AUXI_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 6	668	Pro-rich.				cell death (GO:0008219)|clathrin coat disassembly (GO:0072318)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of clathrin-mediated endocytosis (GO:2000369)	cytosol (GO:0005829)|synapse (GO:0045202)	protein tyrosine phosphatase activity (GO:0004725)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(22)|ovary(1)|prostate(2)|skin(1)	39						GTACTCCCACCCATCAAAGCA	0.448																																					p.T725T		Atlas-SNP	.											.	DNAJC6	104	.	0			c.C2175A						.						96	96	96					1																	65867511		2203	4300	6503	SO:0001819	synonymous_variant	9829	exon15			TCCCACCCATCAA	AB007942	CCDS30739.1, CCDS58004.1, CCDS58005.1	1p31.3	2011-09-02			ENSG00000116675	ENSG00000116675		"Heat shock proteins / DNAJ (HSP40)"	15469	protein-coding gene	gene with protein product	"auxilin"	608375				9455484, 11147971	Standard	NM_001256864		Approved	KIAA0473	uc001dce.2	O75061	OTTHUMG00000009066	ENST00000395325.3:c.2004C>A	chr1.hg19:g.65867511C>A		110.0	0.0		73.0	4.0	NM_001256864	B7Z3V8|D3DQ65|D3DQ66|Q32M66|Q4G0K1|Q5T614|Q5T615	Silent	SNP	ENST00000395325.3	hg19	CCDS30739.1																																																																																			.	.		0.448	DNAJC6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025134.1			A	65867511	C	A	65867511	2	1	259	1	0	0	0	0	0	0	0	1	4655	610	22	3		3	DNAJC6	1	65867511	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	2768294	65867511	183383110	40	36358										
WLS	79971	hgsc.bcm.edu	37	chr1	68611689	68611689	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gattccagccacgatgatgaAggccatctggtcgtgtccag	12	11	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:68611689A>G	ENST00000262348.4	-	9	1394	c.1141T>C	c.(1141-1143)Ttc>Ctc	p.F381L	WLS_ENST00000491811.1_5'UTR|WLS_ENST00000354777.2_Missense_Mutation_p.F379L|GNG12-AS1_ENST00000413628.1_RNA|GNG12-AS1_ENST00000420587.1_RNA|WLS_ENST00000370976.3_Missense_Mutation_p.F290L|WLS_ENST00000540432.1_Missense_Mutation_p.F381L	NM_024911.6	NP_079187.3	Q5T9L3	WLS_HUMAN	wntless Wnt ligand secretion mediator	381					anterior/posterior axis specification (GO:0009948)|mesoderm formation (GO:0001707)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|Wnt signaling pathway (GO:0016055)	cytoplasmic vesicle (GO:0031410)|early endosome membrane (GO:0031901)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(4)|prostate(3)|urinary_tract(1)	20						ACGATGATGAAGGCCATCTGG	0.527																																					p.F381L		Atlas-SNP	.											.	WLS	97	.	0			c.T1141C						.						86	85	85					1																	68611689		2203	4300	6503	SO:0001583	missense	79971	exon9			TGATGAAGGCCAT	BX538320	CCDS642.1, CCDS30750.1, CCDS53331.1	1p31.2	2013-10-03	2013-10-03	2010-03-02	ENSG00000116729	ENSG00000116729			30238	protein-coding gene	gene with protein product	"wntless homolog"	611514	"chromosome 1 open reading frame 139", "G protein-coupled receptor 177", "wntless homolog (Drosophila)"	C1orf139, GPR177		12761501	Standard	NM_024911		Approved	FLJ23091, MRP, wls, EVI, mig-14	uc001dee.3	Q5T9L3	OTTHUMG00000009153	ENST00000262348.4:c.1141T>C	chr1.hg19:g.68611689A>G	ENSP00000262348:p.Phe381Leu	100.0	0.0		59.0	4.0	NM_024911	B2RNT2|Q5JRS7|Q7Z2Z9|Q8NC43	Missense_Mutation	SNP	ENST00000262348.4	hg19	CCDS642.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.949806	0.73787	.	.	ENSG00000116729	ENST00000540432;ENST00000354777;ENST00000262348;ENST00000370976	T;T;T;T	0.46819	0.86;0.86;0.86;0.86	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.35335	0.0928	L	0.59436	1.845	0.80722	D	1	B;B;B;B	0.26318	0.146;0.077;0.011;0.146	B;B;B;B	0.30316	0.034;0.114;0.027;0.034	T	0.33854	-0.9852	10	0.52906	T	0.07	-26.0661	15.6915	0.77457	1.0:0.0:0.0:0.0	.	381;290;381;379	F5H4K0;Q5JRS7;Q5T9L3;Q5T9L3-2	.;.;WLS_HUMAN;.	L	381;379;381;290	ENSP00000446112:F381L;ENSP00000346829:F379L;ENSP00000262348:F381L;ENSP00000360015:F290L	ENSP00000262348:F381L	F	-	1	0	WLS	68384277	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.962000	0.93254	2.107000	0.64212	0.533000	0.62120	TTC	.	.		0.527	WLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025368.1	NM_024911		G	68611689	A	G	68611689	3	3	259	1	0	0	0	0	1	0	0	0	17391	72	3	2	626	2	WLS	1	68611689	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2744178	68611689	180638932	41	36359										
RABGGTB	5876	hgsc.bcm.edu	37	chr1	76253187	76253187	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	actttattttgaaagggcacTccacagaaggatgttattat	8	6	0	2	rs542064322		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:76253187T>C	ENST00000319942.3	+	2	80	c.9T>C	c.(7-9)acT>acC	p.T3T	RABGGTB_ENST00000496055.1_3'UTR|RABGGTB_ENST00000535300.1_5'UTR|RABGGTB_ENST00000370826.3_Silent_p.T3T|SNORD45B_ENST00000364617.1_RNA|SNORD45A_ENST00000384512.1_RNA|SNORD45C_ENST00000383893.1_RNA	NM_004582.3	NP_004573.2	P53611	PGTB2_HUMAN	Rab geranylgeranyltransferase, beta subunit	3					cellular protein modification process (GO:0006464)|protein geranylgeranylation (GO:0018344)|visual perception (GO:0007601)	Rab-protein geranylgeranyltransferase complex (GO:0005968)	Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)	19						GAAAGGGCACTCCACAGAAGG	0.383																																					p.T3T		Atlas-SNP	.											.	RABGGTB	37	.	0			c.T9C						.						131	118	123					1																	76253187		2203	4300	6503	SO:0001819	synonymous_variant	5876	exon2			GGGCACTCCACAG	U49245	CCDS669.1	1p31	2008-02-05			ENSG00000137955	ENSG00000137955			9796	protein-coding gene	gene with protein product		179080				8706741, 8954794	Standard	NM_004582		Approved		uc001dgy.2	P53611	OTTHUMG00000009786	ENST00000319942.3:c.9T>C	chr1.hg19:g.76253187T>C		218.0	0.0		122.0	6.0	NM_004582	Q92697	Silent	SNP	ENST00000319942.3	hg19	CCDS669.1																																																																																			.	.		0.383	RABGGTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026972.1	NM_004582		C	76253187	T	C	76253187	2	2	259	1	0	0	0	0	0	0	0	1	12983	1538	54	2		2	RABGGTB	1	76253187	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	7641498	76253187	172997434	42	36360										
LPHN2	23266	hgsc.bcm.edu	37	chr1	82409131	82409131	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atagttattagccagctgaaTccatacactcttcgatttga	6	9	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:82409131T>C	ENST00000370728.1	+	8	1521	c.876T>C	c.(874-876)aaT>aaC	p.N292N	LPHN2_ENST00000319517.6_Silent_p.N292N|LPHN2_ENST00000370723.1_Silent_p.N292N|LPHN2_ENST00000370727.1_Silent_p.N292N|LPHN2_ENST00000370730.1_Silent_p.N292N|LPHN2_ENST00000271029.4_Silent_p.N292N|LPHN2_ENST00000335786.5_Silent_p.N292N|LPHN2_ENST00000359929.3_Silent_p.N292N|LPHN2_ENST00000370717.2_Silent_p.N292N|LPHN2_ENST00000370721.1_Silent_p.N296N|LPHN2_ENST00000370715.1_Silent_p.N292N|LPHN2_ENST00000370713.1_Silent_p.N292N|LPHN2_ENST00000370725.1_Silent_p.N292N|LPHN2_ENST00000394879.1_Silent_p.N292N|LPHN2_ENST00000469377.2_Intron			O95490	LPHN2_HUMAN	latrophilin 2	292	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)			NS(3)|breast(6)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(37)|ovary(3)|pancreas(1)|prostate(3)|skin(22)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	119				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)		GCCAGCTGAATCCATACACTC	0.423																																					p.N292N		Atlas-SNP	.											.	LPHN2	464	.	0			c.T876C						.						134	124	127					1																	82409131		2203	4300	6503	SO:0001819	synonymous_variant	23266	exon5			GCTGAATCCATAC	AJ131581	CCDS689.1, CCDS72811.1	1p31.1	2014-08-08	2003-03-17	2003-05-02	ENSG00000117114	ENSG00000117114		"-", "GPCR / Class B : Orphans"	18582	protein-coding gene	gene with protein product		607018	"latrophilin 1"	LPHH1		10760572	Standard	XR_248786		Approved	KIAA0786, LEC1	uc001diu.3	O95490	OTTHUMG00000009844	ENST00000370728.1:c.876T>C	chr1.hg19:g.82409131T>C		143.0	0.0		99.0	4.0	NM_012302	A5XEI2|B1ALT8|B1ALT9|B1ALU0|B1ALU2|B1ALU4|B1ALU5|B1ALU6|O94882|Q5VX76|Q9UKY5|Q9UKY6	Silent	SNP	ENST00000370728.1	hg19		.	.	.	.	.	.	.	.	.	.	T	4.305	0.055913	0.08291	.	.	ENSG00000117114	ENST00000449420	.	.	.	5.52	1.84	0.25277	.	.	.	.	.	T	0.40119	0.1104	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.24048	-1.0171	4	.	.	.	.	7.3061	0.26449	0.0:0.5143:0.0:0.4857	.	.	.	.	T	160	.	.	I	+	2	0	LPHN2	82181719	0.958000	0.32768	1.000000	0.80357	0.985000	0.73830	0.087000	0.14958	0.347000	0.23924	0.374000	0.22700	ATC	.	.		0.423	LPHN2-007	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000027188.1	NM_012302		C	82409131	T	C	82409131	2	2	259	1	0	0	0	0	0	0	0	1	8925	1432	50	2		2	LPHN2	1	82409131	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	6155944	82409131	166841490	43	36361										
EPHX4	253152	hgsc.bcm.edu	37	chr1	92528663	92528663	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	actccaacactactactgtgGggagagaatgacgcattcat	9	10	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:92528663G>T	ENST00000370383.4	+	7	1007	c.909G>T	c.(907-909)tgG>tgT	p.W303C		NM_173567.4	NP_775838.3	Q8IUS5	EPHX4_HUMAN	epoxide hydrolase 4	303						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)			central_nervous_system(1)|large_intestine(3)|lung(8)	12						TACTACTGTGGGGAGAGAATG	0.393																																					p.W303C	GBM(140;473 1857 5172 22066 49719)	Atlas-SNP	.											.	EPHX4	46	.	0			c.G909T						.						130	134	133					1																	92528663		2203	4300	6503	SO:0001583	missense	253152	exon7			ACTGTGGGGAGAG	AK074822	CCDS736.1	1p22.1	2011-10-05	2009-04-06	2009-04-06	ENSG00000172031	ENSG00000172031		"Abhydrolase domain containing"	23758	protein-coding gene	gene with protein product			"abhydrolase domain containing 7"	ABHD7		12477932	Standard	NM_173567		Approved	EPHXRP, FLJ90341	uc001don.2	Q8IUS5	OTTHUMG00000010114	ENST00000370383.4:c.909G>T	chr1.hg19:g.92528663G>T	ENSP00000359410:p.Trp303Cys	207.0	0.0		94.0	4.0	NM_173567	Q8NCC6	Missense_Mutation	SNP	ENST00000370383.4	hg19	CCDS736.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.227482	0.79576	.	.	ENSG00000172031	ENST00000370383	T	0.04758	3.56	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.22475	0.0542	M	0.90483	3.12	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.03259	-1.1055	10	0.49607	T	0.09	.	19.904	0.97001	0.0:0.0:1.0:0.0	.	303	Q8IUS5	EPHX4_HUMAN	C	303	ENSP00000359410:W303C	ENSP00000359410:W303C	W	+	3	0	EPHX4	92301251	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.366000	0.97143	2.698000	0.92095	0.650000	0.86243	TGG	.	.		0.393	EPHX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027985.1	NM_173567		T	92528663	G	T	92528663	3	4	259	1	0	0	0	0	1	0	0	0	5184	1241	43	3	935	3	EPHX4	1	92528663	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	10119532	92528663	156721958	44	36362										
EPHX4	253152	hgsc.bcm.edu	37	chr1	92528734	92528734	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttatgttaaaaactatttcaGgctaactattttgtcagaag	6	5	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:92528734G>T	ENST00000370383.4	+	7	1078	c.980G>T	c.(979-981)aGg>aTg	p.R327M		NM_173567.4	NP_775838.3	Q8IUS5	EPHX4_HUMAN	epoxide hydrolase 4	327						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)			central_nervous_system(1)|large_intestine(3)|lung(8)	12						AACTATTTCAGGCTAACTATT	0.388																																					p.R327M	GBM(140;473 1857 5172 22066 49719)	Atlas-SNP	.											.	EPHX4	46	.	0			c.G980T						.						88	93	91					1																	92528734		2203	4300	6503	SO:0001583	missense	253152	exon7			ATTTCAGGCTAAC	AK074822	CCDS736.1	1p22.1	2011-10-05	2009-04-06	2009-04-06	ENSG00000172031	ENSG00000172031		"Abhydrolase domain containing"	23758	protein-coding gene	gene with protein product			"abhydrolase domain containing 7"	ABHD7		12477932	Standard	NM_173567		Approved	EPHXRP, FLJ90341	uc001don.2	Q8IUS5	OTTHUMG00000010114	ENST00000370383.4:c.980G>T	chr1.hg19:g.92528734G>T	ENSP00000359410:p.Arg327Met	93.0	0.0		80.0	4.0	NM_173567	Q8NCC6	Missense_Mutation	SNP	ENST00000370383.4	hg19	CCDS736.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.199073	0.79015	.	.	ENSG00000172031	ENST00000370383	T	0.70399	-0.48	5.84	5.84	0.93424	.	0.043531	0.85682	D	0.000000	T	0.79221	0.4409	M	0.86268	2.805	0.53688	D	0.999975	P	0.49358	0.923	P	0.56343	0.796	T	0.82234	-0.0558	10	0.72032	D	0.01	.	13.3592	0.60646	0.0719:0.0:0.9281:0.0	.	327	Q8IUS5	EPHX4_HUMAN	M	327	ENSP00000359410:R327M	ENSP00000359410:R327M	R	+	2	0	EPHX4	92301322	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.227000	0.72282	2.756000	0.94617	0.650000	0.86243	AGG	.	.		0.388	EPHX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027985.1	NM_173567		T	92528734	G	T	92528734	3	4	259	1	0	0	0	0	1	0	0	0	5184	1000	35	3	1006	3	EPHX4	1	92528734	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	71	92528734	156721887	45	36363										
GLMN	11146	hgsc.bcm.edu	37	chr1	92713534	92713534	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctcaatatttccaagttctgTccataatccagtctgttaag	5	10	3	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:92713534T>C	ENST00000370360.3	-	17	1567	c.1486A>G	c.(1486-1488)Aca>Gca	p.T496A	GLMN_ENST00000534881.1_Missense_Mutation_p.T482A	NM_053274.2	NP_444504.1	Q92990	GLMN_HUMAN	glomulin, FKBP associated protein	496					muscle cell differentiation (GO:0042692)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of T cell proliferation (GO:0042130)|neural tube closure (GO:0001843)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of phosphorylation (GO:0042327)|regulation of gene expression, epigenetic (GO:0040029)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|vasculogenesis (GO:0001570)	Cul2-RING ubiquitin ligase complex (GO:0031462)|Cul3-RING ubiquitin ligase complex (GO:0031463)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|cullin-RING ubiquitin ligase complex (GO:0031461)|intracellular (GO:0005622)	hepatocyte growth factor receptor binding (GO:0005171)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase inhibitor activity (GO:0055105)			endometrium(5)|kidney(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)	17		all_lung(203;0.00827)|Lung NSC(277;0.0295)		all cancers(265;0.00702)|GBM - Glioblastoma multiforme(16;0.0381)|Epithelial(280;0.0989)		CCAAGTTCTGTCCATAATCCA	0.294									Multiple Glomus Tumors (of the Skin), Familial																												p.T496A		Atlas-SNP	.											GLMN,NS,carcinoma,+2,1	GLMN	37	.	0			c.A1486G						.						84	88	87					1																	92713534		2202	4290	6492	SO:0001583	missense	11146	exon17	Familial Cancer Database	Multiple Familial Glomangiomas, Hereditary Multiple Glomus Tumors, Familial Multiple Glomangiomatosis, Inherited Cutaneous Venous Anomalies, incl. Familial Multiple Glomangiomyoma	GTTCTGTCCATAA	U73704	CCDS738.1	1p22.1	2008-02-05	2004-07-01		ENSG00000174842	ENSG00000174842			14373	protein-coding gene	gene with protein product		601749	"venous malformation with glomus cells"	VMGLOM		8955134	Standard	XM_005270400		Approved	FAP48, GLML, GVM, FKBPAP	uc001dor.3	Q92990	OTTHUMG00000010283	ENST00000370360.3:c.1486A>G	chr1.hg19:g.92713534T>C	ENSP00000359385:p.Thr496Ala	158.0	0.0		86.0	4.0	NM_053274	Q5VVC3|Q9BVE8	Missense_Mutation	SNP	ENST00000370360.3	hg19	CCDS738.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.568284	0.86439	.	.	ENSG00000174842	ENST00000370360;ENST00000534881	T;T	0.44482	0.92;0.92	6.17	6.17	0.99709	.	0.043410	0.85682	D	0.000000	T	0.46814	0.1412	L	0.55834	1.745	0.58432	D	0.999997	P;P	0.52463	0.924;0.953	P;P	0.55508	0.777;0.76	T	0.48747	-0.9008	10	0.72032	D	0.01	-13.1409	16.8222	0.85835	0.0:0.0:0.0:1.0	.	482;496	B4DJ85;Q92990	.;GLMN_HUMAN	A	496;482	ENSP00000359385:T496A;ENSP00000440156:T482A	ENSP00000359385:T496A	T	-	1	0	GLMN	92486122	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	6.378000	0.73150	2.371000	0.80710	0.533000	0.62120	ACA	.	.		0.294	GLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028358.1	NM_007070		C	92713534	T	C	92713534	3	2	259	1	0	0	0	0	1	0	0	0	6456	1667	58	2	310	2	GLMN	1	92713534	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	184800	92713534	156537087	46	36364										
DPYD	1806	hgsc.bcm.edu	37	chr1	97770913	97770913	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gacctgagacagtgttggtgGctgtaacgccattggcacca	13	10	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:97770913G>T	ENST00000370192.3	-	18	2301	c.2201C>A	c.(2200-2202)gCc>gAc	p.A734D	DPYD-AS1_ENST00000422980.1_RNA	NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	734					beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase catabolic process (GO:0006145)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymidine catabolic process (GO:0006214)|thymine catabolic process (GO:0006210)|UMP biosynthetic process (GO:0006222)|uracil catabolic process (GO:0006212)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|dihydroorotate dehydrogenase activity (GO:0004152)|dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(18)|lung(30)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	AGTGTTGGTGGCTGTAACGCC	0.468																																					p.A734D		Atlas-SNP	.											.	DPYD	219	.	0			c.C2201A						.						197	167	177					1																	97770913		2203	4300	6503	SO:0001583	missense	1806	exon18			TTGGTGGCTGTAA	U20938	CCDS30777.1, CCDS53346.1	1p22	2014-09-17			ENSG00000188641	ENSG00000188641	1.3.1.2		3012	protein-coding gene	gene with protein product		612779				7713523	Standard	NM_000110		Approved	DPD	uc001drv.3	Q12882	OTTHUMG00000039683	ENST00000370192.3:c.2201C>A	chr1.hg19:g.97770913G>T	ENSP00000359211:p.Ala734Asp	156.0	0.0		97.0	5.0	NM_000110	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Missense_Mutation	SNP	ENST00000370192.3	hg19	CCDS30777.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.035026	0.93575	.	.	ENSG00000188641	ENST00000370192	T	0.75938	-0.98	5.55	5.55	0.83447	Aldolase-type TIM barrel (1);	0.000000	0.85682	D	0.000000	D	0.90573	0.7045	H	0.96518	3.835	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92729	0.6198	10	0.87932	D	0	-15.1721	19.8696	0.96845	0.0:0.0:1.0:0.0	.	734	Q12882	DPYD_HUMAN	D	734	ENSP00000359211:A734D	ENSP00000359211:A734D	A	-	2	0	DPYD	97543501	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	9.416000	0.97383	2.773000	0.95371	0.585000	0.79938	GCC	.	.		0.468	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110		T	97770913	G	T	97770913	3	4	259	1	0	0	0	0	1	0	0	0	4747	1203	42	3	900	3	DPYD	1	97770913	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	5057379	97770913	151479708	47	36365										
DBT	1629	hgsc.bcm.edu	37	chr1	100672056	100672056	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	taagatcagtggtgctgagcTgactcacagagcccaatttc	10	10	2	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:100672056T>C	ENST00000370132.4	-	9	1167	c.1154A>G	c.(1153-1155)cAg>cGg	p.Q385R		NM_001918.3	NP_001909.3	P11182	ODB2_HUMAN	dihydrolipoamide branched chain transacylase E2	385					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	dihydrolipoyllysine-residue (2-methylpropanoyl)transferase activity (GO:0043754)			NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|pancreas(1)|prostate(1)|skin(1)	19		all_epithelial(167;5.4e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.0739)|all cancers(265;0.123)|COAD - Colon adenocarcinoma(174;0.154)|Lung(183;0.199)		GGTGCTGAGCTGACTCACAGA	0.403																																					p.Q385R		Atlas-SNP	.											.	DBT	39	.	0			c.A1154G						.						185	188	187					1																	100672056		2203	4300	6503	SO:0001583	missense	1629	exon9			CTGAGCTGACTCA	BC016675	CCDS767.1	1p31	2008-02-05	2004-11-15		ENSG00000137992	ENSG00000137992			2698	protein-coding gene	gene with protein product		248610	"dihydrolipoamide branched chain transacylase (E2 component of branched chain keto acid dehydrogenase complex; maple syrup urine disease)"			1420314, 1429740	Standard	NM_001918		Approved		uc001dta.3	P11182	OTTHUMG00000010921	ENST00000370132.4:c.1154A>G	chr1.hg19:g.100672056T>C	ENSP00000359151:p.Gln385Arg	140.0	0.0		92.0	4.0	NM_001918	B2R811|Q5VVL8	Missense_Mutation	SNP	ENST00000370132.4	hg19	CCDS767.1	.	.	.	.	.	.	.	.	.	.	T	16.45	3.126641	0.56721	.	.	ENSG00000137992	ENST00000543138;ENST00000370132	T	0.40476	1.03	5.54	5.54	0.83059	2-oxoacid dehydrogenase acyltransferase, catalytic domain (1);Chloramphenicol acetyltransferase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.15998	0.0385	N	0.20357	0.565	0.80722	D	1	B;B	0.22211	0.008;0.066	B;B	0.23018	0.014;0.043	T	0.06625	-1.0816	10	0.21014	T	0.42	-11.8926	15.969	0.79998	0.0:0.0:0.0:1.0	.	204;385	F5H1F9;P11182	.;ODB2_HUMAN	R	204;385	ENSP00000359151:Q385R	ENSP00000359151:Q385R	Q	-	2	0	DBT	100444644	1.000000	0.71417	0.965000	0.40720	0.731000	0.41821	7.565000	0.82337	2.234000	0.73211	0.459000	0.35465	CAG	.	.		0.403	DBT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030101.2	NM_001918		C	100672056	T	C	100672056	3	2	259	1	0	0	0	0	1	0	0	0	4260	1580	55	2	306	2	DBT	1	100672056	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	2901143	100672056	148578565	48	36366										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103491374	103491374	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acctttacccctagtttggcTtttgctgatgcttgataact	7	10	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:103491374T>C	ENST00000370096.3	-	7	1210				COL11A1_ENST00000353414.4_Intron|COL11A1_ENST00000358392.2_Silent_p.K305K|COL11A1_ENST00000512756.1_Intron	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1						cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		CTAGTTTGGCTTTTGCTGATG	0.368																																					p.K305K		Atlas-SNP	.											.	COL11A1	972	.	0			c.A915G						.						171	165	167					1																	103491374		2203	4300	6503	SO:0001627	intron_variant	1301	exon6			TTTGGCTTTTGCT	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.898-205A>G	chr1.hg19:g.103491374T>C		214.0	0.0		138.0	6.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Silent	SNP	ENST00000370096.3	hg19	CCDS778.1																																																																																			.	.		0.368	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		C	103491374	T	C	103491374	1	2	259	0	1	0	0	0	0	0	0	0	3669	1606	56	2		2	COL11A1	1	103491374	Intron	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	2819318	103491374	145759247	49	36367										
KIAA1324	57535	hgsc.bcm.edu	37	chr1	109715162	109715162	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgactccaggtggatgaagaCcacagagaaaggatgggaat	14	6	0	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:109715162C>A	ENST00000369939.3	+	5	851	c.668C>A	c.(667-669)aCc>aAc	p.T223N	KIAA1324_ENST00000529753.1_Missense_Mutation_p.T223N	NM_020775.4	NP_065826	Q6UXG2	K1324_HUMAN	KIAA1324	223					cellular response to starvation (GO:0009267)|macroautophagy (GO:0016236)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|positive regulation of autophagic vacuole assembly (GO:2000786)|positive regulation of vacuole organization (GO:0044090)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34		all_epithelial(167;0.000102)|all_lung(203;0.000323)|Lung NSC(277;0.00063)		Colorectal(144;0.0188)|Lung(183;0.0527)|COAD - Colon adenocarcinoma(174;0.14)|Epithelial(280;0.21)|all cancers(265;0.249)		TGGATGAAGACCACAGAGAAA	0.498																																					p.T223N		Atlas-SNP	.											.	KIAA1324	77	.	0			c.C668A						.						78	75	76					1																	109715162		2203	4300	6503	SO:0001583	missense	57535	exon5			TGAAGACCACAGA	AK057647	CCDS794.1, CCDS58015.1	1p13.3	2008-09-18			ENSG00000116299	ENSG00000116299			29618	protein-coding gene	gene with protein product	"estrogen induced gene 121"	611298				10718198, 16322283	Standard	NM_020775		Approved	maba1, EIG121	uc021orb.1	Q6UXG2	OTTHUMG00000011725	ENST00000369939.3:c.668C>A	chr1.hg19:g.109715162C>A	ENSP00000358955:p.Thr223Asn	236.0	0.0		153.0	63.0	NM_020775	Q08AE6|Q5T5C9|Q5T5D0|Q5T5D1|Q9P2M2	Missense_Mutation	SNP	ENST00000369939.3	hg19	CCDS794.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.964348	0.74131	.	.	ENSG00000116299	ENST00000369939;ENST00000457623;ENST00000529753	T;T;T	0.42513	0.97;0.97;0.97	5.69	5.69	0.88448	.	0.222920	0.45867	D	0.000330	T	0.27524	0.0676	N	0.11064	0.09	0.24179	N	0.995594	D;D;D;D	0.63880	0.976;0.993;0.976;0.976	P;P;P;P	0.58520	0.84;0.753;0.84;0.794	T	0.19582	-1.0301	10	0.27785	T	0.31	-7.9859	17.586	0.87981	0.0:1.0:0.0:0.0	.	223;223;223;223	Q6UXG2-4;Q6UXG2-3;C9J810;Q6UXG2	.;.;.;K1324_HUMAN	N	223	ENSP00000358955:T223N;ENSP00000393964:T223N;ENSP00000434595:T223N	ENSP00000358955:T223N	T	+	2	0	KIAA1324	109516685	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	2.872000	0.48467	2.678000	0.91216	0.650000	0.86243	ACC	.	.		0.498	KIAA1324-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032389.2	NM_020775		A	109715162	C	A	109715162	3	1	259	1	0	0	0	0	1	0	0	0	8232	507	18	3	686	3	KIAA1324	1	109715162	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	6223788	109715162	139535459	50	36368										
ATXN7L2	127002	hgsc.bcm.edu	37	chr1	110031709	110031709	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccaagcagacctacccatacTgtgcactgcccaggtacgtc	8	16	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:110031709T>C	ENST00000369870.3	+	7	1039	c.1024T>C	c.(1024-1026)Tgt>Cgt	p.C342R		NM_153340.4	NP_699171.3	Q5T6C5	AT7L2_HUMAN	ataxin 7-like 2	342										breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)	17		all_epithelial(167;0.00197)|all_lung(203;0.00291)|Lung NSC(277;0.00453)		Colorectal(144;0.0129)|Lung(183;0.0426)|Epithelial(280;0.0675)|READ - Rectum adenocarcinoma(129;0.0693)|all cancers(265;0.071)|LUSC - Lung squamous cell carcinoma(189;0.228)		CTACCCATACTGTGCACTGCC	0.622																																					p.C342R		Atlas-SNP	.											.	ATXN7L2	60	.	0			c.T1024C						.						85	76	79					1																	110031709		2203	4300	6503	SO:0001583	missense	127002	exon7			CCATACTGTGCAC	BC037582	CCDS30794.1	1p13.2	2008-02-05			ENSG00000162650	ENSG00000162650			28713	protein-coding gene	gene with protein product						12477932	Standard	NM_153340		Approved	MGC46534, FLJ00381	uc001dxr.3	Q5T6C5	OTTHUMG00000011027	ENST00000369870.3:c.1024T>C	chr1.hg19:g.110031709T>C	ENSP00000358886:p.Cys342Arg	128.0	0.0		91.0	4.0	NM_153340		Missense_Mutation	SNP	ENST00000369870.3	hg19	CCDS30794.1	.	.	.	.	.	.	.	.	.	.	T	17.10	3.303442	0.60195	.	.	ENSG00000162650	ENST00000369870;ENST00000541125	T	0.30714	1.52	5.97	4.85	0.62838	.	0.000000	0.64402	D	0.000002	T	0.13114	0.0318	L	0.50333	1.59	0.80722	D	1	B	0.25441	0.126	B	0.20767	0.031	T	0.04870	-1.0921	10	0.27082	T	0.32	-5.2976	9.2673	0.37650	0.0:0.0817:0.0:0.9183	.	342	Q5T6C5	AT7L2_HUMAN	R	342	ENSP00000358886:C342R	ENSP00000358886:C342R	C	+	1	0	ATXN7L2	109833232	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.145000	0.50623	2.288000	0.76882	0.533000	0.62120	TGT	.	.		0.622	ATXN7L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030331.1	NM_153340		C	110031709	T	C	110031709	3	2	259	1	0	0	0	0	1	0	0	0	1217	1580	55	2	1050	2	ATXN7L2	1	110031709	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	316547	110031709	139218912	51	36369										
EPS8L3	79574	hgsc.bcm.edu	37	chr1	110294654	110294654	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggaccacagtcagttcccgtGggttcctagcttcaaactcg	10	13	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:110294654G>A	ENST00000361965.4	-	15	1503	c.1397C>T	c.(1396-1398)cCa>cTa	p.P466L	EPS8L3_ENST00000361852.4_Missense_Mutation_p.P436L|RP4-735C1.4_ENST00000431955.1_RNA|EPS8L3_ENST00000369805.3_Missense_Mutation_p.P467L	NM_133181.3	NP_573444.2	Q8TE67	ES8L3_HUMAN	EPS8-like 3	466	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.					cytoplasm (GO:0005737)				breast(1)|endometrium(3)|large_intestine(6)|lung(15)|ovary(5)|skin(1)|upper_aerodigestive_tract(1)	32		all_epithelial(167;1.95e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)		Lung(183;0.0245)|Colorectal(144;0.0365)|all cancers(265;0.103)|Epithelial(280;0.109)|LUSC - Lung squamous cell carcinoma(189;0.137)|COAD - Colon adenocarcinoma(174;0.141)		CAGTTCCCGTGGGTTCCTAGC	0.597																																					p.P467L		Atlas-SNP	.											.	EPS8L3	73	.	0			c.C1400T						.						105	106	105					1																	110294654		2203	4300	6503	SO:0001583	missense	79574	exon15			TCCCGTGGGTTCC	AK025175	CCDS813.1, CCDS814.1, CCDS815.1	1p13.2	2008-02-05			ENSG00000198758	ENSG00000198758			21297	protein-coding gene	gene with protein product		614989				12620401	Standard	NM_139053		Approved	FLJ21522, MGC16817	uc001dyq.2	Q8TE67	OTTHUMG00000011651	ENST00000361965.4:c.1397C>T	chr1.hg19:g.110294654G>A	ENSP00000355255:p.Pro466Leu	236.0	0.0		186.0	75.0	NM_139053	A8K833|Q5T8Q6|Q5T8Q7|Q5T8Q8|Q96E47|Q9H719	Missense_Mutation	SNP	ENST00000361965.4	hg19	CCDS814.1	.	.	.	.	.	.	.	.	.	.	G	15.57	2.872393	0.51695	.	.	ENSG00000198758	ENST00000361852;ENST00000369805;ENST00000361965	T;T;T	0.33216	1.42;1.42;1.42	5.57	4.64	0.57946	Src homology-3 domain (4);	0.852789	0.10775	N	0.635539	T	0.28995	0.0720	M	0.85299	2.745	0.35830	D	0.825258	P;B;P	0.42296	0.666;0.434;0.775	B;B;B	0.42282	0.23;0.242;0.382	T	0.25950	-1.0117	10	0.44086	T	0.13	-0.0164	11.7056	0.51595	0.0:0.0:0.8235:0.1765	.	436;466;467	Q8TE67-2;Q8TE67;Q8TE67-3	.;ES8L3_HUMAN;.	L	436;467;466	ENSP00000354551:P436L;ENSP00000358820:P467L;ENSP00000355255:P466L	ENSP00000354551:P436L	P	-	2	0	EPS8L3	110096177	0.114000	0.22134	0.814000	0.32528	0.820000	0.46376	1.671000	0.37513	1.318000	0.45170	0.655000	0.94253	CCA	.	.		0.597	EPS8L3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000032234.1	NM_024526		A	110294654	G	A	110294654	3	1	259	1	0	0	0	0	1	0	0	0	5199	1348	47	3	404	3	EPS8L3	1	110294654	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	262945	110294654	138955967	52	36370										
CHIA	27159	hgsc.bcm.edu	37	chr1	111862847	111862847	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgtttcaggttgcacggctcCagctcagcccattgagccaa	10	13	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:111862847C>T	ENST00000369740.1	+	12	1293	c.1190C>T	c.(1189-1191)cCa>cTa	p.P397L	CHIA_ENST00000343320.6_Missense_Mutation_p.P397L|CHIA_ENST00000451398.2_Missense_Mutation_p.P236L|CHIA_ENST00000483391.1_Missense_Mutation_p.P236L|RP5-1125M8.2_ENST00000426321.1_RNA|CHIA_ENST00000430615.1_Missense_Mutation_p.P289L|CHIA_ENST00000353665.6_Missense_Mutation_p.P236L	NM_001258001.1|NM_201653.3	NP_001244930.1|NP_970615.2	Q9BZP6	CHIA_HUMAN	chitinase, acidic	397					apoptotic process (GO:0006915)|cell wall chitin metabolic process (GO:0006037)|chitin catabolic process (GO:0006032)|chitin metabolic process (GO:0006030)|digestion (GO:0007586)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|positive regulation of chemokine secretion (GO:0090197)|production of molecular mediator involved in inflammatory response (GO:0002532)|response to fungus (GO:0009620)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|chitinase activity (GO:0004568)|kinase binding (GO:0019900)|lysozyme activity (GO:0003796)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		all_cancers(81;3.23e-05)|all_epithelial(167;1.2e-05)|all_lung(203;0.000154)|Lung NSC(277;0.000304)		Colorectal(144;0.0115)|Lung(183;0.0292)|COAD - Colon adenocarcinoma(174;0.0314)|all cancers(265;0.0477)|Epithelial(280;0.0918)|LUSC - Lung squamous cell carcinoma(189;0.154)		TGCACGGCTCCAGCTCAGCCC	0.572																																					p.P397L		Atlas-SNP	.											.	CHIA	115	.	0			c.C1190T						.						67	67	67					1																	111862847		2203	4300	6503	SO:0001583	missense	27159	exon12			CGGCTCCAGCTCA	AF290004	CCDS832.1, CCDS41368.1, CCDS58017.1	1p13.2	2008-05-14			ENSG00000134216	ENSG00000134216			17432	protein-coding gene	gene with protein product		606080				11085997	Standard	NM_021797		Approved	AMCase, TSA1902, CHIT2	uc001eas.4	Q9BZP6	OTTHUMG00000011165	ENST00000369740.1:c.1190C>T	chr1.hg19:g.111862847C>T	ENSP00000358755:p.Pro397Leu	104.0	0.0		82.0	4.0	NM_201653	Q32W79|Q32W80|Q3B866|Q5U5Z5|Q5VUV4|Q86UD8|Q9ULY3|Q9ULY4	Missense_Mutation	SNP	ENST00000369740.1	hg19	CCDS41368.1	.	.	.	.	.	.	.	.	.	.	C	13.88	2.370086	0.42003	.	.	ENSG00000134216	ENST00000422815;ENST00000483391;ENST00000369740;ENST00000343320;ENST00000451398;ENST00000353665;ENST00000489524;ENST00000430615	T;T;T;T;T;T;T;T	0.06068	4.05;3.69;3.35;3.35;3.69;3.69;3.48;3.9	5.07	5.07	0.68467	.	1.360170	0.06346	U	0.708911	T	0.05823	0.0152	M	0.71036	2.16	0.22684	N	0.998854	B	0.33000	0.393	B	0.29862	0.108	T	0.21930	-1.0231	10	0.59425	D	0.04	-1.3337	15.9825	0.80121	0.0:1.0:0.0:0.0	.	397	Q9BZP6	CHIA_HUMAN	L	341;236;397;397;236;236;236;289	ENSP00000387671:P341L;ENSP00000436946:P236L;ENSP00000358755:P397L;ENSP00000341828:P397L;ENSP00000390476:P236L;ENSP00000338970:P236L;ENSP00000433309:P236L;ENSP00000391132:P289L	ENSP00000341828:P397L	P	+	2	0	CHIA	111664370	0.000000	0.05858	0.005000	0.12908	0.049000	0.14656	0.622000	0.24433	2.628000	0.89032	0.655000	0.94253	CCA	.	.		0.572	CHIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030710.1			T	111862847	C	T	111862847	3	4	259	1	0	0	0	0	1	0	0	0	3344	594	21	3	1232	3	CHIA	1	111862847	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	1568193	111862847	137387774	53	36371										
ATP5F1	515	hgsc.bcm.edu	37	chr1	111998810	111998810	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cctatcagtactaggtgtaaTggtctatggaattaaaaaat	8	5	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:111998810T>C	ENST00000369722.3	+	4	932	c.326T>C	c.(325-327)aTg>aCg	p.M109T	ATP5F1_ENST00000483994.1_Missense_Mutation_p.M48T|ATP5F1_ENST00000369721.4_3'UTR	NM_001688.4	NP_001679.2	P24539	AT5F1_HUMAN	ATP synthase, H+ transporting, mitochondrial Fo complex, subunit B1	109					ATP catabolic process (GO:0006200)|ATP synthesis coupled proton transport (GO:0015986)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) (GO:0000276)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	hydrogen ion transmembrane transporter activity (GO:0015078)|transmembrane transporter activity (GO:0022857)			breast(1)|cervix(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	8		all_cancers(81;8.16e-06)|all_epithelial(167;5.63e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0238)|Colorectal(144;0.0296)|all cancers(265;0.0488)|Epithelial(280;0.0732)|COAD - Colon adenocarcinoma(174;0.114)|LUSC - Lung squamous cell carcinoma(189;0.135)		CTAGGTGTAATGGTCTATGGA	0.378																																					p.M109T		Atlas-SNP	.											.	ATP5F1	20	.	0			c.T326C						.						143	143	143					1																	111998810		2203	4297	6500	SO:0001583	missense	515	exon4			GTGTAATGGTCTA	X60221	CCDS836.1	1p13.2	2012-10-12	2010-06-11		ENSG00000116459	ENSG00000116459		"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	840	protein-coding gene	gene with protein product		603270	"ATP synthase, H+ transporting, mitochondrial F0 complex, subunit b, isoform 1", "ATP synthase, H+ transporting, mitochondrial F0 complex, subunit B1"			1831354	Standard	XM_005270929		Approved		uc001ebc.3	P24539	OTTHUMG00000011745	ENST00000369722.3:c.326T>C	chr1.hg19:g.111998810T>C	ENSP00000358737:p.Met109Thr	113.0	0.0		90.0	4.0	NM_001688	Q9BQ68|Q9BRU8	Missense_Mutation	SNP	ENST00000369722.3	hg19	CCDS836.1	.	.	.	.	.	.	.	.	.	.	T	6.407	0.443303	0.12164	.	.	ENSG00000116459	ENST00000369722;ENST00000483994	T;T	0.28069	1.63;1.63	5.37	4.23	0.50019	.	0.431403	0.27420	N	0.019450	T	0.08758	0.0217	L	0.29908	0.895	0.23762	N	0.996912	B;B	0.15473	0.013;0.013	B;B	0.18561	0.022;0.022	T	0.25152	-1.0140	9	.	.	.	.	11.699	0.51560	0.1327:0.0:0.0:0.8673	.	109;109	Q08ET0;P24539	.;AT5F1_HUMAN	T	109;48	ENSP00000358737:M109T;ENSP00000420366:M48T	.	M	+	2	0	ATP5F1	111800333	0.864000	0.29904	0.003000	0.11579	0.000000	0.00434	5.684000	0.68197	0.964000	0.38108	-0.301000	0.09380	ATG	.	.		0.378	ATP5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032455.1	NM_001688		C	111998810	T	C	111998810	3	2	259	1	0	0	0	0	1	0	0	0	1152	1464	51	2	340	2	ATP5F1	1	111998810	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	135963	111998810	137251811	54	36372										
TTF2	8458	hgsc.bcm.edu	37	chr1	117641477	117641477	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atccatcacttgaagatcaaGcttgtgaccgaatttaccga	7	10	2	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:117641477G>T	ENST00000369466.4	+	22	3336	c.3292G>T	c.(3292-3294)Gct>Tct	p.A1098S	TTF2_ENST00000480701.1_3'UTR	NM_003594.3	NP_003585.3	Q9UNY4	TTF2_HUMAN	transcription termination factor, RNA polymerase II	1098	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(24)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	50	Lung SC(450;0.225)	all_cancers(81;4.23e-06)|all_epithelial(167;3.65e-07)|all_lung(203;2.81e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0553)|Colorectal(144;0.179)|LUSC - Lung squamous cell carcinoma(189;0.19)		TGAAGATCAAGCTTGTGACCG	0.453																																					p.A1098S		Atlas-SNP	.											.	TTF2	92	.	0			c.G3292T						.						148	136	140					1																	117641477		2203	4300	6503	SO:0001583	missense	8458	exon22			GATCAAGCTTGTG	AF073771	CCDS892.1	1p13.1	2014-02-18			ENSG00000116830	ENSG00000116830			12398	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 6"	604718				9748214	Standard	NM_003594		Approved	HuF2, ZGRF6	uc001egy.3	Q9UNY4	OTTHUMG00000012030	ENST00000369466.4:c.3292G>T	chr1.hg19:g.117641477G>T	ENSP00000358478:p.Ala1098Ser	124.0	0.0		81.0	4.0	NM_003594	A8K4Q2|O75921|Q5T2K7|Q5VVU8|Q8N6I8	Missense_Mutation	SNP	ENST00000369466.4	hg19	CCDS892.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.034997	0.93575	.	.	ENSG00000116830	ENST00000369466;ENST00000427271	T;T	0.74209	-0.82;-0.82	5.22	5.22	0.72569	Helicase, C-terminal (3);	0.000000	0.37809	N	0.001922	D	0.85944	0.5815	M	0.88377	2.95	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85642	0.1277	10	0.38643	T	0.18	-15.5364	16.6163	0.84917	0.0:0.0:1.0:0.0	.	1098	Q9UNY4	TTF2_HUMAN	S	1098;79	ENSP00000358478:A1098S;ENSP00000408111:A79S	ENSP00000358478:A1098S	A	+	1	0	TTF2	117443000	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.301000	0.96167	2.594000	0.87642	0.462000	0.41574	GCT	.	.		0.453	TTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033277.3			T	117641477	G	T	117641477	3	4	259	1	0	0	0	0	1	0	0	0	16734	971	34	3	3378	3	TTF2	1	117641477	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	5642667	117641477	131609144	55	36373										
POLR3C	10623	hgsc.bcm.edu	37	chr1	145598543	145598543	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aaaacagacttactggatcaTctgccagcagagtgagatac	9	9	2	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:145598543T>C	ENST00000334163.3	-	8	1110	c.950A>G	c.(949-951)gAt>gGt	p.D317G	POLR3C_ENST00000471254.1_5'UTR|POLR3C_ENST00000369294.1_Missense_Mutation_p.D317G	NM_006468.6	NP_006459.3	Q9BUI4	RPC3_HUMAN	polymerase (RNA) III (DNA directed) polypeptide C (62kD)	317					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			breast(2)|endometrium(4)|kidney(1)|large_intestine(3)|liver(1)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)		Epithelial(2;7.55e-13)			TACTGGATCATCTGCCAGCAG	0.388																																					p.D317G		Atlas-SNP	.											.	POLR3C	41	.	0			c.A950G						.						137	135	136					1																	145598543		2203	4300	6503	SO:0001583	missense	10623	exon8			GGATCATCTGCCA	AJ238234	CCDS72864.1	1q21	2013-01-21			ENSG00000186141	ENSG00000186141		"RNA polymerase subunits"	30076	protein-coding gene	gene with protein product						9171375, 12391170	Standard	NM_006468		Approved	RPC62, RPC3	uc001eoh.3	Q9BUI4	OTTHUMG00000013753	ENST00000334163.3:c.950A>G	chr1.hg19:g.145598543T>C	ENSP00000334564:p.Asp317Gly	90.0	0.0		69.0	4.0	NM_006468	O15317|Q9Y3R6	Missense_Mutation	SNP	ENST00000334163.3	hg19	CCDS921.1	.	.	.	.	.	.	.	.	.	.	T	24.5	4.538596	0.85917	.	.	ENSG00000186141	ENST00000334163;ENST00000369294	T;T	0.48522	0.81;0.81	6.17	6.17	0.99709	RNA polymerase III Rpc82, C -terminal (1);	0.090873	0.85682	D	0.000000	T	0.49677	0.1571	M	0.63843	1.955	0.80722	D	1	P;P;P	0.51449	0.637;0.934;0.945	P;P;P	0.57468	0.458;0.725;0.821	T	0.47560	-0.9108	10	0.31617	T	0.26	-21.036	13.214	0.59844	0.0:0.0:0.0:1.0	.	317;317;317	E9PHH9;Q9BUI4;Q53F76	.;RPC3_HUMAN;.	G	317	ENSP00000334564:D317G;ENSP00000358300:D317G	ENSP00000334564:D317G	D	-	2	0	POLR3C	144309900	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.085000	0.76875	2.371000	0.80710	0.533000	0.62120	GAT	.	.		0.388	POLR3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038542.1	NM_006468		C	145598543	T	C	145598543	3	2	259	1	0	0	0	0	1	0	0	0	12239	1435	50	2	686	2	POLR3C	1	145598543	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	27957066	145598543	103652078	56	36374										
ILF2	3608	hgsc.bcm.edu	37	chr1	153635509	153635509	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	caatacctgctgttctagggTcatgactgtgtgtactctaa	9	9	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:153635509T>C	ENST00000361891.4	-	12	1032	c.907A>G	c.(907-909)Acc>Gcc	p.T303A	ILF2_ENST00000480213.1_5'UTR	NM_001267809.1|NM_004515.3	NP_001254738.1|NP_004506.2	Q12905	ILF2_HUMAN	interleukin enhancer binding factor 2	303	DZF. {ECO:0000255|PROSITE- ProRule:PRU01040}.				immune response (GO:0006955)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|transferase activity (GO:0016740)			cervix(1)|kidney(1)|lung(4)|skin(1)	7	all_lung(78;1.84e-32)|Lung NSC(65;6.67e-31)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			TGTTCTAGGGTCATGACTGTG	0.498																																					p.T303A		Atlas-SNP	.											.	ILF2	25	.	0			c.A907G						.						88	85	86					1																	153635509		2203	4300	6503	SO:0001583	missense	3608	exon12			CTAGGGTCATGAC	U10323	CCDS1050.1, CCDS72919.1	1q21.3	2012-12-04	2012-12-04		ENSG00000143621	ENSG00000143621			6037	protein-coding gene	gene with protein product		603181	"interleukin enhancer binding factor 2, 45kD", "interleukin enhancer binding factor 2, 45kDa"			7519613	Standard	NM_004515		Approved	NF45	uc001fcr.4	Q12905	OTTHUMG00000037087	ENST00000361891.4:c.907A>G	chr1.hg19:g.153635509T>C	ENSP00000355011:p.Thr303Ala	162.0	0.0		122.0	5.0	NM_004515	A6NDB0|B2R8G7|Q5SR10|Q5SR11|Q7L7R3|Q9BWD4|Q9P1N0	Missense_Mutation	SNP	ENST00000361891.4	hg19	CCDS1050.1	.	.	.	.	.	.	.	.	.	.	T	18.70	3.680666	0.68042	.	.	ENSG00000143621	ENST00000361891	T	0.50548	0.74	5.28	5.28	0.74379	DZF (2);	0.044922	0.85682	D	0.000000	T	0.50650	0.1628	M	0.85630	2.765	0.80722	D	1	B;B	0.33528	0.363;0.416	B;B	0.43990	0.311;0.438	T	0.60845	-0.7182	10	0.72032	D	0.01	-12.3981	11.5378	0.50648	0.0:0.0:0.0:1.0	.	303;303	F4ZW62;Q12905	.;ILF2_HUMAN	A	303	ENSP00000355011:T303A	ENSP00000355011:T303A	T	-	1	0	ILF2	151902133	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.160000	0.64929	2.225000	0.72522	0.533000	0.62120	ACC	.	.		0.498	ILF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090040.1	NM_004515		C	153635509	T	C	153635509	3	2	259	1	0	0	0	0	1	0	0	0	7720	1667	58	2	277	2	ILF2	1	153635509	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	8036966	153635509	95615112	57	36375										
DENND4B	9909	hgsc.bcm.edu	37	chr1	153903522	153903522	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aacagaggctggatcaggggTtagccaaggagatggggcct	17	7	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:153903522T>C	ENST00000361217.4	-	25	4433	c.4015A>G	c.(4015-4017)Acc>Gcc	p.T1339A	DENND4B_ENST00000474386.1_5'UTR	NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	1339					positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab protein signal transduction (GO:0032483)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	36	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			GGATCAGGGGTTAGCCAAGGA	0.572																																					p.T1339A		Atlas-SNP	.											.	DENND4B	210	.	0			c.A4015G						.						26	30	29					1																	153903522		2004	4169	6173	SO:0001583	missense	9909	exon25			CAGGGGTTAGCCA	AB007945	CCDS44228.1	1q21.3	2012-10-03	2006-01-27	2006-01-27	ENSG00000198837	ENSG00000198837		"DENN/MADD domain containing"	29044	protein-coding gene	gene with protein product			"KIAA0476"	KIAA0476		9455484, 12906859	Standard	NM_014856		Approved		uc001fdd.1	O75064	OTTHUMG00000037157	ENST00000361217.4:c.4015A>G	chr1.hg19:g.153903522T>C	ENSP00000354597:p.Thr1339Ala	110.0	0.0		70.0	4.0	NM_014856	Q5T4K0	Missense_Mutation	SNP	ENST00000361217.4	hg19	CCDS44228.1	.	.	.	.	.	.	.	.	.	.	T	7.862	0.726343	0.15439	.	.	ENSG00000198837	ENST00000361217	T	0.06068	3.35	5.14	2.77	0.32553	.	0.689341	0.13633	N	0.373562	T	0.00875	0.0029	N	0.03608	-0.345	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.48364	-0.9042	10	0.40728	T	0.16	-2.4136	5.4973	0.16809	0.0:0.1716:0.1604:0.6679	.	1339	O75064	DEN4B_HUMAN	A	1339	ENSP00000354597:T1339A	ENSP00000354597:T1339A	T	-	1	0	DENND4B	152170146	0.001000	0.12720	0.007000	0.13788	0.804000	0.45430	-0.031000	0.12287	0.974000	0.38366	0.455000	0.32223	ACC	.	.		0.572	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806		C	153903522	T	C	153903522	3	2	259	1	0	0	0	0	1	0	0	0	4436	1725	60	2	491	2	DENND4B	1	153903522	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	268013	153903522	95347099	58	36376										
SLC39A1	27173	hgsc.bcm.edu	37	chr1	153935029	153935029	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gccttcatggttagctcctgGccggcgcagcacacagatgg	13	13	1	1	rs3211049		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:153935029G>A	ENST00000368623.3	-	1	922	c.163C>T	c.(163-165)Cca>Tca	p.P55S	SLC39A1_ENST00000368621.1_Missense_Mutation_p.P55S|SLC39A1_ENST00000537590.1_5'UTR|SLC39A1_ENST00000310483.6_Missense_Mutation_p.P55S|SLC39A1_ENST00000461071.1_5'UTR|SLC39A1_ENST00000356205.4_Missense_Mutation_p.P55S			Q9NY26	S39A1_HUMAN	solute carrier family 39 (zinc transporter), member 1	55				P -> T (in Ref. 1; CAB59979/CAB59980). {ECO:0000305}.	cation transport (GO:0006812)|transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic cation transmembrane transporter activity (GO:0022890)|zinc ion transmembrane transporter activity (GO:0005385)			kidney(2)|large_intestine(2)|lung(7)|urinary_tract(1)	12	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)	Colorectal(1306;0.019)		TTAGCTCCTGGCCGGCGCAGC	0.632																																					p.P55S		Atlas-SNP	.											.	SLC39A1	24	.	0			c.C163T						.						37	44	41					1																	153935029		2203	4300	6503	SO:0001583	missense	27173	exon2			CTCCTGGCCGGCG	BC007886	CCDS1055.1, CCDS72920.1	1q21	2013-05-22		2002-02-15	ENSG00000143570	ENSG00000143570		"Solute carriers"	12876	protein-coding gene	gene with protein product		604740	"zinc/iron regulated transporter-like"	ZIRTL		10610721, 10681536	Standard	NM_014437		Approved	ZIP1	uc031ppi.1	Q9NY26	OTTHUMG00000037158	ENST00000368623.3:c.163C>T	chr1.hg19:g.153935029G>A	ENSP00000357612:p.Pro55Ser	179.0	0.0		118.0	5.0	NM_001271957	B4DDY7|Q5T4K1|Q8N2H7|Q9BTV0|Q9UBI7|Q9Y2Z7|Q9Y380	Missense_Mutation	SNP	ENST00000368623.3	hg19	CCDS1055.1	.	.	.	.	.	.	.	.	.	.	G	1.547	-0.540142	0.04053	.	.	ENSG00000143570	ENST00000356205;ENST00000368623;ENST00000368621;ENST00000310483;ENST00000543075;ENST00000429040;ENST00000413622;ENST00000417348	T;T;T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96;0.96;0.96	5.64	-0.156	0.13391	.	0.369343	0.24506	N	0.037935	T	0.06050	0.0157	N	0.12746	0.255	0.23816	N	0.996769	B	0.02656	0.0	B	0.12156	0.007	T	0.36866	-0.9730	10	0.20046	T	0.44	-2.6953	3.6124	0.08065	0.0792:0.2628:0.389:0.269	.	55	Q9NY26	S39A1_HUMAN	S	55;55;55;55;44;55;55;55	ENSP00000348535:P55S;ENSP00000357612:P55S;ENSP00000357610:P55S;ENSP00000309710:P55S;ENSP00000392950:P55S;ENSP00000392229:P55S;ENSP00000407717:P55S	ENSP00000309710:P55S	P	-	1	0	SLC39A1	152201653	0.000000	0.05858	0.283000	0.24790	0.287000	0.27160	-0.205000	0.09411	0.004000	0.14682	0.655000	0.94253	CCA	.	.		0.632	SLC39A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090284.1	NM_014437		A	153935029	G	A	153935029	3	1	259	1	0	0	0	0	1	0	0	0	14627	1203	42	3	823	3	SLC39A1	1	153935029	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	31507	153935029	95315592	59	36377										
CREB3L4	148327	hgsc.bcm.edu	37	chr1	153945673	153945673	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tacctccctacattctagggTggcagcctgttctgcacaga	9	13	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:153945673T>C	ENST00000368607.3	+	7	1012	c.746T>C	c.(745-747)gTg>gCg	p.V249A	CREB3L4_ENST00000271889.4_Missense_Mutation_p.V249A|JTB_ENST00000471173.1_5'Flank|CREB3L4_ENST00000368600.3_Missense_Mutation_p.V229A|CREB3L4_ENST00000405694.3_Missense_Mutation_p.V102A|CREB3L4_ENST00000368603.1_Missense_Mutation_p.V249A|CREB3L4_ENST00000468845.1_3'UTR	NM_001255978.1|NM_001255980.1|NM_130898.3	NP_001242907.1|NP_001242909.1|NP_570968.1	Q8TEY5	CR3L4_HUMAN	cAMP responsive element binding protein 3-like 4	249	bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				response to unfolded protein (GO:0006986)|spermatogenesis (GO:0007283)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(3)	13	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			CATTCTAGGGTGGCAGCCTGT	0.512																																					p.V249A		Atlas-SNP	.											.	CREB3L4	36	.	0			c.T746C						.						63	64	63					1																	153945673		2203	4300	6503	SO:0001583	missense	148327	exon7			CTAGGGTGGCAGC	AF394167	CCDS1056.1, CCDS58029.1	1q21.2	2013-01-10			ENSG00000143578	ENSG00000143578		"basic leucine zipper proteins"	18854	protein-coding gene	gene with protein product		607138					Standard	NM_130898		Approved	AIbZIP, CREB4, CREB3, hJAL, ATCE1	uc001fdr.3	Q8TEY5	OTTHUMG00000037159	ENST00000368607.3:c.746T>C	chr1.hg19:g.153945673T>C	ENSP00000357596:p.Val249Ala	124.0	0.0		100.0	4.0	NM_001255978	D3DV62|Q5T4L0|Q86YW6	Missense_Mutation	SNP	ENST00000368607.3	hg19	CCDS1056.1	.	.	.	.	.	.	.	.	.	.	T	15.12	2.738148	0.49045	.	.	ENSG00000143578	ENST00000405694;ENST00000368607;ENST00000271889;ENST00000368603;ENST00000368600	T;T;T;T;T	0.60171	0.21;0.21;0.21;0.21;0.21	5.26	4.13	0.48395	Basic-leucine zipper (bZIP) transcription factor (2);bZIP transcription factor, bZIP-1 (1);	0.242965	0.32671	N	0.005787	T	0.27967	0.0689	L	0.35542	1.07	0.41438	D	0.987902	B;B	0.32409	0.046;0.37	B;B	0.30316	0.068;0.114	T	0.20907	-1.0261	10	0.59425	D	0.04	-12.8755	9.3244	0.37984	0.0:0.0849:0.0:0.9151	.	229;249	Q5T4L0;Q8TEY5	.;CR3L4_HUMAN	A	102;249;249;249;229	ENSP00000385104:V102A;ENSP00000357596:V249A;ENSP00000271889:V249A;ENSP00000357592:V249A;ENSP00000357589:V229A	ENSP00000271889:V249A	V	+	2	0	CREB3L4	152212297	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	1.545000	0.36169	1.008000	0.39264	0.533000	0.62120	GTG	.	.		0.512	CREB3L4-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090291.1	NM_130898		C	153945673	T	C	153945673	3	2	259	1	0	0	0	0	1	0	0	0	3861	1696	59	2	768	2	CREB3L4	1	153945673	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	10644	153945673	95304948	60	36378										
UBAP2L	9898	hgsc.bcm.edu	37	chr1	154218760	154218760	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tctggatccgtctcaggctcCttctctggcccagcctctgg	10	16	4	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:154218760C>A	ENST00000361546.2	+	10	965	c.923C>A	c.(922-924)cCt>cAt	p.P308H	UBAP2L_ENST00000271877.7_Missense_Mutation_p.P319H|UBAP2L_ENST00000343815.6_Missense_Mutation_p.P308H|UBAP2L_ENST00000428931.1_Missense_Mutation_p.P308H			Q14157	UBP2L_HUMAN	ubiquitin associated protein 2-like	308					binding of sperm to zona pellucida (GO:0007339)		poly(A) RNA binding (GO:0044822)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(20)|ovary(1)|prostate(1)|urinary_tract(2)	50	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			TCTCAGGCTCCTTCTCTGGCC	0.488																																					p.P308H		Atlas-SNP	.											.	UBAP2L	197	.	0			c.C923A						.						129	124	125					1																	154218760		2203	4300	6503	SO:0001583	missense	9898	exon11			AGGCTCCTTCTCT	BC003170	CCDS1063.1, CCDS44229.1, CCDS72925.1	1q21.3	2008-02-05			ENSG00000143569	ENSG00000143569			29877	protein-coding gene	gene with protein product						8590280, 11230159	Standard	NM_014847		Approved	NICE-4, KIAA0144	uc001fep.4	Q14157	OTTHUMG00000035983	ENST00000361546.2:c.923C>A	chr1.hg19:g.154218760C>A	ENSP00000355343:p.Pro308His	114.0	0.0		78.0	4.0	NM_001127320	B4E0U8|Q5VU75|Q5VU76|Q9BTU3|Q9UGL2|Q9UGL3|Q9UGL4|Q9UGL5	Missense_Mutation	SNP	ENST00000361546.2	hg19	CCDS1063.1	.	.	.	.	.	.	.	.	.	.	C	19.59	3.855341	0.71719	.	.	ENSG00000143569	ENST00000343815;ENST00000428931;ENST00000271877;ENST00000368504;ENST00000361546	T;T;T;T;T	0.44083	2.71;2.72;2.73;0.93;2.72	5.29	5.29	0.74685	.	0.116551	0.64402	D	0.000014	T	0.29389	0.0732	N	0.08118	0	0.32691	N	0.514171	P;D;P;P;P	0.69078	0.838;0.997;0.899;0.899;0.838	B;D;P;P;B	0.66716	0.276;0.946;0.466;0.466;0.364	T	0.33189	-0.9878	10	0.56958	D	0.05	-9.7163	11.5156	0.50520	0.0:0.9194:0.0:0.0806	.	222;319;301;308;308	B4DZJ6;F8W726;Q14157-4;Q14157-1;Q14157	.;.;.;.;UBP2L_HUMAN	H	308;308;319;319;308	ENSP00000345308:P308H;ENSP00000389445:P308H;ENSP00000271877:P319H;ENSP00000357490:P319H;ENSP00000355343:P308H	ENSP00000271877:P319H	P	+	2	0	UBAP2L	152485384	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.331000	0.59273	2.752000	0.94435	0.655000	0.94253	CCT	.	.		0.488	UBAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087673.1	NM_014847		A	154218760	C	A	154218760	3	1	259	1	0	0	0	0	1	0	0	0	16853	681	24	3	961	3	UBAP2L	1	154218760	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	273087	154218760	95031861	61	36379										
ATP8B2	57198	hgsc.bcm.edu	37	chr1	154317184	154317184	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gcttcacctatcaggacaagCtttcttcttccaagctaact	5	13	4	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:154317184C>A	ENST00000368489.3	+	21	2308	c.2308C>A	c.(2308-2310)Ctt>Att	p.L770I		NM_020452.3	NP_065185.1	P98198	AT8B2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 2	756					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)		IL6R/ATP8B2(2)	breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			TCAGGACAAGCTTTCTTCTTC	0.532											OREG0013835	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L770I		Atlas-SNP	.											.	ATP8B2	158	.	0			c.C2308A						.						146	136	139					1																	154317184		2203	4300	6503	SO:0001583	missense	57198	exon21			GACAAGCTTTCTT	AB032963	CCDS1066.1, CCDS41405.1	1q21.3	2012-03-09	2012-03-09		ENSG00000143515	ENSG00000143515		"ATPases / P-type"	13534	protein-coding gene	gene with protein product		605867	"ATPase, class I, type 8B, member 2"			10574461, 11015572	Standard	NM_020452		Approved	ATPID, KIAA1137	uc001fex.3	P98198	OTTHUMG00000035979	ENST00000368489.3:c.2308C>A	chr1.hg19:g.154317184C>A	ENSP00000357475:p.Leu770Ile	100.0	0.0	1762	76.0	4.0	NM_020452	B4E3P4|Q6NT69|Q7Z486|Q96I43|Q96NQ7	Missense_Mutation	SNP	ENST00000368489.3	hg19	CCDS1066.1	.	.	.	.	.	.	.	.	.	.	C	5.724	0.318030	0.10845	.	.	ENSG00000143515	ENST00000368489	T	0.09817	2.94	5.62	2.52	0.30459	.	1.074510	0.07109	N	0.841811	T	0.02304	0.0071	N	0.11892	0.195	0.19575	N	0.999964	B	0.28470	0.213	B	0.29862	0.108	T	0.47911	-0.9080	10	0.31617	T	0.26	.	10.7602	0.46259	0.1356:0.474:0.3904:0.0	.	770	P98198-3	.	I	770	ENSP00000357475:L770I	ENSP00000357475:L770I	L	+	1	0	ATP8B2	152583808	0.000000	0.05858	0.003000	0.11579	0.257000	0.26127	0.640000	0.24705	0.694000	0.31654	0.591000	0.81541	CTT	.	.		0.532	ATP8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087658.2	NM_020452		A	154317184	C	A	154317184	3	1	259	1	0	0	0	0	1	0	0	0	1195	797	28	3	2520	3	ATP8B2	1	154317184	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	98424	154317184	94933437	62	36380										
IL6R	3570	hgsc.bcm.edu	37	chr1	154437808	154437808	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cgaccagatgccagggacccAcggagcccttatgacatcag	11	14	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:154437808A>G	ENST00000368485.3	+	10	1796	c.1359A>G	c.(1357-1359)ccA>ccG	p.P453P	IL6R_ENST00000344086.4_3'UTR	NM_000565.3	NP_000556.1	P08887	IL6RA_HUMAN	interleukin 6 receptor	453					acute-phase response (GO:0006953)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|endocrine pancreas development (GO:0031018)|extrinsic apoptotic signaling pathway (GO:0097191)|hepatic immune response (GO:0002384)|interleukin-6-mediated signaling pathway (GO:0070102)|monocyte chemotaxis (GO:0002548)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of interleukin-8 production (GO:0032717)|neutrophil mediated immunity (GO:0002446)|positive regulation of activation of Janus kinase activity (GO:0010536)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine production (GO:0032722)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|response to cytokine (GO:0034097)	apical plasma membrane (GO:0016324)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|interleukin-6 receptor complex (GO:0005896)|plasma membrane (GO:0005886)	ciliary neurotrophic factor binding (GO:0070119)|cytokine receptor activity (GO:0004896)|enzyme binding (GO:0019899)|interleukin-6 binding (GO:0019981)|protein homodimerization activity (GO:0042803)		IL6R/ATP8B2(2)	breast(2)|large_intestine(1)|ovary(3)	6	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)		Tocilizumab(DB06273)	CCAGGGACCCACGGAGCCCTT	0.582																																					p.P453P		Atlas-SNP	.											.	IL6R	47	.	0			c.A1359G						.						67	70	69					1																	154437808		2203	4300	6503	SO:0001819	synonymous_variant	3570	exon10			GGACCCACGGAGC	X12830	CCDS1067.1, CCDS1068.1, CCDS72927.1	1q21	2013-01-11			ENSG00000160712	ENSG00000160712		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6019	protein-coding gene	gene with protein product		147880					Standard	NM_000565		Approved	CD126	uc001fez.2	P08887	OTTHUMG00000036073	ENST00000368485.3:c.1359A>G	chr1.hg19:g.154437808A>G		197.0	0.0		105.0	5.0	NM_000565	A8KAE8|B2R6V4|Q16202|Q53EQ7|Q5FWG2|Q5VZ23	Silent	SNP	ENST00000368485.3	hg19	CCDS1067.1																																																																																			.	.		0.582	IL6R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087911.1	NM_000565		G	154437808	A	G	154437808	2	3	259	1	0	0	0	0	0	0	0	1	7711	146	6	2		2	IL6R	1	154437808	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	120624	154437808	94812813	63	36381										
TDRD10	126668	hgsc.bcm.edu	37	chr1	154515291	154515291	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cttctttgcagtcccgttggAaatgaggtgagcaaggtata	12	7	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:154515291A>G	ENST00000368480.3	+	8	582	c.497A>G	c.(496-498)gAa>gGa	p.E166G	TDRD10_ENST00000479937.1_3'UTR|TDRD10_ENST00000368482.4_Missense_Mutation_p.E166G			Q5VZ19	TDR10_HUMAN	tudor domain containing 10	166							nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			GTCCCGTTGGAAATGAGGTGA	0.512																																					p.E166G		Atlas-SNP	.											.	TDRD10	48	.	0			c.A497G						.						83	74	77					1																	154515291		2203	4300	6503	SO:0001583	missense	126668	exon8			CGTTGGAAATGAG	AL713777	CCDS30878.2, CCDS41406.1	1q21.3	2013-02-12			ENSG00000163239	ENSG00000163239		"Tudor domain containing", "RNA binding motif (RRM) containing"	25316	protein-coding gene	gene with protein product						12975309	Standard	NM_182499		Approved	DKFZp434M202	uc009wow.3	Q5VZ19	OTTHUMG00000037264	ENST00000368480.3:c.497A>G	chr1.hg19:g.154515291A>G	ENSP00000357465:p.Glu166Gly	166.0	0.0		93.0	4.0	NM_182499	A4FU09|B0QZ53|B4DXV4|Q3ZCP1|Q3ZCS7|Q5SXY7|Q6UXV2|Q8TCN3	Missense_Mutation	SNP	ENST00000368480.3	hg19	CCDS41406.1	.	.	.	.	.	.	.	.	.	.	A	15.33	2.801146	0.50315	.	.	ENSG00000163239	ENST00000368482;ENST00000368480	T;T	0.38240	1.19;1.15	3.27	3.27	0.37495	.	0.000000	0.36002	U	0.002843	T	0.14313	0.0346	L	0.32530	0.975	0.23862	N	0.996631	P;P	0.48694	0.914;0.801	B;P	0.45558	0.404;0.485	T	0.03384	-1.1042	10	0.37606	T	0.19	-6.3717	7.9501	0.30010	1.0:0.0:0.0:0.0	.	166;166	Q5VZ19;Q5VZ19-2	TDR10_HUMAN;.	G	166	ENSP00000357467:E166G;ENSP00000357465:E166G	ENSP00000357465:E166G	E	+	2	0	TDRD10	152781915	0.998000	0.40836	0.959000	0.39883	0.861000	0.49209	1.022000	0.30052	1.375000	0.46248	0.369000	0.22263	GAA	.	.		0.512	TDRD10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090700.2	NM_182499		G	154515291	A	G	154515291	3	3	259	1	0	0	0	0	1	0	0	0	15746	246	9	2	523	2	TDRD10	1	154515291	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	77483	154515291	94735330	64	36382										
DCST2	127579	hgsc.bcm.edu	37	chr1	155005955	155005955	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gaggacagtggctcggacctGgcgagagaatcccatgccca	14	12	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:155005955G>T	ENST00000368424.3	-	1	281	c.223C>A	c.(223-225)Cag>Aag	p.Q75K	DCST1_ENST00000368419.2_5'Flank|DCST1_ENST00000392480.1_5'Flank|DCST1_ENST00000295542.1_5'Flank|DCST2_ENST00000295536.5_Missense_Mutation_p.Q75K|DCST1_ENST00000423025.2_5'Flank	NM_144622.2	NP_653223.2	Q5T1A1	DCST2_HUMAN	DC-STAMP domain containing 2	75						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(13)|ovary(3)|prostate(1)|skin(1)	38	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			GCTCGGACCTGGCGAGAGAAT	0.657																																					p.Q75K		Atlas-SNP	.											.	DCST2	80	.	0			c.C223A						.						48	46	47					1																	155005955		2203	4300	6503	SO:0001583	missense	127579	exon1			GGACCTGGCGAGA	AK057496	CCDS1082.2	1q22	2008-02-05		2005-08-09	ENSG00000163354	ENSG00000163354			26562	protein-coding gene	gene with protein product							Standard	NM_144622		Approved	FLJ32934	uc001fgm.3	Q5T1A1	OTTHUMG00000037371	ENST00000368424.3:c.223C>A	chr1.hg19:g.155005955G>T	ENSP00000357409:p.Gln75Lys	173.0	0.0		88.0	5.0	NM_144622	Q2M2R2|Q8N810|Q96M03	Missense_Mutation	SNP	ENST00000368424.3	hg19	CCDS1082.2	.	.	.	.	.	.	.	.	.	.	G	8.969	0.972544	0.18736	.	.	ENSG00000163354	ENST00000368424;ENST00000295536	T;T	0.23552	1.9;1.93	5.44	4.33	0.51752	.	0.968381	0.08463	N	0.942162	T	0.05686	0.0149	L	0.38175	1.15	0.20403	N	0.99991	B	0.19331	0.035	B	0.14023	0.01	T	0.43065	-0.9414	10	0.02654	T	1	-31.6972	7.057	0.25106	0.0995:0.0:0.7252:0.1753	.	75	Q5T1A1	DCST2_HUMAN	K	75	ENSP00000357409:Q75K;ENSP00000295536:Q75K	ENSP00000295536:Q75K	Q	-	1	0	DCST2	153272579	0.870000	0.30015	1.000000	0.80357	0.867000	0.49689	2.247000	0.43151	2.564000	0.86499	0.561000	0.74099	CAG	.	.		0.657	DCST2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090953.3	NM_144622		T	155005955	G	T	155005955	3	4	259	1	0	0	0	0	1	0	0	0	4305	1357	47	3	2158	3	DCST2	1	155005955	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	490664	155005955	94244666	65	36383										
ARHGEF2	9181	hgsc.bcm.edu	37	chr1	155927648	155927648	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgtctcgtacgattagattcTgcagcgataccactgaaggc	10	10	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:155927648T>C	ENST00000361247.4	-	13	1670	c.1571A>G	c.(1570-1572)cAg>cGg	p.Q524R	ARHGEF2_ENST00000313695.7_Missense_Mutation_p.Q496R|ARHGEF2_ENST00000313667.4_Missense_Mutation_p.Q523R|ARHGEF2_ENST00000477754.2_Intron|ARHGEF2_ENST00000368315.4_Missense_Mutation_p.Q525R|ARHGEF2_ENST00000462460.2_Missense_Mutation_p.Q569R|ARHGEF2_ENST00000368316.1_Missense_Mutation_p.Q496R	NM_001162383.1|NM_001162384.1	NP_001155855.1|NP_001155856.1	Q92974	ARHG2_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 2	524	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin filament organization (GO:0007015)|apoptotic signaling pathway (GO:0097190)|cell morphogenesis (GO:0000902)|cellular hyperosmotic response (GO:0071474)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to tumor necrosis factor (GO:0071356)|establishment of mitotic spindle orientation (GO:0000132)|innate immune response (GO:0045087)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress (GO:1902219)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of necroptotic process (GO:0060546)|negative regulation of neurogenesis (GO:0050768)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cell proliferation (GO:0042127)|regulation of Rho protein signal transduction (GO:0035023)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)|vesicle (GO:0031982)	microtubule binding (GO:0008017)|Rac GTPase binding (GO:0048365)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho GTPase binding (GO:0017048)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(4)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|skin(2)	40	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					GATTAGATTCTGCAGCGATAC	0.522																																					p.Q524R	Melanoma(178;35 2768 6610 28839)	Atlas-SNP	.											.	ARHGEF2	81	.	0			c.A1571G						.						89	64	72					1																	155927648		2203	4300	6503	SO:0001583	missense	9181	exon13			AGATTCTGCAGCG	AB014551	CCDS1125.1, CCDS53375.1, CCDS53376.1	1q21-q22	2013-01-10	2009-06-12		ENSG00000116584	ENSG00000116584		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	682	protein-coding gene	gene with protein product		607560	"rho/rac guanine nucleotide exchange factor (GEF) 2"			9857026, 9734811	Standard	NM_004723		Approved	LFP40, GEF-H1, KIAA0651, P40	uc001fmt.2	Q92974	OTTHUMG00000017464	ENST00000361247.4:c.1571A>G	chr1.hg19:g.155927648T>C	ENSP00000354837:p.Gln524Arg	131.0	0.0		101.0	5.0	NM_001162383	D3DVA6|O75142|Q15079|Q5VY92|Q8TDA3|Q8WUG4|Q9H023	Missense_Mutation	SNP	ENST00000361247.4	hg19	CCDS53376.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.579088	0.86645	.	.	ENSG00000116584	ENST00000313695;ENST00000361247;ENST00000368315;ENST00000368316;ENST00000313667	T;T;T;T;T	0.75367	-0.93;-0.93;-0.93;-0.93;-0.93	5.28	5.28	0.74379	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.45606	D	0.000343	T	0.74884	0.3775	L	0.55834	1.745	0.49389	D	0.999789	P;D;P	0.57257	0.883;0.979;0.858	P;P;P	0.57846	0.771;0.828;0.535	T	0.78677	-0.2111	10	0.66056	D	0.02	-39.65	13.1991	0.59756	0.0:0.0:0.0:1.0	.	568;524;523	D3DVA5;Q92974;Q92974-2	.;ARHG2_HUMAN;.	R	496;524;525;496;523	ENSP00000315325:Q496R;ENSP00000354837:Q524R;ENSP00000357298:Q525R;ENSP00000357299:Q496R;ENSP00000314787:Q523R	ENSP00000314787:Q523R	Q	-	2	0	ARHGEF2	154194272	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.632000	0.54287	2.213000	0.71641	0.528000	0.53228	CAG	.	.		0.522	ARHGEF2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046204.2	NM_004723		C	155927648	T	C	155927648	3	2	259	1	0	0	0	0	1	0	0	0	903	1580	55	2	1429	2	ARHGEF2	1	155927648	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	921693	155927648	93322973	66	36384										
INSRR	3645	hgsc.bcm.edu	37	chr1	156813015	156813015	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cgaggcacctcccattcatcAgggacatacactgcaaggag	10	13	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:156813015A>G	ENST00000368195.3	-	17	3303	c.2907T>C	c.(2905-2907)ccT>ccC	p.P969P	NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	969					actin cytoskeleton reorganization (GO:0031532)|cellular response to alkaline pH (GO:0071469)|male sex determination (GO:0030238)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(7)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	42	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CCCATTCATCAGGGACATACA	0.572																																					p.P969P		Atlas-SNP	.											.	INSRR	309	.	0			c.T2907C						.						56	50	52					1																	156813015		2203	4300	6503	SO:0001819	synonymous_variant	3645	exon17			TTCATCAGGGACA	J05046	CCDS1160.1	1q21-q23	2013-02-11			ENSG00000027644	ENSG00000027644		"Fibronectin type III domain containing"	6093	protein-coding gene	gene with protein product		147671				2768234, 2249481	Standard	NM_014215		Approved	IRR	uc010pht.2	P14616	OTTHUMG00000041291	ENST00000368195.3:c.2907T>C	chr1.hg19:g.156813015A>G		131.0	0.0		75.0	4.0	NM_014215	O60724|Q5VZS3	Silent	SNP	ENST00000368195.3	hg19	CCDS1160.1																																																																																			.	.		0.572	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215		G	156813015	A	G	156813015	2	3	259	1	0	0	0	0	0	0	0	1	7783	175	7	2		2	INSRR	1	156813015	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	885367	156813015	92437606	67	36385										
PEAR1	375033	hgsc.bcm.edu	37	chr1	156879570	156879570	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gcgtggtaactgctctgtgcCctgcccacccggaacctggg	13	15	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:156879570C>G	ENST00000338302.3	+	13	1664	c.1439C>G	c.(1438-1440)cCc>cGc	p.P480R	PEAR1_ENST00000292357.7_Missense_Mutation_p.P480R			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	480					recognition of apoptotic cell (GO:0043654)	integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(6)|lung(22)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)	43	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					TGCTCTGTGCCCTGCCCACCC	0.627																																					p.P480R		Atlas-SNP	.											.	PEAR1	118	.	0			c.C1439G						.						55	52	53					1																	156879570		2203	4300	6503	SO:0001583	missense	375033	exon12			CTGTGCCCTGCCC	AK098809	CCDS30892.1	1q23.1	2008-02-05	2007-10-25	2007-10-25	ENSG00000187800	ENSG00000187800			33631	protein-coding gene	gene with protein product		610278	"multiple EGF-like-domains 12"	MEGF12		15851471	Standard	NM_001080471		Approved	JEDI, FLJ00193	uc001fqj.1	Q5VY43	OTTHUMG00000041293	ENST00000338302.3:c.1439C>G	chr1.hg19:g.156879570C>G	ENSP00000344465:p.Pro480Arg	105.0	0.0		82.0	4.0	NM_001080471	Q8TEK2	Missense_Mutation	SNP	ENST00000338302.3	hg19	CCDS30892.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.184356	0.78677	.	.	ENSG00000187800	ENST00000338302;ENST00000292357	D;D	0.85955	-2.05;-2.05	5.16	5.16	0.70880	EGF-like region, conserved site (1);	0.135578	0.34245	N	0.004137	T	0.74809	0.3765	N	0.05574	-0.02	0.47441	D	0.999423	D	0.59767	0.986	P	0.58454	0.839	T	0.74731	-0.3566	10	0.17832	T	0.49	.	16.1843	0.81939	0.0:1.0:0.0:0.0	.	480	Q5VY43	PEAR1_HUMAN	R	480	ENSP00000344465:P480R;ENSP00000292357:P480R	ENSP00000292357:P480R	P	+	2	0	PEAR1	155146194	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.575000	0.67430	2.679000	0.91253	0.561000	0.74099	CCC	.	.		0.627	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471		G	156879570	C	G	156879570	3	3	259	1	0	0	0	0	1	0	0	0	11721	623	22	4	1481	4	PEAR1	1	156879570	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	66555	156879570	92371051	68	36386										
OR6K2	81448	hgsc.bcm.edu	37	chr1	158670333	158670333	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccaggtttccaacaacaatgAaagcatagatgaagagcagt	9	8	0	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:158670333A>G	ENST00000359610.2	-	1	153	c.110T>C	c.(109-111)tTc>tCc	p.F37S		NM_001005279.1	NP_001005279.1	Q8NGY2	OR6K2_HUMAN	olfactory receptor, family 6, subfamily K, member 2	37						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	46	all_hematologic(112;0.0378)					AACAACAATGAAAGCATAGAT	0.443																																					p.F37S		Atlas-SNP	.											.	OR6K2	104	.	0			c.T110C						.						110	107	108					1																	158670333		2203	4300	6503	SO:0001583	missense	81448	exon1			ACAATGAAAGCAT	BK004196	CCDS30902.1	1q23.1	2012-08-09			ENSG00000196171	ENSG00000196171		"GPCR / Class A : Olfactory receptors"	15029	protein-coding gene	gene with protein product							Standard	NM_001005279		Approved		uc001fsu.1	Q8NGY2	OTTHUMG00000022768	ENST00000359610.2:c.110T>C	chr1.hg19:g.158670333A>G	ENSP00000352626:p.Phe37Ser	132.0	0.0		87.0	5.0	NM_001005279	B9EH33|Q6IFR6	Missense_Mutation	SNP	ENST00000359610.2	hg19	CCDS30902.1	.	.	.	.	.	.	.	.	.	.	A	12.07	1.827340	0.32329	.	.	ENSG00000196171	ENST00000359610	T	0.00428	7.44	4.47	4.47	0.54385	.	0.000000	0.40064	N	0.001188	T	0.00440	0.0014	L	0.54323	1.7	0.26318	N	0.977725	D	0.89917	1.0	D	0.91635	0.999	T	0.50676	-0.8800	10	0.87932	D	0	-15.1693	12.8974	0.58108	1.0:0.0:0.0:0.0	.	37	Q8NGY2	OR6K2_HUMAN	S	37	ENSP00000352626:F37S	ENSP00000352626:F37S	F	-	2	0	OR6K2	156936957	0.923000	0.31300	0.346000	0.25655	0.184000	0.23303	3.836000	0.55813	1.854000	0.53819	0.533000	0.62120	TTC	.	.		0.443	OR6K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059061.1	NM_001005279		G	158670333	A	G	158670333	3	3	259	1	0	0	0	0	1	0	0	0	11211	246	9	2	868	2	OR6K2	1	158670333	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1790763	158670333	90580288	69	36387										
ITLN2	142683	hgsc.bcm.edu	37	chr1	160919847	160919847	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aacactcacgttgaccatacGgtgagtaataagatgcagtc	9	9	1	3	rs201391588		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:160919847G>T	ENST00000368029.3	-	6	767	c.710C>A	c.(709-711)cCg>cAg	p.P237Q	ITLN2_ENST00000494442.1_5'UTR|RP11-544M22.1_ENST00000356006.3_RNA	NM_080878.2	NP_543154.1	Q8WWU7	ITLN2_HUMAN	intelectin 2	237	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.					extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			endometrium(4)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(1)	19	all_cancers(52;2.99e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			TTGACCATACGGTGAGTAATA	0.398																																					p.P237Q		Atlas-SNP	.											.	ITLN2	35	.	0			c.C710A						.						130	116	121					1																	160919847		2203	4300	6503	SO:0001583	missense	142683	exon6			CCATACGGTGAGT	AY065973	CCDS1212.1	1q22-q23.5	2013-02-06			ENSG00000158764	ENSG00000158764		"Fibrinogen C domain containing"	20599	protein-coding gene	gene with protein product		609874				11181563	Standard	NM_080878		Approved	HL-2	uc001fxd.3	Q8WWU7	OTTHUMG00000028605	ENST00000368029.3:c.710C>A	chr1.hg19:g.160919847G>T	ENSP00000357008:p.Pro237Gln	129.0	0.0		93.0	4.0	NM_080878	Q17RR2|Q5VYI0	Missense_Mutation	SNP	ENST00000368029.3	hg19	CCDS1212.1	.	.	.	.	.	.	.	.	.	.	G	12.07	1.829002	0.32329	.	.	ENSG00000158764	ENST00000368029	T	0.21932	1.98	4.72	4.72	0.59763	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (1);	0.000000	0.53938	U	0.000056	T	0.24236	0.0587	M	0.85373	2.75	0.36106	D	0.844452	P;P	0.52842	0.886;0.956	B;P	0.44359	0.433;0.447	T	0.37572	-0.9700	10	0.72032	D	0.01	-0.81	15.5105	0.75776	0.0:0.0:1.0:0.0	.	236;237	A6NI51;Q8WWU7	.;ITLN2_HUMAN	Q	237	ENSP00000357008:P237Q	ENSP00000357008:P237Q	P	-	2	0	ITLN2	159186471	0.989000	0.36119	0.431000	0.26735	0.005000	0.04900	2.768000	0.47645	2.285000	0.76669	0.561000	0.74099	CCG	.	.		0.398	ITLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071465.1	NM_080878		T	160919847	G	T	160919847	3	4	259	1	0	0	0	0	1	0	0	0	7920	1116	39	1	279	1	ITLN2	1	160919847	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	2249514	160919847	88330774	70	36388										
C1orf111	284680	hgsc.bcm.edu	37	chr1	162344320	162344320	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctctttgtctgcacacacgaAgtagctgtagggggagaacc	12	10	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:162344320A>G	ENST00000367935.5	-	3	383	c.304T>C	c.(304-306)Ttc>Ctc	p.F102L	RP11-565P22.6_ENST00000431696.1_Intron	NM_182581.3	NP_872387.2	Q5T0L3	CA111_HUMAN	chromosome 1 open reading frame 111	102										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)	11	all_hematologic(112;0.15)		BRCA - Breast invasive adenocarcinoma(70;0.0938)			GCACACACGAAGTAGCTGTAG	0.577																																					p.F102L		Atlas-SNP	.											.	C1orf111	26	.	0			c.T304C						.						121	120	120					1																	162344320		2203	4300	6503	SO:0001583	missense	284680	exon3			ACACGAAGTAGCT	BC032957	CCDS1238.1	1q23.3	2008-02-05			ENSG00000171722	ENSG00000171722			27648	protein-coding gene	gene with protein product						12477932	Standard	NM_182581		Approved		uc001gbx.2	Q5T0L3	OTTHUMG00000031375	ENST00000367935.5:c.304T>C	chr1.hg19:g.162344320A>G	ENSP00000356912:p.Phe102Leu	142.0	0.0		83.0	4.0	NM_182581	Q6X961|Q8NEC3	Missense_Mutation	SNP	ENST00000367935.5	hg19	CCDS1238.1	.	.	.	.	.	.	.	.	.	.	A	19.70	3.877366	0.72294	.	.	ENSG00000171722	ENST00000367935	T	0.37915	1.17	4.98	4.98	0.66077	.	0.000000	0.64402	D	0.000005	T	0.49304	0.1549	M	0.73598	2.24	0.33288	D	0.563115	D	0.67145	0.996	D	0.77557	0.99	T	0.59669	-0.7411	9	0.87932	D	0	-19.8356	12.0718	0.53620	1.0:0.0:0.0:0.0	.	102	Q5T0L3	CA111_HUMAN	L	102	ENSP00000356912:F102L	ENSP00000356912:F102L	F	-	1	0	C1orf111	160610944	1.000000	0.71417	0.993000	0.49108	0.708000	0.40852	3.692000	0.54727	1.859000	0.53934	0.533000	0.62120	TTC	.	.		0.577	C1orf111-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076791.2	NM_182581		G	162344320	A	G	162344320	3	3	259	1	0	0	0	0	1	0	0	0	1986	72	3	2	485	2	C1orf111	1	162344320	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1424473	162344320	86906301	71	36389										
RXRG	6258	hgsc.bcm.edu	37	chr1	165398198	165398198	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgtagagccagtgtggccagGggagcctgtaagaagaagaa	16	6	0	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:165398198G>A	ENST00000359842.5	-	2	357	c.55C>T	c.(55-57)Cct>Tct	p.P19S		NM_001256570.1|NM_006917.4	NP_001243499.1|NP_008848.1	P48443	RXRG_HUMAN	retinoid X receptor, gamma	19	Modulating. {ECO:0000250}.				gene expression (GO:0010467)|heart development (GO:0007507)|neuron differentiation (GO:0030182)|peripheral nervous system development (GO:0007422)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of myelination (GO:0031641)|response to retinoic acid (GO:0032526)|skeletal muscle tissue development (GO:0007519)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	9-cis retinoic acid receptor activity (GO:0004886)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.P19T(1)		endometrium(1)|kidney(3)|large_intestine(6)|lung(22)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	38	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)				Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Tretinoin(DB00755)	GTGTGGCCAGGGGAGCCTGTA	0.572																																					p.P19S		Atlas-SNP	.											RXRG,NS,carcinoma,0,1	RXRG	91	.	1	Substitution - Missense(1)	lung(1)	c.C55T						.						44	40	41					1																	165398198		2203	4300	6503	SO:0001583	missense	6258	exon2			GGCCAGGGGAGCC	U38480	CCDS1248.1, CCDS72970.1	1q22-q23	2013-01-16			ENSG00000143171	ENSG00000143171		"Nuclear hormone receptors"	10479	protein-coding gene	gene with protein product	"nuclear receptor subfamily 2 group B member 3"	180247				8034312	Standard	NR_033824		Approved	NR2B3	uc001gda.3	P48443	OTTHUMG00000034626	ENST00000359842.5:c.55C>T	chr1.hg19:g.165398198G>A	ENSP00000352900:p.Pro19Ser	140.0	0.0		93.0	4.0	NM_006917	A6NIP1|Q6IBU7	Missense_Mutation	SNP	ENST00000359842.5	hg19	CCDS1248.1	.	.	.	.	.	.	.	.	.	.	G	11.95	1.790428	0.31685	.	.	ENSG00000143171	ENST00000359842	D	0.91894	-2.93	4.56	3.65	0.41850	.	0.846178	0.10999	N	0.610725	T	0.79423	0.4443	L	0.27053	0.805	0.43439	D	0.995615	B	0.02656	0.0	B	0.01281	0.0	T	0.70475	-0.4861	9	0.54805	T	0.06	.	11.3765	0.49730	0.0887:0.0:0.9113:0.0	.	19	P48443	RXRG_HUMAN	S	19	ENSP00000352900:P19S	ENSP00000352900:P19S	P	-	1	0	RXRG	163664822	0.999000	0.42202	0.989000	0.46669	0.928000	0.56348	1.311000	0.33562	1.142000	0.42291	0.561000	0.74099	CCT	.	.		0.572	RXRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083794.2	NM_006917		A	165398198	G	A	165398198	3	1	259	1	0	0	0	0	1	0	0	0	13780	1232	43	3	1372	3	RXRG	1	165398198	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	3053878	165398198	83852423	72	36390										
TIPRL	261726	hgsc.bcm.edu	37	chr1	168169255	168169255	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gaattgatcctaacccagcaGactcacaaaaaagtacacaa	5	11	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:168169255G>T	ENST00000367833.2	+	7	935	c.790G>T	c.(790-792)Gac>Tac	p.D264Y		NM_152902.3	NP_690866.1	O75663	TIPRL_HUMAN	TOR signaling pathway regulator	264	Interaction with PPP2CA.				DNA damage checkpoint (GO:0000077)|negative regulation of protein phosphatase type 2A activity (GO:0034048)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				breast(1)|kidney(1)|large_intestine(1)|ovary(2)|skin(1)	6	all_hematologic(923;0.215)					TAACCCAGCAGACTCACAAAA	0.363																																					p.D264Y		Atlas-SNP	.											.	TIPRL	16	.	0			c.G790T						.						61	60	60					1																	168169255		2203	4299	6502	SO:0001583	missense	261726	exon7			CCAGCAGACTCAC	AB097034	CCDS1270.1, CCDS30935.1	1q23.2	2014-03-07	2014-03-07		ENSG00000143155	ENSG00000143155			30231	protein-coding gene	gene with protein product		611807	"TIP41, TOR signaling pathway regulator-like (S. cerevisiae)"			12761501	Standard	NM_001031800		Approved	MGC3794, dJ69E11.3, TIP41	uc001gfg.3	O75663	OTTHUMG00000034646	ENST00000367833.2:c.790G>T	chr1.hg19:g.168169255G>T	ENSP00000356807:p.Asp264Tyr	101.0	0.0		91.0	4.0	NM_152902	B2R8V3|Q5HYB2|Q8IZ86	Missense_Mutation	SNP	ENST00000367833.2	hg19	CCDS1270.1	.	.	.	.	.	.	.	.	.	.	G	11.06	1.527741	0.27299	.	.	ENSG00000143155	ENST00000367833	.	.	.	5.91	5.0	0.66597	.	0.543934	0.21397	N	0.075209	T	0.30262	0.0759	L	0.47716	1.5	0.32833	D	0.504357	B	0.31790	0.34	B	0.31016	0.123	T	0.32745	-0.9895	8	0.56958	D	0.05	-10.2752	11.6011	0.51003	0.1431:0.0:0.8569:0.0	.	264	O75663	TIPRL_HUMAN	Y	264	.	ENSP00000356807:D264Y	D	+	1	0	TIPRL	166435879	0.010000	0.17322	0.999000	0.59377	0.549000	0.35272	0.634000	0.24614	1.504000	0.48704	0.655000	0.94253	GAC	.	.		0.363	TIPRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083822.1	NM_152902		T	168169255	G	T	168169255	3	4	259	1	0	0	0	0	1	0	0	0	15941	942	33	3	841	3	TIPRL	1	168169255	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	2771057	168169255	81081366	73	36391										
C1orf114	57821	hgsc.bcm.edu	37	chr1	169388397	169388397	+	Splice_Site	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttctatttttcgtcgctcttCctagtaaaagaatatgaaaa	5	7	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:169388397C>A	ENST00000367806.3	-	4	1221	c.1069G>T	c.(1069-1071)Gaa>Taa	p.E357*	CCDC181_ENST00000545005.1_Splice_Site_p.E357*|CCDC181_ENST00000367805.3_Splice_Site_p.E357*|CCDC181_ENST00000491570.1_5'UTR	NM_021179.1	NP_067002.1	Q5TID7	CC181_HUMAN	coiled-coil domain containing 181	357						nucleus (GO:0005634)											CGTCGCTCTTCCTAGTAAAAG	0.308																																					p.E357X		Atlas-SNP	.											.	C1orf114	67	.	0			c.G1069T						.						45	42	43					1																	169388397		2202	4295	6497	SO:0001630	splice_region_variant	57821	exon4			GCTCTTCCTAGTA	AL049687	CCDS1279.1, CCDS72979.1	1q24	2013-03-14	2013-03-14	2013-03-14	ENSG00000117477	ENSG00000117477			28051	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 114"	C1orf114			Standard	XM_005245381		Approved	FLJ25846	uc001gfz.1	Q5TID7	OTTHUMG00000035448	ENST00000367806.3:c.1069-1G>T	chr1.hg19:g.169388397C>A		91.0	0.0		59.0	4.0	NM_021179	O60780|Q53FD5|Q5TID9|Q8TC48	Nonsense_Mutation	SNP	ENST00000367806.3	hg19		.	.	.	.	.	.	.	.	.	.	C	37	6.585705	0.97684	.	.	ENSG00000117477	ENST00000367805;ENST00000367806;ENST00000545005	.	.	.	5.98	5.98	0.97165	.	0.348808	0.31859	N	0.006945	.	.	.	.	.	.	0.80722	A	1.000000	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-8.2959	20.0532	0.97636	0.0:1.0:0.0:0.0	.	.	.	.	X	357	.	ENSP00000356779:E357X	E	-	1	0	C1orf114	167655021	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.070000	0.71220	2.835000	0.97688	0.650000	0.86243	GAA	.	.		0.308	CCDC181-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086099.1	NM_021179	Nonsense_Mutation	A	169388397	C	A	169388397	5	1	259	1	0	0	0	0	0	0	1	0	1989	869	30	3	469	3	C1orf114	1	169388397	Splice_Site	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	1219142	169388397	79862224	74	36392										
F5	2153	hgsc.bcm.edu	37	chr1	169512354	169512354	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gaagttaacatccaagttccTacagaagagagacagacaga	9	8	0	5			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:169512354T>C	ENST00000367797.3	-	13	2177		c.e13-2		F5_ENST00000367796.3_Splice_Site	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)						blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	TCCAAGTTCCTACAGAAGAGA	0.383																																					.		Atlas-SNP	.											.	F5	301	.	0			c.1976-2A>G						.						50	50	50					1																	169512354		2202	4300	6502	SO:0001630	splice_region_variant	2153	exon14			AGTTCCTACAGAA	M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.1976-2A>G	chr1.hg19:g.169512354T>C		103.0	0.0		73.0	23.0	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Splice_Site	SNP	ENST00000367797.3	hg19	CCDS1281.1	.	.	.	.	.	.	.	.	.	.	T	17.22	3.333513	0.60853	.	.	ENSG00000198734	ENST00000367797;ENST00000367796	.	.	.	5.98	4.82	0.62117	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.9103	0.58177	0.0:0.0:0.1358:0.8642	.	.	.	.	.	-1	.	.	.	-	.	.	F5	167778978	1.000000	0.71417	0.806000	0.32338	0.751000	0.42716	6.275000	0.72594	1.035000	0.39972	0.482000	0.46254	.	.	.		0.383	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	Intron	C	169512354	T	C	169512354	5	2	259	1	0	0	0	0	0	0	1	0	5350	1536	53	2	4752	2	F5	1	169512354	Splice_Site	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	123957	169512354	79738267	75	36393										
DNM3	26052	hgsc.bcm.edu	37	chr1	171958288	171958288	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctaaagaagttgatcctcaaGgtgagtgtgtgactactaag	11	6	1	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:171958288G>T	ENST00000355305.5	+	4	746	c.589G>T	c.(589-591)Ggt>Tgt	p.G197C	DNM3_ENST00000520906.1_Splice_Site_p.G197C|DNM3_ENST00000358155.4_Splice_Site_p.G197C|DNM3_ENST00000367733.2_Splice_Site_p.G197C|DNM3_ENST00000367731.1_Splice_Site_p.G197C			Q9UQ16	DYN3_HUMAN	dynamin 3	197	Dynamin-type G.				endocytosis (GO:0006897)|filopodium assembly (GO:0046847)|GTP catabolic process (GO:0006184)|synapse assembly (GO:0007416)	dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(16)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						TGATCCTCAAGGTGAGTGTGT	0.378																																					p.G197C		Atlas-SNP	.											.	DNM3	85	.	0			c.G589T						.						50	47	48					1																	171958288		1912	4143	6055	SO:0001630	splice_region_variant	26052	exon4			CCTCAAGGTGAGT	AL136712	CCDS44276.1, CCDS60356.1	1q24.1	2013-01-10			ENSG00000197959	ENSG00000197959		"Pleckstrin homology (PH) domain containing"	29125	protein-coding gene	gene with protein product	"Dyna III"	611445				10048485	Standard	NM_015569		Approved	KIAA0820	uc001gie.4	Q9UQ16	OTTHUMG00000034913	ENST00000355305.5:c.589+1G>T	chr1.hg19:g.171958288G>T		131.0	0.0		76.0	4.0	NM_001136127	A9Z1Y1|O14982|O95555|Q1MTM8|Q5W129|Q6P2G1|Q9H0P3|Q9H548|Q9NQ68|Q9NQN6	Missense_Mutation	SNP	ENST00000355305.5	hg19		.	.	.	.	.	.	.	.	.	.	G	26.5	4.743055	0.89663	.	.	ENSG00000197959	ENST00000359070;ENST00000358155;ENST00000367733;ENST00000355305;ENST00000367731;ENST00000520906;ENST00000523513	D;D;D;D;D;D	0.97404	-4.23;-4.23;-4.23;-4.23;-4.23;-4.37	5.9	5.9	0.94986	.	0.047955	0.85682	D	0.000000	D	0.99417	0.9794	H	0.99834	4.825	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.85130	0.997;0.997;0.995;0.997	D	0.98227	1.0481	10	0.87932	D	0	.	18.8427	0.92190	0.0:0.0:1.0:0.0	.	197;197;197;197	E5RHK8;Q9UQ16-2;Q9UQ16-3;Q6P2G1	.;.;.;.	C	197;197;197;197;197;197;87	ENSP00000350876:G197C;ENSP00000356707:G197C;ENSP00000347457:G197C;ENSP00000356705:G197C;ENSP00000429701:G197C;ENSP00000429416:G87C	ENSP00000347457:G197C	G	+	1	0	DNM3	170224911	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	9.793000	0.99091	2.788000	0.95919	0.650000	0.86243	GGT	.	.		0.378	DNM3-003	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000084531.1	NM_015569	Missense_Mutation	T	171958288	G	T	171958288	5	4	259	1	0	0	0	0	0	0	1	0	4675	1014	35	3	603	3	DNM3	1	171958288	Splice_Site	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	2445934	171958288	77292333	76	36394										
PAPPA2	60676	hgsc.bcm.edu	37	chr1	176564279	176564279	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gtggaattgatctcccagtaCaatggatactggccccttcg	10	11	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:176564279C>T	ENST00000367662.3	+	3	2703	c.1539C>T	c.(1537-1539)taC>taT	p.Y513Y	PAPPA2_ENST00000367661.3_Silent_p.Y513Y	NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	513	Metalloprotease.				bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.Y513*(2)		NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						TCTCCCAGTACAATGGATACT	0.532																																					p.Y513Y		Atlas-SNP	.											PAPPA2_ENST00000367661,NS,carcinoma,0,2	PAPPA2	665	.	2	Substitution - Nonsense(2)	lung(2)	c.C1539T						.						55	55	55					1																	176564279		1979	4172	6151	SO:0001819	synonymous_variant	60676	exon3			CCAGTACAATGGA	BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"placenta-specific 3"	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.1539C>T	chr1.hg19:g.176564279C>T		68.0	1.0		61.0	3.0	NM_021936	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Silent	SNP	ENST00000367662.3	hg19	CCDS41438.1																																																																																			.	.		0.532	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1			T	176564279	C	T	176564279	2	4	259	1	0	0	0	0	0	0	0	1	11442	489	17	3		3	PAPPA2	1	176564279	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	4605991	176564279	72686342	77	36395										
ZNF648	127665	hgsc.bcm.edu	37	chr1	182026597	182026597	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aacagagaagagttccctgcGgacgtgtctacacttttgtg	11	9	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:182026597G>T	ENST00000339948.3	-	2	756	c.549C>A	c.(547-549)tcC>tcA	p.S183S		NM_001009992.1	NP_001009992.1	Q5T619	ZN648_HUMAN	zinc finger protein 648	183					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(7)|large_intestine(10)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	40						AGTTCCCTGCGGACGTGTCTA	0.587																																					p.S183S	NSCLC(71;908 1374 5429 20458 35642)	Atlas-SNP	.											.	ZNF648	111	.	0			c.C549A						.						58	63	61					1																	182026597		2203	4300	6503	SO:0001819	synonymous_variant	127665	exon2			CCCTGCGGACGTG	AK128654	CCDS30952.1	1q25.3	2013-01-08			ENSG00000179930	ENSG00000179930		"Zinc fingers, C2H2-type"	18190	protein-coding gene	gene with protein product							Standard	NM_001009992		Approved	FLJ46813	uc001goz.3	Q5T619	OTTHUMG00000037302	ENST00000339948.3:c.549C>A	chr1.hg19:g.182026597G>T		152.0	0.0		96.0	6.0	NM_001009992	B2RP16	Silent	SNP	ENST00000339948.3	hg19	CCDS30952.1																																																																																			.	.		0.587	ZNF648-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090794.1	XM_060597		T	182026597	G	T	182026597	2	4	259	1	0	0	0	0	0	0	0	1	18078	1103	39	1		1	ZNF648	1	182026597	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	5462318	182026597	67224024	78	36396										
LAMC1	3915	hgsc.bcm.edu	37	chr1	183111868	183111868	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gacattcgcaatctggaggaCatcaggaagaccttaccatc	9	11	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:183111868C>T	ENST00000258341.4	+	28	5030	c.4773C>T	c.(4771-4773)gaC>gaT	p.D1591D	RP11-181K3.4_ENST00000457852.3_RNA	NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	1591	Domain II and I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						ATCTGGAGGACATCAGGAAGA	0.522																																					p.D1591D		Atlas-SNP	.											.	LAMC1	176	.	0			c.C4773T						.						130	113	118					1																	183111868		2203	4300	6503	SO:0001819	synonymous_variant	3915	exon28			GGAGGACATCAGG	J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"Laminins"	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.4773C>T	chr1.hg19:g.183111868C>T		113.0	0.0		95.0	4.0	NM_002293	Q5VYE7	Silent	SNP	ENST00000258341.4	hg19	CCDS1351.1																																																																																			.	.		0.522	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293		T	183111868	C	T	183111868	2	4	259	1	0	0	0	0	0	0	0	1	8623	477	17	3		3	LAMC1	1	183111868	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	1085271	183111868	66138753	79	36397										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186031705	186031705	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgaaggtaaaagagaaacagAgtgttacgctgacttgtgaa	12	4	0	5			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:186031705A>G	ENST00000271588.4	+	48	7715	c.7486A>G	c.(7486-7488)Agt>Ggt	p.S2496G	HMCN1_ENST00000367492.2_Missense_Mutation_p.S2496G	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2496	Ig-like C2-type 23.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						AGAGAAACAGAGTGTTACGCT	0.408																																					p.S2496G		Atlas-SNP	.											.	HMCN1	797	.	0			c.A7486G						.						106	100	102					1																	186031705		2203	4300	6503	SO:0001583	missense	83872	exon48			AAACAGAGTGTTA	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.7486A>G	chr1.hg19:g.186031705A>G	ENSP00000271588:p.Ser2496Gly	123.0	0.0		86.0	5.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	A	14.97	2.694899	0.48202	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.70164	-0.46;-0.46	5.51	3.15	0.36227	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.177069	0.64402	D	0.000007	T	0.66934	0.2840	M	0.75777	2.31	0.28600	N	0.909212	B	0.24823	0.112	B	0.37015	0.239	T	0.59193	-0.7500	10	0.24483	T	0.36	.	8.9866	0.35997	0.7857:0.0:0.2143:0.0	.	2496	Q96RW7	HMCN1_HUMAN	G	2496	ENSP00000271588:S2496G;ENSP00000356462:S2496G	ENSP00000271588:S2496G	S	+	1	0	HMCN1	184298328	0.998000	0.40836	0.976000	0.42696	0.985000	0.73830	3.670000	0.54569	0.921000	0.36994	0.482000	0.46254	AGT	.	.		0.408	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		G	186031705	A	G	186031705	3	3	259	1	0	0	0	0	1	0	0	0	7229	304	11	2	7676	2	HMCN1	1	186031705	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2919837	186031705	63218916	80	36398										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186157064	186157064	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cactgtggacccaatcgcatGtgcttcaacatgagaggaag	11	10	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:186157064G>A	ENST00000271588.4	+	106	16693	c.16464G>A	c.(16462-16464)atG>atA	p.M5488I	HMCN1_ENST00000367492.2_Missense_Mutation_p.M5371I	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	5488					response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						CCAATCGCATGTGCTTCAACA	0.517																																					p.M5488I		Atlas-SNP	.											.	HMCN1	797	.	0			c.G16464A						.						345	248	280					1																	186157064		2203	4300	6503	SO:0001583	missense	83872	exon106			TCGCATGTGCTTC	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.16464G>A	chr1.hg19:g.186157064G>A	ENSP00000271588:p.Met5488Ile	186.0	0.0		119.0	6.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	G	19.22	3.784983	0.70222	.	.	ENSG00000143341	ENST00000271588;ENST00000367492;ENST00000414277	T;T;T	0.75367	-0.03;-0.02;-0.93	5.72	5.72	0.89469	EGF-like calcium-binding, conserved site (1);Growth factor, receptor (1);Epidermal growth factor-like (1);	0.035367	0.85682	D	0.000000	T	0.70290	0.3207	L	0.48362	1.52	0.39946	D	0.974476	B	0.30406	0.278	B	0.26517	0.07	T	0.68239	-0.5461	10	0.39692	T	0.17	.	19.8968	0.96969	0.0:0.0:1.0:0.0	.	5488	Q96RW7	HMCN1_HUMAN	I	5488;5371;163	ENSP00000271588:M5488I;ENSP00000356462:M5371I;ENSP00000406205:M163I	ENSP00000271588:M5488I	M	+	3	0	HMCN1	184423687	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	9.807000	0.99171	2.691000	0.91804	0.655000	0.94253	ATG	.	.		0.517	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		A	186157064	G	A	186157064	3	1	259	1	0	0	0	0	1	0	0	0	7229	1377	48	3	16886	3	HMCN1	1	186157064	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	125359	186157064	63093557	81	36399										
IGFN1	91156	hgsc.bcm.edu	37	chr1	201186487	201186487	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	catcacactgacatggacagCacctcggggccccggcagcg	12	16	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:201186487C>T	ENST00000335211.4	+	17	9798	c.9668C>T	c.(9667-9669)gCa>gTa	p.A3223V	IGFN1_ENST00000295591.8_Missense_Mutation_p.A383V	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	766						nucleus (GO:0005634)|Z disc (GO:0030018)				autonomic_ganglia(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						ACATGGACAGCACCTCGGGGC	0.652																																					p.A3223V		Atlas-SNP	.											.	IGFN1	220	.	0			c.C9668T						.						63	64	64					1																	201186487		2203	4300	6503	SO:0001583	missense	91156	exon17			GGACAGCACCTCG	AY245430	CCDS53455.1	1q32.1	2013-02-11			ENSG00000163395	ENSG00000163395		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	24607	protein-coding gene	gene with protein product							Standard	NM_001164586		Approved	DKFZp434B1231, EEF1A2BP1	uc001gwc.3	Q86VF2	OTTHUMG00000035728	ENST00000335211.4:c.9668C>T	chr1.hg19:g.201186487C>T	ENSP00000334714:p.Ala3223Val	235.0	0.0		182.0	23.0	NM_001164586	F8WAI1|Q9NT72	Missense_Mutation	SNP	ENST00000335211.4	hg19	CCDS53455.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.607853	0.87258	.	.	ENSG00000163395	ENST00000335211;ENST00000295591	T;T	0.58940	0.3;0.3	4.68	4.68	0.58851	.	0.227102	0.37393	N	0.002106	T	0.63271	0.2497	L	0.58969	1.84	0.38149	D	0.938696	P	0.39520	0.676	P	0.48488	0.579	T	0.63642	-0.6591	10	0.24483	T	0.36	.	15.7862	0.78306	0.0:1.0:0.0:0.0	.	3223	F8WAI1	.	V	3223;383	ENSP00000334714:A3223V;ENSP00000295591:A383V	ENSP00000295591:A383V	A	+	2	0	IGFN1	199453110	0.885000	0.30320	0.114000	0.21550	0.008000	0.06430	4.271000	0.58902	2.129000	0.65627	0.561000	0.74099	GCA	.	.		0.652	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275		T	201186487	C	T	201186487	3	4	259	1	0	0	0	0	1	0	0	0	7599	710	25	3	9730	3	IGFN1	1	201186487	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	15029423	201186487	48064134	82	36400										
LGR6	59352	hgsc.bcm.edu	37	chr1	202287998	202287998	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gcccctagcctatgctgcggCcggggagctggagaagagct	16	12	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:202287998C>T	ENST00000367278.3	+	18	2656	c.2567C>T	c.(2566-2568)gCc>gTc	p.A856V	LGR6_ENST00000439764.2_Missense_Mutation_p.A717V|LGR6_ENST00000255432.7_Missense_Mutation_p.A804V	NM_001017403.1	NP_001017403.1	Q9HBX8	LGR6_HUMAN	leucine-rich repeat containing G protein-coupled receptor 6	856					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of Wnt signaling pathway (GO:0030177)|Wnt signaling pathway (GO:0016055)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	36						TATGCTGCGGCCGGGGAGCTG	0.632																																					p.A856V		Atlas-SNP	.											.	LGR6	102	.	0			c.C2567T						.						48	58	54					1																	202287998		2203	4300	6503	SO:0001583	missense	59352	exon18			CTGCGGCCGGGGA	AF190501	CCDS1424.1, CCDS30971.1, CCDS30972.1	1q32.1	2012-08-21	2011-01-25		ENSG00000133067	ENSG00000133067		"GPCR / Class A : Orphans"	19719	protein-coding gene	gene with protein product		606653	"leucine-rich repeat-containing G protein-coupled receptor 6"			10935549	Standard	XM_005245404		Approved	FLJ14471	uc001gxu.3	Q9HBX8	OTTHUMG00000041383	ENST00000367278.3:c.2567C>T	chr1.hg19:g.202287998C>T	ENSP00000356247:p.Ala856Val	167.0	0.0		94.0	4.0	NM_001017403	Q5T509|Q5T512|Q6UY15|Q86VU0|Q96K69|Q9BYD7	Missense_Mutation	SNP	ENST00000367278.3	hg19	CCDS30971.1	.	.	.	.	.	.	.	.	.	.	C	10.12	1.263462	0.23051	.	.	ENSG00000133067	ENST00000367278;ENST00000255432;ENST00000439764	T;T;T	0.59638	0.25;0.65;0.68	4.18	3.27	0.37495	.	0.384683	0.21905	N	0.067385	T	0.43255	0.1239	L	0.40543	1.245	0.09310	N	0.999999	P;B;B	0.38078	0.617;0.202;0.128	B;B;B	0.30855	0.121;0.098;0.101	T	0.36720	-0.9736	10	0.51188	T	0.08	.	10.7001	0.45922	0.0:0.8359:0.0:0.1641	.	717;804;856	Q9HBX8-1;Q9HBX8-2;Q9HBX8	.;.;LGR6_HUMAN	V	856;804;717	ENSP00000356247:A856V;ENSP00000255432:A804V;ENSP00000387869:A717V	ENSP00000255432:A804V	A	+	2	0	LGR6	200554621	0.922000	0.31269	0.013000	0.15412	0.216000	0.24613	2.333000	0.43912	1.121000	0.41925	0.485000	0.47835	GCC	.	.		0.632	LGR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099143.1	NM_021636		T	202287998	C	T	202287998	3	4	259	1	0	0	0	0	1	0	0	0	8767	739	26	3	2784	3	LGR6	1	202287998	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	1101511	202287998	46962623	83	36401										
LAX1	54900	hgsc.bcm.edu	37	chr1	203741220	203741220	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acatgagtcgaggagtatgcGcattttcagtactgagagcc	12	8	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:203741220G>T	ENST00000442561.2	+	4	725	c.335G>T	c.(334-336)cGc>cTc	p.R112L	LAX1_ENST00000367217.5_Missense_Mutation_p.R96L|LAX1_ENST00000367215.1_3'UTR	NM_017773.3	NP_060243.2	Q8IWV1	LAX1_HUMAN	lymphocyte transmembrane adaptor 1	112					antigen receptor-mediated signaling pathway (GO:0050851)|B cell activation (GO:0042113)|immune response (GO:0006955)|immunoglobulin secretion (GO:0048305)|inactivation of MAPK activity (GO:0000188)|intracellular signal transduction (GO:0035556)|negative regulation of T cell activation (GO:0050868)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)			central_nervous_system(2)|endometrium(3)|large_intestine(2)|lung(13)|prostate(1)|stomach(1)|urinary_tract(2)	24	all_cancers(21;0.0915)		BRCA - Breast invasive adenocarcinoma(75;0.109)			AGGAGTATGCGCATTTTCAGT	0.488																																					p.R112L		Atlas-SNP	.											.	LAX1	48	.	0			c.G335T						.						139	128	132					1																	203741220		2203	4300	6503	SO:0001583	missense	54900	exon4			GTATGCGCATTTT	AK000347	CCDS1441.2, CCDS44297.1	1q32.1	2008-02-05			ENSG00000122188	ENSG00000122188			26005	protein-coding gene	gene with protein product	"LAT-like membrane associated protein", "linker for activation of x cells"					12359715	Standard	NM_017773		Approved	LAX, FLJ20340	uc001haa.3	Q8IWV1	OTTHUMG00000035908	ENST00000442561.2:c.335G>T	chr1.hg19:g.203741220G>T	ENSP00000406970:p.Arg112Leu	107.0	0.0		67.0	4.0	NM_017773	B7Z744|J3KP69|Q6NSZ6|Q9NXB4	Missense_Mutation	SNP	ENST00000442561.2	hg19	CCDS1441.2	.	.	.	.	.	.	.	.	.	.	G	13.10	2.137429	0.37728	.	.	ENSG00000122188	ENST00000442561;ENST00000367217	.	.	.	4.56	3.64	0.41730	.	0.217303	0.32935	N	0.005472	T	0.49457	0.1558	L	0.53249	1.67	0.09310	N	1	D;D	0.63046	0.992;0.992	P;P	0.56278	0.795;0.72	T	0.38564	-0.9655	9	0.62326	D	0.03	-3.9142	9.0249	0.36222	0.1046:0.0:0.8954:0.0	.	96;112	B7Z744;Q8IWV1	.;LAX1_HUMAN	L	112;96	.	ENSP00000356186:R96L	R	+	2	0	LAX1	202007843	0.024000	0.19004	0.005000	0.12908	0.071000	0.16799	0.720000	0.25896	1.033000	0.39918	0.655000	0.94253	CGC	.	.		0.488	LAX1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087468.3	NM_017773		T	203741220	G	T	203741220	3	4	259	1	0	0	0	0	1	0	0	0	8657	1087	38	1	394	1	LAX1	1	203741220	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1453222	203741220	45509401	84	36402										
SOX13	9580	hgsc.bcm.edu	37	chr1	204083543	204083543	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccaggagaagctggacttcaAccgaaatttgaaagaaggta	11	7	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:204083543A>G	ENST00000367204.1	+	3	423	c.314A>G	c.(313-315)aAc>aGc	p.N105S	SOX13_ENST00000367203.4_3'UTR	NM_005686.2	NP_005677.2	Q9UN79	SOX13_HUMAN	SRY (sex determining region Y)-box 13	105					anatomical structure morphogenesis (GO:0009653)|regulation of gamma-delta T cell differentiation (GO:0045586)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(2)|prostate(2)	13	all_cancers(21;0.0754)|Breast(84;0.116)|all_epithelial(62;0.189)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.109)			CTGGACTTCAACCGAAATTTG	0.537																																					p.N105S		Atlas-SNP	.											.	SOX13	38	.	0			c.A314G						.						52	51	52					1																	204083543		1949	4153	6102	SO:0001583	missense	9580	exon3			ACTTCAACCGAAA		CCDS44299.1	1q32	2008-07-18			ENSG00000143842	ENSG00000143842		"SRY (sex determining region Y)-boxes"	11192	protein-coding gene	gene with protein product	"islet cell antibody 12", "SRY-related HMG-box gene 13", "type 1 diabetes autoantigen", "SRY-box 13"	604748				10198172	Standard	NM_005686		Approved	Sox-13, ICA12, MGC117216	uc001ham.3	Q9UN79	OTTHUMG00000036050	ENST00000367204.1:c.314A>G	chr1.hg19:g.204083543A>G	ENSP00000356172:p.Asn105Ser	166.0	0.0		92.0	4.0	NM_005686	B4E2B0|O95275|O95826|Q3KQV7|Q5SXX1|Q9UHW7	Missense_Mutation	SNP	ENST00000367204.1	hg19	CCDS44299.1	.	.	.	.	.	.	.	.	.	.	A	5.148	0.212914	0.09757	.	.	ENSG00000143842	ENST00000367204;ENST00000528591	D	0.97505	-4.41	4.65	3.5	0.40072	.	0.221487	0.45867	N	0.000321	D	0.92289	0.7554	L	0.35414	1.06	0.25626	N	0.986358	B;B	0.12630	0.0;0.006	B;B	0.15052	0.001;0.012	T	0.81484	-0.0912	10	0.19590	T	0.45	.	6.9016	0.24285	0.8813:0.0:0.1187:0.0	.	105;87	Q9UN79;Q5SXX2	SOX13_HUMAN;.	S	105	ENSP00000356172:N105S	ENSP00000356172:N105S	N	+	2	0	SOX13	202350166	1.000000	0.71417	0.993000	0.49108	0.945000	0.59286	2.984000	0.49353	0.622000	0.30249	0.460000	0.39030	AAC	.	.		0.537	SOX13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087881.2	NM_005686		G	204083543	A	G	204083543	3	3	259	1	0	0	0	0	1	0	0	0	14959	43	2	2	320	2	SOX13	1	204083543	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	342323	204083543	45167078	85	36403										
PIK3C2B	5287	hgsc.bcm.edu	37	chr1	204403607	204403607	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctgggcatggcccaggaagcGgccaaaatcaatgtggaaca	13	10	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:204403607G>T	ENST00000367187.3	-	25	4202	c.3646C>A	c.(3646-3648)Cgc>Agc	p.R1216S	PIK3C2B_ENST00000424712.2_Missense_Mutation_p.R1188S|RP11-739N20.2_ENST00000443515.1_RNA	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	1216	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			CCCAGGAAGCGGCCAAAATCA	0.522																																					p.R1216S		Atlas-SNP	.											.	PIK3C2B	142	.	0			c.C3646A						.						80	62	68					1																	204403607		2203	4300	6503	SO:0001583	missense	5287	exon25			GGAAGCGGCCAAA	Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"phosphoinositide-3-kinase, class 2, beta polypeptide"			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.3646C>A	chr1.hg19:g.204403607G>T	ENSP00000356155:p.Arg1216Ser	135.0	0.0		99.0	4.0	NM_002646	O95666|Q5SW99	Missense_Mutation	SNP	ENST00000367187.3	hg19	CCDS1446.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.946665	0.92593	.	.	ENSG00000133056	ENST00000367187;ENST00000424712	T;T	0.75367	-0.93;-0.93	5.69	5.69	0.88448	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.173359	0.47093	D	0.000249	T	0.80132	0.4567	L	0.50333	1.59	0.41599	D	0.988844	P;D	0.58620	0.888;0.983	P;P	0.59948	0.711;0.866	T	0.81716	-0.0806	10	0.87932	D	0	.	12.6528	0.56772	0.0:0.0:0.7285:0.2715	.	1188;1216	F5GWN5;O00750	.;P3C2B_HUMAN	S	1216;1188	ENSP00000356155:R1216S;ENSP00000400561:R1188S	ENSP00000356155:R1216S	R	-	1	0	PIK3C2B	202670230	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.790000	0.62453	2.692000	0.91855	0.563000	0.77884	CGC	.	.		0.522	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646		T	204403607	G	T	204403607	3	4	259	1	0	0	0	0	1	0	0	0	11919	1116	39	1	1298	1	PIK3C2B	1	204403607	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	320064	204403607	44847014	86	36404										
NFASC	23114	hgsc.bcm.edu	37	chr1	204938107	204938107	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acacgatctcggtgagagtaAagggtacgttgtgtgtattt	13	5	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:204938107A>G	ENST00000401399.1	+	9	1199	c.1000A>G	c.(1000-1002)Aag>Gag	p.K334E	NFASC_ENST00000513543.1_Missense_Mutation_p.K345E|NFASC_ENST00000367169.4_Missense_Mutation_p.K334E|NFASC_ENST00000338586.6_Missense_Mutation_p.K334E|NFASC_ENST00000367172.4_Missense_Mutation_p.K334E|NFASC_ENST00000338515.6_Missense_Mutation_p.K334E|NFASC_ENST00000339876.6_Missense_Mutation_p.K334E|NFASC_ENST00000367170.4_Missense_Mutation_p.K334E|NFASC_ENST00000404076.1_Missense_Mutation_p.K328E|NFASC_ENST00000367171.4_Missense_Mutation_p.K334E|NFASC_ENST00000360049.4_Missense_Mutation_p.K345E|NFASC_ENST00000403080.1_Missense_Mutation_p.K334E|NFASC_ENST00000539706.1_Missense_Mutation_p.K345E|NFASC_ENST00000404907.1_Missense_Mutation_p.K345E			O94856	NFASC_HUMAN	neurofascin	334					axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			GGTGAGAGTAAAGGGTACGTT	0.527																																					p.K345E		Atlas-SNP	.											.	NFASC	396	.	0			c.A1033G						.						64	69	67					1																	204938107		2203	4300	6503	SO:0001583	missense	23114	exon10			AGAGTAAAGGGTA	AK027553	CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1	1q32.1	2013-02-11	2010-06-24		ENSG00000163531	ENSG00000163531		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	29866	protein-coding gene	gene with protein product		609145	"neurofascin homolog (chicken)"			1377696, 8672144	Standard	NM_015090		Approved	NRCAML, KIAA0756, FLJ46866, NF	uc001hbj.3	O94856	OTTHUMG00000151697	ENST00000401399.1:c.1000A>G	chr1.hg19:g.204938107A>G	ENSP00000385637:p.Lys334Glu	188.0	0.0		89.0	4.0	NM_015090	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Missense_Mutation	SNP	ENST00000401399.1	hg19	CCDS53460.1	.	.	.	.	.	.	.	.	.	.	A	19.80	3.894541	0.72639	.	.	ENSG00000163531	ENST00000367172;ENST00000367171;ENST00000367170;ENST00000338515;ENST00000339876;ENST00000338586;ENST00000295776;ENST00000539706;ENST00000360049;ENST00000367169;ENST00000403080;ENST00000404076;ENST00000401399;ENST00000404907;ENST00000513543;ENST00000430393	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.77229	-1.08;-1.08;-1.08;-1.08;-1.08;-1.08;-1.08;-1.08;-1.08;-1.08;-1.08;-1.08;-1.08;-1.08;-1.08	5.8	5.8	0.92144	.	0.000000	0.56097	D	0.000027	T	0.73466	0.3590	N	0.04746	-0.17	0.80722	D	1	D;B;D;P;D;P;D	0.89917	1.0;0.322;1.0;0.815;1.0;0.517;1.0	D;B;D;P;D;B;D	0.91635	0.994;0.05;0.967;0.601;0.996;0.074;0.999	T	0.69899	-0.5020	10	0.07175	T	0.84	.	15.8152	0.78595	1.0:0.0:0.0:0.0	.	345;345;430;334;334;345;334	O94856-11;O94856-8;B4DRH7;F8W791;O94856-9;O94856-3;O94856-2	.;.;.;.;.;.;.	E	334;334;334;334;334;334;345;345;345;334;334;328;334;345;345;321	ENSP00000356140:K334E;ENSP00000356139:K334E;ENSP00000356138:K334E;ENSP00000342128:K334E;ENSP00000344786:K334E;ENSP00000343509:K334E;ENSP00000438614:K345E;ENSP00000353154:K345E;ENSP00000356137:K334E;ENSP00000384875:K334E;ENSP00000385676:K328E;ENSP00000385637:K334E;ENSP00000384061:K345E;ENSP00000425908:K345E;ENSP00000415031:K321E	ENSP00000295776:K345E	K	+	1	0	NFASC	203204730	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.444000	0.80532	2.213000	0.71641	0.528000	0.53228	AAG	.	.		0.527	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388		G	204938107	A	G	204938107	3	3	259	1	0	0	0	0	1	0	0	0	10368	15	1	2	1085	2	NFASC	1	204938107	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	534500	204938107	44312514	87	36405										
NUAK2	81788	hgsc.bcm.edu	37	chr1	205273191	205273191	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttgggctgagctccggagggTcctcctgtaccccttctgca	12	14	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:205273191T>C	ENST00000367157.3	-	7	1400	c.1274A>G	c.(1273-1275)gAc>gGc	p.D425G		NM_030952.1	NP_112214.1			NUAK family, SNF1-like kinase, 2											breast(3)|kidney(3)|large_intestine(4)|lung(4)|ovary(3)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23	Breast(84;0.186)		BRCA - Breast invasive adenocarcinoma(75;0.117)			CTCCGGAGGGTCCTCCTGTAC	0.627																																					p.D425G		Atlas-SNP	.											.	NUAK2	107	.	0			c.A1274G						.						73	69	70					1																	205273191		2203	4300	6503	SO:0001583	missense	81788	exon7			GGAGGGTCCTCCT	AK074830	CCDS1453.1	1q32.1	2008-02-05			ENSG00000163545	ENSG00000163545			29558	protein-coding gene	gene with protein product	"SNF1/AMP activated protein kinase"	608131				11230166	Standard	NM_030952		Approved	SNARK, FLJ90349	uc001hce.3	Q9H093	OTTHUMG00000037196	ENST00000367157.3:c.1274A>G	chr1.hg19:g.205273191T>C	ENSP00000356125:p.Asp425Gly	115.0	0.0		81.0	4.0	NM_030952		Missense_Mutation	SNP	ENST00000367157.3	hg19	CCDS1453.1	.	.	.	.	.	.	.	.	.	.	T	0.014	-1.582617	0.00879	.	.	ENSG00000163545	ENST00000367157	T	0.72394	-0.65	4.84	0.918	0.19386	.	0.448909	0.18701	N	0.133563	T	0.44664	0.1304	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18241	-1.0343	10	0.15066	T	0.55	.	4.8344	0.13456	0.0:0.2661:0.1515:0.5824	.	425	Q9H093	NUAK2_HUMAN	G	425	ENSP00000356125:D425G	ENSP00000356125:D425G	D	-	2	0	NUAK2	203539814	0.000000	0.05858	0.021000	0.16686	0.032000	0.12392	0.193000	0.17116	-0.108000	0.12066	0.334000	0.21626	GAC	.	.		0.627	NUAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090390.1	NM_030952		C	205273191	T	C	205273191	3	2	259	1	0	0	0	0	1	0	0	0	10722	1667	58	2	616	2	NUAK2	1	205273191	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	335084	205273191	43977430	88	36406										
INTS7	25896	hgsc.bcm.edu	37	chr1	212139822	212139822	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tctattgcatgagatatcagTaaacagctctgctgctgtct	8	9	4	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:212139822T>A	ENST00000366994.3	-	16	2237	c.2133A>T	c.(2131-2133)ttA>ttT	p.L711F	INTS7_ENST00000366992.3_Missense_Mutation_p.L711F|INTS7_ENST00000469606.1_5'UTR|INTS7_ENST00000366993.3_Missense_Mutation_p.L711F|INTS7_ENST00000440600.2_Missense_Mutation_p.L662F	NM_001199811.1|NM_001199812.1|NM_015434.3	NP_001186740.1|NP_001186741.1|NP_056249.1	Q9NVH2	INT7_HUMAN	integrator complex subunit 7	711					cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|snRNA processing (GO:0016180)	chromosome (GO:0005694)|integrator complex (GO:0032039)				NS(1)|breast(1)|kidney(1)|large_intestine(8)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20				OV - Ovarian serous cystadenocarcinoma(81;0.00584)|all cancers(67;0.0318)|Epithelial(68;0.0852)		GAGATATCAGTAAACAGCTCT	0.348																																					p.L711F		Atlas-SNP	.											.	INTS7	68	.	0			c.A2133T						.						80	86	84					1																	212139822		2203	4300	6503	SO:0001583	missense	25896	exon16			TATCAGTAAACAG	AK022509	CCDS1501.1, CCDS55684.1, CCDS55683.1, CCDS55685.1	1q32.3	2008-02-05	2006-03-15	2006-03-15	ENSG00000143493	ENSG00000143493			24484	protein-coding gene	gene with protein product		611350	"chromosome 1 open reading frame 73"	C1orf73		16239144	Standard	NM_015434		Approved	DKFZP434B168, INT7	uc001hiw.2	Q9NVH2	OTTHUMG00000037119	ENST00000366994.3:c.2133A>T	chr1.hg19:g.212139822T>A	ENSP00000355961:p.Leu711Phe	111.0	0.0		90.0	39.0	NM_015434	B4DLZ6|B7WNP6|B7WPB6|Q8N4K7|Q8WUH5|Q9H9V3|Q9NVU5|Q9UFC6|Q9UFM3	Missense_Mutation	SNP	ENST00000366994.3	hg19	CCDS1501.1	.	.	.	.	.	.	.	.	.	.	T	14.83	2.652261	0.47362	.	.	ENSG00000143493	ENST00000366994;ENST00000366993;ENST00000366992;ENST00000440600	T;T;T;T	0.49139	0.79;0.81;0.8;0.8	4.98	-3.46	0.04767	.	0.000000	0.64402	D	0.000001	T	0.22244	0.0536	L	0.27053	0.805	0.49687	D	0.999817	B;B;B;B	0.27229	0.172;0.046;0.046;0.046	B;B;B;B	0.25291	0.04;0.04;0.04;0.059	T	0.11131	-1.0600	10	0.09843	T	0.71	-12.6108	4.9809	0.14164	0.1385:0.5431:0.1413:0.1771	.	662;711;711;711	B4DLZ6;Q9NVH2-3;Q9NVH2-2;Q9NVH2	.;.;.;INT7_HUMAN	F	711;711;711;662	ENSP00000355961:L711F;ENSP00000355960:L711F;ENSP00000355959:L711F;ENSP00000388908:L662F	ENSP00000355959:L711F	L	-	3	2	INTS7	210206445	0.997000	0.39634	0.994000	0.49952	0.996000	0.88848	0.448000	0.21726	-0.262000	0.09392	0.454000	0.30748	TTA	.	.		0.348	INTS7-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090142.1	NM_015434		A	212139822	T	A	212139822	3	1	259	1	0	0	0	0	1	0	0	0	7792	1635	57	4	775	4	INTS7	1	212139822	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	6866631	212139822	37110799	89	36407										
USH2A	7399	hgsc.bcm.edu	37	chr1	215963585	215963585	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aagctgagcagcatatggtaTctgacatattcacataatcc	7	9	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:215963585T>C	ENST00000307340.3	-	51	10384	c.9998A>G	c.(9997-9999)gAt>gGt	p.D3333G	USH2A_ENST00000366943.2_Missense_Mutation_p.D3333G	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3333					hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			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)		GCATATGGTATCTGACATATT	0.378										HNSCC(13;0.011)																											p.D3333G		Atlas-SNP	.											.	USH2A	1168	.	0			c.A9998G						.						122	114	117					1																	215963585		2203	4300	6503	SO:0001583	missense	7399	exon51			ATGGTATCTGACA	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.9998A>G	chr1.hg19:g.215963585T>C	ENSP00000305941:p.Asp3333Gly	156.0	0.0		122.0	5.0	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	T	12.64	1.999505	0.35320	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.13420	2.6;2.59	5.91	5.91	0.95273	Fibronectin, type III (2);	0.143817	0.31370	N	0.007773	T	0.12305	0.0299	L	0.53249	1.67	0.30027	N	0.813858	P	0.43094	0.799	B	0.33339	0.162	T	0.17137	-1.0379	10	0.33141	T	0.24	.	11.387	0.49791	0.0:0.0697:0.0:0.9303	.	3333	O75445	USH2A_HUMAN	G	3333	ENSP00000305941:D3333G;ENSP00000355910:D3333G	ENSP00000305941:D3333G	D	-	2	0	USH2A	214030208	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.843000	0.48238	2.254000	0.74563	0.533000	0.62120	GAT	.	.		0.378	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		C	215963585	T	C	215963585	3	2	259	1	0	0	0	0	1	0	0	0	17051	1435	50	2	5698	2	USH2A	1	215963585	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	3823763	215963585	33287036	90	36408										
EPRS	2058	hgsc.bcm.edu	37	chr1	220203778	220203778	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acctttcccatctccgcaccTggaagctcaacaaatttccc	4	17	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:220203778T>C	ENST00000366923.3	-	6	842	c.573A>G	c.(571-573)ccA>ccG	p.P191P		NM_004446.2	NP_004437.2	P07814	SYEP_HUMAN	glutamyl-prolyl-tRNA synthetase	191	Glutamate--tRNA ligase.				cellular response to interferon-gamma (GO:0071346)|gene expression (GO:0010467)|glutamyl-tRNA aminoacylation (GO:0006424)|negative regulation of translation (GO:0017148)|prolyl-tRNA aminoacylation (GO:0006433)|protein complex assembly (GO:0006461)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|GAIT complex (GO:0097452)|membrane (GO:0016020)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|glutamate-tRNA ligase activity (GO:0004818)|proline-tRNA ligase activity (GO:0004827)|RNA stem-loop binding (GO:0035613)			breast(2)|endometrium(11)|kidney(2)|large_intestine(13)|lung(24)|ovary(1)|prostate(3)|skin(2)|stomach(2)|urinary_tract(3)	63				GBM - Glioblastoma multiforme(131;0.0735)	L-Proline(DB00172)	TCTCCGCACCTGGAAGCTCAA	0.398																																					p.P191P		Atlas-SNP	.											.	EPRS	140	.	0			c.A573G						.						90	89	89					1																	220203778		2203	4300	6503	SO:0001819	synonymous_variant	2058	exon6			CGCACCTGGAAGC	X54326	CCDS31027.1	1q41	2011-07-01			ENSG00000136628	ENSG00000136628	6.1.1.15, 6.1.1.17	"Aminoacyl tRNA synthetases / Class I", "Aminoacyl tRNA synthetases / Class II"	3418	protein-coding gene	gene with protein product	"glutamate tRNA ligase", "proline tRNA ligase"	138295		QPRS, QARS		1988429	Standard	NM_004446		Approved	EARS, PARS, GLUPRORS	uc001hly.1	P07814	OTTHUMG00000037433	ENST00000366923.3:c.573A>G	chr1.hg19:g.220203778T>C		92.0	0.0		62.0	4.0	NM_004446	A0AVA9|B9EGH3|Q05BP6|Q05DF8|Q5DSM1|Q5H9S5|Q6PD57|Q86X73	Silent	SNP	ENST00000366923.3	hg19	CCDS31027.1																																																																																			.	.		0.398	EPRS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091133.2	NM_004446		C	220203778	T	C	220203778	2	2	259	1	0	0	0	0	0	0	0	1	5193	1567	55	2		2	EPRS	1	220203778	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	4240193	220203778	29046843	91	36409										
TLR5	7100	hgsc.bcm.edu	37	chr1	223286028	223286028	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aaacagatggaacagtccctGaaaagcatctggatgcaaga	10	8	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:223286028G>A	ENST00000540964.1	-	4	807	c.346C>T	c.(346-348)Cag>Tag	p.Q116*	TLR5_ENST00000342210.6_Nonsense_Mutation_p.Q116*			O60602	TLR5_HUMAN	toll-like receptor 5	116					cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				GBM - Glioblastoma multiforme(131;0.0851)		AACAGTCCCTGAAAAGCATCT	0.413																																					p.Q116X		Atlas-SNP	.											.	TLR5	86	.	0			c.C346T						.						94	92	92					1																	223286028		2203	4300	6503	SO:0001587	stop_gained	7100	exon6			GTCCCTGAAAAGC		CCDS31033.1	1q32.3-q42	2014-01-29			ENSG00000187554	ENSG00000187554			11851	protein-coding gene	gene with protein product	"Toll/interleukin-1 receptor-like protein 3"	603031	"systemic lupus erythematosus susceptibility 1"	SLEB1		9435236, 16027372	Standard	NM_003268		Approved	TIL3, FLJ10052, MGC126430, MGC126431	uc001hnw.2	O60602	OTTHUMG00000037937	ENST00000540964.1:c.346C>T	chr1.hg19:g.223286028G>A	ENSP00000440643:p.Gln116*	156.0	0.0		121.0	5.0	NM_003268	B1AZ05|B3Y633|B9VJ63|D1CS80|D3DTB8|O15456|Q32MI2|Q32MI3	Nonsense_Mutation	SNP	ENST00000540964.1	hg19	CCDS31033.1	.	.	.	.	.	.	.	.	.	.	G	36	5.741443	0.96873	.	.	ENSG00000187554	ENST00000540964;ENST00000366881;ENST00000342210	.	.	.	5.03	5.03	0.67393	.	0.460355	0.21479	N	0.073863	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.3781	0.66892	0.0:0.2626:0.7374:0.0	.	.	.	.	X	116	.	ENSP00000340089:Q116X	Q	-	1	0	TLR5	221352651	0.956000	0.32656	0.563000	0.28383	0.969000	0.65631	2.578000	0.46051	2.483000	0.83821	0.655000	0.94253	CAG	.	.		0.413	TLR5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_003268		A	223286028	G	A	223286028	4	1	259	1	0	0	0	0	0	1	0	0	15969	1299	45	3	2234	3	TLR5	1	223286028	Nonsense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	3082250	223286028	25964593	92	36410										
TLR5	7100	hgsc.bcm.edu	37	chr1	223286221	223286221	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atatagttgaagctcagcagGagcctctcagtggtgttgag	13	7	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:223286221G>T	ENST00000540964.1	-	4	614	c.153C>A	c.(151-153)ctC>ctA	p.L51L	TLR5_ENST00000342210.6_Silent_p.L51L			O60602	TLR5_HUMAN	toll-like receptor 5	51					cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				GBM - Glioblastoma multiforme(131;0.0851)		AGCTCAGCAGGAGCCTCTCAG	0.532																																					p.L51L		Atlas-SNP	.											.	TLR5	86	.	0			c.C153A						.						65	66	65					1																	223286221		2203	4300	6503	SO:0001819	synonymous_variant	7100	exon6			CAGCAGGAGCCTC		CCDS31033.1	1q32.3-q42	2014-01-29			ENSG00000187554	ENSG00000187554			11851	protein-coding gene	gene with protein product	"Toll/interleukin-1 receptor-like protein 3"	603031	"systemic lupus erythematosus susceptibility 1"	SLEB1		9435236, 16027372	Standard	NM_003268		Approved	TIL3, FLJ10052, MGC126430, MGC126431	uc001hnw.2	O60602	OTTHUMG00000037937	ENST00000540964.1:c.153C>A	chr1.hg19:g.223286221G>T		122.0	0.0		123.0	5.0	NM_003268	B1AZ05|B3Y633|B9VJ63|D1CS80|D3DTB8|O15456|Q32MI2|Q32MI3	Silent	SNP	ENST00000540964.1	hg19	CCDS31033.1																																																																																			.	.		0.532	TLR5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_003268		T	223286221	G	T	223286221	2	4	259	1	0	0	0	0	0	0	0	1	15969	1161	41	3		3	TLR5	1	223286221	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	193	223286221	25964400	93	36411										
CDC42BPA	8476	hgsc.bcm.edu	37	chr1	227216408	227216408	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	attcctgttgtctagatcttCggccctggcagtcagtgtat	10	10	3	1	rs369641713		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:227216408C>T	ENST00000366769.3	-	29	5568	c.4277G>A	c.(4276-4278)cGa>cAa	p.R1426Q	CDC42BPA_ENST00000366765.3_Missense_Mutation_p.R1439Q|CDC42BPA_ENST00000366766.2_Missense_Mutation_p.R1461Q|CDC42BPA_ENST00000366767.3_Missense_Mutation_p.R1345Q|CDC42BPA_ENST00000535525.1_Missense_Mutation_p.R1406Q|CDC42BPA_ENST00000366764.2_Missense_Mutation_p.R1398Q|CDC42BPA_ENST00000334218.5_Missense_Mutation_p.R1426Q	NM_003607.3	NP_003598.2			CDC42 binding protein kinase alpha (DMPK-like)											NS(1)|breast(4)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(12)|lung(32)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|urinary_tract(2)	77		all_cancers(173;0.156)|Prostate(94;0.0792)				TCTAGATCTTCGGCCCTGGCA	0.423																																					p.R1426Q		Atlas-SNP	.											.	CDC42BPA	528	.	0			c.G4277A						.	C	GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	123	110	115		4277,4034	4.6	1	1		115	0,8600		0,0,4300	no	missense,missense	CDC42BPA	NM_003607.3,NM_014826.4	43,43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	1426/1720,1345/1639	227216408	1,13005	2203	4300	6503	SO:0001583	missense	8476	exon29			GATCTTCGGCCCT	U59305	CCDS1558.1, CCDS1559.1	1q42.11	2011-11-23	2001-11-28		ENSG00000143776	ENSG00000143776			1737	protein-coding gene	gene with protein product	"myotonic dystrophy kinase-related Cdc42-binding kinase"	603412	"CDC42-binding protein kinase alpha (DMPK-like)"				Standard	NM_003607		Approved	MRCKA, PK428, FLJ23347, KIAA0451, MRCK	uc001hqr.3	Q5VT25	OTTHUMG00000037618	ENST00000366769.3:c.4277G>A	chr1.hg19:g.227216408C>T	ENSP00000355731:p.Arg1426Gln	166.0	0.0		85.0	4.0	NM_003607		Missense_Mutation	SNP	ENST00000366769.3	hg19	CCDS1558.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.496204	0.85069	2.27E-4	0.0	ENSG00000143776	ENST00000366769;ENST00000366767;ENST00000334218;ENST00000366766;ENST00000366764;ENST00000366762;ENST00000535525;ENST00000366765	T;T;T;T;T;T;T	0.05081	3.5;3.5;3.5;3.5;3.5;3.5;3.5	5.53	4.62	0.57501	.	0.060172	0.64402	D	0.000003	T	0.28599	0.0708	M	0.84773	2.715	0.58432	D	0.999996	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;0.999;0.994;0.999;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.87578	0.996;0.998;0.958;0.952;0.997;0.973;0.983;0.986	T	0.10245	-1.0638	10	0.72032	D	0.01	.	14.5294	0.67915	0.0:0.9296:0.0:0.0704	.	1406;1398;741;323;1345;1426;1461;628	F5H5N0;Q5VT25-4;E9PEF7;Q5T7A7;Q5VT25-3;Q5VT25-5;Q5VT25-2;Q5T799	.;.;.;.;.;.;.;.	Q	1426;1345;1426;1461;1398;741;1406;1439	ENSP00000355731:R1426Q;ENSP00000355729:R1345Q;ENSP00000335341:R1426Q;ENSP00000355728:R1461Q;ENSP00000355726:R1398Q;ENSP00000443275:R1406Q;ENSP00000355727:R1439Q	ENSP00000335341:R1426Q	R	-	2	0	CDC42BPA	225283031	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	6.034000	0.70933	1.484000	0.48361	0.585000	0.79938	CGA	.	.		0.423	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	NM_014826		T	227216408	C	T	227216408	3	4	259	1	0	0	0	0	1	0	0	0	3074	884	31	1	914	1	CDC42BPA	1	227216408	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	3930187	227216408	22034213	94	36412										
PGBD5	79605	hgsc.bcm.edu	37	chr1	230486728	230486728	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atgatgaagccagtggaagaAcattgtctgacccagaggct	12	8	1	5			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:230486728A>G	ENST00000525115.1	-	3	686	c.663T>C	c.(661-663)tgT>tgC	p.C221C	PGBD5_ENST00000321327.2_Silent_p.C320C|PGBD5_ENST00000391860.1_Silent_p.C175C			Q8N414	PGBD5_HUMAN	piggyBac transposable element derived 5	221						integral component of membrane (GO:0016021)				biliary_tract(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(2)|skin(1)	33	Breast(184;0.0397)	Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;0.201)		CAGTGGAAGAACATTGTCTGA	0.567																																					p.C290C		Atlas-SNP	.											.	PGBD5	73	.	0			c.T870C						.						115	110	112					1																	230486728		2203	4300	6503	SO:0001819	synonymous_variant	79605	exon3			GGAAGAACATTGT	AK021475		1q42.13	2008-02-05			ENSG00000177614	ENSG00000177614			19405	protein-coding gene	gene with protein product							Standard	NM_001258311		Approved	DKFZp761A0620, FLJ11413	uc031psq.1	Q8N414	OTTHUMG00000037759	ENST00000525115.1:c.663T>C	chr1.hg19:g.230486728A>G		123.0	0.0		93.0	4.0	NM_001258311	A0PJF3|B9EK58|Q5SR37|Q6PJN2	Silent	SNP	ENST00000525115.1	hg19																																																																																				.	.		0.567	PGBD5-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000382617.1	NM_024554		G	230486728	A	G	230486728	2	3	259	1	0	0	0	0	0	0	0	1	11793	41	2	2		2	PGBD5	1	230486728	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	3270320	230486728	18763893	95	36413										
NID1	4811	hgsc.bcm.edu	37	chr1	236157008	236157008	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gcggccgtcgcgatccacgcAccagcagtagccggtgctgc	14	16	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:236157008A>G	ENST00000264187.6	-	13	2774	c.2692T>C	c.(2692-2694)Tgc>Cgc	p.C898R	NID1_ENST00000366595.3_Missense_Mutation_p.C765R	NM_002508.2	NP_002499.2	P14543	NID1_HUMAN	nidogen 1	898	Thyroglobulin type-1. {ECO:0000255|PROSITE-ProRule:PRU00500}.				basement membrane organization (GO:0071711)|cell-matrix adhesion (GO:0007160)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|positive regulation of cell-substrate adhesion (GO:0010811)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|cell periphery (GO:0071944)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|laminin binding (GO:0043236)|proteoglycan binding (GO:0043394)			breast(4)|endometrium(9)|kidney(1)|large_intestine(23)|lung(20)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(1)	66	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Urokinase(DB00013)	CGATCCACGCACCAGCAGTAG	0.701																																					p.C898R		Atlas-SNP	.											.	NID1	196	.	0			c.T2692C						.						21	22	22					1																	236157008		2200	4297	6497	SO:0001583	missense	4811	exon13			CCACGCACCAGCA	BC045606	CCDS1608.1	1q43	2011-05-08	2005-06-02	2005-06-02	ENSG00000116962	ENSG00000116962			7821	protein-coding gene	gene with protein product		131390	"nidogen (enactin)"	NID		2471408, 7557988	Standard	NM_002508		Approved	entactin	uc001hxo.3	P14543	OTTHUMG00000040071	ENST00000264187.6:c.2692T>C	chr1.hg19:g.236157008A>G	ENSP00000264187:p.Cys898Arg	161.0	0.0		77.0	4.0	NM_002508	Q14942|Q59FL2|Q5TAF2|Q5TAF3|Q86XD7	Missense_Mutation	SNP	ENST00000264187.6	hg19	CCDS1608.1	.	.	.	.	.	.	.	.	.	.	A	28.0	4.880061	0.91740	.	.	ENSG00000116962	ENST00000264187;ENST00000366595	D;D	0.87491	-2.26;-2.26	5.69	5.69	0.88448	Thyroglobulin type-1 (6);	0.000000	0.85682	D	0.000000	D	0.96278	0.8786	H	0.98351	4.21	0.80722	D	1	D;P	0.89917	1.0;0.931	D;P	0.91635	0.999;0.739	D	0.97936	1.0323	10	0.87932	D	0	.	15.5931	0.76554	1.0:0.0:0.0:0.0	.	765;898	P14543-2;P14543	.;NID1_HUMAN	R	898;765	ENSP00000264187:C898R;ENSP00000355554:C765R	ENSP00000264187:C898R	C	-	1	0	NID1	234223631	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	8.751000	0.91628	2.162000	0.67917	0.454000	0.30748	TGC	.	.		0.701	NID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096647.2	NM_002508		G	236157008	A	G	236157008	3	3	259	1	0	0	0	0	1	0	0	0	10423	159	6	2	1083	2	NID1	1	236157008	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	5670280	236157008	13093613	96	36414										
EDARADD	128178	hgsc.bcm.edu	37	chr1	236645629	236645629	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cctcctgcttgctccgggccCccaccataagtgacttgctc	8	18	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:236645629C>T	ENST00000334232.4	+	6	495	c.328C>T	c.(328-330)Ccc>Tcc	p.P110S	EDARADD_ENST00000359362.5_Missense_Mutation_p.P100S	NM_145861.2	NP_665860.2	Q8WWZ3	EDAD_HUMAN	EDAR-associated death domain	110					cell differentiation (GO:0030154)|hair follicle development (GO:0001942)|odontogenesis of dentin-containing tooth (GO:0042475)|signal transduction (GO:0007165)|trachea gland development (GO:0061153)	cytoplasm (GO:0005737)		p.P110T(1)		endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)|stomach(1)	12	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.0232)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			GCTCCGGGCCCCCACCATAAG	0.478																																					p.P110S		Atlas-SNP	.											EDARADD,NS,carcinoma,0,1	EDARADD	31	.	1	Substitution - Missense(1)	lung(1)	c.C328T						.						82	79	80					1																	236645629		2203	4300	6503	SO:0001583	missense	128178	exon6			CGGGCCCCCACCA	AY028914	CCDS1610.1, CCDS31065.1	1q42.3	2013-05-22			ENSG00000186197	ENSG00000186197			14341	protein-coding gene	gene with protein product		606603				11780064	Standard	NM_145861		Approved		uc001hxu.1	Q8WWZ3	OTTHUMG00000039954	ENST00000334232.4:c.328C>T	chr1.hg19:g.236645629C>T	ENSP00000335076:p.Pro110Ser	143.0	0.0		73.0	4.0	NM_145861	A2VCK5|A8K7B5|B1AL54|B9ZVW5|Q5VYJ7	Missense_Mutation	SNP	ENST00000334232.4	hg19	CCDS1610.1	.	.	.	.	.	.	.	.	.	.	C	16.57	3.160516	0.57368	.	.	ENSG00000186197	ENST00000334232;ENST00000359362	T;D	0.82433	-1.04;-1.61	5.22	5.22	0.72569	.	0.000000	0.64402	U	0.000001	D	0.84678	0.5525	M	0.70275	2.135	0.52099	D	0.999943	P;P	0.42692	0.787;0.787	B;B	0.43251	0.322;0.413	D	0.84472	0.0600	9	.	.	.	.	18.9765	0.92738	0.0:1.0:0.0:0.0	.	100;110	A8K7B5;Q8WWZ3	.;EDAD_HUMAN	S	110;100	ENSP00000335076:P110S;ENSP00000352320:P100S	.	P	+	1	0	EDARADD	234712252	1.000000	0.71417	0.981000	0.43875	0.401000	0.30781	5.547000	0.67249	2.720000	0.93068	0.655000	0.94253	CCC	.	.		0.478	EDARADD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000096368.1	NM_145861		T	236645629	C	T	236645629	3	4	259	1	0	0	0	0	1	0	0	0	4908	623	22	3	385	3	EDARADD	1	236645629	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	488621	236645629	12604992	97	36415										
RYR2	6262	hgsc.bcm.edu	37	chr1	237947885	237947885	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tcatcctactggagtattttCatgaccctcttgcacttcgt	6	12	3	1	rs267598440		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:237947885C>T	ENST00000366574.2	+	90	13190	c.12873C>T	c.(12871-12873)ttC>ttT	p.F4291F	RYR2_ENST00000542537.1_Silent_p.F4275F|RYR2_ENST00000609119.1_3'UTR|RYR2_ENST00000360064.6_Silent_p.F4297F	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	4291					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GGAGTATTTTCATGACCCTCT	0.478																																					p.F4291F		Atlas-SNP	.											.	RYR2	1273	.	0			c.C12873T						.						77	75	76					1																	237947885		1903	4117	6020	SO:0001819	synonymous_variant	6262	exon90			TATTTTCATGACC	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.12873C>T	chr1.hg19:g.237947885C>T		69.0	0.0		42.0	4.0	NM_001035	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	hg19	CCDS55691.1																																																																																			.	.		0.478	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		T	237947885	C	T	237947885	2	4	259	1	0	0	0	0	0	0	0	1	13784	825	29	3		3	RYR2	1	237947885	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	1302256	237947885	11302736	98	36416										
KMO	8564	hgsc.bcm.edu	37	chr1	241718930	241718930	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agtatattctttctgtaagcAgagaaaatctaaacaaggat	7	5	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:241718930A>G	ENST00000366559.4	+	5	642	c.331A>G	c.(331-333)Aga>Gga	p.R111G	KMO_ENST00000366557.4_Missense_Mutation_p.R111G|KMO_ENST00000484628.1_3'UTR|KMO_ENST00000366558.3_Missense_Mutation_p.R111G	NM_003679.4	NP_003670.2			kynurenine 3-monooxygenase (kynurenine 3-hydroxylase)											NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)	33	Ovarian(103;0.103)|all_lung(81;0.23)		OV - Ovarian serous cystadenocarcinoma(106;0.0176)			TTCTGTAAGCAGAGAAAATCT	0.313																																					p.R111G		Atlas-SNP	.											.	KMO	69	.	0			c.A331G						.						91	93	92					1																	241718930		2202	4298	6500	SO:0001583	missense	8564	exon5			GTAAGCAGAGAAA	AF056032	CCDS1618.1	1q42-q44	2010-11-23			ENSG00000117009	ENSG00000117009	1.14.13.9		6381	protein-coding gene	gene with protein product		603538				9237672	Standard	NM_003679		Approved		uc009xgp.3	O15229	OTTHUMG00000039635	ENST00000366559.4:c.331A>G	chr1.hg19:g.241718930A>G	ENSP00000355517:p.Arg111Gly	94.0	0.0		84.0	4.0	NM_003679		Missense_Mutation	SNP	ENST00000366559.4	hg19	CCDS1618.1	.	.	.	.	.	.	.	.	.	.	A	19.66	3.869480	0.72065	.	.	ENSG00000117009	ENST00000366559;ENST00000366558;ENST00000366557	T;T;T	0.51071	0.72;0.72;0.72	5.54	5.54	0.83059	Monooxygenase, FAD-binding (1);	0.000000	0.85682	D	0.000000	T	0.79317	0.4425	H	0.97465	4.01	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.998;0.999	D	0.86406	0.1745	10	0.87932	D	0	.	13.6034	0.62033	1.0:0.0:0.0:0.0	.	111;111;111	O15229;A8K693;O15229-2	KMO_HUMAN;.;.	G	111	ENSP00000355517:R111G;ENSP00000355516:R111G;ENSP00000355515:R111G	ENSP00000355515:R111G	R	+	1	2	KMO	239785553	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	5.383000	0.66219	2.093000	0.63338	0.482000	0.46254	AGA	.	.		0.313	KMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095612.1	NM_003679		G	241718930	A	G	241718930	3	3	259	1	0	0	0	0	1	0	0	0	8433	180	7	2	349	2	KMO	1	241718930	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	3771045	241718930	7531691	99	36417										
WDR64	128025	hgsc.bcm.edu	37	chr1	241886642	241886642	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tggcaccccaatatcagcacCaagccagtagggaaacttgt	9	12	1	0	rs145843472		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:241886642C>A	ENST00000366552.2	+	9	1275	c.1068C>A	c.(1066-1068)acC>acA	p.T356T	WDR64_ENST00000437684.2_Silent_p.T356T	NM_144625.4	NP_653226.4	B1ANS9	WDR64_HUMAN	WD repeat domain 64	356										breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(17)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			ATATCAGCACCAAGCCAGTAG	0.453																																					p.T356T		Atlas-SNP	.											.	WDR64	234	.	0			c.C1068A						.						113	105	107					1																	241886642		2203	4300	6503	SO:0001819	synonymous_variant	128025	exon9			CAGCACCAAGCCA	AK057540		1q43	2013-01-09			ENSG00000162843	ENSG00000162843		"WD repeat domain containing"	26570	protein-coding gene	gene with protein product							Standard	NM_144625		Approved	FLJ32978	uc001hzg.2	B1ANS9	OTTHUMG00000039705	ENST00000366552.2:c.1068C>A	chr1.hg19:g.241886642C>A		110.0	0.0		76.0	4.0	NM_144625	B1ANT0|Q7Z573|Q96LY9	Silent	SNP	ENST00000366552.2	hg19																																																																																				.	C|1.000;T|0.000		0.453	WDR64-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144625		A	241886642	C	A	241886642	2	1	259	1	0	0	0	0	0	0	0	1	17330	581	21	3		3	WDR64	1	241886642	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	167712	241886642	7363979	100	36418										
CNST	163882	hgsc.bcm.edu	37	chr1	246810803	246810803	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gcaagtcaaagacagagccgTtgatttcaccaggctgtgac	11	10	2	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:246810803T>C	ENST00000366513.4	+	9	1569	c.1300T>C	c.(1300-1302)Ttg>Ctg	p.L434L	CNST_ENST00000483271.1_3'UTR|CNST_ENST00000366512.3_Silent_p.L434L	NM_152609.2	NP_689822.2	Q6PJW8	CNST_HUMAN	consortin, connexin sorting protein	434					negative regulation of phosphatase activity (GO:0010923)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)	connexin binding (GO:0071253)|phosphatase binding (GO:0019902)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|prostate(1)|urinary_tract(2)	28						GACAGAGCCGTTGATTTCACC	0.507											OREG0014367	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L434L		Atlas-SNP	.											.	CNST	73	.	0			c.T1300C						.						192	207	202					1																	246810803		2203	4300	6503	SO:0001819	synonymous_variant	163882	exon9			GAGCCGTTGATTT	AK056563	CCDS1628.1, CCDS44343.1	1q44	2012-04-17	2009-11-03	2009-11-03	ENSG00000162852	ENSG00000162852		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	26486	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 64"	613439	"chromosome 1 open reading frame 71"	C1orf71		19864490	Standard	NM_152609		Approved	FLJ32001, PPP1R64	uc001ibp.3	Q6PJW8	OTTHUMG00000040090	ENST00000366513.4:c.1300T>C	chr1.hg19:g.246810803T>C		121.0	0.0	2468	94.0	4.0	NM_152609	Q5VSY9|Q5VTM7|Q8IYA9|Q8N3L5|Q8NB09|Q8TEI2|Q96MR5	Silent	SNP	ENST00000366513.4	hg19	CCDS1628.1																																																																																			.	.		0.507	CNST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096780.1	NM_152609		C	246810803	T	C	246810803	2	2	259	1	0	0	0	0	0	0	0	1	3636	1722	60	2		2	CNST	1	246810803	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	4924161	246810803	2439818	101	36419										
SNTG2	54221	hgsc.bcm.edu	37	chr2	1168816	1168816	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gcgaccacagcagtggggccTcctctcccctctttgacagc	10	17	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:1168816T>C	ENST00000308624.5	+	8	667	c.538T>C	c.(538-540)Tcc>Ccc	p.S180P	SNTG2_ENST00000407292.1_Intron|SNTG2_ENST00000467759.1_3'UTR	NM_018968.3	NP_061841.2	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2	180					central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|syntrophin complex (GO:0016013)	PDZ domain binding (GO:0030165)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		CAGTGGGGCCTCCTCTCCCCT	0.473																																					p.S180P		Atlas-SNP	.											.	SNTG2	125	.	0			c.T538C						.						146	152	150					2																	1168816		1964	4141	6105	SO:0001583	missense	54221	exon8			GGGGCCTCCTCTC	AJ003029	CCDS46220.1	2p25	2008-05-23			ENSG00000172554	ENSG00000172554			13741	protein-coding gene	gene with protein product		608715				10747910	Standard	NM_018968		Approved	SYN5, G2SYN	uc002qwq.3	Q9NY99	OTTHUMG00000151370	ENST00000308624.5:c.538T>C	chr2.hg19:g.1168816T>C	ENSP00000311837:p.Ser180Pro	128.0	0.0		121.0	5.0	NM_018968	Q05AH5	Missense_Mutation	SNP	ENST00000308624.5	hg19	CCDS46220.1	.	.	.	.	.	.	.	.	.	.	T	17.73	3.461101	0.63513	.	.	ENSG00000172554	ENST00000308624	T	0.43294	0.95	4.73	4.73	0.59995	.	0.060105	0.64402	D	0.000002	T	0.56630	0.1998	M	0.72894	2.215	0.80722	D	1	D	0.64830	0.994	P	0.58077	0.832	T	0.58940	-0.7547	10	0.45353	T	0.12	.	12.4711	0.55787	0.0:0.0:0.0:1.0	.	180	Q9NY99	SNTG2_HUMAN	P	180	ENSP00000311837:S180P	ENSP00000311837:S180P	S	+	1	0	SNTG2	1158816	1.000000	0.71417	0.646000	0.29493	0.628000	0.37860	5.105000	0.64591	1.748000	0.51833	0.523000	0.50628	TCC	.	.		0.473	SNTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322454.1	NM_018968		C	1168816	T	C	1168816	3	2	259	1	0	0	0	0	1	0	0	0	14890	1551	54	2	568	2	SNTG2	2	1168816	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10		1168816	242030557	102	36420										
GREB1	9687	hgsc.bcm.edu	37	chr2	11778934	11778934	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aaaaagtttcattttctgaaAggtaacttttgtactcttaa	5	5	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:11778934A>G	ENST00000381486.2	+	32	5985	c.5685A>G	c.(5683-5685)aaA>aaG	p.K1895K	GREB1_ENST00000234142.5_Splice_Site_p.K1895K|GREB1_ENST00000396123.1_Splice_Site_p.K893K	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1895						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		ATTTTCTGAAAGGTAACTTTT	0.463																																					p.K1895K	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											.	GREB1	308	.	0			c.A5685G						.						114	102	106					2																	11778934		1881	4119	6000	SO:0001630	splice_region_variant	9687	exon32			TCTGAAAGGTAAC		CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"gene regulated by estrogen in breast cancer"	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.5686+1A>G	chr2.hg19:g.11778934A>G		178.0	0.0		141.0	6.0	NM_014668	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Silent	SNP	ENST00000381486.2	hg19	CCDS42655.1																																																																																			.	.		0.463	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668	Silent	G	11778934	A	G	11778934	5	3	259	1	0	0	0	0	0	0	1	0	6769	86	3	2	5915	2	GREB1	2	11778934	Splice_Site	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	10610118	11778934	231420439	103	36421										
NBAS	51594	hgsc.bcm.edu	37	chr2	15694236	15694236	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tattaaccaagcgaaccagtCcatcagggagcaaaaaaggt	9	9	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:15694236C>A	ENST00000281513.5	-	4	261	c.236G>T	c.(235-237)gGa>gTa	p.G79V	NBAS_ENST00000441750.1_Missense_Mutation_p.G79V	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	79					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				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						GCGAACCAGTCCATCAGGGAG	0.368																																					p.G79V		Atlas-SNP	.											.	NBAS	246	.	0			c.G236T						.						102	100	101					2																	15694236		2203	4300	6503	SO:0001583	missense	51594	exon4			ACCAGTCCATCAG	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.236G>T	chr2.hg19:g.15694236C>A	ENSP00000281513:p.Gly79Val	124.0	0.0		124.0	5.0	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	hg19	CCDS1685.1	.	.	.	.	.	.	.	.	.	.	C	14.21	2.468217	0.43839	.	.	ENSG00000151779	ENST00000441750;ENST00000281513	T;T	0.09445	2.98;3.13	5.33	4.45	0.53987	.	0.057690	0.64402	D	0.000001	T	0.24736	0.0600	L	0.51422	1.61	0.43959	D	0.996633	D	0.89917	1.0	D	0.70227	0.968	T	0.00677	-1.1614	10	0.87932	D	0	.	10.9663	0.47414	0.0:0.9114:0.0:0.0886	.	79	A2RRP1	NBAS_HUMAN	V	79	ENSP00000413201:G79V;ENSP00000281513:G79V	ENSP00000281513:G79V	G	-	2	0	NBAS	15611687	1.000000	0.71417	1.000000	0.80357	0.869000	0.49853	4.005000	0.57075	1.238000	0.43771	0.305000	0.20034	GGA	.	.		0.368	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		A	15694236	C	A	15694236	3	1	259	1	0	0	0	0	1	0	0	0	10195	855	30	3	7075	3	NBAS	2	15694236	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	3915302	15694236	227505137	104	36422										
UBXN2A	165324	hgsc.bcm.edu	37	chr2	24199877	24199877	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttatggaaaaacggattcacCgtcaacgacgatttcagaag	9	8	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:24199877C>A	ENST00000309033.4	+	4	463	c.219C>A	c.(217-219)acC>acA	p.T73T	UBXN2A_ENST00000446425.2_3'UTR|UBXN2A_ENST00000535786.1_Silent_p.T73T|UBXN2A_ENST00000404924.1_Silent_p.T73T	NM_181713.3	NP_859064.2	P68543	UBX2A_HUMAN	UBX domain protein 2A	73	SEP. {ECO:0000255|PROSITE- ProRule:PRU00732}.				regulation of gene expression (GO:0010468)|regulation of protein catabolic process (GO:0042176)|regulation of protein ubiquitination (GO:0031396)	cis-Golgi network (GO:0005801)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)				endometrium(1)|large_intestine(3)|liver(1)|lung(6)	11						ACGGATTCACCGTCAACGACG	0.398																																					p.T73T		Atlas-SNP	.											UBXN2A,colon,carcinoma,0,1	UBXN2A	20	.	0			c.C219A						.						81	80	80					2																	24199877		2203	4300	6503	SO:0001819	synonymous_variant	165324	exon4			ATTCACCGTCAAC	BC037901	CCDS1704.1	2p24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000173960	ENSG00000173960		"UBX domain containing"	27265	protein-coding gene	gene with protein product			"UBX domain containing 4"	UBXD4		12477932	Standard	NM_181713		Approved		uc002ren.3	P68543	OTTHUMG00000125497	ENST00000309033.4:c.219C>A	chr2.hg19:g.24199877C>A		82.0	0.0		52.0	3.0	NM_181713	A8K577|B7ZKP8|Q569G8	Silent	SNP	ENST00000309033.4	hg19	CCDS1704.1																																																																																			.	.		0.398	UBXN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246824.2	NM_181713		A	24199877	C	A	24199877	2	1	259	1	0	0	0	0	0	0	0	1	16929	639	23	1		1	UBXN2A	2	24199877	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	8505641	24199877	218999496	105	36423										
HADHB	3032	hgsc.bcm.edu	37	chr2	26502146	26502146	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gccaagaaggcacaggatgaAggactcctttctgatgtggt	13	8	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:26502146A>G	ENST00000317799.5	+	9	878	c.774A>G	c.(772-774)gaA>gaG	p.E258E	HADHB_ENST00000537713.1_Silent_p.E243E|HADHB_ENST00000545822.1_Silent_p.E236E|HADHB_ENST00000405867.3_Intron|HADHB_ENST00000494615.1_3'UTR	NM_000183.2	NP_000174.1	P55084	ECHB_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), beta subunit	258					cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrial envelope (GO:0005740)|mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acyltransferase activity (GO:0003988)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CACAGGATGAAGGACTCCTTT	0.473																																					p.E258E		Atlas-SNP	.											.	HADHB	50	.	0			c.A774G						.						98	92	94					2																	26502146		2203	4300	6503	SO:0001819	synonymous_variant	3032	exon9			GGATGAAGGACTC		CCDS1722.1, CCDS62871.1, CCDS62872.1	2p23	2010-04-30	2010-04-30		ENSG00000138029	ENSG00000138029	2.3.1.16		4803	protein-coding gene	gene with protein product	"mitochondrial trifunctional protein, beta subunit"	143450	"hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), beta subunit"			9605857	Standard	NM_000183		Approved	MTPB	uc002rgz.3	P55084	OTTHUMG00000096978	ENST00000317799.5:c.774A>G	chr2.hg19:g.26502146A>G		131.0	0.0		83.0	4.0	NM_000183	B2RB16|B4E2W0|O14969|Q53TA6|Q96C77|Q9H3F5|Q9T2V8	Silent	SNP	ENST00000317799.5	hg19	CCDS1722.1																																																																																			.	.		0.473	HADHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214050.2	NM_000183		G	26502146	A	G	26502146	2	3	259	1	0	0	0	0	0	0	0	1	6953	69	3	2		2	HADHB	2	26502146	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2302269	26502146	216697227	106	36424										
OTOF	9381	hgsc.bcm.edu	37	chr2	26699053	26699053	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gcccaggccctgggctgcctTgacctcctggaagccacagg	13	16	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:26699053T>C	ENST00000272371.2	-	23	2935	c.2809A>G	c.(2809-2811)Aag>Gag	p.K937E	OTOF_ENST00000402415.3_Missense_Mutation_p.K247E|OTOF_ENST00000338581.6_Missense_Mutation_p.K190E|OTOF_ENST00000339598.3_Missense_Mutation_p.K190E|OTOF_ENST00000403946.3_Missense_Mutation_p.K937E	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	937					membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			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)					TGGGCTGCCTTGACCTCCTGG	0.657																																					p.K937E	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											.	OTOF	524	.	0			c.A2809G						.						35	35	35					2																	26699053		2200	4297	6497	SO:0001583	missense	9381	exon23			CTGCCTTGACCTC	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"fer-1-like family member 2"	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.2809A>G	chr2.hg19:g.26699053T>C	ENSP00000272371:p.Lys937Glu	56.0	0.0		51.0	4.0	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Missense_Mutation	SNP	ENST00000272371.2	hg19	CCDS1725.1	.	.	.	.	.	.	.	.	.	.	T	18.06	3.539003	0.65085	.	.	ENSG00000115155	ENST00000338581;ENST00000339598;ENST00000402415;ENST00000272371;ENST00000403946	T;T;T;T;T	0.80214	-1.11;-1.12;-1.08;-1.35;-1.35	5.41	4.24	0.50183	.	0.377728	0.31989	N	0.006744	T	0.77725	0.4173	L	0.49126	1.545	0.58432	D	0.999992	P;B;P;B	0.52061	0.799;0.042;0.95;0.356	B;B;P;B	0.48334	0.255;0.037;0.574;0.138	T	0.72711	-0.4211	10	0.22706	T	0.39	-38.1605	10.695	0.45894	0.1432:0.0:0.0:0.8568	.	937;190;247;190	Q9HC10;Q9HC10-2;Q9HC10-3;Q9HC10-4	OTOF_HUMAN;.;.;.	E	190;190;247;937;937	ENSP00000345137:K190E;ENSP00000344521:K190E;ENSP00000383906:K247E;ENSP00000272371:K937E;ENSP00000385255:K937E	ENSP00000272371:K937E	K	-	1	0	OTOF	26552557	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	6.084000	0.71335	0.878000	0.35920	0.459000	0.35465	AAG	.	.		0.657	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3			C	26699053	T	C	26699053	3	2	259	1	0	0	0	0	1	0	0	0	11312	1821	63	2	3465	2	OTOF	2	26699053	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	196907	26699053	216500320	107	36425										
DPYSL5	56896	hgsc.bcm.edu	37	chr2	27147810	27147810	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccacgtcctgcccgacaaggAgacctcccttgtggacgctt	10	16	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:27147810A>G	ENST00000288699.6	+	3	475	c.317A>G	c.(316-318)gAg>gGg	p.E106G	DPYSL5_ENST00000401478.1_Missense_Mutation_p.E106G	NM_001253724.1|NM_020134.3	NP_001240653.1|NP_064519.2	Q9BPU6	DPYL5_HUMAN	dihydropyrimidinase-like 5	106					axon guidance (GO:0007411)|nervous system development (GO:0007399)|pyrimidine nucleobase catabolic process (GO:0006208)|signal transduction (GO:0007165)	cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			breast(1)|endometrium(5)|large_intestine(2)|lung(13)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	27	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCCGACAAGGAGACCTCCCTT	0.637																																					p.E106G		Atlas-SNP	.											.	DPYSL5	69	.	0			c.A317G						.						92	80	84					2																	27147810		2203	4300	6503	SO:0001583	missense	56896	exon3			ACAAGGAGACCTC	AF264015	CCDS1730.1	2p23.3	2008-02-05			ENSG00000157851	ENSG00000157851			20637	protein-coding gene	gene with protein product		608383				10851247, 11034345	Standard	NM_020134		Approved	CRMP5, Ulip6, CRMP-5, CRAM	uc002rhu.4	Q9BPU6	OTTHUMG00000097071	ENST00000288699.6:c.317A>G	chr2.hg19:g.27147810A>G	ENSP00000288699:p.Glu106Gly	101.0	0.0		81.0	4.0	NM_001253724	Q8TCL6|Q9NQC4|Q9NRY9	Missense_Mutation	SNP	ENST00000288699.6	hg19	CCDS1730.1	.	.	.	.	.	.	.	.	.	.	A	6.794	0.515436	0.12944	.	.	ENSG00000157851	ENST00000450961;ENST00000288699;ENST00000401478;ENST00000431402;ENST00000434719	T;D;D;T;T	0.89343	-0.95;-2.5;-2.5;-0.92;-0.94	4.96	4.96	0.65561	Amidohydrolase 1 (1);	0.262941	0.43110	D	0.000611	T	0.60560	0.2278	N	0.00150	-1.985	0.40576	D	0.981343	B	0.02656	0.0	B	0.04013	0.001	T	0.68383	-0.5423	10	0.02654	T	1	-31.3377	13.9042	0.63823	1.0:0.0:0.0:0.0	.	106	Q9BPU6	DPYL5_HUMAN	G	106	ENSP00000407174:E106G;ENSP00000288699:E106G;ENSP00000385549:E106G;ENSP00000399581:E106G;ENSP00000413075:E106G	ENSP00000288699:E106G	E	+	2	0	DPYSL5	27001314	1.000000	0.71417	1.000000	0.80357	0.713000	0.41058	4.858000	0.62947	1.993000	0.58246	0.482000	0.46254	GAG	.	.		0.637	DPYSL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214187.2	NM_020134		G	27147810	A	G	27147810	3	3	259	1	0	0	0	0	1	0	0	0	4752	304	11	2	323	2	DPYSL5	2	27147810	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	448757	27147810	216051563	108	36426										
MAPRE3	22924	hgsc.bcm.edu	37	chr2	27248785	27248785	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gacagtggatgggctggagaAggaacgtgacttctacttca	14	7	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:27248785A>G	ENST00000233121.2	+	6	860	c.662A>G	c.(661-663)aAg>aGg	p.K221R	MAPRE3_ENST00000405074.3_Missense_Mutation_p.K206R|MAPRE3_ENST00000402218.1_Missense_Mutation_p.K206R			Q9UPY8	MARE3_HUMAN	microtubule-associated protein, RP/EB family, member 3	221	APC-binding.|DCTN1-binding.|EB1 C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00576}.				mitotic nuclear division (GO:0007067)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of microtubule plus-end binding (GO:1903033)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)	microtubule binding (GO:0008017)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(3)|upper_aerodigestive_tract(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGGCTGGAGAAGGAACGTGAC	0.532																																					p.K221R		Atlas-SNP	.											.	MAPRE3	40	.	0			c.A662G						.						113	100	104					2																	27248785		2203	4300	6503	SO:0001583	missense	22924	exon6			TGGAGAAGGAACG	Y11174	CCDS1731.1	2p23.3-p23.1	2008-06-04			ENSG00000084764	ENSG00000084764			6892	protein-coding gene	gene with protein product		605788				9233623	Standard	NM_012326		Approved	RP3, EB3	uc002rhw.3	Q9UPY8	OTTHUMG00000097067	ENST00000233121.2:c.662A>G	chr2.hg19:g.27248785A>G	ENSP00000233121:p.Lys221Arg	96.0	0.0		86.0	4.0	NM_012326	B7WPK5|O00265|Q6FHB0|Q6FI15|Q9BZP7|Q9BZP8	Missense_Mutation	SNP	ENST00000233121.2	hg19	CCDS1731.1	.	.	.	.	.	.	.	.	.	.	a	23.3	4.402264	0.83230	.	.	ENSG00000084764	ENST00000233121;ENST00000405074;ENST00000402218	T;T;T	0.49139	0.79;0.81;0.81	5.68	4.49	0.54785	EB1, C-terminal (2);	0.090131	0.64402	D	0.000003	T	0.59418	0.2192	L	0.60067	1.865	0.80722	D	1	P;P	0.49961	0.552;0.93	P;P	0.59643	0.584;0.861	T	0.59841	-0.7378	10	0.59425	D	0.04	-17.9221	11.0054	0.47631	0.86:0.0:0.0:0.14	.	206;221	Q9UPY8-2;Q9UPY8	.;MARE3_HUMAN	R	221;206;206	ENSP00000233121:K221R;ENSP00000383915:K206R;ENSP00000385715:K206R	ENSP00000233121:K221R	K	+	2	0	MAPRE3	27102289	1.000000	0.71417	0.978000	0.43139	0.764000	0.43329	9.262000	0.95591	0.932000	0.37266	0.529000	0.55759	AAG	.	.		0.532	MAPRE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214183.1	NM_012326		G	27248785	A	G	27248785	3	3	259	1	0	0	0	0	1	0	0	0	9305	72	3	2	680	2	MAPRE3	2	27248785	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	100975	27248785	215950588	109	36427										
TMEM214	54867	hgsc.bcm.edu	37	chr2	27258486	27258486	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tccctacagcctggtgagccGggagctacgtgggatcatcc	13	13	1	1	rs375315795		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:27258486G>A	ENST00000238788.9	+	4	589	c.527G>A	c.(526-528)cGg>cAg	p.R176Q	TMEM214_ENST00000404032.3_Intron	NM_017727.4	NP_060197.4	Q6NUQ4	TM214_HUMAN	transmembrane protein 214	176					apoptotic process (GO:0006915)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)	18						CTGGTGAGCCGGGAGCTACGT	0.562																																					p.R176Q		Atlas-SNP	.											.	TMEM214	41	.	0			c.G527A						.	G	,GLN/ARG	1,3907		0,1,1953	87	91	90		,527	1.7	0.7	2		90	0,8296		0,0,4148	no	intron,missense	TMEM214	NM_001083590.1,NM_017727.4	,43	0,1,6101	AA,AG,GG		0.0,0.0256,0.0082	,benign	,176/690	27258486	1,12203	1954	4148	6102	SO:0001583	missense	54867	exon4			TGAGCCGGGAGCT		CCDS42664.1, CCDS46242.1	2p23.3	2013-06-19			ENSG00000119777	ENSG00000119777			25983	protein-coding gene	gene with protein product						23661706	Standard	NM_001083590		Approved	FLJ20254	uc002ria.4	Q6NUQ4	OTTHUMG00000151999	ENST00000238788.9:c.527G>A	chr2.hg19:g.27258486G>A	ENSP00000238788:p.Arg176Gln	88.0	0.0		59.0	15.0	NM_017727	A6NNF2|B3KUI9|B5MCD8|D6W547|Q53SW1|Q69YH4|Q8NC45|Q8WZ37|Q9NXH2	Missense_Mutation	SNP	ENST00000238788.9	hg19	CCDS42664.1	.	.	.	.	.	.	.	.	.	.	G	15.38	2.816211	0.50527	2.56E-4	0.0	ENSG00000119777	ENST00000238788	T	0.43294	0.95	5.67	1.66	0.24008	.	0.405771	0.25372	N	0.031153	T	0.31513	0.0799	L	0.51422	1.61	0.80722	D	1	B	0.13594	0.008	B	0.04013	0.001	T	0.07102	-1.0790	10	0.41790	T	0.15	-5.0376	5.3239	0.15895	0.4238:0.1366:0.4395:0.0	.	176	Q6NUQ4	TM214_HUMAN	Q	176	ENSP00000238788:R176Q	ENSP00000238788:R176Q	R	+	2	0	TMEM214	27111990	1.000000	0.71417	0.698000	0.30274	0.956000	0.61745	1.941000	0.40233	0.011000	0.14865	0.561000	0.74099	CGG	.	.		0.562	TMEM214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324748.1	NM_017727		A	27258486	G	A	27258486	3	1	259	1	0	0	0	0	1	0	0	0	16152	1116	39	1	541	1	TMEM214	2	27258486	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	9701	27258486	215940887	110	36428										
YPEL5	51646	hgsc.bcm.edu	37	chr2	30381672	30381672	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgctctagttcgagagagtgAgggctttgaggagcatgtac	15	6	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:30381672A>G	ENST00000379520.3	+	5	833	c.329A>G	c.(328-330)gAg>gGg	p.E110G	YPEL5_ENST00000495673.1_3'UTR|YPEL5_ENST00000261353.4_Missense_Mutation_p.E110G|YPEL5_ENST00000402003.3_Missense_Mutation_p.E110G|YPEL5_ENST00000379519.3_Missense_Mutation_p.E110G|YPEL5_ENST00000402708.1_Missense_Mutation_p.E110G	NM_001127401.1	NP_001120873.1	P62699	YPEL5_HUMAN	yippee-like 5 (Drosophila)	110										NS(1)|endometrium(1)|kidney(1)|lung(3)|prostate(1)	7	Acute lymphoblastic leukemia(172;0.155)					CGAGAGAGTGAGGGCTTTGAG	0.448																																					p.E110G		Atlas-SNP	.											.	YPEL5	16	.	0			c.A329G						.						103	80	88					2																	30381672		2203	4300	6503	SO:0001583	missense	51646	exon4			AGAGTGAGGGCTT	AF135161	CCDS1771.1	2p23	2004-06-28			ENSG00000119801	ENSG00000119801			18329	protein-coding gene	gene with protein product		609726					Standard	NM_016061		Approved	CGI-127	uc002rmz.4	P62699	OTTHUMG00000097839	ENST00000379520.3:c.329A>G	chr2.hg19:g.30381672A>G	ENSP00000368835:p.Glu110Gly	84.0	0.0		76.0	4.0	NM_001127400	D6W568|Q65Z97|Q8R174|Q9D6M1|Q9UMX7|Q9Y3C9	Missense_Mutation	SNP	ENST00000379520.3	hg19	CCDS1771.1	.	.	.	.	.	.	.	.	.	.	.	16.99	3.274272	0.59649	.	.	ENSG00000119801	ENST00000379520;ENST00000379519;ENST00000261353;ENST00000402003;ENST00000402708	.	.	.	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.42200	0.1192	N	0.11818	0.18	0.80722	D	1	B	0.29188	0.236	B	0.30029	0.11	T	0.41179	-0.9523	9	0.48119	T	0.1	-1.1754	15.0511	0.71872	1.0:0.0:0.0:0.0	.	110	P62699	YPEL5_HUMAN	G	110	.	ENSP00000261353:E110G	E	+	2	0	YPEL5	30235176	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.090000	0.94144	2.145000	0.66743	0.533000	0.62120	GAG	.	.		0.448	YPEL5-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215128.1	NM_016061		G	30381672	A	G	30381672	3	3	259	1	0	0	0	0	1	0	0	0	17508	304	11	2	335	2	YPEL5	2	30381672	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	3123186	30381672	212817701	111	36429										
HEATR5B	54497	hgsc.bcm.edu	37	chr2	37246965	37246965	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttcttacctggcaagctttcGctattatatctgatggtgta	8	8	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:37246965G>T	ENST00000233099.5	-	26	4186	c.4091C>A	c.(4090-4092)gCg>gAg	p.A1364E	HEATR5B_ENST00000354531.2_Missense_Mutation_p.A1364E	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	1364						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				GCAAGCTTTCGCTATTATATC	0.308																																					p.A1364E		Atlas-SNP	.											HEATR5B,NS,carcinoma,0,1	HEATR5B	185	.	0			c.C4091A						.						77	83	81					2																	37246965		2203	4300	6503	SO:0001583	missense	54497	exon26			GCTTTCGCTATTA	AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.4091C>A	chr2.hg19:g.37246965G>T	ENSP00000233099:p.Ala1364Glu	51.0	0.0		39.0	2.0	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Missense_Mutation	SNP	ENST00000233099.5	hg19	CCDS33181.1	.	.	.	.	.	.	.	.	.	.	G	32	5.118482	0.94385	.	.	ENSG00000008869	ENST00000233099;ENST00000354531	T;T	0.52057	0.68;0.68	5.73	5.73	0.89815	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.68109	0.2965	M	0.65320	2	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.64884	-0.6302	10	0.42905	T	0.14	-20.3084	19.9026	0.96993	0.0:0.0:1.0:0.0	.	1364	Q9P2D3	HTR5B_HUMAN	E	1364	ENSP00000233099:A1364E;ENSP00000346531:A1364E	ENSP00000233099:A1364E	A	-	2	0	HEATR5B	37100469	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.763000	0.98947	2.707000	0.92482	0.643000	0.83706	GCG	.	.		0.308	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024		T	37246965	G	T	37246965	3	4	259	1	0	0	0	0	1	0	0	0	7041	1087	38	1	2168	1	HEATR5B	2	37246965	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	6865293	37246965	205952408	112	36430										
FBXO11	80204	hgsc.bcm.edu	37	chr2	48132835	48132835	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cgacactcgcctgggtctccGgttggcggctcggacggagt	16	13	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:48132835G>A	ENST00000403359.3	-	1	97	c.25C>T	c.(25-27)Cgg>Tgg	p.R9W	FBXO11_ENST00000378314.3_5'Flank|AC079807.2_ENST00000439870.1_RNA|AC079807.2_ENST00000417692.1_RNA|AC079807.2_ENST00000432064.1_RNA|FBXO11_ENST00000316377.4_5'Flank	NM_001190274.1	NP_001177203.1	Q86XK2	FBX11_HUMAN	F-box protein 11	9					cellular protein modification process (GO:0006464)|peptidyl-arginine N-methylation (GO:0035246)|protein ubiquitination (GO:0016567)|sensory perception of sound (GO:0007605)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	protein-arginine N-methyltransferase activity (GO:0016274)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.0?(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	26		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			CTGGGTCTCCGGTTGGCGGCT	0.726			"Mis, F, D"		DLBCL																																p.R9W		Atlas-SNP	.		Rec	yes		2	2p16.3	80204	F-box protein 11		L	.	FBXO11	127	.	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.C25T						.						3	3	3					2																	48132835		756	1788	2544	SO:0001583	missense	80204	exon1			GTCTCCGGTTGGC	AF174599	CCDS1837.1, CCDS54357.1	2p16.3	2014-01-29	2008-06-23	2008-06-23	ENSG00000138081	ENSG00000138081		"Ubiquitin protein ligase E3 component n-recognins", "F-boxes /  "other""	13590	protein-coding gene	gene with protein product	"ubiquitin protein ligase E3 component n-recognin 6"	607871	"F-box only protein 11"			10531035, 16487488, 18162545	Standard	NM_025133		Approved	FBX11, UBR6	uc002rwe.3	Q86XK2	OTTHUMG00000129130	ENST00000403359.3:c.25C>T	chr2.hg19:g.48132835G>A	ENSP00000384823:p.Arg9Trp	111.0	0.0		86.0	4.0	NM_001190274	A1L491|Q52ZP1|Q53EP7|Q53RT5|Q8IXG3|Q96E90|Q9H6V8|Q9H9L1|Q9NR14|Q9UFK1|Q9UHI1|Q9UKC2	Missense_Mutation	SNP	ENST00000403359.3	hg19	CCDS54357.1	.	.	.	.	.	.	.	.	.	.	G	13.86	2.364292	0.41902	.	.	ENSG00000138081	ENST00000403359	T	0.55413	0.52	2.23	2.23	0.28157	.	.	.	.	.	T	0.34308	0.0893	N	0.08118	0	0.80722	D	1	.	.	.	.	.	.	T	0.26643	-1.0097	7	0.87932	D	0	-8.703	6.137	0.20239	0.0:0.0:0.6988:0.3012	.	.	.	.	W	9	ENSP00000384823:R9W	ENSP00000384823:R9W	R	-	1	2	FBXO11	47986339	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	1.517000	0.35867	1.225000	0.43566	0.491000	0.48974	CGG	.	.		0.726	FBXO11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251181.3	NM_012167, NM_018693, NM_025133		A	48132835	G	A	48132835	3	1	259	1	0	0	0	0	1	0	0	0	5735	1115	39	1	2940	1	FBXO11	2	48132835	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	10885870	48132835	195066538	113	36431										
C2orf63	130162	hgsc.bcm.edu	37	chr2	55433452	55433452	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tttcgaagaattcttctaggActgtttgctgcataacaagc	8	8	2	1	rs151168260		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:55433452A>G	ENST00000401408.1	-	9	1305	c.960T>C	c.(958-960)agT>agC	p.S320S	CLHC1_ENST00000407122.1_Silent_p.S320S|CLHC1_ENST00000494539.1_Intron|CLHC1_ENST00000406437.2_Intron|CLHC1_ENST00000406076.1_Silent_p.S198S	NM_152385.2	NP_689598.2	Q8NHS4	CLHC1_HUMAN	clathrin heavy chain linker domain containing 1	320																	TTCTTCTAGGACTGTTTGCTG	0.313																																					p.S320S		Atlas-SNP	.											.	.	.	.	0			c.T960C						.	A	,	0,4404		0,0,2202	104	105	104		594,960	3.3	1	2	dbSNP_134	104	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous,coding-synonymous	C2orf63	NM_001135598.1,NM_152385.2	,	0,1,6500	GG,GA,AA		0.0116,0.0,0.0077	,	198/465,320/587	55433452	1,13001	2202	4299	6501	SO:0001819	synonymous_variant	130162	exon9			TCTAGGACTGTTT		CCDS33201.1, CCDS46287.1	2p16.1	2012-08-03	2012-08-03	2012-08-03	ENSG00000162994	ENSG00000162994			26453	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 63"	C2orf63			Standard	NM_152385		Approved	FLJ31438	uc002ryi.2	Q8NHS4	OTTHUMG00000151918	ENST00000401408.1:c.960T>C	chr2.hg19:g.55433452A>G		97.0	0.0		97.0	4.0	NM_152385	B2RDV1|Q53R93|Q8N403	Silent	SNP	ENST00000401408.1	hg19	CCDS33201.1																																																																																			.	A|1.000;G|0.000		0.313	CLHC1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324412.4	NM_152385		G	55433452	A	G	55433452	2	3	259	1	0	0	0	0	0	0	0	1	2184	272	10	2		2	C2orf63	2	55433452	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	7300617	55433452	187765921	114	36432										
ARHGAP25	9938	hgsc.bcm.edu	37	chr2	69043419	69043419	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acttgtgtaaatctcttcccAggctcagcaggagttgatga	10	9	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:69043419A>G	ENST00000295381.3	+	7	1223		c.e7-1		ARHGAP25_ENST00000544262.1_3'UTR|ARHGAP25_ENST00000409202.3_Splice_Site|ARHGAP25_ENST00000409030.3_Splice_Site|ARHGAP25_ENST00000467265.1_Splice_Site|ARHGAP25_ENST00000497079.1_Splice_Site|ARHGAP25_ENST00000409220.1_Splice_Site|ARHGAP25_ENST00000479844.1_5'Flank	NM_001007231.2	NP_001007232.2	P42331	RHG25_HUMAN	Rho GTPase activating protein 25						regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(20)|ovary(3)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	52						ATCTCTTCCCAGGCTCAGCAG	0.493																																					.		Atlas-SNP	.											.	ARHGAP25	175	.	0			c.688-2A>G						.						97	90	93					2																	69043419		2203	4300	6503	SO:0001630	splice_region_variant	9938	exon6			CTTCCCAGGCTCA	D29642	CCDS33214.1, CCDS46312.1, CCDS33214.2, CCDS54363.1, CCDS54364.1	2p13.3	2013-01-10			ENSG00000163219	ENSG00000163219		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	28951	protein-coding gene	gene with protein product		610587				7584044	Standard	NM_001007231		Approved	KIAA0053	uc010fdg.3	P42331	OTTHUMG00000152621	ENST00000295381.3:c.805-1A>G	chr2.hg19:g.69043419A>G		88.0	0.0		78.0	4.0	NM_001166277	A8K2Y1|B7Z498|E9PFQ7|G5E9G2|Q8IXQ2	Splice_Site	SNP	ENST00000295381.3	hg19		.	.	.	.	.	.	.	.	.	.	A	23.0	4.361753	0.82353	.	.	ENSG00000163219	ENST00000295381;ENST00000409202;ENST00000467265;ENST00000409030;ENST00000409220;ENST00000482106;ENST00000497079;ENST00000543533;ENST00000497259	.	.	.	5.85	5.85	0.93711	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4228	0.75025	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ARHGAP25	68896923	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.938000	0.92943	2.241000	0.73720	0.477000	0.44152	.	.	.		0.493	ARHGAP25-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014882	Intron	G	69043419	A	G	69043419	5	3	259	1	0	0	0	0	0	0	1	0	874	202	7	2	872	2	ARHGAP25	2	69043419	Splice_Site	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	13609967	69043419	174155954	115	36433										
C2orf42	54980	hgsc.bcm.edu	37	chr2	70408789	70408789	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cataacaccgtccagagctcAgctgagtgatgatcgtccca	9	13	1	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:70408789A>G	ENST00000264434.2	-	3	708	c.329T>C	c.(328-330)cTg>cCg	p.L110P	C2orf42_ENST00000420306.1_Missense_Mutation_p.L110P|C2orf42_ENST00000470096.1_5'UTR	NM_017880.1	NP_060350.1	Q9NWW7	CB042_HUMAN	chromosome 2 open reading frame 42	110										endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|urinary_tract(1)	12						TCCAGAGCTCAGCTGAGTGAT	0.562																																					p.L110P		Atlas-SNP	.											.	C2orf42	30	.	0			c.T329C						.						85	74	78					2																	70408789		2203	4300	6503	SO:0001583	missense	54980	exon3			GAGCTCAGCTGAG	AK000565	CCDS1899.1	2p14	2011-03-08			ENSG00000115998	ENSG00000115998			26056	protein-coding gene	gene with protein product						12477932	Standard	XM_005264389		Approved	FLJ20558	uc002sgh.3	Q9NWW7	OTTHUMG00000129642	ENST00000264434.2:c.329T>C	chr2.hg19:g.70408789A>G	ENSP00000264434:p.Leu110Pro	120.0	0.0		100.0	4.0	NM_017880	D6W5G3|Q9H629	Missense_Mutation	SNP	ENST00000264434.2	hg19	CCDS1899.1	.	.	.	.	.	.	.	.	.	.	A	19.91	3.913753	0.72983	.	.	ENSG00000115998	ENST00000264434;ENST00000420306;ENST00000447804;ENST00000417865;ENST00000419381;ENST00000457952	T;T	0.49720	0.77;0.77	4.96	4.96	0.65561	.	0.075820	0.49916	D	0.000128	T	0.50939	0.1645	L	0.43152	1.355	0.80722	D	1	D	0.54207	0.965	P	0.53649	0.731	T	0.42682	-0.9437	10	0.27082	T	0.32	-9.575	13.6431	0.62265	1.0:0.0:0.0:0.0	.	110	Q9NWW7	CB042_HUMAN	P	110	ENSP00000264434:L110P;ENSP00000404515:L110P	ENSP00000264434:L110P	L	-	2	0	C2orf42	70262293	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.090000	0.89526	2.082000	0.62665	0.397000	0.26171	CTG	.	.		0.562	C2orf42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251840.1	NM_017880		G	70408789	A	G	70408789	3	3	259	1	0	0	0	0	1	0	0	0	2168	188	7	2	1427	2	C2orf42	2	70408789	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1365370	70408789	172790584	116	36434										
TIA1	7072	hgsc.bcm.edu	37	chr2	70441567	70441567	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atatactggccaatttgttgTgcatttccataccactggcc	7	11	0	0	rs373531585		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:70441567T>C	ENST00000433529.2	-	12	1158	c.948A>G	c.(946-948)gcA>gcG	p.A316A	TIA1_ENST00000282574.4_Silent_p.A315A|C2orf42_ENST00000470096.1_Intron|TIA1_ENST00000415783.2_Silent_p.A305A|TIA1_ENST00000445587.1_Intron|TIA1_ENST00000482876.1_5'Flank	NM_022173.2	NP_071505.2	P31483	TIA1_HUMAN	TIA1 cytotoxic granule-associated RNA binding protein	316					apoptotic process (GO:0006915)|negative regulation of cytokine biosynthetic process (GO:0042036)|negative regulation of translation (GO:0017148)|regulation of mRNA splicing, via spliceosome (GO:0048024)	cytoplasmic stress granule (GO:0010494)|nuclear stress granule (GO:0097165)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|skin(1)|urinary_tract(1)	17						CAATTTGTTGTGCATTTCCAT	0.383																																					p.A316A		Atlas-SNP	.											.	TIA1	37	.	0			c.A948G						.						109	92	98					2																	70441567		2203	4300	6503	SO:0001819	synonymous_variant	7072	exon12			TTGTTGTGCATTT		CCDS1900.1, CCDS1901.1	2p13	2013-02-12	2001-11-28		ENSG00000116001	ENSG00000116001		"RNA binding motif (RRM) containing"	11802	protein-coding gene	gene with protein product	"T-cell-restricted intracellular antigen-1", "nucleolysin TIA-1 isoform p40"	603518	"TIA1 cytotoxic granule-associated RNA-binding protein"			8176212, 12486009	Standard	NM_022173		Approved		uc002sgj.4	P31483	OTTHUMG00000129644	ENST00000433529.2:c.948A>G	chr2.hg19:g.70441567T>C		152.0	0.0		123.0	5.0	NM_022173	Q53SS9	Silent	SNP	ENST00000433529.2	hg19	CCDS1901.1																																																																																			.	.		0.383	TIA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251842.2	NM_022037		C	70441567	T	C	70441567	2	2	259	1	0	0	0	0	0	0	0	1	15902	1683	59	2		2	TIA1	2	70441567	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	32778	70441567	172757806	117	36435										
DYSF	8291	hgsc.bcm.edu	37	chr2	71892352	71892352	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cagctcctccacctcttctgCcagcagcatagagtcaaggc	8	16	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:71892352C>T	ENST00000258104.3	+	46	5395	c.5118C>T	c.(5116-5118)tgC>tgT	p.C1706C	DYSF_ENST00000409762.1_Silent_p.C1723C|DYSF_ENST00000479049.2_3'UTR|DYSF_ENST00000413539.2_Silent_p.C1737C|DYSF_ENST00000409366.1_Silent_p.C1728C|DYSF_ENST00000409744.1_Silent_p.C1714C|DYSF_ENST00000394120.2_Silent_p.C1707C|DYSF_ENST00000409582.3_Silent_p.C1744C|DYSF_ENST00000409651.1_Silent_p.C1738C|DYSF_ENST00000410020.3_Silent_p.C1745C|DYSF_ENST00000429174.2_Silent_p.C1727C|DYSF_ENST00000410041.1_Silent_p.C1724C	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	1706					plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						ACCTCTTCTGCCAGCAGCATA	0.537																																					p.C1745C		Atlas-SNP	.											.	DYSF	536	.	0			c.C5235T						.						103	104	104					2																	71892352		2203	4300	6503	SO:0001819	synonymous_variant	8291	exon47			CTTCTGCCAGCAG	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"fer-1-like family member 1"	603009	"limb girdle muscular dystrophy 2B (autosomal recessive)"	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.5118C>T	chr2.hg19:g.71892352C>T		83.0	0.0		57.0	4.0	NM_001130987	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Silent	SNP	ENST00000258104.3	hg19	CCDS1918.1																																																																																			.	.		0.537	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494		T	71892352	C	T	71892352	2	4	259	1	0	0	0	0	0	0	0	1	4861	747	26	3		3	DYSF	2	71892352	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	1450785	71892352	171307021	118	36436										
DCTN1	1639	hgsc.bcm.edu	37	chr2	74590545	74590545	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cagaccctggagcctgcccaGggatggctcctgtggggacc	15	14	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:74590545G>A	ENST00000361874.3	-	28	3538	c.3221C>T	c.(3220-3222)cCt>cTt	p.P1074L	DCTN1_ENST00000407639.2_Missense_Mutation_p.P940L|DCTN1_ENST00000495643.1_5'Flank|RP11-287D1.3_ENST00000451608.2_5'Flank|DCTN1_ENST00000394003.3_Missense_Mutation_p.P1067L|DCTN1_ENST00000409438.1_Missense_Mutation_p.P935L|DCTN1_ENST00000409567.3_Missense_Mutation_p.P1049L|DCTN1_ENST00000409240.1_Missense_Mutation_p.P1032L|DCTN1_ENST00000409868.1_Missense_Mutation_p.P1052L	NM_004082.4	NP_004073.2	Q14203	DCTN1_HUMAN	dynactin 1	1074					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|G2/M transition of mitotic cell cycle (GO:0000086)|melanosome transport (GO:0032402)|microtubule-based transport (GO:0010970)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|nervous system development (GO:0007399)	cell leading edge (GO:0031252)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|dynein complex (GO:0030286)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(1)|skin(3)	45						AGCCTGCCCAGGGATGGCTCC	0.577																																					p.P1074L		Atlas-SNP	.											.	DCTN1	110	.	0			c.C3221T						.						19	19	19					2																	74590545		2202	4300	6502	SO:0001583	missense	1639	exon28			TGCCCAGGGATGG		CCDS1939.1, CCDS46341.1, CCDS46342.1, CCDS54368.1, CCDS54369.1	2p13	2014-09-17	2010-06-24		ENSG00000204843	ENSG00000204843			2711	protein-coding gene	gene with protein product	"p150 glued homolog (Drosophila)"	601143	"dynactin 1 (p150, Glued (Drosophila) homolog)"			1828535	Standard	NM_001190836		Approved		uc002skx.3	Q14203	OTTHUMG00000129963	ENST00000361874.3:c.3221C>T	chr2.hg19:g.74590545G>A	ENSP00000354791:p.Pro1074Leu	64.0	0.0		50.0	4.0	NM_004082	A8MY36|B4DM45|E9PFS5|E9PGE1|G5E9H4|O95296|Q6IQ37|Q9BRM9|Q9UIU1|Q9UIU2	Missense_Mutation	SNP	ENST00000361874.3	hg19	CCDS1939.1	.	.	.	.	.	.	.	.	.	.	G	4.597	0.110890	0.08831	.	.	ENSG00000204843	ENST00000361874;ENST00000394003;ENST00000393999;ENST00000407639;ENST00000409438;ENST00000409240;ENST00000409868;ENST00000409567	T;T;T;T;T;T;T	0.78481	-0.78;-0.96;-0.78;-0.78;-1.18;-0.96;-0.96	4.72	4.72	0.59763	.	0.192725	0.25683	N	0.028992	T	0.60856	0.2301	N	0.05230	-0.09	0.21445	N	0.999685	B;B;B;B;B;B;B	0.12013	0.001;0.0;0.003;0.0;0.0;0.005;0.0	B;B;B;B;B;B;B	0.19391	0.001;0.0;0.011;0.003;0.0;0.025;0.0	T	0.50775	-0.8788	10	0.32370	T	0.25	-3.8028	16.6006	0.84815	0.0:0.0:1.0:0.0	.	1049;1032;1074;1067;940;935;1057	E9PGE1;E9PFS5;Q14203;A8MY36;Q14203-2;G5E9H4;A8MWX9	.;.;DCTN1_HUMAN;.;.;.;.	L	1074;1067;1057;940;935;1032;1052;1049	ENSP00000354791:P1074L;ENSP00000377571:P1067L;ENSP00000384844:P940L;ENSP00000387270:P935L;ENSP00000386406:P1032L;ENSP00000387327:P1052L;ENSP00000386843:P1049L	ENSP00000354791:P1074L	P	-	2	0	DCTN1	74444053	0.404000	0.25328	0.669000	0.29828	0.678000	0.39670	2.786000	0.47790	2.424000	0.82194	0.643000	0.83706	CCT	.	.		0.577	DCTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252227.3	NM_004082		A	74590545	G	A	74590545	3	1	259	1	0	0	0	0	1	0	0	0	4308	1000	35	3	635	3	DCTN1	2	74590545	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	2698193	74590545	168608828	119	36437										
CTNNA2	1496	hgsc.bcm.edu	37	chr2	80101205	80101205	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atgtgttacacacacaggagCtgaaggatcctcactgtcgg	11	10	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:80101205C>A	ENST00000402739.4	+	5	594	c.589C>A	c.(589-591)Ctg>Atg	p.L197M	CTNNA2_ENST00000361291.4_Missense_Mutation_p.L231M|CTNNA2_ENST00000541047.1_Missense_Mutation_p.L197M|CTNNA2_ENST00000496558.1_Missense_Mutation_p.L197M|CTNNA2_ENST00000466387.1_Missense_Mutation_p.L197M|CTNNA2_ENST00000540488.1_Missense_Mutation_p.L197M	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	197					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						CACACAGGAGCTGAAGGATCC	0.483																																					p.L197M		Atlas-SNP	.											.	CTNNA2	462	.	0			c.C589A						.						39	41	40					2																	80101205		1984	4172	6156	SO:0001583	missense	1496	exon6			CAGGAGCTGAAGG		CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"cadherin-associated protein, related", "cancer/testis antigen 114"	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.589C>A	chr2.hg19:g.80101205C>A	ENSP00000384638:p.Leu197Met	60.0	0.0		72.0	4.0	NM_001164883	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Missense_Mutation	SNP	ENST00000402739.4	hg19		.	.	.	.	.	.	.	.	.	.	C	19.20	3.782220	0.70222	.	.	ENSG00000066032	ENST00000466387;ENST00000496558;ENST00000361291;ENST00000402739;ENST00000541047;ENST00000540488	T;T;T;T;T;T	0.64803	-0.12;-0.12;-0.12;-0.12;-0.12;-0.12	5.7	3.89	0.44902	Vinculin, conserved site (1);	0.000000	0.64402	D	0.000005	D	0.82365	0.5021	M	0.92122	3.275	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.994;0.997	D	0.86239	0.1642	10	0.72032	D	0.01	.	12.5675	0.56318	0.0:0.863:0.0:0.137	.	197;197;197	P26232;P26232-3;P26232-2	CTNA2_HUMAN;.;.	M	197;197;231;197;197;197	ENSP00000418191:L197M;ENSP00000419295:L197M;ENSP00000355398:L231M;ENSP00000384638:L197M;ENSP00000444675:L197M;ENSP00000441705:L197M	ENSP00000355398:L231M	L	+	1	2	CTNNA2	79954713	1.000000	0.71417	1.000000	0.80357	0.809000	0.45718	4.079000	0.57613	1.413000	0.46997	0.650000	0.86243	CTG	.	.		0.483	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389		A	80101205	C	A	80101205	3	1	259	1	0	0	0	0	1	0	0	0	4015	796	28	3	607	3	CTNNA2	2	80101205	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	5510660	80101205	163098168	120	36438										
CAPG	822	hgsc.bcm.edu	37	chr2	85628289	85628289	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gtctggccagcctacccaccTggcccaggtccaggatgaag	12	15	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:85628289T>C	ENST00000409921.1	-	5	581	c.515A>G	c.(514-516)cAg>cGg	p.Q172R	CAPG_ENST00000409670.1_Splice_Site_p.Q172R|CAPG_ENST00000483659.1_5'UTR|CAPG_ENST00000263867.4_Splice_Site_p.Q172R|CAPG_ENST00000409724.1_Splice_Site_p.Q172R			Q9BPX3	CND3_HUMAN	capping protein (actin filament), gelsolin-like	0					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(6)	11						CCTACCCACCTGGCCCAGGTC	0.592																																					p.Q172R		Atlas-SNP	.											.	CAPG	32	.	0			c.A515G						.						126	119	121					2																	85628289		2203	4300	6503	SO:0001630	splice_region_variant	822	exon5			CCCACCTGGCCCA	M94345	CCDS1974.1, CCDS58715.1	2p11.2	2008-06-04			ENSG00000042493	ENSG00000042493			1474	protein-coding gene	gene with protein product	"macrophage capping protein"	153615		AFCP		1322908, 12754261	Standard	NM_001747		Approved	MCP	uc010fgi.2	P40121	OTTHUMG00000130183	ENST00000409921.1:c.516+1A>G	chr2.hg19:g.85628289T>C		159.0	0.0		144.0	6.0	NM_001256140	Q3MJE0|Q96SV9|Q9BUR3|Q9BVY1|Q9H914|Q9H9Z6|Q9HBI9	Missense_Mutation	SNP	ENST00000409921.1	hg19	CCDS58715.1	.	.	.	.	.	.	.	.	.	.	T	14.69	2.610289	0.46527	.	.	ENSG00000042493	ENST00000542681;ENST00000263867;ENST00000409921;ENST00000409670;ENST00000409724;ENST00000439385;ENST00000449030;ENST00000447219;ENST00000409275	T;T;T;T;T;T;T;T	0.56275	0.47;0.47;0.47;0.47;0.47;0.47;0.47;0.47	5.97	2.21	0.28008	Gelsolin domain (1);	0.316113	0.38720	N	0.001581	T	0.31389	0.0795	N	0.17594	0.5	0.35580	D	0.80621	B;B;B	0.15930	0.001;0.0;0.015	B;B;B	0.21917	0.002;0.001;0.037	T	0.14727	-1.0462	10	0.35671	T	0.21	.	5.3512	0.16036	0.0:0.1584:0.1483:0.6933	.	151;172;172	B4DU58;B8ZZS7;P40121	.;.;CAPG_HUMAN	R	151;172;172;172;172;172;172;172;172	ENSP00000263867:Q172R;ENSP00000387063:Q172R;ENSP00000386315:Q172R;ENSP00000386965:Q172R;ENSP00000391923:Q172R;ENSP00000403330:Q172R;ENSP00000398232:Q172R;ENSP00000386596:Q172R	ENSP00000263867:Q172R	Q	-	2	0	CAPG	85481800	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	1.744000	0.38268	0.495000	0.27882	0.533000	0.62120	CAG	.	.		0.592	CAPG-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000329383.1	NM_001747	Missense_Mutation	C	85628289	T	C	85628289	5	2	259	1	0	0	0	0	0	0	1	0	2623	1594	55	2	555	2	CAPG	2	85628289	Splice_Site	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	5527084	85628289	157571084	121	36439										
RPIA	22934	hgsc.bcm.edu	37	chr2	89036184	89036184	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gttgaacttcgaatggctgtCaacaaggctgtgagtggcct	13	8	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:89036184C>T	ENST00000283646.4	+	7	784	c.729C>T	c.(727-729)gtC>gtT	p.V243V		NM_144563.2	NP_653164.2	P49247	RPIA_HUMAN	ribose 5-phosphate isomerase A	243					carbohydrate metabolic process (GO:0005975)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, non-oxidative branch (GO:0009052)|ribose phosphate metabolic process (GO:0019693)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	monosaccharide binding (GO:0048029)|ribose-5-phosphate isomerase activity (GO:0004751)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|skin(1)	18		Acute lymphoblastic leukemia(2;0.000456)|all_hematologic(2;0.00287)				GAATGGCTGTCAACAAGGCTG	0.572																																					p.V243V		Atlas-SNP	.											.	RPIA	35	.	0			c.C729T						.						133	146	142					2																	89036184		2030	4187	6217	SO:0001819	synonymous_variant	22934	exon7			GGCTGTCAACAAG	L35035	CCDS2004.2	2p11.2	2008-07-31	2008-07-31		ENSG00000153574	ENSG00000153574	5.3.1.6		10297	protein-coding gene	gene with protein product	"ribose 5-phosphate epimerase"	180430				7758956	Standard	NM_144563		Approved		uc002ste.3	P49247	OTTHUMG00000130333	ENST00000283646.4:c.729C>T	chr2.hg19:g.89036184C>T		94.0	0.0		70.0	4.0	NM_144563	Q541P9|Q96BJ6	Silent	SNP	ENST00000283646.4	hg19	CCDS2004.2																																																																																			.	.		0.572	RPIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252683.2			T	89036184	C	T	89036184	2	4	259	1	0	0	0	0	0	0	0	1	13568	813	29	3		3	RPIA	2	89036184	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	3407895	89036184	154163189	122	36440										
ZNF514	84874	hgsc.bcm.edu	37	chr2	95815310	95815310	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tttctccagtatgagtcctcTgatgcttaataagggatgaa	9	7	2	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:95815310T>C	ENST00000295208.2	-	5	1382	c.920A>G	c.(919-921)cAg>cGg	p.Q307R	ZNF514_ENST00000411425.1_Missense_Mutation_p.Q307R|MRPS5_ENST00000475040.1_5'Flank	NM_032788.1	NP_116177.1	Q96K75	ZN514_HUMAN	zinc finger protein 514	307					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(4)|lung(6)|urinary_tract(1)	11						ATGAGTCCTCTGATGCTTAAT	0.438																																					p.Q307R		Atlas-SNP	.											.	ZNF514	34	.	0			c.A920G						.						66	70	69					2																	95815310		2203	4300	6503	SO:0001583	missense	84874	exon5			GTCCTCTGATGCT	AL832263	CCDS2011.1	2q11.2	2013-01-08			ENSG00000144026	ENSG00000144026		"Zinc fingers, C2H2-type", "-"	25894	protein-coding gene	gene with protein product							Standard	NM_032788		Approved	FLJ14457	uc002sue.1	Q96K75	OTTHUMG00000130391	ENST00000295208.2:c.920A>G	chr2.hg19:g.95815310T>C	ENSP00000295208:p.Gln307Arg	142.0	0.0		119.0	5.0	NM_032788	Q5JPJ3	Missense_Mutation	SNP	ENST00000295208.2	hg19	CCDS2011.1	.	.	.	.	.	.	.	.	.	.	T	11.92	1.783415	0.31593	.	.	ENSG00000144026	ENST00000295208;ENST00000411425	T;T	0.07327	3.2;3.2	2.65	1.5	0.22942	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07279	0.0184	N	0.21194	0.64	0.26677	N	0.971611	B;P	0.37612	0.001;0.602	B;B	0.42653	0.004;0.394	T	0.32134	-0.9918	9	0.54805	T	0.06	.	5.9899	0.19454	0.0:0.1365:0.0:0.8635	.	307;126	Q96K75;Q658L7	ZN514_HUMAN;.	R	307	ENSP00000295208:Q307R;ENSP00000405509:Q307R	ENSP00000295208:Q307R	Q	-	2	0	ZNF514	95179037	0.000000	0.05858	1.000000	0.80357	0.951000	0.60555	-0.086000	0.11233	0.439000	0.26476	0.533000	0.62120	CAG	.	.		0.438	ZNF514-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252769.1	NM_032788		C	95815310	T	C	95815310	3	2	259	1	0	0	0	0	1	0	0	0	17974	1580	55	2	286	2	ZNF514	2	95815310	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	6779126	95815310	147384063	123	36441										
FAM178B	51252	hgsc.bcm.edu	37	chr2	97586981	97586981	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gtcagacacccagctcagggTgcagcacagttcctggagct	12	13	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:97586981T>C	ENST00000417561.3	-	16	1926	c.1927A>G	c.(1927-1929)Acc>Gcc	p.T643A	FAM178B_ENST00000327896.3_Missense_Mutation_p.T463A|FAM178B_ENST00000490605.2_Missense_Mutation_p.T495A			Q8IXR5	F178B_HUMAN	family with sequence similarity 178, member B	643										large_intestine(1)|ovary(1)	2						CAGCTCAGGGTGCAGCACAGT	0.657																																					p.T495A		Atlas-SNP	.											.	FAM178B	35	.	0			c.A1483G						.						60	64	63					2																	97586981		692	1591	2283	SO:0001583	missense	51252	exon12			TCAGGGTGCAGCA	AF151068, BC039488	CCDS33252.1, CCDS46366.1, CCDS46366.2	2q11.2	2008-08-08			ENSG00000168754	ENSG00000168754			28036	protein-coding gene	gene with protein product						11042152	Standard	NM_001122646		Approved	LOC51252	uc002sxl.4	Q8IXR5	OTTHUMG00000155257	ENST00000417561.3:c.1927A>G	chr2.hg19:g.97586981T>C	ENSP00000413245:p.Thr643Ala	94.0	0.0		59.0	4.0	NM_001122646	A8MXN2|E9PD86|Q8IUY0|Q9P0P4	Missense_Mutation	SNP	ENST00000417561.3	hg19		.	.	.	.	.	.	.	.	.	.	T	0.011	-1.710213	0.00712	.	.	ENSG00000168754	ENST00000417561;ENST00000327896;ENST00000490605	T;T;T	0.39997	1.05;1.09;1.08	5.21	-4.31	0.03698	.	0.787278	0.10183	N	0.705656	T	0.09686	0.0238	N	0.01576	-0.805	0.09310	N	1	.	.	.	.	.	.	T	0.32508	-0.9904	8	0.02654	T	1	-1.9274	1.9878	0.03440	0.1416:0.2285:0.139:0.4909	.	.	.	.	A	643;463;495	ENSP00000413245:T643A;ENSP00000333553:T463A;ENSP00000429896:T495A	ENSP00000333553:T463A	T	-	1	0	FAM178B	96950708	0.000000	0.05858	0.008000	0.14137	0.038000	0.13279	-3.548000	0.00434	-0.351000	0.08249	-1.133000	0.01973	ACC	.	.		0.657	FAM178B-202	KNOWN	basic	protein_coding	protein_coding		NM_016490		C	97586981	T	C	97586981	3	2	259	1	0	0	0	0	1	0	0	0	5509	1696	59	2	611	2	FAM178B	2	97586981	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1771671	97586981	145612392	124	36442										
MAP4K4	9448	hgsc.bcm.edu	37	chr2	102490567	102490567	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gattttcctgtgatgggatgAgaccagaagccataaggcaa	12	7	0	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:102490567A>G	ENST00000347699.4	+	23	2659	c.2659A>G	c.(2659-2661)Aga>Gga	p.R887G	MAP4K4_ENST00000425019.1_Missense_Mutation_p.R920G|MAP4K4_ENST00000413150.2_Missense_Mutation_p.R802G|MAP4K4_ENST00000350878.4_Missense_Mutation_p.R927G|MAP4K4_ENST00000302217.5_Missense_Mutation_p.R690G|MAP4K4_ENST00000456652.1_Missense_Mutation_p.R686G|MAP4K4_ENST00000350198.4_Missense_Mutation_p.R806G|MAP4K4_ENST00000324219.4_Missense_Mutation_p.R968G	NM_001242559.1|NM_145687.3	NP_001229488.1|NP_663720.1	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase kinase 4	887	Mediates interaction with RAP2A.				intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of JNK cascade (GO:0046328)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						TGATGGGATGAGACCAGAAGC	0.458																																					p.R921G		Atlas-SNP	.											.	MAP4K4	111	.	0			c.A2761G						.						94	93	93					2																	102490567		1931	4126	6057	SO:0001583	missense	9448	exon24			GGGATGAGACCAG	AF096300	CCDS56130.1, CCDS74546.1	2q11.2-q12	2011-06-09			ENSG00000071054	ENSG00000071054		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6866	protein-coding gene	gene with protein product	"HPK/GCK-like kinase", "hepatocyte progenitor kinase-like/germinal center kinase-like kinase"	604666				9890973, 9734811, 9135144	Standard	NM_004834		Approved	HGK, NIK, FLH21957	uc002tbf.3	O95819	OTTHUMG00000155394	ENST00000347699.4:c.2659A>G	chr2.hg19:g.102490567A>G	ENSP00000314363:p.Arg887Gly	158.0	0.0		111.0	6.0	NM_145686	O75172|Q9NST7	Missense_Mutation	SNP	ENST00000347699.4	hg19	CCDS56130.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.35|15.35	2.806641|2.806641	0.50421|0.50421	.|.	.|.	ENSG00000071054|ENSG00000071054	ENST00000421882|ENST00000425019;ENST00000324219;ENST00000350198;ENST00000302217;ENST00000413150;ENST00000456652;ENST00000347699;ENST00000417294;ENST00000350878	.|T;T;T;T;T;T;T;T;T	.|0.75050	.|-0.81;-0.76;-0.76;-0.26;-0.77;-0.26;-0.77;-0.9;-0.78	5.22|5.22	5.22|5.22	0.72569|0.72569	.|.	.|0.066200	.|0.64402	.|D	.|0.000007	D|D	0.82365|0.82365	0.5021|0.5021	L|L	0.58810|0.58810	1.83|1.83	0.58432|0.58432	D|D	0.999992|0.999992	.|D;P;B;B;P;D;B;P;D;B	.|0.64830	.|0.967;0.717;0.047;0.069;0.814;0.99;0.073;0.814;0.994;0.443	.|P;P;B;B;P;P;B;P;D;B	.|0.68483	.|0.879;0.478;0.05;0.028;0.677;0.718;0.008;0.677;0.958;0.108	T|T	0.80527|0.80527	-0.1343|-0.1343	5|10	.|0.29301	.|T	.|0.29	.|.	15.1029|15.1029	0.72296|0.72296	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|927;883;686;690;805;887;920;806;859;968	.|B7Z388;B7Z3V5;E7EX83;C9J840;O95819-4;O95819;E7EN19;G3XAA2;O95819-2;G5E948	.|.;.;.;.;.;M4K4_HUMAN;.;.;.;.	G|G	703|920;968;806;690;802;686;887;818;927	.|ENSP00000392830:R920G;ENSP00000313644:R968G;ENSP00000281111:R806G;ENSP00000303600:R690G;ENSP00000389752:R802G;ENSP00000387370:R686G;ENSP00000314363:R887G;ENSP00000409720:R818G;ENSP00000343658:R927G	.|ENSP00000303600:R690G	E|R	+|+	2|1	0|2	MAP4K4|MAP4K4	101856999|101856999	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	4.478000|4.478000	0.60230|0.60230	1.972000|1.972000	0.57404|0.57404	0.533000|0.533000	0.62120|0.62120	GAG|AGA	.	.		0.458	MAP4K4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339839.1	NM_004834		G	102490567	A	G	102490567	3	3	259	1	0	0	0	0	1	0	0	0	9271	296	11	2	3000	2	MAP4K4	2	102490567	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	4903586	102490567	140708806	125	36443										
SH3RF3	344558	hgsc.bcm.edu	37	chr2	110015186	110015186	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	actttaagcagctcaggggcGgtcagtgcctttcagcggcg	14	11	3	0	rs542535234		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:110015186G>T	ENST00000309415.6	+	4	1086	c.1086G>T	c.(1084-1086)gcG>gcT	p.A362A		NM_001099289.1	NP_001092759.1	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3	362							zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(5)|ovary(2)	18						GCTCAGGGGCGGTCAGTGCCT	0.632																																					p.A362A		Atlas-SNP	.											SH3RF3,right_upper_lobe,carcinoma,0,1	SH3RF3	62	.	0			c.G1086T						.						40	47	45					2																	110015186		2203	4300	6503	SO:0001819	synonymous_variant	344558	exon4			AGGGGCGGTCAGT	AK074131	CCDS74557.1	2q13	2013-01-11	2008-05-14	2008-05-14	ENSG00000172985	ENSG00000172985		"RING-type (C3HC4) zinc fingers"	24699	protein-coding gene	gene with protein product			"SH3 multiple domains 4"	SH3MD4		16374509	Standard	XM_006712493		Approved	FLJ00204, POSH2	uc010ywt.1	Q8TEJ3	OTTHUMG00000153439	ENST00000309415.6:c.1086G>T	chr2.hg19:g.110015186G>T		104.0	0.0		78.0	4.0	NM_001099289	A0SDZ7|A8MPR1|Q8NDU1	Silent	SNP	ENST00000309415.6	hg19																																																																																				.	.		0.632	SH3RF3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001099289		T	110015186	G	T	110015186	2	4	259	1	0	0	0	0	0	0	0	1	14275	1103	39	1		1	SH3RF3	2	110015186	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	7524619	110015186	133184187	126	36444										
FBLN7	129804	hgsc.bcm.edu	37	chr2	112933383	112933383	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gcatttgtcctccaggaaggActgggaaccgctgtcagcat	12	11	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:112933383A>G	ENST00000331203.2	+	4	770	c.499A>G	c.(499-501)Act>Gct	p.T167A	FBLN7_ENST00000472377.1_3'UTR|FBLN7_ENST00000409667.3_Intron|FBLN7_ENST00000409903.1_Missense_Mutation_p.T167A|FBLN7_ENST00000409450.3_Missense_Mutation_p.T167A	NM_001128165.1|NM_153214.2	NP_001121637.1|NP_694946.2	Q53RD9	FBLN7_HUMAN	fibulin 7	167	EGF-like 1; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						TCCAGGAAGGACTGGGAACCG	0.537																																					p.T167A		Atlas-SNP	.											.	FBLN7	49	.	0			c.A499G						.						129	109	115					2																	112933383		2203	4300	6503	SO:0001583	missense	129804	exon4			GGAAGGACTGGGA		CCDS2095.1, CCDS46391.1	2q13	2010-06-15			ENSG00000144152	ENSG00000144152		"Fibulins"	26740	protein-coding gene	gene with protein product		611551				17699513	Standard	NM_153214		Approved	FLJ37440, TM14	uc002tho.1	Q53RD9	OTTHUMG00000153267	ENST00000331203.2:c.499A>G	chr2.hg19:g.112933383A>G	ENSP00000331411:p.Thr167Ala	91.0	0.0		72.0	4.0	NM_153214	A0JNV1|A0JNV2|Q5H9P5|Q8N9G0	Missense_Mutation	SNP	ENST00000331203.2	hg19	CCDS2095.1	.	.	.	.	.	.	.	.	.	.	A	13.25	2.180743	0.38511	.	.	ENSG00000144152	ENST00000331203;ENST00000409903;ENST00000409450;ENST00000441565	D;D;D;D	0.94457	-3.43;-3.43;-3.43;-3.43	5.66	1.81	0.25067	EGF (1);Epidermal growth factor-like (1);EGF-like region, conserved site (1);Epidermal growth factor-like, type 3 (1);	0.215378	0.47852	N	0.000202	D	0.92071	0.7487	M	0.71036	2.16	0.34385	D	0.69357	P;P;P	0.45957	0.459;0.566;0.869	B;B;P	0.48425	0.225;0.438;0.577	D	0.87482	0.2421	10	0.12103	T	0.63	-2.153	2.5345	0.04711	0.54:0.1335:0.07:0.2565	.	167;167;167	Q53RD9-2;Q53RD9;B8ZZC1	.;FBLN7_HUMAN;.	A	167;167;167;61	ENSP00000331411:T167A;ENSP00000386295:T167A;ENSP00000387000:T167A;ENSP00000388025:T61A	ENSP00000331411:T167A	T	+	1	0	FBLN7	112649854	1.000000	0.71417	0.510000	0.27712	0.921000	0.55340	2.912000	0.48782	0.063000	0.16370	0.533000	0.62120	ACT	.	.		0.537	FBLN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330505.1	NM_153214		G	112933383	A	G	112933383	3	3	259	1	0	0	0	0	1	0	0	0	5709	275	10	2	513	2	FBLN7	2	112933383	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2918197	112933383	130265990	127	36445										
AMMECR1L	83607	hgsc.bcm.edu	37	chr2	128628438	128628438	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aaagttagtaaggagggagaCagagcagaaaagtttaggca	14	3	0	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:128628438C>T	ENST00000272647.5	-	5	843	c.583G>A	c.(583-585)Gtc>Atc	p.V195I	AMMECR1L_ENST00000393001.1_Missense_Mutation_p.V195I	NM_001199140.1	NP_001186069.1	Q6DCA0	AMERL_HUMAN	AMMECR1-like	195	AMMECR1. {ECO:0000255|PROSITE- ProRule:PRU00467}.							p.V195L(1)		central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)	9	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.07)		AGGAGGGAGACAGAGCAGAAA	0.522																																					p.V195I		Atlas-SNP	.											AMMECR1L,NS,carcinoma,0,1	AMMECR1L	22	.	1	Substitution - Missense(1)	lung(1)	c.G583A						.						64	59	60					2																	128628438		2203	4300	6503	SO:0001583	missense	83607	exon5			GGGAGACAGAGCA		CCDS2152.1	2q21	2012-11-15	2012-11-15		ENSG00000144233	ENSG00000144233			28658	protein-coding gene	gene with protein product			"AMME chromosomal region gene 1-like"				Standard	NM_001199140		Approved	MGC4268	uc002tpl.3	Q6DCA0	OTTHUMG00000131535	ENST00000272647.5:c.583G>A	chr2.hg19:g.128628438C>T	ENSP00000272647:p.Val195Ile	157.0	0.0		125.0	70.0	NM_031445	B4E276	Missense_Mutation	SNP	ENST00000272647.5	hg19	CCDS2152.1	.	.	.	.	.	.	.	.	.	.	C	36	5.707123	0.96821	.	.	ENSG00000144233	ENST00000272647;ENST00000393001	.	.	.	5.46	5.46	0.80206	AMMECR1 domain (2);	0.000000	0.64402	D	0.000002	T	0.75287	0.3829	L	0.54908	1.71	0.80722	D	1	P	0.51351	0.944	D	0.64237	0.923	T	0.72337	-0.4324	9	0.40728	T	0.16	-15.9275	19.6629	0.95879	0.0:1.0:0.0:0.0	.	195	Q6DCA0	AMERL_HUMAN	I	195	.	ENSP00000272647:V195I	V	-	1	0	AMMECR1L	128344908	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.445000	0.80570	2.726000	0.93360	0.655000	0.94253	GTC	.	.		0.522	AMMECR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254392.1	NM_031445		T	128628438	C	T	128628438	3	4	259	1	0	0	0	0	1	0	0	0	579	478	17	3	365	3	AMMECR1L	2	128628438	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	15695055	128628438	114570935	128	36446										
THSD7B	80731	hgsc.bcm.edu	37	chr2	138400205	138400205	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gtctgcatgtaaattggaggTaggtcatgtaatgacagtta	12	4	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:138400205T>A	ENST00000409968.1	+	21	4123		c.e21+2		THSD7B_ENST00000272643.3_Splice_Site|THSD7B_ENST00000543459.1_Intron|THSD7B_ENST00000413152.2_Splice_Site			Q9C0I4	THS7B_HUMAN	thrombospondin, type I, domain containing 7B							integral component of membrane (GO:0016021)				NS(3)|breast(3)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(14)|lung(57)|ovary(4)|pancreas(3)|prostate(11)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	134				BRCA - Breast invasive adenocarcinoma(221;0.19)		AAATTGGAGGTAGGTCATGTA	0.493																																					.		Atlas-SNP	.											.	THSD7B	506	.	0			c.3857+2T>A						.						62	64	64					2																	138400205		1894	4123	6017	SO:0001630	splice_region_variant	80731	exon20			TGGAGGTAGGTCA			2q22.1	2006-11-24			ENSG00000144229	ENSG00000144229			29348	protein-coding gene	gene with protein product						11214970	Standard	NM_001080427		Approved	KIAA1679	uc002tva.1	Q9C0I4	OTTHUMG00000153590	ENST00000409968.1:c.3945+2T>A	chr2.hg19:g.138400205T>A		70.0	0.0		52.0	4.0	NM_001080427		Splice_Site	SNP	ENST00000409968.1	hg19		.	.	.	.	.	.	.	.	.	.	T	17.90	3.502889	0.64298	.	.	ENSG00000144229	ENST00000409968;ENST00000272643;ENST00000413152	.	.	.	5.33	5.33	0.75918	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.413	0.67128	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	THSD7B	138116675	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.849000	0.62882	2.234000	0.73211	0.533000	0.62120	.	.	.		0.493	THSD7B-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000331769.2	XM_046570.9	Intron	A	138400205	T	A	138400205	5	1	259	1	0	0	0	0	0	0	1	0	15895	1652	57	4	3937	4	THSD7B	2	138400205	Splice_Site	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	9771767	138400205	104799168	129	36447										
UPP2	151531	hgsc.bcm.edu	37	chr2	158971674	158971674	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgcactgtttatgcacaaggAgctcgggtttgaggaagctg	14	7	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:158971674A>G	ENST00000005756.4	+	3	436	c.242A>G	c.(241-243)gAg>gGg	p.E81G	UPP2_ENST00000605860.1_Missense_Mutation_p.E138G|UPP2_ENST00000409859.4_Missense_Mutation_p.E138G|UPP2_ENST00000460456.1_Intron	NM_173355.3	NP_775491.1	O95045	UPP2_HUMAN	uridine phosphorylase 2	81					nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|nucleotide catabolic process (GO:0009166)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside salvage (GO:0043097)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)|uridine metabolic process (GO:0046108)	cytosol (GO:0005829)|type III intermediate filament (GO:0045098)	uridine phosphorylase activity (GO:0004850)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31					Fluorouracil(DB00544)	ATGCACAAGGAGCTCGGGTTT	0.458																																					p.E138G		Atlas-SNP	.											.	UPP2	60	.	0			c.A413G						.						105	105	105					2																	158971674		2203	4300	6503	SO:0001583	missense	151531	exon5			ACAAGGAGCTCGG	AY225131	CCDS2207.1, CCDS46435.1	2q24.2	2008-02-05			ENSG00000007001	ENSG00000007001			23061	protein-coding gene	gene with protein product						12849978	Standard	NM_173355		Approved	UPASE2, UP2, UDRPASE2	uc002tzo.3	O95045	OTTHUMG00000131969	ENST00000005756.4:c.242A>G	chr2.hg19:g.158971674A>G	ENSP00000005756:p.Glu81Gly	125.0	0.0		133.0	6.0	NM_001135098	B3KV87	Missense_Mutation	SNP	ENST00000005756.4	hg19	CCDS2207.1	.	.	.	.	.	.	.	.	.	.	A	15.99	2.995626	0.54147	.	.	ENSG00000007001	ENST00000409859;ENST00000005756	D;D	0.88741	-2.42;-2.42	5.7	4.55	0.56014	Nucleoside phosphorylase domain (1);	0.221802	0.45126	D	0.000383	D	0.93835	0.8028	M	0.87381	2.88	0.58432	D	0.999997	D	0.76494	0.999	D	0.65323	0.934	D	0.93291	0.6668	10	0.52906	T	0.07	.	10.5443	0.45052	0.9237:0.0:0.0763:0.0	.	81	O95045	UPP2_HUMAN	G	138;81	ENSP00000387230:E138G;ENSP00000005756:E81G	ENSP00000005756:E81G	E	+	2	0	UPP2	158679920	1.000000	0.71417	0.793000	0.32043	0.090000	0.18270	6.190000	0.72057	1.000000	0.39049	0.533000	0.62120	GAG	.	.		0.458	UPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254929.2	NM_173355		G	158971674	A	G	158971674	3	3	259	1	0	0	0	0	1	0	0	0	17028	304	11	2	431	2	UPP2	2	158971674	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	20571469	158971674	84227699	130	36448										
LRP2	4036	hgsc.bcm.edu	37	chr2	170058302	170058302	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgccatcaccacagtcattgTagtaatcacagcggtaagag	9	10	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:170058302T>C	ENST00000263816.3	-	44	8573	c.8288A>G	c.(8287-8289)tAc>tGc	p.Y2763C		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	2763	LDL-receptor class A 17. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	ACAGTCATTGTAGTAATCACA	0.502																																					p.Y2763C		Atlas-SNP	.											.	LRP2	751	.	0			c.A8288G						.						157	133	141					2																	170058302		2203	4300	6503	SO:0001583	missense	4036	exon44			TCATTGTAGTAAT		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.8288A>G	chr2.hg19:g.170058302T>C	ENSP00000263816:p.Tyr2763Cys	81.0	0.0		70.0	4.0	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	hg19	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	T	17.90	3.503190	0.64298	.	.	ENSG00000081479	ENST00000263816	D	0.95554	-3.74	5.7	5.7	0.88788	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.96800	0.8955	L	0.52905	1.665	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96450	0.9333	10	0.39692	T	0.17	.	15.9722	0.80027	0.0:0.0:0.0:1.0	.	2763	P98164	LRP2_HUMAN	C	2763	ENSP00000263816:Y2763C	ENSP00000263816:Y2763C	Y	-	2	0	LRP2	169766548	1.000000	0.71417	0.998000	0.56505	0.905000	0.53344	4.938000	0.63519	2.169000	0.68431	0.528000	0.53228	TAC	.	.		0.502	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		C	170058302	T	C	170058302	3	2	259	1	0	0	0	0	1	0	0	0	8965	1638	57	2	5823	2	LRP2	2	170058302	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	11086628	170058302	73141071	131	36449										
PDK1	5163	hgsc.bcm.edu	37	chr2	173423557	173423557	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aatcttctcaggacaccatcCgttcaattggtacaaagctg	7	11	3	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:173423557C>T	ENST00000282077.3	+	2	500	c.318C>T	c.(316-318)tcC>tcT	p.S106S	PDK1_ENST00000410055.1_Silent_p.S106S|AC093818.1_ENST00000450443.1_RNA|Y_RNA_ENST00000362996.1_RNA|AC093818.1_ENST00000442417.1_RNA|AC093818.1_ENST00000444919.1_RNA|PDK1_ENST00000392571.2_Silent_p.S106S|PDK1_ENST00000543905.1_Silent_p.S30S|PDK1_ENST00000544863.1_5'UTR|AC093818.1_ENST00000436922.1_RNA			Q15118	PDK1_HUMAN	pyruvate dehydrogenase kinase, isozyme 1	106					cell proliferation (GO:0008283)|cellular metabolic process (GO:0044237)|glucose metabolic process (GO:0006006)|hypoxia-inducible factor-1alpha signaling pathway (GO:0097411)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|protein phosphorylation (GO:0006468)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of glucose metabolic process (GO:0010906)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)			central_nervous_system(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)	16			OV - Ovarian serous cystadenocarcinoma(117;0.12)			GGACACCATCCGTTCAATTGG	0.383									Autosomal Dominant Polycystic Kidney Disease																												p.S106S		Atlas-SNP	.											.	PDK1	39	.	0			c.C318T						.						95	92	93					2																	173423557		2203	4300	6503	SO:0001819	synonymous_variant	5163	exon2	Familial Cancer Database	ADPKD	ACCATCCGTTCAA	L42450	CCDS2250.1, CCDS63059.1	2q31.1	2008-05-23	2005-11-16		ENSG00000152256	ENSG00000152256			8809	protein-coding gene	gene with protein product		602524	"pyruvate dehydrogenase kinase, isoenzyme 1"			7499431	Standard	NR_103731		Approved		uc002uhs.3	Q15118	OTTHUMG00000132285	ENST00000282077.3:c.318C>T	chr2.hg19:g.173423557C>T		138.0	0.0		99.0	5.0	NM_002610	B2R6T1|B7Z937|D3DPD8|E9PD65|Q308M4	Silent	SNP	ENST00000282077.3	hg19	CCDS2250.1																																																																																			.	.		0.383	PDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255380.3	NM_002610		T	173423557	C	T	173423557	2	4	259	1	0	0	0	0	0	0	0	1	11684	639	23	1		1	PDK1	2	173423557	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	3365255	173423557	69775816	132	36450										
HNRNPA3	220988	hgsc.bcm.edu	37	chr2	178083814	178083814	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gattttggaaattatagtggAcaacagcaatcaaattatgg	9	4	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:178083814A>G	ENST00000392524.2	+	9	1248	c.1011A>G	c.(1009-1011)ggA>ggG	p.G337G	HNRNPA3_ENST00000411529.2_Silent_p.G315G|HNRNPA3_ENST00000435711.1_Silent_p.G337G			P51991	ROA3_HUMAN	heterogeneous nuclear ribonucleoprotein A3	337	Gly-rich.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|urinary_tract(1)	16						ATTATAGTGGACAACAGCAAT	0.388																																					p.G337G		Atlas-SNP	.											.	HNRNPA3	42	.	0			c.A1011G						.						85	92	90					2																	178083814		2203	4297	6500	SO:0001819	synonymous_variant	220988	exon9			TAGTGGACAACAG	AF517524	CCDS2273.1	2q31.2	2013-02-12		2008-04-18	ENSG00000170144	ENSG00000170144		"RNA binding motif (RRM) containing"	24941	protein-coding gene	gene with protein product		605372		HNRPA3		11886857, 15776420	Standard	XM_005246380		Approved		uc002ulc.1	P51991	OTTHUMG00000132529	ENST00000392524.2:c.1011A>G	chr2.hg19:g.178083814A>G		116.0	0.0		87.0	4.0	NM_194247	D3DPF4|Q53RW7|Q6URK5	Silent	SNP	ENST00000392524.2	hg19	CCDS2273.1																																																																																			.	.		0.388	HNRNPA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255729.3	NM_194247		G	178083814	A	G	178083814	2	3	259	1	0	0	0	0	0	0	0	1	7269	262	10	2		2	HNRNPA3	2	178083814	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	4660257	178083814	65115559	133	36451										
TTN	7273	hgsc.bcm.edu	37	chr2	179413062	179413062	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atttcatagggctcaccaacAccatactcatttactgcaga	5	12	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:179413062A>G	ENST00000591111.1	-	289	88592	c.88368T>C	c.(88366-88368)ggT>ggC	p.G29456G	TTN_ENST00000359218.5_Silent_p.G22157G|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000460472.2_Silent_p.G22032G|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000342175.6_Silent_p.G22224G|RP11-65L3.2_ENST00000603415.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000589042.1_Silent_p.G31097G|TTN_ENST00000342992.6_Silent_p.G28529G|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	29456	Fibronectin type-III 114. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCTCACCAACACCATACTCAT	0.463																																					p.G31097G		Atlas-SNP	.											.	TTN	18412	.	0			c.T93291C						.						211	211	211					2																	179413062		2059	4199	6258	SO:0001819	synonymous_variant	7273	exon339			ACCAACACCATAC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.88368T>C	chr2.hg19:g.179413062A>G		86.0	0.0		56.0	4.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.463	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179413062	A	G	179413062	2	3	259	1	0	0	0	0	0	0	0	1	16750	146	6	2		2	TTN	2	179413062	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1329248	179413062	63786311	134	36452										
TTN	7273	hgsc.bcm.edu	37	chr2	179419855	179419855	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgacaacttctgtatattctAgaggcaaatcaattacagga	7	7	3	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:179419855A>G	ENST00000591111.1	-	281	83632	c.83408T>C	c.(83407-83409)cTa>cCa	p.L27803P	TTN_ENST00000359218.5_Missense_Mutation_p.L20504P|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.L20379P|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.L20571P|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.L29444P|TTN_ENST00000342992.6_Missense_Mutation_p.L26876P|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	27803	Ig-like 130.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGTATATTCTAGAGGCAAATC	0.363																																					p.L29444P		Atlas-SNP	.											.	TTN	18412	.	0			c.T88331C						.						74	71	72					2																	179419855		1824	4080	5904	SO:0001583	missense	7273	exon331			TATTCTAGAGGCA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.83408T>C	chr2.hg19:g.179419855A>G	ENSP00000465570:p.Leu27803Pro	98.0	0.0		98.0	4.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	14.41	2.526121	0.44969	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.63580	-0.05;0.18;0.18;0.15	5.66	5.66	0.87406	Fibronectin, type III (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.52597	0.1744	L	0.46157	1.445	0.53688	D	0.999973	B;B;B;B	0.06786	0.001;0.001;0.001;0.001	B;B;B;B	0.10450	0.005;0.005;0.005;0.005	T	0.55503	-0.8131	9	0.87932	D	0	.	6.3004	0.21109	0.8067:0.0:0.1933:0.0	.	20379;20504;20571;27803	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	P	26876;20379;20571;20504;20376	ENSP00000343764:L26876P;ENSP00000434586:L20379P;ENSP00000340554:L20571P;ENSP00000352154:L20504P	ENSP00000340554:L20571P	L	-	2	0	TTN	179128101	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	4.012000	0.57131	2.279000	0.76181	0.533000	0.62120	CTA	.	.		0.363	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179419855	A	G	179419855	3	3	259	1	0	0	0	0	1	0	0	0	16750	420	15	2	19776	2	TTN	2	179419855	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	6793	179419855	63779518	135	36453										
CCDC141	285025	hgsc.bcm.edu	37	chr2	179742806	179742806	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aatgcttggctttagcatcaTcctgctccttctgagggatt	9	10	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:179742806T>C	ENST00000409284.1	-	12	1901	c.1784A>G	c.(1783-1785)gAt>gGt	p.D595G	CCDC141_ENST00000420890.2_Missense_Mutation_p.D595G|CCDC141_ENST00000295723.5_Missense_Mutation_p.D20G			Q6ZP82	CC141_HUMAN	coiled-coil domain containing 141	595										NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(37)|ovary(8)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)	78			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147)			TTTAGCATCATCCTGCTCCTT	0.378																																					p.D595G		Atlas-SNP	.											.	CCDC141	362	.	0			c.A1784G						.						90	87	88					2																	179742806		2203	4300	6503	SO:0001583	missense	285025	exon12			GCATCATCCTGCT	AK096821		2q31.2	2013-01-14			ENSG00000163492	ENSG00000163492		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	26821	protein-coding gene	gene with protein product	"coiled-coil protein associated with myosin II and DISC1"					20956536	Standard	NM_173648		Approved	FLJ39502, CAMDI	uc002une.2	Q6ZP82	OTTHUMG00000132578	ENST00000409284.1:c.1784A>G	chr2.hg19:g.179742806T>C	ENSP00000386503:p.Asp595Gly	95.0	0.0		75.0	4.0	NM_173648	H7C0P1|J3KNW6|Q8N8H3	Missense_Mutation	SNP	ENST00000409284.1	hg19		.	.	.	.	.	.	.	.	.	.	t	9.057	0.993584	0.19043	.	.	ENSG00000163492	ENST00000420890;ENST00000343876;ENST00000295723;ENST00000443758;ENST00000446116;ENST00000409284	T;T;T;T	0.48522	0.81;1.44;1.46;1.44	5.23	2.5	0.30297	.	0.480260	0.18515	N	0.138929	T	0.27205	0.0667	N	0.17082	0.46	0.09310	N	1	B;B	0.11235	0.0;0.004	B;B	0.11329	0.0;0.006	T	0.16541	-1.0399	10	0.18276	T	0.48	-6.0665	8.2729	0.31855	0.0:0.1948:0.0:0.8052	.	595;20	B8ZZB3;Q6ZP82	.;CC141_HUMAN	G	595;39;20;595;530;595	ENSP00000395995:D595G;ENSP00000344627:D39G;ENSP00000295723:D20G;ENSP00000390190:D595G	ENSP00000295723:D20G	D	-	2	0	CCDC141	179451051	0.000000	0.05858	0.162000	0.22713	0.439000	0.31926	-0.319000	0.08039	0.825000	0.34637	0.473000	0.43528	GAT	.	.		0.378	CCDC141-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000335873.1	NM_173648		C	179742806	T	C	179742806	3	2	259	1	0	0	0	0	1	0	0	0	2777	1435	50	2	2616	2	CCDC141	2	179742806	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	322951	179742806	63456567	136	36454										
ZSWIM2	151112	hgsc.bcm.edu	37	chr2	187698746	187698746	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggcataagtgatattctatgCattcggtacacctaaaaata	7	7	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:187698746C>T	ENST00000295131.2	-	6	794	c.755G>A	c.(754-756)tGc>tAc	p.C252Y		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	252					apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			ATATTCTATGCATTCGGTACA	0.358																																					p.C252Y		Atlas-SNP	.											.	ZSWIM2	119	.	0			c.G755A						.						116	100	106					2																	187698746		2203	4300	6503	SO:0001583	missense	151112	exon6			TCTATGCATTCGG	AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"Zinc fingers, SWIM-type", "Zinc fingers, ZZ-type"	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.755G>A	chr2.hg19:g.187698746C>T	ENSP00000295131:p.Cys252Tyr	122.0	0.0		96.0	4.0	NM_182521	B3KXV6|Q53SI3|Q57ZY3	Missense_Mutation	SNP	ENST00000295131.2	hg19	CCDS33348.1	.	.	.	.	.	.	.	.	.	.	C	17.35	3.367338	0.61513	.	.	ENSG00000163012	ENST00000295131	D	0.96073	-3.9	5.78	5.78	0.91487	Zinc finger, ZZ-type (4);	0.000000	0.64402	D	0.000012	D	0.98321	0.9443	M	0.93375	3.41	0.50632	D	0.999886	D	0.89917	1.0	D	0.79108	0.992	D	0.99191	1.0870	10	0.87932	D	0	-10.6671	16.9191	0.86159	0.0:1.0:0.0:0.0	.	252	Q8NEG5	ZSWM2_HUMAN	Y	252	ENSP00000295131:C252Y	ENSP00000295131:C252Y	C	-	2	0	ZSWIM2	187406991	0.997000	0.39634	0.309000	0.25155	0.710000	0.40934	5.004000	0.63966	2.722000	0.93159	0.467000	0.42956	TGC	.	.		0.358	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521		T	187698746	C	T	187698746	3	4	259	1	0	0	0	0	1	0	0	0	18256	710	25	3	1162	3	ZSWIM2	2	187698746	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	7955940	187698746	55500627	137	36455										
ANKRD44	91526	hgsc.bcm.edu	37	chr2	197954757	197954757	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acatgctatggattccacacCtgaggagtaagaaaacagag	10	8	0	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:197954757C>A	ENST00000328737.2	-	11	1102		c.e11-1		ANKRD44_ENST00000409153.1_Splice_Site|ANKRD44_ENST00000450567.1_Splice_Site|ANKRD44_ENST00000539527.1_Splice_Site|ANKRD44_ENST00000282272.8_Splice_Site|ANKRD44_ENST00000477852.1_5'Flank|ANKRD44_ENST00000337207.5_Splice_Site			Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44											NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(20)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.246)			GATTCCACACCTGAGGAGTAA	0.413																																					.		Atlas-SNP	.											.	ANKRD44	281	.	0			c.1101-1G>T						.						102	93	96					2																	197954757		2203	4300	6503	SO:0001630	splice_region_variant	91526	exon12			CCACACCTGAGGA	AK097086	CCDS33355.1, CCDS33355.2, CCDS74619.1	2q33.1	2013-01-10			ENSG00000065413	ENSG00000065413		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits", "Ankyrin repeat domain containing"	25259	protein-coding gene	gene with protein product	"protein phosphatase 6 ankyrin repeat subunit B"						Standard	NM_153697		Approved	PP6-ARS-B	uc021vuj.1	Q8N8A2	OTTHUMG00000154411	ENST00000328737.2:c.1026-1G>T	chr2.hg19:g.197954757C>A		95.0	0.0		105.0	5.0	NM_001195144	Q53SL9|Q6P480|Q86VL5|Q8IZ72|Q9UFA4	Splice_Site	SNP	ENST00000328737.2	hg19		.	.	.	.	.	.	.	.	.	.	C	25.0	4.590966	0.86851	.	.	ENSG00000065413	ENST00000424317;ENST00000282272;ENST00000328737;ENST00000450567;ENST00000337207;ENST00000422886;ENST00000409153;ENST00000539527	.	.	.	5.31	5.31	0.75309	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.1694	0.93570	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ANKRD44	197663002	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.434000	0.80377	2.765000	0.95021	0.655000	0.94253	.	.	.		0.413	ANKRD44-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335113.1	NM_153697	Intron	A	197954757	C	A	197954757	5	1	259	1	0	0	0	0	0	0	1	0	672	695	24	3	1798	3	ANKRD44	2	197954757	Splice_Site	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	10256011	197954757	45244616	138	36456										
ALS2	57679	hgsc.bcm.edu	37	chr2	202568849	202568849	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	taataactatactcaccttcAaggtggtgaacattataccc	5	10	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:202568849A>G	ENST00000264276.6	-	33	5303	c.4931T>C	c.(4930-4932)tTg>tCg	p.L1644S	ALS2_ENST00000457679.2_3'UTR	NM_020919.3	NP_065970.2	Q96Q42	ALS2_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	1644	VPS9. {ECO:0000255|PROSITE- ProRule:PRU00550}.				behavioral fear response (GO:0001662)|cell death (GO:0008219)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|locomotory behavior (GO:0007626)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Rab GTPase activity (GO:0032851)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of Ran GTPase activity (GO:0032853)|protein localization (GO:0008104)|receptor recycling (GO:0001881)|regulation of endosome size (GO:0051036)|response to oxidative stress (GO:0006979)|synaptic transmission, glutamatergic (GO:0035249)|vesicle organization (GO:0016050)	centrosome (GO:0005813)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome (GO:0005769)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|ruffle (GO:0001726)|vesicle (GO:0031982)	protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(22)|ovary(1)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	72						ACTCACCTTCAAGGTGGTGAA	0.358																																					p.L1644S		Atlas-SNP	.											.	ALS2	172	.	0			c.T4931C						.						72	65	67					2																	202568849		1828	4079	5907	SO:0001583	missense	57679	exon33			ACCTTCAAGGTGG	AB053305	CCDS42800.1, CCDS46492.1	2q33-q35	2014-09-17	2004-06-23		ENSG00000003393	ENSG00000003393		"Rho guanine nucleotide exchange factors"	443	protein-coding gene	gene with protein product	"alsin"	606352	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 6"	ALS2CR6		11586298	Standard	NM_020919		Approved		uc002uyo.3	Q96Q42	OTTHUMG00000154507	ENST00000264276.6:c.4931T>C	chr2.hg19:g.202568849A>G	ENSP00000264276:p.Leu1644Ser	122.0	0.0		112.0	6.0	NM_020919	Q53TT1|Q53TV2|Q8N1E0|Q96PC4|Q96Q41|Q9H973|Q9HCK9	Missense_Mutation	SNP	ENST00000264276.6	hg19	CCDS42800.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.405316	0.83230	.	.	ENSG00000003393	ENST00000264276	T	0.49139	0.79	5.78	5.78	0.91487	Vacuolar sorting protein 9 (2);	0.142767	0.47852	D	0.000211	T	0.71904	0.3395	M	0.83012	2.62	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.76666	-0.2875	10	0.87932	D	0	.	16.1138	0.81283	1.0:0.0:0.0:0.0	.	1644	Q96Q42	ALS2_HUMAN	S	1644	ENSP00000264276:L1644S	ENSP00000264276:L1644S	L	-	2	0	ALS2	202277094	1.000000	0.71417	1.000000	0.80357	0.763000	0.43281	9.288000	0.96055	2.220000	0.72140	0.533000	0.62120	TTG	.	.		0.358	ALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335562.3	NM_020919		G	202568849	A	G	202568849	3	3	259	1	0	0	0	0	1	0	0	0	550	131	5	2	50	2	ALS2	2	202568849	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	4614092	202568849	40630524	139	36457										
BMPR2	659	hgsc.bcm.edu	37	chr2	203420956	203420956	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cagtttattggtgaggacacCcggctgaatattaattccag	10	8	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:203420956C>A	ENST00000374580.4	+	12	3107	c.2568C>A	c.(2566-2568)acC>acA	p.T856T	BMPR2_ENST00000374574.2_Intron	NM_001204.6	NP_001195.2	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor, type II (serine/threonine kinase)	856					activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|brain development (GO:0007420)|cellular response to starvation (GO:0009267)|chondrocyte development (GO:0002063)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm formation (GO:0001707)|negative regulation of cell growth (GO:0030308)|negative regulation of chondrocyte proliferation (GO:1902731)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of vasoconstriction (GO:0045906)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of bone mineralization (GO:0030501)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|regulation of cell proliferation (GO:0042127)|regulation of lung blood pressure (GO:0014916)|retina vasculature development in camera-type eye (GO:0061298)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|venous blood vessel development (GO:0060841)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|fully spanning plasma membrane (GO:0044214)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	activin receptor activity, type II (GO:0016362)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(11)|lung(7)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	42						GTGAGGACACCCGGCTGAATA	0.468																																					p.T856T		Atlas-SNP	.											.	BMPR2	142	.	0			c.C2568A						.						128	122	124					2																	203420956		2203	4300	6503	SO:0001819	synonymous_variant	659	exon12			GGACACCCGGCTG	Z48923	CCDS33361.1	2q33-q34	2014-09-17			ENSG00000204217	ENSG00000204217			1078	protein-coding gene	gene with protein product		600799	"primary pulmonary hypertension 1"	PPH1		7791754	Standard	NM_001204		Approved	BRK-3, T-ALK, BMPR3, BMPR-II	uc002uzf.4	Q13873	OTTHUMG00000133617	ENST00000374580.4:c.2568C>A	chr2.hg19:g.203420956C>A		85.0	0.0		90.0	5.0	NM_001204	Q13161|Q16569|Q4ZG08|Q53SA5|Q585T8	Silent	SNP	ENST00000374580.4	hg19	CCDS33361.1																																																																																			.	.		0.468	BMPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257743.1	NM_001204		A	203420956	C	A	203420956	2	1	259	1	0	0	0	0	0	0	0	1	1471	610	22	3		3	BMPR2	2	203420956	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	852107	203420956	39778417	140	36458										
ZDBF2	57683	hgsc.bcm.edu	37	chr2	207170906	207170906	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cactgcagtcagtggttgacAgacccccagtggctgtcaca	11	13	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:207170906A>G	ENST00000374423.3	+	5	2040	c.1654A>G	c.(1654-1656)Aga>Gga	p.R552G		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	552							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						AGTGGTTGACAGACCCCCAGT	0.438																																					p.R552G		Atlas-SNP	.											.	ZDBF2	531	.	0			c.A1654G						.						98	92	94					2																	207170906		1866	4113	5979	SO:0001583	missense	57683	exon5			GTTGACAGACCCC	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"Zinc fingers, DBF-type"	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.1654A>G	chr2.hg19:g.207170906A>G	ENSP00000363545:p.Arg552Gly	84.0	0.0		63.0	5.0	NM_020923	Q6ZNP7|Q6ZSN8	Missense_Mutation	SNP	ENST00000374423.3	hg19	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	C	17.09	3.300258	0.60195	.	.	ENSG00000204186	ENST00000374423	T	0.44083	0.93	4.09	-0.325	0.12702	.	1.722310	0.04110	N	0.314521	T	0.29817	0.0745	L	0.34521	1.04	0.09310	N	1	B	0.19817	0.039	B	0.19391	0.025	T	0.23619	-1.0183	10	0.56958	D	0.05	.	0.8148	0.01100	0.3866:0.2781:0.1415:0.1938	.	552	Q9HCK1	ZDBF2_HUMAN	G	552	ENSP00000363545:R552G	ENSP00000363545:R552G	R	+	1	2	ZDBF2	206879151	0.001000	0.12720	0.000000	0.03702	0.024000	0.10985	0.071000	0.14594	-0.324000	0.08589	-0.127000	0.14921	AGA	.	.		0.438	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		G	207170906	A	G	207170906	3	3	259	1	0	0	0	0	1	0	0	0	17614	180	7	2	1664	2	ZDBF2	2	207170906	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	3749950	207170906	36028467	141	36459										
DNPEP	23549	hgsc.bcm.edu	37	chr2	220251502	220251502	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agttcctggtcatgaagtacTgaggagaaggggaggaaaga	16	4	1	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:220251502T>C	ENST00000273075.4	-	4	440		c.e4-2		DNPEP_ENST00000373972.1_Splice_Site|DNPEP_ENST00000523282.1_Splice_Site|AC053503.4_ENST00000420563.1_RNA	NM_012100.2	NP_036232	Q9ULA0	DNPEP_HUMAN	aspartyl aminopeptidase						peptide metabolic process (GO:0006518)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Renal(207;0.0474)		Epithelial(149;1.09e-06)|all cancers(144;0.000179)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CATGAAGTACTGAGGAGAAGG	0.587																																					.		Atlas-SNP	.											.	DNPEP	40	.	0			c.220-2A>G						.						39	42	41					2																	220251502		2066	4208	6274	SO:0001630	splice_region_variant	23549	exon5			AAGTACTGAGGAG		CCDS42823.1	2q36.1	2008-05-22			ENSG00000123992	ENSG00000123992			2981	protein-coding gene	gene with protein product		611367				9632644	Standard	NM_012100		Approved	DAP, ASPEP	uc002vle.2	Q9ULA0	OTTHUMG00000058919	ENST00000273075.4:c.220-2A>G	chr2.hg19:g.220251502T>C		68.0	0.0		63.0	4.0	NM_012100	Q9BW44|Q9NUV5	Splice_Site	SNP	ENST00000273075.4	hg19	CCDS42823.1	.	.	.	.	.	.	.	.	.	.	T	15.90	2.969727	0.53614	.	.	ENSG00000123992	ENST00000273075;ENST00000337010;ENST00000523282;ENST00000457935;ENST00000429013;ENST00000521459;ENST00000322176;ENST00000519905	.	.	.	3.59	3.59	0.41128	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.733	0.34512	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	DNPEP	219959746	1.000000	0.71417	0.998000	0.56505	0.773000	0.43773	7.617000	0.83032	1.641000	0.50575	0.402000	0.26972	.	.	.		0.587	DNPEP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000130212.1	NM_012100	Intron	C	220251502	T	C	220251502	5	2	259	1	0	0	0	0	0	0	1	0	4681	1594	55	2	1287	2	DNPEP	2	220251502	Splice_Site	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	13080596	220251502	22947871	142	36460										
SPEG	10290	hgsc.bcm.edu	37	chr2	220333748	220333748	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agctgtatgtagaagagcccCggacagccgcctcaggcccc	12	15	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:220333748C>A	ENST00000312358.7	+	12	3601	c.3469C>A	c.(3469-3471)Cgg>Agg	p.R1157R	SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	1157					cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		AGAAGAGCCCCGGACAGCCGC	0.682																																					p.R1157R		Atlas-SNP	.											SPEG,NS,carcinoma,0,1	SPEG	272	.	0			c.C3469A						.						29	36	34					2																	220333748		1917	4120	6037	SO:0001819	synonymous_variant	10290	exon12			GAGCCCCGGACAG	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"Immunoglobulin superfamily / I-set domain containing"	16901	protein-coding gene	gene with protein product		615950	"aortic preferentially expressed gene 1"	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.3469C>A	chr2.hg19:g.220333748C>A		114.0	0.0		47.0	3.0	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Silent	SNP	ENST00000312358.7	hg19	CCDS42824.1																																																																																			.	.		0.682	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		A	220333748	C	A	220333748	2	1	259	1	0	0	0	0	0	0	0	1	15051	643	23	1		1	SPEG	2	220333748	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	82246	220333748	22865625	143	36461										
WDFY1	57590	hgsc.bcm.edu	37	chr2	224760297	224760297	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gatgctgttgtcagatgctcCtgagaagagtaaccgctgaa	12	8	1	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:224760297C>A	ENST00000233055.4	-	7	751	c.649G>T	c.(649-651)Gga>Tga	p.G217*		NM_020830.3	NP_065881.1	Q8IWB7	WDFY1_HUMAN	WD repeat and FYVE domain containing 1	217						cytosol (GO:0005829)|early endosome (GO:0005769)|nucleus (GO:0005634)	1-phosphatidylinositol binding (GO:0005545)|zinc ion binding (GO:0008270)	p.G217R(1)		NS(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(6)|prostate(2)	18		all_lung(227;0.00682)|Lung NSC(271;0.00859)|Renal(207;0.0112)|all_hematologic(139;0.189)		Epithelial(121;5.34e-10)|all cancers(144;1.67e-07)|Lung(261;0.00807)|LUSC - Lung squamous cell carcinoma(224;0.00843)		TCAGATGCTCCTGAGAAGAGT	0.552																																					p.G217X		Atlas-SNP	.											WDFY1,colon,carcinoma,0,1	WDFY1	46	.	1	Substitution - Missense(1)	large_intestine(1)	c.G649T						.						101	87	92					2																	224760297		2203	4300	6503	SO:0001587	stop_gained	57590	exon7			ATGCTCCTGAGAA	AB037856	CCDS33387.1	2q36.2	2013-01-09	2003-03-13		ENSG00000085449	ENSG00000085449		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20451	protein-coding gene	gene with protein product			"WD40 and FYVE domain containing 1"			11739631	Standard	NM_020830		Approved	KIAA1435, FENS-1, WDF1, ZFYVE17	uc002vnq.3	Q8IWB7	OTTHUMG00000153370	ENST00000233055.4:c.649G>T	chr2.hg19:g.224760297C>A	ENSP00000233055:p.Gly217*	100.0	0.0		69.0	3.0	NM_020830	Q53S17|Q9H9D5|Q9P2B3	Nonsense_Mutation	SNP	ENST00000233055.4	hg19	CCDS33387.1	.	.	.	.	.	.	.	.	.	.	C	37	6.256075	0.97417	.	.	ENSG00000085449	ENST00000233055;ENST00000429915	.	.	.	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-13.4219	19.575	0.95439	0.0:1.0:0.0:0.0	.	.	.	.	X	217;174	.	ENSP00000233055:G217X	G	-	1	0	WDFY1	224468541	1.000000	0.71417	0.997000	0.53966	0.994000	0.84299	7.314000	0.78988	2.630000	0.89119	0.491000	0.48974	GGA	.	.		0.552	WDFY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330908.1	NM_020830		A	224760297	C	A	224760297	4	1	259	1	0	0	0	0	0	1	0	0	17283	690	24	3	607	3	WDFY1	2	224760297	Nonsense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	4426549	224760297	18439076	144	36462										
SPHKAP	80309	hgsc.bcm.edu	37	chr2	228881964	228881964	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctttctctgctgtctctttcGatgtccctcagcatgtacct	6	14	3	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:228881964G>T	ENST00000392056.3	-	7	3652	c.3606C>A	c.(3604-3606)atC>atA	p.I1202I	SPHKAP_ENST00000344657.5_Silent_p.I1202I	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	1202						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)			NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		TGTCTCTTTCGATGTCCCTCA	0.567																																					p.I1202I		Atlas-SNP	.											SPHKAP_ENST00000392056,NS,carcinoma,0,4	SPHKAP	750	.	0			c.C3606A						.						103	101	102					2																	228881964		2203	4300	6503	SO:0001819	synonymous_variant	80309	exon7			TCTTTCGATGTCC		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"A-kinase anchor proteins"	30619	protein-coding gene	gene with protein product	"sphingosine kinase type 1-interacting protein"	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.3606C>A	chr2.hg19:g.228881964G>T		83.0	0.0		37.0	2.0	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Silent	SNP	ENST00000392056.3	hg19	CCDS46537.1																																																																																			.	.		0.567	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623		T	228881964	G	T	228881964	2	4	259	1	0	0	0	0	0	0	0	1	15063	1048	37	1		1	SPHKAP	2	228881964	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	4121667	228881964	14317409	145	36463										
COL6A3	1293	hgsc.bcm.edu	37	chr2	238289710	238289710	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gatcggcacccttgttcccaAtggcaaaggccattatgctg	10	12	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:238289710A>G	ENST00000295550.4	-	5	2197	c.1745T>C	c.(1744-1746)aTt>aCt	p.I582T	COL6A3_ENST00000353578.4_Missense_Mutation_p.I376T|COL6A3_ENST00000409809.1_Missense_Mutation_p.I376T|COL6A3_ENST00000392003.2_Missense_Mutation_p.I175T|COL6A3_ENST00000347401.3_Missense_Mutation_p.I381T|COL6A3_ENST00000346358.4_Missense_Mutation_p.I582T|COL6A3_ENST00000392004.3_Missense_Mutation_p.I376T|COL6A3_ENST00000472056.1_Missense_Mutation_p.I175T	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	582	Nonhelical region.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		CTTGTTCCCAATGGCAAAGGC	0.547																																					p.I582T		Atlas-SNP	.											.	COL6A3	608	.	0			c.T1745C						.						92	90	90					2																	238289710		2203	4300	6503	SO:0001583	missense	1293	exon5			TTCCCAATGGCAA	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.1745T>C	chr2.hg19:g.238289710A>G	ENSP00000295550:p.Ile582Thr	84.0	0.0		66.0	4.0	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	hg19	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	A	12.40	1.925465	0.34002	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358;ENST00000392004;ENST00000392003;ENST00000433762	T;T;T;T;T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68	5.81	5.81	0.92471	von Willebrand factor, type A (3);	0.821953	0.10433	N	0.675328	T	0.74711	0.3752	M	0.89968	3.075	0.09310	N	1	P;D;P;B;P;P	0.60160	0.505;0.987;0.482;0.268;0.876;0.549	B;P;B;B;P;B	0.62298	0.305;0.9;0.297;0.392;0.755;0.239	T	0.68213	-0.5468	10	0.87932	D	0	.	16.167	0.81768	1.0:0.0:0.0:0.0	.	582;175;175;376;376;582	E9PCV6;E9PFQ6;A8MT30;E9PGQ9;P12111-2;P12111	.;.;.;.;.;CO6A3_HUMAN	T	582;381;376;175;376;582;376;175;582	ENSP00000295550:I582T;ENSP00000315609:I381T;ENSP00000315873:I376T;ENSP00000418285:I175T;ENSP00000386844:I376T;ENSP00000295546:I582T;ENSP00000375861:I376T;ENSP00000375860:I175T;ENSP00000389539:I582T	ENSP00000295550:I582T	I	-	2	0	COL6A3	237954449	0.669000	0.27502	0.003000	0.11579	0.091000	0.18340	5.250000	0.65432	2.210000	0.71456	0.533000	0.62120	ATT	.	.		0.547	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		G	238289710	A	G	238289710	3	3	259	1	0	0	0	0	1	0	0	0	3703	101	4	2	7995	2	COL6A3	2	238289710	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	9407746	238289710	4909663	146	36464										
KLHL30	377007	hgsc.bcm.edu	37	chr2	239056574	239056574	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atacgtcagcaacttctcggCtgccggctgccggggccggc	14	15	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:239056574C>T	ENST00000409223.1	+	6	1357	c.1250C>T	c.(1249-1251)gCt>gTt	p.A417V	KLHL30_ENST00000305959.4_Missense_Mutation_p.A399V			Q0D2K2	KLH30_HUMAN	kelch-like family member 30	417										lung(4)	4		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		AACTTCTCGGCTGCCGGCTGC	0.672																																					p.A417V		Atlas-SNP	.											.	KLHL30	79	.	0			c.C1250T						.						14	19	17					2																	239056574		1870	4091	5961	SO:0001583	missense	377007	exon6			TCTCGGCTGCCGG		CCDS46555.1, CCDS46555.2	2q37.3	2013-02-22	2013-02-22		ENSG00000168427	ENSG00000168427		"Kelch-like", "BTB/POZ domain containing"	24770	protein-coding gene	gene with protein product			"kelch-like 30 (Drosophila)"				Standard	NM_198582		Approved	FLJ43374	uc002vxr.2	Q0D2K2	OTTHUMG00000152905	ENST00000409223.1:c.1250C>T	chr2.hg19:g.239056574C>T	ENSP00000386389:p.Ala417Val	95.0	0.0		76.0	4.0	NM_198582	Q6ZUS1	Missense_Mutation	SNP	ENST00000409223.1	hg19	CCDS46555.2	.	.	.	.	.	.	.	.	.	.	c	9.475	1.096539	0.20552	.	.	ENSG00000168427	ENST00000409223;ENST00000305959	T;T	0.67865	-0.29;-0.29	3.89	3.01	0.34805	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.43188	0.1236	N	0.20881	0.62	0.39544	D	0.968868	B	0.14438	0.01	B	0.12837	0.008	T	0.31447	-0.9943	10	0.02654	T	1	.	7.611	0.28131	0.0:0.7907:0.0:0.2093	.	417	Q0D2K2	KLH30_HUMAN	V	417;399	ENSP00000386389:A417V;ENSP00000302386:A399V	ENSP00000302386:A399V	A	+	2	0	KLHL30	238721313	0.997000	0.39634	0.130000	0.21974	0.565000	0.35776	3.537000	0.53590	0.864000	0.35578	0.651000	0.88453	GCT	.	.		0.672	KLHL30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328518.1	NM_198582		T	239056574	C	T	239056574	3	4	259	1	0	0	0	0	1	0	0	0	8393	797	28	3	1268	3	KLHL30	2	239056574	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	766864	239056574	4142799	147	36465										
SNED1	25992	hgsc.bcm.edu	37	chr2	241979607	241979607	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggagcagcctgcgagatgggTgagtggcctggcttcggatt	18	8	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:241979607T>A	ENST00000310397.8	+	7	1159		c.e7+2		SNED1_ENST00000342631.6_Splice_Site|SNED1_ENST00000401884.1_Splice_Site|AC005237.4_ENST00000458377.1_RNA|SNED1_ENST00000405547.3_Splice_Site	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1						cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	24		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		GCGAGATGGGTGAGTGGCCTG	0.642																																					.		Atlas-SNP	.											.	SNED1	76	.	0			c.1159+2T>A						.						30	38	35					2																	241979607		2127	4234	6361	SO:0001630	splice_region_variant	25992	exon7			GATGGGTGAGTGG	AK074062	CCDS46562.1	2q37.3	2014-01-28			ENSG00000162804	ENSG00000162804		"Fibronectin type III domain containing"	24696	protein-coding gene	gene with protein product						12477932	Standard	NM_001080437		Approved	FLJ00133, SST3, Snep	uc002wah.1	Q8TER0	OTTHUMG00000151803	ENST00000310397.8:c.1159+2T>A	chr2.hg19:g.241979607T>A		110.0	0.0		82.0	5.0	NM_001080437	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Splice_Site	SNP	ENST00000310397.8	hg19	CCDS46562.1	.	.	.	.	.	.	.	.	.	.	T	8.512	0.866695	0.17250	.	.	ENSG00000162804	ENST00000401884;ENST00000405547;ENST00000310397;ENST00000342631;ENST00000401644;ENST00000431690;ENST00000420591	.	.	.	4.73	3.54	0.40534	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.1866	0.43002	0.0:0.0813:0.0:0.9187	.	.	.	.	.	-1	.	.	.	+	.	.	SNED1	241628280	1.000000	0.71417	0.504000	0.27639	0.040000	0.13550	4.521000	0.60532	0.619000	0.30197	0.482000	0.46254	.	.	.		0.642	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482	Intron	A	241979607	T	A	241979607	5	1	259	1	0	0	0	0	0	0	1	0	14860	1710	59	4	1187	4	SNED1	2	241979607	Splice_Site	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	2923033	241979607	1219766	148	36466										
HDLBP	3069	hgsc.bcm.edu	37	chr2	242186199	242186199	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aatagacagaatcctgctccGggcagcttcgcagttggctc	11	12	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:242186199G>T	ENST00000391975.1	-	16	2145	c.1918C>A	c.(1918-1920)Cgg>Agg	p.R640R	HDLBP_ENST00000476807.1_5'Flank|HDLBP_ENST00000310931.4_Silent_p.R640R|HDLBP_ENST00000427183.2_Silent_p.R607R|AC104841.1_ENST00000578965.1_RNA|HDLBP_ENST00000391976.2_Silent_p.R640R	NM_203346.3	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	640	KH 7. {ECO:0000255|PROSITE- ProRule:PRU00117}.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)	cytoplasm (GO:0005737)|high-density lipoprotein particle (GO:0034364)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)	p.R640W(1)		breast(7)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(11)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)		ATCCTGCTCCGGGCAGCTTCG	0.458																																					p.R640R		Atlas-SNP	.											HDLBP,NS,carcinoma,0,1	HDLBP	118	.	1	Substitution - Missense(1)	endometrium(1)	c.C1918A						.						131	135	134					2																	242186199		2203	4300	6503	SO:0001819	synonymous_variant	3069	exon16			TGCTCCGGGCAGC		CCDS2547.1, CCDS58760.1	2q37.3	2008-07-18	2008-07-18		ENSG00000115677	ENSG00000115677			4857	protein-coding gene	gene with protein product		142695	"vigilin"	VGL		1318310, 8390966	Standard	NM_005336		Approved	HBP	uc002waz.3	Q00341	OTTHUMG00000133391	ENST00000391975.1:c.1918C>A	chr2.hg19:g.242186199G>T		121.0	0.0		122.0	5.0	NM_005336	B4DTQ2|E7EM71|Q53QU2|Q9UCY3	Silent	SNP	ENST00000391975.1	hg19	CCDS2547.1	.	.	.	.	.	.	.	.	.	.	G	0.112	-1.136950	0.01742	.	.	ENSG00000115677	ENST00000373292	.	.	.	6.16	1.38	0.22167	.	.	.	.	.	T	0.39835	0.1093	.	.	.	0.34007	D	0.650997	.	.	.	.	.	.	T	0.44559	-0.9320	4	.	.	.	-6.8468	4.7722	0.13162	0.2467:0.0:0.5192:0.2341	.	.	.	.	Q	448	.	.	P	-	2	0	HDLBP	241834872	1.000000	0.71417	0.000000	0.03702	0.004000	0.04260	3.222000	0.51223	-0.018000	0.14079	-0.188000	0.12872	CCG	.	.		0.458	HDLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257245.5	NM_203346		T	242186199	G	T	242186199	2	4	259	1	0	0	0	0	0	0	0	1	7034	1115	39	1		1	HDLBP	2	242186199	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	206592	242186199	1013174	149	36467										
CRBN	51185	hgsc.bcm.edu	37	chr3	3221342	3221342	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tggttgcccatgttgtgcgcAgcgtcctgctgatctccttc	11	13	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:3221342A>G	ENST00000231948.4	-	1	52	c.30T>C	c.(28-30)gcT>gcC	p.A10A	CRBN_ENST00000432408.2_Silent_p.A10A	NM_016302.3	NP_057386.2	Q96SW2	CRBN_HUMAN	cereblon	10					negative regulation of ion transmembrane transport (GO:0034766)|negative regulation of protein homooligomerization (GO:0032463)|positive regulation of protein homodimerization activity (GO:0090073)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP-dependent peptidase activity (GO:0004176)			endometrium(1)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	11				Epithelial(13;0.00244)|OV - Ovarian serous cystadenocarcinoma(96;0.00617)|all cancers(10;0.0079)	Lenalidomide(DB00480)|Pomalidomide(DB08910)|Thalidomide(DB01041)	TGTTGTGCGCAGCGTCCTGCT	0.677											OREG0015364	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A10A		Atlas-SNP	.											.	CRBN	29	.	0			c.T30C						.						40	37	38					3																	3221342		2202	4300	6502	SO:0001819	synonymous_variant	51185	exon1			GTGCGCAGCGTCC	BC017419	CCDS2562.1, CCDS54547.1	3p26.3	2014-05-27			ENSG00000113851	ENSG00000113851			30185	protein-coding gene	gene with protein product		609262	"mental retardation, non-syndromic, autosomal recessive, 2A"	MRT2A		15557513	Standard	NM_016302		Approved	MRT2	uc003bpq.3	Q96SW2	OTTHUMG00000090261	ENST00000231948.4:c.30T>C	chr3.hg19:g.3221342A>G		234.0	0.0	609	161.0	8.0	NM_001173482	B2R6H4|C9IZA9|C9JAH6|Q6AI62|Q6NVZ0|Q9UHW4	Silent	SNP	ENST00000231948.4	hg19	CCDS2562.1	.	.	.	.	.	.	.	.	.	.	A	11.97	1.797374	0.31777	.	.	ENSG00000113851	ENST00000424814;ENST00000450014	.	.	.	2.87	0.479	0.16796	.	.	.	.	.	T	0.45418	0.1341	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.24657	-1.0154	4	.	.	.	-1.3199	3.9654	0.09429	0.344:0.0:0.4575:0.1985	.	.	.	.	P	6	.	.	L	-	2	0	CRBN	3196342	1.000000	0.71417	0.961000	0.40146	0.888000	0.51559	1.650000	0.37292	0.083000	0.17047	0.455000	0.32223	CTG	.	.		0.677	CRBN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206579.3	NM_016302		G	3221342	A	G	3221342	2	3	259	1	0	0	0	0	0	0	0	1	3853	175	7	2		2	CRBN	3	3221342	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10		3221342	194801088	150	36468										
LRRN1	57633	hgsc.bcm.edu	37	chr3	3887042	3887042	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aatgctttggtgggtctggaTagccttgagagcctgtcttt	13	7	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:3887042T>C	ENST00000319331.3	+	2	1478	c.717T>C	c.(715-717)gaT>gaC	p.D239D	SUMF1_ENST00000534863.1_Intron	NM_020873.5	NP_065924.3	Q6UXK5	LRRN1_HUMAN	leucine rich repeat neuronal 1	239						integral component of membrane (GO:0016021)				NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|skin(1)|urinary_tract(2)	26				Epithelial(13;0.000886)|all cancers(10;0.0032)|OV - Ovarian serous cystadenocarcinoma(96;0.00608)|STAD - Stomach adenocarcinoma(44;0.0617)		TGGGTCTGGATAGCCTTGAGA	0.393																																					p.D239D		Atlas-SNP	.											.	LRRN1	82	.	0			c.T717C						.						101	107	105					3																	3887042		2203	4300	6503	SO:0001819	synonymous_variant	57633	exon2			TCTGGATAGCCTT	AB040930	CCDS33685.1	3p26.2	2013-01-11			ENSG00000175928	ENSG00000175928		"Immunoglobulin superfamily / I-set domain containing"	20980	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 3"					10819331	Standard	NM_020873		Approved	FIGLER3	uc003bpt.4	Q6UXK5	OTTHUMG00000154934	ENST00000319331.3:c.717T>C	chr3.hg19:g.3887042T>C		79.0	0.0		66.0	4.0	NM_020873	Q3LID5|Q8IYV5|Q9H8V1|Q9P231	Silent	SNP	ENST00000319331.3	hg19	CCDS33685.1																																																																																			.	.		0.393	LRRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337704.2	NM_020873		C	3887042	T	C	3887042	2	2	259	1	0	0	0	0	0	0	0	1	9043	1403	49	2		2	LRRN1	3	3887042	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	665700	3887042	194135388	151	36469										
RAF1	5894	hgsc.bcm.edu	37	chr3	12653516	12653516	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	caggcccctcaccttgagtgCtttcataaggcagtcatgca	9	13	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:12653516C>A	ENST00000251849.4	-	3	692	c.253G>T	c.(253-255)Gca>Tca	p.A85S	RAF1_ENST00000534997.1_5'Flank|RAF1_ENST00000542177.1_Intron|RAF1_ENST00000442415.2_Missense_Mutation_p.A85S	NM_002880.3	NP_002871.1	P04049	RAF1_HUMAN	Raf-1 proto-oncogene, serine/threonine kinase	85	RBD. {ECO:0000255|PROSITE- ProRule:PRU00262}.				activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|death-inducing signaling complex assembly (GO:0071550)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intermediate filament cytoskeleton organization (GO:0045104)|ion transmembrane transport (GO:0034220)|MAPK cascade (GO:0000165)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of protein complex assembly (GO:0031333)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of cell differentiation (GO:0045595)|regulation of cell motility (GO:2000145)|regulation of Rho protein signal transduction (GO:0035023)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)		ESRP1/RAF1(4)|RAF1/DAZL(2)|SRGAP3/RAF1(6)	biliary_tract(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	32					Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)	ACCTTGAGTGCTTTCATAAGG	0.483			T	SRGAP3	pilocytic astrocytoma				Noonan syndrome																												p.A85S		Atlas-SNP	.		Dom	yes		3	3p25	5894	v-raf-1 murine leukemia viral oncogene homolog 1		M	.	RAF1	66	.	0			c.G253T						.						171	158	163					3																	12653516		2203	4300	6503	SO:0001583	missense	5894	exon3	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	TGAGTGCTTTCAT	X03484	CCDS2612.1	3p25	2014-09-17	2014-06-26		ENSG00000132155	ENSG00000132155			9829	protein-coding gene	gene with protein product	"C-Raf proto-oncogene, serine/threonine kinase"	164760	"v-raf-1 murine leukemia viral oncogene homolog 1"			1611909	Standard	NM_002880		Approved	Raf-1, c-Raf, CRAF	uc003bxf.4	P04049	OTTHUMG00000129789	ENST00000251849.4:c.253G>T	chr3.hg19:g.12653516C>A	ENSP00000251849:p.Ala85Ser	90.0	0.0		86.0	4.0	NM_002880	B0LPH8|B2R5N3|Q15278|Q9UC20	Missense_Mutation	SNP	ENST00000251849.4	hg19	CCDS2612.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.635569	0.87760	.	.	ENSG00000132155	ENST00000251849;ENST00000442415	T;T	0.76839	-1.04;-1.05	5.7	5.7	0.88788	Raf-like Ras-binding (3);	0.000000	0.85682	D	0.000000	D	0.85075	0.5614	M	0.81942	2.565	0.80722	D	1	P	0.42296	0.775	P	0.48227	0.571	D	0.86103	0.1557	10	0.62326	D	0.03	.	19.8438	0.96701	0.0:1.0:0.0:0.0	.	85	P04049	RAF1_HUMAN	S	85	ENSP00000251849:A85S;ENSP00000401888:A85S	ENSP00000251849:A85S	A	-	1	0	RAF1	12628516	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	7.797000	0.85911	2.705000	0.92388	0.508000	0.49915	GCA	.	.		0.483	RAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252015.2	NM_002880		A	12653516	C	A	12653516	3	1	259	1	0	0	0	0	1	0	0	0	13017	797	28	3	1753	3	RAF1	3	12653516	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	8766474	12653516	185368914	152	36470										
SATB1	6304	hgsc.bcm.edu	37	chr3	18458441	18458441	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aataacctagagacagcaatGccatttcgatcagctggttg	9	9	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:18458441G>A	ENST00000338745.6	-	3	2075	c.341C>T	c.(340-342)gCa>gTa	p.A114V	TBC1D5_ENST00000414318.2_Intron|SATB1_ENST00000417717.2_Missense_Mutation_p.A114V|SATB1_ENST00000454909.2_Missense_Mutation_p.A114V|SATB1_ENST00000475083.1_5'UTR	NM_002971.4	NP_002962.1	Q01826	SATB1_HUMAN	SATB homeobox 1	114	PDZ-like dimerization domain.				activated T cell proliferation (GO:0050798)|apoptotic process (GO:0006915)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|epidermis development (GO:0008544)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|reflex (GO:0060004)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(2)|endometrium(6)|large_intestine(4)|lung(10)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	32						AGACAGCAATGCCATTTCGAT	0.418																																					p.A114V		Atlas-SNP	.											.	SATB1	96	.	0			c.C341T						.						185	164	171					3																	18458441		2203	4300	6503	SO:0001583	missense	6304	exon3			AGCAATGCCATTT		CCDS2631.1, CCDS56242.1	3p24.3	2011-07-19	2007-02-15		ENSG00000182568	ENSG00000182568		"Homeoboxes / CUT class"	10541	protein-coding gene	gene with protein product		602075	"special AT-rich sequence binding protein 1 (binds to nuclear matrix/scaffold-associating DNA)"			1505028	Standard	NM_002971		Approved		uc003cbj.3	Q01826	OTTHUMG00000129890	ENST00000338745.6:c.341C>T	chr3.hg19:g.18458441G>A	ENSP00000341024:p.Ala114Val	114.0	0.0		96.0	4.0	NM_002971	B3KXF1|C9JTR6|Q59EQ0	Missense_Mutation	SNP	ENST00000338745.6	hg19	CCDS2631.1	.	.	.	.	.	.	.	.	.	.	G	19.06	3.753662	0.69648	.	.	ENSG00000182568	ENST00000338745;ENST00000454909;ENST00000417717;ENST00000440737;ENST00000452260;ENST00000415069;ENST00000457005;ENST00000414509	T;T;T;T;T;T;T;T	0.53857	0.6;0.6;0.6;0.6;0.6;0.6;0.6;0.6	5.33	5.33	0.75918	.	0.104703	0.64402	D	0.000004	T	0.67998	0.2953	L	0.45581	1.43	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.65672	-0.6111	10	0.42905	T	0.14	-14.0945	19.3886	0.94570	0.0:0.0:1.0:0.0	.	114;114	Q01826-2;Q01826	.;SATB1_HUMAN	V	114	ENSP00000341024:A114V;ENSP00000399708:A114V;ENSP00000399518:A114V;ENSP00000402982:A114V;ENSP00000406727:A114V;ENSP00000390529:A114V;ENSP00000398072:A114V;ENSP00000408871:A114V	ENSP00000341024:A114V	A	-	2	0	SATB1	18433445	1.000000	0.71417	0.988000	0.46212	0.995000	0.86356	9.813000	0.99286	2.646000	0.89796	0.561000	0.74099	GCA	.	.		0.418	SATB1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252138.4	NM_001131010		A	18458441	G	A	18458441	3	1	259	1	0	0	0	0	1	0	0	0	13868	1319	46	3	1986	3	SATB1	3	18458441	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	5804925	18458441	179563989	153	36471										
STT3B	201595	hgsc.bcm.edu	37	chr3	31574743	31574743	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tcctggcctggcttgccggcTtcagctcgcgcctcttcgcc	11	18	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:31574743T>C	ENST00000295770.2	+	1	462	c.253T>C	c.(253-255)Ttc>Ctc	p.F85L	STT3B_ENST00000453168.1_3'UTR	NM_178862.1	NP_849193.1	Q8TCJ2	STT3B_HUMAN	STT3B, subunit of the oligosaccharyltransferase complex (catalytic)	85					co-translational protein modification (GO:0043686)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			autonomic_ganglia(1)|biliary_tract(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	19						GCTTGCCGGCTTCAGCTCGCG	0.706																																					p.F85L		Atlas-SNP	.											.	STT3B	52	.	0			c.T253C						.						11	11	11					3																	31574743		2127	4172	6299	SO:0001583	missense	201595	exon1			GCCGGCTTCAGCT	AK027789	CCDS2650.1	3p24.1	2013-03-06	2013-03-06		ENSG00000163527	ENSG00000163527	2.4.99.18		30611	protein-coding gene	gene with protein product	"source of immunodominant MHC associated peptides", "dolichyl-diphosphooligosaccharide protein glycotransferase"	608605	"STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)"			12887896, 12439619	Standard	XM_006713017		Approved	SIMP, FLJ90106, STT3-B	uc011axe.2	Q8TCJ2	OTTHUMG00000130673	ENST00000295770.2:c.253T>C	chr3.hg19:g.31574743T>C	ENSP00000295770:p.Phe85Leu	114.0	0.0		83.0	4.0	NM_178862	Q96JZ4|Q96KY7	Missense_Mutation	SNP	ENST00000295770.2	hg19	CCDS2650.1	.	.	.	.	.	.	.	.	.	.	T	29.0	4.972636	0.92919	.	.	ENSG00000163527	ENST00000295770	.	.	.	4.13	4.13	0.48395	.	0.053416	0.85682	D	0.000000	T	0.82006	0.4943	M	0.94142	3.5	0.80722	D	1	P	0.42584	0.784	P	0.51657	0.676	D	0.86183	0.1607	9	0.66056	D	0.02	0.6074	12.4573	0.55712	0.0:0.0:0.0:1.0	.	85	Q8TCJ2	STT3B_HUMAN	L	85	.	ENSP00000295770:F85L	F	+	1	0	STT3B	31549747	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	4.166000	0.58203	1.633000	0.50488	0.248000	0.18094	TTC	.	.		0.706	STT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253166.2	NM_178862		C	31574743	T	C	31574743	3	2	259	1	0	0	0	0	1	0	0	0	15349	1609	56	2	255	2	STT3B	3	31574743	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	13116302	31574743	166447687	154	36472										
CLASP2	23122	hgsc.bcm.edu	37	chr3	33759302	33759302	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctcgccgccgtcgcttacccGgtagttgctcgaacccaccc	9	19	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:33759302G>T	ENST00000468888.2	-	1	239	c.193C>A	c.(193-195)Cgg>Agg	p.R65R	CLASP2_ENST00000359576.5_Silent_p.R65R|CLASP2_ENST00000307312.7_5'UTR|CLASP2_ENST00000399362.4_Silent_p.R65R			O75122	CLAP2_HUMAN	cytoplasmic linker associated protein 2	1117					axon guidance (GO:0007411)|establishment or maintenance of cell polarity (GO:0007163)|fucosylation (GO:0036065)|microtubule anchoring (GO:0034453)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)|regulation of microtubule polymerization or depolymerization (GO:0031110)|regulation of microtubule-based process (GO:0032886)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)|microtubule plus-end binding (GO:0051010)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	48						TCGCTTACCCGGTAGTTGCTC	0.716																																					p.R65R		Atlas-SNP	.											.	CLASP2	138	.	0			c.C193A						.						8	12	11					3																	33759302		1907	4067	5974	SO:0001819	synonymous_variant	23122	exon1			TTACCCGGTAGTT	AB014527		3p24.3	2013-01-18			ENSG00000163539	ENSG00000163539			17078	protein-coding gene	gene with protein product		605853				9734811, 10899121	Standard	NM_015097		Approved	KIAA0627	uc021wvc.1	O75122	OTTHUMG00000156489	ENST00000468888.2:c.193C>A	chr3.hg19:g.33759302G>T		113.0	0.0		86.0	5.0	NM_015097	Q7L8F6|Q8N6R6|Q9BQT3|Q9BQT4|Q9H7A3|Q9NSZ2	Silent	SNP	ENST00000468888.2	hg19																																																																																				.	.		0.716	CLASP2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000344320.4	NM_001207044		T	33759302	G	T	33759302	2	4	259	1	0	0	0	0	0	0	0	1	3457	1115	39	1		1	CLASP2	3	33759302	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	2184559	33759302	164263128	155	36473										
TRANK1	9881	hgsc.bcm.edu	37	chr3	36880152	36880152	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tcagggcagtgtcatgggccAgggccaacttctccttctca	11	13	4	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:36880152A>G	ENST00000429976.2	-	18	5451	c.5204T>C	c.(5203-5205)cTg>cCg	p.L1735P	TRANK1_ENST00000301807.6_Missense_Mutation_p.L1185P|TRANK1_ENST00000428977.2_Missense_Mutation_p.L1185P	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	1735							ATP binding (GO:0005524)|hydrolase activity (GO:0016787)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(20)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	73						GTCATGGGCCAGGGCCAACTT	0.483																																					p.L1735P		Atlas-SNP	.											.	TRANK1	398	.	0			c.T5204C						.						79	75	76					3																	36880152		1933	4126	6059	SO:0001583	missense	9881	exon18			TGGGCCAGGGCCA	AK096678	CCDS46789.1, CCDS46789.2	3p22.2	2013-01-11			ENSG00000168016	ENSG00000168016		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29011	protein-coding gene	gene with protein product	"lupus brain antigen 1", "KIAA0342"					9205841	Standard	NM_014831		Approved	LBA1, KIAA0342	uc003cgj.3	O15050	OTTHUMG00000155848	ENST00000429976.2:c.5204T>C	chr3.hg19:g.36880152A>G	ENSP00000416168:p.Leu1735Pro	117.0	0.0		136.0	7.0	NM_014831	Q8N8K0	Missense_Mutation	SNP	ENST00000429976.2	hg19	CCDS46789.2	.	.	.	.	.	.	.	.	.	.	A	16.48	3.136388	0.56936	.	.	ENSG00000168016	ENST00000428977;ENST00000429976;ENST00000301807	T;T;T	0.34472	1.36;1.78;1.36	5.04	5.04	0.67666	Tetratricopeptide-like helical (1);	.	.	.	.	T	0.33206	0.0855	N	0.24115	0.695	0.58432	D	0.999995	D	0.56521	0.976	P	0.47744	0.556	T	0.13335	-1.0513	9	0.52906	T	0.07	.	15.4909	0.75605	1.0:0.0:0.0:0.0	.	1735	O15050	TRNK1_HUMAN	P	1185;1735;1185	ENSP00000416826:L1185P;ENSP00000416168:L1735P;ENSP00000301807:L1185P	ENSP00000301807:L1185P	L	-	2	0	TRANK1	36855156	0.988000	0.35896	0.528000	0.27938	0.544000	0.35116	4.852000	0.62904	2.202000	0.70862	0.533000	0.62120	CTG	.	.		0.483	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831		G	36880152	A	G	36880152	3	3	259	1	0	0	0	0	1	0	0	0	16469	188	7	2	3597	2	TRANK1	3	36880152	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	3120850	36880152	161142278	156	36474										
VILL	50853	hgsc.bcm.edu	37	chr3	38044780	38044780	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctgggaggccctgggaggccGggccccctaccccagcaaca	14	17	0	0	rs373953862		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:38044780G>T	ENST00000283713.6	+	15	2047	c.1781G>T	c.(1780-1782)cGg>cTg	p.R594L	VILL_ENST00000465644.1_Missense_Mutation_p.R312L|VILL_ENST00000383759.2_Missense_Mutation_p.R594L			O15195	VILL_HUMAN	villin-like	594					actin filament capping (GO:0051693)|cytoskeleton organization (GO:0007010)	actin cytoskeleton (GO:0015629)	structural constituent of cytoskeleton (GO:0005200)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(3)|stomach(3)|urinary_tract(2)	28				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)		CTGGGAGGCCGGGCCCCCTAC	0.607											OREG0015475	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R594L		Atlas-SNP	.											.	VILL	61	.	0			c.G1781T						.						33	33	33					3																	38044780		2203	4300	6503	SO:0001583	missense	50853	exon14			GAGGCCGGGCCCC		CCDS2670.2	3p21	2004-07-28			ENSG00000136059	ENSG00000136059			30906	protein-coding gene	gene with protein product						9179494	Standard	XM_005265191		Approved		uc003chl.3	O15195	OTTHUMG00000130814	ENST00000283713.6:c.1781G>T	chr3.hg19:g.38044780G>T	ENSP00000283713:p.Arg594Leu	58.0	0.0	875	74.0	4.0	NM_015873	A8MZP1|Q9BT80|Q9BWH7	Missense_Mutation	SNP	ENST00000283713.6	hg19	CCDS2670.2	.	.	.	.	.	.	.	.	.	.	g	13.40	2.224929	0.39300	.	.	ENSG00000136059	ENST00000283713;ENST00000383759;ENST00000356246;ENST00000465644	T;T;T	0.21191	2.02;2.02;2.02	4.55	1.69	0.24217	.	0.240429	0.38959	N	0.001508	T	0.28732	0.0712	M	0.77103	2.36	0.30013	N	0.814963	P	0.38110	0.618	P	0.45506	0.483	T	0.23048	-1.0199	10	0.87932	D	0	-11.4828	4.879	0.13670	0.2874:0.3475:0.3651:0.0	.	594	O15195	VILL_HUMAN	L	594;594;580;312	ENSP00000283713:R594L;ENSP00000373266:R594L;ENSP00000422096:R312L	ENSP00000283713:R594L	R	+	2	0	VILL	38019784	0.964000	0.33143	0.994000	0.49952	0.035000	0.12851	1.397000	0.34543	0.099000	0.17552	-0.420000	0.06012	CGG	.	.		0.607	VILL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253360.3	NM_015873		T	38044780	G	T	38044780	3	4	259	1	0	0	0	0	1	0	0	0	17180	1116	39	1	1835	1	VILL	3	38044780	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1164628	38044780	159977650	157	36475										
DLEC1	9940	hgsc.bcm.edu	37	chr3	38080908	38080908	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agcttcgcagcccggccccgCcgcctcacgcagcttgcgct	11	20	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:38080908C>T	ENST00000308059.6	+	1	213	c.192C>T	c.(190-192)cgC>cgT	p.R64R	DLEC1_ENST00000346219.3_Silent_p.R64R|DLEC1_ENST00000452631.2_Silent_p.R64R					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		CCCGGCCCCGCCGCCTCACGC	0.677																																					p.R64R		Atlas-SNP	.											.	DLEC1	278	.	0			c.C192T						.						35	43	40					3																	38080908		1996	4174	6170	SO:0001819	synonymous_variant	9940	exon1			GCCCCGCCGCCTC	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"cilia and flagella associated protein 81"	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.192C>T	chr3.hg19:g.38080908C>T		176.0	0.0		138.0	46.0	NM_007337		Silent	SNP	ENST00000308059.6	hg19	CCDS2672.2																																																																																			.	.		0.677	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337		T	38080908	C	T	38080908	2	4	259	1	0	0	0	0	0	0	0	1	4554	726	26	3		3	DLEC1	3	38080908	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	36128	38080908	159941522	158	36476										
XYLB	9942	hgsc.bcm.edu	37	chr3	38416703	38416703	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atgcctgccctggaaggccaCatcttctgcaacccggttga	10	14	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:38416703C>T	ENST00000207870.3	+	12	1047	c.957C>T	c.(955-957)caC>caT	p.H319H	XYLB_ENST00000542835.1_Silent_p.H182H	NM_005108.3	NP_005099.2	O75191	XYLB_HUMAN	xylulokinase homolog (H. influenzae)	319					carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|D-xylose metabolic process (GO:0042732)|generation of precursor metabolites and energy (GO:0006091)|xylulose catabolic process (GO:0005998)|xylulose metabolic process (GO:0005997)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|xylulokinase activity (GO:0004856)			endometrium(3)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|ovary(1)|prostate(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.00372)|Kidney(284;0.00405)		TGGAAGGCCACATCTTCTGCA	0.607																																					p.H319H		Atlas-SNP	.											.	XYLB	50	.	0			c.C957T						.						124	88	100					3																	38416703		2203	4300	6503	SO:0001819	synonymous_variant	9942	exon12			AGGCCACATCTTC	AB015046	CCDS2678.1	3p22-p21.3	2006-12-18	2001-12-04		ENSG00000093217	ENSG00000093217			12839	protein-coding gene	gene with protein product		604049	"xylulokinase (H. influenzae) homolog"			9763671	Standard	NM_005108		Approved	FLJ10343, FLJ12539	uc003cic.2	O75191	OTTHUMG00000131294	ENST00000207870.3:c.957C>T	chr3.hg19:g.38416703C>T		134.0	0.0		88.0	4.0	NM_005108	B2RAW4|B4DDT2|B9EH64	Silent	SNP	ENST00000207870.3	hg19	CCDS2678.1																																																																																			.	.		0.607	XYLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254062.2	NM_005108		T	38416703	C	T	38416703	2	4	259	1	0	0	0	0	0	0	0	1	17477	477	17	3		3	XYLB	3	38416703	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	335795	38416703	159605727	159	36477										
ZNF662	389114	hgsc.bcm.edu	37	chr3	42956424	42956424	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aatgtgggaagggctttagtCagaacacaagccttacgcaa	11	8	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:42956424C>A	ENST00000541208.1	+	5	1228	c.859C>A	c.(859-861)Cag>Aag	p.Q287K	ZNF662_ENST00000422021.1_Intron|ZNF662_ENST00000328199.6_Missense_Mutation_p.Q313K|KRBOX1_ENST00000426937.1_Intron|ZNF662_ENST00000440367.2_Missense_Mutation_p.Q287K			Q6ZS27	ZN662_HUMAN	zinc finger protein 662	287					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|large_intestine(6)|lung(5)|upper_aerodigestive_tract(1)	15				KIRC - Kidney renal clear cell carcinoma(284;0.217)		GGGCTTTAGTCAGAACACAAG	0.448																																					p.Q313K		Atlas-SNP	.											.	ZNF662	112	.	0			c.C937A						.						99	90	93					3																	42956424		2203	4300	6503	SO:0001583	missense	389114	exon4			TTTAGTCAGAACA	AK127779	CCDS2708.1, CCDS46807.1	3p22.1	2013-01-08			ENSG00000182983	ENSG00000182983		"Zinc fingers, C2H2-type", "-"	31930	protein-coding gene	gene with protein product							Standard	NM_207404		Approved	FLJ45880	uc003cmk.2	Q6ZS27	OTTHUMG00000133041	ENST00000541208.1:c.859C>A	chr3.hg19:g.42956424C>A	ENSP00000446208:p.Gln287Lys	87.0	0.0		91.0	4.0	NM_001134656	A1A4T9|F8W7S8|Q6ZNF8|Q6ZQW8	Missense_Mutation	SNP	ENST00000541208.1	hg19	CCDS2708.1	.	.	.	.	.	.	.	.	.	.	C	7.980	0.750912	0.15778	.	.	ENSG00000182983	ENST00000440367;ENST00000328199;ENST00000541208	T;T;T	0.07021	3.23;3.23;3.23	3.17	3.17	0.36434	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07413	0.0187	N	0.11927	0.2	0.22050	N	0.99939	D;D	0.54601	0.959;0.967	B;P	0.50570	0.434;0.644	T	0.33548	-0.9864	9	0.33940	T	0.23	.	8.4601	0.32923	0.0:0.7589:0.2411:0.0	.	313;287	F8W7S8;Q6ZS27	.;ZN662_HUMAN	K	287;313;287	ENSP00000405047:Q287K;ENSP00000329264:Q313K;ENSP00000446208:Q287K	ENSP00000329264:Q313K	Q	+	1	0	ZNF662	42931428	0.000000	0.05858	1.000000	0.80357	0.990000	0.78478	-0.353000	0.07691	1.797000	0.52628	0.555000	0.69702	CAG	.	.		0.448	ZNF662-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256646.4	NM_207404		A	42956424	C	A	42956424	3	1	259	1	0	0	0	0	1	0	0	0	18086	827	29	3	1060	3	ZNF662	3	42956424	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	4539721	42956424	155066006	160	36478										
CDCP1	64866	hgsc.bcm.edu	37	chr3	45135024	45135024	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggctggcaccagcaccaggcTgagcctgtccttgggcacca	13	15	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:45135024T>C	ENST00000296129.1	-	6	1506	c.1372A>G	c.(1372-1374)Agc>Ggc	p.S458G		NM_022842.3	NP_073753.3	Q9H5V8	CDCP1_HUMAN	CUB domain containing protein 1	458	CUB.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|skin(4)|urinary_tract(1)	29				BRCA - Breast invasive adenocarcinoma(193;0.00928)|KIRC - Kidney renal clear cell carcinoma(197;0.0519)|Kidney(197;0.0651)		AGCACCAGGCTGAGCCTGTCC	0.597																																					p.S458G		Atlas-SNP	.											.	CDCP1	61	.	0			c.A1372G						.						93	84	87					3																	45135024		2203	4300	6503	SO:0001583	missense	64866	exon6			CCAGGCTGAGCCT	AF468010	CCDS2727.1, CCDS46812.1	3p21.3	2006-03-28			ENSG00000163814	ENSG00000163814		"CD molecules"	24357	protein-coding gene	gene with protein product		611735				11466621	Standard	NM_022842		Approved	CD318, SIMA135	uc003com.3	Q9H5V8	OTTHUMG00000133090	ENST00000296129.1:c.1372A>G	chr3.hg19:g.45135024T>C	ENSP00000296129:p.Ser458Gly	84.0	0.0		78.0	4.0	NM_022842	Q49UB4|Q6NT71|Q6U9Y2|Q8WU91|Q96QU7|Q9H676|Q9H8C2	Missense_Mutation	SNP	ENST00000296129.1	hg19	CCDS2727.1	.	.	.	.	.	.	.	.	.	.	T	14.23	2.472378	0.43942	.	.	ENSG00000163814	ENST00000296129	T	0.23754	1.89	5.85	4.67	0.58626	.	0.270974	0.44483	N	0.000441	T	0.21062	0.0507	L	0.38838	1.175	0.80722	D	1	B	0.12013	0.005	B	0.11329	0.006	T	0.02705	-1.1121	10	0.52906	T	0.07	.	10.5696	0.45192	0.0:0.0744:0.0:0.9256	.	458	Q9H5V8	CDCP1_HUMAN	G	458	ENSP00000296129:S458G	ENSP00000296129:S458G	S	-	1	0	CDCP1	45110028	0.994000	0.37717	0.974000	0.42286	0.772000	0.43724	2.542000	0.45744	1.000000	0.39049	0.459000	0.35465	AGC	.	.		0.597	CDCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256748.3	NM_022842		C	45135024	T	C	45135024	3	2	259	1	0	0	0	0	1	0	0	0	3095	1580	55	2	1154	2	CDCP1	3	45135024	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	2178600	45135024	152887406	161	36479										
C3orf75	54859	hgsc.bcm.edu	37	chr3	47552681	47552681	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tggtgtacaaggaaactcccAtctgtcttggcatcacagag	10	10	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:47552681A>G	ENST00000296149.4	-	2	260	c.90T>C	c.(88-90)gaT>gaC	p.D30D	ELP6_ENST00000439305.1_5'UTR|ELP6_ENST00000446787.1_5'UTR|ELP6_ENST00000460502.1_5'Flank	NM_001031703.2	NP_001026873.2	Q0PNE2	ELP6_HUMAN	elongator acetyltransferase complex subunit 6	30					chromatin organization (GO:0006325)|positive regulation of cell migration (GO:0030335)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Elongator holoenzyme complex (GO:0033588)											GGAAACTCCCATCTGTCTTGG	0.418																																					p.D30D		Atlas-SNP	.											.	.	.	.	0			c.T90C						.						106	100	102					3																	47552681		1874	4117	5991	SO:0001819	synonymous_variant	54859	exon2			ACTCCCATCTGTC	AK000218	CCDS43082.1	3p21.31	2012-08-14	2012-08-08	2012-08-08	ENSG00000163832	ENSG00000163832		"Elongator acetyltransferase complex subunits"	25976	protein-coding gene	gene with protein product		615020	"transmembrane protein 103", "chromosome 3 open reading frame 75"	TMEM103, C3orf75		22854966	Standard	XM_005265241		Approved	FLJ20211	uc003crk.3	Q0PNE2	OTTHUMG00000133521	ENST00000296149.4:c.90T>C	chr3.hg19:g.47552681A>G		96.0	0.0		98.0	4.0	NM_001031703	Q9BW57|Q9NXJ3	Silent	SNP	ENST00000296149.4	hg19	CCDS43082.1																																																																																			.	.		0.418	ELP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257493.1	NM_017713		G	47552681	A	G	47552681	2	3	259	1	0	0	0	0	0	0	0	1	2247	214	8	2		2	C3orf75	3	47552681	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2417657	47552681	150469749	162	36480										
COL7A1	1294	hgsc.bcm.edu	37	chr3	48609831	48609831	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	accggctcacccaccaggtcTccagcaaggcctccaggggc	11	18	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:48609831T>C	ENST00000328333.8	-	89	7067	c.6960A>G	c.(6958-6960)ggA>ggG	p.G2320G	COL7A1_ENST00000454817.1_Silent_p.G2288G	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	2320	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CCACCAGGTCTCCAGCAAGGC	0.607																																					p.G2320G		Atlas-SNP	.											.	COL7A1	320	.	0			c.A6960G						.						84	89	87					3																	48609831		2203	4300	6503	SO:0001819	synonymous_variant	1294	exon89			CAGGTCTCCAGCA	L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"Collagens", "Fibronectin type III domain containing"	2214	protein-coding gene	gene with protein product	"collagen VII, alpha-1 polypeptide", "LC collagen"	120120	"epidermolysis bullosa, dystrophic, dominant and recessive"	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.6960A>G	chr3.hg19:g.48609831T>C		184.0	0.0		153.0	7.0	NM_000094	Q14054|Q16507	Silent	SNP	ENST00000328333.8	hg19	CCDS2773.1																																																																																			.	.		0.607	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094		C	48609831	T	C	48609831	2	2	259	1	0	0	0	0	0	0	0	1	3706	1538	54	2		2	COL7A1	3	48609831	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1057150	48609831	149412599	163	36481										
P4HTM	54681	hgsc.bcm.edu	37	chr3	49043519	49043519	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tctgattcaggatgacgtggAcctccgtgacacacggaggc	13	11	2	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:49043519A>G	ENST00000383729.4	+	8	1558	c.1187A>G	c.(1186-1188)gAc>gGc	p.D396G	P4HTM_ENST00000343546.4_Missense_Mutation_p.D457G|WDR6_ENST00000608424.1_5'Flank|WDR6_ENST00000415265.2_5'Flank|WDR6_ENST00000395474.3_5'Flank|WDR6_ENST00000448293.1_5'Flank	NM_177939.2	NP_808808.1	Q9NXG6	P4HTM_HUMAN	prolyl 4-hydroxylase, transmembrane (endoplasmic reticulum)	396	Fe2OG dioxygenase. {ECO:0000255|PROSITE- ProRule:PRU00805}.					endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)			NS(1)|breast(2)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	21					Vitamin C(DB00126)	GATGACGTGGACCTCCGTGAC	0.582																																					p.D457G		Atlas-SNP	.											.	P4HTM	71	.	0			c.A1370G						.						104	97	99					3																	49043519		2203	4300	6503	SO:0001583	missense	54681	exon8			ACGTGGACCTCCG		CCDS2781.2, CCDS43089.1	3p21.31	2009-01-14			ENSG00000178467	ENSG00000178467			28858	protein-coding gene	gene with protein product	"Prolyl hydroxlase domain-containing 4", "hypoxia inducible factor prolyl 4 hydroxylase"	614584				12163023, 17726031	Standard	XR_245139		Approved	P4H-TM, PHD4, PH4, HIFPH4, FLJ20262, EGLN4, PH-4	uc003cvh.3	Q9NXG6	OTTHUMG00000074057	ENST00000383729.4:c.1187A>G	chr3.hg19:g.49043519A>G	ENSP00000373235:p.Asp396Gly	112.0	0.0		91.0	4.0	NM_177938	Q6PAG6|Q8TCJ9|Q8WV55|Q96F22|Q9BW77	Missense_Mutation	SNP	ENST00000383729.4	hg19	CCDS43089.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.648164	0.87958	.	.	ENSG00000178467	ENST00000383729;ENST00000343546	T	0.79247	-1.25	5.85	5.85	0.93711	Oxoglutarate/iron-dependent oxygenase (2);Prolyl 4-hydroxylase, alpha subunit (1);	0.000000	0.85682	D	0.000000	D	0.83723	0.5316	L	0.48642	1.525	0.48632	D	0.999688	P;D	0.89917	0.659;1.0	P;D	0.87578	0.789;0.998	T	0.80360	-0.1415	10	0.20519	T	0.43	-35.4512	16.2303	0.82332	1.0:0.0:0.0:0.0	.	457;396	Q9NXG6-3;Q9NXG6	.;P4HTM_HUMAN	G	396;457	ENSP00000373235:D396G	ENSP00000341422:D457G	D	+	2	0	P4HTM	49018523	1.000000	0.71417	0.998000	0.56505	0.945000	0.59286	8.393000	0.90182	2.233000	0.73108	0.533000	0.62120	GAC	.	.		0.582	P4HTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157211.1	NM_177938		G	49043519	A	G	49043519	3	3	259	1	0	0	0	0	1	0	0	0	11369	275	10	2	1400	2	P4HTM	3	49043519	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	433688	49043519	148978911	164	36482										
LAMB2	3913	hgsc.bcm.edu	37	chr3	49159200	49159200	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cagactatttcctgcccgttTcaatttcagagcctccagga	7	13	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:49159200T>C	ENST00000418109.1	-	31	5181	c.5017A>G	c.(5017-5019)Aaa>Gaa	p.K1673E	USP19_ENST00000398888.2_5'Flank|USP19_ENST00000453664.1_5'Flank|LAMB2_ENST00000305544.4_Missense_Mutation_p.K1673E|USP19_ENST00000434032.2_5'Flank|USP19_ENST00000398898.2_5'Flank|USP19_ENST00000417901.1_5'Flank|USP19_ENST00000398892.3_5'Flank|USP19_ENST00000488993.1_5'Flank	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	1673	Domain I.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		CCTGCCCGTTTCAATTTCAGA	0.602																																					p.K1673E		Atlas-SNP	.											.	LAMB2	156	.	0			c.A5017G						.						75	76	75					3																	49159200		2203	4300	6503	SO:0001583	missense	3913	exon30			CCCGTTTCAATTT		CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"Laminins"	6487	protein-coding gene	gene with protein product	"laminin S"	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.5017A>G	chr3.hg19:g.49159200T>C	ENSP00000388325:p.Lys1673Glu	88.0	0.0		86.0	4.0	NM_002292	Q16321	Missense_Mutation	SNP	ENST00000418109.1	hg19	CCDS2789.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.052051	0.75960	.	.	ENSG00000172037	ENST00000418109;ENST00000305544	T;T	0.36520	1.25;1.25	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.59059	0.2166	M	0.69823	2.125	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.58381	-0.7646	10	0.38643	T	0.18	.	15.6945	0.77484	0.0:0.0:0.0:1.0	.	1673	P55268	LAMB2_HUMAN	E	1673	ENSP00000388325:K1673E;ENSP00000307156:K1673E	ENSP00000307156:K1673E	K	-	1	0	LAMB2	49134204	1.000000	0.71417	1.000000	0.80357	0.359000	0.29487	7.619000	0.83057	2.118000	0.64928	0.533000	0.62120	AAA	.	.		0.602	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292		C	49159200	T	C	49159200	3	2	259	1	0	0	0	0	1	0	0	0	8620	1792	62	2	391	2	LAMB2	3	49159200	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	115681	49159200	148863230	165	36483										
MST1R	4486	hgsc.bcm.edu	37	chr3	49940121	49940121	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gccttctggggccccccggcGcctgcgttttggagcaaatc	13	15	1	0	rs541331773		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:49940121G>A	ENST00000296474.3	-	1	949	c.922C>T	c.(922-924)Cgc>Tgc	p.R308C	CTD-2330K9.3_ENST00000419183.1_5'Flank|CTD-2330K9.2_ENST00000435478.1_RNA|MST1R_ENST00000344206.4_Missense_Mutation_p.R308C	NM_002447.2	NP_002438	Q04912	RON_HUMAN	macrophage stimulating 1 receptor (c-met-related tyrosine kinase)	308	Poly-Arg.|Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cellular component movement (GO:0006928)|defense response (GO:0006952)|innate immune response (GO:0045087)|macrophage colony-stimulating factor signaling pathway (GO:0038145)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|response to virus (GO:0009615)|signal transduction (GO:0007165)|single fertilization (GO:0007338)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|macrophage colony-stimulating factor receptor activity (GO:0005011)			cervix(1)|endometrium(5)|large_intestine(3)|lung(17)|ovary(5)|prostate(2)|skin(1)|urinary_tract(3)	37				BRCA - Breast invasive adenocarcinoma(193;4.65e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)		GCCCCCCGGCGCCTGCGTTTT	0.662													G|||	1	0.000199681	0	0	5008	,	,		15347	0		0	False		,,,				2504	0.001				p.R308C		Atlas-SNP	.											.	MST1R	205	.	0			c.C922T						.						59	71	67					3																	49940121		2203	4300	6503	SO:0001583	missense	4486	exon1			CCCGGCGCCTGCG	X70040	CCDS2807.1, CCDS58833.1	3p21	2008-08-18			ENSG00000164078	ENSG00000164078		"CD molecules"	7381	protein-coding gene	gene with protein product		600168	"PTK8 protein tyrosine kinase 8"	RON, PTK8		8386824	Standard	NM_002447		Approved	CDw136, CD136	uc003cxy.4	Q04912	OTTHUMG00000156709	ENST00000296474.3:c.922C>T	chr3.hg19:g.49940121G>A	ENSP00000296474:p.Arg308Cys	72.0	0.0		55.0	24.0	NM_001244937	B5A944|B5A945|B5A946|B5A947	Missense_Mutation	SNP	ENST00000296474.3	hg19	CCDS2807.1	.	.	.	.	.	.	.	.	.	.	G	15.17	2.753547	0.49362	.	.	ENSG00000164078	ENST00000296474;ENST00000344206	T;T	0.07021	3.23;3.23	4.7	3.75	0.43078	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.046283	0.85682	D	0.000000	T	0.25901	0.0631	M	0.80746	2.51	0.53005	D	0.999967	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.998;1.0;1.0;0.999	T	0.00909	-1.1518	10	0.87932	D	0	-17.5197	7.3058	0.26447	0.0:0.1414:0.4771:0.3815	.	308;308;308;308;308	Q04912-3;Q04912-4;Q04912-6;Q04912-5;Q04912	.;.;.;.;RON_HUMAN	C	308	ENSP00000296474:R308C;ENSP00000341325:R308C	ENSP00000296474:R308C	R	-	1	0	MST1R	49915125	0.792000	0.28813	0.693000	0.30195	0.185000	0.23345	1.383000	0.34385	2.151000	0.67156	0.561000	0.74099	CGC	.	.		0.662	MST1R-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345403.1			A	49940121	G	A	49940121	3	1	259	1	0	0	0	0	1	0	0	0	9900	1087	38	1	3360	1	MST1R	3	49940121	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	780921	49940121	148082309	166	36484										
STAB1	23166	hgsc.bcm.edu	37	chr3	52556640	52556640	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tctgaacttttcggaggctgAggcggcatgcgaagcacagg	15	9	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:52556640A>G	ENST00000321725.6	+	61	6756	c.6680A>G	c.(6679-6681)gAg>gGg	p.E2227G		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	2227	Link. {ECO:0000255|PROSITE- ProRule:PRU00323, ECO:0000305}.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)			breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		TCGGAGGCTGAGGCGGCATGC	0.617																																					p.E2227G		Atlas-SNP	.											.	STAB1	178	.	0			c.A6680G						.						65	69	68					3																	52556640		2203	4300	6503	SO:0001583	missense	23166	exon61			AGGCTGAGGCGGC	AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"MS-1 antigen", "fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1", "common lymphatic endothelial and vascular endothelial receptor-1"	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.6680A>G	chr3.hg19:g.52556640A>G	ENSP00000312946:p.Glu2227Gly	116.0	0.0		88.0	4.0	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Missense_Mutation	SNP	ENST00000321725.6	hg19	CCDS33768.1	.	.	.	.	.	.	.	.	.	.	A	14.56	2.570899	0.45798	.	.	ENSG00000010327	ENST00000321725	T	0.32753	1.44	5.75	4.61	0.57282	C-type lectin fold (1);Link (3);C-type lectin-like (1);	0.540280	0.21175	N	0.078918	T	0.33498	0.0865	M	0.71206	2.165	0.24342	N	0.994953	P;P	0.35872	0.525;0.525	B;B	0.37731	0.257;0.257	T	0.20505	-1.0273	10	0.28530	T	0.3	.	10.9201	0.47158	0.9264:0.0:0.0736:0.0	.	114;2227	B3KSK0;Q9NY15	.;STAB1_HUMAN	G	2227	ENSP00000312946:E2227G	ENSP00000312946:E2227G	E	+	2	0	STAB1	52531680	0.000000	0.05858	0.233000	0.24025	0.493000	0.33554	0.589000	0.23939	2.192000	0.70111	0.459000	0.35465	GAG	.	.		0.617	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136		G	52556640	A	G	52556640	3	3	259	1	0	0	0	0	1	0	0	0	15252	304	11	2	6922	2	STAB1	3	52556640	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2616519	52556640	145465790	167	36485										
ADAMTS9	56999	hgsc.bcm.edu	37	chr3	64599079	64599079	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gctgctgacaagtctgcataGatgttggcttggtctcaggg	14	8	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:64599079G>T	ENST00000498707.1	-	22	3638	c.3296C>A	c.(3295-3297)tCt>tAt	p.S1099Y	ADAMTS9_ENST00000295903.4_Missense_Mutation_p.S1071Y	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	1099	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.				glycoprotein catabolic process (GO:0006516)|multicellular organismal development (GO:0007275)|positive regulation of melanocyte differentiation (GO:0045636)|protein transport (GO:0015031)|proteolysis (GO:0006508)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(17)|liver(4)|lung(43)|ovary(3)|prostate(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	100		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		AGTCTGCATAGATGTTGGCTT	0.488																																					p.S1099Y		Atlas-SNP	.											.	ADAMTS9	206	.	0			c.C3296A						.						108	105	106					3																	64599079		2203	4300	6503	SO:0001583	missense	56999	exon22			TGCATAGATGTTG	AF261918	CCDS2903.1	3p14.1	2008-05-15	2005-08-19		ENSG00000163638	ENSG00000163638		"ADAM metallopeptidases with thrombospondin type 1 motif"	13202	protein-coding gene	gene with protein product		605421	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 9"			10936055	Standard	NM_182920		Approved	KIAA1312	uc003dmg.3	Q9P2N4	OTTHUMG00000158722	ENST00000498707.1:c.3296C>A	chr3.hg19:g.64599079G>T	ENSP00000418735:p.Ser1099Tyr	111.0	0.0		94.0	4.0	NM_182920	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	Missense_Mutation	SNP	ENST00000498707.1	hg19	CCDS2903.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.6|24.6	4.549995|4.549995	0.86127|0.86127	.|.	.|.	ENSG00000163638|ENSG00000163638	ENST00000481060|ENST00000295903;ENST00000498707	.|T;T	.|0.61627	.|0.09;0.09	6.06|6.06	6.06|6.06	0.98353|0.98353	.|.	.|0.066684	.|0.64402	.|D	.|0.000006	T|T	0.76912|0.76912	0.4054|0.4054	M|M	0.84082|0.84082	2.675|2.675	0.80722|0.80722	D|D	1|1	.|B;D;B	.|0.76494	.|0.219;0.999;0.052	.|B;D;B	.|0.65323	.|0.158;0.934;0.082	T|T	0.71002|0.71002	-0.4718|-0.4718	5|10	.|0.18276	.|T	.|0.48	.|.	20.6282|20.6282	0.99521|0.99521	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1071;1099;1099	.|B7ZVX9;Q9P2N4-1;Q9P2N4	.|.;.;ATS9_HUMAN	I|Y	155|1071;1099	.|ENSP00000295903:S1071Y;ENSP00000418735:S1099Y	.|ENSP00000295903:S1071Y	L|S	-|-	1|2	2|0	ADAMTS9|ADAMTS9	64574119|64574119	1.000000|1.000000	0.71417|0.71417	0.726000|0.726000	0.30738|0.30738	0.766000|0.766000	0.43426|0.43426	7.536000|7.536000	0.82023|0.82023	2.871000|2.871000	0.98454|0.98454	0.655000|0.655000	0.94253|0.94253	CTA|TCT	.	.		0.488	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351891.1			T	64599079	G	T	64599079	3	4	259	1	0	0	0	0	1	0	0	0	273	942	33	3	2583	3	ADAMTS9	3	64599079	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	12042439	64599079	133423351	168	36486										
EPHA3	2042	hgsc.bcm.edu	37	chr3	89390186	89390186	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gtgtgagaataattacttccGggcagacaaagaccctccat	9	10	0	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:89390186G>T	ENST00000336596.2	+	4	1160	c.935G>T	c.(934-936)cGg>cTg	p.R312L	EPHA3_ENST00000494014.1_Missense_Mutation_p.R312L|EPHA3_ENST00000452448.2_Missense_Mutation_p.R312L	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	312	Cys-rich.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)	p.R312L(2)		NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		AATTACTTCCGGGCAGACAAA	0.458										TSP Lung(6;0.00050)																											p.R312L		Atlas-SNP	.											EPHA3_ENST00000452448,colon,carcinoma,+1,4	EPHA3	501	.	2	Substitution - Missense(2)	lung(2)	c.G935T						.						157	156	156					3																	89390186		2203	4300	6503	SO:0001583	missense	2042	exon4			ACTTCCGGGCAGA	M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3387	protein-coding gene	gene with protein product		179611	"EphA3"	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.935G>T	chr3.hg19:g.89390186G>T	ENSP00000337451:p.Arg312Leu	74.0	0.0		94.0	4.0	NM_005233	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	hg19	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.914940	0.92178	.	.	ENSG00000044524	ENST00000336596;ENST00000452448;ENST00000494014	D;D;D	0.96168	-3.93;-3.93;-3.93	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.98592	0.9529	H	0.95574	3.69	0.80722	D	1	D;D	0.65815	0.995;0.995	D;P	0.70227	0.968;0.886	D	0.98701	1.0700	9	.	.	.	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	312;312	P29320;P29320-2	EPHA3_HUMAN;.	L	312	ENSP00000337451:R312L;ENSP00000399926:R312L;ENSP00000419190:R312L	.	R	+	2	0	EPHA3	89472876	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.941000	0.99782	0.655000	0.94253	CGG	.	.		0.458	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		T	89390186	G	T	89390186	3	4	259	1	0	0	0	0	1	0	0	0	5170	1116	39	1	949	1	EPHA3	3	89390186	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	24791107	89390186	108632244	169	36487										
TBC1D23	55773	hgsc.bcm.edu	37	chr3	100002653	100002653	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ataatgaataagtacattccCaggtaaaatatgattcagtt	6	5	1	2	rs200870879		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:100002653C>T	ENST00000394144.4	+	4	481	c.474C>T	c.(472-474)ccC>ccT	p.P158P	TBC1D23_ENST00000486274.1_3'UTR|TBC1D23_ENST00000475134.1_Intron|TBC1D23_ENST00000344949.5_Silent_p.P158P	NM_001199198.2	NP_001186127.1	Q9NUY8	TBC23_HUMAN	TBC1 domain family, member 23	158	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				positive regulation of interleukin-6 production (GO:0032755)|regulation of inflammatory response (GO:0050727)|regulation of tumor necrosis factor production (GO:0032680)		Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(1)|large_intestine(7)|liver(1)|lung(10)|ovary(1)|prostate(2)|skin(2)	25						AGTACATTCCCAGGTAAAATA	0.368																																					p.P158P		Atlas-SNP	.											.	TBC1D23	133	.	0			c.C474T						.						69	67	68					3																	100002653		2203	4300	6503	SO:0001819	synonymous_variant	55773	exon4			CATTCCCAGGTAA	AK001908	CCDS2936.1, CCDS56265.1	3q12.2	2013-07-10			ENSG00000036054	ENSG00000036054			25622	protein-coding gene	gene with protein product						22312129	Standard	NM_001199198		Approved	FLJ11046	uc003dtt.4	Q9NUY8	OTTHUMG00000159067	ENST00000394144.4:c.474C>T	chr3.hg19:g.100002653C>T		108.0	0.0		83.0	4.0	NM_001199198	B9A6M5|Q8TCN8|Q8WUB7|Q96D90|Q9NV75	Silent	SNP	ENST00000394144.4	hg19	CCDS56265.1																																																																																			.	C|1.000;G|0.000		0.368	TBC1D23-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353150.1	NM_018309		T	100002653	C	T	100002653	2	4	259	1	0	0	0	0	0	0	0	1	15628	581	21	3		3	TBC1D23	3	100002653	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	10612467	100002653	98019777	170	36488										
FAM55C	91775	hgsc.bcm.edu	37	chr3	101520615	101520615	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aaaccagacagggtctatttCaagagtctcttccgttcagg	9	10	4	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:101520615C>T	ENST00000491511.2	+	5	1586	c.630C>T	c.(628-630)ttC>ttT	p.F210F	NXPE3_ENST00000477909.1_Silent_p.F210F|NXPE3_ENST00000273347.5_Silent_p.F210F|NXPE3_ENST00000422132.1_Silent_p.F210F	NM_001134456.1	NP_001127928.1	Q969Y0	NXPE3_HUMAN	neurexophilin and PC-esterase domain family, member 3	210						extracellular region (GO:0005576)											GGGTCTATTTCAAGAGTCTCT	0.473																																					p.F210F		Atlas-SNP	.											.	.	.	.	0			c.C630T						.						68	70	70					3																	101520615		2203	4300	6503	SO:0001819	synonymous_variant	91775	exon5			CTATTTCAAGAGT	AK054664	CCDS2945.1	3q12.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000144815	ENSG00000144815			28238	protein-coding gene	gene with protein product			"family with sequence similarity 55, member C"	FAM55C		12975309	Standard	NM_001134456		Approved	MGC15606	uc003dvn.3	Q969Y0	OTTHUMG00000159179	ENST00000491511.2:c.630C>T	chr3.hg19:g.101520615C>T		87.0	0.0		78.0	4.0	NM_145037	A8K0X4|D3DN53|Q7Z2S8	Silent	SNP	ENST00000491511.2	hg19	CCDS2945.1																																																																																			.	.		0.473	NXPE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353711.2	NM_145037		T	101520615	C	T	101520615	2	4	259	1	0	0	0	0	0	0	0	1	5594	825	29	3		3	FAM55C	3	101520615	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	1517962	101520615	96501815	171	36489										
PLCXD2	257068	hgsc.bcm.edu	37	chr3	111432809	111432809	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gaaagaagattccagcgcccTgggcaaacaccacaagtgtg	11	11	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:111432809T>C	ENST00000477665.1	+	3	1024	c.700T>C	c.(700-702)Tgg>Cgg	p.W234R	PLCXD2_ENST00000393934.3_Missense_Mutation_p.W234R|PLCXD2_ENST00000472215.1_3'UTR	NM_001185106.1	NP_001172035.1	Q0VAA5	PLCX2_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 2	234					lipid catabolic process (GO:0016042)		phosphoric diester hydrolase activity (GO:0008081)|signal transducer activity (GO:0004871)			endometrium(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)	17						TCCAGCGCCCTGGGCAAACAC	0.507																																					p.W234R		Atlas-SNP	.											PLCXD2,NS,carcinoma,0,1	PLCXD2	36	.	0			c.T700C						.						78	79	79					3																	111432809		2203	4300	6503	SO:0001583	missense	257068	exon3			GCGCCCTGGGCAA	AK056141	CCDS2961.1, CCDS54619.1	3q13.2	2004-09-09			ENSG00000240891	ENSG00000240891			26462	protein-coding gene	gene with protein product							Standard	NM_001185106		Approved	FLJ31579	uc003dxz.3	Q0VAA5	OTTHUMG00000159279	ENST00000477665.1:c.700T>C	chr3.hg19:g.111432809T>C	ENSP00000420686:p.Trp234Arg	93.0	1.0		53.0	3.0	NM_001185106	Q96N12	Missense_Mutation	SNP	ENST00000477665.1	hg19	CCDS54619.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.159586	0.78226	.	.	ENSG00000240891	ENST00000393934;ENST00000477665	.	.	.	5.39	5.39	0.77823	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);	.	.	.	.	T	0.81118	0.4756	M	0.87381	2.88	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.997;0.998	D	0.84613	0.0679	8	0.87932	D	0	-9.1565	13.3815	0.60770	0.0:0.0:0.0:1.0	.	234;234	Q0VAA5;Q0VAA5-2	PLCX2_HUMAN;.	R	234	.	ENSP00000377511:W234R	W	+	1	0	PLCXD2	112915499	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.584000	0.82572	2.034000	0.60081	0.460000	0.39030	TGG	.	.		0.507	PLCXD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354322.1	NM_153268		C	111432809	T	C	111432809	3	2	259	1	0	0	0	0	1	0	0	0	12051	1580	55	2	710	2	PLCXD2	3	111432809	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	9912194	111432809	86589621	172	36490										
PHLDB2	90102	hgsc.bcm.edu	37	chr3	111658351	111658351	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctgttggatgttgaaagcaaAcactttgaagacctggagtt	11	6	0	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:111658351A>G	ENST00000431670.2	+	7	2571	c.2160A>G	c.(2158-2160)aaA>aaG	p.K720K	PHLDB2_ENST00000393925.3_Silent_p.K720K|PHLDB2_ENST00000481953.1_Silent_p.K677K|PHLDB2_ENST00000393923.3_Silent_p.K704K|PHLDB2_ENST00000412622.1_Silent_p.K677K|PHLDB2_ENST00000495180.1_Silent_p.K306K	NM_001134438.1	NP_001127910.1	Q86SQ0	PHLB2_HUMAN	pleckstrin homology-like domain, family B, member 2	720						cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(8)|lung(23)|ovary(6)|skin(7)|stomach(1)	55						TTGAAAGCAAACACTTTGAAG	0.418																																					p.K720K		Atlas-SNP	.											.	PHLDB2	449	.	0			c.A2160G						.						125	118	120					3																	111658351		2203	4300	6503	SO:0001819	synonymous_variant	90102	exon7			AAGCAAACACTTT		CCDS2962.1, CCDS46885.1, CCDS46886.1	3q13.13	2013-01-10			ENSG00000144824	ENSG00000144824		"Pleckstrin homology (PH) domain containing"	29573	protein-coding gene	gene with protein product		610298				12376540	Standard	NM_145753		Approved	LL5beta, FLJ21791, LL5b	uc003dyg.3	Q86SQ0	OTTHUMG00000159282	ENST00000431670.2:c.2160A>G	chr3.hg19:g.111658351A>G		85.0	0.0		64.0	4.0	NM_001134439	A5PKZ3|Q59EA8|Q68CY3|Q6NT98|Q8N8U8|Q8NAB1|Q8NCU5	Silent	SNP	ENST00000431670.2	hg19	CCDS46886.1																																																																																			.	.		0.418	PHLDB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354337.1	NM_145753		G	111658351	A	G	111658351	2	3	259	1	0	0	0	0	0	0	0	1	11861	40	2	2		2	PHLDB2	3	111658351	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	225542	111658351	86364079	173	36491										
BOC	91653	hgsc.bcm.edu	37	chr3	112989741	112989741	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gtgtgcagcctacaacccagTgacccaggaagtgaaaacct	10	12	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:112989741T>C	ENST00000495514.1	+	6	1321	c.617T>C	c.(616-618)gTg>gCg	p.V206A	BOC_ENST00000355385.3_Missense_Mutation_p.V206A|BOC_ENST00000273395.4_Missense_Mutation_p.V206A			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	206	Ig-like C2-type 2.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			TACAACCCAGTGACCCAGGAA	0.602																																					p.V206A		Atlas-SNP	.											.	BOC	139	.	0			c.T617C						.						147	144	145					3																	112989741		2203	4300	6503	SO:0001583	missense	91653	exon6			ACCCAGTGACCCA	AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	17173	protein-coding gene	gene with protein product	"brother of CDO", "brother of CDON", "cell adhesion associated, oncogene regulated 2"	608708	"Boc homolog (mouse)"			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.617T>C	chr3.hg19:g.112989741T>C	ENSP00000418663:p.Val206Ala	130.0	0.0		89.0	4.0	NM_033254	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Missense_Mutation	SNP	ENST00000495514.1	hg19	CCDS2971.1	.	.	.	.	.	.	.	.	.	.	T	31	5.088557	0.94100	.	.	ENSG00000144857	ENST00000495514;ENST00000273395;ENST00000355385	T;T;T	0.12147	2.71;2.71;2.71	5.8	5.8	0.92144	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.061508	0.64402	D	0.000004	T	0.24547	0.0595	L	0.42487	1.325	0.58432	D	0.999999	P;P	0.47409	0.895;0.716	P;P	0.56648	0.779;0.803	T	0.01524	-1.1333	10	0.20519	T	0.43	.	16.1549	0.81657	0.0:0.0:0.0:1.0	.	206;206	Q9BWV1-3;Q9BWV1	.;BOC_HUMAN	A	206	ENSP00000418663:V206A;ENSP00000273395:V206A;ENSP00000347546:V206A	ENSP00000273395:V206A	V	+	2	0	BOC	114472431	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.698000	0.84413	2.209000	0.71365	0.533000	0.62120	GTG	.	.		0.602	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254		C	112989741	T	C	112989741	3	2	259	1	0	0	0	0	1	0	0	0	1481	1696	59	2	631	2	BOC	3	112989741	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1331390	112989741	85032689	174	36492										
WDR52	55779	hgsc.bcm.edu	37	chr3	113119484	113119484	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aggagaagaggcattctgggTcctgggtctgagaatagata	15	5	2	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:113119484T>C	ENST00000295868.2	-	12	1544	c.1382A>G	c.(1381-1383)gAc>gGc	p.D461G	WDR52_ENST00000393845.2_Missense_Mutation_p.D461G	NM_018338.3	NP_060808.2														breast(2)|central_nervous_system(3)|endometrium(3)|kidney(5)|large_intestine(7)|lung(26)|prostate(1)|urinary_tract(2)	49						GCATTCTGGGTCCTGGGTCTG	0.398																																					p.D461G		Atlas-SNP	.											.	WDR52	151	.	0			c.A1382G						.						51	56	54					3																	113119484		2203	4300	6503	SO:0001583	missense	55779	exon12			TCTGGGTCCTGGG																												ENST00000295868.2:c.1382A>G	chr3.hg19:g.113119484T>C	ENSP00000295868:p.Asp461Gly	129.0	0.0		89.0	4.0	NM_001164496		Missense_Mutation	SNP	ENST00000295868.2	hg19	CCDS2972.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.481913	0.84747	.	.	ENSG00000206530	ENST00000393845;ENST00000295868	T;T	0.65549	-0.16;0.87	5.98	5.98	0.97165	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	.	.	.	.	T	0.73938	0.3651	M	0.68317	2.08	0.80722	D	1	D	0.58970	0.984	P	0.60173	0.87	T	0.71417	-0.4599	9	0.27785	T	0.31	.	15.6593	0.77169	0.0:0.0:0.0:1.0	.	461	Q96MT7	WDR52_HUMAN	G	461	ENSP00000377428:D461G;ENSP00000295868:D461G	ENSP00000295868:D461G	D	-	2	0	WDR52	114602174	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.007000	0.76335	2.288000	0.76882	0.528000	0.53228	GAC	.	.		0.398	WDR52-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354128.3			C	113119484	T	C	113119484	3	2	259	1	0	0	0	0	1	0	0	0	17319	1667	58	2	4293	2	WDR52	3	113119484	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	129743	113119484	84902946	175	36493										
C3orf30	152405	hgsc.bcm.edu	37	chr3	118870130	118870130	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cccctgaattttatgctgtgCcaggtatagaattggagaaa	10	7	0	3	rs570667131		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:118870130C>T	ENST00000295622.1	+	3	1642	c.1602C>T	c.(1600-1602)tgC>tgT	p.C534C	RP11-484M3.5_ENST00000490594.1_Intron	NM_152539.2	NP_689752.2	Q96M34	CC030_HUMAN	chromosome 3 open reading frame 30	534										NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(20)|ovary(2)|prostate(1)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(114;0.222)		TTATGCTGTGCCAGGTATAGA	0.373																																					p.C534C		Atlas-SNP	.											.	C3orf30	64	.	0			c.C1602T						.						165	177	173					3																	118870130		2203	4300	6503	SO:0001819	synonymous_variant	152405	exon3			GCTGTGCCAGGTA	AK057421	CCDS2984.1	3q13.32	2011-08-09			ENSG00000163424	ENSG00000163424			26553	protein-coding gene	gene with protein product							Standard	NM_152539		Approved	FLJ32859	uc003ecb.1	Q96M34	OTTHUMG00000159349	ENST00000295622.1:c.1602C>T	chr3.hg19:g.118870130C>T		100.0	0.0		88.0	4.0	NM_152539	A1L4B7	Silent	SNP	ENST00000295622.1	hg19	CCDS2984.1	.	.	.	.	.	.	.	.	.	.	C	5.104	0.204832	0.09704	.	.	ENSG00000163424	ENST00000492792	.	.	.	5.01	-1.78	0.07957	.	.	.	.	.	T	0.19805	0.0476	.	.	.	0.29470	N	0.857114	.	.	.	.	.	.	T	0.29822	-0.9999	4	.	.	.	6.9124	1.057	0.01592	0.1438:0.2677:0.3112:0.2773	.	.	.	.	S	220	.	.	P	+	1	0	C3orf30	120352820	0.003000	0.15002	0.037000	0.18230	0.866000	0.49608	-0.420000	0.07062	-0.197000	0.10350	-0.218000	0.12543	CCA	.	.		0.373	C3orf30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354838.1	NM_152539		T	118870130	C	T	118870130	2	4	259	1	0	0	0	0	0	0	0	1	2222	747	26	3		3	C3orf30	3	118870130	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	5750646	118870130	79152300	176	36494										
ARHGAP31	57514	hgsc.bcm.edu	37	chr3	119109740	119109740	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cctggccactaaccatcctgCtcgcaaggaaaggagggaga	12	12	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:119109740C>T	ENST00000264245.4	+	7	1323	c.791C>T	c.(790-792)gCt>gTt	p.A264V		NM_020754.2	NP_065805.2	Q2M1Z3	RHG31_HUMAN	Rho GTPase activating protein 31	264					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(3)|large_intestine(11)|lung(29)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	67						AACCATCCTGCTCGCAAGGAA	0.577																																					p.A264V	Pancreas(7;176 297 5394 51128 51241)	Atlas-SNP	.											.	ARHGAP31	175	.	0			c.C791T						.						70	75	74					3																	119109740		1980	4167	6147	SO:0001583	missense	57514	exon7			ATCCTGCTCGCAA		CCDS43135.1	3q13.33	2011-06-29			ENSG00000031081	ENSG00000031081		"Rho GTPase activating proteins"	29216	protein-coding gene	gene with protein product		610911				9786927, 12819203, 16519628	Standard	NM_020754		Approved	CDGAP	uc003ecj.4	Q2M1Z3	OTTHUMG00000159362	ENST00000264245.4:c.791C>T	chr3.hg19:g.119109740C>T	ENSP00000264245:p.Ala264Val	118.0	0.0		94.0	4.0	NM_020754	Q9ULL6	Missense_Mutation	SNP	ENST00000264245.4	hg19	CCDS43135.1	.	.	.	.	.	.	.	.	.	.	C	16.36	3.100690	0.56183	.	.	ENSG00000031081	ENST00000264245;ENST00000543280	T	0.07216	3.21	5.8	5.8	0.92144	.	0.240214	0.34603	N	0.003838	T	0.05044	0.0135	N	0.02539	-0.55	0.42281	D	0.992091	B	0.11235	0.004	B	0.14023	0.01	T	0.51100	-0.8748	10	0.38643	T	0.18	.	19.1007	0.93272	0.0:1.0:0.0:0.0	.	264	Q2M1Z3	RHG31_HUMAN	V	264	ENSP00000264245:A264V	ENSP00000264245:A264V	A	+	2	0	ARHGAP31	120592430	1.000000	0.71417	0.702000	0.30337	0.933000	0.57130	4.989000	0.63870	2.760000	0.94817	0.478000	0.44815	GCT	.	.		0.577	ARHGAP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354942.2			T	119109740	C	T	119109740	3	4	259	1	0	0	0	0	1	0	0	0	880	797	28	3	817	3	ARHGAP31	3	119109740	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	239610	119109740	78912690	177	36495										
GSK3B	2932	hgsc.bcm.edu	37	chr3	119642320	119642320	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccagcaccagattaagatagAcctcatctttctgaaagagt	7	10	3	5			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:119642320A>G	ENST00000264235.8	-	4	1359	c.377T>C	c.(376-378)gTc>gCc	p.V126A	GSK3B_ENST00000316626.5_Missense_Mutation_p.V126A	NM_001146156.1|NM_002093.3	NP_001139628.1|NP_002084.2	P49841	GSK3B_HUMAN	glycogen synthase kinase 3 beta	126	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell migration (GO:0016477)|cellular response to interleukin-3 (GO:0036016)|cellular response to mechanical stimulus (GO:0071260)|circadian rhythm (GO:0007623)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial to mesenchymal transition (GO:0001837)|ER overload response (GO:0006983)|establishment of cell polarity (GO:0030010)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fat cell differentiation (GO:0045444)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glycogen metabolic process (GO:0005977)|hippocampus development (GO:0021766)|hypermethylation of CpG island (GO:0044027)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|myoblast fusion (GO:0007520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of neuron maturation (GO:0014043)|negative regulation of neuron projection development (GO:0010977)|negative regulation of NFAT protein import into nucleus (GO:0051534)|negative regulation of protein binding (GO:0032091)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of type B pancreatic cell development (GO:2000077)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein binding (GO:0032092)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of stem cell differentiation (GO:2000738)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|protein localization to microtubule (GO:0035372)|protein phosphorylation (GO:0006468)|re-entry into mitotic cell cycle (GO:0000320)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of microtubule-based process (GO:0032886)|regulation of neuronal synaptic plasticity (GO:0048168)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|superior temporal gyrus development (GO:0071109)	beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|kinase activity (GO:0016301)|NF-kappaB binding (GO:0051059)|p53 binding (GO:0002039)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II transcription factor binding (GO:0001085)|tau-protein kinase activity (GO:0050321)|ubiquitin protein ligase binding (GO:0031625)			endometrium(1)|large_intestine(8)|lung(7)|prostate(2)	18				GBM - Glioblastoma multiforme(114;0.24)	Lithium(DB01356)	ATTAAGATAGACCTCATCTTT	0.338																																					p.V126A		Atlas-SNP	.											.	GSK3B	119	.	0			c.T377C						.						48	45	46					3																	119642320		2202	4300	6502	SO:0001583	missense	2932	exon4			AGATAGACCTCAT	BC012760	CCDS2996.1, CCDS54628.1	3q13.3	2008-02-15			ENSG00000082701	ENSG00000082701			4617	protein-coding gene	gene with protein product		605004				10486203	Standard	NM_002093		Approved		uc003edm.3	P49841	OTTHUMG00000133765	ENST00000264235.8:c.377T>C	chr3.hg19:g.119642320A>G	ENSP00000264235:p.Val126Ala	95.0	0.0		70.0	4.0	NM_002093	D3DN89|Q9BWH3|Q9UL47	Missense_Mutation	SNP	ENST00000264235.8	hg19	CCDS54628.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.123558	0.77436	.	.	ENSG00000082701	ENST00000264235;ENST00000316626	T;T	0.66280	-0.2;-0.2	4.28	4.28	0.50868	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.66694	0.2815	L	0.31371	0.925	0.80722	D	1	D;P	0.54207	0.965;0.956	D;P	0.63033	0.91;0.854	T	0.71144	-0.4678	10	0.87932	D	0	-5.4231	13.5977	0.62000	1.0:0.0:0.0:0.0	.	126;126	P49841;P49841-2	GSK3B_HUMAN;.	A	126	ENSP00000264235:V126A;ENSP00000324806:V126A	ENSP00000264235:V126A	V	-	2	0	GSK3B	121125010	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.761000	0.91691	1.804000	0.52760	0.460000	0.39030	GTC	.	.		0.338	GSK3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258240.2			G	119642320	A	G	119642320	3	3	259	1	0	0	0	0	1	0	0	0	6833	275	10	2	960	2	GSK3B	3	119642320	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	532580	119642320	78380110	178	36496										
PARP14	54625	hgsc.bcm.edu	37	chr3	122437412	122437412	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aagactttgatgaaaaggagTatcaggagttgaatgagctg	13	3	1	5			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:122437412T>C	ENST00000474629.2	+	14	4680	c.4414T>C	c.(4414-4416)Tat>Cat	p.Y1472H	PARP14_ENST00000475640.1_3'UTR	NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	1472					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		TGAAAAGGAGTATCAGGAGTT	0.388																																					p.Y1472H		Atlas-SNP	.											.	PARP14	242	.	0			c.T4414C						.						100	102	101					3																	122437412		2038	4200	6238	SO:0001583	missense	54625	exon14			AAGGAGTATCAGG	AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"Poly (ADP-ribose) polymerases"	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.4414T>C	chr3.hg19:g.122437412T>C	ENSP00000418194:p.Tyr1472His	93.0	0.0		86.0	4.0	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Missense_Mutation	SNP	ENST00000474629.2	hg19	CCDS46894.1	.	.	.	.	.	.	.	.	.	.	T	8.965	0.971614	0.18736	.	.	ENSG00000173193	ENST00000474629;ENST00000398162;ENST00000310290;ENST00000398157	T	0.09630	2.96	5.23	2.75	0.32379	.	0.690200	0.13861	N	0.357641	T	0.16938	0.0407	M	0.70595	2.14	0.09310	N	1	D;P	0.59767	0.986;0.85	P;B	0.54100	0.742;0.37	T	0.16600	-1.0397	10	0.23891	T	0.37	.	1.4913	0.02457	0.3035:0.0819:0.1579:0.4567	.	1472;1472	Q460N5-4;Q460N5	.;PAR14_HUMAN	H	1472;1391;75;468	ENSP00000418194:Y1472H	ENSP00000310633:Y75H	Y	+	1	0	PARP14	123920102	0.000000	0.05858	0.066000	0.19879	0.064000	0.16182	-0.525000	0.06214	0.401000	0.25424	0.528000	0.53228	TAT	.	.		0.388	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554		C	122437412	T	C	122437412	3	2	259	1	0	0	0	0	1	0	0	0	11467	1638	57	2	4468	2	PARP14	3	122437412	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	2795092	122437412	75585018	179	36497										
PARP14	54625	hgsc.bcm.edu	37	chr3	122439215	122439215	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gcaagtttaatcagacctgcTcacacttcagaatagagaag	8	9	3	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:122439215T>C	ENST00000474629.2	+	15	5187	c.4921T>C	c.(4921-4923)Tca>Cca	p.S1641P	PARP14_ENST00000475640.1_3'UTR	NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	1641	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		TCAGACCTGCTCACACTTCAG	0.433																																					p.S1641P		Atlas-SNP	.											.	PARP14	242	.	0			c.T4921C						.						87	81	83					3																	122439215		1985	4160	6145	SO:0001583	missense	54625	exon15			ACCTGCTCACACT	AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"Poly (ADP-ribose) polymerases"	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.4921T>C	chr3.hg19:g.122439215T>C	ENSP00000418194:p.Ser1641Pro	103.0	0.0		95.0	4.0	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Missense_Mutation	SNP	ENST00000474629.2	hg19	CCDS46894.1	.	.	.	.	.	.	.	.	.	.	T	7.840	0.721787	0.15372	.	.	ENSG00000173193	ENST00000474629;ENST00000398162;ENST00000310290;ENST00000398157	T	0.14640	2.49	5.06	-10.1	0.00402	Poly(ADP-ribose) polymerase, catalytic domain (2);	0.934638	0.08919	N	0.874661	T	0.05593	0.0147	N	0.12637	0.245	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.11329	0.006;0.003	T	0.41215	-0.9521	10	0.18710	T	0.47	.	11.276	0.49168	0.0:0.2472:0.5103:0.2424	.	1641;1641	Q460N5-4;Q460N5	.;PAR14_HUMAN	P	1641;1560;244;637	ENSP00000418194:S1641P	ENSP00000310633:S244P	S	+	1	0	PARP14	123921905	0.000000	0.05858	0.004000	0.12327	0.025000	0.11179	-5.482000	0.00119	-2.079000	0.00871	-1.333000	0.01266	TCA	.	.		0.433	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554		C	122439215	T	C	122439215	3	2	259	1	0	0	0	0	1	0	0	0	11467	1551	54	2	4979	2	PARP14	3	122439215	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1803	122439215	75583215	180	36498										
KALRN	8997	hgsc.bcm.edu	37	chr3	124385357	124385357	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	attctatgtgatcgagctggAtgcaggcatgcagtcccgga	13	9	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:124385357A>G	ENST00000291478.5	+	13	1476	c.1313A>G	c.(1312-1314)gAt>gGt	p.D438G	KALRN_ENST00000428018.2_Missense_Mutation_p.D406G|KALRN_ENST00000360013.3_Missense_Mutation_p.D2135G|KALRN_ENST00000459915.1_Missense_Mutation_p.D227G|KALRN_ENST00000393496.1_Missense_Mutation_p.D476G	NM_007064.3	NP_008995.2	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	2134					apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						ATCGAGCTGGATGCAGGCATG	0.552																																					p.D2135G		Atlas-SNP	.											.	KALRN	556	.	0			c.A6404G						.						86	78	81					3																	124385357		2203	4300	6503	SO:0001583	missense	8997	exon46			AGCTGGATGCAGG	U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	4814	protein-coding gene	gene with protein product	"serine/threonine kinase with Dbl and pleckstrin homology domains"	604605	"huntingtin-associated protein interacting protein (duo)"	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000291478.5:c.1313A>G	chr3.hg19:g.124385357A>G	ENSP00000291478:p.Asp438Gly	121.0	0.0		95.0	5.0	NM_001024660	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Missense_Mutation	SNP	ENST00000291478.5	hg19	CCDS3028.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.3|22.3	4.274944|4.274944	0.80580|0.80580	.|.	.|.	ENSG00000160145|ENSG00000160145	ENST00000360013;ENST00000393496;ENST00000291478;ENST00000428018;ENST00000459915|ENST00000354186	T;T;T;T;T|.	0.12361|.	2.69;2.69;2.69;2.69;2.69|.	5.15|5.15	5.15|5.15	0.70609|0.70609	Pleckstrin homology-type (1);Pleckstrin homology domain (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.74473|0.74473	0.3721|0.3721	M|M	0.75447|0.75447	2.3|2.3	0.58432|0.58432	D|D	0.999997|0.999997	B;D;D;P|.	0.76494|.	0.054;0.999;0.999;0.598|.	B;D;D;B|.	0.70935|.	0.027;0.941;0.971;0.243|.	T|T	0.75575|0.75575	-0.3270|-0.3270	10|5	0.72032|.	D|.	0.01|.	.|.	15.1548|15.1548	0.72733|0.72733	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	227;438;476;2134|.	E7EUZ8;C9JQ37;O60229-5;O60229|.	.;.;.;KALRN_HUMAN|.	G|V	2135;476;438;406;227|2104	ENSP00000353109:D2135G;ENSP00000377134:D476G;ENSP00000291478:D438G;ENSP00000402419:D406G;ENSP00000420318:D227G|.	ENSP00000291478:D438G|.	D|M	+|+	2|1	0|0	KALRN|KALRN	125868047|125868047	1.000000|1.000000	0.71417|0.71417	0.989000|0.989000	0.46669|0.46669	0.829000|0.829000	0.46940|0.46940	9.139000|9.139000	0.94554|0.94554	2.170000|2.170000	0.68504|0.68504	0.460000|0.460000	0.39030|0.39030	GAT|ATG	.	.		0.552	KALRN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000246891.5	NM_003947		G	124385357	A	G	124385357	3	3	259	1	0	0	0	0	1	0	0	0	7984	333	12	2	6742	2	KALRN	3	124385357	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1946142	124385357	73637073	181	36499										
MCM2	4171	hgsc.bcm.edu	37	chr3	127325501	127325501	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	accagtggggtggtgaccagCtgcactggcgtcctgcccca	14	14	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:127325501C>A	ENST00000265056.7	+	6	1186	c.942C>A	c.(940-942)agC>agA	p.S314R		NM_004526.2	NP_004517.2	P49736	MCM2_HUMAN	minichromosome maintenance complex component 2	314					cell cycle (GO:0007049)|cellular response to interleukin-4 (GO:0071353)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|MCM complex (GO:0042555)|microtubule cytoskeleton (GO:0015630)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA replication origin binding (GO:0003688)|metal ion binding (GO:0046872)			ovary(3)|skin(2)|stomach(1)	6						TGGTGACCAGCTGCACTGGCG	0.607																																					p.S314R		Atlas-SNP	.											.	MCM2	79	.	0			c.C942A						.						77	71	73					3																	127325501		2203	4300	6503	SO:0001583	missense	4171	exon6			GACCAGCTGCACT	X67334	CCDS3043.1	3q21	2007-04-04	2007-04-04		ENSG00000073111	ENSG00000073111			6944	protein-coding gene	gene with protein product	"mitotin"	116945	"minichromosome maintenance deficient (S. cerevisiae) 2 (mitotin)", "MCM2 minichromosome maintenance deficient 2, mitotin (S. cerevisiae)"	CCNL1, CDCL1		1710453, 8258304	Standard	NM_004526		Approved	D3S3194, KIAA0030, BM28, cdc19	uc003ejp.4	P49736	OTTHUMG00000159637	ENST00000265056.7:c.942C>A	chr3.hg19:g.127325501C>A	ENSP00000265056:p.Ser314Arg	84.0	0.0		57.0	4.0	NM_004526	Q14577|Q15023|Q8N2V1|Q969W7|Q96AE1|Q9BRM7	Missense_Mutation	SNP	ENST00000265056.7	hg19	CCDS3043.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	4.367|4.367	0.067726|0.067726	0.08436|0.08436	.|.	.|.	ENSG00000073111|ENSG00000073111	ENST00000491422|ENST00000265056;ENST00000539922;ENST00000543142	.|T	.|0.02631	.|4.22	4.99|4.99	4.12|4.12	0.48240|0.48240	.|Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);	.|0.078244	.|0.85682	.|D	.|0.000000	T|T	0.01940|0.01940	0.0061|0.0061	N|N	0.16098|0.16098	0.37|0.37	0.58432|0.58432	D|D	0.999991|0.999991	.|P;B;B	.|0.49559	.|0.925;0.001;0.003	.|P;B;B	.|0.44990	.|0.466;0.015;0.009	T|T	0.53258|0.53258	-0.8464|-0.8464	5|10	.|0.02654	.|T	.|1	-41.6488|-41.6488	7.9871|7.9871	0.30218|0.30218	0.0:0.7367:0.0:0.2633|0.0:0.7367:0.0:0.2633	.|.	.|295;184;314	.|F5H1E9;B4DSV5;P49736	.|.;.;MCM2_HUMAN	D|R	177|314;218;295	.|ENSP00000265056:S314R	.|ENSP00000265056:S314R	A|S	+|+	2|3	0|2	MCM2|MCM2	128808191|128808191	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	2.255000|2.255000	0.43222|0.43222	1.087000|1.087000	0.41251|0.41251	0.585000|0.585000	0.79938|0.79938	GCT|AGC	.	.		0.607	MCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356612.1			A	127325501	C	A	127325501	3	1	259	1	0	0	0	0	1	0	0	0	9395	796	28	3	964	3	MCM2	3	127325501	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	2940144	127325501	70696929	182	36500										
TXNDC6	347736	hgsc.bcm.edu	37	chr3	138023727	138023727	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gacatcacctttctggctgcTccctcctggccacattgggg	10	15	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:138023727T>C	ENST00000333911.3	-	9	806	c.779A>G	c.(778-780)gAg>gGg	p.E260G	NME9_ENST00000317876.4_Missense_Mutation_p.E199G|NME9_ENST00000341790.5_Missense_Mutation_p.E197G|NME9_ENST00000383180.2_Missense_Mutation_p.E199G|NME9_ENST00000484930.1_Missense_Mutation_p.E197G|NME9_ENST00000536478.1_Missense_Mutation_p.E199G			Q86XW9	TXND6_HUMAN	NME/NM23 family member 9	260	NDK.				cell redox homeostasis (GO:0045454)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|UTP biosynthetic process (GO:0006228)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)										TTCTGGCTGCTCCCTCCTGGC	0.577																																					p.E199G		Atlas-SNP	.											.	.	.	.	0			c.A596G						.						121	108	112					3																	138023727		2203	4300	6503	SO:0001583	missense	347736	exon10			GGCTGCTCCCTCC	AF196568	CCDS3099.1	3q22.3	2012-05-18	2012-05-18	2011-08-24	ENSG00000181322	ENSG00000181322			21343	protein-coding gene	gene with protein product			"thioredoxin domain containing 6", "NME gene family member 9", "NME family member 9"	TXNDC6		12569107, 19852809	Standard	NM_178130		Approved	TXL-2, NM23-H9	uc003ese.1	Q86XW9	OTTHUMG00000159823	ENST00000333911.3:c.779A>G	chr3.hg19:g.138023727T>C	ENSP00000335444:p.Glu260Gly	91.0	0.0		65.0	4.0	NM_178130	Q7Z4A8|Q8N1V7	Missense_Mutation	SNP	ENST00000333911.3	hg19		.	.	.	.	.	.	.	.	.	.	T	17.83	3.484498	0.63962	.	.	ENSG00000181322	ENST00000383180;ENST00000317876;ENST00000484930;ENST00000341790;ENST00000536478;ENST00000333911	T;T;T;T;T;T	0.49432	0.8;0.8;0.8;0.8;0.8;0.78	5.02	5.02	0.67125	.	0.052863	0.64402	D	0.000001	T	0.67924	0.2945	.	.	.	0.47949	D	0.999551	D;D;D	0.76494	0.998;0.999;0.999	D;D;D	0.78314	0.933;0.991;0.963	T	0.72418	-0.4300	9	0.72032	D	0.01	-28.0486	12.7046	0.57054	0.0:0.0:0.0:1.0	.	197;260;199	Q86XW9-3;Q86XW9;Q86XW9-2	.;TXND6_HUMAN;.	G	199;199;197;197;199;260	ENSP00000372667:E199G;ENSP00000321929:E199G;ENSP00000419882:E197G;ENSP00000341084:E197G;ENSP00000440143:E199G;ENSP00000335444:E260G	ENSP00000321929:E199G	E	-	2	0	TXNDC6	139506417	1.000000	0.71417	1.000000	0.80357	0.451000	0.32288	5.841000	0.69409	1.881000	0.54492	0.482000	0.46254	GAG	.	.		0.577	NME9-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000357583.1	NM_178130		C	138023727	T	C	138023727	3	2	259	1	0	0	0	0	1	0	0	0	16815	1551	54	2	207	2	TXNDC6	3	138023727	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	10698226	138023727	59998703	183	36501										
PIK3CB	5291	hgsc.bcm.edu	37	chr3	138376626	138376626	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cactcgctcccttttaatgcCaaacttagatttgaaatttc	4	11	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:138376626C>T	ENST00000477593.1	-	21	2921	c.2848G>A	c.(2848-2850)Ggc>Agc	p.G950S	PIK3CB_ENST00000289153.2_Missense_Mutation_p.G950S|PIK3CB_ENST00000544716.1_Missense_Mutation_p.G401S			P42338	PK3CB_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit beta	950	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|embryonic cleavage (GO:0040016)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of autophagy (GO:0010508)|regulation of cell-matrix adhesion (GO:0001952)|regulation of clathrin-mediated endocytosis (GO:2000369)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	41					Caffeine(DB00201)	CTTTTAATGCCAAACTTAGAT	0.368																																					p.G950S		Atlas-SNP	.											.	PIK3CB	103	.	0			c.G2848A						.						92	93	93					3																	138376626		2203	4300	6503	SO:0001583	missense	5291	exon20			TAATGCCAAACTT		CCDS3104.1	3q22.3	2013-09-19	2012-07-13		ENSG00000051382	ENSG00000051382	2.7.1.153		8976	protein-coding gene	gene with protein product		602925	"phosphoinositide-3-kinase, catalytic, beta polypeptide"	PIK3C1		8246984	Standard	NM_006219		Approved		uc011bmq.3	P42338	OTTHUMG00000159893	ENST00000477593.1:c.2848G>A	chr3.hg19:g.138376626C>T	ENSP00000418143:p.Gly950Ser	134.0	0.0		97.0	4.0	NM_006219	D3DNF0|Q24JU2	Missense_Mutation	SNP	ENST00000477593.1	hg19	CCDS3104.1	.	.	.	.	.	.	.	.	.	.	C	29.4	5.005252	0.93287	.	.	ENSG00000051382	ENST00000477593;ENST00000544716;ENST00000289153	D;D;D	0.82433	-1.61;-1.61;-1.61	5.72	5.72	0.89469	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.103125	0.64402	D	0.000002	D	0.91178	0.7221	M	0.86268	2.805	0.80722	D	1	D;D;D	0.71674	0.997;0.998;0.976	D;D;D	0.77004	0.939;0.989;0.951	D	0.91478	0.5202	10	0.54805	T	0.06	-13.5388	13.128	0.59366	0.0:0.9271:0.0:0.0729	.	950;537;401	P42338;B4DZI3;Q68DL0	PK3CB_HUMAN;.;.	S	950;401;950	ENSP00000418143:G950S;ENSP00000438259:G401S;ENSP00000289153:G950S	ENSP00000289153:G950S	G	-	1	0	PIK3CB	139859316	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.088000	0.71371	2.684000	0.91462	0.650000	0.86243	GGC	.	.		0.368	PIK3CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358019.1			T	138376626	C	T	138376626	3	4	259	1	0	0	0	0	1	0	0	0	11923	594	21	3	374	3	PIK3CB	3	138376626	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	352899	138376626	59645804	184	36502										
ZBTB38	253461	hgsc.bcm.edu	37	chr3	141164366	141164366	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agtgcaagacctgcggacggTgcttttcggtgcaaggaaac	14	9	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:141164366T>C	ENST00000514251.1	+	4	3415	c.3136T>C	c.(3136-3138)Tgc>Cgc	p.C1046R	ZBTB38_ENST00000321464.5_Missense_Mutation_p.C1047R|ZBTB38_ENST00000441582.2_Missense_Mutation_p.C1046R					zinc finger and BTB domain containing 38											breast(3)|cervix(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	41						CTGCGGACGGTGCTTTTCGGT	0.517																																					p.C1046R		Atlas-SNP	.											.	ZBTB38	92	.	0			c.T3136C						.						83	85	84					3																	141164366		2070	4200	6270	SO:0001583	missense	253461	exon8			GGACGGTGCTTTT	BC015444	CCDS43157.1	3q23	2014-06-13			ENSG00000177311	ENSG00000177311		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	26636	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 171"	612218				12477932	Standard	NM_001080412		Approved	FLJ35036, CIBZ, ZNF921, PPP1R171	uc003etw.3	Q8NAP3	OTTHUMG00000160128	ENST00000514251.1:c.3136T>C	chr3.hg19:g.141164366T>C	ENSP00000426387:p.Cys1046Arg	103.0	0.0		107.0	6.0	NM_001080412		Missense_Mutation	SNP	ENST00000514251.1	hg19	CCDS43157.1	.	.	.	.	.	.	.	.	.	.	T	3.592	-0.083306	0.07141	.	.	ENSG00000177311	ENST00000514251;ENST00000441582;ENST00000321464	T;T;T	0.07216	3.21;3.21;3.21	5.76	-3.08	0.05347	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.293174	0.35555	N	0.003129	T	0.02047	0.0064	N	0.03071	-0.42	0.39004	D	0.959415	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.46569	-0.9182	9	.	.	.	-11.9993	1.957	0.03378	0.1022:0.2343:0.2105:0.453	.	1047;1046	B4DYR8;Q8NAP3	.;ZBT38_HUMAN	R	1046;1046;1047	ENSP00000426387:C1046R;ENSP00000406955:C1046R;ENSP00000372635:C1047R	.	C	+	1	0	ZBTB38	142647056	0.997000	0.39634	0.037000	0.18230	0.440000	0.31957	0.772000	0.26647	-0.403000	0.07622	0.533000	0.62120	TGC	.	.		0.517	ZBTB38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359329.2			C	141164366	T	C	141164366	3	2	259	1	0	0	0	0	1	0	0	0	17554	1696	59	2	3138	2	ZBTB38	3	141164366	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	2787740	141164366	56858064	185	36503										
GK5	256356	hgsc.bcm.edu	37	chr3	141884509	141884509	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gagcgtttcactgctttggcCcagttttccagactcatttc	8	12	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:141884509C>A	ENST00000392993.2	-	16	1696	c.1545G>T	c.(1543-1545)tgG>tgT	p.W515C		NM_001039547.2	NP_001034636.1	Q6ZS86	GLPK5_HUMAN	glycerol kinase 5 (putative)	515					glycerol catabolic process (GO:0019563)		ATP binding (GO:0005524)|glycerol kinase activity (GO:0004370)			kidney(1)|large_intestine(1)|lung(7)|urinary_tract(1)	10						CTGCTTTGGCCCAGTTTTCCA	0.388																																					p.W515C		Atlas-SNP	.											.	GK5	45	.	0			c.G1545T						.						222	202	209					3																	141884509		2203	4300	6503	SO:0001583	missense	256356	exon16			TTTGGCCCAGTTT	BX648681	CCDS33871.1	3q23	2014-02-12	2006-09-21		ENSG00000175066	ENSG00000175066		"Glycerol kinases"	28635	protein-coding gene	gene with protein product						12477932	Standard	NM_001039547		Approved	MGC40579	uc003euq.2	Q6ZS86	OTTHUMG00000133572	ENST00000392993.2:c.1545G>T	chr3.hg19:g.141884509C>A	ENSP00000418001:p.Trp515Cys	651.0	1.0		514.0	246.0	NM_001039547	B2R9I2|D3DNG2|Q8N2A7|Q8N5E6	Missense_Mutation	SNP	ENST00000392993.2	hg19	CCDS33871.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.421896	0.83559	.	.	ENSG00000175066	ENST00000392993	D	0.91124	-2.79	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	D	0.97052	0.9037	H	0.95365	3.66	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97577	1.0108	10	0.87932	D	0	-10.5498	19.2235	0.93808	0.0:1.0:0.0:0.0	.	515	Q6ZS86	GLPK5_HUMAN	C	515	ENSP00000418001:W515C	ENSP00000418001:W515C	W	-	3	0	GK5	143367199	1.000000	0.71417	0.998000	0.56505	0.983000	0.72400	6.578000	0.74032	2.838000	0.97847	0.591000	0.81541	TGG	.	.		0.388	GK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353999.1	NM_001039547		A	141884509	C	A	141884509	3	1	259	1	0	0	0	0	1	0	0	0	6430	624	22	3	48	3	GK5	3	141884509	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	720143	141884509	56137921	186	36504										
MED12L	116931	hgsc.bcm.edu	37	chr3	150911407	150911407	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aatttttccatctaattatgAcctccttcgccacttacagt	3	12	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:150911407A>G	ENST00000474524.1	+	14	2137	c.2099A>G	c.(2098-2100)gAc>gGc	p.D700G	MED12L_ENST00000422248.2_Missense_Mutation_p.D700G|MED12L_ENST00000309237.4_Missense_Mutation_p.D735G|MED12L_ENST00000273432.4_Missense_Mutation_p.D560G	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	700						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TCTAATTATGACCTCCTTCGC	0.368																																					p.D700G		Atlas-SNP	.											.	MED12L	271	.	0			c.A2099G						.						142	142	142					3																	150911407		2203	4300	6503	SO:0001583	missense	116931	exon14			ATTATGACCTCCT	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.2099A>G	chr3.hg19:g.150911407A>G	ENSP00000417235:p.Asp700Gly	133.0	0.0		121.0	5.0	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Missense_Mutation	SNP	ENST00000474524.1	hg19	CCDS33876.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.81|13.81	2.348768|2.348768	0.41599|0.41599	.|.	.|.	ENSG00000144893|ENSG00000144893	ENST00000422248;ENST00000309237;ENST00000474524;ENST00000273432|ENST00000480026	T;T;T;T|.	0.33438|.	1.41;1.41;1.41;1.41|.	5.18|5.18	3.88|3.88	0.44766|0.44766	Mediator complex, subunit Med12, LCEWAV-domain (1);|.	0.216134|.	0.47455|.	N|.	0.000224|.	T|.	0.61664|.	0.2365|.	L|L	0.58669|0.58669	1.825|1.825	0.42457|0.42457	D|D	0.992776|0.992776	B;B;B;B|.	0.18741|.	0.03;0.001;0.003;0.001|.	B;B;B;B|.	0.21708|.	0.036;0.006;0.004;0.0|.	T|.	0.58640|.	-0.7601|.	10|.	0.72032|.	D|.	0.01|.	-9.8062|-9.8062	10.561|10.561	0.45146|0.45146	0.9159:0.0:0.0841:0.0|0.9159:0.0:0.0841:0.0	.|.	560;700;700;735|.	F8WAE6;Q86YW9;Q86YW9-2;Q86YW9-3|.	.;MD12L_HUMAN;.;.|.	G|W	700;735;700;560|49	ENSP00000403308:D700G;ENSP00000310760:D735G;ENSP00000417235:D700G;ENSP00000273432:D560G|.	ENSP00000273432:D560G|.	D|X	+|+	2|3	0|0	MED12L|MED12L	152394097|152394097	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.926000|0.926000	0.56050|0.56050	4.683000|4.683000	0.61679|0.61679	0.780000|0.780000	0.33566|0.33566	0.496000|0.496000	0.49642|0.49642	GAC|TGA	.	.		0.368	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002		G	150911407	A	G	150911407	3	3	259	1	0	0	0	0	1	0	0	0	9438	275	10	2	2153	2	MED12L	3	150911407	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	9026898	150911407	47111023	187	36505										
OTOL1	131149	hgsc.bcm.edu	37	chr3	161221321	161221321	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgagttggctagagtgccccGgtcggctttcagcgctggtt	15	10	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:161221321G>T	ENST00000327928.4	+	4	1025	c.1025G>T	c.(1024-1026)cGg>cTg	p.R342L		NM_001080440.1	NP_001073909.1	A6NHN0	OTOL1_HUMAN	otolin 1	342	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.					collagen trimer (GO:0005581)|extracellular region (GO:0005576)				central_nervous_system(2)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)	27						AGAGTGCCCCGGTCGGCTTTC	0.522																																					p.R342L		Atlas-SNP	.											.	OTOL1	63	.	0			c.G1025T						.						39	38	38					3																	161221321		1872	4099	5971	SO:0001583	missense	131149	exon4			TGCCCCGGTCGGC		CCDS46948.1	3q26.1	2011-05-19	2011-05-19			ENSG00000182447			34071	protein-coding gene	gene with protein product	"C1q and tumor necrosis factor related protein 15"		"otolin 1 homolog (zebrafish)"			17544811, 15905077	Standard	NM_001080440		Approved	C1QTNF15	uc011bpb.2	A6NHN0		ENST00000327928.4:c.1025G>T	chr3.hg19:g.161221321G>T	ENSP00000330808:p.Arg342Leu	164.0	0.0		106.0	5.0	NM_001080440		Missense_Mutation	SNP	ENST00000327928.4	hg19	CCDS46948.1	.	.	.	.	.	.	.	.	.	.	G	5.140	0.211399	0.09757	.	.	ENSG00000182447	ENST00000327928	D	0.86297	-2.1	5.23	-2.2	0.06994	Tumour necrosis factor-like (2);Complement C1q protein (2);	0.298148	0.35407	N	0.003223	D	0.83552	0.5279	M	0.79123	2.44	0.09310	N	0.999994	P	0.49862	0.929	B	0.41440	0.357	T	0.77032	-0.2738	10	0.25106	T	0.35	.	11.4066	0.49902	0.5857:0.0:0.4143:0.0	.	342	A6NHN0	OTOL1_HUMAN	L	342	ENSP00000330808:R342L	ENSP00000330808:R342L	R	+	2	0	OTOL1	162704015	0.062000	0.20869	0.000000	0.03702	0.001000	0.01503	0.639000	0.24690	-0.955000	0.03636	-1.031000	0.02408	CGG	.	.		0.522	OTOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353184.1	NM_001080440		T	161221321	G	T	161221321	3	4	259	1	0	0	0	0	1	0	0	0	11313	1116	39	1	1039	1	OTOL1	3	161221321	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	10309914	161221321	36801109	188	36506										
SLITRK3	22865	hgsc.bcm.edu	37	chr3	164907028	164907028	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gttcttcctcaggttgagccGggccagggatgtgccagcaa	14	11	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:164907028G>T	ENST00000475390.1	-	2	2034	c.1591C>A	c.(1591-1593)Cgg>Agg	p.R531R	SLITRK3_ENST00000241274.3_Silent_p.R531R			O94933	SLIK3_HUMAN	SLIT and NTRK-like family, member 3	531					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(66)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(5)	119						AGGTTGAGCCGGGCCAGGGAT	0.507										HNSCC(40;0.11)																											p.R531R		Atlas-SNP	.											SLITRK3,right_upper_lobe,carcinoma,0,1	SLITRK3	263	.	0			c.C1591A						.						56	59	58					3																	164907028		2203	4300	6503	SO:0001819	synonymous_variant	22865	exon2			TGAGCCGGGCCAG	AB020655	CCDS3197.1	3q26.1	2004-07-28			ENSG00000121871	ENSG00000121871			23501	protein-coding gene	gene with protein product		609679				10048485, 14557068	Standard	NM_014926		Approved	KIAA0848	uc003fek.3	O94933	OTTHUMG00000158072	ENST00000475390.1:c.1591C>A	chr3.hg19:g.164907028G>T		88.0	0.0		60.0	3.0	NM_014926	Q1RMY6	Silent	SNP	ENST00000475390.1	hg19	CCDS3197.1																																																																																			.	.		0.507	SLITRK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350126.1	NM_014926		T	164907028	G	T	164907028	2	4	259	1	0	0	0	0	0	0	0	1	14759	1115	39	1		1	SLITRK3	3	164907028	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	3685707	164907028	33115402	189	36507										
TBL1XR1	79718	hgsc.bcm.edu	37	chr3	176744244	176744244	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tccacctgttcccctatagcTgtgaactagagcacctgtct	7	14	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:176744244T>C	ENST00000430069.1	-	15	1694	c.1435A>G	c.(1435-1437)Agc>Ggc	p.S479G	TBL1XR1_ENST00000457928.2_Missense_Mutation_p.S479G			Q9BZK7	TBL1R_HUMAN	transducin (beta)-like 1 X-linked receptor 1	479					canonical Wnt signaling pathway (GO:0060070)|cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|histone binding (GO:0042393)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(7)|liver(1)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	31	all_cancers(143;1.44e-17)|Ovarian(172;0.00163)|Breast(254;0.214)	Acute lymphoblastic leukemia(1;0.00599)|all_hematologic(1;0.0632)|Prostate(884;0.215)	OV - Ovarian serous cystadenocarcinoma(80;9.83e-31)			CCCCTATAGCTGTGAACTAGA	0.338																																					p.S479G		Atlas-SNP	.											.	TBL1XR1	87	.	0			c.A1435G						.						92	80	84					3																	176744244		1841	4093	5934	SO:0001583	missense	79718	exon15			TATAGCTGTGAAC	AK022956	CCDS46961.1	3q26.33	2013-01-10	2008-01-17		ENSG00000177565	ENSG00000177565		"WD repeat domain containing"	29529	protein-coding gene	gene with protein product		608628	"transducin (beta)-like 1X-linked receptor 1"			11063877, 11931768	Standard	NM_024665		Approved	IRA1, FLJ12894, TBLR1, C21, DC42	uc003fix.4	Q9BZK7	OTTHUMG00000157140	ENST00000430069.1:c.1435A>G	chr3.hg19:g.176744244T>C	ENSP00000405574:p.Ser479Gly	96.0	0.0		99.0	4.0	NM_024665	D3DNQ9|Q14DC3|Q9H2I1|Q9H9A1	Missense_Mutation	SNP	ENST00000430069.1	hg19	CCDS46961.1	.	.	.	.	.	.	.	.	.	.	T	20.5	3.994341	0.74703	.	.	ENSG00000177565	ENST00000430069;ENST00000457928;ENST00000536758	D;D	0.81739	-1.53;-1.53	6.17	6.17	0.99709	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.84197	0.5419	M	0.84511	2.7	0.80722	D	1	P	0.42010	0.768	B	0.41088	0.347	D	0.86669	0.1909	10	0.72032	D	0.01	-6.0741	16.0034	0.80327	0.0:0.0:0.0:1.0	.	479	Q9BZK7	TBL1R_HUMAN	G	479;479;341	ENSP00000405574:S479G;ENSP00000413251:S479G	ENSP00000405574:S479G	S	-	1	0	TBL1XR1	178226938	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	2.371000	0.80710	0.533000	0.62120	AGC	.	.		0.338	TBL1XR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347587.3	NM_024665		C	176744244	T	C	176744244	3	2	259	1	0	0	0	0	1	0	0	0	15655	1580	55	2	117	2	TBL1XR1	3	176744244	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	11837216	176744244	21278186	190	36508										
ZMAT3	64393	hgsc.bcm.edu	37	chr3	178745434	178745434	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gagaaaatggcaatacctacGagaatgagttactctgagct	10	7	1	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:178745434G>T	ENST00000311417.2	-	4	1298	c.557C>A	c.(556-558)tCg>tAg	p.S186*	ZMAT3_ENST00000432729.1_Splice_Site_p.S186*	NM_022470.3	NP_071915.1			zinc finger, matrin-type 3											breast(1)|endometrium(1)|large_intestine(6)|lung(2)|ovary(2)|prostate(1)|skin(1)	14	all_cancers(143;3.31e-18)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;6.74e-27)|GBM - Glioblastoma multiforme(14;0.00448)|BRCA - Breast invasive adenocarcinoma(182;0.0527)			CAATACCTACGAGAATGAGTT	0.463																																					p.S186X		Atlas-SNP	.											.	ZMAT3	42	.	0			c.C557A						.						61	64	63					3																	178745434		2203	4300	6503	SO:0001630	splice_region_variant	64393	exon4			ACCTACGAGAATG	AK122768	CCDS3224.1, CCDS46962.1	3q26.32	2012-10-05	2010-09-15		ENSG00000172667	ENSG00000172667		"Zinc fingers, matrin-type"	29983	protein-coding gene	gene with protein product		606452				9400996, 11689294	Standard	NM_022470		Approved	WIG1, MGC10613, FLJ12296, WIG-1, PAG608	uc003fjg.3	Q9HA38	OTTHUMG00000157290	ENST00000311417.2:c.557+1C>A	chr3.hg19:g.178745434G>T		104.0	0.0		81.0	4.0	NM_022470		Nonsense_Mutation	SNP	ENST00000311417.2	hg19	CCDS3224.1	.	.	.	.	.	.	.	.	.	.	G	42	9.424593	0.99167	.	.	ENSG00000172667	ENST00000311417;ENST00000432729	.	.	.	5.6	4.54	0.55810	.	0.471891	0.24454	N	0.038381	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-28.5812	11.8513	0.52413	0.15:0.0:0.85:0.0	.	.	.	.	X	186	.	.	S	-	2	0	ZMAT3	180228128	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.682000	0.54656	2.635000	0.89317	0.650000	0.86243	TCG	.	.		0.463	ZMAT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348336.2	NM_152240	Nonsense_Mutation	T	178745434	G	T	178745434	5	4	259	1	0	0	0	0	0	0	1	0	17708	1072	37	1	324	1	ZMAT3	3	178745434	Splice_Site	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	2001190	178745434	19276996	191	36509										
EPHB3	2049	hgsc.bcm.edu	37	chr3	184290572	184290572	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctggatggagaacccctacgTgaaagtggacaccattgcac	11	11	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:184290572T>C	ENST00000330394.2	+	3	916	c.464T>C	c.(463-465)gTg>gCg	p.V155A	EIF2B5_ENST00000444495.1_Intron	NM_004443.3	NP_004434.2	P54753	EPHB3_HUMAN	EPH receptor B3	155	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell migration (GO:0016477)|central nervous system projection neuron axonogenesis (GO:0021952)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|digestive tract morphogenesis (GO:0048546)|ephrin receptor signaling pathway (GO:0048013)|palate development (GO:0060021)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of axonogenesis (GO:0050770)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell-cell adhesion (GO:0022407)|regulation of Rac GTPase activity (GO:0032314)|retinal ganglion cell axon guidance (GO:0031290)|substrate adhesion-dependent cell spreading (GO:0034446)|thymus development (GO:0048538)|urogenital system development (GO:0001655)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|ephrin receptor activity (GO:0005003)			breast(5)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_cancers(143;1.89e-10)|Ovarian(172;0.0339)		Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22)			AACCCCTACGTGAAAGTGGAC	0.602																																					p.V155A		Atlas-SNP	.											.	EPHB3	114	.	0			c.T464C						.						75	74	74					3																	184290572		2203	4300	6503	SO:0001583	missense	2049	exon3			CCTACGTGAAAGT	X75208	CCDS3268.1	3q27.1	2013-09-19	2004-10-28		ENSG00000182580	ENSG00000182580		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3394	protein-coding gene	gene with protein product		601839	"EphB3"	ETK2		8397371	Standard	NM_004443		Approved	Hek2, Tyro6	uc003foz.3	P54753	OTTHUMG00000156710	ENST00000330394.2:c.464T>C	chr3.hg19:g.184290572T>C	ENSP00000332118:p.Val155Ala	91.0	0.0		60.0	4.0	NM_004443	Q7Z740	Missense_Mutation	SNP	ENST00000330394.2	hg19	CCDS3268.1	.	.	.	.	.	.	.	.	.	.	T	17.98	3.520275	0.64747	.	.	ENSG00000182580	ENST00000330394	T	0.03496	3.91	5.48	5.48	0.80851	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.147656	0.48286	D	0.000200	T	0.07638	0.0192	L	0.59912	1.85	0.58432	D	0.999995	P	0.36990	0.577	B	0.40825	0.341	T	0.15954	-1.0419	10	0.44086	T	0.13	.	14.7622	0.69614	0.0:0.0:0.0:1.0	.	155	P54753	EPHB3_HUMAN	A	155	ENSP00000332118:V155A	ENSP00000332118:V155A	V	+	2	0	EPHB3	185773266	1.000000	0.71417	0.997000	0.53966	0.989000	0.77384	8.040000	0.89188	2.074000	0.62210	0.459000	0.35465	GTG	.	.		0.602	EPHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345413.1	NM_004443		C	184290572	T	C	184290572	3	2	259	1	0	0	0	0	1	0	0	0	5178	1696	59	2	474	2	EPHB3	3	184290572	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	5545138	184290572	13731858	192	36510										
OSTalpha	200931	hgsc.bcm.edu	37	chr3	195955119	195955119	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cctgctgctgctgctgccccTgctgtccacggctgctgctc	11	18	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:195955119T>C	ENST00000296327.5	+	5	705	c.496T>C	c.(496-498)Tgc>Cgc	p.C166R		NM_152672.5	NP_689885.4	Q86UW1	OSTA_HUMAN	solute carrier family 51, alpha subunit	166	Poly-Cys.				bile acid and bile salt transport (GO:0015721)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)									Conjugated Estrogens(DB00286)|Digoxin(DB00390)|Dinoprostone(DB00917)	ctgctgcccctgctgtccacg	0.677																																					p.C166R		Atlas-SNP	.											.	.	.	.	0			c.T496C						.						66	66	66					3																	195955119		2203	4300	6503	SO:0001583	missense	200931	exon5			TGCCCCTGCTGTC		CCDS3314.1	3q29	2013-05-22			ENSG00000163959	ENSG00000163959		"Solute carriers"	29955	protein-coding gene	gene with protein product	"organic solute transporter, alpha subunit"	612084				12719432, 20538072	Standard	NM_152672		Approved	OSTalpha	uc003fwd.3	Q86UW1	OTTHUMG00000155684	ENST00000296327.5:c.496T>C	chr3.hg19:g.195955119T>C	ENSP00000296327:p.Cys166Arg	82.0	0.0		59.0	4.0	NM_152672	Q6ZMC7	Missense_Mutation	SNP	ENST00000296327.5	hg19	CCDS3314.1	.	.	.	.	.	.	.	.	.	.	T	14.87	2.665807	0.47677	.	.	ENSG00000163959	ENST00000296327	T	0.42131	0.98	5.5	5.5	0.81552	.	0.000000	0.53938	D	0.000046	T	0.67468	0.2896	M	0.83012	2.62	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.72567	-0.4254	10	0.72032	D	0.01	-14.1685	14.9457	0.71029	0.0:0.0:0.0:1.0	.	166	Q86UW1	OSTA_HUMAN	R	166	ENSP00000296327:C166R	ENSP00000296327:C166R	C	+	1	0	AC069257.9	197439516	1.000000	0.71417	1.000000	0.80357	0.103000	0.19146	4.997000	0.63921	2.308000	0.77769	0.533000	0.62120	TGC	.	.		0.677	SLC51A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341253.1	NM_152672		C	195955119	T	C	195955119	3	2	259	1	0	0	0	0	1	0	0	0	11309	1580	55	2	514	2	OSTalpha	3	195955119	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	11664547	195955119	2067311	193	36511										
FBXO45	200933	hgsc.bcm.edu	37	chr3	196304623	196304623	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctggtggacaataatctactAcataatggagaagtcaatgg	10	6	2	1	rs374910244		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:196304623A>T	ENST00000311630.6	+	2	915	c.618A>T	c.(616-618)ctA>ctT	p.L206L	FBXO45_ENST00000440469.1_Silent_p.L27L	NM_001105573.1	NP_001099043.1	P0C2W1	FBSP1_HUMAN	F-box protein 45	206	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				anterior commissure morphogenesis (GO:0021960)|cellular response to DNA damage stimulus (GO:0006974)|cerebral cortex radially oriented cell migration (GO:0021799)|cerebral cortex tangential migration (GO:0021800)|corticospinal tract morphogenesis (GO:0021957)|neuron migration (GO:0001764)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|synapse assembly involved in innervation (GO:0060386)	cell junction (GO:0030054)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				cervix(1)|kidney(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	7	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;2.75e-23)|all cancers(36;2.47e-21)|OV - Ovarian serous cystadenocarcinoma(49;2.32e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)		ATAATCTACTACATAATGGAG	0.478																																					p.L206L		Atlas-SNP	.											.	FBXO45	18	.	0			c.A618T						.						58	58	58					3																	196304623		1947	4155	6102	SO:0001819	synonymous_variant	200933	exon2			TCTACTACATAAT	AK025697	CCDS46985.1	3q29	2008-02-05			ENSG00000174013	ENSG00000174013		"F-boxes /  "other""	29148	protein-coding gene	gene with protein product		609112					Standard	NM_001105573		Approved	Fbx45	uc010iai.3	P0C2W1	OTTHUMG00000155571	ENST00000311630.6:c.618A>T	chr3.hg19:g.196304623A>T		94.0	0.0		49.0	4.0	NM_001105573	A6NF90|D3DXB5	Silent	SNP	ENST00000311630.6	hg19	CCDS46985.1																																																																																			.	.		0.478	FBXO45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340687.2			T	196304623	A	T	196304623	2	4	259	1	0	0	0	0	0	0	0	1	5762	378	14	4		4	FBXO45	3	196304623	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	349504	196304623	1717807	194	36512										
ZNF141	7700	hgsc.bcm.edu	37	chr4	367349	367349	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aatgtgatgaatgtggcaaaGcctttggacggtccagggtc	14	7	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:367349G>T	ENST00000240499.7	+	4	1272	c.1123G>T	c.(1123-1125)Gcc>Tcc	p.A375S	ZNF141_ENST00000505939.1_Intron|ZNF141_ENST00000512994.1_Intron	NM_003441.2	NP_003432.1	Q15928	ZN141_HUMAN	zinc finger protein 141	375					anatomical structure morphogenesis (GO:0009653)|limb morphogenesis (GO:0035108)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|kidney(3)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(1)	18						ATGTGGCAAAGCCTTTGGACG	0.423																																					p.A375S		Atlas-SNP	.											.	ZNF141	48	.	0			c.G1123T						.						44	47	46					4																	367349		2203	4299	6502	SO:0001583	missense	7700	exon4			GGCAAAGCCTTTG	L15309	CCDS33931.1	4p16.3	2013-01-08	2006-06-13			ENSG00000131127		"Zinc fingers, C2H2-type", "-"	12926	protein-coding gene	gene with protein product		194648	"zinc finger protein 141 (clone pHZ-44)"	D4S90		8268908	Standard	NM_003441		Approved	pHZ-44	uc003gaa.2	Q15928		ENST00000240499.7:c.1123G>T	chr4.hg19:g.367349G>T	ENSP00000240499:p.Ala375Ser	122.0	0.0		91.0	4.0	NM_003441	Q6DK07	Missense_Mutation	SNP	ENST00000240499.7	hg19	CCDS33931.1	.	.	.	.	.	.	.	.	.	.	G	17.95	3.513547	0.64522	.	.	ENSG00000131127	ENST00000240499	T	0.18338	2.22	1.24	1.24	0.21308	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10723	0.0262	N	0.16790	0.44	0.24477	N	0.994366	P	0.42337	0.776	P	0.44811	0.461	T	0.18366	-1.0339	8	.	.	.	.	3.6174	0.08082	0.2802:0.0:0.7198:0.0	.	375	Q15928	ZN141_HUMAN	S	375	ENSP00000240499:A375S	.	A	+	1	0	ZNF141	357349	0.000000	0.05858	0.192000	0.23308	0.899000	0.52679	0.077000	0.14738	0.591000	0.29711	0.313000	0.20887	GCC	.	.		0.423	ZNF141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357710.1	NM_003441		T	367349	G	T	367349	3	4	259	1	0	0	0	0	1	0	0	0	17745	971	34	3	1137	3	ZNF141	4	367349	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10		367349	190786927	195	36513										
ZFYVE28	57732	hgsc.bcm.edu	37	chr4	2306996	2306996	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atgggcggtgaaagcaaagaGgacatctcgtcccccgccct	12	13	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:2306996G>A	ENST00000290974.2	-	8	1410	c.1071C>T	c.(1069-1071)tcC>tcT	p.S357S	ZFYVE28_ENST00000511071.1_Silent_p.S327S|ZFYVE28_ENST00000515312.1_Silent_p.S287S|RP11-478C1.7_ENST00000510632.1_RNA	NM_020972.2	NP_066023.2	Q9HCC9	LST2_HUMAN	zinc finger, FYVE domain containing 28	357					negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)	cytosol (GO:0005829)|early endosome membrane (GO:0031901)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	31						AAAGCAAAGAGGACATCTCGT	0.672																																					p.S357S		Atlas-SNP	.											.	ZFYVE28	79	.	0			c.C1071T						.						46	46	46					4																	2306996		2203	4299	6502	SO:0001819	synonymous_variant	57732	exon8			CAAAGAGGACATC	AK126692	CCDS33942.1, CCDS54708.1, CCDS54709.1, CCDS54710.1, CCDS54711.1, CCDS54712.1	4p16.3	2008-05-02			ENSG00000159733	ENSG00000159733		"Zinc fingers, FYVE domain containing"	29334	protein-coding gene	gene with protein product		614176				10997877	Standard	NM_020972		Approved	KIAA1643	uc003gex.2	Q9HCC9	OTTHUMG00000160292	ENST00000290974.2:c.1071C>T	chr4.hg19:g.2306996G>A		109.0	0.0		94.0	4.0	NM_020972	B2RP83|B3KX50|B7Z1Q7|B7Z2G9|B7Z2M2|B7ZB19|E9PB54|E9PB64|E9PG77|Q7Z6J3	Silent	SNP	ENST00000290974.2	hg19	CCDS33942.1																																																																																			.	.		0.672	ZFYVE28-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360078.1	XM_035371		A	2306996	G	A	2306996	2	1	259	1	0	0	0	0	0	0	0	1	17685	987	35	3		3	ZFYVE28	4	2306996	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1939647	2306996	188847280	196	36514										
ADRA2C	152	hgsc.bcm.edu	37	chr4	3768868	3768868	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tcgtggccgtgtggctcatcTcggccgtcatctccttcccg	11	16	4	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:3768868T>C	ENST00000330055.5	+	1	744	c.535T>C	c.(535-537)Tcg>Ccg	p.S179P	ADRA2C_ENST00000509482.1_Missense_Mutation_p.S179P	NM_000683.3	NP_000674.2	P18825	ADA2C_HUMAN	adrenoceptor alpha 2C	179					activation of MAPK activity by adrenergic receptor signaling pathway (GO:0071883)|activation of protein kinase B activity (GO:0032148)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|energy reserve metabolic process (GO:0006112)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|female pregnancy (GO:0007565)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of norepinephrine secretion (GO:0010700)|negative regulation of uterine smooth muscle contraction (GO:0070473)|platelet activation (GO:0030168)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of vasoconstriction (GO:0045907)|regulation of insulin secretion (GO:0050796)|regulation of sensory perception of pain (GO:0051930)|small molecule metabolic process (GO:0044281)	axon terminus (GO:0043679)|cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|alpha2-adrenergic receptor activity (GO:0004938)|epinephrine binding (GO:0051379)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)	8				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)	Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bethanidine(DB00217)|Brimonidine(DB00484)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Clozapine(DB00363)|Desipramine(DB01151)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Fenoldopam(DB00800)|Iloperidone(DB04946)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methamphetamine(DB01577)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxymetazoline(DB00935)|Paliperidone(DB01267)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Pramipexole(DB00413)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Tizanidine(DB00697)|Tolazoline(DB00797)|Xylometazoline(DB06694)|Yohimbine(DB01392)|Ziprasidone(DB00246)	GTGGCTCATCTCGGCCGTCAT	0.677																																					p.S179P	Esophageal Squamous(12;454 628 4517 14479)	Atlas-SNP	.											.	ADRA2C	24	.	0			c.T535C						.						30	30	30					4																	3768868		2201	4295	6496	SO:0001583	missense	152	exon1			CTCATCTCGGCCG	AY455666	CCDS47004.1	4p16.3	2013-10-22	2012-05-09		ENSG00000184160	ENSG00000184160		"GPCR / Class A : Adrenoceptors : alpha"	283	protein-coding gene	gene with protein product		104250	"adrenergic, alpha-2C-, receptor"	ADRA2L2, ADRA2RL2		1849485	Standard	NM_000683		Approved	ADRARL2	uc003ghm.3	P18825	OTTHUMG00000159830	ENST00000330055.5:c.535T>C	chr4.hg19:g.3768868T>C	ENSP00000386069:p.Ser179Pro	157.0	0.0		91.0	5.0	NM_000683	P35369|Q9HB49	Missense_Mutation	SNP	ENST00000330055.5	hg19	CCDS47004.1	.	.	.	.	.	.	.	.	.	.	T	18.41	3.618455	0.66787	.	.	ENSG00000184160	ENST00000509482;ENST00000330055	T;T	0.46063	0.88;0.88	3.37	3.37	0.38596	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.61299	0.2336	M	0.74389	2.26	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.77557	0.985;0.99	T	0.65307	-0.6200	9	0.72032	D	0.01	.	11.1249	0.48312	0.0:0.0:0.0:1.0	.	179;179	D6RGL0;P18825	.;ADA2C_HUMAN	P	179	ENSP00000426268:S179P;ENSP00000386069:S179P	ENSP00000386069:S179P	S	+	1	0	ADRA2C	3738666	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.806000	0.38892	1.394000	0.46624	0.459000	0.35465	TCG	.	.		0.677	ADRA2C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357607.1	NM_000683		C	3768868	T	C	3768868	3	2	259	1	0	0	0	0	1	0	0	0	339	1551	54	2	537	2	ADRA2C	4	3768868	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1461872	3768868	187385408	197	36515										
SLC34A2	10568	hgsc.bcm.edu	37	chr4	25678341	25678341	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cagggtgaggtccctgcctcGgactcaaagaccgaatgcac	12	13	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:25678341G>T	ENST00000382051.3	+	13	2093	c.2043G>T	c.(2041-2043)tcG>tcT	p.S681S	SLC34A2_ENST00000503434.1_Silent_p.S680S|SLC34A2_ENST00000504570.1_Silent_p.S680S	NM_001177998.1|NM_006424.2	NP_001171469.1|NP_006415	O95436	NPT2B_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 2	681					aging (GO:0007568)|cellular phosphate ion homeostasis (GO:0030643)|in utero embryonic development (GO:0001701)|ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|response to fructose (GO:0009750)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	phosphate ion binding (GO:0042301)|sodium ion binding (GO:0031402)|sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|sodium:phosphate symporter activity (GO:0005436)	p.S681S(1)	SLC34A2/ROS1(14)	breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|skin(4)	41		Breast(46;0.0503)				TCCCTGCCTCGGACTCAAAGA	0.582			T	ROS1	NSCLC																																p.S681S		Atlas-SNP	.		Dom	yes		4	4p15.2	10568	"solute carrier family 34 (sodium phosphate), member 2"		E	SLC34A2,NS,carcinoma,0,2	SLC34A2	93	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2043T						.						56	57	57					4																	25678341		2203	4300	6503	SO:0001819	synonymous_variant	10568	exon13			TGCCTCGGACTCA	AF111856	CCDS3435.1, CCDS54750.1	4p15.2	2013-07-17	2013-07-17		ENSG00000157765	ENSG00000157765		"Solute carriers"	11020	protein-coding gene	gene with protein product		604217	"solute carrier family 34 (sodium phosphate), member 2"			10329428, 10610722	Standard	NM_006424		Approved	NAPI-3B	uc003grr.3	O95436	OTTHUMG00000097757	ENST00000382051.3:c.2043G>T	chr4.hg19:g.25678341G>T		99.0	1.0		66.0	3.0	NM_006424	A5PL17|Q8N2K2|Q8WYA9|Q9P0V7	Silent	SNP	ENST00000382051.3	hg19	CCDS3435.1																																																																																			.	.		0.582	SLC34A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214990.1	NM_006424		T	25678341	G	T	25678341	2	4	259	1	0	0	0	0	0	0	0	1	14583	1103	39	1		1	SLC34A2	4	25678341	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	21909473	25678341	165475935	198	36516										
PGM2	55276	hgsc.bcm.edu	37	chr4	37847313	37847313	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	attgttttagctaacgacccGgatgctgatagacttgctgt	10	8	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:37847313G>T	ENST00000381967.4	+	8	1069	c.969G>T	c.(967-969)ccG>ccT	p.P323P	PGM2_ENST00000537241.1_Silent_p.P163P|PGM2_ENST00000544359.1_Silent_p.P184P	NM_018290.3	NP_060760.2	Q96G03	PGM2_HUMAN	phosphoglucomutase 2	323					carbohydrate metabolic process (GO:0005975)|deoxyribose phosphate catabolic process (GO:0046386)|galactose catabolic process (GO:0019388)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	magnesium ion binding (GO:0000287)|phosphoglucomutase activity (GO:0004614)|phosphopentomutase activity (GO:0008973)			breast(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(2)|urinary_tract(1)	19						CTAACGACCCGGATGCTGATA	0.333																																					p.P323P		Atlas-SNP	.											.	PGM2	45	.	0			c.G969T						.						104	108	107					4																	37847313		2203	4300	6503	SO:0001819	synonymous_variant	55276	exon8			CGACCCGGATGCT	BC010087	CCDS3443.1	4p14	2012-10-02			ENSG00000169299	ENSG00000169299	5.4.2.2		8906	protein-coding gene	gene with protein product	"phosphopentomutase"	172000				9549096	Standard	NM_018290		Approved	FLJ10983	uc011byb.1	Q96G03	OTTHUMG00000097813	ENST00000381967.4:c.969G>T	chr4.hg19:g.37847313G>T		128.0	0.0		98.0	4.0	NM_018290	B4E0G8|Q53FP5|Q5QTR0|Q9H0P9|Q9NV22	Silent	SNP	ENST00000381967.4	hg19	CCDS3443.1																																																																																			.	.		0.333	PGM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215079.2	NM_018290		T	37847313	G	T	37847313	2	4	259	1	0	0	0	0	0	0	0	1	11807	1103	39	1		1	PGM2	4	37847313	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	12168972	37847313	153306963	199	36517										
TBC1D1	23216	hgsc.bcm.edu	37	chr4	38055861	38055861	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccatcttggtgattctggtgGgactcctgtgaagacccgga	13	10	2	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:38055861G>T	ENST00000261439.4	+	12	2307	c.1952G>T	c.(1951-1953)gGg>gTg	p.G651V	TBC1D1_ENST00000508802.1_Missense_Mutation_p.G745V	NM_001253914.1|NM_001253915.1|NM_015173.3	NP_001240843.1|NP_001240844.1|NP_055988.2	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1	651					membrane organization (GO:0061024)|regulation of protein localization (GO:0032880)	cytosol (GO:0005829)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)			NS(1)|breast(3)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	36						GATTCTGGTGGGACTCCTGTG	0.473																																					p.G745V		Atlas-SNP	.											.	TBC1D1	94	.	0			c.G2234T						.						111	122	118					4																	38055861		2203	4300	6503	SO:0001583	missense	23216	exon14			CTGGTGGGACTCC	AB029031	CCDS33972.1, CCDS58897.1	4p14	2013-07-09			ENSG00000065882	ENSG00000065882			11578	protein-coding gene	gene with protein product		609850				10965142, 18258599	Standard	NM_015173		Approved	TBC, TBC1, KIAA1108	uc003gtb.3	Q86TI0	OTTHUMG00000150302	ENST00000261439.4:c.1952G>T	chr4.hg19:g.38055861G>T	ENSP00000261439:p.Gly651Val	92.0	0.0		70.0	4.0	NM_001253912	B7Z3D9|E9PGH8|Q96K82|Q9UPP4	Missense_Mutation	SNP	ENST00000261439.4	hg19	CCDS33972.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	10.64|10.64|10.64	1.408372|1.408372|1.408372	0.25378|0.25378|0.25378	.|.|.	.|.|.	ENSG00000065882|ENSG00000065882|ENSG00000065882	ENST00000508802;ENST00000261439;ENST00000446803;ENST00000421339|ENST00000513936;ENST00000443855|ENST00000510573	T;T;T;T|.|.	0.56611|.|.	3.49;0.45;0.45;0.45|.|.	5.55|5.55|5.55	2.46|2.46|2.46	0.29980|0.29980|0.29980	.|.|.	0.436222|0.436222|.	0.21738|0.21738|.	N|N|.	0.069863|0.069863|.	T|.|T	0.55081|.|0.55081	0.1898|.|0.1898	L|L|L	0.49778|0.49778|0.49778	1.585|1.585|1.585	0.80722|0.80722|0.80722	D|D|D	1|1|1	P;P;B;P|.|.	0.40660|.|.	0.726;0.59;0.314;0.726|.|.	P;B;B;P|.|.	0.50970|.|.	0.655;0.424;0.174;0.655|.|.	T|.|T	0.48103|.|0.48103	-0.9064|.|-0.9064	10|.|5	0.87932|0.54805|.	D|T|.	0|0.06|.	-12.8101|-12.8101|-12.8101	6.9507|6.9507|6.9507	0.24544|0.24544|0.24544	0.4656:0.0:0.5343:0.0|0.4656:0.0:0.5343:0.0|0.4656:0.0:0.5343:0.0	.|.|.	651;745;383;651|.|.	B9A6J6;E9PGH8;Q6PJJ8;Q86TI0|.|.	.;.;.;TBCD1_HUMAN|.|.	V|X|C	745;651;522;119|176;197|338	ENSP00000423651:G745V;ENSP00000261439:G651V;ENSP00000396877:G522V;ENSP00000410167:G119V|.|.	ENSP00000261439:G651V|ENSP00000397640:G197X|.	G|G|W	+|+|+	2|1|3	0|0|0	TBC1D1|TBC1D1|TBC1D1	37732256|37732256|37732256	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.831000|0.831000|0.831000	0.32960|0.32960|0.32960	0.241000|0.241000|0.241000	0.25554|0.25554|0.25554	2.314000|2.314000|2.314000	0.43743|0.43743|0.43743	0.720000|0.720000|0.720000	0.32209|0.32209|0.32209	-0.136000|-0.136000|-0.136000	0.14681|0.14681|0.14681	GGG|GGA|TGG	.	.		0.473	TBC1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317443.2	NM_015173		T	38055861	G	T	38055861	3	4	259	1	0	0	0	0	1	0	0	0	15612	1232	43	3	1994	3	TBC1D1	4	38055861	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	208548	38055861	153098415	200	36518										
TLR10	81793	hgsc.bcm.edu	37	chr4	38776477	38776477	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	actttattaagcaatagaacCgatgtcttagcattttctaa	5	7	2	1	rs578031272		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:38776477C>A	ENST00000308973.4	-	4	1340	c.735G>T	c.(733-735)tcG>tcT	p.S245S	TLR10_ENST00000507953.1_5'Flank|TLR10_ENST00000361424.2_Silent_p.S245S|TLR10_ENST00000506111.1_Silent_p.S245S|TLR10_ENST00000508334.1_Silent_p.S245S	NM_001017388.2|NM_001195107.1|NM_030956.3	NP_001017388.1|NP_001182036.1|NP_112218.2	Q9BXR5	TLR10_HUMAN	toll-like receptor 10	245					immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of inflammatory response (GO:0050729)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(2)	25						GCAATAGAACCGATGTCTTAG	0.323																																					p.S245S		Atlas-SNP	.											.	TLR10	87	.	0			c.G735T						.						63	62	62					4																	38776477		2203	4300	6503	SO:0001819	synonymous_variant	81793	exon2			TAGAACCGATGTC	AF296673	CCDS3445.1	4p14	2009-11-23			ENSG00000174123	ENSG00000174123		"CD molecules"	15634	protein-coding gene	gene with protein product		606270				11267672	Standard	NM_030956		Approved	CD290	uc003gtk.3	Q9BXR5	OTTHUMG00000128578	ENST00000308973.4:c.735G>T	chr4.hg19:g.38776477C>A		130.0	0.0		109.0	5.0	NM_001017388	A8K7L1|B3Y668|D1CS21|D1CS22|Q32MI7|Q32MI8|Q5FWG4|Q6UXL3	Silent	SNP	ENST00000308973.4	hg19	CCDS3445.1																																																																																			.	.		0.323	TLR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250430.1			A	38776477	C	A	38776477	2	1	259	1	0	0	0	0	0	0	0	1	15965	639	23	1		1	TLR10	4	38776477	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	720616	38776477	152377799	201	36519										
UGDH	7358	hgsc.bcm.edu	37	chr4	39511398	39511398	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	accaacactggcttttagaaActtgtttccaattctctggt	6	10	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:39511398A>G	ENST00000316423.6	-	6	1135	c.793T>C	c.(793-795)Ttt>Ctt	p.F265L	UGDH_ENST00000501493.2_Missense_Mutation_p.F198L|UGDH_ENST00000515398.1_5'Flank|UGDH_ENST00000507089.1_Missense_Mutation_p.F168L|UGDH_ENST00000506179.1_Missense_Mutation_p.F265L	NM_001184701.1|NM_003359.3	NP_001171630.1|NP_003350.1	O60701	UGDH_HUMAN	UDP-glucose 6-dehydrogenase	265	Substrate binding.				cellular glucuronidation (GO:0052695)|gastrulation with mouth forming second (GO:0001702)|glycosaminoglycan biosynthetic process (GO:0006024)|small molecule metabolic process (GO:0044281)|UDP-glucose metabolic process (GO:0006011)|UDP-glucuronate biosynthetic process (GO:0006065)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|NAD binding (GO:0051287)|UDP-glucose 6-dehydrogenase activity (GO:0003979)			breast(1)|central_nervous_system(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(2)	27						GCTTTTAGAAACTTGTTTCCA	0.388																																					p.F265L		Atlas-SNP	.											.	UGDH	52	.	0			c.T793C						.						132	131	132					4																	39511398		2203	4300	6503	SO:0001583	missense	7358	exon6			TTAGAAACTTGTT	AF061016	CCDS3455.1, CCDS54757.1, CCDS54758.1	4p14	2011-11-16	2010-04-28		ENSG00000109814	ENSG00000109814	1.1.1.22		12525	protein-coding gene	gene with protein product		603370	"UDP-glucose dehydrogenase"			9737970, 10575217	Standard	NM_003359		Approved		uc003guk.2	O60701	OTTHUMG00000099371	ENST00000316423.6:c.793T>C	chr4.hg19:g.39511398A>G	ENSP00000319501:p.Phe265Leu	90.0	0.0		77.0	4.0	NM_003359	B3KUU2|B4DN25|O60589	Missense_Mutation	SNP	ENST00000316423.6	hg19	CCDS3455.1	.	.	.	.	.	.	.	.	.	.	A	29.7	5.027330	0.93518	.	.	ENSG00000109814	ENST00000316423;ENST00000501493;ENST00000506179;ENST00000507089	D;T;D;D	0.84873	-1.91;-1.29;-1.91;-1.89	5.51	5.51	0.81932	UDP-glucose/GDP-mannose dehydrogenase, dimerisation (1);NAD(P)-binding domain (1);6-phosphogluconate dehydrogenase, C-terminal-like (1);	0.000000	0.85682	D	0.000000	D	0.95642	0.8583	H	0.99011	4.4	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.951	D	0.97443	1.0023	10	0.87932	D	0	-9.485	15.1102	0.72349	1.0:0.0:0.0:0.0	.	198;265	B3KUU2;O60701	.;UGDH_HUMAN	L	265;198;265;168	ENSP00000319501:F265L;ENSP00000422909:F198L;ENSP00000421757:F265L;ENSP00000426560:F168L	ENSP00000319501:F265L	F	-	1	0	UGDH	39187793	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.569000	0.90744	2.213000	0.71641	0.528000	0.53228	TTT	.	.		0.388	UGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216818.3	NM_003359		G	39511398	A	G	39511398	3	3	259	1	0	0	0	0	1	0	0	0	16955	43	2	2	719	2	UGDH	4	39511398	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	734921	39511398	151642878	202	36520										
PDS5A	23244	hgsc.bcm.edu	37	chr4	39850470	39850470	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aaatgagaggaagaaaattaCcttttcaggttgtgtaaaaa	9	3	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:39850470C>T	ENST00000303538.8	-	28	3879		c.e28+1			NM_001100399.1	NP_001093869.1			PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae)											breast(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(14)|prostate(3)|skin(1)|urinary_tract(1)	39						AAGAAAATTACCTTTTCAGGT	0.368																																					.		Atlas-SNP	.											.	PDS5A	114	.	0			c.3339+1G>A						.						77	75	76					4																	39850470		1830	4087	5917	SO:0001630	splice_region_variant	23244	exon29			AAATTACCTTTTC	AF294791	CCDS47045.1, CCDS54759.1	4p14	2007-06-20			ENSG00000121892	ENSG00000121892			29088	protein-coding gene	gene with protein product		613200				11076961, 15855230	Standard	NM_001100399		Approved	KIAA0648, PIG54, SCC-112	uc003guv.4	Q29RF7	OTTHUMG00000160582	ENST00000303538.8:c.3339+1G>A	chr4.hg19:g.39850470C>T		80.0	0.0		65.0	4.0	NM_001100399		Splice_Site	SNP	ENST00000303538.8	hg19	CCDS47045.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.364380	0.82463	.	.	ENSG00000121892	ENST00000303538	.	.	.	5.47	5.47	0.80525	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.3219	0.94245	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PDS5A	39526865	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.298000	0.78815	2.538000	0.85594	0.655000	0.94253	.	.	.		0.368	PDS5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361287.1	NM_015200	Intron	T	39850470	C	T	39850470	5	4	259	1	0	0	0	0	0	0	1	0	11700	521	18	3	697	3	PDS5A	4	39850470	Splice_Site	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	339072	39850470	151303806	203	36521										
NSUN7	79730	hgsc.bcm.edu	37	chr4	40800850	40800850	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgcacatgttcagtttttccAgaagaaaatgaagctgttgt	9	6	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:40800850A>G	ENST00000381782.2	+	10	1824	c.1329A>G	c.(1327-1329)ccA>ccG	p.P443P	NSUN7_ENST00000316607.5_Silent_p.P443P	NM_024677.4	NP_078953	Q8NE18	NSUN7_HUMAN	NOP2/Sun domain family, member 7	443							methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|cervix(1)|large_intestine(1)|lung(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	12						CAGTTTTTCCAGAAGAAAATG	0.338																																					p.P443P		Atlas-SNP	.											.	NSUN7	70	.	0			c.A1329G						.						96	100	98					4																	40800850		2202	4299	6501	SO:0001819	synonymous_variant	79730	exon10			TTTTCCAGAAGAA	BC036568	CCDS3461.2	4p14	2013-10-11	2009-11-23		ENSG00000179299	ENSG00000179299		"NOP2/Sun domain containing"	25857	protein-coding gene	gene with protein product			"NOL1/NOP2/Sun domain family, member 7"			17442852	Standard	NM_024677		Approved	FLJ14001	uc003gvj.4	Q8NE18	OTTHUMG00000128597	ENST00000381782.2:c.1329A>G	chr4.hg19:g.40800850A>G		109.0	0.0		94.0	4.0	NM_024677	C9JI19|Q8N9K8|Q9H815	Silent	SNP	ENST00000381782.2	hg19	CCDS3461.2																																																																																			.	.		0.338	NSUN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250454.2	NM_024677		G	40800850	A	G	40800850	2	3	259	1	0	0	0	0	0	0	0	1	10692	175	7	2		2	NSUN7	4	40800850	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	950380	40800850	150353426	204	36522										
GABRB1	2560	hgsc.bcm.edu	37	chr4	47427703	47427703	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gccatcaggtcgacgcccacGgtaacattctcctcagcacc	8	17	3	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:47427703G>T	ENST00000295454.3	+	9	1385	c.1093G>T	c.(1093-1095)Ggt>Tgt	p.G365C	GABRB1_ENST00000538619.1_Missense_Mutation_p.G295C	NM_000812.3	NP_000803.2	P18505	GBRB1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 1	365					cellular response to histamine (GO:0071420)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|ligand-gated ion channel activity (GO:0015276)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44					Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Gamma Hydroxybutyric Acid(DB01440)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lindane(DB00431)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CGACGCCCACGGTAACATTCT	0.522																																					p.G365C		Atlas-SNP	.											.	GABRB1	107	.	0			c.G1093T						.						78	74	76					4																	47427703		2203	4300	6503	SO:0001583	missense	2560	exon9			GCCCACGGTAACA		CCDS3474.1	4p12	2012-06-22			ENSG00000163288	ENSG00000163288		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4081	protein-coding gene	gene with protein product	"GABA(A) receptor, beta 1"	137190					Standard	NM_000812		Approved		uc003gxh.3	P18505	OTTHUMG00000044269	ENST00000295454.3:c.1093G>T	chr4.hg19:g.47427703G>T	ENSP00000295454:p.Gly365Cys	85.0	0.0		96.0	4.0	NM_000812	B2R6U7|D6REL3|Q16166|Q8TBK3	Missense_Mutation	SNP	ENST00000295454.3	hg19	CCDS3474.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.685643	0.88639	.	.	ENSG00000163288	ENST00000295454;ENST00000538619	D;D	0.85556	-2.0;-2.0	5.48	5.48	0.80851	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.915575	0.09463	N	0.798742	D	0.93390	0.7892	M	0.79258	2.445	0.80722	D	1	D;D	0.89917	0.996;1.0	D;D	0.78314	0.931;0.991	D	0.90947	0.4802	10	0.87932	D	0	-23.5004	19.5559	0.95347	0.0:0.0:1.0:0.0	.	295;365	F5GXV5;P18505	.;GBRB1_HUMAN	C	365;295	ENSP00000295454:G365C;ENSP00000440330:G295C	ENSP00000295454:G365C	G	+	1	0	GABRB1	47122460	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	9.519000	0.98025	2.861000	0.98227	0.650000	0.86243	GGT	.	.		0.522	GABRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216896.1			T	47427703	G	T	47427703	3	4	259	1	0	0	0	0	1	0	0	0	6174	1116	39	1	1127	1	GABRB1	4	47427703	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	6626853	47427703	143726573	205	36523										
CORIN	10699	hgsc.bcm.edu	37	chr4	47628491	47628491	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tggagtgtaatgtcagccacCgcggctctttctcctgttcc	10	13	3	0	rs373955478		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:47628491C>A	ENST00000273857.4	-	17	2245	c.2246G>T	c.(2245-2247)cGg>cTg	p.R749L	CORIN_ENST00000508498.1_Missense_Mutation_p.R610L|CORIN_ENST00000515827.1_5'UTR|CORIN_ENST00000502252.1_Missense_Mutation_p.R682L|CORIN_ENST00000505909.1_Missense_Mutation_p.R712L	NM_006587.2	NP_006578.2	Q9Y5Q5	CORIN_HUMAN	corin, serine peptidase	749	SRCR.				female pregnancy (GO:0007565)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of blood pressure (GO:0008217)|regulation of renal sodium excretion (GO:0035813)|regulation of systemic arterial blood pressure by atrial natriuretic peptide (GO:0003050)	cell surface (GO:0009986)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)			NS(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(18)|lung(39)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)	79						TGTCAGCCACCGCGGCTCTTT	0.418																																					p.R749L		Atlas-SNP	.											.	CORIN	154	.	0			c.G2246T						.						179	170	173					4																	47628491		2203	4300	6503	SO:0001583	missense	10699	exon17			AGCCACCGCGGCT	AF133845	CCDS3477.1, CCDS63958.1, CCDS75122.1	4p13-p12	2011-08-31	2005-08-17		ENSG00000145244	ENSG00000145244		"Serine peptidases / Transmembrane"	19012	protein-coding gene	gene with protein product		605236	"corin, serine protease"			10329693	Standard	NM_006587		Approved	PRSC, CRN, ATC2, Lrp4, TMPRSS10	uc003gxm.3	Q9Y5Q5	OTTHUMG00000099441	ENST00000273857.4:c.2246G>T	chr4.hg19:g.47628491C>A	ENSP00000273857:p.Arg749Leu	156.0	0.0		122.0	5.0	NM_006587	B0ZBE3|Q2TBD2|Q4W5E5|Q4W5G6|Q9UHY2	Missense_Mutation	SNP	ENST00000273857.4	hg19	CCDS3477.1	.	.	.	.	.	.	.	.	.	.	C	2.407	-0.336151	0.05278	.	.	ENSG00000145244	ENST00000273857;ENST00000508498;ENST00000502252;ENST00000505909	T;T;T;T	0.59772	0.24;0.24;0.24;0.78	5.26	-7.29	0.01451	Speract/scavenger receptor-related (2);	0.847295	0.10512	N	0.665971	T	0.27765	0.0683	N	0.12182	0.205	0.19775	N	0.999954	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.40515	-0.9559	10	0.06891	T	0.86	.	9.922	0.41470	0.0:0.1303:0.5796:0.29	.	682;749	B4E1Y7;Q9Y5Q5	.;CORIN_HUMAN	L	749;610;682;712	ENSP00000273857:R749L;ENSP00000425597:R610L;ENSP00000424212:R682L;ENSP00000425401:R712L	ENSP00000273857:R749L	R	-	2	0	CORIN	47323248	0.000000	0.05858	0.023000	0.16930	0.004000	0.04260	-0.340000	0.07821	-1.267000	0.02443	-1.910000	0.00522	CGG	.	.		0.418	CORIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216906.2			A	47628491	C	A	47628491	3	1	259	1	0	0	0	0	1	0	0	0	3754	652	23	1	906	1	CORIN	4	47628491	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	200788	47628491	143525785	206	36524										
SGCB	6443	hgsc.bcm.edu	37	chr4	52890227	52890227	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agcacacatgcagagcttgtAgcgtacccagtcaccactac	8	14	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:52890227A>G	ENST00000381431.5	-	6	1075	c.853T>C	c.(853-855)Tac>Cac	p.Y285H	SGCB_ENST00000535450.1_Missense_Mutation_p.Y215H	NM_000232.4	NP_000223.1	Q16585	SGCB_HUMAN	sarcoglycan, beta (43kDa dystrophin-associated glycoprotein)	285	Cys-rich.				cardiac muscle cell development (GO:0055013)|muscle fiber development (GO:0048747)|muscle organ development (GO:0007517)|vascular smooth muscle cell development (GO:0097084)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of plasma membrane (GO:0005887)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)				breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(6)|prostate(1)	17			GBM - Glioblastoma multiforme(4;7.63e-12)|LUSC - Lung squamous cell carcinoma(32;0.00204)			CAGAGCTTGTAGCGTACCCAG	0.527																																					p.Y285H		Atlas-SNP	.											.	SGCB	35	.	0			c.T853C						.						120	102	108					4																	52890227		2203	4300	6503	SO:0001583	missense	6443	exon6			GCTTGTAGCGTAC	U29586	CCDS3488.1	4q12	2014-09-17	2002-08-29		ENSG00000163069	ENSG00000163069			10806	protein-coding gene	gene with protein product		600900	"sarcoglycan, beta (43kD dystrophin-associated glycoprotein)"	LGMD2E		8968749	Standard	NM_000232		Approved	SGC, A3b	uc003gzj.2	Q16585	OTTHUMG00000128697	ENST00000381431.5:c.853T>C	chr4.hg19:g.52890227A>G	ENSP00000370839:p.Tyr285His	183.0	0.0		133.0	17.0	NM_000232	B7Z635|O00661	Missense_Mutation	SNP	ENST00000381431.5	hg19	CCDS3488.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.982405	0.74474	.	.	ENSG00000163069	ENST00000381431;ENST00000535450	D;D	0.96885	-4.16;-4.16	5.3	5.3	0.74995	.	0.055782	0.64402	D	0.000001	D	0.97433	0.9160	M	0.73217	2.22	0.53688	D	0.999974	D;D	0.56287	0.975;0.975	P;P	0.62298	0.9;0.845	D	0.98100	1.0414	10	0.87932	D	0	-31.5733	14.7196	0.69297	1.0:0.0:0.0:0.0	.	215;285	B7Z635;Q16585	.;SGCB_HUMAN	H	285;215	ENSP00000370839:Y285H;ENSP00000441199:Y215H	ENSP00000370839:Y285H	Y	-	1	0	SGCB	52584984	1.000000	0.71417	0.993000	0.49108	0.235000	0.25334	9.134000	0.94467	2.129000	0.65627	0.482000	0.46254	TAC	.	.		0.527	SGCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250596.2			G	52890227	A	G	52890227	3	3	259	1	0	0	0	0	1	0	0	0	14215	420	15	2	107	2	SGCB	4	52890227	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	5261736	52890227	138264049	207	36525										
KIAA1211	57482	hgsc.bcm.edu	37	chr4	57181298	57181298	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acacgttccaggtgtcctccGgagggaagcagattctcttt	11	11	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:57181298G>T	ENST00000504228.1	+	6	1735	c.1630G>T	c.(1630-1632)Gga>Tga	p.G544*	KIAA1211_ENST00000264229.6_Nonsense_Mutation_p.G544*|KIAA1211_ENST00000541073.1_Nonsense_Mutation_p.G537*			Q6ZU35	K1211_HUMAN	KIAA1211	544										endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					GGTGTCCTCCGGAGGGAAGCA	0.647																																					p.G544X		Atlas-SNP	.											.	KIAA1211	178	.	0			c.G1630T						.						15	21	19					4																	57181298		2035	4174	6209	SO:0001587	stop_gained	57482	exon8			TCCTCCGGAGGGA	AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.1630G>T	chr4.hg19:g.57181298G>T	ENSP00000423366:p.Gly544*	152.0	0.0		91.0	4.0	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Nonsense_Mutation	SNP	ENST00000504228.1	hg19	CCDS43230.1	.	.	.	.	.	.	.	.	.	.	G	39	7.345149	0.98224	.	.	ENSG00000109265	ENST00000264229;ENST00000504228;ENST00000541073;ENST00000546221	.	.	.	4.86	4.86	0.63082	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-27.0663	17.9911	0.89169	0.0:0.0:1.0:0.0	.	.	.	.	X	544;544;537;454	.	ENSP00000264229:G544X	G	+	1	0	KIAA1211	56876055	1.000000	0.71417	0.070000	0.20053	0.886000	0.51366	7.489000	0.81451	2.229000	0.72834	0.561000	0.74099	GGA	.	.		0.647	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722		T	57181298	G	T	57181298	4	4	259	1	0	0	0	0	0	1	0	0	8224	1117	39	1	1648	1	KIAA1211	4	57181298	Nonsense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	4291071	57181298	133972978	208	36526										
SLC4A4	8671	hgsc.bcm.edu	37	chr4	72412214	72412214	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tggagacagagacttctgcaCctggagaacaaccaaagttt	10	9	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:72412214C>A	ENST00000264485.5	+	19	2707	c.2590C>A	c.(2590-2592)Cct>Act	p.P864T	SLC4A4_ENST00000351898.6_Intron|SLC4A4_ENST00000340595.3_Missense_Mutation_p.P820T|SLC4A4_ENST00000425175.1_Missense_Mutation_p.P864T	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4	864					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	58			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)		Sodium bicarbonate(DB01390)	GACTTCTGCACCTGGAGAACA	0.473																																					p.P864T		Atlas-SNP	.											.	SLC4A4	269	.	0			c.C2590A						.						110	88	96					4																	72412214		2203	4300	6503	SO:0001583	missense	8671	exon19			TCTGCACCTGGAG	AF007216	CCDS3549.1, CCDS43236.1, CCDS47071.1	4q13.3	2013-07-19	2013-07-19		ENSG00000080493	ENSG00000080493		"Solute carriers"	11030	protein-coding gene	gene with protein product		603345	"solute carrier family 4, sodium bicarbonate cotransporter, member 4"	SLC4A5		9235899, 9651366	Standard	NM_001098484		Approved	NBC1, HNBC1, NBC2, pNBC, hhNMC	uc010iic.3	Q9Y6R1	OTTHUMG00000129907	ENST00000264485.5:c.2590C>A	chr4.hg19:g.72412214C>A	ENSP00000264485:p.Pro864Thr	67.0	0.0		80.0	4.0	NM_001098484	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Missense_Mutation	SNP	ENST00000264485.5	hg19	CCDS43236.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.993049	0.93167	.	.	ENSG00000080493	ENST00000264485;ENST00000425175;ENST00000340595	D;D;D	0.88354	-2.37;-2.37;-2.37	5.76	5.76	0.90799	Bicarbonate transporter, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.94938	0.8363	M	0.80616	2.505	0.80722	D	1	D;D;D	0.76494	0.999;0.998;0.999	D;D;D	0.77557	0.99;0.972;0.99	D	0.94949	0.8098	10	0.87932	D	0	.	19.976	0.97309	0.0:1.0:0.0:0.0	.	864;820;864	A5JJ20;Q9Y6R1-2;Q9Y6R1	.;.;S4A4_HUMAN	T	864;864;820	ENSP00000264485:P864T;ENSP00000393557:P864T;ENSP00000344272:P820T	ENSP00000264485:P864T	P	+	1	0	SLC4A4	72631078	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.818000	0.86416	2.713000	0.92767	0.655000	0.94253	CCT	.	.		0.473	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759		A	72412214	C	A	72412214	3	1	259	1	0	0	0	0	1	0	0	0	14671	507	18	3	2781	3	SLC4A4	4	72412214	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	15230916	72412214	118742062	209	36527										
ALB	213	hgsc.bcm.edu	37	chr4	74275125	74275126	+	Frame_Shift_Ins	INS	-	-	C													0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttttatgccccggaactcctINStttctttgctaaaaggtata							TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:74275125_74275126insC	ENST00000503124.1	+	3	293_294	c.86_87insC	c.(85-90)cttttcfs	p.LF29fs	ALB_ENST00000509063.1_Frame_Shift_Ins_p.LF179fs|ALB_ENST00000415165.2_Intron|ALB_ENST00000401494.3_Frame_Shift_Ins_p.LF64fs|ALB_ENST00000295897.4_Frame_Shift_Ins_p.LF179fs|ALB_ENST00000505649.1_3'UTR			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CCGGAACTCCTTTTCTTTGCTA	0.351																																					p.L179fs		Atlas-INDEL	.											.	ALB	132	.	0			c.536_537insC						.																																			SO:0001589	frameshift_variant	213	exon5			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	Exception_encountered	chr4.hg19:g.74275125_74275126insC	ENSP00000421027:p.Leu29fs	388.0	0.0		297.0	154.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Frame_Shift_Ins	INS	ENST00000503124.1	hg19																																																																																				.	.		0.351	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		C	74275126	-	C	74275125	7	5	259	1	0	1	1	0	0	0	0	0	486	1609	56	0	554	0	ALB	4	74275125	Frame_Shift_Ins	INS	-	TCGA-ES-A2HS-01A-11D-A183-10	1862911	74275125	116879151	210	36528	184	2								
ALB	213	hgsc.bcm.edu	37	chr4	74275126	74275126	+	Silent	SNP	T	T	C													0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttttatgccccggaactcctTttctttgctaaaaggtataa							TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:74275126T>C	ENST00000503124.1	+	3	294	c.87T>C	c.(85-87)ctT>ctC	p.L29L	ALB_ENST00000509063.1_Silent_p.L179L|ALB_ENST00000415165.2_Intron|ALB_ENST00000401494.3_Silent_p.L64L|ALB_ENST00000295897.4_Silent_p.L179L|ALB_ENST00000505649.1_3'UTR			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CGGAACTCCTTTTCTTTGCTA	0.353																																					p.L179L		Atlas-SNP	.											.	ALB	132	.	0			c.T537C						.						72	76	75					4																	74275126		2203	4299	6502	SO:0001819	synonymous_variant	213	exon5			ACTCCTTTTCTTT	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.87T>C	chr4.hg19:g.74275126T>C		388.0	0.0		293.0	172.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Silent	SNP	ENST00000503124.1	hg19		.	.	.	.	.	.	.	.	.	.	T	14.14	2.447201	0.43429	.	.	ENSG00000163631	ENST00000511370	.	.	.	5.55	-3.31	0.04988	.	.	.	.	.	T	0.41696	0.1170	.	.	.	0.46149	D	0.998893	.	.	.	.	.	.	T	0.33624	-0.9861	4	.	.	.	-11.4619	3.7631	0.08611	0.1125:0.1341:0.462:0.2914	.	.	.	.	L	24	.	.	F	+	1	0	ALB	74493990	0.001000	0.12720	0.195000	0.23364	0.710000	0.40934	-0.314000	0.08092	-0.676000	0.05238	0.482000	0.46254	TTT	.	.		0.353	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		C	74275126	T	C	74275126	2	2	259	1	0	0	0	0	0	0	0	1	486	1828	64	2		2	ALB	4	74275126	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1	74275126	116879150	211	36529	184	2								
ALB	213	hgsc.bcm.edu	37	chr4	74275205	74275205	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctgcctgcctgttgccaaagGtattatgcaaaagaatagaa	9	8	0	2	rs75828235		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:74275205G>A	ENST00000503124.1	+	3	372		c.e3+1		ALB_ENST00000509063.1_Splice_Site|ALB_ENST00000415165.2_Intron|ALB_ENST00000401494.3_Splice_Site|ALB_ENST00000295897.4_Splice_Site|ALB_ENST00000505649.1_Splice_Site			Q8TES7	FBF1_HUMAN	albumin						apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GTTGCCAAAGGTATTATGCAA	0.388																																					.		Atlas-SNP	.											.	ALB	132	.	0			c.615+1G>A						.						71	74	73					4																	74275205		2203	4299	6502	SO:0001630	splice_region_variant	213	exon5			CCAAAGGTATTAT	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.165+1G>A	chr4.hg19:g.74275205G>A		198.0	0.0		144.0	41.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Splice_Site	SNP	ENST00000503124.1	hg19		.	.	.	.	.	.	.	.	.	.	G	11.04	1.521991	0.27211	.	.	ENSG00000163631	ENST00000295897;ENST00000503124;ENST00000509063;ENST00000401494;ENST00000430202;ENST00000511370	.	.	.	5.25	5.25	0.73442	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.9449	0.89036	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ALB	74494069	1.000000	0.71417	1.000000	0.80357	0.133000	0.20885	5.592000	0.67543	2.894000	0.99253	0.591000	0.81541	.	.	.		0.388	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477	Intron	A	74275205	G	A	74275205	5	1	259	1	0	0	0	0	0	0	1	0	486	1275	44	3	634	3	ALB	4	74275205	Splice_Site	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	79	74275205	116879071	212	36530										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79418004	79418004	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acgatgactccatgtttgagCcagaggaacagttcagggtc	12	9	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:79418004C>T	ENST00000264895.6	+	60	9444	c.9004C>T	c.(9004-9006)Cca>Tca	p.P3002S		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	2998	Calx-beta 4.				cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						CATGTTTGAGCCAGAGGAACA	0.448																																					p.P3002S		Atlas-SNP	.											.	FRAS1	779	.	0			c.C9004T						.						184	178	180					4																	79418004		1941	4157	6098	SO:0001583	missense	80144	exon60			TTTGAGCCAGAGG	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.9004C>T	chr4.hg19:g.79418004C>T	ENSP00000264895:p.Pro3002Ser	120.0	0.0		91.0	4.0	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000264895.6	hg19	CCDS54771.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.14|17.14	3.312455|3.312455	0.60414|0.60414	.|.	.|.	ENSG00000138759|ENSG00000138759	ENST00000512123|ENST00000264895	.|T	.|0.28666	.|1.6	5.51|5.51	5.51|5.51	0.81932|0.81932	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.47303|0.47303	0.1438|0.1438	L|L	0.38175|0.38175	1.15|1.15	0.80722|0.80722	D|D	1|1	.|D;D	.|0.76494	.|0.965;0.999	.|P;D	.|0.71656	.|0.791;0.974	T|T	0.28332|0.28332	-1.0047|-1.0047	5|10	.|0.40728	.|T	.|0.16	.|.	19.4366|19.4366	0.94798|0.94798	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|3001;3002	.|Q86XX4-2;E9PHH6	.|.;.	V|S	1230|3002	.|ENSP00000264895:P3002S	.|ENSP00000264895:P3002S	A|P	+|+	2|1	0|0	FRAS1|FRAS1	79637028|79637028	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.757000|0.757000	0.42996|0.42996	5.796000|5.796000	0.69080|0.69080	2.580000|2.580000	0.87095|0.87095	0.650000|0.650000	0.86243|0.86243	GCC|CCA	.	.		0.448	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	79418004	C	T	79418004	3	4	259	1	0	0	0	0	1	0	0	0	6050	739	26	3	9317	3	FRAS1	4	79418004	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	5142799	79418004	111736272	213	36531										
BMP3	651	hgsc.bcm.edu	37	chr4	81967507	81967507	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggcagaataccagtataaaaAggatgaggtgtgggaggaga	16	3	0	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:81967507A>G	ENST00000282701.2	+	2	1252	c.932A>G	c.(931-933)aAg>aGg	p.K311R		NM_001201.2	NP_001192.2	P12645	BMP3_HUMAN	bone morphogenetic protein 3	311					cartilage development (GO:0051216)|cell differentiation (GO:0030154)|cell-cell signaling (GO:0007267)|growth (GO:0040007)|ossification (GO:0001503)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	BMP receptor binding (GO:0070700)|receptor binding (GO:0005102)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	29						CAGTATAAAAAGGATGAGGTG	0.512																																					p.K311R		Atlas-SNP	.											.	BMP3	59	.	0			c.A932G						.						44	50	48					4																	81967507		2203	4299	6502	SO:0001583	missense	651	exon2			ATAAAAAGGATGA	M22491	CCDS3588.1	4q21	2013-02-06	2008-05-22		ENSG00000152785	ENSG00000152785		"Bone morphogenetic proteins"	1070	protein-coding gene	gene with protein product	"osteogenin"	112263	"bone morphogenetic protein 3 (osteogenic)"				Standard	NM_001201		Approved		uc003hmg.4	P12645	OTTHUMG00000130292	ENST00000282701.2:c.932A>G	chr4.hg19:g.81967507A>G	ENSP00000282701:p.Lys311Arg	155.0	0.0		92.0	4.0	NM_001201	Q4VAS5	Missense_Mutation	SNP	ENST00000282701.2	hg19	CCDS3588.1	.	.	.	.	.	.	.	.	.	.	A	4.253	0.045891	0.08196	.	.	ENSG00000152785	ENST00000282701	T	0.74632	-0.86	5.16	2.67	0.31697	.	0.352028	0.35555	N	0.003139	T	0.54886	0.1886	N	0.24115	0.695	0.20074	N	0.999935	B	0.06786	0.001	B	0.01281	0.0	T	0.39121	-0.9629	10	0.33940	T	0.23	.	5.4368	0.16486	0.6584:0.0:0.0735:0.2681	.	311	P12645	BMP3_HUMAN	R	311	ENSP00000282701:K311R	ENSP00000282701:K311R	K	+	2	0	BMP3	82186531	1.000000	0.71417	0.830000	0.32933	0.011000	0.07611	2.110000	0.41873	0.359000	0.24239	-1.229000	0.01577	AAG	.	.		0.512	BMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252634.1			G	81967507	A	G	81967507	3	3	259	1	0	0	0	0	1	0	0	0	1461	72	3	2	938	2	BMP3	4	81967507	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2549503	81967507	109186769	214	36532										
SCD5	79966	hgsc.bcm.edu	37	chr4	83601881	83601881	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttctctggatccggaccacaGgatcagcaagcaggtcagtg	12	11	3	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:83601881G>T	ENST00000319540.4	-	3	867	c.548C>A	c.(547-549)cCt>cAt	p.P183H	SCD5_ENST00000273908.4_Missense_Mutation_p.P183H	NM_001037582.2	NP_001032671.2	Q86SK9	SCD5_HUMAN	stearoyl-CoA desaturase 5	183					fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	iron ion binding (GO:0005506)|stearoyl-CoA 9-desaturase activity (GO:0004768)			endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)	13		Colorectal(4;0.0323)|Hepatocellular(203;0.115)				CCGGACCACAGGATCAGCAAG	0.512																																					p.P183H		Atlas-SNP	.											SCD5_ENST00000273908,NS,malignant_melanoma,-1,2	SCD5	58	.	0			c.C548A						.						92	87	89					4																	83601881		2203	4300	6503	SO:0001583	missense	79966	exon3			ACCACAGGATCAG	AF389338	CCDS3595.1, CCDS34024.1	4q21.3	2013-01-25	2005-06-09	2005-06-09	ENSG00000145284	ENSG00000145284		"Fatty acid desaturases"	21088	protein-coding gene	gene with protein product		608370	"stearoyl-CoA desaturase 4"	SCD4		12477932	Standard	NM_024906		Approved	ACOD4, FLJ21032, FADS4, HSCD5	uc003hna.2	Q86SK9	OTTHUMG00000130293	ENST00000319540.4:c.548C>A	chr4.hg19:g.83601881G>T	ENSP00000316329:p.Pro183His	70.0	0.0		51.0	3.0	NM_024906	B2RPG0|Q4W5Q5|Q8NDS0|Q9H7D1	Missense_Mutation	SNP	ENST00000319540.4	hg19	CCDS34024.1	.	.	.	.	.	.	.	.	.	.	G	17.15	3.316324	0.60524	.	.	ENSG00000145284	ENST00000319540;ENST00000273908	T;T	0.15256	2.44;2.44	5.44	4.59	0.56863	Fatty acid desaturase, type 1 (1);	0.329489	0.31301	N	0.007883	T	0.45994	0.1370	M	0.91818	3.245	0.27273	N	0.958306	D;D	0.89917	1.0;1.0	D;D	0.72982	0.973;0.979	T	0.50101	-0.8867	10	0.87932	D	0	-10.1797	8.5047	0.33179	0.0776:0.0:0.7698:0.1526	.	183;183	Q86SK9-2;Q86SK9	.;SCD5_HUMAN	H	183	ENSP00000316329:P183H;ENSP00000273908:P183H	ENSP00000273908:P183H	P	-	2	0	SCD5	83820905	0.939000	0.31865	0.981000	0.43875	0.933000	0.57130	2.169000	0.42434	1.506000	0.48736	0.591000	0.81541	CCT	.	.		0.512	SCD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252635.1	NM_024906		T	83601881	G	T	83601881	3	4	259	1	0	0	0	0	1	0	0	0	13902	1000	35	3	662	3	SCD5	4	83601881	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1634374	83601881	107552395	215	36533										
SCD5	79966	hgsc.bcm.edu	37	chr4	83601977	83601977	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acccaatatgggagaagaagAagccccggcgggcattgtgg	15	9	0	3	rs138660783	byFrequency	TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:83601977A>G	ENST00000319540.4	-	3	771	c.452T>C	c.(451-453)tTc>tCc	p.F151S	SCD5_ENST00000273908.4_Missense_Mutation_p.F151S	NM_001037582.2	NP_001032671.2	Q86SK9	SCD5_HUMAN	stearoyl-CoA desaturase 5	151					fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	iron ion binding (GO:0005506)|stearoyl-CoA 9-desaturase activity (GO:0004768)			endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)	13		Colorectal(4;0.0323)|Hepatocellular(203;0.115)				GGAGAAGAAGAAGCCCCGGCG	0.542																																					p.F151S		Atlas-SNP	.											.	SCD5	58	.	0			c.T452C						.						104	111	109					4																	83601977		2203	4300	6503	SO:0001583	missense	79966	exon3			AAGAAGAAGCCCC	AF389338	CCDS3595.1, CCDS34024.1	4q21.3	2013-01-25	2005-06-09	2005-06-09	ENSG00000145284	ENSG00000145284		"Fatty acid desaturases"	21088	protein-coding gene	gene with protein product		608370	"stearoyl-CoA desaturase 4"	SCD4		12477932	Standard	NM_024906		Approved	ACOD4, FLJ21032, FADS4, HSCD5	uc003hna.2	Q86SK9	OTTHUMG00000130293	ENST00000319540.4:c.452T>C	chr4.hg19:g.83601977A>G	ENSP00000316329:p.Phe151Ser	118.0	0.0		81.0	4.0	NM_024906	B2RPG0|Q4W5Q5|Q8NDS0|Q9H7D1	Missense_Mutation	SNP	ENST00000319540.4	hg19	CCDS34024.1	.	.	.	.	.	.	.	.	.	.	A	27.8	4.861183	0.91433	.	.	ENSG00000145284	ENST00000319540;ENST00000273908	T;T	0.15487	2.42;2.42	5.27	5.27	0.74061	Fatty acid desaturase, type 1 (1);	0.049186	0.85682	D	0.000000	T	0.57110	0.2031	H	0.96996	3.92	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.994;0.996	T	0.73170	-0.4067	10	0.87932	D	0	-12.9515	15.3641	0.74507	1.0:0.0:0.0:0.0	.	151;151	Q86SK9-2;Q86SK9	.;SCD5_HUMAN	S	151	ENSP00000316329:F151S;ENSP00000273908:F151S	ENSP00000273908:F151S	F	-	2	0	SCD5	83821001	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.241000	0.78201	2.220000	0.72140	0.383000	0.25322	TTC	.	A|0.999;C|0.001		0.542	SCD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252635.1	NM_024906		G	83601977	A	G	83601977	3	3	259	1	0	0	0	0	1	0	0	0	13902	246	9	2	758	2	SCD5	4	83601977	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	96	83601977	107552299	216	36534										
AGPAT9	84803	hgsc.bcm.edu	37	chr4	84519219	84519219	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctcagtataaccctcagttcGgtgatgcattttggaacagt	9	9	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:84519219G>T	ENST00000395226.2	+	11	1230	c.1012G>T	c.(1012-1014)Ggt>Tgt	p.G338C	AGPAT9_ENST00000264409.4_Missense_Mutation_p.G338C	NM_001256421.1	NP_001243350.1	Q53EU6	GPAT3_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 9	338					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|regulation of TOR signaling (GO:0032006)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)|glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(3)	13		Hepatocellular(203;0.114)				CCCTCAGTTCGGTGATGCATT	0.448																																					p.G338C		Atlas-SNP	.											.	AGPAT9	41	.	0			c.G1012T						.						124	116	119					4																	84519219		2203	4300	6503	SO:0001583	missense	84803	exon11			CAGTTCGGTGATG	AK055749	CCDS3606.1	4q21.23	2014-02-13	2008-01-29		ENSG00000138678	ENSG00000138678	2.3.1.15	"1-acylglycerol-3-phosphate O-acyltransferases"	28157	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, theta"	610958	"1-acylglycerol-3-phosphate O-acyltransferase 9 (lysophosphatidic acid acyltransferase, theta)"			12975309	Standard	NM_001256421		Approved	MGC11324, LPAAT-theta, MAG1, HMFN0839	uc003how.4	Q53EU6	OTTHUMG00000130431	ENST00000395226.2:c.1012G>T	chr4.hg19:g.84519219G>T	ENSP00000378651:p.Gly338Cys	44.0	0.0		45.0	4.0	NM_001256421	Q68CJ4|Q6GPI6|Q96NA3	Missense_Mutation	SNP	ENST00000395226.2	hg19	CCDS3606.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.295114	0.81025	.	.	ENSG00000138678	ENST00000395226;ENST00000264409	T;T	0.48522	0.81;0.81	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.76644	0.4016	M	0.91818	3.245	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.79708	-0.1690	10	0.48119	T	0.1	-16.6768	19.6718	0.95914	0.0:0.0:1.0:0.0	.	338	Q53EU6	GPAT3_HUMAN	C	338	ENSP00000378651:G338C;ENSP00000264409:G338C	ENSP00000264409:G338C	G	+	1	0	AGPAT9	84738243	1.000000	0.71417	1.000000	0.80357	0.643000	0.38383	9.764000	0.98949	2.639000	0.89480	0.557000	0.71058	GGT	.	.		0.448	AGPAT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252821.3	NM_032717		T	84519219	G	T	84519219	3	4	259	1	0	0	0	0	1	0	0	0	392	1116	39	1	1050	1	AGPAT9	4	84519219	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	917242	84519219	106635057	217	36535										
AFF1	4299	hgsc.bcm.edu	37	chr4	87967360	87967360	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctgcttcgaattagagagaaGgaaagacgcaaccaggaagc	12	8	0	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:87967360G>T	ENST00000307808.6	+	2	480	c.60G>T	c.(58-60)aaG>aaT	p.K20N	AFF1_ENST00000395146.4_Missense_Mutation_p.K27N|AFF1_ENST00000544085.1_Intron	NM_005935.2	NP_005926.1	P51825	AFF1_HUMAN	AF4/FMR2 family, member 1	20					positive regulation of transcription, DNA-templated (GO:0045893)	transcription elongation factor complex (GO:0008023)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|large_intestine(2)	3		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)		TTAGAGAGAAGGAAAGACGCA	0.398																																					p.K27N		Atlas-SNP	.											.	AFF1	102	.	0			c.G81T						.						107	106	107					4																	87967360		2203	4300	6503	SO:0001583	missense	4299	exon3			AGAGAAGGAAAGA	L22179	CCDS3616.1, CCDS54775.1	4q21.3	2009-08-04	2005-06-27	2005-06-27	ENSG00000172493	ENSG00000172493			7135	protein-coding gene	gene with protein product		159557	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 2", "pre-B-cell monocytic leukemia partner 1"	PBM1, MLLT2		7689231, 1423625, 8353274	Standard	NM_005935		Approved	AF-4, AF4	uc011ccz.2	P51825	OTTHUMG00000130603	ENST00000307808.6:c.60G>T	chr4.hg19:g.87967360G>T	ENSP00000305689:p.Lys20Asn	148.0	0.0		99.0	4.0	NM_001166693	B4DTU1|E9PBM3	Missense_Mutation	SNP	ENST00000307808.6	hg19	CCDS3616.1	.	.	.	.	.	.	.	.	.	.	G	18.81	3.702663	0.68501	.	.	ENSG00000172493	ENST00000395146;ENST00000395142;ENST00000507468;ENST00000503477;ENST00000307808	T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26	5.73	3.02	0.34903	.	0.068104	0.64402	D	0.000015	T	0.76198	0.3954	M	0.67953	2.075	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.997;0.994;0.994;1.0	D;D;D;D;D	0.79784	0.993;0.967;0.918;0.918;0.993	T	0.74090	-0.3777	10	0.62326	D	0.03	-29.5459	7.7224	0.28740	0.4644:0.0:0.5356:0.0	.	27;27;20;20;27	E9PBM3;B4DXZ8;Q14C88;P51825;B4DTU1	.;.;.;AFF1_HUMAN;.	N	27;27;27;27;20	ENSP00000378578:K27N;ENSP00000427593:K27N;ENSP00000424483:K27N;ENSP00000305689:K20N	ENSP00000305689:K20N	K	+	3	2	AFF1	88186384	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	0.800000	0.27042	0.407000	0.25591	0.655000	0.94253	AAG	.	.		0.398	AFF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253053.3	NM_005935		T	87967360	G	T	87967360	3	4	259	1	0	0	0	0	1	0	0	0	356	991	35	3	108	3	AFF1	4	87967360	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	3448141	87967360	103186916	218	36536										
PDHA2	5161	hgsc.bcm.edu	37	chr4	96762199	96762199	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gtgatcctggagtcagttatCgtacacgagaagaaattcag	11	7	2	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:96762199C>A	ENST00000295266.4	+	1	961	c.898C>A	c.(898-900)Cgt>Agt	p.R300S		NM_005390.4	NP_005381.1	P29803	ODPAT_HUMAN	pyruvate dehydrogenase (lipoamide) alpha 2	300					glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|pyruvate metabolic process (GO:0006090)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	pyruvate dehydrogenase (acetyl-transferring) activity (GO:0004739)	p.R300C(1)		NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(23)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	46		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.23e-06)		AGTCAGTTATCGTACACGAGA	0.433																																					p.R300S		Atlas-SNP	.											PDHA2,caecum,carcinoma,0,2	PDHA2	118	.	1	Substitution - Missense(1)	large_intestine(1)	c.C898A						.						103	100	101					4																	96762199		2203	4300	6503	SO:0001583	missense	5161	exon1			AGTTATCGTACAC		CCDS3644.1	4q22-q23	2009-11-09			ENSG00000163114	ENSG00000163114	1.2.4.1		8807	protein-coding gene	gene with protein product		179061		PDHAL			Standard	NM_005390		Approved		uc003htr.4	P29803	OTTHUMG00000130990	ENST00000295266.4:c.898C>A	chr4.hg19:g.96762199C>A	ENSP00000295266:p.Arg300Ser	110.0	0.0		71.0	37.0	NM_005390	B2R9Q3|Q0VDI5|Q4VC02|Q6NXQ1	Missense_Mutation	SNP	ENST00000295266.4	hg19	CCDS3644.1	.	.	.	.	.	.	.	.	.	.	C	15.90	2.969579	0.53614	.	.	ENSG00000163114	ENST00000295266	D	0.97870	-4.58	4.91	4.07	0.47477	Dehydrogenase, E1 component (1);	0.000000	0.85682	D	0.000000	D	0.99168	0.9712	H	0.98682	4.3	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98674	1.0689	10	0.87932	D	0	-10.2397	11.2932	0.49263	0.0:0.9113:0.0:0.0887	.	300	P29803	ODPAT_HUMAN	S	300	ENSP00000295266:R300S	ENSP00000295266:R300S	R	+	1	0	PDHA2	96981222	1.000000	0.71417	0.053000	0.19242	0.437000	0.31866	5.205000	0.65186	1.456000	0.47831	0.467000	0.42956	CGT	.	.		0.433	PDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253608.1			A	96762199	C	A	96762199	3	1	259	1	0	0	0	0	1	0	0	0	11674	884	31	1	900	1	PDHA2	4	96762199	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	8794839	96762199	94392077	219	36537										
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123265683	123265683	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agtctgtaagcaagtctgcaAgcaaaatggatactacgtta	9	7	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:123265683A>T	ENST00000264501.4	+	74	13073	c.12700A>T	c.(12700-12702)Agc>Tgc	p.S4234C	KIAA1109_ENST00000388738.3_Missense_Mutation_p.S4234C			Q2LD37	K1109_HUMAN	KIAA1109	4234					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						CAAGTCTGCAAGCAAAATGGA	0.323																																					p.S4234C		Atlas-SNP	.											.	KIAA1109	424	.	0			c.A12700T						.						131	124	126					4																	123265683		1849	4099	5948	SO:0001583	missense	84162	exon72			TCTGCAAGCAAAA	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.12700A>T	chr4.hg19:g.123265683A>T	ENSP00000264501:p.Ser4234Cys	157.0	0.0		87.0	4.0	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	A|A|A	17.81|17.81|17.81	3.481623|3.481623|3.481623	0.63849|0.63849|0.63849	.|.|.	.|.|.	ENSG00000138688|ENSG00000138688|ENSG00000138688	ENST00000442707|ENST00000306802|ENST00000264501;ENST00000388738;ENST00000438707	.|.|T;T;T	.|.|0.34859	.|.|2.32;2.32;1.34	5.52|5.52|5.52	5.52|5.52|5.52	0.82312|0.82312|0.82312	.|.|.	.|.|0.167446	.|.|0.53938	.|.|D	.|.|0.000051	T|T|T	0.38268|0.38268|0.38268	0.1034|0.1034|0.1034	L|L|L	0.46157|0.46157|0.46157	1.445|1.445|1.445	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|.|P;P	.|.|0.42123	.|.|0.771;0.661	.|.|B;B	.|.|0.42653	.|.|0.394;0.299	T|T|T	0.26815|0.26815|0.26815	-1.0092|-1.0092|-1.0092	5|5|10	.|.|0.59425	.|.|D	.|.|0.04	.|.|.	15.6544|15.6544|15.6544	0.77121|0.77121|0.77121	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.|.	.|.|4233;4234	.|.|Q2LD37-4;Q2LD37	.|.|.;K1109_HUMAN	M|H|C	179|609|4234;4234;903	.|.|ENSP00000264501:S4234C;ENSP00000373390:S4234C;ENSP00000410874:S903C	.|.|ENSP00000264501:S4234C	K|Q|S	+|+|+	2|3|1	0|2|0	KIAA1109|KIAA1109|KIAA1109	123485133|123485133|123485133	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.957000|0.957000|0.957000	0.61999|0.61999|0.61999	4.347000|4.347000|4.347000	0.59373|0.59373|0.59373	2.094000|2.094000|2.094000	0.63399|0.63399|0.63399	0.533000|0.533000|0.533000	0.62120|0.62120|0.62120	AAG|CAA|AGC	.	.		0.323	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		T	123265683	A	T	123265683	3	4	259	1	0	0	0	0	1	0	0	0	8217	72	3	4	12986	4	KIAA1109	4	123265683	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	26503484	123265683	67888593	220	36538										
PLK4	10733	hgsc.bcm.edu	37	chr4	128803010	128803010	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttaaagttggaaatctgcttGgtaaaggatcatttgctggt	11	4	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:128803010G>T	ENST00000270861.5	+	2	329	c.55G>T	c.(55-57)Ggt>Tgt	p.G19C	PLK4_ENST00000513090.1_Missense_Mutation_p.G19C|PLK4_ENST00000511942.1_3'UTR|PLK4_ENST00000507249.1_Missense_Mutation_p.G19C|PLK4_ENST00000514379.1_5'UTR|PLK4_ENST00000515069.1_Missense_Mutation_p.G19C	NM_014264.4	NP_055079.3	O00444	PLK4_HUMAN	polo-like kinase 4	19	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				centriole replication (GO:0007099)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of centriole replication (GO:0046601)|protein phosphorylation (GO:0006468)|trophoblast giant cell differentiation (GO:0060707)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	31						AAATCTGCTTGGTAAAGGATC	0.368																																					p.G19C	Colon(135;508 1718 19061 31832 42879)	Atlas-SNP	.											.	PLK4	65	.	0			c.G55T						.						95	94	94					4																	128803010		2203	4300	6503	SO:0001583	missense	10733	exon2			CTGCTTGGTAAAG	Y13115	CCDS3735.1, CCDS54803.1, CCDS54804.1	4q27-q28	2013-01-18	2010-06-24	2004-01-28	ENSG00000142731	ENSG00000142731			11397	protein-coding gene	gene with protein product		605031	"serine/threonine kinase 18", "polo-like kinase 4 (Drosophila)"	STK18			Standard	NM_014264		Approved	Sak	uc003ifo.3	O00444	OTTHUMG00000133301	ENST00000270861.5:c.55G>T	chr4.hg19:g.128803010G>T	ENSP00000270861:p.Gly19Cys	181.0	0.0		98.0	4.0	NM_001190799	B2RAL0|B7Z837|B7Z8G7|Q8IYF0|Q96Q95|Q9UD84|Q9UDE2	Missense_Mutation	SNP	ENST00000270861.5	hg19	CCDS3735.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.472526	0.84640	.	.	ENSG00000142731	ENST00000270861;ENST00000515069;ENST00000513090;ENST00000507249	T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1	3.97	3.97	0.46021	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.87497	0.6192	H	0.98769	4.325	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.93053	0.6467	10	0.87932	D	0	-7.6902	16.6235	0.84936	0.0:0.0:1.0:0.0	.	19;19	O00444-2;O00444	.;PLK4_HUMAN	C	19	ENSP00000270861:G19C;ENSP00000421774:G19C;ENSP00000427554:G19C;ENSP00000423412:G19C	ENSP00000270861:G19C	G	+	1	0	PLK4	129022460	1.000000	0.71417	0.996000	0.52242	0.962000	0.63368	8.776000	0.91776	2.211000	0.71520	0.561000	0.74099	GGT	.	.		0.368	PLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257095.3			T	128803010	G	T	128803010	3	4	259	1	0	0	0	0	1	0	0	0	12107	1348	47	3	61	3	PLK4	4	128803010	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	5537327	128803010	62351266	221	36539										
ODZ3	55714	hgsc.bcm.edu	37	chr4	183676072	183676072	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atgaagttgcgtctccaactGatcaagaactctacatcttt	6	10	4	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:183676072G>T	ENST00000511685.1	+	22	4675	c.4552G>T	c.(4552-4554)Gat>Tat	p.D1518Y	TENM3_ENST00000502950.1_3'UTR|TENM3_ENST00000406950.2_Missense_Mutation_p.D1518Y			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1518					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										GTCTCCAACTGATCAAGAACT	0.378																																					p.D1518Y		Atlas-SNP	.											.	.	.	.	0			c.G4552T						.						78	78	78					4																	183676072		1909	4121	6030	SO:0001583	missense	55714	exon21			CCAACTGATCAAG	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.4552G>T	chr4.hg19:g.183676072G>T	ENSP00000424226:p.Asp1518Tyr	73.0	0.0		53.0	4.0	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	hg19	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	G	14.89	2.669295	0.47677	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	T;T	0.17854	2.25;2.25	5.25	5.25	0.73442	.	.	.	.	.	T	0.18923	0.0454	L	0.36672	1.1	0.52501	D	0.999955	P	0.47350	0.894	B	0.41813	0.367	T	0.01140	-1.1439	9	0.72032	D	0.01	.	19.0324	0.92963	0.0:0.0:1.0:0.0	.	1518	Q9P273	TEN3_HUMAN	Y	1518	ENSP00000424226:D1518Y;ENSP00000385276:D1518Y	ENSP00000385276:D1518Y	D	+	1	0	ODZ3	183913066	1.000000	0.71417	0.998000	0.56505	0.985000	0.73830	7.492000	0.81482	2.737000	0.93849	0.563000	0.77884	GAT	.	.		0.378	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			T	183676072	G	T	183676072	3	4	259	1	0	0	0	0	1	0	0	0	10845	1290	45	3	4634	3	ODZ3	4	183676072	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	54873062	183676072	7478204	222	36540										
MLF1IP	79682	hgsc.bcm.edu	37	chr4	185646185	185646185	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttggagaattcttcttcatcAgcatatatagctgtgctatg	8	7	4	1	rs374160243		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:185646185A>G	ENST00000281453.5	-	4	316	c.246T>C	c.(244-246)gcT>gcC	p.A82A	MLF1IP_ENST00000541971.1_Silent_p.A82A	NM_024629.3	NP_078905.2														endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|stomach(1)	13		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Hepatocellular(41;0.000519)|Colorectal(36;0.00172)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.0299)|all_hematologic(60;0.0592)|Medulloblastoma(177;0.146)		all cancers(43;7.83e-28)|Epithelial(43;2.56e-24)|OV - Ovarian serous cystadenocarcinoma(60;4.5e-11)|Colorectal(24;3.27e-06)|STAD - Stomach adenocarcinoma(60;2.66e-05)|GBM - Glioblastoma multiforme(59;3.16e-05)|BRCA - Breast invasive adenocarcinoma(30;0.000252)|COAD - Colon adenocarcinoma(29;0.000512)|LUSC - Lung squamous cell carcinoma(40;0.01)|READ - Rectum adenocarcinoma(43;0.0419)		CTTCTTCATCAGCATATATAG	0.373																																					p.A82A		Atlas-SNP	.											.	MLF1IP	33	.	0			c.T246C						.	A		0,4406		0,0,2203	142	135	137		246	-5.4	0.3	4		137	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MLF1IP	NM_024629.3		0,1,6502	GG,GA,AA		0.0116,0.0,0.0077		82/419	185646185	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	79682	exon4			TTCATCAGCATAT																												ENST00000281453.5:c.246T>C	chr4.hg19:g.185646185A>G		111.0	0.0		83.0	5.0	NM_024629		Silent	SNP	ENST00000281453.5	hg19	CCDS3838.1																																																																																			.	.		0.373	MLF1IP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360841.2			G	185646185	A	G	185646185	2	3	259	1	0	0	0	0	0	0	0	1	9624	175	7	2		2	MLF1IP	4	185646185	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1970113	185646185	5508091	223	36541										
CCT5	22948	hgsc.bcm.edu	37	chr5	10254914	10254914	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tggaactgtccaagtctcagGatgatgaaattggagatgga	13	5	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:10254914G>A	ENST00000280326.4	+	3	715	c.295G>A	c.(295-297)Gat>Aat	p.D99N	CCT5_ENST00000503026.1_Missense_Mutation_p.D78N|CCT5_ENST00000515676.1_Missense_Mutation_p.D61N|CCT5_ENST00000506600.1_Intron|CCT5_ENST00000515390.1_Intron	NM_012073.3	NP_036205.1	P48643	TCPE_HUMAN	chaperonin containing TCP1, subunit 5 (epsilon)	99					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|response to virus (GO:0009615)	cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleolus (GO:0005730)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|G-protein beta-subunit binding (GO:0031681)	p.D99Y(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(2)	26						CAAGTCTCAGGATGATGAAAT	0.428																																					p.D99N		Atlas-SNP	.											CCT5,NS,carcinoma,0,1	CCT5	49	.	1	Substitution - Missense(1)	lung(1)	c.G295A						.						141	122	129					5																	10254914		2203	4300	6503	SO:0001583	missense	22948	exon3			TCTCAGGATGATG	D43950	CCDS3877.1	5p15.2	2014-09-17			ENSG00000150753	ENSG00000150753		"Heat Shock Proteins / Chaperonins"	1618	protein-coding gene	gene with protein product		610150					Standard	NM_012073		Approved	KIAA0098	uc003jeq.3	P48643	OTTHUMG00000131042	ENST00000280326.4:c.295G>A	chr5.hg19:g.10254914G>A	ENSP00000280326:p.Asp99Asn	169.0	1.0		94.0	4.0	NM_012073	A8JZY8|A8K2X8|B4DYD8	Missense_Mutation	SNP	ENST00000280326.4	hg19	CCDS3877.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	36|36	5.777527|5.777527	0.96929|0.96929	.|.	.|.	ENSG00000150753|ENSG00000150753	ENST00000440011|ENST00000280326;ENST00000503026;ENST00000515676	.|T;T;T	.|0.15256	.|2.44;2.44;2.44	5.64|5.64	5.64|5.64	0.86602|0.86602	.|Chaperonin TCP-1, conserved site (1);	.|0.000000	.|0.85682	.|D	.|0.000000	.|T	.|0.59348	.|0.2187	H|H	0.96916|0.96916	3.905|3.905	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.97110	.|1.0;1.0;1.0	.|T	.|0.73914	.|-0.3832	.|10	.|0.87932	.|D	.|0	.|-28.1245	18.761|18.761	0.91851|0.91851	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|97;99;99	.|Q9BU08;A8K2X8;P48643	.|.;.;TCPE_HUMAN	.|N	-1|99;78;61	.|ENSP00000280326:D99N;ENSP00000423318:D78N;ENSP00000427297:D61N	.|ENSP00000280326:D99N	.|D	+|+	.|1	.|0	CCT5|CCT5	10307914|10307914	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	9.288000|9.288000	0.96055|0.96055	2.656000|2.656000	0.90262|0.90262	0.644000|0.644000	0.83932|0.83932	.|GAT	.	.		0.428	CCT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253688.2			A	10254914	G	A	10254914	3	1	259	1	0	0	0	0	1	0	0	0	2958	1174	41	3	305	3	CCT5	5	10254914	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10		10254914	170660346	224	36542										
RAI14	26064	hgsc.bcm.edu	37	chr5	34796132	34796132	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgacagcccaagatactaccGgtatgtggtttttagtctct	9	9	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:34796132G>T	ENST00000265109.3	+	4	543	c.256G>T	c.(256-258)Gga>Tga	p.G86*	RAI14_ENST00000512629.1_Splice_Site_p.G86*|RAI14_ENST00000397449.1_Splice_Site_p.G79*|RAI14_ENST00000506376.1_Splice_Site_p.G78*|RAI14_ENST00000503673.1_Splice_Site_p.G86*|RAI14_ENST00000507276.1_3'UTR|RAI14_ENST00000428746.2_Splice_Site_p.G86*|RAI14_ENST00000515799.1_Splice_Site_p.G89*	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	86						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(19)|lung(22)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(31;0.000191)					AGATACTACCGGTATGTGGTT	0.428																																					p.G89X		Atlas-SNP	.											.	RAI14	100	.	0			c.G265T						.						196	174	182					5																	34796132		2203	4300	6503	SO:0001630	splice_region_variant	26064	exon6			ACTACCGGTATGT	AB037755	CCDS34142.1, CCDS54837.1, CCDS54838.1, CCDS54839.1	5p13.3-p13.2	2013-01-10			ENSG00000039560	ENSG00000039560		"Ankyrin repeat domain containing"	14873	protein-coding gene	gene with protein product	"novel retinal pigment epithelial"	606586				11042181	Standard	NM_015577		Approved	NORPEG, KIAA1334, RAI13, DKFZp564G013	uc011coj.2	Q9P0K7	OTTHUMG00000162019	ENST00000265109.3:c.256+1G>T	chr5.hg19:g.34796132G>T		187.0	0.0		119.0	5.0	NM_001145525	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Nonsense_Mutation	SNP	ENST00000265109.3	hg19	CCDS34142.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.791353	0.90367	.	.	ENSG00000039560	ENST00000265109;ENST00000514527;ENST00000513974;ENST00000512629;ENST00000428746;ENST00000514873;ENST00000503673;ENST00000504052;ENST00000512305;ENST00000514036;ENST00000515799;ENST00000508315;ENST00000512625;ENST00000506376;ENST00000397449	.	.	.	6.08	6.08	0.98989	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-18.9939	17.5802	0.87965	0.0:0.0:1.0:0.0	.	.	.	.	X	86;86;86;86;86;86;86;86;86;86;89;86;86;78;79	.	ENSP00000265109:G86X	G	+	1	0	RAI14	34831889	1.000000	0.71417	0.982000	0.44146	0.935000	0.57460	6.310000	0.72830	2.894000	0.99253	0.655000	0.94253	GGA	.	.		0.428	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577	Nonsense_Mutation	T	34796132	G	T	34796132	5	4	259	1	0	0	0	0	0	0	1	0	13023	1130	39	1	331	1	RAI14	5	34796132	Splice_Site	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	24541218	34796132	146119128	225	36543										
C5orf33	133686	hgsc.bcm.edu	37	chr5	36226594	36226594	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tacctcctgcagctatgacaGcatctgcccatcgaacagtc	7	15	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:36226594G>A	ENST00000381937.4	-	3	460	c.461C>T	c.(460-462)gCt>gTt	p.A154V	NADK2_ENST00000397338.1_5'UTR|NADK2_ENST00000506945.1_5'UTR|NADK2_ENST00000514504.1_Missense_Mutation_p.A154V|NADK2_ENST00000282512.3_5'UTR	NM_001085411.1	NP_001078880.1	Q4G0N4	NAKD2_HUMAN	NAD kinase 2, mitochondrial	154					NAD metabolic process (GO:0019674)|NADP biosynthetic process (GO:0006741)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|NAD+ kinase activity (GO:0003951)|protein homodimerization activity (GO:0042803)										AGCTATGACAGCATCTGCCCA	0.373																																					p.A154V		Atlas-SNP	.											.	NADKD1	47	.	0			c.C461T						.						144	137	139					5																	36226594		1915	4135	6050	SO:0001583	missense	133686	exon3			ATGACAGCATCTG	BC062567	CCDS3917.1, CCDS47197.1, CCDS75235.1	5p13.2	2013-04-30	2013-04-30	2013-04-30	ENSG00000152620	ENSG00000152620			26404	protein-coding gene	gene with protein product	"mitochondrial NAD kinase"	615787	"chromosome 5 open reading frame 33", "NAD kinase domain containing 1"	C5orf33, NADKD1		23616928	Standard	NM_001085411		Approved	FLJ30596, MNADK	uc003jkf.4	Q4G0N4	OTTHUMG00000131105	ENST00000381937.4:c.461C>T	chr5.hg19:g.36226594G>A	ENSP00000371362:p.Ala154Val	113.0	0.0		71.0	4.0	NM_001085411	B5MC93|Q6UTX5|Q96NM0	Missense_Mutation	SNP	ENST00000381937.4	hg19	CCDS47197.1	.	.	.	.	.	.	.	.	.	.	G	16.89	3.247985	0.59103	.	.	ENSG00000152620	ENST00000381937;ENST00000514504	T;T	0.40225	1.04;1.04	5.87	5.87	0.94306	ATP-NAD kinase, PpnK-type, alpha/beta (1);ATP-NAD kinase, PpnK-type (1);	.	.	.	.	T	0.39145	0.1067	N	0.02674	-0.535	0.80722	D	1	D	0.69078	0.997	D	0.80764	0.994	T	0.48007	-0.9072	9	0.13853	T	0.58	.	18.9723	0.92719	0.0:0.0:1.0:0.0	.	154	Q4G0N4	NAKD1_HUMAN	V	154	ENSP00000371362:A154V;ENSP00000421029:A154V	ENSP00000371362:A154V	A	-	2	0	NADKD1	36262351	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.683000	0.91236	2.767000	0.95098	0.591000	0.81541	GCT	.	.		0.373	NADK2-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367541.1	NM_153013		A	36226594	G	A	36226594	3	1	259	1	0	0	0	0	1	0	0	0	2294	971	34	3	907	3	C5orf33	5	36226594	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1430462	36226594	144688666	226	36544										
LIFR	3977	hgsc.bcm.edu	37	chr5	38481738	38481738	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aaaaaagtttgtaaaggaccAccctcctccattagatttag	6	9	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:38481738A>G	ENST00000263409.4	-	20	3415	c.3253T>C	c.(3253-3255)Tgg>Cgg	p.W1085R	LIFR_ENST00000453190.2_Missense_Mutation_p.W1085R	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	1085					cell surface receptor signaling pathway (GO:0007166)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|leukemia inhibitory factor signaling pathway (GO:0048861)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|leukemia inhibitory factor receptor activity (GO:0004923)			NS(2)|breast(4)|endometrium(6)|kidney(2)|large_intestine(30)|liver(2)|lung(21)|ovary(3)|skin(5)|stomach(1)|urinary_tract(2)	78	all_lung(31;0.00021)					GTAAAGGACCACCCTCCTCCA	0.408			T	PLAG1	salivary adenoma																																p.W1085R	Melanoma(13;4 730 6426 9861 34751)	Atlas-SNP	.		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	.	LIFR	348	.	0			c.T3253C						.						123	128	126					5																	38481738		2203	4300	6503	SO:0001583	missense	3977	exon20			AGGACCACCCTCC	X61615	CCDS3927.1	5p13-p12	2013-02-11	2006-05-17		ENSG00000113594	ENSG00000113594		"CD molecules", "Fibronectin type III domain containing"	6597	protein-coding gene	gene with protein product		151443	"leukemia inhibitory factor receptor"			1915266	Standard	NM_001127671		Approved	CD118	uc003jli.2	P42702	OTTHUMG00000131138	ENST00000263409.4:c.3253T>C	chr5.hg19:g.38481738A>G	ENSP00000263409:p.Trp1085Arg	144.0	0.0		96.0	4.0	NM_002310	Q6LCD9	Missense_Mutation	SNP	ENST00000263409.4	hg19	CCDS3927.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.054177	0.75960	.	.	ENSG00000113594	ENST00000263409;ENST00000453190	T;T	0.72725	-0.68;-0.68	5.94	5.94	0.96194	.	0.255835	0.38005	N	0.001855	D	0.82664	0.5086	M	0.62723	1.935	0.53688	D	0.99997	D	0.89917	1.0	D	0.87578	0.998	D	0.84307	0.0508	10	0.87932	D	0	-10.4001	16.3908	0.83537	1.0:0.0:0.0:0.0	.	1085	P42702	LIFR_HUMAN	R	1085	ENSP00000263409:W1085R;ENSP00000398368:W1085R	ENSP00000263409:W1085R	W	-	1	0	LIFR	38517495	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.125000	0.71627	2.269000	0.75478	0.455000	0.32223	TGG	.	.		0.408	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310		G	38481738	A	G	38481738	3	3	259	1	0	0	0	0	1	0	0	0	8789	159	6	2	44	2	LIFR	5	38481738	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2255144	38481738	142433522	227	36545										
RICTOR	253260	hgsc.bcm.edu	37	chr5	38952348	38952348	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gtctagagctggttgactccGagttcaaacttagagtgctt	11	8	2	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:38952348G>T	ENST00000357387.3	-	30	3107	c.3077C>A	c.(3076-3078)tCg>tAg	p.S1026*	RICTOR_ENST00000503698.1_5'Flank|RICTOR_ENST00000296782.5_Nonsense_Mutation_p.S1026*	NM_152756.3	NP_689969.2			RPTOR independent companion of MTOR, complex 2											NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|prostate(3)|skin(5)	75	all_lung(31;0.000396)					GGTTGACTCCGAGTTCAAACT	0.413																																					p.S1026X		Atlas-SNP	.											.	RICTOR	182	.	0			c.C3077A						.						113	108	110					5																	38952348		2203	4300	6503	SO:0001587	stop_gained	253260	exon30			GACTCCGAGTTCA		CCDS34148.1, CCDS68861.1	5p13.1	2009-07-09			ENSG00000164327	ENSG00000164327			28611	protein-coding gene	gene with protein product	"rapamycin-insensitive companion of mTOR", "pianissimo"	609022				12477932	Standard	XM_005248278		Approved	MGC39830, AVO3, PIA, KIAA1999	uc003jlp.2	Q6R327	OTTHUMG00000162037	ENST00000357387.3:c.3077C>A	chr5.hg19:g.38952348G>T	ENSP00000349959:p.Ser1026*	174.0	0.0		91.0	4.0	NM_152756		Nonsense_Mutation	SNP	ENST00000357387.3	hg19	CCDS34148.1	.	.	.	.	.	.	.	.	.	.	G	41	8.702961	0.98920	.	.	ENSG00000164327	ENST00000357387;ENST00000296782	.	.	.	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.4694	19.4443	0.94840	0.0:0.0:1.0:0.0	.	.	.	.	X	1026	.	ENSP00000296782:S1026X	S	-	2	0	RICTOR	38988105	1.000000	0.71417	0.995000	0.50966	0.975000	0.68041	9.434000	0.97515	2.590000	0.87494	0.460000	0.39030	TCG	.	.		0.413	RICTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366985.1	NM_152756		T	38952348	G	T	38952348	4	4	259	1	0	0	0	0	0	1	0	0	13373	1059	37	1	2085	1	RICTOR	5	38952348	Nonsense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	470610	38952348	141962912	228	36546										
DAB2	1601	hgsc.bcm.edu	37	chr5	39390554	39390554	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cttagagctcacctgttgccCggtttttatggcaaaaaact	8	10	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:39390554C>A	ENST00000320816.6	-	5	921	c.454G>T	c.(454-456)Ggg>Tgg	p.G152W	DAB2_ENST00000545653.1_Missense_Mutation_p.G152W|DAB2_ENST00000339788.6_Missense_Mutation_p.G152W|DAB2_ENST00000512525.1_5'UTR|DAB2_ENST00000509337.1_Missense_Mutation_p.G152W	NM_001343.3	NP_001334.2	P98082	DAB2_HUMAN	Dab, mitogen-responsive phosphoprotein, homolog 2 (Drosophila)	152	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cell morphogenesis involved in differentiation (GO:0000904)|cell proliferation (GO:0008283)|cellular response to transforming growth factor beta stimulus (GO:0071560)|clathrin coat assembly (GO:0048268)|endoderm development (GO:0007492)|excretion (GO:0007588)|in utero embryonic development (GO:0001701)|leading edge cell differentiation (GO:0035026)|membrane organization (GO:0061024)|myeloid cell differentiation (GO:0030099)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of protein binding (GO:0032091)|negative regulation of protein localization to plasma membrane (GO:1903077)|negative regulation of transcription, DNA-templated (GO:0045892)|pinocytosis (GO:0006907)|positive regulation of cell migration (GO:0030335)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of endocytosis (GO:0045807)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of receptor recycling (GO:0001921)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|clathrin coat of coated pit (GO:0030132)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	cargo receptor activity (GO:0038024)|clathrin adaptor activity (GO:0035615)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein C-terminus binding (GO:0008022)|SMAD binding (GO:0046332)	p.G152R(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(9)|lung(19)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	47	all_lung(31;0.000197)		Epithelial(62;0.137)			ACCTGTTGCCCGGTTTTTATG	0.443																																					p.G152W		Atlas-SNP	.											DAB2,NS,carcinoma,0,1	DAB2	124	.	1	Substitution - Missense(1)	endometrium(1)	c.G454T						.						90	88	89					5																	39390554		2203	4300	6503	SO:0001583	missense	1601	exon5			GTTGCCCGGTTTT	U53446	CCDS34149.1, CCDS58946.1	5p13.1	2013-10-03	2013-03-08		ENSG00000153071	ENSG00000153071			2662	protein-coding gene	gene with protein product		601236	"disabled (Drosophila) homolog 2 (mitogen-responsive phosphoprotein)", "disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)"			8660969, 9620555	Standard	NM_001343		Approved	DOC-2	uc003jlx.3	P98082	OTTHUMG00000162043	ENST00000320816.6:c.454G>T	chr5.hg19:g.39390554C>A	ENSP00000313391:p.Gly152Trp	91.0	0.0		58.0	4.0	NM_001343	A6NES5|Q13598|Q9BTY0|Q9UK04	Missense_Mutation	SNP	ENST00000320816.6	hg19	CCDS34149.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.885439	0.91814	.	.	ENSG00000153071	ENST00000320816;ENST00000339788;ENST00000545653;ENST00000509337	T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06	5.6	5.6	0.85130	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.045830	0.85682	D	0.000000	T	0.72011	0.3408	L	0.29908	0.895	0.53688	D	0.99997	D;D	0.89917	1.0;1.0	D;D	0.77557	0.99;0.983	T	0.74321	-0.3703	10	0.87932	D	0	-7.8572	19.9823	0.97331	0.0:1.0:0.0:0.0	.	152;152	P98082;P98082-3	DAB2_HUMAN;.	W	152	ENSP00000313391:G152W;ENSP00000345508:G152W;ENSP00000439919:G152W;ENSP00000426245:G152W	ENSP00000313391:G152W	G	-	1	0	DAB2	39426311	1.000000	0.71417	0.995000	0.50966	0.965000	0.64279	5.545000	0.67237	2.788000	0.95919	0.650000	0.86243	GGG	.	.		0.443	DAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367014.1	NM_001343		A	39390554	C	A	39390554	3	1	259	1	0	0	0	0	1	0	0	0	4220	652	23	1	1898	1	DAB2	5	39390554	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	438206	39390554	141524706	229	36547										
CARD6	84674	hgsc.bcm.edu	37	chr5	40853234	40853234	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	caaatttttcagaggatactGaacttgaagccagcacagct	8	9	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:40853234G>A	ENST00000254691.5	+	3	1999	c.1800G>A	c.(1798-1800)ctG>ctA	p.L600L	CARD6_ENST00000381677.3_Intron	NM_032587.3	NP_115976.2	Q9BX69	CARD6_HUMAN	caspase recruitment domain family, member 6	600					apoptotic process (GO:0006915)|regulation of apoptotic process (GO:0042981)					NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(2)|lung(29)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	62						AGAGGATACTGAACTTGAAGC	0.483																																					p.L600L		Atlas-SNP	.											.	CARD6	141	.	0			c.G1800A						.						118	119	118					5																	40853234		2203	4300	6503	SO:0001819	synonymous_variant	84674	exon3			GATACTGAACTTG	AF356193	CCDS3935.1	5p13.1	2008-05-23			ENSG00000132357	ENSG00000132357			16394	protein-coding gene	gene with protein product		609986				12775719	Standard	NM_032587		Approved	CINCIN1	uc003jmg.3	Q9BX69	OTTHUMG00000094775	ENST00000254691.5:c.1800G>A	chr5.hg19:g.40853234G>A		193.0	0.0		93.0	4.0	NM_032587	Q52LR2	Silent	SNP	ENST00000254691.5	hg19	CCDS3935.1																																																																																			.	.		0.483	CARD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211584.3			A	40853234	G	A	40853234	2	1	259	1	0	0	0	0	0	0	0	1	2652	1277	45	3		3	CARD6	5	40853234	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1462680	40853234	140062026	230	36548										
C6	729	hgsc.bcm.edu	37	chr5	41186295	41186295	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acttctcctctgggctctccTgccagaaaatgaaacctaga	7	13	3	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:41186295T>C	ENST00000263413.3	-	6	867	c.603A>G	c.(601-603)gcA>gcG	p.A201A	C6_ENST00000475349.1_Intron|C6_ENST00000337836.5_Silent_p.A201A	NM_001115131.1	NP_001108603.2	P13671	CO6_HUMAN	complement component 6	201	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)				central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(7)|large_intestine(16)|liver(1)|lung(51)|ovary(3)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)	96		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)				TGGGCTCTCCTGCCAGAAAAT	0.373																																					p.A201A		Atlas-SNP	.											.	C6	197	.	0			c.A603G						.						68	67	68					5																	41186295		2203	4300	6503	SO:0001819	synonymous_variant	729	exon6			CTCTCCTGCCAGA	J05024	CCDS3936.1	5p13.1	2014-09-17			ENSG00000039537	ENSG00000039537		"Complement system"	1339	protein-coding gene	gene with protein product		217050					Standard	NM_001115131		Approved		uc003jmk.3	P13671	OTTHUMG00000094781	ENST00000263413.3:c.603A>G	chr5.hg19:g.41186295T>C		174.0	0.0		97.0	4.0	NM_001115131		Silent	SNP	ENST00000263413.3	hg19	CCDS3936.1																																																																																			.	.		0.373	C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211592.1			C	41186295	T	C	41186295	2	2	259	1	0	0	0	0	0	0	0	1	2317	1567	55	2		2	C6	5	41186295	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	333061	41186295	139728965	231	36549										
C5orf34	375444	hgsc.bcm.edu	37	chr5	43490731	43490731	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tttaagtttaaaagaaaaatAccaattttcttggagaacag	6	4	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:43490731A>G	ENST00000306862.2	-	11	2055		c.e11+1		RP11-159F24.3_ENST00000505645.1_RNA	NM_198566.2	NP_940968	Q96MH7	CE034_HUMAN	chromosome 5 open reading frame 34											breast(2)|endometrium(2)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|stomach(2)	21	Lung NSC(6;2.07e-05)					AAAGAAAAATACCAATTTTCT	0.338																																					.		Atlas-SNP	.											.	C5orf34	47	.	0			c.1679+2T>C						.						58	57	57					5																	43490731		2203	4299	6502	SO:0001630	splice_region_variant	375444	exon12			AAAAATACCAATT	AK056925	CCDS3946.1	5p12	2012-02-23			ENSG00000172244	ENSG00000172244			24738	protein-coding gene	gene with protein product						12477932	Standard	XM_006714473		Approved	FLJ32363	uc003jnz.2	Q96MH7	OTTHUMG00000131151	ENST00000306862.2:c.1679+1T>C	chr5.hg19:g.43490731A>G		128.0	0.0		82.0	4.0	NM_198566		Splice_Site	SNP	ENST00000306862.2	hg19	CCDS3946.1	.	.	.	.	.	.	.	.	.	.	A	16.95	3.262381	0.59431	.	.	ENSG00000172244	ENST00000306862	.	.	.	5.44	5.44	0.79542	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.1728	0.59609	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	C5orf34	43526488	1.000000	0.71417	0.996000	0.52242	0.703000	0.40648	4.739000	0.62080	2.190000	0.69967	0.528000	0.53228	.	.	.		0.338	C5orf34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253843.1	NM_198566	Intron	G	43490731	A	G	43490731	5	3	259	1	0	0	0	0	0	0	1	0	2295	405	14	2	247	2	C5orf34	5	43490731	Splice_Site	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2304436	43490731	137424529	232	36550										
MRPS30	10884	hgsc.bcm.edu	37	chr5	44815068	44815068	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttgtctcccaggctgtgatcAcagatggaaaatacttttcc	8	10	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:44815068A>G	ENST00000507110.1	+	5	1122	c.1084A>G	c.(1084-1086)Aca>Gca	p.T362A		NM_016640.3	NP_057724.2	Q9NP92	RT30_HUMAN	mitochondrial ribosomal protein S30	362					apoptotic process (GO:0006915)|translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.T362A(2)		central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(2)|lung(11)|prostate(1)	20	Lung NSC(6;8.08e-07)					GGCTGTGATCACAGATGGAAA	0.378																																					p.T362A		Atlas-SNP	.											MRPS30_ENST00000507110,NS,carcinoma,0,2	MRPS30	90	.	2	Substitution - Missense(2)	endometrium(2)	c.A1084G						.						162	166	164					5																	44815068		2203	4300	6503	SO:0001583	missense	10884	exon5			GTGATCACAGATG	AF146192	CCDS3951.1	5q11	2012-09-13		2001-11-09	ENSG00000112996	ENSG00000112996		"Mitochondrial ribosomal proteins / small subunits"	8769	protein-coding gene	gene with protein product		611991		PDCD9		10640817, 11279123	Standard	NM_016640		Approved	PAP	uc003joh.3	Q9NP92	OTTHUMG00000096967	ENST00000507110.1:c.1084A>G	chr5.hg19:g.44815068A>G	ENSP00000424328:p.Thr362Ala	144.0	0.0		75.0	3.0	NM_016640	Q96I91|Q96Q19|Q9H0P8|Q9NSF9|Q9NZ76	Missense_Mutation	SNP	ENST00000507110.1	hg19	CCDS3951.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.323158	0.81580	.	.	ENSG00000112996	ENST00000507110	T	0.30448	1.53	5.86	5.86	0.93980	.	0.047675	0.85682	D	0.000000	T	0.54951	0.1890	M	0.81341	2.54	0.58432	D	0.999999	D	0.63046	0.992	D	0.66716	0.946	T	0.60301	-0.7290	10	0.72032	D	0.01	-23.2635	11.3486	0.49575	0.8646:0.0:0.0:0.1354	.	362	Q9NP92	RT30_HUMAN	A	362	ENSP00000424328:T362A	ENSP00000424328:T362A	T	+	1	0	MRPS30	44850825	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.139000	0.77314	2.237000	0.73441	0.528000	0.53228	ACA	.	.		0.378	MRPS30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214033.2	NM_016640		G	44815068	A	G	44815068	3	3	259	1	0	0	0	0	1	0	0	0	9849	159	6	2	1102	2	MRPS30	5	44815068	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1324337	44815068	136100192	233	36551										
GPX8	493869	hgsc.bcm.edu	37	chr5	54456944	54456944	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gtgttggcttttccctgcaaTcagtttggagaatcggagcc	12	9	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:54456944T>C	ENST00000503787.1	+	2	402	c.327T>C	c.(325-327)aaT>aaC	p.N109N	GPX8_ENST00000515370.1_Silent_p.N58N|CDC20B_ENST00000331730.3_Intron|CDC20B_ENST00000296733.1_Intron|GPX8_ENST00000506123.1_3'UTR|CDC20B_ENST00000381375.2_Intron|CDC20B_ENST00000334206.5_Intron|GPX8_ENST00000296734.6_Intron|CDC20B_ENST00000322374.6_Intron	NM_001008397.2	NP_001008398.2	Q8TED1	GPX8_HUMAN	glutathione peroxidase 8 (putative)	109					response to oxidative stress (GO:0006979)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	glutathione peroxidase activity (GO:0004602)|peroxidase activity (GO:0004601)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|prostate(1)	11					Glutathione(DB00143)	TTCCCTGCAATCAGTTTGGAG	0.463																																					p.N109N		Atlas-SNP	.											.	GPX8	20	.	0			c.T327C						.						86	83	84					5																	54456944		2203	4300	6503	SO:0001819	synonymous_variant	493869	exon2			CTGCAATCAGTTT	BC029424	CCDS34156.1	5q11.2	2008-09-29				ENSG00000164294			33100	protein-coding gene	gene with protein product							Standard	NM_001008397		Approved	UNQ847, EPLA847	uc003jpq.2	Q8TED1		ENST00000503787.1:c.327T>C	chr5.hg19:g.54456944T>C		143.0	0.0		77.0	4.0	NM_001008397		Silent	SNP	ENST00000503787.1	hg19	CCDS34156.1																																																																																			.	.		0.463	GPX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369717.1	NM_001008397		C	54456944	T	C	54456944	2	2	259	1	0	0	0	0	0	0	0	1	6755	1432	50	2		2	GPX8	5	54456944	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	9641876	54456944	126458316	234	36552										
IL6ST	3572	hgsc.bcm.edu	37	chr5	55237449	55237449	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttcatcactgctagaaatgcTtggcctagaagatgacatgc	9	9	2	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:55237449T>A	ENST00000381298.2	-	17	2530	c.2218A>T	c.(2218-2220)Agc>Tgc	p.S740C	IL6ST_ENST00000381294.3_Missense_Mutation_p.S679C|IL6ST_ENST00000536319.1_3'UTR|IL6ST_ENST00000381287.4_3'UTR|IL6ST_ENST00000336909.5_Missense_Mutation_p.S740C|IL6ST_ENST00000502326.3_Missense_Mutation_p.S740C|CTD-2031P19.5_ENST00000576302.1_RNA	NM_001190981.1|NM_002184.3|NM_175767.2	NP_001177910.1|NP_002175.2|NP_786943.1	P40189	IL6RB_HUMAN	interleukin 6 signal transducer	740	Ser-rich.				ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|glycogen metabolic process (GO:0005977)|interleukin-27-mediated signaling pathway (GO:0070106)|interleukin-6-mediated signaling pathway (GO:0070102)|leukemia inhibitory factor signaling pathway (GO:0048861)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of Notch signaling pathway (GO:0008593)|response to cytokine (GO:0034097)|viral process (GO:0016032)	ciliary neurotrophic factor receptor complex (GO:0070110)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|interleukin-6 receptor complex (GO:0005896)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|oncostatin-M receptor complex (GO:0005900)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|interleukin-11 receptor activity (GO:0004921)|interleukin-27 receptor activity (GO:0045509)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(5)|kidney(5)|large_intestine(4)|liver(2)|lung(1)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)				CTAGAAATGCTTGGCCTAGAA	0.428			O		hepatocellular ca																																p.S740C		Atlas-SNP	.		Dom	yes		5	5q11	3572	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"		E	.	IL6ST	75	.	0			c.A2218T						.						180	179	180					5																	55237449		2203	4300	6503	SO:0001583	missense	3572	exon17			AAATGCTTGGCCT	M57230	CCDS3971.1, CCDS47209.1, CCDS54856.1	5q11.2	2014-04-04	2014-04-04		ENSG00000134352	ENSG00000134352		"Interleukins and interleukin receptors", "CD molecules", "Fibronectin type III domain containing"	6021	protein-coding gene	gene with protein product	"gp130, oncostatin M receptor"	600694	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"			2261637	Standard	NM_002184		Approved	GP130, CD130	uc003jqq.3	P40189	OTTHUMG00000097043	ENST00000381298.2:c.2218A>T	chr5.hg19:g.55237449T>A	ENSP00000370698:p.Ser740Cys	155.0	0.0		97.0	4.0	NM_002184	A0N0L4|Q5FC04|Q9UQ41	Missense_Mutation	SNP	ENST00000381298.2	hg19	CCDS3971.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.398179	0.83120	.	.	ENSG00000134352	ENST00000381298;ENST00000336909;ENST00000381294	T;T;T	0.44482	1.2;1.2;0.92	5.4	5.4	0.78164	.	0.161133	0.64402	D	0.000002	T	0.55768	0.1941	L	0.36672	1.1	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.59295	-0.7481	10	0.87932	D	0	.	15.7345	0.77831	0.0:0.0:0.0:1.0	.	740;679;740	Q17RA0;Q5FC04;P40189	.;.;IL6RB_HUMAN	C	740;740;679	ENSP00000370698:S740C;ENSP00000338799:S740C;ENSP00000370694:S679C	ENSP00000338799:S740C	S	-	1	0	IL6ST	55273206	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.299000	0.78831	2.170000	0.68504	0.455000	0.32223	AGC	.	.		0.428	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184		A	55237449	T	A	55237449	3	1	259	1	0	0	0	0	1	0	0	0	7712	1609	56	4	542	4	IL6ST	5	55237449	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	780505	55237449	125677811	235	36553										
PLK2	10769	hgsc.bcm.edu	37	chr5	57753099	57753099	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tagcaattaagtgcttggcaGgagccagcaatgaggacggc	14	8	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:57753099G>T	ENST00000274289.3	-	7	1217	c.917C>A	c.(916-918)cCt>cAt	p.P306H	PLK2_ENST00000502671.1_5'UTR	NM_001252226.1|NM_006622.3	NP_001239155.1|NP_006613.2	Q9NYY3	PLK2_HUMAN	polo-like kinase 2	306	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				G1/S transition of mitotic cell cycle (GO:0000082)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|mitotic cell cycle checkpoint (GO:0007093)|mitotic spindle organization (GO:0007052)|negative regulation of apoptotic process (GO:0043066)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein phosphorylation (GO:0006468)|Rap protein signal transduction (GO:0032486)|Ras protein signal transduction (GO:0007265)|regulation of centriole replication (GO:0046599)|regulation of synaptic plasticity (GO:0048167)	centriole (GO:0005814)|centrosome (GO:0005813)|dendrite (GO:0030425)|intracellular (GO:0005622)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			endometrium(7)|large_intestine(7)|lung(5)|ovary(3)|prostate(2)|skin(2)	26		all_cancers(5;1.76e-12)|all_epithelial(5;2.09e-13)|all_lung(5;6.64e-05)|Lung NSC(5;0.000127)|Prostate(74;0.055)|Breast(144;0.0602)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;7.03e-37)		GTGCTTGGCAGGAGCCAGCAA	0.438																																					p.P306H		Atlas-SNP	.											.	PLK2	71	.	0			c.C917A						.						86	81	83					5																	57753099		2203	4300	6503	SO:0001583	missense	10769	exon7			TTGGCAGGAGCCA		CCDS3974.1, CCDS75250.1	5q12.1-q13.2	2013-01-18	2010-06-24		ENSG00000145632	ENSG00000145632			19699	protein-coding gene	gene with protein product	"serum-inducible kinase"	607023	"polo-like kinase 2 (Drosophila)"				Standard	NM_006622		Approved	SNK	uc003jrn.3	Q9NYY3	OTTHUMG00000097047	ENST00000274289.3:c.917C>A	chr5.hg19:g.57753099G>T	ENSP00000274289:p.Pro306His	46.0	0.0		20.0	4.0	NM_006622	O60679|Q96CV7|Q9UE61	Missense_Mutation	SNP	ENST00000274289.3	hg19	CCDS3974.1	.	.	.	.	.	.	.	.	.	.	G	14.05	2.419916	0.42918	.	.	ENSG00000145632	ENST00000274289;ENST00000537944;ENST00000442330	T	0.65178	-0.14	5.27	5.27	0.74061	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.168065	0.56097	D	0.000040	T	0.59473	0.2196	L	0.39020	1.185	0.45662	D	0.998584	B	0.24186	0.099	B	0.32762	0.152	T	0.57676	-0.7770	10	0.49607	T	0.09	-15.0317	18.9292	0.92558	0.0:0.0:1.0:0.0	.	306	Q9NYY3	PLK2_HUMAN	H	306;306;292	ENSP00000274289:P306H	ENSP00000274289:P306H	P	-	2	0	PLK2	57788856	1.000000	0.71417	0.999000	0.59377	0.987000	0.75469	5.947000	0.70242	2.461000	0.83175	0.655000	0.94253	CCT	.	.		0.438	PLK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214150.1	NM_006622		T	57753099	G	T	57753099	3	4	259	1	0	0	0	0	1	0	0	0	12105	1000	35	3	1172	3	PLK2	5	57753099	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	2515650	57753099	123162161	236	36554										
MAP1B	4131	hgsc.bcm.edu	37	chr5	71489755	71489755	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agcttaaccctgttctgtccTgaagaaggggactggaagaa	12	8	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:71489755T>C	ENST00000296755.7	+	5	871	c.573T>C	c.(571-573)ccT>ccC	p.P191P		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	191					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)	p.P191P(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		TGTTCTGTCCTGAAGAAGGGG	0.423																																					p.P191P	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											MAP1B,NS,carcinoma,0,1	MAP1B	243	.	1	Substitution - coding silent(1)	lung(1)	c.T573C						.						81	78	79					5																	71489755		2203	4300	6503	SO:0001819	synonymous_variant	4131	exon5			CTGTCCTGAAGAA	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.573T>C	chr5.hg19:g.71489755T>C		98.0	0.0		37.0	2.0	NM_005909	A2BDK5	Silent	SNP	ENST00000296755.7	hg19	CCDS4012.1																																																																																			.	.		0.423	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		C	71489755	T	C	71489755	2	2	259	1	0	0	0	0	0	0	0	1	9237	1567	55	2		2	MAP1B	5	71489755	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	13736656	71489755	109425505	237	36555										
MAP1B	4131	hgsc.bcm.edu	37	chr5	71493402	71493402	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cccgcccctcattggatccgAgtctgcttatgaaagttttc	8	13	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:71493402A>G	ENST00000296755.7	+	5	4518	c.4220A>G	c.(4219-4221)gAg>gGg	p.E1407G		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1407					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		ATTGGATCCGAGTCTGCTTAT	0.493																																					p.E1407G	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.A4220G						.						46	48	48					5																	71493402		2202	4300	6502	SO:0001583	missense	4131	exon5			GATCCGAGTCTGC	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.4220A>G	chr5.hg19:g.71493402A>G	ENSP00000296755:p.Glu1407Gly	121.0	0.0		70.0	4.0	NM_005909	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	hg19	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	A	14.40	2.522854	0.44866	.	.	ENSG00000131711	ENST00000296755	T	0.04275	3.66	5.55	5.55	0.83447	.	0.082420	0.51477	D	0.000082	T	0.04724	0.0128	N	0.24115	0.695	0.49130	D	0.999753	P;P	0.39665	0.682;0.546	B;B	0.34590	0.186;0.186	T	0.44636	-0.9315	10	0.87932	D	0	-17.0322	15.6992	0.77528	1.0:0.0:0.0:0.0	.	1281;1407	A2BDK6;P46821	.;MAP1B_HUMAN	G	1407	ENSP00000296755:E1407G	ENSP00000296755:E1407G	E	+	2	0	MAP1B	71529158	1.000000	0.71417	0.984000	0.44739	0.566000	0.35808	3.881000	0.56152	2.122000	0.65172	0.459000	0.35465	GAG	.	.		0.493	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		G	71493402	A	G	71493402	3	3	259	1	0	0	0	0	1	0	0	0	9237	304	11	2	4238	2	MAP1B	5	71493402	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	3647	71493402	109421858	238	36556										
RGNEF	64283	hgsc.bcm.edu	37	chr5	73189069	73189069	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aagtgaatctgatgaagacaAgaggaaagctgaagccagag	13	5	1	7			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:73189069A>G	ENST00000426542.2	+	27	3634	c.3614A>G	c.(3613-3615)aAg>aGg	p.K1205R	ARHGEF28_ENST00000512883.1_Missense_Mutation_p.K169R|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.K1205R|ARHGEF28_ENST00000287898.5_Missense_Mutation_p.K1205R|ARHGEF28_ENST00000296799.4_Missense_Mutation_p.K892R|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.K1205R|ARHGEF28_ENST00000545377.1_Missense_Mutation_p.K1205R|ARHGEF28_ENST00000437974.1_Missense_Mutation_p.K1205R			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	1205					central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)										GATGAAGACAAGAGGAAAGCT	0.458																																					p.K1205R		Atlas-SNP	.											.	.	.	.	0			c.A3614G						.						78	75	76					5																	73189069		1947	4124	6071	SO:0001583	missense	64283	exon28			AAGACAAGAGGAA		CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.3614A>G	chr5.hg19:g.73189069A>G	ENSP00000412175:p.Lys1205Arg	152.0	0.0		97.0	4.0	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	hg19	CCDS54870.1	.	.	.	.	.	.	.	.	.	.	A	3.469	-0.108308	0.06924	.	.	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542;ENST00000296799;ENST00000512883	T;T;T;T;T;T;T;T	0.30714	3.17;3.18;3.17;2.86;3.18;3.17;3.0;1.52	4.87	0.227	0.15359	.	.	.	.	.	T	0.12518	0.0304	N	0.04335	-0.225	0.18873	N	0.999981	B;B;B;B;B	0.09022	0.001;0.001;0.0;0.002;0.0	B;B;B;B;B	0.11329	0.004;0.005;0.004;0.006;0.003	T	0.35895	-0.9770	9	0.12430	T	0.62	.	9.1023	0.36676	0.4434:0.0:0.5566:0.0	.	892;1205;1205;169;1205	B5MDA3;Q8N1W1;E9PC75;D6RGZ3;Q8N1W1-4	.;RGNEF_HUMAN;.;.;.	R	1205;1205;1205;1205;1205;1205;892;169	ENSP00000296794:K1205R;ENSP00000441913:K1205R;ENSP00000441436:K1205R;ENSP00000287898:K1205R;ENSP00000411459:K1205R;ENSP00000412175:K1205R;ENSP00000296799:K892R;ENSP00000421081:K169R	ENSP00000287898:K1205R	K	+	2	0	RP11-428C6.1	73224825	1.000000	0.71417	0.999000	0.59377	0.926000	0.56050	1.135000	0.31454	0.211000	0.20683	-0.177000	0.13119	AAG	.	.		0.458	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1			G	73189069	A	G	73189069	3	3	259	1	0	0	0	0	1	0	0	0	13298	72	3	2	3720	2	RGNEF	5	73189069	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1695667	73189069	107726191	239	36557										
HMGCR	3156	hgsc.bcm.edu	37	chr5	74638583	74638583	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggttggaattatgaatgtccAaagtttgaagaggttagtga	13	2	0	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:74638583A>G	ENST00000287936.4	+	2	309	c.153A>G	c.(151-153)ccA>ccG	p.P51P	HMGCR_ENST00000343975.5_Silent_p.P51P|HMGCR_ENST00000511206.1_Silent_p.P51P	NM_000859.2	NP_000850.1	P04035	HMDH_HUMAN	3-hydroxy-3-methylglutaryl-CoA reductase	51					aging (GO:0007568)|cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|coenzyme A metabolic process (GO:0015936)|isoprenoid biosynthetic process (GO:0008299)|myoblast differentiation (GO:0045445)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of striated muscle cell apoptotic process (GO:0010664)|negative regulation of vasodilation (GO:0045908)|negative regulation of wound healing (GO:0061045)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein tetramerization (GO:0051262)|response to ethanol (GO:0045471)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|ubiquinone metabolic process (GO:0006743)|visual learning (GO:0008542)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|peroxisomal membrane (GO:0005778)	coenzyme binding (GO:0050662)|hydroxymethylglutaryl-CoA reductase (NADPH) activity (GO:0004420)|hydroxymethylglutaryl-CoA reductase activity (GO:0042282)|NADPH binding (GO:0070402)			breast(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	20		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;2.24e-54)	Atorvastatin(DB01076)|Fluvastatin(DB01095)|Lovastatin(DB00227)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rosuvastatin(DB01098)|Simvastatin(DB00641)	ATGAATGTCCAAAGTTTGAAG	0.373																																					p.P51P		Atlas-SNP	.											.	HMGCR	53	.	0			c.A153G						.						101	93	95					5																	74638583		2203	4300	6503	SO:0001819	synonymous_variant	3156	exon2			ATGTCCAAAGTTT		CCDS4027.1, CCDS47234.1	5q13.3-q14	2012-10-02	2010-04-30		ENSG00000113161	ENSG00000113161	1.1.1.88, 1.1.1.34		5006	protein-coding gene	gene with protein product	"hydroxymethylglutaryl-CoA reductase", "3-hydroxy-3-methylglutaryl CoA reductase (NADPH)"	142910	"3-hydroxy-3-methylglutaryl-Coenzyme A reductase"				Standard	NM_000859		Approved		uc003kdp.3	P04035	OTTHUMG00000102069	ENST00000287936.4:c.153A>G	chr5.hg19:g.74638583A>G		159.0	0.0		91.0	5.0	NM_001130996	B7Z3Y9|Q8N190	Silent	SNP	ENST00000287936.4	hg19	CCDS4027.1																																																																																			.	.		0.373	HMGCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219877.2			G	74638583	A	G	74638583	2	3	259	1	0	0	0	0	0	0	0	1	7240	117	5	2		2	HMGCR	5	74638583	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1449514	74638583	106276677	240	36558										
JMY	133746	hgsc.bcm.edu	37	chr5	78587025	78587025	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggcagcggctgctgaacggaTggaaaaactccagtatgcag	14	9	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:78587025T>C	ENST00000396137.4	+	4	1892	c.1430T>C	c.(1429-1431)aTg>aCg	p.M477T		NM_152405.4	NP_689618.4	Q8N9B5	JMY_HUMAN	junction mediating and regulatory protein, p53 cofactor	477					'de novo' actin filament nucleation (GO:0070060)|actin polymerization-dependent cell motility (GO:0070358)|Arp2/3 complex-mediated actin nucleation (GO:0034314)|cell cycle arrest (GO:0007050)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of apoptotic process (GO:0043065)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			endometrium(4)|kidney(2)|large_intestine(2)|lung(6)|skin(1)|urinary_tract(1)	16		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;4.45e-45)|Epithelial(54;5.85e-40)|all cancers(79;2.89e-35)		GCTGAACGGATGGAAAAACTC	0.393																																					p.M477T		Atlas-SNP	.											.	JMY	82	.	0			c.T1430C						.						72	71	71					5																	78587025		1874	4096	5970	SO:0001583	missense	133746	exon4			AACGGATGGAAAA	AK095189	CCDS4047.3	5q14.1	2010-03-23			ENSG00000152409	ENSG00000152409			28916	protein-coding gene	gene with protein product		604279				10518217	Standard	NM_152405		Approved	FLJ37870	uc003kfx.4	Q8N9B5	OTTHUMG00000131301	ENST00000396137.4:c.1430T>C	chr5.hg19:g.78587025T>C	ENSP00000379441:p.Met477Thr	119.0	0.0		77.0	4.0	NM_152405	A1L4P5|B5MDS2|B5MDT0	Missense_Mutation	SNP	ENST00000396137.4	hg19	CCDS4047.3	.	.	.	.	.	.	.	.	.	.	T	19.35	3.811531	0.70797	.	.	ENSG00000152409	ENST00000282259;ENST00000396137	T	0.08807	3.05	5.31	5.31	0.75309	.	0.081869	0.85682	D	0.000000	T	0.14570	0.0352	M	0.66939	2.045	0.53688	D	0.999973	P	0.47910	0.902	B	0.43301	0.415	T	0.01027	-1.1476	10	0.87932	D	0	.	15.2486	0.73526	0.0:0.0:0.0:1.0	.	477	Q8N9B5	JMY_HUMAN	T	477	ENSP00000379441:M477T	ENSP00000282259:M477T	M	+	2	0	JMY	78622781	1.000000	0.71417	0.993000	0.49108	0.824000	0.46624	7.226000	0.78060	1.999000	0.58509	0.454000	0.30748	ATG	.	.		0.393	JMY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254070.4	NM_152405		C	78587025	T	C	78587025	3	2	259	1	0	0	0	0	1	0	0	0	7966	1464	51	2	1444	2	JMY	5	78587025	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	3948442	78587025	102328235	241	36559										
HOMER1	9456	hgsc.bcm.edu	37	chr5	78692728	78692728	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gttttaacctttctatttccTagaaaagacagagcaatgtc	6	8	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:78692728T>C	ENST00000334082.6	-	8	2238		c.e8-2		HOMER1_ENST00000535690.1_Splice_Site|HOMER1_ENST00000508576.1_Intron|HOMER1_ENST00000282260.6_Splice_Site	NM_004272.3	NP_004263.1	Q86YM7	HOME1_HUMAN	homer homolog 1 (Drosophila)						behavioral response to cocaine (GO:0048148)|chemical homeostasis within a tissue (GO:0048875)|circadian rhythm (GO:0007623)|phospholipase C-activating G-protein coupled glutamate receptor signaling pathway (GO:0007206)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of signal transduction (GO:0009967)|protein localization to synapse (GO:0035418)|regulation of calcium ion import (GO:0090279)|regulation of cation channel activity (GO:2001257)|regulation of store-operated calcium entry (GO:2001256)|response to calcium ion (GO:0051592)|response to nicotine (GO:0035094)|skeletal muscle contraction (GO:0003009)|skeletal muscle fiber development (GO:0048741)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell junction (GO:0030054)|costamere (GO:0043034)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|Z disc (GO:0030018)	ion channel binding (GO:0044325)|signaling adaptor activity (GO:0035591)			endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|prostate(2)|skin(1)	14		Lung NSC(167;0.00131)|all_lung(232;0.00151)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;1.87e-44)|Epithelial(54;7.07e-41)|all cancers(79;5.5e-36)		TTCTATTTCCTAGAAAAGACA	0.338																																					.		Atlas-SNP	.											.	HOMER1	37	.	0			c.406-2A>G						.						98	86	89					5																	78692728		1822	4077	5899	SO:0001630	splice_region_variant	9456	exon6			ATTTCCTAGAAAA	BC015502	CCDS43335.1, CCDS64188.1, CCDS64189.1	5q14.2	2008-02-05			ENSG00000152413	ENSG00000152413			17512	protein-coding gene	gene with protein product		604798				9808459, 9808458	Standard	NM_004272		Approved	Ves-1, SYN47, HOMER-1B	uc003kfy.4	Q86YM7	OTTHUMG00000134278	ENST00000334082.6:c.796-2A>G	chr5.hg19:g.78692728T>C		240.0	0.0		123.0	5.0	NM_001277077	B2R688|O96003|Q86YM5	Splice_Site	SNP	ENST00000334082.6	hg19	CCDS43335.1	.	.	.	.	.	.	.	.	.	.	T	19.33	3.806032	0.70682	.	.	ENSG00000152413	ENST00000334082;ENST00000282260;ENST00000535690	.	.	.	5.63	5.63	0.86233	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1139	0.72384	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	HOMER1	78728484	1.000000	0.71417	0.998000	0.56505	0.884000	0.51177	7.063000	0.76714	2.267000	0.75376	0.533000	0.62120	.	.	.		0.338	HOMER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258856.1	NM_004272	Intron	C	78692728	T	C	78692728	5	2	259	1	0	0	0	0	0	0	1	0	7287	1536	53	2	278	2	HOMER1	5	78692728	Splice_Site	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	105703	78692728	102222532	242	36560										
SPZ1	84654	hgsc.bcm.edu	37	chr5	79616053	79616053	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgatggccagctctgctaagTcagctgagatgcccaccatc	10	13	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:79616053T>C	ENST00000296739.4	+	1	264	c.19T>C	c.(19-21)Tca>Cca	p.S7P		NM_032567.3	NP_115956.3	Q9BXG8	SPZ1_HUMAN	spermatogenic leucine zipper 1	7					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(5)|large_intestine(4)|lung(12)|ovary(1)|skin(2)	26		Lung NSC(167;0.0393)|all_lung(232;0.0428)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;3.43e-47)|Epithelial(54;2.25e-41)|all cancers(79;4.19e-36)		CTCTGCTAAGTCAGCTGAGAT	0.473																																					p.S7P		Atlas-SNP	.											.	SPZ1	60	.	0			c.T19C						.						197	197	197					5																	79616053		1960	4163	6123	SO:0001583	missense	84654	exon1			GCTAAGTCAGCTG		CCDS43336.1	5q14.1	2014-06-13				ENSG00000164299			30721	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 148"					11165476, 12778315, 15226296, 15829580, 15899793	Standard	NM_032567		Approved	NYD-TSP1, FLJ25709, PPP1R148	uc003kgn.3	Q9BXG8		ENST00000296739.4:c.19T>C	chr5.hg19:g.79616053T>C	ENSP00000369611:p.Ser7Pro	144.0	0.0		82.0	4.0	NM_032567	B2RA21|Q8N4P1|Q8N7E9	Missense_Mutation	SNP	ENST00000296739.4	hg19	CCDS43336.1	.	.	.	.	.	.	.	.	.	.	T	15.54	2.865170	0.51482	.	.	ENSG00000164299	ENST00000511881;ENST00000296739	T;T	0.52983	0.64;1.26	4.19	-1.18	0.09617	.	1.029180	0.07769	N	0.951371	T	0.36386	0.0965	L	0.42245	1.32	0.09310	N	1	B	0.17667	0.023	B	0.19391	0.025	T	0.39961	-0.9588	10	0.66056	D	0.02	-3.7233	4.0791	0.09917	0.0:0.2015:0.3598:0.4387	.	7	Q9BXG8	SPZ1_HUMAN	P	7	ENSP00000426530:S7P;ENSP00000369611:S7P	ENSP00000369611:S7P	S	+	1	0	SPZ1	79651809	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	0.014000	0.13333	-0.176000	0.10707	0.379000	0.24179	TCA	.	.		0.473	SPZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369322.1	NM_032567		C	79616053	T	C	79616053	3	2	259	1	0	0	0	0	1	0	0	0	15142	1667	58	2	21	2	SPZ1	5	79616053	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	923325	79616053	101299207	243	36561										
GPR98	84059	hgsc.bcm.edu	37	chr5	89971070	89971070	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tctccactaggcttgctgcaGttctccacagggctgcctcc	9	16	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:89971070G>A	ENST00000405460.2	+	24	5217	c.5121G>A	c.(5119-5121)caG>caA	p.Q1707Q	GPR98_ENST00000450321.2_3'UTR	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	1707					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		GCTTGCTGCAGTTCTCCACAG	0.483																																					p.Q1707Q		Atlas-SNP	.											.	GPR98	605	.	0			c.G5121A						.						47	49	48					5																	89971070		2067	4215	6282	SO:0001819	synonymous_variant	84059	exon24			GCTGCAGTTCTCC	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.5121G>A	chr5.hg19:g.89971070G>A		84.0	0.0		53.0	41.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	hg19	CCDS47246.1																																																																																			.	.		0.483	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		A	89971070	G	A	89971070	2	1	259	1	0	0	0	0	0	0	0	1	6730	1020	36	3		3	GPR98	5	89971070	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	10355017	89971070	90944190	244	36562										
MCTP1	79772	hgsc.bcm.edu	37	chr5	94245051	94245051	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	taaaggtgaaaatcaaattgTtccctccactgaggattcaa	7	8	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:94245051T>C	ENST00000515393.1	-	10	1556	c.1557A>G	c.(1555-1557)gaA>gaG	p.E519E	MCTP1_ENST00000312216.8_Silent_p.E298E|MCTP1_ENST00000505078.1_Silent_p.E35E|MCTP1_ENST00000505208.1_Silent_p.E298E|MCTP1_ENST00000429576.2_Silent_p.E252E	NM_024717.4	NP_078993.4	Q6DN14	MCTP1_HUMAN	multiple C2 domains, transmembrane 1	519	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(13)|liver(2)|lung(13)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	41		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)		AATCAAATTGTTCCCTCCACT	0.368																																					p.E519E		Atlas-SNP	.											.	MCTP1	110	.	0			c.A1557G						.						80	78	79					5																	94245051		2203	4300	6503	SO:0001819	synonymous_variant	79772	exon10			AAATTGTTCCCTC		CCDS34203.1, CCDS47247.1, CCDS75275.1	5q15	2008-02-05			ENSG00000175471	ENSG00000175471			26183	protein-coding gene	gene with protein product						15528213	Standard	XM_005272082		Approved	FLJ22344	uc003kkx.2	Q6DN14	OTTHUMG00000162742	ENST00000515393.1:c.1557A>G	chr5.hg19:g.94245051T>C		175.0	0.0		105.0	6.0	NM_024717	Q6DN13|Q8N2W1|Q8NBA2|Q96LX0|Q9H6E8	Silent	SNP	ENST00000515393.1	hg19	CCDS34203.1	.	.	.	.	.	.	.	.	.	.	T	9.049	0.991491	0.18966	.	.	ENSG00000175471	ENST00000503301	.	.	.	5.68	3.35	0.38373	.	.	.	.	.	T	0.55768	0.1941	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50634	-0.8805	4	.	.	.	-20.4283	6.8803	0.24168	0.0:0.3275:0.0:0.6725	.	.	.	.	A	282	.	.	T	-	1	0	MCTP1	94270807	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.993000	0.29680	1.003000	0.39130	0.477000	0.44152	ACA	.	.		0.368	MCTP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370280.3	NM_024717		C	94245051	T	C	94245051	2	2	259	1	0	0	0	0	0	0	0	1	9409	1722	60	2		2	MCTP1	5	94245051	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	4273981	94245051	86670209	245	36563										
CHD1	1105	hgsc.bcm.edu	37	chr5	98204197	98204197	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aatcagaaagtctaaggcttAcaatgctgaatgtcttctga	8	7	4	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:98204197A>T	ENST00000284049.3	-	30	4398		c.e30+1		CHD1_ENST00000511067.1_Splice_Site	NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1						chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	49		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	TCTAAGGCTTACAATGCTGAA	0.343																																					.		Atlas-SNP	.											.	CHD1	137	.	0			c.4248+2T>A						.						97	98	97					5																	98204197		2203	4300	6503	SO:0001630	splice_region_variant	1105	exon31			AGGCTTACAATGC	AF006513	CCDS34204.1	5q15-q21	2008-07-18			ENSG00000153922	ENSG00000153922			1915	protein-coding gene	gene with protein product		602118				8460153, 9326634	Standard	XM_005271866		Approved		uc003knf.3	O14646	OTTHUMG00000162744	ENST00000284049.3:c.4248+1T>A	chr5.hg19:g.98204197A>T		90.0	0.0		53.0	4.0	NM_001270	Q17RZ3	Splice_Site	SNP	ENST00000284049.3	hg19	CCDS34204.1	.	.	.	.	.	.	.	.	.	.	A	15.63	2.891018	0.52014	.	.	ENSG00000153922	ENST00000284049	.	.	.	5.32	5.32	0.75619	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.5806	0.76432	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CHD1	98232097	1.000000	0.71417	1.000000	0.80357	0.549000	0.35272	8.878000	0.92393	2.157000	0.67596	0.533000	0.62120	.	.	.		0.343	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270	Intron	T	98204197	A	T	98204197	5	4	259	1	0	0	0	0	0	0	1	0	3325	405	14	4	906	4	CHD1	5	98204197	Splice_Site	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	3959146	98204197	82711063	246	36564										
ST8SIA4	7903	hgsc.bcm.edu	37	chr5	100231449	100231449	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctttcgaatgattttatcagAgctattgacaagtgaccgac	8	8	1	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:100231449A>G	ENST00000231461.5	-	2	464	c.154T>C	c.(154-156)Tct>Cct	p.S52P	ST8SIA4_ENST00000451528.2_Missense_Mutation_p.S52P	NM_005668.4	NP_005659.1	Q92187	SIA8D_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	52					axon guidance (GO:0007411)|cellular protein modification process (GO:0006464)|ganglioside biosynthetic process (GO:0001574)|N-glycan processing (GO:0006491)|nervous system development (GO:0007399)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(11)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)	25		all_cancers(142;1.5e-07)|all_epithelial(76;1.43e-10)|Prostate(80;0.000644)|Lung NSC(167;0.0059)|all_lung(232;0.00914)|Ovarian(225;0.024)|Colorectal(57;0.09)|Breast(839;0.203)		COAD - Colon adenocarcinoma(37;0.00402)		ATTTTATCAGAGCTATTGACA	0.383																																					p.S52P		Atlas-SNP	.											.	ST8SIA4	77	.	0			c.T154C						.						114	110	112					5																	100231449		2203	4299	6502	SO:0001583	missense	7903	exon2			TATCAGAGCTATT	L41680	CCDS4091.1, CCDS47252.1	5q21	2013-03-01	2003-01-14	2005-02-07	ENSG00000113532	ENSG00000113532		"Sialyltransferases"	10871	protein-coding gene	gene with protein product	"ST8Sia IV"	602547	"sialyltransferase 8 (alpha-2, 8-polysialytransferase) D"	SIAT8D		7624364	Standard	NM_005668		Approved	PST, PST1	uc003knk.3	Q92187	OTTHUMG00000128727	ENST00000231461.5:c.154T>C	chr5.hg19:g.100231449A>G	ENSP00000231461:p.Ser52Pro	171.0	0.0		105.0	5.0	NM_175052	A8KA07|G3V104|Q8N1F4|Q92693	Missense_Mutation	SNP	ENST00000231461.5	hg19	CCDS4091.1	.	.	.	.	.	.	.	.	.	.	A	16.64	3.180082	0.57800	.	.	ENSG00000113532	ENST00000231461;ENST00000451528	T;T	0.37584	2.03;1.19	6.06	4.88	0.63580	.	0.064453	0.64402	D	0.000006	T	0.29190	0.0726	L	0.32530	0.975	0.51233	D	0.999912	P	0.37466	0.596	B	0.37267	0.245	T	0.05084	-1.0907	10	0.52906	T	0.07	.	11.9112	0.52739	0.8696:0.0:0.0:0.1304	.	52	Q92187	SIA8D_HUMAN	P	52	ENSP00000231461:S52P;ENSP00000428914:S52P	ENSP00000231461:S52P	S	-	1	0	ST8SIA4	100259348	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.017000	0.64047	1.064000	0.40671	0.533000	0.62120	TCT	.	.		0.383	ST8SIA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250632.3	NM_005668		G	100231449	A	G	100231449	3	3	259	1	0	0	0	0	1	0	0	0	15249	304	11	2	945	2	ST8SIA4	5	100231449	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2027252	100231449	80683811	247	36565										
EFNA5	1946	hgsc.bcm.edu	37	chr5	106723416	106723416	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agtgaacttacttgttggtcTcacaaagactttgagcttta	8	7	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:106723416T>C	ENST00000333274.6	-	3	756	c.475A>G	c.(475-477)Aga>Gga	p.R159G	EFNA5_ENST00000509503.1_Missense_Mutation_p.R159G|EFNA5_ENST00000510359.1_5'UTR	NM_001962.2	NP_001953.1	P52803	EFNA5_HUMAN	ephrin-A5	159	Ephrin RBD. {ECO:0000255|PROSITE- ProRule:PRU00884}.				axon guidance (GO:0007411)|ephrin receptor signaling pathway (GO:0048013)|nervous system development (GO:0007399)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell-cell adhesion (GO:0022407)|regulation of focal adhesion assembly (GO:0051893)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rho GTPase activity (GO:0032319)|retinal ganglion cell axon guidance (GO:0031290)	anchored component of external side of plasma membrane (GO:0031362)|plasma membrane (GO:0005886)	chemorepellent activity (GO:0045499)|ephrin receptor binding (GO:0046875)			large_intestine(6)	6		all_cancers(142;5.15e-06)|all_epithelial(76;4.39e-07)|Prostate(80;0.00726)|Lung NSC(167;0.0736)|Ovarian(225;0.0797)|all_lung(232;0.0854)|Colorectal(57;0.241)		Epithelial(69;1.25e-12)|OV - Ovarian serous cystadenocarcinoma(64;1.32e-11)|BRCA - Breast invasive adenocarcinoma(61;0.0376)|COAD - Colon adenocarcinoma(37;0.109)		CTTGTTGGTCTCACAAAGACT	0.448																																					p.R159G		Atlas-SNP	.											.	EFNA5	16	.	0			c.A475G						.						169	156	160					5																	106723416		2202	4300	6502	SO:0001583	missense	1946	exon3			TTGGTCTCACAAA	U26403	CCDS4097.1	5q21	2011-03-09			ENSG00000184349	ENSG00000184349		"Ephrins"	3225	protein-coding gene	gene with protein product		601535		EPLG7		8661153, 9245480	Standard	NM_001962		Approved	AF1, LERK7	uc003kol.3	P52803	OTTHUMG00000128741	ENST00000333274.6:c.475A>G	chr5.hg19:g.106723416T>C	ENSP00000328777:p.Arg159Gly	168.0	0.0		66.0	4.0	NM_001962		Missense_Mutation	SNP	ENST00000333274.6	hg19	CCDS4097.1	.	.	.	.	.	.	.	.	.	.	T	15.24	2.775925	0.49786	.	.	ENSG00000184349	ENST00000333274;ENST00000509503	D;D	0.93133	-3.17;-3.17	5.56	3.26	0.37387	Cupredoxin (2);	0.000000	0.85682	D	0.000000	D	0.91372	0.7278	M	0.80028	2.48	0.80722	D	1	P	0.35226	0.491	B	0.30646	0.118	D	0.88244	0.2912	10	0.18276	T	0.48	-13.5014	13.3692	0.60703	0.0:0.0:0.476:0.524	.	159	P52803	EFNA5_HUMAN	G	159	ENSP00000328777:R159G;ENSP00000426989:R159G	ENSP00000328777:R159G	R	-	1	2	EFNA5	106751315	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.711000	0.54868	0.932000	0.37266	0.533000	0.62120	AGA	.	.		0.448	EFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250652.1	NM_001962		C	106723416	T	C	106723416	3	2	259	1	0	0	0	0	1	0	0	0	4956	1559	54	2	223	2	EFNA5	5	106723416	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	6491967	106723416	74191844	248	36566										
STARD4	134429	hgsc.bcm.edu	37	chr5	110837775	110837775	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	caaggtcatctataacacctTgggctttgtagctggagaaa	10	8	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:110837775T>C	ENST00000296632.3	-	4	301	c.167A>G	c.(166-168)cAa>cGa	p.Q56R	STARD4_ENST00000509887.1_Intron|STARD4_ENST00000502322.1_Missense_Mutation_p.Q56R|STARD4_ENST00000511569.1_5'UTR|STARD4_ENST00000512160.1_Intron	NM_139164.1	NP_631903.1	Q96DR4	STAR4_HUMAN	StAR-related lipid transfer (START) domain containing 4	56	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				lipid transport (GO:0006869)		lipid binding (GO:0008289)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)	12		all_cancers(142;0.00259)|all_epithelial(76;8.32e-05)|Prostate(80;0.0115)|Colorectal(10;0.0959)|Ovarian(225;0.156)|all_lung(232;0.18)|Lung NSC(167;0.248)		OV - Ovarian serous cystadenocarcinoma(64;4.91e-09)|Epithelial(69;1.39e-08)|all cancers(49;2.34e-06)|COAD - Colon adenocarcinoma(37;0.049)|Colorectal(14;0.138)		TATAACACCTTGGGCTTTGTA	0.383																																					p.Q56R		Atlas-SNP	.											.	STARD4	31	.	0			c.A167G						.						109	117	114					5																	110837775		2202	4300	6502	SO:0001583	missense	134429	exon4			ACACCTTGGGCTT	AF480299	CCDS4104.1	5q22	2011-09-12	2007-08-16		ENSG00000164211	ENSG00000164211		"StAR-related lipid transfer (START) domain containing"	18058	protein-coding gene	gene with protein product		607049	"START domain containing 4, sterol regulated"			12011452	Standard	NM_139164		Approved		uc003kph.1	Q96DR4	OTTHUMG00000128793	ENST00000296632.3:c.167A>G	chr5.hg19:g.110837775T>C	ENSP00000296632:p.Gln56Arg	99.0	0.0		70.0	4.0	NM_139164	Q86TN9	Missense_Mutation	SNP	ENST00000296632.3	hg19	CCDS4104.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.964345	0.74131	.	.	ENSG00000164211	ENST00000296632;ENST00000505803;ENST00000502322	T;T;T	0.78126	-1.15;-1.15;-1.15	5.94	5.94	0.96194	Lipid-binding START (2);START-like domain (1);	0.081196	0.52532	D	0.000068	D	0.83202	0.5203	M	0.67953	2.075	0.80722	D	1	P;P	0.51449	0.942;0.945	P;P	0.53988	0.739;0.523	T	0.81623	-0.0849	10	0.30854	T	0.27	-6.1773	16.3871	0.83514	0.0:0.0:0.0:1.0	.	56;56	Q86TN9;Q96DR4	.;STAR4_HUMAN	R	56	ENSP00000296632:Q56R;ENSP00000427478:Q56R;ENSP00000427639:Q56R	ENSP00000296632:Q56R	Q	-	2	0	STARD4	110865674	1.000000	0.71417	1.000000	0.80357	0.611000	0.37282	6.199000	0.72112	2.276000	0.75962	0.533000	0.62120	CAA	.	.		0.383	STARD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250720.1	NM_139164		C	110837775	T	C	110837775	3	2	259	1	0	0	0	0	1	0	0	0	15274	1812	63	2	462	2	STARD4	5	110837775	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	4114359	110837775	70077485	249	36567										
DMXL1	1657	hgsc.bcm.edu	37	chr5	118576151	118576151	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atactcttgtagcacctgccAatagtttagtccatggtaag	8	9	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:118576151A>G	ENST00000311085.8	+	41	8706	c.8626A>G	c.(8626-8628)Aat>Gat	p.N2876D	DMXL1_ENST00000505312.1_3'UTR|DMXL1_ENST00000539542.1_Missense_Mutation_p.N2897D	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	2876				N -> D (in Ref. 1; CAA06718). {ECO:0000305}.						breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		AGCACCTGCCAATAGTTTAGT	0.289																																					p.N2876D		Atlas-SNP	.											DMXL1,colon,carcinoma,0,2	DMXL1	268	.	0			c.A8626G						.						84	95	91					5																	118576151		2202	4300	6502	SO:0001583	missense	1657	exon41			CCTGCCAATAGTT	AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"WD repeat domain containing"	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.8626A>G	chr5.hg19:g.118576151A>G	ENSP00000309690:p.Asn2876Asp	101.0	0.0		40.0	2.0	NM_005509		Missense_Mutation	SNP	ENST00000311085.8	hg19	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	A	14.36	2.512316	0.44660	.	.	ENSG00000172869	ENST00000311085;ENST00000539542	T;T	0.01335	5.0;5.0	5.34	4.19	0.49359	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.097095	0.64402	D	0.000002	T	0.01870	0.0059	L	0.43152	1.355	0.41062	D	0.985381	B;B	0.15141	0.012;0.004	B;B	0.11329	0.006;0.004	T	0.52283	-0.8596	10	0.66056	D	0.02	-22.0096	10.5741	0.45217	0.9243:0.0:0.0757:0.0	.	2897;2876	F5H269;Q9Y485	.;DMXL1_HUMAN	D	2876;2897	ENSP00000309690:N2876D;ENSP00000439479:N2897D	ENSP00000309690:N2876D	N	+	1	0	DMXL1	118604050	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.261000	0.65496	2.031000	0.59945	0.528000	0.53228	AAT	.	.		0.289	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		G	118576151	A	G	118576151	3	3	259	1	0	0	0	0	1	0	0	0	4596	130	5	2	8788	2	DMXL1	5	118576151	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	7738376	118576151	62339109	250	36568										
HSD17B4	3295	hgsc.bcm.edu	37	chr5	118867101	118867101	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aatattggggctaagtggagTaagttatagccctgatttta	11	4	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:118867101T>A	ENST00000256216.6	+	22	2126		c.e22+2		HSD17B4_ENST00000522415.1_Splice_Site|HSD17B4_ENST00000504811.1_Splice_Site|HSD17B4_ENST00000513628.1_Splice_Site|HSD17B4_ENST00000414835.2_Splice_Site|HSD17B4_ENST00000510025.1_Splice_Site|HSD17B4_ENST00000509514.1_Splice_Site|HSD17B4_ENST00000515320.1_Splice_Site	NM_000414.3	NP_000405.1	P51659	DHB4_HUMAN	hydroxysteroid (17-beta) dehydrogenase 4						alpha-linolenic acid metabolic process (GO:0036109)|androgen metabolic process (GO:0008209)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|estrogen metabolic process (GO:0008210)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|medium-chain fatty-acyl-CoA metabolic process (GO:0036112)|metabolic process (GO:0008152)|osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|Sertoli cell development (GO:0060009)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)|very long-chain fatty-acyl-CoA metabolic process (GO:0036111)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	17-beta-hydroxysteroid dehydrogenase (NAD+) activity (GO:0044594)|3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity (GO:0033989)|isomerase activity (GO:0016853)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(2)	25		all_cancers(142;0.0206)|Prostate(80;0.0322)		OV - Ovarian serous cystadenocarcinoma(64;0.000247)|Epithelial(69;0.000849)|all cancers(49;0.0122)		CTAAGTGGAGTAAGTTATAGC	0.358																																					.	Colon(35;490 801 34689 41394 43344)	Atlas-SNP	.											.	HSD17B4	63	.	0			c.1939+2T>A						.						80	80	80					5																	118867101		2202	4300	6502	SO:0001630	splice_region_variant	3295	exon21			GTGGAGTAAGTTA		CCDS4126.1, CCDS56378.1, CCDS56379.1	5q2	2011-09-20			ENSG00000133835	ENSG00000133835	4.2.1.107, 1.1.1.35	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	5213	protein-coding gene	gene with protein product	"17beta-estradiol dehydrogenase type IV", "peroxisomal multifunctional protein 2", "17-beta-HSD IV", "17-beta-hydroxysteroid dehydrogenase 4", "D-bifunctional protein, peroxisomal", "D-3-hydroxyacyl-CoA dehydratase", "3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholest-24-enoyl-CoA hydratase", "beta-keto-reductase", "beta-hydroxyacyl dehydrogenase", "short chain dehydrogenase/reductase family 8C, member 1"	601860				8938456, 19027726	Standard	NM_000414		Approved	MFE-2, DBP, SDR8C1	uc003ksj.3	P51659	OTTHUMG00000128899	ENST00000256216.6:c.1993+2T>A	chr5.hg19:g.118867101T>A		141.0	0.0		84.0	4.0	NM_001199292	B4DNV1|B4DVS5|E9PB82|F5HE57	Splice_Site	SNP	ENST00000256216.6	hg19	CCDS4126.1	.	.	.	.	.	.	.	.	.	.	T	17.90	3.501994	0.64298	.	.	ENSG00000133835	ENST00000256216;ENST00000515320;ENST00000510025;ENST00000504811;ENST00000414835;ENST00000513628;ENST00000509514	.	.	.	5.49	5.49	0.81192	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5759	0.68246	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	HSD17B4	118895000	1.000000	0.71417	1.000000	0.80357	0.658000	0.38924	6.937000	0.75898	2.087000	0.62958	0.528000	0.53228	.	.	.		0.358	HSD17B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250863.3	NM_000414	Intron	A	118867101	T	A	118867101	5	1	259	1	0	0	0	0	0	0	1	0	7395	1652	57	4	2081	4	HSD17B4	5	118867101	Splice_Site	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	290950	118867101	62048159	251	36569										
SNCAIP	9627	hgsc.bcm.edu	37	chr5	121739502	121739502	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gttcagtattcagtcacatcActcaagacgatcccagaact	6	12	5	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:121739502A>G	ENST00000261368.8	+	3	334	c.72A>G	c.(70-72)tcA>tcG	p.S24S	SNCAIP_ENST00000414317.2_Missense_Mutation_p.H15R|SNCAIP_ENST00000379533.2_Silent_p.S71S|SNCAIP_ENST00000261367.7_Silent_p.S71S|SNCAIP_ENST00000504884.2_Silent_p.S24S|SNCAIP_ENST00000379538.3_Missense_Mutation_p.H9R|SNCAIP_ENST00000542191.1_5'UTR|SNCAIP_ENST00000503116.2_Silent_p.S71S|SNCAIP_ENST00000379536.2_Silent_p.S24S	NM_005460.2	NP_005451.2	Q9Y6H5	SNCAP_HUMAN	synuclein, alpha interacting protein	24					cell death (GO:0008219)|dopamine metabolic process (GO:0042417)|regulation of inclusion body assembly (GO:0090083)|regulation of neurotransmitter secretion (GO:0046928)	cytoplasm (GO:0005737)|neuronal cell body (GO:0043025)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	identical protein binding (GO:0042802)|ubiquitin protein ligase binding (GO:0031625)			NS(3)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(9)|ovary(2)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	39		all_cancers(142;0.00787)|Prostate(80;0.0327)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000625)|Epithelial(69;0.00216)|all cancers(49;0.0232)		CAGTCACATCACTCAAGACGA	0.443																																					p.H9R		Atlas-SNP	.											.	SNCAIP	308	.	0			c.A26G						.						221	203	209					5																	121739502		2203	4300	6503	SO:0001819	synonymous_variant	9627	exon3			CACATCACTCAAG	AF167306	CCDS4131.1, CCDS58964.1	5q23.2	2013-01-10	2008-07-31		ENSG00000064692	ENSG00000064692		"Ankyrin repeat domain containing"	11139	protein-coding gene	gene with protein product	"synphilin"	603779				10319874	Standard	NM_001242935		Approved	SYPH1	uc003ksw.1	Q9Y6H5	OTTHUMG00000128915	ENST00000261368.8:c.72A>G	chr5.hg19:g.121739502A>G		142.0	0.0		95.0	6.0	NM_001242935	D3DSZ1|Q05BS1|Q1PSC2|Q49AC6|Q504U9|Q6L984|Q6L985|Q6L986|Q9HC59	Missense_Mutation	SNP	ENST00000261368.8	hg19	CCDS4131.1	.	.	.	.	.	.	.	.	.	.	A	15.15	2.749419	0.49257	.	.	ENSG00000064692	ENST00000379538;ENST00000414317;ENST00000447854	T;T	0.01629	5.05;4.72	5.64	-11.3	0.00108	.	.	.	.	.	T	0.01061	0.0035	.	.	.	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.48210	-0.9055	8	0.48119	T	0.1	-14.8217	1.8704	0.03207	0.1616:0.2743:0.3298:0.2343	.	15;9;9	B7Z995;Q9Y6H5-5;Q9Y6H5-2	.;.;.	R	9;15;15	ENSP00000368854:H9R;ENSP00000394392:H15R	ENSP00000368854:H9R	H	+	2	0	SNCAIP	121767401	0.510000	0.26171	0.513000	0.27749	0.993000	0.82548	-0.524000	0.06222	-1.933000	0.01052	-0.290000	0.09829	CAC	.	.		0.443	SNCAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250888.1			G	121739502	A	G	121739502	2	3	259	1	0	0	0	0	0	0	0	1	14856	146	6	2		2	SNCAIP	5	121739502	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2872401	121739502	59175758	252	36570										
GRAMD3	65983	hgsc.bcm.edu	37	chr5	125813387	125813387	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgctgattctgtttcagatcTctattccagctttctcggta	7	10	4	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:125813387T>C	ENST00000285689.3	+	6	951	c.490T>C	c.(490-492)Tct>Cct	p.S164P	GRAMD3_ENST00000515200.1_Missense_Mutation_p.S141P|GRAMD3_ENST00000544396.1_Missense_Mutation_p.S60P|RP11-517I3.1_ENST00000512500.1_RNA|GRAMD3_ENST00000543198.1_Missense_Mutation_p.S141P|RP11-517I3.1_ENST00000515808.1_RNA|GRAMD3_ENST00000502348.1_Missense_Mutation_p.S55P|GRAMD3_ENST00000542322.1_Missense_Mutation_p.S172P|GRAMD3_ENST00000511134.1_Missense_Mutation_p.S148P|GRAMD3_ENST00000513040.1_Missense_Mutation_p.S179P	NM_023927.2	NP_076416.2	Q96HH9	GRAM3_HUMAN	GRAM domain containing 3	164	GRAM.					cytoplasmic microtubule (GO:0005881)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		Prostate(80;0.0928)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0401)|OV - Ovarian serous cystadenocarcinoma(64;0.0604)|all cancers(49;0.108)		GTTTCAGATCTCTATTCCAGC	0.388																																					p.S179P		Atlas-SNP	.											.	GRAMD3	30	.	0			c.T535C						.						117	124	122					5																	125813387		2203	4300	6503	SO:0001583	missense	65983	exon6			CAGATCTCTATTC	BC008590	CCDS4136.1, CCDS54891.1, CCDS54892.1, CCDS54893.1, CCDS54894.1	5q23.2	2014-02-12	2005-11-03		ENSG00000155324	ENSG00000155324			24911	protein-coding gene	gene with protein product	"HCV NS3 transactivated protein 2"					12477932	Standard	NM_023927		Approved	NS3TP2, FLJ21313	uc011cwt.2	Q96HH9	OTTHUMG00000128943	ENST00000285689.3:c.490T>C	chr5.hg19:g.125813387T>C	ENSP00000285689:p.Ser164Pro	213.0	0.0		130.0	6.0	NM_001146319	B7Z1F2|B7Z3R1|B7Z6D8|B7Z8T2|D3DSZ3|Q9H753	Missense_Mutation	SNP	ENST00000285689.3	hg19	CCDS4136.1	.	.	.	.	.	.	.	.	.	.	T	15.88	2.964473	0.53507	.	.	ENSG00000155324	ENST00000513040;ENST00000506445;ENST00000543367;ENST00000285689;ENST00000515200;ENST00000542322;ENST00000544396;ENST00000543198;ENST00000502348;ENST00000511134	D;D;D;D;D;D;D;D;D	0.87491	-2.26;-2.26;-2.26;-2.26;-2.26;-2.26;-2.26;-2.26;-2.26	5.55	4.36	0.52297	GRAM (2);	0.325774	0.36167	N	0.002749	D	0.89818	0.6825	M	0.64404	1.975	0.41316	D	0.987143	D;P;D;D;D	0.64830	0.991;0.952;0.994;0.991;0.991	P;P;D;P;P	0.64506	0.876;0.828;0.926;0.885;0.876	D	0.88502	0.3083	10	0.54805	T	0.06	.	6.1935	0.20538	0.3273:0.0:0.1302:0.5425	.	148;60;172;179;164	B7Z8T2;B7Z1F2;B7Z3R1;B7Z6D8;Q96HH9	.;.;.;.;GRAM3_HUMAN	P	179;178;148;164;141;172;60;141;55;148	ENSP00000426120:S179P;ENSP00000424985:S178P;ENSP00000285689:S164P;ENSP00000426143:S141P;ENSP00000441876:S172P;ENSP00000444049:S60P;ENSP00000442902:S141P;ENSP00000427596:S55P;ENSP00000426088:S148P	ENSP00000285689:S164P	S	+	1	0	GRAMD3	125841286	0.594000	0.26849	0.997000	0.53966	0.984000	0.73092	1.433000	0.34947	1.002000	0.39104	0.533000	0.62120	TCT	.	.		0.388	GRAMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250922.2	NM_023927		C	125813387	T	C	125813387	3	2	259	1	0	0	0	0	1	0	0	0	6760	1551	54	2	726	2	GRAMD3	5	125813387	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	4073885	125813387	55101873	253	36571										
ISOC1	51015	hgsc.bcm.edu	37	chr5	128442751	128442751	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gatggacaggatgtttgcccTcgaggtaattgtcctgcttg	13	8	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:128442751T>C	ENST00000173527.5	+	4	762	c.746T>C	c.(745-747)cTc>cCc	p.L249P		NM_016048.2	NP_057132.2	Q96CN7	ISOC1_HUMAN	isochorismatase domain containing 1	249						extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)	catalytic activity (GO:0003824)			kidney(2)|lung(7)	9		all_cancers(142;0.0813)|Prostate(80;0.0865)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.138)|OV - Ovarian serous cystadenocarcinoma(64;0.164)		ATGTTTGCCCTCGAGGTAATT	0.428																																					p.L249P		Atlas-SNP	.											.	ISOC1	26	.	0			c.T746C						.						132	128	129					5																	128442751		2012	4190	6202	SO:0001583	missense	51015	exon4			TTGCCCTCGAGGT	AF151869	CCDS43357.1	5q22.1-q33.3	2010-03-19			ENSG00000066583	ENSG00000066583			24254	protein-coding gene	gene with protein product						10810093, 18566572	Standard	NM_016048		Approved	CGI-111	uc003kva.3	Q96CN7	OTTHUMG00000163144	ENST00000173527.5:c.746T>C	chr5.hg19:g.128442751T>C	ENSP00000173527:p.Leu249Pro	150.0	0.0		94.0	4.0	NM_016048	Q7Z770	Missense_Mutation	SNP	ENST00000173527.5	hg19	CCDS43357.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.954526	0.73902	.	.	ENSG00000066583	ENST00000506986;ENST00000173527	.	.	.	5.07	3.92	0.45320	Isochorismatase-like (3);	0.174261	0.36482	N	0.002574	T	0.74199	0.3685	M	0.88241	2.94	0.80722	D	1	P	0.37176	0.586	P	0.48089	0.566	T	0.75091	-0.3440	8	.	.	.	-17.3297	10.7276	0.46077	0.0:0.0752:0.0:0.9248	.	249	Q96CN7	ISOC1_HUMAN	P	228;249	.	.	L	+	2	0	ISOC1	128470650	1.000000	0.71417	0.996000	0.52242	0.955000	0.61496	6.461000	0.73522	1.086000	0.41228	0.528000	0.53228	CTC	.	.		0.428	ISOC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371826.1	NM_016048		C	128442751	T	C	128442751	3	2	259	1	0	0	0	0	1	0	0	0	7871	1551	54	2	760	2	ISOC1	5	128442751	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	2629364	128442751	52472509	254	36572										
RAD50	10111	hgsc.bcm.edu	37	chr5	131911482	131911482	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttcaaaggttgctcaagaaaCagatgtgagagcccagattc	10	8	2	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:131911482C>T	ENST00000265335.6	+	3	614	c.227C>T	c.(226-228)aCa>aTa	p.T76I	RAD50_ENST00000378823.3_5'UTR			Q92878	RAD50_HUMAN	RAD50 homolog (S. cerevisiae)	76					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|reciprocal meiotic recombination (GO:0007131)|regulation of mitotic recombination (GO:0000019)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	membrane (GO:0016020)|Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|nuclease activity (GO:0004518)|protein binding, bridging (GO:0030674)|zinc ion binding (GO:0008270)			breast(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		all_cancers(142;0.0368)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GCTCAAGAAACAGATGTGAGA	0.383								Homologous recombination																													p.T76I		Atlas-SNP	.											.	RAD50	246	.	0			c.C227T						.						101	91	94					5																	131911482		2203	4300	6503	SO:0001583	missense	10111	exon3			AAGAAACAGATGT	Z75311	CCDS34233.1	5q23-q31	2008-05-30	2001-11-28		ENSG00000113522	ENSG00000113522			9816	protein-coding gene	gene with protein product		604040	"RAD50 (S. cerevisiae) homolog"			8756642, 9705271	Standard	NM_005732		Approved	hRad50, RAD50-2	uc003kxi.3	Q92878	OTTHUMG00000059613	ENST00000265335.6:c.227C>T	chr5.hg19:g.131911482C>T	ENSP00000265335:p.Thr76Ile	151.0	0.0		92.0	4.0	NM_005732	B9EGF5|O43254|Q6GMT7|Q6P5X3|Q9UP86	Missense_Mutation	SNP	ENST00000265335.6	hg19	CCDS34233.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.977597	0.92982	.	.	ENSG00000113522	ENST00000265335;ENST00000453394	T;T	0.06608	3.28;3.28	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.21921	0.0528	L	0.52126	1.63	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.00028	-1.2296	10	0.56958	D	0.05	-15.9137	18.9261	0.92546	0.0:1.0:0.0:0.0	.	76	Q92878	RAD50_HUMAN	I	76	ENSP00000265335:T76I;ENSP00000400049:T76I	ENSP00000265335:T76I	T	+	2	0	RAD50	131939381	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	7.497000	0.81536	2.710000	0.92621	0.555000	0.69702	ACA	.	.		0.383	RAD50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132566.5	NM_005732		T	131911482	C	T	131911482	3	4	259	1	0	0	0	0	1	0	0	0	12999	478	17	3	237	3	RAD50	5	131911482	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	3468731	131911482	49003778	255	36573										
SEC24A	10802	hgsc.bcm.edu	37	chr5	134022523	134022523	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gtatctctttgtatttgatgTgtctcacaatgcagtcgaaa	8	7	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:134022523T>C	ENST00000398844.2	+	10	1823	c.1535T>C	c.(1534-1536)gTg>gCg	p.V512A	SEC24A_ENST00000322887.4_Missense_Mutation_p.V512A	NM_021982.2	NP_068817.1	O95486	SC24A_HUMAN	SEC24 family member A	512					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of protein secretion (GO:0050714)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045714)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	36			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GTATTTGATGTGTCTCACAAT	0.333																																					p.V512A		Atlas-SNP	.											.	SEC24A	77	.	0			c.T1535C						.						123	111	115					5																	134022523		1854	4105	5959	SO:0001583	missense	10802	exon10			TTGATGTGTCTCA	AJ131244	CCDS43363.1, CCDS58967.1	5q31.1	2013-10-21	2013-10-21		ENSG00000113615	ENSG00000113615			10703	protein-coding gene	gene with protein product		607183	"SEC24 (S. cerevisiae) related gene family, member A", "SEC24 family, member A (S. cerevisiae)"			10075675, 10329445	Standard	NM_021982		Approved		uc003kzs.3	O95486	OTTHUMG00000163064	ENST00000398844.2:c.1535T>C	chr5.hg19:g.134022523T>C	ENSP00000381823:p.Val512Ala	202.0	0.0		105.0	5.0	NM_001252231	A8MVW3|Q8WUV2|Q96GP7	Missense_Mutation	SNP	ENST00000398844.2	hg19	CCDS43363.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	28.3|28.3	4.909637|4.909637	0.92107|0.92107	.|.	.|.	ENSG00000113615|ENSG00000113615	ENST00000513123|ENST00000398844;ENST00000322887	.|T;T	.|0.80653	.|-1.4;-1.4	5.8|5.8	5.8|5.8	0.92144|0.92144	.|Sec23/Sec24, trunk domain (1);	.|0.109172	.|0.64402	.|D	.|0.000009	D|D	0.91744|0.91744	0.7389|0.7389	M|M	0.91459|0.91459	3.21|3.21	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;0.997	.|D;D	.|0.80764	.|0.994;0.989	D|D	0.93471|0.93471	0.6819|0.6819	5|10	.|0.87932	.|D	.|0	-13.5895|-13.5895	16.1502|16.1502	0.81611|0.81611	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|276;512	.|B4E205;O95486	.|.;SC24A_HUMAN	R|A	58|512	.|ENSP00000381823:V512A;ENSP00000321749:V512A	.|ENSP00000321749:V512A	C|V	+|+	1|2	0|0	SEC24A|SEC24A	134050422|134050422	1.000000|1.000000	0.71417|0.71417	0.965000|0.965000	0.40720|0.40720	0.988000|0.988000	0.76386|0.76386	7.671000|7.671000	0.83941|0.83941	2.203000|2.203000	0.70933|0.70933	0.460000|0.460000	0.39030|0.39030	TGT|GTG	.	.		0.333	SEC24A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371563.1			C	134022523	T	C	134022523	3	2	259	1	0	0	0	0	1	0	0	0	14009	1696	59	2	1573	2	SEC24A	5	134022523	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	2111041	134022523	46892737	256	36574										
PCDHB16	57717	hgsc.bcm.edu	37	chr5	140563037	140563037	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aatcctatgacaggggaagtTcgactgagaaagcaagtaga	12	6	0	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:140563037T>A	ENST00000361016.2	+	1	2058	c.903T>A	c.(901-903)gtT>gtA	p.V301V		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	301	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CAGGGGAAGTTCGACTGAGAA	0.438																																					p.V301V		Atlas-SNP	.											.	PCDHB16	159	.	0			c.T903A						.						80	87	85					5																	140563037		2203	4300	6503	SO:0001819	synonymous_variant	57717	exon1			GGAAGTTCGACTG	AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"Cadherins / Protocadherins : Clustered"	14546	other	protocadherin	"cadherin ME1", "protocadherin-3x", "PCDHbeta 16"	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325	ENST00000361016.2:c.903T>A	chr5.hg19:g.140563037T>A		72.0	0.0		39.0	27.0	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Silent	SNP	ENST00000361016.2	hg19	CCDS4251.1																																																																																			.	.		0.438	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957		A	140563037	T	A	140563037	2	1	259	1	0	0	0	0	0	0	0	1	11550	1770	62	4		4	PCDHB16	5	140563037	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	6540514	140563037	40352223	257	36575										
PCDHGA8	9708	hgsc.bcm.edu	37	chr5	140774716	140774716	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gcccaactacgcagacatgcTcatcagtcaggagggctgtg	12	12	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:140774716T>C	ENST00000398604.2	+	1	2336	c.2336T>C	c.(2335-2337)cTc>cCc	p.L779P	PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron	NM_032088.1	NP_114477.1	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8	779					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			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)			GCAGACATGCTCATCAGTCAG	0.473																																					p.L779P		Atlas-SNP	.											.	PCDHGA8	146	.	0			c.T2336C						.						77	81	80					5																	140774716		2196	4298	6494	SO:0001583	missense	9708	exon1			ACATGCTCATCAG	AF152515	CCDS47291.1, CCDS75338.1	5q31	2010-01-26			ENSG00000253767	ENSG00000253767		"Cadherins / Protocadherins : Clustered"	8706	other	protocadherin		606295				10380929	Standard	NM_014004		Approved	KIAA0327, PCDH-GAMMA-A8		Q9Y5G5	OTTHUMG00000164053	ENST00000398604.2:c.2336T>C	chr5.hg19:g.140774716T>C	ENSP00000381605:p.Leu779Pro	255.0	0.0		163.0	7.0	NM_014004	A7MCZ4|O15039	Missense_Mutation	SNP	ENST00000398604.2	hg19	CCDS47291.1	.	.	.	.	.	.	.	.	.	.	.	11.79	1.743982	0.30865	.	.	ENSG00000253767	ENST00000398604	T	0.50277	0.75	4.5	4.5	0.54988	.	.	.	.	.	T	0.72252	0.3437	M	0.92169	3.28	0.26051	N	0.981476	D;D	0.89917	1.0;1.0	D;D	0.81914	0.989;0.995	T	0.65450	-0.6165	9	0.62326	D	0.03	.	7.7621	0.28959	0.0:0.0946:0.0:0.9054	.	779;779	Q9Y5G5;Q9Y5G5-2	PCDG8_HUMAN;.	P	779	ENSP00000381605:L779P	ENSP00000381605:L779P	L	+	2	0	PCDHGA8	140754900	0.722000	0.28017	0.927000	0.36925	0.189000	0.23516	2.857000	0.48349	1.905000	0.55150	0.533000	0.62120	CTC	.	.		0.473	PCDHGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376972.1	NM_032088		C	140774716	T	C	140774716	3	2	259	1	0	0	0	0	1	0	0	0	11569	1551	54	2	2338	2	PCDHGA8	5	140774716	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	211679	140774716	40140544	258	36576										
PCDHGA1	26025	hgsc.bcm.edu	37	chr5	140884982	140884982	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cccaaaatggcgatgacaccGgcacctggcccaacaaccag	9	16	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:140884982G>T	ENST00000252085.3	+	3	2648	c.2506G>T	c.(2506-2508)Ggc>Tgc	p.G836C	PCDHGA11_ENST00000518882.1_Missense_Mutation_p.G654C|PCDHGB4_ENST00000519479.1_Missense_Mutation_p.G827C|PCDHGB3_ENST00000576222.1_Missense_Mutation_p.G833C|PCDHGB6_ENST00000520790.1_Missense_Mutation_p.G834C|PCDHGA11_ENST00000398587.2_Missense_Mutation_p.G839C|PCDHGA10_ENST00000398610.2_Missense_Mutation_p.G840C|PCDHGA7_ENST00000518325.1_Missense_Mutation_p.G836C|PCDHGB7_ENST00000398594.2_Missense_Mutation_p.G833C|PCDHGA3_ENST00000253812.6_Missense_Mutation_p.G836C|PCDHGB1_ENST00000523390.1_Missense_Mutation_p.G831C|PCDHGB2_ENST00000522605.1_Missense_Mutation_p.G835C|PCDHGA2_ENST00000394576.2_Missense_Mutation_p.G836C|PCDHGA1_ENST00000517417.1_Missense_Mutation_p.G835C|PCDHGA4_ENST00000571252.1_Missense_Mutation_p.G835C|PCDHGA5_ENST00000518069.1_Missense_Mutation_p.G835C|PCDHGA6_ENST00000517434.1_Missense_Mutation_p.G836C|PCDHGA8_ENST00000398604.2_Missense_Mutation_p.G836C|PCDHGC4_ENST00000306593.1_Missense_Mutation_p.G842C|PCDHGC3_ENST00000308177.3_Missense_Mutation_p.G838C|PCDHGC5_ENST00000252087.1_Missense_Mutation_p.G848C|PCDHGA9_ENST00000573521.1_Missense_Mutation_p.G836C	NM_003735.2|NM_032094.1	NP_003726.1|NP_115265.1	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12	836					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(23)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	58			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGATGACACCGGCACCTGGCC	0.592																																					p.G848C		Atlas-SNP	.											.	PCDHGC5	199	.	0			c.G2542T						.						190	184	186					5																	140884982		2203	4300	6503	SO:0001583	missense	56097	exon3			GACACCGGCACCT	AF152506	CCDS4260.1, CCDS75346.1	5q31	2010-01-26	2002-05-23		ENSG00000253159	ENSG00000253159		"Cadherins / Protocadherins : Clustered"	8699	other	protocadherin	"fibroblast cadherin FIB3"	603059	"cadherin 21"	CDH21		10380929	Standard	NM_003735		Approved	KIAA0588, FIB3, PCDH-GAMMA-A12		O60330	OTTHUMG00000129611	ENST00000252085.3:c.2506G>T	chr5.hg19:g.140884982G>T	ENSP00000252085:p.Gly836Cys	161.0	0.0		99.0	4.0	NM_018929	O15100|Q6UW70|Q9Y5D7	Missense_Mutation	SNP	ENST00000252085.3	hg19	CCDS4260.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.474072	0.84640	.	.	ENSG00000204956;ENSG00000081853;ENSG00000254245;ENSG00000254221;ENSG00000253910;ENSG00000253485;ENSG00000253731;ENSG00000253537;ENSG00000253953;ENSG00000253767;ENSG00000253305;ENSG00000253846;ENSG00000254122;ENSG00000253873;ENSG00000253873;ENSG00000253159;ENSG00000240184;ENSG00000242419;ENSG00000240764	ENST00000517417;ENST00000394576;ENST00000253812;ENST00000523390;ENST00000522605;ENST00000518069;ENST00000517434;ENST00000518325;ENST00000519479;ENST00000398604;ENST00000520790;ENST00000398610;ENST00000398594;ENST00000398587;ENST00000518882;ENST00000252085;ENST00000308177;ENST00000306593;ENST00000252087	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.96396	-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0	5.32	5.32	0.75619	.	0.000000	0.48767	D	0.000170	D	0.98311	0.9440	M	0.87180	2.865	0.52099	D	0.999947	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.999;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	1.0;1.0;0.995;1.0;0.997;1.0;1.0;1.0;0.998;0.999;0.998;1.0;0.996;0.999;0.997;0.99;1.0;0.998;0.995;0.993;1.0;0.997;0.998;0.984	D	0.99047	1.0826	10	0.87932	D	0	.	17.7507	0.88432	0.0:0.0:1.0:0.0	.	848;842;38;838;836;839;654;833;840;834;836;827;836;827;836;836;833;835;835;835;831;836;836;835	Q9Y5F6;Q9Y5F7;Q9BR81;Q9UN70;O60330;Q9Y5H2;Q9Y5H2-3;Q9Y5F8;Q9Y5H3;Q9Y5F9;Q9Y5G4;Q9Y5G0;Q9Y5G5;Q9UN71;Q9Y5G6;Q9Y5G7;Q9Y5G1;Q9Y5G8;Q9Y5G2;Q9Y5G9;Q9Y5G3;Q9Y5H0;Q9Y5H1;Q9Y5H4	PCDGM_HUMAN;PCDGL_HUMAN;.;PCDGK_HUMAN;PCDGC_HUMAN;PCDGB_HUMAN;.;PCDGJ_HUMAN;PCDGA_HUMAN;PCDGI_HUMAN;PCDG9_HUMAN;PCDGH_HUMAN;PCDG8_HUMAN;PCDGG_HUMAN;PCDG7_HUMAN;PCDG6_HUMAN;PCDGF_HUMAN;PCDG5_HUMAN;PCDGE_HUMAN;PCDG4_HUMAN;PCDGD_HUMAN;PCDG3_HUMAN;PCDG2_HUMAN;PCDG1_HUMAN	C	835;836;836;831;835;835;836;836;827;836;834;840;833;839;654;836;838;842;848	ENSP00000431083:G835C;ENSP00000378077:G836C;ENSP00000253812:G836C;ENSP00000429273:G831C;ENSP00000429018:G835C;ENSP00000429834:G835C;ENSP00000429601:G836C;ENSP00000430024:G836C;ENSP00000428288:G827C;ENSP00000381605:G836C;ENSP00000428603:G834C;ENSP00000381611:G840C;ENSP00000381594:G833C;ENSP00000381589:G839C;ENSP00000428333:G654C;ENSP00000252085:G836C;ENSP00000312070:G838C;ENSP00000306918:G842C;ENSP00000252087:G848C	ENSP00000381611:G840C	G	+	1	0	PCDHGA12;PCDHGA10;PCDHGA11;PCDHGB7;PCDHGA8;PCDHGC5;PCDHGA7;PCDHGB6;PCDHGC4;PCDHGA6;PCDHGC3;PCDHGA5;PCDHGA3;PCDHGB2;PCDHGA2;PCDHGA1;PCDHGB4;PCDHGB1	140865166	1.000000	0.71417	0.995000	0.50966	0.993000	0.82548	5.820000	0.69250	2.772000	0.95346	0.650000	0.86243	GGC	.	.		0.592	PCDHGA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251806.2	NM_003735		T	140884982	G	T	140884982	3	4	259	1	0	0	0	0	1	0	0	0	11559	1116	39	1	2563	1	PCDHGA1	5	140884982	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	110266	140884982	40030278	259	36577										
PDE6A	5145	hgsc.bcm.edu	37	chr5	149294528	149294528	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gatgactttgatgtcctcttTgccatgcaggatgtagtcaa	10	8	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:149294528T>C	ENST00000255266.5	-	6	1095	c.976A>G	c.(976-978)Aaa>Gaa	p.K326E		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	326	GAF 2.				cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	44			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Caffeine(DB00201)	ATGTCCTCTTTGCCATGCAGG	0.328																																					p.K326E		Atlas-SNP	.											.	PDE6A	98	.	0			c.A976G						.						145	137	140					5																	149294528		2203	4300	6503	SO:0001583	missense	5145	exon6			CCTCTTTGCCATG		CCDS4299.1	5q31.2-q34	2013-02-14			ENSG00000132915	ENSG00000132915	3.1.4.17	"Phosphodiesterases"	8785	protein-coding gene	gene with protein product		180071		PDEA		2155175	Standard	NM_000440		Approved	RP43	uc003lrg.4	P16499	OTTHUMG00000130047	ENST00000255266.5:c.976A>G	chr5.hg19:g.149294528T>C	ENSP00000255266:p.Lys326Glu	126.0	0.0		86.0	4.0	NM_000440	Q0P638	Missense_Mutation	SNP	ENST00000255266.5	hg19	CCDS4299.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.094954	0.76870	.	.	ENSG00000132915	ENST00000255266	T	0.67171	-0.25	5.19	5.19	0.71726	GAF (2);	0.123303	0.56097	D	0.000028	T	0.78278	0.4258	M	0.78456	2.415	0.53688	D	0.999972	P	0.49559	0.925	P	0.59012	0.85	T	0.78003	-0.2374	10	0.35671	T	0.21	.	13.2885	0.60258	0.0:0.0:0.0:1.0	.	326	P16499	PDE6A_HUMAN	E	326	ENSP00000255266:K326E	ENSP00000255266:K326E	K	-	1	0	PDE6A	149274721	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	6.664000	0.74437	2.084000	0.62774	0.482000	0.46254	AAA	.	.		0.328	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2			C	149294528	T	C	149294528	3	2	259	1	0	0	0	0	1	0	0	0	11654	1821	63	2	1674	2	PDE6A	5	149294528	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	8409546	149294528	31620732	260	36578										
SLC36A2	153201	hgsc.bcm.edu	37	chr5	150712834	150712834	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctgttccgaagaagagagggTaggtcttccagcttgctacc	12	10	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:150712834T>A	ENST00000335244.4	-	7	923	c.794A>T	c.(793-795)tAc>tTc	p.Y265F	SLC36A2_ENST00000521967.1_Missense_Mutation_p.Y265F|SLC36A2_ENST00000450886.1_5'Flank	NM_181776.2	NP_861441.2	Q495M3	S36A2_HUMAN	solute carrier family 36 (proton/amino acid symporter), member 2	265					amino acid transport (GO:0006865)|ion transport (GO:0006811)|proline transmembrane transport (GO:0035524)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine transmembrane transporter activity (GO:0015187)|hydrogen:amino acid symporter activity (GO:0005280)|L-alanine transmembrane transporter activity (GO:0015180)|L-proline transmembrane transporter activity (GO:0015193)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(14)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Cycloserine(DB00260)	GAAGAGAGGGTAGGTCTTCCA	0.458																																					p.Y265F		Atlas-SNP	.											.	SLC36A2	71	.	0			c.A794T						.						113	111	112					5																	150712834		2203	4300	6503	SO:0001583	missense	153201	exon7			AGAGGGTAGGTCT	AY162214	CCDS4315.1	5q33.1	2013-05-22			ENSG00000186335	ENSG00000186335		"Solute carriers"	18762	protein-coding gene	gene with protein product		608331				11959859	Standard	NM_181776		Approved	PAT2, tramdorin, TRAMD1	uc003lty.3	Q495M3	OTTHUMG00000130129	ENST00000335244.4:c.794A>T	chr5.hg19:g.150712834T>A	ENSP00000334223:p.Tyr265Phe	185.0	0.0		123.0	7.0	NM_181776	Q495M4|Q495M6|Q6ZWK5|Q7Z6B5	Missense_Mutation	SNP	ENST00000335244.4	hg19	CCDS4315.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.77|12.77	2.037639|2.037639	0.35989|0.35989	.|.	.|.	ENSG00000186335|ENSG00000186335	ENST00000523044|ENST00000335244;ENST00000521967	.|T;T	.|0.02085	.|4.46;4.46	4.71|4.71	4.71|4.71	0.59529|0.59529	.|.	.|0.059999	.|0.64402	.|D	.|0.000002	T|T	0.01558|0.01558	0.0050|0.0050	N|N	0.12887|0.12887	0.27|0.27	0.80722|0.80722	D|D	1|1	.|B;B	.|0.15141	.|0.005;0.012	.|B;B	.|0.21360	.|0.023;0.034	T|T	0.56208|0.56208	-0.8017|-0.8017	5|10	.|0.12430	.|T	.|0.62	-14.1951|-14.1951	10.298|10.298	0.43635|0.43635	0.1476:0.0:0.0:0.8524|0.1476:0.0:0.0:0.8524	.|.	.|265;265	.|E5RJJ5;Q495M3	.|.;S36A2_HUMAN	S|F	18|265	.|ENSP00000334223:Y265F;ENSP00000430535:Y265F	.|ENSP00000334223:Y265F	T|Y	-|-	1|2	0|0	SLC36A2|SLC36A2	150693027|150693027	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	2.751000|2.751000	0.47508|0.47508	2.111000|2.111000	0.64477|0.64477	0.477000|0.477000	0.44152|0.44152	ACC|TAC	.	.		0.458	SLC36A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252437.1			A	150712834	T	A	150712834	3	1	259	1	0	0	0	0	1	0	0	0	14609	1638	57	4	673	4	SLC36A2	5	150712834	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1418306	150712834	30202426	261	36579										
FAT2	2196	hgsc.bcm.edu	37	chr5	150905386	150905386	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cttaggccctcagcagtcacCagccatccatccggggtcac	9	17	3	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:150905386C>A	ENST00000261800.5	-	17	10461	c.10449G>T	c.(10447-10449)ctG>ctT	p.L3483L		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3483	Cadherin 31. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CAGCAGTCACCAGCCATCCAT	0.577																																					p.L3483L		Atlas-SNP	.											.	FAT2	465	.	0			c.G10449T						.						82	75	78					5																	150905386		2203	4300	6503	SO:0001819	synonymous_variant	2196	exon17			AGTCACCAGCCAT	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.10449G>T	chr5.hg19:g.150905386C>A		87.0	0.0		64.0	4.0	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	hg19	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	C	8.305	0.820831	0.16678	.	.	ENSG00000086570	ENST00000520200	.	.	.	5.11	2.33	0.28932	.	.	.	.	.	T	0.54532	0.1864	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46857	-0.9161	4	.	.	.	.	6.3892	0.21577	0.1287:0.6561:0.0:0.2152	.	.	.	.	C	342	.	.	G	-	1	0	FAT2	150885579	0.963000	0.33076	1.000000	0.80357	0.831000	0.47069	0.512000	0.22755	0.667000	0.31107	-0.252000	0.11476	GGT	.	.		0.577	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		A	150905386	C	A	150905386	2	1	259	1	0	0	0	0	0	0	0	1	5698	581	21	3		3	FAT2	5	150905386	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	192552	150905386	30009874	262	36580										
FAT2	2196	hgsc.bcm.edu	37	chr5	150908752	150908752	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tccttaccgtgaggatgacgTcacccacaagggcattctct	9	13	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:150908752T>C	ENST00000261800.5	-	14	10025	c.10013A>G	c.(10012-10014)gAc>gGc	p.D3338G		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3338	Cadherin 30. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GAGGATGACGTCACCCACAAG	0.512																																					p.D3338G		Atlas-SNP	.											.	FAT2	465	.	0			c.A10013G						.						103	96	98					5																	150908752		2203	4300	6503	SO:0001583	missense	2196	exon14			ATGACGTCACCCA	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.10013A>G	chr5.hg19:g.150908752T>C	ENSP00000261800:p.Asp3338Gly	134.0	0.0		90.0	4.0	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	hg19	CCDS4317.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	6.202|6.202	0.405372|0.405372	0.11754|0.11754	.|.	.|.	ENSG00000086570|ENSG00000086570	ENST00000261800|ENST00000520200	T|.	0.50277|.	0.75|.	5.78|5.78	3.27|3.27	0.37495|0.37495	Cadherin (3);Cadherin-like (1);|.	0.350897|.	0.27315|.	N|.	0.019932|.	T|.	0.29126|.	0.0724|.	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	B;B|.	0.06786|.	0.001;0.001|.	B;B|.	0.12156|.	0.006;0.007|.	T|.	0.17992|.	-1.0351|.	10|.	0.33141|.	T|.	0.24|.	.|.	12.6955|12.6955	0.57001|0.57001	0.0:0.0:0.2595:0.7405|0.0:0.0:0.2595:0.7405	.|.	3338;529|.	Q9NYQ8;E9PDJ8|.	FAT2_HUMAN;.|.	G|W	3338|196	ENSP00000261800:D3338G|.	ENSP00000261800:D3338G|.	D|X	-|-	2|3	0|0	FAT2|FAT2	150888945|150888945	0.079000|0.079000	0.21365|0.21365	0.003000|0.003000	0.11579|0.11579	0.101000|0.101000	0.19017|0.19017	1.767000|1.767000	0.38501|0.38501	0.399000|0.399000	0.25367|0.25367	0.519000|0.519000	0.50382|0.50382	GAC|TGA	.	.		0.512	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		C	150908752	T	C	150908752	3	2	259	1	0	0	0	0	1	0	0	0	5698	1667	58	2	3076	2	FAT2	5	150908752	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	3366	150908752	30006508	263	36581										
SPARC	6678	hgsc.bcm.edu	37	chr5	151049257	151049257	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cgatgtagtccaggtggagcTtgtggcccttcttggtgccc	14	11	1	0	rs200223394		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:151049257T>C	ENST00000231061.4	-	6	732	c.419A>G	c.(418-420)aAg>aGg	p.K140R	SPARC_ENST00000537849.1_5'Flank	NM_003118.3	NP_003109.1	P09486	SPRC_HUMAN	secreted protein, acidic, cysteine-rich (osteonectin)	140	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				blood coagulation (GO:0007596)|bone development (GO:0060348)|cellular response to growth factor stimulus (GO:0071363)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|inner ear development (GO:0048839)|lung development (GO:0030324)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|ossification (GO:0001503)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of endothelial cell migration (GO:0010595)|regulation of cell morphogenesis (GO:0022604)|response to cadmium ion (GO:0046686)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to gravity (GO:0009629)|response to L-ascorbic acid (GO:0033591)|response to lead ion (GO:0010288)|response to lipopolysaccharide (GO:0032496)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)	basement membrane (GO:0005604)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nuclear matrix (GO:0016363)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|platelet alpha granule membrane (GO:0031092)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix binding (GO:0050840)			central_nervous_system(3)|large_intestine(5)|lung(5)|ovary(1)|urinary_tract(1)	15		Medulloblastoma(196;0.109)|all_hematologic(541;0.122)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)	OV - Ovarian serous cystadenocarcinoma(192;0.00118)		CAGGTGGAGCTTGTGGCCCTT	0.557																																					p.K140R		Atlas-SNP	.											.	SPARC	38	.	0			c.A419G						.	T	ARG/LYS	0,4406		0,0,2203	125	110	115		419	5.7	1	5		115	2,8598	2.2+/-6.3	0,2,4298	no	missense	SPARC	NM_003118.2	26	0,2,6501	CC,CT,TT		0.0233,0.0,0.0154	benign	140/304	151049257	2,13004	2203	4300	6503	SO:0001583	missense	6678	exon6			TGGAGCTTGTGGC		CCDS4318.1	5q31-q33	2012-10-02			ENSG00000113140	ENSG00000113140			11219	protein-coding gene	gene with protein product	"cysteine-rich protein", "osteonectin"	182120		ON		2838412, 3410046	Standard	NM_003118		Approved		uc003lui.4	P09486	OTTHUMG00000130122	ENST00000231061.4:c.419A>G	chr5.hg19:g.151049257T>C	ENSP00000231061:p.Lys140Arg	163.0	0.0		123.0	5.0	NM_003118	D3DQH9|Q6IBK4	Missense_Mutation	SNP	ENST00000231061.4	hg19	CCDS4318.1	.	.	.	.	.	.	.	.	.	.	T	16.10	3.027083	0.54683	0.0	2.33E-4	ENSG00000113140	ENST00000231061;ENST00000538026;ENST00000521569	T;T;T	0.75367	-0.93;-0.93;-0.93	5.7	5.7	0.88788	Proteinase inhibitor I1, Kazal (2);	0.000000	0.85682	D	0.000000	T	0.64080	0.2566	L	0.27975	0.815	0.80722	D	1	B	0.14805	0.011	B	0.21360	0.034	T	0.58595	-0.7609	10	0.25106	T	0.35	-25.5431	15.9765	0.80071	0.0:0.0:0.0:1.0	.	140	P09486	SPRC_HUMAN	R	140;49;49	ENSP00000231061:K140R;ENSP00000440127:K49R;ENSP00000428119:K49R	ENSP00000231061:K140R	K	-	2	0	SPARC	151029450	1.000000	0.71417	0.997000	0.53966	0.999000	0.98932	7.516000	0.81772	2.172000	0.68678	0.533000	0.62120	AAG	.	T|0.999;C|0.001		0.557	SPARC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252430.1	NM_003118		C	151049257	T	C	151049257	3	2	259	1	0	0	0	0	1	0	0	0	15010	1609	56	2	512	2	SPARC	5	151049257	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	140505	151049257	29866003	264	36582										
MFAP3	4238	hgsc.bcm.edu	37	chr5	153432861	153432861	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agtcacacaatttaagaccaTggagtttgctcgttatattg	8	7	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:153432861T>C	ENST00000436816.1	+	3	896	c.677T>C	c.(676-678)aTg>aCg	p.M226T	MFAP3_ENST00000439768.2_Missense_Mutation_p.M80T|MFAP3_ENST00000322602.5_Missense_Mutation_p.M226T	NM_001242336.1|NM_005927.4	NP_001229265.1|NP_005918.1	P55082	MFAP3_HUMAN	microfibrillar-associated protein 3	226					extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|kidney(2)|large_intestine(1)|lung(2)|pancreas(1)	7	Renal(175;0.00488)	Lung NSC(249;0.00145)|all_lung(500;0.00226)|all_neural(177;0.122)|Breast(839;0.14)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)	OV - Ovarian serous cystadenocarcinoma(192;9.69e-06)|GBM - Glioblastoma multiforme(465;0.0201)		TTTAAGACCATGGAGTTTGCT	0.448																																					p.M226T		Atlas-SNP	.											.	MFAP3	20	.	0			c.T677C						.						109	110	110					5																	153432861		2203	4300	6503	SO:0001583	missense	4238	exon3			AGACCATGGAGTT		CCDS4324.1, CCDS47319.1	5q32-q33.2	2013-01-11			ENSG00000037749	ENSG00000037749		"Immunoglobulin superfamily / I-set domain containing"	7034	protein-coding gene	gene with protein product		600491				7782085	Standard	NM_005927		Approved		uc010jib.2	P55082	OTTHUMG00000130149	ENST00000436816.1:c.677T>C	chr5.hg19:g.153432861T>C	ENSP00000409933:p.Met226Thr	206.0	0.0		100.0	4.0	NM_005927	B2RDK0|B4DKA1|Q9NXA7	Missense_Mutation	SNP	ENST00000436816.1	hg19	CCDS4324.1	.	.	.	.	.	.	.	.	.	.	T	19.50	3.839339	0.71488	.	.	ENSG00000037749	ENST00000439768;ENST00000436816;ENST00000322602	T;T	0.27256	1.68;1.68	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.49218	0.1544	M	0.65975	2.015	0.58432	D	0.999995	D	0.71674	0.998	D	0.72338	0.977	T	0.44065	-0.9352	9	.	.	.	-19.8981	15.9374	0.79723	0.0:0.0:0.0:1.0	.	226	P55082	MFAP3_HUMAN	T	80;226;226	ENSP00000409933:M226T;ENSP00000322956:M226T	.	M	+	2	0	MFAP3	153413054	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.063000	0.71162	2.228000	0.72767	0.533000	0.62120	ATG	.	.		0.448	MFAP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252457.2	NM_005927		C	153432861	T	C	153432861	3	2	259	1	0	0	0	0	1	0	0	0	9524	1464	51	2	683	2	MFAP3	5	153432861	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	2383604	153432861	27482399	265	36583										
TIMD4	91937	hgsc.bcm.edu	37	chr5	156375500	156375500	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gatgttgatgggagatcccaAactttggactctttggaaaa	11	6	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:156375500A>G	ENST00000274532.2	-	5	827	c.771T>C	c.(769-771)gtT>gtC	p.V257V	TIMD4_ENST00000407087.3_Intron	NM_138379.2	NP_612388.2	Q96H15	TIMD4_HUMAN	T-cell immunoglobulin and mucin domain containing 4	257	Ser-rich.					integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(23)|ovary(2)|skin(2)	37	Renal(175;0.00488)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GGAGATCCCAAACTTTGGACT	0.423																																					p.V257V		Atlas-SNP	.											.	TIMD4	94	.	0			c.T771C						.						71	60	64					5																	156375500		2203	4300	6503	SO:0001819	synonymous_variant	91937	exon5			ATCCCAAACTTTG	BC008988	CCDS4332.1, CCDS54943.1	5q33.3	2013-01-11			ENSG00000145850	ENSG00000145850		"Immunoglobulin superfamily / V-set domain containing"	25132	protein-coding gene	gene with protein product		610096				12477932	Standard	NM_001146726		Approved		uc003lwh.2	Q96H15	OTTHUMG00000130244	ENST00000274532.2:c.771T>C	chr5.hg19:g.156375500A>G		154.0	0.0		93.0	4.0	NM_138379	B5MCL9	Silent	SNP	ENST00000274532.2	hg19	CCDS4332.1																																																																																			.	.		0.423	TIMD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252568.1	NM_138379		G	156375500	A	G	156375500	2	3	259	1	0	0	0	0	0	0	0	1	15918	1	1	2		2	TIMD4	5	156375500	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2942639	156375500	24539760	266	36584										
GABRA6	2559	hgsc.bcm.edu	37	chr5	161128527	161128527	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cctgactccaaatatcatctGaagaaaaggatcacttctct	5	11	4	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:161128527G>A	ENST00000274545.5	+	9	1543	c.1110G>A	c.(1108-1110)ctG>ctA	p.L370L	GABRA6_ENST00000523217.1_Silent_p.L360L			Q16445	GBRA6_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 6	370					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.L370L(1)		breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|liver(2)|lung(22)|ovary(7)|skin(6)|urinary_tract(2)	57	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	AATATCATCTGAAGAAAAGGA	0.383										TCGA Ovarian(5;0.080)																											p.L370L		Atlas-SNP	.											GABRA6,NS,carcinoma,0,1	GABRA6	139	.	1	Substitution - coding silent(1)	lung(1)	c.G1110A						.						105	110	108					5																	161128527		2203	4300	6503	SO:0001819	synonymous_variant	2559	exon9			TCATCTGAAGAAA		CCDS4356.1	5q34	2012-06-22			ENSG00000145863	ENSG00000145863		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4080	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 6"	137143				8020978	Standard	NM_000811		Approved		uc003lyu.2	Q16445	OTTHUMG00000130351	ENST00000274545.5:c.1110G>A	chr5.hg19:g.161128527G>A		88.0	0.0		40.0	2.0	NM_000811	A8K096|Q4VAV2	Silent	SNP	ENST00000274545.5	hg19	CCDS4356.1																																																																																			.	.		0.383	GABRA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252707.2			A	161128527	G	A	161128527	2	1	259	1	0	0	0	0	0	0	0	1	6173	1277	45	3		3	GABRA6	5	161128527	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	4753027	161128527	19786733	267	36585										
ODZ2	57451	hgsc.bcm.edu	37	chr5	167489119	167489119	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tggtgaagcagaagttggtcGgcgggtaacacaagaagtcc	15	7	0	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:167489119G>T	ENST00000518659.1	+	7	1403	c.1364G>T	c.(1363-1365)cGg>cTg	p.R455L	TENM2_ENST00000519204.1_Missense_Mutation_p.R334L|TENM2_ENST00000403607.2_Missense_Mutation_p.R288L|TENM2_ENST00000520394.1_Missense_Mutation_p.R223L|TENM2_ENST00000545108.1_Missense_Mutation_p.R455L	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	455					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R288Q(1)									GAAGTTGGTCGGCGGGTAACA	0.463																																					p.R455L		Atlas-SNP	.											ODZ2,colon,carcinoma,0,1	.	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1364T						.						81	84	83					5																	167489119		1851	4098	5949	SO:0001583	missense	57451	exon7			TTGGTCGGCGGGT	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"odz, odd Oz/ten-m homolog 2 (Drosophila)"	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.1364G>T	chr5.hg19:g.167489119G>T	ENSP00000429430:p.Arg455Leu	127.0	1.0		75.0	3.0	NM_001122679	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	hg19		.	.	.	.	.	.	.	.	.	.	G	16.12	3.033741	0.54896	.	.	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	T;T;T;T;T	0.20738	2.05;2.05;2.05;2.05;2.05	5.63	5.63	0.86233	.	0.055296	0.64402	D	0.000002	T	0.34861	0.0912	M	0.69823	2.125	0.45979	D	0.998796	P;P;P	0.46784	0.884;0.785;0.853	P;B;P	0.48738	0.588;0.355;0.507	T	0.06110	-1.0845	10	0.56958	D	0.05	.	14.8382	0.70201	0.0705:0.0:0.9295:0.0	.	455;223;334	Q9NT68;F8VNQ3;G3V106	TEN2_HUMAN;.;.	L	455;455;334;223;288	ENSP00000429430:R455L;ENSP00000438635:R455L;ENSP00000428964:R334L;ENSP00000427874:R223L;ENSP00000384905:R288L	ENSP00000384905:R288L	R	+	2	0	ODZ2	167421697	1.000000	0.71417	0.440000	0.26846	0.961000	0.63080	8.017000	0.88712	2.644000	0.89710	0.655000	0.94253	CGG	.	.		0.463	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		T	167489119	G	T	167489119	3	4	259	1	0	0	0	0	1	0	0	0	10844	1116	39	1	1390	1	ODZ2	5	167489119	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	6360592	167489119	13426141	268	36586										
WWC1	23286	hgsc.bcm.edu	37	chr5	167882362	167882362	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggtgtgacttcttcctcaggTggacaaagagaccaacacgg	12	10	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:167882362T>C	ENST00000265293.4	+	19	3162	c.2660T>C	c.(2659-2661)gTg>gCg	p.V887A	WWC1_ENST00000522140.1_3'UTR|WWC1_ENST00000521089.1_Splice_Site_p.V887A	NM_001161661.1|NM_001161662.1|NM_015238.2	NP_001155133.1|NP_001155134.1|NP_056053.1	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1	887	Interaction with histone H3.				cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|hippo signaling (GO:0035329)|negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of MAPK cascade (GO:0043410)|regulation of hippo signaling (GO:0035330)|regulation of intracellular transport (GO:0032386)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)|transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(2)|prostate(1)|skin(4)	43	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)		CTTCCTCAGGTGGACAAAGAG	0.612																																					p.V887A		Atlas-SNP	.											.	WWC1	98	.	0			c.T2660C						.						108	113	111					5																	167882362		2203	4300	6503	SO:0001630	splice_region_variant	23286	exon19			CTCAGGTGGACAA	AF506799	CCDS4366.1, CCDS54945.1	5q34	2014-06-13	2006-11-09		ENSG00000113645	ENSG00000113645		"WW, C2 and coiled-coil domain containing"	29435	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 168"	610533	"WW, C2 and coiled-coil domain containing 1"			10048485, 12559952	Standard	NM_001161661		Approved	KIBRA, KIAA0869, PPP1R168	uc011den.2	Q8IX03	OTTHUMG00000130408	ENST00000265293.4:c.2659-1T>C	chr5.hg19:g.167882362T>C		199.0	0.0		99.0	4.0	NM_015238	B4DK05|O94946|Q6MZX4|Q6Y2F8|Q7Z4G8|Q8WVM4|Q9BT29	Missense_Mutation	SNP	ENST00000265293.4	hg19	CCDS4366.1	.	.	.	.	.	.	.	.	.	.	T	27.8	4.862617	0.91511	.	.	ENSG00000113645	ENST00000265293;ENST00000521089;ENST00000524038	T;T;T	0.58940	0.3;0.3;0.3	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.72285	0.3441	L	0.60455	1.87	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.80764	0.99;0.994	T	0.73107	-0.4087	10	0.48119	T	0.1	.	15.5525	0.76164	0.0:0.0:0.0:1.0	.	887;887	Q8IX03-2;Q8IX03	.;KIBRA_HUMAN	A	887;887;213	ENSP00000265293:V887A;ENSP00000427772:V887A;ENSP00000428084:V213A	ENSP00000265293:V887A	V	+	2	0	WWC1	167814940	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.203000	0.72137	2.070000	0.61991	0.533000	0.62120	GTG	.	.		0.612	WWC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252791.2	NM_015238	Missense_Mutation	C	167882362	T	C	167882362	5	2	259	1	0	0	0	0	0	0	1	0	17426	1710	59	2	2734	2	WWC1	5	167882362	Splice_Site	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	393243	167882362	13032898	269	36587										
STK10	6793	hgsc.bcm.edu	37	chr5	171520874	171520874	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctgagactggctgggtgccaGcggggtggaaggtgactcct	18	9	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:171520874G>A	ENST00000176763.5	-	9	1439	c.1096C>T	c.(1096-1098)Ctg>Ttg	p.L366L	STK10_ENST00000517775.1_5'Flank	NM_005990.3	NP_005981.3	O94804	STK10_HUMAN	serine/threonine kinase 10	366					cell cycle (GO:0007049)|lymphocyte aggregation (GO:0071593)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of lymphocyte migration (GO:2000401)|signal transduction by phosphorylation (GO:0023014)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|polo kinase kinase activity (GO:0042801)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(6)|pancreas(1)|prostate(1)|testis(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CTGGGTGCCAGCGGGGTGGAA	0.597																																					p.L366L		Atlas-SNP	.											.	STK10	100	.	0			c.C1096T						.						44	49	47					5																	171520874		2202	4299	6501	SO:0001819	synonymous_variant	6793	exon9			GTGCCAGCGGGGT	AB015718	CCDS34290.1	5q35.1	2008-07-18			ENSG00000072786	ENSG00000072786			11388	protein-coding gene	gene with protein product		603919				10199912	Standard	NM_005990		Approved	LOK, PRO2729	uc003mbo.1	O94804	OTTHUMG00000163265	ENST00000176763.5:c.1096C>T	chr5.hg19:g.171520874G>A		150.0	0.0		95.0	4.0	NM_005990	A6ND35|B2R8F5|B3KMY1|Q6NSK0|Q9UIW4	Silent	SNP	ENST00000176763.5	hg19	CCDS34290.1																																																																																			.	.		0.597	STK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372374.2	NM_005990		A	171520874	G	A	171520874	2	1	259	1	0	0	0	0	0	0	0	1	15301	962	34	3		3	STK10	5	171520874	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	3638512	171520874	9394386	270	36588										
TRIM41	90933	hgsc.bcm.edu	37	chr5	180651508	180651508	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggatctagaccccgtcacccCactgcccccgcctccagccc	7	23	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:180651508C>T	ENST00000315073.5	+	1	1219	c.509C>T	c.(508-510)cCa>cTa	p.P170L	TRIM41_ENST00000351937.5_Missense_Mutation_p.P170L|MIR4638_ENST00000581158.1_RNA|CTC-338M12.7_ENST00000499096.2_RNA	NM_033549.4	NP_291027.3	Q8WV44	TRI41_HUMAN	tripartite motif containing 41	170					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(3)|prostate(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	26	all_cancers(89;9.17e-06)|all_epithelial(37;1.19e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0684)	all_cancers(40;0.000209)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCCGTCACCCCACTGCCCCCG	0.642																																					p.P170L		Atlas-SNP	.											.	TRIM41	96	.	0			c.C509T						.						45	51	49					5																	180651508		2203	4300	6503	SO:0001583	missense	90933	exon1			TCACCCCACTGCC	AF258579	CCDS4465.1, CCDS4466.1	5q35.3	2013-01-09	2011-01-25		ENSG00000146063	ENSG00000146063		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19013	protein-coding gene	gene with protein product	"RING-finger protein that interacts with C kinase"	610530	"tripartite motif-containing 41"			16022281	Standard	NM_033549		Approved	MGC1127, RINCK	uc003mne.2	Q8WV44	OTTHUMG00000130965	ENST00000315073.5:c.509C>T	chr5.hg19:g.180651508C>T	ENSP00000320869:p.Pro170Leu	164.0	0.0		95.0	4.0	NM_201627	B3KNJ6|D3DWR9|Q5BKT0|Q7L484|Q96Q10|Q9BSL8	Missense_Mutation	SNP	ENST00000315073.5	hg19	CCDS4466.1	.	.	.	.	.	.	.	.	.	.	C	13.42	2.231936	0.39399	.	.	ENSG00000146063	ENST00000351937;ENST00000315073;ENST00000421508	T;T	0.54279	1.04;0.58	4.55	2.7	0.31948	Zinc finger, RING-type (1);	0.407810	0.20910	N	0.083485	T	0.36608	0.0973	L	0.36672	1.1	0.34627	D	0.719231	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.001	T	0.32402	-0.9908	10	0.21540	T	0.41	.	6.7474	0.23468	0.1827:0.7214:0.0:0.096	.	170;170;170	Q8WV44;Q8WV44-2;Q8WV44-4	TRI41_HUMAN;.;.	L	170;170;49	ENSP00000336749:P170L;ENSP00000320869:P170L	ENSP00000320869:P170L	P	+	2	0	TRIM41	180584114	0.358000	0.24947	0.997000	0.53966	0.767000	0.43475	2.033000	0.41136	0.482000	0.27582	0.491000	0.48974	CCA	.	.		0.642	TRIM41-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253574.3	NM_201627		T	180651508	C	T	180651508	3	4	259	1	0	0	0	0	1	0	0	0	16531	594	21	3	511	3	TRIM41	5	180651508	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	9130634	180651508	263752	271	36589										
HIVEP1	3096	hgsc.bcm.edu	37	chr6	12161737	12161737	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aagaatctgatggcccagatGaggatgacaatgaaaatgaa	11	5	1	7			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:12161737G>T	ENST00000379388.2	+	8	6885	c.6553G>T	c.(6553-6555)Gag>Tag	p.E2185*	HIVEP1_ENST00000541134.1_Nonsense_Mutation_p.E50*	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	2185					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				TGGCCCAGATGAGGATGACAA	0.453																																					p.E2185X		Atlas-SNP	.											.	HIVEP1	242	.	0			c.G6553T						.						79	87	84					6																	12161737		2050	4198	6248	SO:0001587	stop_gained	3096	exon8			CCAGATGAGGATG	J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"Zinc fingers, C2H2-type"	4920	protein-coding gene	gene with protein product		194540	"human immunodeficiency virus type I enhancer-binding protein 1", "zinc finger protein 40"	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.6553G>T	chr6.hg19:g.12161737G>T	ENSP00000368698:p.Glu2185*	116.0	0.0		99.0	4.0	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Nonsense_Mutation	SNP	ENST00000379388.2	hg19	CCDS43426.1	.	.	.	.	.	.	.	.	.	.	G	36	5.874478	0.97055	.	.	ENSG00000095951	ENST00000379388;ENST00000442081;ENST00000541134;ENST00000542327	.	.	.	5.77	5.77	0.91146	.	0.227351	0.22489	N	0.059383	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	-27.6047	19.9827	0.97334	0.0:0.0:1.0:0.0	.	.	.	.	X	2185;112;50;167	.	ENSP00000368698:E2185X	E	+	1	0	HIVEP1	12269723	1.000000	0.71417	1.000000	0.80357	0.814000	0.46013	8.955000	0.93058	2.728000	0.93425	0.655000	0.94253	GAG	.	.		0.453	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114		T	12161737	G	T	12161737	4	4	259	1	0	0	0	0	0	1	0	0	7195	1291	45	3	6579	3	HIVEP1	6	12161737	Nonsense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10		12161737	158953330	272	36590										
TDP2	51567	hgsc.bcm.edu	37	chr6	24653322	24653322	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttcattcgttccgcagcatgCcctctggtgctctccaaatg	8	14	3	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:24653322C>T	ENST00000378198.4	-	6	866	c.696G>A	c.(694-696)ggG>ggA	p.G232G	TDP2_ENST00000545995.1_Silent_p.G262G|TDP2_ENST00000341060.3_Silent_p.G174G|TDP2_ENST00000478285.1_5'Flank			O95551	TYDP2_HUMAN	tyrosyl-DNA phosphodiesterase 2	232					cell surface receptor signaling pathway (GO:0007166)|double-strand break repair (GO:0006302)|regulation of RNA biosynthetic process (GO:2001141)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)|PML body (GO:0016605)	5'-tyrosyl-DNA phosphodiesterase activity (GO:0070260)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|nuclease activity (GO:0004518)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)|tyrosyl-RNA phosphodiesterase activity (GO:0036317)			kidney(2)|large_intestine(1)|lung(5)|ovary(1)	9						CCGCAGCATGCCCTCTGGTGC	0.423								Direct reversal of damage																													p.G232G		Atlas-SNP	.											.	TDP2	29	.	0			c.G696A						.						231	244	239					6																	24653322		2203	4300	6503	SO:0001819	synonymous_variant	51567	exon6			AGCATGCCCTCTG	AJ269473	CCDS4557.1	6p22.3-p22.1	2010-05-07	2010-05-07	2010-05-07	ENSG00000111802	ENSG00000111802	3.1.4.-		17768	protein-coding gene	gene with protein product		605764	"TRAF and TNF receptor associated protein"	TTRAP		11478795	Standard	NM_016614		Approved		uc003nej.3	O95551	OTTHUMG00000014360	ENST00000378198.4:c.696G>A	chr6.hg19:g.24653322C>T		138.0	0.0		113.0	5.0	NM_016614	B4DKL8|B4DQ95|Q2TBE2|Q5JYM0|Q7Z6U5|Q9NUK5|Q9NYY9	Silent	SNP	ENST00000378198.4	hg19	CCDS4557.1																																																																																			.	.		0.423	TDP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000040012.1			T	24653322	C	T	24653322	2	4	259	1	0	0	0	0	0	0	0	1	15744	726	26	3		3	TDP2	6	24653322	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	12491585	24653322	146461745	273	36591										
BTN2A1	11120	hgsc.bcm.edu	37	chr6	26463600	26463600	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acccctacggtggggttgcgCctgccctgaaagaggtctcc	13	14	1	2	rs368618565		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:26463600C>T	ENST00000312541.5	+	4	807	c.559C>T	c.(559-561)Cct>Tct	p.P187S	BTN2A1_ENST00000469185.1_Missense_Mutation_p.P187S|BTN2A1_ENST00000429381.1_Missense_Mutation_p.P187S|BTN2A1_ENST00000541522.1_Missense_Mutation_p.P126S	NM_007049.3|NM_078476.2	NP_008980.1|NP_510961.1	Q7KYR7	BT2A1_HUMAN	butyrophilin, subfamily 2, member A1	187					lipid metabolic process (GO:0006629)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(3)	27						TGGGGTTGCGCCTGCCCTGAA	0.597																																					p.P187S		Atlas-SNP	.											.	BTN2A1	118	.	0			c.C559T						.	C	SER/PRO,SER/PRO,SER/PRO,SER/PRO	0,4406		0,0,2203	96	86	89		376,559,559,559	2.9	0	6		89	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense,missense,missense	BTN2A1	NM_001197233.1,NM_001197234.1,NM_007049.3,NM_078476.2	74,74,74,74	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	126/467,187/331,187/528,187/335	26463600	2,13004	2203	4300	6503	SO:0001583	missense	11120	exon4			GTTGCGCCTGCCC	U90543	CCDS4613.1, CCDS47390.1, CCDS56404.1, CCDS56405.1	6p22.1	2014-01-14			ENSG00000112763	ENSG00000112763		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Butyrophilins"	1136	protein-coding gene	gene with protein product		613590				9382921, 9149941	Standard	NM_007049		Approved	BT2.1, BTF1, BTN2.1	uc003nib.2	Q7KYR7	OTTHUMG00000014457	ENST00000312541.5:c.559C>T	chr6.hg19:g.26463600C>T	ENSP00000312158:p.Pro187Ser	79.0	0.0		67.0	4.0	NM_001197234	B4DLP9|E9PGR4|O00475|P78408|Q59EN4|Q7KYQ7|Q7Z386|Q96AV7|Q9NU62	Missense_Mutation	SNP	ENST00000312541.5	hg19	CCDS4613.1	.	.	.	.	.	.	.	.	.	.	C	11.17	1.559823	0.27827	0.0	2.33E-4	ENSG00000112763	ENST00000312541;ENST00000541522;ENST00000429381;ENST00000265424;ENST00000469185	T;T;T;T	0.12255	2.7;2.7;2.7;2.7	2.88	2.88	0.33553	CD80-like, immunoglobulin C2-set (1);	0.271298	0.27176	N	0.020578	T	0.19208	0.0461	M	0.64170	1.965	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.01225	-1.1413	10	0.41790	T	0.15	.	11.9438	0.52915	0.0:1.0:0.0:0.0	.	187;187	Q96AV7;Q7KYR7	.;BT2A1_HUMAN	S	187;126;187;187;187	ENSP00000312158:P187S;ENSP00000443909:P126S;ENSP00000416945:P187S;ENSP00000419043:P187S	ENSP00000265424:P187S	P	+	1	0	BTN2A1	26571579	0.000000	0.05858	0.018000	0.16275	0.004000	0.04260	0.167000	0.16602	1.896000	0.54893	0.561000	0.74099	CCT	.	.		0.597	BTN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040122.2	NM_007049		T	26463600	C	T	26463600	3	4	259	1	0	0	0	0	1	0	0	0	1562	739	26	3	569	3	BTN2A1	6	26463600	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	1810278	26463600	144651467	274	36592										
ZNF192	7745	hgsc.bcm.edu	37	chr6	28121227	28121227	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tggcaaagccttcagtcagaAcacaggcctgattctgcacc	9	13	3	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:28121227A>G	ENST00000330236.6	+	6	1353	c.1169A>G	c.(1168-1170)aAc>aGc	p.N390S	ZKSCAN8_ENST00000457389.2_Missense_Mutation_p.N390S	NM_001278119.1|NM_001278121.1|NM_001278122.1|NM_006298.2	NP_001265048.1|NP_001265050.1|NP_001265051.1|NP_006289.2	Q15776	ZKSC8_HUMAN	zinc finger with KRAB and SCAN domains 8	390					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TTCAGTCAGAACACAGGCCTG	0.483																																					p.N390S		Atlas-SNP	.											.	.	.	.	0			c.A1169G						.						157	160	159					6																	28121227		2203	4300	6503	SO:0001583	missense	7745	exon6			GTCAGAACACAGG		CCDS4645.1	6p21	2013-01-09	2013-01-09	2013-01-09	ENSG00000198315	ENSG00000198315		"Zinc fingers, C2H2-type", "-", "-", "-"	12983	protein-coding gene	gene with protein product		602240	"zinc finger protein 192"	ZNF192			Standard	NM_001278119		Approved	LD5-1, ZSCAN40	uc003nkn.2	Q15776	OTTHUMG00000014510	ENST00000330236.6:c.1169A>G	chr6.hg19:g.28121227A>G	ENSP00000332750:p.Asn390Ser	181.0	0.0		161.0	8.0	NM_006298	A1L3D4|B4DYF1|Q4VAR1|Q4VAR2|Q4VAR3|Q9H4T1	Missense_Mutation	SNP	ENST00000330236.6	hg19	CCDS4645.1	.	.	.	.	.	.	.	.	.	.	A	1.016	-0.686274	0.03328	.	.	ENSG00000198315	ENST00000330236;ENST00000457389	T;T	0.13778	2.56;2.56	5.99	5.99	0.97316	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	D	0.000004	T	0.01976	0.0062	N	0.01219	-0.95	0.80722	D	1	B	0.25850	0.136	B	0.35859	0.212	T	0.34527	-0.9825	10	0.02654	T	1	.	15.4737	0.75461	1.0:0.0:0.0:0.0	.	390	Q15776	ZN192_HUMAN	S	390	ENSP00000332750:N390S;ENSP00000402948:N390S	ENSP00000332750:N390S	N	+	2	0	ZNF192	28229206	0.000000	0.05858	0.998000	0.56505	0.995000	0.86356	-0.014000	0.12656	2.300000	0.77407	0.533000	0.62120	AAC	.	.		0.483	ZKSCAN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040178.2			G	28121227	A	G	28121227	3	3	259	1	0	0	0	0	1	0	0	0	17771	43	2	2	1187	2	ZNF192	6	28121227	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1657627	28121227	142993840	275	36593										
NKAPL	222698	hgsc.bcm.edu	37	chr6	28227461	28227461	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cgtcactgctatgcagaagaAcggcagtcagcggaagacta	12	10	2	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:28227461A>G	ENST00000343684.3	+	1	364	c.312A>G	c.(310-312)gaA>gaG	p.E104E	ZKSCAN4_ENST00000423974.2_5'Flank	NM_001007531.1	NP_001007532.1	Q5M9Q1	NKAPL_HUMAN	NFKB activating protein-like	104										breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31						ATGCAGAAGAACGGCAGTCAG	0.582																																					p.E104E		Atlas-SNP	.											.	NKAPL	72	.	0			c.A312G						.						69	68	69					6																	28227461		2203	4300	6503	SO:0001819	synonymous_variant	222698	exon1			AGAAGAACGGCAG	BC038240	CCDS34353.1	6p21.33	2008-02-05	2007-08-16	2007-08-16	ENSG00000189134	ENSG00000189134			21584	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 194"	C6orf194			Standard	NM_001007531		Approved	bA424I5.1	uc003nkt.4	Q5M9Q1	OTTHUMG00000014517	ENST00000343684.3:c.312A>G	chr6.hg19:g.28227461A>G		74.0	0.0		92.0	4.0	NM_001007531	Q3MIV1|Q9H4Q7	Silent	SNP	ENST00000343684.3	hg19	CCDS34353.1																																																																																			.	.		0.582	NKAPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040185.1			G	28227461	A	G	28227461	2	3	259	1	0	0	0	0	0	0	0	1	10449	40	2	2		2	NKAPL	6	28227461	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	106234	28227461	142887606	276	36594										
ZNF323	64288	hgsc.bcm.edu	37	chr6	28297130	28297130	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cagatcttcaactacagccaCagcctcctccccactctccg	4	20	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:28297130C>T	ENST00000414429.1	-	6	1234	c.331G>A	c.(331-333)Gtg>Atg	p.V111M	ZSCAN31_ENST00000344279.6_Missense_Mutation_p.V111M|ZSCAN31_ENST00000439158.1_Missense_Mutation_p.V111M|ZSCAN31_ENST00000396838.2_Missense_Mutation_p.V111M|ZSCAN31_ENST00000446474.1_Intron|ZSCAN31_ENST00000481934.1_5'Flank			Q96LW9	ZSC31_HUMAN	zinc finger and SCAN domain containing 31	111	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)										ACTACAGCCACAGCCTCCTCC	0.527																																					p.V111M		Atlas-SNP	.											.	.	.	.	0			c.G331A						.						142	159	153					6																	28297130		2203	4300	6503	SO:0001583	missense	64288	exon2			CAGCCACAGCCTC		CCDS4649.1, CCDS59001.1	6p	2013-01-09	2013-01-08	2013-01-08	ENSG00000235109	ENSG00000235109		"-", "Zinc fingers, C2H2-type"	14097	protein-coding gene	gene with protein product		610794	"zinc finger protein 310 pseudogene", "zinc finger protein 323"	ZNF310P, ZNF323			Standard	NM_001135216		Approved		uc003nla.3	Q96LW9	OTTHUMG00000014518	ENST00000414429.1:c.331G>A	chr6.hg19:g.28297130C>T	ENSP00000390076:p.Val111Met	124.0	0.0		99.0	4.0	NM_030899	Q6P178|Q8WWS5	Missense_Mutation	SNP	ENST00000414429.1	hg19	CCDS4649.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.459795	0.84317	.	.	ENSG00000235109	ENST00000396838;ENST00000439158;ENST00000414429;ENST00000344279;ENST00000453745;ENST00000439636;ENST00000447021	T;T;T;T;T;T;T	0.06294	3.32;3.32;3.32;3.32;3.32;3.32;3.32	4.68	2.89	0.33648	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	.	.	.	.	T	0.14874	0.0359	H	0.99404	4.55	0.09310	N	1	P	0.38551	0.636	P	0.44732	0.459	T	0.21245	-1.0251	9	0.87932	D	0	.	7.454	0.27255	0.0:0.7255:0.0:0.2745	.	111	Q96LW9	ZN323_HUMAN	M	111	ENSP00000380050:V111M;ENSP00000413705:V111M;ENSP00000390076:V111M;ENSP00000345339:V111M;ENSP00000389479:V111M;ENSP00000412519:V111M;ENSP00000416108:V111M	ENSP00000345339:V111M	V	-	1	0	ZNF323	28405109	0.002000	0.14202	0.001000	0.08648	0.941000	0.58515	0.911000	0.28584	0.515000	0.28320	0.563000	0.77884	GTG	.	.		0.527	ZSCAN31-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346804.1	NM_030899		T	28297130	C	T	28297130	3	4	259	1	0	0	0	0	1	0	0	0	17858	478	17	3	901	3	ZNF323	6	28297130	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	69669	28297130	142817937	277	36595										
ZKSCAN3	80317	hgsc.bcm.edu	37	chr6	28333988	28333988	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atcagtgtaatgcgtgtggaAaaggcttcacccgaatttca	10	8	3	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:28333988A>G	ENST00000377255.3	+	7	1840	c.1543A>G	c.(1543-1545)Aaa>Gaa	p.K515E	ZKSCAN3_ENST00000341464.5_Missense_Mutation_p.K367E|ZKSCAN3_ENST00000252211.2_Missense_Mutation_p.K515E	NM_001242894.1	NP_001229823.1	Q9BRR0	ZKSC3_HUMAN	zinc finger with KRAB and SCAN domains 3	515					autophagy (GO:0006914)|lysosome organization (GO:0007040)|negative regulation of autophagy (GO:0010507)|negative regulation of cellular senescence (GO:2000773)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(4)|large_intestine(3)|lung(8)|pancreas(1)|skin(2)|stomach(2)|urinary_tract(1)	21						TGCGTGTGGAAAAGGCTTCAC	0.423																																					p.K515E		Atlas-SNP	.											.	ZKSCAN3	50	.	0			c.A1543G						.						104	103	104					6																	28333988		2203	4300	6503	SO:0001583	missense	80317	exon6			TGTGGAAAAGGCT	U71601	CCDS4650.1, CCDS56408.1	6p22.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000189298		"Zinc fingers, C2H2-type", "-", "-", "-"	13853	protein-coding gene	gene with protein product		612791	"zinc finger protein 306", "zinc finger protein 309"	ZNF306, ZNF309		10520746, 22531714	Standard	NM_024493		Approved	Zfp47, ZF47, ZSCAN35	uc003nle.4	Q9BRR0	OTTHUMG00000014521	ENST00000377255.3:c.1543A>G	chr6.hg19:g.28333988A>G	ENSP00000366465:p.Lys515Glu	88.0	0.0		72.0	4.0	NM_024493	B2R8W2|B3KVC0|H7BXX1|Q5VXH3|Q92972|Q9H4T3	Missense_Mutation	SNP	ENST00000377255.3	hg19	CCDS4650.1	.	.	.	.	.	.	.	.	.	.	A	18.29	3.592151	0.66219	.	.	ENSG00000189298	ENST00000252211;ENST00000341464;ENST00000377255	T;T;T	0.27104	1.69;1.69;1.69	3.97	3.97	0.46021	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.32645	0.0836	L	0.53729	1.69	0.31381	N	0.678991	D	0.76494	0.999	D	0.83275	0.996	T	0.09443	-1.0674	9	0.66056	D	0.02	.	11.9945	0.53194	1.0:0.0:0.0:0.0	.	515	Q9BRR0	ZKSC3_HUMAN	E	515;367;515	ENSP00000252211:K515E;ENSP00000341883:K367E;ENSP00000366465:K515E	ENSP00000252211:K515E	K	+	1	0	ZKSCAN3	28441967	1.000000	0.71417	1.000000	0.80357	0.296000	0.27459	4.047000	0.57383	1.666000	0.50821	0.533000	0.62120	AAA	.	.		0.423	ZKSCAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040189.3	NM_024493		G	28333988	A	G	28333988	3	3	259	1	0	0	0	0	1	0	0	0	17703	15	1	2	1561	2	ZKSCAN3	6	28333988	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	36858	28333988	142781079	278	36596										
PPP1R10	5514	hgsc.bcm.edu	37	chr6	30571268	30571268	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccatgatggaggtgaggatcTcttggacattaatgcctcct	11	9	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:30571268T>C	ENST00000376511.2	-	16	2300	c.1748A>G	c.(1747-1749)gAg>gGg	p.E583G		NM_002714.3	NP_002705.2	Q96QC0	PP1RA_HUMAN	protein phosphatase 1, regulatory subunit 10	583	Gly-rich.|Interaction with WDR82. {ECO:0000250}.				protein import into nucleus (GO:0006606)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|nucleus (GO:0005634)|PTW/PP1 phosphatase complex (GO:0072357)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein phosphatase inhibitor activity (GO:0004864)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(3)|skin(1)	25						GGTGAGGATCTCTTGGACATT	0.567																																					p.E583G		Atlas-SNP	.											.	PPP1R10	60	.	0			c.A1748G						.						97	84	89					6																	30571268		2203	4300	6503	SO:0001583	missense	5514	exon16			AGGATCTCTTGGA	Y13247	CCDS4681.1	6p21.3	2012-04-17	2011-10-04		ENSG00000204569	ENSG00000204569		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9284	protein-coding gene	gene with protein product	"phosphatase 1 nuclear targeting subunit", "HLA-C associated transcript 53"	603771	"protein phosphatase 1, regulatory (inhibitor) subunit 10"			9461602, 9784381	Standard	NM_002714		Approved	PNUTS, FB19, CAT53, p99	uc003nqn.2	Q96QC0	OTTHUMG00000031259	ENST00000376511.2:c.1748A>G	chr6.hg19:g.30571268T>C	ENSP00000365694:p.Glu583Gly	112.0	0.0		72.0	4.0	NM_002714	O00405	Missense_Mutation	SNP	ENST00000376511.2	hg19	CCDS4681.1	.	.	.	.	.	.	.	.	.	.	T	12.90	2.077578	0.36662	.	.	ENSG00000204569	ENST00000376511	T	0.52295	0.67	4.9	4.9	0.64082	.	0.000000	0.85682	D	0.000000	T	0.42877	0.1222	N	0.19112	0.55	0.58432	D	0.999996	D	0.71674	0.998	D	0.78314	0.991	T	0.49634	-0.8919	10	0.49607	T	0.09	-23.2507	13.8155	0.63290	0.0:0.0:0.0:1.0	.	583	Q96QC0	PP1RA_HUMAN	G	583	ENSP00000365694:E583G	ENSP00000365694:E583G	E	-	2	0	PPP1R10	30679247	1.000000	0.71417	1.000000	0.80357	0.172000	0.22775	7.040000	0.76551	1.958000	0.56883	0.383000	0.25322	GAG	.	.		0.567	PPP1R10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076556.2	NM_002714		C	30571268	T	C	30571268	3	2	259	1	0	0	0	0	1	0	0	0	12364	1551	54	2	1094	2	PPP1R10	6	30571268	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	2237280	30571268	140543799	279	36597										
GTF2H4	2968	hgsc.bcm.edu	37	chr6	30876860	30876860	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gaaccgagtacacctacaatGcaggaatctgcaggaattct	9	10	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:30876860G>A	ENST00000259895.4	+	2	270	c.47G>A	c.(46-48)tGc>tAc	p.C16Y	GTF2H4_ENST00000539324.1_Intron|GTF2H4_ENST00000376316.2_Missense_Mutation_p.C16Y|RN7SL175P_ENST00000580375.1_RNA	NM_001517.4	NP_001508.1	Q92759	TF2H4_HUMAN	general transcription factor IIH, polypeptide 4, 52kDa	16					7-methylguanosine mRNA capping (GO:0006370)|ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|gene expression (GO:0010467)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	core TFIIH complex (GO:0000439)|holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)	ATP-dependent DNA helicase activity (GO:0004003)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11						CACCTACAATGCAGGAATCTG	0.547								Nucleotide excision repair (NER)																													p.C16Y		Atlas-SNP	.											GTF2H4_ENST00000259895,colon,carcinoma,0,2	GTF2H4	38	.	0			c.G47A						.						89	80	83					6																	30876860		2203	4300	6503	SO:0001583	missense	2968	exon2			TACAATGCAGGAA	Y07595	CCDS34386.1	6p21.3	2012-11-05	2002-08-29		ENSG00000213780	ENSG00000213780		"General transcription factors", "General transcription factor IIH complex subunits"	4658	protein-coding gene	gene with protein product		601760	"general transcription factor IIH, polypeptide 4 (52kD subunit)"			9118947	Standard	NM_001517		Approved	TFB2, TFIIH, P52	uc003nsa.1	Q92759	OTTHUMG00000031043	ENST00000259895.4:c.47G>A	chr6.hg19:g.30876860G>A	ENSP00000259895:p.Cys16Tyr	43.0	0.0		27.0	2.0	NM_001517	B4DTJ5|Q76KU4	Missense_Mutation	SNP	ENST00000259895.4	hg19	CCDS34386.1	.	.	.	.	.	.	.	.	.	.	G	17.70	3.454752	0.63290	.	.	ENSG00000213780	ENST00000259895;ENST00000376316;ENST00000453897	T;T	0.45276	0.9;0.9	4.44	4.44	0.53790	.	0.072462	0.56097	U	0.000030	T	0.34948	0.0915	L	0.54323	1.7	0.80722	D	1	P;P;P	0.48998	0.918;0.814;0.814	P;P;P	0.47015	0.534;0.534;0.534	T	0.29671	-1.0004	10	0.59425	D	0.04	-25.7827	14.6358	0.68689	0.0:0.0:1.0:0.0	.	22;16;16	B4DNU0;Q53HH3;Q92759	.;.;TF2H4_HUMAN	Y	16	ENSP00000259895:C16Y;ENSP00000365493:C16Y	ENSP00000259895:C16Y	C	+	2	0	GTF2H4	30984839	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	8.202000	0.89737	2.300000	0.77407	0.561000	0.74099	TGC	.	.		0.547	GTF2H4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076044.3	NM_001517		A	30876860	G	A	30876860	3	1	259	1	0	0	0	0	1	0	0	0	6874	1319	46	3	49	3	GTF2H4	6	30876860	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	305592	30876860	140238207	280	36598										
CCHCR1	54535	hgsc.bcm.edu	37	chr6	31113070	31113070	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acgtctgtgaccggtggtggTaggggacagctgggacgggg	21	7	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:31113070T>C	ENST00000376266.5	-	13	1604	c.1482A>G	c.(1480-1482)ctA>ctG	p.L494L	CCHCR1_ENST00000396263.2_Silent_p.L441L|CCHCR1_ENST00000451521.2_Silent_p.L547L|CCHCR1_ENST00000396268.3_Silent_p.L583L	NM_019052.3	NP_061925.2	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1	494					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein export from nucleus (GO:0006611)	centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(13)|skin(1)	23						CCGGTGGTGGTAGGGGACAGC	0.597																																					p.L583L		Atlas-SNP	.											.	CCHCR1	68	.	0			c.A1749G						.						36	31	33					6																	31113070		1511	2709	4220	SO:0001819	synonymous_variant	54535	exon13			TGGTGGTAGGGGA	AF216493	CCDS4695.1, CCDS43445.1, CCDS47397.1	6p21.3	2007-08-01	2005-02-15	2005-02-16	ENSG00000204536	ENSG00000204536			13930	protein-coding gene	gene with protein product		605310	"chromosome 6 open reading frame 18"	C6orf18		10888604, 10545595	Standard	NM_019052		Approved	HCR	uc003nsp.4	Q8TD31	OTTHUMG00000031112	ENST00000376266.5:c.1482A>G	chr6.hg19:g.31113070T>C		69.0	0.0		66.0	4.0	NM_001105564	A2ABH6|E9PE84|Q2TB67|Q5SQ82|Q5STE9|Q9NRK8|Q9NWY9|Q9NXJ4|Q9NXK3|Q9Y6W1|Q9Y6W2	Silent	SNP	ENST00000376266.5	hg19	CCDS4695.1																																																																																			.	.		0.597	CCHCR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076190.5	NM_019052		C	31113070	T	C	31113070	2	2	259	1	0	0	0	0	0	0	0	1	2879	1625	57	2		2	CCHCR1	6	31113070	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	236210	31113070	140001997	281	36599										
TNXB	7148	hgsc.bcm.edu	37	chr6	32020470	32020470	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tcacacccacagcggacactGggcccacgcgctgcccctcg	10	20	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:32020470G>A	ENST00000375244.3	-	26	9293	c.9092C>T	c.(9091-9093)cCa>cTa	p.P3031L	TNXB_ENST00000375247.2_Missense_Mutation_p.P3029L			P22105	TENX_HUMAN	tenascin XB	3076	Fibronectin type-III 22. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						AGCGGACACTGGGCCCACGCG	0.632																																					p.P3029L		Atlas-SNP	.											.	TNXB	553	.	0			c.C9086T						.						54	61	58					6																	32020470		1401	2620	4021	SO:0001583	missense	7148	exon26			GACACTGGGCCCA	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.9092C>T	chr6.hg19:g.32020470G>A	ENSP00000364393:p.Pro3031Leu	182.0	0.0		118.0	5.0	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	hg19		.	.	.	.	.	.	.	.	.	.	g	20.5	4.002323	0.74932	.	.	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.05649	3.41;3.41	4.42	4.42	0.53409	.	0.000000	0.37669	U	0.001999	T	0.22936	0.0554	M	0.93978	3.48	0.41187	D	0.986274	D	0.89917	1.0	D	0.80764	0.994	T	0.16453	-1.0402	10	0.35671	T	0.21	.	13.9305	0.63991	0.0:0.0:1.0:0.0	.	3029	P22105-3	.	L	3031;3029	ENSP00000364393:P3031L;ENSP00000364396:P3029L	ENSP00000364393:P3031L	P	-	2	0	TNXB	32128448	0.998000	0.40836	0.990000	0.47175	0.030000	0.12068	3.413000	0.52686	1.968000	0.57251	0.561000	0.74099	CCA	.	.		0.632	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		A	32020470	G	A	32020470	3	1	259	1	0	0	0	0	1	0	0	0	16361	1348	47	3	5703	3	TNXB	6	32020470	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	907400	32020470	139094597	282	36600										
TNXB	7148	hgsc.bcm.edu	37	chr6	32057134	32057134	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agcttggaacccgtgctgtgAatggggggctcgccccctct	14	13	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:32057134A>G	ENST00000375244.3	-	5	2582	c.2381T>C	c.(2380-2382)tTc>tCc	p.F794S	TNXB_ENST00000375247.2_Missense_Mutation_p.F794S			P22105	TENX_HUMAN	tenascin XB	747	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						CCGTGCTGTGAATGGGGGGCT	0.612																																					p.F794S		Atlas-SNP	.											.	TNXB	553	.	0			c.T2381C						.						31	35	33					6																	32057134		1947	4146	6093	SO:0001583	missense	7148	exon5			GCTGTGAATGGGG	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.2381T>C	chr6.hg19:g.32057134A>G	ENSP00000364393:p.Phe794Ser	58.0	0.0		65.0	4.0	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	hg19		.	.	.	.	.	.	.	.	.	.	A	18.32	3.597752	0.66332	.	.	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.56103	0.48;0.48	5.3	5.3	0.74995	.	.	.	.	.	T	0.36441	0.0967	N	0.05078	-0.115	0.31808	N	0.627477	D	0.76494	0.999	D	0.85130	0.997	T	0.35822	-0.9773	9	0.22706	T	0.39	.	13.2394	0.59987	1.0:0.0:0.0:0.0	.	794	P22105-3	.	S	794	ENSP00000364393:F794S;ENSP00000364396:F794S	ENSP00000364393:F794S	F	-	2	0	TNXB	32165112	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.204000	0.51082	2.231000	0.72958	0.460000	0.39030	TTC	.	.		0.612	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		G	32057134	A	G	32057134	3	3	259	1	0	0	0	0	1	0	0	0	16361	246	9	2	12492	2	TNXB	6	32057134	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	36664	32057134	139057933	283	36601										
ATF6B	1388	hgsc.bcm.edu	37	chr6	32085736	32085736	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aactggctcttgctctgagaAccccagcaagtgtctccggg	11	13	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:32085736A>G	ENST00000375203.3	-	12	1356	c.1324T>C	c.(1324-1326)Ttc>Ctc	p.F442L	ATF6B_ENST00000375201.4_Missense_Mutation_p.F439L	NM_001136153.1|NM_004381.4	NP_001129625.1|NP_004372.3	Q99941	ATF6B_HUMAN	activating transcription factor 6 beta	442					response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	22						TGCTCTGAGAACCCCAGCAAG	0.597																																					p.F442L		Atlas-SNP	.											.	ATF6B	40	.	0			c.T1324C						.						53	54	54					6																	32085736		2203	4300	6503	SO:0001583	missense	1388	exon12			CTGAGAACCCCAG		CCDS47408.1, CCDS4737.1	6p21.3	2013-01-10	2008-10-21	2008-10-21	ENSG00000213676	ENSG00000213676		"basic leucine zipper proteins"	2349	protein-coding gene	gene with protein product		600984	"cAMP responsive element binding protein-like 1"	CREBL1		11256944, 14973138	Standard	NM_004381		Approved	G13	uc003nzn.3	Q99941	OTTHUMG00000031296	ENST00000375203.3:c.1324T>C	chr6.hg19:g.32085736A>G	ENSP00000364349:p.Phe442Leu	137.0	0.0		91.0	4.0	NM_004381	B0UYX6|Q13269|Q14343|Q14345|Q5SSW7|Q99635|Q99637|Q9H3V9|Q9H3W1|Q9NPL0	Missense_Mutation	SNP	ENST00000375203.3	hg19	CCDS4737.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.623135	0.87460	.	.	ENSG00000213676	ENST00000375203;ENST00000375201	T;T	0.58060	0.36;1.1	5.87	5.87	0.94306	.	0.673373	0.13546	U	0.379841	T	0.48750	0.1517	M	0.79926	2.475	0.36535	D	0.870938	P;P;P	0.47191	0.891;0.553;0.826	P;B;B	0.45610	0.487;0.143;0.292	T	0.53767	-0.8392	10	0.31617	T	0.26	-18.2328	12.6731	0.56878	1.0:0.0:0.0:0.0	.	439;442;442	Q99941-2;Q99941;Q6AZW6	.;ATF6B_HUMAN;.	L	442;439	ENSP00000364349:F442L;ENSP00000364347:F439L	ENSP00000364347:F439L	F	-	1	0	ATF6B	32193714	1.000000	0.71417	0.999000	0.59377	0.947000	0.59692	2.983000	0.49345	2.244000	0.73946	0.533000	0.62120	TTC	.	.		0.597	ATF6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076638.2			G	32085736	A	G	32085736	3	3	259	1	0	0	0	0	1	0	0	0	1085	43	2	2	815	2	ATF6B	6	32085736	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	28602	32085736	139029331	284	36602										
TAP1	6890	hgsc.bcm.edu	37	chr6	32816572	32816572	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gtactcaaatattttctctgAggagcccacagccttctgta	7	11	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:32816572A>G	ENST00000354258.4	-	7	1764	c.1603T>C	c.(1603-1605)Tca>Cca	p.S535P	TAP1_ENST00000425148.2_Missense_Mutation_p.S274P|PSMB9_ENST00000395330.1_Intron|TAPSAR1_ENST00000453426.1_lincRNA	NM_000593.5	NP_000584.2	Q03518	TAP1_HUMAN	transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)	535	Involved in peptide-binding site.				antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytosol to ER transport (GO:0046967)|defense response (GO:0006952)|intracellular transport of viral protein in host cell (GO:0019060)|peptide transport (GO:0015833)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)|TAP complex (GO:0042825)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|MHC class Ib protein binding (GO:0023029)|peptide antigen binding (GO:0042605)|peptide transporter activity (GO:0015197)|protein homodimerization activity (GO:0042803)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(4)|prostate(1)|skin(1)	21					Lapatinib(DB01259)	ATTTTCTCTGAGGAGCCCACA	0.522																																					p.S535P		Atlas-SNP	.											.	TAP1	39	.	0			c.T1603C						.						110	110	110					6																	32816572		2203	4300	6503	SO:0001583	missense	6890	exon7			TCTCTGAGGAGCC		CCDS4758.1	6p21.3	2014-09-17			ENSG00000168394	ENSG00000168394		"ATP binding cassette transporters / subfamily B"	43	protein-coding gene	gene with protein product		170260		ABCB2		1529427, 1946428	Standard	NM_000593		Approved	PSF1, RING4, D6S114E	uc003ocg.3	Q03518	OTTHUMG00000031067	ENST00000354258.4:c.1603T>C	chr6.hg19:g.32816572A>G	ENSP00000346206:p.Ser535Pro	99.0	0.0		89.0	4.0	NM_000593	Q16149|Q96CP4	Missense_Mutation	SNP	ENST00000354258.4	hg19	CCDS4758.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.030456	0.75504	.	.	ENSG00000168394	ENST00000354258;ENST00000425148	T;T	0.80653	-1.4;-1.4	5.02	5.02	0.67125	ABC transporter, transmembrane domain, type 1 (1);	.	.	.	.	D	0.87977	0.6314	M	0.86097	2.795	0.58432	D	0.999999	D	0.89917	1.0	D	0.78314	0.991	D	0.89888	0.4035	9	0.72032	D	0.01	-2.3668	12.7438	0.57268	1.0:0.0:0.0:0.0	.	535	Q03518	TAP1_HUMAN	P	535;274	ENSP00000346206:S535P;ENSP00000401919:S274P	ENSP00000346206:S535P	S	-	1	0	TAP1	32924550	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	5.998000	0.70653	2.106000	0.64143	0.523000	0.50628	TCA	.	.		0.522	TAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076087.2	NM_000593		G	32816572	A	G	32816572	3	3	259	1	0	0	0	0	1	0	0	0	15565	304	11	2	843	2	TAP1	6	32816572	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	730836	32816572	138298495	285	36603										
TAP1	6890	hgsc.bcm.edu	37	chr6	32820940	32820940	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccgccgggcacccagaggctCccgagtttgtgccacagggc	14	16	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:32820940C>A	ENST00000354258.4	-	1	815	c.654G>T	c.(652-654)ggG>ggT	p.G218G	PSMB9_ENST00000453265.2_5'Flank|PSMB9_ENST00000374859.2_5'Flank|TAP1_ENST00000425148.2_5'Flank|PSMB9_ENST00000395330.1_Intron	NM_000593.5	NP_000584.2	Q03518	TAP1_HUMAN	transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)	218					antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytosol to ER transport (GO:0046967)|defense response (GO:0006952)|intracellular transport of viral protein in host cell (GO:0019060)|peptide transport (GO:0015833)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)|TAP complex (GO:0042825)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|MHC class Ib protein binding (GO:0023029)|peptide antigen binding (GO:0042605)|peptide transporter activity (GO:0015197)|protein homodimerization activity (GO:0042803)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(4)|prostate(1)|skin(1)	21					Lapatinib(DB01259)	CCCAGAGGCTCCCGAGTTTGT	0.667																																					p.G218G		Atlas-SNP	.											.	TAP1	39	.	0			c.G654T						.						20	21	21					6																	32820940		1508	2707	4215	SO:0001819	synonymous_variant	6890	exon1			GAGGCTCCCGAGT		CCDS4758.1	6p21.3	2014-09-17			ENSG00000168394	ENSG00000168394		"ATP binding cassette transporters / subfamily B"	43	protein-coding gene	gene with protein product		170260		ABCB2		1529427, 1946428	Standard	NM_000593		Approved	PSF1, RING4, D6S114E	uc003ocg.3	Q03518	OTTHUMG00000031067	ENST00000354258.4:c.654G>T	chr6.hg19:g.32820940C>A		129.0	0.0		103.0	32.0	NM_000593	Q16149|Q96CP4	Silent	SNP	ENST00000354258.4	hg19	CCDS4758.1																																																																																			.	.		0.667	TAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076087.2	NM_000593		A	32820940	C	A	32820940	2	1	259	1	0	0	0	0	0	0	0	1	15565	842	30	3		3	TAP1	6	32820940	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	4368	32820940	138294127	286	36604										
ZBTB9	221504	hgsc.bcm.edu	37	chr6	33423704	33423704	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acttgagcttcctgcccctcCtgcactgccccccaaaatct	5	19	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:33423704C>T	ENST00000395064.2	+	2	1095	c.827C>T	c.(826-828)cCt>cTt	p.P276L		NM_152735.3	NP_689948.1	Q96C00	ZBTB9_HUMAN	zinc finger and BTB domain containing 9	276	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|skin(1)|upper_aerodigestive_tract(2)	11						CCTGCCCCTCCTGCACTGCCC	0.562																																					p.P276L		Atlas-SNP	.											.	ZBTB9	23	.	0			c.C827T						.						57	59	58					6																	33423704		2203	4300	6503	SO:0001583	missense	221504	exon2			CCCCTCCTGCACT	AK122644	CCDS4780.1	6p21.31	2013-01-09			ENSG00000213588	ENSG00000213588		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	28323	protein-coding gene	gene with protein product						12477932	Standard	NM_152735		Approved	MGC23166, ZNF919	uc003oeq.3	Q96C00	OTTHUMG00000140180	ENST00000395064.2:c.827C>T	chr6.hg19:g.33423704C>T	ENSP00000378503:p.Pro276Leu	91.0	0.0		96.0	5.0	NM_152735	A2AB19	Missense_Mutation	SNP	ENST00000395064.2	hg19	CCDS4780.1	.	.	.	.	.	.	.	.	.	.	C	12.13	1.846482	0.32606	.	.	ENSG00000213588	ENST00000395064	T	0.06608	3.28	4.54	4.54	0.55810	.	7.925470	0.01955	U	0.042929	T	0.02156	0.0067	N	0.19112	0.55	0.21897	N	0.999486	P	0.37423	0.594	B	0.34722	0.188	T	0.32214	-0.9915	10	0.27785	T	0.31	.	12.6515	0.56764	0.0:1.0:0.0:0.0	.	276	Q96C00	ZBTB9_HUMAN	L	276	ENSP00000378503:P276L	ENSP00000378503:P276L	P	+	2	0	ZBTB9	33531682	0.003000	0.15002	0.007000	0.13788	0.850000	0.48378	1.805000	0.38883	2.368000	0.80403	0.655000	0.94253	CCT	.	.		0.562	ZBTB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276533.1	NM_152735		T	33423704	C	T	33423704	3	4	259	1	0	0	0	0	1	0	0	0	17573	681	24	3	829	3	ZBTB9	6	33423704	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	602764	33423704	137691363	287	36605										
BRPF3	27154	hgsc.bcm.edu	37	chr6	36175193	36175193	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gctgctgattgagctgattcGgaagagagagaagctcaaac	13	7	1	5			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:36175193G>T	ENST00000357641.6	+	4	1962	c.1709G>T	c.(1708-1710)cGg>cTg	p.R570L	BRPF3_ENST00000534400.1_Missense_Mutation_p.R570L|BRPF3_ENST00000443324.2_Missense_Mutation_p.R570L|BRPF3_ENST00000534694.1_Missense_Mutation_p.R570L|BRPF3_ENST00000543502.1_Missense_Mutation_p.R570L|BRPF3_ENST00000339717.7_Missense_Mutation_p.R570L	NM_015695.2	NP_056510.2	Q9ULD4	BRPF3_HUMAN	bromodomain and PHD finger containing, 3	570					blood coagulation (GO:0007596)|histone H3 acetylation (GO:0043966)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	cytosol (GO:0005829)|extracellular region (GO:0005576)|MOZ/MORF histone acetyltransferase complex (GO:0070776)	zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(1)|skin(4)|urinary_tract(2)	40						GAGCTGATTCGGAAGAGAGAG	0.547																																					p.R570L		Atlas-SNP	.											.	BRPF3	93	.	0			c.G1709T						.						49	47	47					6																	36175193		2203	4300	6503	SO:0001583	missense	27154	exon4			TGATTCGGAAGAG	AB033112	CCDS34437.1	6p21.31	2008-02-05			ENSG00000096070	ENSG00000096070			14256	protein-coding gene	gene with protein product						10574462	Standard	NM_015695		Approved	KIAA1286	uc003olv.4	Q9ULD4	OTTHUMG00000014589	ENST00000357641.6:c.1709G>T	chr6.hg19:g.36175193G>T	ENSP00000350267:p.Arg570Leu	181.0	0.0		136.0	7.0	NM_015695	A6ND56|A6NJE2|B7ZLN5|E7EX85|Q17RB6|Q5R3K8	Missense_Mutation	SNP	ENST00000357641.6	hg19	CCDS34437.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.319944	0.81469	.	.	ENSG00000096070	ENST00000357641;ENST00000339717;ENST00000534694;ENST00000543502;ENST00000443324;ENST00000534400	T;T;T;T;T;T	0.20738	2.28;2.31;2.3;2.31;2.3;2.05	4.86	4.86	0.63082	Bromodomain (1);	0.000000	0.85682	D	0.000000	T	0.41604	0.1166	M	0.74546	2.27	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.85130	0.993;0.993;0.997	T	0.43972	-0.9358	10	0.87932	D	0	.	18.3462	0.90322	0.0:0.0:1.0:0.0	.	570;570;570	B7ZLN5;Q17RB6;Q9ULD4	.;.;BRPF3_HUMAN	L	570	ENSP00000350267:R570L;ENSP00000345419:R570L;ENSP00000434501:R570L;ENSP00000445352:R570L;ENSP00000387368:R570L;ENSP00000436504:R570L	ENSP00000345419:R570L	R	+	2	0	BRPF3	36283171	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.751000	0.98889	2.409000	0.81822	0.655000	0.94253	CGG	.	.		0.547	BRPF3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040335.3	NM_015695		T	36175193	G	T	36175193	3	4	259	1	0	0	0	0	1	0	0	0	1523	1116	39	1	1719	1	BRPF3	6	36175193	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	2751489	36175193	134939874	288	36606										
PPIL1	51645	hgsc.bcm.edu	37	chr6	36842499	36842499	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccgaaccccctcacctggtcTccaagtaaacgttgggtggc	10	15	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:36842499T>C	ENST00000373699.5	-	1	301	c.50A>G	c.(49-51)gAg>gGg	p.E17G	C6orf89_ENST00000359359.2_Intron|C6orf89_ENST00000510325.2_Intron	NM_016059.4	NP_057143.1	Q9Y3C6	PPIL1_HUMAN	peptidylprolyl isomerase (cyclophilin)-like 1	17	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)|extracellular vesicular exosome (GO:0070062)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			lung(1)|ovary(1)	2						TCACCTGGTCTCCAAGTAAAC	0.657																																					p.E17G		Atlas-SNP	.											.	PPIL1	6	.	0			c.A50G						.						29	31	30					6																	36842499		2203	4300	6503	SO:0001583	missense	51645	exon1			CTGGTCTCCAAGT	AF090992	CCDS4826.1	6p21.1	2008-08-29			ENSG00000137168	ENSG00000137168			9260	protein-coding gene	gene with protein product		601301				10072585, 8978786	Standard	NM_016059		Approved	CYPL1	uc003omu.2	Q9Y3C6	OTTHUMG00000014612	ENST00000373699.5:c.50A>G	chr6.hg19:g.36842499T>C	ENSP00000362803:p.Glu17Gly	158.0	0.0		120.0	5.0	NM_016059	O15001|Q5TDC9	Missense_Mutation	SNP	ENST00000373699.5	hg19	CCDS4826.1	.	.	.	.	.	.	.	.	.	.	T	31	5.063038	0.93898	.	.	ENSG00000137168	ENST00000373699	T	0.24908	1.83	5.62	5.62	0.85841	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (3);Cyclophilin-like (1);	0.114392	0.56097	D	0.000021	T	0.28896	0.0717	M	0.84846	2.72	0.80722	D	1	P	0.37101	0.582	B	0.41466	0.358	T	0.20273	-1.0280	10	0.66056	D	0.02	.	13.778	0.63066	0.0:0.0:0.0:1.0	.	17	Q9Y3C6	PPIL1_HUMAN	G	17	ENSP00000362803:E17G	ENSP00000362803:E17G	E	-	2	0	PPIL1	36950477	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.465000	0.66725	2.153000	0.67306	0.528000	0.53228	GAG	.	.		0.657	PPIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040382.1			C	36842499	T	C	36842499	3	2	259	1	0	0	0	0	1	0	0	0	12338	1551	54	2	466	2	PPIL1	6	36842499	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	667306	36842499	134272568	289	36607										
KIF6	221458	hgsc.bcm.edu	37	chr6	39552745	39552745	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cactcgctgtgcaaatctgcAggttgatatagactcctaag	9	10	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:39552745A>G	ENST00000287152.7	-	9	1100	c.1006T>C	c.(1006-1008)Tgc>Cgc	p.C336R	KIF6_ENST00000373216.3_Missense_Mutation_p.C336R|KIF6_ENST00000373213.4_Missense_Mutation_p.C175R|KIF6_ENST00000373215.3_Missense_Mutation_p.C336R|KIF6_ENST00000538893.1_Missense_Mutation_p.C336R	NM_145027.4	NP_659464.3	Q6ZMV9	KIF6_HUMAN	kinesin family member 6	336	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|male germ cell nucleus (GO:0001673)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(16)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						GCAAATCTGCAGGTTGATATA	0.303																																					p.C336R		Atlas-SNP	.											.	KIF6	233	.	0			c.T1006C						.						87	95	92					6																	39552745		2203	4300	6503	SO:0001583	missense	221458	exon9			ATCTGCAGGTTGA	AL832634	CCDS4844.1, CCDS75449.1	6p21.2	2010-03-30			ENSG00000164627	ENSG00000164627		"Kinesins"	21202	protein-coding gene	gene with protein product		613919	"chromosome 6 open reading frame 102"	C6orf102			Standard	NM_145027		Approved	dJ1043E3.1, MGC33317, dJ137F1.4, dJ188D3.1, DKFZp451I2418	uc003oot.2	Q6ZMV9	OTTHUMG00000014648	ENST00000287152.7:c.1006T>C	chr6.hg19:g.39552745A>G	ENSP00000287152:p.Cys336Arg	97.0	0.0		77.0	4.0	NM_145027	Q2MDE3|Q2MDE4|Q5T8J6|Q6ZWE3|Q86T87|Q8WTV4	Missense_Mutation	SNP	ENST00000287152.7	hg19	CCDS4844.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.163189	0.78226	.	.	ENSG00000164627	ENST00000287152;ENST00000373216;ENST00000373213;ENST00000373215;ENST00000538893;ENST00000441975;ENST00000373211	T;T;T;T;T;T	0.72505	-0.66;-0.66;-0.66;-0.66;-0.66;-0.66	5.65	5.65	0.86999	Kinesin, motor domain (3);	.	.	.	.	T	0.81029	0.4738	M	0.78637	2.42	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.994;0.996;0.996;0.998	D	0.84046	0.0367	9	0.87932	D	0	.	14.4154	0.67145	1.0:0.0:0.0:0.0	.	336;336;336;336	E7EUN7;F6VGH2;Q6ZMV9-3;Q6ZMV9	.;.;.;KIF6_HUMAN	R	336;336;175;336;336;123;127	ENSP00000287152:C336R;ENSP00000362312:C336R;ENSP00000362309:C175R;ENSP00000362311:C336R;ENSP00000441435:C336R;ENSP00000404856:C123R	ENSP00000287152:C336R	C	-	1	0	KIF6	39660723	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.770000	0.91746	2.281000	0.76405	0.528000	0.53228	TGC	.	.		0.303	KIF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040455.2	NM_145027		G	39552745	A	G	39552745	3	3	259	1	0	0	0	0	1	0	0	0	8317	188	7	2	1498	2	KIF6	6	39552745	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2710246	39552745	131562322	290	36608										
KIAA0240	23506	hgsc.bcm.edu	37	chr6	42819934	42819934	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctcttgagcaccacactgccAggtcaggagcttcctcagtt	9	14	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:42819934A>G	ENST00000314073.5	+	7	2120	c.1944A>G	c.(1942-1944)ccA>ccG	p.P648P	GLTSCR1L_ENST00000394168.1_Splice_Site_p.P648P			Q6AI39	GSC1L_HUMAN	GLTSCR1-like	648																	CCACACTGCCAGGTCAGGAGC	0.522																																					p.P648P		Atlas-SNP	.											.	.	.	.	0			c.A1944G						.						92	73	79					6																	42819934		2203	4300	6503	SO:0001630	splice_region_variant	23506	exon6			ACTGCCAGGTCAG	AL833540	CCDS34451.1	6p21.1	2012-11-29	2012-11-29	2012-11-29	ENSG00000112624	ENSG00000112624			21111	protein-coding gene	gene with protein product			"KIAA0240"	KIAA0240			Standard	XM_005248972		Approved		uc003osp.1	Q6AI39	OTTHUMG00000014706	ENST00000314073.5:c.1945+1A>G	chr6.hg19:g.42819934A>G		115.0	0.0		123.0	5.0	NM_015349	A1L3W2|Q5TFZ3|Q92514	Silent	SNP	ENST00000314073.5	hg19	CCDS34451.1																																																																																			.	.		0.522	GLTSCR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040562.3	NM_015349	Silent	G	42819934	A	G	42819934	5	3	259	1	0	0	0	0	0	0	1	0	8173	202	7	2	1962	2	KIAA0240	6	42819934	Splice_Site	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	3267189	42819934	128295133	291	36609										
ZNF318	24149	hgsc.bcm.edu	37	chr6	43308192	43308192	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cacagccaagccagcttggcGgtccagattccgccgctcct	10	17	0	1	rs377285454		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:43308192G>T	ENST00000361428.2	-	10	3621	c.3544C>A	c.(3544-3546)Cgc>Agc	p.R1182S	ZNF318_ENST00000318149.3_Intron	NM_014345.2	NP_055160.2	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	1182					meiotic nuclear division (GO:0007126)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(21)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	61			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)			CCAGCTTGGCGGTCCAGATTC	0.443																																					p.R1182S		Atlas-SNP	.											.	ZNF318	175	.	0			c.C3544A						.						41	44	43					6																	43308192		2197	4289	6486	SO:0001583	missense	24149	exon10			CTTGGCGGTCCAG	AF090114	CCDS4895.2	6p21.1	2013-09-19			ENSG00000171467	ENSG00000171467		"Zinc fingers, C2H2-type"	13578	protein-coding gene	gene with protein product						10873617	Standard	NM_014345		Approved	HRIHFB2436, ZFP318	uc003oux.3	Q5VUA4	OTTHUMG00000014732	ENST00000361428.2:c.3544C>A	chr6.hg19:g.43308192G>T	ENSP00000354964:p.Arg1182Ser	89.0	0.0		59.0	4.0	NM_014345	O94796|Q4G0E4|Q8NEM6|Q9UNU8|Q9Y2W9	Missense_Mutation	SNP	ENST00000361428.2	hg19	CCDS4895.2	.	.	.	.	.	.	.	.	.	.	G	17.62	3.435694	0.62955	.	.	ENSG00000171467	ENST00000361428	T	0.49720	0.77	5.69	5.69	0.88448	.	0.057492	0.64402	D	0.000001	T	0.49695	0.1572	M	0.61703	1.905	0.80722	D	1	D	0.54964	0.969	P	0.54460	0.753	T	0.55003	-0.8208	10	0.87932	D	0	-3.3998	13.0671	0.59041	0.0732:0.0:0.9268:0.0	.	1182	Q5VUA4	ZN318_HUMAN	S	1182	ENSP00000354964:R1182S	ENSP00000354964:R1182S	R	-	1	0	ZNF318	43416170	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.058000	0.71126	2.683000	0.91414	0.655000	0.94253	CGC	.	.		0.443	ZNF318-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040601.2	NM_014345		T	43308192	G	T	43308192	3	4	259	1	0	0	0	0	1	0	0	0	17851	1116	39	1	3299	1	ZNF318	6	43308192	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	488258	43308192	127806875	292	36610										
CDC5L	988	hgsc.bcm.edu	37	chr6	44371614	44371614	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agaaattcagaagaaaagaaAaaggaagagaggagttgatt	12	1	1	6	rs370695015		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:44371614A>G	ENST00000371477.3	+	6	907	c.608A>G	c.(607-609)aAa>aGa	p.K203R		NM_001253.3	NP_001244.1	Q99459	CDC5L_HUMAN	cell division cycle 5-like	203	Nuclear localization signal. {ECO:0000255}.|Required for interaction with CTNNBL1. {ECO:0000269|PubMed:21385873}.				cell cycle (GO:0007049)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)|Prp19 complex (GO:0000974)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|WD40-repeat domain binding (GO:0071987)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|skin(4)	29	all_lung(25;0.00433)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			AAGAAAAGAAAAAGGAAGAGA	0.383																																					p.K203R		Atlas-SNP	.											.	CDC5L	86	.	0			c.A608G						.						57	62	61					6																	44371614		2201	4299	6500	SO:0001583	missense	988	exon6			AAAGAAAAAGGAA	D85423	CCDS4912.1	6p21.1	2013-01-17	2013-01-17		ENSG00000096401	ENSG00000096401			1743	protein-coding gene	gene with protein product		602868	"CDC5 (cell division cycle 5, S. pombe, homolog)-like", "CDC5 cell division cycle 5-like (S. pombe)"			9598309, 9038199	Standard	NM_001253		Approved	PCDC5RP, hCDC5, CEF1, CDC5	uc003oxl.3	Q99459	OTTHUMG00000014767	ENST00000371477.3:c.608A>G	chr6.hg19:g.44371614A>G	ENSP00000360532:p.Lys203Arg	118.0	0.0		99.0	4.0	NM_001253	Q76N46|Q99974	Missense_Mutation	SNP	ENST00000371477.3	hg19	CCDS4912.1	.	.	.	.	.	.	.	.	.	.	A	13.78	2.338606	0.41398	.	.	ENSG00000096401	ENST00000371477	T	0.50277	0.75	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	T	0.17365	0.0417	N	0.13140	0.3	0.80722	D	1	B	0.21071	0.051	B	0.24006	0.05	T	0.12293	-1.0553	10	0.13108	T	0.6	-29.085	16.5885	0.84745	1.0:0.0:0.0:0.0	.	203	Q99459	CDC5L_HUMAN	R	203	ENSP00000360532:K203R	ENSP00000360532:K203R	K	+	2	0	CDC5L	44479592	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.093000	0.94163	2.317000	0.78254	0.460000	0.39030	AAA	.	.		0.383	CDC5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040743.1			G	44371614	A	G	44371614	3	3	259	1	0	0	0	0	1	0	0	0	3084	14	1	2	630	2	CDC5L	6	44371614	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1063422	44371614	126743453	293	36611										
TNFRSF21	27242	hgsc.bcm.edu	37	chr6	47202533	47202533	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tcctgtggggaaggctccacCgtcaggagagcggaattctc	14	11	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:47202533C>T	ENST00000296861.2	-	5	2004	c.1611G>A	c.(1609-1611)acG>acA	p.T537T		NM_014452.3	NP_055267.1	O75509	TNR21_HUMAN	tumor necrosis factor receptor superfamily, member 21	537					adaptive immune response (GO:0002250)|apoptotic process (GO:0006915)|B cell apoptotic process (GO:0001783)|cellular lipid metabolic process (GO:0044255)|cellular response to tumor necrosis factor (GO:0071356)|humoral immune response (GO:0006959)|myelination (GO:0042552)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-13 secretion (GO:2000666)|negative regulation of interleukin-5 secretion (GO:2000663)|negative regulation of myelination (GO:0031642)|negative regulation of T cell proliferation (GO:0042130)|neuron apoptotic process (GO:0051402)|oligodendrocyte apoptotic process (GO:0097252)|regulation of oligodendrocyte differentiation (GO:0048713)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|lung(7)|pancreas(1)|skin(2)	21			Lung(136;0.189)			AAGGCTCCACCGTCAGGAGAG	0.607																																					p.T537T		Atlas-SNP	.											.	TNFRSF21	61	.	0			c.G1611A						.						45	42	43					6																	47202533		2203	4300	6503	SO:0001819	synonymous_variant	27242	exon5			CTCCACCGTCAGG	AF068868	CCDS4921.1	6p21.1	2011-08-11			ENSG00000146072	ENSG00000146072		"Tumor necrosis factor receptor superfamily", "CD molecules"	13469	protein-coding gene	gene with protein product	"death receptor 6"	605732				9714541	Standard	NM_014452		Approved	DR6, CD358	uc003oyv.3	O75509	OTTHUMG00000014796	ENST00000296861.2:c.1611G>A	chr6.hg19:g.47202533C>T		78.0	0.0		48.0	4.0	NM_014452	B2RDI9|Q0D2P5|Q96D86	Silent	SNP	ENST00000296861.2	hg19	CCDS4921.1																																																																																			.	.		0.607	TNFRSF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040814.1	NM_014452		T	47202533	C	T	47202533	2	4	259	1	0	0	0	0	0	0	0	1	16310	639	23	1		1	TNFRSF21	6	47202533	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	2830919	47202533	123912534	294	36612										
OPN5	221391	hgsc.bcm.edu	37	chr6	47763294	47763294	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atgtgctggaaatgaaactgAcaaaggtaagtgcactaata	10	5	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:47763294A>G	ENST00000371211.2	+	4	779	c.751A>G	c.(751-753)Aca>Gca	p.T251A	OPN5_ENST00000489301.2_Missense_Mutation_p.T251A|OPN5_ENST00000393699.2_Missense_Mutation_p.T251A|OPN5_ENST00000244799.4_3'UTR	NM_181744.3	NP_859528.1	Q6U736	OPN5_HUMAN	opsin 5	251					phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)	G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)			endometrium(1)|large_intestine(3)|lung(14)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(2)	29						AATGAAACTGACAAAGGTAAG	0.413																																					p.T251A	Melanoma(28;740 973 10870 42660 45347)	Atlas-SNP	.											.	OPN5	58	.	0			c.A751G						.						83	74	77					6																	47763294		2203	4300	6503	SO:0001583	missense	221391	exon4			AAACTGACAAAGG	AY288419	CCDS4923.1	6p12.3	2012-08-08	2004-01-23		ENSG00000124818	ENSG00000124818		"GPCR / Class A : Opsin receptors"	19992	protein-coding gene	gene with protein product	"neuropsin"	609042	"transmembrane protein 13"	TMEM13		14623103, 14623098	Standard	NR_033806		Approved	neuropsin, dJ402H5.1	uc003ozc.3	Q6U736	OTTHUMG00000014803	ENST00000371211.2:c.751A>G	chr6.hg19:g.47763294A>G	ENSP00000360255:p.Thr251Ala	89.0	0.0		92.0	4.0	NM_181744	A0AV33|Q5T5B9|Q5T886|Q7Z603|Q86SL5	Missense_Mutation	SNP	ENST00000371211.2	hg19	CCDS4923.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.165161	0.78339	.	.	ENSG00000124818	ENST00000489301;ENST00000371211;ENST00000393699	T;T;T	0.69926	-0.44;-0.44;-0.44	5.48	5.48	0.80851	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.27454	0.0674	N	0.11892	0.195	0.44268	D	0.997121	P	0.36330	0.548	B	0.35727	0.209	T	0.43180	-0.9407	10	0.02654	T	1	.	15.5684	0.76313	1.0:0.0:0.0:0.0	.	251	Q6U736	OPN5_HUMAN	A	251	ENSP00000426991:T251A;ENSP00000360255:T251A;ENSP00000377302:T251A	ENSP00000360255:T251A	T	+	1	0	OPN5	47871253	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	8.962000	0.93254	2.075000	0.62263	0.454000	0.30748	ACA	.	.		0.413	OPN5-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359451.1	NM_181744		G	47763294	A	G	47763294	3	3	259	1	0	0	0	0	1	0	0	0	10892	275	10	2	765	2	OPN5	6	47763294	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	560761	47763294	123351773	295	36613										
EFHC1	114327	hgsc.bcm.edu	37	chr6	52329890	52329890	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cacgtattgatgtgagcaagCgggaaccacctccagtaaaa	10	10	0	2	rs371151471	byFrequency	TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:52329890C>A	ENST00000371068.5	+	6	1217	c.1114C>A	c.(1114-1116)Cgg>Agg	p.R372R	EFHC1_ENST00000433625.2_Silent_p.R281R|EFHC1_ENST00000538167.1_Silent_p.R353R	NM_018100.3	NP_060570.2	Q5JVL4	EFHC1_HUMAN	EF-hand domain (C-terminal) containing 1	372						axoneme (GO:0005930)|neuronal cell body (GO:0043025)	calcium ion binding (GO:0005509)|protein C-terminus binding (GO:0008022)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(8)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	27	Lung NSC(77;0.109)					TGTGAGCAAGCGGGAACCACC	0.353																																					p.R372R		Atlas-SNP	.											.	EFHC1	68	.	0			c.C1114A						.						61	57	58					6																	52329890		2203	4300	6503	SO:0001819	synonymous_variant	114327	exon6			AGCAAGCGGGAAC	AK001328	CCDS4942.1, CCDS55021.1	6p12.3	2014-02-04			ENSG00000096093	ENSG00000096093		"EF-hand domain containing"	16406	protein-coding gene	gene with protein product	"myoclonin-1"	608815	"epilepsy, juvenile myoclonic 1"	EJM1, EJM		15258581	Standard	NM_018100		Approved	FLJ10466	uc003pap.4	Q5JVL4	OTTHUMG00000014848	ENST00000371068.5:c.1114C>A	chr6.hg19:g.52329890C>A		121.0	0.0		99.0	4.0	NM_018100	B4DMU3|F5GZD8|Q5XKM4|Q6E1U7|Q6E1U8|Q8WUL2|Q9NVW6	Silent	SNP	ENST00000371068.5	hg19	CCDS4942.1																																																																																			.	.		0.353	EFHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040905.2	NM_018100		A	52329890	C	A	52329890	2	1	259	1	0	0	0	0	0	0	0	1	4948	759	27	1		1	EFHC1	6	52329890	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	4566596	52329890	118785177	296	36614										
GFRAL	389400	hgsc.bcm.edu	37	chr6	55223877	55223877	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tacctgtaggaccattacacAaagtgaggaatctttgtgta	9	7	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:55223877A>C	ENST00000340465.2	+	6	979	c.893A>C	c.(892-894)cAa>cCa	p.Q298P		NM_207410.2	NP_997293.2	Q6UXV0	GFRAL_HUMAN	GDNF family receptor alpha like	298					negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|stress-activated protein kinase signaling cascade (GO:0031098)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(2)|kidney(5)|large_intestine(2)|liver(1)|lung(31)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	48	Lung NSC(77;0.0875)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			ACCATTACACAAAGTGAGGAA	0.393																																					p.Q298P		Atlas-SNP	.											.	GFRAL	91	.	0			c.A893C						.						124	115	118					6																	55223877		2203	4299	6502	SO:0001583	missense	389400	exon6			TTACACAAAGTGA	AY358198	CCDS4957.1	6p12.1	2007-06-22			ENSG00000187871	ENSG00000187871			32789	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 144"	C6orf144		16086688	Standard	NM_207410		Approved	GRAL, UNQ9356, bA360D14.1	uc003pcm.1	Q6UXV0	OTTHUMG00000014900	ENST00000340465.2:c.893A>C	chr6.hg19:g.55223877A>C	ENSP00000343636:p.Gln298Pro	134.0	0.0		120.0	63.0	NM_207410	Q5VTF6	Missense_Mutation	SNP	ENST00000340465.2	hg19	CCDS4957.1	.	.	.	.	.	.	.	.	.	.	A	7.534	0.659246	0.14645	.	.	ENSG00000187871	ENST00000340465	T	0.64803	-0.12	5.67	1.57	0.23409	GDNF/GAS1 (2);	0.937809	0.09022	N	0.860045	T	0.24084	0.0583	L	0.39633	1.23	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.13548	-1.0505	10	0.27082	T	0.32	-13.4037	1.733	0.02936	0.3225:0.3345:0.0849:0.2581	.	298	Q6UXV0	GFRAL_HUMAN	P	298	ENSP00000343636:Q298P	ENSP00000343636:Q298P	Q	+	2	0	GFRAL	55331836	0.000000	0.05858	0.113000	0.21522	0.899000	0.52679	0.198000	0.17217	0.385000	0.24970	-0.429000	0.05907	CAA	.	.		0.393	GFRAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040995.2	NM_207410		C	55223877	A	C	55223877	3	2	259	1	0	0	0	0	1	0	0	0	6359	130	5	5	915	5	GFRAL	6	55223877	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2893987	55223877	115891190	297	36615										
KIAA1586	57691	hgsc.bcm.edu	37	chr6	56917492	56917492	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	attatttttcagattctgttTcctaaaatgccaaaacgaca	4	8	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:56917492T>C	ENST00000370733.4	+	4	402	c.195T>C	c.(193-195)ttT>ttC	p.F65F	KIAA1586_ENST00000545356.1_Silent_p.F38F|KIAA1586_ENST00000488682.1_3'UTR	NM_020931.2	NP_065982.1	Q9HCI6	K1586_HUMAN	KIAA1586	65							nucleic acid binding (GO:0003676)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|skin(1)	18	Lung NSC(77;0.0969)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			AGATTCTGTTTCCTAAAATGC	0.284																																					p.F65F		Atlas-SNP	.											.	KIAA1586	59	.	0			c.T195C						.						34	39	37					6																	56917492		2196	4297	6493	SO:0001819	synonymous_variant	57691	exon4			TCTGTTTCCTAAA	AB046806	CCDS34480.1, CCDS69138.1	6p12.1	2014-03-27			ENSG00000168116	ENSG00000168116			21360	protein-coding gene	gene with protein product						10997877	Standard	NM_001286274		Approved		uc003pdj.3	Q9HCI6	OTTHUMG00000014915	ENST00000370733.4:c.195T>C	chr6.hg19:g.56917492T>C		96.0	0.0		81.0	4.0	NM_020931	A8K4M3|Q8IW25	Silent	SNP	ENST00000370733.4	hg19	CCDS34480.1																																																																																			.	.		0.284	KIAA1586-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041033.1	NM_020931		C	56917492	T	C	56917492	2	2	259	1	0	0	0	0	0	0	0	1	8254	1780	62	2		2	KIAA1586	6	56917492	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1693615	56917492	114197575	298	36616										
C6orf165	154313	hgsc.bcm.edu	37	chr6	88128042	88128042	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tccttgagaaggcagccaacGacccactcatgagggctgaa	11	12	1	3	rs267601154		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:88128042G>A	ENST00000507897.1	+	7	831	c.748G>A	c.(748-750)Gac>Aac	p.D250N	C6ORF165_ENST00000369562.4_Missense_Mutation_p.D250N			Q8IYR0	CF165_HUMAN	chromosome 6 open reading frame 165	250										NS(1)|central_nervous_system(1)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0419)		GGCAGCCAACGACCCACTCAT	0.463																																					p.D250N		Atlas-SNP	.											.	C6orf165	116	.	0			c.G748A						.						101	100	100					6																	88128042		2203	4300	6503	SO:0001583	missense	154313	exon7			GCCAACGACCCAC	BC035083	CCDS34498.1	6q15	2012-02-07			ENSG00000213204	ENSG00000213204			21405	protein-coding gene	gene with protein product							Standard	NM_001031743		Approved	FLJ25974, dJ382I10.1	uc003plv.3	Q8IYR0	OTTHUMG00000015173	ENST00000507897.1:c.748G>A	chr6.hg19:g.88128042G>A	ENSP00000426769:p.Asp250Asn	140.0	0.0		81.0	4.0	NM_001031743	A8K969|E1P507|Q8N9U4	Missense_Mutation	SNP	ENST00000507897.1	hg19	CCDS34498.1	.	.	.	.	.	.	.	.	.	.	G	0.023	-1.405130	0.01155	.	.	ENSG00000213204	ENST00000369562;ENST00000480123	T;T	0.32023	1.47;1.49	5.16	3.92	0.45320	.	0.228682	0.49916	N	0.000121	T	0.03136	0.0092	N	0.01817	-0.705	0.22354	N	0.999172	B;B	0.11235	0.003;0.004	B;B	0.06405	0.002;0.002	T	0.44360	-0.9333	10	0.14252	T	0.57	.	9.1397	0.36897	0.8434:0.0:0.1566:0.0	.	250;250	Q8IYR0;E1P509	CF165_HUMAN;.	N	250	ENSP00000358575:D250N;ENSP00000422494:D250N	ENSP00000358575:D250N	D	+	1	0	C6orf165	88184761	0.954000	0.32549	0.606000	0.28943	0.009000	0.06853	2.473000	0.45145	0.908000	0.36671	-0.423000	0.05987	GAC	.	.		0.463	C6orf165-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000470406.1	NM_178823		A	88128042	G	A	88128042	3	1	259	1	0	0	0	0	1	0	0	0	2343	1058	37	1	770	1	C6orf165	6	88128042	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	31210550	88128042	82987025	299	36617										
RARS2	57038	hgsc.bcm.edu	37	chr6	88229903	88229903	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccatgcagacattacctttcTgcccagtcatatcccatgat	5	14	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:88229903T>C	ENST00000369536.5	-	13	1152	c.1107A>G	c.(1105-1107)gcA>gcG	p.A369A	RARS2_ENST00000497828.1_5'Flank	NM_020320.3	NP_064716.2	Q5T160	SYRM_HUMAN	arginyl-tRNA synthetase 2, mitochondrial	369					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	22		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0456)		ATTACCTTTCTGCCCAGTCAT	0.353																																					p.A369A		Atlas-SNP	.											.	RARS2	61	.	0			c.A1107G						.						237	229	232					6																	88229903		2203	4300	6503	SO:0001819	synonymous_variant	57038	exon13			CCTTTCTGCCCAG	AK093934	CCDS5011.1	6q16.1	2011-07-01	2007-09-27	2007-02-23	ENSG00000146282	ENSG00000146282	6.1.1.19	"Aminoacyl tRNA synthetases / Class I"	21406	protein-coding gene	gene with protein product	"arginine tRNA ligase 2, mitochondrial (putative)"	611524	"arginyl-tRNA synthetase-like"	RARSL		17847012	Standard	NM_020320		Approved	MGC14993, MGC23778, PRO1992, dJ382I10.6, DALRD2	uc003pme.3	Q5T160	OTTHUMG00000015178	ENST00000369536.5:c.1107A>G	chr6.hg19:g.88229903T>C		179.0	0.0		85.0	4.0	NM_020320	B2RDT7|Q96FU5|Q9H8K8	Silent	SNP	ENST00000369536.5	hg19	CCDS5011.1																																																																																			.	.		0.353	RARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041448.1	NM_020320		C	88229903	T	C	88229903	2	2	259	1	0	0	0	0	0	0	0	1	13074	1567	55	2		2	RARS2	6	88229903	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	101861	88229903	82885164	300	36618										
MDN1	23195	hgsc.bcm.edu	37	chr6	90393616	90393616	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cattccacttggaaatcttaAcaaattcctgtaagataaat	4	8	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:90393616A>G	ENST00000369393.3	-	72	11952	c.11837T>C	c.(11836-11838)gTt>gCt	p.V3946A	MDN1_ENST00000428876.1_Missense_Mutation_p.V3946A			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	3946					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		GGAAATCTTAACAAATTCCTG	0.358																																					p.V3946A		Atlas-SNP	.											.	MDN1	478	.	0			c.T11837C						.						86	82	84					6																	90393616		2203	4300	6503	SO:0001583	missense	23195	exon72			ATCTTAACAAATT	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.11837T>C	chr6.hg19:g.90393616A>G	ENSP00000358400:p.Val3946Ala	157.0	0.0		93.0	4.0	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	hg19	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	A	18.10	3.548634	0.65311	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.50548	0.74;0.74	5.28	5.28	0.74379	.	0.000000	0.64402	D	0.000001	T	0.61553	0.2356	M	0.76838	2.35	0.58432	D	0.999998	D	0.76494	0.999	D	0.78314	0.991	T	0.64373	-0.6423	10	0.42905	T	0.14	.	15.2069	0.73186	1.0:0.0:0.0:0.0	.	3946	Q9NU22	MDN1_HUMAN	A	3946	ENSP00000358400:V3946A;ENSP00000413970:V3946A	ENSP00000358400:V3946A	V	-	2	0	MDN1	90450337	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.339000	0.96797	2.005000	0.58758	0.459000	0.35465	GTT	.	.		0.358	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			G	90393616	A	G	90393616	3	3	259	1	0	0	0	0	1	0	0	0	9424	43	2	2	5077	2	MDN1	6	90393616	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2163713	90393616	80721451	301	36619										
GJA10	84694	hgsc.bcm.edu	37	chr6	90605295	90605295	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	caatgtctcagtcctggctaGgtacaactacggctcctaga	9	12	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:90605295G>T	ENST00000369352.1	+	1	1108	c.1108G>T	c.(1108-1110)Ggt>Tgt	p.G370C	Y_RNA_ENST00000517082.1_RNA	NM_032602.1	NP_115991.1	P57773	CXA9_HUMAN	gap junction protein, alpha 10, 62kDa	407					cell communication (GO:0007154)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(17)|ovary(1)|skin(3)|urinary_tract(1)	37		all_cancers(76;5.71e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00527)		BRCA - Breast invasive adenocarcinoma(108;0.0915)		GTCCTGGCTAGGTACAACTAC	0.547																																					p.G370C		Atlas-SNP	.											.	GJA10	83	.	0			c.G1108T						.						112	105	107					6																	90605295		2203	4300	6503	SO:0001583	missense	84694	exon1			TGGCTAGGTACAA	AF296766	CCDS5025.1	6q15-q16	2008-02-05			ENSG00000135355	ENSG00000135355		"Ion channels / Gap junction proteins (connexins)"	16995	protein-coding gene	gene with protein product	"connexin 62"	611924					Standard	NM_032602		Approved	CX62	uc011eaa.2	Q969M2	OTTHUMG00000015210	ENST00000369352.1:c.1108G>T	chr6.hg19:g.90605295G>T	ENSP00000358358:p.Gly370Cys	88.0	0.0		71.0	4.0	NM_032602	B2R722|B3KVQ2|Q5TA63|Q96KG0	Missense_Mutation	SNP	ENST00000369352.1	hg19	CCDS5025.1	.	.	.	.	.	.	.	.	.	.	G	10.80	1.453198	0.26161	.	.	ENSG00000135355	ENST00000369352	D	0.99080	-5.4	5.3	3.43	0.39272	.	1.147620	0.06486	N	0.733689	D	0.97832	0.9288	L	0.59436	1.845	0.09310	N	1	D	0.63880	0.993	P	0.53185	0.72	D	0.94379	0.7603	10	0.66056	D	0.02	.	9.0761	0.36522	0.0848:0.1514:0.7638:0.0	.	370	Q969M2	CXA10_HUMAN	C	370	ENSP00000358358:G370C	ENSP00000358358:G370C	G	+	1	0	GJA10	90662016	0.027000	0.19231	0.011000	0.14972	0.199000	0.23934	2.165000	0.42396	1.319000	0.45190	0.563000	0.77884	GGT	.	.		0.547	GJA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041505.1	NM_032602		T	90605295	G	T	90605295	3	4	259	1	0	0	0	0	1	0	0	0	6409	1000	35	3	1110	3	GJA10	6	90605295	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	211679	90605295	80509772	302	36620										
EPHA7	2045	hgsc.bcm.edu	37	chr6	93967190	93967190	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tggtacttaccctgagaaatGcatctagggctccattttcc	8	11	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:93967190G>A	ENST00000369303.4	-	12	2346	c.2162C>T	c.(2161-2163)gCa>gTa	p.A721V		NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	721	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|ephrin receptor signaling pathway (GO:0048013)|negative chemotaxis (GO:0050919)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cell-cell adhesion (GO:0022407)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of protein autophosphorylation (GO:0031952)|retinal ganglion cell axon guidance (GO:0031290)	dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|chemorepellent activity (GO:0045499)|GPI-linked ephrin receptor activity (GO:0005004)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(1)|central_nervous_system(7)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|lung(43)|ovary(8)|pancreas(1)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(13)|urinary_tract(1)	112		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		CCTGAGAAATGCATCTAGGGC	0.343																																					p.A721V		Atlas-SNP	.											.	EPHA7	251	.	0			c.C2162T						.						84	87	86					6																	93967190		2203	4300	6503	SO:0001583	missense	2045	exon12			AGAAATGCATCTA	L36642	CCDS5031.1, CCDS75494.1	6q16.3	2013-02-11	2004-10-28		ENSG00000135333	ENSG00000135333		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3390	protein-coding gene	gene with protein product		602190	"EphA7"			9267020	Standard	NM_004440		Approved	Hek11	uc003poe.3	Q15375	OTTHUMG00000015228	ENST00000369303.4:c.2162C>T	chr6.hg19:g.93967190G>A	ENSP00000358309:p.Ala721Val	173.0	0.0		100.0	4.0	NM_004440	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Missense_Mutation	SNP	ENST00000369303.4	hg19	CCDS5031.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.972590	0.74246	.	.	ENSG00000135333	ENST00000369303	T	0.62498	0.02	5.87	5.87	0.94306	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.055365	0.64402	D	0.000001	T	0.44829	0.1312	L	0.41236	1.265	0.80722	D	1	B;P;D	0.53619	0.315;0.951;0.961	B;B;B	0.37267	0.025;0.158;0.245	T	0.57051	-0.7877	10	0.87932	D	0	.	20.2119	0.98289	0.0:0.0:1.0:0.0	.	717;716;721	Q15375-4;Q15375-2;Q15375	.;.;EPHA7_HUMAN	V	721	ENSP00000358309:A721V	ENSP00000358309:A721V	A	-	2	0	EPHA7	94023911	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	7.721000	0.84768	2.784000	0.95788	0.585000	0.79938	GCA	.	.		0.343	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1			A	93967190	G	A	93967190	3	1	259	1	0	0	0	0	1	0	0	0	5174	1319	46	3	858	3	EPHA7	6	93967190	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	3361895	93967190	77147877	303	36621										
C6orf167	253714	hgsc.bcm.edu	37	chr6	97613138	97613138	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gtaccttatgacttgcacaaTgcatttctttagagatgata	7	7	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:97613138T>C	ENST00000275053.4	-	21	3470	c.3205A>G	c.(3205-3207)Att>Gtt	p.I1069V	MMS22L_ENST00000369251.2_Missense_Mutation_p.I1029V	NM_198468.2	NP_940870.2	Q6ZRQ5	MMS22_HUMAN	MMS22-like, DNA repair protein	1069					double-strand break repair via homologous recombination (GO:0000724)|replication fork processing (GO:0031297)	nuclear replication fork (GO:0043596)				breast(1)|endometrium(9)|kidney(2)|large_intestine(12)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	50						ACTTGCACAATGCATTTCTTT	0.343																																					p.I1069V		Atlas-SNP	.											.	MMS22L	102	.	0			c.A3205G						.						101	101	101					6																	97613138		2203	4300	6503	SO:0001583	missense	253714	exon21			GCACAATGCATTT		CCDS5039.1	6q16.3	2010-11-11	2010-11-11	2010-11-11	ENSG00000146263	ENSG00000146263			21475	protein-coding gene	gene with protein product		615614	"chromosome 6 open reading frame 167"	C6orf167		21055983, 21055984	Standard	NM_198468		Approved	dJ39B17.2	uc003ppb.3	Q6ZRQ5	OTTHUMG00000015248	ENST00000275053.4:c.3205A>G	chr6.hg19:g.97613138T>C	ENSP00000275053:p.Ile1069Val	104.0	0.0		73.0	4.0	NM_198468	D6R9Y8|D6RBQ4|E1P529|Q5THT2|Q68CQ6|Q68D32	Missense_Mutation	SNP	ENST00000275053.4	hg19	CCDS5039.1	.	.	.	.	.	.	.	.	.	.	T	1.018	-0.685723	0.03328	.	.	ENSG00000146263	ENST00000275053;ENST00000369251	T;T	0.30182	1.54;1.54	5.79	-1.5	0.08691	.	0.209158	0.47455	D	0.000227	T	0.06781	0.0173	L	0.34521	1.04	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.39187	-0.9626	10	0.25751	T	0.34	-15.3407	9.128	0.36828	0.0:0.2479:0.0949:0.6572	.	1029;1069	E2QRD4;Q6ZRQ5	.;MMS22_HUMAN	V	1069;1029	ENSP00000275053:I1069V;ENSP00000358254:I1029V	ENSP00000275053:I1069V	I	-	1	0	MMS22L	97719859	0.995000	0.38212	0.144000	0.22314	0.083000	0.17756	0.611000	0.24268	-0.404000	0.07610	-1.139000	0.01908	ATT	.	.		0.343	MMS22L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041573.3	NM_198468		C	97613138	T	C	97613138	3	2	259	1	0	0	0	0	1	0	0	0	2344	1464	51	2	546	2	C6orf167	6	97613138	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	3645948	97613138	73501929	304	36622										
SFRS18	25957	hgsc.bcm.edu	37	chr6	99856127	99856127	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttcgcgaatccaagcgggaaGagtcctgcgttttactgcgt	12	10	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:99856127G>T	ENST00000369239.5	-	7	898	c.694C>A	c.(694-696)Ctt>Att	p.L232I	PNISR_ENST00000438806.1_Missense_Mutation_p.L232I	NM_032870.2	NP_116259.2	Q8TF01	PNISR_HUMAN	PNN-interacting serine/arginine-rich protein	232						cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24						CAAGCGGGAAGAGTCCTGCGT	0.363																																					p.L232I		Atlas-SNP	.											.	PNISR	74	.	0			c.C694A						.						85	79	81					6																	99856127		2203	4300	6503	SO:0001583	missense	25957	exon6			CGGGAAGAGTCCT	AK027759	CCDS5043.1	6q16.3	2011-06-06	2011-06-06	2011-06-06	ENSG00000132424	ENSG00000132424			21222	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 111", "splicing factor, arginine/serine-rich 18"	C6orf111, SFRS18		14578391	Standard	NM_032870		Approved	FLJ14752, bA98I9.2, DKFZp564B0769, SRrp130	uc021zdd.1	Q8TF01	OTTHUMG00000015262	ENST00000369239.5:c.694C>A	chr6.hg19:g.99856127G>T	ENSP00000358242:p.Leu232Ile	173.0	0.0		121.0	5.0	NM_015491	A8K540|E1P5D2|Q5T064|Q5T065|Q6P2B4|Q6P2N4|Q6PJ93|Q6PK36|Q7Z640|Q8N2L1|Q8TF00|Q96K10|Q96SI3|Q96SM5|Q9P076|Q9P0C0|Q9Y4N3	Missense_Mutation	SNP	ENST00000369239.5	hg19	CCDS5043.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.028756	0.93518	.	.	ENSG00000132424	ENST00000369239;ENST00000438806	T;T	0.44482	0.92;0.92	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.65873	0.2733	M	0.83483	2.645	0.80722	D	1	D	0.67145	0.996	D	0.80764	0.994	T	0.68062	-0.5508	10	0.87932	D	0	.	20.5827	0.99408	0.0:0.0:1.0:0.0	.	232	Q8TF01	PNISR_HUMAN	I	232	ENSP00000358242:L232I;ENSP00000387997:L232I	ENSP00000358242:L232I	L	-	1	0	PNISR	99962848	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.328000	0.65887	2.941000	0.99782	0.655000	0.94253	CTT	.	.		0.363	PNISR-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041598.1	NM_032870		T	99856127	G	T	99856127	3	4	259	1	0	0	0	0	1	0	0	0	14189	942	33	3	1747	3	SFRS18	6	99856127	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	2242989	99856127	71258940	305	36623										
HACE1	57531	hgsc.bcm.edu	37	chr6	105259252	105259252	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	taatatcagcaccactgtctAgcaagcactgcactgtctga	7	12	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:105259252A>G	ENST00000262903.4	-	7	827	c.551T>C	c.(550-552)cTa>cCa	p.L184P	HACE1_ENST00000369125.2_Missense_Mutation_p.L184P	NM_020771.3	NP_065822.2	Q8IYU2	HACE1_HUMAN	HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1	184					cell cycle (GO:0007049)|Golgi organization (GO:0007030)|membrane fusion (GO:0061025)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|Rac protein signal transduction (GO:0016601)|regulation of cell migration (GO:0030334)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Rab GTPase binding (GO:0017137)|Rac GTPase binding (GO:0048365)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	44		all_cancers(87;6.89e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0216)|Colorectal(196;0.202)		BRCA - Breast invasive adenocarcinoma(108;0.122)|Epithelial(106;0.204)		ACCACTGTCTAGCAAGCACTG	0.358																																					p.L184P		Atlas-SNP	.											.	HACE1	96	.	0			c.T551C						.						107	106	106					6																	105259252		2203	4299	6502	SO:0001583	missense	57531	exon7			CTGTCTAGCAAGC	BC034982	CCDS5050.1	6q21	2013-01-10	2012-02-23		ENSG00000085382	ENSG00000085382		"Ankyrin repeat domain containing"	21033	protein-coding gene	gene with protein product		610876				10718198	Standard	NM_020771		Approved	KIAA1320	uc003pqu.1	Q8IYU2	OTTHUMG00000015287	ENST00000262903.4:c.551T>C	chr6.hg19:g.105259252A>G	ENSP00000262903:p.Leu184Pro	117.0	0.0		67.0	4.0	NM_020771	A8K6U5|B3KY89|B4DFM6|B4DTQ4|B7Z9X6|E9PGP0|Q5VU99|Q5VUA0|Q8ND12|Q9P2M6	Missense_Mutation	SNP	ENST00000262903.4	hg19	CCDS5050.1	.	.	.	.	.	.	.	.	.	.	A	16.33	3.094336	0.56075	.	.	ENSG00000085382	ENST00000262903;ENST00000369125;ENST00000519645	T;T;T	0.72725	-0.68;-0.68;-0.68	5.34	5.34	0.76211	Ankyrin repeat-containing domain (4);	0.000000	0.64402	D	0.000001	D	0.87597	0.6217	H	0.96777	3.88	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.81914	0.995;0.977	D	0.91854	0.5494	10	0.87932	D	0	.	14.9585	0.71138	1.0:0.0:0.0:0.0	.	184;184	E9PGP0;Q8IYU2	.;HACE1_HUMAN	P	184;184;140	ENSP00000262903:L184P;ENSP00000358121:L184P;ENSP00000429765:L140P	ENSP00000262903:L184P	L	-	2	0	HACE1	105365945	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.563000	0.82314	2.008000	0.58898	0.460000	0.39030	CTA	.	.		0.358	HACE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041643.2	XM_045095		G	105259252	A	G	105259252	3	3	259	1	0	0	0	0	1	0	0	0	6949	420	15	2	2250	2	HACE1	6	105259252	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	5403125	105259252	65855815	306	36624										
AIM1	202	hgsc.bcm.edu	37	chr6	106999726	106999726	+	Splice_Site	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gtgattgcttttgtttcttaGatgggtagcctatgaaaatc	10	5	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:106999726G>T	ENST00000369066.3	+	12	4575		c.e12-1		AIM1_ENST00000535438.1_Splice_Site|AIM1_ENST00000487681.1_Splice_Site	NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1						developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		TTGTTTCTTAGATGGGTAGCC	0.328																																					.		Atlas-SNP	.											.	AIM1	161	.	0			c.4089-1G>T						.						79	88	85					6																	106999726		2203	4298	6501	SO:0001630	splice_region_variant	202	exon12			TTCTTAGATGGGT	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"suppression of tumorigenicity 4", "beta-gamma crystallin domain containing 1"	601797	"suppression of tumorigenicity 4 (malignant melanoma)"	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.4089-1G>T	chr6.hg19:g.106999726G>T		161.0	0.0		98.0	4.0	NM_001624	Q6P2P0|Q9BTM3	Splice_Site	SNP	ENST00000369066.3	hg19	CCDS34506.1	.	.	.	.	.	.	.	.	.	.	G	36	5.621912	0.96660	.	.	ENSG00000112297	ENST00000369066;ENST00000457437;ENST00000535438	.	.	.	5.9	5.9	0.94986	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.2723	0.98479	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	AIM1	107106419	1.000000	0.71417	0.770000	0.31555	0.944000	0.59088	9.463000	0.97652	2.793000	0.96121	0.563000	0.77884	.	.	.		0.328	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1		Intron	T	106999726	G	T	106999726	5	4	259	1	0	0	0	0	0	0	1	0	430	956	33	3	4134	3	AIM1	6	106999726	Splice_Site	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1740474	106999726	64115341	307	36625										
REV3L	5980	hgsc.bcm.edu	37	chr6	111686477	111686477	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agtatagttacctttgcttgTgttaacagtactcttctaag	7	7	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:111686477T>C	ENST00000358835.3	-	16	7198	c.6744A>G	c.(6742-6744)acA>acG	p.T2248T	REV3L_ENST00000368805.1_Silent_p.T2248T|REV3L_ENST00000368802.3_Silent_p.T2248T|REV3L_ENST00000435970.1_Silent_p.T2170T			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	2248					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		CCTTTGCTTGTGTTAACAGTA	0.294								DNA polymerases (catalytic subunits)																													p.T2248T		Atlas-SNP	.											.	REV3L	386	.	0			c.A6744G						.						129	120	123					6																	111686477		2198	4297	6495	SO:0001819	synonymous_variant	5980	exon15			TGCTTGTGTTAAC	AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"DNA polymerases"	9968	protein-coding gene	gene with protein product	"polymerase, DNA, zeta"	602776	"REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta", "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.6744A>G	chr6.hg19:g.111686477T>C		162.0	0.0		89.0	4.0	NM_002912	O43214|Q5TC33	Silent	SNP	ENST00000358835.3	hg19	CCDS5091.2																																																																																			.	.		0.294	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		C	111686477	T	C	111686477	2	2	259	1	0	0	0	0	0	0	0	1	13255	1683	59	2		2	REV3L	6	111686477	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	4686751	111686477	59428590	308	36626										
LAMA4	3910	hgsc.bcm.edu	37	chr6	112466014	112466014	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	accttgctggcaacacttctGgtctgagcaatgagctctcg	10	12	3	2	rs189313630	byFrequency	TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:112466014G>T	ENST00000230538.7	-	19	2872	c.2475C>A	c.(2473-2475)acC>acA	p.T825T	LAMA4_ENST00000389463.4_Silent_p.T818T|LAMA4_ENST00000424408.2_Silent_p.T818T|LAMA4_ENST00000522006.1_Silent_p.T818T	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	825	Domain II and I.				blood vessel development (GO:0001568)|brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(42)|ovary(4)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(8)	100		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		CAACACTTCTGGTCTGAGCAA	0.517																																					p.T825T		Atlas-SNP	.											LAMA4,right_upper_lobe,carcinoma,0,1	LAMA4	227	.	0			c.C2475A						.						111	110	110					6																	112466014		2203	4300	6503	SO:0001819	synonymous_variant	3910	exon19			ACTTCTGGTCTGA		CCDS34514.1, CCDS43491.1, CCDS43492.1	6q21	2014-09-17			ENSG00000112769	ENSG00000112769		"Laminins"	6484	protein-coding gene	gene with protein product		600133				7959779	Standard	NM_001105206		Approved	LAMA3	uc003pvu.3	Q16363	OTTHUMG00000015386	ENST00000230538.7:c.2475C>A	chr6.hg19:g.112466014G>T		45.0	0.0		39.0	2.0	NM_001105206	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Silent	SNP	ENST00000230538.7	hg19	CCDS43491.1																																																																																			.	G|1.000;A|0.000		0.517	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206		T	112466014	G	T	112466014	2	4	259	1	0	0	0	0	0	0	0	1	8617	1335	47	3		3	LAMA4	6	112466014	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	779537	112466014	58649053	309	36627										
RSPH4A	345895	hgsc.bcm.edu	37	chr6	116943931	116943931	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aattttctctgtttggatagAtatgatcatctttctaatat	5	5	4	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:116943931A>G	ENST00000229554.5	+	2	824	c.687A>G	c.(685-687)ctA>ctG	p.L229L	RSPH4A_ENST00000368581.4_Splice_Site_p.L229L|RSPH4A_ENST00000368580.4_Splice_Site_p.L229L	NM_001010892.2	NP_001010892.1	Q5TD94	RSH4A_HUMAN	radial spoke head 4 homolog A (Chlamydomonas)	229					axoneme assembly (GO:0035082)|cilium movement (GO:0003341)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|radial spoke (GO:0001534)				breast(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						GTTTGGATAGATATGATCATC	0.328									Kartagener syndrome																												p.L229L		Atlas-SNP	.											.	RSPH4A	54	.	0			c.A687G						.						56	61	60					6																	116943931		2203	4298	6501	SO:0001630	splice_region_variant	345895	exon2	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GGATAGATATGAT		CCDS34521.1, CCDS55051.1	6q22.1	2012-05-03	2009-02-17	2009-02-17	ENSG00000111834	ENSG00000111834			21558	protein-coding gene	gene with protein product		612647	"radial spokehead-like 3"	RSHL3		19200523	Standard	NM_001010892		Approved	dJ412I7.1, FLJ37974, RSPH6B, CILD11	uc003pxe.2	Q5TD94	OTTHUMG00000015444	ENST00000229554.5:c.687-1A>G	chr6.hg19:g.116943931A>G		113.0	0.0		97.0	4.0	NM_001161664	B4DSI1|Q3KP24|Q5TD95	Silent	SNP	ENST00000229554.5	hg19	CCDS34521.1																																																																																			.	.		0.328	RSPH4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041960.1	NM_001010892	Silent	G	116943931	A	G	116943931	5	3	259	1	0	0	0	0	0	0	1	0	13721	347	12	2	693	2	RSPH4A	6	116943931	Splice_Site	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	4477917	116943931	54171136	310	36628										
C6orf174	387104	hgsc.bcm.edu	37	chr6	127837004	127837004	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agctcagactgcagacatccTtctttccagtagctccctcc	6	16	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:127837004T>C	ENST00000525778.1	-	2	1501	c.756A>G	c.(754-756)gaA>gaG	p.E252E	SOGA3_ENST00000556132.1_Silent_p.E252E|SOGA3_ENST00000465909.2_Silent_p.E252E|SOGA3_ENST00000481848.2_Silent_p.E252E|SOGA3_ENST00000368268.2_Silent_p.E252E			Q5TF21	SOGA3_HUMAN	SOGA family member 3	252					regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											GCAGACATCCTTCTTTCCAGT	0.657																																					p.E252E		Atlas-SNP	.											.	.	.	.	0			c.A756G						.						19	24	23					6																	127837004		1927	4111	6038	SO:0001819	synonymous_variant	387104	exon2			ACATCCTTCTTTC	AK096490	CCDS43505.1	6q22.33	2013-03-28	2012-02-27	2012-02-27	ENSG00000214338	ENSG00000214338			21494	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 174"	C6orf174			Standard	NM_001012279		Approved	dJ403A15.3	uc003qbd.3	Q5TF21	OTTHUMG00000166438	ENST00000525778.1:c.756A>G	chr6.hg19:g.127837004T>C		139.0	0.0		82.0	4.0	NM_001012279		Silent	SNP	ENST00000525778.1	hg19	CCDS43505.1																																																																																			.	.		0.657	SOGA3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388246.1	NM_001012279		C	127837004	T	C	127837004	2	2	259	1	0	0	0	0	0	0	0	1	2347	1606	56	2		2	C6orf174	6	127837004	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	10893073	127837004	43278063	311	36629										
C6orf58	352999	hgsc.bcm.edu	37	chr6	127902353	127902353	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cagtcaccttttagtaagttTgatgatctgttgaagtactt	8	6	2	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:127902353T>C	ENST00000329722.7	+	4	612	c.600T>C	c.(598-600)ttT>ttC	p.F200F		NM_001010905.1	NP_001010905.1	Q6P5S2	CF058_HUMAN	chromosome 6 open reading frame 58	200						extracellular vesicular exosome (GO:0070062)				kidney(3)|large_intestine(3)|liver(1)|lung(7)|pancreas(1)	15				GBM - Glioblastoma multiforme(226;0.0405)|all cancers(137;0.156)		TTAGTAAGTTTGATGATCTGT	0.328																																					p.F200F		Atlas-SNP	.											.	C6orf58	35	.	0			c.T600C						.						108	104	105					6																	127902353		2203	4295	6498	SO:0001819	synonymous_variant	352999	exon4			TAAGTTTGATGAT	BC062712	CCDS34533.1	6q22.33	2011-12-13			ENSG00000184530	ENSG00000184530			20960	protein-coding gene	gene with protein product							Standard	NM_001010905		Approved		uc003qbh.4	Q6P5S2	OTTHUMG00000015530	ENST00000329722.7:c.600T>C	chr6.hg19:g.127902353T>C		128.0	0.0		89.0	4.0	NM_001010905	B4E1I0|Q5VUP2	Silent	SNP	ENST00000329722.7	hg19	CCDS34533.1																																																																																			.	.		0.328	C6orf58-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042152.1	NM_001010905		C	127902353	T	C	127902353	2	2	259	1	0	0	0	0	0	0	0	1	2369	1809	63	2		2	C6orf58	6	127902353	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	65349	127902353	43212714	312	36630										
PTPRK	5796	hgsc.bcm.edu	37	chr6	128643368	128643368	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggtaactgaaatcaatgcagTgagtgtcgttctccttcatt	9	8	3	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:128643368T>A	ENST00000368215.3	-	3	310	c.311A>T	c.(310-312)cAc>cTc	p.H104L	PTPRK_ENST00000368213.5_Missense_Mutation_p.H104L|PTPRK_ENST00000368227.3_Missense_Mutation_p.H104L|PTPRK_ENST00000524481.1_5'UTR|PTPRK_ENST00000532331.1_Missense_Mutation_p.H104L|PTPRK_ENST00000368207.3_Missense_Mutation_p.H104L|PTPRK_ENST00000368210.3_Missense_Mutation_p.H104L|PTPRK_ENST00000368226.4_Missense_Mutation_p.H104L|PTPRK_ENST00000525459.1_Missense_Mutation_p.H104L			Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	104	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to reactive oxygen species (GO:0034614)|cellular response to UV (GO:0034644)|focal adhesion assembly (GO:0048041)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)		PTPRK/RSPO3(10)	autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(14)|lung(24)|ovary(3)|pancreas(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	72				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		ATCAATGCAGTGAGTGTCGTT	0.418																																					p.H104L		Atlas-SNP	.											.	PTPRK	330	.	0			c.A311T						.						156	147	150					6																	128643368		2203	4299	6502	SO:0001583	missense	5796	exon3			ATGCAGTGAGTGT	L77886	CCDS5137.1, CCDS47473.1, CCDS75517.1	6q22.2-q22.3	2013-02-11			ENSG00000152894	ENSG00000152894		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9674	protein-coding gene	gene with protein product		602545				9047348, 8663237	Standard	NM_002844		Approved	R-PTP-kappa	uc010kfc.3	Q15262	OTTHUMG00000015536	ENST00000368215.3:c.311A>T	chr6.hg19:g.128643368T>A	ENSP00000357198:p.His104Leu	134.0	0.0		95.0	4.0	NM_001135648	B2RTQ8|B7ZMG0|Q14763|Q5TG10|Q5TG11	Missense_Mutation	SNP	ENST00000368215.3	hg19		.	.	.	.	.	.	.	.	.	.	T	32	5.151204	0.94645	.	.	ENSG00000152894	ENST00000368226;ENST00000368227;ENST00000532331;ENST00000368213;ENST00000368210;ENST00000368215;ENST00000368207;ENST00000525459	T;T;T;T;T;T;T;T	0.02140	4.43;4.43;4.43;4.43;4.43;4.43;4.43;4.43	6.06	6.06	0.98353	Concanavalin A-like lectin/glucanase (1);MAM domain (5);	0.122378	0.53938	D	0.000045	T	0.06188	0.0160	L	0.54965	1.715	0.58432	D	0.999993	D;D;D;D;D;D	0.89917	1.0;0.994;0.998;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;0.969;0.948;0.999;1.0;0.999	T	0.15694	-1.0428	10	0.87932	D	0	.	15.8056	0.78506	0.0:0.0:0.0:1.0	.	104;104;104;104;104;104	B4DHC3;B7ZMG0;Q15262-3;E9PRW2;Q15262;Q15262-2	.;.;.;.;PTPRK_HUMAN;.	L	104	ENSP00000357209:H104L;ENSP00000357210:H104L;ENSP00000432973:H104L;ENSP00000357196:H104L;ENSP00000357193:H104L;ENSP00000357198:H104L;ENSP00000357190:H104L;ENSP00000434116:H104L	ENSP00000357190:H104L	H	-	2	0	PTPRK	128685061	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.040000	0.89188	2.323000	0.78572	0.528000	0.53228	CAC	.	.		0.418	PTPRK-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000042163.1			A	128643368	T	A	128643368	3	1	259	1	0	0	0	0	1	0	0	0	12820	1696	59	4	4145	4	PTPRK	6	128643368	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	741015	128643368	42471699	313	36631										
ARHGAP18	93663	hgsc.bcm.edu	37	chr6	129950526	129950526	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tggcatcatcgcctttgctcTtctggattttctccttggag	9	11	4	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:129950526T>C	ENST00000368149.2	-	5	846	c.758A>G	c.(757-759)aAg>aGg	p.K253R		NM_033515.2	NP_277050.2			Rho GTPase activating protein 18											NS(2)|endometrium(1)|large_intestine(4)|lung(4)|ovary(2)|prostate(2)|skin(3)	18				OV - Ovarian serous cystadenocarcinoma(136;0.0621)|GBM - Glioblastoma multiforme(226;0.0638)|all cancers(137;0.074)		GCCTTTGCTCTTCTGGATTTT	0.413																																					p.K253R		Atlas-SNP	.											.	ARHGAP18	52	.	0			c.A758G						.						130	128	129					6																	129950526		2203	4300	6503	SO:0001583	missense	93663	exon5			TTGCTCTTCTGGA	AB053293	CCDS34535.1	6q23.1	2011-06-29			ENSG00000146376	ENSG00000146376		"Rho GTPase activating proteins"	21035	protein-coding gene	gene with protein product		613351					Standard	NM_033515		Approved	MacGAP, bA307O14.2	uc003qbr.3	Q8N392	OTTHUMG00000015547	ENST00000368149.2:c.758A>G	chr6.hg19:g.129950526T>C	ENSP00000357131:p.Lys253Arg	158.0	0.0		89.0	4.0	NM_033515		Missense_Mutation	SNP	ENST00000368149.2	hg19	CCDS34535.1	.	.	.	.	.	.	.	.	.	.	T	4.882	0.163997	0.09287	.	.	ENSG00000146376	ENST00000368149;ENST00000275189	.	.	.	5.49	-1.45	0.08828	.	0.471085	0.25561	N	0.029835	T	0.05593	0.0147	N	0.17723	0.515	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.36456	-0.9747	8	.	.	.	.	4.3617	0.11205	0.2118:0.2751:0.0:0.5131	.	253;253	A9UK01;Q8N392	.;RHG18_HUMAN	R	208;253	.	.	K	-	2	0	ARHGAP18	129992219	0.000000	0.05858	0.013000	0.15412	0.058000	0.15608	0.200000	0.17257	-0.083000	0.12618	-0.250000	0.11733	AAG	.	.		0.413	ARHGAP18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042185.2	NM_033515		C	129950526	T	C	129950526	3	2	259	1	0	0	0	0	1	0	0	0	868	1609	56	2	1277	2	ARHGAP18	6	129950526	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1307158	129950526	41164541	314	36632										
L3MBTL3	84456	hgsc.bcm.edu	37	chr6	130407320	130407320	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttccagaaaaaaatgaagctTgaggttgtagacaaaaggaa	10	4	0	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:130407320T>C	ENST00000529410.1	+	18	1922	c.1443T>C	c.(1441-1443)ctT>ctC	p.L481L	L3MBTL3_ENST00000368136.2_Silent_p.L481L|L3MBTL3_ENST00000368139.2_Silent_p.L456L|L3MBTL3_ENST00000361794.2_Silent_p.L481L|L3MBTL3_ENST00000533560.1_Silent_p.L456L|L3MBTL3_ENST00000526019.1_Silent_p.L456L			Q96JM7	LMBL3_HUMAN	l(3)mbt-like 3 (Drosophila)	481					chromatin modification (GO:0016568)|erythrocyte maturation (GO:0043249)|granulocyte differentiation (GO:0030851)|macrophage differentiation (GO:0030225)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				cervix(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|skin(4)|stomach(1)|urinary_tract(1)	43				GBM - Glioblastoma multiforme(226;0.0266)|OV - Ovarian serous cystadenocarcinoma(155;0.154)		AAATGAAGCTTGAGGTTGTAG	0.398																																					p.L481L		Atlas-SNP	.											.	L3MBTL3	99	.	0			c.T1443C						.						151	171	164					6																	130407320		2203	4300	6503	SO:0001819	synonymous_variant	84456	exon16			GAAGCTTGAGGTT	AB058701	CCDS34537.1, CCDS34538.1	6q23	2013-01-10			ENSG00000198945	ENSG00000198945		"Sterile alpha motif (SAM) domain containing"	23035	protein-coding gene	gene with protein product							Standard	NM_032438		Approved	KIAA1798	uc003qbt.3	Q96JM7	OTTHUMG00000015554	ENST00000529410.1:c.1443T>C	chr6.hg19:g.130407320T>C		159.0	0.0		98.0	4.0	NM_032438	Q4VXE1|Q5VUM9|Q6P9B5	Silent	SNP	ENST00000529410.1	hg19	CCDS34537.1																																																																																			.	.		0.398	L3MBTL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042195.2	XM_027074		C	130407320	T	C	130407320	2	2	259	1	0	0	0	0	0	0	0	1	8602	1799	63	2		2	L3MBTL3	6	130407320	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	456794	130407320	40707747	315	36633										
TMEM200A	114801	hgsc.bcm.edu	37	chr6	130762130	130762130	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gaacggcatgtacactggttTgatgggagaaacagaagtaa	13	5	0	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:130762130T>A	ENST00000296978.3	+	3	1434	c.563T>A	c.(562-564)tTg>tAg	p.L188*	TMEM200A_ENST00000392429.1_Nonsense_Mutation_p.L188*|TMEM200A_ENST00000545622.1_Nonsense_Mutation_p.L188*	NM_001258276.1|NM_001258277.1|NM_001258278.1	NP_001245205.1|NP_001245206.1|NP_001245207.1	Q86VY9	T200A_HUMAN	transmembrane protein 200A	188						integral component of membrane (GO:0016021)				NS(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(30)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52				GBM - Glioblastoma multiforme(226;0.0139)|OV - Ovarian serous cystadenocarcinoma(155;0.12)		TACACTGGTTTGATGGGAGAA	0.448																																					p.L188X		Atlas-SNP	.											.	TMEM200A	108	.	0			c.T563A						.						96	89	91					6																	130762130		2203	4300	6503	SO:0001587	stop_gained	114801	exon3			CTGGTTTGATGGG	AB067500	CCDS5140.1	6q23.1	2009-09-04	2007-12-18	2007-12-18	ENSG00000164484	ENSG00000164484			21075	protein-coding gene	gene with protein product			"KIAA1913"	KIAA1913		15722956	Standard	NM_001258276		Approved	TTMC	uc010kfh.4	Q86VY9	OTTHUMG00000015557	ENST00000296978.3:c.563T>A	chr6.hg19:g.130762130T>A	ENSP00000296978:p.Leu188*	194.0	0.0		80.0	4.0	NM_001258277	Q96PX5	Nonsense_Mutation	SNP	ENST00000296978.3	hg19	CCDS5140.1	.	.	.	.	.	.	.	.	.	.	T	53	20.462260	0.99931	.	.	ENSG00000164484	ENST00000296978;ENST00000545622;ENST00000392429	.	.	.	5.46	3.01	0.34805	.	0.596635	0.18460	N	0.140553	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.0425	0.30529	0.0:0.0706:0.1365:0.7928	.	.	.	.	X	188	.	ENSP00000296978:L188X	L	+	2	0	TMEM200A	130803823	0.172000	0.23043	0.109000	0.21407	0.920000	0.55202	1.661000	0.37408	0.348000	0.23949	0.533000	0.62120	TTG	.	.		0.448	TMEM200A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042201.1	NM_052913		A	130762130	T	A	130762130	4	1	259	1	0	0	0	0	0	1	0	0	16138	1821	63	4	565	4	TMEM200A	6	130762130	Nonsense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	354810	130762130	40352937	316	36634										
TBPL1	9519	hgsc.bcm.edu	37	chr6	134304019	134304019	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgcagaaactaggttttcagGtaacgttttcaaatagtatc	8	6	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:134304019G>A	ENST00000237264.4	+	4	557		c.e4+1		TBPL1_ENST00000477527.1_Splice_Site|TBPL1_ENST00000367871.1_Splice_Site	NM_001253676.1|NM_004865.3	NP_001240605.1|NP_004856.1	P62380	TBPL1_HUMAN	TBP-like 1						acrosome assembly (GO:0001675)|DNA-templated transcription, initiation (GO:0006352)|dTTP biosynthetic process (GO:0006235)|regulation of transcription, DNA-templated (GO:0006355)|spermatid nucleus differentiation (GO:0007289)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|transcription factor TFIIA complex (GO:0005672)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	6	Colorectal(23;0.221)|Breast(56;0.247)			GBM - Glioblastoma multiforme(68;0.00591)|OV - Ovarian serous cystadenocarcinoma(155;0.00848)		AGGTTTTCAGGTAACGTTTTC	0.323																																					.		Atlas-SNP	.											.	TBPL1	20	.	0			c.282+1G>A						.						68	66	67					6																	134304019		2201	4299	6500	SO:0001630	splice_region_variant	9519	exon4			TTTCAGGTAACGT	AB020881	CCDS5168.1	6q22.1-q22.3	2008-05-23			ENSG00000028839	ENSG00000028839			11589	protein-coding gene	gene with protein product		605521				10082669, 10220372, 15767669	Standard	NM_001253676		Approved	TLP, STUD, TRF2, TLF	uc010kgg.3	P62380	OTTHUMG00000015609	ENST00000237264.4:c.282+1G>A	chr6.hg19:g.134304019G>A		195.0	0.0		121.0	5.0	NM_001253676	A8K8F5|O95753|Q9BWD5|Q9Z2Z0	Splice_Site	SNP	ENST00000237264.4	hg19	CCDS5168.1	.	.	.	.	.	.	.	.	.	.	G	16.69	3.193057	0.58017	.	.	ENSG00000028839	ENST00000416965;ENST00000367871;ENST00000237264	.	.	.	5.99	5.11	0.69529	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.4606	0.61225	0.0:0.0:0.8431:0.1569	.	.	.	.	.	-1	.	.	.	+	.	.	TBPL1	134345712	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	7.371000	0.79600	1.501000	0.48654	0.655000	0.94253	.	.	.		0.323	TBPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042294.2		Intron	A	134304019	G	A	134304019	5	1	259	1	0	0	0	0	0	0	1	0	15660	1275	44	3	293	3	TBPL1	6	134304019	Splice_Site	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	3541889	134304019	36811048	317	36635										
HBS1L	10767	hgsc.bcm.edu	37	chr6	135358603	135358603	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aattatcaacagtcatatttTccaacgagctagttaagtac	5	8	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:135358603T>C	ENST00000367837.5	-	4	637				HBS1L_ENST00000415177.2_Intron|HBS1L_ENST00000367820.2_Intron|HBS1L_ENST00000367826.2_Intron|HBS1L_ENST00000314674.3_Intron|HBS1L_ENST00000445176.2_Intron|HBS1L_ENST00000367822.5_Missense_Mutation_p.E331G|HBS1L_ENST00000367824.4_Intron	NM_001145158.1|NM_006620.3	NP_001138630.1|NP_006611.1	Q9Y450	HBS1L_HUMAN	HBS1-like translational GTPase						signal transduction (GO:0007165)|translation (GO:0006412)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation elongation factor activity (GO:0003746)			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	20	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)		AGTCATATTTTCCAACGAGCT	0.289																																					p.E331G		Atlas-SNP	.											.	HBS1L	75	.	0			c.A992G						.						32	26	28					6																	135358603		692	1590	2282	SO:0001627	intron_variant	10767	exon5			ATATTTTCCAACG	U87791	CCDS5173.1, CCDS47479.1, CCDS47480.1	6q23.3	2014-04-30	2014-04-30		ENSG00000112339	ENSG00000112339			4834	protein-coding gene	gene with protein product	"eRF3 family member"	612450	"HBS1 (S. cerevisiae)-like", "HBS1-like (S. cerevisiae)"			9872408, 23667253	Standard	NM_006620		Approved	ERFS, HBS1, HSPC276, KIAA1038, DKFZp434g247, EF-1a, eRF3c	uc003qez.2	Q9Y450	OTTHUMG00000015626	ENST00000367837.5:c.430+2107A>G	chr6.hg19:g.135358603T>C		214.0	0.0		122.0	5.0	NM_001145207	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	Missense_Mutation	SNP	ENST00000367837.5	hg19	CCDS5173.1	.	.	.	.	.	.	.	.	.	.	T	13.07	2.128182	0.37533	.	.	ENSG00000112339	ENST00000367822	.	.	.	5.49	5.49	0.81192	.	.	.	.	.	T	0.31104	0.0786	.	.	.	0.80722	D	1	B	0.27559	0.181	B	0.30646	0.118	T	0.42599	-0.9442	7	0.54805	T	0.06	.	4.8834	0.13690	0.0:0.1141:0.1863:0.6996	.	331	Q9Y450-2	.	G	331	.	ENSP00000356796:E331G	E	-	2	0	HBS1L	135400296	1.000000	0.71417	0.998000	0.56505	0.510000	0.34073	2.111000	0.41883	2.194000	0.70268	0.533000	0.62120	GAA	.	.		0.289	HBS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042339.2			C	135358603	T	C	135358603	1	2	259	0	1	0	0	0	0	0	0	0	6996	1783	62	2		2	HBS1L	6	135358603	Intron	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1054584	135358603	35756464	318	36636										
MAP3K5	4217	hgsc.bcm.edu	37	chr6	136882716	136882716	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccattcactctcagccagtcGgtaagttcagaatcttcagt	7	12	5	1	rs371929460		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:136882716G>T	ENST00000359015.4	-	28	4302	c.3942C>A	c.(3940-3942)acC>acA	p.T1314T	MAP3K5_ENST00000355845.4_Silent_p.T561T	NM_005923.3	NP_005914.1	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase 5	1314			T -> I (in dbSNP:rs45599539). {ECO:0000269|PubMed:17344846}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JNK cascade (GO:0007254)|MAPK cascade (GO:0000165)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of neuron death (GO:1901216)|programmed necrotic cell death (GO:0097300)|protein phosphorylation (GO:0006468)|response to ischemia (GO:0002931)|viral process (GO:0016032)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(6)|large_intestine(6)|lung(24)|ovary(2)|prostate(1)|skin(4)|urinary_tract(4)	58	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		TCAGCCAGTCGGTAAGTTCAG	0.373																																					p.T1314T		Atlas-SNP	.											.	MAP3K5	136	.	0			c.C3942A						.						94	93	93					6																	136882716		2203	4300	6503	SO:0001819	synonymous_variant	4217	exon28			CCAGTCGGTAAGT	U67156	CCDS5179.1	6q22.33	2011-06-09			ENSG00000197442	ENSG00000197442		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6857	protein-coding gene	gene with protein product	"apoptosis signal regulating kinase 1"	602448		MEKK5		9465908	Standard	NM_005923		Approved	MAPKKK5, ASK1	uc003qhc.3	Q99683	OTTHUMG00000015647	ENST00000359015.4:c.3942C>A	chr6.hg19:g.136882716G>T		218.0	0.0		128.0	9.0	NM_005923	A6NIA0|B4DGB2|Q5THN3|Q99461	Silent	SNP	ENST00000359015.4	hg19	CCDS5179.1																																																																																			.	.		0.373	MAP3K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042383.1			T	136882716	G	T	136882716	2	4	259	1	0	0	0	0	0	0	0	1	9262	1103	39	1		1	MAP3K5	6	136882716	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1524113	136882716	34232351	319	36637										
HECA	51696	hgsc.bcm.edu	37	chr6	139487731	139487731	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gacacagactggtatcaggtGaagcggatgcaggacgagaa	15	7	1	3	rs529104889		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:139487731G>T	ENST00000367658.2	+	2	867	c.582G>T	c.(580-582)gtG>gtT	p.V194V	RP1-225E12.2_ENST00000589192.1_RNA|RP1-225E12.2_ENST00000588638.1_RNA|RP1-225E12.2_ENST00000588529.1_RNA|RP1-225E12.2_ENST00000586266.1_RNA|RP1-225E12.2_ENST00000586229.1_RNA|RP1-225E12.2_ENST00000590679.1_RNA|RP1-225E12.2_ENST00000587577.1_RNA|RP1-225E12.3_ENST00000585874.1_RNA|RP1-225E12.2_ENST00000415194.2_RNA|RP1-225E12.2_ENST00000591102.1_RNA	NM_016217.2	NP_057301.1	Q9UBI9	HDC_HUMAN	headcase homolog (Drosophila)	194					respiratory tube development (GO:0030323)	membrane (GO:0016020)				endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)	15				GBM - Glioblastoma multiforme(68;0.000252)|OV - Ovarian serous cystadenocarcinoma(155;0.000387)		GGTATCAGGTGAAGCGGATGC	0.577																																					p.V194V		Atlas-SNP	.											.	HECA	45	.	0			c.G582T						.						71	77	75					6																	139487731		2203	4300	6503	SO:0001819	synonymous_variant	51696	exon2			TCAGGTGAAGCGG	AB033492	CCDS5194.1	6q23-q24	2010-11-25			ENSG00000112406	ENSG00000112406			21041	protein-coding gene	gene with protein product		607977				11696983, 19643820	Standard	NM_016217		Approved	HDCL, hHDC, HDC, dJ225E12.1	uc003qin.3	Q9UBI9	OTTHUMG00000015686	ENST00000367658.2:c.582G>T	chr6.hg19:g.139487731G>T		162.0	0.0		65.0	4.0	NM_016217		Silent	SNP	ENST00000367658.2	hg19	CCDS5194.1																																																																																			.	.		0.577	HECA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042456.1	NM_016217		T	139487731	G	T	139487731	2	4	259	1	0	0	0	0	0	0	0	1	7047	1277	45	3		3	HECA	6	139487731	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	2605015	139487731	31627336	320	36638										
ADAT2	134637	hgsc.bcm.edu	37	chr6	143755117	143755117	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccatttctgcatgtcgagtaGcctgaaaagagaaaggggct	12	8	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:143755117G>A	ENST00000237283.8	-	3	217	c.203C>T	c.(202-204)gCt>gTt	p.A68V	ADAT2_ENST00000606514.1_Splice_Site_p.A21V	NM_182503.2	NP_872309.2	Q7Z6V5	ADAT2_HUMAN	adenosine deaminase, tRNA-specific 2	68					tRNA wobble adenosine to inosine editing (GO:0002100)		tRNA-specific adenosine deaminase activity (GO:0008251)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(3)|lung(3)	8				OV - Ovarian serous cystadenocarcinoma(155;5.61e-06)|GBM - Glioblastoma multiforme(68;0.0115)		ATGTCGAGTAGCCTGAAAAGA	0.418																																					p.A68V		Atlas-SNP	.											.	ADAT2	18	.	0			c.C203T						.						131	125	127					6																	143755117		1979	4158	6137	SO:0001630	splice_region_variant	134637	exon3			CGAGTAGCCTGAA	BC037955	CCDS43511.1, CCDS69219.1	6q24.2	2014-01-28	2011-05-19	2007-08-16	ENSG00000189007	ENSG00000189007			21172	protein-coding gene	gene with protein product	tRNA-specific adenosine deaminase 2 homolog (S. cerevisiae)	615388	"deaminase domain containing 1", "adenosine deaminase, tRNA-specific 2, TAD2 homolog (S. cerevisiae)"	DEADC1		12457566	Standard	NM_182503		Approved	dJ20N2.1, TAD2	uc003qjj.3	Q7Z6V5	OTTHUMG00000015725	ENST00000237283.8:c.202-1C>T	chr6.hg19:g.143755117G>A		37.0	0.0		25.0	17.0	NM_182503	A6NL12|B3KWY3|Q7Z327|Q8IY39	Missense_Mutation	SNP	ENST00000237283.8	hg19	CCDS43511.1	.	.	.	.	.	.	.	.	.	.	G	32	5.119043	0.94385	.	.	ENSG00000189007	ENST00000367594;ENST00000237283	T	0.41758	0.99	4.37	4.37	0.52481	Cytidine deaminase-like (1);CMP/dCMP deaminase, zinc-binding (1);	0.000000	0.85682	D	0.000000	T	0.52853	0.1760	L	0.55017	1.72	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.56811	-0.7917	10	0.59425	D	0.04	-17.6129	17.1223	0.86705	0.0:0.0:1.0:0.0	.	68	Q7Z6V5	ADAT2_HUMAN	V	21;68	ENSP00000237283:A68V	ENSP00000237283:A68V	A	-	2	0	ADAT2	143796810	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.782000	0.91809	2.254000	0.74563	0.650000	0.86243	GCT	.	.		0.418	ADAT2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042517.1	XM_059727	Missense_Mutation	A	143755117	G	A	143755117	5	1	259	1	0	0	0	0	0	0	1	0	285	985	34	3	388	3	ADAT2	6	143755117	Splice_Site	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	4267386	143755117	27359950	321	36639										
SHPRH	257218	hgsc.bcm.edu	37	chr6	146243830	146243830	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aagtctggctggtcggaggtGacagactgttgcagactcaa	14	8	2	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:146243830G>T	ENST00000367505.2	-	19	3952	c.3688C>A	c.(3688-3690)Cac>Aac	p.H1230N	SHPRH_ENST00000438092.2_Missense_Mutation_p.H1234N|SHPRH_ENST00000275233.7_Missense_Mutation_p.H1230N|SHPRH_ENST00000367503.3_Missense_Mutation_p.H1234N			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	1230					DNA repair (GO:0006281)|nucleosome assembly (GO:0006334)|protein polyubiquitination (GO:0000209)	nucleosome (GO:0000786)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1)	79		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		GGTCGGAGGTGACAGACTGTT	0.403																																					p.H1234N		Atlas-SNP	.											.	SHPRH	169	.	0			c.C3700A						.						87	87	87					6																	146243830		1888	4104	5992	SO:0001583	missense	257218	exon19			GGAGGTGACAGAC	AB095943	CCDS43513.1, CCDS47496.1, CCDS43513.2	6q24.2	2012-02-23	2012-02-23		ENSG00000146414	ENSG00000146414		"RING-type (C3HC4) zinc fingers"	19336	protein-coding gene	gene with protein product		608048	"SNF2 histone linker PHD RING helicase"			12837266	Standard	NM_001042683		Approved	FLJ90837, KIAA2023, bA545I5.2	uc003qlf.3	Q149N8	OTTHUMG00000015750	ENST00000367505.2:c.3688C>A	chr6.hg19:g.146243830G>T	ENSP00000356475:p.His1230Asn	94.0	0.0		82.0	4.0	NM_173082	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Missense_Mutation	SNP	ENST00000367505.2	hg19	CCDS43513.2	.	.	.	.	.	.	.	.	.	.	G	23.1	4.379883	0.82682	.	.	ENSG00000146414	ENST00000367505;ENST00000367503;ENST00000438092;ENST00000275233	T;T;T;T	0.74526	-0.84;-0.85;-0.84;-0.84	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	D	0.83188	0.5200	M	0.66939	2.045	0.80722	D	1	P;D;D	0.76494	0.956;0.999;0.999	P;D;D	0.83275	0.63;0.991;0.996	T	0.83196	-0.0081	10	0.52906	T	0.07	-17.2231	19.0974	0.93258	0.0:0.0:1.0:0.0	.	429;1230;1234	B3KX98;Q149N8;Q149N8-4	.;SHPRH_HUMAN;.	N	1230;1234;1234;1230	ENSP00000356475:H1230N;ENSP00000356473:H1234N;ENSP00000412797:H1234N;ENSP00000275233:H1230N	ENSP00000275233:H1230N	H	-	1	0	SHPRH	146285523	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.599000	0.98280	2.593000	0.87608	0.650000	0.86243	CAC	.	.		0.403	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082		T	146243830	G	T	146243830	3	4	259	1	0	0	0	0	1	0	0	0	14306	1290	45	3	1428	3	SHPRH	6	146243830	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	2488713	146243830	24871237	322	36640										
NUP43	348995	hgsc.bcm.edu	37	chr6	150067096	150067096	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctgtaaatccattacatcacCatggtgtctgatatcacaca	5	11	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:150067096C>T	ENST00000340413.2	-	2	299	c.223G>A	c.(223-225)Ggt>Agt	p.G75S	NUP43_ENST00000460354.2_Missense_Mutation_p.G75S|NUP43_ENST00000367403.3_Missense_Mutation_p.G136S|NUP43_ENST00000463048.3_5'UTR|NUP43_ENST00000367404.4_Missense_Mutation_p.G75S	NM_198887.1	NP_942590.1	Q8NFH3	NUP43_HUMAN	nucleoporin 43kDa	75					carbohydrate metabolic process (GO:0005975)|chromosome segregation (GO:0007059)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)		p.G75C(1)		breast(1)|large_intestine(2)|lung(8)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	18		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;4.71e-13)|GBM - Glioblastoma multiforme(68;0.101)		ATTACATCACCATGGTGTCTG	0.363																																					p.G75S		Atlas-SNP	.											NUP43,NS,carcinoma,0,1	NUP43	32	.	1	Substitution - Missense(1)	lung(1)	c.G223A						.						127	124	125					6																	150067096		2203	4300	6503	SO:0001583	missense	348995	exon2			CATCACCATGGTG	AF514997	CCDS5218.1	6q25.1	2013-01-10			ENSG00000120253	ENSG00000120253		"WD repeat domain containing"	21182	protein-coding gene	gene with protein product		608141				12196509	Standard	XM_005266961		Approved	bA350J20.1, FLJ13287	uc003qmz.3	Q8NFH3	OTTHUMG00000015795	ENST00000340413.2:c.223G>A	chr6.hg19:g.150067096C>T	ENSP00000342262:p.Gly75Ser	80.0	0.0		44.0	2.0	NM_198887	B4E2F0|Q9H8S0	Missense_Mutation	SNP	ENST00000340413.2	hg19	CCDS5218.1	.	.	.	.	.	.	.	.	.	.	C	36	5.940959	0.97128	.	.	ENSG00000120253	ENST00000340413;ENST00000460354;ENST00000367403;ENST00000367404;ENST00000543637	T;T;T;T;T	0.70869	-0.06;-0.06;-0.52;-0.52;-0.52	6.08	6.08	0.98989	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.82536	0.5058	M	0.71581	2.175	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.81265	-0.1011	10	0.56958	D	0.05	-26.5731	20.6647	0.99678	0.0:1.0:0.0:0.0	.	75;75	B4E2F0;Q8NFH3	.;NUP43_HUMAN	S	75;75;136;75;82	ENSP00000342262:G75S;ENSP00000432401:G75S;ENSP00000356373:G136S;ENSP00000356374:G75S;ENSP00000438031:G82S	ENSP00000342262:G75S	G	-	1	0	NUP43	150108789	1.000000	0.71417	0.996000	0.52242	0.995000	0.86356	7.487000	0.81328	2.890000	0.99128	0.655000	0.94253	GGT	.	.		0.363	NUP43-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396947.1	NM_198887		T	150067096	C	T	150067096	3	4	259	1	0	0	0	0	1	0	0	0	10774	594	21	3	947	3	NUP43	6	150067096	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	3823266	150067096	21047971	323	36641										
LRP11	84918	hgsc.bcm.edu	37	chr6	150147437	150147437	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgttcccctcctcctccatcAccctttgactcaaatatata	2	16	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:150147437A>G	ENST00000239367.2	-	6	1316	c.1311T>C	c.(1309-1311)ggT>ggC	p.G437G	LRP11_ENST00000546019.1_Silent_p.G182G|LRP11_ENST00000463728.1_5'UTR	NM_032832.5	NP_116221.3	Q86VZ4	LRP11_HUMAN	low density lipoprotein receptor-related protein 11	437						integral component of membrane (GO:0016021)				cervix(1)|kidney(5)|large_intestine(1)|lung(1)	8		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;4.56e-12)|GBM - Glioblastoma multiforme(68;0.225)		CTCCTCCATCACCCTTTGACT	0.448																																					p.G437G		Atlas-SNP	.											.	LRP11	27	.	0			c.T1311C						.						197	190	192					6																	150147437		2203	4300	6503	SO:0001819	synonymous_variant	84918	exon6			TCCATCACCCTTT	AK027641	CCDS5220.1	6q24.3	2013-02-27			ENSG00000120256	ENSG00000120256		"Low density lipoprotein receptors"	16936	protein-coding gene	gene with protein product							Standard	NM_032832		Approved	bA350J20.3, MANSC3	uc003qng.2	Q86VZ4	OTTHUMG00000015801	ENST00000239367.2:c.1311T>C	chr6.hg19:g.150147437A>G		168.0	0.0		99.0	5.0	NM_032832	Q5VYC0|Q96SN6	Silent	SNP	ENST00000239367.2	hg19	CCDS5220.1																																																																																			.	.		0.448	LRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042664.1	NM_032832		G	150147437	A	G	150147437	2	3	259	1	0	0	0	0	0	0	0	1	8962	146	6	2		2	LRP11	6	150147437	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	80341	150147437	20967630	324	36642										
ESR1	2099	hgsc.bcm.edu	37	chr6	152382169	152382169	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gcatggtggagatcttcgacAtgctgctggctacatcatct	11	10	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:152382169A>G	ENST00000206249.3	+	6	1641	c.1279A>G	c.(1279-1281)Atg>Gtg	p.M427V	ESR1_ENST00000338799.5_Missense_Mutation_p.M427V|ESR1_ENST00000406599.1_Missense_Mutation_p.M166V|ESR1_ENST00000427531.2_Missense_Mutation_p.M254V|ESR1_ENST00000456483.2_Missense_Mutation_p.M315V|ESR1_ENST00000443427.1_Missense_Mutation_p.M427V|ESR1_ENST00000440973.1_Missense_Mutation_p.M427V	NM_000125.3	NP_000116.2	P03372	ESR1_HUMAN	estrogen receptor 1	427	Interaction with AKAP13.|Self-association.|Steroid-binding.|Transactivation AF-2.				androgen metabolic process (GO:0008209)|antral ovarian follicle growth (GO:0001547)|cellular response to estradiol stimulus (GO:0071392)|chromatin remodeling (GO:0006338)|epithelial cell development (GO:0002064)|epithelial cell proliferation involved in mammary gland duct elongation (GO:0060750)|gene expression (GO:0010467)|intracellular estrogen receptor signaling pathway (GO:0030520)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|male gonad development (GO:0008584)|mammary gland alveolus development (GO:0060749)|mammary gland branching involved in pregnancy (GO:0060745)|negative regulation of gene expression (GO:0010629)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|uterus development (GO:0060065)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|transcriptionally active chromatin (GO:0035327)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enzyme binding (GO:0019899)|estrogen receptor activity (GO:0030284)|estrogen response element binding (GO:0034056)|estrogen-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0038052)|identical protein binding (GO:0042802)|nitric-oxide synthase regulator activity (GO:0030235)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(19)|ovary(1)|prostate(2)|skin(1)	49		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Allylestrenol(DB01431)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Estropipate(DB04574)|Ethinyl Estradiol(DB00977)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Ospemifene(DB04938)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)|Trilostane(DB01108)	GATCTTCGACATGCTGCTGGC	0.373																																					p.M427V		Atlas-SNP	.											.	ESR1	94	.	0			c.A1279G						.						110	99	103					6																	152382169		2203	4300	6503	SO:0001583	missense	2099	exon6			TTCGACATGCTGC	X03635	CCDS5234.1	6q24-q27	2013-01-16			ENSG00000091831	ENSG00000091831		"Nuclear hormone receptors"	3467	protein-coding gene	gene with protein product		133430		ESR		3754034	Standard	NM_000125		Approved	NR3A1, Era	uc003qon.4	P03372	OTTHUMG00000016103	ENST00000206249.3:c.1279A>G	chr6.hg19:g.152382169A>G	ENSP00000206249:p.Met427Val	147.0	0.0		74.0	4.0	NM_000125	Q13511|Q14276|Q5T5H7|Q6MZQ9|Q9NU51|Q9UDZ7|Q9UIS7	Missense_Mutation	SNP	ENST00000206249.3	hg19	CCDS5234.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.528128	0.85706	.	.	ENSG00000091831	ENST00000440973;ENST00000338799;ENST00000456483;ENST00000443427;ENST00000206249;ENST00000406599;ENST00000431590;ENST00000544394;ENST00000415488	D;D;D;D;D;D;D;D	0.96396	-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0	5.38	5.38	0.77491	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.85682	D	0.000000	D	0.97291	0.9114	M	0.65498	2.005	0.58432	D	0.999999	P;D;D;P;P;P;P	0.65815	0.704;0.968;0.995;0.607;0.514;0.458;0.514	P;P;D;B;B;B;B	0.72075	0.543;0.906;0.976;0.227;0.34;0.311;0.438	D	0.98336	1.0536	10	0.87932	D	0	.	15.4108	0.74917	1.0:0.0:0.0:0.0	.	331;122;166;354;426;427;427	B0QYW6;C8CJL6;Q9H2M1;B4E3R5;A8KAF4;G4XH65;P03372	.;.;.;.;.;.;ESR1_HUMAN	V	427;427;315;427;427;166;355;254;100	ENSP00000405330:M427V;ENSP00000342630:M427V;ENSP00000415934:M315V;ENSP00000387500:M427V;ENSP00000206249:M427V;ENSP00000384064:M166V;ENSP00000445454:M254V;ENSP00000401995:M100V	ENSP00000206249:M427V	M	+	1	0	ESR1	152423862	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.323000	0.96364	2.039000	0.60335	0.533000	0.62120	ATG	.	.		0.373	ESR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043308.1			G	152382169	A	G	152382169	3	3	259	1	0	0	0	0	1	0	0	0	5258	217	8	2	1301	2	ESR1	6	152382169	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2234732	152382169	18732898	325	36643										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152457873	152457873	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aggtcccggctctccttgctGtcagcctgggtgaactcagg	13	13	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:152457873G>A	ENST00000367255.5	-	141	26140	c.25539C>T	c.(25537-25539)gaC>gaT	p.D8513D	SYNE1_ENST00000341594.5_Silent_p.D8125D|SYNE1_ENST00000347037.5_5'UTR|SYNE1_ENST00000265368.4_Silent_p.D8513D|SYNE1_ENST00000354674.4_Silent_p.D691D|SYNE1_ENST00000448038.1_Silent_p.D8465D|SYNE1_ENST00000423061.1_Silent_p.D8465D|SYNE1_ENST00000356820.4_Silent_p.D3037D|SYNE1_ENST00000539504.1_Silent_p.D668D	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	8513					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TCTCCTTGCTGTCAGCCTGGG	0.587										HNSCC(10;0.0054)																											p.D8513D		Atlas-SNP	.											.	SYNE1	3227	.	0			c.C25539T						.						93	87	89					6																	152457873		2203	4300	6503	SO:0001819	synonymous_variant	23345	exon141			CTTGCTGTCAGCC	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.25539C>T	chr6.hg19:g.152457873G>A		155.0	0.0		82.0	5.0	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	hg19	CCDS5236.2																																																																																			.	.		0.587	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152457873	G	A	152457873	2	1	259	1	0	0	0	0	0	0	0	1	15460	1368	48	3		3	SYNE1	6	152457873	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	75704	152457873	18657194	326	36644										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152577846	152577846	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agatttatcttgggttggcaCgtcccctttgtacagtggca	11	9	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:152577846C>T	ENST00000367255.5	-	102	19628	c.19027G>A	c.(19027-19029)Gtg>Atg	p.V6343M	SYNE1_ENST00000341594.5_Missense_Mutation_p.V5955M|SYNE1_ENST00000265368.4_Missense_Mutation_p.V6343M|SYNE1_ENST00000448038.1_Missense_Mutation_p.V6272M|SYNE1_ENST00000423061.1_Missense_Mutation_p.V6272M|SYNE1_ENST00000356820.4_Missense_Mutation_p.V867M	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	6343					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.V6343L(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TGGGTTGGCACGTCCCCTTTG	0.468										HNSCC(10;0.0054)																											p.V6343M		Atlas-SNP	.											SYNE1_ENST00000423061,rectum,carcinoma,0,5	SYNE1	3227	.	2	Substitution - Missense(2)	prostate(2)	c.G19027A						.						179	149	159					6																	152577846		2203	4300	6503	SO:0001583	missense	23345	exon102			TTGGCACGTCCCC	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.19027G>A	chr6.hg19:g.152577846C>T	ENSP00000356224:p.Val6343Met	92.0	0.0		46.0	2.0	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	5.689	0.311623	0.10789	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820	T;T;T;T;T;T	0.53857	0.7;0.69;0.6;0.69;0.79;2.65	5.29	4.43	0.53597	.	0.206659	0.33854	N	0.004500	T	0.15522	0.0374	N	0.08118	0	0.09310	N	1	P;P;P	0.44578	0.75;0.75;0.838	B;B;B	0.40565	0.115;0.115;0.333	T	0.02721	-1.1119	10	0.44086	T	0.13	.	9.6366	0.39811	0.0:0.7808:0.0:0.2192	.	6343;6343;6272	Q8NF91;E7EQI5;Q8NF91-4	SYNE1_HUMAN;.;.	M	6343;6272;6343;6272;5955;867	ENSP00000356224:V6343M;ENSP00000396024:V6272M;ENSP00000265368:V6343M;ENSP00000390975:V6272M;ENSP00000341887:V5955M;ENSP00000349276:V867M	ENSP00000265368:V6343M	V	-	1	0	SYNE1	152619539	0.005000	0.15991	0.013000	0.15412	0.233000	0.25261	1.384000	0.34396	1.373000	0.46208	-0.142000	0.14014	GTG	.	.		0.468	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152577846	C	T	152577846	3	4	259	1	0	0	0	0	1	0	0	0	15460	536	19	1	7619	1	SYNE1	6	152577846	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	119973	152577846	18537221	327	36645										
SYNJ2	8871	hgsc.bcm.edu	37	chr6	158449995	158449995	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aaacgatgggtctcgctttgAcctgactgtccgcacgcaga	11	12	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:158449995A>G	ENST00000355585.4	+	3	497	c.422A>G	c.(421-423)gAc>gGc	p.D141G	SYNJ2_ENST00000367122.2_Missense_Mutation_p.D141G|SYNJ2_ENST00000449859.2_Missense_Mutation_p.D90G|SYNJ2_ENST00000367121.3_Missense_Mutation_p.D141G	NM_001178088.1|NM_003898.3	NP_001171559.1|NP_003889.1	O15056	SYNJ2_HUMAN	synaptojanin 2	141	SAC. {ECO:0000255|PROSITE- ProRule:PRU00183}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			biliary_tract(1)|endometrium(9)|kidney(3)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)		TCTCGCTTTGACCTGACTGTC	0.582																																					p.D141G		Atlas-SNP	.											.	SYNJ2	111	.	0			c.A422G						.						66	68	68					6																	158449995		2203	4300	6503	SO:0001583	missense	8871	exon3			GCTTTGACCTGAC	AB002346	CCDS5254.1	6q25.3	2008-05-15			ENSG00000078269	ENSG00000078269			11504	protein-coding gene	gene with protein product		609410					Standard	NM_003898		Approved	INPP5H	uc003qqx.2	O15056	OTTHUMG00000015904	ENST00000355585.4:c.422A>G	chr6.hg19:g.158449995A>G	ENSP00000347792:p.Asp141Gly	114.0	0.0		61.0	5.0	NM_003898	Q5TA13|Q5TA16|Q5TA19|Q86XK0|Q8IZA8|Q9H226	Missense_Mutation	SNP	ENST00000355585.4	hg19	CCDS5254.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.57|16.57	3.160442|3.160442	0.57368|0.57368	.|.	.|.	ENSG00000078269|ENSG00000078269	ENST00000367122;ENST00000367121;ENST00000355585;ENST00000449320;ENST00000449859|ENST00000367113	T;T;T;T;T|.	0.72167|.	-0.63;-0.63;-0.63;-0.63;-0.63|.	4.62|4.62	4.62|4.62	0.57501|0.57501	Synaptojanin, N-terminal (2);|.	0.000000|.	0.64402|.	D|.	0.000018|.	D|D	0.85579|0.85579	0.5729|0.5729	H|H	0.98027|0.98027	4.13|4.13	0.49915|0.49915	D|D	0.999838|0.999838	D;D;D;D|.	0.58620|.	0.969;0.983;0.983;0.962|.	P;D;P;P|.	0.63113|.	0.676;0.911;0.676;0.547|.	D|D	0.90043|0.90043	0.4143|0.4143	10|5	0.87932|.	D|.	0|.	.|.	14.2246|14.2246	0.65850|0.65850	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	90;141;141;141|.	B4DJU8;E7ER60;O15056;O15056-3|.	.;.;SYNJ2_HUMAN;.|.	G|A	141;141;141;90;90|116	ENSP00000356089:D141G;ENSP00000356088:D141G;ENSP00000347792:D141G;ENSP00000411202:D90G;ENSP00000388371:D90G|.	ENSP00000347792:D141G|.	D|T	+|+	2|1	0|0	SYNJ2|SYNJ2	158369983|158369983	1.000000|1.000000	0.71417|0.71417	0.992000|0.992000	0.48379|0.48379	0.017000|0.017000	0.09413|0.09413	8.614000|8.614000	0.90917|0.90917	0.546000|0.546000	0.28920|0.28920	0.655000|0.655000	0.94253|0.94253	GAC|ACC	.	.		0.582	SYNJ2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042858.2			G	158449995	A	G	158449995	3	3	259	1	0	0	0	0	1	0	0	0	15468	275	10	2	432	2	SYNJ2	6	158449995	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	5872149	158449995	12665072	328	36646										
IGF2R	3482	hgsc.bcm.edu	37	chr6	160491044	160491044	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cttatgtccagatgggattcGgaaaaagtcaaccaccatcc	8	11	1	1	rs368697729		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:160491044G>T	ENST00000356956.1	+	31	4545	c.4397G>T	c.(4396-4398)cGg>cTg	p.R1466L		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	1466					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	GATGGGATTCGGAAAAAGTCA	0.522																																					p.R1466L		Atlas-SNP	.											.	IGF2R	251	.	0			c.G4397T						.						106	87	93					6																	160491044		2203	4300	6503	SO:0001583	missense	3482	exon31			GGATTCGGAAAAA	J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"CD molecules"	5467	protein-coding gene	gene with protein product	"cation-independent mannose-6 phosphate receptor"	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.4397G>T	chr6.hg19:g.160491044G>T	ENSP00000349437:p.Arg1466Leu	175.0	0.0		95.0	4.0	NM_000876	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	hg19	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.840838	0.91197	.	.	ENSG00000197081	ENST00000356956	T	0.13089	2.62	5.62	5.62	0.85841	Mannose-6-phosphate receptor, binding (1);	0.058799	0.64402	D	0.000005	T	0.34077	0.0885	M	0.77616	2.38	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.06023	-1.0850	10	0.54805	T	0.06	-11.632	19.6758	0.95932	0.0:0.0:1.0:0.0	.	1466	P11717	MPRI_HUMAN	L	1466	ENSP00000349437:R1466L	ENSP00000349437:R1466L	R	+	2	0	IGF2R	160411034	1.000000	0.71417	0.971000	0.41717	0.723000	0.41478	5.738000	0.68613	2.644000	0.89710	0.561000	0.74099	CGG	.	.		0.522	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876		T	160491044	G	T	160491044	3	4	259	1	0	0	0	0	1	0	0	0	7585	1116	39	1	4519	1	IGF2R	6	160491044	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	2041049	160491044	10624023	329	36647										
LPA	4018	hgsc.bcm.edu	37	chr6	160978594	160978594	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggattcctgcagtagttctcGgtcaggccactgcaaattcc	10	12	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:160978594G>T	ENST00000316300.5	-	29	4685	c.4641C>A	c.(4639-4641)acC>acA	p.T1547T	LPA_ENST00000447678.1_Silent_p.T1547T			P08519	APOA_HUMAN	lipoprotein, Lp(a)	4055	Kringle 14. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	AGTAGTTCTCGGTCAGGCCAC	0.478																																					p.T1547T		Atlas-SNP	.											.	LPA	237	.	0			c.C4641A						.						67	69	68					6																	160978594		2113	4264	6377	SO:0001819	synonymous_variant	4018	exon30			GTTCTCGGTCAGG	X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.4641C>A	chr6.hg19:g.160978594G>T		173.0	0.0		100.0	4.0	NM_005577	Q5VTD7|Q9UD88	Silent	SNP	ENST00000316300.5	hg19	CCDS43523.1																																																																																			.	.		0.478	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577		T	160978594	G	T	160978594	2	4	259	1	0	0	0	0	0	0	0	1	8912	1103	39	1		1	LPA	6	160978594	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	487550	160978594	10136473	330	36648										
RPS6KA2	6196	hgsc.bcm.edu	37	chr6	166912091	166912091	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctcgatcgtcccgcagaaggAgtacgctctcttgtcgtggt	12	12	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:166912091A>G	ENST00000265678.4	-	8	875	c.652T>C	c.(652-654)Tcc>Ccc	p.S218P	RPS6KA2_ENST00000503859.1_Missense_Mutation_p.S226P|RPS6KA2_ENST00000481261.2_Missense_Mutation_p.S129P|RPS6KA2_ENST00000510118.1_Missense_Mutation_p.S243P|RPS6KA2_ENST00000405189.3_Missense_Mutation_p.S129P|RPS6KA2_ENST00000366863.2_Missense_Mutation_p.S64P	NM_021135.4	NP_066958.2	Q15349	KS6A2_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 2	218	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|brain renin-angiotensin system (GO:0002035)|cardiac muscle cell apoptotic process (GO:0010659)|cellular response to carbohydrate stimulus (GO:0071322)|heart contraction (GO:0060047)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of meiosis (GO:0045835)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oocyte maturation (GO:0001556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of gene expression (GO:0010628)|regulation of protein processing (GO:0070613)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|ribosomal protein S6 kinase activity (GO:0004711)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	45		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)		CCGCAGAAGGAGTACGCTCTC	0.597																																					p.S226P		Atlas-SNP	.											.	RPS6KA2	212	.	0			c.T676C						.						212	143	167					6																	166912091		2203	4300	6503	SO:0001583	missense	6196	exon9			AGAAGGAGTACGC	L07598	CCDS5294.1, CCDS34570.1	6q27	2011-04-05	2002-08-29		ENSG00000071242	ENSG00000071242			10431	protein-coding gene	gene with protein product		601685	"ribosomal protein S6 kinase, 90kD, polypeptide 2"			8141249	Standard	NM_001006932		Approved	RSK, RSK3, HU-2	uc003qvc.1	Q15349	OTTHUMG00000016007	ENST00000265678.4:c.652T>C	chr6.hg19:g.166912091A>G	ENSP00000265678:p.Ser218Pro	144.0	0.0		85.0	4.0	NM_001006932	B3KTK9|Q15419|Q59GJ3|Q5TI68|Q96J38|Q9UJN5	Missense_Mutation	SNP	ENST00000265678.4	hg19	CCDS5294.1	.	.	.	.	.	.	.	.	.	.	A	29.4	5.002768	0.93287	.	.	ENSG00000071242	ENST00000265678;ENST00000510118;ENST00000503859;ENST00000481261;ENST00000405189;ENST00000366863	T;T;T;T;T;T	0.67345	1.74;1.74;1.74;1.74;1.74;-0.26	4.89	4.89	0.63831	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.77445	0.4131	M	0.77820	2.39	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.87578	0.998;0.997;0.996	T	0.81627	-0.0847	10	0.87932	D	0	.	13.9945	0.64388	1.0:0.0:0.0:0.0	.	243;226;218	F2Z2J1;Q15349-3;Q15349	.;.;KS6A2_HUMAN	P	218;243;226;129;129;64	ENSP00000265678:S218P;ENSP00000422435:S243P;ENSP00000427015:S226P;ENSP00000422484:S129P;ENSP00000386050:S129P;ENSP00000355828:S64P	ENSP00000265678:S218P	S	-	1	0	RPS6KA2	166832081	1.000000	0.71417	0.832000	0.32986	0.955000	0.61496	8.576000	0.90770	1.947000	0.56498	0.533000	0.62120	TCC	.	.		0.597	RPS6KA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043075.3	NM_021135		G	166912091	A	G	166912091	3	3	259	1	0	0	0	0	1	0	0	0	13666	304	11	2	1605	2	RPS6KA2	6	166912091	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	5933497	166912091	4202976	331	36649										
C6orf70	55780	hgsc.bcm.edu	37	chr6	170154032	170154032	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	taatttgtaatcttgggtttCaactcagagaaaattgtgat	8	4	3	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:170154032C>T	ENST00000366773.3	+	2	112	c.79C>T	c.(79-81)Caa>Taa	p.Q27*	ERMARD_ENST00000392095.4_Intron|ERMARD_ENST00000588451.1_5'UTR|ERMARD_ENST00000366772.2_Nonsense_Mutation_p.Q27*|ERMARD_ENST00000418781.3_Nonsense_Mutation_p.Q27*|TCTE3_ENST00000366774.3_5'Flank	NM_001278532.1|NM_018341.1	NP_001265461.1|NP_060811.1	Q5T6L9	EMARD_HUMAN	ER membrane-associated RNA degradation	27					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											TCTTGGGTTTCAACTCAGAGA	0.348																																					p.Q27X		Atlas-SNP	.											.	C6orf70	63	.	0			c.C79T						.						82	78	79					6																	170154032		2203	4300	6503	SO:0001587	stop_gained	55780	exon2			GGGTTTCAACTCA	AK002014	CCDS34576.1, CCDS64572.1, CCDS64573.1, CCDS64574.1	6q27	2013-08-28	2013-08-28	2013-08-28	ENSG00000130023	ENSG00000130023			21056	protein-coding gene	gene with protein product		615532	"chromosome 6 open reading frame 70"	C6orf70		23768067	Standard	NM_018341		Approved	FLJ11152, dJ266L20.3	uc003qxg.1	Q5T6L9	OTTHUMG00000016067	ENST00000366773.3:c.79C>T	chr6.hg19:g.170154032C>T	ENSP00000355735:p.Gln27*	124.0	0.0		62.0	4.0	NM_018341	B4DFH0|F8WAF1|Q3ZCS8|Q5T6L8|Q9NUT5|Q9NVU2	Nonsense_Mutation	SNP	ENST00000366773.3	hg19	CCDS34576.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.939366	0.73557	.	.	ENSG00000130023	ENST00000366773;ENST00000366772;ENST00000418781	.	.	.	5.66	4.79	0.61399	.	0.212077	0.32802	N	0.005635	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	14.4984	0.67704	0.0:0.1503:0.8497:0.0	.	.	.	.	X	27	.	ENSP00000355734:Q27X	Q	+	1	0	C6orf70	169895957	1.000000	0.71417	0.965000	0.40720	0.389000	0.30415	4.290000	0.59019	1.388000	0.46506	-0.153000	0.13522	CAA	.	.		0.348	ERMARD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043238.2	NM_018341		T	170154032	C	T	170154032	4	4	259	1	0	0	0	0	0	1	0	0	2372	827	29	3	85	3	C6orf70	6	170154032	Nonsense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	3241941	170154032	961035	332	36650										
PRKAR1B	5575	hgsc.bcm.edu	37	chr7	635799	635799	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tcaccataaggatgcgccggTagctgtcccggtcgatcccc	11	15	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:635799T>C	ENST00000406797.1	-	7	866	c.692A>G	c.(691-693)tAc>tGc	p.Y231C	PRKAR1B_ENST00000544935.1_Missense_Mutation_p.Y231C|PRKAR1B_ENST00000360274.4_Missense_Mutation_p.Y231C|PRKAR1B_ENST00000403562.1_Missense_Mutation_p.Y231C|PRKAR1B_ENST00000537384.1_Missense_Mutation_p.Y231C	NM_001164761.1	NP_001158233.1	P31321	KAP1_HUMAN	protein kinase, cAMP-dependent, regulatory, type I, beta	231					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)			endometrium(4)|large_intestine(1)|liver(1)|lung(10)|prostate(1)	17		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|Epithelial(4;5.75e-19)|OV - Ovarian serous cystadenocarcinoma(56;2.01e-18)|all cancers(6;3.96e-16)|BRCA - Breast invasive adenocarcinoma(126;0.152)		GATGCGCCGGTAGCTGTCCCG	0.637																																					p.Y231C		Atlas-SNP	.											.	PRKAR1B	32	.	0			c.A692G						.						97	76	83					7																	635799		2203	4296	6499	SO:0001583	missense	5575	exon7			CGCCGGTAGCTGT	M65066	CCDS34579.1	7p22.3	2013-09-19			ENSG00000188191	ENSG00000188191	2.7.11.1		9390	protein-coding gene	gene with protein product		176911				1358799, 3479018	Standard	NM_002735		Approved		uc003siw.2	P31321	OTTHUMG00000151411	ENST00000406797.1:c.692A>G	chr7.hg19:g.635799T>C	ENSP00000385749:p.Tyr231Cys	176.0	0.0		121.0	5.0	NM_001164760	Q8N422	Missense_Mutation	SNP	ENST00000406797.1	hg19	CCDS34579.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	21.4|21.4	4.148129|4.148129	0.78001|0.78001	.|.	.|.	ENSG00000188191|ENSG00000188191	ENST00000400758|ENST00000537384;ENST00000544935;ENST00000406797;ENST00000403562;ENST00000360274;ENST00000430040	.|D;D;D;D;D;D	.|0.84873	.|-1.91;-1.91;-1.91;-1.91;-1.91;-1.91	4.88|4.88	4.88|4.88	0.63580|0.63580	.|Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	.|0.000000	.|0.85682	.|U	.|0.000000	D|D	0.91646|0.91646	0.7360|0.7360	M|M	0.75777|0.75777	2.31|2.31	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.91635	.|0.999	D|D	0.92734|0.92734	0.6202|0.6202	5|10	.|0.87932	.|D	.|0	-2.1353|-2.1353	14.5236|14.5236	0.67870|0.67870	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|231	.|P31321	.|KAP1_HUMAN	A|C	92|231	.|ENSP00000440449:Y231C;ENSP00000444487:Y231C;ENSP00000385749:Y231C;ENSP00000385349:Y231C;ENSP00000353415:Y231C;ENSP00000402648:Y231C	.|ENSP00000353415:Y231C	T|Y	-|-	1|2	0|0	PRKAR1B|PRKAR1B	602325|602325	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.960000|0.960000	0.62799|0.62799	7.487000|7.487000	0.81328|0.81328	1.851000|1.851000	0.53745|0.53745	0.449000|0.449000	0.29647|0.29647	ACC|TAC	.	.		0.637	PRKAR1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322525.1			C	635799	T	C	635799	3	2	259	1	0	0	0	0	1	0	0	0	12516	1638	57	2	473	2	PRKAR1B	7	635799	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10		635799	158502864	333	36651										
SUN1	23353	hgsc.bcm.edu	37	chr7	881715	881715	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gctgtgactcgacggcctccTgtattggacgagtcttggat	13	10	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:881715T>C	ENST00000405266.1	+	3	423	c.399T>C	c.(397-399)ccT>ccC	p.P133P	SUN1_ENST00000403868.1_Silent_p.P133P|SUN1_ENST00000452783.2_Silent_p.P133P|SUN1_ENST00000425407.2_Silent_p.P83P|SUN1_ENST00000401592.1_Silent_p.P133P|SUN1_ENST00000389574.3_Silent_p.P83P|SUN1_ENST00000457378.2_Silent_p.P154P|SUN1_ENST00000456758.2_Silent_p.P191P			O94901	SUN1_HUMAN	Sad1 and UNC84 domain containing 1	133	LMNA-binding.				cytoskeletal anchoring at nuclear membrane (GO:0090286)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)	acrosomal membrane (GO:0002080)|integral component of nuclear inner membrane (GO:0005639)|nuclear envelope (GO:0005635)|SUN-KASH complex (GO:0034993)				NS(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(17)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GACGGCCTCCTGTATTGGACG	0.572																																					p.P154P		Atlas-SNP	.											.	SUN1	157	.	0			c.T462C						.						79	80	79					7																	881715		2072	4211	6283	SO:0001819	synonymous_variant	23353	exon5			GCCTCCTGTATTG	AF202724	CCDS43533.1, CCDS47525.1, CCDS55078.1, CCDS55079.1, CCDS55080.1	7p22.3	2010-01-27	2010-01-27	2010-01-27	ENSG00000164828	ENSG00000164828			18587	protein-coding gene	gene with protein product	"Sad1 unc-84 domain protein 1"	607723	"unc-84 homolog A (C. elegans)"	UNC84A		11593002	Standard	NM_001130965		Approved	KIAA0810, FLJ12407	uc021zym.1	O94901	OTTHUMG00000151426	ENST00000405266.1:c.399T>C	chr7.hg19:g.881715T>C		111.0	0.0		69.0	4.0	NM_001171945	A5PL20|B3KMV7|B4DZF7|B7WNY4|B7WP53|E9PDU4|E9PF23|F8WD13|Q96CZ7|Q9HA14|Q9UH98	Silent	SNP	ENST00000405266.1	hg19																																																																																				.	.		0.572	SUN1-001	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000322566.1	NM_025154		C	881715	T	C	881715	2	2	259	1	0	0	0	0	0	0	0	1	15406	1567	55	2		2	SUN1	7	881715	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	245916	881715	158256948	334	36652										
CHST12	55501	hgsc.bcm.edu	37	chr7	2472863	2472863	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgcaccgcggtgcgccctacCgcgacccgctgcgcatcccg	12	20	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:2472863C>A	ENST00000258711.6	+	2	724	c.589C>A	c.(589-591)Cgc>Agc	p.R197S		NM_001243794.1|NM_001243795.1|NM_018641.4	NP_001230723.1|NP_001230724.1|NP_061111.1	Q9NRB3	CHSTC_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 12	197					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|chondroitin 4-sulfotransferase activity (GO:0047756)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	21		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0847)|OV - Ovarian serous cystadenocarcinoma(56;2.25e-13)		TGCGCCCTACCGCGACCCGCT	0.677																																					p.R197S		Atlas-SNP	.											.	CHST12	39	.	0			c.C589A						.						49	41	44					7																	2472863		2203	4299	6502	SO:0001583	missense	55501	exon2			CCCTACCGCGACC	AF239822	CCDS5333.1	7p22	2007-03-14			ENSG00000136213	ENSG00000136213	2.8.2.5	"Sulfotransferases, membrane-bound"	17423	protein-coding gene	gene with protein product		610129				10781601	Standard	NM_018641		Approved	C4S-2, C4ST2	uc021zyu.1	Q9NRB3	OTTHUMG00000023849	ENST00000258711.6:c.589C>A	chr7.hg19:g.2472863C>A	ENSP00000258711:p.Arg197Ser	145.0	0.0		94.0	4.0	NM_018641	A4D1Z9|Q502W3|Q9NXY7	Missense_Mutation	SNP	ENST00000258711.6	hg19	CCDS5333.1	.	.	.	.	.	.	.	.	.	.	C	6.407	0.443189	0.12164	.	.	ENSG00000136213	ENST00000258711;ENST00000432336	T;T	0.72835	-0.69;-0.69	5.23	4.25	0.50352	.	0.422384	0.25792	N	0.028274	T	0.52549	0.1741	N	0.20845	0.615	0.32470	N	0.542986	P	0.37158	0.585	B	0.39419	0.299	T	0.55964	-0.8057	10	0.05525	T	0.97	-8.4503	12.9136	0.58192	0.1318:0.7528:0.1154:0.0	.	197	Q9NRB3	CHSTC_HUMAN	S	197	ENSP00000258711:R197S;ENSP00000411207:R197S	ENSP00000258711:R197S	R	+	1	0	CHST12	2439389	0.717000	0.27966	1.000000	0.80357	0.894000	0.52154	2.056000	0.41355	2.451000	0.82905	0.561000	0.74099	CGC	.	.		0.677	CHST12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060170.3	NM_018641		A	2472863	C	A	2472863	3	1	259	1	0	0	0	0	1	0	0	0	3402	652	23	1	591	1	CHST12	7	2472863	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	1591148	2472863	156665800	335	36653										
LFNG	3955	hgsc.bcm.edu	37	chr7	2552813	2552813	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccaagcagatctgggcatggAgcaaatgctcaggaaggctg	14	9	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:2552813A>G	ENST00000402506.1	+	2	196	c.70A>G	c.(70-72)Agc>Ggc	p.S24G		NM_001166355.1	NP_001159827.1	Q8NES3	LFNG_HUMAN	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	0					compartment pattern specification (GO:0007386)|female meiotic division (GO:0007143)|metabolic process (GO:0008152)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|ovarian follicle development (GO:0001541)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of protein binding (GO:0032092)|regulation of Notch signaling pathway (GO:0008593)|regulation of somitogenesis (GO:0014807)|somitogenesis (GO:0001756)	extracellular region (GO:0005576)|integral component of Golgi membrane (GO:0030173)|vesicle (GO:0031982)	metal ion binding (GO:0046872)|O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity (GO:0033829)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)|urinary_tract(2)	6		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.54e-14)		CTGGGCATGGAGCAAATGCTC	0.542																																					p.S24G		Atlas-SNP	.											.	LFNG	57	.	0			c.A70G						.						150	138	141					7																	2552813		1568	3582	5150	SO:0001583	missense	3955	exon2			GCATGGAGCAAAT	BC014851	CCDS34586.1, CCDS34587.1, CCDS55081.1, CCDS55082.1	7p22.3	2013-02-19	2006-11-13		ENSG00000106003	ENSG00000106003	2.4.1.222	"Beta 3-glycosyltransferases"	6560	protein-coding gene	gene with protein product		602576	"lunatic fringe (Drosophila) homolog", "lunatic fringe homolog (Drosophila)"			9878264, 9187150	Standard	NM_001166355		Approved	SCDO3	uc003smf.3	Q8NES3	OTTHUMG00000152043	ENST00000402506.1:c.70A>G	chr7.hg19:g.2552813A>G	ENSP00000385764:p.Ser24Gly	140.0	0.0		98.0	4.0	NM_001166355	B3KTY6|B5MCR5|O00589|Q96C39|Q9UJW5	Missense_Mutation	SNP	ENST00000402506.1	hg19	CCDS55081.1	.	.	.	.	.	.	.	.	.	.	A	10.57	1.386861	0.25031	.	.	ENSG00000106003	ENST00000402506	T	0.56275	0.47	2.87	-5.74	0.02391	.	.	.	.	.	T	0.23330	0.0564	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.15954	-1.0419	7	0.30078	T	0.28	.	3.2979	0.06973	0.231:0.0:0.2547:0.5143	.	.	.	.	G	24	ENSP00000385764:S24G	ENSP00000385764:S24G	S	+	1	0	LFNG	2519339	0.013000	0.17824	0.000000	0.03702	0.010000	0.07245	0.353000	0.20130	-0.999000	0.03442	-0.415000	0.06103	AGC	.	.		0.542	LFNG-003	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000325023.1	NM_002304		G	2552813	A	G	2552813	3	3	259	1	0	0	0	0	1	0	0	0	8746	304	11	2	76	2	LFNG	7	2552813	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	79950	2552813	156585850	336	36654										
TNRC18	84629	hgsc.bcm.edu	37	chr7	5391469	5391469	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccttggtcaaacgattcctcCgaagagtcgctgaaggagga	12	10	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:5391469C>A	ENST00000430969.1	-	17	5799	c.5451G>T	c.(5449-5451)tcG>tcT	p.S1817S	TNRC18_ENST00000399537.4_Silent_p.S1817S	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1817							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		ACGATTCCTCCGAAGAGTCGC	0.582																																					p.S1817S		Atlas-SNP	.											.	TNRC18	311	.	0			c.G5451T						.						18	16	17					7																	5391469		1567	3582	5149	SO:0001819	synonymous_variant	84629	exon17			TTCCTCCGAAGAG	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"Trinucleotide (CAG) repeat containing"	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.5451G>T	chr7.hg19:g.5391469C>A		163.0	0.0		99.0	4.0	NM_001080495	A8MX41|Q96JH1|Q96K91	Silent	SNP	ENST00000430969.1	hg19	CCDS47534.1																																																																																			.	.		0.582	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				A	5391469	C	A	5391469	2	1	259	1	0	0	0	0	0	0	0	1	16354	639	23	1		1	TNRC18	7	5391469	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	2838656	5391469	153747194	337	36655										
TNRC18	84629	hgsc.bcm.edu	37	chr7	5396822	5396822	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgaagggcgacttcaacttgTcctgcttggtgagggagagg	16	7	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:5396822T>C	ENST00000430969.1	-	16	5267	c.4919A>G	c.(4918-4920)gAc>gGc	p.D1640G	TNRC18_ENST00000399537.4_Missense_Mutation_p.D1640G	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1640							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		CTTCAACTTGTCCTGCTTGGT	0.552																																					p.D1640G		Atlas-SNP	.											.	TNRC18	311	.	0			c.A4919G						.						45	45	45					7																	5396822		2033	4184	6217	SO:0001583	missense	84629	exon16			AACTTGTCCTGCT	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"Trinucleotide (CAG) repeat containing"	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.4919A>G	chr7.hg19:g.5396822T>C	ENSP00000395538:p.Asp1640Gly	212.0	0.0		199.0	9.0	NM_001080495	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	hg19	CCDS47534.1	.	.	.	.	.	.	.	.	.	.	t	15.07	2.725089	0.48833	.	.	ENSG00000182095	ENST00000399537;ENST00000430969;ENST00000399544;ENST00000440081	T;T;T	0.42900	2.67;2.69;0.96	5.25	5.25	0.73442	.	0.000000	0.41938	D	0.000788	T	0.39759	0.1090	M	0.61703	1.905	0.33662	D	0.609793	B;B	0.33940	0.433;0.236	B;B	0.30029	0.11;0.031	T	0.53830	-0.8383	10	0.23891	T	0.37	.	15.1664	0.72828	0.0:0.0:0.0:1.0	.	695;1640	A8MSW5;O15417	.;TNC18_HUMAN	G	1640;1640;695;130	ENSP00000382452:D1640G;ENSP00000395538:D1640G;ENSP00000395990:D130G	ENSP00000382452:D1640G	D	-	2	0	TNRC18	5363348	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.801000	0.62532	1.988000	0.58038	0.459000	0.35465	GAC	.	.		0.552	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				C	5396822	T	C	5396822	3	2	259	1	0	0	0	0	1	0	0	0	16354	1667	58	2	4047	2	TNRC18	7	5396822	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	5353	5396822	153741841	338	36656										
EIF2AK1	27102	hgsc.bcm.edu	37	chr7	6078226	6078226	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	catactcccggccccgcttgTttctctcgactatccaatcc	5	18	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:6078226T>C	ENST00000199389.6	-	10	1342	c.1196A>G	c.(1195-1197)aAc>aGc	p.N399S	EIF2AK1_ENST00000495565.1_5'Flank|EIF2AK1_ENST00000536084.1_Missense_Mutation_p.N275S	NM_001134335.1|NM_014413.3	NP_001127807.1|NP_055228.2	Q9BQI3	E2AK1_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 1	399	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of cell proliferation (GO:0008285)|negative regulation of hemoglobin biosynthetic process (GO:0046986)|negative regulation of translational initiation by iron (GO:0045993)|protein autophosphorylation (GO:0046777)|protoporphyrinogen IX metabolic process (GO:0046501)|regulation of eIF2 alpha phosphorylation by heme (GO:0010999)|response to external stimulus (GO:0009605)|response to stress (GO:0006950)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|heme binding (GO:0020037)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	27		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.106)|OV - Ovarian serous cystadenocarcinoma(56;5.22e-14)		GCCCCGCTTGTTTCTCTCGAC	0.562																																					p.N399S		Atlas-SNP	.											.	EIF2AK1	76	.	0			c.A1196G						.						136	127	130					7																	6078226		2203	4300	6503	SO:0001583	missense	27102	exon10			CGCTTGTTTCTCT	BC006524	CCDS5345.1	7p22	2005-01-20			ENSG00000086232	ENSG00000086232			24921	protein-coding gene	gene with protein product	"heme regulated initiation factor 2 alpha kinase"	613635				7709427, 10718198	Standard	NM_014413		Approved	HRI, KIAA1369	uc003spp.3	Q9BQI3	OTTHUMG00000090689	ENST00000199389.6:c.1196A>G	chr7.hg19:g.6078226T>C	ENSP00000199389:p.Asn399Ser	84.0	0.0		86.0	4.0	NM_014413	A8K2R2|Q549K6|Q8NBW3|Q9HC02|Q9NYE0|Q9P0V6|Q9P1J5|Q9P2H8|Q9UHG4	Missense_Mutation	SNP	ENST00000199389.6	hg19	CCDS5345.1	.	.	.	.	.	.	.	.	.	.	.	22.6	4.317420	0.81469	.	.	ENSG00000086232	ENST00000199389;ENST00000536084;ENST00000426957	T;T	0.69175	-0.38;1.88	5.74	5.74	0.90152	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.042140	0.85682	D	0.000000	T	0.75583	0.3869	L	0.47078	1.49	0.54753	D	0.999984	D;D;P	0.71674	0.998;0.981;0.62	D;P;B	0.66196	0.942;0.661;0.422	T	0.75071	-0.3447	10	0.41790	T	0.15	-22.7794	15.7044	0.77565	0.0:0.0:0.0:1.0	.	275;398;399	B4DIP4;Q9BQI3-2;Q9BQI3	.;.;E2AK1_HUMAN	S	399;275;26	ENSP00000199389:N399S;ENSP00000445784:N275S	ENSP00000199389:N399S	N	-	2	0	EIF2AK1	6044752	1.000000	0.71417	0.443000	0.26883	0.060000	0.15804	4.807000	0.62576	2.181000	0.69327	0.528000	0.53228	AAC	.	.		0.562	EIF2AK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207373.2	NM_014413		C	6078226	T	C	6078226	3	2	259	1	0	0	0	0	1	0	0	0	4998	1725	60	2	720	2	EIF2AK1	7	6078226	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	681404	6078226	153060437	339	36657										
COL28A1	340267	hgsc.bcm.edu	37	chr7	7572478	7572478	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	taaacgctgacaaaagcaggAgatagaagacaaaatatctg	9	6	1	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:7572478A>G	ENST00000399429.3	-	2	169	c.29T>C	c.(28-30)cTc>cCc	p.L10P		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	10					cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		CAAAAGCAGGAGATAGAAGAC	0.353																																					p.L10P		Atlas-SNP	.											.	COL28A1	113	.	0			c.T29C						.						134	124	127					7																	7572478		1867	4112	5979	SO:0001583	missense	340267	exon2			AGCAGGAGATAGA	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"Collagens"	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.29T>C	chr7.hg19:g.7572478A>G	ENSP00000382356:p.Leu10Pro	81.0	0.0		81.0	4.0	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Missense_Mutation	SNP	ENST00000399429.3	hg19	CCDS43553.1	.	.	.	.	.	.	.	.	.	.	A	8.338	0.828124	0.16749	.	.	ENSG00000215018	ENST00000399429;ENST00000399419;ENST00000448652	D	0.89617	-2.54	4.28	3.11	0.35812	.	0.536026	0.15628	U	0.252502	D	0.87589	0.6215	N	0.24115	0.695	0.30233	N	0.795696	D	0.64830	0.994	P	0.59288	0.855	T	0.82855	-0.0251	10	0.72032	D	0.01	-4.7079	9.4504	0.38723	0.8389:0.0:0.1611:0.0	.	10	Q2UY09	COSA1_HUMAN	P	10	ENSP00000382356:L10P	ENSP00000382347:L10P	L	-	2	0	COL28A1	7539003	0.265000	0.24102	0.648000	0.29521	0.008000	0.06430	1.247000	0.32815	0.284000	0.22305	-1.450000	0.01041	CTC	.	.		0.353	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763		G	7572478	A	G	7572478	3	3	259	1	0	0	0	0	1	0	0	0	3688	304	11	2	3484	2	COL28A1	7	7572478	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1494252	7572478	151566185	340	36658										
SCIN	85477	hgsc.bcm.edu	37	chr7	12662452	12662452	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggggaaaagccagagcttccAgatggaggtgatgatgatga	16	5	0	6			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:12662452A>G	ENST00000297029.5	+	5	794	c.693A>G	c.(691-693)ccA>ccG	p.P231P	SCIN_ENST00000519209.1_5'UTR|SCIN_ENST00000445618.2_5'UTR|SCIN_ENST00000473722.1_3'UTR	NM_001112706.2	NP_001106177.1	Q9Y6U3	ADSV_HUMAN	scinderin	231	Actin-severing. {ECO:0000255}.				actin filament capping (GO:0051693)|actin filament severing (GO:0051014)|actin nucleation (GO:0045010)|calcium ion-dependent exocytosis (GO:0017156)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of secretion (GO:0051047)|regulation of chondrocyte differentiation (GO:0032330)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	1-phosphatidylinositol binding (GO:0005545)|actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	17				UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		CAGAGCTTCCAGATGGAGGTG	0.383																																					p.P231P		Atlas-SNP	.											.	SCIN	105	.	0			c.A693G						.						160	156	157					7																	12662452		1887	4124	6011	SO:0001819	synonymous_variant	85477	exon5			GCTTCCAGATGGA	AF276507	CCDS47545.1, CCDS47546.1	7p21.3	2006-04-25			ENSG00000006747	ENSG00000006747			21695	protein-coding gene	gene with protein product		613416					Standard	NM_033128		Approved	adseverin, KIAA1905	uc003ssn.4	Q9Y6U3	OTTHUMG00000152385	ENST00000297029.5:c.693A>G	chr7.hg19:g.12662452A>G		83.0	0.0		89.0	4.0	NM_001112706	A8K2U8|Q8NBZ6|Q8WU97|Q96JC7|Q96PY2	Silent	SNP	ENST00000297029.5	hg19	CCDS47545.1																																																																																			.	.		0.383	SCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326041.1	NM_033128		G	12662452	A	G	12662452	2	3	259	1	0	0	0	0	0	0	0	1	13920	175	7	2		2	SCIN	7	12662452	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	5089974	12662452	146476211	341	36659										
KLHL7	55975	hgsc.bcm.edu	37	chr7	23180386	23180386	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tttattttctttctgtgtttAggtataagtgtgctagcgga	10	4	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:23180386A>G	ENST00000339077.5	+	5	685		c.e5-1		KLHL7_ENST00000409689.1_Splice_Site|KLHL7_ENST00000539124.1_Splice_Site|KLHL7_ENST00000322231.7_Splice_Site|KLHL7_ENST00000545443.1_Splice_Site|KLHL7_ENST00000542558.1_Splice_Site|KLHL7_ENST00000479288.1_Splice_Site	NM_001031710.2	NP_001026880.2	Q8IXQ5	KLHL7_HUMAN	kelch-like family member 7						protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TTCTGTGTTTAGGTATAAGTG	0.318																																					.		Atlas-SNP	.											KLHL7_ENST00000339077,NS,carcinoma,0,4	KLHL7	102	.	0			c.443-2A>G						.						59	59	59					7																	23180386		2203	4300	6503	SO:0001630	splice_region_variant	55975	exon5			GTGTTTAGGTATA		CCDS5378.1, CCDS34609.1, CCDS5378.2, CCDS55095.1	7p15.3	2013-01-30	2013-01-30		ENSG00000122550	ENSG00000122550		"Kelch-like", "BTB/POZ domain containing"	15646	protein-coding gene	gene with protein product	"retinitis pigmentosa 42"	611119	"kelch-like 7 (Drosophila)"			19520207	Standard	NM_001031710		Approved	KLHL6, SBBI26, RP42	uc003svs.4	Q8IXQ5	OTTHUMG00000094813	ENST00000339077.5:c.443-1A>G	chr7.hg19:g.23180386A>G		77.0	0.0		70.0	3.0	NM_001031710	A4D144|B7Z5I9|G5E9G3|Q7Z765|Q96MV2|Q9BQF8|Q9UDQ9	Splice_Site	SNP	ENST00000339077.5	hg19	CCDS34609.1	.	.	.	.	.	.	.	.	.	.	A	13.38	2.220187	0.39201	.	.	ENSG00000122550	ENST00000322231;ENST00000339077;ENST00000539124;ENST00000409689;ENST00000545443	.	.	.	5.07	5.07	0.68467	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1304	0.72517	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	KLHL7	23146911	1.000000	0.71417	0.978000	0.43139	0.327000	0.28475	8.606000	0.90888	2.032000	0.59987	0.379000	0.24179	.	.	.		0.318	KLHL7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326860.3	NM_018846	Intron	G	23180386	A	G	23180386	5	3	259	1	0	0	0	0	0	0	1	0	8403	434	15	2	522	2	KLHL7	7	23180386	Splice_Site	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	10517934	23180386	135958277	342	36660										
HIBADH	11112	hgsc.bcm.edu	37	chr7	27672052	27672052	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tttttcagcaacatctgctgGggaagatactacctttaaaa	7	8	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:27672052G>T	ENST00000265395.2	-	3	471	c.265C>A	c.(265-267)Cca>Aca	p.P89T		NM_152740.3	NP_689953.1	P31937	3HIDH_HUMAN	3-hydroxyisobutyrate dehydrogenase	89					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|pentose-phosphate shunt (GO:0006098)|small molecule metabolic process (GO:0044281)|valine catabolic process (GO:0006574)	mitochondrial matrix (GO:0005759)	3-hydroxyisobutyrate dehydrogenase activity (GO:0008442)|NAD binding (GO:0051287)|phosphogluconate dehydrogenase (decarboxylating) activity (GO:0004616)			endometrium(4)|kidney(2)|lung(3)|ovary(2)|prostate(1)	12			GBM - Glioblastoma multiforme(3;0.0368)			ACATCTGCTGGGGAAGATACT	0.368																																					p.P89T		Atlas-SNP	.											.	HIBADH	28	.	0			c.C265A						.						110	106	107					7																	27672052		2203	4300	6503	SO:0001583	missense	11112	exon3			CTGCTGGGGAAGA	AF529362	CCDS5414.1	7p15	2009-06-12			ENSG00000106049	ENSG00000106049	1.1.1.31		4907	protein-coding gene	gene with protein product		608475					Standard	NM_152740		Approved	NS5ATP1	uc003szf.3	P31937	OTTHUMG00000097035	ENST00000265395.2:c.265C>A	chr7.hg19:g.27672052G>T	ENSP00000265395:p.Pro89Thr	86.0	0.0		76.0	4.0	NM_152740	Q546Z2|Q9UDN3	Missense_Mutation	SNP	ENST00000265395.2	hg19	CCDS5414.1	.	.	.	.	.	.	.	.	.	.	G	15.19	2.759483	0.49468	.	.	ENSG00000106049	ENST00000265395	T	0.37915	1.17	5.8	5.8	0.92144	6-phosphogluconate dehydrogenase, NADP-binding (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.50633	0.1627	M	0.77103	2.36	0.80722	D	1	P;P	0.37997	0.614;0.614	B;B	0.43155	0.41;0.41	T	0.47129	-0.9141	10	0.39692	T	0.17	-23.3127	20.0643	0.97702	0.0:0.0:1.0:0.0	.	89;89	Q546Z2;P31937	.;3HIDH_HUMAN	T	89	ENSP00000265395:P89T	ENSP00000265395:P89T	P	-	1	0	HIBADH	27638577	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.138000	0.94501	2.737000	0.93849	0.650000	0.86243	CCA	.	.		0.368	HIBADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214132.1	NM_152740		T	27672052	G	T	27672052	3	4	259	1	0	0	0	0	1	0	0	0	7108	1232	43	3	769	3	HIBADH	7	27672052	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	4491666	27672052	131466611	343	36661										
TAX1BP1	8887	hgsc.bcm.edu	37	chr7	27832797	27832797	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atttaaggaatgccaaaggcTccaaaaacaaataaacaaac	5	8	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:27832797T>C	ENST00000396319.2	+	10	1464	c.1376T>C	c.(1375-1377)cTc>cCc	p.L459P	TAX1BP1_ENST00000433216.2_Missense_Mutation_p.L302P|TAX1BP1_ENST00000543117.1_Missense_Mutation_p.L459P|TAX1BP1_ENST00000265393.6_Missense_Mutation_p.L459P|TAX1BP1_ENST00000409980.1_Missense_Mutation_p.L459P	NM_006024.6	NP_006015.4	Q86VP1	TAXB1_HUMAN	Tax1 (human T-cell leukemia virus type I) binding protein 1	459					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)	cytosol (GO:0005829)	kinase binding (GO:0019900)			breast(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(8)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31			GBM - Glioblastoma multiforme(3;0.0823)			TGCCAAAGGCTCCAAAAACAA	0.313																																					p.L459P		Atlas-SNP	.											.	TAX1BP1	71	.	0			c.T1376C						.						34	36	35					7																	27832797		2203	4300	6503	SO:0001583	missense	8887	exon10			AAAGGCTCCAAAA	U33821	CCDS5415.1, CCDS43561.1, CCDS56471.1	7p15	2010-08-05			ENSG00000106052	ENSG00000106052			11575	protein-coding gene	gene with protein product		605326				10435631	Standard	NM_006024		Approved	TXBP151, CALCOCO3	uc003szl.3	Q86VP1	OTTHUMG00000023377	ENST00000396319.2:c.1376T>C	chr7.hg19:g.27832797T>C	ENSP00000379612:p.Leu459Pro	142.0	0.0		122.0	5.0	NM_006024	B4DKU7|E7ENV2|O60398|O95770|Q13311|Q9BQG5|Q9UI88	Missense_Mutation	SNP	ENST00000396319.2	hg19	CCDS5415.1	.	.	.	.	.	.	.	.	.	.	T	16.88	3.245160	0.59103	.	.	ENSG00000106052	ENST00000543117;ENST00000265393;ENST00000409980;ENST00000433216;ENST00000396319;ENST00000457186	T;T;T;T;T	0.16457	2.34;2.34;2.34;2.34;2.34	5.9	4.74	0.60224	.	0.000000	0.48286	D	0.000193	T	0.39963	0.1098	M	0.66939	2.045	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.998	T	0.23476	-1.0187	10	0.87932	D	0	-6.0552	13.3552	0.60623	0.0:0.0:0.1316:0.8684	.	302;459;459	E7ENV2;Q86VP1;Q86VP1-2	.;TAXB1_HUMAN;.	P	459;459;459;302;459;14	ENSP00000444811:L459P;ENSP00000265393:L459P;ENSP00000386515:L459P;ENSP00000391907:L302P;ENSP00000379612:L459P	ENSP00000265393:L459P	L	+	2	0	TAX1BP1	27799322	1.000000	0.71417	1.000000	0.80357	0.500000	0.33767	7.537000	0.82033	1.038000	0.40049	0.528000	0.53228	CTC	.	.		0.313	TAX1BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214142.1	NM_006024		C	27832797	T	C	27832797	3	2	259	1	0	0	0	0	1	0	0	0	15609	1551	54	2	1410	2	TAX1BP1	7	27832797	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	160745	27832797	131305866	344	36662										
ADCYAP1R1	117	hgsc.bcm.edu	37	chr7	31125006	31125006	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gcgatctccgtcttcatcaaAgactggattctgtatgcgga	10	10	5	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:31125006A>G	ENST00000304166.4	+	9	907	c.618A>G	c.(616-618)aaA>aaG	p.K206K	ADCYAP1R1_ENST00000396211.2_Silent_p.K206K|ADCYAP1R1_ENST00000409363.1_Silent_p.K185K|ADCYAP1R1_ENST00000409489.1_Silent_p.K206K	NM_001118.4|NM_001199635.1|NM_001199636.1	NP_001109.2|NP_001186564.1|NP_001186565.1	P41586	PACR_HUMAN	adenylate cyclase activating polypeptide 1 (pituitary) receptor type I	206					activation of adenylate cyclase activity (GO:0007190)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)|vasoactive intestinal polypeptide receptor activity (GO:0004999)			endometrium(1)|large_intestine(4)|liver(2)|lung(24)|ovary(1)|skin(2)|stomach(1)	35						TCTTCATCAAAGACTGGATTC	0.552																																					p.K206K	Ovarian(44;225 1186 2158 11092)	Atlas-SNP	.											.	ADCYAP1R1	78	.	0			c.A618G						.						191	152	165					7																	31125006		2203	4300	6503	SO:0001819	synonymous_variant	117	exon9			CATCAAAGACTGG		CCDS5433.1, CCDS56480.1, CCDS56481.1	7p14.3	2012-09-20			ENSG00000078549	ENSG00000078549		"GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"	242	protein-coding gene	gene with protein product	"PACAP receptor 1"	102981				7902709	Standard	NM_001199635		Approved	PAC1, PACAPR, PAC1R	uc003tcg.3	P41586	OTTHUMG00000023884	ENST00000304166.4:c.618A>G	chr7.hg19:g.31125006A>G		39.0	0.0		39.0	4.0	NM_001118	A8K1Y1|B7ZLA7|B8ZZK3|Q17S10	Silent	SNP	ENST00000304166.4	hg19	CCDS5433.1																																																																																			.	.		0.552	ADCYAP1R1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000215041.3	NM_001118		G	31125006	A	G	31125006	2	3	259	1	0	0	0	0	0	0	0	1	303	69	3	2		2	ADCYAP1R1	7	31125006	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	3292209	31125006	128013657	345	36663										
FKBP9	11328	hgsc.bcm.edu	37	chr7	33028263	33028263	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gggtatggagaggaaggaagAggtgagcatcagcatcacct	16	6	2	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:33028263A>G	ENST00000242209.4	+	6	1207	c.1038A>G	c.(1036-1038)agA>agG	p.R346R	FKBP9_ENST00000538443.1_Splice_Site_p.R208R|FKBP9_ENST00000490776.2_Splice_Site_p.R114R|AVL9_ENST00000404479.1_Intron|FKBP9_ENST00000538336.1_Splice_Site_p.R399R|FKBP9_ENST00000489038.1_3'UTR	NM_001284343.1|NM_007270.3	NP_001271272.1|NP_009201.2	O95302	FKBP9_HUMAN	FK506 binding protein 9, 63 kDa	346	PPIase FKBP-type 3. {ECO:0000255|PROSITE- ProRule:PRU00277}.				chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			central_nervous_system(13)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	39			GBM - Glioblastoma multiforme(11;0.0156)			AGGAAGGAAGAGGTGAGCATC	0.478																																					p.R346R		Atlas-SNP	.											.	FKBP9	335	.	0			c.A1038G						.						108	91	97					7																	33028263		2203	4300	6503	SO:0001630	splice_region_variant	11328	exon6			AGGAAGAGGTGAG	AF089745	CCDS5439.1, CCDS64622.1, CCDS64623.1	7p11.1	2013-01-10	2002-08-29		ENSG00000122642	ENSG00000122642		"EF-hand domain containing"	3725	protein-coding gene	gene with protein product			"FK506-binding protein 9 (63 kD)"			12036304	Standard	NM_007270		Approved	FKBP60, FKBP63	uc003tdh.3	O95302	OTTHUMG00000097847	ENST00000242209.4:c.1039+1A>G	chr7.hg19:g.33028263A>G		106.0	0.0		70.0	4.0	NM_007270	B3KY35|B7Z1G9|B7Z6H3|Q2M2A1|Q3MIR7|Q6IN76|Q6P2N1|Q96EX5|Q96IJ9	Silent	SNP	ENST00000242209.4	hg19	CCDS5439.1																																																																																			.	.		0.478	FKBP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215137.1	NM_007270	Silent	G	33028263	A	G	33028263	5	3	259	1	0	0	0	0	0	0	1	0	5923	318	11	2	1060	2	FKBP9	7	33028263	Splice_Site	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1903257	33028263	126110400	346	36664										
NT5C3	51251	hgsc.bcm.edu	37	chr7	33057200	33057200	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttggagcttatcaaagaaatTctcatatccttctctgtaag	6	8	3	1	rs186325627	byFrequency	TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:33057200T>C	ENST00000242210.7	-	7	635	c.559A>G	c.(559-561)Aat>Gat	p.N187D	NT5C3A_ENST00000405342.1_Missense_Mutation_p.N148D|NT5C3A_ENST00000381626.2_Missense_Mutation_p.N136D|NT5C3A_ENST00000396152.2_Missense_Mutation_p.N148D|NT5C3A_ENST00000409467.1_Missense_Mutation_p.N136D|AVL9_ENST00000404479.1_Intron|NT5C3A_ENST00000409787.1_Missense_Mutation_p.N148D|NT5C3A_ENST00000610140.1_Missense_Mutation_p.N182D	NM_001002009.2|NM_001002010.2	NP_001002009.1|NP_001002010.1	Q9H0P0	5NT3A_HUMAN	5'-nucleotidase, cytosolic IIIA	187					dephosphorylation (GO:0016311)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside metabolic process (GO:0006213)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	2'-phosphotransferase activity (GO:0008665)|5'-nucleotidase activity (GO:0008253)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)										TCAAAGAAATTCTCATATCCT	0.363																																					p.N187D		Atlas-SNP	.											.	.	.	.	0			c.A559G						.						128	126	127					7																	33057200		2203	4300	6503	SO:0001583	missense	0	exon7			AGAAATTCTCATA	AF312735	CCDS34616.1, CCDS34617.1, CCDS55101.1	7p14.3	2013-03-06	2013-03-06	2013-03-06	ENSG00000122643	ENSG00000122643	3.1.3.5		17820	protein-coding gene	gene with protein product	"lupin"	606224	"5'-nucleotidase, cytosolic III"	NT5C3		11042152, 10942414	Standard	NM_001002010		Approved	UMPH1, PSN1, PN-I, UMPH, P5'N-1, cN-III, p36, POMP, hUMP1	uc003tdk.4	Q9H0P0	OTTHUMG00000152983	ENST00000242210.7:c.559A>G	chr7.hg19:g.33057200T>C	ENSP00000242210:p.Asn187Asp	124.0	0.0		99.0	4.0	NM_001002010	A8K253|B2RAA5|B8ZZC4|Q6IPZ1|Q6NXS6|Q7L3G6|Q9P0P5|Q9UC42|Q9UC43|Q9UC44|Q9UC45	Missense_Mutation	SNP	ENST00000242210.7	hg19	CCDS34616.1	.	.	.	.	.	.	.	.	.	.	T	10.39	1.337953	0.24253	.	.	ENSG00000122643	ENST00000381626;ENST00000396152;ENST00000242210;ENST00000405342;ENST00000409467;ENST00000409787	D;D;D;D;D;D	0.82526	-1.62;-1.62;-1.62;-1.62;-1.62;-1.62	5.19	-2.49	0.06403	HAD-like domain (2);	0.456245	0.25532	N	0.030036	T	0.58906	0.2155	N	0.16567	0.415	0.25846	N	0.983995	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.41840	-0.9486	10	0.14252	T	0.57	.	2.588	0.04835	0.0942:0.2194:0.1763:0.5101	.	187;148	Q9H0P0;Q9H0P0-1	5NT3_HUMAN;.	D	136;148;187;148;136;148	ENSP00000371039:N136D;ENSP00000379456:N148D;ENSP00000242210:N187D;ENSP00000385261:N148D;ENSP00000387166:N136D;ENSP00000387205:N148D	ENSP00000242210:N187D	N	-	1	0	NT5C3	33023725	0.199000	0.23386	0.995000	0.50966	0.991000	0.79684	0.377000	0.20552	-0.239000	0.09710	0.533000	0.62120	AAT	.	T|0.999;G|0.001		0.363	NT5C3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328880.1	NM_016489		C	33057200	T	C	33057200	3	2	259	1	0	0	0	0	1	0	0	0	10697	1783	62	2	463	2	NT5C3	7	33057200	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	28937	33057200	126081463	347	36665										
AOAH	313	hgsc.bcm.edu	37	chr7	36763688	36763688	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tcatcgttggctggagaggcCgaggactgaagagacaggag	17	7	1	3	rs2228411	byFrequency	TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:36763688C>A	ENST00000258749.5	-	1	465	c.66G>T	c.(64-66)tcG>tcT	p.S22S	AOAH_ENST00000535891.1_Silent_p.S22S|AOAH_ENST00000431169.1_Silent_p.S22S	NM_001637.3	NP_001628.1	P28039	AOAH_HUMAN	acyloxyacyl hydrolase (neutrophil)	22					inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|lipopolysaccharide metabolic process (GO:0008653)|negative regulation of inflammatory response (GO:0050728)	extracellular region (GO:0005576)	acyloxyacyl hydrolase activity (GO:0050528)|catalytic activity (GO:0003824)|lipoprotein lipase activity (GO:0004465)	p.S22S(1)		NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(21)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	41						CTGGAGAGGCCGAGGACTGAA	0.512																																					p.S22S		Atlas-SNP	.											AOAH,NS,carcinoma,0,2	AOAH	79	.	1	Substitution - coding silent(1)	stomach(1)	c.G66T						.						57	63	61					7																	36763688		2203	4300	6503	SO:0001819	synonymous_variant	313	exon1			AGAGGCCGAGGAC	BC025698	CCDS5448.1, CCDS55102.1, CCDS75584.1	7p14-p12	2014-03-14			ENSG00000136250	ENSG00000136250	3.1.1.77		548	protein-coding gene	gene with protein product		102593				1883828	Standard	NM_001637		Approved		uc022abu.1	P28039	OTTHUMG00000023566	ENST00000258749.5:c.66G>T	chr7.hg19:g.36763688C>A		79.0	0.0		70.0	3.0	NM_001177507	A4D1Y5|B7Z490|Q53F13	Silent	SNP	ENST00000258749.5	hg19	CCDS5448.1																																																																																			.	C|0.590;T|0.410		0.512	AOAH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219829.2	NM_001637		A	36763688	C	A	36763688	2	1	259	1	0	0	0	0	0	0	0	1	726	639	23	1		1	AOAH	7	36763688	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	3706488	36763688	122374975	348	36666										
VPS41	27072	hgsc.bcm.edu	37	chr7	38781711	38781711	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccaatgttgtttaacaagccAgtaataaatgctacaaaata	5	7	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:38781711A>G	ENST00000310301.4	-	25	2187	c.2133T>C	c.(2131-2133)acT>acC	p.T711T	VPS41_ENST00000395969.2_Silent_p.T686T	NM_014396.3	NP_055211.2	P49754	VPS41_HUMAN	vacuolar protein sorting 41 homolog (S. cerevisiae)	711					Golgi vesicle transport (GO:0048193)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	cytosol (GO:0005829)|early endosome (GO:0005769)|Golgi-associated vesicle (GO:0005798)|HOPS complex (GO:0030897)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	44						TTAACAAGCCAGTAATAAATG	0.318																																					p.T711T		Atlas-SNP	.											.	VPS41	102	.	0			c.T2133C						.						53	53	53					7																	38781711		2203	4299	6502	SO:0001819	synonymous_variant	27072	exon25			CAAGCCAGTAATA	U87309	CCDS5457.1, CCDS5458.2	7p14.1-p13	2009-05-08	2006-12-19		ENSG00000006715	ENSG00000006715			12713	protein-coding gene	gene with protein product		605485	"vacuolar protein sorting 41 (yeast homolog)", "vacuolar protein sorting 41 (yeast)"			9159129	Standard	NM_080631		Approved	HVSP41	uc003tgy.3	P49754	OTTHUMG00000023629	ENST00000310301.4:c.2133T>C	chr7.hg19:g.38781711A>G		135.0	0.0		96.0	4.0	NM_014396	E9PF36|Q86TP8|Q99851|Q99852	Silent	SNP	ENST00000310301.4	hg19	CCDS5457.1																																																																																			.	.		0.318	VPS41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226986.3			G	38781711	A	G	38781711	2	3	259	1	0	0	0	0	0	0	0	1	17225	175	7	2		2	VPS41	7	38781711	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2018023	38781711	120356952	349	36667										
STK17A	9263	hgsc.bcm.edu	37	chr7	43663335	43663335	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggagtgttaacatatgtcatGcttacaggaatatcaccttt	8	7	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:43663335G>T	ENST00000319357.5	+	6	947	c.768G>T	c.(766-768)atG>atT	p.M256I		NM_004760.2	NP_004751.2	Q9UEE5	ST17A_HUMAN	serine/threonine kinase 17a	256	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast apoptotic process (GO:2000271)|protein phosphorylation (GO:0006468)|regulation of reactive oxygen species metabolic process (GO:2000377)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2)	11						CATATGTCATGCTTACAGGAA	0.289																																					p.M256I		Atlas-SNP	.											.	STK17A	31	.	0			c.G768T						.						97	96	96					7																	43663335		2201	4297	6498	SO:0001583	missense	9263	exon6			TGTCATGCTTACA	AB011420	CCDS5470.1	7p13	2008-05-15	2007-02-12		ENSG00000164543	ENSG00000164543			11395	protein-coding gene	gene with protein product	"death-associated protein kinase-related 1"	604726	"serine/threonine kinase 17a (apoptosis-inducing)"			9786912	Standard	NM_004760		Approved	DRAK1	uc003tih.3	Q9UEE5	OTTHUMG00000022825	ENST00000319357.5:c.768G>T	chr7.hg19:g.43663335G>T	ENSP00000319192:p.Met256Ile	81.0	0.0		82.0	5.0	NM_004760	A4D1V6|Q8IVC8	Missense_Mutation	SNP	ENST00000319357.5	hg19	CCDS5470.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.863338	0.91511	.	.	ENSG00000164543	ENST00000319357	T	0.41758	0.99	4.98	4.98	0.66077	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000020	T	0.52901	0.1763	N	0.25031	0.7	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.59904	-0.7366	10	0.87932	D	0	.	18.2488	0.89996	0.0:0.0:1.0:0.0	.	256	Q9UEE5	ST17A_HUMAN	I	256	ENSP00000319192:M256I	ENSP00000319192:M256I	M	+	3	0	STK17A	43629860	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.183000	0.94887	2.278000	0.76064	0.563000	0.77884	ATG	.	.		0.289	STK17A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250902.1	NM_004760		T	43663335	G	T	43663335	3	4	259	1	0	0	0	0	1	0	0	0	15305	1319	46	3	790	3	STK17A	7	43663335	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	4881624	43663335	115475328	350	36668										
DBNL	28988	hgsc.bcm.edu	37	chr7	44098959	44098959	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acccgggtttgcaggcaagcTgaggagccccttcctgcaga	13	13	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:44098959T>C	ENST00000448521.1	+	10	940	c.842T>C	c.(841-843)cTg>cCg	p.L281P	DBNL_ENST00000456905.1_Missense_Mutation_p.L233P|DBNL_ENST00000468694.1_Missense_Mutation_p.L290P|DBNL_ENST00000452943.1_Missense_Mutation_p.L257P|DBNL_ENST00000440166.1_Missense_Mutation_p.L178P|DBNL_ENST00000494774.1_Missense_Mutation_p.L282P|DBNL_ENST00000497184.1_3'UTR|DBNL_ENST00000490734.2_Missense_Mutation_p.L187P	NM_001014436.2	NP_001014436.1	Q9UJU6	DBNL_HUMAN	drebrin-like	281					activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|endocytosis (GO:0006897)|immune system process (GO:0002376)|neuron projection morphogenesis (GO:0048812)|podosome assembly (GO:0071800)|Rac protein signal transduction (GO:0016601)|synapse assembly (GO:0007416)	cell cortex (GO:0005938)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|podosome (GO:0002102)|postsynaptic density (GO:0014069)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|enzyme activator activity (GO:0008047)			breast(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)|stomach(1)	12						GCAGGCAAGCTGAGGAGCCCC	0.597																																					p.L290P	NSCLC(68;573 1327 18604 34760 37992)	Atlas-SNP	.											.	DBNL	26	.	0			c.T869C						.						38	39	38					7																	44098959		2203	4300	6503	SO:0001583	missense	28988	exon10			GCAAGCTGAGGAG	AF151364	CCDS34622.1, CCDS34623.1, CCDS47579.1, CCDS64633.1, CCDS64634.1	7p13	2004-07-22			ENSG00000136279	ENSG00000136279			2696	protein-coding gene	gene with protein product		610106				10087302	Standard	NM_014063		Approved	SH3P7, HIP-55	uc003tjq.4	Q9UJU6	OTTHUMG00000155350	ENST00000448521.1:c.842T>C	chr7.hg19:g.44098959T>C	ENSP00000411701:p.Leu281Pro	86.0	0.0		58.0	4.0	NM_001122956	A4D2I9|B4DEM2|C9J7P1|P84070|Q6IAI8|Q96F30|Q96K74|Q9HBN8|Q9NR72	Missense_Mutation	SNP	ENST00000448521.1	hg19	CCDS34623.1	.	.	.	.	.	.	.	.	.	.	T	16.59	3.166408	0.57476	.	.	ENSG00000136279	ENST00000448521;ENST00000456905;ENST00000440166;ENST00000452943;ENST00000468694;ENST00000494774;ENST00000490734;ENST00000539475	T;T;T;T;T;T;T	0.35048	1.71;2.04;1.99;2.03;1.33;1.73;2.0	5.32	5.32	0.75619	.	0.800992	0.11347	N	0.573412	T	0.60183	0.2249	M	0.66939	2.045	0.80722	D	1	D;D;P;D;P;D;D;B;D	0.89917	1.0;1.0;0.488;0.999;0.919;0.999;0.997;0.36;1.0	D;D;B;D;P;D;D;B;D	0.75484	0.957;0.959;0.23;0.959;0.548;0.959;0.973;0.173;0.986	T	0.53961	-0.8364	10	0.48119	T	0.1	-29.9077	14.9982	0.71449	0.0:0.0:0.0:1.0	.	178;230;211;233;187;257;290;281;282	B4DEM2;B4DXL9;B4DDU5;B4DDP6;C9J7P1;B4DDD6;Q9UJU6-3;Q9UJU6;Q9UJU6-2	.;.;.;.;.;.;.;DBNL_HUMAN;.	P	281;233;178;257;290;282;187;211	ENSP00000411701:L281P;ENSP00000416421:L233P;ENSP00000415173:L178P;ENSP00000405343:L257P;ENSP00000417653:L290P;ENSP00000419992:L282P;ENSP00000417749:L187P	ENSP00000415173:L178P	L	+	2	0	DBNL	44065484	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.929000	0.70096	2.024000	0.59613	0.456000	0.33151	CTG	.	.		0.597	DBNL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339572.2	NM_014063		C	44098959	T	C	44098959	3	2	259	1	0	0	0	0	1	0	0	0	4257	1580	55	2	907	2	DBNL	7	44098959	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	435624	44098959	115039704	351	36669										
OGDH	4967	hgsc.bcm.edu	37	chr7	44687303	44687303	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gaccccctggggattttggaTgctgatctggactcctccgt	12	12	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:44687303T>C	ENST00000222673.5	+	4	504	c.462T>C	c.(460-462)gaT>gaC	p.D154D	OGDH_ENST00000543843.1_Intron|OGDH_ENST00000443864.2_Silent_p.D154D|OGDH_ENST00000439616.2_Intron|OGDH_ENST00000444676.1_Silent_p.D154D|OGDH_ENST00000449767.1_Intron|OGDH_ENST00000447398.1_Intron	NM_002541.3	NP_002532.2	Q02218	ODO1_HUMAN	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	154					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|cerebellar cortex development (GO:0021695)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hippocampus development (GO:0021766)|lysine catabolic process (GO:0006554)|NADH metabolic process (GO:0006734)|olfactory bulb mitral cell layer development (GO:0061034)|pyramidal neuron development (GO:0021860)|small molecule metabolic process (GO:0044281)|striatum development (GO:0021756)|succinyl-CoA metabolic process (GO:0006104)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)|thalamus development (GO:0021794)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)|oxoglutarate dehydrogenase complex (GO:0045252)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (NAD+) activity (GO:0034602)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			breast(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	36					Valproic Acid(DB00313)	GGATTTTGGATGCTGATCTGG	0.537																																					p.D154D		Atlas-SNP	.											.	OGDH	145	.	0			c.T462C						.						121	112	115					7																	44687303		2203	4300	6503	SO:0001819	synonymous_variant	4967	exon4			TTTGGATGCTGAT	D10523	CCDS34627.1, CCDS47580.1, CCDS55107.1	7p13-p11.2	2010-11-23			ENSG00000105953	ENSG00000105953	1.2.4.2		8124	protein-coding gene	gene with protein product		613022				8020988, 1542694	Standard	NM_002541		Approved	E1k	uc003tln.3	Q02218	OTTHUMG00000155304	ENST00000222673.5:c.462T>C	chr7.hg19:g.44687303T>C		96.0	0.0		94.0	4.0	NM_002541	B4E2U9|D3DVL0|E9PBM1|Q96DD3|Q9UDX0	Silent	SNP	ENST00000222673.5	hg19	CCDS34627.1																																																																																			.	.		0.537	OGDH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339391.1			C	44687303	T	C	44687303	2	2	259	1	0	0	0	0	0	0	0	1	10848	1461	51	2		2	OGDH	7	44687303	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	588344	44687303	114451360	352	36670										
STX1A	6804	hgsc.bcm.edu	37	chr7	73119552	73119552	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttcttccagctcctccttcgTctctggggaggtagaaaggg	12	11	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:73119552T>C	ENST00000222812.3	-	4	237	c.211A>G	c.(211-213)Acg>Gcg	p.T71A	STX1A_ENST00000395156.3_Missense_Mutation_p.T71A|STX1A_ENST00000395154.3_Missense_Mutation_p.T71A|STX1A_ENST00000395155.3_Missense_Mutation_p.T71A	NM_004603.3	NP_004594.1	Q16623	STX1A_HUMAN	syntaxin 1A (brain)	71					calcium ion-dependent exocytosis (GO:0017156)|cellular protein metabolic process (GO:0044267)|energy reserve metabolic process (GO:0006112)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|neurotransmitter secretion (GO:0007269)|positive regulation of exocytosis (GO:0045921)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of insulin secretion (GO:0050796)|response to gravity (GO:0009629)|secretion by cell (GO:0032940)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|synaptic vesicle docking involved in exocytosis (GO:0016081)	actomyosin (GO:0042641)|cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|SNARE complex (GO:0031201)|synaptic vesicle membrane (GO:0030672)|synaptobrevin 2-SNAP-25-syntaxin-1a complex (GO:0070044)|synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex (GO:0070032)|synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex (GO:0070033)	calcium channel inhibitor activity (GO:0019855)			large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	5		Lung NSC(55;0.0908)|all_lung(88;0.198)				TCCTCCTTCGTCTCTGGGGAG	0.587																																					p.T71A		Atlas-SNP	.											.	STX1A	16	.	0			c.A211G						.						149	130	136					7																	73119552		2203	4300	6503	SO:0001583	missense	6804	exon4			CCTTCGTCTCTGG		CCDS34655.1, CCDS55120.1	7q11.2	2008-07-18			ENSG00000106089	ENSG00000106089			11433	protein-coding gene	gene with protein product		186590		STX1		1321498	Standard	NM_001165903		Approved	HPC-1, p35-1	uc003tyx.3	Q16623	OTTHUMG00000137422	ENST00000222812.3:c.211A>G	chr7.hg19:g.73119552T>C	ENSP00000222812:p.Thr71Ala	171.0	0.0		112.0	5.0	NM_004603	O15447|O15448|Q12936|Q75MD9|Q7Z5K3|Q9BPZ6	Missense_Mutation	SNP	ENST00000222812.3	hg19	CCDS34655.1	.	.	.	.	.	.	.	.	.	.	T	17.45	3.392774	0.62066	.	.	ENSG00000106089	ENST00000222812;ENST00000395156;ENST00000395154;ENST00000395155	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	4.67	4.67	0.58626	t-SNARE (1);Syntaxin, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.39682	0.1087	M	0.71036	2.16	0.80722	D	1	B;B;B	0.12630	0.006;0.002;0.0	B;B;B	0.10450	0.005;0.001;0.003	T	0.25813	-1.0121	10	0.12103	T	0.63	-27.0427	12.1051	0.53807	0.0:0.0:0.0:1.0	.	71;71;71	Q7Z5K3;Q16623-3;Q16623	.;.;STX1A_HUMAN	A	71	ENSP00000222812:T71A;ENSP00000378585:T71A;ENSP00000378583:T71A;ENSP00000378584:T71A	ENSP00000222812:T71A	T	-	1	0	STX1A	72757488	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	5.965000	0.70387	1.961000	0.56991	0.454000	0.30748	ACG	.	.		0.587	STX1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268422.1	NM_004603		C	73119552	T	C	73119552	3	2	259	1	0	0	0	0	1	0	0	0	15358	1667	58	2	683	2	STX1A	7	73119552	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	28432249	73119552	86019111	353	36671										
HIP1	3092	hgsc.bcm.edu	37	chr7	75186064	75186064	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aacctgaagctcccgttggcTtgtggcaagttcctgcttca	10	12	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:75186064T>C	ENST00000336926.6	-	17	1659	c.1633A>G	c.(1633-1635)Agc>Ggc	p.S545G	HIP1_ENST00000434438.2_Missense_Mutation_p.S545G	NM_005338.5	NP_005329.3	O00291	HIP1_HUMAN	huntingtin interacting protein 1	545					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell differentiation (GO:0030154)|clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|positive regulation of receptor-mediated endocytosis (GO:0048260)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|phosphatidylinositol binding (GO:0035091)|structural constituent of cytoskeleton (GO:0005200)			breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						TCCCGTTGGCTTGTGGCAAGT	0.463			T	PDGFRB	CMML																																p.S545G		Atlas-SNP	.		Dom	yes		7	7q11.23	3092	huntingtin interacting protein 1		L	.	HIP1	91	.	0			c.A1633G						.						113	115	114					7																	75186064		2203	4300	6503	SO:0001583	missense	3092	exon17			GTTGGCTTGTGGC	AF052288	CCDS34669.1, CCDS59060.1	7q11.23	2008-07-18			ENSG00000127946	ENSG00000127946			4913	protein-coding gene	gene with protein product		601767				9140394, 9147654	Standard	NM_005338		Approved	ILWEQ	uc003uds.2	O00291	OTTHUMG00000156050	ENST00000336926.6:c.1633A>G	chr7.hg19:g.75186064T>C	ENSP00000336747:p.Ser545Gly	70.0	0.0		43.0	4.0	NM_005338	B4E3I7|E7ES17|O00328|Q2TB58|Q8TDL4	Missense_Mutation	SNP	ENST00000336926.6	hg19	CCDS34669.1	.	.	.	.	.	.	.	.	.	.	T	8.497	0.863309	0.17250	.	.	ENSG00000127946	ENST00000336926;ENST00000434438	T;T	0.14516	2.72;2.5	5.93	5.93	0.95920	.	0.226266	0.64402	D	0.000011	T	0.14270	0.0345	L	0.50919	1.6	0.45502	D	0.998461	B;B	0.21225	0.0;0.053	B;B	0.19391	0.0;0.025	T	0.08371	-1.0725	10	0.15952	T	0.53	-15.3367	13.7453	0.62872	0.0:0.0:0.0:1.0	.	545;545	E7ES17;O00291	.;HIP1_HUMAN	G	545	ENSP00000336747:S545G;ENSP00000410300:S545G	ENSP00000336747:S545G	S	-	1	0	HIP1	75024000	1.000000	0.71417	0.983000	0.44433	0.051000	0.14879	4.648000	0.61425	2.257000	0.74773	0.533000	0.62120	AGC	.	.		0.463	HIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342863.2	NM_005338		C	75186064	T	C	75186064	3	2	259	1	0	0	0	0	1	0	0	0	7123	1609	56	2	1540	2	HIP1	7	75186064	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	2066512	75186064	83952599	354	36672										
FGL2	10875	hgsc.bcm.edu	37	chr7	76829024	76829024	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tttgctctttcatctttaatTtcctctgtttcattgtttgc	4	9	5	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:76829024T>C	ENST00000248598.5	-	1	119	c.87A>G	c.(85-87)gaA>gaG	p.E29E	RP11-467H10.2_ENST00000459742.1_RNA|CCDC146_ENST00000431197.1_Intron|CCDC146_ENST00000285871.4_Intron	NM_006682.2	NP_006673.1	Q14314	FGL2_HUMAN	fibrinogen-like 2	29						extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)				breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|skin(2)	13						CATCTTTAATTTCCTCTGTTT	0.498																																					p.E29E		Atlas-SNP	.											.	FGL2	40	.	0			c.A87G						.						96	95	95					7																	76829024		2203	4300	6503	SO:0001819	synonymous_variant	10875	exon1			TTTAATTTCCTCT	Z36531	CCDS5591.1	7q11.23	2013-02-06			ENSG00000127951	ENSG00000127951		"Fibrinogen C domain containing"	3696	protein-coding gene	gene with protein product		605351				7642106	Standard	NM_006682		Approved	pT49, T49	uc003ugb.3	Q14314	OTTHUMG00000130681	ENST00000248598.5:c.87A>G	chr7.hg19:g.76829024T>C		79.0	0.0		78.0	4.0	NM_006682		Silent	SNP	ENST00000248598.5	hg19	CCDS5591.1																																																																																			.	.		0.498	FGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253176.1	NM_006682		C	76829024	T	C	76829024	2	2	259	1	0	0	0	0	0	0	0	1	5881	1838	64	2		2	FGL2	7	76829024	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1642960	76829024	82309639	355	36673										
SEMA3D	223117	hgsc.bcm.edu	37	chr7	84666257	84666257	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	catactgcacccaacgatggTctgcactttccttatgagca	7	13	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:84666257T>C	ENST00000284136.6	-	10	1182	c.1139A>G	c.(1138-1140)gAc>gGc	p.D380G	SEMA3D_ENST00000484038.1_5'UTR	NM_152754.2	NP_689967.2	O95025	SEM3D_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	380	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(1)|breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(19)|lung(29)|ovary(3)|pancreas(1)|prostate(4)|skin(2)	73						CCAACGATGGTCTGCACTTTC	0.398																																					p.D380G	Ovarian(63;442 1191 17318 29975 31528)	Atlas-SNP	.											.	SEMA3D	177	.	0			c.A1139G						.						138	121	127					7																	84666257		2203	4300	6503	SO:0001583	missense	223117	exon10			CGATGGTCTGCAC	BC029590	CCDS34676.1	7q21.11	2013-01-11			ENSG00000153993	ENSG00000153993		"Semaphorins", "Immunoglobulin superfamily / V-set domain containing"	10726	protein-coding gene	gene with protein product		609907					Standard	NM_152754		Approved	coll-2, Sema-Z2	uc003uic.3	O95025	OTTHUMG00000154569	ENST00000284136.6:c.1139A>G	chr7.hg19:g.84666257T>C	ENSP00000284136:p.Asp380Gly	157.0	0.0		120.0	5.0	NM_152754	A6NK46|Q6UW77|Q8NCQ1	Missense_Mutation	SNP	ENST00000284136.6	hg19	CCDS34676.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.319342	0.81469	.	.	ENSG00000153993	ENST00000284136	T	0.22743	1.94	5.89	5.89	0.94794	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.43389	0.1245	L	0.55990	1.75	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.28459	-1.0043	10	0.72032	D	0.01	.	16.3071	0.82852	0.0:0.0:0.0:1.0	.	380	O95025	SEM3D_HUMAN	G	380	ENSP00000284136:D380G	ENSP00000284136:D380G	D	-	2	0	SEMA3D	84504193	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.965000	0.87945	2.250000	0.74265	0.477000	0.44152	GAC	.	.		0.398	SEMA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336084.2	NM_152754		C	84666257	T	C	84666257	3	2	259	1	0	0	0	0	1	0	0	0	14042	1667	58	2	1226	2	SEMA3D	7	84666257	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	7837233	84666257	74472406	356	36674										
ABCB1	5243	hgsc.bcm.edu	37	chr7	87214929	87214929	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tcatgagaggaagtccagccCcatggatgatggcagccaaa	12	10	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:87214929C>A	ENST00000265724.3	-	5	602	c.185G>T	c.(184-186)gGg>gTg	p.G62V	ABCB1_ENST00000543898.1_Missense_Mutation_p.G62V	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	62	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				drug transmembrane transport (GO:0006855)|G2/M transition of mitotic cell cycle (GO:0000086)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|stem cell proliferation (GO:0072089)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(14)|kidney(9)|large_intestine(14)|lung(48)|ovary(4)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	111	Esophageal squamous(14;0.00164)				Acebutolol(DB01193)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Adenosine triphosphate(DB00171)|ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Albendazole(DB00518)|Alfentanil(DB00802)|Alitretinoin(DB00523)|Amantadine(DB00915)|Aminohippurate(DB00345)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Amsacrine(DB00276)|Apixaban(DB06605)|Arsenic trioxide(DB01169)|Astemizole(DB00637)|Atazanavir(DB01072)|Atenolol(DB00335)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzocaine(DB01086)|Bepridil(DB01244)|Betamethasone(DB00443)|Biperiden(DB00810)|Boceprevir(DB08873)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Bromocriptine(DB01200)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Canagliflozin(DB08907)|Candesartan(DB00796)|Captopril(DB01197)|Carbamazepine(DB00564)|Carfilzomib(DB08889)|Carvedilol(DB01136)|Caspofungin(DB00520)|Chloroquine(DB00608)|Chlorpromazine(DB00477)|Chlorpropamide(DB00672)|Chlorprothixene(DB01239)|Cilazapril(DB01340)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisplatin(DB00515)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Clofazimine(DB00845)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabigatran etexilate(DB06695)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dipyridamole(DB00975)|Docetaxel(DB01248)|Domperidone(DB01184)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Dronedarone(DB04855)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Etravirine(DB06414)|Ezetimibe(DB00973)|Felodipine(DB01023)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fidaxomicin(DB08874)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluticasone furoate(DB08906)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gemcitabine(DB00441)|Glyburide(DB01016)|Gramicidin D(DB00027)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Imatinib(DB00619)|Imipramine(DB00458)|Indacaterol(DB05039)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketoconazole(DB01026)|Lamivudine(DB00709)|Lamotrigine(DB00555)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lenalidomide(DB00480)|Levetiracetam(DB01202)|Levofloxacin(DB01137)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Liothyronine(DB00279)|Liotrix(DB01583)|Lisinopril(DB00722)|Lomitapide(DB08827)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Mannitol(DB00742)|Maprotiline(DB00934)|Mebendazole(DB00643)|Mefloquine(DB00358)|Megestrol acetate(DB00351)|Meprobamate(DB00371)|Methadone(DB00333)|Methotrexate(DB00563)|Methylprednisolone(DB00959)|Metoprolol(DB00264)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mitomycin(DB00305)|Mitoxantrone(DB01204)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nadolol(DB01203)|Naloxone(DB01183)|Naltrexone(DB00704)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Neostigmine(DB01400)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nizatidine(DB00585)|Norethindrone(DB00717)|Olanzapine(DB00334)|Omeprazole(DB00338)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paroxetine(DB00715)|Pazopanib(DB06589)|Perindopril(DB00790)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Pitavastatin(DB08860)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pravastatin(DB00175)|Prazosin(DB00457)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Progesterone(DB00396)|Promethazine(DB01069)|Propafenone(DB01182)|Propranolol(DB00571)|Protriptyline(DB00344)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reboxetine(DB00234)|Regorafenib(DB08896)|Reserpine(DB00206)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Roxithromycin(DB00778)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Scopolamine(DB00747)|Selegiline(DB01037)|Sertraline(DB01104)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|SOFOSBUVIR(DB08934)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Streptozocin(DB00428)|Sulfinpyrazone(DB01138)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telaprevir(DB05521)|Telmisartan(DB00966)|Temsirolimus(DB06287)|Terazosin(DB01162)|Testosterone(DB00624)|Ticagrelor(DB08816)|Timolol(DB00373)|Tolvaptan(DB06212)|Topotecan(DB01030)|Toremifene(DB00539)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Vecuronium(DB01339)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voacamine(DB04877)|Zidovudine(DB00495)	AAGTCCAGCCCCATGGATGAT	0.393																																					p.G62V		Atlas-SNP	.											.	ABCB1	263	.	0			c.G185T						.						93	94	94					7																	87214929		2203	4300	6503	SO:0001583	missense	5243	exon5			CCAGCCCCATGGA	M14758	CCDS5608.1	7q21.12	2012-03-14	2004-05-12		ENSG00000085563	ENSG00000085563		"CD molecules", "ATP binding cassette transporters / subfamily B"	40	protein-coding gene	gene with protein product	"multidrug resistance protein 1"	171050	"colchicin sensitivity"	PGY1, MDR1, CLCS		3027054	Standard	NM_000927		Approved	P-gp, CD243, GP170, ABC20	uc003uiz.2	P08183	OTTHUMG00000023393	ENST00000265724.3:c.185G>T	chr7.hg19:g.87214929C>A	ENSP00000265724:p.Gly62Val	106.0	0.0		116.0	6.0	NM_000927	A8K294|B5AK60|Q12755|Q14812	Missense_Mutation	SNP	ENST00000265724.3	hg19	CCDS5608.1	.	.	.	.	.	.	.	.	.	.	C	10.85	1.467954	0.26335	.	.	ENSG00000085563	ENST00000265724;ENST00000543898	T;T	0.79033	-1.23;-1.23	5.72	5.72	0.89469	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.92283	0.7552	H	0.97440	4.005	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.949;1.0	D	0.94357	0.7584	10	0.72032	D	0.01	-22.2302	15.3886	0.74723	0.0:1.0:0.0:0.0	.	62;62	B5AK60;P08183	.;MDR1_HUMAN	V	62	ENSP00000265724:G62V;ENSP00000444095:G62V	ENSP00000265724:G62V	G	-	2	0	ABCB1	87052865	1.000000	0.71417	0.928000	0.36995	0.477000	0.33069	3.949000	0.56668	2.700000	0.92200	0.563000	0.77884	GGG	.	.		0.393	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2	NM_000927		A	87214929	C	A	87214929	3	1	259	1	0	0	0	0	1	0	0	0	40	623	22	3	3757	3	ABCB1	7	87214929	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	2548672	87214929	71923734	357	36675										
HEPACAM2	253012	hgsc.bcm.edu	37	chr7	92825188	92825188	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agcaacaaattcatatattcCgaagtcatccagagcatctt	5	10	3	1	rs145244580	byFrequency	TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:92825188C>A	ENST00000394468.2	-	8	1305	c.1228G>T	c.(1228-1230)Gga>Tga	p.G410*	HEPACAM2_ENST00000341723.4_Nonsense_Mutation_p.G398*|HEPACAM2_ENST00000440868.1_Silent_p.S389S|HEPACAM2_ENST00000492616.1_5'UTR|HEPACAM2_ENST00000453812.2_Nonsense_Mutation_p.G433*	NM_001039372.1	NP_001034461.1	A8MVW5	HECA2_HUMAN	HEPACAM family member 2	410					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|midbody (GO:0030496)|spindle (GO:0005819)				breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|ovary(4)|skin(1)	28						TCATATATTCCGAAGTCATCC	0.383																																					p.G410X		Atlas-SNP	.											.	HEPACAM2	132	.	0			c.G1228T						.						116	113	114					7																	92825188		2203	4300	6503	SO:0001587	stop_gained	253012	exon8			ATATTCCGAAGTC	AK096002	CCDS5629.1, CCDS43616.1, CCDS75631.1, CCDS75632.1	7q21.3	2013-01-29	2008-07-11		ENSG00000188175	ENSG00000188175		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	27364	protein-coding gene	gene with protein product		614133				12975309	Standard	NM_001288804		Approved	FLJ38683	uc003umm.3	A8MVW5	OTTHUMG00000131732	ENST00000394468.2:c.1228G>T	chr7.hg19:g.92825188C>A	ENSP00000377980:p.Gly410*	70.0	0.0		79.0	4.0	NM_001039372	B3KTT4|B4DPJ1|B9EG93|E9PDV5|Q6UXI0	Nonsense_Mutation	SNP	ENST00000394468.2	hg19	CCDS43616.1	.	.	.	.	.	.	.	.	.	.	C	37	6.197908	0.97367	.	.	ENSG00000188175	ENST00000394468;ENST00000341723;ENST00000453812	.	.	.	4.89	4.89	0.63831	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-15.3871	16.7918	0.85591	0.0:1.0:0.0:0.0	.	.	.	.	X	410;398;433	.	ENSP00000340532:G398X	G	-	1	0	HEPACAM2	92663124	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	4.510000	0.60455	2.692000	0.91855	0.650000	0.86243	GGA	.	C|0.998;T|0.002		0.383	HEPACAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254651.1	NM_198151		A	92825188	C	A	92825188	4	1	259	1	0	0	0	0	0	1	0	0	7062	661	23	1	172	1	HEPACAM2	7	92825188	Nonsense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	5610259	92825188	66313475	358	36676										
SMURF1	57154	hgsc.bcm.edu	37	chr7	98628253	98628253	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cctccacggctgtcagcagcTtctcgtagagcttctcatag	9	14	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:98628253T>C	ENST00000361125.1	-	19	2547	c.2228A>G	c.(2227-2229)aAg>aGg	p.K743R	AC004893.11_ENST00000360902.1_RNA|AC004893.11_ENST00000468960.2_RNA|SMURF1_ENST00000361368.2_Missense_Mutation_p.K717R	NM_020429.2	NP_065162.1	Q9HCE7	SMUF1_HUMAN	SMAD specific E3 ubiquitin protein ligase 1	743	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				BMP signaling pathway (GO:0030509)|cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of ossification (GO:0030279)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein export from nucleus (GO:0006611)|protein localization to cell surface (GO:0034394)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	activin binding (GO:0048185)|I-SMAD binding (GO:0070411)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|urinary_tract(1)	25	all_cancers(62;1.05e-08)|all_epithelial(64;4.34e-09)|Lung NSC(181;0.00902)|all_lung(186;0.0145)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)|Lung(104;0.224)			TGTCAGCAGCTTCTCGTAGAG	0.522																																					p.K743R		Atlas-SNP	.											.	SMURF1	58	.	0			c.A2228G						.						122	111	115					7																	98628253		2203	4300	6503	SO:0001583	missense	57154	exon19			AGCAGCTTCTCGT	AB046845	CCDS34689.1, CCDS34690.1	7q21.1-q31.1	2004-07-29			ENSG00000198742	ENSG00000198742			16807	protein-coding gene	gene with protein product		605568				10458166	Standard	NM_020429		Approved	KIAA1625	uc003upu.2	Q9HCE7	OTTHUMG00000150272	ENST00000361125.1:c.2228A>G	chr7.hg19:g.98628253T>C	ENSP00000354621:p.Lys743Arg	96.0	0.0		74.0	5.0	NM_020429	A4D279|B7ZMB6|B9EGV3|O75853|Q547Q3|Q9UJT8	Missense_Mutation	SNP	ENST00000361125.1	hg19	CCDS34690.1	.	.	.	.	.	.	.	.	.	.	T	29.1	4.981217	0.93044	.	.	ENSG00000198742	ENST00000361368;ENST00000361125	T;T	0.52526	0.66;0.66	5.26	5.26	0.73747	HECT (4);	0.000000	0.85682	D	0.000000	T	0.61714	0.2369	L	0.43646	1.37	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	T	0.64859	-0.6308	10	0.72032	D	0.01	.	15.1696	0.72862	0.0:0.0:0.0:1.0	.	717;743;714	Q9HCE7-2;Q9HCE7;B9EGV3	.;SMUF1_HUMAN;.	R	717;743	ENSP00000355326:K717R;ENSP00000354621:K743R	ENSP00000354621:K743R	K	-	2	0	SMURF1	98466189	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.668000	0.83897	1.993000	0.58246	0.391000	0.25812	AAG	.	.		0.522	SMURF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000335001.2	NM_020429		C	98628253	T	C	98628253	3	2	259	1	0	0	0	0	1	0	0	0	14834	1609	56	2	49	2	SMURF1	7	98628253	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	5803065	98628253	60510410	359	36677										
AP4M1	9179	hgsc.bcm.edu	37	chr7	99703069	99703069	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttgctctctggtctctcagcTgactgtgatgcggtaccaac	10	12	3	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:99703069T>C	ENST00000359593.4	+	11	994	c.836T>C	c.(835-837)cTg>cCg	p.L279P	AP4M1_ENST00000429084.1_Splice_Site_p.L286P|AP4M1_ENST00000421755.1_Splice_Site_p.L279P|AP4M1_ENST00000422582.1_Splice_Site_p.L151P	NM_004722.3	NP_004713.2	O00189	AP4M1_HUMAN	adaptor-related protein complex 4, mu 1 subunit	279	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				Golgi to endosome transport (GO:0006895)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|Golgi trans cisterna (GO:0000138)|trans-Golgi network (GO:0005802)	transporter activity (GO:0005215)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)	17	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GTCTCTCAGCTGACTGTGATG	0.612																																					p.L279P	Pancreas(174;1182 2812 29595 49511)	Atlas-SNP	.											.	AP4M1	39	.	0			c.T836C						.						120	101	108					7																	99703069		2203	4300	6503	SO:0001630	splice_region_variant	9179	exon11			CTCAGCTGACTGT	Y08387	CCDS5685.1	7q22.1	2012-06-29			ENSG00000221838	ENSG00000221838			574	protein-coding gene	gene with protein product	"mu-adaptin-related protein-2", "mu subunit of AP-4", "AP-4 adapter complex mu subunit", "adaptor-related protein complex AP-4 mu4 subunit"	602296				9013859, 10066790, 21620353	Standard	NM_004722		Approved	MU-ARP2, MU-4, SPG50	uc003utb.4	O00189	OTTHUMG00000154722	ENST00000359593.4:c.835-1T>C	chr7.hg19:g.99703069T>C		117.0	0.0		90.0	4.0	NM_004722	D6W5U1|Q8WV65|Q9UHK9	Missense_Mutation	SNP	ENST00000359593.4	hg19	CCDS5685.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.4|20.4	3.985015|3.985015	0.74474|0.74474	.|.	.|.	ENSG00000221838|ENSG00000221838	ENST00000438383;ENST00000429084;ENST00000359593;ENST00000439416;ENST00000421755;ENST00000422582;ENST00000450807|ENST00000445295	T;T;T;T;T;T;T|.	0.20598|.	2.06;2.06;2.06;2.06;2.06;2.06;2.06|.	5.38|5.38	5.38|5.38	0.77491|0.77491	Clathrin adaptor, mu subunit, conserved site (1);Clathrin adaptor, mu subunit, C-terminal (3);|.	0.071876|.	0.56097|.	D|.	0.000023|.	T|.	0.56572|.	0.1994|.	L|L	0.36672|0.36672	1.1|1.1	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	0.998;1.0;1.0|.	D;D;D|.	0.69307|.	0.947;0.963;0.963|.	T|.	0.53436|.	-0.8439|.	10|.	0.87932|.	D|.	0|.	2.8916|2.8916	13.3999|13.3999	0.60876|0.60876	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	235;286;279|.	C9JMG3;C9JC87;O00189|.	.;.;AP4M1_HUMAN|.	P|R	211;286;279;235;279;151;31|5	ENSP00000401613:L211P;ENSP00000403663:L286P;ENSP00000352603:L279P;ENSP00000414286:L235P;ENSP00000412185:L279P;ENSP00000406676:L151P;ENSP00000391585:L31P|.	ENSP00000352603:L279P|.	L|X	+|+	2|1	0|0	AP4M1|AP4M1	99541005|99541005	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	5.015000|5.015000	0.64035|0.64035	2.254000|2.254000	0.74563|0.74563	0.533000|0.533000	0.62120|0.62120	CTG|TGA	.	.		0.612	AP4M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336772.4	NM_004722	Missense_Mutation	C	99703069	T	C	99703069	5	2	259	1	0	0	0	0	0	0	1	0	753	1594	55	2	878	2	AP4M1	7	99703069	Splice_Site	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1074816	99703069	59435594	360	36678										
TFR2	7036	hgsc.bcm.edu	37	chr7	100225214	100225214	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tctcacctccataaaggagaActcgacggcagggactccca	9	14	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:100225214A>G	ENST00000462107.1	-	16	2040	c.1753T>C	c.(1753-1755)Ttc>Ctc	p.F585L	TFR2_ENST00000431692.1_3'UTR|TFR2_ENST00000223051.3_Missense_Mutation_p.F585L|TFR2_ENST00000544242.1_Missense_Mutation_p.F126L			Q9UP52	TFR2_HUMAN	transferrin receptor 2	585					cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)|receptor-mediated endocytosis (GO:0006898)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transferrin receptor activity (GO:0004998)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	23	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)				Gallium nitrate(DB05260)	ATAAAGGAGAACTCGACGGCA	0.642																																					p.F585L		Atlas-SNP	.											.	TFR2	53	.	0			c.T1753C						.						58	58	58					7																	100225214		2203	4300	6503	SO:0001583	missense	7036	exon15			AGGAGAACTCGAC	AF053356	CCDS34707.1	7q22	2003-01-27			ENSG00000106327	ENSG00000106327			11762	protein-coding gene	gene with protein product		604720				9799793, 12130528	Standard	NM_003227		Approved	HFE3, TFRC2	uc003uvv.1	Q9UP52	OTTHUMG00000159598	ENST00000462107.1:c.1753T>C	chr7.hg19:g.100225214A>G	ENSP00000420525:p.Phe585Leu	64.0	0.0		65.0	4.0	NM_003227	A6NGM7|O75422|Q1HE13|Q9HA99|Q9NX67	Missense_Mutation	SNP	ENST00000462107.1	hg19	CCDS34707.1	.	.	.	.	.	.	.	.	.	.	A	15.07	2.723543	0.48728	.	.	ENSG00000106327	ENST00000223051;ENST00000462107;ENST00000544242	T;T;T	0.37915	1.17;1.17;1.17	4.9	4.9	0.64082	Peptidase M28 (1);	0.132555	0.51477	D	0.000085	T	0.29190	0.0726	L	0.28649	0.875	0.80722	D	1	B	0.28667	0.219	B	0.31946	0.138	T	0.10086	-1.0645	10	0.44086	T	0.13	-28.6179	12.5712	0.56339	1.0:0.0:0.0:0.0	.	585	Q9UP52	TFR2_HUMAN	L	585;585;126	ENSP00000223051:F585L;ENSP00000420525:F585L;ENSP00000443656:F126L	ENSP00000223051:F585L	F	-	1	0	TFR2	100063150	1.000000	0.71417	1.000000	0.80357	0.475000	0.33008	2.953000	0.49105	2.077000	0.62373	0.374000	0.22700	TTC	.	.		0.642	TFR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356392.3	NM_003227		G	100225214	A	G	100225214	3	3	259	1	0	0	0	0	1	0	0	0	15826	43	2	2	668	2	TFR2	7	100225214	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	522145	100225214	58913449	361	36679										
GNB2	2783	hgsc.bcm.edu	37	chr7	100275432	100275432	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aatcatcaccagctctggggAtaccacctggtgaggctctg	11	12	4	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:100275432A>G	ENST00000303210.4	+	7	970	c.488A>G	c.(487-489)gAt>gGt	p.D163G	GNB2_ENST00000427895.1_Missense_Mutation_p.D63G|GNB2_ENST00000419828.1_Missense_Mutation_p.D63G|GNB2_ENST00000436220.1_Missense_Mutation_p.D119G|GNB2_ENST00000393926.1_Missense_Mutation_p.D163G|GNB2_ENST00000393924.1_Missense_Mutation_p.D163G|GNB2_ENST00000424361.1_Missense_Mutation_p.D119G	NM_005273.3	NP_005264.2	P62879	GBB2_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 2	163					cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|GTP catabolic process (GO:0006184)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cell body (GO:0044297)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	calcium channel regulator activity (GO:0005246)|GTPase activity (GO:0003924)|GTPase binding (GO:0051020)|protein complex binding (GO:0032403)|signal transducer activity (GO:0004871)			endometrium(1)|lung(3)|ovary(2)|prostate(1)	7	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)	Ovarian(593;0.238)				AGCTCTGGGGATACCACCTGG	0.622																																					p.D163G		Atlas-SNP	.											.	GNB2	29	.	0			c.A488G						.						55	45	49					7																	100275432		2203	4300	6503	SO:0001583	missense	2783	exon7			CTGGGGATACCAC	M16514	CCDS5703.1	7q21.3-q22.1	2013-01-10			ENSG00000172354	ENSG00000172354		"WD repeat domain containing"	4398	protein-coding gene	gene with protein product	"G protein, beta-2 subunit", "guanine nucleotide-binding protein G(I)/G(S)/G(T) beta subunit 2", "signal-transducing guanine nucleotide-binding regulatory protein beta subunit", "transducin beta chain 2"	139390				9799793	Standard	NM_005273		Approved		uc003uwb.3	P62879	OTTHUMG00000137419	ENST00000303210.4:c.488A>G	chr7.hg19:g.100275432A>G	ENSP00000305260:p.Asp163Gly	105.0	0.0		93.0	4.0	NM_005273	B3KPU1|P11016|P54312	Missense_Mutation	SNP	ENST00000303210.4	hg19	CCDS5703.1	.	.	.	.	.	.	.	.	.	.	.	25.9	4.680853	0.88542	.	.	ENSG00000172354	ENST00000303210;ENST00000451587;ENST00000436220;ENST00000424361;ENST00000419828;ENST00000427895;ENST00000393926;ENST00000431068;ENST00000393924	D;D;D;D;D;D;D;D;D	0.89270	-2.49;-2.49;-2.49;-2.49;-2.49;-2.49;-2.49;-2.49;-2.49	4.79	4.79	0.61399	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.95959	0.8684	H	0.96430	3.82	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96816	0.9600	10	0.87932	D	0	-1.7218	12.3252	0.55007	1.0:0.0:0.0:0.0	.	163	P62879	GBB2_HUMAN	G	163;163;119;119;63;63;163;163;163	ENSP00000305260:D163G;ENSP00000399904:D163G;ENSP00000401873:D119G;ENSP00000389391:D119G;ENSP00000390543:D63G;ENSP00000400286:D63G;ENSP00000377503:D163G;ENSP00000390077:D163G;ENSP00000377501:D163G	ENSP00000305260:D163G	D	+	2	0	GNB2	100113368	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.088000	0.76901	2.014000	0.59158	0.379000	0.24179	GAT	.	.		0.622	GNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268391.2	NM_005273		G	100275432	A	G	100275432	3	3	259	1	0	0	0	0	1	0	0	0	6525	333	12	2	510	2	GNB2	7	100275432	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	50218	100275432	58863231	362	36680										
ACHE	43	hgsc.bcm.edu	37	chr7	100487872	100487872	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gatcctgcttgctgtagtggTcgaactggttcttccagtgc	12	10	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:100487872T>C	ENST00000412389.1	-	4	1963	c.1808A>G	c.(1807-1809)gAc>gGc	p.D603G	ACHE_ENST00000302913.4_3'UTR|UFSP1_ENST00000388761.2_5'Flank|ACHE_ENST00000428317.1_Missense_Mutation_p.D603G|ACHE_ENST00000241069.5_Missense_Mutation_p.D603G|ACHE_ENST00000419336.2_Missense_Mutation_p.D515G			P22303	ACES_HUMAN	acetylcholinesterase (Yt blood group)	603					acetylcholine catabolic process (GO:0006581)|acetylcholine catabolic process in synaptic cleft (GO:0001507)|amyloid precursor protein metabolic process (GO:0042982)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|choline metabolic process (GO:0019695)|DNA replication (GO:0006260)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|negative regulation of synaptic transmission, cholinergic (GO:0032223)|nervous system development (GO:0007399)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter receptor biosynthetic process (GO:0045212)|osteoblast development (GO:0002076)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of protein secretion (GO:0050714)|protein tetramerization (GO:0051262)|receptor internalization (GO:0031623)|regulation of axonogenesis (GO:0050770)|regulation of dendrite morphogenesis (GO:0048814)|regulation of receptor recycling (GO:0001919)|response to wounding (GO:0009611)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	acetylcholine binding (GO:0042166)|acetylcholinesterase activity (GO:0003990)|beta-amyloid binding (GO:0001540)|cholinesterase activity (GO:0004104)|collagen binding (GO:0005518)|hydrolase activity (GO:0016787)|laminin binding (GO:0043236)|protein homodimerization activity (GO:0042803)|serine hydrolase activity (GO:0017171)			large_intestine(3)|lung(7)|skin(3)|urinary_tract(3)	16	Lung NSC(181;0.041)|all_lung(186;0.0581)				Ambenonium(DB01122)|Choline(DB00122)|Decamethonium(DB01245)|Demecarium(DB00944)|Dipivefrin(DB00449)|Donepezil(DB00843)|Edrophonium(DB01010)|Ephedrine(DB01364)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Isoflurophate(DB00677)|Mefloquine(DB00358)|Minaprine(DB00805)|Neostigmine(DB01400)|Physostigmine(DB00981)|Pralidoxime(DB00733)|Pyridostigmine(DB00545)|Rivastigmine(DB00989)|Tubocurarine(DB01199)	GCTGTAGTGGTCGAACTGGTT	0.632																																					p.D603G		Atlas-SNP	.											.	ACHE	80	.	0			c.A1808G						.						66	57	60					7																	100487872		2203	4300	6503	SO:0001583	missense	43	exon5			TAGTGGTCGAACT		CCDS5709.1, CCDS5710.1, CCDS64736.1	7q22	2014-07-19	2014-01-02		ENSG00000087085	ENSG00000087085	3.1.1.7	"Blood group antigens"	108	protein-coding gene	gene with protein product	"Yt blood group"	100740	"acetylcholinesterase (YT blood group)", "acetylcholinesterase (Yt blood group)", "acetylcholinesterase"	YT		1380483	Standard	XM_005250357		Approved		uc003uxe.3	P22303	OTTHUMG00000157033	ENST00000412389.1:c.1808A>G	chr7.hg19:g.100487872T>C	ENSP00000394976:p.Asp603Gly	207.0	0.0		141.0	6.0	NM_000665	A4D2E2|B7ZKZ0|D6W5X7|Q16169|Q29S23|Q2M324|Q504V3|Q53F46|Q86TM9|Q86YX9|Q9BXP7	Missense_Mutation	SNP	ENST00000412389.1	hg19	CCDS5709.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.2|25.2	4.615153|4.615153	0.87359|0.87359	.|.	.|.	ENSG00000087085|ENSG00000087085	ENST00000419336;ENST00000241069;ENST00000428317;ENST00000412389|ENST00000426415;ENST00000430554	T;T;T;T|T;T	0.69435|0.68479	-0.4;-0.28;-0.28;-0.28|-0.33;-0.1	4.32|4.32	4.32|4.32	0.51571|0.51571	Acetylcholinesterase, tetramerisation (2);|.	0.000000|.	0.64402|.	U|.	0.000003|.	T|T	0.71082|0.71082	0.3298|0.3298	L|L	0.53249|0.53249	1.67|1.67	0.80722|0.80722	D|D	1|1	D;D|.	0.76494|.	0.987;0.999|.	P;D|.	0.74674|.	0.797;0.984|.	T|T	0.74150|0.74150	-0.3758|-0.3758	10|7	0.56958|0.87932	D|D	0.05|0	.|.	11.4294|11.4294	0.50032|0.50032	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	515;603|.	P22303-3;P22303|.	.;ACES_HUMAN|.	G|A	515;603;603;603|385;422	ENSP00000403474:D515G;ENSP00000241069:D603G;ENSP00000414858:D603G;ENSP00000394976:D603G|ENSP00000397143:T385A;ENSP00000399725:T422A	ENSP00000241069:D603G|ENSP00000397143:T385A	D|T	-|-	2|1	0|0	ACHE|ACHE	100325808|100325808	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.984000|0.984000	0.73092|0.73092	5.040000|5.040000	0.64191|0.64191	1.599000|1.599000	0.50093|0.50093	0.260000|0.260000	0.18958|0.18958	GAC|ACC	.	.		0.632	ACHE-013	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347201.1	NM_015831		C	100487872	T	C	100487872	3	2	259	1	0	0	0	0	1	0	0	0	141	1667	58	2	40	2	ACHE	7	100487872	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	212440	100487872	58650791	363	36681										
CUX1	1523	hgsc.bcm.edu	37	chr7	101840082	101840082	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tcaagactttttcagctcatCcctggcaagccccagcctac	6	16	3	1	rs569218052		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:101840082C>A	ENST00000292535.7	+	15	1429	c.1391C>A	c.(1390-1392)tCc>tAc	p.S464Y	CUX1_ENST00000556210.1_Intron|CUX1_ENST00000393824.3_Intron|CUX1_ENST00000437600.4_Intron|CUX1_ENST00000360264.3_Missense_Mutation_p.S475Y|CUX1_ENST00000549414.2_Missense_Mutation_p.S464Y|CUX1_ENST00000550008.2_Missense_Mutation_p.S464Y|CUX1_ENST00000547394.2_Intron|CUX1_ENST00000560541.1_Intron|CUX1_ENST00000425244.2_Intron|CUX1_ENST00000546411.2_Intron|CUX1_ENST00000292538.4_Intron|SNORA48_ENST00000517015.1_RNA	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	464					auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						TTCAGCTCATCCCTGGCAAGC	0.532													C|||	1	0.000199681	8e-04	0	5008	,	,		16575	0		0	False		,,,				2504	0				p.S475Y		Atlas-SNP	.											.	CUX1	253	.	0			c.C1424A						.						70	73	72					7																	101840082		2203	4300	6503	SO:0001583	missense	1523	exon15			GCTCATCCCTGGC	M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923		"Homeoboxes / CUT class"	2557	protein-coding gene	gene with protein product	"golgi integral membrane protein 6"	116896	"cut (Drosophila)-like 1 (CCAAT displacement protein)", "cut-like 1, CCAAT displacement protein (Drosophila)"	CUTL1		8468066, 9799793, 15004235	Standard	NM_001202543		Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000292535.7:c.1391C>A	chr7.hg19:g.101840082C>A	ENSP00000292535:p.Ser464Tyr	174.0	0.0		138.0	44.0	NM_001202543	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Missense_Mutation	SNP	ENST00000292535.7	hg19	CCDS5721.1	.	.	.	.	.	.	.	.	.	.	C	14.24	2.476486	0.44044	.	.	ENSG00000257923	ENST00000360264;ENST00000292535;ENST00000549414;ENST00000550008	T;T;T;T	0.60797	0.18;0.17;0.16;0.17	5.71	4.8	0.61643	.	0.294006	0.28635	N	0.014644	T	0.52500	0.1738	N	0.22421	0.69	0.80722	D	1	P;P	0.42649	0.681;0.786	B;P	0.47251	0.254;0.542	T	0.53012	-0.8498	10	0.40728	T	0.16	-6.8901	15.6421	0.77012	0.1423:0.8577:0.0:0.0	.	464;475	P39880;P39880-3	CUX1_HUMAN;.	Y	475;464;464;464	ENSP00000353401:S475Y;ENSP00000292535:S464Y;ENSP00000446630:S464Y;ENSP00000447373:S464Y	ENSP00000292535:S464Y	S	+	2	0	CUX1	101626802	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.111000	0.50360	1.350000	0.45770	0.561000	0.74099	TCC	.	.		0.532	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913		A	101840082	C	A	101840082	3	1	259	1	0	0	0	0	1	0	0	0	4066	855	30	3	1516	3	CUX1	7	101840082	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	1352210	101840082	57298581	364	36682										
NRCAM	4897	hgsc.bcm.edu	37	chr7	107807398	107807398	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	caaacacatcctctgaactcAcaaaaccagagtcccccaca	3	17	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:107807398A>G	ENST00000425651.2	-	27	3433	c.3434T>C	c.(3433-3435)gTg>gCg	p.V1145A	NRCAM_ENST00000351718.4_Intron|NRCAM_ENST00000379024.4_Intron|NRCAM_ENST00000379028.3_Missense_Mutation_p.V1145A|NRCAM_ENST00000413765.2_Intron|NRCAM_ENST00000379022.4_Missense_Mutation_p.V1145A	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	1145	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						CTCTGAACTCACAAAACCAGA	0.537																																					p.V1145A		Atlas-SNP	.											.	NRCAM	267	.	0			c.T3434C						.						53	58	57					7																	107807398		2060	4191	6251	SO:0001583	missense	4897	exon27			GAACTCACAAAAC		CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7994	protein-coding gene	gene with protein product	"NgCAM-related cell adhesion molecule"	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.3434T>C	chr7.hg19:g.107807398A>G	ENSP00000401244:p.Val1145Ala	111.0	0.0		86.0	4.0	NM_001037132	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Missense_Mutation	SNP	ENST00000425651.2	hg19	CCDS47686.1	.	.	.	.	.	.	.	.	.	.	A	10.03	1.240010	0.22711	.	.	ENSG00000091129	ENST00000379032;ENST00000379028;ENST00000425651;ENST00000379022	T;T;T	0.58358	0.34;0.34;0.38	5.67	5.67	0.87782	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.382752	0.29892	N	0.010929	T	0.26376	0.0644	N	0.08118	0	0.31329	N	0.685032	B	0.02656	0.0	B	0.09377	0.004	T	0.27640	-1.0068	10	0.07644	T	0.81	.	7.4738	0.27363	0.6361:0.2434:0.0:0.1205	.	1145	Q92823	NRCAM_HUMAN	A	1145	ENSP00000368314:V1145A;ENSP00000401244:V1145A;ENSP00000368308:V1145A	ENSP00000368308:V1145A	V	-	2	0	NRCAM	107594634	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.123000	0.41996	2.284000	0.76573	0.523000	0.50628	GTG	.	.		0.537	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132		G	107807398	A	G	107807398	3	3	259	1	0	0	0	0	1	0	0	0	10653	159	6	2	526	2	NRCAM	7	107807398	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	5967316	107807398	51331265	365	36683										
PTPRZ1	5803	hgsc.bcm.edu	37	chr7	121679517	121679517	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttcttttgcagagaaaatgtGatcagtactggcctgccgat	10	8	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:121679517G>A	ENST00000393386.2	+	20	5923	c.5512G>A	c.(5512-5514)Gat>Aat	p.D1838N	PTPRZ1_ENST00000449182.1_Missense_Mutation_p.D971N	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	1838	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						GAGAAAATGTGATCAGTACTG	0.418																																					p.D1838N		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.G5512A						.						87	86	86					7																	121679517		2203	4300	6503	SO:0001583	missense	5803	exon20			AAATGTGATCAGT	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.5512G>A	chr7.hg19:g.121679517G>A	ENSP00000377047:p.Asp1838Asn	39.0	0.0		53.0	4.0	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	hg19	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	G	36	5.724235	0.96847	.	.	ENSG00000106278	ENST00000393386;ENST00000449182	D;D	0.84070	-1.8;-1.8	5.88	5.88	0.94601	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	D	0.000000	D	0.92296	0.7556	M	0.82923	2.615	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.994;0.997	D	0.92393	0.5923	10	0.72032	D	0.01	.	20.2441	0.98394	0.0:0.0:1.0:0.0	.	977;971;1838	P23471-2;C9JFM0;P23471	.;.;PTPRZ_HUMAN	N	1838;971	ENSP00000377047:D1838N;ENSP00000410000:D971N	ENSP00000377047:D1838N	D	+	1	0	PTPRZ1	121466753	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.813000	0.99286	2.774000	0.95407	0.655000	0.94253	GAT	.	.		0.418	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		A	121679517	G	A	121679517	3	1	259	1	0	0	0	0	1	0	0	0	12829	1290	45	3	5590	3	PTPRZ1	7	121679517	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	13872119	121679517	37459146	366	36684										
FLNC	2318	hgsc.bcm.edu	37	chr7	128494663	128494663	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tttcagttcactgtggggccGctgggtgaaggtggtgccca	16	9	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:128494663G>A	ENST00000325888.8	+	41	7185	c.6924G>A	c.(6922-6924)ccG>ccA	p.P2308P	RP11-309L24.2_ENST00000469965.1_RNA|FLNC_ENST00000346177.6_Silent_p.P2275P	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	2308					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						CTGTGGGGCCGCTGGGTGAAG	0.692																																					p.P2308P		Atlas-SNP	.											.	FLNC	339	.	0			c.G6924A						.						13	16	15					7																	128494663		2147	4249	6396	SO:0001819	synonymous_variant	2318	exon41			GGGGCCGCTGGGT	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"actin binding protein 280"	102565	"filamin C, gamma (actin binding protein 280)"	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.6924G>A	chr7.hg19:g.128494663G>A		160.0	0.0		107.0	5.0	NM_001458	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Silent	SNP	ENST00000325888.8	hg19	CCDS43644.1																																																																																			.	.		0.692	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3			A	128494663	G	A	128494663	2	1	259	1	0	0	0	0	0	0	0	1	5943	1074	38	1		1	FLNC	7	128494663	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	6815146	128494663	30644000	367	36685										
KIAA1147	57189	hgsc.bcm.edu	37	chr7	141362629	141362629	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	caacaaagtctgaaatatccGgttgttttgttctaggaaaa	8	6	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:141362629G>T	ENST00000536163.1	-	9	1194	c.1195C>A	c.(1195-1197)Cgg>Agg	p.R399R	KIAA1147_ENST00000482493.1_Silent_p.R295R|RP5-894A10.6_ENST00000602609.1_RNA	NM_001080392.1	NP_001073861.1	A4D1U4	LCHN_HUMAN	KIAA1147	399										breast(3)|endometrium(4)|kidney(2)|large_intestine(1)|ovary(1)|skin(1)	12	Melanoma(164;0.0171)					TGAAATATCCGGTTGTTTTGT	0.502																																					p.R399R		Atlas-SNP	.											.	KIAA1147	32	.	0			c.C1195A						.						30	30	30					7																	141362629		1845	4088	5933	SO:0001819	synonymous_variant	57189	exon9			ATATCCGGTTGTT	AB032973	CCDS47726.1	7q34	2012-10-04			ENSG00000257093	ENSG00000257093			29472	protein-coding gene	gene with protein product							Standard	NM_001080392		Approved	LCHN	uc003vwk.3	A4D1U4	OTTHUMG00000157539	ENST00000536163.1:c.1195C>A	chr7.hg19:g.141362629G>T		117.0	0.0		95.0	4.0	NM_001080392	Q9ULS3	Silent	SNP	ENST00000536163.1	hg19	CCDS47726.1																																																																																			.	.		0.502	KIAA1147-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349104.1			T	141362629	G	T	141362629	2	4	259	1	0	0	0	0	0	0	0	1	8219	1115	39	1		1	KIAA1147	7	141362629	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	12867966	141362629	17776034	368	36686										
TRPV6	55503	hgsc.bcm.edu	37	chr7	142569466	142569466	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gtgagaacacgcagtcagatCtgatattcccagctctcccc	8	14	3	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:142569466C>T	ENST00000359396.3	-	15	2417	c.2172G>A	c.(2170-2172)caG>caA	p.Q724Q		NM_018646.3	NP_061116	Q9H1D0	TRPV6_HUMAN	transient receptor potential cation channel, subfamily V, member 6	724					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|regulation of calcium ion-dependent exocytosis (GO:0017158)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)			breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	42	Melanoma(164;0.059)					GCAGTCAGATCTGATATTCCC	0.527																																					p.Q724Q		Atlas-SNP	.											.	TRPV6	108	.	0			c.G2172A						.						76	75	75					7																	142569466		2203	4300	6503	SO:0001819	synonymous_variant	55503	exon15			TCAGATCTGATAT	AJ277909	CCDS5874.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000165125	ENSG00000165125		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	14006	protein-coding gene	gene with protein product		606680	"epithelial calcium channel 2"	ECAC2		11097838, 11549322, 16382100, 16717058	Standard	NM_018646		Approved	CaT1	uc003wbx.2	Q9H1D0	OTTHUMG00000157158	ENST00000359396.3:c.2172G>A	chr7.hg19:g.142569466C>T		126.0	0.0		91.0	5.0	NM_018646	A4D2I8|Q8TDL3|Q8WXR8|Q96LC5|Q9H1D1|Q9H296	Silent	SNP	ENST00000359396.3	hg19	CCDS5874.1																																																																																			.	.		0.527	TRPV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347662.1	NM_014274		T	142569466	C	T	142569466	2	4	259	1	0	0	0	0	0	0	0	1	16615	912	32	3		3	TRPV6	7	142569466	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	1206837	142569466	16569197	369	36687										
CUL1	8454	hgsc.bcm.edu	37	chr7	148451110	148451110	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agtgttcaccagtcaaaccaAgcacgaggagctggagttcc	11	11	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:148451110A>G	ENST00000325222.4	+	3	462	c.183A>G	c.(181-183)caA>caG	p.Q61Q	CUL1_ENST00000602748.1_Silent_p.Q61Q|CUL1_ENST00000409469.1_Silent_p.Q61Q	NM_003592.2	NP_003583.2	Q13616	CUL1_HUMAN	cullin 1	61				Missing (in Ref. 1; AAC50544). {ECO:0000305}.	anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic cell cycle (GO:0000278)|negative regulation of cell proliferation (GO:0008285)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|viral process (GO:0016032)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|SCF ubiquitin ligase complex (GO:0019005)				breast(2)|central_nervous_system(2)|endometrium(1)|kidney(5)|large_intestine(10)|liver(2)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	40	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)			AGTCAAACCAAGCACGAGGAG	0.413																																					p.Q61Q		Atlas-SNP	.											.	CUL1	80	.	0			c.A183G						.						59	56	57					7																	148451110		2203	4300	6503	SO:0001819	synonymous_variant	8454	exon3			AAACCAAGCACGA	U58087	CCDS34772.1	7q36.1	2011-05-24			ENSG00000055130	ENSG00000055130			2551	protein-coding gene	gene with protein product		603134				8681378	Standard	NM_003592		Approved		uc003wey.3	Q13616	OTTHUMG00000152776	ENST00000325222.4:c.183A>G	chr7.hg19:g.148451110A>G		100.0	0.0		93.0	5.0	NM_003592	D3DWG3|O60719|Q08AL6|Q8IYW1	Silent	SNP	ENST00000325222.4	hg19	CCDS34772.1																																																																																			.	.		0.413	CUL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467785.1	NM_003592		G	148451110	A	G	148451110	2	3	259	1	0	0	0	0	0	0	0	1	4056	69	3	2		2	CUL1	7	148451110	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	5881644	148451110	10687553	370	36688										
ZNF862	643641	hgsc.bcm.edu	37	chr7	149545056	149545056	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atgaatgaggagcagacggcTctgttctgctctgcttgccg	13	10	3	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:149545056T>C	ENST00000223210.4	+	4	719	c.474T>C	c.(472-474)gcT>gcC	p.A158A		NM_001099220.1	NP_001092690.1	O60290	ZN862_HUMAN	zinc finger protein 862	158					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(1)	34						AGCAGACGGCTCTGTTCTGCT	0.507																																					p.A158A		Atlas-SNP	.											.	ZNF862	97	.	0			c.T474C						.						49	49	49					7																	149545056		2022	4180	6202	SO:0001819	synonymous_variant	643641	exon4			GACGGCTCTGTTC	AB011115	CCDS47741.1	7q36.1	2013-01-11			ENSG00000106479	ENSG00000106479		"Zinc fingers, C2H2-type", "-"	34519	protein-coding gene	gene with protein product							Standard	NM_001099220		Approved		uc010lpn.3	O60290	OTTHUMG00000158093	ENST00000223210.4:c.474T>C	chr7.hg19:g.149545056T>C		128.0	0.0		119.0	6.0	NM_001099220	A0AUL8	Silent	SNP	ENST00000223210.4	hg19	CCDS47741.1																																																																																			.	.		0.507	ZNF862-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350165.1	NM_001099220		C	149545056	T	C	149545056	2	2	259	1	0	0	0	0	0	0	0	1	18210	1538	54	2		2	ZNF862	7	149545056	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1093946	149545056	9593607	371	36689										
GIMAP1	170575	hgsc.bcm.edu	37	chr7	150417814	150417814	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aggccctgaggagcggctccGgcgggtggcggagcgcgtgg	22	11	0	1	rs537240577	byFrequency	TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:150417814G>A	ENST00000307194.5	+	3	862	c.722G>A	c.(721-723)cGg>cAg	p.R241Q		NM_130759.3	NP_570115.1	Q8WWP7	GIMA1_HUMAN	GTPase, IMAP family member 1	241					B cell differentiation (GO:0030183)|T cell differentiation (GO:0030217)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	28			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GAGCGGCTCCGGCGGGTGGCG	0.706													G|||	3	0.000599042	0	0.0029	5008	,	,		14481	0		0	False		,,,				2504	0.001				p.R241Q		Atlas-SNP	.											GIMAP1,NS,carcinoma,0,1	GIMAP1	61	.	0			c.G722A						.						10	12	11					7																	150417814		2123	4150	6273	SO:0001583	missense	170575	exon3			GGCTCCGGCGGGT	AJ306287	CCDS5906.1	7q36.1	2014-04-04			ENSG00000213203	ENSG00000213203		"GTPases, IMAP"	23237	protein-coding gene	gene with protein product	"immune-associated nucleotide-binding protein 2"	608084				15474311, 18701445	Standard	NM_130759		Approved	HIMAP1, IMAP38, IMAP1, IAN2		Q8WWP7	OTTHUMG00000157489	ENST00000307194.5:c.722G>A	chr7.hg19:g.150417814G>A	ENSP00000302833:p.Arg241Gln	65.0	0.0		57.0	6.0	NM_130759	B2RCI3|Q8NAZ0	Missense_Mutation	SNP	ENST00000307194.5	hg19	CCDS5906.1	.	.	.	.	.	.	.	.	.	.	G	14.19	2.461332	0.43736	.	.	ENSG00000213203	ENST00000307194	T	0.07021	3.23	4.51	-0.551	0.11822	.	1.927680	0.04097	U	0.312211	T	0.06416	0.0165	L	0.29908	0.895	0.09310	N	1	B	0.22909	0.077	B	0.08055	0.003	T	0.38156	-0.9674	10	0.34782	T	0.22	.	4.3474	0.11139	0.297:0.3023:0.4007:0.0	.	241	Q8WWP7	GIMA1_HUMAN	Q	241	ENSP00000302833:R241Q	ENSP00000302833:R241Q	R	+	2	0	GIMAP1	150048747	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.355000	0.02612	-0.187000	0.10516	-0.145000	0.13849	CGG	.	.		0.706	GIMAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348951.2	NM_130759		A	150417814	G	A	150417814	3	1	259	1	0	0	0	0	1	0	0	0	6387	1116	39	1	728	1	GIMAP1	7	150417814	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	872758	150417814	8720849	372	36690										
ABP1	26	hgsc.bcm.edu	37	chr7	150553813	150553813	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aagtaccatgtgctgaggttTctggataaaggtgaaaggca	13	5	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:150553813T>C	ENST00000493429.1	+	4	839	c.255T>C	c.(253-255)ttT>ttC	p.F85F	AOC1_ENST00000360937.4_Silent_p.F85F|AOC1_ENST00000467291.1_Silent_p.F85F|AOC1_ENST00000416793.2_Silent_p.F85F			P19801	AOC1_HUMAN	amine oxidase, copper containing 1	85					amine metabolic process (GO:0009308)|cellular response to azide (GO:0097185)|cellular response to copper ion (GO:0071280)|cellular response to copper ion starvation (GO:0035874)|cellular response to heparin (GO:0071504)|cellular response to histamine (GO:0071420)|oxidation-reduction process (GO:0055114)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|diamine oxidase activity (GO:0052597)|drug binding (GO:0008144)|heparin binding (GO:0008201)|histamine oxidase activity (GO:0052598)|methylputrescine oxidase activity (GO:0052599)|primary amine oxidase activity (GO:0008131)|propane-1,3-diamine oxidase activity (GO:0052600)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|receptor activity (GO:0004872)|sodium channel activity (GO:0005272)|zinc ion binding (GO:0008270)									Amiloride(DB00594)	TGCTGAGGTTTCTGGATAAAG	0.567																																					p.F85F		Atlas-SNP	.											.	ABP1	92	.	0			c.T255C						.						153	152	152					7																	150553813		2074	4213	6287	SO:0001819	synonymous_variant	26	exon2			GAGGTTTCTGGAT	AK092514	CCDS43679.1, CCDS64797.1	7q36.1	2013-06-19	2013-06-19	2013-06-19	ENSG00000002726	ENSG00000002726	1.4.3.22		80	protein-coding gene	gene with protein product	"diamine oxidase"	104610	"amiloride binding protein 1 (amine oxidase (copper-containing))"	ABP1		8182053	Standard	NM_001091		Approved	DAO	uc003wia.2	P19801	OTTHUMG00000158306	ENST00000493429.1:c.255T>C	chr7.hg19:g.150553813T>C		121.0	0.0		92.0	4.0	NM_001091	C9J690|Q16683|Q16684|Q56II4|Q6GU42	Silent	SNP	ENST00000493429.1	hg19	CCDS43679.1																																																																																			.	.		0.567	AOC1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350628.1	NM_001091		C	150553813	T	C	150553813	2	2	259	1	0	0	0	0	0	0	0	1	98	1780	62	2		2	ABP1	7	150553813	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	135999	150553813	8584850	373	36691										
NOS3	4846	hgsc.bcm.edu	37	chr7	150707785	150707785	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gctgcctgccccactgctccTcacccagctgcctctgctcc	7	22	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:150707785T>C	ENST00000297494.3	+	22	3143	c.2786T>C	c.(2785-2787)cTc>cCc	p.L929P	NOS3_ENST00000461406.1_Missense_Mutation_p.L723P|ATG9B_ENST00000494791.1_5'Flank|NOS3_ENST00000477227.1_3'UTR	NM_000603.4	NP_000594.2	P60323	NANO3_HUMAN	nitric oxide synthase 3 (endothelial cell)	0					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|oogenesis (GO:0048477)|regulation of cell cycle (GO:0051726)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(11)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	50	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CCACTGCTCCTCACCCAGCTG	0.657																																					p.L929P		Atlas-SNP	.											.	NOS3	131	.	0			c.T2786C						.						31	31	31					7																	150707785		2202	4300	6502	SO:0001583	missense	4846	exon22			TGCTCCTCACCCA		CCDS5912.1, CCDS55182.1, CCDS55183.1	7q36	2007-02-15			ENSG00000164867	ENSG00000164867	1.14.13.39		7876	protein-coding gene	gene with protein product	"endothelial nitric oxide synthase"	163729				1379542	Standard	NM_000603		Approved	ECNOS, eNOS	uc003wif.3	P29474	OTTHUMG00000158343	ENST00000297494.3:c.2786T>C	chr7.hg19:g.150707785T>C	ENSP00000297494:p.Leu929Pro	133.0	0.0		95.0	4.0	NM_000603	Q495E5	Missense_Mutation	SNP	ENST00000297494.3	hg19	CCDS5912.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	28.2|28.2	4.897313|4.897313	0.91962|0.91962	.|.	.|.	ENSG00000164867|ENSG00000164867	ENST00000297494;ENST00000461406|ENST00000475017	T;T|.	0.70631|.	-0.5;-0.5|.	4.86|4.86	4.86|4.86	0.63082|0.63082	Riboflavin synthase-like beta-barrel (1);FAD-binding, type 1 (1);NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain-3 (1);Ferredoxin reductase-type FAD-binding domain (1);|.	0.000000|.	0.53938|.	D|.	0.000054|.	T|T	0.78880|0.78880	0.4353|0.4353	M|M	0.88640|0.88640	2.97|2.97	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;0.999|.	T|T	0.82339|0.82339	-0.0506|-0.0506	10|5	0.87932|.	D|.	0|.	3.8375|3.8375	12.443|12.443	0.55635|0.55635	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	723;929|.	E7ESA7;P29474|.	.;NOS3_HUMAN|.	P|P	929;723|223	ENSP00000297494:L929P;ENSP00000417143:L723P|.	ENSP00000297494:L929P|.	L|S	+|+	2|1	0|0	NOS3|NOS3	150338718|150338718	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.976000|0.976000	0.68499|0.68499	7.811000|7.811000	0.86092|0.86092	2.041000|2.041000	0.60428|0.60428	0.402000|0.402000	0.26972|0.26972	CTC|TCA	.	.		0.657	NOS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350750.2	NM_000603		C	150707785	T	C	150707785	3	2	259	1	0	0	0	0	1	0	0	0	10553	1551	54	2	3150	2	NOS3	7	150707785	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	153972	150707785	8430878	374	36692										
NCAPG2	54892	hgsc.bcm.edu	37	chr7	158472756	158472756	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aaacaacaatgcagcatttgAtcgaacttcagagtttctgg	8	8	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:158472756A>G	ENST00000409423.1	-	12	1214	c.1042T>C	c.(1042-1044)Tca>Cca	p.S348P	NCAPG2_ENST00000275830.10_Missense_Mutation_p.S140P|NCAPG2_ENST00000449727.2_Missense_Mutation_p.S348P|NCAPG2_ENST00000356309.3_Missense_Mutation_p.S348P|NCAPG2_ENST00000409339.3_Missense_Mutation_p.S348P	NM_001281932.1	NP_001268861.1	Q86XI2	CNDG2_HUMAN	non-SMC condensin II complex, subunit G2	348					chromosome condensation (GO:0030261)|inner cell mass cell proliferation (GO:0001833)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	methylated histone binding (GO:0035064)			NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(7)|liver(1)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	39	Ovarian(565;0.152)	all_cancers(7;3.44e-11)|all_epithelial(9;3.05e-05)|all_hematologic(28;0.014)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.187)|STAD - Stomach adenocarcinoma(7;0.18)		GCAGCATTTGATCGAACTTCA	0.363																																					p.S348P		Atlas-SNP	.											.	NCAPG2	80	.	0			c.T1042C						.						115	106	109					7																	158472756		1841	4099	5940	SO:0001583	missense	54892	exon11			CATTTGATCGAAC	BC043404	CCDS43686.1, CCDS64816.1	7q36.3	2006-09-04	2006-09-04	2006-09-04	ENSG00000146918	ENSG00000146918			21904	protein-coding gene	gene with protein product		608532	"leucine zipper protein 5"	LUZP5		14532007	Standard	NM_001281933		Approved	FLJ20311, MTB, CAP-G2, hCAP-G2	uc003wnv.1	Q86XI2	OTTHUMG00000151438	ENST00000409423.1:c.1042T>C	chr7.hg19:g.158472756A>G	ENSP00000386569:p.Ser348Pro	146.0	0.0		120.0	5.0	NM_017760	A4D228|Q7Z3J9|Q8WUG8|Q9BRX6|Q9H8S2|Q9H9K6	Missense_Mutation	SNP	ENST00000409423.1	hg19	CCDS43686.1	.	.	.	.	.	.	.	.	.	.	A	18.42	3.619619	0.66787	.	.	ENSG00000146918	ENST00000356309;ENST00000409423;ENST00000275830;ENST00000409339;ENST00000449727	T;T;T;T;T	0.48522	1.41;1.41;0.81;1.41;1.41	6.17	5.0	0.66597	Armadillo-like helical (1);Armadillo-type fold (1);	0.063219	0.64402	D	0.000003	T	0.60856	0.2301	L	0.51422	1.61	0.46458	D	0.999057	D;D;D	0.71674	0.997;0.997;0.998	D;D;D	0.66847	0.911;0.939;0.947	T	0.61302	-0.7090	10	0.52906	T	0.07	-10.6941	13.2852	0.60239	0.752:0.248:0.0:0.0	.	348;140;348	Q86XI2-2;E7EUH9;Q86XI2	.;.;CNDG2_HUMAN	P	348;348;140;348;348	ENSP00000348657:S348P;ENSP00000386569:S348P;ENSP00000275830:S140P;ENSP00000387007:S348P;ENSP00000388326:S348P	ENSP00000275830:S140P	S	-	1	0	NCAPG2	158165517	0.998000	0.40836	0.696000	0.30242	0.839000	0.47603	2.303000	0.43646	1.123000	0.41961	0.533000	0.62120	TCA	.	.		0.363	NCAPG2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327111.1	NM_017760		G	158472756	A	G	158472756	3	3	259	1	0	0	0	0	1	0	0	0	10217	333	12	2	2461	2	NCAPG2	7	158472756	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	7764971	158472756	665907	375	36693										
CSMD1	64478	hgsc.bcm.edu	37	chr8	2823315	2823315	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acctttgcagacaggtttgcTcggattccacctgccgtctt	9	13	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:2823315T>C	ENST00000520002.1	-	60	9820	c.9265A>G	c.(9265-9267)Agc>Ggc	p.S3089G	CSMD1_ENST00000537824.1_Missense_Mutation_p.S3088G|CSMD1_ENST00000602723.1_Intron|CSMD1_ENST00000400186.3_Intron|CSMD1_ENST00000542608.1_Intron|CSMD1_ENST00000602557.1_Missense_Mutation_p.S3089G			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	3089	Sushi 24. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		ACAGGTTTGCTCGGATTCCAC	0.418																																					p.S3088G		Atlas-SNP	.											.	CSMD1	1469	.	0			c.A9262G						.						80	78	78					8																	2823315		1988	4181	6169	SO:0001583	missense	64478	exon59			GTTTGCTCGGATT			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.9265A>G	chr8.hg19:g.2823315T>C	ENSP00000430733:p.Ser3089Gly	145.0	0.0		75.0	4.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.86|11.86	1.765752|1.765752	0.31228|0.31228	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000335551|ENST00000520002;ENST00000318252;ENST00000537824	.|T;T	.|0.66460	.|-0.21;-0.21	5.42|5.42	5.42|5.42	0.78866|0.78866	.|Complement control module (2);Sushi/SCR/CCP (3);	.|0.133108	.|0.50627	.|D	.|0.000113	T|T	0.65154|0.65154	0.2664|0.2664	L|L	0.56199|0.56199	1.76|1.76	0.80722|0.80722	D|D	1|1	.|B;B	.|0.21147	.|0.052;0.018	.|B;B	.|0.29176	.|0.055;0.099	T|T	0.61893|0.61893	-0.6969|-0.6969	5|10	.|0.37606	.|T	.|0.19	.|.	15.475|15.475	0.75471|0.75471	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|3089;3089	.|E5RIG2;Q96PZ7	.|.;CSMD1_HUMAN	G|G	2505|3089;2950;3088	.|ENSP00000430733:S3089G;ENSP00000441462:S3088G	.|ENSP00000320445:S2950G	E|S	-|-	2|1	0|0	CSMD1|CSMD1	2810722|2810722	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.027000|0.027000	0.11550|0.11550	4.845000|4.845000	0.62853|0.62853	2.056000|2.056000	0.61249|0.61249	0.533000|0.533000	0.62120|0.62120	GAG|AGC	.	.		0.418	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		C	2823315	T	C	2823315	3	2	259	1	0	0	0	0	1	0	0	0	3946	1551	54	2	1480	2	CSMD1	8	2823315	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10		2823315	143540707	376	36694										
SLC7A2	6542	hgsc.bcm.edu	37	chr8	17422622	17422622	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccaagaaatctcagttcaccTttcatattccatgaaaagac	4	11	3	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:17422622T>C	ENST00000494857.1	+	13	2162	c.1944T>C	c.(1942-1944)ccT>ccC	p.P648P	SLC7A2_ENST00000398090.3_Silent_p.P687P|SLC7A2_ENST00000470360.1_Silent_p.P687P|SLC7A2_ENST00000004531.10_Silent_p.P688P|SLC7A2_ENST00000522656.1_Silent_p.P648P	NM_001008539.3	NP_001008539.3	P52569	CTR2_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	648					amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|macrophage activation (GO:0042116)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide production involved in inflammatory response (GO:0002537)|regulation of inflammatory response (GO:0050727)|regulation of macrophage activation (GO:0043030)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	basic amino acid transmembrane transporter activity (GO:0015174)|high-affinity arginine transmembrane transporter activity (GO:0005289)|L-lysine transmembrane transporter activity (GO:0015189)|L-ornithine transmembrane transporter activity (GO:0000064)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(4)|lung(8)|ovary(2)|skin(1)|stomach(1)	25				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	L-Lysine(DB00123)|L-Ornithine(DB00129)	TCAGTTCACCTTTCATATTCC	0.418																																					p.P688P		Atlas-SNP	.											.	SLC7A2	157	.	0			c.T2064C						.						112	89	97					8																	17422622		2203	4300	6503	SO:0001819	synonymous_variant	6542	exon12			TTCACCTTTCATA	D29990	CCDS6002.2, CCDS34852.1, CCDS55203.1	8p22	2013-05-22			ENSG00000003989	ENSG00000003989		"Solute carriers"	11060	protein-coding gene	gene with protein product		601872		ATRC2		8954799	Standard	NM_001164771		Approved	CAT-2, HCAT2	uc011kye.2	P52569	OTTHUMG00000130819	ENST00000494857.1:c.1944T>C	chr8.hg19:g.17422622T>C		169.0	0.0		87.0	4.0	NM_001164771	B7ZL54|O15291|O15292|Q14CQ6|Q6NSZ7|Q86TC6	Silent	SNP	ENST00000494857.1	hg19	CCDS34852.1																																																																																			.	.		0.418	SLC7A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253367.3	NM_003046		C	17422622	T	C	17422622	2	2	259	1	0	0	0	0	0	0	0	1	14712	1596	56	2		2	SLC7A2	8	17422622	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	14599307	17422622	128941400	377	36695										
PCM1	5108	hgsc.bcm.edu	37	chr8	17867212	17867212	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttaaacagagatgcaaaaggAaaatagaagcaactggagtg	11	4	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:17867212A>G	ENST00000519253.1	+	31	5346	c.5095A>G	c.(5095-5097)Aaa>Gaa	p.K1699E	PCM1_ENST00000524226.1_Missense_Mutation_p.K1653E|PCM1_ENST00000325083.8_Missense_Mutation_p.K1707E|PCM1_ENST00000327578.8_Missense_Mutation_p.K406E			Q15154	PCM1_HUMAN	pericentriolar material 1	1707	Interaction with HAP1.				centrosome organization (GO:0051297)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|interkinetic nuclear migration (GO:0022027)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|microtubule anchoring (GO:0034453)|microtubule anchoring at centrosome (GO:0034454)|mitotic cell cycle (GO:0000278)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|positive regulation of intracellular protein transport (GO:0090316)|protein localization to centrosome (GO:0071539)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|pericentriolar material (GO:0000242)|protein complex (GO:0043234)	identical protein binding (GO:0042802)		PCM1/JAK2(30)	breast(4)|endometrium(8)|kidney(5)|large_intestine(16)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	48				Colorectal(111;0.0789)		ATGCAAAAGGAAAATAGAAGC	0.308			T	"RET, JAK2"	"papillary thyroid, CML, MPD"																																p.K1707E		Atlas-SNP	.		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"E, L"	.	PCM1	120	.	0			c.A5119G						.						54	52	52					8																	17867212		1830	4074	5904	SO:0001583	missense	5108	exon31			AAAAGGAAAATAG		CCDS47812.1	8p22-p21.3	2008-08-08			ENSG00000078674	ENSG00000078674			8727	protein-coding gene	gene with protein product		600299				8120099, 15659651	Standard	NM_006197		Approved	PTC4	uc003wyi.4	Q15154	OTTHUMG00000163699	ENST00000519253.1:c.5095A>G	chr8.hg19:g.17867212A>G	ENSP00000431099:p.Lys1699Glu	138.0	0.0		67.0	4.0	NM_006197	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Missense_Mutation	SNP	ENST00000519253.1	hg19		.	.	.	.	.	.	.	.	.	.	A	17.25	3.342073	0.61073	.	.	ENSG00000078674	ENST00000325083;ENST00000519253;ENST00000524226;ENST00000327578	T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3	4.91	4.91	0.64330	.	0.316425	0.32769	N	0.005662	T	0.71804	0.3383	L	0.50333	1.59	0.39847	D	0.973192	P;P;B;P;P;P;P	0.50272	0.79;0.79;0.379;0.79;0.827;0.933;0.79	P;P;B;P;B;P;P	0.53760	0.561;0.561;0.187;0.561;0.442;0.734;0.561	T	0.76094	-0.3085	10	0.59425	D	0.04	-25.7633	14.8517	0.70300	1.0:0.0:0.0:0.0	.	1699;1707;506;1699;1652;1653;1707	B9EIS5;D3DSQ0;B4DJ00;E7ETA6;Q15154-2;E7EV56;Q15154	.;.;.;.;.;.;PCM1_HUMAN	E	1707;1699;1653;406	ENSP00000327077:K1707E;ENSP00000431099:K1699E;ENSP00000430521:K1653E;ENSP00000328332:K406E	ENSP00000327077:K1707E	K	+	1	0	PCM1	17911492	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.778000	0.75043	1.982000	0.57802	0.377000	0.23210	AAA	.	.		0.308	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197		G	17867212	A	G	17867212	3	3	259	1	0	0	0	0	1	0	0	0	11593	247	9	2	5233	2	PCM1	8	17867212	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	444590	17867212	128496810	378	36696										
PCM1	5108	hgsc.bcm.edu	37	chr8	17868140	17868140	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	taaaaggattcttgaagatcAtggctcacctgctggagaga	11	7	3	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:17868140A>G	ENST00000519253.1	+	32	5410	c.5159A>G	c.(5158-5160)cAt>cGt	p.H1720R	PCM1_ENST00000524226.1_Missense_Mutation_p.H1674R|PCM1_ENST00000325083.8_Missense_Mutation_p.H1728R|PCM1_ENST00000327578.8_Missense_Mutation_p.H427R			Q15154	PCM1_HUMAN	pericentriolar material 1	1728	Interaction with HAP1.				centrosome organization (GO:0051297)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|interkinetic nuclear migration (GO:0022027)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|microtubule anchoring (GO:0034453)|microtubule anchoring at centrosome (GO:0034454)|mitotic cell cycle (GO:0000278)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|positive regulation of intracellular protein transport (GO:0090316)|protein localization to centrosome (GO:0071539)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|pericentriolar material (GO:0000242)|protein complex (GO:0043234)	identical protein binding (GO:0042802)		PCM1/JAK2(30)	breast(4)|endometrium(8)|kidney(5)|large_intestine(16)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	48				Colorectal(111;0.0789)		CTTGAAGATCATGGCTCACCT	0.393			T	"RET, JAK2"	"papillary thyroid, CML, MPD"																																p.H1728R		Atlas-SNP	.		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"E, L"	.	PCM1	120	.	0			c.A5183G						.						128	125	126					8																	17868140		1871	4104	5975	SO:0001583	missense	5108	exon32			AAGATCATGGCTC		CCDS47812.1	8p22-p21.3	2008-08-08			ENSG00000078674	ENSG00000078674			8727	protein-coding gene	gene with protein product		600299				8120099, 15659651	Standard	NM_006197		Approved	PTC4	uc003wyi.4	Q15154	OTTHUMG00000163699	ENST00000519253.1:c.5159A>G	chr8.hg19:g.17868140A>G	ENSP00000431099:p.His1720Arg	156.0	0.0		71.0	4.0	NM_006197	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Missense_Mutation	SNP	ENST00000519253.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	6.128|6.128	0.391823|0.391823	0.11581|0.11581	.|.	.|.	ENSG00000078674|ENSG00000078674	ENST00000325083;ENST00000519253;ENST00000524226;ENST00000327578|ENST00000522275	T;T;T;T|.	0.63417|.	-0.04;-0.04;-0.04;-0.04|.	4.85|4.85	-0.802|-0.802	0.10889|0.10889	.|.	0.805653|.	0.11459|.	N|.	0.561977|.	T|T	0.09291|0.09291	0.0229|0.0229	N|N	0.03608|0.03608	-0.345|-0.345	0.22500|0.22500	N|N	0.999041|0.999041	B;B;B;B;B;B;B|.	0.10296|.	0.0;0.0;0.0;0.0;0.0;0.003;0.0|.	B;B;B;B;B;B;B|.	0.15484|.	0.002;0.002;0.001;0.002;0.001;0.013;0.002|.	T|T	0.28870|0.28870	-1.0030|-1.0030	10|5	0.22109|.	T|.	0.4|.	-8.7879|-8.7879	1.8844|1.8844	0.03235|0.03235	0.3329:0.3663:0.0902:0.2106|0.3329:0.3663:0.0902:0.2106	.|.	1720;1728;527;1720;1673;1674;1728|.	B9EIS5;D3DSQ0;B4DJ00;E7ETA6;Q15154-2;E7EV56;Q15154|.	.;.;.;.;.;.;PCM1_HUMAN|.	R|V	1728;1720;1674;427|468	ENSP00000327077:H1728R;ENSP00000431099:H1720R;ENSP00000430521:H1674R;ENSP00000328332:H427R|.	ENSP00000327077:H1728R|.	H|M	+|+	2|1	0|0	PCM1|PCM1	17912420|17912420	0.817000|0.817000	0.29147|0.29147	0.939000|0.939000	0.37840|0.37840	0.951000|0.951000	0.60555|0.60555	0.318000|0.318000	0.19504|0.19504	0.256000|0.256000	0.21614|0.21614	0.459000|0.459000	0.35465|0.35465	CAT|ATG	.	.		0.393	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197		G	17868140	A	G	17868140	3	3	259	1	0	0	0	0	1	0	0	0	11593	217	8	2	5301	2	PCM1	8	17868140	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	928	17868140	128495882	379	36697										
LGI3	203190	hgsc.bcm.edu	37	chr8	22012911	22012911	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggccctatccatacaagaacTgcagcagcgggaggtgggag	15	10	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:22012911T>C	ENST00000306317.2	-	2	561	c.272A>G	c.(271-273)cAg>cGg	p.Q91R	LGI3_ENST00000424267.2_Missense_Mutation_p.Q91R	NM_139278.2	NP_644807.1	Q8N145	LGI3_HUMAN	leucine-rich repeat LGI family, member 3	91					exocytosis (GO:0006887)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|extracellular region (GO:0005576)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	catalytic activity (GO:0003824)			endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	17				Colorectal(74;0.00189)|COAD - Colon adenocarcinoma(73;0.0612)|READ - Rectum adenocarcinoma(644;0.0999)		ATACAAGAACTGCAGCAGCGG	0.607																																					p.Q91R		Atlas-SNP	.											.	LGI3	44	.	0			c.A272G						.						162	157	158					8																	22012911		2203	4300	6503	SO:0001583	missense	203190	exon2			AAGAACTGCAGCA	AJ487518	CCDS6025.1	8p21.2	2008-07-28			ENSG00000168481	ENSG00000168481			18711	protein-coding gene	gene with protein product		608302				12023020, 18628660	Standard	NM_139278		Approved		uc003xav.3	Q8N145	OTTHUMG00000131599	ENST00000306317.2:c.272A>G	chr8.hg19:g.22012911T>C	ENSP00000302297:p.Gln91Arg	113.0	0.0		32.0	4.0	NM_139278	A5PLP2|Q86TL4|Q8N296	Missense_Mutation	SNP	ENST00000306317.2	hg19	CCDS6025.1	.	.	.	.	.	.	.	.	.	.	T	15.76	2.929034	0.52759	.	.	ENSG00000168481	ENST00000306317;ENST00000424267;ENST00000517694	T;T;D	0.89810	0.35;0.51;-2.57	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	D	0.88822	0.6541	N	0.20445	0.575	0.50467	D	0.999871	D;B	0.59357	0.985;0.192	D;B	0.71414	0.973;0.052	D	0.88685	0.3205	10	0.44086	T	0.13	-27.5892	11.6456	0.51259	0.0:0.0:0.0:1.0	.	91;91	A5PLP2;Q8N145	.;LGI3_HUMAN	R	91;91;52	ENSP00000302297:Q91R;ENSP00000399121:Q91R;ENSP00000427817:Q52R	ENSP00000302297:Q91R	Q	-	2	0	LGI3	22068856	1.000000	0.71417	1.000000	0.80357	0.233000	0.25261	6.856000	0.75450	2.056000	0.61249	0.528000	0.53228	CAG	.	.		0.607	LGI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254482.1			C	22012911	T	C	22012911	3	2	259	1	0	0	0	0	1	0	0	0	8762	1580	55	2	1402	2	LGI3	8	22012911	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	4144771	22012911	124351111	380	36698										
C8orf58	541565	hgsc.bcm.edu	37	chr8	22458617	22458617	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cgccttaccgggcctttctcAggactccctggactttgaat	9	14	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:22458617A>G	ENST00000289989.5	+	2	337	c.263A>G	c.(262-264)cAg>cGg	p.Q88R	C8orf58_ENST00000453427.2_3'UTR|C8orf58_ENST00000409586.3_Missense_Mutation_p.Q88R			Q8NAV2	CH058_HUMAN	chromosome 8 open reading frame 58	88										endometrium(1)|lung(1)|ovary(1)|skin(1)	4		Prostate(55;0.0421)|Breast(100;0.102)|all_epithelial(46;0.142)		BRCA - Breast invasive adenocarcinoma(99;0.00563)|Colorectal(74;0.0145)|COAD - Colon adenocarcinoma(73;0.0608)		GGCCTTTCTCAGGACTCCCTG	0.652																																					p.Q88R		Atlas-SNP	.											.	C8orf58	17	.	0			c.A263G						.						25	30	28					8																	22458617		2193	4297	6490	SO:0001583	missense	541565	exon2			TTTCTCAGGACTC	BC012750	CCDS34862.1, CCDS56527.1, CCDS75708.1	8p21.3	2010-08-17			ENSG00000241852	ENSG00000241852			32233	protein-coding gene	gene with protein product							Standard	NM_001013842		Approved	FLJ34715	uc003xce.3	Q8NAV2	OTTHUMG00000154160	ENST00000289989.5:c.263A>G	chr8.hg19:g.22458617A>G	ENSP00000289989:p.Gln88Arg	93.0	0.0		36.0	4.0	NM_001013842	B4DI44	Missense_Mutation	SNP	ENST00000289989.5	hg19	CCDS34862.1	.	.	.	.	.	.	.	.	.	.	a	17.97	3.518831	0.64634	.	.	ENSG00000248235;ENSG00000241852;ENSG00000241852;ENSG00000241852	ENST00000450780;ENST00000409586;ENST00000289989;ENST00000381191	.	.	.	4.1	-0.126	0.13515	.	0.364625	0.19601	N	0.110389	T	0.52256	0.1723	M	0.68317	2.08	0.26117	N	0.980603	D;D;D	0.71674	0.998;0.998;0.998	D;D;D	0.80764	0.994;0.994;0.994	T	0.38972	-0.9636	9	0.72032	D	0.01	-7.5099	2.9471	0.05849	0.5033:0.0:0.1114:0.3853	.	88;16;88	Q8NAV2-2;E7EQH9;Q8NAV2	.;.;CH058_HUMAN	R	157;88;88;16	.	ENSP00000399696:Q157R	Q	+	2	0	AC037459.4;C8orf58	22514562	0.939000	0.31865	0.997000	0.53966	0.880000	0.50808	1.026000	0.30103	0.205000	0.20568	0.368000	0.22195	CAG	.	.		0.652	C8orf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334183.1	NM_001013842		G	22458617	A	G	22458617	3	3	259	1	0	0	0	0	1	0	0	0	2435	188	7	2	269	2	C8orf58	8	22458617	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	445706	22458617	123905405	381	36699										
TNFRSF10D	8793	hgsc.bcm.edu	37	chr8	22995463	22995463	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	caccagttggtcctgaattgTttcctttgcatgtccttctt	7	11	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:22995463T>C	ENST00000312584.3	-	9	1175	c.1081A>G	c.(1081-1083)Aca>Gca	p.T361A		NM_003840.4	NP_003831.2	Q9UBN6	TR10D_HUMAN	tumor necrosis factor receptor superfamily, member 10d, decoy with truncated death domain	361	Death; truncated.				apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0147)|COAD - Colon adenocarcinoma(73;0.0612)		TCCTGAATTGTTTCCTTTGCA	0.493																																					p.T361A		Atlas-SNP	.											.	TNFRSF10D	21	.	0			c.A1081G						.						98	80	86					8																	22995463		2203	4300	6503	SO:0001583	missense	8793	exon9			GAATTGTTTCCTT	AF029761	CCDS6038.1	8p21	2006-02-22			ENSG00000173530	ENSG00000173530		"Tumor necrosis factor receptor superfamily", "CD molecules"	11907	protein-coding gene	gene with protein product		603614				9382840, 9537512	Standard	NM_003840		Approved	DcR2, TRUNDD, TRAILR4, CD264	uc003xcz.2	Q9UBN6	OTTHUMG00000097845	ENST00000312584.3:c.1081A>G	chr8.hg19:g.22995463T>C	ENSP00000310263:p.Thr361Ala	195.0	0.0		98.0	4.0	NM_003840	B2R8W0|Q9Y6Q4	Missense_Mutation	SNP	ENST00000312584.3	hg19	CCDS6038.1	.	.	.	.	.	.	.	.	.	.	T	7.948	0.744320	0.15710	.	.	ENSG00000173530	ENST00000312584	D	0.82619	-1.63	1.96	0.795	0.18643	.	3.827150	0.01571	U	0.020596	T	0.72095	0.3418	L	0.29908	0.895	0.09310	N	1	P	0.36222	0.544	B	0.34873	0.191	T	0.59069	-0.7523	10	0.23302	T	0.38	.	3.4681	0.07557	0.0:0.2172:0.0:0.7828	.	361	Q9UBN6	TR10D_HUMAN	A	361	ENSP00000310263:T361A	ENSP00000310263:T361A	T	-	1	0	TNFRSF10D	23051408	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-0.540000	0.06106	0.218000	0.20820	0.379000	0.24179	ACA	.	.		0.493	TNFRSF10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215135.1			C	22995463	T	C	22995463	3	2	259	1	0	0	0	0	1	0	0	0	16298	1725	60	2	83	2	TNFRSF10D	8	22995463	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	536846	22995463	123368559	382	36700										
SCARA3	51435	hgsc.bcm.edu	37	chr8	27509080	27509080	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aacctatctttgcacacatcGgtgcggattctttacctctt	6	12	3	0	rs371890046		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:27509080G>T	ENST00000301904.3	+	3	182	c.162G>T	c.(160-162)tcG>tcT	p.S54S	SCARA3_ENST00000337221.4_Silent_p.S54S	NM_016240.2	NP_057324.2	Q6AZY7	SCAR3_HUMAN	scavenger receptor class A, member 3	54					receptor-mediated endocytosis (GO:0006898)|response to oxidative stress (GO:0006979)|UV protection (GO:0009650)	collagen trimer (GO:0005581)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)			breast(1)|large_intestine(3)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	9		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0219)|Colorectal(74;0.148)		TGCACACATCGGTGCGGATTC	0.662																																					p.S54S		Atlas-SNP	.											.	SCARA3	93	.	0			c.G162T						.						86	83	84					8																	27509080		2203	4300	6503	SO:0001819	synonymous_variant	51435	exon3			CACATCGGTGCGG	AB007829	CCDS34870.1, CCDS34871.1	8p21	2010-03-24			ENSG00000168077	ENSG00000168077			19000	protein-coding gene	gene with protein product	"macrophage scavenger receptor-like 1"	602728				9747040, 9580669	Standard	NM_182826		Approved	CSR1, CSR, MSLR1, APC7, MSRL1	uc003xga.1	Q6AZY7	OTTHUMG00000163898	ENST00000301904.3:c.162G>T	chr8.hg19:g.27509080G>T		251.0	0.0		79.0	4.0	NM_182826	Q9UM15|Q9UM16	Silent	SNP	ENST00000301904.3	hg19	CCDS34871.1																																																																																			.	.		0.662	SCARA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376258.2	NM_016240		T	27509080	G	T	27509080	2	4	259	1	0	0	0	0	0	0	0	1	13894	1103	39	1		1	SCARA3	8	27509080	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	4513617	27509080	118854942	383	36701										
CCDC25	55246	hgsc.bcm.edu	37	chr8	27605739	27605739	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgggaaccgctcgactttggTcttttctaatcggttcagga	11	9	3	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:27605739T>C	ENST00000356537.4	-	7	499	c.406A>G	c.(406-408)Acc>Gcc	p.T136A	RP11-16P20.3_ENST00000521510.1_RNA|CCDC25_ENST00000539095.1_Missense_Mutation_p.T68A|CCDC25_ENST00000522915.1_Missense_Mutation_p.T68A	NM_018246.2	NP_060716.2	Q86WR0	CCD25_HUMAN	coiled-coil domain containing 25	136						extracellular vesicular exosome (GO:0070062)		p.T136P(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)	7		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0223)|KIRC - Kidney renal clear cell carcinoma(542;0.11)|Kidney(114;0.131)|Colorectal(74;0.154)		TCGACTTTGGTCTTTTCTAAT	0.388																																					p.T136A		Atlas-SNP	.											CCDC25,NS,carcinoma,0,1	CCDC25	14	.	1	Substitution - Missense(1)	kidney(1)	c.A406G						.						122	118	119					8																	27605739		2203	4300	6503	SO:0001583	missense	55246	exon7			CTTTGGTCTTTTC	AK001715	CCDS6062.2	8p21.1	2006-09-20			ENSG00000147419	ENSG00000147419			25591	protein-coding gene	gene with protein product						12477932	Standard	NM_018246		Approved	FLJ10853	uc003xgc.3	Q86WR0	OTTHUMG00000132173	ENST00000356537.4:c.406A>G	chr8.hg19:g.27605739T>C	ENSP00000348933:p.Thr136Ala	249.0	0.0		110.0	5.0	NM_018246	Q0P663|Q96SI2|Q9NV98	Missense_Mutation	SNP	ENST00000356537.4	hg19	CCDS6062.2	.	.	.	.	.	.	.	.	.	.	T	19.67	3.871617	0.72065	.	.	ENSG00000147419	ENST00000356537;ENST00000539095;ENST00000522915	.	.	.	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.68063	0.2960	M	0.93016	3.37	0.80722	D	1	P	0.41393	0.748	B	0.33339	0.162	T	0.77474	-0.2574	9	0.87932	D	0	-8.3639	13.7503	0.62904	0.0:0.0:0.0:1.0	.	136	Q86WR0	CCD25_HUMAN	A	136;68;68	.	ENSP00000348933:T136A	T	-	1	0	CCDC25	27661658	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.850000	0.75420	2.132000	0.65825	0.533000	0.62120	ACC	.	.		0.388	CCDC25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255224.1	NM_018246		C	27605739	T	C	27605739	3	2	259	1	0	0	0	0	1	0	0	0	2802	1667	58	2	232	2	CCDC25	8	27605739	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	96659	27605739	118758283	384	36702										
FZD3	7976	hgsc.bcm.edu	37	chr8	28385289	28385289	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttcacgccagtgcatggggcAtccccggaactctaaccatc	9	15	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:28385289A>G	ENST00000240093.3	+	5	1490	c.1012A>G	c.(1012-1014)Atc>Gtc	p.I338V	RNA5SP259_ENST00000365541.1_RNA|FZD3_ENST00000537916.1_Missense_Mutation_p.I338V	NM_017412.3	NP_059108.1	Q9NPG1	FZD3_HUMAN	frizzled class receptor 3	338					canonical Wnt signaling pathway (GO:0060070)|cell proliferation in midbrain (GO:0033278)|commissural neuron axon guidance (GO:0071679)|establishment of planar polarity (GO:0001736)|facial nucleus development (GO:0021754)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hair follicle development (GO:0001942)|inner ear morphogenesis (GO:0042472)|neural tube closure (GO:0001843)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|post-anal tail morphogenesis (GO:0036342)|vasculature development (GO:0001944)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|neuron projection membrane (GO:0032589)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(15)|ovary(1)|prostate(1)|skin(1)	41		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.109)|Kidney(114;0.13)|Colorectal(74;0.23)		TGCATGGGGCATCCCCGGAAC	0.438																																					p.I338V		Atlas-SNP	.											.	FZD3	65	.	0			c.A1012G						.						147	143	145					8																	28385289		2203	4300	6503	SO:0001583	missense	7976	exon5			TGGGGCATCCCCG	AJ272427	CCDS6069.1	8p21	2014-06-27	2014-01-29		ENSG00000104290	ENSG00000104290		"GPCR / Class F : Frizzled receptors"	4041	protein-coding gene	gene with protein product		606143	"frizzled (Drosophila) homolog 3", "frizzled homolog 3 (Drosophila)", "frizzled 3, seven transmembrane spanning receptor", "frizzled family receptor 3"			10777673, 10873558	Standard	NM_145866		Approved		uc010lvb.3	Q9NPG1	OTTHUMG00000102145	ENST00000240093.3:c.1012A>G	chr8.hg19:g.28385289A>G	ENSP00000240093:p.Ile338Val	133.0	0.0		59.0	4.0	NM_017412	A8K615	Missense_Mutation	SNP	ENST00000240093.3	hg19	CCDS6069.1	.	.	.	.	.	.	.	.	.	.	A	2.075	-0.412164	0.04799	.	.	ENSG00000104290	ENST00000537916;ENST00000240093	T;T	0.81330	-1.48;-1.48	5.32	5.32	0.75619	GPCR, family 2-like (1);	0.110358	0.64402	D	0.000011	T	0.63988	0.2558	N	0.13003	0.285	0.45205	D	0.998214	B	0.13594	0.008	B	0.23150	0.044	T	0.59490	-0.7445	10	0.02654	T	1	.	14.0788	0.64907	1.0:0.0:0.0:0.0	.	338	Q9NPG1	FZD3_HUMAN	V	338	ENSP00000437489:I338V;ENSP00000240093:I338V	ENSP00000240093:I338V	I	+	1	0	FZD3	28441208	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.298000	0.43602	2.007000	0.58848	0.460000	0.39030	ATC	.	.		0.438	FZD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219986.2	NM_145866		G	28385289	A	G	28385289	3	3	259	1	0	0	0	0	1	0	0	0	6139	217	8	2	1022	2	FZD3	8	28385289	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	779550	28385289	117978733	385	36703										
FUT10	84750	hgsc.bcm.edu	37	chr8	33230192	33230192	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gggcttctttcttggattgtTcaaagctggaaatccacatc	9	9	3	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:33230192T>C	ENST00000327671.5	-	5	1974	c.1343A>G	c.(1342-1344)gAa>gGa	p.E448G	FUT10_ENST00000524021.1_Missense_Mutation_p.E420G|FUT10_ENST00000518672.1_Missense_Mutation_p.E420G	NM_032664.3	NP_116053.3	Q6P4F1	FUT10_HUMAN	fucosyltransferase 10 (alpha (1,3) fucosyltransferase)	448					embryo development (GO:0009790)|fertilization (GO:0009566)|fucosylation (GO:0036065)|hemopoiesis (GO:0030097)|L-fucose catabolic process (GO:0042355)|nervous system development (GO:0007399)|protein folding (GO:0006457)|protein glycosylation (GO:0006486)|protein targeting (GO:0006605)|wound healing (GO:0042060)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)			cervix(1)|endometrium(1)|large_intestine(7)|liver(1)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2)	29				KIRC - Kidney renal clear cell carcinoma(67;0.129)|Kidney(114;0.154)		CTTGGATTGTTCAAAGCTGGA	0.473																																					p.E448G		Atlas-SNP	.											.	FUT10	62	.	0			c.A1343G						.						93	89	91					8																	33230192		2203	4300	6503	SO:0001583	missense	84750	exon5			GATTGTTCAAAGC	AJ512465	CCDS6088.1	8p12	2013-02-26			ENSG00000172728	ENSG00000172728		"Fucosyltransferases"	19234	protein-coding gene	gene with protein product							Standard	NM_032664		Approved		uc003xje.3	Q6P4F1	OTTHUMG00000163954	ENST00000327671.5:c.1343A>G	chr8.hg19:g.33230192T>C	ENSP00000332757:p.Glu448Gly	174.0	0.0		94.0	4.0	NM_032664	A8KAC8|Q70GG3|Q8IVI6|Q8IVI7|Q8IVJ3|Q8TE43|Q9BSR3	Missense_Mutation	SNP	ENST00000327671.5	hg19	CCDS6088.1	.	.	.	.	.	.	.	.	.	.	T	14.63	2.594131	0.46214	.	.	ENSG00000172728	ENST00000327671;ENST00000380081;ENST00000518672;ENST00000524021	T;T;T	0.39787	1.06;1.07;1.07	5.45	4.26	0.50523	.	0.469911	0.20431	N	0.092465	T	0.38506	0.1043	M	0.72894	2.215	0.80722	D	1	P;B;B	0.40144	0.704;0.181;0.022	B;B;B	0.35182	0.197;0.051;0.04	T	0.14755	-1.0461	10	0.30078	T	0.28	-1.4095	9.6994	0.40178	0.0:0.0839:0.0:0.9161	.	498;448;490	B4E056;Q6P4F1;E7EU36	.;FUT10_HUMAN;.	G	448;490;420;420	ENSP00000332757:E448G;ENSP00000430428:E420G;ENSP00000429870:E420G	ENSP00000332757:E448G	E	-	2	0	FUT10	33349734	1.000000	0.71417	0.935000	0.37517	0.969000	0.65631	4.397000	0.59690	0.875000	0.35847	0.482000	0.46254	GAA	.	.		0.473	FUT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376540.1	NM_032664		C	33230192	T	C	33230192	3	2	259	1	0	0	0	0	1	0	0	0	6110	1783	62	2	100	2	FUT10	8	33230192	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	4844903	33230192	113133830	386	36704										
KCNU1	157855	hgsc.bcm.edu	37	chr8	36693822	36693822	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gggtttatatagggtgctctCtatcaagaactatgattcta	9	6	3	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:36693822C>T	ENST00000399881.3	+	13	1341	c.1304C>T	c.(1303-1305)tCt>tTt	p.S435F		NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	435	RCK N-terminal.				multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)	p.S435F(2)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		AGGGTGCTCTCTATCAAGAAC	0.348																																					p.S435F		Atlas-SNP	.											KCNU1_ENST00000399881,rectum,carcinoma,0,2	KCNU1	359	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1304T						.						140	133	135					8																	36693822		1827	4079	5906	SO:0001583	missense	157855	exon13			TGCTCTCTATCAA	BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.1304C>T	chr8.hg19:g.36693822C>T	ENSP00000382770:p.Ser435Phe	89.0	0.0		35.0	2.0	NM_001031836		Missense_Mutation	SNP	ENST00000399881.3	hg19	CCDS55220.1	.	.	.	.	.	.	.	.	.	.	C	16.18	3.049503	0.55218	.	.	ENSG00000215262	ENST00000399881	T	0.70282	-0.47	5.6	4.71	0.59529	NAD(P)-binding domain (1);	0.000000	0.35151	U	0.003416	D	0.84074	0.5392	M	0.77313	2.365	0.80722	D	1	D	0.89917	1.0	D	0.72338	0.977	D	0.86779	0.1978	10	0.87932	D	0	-4.1264	16.6359	0.85059	0.0:0.87:0.13:0.0	.	435	A8MYU2	KCNU1_HUMAN	F	435	ENSP00000382770:S435F	ENSP00000382770:S435F	S	+	2	0	KCNU1	36812980	0.998000	0.40836	0.929000	0.37066	0.298000	0.27526	4.151000	0.58105	1.466000	0.48025	0.650000	0.86243	TCT	.	.		0.348	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836		T	36693822	C	T	36693822	3	4	259	1	0	0	0	0	1	0	0	0	8102	913	32	3	1354	3	KCNU1	8	36693822	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	3463630	36693822	109670200	387	36705										
HOOK3	84376	hgsc.bcm.edu	37	chr8	42819473	42819473	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggttgcagcattgcaggaagAgaaaagtagtttgttggcag	15	4	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:42819473A>G	ENST00000307602.4	+	9	835	c.635A>G	c.(634-636)gAg>gGg	p.E212G		NM_032410.3	NP_115786.1	Q86VS8	HOOK3_HUMAN	hook microtubule-tethering protein 3	212					cytoplasmic microtubule organization (GO:0031122)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|Golgi localization (GO:0051645)|interkinetic nuclear migration (GO:0022027)|lysosome organization (GO:0007040)|microtubule anchoring at centrosome (GO:0034454)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|protein localization to centrosome (GO:0071539)|protein transport (GO:0015031)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|FHF complex (GO:0070695)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule organizing center (GO:0005815)|pericentriolar material (GO:0000242)	identical protein binding (GO:0042802)|microtubule binding (GO:0008017)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	31	Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.000105)|Lung NSC(58;0.000419)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)			TTGCAGGAAGAGAAAAGTAGT	0.408			T	RET	papillary thyroid																																p.E212G		Atlas-SNP	.		Dom	yes		8	8p11.21	84376	hook homolog 3		E	.	HOOK3	71	.	0			c.A635G						.						121	117	118					8																	42819473		2203	4300	6503	SO:0001583	missense	84376	exon9			AGGAAGAGAAAAG	AK090540	CCDS6139.1	8p11.21	2013-08-21	2013-08-21		ENSG00000168172	ENSG00000168172			23576	protein-coding gene	gene with protein product		607825	"hook homolog 3 (Drosophila)"			9927460	Standard	NM_032410		Approved	HK3	uc003xpr.3	Q86VS8	OTTHUMG00000165278	ENST00000307602.4:c.635A>G	chr8.hg19:g.42819473A>G	ENSP00000305699:p.Glu212Gly	86.0	0.0		80.0	5.0	NM_032410	D3DSY8|Q8NBH0|Q9BY13	Missense_Mutation	SNP	ENST00000307602.4	hg19	CCDS6139.1	.	.	.	.	.	.	.	.	.	.	A	25.6	4.655876	0.88056	.	.	ENSG00000168172	ENST00000307602	T	0.35236	1.32	5.93	5.93	0.95920	.	0.100609	0.64402	D	0.000003	T	0.65417	0.2689	M	0.84683	2.71	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	T	0.69903	-0.5019	10	0.56958	D	0.05	-6.9643	16.418	0.83748	1.0:0.0:0.0:0.0	.	212;212	Q2VJ45;Q86VS8	.;HOOK3_HUMAN	G	212	ENSP00000305699:E212G	ENSP00000305699:E212G	E	+	2	0	HOOK3	42938630	1.000000	0.71417	1.000000	0.80357	0.888000	0.51559	8.899000	0.92544	2.281000	0.76405	0.524000	0.50904	GAG	.	.		0.408	HOOK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383172.2	NM_032410		G	42819473	A	G	42819473	3	3	259	1	0	0	0	0	1	0	0	0	7293	304	11	2	669	2	HOOK3	8	42819473	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	6125651	42819473	103544549	388	36706										
PXDNL	137902	hgsc.bcm.edu	37	chr8	52321594	52321594	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggcacacgcggggctggagcGcgcgaagagcatgcagggcg	20	11	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:52321594G>A	ENST00000356297.4	-	17	2690	c.2590C>T	c.(2590-2592)Cgc>Tgc	p.R864C	PXDNL_ENST00000543296.1_Missense_Mutation_p.R864C	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	864					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.R864C(1)|p.R63C(1)		NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				GGGCTGGAGCGCGCGAAGAGC	0.662																																					p.R864C		Atlas-SNP	.											PXDNL_ENST00000356297,colon,carcinoma,0,2	PXDNL	414	.	2	Substitution - Missense(2)	large_intestine(2)	c.C2590T						.						22	26	25					8																	52321594		2026	4158	6184	SO:0001583	missense	137902	exon17			TGGAGCGCGCGAA		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"Immunoglobulin superfamily / I-set domain containing"	26359	protein-coding gene	gene with protein product	"polysomal ribonuclease 1 homolog (Xenopus)"	615904	"peroxidasin homolog-like (Drosophila)"			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.2590C>T	chr8.hg19:g.52321594G>A	ENSP00000348645:p.Arg864Cys	87.0	0.0		100.0	6.0	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	hg19	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	G	10.39	1.336473	0.24253	.	.	ENSG00000147485	ENST00000356297;ENST00000543296	D;D	0.84800	-1.9;-1.9	3.31	0.304	0.15796	.	0.272281	0.26156	N	0.026002	D	0.94128	0.8117	H	0.99286	4.5	0.44123	D	0.996903	D	0.89917	1.0	D	0.91635	0.999	D	0.89382	0.3682	10	0.87932	D	0	.	4.8892	0.13719	0.22:0.1755:0.6045:0.0	.	864	A1KZ92	PXDNL_HUMAN	C	864	ENSP00000348645:R864C;ENSP00000444865:R864C	ENSP00000348645:R864C	R	-	1	0	PXDNL	52484147	1.000000	0.71417	0.029000	0.17559	0.003000	0.03518	2.981000	0.49329	-0.220000	0.09988	-0.898000	0.02899	CGC	.	.		0.662	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		A	52321594	G	A	52321594	3	1	259	1	0	0	0	0	1	0	0	0	12863	1087	38	1	1829	1	PXDNL	8	52321594	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	9502121	52321594	94042428	389	36707										
CNBD1	168975	hgsc.bcm.edu	37	chr8	88218349	88218349	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gactgtcttttccgaaacctGgttgaaaggcagcacaggta	11	9	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:88218349G>T	ENST00000518476.1	+	5	611	c.560G>T	c.(559-561)tGg>tTg	p.W187L	CNBD1_ENST00000522427.1_3'UTR	NM_173538.2	NP_775809.1	Q8NA66	CNBD1_HUMAN	cyclic nucleotide binding domain containing 1	187										breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(4)|urinary_tract(1)	32						TCCGAAACCTGGTTGAAAGGC	0.358																																					p.W187L		Atlas-SNP	.											.	CNBD1	206	.	0			c.G560T						.						77	72	74					8																	88218349		1850	4102	5952	SO:0001583	missense	168975	exon5			AAACCTGGTTGAA	AK093121	CCDS55259.1	8q21.3	2005-08-09				ENSG00000176571			26663	protein-coding gene	gene with protein product							Standard	NM_173538		Approved	FLJ35802	uc003ydy.2	Q8NA66		ENST00000518476.1:c.560G>T	chr8.hg19:g.88218349G>T	ENSP00000430073:p.Trp187Leu	72.0	0.0		98.0	4.0	NM_173538		Missense_Mutation	SNP	ENST00000518476.1	hg19	CCDS55259.1	.	.	.	.	.	.	.	.	.	.	G	11.26	1.586120	0.28268	.	.	ENSG00000176571	ENST00000518476	D	0.95949	-3.86	5.02	5.02	0.67125	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);	0.288280	0.25313	N	0.031579	D	0.96778	0.8948	L	0.58101	1.795	0.30793	N	0.74072	D	0.89917	1.0	D	0.83275	0.996	D	0.94992	0.8135	10	0.52906	T	0.07	-0.3155	13.8978	0.63783	0.0:0.0:1.0:0.0	.	187	Q8NA66	CNBD1_HUMAN	L	187	ENSP00000430073:W187L	ENSP00000430073:W187L	W	+	2	0	CNBD1	88287465	1.000000	0.71417	0.997000	0.53966	0.218000	0.24690	4.489000	0.60309	2.335000	0.79485	0.460000	0.39030	TGG	.	.		0.358	CNBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375113.2	NM_173538		T	88218349	G	T	88218349	3	4	259	1	0	0	0	0	1	0	0	0	3593	1357	47	3	578	3	CNBD1	8	88218349	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	35896755	88218349	58145673	390	36708										
RIPK2	8767	hgsc.bcm.edu	37	chr8	90782012	90782012	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccttacagattgcagattttGgtttatcaaagtggcgcatg	10	7	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:90782012G>T	ENST00000220751.4	+	4	810	c.496G>T	c.(496-498)Ggt>Tgt	p.G166C	RIPK2_ENST00000540020.1_Missense_Mutation_p.G29C	NM_003821.5	NP_003812.1	O43353	RIPK2_HUMAN	receptor-interacting serine-threonine kinase 2	166	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|adaptive immune response (GO:0002250)|apoptotic process (GO:0006915)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to peptidoglycan (GO:0071224)|defense response to Gram-positive bacterium (GO:0050830)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070427)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of immature T cell proliferation (GO:0033091)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|response to exogenous dsRNA (GO:0043330)|response to interleukin-1 (GO:0070555)|response to interleukin-12 (GO:0070671)|response to interleukin-18 (GO:0070673)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|T cell proliferation (GO:0042098)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|protein complex (GO:0043234)|vesicle (GO:0031982)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|LIM domain binding (GO:0030274)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)	p.G166C(1)		kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(2)	10			BRCA - Breast invasive adenocarcinoma(11;0.0474)			TGCAGATTTTGGTTTATCAAA	0.363																																					p.G166C		Atlas-SNP	.											RIPK2,NS,carcinoma,0,1	RIPK2	37	.	1	Substitution - Missense(1)	lung(1)	c.G496T						.						147	153	151					8																	90782012		2203	4299	6502	SO:0001583	missense	8767	exon4			GATTTTGGTTTAT	AC004003	CCDS6247.1	8q21	2008-05-02			ENSG00000104312	ENSG00000104312			10020	protein-coding gene	gene with protein product		603455				9575181, 9705938	Standard	XM_005251092		Approved	RICK, RIP2, CARDIAK, CARD3	uc003yee.3	O43353	OTTHUMG00000163809	ENST00000220751.4:c.496G>T	chr8.hg19:g.90782012G>T	ENSP00000220751:p.Gly166Cys	56.0	0.0		75.0	3.0	NM_003821	B7Z748|Q6UWF0	Missense_Mutation	SNP	ENST00000220751.4	hg19	CCDS6247.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.601674	0.87055	.	.	ENSG00000104312	ENST00000220751;ENST00000540020	D;D	0.92858	-1.63;-3.12	5.41	5.41	0.78517	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.43747	D	0.000531	D	0.97682	0.9240	H	0.96833	3.89	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98474	1.0602	10	0.87932	D	0	-19.8595	19.3887	0.94570	0.0:0.0:1.0:0.0	.	166	O43353	RIPK2_HUMAN	C	166;29	ENSP00000220751:G166C;ENSP00000441623:G29C	ENSP00000220751:G166C	G	+	1	0	RIPK2	90851149	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	9.350000	0.97070	2.826000	0.97356	0.655000	0.94253	GGT	.	.		0.363	RIPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375686.1			T	90782012	G	T	90782012	3	4	259	1	0	0	0	0	1	0	0	0	13396	1348	47	3	510	3	RIPK2	8	90782012	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	2563663	90782012	55582010	391	36709										
CALB1	793	hgsc.bcm.edu	37	chr8	91072909	91072909	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aagcatccagttcattttcaTctatgtatccattgccgtcc	5	12	3	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:91072909T>G	ENST00000265431.3	-	10	801	c.620A>C	c.(619-621)gAt>gCt	p.D207A	CALB1_ENST00000518457.1_Missense_Mutation_p.D150A	NM_004929.2	NP_004920.1	P05937	CALB1_HUMAN	calbindin 1, 28kDa	207	EF-hand 5. {ECO:0000255|PROSITE- ProRule:PRU00448}.				cellular response to organic substance (GO:0071310)|cytosolic calcium ion homeostasis (GO:0051480)|locomotory behavior (GO:0007626)|long-term memory (GO:0007616)|metanephric collecting duct development (GO:0072205)|metanephric connecting tubule development (GO:0072286)|metanephric distal convoluted tubule development (GO:0072221)|metanephric part of ureteric bud development (GO:0035502)|regulation of synaptic plasticity (GO:0048167)|retina layer formation (GO:0010842)|short-term memory (GO:0007614)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|vitamin D binding (GO:0005499)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|lung(8)|pancreas(1)	11			BRCA - Breast invasive adenocarcinoma(11;0.00953)			TTCATTTTCATCTATGTATCC	0.383																																					p.D207A	Melanoma(46;573 1182 27367 39727 48386)	Atlas-SNP	.											.	CALB1	25	.	0			c.A620C						.						199	195	196					8																	91072909		2203	4300	6503	SO:0001583	missense	793	exon10			TTTTCATCTATGT		CCDS6251.1	8q21.3	2013-01-10	2002-08-29		ENSG00000104327	ENSG00000104327		"EF-hand domain containing"	1434	protein-coding gene	gene with protein product		114050		CALB			Standard	NM_004929		Approved		uc003yel.1	P05937	OTTHUMG00000134314	ENST00000265431.3:c.620A>C	chr8.hg19:g.91072909T>G	ENSP00000265431:p.Asp207Ala	105.0	0.0		137.0	40.0	NM_004929	B2R696|B7Z9J4	Missense_Mutation	SNP	ENST00000265431.3	hg19	CCDS6251.1	.	.	.	.	.	.	.	.	.	.	T	18.34	3.601966	0.66445	.	.	ENSG00000104327	ENST00000265431;ENST00000518457	T;T	0.73681	-0.77;-0.77	5.8	5.8	0.92144	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.83714	0.5314	L	0.55213	1.73	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.85133	0.0976	10	0.72032	D	0.01	-21.197	16.1606	0.81704	0.0:0.0:0.0:1.0	.	207	P05937	CALB1_HUMAN	A	207;150	ENSP00000265431:D207A;ENSP00000429602:D150A	ENSP00000265431:D207A	D	-	2	0	CALB1	91142085	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.948000	0.75965	2.227000	0.72691	0.460000	0.39030	GAT	.	.		0.383	CALB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259338.2	NM_004929		G	91072909	T	G	91072909	3	3	259	1	0	0	0	0	1	0	0	0	2575	1435	50	5	173	5	CALB1	8	91072909	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	290897	91072909	55291113	392	36710										
RNF139	11236	hgsc.bcm.edu	37	chr8	125487462	125487462	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tttacatcatcgacgccatcTtcaactcctacccggattcc	4	16	3	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:125487462T>C	ENST00000303545.3	+	1	484	c.112T>C	c.(112-114)Ttc>Ctc	p.F38L	RNF139-AS1_ENST00000499418.2_lincRNA	NM_007218.3	NP_009149.2			ring finger protein 139											breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|liver(1)|lung(4)|prostate(1)|skin(1)	20	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			CGACGCCATCTTCAACTCCTA	0.637																																					p.F38L		Atlas-SNP	.											.	RNF139	57	.	0			c.T112C						.						81	84	83					8																	125487462		2203	4300	6503	SO:0001583	missense	11236	exon1			GCCATCTTCAACT	AF064801	CCDS6350.1	8q24	2013-01-09			ENSG00000170881	ENSG00000170881		"RING-type (C3HC4) zinc fingers"	17023	protein-coding gene	gene with protein product		603046				9689122	Standard	NM_007218		Approved	TRC8, RCA1, HRCA1	uc003yrc.3	Q8WU17	OTTHUMG00000165072	ENST00000303545.3:c.112T>C	chr8.hg19:g.125487462T>C	ENSP00000304051:p.Phe38Leu	66.0	0.0		58.0	6.0	NM_007218		Missense_Mutation	SNP	ENST00000303545.3	hg19	CCDS6350.1	.	.	.	.	.	.	.	.	.	.	T	6.611	0.481042	0.12581	.	.	ENSG00000170881	ENST00000303545	T	0.28069	1.63	4.44	3.3	0.37823	.	0.214512	0.40469	N	0.001094	T	0.12220	0.0297	N	0.04090	-0.28	0.37178	D	0.903345	B	0.06786	0.001	B	0.08055	0.003	T	0.13229	-1.0517	10	0.17832	T	0.49	-8.4438	7.4699	0.27342	0.0:0.1002:0.0:0.8998	.	38	Q8WU17	RN139_HUMAN	L	38	ENSP00000304051:F38L	ENSP00000304051:F38L	F	+	1	0	RNF139	125556643	1.000000	0.71417	1.000000	0.80357	0.417000	0.31264	5.377000	0.66184	0.759000	0.33084	0.459000	0.35465	TTC	.	.		0.637	RNF139-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000381692.1	NM_007218		C	125487462	T	C	125487462	3	2	259	1	0	0	0	0	1	0	0	0	13457	1609	56	2	114	2	RNF139	8	125487462	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	34414553	125487462	20876560	393	36711										
KIAA0196	9897	hgsc.bcm.edu	37	chr8	126062907	126062907	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cagcaactgctttggatccaCctaagtgccaatcaaaagta	7	11	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:126062907C>T	ENST00000318410.7	-	18	2447	c.2098G>A	c.(2098-2100)Gtg>Atg	p.V700M	KIAA0196_ENST00000517845.1_Splice_Site_p.V552M	NM_014846.3	NP_055661.3	Q12768	STRUM_HUMAN	KIAA0196	700					cell death (GO:0008219)|endosomal transport (GO:0016197)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|WASH complex (GO:0071203)				NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	42	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)			TTTGGATCCACCTAAGTGCCA	0.438																																					p.V700M		Atlas-SNP	.											.	KIAA0196	90	.	0			c.G2098A						.						101	93	96					8																	126062907		2203	4300	6503	SO:0001630	splice_region_variant	9897	exon18			GATCCACCTAAGT		CCDS6355.1	8q24.13	2014-05-09			ENSG00000164961	ENSG00000164961			28984	protein-coding gene	gene with protein product	"strumpellin"	610657	"spastic paraplegia 8 (autosomal dominant)"	SPG8		9973294, 17160902, 23085491	Standard	NM_014846		Approved		uc003yrt.3	Q12768	OTTHUMG00000164991	ENST00000318410.7:c.2098-1G>A	chr8.hg19:g.126062907C>T		77.0	0.0		87.0	4.0	NM_014846	A8K4R7|Q3KQX5|Q8TBQ2	Missense_Mutation	SNP	ENST00000318410.7	hg19	CCDS6355.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.729058	0.89390	.	.	ENSG00000164961	ENST00000318410;ENST00000517845	D;D	0.89810	-2.57;-2.57	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	D	0.94739	0.8302	M	0.80616	2.505	0.80722	D	1	D;D	0.67145	0.984;0.996	P;D	0.81914	0.865;0.995	D	0.95079	0.8211	10	0.72032	D	0.01	-19.1397	19.0437	0.93011	0.0:1.0:0.0:0.0	.	552;700	E7EQI7;Q12768	.;STRUM_HUMAN	M	700;552	ENSP00000318016:V700M;ENSP00000429676:V552M	ENSP00000318016:V700M	V	-	1	0	KIAA0196	126132089	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	7.772000	0.85439	2.575000	0.86900	0.655000	0.94253	GTG	.	.		0.438	KIAA0196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381369.1	NM_014846	Missense_Mutation	T	126062907	C	T	126062907	5	4	259	1	0	0	0	0	0	0	1	0	8170	521	18	3	1429	3	KIAA0196	8	126062907	Splice_Site	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	575445	126062907	20301115	394	36712										
ASAP1	50807	hgsc.bcm.edu	37	chr8	131130888	131130888	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cttgaaaacctatgatctacAtactttgcagtgatatattc	5	8	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:131130888A>G	ENST00000518721.1	-	19	1868	c.1641T>C	c.(1639-1641)taT>taC	p.Y547Y	ASAP1_ENST00000357668.1_Silent_p.Y547Y	NM_001247996.1|NM_018482.3	NP_001234925.1|NP_060952.2	Q9ULH1	ASAP1_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 1	547	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				cilium morphogenesis (GO:0060271)|regulation of ARF GTPase activity (GO:0032312)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|zinc ion binding (GO:0008270)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(22)|ovary(6)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	68						TATGATCTACATACTTTGCAG	0.333																																					p.Y547Y		Atlas-SNP	.											.	ASAP1	133	.	0			c.T1641C						.						81	77	78					8																	131130888		2203	4300	6503	SO:0001819	synonymous_variant	50807	exon19			ATCTACATACTTT	AB033075	CCDS6362.1, CCDS75788.1	8q24.1-q24.2	2013-01-11	2008-09-22	2008-09-22	ENSG00000153317	ENSG00000153317		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	2720	protein-coding gene	gene with protein product	"centaurin, beta 4"	605953	"development and differentiation enhancing factor 1"	DDEF1		9819391	Standard	NM_018482		Approved	PAP, KIAA1249, ZG14P, CENTB4	uc003yta.2	Q9ULH1	OTTHUMG00000164772	ENST00000518721.1:c.1641T>C	chr8.hg19:g.131130888A>G		177.0	0.0		263.0	72.0	NM_018482	B2RNV3	Silent	SNP	ENST00000518721.1	hg19	CCDS6362.1	.	.	.	.	.	.	.	.	.	.	A	8.808	0.934450	0.18206	.	.	ENSG00000153317	ENST00000524124	.	.	.	5.86	0.792	0.18625	.	.	.	.	.	T	0.57036	0.2026	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48681	-0.9014	4	.	.	.	.	9.2609	0.37612	0.6503:0.0:0.3497:0.0	.	.	.	.	R	368	.	.	C	-	1	0	ASAP1	131200070	1.000000	0.71417	0.935000	0.37517	0.941000	0.58515	1.649000	0.37281	-0.075000	0.12798	-0.261000	0.10672	TGT	.	.		0.333	ASAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380170.1	NM_018482		G	131130888	A	G	131130888	2	3	259	1	0	0	0	0	0	0	0	1	1010	224	8	2		2	ASAP1	8	131130888	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	5067981	131130888	15233134	395	36713										
ADCY8	114	hgsc.bcm.edu	37	chr8	131795974	131795974	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttgttgaatgaatgcttgttGatctcctgtatgctttctgt	9	6	2	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:131795974G>T	ENST00000286355.5	-	17	5323	c.3231C>A	c.(3229-3231)atC>atA	p.I1077I	ADCY8_ENST00000377928.3_Silent_p.I946I	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	1077					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)	p.I1077I(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			AATGCTTGTTGATCTCCTGTA	0.502										HNSCC(32;0.087)																											p.I1077I		Atlas-SNP	.											ADCY8,NS,carcinoma,0,1	ADCY8	291	.	1	Substitution - coding silent(1)	lung(1)	c.C3231A						.						163	148	153					8																	131795974		2203	4300	6503	SO:0001819	synonymous_variant	114	exon17			CTTGTTGATCTCC	Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"Adenylate cyclases"	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.3231C>A	chr8.hg19:g.131795974G>T		115.0	0.0		110.0	6.0	NM_001115		Silent	SNP	ENST00000286355.5	hg19	CCDS6363.1																																																																																			.	.		0.502	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			T	131795974	G	T	131795974	2	4	259	1	0	0	0	0	0	0	0	1	300	1280	45	3		3	ADCY8	8	131795974	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	665086	131795974	14568048	396	36714										
FAM83H	286077	hgsc.bcm.edu	37	chr8	144812417	144812417	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccctggaagccgaaggtcagAggccagcccaaatcaagctc	11	14	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:144812417A>G	ENST00000388913.3	-	2	461	c.336T>C	c.(334-336)ccT>ccC	p.P112P	MIR4664_ENST00000583819.1_RNA	NM_198488.3	NP_940890	Q6ZRV2	FA83H_HUMAN	family with sequence similarity 83, member H	112					biomineral tissue development (GO:0031214)					central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(12)|pancreas(1)|prostate(3)|urinary_tract(1)	21	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			CGAAGGTCAGAGGCCAGCCCA	0.622																																					p.P112P		Atlas-SNP	.											.	FAM83H	68	.	0			c.T336C						.						46	52	50					8																	144812417		2056	4180	6236	SO:0001819	synonymous_variant	286077	exon2			GGTCAGAGGCCAG	AK127960	CCDS6410.2	8q24.3	2014-03-13			ENSG00000180921	ENSG00000180921			24797	protein-coding gene	gene with protein product		611927				18252228	Standard	NM_198488		Approved	FLJ46072	uc003yzk.3	Q6ZRV2	OTTHUMG00000133559	ENST00000388913.3:c.336T>C	chr8.hg19:g.144812417A>G		84.0	0.0		72.0	4.0	NM_198488	A0JLS2|Q8N4W0	Silent	SNP	ENST00000388913.3	hg19	CCDS6410.2																																																																																			.	.		0.622	FAM83H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257632.2	NM_198488		G	144812417	A	G	144812417	2	3	259	1	0	0	0	0	0	0	0	1	5648	291	11	2		2	FAM83H	8	144812417	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	13016443	144812417	1551605	397	36715										
SCRIB	23513	hgsc.bcm.edu	37	chr8	144891811	144891811	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gcctcagccgacgggccctcGggctcagcctcagagactgt	13	16	3	1	rs546935238		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:144891811G>C	ENST00000320476.3	-	14	1614	c.1608C>G	c.(1606-1608)ccC>ccG	p.P536P	SCRIB_ENST00000377533.3_Silent_p.P455P|SCRIB_ENST00000356994.2_Silent_p.P536P	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	536	Sufficient for targeting to adherens junction and to inhibit cell proliferation.				activation of Rac GTPase activity (GO:0032863)|apoptotic process involved in morphogenesis (GO:0060561)|astrocyte cell migration (GO:0043615)|asymmetric protein localization (GO:0008105)|auditory receptor cell stereocilium organization (GO:0060088)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cochlear nucleus development (GO:0021747)|establishment of apical/basal cell polarity (GO:0035089)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of mitotic cell cycle (GO:0045930)|neural tube closure (GO:0001843)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of receptor recycling (GO:0001921)|protein localization to adherens junction (GO:0071896)|single organismal cell-cell adhesion (GO:0016337)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle targeting (GO:0016080)|viral process (GO:0016032)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)|Scrib-APC-beta-catenin complex (GO:0034750)				NS(1)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(20)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	42	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			ACGGGCCCTCGGGCTCAGCCT	0.662																																					p.P536P	Pancreas(51;966 1133 10533 14576 29674)	Atlas-SNP	.											.	SCRIB	192	.	0			c.C1608G						.						57	55	55					8																	144891811		2203	4300	6503	SO:0001819	synonymous_variant	23513	exon14			GCCCTCGGGCTCA	AY062238	CCDS6411.1, CCDS6412.1	8q24.3	2013-03-05	2013-03-05		ENSG00000180900	ENSG00000180900			30377	protein-coding gene	gene with protein product		607733	"scribbled homolog (Drosophila)"			11027293, 14681682	Standard	NM_182706		Approved	KIAA0147, SCRB1, Vartul	uc003yzo.1	Q14160	OTTHUMG00000165154	ENST00000320476.3:c.1608C>G	chr8.hg19:g.144891811G>C		90.0	0.0		93.0	4.0	NM_015356	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Silent	SNP	ENST00000320476.3	hg19	CCDS6411.1																																																																																			.	.		0.662	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356		C	144891811	G	C	144891811	2	2	259	1	0	0	0	0	0	0	0	1	13952	1103	39	4		4	SCRIB	8	144891811	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	79394	144891811	1472211	398	36716										
PLEC	5339	hgsc.bcm.edu	37	chr8	144990726	144990726	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acgtcacgcagcttctgtgcGgtgcgggcgtccaccgtgcc	14	15	2	0	rs369202116		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:144990726G>T	ENST00000322810.4	-	32	13843	c.13674C>A	c.(13672-13674)acC>acA	p.T4558T	PLEC_ENST00000356346.3_Silent_p.T4407T|PLEC_ENST00000354589.3_Silent_p.T4421T|PLEC_ENST00000398774.2_Silent_p.T4389T|PLEC_ENST00000357649.2_Silent_p.T4425T|PLEC_ENST00000345136.3_Silent_p.T4421T|PLEC_ENST00000527096.1_Silent_p.T4444T|PLEC_ENST00000354958.2_Silent_p.T4399T|PLEC_ENST00000436759.2_Silent_p.T4448T	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	4558	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						GCTTCTGTGCGGTGCGGGCGT	0.672																																					p.T4558T		Atlas-SNP	.											.	PLEC	1144	.	0			c.C13674A						.						56	60	59					8																	144990726		2002	4131	6133	SO:0001819	synonymous_variant	5339	exon32			CTGTGCGGTGCGG	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"plectin 1, intermediate filament binding protein, 500kD", "epidermolysis bullosa simplex 1 (Ogna)", "plectin 1, intermediate filament binding protein 500kDa"	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.13674C>A	chr8.hg19:g.144990726G>T		69.0	0.0		80.0	4.0	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	hg19	CCDS43772.1																																																																																			.	.		0.672	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		T	144990726	G	T	144990726	2	4	259	1	0	0	0	0	0	0	0	1	12061	1103	39	1		1	PLEC	8	144990726	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	98915	144990726	1373296	399	36717										
PLEC	5339	hgsc.bcm.edu	37	chr8	144991010	144991010	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggtgacagggaagcgctcacCggtgctggggtcgatgatgc	18	9	1	2	rs368027812		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:144991010C>A	ENST00000322810.4	-	32	13559	c.13390G>T	c.(13390-13392)Ggt>Tgt	p.G4464C	PLEC_ENST00000356346.3_Missense_Mutation_p.G4313C|PLEC_ENST00000354589.3_Missense_Mutation_p.G4327C|PLEC_ENST00000398774.2_Missense_Mutation_p.G4295C|PLEC_ENST00000357649.2_Missense_Mutation_p.G4331C|PLEC_ENST00000345136.3_Missense_Mutation_p.G4327C|PLEC_ENST00000527096.1_Missense_Mutation_p.G4350C|PLEC_ENST00000354958.2_Missense_Mutation_p.G4305C|PLEC_ENST00000436759.2_Missense_Mutation_p.G4354C	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	4464	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						AAGCGCTCACCGGTGCTGGGG	0.652																																					p.G4464C		Atlas-SNP	.											.	PLEC	1144	.	0			c.G13390T						.						49	55	53					8																	144991010		2123	4226	6349	SO:0001583	missense	5339	exon32			GCTCACCGGTGCT	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"plectin 1, intermediate filament binding protein, 500kD", "epidermolysis bullosa simplex 1 (Ogna)", "plectin 1, intermediate filament binding protein 500kDa"	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.13390G>T	chr8.hg19:g.144991010C>A	ENSP00000323856:p.Gly4464Cys	155.0	0.0		138.0	7.0	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	hg19	CCDS43772.1	.	.	.	.	.	.	.	.	.	.	C	6.324	0.427898	0.11987	.	.	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	T;T;T;T;T;T;T;T;T	0.80033	-1.33;-1.33;-1.33;-1.33;-1.33;-1.33;-1.33;-1.33;-1.33	5.19	5.19	0.71726	.	0.000000	0.64402	U	0.000006	D	0.91499	0.7316	M	0.88450	2.955	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.999;0.999;0.999;0.999	D	0.92759	0.6222	10	0.87932	D	0	.	18.5216	0.90954	0.0:1.0:0.0:0.0	.	4354;4313;4305;4464;4295;4327;4331;4327	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	C	4327;4331;4327;4295;4464;4305;4313;4354;4350	ENSP00000344848:G4327C;ENSP00000350277:G4331C;ENSP00000346602:G4327C;ENSP00000381756:G4295C;ENSP00000323856:G4464C;ENSP00000347044:G4305C;ENSP00000348702:G4313C;ENSP00000388180:G4354C;ENSP00000434583:G4350C	ENSP00000323856:G4464C	G	-	1	0	PLEC	145062998	1.000000	0.71417	0.107000	0.21349	0.025000	0.11179	7.593000	0.82686	2.693000	0.91896	0.643000	0.83706	GGT	.	.		0.652	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		A	144991010	C	A	144991010	3	1	259	1	0	0	0	0	1	0	0	0	12061	652	23	1	668	1	PLEC	8	144991010	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	284	144991010	1373012	400	36718										
RECQL4	9684	hgsc.bcm.edu	37	chr8	145740718	145740718	+	5'Flank	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctgactgctcacctgccaacTgccctgagggccccagggag	12	16	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:145740718T>A	ENST00000292524.1	+	0	0				RECQL4_ENST00000428558.2_Missense_Mutation_p.Q461L|RECQL4_ENST00000532237.1_5'UTR|LRRC14_ENST00000529022.1_5'Flank|CTD-2517M22.17_ENST00000580385.1_RNA	NM_001272036.1|NM_014665.2	NP_001258965.1|NP_055480.1	Q15048	LRC14_HUMAN	leucine rich repeat containing 14											endometrium(1)|lung(3)|prostate(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			ACCTGCCAACTGCCCTGAGGG	0.617																																					p.Q461L		Atlas-SNP	.											.	RECQL4	75	.	0			c.A1382T						.						38	44	42					8																	145740718		2050	4208	6258	SO:0001631	upstream_gene_variant	9401	exon7			GCCAACTGCCCTG	BC011377	CCDS6432.1	8q24.3	2012-08-20			ENSG00000160959	ENSG00000160959			20419	protein-coding gene	gene with protein product						7584026	Standard	NM_001272036		Approved	KIAA0014, LRRC14A	uc003zdk.3	Q15048	OTTHUMG00000165179		chr8.hg19:g.145740718T>A	Exception_encountered	154.0	0.0		166.0	10.0	NM_004260	A8K0A8|D3DWM8	Missense_Mutation	SNP	ENST00000292524.1	hg19	CCDS6432.1																																																																																			.	.		0.617	LRRC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382494.1	NM_014665		A	145740718	T	A	145740718	1	1	259	0	1	0	0	0	0	0	0	0	13217	1580	55	4		4	RECQL4	8	145740718	5'Flank	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	749708	145740718	623304	401	36719										
LRRC24	441381	hgsc.bcm.edu	37	chr8	145749598	145749598	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gcagtgctagggaggacagcCccgctagagcctggtcctcc	14	14	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:145749598C>T	ENST00000529415.2	-	4	620	c.503G>A	c.(502-504)gGg>gAg	p.G168E	LRRC14_ENST00000292524.1_3'UTR|LRRC14_ENST00000528528.1_Intron|LRRC24_ENST00000533758.1_Missense_Mutation_p.G165E			Q50LG9	LRC24_HUMAN	leucine rich repeat containing 24	168						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(1)|lung(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			GGAGGACAGCCCCGCTAGAGC	0.612																																					p.G168E		Atlas-SNP	.											.	LRRC24	11	.	0			c.G503A						.						67	71	70					8																	145749598		2203	4300	6503	SO:0001583	missense	441381	exon4			GACAGCCCCGCTA	AB178281	CCDS34969.1	8q24.3	2013-01-11			ENSG00000254402	ENSG00000254402		"Immunoglobulin superfamily / I-set domain containing"	28947	protein-coding gene	gene with protein product						7584026	Standard	NM_001024678		Approved	LRRC14OS	uc003zdm.3	Q50LG9	OTTHUMG00000165180	ENST00000529415.2:c.503G>A	chr8.hg19:g.145749598C>T	ENSP00000434849:p.Gly168Glu	76.0	0.0		66.0	4.0	NM_001024678		Missense_Mutation	SNP	ENST00000529415.2	hg19	CCDS34969.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.906734	0.92107	.	.	ENSG00000254402	ENST00000529415;ENST00000533758	T;T	0.60548	0.18;0.18	4.55	4.55	0.56014	.	0.057736	0.64402	D	0.000001	T	0.71685	0.3369	M	0.64404	1.975	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.85130	0.982;0.997	T	0.74411	-0.3674	10	0.72032	D	0.01	.	12.6709	0.56866	0.0:1.0:0.0:0.0	.	165;168	G3V1D8;Q50LG9	.;LRC24_HUMAN	E	168;165	ENSP00000434849:G168E;ENSP00000435653:G165E	ENSP00000434849:G168E	G	-	2	0	LRRC24	145720406	0.998000	0.40836	0.995000	0.50966	0.954000	0.61252	4.090000	0.57693	2.350000	0.79820	0.561000	0.74099	GGG	.	.		0.612	LRRC24-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382501.2	NM_001024678		T	145749598	C	T	145749598	3	4	259	1	0	0	0	0	1	0	0	0	8988	623	22	3	1046	3	LRRC24	8	145749598	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	8880	145749598	614424	402	36720										
KCNV2	169522	hgsc.bcm.edu	37	chr9	2729648	2729648	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggagaggggagaggtgaactTcatgcagagagccagaaaga	17	5	1	6			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:2729648T>G	ENST00000382082.3	+	2	1797	c.1559T>G	c.(1558-1560)tTc>tGc	p.F520C		NM_133497.3	NP_598004.1	Q8TDN2	KCNV2_HUMAN	potassium channel, subfamily V, member 2	520					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(2)	35				GBM - Glioblastoma multiforme(50;0.0257)		GAGGTGAACTTCATGCAGAGA	0.453																																					p.F520C		Atlas-SNP	.											.	KCNV2	72	.	0			c.T1559G						.						113	103	107					9																	2729648		2203	4300	6503	SO:0001583	missense	169522	exon2			TGAACTTCATGCA	AF348983	CCDS6447.1	9p24.2	2011-07-05			ENSG00000168263	ENSG00000168263		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	19698	protein-coding gene	gene with protein product		607604				12060745, 16382104	Standard	NM_133497		Approved	Kv8.2	uc003zho.2	Q8TDN2	OTTHUMG00000019449	ENST00000382082.3:c.1559T>G	chr9.hg19:g.2729648T>G	ENSP00000371514:p.Phe520Cys	187.0	0.0		113.0	11.0	NM_133497	Q5T6X0	Missense_Mutation	SNP	ENST00000382082.3	hg19	CCDS6447.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.352445	0.82132	.	.	ENSG00000168263	ENST00000382082	D	0.96992	-4.2	5.37	5.37	0.77165	.	1.777150	0.03575	N	0.229189	D	0.98261	0.9424	M	0.78916	2.43	0.80722	D	1	D	0.89917	1.0	D	0.67725	0.953	D	0.91921	0.5547	10	0.38643	T	0.18	.	15.6629	0.77203	0.0:0.0:0.0:1.0	.	520	Q8TDN2	KCNV2_HUMAN	C	520	ENSP00000371514:F520C	ENSP00000371514:F520C	F	+	2	0	KCNV2	2719648	1.000000	0.71417	0.990000	0.47175	0.993000	0.82548	7.997000	0.88414	2.165000	0.68154	0.533000	0.62120	TTC	.	.		0.453	KCNV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051528.1	NM_133497		G	2729648	T	G	2729648	3	3	259	1	0	0	0	0	1	0	0	0	8104	1783	62	5	1565	5	KCNV2	9	2729648	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10		2729648	138483783	403	36721										
MPDZ	8777	hgsc.bcm.edu	37	chr9	13193255	13193255	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gataaaatgatgtcccactgTcgcttccaggcttatcccca	7	13	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:13193255T>C	ENST00000319217.7	-	14	1961	c.1714A>G	c.(1714-1716)Aca>Gca	p.T572A	MPDZ_ENST00000546205.1_Missense_Mutation_p.T572A|MPDZ_ENST00000541718.1_Missense_Mutation_p.T572A|MPDZ_ENST00000381022.2_Missense_Mutation_p.T572A|MPDZ_ENST00000536827.1_Missense_Mutation_p.T572A|MPDZ_ENST00000381015.4_Missense_Mutation_p.T572A|MPDZ_ENST00000447879.1_Missense_Mutation_p.T572A	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	572	PDZ 4. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		TGTCCCACTGTCGCTTCCAGG	0.443																																					p.T572A		Atlas-SNP	.											MPDZ_ENST00000541718,NS,carcinoma,0,2	MPDZ	324	.	0			c.A1714G						.						89	89	89					9																	13193255		1925	4123	6048	SO:0001583	missense	8777	exon14			CCACTGTCGCTTC	AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.1714A>G	chr9.hg19:g.13193255T>C	ENSP00000320006:p.Thr572Ala	78.0	0.0		60.0	4.0	NM_003829	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Missense_Mutation	SNP	ENST00000319217.7	hg19		.	.	.	.	.	.	.	.	.	.	T	14.32	2.500367	0.44455	.	.	ENSG00000107186	ENST00000319217;ENST00000541718;ENST00000381022;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000399902;ENST00000546205	T;T;T;T;T;T;T	0.26518	1.73;1.73;1.73;1.73;1.73;1.73;1.73	5.87	4.73	0.59995	.	0.000000	0.48286	D	0.000187	T	0.21267	0.0512	L	0.41710	1.295	0.80722	D	1	P;P;P	0.44578	0.693;0.644;0.838	P;B;B	0.45660	0.489;0.356;0.356	T	0.07462	-1.0771	10	0.11485	T	0.65	.	6.923	0.24399	0.1329:0.0701:0.0:0.797	.	572;572;572	B7ZMI4;O75970-3;O75970-2	.;.;.	A	572	ENSP00000320006:T572A;ENSP00000439807:T572A;ENSP00000370410:T572A;ENSP00000444151:T572A;ENSP00000415208:T572A;ENSP00000370403:T572A;ENSP00000446358:T572A	ENSP00000320006:T572A	T	-	1	0	MPDZ	13183255	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.685000	0.37659	1.052000	0.40392	0.533000	0.62120	ACA	.	.		0.443	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829		C	13193255	T	C	13193255	3	2	259	1	0	0	0	0	1	0	0	0	9731	1667	58	2	4543	2	MPDZ	9	13193255	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	10463607	13193255	128020176	404	36722										
ADAMTSL1	92949	hgsc.bcm.edu	37	chr9	18829938	18829938	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctgacgtctcctctgggaacAcagctggtcctggatcctgg	12	13	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:18829938A>G	ENST00000380548.4	+	23	4551	c.4212A>G	c.(4210-4212)acA>acG	p.T1404T	ADAMTSL1_ENST00000380545.5_Silent_p.T105T	NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	1404	Ig-like C2-type 4.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(2)|lung(17)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(50;1.29e-17)		CTCTGGGAACACAGCTGGTCC	0.562																																					p.T1404T		Atlas-SNP	.											.	ADAMTSL1	306	.	0			c.A4212G						.						71	72	72					9																	18829938		2069	4208	6277	SO:0001819	synonymous_variant	92949	exon23			GGGAACACAGCTG	AF176313	CCDS6485.1, CCDS47954.1	9p21.3	2013-01-11			ENSG00000178031	ENSG00000178031		"Immunoglobulin superfamily / I-set domain containing"	14632	protein-coding gene	gene with protein product	"punctin"	609198	"chromosome 9 open reading frame 94"	C9orf94		9628581, 11805097	Standard	NM_001040272		Approved	ADAMTSR1, FLJ35283	uc003zne.4	Q8N6G6	OTTHUMG00000019604	ENST00000380548.4:c.4212A>G	chr9.hg19:g.18829938A>G		139.0	0.0		96.0	4.0	NM_001040272	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Silent	SNP	ENST00000380548.4	hg19	CCDS47954.1																																																																																			.	.		0.562	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1			G	18829938	A	G	18829938	2	3	259	1	0	0	0	0	0	0	0	1	274	146	6	2		2	ADAMTSL1	9	18829938	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	5636683	18829938	122383493	405	36723										
DENND4C	55667	hgsc.bcm.edu	37	chr9	19346681	19346681	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atcttctagtatggaattacAcagagaggaaaacagagagt	10	5	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:19346681A>G	ENST00000380432.2	+	18	3092	c.3059A>G	c.(3058-3060)cAc>cGc	p.H1020R	DENND4C_ENST00000602925.1_Missense_Mutation_p.H1256R|DENND4C_ENST00000434457.2_Missense_Mutation_p.H1305R			Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	1020					cellular response to insulin stimulus (GO:0032869)|positive regulation of Rab GTPase activity (GO:0032851)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)	cytosol (GO:0005829)|insulin-responsive compartment (GO:0032593)|plasma membrane (GO:0005886)|retromer complex (GO:0030904)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(8)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						ATGGAATTACACAGAGAGGAA	0.398																																					p.H1256R		Atlas-SNP	.											.	DENND4C	120	.	0			c.A3767G						.						75	76	75					9																	19346681		2203	4300	6503	SO:0001583	missense	55667	exon22			AATTACACAGAGA	AK000693	CCDS6491.2, CCDS6491.3	9p22.1	2012-10-03	2006-01-27	2006-01-27	ENSG00000137145	ENSG00000137145		"DENN/MADD domain containing"	26079	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 55B", "chromosome 9 open reading frame 55"	C9orf55B, C9orf55		12906859	Standard	NM_017925		Approved	FLJ20686, bA513M16.3	uc031tcw.1	Q5VZ89	OTTHUMG00000019627	ENST00000380432.2:c.3059A>G	chr9.hg19:g.19346681A>G	ENSP00000369797:p.His1020Arg	146.0	0.0		103.0	5.0	NM_017925	A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	Missense_Mutation	SNP	ENST00000380432.2	hg19		.	.	.	.	.	.	.	.	.	.	A	9.427	1.084460	0.20309	.	.	ENSG00000137145	ENST00000380437;ENST00000307015;ENST00000453857;ENST00000540671;ENST00000380432;ENST00000380427;ENST00000361024	T;T	0.22945	1.94;1.93	5.81	5.81	0.92471	.	0.088740	0.47093	D	0.000251	T	0.20414	0.0491	L	0.44542	1.39	0.35516	D	0.801045	P;P;P;P	0.47910	0.508;0.902;0.508;0.872	B;B;B;B	0.38225	0.135;0.268;0.226;0.213	T	0.28839	-1.0031	10	0.36615	T	0.2	-8.3174	10.5039	0.44821	0.9281:0.0:0.0719:0.0	.	350;1020;202;1020	B7Z660;Q5VZ89-5;Q5VZ89-3;Q5VZ89	.;.;.;DEN4C_HUMAN	R	1020;493;202;350;493;202;17	ENSP00000305795:H493R;ENSP00000443804:H350R	ENSP00000305795:H493R	H	+	2	0	DENND4C	19336681	0.998000	0.40836	0.230000	0.23976	0.231000	0.25187	5.457000	0.66672	2.213000	0.71641	0.528000	0.53228	CAC	.	.		0.398	DENND4C-201	KNOWN	basic	protein_coding	protein_coding		NM_017925		G	19346681	A	G	19346681	3	3	259	1	0	0	0	0	1	0	0	0	4437	159	6	2	3129	2	DENND4C	9	19346681	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	516743	19346681	121866750	406	36724										
UBAP2	55833	hgsc.bcm.edu	37	chr9	33996317	33996317	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cattcatcctgatttttcccTgtcacttccataagctagtg	5	12	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:33996317T>C	ENST00000379238.1	-	4	309	c.192A>G	c.(190-192)acA>acG	p.T64T	UBAP2_ENST00000480885.1_5'UTR|UBAP2_ENST00000360802.1_Silent_p.T64T|UBAP2_ENST00000379239.4_5'UTR|UBAP2_ENST00000418786.2_Silent_p.T64T|UBAP2_ENST00000449054.1_Silent_p.T64T|UBAP2_ENST00000539807.1_Intron					ubiquitin associated protein 2											endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(13)|ovary(3)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)		GATTTTTCCCTGTCACTTCCA	0.353																																					p.T64T		Atlas-SNP	.											.	UBAP2	82	.	0			c.A192G						.						178	165	170					9																	33996317		2203	4300	6503	SO:0001819	synonymous_variant	55833	exon4			TTTCCCTGTCACT	AB040924	CCDS6547.1, CCDS75828.1	9p11.2	2008-02-05			ENSG00000137073	ENSG00000137073			14185	protein-coding gene	gene with protein product						8871400	Standard	NM_018449		Approved	KIAA1491, bA176F3.5, FLJ22435	uc003ztq.1	Q5T6F2	OTTHUMG00000000427	ENST00000379238.1:c.192A>G	chr9.hg19:g.33996317T>C		168.0	0.0		119.0	5.0	NM_018449		Silent	SNP	ENST00000379238.1	hg19	CCDS6547.1																																																																																			.	.		0.353	UBAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001071.1	NM_018449		C	33996317	T	C	33996317	2	2	259	1	0	0	0	0	0	0	0	1	16852	1567	55	2		2	UBAP2	9	33996317	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	14649636	33996317	107217114	407	36725										
VCP	7415	hgsc.bcm.edu	37	chr9	35060881	35060881	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctgtggcacctctaccacggTttcccgcagtgctgatgggt	12	13	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:35060881T>C	ENST00000358901.6	-	12	2294	c.1399A>G	c.(1399-1401)Acc>Gcc	p.T467A		NM_007126.3	NP_009057.1	P55072	TERA_HUMAN	valosin containing protein	467					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|aggresome assembly (GO:0070842)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|establishment of protein localization (GO:0045184)|positive regulation of Lys63-specific deubiquitinase activity (GO:1903007)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein K63-linked deubiquitination (GO:1903006)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein homooligomerization (GO:0051260)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|retrograde protein transport, ER to cytosol (GO:0030970)|translesion synthesis (GO:0019985)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Hrd1p ubiquitin ligase complex (GO:0000836)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|proteasome complex (GO:0000502)|site of double-strand break (GO:0035861)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|deubiquitinase activator activity (GO:0035800)|lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|protein domain specific binding (GO:0019904)|protein phosphatase binding (GO:0019903)|ubiquitin-specific protease binding (GO:1990381)			breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			TCTACCACGGTTTCCCGCAGT	0.552																																					p.T467A		Atlas-SNP	.											.	VCP	64	.	0			c.A1399G						.						143	128	133					9																	35060881		2203	4300	6503	SO:0001583	missense	7415	exon12			CCACGGTTTCCCG	AC004472	CCDS6573.1	9p13.3	2014-09-17	2011-01-25		ENSG00000165280	ENSG00000165280		"ATPases / AAA-type"	12666	protein-coding gene	gene with protein product		601023	"valosin-containing protein"			8595912, 7553851	Standard	NM_007126		Approved	IBMPFD, p97	uc003zvy.2	P55072	OTTHUMG00000019855	ENST00000358901.6:c.1399A>G	chr9.hg19:g.35060881T>C	ENSP00000351777:p.Thr467Ala	145.0	0.0		119.0	5.0	NM_007126	B2R5T8|Q0V924|Q2TAI5|Q969G7|Q9UCD5	Missense_Mutation	SNP	ENST00000358901.6	hg19	CCDS6573.1	.	.	.	.	.	.	.	.	.	.	T	15.49	2.850296	0.51270	.	.	ENSG00000165280	ENST00000358901	D	0.86627	-2.15	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	D	0.87728	0.6250	M	0.77103	2.36	0.80722	D	1	B	0.06786	0.001	B	0.09377	0.004	D	0.84750	0.0756	10	0.56958	D	0.05	-20.532	15.9966	0.80256	0.0:0.0:0.0:1.0	.	467	P55072	TERA_HUMAN	A	467	ENSP00000351777:T467A	ENSP00000351777:T467A	T	-	1	0	VCP	35050881	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	8.040000	0.89188	2.179000	0.69175	0.460000	0.39030	ACC	.	.		0.552	VCP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052290.1	NM_007126		C	35060881	T	C	35060881	3	2	259	1	0	0	0	0	1	0	0	0	17155	1725	60	2	1045	2	VCP	9	35060881	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1064564	35060881	106152550	408	36726										
SIT1	27240	hgsc.bcm.edu	37	chr9	35650500	35650501	+	Splice_Site	DNP	GT	GT	AC													0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cctgttgtccttcacccaccGtccctgccccggatggctcc					rs199515871		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G|T	G|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:35650500_35650501GT>AC	ENST00000259608.3	-	2	320_321	c.234_235AC>GT	c.(232-237)ggACgc>ggGTgc	p.R79C	SIT1_ENST00000474403.1_Intron	NM_014450.2	NP_055265.1	Q9Y3P8	SIT1_HUMAN	signaling threshold regulating transmembrane adaptor 1	79					immune system process (GO:0002376)|regulation of T cell activation (GO:0050863)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	kinase binding (GO:0019900)|SH2 domain binding (GO:0042169)			endometrium(2)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	9			Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TTCACCCACCGTCCCTGCCCCG	0.594																																					p.R79C|p.G78G		Atlas-SNP	.											.	SIT1	15	.	0			c.C235T|c.A234G						.																																			SO:0001630	splice_region_variant	27240	exon2			CCCACCGTCCCTG|CCACCGTCCCTGC		CCDS6582.1	9p13-p12	2008-02-05	2005-04-26		ENSG00000137078	ENSG00000137078			17710	protein-coding gene	gene with protein product	"SHP2 interacting transmembrane adaptor"	604964	"suppression inducing transmembrane adaptor 1"			11491537, 10209036	Standard	NM_014450		Approved	SIT	uc003zxe.1	Q9Y3P8	OTTHUMG00000019867	ENST00000259608.3:c.234_235delinsAC	chr9.hg19:g.35650500_35650501delinsAC		199.0|195.0	0.0		99.0|98.0	4.0	NM_014450	B2RBP9	Missense_Mutation|Silent	SNP	ENST00000259608.3	hg19	CCDS6582.1																																																																																			.	.		0.594	SIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052322.1	NM_014450	Missense_Mutation	AC	35650501	GT	AC	35650500	5	1	259	1	0	0	0	0	0	0	1	0	14359	1159	40	1	371	1	SIT1	9	35650500	Splice_Site	DNP	GT	TCGA-ES-A2HS-01A-11D-A183-10	589619	35650500	105562931	409	36727										
TPM2	7169	hgsc.bcm.edu	37	chr9	35685445	35685445	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgtcacctcttcatatttgcGgtctgaatcctcagcgatgt	8	11	5	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:35685445G>T	ENST00000360958.2	-	4	582	c.478C>A	c.(478-480)Cgc>Agc	p.R160S	TPM2_ENST00000378292.3_Missense_Mutation_p.R160S|TPM2_ENST00000329305.2_Missense_Mutation_p.R160S|TPM2_ENST00000378300.5_Missense_Mutation_p.R160S	NM_003289.3	NP_003280.2	P07951	TPM2_HUMAN	tropomyosin 2 (beta)	160					muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of ATPase activity (GO:0043462)	cytosol (GO:0005829)|muscle thin filament tropomyosin (GO:0005862)	actin binding (GO:0003779)|structural constituent of muscle (GO:0008307)	p.R160S(2)		NS(1)|breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_epithelial(49;0.121)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TCATATTTGCGGTCTGAATCC	0.542																																					p.R160S		Atlas-SNP	.											.	TPM2	64	.	2	Substitution - Missense(2)	lung(2)	c.C478A						.						193	153	166					9																	35685445		2203	4300	6503	SO:0001583	missense	7169	exon4			ATTTGCGGTCTGA		CCDS6586.1, CCDS6587.1	9p13	2014-09-17	2003-12-02		ENSG00000198467	ENSG00000198467		"Tropomyosins"	12011	protein-coding gene	gene with protein product	"nemaline myopathy type 4"	190990	"arthrogryposis multiplex congenital, distal, type 1"	AMCD1		7606936	Standard	NM_003289		Approved	DA1, NEM4	uc003zxq.3	P07951	OTTHUMG00000019878	ENST00000360958.2:c.478C>A	chr9.hg19:g.35685445G>T	ENSP00000354219:p.Arg160Ser	103.0	0.0		95.0	4.0	NM_213674	A6NM85|P06468|Q13894|Q53FM4|Q5TCU4|Q5TCU7|Q9UH67	Missense_Mutation	SNP	ENST00000360958.2	hg19	CCDS6587.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.080699	0.76528	.	.	ENSG00000198467	ENST00000378300;ENST00000378292;ENST00000329305;ENST00000360958	T;D;D;D	0.97553	1.51;-4.43;-4.43;-4.43	4.92	3.96	0.45880	.	.	.	.	.	D	0.98658	0.9550	M	0.92691	3.335	0.49051	D	0.999741	P;D;D;P;D	0.61697	0.905;0.974;0.987;0.951;0.99	P;D;D;D;D	0.72982	0.897;0.97;0.979;0.914;0.974	D	0.98776	1.0730	9	0.72032	D	0.01	.	15.3262	0.74164	0.0:0.0:0.86:0.14	.	160;160;160;160;160	B4DGC2;A7XZE4;P07951;Q5TCU8;P07951-2	.;.;TPM2_HUMAN;.;.	S	160	ENSP00000367550:R160S;ENSP00000367542:R160S;ENSP00000367541:R160S;ENSP00000354219:R160S	ENSP00000367541:R160S	R	-	1	0	TPM2	35675445	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.411000	0.73298	2.714000	0.92807	0.561000	0.74099	CGC	.	.		0.542	TPM2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052376.1	NM_003289		T	35685445	G	T	35685445	3	4	259	1	0	0	0	0	1	0	0	0	16421	1116	39	1	567	1	TPM2	9	35685445	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	34945	35685445	105527986	410	36728										
RGP1	692094	hgsc.bcm.edu	37	chr9	35752822	35752822	+	IGR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gctgcctactagccccacccTggcctcatatgctgccccag	8	19	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:35752822T>C	ENST00000436428.2	-	0	670				RGP1_ENST00000378078.4_Missense_Mutation_p.L376P|MSMP_ENST00000414286.1_5'Flank|GBA2_ENST00000545786.1_5'Flank|RGP1_ENST00000456972.2_Missense_Mutation_p.L416P	NM_001044264.2	NP_001037729.1	Q1L6U9	MSMP_HUMAN	microseminoprotein, prostate associated							cytoplasm (GO:0005737)|extracellular space (GO:0005615)				endometrium(2)|kidney(1)|lung(3)|prostate(3)	9						AGCCCCACCCTGGCCTCATAT	0.592																																					p.L376P		Atlas-SNP	.											RGP1_ENST00000378078,colon,carcinoma,0,2	RGP1	60	.	0			c.T1127C						.						36	36	36					9																	35752822		1987	4146	6133	SO:0001628	intergenic_variant	9827	exon9			CCACCCTGGCCTC	DQ012170	CCDS43797.1	9p13.3	2012-10-02			ENSG00000215183	ENSG00000215183			29663	protein-coding gene	gene with protein product		612191				17338636	Standard	NM_001044264		Approved	PC-3, PSMP	uc003zyb.2	Q1L6U9	OTTHUMG00000019882		chr9.hg19:g.35752822T>C		126.0	0.0		91.0	6.0	NM_001080496		Missense_Mutation	SNP	ENST00000436428.2	hg19	CCDS43797.1	.	.	.	.	.	.	.	.	.	.	T	13.42	2.232296	0.39498	.	.	ENSG00000107185	ENST00000456972;ENST00000378078	.	.	.	5.93	4.73	0.59995	.	0.173543	0.43579	D	0.000541	T	0.57548	0.2061	M	0.62723	1.935	0.80722	D	1	B;B	0.09022	0.002;0.002	B;B	0.11329	0.006;0.006	T	0.55585	-0.8118	9	0.34782	T	0.22	-7.8366	11.3719	0.49704	0.1355:0.0:0.0:0.8645	.	376;376	Q92546;A8K0K1	RGP1_HUMAN;.	P	416;376	.	ENSP00000367318:L376P	L	+	2	0	RGP1	35742822	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.073000	0.64395	2.263000	0.75096	0.533000	0.62120	CTG	.	.		0.592	MSMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052384.2	NM_001044264		C	35752822	T	C	35752822	1	2	259	0	1	0	0	0	0	0	0	0	13299	1580	55	2		2	RGP1	9	35752822	IGR	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	67377	35752822	105460609	411	36729										
TJP2	9414	hgsc.bcm.edu	37	chr9	71845110	71845110	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttcaagaagggacctcggcgGagcaggagggccttcaagaa	15	9	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:71845110G>T	ENST00000377245.4	+	11	1841	c.1633G>T	c.(1633-1635)Gag>Tag	p.E545*	TJP2_ENST00000265384.7_Nonsense_Mutation_p.E545*|TJP2_ENST00000348208.4_Nonsense_Mutation_p.E545*|TJP2_ENST00000535702.1_Nonsense_Mutation_p.E549*|TJP2_ENST00000453658.2_Nonsense_Mutation_p.E522*|TJP2_ENST00000539225.1_Nonsense_Mutation_p.E576*	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	545	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|hippo signaling (GO:0035329)|nucleotide phosphorylation (GO:0046939)|response to organic substance (GO:0010033)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	guanylate kinase activity (GO:0004385)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(5)|lung(9)|prostate(3)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	35						GACCTCGGCGGAGCAGGAGGG	0.512																																					p.E576X		Atlas-SNP	.											.	TJP2	120	.	0			c.G1726T						.						73	77	75					9																	71845110		2203	4300	6503	SO:0001587	stop_gained	9414	exon11			TCGGCGGAGCAGG	L27476	CCDS6627.1, CCDS6628.1, CCDS55314.1, CCDS55315.1, CCDS55316.1, CCDS55317.1	9q13-q21	2012-07-12	2012-07-12		ENSG00000119139	ENSG00000119139			11828	protein-coding gene	gene with protein product	"Friedreich ataxia region gene X104 (tight junction protein ZO-2)", "zona occludens 2"	607709	"deafness, autosomal dominant 51"	DFNA51		7951235, 20602916	Standard	NM_001170630		Approved	ZO-2, X104, ZO2	uc011lrv.2	Q9UDY2	OTTHUMG00000019978	ENST00000377245.4:c.1633G>T	chr9.hg19:g.71845110G>T	ENSP00000366453:p.Glu545*	96.0	0.0		83.0	4.0	NM_001170416	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Nonsense_Mutation	SNP	ENST00000377245.4	hg19	CCDS6627.1	.	.	.	.	.	.	.	.	.	.	G	41	9.092042	0.99062	.	.	ENSG00000119139	ENST00000453658;ENST00000377245;ENST00000348208;ENST00000265384;ENST00000535702;ENST00000539225	.	.	.	5.86	5.86	0.93980	.	0.171732	0.51477	D	0.000100	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	.	20.5632	0.99335	0.0:0.0:1.0:0.0	.	.	.	.	X	522;545;545;545;549;576	.	ENSP00000265384:E545X	E	+	1	0	TJP2	71034930	1.000000	0.71417	0.949000	0.38748	0.949000	0.60115	9.813000	0.99286	2.937000	0.99478	0.650000	0.86243	GAG	.	.		0.512	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629		T	71845110	G	T	71845110	4	4	259	1	0	0	0	0	0	1	0	0	15945	1175	41	3	1832	3	TJP2	9	71845110	Nonsense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	36092288	71845110	69368321	412	36730										
TLE4	7091	hgsc.bcm.edu	37	chr9	82337475	82337475	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agacaaataccaactacatcTtcatgagagctgtgtgctgt	8	9	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:82337475T>C	ENST00000376552.2	+	18	3114	c.2096T>C	c.(2095-2097)cTt>cCt	p.L699P	TLE4_ENST00000376537.4_Missense_Mutation_p.L731P|TLE4_ENST00000376534.4_Missense_Mutation_p.L336P|TLE4_ENST00000376520.4_Missense_Mutation_p.L731P|TLE4_ENST00000376544.3_Missense_Mutation_p.L630P|TLE4_ENST00000265284.6_Missense_Mutation_p.L674P	NM_007005.3	NP_008936.2	Q04727	TLE4_HUMAN	transducin-like enhancer of split 4	699					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|Wnt signaling pathway (GO:0016055)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	39						CAACTACATCTTCATGAGAGC	0.498																																					p.L699P		Atlas-SNP	.											.	TLE4	187	.	0			c.T2096C						.						138	136	137					9																	82337475		2031	4221	6252	SO:0001583	missense	7091	exon18			TACATCTTCATGA	M99439	CCDS43837.1, CCDS65069.1, CCDS65070.1, CCDS75851.1	9q21.32	2014-03-07	2014-03-07		ENSG00000106829	ENSG00000106829		"WD repeat domain containing"	11840	protein-coding gene	gene with protein product		605132	"transducin-like enhancer of split 4, homolog of Drosophila E(sp1)", "transducin-like enhancer of split 4 (E(sp1) homolog, Drosophila)"			8365415	Standard	XM_005252167		Approved	E(spI), ESG, GRG4	uc004alc.3	Q04727	OTTHUMG00000020072	ENST00000376552.2:c.2096T>C	chr9.hg19:g.82337475T>C	ENSP00000365735:p.Leu699Pro	207.0	0.0		125.0	5.0	NM_007005	F8W6T6|Q3ZCS1|Q5T1Y2|Q6PCB3|Q9BZ07|Q9BZ08|Q9BZ09|Q9NSL3|Q9ULF9	Missense_Mutation	SNP	ENST00000376552.2	hg19	CCDS43837.1	.	.	.	.	.	.	.	.	.	.	T	28.0	4.883456	0.91740	.	.	ENSG00000106829	ENST00000376552;ENST00000376544;ENST00000376520;ENST00000376537;ENST00000376534;ENST00000265284	T;T;T;T;T;T	0.60040	0.22;0.22;0.22;0.22;0.22;0.22	6.17	6.17	0.99709	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.73674	0.3617	L	0.58669	1.825	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.97110	0.987;0.999;0.969;1.0	T	0.74435	-0.3666	10	0.56958	D	0.05	-18.4225	16.8222	0.85835	0.0:0.0:0.0:1.0	.	674;630;731;699	F8W6T6;Q04727-2;Q04727-3;Q04727	.;.;.;TLE4_HUMAN	P	699;630;731;731;336;674	ENSP00000365735:L699P;ENSP00000365727:L630P;ENSP00000365703:L731P;ENSP00000365720:L731P;ENSP00000365717:L336P;ENSP00000265284:L674P	ENSP00000265284:L674P	L	+	2	0	TLE4	81527295	1.000000	0.71417	0.968000	0.41197	0.994000	0.84299	8.040000	0.89188	2.371000	0.80710	0.533000	0.62120	CTT	.	.		0.498	TLE4-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052792.4	XM_212237		C	82337475	T	C	82337475	3	2	259	1	0	0	0	0	1	0	0	0	15956	1609	56	2	2166	2	TLE4	9	82337475	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	10492365	82337475	58875956	413	36731										
FLJ46321	389763	hgsc.bcm.edu	37	chr9	84608910	84608910	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgctcactgacaaatgtgaaAgcaagcacttccaatgaaac	7	10	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:84608910A>G	ENST00000344803.2	+	4	3572	c.3525A>G	c.(3523-3525)aaA>aaG	p.K1175K		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	1175					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CAAATGTGAAAGCAAGCACTT	0.398																																					p.K1175K		Atlas-SNP	.											.	.	.	.	0			c.A3525G						.						56	54	54					9																	84608910		1869	4124	5993	SO:0001819	synonymous_variant	389763	exon4			TGTGAAAGCAAGC		CCDS47986.1	9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000214929	ENSG00000214929			37283	protein-coding gene	gene with protein product			"family with sequence similarity 75, member D1"	FAM75D1			Standard	NM_001001670		Approved	FLJ46321	uc004amn.3	Q6ZQQ2	OTTHUMG00000169122	ENST00000344803.2:c.3525A>G	chr9.hg19:g.84608910A>G		125.0	0.0		82.0	4.0	NM_001001670		Silent	SNP	ENST00000344803.2	hg19	CCDS47986.1																																																																																			.	.		0.398	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		G	84608910	A	G	84608910	2	3	259	1	0	0	0	0	0	0	0	1	5940	69	3	2		2	FLJ46321	9	84608910	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2271435	84608910	56604521	414	36732										
IARS	3376	hgsc.bcm.edu	37	chr9	95033301	95033301	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gtagctgtgagtgaaggtggTggcaaccagaagtcggcctt	16	7	0	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:95033301T>C	ENST00000375643.3	-	12	1437	c.1171A>G	c.(1171-1173)Acc>Gcc	p.T391A	IARS_ENST00000443024.2_Missense_Mutation_p.T391A|IARS_ENST00000447699.2_Missense_Mutation_p.T281A|IARS_ENST00000375629.3_5'UTR	NM_013417.2	NP_038203.2	P41252	SYIC_HUMAN	isoleucyl-tRNA synthetase	391					gene expression (GO:0010467)|isoleucyl-tRNA aminoacylation (GO:0006428)|osteoblast differentiation (GO:0001649)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|isoleucine-tRNA ligase activity (GO:0004822)			breast(3)|endometrium(2)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	35					L-Isoleucine(DB00167)	GTGAAGGTGGTGGCAACCAGA	0.388																																					p.T391A		Atlas-SNP	.											.	IARS	74	.	0			c.A1171G						.						178	167	171					9																	95033301		2203	4300	6503	SO:0001583	missense	3376	exon12			AGGTGGTGGCAAC	AB209234	CCDS6694.1	9q21	2011-07-01	2007-02-26		ENSG00000196305	ENSG00000196305	6.1.1.5	"Aminoacyl tRNA synthetases / Class I"	5330	protein-coding gene	gene with protein product	"isoleucine tRNA ligase 1, cytoplasmic"	600709				8812440	Standard	NM_002161		Approved	ILRS, IARS1	uc004aru.4	P41252	OTTHUMG00000020219	ENST00000375643.3:c.1171A>G	chr9.hg19:g.95033301T>C	ENSP00000364794:p.Thr391Ala	96.0	0.0		65.0	4.0	NM_013417	A8KAE9|Q5TCD0|Q7Z3T4|Q9H588	Missense_Mutation	SNP	ENST00000375643.3	hg19	CCDS6694.1	.	.	.	.	.	.	.	.	.	.	T	10.76	1.439961	0.25900	.	.	ENSG00000196305	ENST00000375643;ENST00000443024;ENST00000447699;ENST00000375660	T;T;T	0.34667	1.35;1.35;1.35	6.08	1.96	0.26148	Valyl/Leucyl/Isoleucyl-tRNA synthetase, class Ia, editing domain (2);Aminoacyl-tRNA synthetase, class Ia (1);	0.208495	0.56097	N	0.000021	T	0.15003	0.0362	N	0.02721	-0.515	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.002	T	0.05305	-1.0893	10	0.32370	T	0.25	-5.9685	10.4604	0.44577	0.0:0.2253:0.0:0.7747	.	391;236	P41252;Q6P0M4	SYIC_HUMAN;.	A	391;391;281;391	ENSP00000364794:T391A;ENSP00000406448:T391A;ENSP00000415020:T281A	ENSP00000364794:T391A	T	-	1	0	IARS	94073122	1.000000	0.71417	0.497000	0.27552	0.369000	0.29798	2.361000	0.44160	0.502000	0.28037	0.533000	0.62120	ACC	.	.		0.388	IARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053059.2	NM_002161		C	95033301	T	C	95033301	3	2	259	1	0	0	0	0	1	0	0	0	7482	1696	59	2	2709	2	IARS	9	95033301	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	10424391	95033301	46180130	415	36733										
FBP2	8789	hgsc.bcm.edu	37	chr9	97346891	97346891	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggcaaagatggttccgatggAggccaggcagtcaatattgg	15	7	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:97346891A>G	ENST00000375337.3	-	3	460	c.394T>C	c.(394-396)Tcc>Ccc	p.S132P		NM_003837.2	NP_003828.2	O00757	F16P2_HUMAN	fructose-1,6-bisphosphatase 2	132					carbohydrate metabolic process (GO:0005975)|fructose metabolic process (GO:0006000)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|small molecule metabolic process (GO:0044281)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	fructose 1,6-bisphosphate 1-phosphatase activity (GO:0042132)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(3)|lung(5)	9		Acute lymphoblastic leukemia(62;0.136)				GTTCCGATGGAGGCCAGGCAG	0.483																																					p.S132P		Atlas-SNP	.											.	FBP2	26	.	0			c.T394C						.						150	122	132					9																	97346891		2203	4300	6503	SO:0001583	missense	8789	exon3			CGATGGAGGCCAG	Y10812	CCDS6711.1	9q22.3	2012-08-13			ENSG00000130957	ENSG00000130957	3.1.3.11		3607	protein-coding gene	gene with protein product		603027				9678974	Standard	NM_003837		Approved		uc004auv.3	O00757	OTTHUMG00000020269	ENST00000375337.3:c.394T>C	chr9.hg19:g.97346891A>G	ENSP00000364486:p.Ser132Pro	151.0	0.0		115.0	5.0	NM_003837	Q17R39|Q6FI53	Missense_Mutation	SNP	ENST00000375337.3	hg19	CCDS6711.1	.	.	.	.	.	.	.	.	.	.	A	14.11	2.437382	0.43224	.	.	ENSG00000130957	ENST00000375337	T	0.79247	-1.25	4.87	4.87	0.63330	.	0.169189	0.53938	D	0.000045	T	0.73426	0.3585	L	0.58354	1.805	0.53005	D	0.999961	B	0.21309	0.054	B	0.25506	0.061	T	0.72782	-0.4189	10	0.66056	D	0.02	-19.1055	9.6905	0.40125	0.9098:0.0:0.0902:0.0	.	132	O00757	F16P2_HUMAN	P	132	ENSP00000364486:S132P	ENSP00000364486:S132P	S	-	1	0	FBP2	96386712	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	3.742000	0.55097	1.941000	0.56285	0.533000	0.62120	TCC	.	.		0.483	FBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053189.1	NM_003837		G	97346891	A	G	97346891	3	3	259	1	0	0	0	0	1	0	0	0	5714	304	11	2	645	2	FBP2	9	97346891	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2313590	97346891	43866540	416	36734										
FKTN	2218	hgsc.bcm.edu	37	chr9	108363469	108363469	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gttaacatccaaccaaaatgTaccagtgtttcttattgatc	5	9	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:108363469T>C	ENST00000223528.2	+	4	333	c.209T>C	c.(208-210)gTa>gCa	p.V70A	FKTN_ENST00000357998.5_Missense_Mutation_p.V70A|FKTN_ENST00000448551.2_Missense_Mutation_p.V70A|FKTN_ENST00000602661.1_Missense_Mutation_p.V70A|FKTN_ENST00000540160.1_Missense_Mutation_p.V70A	NM_006731.2	NP_006722.2	O75072	FKTN_HUMAN	fukutin	70					muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|negative regulation of JNK cascade (GO:0046329)|nervous system development (GO:0007399)|regulation of protein glycosylation (GO:0060049)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	transferase activity (GO:0016740)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	25						AACCAAAATGTACCAGTGTTT	0.318																																					p.V70A		Atlas-SNP	.											.	FKTN	47	.	0			c.T209C						.						64	64	64					9																	108363469		2203	4299	6502	SO:0001583	missense	2218	exon4			AAAATGTACCAGT		CCDS6766.1	9q31-q33	2014-09-17	2007-11-21	2007-11-21	ENSG00000106692	ENSG00000106692			3622	protein-coding gene	gene with protein product		607440	"Fukuyama type congenital muscular dystrophy (fukutin)"	FCMD		8275093, 17036286, 17044012	Standard	NM_001079802		Approved	LGMD2M	uc004bcs.3	O75072	OTTHUMG00000020425	ENST00000223528.2:c.209T>C	chr9.hg19:g.108363469T>C	ENSP00000223528:p.Val70Ala	108.0	0.0		91.0	5.0	NM_006731	B4DUX9|J3KP13|Q3MIJ1|Q96TE1|Q9P295	Missense_Mutation	SNP	ENST00000223528.2	hg19	CCDS6766.1	.	.	.	.	.	.	.	.	.	.	T	17.68	3.449337	0.63178	.	.	ENSG00000106692	ENST00000223528;ENST00000448551;ENST00000540160;ENST00000357998;ENST00000374705	D;D;D;D;D	0.92199	-2.66;-2.99;-1.84;-2.99;-1.89	5.65	5.65	0.86999	.	0.222664	0.40144	N	0.001170	D	0.88654	0.6495	L	0.44542	1.39	0.40163	D	0.977088	P;P;P	0.41131	0.739;0.495;0.682	B;B;B	0.36464	0.225;0.079;0.079	D	0.90327	0.4349	10	0.87932	D	0	-12.5197	15.0542	0.71901	0.0:0.0:0.0:1.0	.	70;70;70	B4E2W4;B4DUX9;O75072	.;.;FKTN_HUMAN	A	70;70;70;70;47	ENSP00000223528:V70A;ENSP00000399140:V70A;ENSP00000439423:V70A;ENSP00000350687:V70A;ENSP00000363837:V47A	ENSP00000223528:V70A	V	+	2	0	FKTN	107403290	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	4.575000	0.60908	2.155000	0.67459	0.383000	0.25322	GTA	.	.		0.318	FKTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053505.1	NM_006731		C	108363469	T	C	108363469	3	2	259	1	0	0	0	0	1	0	0	0	5927	1638	57	2	219	2	FKTN	9	108363469	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	11016578	108363469	32849962	417	36735										
C9orf84	158401	hgsc.bcm.edu	37	chr9	114454021	114454021	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cagaaagtctcatcttttgaActttcacatgtgaggccttc	7	10	3	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:114454021A>G	ENST00000318737.4	-	25	4172	c.4044T>C	c.(4042-4044)agT>agC	p.S1348S	C9orf84_ENST00000374287.3_Silent_p.S1348S|C9orf84_ENST00000394779.3_Silent_p.S1309S|C9orf84_ENST00000394777.4_Silent_p.S1274S	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	1348										breast(1)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(10)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						CATCTTTTGAACTTTCACATG	0.373																																					p.S1348S		Atlas-SNP	.											.	C9orf84	207	.	0			c.T4044C						.						72	74	73					9																	114454021		2203	4300	6503	SO:0001819	synonymous_variant	158401	exon25			TTTTGAACTTTCA	AL833535	CCDS6781.3, CCDS43863.1	9q32	2012-03-16			ENSG00000165181	ENSG00000165181			26535	protein-coding gene	gene with protein product							Standard	XM_005251738		Approved	FLJ32779	uc004bfr.3	Q5VXU9	OTTHUMG00000020495	ENST00000318737.4:c.4044T>C	chr9.hg19:g.114454021A>G		118.0	0.0		90.0	4.0	NM_173521	A2A2V3|Q2M1H8|Q96M73	Silent	SNP	ENST00000318737.4	hg19	CCDS6781.3																																																																																			.	.		0.373	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521		G	114454021	A	G	114454021	2	3	259	1	0	0	0	0	0	0	0	1	2502	40	2	2		2	C9orf84	9	114454021	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	6090552	114454021	26759410	418	36736										
TTC16	158248	hgsc.bcm.edu	37	chr9	130482418	130482418	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gaatgtcttctcacatgctgCtgagctccagcctgagaaac	9	12	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:130482418C>T	ENST00000373289.3	+	5	568	c.488C>T	c.(487-489)gCt>gTt	p.A163V	TTC16_ENST00000393748.4_5'UTR|PTRH1_ENST00000429848.1_Intron|PTRH1_ENST00000419060.1_Intron	NM_144965.1	NP_659402.1	Q8NEE8	TTC16_HUMAN	tetratricopeptide repeat domain 16	163										central_nervous_system(2)|endometrium(3)|lung(7)|ovary(3)|pancreas(2)|prostate(4)|skin(1)	22						TCACATGCTGCTGAGCTCCAG	0.597																																					p.A163V		Atlas-SNP	.											.	TTC16	55	.	0			c.C488T						.						204	157	173					9																	130482418		2203	4300	6503	SO:0001583	missense	158248	exon5			ATGCTGCTGAGCT	AK057342	CCDS6875.1	9q34.13	2013-01-10			ENSG00000167094	ENSG00000167094		"Tetratricopeptide (TTC) repeat domain containing"	26536	protein-coding gene	gene with protein product						12477932	Standard	NM_144965		Approved	FLJ32780	uc004brq.1	Q8NEE8	OTTHUMG00000020711	ENST00000373289.3:c.488C>T	chr9.hg19:g.130482418C>T	ENSP00000362386:p.Ala163Val	152.0	0.0		96.0	5.0	NM_144965	B4DYG4|B5ME24|Q5JU66|Q96M72	Missense_Mutation	SNP	ENST00000373289.3	hg19	CCDS6875.1	.	.	.	.	.	.	.	.	.	.	C	3.684	-0.064900	0.07273	.	.	ENSG00000167094	ENST00000373289;ENST00000316259	T	0.50548	0.74	4.84	0.946	0.19549	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.892206	0.09685	N	0.769180	T	0.29158	0.0725	N	0.24115	0.695	0.09310	N	0.999994	B;B;B	0.27450	0.179;0.048;0.179	B;B;B	0.21151	0.033;0.013;0.033	T	0.16867	-1.0388	10	0.33940	T	0.23	-0.4035	6.0062	0.19547	0.0:0.6302:0.1385:0.2313	.	150;115;163	B4DZ42;B4DH05;Q8NEE8	.;.;TTC16_HUMAN	V	163;108	ENSP00000362386:A163V	ENSP00000319048:A108V	A	+	2	0	TTC16	129522239	0.006000	0.16342	0.000000	0.03702	0.391000	0.30476	1.605000	0.36815	0.012000	0.14892	0.195000	0.17529	GCT	.	.		0.597	TTC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054224.1	NM_144965		T	130482418	C	T	130482418	3	4	259	1	0	0	0	0	1	0	0	0	16698	797	28	3	506	3	TTC16	9	130482418	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	16028397	130482418	10731013	419	36737										
ZER1	10444	hgsc.bcm.edu	37	chr9	131515870	131515870	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gcagttagtcaggtacagctCcaccaggtcctgggagtggg	15	10	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:131515870C>T	ENST00000291900.2	-	4	725	c.319G>A	c.(319-321)Gag>Aag	p.E107K	ZER1_ENST00000494461.1_5'UTR	NM_006336.2	NP_006327.2	Q7Z7L7	ZER1_HUMAN	zyg-11 related, cell cycle regulator	107					protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein transferase activity (GO:0051438)	Cul2-RING ubiquitin ligase complex (GO:0031462)	ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	15						AGGTACAGCTCCACCAGGTCC	0.622																																					p.E107K		Atlas-SNP	.											.	ZER1	49	.	0			c.G319A						.						40	41	40					9																	131515870		2203	4300	6503	SO:0001583	missense	10444	exon4			ACAGCTCCACCAG	X99802	CCDS6910.1	9q33.3	2013-01-17	2012-12-10	2007-01-04	ENSG00000160445	ENSG00000160445		"ZYG11 cell cycle regulator family"	30960	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 60", "zyg-11 homolog B (C. elegans)-like", "zer-1 homolog (C. elegans)"	C9orf60, ZYG11BL		11719588	Standard	NM_006336		Approved	ZYG, Hzyg	uc004bwa.2	Q7Z7L7	OTTHUMG00000020759	ENST00000291900.2:c.319G>A	chr9.hg19:g.131515870C>T	ENSP00000291900:p.Glu107Lys	96.0	0.0		62.0	4.0	NM_006336	O00156|Q5T272|Q5T273	Missense_Mutation	SNP	ENST00000291900.2	hg19	CCDS6910.1	.	.	.	.	.	.	.	.	.	.	C	34	5.344655	0.95807	.	.	ENSG00000160445	ENST00000291900;ENST00000414921	T;T	0.18174	2.23;2.23	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.31263	0.0791	L	0.32530	0.975	0.80722	D	1	D	0.63880	0.993	D	0.70935	0.971	T	0.01068	-1.1462	10	0.23302	T	0.38	-35.5407	18.8072	0.92041	0.0:1.0:0.0:0.0	.	107	Q7Z7L7	ZER1_HUMAN	K	107	ENSP00000291900:E107K;ENSP00000393051:E107K	ENSP00000291900:E107K	E	-	1	0	ZER1	130555691	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.374000	0.66167	2.691000	0.91804	0.655000	0.94253	GAG	.	.		0.622	ZER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054491.1	NM_006336		T	131515870	C	T	131515870	3	4	259	1	0	0	0	0	1	0	0	0	17640	864	30	3	2033	3	ZER1	9	131515870	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	1033452	131515870	9697561	420	36738										
PHYHD1	254295	hgsc.bcm.edu	37	chr9	131702690	131702690	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cttcctgtacacggagccccTgggccgggtgctgggcgtgt	16	13	0	0	rs569532899		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:131702690T>C	ENST00000372592.3	+	10	1433	c.500T>C	c.(499-501)cTg>cCg	p.L167P	RP11-101E3.5_ENST00000482796.1_5'Flank|PHYHD1_ENST00000421063.2_Missense_Mutation_p.L146P|PHYHD1_ENST00000487504.1_3'UTR|PHYHD1_ENST00000353176.5_Missense_Mutation_p.L146P|PHYHD1_ENST00000308941.5_Missense_Mutation_p.W160R	NM_001100876.1	NP_001094346.1	Q5SRE7	PHYD1_HUMAN	phytanoyl-CoA dioxygenase domain containing 1	167							dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|skin(1)|stomach(3)	10						ACGGAGCCCCTGGGCCGGGTG	0.627													T|||	1	0.000199681	0	0	5008	,	,		17838	0		0	False		,,,				2504	0.001				p.L167P		Atlas-SNP	.											.	PHYHD1	29	.	0			c.T500C						.						71	77	75					9																	131702690		2203	4300	6503	SO:0001583	missense	254295	exon10			AGCCCCTGGGCCG	BC051300	CCDS6914.1, CCDS43885.1, CCDS43886.1	9q34.13	2010-08-13			ENSG00000175287	ENSG00000175287			23396	protein-coding gene	gene with protein product						12477932	Standard	NM_174933		Approved	MGC16638	uc004bwp.2	Q5SRE7	OTTHUMG00000020764	ENST00000372592.3:c.500T>C	chr9.hg19:g.131702690T>C	ENSP00000361673:p.Leu167Pro	107.0	0.0		87.0	4.0	NM_001100876	A6PWN9|A6PWP0|B3KT57|B4E3X8|Q5SRE9|Q5SRF0|Q7Z623|Q7Z7P9|Q96GM4	Missense_Mutation	SNP	ENST00000372592.3	hg19	CCDS43885.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.93|18.93	3.726987|3.726987	0.69074|0.69074	.|.	.|.	ENSG00000175287|ENSG00000175287	ENST00000372592;ENST00000353176;ENST00000426694;ENST00000421063|ENST00000308941;ENST00000419872	D;D;D;D|.	0.88664|.	-2.41;-2.41;-2.41;-2.41|.	5.25|5.25	5.25|5.25	0.73442|0.73442	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.78717|0.78717	0.4327|0.4327	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	B;B|D	0.19706|0.76494	0.029;0.038|0.999	B;B|D	0.25291|0.74023	0.059;0.027|0.982	T|T	0.81949|0.81949	-0.0699|-0.0699	8|8	0.30078|0.87932	T|D	0.28|0	-3.8361|-3.8361	14.3375|14.3375	0.66600|0.66600	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	146;167|160	Q5SRE7-2;Q5SRE7|Q5SRE7-3	.;PHYD1_HUMAN|.	P|R	167;146;167;146|160;25	ENSP00000361673:L167P;ENSP00000340945:L146P;ENSP00000412377:L167P;ENSP00000409928:L146P|.	ENSP00000340945:L146P|ENSP00000309515:W160R	L|W	+|+	2|1	0|0	PHYHD1|PHYHD1	130742511|130742511	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.980000|0.980000	0.70556|0.70556	5.150000|5.150000	0.64869|0.64869	1.998000|1.998000	0.58463|0.58463	0.454000|0.454000	0.30748|0.30748	CTG|TGG	.	.		0.627	PHYHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054506.2	NM_174933		C	131702690	T	C	131702690	3	2	259	1	0	0	0	0	1	0	0	0	11874	1580	55	2	530	2	PHYHD1	9	131702690	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	186820	131702690	9510741	421	36739										
BAT2L1	84726	hgsc.bcm.edu	37	chr9	134353913	134353913	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggggaggagagtgaggtgggTtctatggtgggcgaaggctt	22	3	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:134353913T>C	ENST00000357304.4	+	17	4720	c.4665T>C	c.(4663-4665)ggT>ggC	p.G1555G	PRRC2B_ENST00000458550.1_Silent_p.G861G|PRRC2B_ENST00000405995.1_Silent_p.G861G|PRRC2B_ENST00000372249.1_5'UTR	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	1555							poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						GTGAGGTGGGTTCTATGGTGG	0.567											OREG0019562	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G1555G		Atlas-SNP	.											.	PRRC2B	266	.	0			c.T4665C						.						134	142	140					9																	134353913		1903	4118	6021	SO:0001819	synonymous_variant	84726	exon17			GGTGGGTTCTATG	AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"KIAA0515", "HLA-B associated transcript 2-like", "HLA-B associated transcript 2-like 1"	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.4665T>C	chr9.hg19:g.134353913T>C		154.0	0.0	1610	96.0	4.0	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Silent	SNP	ENST00000357304.4	hg19	CCDS48044.1	.	.	.	.	.	.	.	.	.	.	T	6.142	0.394323	0.11638	.	.	ENSG00000130723	ENST00000451855	.	.	.	5.42	0.937	0.19494	.	.	.	.	.	T	0.40839	0.1133	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.29181	-1.0020	4	.	.	.	-26.4667	0.8187	0.01107	0.1653:0.2618:0.1618:0.4111	.	.	.	.	L	289	.	.	F	+	1	0	PRRC2B	133343734	0.893000	0.30496	0.804000	0.32291	0.479000	0.33129	0.211000	0.17474	0.643000	0.30638	-0.366000	0.07423	TTC	.	.		0.567	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	134353913	T	C	134353913	2	2	259	1	0	0	0	0	0	0	0	1	1320	1712	60	2		2	BAT2L1	9	134353913	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	2651223	134353913	6859518	422	36740										
GBGT1	26301	hgsc.bcm.edu	37	chr9	136029497	136029497	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctcccagtgggagtgaccctGgatggggatggagctgagaa	17	8	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:136029497G>T	ENST00000372040.3	-	7	822	c.511C>A	c.(511-513)Cag>Aag	p.Q171K	GBGT1_ENST00000372038.3_3'UTR|GBGT1_ENST00000372043.3_Silent_p.S164S|RALGDS_ENST00000542690.1_Intron|GBGT1_ENST00000540636.1_Missense_Mutation_p.Q154K|GBGT1_ENST00000472281.1_5'UTR	NM_001282629.1	NP_001269558.1	Q8N5D6	GBGT1_HUMAN	globoside alpha-1,3-N-acetylgalactosaminyltransferase 1	171					glycolipid biosynthetic process (GO:0009247)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	globoside alpha-N-acetylgalactosaminyltransferase activity (GO:0047277)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(4)|lung(2)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(145;3.49e-06)|Epithelial(140;2.59e-05)		GAGTGACCCTGGATGGGGATG	0.627																																					p.Q171K		Atlas-SNP	.											.	GBGT1	25	.	0			c.C511A						.						39	35	37					9																	136029497		2203	4299	6502	SO:0001583	missense	26301	exon7			GACCCTGGATGGG	AY358175	CCDS6960.1, CCDS65175.1, CCDS65176.1	9q34.13-q34.3	2014-07-18			ENSG00000148288	ENSG00000148288		"Glycosyltransferase family 6 domain containing"	20460	protein-coding gene	gene with protein product	"Forssman glycolipid synthetase (FS)", "Forssman synthetase"	606074				10506200, 8855242	Standard	NM_021996		Approved	UDP-GalNAc, A3GALNT, MGC44848, FS		Q8N5D6	OTTHUMG00000020853	ENST00000372040.3:c.511C>A	chr9.hg19:g.136029497G>T	ENSP00000361110:p.Gln171Lys	90.0	0.0		81.0	4.0	NM_021996	A8K633|B2RA95|B7Z8S5|Q45F07|Q5T7U9|Q5T7V1|Q8N2K4|Q9UKI5	Missense_Mutation	SNP	ENST00000372040.3	hg19	CCDS6960.1	.	.	.	.	.	.	.	.	.	.	G	0.042	-1.280718	0.01398	.	.	ENSG00000148288	ENST00000372040;ENST00000540636	T;T	0.01099	5.34;5.34	5.38	4.47	0.54385	.	0.981452	0.08357	N	0.958368	T	0.01189	0.0039	N	0.24115	0.695	0.21325	N	0.999724	B;B	0.12013	0.005;0.005	B;B	0.12837	0.008;0.005	T	0.46275	-0.9203	10	0.05525	T	0.97	-0.2384	13.695	0.62572	0.0:0.0:0.7209:0.2791	.	154;171	B7Z8S5;Q8N5D6	.;GBGT1_HUMAN	K	171;154	ENSP00000361110:Q171K;ENSP00000437663:Q154K	ENSP00000361110:Q171K	Q	-	1	0	GBGT1	135019318	0.064000	0.20934	0.818000	0.32626	0.313000	0.28021	0.698000	0.25571	1.237000	0.43756	0.491000	0.48974	CAG	.	.		0.627	GBGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054815.1	NM_021996		T	136029497	G	T	136029497	3	4	259	1	0	0	0	0	1	0	0	0	6280	1357	47	3	536	3	GBGT1	9	136029497	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1675584	136029497	5183934	423	36741										
COL5A1	1289	hgsc.bcm.edu	37	chr9	137716488	137716488	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agcccctgccaatccaggcaTccaggacgcggcggaacatc	11	16	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:137716488T>C	ENST00000371817.3	+	62	5155	c.4741T>C	c.(4741-4743)Tcc>Ccc	p.S1581P		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	1581	Nonhelical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		AATCCAGGCATCCAGGACGCG	0.647																																					p.S1581P		Atlas-SNP	.											.	COL5A1	323	.	0			c.T4741C						.						47	42	44					9																	137716488		2203	4300	6503	SO:0001583	missense	1289	exon62			CAGGCATCCAGGA	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"Collagens"	2209	protein-coding gene	gene with protein product	"alpha 1 type V collagen"	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.4741T>C	chr9.hg19:g.137716488T>C	ENSP00000360882:p.Ser1581Pro	168.0	0.0		96.0	6.0	NM_000093	Q15094|Q5SUX4	Missense_Mutation	SNP	ENST00000371817.3	hg19	CCDS6982.1	.	.	.	.	.	.	.	.	.	.	T	10.22	1.290693	0.23564	.	.	ENSG00000130635	ENST00000371817;ENST00000355306	D	0.89810	-2.57	4.21	4.21	0.49690	.	0.440276	0.21317	U	0.076538	T	0.79992	0.4542	L	0.27944	0.81	0.34759	D	0.732579	B	0.06786	0.001	B	0.08055	0.003	T	0.76438	-0.2959	10	0.14252	T	0.57	.	10.983	0.47506	0.0:0.0:0.156:0.844	.	1581	P20908	CO5A1_HUMAN	P	1581;118	ENSP00000360882:S1581P	ENSP00000347458:S118P	S	+	1	0	COL5A1	136856309	0.937000	0.31787	0.131000	0.22000	0.957000	0.61999	1.675000	0.37555	1.673000	0.50895	0.363000	0.22086	TCC	.	.		0.647	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093		C	137716488	T	C	137716488	3	2	259	1	0	0	0	0	1	0	0	0	3698	1435	50	2	4987	2	COL5A1	9	137716488	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1686991	137716488	3496943	424	36742										
ABCA2	20	hgsc.bcm.edu	37	chr9	139910924	139910924	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctccatgccacgggtctcctCtgcaccagggctgtggatca	11	15	3	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:139910924C>A	ENST00000371605.3	-	20	3068		c.e20-1		ABCA2_ENST00000492260.1_5'Flank|ABCA2_ENST00000265662.5_Splice_Site|ABCA2_ENST00000341511.6_Splice_Site			Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 2						ATP catabolic process (GO:0006200)|cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|regulation of intracellular cholesterol transport (GO:0032383)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|nucleotide binding (GO:0000166)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|liver(1)|lung(25)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	41	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		CGGGTCTCCTCTGCACCAGGG	0.642																																					.		Atlas-SNP	.											.	ABCA2	113	.	0			c.3014-1G>T						.						74	83	80					9																	139910924		2095	4202	6297	SO:0001630	splice_region_variant	20	exon22			TCTCCTCTGCACC	U18235	CCDS43909.1	9q34	2012-03-14			ENSG00000107331	ENSG00000107331		"ATP binding cassette transporters / subfamily A"	32	protein-coding gene	gene with protein product		600047		ABC2		8088782	Standard	NM_212533		Approved		uc022bpy.1	Q9BZC7	OTTHUMG00000020958	ENST00000371605.3:c.2921-1G>T	chr9.hg19:g.139910924C>A		144.0	0.0		95.0	4.0	NM_212533	A6NED5|Q5SPY5|Q5W9G5|Q76MW7|Q9HC28	Splice_Site	SNP	ENST00000371605.3	hg19		.	.	.	.	.	.	.	.	.	.	C	14.15	2.450280	0.43531	.	.	ENSG00000107331	ENST00000265662;ENST00000371605;ENST00000355090;ENST00000341511	.	.	.	4.23	4.23	0.50019	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5922	0.84769	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ABCA2	139030745	1.000000	0.71417	0.998000	0.56505	0.447000	0.32167	3.667000	0.54547	1.898000	0.54952	0.306000	0.20318	.	.	.		0.642	ABCA2-202	KNOWN	basic	protein_coding	protein_coding		NM_001606	Intron	A	139910924	C	A	139910924	5	1	259	1	0	0	0	0	0	0	1	0	32	927	32	3	4503	3	ABCA2	9	139910924	Splice_Site	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	2194436	139910924	1302507	425	36743										
RNF208	727800	hgsc.bcm.edu	37	chr9	140115610	140115610	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atggggacccttcaggcaggAcatgaggaggcccggccagc	16	12	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:140115610A>G	ENST00000392827.1	-	2	223	c.55T>C	c.(55-57)Tcc>Ccc	p.S19P	RNF208_ENST00000391553.1_Missense_Mutation_p.S19P			Q9H0X6	RN208_HUMAN	ring finger protein 208	19					protein autoubiquitination (GO:0051865)		ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			lung(1)	1	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		TTCAGGCAGGACATGAGGAGG	0.652																																					p.S19P		Atlas-SNP	.											.	RNF208	11	.	0			c.T55C						.						12	14	14					9																	140115610		1928	4112	6040	SO:0001583	missense	727800	exon1			GGCAGGACATGAG	AF416715	CCDS7037.2	9q34.3	2007-01-19				ENSG00000212864		"RING-type (C3HC4) zinc fingers"	25420	protein-coding gene	gene with protein product						11230166	Standard	NM_031297		Approved	DKFZP761H1710	uc004clz.2	Q9H0X6		ENST00000392827.1:c.55T>C	chr9.hg19:g.140115610A>G	ENSP00000376572:p.Ser19Pro	146.0	0.0		104.0	5.0	NM_031297	A2BFA0	Missense_Mutation	SNP	ENST00000392827.1	hg19	CCDS7037.2	.	.	.	.	.	.	.	.	.	.	a	13.72	2.321905	0.41096	.	.	ENSG00000212864	ENST00000392827;ENST00000391553	T;T	0.39997	1.05;1.05	3.58	2.39	0.29439	.	.	.	.	.	T	0.31167	0.0788	N	0.19112	0.55	0.40669	D	0.982191	P	0.39250	0.665	B	0.43018	0.405	T	0.13202	-1.0518	9	0.87932	D	0	-5.8566	8.7227	0.34449	0.8074:0.1926:0.0:0.0	.	19	Q9H0X6	RN208_HUMAN	P	19	ENSP00000376572:S19P;ENSP00000375397:S19P	ENSP00000375397:S19P	S	-	1	0	RNF208	139235431	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.163000	0.50763	0.425000	0.26087	0.454000	0.30748	TCC	.	.		0.652	RNF208-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254714.1	NM_031297		G	140115610	A	G	140115610	3	3	259	1	0	0	0	0	1	0	0	0	13490	275	10	2	734	2	RNF208	9	140115610	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	204686	140115610	1097821	426	36744										
ADARB2	105	hgsc.bcm.edu	37	chr10	1229197	1229197	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cccaggtgcccaggccagccTtctgaaaggccttgaacagc	11	15	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:1229197T>C	ENST00000381312.1	-	10	2481	c.2156A>G	c.(2155-2157)aAg>aGg	p.K719R	ADARB2_ENST00000381305.1_Missense_Mutation_p.K121R|ADARB2_ENST00000381310.3_Missense_Mutation_p.K228R	NM_018702.3	NP_061172.1	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2 (non-functional)	719	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				mRNA processing (GO:0006397)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	41		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		CAGGCCAGCCTTCTGAAAGGC	0.622																																					p.K719R		Atlas-SNP	.											.	ADARB2	95	.	0			c.A2156G						.						61	54	56					10																	1229197		2203	4300	6503	SO:0001583	missense	105	exon10			CCAGCCTTCTGAA	AF034837	CCDS7058.1	10p15.3	2013-05-20	2013-05-20		ENSG00000185736	ENSG00000185736	3.5.-.-		227	protein-coding gene	gene with protein product	"RED2 homolog (rat)"	602065	"adenosine deaminase, RNA-specific, B2 (RED2 homolog rat)", "adenosine deaminase, RNA-specific, B2"			9272162, 10836796	Standard	NM_018702		Approved	RED2, hRED2, ADAR3	uc009xhq.3	Q9NS39	OTTHUMG00000017543	ENST00000381312.1:c.2156A>G	chr10.hg19:g.1229197T>C	ENSP00000370713:p.Lys719Arg	176.0	0.0		125.0	5.0	NM_018702	B2RPJ5|Q5VUT6|Q5VW42	Missense_Mutation	SNP	ENST00000381312.1	hg19	CCDS7058.1	.	.	.	.	.	.	.	.	.	.	T	12.90	2.077815	0.36662	.	.	ENSG00000185736	ENST00000381312;ENST00000381310;ENST00000381305	D;D;D	0.93859	-3.3;-3.3;-3.3	5.32	5.32	0.75619	Adenosine deaminase/editase (3);	0.093502	0.85682	D	0.000000	D	0.88243	0.6384	L	0.35249	1.045	0.42091	D	0.991298	B;B;B	0.18610	0.004;0.029;0.014	B;B;B	0.22601	0.04;0.039;0.032	D	0.84155	0.0425	10	0.42905	T	0.14	-28.3273	8.6606	0.34091	0.0:0.149:0.0:0.851	.	719;121;228	Q9NS39;Q5VW43;Q5VW42	RED2_HUMAN;.;.	R	719;228;121	ENSP00000370713:K719R;ENSP00000370711:K228R;ENSP00000370706:K121R	ENSP00000370706:K121R	K	-	2	0	ADARB2	1219197	1.000000	0.71417	0.999000	0.59377	0.788000	0.44548	2.792000	0.47837	2.025000	0.59659	0.459000	0.35465	AAG	.	.		0.622	ADARB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046426.1	NM_018702		C	1229197	T	C	1229197	3	2	259	1	0	0	0	0	1	0	0	0	283	1609	56	2	67	2	ADARB2	10	1229197	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10		1229197	134305550	427	36745										
RBM17	84991	hgsc.bcm.edu	37	chr10	6143232	6143232	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tccttgtttttgatgattttAgagccaaaggacgaaacaaa	8	6	0	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:6143232A>G	ENST00000446108.1	+	3	767		c.e3-1		RBM17_ENST00000379888.4_Splice_Site	NM_001145547.1	NP_001139019.1	Q96I25	SPF45_HUMAN	RNA binding motif protein 17						alternative mRNA splicing, via spliceosome (GO:0000380)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(2)	19						TGATGATTTTAGAGCCAAAGG	0.428																																					.		Atlas-SNP	.											.	RBM17	45	.	0			c.124-2A>G						.						54	47	50					10																	6143232		2203	4300	6503	SO:0001630	splice_region_variant	84991	exon3			GATTTTAGAGCCA	AF083384	CCDS7077.1	10p15.1	2013-01-28			ENSG00000134453	ENSG00000134453		"RNA binding motif (RRM) containing", "G patch domain containing"	16944	protein-coding gene	gene with protein product	"splicing factor 45kDa"	606935				9731529	Standard	NM_032905		Approved	SPF45, MGC14439	uc001ijb.3	Q96I25	OTTHUMG00000017618	ENST00000446108.1:c.124-1A>G	chr10.hg19:g.6143232A>G		92.0	0.0		76.0	4.0	NM_032905	Q96GY6	Splice_Site	SNP	ENST00000446108.1	hg19	CCDS7077.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.093478	0.76756	.	.	ENSG00000134453	ENST00000372795;ENST00000379888;ENST00000437845;ENST00000432931;ENST00000446108;ENST00000418631	.	.	.	4.67	4.67	0.58626	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4099	0.67109	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	RBM17	6183238	1.000000	0.71417	0.994000	0.49952	0.956000	0.61745	9.014000	0.93635	1.862000	0.54008	0.460000	0.39030	.	.	.		0.428	RBM17-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046635.1	NM_032905	Intron	G	6143232	A	G	6143232	5	3	259	1	0	0	0	0	0	0	1	0	13134	434	15	2	128	2	RBM17	10	6143232	Splice_Site	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	4914035	6143232	129391515	428	36746										
NUDT5	11164	hgsc.bcm.edu	37	chr10	12215770	12215770	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cagtttcttcttcaagctccCggagagcagctgcttctggg	11	12	4	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:12215770C>T	ENST00000491614.1	-	6	727	c.332G>A	c.(331-333)cGg>cAg	p.R111Q	NUDT5_ENST00000378940.3_Missense_Mutation_p.R111Q|NUDT5_ENST00000537776.1_Missense_Mutation_p.R111Q|NUDT5_ENST00000378937.3_Missense_Mutation_p.R124Q|NUDT5_ENST00000378952.3_5'UTR|NUDT5_ENST00000378927.3_Missense_Mutation_p.R111Q			Q9UKK9	NUDT5_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 5	111	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				D-ribose catabolic process (GO:0019303)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|ribonucleoside diphosphate catabolic process (GO:0009191)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	ADP-ribose diphosphatase activity (GO:0047631)|ADP-sugar diphosphatase activity (GO:0019144)|magnesium ion binding (GO:0000287)|nucleoside-diphosphatase activity (GO:0017110)|snoRNA binding (GO:0030515)			breast(1)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)	8		Renal(717;0.228)				TTCAAGCTCCCGGAGAGCAGC	0.493																																					p.R111Q		Atlas-SNP	.											.	NUDT5	10	.	0			c.G332A						.						174	177	176					10																	12215770		2203	4300	6503	SO:0001583	missense	11164	exon6			AGCTCCCGGAGAG	AF155832	CCDS7089.1	10p14	2008-05-14			ENSG00000165609	ENSG00000165609		"Nudix motif containing"	8052	protein-coding gene	gene with protein product		609230				10373642	Standard	NM_014142		Approved	hYSAH1, YSA1H	uc001ilj.3	Q9UKK9	OTTHUMG00000017682	ENST00000491614.1:c.332G>A	chr10.hg19:g.12215770C>T	ENSP00000419628:p.Arg111Gln	149.0	0.0		125.0	5.0	NM_014142	A8K516|Q6IAG0|Q9UH49	Missense_Mutation	SNP	ENST00000491614.1	hg19	CCDS7089.1	.	.	.	.	.	.	.	.	.	.	C	35	5.424703	0.96111	.	.	ENSG00000165609	ENST00000491614;ENST00000378929;ENST00000378937;ENST00000537776;ENST00000378940;ENST00000378927	T;T;T;T;T	0.54479	0.57;0.57;0.57;0.57;0.57	5.76	5.76	0.90799	NUDIX hydrolase (1);NUDIX hydrolase domain (3);NUDIX hydrolase, conserved site (1);NUDIX hydrolase domain-like (1);	0.000000	0.85682	D	0.000000	D	0.86041	0.5838	H	0.99379	4.54	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.91491	0.5212	10	0.87932	D	0	-19.7435	20.3242	0.98691	0.0:1.0:0.0:0.0	.	111;111	A6NCQ0;Q9UKK9	.;NUDT5_HUMAN	Q	111;111;124;111;111;111	ENSP00000419628:R111Q;ENSP00000368219:R124Q;ENSP00000445116:R111Q;ENSP00000368222:R111Q;ENSP00000368209:R111Q	ENSP00000368209:R111Q	R	-	2	0	NUDT5	12255776	1.000000	0.71417	0.999000	0.59377	0.869000	0.49853	6.507000	0.73717	2.882000	0.98803	0.655000	0.94253	CGG	.	.		0.493	NUDT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046811.1			T	12215770	C	T	12215770	3	4	259	1	0	0	0	0	1	0	0	0	10751	652	23	1	347	1	NUDT5	10	12215770	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	6072538	12215770	123318977	429	36747										
MCM10	55388	hgsc.bcm.edu	37	chr10	13212949	13212949	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agacaatctgtctctgctgaCcgcactgctggaagaaaatg	10	10	2	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:13212949C>T	ENST00000484800.2	+	3	138	c.35C>T	c.(34-36)aCc>aTc	p.T12I	MCM10_ENST00000378694.1_Missense_Mutation_p.T12I|MCM10_ENST00000378714.3_Missense_Mutation_p.T12I			Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	12	N-terminal domain. {ECO:0000250}.				cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(4)|ovary(2)|skin(1)|stomach(1)	9						TCTCTGCTGACCGCACTGCTG	0.438																																					p.T12I		Atlas-SNP	.											.	MCM10	76	.	0			c.C35T						.						68	70	69					10																	13212949		2203	4300	6503	SO:0001583	missense	55388	exon3			TGCTGACCGCACT	AB042719	CCDS7095.1, CCDS7096.1	10p13	2008-08-01	2007-04-04		ENSG00000065328	ENSG00000065328			18043	protein-coding gene	gene with protein product		609357	"MCM10 minichromosome maintenance deficient 10 (S. cerevisiae)"			11095689, 17699597	Standard	NM_018518		Approved	PRO2249, CNA43, DNA43	uc001ima.3	Q7L590	OTTHUMG00000017694	ENST00000484800.2:c.35C>T	chr10.hg19:g.13212949C>T	ENSP00000418268:p.Thr12Ile	138.0	0.0		121.0	5.0	NM_182751	A8K9I6|B7ZKZ8|Q3MIR3|Q7LD55|Q96GX4|Q96NB6|Q9H0D7|Q9H3P9|Q9P177	Missense_Mutation	SNP	ENST00000484800.2	hg19	CCDS7096.1	.	.	.	.	.	.	.	.	.	.	C	18.89	3.718569	0.68844	.	.	ENSG00000065328	ENST00000378714;ENST00000361282;ENST00000484800;ENST00000378694	T;T;T	0.19105	2.19;2.18;2.17	5.91	5.91	0.95273	.	0.263978	0.42682	D	0.000671	T	0.33177	0.0854	M	0.64997	1.995	0.45914	D	0.998755	D;D;D	0.58970	0.973;0.984;0.973	P;P;P	0.51266	0.463;0.664;0.463	T	0.00984	-1.1491	10	0.32370	T	0.25	0.7561	15.43	0.75084	0.0:0.9322:0.0:0.0678	.	12;12;12	Q5T670;Q7L590-2;Q7L590	.;.;MCM10_HUMAN	I	12	ENSP00000367986:T12I;ENSP00000418268:T12I;ENSP00000367966:T12I	ENSP00000354945:T12I	T	+	2	0	MCM10	13252955	0.999000	0.42202	0.990000	0.47175	0.936000	0.57629	4.445000	0.60007	2.793000	0.96121	0.655000	0.94253	ACC	.	.		0.438	MCM10-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356853.1	NM_182751		T	13212949	C	T	13212949	3	4	259	1	0	0	0	0	1	0	0	0	9394	507	18	3	41	3	MCM10	10	13212949	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	997179	13212949	122321798	430	36748										
CUBN	8029	hgsc.bcm.edu	37	chr10	17157511	17157511	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	taaatcctcacagatgccatGgacacagcgtgccacagaac	8	13	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:17157511G>T	ENST00000377833.4	-	7	744	c.679C>A	c.(679-681)Cat>Aat	p.H227N		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	227					cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CAGATGCCATGGACACAGCGT	0.542																																					p.H227N		Atlas-SNP	.											.	CUBN	515	.	0			c.C679A						.						139	117	124					10																	17157511		2203	4300	6503	SO:0001583	missense	8029	exon7			TGCCATGGACACA	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.679C>A	chr10.hg19:g.17157511G>T	ENSP00000367064:p.His227Asn	91.0	0.0		92.0	4.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.478655	0.84747	.	.	ENSG00000107611	ENST00000377833	D	0.86366	-2.11	5.75	5.75	0.90469	Growth factor, receptor (1);Epidermal growth factor-like (1);	0.000000	0.48286	D	0.000198	D	0.94460	0.8217	M	0.85462	2.755	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.94680	0.7864	10	0.87932	D	0	.	19.5261	0.95208	0.0:0.0:1.0:0.0	.	227	O60494	CUBN_HUMAN	N	227	ENSP00000367064:H227N	ENSP00000367064:H227N	H	-	1	0	CUBN	17197517	1.000000	0.71417	0.065000	0.19835	0.739000	0.42172	6.220000	0.72237	2.721000	0.93114	0.655000	0.94253	CAT	.	.		0.542	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		T	17157511	G	T	17157511	3	4	259	1	0	0	0	0	1	0	0	0	4053	1348	47	3	10436	3	CUBN	10	17157511	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	3944562	17157511	118377236	431	36749										
MYO3A	53904	hgsc.bcm.edu	37	chr10	26312957	26312957	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tcttatttttctaggaatccAcccccaaaactaaggcagcc	5	13	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:26312957A>G	ENST00000265944.5	+	9	904	c.738A>G	c.(736-738)ccA>ccG	p.P246P	MYO3A_ENST00000543632.1_Silent_p.P246P	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	246	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						CTAGGAATCCACCCCCAAAAC	0.383																																					p.P246P		Atlas-SNP	.											.	MYO3A	371	.	0			c.A738G						.						133	136	135					10																	26312957		2203	4300	6503	SO:0001819	synonymous_variant	53904	exon9			GAATCCACCCCCA	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.738A>G	chr10.hg19:g.26312957A>G		163.0	0.0		124.0	5.0	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Silent	SNP	ENST00000265944.5	hg19	CCDS7148.1																																																																																			.	.		0.383	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		G	26312957	A	G	26312957	2	3	259	1	0	0	0	0	0	0	0	1	10085	146	6	2		2	MYO3A	10	26312957	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	9155446	26312957	109221790	432	36750										
ABI1	10006	hgsc.bcm.edu	37	chr10	27044647	27044647	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tggagtcaactgaggcatagGgggagggggtggagcaatag	20	4	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:27044647G>T	ENST00000376142.2	-	10	1173	c.1102C>A	c.(1102-1104)Cct>Act	p.P368T	ABI1_ENST00000536334.1_Intron|ABI1_ENST00000355394.4_Missense_Mutation_p.P369T|ABI1_ENST00000376138.3_Intron|ABI1_ENST00000376170.4_Intron|ABI1_ENST00000346832.5_Intron|ABI1_ENST00000376166.1_Intron|ABI1_ENST00000376134.3_Missense_Mutation_p.P342T|ABI1_ENST00000359188.4_Missense_Mutation_p.P340T|ABI1_ENST00000376140.3_Missense_Mutation_p.P341T|ABI1_ENST00000376139.2_Missense_Mutation_p.P336T|ABI1_ENST00000376160.1_Missense_Mutation_p.P335T|ABI1_ENST00000490841.2_Intron|ABI1_ENST00000376137.4_Missense_Mutation_p.P283T	NM_005470.3	NP_005461.2	Q8IZP0	ABI1_HUMAN	abl-interactor 1	368	Pro-rich.				actin polymerization or depolymerization (GO:0008154)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|lamellipodium morphogenesis (GO:0072673)|megakaryocyte development (GO:0035855)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|SCAR complex (GO:0031209)	cytoskeletal protein binding (GO:0008092)|protein complex binding (GO:0032403)|protein tyrosine kinase activator activity (GO:0030296)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(9)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TGAGGCATAGGGGGAGGGGGT	0.458																																					p.P368T		Atlas-SNP	.											.	ABI1	38	.	0			c.C1102A						.						93	95	94					10																	27044647		2203	4300	6503	SO:0001583	missense	10006	exon10			GCATAGGGGGAGG	U87166	CCDS7150.1, CCDS31169.1, CCDS31170.1, CCDS31171.1, CCDS53497.1, CCDS53498.1, CCDS53499.1, CCDS53500.1, CCDS53501.1, CCDS73077.1, CCDS73078.1	10p12.1	2009-05-29	2004-03-17	2004-03-19	ENSG00000136754	ENSG00000136754			11320	protein-coding gene	gene with protein product		603050	"spectrin SH3 domain binding protein 1"	SSH3BP1		9593709, 9010225	Standard	NM_005470		Approved	E3B1, ABI-1	uc001isx.3	Q8IZP0	OTTHUMG00000017848	ENST00000376142.2:c.1102C>A	chr10.hg19:g.27044647G>T	ENSP00000365312:p.Pro368Thr	85.0	0.0		84.0	4.0	NM_005470	A9Z1Y6|B3KX62|B4DQ58|H7BXI6|O15147|O76049|O95060|Q5T2R3|Q5T2R4|Q5T2R6|Q5T2R7|Q5T2R9|Q5W070|Q5W072|Q8TB63|Q96S81|Q9NXZ9|Q9NYB8	Missense_Mutation	SNP	ENST00000376142.2	hg19	CCDS7150.1	.	.	.	.	.	.	.	.	.	.	G	19.36	3.812514	0.70912	.	.	ENSG00000136754	ENST00000376160;ENST00000376142;ENST00000359188;ENST00000376139;ENST00000355394;ENST00000376134;ENST00000376137;ENST00000376140	T;T;T;T;T;T;T;T	0.47528	0.98;0.88;0.94;0.88;1.06;0.84;1.02;0.95	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.65365	0.2684	L	0.50333	1.59	0.80722	D	1	D;P;P;P;B	0.71674	0.998;0.746;0.746;0.746;0.376	D;P;P;P;B	0.73708	0.981;0.557;0.557;0.557;0.164	T	0.65389	-0.6180	10	0.62326	D	0.03	-9.3667	19.6869	0.95982	0.0:0.0:1.0:0.0	.	282;340;336;341;368	B6VEX3;Q8IZP0-6;Q8IZP0-5;Q8IZP0-9;Q8IZP0	.;.;.;.;ABI1_HUMAN	T	335;368;340;336;369;342;283;341	ENSP00000365330:P335T;ENSP00000365312:P368T;ENSP00000352114:P340T;ENSP00000365309:P336T;ENSP00000347555:P369T;ENSP00000365304:P342T;ENSP00000365307:P283T;ENSP00000365310:P341T	ENSP00000347555:P369T	P	-	1	0	ABI1	27084653	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.751000	0.98889	2.726000	0.93360	0.655000	0.94253	CCT	.	.		0.458	ABI1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047287.1	NM_005470		T	27044647	G	T	27044647	3	4	259	1	0	0	0	0	1	0	0	0	88	1232	43	3	436	3	ABI1	10	27044647	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	731690	27044647	108490100	433	36751										
YME1L1	10730	hgsc.bcm.edu	37	chr10	27409405	27409405	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgagataccatttcaaaattTctgttcgaccttttacatct	4	9	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:27409405T>C	ENST00000326799.3	-	14	1689	c.1541A>G	c.(1540-1542)gAa>gGa	p.E514G	YME1L1_ENST00000376016.3_Missense_Mutation_p.E457G|YME1L1_ENST00000375972.3_Missense_Mutation_p.E424G	NM_139312.2	NP_647473.1	Q96TA2	YMEL1_HUMAN	YME1-like 1 ATPase	514					cell proliferation (GO:0008283)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|mitochondrion organization (GO:0007005)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	23						TTTCAAAATTTCTGTTCGACC	0.343																																					p.E514G		Atlas-SNP	.											.	YME1L1	71	.	0			c.A1541G						.						95	91	92					10																	27409405		2203	4300	6503	SO:0001583	missense	10730	exon14			AAAATTTCTGTTC	AJ132637	CCDS7151.1, CCDS7152.1, CCDS58072.1	10p14	2013-06-10	2013-06-10		ENSG00000136758	ENSG00000136758		"ATPases / AAA-type"	12843	protein-coding gene	gene with protein product		607472	"YME1 (S.cerevisiae)-like 1", "YME1-like 1 (S. cerevisiae)"			22262461	Standard	NM_139312		Approved		uc001itj.3	Q96TA2	OTTHUMG00000017853	ENST00000326799.3:c.1541A>G	chr10.hg19:g.27409405T>C	ENSP00000318480:p.Glu514Gly	117.0	0.0		88.0	4.0	NM_139312	B4DNM1|D3DRV8|D3DRV9|Q5T8D9|Q9H1Q0|Q9UMR9	Missense_Mutation	SNP	ENST00000326799.3	hg19	CCDS7152.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.325619	0.81580	.	.	ENSG00000136758	ENST00000376016;ENST00000326799;ENST00000375969;ENST00000375972;ENST00000546122	T;T;T	0.79845	-1.31;-1.31;-1.31	5.72	5.72	0.89469	Peptidase M41, FtsH (2);	0.000000	0.85682	D	0.000000	D	0.89663	0.6780	M	0.78916	2.43	0.80722	D	1	D;D;D	0.76494	0.999;0.968;0.999	D;P;D	0.75484	0.986;0.852;0.96	D	0.90862	0.4739	10	0.87932	D	0	-30.5238	16.2988	0.82793	0.0:0.0:0.0:1.0	.	424;457;514	B4DNM1;Q96TA2-2;Q96TA2	.;.;YMEL1_HUMAN	G	457;514;514;424;260	ENSP00000365184:E457G;ENSP00000318480:E514G;ENSP00000365139:E424G	ENSP00000318480:E514G	E	-	2	0	YME1L1	27449411	1.000000	0.71417	1.000000	0.80357	0.551000	0.35334	7.954000	0.87848	2.311000	0.77944	0.533000	0.62120	GAA	.	.		0.343	YME1L1-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047306.1	NM_139312		C	27409405	T	C	27409405	3	2	259	1	0	0	0	0	1	0	0	0	17502	1783	62	2	808	2	YME1L1	10	27409405	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	364758	27409405	108125342	434	36752										
SVIL	6840	hgsc.bcm.edu	37	chr10	29820188	29820188	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gaaacaggtacttgccatcgAcagttggcgtttctgaatgt	11	8	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:29820188A>G	ENST00000355867.4	-	10	2791	c.2039T>C	c.(2038-2040)gTc>gCc	p.V680A	SVIL_ENST00000375398.2_Missense_Mutation_p.V680A|SVIL_ENST00000375400.3_Missense_Mutation_p.V286A	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	680					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				CTTGCCATCGACAGTTGGCGT	0.353																																					p.V680A		Atlas-SNP	.											.	SVIL	226	.	0			c.T2039C						.						134	113	120					10																	29820188		2203	4300	6503	SO:0001583	missense	6840	exon10			CCATCGACAGTTG	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"archvillin"	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.2039T>C	chr10.hg19:g.29820188A>G	ENSP00000348128:p.Val680Ala	78.0	0.0		79.0	4.0	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	hg19	CCDS7164.1	.	.	.	.	.	.	.	.	.	.	A	0.349	-0.945961	0.02304	.	.	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867	T;T;T	0.52057	0.68;0.68;0.68	5.81	2.71	0.32032	.	1.813340	0.02448	N	0.085221	T	0.21509	0.0518	N	0.01297	-0.9	0.29181	N	0.876508	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.29731	-1.0002	9	.	.	.	-0.9066	6.7409	0.23435	0.3201:0.0:0.6799:0.0	.	286;680	O95425-2;O95425	.;SVIL_HUMAN	A	286;680;680	ENSP00000364549:V286A;ENSP00000364547:V680A;ENSP00000348128:V680A	.	V	-	2	0	SVIL	29860194	0.004000	0.15560	0.009000	0.14445	0.002000	0.02628	0.960000	0.29253	0.622000	0.30249	0.533000	0.62120	GTC	.	.		0.353	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1			G	29820188	A	G	29820188	3	3	259	1	0	0	0	0	1	0	0	0	15436	275	10	2	4721	2	SVIL	10	29820188	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2410783	29820188	105714559	435	36753										
ZNF33A	7581	hgsc.bcm.edu	37	chr10	38344489	38344489	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gagtgtgggaaatcctttagTgaaaagtcaaatcttacaca	9	6	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:38344489T>C	ENST00000458705.2	+	5	1592	c.1434T>C	c.(1432-1434)agT>agC	p.S478S	ZNF33A_ENST00000307441.9_Silent_p.S478S|ZNF33A_ENST00000469037.2_Intron|ZNF33A_ENST00000432900.2_Silent_p.S485S|ZNF33A_ENST00000374618.3_Silent_p.S479S			Q06730	ZN33A_HUMAN	zinc finger protein 33A	478					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(2)|large_intestine(8)|liver(2)|lung(27)|ovary(2)|prostate(1)|skin(2)	46						AATCCTTTAGTGAAAAGTCAA	0.388																																					p.S479S		Atlas-SNP	.											.	ZNF33A	103	.	0			c.T1437C						.						60	59	59					10																	38344489		2202	4300	6502	SO:0001819	synonymous_variant	7581	exon5			CTTTAGTGAAAAG	D31763	CCDS31182.1, CCDS60514.1, CCDS73088.1, CCDS73089.1	10p11.2	2013-01-08	2005-03-18		ENSG00000189180	ENSG00000189180		"Zinc fingers, C2H2-type", "-"	13096	protein-coding gene	gene with protein product	"zinc finger and ZAK associated protein with KRAB domain"	194521	"zinc finger protein 33a (KOX 31)", "zinc finger protein 11A"	ZNF33, ZNF11A		2014798, 8464732	Standard	NM_006974		Approved	KOX5, KOX31, KIAA0065, FLJ23404, ZZAPK	uc031pui.1	Q06730	OTTHUMG00000017983	ENST00000458705.2:c.1434T>C	chr10.hg19:g.38344489T>C		91.0	0.0		97.0	4.0	NM_006954	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Silent	SNP	ENST00000458705.2	hg19	CCDS31182.1																																																																																			.	.		0.388	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974		C	38344489	T	C	38344489	2	2	259	1	0	0	0	0	0	0	0	1	17869	1693	59	2		2	ZNF33A	10	38344489	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	8524301	38344489	97190258	436	36754										
ARHGAP22	58504	hgsc.bcm.edu	37	chr10	49667827	49667827	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cagcccctcctcagtgagccCgcgctcccggatgaagtcca	10	18	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:49667827C>T	ENST00000249601.4	-	5	855	c.559G>A	c.(559-561)Ggg>Agg	p.G187R	ARHGAP22_ENST00000417912.2_Missense_Mutation_p.G203R|ARHGAP22_ENST00000374172.1_Missense_Mutation_p.G78R|ARHGAP22_ENST00000435790.2_Missense_Mutation_p.G193R|ARHGAP22_ENST00000417247.2_Missense_Mutation_p.G97R|ARHGAP22_ENST00000374170.1_Missense_Mutation_p.G97R	NM_001256024.1|NM_021226.3	NP_001242953.1|NP_067049.2	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 22	187	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TCAGTGAGCCCGCGCTCCCGG	0.647																																					p.G203R		Atlas-SNP	.											.	ARHGAP22	94	.	0			c.G607A						.						101	94	96					10																	49667827		2203	4300	6503	SO:0001583	missense	58504	exon5			TGAGCCCGCGCTC	AY324801	CCDS7227.1, CCDS58079.1, CCDS58080.1, CCDS58081.1	10q11.23	2013-01-10			ENSG00000128805	ENSG00000128805		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	30320	protein-coding gene	gene with protein product		610585				8619474	Standard	NM_021226		Approved	RhoGAP2	uc010qgm.3	Q7Z5H3	OTTHUMG00000018176	ENST00000249601.4:c.559G>A	chr10.hg19:g.49667827C>T	ENSP00000249601:p.Gly187Arg	120.0	0.0		97.0	4.0	NM_001256024	A0AVP7|A5YM75|B4DED8|B9EGA0|C9JDM2|O00152|Q6ZSB0	Missense_Mutation	SNP	ENST00000249601.4	hg19	CCDS7227.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.745759	0.89663	.	.	ENSG00000128805	ENST00000249601;ENST00000374172;ENST00000374170;ENST00000417247;ENST00000435790;ENST00000417912	T;T;T;T;T;T	0.57752	2.25;0.38;2.25;2.25;2.25;0.38	4.9	4.9	0.64082	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.80523	0.4639	H	0.94264	3.515	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.998;1.0;1.0;1.0;0.991	D	0.86287	0.1671	10	0.87932	D	0	.	17.2419	0.87015	0.0:1.0:0.0:0.0	.	193;187;203;187;97	B4DED8;A6NDI7;Q7Z5H3-2;Q7Z5H3;Q7Z5H3-3	.;.;.;RHG22_HUMAN;.	R	187;78;97;97;193;203	ENSP00000249601:G187R;ENSP00000363287:G78R;ENSP00000363285:G97R;ENSP00000410054:G97R;ENSP00000416701:G193R;ENSP00000412461:G203R	ENSP00000249601:G187R	G	-	1	0	ARHGAP22	49337833	1.000000	0.71417	0.942000	0.38095	0.639000	0.38242	7.564000	0.82326	2.565000	0.86533	0.313000	0.20887	GGG	.	.		0.647	ARHGAP22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358767.1	NM_021226		T	49667827	C	T	49667827	3	4	259	1	0	0	0	0	1	0	0	0	872	652	23	1	1561	1	ARHGAP22	10	49667827	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	11323338	49667827	85866920	437	36755										
JMJD1C	221037	hgsc.bcm.edu	37	chr10	64946064	64946064	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tcaggagatcagcttggtggTctccaaaatcaagactaatt	9	8	4	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:64946064T>C	ENST00000399262.2	-	19	6868	c.6650A>G	c.(6649-6651)gAc>gGc	p.D2217G	JMJD1C_ENST00000399251.1_3'UTR|JMJD1C_ENST00000542921.1_Missense_Mutation_p.D2035G|JMJD1C_ENST00000402544.1_Missense_Mutation_p.D1980G	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	2217					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					AGCTTGGTGGTCTCCAAAATC	0.368																																					p.D2217G		Atlas-SNP	.											.	JMJD1C	347	.	0			c.A6650G						.						109	103	105					10																	64946064		1861	4098	5959	SO:0001583	missense	221037	exon19			TGGTGGTCTCCAA	L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"thyroid hormone receptor interactor 8"	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.6650A>G	chr10.hg19:g.64946064T>C	ENSP00000382204:p.Asp2217Gly	132.0	0.0		94.0	4.0	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Missense_Mutation	SNP	ENST00000399262.2	hg19	CCDS41532.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.67|19.67	3.871796|3.871796	0.72180|0.72180	.|.	.|.	ENSG00000171988|ENSG00000171988	ENST00000399262;ENST00000402544;ENST00000542921|ENST00000327520	T;T;T|.	0.74002|.	-0.8;-0.8;-0.8|.	5.66|5.66	5.66|5.66	0.87406|0.87406	.|.	0.047245|.	0.85682|.	D|.	0.000000|.	T|T	0.69495|0.69495	0.3117|0.3117	L|L	0.53617|0.53617	1.68|1.68	0.80722|0.80722	D|D	1|1	P;P;B|.	0.48294|.	0.908;0.908;0.004|.	B;B;B|.	0.43950|.	0.437;0.437;0.027|.	T|T	0.67337|0.67337	-0.5696|-0.5696	10|5	0.72032|.	D|.	0.01|.	-13.429|-13.429	15.8601|15.8601	0.79014|0.79014	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	2035;2217;2035|.	B7ZLC8;Q15652;A0T124|.	.;JHD2C_HUMAN;.|.	G|A	2217;1980;2035|764	ENSP00000382204:D2217G;ENSP00000384990:D1980G;ENSP00000444682:D2035G|.	ENSP00000382204:D2217G|.	D|T	-|-	2|1	0|0	JMJD1C|JMJD1C	64616070|64616070	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	4.773000|4.773000	0.62331|0.62331	2.284000|2.284000	0.76573|0.76573	0.528000|0.528000	0.53228|0.53228	GAC|ACC	.	.		0.368	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241		C	64946064	T	C	64946064	3	2	259	1	0	0	0	0	1	0	0	0	7959	1667	58	2	1004	2	JMJD1C	10	64946064	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	15278237	64946064	70588683	438	36756										
LRRTM3	347731	hgsc.bcm.edu	37	chr10	68857536	68857536	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gctggccgaatcagtgaccaTaaacagcagctagcttaact	9	11	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:68857536T>A	ENST00000361320.4	+	3	2306	c.1728T>A	c.(1726-1728)caT>caA	p.H576Q	CTNNA3_ENST00000433211.2_Intron|CTNNA3_ENST00000373744.4_Intron|LRRTM3_ENST00000485868.1_3'UTR	NM_178011.3	NP_821079.3	Q86VH5	LRRT3_HUMAN	leucine rich repeat transmembrane neuronal 3	576					positive regulation of beta-amyloid formation (GO:1902004)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	41						TCAGTGACCATAAACAGCAGC	0.458																																					p.H576Q		Atlas-SNP	.											.	LRRTM3	241	.	0			c.T1728A						.						125	108	114					10																	68857536		2203	4300	6503	SO:0001583	missense	347731	exon3			TGACCATAAACAG	BX640611	CCDS7270.1	10q22.1	2007-01-22				ENSG00000198739			19410	protein-coding gene	gene with protein product		610869				12676565	Standard	XR_247527		Approved		uc001jmz.1	Q86VH5		ENST00000361320.4:c.1728T>A	chr10.hg19:g.68857536T>A	ENSP00000355187:p.His576Gln	93.0	0.0		91.0	4.0	NM_178011	A8K2A3|Q2NKX7|Q6N0A3	Missense_Mutation	SNP	ENST00000361320.4	hg19	CCDS7270.1	.	.	.	.	.	.	.	.	.	.	T	12.88	2.069775	0.36566	.	.	ENSG00000198739	ENST00000361320;ENST00000373722	T	0.41758	0.99	5.62	3.26	0.37387	.	0.000000	0.49305	D	0.000149	T	0.21145	0.0509	N	0.08118	0	0.29259	N	0.871486	B	0.17852	0.024	B	0.06405	0.002	T	0.12630	-1.0540	10	0.87932	D	0	.	7.2321	0.26049	0.0:0.235:0.0:0.7649	.	576	Q86VH5	LRRT3_HUMAN	Q	576	ENSP00000355187:H576Q	ENSP00000355187:H576Q	H	+	3	2	LRRTM3	68527542	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	0.183000	0.16919	1.074000	0.40909	0.528000	0.53228	CAT	.	.		0.458	LRRTM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048277.2	NM_178011		A	68857536	T	A	68857536	3	1	259	1	0	0	0	0	1	0	0	0	9050	1403	49	4	1738	4	LRRTM3	10	68857536	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	3911472	68857536	66677211	439	36757										
MYPN	84665	hgsc.bcm.edu	37	chr10	69925542	69925542	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctgcaagcaacaaatacggcAcagtgtcaagcattgcacag	9	11	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:69925542A>G	ENST00000358913.5	+	9	2055	c.1567A>G	c.(1567-1569)Aca>Gca	p.T523A	MYPN_ENST00000540630.1_Missense_Mutation_p.T523A|MYPN_ENST00000354393.2_Missense_Mutation_p.T248A	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	523	Ig-like 2.				sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						CAAATACGGCACAGTGTCAAG	0.438																																					p.T523A		Atlas-SNP	.											.	MYPN	189	.	0			c.A1567G						.						169	136	147					10																	69925542		2203	4300	6503	SO:0001583	missense	84665	exon9			TACGGCACAGTGT	AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347		"Immunoglobulin superfamily / I-set domain containing"	23246	protein-coding gene	gene with protein product	"sarcomeric protein myopalladin, 145 kDa"	608517				11309420, 12482578	Standard	NM_032578		Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.1567A>G	chr10.hg19:g.69925542A>G	ENSP00000351790:p.Thr523Ala	85.0	0.0		76.0	4.0	NM_032578	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Missense_Mutation	SNP	ENST00000358913.5	hg19	CCDS7275.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.172926	0.78452	.	.	ENSG00000138347	ENST00000354393;ENST00000542332;ENST00000358913;ENST00000540630	T;T;T	0.66638	-0.22;-0.22;-0.22	5.23	4.06	0.47325	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.72542	0.3473	L	0.39566	1.225	0.58432	D	0.999991	D;D;D	0.76494	0.996;0.999;0.999	D;D;D	0.83275	0.987;0.978;0.996	T	0.69250	-0.5194	9	.	.	.	.	11.1945	0.48704	0.8623:0.0:0.0:0.1377	.	523;248;523	F5GWA6;Q86TC9-2;Q86TC9	.;.;MYPN_HUMAN	A	248;248;523;523	ENSP00000346369:T248A;ENSP00000351790:T523A;ENSP00000441668:T523A	.	T	+	1	0	MYPN	69595548	1.000000	0.71417	0.908000	0.35775	0.884000	0.51177	8.923000	0.92808	0.779000	0.33543	0.459000	0.35465	ACA	.	.		0.438	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578		G	69925542	A	G	69925542	3	3	259	1	0	0	0	0	1	0	0	0	10107	159	6	2	1597	2	MYPN	10	69925542	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1068006	69925542	65609205	440	36758										
DDX21	9188	hgsc.bcm.edu	37	chr10	70723119	70723119	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttacagcgggaaggacttaaTtgcacaggcacggacaggaa	13	8	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:70723119T>C	ENST00000354185.4	+	4	778	c.680T>C	c.(679-681)aTt>aCt	p.I227T	RN7SL373P_ENST00000577512.1_RNA	NM_001256910.1|NM_004728.3	NP_001243839.1|NP_004719.2	Q9NR30	DDX21_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 21	227	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|osteoblast differentiation (GO:0001649)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	20						AAGGACTTAATTGCACAGGCA	0.463																																					p.I227T		Atlas-SNP	.											.	DDX21	57	.	0			c.T680C						.						143	125	131					10																	70723119		2203	4300	6503	SO:0001583	missense	9188	exon4			ACTTAATTGCACA	U41387	CCDS31211.1, CCDS73144.1	10q21	2013-05-13	2012-02-23		ENSG00000165732	ENSG00000165732		"DEAD-boxes"	2744	protein-coding gene	gene with protein product		606357	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 21", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 21"			8614622, 18180292	Standard	NM_004728		Approved	RH-II/GU, GURDB	uc001jov.2	Q9NR30	OTTHUMG00000018366	ENST00000354185.4:c.680T>C	chr10.hg19:g.70723119T>C	ENSP00000346120:p.Ile227Thr	95.0	0.0		100.0	4.0	NM_004728	B2RDL0|Q13436|Q5VX41|Q68D35	Missense_Mutation	SNP	ENST00000354185.4	hg19	CCDS31211.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.979987	0.74360	.	.	ENSG00000165732	ENST00000354185	T	0.58060	0.36	5.4	4.27	0.50696	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.204155	0.52532	N	0.000080	T	0.72439	0.3460	M	0.84683	2.71	0.51012	D	0.999905	D	0.71674	0.998	D	0.71870	0.975	T	0.75752	-0.3207	10	0.72032	D	0.01	-4.9461	11.1026	0.48184	0.0:0.0721:0.0:0.9279	.	227	Q9NR30	DDX21_HUMAN	T	227	ENSP00000346120:I227T	ENSP00000346120:I227T	I	+	2	0	DDX21	70393125	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	7.655000	0.83696	1.004000	0.39156	0.533000	0.62120	ATT	.	.		0.463	DDX21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048374.1	NM_004728		C	70723119	T	C	70723119	3	2	259	1	0	0	0	0	1	0	0	0	4351	1493	52	2	694	2	DDX21	10	70723119	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	797577	70723119	64811628	441	36759										
CDH23	64072	hgsc.bcm.edu	37	chr10	73375297	73375297	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctttgccctggactacatcaGcggagtgctgaccttgaatg	11	11	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:73375297G>T	ENST00000224721.6	+	9	889	c.884G>T	c.(883-885)aGc>aTc	p.S295I	CDH23_ENST00000398809.4_Missense_Mutation_p.S290I|CDH23_ENST00000461841.3_Missense_Mutation_p.S335I|CDH23_ENST00000299366.7_Missense_Mutation_p.S335I|CDH23_ENST00000398842.3_Missense_Mutation_p.S290I	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	290	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						GACTACATCAGCGGAGTGCTG	0.592																																					p.S290I		Atlas-SNP	.											.	CDH23	365	.	0			c.G869T						.						86	89	88					10																	73375297		2034	4178	6212	SO:0001583	missense	64072	exon10			ACATCAGCGGAGT	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"Cadherins / Cadherin-related"	13733	protein-coding gene	gene with protein product	"cadherin-related family member 23"	605516	"cadherin related 23", "cadherin-like 23"	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.884G>T	chr10.hg19:g.73375297G>T	ENSP00000224721:p.Ser295Ile	130.0	0.0		79.0	4.0	NM_052836	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	hg19		.	.	.	.	.	.	.	.	.	.	G	19.76	3.888389	0.72524	.	.	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000398828;ENST00000398809;ENST00000398842;ENST00000299366;ENST00000224721;ENST00000416060	T;T	0.63744	-0.06;-0.06	4.22	4.22	0.49857	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.82033	0.4949	M	0.88979	2.995	0.80722	D	1	D;D;D	0.69078	0.973;0.997;0.997	P;D;D	0.80764	0.677;0.988;0.994	D	0.86633	0.1887	10	0.87932	D	0	.	16.7626	0.85516	0.0:0.0:1.0:0.0	.	290;290;290	A5D6V9;Q9H251;Q9H251-5	.;CAD23_HUMAN;.	I	297;290;290;290;290;295;295;207	ENSP00000381789:S290I;ENSP00000381822:S290I	ENSP00000224721:S297I	S	+	2	0	CDH23	73045303	1.000000	0.71417	0.985000	0.45067	0.604000	0.37047	7.210000	0.77924	2.182000	0.69389	0.557000	0.71058	AGC	.	.		0.592	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836		T	73375297	G	T	73375297	3	4	259	1	0	0	0	0	1	0	0	0	3110	971	34	3	903	3	CDH23	10	73375297	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	2652178	73375297	62159450	442	36760										
C10orf54	64115	hgsc.bcm.edu	37	chr10	73511594	73511594	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggtggtgaggcttcaaagccGgggttttcaatcccttgaat	13	8	2	2	rs201880754		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:73511594G>T	ENST00000394957.3	-	6	787	c.729C>A	c.(727-729)ccC>ccA	p.P243P	CDH23_ENST00000224721.6_Intron	NM_022153.1	NP_071436.1	Q9H7M9	GI24_HUMAN	chromosome 10 open reading frame 54	243					BMP signaling pathway (GO:0030509)|negative regulation of CD4-positive, alpha-beta T cell proliferation (GO:2000562)|negative regulation of T cell cytokine production (GO:0002725)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of stem cell differentiation (GO:2000738)|stem cell differentiation (GO:0048863)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|endometrium(1)|lung(1)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	9						CTTCAAAGCCGGGGTTTTCAA	0.602																																					p.P243P		Atlas-SNP	.											.	C10orf54	29	.	0			c.C729A						.						48	49	49					10																	73511594		2203	4300	6503	SO:0001819	synonymous_variant	64115	exon6			AAAGCCGGGGTTT	AF193048	CCDS31218.1	10q22.1	2013-11-28			ENSG00000107738	ENSG00000107738		"Immunoglobulin superfamily / V-set domain containing"	30085	protein-coding gene	gene with protein product	"stress induced secreted protein 1"	615608				12975309	Standard	NM_022153		Approved	SISP1, GI24, B7-H5, B7H5	uc001jsd.3	Q9H7M9	OTTHUMG00000018426	ENST00000394957.3:c.729C>A	chr10.hg19:g.73511594G>T		125.0	0.0		110.0	5.0	NM_022153	A1L0X9|A4ZYV1|A8MVH5|Q6UXF3|Q8WUG3|Q8WYZ8	Silent	SNP	ENST00000394957.3	hg19	CCDS31218.1																																																																																			.	G|1.000;A|0.000		0.602	C10orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048548.1	NM_022153		T	73511594	G	T	73511594	2	4	259	1	0	0	0	0	0	0	0	1	1609	1103	39	1		1	C10orf54	10	73511594	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	136297	73511594	62023153	443	36761										
CCDC109A	90550	hgsc.bcm.edu	37	chr10	74631338	74631338	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tattttgtaatgacacgccaGgtaagaattctcttcaagta	7	7	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:74631338G>T	ENST00000373053.3	+	6	882	c.861G>T	c.(859-861)caG>caT	p.Q287H	MCU_ENST00000357157.6_Splice_Site_p.Q266H|MCU_ENST00000605416.1_3'UTR|MCU_ENST00000536019.1_Splice_Site_p.Q238H	NM_138357.2	NP_612366.1	Q8NE86	MCU_HUMAN	mitochondrial calcium uniporter	287					calcium ion transmembrane import into mitochondrion (GO:0036444)|calcium-mediated signaling (GO:0019722)|glucose homeostasis (GO:0042593)|mitochondrial calcium ion transport (GO:0006851)|positive regulation of insulin secretion (GO:0032024)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|protein complex oligomerization (GO:0035786)	calcium channel complex (GO:0034704)|integral component of mitochondrial inner membrane (GO:0031305)|mitochondrial inner membrane (GO:0005743)|uniplex complex (GO:1990246)	calcium channel activity (GO:0005262)|uniporter activity (GO:0015292)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|urinary_tract(1)	14						TGACACGCCAGGTAAGAATTC	0.358																																					p.Q287H		Atlas-SNP	.											.	MCU	29	.	0			c.G861T						.						75	73	74					10																	74631338		2203	4300	6503	SO:0001630	splice_region_variant	90550	exon6			ACGCCAGGTAAGA	BC034235	CCDS7317.1, CCDS59218.1, CCDS59219.1	10q22.2	2011-06-23	2011-06-23	2011-06-23	ENSG00000156026	ENSG00000156026			23526	protein-coding gene	gene with protein product		614197	"coiled-coil domain containing 109A"	C10orf42, CCDC109A		21685886, 21685888	Standard	NM_138357		Approved	FLJ46135	uc001jtc.3	Q8NE86	OTTHUMG00000018443	ENST00000373053.3:c.861+1G>T	chr10.hg19:g.74631338G>T		52.0	0.0		82.0	4.0	NM_138357	B2RDF3|B3KXV7|Q96FL3	Missense_Mutation	SNP	ENST00000373053.3	hg19	CCDS7317.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.577859	0.86645	.	.	ENSG00000156026	ENST00000373053;ENST00000357157;ENST00000536019	T;T;T	0.32272	1.46;1.46;1.46	5.92	5.0	0.66597	Coiled-coil domain containing protein 109, C-terminal (1);	0.050514	0.85682	N	0.000000	T	0.59959	0.2232	M	0.82517	2.595	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.74674	0.973;0.951;0.984	T	0.67929	-0.5543	10	0.87932	D	0	-11.0743	16.9087	0.86135	0.0:0.1281:0.8719:0.0	.	266;238;287	Q8NE86-2;Q8NE86-3;Q8NE86	.;.;MCU_HUMAN	H	287;266;238	ENSP00000362144:Q287H;ENSP00000349680:Q266H;ENSP00000440913:Q238H	ENSP00000349680:Q266H	Q	+	3	2	MCU	74301344	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.869000	0.99810	1.439000	0.47511	0.650000	0.86243	CAG	.	.		0.358	MCU-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048594.1	NM_138357	Missense_Mutation	T	74631338	G	T	74631338	5	4	259	1	0	0	0	0	0	0	1	0	2746	1014	35	3	883	3	CCDC109A	10	74631338	Splice_Site	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1119744	74631338	60903409	444	36762										
SEC24C	9632	hgsc.bcm.edu	37	chr10	75525917	75525917	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	caatgccatcaggactggtcTtgttaggctcctctgtgagg	12	10	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:75525917T>C	ENST00000339365.2	+	12	1718	c.1556T>C	c.(1555-1557)cTt>cCt	p.L519P	SEC24C_ENST00000411652.2_Missense_Mutation_p.L400P|SEC24C_ENST00000546025.1_Intron|SEC24C_ENST00000535742.1_Intron|SEC24C_ENST00000540668.1_Intron|SEC24C_ENST00000345254.4_Missense_Mutation_p.L519P	NM_004922.3	NP_004913.2	P53992	SC24C_HUMAN	SEC24 family member C	519					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)	p.L519H(1)		breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(3)|lung(12)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	Prostate(51;0.0112)					AGGACTGGTCTTGTTAGGCTC	0.468																																					p.L519P		Atlas-SNP	.											SEC24C,NS,carcinoma,0,1	SEC24C	86	.	1	Substitution - Missense(1)	endometrium(1)	c.T1556C						.						123	123	123					10																	75525917		2203	4300	6503	SO:0001583	missense	9632	exon11			CTGGTCTTGTTAG	D38555	CCDS7332.1	10q22	2013-10-21	2013-10-21		ENSG00000176986	ENSG00000176986			10705	protein-coding gene	gene with protein product		607185	"SEC24 (S. cerevisiae) related gene family, member C", "SEC24 family, member C (S. cerevisiae)"			10214955, 7584044	Standard	NM_004922		Approved	KIAA0079	uc001jux.3	P53992	OTTHUMG00000018476	ENST00000339365.2:c.1556T>C	chr10.hg19:g.75525917T>C	ENSP00000343405:p.Leu519Pro	57.0	0.0		50.0	3.0	NM_198597	B4DZT4|Q8WV25	Missense_Mutation	SNP	ENST00000339365.2	hg19	CCDS7332.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.968865	0.74131	.	.	ENSG00000176986	ENST00000345254;ENST00000339365;ENST00000411652	T;T;T	0.49432	0.78;0.78;0.78	5.71	5.71	0.89125	Sec23/Sec24, trunk domain (1);	0.109254	0.64402	D	0.000015	T	0.74107	0.3673	M	0.88377	2.95	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	T	0.79914	-0.1602	10	0.87932	D	0	-17.1134	15.9812	0.80111	0.0:0.0:0.0:1.0	.	400;519;519	E7EP00;G5EA31;P53992	.;.;SC24C_HUMAN	P	519;519;400	ENSP00000321845:L519P;ENSP00000343405:L519P;ENSP00000402913:L400P	ENSP00000343405:L519P	L	+	2	0	SEC24C	75195923	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.040000	0.89188	2.178000	0.69098	0.533000	0.62120	CTT	.	.		0.468	SEC24C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048679.1			C	75525917	T	C	75525917	3	2	259	1	0	0	0	0	1	0	0	0	14011	1609	56	2	1594	2	SEC24C	10	75525917	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	894579	75525917	60008830	445	36763										
VCL	7414	hgsc.bcm.edu	37	chr10	75854142	75854142	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	caacagcagaccggccaaagCagctgtacaccttgagggca	11	13	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:75854142C>T	ENST00000211998.4	+	11	1560	c.1466C>T	c.(1465-1467)gCa>gTa	p.A489V	VCL_ENST00000478896.2_Intron|VCL_ENST00000417648.2_Intron|VCL_ENST00000372755.3_Missense_Mutation_p.A489V	NM_014000.2	NP_054706.1	P18206	VINC_HUMAN	vinculin	489	3 X 112 AA tandem repeats.|N-terminal globular head.				adherens junction assembly (GO:0034333)|apical junction assembly (GO:0043297)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|epithelial cell-cell adhesion (GO:0090136)|lamellipodium assembly (GO:0030032)|morphogenesis of an epithelium (GO:0002009)|muscle contraction (GO:0006936)|negative regulation of cell migration (GO:0030336)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|protein localization to cell surface (GO:0034394)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cell-substrate junction (GO:0030055)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	actin binding (GO:0003779)|alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)		VCL/ALK(4)	breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	20	Prostate(51;0.0112)					CCGGCCAAAGCAGCTGTACAC	0.577																																					p.A489V		Atlas-SNP	.											.	VCL	77	.	0			c.C1466T						.						65	54	58					10																	75854142		2203	4300	6503	SO:0001583	missense	7414	exon11			CCAAAGCAGCTGT	M33308	CCDS7340.1, CCDS7341.1	10q22.1-q23	2014-09-17			ENSG00000035403	ENSG00000035403			12665	protein-coding gene	gene with protein product	"metavinculin"	193065				1339348	Standard	NM_014000		Approved		uc001jwd.3	P18206	OTTHUMG00000018498	ENST00000211998.4:c.1466C>T	chr10.hg19:g.75854142C>T	ENSP00000211998:p.Ala489Val	258.0	0.0		239.0	11.0	NM_003373	Q16450|Q5SWX2|Q7Z3B8|Q8IXU7	Missense_Mutation	SNP	ENST00000211998.4	hg19	CCDS7341.1	.	.	.	.	.	.	.	.	.	.	C	32	5.111533	0.94339	.	.	ENSG00000035403	ENST00000372755;ENST00000211998;ENST00000415462;ENST00000537043;ENST00000436396	T;T;T	0.39229	1.09;1.09;1.09	5.47	5.47	0.80525	.	0.056220	0.64402	D	0.000001	T	0.35799	0.0944	L	0.47716	1.5	0.80722	D	1	P;B;B	0.42993	0.797;0.097;0.134	B;B;B	0.34038	0.101;0.042;0.174	T	0.15321	-1.0441	10	0.24483	T	0.36	.	19.378	0.94519	0.0:1.0:0.0:0.0	.	416;489;489	F5H7T3;P18206-2;P18206	.;.;VINC_HUMAN	V	489;489;396;416;161	ENSP00000361841:A489V;ENSP00000211998:A489V;ENSP00000415489:A161V	ENSP00000211998:A489V	A	+	2	0	VCL	75524148	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.441000	0.80485	2.583000	0.87209	0.585000	0.79938	GCA	.	.		0.577	VCL-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_003373, NM_014000		T	75854142	C	T	75854142	3	4	259	1	0	0	0	0	1	0	0	0	17154	710	25	3	1508	3	VCL	10	75854142	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	328225	75854142	59680605	446	36764										
MYST4	23522	hgsc.bcm.edu	37	chr10	76788578	76788578	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agggaagaaacatgtgccccTgtaagtccaaacacatcacc	8	12	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:76788578T>C	ENST00000287239.4	+	18	4485	c.3996T>C	c.(3994-3996)ccT>ccC	p.P1332P	KAT6B_ENST00000372724.1_Silent_p.P1040P|KAT6B_ENST00000372714.1_Silent_p.P1040P|KAT6B_ENST00000372711.1_Silent_p.P1149P|KAT6B_ENST00000372725.1_Silent_p.P1040P	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	1332					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										CATGTGCCCCTGTAAGTCCAA	0.502																																					p.P1332P		Atlas-SNP	.											.	.	.	.	0			c.T3996C						.						73	71	72					10																	76788578		2203	4300	6503	SO:0001819	synonymous_variant	23522	exon18			TGCCCCTGTAAGT	AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	17582	protein-coding gene	gene with protein product	"MOZ-related factor"	605880	"MYST histone acetyltransferase (monocytic leukemia) 4"	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.3996T>C	chr10.hg19:g.76788578T>C		114.0	0.0		103.0	5.0	NM_012330	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Silent	SNP	ENST00000287239.4	hg19	CCDS7345.1																																																																																			.	.		0.502	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330		C	76788578	T	C	76788578	2	2	259	1	0	0	0	0	0	0	0	1	10114	1567	55	2		2	MYST4	10	76788578	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	934436	76788578	58746169	447	36765										
GRID1	2894	hgsc.bcm.edu	37	chr10	87628897	87628897	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccacggtcatccttccaaggGcactatggaccagatccagg	10	14	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:87628897G>T	ENST00000327946.7	-	6	906	c.821C>A	c.(820-822)gCc>gAc	p.A274D		NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	274					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|social behavior (GO:0035176)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|ionotropic glutamate receptor complex (GO:0008328)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(46)|ovary(5)|prostate(4)|skin(5)|stomach(4)|upper_aerodigestive_tract(5)	106						CCTTCCAAGGGCACTATGGAC	0.517										Multiple Myeloma(13;0.14)																											p.A274D		Atlas-SNP	.											.	GRID1	204	.	0			c.C821A						.						157	136	143					10																	87628897		2203	4300	6503	SO:0001583	missense	2894	exon6			CCAAGGGCACTAT	AB033046	CCDS31236.1	10q22	2012-08-29			ENSG00000182771	ENSG00000182771		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4575	protein-coding gene	gene with protein product		610659					Standard	NM_017551		Approved	GluD1, KIAA1220	uc001kdl.1	Q9ULK0	OTTHUMG00000018650	ENST00000327946.7:c.821C>A	chr10.hg19:g.87628897G>T	ENSP00000330148:p.Ala274Asp	146.0	0.0		107.0	5.0	NM_017551	B3KXD5|B7Z7L0|Q8IXT3	Missense_Mutation	SNP	ENST00000327946.7	hg19	CCDS31236.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.488424	0.84854	.	.	ENSG00000182771	ENST00000327946	D	0.85556	-2.0	5.82	5.82	0.92795	Extracellular ligand-binding receptor (1);	0.097857	0.64402	D	0.000001	D	0.87030	0.6076	L	0.44542	1.39	0.80722	D	1	D	0.58268	0.982	P	0.52159	0.691	D	0.87980	0.2742	10	0.87932	D	0	.	19.0974	0.93258	0.0:0.0:1.0:0.0	.	274	Q9ULK0	GRID1_HUMAN	D	274	ENSP00000330148:A274D	ENSP00000330148:A274D	A	-	2	0	GRID1	87618877	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.848000	0.99507	2.745000	0.94114	0.655000	0.94253	GCC	.	.		0.517	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3	XM_043613		T	87628897	G	T	87628897	3	4	259	1	0	0	0	0	1	0	0	0	6780	1203	42	3	2252	3	GRID1	10	87628897	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	10840319	87628897	47905850	448	36766										
PPP1R3C	5507	hgsc.bcm.edu	37	chr10	93390552	93390552	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	caggtggtgaatgtgccaagCaaagcctcatggccacatcc	11	12	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:93390552C>A	ENST00000238994.5	-	2	170	c.86G>T	c.(85-87)tGc>tTc	p.C29F		NM_005398.5	NP_005389.1			protein phosphatase 1, regulatory subunit 3C											breast(1)|endometrium(1)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(1)	12		Colorectal(252;0.235)				ATGTGCCAAGCAAAGCCTCAT	0.453																																					p.C29F		Atlas-SNP	.											.	PPP1R3C	30	.	0			c.G86T						.						81	83	82					10																	93390552		2203	4300	6503	SO:0001583	missense	5507	exon2			GCCAAGCAAAGCC	Y18207	CCDS7416.1	10q23-q24	2012-04-17	2011-10-04	2001-08-01	ENSG00000119938	ENSG00000119938		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9293	protein-coding gene	gene with protein product	"Phosphatase 1, regulatory inhibitor subunit 5", "protein targeting to glycogen"	602999	"protein phosphatase 1, regulatory (inhibitor) subunit 3C"	PPP1R5		8985175	Standard	NM_005398		Approved	PTG	uc001kho.3	Q9UQK1	OTTHUMG00000018745	ENST00000238994.5:c.86G>T	chr10.hg19:g.93390552C>A	ENSP00000238994:p.Cys29Phe	96.0	0.0		79.0	4.0	NM_005398		Missense_Mutation	SNP	ENST00000238994.5	hg19	CCDS7416.1	.	.	.	.	.	.	.	.	.	.	C	9.503	1.103720	0.20632	.	.	ENSG00000119938	ENST00000238994;ENST00000438999	T	0.41400	1.0	5.68	5.68	0.88126	.	0.104848	0.64402	D	0.000002	T	0.41050	0.1142	L	0.56769	1.78	0.52099	D	0.999943	B	0.30889	0.299	B	0.26517	0.07	T	0.26087	-1.0113	10	0.15499	T	0.54	-13.9965	19.7888	0.96450	0.0:1.0:0.0:0.0	.	29	Q9UQK1	PPR3C_HUMAN	F	29	ENSP00000238994:C29F	ENSP00000238994:C29F	C	-	2	0	PPP1R3C	93380532	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	3.173000	0.50839	2.662000	0.90505	0.655000	0.94253	TGC	.	.		0.453	PPP1R3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049372.1	NM_005398		A	93390552	C	A	93390552	3	1	259	1	0	0	0	0	1	0	0	0	12385	710	25	3	871	3	PPP1R3C	10	93390552	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	5761655	93390552	42144195	449	36767										
CEP55	55165	hgsc.bcm.edu	37	chr10	95279490	95279490	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aaaaactcgaccgtcaacatGtgcagcatcaattgcatgta	7	10	2	0	rs542873829		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:95279490G>A	ENST00000371485.3	+	8	1421	c.1117G>A	c.(1117-1119)Gtg>Atg	p.V373M	CEP55_ENST00000496302.1_3'UTR	NM_001127182.1|NM_018131.4	NP_001120654|NP_060601	Q53EZ4	CEP55_HUMAN	centrosomal protein 55kDa	373	Required for localization to the interphase centrosome and to the midbody during cytokinesis.				establishment of protein localization (GO:0045184)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|midbody (GO:0030496)				kidney(1)|large_intestine(5)|lung(6)|stomach(1)	13		Colorectal(252;0.207)				CCGTCAACATGTGCAGCATCA	0.393													g|||	1	0.000199681	8e-04	0	5008	,	,		20466	0		0	False		,,,				2504	0				p.V373M		Atlas-SNP	.											.	CEP55	35	.	0			c.G1117A						.						117	102	107					10																	95279490		2203	4300	6503	SO:0001583	missense	55165	exon8			CAACATGTGCAGC	AK001402	CCDS7428.1	10q24.1	2014-02-20	2005-12-01	2005-12-01	ENSG00000138180	ENSG00000138180			1161	protein-coding gene	gene with protein product	"cancer/testis antigen 111"	610000	"chromosome 10 open reading frame 3"	C10orf3		16198290	Standard	NM_018131		Approved	FLJ10540, CT111	uc009xug.3	Q53EZ4	OTTHUMG00000018774	ENST00000371485.3:c.1117G>A	chr10.hg19:g.95279490G>A	ENSP00000360540:p.Val373Met	93.0	0.0		84.0	4.0	NM_018131	B2RDG8|Q32WF5|Q3MV20|Q5VY28|Q6N034|Q96H32|Q9NVS7	Missense_Mutation	SNP	ENST00000371485.3	hg19	CCDS7428.1	.	.	.	.	.	.	.	.	.	.	g	1.489	-0.555262	0.03967	.	.	ENSG00000138180	ENST00000371485;ENST00000358339	T	0.15952	2.38	5.79	3.46	0.39613	.	0.262502	0.46758	N	0.000267	T	0.02727	0.0082	N	0.00289	-1.7	0.22096	N	0.999361	B	0.02656	0.0	B	0.04013	0.001	T	0.41645	-0.9497	10	0.02654	T	1	-10.0504	4.4531	0.11630	0.6671:0.0:0.1569:0.1761	.	373	Q53EZ4	CEP55_HUMAN	M	373	ENSP00000360540:V373M	ENSP00000351102:V373M	V	+	1	0	CEP55	95269480	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	1.307000	0.33516	0.455000	0.26910	-0.405000	0.06341	GTG	.	.		0.393	CEP55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049434.1	NM_018131		A	95279490	G	A	95279490	3	1	259	1	0	0	0	0	1	0	0	0	3257	1377	48	3	1143	3	CEP55	10	95279490	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1888938	95279490	40255257	450	36768										
PLCE1	51196	hgsc.bcm.edu	37	chr10	96076352	96076352	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctgttaccacagactattttTtgatggaagaaaaatatttt	6	5	0	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:96076352T>C	ENST00000371380.3	+	28	6416	c.6181T>C	c.(6181-6183)Ttg>Ctg	p.L2061L	RP11-76P2.4_ENST00000609123.1_RNA|NOC3L_ENST00000543788.1_Intron|PLCE1_ENST00000371385.3_Silent_p.L1753L|PLCE1_ENST00000260766.3_Silent_p.L2061L|PLCE1_ENST00000371375.1_Silent_p.L1753L			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1	2061	Ras-associating 1. {ECO:0000255|PROSITE- ProRule:PRU00166}.				activation of MAPK activity (GO:0000187)|calcium-mediated signaling (GO:0019722)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|diacylglycerol biosynthetic process (GO:0006651)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerulus development (GO:0032835)|heart development (GO:0007507)|inositol phosphate metabolic process (GO:0043647)|inositol phosphate-mediated signaling (GO:0048016)|lipid catabolic process (GO:0016042)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|phospholipid metabolic process (GO:0006644)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of GTPase activity (GO:0043547)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|Ras protein signal transduction (GO:0007265)|regulation of cell growth (GO:0001558)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of protein kinase activity (GO:0045859)|regulation of Ras protein signal transduction (GO:0046578)|regulation of smooth muscle contraction (GO:0006940)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)|guanyl-nucleotide exchange factor activity (GO:0005085)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|Ras GTPase binding (GO:0017016)|receptor signaling protein activity (GO:0005057)			liver(1)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	8		Colorectal(252;0.0458)				AGACTATTTTTTGATGGAAGA	0.333																																					p.L2061L		Atlas-SNP	.											PLCE1_ENST00000371375,NS,carcinoma,0,3	PLCE1	543	.	0			c.T6181C						.						46	45	45					10																	96076352		1793	4065	5858	SO:0001819	synonymous_variant	51196	exon29			TATTTTTTGATGG		CCDS41552.1, CCDS53555.1	10q23	2010-02-22			ENSG00000138193	ENSG00000138193	3.1.4.11		17175	protein-coding gene	gene with protein product	"nephrosis type 3"	608414				11022047, 11022048	Standard	NM_016341		Approved	KIAA1516, PLCE, NPHS3	uc001kjk.3	Q9P212	OTTHUMG00000018789	ENST00000371380.3:c.6181T>C	chr10.hg19:g.96076352T>C		56.0	0.0		38.0	2.0	NM_016341	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Silent	SNP	ENST00000371380.3	hg19	CCDS41552.1																																																																																			.	.		0.333	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049469.3	NM_016341		C	96076352	T	C	96076352	2	2	259	1	0	0	0	0	0	0	0	1	12043	1838	64	2		2	PLCE1	10	96076352	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	796862	96076352	39458395	451	36769										
MMS19	64210	hgsc.bcm.edu	37	chr10	99220678	99220678	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccttacccagagaagaagagTgaaggcctgactacgacagg	12	10	0	5			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:99220678T>C	ENST00000438925.2	-	24	2733	c.2398A>G	c.(2398-2400)Act>Gct	p.T800A	MMS19_ENST00000370782.2_Missense_Mutation_p.T800A|MMS19_ENST00000355839.6_Missense_Mutation_p.T757A|MMS19_ENST00000327238.10_Missense_Mutation_p.T702A|MMS19_ENST00000327277.7_3'UTR	NM_022362.4	NP_071757.4	Q96T76	MMS19_HUMAN	MMS19 nucleotide excision repair homolog (S. cerevisiae)	800					cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|iron-sulfur cluster assembly (GO:0016226)|nucleotide-excision repair (GO:0006289)|phosphorelay signal transduction system (GO:0000160)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	CIA complex (GO:0097361)|cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|membrane (GO:0016020)|MMXD complex (GO:0071817)|nucleus (GO:0005634)|spindle (GO:0005819)	estrogen receptor binding (GO:0030331)|protein binding, bridging (GO:0030674)|receptor signaling complex scaffold activity (GO:0030159)|transcription coactivator activity (GO:0003713)			endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|stomach(1)	16		Colorectal(252;0.0846)		Epithelial(162;3.33e-10)|all cancers(201;2.74e-08)		AGAAGAAGAGTGAAGGCCTGA	0.498								Direct reversal of damage																													p.T800A		Atlas-SNP	.											.	MMS19	36	.	0			c.A2398G						.						37	35	36					10																	99220678		2203	4297	6500	SO:0001583	missense	64210	exon24			GAAGAGTGAAGGC	AF007151	CCDS7464.1, CCDS73177.1	10q24-q25	2007-08-15	2007-08-15	2007-08-15	ENSG00000155229	ENSG00000155229			13824	protein-coding gene	gene with protein product	"MET18 homolog (S. cerevisiae)"	614777		MMS19L		11071939	Standard	NM_022362		Approved	MET18, hMMS19	uc001kns.4	Q96T76	OTTHUMG00000018857	ENST00000438925.2:c.2398A>G	chr10.hg19:g.99220678T>C	ENSP00000412698:p.Thr800Ala	86.0	0.0		98.0	4.0	NM_022362	B0QZ75|B3KPE5|B4DQX2|B4E2I3|D3DR55|F8W9Y2|Q17RZ8|Q5T455|Q66K82|Q7L4W8|Q969Z1|Q96DF1|Q96MR1|Q96RK5|Q96SK1|Q9BUE2|Q9BYS9	Missense_Mutation	SNP	ENST00000438925.2	hg19	CCDS7464.1	.	.	.	.	.	.	.	.	.	.	T	15.46	2.839897	0.51057	.	.	ENSG00000155229	ENST00000438925;ENST00000370782;ENST00000327238;ENST00000422291;ENST00000355839	T;T;T;T	0.28666	1.6;1.6;1.6;1.6	5.66	5.66	0.87406	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.46502	0.1396	M	0.61703	1.905	0.80722	D	1	P;D;D;B;D	0.71674	0.911;0.996;0.998;0.138;0.966	B;P;P;B;P	0.62560	0.288;0.834;0.904;0.082;0.493	T	0.38134	-0.9675	10	0.08837	T	0.75	.	15.5432	0.76074	0.0:0.0:0.0:1.0	.	821;702;757;800;757	B4DQX2;Q96T76-5;F8W9Y2;Q96T76;B4E2I3	.;.;.;MMS19_HUMAN;.	A	800;800;702;779;757	ENSP00000412698:T800A;ENSP00000359818:T800A;ENSP00000320059:T702A;ENSP00000348097:T757A	ENSP00000320059:T702A	T	-	1	0	MMS19	99210668	1.000000	0.71417	1.000000	0.80357	0.854000	0.48673	3.458000	0.53014	2.154000	0.67381	0.397000	0.26171	ACT	.	.		0.498	MMS19-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049706.2			C	99220678	T	C	99220678	3	2	259	1	0	0	0	0	1	0	0	0	9681	1696	59	2	726	2	MMS19	10	99220678	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	3144326	99220678	36314069	452	36770										
ERLIN1	10613	hgsc.bcm.edu	37	chr10	101937926	101937926	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	catattaaccacttctattcGgtcaatatagatcatgaccc	4	11	3	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:101937926G>T	ENST00000421367.2	-	4	2975	c.268C>A	c.(268-270)Cga>Aga	p.R90R	ERLIN1_ENST00000407654.3_Silent_p.R90R	NM_001100626.1|NM_006459.3	NP_001094096.1|NP_006450.2	O75477	ERLN1_HUMAN	ER lipid raft associated 1	88					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)							Colorectal(252;0.234)		Epithelial(162;3.85e-10)|all cancers(201;3.25e-08)		ACTTCTATTCGGTCAATATAG	0.373																																					p.R90R		Atlas-SNP	.											.	.	.	.	0			c.C268A						.						64	54	57					10																	101937926		2199	4296	6495	SO:0001819	synonymous_variant	10613	exon4			CTATTCGGTCAAT	AF064093	CCDS7487.2	10q24.31	2014-03-03	2007-01-26	2007-01-26	ENSG00000107566	ENSG00000107566			16947	protein-coding gene	gene with protein product	"Band_7 23-211 Keo4 (Interim) similar to C.elegans protein C42C1.9"	611604	"chromosome 10 open reading frame 69", "SPFH domain family, member 1"	C10orf69, SPFH1		11118313, 16835267, 24482476	Standard	NM_006459		Approved	KE04, Erlin-1, SPG62	uc001kqo.4	O75477	OTTHUMG00000018900	ENST00000421367.2:c.268C>A	chr10.hg19:g.101937926G>T		62.0	0.0		72.0	4.0	NM_006459	B0QZ42|Q53HV0	Silent	SNP	ENST00000421367.2	hg19	CCDS7487.2																																																																																			.	.		0.373	ERLIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049840.2	NM_006459		T	101937926	G	T	101937926	2	4	259	1	0	0	0	0	0	0	0	1	5234	1124	39	1		1	ERLIN1	10	101937926	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	2717248	101937926	33596821	453	36771										
ELOVL3	83401	hgsc.bcm.edu	37	chr10	103988767	103988767	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	actacactctgaaggctgccAacgtgaagccccccaagatg	9	14	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:103988767A>T	ENST00000370005.3	+	4	792	c.571A>T	c.(571-573)Aac>Tac	p.N191Y		NM_152310.1	NP_689523.1	Q9HB03	ELOV3_HUMAN	ELOVL fatty acid elongase 3	191					cellular lipid metabolic process (GO:0044255)|fatty acid elongation, monounsaturated fatty acid (GO:0034625)|fatty acid elongation, polyunsaturated fatty acid (GO:0034626)|fatty acid elongation, saturated fatty acid (GO:0019367)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|very long-chain fatty acid biosynthetic process (GO:0042761)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transferase activity (GO:0016740)			breast(2)|lung(10)|ovary(2)|prostate(1)|skin(1)	16		Colorectal(252;0.207)		Epithelial(162;4.47e-08)|all cancers(201;7.96e-07)		GAAGGCTGCCAACGTGAAGCC	0.517																																					p.N191Y		Atlas-SNP	.											.	ELOVL3	39	.	0			c.A571T						.						128	118	121					10																	103988767		2203	4300	6503	SO:0001583	missense	83401	exon4			GCTGCCAACGTGA	AF292387	CCDS7531.1	10q24	2011-05-25	2011-05-25		ENSG00000119915	ENSG00000119915			18047	protein-coding gene	gene with protein product		611815	"elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 3"				Standard	NM_152310		Approved	CIG-30	uc001kut.3	Q9HB03	OTTHUMG00000018951	ENST00000370005.3:c.571A>T	chr10.hg19:g.103988767A>T	ENSP00000359022:p.Asn191Tyr	149.0	0.0		122.0	5.0	NM_152310	Q5VZL3|Q8N180	Missense_Mutation	SNP	ENST00000370005.3	hg19	CCDS7531.1	.	.	.	.	.	.	.	.	.	.	A	16.24	3.067863	0.55539	.	.	ENSG00000119915	ENST00000370005	T	0.22336	1.96	5.57	1.96	0.26148	.	0.684456	0.13693	N	0.369386	T	0.19005	0.0456	L	0.33339	1.005	0.26067	N	0.981271	B	0.16603	0.018	B	0.35073	0.195	T	0.35400	-0.9790	10	0.87932	D	0	-15.7707	6.2622	0.20907	0.4996:0.0:0.5004:0.0	.	191	Q9HB03	ELOV3_HUMAN	Y	191	ENSP00000359022:N191Y	ENSP00000359022:N191Y	N	+	1	0	ELOVL3	103978757	0.998000	0.40836	0.462000	0.27118	0.979000	0.70002	3.902000	0.56310	0.410000	0.25675	0.528000	0.53228	AAC	.	.		0.517	ELOVL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050030.1	NM_152310		T	103988767	A	T	103988767	3	4	259	1	0	0	0	0	1	0	0	0	5077	130	5	4	585	4	ELOVL3	10	103988767	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2050841	103988767	31545980	454	36772										
SFXN2	118980	hgsc.bcm.edu	37	chr10	104486433	104486433	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gctttaacatcgatgcccccCgttgggaccagcgcaccttc	9	16	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:104486433C>A	ENST00000369893.5	+	2	207	c.40C>A	c.(40-42)Cgt>Agt	p.R14S	SFXN2_ENST00000602785.1_3'UTR	NM_178858.4	NP_849189.1	Q96NB2	SFXN2_HUMAN	sideroflexin 2	14					iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|prostate(1)	13		Colorectal(252;0.207)		Epithelial(162;4.53e-09)|all cancers(201;1.2e-07)|BRCA - Breast invasive adenocarcinoma(275;0.218)		CGATGCCCCCCGTTGGGACCA	0.542																																					p.R14S		Atlas-SNP	.											.	SFXN2	40	.	0			c.C40A						.						113	112	113					10																	104486433		2203	4300	6503	SO:0001583	missense	118980	exon2			GCCCCCCGTTGGG	AF462052	CCDS7539.1	10q24.32	2006-03-13			ENSG00000156398	ENSG00000156398		"Sideroflexins"	16086	protein-coding gene	gene with protein product		615570					Standard	NM_178858		Approved		uc001kwb.2	Q96NB2	OTTHUMG00000018967	ENST00000369893.5:c.40C>A	chr10.hg19:g.104486433C>A	ENSP00000358909:p.Arg14Ser	99.0	0.0		64.0	4.0	NM_178858	Q5JSM6	Missense_Mutation	SNP	ENST00000369893.5	hg19	CCDS7539.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.357748	0.82243	.	.	ENSG00000156398	ENST00000369893	T	0.36340	1.26	5.49	5.49	0.81192	.	0.052777	0.85682	D	0.000000	T	0.55130	0.1901	M	0.90082	3.085	0.80722	D	1	P	0.43287	0.802	B	0.43445	0.42	T	0.66834	-0.5823	10	0.72032	D	0.01	0.0231	19.3785	0.94521	0.0:1.0:0.0:0.0	.	14	Q96NB2	SFXN2_HUMAN	S	14	ENSP00000358909:R14S	ENSP00000358909:R14S	R	+	1	0	SFXN2	104476423	1.000000	0.71417	1.000000	0.80357	0.713000	0.41058	4.918000	0.63376	2.566000	0.86566	0.561000	0.74099	CGT	.	.		0.542	SFXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050096.2	XM_058359		A	104486433	C	A	104486433	3	1	259	1	0	0	0	0	1	0	0	0	14210	652	23	1	42	1	SFXN2	10	104486433	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	497666	104486433	31048314	455	36773										
PDCD11	22984	hgsc.bcm.edu	37	chr10	105184772	105184772	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cagcgaacaccaggcgattgTgcagcacttggagaagtcct	12	11	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:105184772T>C	ENST00000369797.3	+	20	2889	c.2795T>C	c.(2794-2796)gTg>gCg	p.V932A	PDCD11_ENST00000490787.1_3'UTR	NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	932					mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	64		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		CAGGCGATTGTGCAGCACTTG	0.552																																					p.V932A		Atlas-SNP	.											.	PDCD11	160	.	0			c.T2795C						.						125	112	117					10																	105184772		2203	4300	6503	SO:0001583	missense	22984	exon20			CGATTGTGCAGCA	D80007	CCDS31276.1	10q24.32	2010-07-06			ENSG00000148843	ENSG00000148843			13408	protein-coding gene	gene with protein product		612333				10229231	Standard	XM_005269647		Approved	KIAA0185, ALG-4, RRP5	uc001kwy.1	Q14690	OTTHUMG00000018988	ENST00000369797.3:c.2795T>C	chr10.hg19:g.105184772T>C	ENSP00000358812:p.Val932Ala	91.0	0.0		77.0	4.0	NM_014976	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Missense_Mutation	SNP	ENST00000369797.3	hg19	CCDS31276.1	.	.	.	.	.	.	.	.	.	.	T	31	5.078234	0.94000	.	.	ENSG00000148843	ENST00000369797;ENST00000543503	T	0.15372	2.43	5.74	5.74	0.90152	.	0.057567	0.64402	D	0.000001	T	0.35158	0.0922	M	0.65498	2.005	0.80722	D	1	D	0.58268	0.982	P	0.55112	0.769	T	0.07849	-1.0751	10	0.87932	D	0	-20.9168	16.3305	0.83010	0.0:0.0:0.0:1.0	.	932	Q14690	RRP5_HUMAN	A	932	ENSP00000358812:V932A	ENSP00000358812:V932A	V	+	2	0	PDCD11	105174762	1.000000	0.71417	0.998000	0.56505	0.969000	0.65631	7.310000	0.78947	2.317000	0.78254	0.459000	0.35465	GTG	.	.		0.552	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1			C	105184772	T	C	105184772	3	2	259	1	0	0	0	0	1	0	0	0	11626	1696	59	2	2869	2	PDCD11	10	105184772	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	698339	105184772	30349975	456	36774										
SLK	9748	hgsc.bcm.edu	37	chr10	105762224	105762224	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aaagagagaagaggcccaagCttgaaaatctgcctgacaca	10	9	1	5			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:105762224C>T	ENST00000369755.3	+	9	1833	c.1288C>T	c.(1288-1290)Ctt>Ttt	p.L430F	SLK_ENST00000335753.4_Missense_Mutation_p.L430F	NM_014720.2	NP_055535.2	Q9H2G2	SLK_HUMAN	STE20-like kinase	430	Glu-rich.				apoptotic process (GO:0006915)|protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			kidney(1)|lung(1)|ovary(2)|skin(2)|stomach(2)	8		Colorectal(252;0.178)		Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		GAGGCCCAAGCTTGAAAATCT	0.363																																					p.L430F	NSCLC(111;540 1651 1927 4474 17706)	Atlas-SNP	.											.	SLK	107	.	0			c.C1288T						.						109	120	117					10																	105762224		2203	4300	6503	SO:0001583	missense	9748	exon9			CCCAAGCTTGAAA		CCDS7553.1	10q25.1	2010-06-25	2010-06-25		ENSG00000065613	ENSG00000065613			11088	protein-coding gene	gene with protein product			"SNF1 (sucrose nonfermenting, yeast, homolog)-like kinase, SNF1 sucrose nonfermenting like kinase (yeast)", "STE20-like kinase (yeast)"			3526554	Standard	NM_014720		Approved	STK2, se20-9, KIAA0204	uc001kxo.1	Q9H2G2	OTTHUMG00000018999	ENST00000369755.3:c.1288C>T	chr10.hg19:g.105762224C>T	ENSP00000358770:p.Leu430Phe	104.0	0.0		97.0	4.0	NM_014720	D3DRA0|D3DRA1|O00211|Q6P1Z4|Q86WU7|Q86WW1|Q92603|Q9NQL0|Q9NQL1	Missense_Mutation	SNP	ENST00000369755.3	hg19	CCDS7553.1	.	.	.	.	.	.	.	.	.	.	C	9.783	1.175873	0.21704	.	.	ENSG00000065613	ENST00000335753;ENST00000369755	T;T	0.69685	-0.42;-0.41	5.62	0.391	0.16282	Protein kinase-like domain (1);	1.163690	0.06371	N	0.713543	T	0.53818	0.1820	L	0.54323	1.7	0.09310	N	1	P;P	0.43701	0.815;0.718	B;B	0.40228	0.323;0.172	T	0.41233	-0.9520	10	0.14252	T	0.57	.	1.1987	0.01880	0.1395:0.3639:0.1506:0.3459	.	430;430	Q9H2G2-2;Q9H2G2	.;SLK_HUMAN	F	430	ENSP00000336824:L430F;ENSP00000358770:L430F	ENSP00000336824:L430F	L	+	1	0	SLK	105752214	0.000000	0.05858	0.661000	0.29709	0.652000	0.38707	-0.707000	0.05041	0.332000	0.23536	-0.300000	0.09419	CTT	.	.		0.363	SLK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050188.1	NM_014720		T	105762224	C	T	105762224	3	4	259	1	0	0	0	0	1	0	0	0	14763	797	28	3	1322	3	SLK	10	105762224	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	577452	105762224	29772523	457	36775										
KIAA1598	57698	hgsc.bcm.edu	37	chr10	118719735	118719735	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	taacttcctctatgaccatgTgagaaactaggaatgagggg	11	7	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:118719735T>C	ENST00000355371.4	-	4	676	c.179A>G	c.(178-180)cAc>cGc	p.H60R	KIAA1598_ENST00000392901.4_5'UTR|KIAA1598_ENST00000392903.2_Missense_Mutation_p.H60R|KIAA1598_ENST00000260777.10_Missense_Mutation_p.H60R|KIAA1598_ENST00000497044.1_5'UTR	NM_001127211.2|NM_001258298.1|NM_001258299.1	NP_001120683.1|NP_001245227.1|NP_001245228.1	A0MZ66	SHOT1_HUMAN	KIAA1598	60					axon guidance (GO:0007411)|regulation of establishment of cell polarity (GO:2000114)|regulation of neuron migration (GO:2001222)	axonal growth cone (GO:0044295)				endometrium(1)|kidney(1)|large_intestine(5)|lung(3)	10				all cancers(201;0.00494)		TATGACCATGTGAGAAACTAG	0.403																																					p.H60R		Atlas-SNP	.											.	KIAA1598	74	.	0			c.A179G						.						67	66	66					10																	118719735		2203	4300	6503	SO:0001583	missense	57698	exon4			ACCATGTGAGAAA	BC022348	CCDS31293.1, CCDS44482.1, CCDS58097.1, CCDS73207.1, CCDS73208.1	10q26.12	2007-01-30			ENSG00000187164	ENSG00000187164			29319	protein-coding gene	gene with protein product		611171				10997877, 17030985	Standard	NM_001127211		Approved	shootin1, shootin-1	uc009xyw.4	A0MZ66	OTTHUMG00000019114	ENST00000355371.4:c.179A>G	chr10.hg19:g.118719735T>C	ENSP00000347532:p.His60Arg	78.0	0.0		76.0	4.0	NM_001258299	A8MYU7|B3KRD3|B3KRH2|B3KTE0|B3KTJ7|B3KTJ8|B4E3U1|B7Z7Z9|Q68DG1|Q6PIM5|Q9HCH4|Q9NUV0	Missense_Mutation	SNP	ENST00000355371.4	hg19	CCDS44482.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.399350	0.83120	.	.	ENSG00000187164	ENST00000392903;ENST00000260777;ENST00000355371	D;D;D	0.91843	-2.92;-2.92;-2.92	5.98	5.98	0.97165	.	0.045076	0.85682	D	0.000000	D	0.93612	0.7960	L	0.41710	1.295	0.80722	D	1	D;D;D	0.89917	1.0;0.989;0.974	D;D;P	0.83275	0.996;0.985;0.796	D	0.91555	0.5260	10	0.19147	T	0.46	-15.2069	16.4728	0.84119	0.0:0.0:0.0:1.0	.	60;60;30	A0MZ66;A0MZ66-2;A0MZ66-6	SHOT1_HUMAN;.;.	R	60	ENSP00000376636:H60R;ENSP00000260777:H60R;ENSP00000347532:H60R	ENSP00000260777:H60R	H	-	2	0	KIAA1598	118709725	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.257000	0.78362	2.296000	0.77279	0.482000	0.46254	CAC	.	.		0.403	KIAA1598-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018330		C	118719735	T	C	118719735	3	2	259	1	0	0	0	0	1	0	0	0	8255	1696	59	2	1772	2	KIAA1598	10	118719735	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	12957511	118719735	16815012	458	36776										
SLC18A2	6571	hgsc.bcm.edu	37	chr10	119003656	119003656	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	taccagagacctgacacttcAtcagaccgccacacagcaca	6	16	2	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:119003656A>G	ENST00000298472.5	+	3	439	c.296A>G	c.(295-297)cAt>cGt	p.H99R	SLC18A2_ENST00000497497.1_3'UTR|RP11-501J20.5_ENST00000425264.1_RNA	NM_003054.4	NP_003045.2	Q05940	VMAT2_HUMAN	solute carrier family 18 (vesicular monoamine transporter), member 2	99					aging (GO:0007568)|cellular response to ammonium ion (GO:0071242)|cellular response to drug (GO:0035690)|death (GO:0016265)|dopamine transport (GO:0015872)|endocytic recycling (GO:0032456)|glucose homeostasis (GO:0042593)|insulin secretion (GO:0030073)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|negative regulation of neurotransmitter transport (GO:0051589)|neurotransmitter loading into synaptic vesicle (GO:0098700)|neurotransmitter secretion (GO:0007269)|post-embryonic development (GO:0009791)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to corticosterone (GO:0051412)|response to herbicide (GO:0009635)|response to starvation (GO:0042594)|response to zinc ion (GO:0010043)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|dense core granule (GO:0031045)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)|terminal bouton (GO:0043195)	amine transmembrane transporter activity (GO:0005275)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)|serotonin transmembrane transporter activity (GO:0015222)			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)	Amphetamine(DB00182)|Benzphetamine(DB00865)|Deserpidine(DB01089)|Dextroamphetamine(DB01576)|Ephedra(DB01363)|Ephedrine(DB01364)|Isometheptene(DB06706)|Methamphetamine(DB01577)|Norepinephrine(DB00368)|Propylhexedrine(DB06714)|Reserpine(DB00206)|Tetrabenazine(DB04844)	CTGACACTTCATCAGACCGCC	0.517																																					p.H99R		Atlas-SNP	.											.	SLC18A2	58	.	0			c.A296G						.						119	103	108					10																	119003656		2203	4300	6503	SO:0001583	missense	6571	exon3			CACTTCATCAGAC	L14269	CCDS7599.1	10q25	2013-07-18	2013-07-18		ENSG00000165646	ENSG00000165646		"Solute carriers"	10935	protein-coding gene	gene with protein product		193001		VMAT2			Standard	NM_003054		Approved	SVMT, SVAT	uc001ldd.2	Q05940	OTTHUMG00000019121	ENST00000298472.5:c.296A>G	chr10.hg19:g.119003656A>G	ENSP00000298472:p.His99Arg	92.0	0.0		83.0	4.0	NM_003054	B2RC96|D3DRC4|Q15876|Q4G147|Q5VW49|Q9H3P6	Missense_Mutation	SNP	ENST00000298472.5	hg19	CCDS7599.1	.	.	.	.	.	.	.	.	.	.	A	1.201	-0.632442	0.03584	.	.	ENSG00000165646	ENST00000298472	T	0.03524	3.9	5.58	-8.56	0.00904	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	2.472560	0.01099	N	0.005329	T	0.01695	0.0054	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43163	-0.9408	10	0.23302	T	0.38	6.9713	2.3047	0.04171	0.4916:0.2249:0.121:0.1625	.	99	Q05940	VMAT2_HUMAN	R	99	ENSP00000298472:H99R	ENSP00000298472:H99R	H	+	2	0	SLC18A2	118993646	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.241000	0.02911	-2.053000	0.00901	-0.376000	0.06991	CAT	.	.		0.517	SLC18A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050563.1	NM_003054		G	119003656	A	G	119003656	3	3	259	1	0	0	0	0	1	0	0	0	14441	217	8	2	302	2	SLC18A2	10	119003656	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	283921	119003656	16531091	459	36777										
C10orf90	118611	hgsc.bcm.edu	37	chr10	128114440	128114440	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gggcagcctgtggttagaccGcattcctttgaaggagctgg	15	9	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:128114440G>T	ENST00000284694.7	-	9	2213	c.2093C>A	c.(2092-2094)gCg>gAg	p.A698E	C10orf90_ENST00000356858.3_3'UTR|C10orf90_ENST00000544758.1_Missense_Mutation_p.A795E|C10orf90_ENST00000480379.1_Missense_Mutation_p.A102E|C10orf90_ENST00000454341.1_Missense_Mutation_p.A601E	NM_001004298.2	NP_001004298.2	Q96M02	CJ090_HUMAN	chromosome 10 open reading frame 90	698	ALMS motif. {ECO:0000250}.				mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell growth (GO:0030308)|protein stabilization (GO:0050821)|response to ionizing radiation (GO:0010212)|response to UV (GO:0009411)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.A698V(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(19)|liver(1)|lung(29)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	65		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)		TGGTTAGACCGCATTCCTTTG	0.483																																					p.A698E		Atlas-SNP	.											C10orf90,NS,carcinoma,0,1	C10orf90	121	.	1	Substitution - Missense(1)	prostate(1)	c.C2093A						.						105	98	100					10																	128114440		2203	4300	6503	SO:0001583	missense	118611	exon9			TAGACCGCATTCC	BC034828	CCDS31310.1	10q26.2	2012-05-31			ENSG00000154493	ENSG00000154493			26563	protein-coding gene	gene with protein product	"fragile-site associated tumor suppressor"					20843368, 20154723	Standard	NM_001004298		Approved	FLJ32938, bA422P15.2, FATS	uc001ljq.3	Q96M02	OTTHUMG00000019245	ENST00000284694.7:c.2093C>A	chr10.hg19:g.128114440G>T	ENSP00000284694:p.Ala698Glu	80.0	0.0		74.0	4.0	NM_001004298	B9EIQ9|Q5JRP6|Q5T023|Q8NCV5|Q8WU75	Missense_Mutation	SNP	ENST00000284694.7	hg19	CCDS31310.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.135846	0.77662	.	.	ENSG00000154493	ENST00000356858;ENST00000284694;ENST00000454341;ENST00000544758	T;T;T	0.22539	1.95;2.04;1.97	5.58	4.63	0.57726	.	0.000000	0.43919	D	0.000505	T	0.24275	0.0588	N	0.08118	0	0.38645	D	0.951701	D;D;D	0.76494	0.997;0.999;0.997	P;D;P	0.65323	0.851;0.934;0.89	T	0.21827	-1.0234	10	0.72032	D	0.01	-21.9319	13.9111	0.63866	0.0:0.0:0.8492:0.1508	.	795;698;601	F5GZL2;Q96M02;Q96M02-2	.;CJ090_HUMAN;.	E	651;698;601;795	ENSP00000284694:A698E;ENSP00000398786:A601E;ENSP00000444369:A795E	ENSP00000284694:A698E	A	-	2	0	C10orf90	128104430	0.993000	0.37304	0.072000	0.20136	0.343000	0.28985	4.314000	0.59166	2.782000	0.95742	0.655000	0.94253	GCG	.	.		0.483	C10orf90-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004298		T	128114440	G	T	128114440	3	4	259	1	0	0	0	0	1	0	0	0	1625	1087	38	1	10	1	C10orf90	10	128114440	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	9110784	128114440	7420307	460	36778										
ZNF511	118472	hgsc.bcm.edu	37	chr10	135123793	135123793	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aagccaaagaaaagcagaagGtagggagccgccaggctcag	14	9	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:135123793G>A	ENST00000359035.3	+	4	557		c.e4+1		TUBGCP2_ENST00000470829.1_5'Flank|TUBGCP2_ENST00000368563.2_5'Flank|ZNF511_ENST00000361518.5_Splice_Site|ZNF511_ENST00000368554.4_Splice_Site|ZNF511_ENST00000463816.2_Splice_Site|TUBGCP2_ENST00000417178.2_5'Flank			Q8NB15	ZN511_HUMAN	zinc finger protein 511						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)	8		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		all cancers(32;7.56e-06)|OV - Ovarian serous cystadenocarcinoma(35;8.15e-06)|Epithelial(32;9.99e-06)		AAAGCAGAAGGTAGGGAGCCG	0.502																																					.		Atlas-SNP	.											.	ZNF511	17	.	0			c.554+1G>A						.						58	63	61					10																	135123793		2203	4300	6503	SO:0001630	splice_region_variant	118472	exon4			CAGAAGGTAGGGA	AK091711	CCDS7677.1	10q26.3	2010-04-12			ENSG00000198546	ENSG00000198546		"Zinc fingers, C2H2-type"	28445	protein-coding gene	gene with protein product						12477932	Standard	NM_145806		Approved	MGC30006	uc001lmj.1	Q8NB15	OTTHUMG00000019317	ENST00000359035.3:c.554+1G>A	chr10.hg19:g.135123793G>A		34.0	0.0		44.0	16.0	NM_145806	A8K8L5|Q8WUP1|Q96BV2	Splice_Site	SNP	ENST00000359035.3	hg19		.	.	.	.	.	.	.	.	.	.	G	15.68	2.905908	0.52333	.	.	ENSG00000198546	ENST00000361518;ENST00000359035;ENST00000368554	.	.	.	4.93	4.93	0.64822	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.0977	0.86639	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ZNF511	134973783	1.000000	0.71417	0.971000	0.41717	0.426000	0.31534	8.496000	0.90485	2.475000	0.83589	0.655000	0.94253	.	.	.		0.502	ZNF511-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000051143.1	NM_145806	Intron	A	135123793	G	A	135123793	5	1	259	1	0	0	0	0	0	0	1	0	17970	1275	44	3	569	3	ZNF511	10	135123793	Splice_Site	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	7009353	135123793	410954	461	36779										
MTG1	92170	hgsc.bcm.edu	37	chr10	135215725	135215725	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctcggattgaaagtgtggagAcaggcctgaagctggccctg	15	9	0	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:135215725A>G	ENST00000317502.6	+	8	696	c.646A>G	c.(646-648)Aca>Gca	p.T216A	RP11-108K14.8_ENST00000468317.2_Missense_Mutation_p.T221A|MTG1_ENST00000477902.2_Missense_Mutation_p.T175A	NM_138384.2	NP_612393.2	Q9BT17	MTG1_HUMAN	mitochondrial ribosome-associated GTPase 1	216					GTP catabolic process (GO:0006184)|regulation of mitochondrial translation (GO:0070129)|regulation of respiratory system process (GO:0044065)|ribosome biogenesis (GO:0042254)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial ribosome (GO:0005761)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|urinary_tract(1)	15		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;1.21e-06)|all cancers(32;1.69e-06)|Epithelial(32;1.94e-06)		AAGTGTGGAGACAGGCCTGAA	0.662																																					p.T216A		Atlas-SNP	.											.	MTG1	38	.	0			c.A646G						.						74	76	75					10																	135215725		2203	4300	6503	SO:0001583	missense	92170	exon8			GTGGAGACAGGCC		CCDS31320.1	10q26.3	2013-05-24	2013-05-24	2006-01-09	ENSG00000148824	ENSG00000148824			32159	protein-coding gene	gene with protein product			"GTP-binding protein 7", "GTP-binding protein 7 (putative)", "mitochondrial GTPase 1 homolog (S. cerevisiae)"	GTPBP7		12808030, 23396448	Standard	NM_138384		Approved		uc001lnd.3	Q9BT17	OTTHUMG00000166564	ENST00000317502.6:c.646A>G	chr10.hg19:g.135215725A>G	ENSP00000323047:p.Thr216Ala	113.0	0.0		89.0	4.0	NM_138384	Q5VWX8|Q6PIY9|Q8IYJ4|Q8NC48|Q9BVU8	Missense_Mutation	SNP	ENST00000317502.6	hg19	CCDS31320.1	.	.	.	.	.	.	.	.	.	.	a	15.59	2.879426	0.51801	.	.	ENSG00000254536;ENSG00000148824;ENSG00000148824	ENST00000468317;ENST00000317502;ENST00000432508	T;T;T	0.13657	2.57;2.57;2.57	5.59	5.59	0.84812	GTP-binding protein, orthogonal bundle domain (1);	0.141126	0.64402	N	0.000005	T	0.13329	0.0323	L	0.33245	0.995	0.50813	D	0.999896	B;B	0.18610	0.029;0.011	B;B	0.26310	0.06;0.068	T	0.05716	-1.0868	10	0.40728	T	0.16	-3.6768	13.7015	0.62611	1.0:0.0:0.0:0.0	.	165;216	E7EVK2;Q9BT17	.;MTG1_HUMAN	A	221;216;165	ENSP00000436767:T221A;ENSP00000323047:T216A;ENSP00000393480:T165A	ENSP00000323047:T216A	T	+	1	0	AL360181.1;MTG1	135065715	1.000000	0.71417	0.978000	0.43139	0.819000	0.46315	4.693000	0.61753	2.126000	0.65437	0.366000	0.22137	ACA	.	.		0.662	MTG1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051166.1	NM_138384		G	135215725	A	G	135215725	3	3	259	1	0	0	0	0	1	0	0	0	9935	275	10	2	676	2	MTG1	10	135215725	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	91932	135215725	319022	462	36780										
B4GALNT4	338707	hgsc.bcm.edu	37	chr11	377213	377213	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cgtggacttcgagctgctgcGctcggactggaacgacctgc	14	13	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:377213G>T	ENST00000329962.6	+	14	2090	c.2090G>T	c.(2089-2091)cGc>cTc	p.R697L		NM_178537.4	NP_848632.2	Q76KP1	B4GN4_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 4	697					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			endometrium(2)|kidney(4)|large_intestine(1)|liver(2)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	24		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GAGCTGCTGCGCTCGGACTGG	0.697																																					p.R697L		Atlas-SNP	.											.	B4GALNT4	83	.	0			c.G2090T						.						17	12	14					11																	377213		2143	4203	6346	SO:0001583	missense	338707	exon14			TGCTGCGCTCGGA	AB089939	CCDS7694.1	11p15.5	2013-02-19			ENSG00000182272	ENSG00000182272	2.4.1.-	"Beta 4-glycosyltransferases"	26315	protein-coding gene	gene with protein product						15044014	Standard	NM_178537		Approved	FLJ25045, NGalNAc-T1	uc001lpb.3	Q76KP1	OTTHUMG00000119075	ENST00000329962.6:c.2090G>T	chr11.hg19:g.377213G>T	ENSP00000328277:p.Arg697Leu	148.0	0.0		90.0	4.0	NM_178537	Q96LV2	Missense_Mutation	SNP	ENST00000329962.6	hg19	CCDS7694.1	.	.	.	.	.	.	.	.	.	.	g	23.6	4.439040	0.83885	.	.	ENSG00000182272	ENST00000329962	T	0.21932	1.98	3.12	3.12	0.35913	.	0.000000	0.85682	D	0.000000	T	0.38878	0.1057	L	0.52126	1.63	0.54753	D	0.999988	D	0.61697	0.99	D	0.71414	0.973	T	0.38887	-0.9640	10	0.87932	D	0	-23.6486	14.7266	0.69349	0.0:0.0:1.0:0.0	.	697	Q76KP1	B4GN4_HUMAN	L	697	ENSP00000328277:R697L	ENSP00000328277:R697L	R	+	2	0	B4GALNT4	367213	1.000000	0.71417	1.000000	0.80357	0.657000	0.38888	9.511000	0.98006	1.764000	0.52075	0.205000	0.17691	CGC	.	.		0.697	B4GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239289.2	NM_178537		T	377213	G	T	377213	3	4	259	1	0	0	0	0	1	0	0	0	1269	1087	38	1	2144	1	B4GALNT4	11	377213	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10		377213	134629303	463	36781										
MUC2	4583	hgsc.bcm.edu	37	chr11	1092653	1092653	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cagccctccaacaaccaccaCaaccacccctccaccaacca	1	24	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:1092653C>A	ENST00000441003.2	+	30	4499	c.4472C>A	c.(4471-4473)aCa>aAa	p.T1491K	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Missense_Mutation_p.T1492K	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4226	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ACAaccaccacaaccacccct	0.627																																					p.T1491K		Atlas-SNP	.											.	MUC2	614	.	0			c.C4472A						.						331	486	432					11																	1092653		1708	3175	4883	SO:0001583	missense	4583	exon30			CCACCACAACCAC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4472C>A	chr11.hg19:g.1092653C>A	ENSP00000415183:p.Thr1491Lys	3967.0	2.0		2125.0	392.0	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	hg19		.	.	.	.	.	.	.	.	.	.	-	3.506	-0.100813	0.06967	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.13778	2.59;2.56	0.924	0.924	0.19418	.	260.082000	0.01025	U	0.004044	T	0.04634	0.0126	.	.	.	0.21473	N	0.999671	P	0.45531	0.86	B	0.33890	0.172	T	0.32161	-0.9917	9	0.06365	T	0.9	.	5.0734	0.14618	0.0:0.7871:0.0:0.2129	.	1491	E7EUV1	.	K	1491;1492	ENSP00000415183:T1491K;ENSP00000351956:T1492K	ENSP00000351956:T1492K	T	+	2	0	MUC2	1082653	0.003000	0.15002	0.024000	0.17045	0.000000	0.00434	0.330000	0.19715	0.935000	0.37341	0.000000	0.15137	ACA	.	.		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		A	1092653	C	A	1092653	3	1	259	1	0	0	0	0	1	0	0	0	9984	478	17	3	4590	3	MUC2	11	1092653	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	715440	1092653	133913863	464	36782										
OR52M1	119772	hgsc.bcm.edu	37	chr11	4566442	4566442	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgctcacttttcataatgtcTgctcagtacccagctccttc	5	14	4	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:4566442T>A	ENST00000360213.1	+	1	22	c.22T>A	c.(22-24)Tgc>Agc	p.C8S		NM_001004137.1	NP_001004137.1	Q8NGK5	O52M1_HUMAN	olfactory receptor, family 52, subfamily M, member 1	8						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(2)|lung(9)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		TCATAATGTCTGCTCAGTACC	0.478																																					p.C8S		Atlas-SNP	.											.	OR52M1	53	.	0			c.T22A						.						90	82	85					11																	4566442		2201	4298	6499	SO:0001583	missense	119772	exon1			AATGTCTGCTCAG	AB065789	CCDS31353.1	11p15.4	2012-08-09	2002-11-13	2002-11-15	ENSG00000197790	ENSG00000197790		"GPCR / Class A : Olfactory receptors"	15225	protein-coding gene	gene with protein product			"olfactory receptor, family 52, subfamily M, member 1 pseudogene"	OR52M1P			Standard	NM_001004137		Approved		uc010qyf.2	Q8NGK5	OTTHUMG00000165706	ENST00000360213.1:c.22T>A	chr11.hg19:g.4566442T>A	ENSP00000353343:p.Cys8Ser	139.0	0.0		125.0	6.0	NM_001004137		Missense_Mutation	SNP	ENST00000360213.1	hg19	CCDS31353.1	.	.	.	.	.	.	.	.	.	.	T	13.34	2.207980	0.39003	.	.	ENSG00000197790	ENST00000360213	T	0.01092	5.35	4.12	4.12	0.48240	.	0.000000	0.51477	D	0.000084	T	0.00906	0.0030	N	0.00385	-1.57	0.26071	N	0.981229	D	0.76494	0.999	D	0.80764	0.994	T	0.58411	-0.7641	10	0.02654	T	1	.	11.7384	0.51778	0.0:0.0:0.0:1.0	.	8	Q8NGK5	O52M1_HUMAN	S	8	ENSP00000353343:C8S	ENSP00000353343:C8S	C	+	1	0	OR52M1	4523018	0.969000	0.33509	0.153000	0.22517	0.954000	0.61252	2.059000	0.41384	2.085000	0.62840	0.533000	0.62120	TGC	.	.		0.478	OR52M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385847.1	NM_001004137		A	4566442	T	A	4566442	3	1	259	1	0	0	0	0	1	0	0	0	11135	1580	55	4	24	4	OR52M1	11	4566442	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	3473789	4566442	130440074	465	36783										
OR51V1	283111	hgsc.bcm.edu	37	chr11	5221456	5221456	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aataaagaaaaaactcctacCtattatagtgagcccaattt	4	8	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:5221456C>A	ENST00000321255.1	-	1	474	c.475G>T	c.(475-477)Ggt>Tgt	p.G159C		NM_001004760.2	NP_001004760.2	Q9H2C8	O51V1_HUMAN	olfactory receptor, family 51, subfamily V, member 1	159					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(13)|lung(19)|skin(2)|upper_aerodigestive_tract(2)	39		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.83e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AAACTCCTACCTATTATAGTG	0.393																																					p.G159C		Atlas-SNP	.											.	OR51V1	77	.	0			c.G475T						.						48	54	52					11																	5221456		2200	4298	6498	SO:0001583	missense	283111	exon1			TCCTACCTATTAT	BK004432	CCDS31375.1	11p15.4	2012-08-09			ENSG00000176742	ENSG00000176742		"GPCR / Class A : Olfactory receptors"	19597	protein-coding gene	gene with protein product				OR51A12			Standard	NM_001004760		Approved		uc010qyz.2	Q9H2C8	OTTHUMG00000066671	ENST00000321255.1:c.475G>T	chr11.hg19:g.5221456C>A	ENSP00000321729:p.Gly159Cys	89.0	0.0		88.0	4.0	NM_001004760		Missense_Mutation	SNP	ENST00000321255.1	hg19	CCDS31375.1	.	.	.	.	.	.	.	.	.	.	C	2.357	-0.347590	0.05208	.	.	ENSG00000176742	ENST00000321255	T	0.37915	1.17	5.27	-5.05	0.02955	GPCR, rhodopsin-like superfamily (1);	1.346060	0.05003	N	0.469573	T	0.27489	0.0675	L	0.39085	1.19	0.09310	N	1	B	0.11235	0.004	B	0.17979	0.02	T	0.39901	-0.9591	10	0.48119	T	0.1	.	9.0537	0.36392	0.7026:0.1152:0.0:0.1822	.	159	Q9H2C8	O51V1_HUMAN	C	159	ENSP00000321729:G159C	ENSP00000321729:G159C	G	-	1	0	OR51V1	5178032	0.000000	0.05858	0.002000	0.10522	0.032000	0.12392	-2.274000	0.01163	-0.745000	0.04772	-0.182000	0.12963	GGT	.	.		0.393	OR51V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142965.1	NM_001004760		A	5221456	C	A	5221456	3	1	259	1	0	0	0	0	1	0	0	0	11116	681	24	3	493	3	OR51V1	11	5221456	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	655014	5221456	129785060	466	36784										
OR56B4	196335	hgsc.bcm.edu	37	chr11	6129433	6129433	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tcttcagtacccctccatagTcactaaagcttttgtcttca	4	13	5	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:6129433T>C	ENST00000316529.3	+	1	520	c.425T>C	c.(424-426)gTc>gCc	p.V142A	RP11-290F24.3_ENST00000529961.1_RNA	NM_001005181.1	NP_001005181.1	Q8NH76	O56B4_HUMAN	olfactory receptor, family 56, subfamily B, member 4	142						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|endometrium(1)|lung(10)|skin(6)|urinary_tract(2)	21		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.31e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CCCTCCATAGTCACTAAAGCT	0.502																																					p.V142A		Atlas-SNP	.											.	OR56B4	50	.	0			c.T425C						.						127	112	117					11																	6129433		2201	4296	6497	SO:0001583	missense	196335	exon1			CCATAGTCACTAA	AB065513	CCDS31406.1	11p15.4	2012-08-09			ENSG00000180919	ENSG00000180919		"GPCR / Class A : Olfactory receptors"	15248	protein-coding gene	gene with protein product							Standard	NM_001005181		Approved		uc010qzx.2	Q8NH76	OTTHUMG00000165531	ENST00000316529.3:c.425T>C	chr11.hg19:g.6129433T>C	ENSP00000321196:p.Val142Ala	167.0	0.0		97.0	4.0	NM_001005181	Q6IFD7	Missense_Mutation	SNP	ENST00000316529.3	hg19	CCDS31406.1	.	.	.	.	.	.	.	.	.	.	T	16.10	3.026492	0.54683	.	.	ENSG00000180919	ENST00000316529	T	0.20598	2.06	4.06	4.06	0.47325	GPCR, rhodopsin-like superfamily (1);	0.257961	0.20024	U	0.100857	T	0.39784	0.1091	M	0.64997	1.995	0.27968	N	0.936522	D	0.53619	0.961	P	0.61328	0.887	T	0.18967	-1.0320	10	0.87932	D	0	.	12.9386	0.58329	0.0:0.0:0.0:1.0	.	142	Q8NH76	O56B4_HUMAN	A	142	ENSP00000321196:V142A	ENSP00000321196:V142A	V	+	2	0	OR56B4	6086009	0.991000	0.36638	0.998000	0.56505	0.058000	0.15608	7.628000	0.83189	1.804000	0.52760	0.454000	0.30748	GTC	.	.		0.502	OR56B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384668.1	NM_001005181		C	6129433	T	C	6129433	3	2	259	1	0	0	0	0	1	0	0	0	11147	1667	58	2	427	2	OR56B4	11	6129433	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	907977	6129433	128877083	467	36785										
TRIM3	10612	hgsc.bcm.edu	37	chr11	6472512	6472512	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gcctctcaccttgaacttgcCctcaggggagaagatgctga	11	12	2	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:6472512C>T	ENST00000525074.1	-	8	2084	c.1690G>A	c.(1690-1692)Ggc>Agc	p.G564S	TRIM3_ENST00000536344.1_Missense_Mutation_p.G445S|TRIM3_ENST00000359518.3_Missense_Mutation_p.G564S|TRIM3_ENST00000345851.3_Missense_Mutation_p.G564S|TRIM3_ENST00000537602.1_Missense_Mutation_p.G486S	NM_001248006.1	NP_001234935.1	O75382	TRIM3_HUMAN	tripartite motif containing 3	564					nervous system development (GO:0007399)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|endosome (GO:0005768)	protein C-terminus binding (GO:0008022)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(3)	27		all_lung(207;9.97e-06)|Lung NSC(207;1.74e-05)|Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;9.34e-10)|Lung(200;0.0234)|LUSC - Lung squamous cell carcinoma(625;0.133)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TTGAACTTGCCCTCAGGGGAG	0.557																																					p.G564S	Melanoma(6;5 510 1540 25169 29084)	Atlas-SNP	.											.	TRIM3	67	.	0			c.G1690A						.						110	87	95					11																	6472512		2201	4296	6497	SO:0001583	missense	10612	exon8			ACTTGCCCTCAGG	AF045239	CCDS7764.1, CCDS58115.1	11p15.5	2013-01-09	2011-01-25	2001-11-23	ENSG00000110171	ENSG00000110171		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	10064	protein-coding gene	gene with protein product	"ring finger protein 22", "brain expressed ring finger", "tripartite motif protein TRIM3"	605493	"tripartite motif-containing 3"	RNF22		10391919	Standard	NM_006458		Approved	HAC1, BERP, RNF97	uc009yfd.3	O75382	OTTHUMG00000133405	ENST00000525074.1:c.1690G>A	chr11.hg19:g.6472512C>T	ENSP00000433102:p.Gly564Ser	85.0	0.0		53.0	4.0	NM_001248006	B7Z5E6|F5H2Q8|Q4V9L4|Q9C038|Q9C039	Missense_Mutation	SNP	ENST00000525074.1	hg19	CCDS7764.1	.	.	.	.	.	.	.	.	.	.	C	32	5.110732	0.94292	.	.	ENSG00000110171	ENST00000530899;ENST00000525074;ENST00000545029;ENST00000345851;ENST00000336043;ENST00000537602;ENST00000359518;ENST00000536344	D;D;D;D;D	0.91894	-2.93;-2.93;-2.93;-2.93;-2.93	5.25	5.25	0.73442	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	D	0.96667	0.8912	M	0.88775	2.98	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97137	0.9822	10	0.62326	D	0.03	-21.2117	17.4604	0.87619	0.0:1.0:0.0:0.0	.	445;564	F5H2Q8;O75382	.;TRIM3_HUMAN	S	564;564;564;564;553;486;564;445	ENSP00000433102:G564S;ENSP00000340797:G564S;ENSP00000441091:G486S;ENSP00000352508:G564S;ENSP00000445460:G445S	ENSP00000337094:G553S	G	-	1	0	TRIM3	6429088	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.446000	0.82766	0.563000	0.77884	GGC	.	.		0.557	TRIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384224.2	NM_006458		T	6472512	C	T	6472512	3	4	259	1	0	0	0	0	1	0	0	0	16519	623	22	3	564	3	TRIM3	11	6472512	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	343079	6472512	128534004	468	36786										
ARFIP2	23647	hgsc.bcm.edu	37	chr11	6501223	6501223	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgtggggatgagtccatcacCagagcccccatagccaccag	11	14	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:6501223C>A	ENST00000254584.2	-	3	258	c.175G>T	c.(175-177)Ggt>Tgt	p.G59C	ARFIP2_ENST00000445086.2_Silent_p.L13L|TIMM10B_ENST00000254616.6_5'Flank|ARFIP2_ENST00000396777.3_Missense_Mutation_p.G59C|TIMM10B_ENST00000472836.1_5'Flank|ARFIP2_ENST00000423813.2_Missense_Mutation_p.G21C|TIMM10B_ENST00000530751.1_5'Flank|ARFIP2_ENST00000525235.1_Missense_Mutation_p.G59C	NM_012402.3	NP_036534.1	P53365	ARFP2_HUMAN	ADP-ribosylation factor interacting protein 2	59					actin cytoskeleton organization (GO:0030036)|cellular component movement (GO:0006928)|lamellipodium assembly (GO:0030032)|ruffle organization (GO:0031529)|small GTPase mediated signal transduction (GO:0007264)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	GTP binding (GO:0005525)|GTP-dependent protein binding (GO:0030742)|Rac GTPase binding (GO:0048365)			endometrium(2)|large_intestine(4)|liver(1)|lung(4)|pancreas(1)|prostate(1)|skin(2)	15		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;3.41e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		AGTCCATCACCAGAGCCCCCA	0.527																																					p.G59C	Melanoma(119;796 1674 9049 20480 24794)	Atlas-SNP	.											ARFIP2,right_upper_lobe,carcinoma,0,1	ARFIP2	23	.	0			c.G175T						.						188	181	184					11																	6501223		2201	4296	6497	SO:0001583	missense	23647	exon3			CATCACCAGAGCC	BC000392	CCDS7765.1, CCDS55739.1, CCDS55740.1, CCDS73250.1	11p15	2008-08-01	2008-08-01		ENSG00000132254	ENSG00000132254			17160	protein-coding gene	gene with protein product	"arfaptin 2"	601638				8670882, 9038142	Standard	NM_012402		Approved	POR1	uc010ran.2	P53365	OTTHUMG00000133406	ENST00000254584.2:c.175G>T	chr11.hg19:g.6501223C>A	ENSP00000254584:p.Gly59Cys	76.0	0.0		41.0	3.0	NM_012402	B4DX86|B4E306|D3DQT5	Missense_Mutation	SNP	ENST00000254584.2	hg19	CCDS7765.1	.	.	.	.	.	.	.	.	.	.	C	17.67	3.446162	0.63178	.	.	ENSG00000132254	ENST00000254584;ENST00000396777;ENST00000423813;ENST00000525235	T;T;T	0.78364	-1.09;-1.09;-1.17	5.12	5.12	0.69794	.	0.102417	0.64402	D	0.000003	T	0.78978	0.4369	.	.	.	0.80722	D	1	P;P;P	0.48998	0.918;0.877;0.8	P;B;B	0.46076	0.503;0.436;0.436	T	0.81604	-0.0857	9	0.56958	D	0.05	.	17.125	0.86711	0.0:1.0:0.0:0.0	.	59;59;59	B4DUZ3;E9PPY7;P53365	.;.;ARFP2_HUMAN	C	59;59;21;59	ENSP00000254584:G59C;ENSP00000379998:G59C;ENSP00000398375:G21C	ENSP00000254584:G59C	G	-	1	0	ARFIP2	6457799	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.026000	0.64103	2.373000	0.80994	0.563000	0.77884	GGT	.	.		0.527	ARFIP2-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387044.1	NM_012402		A	6501223	C	A	6501223	3	1	259	1	0	0	0	0	1	0	0	0	855	594	21	3	874	3	ARFIP2	11	6501223	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	28711	6501223	128505293	469	36787										
DNHD1	144132	hgsc.bcm.edu	37	chr11	6561171	6561171	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cggcggttgcagcggtactgGgaagcgcgccagctgcgcct	17	13	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:6561171G>T	ENST00000527990.2	+	16	3486	c.3486G>T	c.(3484-3486)tgG>tgT	p.W1162C	DNHD1_ENST00000254579.6_Missense_Mutation_p.W1162C			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	1162					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		AGCGGTACTGGGAAGCGCGCC	0.592																																					p.W1162C		Atlas-SNP	.											.	DNHD1	198	.	0			c.G3486T						.						57	60	59					11																	6561171		692	1591	2283	SO:0001583	missense	144132	exon18			GTACTGGGAAGCG	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 47", "dynein heavy chain domain 1-like", "coiled-coil domain containing 35"	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.3486G>T	chr11.hg19:g.6561171G>T	ENSP00000436180:p.Trp1162Cys	122.0	0.0		87.0	4.0	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	hg19	CCDS44532.1	.	.	.	.	.	.	.	.	.	.	G	15.22	2.769358	0.49680	.	.	ENSG00000179532	ENST00000254579;ENST00000527990	T;T	0.68765	-0.35;-0.35	5.57	5.57	0.84162	Dynein heavy chain, domain-2 (1);	.	.	.	.	T	0.68622	0.3021	N	0.08118	0	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.76528	-0.2926	9	0.87932	D	0	.	18.3162	0.90221	0.0:0.0:1.0:0.0	.	1162	Q96M86	DNHD1_HUMAN	C	1162	ENSP00000254579:W1162C;ENSP00000436180:W1162C	ENSP00000254579:W1162C	W	+	3	0	DNHD1	6517747	1.000000	0.71417	1.000000	0.80357	0.088000	0.18126	5.613000	0.67688	2.611000	0.88343	0.561000	0.74099	TGG	.	.		0.592	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666		T	6561171	G	T	6561171	3	4	259	1	0	0	0	0	1	0	0	0	4670	1241	43	3	3557	3	DNHD1	11	6561171	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	59948	6561171	128445345	470	36788										
PPFIBP2	8495	hgsc.bcm.edu	37	chr11	7670813	7670813	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	caactacatcatctcagcatCaaatgtgccattcacgtgct	5	13	4	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:7670813C>G	ENST00000299492.4	+	21	2437	c.2049C>G	c.(2047-2049)atC>atG	p.I683M	PPFIBP2_ENST00000528883.1_Missense_Mutation_p.I571M|PPFIBP2_ENST00000530582.1_3'UTR|PPFIBP2_ENST00000533792.1_Missense_Mutation_p.I525M|PPFIBP2_ENST00000530181.1_Missense_Mutation_p.I540M	NM_003621.3	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2 (liprin beta 2)	683	SAM 2. {ECO:0000255|PROSITE- ProRule:PRU00184}.				cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)	DNA binding (GO:0003677)|integrase activity (GO:0008907)			breast(8)|cervix(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				Epithelial(150;2.01e-07)|BRCA - Breast invasive adenocarcinoma(625;0.236)		ATCTCAGCATCAAATGTGCCA	0.453																																					p.I683M		Atlas-SNP	.											.	PPFIBP2	87	.	0			c.C2049G						.						246	247	246					11																	7670813		2201	4296	6497	SO:0001583	missense	8495	exon21			CAGCATCAAATGT	AF034803	CCDS31419.1, CCDS58116.1, CCDS58117.1	11p15.4	2013-01-10			ENSG00000166387	ENSG00000166387		"Sterile alpha motif (SAM) domain containing"	9250	protein-coding gene	gene with protein product		603142				9624153	Standard	NM_003621		Approved	Cclp1	uc001mfj.5	Q8ND30	OTTHUMG00000165617	ENST00000299492.4:c.2049C>G	chr11.hg19:g.7670813C>G	ENSP00000299492:p.Ile683Met	303.0	0.0		199.0	67.0	NM_003621	B7Z433|E9PK77|O75337|Q8WW26	Missense_Mutation	SNP	ENST00000299492.4	hg19	CCDS31419.1	.	.	.	.	.	.	.	.	.	.	C	18.13	3.555140	0.65425	.	.	ENSG00000166387	ENST00000299492;ENST00000537211;ENST00000533792;ENST00000541115;ENST00000528883;ENST00000530181	T;T;T;T	0.67171	-0.25;-0.25;-0.25;-0.25	5.2	3.25	0.37280	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.000000	0.64402	D	0.000001	T	0.72285	0.3441	L	0.50993	1.605	0.45930	D	0.998769	D;D;D;D;D;D	0.89917	1.0;0.973;1.0;0.998;1.0;1.0	D;D;D;D;D;D	0.97110	0.998;0.949;0.995;0.998;0.999;1.0	T	0.72286	-0.4338	10	0.72032	D	0.01	-16.1897	5.3238	0.15895	0.1765:0.6576:0.0:0.1659	.	571;571;606;525;540;683	E9PK77;B7Z433;F5GWB0;E9PP16;E9PMU1;Q8ND30	.;.;.;.;.;LIPB2_HUMAN	M	683;24;525;606;571;540	ENSP00000299492:I683M;ENSP00000436498:I525M;ENSP00000435469:I571M;ENSP00000437321:I540M	ENSP00000299492:I683M	I	+	3	3	PPFIBP2	7627389	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.503000	0.35715	1.269000	0.44280	0.563000	0.77884	ATC	.	.		0.453	PPFIBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385345.2	NM_003621		G	7670813	C	G	7670813	3	3	259	1	0	0	0	0	1	0	0	0	12323	816	29	4	2127	4	PPFIBP2	11	7670813	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	1109642	7670813	127335703	471	36789										
OVCH2	341277	hgsc.bcm.edu	37	chr11	7718054	7718054	+	RNA	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atacattgacaggtaactgtGgtgacaagactcaacatcta	8	8	2	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:7718054G>T	ENST00000533663.1	-	0	0				OVCH2_ENST00000534193.2_RNA|OVCH2_ENST00000454689.1_RNA			Q7RTZ1	OVCH2_HUMAN	ovochymase 2 (gene/pseudogene)							extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			cervix(1)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(2)	15				Epithelial(150;7.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.197)		AGGTAACTGTGGTGACAAGAC	0.473																																					p.H367N		Atlas-SNP	.											.	OVCH2	47	.	0			c.C1099A						.						105	100	102					11																	7718054		1958	4148	6106			341277	exon10			AACTGTGGTGACA	BN000120	CCDS73251.1	11p15.4	2012-10-02	2010-06-08		ENSG00000183378	ENSG00000183378			29970	protein-coding gene	gene with protein product			"ovochymase 2"			12838346	Standard	XM_006718221		Approved	OVTN	uc031pyw.1	Q7RTZ1	OTTHUMG00000165418		chr11.hg19:g.7718054G>T		72.0	0.0		54.0	4.0	NM_198185		Missense_Mutation	SNP	ENST00000533663.1	hg19		.	.	.	.	.	.	.	.	.	.	G	16.08	3.022077	0.54576	.	.	ENSG00000183378	ENST00000454689	T	0.16897	2.31	5.69	5.69	0.88448	CUB (5);	0.172702	0.29015	N	0.013415	T	0.20901	0.0503	L	0.35341	1.055	0.24520	N	0.994167	P	0.48589	0.912	P	0.50049	0.629	T	0.10291	-1.0636	10	0.24483	T	0.36	-15.649	15.3063	0.73995	0.0:0.0:1.0:0.0	.	367	Q7RTZ1	OVCH2_HUMAN	N	367	ENSP00000407158:H367N	ENSP00000407158:H367N	H	-	1	0	OVCH2	7674630	1.000000	0.71417	0.978000	0.43139	0.641000	0.38312	4.061000	0.57485	2.679000	0.91253	0.655000	0.94253	CAC	.	.		0.473	OVCH2-002	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000383928.1	NM_198185		T	7718054	G	T	7718054	1	4	259	0	1	0	0	0	0	0	0	0	11333	1348	47	3		3	OVCH2	11	7718054	RNA	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	47241	7718054	127288462	472	36790										
SCUBE2	57758	hgsc.bcm.edu	37	chr11	9069079	9069079	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tacggagccgcttctcggttCgctttacgatgcagctcagg	12	12	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:9069079C>A	ENST00000309263.3	-	15	1811	c.1739G>T	c.(1738-1740)cGa>cTa	p.R580L	SCUBE2_ENST00000457346.2_Missense_Mutation_p.R609L|SCUBE2_ENST00000450649.2_Missense_Mutation_p.R454L|RP11-467K18.2_ENST00000531592.1_RNA|SCUBE2_ENST00000520467.1_Missense_Mutation_p.R609L			Q9NQ36	SCUB2_HUMAN	signal peptide, CUB domain, EGF-like 2	580						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			breast(1)|endometrium(5)|kidney(3)|large_intestine(15)|liver(1)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	42				all cancers(16;8.57e-09)|Epithelial(150;4.42e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0116)		CTTCTCGGTTCGCTTTACGAT	0.572																																					p.R609L		Atlas-SNP	.											SCUBE2,NS,carcinoma,0,1	SCUBE2	102	.	0			c.G1826T						.						69	56	60					11																	9069079		2201	4296	6497	SO:0001583	missense	57758	exon16			TCGGTTCGCTTTA	AK131552	CCDS7797.1, CCDS7797.2, CCDS53599.1	11p15.4	2014-09-04			ENSG00000175356	ENSG00000175356			30425	protein-coding gene	gene with protein product		611747				12270931, 11528127	Standard	NM_020974		Approved	Cegf1, Cegb1, FLJ16792	uc001mhi.2	Q9NQ36	OTTHUMG00000163880	ENST00000309263.3:c.1739G>T	chr11.hg19:g.9069079C>A	ENSP00000310658:p.Arg580Leu	228.0	0.0		174.0	17.0	NM_020974	Q2NKQ8|Q6ZWI1	Missense_Mutation	SNP	ENST00000309263.3	hg19		.	.	.	.	.	.	.	.	.	.	C	15.36	2.810857	0.50421	.	.	ENSG00000175356	ENST00000457346;ENST00000309263;ENST00000450649;ENST00000520467	D;D;D;D	0.84370	-1.55;-1.65;-1.84;-1.81	5.21	4.28	0.50868	.	0.163887	0.49916	D	0.000133	D	0.85566	0.5726	M	0.73962	2.25	0.43959	D	0.996634	P;P;P	0.51537	0.946;0.664;0.534	P;B;B	0.47118	0.538;0.307;0.228	D	0.86791	0.1985	10	0.87932	D	0	.	9.3048	0.37867	0.0:0.7914:0.0:0.2086	.	454;609;580	Q9NQ36-3;Q9NQ36-2;Q9NQ36	.;.;SCUB2_HUMAN	L	609;580;454;609	ENSP00000390481:R609L;ENSP00000310658:R580L;ENSP00000415187:R454L;ENSP00000429969:R609L	ENSP00000310658:R580L	R	-	2	0	SCUBE2	9025655	0.932000	0.31603	0.974000	0.42286	0.772000	0.43724	1.679000	0.37597	2.603000	0.88011	0.655000	0.94253	CGA	.	.		0.572	SCUBE2-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000385812.2	NM_020974		A	9069079	C	A	9069079	3	1	259	1	0	0	0	0	1	0	0	0	13960	884	31	1	1292	1	SCUBE2	11	9069079	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	1351025	9069079	125937437	473	36791										
INSC	387755	hgsc.bcm.edu	37	chr11	15247245	15247245	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gtcttcctactggcctctgcGgcccttgccaacatcacgtt	8	16	3	0	rs111784838		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:15247245G>T	ENST00000379554.3	+	9	1228	c.1182G>T	c.(1180-1182)gcG>gcT	p.A394A	INSC_ENST00000424273.1_Silent_p.A305A|INSC_ENST00000525218.1_Silent_p.A305A|INSC_ENST00000447214.2_3'UTR|INSC_ENST00000530161.1_Silent_p.A347A|INSC_ENST00000379556.3_Silent_p.A347A|INSC_ENST00000528567.1_Silent_p.A347A	NM_001031853.3	NP_001027024.3	Q1MX18	INSC_HUMAN	inscuteable homolog (Drosophila)	394					establishment of mitotic spindle orientation (GO:0000132)|lung epithelial cell differentiation (GO:0060487)|nervous system development (GO:0007399)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)				NS(2)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(3)|lung(24)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49						TGGCCTCTGCGGCCCTTGCCA	0.512																																					p.A394A		Atlas-SNP	.											.	INSC	104	.	0			c.G1182T						.						67	66	66					11																	15247245		1951	4142	6093	SO:0001819	synonymous_variant	387755	exon9			CTCTGCGGCCCTT	AB231744	CCDS41621.1, CCDS41622.1, CCDS60735.1, CCDS60736.1	11p15.2	2014-02-05			ENSG00000188487	ENSG00000188487			33116	protein-coding gene	gene with protein product	"inscuteable spindle orientation adaptor protein"	610668				16458856	Standard	NM_001031853		Approved		uc001mly.4	Q1MX18	OTTHUMG00000165838	ENST00000379554.3:c.1182G>T	chr11.hg19:g.15247245G>T		96.0	0.0		66.0	4.0	NM_001031853	A0PJX5|Q1MX19|Q3C1V6|Q4AC95|Q4AC96|Q4AC97|Q4AC98	Silent	SNP	ENST00000379554.3	hg19	CCDS41621.1																																																																																			.	G|0.999;A|0.001		0.512	INSC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386590.1	NM_001031853		T	15247245	G	T	15247245	2	4	259	1	0	0	0	0	0	0	0	1	7773	1103	39	1		1	INSC	11	15247245	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	6178166	15247245	119759271	474	36792										
INSC	387755	hgsc.bcm.edu	37	chr11	15262003	15262003	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tctcctacaggcatgtcccgTctcatcgagctctgcagatc	8	15	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:15262003T>C	ENST00000379554.3	+	12	1591	c.1545T>C	c.(1543-1545)cgT>cgC	p.R515R	INSC_ENST00000424273.1_Silent_p.R426R|INSC_ENST00000525218.1_Silent_p.R426R|INSC_ENST00000447214.2_3'UTR|INSC_ENST00000530161.1_Silent_p.R468R|INSC_ENST00000379556.3_Silent_p.R468R|INSC_ENST00000528567.1_Silent_p.R468R	NM_001031853.3	NP_001027024.3	Q1MX18	INSC_HUMAN	inscuteable homolog (Drosophila)	515					establishment of mitotic spindle orientation (GO:0000132)|lung epithelial cell differentiation (GO:0060487)|nervous system development (GO:0007399)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)				NS(2)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(3)|lung(24)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49						GCATGTCCCGTCTCATCGAGC	0.622																																					p.R515R		Atlas-SNP	.											.	INSC	104	.	0			c.T1545C						.						57	60	59					11																	15262003		2022	4177	6199	SO:0001819	synonymous_variant	387755	exon12			GTCCCGTCTCATC	AB231744	CCDS41621.1, CCDS41622.1, CCDS60735.1, CCDS60736.1	11p15.2	2014-02-05			ENSG00000188487	ENSG00000188487			33116	protein-coding gene	gene with protein product	"inscuteable spindle orientation adaptor protein"	610668				16458856	Standard	NM_001031853		Approved		uc001mly.4	Q1MX18	OTTHUMG00000165838	ENST00000379554.3:c.1545T>C	chr11.hg19:g.15262003T>C		165.0	0.0		111.0	5.0	NM_001031853	A0PJX5|Q1MX19|Q3C1V6|Q4AC95|Q4AC96|Q4AC97|Q4AC98	Silent	SNP	ENST00000379554.3	hg19	CCDS41621.1																																																																																			.	.		0.622	INSC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386590.1	NM_001031853		C	15262003	T	C	15262003	2	2	259	1	0	0	0	0	0	0	0	1	7773	1654	58	2		2	INSC	11	15262003	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	14758	15262003	119744513	475	36793										
HPS5	11234	hgsc.bcm.edu	37	chr11	18317630	18317630	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acgggagaaaagtttcattcTtatctgtctcaaacatcact	6	9	5	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:18317630T>C	ENST00000349215.3	-	13	1827	c.1550A>G	c.(1549-1551)aAg>aGg	p.K517R	HPS5_ENST00000396253.3_Missense_Mutation_p.K403R|HPS5_ENST00000438420.2_Missense_Mutation_p.K403R|HPS5_ENST00000352460.3_5'UTR	NM_181507.1	NP_852608.1	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5	517					blood coagulation (GO:0007596)|organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						AGTTTCATTCTTATCTGTCTC	0.378									Hermansky-Pudlak syndrome																												p.K517R		Atlas-SNP	.											HPS5,NS,carcinoma,0,1	HPS5	70	.	0			c.A1550G						.						132	127	129					11																	18317630		2199	4293	6492	SO:0001583	missense	11234	exon13	Familial Cancer Database	HPS, HPS1-8	TCATTCTTATCTG	AB023234	CCDS7836.1, CCDS7837.1	11p14	2014-06-18			ENSG00000110756	ENSG00000110756			17022	protein-coding gene	gene with protein product		607521				10231032, 10094488	Standard	NM_181507		Approved		uc001mod.1	Q9UPZ3	OTTHUMG00000166612	ENST00000349215.3:c.1550A>G	chr11.hg19:g.18317630T>C	ENSP00000265967:p.Lys517Arg	97.0	0.0		72.0	4.0	NM_181507	A8K6J8|A8K8S1|D3DQX9|D3DQY0|O95942|Q8N4U0	Missense_Mutation	SNP	ENST00000349215.3	hg19	CCDS7836.1	.	.	.	.	.	.	.	.	.	.	T	5.721	0.317550	0.10845	.	.	ENSG00000110756	ENST00000396253;ENST00000438420;ENST00000349215	T;T;T	0.49720	0.78;0.78;0.77	5.35	4.23	0.50019	.	0.059785	0.64402	D	0.000002	T	0.19967	0.0480	N	0.11560	0.145	0.80722	D	1	B	0.09022	0.002	B	0.09377	0.004	T	0.16012	-1.0417	10	0.07030	T	0.85	.	3.1692	0.06546	0.0:0.3692:0.0:0.6308	.	517	Q9UPZ3	HPS5_HUMAN	R	403;403;517	ENSP00000379552:K403R;ENSP00000399590:K403R;ENSP00000265967:K517R	ENSP00000265967:K517R	K	-	2	0	HPS5	18274206	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.466000	0.53071	2.035000	0.60131	0.528000	0.53228	AAG	.	.		0.378	HPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390808.1	NM_181507		C	18317630	T	C	18317630	3	2	259	1	0	0	0	0	1	0	0	0	7351	1609	56	2	1883	2	HPS5	11	18317630	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	3055627	18317630	116688886	476	36794										
TSG101	7251	hgsc.bcm.edu	37	chr11	18502150	18502150	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttttgcattagtgccctcagCtggaactgtttacgggacag	11	9	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:18502150C>T	ENST00000251968.3	-	10	1531	c.1116G>A	c.(1114-1116)caG>caA	p.Q372Q	TSG101_ENST00000536719.1_Intron|TSG101_ENST00000357193.3_Silent_p.Q267Q	NM_006292.3	NP_006283.1	Q99816	TS101_HUMAN	tumor susceptibility 101	372	SB. {ECO:0000255|PROSITE- ProRule:PRU00644}.				cell cycle arrest (GO:0007050)|cell division (GO:0051301)|cellular protein modification process (GO:0006464)|endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|keratinocyte differentiation (GO:0030216)|membrane organization (GO:0061024)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell growth (GO:0001558)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|viral budding (GO:0046755)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|multivesicular body (GO:0005771)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	calcium-dependent protein binding (GO:0048306)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transcription corepressor activity (GO:0003714)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)			kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	22						GTGCCCTCAGCTGGAACTGTT	0.443																																					p.Q372Q	GBM(99;1348 1396 8611 26475 50572)	Atlas-SNP	.											.	TSG101	43	.	0			c.G1116A						.						91	86	88					11																	18502150		2199	4293	6492	SO:0001819	synonymous_variant	7251	exon10			CCTCAGCTGGAAC	U82130	CCDS7842.1	11p15	2013-08-22	2013-08-22		ENSG00000074319	ENSG00000074319			15971	protein-coding gene	gene with protein product		601387	"tumor susceptibility gene 10", "tumor susceptibility gene 101"	TSG10		9019400, 9241264	Standard	NM_006292		Approved	VPS23	uc001mor.3	Q99816	OTTHUMG00000167725	ENST00000251968.3:c.1116G>A	chr11.hg19:g.18502150C>T		215.0	0.0		127.0	50.0	NM_006292	Q9BUM5	Silent	SNP	ENST00000251968.3	hg19	CCDS7842.1																																																																																			.	.		0.443	TSG101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395906.1	NM_006292		T	18502150	C	T	18502150	2	4	259	1	0	0	0	0	0	0	0	1	16631	796	28	3		3	TSG101	11	18502150	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	184520	18502150	116504366	477	36795										
SPTY2D1	144108	hgsc.bcm.edu	37	chr11	18655797	18655797	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctatcatgagaatttctctgAagtccatgttgggccgaggc	11	9	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:18655797A>G	ENST00000336349.5	-	1	243	c.8T>C	c.(7-9)tTc>tCc	p.F3S	SPTY2D1_ENST00000543776.1_Intron	NM_194285.2	NP_919261.2	Q68D10	SPT2_HUMAN	SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae)	3										breast(4)|cervix(3)|endometrium(2)|kidney(3)|large_intestine(7)|lung(9)|skin(1)|stomach(1)	30						AATTTCTCTGAAGTCCATGTT	0.567																																					p.F3S		Atlas-SNP	.											.	SPTY2D1	72	.	0			c.T8C						.						154	141	146					11																	18655797		2199	4293	6492	SO:0001583	missense	144108	exon1			TCTCTGAAGTCCA	BX647798	CCDS31441.1	11p15.1	2005-10-28			ENSG00000179119	ENSG00000179119			26818	protein-coding gene	gene with protein product							Standard	NM_194285		Approved	FLJ39441, DKFZp686I068	uc001moy.3	Q68D10	OTTHUMG00000167733	ENST00000336349.5:c.8T>C	chr11.hg19:g.18655797A>G	ENSP00000337991:p.Phe3Ser	95.0	0.0		80.0	4.0	NM_194285	Q6AWA5|Q6MZI5|Q7Z390|Q7Z470|Q86VG8|Q8N3E7|Q8N417|Q8N8I3	Missense_Mutation	SNP	ENST00000336349.5	hg19	CCDS31441.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.067782	0.76301	.	.	ENSG00000179119	ENST00000336349;ENST00000333429	T	0.38722	1.12	5.65	5.65	0.86999	.	0.160682	0.56097	D	0.000029	T	0.57388	0.2050	L	0.49778	1.585	0.52501	D	0.999957	D	0.71674	0.998	D	0.78314	0.991	T	0.59773	-0.7391	10	0.87932	D	0	-9.5335	12.1892	0.54261	1.0:0.0:0.0:0.0	.	3	Q68D10	SPT2_HUMAN	S	3	ENSP00000337991:F3S	ENSP00000331447:F3S	F	-	2	0	SPTY2D1	18612373	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.944000	0.56629	2.371000	0.80710	0.533000	0.62120	TTC	.	.		0.567	SPTY2D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395941.1	NM_194285		G	18655797	A	G	18655797	3	3	259	1	0	0	0	0	1	0	0	0	15141	246	9	2	2073	2	SPTY2D1	11	18655797	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	153647	18655797	116350719	478	36796										
IGSF22	283284	hgsc.bcm.edu	37	chr11	18735929	18735929	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gatgagcttgtgcactgcacCctgcttcacaatctgcatgc	9	13	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:18735929C>A	ENST00000513874.1	-	13	1832	c.1693G>T	c.(1693-1695)Ggt>Tgt	p.G565C	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	565										NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						TGCACTGCACCCTGCTTCACA	0.582																																					p.G565C		Atlas-SNP	.											.	IGSF22	211	.	0			c.G1693T						.						101	106	105					11																	18735929		2082	4200	6282	SO:0001583	missense	283284	exon13			CTGCACCCTGCTT	AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	26750	protein-coding gene	gene with protein product							Standard	NM_173588		Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.1693G>T	chr11.hg19:g.18735929C>A	ENSP00000421191:p.Gly565Cys	98.0	0.0		99.0	4.0	NM_173588	A6NNA0|D6RGV7	Missense_Mutation	SNP	ENST00000513874.1	hg19	CCDS41625.2	.	.	.	.	.	.	.	.	.	.	C	17.16	3.319693	0.60524	.	.	ENSG00000179057	ENST00000513874	T	0.51817	0.69	4.42	3.51	0.40186	.	0.000000	0.37437	U	0.002097	T	0.64034	0.2562	M	0.72479	2.2	0.31587	N	0.654372	D	0.89917	1.0	D	0.87578	0.998	T	0.69243	-0.5196	10	0.87932	D	0	.	9.3646	0.38217	0.0:0.8962:0.0:0.1038	.	565	D6RGV7	.	C	565	ENSP00000421191:G565C	ENSP00000322422:G565C	G	-	1	0	IGSF22	18692505	1.000000	0.71417	0.971000	0.41717	0.811000	0.45836	3.997000	0.57016	0.861000	0.35504	0.551000	0.68910	GGT	.	.		0.582	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588		A	18735929	C	A	18735929	3	1	259	1	0	0	0	0	1	0	0	0	7609	623	22	3	2331	3	IGSF22	11	18735929	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	80132	18735929	116270587	479	36797										
PTPN5	84867	hgsc.bcm.edu	37	chr11	18754887	18754887	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctgacgatgggtccctgagtGgcgatgtacaccttctcctc	11	13	1	2	rs144666949		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:18754887G>A	ENST00000358540.2	-	11	1543	c.1113C>T	c.(1111-1113)gcC>gcT	p.A371A	PTPN5_ENST00000477854.1_Silent_p.A175A|PTPN5_ENST00000396168.1_Silent_p.A347A|PTPN5_ENST00000396166.3_5'Flank|RP11-1081L13.4_ENST00000527285.1_RNA|PTPN5_ENST00000396167.2_Silent_p.A339A|PTPN5_ENST00000396171.4_Silent_p.A371A|PTPN5_ENST00000396170.1_Silent_p.A339A	NM_006906.1	NP_008837.1	P54829	PTN5_HUMAN	protein tyrosine phosphatase, non-receptor type 5 (striatum-enriched)	371	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	phosphotyrosine binding (GO:0001784)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(13)|ovary(2)|prostate(1)|skin(4)	27						GTCCCTGAGTGGCGATGTACA	0.612																																					p.A371A		Atlas-SNP	.											.	PTPN5	163	.	0			c.C1113T						.	G	,,	1,4397	2.1+/-5.4	0,1,2198	180	143	155		1017,1113,1113	4.5	1	11	dbSNP_134	155	0,8586		0,0,4293	no	coding-synonymous,coding-synonymous,coding-synonymous	PTPN5	NM_001039970.1,NM_006906.1,NM_032781.3	,,	0,1,6491	AA,AG,GG		0.0,0.0227,0.0077	,,	339/534,371/566,371/566	18754887	1,12983	2199	4293	6492	SO:0001819	synonymous_variant	84867	exon11			CTGAGTGGCGATG	BC064807	CCDS7845.1, CCDS41626.1, CCDS60746.1	11p15.1	2011-06-09			ENSG00000110786	ENSG00000110786		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9657	protein-coding gene	gene with protein product		176879				1714595	Standard	NM_001278236		Approved	STEP, PTPSTEP	uc001mpc.4	P54829	OTTHUMG00000134304	ENST00000358540.2:c.1113C>T	chr11.hg19:g.18754887G>A		95.0	0.0		86.0	27.0	NM_032781	B3KXG7|B7Z386|B7ZAF5|D3DQY7|Q6P1Z2|Q8N2A1|Q8NDP8	Silent	SNP	ENST00000358540.2	hg19	CCDS7845.1																																																																																			.	G|1.000;A|0.000		0.612	PTPN5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259196.2	NM_001039970		A	18754887	G	A	18754887	2	1	259	1	0	0	0	0	0	0	0	1	12806	1335	47	3		3	PTPN5	11	18754887	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	18958	18754887	116251629	480	36798										
FBXO3	26273	hgsc.bcm.edu	37	chr11	33763518	33763518	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agactctcctccgtctctccTcttcatcatcttcatctgat	3	16	8	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:33763518T>C	ENST00000265651.3	-	11	1370	c.1352A>G	c.(1351-1353)gAg>gGg	p.E451G	FBXO3_ENST00000526785.1_Missense_Mutation_p.E338G|FBXO3_ENST00000532057.1_Missense_Mutation_p.E138G|FBXO3_ENST00000531080.1_Missense_Mutation_p.E138G|FBXO3_ENST00000530401.1_3'UTR	NM_012175.3	NP_036307.2	Q9UK99	FBX3_HUMAN	F-box protein 3	451	Asp/Glu-rich (highly acidic).				proteolysis (GO:0006508)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|pancreas(1)|stomach(1)	13		Lung NSC(402;0.0804)		BRCA - Breast invasive adenocarcinoma(625;0.00315)|Lung(977;0.00488)|LUSC - Lung squamous cell carcinoma(625;0.008)		CCGTCTCTCCTCTTCATCATC	0.473																																					p.E451G		Atlas-SNP	.											.	FBXO3	37	.	0			c.A1352G						.						228	173	192					11																	33763518		2202	4298	6500	SO:0001583	missense	26273	exon11			CTCTCCTCTTCAT	AK001943	CCDS7887.1, CCDS44566.1	11p13	2006-07-07	2004-06-15		ENSG00000110429	ENSG00000110429		"F-boxes /  "other""	13582	protein-coding gene	gene with protein product		609089	"F-box only protein 3"			10531037	Standard	NM_033406		Approved	FBX3, FBA	uc001muz.3	Q9UK99	OTTHUMG00000166244	ENST00000265651.3:c.1352A>G	chr11.hg19:g.33763518T>C	ENSP00000265651:p.Glu451Gly	113.0	0.0		78.0	4.0	NM_012175	B3KY16|D3DR05|Q86X90|Q9H0V2|Q9NUX2	Missense_Mutation	SNP	ENST00000265651.3	hg19	CCDS7887.1	.	.	.	.	.	.	.	.	.	.	T	13.15	2.151073	0.38021	.	.	ENSG00000110429	ENST00000526785;ENST00000265651;ENST00000531080;ENST00000532057	T;T;T;T	0.33865	1.39;1.39;1.39;1.39	3.69	3.69	0.42338	.	0.135863	0.34067	N	0.004282	T	0.35451	0.0932	N	0.14661	0.345	0.80722	D	1	P	0.39094	0.659	P	0.55391	0.775	T	0.20907	-1.0261	10	0.48119	T	0.1	-14.3224	9.0552	0.36401	0.0:0.0:0.0:1.0	.	451	Q9UK99	FBX3_HUMAN	G	338;451;138;138	ENSP00000435680:E338G;ENSP00000265651:E451G;ENSP00000435165:E138G;ENSP00000434001:E138G	ENSP00000265651:E451G	E	-	2	0	FBXO3	33720094	0.975000	0.34042	0.979000	0.43373	0.830000	0.47004	1.729000	0.38115	1.897000	0.54924	0.459000	0.35465	GAG	.	.		0.473	FBXO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388665.1	NM_012175		C	33763518	T	C	33763518	3	2	259	1	0	0	0	0	1	0	0	0	5747	1551	54	2	67	2	FBXO3	11	33763518	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	15008631	33763518	101242998	481	36799										
NAT10	55226	hgsc.bcm.edu	37	chr11	34152409	34152409	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tcaagctaattcagcagctcCgtcaacagagcgcccagagc	9	14	3	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:34152409C>A	ENST00000257829.3	+	13	1500	c.1294C>A	c.(1294-1296)Cgt>Agt	p.R432S	NAT10_ENST00000527971.1_Intron|NAT10_ENST00000531159.2_Missense_Mutation_p.R360S	NM_024662.2	NP_078938	Q9H0A0	NAT10_HUMAN	N-acetyltransferase 10 (GCN5-related)	432						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|N-acetyltransferase activity (GO:0008080)|poly(A) RNA binding (GO:0044822)			endometrium(4)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	23		Acute lymphoblastic leukemia(5;0.0119)|all_hematologic(20;0.0231)				TCAGCAGCTCCGTCAACAGAG	0.557																																					p.R432S		Atlas-SNP	.											.	NAT10	78	.	0			c.C1294A						.						109	100	103					11																	34152409		2202	4298	6500	SO:0001583	missense	55226	exon13			CAGCTCCGTCAAC	AF489535	CCDS7889.1, CCDS44568.1	11p13	2011-11-16	2008-09-24		ENSG00000135372	ENSG00000135372	2.3.1.-		29830	protein-coding gene	gene with protein product		609221	"N-acetyltransferase 10"			14592445, 21177859	Standard	NM_024662		Approved	hALP, FLJ10774, FLJ12179, NET43, KIAA1709	uc001mvk.3	Q9H0A0	OTTHUMG00000166249	ENST00000257829.3:c.1294C>A	chr11.hg19:g.34152409C>A	ENSP00000257829:p.Arg432Ser	100.0	0.0		94.0	5.0	NM_024662	B4DFD5|E7ESU4|E9PMN9|Q86WK5|Q9C0F4|Q9HA61|Q9NVF2	Missense_Mutation	SNP	ENST00000257829.3	hg19	CCDS7889.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.442045	0.83993	.	.	ENSG00000135372	ENST00000257829;ENST00000531159	T;T	0.44083	0.93;0.93	5.53	5.53	0.82687	Domain of unknown function DUF699, exodeoxyribonuclease V alpha chain (1);	0.000000	0.85682	D	0.000000	T	0.68220	0.2977	M	0.79805	2.47	0.80722	D	1	D	0.76494	0.999	D	0.74348	0.983	T	0.69235	-0.5198	10	0.52906	T	0.07	-14.4578	19.8251	0.96614	0.0:1.0:0.0:0.0	.	432	Q9H0A0	NAT10_HUMAN	S	432;360	ENSP00000257829:R432S;ENSP00000433011:R360S	ENSP00000257829:R432S	R	+	1	0	NAT10	34108985	0.998000	0.40836	0.994000	0.49952	0.997000	0.91878	3.745000	0.55119	2.763000	0.94921	0.561000	0.74099	CGT	.	.		0.557	NAT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388693.1	NM_024662		A	34152409	C	A	34152409	3	1	259	1	0	0	0	0	1	0	0	0	10183	652	23	1	1340	1	NAT10	11	34152409	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	388891	34152409	100854107	482	36800										
CD82	3732	hgsc.bcm.edu	37	chr11	44639811	44639811	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cctgttcctgcgaagtcaagGgggaagaggacaacagcctt	13	10	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:44639811G>T	ENST00000227155.4	+	8	786	c.538G>T	c.(538-540)Ggg>Tgg	p.G180W	CD82_ENST00000530931.1_3'UTR|CD82_ENST00000342935.3_Missense_Mutation_p.G155W	NM_002231.3	NP_002222.1	P27701	CD82_HUMAN	CD82 molecule	180						extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				large_intestine(1)|ovary(1)	2						CGAAGTCAAGGGGGAAGAGGA	0.597																																					p.G180W		Atlas-SNP	.											.	CD82	27	.	0			c.G538T						.						68	60	63					11																	44639811		2203	4299	6502	SO:0001583	missense	3732	exon8			GTCAAGGGGGAAG	U20770	CCDS7909.1, CCDS31469.1	11p11.2	2013-02-14	2006-03-28	2005-03-03		ENSG00000085117		"CD molecules", "Tetraspanins"	6210	protein-coding gene	gene with protein product	"suppression of tumorigenicity 6", "R2 leukocyte antigen"	600623	"kangai 1 (suppression of tumorigenicity 6, prostate; CD82 antigen (R2 leukocyte antigen, antigen detected by monoclonal and antibody IA4))", "CD82 antigen"	ST6, KAI1			Standard	XM_006718222		Approved	R2, IA4, TSPAN27	uc001myc.3	P27701		ENST00000227155.4:c.538G>T	chr11.hg19:g.44639811G>T	ENSP00000227155:p.Gly180Trp	115.0	0.0		91.0	4.0	NM_002231	D3DQN6|E9PC70|Q7Z2D4|Q7Z5N2	Missense_Mutation	SNP	ENST00000227155.4	hg19	CCDS7909.1	.	.	.	.	.	.	.	.	.	.	G	15.89	2.967788	0.53507	.	.	ENSG00000085117	ENST00000227155;ENST00000342935	T;T	0.51325	0.96;0.71	4.86	-5.09	0.02920	Tetraspanin, EC2 domain (1);	.	.	.	.	T	0.40522	0.1120	N	0.24115	0.695	0.09310	N	1	P;D	0.59767	0.733;0.986	P;P	0.58520	0.84;0.799	T	0.38672	-0.9650	9	0.72032	D	0.01	.	4.489	0.11805	0.5078:0.0:0.2271:0.2651	.	155;180	E9PC70;P27701	.;CD82_HUMAN	W	180;155	ENSP00000227155:G180W;ENSP00000339686:G155W	ENSP00000227155:G180W	G	+	1	0	CD82	44596387	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-2.311000	0.01128	-0.657000	0.05373	-0.258000	0.10820	GGG	.	.		0.597	CD82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389886.1			T	44639811	G	T	44639811	3	4	259	1	0	0	0	0	1	0	0	0	3042	1232	43	3	560	3	CD82	11	44639811	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	10487402	44639811	90366705	483	36801										
AMBRA1	55626	hgsc.bcm.edu	37	chr11	46569854	46569854	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccagctcctgcagaagccgcTgagctcccatggcccgagca	11	17	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:46569854T>C	ENST00000458649.2	-	2	495	c.77A>G	c.(76-78)cAg>cGg	p.Q26R	AMBRA1_ENST00000534300.1_Missense_Mutation_p.Q26R|AMBRA1_ENST00000426438.1_Missense_Mutation_p.Q26R|AMBRA1_ENST00000533727.1_Missense_Mutation_p.Q26R|AMBRA1_ENST00000528950.1_Missense_Mutation_p.Q26R|AMBRA1_ENST00000298834.3_Missense_Mutation_p.Q26R|AMBRA1_ENST00000314845.3_Missense_Mutation_p.Q26R			Q9C0C7	AMRA1_HUMAN	autophagy/beclin-1 regulator 1	26					autophagy (GO:0006914)|cell differentiation (GO:0030154)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neural tube development (GO:0021915)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|phagocytic vesicle (GO:0045335)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	39				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)		CAGAAGCCGCTGAGCTCCCAT	0.537																																					p.Q26R		Atlas-SNP	.											.	AMBRA1	201	.	0			c.A77G						.						172	187	182					11																	46569854		2201	4299	6500	SO:0001583	missense	55626	exon2			AGCCGCTGAGCTC	AB051523	CCDS31475.1, CCDS58132.1, CCDS73281.1	11p11.2	2013-01-09			ENSG00000110497	ENSG00000110497		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	25990	protein-coding gene	gene with protein product	"WD repeat domain 94", "DDB1 and CUL4 associated factor 3"	611359				17622796, 17603510, 17589504	Standard	NM_001267782		Approved	FLJ20294, KIAA1736, WDR94, DCAF3	uc001ncv.3	Q9C0C7	OTTHUMG00000166500	ENST00000458649.2:c.77A>G	chr11.hg19:g.46569854T>C	ENSP00000415327:p.Gln26Arg	160.0	0.0		97.0	5.0	NM_001267783	A6XN33|D3DQP8|G3V193|Q86XD6|Q9H8Z0|Q9NXE7	Missense_Mutation	SNP	ENST00000458649.2	hg19		.	.	.	.	.	.	.	.	.	.	T	21.0	4.075037	0.76415	.	.	ENSG00000110497	ENST00000314845;ENST00000533727;ENST00000534300;ENST00000426438;ENST00000298834;ENST00000314823;ENST00000458649;ENST00000528950	T;T;T;T;T;T;T	0.70282	-0.31;-0.47;-0.19;-0.31;-0.19;-0.29;-0.31	6.08	6.08	0.98989	.	0.104010	0.64402	D	0.000002	T	0.75547	0.3864	N	0.22421	0.69	0.58432	D	0.999998	D;D;D;D;D;D	0.63046	0.987;0.992;0.992;0.992;0.992;0.992	D;D;D;D;D;D	0.72982	0.953;0.979;0.979;0.979;0.979;0.979	T	0.77239	-0.2661	10	0.49607	T	0.09	.	16.6512	0.85203	0.0:0.0:0.0:1.0	.	26;26;26;26;26;26	Q9C0C7;Q9C0C7-3;Q9C0C7-2;G3V193;Q9C0C7-5;Q9C0C7-4	AMRA1_HUMAN;.;.;.;.;.	R	26	ENSP00000318313:Q26R;ENSP00000433372:Q26R;ENSP00000431926:Q26R;ENSP00000410899:Q26R;ENSP00000298834:Q26R;ENSP00000415327:Q26R;ENSP00000433945:Q26R	ENSP00000298834:Q26R	Q	-	2	0	AMBRA1	46526430	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.331000	0.79192	2.333000	0.79357	0.482000	0.46254	CAG	.	.		0.537	AMBRA1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000390103.1	NM_017749		C	46569854	T	C	46569854	3	2	259	1	0	0	0	0	1	0	0	0	565	1580	55	2	3621	2	AMBRA1	11	46569854	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1930043	46569854	88436662	484	36802										
FNBP4	23360	hgsc.bcm.edu	37	chr11	47755663	47755663	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tttacttgtcagggtatttgCcagttctccaatctgaaact	7	9	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:47755663C>T	ENST00000263773.5	-	10	1612	c.1600G>A	c.(1600-1602)Gca>Aca	p.A534T	FNBP4_ENST00000534003.1_5'UTR	NM_015308.2	NP_056123.2	Q8N3X1	FNBP4_HUMAN	formin binding protein 4	534						nucleus (GO:0005634)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	44						AGGGTATTTGCCAGTTCTCCA	0.323																																					p.A534T		Atlas-SNP	.											.	FNBP4	99	.	0			c.G1600A						.						107	101	103					11																	47755663		1827	4084	5911	SO:0001583	missense	23360	exon10			TATTTGCCAGTTC	BC037404	CCDS41644.1	11q12.1	2008-02-05			ENSG00000109920	ENSG00000109920			19752	protein-coding gene	gene with protein product		615265				10231032	Standard	NM_015308		Approved	KIAA1014	uc009ylv.3	Q8N3X1	OTTHUMG00000166533	ENST00000263773.5:c.1600G>A	chr11.hg19:g.47755663C>T	ENSP00000263773:p.Ala534Thr	73.0	0.0		74.0	4.0	NM_015308	Q9H985|Q9NT81|Q9Y2L7	Missense_Mutation	SNP	ENST00000263773.5	hg19	CCDS41644.1	.	.	.	.	.	.	.	.	.	.	C	36	5.658373	0.96734	.	.	ENSG00000109920	ENST00000263773	T	0.11063	2.81	6.02	6.02	0.97574	.	0.089636	0.85682	D	0.000000	T	0.24812	0.0602	L	0.27053	0.805	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.00613	-1.1644	10	0.54805	T	0.06	-24.6893	20.5373	0.99239	0.0:1.0:0.0:0.0	.	534	Q8N3X1	FNBP4_HUMAN	T	534	ENSP00000263773:A534T	ENSP00000263773:A534T	A	-	1	0	FNBP4	47712239	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.796000	0.85898	2.857000	0.98124	0.650000	0.86243	GCA	.	.		0.323	FNBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390237.3			T	47755663	C	T	47755663	3	4	259	1	0	0	0	0	1	0	0	0	5975	739	26	3	1485	3	FNBP4	11	47755663	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	1185809	47755663	87250853	485	36803										
SPRYD5	84767	hgsc.bcm.edu	37	chr11	55653258	55653258	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgtttgccgtgctccaactcTcaggagcaccggaatcacat	9	13	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:55653258T>C	ENST00000449290.2	+	2	446	c.354T>C	c.(352-354)tcT>tcC	p.S118S	TRIM51_ENST00000244891.3_5'Flank	NM_032681.3	NP_116070.2	Q9BSJ1	TRI51_HUMAN	tripartite motif-containing 51	118						intracellular (GO:0005622)	zinc ion binding (GO:0008270)										GCTCCAACTCTCAGGAGCACC	0.498																																					p.S118S		Atlas-SNP	.											.	.	.	.	0			c.T354C						.						18	17	17					11																	55653258		692	1591	2283	SO:0001819	synonymous_variant	84767	exon2			CAACTCTCAGGAG	BC005014		11p11	2013-01-09	2012-05-18	2012-05-18	ENSG00000124900	ENSG00000124900		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19023	protein-coding gene	gene with protein product			"SPRY domain containing 5"	SPRYD5			Standard	NM_032681		Approved	TRIM51A	uc010rip.2	Q9BSJ1	OTTHUMG00000156437	ENST00000449290.2:c.354T>C	chr11.hg19:g.55653258T>C		158.0	0.0		96.0	5.0	NM_032681	A6NMG2	Silent	SNP	ENST00000449290.2	hg19																																																																																				.	.		0.498	TRIM51-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000391522.1	NM_032681		C	55653258	T	C	55653258	2	2	259	1	0	0	0	0	0	0	0	1	15126	1538	54	2		2	SPRYD5	11	55653258	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	7897595	55653258	79353258	486	36804										
OR8J1	219477	hgsc.bcm.edu	37	chr11	56128618	56128618	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cctgaggaataaggatgtgaAgactgctctacagagattca	11	7	2	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:56128618A>G	ENST00000303039.3	+	1	928	c.896A>G	c.(895-897)aAg>aGg	p.K299R		NM_001005205.2	NP_001005205.2	Q8NGP2	OR8J1_HUMAN	olfactory receptor, family 8, subfamily J, member 1	299						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	47	Esophageal squamous(21;0.00448)					AAGGATGTGAAGACTGCTCTA	0.373																																					p.K299R		Atlas-SNP	.											.	OR8J1	87	.	0			c.A896G						.						81	73	76					11																	56128618		2201	4296	6497	SO:0001583	missense	219477	exon1			ATGTGAAGACTGC	AB065748	CCDS31529.1	11q11	2012-08-09			ENSG00000172487	ENSG00000172487		"GPCR / Class A : Olfactory receptors"	14855	protein-coding gene	gene with protein product							Standard	NM_001005205		Approved		uc010rjh.2	Q8NGP2	OTTHUMG00000166859	ENST00000303039.3:c.896A>G	chr11.hg19:g.56128618A>G	ENSP00000304060:p.Lys299Arg	119.0	0.0		86.0	4.0	NM_001005205	B2RNQ6|B9EH63|Q6IFC2|Q96RC3	Missense_Mutation	SNP	ENST00000303039.3	hg19	CCDS31529.1	.	.	.	.	.	.	.	.	.	.	A	7.016	0.557679	0.13436	.	.	ENSG00000172487	ENST00000303039	T	0.23552	1.9	3.76	3.76	0.43208	.	0.087193	0.49305	D	0.000141	T	0.17534	0.0421	L	0.31526	0.94	0.21604	N	0.999628	B	0.10296	0.003	B	0.16722	0.016	T	0.14671	-1.0464	10	0.72032	D	0.01	.	6.8501	0.24010	0.8904:0.0:0.1096:0.0	.	299	Q8NGP2	OR8J1_HUMAN	R	299	ENSP00000304060:K299R	ENSP00000304060:K299R	K	+	2	0	OR8J1	55885194	0.852000	0.29690	0.990000	0.47175	0.045000	0.14185	1.513000	0.35823	1.707000	0.51288	0.448000	0.29417	AAG	.	.		0.373	OR8J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391606.2	NM_001005205		G	56128618	A	G	56128618	3	3	259	1	0	0	0	0	1	0	0	0	11250	72	3	2	898	2	OR8J1	11	56128618	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	475360	56128618	78877898	487	36805										
OR5M11	219487	hgsc.bcm.edu	37	chr11	56310189	56310189	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aacaagaaagcttaatgagcGgcgggtcagcacagtagaag	13	7	1	3	rs200285217		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:56310189G>T	ENST00000528616.2	-	1	568	c.545C>A	c.(544-546)cCg>cAg	p.P182Q		NM_001005245.1	NP_001005245.1	Q96RB7	OR5MB_HUMAN	olfactory receptor, family 5, subfamily M, member 11	182						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(14)	18						CTTAATGAGCGGCGGGTCAGC	0.502																																					p.P182Q		Atlas-SNP	.											OR5M11,caecum,carcinoma,0,2	OR5M11	60	.	0			c.C545A						.						46	48	48					11																	56310189		2063	4220	6283	SO:0001583	missense	219487	exon1			ATGAGCGGCGGGT	AP002517	CCDS53629.1	11q11	2012-08-09				ENSG00000255223		"GPCR / Class A : Olfactory receptors"	15291	protein-coding gene	gene with protein product							Standard	NM_001005245		Approved	OR11-199	uc010rjl.2	Q96RB7		ENST00000528616.2:c.545C>A	chr11.hg19:g.56310189G>T	ENSP00000432417:p.Pro182Gln	146.0	0.0		100.0	4.0	NM_001005245	B2RNL5|B2RNL7	Missense_Mutation	SNP	ENST00000528616.2	hg19	CCDS53629.1	.	.	.	.	.	.	.	.	.	.	A	10.50	1.366503	0.24771	.	.	ENSG00000255223	ENST00000528616	T	0.00137	8.68	4.89	1.97	0.26223	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00328	0.0010	L	0.58969	1.84	0.09310	N	0.999999	D	0.89917	1.0	D	0.85130	0.997	T	0.51679	-0.8675	9	0.87932	D	0	.	7.6395	0.28286	0.1337:0.0:0.6314:0.2349	.	182	Q96RB7	OR5MB_HUMAN	Q	182	ENSP00000432417:P182Q	ENSP00000432417:P182Q	P	-	2	0	OR5M11	56066765	0.003000	0.15002	0.493000	0.27502	0.234000	0.25298	1.152000	0.31663	0.040000	0.15660	-1.789000	0.00628	CCG	.	.		0.502	OR5M11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391608.1	NM_001005245		T	56310189	G	T	56310189	3	4	259	1	0	0	0	0	1	0	0	0	11183	1116	39	1	375	1	OR5M11	11	56310189	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	181571	56310189	78696327	488	36806										
YPEL4	219539	hgsc.bcm.edu	37	chr11	57413535	57413535	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tacttctggctcgtctcaaaAgcttgctcctggtgaaggag	11	10	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:57413535A>G	ENST00000524669.1	-	5	3025	c.303T>C	c.(301-303)gcT>gcC	p.A101A	AP000662.4_ENST00000530595.1_RNA|YPEL4_ENST00000300022.3_Silent_p.A101A|YPEL4_ENST00000531442.1_5'Flank|YPEL4_ENST00000534711.1_Silent_p.A101A|YPEL4_ENST00000544993.1_Silent_p.A101A			Q96NS1	YPEL4_HUMAN	yippee-like 4 (Drosophila)	101						nucleus (GO:0005634)				lung(2)|skin(1)	3						TCGTCTCAAAAGCTTGCTCCT	0.532																																					p.A101A		Atlas-SNP	.											.	YPEL4	5	.	0			c.T303C						.						149	111	124					11																	57413535		2201	4296	6497	SO:0001819	synonymous_variant	219539	exon5			CTCAAAAGCTTGC	AK054775	CCDS7963.1	11q12	2008-02-05				ENSG00000166793			18328	protein-coding gene	gene with protein product		609725					Standard	NM_145008		Approved	FLJ30213	uc001nkv.4	Q96NS1		ENST00000524669.1:c.303T>C	chr11.hg19:g.57413535A>G		93.0	0.0		79.0	5.0	NM_145008	B3KW92|Q2M3U7|Q65Z98	Silent	SNP	ENST00000524669.1	hg19	CCDS7963.1																																																																																			.	.		0.532	YPEL4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393370.1	NM_145008		G	57413535	A	G	57413535	2	3	259	1	0	0	0	0	0	0	0	1	17507	59	3	2		2	YPEL4	11	57413535	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1103346	57413535	77592981	489	36807										
MS4A4A	51338	hgsc.bcm.edu	37	chr11	60073590	60073590	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tagggtctggatggcatggtGctcctcctaagtgtgctgga	15	8	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:60073590G>A	ENST00000337908.4	+	6	654	c.564G>A	c.(562-564)gtG>gtA	p.V188V	MS4A4A_ENST00000355131.3_Silent_p.V169V|MS4A4A_ENST00000532114.1_Silent_p.V135V|MS4A4A_ENST00000395016.3_Silent_p.V169V	NM_148975.2	NP_683876.1	Q96JQ5	M4A4A_HUMAN	membrane-spanning 4-domains, subfamily A, member 4A	188						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(12)|prostate(1)|skin(4)	23						ATGGCATGGTGCTCCTCCTAA	0.463																																					p.V188V		Atlas-SNP	.											.	MS4A4A	76	.	0			c.G564A						.						281	239	253					11																	60073590		2203	4300	6503	SO:0001819	synonymous_variant	51338	exon6			CATGGTGCTCCTC	AB013102	CCDS7982.1, CCDS58135.1	11q12	2012-02-28	2012-02-28		ENSG00000110079	ENSG00000110079			13371	protein-coding gene	gene with protein product		606547	"membrane-spanning 4-domains, subfamily A, member 4"	MS4A4		11245982, 11401424	Standard	NM_148975		Approved	CD20L1, MS4A7	uc001noz.3	Q96JQ5	OTTHUMG00000154949	ENST00000337908.4:c.564G>A	chr11.hg19:g.60073590G>A		675.0	0.0		458.0	95.0	NM_148975	Q8TEZ6|Q96PG7|Q9BY18|Q9H3V3|Q9P1S3	Silent	SNP	ENST00000337908.4	hg19	CCDS7982.1																																																																																			.	.		0.463	MS4A4A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337774.2			A	60073590	G	A	60073590	2	1	259	1	0	0	0	0	0	0	0	1	9871	1306	46	3		3	MS4A4A	11	60073590	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	2660055	60073590	74932926	490	36808										
MS4A8B	83661	hgsc.bcm.edu	37	chr11	60476245	60476245	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cccgactattatccttacgcCtggggtgtggtgagtatccc	11	12	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:60476245C>A	ENST00000300226.2	+	5	728	c.525C>A	c.(523-525)gcC>gcA	p.A175A		NM_031457.1	NP_113645.1	Q9BY19	M4A8_HUMAN	membrane-spanning 4-domains, subfamily A, member 8	175						integral component of membrane (GO:0016021)											ATCCTTACGCCTGGGGTGTGG	0.463																																					p.A175A		Atlas-SNP	.											.	.	.	.	0			c.C525A						.						125	112	116					11																	60476245		2203	4300	6503	SO:0001819	synonymous_variant	83661	exon5			TTACGCCTGGGGT	AF237905	CCDS7990.1	11q12	2013-03-01	2013-03-01	2013-03-01	ENSG00000166959	ENSG00000166959			13380	protein-coding gene	gene with protein product		606549	"membrane-spanning 4-domains, subfamily A, member 8B"	MS4A8B		11245982, 11401424	Standard	NM_031457		Approved	MS4A4, CD20L5	uc001npv.3	Q9BY19	OTTHUMG00000167686	ENST00000300226.2:c.525C>A	chr11.hg19:g.60476245C>A		238.0	0.0		151.0	56.0	NM_031457	Q8TCA5	Silent	SNP	ENST00000300226.2	hg19	CCDS7990.1	.	.	.	.	.	.	.	.	.	.	C	3.417	-0.118946	0.06838	.	.	ENSG00000166959	ENST00000525458	.	.	.	4.0	2.07	0.26955	.	.	.	.	.	T	0.31827	0.0809	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.20107	-1.0285	4	.	.	.	3.6068	6.33	0.21264	0.0:0.7636:0.0:0.2364	.	.	.	.	H	157	.	.	P	+	2	0	MS4A8B	60232821	0.002000	0.14202	0.004000	0.12327	0.097000	0.18754	0.687000	0.25407	0.903000	0.36546	-0.218000	0.12543	CCT	.	.		0.463	MS4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395605.1			A	60476245	C	A	60476245	2	1	259	1	0	0	0	0	0	0	0	1	9876	668	24	3		3	MS4A8B	11	60476245	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	402655	60476245	74530271	491	36809										
PRPF19	27339	hgsc.bcm.edu	37	chr11	60670241	60670241	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cagcagtgacttccttggtgAgacgggcaatgacacggcag	14	10	0	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:60670241A>G	ENST00000227524.4	-	4	564	c.359T>C	c.(358-360)cTc>cCc	p.L120P		NM_014502.4	NP_055317.1			pre-mRNA processing factor 19											haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|urinary_tract(1)	22						TTCCTTGGTGAGACGGGCAAT	0.592																																					p.L120P		Atlas-SNP	.											.	PRPF19	62	.	0			c.T359C						.						63	55	58					11																	60670241		2203	4299	6502	SO:0001583	missense	27339	exon4			TTGGTGAGACGGG	BC018698	CCDS7995.1	11q12.2	2014-05-20	2013-06-10	2005-04-01	ENSG00000110107	ENSG00000110107		"WD repeat domain containing", "U-box domain containing"	17896	protein-coding gene	gene with protein product	"nuclear matrix protein NMP200 related to splicing factor PRP19", "psoralen 4"	608330	"PRP19/PSO4 homolog (S. cerevisiae)", "PRP19/PSO4 pre-mRNA processing factor 19 homolog (S. cerevisiae)"	PRP19		12960389	Standard	NM_014502		Approved	UBOX4, NMP200, PSO4, hPSO4	uc001nqf.3	Q9UMS4	OTTHUMG00000167798	ENST00000227524.4:c.359T>C	chr11.hg19:g.60670241A>G	ENSP00000227524:p.Leu120Pro	121.0	0.0		97.0	4.0	NM_014502		Missense_Mutation	SNP	ENST00000227524.4	hg19	CCDS7995.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.392617	0.83011	.	.	ENSG00000110107	ENST00000227524;ENST00000541371;ENST00000546152	T	0.70749	-0.51	4.62	4.62	0.57501	Pre-mRNA-splicing factor 19 (1);	0.131926	0.52532	D	0.000075	D	0.87083	0.6089	M	0.92367	3.3	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90297	0.4327	10	0.87932	D	0	-22.4155	14.1796	0.65564	1.0:0.0:0.0:0.0	.	120	Q9UMS4	PRP19_HUMAN	P	120;120;35	ENSP00000227524:L120P	ENSP00000227524:L120P	L	-	2	0	PRPF19	60426817	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.547000	0.90665	2.064000	0.61679	0.533000	0.62120	CTC	.	.		0.592	PRPF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396334.1	NM_014502		G	60670241	A	G	60670241	3	3	259	1	0	0	0	0	1	0	0	0	12576	304	11	2	1207	2	PRPF19	11	60670241	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	193996	60670241	74336275	492	36810										
CD6	923	hgsc.bcm.edu	37	chr11	60785418	60785418	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aacccccaggtgttttcttcAgagaggagttccttcctgga	10	11	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:60785418A>G	ENST00000313421.7	+	11	1956	c.1770A>G	c.(1768-1770)tcA>tcG	p.S590S	CD6_ENST00000352009.5_Silent_p.S558S|CD6_ENST00000452451.2_Silent_p.S549S|CD6_ENST00000346437.4_Silent_p.S517S|CD6_ENST00000344028.5_Silent_p.S558S	NM_006725.4	NP_006716.3	P30203	CD6_HUMAN	CD6 molecule	590					cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	scavenger receptor activity (GO:0005044)			endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)	18						TGTTTTCTTCAGAGAGGAGTT	0.577																																					p.S590S	Pancreas(169;904 2017 4767 38890 42505)	Atlas-SNP	.											.	CD6	122	.	0			c.A1770G						.						59	63	62					11																	60785418		2203	4299	6502	SO:0001819	synonymous_variant	923	exon11			TTCTTCAGAGAGG		CCDS7999.1, CCDS58137.1, CCDS58138.1	11q12.2	2006-03-28	2006-03-28		ENSG00000013725	ENSG00000013725		"CD molecules"	1691	protein-coding gene	gene with protein product		186720	"CD6 antigen"			9013954	Standard	NM_006725		Approved	Tp120	uc001nqq.3	P30203	OTTHUMG00000167823	ENST00000313421.7:c.1770A>G	chr11.hg19:g.60785418A>G		81.0	0.0		58.0	4.0	NM_006725	A4KAD4|A4KAD5|Q9UMF2|Q9Y4K7|Q9Y4K8|Q9Y4K9|Q9Y4L0	Silent	SNP	ENST00000313421.7	hg19	CCDS7999.1																																																																																			.	.		0.577	CD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396449.1	NM_006725		G	60785418	A	G	60785418	2	3	259	1	0	0	0	0	0	0	0	1	3030	175	7	2		2	CD6	11	60785418	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	115177	60785418	74221098	493	36811										
AHNAK	79026	hgsc.bcm.edu	37	chr11	62300901	62300901	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gacttcaggtgcagaaacccTcagccctgcctttggtgtct	10	13	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:62300901T>C	ENST00000378024.4	-	5	1262	c.988A>G	c.(988-990)Agg>Ggg	p.R330G	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	330					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				GCAGAAACCCTCAGCCCTGCC	0.542																																					p.R330G		Atlas-SNP	.											.	AHNAK	532	.	0			c.A988G						.						61	65	63					11																	62300901		2202	4299	6501	SO:0001583	missense	79026	exon5			AAACCCTCAGCCC	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.988A>G	chr11.hg19:g.62300901T>C	ENSP00000367263:p.Arg330Gly	106.0	0.0		76.0	4.0	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	hg19	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	T	6.865	0.529006	0.13127	.	.	ENSG00000124942	ENST00000378024	T	0.00730	5.77	5.05	2.36	0.29203	.	1.083490	0.07313	U	0.876171	T	0.00580	0.0019	N	0.03608	-0.345	0.09310	N	1	B	0.24132	0.098	B	0.23716	0.048	T	0.47459	-0.9116	10	0.39692	T	0.17	-0.5385	8.1366	0.31058	0.0:0.1978:0.0:0.8022	.	330	Q09666	AHNK_HUMAN	G	330	ENSP00000367263:R330G	ENSP00000367263:R330G	R	-	1	2	AHNAK	62057477	0.004000	0.15560	0.636000	0.29352	0.484000	0.33280	0.859000	0.27858	0.770000	0.33336	0.528000	0.53228	AGG	.	.		0.542	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		C	62300901	T	C	62300901	3	2	259	1	0	0	0	0	1	0	0	0	414	1550	54	2	16804	2	AHNAK	11	62300901	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1515483	62300901	72705615	494	36812										
ZBTB3	79842	hgsc.bcm.edu	37	chr11	62520653	62520653	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tttgccccagtggcctgatgTctcagcagatgccaacgaag	11	12	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:62520653T>C	ENST00000394807.3	-	2	759	c.634A>G	c.(634-636)Aca>Gca	p.T212A		NM_024784.3	NP_079060.1	Q9H5J0	ZBTB3_HUMAN	zinc finger and BTB domain containing 3	212					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(9)|ovary(2)|prostate(2)	24						TGGCCTGATGTCTCAGCAGAT	0.542																																					p.T212A		Atlas-SNP	.											.	ZBTB3	47	.	0			c.A634G						.						99	84	89					11																	62520653		2202	4299	6501	SO:0001583	missense	79842	exon2			CTGATGTCTCAGC	AK027045	CCDS8034.1	11q12.3	2013-01-09				ENSG00000185670		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	22918	protein-coding gene	gene with protein product							Standard	NM_024784		Approved	FLJ23392	uc001nuz.3	Q9H5J0		ENST00000394807.3:c.634A>G	chr11.hg19:g.62520653T>C	ENSP00000378286:p.Thr212Ala	93.0	0.0		94.0	4.0	NM_024784		Missense_Mutation	SNP	ENST00000394807.3	hg19	CCDS8034.1	.	.	.	.	.	.	.	.	.	.	T	0.039	-1.291688	0.01375	.	.	ENSG00000185670	ENST00000394807	T	0.11495	2.77	5.22	2.7	0.31948	.	0.893105	0.09879	N	0.743895	T	0.05547	0.0146	N	0.14661	0.345	0.19945	N	0.999942	B	0.22800	0.075	B	0.19946	0.027	T	0.45264	-0.9273	10	0.07644	T	0.81	.	6.4125	0.21698	0.1467:0.0:0.4211:0.4322	.	212	Q9H5J0	ZBTB3_HUMAN	A	212	ENSP00000378286:T212A	ENSP00000378286:T212A	T	-	1	0	ZBTB3	62277229	0.004000	0.15560	0.996000	0.52242	0.480000	0.33159	0.285000	0.18883	0.334000	0.23590	0.459000	0.35465	ACA	.	.		0.542	ZBTB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395342.1	NM_024784		C	62520653	T	C	62520653	3	2	259	1	0	0	0	0	1	0	0	0	17549	1667	58	2	1094	2	ZBTB3	11	62520653	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	219752	62520653	72485863	495	36813										
RCOR2	283248	hgsc.bcm.edu	37	chr11	63680389	63680389	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gccctccagggcttggcgcaGgctgctgttcgtctgcttca	13	14	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:63680389G>A	ENST00000301459.4	-	9	1309	c.922C>T	c.(922-924)Ctg>Ttg	p.L308L	RCOR2_ENST00000473926.2_5'Flank	NM_173587.3	NP_775858.2	Q8IZ40	RCOR2_HUMAN	REST corepressor 2	308					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			kidney(2)|large_intestine(3)|liver(1)|lung(5)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	17						GCTTGGCGCAGGCTGCTGTTC	0.587																																					p.L308L		Atlas-SNP	.											.	RCOR2	43	.	0			c.C922T						.						56	44	48					11																	63680389		2201	4297	6498	SO:0001819	synonymous_variant	283248	exon9			GGCGCAGGCTGCT	BC010608	CCDS8052.1	11q13.1	2008-02-05			ENSG00000167771	ENSG00000167771			27455	protein-coding gene	gene with protein product						12477932	Standard	NM_173587		Approved		uc001nyc.3	Q8IZ40	OTTHUMG00000150472	ENST00000301459.4:c.922C>T	chr11.hg19:g.63680389G>A		101.0	0.0		54.0	14.0	NM_173587	Q96FP3	Silent	SNP	ENST00000301459.4	hg19	CCDS8052.1																																																																																			.	.		0.587	RCOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318233.1	NM_173587		A	63680389	G	A	63680389	2	1	259	1	0	0	0	0	0	0	0	1	13198	991	35	3		3	RCOR2	11	63680389	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1159736	63680389	71326127	496	36814										
RCOR2	283248	hgsc.bcm.edu	37	chr11	63680410	63680410	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gctgctgttcgtctgcttcaTgctctgtacctgggaaggcc	12	12	3	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:63680410T>C	ENST00000301459.4	-	9	1288	c.901A>G	c.(901-903)Atg>Gtg	p.M301V	RCOR2_ENST00000473926.2_5'Flank	NM_173587.3	NP_775858.2	Q8IZ40	RCOR2_HUMAN	REST corepressor 2	301					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			kidney(2)|large_intestine(3)|liver(1)|lung(5)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	17						GTCTGCTTCATGCTCTGTACC	0.577																																					p.M301V		Atlas-SNP	.											.	RCOR2	43	.	0			c.A901G						.						52	40	44					11																	63680410		2200	4297	6497	SO:0001583	missense	283248	exon9			GCTTCATGCTCTG	BC010608	CCDS8052.1	11q13.1	2008-02-05			ENSG00000167771	ENSG00000167771			27455	protein-coding gene	gene with protein product						12477932	Standard	NM_173587		Approved		uc001nyc.3	Q8IZ40	OTTHUMG00000150472	ENST00000301459.4:c.901A>G	chr11.hg19:g.63680410T>C	ENSP00000301459:p.Met301Val	89.0	0.0		52.0	4.0	NM_173587	Q96FP3	Missense_Mutation	SNP	ENST00000301459.4	hg19	CCDS8052.1	.	.	.	.	.	.	.	.	.	.	T	12.48	1.950469	0.34377	.	.	ENSG00000167771	ENST00000301459	T	0.40476	1.03	4.56	4.56	0.56223	.	0.097021	0.64402	D	0.000001	T	0.20659	0.0497	N	0.03608	-0.345	0.28674	N	0.905484	B	0.02656	0.0	B	0.04013	0.001	T	0.09015	-1.0694	10	0.23891	T	0.37	.	13.3293	0.60477	0.0:0.0:0.0:1.0	.	301	Q8IZ40	RCOR2_HUMAN	V	301	ENSP00000301459:M301V	ENSP00000301459:M301V	M	-	1	0	RCOR2	63436986	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	3.651000	0.54431	2.053000	0.61076	0.459000	0.35465	ATG	.	.		0.577	RCOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318233.1	NM_173587		C	63680410	T	C	63680410	3	2	259	1	0	0	0	0	1	0	0	0	13198	1464	51	2	686	2	RCOR2	11	63680410	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	21	63680410	71326106	497	36815										
C11orf20	25858	hgsc.bcm.edu	37	chr11	64071271	64071271	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctgcccctgatggaactcatGgagaatgaagctctggaaat	11	9	2	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:64071271G>T	ENST00000328404.6	+	4	479	c.459G>T	c.(457-459)atG>atT	p.M153I	TEX40_ENST00000539943.1_Missense_Mutation_p.M111I|RP11-783K16.10_ENST00000539086.1_RNA|ESRRA_ENST00000000442.6_5'Flank|ESRRA_ENST00000406310.1_5'Flank|ESRRA_ENST00000405666.1_5'Flank	NM_001039496.1	NP_001034585.1	Q9NTU4	TEX40_HUMAN	testis expressed 40	153					cell differentiation (GO:0030154)|male meiosis (GO:0007140)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)											TGGAACTCATGGAGAATGAAG	0.572																																					p.M153I		Atlas-SNP	.											.	.	.	.	0			c.G459T						.						32	35	34					11																	64071271		2001	4157	6158	SO:0001583	missense	25858	exon4			ACTCATGGAGAAT			11q13.1	2013-01-11	2013-01-11	2013-01-11	ENSG00000219435	ENSG00000219435			19231	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 20"	C11orf20			Standard	NM_001039496		Approved	DKFZP566E164	uc009ypm.3	Q9NTU4	OTTHUMG00000167820	ENST00000328404.6:c.459G>T	chr11.hg19:g.64071271G>T	ENSP00000330877:p.Met153Ile	127.0	0.0		95.0	4.0	NM_001039496		Missense_Mutation	SNP	ENST00000328404.6	hg19		.	.	.	.	.	.	.	.	.	.	G	14.78	2.638230	0.47153	.	.	ENSG00000219435	ENST00000328404;ENST00000539943	T;T	0.52526	0.66;0.67	4.22	4.22	0.49857	.	.	.	.	.	T	0.56077	0.1961	L	0.29908	0.895	0.29521	N	0.853477	D	0.76494	0.999	D	0.83275	0.996	T	0.52533	-0.8563	9	0.66056	D	0.02	-18.6491	12.29	0.54812	0.0:0.0:1.0:0.0	.	153	Q9NTU4	CK020_HUMAN	I	153;111	ENSP00000330877:M153I;ENSP00000443917:M111I	ENSP00000330877:M153I	M	+	3	0	C11orf20	63827847	1.000000	0.71417	1.000000	0.80357	0.833000	0.47200	4.427000	0.59888	2.365000	0.80145	0.555000	0.69702	ATG	.	.		0.572	TEX40-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001039496		T	64071271	G	T	64071271	3	4	259	1	0	0	0	0	1	0	0	0	1636	1348	47	3	473	3	C11orf20	11	64071271	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	390861	64071271	70935245	498	36816										
SLC22A11	55867	hgsc.bcm.edu	37	chr11	64323631	64323631	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	accgatgctggacacacatgCtggacaatggctctgcggtt	12	11	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:64323631C>T	ENST00000301891.4	+	1	534	c.160C>T	c.(160-162)Ctg>Ttg	p.L54L	SLC22A11_ENST00000377585.3_Silent_p.L54L|SLC22A11_ENST00000490834.1_3'UTR|SLC22A11_ENST00000377581.3_Silent_p.L54L	NM_018484.2	NP_060954.1	Q9NSA0	S22AB_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 11	54					organic anion transport (GO:0015711)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|organic anion transmembrane transporter activity (GO:0008514)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	23					Aminohippurate(DB00345)|Aspartame(DB00168)|Benzylpenicillin(DB01053)|Bumetanide(DB00887)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefazolin(DB01327)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Ceftriaxone(DB01212)|Cimetidine(DB00501)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Doxycycline(DB00254)|Estradiol(DB00783)|Furosemide(DB00695)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Methotrexate(DB00563)|Minocycline(DB01017)|Novobiocin(DB01051)|Oxytetracycline(DB00595)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pravastatin(DB00175)|Probenecid(DB01032)|Salicylic acid(DB00936)|Tetracycline(DB00759)|Zidovudine(DB00495)	GACACACATGCTGGACAATGG	0.622											OREG0004031	type=REGULATORY REGION|Gene=SLC22A11|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.L54L		Atlas-SNP	.											.	SLC22A11	54	.	0			c.C160T						.						170	148	155					11																	64323631		2201	4297	6498	SO:0001819	synonymous_variant	55867	exon1			CACATGCTGGACA	AB026116	CCDS8074.1	11q13.3	2013-05-22	2008-01-11		ENSG00000168065	ENSG00000168065		"Solute carriers"	18120	protein-coding gene	gene with protein product		607097				10660625, 15576633, 17229912	Standard	NM_018484		Approved	OAT4	uc001oai.3	Q9NSA0	OTTHUMG00000045142	ENST00000301891.4:c.160C>T	chr11.hg19:g.64323631C>T		177.0	0.0	1075	90.0	34.0	NM_018484	A8K426|Q53GR2|Q6ZP72|Q8NBU4	Silent	SNP	ENST00000301891.4	hg19	CCDS8074.1																																																																																			.	.		0.622	SLC22A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104886.4	NM_018484		T	64323631	C	T	64323631	2	4	259	1	0	0	0	0	0	0	0	1	14457	796	28	3		3	SLC22A11	11	64323631	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	252360	64323631	70682885	499	36817										
NRXN2	9379	hgsc.bcm.edu	37	chr11	64436058	64436058	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gcctgtggtggtcaggatccCgtccaccgagatggtcacct	13	13	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:64436058C>A	ENST00000377551.1	-	7	1427	c.1216G>T	c.(1216-1218)Ggg>Tgg	p.G406W	NRXN2_ENST00000377559.3_Missense_Mutation_p.G375W|NRXN2_ENST00000265459.6_Missense_Mutation_p.G406W|NRXN2_ENST00000409571.1_Missense_Mutation_p.G399W			Q9P2S2	NRX2A_HUMAN	neurexin 2	406	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|gephyrin clustering (GO:0097116)|neuroligin clustering (GO:0097118)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	calcium channel regulator activity (GO:0005246)|cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|neuroligin family protein binding (GO:0097109)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	71						GTCAGGATCCCGTCCACCGAG	0.572																																					p.G406W		Atlas-SNP	.											.	NRXN2	247	.	0			c.G1216T						.						124	111	115					11																	64436058		2201	4297	6498	SO:0001583	missense	9379	exon8			GGATCCCGTCCAC		CCDS8077.1, CCDS31597.1, CCDS8078.1	11q13	2008-07-18			ENSG00000110076	ENSG00000110076			8009	protein-coding gene	gene with protein product	"neurexin II"	600566				1621094	Standard	NM_015080		Approved		uc021qkw.1	P58401	OTTHUMG00000045214	ENST00000377551.1:c.1216G>T	chr11.hg19:g.64436058C>A	ENSP00000366774:p.Gly406Trp	123.0	0.0		81.0	4.0	NM_015080	A7E2C1|Q9Y2D6	Missense_Mutation	SNP	ENST00000377551.1	hg19	CCDS8077.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.2|24.2	4.501927|4.501927	0.85176|0.85176	.|.	.|.	ENSG00000110076|ENSG00000110076	ENST00000377551;ENST00000377559;ENST00000265459;ENST00000345863;ENST00000409571;ENST00000442300|ENST00000437746	D;D;D;D;D|.	0.82167|.	-1.58;-1.5;-1.58;-1.58;-1.58|.	4.91|4.91	4.91|4.91	0.64330|0.64330	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);|.	0.000000|.	0.43416|.	U|.	0.000563|.	T|T	0.78780|0.78780	0.4337|0.4337	M|M	0.84773|0.84773	2.715|2.715	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	1.0;1.0;0.999|.	T|T	0.81152|0.81152	-0.1063|-0.1063	10|5	0.87932|.	D|.	0|.	.|.	15.6315|15.6315	0.76912|0.76912	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	375;406;152|.	Q9P2S2-2;Q9P2S2;E7EV67|.	.;NRX2A_HUMAN;.|.	W|L	406;375;406;375;399;162|180	ENSP00000366774:G406W;ENSP00000366782:G375W;ENSP00000265459:G406W;ENSP00000386416:G399W;ENSP00000388971:G162W|.	ENSP00000265459:G406W|.	G|R	-|-	1|2	0|0	NRXN2|NRXN2	64192634|64192634	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	7.600000|7.600000	0.82769|0.82769	2.531000|2.531000	0.85337|0.85337	0.650000|0.650000	0.86243|0.86243	GGG|CGG	.	.		0.572	NRXN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104967.3	NM_015080		A	64436058	C	A	64436058	3	1	259	1	0	0	0	0	1	0	0	0	10675	652	23	1	4255	1	NRXN2	11	64436058	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	112427	64436058	70570458	500	36818										
ATG2A	23130	hgsc.bcm.edu	37	chr11	64681337	64681337	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acaccacgttccccatcaccCggagagtgctccaccctcac	6	20	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:64681337C>T	ENST00000377264.3	-	4	658	c.546G>A	c.(544-546)ccG>ccA	p.P182P	ATG2A_ENST00000421419.2_Silent_p.P182P	NM_015104.2	NP_055919.2	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	182					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(19)|ovary(3)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	55						CCCCATCACCCGGAGAGTGCT	0.617																																					p.P182P		Atlas-SNP	.											.	ATG2A	133	.	0			c.G546A						.						116	98	104					11																	64681337		2201	4297	6498	SO:0001819	synonymous_variant	23130	exon4			ATCACCCGGAGAG		CCDS31602.1	11q13.1	2014-02-12	2012-06-06		ENSG00000110046	ENSG00000110046			29028	protein-coding gene	gene with protein product			"ATG2 autophagy related 2 homolog A (S. cerevisiae)"			21887408	Standard	NM_015104		Approved	KIAA0404	uc001obx.3	Q2TAZ0	OTTHUMG00000066831	ENST00000377264.3:c.546G>A	chr11.hg19:g.64681337C>T		143.0	0.0		79.0	4.0	NM_015104	O43154|Q14DM2|Q6ZTV2|Q7Z6K8|Q8IVY5|Q8TAI8|Q96HH7	Silent	SNP	ENST00000377264.3	hg19	CCDS31602.1																																																																																			.	.		0.617	ATG2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000143224.1	NM_015104		T	64681337	C	T	64681337	2	4	259	1	0	0	0	0	0	0	0	1	1093	639	23	1		1	ATG2A	11	64681337	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	245279	64681337	70325179	501	36819										
CAPN1	823	hgsc.bcm.edu	37	chr11	64977828	64977828	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cttcaagctcaacaagaagcTgtacgagctcatcatcaccc	6	14	5	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:64977828T>C	ENST00000527323.1	+	19	2204	c.1964T>C	c.(1963-1965)cTg>cCg	p.L655P	CAPN1_ENST00000524773.1_Missense_Mutation_p.L655P|CAPN1_ENST00000533129.1_Missense_Mutation_p.L655P|CAPN1_ENST00000279247.6_Missense_Mutation_p.L655P|CAPN1_ENST00000533820.1_Missense_Mutation_p.L655P			P07384	CAN1_HUMAN	calpain 1, (mu/I) large subunit	655	Domain IV.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of cell proliferation (GO:0008284)|proteolysis (GO:0006508)|receptor catabolic process (GO:0032801)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	13		Lung NSC(402;0.094)|Melanoma(852;0.16)		Lung(977;0.00168)|LUSC - Lung squamous cell carcinoma(976;0.00813)		AACAAGAAGCTGTACGAGCTC	0.597																																					p.L655P		Atlas-SNP	.											.	CAPN1	44	.	0			c.T1964C						.						54	56	55					11																	64977828		2020	4191	6211	SO:0001583	missense	823	exon20			AGAAGCTGTACGA	X04366	CCDS44644.1	11q13	2013-01-10			ENSG00000014216	ENSG00000014216	3.4.22.52	"EF-hand domain containing"	1476	protein-coding gene	gene with protein product		114220				3017764, 2209092	Standard	NM_005186		Approved	muCANP, muCL, CANP, CANPL1	uc009yqd.2	P07384	OTTHUMG00000165614	ENST00000527323.1:c.1964T>C	chr11.hg19:g.64977828T>C	ENSP00000431984:p.Leu655Pro	116.0	0.0		108.0	5.0	NM_001198869	Q2TTR0|Q6DHV4	Missense_Mutation	SNP	ENST00000527323.1	hg19	CCDS44644.1	.	.	.	.	.	.	.	.	.	.	T	19.09	3.759861	0.69763	.	.	ENSG00000014216	ENST00000533820;ENST00000533129;ENST00000524773;ENST00000279247;ENST00000259755;ENST00000527323	T;T;T;T;T	0.32515	1.45;1.45;1.45;1.45;1.45	4.21	4.21	0.49690	EF-hand-like domain (1);	0.000000	0.64402	D	0.000003	T	0.55369	0.1916	M	0.85462	2.755	0.80722	D	1	D	0.71674	0.998	D	0.64776	0.929	T	0.63207	-0.6689	10	0.87932	D	0	.	11.5655	0.50802	0.0:0.0:0.0:1.0	.	655	P07384	CAN1_HUMAN	P	655;655;655;655;601;655	ENSP00000435272:L655P;ENSP00000431686:L655P;ENSP00000434176:L655P;ENSP00000279247:L655P;ENSP00000431984:L655P	ENSP00000259755:L601P	L	+	2	0	CAPN1	64734404	1.000000	0.71417	0.991000	0.47740	0.683000	0.39861	7.682000	0.84083	1.701000	0.51217	0.460000	0.39030	CTG	.	.		0.597	CAPN1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385325.1			C	64977828	T	C	64977828	3	2	259	1	0	0	0	0	1	0	0	0	2624	1580	55	2	2038	2	CAPN1	11	64977828	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	296491	64977828	70028688	502	36820										
DPF2	5977	hgsc.bcm.edu	37	chr11	65113180	65113180	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cgaccaggcctcagttaccaCtatgcccactcccacttggc	7	18	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:65113180C>G	ENST00000528416.1	+	7	814	c.681C>G	c.(679-681)caC>caG	p.H227Q	DPF2_ENST00000415073.2_Intron|DPF2_ENST00000532264.1_3'UTR|DPF2_ENST00000252268.4_Missense_Mutation_p.H241Q	NM_006268.4	NP_006259.1	Q92785	REQU_HUMAN	D4, zinc and double PHD fingers family 2	227					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|prostate(1)	23						TCAGTTACCACTATGCCCACT	0.522																																					p.H227Q		Atlas-SNP	.											.	DPF2	54	.	0			c.C681G						.						86	77	80					11																	65113180		2201	4297	6498	SO:0001583	missense	5977	exon7			TTACCACTATGCC	U94585	CCDS8100.1	11q13.1	2014-05-13	2003-10-06	2003-10-08	ENSG00000133884	ENSG00000133884		"Zinc fingers, PHD-type"	9964	protein-coding gene	gene with protein product		601671	"requiem, apoptosis response zinc finger gene"	REQ		11845289	Standard	NM_006268		Approved	ubi-d4, BAF45d	uc001odm.3	Q92785	OTTHUMG00000165985	ENST00000528416.1:c.681C>G	chr11.hg19:g.65113180C>G	ENSP00000436901:p.His227Gln	79.0	0.0		57.0	4.0	NM_006268	A8K7C9|B4DT58	Missense_Mutation	SNP	ENST00000528416.1	hg19	CCDS8100.1	.	.	.	.	.	.	.	.	.	.	C	17.67	3.447906	0.63178	.	.	ENSG00000133884	ENST00000528416;ENST00000252268	D;D	0.94793	-3.52;-3.06	5.24	4.34	0.51931	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.39834	N	0.001260	D	0.92984	0.7767	M	0.83774	2.66	0.48975	D	0.999737	P	0.37864	0.61	B	0.35550	0.205	D	0.91947	0.5568	10	0.59425	D	0.04	-32.7354	7.682	0.28520	0.0:0.8178:0.0:0.1822	.	227	Q92785	REQU_HUMAN	Q	227;241	ENSP00000436901:H227Q;ENSP00000252268:H241Q	ENSP00000252268:H241Q	H	+	3	2	DPF2	64869756	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	1.871000	0.39539	1.446000	0.47643	0.561000	0.74099	CAC	.	.		0.522	DPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387293.3	NM_006268		G	65113180	C	G	65113180	3	3	259	1	0	0	0	0	1	0	0	0	4719	564	20	4	707	4	DPF2	11	65113180	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	135352	65113180	69893336	503	36821										
FIBP	9158	hgsc.bcm.edu	37	chr11	65652450	65652450	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gaagacgcccagctttccccGgagagcagtgcacaccaggc	12	15	0	2	rs368306000		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:65652450G>T	ENST00000338369.2	-	7	908	c.796C>A	c.(796-798)Cgg>Agg	p.R266R	FIBP_ENST00000533045.1_Silent_p.R256R|FIBP_ENST00000357519.4_Silent_p.R259R|FIBP_ENST00000426652.2_5'Flank	NM_198897.1	NP_942600.1	O43427	FIBP_HUMAN	fibroblast growth factor (acidic) intracellular binding protein	266					fibroblast growth factor receptor signaling pathway (GO:0008543)|platelet aggregation (GO:0070527)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	fibroblast growth factor binding (GO:0017134)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(1)	10				READ - Rectum adenocarcinoma(159;0.166)		AGCTTTCCCCGGAGAGCAGTG	0.622											OREG0021089	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R266R		Atlas-SNP	.											.	FIBP	28	.	0			c.C796A						.						69	66	67					11																	65652450		2201	4296	6497	SO:0001819	synonymous_variant	9158	exon7			TTCCCCGGAGAGC	AF010187	CCDS8118.1, CCDS8119.1	11q13.1	2006-06-15			ENSG00000172500	ENSG00000172500			3705	protein-coding gene	gene with protein product		608296				9806903	Standard	NM_004214		Approved	FGFIBP	uc001ogd.3	O43427	OTTHUMG00000166846	ENST00000338369.2:c.796C>A	chr11.hg19:g.65652450G>T		132.0	0.0	1085	89.0	4.0	NM_198897	A8K0J7|Q27Q85|Q6IBQ3|Q9HD65	Silent	SNP	ENST00000338369.2	hg19	CCDS8119.1																																																																																			.	.		0.622	FIBP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000391575.2	NM_198897		T	65652450	G	T	65652450	2	4	259	1	0	0	0	0	0	0	0	1	5894	1115	39	1		1	FIBP	11	65652450	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	539270	65652450	69354066	504	36822										
POLD4	57804	hgsc.bcm.edu	37	chr11	67120247	67120247	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	caagcccatctgcttggcccGacaccagcgctgcagccgtg	11	17	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:67120247G>A	ENST00000312419.3	-	3	360	c.214C>T	c.(214-216)Cgg>Tgg	p.R72W	AP003419.11_ENST00000543494.1_RNA|POLD4_ENST00000539074.1_Intron|POLD4_ENST00000529704.1_5'UTR	NM_021173.4	NP_066996.3	Q9HCU8	DPOD4_HUMAN	polymerase (DNA-directed), delta 4, accessory subunit	72					base-excision repair (GO:0006284)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)	p.R72W(1)		breast(1)|endometrium(1)|lung(1)	3			BRCA - Breast invasive adenocarcinoma(15;3.08e-06)			TGCTTGGCCCGACACCAGCGC	0.637																																					p.R72W		Atlas-SNP	.											POLD4_ENST00000312419,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	POLD4	9	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.C214T						.						23	25	24					11																	67120247		2194	4285	6479	SO:0001583	missense	57804	exon3			TGGCCCGACACCA	AF179890	CCDS8158.1, CCDS58149.1	11q13	2012-05-18	2012-05-18		ENSG00000175482	ENSG00000175482		"DNA polymerases"	14106	protein-coding gene	gene with protein product	"DNA polymerase delta smallest subunit p12"	611525	"polymerase (DNA-directed), delta 4"			10751307	Standard	NM_021173		Approved	p12, POLDS	uc001okm.4	Q9HCU8	OTTHUMG00000167135	ENST00000312419.3:c.214C>T	chr11.hg19:g.67120247G>A	ENSP00000311368:p.Arg72Trp	43.0	0.0		34.0	3.0	NM_021173	F5H506	Missense_Mutation	SNP	ENST00000312419.3	hg19	CCDS8158.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.008205	0.75046	.	.	ENSG00000175482	ENST00000312419	T	0.51817	0.69	4.3	3.36	0.38483	.	0.000000	0.41194	D	0.000935	T	0.69708	0.3141	M	0.88450	2.955	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.72931	-0.4142	10	0.87932	D	0	-14.981	9.1342	0.36863	0.0:0.0:0.7822:0.2178	.	72	Q9HCU8	DPOD4_HUMAN	W	72	ENSP00000311368:R72W	ENSP00000311368:R72W	R	-	1	2	POLD4	66876823	1.000000	0.71417	0.998000	0.56505	0.881000	0.50899	3.198000	0.51035	0.990000	0.38787	0.462000	0.41574	CGG	.	.		0.637	POLD4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393336.1	NM_021173		A	67120247	G	A	67120247	3	1	259	1	0	0	0	0	1	0	0	0	12202	1057	37	1	117	1	POLD4	11	67120247	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1467797	67120247	67886269	505	36823										
PITPNM1	9600	hgsc.bcm.edu	37	chr11	67270152	67270152	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggttggccaggatctccacgCcgctgccctcaccactagac	10	17	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:67270152C>T	ENST00000534749.1	-	2	304	c.116G>A	c.(115-117)gGc>gAc	p.G39D	PITPNM1_ENST00000436757.2_Missense_Mutation_p.G39D|PITPNM1_ENST00000356404.3_Missense_Mutation_p.G39D			O00562	PITM1_HUMAN	phosphatidylinositol transfer protein, membrane-associated 1	39					brain development (GO:0007420)|lipid metabolic process (GO:0006629)|phospholipid transport (GO:0015914)|phototransduction (GO:0007602)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lipid particle (GO:0005811)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphatidylinositol transporter activity (GO:0008526)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(3)	18						GATCTCCACGCCGCTGCCCTC	0.652																																					p.G39D	GBM(28;144 709 4607 5525)	Atlas-SNP	.											.	PITPNM1	84	.	0			c.G116A						.						57	57	57					11																	67270152		2200	4295	6495	SO:0001583	missense	9600	exon3			TCCACGCCGCTGC	X98654	CCDS31620.1, CCDS44659.1	11q13	2008-07-21		2003-05-16	ENSG00000110697	ENSG00000110697			9003	protein-coding gene	gene with protein product	"PYK2 N-terminal domain-interacting receptor 2", "retinal degeneration B alpha 1"	608794		PITPNM		9680295	Standard	NM_004910		Approved	DRES9, NIR2, RDGB1, RDGBA1, Rd9, RDGB	uc001oly.3	O00562	OTTHUMG00000167675	ENST00000534749.1:c.116G>A	chr11.hg19:g.67270152C>T	ENSP00000437286:p.Gly39Asp	118.0	0.0		91.0	4.0	NM_001130848	A6NME4|Q6T7X3|Q8TBN3|Q9BZ73	Missense_Mutation	SNP	ENST00000534749.1	hg19	CCDS31620.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.830897	0.91036	.	.	ENSG00000110697	ENST00000534749;ENST00000436757;ENST00000356404;ENST00000533391;ENST00000532703;ENST00000528559;ENST00000524901	T;T;T;T;T;T;T	0.62498	0.02;0.02;0.02;0.02;0.02;0.02;0.02	4.17	4.17	0.49024	START-like domain (1);	0.000000	0.46145	D	0.000320	D	0.85141	0.5629	H	0.96301	3.8	0.52501	D	0.999955	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.90218	0.4269	10	0.87932	D	0	-26.5468	15.5871	0.76491	0.0:1.0:0.0:0.0	.	39;39	O00562-2;O00562	.;PITM1_HUMAN	D	39	ENSP00000437286:G39D;ENSP00000398787:G39D;ENSP00000348772:G39D;ENSP00000434046:G39D;ENSP00000432977:G39D;ENSP00000434904:G39D;ENSP00000432746:G39D	ENSP00000348772:G39D	G	-	2	0	PITPNM1	67026728	1.000000	0.71417	0.989000	0.46669	0.996000	0.88848	7.417000	0.80156	2.313000	0.78055	0.561000	0.74099	GGC	.	.		0.652	PITPNM1-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395520.1	NM_004910		T	67270152	C	T	67270152	3	4	259	1	0	0	0	0	1	0	0	0	11959	739	26	3	3706	3	PITPNM1	11	67270152	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	149905	67270152	67736364	506	36824										
ALDH3B1	221	hgsc.bcm.edu	37	chr11	67787182	67787182	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cctcacccatcccgccttgcAgagctgctttgctgtggtgc	10	16	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:67787182A>G	ENST00000434449.1	+	6	521		c.e6-1		ALDH3B1_ENST00000316367.6_Splice_Site|ALDH3B1_ENST00000539229.1_Splice_Site|ALDH3B1_ENST00000342456.6_Splice_Site|ALDH3B1_ENST00000007633.8_Splice_Site			P43353	AL3B1_HUMAN	aldehyde dehydrogenase 3 family, member B1						alcohol metabolic process (GO:0006066)|aldehyde catabolic process (GO:0046185)|cellular response to oxidative stress (GO:0034599)|ethanol catabolic process (GO:0006068)|lipid metabolic process (GO:0006629)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)										CCCGCCTTGCAGAGCTGCTTT	0.672																																					.		Atlas-SNP	.											.	.	.	.	0			c.480-2A>G						.						69	80	76					11																	67787182		2200	4294	6494	SO:0001630	splice_region_variant	221	exon6			CCTTGCAGAGCTG	U10868	CCDS73335.1, CCDS73336.1	11q13	2010-04-27			ENSG00000006534	ENSG00000006534	1.2.1.5	"Aldehyde dehydrogenases"	410	protein-coding gene	gene with protein product	"aldehyde dehydrogenase 7", "aldehyde dehydrogenase 3B1"	600466		ALDH7		9161417, 7828891	Standard	NM_000694		Approved		uc001ona.3	P43353	OTTHUMG00000154910	ENST00000434449.1:c.522-1A>G	chr11.hg19:g.67787182A>G		211.0	0.0		98.0	4.0	NM_001161473	A3FMP9|Q53XL5|Q8N515|Q96CK8	Splice_Site	SNP	ENST00000434449.1	hg19																																																																																				.	.		0.672	ALDH3B1-001	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000337614.1	NM_000694	Intron	G	67787182	A	G	67787182	5	3	259	1	0	0	0	0	0	0	1	0	499	202	7	2	496	2	ALDH3B1	11	67787182	Splice_Site	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	517030	67787182	67219334	507	36825										
CPT1A	1374	hgsc.bcm.edu	37	chr11	68580046	68580046	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cgccagtgatgatgccgttcTaaagacagacacccgggccg	12	13	1	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:68580046T>A	ENST00000265641.5	-	3	296		c.e3-2		CPT1A_ENST00000539743.1_Splice_Site|CPT1A_ENST00000376618.2_Splice_Site|CPT1A_ENST00000540367.1_Splice_Site	NM_001876.3	NP_001867.2	P50416	CPT1A_HUMAN	carnitine palmitoyltransferase 1A (liver)						carnitine metabolic process (GO:0009437)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|cellular response to fatty acid (GO:0071398)|eating behavior (GO:0042755)|epithelial cell differentiation (GO:0030855)|fatty acid beta-oxidation (GO:0006635)|glucose metabolic process (GO:0006006)|long-chain fatty acid metabolic process (GO:0001676)|positive regulation of fatty acid beta-oxidation (GO:0032000)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	carnitine O-palmitoyltransferase activity (GO:0004095)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	Esophageal squamous(3;3.28e-14)		LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.142)		Glyburide(DB01016)|L-Carnitine(DB00583)|Perhexiline(DB01074)	GATGCCGTTCTAAAGACAGAC	0.622																																					.		Atlas-SNP	.											.	CPT1A	89	.	0			c.142-2A>T						.						91	71	78					11																	68580046		2200	4294	6494	SO:0001630	splice_region_variant	1374	exon4			CCGTTCTAAAGAC	L39211	CCDS8185.1, CCDS31624.1	11q13.2	2007-07-26				ENSG00000110090	2.3.1.21		2328	protein-coding gene	gene with protein product		600528		CPT1		7892212, 9070950	Standard	NM_001876		Approved	CPT1-L, L-CPT1	uc001oog.4	P50416		ENST00000265641.5:c.142-2A>T	chr11.hg19:g.68580046T>A		126.0	0.0		98.0	4.0	NM_001031847	Q8TCU0|Q9BWK0	Splice_Site	SNP	ENST00000265641.5	hg19	CCDS8185.1	.	.	.	.	.	.	.	.	.	.	T	16.45	3.128112	0.56721	.	.	ENSG00000110090	ENST00000540367;ENST00000376618;ENST00000265641;ENST00000538308;ENST00000539743	.	.	.	4.64	4.64	0.57946	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.2355	0.65925	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	CPT1A	68336622	1.000000	0.71417	0.870000	0.34147	0.522000	0.34438	7.572000	0.82409	1.945000	0.56424	0.402000	0.26972	.	.	.		0.622	CPT1A-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397457.2	NM_001876	Intron	A	68580046	T	A	68580046	5	1	259	1	0	0	0	0	0	0	1	0	3833	1536	53	4	2289	4	CPT1A	11	68580046	Splice_Site	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	792864	68580046	66426470	508	36826										
KRTAP5-11	440051	hgsc.bcm.edu	37	chr11	71293531	71293531	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agggcttgcagcagctggacTggcagcagctggattggcag	17	9	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:71293531T>C	ENST00000398530.1	-	1	390	c.353A>G	c.(352-354)cAg>cGg	p.Q118R	KRTAP5-11_ENST00000526239.1_Intron|AP000867.1_ENST00000343767.3_Intron	NM_001005405.2	NP_001005405.1	Q6L8G4	KR511_HUMAN	keratin associated protein 5-11	118	6 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						gcagctggactggcagcagct	0.622																																					p.Q118R		Atlas-SNP	.											.	KRTAP5-11	36	.	0			c.A353G						.						55	69	64					11																	71293531		2200	4293	6493	SO:0001583	missense	440051	exon1			CTGGACTGGCAGC	AB126080	CCDS41685.1	11q13.4	2008-11-06			ENSG00000204571	ENSG00000204571		"Keratin associated proteins"	23606	protein-coding gene	gene with protein product						15144888	Standard	NM_001005405		Approved	KRTAP5.11, KRTAP5-6	uc001oqu.3	Q6L8G4	OTTHUMG00000057586	ENST00000398530.1:c.353A>G	chr11.hg19:g.71293531T>C	ENSP00000381541:p.Gln118Arg	165.0	0.0		102.0	7.0	NM_001005405		Missense_Mutation	SNP	ENST00000398530.1	hg19	CCDS41685.1	.	.	.	.	.	.	.	.	.	.	.	3.786	-0.044685	0.07452	.	.	ENSG00000204571	ENST00000376535;ENST00000398530	T	0.01464	4.86	1.87	0.597	0.17504	.	.	.	.	.	T	0.01661	0.0053	M	0.71581	2.175	0.21782	N	0.999545	P	0.48016	0.904	B	0.34385	0.181	T	0.38112	-0.9676	9	0.07813	T	0.8	.	3.9756	0.09473	0.3203:0.0:0.0:0.6797	.	118	Q6L8G4	KR511_HUMAN	R	118	ENSP00000381541:Q118R	ENSP00000365718:Q118R	Q	-	2	0	KRTAP5-11	70971179	0.997000	0.39634	0.983000	0.44433	0.701000	0.40568	0.913000	0.28611	0.153000	0.19213	0.361000	0.22055	CAG	.	.		0.622	KRTAP5-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127969.1	NM_001005405		C	71293531	T	C	71293531	3	2	259	1	0	0	0	0	1	0	0	0	8569	1580	55	2	121	2	KRTAP5-11	11	71293531	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	2713485	71293531	63712985	509	36827										
RNF169	254225	hgsc.bcm.edu	37	chr11	74546594	74546594	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tttttaatctctttcaggtcAcaactatgactccagcctcc	4	13	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:74546594A>G	ENST00000299563.4	+	6	959	c.946A>G	c.(946-948)Aca>Gca	p.T316A		NM_001098638.1	NP_001092108.1	Q8NCN4	RN169_HUMAN	ring finger protein 169	316					cellular response to DNA damage stimulus (GO:0006974)|negative regulation of double-strand break repair (GO:2000780)|protein ubiquitination (GO:0016567)	intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|site of double-strand break (GO:0035861)	K63-linked polyubiquitin binding (GO:0070530)|ligase activity (GO:0016874)|nucleosome binding (GO:0031491)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|urinary_tract(1)	15						CTTTCAGGTCACAACTATGAC	0.458																																					p.T316A		Atlas-SNP	.											.	RNF169	36	.	0			c.A946G						.						65	68	67					11																	74546594		2011	4164	6175	SO:0001583	missense	254225	exon6			CAGGTCACAACTA	AB082522	CCDS41691.1	11q13.4	2008-02-05			ENSG00000166439	ENSG00000166439		"RING-type (C3HC4) zinc fingers"	26961	protein-coding gene	gene with protein product						12056414	Standard	NM_001098638		Approved	KIAA1991	uc001ovl.4	Q8NCN4	OTTHUMG00000165516	ENST00000299563.4:c.946A>G	chr11.hg19:g.74546594A>G	ENSP00000299563:p.Thr316Ala	98.0	0.0		87.0	4.0	NM_001098638	Q6N015	Missense_Mutation	SNP	ENST00000299563.4	hg19	CCDS41691.1	.	.	.	.	.	.	.	.	.	.	A	9.720	1.159330	0.21454	.	.	ENSG00000166439	ENST00000299563	T	0.43688	0.94	5.82	3.52	0.40303	.	0.378221	0.31102	N	0.008254	T	0.39682	0.1087	M	0.70595	2.14	0.80722	D	1	P	0.52170	0.951	B	0.44224	0.444	T	0.19549	-1.0302	10	0.35671	T	0.21	-19.5797	4.9872	0.14196	0.6842:0.1555:0.1603:0.0	.	316	Q8NCN4	RN169_HUMAN	A	316	ENSP00000299563:T316A	ENSP00000299563:T316A	T	+	1	0	RNF169	74224242	0.025000	0.19082	0.998000	0.56505	0.262000	0.26303	1.020000	0.30027	0.483000	0.27608	-0.264000	0.10439	ACA	.	.		0.458	RNF169-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384741.1	XM_495886		G	74546594	A	G	74546594	3	3	259	1	0	0	0	0	1	0	0	0	13475	159	6	2	968	2	RNF169	11	74546594	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	3253063	74546594	60459922	510	36828										
UVRAG	7405	hgsc.bcm.edu	37	chr11	75851784	75851784	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tcacacctccagtgcaatccCtgttcctaagagacaaagct	6	14	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:75851784C>A	ENST00000356136.3	+	15	1668	c.1427C>A	c.(1426-1428)cCt>cAt	p.P476H	UVRAG_ENST00000538870.1_Missense_Mutation_p.P32H|UVRAG_ENST00000532130.1_Missense_Mutation_p.P104H|UVRAG_ENST00000533454.1_Missense_Mutation_p.P104H|UVRAG_ENST00000528420.1_Missense_Mutation_p.P375H|UVRAG_ENST00000531818.1_Missense_Mutation_p.P104H|UVRAG_ENST00000539288.1_Missense_Mutation_p.P104H	NM_003369.3	NP_003360.2	Q9P2Y5	UVRAG_HUMAN	UV radiation resistance associated	476					DNA repair (GO:0006281)|positive regulation of autophagy (GO:0010508)|SNARE complex assembly (GO:0035493)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)|phagocytic vesicle (GO:0045335)|protein complex (GO:0043234)				central_nervous_system(1)|cervix(3)|endometrium(3)|kidney(1)|large_intestine(2)|lung(15)|skin(5)|urinary_tract(2)	32						AGTGCAATCCCTGTTCCTAAG	0.478																																					p.P476H		Atlas-SNP	.											.	UVRAG	69	.	0			c.C1427A						.						67	70	69					11																	75851784		2200	4293	6493	SO:0001583	missense	7405	exon15			CAATCCCTGTTCC	X99050, AB012958	CCDS8241.1	11q13	2012-11-15	2012-11-15		ENSG00000198382	ENSG00000198382			12640	protein-coding gene	gene with protein product	"beclin 1 binding protein"	602493	"UV radiation resistance associated gene"			9169138, 16799551, 18843052	Standard	NM_003369		Approved	VPS38	uc001oxc.3	Q9P2Y5	OTTHUMG00000165319	ENST00000356136.3:c.1427C>A	chr11.hg19:g.75851784C>A	ENSP00000348455:p.Pro476His	119.0	0.0		74.0	4.0	NM_003369	B3KTC1|O00392	Missense_Mutation	SNP	ENST00000356136.3	hg19	CCDS8241.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.440907	0.83993	.	.	ENSG00000198382	ENST00000356136;ENST00000528420;ENST00000533454;ENST00000531818;ENST00000532130;ENST00000539288;ENST00000538870	T	0.52526	0.66	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.60599	0.2281	L	0.34521	1.04	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.95	T	0.61855	-0.6977	10	0.66056	D	0.02	-13.7312	18.8301	0.92135	0.0:1.0:0.0:0.0	.	32;476	B7Z6A0;Q9P2Y5	.;UVRAG_HUMAN	H	476;375;104;104;104;104;32	ENSP00000348455:P476H	ENSP00000348455:P476H	P	+	2	0	UVRAG	75529432	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.206000	0.77891	2.764000	0.94973	0.655000	0.94253	CCT	.	.		0.478	UVRAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383430.1	NM_003369		A	75851784	C	A	75851784	3	1	259	1	0	0	0	0	1	0	0	0	17123	681	24	3	1485	3	UVRAG	11	75851784	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	1305190	75851784	59154732	511	36829										
INTS4	92105	hgsc.bcm.edu	37	chr11	77692604	77692604	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	caatgatgcaattttcagtcTcacagatggatcattctcct	6	10	4	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:77692604T>C	ENST00000534064.1	-	3	299	c.265A>G	c.(265-267)Aga>Gga	p.R89G	INTS4_ENST00000529807.1_Missense_Mutation_p.R89G	NM_033547.3	NP_291025.3	Q96HW7	INT4_HUMAN	integrator complex subunit 4	89					snRNA processing (GO:0016180)	integrator complex (GO:0032039)			INTS4/GAB2(2)	NS(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(5)|upper_aerodigestive_tract(1)	32	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)			ATTTTCAGTCTCACAGATGGA	0.383																																					p.R89G		Atlas-SNP	.											.	INTS4	89	.	0			c.A265G						.						116	106	109					11																	77692604		2200	4292	6492	SO:0001583	missense	92105	exon3			TCAGTCTCACAGA	BC015664	CCDS31644.1	11q14.1	2006-04-26			ENSG00000149262	ENSG00000149262			25048	protein-coding gene	gene with protein product		611348				16239144	Standard	NM_033547		Approved	INT4, MGC16733, MST093	uc001oys.3	Q96HW7	OTTHUMG00000166629	ENST00000534064.1:c.265A>G	chr11.hg19:g.77692604T>C	ENSP00000434466:p.Arg89Gly	166.0	0.0		122.0	5.0	NM_033547	Q2YD62|Q6PJG4|Q7Z4E7|Q96G32|Q96GA1|Q9BRC0	Missense_Mutation	SNP	ENST00000534064.1	hg19	CCDS31644.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.987070	0.74589	.	.	ENSG00000149262	ENST00000534064;ENST00000529807	T;T	0.75477	-0.94;0.67	4.75	3.59	0.41128	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.83857	0.5345	M	0.75777	2.31	0.80722	D	1	D	0.57899	0.981	D	0.69824	0.966	D	0.84611	0.0678	10	0.87932	D	0	-13.7668	11.4727	0.50280	0.0:0.0:0.1508:0.8492	.	89	Q96HW7	INT4_HUMAN	G	89	ENSP00000434466:R89G;ENSP00000433644:R89G	ENSP00000407787:R89G	R	-	1	2	INTS4	77370252	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.329000	0.43876	0.818000	0.34468	0.482000	0.46254	AGA	.	.		0.383	INTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390927.1	NM_033547		C	77692604	T	C	77692604	3	2	259	1	0	0	0	0	1	0	0	0	7789	1559	54	2	2710	2	INTS4	11	77692604	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1840820	77692604	57313912	512	36830										
TMEM135	65084	hgsc.bcm.edu	37	chr11	87029247	87029247	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	catgcagatactatcatctaTtccatctctacagcaatttg	4	11	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:87029247T>C	ENST00000305494.5	+	13	1185	c.1146T>C	c.(1144-1146)taT>taC	p.Y382Y	TMEM135_ENST00000340353.7_Silent_p.Y360Y|TMEM135_ENST00000532959.1_Silent_p.Y253Y|TMEM135_ENST00000535167.1_Silent_p.Y243Y	NM_022918.3	NP_075069.3	Q86UB9	TM135_HUMAN	transmembrane protein 135	382					peroxisome organization (GO:0007031)	integral component of membrane (GO:0016021)|peroxisome (GO:0005777)				NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	17		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				CTATCATCTATTCCATCTCTA	0.348																																					p.Y382Y		Atlas-SNP	.											.	TMEM135	40	.	0			c.T1146C						.						176	165	168					11																	87029247		2201	4299	6500	SO:0001819	synonymous_variant	65084	exon13			CATCTATTCCATC	BX648678	CCDS8280.1, CCDS53692.1	11q14.2	2006-03-09			ENSG00000166575	ENSG00000166575			26167	protein-coding gene	gene with protein product						12477932	Standard	NM_022918		Approved	FLJ22104	uc001pch.3	Q86UB9	OTTHUMG00000167248	ENST00000305494.5:c.1146T>C	chr11.hg19:g.87029247T>C		103.0	0.0		69.0	4.0	NM_022918	Q6AW91|Q8ND01|Q9H6M3	Silent	SNP	ENST00000305494.5	hg19	CCDS8280.1																																																																																			.	.		0.348	TMEM135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393875.1	NM_022918		C	87029247	T	C	87029247	2	2	259	1	0	0	0	0	0	0	0	1	16066	1500	52	2		2	TMEM135	11	87029247	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	9336643	87029247	47977269	513	36831										
AMOTL1	154810	hgsc.bcm.edu	37	chr11	94602390	94602390	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gctggggaaggagcaccatgAgcatgcctctgccccactgc	13	14	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:94602390A>G	ENST00000433060.2	+	12	2657	c.2516A>G	c.(2515-2517)gAg>gGg	p.E839G	AMOTL1_ENST00000317829.8_Missense_Mutation_p.E789G|AMOTL1_ENST00000317837.9_Missense_Mutation_p.E426G	NM_130847.2	NP_570899.1	Q8IY63	AMOL1_HUMAN	angiomotin like 1	839					establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|hippo signaling (GO:0035329)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|tight junction (GO:0005923)	identical protein binding (GO:0042802)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	36		Acute lymphoblastic leukemia(157;2.38e-05)|all_hematologic(158;0.00824)				GAGCACCATGAGCATGCCTCT	0.522																																					p.E839G		Atlas-SNP	.											.	AMOTL1	95	.	0			c.A2516G						.						29	37	34					11																	94602390		2138	4240	6378	SO:0001583	missense	154810	exon12			ACCATGAGCATGC	AF453742	CCDS44712.1, CCDS73368.1	11q21	2008-07-18				ENSG00000166025			17811	protein-coding gene	gene with protein product	"junction-enriched and associated protein"	614657				11733531	Standard	XM_005273798		Approved	JEAP	uc001pfb.3	Q8IY63		ENST00000433060.2:c.2516A>G	chr11.hg19:g.94602390A>G	ENSP00000387739:p.Glu839Gly	108.0	0.0		93.0	5.0	NM_130847	Q63HK7|Q8NDN0|Q8TEN8|Q8WXD1|Q96CM5	Missense_Mutation	SNP	ENST00000433060.2	hg19	CCDS44712.1	.	.	.	.	.	.	.	.	.	.	A	13.50	2.257003	0.39896	.	.	ENSG00000166025	ENST00000317829;ENST00000317837;ENST00000433060	T;T;T	0.46451	2.2;0.87;2.19	5.59	4.47	0.54385	.	0.389493	0.26286	N	0.025245	T	0.25754	0.0627	N	0.16478	0.41	0.22762	N	0.998762	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.14615	-1.0466	10	0.24483	T	0.36	-4.8031	10.6353	0.45560	0.9243:0.0:0.0757:0.0	.	789;839	Q8IY63-2;Q8IY63	.;AMOL1_HUMAN	G	789;426;839	ENSP00000320968:E789G;ENSP00000323474:E426G;ENSP00000387739:E839G	ENSP00000320968:E789G	E	+	2	0	AMOTL1	94242038	0.994000	0.37717	0.020000	0.16555	0.056000	0.15407	3.144000	0.50616	0.984000	0.38629	0.459000	0.35465	GAG	.	.		0.522	AMOTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396474.3	NM_130847		G	94602390	A	G	94602390	3	3	259	1	0	0	0	0	1	0	0	0	583	304	11	2	2562	2	AMOTL1	11	94602390	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	7573143	94602390	40404126	514	36832										
MMP1	4312	hgsc.bcm.edu	37	chr11	102663360	102663360	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gaaaaaccggacttcatctcTgtcggcaaattcgtaagcag	9	10	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:102663360T>C	ENST00000315274.6	-	7	1076	c.1009A>G	c.(1009-1011)Aga>Gga	p.R337G	WTAPP1_ENST00000525739.2_RNA	NM_001145938.1|NM_002421.3	NP_001139410.1|NP_002412.1	P03956	MMP1_HUMAN	matrix metallopeptidase 1 (interstitial collagenase)	337					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|proteolysis (GO:0006508)|viral process (GO:0016032)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(2)|lung(18)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	30	all_epithelial(12;0.0127)	all_neural(303;0.000318)|all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.072)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.233)	OV - Ovarian serous cystadenocarcinoma(223;1.82e-07)|Epithelial(105;1.51e-06)|BRCA - Breast invasive adenocarcinoma(274;0.014)	Marimastat(DB00786)	ACTTCATCTCTGTCGGCAAAT	0.398																																					p.R337G		Atlas-SNP	.											.	MMP1	74	.	0			c.A1009G						.						122	125	124					11																	102663360		2203	4299	6502	SO:0001583	missense	4312	exon7			CATCTCTGTCGGC	X54925	CCDS8322.1	11q21-q22	2014-01-30	2005-08-08		ENSG00000196611	ENSG00000196611	3.4.24.7	"Endogenous ligands"	7155	protein-coding gene	gene with protein product		120353	"matrix metalloproteinase 1 (interstitial collagenase)"	CLG			Standard	NM_002421		Approved		uc001phi.2	P03956	OTTHUMG00000048192	ENST00000315274.6:c.1009A>G	chr11.hg19:g.102663360T>C	ENSP00000322788:p.Arg337Gly	105.0	0.0		83.0	4.0	NM_002421	P08156	Missense_Mutation	SNP	ENST00000315274.6	hg19	CCDS8322.1	.	.	.	.	.	.	.	.	.	.	t	12.15	1.852757	0.32699	.	.	ENSG00000196611	ENST00000315274	T	0.13196	2.61	6.16	5.05	0.67936	Hemopexin/matrixin (2);	0.280687	0.33161	N	0.005207	T	0.16300	0.0392	L	0.58428	1.81	0.09310	N	1	B	0.24426	0.103	B	0.31614	0.133	T	0.23368	-1.0190	10	0.72032	D	0.01	.	7.2058	0.25907	0.0:0.0735:0.1465:0.7799	.	337	P03956	MMP1_HUMAN	G	337	ENSP00000322788:R337G	ENSP00000322788:R337G	R	-	1	2	MMP1	102168570	0.004000	0.15560	0.045000	0.18777	0.727000	0.41649	1.439000	0.35013	1.163000	0.42636	0.528000	0.53228	AGA	.	.		0.398	MMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109632.1	NM_002421		C	102663360	T	C	102663360	3	2	259	1	0	0	0	0	1	0	0	0	9657	1588	55	2	416	2	MMP1	11	102663360	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	8060970	102663360	32343156	515	36833										
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	103058312	103058312	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	actttggtagcattcctacaAcaggtaagtcatattgcttg	8	8	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:103058312A>G	ENST00000375735.2	+	43	7281	c.7137A>G	c.(7135-7137)caA>caG	p.Q2379Q	DYNC2H1_ENST00000398093.3_Silent_p.Q2379Q|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	2379	AAA 3. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		CATTCCTACAACAGGTAAGTC	0.328																																					p.Q2379Q		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.A7137G						.						66	60	62					11																	103058312		1835	4084	5919	SO:0001819	synonymous_variant	79659	exon43			CCTACAACAGGTA	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.7137A>G	chr11.hg19:g.103058312A>G		106.0	0.0		88.0	4.0	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Silent	SNP	ENST00000375735.2	hg19	CCDS53701.1																																																																																			.	.		0.328	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		G	103058312	A	G	103058312	2	3	259	1	0	0	0	0	0	0	0	1	4848	40	2	2		2	DYNC2H1	11	103058312	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	394952	103058312	31948204	516	36834										
PCSK7	9159	hgsc.bcm.edu	37	chr11	117100222	117100222	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acagcctccacctgctgccgGatggcctccacctccagggc	10	19	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:117100222G>T	ENST00000320934.3	-	3	969	c.339C>A	c.(337-339)atC>atA	p.I113I		NM_004716.2	NP_004707.2	Q16549	PCSK7_HUMAN	proprotein convertase subtilisin/kexin type 7	113					peptide hormone processing (GO:0016486)|protein processing (GO:0016485)	integral component of Golgi membrane (GO:0030173)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|skin(1)	16	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|Epithelial(105;6.71e-05)|all cancers(92;0.000537)		CCTGCTGCCGGATGGCCTCCA	0.652			T	IGH@	MLCLS																																p.I113I		Atlas-SNP	.		Dom	yes		11	11q23.3	9159	proprotein convertase subtilisin/kexin type 7		L	.	PCSK7	59	.	0			c.C339A						.						52	57	55					11																	117100222		2201	4296	6497	SO:0001819	synonymous_variant	9159	exon3			CTGCCGGATGGCC	U40623	CCDS8382.1	11q23-q24	2008-02-01			ENSG00000160613	ENSG00000160613			8748	protein-coding gene	gene with protein product		604872				8615762, 9820811	Standard	XM_006718938		Approved	PC7, PC8, LPC, SPC7	uc001pqr.3	Q16549	OTTHUMG00000165640	ENST00000320934.3:c.339C>A	chr11.hg19:g.117100222G>T		86.0	0.0		50.0	4.0	NM_004716	B0YJ60|Q3C1X1|Q53GM4|Q96FK8|Q9UL57	Silent	SNP	ENST00000320934.3	hg19	CCDS8382.1																																																																																			.	.		0.652	PCSK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385529.2	NM_004716		T	117100222	G	T	117100222	2	4	259	1	0	0	0	0	0	0	0	1	11614	1164	41	3		3	PCSK7	11	117100222	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	14041910	117100222	17906294	517	36835										
CEP164	22897	hgsc.bcm.edu	37	chr11	117214976	117214976	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggcatcgtggccccactgccTggagagtggaaaccatggta	14	11	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:117214976T>C	ENST00000278935.3	+	4	324	c.177T>C	c.(175-177)ccT>ccC	p.P59P		NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	59	Interaction with ATRIP.|WW. {ECO:0000255|PROSITE- ProRule:PRU00224}.				cilium assembly (GO:0042384)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(7)|large_intestine(12)|lung(18)|ovary(3)|prostate(3)	47	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		CCCCACTGCCTGGAGAGTGGA	0.552																																					p.P59P		Atlas-SNP	.											.	CEP164	121	.	0			c.T177C						.						36	33	34					11																	117214976		2201	4296	6497	SO:0001819	synonymous_variant	22897	exon3			ACTGCCTGGAGAG	AB028975	CCDS31683.1	11q23.3	2014-02-20			ENSG00000110274	ENSG00000110274			29182	protein-coding gene	gene with protein product		614848				10470851, 14654843	Standard	NM_014956		Approved	KIAA1052, NPHP15	uc001prc.3	Q9UPV0	OTTHUMG00000167070	ENST00000278935.3:c.177T>C	chr11.hg19:g.117214976T>C		134.0	0.0		106.0	5.0	NM_001271933	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	Silent	SNP	ENST00000278935.3	hg19	CCDS31683.1																																																																																			.	.		0.552	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1	NM_014956		C	117214976	T	C	117214976	2	2	259	1	0	0	0	0	0	0	0	1	3251	1567	55	2		2	CEP164	11	117214976	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	114754	117214976	17791540	518	36836										
UBE4A	9354	hgsc.bcm.edu	37	chr11	118245776	118245776	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgccagaaatctttttccaaAtgtatgcctcagatgctttc	6	10	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:118245776A>G	ENST00000431736.2	+	9	1375	c.1303A>G	c.(1303-1305)Atg>Gtg	p.M435V	UBE4A_ENST00000252108.3_Missense_Mutation_p.M428V					ubiquitination factor E4A											autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(7)|liver(2)|lung(14)|ovary(3)|prostate(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	56	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)		CTTTTTCCAAATGTATGCCTC	0.468																																					p.M435V		Atlas-SNP	.											.	UBE4A	97	.	0			c.A1303G						.						103	92	96					11																	118245776		2200	4296	6496	SO:0001583	missense	9354	exon9			TTCCAAATGTATG	D50916	CCDS8396.1, CCDS55790.1	11q23.3	2013-01-28	2011-05-19					"U-box domain containing"	12499	protein-coding gene	gene with protein product		603753	"ubiquitination factor E4A (homologous to yeast UFD2)", "ubiquitination factor E4A (UFD2 homolog, yeast)"			10089879	Standard	NM_004788		Approved	UBOX2, UFD2, KIAA0126, E4	uc001psv.3	Q14139	OTTHUMG00000168100	ENST00000431736.2:c.1303A>G	chr11.hg19:g.118245776A>G	ENSP00000387362:p.Met435Val	158.0	0.0		95.0	4.0	NM_004788		Missense_Mutation	SNP	ENST00000431736.2	hg19	CCDS8396.1	.	.	.	.	.	.	.	.	.	.	A	11.85	1.761719	0.31228	.	.	ENSG00000110344	ENST00000252108;ENST00000431736	T;T	0.39997	1.05;1.05	5.85	5.85	0.93711	Ubiquitin conjugation factor E4, core (1);	0.072733	0.85682	D	0.000000	T	0.32071	0.0817	N	0.24115	0.695	0.80722	D	1	B;B	0.20780	0.048;0.012	B;B	0.22386	0.039;0.015	T	0.07712	-1.0758	10	0.25106	T	0.35	-18.7866	16.2268	0.82300	1.0:0.0:0.0:0.0	.	428;435	Q14139;Q14139-2	UBE4A_HUMAN;.	V	428;435	ENSP00000252108:M428V;ENSP00000387362:M435V	ENSP00000252108:M428V	M	+	1	0	UBE4A	117750986	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.967000	0.76079	2.242000	0.73789	0.402000	0.26972	ATG	.	.		0.468	UBE4A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398143.1	NM_004788		G	118245776	A	G	118245776	3	3	259	1	0	0	0	0	1	0	0	0	16897	101	4	2	1333	2	UBE4A	11	118245776	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1030800	118245776	16760740	519	36837										
MLL	4297	hgsc.bcm.edu	37	chr11	118392112	118392112	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccatccagactgacaagcggGaaaagtattacgacagcaag	10	10	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:118392112G>A	ENST00000389506.5	+	35	11614	c.11614G>A	c.(11614-11616)Gaa>Aaa	p.E3872K	RP11-770J1.3_ENST00000528578.1_RNA|KMT2A_ENST00000354520.4_Missense_Mutation_p.E3834K|KMT2A_ENST00000534358.1_Missense_Mutation_p.E3875K|RP11-770J1.3_ENST00000554407.1_RNA|RP11-770J1.3_ENST00000532597.1_RNA|RP11-770J1.3_ENST00000525992.2_RNA|RP11-770J1.3_ENST00000556583.1_RNA			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	3872	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										TGACAAGCGGGAAAAGTATTA	0.483																																					p.E3875K		Atlas-SNP	.											.	MLL	548	.	0			c.G11623A						.						94	85	88					11																	118392112		2200	4295	6495	SO:0001583	missense	4297	exon35			AAGCGGGAAAAGT	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.11614G>A	chr11.hg19:g.118392112G>A	ENSP00000374157:p.Glu3872Lys	113.0	0.0		82.0	4.0	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Missense_Mutation	SNP	ENST00000389506.5	hg19	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.293663	0.80914	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313	T;T;T	0.81078	-1.45;-1.45;-1.45	5.82	5.82	0.92795	SET domain (3);	0.000000	0.85682	D	0.000000	D	0.90263	0.6955	M	0.88979	2.995	0.80722	D	1	D;D	0.65815	0.995;0.995	P;P	0.56916	0.809;0.809	D	0.91460	0.5188	10	0.87932	D	0	.	20.1008	0.97874	0.0:0.0:1.0:0.0	.	3875;3872	E9PQG7;Q03164	.;MLL1_HUMAN	K	3875;3872;3834;2782	ENSP00000436786:E3875K;ENSP00000374157:E3872K;ENSP00000346516:E3834K	ENSP00000346516:E3834K	E	+	1	0	MLL	117897322	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	7.577000	0.82486	2.748000	0.94277	0.591000	0.81541	GAA	.	.		0.483	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		A	118392112	G	A	118392112	3	1	259	1	0	0	0	0	1	0	0	0	9629	1175	41	3	11752	3	MLL	11	118392112	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	146336	118392112	16614404	520	36838										
ABCG4	64137	hgsc.bcm.edu	37	chr11	119029042	119029042	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctgtccatcctcagggacacGgtgaggcgtcaggctggggg	17	11	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:119029042G>T	ENST00000449422.2	+	10	1355	c.1167G>T	c.(1165-1167)acG>acT	p.T389T	ABCG4_ENST00000307417.3_Splice_Site_p.T389T|AP002956.1_ENST00000599663.1_5'Flank|ABCG4_ENST00000531739.1_Splice_Site_p.T389T	NM_001142505.1	NP_001135977.1	Q9H172	ABCG4_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 4	389	ABC transmembrane type-2.				cholesterol efflux (GO:0033344)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cholesterol transporter activity (GO:0017127)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.T389T(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(28)|ovary(2)|prostate(1)|skin(1)	44	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		TCAGGGACACGGTGAGGCGTC	0.587																																					p.T389T		Atlas-SNP	.											ABCG4,NS,carcinoma,0,1	ABCG4	77	.	1	Substitution - coding silent(1)	lung(1)	c.G1167T						.						176	158	164					11																	119029042		2200	4295	6495	SO:0001630	splice_region_variant	64137	exon10			GGACACGGTGAGG	AJ300465	CCDS8415.1	11q23	2012-03-14			ENSG00000172350	ENSG00000172350		"ATP binding cassette transporters / subfamily G"	13884	protein-coding gene	gene with protein product	"putative ABC transporter", "ATP-binding cassette, subfamily G, member 4"	607784				11435397	Standard	NM_022169		Approved	WHITE2	uc001pvs.3	Q9H172	OTTHUMG00000166169	ENST00000449422.2:c.1167+1G>T	chr11.hg19:g.119029042G>T		113.0	0.0		68.0	3.0	NM_022169	A8K1B5|Q8WWH0|Q8WWH1|Q8WWH2	Silent	SNP	ENST00000449422.2	hg19	CCDS8415.1																																																																																			.	.		0.587	ABCG4-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388215.1	NM_022169	Silent	T	119029042	G	T	119029042	5	4	259	1	0	0	0	0	0	0	1	0	70	1130	39	1	1201	1	ABCG4	11	119029042	Splice_Site	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	636930	119029042	15977474	521	36839										
SORL1	6653	hgsc.bcm.edu	37	chr11	121478830	121478830	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aaggtggctgcggtgactagTcgtggaataggaaactggag	17	5	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:121478830T>C	ENST00000260197.7	+	38	5313	c.5184T>C	c.(5182-5184)agT>agC	p.S1728S	SORL1_ENST00000527934.1_Silent_p.S343S|SORL1_ENST00000532694.1_Silent_p.S574S|SORL1_ENST00000534286.1_Silent_p.S638S|SORL1_ENST00000525532.1_Silent_p.S672S	NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	1728	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell death (GO:0008219)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902960)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of neurofibrillary tangle assembly (GO:1902997)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of tau-protein kinase activity (GO:1902948)|positive regulation of choline O-acetyltransferase activity (GO:1902771)|positive regulation of early endosome to recycling endosome transport (GO:1902955)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|positive regulation of protein localization to early endosome (GO:1902966)|post-Golgi vesicle-mediated transport (GO:0006892)|protein maturation (GO:0051604)|protein retention in Golgi apparatus (GO:0045053)|protein targeting (GO:0006605)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|receptor-mediated endocytosis (GO:0006898)|regulation of smooth muscle cell migration (GO:0014910)|signal transduction (GO:0007165)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|nuclear envelope lumen (GO:0005641)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)|beta-amyloid binding (GO:0001540)|low-density lipoprotein particle binding (GO:0030169)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(2)|lung(34)|ovary(5)|pancreas(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(2)	91		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		CGGTGACTAGTCGTGGAATAG	0.363																																					p.S1728S		Atlas-SNP	.											.	SORL1	218	.	0			c.T5184C						.						107	102	104					11																	121478830		2202	4299	6501	SO:0001819	synonymous_variant	6653	exon38			GACTAGTCGTGGA	Y08110	CCDS8436.1	11q23.2-q24.4	2014-06-05	2011-01-25		ENSG00000137642	ENSG00000137642		"Fibronectin type III domain containing"	11185	protein-coding gene	gene with protein product	"LDLR relative with 11 ligand-binding repeats"	602005	"chromosome 11 open reading frame 32", "sortilin-related receptor, L(DLR class) A repeats-containing"	C11orf32		9157966, 8940146	Standard	NM_003105		Approved	gp250, LR11, LRP9, SorLA, SorLA-1	uc001pxx.3	Q92673	OTTHUMG00000166057	ENST00000260197.7:c.5184T>C	chr11.hg19:g.121478830T>C		75.0	0.0		76.0	4.0	NM_003105	B2RNX7|Q92856	Silent	SNP	ENST00000260197.7	hg19	CCDS8436.1																																																																																			.	.		0.363	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2	NM_003105		C	121478830	T	C	121478830	2	2	259	1	0	0	0	0	0	0	0	1	14949	1664	58	2		2	SORL1	11	121478830	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	2449788	121478830	13527686	522	36840										
FOXRED1	55572	hgsc.bcm.edu	37	chr11	126146997	126146997	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggacccggcgaacctggaagTggaccatgatttcttccagg	13	11	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:126146997T>C	ENST00000263578.5	+	10	1207	c.1133T>C	c.(1132-1134)gTg>gCg	p.V378A	FOXRED1_ENST00000532125.1_Missense_Mutation_p.V364A|FOXRED1_ENST00000442061.2_Missense_Mutation_p.V208A|FOXRED1_ENST00000534011.1_3'UTR	NM_017547.3	NP_060017.1	Q96CU9	FXRD1_HUMAN	FAD-dependent oxidoreductase domain containing 1	378						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)			breast(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(1)	15	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0729)		AACCTGGAAGTGGACCATGAT	0.547																																					p.V378A		Atlas-SNP	.											.	FOXRED1	38	.	0			c.T1133C						.						82	75	78					11																	126146997		2201	4298	6499	SO:0001583	missense	55572	exon10			TGGAAGTGGACCA		CCDS8471.1	11q24.2	2006-02-03			ENSG00000110074	ENSG00000110074			26927	protein-coding gene	gene with protein product		613622				10497265	Standard	NM_017547		Approved	H17	uc001qdi.3	Q96CU9	OTTHUMG00000165827	ENST00000263578.5:c.1133T>C	chr11.hg19:g.126146997T>C	ENSP00000263578:p.Val378Ala	189.0	0.0		108.0	5.0	NM_017547	B3KN84|B4DHU2|Q71MG0|Q9BU39|Q9UKY9	Missense_Mutation	SNP	ENST00000263578.5	hg19	CCDS8471.1	.	.	.	.	.	.	.	.	.	.	T	34	5.374574	0.95923	.	.	ENSG00000110074	ENST00000263578;ENST00000442061;ENST00000532125	D;D;D	0.82619	-1.63;-1.63;-1.63	5.79	5.79	0.91817	FAD dependent oxidoreductase (1);	0.000000	0.85682	D	0.000000	D	0.91549	0.7331	M	0.82193	2.58	0.80722	D	1	D;D;D	0.89917	0.985;1.0;0.988	P;D;P	0.91635	0.828;0.999;0.893	D	0.92337	0.5878	10	0.59425	D	0.04	-22.3541	15.7901	0.78350	0.0:0.0:0.0:1.0	.	364;245;378	Q96CU9-3;B4DI59;Q96CU9	.;.;FXRD1_HUMAN	A	378;208;364	ENSP00000263578:V378A;ENSP00000404371:V208A;ENSP00000434178:V364A	ENSP00000263578:V378A	V	+	2	0	FOXRED1	125652207	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.718000	0.84743	2.213000	0.71641	0.477000	0.44152	GTG	.	.		0.547	FOXRED1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386434.1	NM_017547		C	126146997	T	C	126146997	3	2	259	1	0	0	0	0	1	0	0	0	6041	1696	59	2	1171	2	FOXRED1	11	126146997	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	4668167	126146997	8859519	523	36841										
GLB1L2	89944	hgsc.bcm.edu	37	chr11	134238603	134238603	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tcaacctctacatgttccacGgaggcaccaactttggcttc	7	14	2	0	rs138130138	byFrequency	TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:134238603G>T	ENST00000535456.2	+	10	1143	c.955G>T	c.(955-957)Gga>Tga	p.G319*	GLB1L2_ENST00000389881.3_Nonsense_Mutation_p.G319*|GLB1L2_ENST00000529077.1_3'UTR|GLB1L2_ENST00000339772.7_Nonsense_Mutation_p.G319*	NM_138342.3	NP_612351.2	Q8IW92	GLBL2_HUMAN	galactosidase, beta 1-like 2	319					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	beta-galactosidase activity (GO:0004565)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	41	all_hematologic(175;0.127)	all_cancers(12;2.85e-18)|all_epithelial(12;1.21e-12)|all_lung(97;0.000276)|Lung NSC(97;0.000518)|Breast(109;0.00122)|Medulloblastoma(222;0.0399)|all_neural(223;0.0412)|Esophageal squamous(93;0.0844)		Epithelial(10;1.37e-11)|all cancers(11;2.2e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000885)|Lung(977;0.223)		CATGTTCCACGGAGGCACCAA	0.527																																					p.G319X		Atlas-SNP	.											GLB1L2,NS,carcinoma,0,1	GLB1L2	79	.	0			c.G955T						.						112	88	96					11																	134238603		2201	4297	6498	SO:0001587	stop_gained	89944	exon10			TTCCACGGAGGCA		CCDS31724.1	11q25	2008-01-29			ENSG00000149328	ENSG00000149328			25129	protein-coding gene	gene with protein product						12975309	Standard	NM_138342		Approved		uc001qhp.3	Q8IW92	OTTHUMG00000167179	ENST00000535456.2:c.955G>T	chr11.hg19:g.134238603G>T	ENSP00000444628:p.Gly319*	76.0	0.0		52.0	4.0	NM_138342	A6NCE6|Q6UX60|Q8NC62|Q8NCB3|Q8NCJ1|Q96HP3	Nonsense_Mutation	SNP	ENST00000535456.2	hg19	CCDS31724.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	36|36	5.892637|5.892637	0.97074|0.97074	.|.	.|.	ENSG00000149328|ENSG00000149328	ENST00000339772;ENST00000535456;ENST00000389881|ENST00000525089;ENST00000533324	.|.	.|.	.|.	5.19|5.19	5.19|5.19	0.71726|0.71726	.|.	0.055211|.	0.64402|.	D|.	0.000001|.	.|T	.|0.73544	.|0.3600	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.73742	.|-0.3887	.|3	0.87932|.	D|.	0|.	-16.874|-16.874	17.4812|17.4812	0.87673|0.87673	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|L	319|257;146	.|.	ENSP00000344659:G319X|.	G|R	+|+	1|2	0|0	GLB1L2|GLB1L2	133743813|133743813	1.000000|1.000000	0.71417|0.71417	0.558000|0.558000	0.28319|0.28319	0.965000|0.965000	0.64279|0.64279	9.048000|9.048000	0.93830|0.93830	2.408000|2.408000	0.81797|0.81797	0.655000|0.655000	0.94253|0.94253	GGA|CGG	.	G|0.997;A|0.003		0.527	GLB1L2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393629.2	NM_138342		T	134238603	G	T	134238603	4	4	259	1	0	0	0	0	0	1	0	0	6437	1117	39	1	993	1	GLB1L2	11	134238603	Nonsense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	8091606	134238603	767913	524	36842										
WNK1	65125	hgsc.bcm.edu	37	chr12	922831	922831	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cgaaaattaacaaagtctgaGaggcagagatttaaagaaga	10	4	1	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:922831G>T	ENST00000315939.6	+	2	1426	c.783G>T	c.(781-783)gaG>gaT	p.E261D	WNK1_ENST00000447667.2_Missense_Mutation_p.E261D|WNK1_ENST00000530271.2_Missense_Mutation_p.E261D|WNK1_ENST00000535572.1_Missense_Mutation_p.E261D|WNK1_ENST00000537687.1_Missense_Mutation_p.E261D	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	261	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			CAAAGTCTGAGAGGCAGAGAT	0.318																																					p.E261D	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.G783T						.						74	72	72					12																	922831		2203	4300	6503	SO:0001583	missense	65125	exon2			GTCTGAGAGGCAG	AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 167"	605232	"protein kinase, lysine deficient 1", "hereditary sensory neuropathy, type II"	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.783G>T	chr12.hg19:g.922831G>T	ENSP00000313059:p.Glu261Asp	113.0	0.0		74.0	5.0	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	hg19	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.050825	0.75960	.	.	ENSG00000060237	ENST00000535572;ENST00000315939;ENST00000537687;ENST00000447667;ENST00000530271	T;T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21;-0.21	5.83	4.9	0.64082	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000003	T	0.58323	0.2114	N	0.16567	0.415	0.80722	D	1	P;P;B	0.38020	0.56;0.615;0.006	B;P;B	0.47118	0.403;0.538;0.014	T	0.62562	-0.6828	10	0.87932	D	0	-17.5842	8.8647	0.35278	0.1929:0.0:0.8071:0.0	.	261;261;261	F5GWT4;Q9H4A3;F6UYG0	.;WNK1_HUMAN;.	D	261	ENSP00000441972:E261D;ENSP00000313059:E261D;ENSP00000444465:E261D;ENSP00000392542:E261D;ENSP00000433548:E261D	ENSP00000313059:E261D	E	+	3	2	WNK1	793092	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.076000	0.57591	1.332000	0.45431	0.561000	0.74099	GAG	.	.		0.318	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979		T	922831	G	T	922831	3	4	259	1	0	0	0	0	1	0	0	0	17392	933	33	3	789	3	WNK1	12	922831	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10		922831	132929064	525	36843										
WNK1	65125	hgsc.bcm.edu	37	chr12	994233	994233	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agtatcacaatacctgcagtTgtctcaatatctactacatc	4	11	3	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:994233T>C	ENST00000315939.6	+	19	4906	c.4263T>C	c.(4261-4263)gtT>gtC	p.V1421V	WNK1_ENST00000530271.2_Silent_p.V1919V|WNK1_ENST00000535572.1_Silent_p.V1174V|WNK1_ENST00000340908.4_Silent_p.V1014V|WNK1_ENST00000537687.1_Silent_p.V1681V	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	1421					intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			TACCTGCAGTTGTCTCAATAT	0.463																																					p.V1681V	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.T5043C						.						176	176	176					12																	994233		2203	4300	6503	SO:0001819	synonymous_variant	65125	exon19			TGCAGTTGTCTCA	AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 167"	605232	"protein kinase, lysine deficient 1", "hereditary sensory neuropathy, type II"	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.4263T>C	chr12.hg19:g.994233T>C		103.0	0.0		99.0	4.0	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Silent	SNP	ENST00000315939.6	hg19	CCDS8506.1																																																																																			.	.		0.463	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979		C	994233	T	C	994233	2	2	259	1	0	0	0	0	0	0	0	1	17392	1799	63	2		2	WNK1	12	994233	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	71402	994233	132857662	526	36844										
FBXL14	144699	hgsc.bcm.edu	37	chr12	1702401	1702401	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cagccccgagaggcgcaggcTgcccatggccagatgcatga	14	14	0	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:1702401T>C	ENST00000339235.3	-	1	930	c.832A>G	c.(832-834)Agc>Ggc	p.S278G	FBXL14_ENST00000543278.1_5'Flank|WNT5B_ENST00000537031.1_Intron	NM_152441.2	NP_689654.1	Q8N1E6	FXL14_HUMAN	F-box and leucine-rich repeat protein 14	278					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	8	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00115)			AGGCGCAGGCTGCCCATGGCC	0.612																																					p.S278G		Atlas-SNP	.											.	FBXL14	19	.	0			c.A832G						.						61	56	58					12																	1702401		2203	4300	6503	SO:0001583	missense	144699	exon1			GCAGGCTGCCCAT	BC028132	CCDS8509.1	12p13.33	2011-06-09			ENSG00000171823	ENSG00000171823		"F-boxes / Leucine-rich repeats"	28624	protein-coding gene	gene with protein product		609081				12477932	Standard	NM_152441		Approved	MGC40195, Fbl14	uc001qjh.3	Q8N1E6	OTTHUMG00000090369	ENST00000339235.3:c.832A>G	chr12.hg19:g.1702401T>C	ENSP00000344855:p.Ser278Gly	72.0	0.0		60.0	4.0	NM_152441		Missense_Mutation	SNP	ENST00000339235.3	hg19	CCDS8509.1	.	.	.	.	.	.	.	.	.	.	T	8.116	0.779902	0.16120	.	.	ENSG00000171823	ENST00000339235	T	0.02395	4.31	4.71	3.56	0.40772	.	0.244275	0.41712	D	0.000840	T	0.01124	0.0037	N	0.01874	-0.695	0.40520	D	0.980829	B	0.02656	0.0	B	0.01281	0.0	T	0.52734	-0.8536	10	0.15952	T	0.53	.	5.5706	0.17194	0.1512:0.0809:0.0:0.7678	.	278	Q8N1E6	FXL14_HUMAN	G	278	ENSP00000344855:S278G	ENSP00000344855:S278G	S	-	1	0	FBXL14	1572662	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.826000	0.55738	0.813000	0.34350	0.528000	0.53228	AGC	.	.		0.612	FBXL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206741.1	NM_152441		C	1702401	T	C	1702401	3	2	259	1	0	0	0	0	1	0	0	0	5718	1580	55	2	432	2	FBXL14	12	1702401	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	708168	1702401	132149494	527	36845										
DCP1B	196513	hgsc.bcm.edu	37	chr12	2062133	2062133	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aggtcctgtaaaaaattctcCcgcagaatgggtactgccat	9	10	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:2062133C>A	ENST00000280665.6	-	7	1052	c.973G>T	c.(973-975)Gga>Tga	p.G325*	DCP1B_ENST00000397173.4_Nonsense_Mutation_p.G223*|DCP1B_ENST00000541700.1_5'UTR|DCP1B_ENST00000540622.1_Nonsense_Mutation_p.G199*	NM_152640.3	NP_689853.3	Q8IZD4	DCP1B_HUMAN	decapping mRNA 1B	325					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	hydrolase activity (GO:0016787)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(3)|lung(10)|skin(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00193)			AAAAATTCTCCCGCAGAATGG	0.502																																					p.G325X		Atlas-SNP	.											.	DCP1B	63	.	0			c.G973T						.						79	87	85					12																	2062133		2203	4300	6503	SO:0001587	stop_gained	196513	exon7			ATTCTCCCGCAGA	AY146652	CCDS31727.1	12p13.33	2013-05-02	2013-05-02		ENSG00000151065	ENSG00000151065			24451	protein-coding gene	gene with protein product		609843	"DCP1 decapping enzyme homolog B (S. cerevisiae)"			12417715, 15067023	Standard	NM_152640		Approved	FLJ31638	uc001qjx.1	Q8IZD4	OTTHUMG00000168113	ENST00000280665.6:c.973G>T	chr12.hg19:g.2062133C>A	ENSP00000280665:p.Gly325*	98.0	0.0		94.0	4.0	NM_152640	B4DRD1|Q86XH9|Q96BP8|Q96MZ8	Nonsense_Mutation	SNP	ENST00000280665.6	hg19	CCDS31727.1	.	.	.	.	.	.	.	.	.	.	C	13.02	2.113145	0.37339	.	.	ENSG00000151065	ENST00000280665;ENST00000397173;ENST00000540622	.	.	.	4.73	-1.34	0.09143	.	1.130390	0.06354	N	0.710400	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.19147	T	0.46	-0.6889	8.1265	0.31001	0.0:0.5862:0.1027:0.3111	.	.	.	.	X	325;223;199	.	ENSP00000280665:G325X	G	-	1	0	DCP1B	1932394	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.350000	0.07721	-0.863000	0.04084	-1.886000	0.00541	GGA	.	.		0.502	DCP1B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398244.1	NM_152640		A	2062133	C	A	2062133	4	1	259	1	0	0	0	0	0	1	0	0	4301	632	22	3	892	3	DCP1B	12	2062133	Nonsense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	359732	2062133	131789762	528	36846										
PARP11	57097	hgsc.bcm.edu	37	chr12	3923215	3923215	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ataattaccttttccaaagaCagcaccatgtataccattta	3	10	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:3923215C>T	ENST00000228820.4	-	7	832	c.688G>A	c.(688-690)Gtc>Atc	p.V230I	PARP11_ENST00000476985.1_5'UTR|PARP11_ENST00000397096.2_Missense_Mutation_p.V223I|PARP11_ENST00000427057.2_Missense_Mutation_p.V149I|PARP11_ENST00000447133.3_Missense_Mutation_p.V149I	NM_020367.4	NP_065100.2	Q9NR21	PAR11_HUMAN	poly (ADP-ribose) polymerase family, member 11	223	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.						NAD+ ADP-ribosyltransferase activity (GO:0003950)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)	17			all cancers(3;1.58e-07)|OV - Ovarian serous cystadenocarcinoma(31;0.00287)|GBM - Glioblastoma multiforme(3;0.0141)|COAD - Colon adenocarcinoma(12;0.0264)			TTTCCAAAGACAGCACCATGT	0.353																																					p.V230I		Atlas-SNP	.											.	PARP11	39	.	0			c.G688A						.						128	122	124					12																	3923215		2203	4300	6503	SO:0001583	missense	57097	exon7			CAAAGACAGCACC	AF263540	CCDS8523.2, CCDS66281.1	12p13.3	2014-01-28	2004-08-25	2004-08-26	ENSG00000111224	ENSG00000111224		"Poly (ADP-ribose) polymerases"	1186	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 6"	C12orf6		15273990	Standard	NM_001286522		Approved		uc001qml.2	Q9NR21	OTTHUMG00000156442	ENST00000228820.4:c.688G>A	chr12.hg19:g.3923215C>T	ENSP00000228820:p.Val230Ile	134.0	0.0		97.0	4.0	NM_020367	B4DRQ0|Q68DS1|Q8N5Y9	Missense_Mutation	SNP	ENST00000228820.4	hg19	CCDS8523.2	.	.	.	.	.	.	.	.	.	.	C	9.723	1.160185	0.21454	.	.	ENSG00000111224	ENST00000397096;ENST00000427057;ENST00000228820;ENST00000447133	T;T;T;T	0.14266	2.52;2.52;2.52;2.52	5.41	-0.0656	0.13768	Poly(ADP-ribose) polymerase, catalytic domain (2);	0.342248	0.29964	N	0.010747	T	0.16257	0.0391	L	0.55990	1.75	0.36412	D	0.863777	B;B;B	0.23735	0.09;0.008;0.011	B;B;B	0.28011	0.085;0.028;0.047	T	0.20806	-1.0264	10	0.25751	T	0.34	.	19.145	0.93461	0.0:0.759:0.241:0.0	.	149;230;223	Q9NR21-2;Q9NR21-4;Q9NR21	.;.;PAR11_HUMAN	I	223;149;230;149	ENSP00000380284:V223I;ENSP00000397058:V149I;ENSP00000228820:V230I;ENSP00000405385:V149I	ENSP00000228820:V230I	V	-	1	0	PARP11	3793476	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	1.573000	0.36472	0.089000	0.17243	-0.274000	0.10170	GTC	.	.		0.353	PARP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344213.1			T	3923215	C	T	3923215	3	4	259	1	0	0	0	0	1	0	0	0	11465	478	17	3	336	3	PARP11	12	3923215	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	1861082	3923215	129928680	529	36847										
C12orf4	57102	hgsc.bcm.edu	37	chr12	4600397	4600397	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	taagcaccagggtatagtcaTttcctaaaaacagaaacaaa	6	8	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:4600397T>C	ENST00000261250.3	-	12	1531	c.1444A>G	c.(1444-1446)Atg>Gtg	p.M482V	C12orf4_ENST00000545746.1_Missense_Mutation_p.M482V	NM_020374.2	NP_065107.1	Q9NQ89	CL004_HUMAN	chromosome 12 open reading frame 4	482										NS(1)|endometrium(1)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	13			Colorectal(7;0.00165)|COAD - Colon adenocarcinoma(12;0.0229)	BRCA - Breast invasive adenocarcinoma(232;0.0281)		GGTATAGTCATTTCCTAAAAA	0.358																																					p.M482V		Atlas-SNP	.											.	C12orf4	58	.	0			c.A1444G						.						137	124	128					12																	4600397		2203	4300	6503	SO:0001583	missense	57102	exon12			TAGTCATTTCCTA	AJ272205	CCDS8528.1	12p13.3	2012-08-10			ENSG00000047621	ENSG00000047621			1184	protein-coding gene	gene with protein product							Standard	NM_020374		Approved		uc001qms.3	Q9NQ89	OTTHUMG00000168258	ENST00000261250.3:c.1444A>G	chr12.hg19:g.4600397T>C	ENSP00000261250:p.Met482Val	119.0	0.0		100.0	6.0	NM_020374	D3DUQ8|Q6MZH5	Missense_Mutation	SNP	ENST00000261250.3	hg19	CCDS8528.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.178888	0.78564	.	.	ENSG00000047621	ENST00000261250;ENST00000545746	.	.	.	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.76212	0.3956	M	0.84326	2.69	0.80722	D	1	P	0.51791	0.948	P	0.54499	0.754	T	0.81048	-0.1109	9	0.87932	D	0	.	15.5652	0.76287	0.0:0.0:0.0:1.0	.	482	Q9NQ89	CL004_HUMAN	V	482	.	ENSP00000261250:M482V	M	-	1	0	C12orf4	4470658	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.239000	0.78182	2.129000	0.65627	0.477000	0.44152	ATG	.	.		0.358	C12orf4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398992.1	NM_020374		C	4600397	T	C	4600397	3	2	259	1	0	0	0	0	1	0	0	0	1687	1493	52	2	226	2	C12orf4	12	4600397	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	677182	4600397	129251498	530	36848										
AKAP3	10566	hgsc.bcm.edu	37	chr12	4736342	4736342	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttggtcacctacaatgggagCagacttaaggcaagattcat	10	8	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:4736342C>A	ENST00000545990.2	-	5	2250	c.1726G>T	c.(1726-1728)Gct>Tct	p.A576S	RP11-500M8.7_ENST00000536588.1_Intron|AKAP3_ENST00000228850.1_Missense_Mutation_p.A576S	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	576					acrosome reaction (GO:0007340)|cellular component movement (GO:0006928)|protein localization (GO:0008104)|single fertilization (GO:0007338)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	acrosomal vesicle (GO:0001669)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	protein kinase A binding (GO:0051018)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						ACAATGGGAGCAGACTTAAGG	0.468																																					p.A576S		Atlas-SNP	.											AKAP3_ENST00000545990,NS,carcinoma,0,4	AKAP3	212	.	0			c.G1726T						.						67	65	66					12																	4736342		2203	4300	6503	SO:0001583	missense	10566	exon4			TGGGAGCAGACTT	U85715	CCDS8531.1	12p13.3	2009-03-12				ENSG00000111254		"A-kinase anchor proteins"	373	protein-coding gene	gene with protein product	"Fibrous Sheath Protein of 95 kDa", "cancer/testis antigen 82"	604689				10334916, 10319321	Standard	NM_001278309		Approved	FSP95, SOB1, AKAP110, CT82	uc001qnb.4	O75969		ENST00000545990.2:c.1726G>T	chr12.hg19:g.4736342C>A	ENSP00000440994:p.Ala576Ser	66.0	0.0		63.0	3.0	NM_006422	O75945|Q86X01|Q9UM61	Missense_Mutation	SNP	ENST00000545990.2	hg19	CCDS8531.1	.	.	.	.	.	.	.	.	.	.	C	0.005	-2.207578	0.00292	.	.	ENSG00000111254	ENST00000228850;ENST00000545990	T;T	0.07327	3.2;3.2	5.82	-2.48	0.06423	A-kinase anchor 110kDa, C-terminal (1);	0.402656	0.24251	N	0.040167	T	0.02533	0.0077	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.38714	-0.9648	10	0.18710	T	0.47	-2.3172	1.1023	0.01687	0.2296:0.3516:0.1935:0.2253	.	576	O75969	AKAP3_HUMAN	S	576	ENSP00000228850:A576S;ENSP00000440994:A576S	ENSP00000228850:A576S	A	-	1	0	AKAP3	4606603	0.126000	0.22350	0.001000	0.08648	0.009000	0.06853	0.203000	0.17315	-0.107000	0.12088	-1.086000	0.02197	GCT	.	.		0.468	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	NM_006422		A	4736342	C	A	4736342	3	1	259	1	0	0	0	0	1	0	0	0	452	710	25	3	843	3	AKAP3	12	4736342	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	135945	4736342	129115553	531	36849										
VWF	7450	hgsc.bcm.edu	37	chr12	6128323	6128323	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gaggcggatctgcttgaggtTggcatggggcccaatgccca	16	10	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:6128323T>C	ENST00000261405.5	-	28	4515	c.4261A>G	c.(4261-4263)Aac>Gac	p.N1421D		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	1421	VWFA 1; binding site for platelet glycoprotein Ib. {ECO:0000255|PROSITE- ProRule:PRU00219}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	TGCTTGAGGTTGGCATGGGGC	0.592																																					p.N1421D		Atlas-SNP	.											.	VWF	338	.	0			c.A4261G						.						76	77	77					12																	6128323		2203	4300	6503	SO:0001583	missense	7450	exon28			TGAGGTTGGCATG		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"Endogenous ligands"	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.4261A>G	chr12.hg19:g.6128323T>C	ENSP00000261405:p.Asn1421Asp	142.0	0.0		96.0	4.0	NM_000552	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	hg19	CCDS8539.1	.	.	.	.	.	.	.	.	.	.	.	12.82	2.053131	0.36181	.	.	ENSG00000110799	ENST00000261405	D	0.81821	-1.54	4.92	4.92	0.64577	von Willebrand factor, type A (3);	0.817450	0.10796	N	0.633182	D	0.84906	0.5576	M	0.69358	2.11	0.80722	D	1	B	0.29955	0.263	B	0.43251	0.413	T	0.80975	-0.1142	10	0.49607	T	0.09	.	13.8742	0.63643	0.0:0.0:0.0:1.0	.	1421	P04275	VWF_HUMAN	D	1421	ENSP00000261405:N1421D	ENSP00000261405:N1421D	N	-	1	0	VWF	5998584	0.994000	0.37717	0.613000	0.29037	0.423000	0.31445	4.583000	0.60964	2.077000	0.62373	0.454000	0.30748	AAC	.	.		0.592	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		C	6128323	T	C	6128323	3	2	259	1	0	0	0	0	1	0	0	0	17261	1812	63	2	4280	2	VWF	12	6128323	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1391981	6128323	127723572	532	36850										
CD4	920	hgsc.bcm.edu	37	chr12	6926435	6926435	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgggtgctgaaccctgaggcGgggatgtggcagtgtctgct	18	8	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:6926435G>T	ENST00000011653.4	+	7	1353	c.1095G>T	c.(1093-1095)gcG>gcT	p.A365A		NM_000616.4|NM_001195015.2|NM_001195016.2|NM_001195017.2	NP_000607.1|NP_001181944.1|NP_001181945.1|NP_001181946.1	P01730	CD4_HUMAN	CD4 molecule	365	Ig-like C2-type 3.				cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cytokine production (GO:0001816)|defense response to Gram-negative bacterium (GO:0050829)|entry into host cell (GO:0030260)|enzyme linked receptor protein signaling pathway (GO:0007167)|immune response (GO:0006955)|induction by virus of host cell-cell fusion (GO:0006948)|innate immune response (GO:0045087)|maintenance of protein location in cell (GO:0032507)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase activity (GO:0045860)|protein palmitoleylation (GO:0045234)|regulation of defense response to virus by virus (GO:0050690)|regulation of T cell activation (GO:0050863)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)|T cell selection (GO:0045058)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|viral process (GO:0016032)	early endosome (GO:0005769)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	coreceptor activity (GO:0015026)|enzyme binding (GO:0019899)|extracellular matrix structural constituent (GO:0005201)|glycoprotein binding (GO:0001948)|MHC class II protein binding (GO:0042289)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	23		Myeloproliferative disorder(1001;0.0122)			Antithymocyte globulin(DB00098)	ACCCTGAGGCGGGGATGTGGC	0.592																																					p.A365A		Atlas-SNP	.											CD4,NS,carcinoma,0,1	CD4	47	.	0			c.G1095T						.						73	59	63					12																	6926435		2203	4300	6503	SO:0001819	synonymous_variant	920	exon7			TGAGGCGGGGATG	M35160	CCDS8562.1	12p13.31	2013-01-11	2006-03-28		ENSG00000010610	ENSG00000010610		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing"	1678	protein-coding gene	gene with protein product		186940	"CD4 antigen (p55)", "T-cell surface glycoprotein CD4"				Standard	NM_000616		Approved		uc001qqv.2	P01730	OTTHUMG00000168514	ENST00000011653.4:c.1095G>T	chr12.hg19:g.6926435G>T		122.0	1.0		100.0	4.0	NM_000616	B2R737|D3DUS5|Q4ZGK2|Q5U066|Q9UDE5	Silent	SNP	ENST00000011653.4	hg19	CCDS8562.1																																																																																			.	.		0.592	CD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399978.1	NM_000616		T	6926435	G	T	6926435	2	4	259	1	0	0	0	0	0	0	0	1	3016	1103	39	1		1	CD4	12	6926435	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	798112	6926435	126925460	533	36851										
PEX5	5830	hgsc.bcm.edu	37	chr12	7344169	7344169	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctctctctcttttaagccccTggtgtggcagacttggcctt	9	13	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:7344169T>C	ENST00000455147.2	+	6	901	c.321T>C	c.(319-321)ccT>ccC	p.P107P	RP11-273B20.3_ENST00000545794.1_RNA|PEX5_ENST00000266563.5_Silent_p.P107P|PEX5_ENST00000420616.2_Silent_p.P107P|PEX5_ENST00000266564.3_Silent_p.P107P|PEX5_ENST00000545220.1_3'UTR|RP11-273B20.3_ENST00000543061.1_RNA|PEX5_ENST00000434354.2_Silent_p.P122P|PEX5_ENST00000412720.2_Silent_p.P128P	NM_001131026.1	NP_001124498.1	P50542	PEX5_HUMAN	peroxisomal biogenesis factor 5	107					cell development (GO:0048468)|cerebral cortex cell migration (GO:0021795)|cerebral cortex neuron differentiation (GO:0021895)|endoplasmic reticulum organization (GO:0007029)|fatty acid beta-oxidation (GO:0006635)|mitochondrial membrane organization (GO:0007006)|negative regulation of protein homotetramerization (GO:1901094)|neuromuscular process (GO:0050905)|neuron migration (GO:0001764)|positive regulation of multicellular organism growth (GO:0040018)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome matrix, docking (GO:0016560)|protein import into peroxisome matrix, translocation (GO:0016561)|protein import into peroxisome membrane (GO:0045046)|protein targeting to peroxisome (GO:0006625)|protein tetramerization (GO:0051262)|very long-chain fatty acid metabolic process (GO:0000038)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	enzyme binding (GO:0019899)|peroxisome matrix targeting signal-1 binding (GO:0005052)|peroxisome targeting sequence binding (GO:0000268)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|small GTPase binding (GO:0031267)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)	21						TTTAAGCCCCTGGTGTGGCAG	0.448																																					p.P122P		Atlas-SNP	.											.	PEX5	63	.	0			c.T366C						.						68	68	68					12																	7344169		2203	4300	6503	SO:0001819	synonymous_variant	5830	exon5			AGCCCCTGGTGTG	U19721	CCDS8576.1, CCDS44822.1, CCDS44823.1, CCDS44824.1, CCDS73433.1	12p	2013-01-10	2004-03-17	2004-03-19		ENSG00000139197		"Tetratricopeptide (TTC) repeat domain containing"	9719	protein-coding gene	gene with protein product		600414	"peroxisome receptor 1"	PXR1			Standard	NM_000319		Approved	PTS1R	uc010sgc.2	P50542		ENST00000455147.2:c.321T>C	chr12.hg19:g.7344169T>C		82.0	0.0		66.0	4.0	NM_001131023	A8K891|B4DZ45|B7ZAD5|D3DUT8|Q15115|Q15266|Q96FN7	Silent	SNP	ENST00000455147.2	hg19	CCDS44823.1																																																																																			.	.		0.448	PEX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398611.1	NM_000319		C	7344169	T	C	7344169	2	2	259	1	0	0	0	0	0	0	0	1	11757	1567	55	2		2	PEX5	12	7344169	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	417734	7344169	126507726	534	36852										
PZP	5858	hgsc.bcm.edu	37	chr12	9318700	9318700	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aggaaaatagcttcgcaccgTttcagggactggccctgaac	11	11	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:9318700T>C	ENST00000261336.2	-	18	2234	c.2206A>G	c.(2206-2208)Acg>Gcg	p.T736A	PZP_ENST00000539983.1_5'UTR|PZP_ENST00000381997.2_Missense_Mutation_p.T605A	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	736					female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						CTTCGCACCGTTTCAGGGACT	0.448																																					p.T736A	Melanoma(125;1402 1695 4685 34487 38571)	Atlas-SNP	.											.	PZP	422	.	0			c.A2206G						.						143	134	137					12																	9318700		2203	4300	6503	SO:0001583	missense	5858	exon18			GCACCGTTTCAGG	X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.2206A>G	chr12.hg19:g.9318700T>C	ENSP00000261336:p.Thr736Ala	143.0	0.0		74.0	4.0	NM_002864	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	hg19	CCDS8600.1	.	.	.	.	.	.	.	.	.	.	T	13.51	2.258979	0.39896	.	.	ENSG00000126838	ENST00000261336;ENST00000381997	T;T	0.37752	1.47;1.18	3.58	2.42	0.29668	.	0.243635	0.20220	U	0.096705	T	0.38081	0.1027	L	0.29908	0.895	0.20307	N	0.999916	P;D;P	0.54772	0.85;0.968;0.85	P;P;P	0.59115	0.507;0.852;0.507	T	0.10800	-1.0614	10	0.87932	D	0	.	6.6954	0.23195	0.0:0.1177:0.0:0.8823	.	736;605;736	B2R950;P20742-2;P20742	.;.;PZP_HUMAN	A	736;605	ENSP00000261336:T736A;ENSP00000371427:T605A	ENSP00000261336:T736A	T	-	1	0	PZP	9209967	0.963000	0.33076	0.004000	0.12327	0.352000	0.29268	2.567000	0.45956	0.533000	0.28675	0.383000	0.25322	ACG	.	.		0.448	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864		C	9318700	T	C	9318700	3	2	259	1	0	0	0	0	1	0	0	0	12884	1725	60	2	2318	2	PZP	12	9318700	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1974531	9318700	124533195	535	36853										
TAS2R8	50836	hgsc.bcm.edu	37	chr12	10959161	10959161	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	taaggctgaccaacaaggaaAtggcaaagcatcccagcagg	11	10	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:10959161A>G	ENST00000240615.2	-	1	731	c.419T>C	c.(418-420)aTt>aCt	p.I140T		NM_023918.1	NP_076407.1	Q9NYW2	TA2R8_HUMAN	taste receptor, type 2, member 8	140					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						CAACAAGGAAATGGCAAAGCA	0.398																																					p.I140T		Atlas-SNP	.											.	TAS2R8	42	.	0			c.T419C						.						110	99	103					12																	10959161		2203	4300	6503	SO:0001583	missense	50836	exon1			AAGGAAATGGCAA	AF227134	CCDS8632.1	12p13	2012-08-22			ENSG00000121314	ENSG00000121314		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14915	protein-coding gene	gene with protein product		604794				10761934, 10766242	Standard	NM_023918		Approved	T2R8, TRB5	uc010shh.2	Q9NYW2	OTTHUMG00000168506	ENST00000240615.2:c.419T>C	chr12.hg19:g.10959161A>G	ENSP00000240615:p.Ile140Thr	123.0	0.0		84.0	4.0	NM_023918	Q4KN29|Q645Y2	Missense_Mutation	SNP	ENST00000240615.2	hg19	CCDS8632.1	.	.	.	.	.	.	.	.	.	.	A	14.72	2.619150	0.46736	.	.	ENSG00000121314	ENST00000240615	T	0.00922	5.54	4.5	2.02	0.26589	GPCR, rhodopsin-like superfamily (1);	0.549996	0.14943	U	0.289365	T	0.01765	0.0056	M	0.69823	2.125	0.09310	N	1	B	0.30236	0.274	B	0.34301	0.179	T	0.34329	-0.9833	10	0.87932	D	0	.	8.0232	0.30421	0.675:0.0:0.0:0.325	.	140	Q9NYW2	TA2R8_HUMAN	T	140	ENSP00000240615:I140T	ENSP00000240615:I140T	I	-	2	0	TAS2R8	10850428	0.002000	0.14202	0.000000	0.03702	0.264000	0.26372	1.807000	0.38902	0.222000	0.20900	0.455000	0.32223	ATT	.	.		0.398	TAS2R8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399932.1			G	10959161	A	G	10959161	3	3	259	1	0	0	0	0	1	0	0	0	15602	101	4	2	513	2	TAS2R8	12	10959161	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1640461	10959161	122892734	536	36854										
C12orf35	55196	hgsc.bcm.edu	37	chr12	32135858	32135858	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gcagtggacaagaatcctcaAcaaaaggaatgcctgctaaa	9	9	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:32135858A>G	ENST00000312561.4	+	4	2383	c.1969A>G	c.(1969-1971)Aca>Gca	p.T657A	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	657																	AGAATCCTCAACAAAAGGAAT	0.423																																					p.T657A		Atlas-SNP	.											.	.	.	.	0			c.A1969G						.						68	65	66					12																	32135858		2203	4299	6502	SO:0001583	missense	55196	exon4			TCCTCAACAAAAG	AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 35"	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.1969A>G	chr12.hg19:g.32135858A>G	ENSP00000310338:p.Thr657Ala	87.0	0.0		73.0	4.0	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Missense_Mutation	SNP	ENST00000312561.4	hg19	CCDS8725.2	.	.	.	.	.	.	.	.	.	.	A	8.364	0.833877	0.16820	.	.	ENSG00000174718	ENST00000312561;ENST00000381054	T;T	0.05258	4.15;3.47	4.99	-5.19	0.02832	.	1.410390	0.04860	N	0.443996	T	0.02929	0.0087	N	0.12182	0.205	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.44877	-0.9299	9	.	.	.	.	3.1103	0.06356	0.2884:0.1292:0.4554:0.1271	.	657	Q9HCM1	CL035_HUMAN	A	657	ENSP00000310338:T657A;ENSP00000370442:T657A	.	T	+	1	0	C12orf35	32027125	0.000000	0.05858	0.000000	0.03702	0.508000	0.34012	-1.927000	0.01561	-0.440000	0.07211	0.460000	0.39030	ACA	.	.		0.423	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169		G	32135858	A	G	32135858	3	3	259	1	0	0	0	0	1	0	0	0	1684	43	2	2	1971	2	C12orf35	12	32135858	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	21176697	32135858	101716037	537	36855										
DNM1L	10059	hgsc.bcm.edu	37	chr12	32890048	32890048	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gtgtttcttaggaacaaaggAgaaacaggctagccagagaa	12	6	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:32890048A>G	ENST00000549701.1	+	14	1623	c.1549A>G	c.(1549-1551)Aga>Gga	p.R517G	DNM1L_ENST00000547312.1_Missense_Mutation_p.R517G|DNM1L_ENST00000553257.1_Missense_Mutation_p.R530G|DNM1L_ENST00000358214.5_Missense_Mutation_p.R530G|DNM1L_ENST00000266481.6_Missense_Mutation_p.R517G|DNM1L_ENST00000452533.2_Missense_Mutation_p.R517G|DNM1L_ENST00000414834.2_Missense_Mutation_p.R314G|DNM1L_ENST00000381000.4_Missense_Mutation_p.R530G|YARS2_ENST00000551673.1_Intron			O00429	DNM1L_HUMAN	dynamin 1-like	517	B domain.|Interaction with GSK3B.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|dynamin polymerization involved in mitochondrial fission (GO:0003374)|endocytosis (GO:0006897)|GTP catabolic process (GO:0006184)|membrane fission involved in mitochondrial fission (GO:0090149)|membrane fusion (GO:0061025)|mitochondrial fission (GO:0000266)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrion morphogenesis (GO:0070584)|necroptotic process (GO:0070266)|peroxisome fission (GO:0016559)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein secretion (GO:0050714)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein homotetramerization (GO:0051289)|protein localization to mitochondrion (GO:0070585)|regulation of mitochondrion organization (GO:0010821)|regulation of peroxisome organization (GO:1900063)|regulation of protein oligomerization (GO:0032459)|release of cytochrome c from mitochondria (GO:0001836)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)|protein complex (GO:0043234)|synapse (GO:0045202)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	23	Lung NSC(5;2.15e-06)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					GGAACAAAGGAGAAACAGGCT	0.333																																					p.R517G		Atlas-SNP	.											.	DNM1L	52	.	0			c.A1549G						.						125	121	122					12																	32890048		2203	4300	6503	SO:0001583	missense	10059	exon14			CAAAGGAGAAACA	AF000430	CCDS8728.1, CCDS8729.1, CCDS8730.1, CCDS61095.1, CCDS61096.1, CCDS61098.1, CCDS61099.1	12p11.21	2012-10-02			ENSG00000087470	ENSG00000087470			2973	protein-coding gene	gene with protein product		603850				9348079, 9731200	Standard	NM_012062		Approved	DRP1, DVLP, HDYNIV, DYMPLE, VPS1	uc001rld.2	O00429	OTTHUMG00000169451	ENST00000549701.1:c.1549A>G	chr12.hg19:g.32890048A>G	ENSP00000450399:p.Arg517Gly	127.0	0.0		78.0	4.0	NM_012062	A8K4X9|B4DGC9|B4DSU8|J3KPI2|O14541|O60709|Q59GN9|Q7L6B3|Q8TBT7|Q9BWM1|Q9Y5J2	Missense_Mutation	SNP	ENST00000549701.1	hg19	CCDS8729.1	.	.	.	.	.	.	.	.	.	.	A	13.45	2.240152	0.39598	.	.	ENSG00000087470	ENST00000452533;ENST00000411996;ENST00000266479;ENST00000553257;ENST00000549701;ENST00000358214;ENST00000266481;ENST00000547312;ENST00000414834;ENST00000381000	D;D;D;D;D;D;T;D	0.90563	-2.67;-2.69;-2.69;-2.68;-2.68;-2.69;-1.34;-2.69	5.47	3.0	0.34707	.	0.290262	0.34828	N	0.003657	D	0.83473	0.5262	N	0.02916	-0.46	0.80722	D	1	D;B;B;P;B;B	0.58268	0.982;0.001;0.006;0.778;0.001;0.006	P;B;B;P;B;B	0.60236	0.871;0.009;0.016;0.572;0.012;0.016	T	0.80598	-0.1311	10	0.35671	T	0.21	.	6.2486	0.20833	0.635:0.2753:0.0896:0.0	.	314;570;570;583;570;517	B4DGC9;D3DUW6;D3DUW5;F8W8D1;D3DUW7;O00429	.;.;.;.;.;DNM1L_HUMAN	G	517;583;517;530;517;530;517;517;314;530	ENSP00000415131:R517G;ENSP00000449089:R530G;ENSP00000450399:R517G;ENSP00000350948:R530G;ENSP00000266481:R517G;ENSP00000448610:R517G;ENSP00000404160:R314G;ENSP00000370388:R530G	ENSP00000266479:R517G	R	+	1	2	DNM1L	32781315	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.892000	0.39748	0.917000	0.36895	0.533000	0.62120	AGA	.	.		0.333	DNM1L-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404124.1	NM_012062		G	32890048	A	G	32890048	3	3	259	1	0	0	0	0	1	0	0	0	4673	296	11	2	1603	2	DNM1L	12	32890048	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	754190	32890048	100961847	538	36856										
PKP2	5318	hgsc.bcm.edu	37	chr12	33031343	33031343	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctgtgcgtgtagtgagccctCtccgggctgctgtcaggaga	15	11	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:33031343C>T	ENST00000070846.6	-	3	495	c.471G>A	c.(469-471)gaG>gaA	p.E157E	PKP2_ENST00000340811.4_Silent_p.E157E	NM_004572.3	NP_004563.2	Q99959	PKP2_HUMAN	plakophilin 2	157					adherens junction maintenance (GO:0034334)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential (GO:0086001)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cell-cell signaling involved in cardiac conduction (GO:0086019)|desmosome assembly (GO:0002159)|gap junction assembly (GO:0016264)|heart development (GO:0007507)|intermediate filament bundle assembly (GO:0045110)|lipid homeostasis (GO:0055088)|maintenance of organ identity (GO:0048496)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of tight junction assembly (GO:2000810)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	adherens junction (GO:0005912)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|protein kinase C binding (GO:0005080)|sodium channel regulator activity (GO:0017080)			NS(1)|breast(2)|endometrium(1)|kidney(9)|large_intestine(8)|lung(21)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	50	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					AGTGAGCCCTCTCCGGGCTGC	0.592																																					p.E157E		Atlas-SNP	.											.	PKP2	110	.	0			c.G471A						.						120	120	120					12																	33031343		2203	4297	6500	SO:0001819	synonymous_variant	5318	exon3			AGCCCTCTCCGGG	X97675	CCDS8731.1, CCDS31771.1	12p11	2014-09-17				ENSG00000057294		"Armadillo repeat containing"	9024	protein-coding gene	gene with protein product		602861				8922383	Standard	NM_001005242		Approved		uc001rlj.4	Q99959	OTTHUMG00000169500	ENST00000070846.6:c.471G>A	chr12.hg19:g.33031343C>T		138.0	0.0		110.0	15.0	NM_004572	A0AV37|B8QFA1|B8QGS6|B8QGS7|D3DUW9|Q4VC01|Q99960	Silent	SNP	ENST00000070846.6	hg19	CCDS8731.1																																																																																			.	.		0.592	PKP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404449.1	NM_004572		T	33031343	C	T	33031343	2	4	259	1	0	0	0	0	0	0	0	1	11994	912	32	3		3	PKP2	12	33031343	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	141295	33031343	100820552	539	36857										
LRRK2	120892	hgsc.bcm.edu	37	chr12	40677799	40677799	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggtgacagccagatcatcagCttgctcttaaggaggctggc	13	10	3	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:40677799C>T	ENST00000298910.7	+	19	2422	c.2364C>T	c.(2362-2364)agC>agT	p.S788S	LRRK2_ENST00000343742.2_Silent_p.S788S	NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	788					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				AGATCATCAGCTTGCTCTTAA	0.448																																					p.S788S		Atlas-SNP	.											.	LRRK2	763	.	0			c.C2364T						.						166	163	164					12																	40677799		2203	4300	6503	SO:0001819	synonymous_variant	120892	exon19			CATCAGCTTGCTC	AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"Parkinson disease"	18618	protein-coding gene	gene with protein product		609007	"Parkinson disease (autosomal dominant) 8"	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.2364C>T	chr12.hg19:g.40677799C>T		181.0	0.0		104.0	5.0	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Silent	SNP	ENST00000298910.7	hg19	CCDS31774.1																																																																																			.	.		0.448	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		T	40677799	C	T	40677799	2	4	259	1	0	0	0	0	0	0	0	1	9042	796	28	3		3	LRRK2	12	40677799	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	7646456	40677799	93174096	540	36858										
ADAMTS20	80070	hgsc.bcm.edu	37	chr12	43847742	43847742	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cagcgcctggttgcactttcGattccgcctccacatgttct	8	15	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:43847742G>A	ENST00000389420.3	-	12	1727	c.1728C>T	c.(1726-1728)atC>atT	p.I576I	ADAMTS20_ENST00000553158.1_Silent_p.I576I	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	576	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		TTGCACTTTCGATTCCGCCTC	0.413																																					p.I576I		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.C1728T						.						117	92	100					12																	43847742		2203	4300	6503	SO:0001819	synonymous_variant	80070	exon12			ACTTTCGATTCCG	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.1728C>T	chr12.hg19:g.43847742G>A		105.0	0.0		76.0	46.0	NM_025003	A6NNC9|J3QT00	Silent	SNP	ENST00000389420.3	hg19	CCDS31778.2																																																																																			.	.		0.413	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		A	43847742	G	A	43847742	2	1	259	1	0	0	0	0	0	0	0	1	266	1048	37	1		1	ADAMTS20	12	43847742	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	3169943	43847742	90004153	541	36859										
ADAMTS20	80070	hgsc.bcm.edu	37	chr12	43847776	43847776	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atgttcttgaacaagaactgTaaggttcccatggtccccat	8	10	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:43847776T>C	ENST00000389420.3	-	12	1693	c.1694A>G	c.(1693-1695)tAc>tGc	p.Y565C	ADAMTS20_ENST00000553158.1_Missense_Mutation_p.Y565C	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	565	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		ACAAGAACTGTAAGGTTCCCA	0.403																																					p.Y565C		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.A1694G						.						115	93	100					12																	43847776		2203	4300	6503	SO:0001583	missense	80070	exon12			GAACTGTAAGGTT	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.1694A>G	chr12.hg19:g.43847776T>C	ENSP00000374071:p.Tyr565Cys	114.0	0.0		86.0	47.0	NM_025003	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	hg19	CCDS31778.2	.	.	.	.	.	.	.	.	.	.	T	17.96	3.517057	0.64634	.	.	ENSG00000173157	ENST00000389420;ENST00000553158;ENST00000389417	T;T	0.53423	0.62;0.62	4.77	3.6	0.41247	.	0.153604	0.30151	N	0.010297	T	0.70413	0.3221	M	0.87180	2.865	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.75161	-0.3415	10	0.87932	D	0	.	12.1553	0.54072	0.0:0.0:0.1435:0.8565	.	565	P59510	ATS20_HUMAN	C	565	ENSP00000374071:Y565C;ENSP00000448341:Y565C	ENSP00000374068:Y565C	Y	-	2	0	ADAMTS20	42134043	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.276000	0.43408	0.901000	0.36495	0.477000	0.44152	TAC	.	.		0.403	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		C	43847776	T	C	43847776	3	2	259	1	0	0	0	0	1	0	0	0	266	1638	57	2	4149	2	ADAMTS20	12	43847776	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	34	43847776	90004119	542	36860										
COL2A1	1280	hgsc.bcm.edu	37	chr12	48374364	48374364	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccaggtgctccagaggggccCtgaggaccaggggcaccagc	16	14	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:48374364C>T	ENST00000380518.3	-	39	2762	c.2598G>A	c.(2596-2598)caG>caA	p.Q866Q	COL2A1_ENST00000337299.6_Silent_p.Q797Q|COL2A1_ENST00000493991.1_5'UTR	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	866	Triple-helical region.				axon guidance (GO:0007411)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to BMP stimulus (GO:0071773)|central nervous system development (GO:0007417)|chondrocyte differentiation (GO:0002062)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal joint morphogenesis (GO:0060272)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|limb bud formation (GO:0060174)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|notochord development (GO:0030903)|otic vesicle development (GO:0071599)|palate development (GO:0060021)|proteoglycan metabolic process (GO:0006029)|regulation of gene expression (GO:0010468)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|tissue homeostasis (GO:0001894)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen type II trimer (GO:0005585)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(3)	64		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	CAGAGGGGCCCTGAGGACCAG	0.637																																					p.Q866Q		Atlas-SNP	.											.	COL2A1	368	.	0			c.G2598A						.						31	30	30					12																	48374364		2203	4300	6503	SO:0001819	synonymous_variant	1280	exon39			GGGGCCCTGAGGA	X16468	CCDS8759.1, CCDS41778.1	12q12-q13.2	2013-11-14	2008-02-04		ENSG00000139219	ENSG00000139219		"Collagens"	2200	protein-coding gene	gene with protein product		120140	"collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital)", "arthroophthalmopathy, progressive (Stickler syndrome)"	SEDC, AOM		1677770	Standard	NM_033150		Approved	STL1	uc001rqu.3	P02458	OTTHUMG00000149896	ENST00000380518.3:c.2598G>A	chr12.hg19:g.48374364C>T		70.0	0.0		57.0	4.0	NM_001844	A6NGA0|Q12985|Q14009|Q14044|Q14045|Q14046|Q14047|Q14056|Q14058|Q16672|Q1JQ82|Q2V4X7|Q6LBY1|Q6LBY2|Q6LBY3|Q96IT5|Q99227|Q9UE38|Q9UE39|Q9UE40|Q9UE41|Q9UE42|Q9UE43	Silent	SNP	ENST00000380518.3	hg19	CCDS41778.1																																																																																			.	.		0.637	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844		T	48374364	C	T	48374364	2	4	259	1	0	0	0	0	0	0	0	1	3689	680	24	3		3	COL2A1	12	48374364	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	4526588	48374364	85477531	543	36861										
COL2A1	1280	hgsc.bcm.edu	37	chr12	48381091	48381091	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggaattccatctgttccaggGttaccctgaaaagggagaca	11	9	1	2	rs570997824		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:48381091G>A	ENST00000380518.3	-	20	1391	c.1227C>T	c.(1225-1227)aaC>aaT	p.N409N	COL2A1_ENST00000337299.6_Silent_p.N340N|COL2A1_ENST00000493991.1_5'UTR	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	409	Triple-helical region.				axon guidance (GO:0007411)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to BMP stimulus (GO:0071773)|central nervous system development (GO:0007417)|chondrocyte differentiation (GO:0002062)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal joint morphogenesis (GO:0060272)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|limb bud formation (GO:0060174)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|notochord development (GO:0030903)|otic vesicle development (GO:0071599)|palate development (GO:0060021)|proteoglycan metabolic process (GO:0006029)|regulation of gene expression (GO:0010468)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|tissue homeostasis (GO:0001894)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen type II trimer (GO:0005585)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(3)	64		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	CTGTTCCAGGGTTACCCTGAA	0.557																																					p.N409N		Atlas-SNP	.											.	COL2A1	368	.	0			c.C1227T						.						67	70	69					12																	48381091		2203	4300	6503	SO:0001819	synonymous_variant	1280	exon20			TCCAGGGTTACCC	X16468	CCDS8759.1, CCDS41778.1	12q12-q13.2	2013-11-14	2008-02-04		ENSG00000139219	ENSG00000139219		"Collagens"	2200	protein-coding gene	gene with protein product		120140	"collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital)", "arthroophthalmopathy, progressive (Stickler syndrome)"	SEDC, AOM		1677770	Standard	NM_033150		Approved	STL1	uc001rqu.3	P02458	OTTHUMG00000149896	ENST00000380518.3:c.1227C>T	chr12.hg19:g.48381091G>A		172.0	0.0		100.0	4.0	NM_001844	A6NGA0|Q12985|Q14009|Q14044|Q14045|Q14046|Q14047|Q14056|Q14058|Q16672|Q1JQ82|Q2V4X7|Q6LBY1|Q6LBY2|Q6LBY3|Q96IT5|Q99227|Q9UE38|Q9UE39|Q9UE40|Q9UE41|Q9UE42|Q9UE43	Silent	SNP	ENST00000380518.3	hg19	CCDS41778.1																																																																																			.	.		0.557	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844		A	48381091	G	A	48381091	2	1	259	1	0	0	0	0	0	0	0	1	3689	1252	44	3		3	COL2A1	12	48381091	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	6727	48381091	85470804	544	36862										
MLL2	8085	hgsc.bcm.edu	37	chr12	49421091	49421091	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctgtgctgagtgggtggctcTggggcggggctctcctgtag	19	9	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:49421091T>C	ENST00000301067.7	-	48	14657	c.14658A>G	c.(14656-14658)ccA>ccG	p.P4886P		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	4886					chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										TGGGTGGCTCTGGGGCGGGGC	0.602																																					p.P4886P		Atlas-SNP	.											.	MLL2	1173	.	0			c.A14658G						.						95	102	100					12																	49421091		1789	3830	5619	SO:0001819	synonymous_variant	8085	exon48			TGGCTCTGGGGCG	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.14658A>G	chr12.hg19:g.49421091T>C		172.0	0.0		114.0	5.0	NM_003482	O14687	Silent	SNP	ENST00000301067.7	hg19	CCDS44873.1																																																																																			.	.		0.602	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			C	49421091	T	C	49421091	2	2	259	1	0	0	0	0	0	0	0	1	9630	1567	55	2		2	MLL2	12	49421091	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1040000	49421091	84430804	545	36863										
MLL2	8085	hgsc.bcm.edu	37	chr12	49432443	49432443	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aacggggtctctgaggtgggCcctgaccaggaaacggagtg	17	9	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:49432443C>T	ENST00000301067.7	-	34	8695	c.8696G>A	c.(8695-8697)gGc>gAc	p.G2899D	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	2899	Pro-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										CTGAGGTGGGCCCTGACCAGG	0.622																																					p.G2899D		Atlas-SNP	.											.	MLL2	1173	.	0			c.G8696A						.						21	24	23					12																	49432443		1876	4101	5977	SO:0001583	missense	8085	exon34			GGTGGGCCCTGAC	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.8696G>A	chr12.hg19:g.49432443C>T	ENSP00000301067:p.Gly2899Asp	91.0	0.0		57.0	4.0	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	hg19	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	C	8.974	0.973577	0.18736	.	.	ENSG00000167548	ENST00000301067	T	0.80214	-1.35	5.32	5.32	0.75619	.	0.000000	0.39083	N	0.001464	T	0.78502	0.4293	L	0.29908	0.895	0.32354	N	0.558019	D	0.69078	0.997	P	0.57152	0.814	T	0.81538	-0.0887	10	0.87932	D	0	.	7.6716	0.28462	0.1658:0.7506:0.0:0.0835	.	2899	O14686	MLL2_HUMAN	D	2899	ENSP00000301067:G2899D	ENSP00000301067:G2899D	G	-	2	0	MLL2	47718710	0.175000	0.23083	0.979000	0.43373	0.851000	0.48451	1.915000	0.39976	2.878000	0.98634	0.650000	0.86243	GGC	.	.		0.622	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			T	49432443	C	T	49432443	3	4	259	1	0	0	0	0	1	0	0	0	9630	739	26	3	8001	3	MLL2	12	49432443	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	11352	49432443	84419452	546	36864										
DIP2B	57609	hgsc.bcm.edu	37	chr12	51069149	51069149	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agagtatctacaaaaatccaGcagcttctgaacactctgaa	6	10	3	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:51069149G>T	ENST00000301180.5	+	7	868	c.834G>T	c.(832-834)caG>caT	p.Q278H		NM_173602.2	NP_775873.2	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B (Drosophila)	278						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(15)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	60						CAAAAATCCAGCAGCTTCTGA	0.368																																					p.Q278H		Atlas-SNP	.											.	DIP2B	167	.	0			c.G834T						.						92	94	94					12																	51069149		2203	4300	6503	SO:0001583	missense	57609	exon7			AATCCAGCAGCTT	AB040896	CCDS31799.1	12q13.12	2012-10-02	2006-01-13		ENSG00000066084	ENSG00000066084			29284	protein-coding gene	gene with protein product		611379					Standard	XM_005269044		Approved	KIAA1463, FLJ34278	uc001rwv.3	Q9P265	OTTHUMG00000169475	ENST00000301180.5:c.834G>T	chr12.hg19:g.51069149G>T	ENSP00000301180:p.Gln278His	164.0	0.0		102.0	5.0	NM_173602	Q6B011|Q8N1L5|Q8NB38	Missense_Mutation	SNP	ENST00000301180.5	hg19	CCDS31799.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.039648	0.75732	.	.	ENSG00000066084	ENST00000455310;ENST00000301180	T	0.46819	0.86	5.03	2.24	0.28232	.	0.050417	0.85682	D	0.000000	T	0.66187	0.2764	M	0.80616	2.505	0.58432	D	0.999998	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.997	T	0.66164	-0.5992	10	0.66056	D	0.02	-11.9782	9.8151	0.40846	0.2874:0.0:0.7126:0.0	.	278;288	Q9P265;E9PHD6	DIP2B_HUMAN;.	H	288;278	ENSP00000301180:Q278H	ENSP00000301180:Q278H	Q	+	3	2	DIP2B	49355416	1.000000	0.71417	0.998000	0.56505	0.981000	0.71138	2.761000	0.47589	0.307000	0.22880	0.563000	0.77884	CAG	.	.		0.368	DIP2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404243.1	NM_173602		T	51069149	G	T	51069149	3	4	259	1	0	0	0	0	1	0	0	0	4530	962	34	3	860	3	DIP2B	12	51069149	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1636706	51069149	82782746	547	36865										
SLC4A8	9498	hgsc.bcm.edu	37	chr12	51844748	51844748	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	catggccagaagcaccggagAcgagggcggggcaaaggagc	18	10	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:51844748A>G	ENST00000453097.2	+	3	436	c.219A>G	c.(217-219)agA>agG	p.R73R	SLC4A8_ENST00000394856.1_Silent_p.R20R|SLC4A8_ENST00000535225.2_Silent_p.R20R|SLC4A8_ENST00000514353.3_Silent_p.R20R|SLC4A8_ENST00000358657.3_Silent_p.R100R	NM_001039960.2|NM_001258401.2	NP_001035049.1|NP_001245330.1			solute carrier family 4, sodium bicarbonate cotransporter, member 8											NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(18)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(2)|urinary_tract(5)	55				BRCA - Breast invasive adenocarcinoma(357;0.15)		AGCACCGGAGACGAGGGCGGG	0.657																																					p.R73R		Atlas-SNP	.											.	SLC4A8	292	.	0			c.A219G						.						18	19	19					12																	51844748		2203	4300	6503	SO:0001819	synonymous_variant	9498	exon3			CCGGAGACGAGGG	AB018282	CCDS44890.1, CCDS58232.1, CCDS58233.1, CCDS73470.1	12q13.13	2013-05-22			ENSG00000050438	ENSG00000050438		"Solute carriers"	11034	protein-coding gene	gene with protein product		605024				11133997	Standard	NM_001039960		Approved	NBC3	uc001rys.2	Q2Y0W8	OTTHUMG00000169489	ENST00000453097.2:c.219A>G	chr12.hg19:g.51844748A>G		165.0	0.0		109.0	6.0	NM_001039960		Silent	SNP	ENST00000453097.2	hg19	CCDS44890.1																																																																																			.	.		0.657	SLC4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404356.1	NM_004858		G	51844748	A	G	51844748	2	3	259	1	0	0	0	0	0	0	0	1	14674	272	10	2		2	SLC4A8	12	51844748	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	775599	51844748	82007147	548	36866										
KRT85	3891	hgsc.bcm.edu	37	chr12	52754781	52754781	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atctggcgccctggggtggtGctgtaggagaggcccccaca	16	12	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:52754781G>A	ENST00000257901.3	-	9	1455	c.1380C>T	c.(1378-1380)agC>agT	p.S460S	KRT85_ENST00000544265.1_Silent_p.S248S	NM_002283.3	NP_002274.1	P78386	KRT85_HUMAN	keratin 85	460	Tail.				epidermis development (GO:0008544)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(6)|kidney(1)|large_intestine(7)|liver(1)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	36	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		CTGGGGTGGTGCTGTAGGAGA	0.657																																					p.S460S		Atlas-SNP	.											.	KRT85	78	.	0			c.C1380T						.						26	28	27					12																	52754781		2203	4300	6503	SO:0001819	synonymous_variant	3891	exon9			GGTGGTGCTGTAG	X99140	CCDS8824.1, CCDS73472.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000135443	ENSG00000135443		"-", "Intermediate filaments type II, keratins (basic)"	6462	protein-coding gene	gene with protein product	"hard keratin type II"	602767	"keratin, hair, basic, 5"	KRTHB5		9084137, 16831889	Standard	NM_002283		Approved	Hb-5	uc001sag.3	P78386	OTTHUMG00000169633	ENST00000257901.3:c.1380C>T	chr12.hg19:g.52754781G>A		117.0	0.0		79.0	4.0	NM_002283	Q9NSB1	Silent	SNP	ENST00000257901.3	hg19	CCDS8824.1																																																																																			.	.		0.657	KRT85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405184.1	NM_002283		A	52754781	G	A	52754781	2	1	259	1	0	0	0	0	0	0	0	1	8508	1310	46	3		3	KRT85	12	52754781	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	910033	52754781	81097114	549	36867										
TENC1	23371	hgsc.bcm.edu	37	chr12	53456471	53456471	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acagcggcagacctcctgcgTcagggtgctggtagagactt	14	11	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:53456471T>C	ENST00000314250.6	+	25	4103	c.3813T>C	c.(3811-3813)cgT>cgC	p.R1271R	TENC1_ENST00000314276.3_Silent_p.R1281R|TENC1_ENST00000549700.1_Silent_p.R1206R|TENC1_ENST00000552570.1_Silent_p.R1271R|TENC1_ENST00000546602.1_Silent_p.R1174R|TENC1_ENST00000379902.3_Silent_p.R1147R|TENC1_ENST00000451358.1_Silent_p.R1261R	NM_170754.2	NP_736610.2	Q63HR2	TENC1_HUMAN	tensin like C1 domain containing phosphatase (tensin 2)	1271					cellular homeostasis (GO:0019725)|collagen metabolic process (GO:0032963)|intracellular signal transduction (GO:0035556)|kidney development (GO:0001822)|multicellular organism growth (GO:0035264)|multicellular organismal homeostasis (GO:0048871)|negative regulation of cell proliferation (GO:0008285)|response to muscle activity (GO:0014850)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(19)|ovary(1)|pancreas(1)|stomach(3)	34						ACCTCCTGCGTCAGGGTGCTG	0.617																																					p.R1281R		Atlas-SNP	.											.	TENC1	148	.	0			c.T3843C						.						68	54	59					12																	53456471		2203	4300	6503	SO:0001819	synonymous_variant	23371	exon25			CCTGCGTCAGGGT	AF518729	CCDS8842.1, CCDS8843.1, CCDS8844.1	12q13.13	2013-02-14	2004-03-05			ENSG00000111077		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	19737	protein-coding gene	gene with protein product	"tensin 2"	607717	"tensin like C1 domain-containing phosphatase"				Standard	NM_015319		Approved	KIAA1075, C1-TEN, TNS2	uc001sbp.3	Q63HR2	OTTHUMG00000169730	ENST00000314250.6:c.3813T>C	chr12.hg19:g.53456471T>C		86.0	0.0		57.0	4.0	NM_015319	A2VDF2|A2VDF3|A2VDI8|A5PKY4|Q2NL80|Q76MW6|Q7Z5T9|Q8NFF9|Q8NFG0|Q96P25|Q9NT29|Q9UPS7	Silent	SNP	ENST00000314250.6	hg19	CCDS8843.1																																																																																			.	.		0.617	TENC1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405779.1	NM_170754		C	53456471	T	C	53456471	2	2	259	1	0	0	0	0	0	0	0	1	15773	1654	58	2		2	TENC1	12	53456471	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	701690	53456471	80395424	550	36868										
SPRYD3	84926	hgsc.bcm.edu	37	chr12	53467190	53467190	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgcagccgcacctcctcaccCagggagtgcatgcccactgc	10	18	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:53467190C>T	ENST00000301463.4	-	6	659	c.573G>A	c.(571-573)ctG>ctA	p.L191L	SPRYD3_ENST00000547837.1_Silent_p.L228L	NM_032840.2	NP_116229.1	Q8NCJ5	SPRY3_HUMAN	SPRY domain containing 3	191	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.									central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	17						CCTCCTCACCCAGGGAGTGCA	0.632																																					p.L191L		Atlas-SNP	.											.	SPRYD3	29	.	0			c.G573A						.						83	60	67					12																	53467190		2201	4298	6499	SO:0001819	synonymous_variant	84926	exon6			CTCACCCAGGGAG	AK074694	CCDS8845.1	12q13.13	2006-11-29		2006-02-02		ENSG00000167778			25920	protein-coding gene	gene with protein product						14702039	Standard	NM_032840		Approved	FLJ14800	uc001sbt.2	Q8NCJ5	OTTHUMG00000170101	ENST00000301463.4:c.573G>A	chr12.hg19:g.53467190C>T		97.0	0.0		80.0	4.0	NM_032840	B9EG99|Q96SK5	Silent	SNP	ENST00000301463.4	hg19	CCDS8845.1																																																																																			.	.		0.632	SPRYD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407264.1	NM_032840		T	53467190	C	T	53467190	2	4	259	1	0	0	0	0	0	0	0	1	15124	581	21	3		3	SPRYD3	12	53467190	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	10719	53467190	80384705	551	36869										
ITGB7	3695	hgsc.bcm.edu	37	chr12	53586193	53586193	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aagaacagctggttgtccagGgtccgctctttgcaccagcc	11	13	1	1	rs549027525		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:53586193G>A	ENST00000267082.5	-	14	2307	c.2076C>T	c.(2074-2076)acC>acT	p.T692T	ITGB7_ENST00000338737.4_Silent_p.T544T|ITGB7_ENST00000550743.2_Silent_p.T544T|ITGB7_ENST00000422257.3_Silent_p.T692T	NM_000889.1	NP_000880.1	P26010	ITB7_HUMAN	integrin, beta 7	692					cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte tethering or rolling (GO:0050901)|multicellular organismal development (GO:0007275)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alpha4-beta7 complex (GO:0034669)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)			NS(2)|breast(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GGTTGTCCAGGGTCCGCTCTT	0.582													G|||	1	0.000199681	0	0	5008	,	,		22424	0		0	False		,,,				2504	0.001				p.T692T		Atlas-SNP	.											.	ITGB7	60	.	0			c.C2076T						.						140	126	131					12																	53586193		2203	4300	6503	SO:0001819	synonymous_variant	3695	exon14			GTCCAGGGTCCGC		CCDS8849.1	12q13.1	2010-03-23				ENSG00000139626		"Integrins"	6162	protein-coding gene	gene with protein product		147559				2040616	Standard	XM_005268851		Approved		uc001scc.3	P26010		ENST00000267082.5:c.2076C>T	chr12.hg19:g.53586193G>A		55.0	0.0		35.0	5.0	NM_000889	Q9UCP7|Q9UCS7	Silent	SNP	ENST00000267082.5	hg19	CCDS8849.1																																																																																			.	.		0.582	ITGB7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405821.2			A	53586193	G	A	53586193	2	1	259	1	0	0	0	0	0	0	0	1	7909	1219	43	3		3	ITGB7	12	53586193	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	119003	53586193	80265702	552	36870										
NCKAP1L	3071	hgsc.bcm.edu	37	chr12	54932744	54932744	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aaatcgagaatccatttctcTgctcatgcgcttggtaagta	8	9	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:54932744T>C	ENST00000293373.6	+	30	3339	c.3260T>C	c.(3259-3261)cTg>cCg	p.L1087P	NCKAP1L_ENST00000545638.2_Missense_Mutation_p.L1037P	NM_005337.4	NP_005328.2	P55160	NCKPL_HUMAN	NCK-associated protein 1-like	1087					actin polymerization-dependent cell motility (GO:0070358)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|chemotaxis (GO:0006935)|cortical actin cytoskeleton organization (GO:0030866)|erythrocyte development (GO:0048821)|maintenance of cell polarity (GO:0030011)|myeloid cell homeostasis (GO:0002262)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of myosin-light-chain-phosphatase activity (GO:0035509)|neutrophil chemotaxis (GO:0030593)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of CD8-positive, alpha-beta T cell differentiation (GO:0043378)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of lymphocyte differentiation (GO:0045621)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of T cell proliferation (GO:0042102)|protein complex assembly (GO:0006461)|response to drug (GO:0042493)|T cell homeostasis (GO:0043029)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|SCAR complex (GO:0031209)	protein complex binding (GO:0032403)|protein kinase activator activity (GO:0030295)|Rac GTPase activator activity (GO:0030675)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(37)|ovary(3)|prostate(3)|skin(3)|stomach(2)	80						TCCATTTCTCTGCTCATGCGC	0.468																																					p.L1087P		Atlas-SNP	.											.	NCKAP1L	180	.	0			c.T3260C						.						92	80	84					12																	54932744		2203	4300	6503	SO:0001583	missense	3071	exon30			TTTCTCTGCTCAT	AI924363	CCDS31813.1, CCDS53799.1	12q13.1	2005-10-11	2005-10-11	2005-10-11		ENSG00000123338			4862	protein-coding gene	gene with protein product		141180	"hematopoietic protein 1"	HEM1		1932118	Standard	NM_005337		Approved		uc001sgc.4	P55160	OTTHUMG00000169843	ENST00000293373.6:c.3260T>C	chr12.hg19:g.54932744T>C	ENSP00000293373:p.Leu1087Pro	99.0	0.0		66.0	4.0	NM_005337	B4DUT5|Q52LW0	Missense_Mutation	SNP	ENST00000293373.6	hg19	CCDS31813.1	.	.	.	.	.	.	.	.	.	.	T	19.43	3.826512	0.71143	.	.	ENSG00000123338	ENST00000293373;ENST00000545638	T;T	0.41400	1.0;1.0	4.25	4.25	0.50352	.	0.095554	0.43110	D	0.000615	T	0.58850	0.2151	M	0.61703	1.905	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.62760	-0.6786	10	0.87932	D	0	-7.923	11.6366	0.51207	0.0:0.0:0.0:1.0	.	1087	P55160	NCKPL_HUMAN	P	1087;1037	ENSP00000293373:L1087P;ENSP00000445596:L1037P	ENSP00000293373:L1087P	L	+	2	0	NCKAP1L	53219011	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.111000	0.77077	1.930000	0.55929	0.533000	0.62120	CTG	.	.		0.468	NCKAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406195.1	NM_005337		C	54932744	T	C	54932744	3	2	259	1	0	0	0	0	1	0	0	0	10231	1580	55	2	3378	2	NCKAP1L	12	54932744	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1346551	54932744	78919151	553	36871										
METTL7B	196410	hgsc.bcm.edu	37	chr12	56076035	56076035	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggtccggagagtactgagacCggtaagcagggtgggaaggg	20	6	0	2	rs555960398		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:56076035C>A	ENST00000394252.3	+	1	706	c.497C>A	c.(496-498)cCg>cAg	p.P166Q		NM_152637.2	NP_689850.2	Q6UX53	MET7B_HUMAN	methyltransferase like 7B	166							methyltransferase activity (GO:0008168)			kidney(1)|large_intestine(1)|lung(4)	6						GTACTGAGACCGGTAAGCAGG	0.622																																					p.P166Q		Atlas-SNP	.											METTL7B_ENST00000394252,NS,carcinoma,-1,2	METTL7B	35	.	0			c.C497A						.						33	29	30					12																	56076035		2203	4300	6503	SO:0001630	splice_region_variant	196410	exon1			TGAGACCGGTAAG		CCDS8887.2	12q13.2	2012-06-12			ENSG00000170439	ENSG00000170439			28276	protein-coding gene	gene with protein product	"associated with lipid droplets 1"					17004324	Standard	NM_152637		Approved	MGC17301, ALDI	uc010spr.2	Q6UX53	OTTHUMG00000152665	ENST00000394252.3:c.498+1C>A	chr12.hg19:g.56076035C>A		141.0	0.0		73.0	3.0	NM_152637	A8K247|Q8WUI1	Missense_Mutation	SNP	ENST00000394252.3	hg19	CCDS8887.2	.	.	.	.	.	.	.	.	.	.	C	17.20	3.330263	0.60743	.	.	ENSG00000170439	ENST00000394252	T	0.37411	1.2	4.86	4.86	0.63082	Methyltransferase type 11 (1);	0.117466	0.64402	D	0.000015	T	0.69646	0.3134	H	0.94658	3.565	0.80722	D	1	D	0.76494	0.999	D	0.74023	0.982	T	0.78889	-0.2026	10	0.66056	D	0.02	-3.9477	15.5599	0.76237	0.0:1.0:0.0:0.0	.	166	Q6UX53	MET7B_HUMAN	Q	166	ENSP00000377796:P166Q	ENSP00000377796:P166Q	P	+	2	0	METTL7B	54362302	0.961000	0.32948	1.000000	0.80357	0.186000	0.23388	1.997000	0.40786	2.508000	0.84585	0.655000	0.94253	CCG	.	.		0.622	METTL7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327271.1	NM_152637	Missense_Mutation	A	56076035	C	A	56076035	5	1	259	1	0	0	0	0	0	0	1	0	9515	666	23	1	499	1	METTL7B	12	56076035	Splice_Site	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	1143291	56076035	77775860	554	36872										
ERBB3	2065	hgsc.bcm.edu	37	chr12	56493513	56493513	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gatggcccgagacccaccacGgtatctggtcataaaggtga	12	11	2	2	rs376939275		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:56493513G>T	ENST00000267101.3	+	24	3361	c.2921G>T	c.(2920-2922)cGg>cTg	p.R974L	RP11-603J24.9_ENST00000548861.1_5'Flank|ERBB3_ENST00000549832.1_Missense_Mutation_p.R94L|ERBB3_ENST00000415288.2_Missense_Mutation_p.R915L|ERBB3_ENST00000450146.2_Missense_Mutation_p.R331L|ERBB3_ENST00000553131.1_Missense_Mutation_p.R215L	NM_001982.3	NP_001973.2	P21860	ERBB3_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3	974					cranial nerve development (GO:0021545)|endocardial cushion development (GO:0003197)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of cell adhesion (GO:0007162)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of secretion (GO:0051048)|negative regulation of signal transduction (GO:0009968)|neuron apoptotic process (GO:0051402)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell proliferation (GO:0042127)|Schwann cell differentiation (GO:0014037)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein tyrosine kinase activator activity (GO:0030296)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			GACCCACCACGGTATCTGGTC	0.468																																					p.R974L		Atlas-SNP	.											.	ERBB3	350	.	0			c.G2921T						.						82	73	76					12																	56493513		2203	4300	6503	SO:0001583	missense	2065	exon24			CACCACGGTATCT	M34309	CCDS31833.1, CCDS44918.1	12q13	2013-07-09	2013-07-09			ENSG00000065361			3431	protein-coding gene	gene with protein product		190151	"lethal congenital contracture syndrome 2"	LCCS2			Standard	NM_001982		Approved	HER3	uc001sjh.3	P21860	OTTHUMG00000170140	ENST00000267101.3:c.2921G>T	chr12.hg19:g.56493513G>T	ENSP00000267101:p.Arg974Leu	164.0	0.0		92.0	4.0	NM_001982	A8K6L6|B4DIK7|B4DV32|E9PDT8|Q9BUD7	Missense_Mutation	SNP	ENST00000267101.3	hg19	CCDS31833.1	.	.	.	.	.	.	.	.	.	.	G	34	5.408020	0.96051	.	.	ENSG00000065361	ENST00000267101;ENST00000450146;ENST00000415288;ENST00000550070;ENST00000553131;ENST00000549832	T;T;T;T;T	0.61040	0.14;0.14;0.14;0.14;0.14	6.17	6.17	0.99709	Protein kinase-like domain (1);	0.000000	0.64402	D	0.000004	T	0.67998	0.2953	L	0.27053	0.805	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.85130	0.982;0.997;0.994	T	0.69427	-0.5148	10	0.87932	D	0	.	19.6509	0.95805	0.0:0.0:1.0:0.0	.	915;94;974	P21860-4;B3KWG5;P21860	.;.;ERBB3_HUMAN	L	974;331;915;97;215;94	ENSP00000267101:R974L;ENSP00000399178:R331L;ENSP00000408340:R915L;ENSP00000449129:R215L;ENSP00000448729:R94L	ENSP00000267101:R974L	R	+	2	0	ERBB3	54779780	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	9.513000	0.98010	2.941000	0.99782	0.655000	0.94253	CGG	.	.		0.468	ERBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407619.3			T	56493513	G	T	56493513	3	4	259	1	0	0	0	0	1	0	0	0	5210	1116	39	1	3146	1	ERBB3	12	56493513	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	417478	56493513	77358382	555	36873										
PAN2	9924	hgsc.bcm.edu	37	chr12	56726754	56726754	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gagcctccaaggccactcccTctgggtccagctccacattc	8	18	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:56726754T>C	ENST00000425394.2	-	2	501	c.125A>G	c.(124-126)gAg>gGg	p.E42G	PAN2_ENST00000257931.5_Missense_Mutation_p.E42G|PAN2_ENST00000440411.3_Missense_Mutation_p.E42G|PAN2_ENST00000548043.1_Missense_Mutation_p.E42G	NM_001127460.2	NP_001120932	Q9HBH5	RDH14_HUMAN	PAN2 poly(A) specific ribonuclease subunit	0					osteoblast differentiation (GO:0001649)	endoplasmic reticulum (GO:0005783)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	41					Vitamin A(DB00162)	GGCCACTCCCTCTGGGTCCAG	0.562																																					p.E42G		Atlas-SNP	.											.	PAN2	107	.	0			c.A125G						.						116	97	103					12																	56726754		2203	4300	6503	SO:0001583	missense	9924	exon2			ACTCCCTCTGGGT	AB014610	CCDS8915.1, CCDS44922.1, CCDS53802.1	12q13.2	2014-03-27	2014-03-27	2008-01-08		ENSG00000135473		"Ubiquitin-specific peptidases"	20074	protein-coding gene	gene with protein product	"PAN2 homolog, PABP1 dependent poly A specific ribonuclease subunit (S. cerevisiae)"		"ubiquitin specific protease 52", "ubiquitin specific peptidase 52", "PAN2 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)"	USP52		12838346, 14583602	Standard	NM_014871		Approved	KIAA0710, hPAN2	uc001skx.3	Q504Q3	OTTHUMG00000170412	ENST00000425394.2:c.125A>G	chr12.hg19:g.56726754T>C	ENSP00000401721:p.Glu42Gly	57.0	0.0		61.0	4.0	NM_014871		Missense_Mutation	SNP	ENST00000425394.2	hg19	CCDS44922.1	.	.	.	.	.	.	.	.	.	.	T	18.95	3.731979	0.69189	.	.	ENSG00000135473	ENST00000425394;ENST00000440411;ENST00000257931;ENST00000548043	T;T;T;T	0.06294	3.32;3.32;3.32;3.32	4.72	4.72	0.59763	.	0.111020	0.64402	D	0.000012	T	0.05273	0.0140	N	0.25647	0.755	0.47905	D	0.999544	B;B;B	0.09022	0.002;0.002;0.001	B;B;B	0.08055	0.003;0.003;0.001	T	0.39187	-0.9626	10	0.14252	T	0.57	-11.5693	13.6203	0.62134	0.0:0.0:0.0:1.0	.	42;42;42	Q504Q3-3;Q504Q3-2;Q504Q3	.;.;PAN2_HUMAN	G	42	ENSP00000401721:E42G;ENSP00000388231:E42G;ENSP00000257931:E42G;ENSP00000449861:E42G	ENSP00000257931:E42G	E	-	2	0	PAN2	55013021	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.370000	0.79589	2.133000	0.65898	0.477000	0.44152	GAG	.	.		0.562	PAN2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409024.1	NM_014871		C	56726754	T	C	56726754	3	2	259	1	0	0	0	0	1	0	0	0	11423	1551	54	2	3583	2	PAN2	12	56726754	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	233241	56726754	77125141	556	36874										
BAZ2A	11176	hgsc.bcm.edu	37	chr12	56993526	56993526	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agaaccaatctccttctgggAcagcctccatcttgggacga	9	13	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:56993526A>G	ENST00000551812.1	-	26	5331	c.5138T>C	c.(5137-5139)gTc>gCc	p.V1713A	BAZ2A_ENST00000549884.1_Missense_Mutation_p.V1711A|BAZ2A_ENST00000179765.5_Missense_Mutation_p.V1681A|BAZ2A_ENST00000379441.3_Missense_Mutation_p.V1683A|BAZ2A_ENST00000553222.1_5'Flank	NM_013449.3	NP_038477.2	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	1713					chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA methylation (GO:0006306)|heterochromatin assembly involved in chromatin silencing (GO:0070869)|histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|histone H4 deacetylation (GO:0070933)|histone H4-K20 methylation (GO:0034770)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|nucleolus (GO:0005730)|rDNA heterochromatin (GO:0033553)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|lysine-acetylated histone binding (GO:0070577)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(15)|urinary_tract(1)	31						TCCTTCTGGGACAGCCTCCAT	0.483																																					p.V1713A		Atlas-SNP	.											.	BAZ2A	263	.	0			c.T5138C						.						100	104	103					12																	56993526		2028	4187	6215	SO:0001583	missense	11176	exon26			TCTGGGACAGCCT	AB032254	CCDS44924.1, CCDS73483.1	12q13.3	2013-01-28				ENSG00000076108		"Zinc fingers, PHD-type"	962	protein-coding gene	gene with protein product	"TTF-I interacting peptide 5"	605682				10662543, 11532953	Standard	XM_005268596		Approved	KIAA0314, TIP5, WALp3	uc001slq.1	Q9UIF9	OTTHUMG00000170332	ENST00000551812.1:c.5138T>C	chr12.hg19:g.56993526A>G	ENSP00000446880:p.Val1713Ala	105.0	0.0		55.0	4.0	NM_013449	B3KN66|O00536|O15030|Q68DI8|Q96H26	Missense_Mutation	SNP	ENST00000551812.1	hg19	CCDS44924.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.497299	0.85069	.	.	ENSG00000076108	ENST00000379441;ENST00000179765;ENST00000551812;ENST00000549787;ENST00000549884	D;D;D;D;D	0.87887	-2.31;-2.31;-2.31;-2.31;-2.31	5.11	5.11	0.69529	Zinc finger, PHD-finger (2);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.071486	0.56097	D	0.000032	D	0.91971	0.7457	M	0.69248	2.105	0.58432	D	0.999997	D;D;D;D	0.71674	0.994;0.987;0.998;0.997	D;D;D;D	0.74023	0.954;0.958;0.982;0.941	D	0.91769	0.5426	10	0.45353	T	0.12	-15.8885	14.5836	0.68308	1.0:0.0:0.0:0.0	.	1711;1709;1713;1686	F8VU39;Q9UIF9-3;Q9UIF9;Q9UIF9-2	.;.;BAZ2A_HUMAN;.	A	1683;1681;1713;645;1711	ENSP00000368754:V1683A;ENSP00000179765:V1681A;ENSP00000446880:V1713A;ENSP00000448760:V645A;ENSP00000447941:V1711A	ENSP00000179765:V1681A	V	-	2	0	BAZ2A	55279793	0.986000	0.35501	1.000000	0.80357	0.997000	0.91878	8.500000	0.90498	2.223000	0.72356	0.533000	0.62120	GTC	.	.		0.483	BAZ2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408561.1	NM_013449		G	56993526	A	G	56993526	3	3	259	1	0	0	0	0	1	0	0	0	1331	275	10	2	595	2	BAZ2A	12	56993526	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	266772	56993526	76858369	557	36875										
BAZ2A	11176	hgsc.bcm.edu	37	chr12	56998905	56998905	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tggagtgcagccttcagcagCctgaccagcaggtcttgcac	12	13	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:56998905C>T	ENST00000551812.1	-	14	2899	c.2706G>A	c.(2704-2706)agG>agA	p.R902R	BAZ2A_ENST00000549884.1_Silent_p.R900R|BAZ2A_ENST00000179765.5_Silent_p.R870R|BAZ2A_ENST00000379441.3_Silent_p.R872R	NM_013449.3	NP_038477.2	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	902	DDT. {ECO:0000255|PROSITE- ProRule:PRU00063}.				chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA methylation (GO:0006306)|heterochromatin assembly involved in chromatin silencing (GO:0070869)|histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|histone H4 deacetylation (GO:0070933)|histone H4-K20 methylation (GO:0034770)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|nucleolus (GO:0005730)|rDNA heterochromatin (GO:0033553)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|lysine-acetylated histone binding (GO:0070577)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(15)|urinary_tract(1)	31						CCTTCAGCAGCCTGACCAGCA	0.552																																					p.R902R		Atlas-SNP	.											.	BAZ2A	263	.	0			c.G2706A						.						69	70	70					12																	56998905		2107	4231	6338	SO:0001819	synonymous_variant	11176	exon14			CAGCAGCCTGACC	AB032254	CCDS44924.1, CCDS73483.1	12q13.3	2013-01-28				ENSG00000076108		"Zinc fingers, PHD-type"	962	protein-coding gene	gene with protein product	"TTF-I interacting peptide 5"	605682				10662543, 11532953	Standard	XM_005268596		Approved	KIAA0314, TIP5, WALp3	uc001slq.1	Q9UIF9	OTTHUMG00000170332	ENST00000551812.1:c.2706G>A	chr12.hg19:g.56998905C>T		122.0	0.0		83.0	5.0	NM_013449	B3KN66|O00536|O15030|Q68DI8|Q96H26	Silent	SNP	ENST00000551812.1	hg19	CCDS44924.1																																																																																			.	.		0.552	BAZ2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408561.1	NM_013449		T	56998905	C	T	56998905	2	4	259	1	0	0	0	0	0	0	0	1	1331	738	26	3		3	BAZ2A	12	56998905	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	5379	56998905	76852990	558	36876										
SDR9C7	121214	hgsc.bcm.edu	37	chr12	57327864	57327864	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cccgctgaagtttctgggatCcctcctcagtgaagcaagca	10	13	2	2	rs147708476		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:57327864C>T	ENST00000293502.1	-	1	325	c.182G>A	c.(181-183)gGa>gAa	p.G61E		NM_148897.2	NP_683695.1	Q8NEX9	DR9C7_HUMAN	short chain dehydrogenase/reductase family 9C, member 7	61					oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	retinol dehydrogenase activity (GO:0004745)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|pancreas(1)	7						TTTCTGGGATCCCTCCTCAGT	0.592																																					p.G61E		Atlas-SNP	.											.	SDR9C7	31	.	0			c.G182A						.	C	GLU/GLY	0,4406		0,0,2203	82	75	77		182	5	1	12	dbSNP_134	77	1,8599	1.2+/-3.3	0,1,4299	no	missense	SDR9C7	NM_148897.2	98	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	61/314	57327864	1,13005	2203	4300	6503	SO:0001583	missense	121214	exon1			TGGGATCCCTCCT	AY044434	CCDS8926.1	12q13.3	2014-09-04			ENSG00000170426	ENSG00000170426	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	29958	protein-coding gene	gene with protein product		609769				12234675, 19027726	Standard	NM_148897		Approved	SDR-O, RDHS	uc010sqw.2	Q8NEX9	OTTHUMG00000171004	ENST00000293502.1:c.182G>A	chr12.hg19:g.57327864C>T	ENSP00000293502:p.Gly61Glu	87.0	0.0		74.0	4.0	NM_148897	B3KVB4	Missense_Mutation	SNP	ENST00000293502.1	hg19	CCDS8926.1	.	.	.	.	.	.	.	.	.	.	C	18.19	3.569039	0.65765	0.0	1.16E-4	ENSG00000170426	ENST00000293502	T	0.50813	0.73	5.0	5.0	0.66597	NAD(P)-binding domain (1);	0.000000	0.64402	D	0.000014	T	0.66665	0.2812	L	0.61218	1.895	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.68911	-0.5284	10	0.66056	D	0.02	.	17.2355	0.86997	0.0:1.0:0.0:0.0	.	61	Q8NEX9	DR9C7_HUMAN	E	61	ENSP00000293502:G61E	ENSP00000293502:G61E	G	-	2	0	SDR9C7	55614131	1.000000	0.71417	1.000000	0.80357	0.121000	0.20230	5.737000	0.68606	2.602000	0.87976	0.650000	0.86243	GGA	.	C|1.000;T|0.000		0.592	SDR9C7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411211.1	NM_148897		T	57327864	C	T	57327864	3	4	259	1	0	0	0	0	1	0	0	0	13989	855	30	3	775	3	SDR9C7	12	57327864	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	328959	57327864	76524031	559	36877										
RDH16	8608	hgsc.bcm.edu	37	chr12	57351019	57351019	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tccagggtcaccgtctccagCctgtctgaagtctggcccct	10	16	4	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:57351019C>T	ENST00000398138.3	-	1	1084	c.228G>A	c.(226-228)agG>agA	p.R76R	RDH16_ENST00000360752.4_5'UTR	NM_003708.3	NP_003699.3	O75452	RDH16_HUMAN	retinol dehydrogenase 16 (all-trans)	76					lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	electron carrier activity (GO:0009055)|retinol dehydrogenase activity (GO:0004745)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)	16						CCGTCTCCAGCCTGTCTGAAG	0.602																																					p.R76R	GBM(179;741 2921 43105 45298)	Atlas-SNP	.											.	RDH16	33	.	0			c.G228A						.						68	73	71					12																	57351019		2203	4300	6503	SO:0001819	synonymous_variant	8608	exon1			CTCCAGCCTGTCT		CCDS41797.1	12q13.3	2011-09-14	2006-05-09			ENSG00000139547		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	29674	protein-coding gene	gene with protein product	"microsomal NAD+ dependent retinol dehydrogenase 4", "short chain dehydrogenase/reductase family 9C, member 8"		"retinol dehydrogenase 16 (all-trans and 13-cis)"			9677409, 10329026, 19027726	Standard	NM_003708		Approved	RODH-4, SDR9C8	uc001smi.4	O75452		ENST00000398138.3:c.228G>A	chr12.hg19:g.57351019C>T		188.0	0.0		114.0	5.0	NM_003708	Q9UNV2	Silent	SNP	ENST00000398138.3	hg19	CCDS41797.1																																																																																			.	.		0.602	RDH16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410898.1	NM_003708		T	57351019	C	T	57351019	2	4	259	1	0	0	0	0	0	0	0	1	13209	738	26	3		3	RDH16	12	57351019	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	23155	57351019	76500876	560	36878										
SHMT2	6472	hgsc.bcm.edu	37	chr12	57625269	57625269	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cccccaccaccccagaacttCtgcagccgagctgcgctgga	9	19	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:57625269C>A	ENST00000328923.3	+	3	689	c.237C>A	c.(235-237)ttC>ttA	p.F79L	SHMT2_ENST00000393827.4_Intron|SHMT2_ENST00000553474.1_Missense_Mutation_p.F58L|SHMT2_ENST00000557487.1_Missense_Mutation_p.F79L|SHMT2_ENST00000449049.3_Missense_Mutation_p.F58L|SHMT2_ENST00000554600.1_3'UTR|SHMT2_ENST00000414700.3_Missense_Mutation_p.F58L	NM_001166356.1|NM_005412.5	NP_001159828.1|NP_005403.2	P34897	GLYM_HUMAN	serine hydroxymethyltransferase 2 (mitochondrial)	79					glycine biosynthetic process from serine (GO:0019264)|L-serine biosynthetic process (GO:0006564)|one-carbon metabolic process (GO:0006730)|positive regulation of cell proliferation (GO:0008284)|protein homotetramerization (GO:0051289)|tetrahydrofolate interconversion (GO:0035999)	extracellular vesicular exosome (GO:0070062)|microtubule cytoskeleton (GO:0015630)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|chromatin binding (GO:0003682)|glycine hydroxymethyltransferase activity (GO:0004372)|L-allo-threonine aldolase activity (GO:0008732)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(1)|large_intestine(4)|liver(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	15					Glycine(DB00145)|Tetrahydrofolic acid(DB00116)	CCCAGAACTTCTGCAGCCGAG	0.622																																					p.F79L	Esophageal Squamous(150;1369 2416 49071 49364)	Atlas-SNP	.											.	SHMT2	40	.	0			c.C237A						.						42	43	42					12																	57625269		2203	4300	6503	SO:0001583	missense	6472	exon3			GAACTTCTGCAGC	AK223555	CCDS8934.1, CCDS53805.1, CCDS55837.1	12q12-q14	2006-03-27				ENSG00000182199	2.1.2.1		10852	protein-coding gene	gene with protein product		138450		SHMT		8999870	Standard	NM_005412		Approved		uc001snf.2	P34897		ENST00000328923.3:c.237C>A	chr12.hg19:g.57625269C>A	ENSP00000333667:p.Phe79Leu	179.0	0.0		148.0	80.0	NM_005412	B7Z9F1|E7EQ19|E7EU43|O00740|Q8N1A5	Missense_Mutation	SNP	ENST00000328923.3	hg19	CCDS8934.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.387402	0.82902	.	.	ENSG00000182199	ENST00000328923;ENST00000557487;ENST00000556689;ENST00000414700;ENST00000557703;ENST00000553529;ENST00000554310;ENST00000557427;ENST00000553474;ENST00000555773;ENST00000554975;ENST00000449049;ENST00000556737	T;T;T;T;T;T;T;T;T;T;T;T;T	0.44881	1.45;0.91;0.91;1.45;1.45;1.45;1.45;1.45;1.45;1.45;1.45;1.45;1.45	4.49	3.6	0.41247	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	T	0.62380	0.2423	M	0.80422	2.495	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.992;1.0	T	0.65335	-0.6193	10	0.72032	D	0.01	.	9.0184	0.36184	0.0:0.8188:0.0:0.1812	.	79;79	Q8N1A5;P34897	.;GLYM_HUMAN	L	79;79;79;58;58;58;58;58;58;58;58;58;58	ENSP00000333667:F79L;ENSP00000452315:F79L;ENSP00000452035:F79L;ENSP00000406881:F58L;ENSP00000450452:F58L;ENSP00000452161:F58L;ENSP00000450893:F58L;ENSP00000452045:F58L;ENSP00000452419:F58L;ENSP00000451968:F58L;ENSP00000452404:F58L;ENSP00000413770:F58L;ENSP00000451495:F58L	ENSP00000333667:F79L	F	+	3	2	SHMT2	55911536	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	0.956000	0.29202	1.263000	0.44181	0.561000	0.74099	TTC	.	.		0.622	SHMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412525.2	NM_005412		A	57625269	C	A	57625269	3	1	259	1	0	0	0	0	1	0	0	0	14301	912	32	3	247	3	SHMT2	12	57625269	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	274250	57625269	76226626	561	36879										
INHBC	3626	hgsc.bcm.edu	37	chr12	57828719	57828719	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cctcctggctccaaccacagTggccactcccagagctggcg	10	18	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:57828719T>C	ENST00000309668.2	+	1	177	c.50T>C	c.(49-51)gTg>gCg	p.V17A	RP11-756H6.1_ENST00000547552.1_lincRNA	NM_005538.2	NP_005529.1	P55103	INHBC_HUMAN	inhibin, beta C	17					growth (GO:0040007)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	transforming growth factor beta receptor binding (GO:0005160)			breast(2)|endometrium(1)|large_intestine(6)|liver(2)|lung(4)|prostate(1)	16						CCAACCACAGTGGCCACTCCC	0.597																																					p.V17A		Atlas-SNP	.											.	INHBC	28	.	0			c.T50C						.						37	38	38					12																	57828719		2203	4300	6503	SO:0001583	missense	3626	exon1			CCACAGTGGCCAC		CCDS8938.1	12q13	2008-02-05				ENSG00000175189			6068	protein-coding gene	gene with protein product		601233				7826378	Standard	NM_005538		Approved		uc001snv.1	P55103	OTTHUMG00000169994	ENST00000309668.2:c.50T>C	chr12.hg19:g.57828719T>C	ENSP00000308716:p.Val17Ala	114.0	0.0		68.0	4.0	NM_005538	A1L3Y2	Missense_Mutation	SNP	ENST00000309668.2	hg19	CCDS8938.1	.	.	.	.	.	.	.	.	.	.	T	1.176	-0.639654	0.03557	.	.	ENSG00000175189	ENST00000550133;ENST00000309668	T	0.80123	-1.34	4.62	1.04	0.20106	.	1.112010	0.06779	N	0.784892	T	0.74928	0.3781	L	0.58810	1.83	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.55717	-0.8097	10	0.23302	T	0.38	-1.9667	7.5577	0.27833	0.0:0.2773:0.0:0.7227	.	17	P55103	INHBC_HUMAN	A	17	ENSP00000308716:V17A	ENSP00000308716:V17A	V	+	2	0	INHBC	56114986	0.004000	0.15560	0.009000	0.14445	0.004000	0.04260	0.525000	0.22956	0.363000	0.24346	-0.411000	0.06167	GTG	.	.		0.597	INHBC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406770.1	NM_005538		C	57828719	T	C	57828719	3	2	259	1	0	0	0	0	1	0	0	0	7752	1696	59	2	52	2	INHBC	12	57828719	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	203450	57828719	76023176	562	36880										
KIF5A	3798	hgsc.bcm.edu	37	chr12	57944131	57944131	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gaaccaggctgagattctgcGgggagacaagttcatcccca	12	11	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:57944131G>T	ENST00000455537.2	+	1	351	c.77G>T	c.(76-78)cGg>cTg	p.R26L	KIF5A_ENST00000286452.5_Missense_Mutation_p.R26L	NM_004984.2	NP_004975.2	Q12840	KIF5A_HUMAN	kinesin family member 5A	26	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein localization (GO:0008104)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(32)|ovary(2)|prostate(2)|skin(2)	62						GAGATTCTGCGGGGAGACAAG	0.607																																					p.R26L		Atlas-SNP	.											.	KIF5A	143	.	0			c.G77T						.						88	77	81					12																	57944131		2203	4300	6503	SO:0001583	missense	3798	exon1			TTCTGCGGGGAGA	U06698	CCDS8945.1	12q13.13	2011-07-15	2004-02-13			ENSG00000155980		"Kinesins"	6323	protein-coding gene	gene with protein product		602821	"spastic paraplegia 10 (autosomal dominant)"	SPG10		9858832, 10441583, 16489470	Standard	NM_004984		Approved	D12S1889, NKHC, MY050	uc001sor.1	Q12840	OTTHUMG00000170143	ENST00000455537.2:c.77G>T	chr12.hg19:g.57944131G>T	ENSP00000408979:p.Arg26Leu	154.0	0.0		97.0	4.0	NM_004984	A6H8M5|Q4LE26	Missense_Mutation	SNP	ENST00000455537.2	hg19	CCDS8945.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.100487	0.76983	.	.	ENSG00000155980	ENST00000455537;ENST00000286452	T;T	0.72051	-0.62;-0.62	3.58	3.58	0.41010	Kinesin, motor domain (3);	0.060761	0.64402	D	0.000005	T	0.68165	0.2971	N	0.25245	0.725	0.33602	D	0.602487	D;P	0.57571	0.98;0.835	P;B	0.56823	0.807;0.224	T	0.72221	-0.4356	10	0.25106	T	0.35	.	15.2387	0.73452	0.0:0.0:1.0:0.0	.	26;26	B7Z2M7;Q12840	.;KIF5A_HUMAN	L	26	ENSP00000408979:R26L;ENSP00000286452:R26L	ENSP00000286452:R26L	R	+	2	0	KIF5A	56230398	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.941000	0.92964	2.317000	0.78254	0.645000	0.84053	CGG	.	.		0.607	KIF5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407634.1	NM_004984		T	57944131	G	T	57944131	3	4	259	1	0	0	0	0	1	0	0	0	8314	1116	39	1	79	1	KIF5A	12	57944131	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	115412	57944131	75907764	563	36881										
USP15	9958	hgsc.bcm.edu	37	chr12	62783254	62783254	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tggaaacatattagatctttGtacagcattgtctgctttgt	8	6	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:62783254G>T	ENST00000280377.5	+	12	1575	c.1517G>T	c.(1516-1518)tGt>tTt	p.C506F	USP15_ENST00000393654.3_Missense_Mutation_p.C481F|USP15_ENST00000353364.3_Missense_Mutation_p.C477F	NM_001252078.1	NP_001239007.1	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15	506	USP.				BMP signaling pathway (GO:0030509)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|protein deubiquitination (GO:0016579)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|identical protein binding (GO:0042802)|SMAD binding (GO:0046332)|transforming growth factor beta receptor binding (GO:0005160)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(15)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	37			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)		TTAGATCTTTGTACAGCATTG	0.299																																					p.C506F	Melanoma(181;615 2041 39364 49691 50001)	Atlas-SNP	.											USP15,NS,carcinoma,0,2	USP15	105	.	0			c.G1517T						.						106	110	109					12																	62783254		2203	4300	6503	SO:0001583	missense	9958	exon12			ATCTTTGTACAGC	AB011101	CCDS8963.1, CCDS58250.1, CCDS58251.1	12q14	2006-07-18	2005-08-08					"Ubiquitin-specific peptidases"	12613	protein-coding gene	gene with protein product		604731	"ubiquitin specific protease 15"			12838346	Standard	NM_001252078		Approved	KIAA0529, UNPH4	uc001src.2	Q9Y4E8	OTTHUMG00000170186	ENST00000280377.5:c.1517G>T	chr12.hg19:g.62783254G>T	ENSP00000280377:p.Cys506Phe	149.0	0.0		89.0	5.0	NM_001252078	Q08AL5|Q9H8G9|Q9HCA6|Q9UNP0|Q9Y5B5	Missense_Mutation	SNP	ENST00000280377.5	hg19	CCDS58251.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.293338	0.80914	.	.	ENSG00000135655	ENST00000353364;ENST00000280377;ENST00000393654	T;T;T	0.19532	2.16;2.14;2.15	5.59	5.59	0.84812	RNA 3&apos (1);Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta (1);	0.105195	0.64402	D	0.000003	T	0.44393	0.1291	L	0.55990	1.75	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	T	0.07947	-1.0746	9	.	.	.	-12.2114	19.5944	0.95530	0.0:0.0:1.0:0.0	.	506;477	Q9Y4E8;Q9Y4E8-2	UBP15_HUMAN;.	F	477;506;481	ENSP00000258123:C477F;ENSP00000280377:C506F;ENSP00000377264:C481F	.	C	+	2	0	USP15	61069521	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	6.524000	0.73791	2.642000	0.89623	0.561000	0.74099	TGT	.	.		0.299	USP15-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407831.2	NM_006313		T	62783254	G	T	62783254	3	4	259	1	0	0	0	0	1	0	0	0	17061	1377	48	3	1472	3	USP15	12	62783254	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	4839123	62783254	71068641	564	36882										
CPM	1368	hgsc.bcm.edu	37	chr12	69279594	69279594	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	catctccatgcatatttgccAcgtatttgaactctggaatc	6	11	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:69279594A>G	ENST00000551568.1	-	3	296	c.236T>C	c.(235-237)gTg>gCg	p.V79A	CPM_ENST00000338356.3_Missense_Mutation_p.V79A|CPM_ENST00000546373.1_Missense_Mutation_p.V79A	NM_001005502.2|NM_198320.3	NP_001005502.1|NP_938079.1	P14384	CBPM_HUMAN	carboxypeptidase M	79					anatomical structure morphogenesis (GO:0009653)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(6)|prostate(2)	9	all_epithelial(5;1.09e-35)|Lung NSC(4;1.47e-33)|all_lung(4;1.02e-31)|Breast(13;1.59e-06)		all cancers(2;2.69e-50)|GBM - Glioblastoma multiforme(2;7.34e-41)|BRCA - Breast invasive adenocarcinoma(5;5.38e-10)|Lung(24;4.61e-05)|LUAD - Lung adenocarcinoma(15;0.000376)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143)			CATATTTGCCACGTATTTGAA	0.433																																					p.V79A		Atlas-SNP	.											.	CPM	30	.	0			c.T236C						.						177	171	173					12																	69279594		2203	4300	6503	SO:0001583	missense	1368	exon3			TTTGCCACGTATT	AF368463	CCDS8987.1	12q15	2012-02-10			ENSG00000135678	ENSG00000135678	3.4.17.12		2311	protein-coding gene	gene with protein product	"renal carboxypeptidase", "urinary carboxypeptidase B"	114860				8586455	Standard	NM_001874		Approved		uc001suq.3	P14384	OTTHUMG00000169300	ENST00000551568.1:c.236T>C	chr12.hg19:g.69279594A>G	ENSP00000448517:p.Val79Ala	134.0	0.0		98.0	4.0	NM_001005502	B2R800|Q9H2K9	Missense_Mutation	SNP	ENST00000551568.1	hg19	CCDS8987.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.472935	0.84640	.	.	ENSG00000135678	ENST00000551568;ENST00000338356;ENST00000546373;ENST00000548954;ENST00000548262	T;T;T;T;T	0.11277	2.79;2.79;2.79;2.79;2.79	5.08	5.08	0.68730	Peptidase M14, carboxypeptidase A (4);	0.062842	0.64402	D	0.000007	T	0.42040	0.1185	M	0.94063	3.49	0.58432	D	0.999999	D	0.60575	0.988	D	0.72338	0.977	T	0.54708	-0.8253	9	.	.	.	-19.74	12.6851	0.56944	1.0:0.0:0.0:0.0	.	79	P14384	CBPM_HUMAN	A	79	ENSP00000448517:V79A;ENSP00000339157:V79A;ENSP00000447255:V79A;ENSP00000446799:V79A;ENSP00000449911:V79A	.	V	-	2	0	CPM	67565861	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.302000	0.72788	2.048000	0.60808	0.455000	0.32223	GTG	.	.		0.433	CPM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403355.1	NM_198320		G	69279594	A	G	69279594	3	3	259	1	0	0	0	0	1	0	0	0	3810	159	6	2	1123	2	CPM	12	69279594	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	6496340	69279594	64572301	565	36883										
LGR5	8549	hgsc.bcm.edu	37	chr12	71955573	71955573	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctttctagaggatttcatagCaacaatatcaggtcgatacc	7	9	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:71955573C>T	ENST00000266674.5	+	8	1109	c.798C>T	c.(796-798)agC>agT	p.S266S	LGR5_ENST00000540815.2_Intron|LGR5_ENST00000536515.1_Silent_p.S194S			O75473	LGR5_HUMAN	leucine-rich repeat containing G protein-coupled receptor 5	266					G-protein coupled receptor signaling pathway (GO:0007186)|inner ear development (GO:0048839)|positive regulation of canonical Wnt signaling pathway (GO:0090263)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)		NUP107/LGR5(2)	endometrium(2)|kidney(3)|large_intestine(2)|lung(24)|ovary(1)|pancreas(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(3)	48						GATTTCATAGCAACAATATCA	0.373																																					p.S266S		Atlas-SNP	.											.	LGR5	103	.	0			c.C798T						.						71	63	66					12																	71955573		2203	4300	6503	SO:0001819	synonymous_variant	8549	exon8			TCATAGCAACAAT	AF062006	CCDS9000.1, CCDS61194.1, CCDS61195.1	12q22-q23	2012-08-21	2011-01-25	2004-11-12				"GPCR / Class A : Orphans"	4504	protein-coding gene	gene with protein product		606667	"G protein-coupled receptor 49", "leucine-rich repeat-containing G protein-coupled receptor 5"	GPR67, GPR49		9642114	Standard	NM_003667		Approved	HG38, FEX	uc001swl.4	O75473	OTTHUMG00000169543	ENST00000266674.5:c.798C>T	chr12.hg19:g.71955573C>T		81.0	0.0		59.0	4.0	NM_003667	D8MCT0|Q4VAM0|Q4VAM2|Q9UP75	Silent	SNP	ENST00000266674.5	hg19	CCDS9000.1																																																																																			.	.		0.373	LGR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404744.1	NM_003667		T	71955573	C	T	71955573	2	4	259	1	0	0	0	0	0	0	0	1	8766	709	25	3		3	LGR5	12	71955573	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	2675979	71955573	61896322	566	36884										
DUSP6	1848	hgsc.bcm.edu	37	chr12	89744396	89744396	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atggcctcagggaaaaactgGgacaggttttggctccagtg	14	8	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:89744396G>T	ENST00000279488.7	-	2	2038	c.807C>A	c.(805-807)tcC>tcA	p.S269S	DUSP6_ENST00000547291.1_Silent_p.S144S|DUSP6_ENST00000308385.6_Intron|DUSP6_ENST00000547140.1_5'UTR	NM_001946.2	NP_001937.2	Q16828	DUS6_HUMAN	dual specificity phosphatase 6	269	Tyrosine-protein phosphatase.				cell differentiation (GO:0030154)|dorsal/ventral pattern formation (GO:0009953)|inactivation of MAPK activity (GO:0000188)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of apoptotic process (GO:0043065)|regulation of endodermal cell fate specification (GO:0042663)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of heart growth (GO:0060420)|response to drug (GO:0042493)|response to nitrosative stress (GO:0051409)|response to organic cyclic compound (GO:0014070)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)			large_intestine(5)|lung(8)|skin(2)|urinary_tract(1)	16						GGAAAAACTGGGACAGGTTTT	0.423																																					p.S269S	Colon(132;3456 5224)	Atlas-SNP	.											.	DUSP6	30	.	0			c.C807A						.						112	123	120					12																	89744396		2203	4300	6503	SO:0001819	synonymous_variant	1848	exon2			AAACTGGGACAGG	BC037236	CCDS9033.1, CCDS9034.1	12q22-q23	2011-06-09				ENSG00000139318		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3072	protein-coding gene	gene with protein product		602748				8626780, 9205128	Standard	NM_001946		Approved	MKP-3, PYST1	uc001tay.3	Q16828		ENST00000279488.7:c.807C>A	chr12.hg19:g.89744396G>T		105.0	0.0		68.0	4.0	NM_001946	O75109|Q53Y75|Q9BSH6	Silent	SNP	ENST00000279488.7	hg19	CCDS9033.1																																																																																			.	.		0.423	DUSP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406534.2	NM_001946, NM_022652		T	89744396	G	T	89744396	2	4	259	1	0	0	0	0	0	0	0	1	4831	1219	43	3		3	DUSP6	12	89744396	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	17788823	89744396	44107499	567	36885										
ATP2B1	490	hgsc.bcm.edu	37	chr12	89997695	89997695	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gcatctgcacagccttaagcGgtgagtcctagaaaagatat	10	9	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:89997695G>T	ENST00000428670.3	-	17	3098	c.2642C>A	c.(2641-2643)cCg>cAg	p.P881Q	ATP2B1_ENST00000348959.3_Missense_Mutation_p.P881Q|ATP2B1_ENST00000393164.2_Missense_Mutation_p.P624Q|ATP2B1_ENST00000261173.2_Missense_Mutation_p.P881Q|ATP2B1_ENST00000359142.3_Missense_Mutation_p.P881Q			P20020	AT2B1_HUMAN	ATPase, Ca++ transporting, plasma membrane 1	881					blood coagulation (GO:0007596)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	45						AGCCTTAAGCGGTGAGTCCTA	0.463																																					p.P881Q		Atlas-SNP	.											.	ATP2B1	191	.	0			c.C2642A						.						59	54	56					12																	89997695		2203	4300	6503	SO:0001583	missense	490	exon16			TTAAGCGGTGAGT	J04027	CCDS9035.1, CCDS41817.1	12q21.33	2010-04-20			ENSG00000070961	ENSG00000070961	3.6.3.8	"ATPases / P-type"	814	protein-coding gene	gene with protein product	"plasma membrane calcium-transporting ATPase 1"	108731				1674727	Standard	NM_001682		Approved	PMCA1	uc001tbh.3	P20020		ENST00000428670.3:c.2642C>A	chr12.hg19:g.89997695G>T	ENSP00000392043:p.Pro881Gln	168.0	0.0		131.0	7.0	NM_001001323	Q12992|Q12993|Q13819|Q13820|Q13821|Q16504|Q93082	Missense_Mutation	SNP	ENST00000428670.3	hg19	CCDS9035.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.902002	0.92035	.	.	ENSG00000070961	ENST00000261173;ENST00000348959;ENST00000359142;ENST00000428670;ENST00000393164	D;D;D;D;D	0.97665	-4.48;-4.48;-4.48;-4.48;-2.38	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	D	0.99165	0.9711	H	0.97390	3.995	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.998	D	0.98874	1.0767	10	0.87932	D	0	-16.217	20.3242	0.98691	0.0:0.0:1.0:0.0	.	881;881;881	P20020-3;P20020-2;P20020-6	.;.;.	Q	881;881;881;881;624	ENSP00000261173:P881Q;ENSP00000343599:P881Q;ENSP00000352054:P881Q;ENSP00000392043:P881Q;ENSP00000376869:P624Q	ENSP00000261173:P881Q	P	-	2	0	ATP2B1	88521826	1.000000	0.71417	0.978000	0.43139	0.994000	0.84299	9.813000	0.99286	2.882000	0.98803	0.655000	0.94253	CCG	.	.		0.463	ATP2B1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406653.1	NM_001682		T	89997695	G	T	89997695	3	4	259	1	0	0	0	0	1	0	0	0	1139	1116	39	1	1198	1	ATP2B1	12	89997695	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	253299	89997695	43854200	568	36886										
BTG1	694	hgsc.bcm.edu	37	chr12	92538064	92538064	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cataggggtcaacccagagtGtgagttcacttgggagaagc	14	8	2	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:92538064G>A	ENST00000256015.3	-	2	669	c.308C>T	c.(307-309)aCa>aTa	p.T103I	RP11-796E2.4_ENST00000501008.2_RNA|C12orf79_ENST00000549802.1_5'Flank|C12orf79_ENST00000546975.1_5'Flank|RP11-796E2.4_ENST00000499685.2_RNA|C12orf79_ENST00000551843.1_5'Flank|C12orf79_ENST00000551563.2_5'Flank	NM_001731.2	NP_001722.1	P62324	BTG1_HUMAN	B-cell translocation gene 1, anti-proliferative	103					cell migration (GO:0016477)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of myoblast differentiation (GO:0045663)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|transcription cofactor activity (GO:0003712)			haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(1)|lung(2)	16		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)				AACCCAGAGTGTGAGTTCACT	0.507			T	MYC	BCLL						OREG0022024	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T103I		Atlas-SNP	.		Dom	yes		12	12q22	694	"B-cell translocation gene 1, anti-proliferative"		L	.	BTG1	30	.	0			c.C308T						.						120	119	119					12																	92538064		2203	4300	6503	SO:0001583	missense	694	exon2			CAGAGTGTGAGTT		CCDS9043.1	12q21.33	2012-10-02			ENSG00000133639	ENSG00000133639			1130	protein-coding gene	gene with protein product		109580				15033446	Standard	NM_001731		Approved		uc001tby.3	P62324	OTTHUMG00000170092	ENST00000256015.3:c.308C>T	chr12.hg19:g.92538064G>A	ENSP00000256015:p.Thr103Ile	127.0	0.0	1291	83.0	4.0	NM_001731	P31607	Missense_Mutation	SNP	ENST00000256015.3	hg19	CCDS9043.1	.	.	.	.	.	.	.	.	.	.	G	19.25	3.791487	0.70452	.	.	ENSG00000133639	ENST00000256015;ENST00000552315	T;T	0.36340	1.56;1.26	5.8	5.8	0.92144	Anti-proliferative protein (4);	0.000000	0.85682	D	0.000000	T	0.67097	0.2857	M	0.84773	2.715	0.80722	D	1	D	0.76494	0.999	D	0.77004	0.989	T	0.71048	-0.4705	10	0.87932	D	0	-3.4656	20.0608	0.97674	0.0:0.0:1.0:0.0	.	103	P62324	BTG1_HUMAN	I	103;28	ENSP00000256015:T103I;ENSP00000447551:T28I	ENSP00000256015:T103I	T	-	2	0	BTG1	91062195	1.000000	0.71417	0.991000	0.47740	0.996000	0.88848	9.413000	0.97351	2.733000	0.93635	0.650000	0.86243	ACA	.	.		0.507	BTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407227.1			A	92538064	G	A	92538064	3	1	259	1	0	0	0	0	1	0	0	0	1555	1377	48	3	211	3	BTG1	12	92538064	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	2540369	92538064	41313831	569	36887										
NTN4	59277	hgsc.bcm.edu	37	chr12	96180818	96180818	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aaatgtagcggagcagttagTcgcaaagtacttataaggct	11	6	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:96180818T>C	ENST00000343702.4	-	2	932	c.484A>G	c.(484-486)Act>Gct	p.T162A	NTN4_ENST00000344911.4_Missense_Mutation_p.T125A|NTN4_ENST00000538383.1_Missense_Mutation_p.T125A|NTN4_ENST00000553059.1_Missense_Mutation_p.T162A	NM_021229.3	NP_067052.2	Q9HB63	NET4_HUMAN	netrin 4	162	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				axon guidance (GO:0007411)|extracellular matrix organization (GO:0030198)|neuron remodeling (GO:0016322)|regulation of branching involved in salivary gland morphogenesis by extracellular matrix-epithelial cell signaling (GO:0060668)	basement membrane (GO:0005604)|plasma membrane (GO:0005886)				NS(2)|breast(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25						GAGCAGTTAGTCGCAAAGTAC	0.493																																					p.T162A		Atlas-SNP	.											.	NTN4	67	.	0			c.A484G						.						102	96	98					12																	96180818		2203	4300	6503	SO:0001583	missense	59277	exon2			AGTTAGTCGCAAA	AF119916	CCDS9054.1	12q22	2013-03-01			ENSG00000074527	ENSG00000074527		"Netrins"	13658	protein-coding gene	gene with protein product	"beta-netrin", "Netrin-4"	610401				11038171	Standard	NM_021229		Approved		uc001tei.3	Q9HB63	OTTHUMG00000170290	ENST00000343702.4:c.484A>G	chr12.hg19:g.96180818T>C	ENSP00000340998:p.Thr162Ala	169.0	0.0		96.0	4.0	NM_021229	B2RNC2|Q658K9|Q7L3F1|Q7L9D6|Q7Z5B6|Q9BZP1|Q9NT44|Q9P133	Missense_Mutation	SNP	ENST00000343702.4	hg19	CCDS9054.1	.	.	.	.	.	.	.	.	.	.	T	4.683	0.127052	0.08931	.	.	ENSG00000074527	ENST00000343702;ENST00000344911;ENST00000538383;ENST00000553059;ENST00000547980	T;T;T;T;T	0.74315	-0.83;-0.83;-0.83;-0.83;-0.83	5.62	3.26	0.37387	Laminin, N-terminal (3);	0.447252	0.27043	N	0.021205	T	0.48607	0.1509	N	0.11560	0.145	0.18873	N	0.999986	B;B	0.02656	0.0;0.0	B;B	0.08055	0.002;0.003	T	0.28299	-1.0048	10	0.05620	T	0.96	.	9.8162	0.40853	0.0:0.2014:0.0:0.7986	.	162;162	Q9HB63-2;Q9HB63	.;NET4_HUMAN	A	162;125;125;162;125	ENSP00000340998:T162A;ENSP00000339436:T125A;ENSP00000444432:T125A;ENSP00000447292:T162A;ENSP00000447594:T125A	ENSP00000340998:T162A	T	-	1	0	NTN4	94704949	0.000000	0.05858	0.930000	0.37139	0.807000	0.45602	-0.077000	0.11394	0.976000	0.38417	0.454000	0.30748	ACT	.	.		0.493	NTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408372.1	NM_021229		C	96180818	T	C	96180818	3	2	259	1	0	0	0	0	1	0	0	0	10711	1667	58	2	1438	2	NTN4	12	96180818	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	3642754	96180818	37671077	570	36888										
C12orf42	374470	hgsc.bcm.edu	37	chr12	103699815	103699815	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgtgtgtctactgatgtgtaTgccctgagcctccaggtgaa	12	9	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:103699815T>C	ENST00000378113.2	-	5	793	c.568A>G	c.(568-570)Ata>Gta	p.I190V	C12orf42_ENST00000548789.1_5'UTR|C12orf42_ENST00000548883.1_Missense_Mutation_p.I190V|C12orf42_ENST00000548048.1_Missense_Mutation_p.I123V|C12orf42_ENST00000315192.8_Intron	NM_001099336.1	NP_001092806.1	Q96LP6	CL042_HUMAN	chromosome 12 open reading frame 42	190										NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)	22						CTGATGTGTATGCCCTGAGCC	0.458																																					p.I190V		Atlas-SNP	.											.	C12orf42	50	.	0			c.A568G						.						143	141	142					12																	103699815		1935	4128	6063	SO:0001583	missense	374470	exon5			TGTGTATGCCCTG	AK058052	CCDS44963.1	12q23.2	2012-05-30			ENSG00000179088	ENSG00000179088			24729	protein-coding gene	gene with protein product							Standard	NM_001099336		Approved	FLJ25323	uc001tjt.2	Q96LP6	OTTHUMG00000169988	ENST00000378113.2:c.568A>G	chr12.hg19:g.103699815T>C	ENSP00000367353:p.Ile190Val	132.0	0.0		93.0	4.0	NM_001099336	Q49A64|Q4G0S2	Missense_Mutation	SNP	ENST00000378113.2	hg19	CCDS44963.1	.	.	.	.	.	.	.	.	.	.	T	0.745	-0.775082	0.02951	.	.	ENSG00000179088	ENST00000548883;ENST00000548048;ENST00000378113;ENST00000552578	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	2.98	0.605	0.17553	.	3.852820	0.01124	N	0.005841	T	0.26919	0.0659	N	0.19112	0.55	0.09310	N	1	B	0.18013	0.025	B	0.10450	0.005	T	0.09164	-1.0687	10	0.16420	T	0.52	5.8231	4.6812	0.12736	0.0:0.2848:0.0:0.7152	.	190	Q96LP6	CL042_HUMAN	V	190;123;190;190	ENSP00000447908:I190V;ENSP00000449362:I123V;ENSP00000367353:I190V;ENSP00000447795:I190V	ENSP00000367353:I190V	I	-	1	0	C12orf42	102223945	0.001000	0.12720	0.000000	0.03702	0.016000	0.09150	0.400000	0.20932	0.128000	0.18479	0.449000	0.29647	ATA	.	.		0.458	C12orf42-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406754.1	NM_198521		C	103699815	T	C	103699815	3	2	259	1	0	0	0	0	1	0	0	0	1690	1464	51	2	522	2	C12orf42	12	103699815	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	7518997	103699815	30152080	571	36889										
ALDH1L2	160428	hgsc.bcm.edu	37	chr12	105428158	105428158	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acagttctctcctttgttgaAaaatactgctcccatgccct	5	13	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:105428158A>G	ENST00000258494.9	-	19	2304	c.2164T>C	c.(2164-2166)Ttc>Ctc	p.F722L	C12orf45_ENST00000548583.1_Intron	NM_001034173.3	NP_001029345.2	Q3SY69	AL1L2_HUMAN	aldehyde dehydrogenase 1 family, member L2	722	Aldehyde dehydrogenase.				10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|prostate(2)|skin(3)|stomach(2)	35						CCTTTGTTGAAAAATACTGCT	0.428																																					p.F722L		Atlas-SNP	.											.	ALDH1L2	71	.	0			c.T2164C						.						91	78	83					12																	105428158		2203	4300	6503	SO:0001583	missense	160428	exon19			TGTTGAAAAATAC	AK095827	CCDS31891.1	12q23.3	2014-09-11			ENSG00000136010	ENSG00000136010	1.5.1.6	"Aldehyde dehydrogenases"	26777	protein-coding gene	gene with protein product	"mitochondrial 10-formyltetrahydrofolate dehydrogenase"	613584				20498374	Standard	NM_001034173		Approved	FLJ38508, mtFDH	uc001tlc.3	Q3SY69	OTTHUMG00000169823	ENST00000258494.9:c.2164T>C	chr12.hg19:g.105428158A>G	ENSP00000258494:p.Phe722Leu	162.0	0.0		122.0	5.0	NM_001034173	Q3SY68|Q68D62|Q6AI55|Q8N922	Missense_Mutation	SNP	ENST00000258494.9	hg19	CCDS31891.1	.	.	.	.	.	.	.	.	.	.	A	33	5.205711	0.95033	.	.	ENSG00000136010	ENST00000258494	T	0.15372	2.43	5.36	5.36	0.76844	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);Aldehyde dehydrogenase, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.31420	0.0796	L	0.33293	1	0.80722	D	1	D	0.76494	0.999	D	0.70227	0.968	T	0.04373	-1.0956	10	0.87932	D	0	.	15.662	0.77193	1.0:0.0:0.0:0.0	.	722	Q3SY69	AL1L2_HUMAN	L	722	ENSP00000258494:F722L	ENSP00000258494:F722L	F	-	1	0	ALDH1L2	103952288	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.071000	0.93980	2.159000	0.67721	0.454000	0.30748	TTC	.	.		0.428	ALDH1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406098.1	XM_090294		G	105428158	A	G	105428158	3	3	259	1	0	0	0	0	1	0	0	0	495	14	1	2	627	2	ALDH1L2	12	105428158	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1728343	105428158	28423737	572	36890										
RFX4	5992	hgsc.bcm.edu	37	chr12	107109249	107109249	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gactggaggaacgtggacctGaacagcatcaccaagcaaac	11	11	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:107109249G>A	ENST00000392842.1	+	11	1479	c.1065G>A	c.(1063-1065)ctG>ctA	p.L355L	RP11-482D24.3_ENST00000552415.1_RNA|RFX4_ENST00000229387.5_Silent_p.L261L|RP11-144F15.1_ENST00000551505.1_Intron|RFX4_ENST00000357881.4_Silent_p.L364L	NM_213594.2	NP_998759.1	Q33E94	RFX4_HUMAN	regulatory factor X, 4 (influences HLA class II expression)	355	Necessary for dimerization.				cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|dorsal spinal cord development (GO:0021516)|midbrain development (GO:0030901)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein processing (GO:0070613)|telencephalon development (GO:0021537)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(20)|pancreas(1)|upper_aerodigestive_tract(1)	35						ACGTGGACCTGAACAGCATCA	0.493																																					p.L364L		Atlas-SNP	.											.	RFX4	218	.	0			c.G1092A						.						227	170	190					12																	107109249		2203	4300	6503	SO:0001819	synonymous_variant	5992	exon11			GGACCTGAACAGC	AB044245	CCDS9106.1, CCDS9108.1, CCDS55880.1	12q24	2008-08-05			ENSG00000111783	ENSG00000111783			9985	protein-coding gene	gene with protein product		603958				8600444, 11682486	Standard	NM_213594		Approved		uc001tlt.3	Q33E94	OTTHUMG00000169173	ENST00000392842.1:c.1065G>A	chr12.hg19:g.107109249G>A		186.0	0.0		96.0	4.0	NM_001206691	A8K5Y0|B2RDW4|Q33DW6|Q33DW7|Q33E95|Q6YM53|Q8MHQ1|Q8NC78|Q8NDF9|Q8SNA1|Q96S80|Q9BXI0	Silent	SNP	ENST00000392842.1	hg19	CCDS9106.1																																																																																			.	.		0.493	RFX4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402707.1	NM_032491		A	107109249	G	A	107109249	2	1	259	1	0	0	0	0	0	0	0	1	13280	1277	45	3		3	RFX4	12	107109249	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1681091	107109249	26742646	573	36891										
BRAP	8315	hgsc.bcm.edu	37	chr12	112098444	112098444	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aacacttattttcttctactGgctcgggcgtttgacagtac	8	10	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:112098444G>A	ENST00000327551.6	-	7	982	c.842C>T	c.(841-843)cCa>cTa	p.P281L	BRAP_ENST00000419234.4_Missense_Mutation_p.P311L|BRAP_ENST00000539060.1_Missense_Mutation_p.P132L			Q6UWU4	CF089_HUMAN	BRCA1 associated protein	205					epithelial cell proliferation (GO:0050673)|positive regulation of cell cycle (GO:0045787)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	20						TTCTTCTACTGGCTCGGGCGT	0.403																																					p.P311L	Pancreas(146;846 1904 7830 25130 26065)	Atlas-SNP	.											.	BRAP	42	.	0			c.C932T						.						168	161	163					12																	112098444		2203	4300	6503	SO:0001583	missense	8315	exon7			TCTACTGGCTCGG	AF035620	CCDS9154.1	12q24.12	2014-09-11			ENSG00000089234	ENSG00000089234		"RING-type (C3HC4) zinc fingers"	1099	protein-coding gene	gene with protein product	"impedes mitogenic signal propagation", "galectin-2-binding protein"	604986				9497340, 19198608	Standard	XM_005253944		Approved	BRAP2, RNF52, IMP	uc001tsn.4	Q7Z569	OTTHUMG00000169600	ENST00000327551.6:c.842C>T	chr12.hg19:g.112098444G>A	ENSP00000330813:p.Pro281Leu	172.0	0.0		121.0	5.0	NM_006768	B4DTT1|F4NAR0|F4NAR1|Q6ZMG5|Q7Z356|Q8IZ35	Missense_Mutation	SNP	ENST00000327551.6	hg19		.	.	.	.	.	.	.	.	.	.	G	9.696	1.153209	0.21371	.	.	ENSG00000089234	ENST00000419234;ENST00000539060;ENST00000327551;ENST00000547043	T;T;T	0.28895	1.59;1.59;1.59	5.14	5.14	0.70334	Zinc finger, RING/FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	T	0.39009	0.1062	N	0.17564	0.495	0.80722	D	1	D;D	0.71674	0.998;0.994	D;P	0.73708	0.981;0.795	T	0.15037	-1.0451	10	0.18276	T	0.48	-11.8702	18.9406	0.92604	0.0:0.0:1.0:0.0	.	132;311	B4DRM1;Q7Z569	.;BRAP_HUMAN	L	311;132;281;93	ENSP00000403524:P311L;ENSP00000441659:P132L;ENSP00000330813:P281L	ENSP00000330813:P281L	P	-	2	0	BRAP	110582827	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.251000	0.78297	2.551000	0.86045	0.563000	0.77884	CCA	.	.		0.403	BRAP-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404994.2			A	112098444	G	A	112098444	3	1	259	1	0	0	0	0	1	0	0	0	1499	1348	47	3	870	3	BRAP	12	112098444	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	4989195	112098444	21753451	574	36892										
OAS1	4938	hgsc.bcm.edu	37	chr12	113354434	113354434	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cccagggatttcggacggtcTtggaattagtcataaactac	10	9	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:113354434T>C	ENST00000202917.5	+	4	1038	c.775T>C	c.(775-777)Ttg>Ctg	p.L259L	OAS1_ENST00000551241.1_Silent_p.L259L|RP1-71H24.1_ENST00000552784.1_RNA|OAS1_ENST00000445409.2_Silent_p.L259L|OAS1_ENST00000452357.2_Silent_p.L259L	NM_016816.2	NP_058132.2	P00973	OAS1_HUMAN	2'-5'-oligoadenylate synthetase 1, 40/46kDa	259					cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|protein oligomerization (GO:0051259)|purine nucleotide biosynthetic process (GO:0006164)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(2)|skin(1)	16						TCGGACGGTCTTGGAATTAGT	0.473																																					p.L259L		Atlas-SNP	.											.	OAS1	128	.	0			c.T775C						.						119	108	112					12																	113354434		2203	4300	6503	SO:0001819	synonymous_variant	4938	exon4			ACGGTCTTGGAAT	X04371	CCDS31905.1, CCDS41838.1, CCDS44980.1	12q24.2	2014-05-21	2011-07-21				2.7.7.-		8086	protein-coding gene	gene with protein product		164350	"2',5'-oligoadenylate synthetase 1 (40-46 kD)"	OIAS		9344649, 9325053	Standard	XM_006719434		Approved	OIASI, IFI-4	uc001tud.3	P00973		ENST00000202917.5:c.775T>C	chr12.hg19:g.113354434T>C		162.0	0.0		94.0	4.0	NM_001032409	A8K4N8|P04820|P29080|P29081|P78485|P78486|Q16700|Q16701|Q1PG42|Q3ZM01|Q53GC5|Q53YA4|Q6A1Z3|Q6IPC6|Q6P7N9|Q96J61	Silent	SNP	ENST00000202917.5	hg19	CCDS41838.1																																																																																			.	.		0.473	OAS1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405896.2			C	113354434	T	C	113354434	2	2	259	1	0	0	0	0	0	0	0	1	10808	1606	56	2		2	OAS1	12	113354434	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1255990	113354434	20497461	575	36893										
OAS1	4938	hgsc.bcm.edu	37	chr12	113357220	113357220	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agcaacagtgcagacgatgaGaccgacgatcccaggaggta	13	10	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:113357220G>T	ENST00000202917.5	+	6	1328	c.1065G>T	c.(1063-1065)gaG>gaT	p.E355D	OAS1_ENST00000551241.1_Intron|RP1-71H24.1_ENST00000552784.1_RNA|OAS1_ENST00000445409.2_Intron	NM_016816.2	NP_058132.2	P00973	OAS1_HUMAN	2'-5'-oligoadenylate synthetase 1, 40/46kDa	355					cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|protein oligomerization (GO:0051259)|purine nucleotide biosynthetic process (GO:0006164)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(2)|skin(1)	16						CAGACGATGAGACCGACGATC	0.498																																					p.E355D		Atlas-SNP	.											.	OAS1	128	.	0			c.G1065T						.						95	92	93					12																	113357220		2203	4300	6503	SO:0001583	missense	4938	exon6			CGATGAGACCGAC	X04371	CCDS31905.1, CCDS41838.1, CCDS44980.1	12q24.2	2014-05-21	2011-07-21				2.7.7.-		8086	protein-coding gene	gene with protein product		164350	"2',5'-oligoadenylate synthetase 1 (40-46 kD)"	OIAS		9344649, 9325053	Standard	XM_006719434		Approved	OIASI, IFI-4	uc001tud.3	P00973		ENST00000202917.5:c.1065G>T	chr12.hg19:g.113357220G>T	ENSP00000202917:p.Glu355Asp	93.0	0.0		77.0	5.0	NM_016816	A8K4N8|P04820|P29080|P29081|P78485|P78486|Q16700|Q16701|Q1PG42|Q3ZM01|Q53GC5|Q53YA4|Q6A1Z3|Q6IPC6|Q6P7N9|Q96J61	Missense_Mutation	SNP	ENST00000202917.5	hg19	CCDS41838.1	.	.	.	.	.	.	.	.	.	.	G	2.728	-0.265134	0.05754	.	.	ENSG00000089127	ENST00000202917	T	0.04706	3.57	2.29	-2.98	0.05513	.	.	.	.	.	T	0.01976	0.0062	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48186	-0.9057	9	0.13853	T	0.58	.	3.9457	0.09347	0.1466:0.0:0.2602:0.5932	.	355	P00973	OAS1_HUMAN	D	355	ENSP00000202917:E355D	ENSP00000202917:E355D	E	+	3	2	OAS1	111841603	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.568000	0.02144	-0.774000	0.04590	0.557000	0.71058	GAG	.	.		0.498	OAS1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405896.2			T	113357220	G	T	113357220	3	4	259	1	0	0	0	0	1	0	0	0	10808	933	33	3	1144	3	OAS1	12	113357220	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	2786	113357220	20494675	576	36894										
OAS2	4939	hgsc.bcm.edu	37	chr12	113443013	113443013	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cagctttgatgtgcttcctgCctttaatgcactgggtaagg	11	9	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:113443013C>T	ENST00000342315.4	+	7	1668	c.1454C>T	c.(1453-1455)gCc>gTc	p.A485V	RP1-71H24.1_ENST00000552784.1_RNA|OAS2_ENST00000392583.2_Missense_Mutation_p.A485V	NM_016817.2	NP_058197.2	P29728	OAS2_HUMAN	2'-5'-oligoadenylate synthetase 2, 69/71kDa	485	OAS domain 2.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|nucleobase-containing compound metabolic process (GO:0006139)|protein glycosylation (GO:0006486)|protein myristoylation (GO:0018377)|purine nucleotide biosynthetic process (GO:0006164)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						GTGCTTCCTGCCTTTAATGCA	0.522																																					p.A485V	Pancreas(199;709 2232 18410 33584 35052)	Atlas-SNP	.											.	OAS2	86	.	0			c.C1454T						.						84	67	72					12																	113443013		2203	4300	6503	SO:0001583	missense	4939	exon7			TTCCTGCCTTTAA	M87284	CCDS31906.1, CCDS41839.1, CCDS44982.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111335			8087	protein-coding gene	gene with protein product		603350	"2'-5'-oligoadenylate synthetase 2 (69-71 kD)"			9790745	Standard	NM_002535		Approved		uc001tuj.3	P29728	OTTHUMG00000169802	ENST00000342315.4:c.1454C>T	chr12.hg19:g.113443013C>T	ENSP00000342278:p.Ala485Val	80.0	0.0		65.0	4.0	NM_002535	A8K9T1|Q6PJ33|Q86XX8	Missense_Mutation	SNP	ENST00000342315.4	hg19	CCDS31906.1	.	.	.	.	.	.	.	.	.	.	.	18.14	3.556919	0.65425	.	.	ENSG00000111335	ENST00000342315;ENST00000392583	T;T	0.16324	2.35;2.35	4.43	3.53	0.40419	.	0.000000	0.47455	D	0.000225	T	0.40886	0.1135	M	0.83223	2.63	0.52099	D	0.999944	D;D	0.89917	1.0;1.0	D;D	0.87578	0.994;0.998	T	0.33033	-0.9884	10	0.87932	D	0	-25.5517	8.3525	0.32310	0.0:0.8911:0.0:0.1089	.	485;485	P29728;P29728-2	OAS2_HUMAN;.	V	485	ENSP00000342278:A485V;ENSP00000376362:A485V	ENSP00000342278:A485V	A	+	2	0	OAS2	111927396	0.991000	0.36638	0.453000	0.27007	0.100000	0.18952	2.553000	0.45837	1.216000	0.43427	0.655000	0.94253	GCC	.	.		0.522	OAS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405937.1			T	113443013	C	T	113443013	3	4	259	1	0	0	0	0	1	0	0	0	10809	739	26	3	1551	3	OAS2	12	113443013	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	85793	113443013	20408882	577	36895										
DDX54	79039	hgsc.bcm.edu	37	chr12	113607596	113607596	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgagggctccttgaggggtcGggcgagggtgagggagcggc	23	7	0	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:113607596G>T	ENST00000306014.5	-	12	1420	c.1393C>A	c.(1393-1395)Cga>Aga	p.R465R	DDX54_ENST00000314045.7_Silent_p.R465R	NM_024072.3	NP_076977.3	Q8TDD1	DDX54_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 54	465	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|intracellular estrogen receptor signaling pathway (GO:0030520)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						TTGAGGGGTCGGGCGAGGGTG	0.652																																					p.R465R		Atlas-SNP	.											.	DDX54	73	.	0			c.C1393A						.						35	35	35					12																	113607596		2203	4300	6503	SO:0001819	synonymous_variant	79039	exon12			GGGGTCGGGCGAG	AF144056	CCDS31907.1, CCDS44984.1	12q24.11	2006-01-30				ENSG00000123064		"DEAD-boxes"	20084	protein-coding gene	gene with protein product		611665				12466272	Standard	NM_001111322		Approved	MGC2835, APR-5, DP97	uc001tuq.4	Q8TDD1	OTTHUMG00000169676	ENST00000306014.5:c.1393C>A	chr12.hg19:g.113607596G>T		124.0	0.0		82.0	4.0	NM_024072	Q86YT8|Q9BRZ1	Silent	SNP	ENST00000306014.5	hg19	CCDS31907.1																																																																																			.	.		0.652	DDX54-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405435.1	NM_024072		T	113607596	G	T	113607596	2	4	259	1	0	0	0	0	0	0	0	1	4374	1124	39	1		1	DDX54	12	113607596	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	164583	113607596	20244299	578	36896										
KSR2	283455	hgsc.bcm.edu	37	chr12	117969500	117969500	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgaactgctgcttgtatttgTagtagtgggatgcttgcaaa	12	5	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:117969500T>C	ENST00000339824.5	-	11	2427	c.1700A>G	c.(1699-1701)tAc>tGc	p.Y567C	KSR2_ENST00000425217.1_Missense_Mutation_p.Y538C|KSR2_ENST00000302438.5_Missense_Mutation_p.Y264C|KSR2_ENST00000545002.1_5'UTR			Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2	567					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(25)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CTTGTATTTGTAGTAGTGGGA	0.502																																					p.Y538C		Atlas-SNP	.											.	KSR2	208	.	0			c.A1613G						.						95	100	99					12																	117969500		1993	4160	6153	SO:0001583	missense	283455	exon11			TATTTGTAGTAGT	AY345972	CCDS61250.1	12q24.22-q24.23	2014-08-12			ENSG00000171435	ENSG00000171435			18610	protein-coding gene	gene with protein product		610737				12471243	Standard	NM_173598		Approved	FLJ25965	uc001two.2	Q6VAB6	OTTHUMG00000169020	ENST00000339824.5:c.1700A>G	chr12.hg19:g.117969500T>C	ENSP00000339952:p.Tyr567Cys	68.0	0.0		40.0	4.0	NM_173598	A0PJT2|Q3B828|Q8N775	Missense_Mutation	SNP	ENST00000339824.5	hg19		.	.	.	.	.	.	.	.	.	.	T	16.14	3.039148	0.55003	.	.	ENSG00000171435	ENST00000425217;ENST00000339824;ENST00000302438;ENST00000542378	T;T;D	0.85955	-1.17;-1.17;-2.05	4.66	4.66	0.58398	.	0.059761	0.64402	D	0.000001	D	0.82577	0.5067	L	0.44542	1.39	0.49798	D	0.999824	P	0.50710	0.938	P	0.46049	0.502	T	0.83154	-0.0102	10	0.42905	T	0.14	.	14.2572	0.66060	0.0:0.0:0.0:1.0	.	567	Q6VAB6	KSR2_HUMAN	C	538;567;264;239	ENSP00000389715:Y538C;ENSP00000339952:Y567C;ENSP00000305466:Y264C	ENSP00000305466:Y264C	Y	-	2	0	KSR2	116453883	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.691000	0.47010	1.934000	0.56057	0.402000	0.26972	TAC	.	.		0.502	KSR2-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401987.2	NM_173598		C	117969500	T	C	117969500	3	2	259	1	0	0	0	0	1	0	0	0	8591	1638	57	2	1192	2	KSR2	12	117969500	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	4361904	117969500	15882395	579	36897										
WSB2	55884	hgsc.bcm.edu	37	chr12	118472835	118472835	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggaaaaaatgtgcagcaaagCccattggtcataggagcaaa	11	7	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:118472835C>G	ENST00000315436.3	-	8	1149	c.1008G>C	c.(1006-1008)ggG>ggC	p.G336G	WSB2_ENST00000536738.1_5'Flank|WSB2_ENST00000542304.1_Silent_p.G111G|WSB2_ENST00000544233.1_Silent_p.G126G|WSB2_ENST00000441406.2_Silent_p.G353G|WSB2_ENST00000535496.1_Silent_p.G338G	NM_001278557.1|NM_018639.3	NP_001265486.1|NP_061109.1	Q9NYS7	WSB2_HUMAN	WD repeat and SOCS box containing 2	336					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TGCAGCAAAGCCCATTGGTCA	0.478											OREG0022175	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G336G		Atlas-SNP	.											.	WSB2	32	.	0			c.G1008C						.						81	78	79					12																	118472835		2203	4300	6503	SO:0001819	synonymous_variant	55884	exon8			GCAAAGCCCATTG	AF038187	CCDS9186.1, CCDS61251.1, CCDS61252.1	12q24.23	2013-01-09	2011-01-25		ENSG00000176871	ENSG00000176871		"WD repeat domain containing"	19222	protein-coding gene	gene with protein product			"WD repeat and SOCS box-containing 2"			12076535	Standard	NM_018639		Approved	SBA2, MGC10210	uc001twr.2	Q9NYS7	OTTHUMG00000168885	ENST00000315436.3:c.1008G>C	chr12.hg19:g.118472835C>G		113.0	0.0	1488	117.0	9.0	NM_018639	B4DIE6|B4DPV6|Q9NRX9	Silent	SNP	ENST00000315436.3	hg19	CCDS9186.1																																																																																			.	.		0.478	WSB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401515.1	NM_018639		G	118472835	C	G	118472835	2	3	259	1	0	0	0	0	0	0	0	1	17420	726	26	4		4	WSB2	12	118472835	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	503335	118472835	15379060	580	36898										
RAB35	11021	hgsc.bcm.edu	37	chr12	120536685	120536685	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccatctgcccggcgaatttgTaggcatcttccgtctccacc	8	16	3	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:120536685T>C	ENST00000229340.5	-	5	595	c.407A>G	c.(406-408)tAc>tGc	p.Y136C	RAB35_ENST00000534951.1_Intron|RAB35_ENST00000432953.2_Intron|RAB35_ENST00000543364.1_5'UTR	NM_001167606.1|NM_006861.6	NP_001161078.1|NP_006852.1	Q15286	RAB35_HUMAN	RAB35, member RAS oncogene family	136					antigen processing and presentation (GO:0019882)|cellular response to nerve growth factor stimulus (GO:1990090)|cytokinesis (GO:0000910)|endosomal transport (GO:0016197)|GTP catabolic process (GO:0006184)|neuron projection development (GO:0031175)|plasma membrane to endosome transport (GO:0048227)|protein localization (GO:0008104)|protein localization to endosome (GO:0036010)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	cell projection membrane (GO:0031253)|clathrin-coated endocytic vesicle (GO:0045334)|coated pit (GO:0005905)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|intercellular bridge (GO:0045171)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(1)|ovary(1)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.248)		GGCGAATTTGTAGGCATCTTC	0.597																																					p.Y136C		Atlas-SNP	.											.	RAB35	18	.	0			c.A407G						.						118	125	123					12																	120536685		2101	4214	6315	SO:0001583	missense	11021	exon5			AATTTGTAGGCAT	X79781	CCDS41846.1, CCDS53836.1	12q24	2008-07-28			ENSG00000111737	ENSG00000111737		"RAB, member RAS oncogene"	9774	protein-coding gene	gene with protein product		604199					Standard	NM_001167606		Approved	H-ray	uc009zww.2	Q15286	OTTHUMG00000169159	ENST00000229340.5:c.407A>G	chr12.hg19:g.120536685T>C	ENSP00000229340:p.Tyr136Cys	144.0	0.0		94.0	4.0	NM_006861	B2R6E0|B4E390	Missense_Mutation	SNP	ENST00000229340.5	hg19	CCDS41846.1	.	.	.	.	.	.	.	.	.	.	T	15.86	2.958352	0.53400	.	.	ENSG00000111737	ENST00000229340;ENST00000538903	T;T	0.76709	-1.04;-1.04	4.77	4.77	0.60923	Small GTP-binding protein domain (1);	0.120787	0.64402	D	0.000017	T	0.64527	0.2606	N	0.14661	0.345	0.80722	D	1	B	0.25667	0.131	B	0.25614	0.062	T	0.66184	-0.5987	10	0.87932	D	0	.	14.4506	0.67382	0.0:0.0:0.0:1.0	.	136	Q15286	RAB35_HUMAN	C	136;120	ENSP00000229340:Y136C;ENSP00000443994:Y120C	ENSP00000229340:Y136C	Y	-	2	0	RAB35	119021068	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	5.858000	0.69532	1.980000	0.57719	0.533000	0.62120	TAC	.	.		0.597	RAB35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402599.2			C	120536685	T	C	120536685	3	2	259	1	0	0	0	0	1	0	0	0	12940	1638	57	2	206	2	RAB35	12	120536685	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	2063850	120536685	13315210	581	36899										
PXN	5829	hgsc.bcm.edu	37	chr12	120651722	120651722	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	caggatggcccgggcgcagcCgccacacttgggtgcgaaca	15	14	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:120651722C>A	ENST00000228307.7	-	11	1573	c.1432G>T	c.(1432-1434)Ggc>Tgc	p.G478C	PXN_ENST00000267257.7_Missense_Mutation_p.G492C|PXN-AS1_ENST00000542265.1_RNA|PXN-AS1_ENST00000539446.1_RNA|PXN-AS1_ENST00000535200.1_RNA|PXN_ENST00000538144.1_5'UTR|PXN_ENST00000397506.3_Missense_Mutation_p.G290C|PXN_ENST00000424649.2_Missense_Mutation_p.G444C|PXN_ENST00000536957.1_Missense_Mutation_p.G476C|PXN_ENST00000458477.2_Missense_Mutation_p.G311C	NM_001080855.2	NP_001074324.1	P49023	PAXI_HUMAN	paxillin	478	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.				activation of MAPK activity (GO:0000187)|branching morphogenesis of an epithelial tube (GO:0048754)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cellular component movement (GO:0006928)|cellular response to reactive oxygen species (GO:0034614)|cytoskeleton organization (GO:0007010)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|growth hormone receptor signaling pathway (GO:0060396)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|muscle contraction (GO:0006936)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of cell shape (GO:0008360)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	beta-catenin binding (GO:0008013)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			breast(1)|endometrium(5)|kidney(2)|large_intestine(1)|lung(5)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CGGGCGCAGCCGCCACACTTG	0.602																																					p.G492C		Atlas-SNP	.											.	PXN	69	.	0			c.G1474T						.						29	39	35					12																	120651722		2033	4178	6211	SO:0001583	missense	5829	exon10			CGCAGCCGCCACA	U14588	CCDS44996.1, CCDS44997.1, CCDS44998.1, CCDS58281.1	12q24	2006-01-23			ENSG00000089159	ENSG00000089159			9718	protein-coding gene	gene with protein product		602505				7534286	Standard	NM_001080855		Approved		uc001txv.3	P49023	OTTHUMG00000169169	ENST00000228307.7:c.1432G>T	chr12.hg19:g.120651722C>A	ENSP00000228307:p.Gly478Cys	103.0	0.0		71.0	4.0	NM_001243756	B2RAI3|B7ZMB4|O14970|O14971|O60360|Q5HYA4	Missense_Mutation	SNP	ENST00000228307.7	hg19	CCDS44997.1	.	.	.	.	.	.	.	.	.	.	C	33	5.255159	0.95336	.	.	ENSG00000089159	ENST00000458477;ENST00000228307;ENST00000424649;ENST00000536957;ENST00000267257;ENST00000397506;ENST00000331257;ENST00000541856	D;D;D;D;D;D	0.89050	-2.46;-2.46;-2.46;-2.46;-2.46;-2.46	5.51	5.51	0.81932	Zinc finger, LIM-type (5);	.	.	.	.	D	0.96352	0.8810	H	0.94264	3.515	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.998;0.998;0.999	D	0.97152	0.9832	9	0.87932	D	0	.	19.4166	0.94703	0.0:1.0:0.0:0.0	.	444;492;290;478	P49023-2;P49023-3;E7EMK8;P49023	.;.;.;PAXI_HUMAN	C	311;478;444;476;492;290;106;203	ENSP00000395536:G311C;ENSP00000228307:G478C;ENSP00000391283:G444C;ENSP00000443887:G476C;ENSP00000267257:G492C;ENSP00000380643:G290C	ENSP00000228307:G478C	G	-	1	0	PXN	119136105	1.000000	0.71417	0.997000	0.53966	0.989000	0.77384	7.675000	0.84002	2.598000	0.87819	0.561000	0.74099	GGC	.	.		0.602	PXN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402679.4	NM_002859		A	120651722	C	A	120651722	3	1	259	1	0	0	0	0	1	0	0	0	12867	652	23	1	351	1	PXN	12	120651722	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	115037	120651722	13200173	582	36900										
NCOR2	9612	hgsc.bcm.edu	37	chr12	124914172	124914172	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gactcacctcctgctctgagAggccatcgatgatctctgac	9	14	3	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:124914172A>G	ENST00000405201.1	-	10	1136	c.1136T>C	c.(1135-1137)cTc>cCc	p.L379P	NCOR2_ENST00000397355.1_Missense_Mutation_p.L379P|NCOR2_ENST00000404621.1_Missense_Mutation_p.L378P|NCOR2_ENST00000429285.2_Missense_Mutation_p.L378P|NCOR2_ENST00000356219.3_Missense_Mutation_p.L379P|NCOR2_ENST00000404121.2_5'UTR			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	379					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		CTGCTCTGAGAGGCCATCGAT	0.662																																					p.L379P		Atlas-SNP	.											.	NCOR2	475	.	0			c.T1136C						.						28	33	32					12																	124914172		2096	4222	6318	SO:0001583	missense	9612	exon12			TCTGAGAGGCCAT	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"nuclear receptor co-repressor 2"			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.1136T>C	chr12.hg19:g.124914172A>G	ENSP00000384018:p.Leu379Pro	159.0	0.0		103.0	5.0	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	hg19	CCDS41858.2	.	.	.	.	.	.	.	.	.	.	A	11.30	1.598702	0.28445	.	.	ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000429285;ENST00000458234;ENST00000420698	T;T;T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88;0.88;0.88	3.57	3.57	0.40892	.	0.256680	0.30510	N	0.009470	T	0.60996	0.2312	M	0.71206	2.165	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.74023	0.96;0.96;0.982	T	0.66344	-0.5947	10	0.87932	D	0	-32.9859	12.6178	0.56586	1.0:0.0:0.0:0.0	.	378;379;379	C9J0Q5;C9J239;C9JFD3	.;.;.	P	379;378;379;379;379;378;379;379	ENSP00000384018:L379P;ENSP00000384202:L378P;ENSP00000348551:L379P;ENSP00000380513:L379P;ENSP00000400281:L378P;ENSP00000402808:L379P;ENSP00000405367:L379P	ENSP00000348551:L379P	L	-	2	0	NCOR2	123480125	1.000000	0.71417	0.995000	0.50966	0.642000	0.38348	9.127000	0.94417	1.609000	0.50190	0.260000	0.18958	CTC	.	.		0.662	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312		G	124914172	A	G	124914172	3	3	259	1	0	0	0	0	1	0	0	0	10245	304	11	2	6584	2	NCOR2	12	124914172	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	4262450	124914172	8937723	583	36901										
NCOR2	9612	hgsc.bcm.edu	37	chr12	124957667	124957667	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccggttccagcttgcccgtcAggctacggtcctgtggcaga	13	14	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:124957667A>G	ENST00000405201.1	-	4	422	c.422T>C	c.(421-423)cTg>cCg	p.L141P	NCOR2_ENST00000397355.1_Missense_Mutation_p.L141P|NCOR2_ENST00000404621.1_Missense_Mutation_p.L141P|NCOR2_ENST00000429285.2_Missense_Mutation_p.L141P|NCOR2_ENST00000356219.3_Missense_Mutation_p.L141P|NCOR2_ENST00000404121.2_5'UTR			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	141					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		CTTGCCCGTCAGGCTACGGTC	0.612																																					p.L141P		Atlas-SNP	.											.	NCOR2	475	.	0			c.T422C						.						35	40	38					12																	124957667		1971	4140	6111	SO:0001583	missense	9612	exon6			CCCGTCAGGCTAC	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"nuclear receptor co-repressor 2"			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.422T>C	chr12.hg19:g.124957667A>G	ENSP00000384018:p.Leu141Pro	64.0	0.0		59.0	4.0	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	hg19	CCDS41858.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	6.183|6.183	0.401919|0.401919	0.11696|0.11696	.|.	.|.	ENSG00000196498|ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000429285;ENST00000458234;ENST00000420698;ENST00000448008|ENST00000542927	T;T;T;T;T;T|.	0.35048|.	2.06;2.32;2.06;2.32;2.32;1.33|.	5.53|5.53	5.53|5.53	0.82687|0.82687	.|.	0.169966|.	0.41605|.	D|.	0.000857|.	T|.	0.67951|.	0.2948|.	L|L	0.50333|0.50333	1.59|1.59	0.80722|0.80722	D|D	1|1	D;D;D|.	0.65815|.	0.976;0.991;0.995|.	P;P;P|.	0.55161|.	0.454;0.593;0.77|.	T|.	0.65923|.	-0.6050|.	10|.	0.72032|.	D|.	0.01|.	-24.9984|-24.9984	15.6599|15.6599	0.77178|0.77178	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	141;141;141|.	C9J0Q5;C9J239;C9JFD3|.	.;.;.|.	P|R	141;141;141;141;141;141;141;141;62|64	ENSP00000384018:L141P;ENSP00000384202:L141P;ENSP00000348551:L141P;ENSP00000380513:L141P;ENSP00000400281:L141P;ENSP00000402808:L141P|.	ENSP00000348551:L141P|.	L|X	-|-	2|1	0|0	NCOR2|NCOR2	123523620|123523620	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.196000|0.196000	0.23810|0.23810	5.716000|5.716000	0.68437|0.68437	2.099000|2.099000	0.63709|0.63709	0.459000|0.459000	0.35465|0.35465	CTG|TGA	.	.		0.612	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312		G	124957667	A	G	124957667	3	3	259	1	0	0	0	0	1	0	0	0	10245	188	7	2	7322	2	NCOR2	12	124957667	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	43495	124957667	8894228	584	36902										
TMEM132B	114795	hgsc.bcm.edu	37	chr12	126139253	126139253	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gaaagtctgcaagaccagatGtaaactcctttcttatgttt	7	8	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:126139253G>A	ENST00000299308.3	+	9	3242	c.3234G>A	c.(3232-3234)atG>atA	p.M1078I	TMEM132B_ENST00000535886.1_Missense_Mutation_p.M590I	NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	1078						integral component of membrane (GO:0016021)		p.M1078I(1)		NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		AAGACCAGATGTAAACTCCTT	0.408																																					p.M1078I		Atlas-SNP	.											TMEM132B,rectum,carcinoma,0,1	TMEM132B	207	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3234A						.						63	58	59					12																	126139253		1865	4084	5949	SO:0001583	missense	114795	exon9			CCAGATGTAAACT	AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.3234G>A	chr12.hg19:g.126139253G>A	ENSP00000299308:p.Met1078Ile	128.0	0.0		70.0	3.0	NM_052907	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Missense_Mutation	SNP	ENST00000299308.3	hg19	CCDS41859.1	.	.	.	.	.	.	.	.	.	.	G	13.31	2.198471	0.38806	.	.	ENSG00000139364	ENST00000299308;ENST00000535886	T;T	0.08807	3.83;3.05	5.81	5.81	0.92471	.	0.131674	0.53938	D	0.000055	T	0.09949	0.0244	L	0.34521	1.04	0.43766	D	0.99628	B	0.28933	0.228	B	0.28011	0.085	T	0.17289	-1.0374	10	0.38643	T	0.18	.	20.0838	0.97793	0.0:0.0:1.0:0.0	.	1078	Q14DG7	T132B_HUMAN	I	1078;590	ENSP00000299308:M1078I;ENSP00000440436:M590I	ENSP00000299308:M1078I	M	+	3	0	TMEM132B	124705206	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.845000	0.92153	2.741000	0.93983	0.655000	0.94253	ATG	.	.		0.408	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907		A	126139253	G	A	126139253	3	1	259	1	0	0	0	0	1	0	0	0	16061	1377	48	3	3268	3	TMEM132B	12	126139253	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1181586	126139253	7712642	585	36903										
STX2	2054	hgsc.bcm.edu	37	chr12	131311746	131311746	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aaacgctcttacctgatggaAgaaatcatccatgaaatgat	7	8	2	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:131311746A>G	ENST00000392373.2	-	2	191	c.97T>C	c.(97-99)Ttc>Ctc	p.F33L	STX2_ENST00000261653.6_Missense_Mutation_p.F33L	NM_194356.2	NP_919337.1	P32856	STX2_HUMAN	syntaxin 2	33					acrosome reaction (GO:0007340)|cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|intracellular protein transport (GO:0006886)|organ morphogenesis (GO:0009887)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|signal transduction (GO:0007165)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)	calcium-dependent protein binding (GO:0048306)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)	16	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.79e-06)|all cancers(50;5.27e-05)|Epithelial(86;5.29e-05)		ACCTGATGGAAGAAATCATCC	0.443																																					p.F33L		Atlas-SNP	.											.	STX2	66	.	0			c.T97C						.						136	126	129					12																	131311746		2203	4300	6503	SO:0001583	missense	2054	exon2			GATGGAAGAAATC	D14582	CCDS9269.1, CCDS9270.1	12q24	2008-02-05	2006-04-25	2006-04-25	ENSG00000111450	ENSG00000111450			3403	protein-coding gene	gene with protein product		132350	"epimorphin"	STX2B, STX2C, STX2A, EPIM		8938452, 15943887	Standard	NM_001980		Approved	EPM	uc001uio.4	P32856	OTTHUMG00000168365	ENST00000392373.2:c.97T>C	chr12.hg19:g.131311746A>G	ENSP00000376178:p.Phe33Leu	125.0	0.0		83.0	4.0	NM_194356	Q86VW8	Missense_Mutation	SNP	ENST00000392373.2	hg19	CCDS9270.1	.	.	.	.	.	.	.	.	.	.	A	14.90	2.672813	0.47781	.	.	ENSG00000111450	ENST00000261653;ENST00000392373	T;T	0.19806	2.12;2.12	4.65	4.65	0.58169	t-SNARE (1);Syntaxin, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.29061	0.0722	L	0.55990	1.75	0.58432	D	0.999999	B;B;P	0.41102	0.379;0.219;0.738	B;B;P	0.48368	0.097;0.07;0.575	T	0.02087	-1.1216	10	0.36615	T	0.2	-16.5748	12.0741	0.53634	1.0:0.0:0.0:0.0	.	33;33;33	P32856-3;P32856-2;P32856	.;.;STX2_HUMAN	L	33	ENSP00000261653:F33L;ENSP00000376178:F33L	ENSP00000261653:F33L	F	-	1	0	STX2	129877699	1.000000	0.71417	1.000000	0.80357	0.031000	0.12232	5.647000	0.67923	1.743000	0.51761	0.481000	0.45027	TTC	.	.		0.443	STX2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399455.2	NM_194356		G	131311746	A	G	131311746	3	3	259	1	0	0	0	0	1	0	0	0	15360	72	3	2	887	2	STX2	12	131311746	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	5172493	131311746	2540149	586	36904										
POLE	5426	hgsc.bcm.edu	37	chr12	133256186	133256186	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tttgacaagatcctccacagTgtggaaggacagcctgatgt	11	9	0	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:133256186T>C	ENST00000320574.5	-	6	518	c.475A>G	c.(475-477)Act>Gct	p.T159A	POLE_ENST00000535270.1_Missense_Mutation_p.T132A	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	159					base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	cytoplasm (GO:0005737)|epsilon DNA polymerase complex (GO:0008622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)			NS(2)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(41)|ovary(3)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	89	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)	Cladribine(DB00242)	TCCTCCACAGTGTGGAAGGAC	0.493								DNA polymerases (catalytic subunits)																													p.T159A		Atlas-SNP	.											.	POLE	416	.	0			c.A475G						.						130	105	114					12																	133256186		2203	4300	6503	SO:0001583	missense	5426	exon6			CCACAGTGTGGAA		CCDS9278.1	12q24.3	2014-09-17	2012-05-18		ENSG00000177084	ENSG00000177084		"DNA polymerases"	9177	protein-coding gene	gene with protein product	"DNA polymerase epsilon catalytic subunit A"	174762	"polymerase (DNA directed), epsilon"			8020968	Standard	NM_006231		Approved	POLE1	uc001uks.1	Q07864	OTTHUMG00000168045	ENST00000320574.5:c.475A>G	chr12.hg19:g.133256186T>C	ENSP00000322570:p.Thr159Ala	110.0	0.0		78.0	4.0	NM_006231	Q13533|Q86VH9	Missense_Mutation	SNP	ENST00000320574.5	hg19	CCDS9278.1	.	.	.	.	.	.	.	.	.	.	T	12.82	2.051712	0.36181	.	.	ENSG00000177084	ENST00000320574;ENST00000455752;ENST00000535270;ENST00000376577	T;T;T	0.09817	2.94;2.94;2.94	5.95	5.95	0.96441	DNA-directed DNA polymerase, family B, exonuclease domain (1);Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.25158	0.0611	M	0.82193	2.58	0.46798	D	0.999204	P;P	0.41366	0.747;0.639	P;P	0.48921	0.46;0.595	T	0.01393	-1.1366	10	0.62326	D	0.03	.	10.2046	0.43105	0.2556:0.0:0.0:0.7444	.	132;159	F5H1D6;Q07864	.;DPOE1_HUMAN	A	159;170;132;94	ENSP00000322570:T159A;ENSP00000406383:T170A;ENSP00000445753:T132A	ENSP00000322570:T159A	T	-	1	0	POLE	131766259	1.000000	0.71417	0.997000	0.53966	0.171000	0.22731	4.835000	0.62781	2.279000	0.76181	0.402000	0.26972	ACT	.	.		0.493	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231		C	133256186	T	C	133256186	3	2	259	1	0	0	0	0	1	0	0	0	12205	1696	59	2	6561	2	POLE	12	133256186	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1944440	133256186	595709	587	36905										
ZNF140	7699	hgsc.bcm.edu	37	chr12	133682950	133682950	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tctatgaatgtgatgaatgtGgtaaagttttcacttggcat	10	4	2	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:133682950G>T	ENST00000355557.2	+	5	2370	c.1087G>T	c.(1087-1089)Ggt>Tgt	p.G363C	ZNF140_ENST00000544426.1_Missense_Mutation_p.G260C|ZNF140_ENST00000440550.2_3'UTR	NM_003440.2	NP_003431.2	P52738	ZN140_HUMAN	zinc finger protein 140	363					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|large_intestine(4)|lung(1)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;1.28e-06)|all_epithelial(31;0.0051)|Lung NSC(355;0.114)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		TGATGAATGTGGTAAAGTTTT	0.403																																					p.G363C		Atlas-SNP	.											.	ZNF140	18	.	0			c.G1087T						.						113	107	109					12																	133682950		2203	4300	6503	SO:0001583	missense	7699	exon5			GAATGTGGTAAAG	U09368	CCDS9282.1, CCDS73550.1	12q24.33	2013-01-08	2006-06-13		ENSG00000196387	ENSG00000196387		"Zinc fingers, C2H2-type", "-"	12925	protein-coding gene	gene with protein product		604082	"zinc finger protein 140 (clone pHZ-39)"			7557990	Standard	XR_245353		Approved	pHZ-39	uc001ulo.3	P52738	OTTHUMG00000167942	ENST00000355557.2:c.1087G>T	chr12.hg19:g.133682950G>T	ENSP00000347755:p.Gly363Cys	113.0	0.0		88.0	7.0	NM_003440	D3DXJ3|Q05CP6|Q8IV75	Missense_Mutation	SNP	ENST00000355557.2	hg19	CCDS9282.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.087520	0.76642	.	.	ENSG00000196387	ENST00000355557;ENST00000544426;ENST00000433577	T;T	0.01516	4.81;4.81	3.85	3.85	0.44370	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.35708	N	0.003036	T	0.13200	0.0320	M	0.90309	3.105	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.01834	-1.1264	10	0.87932	D	0	.	15.0534	0.71894	0.0:0.0:1.0:0.0	.	363	P52738	ZN140_HUMAN	C	363;260;154	ENSP00000347755:G363C;ENSP00000445411:G260C	ENSP00000347755:G363C	G	+	1	0	ZNF140	132193023	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.688000	0.61715	2.139000	0.66308	0.563000	0.77884	GGT	.	.		0.403	ZNF140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397169.1	NM_003440		T	133682950	G	T	133682950	3	4	259	1	0	0	0	0	1	0	0	0	17744	1348	47	3	1101	3	ZNF140	12	133682950	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	426764	133682950	168945	588	36906										
MPHOSPH8	54737	hgsc.bcm.edu	37	chr13	20237233	20237233	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gcaggagcttttgtaaatgtCcagcaaagcaatggtgagac	12	7	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:20237233C>T	ENST00000361479.5	+	9	2054	c.1986C>T	c.(1984-1986)gtC>gtT	p.V662V	MPHOSPH8_ENST00000414242.2_Silent_p.V662V	NM_017520.3	NP_059990.2	Q99549	MPP8_HUMAN	M-phase phosphoprotein 8	662					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of DNA methylation (GO:0044030)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear heterochromatin (GO:0005720)|nuclear nucleosome (GO:0000788)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	methylated histone binding (GO:0035064)			breast(2)|endometrium(1)|large_intestine(2)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		all_cancers(29;2.83e-16)|all_lung(29;1.16e-17)|all_epithelial(30;8.13e-16)|Lung NSC(5;6.91e-15)|Lung SC(185;0.0367)		all cancers(112;8.43e-05)|Epithelial(112;0.000426)|OV - Ovarian serous cystadenocarcinoma(117;0.00596)|Lung(94;0.015)|LUSC - Lung squamous cell carcinoma(192;0.0795)		TTGTAAATGTCCAGCAAAGCA	0.398																																					p.V662V		Atlas-SNP	.											.	MPHOSPH8	58	.	0			c.C1986T						.						140	144	142					13																	20237233		2203	4300	6503	SO:0001819	synonymous_variant	54737	exon9			AAATGTCCAGCAA	AK056785, AJ293409	CCDS9287.1	13q12.11	2013-01-10			ENSG00000196199	ENSG00000196199		"Ankyrin repeat domain containing"	29810	protein-coding gene	gene with protein product		611626				8885239	Standard	NM_017520		Approved	mpp8, HSMPP8	uc001umh.3	Q99549	OTTHUMG00000016498	ENST00000361479.5:c.1986C>T	chr13.hg19:g.20237233C>T		99.0	0.0		73.0	4.0	NM_017520	B7Z6F9|Q5JPE5|Q5JTQ0|Q86TK3|Q96MK4|Q9BTP1	Silent	SNP	ENST00000361479.5	hg19	CCDS9287.1																																																																																			.	.		0.398	MPHOSPH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044028.2	NM_017520		T	20237233	C	T	20237233	2	4	259	1	0	0	0	0	0	0	0	1	9736	842	30	3		3	MPHOSPH8	13	20237233	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10		20237233	94932645	589	36907										
SGCG	6445	hgsc.bcm.edu	37	chr13	23898576	23898576	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cgtggggtccctctggcagcTcacagagcctctacgaaatc	11	14	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:23898576T>C	ENST00000218867.3	+	8	896	c.772T>C	c.(772-774)Tca>Cca	p.S258P	SGCG_ENST00000545013.1_Missense_Mutation_p.S258P|SGCG_ENST00000537476.1_Missense_Mutation_p.S258P	NM_000231.2	NP_000222	Q13326	SGCG_HUMAN	sarcoglycan, gamma (35kDa dystrophin-associated glycoprotein)	258					muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		all_cancers(29;4.34e-23)|all_epithelial(30;4.4e-19)|all_lung(29;2.45e-18)|Lung SC(185;0.0228)|Breast(139;0.188)		all cancers(112;0.00255)|Epithelial(112;0.0129)|OV - Ovarian serous cystadenocarcinoma(117;0.0365)|Lung(94;0.205)		CTCTGGCAGCTCACAGAGCCT	0.562																																					p.S258P		Atlas-SNP	.											.	SGCG	64	.	0			c.T772C						.						113	92	99					13																	23898576		2203	4300	6503	SO:0001583	missense	6445	exon8			GGCAGCTCACAGA	U34976	CCDS9299.1	13q12-q13	2014-09-17	2002-08-29		ENSG00000102683	ENSG00000102683			10809	protein-coding gene	gene with protein product	"Maghrebian myopathy (autosomal recessive)", "35kD dystrophin-associated glycoprotein", "limb girdle muscular dystrophy 2C (Duchenne-like muscular dystrophy, autosomal recessive)", "gamma sarcoglycan"	608896	"sarcoglycan, gamma (35kD dystrophin-associated glycoprotein)"	DMDA1, MAM, LGMD2C		8968757	Standard	NM_000231		Approved	SCARMD2, DAGA4, SCG3, DMDA, TYPE, A4, MGC130048	uc001uom.2	Q13326	OTTHUMG00000016563	ENST00000218867.3:c.772T>C	chr13.hg19:g.23898576T>C	ENSP00000218867:p.Ser258Pro	144.0	0.0		79.0	4.0	NM_000231	Q32M32|Q5T9J6	Missense_Mutation	SNP	ENST00000218867.3	hg19	CCDS9299.1	.	.	.	.	.	.	.	.	.	.	T	9.539	1.112812	0.20795	.	.	ENSG00000102683	ENST00000218867;ENST00000537476;ENST00000545013	D;D;D	0.94862	-3.54;-3.54;-3.54	5.28	-1.61	0.08399	.	0.452001	0.25164	N	0.032654	D	0.88190	0.6370	L	0.52364	1.645	0.09310	N	0.999993	B	0.06786	0.001	B	0.12156	0.007	T	0.75844	-0.3174	10	0.40728	T	0.16	-2.8715	1.4353	0.02342	0.1175:0.201:0.2427:0.4388	.	258	Q13326	SGCG_HUMAN	P	258	ENSP00000218867:S258P;ENSP00000444100:S258P;ENSP00000442232:S258P	ENSP00000218867:S258P	S	+	1	0	SGCG	22796576	0.014000	0.17966	0.032000	0.17829	0.300000	0.27592	0.752000	0.26362	-0.241000	0.09681	0.454000	0.30748	TCA	.	.		0.562	SGCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044151.1	NM_000231		C	23898576	T	C	23898576	3	2	259	1	0	0	0	0	1	0	0	0	14218	1551	54	2	798	2	SGCG	13	23898576	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	3661343	23898576	91271302	590	36908										
SACS	26278	hgsc.bcm.edu	37	chr13	23910918	23910918	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gataaaggtatggtgccgccTcaaaatttaaatgaaaagaa	9	5	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:23910918T>C	ENST00000382292.3	-	9	7370	c.7097A>G	c.(7096-7098)gAg>gGg	p.E2366G	SACS_ENST00000402364.1_Missense_Mutation_p.E1616G|SACS_ENST00000382298.3_Missense_Mutation_p.E2366G			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	2366					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		TGGTGCCGCCTCAAAATTTAA	0.348																																					p.E2366G		Atlas-SNP	.											.	SACS	871	.	0			c.A7097G						.						51	52	52					13																	23910918		2203	4298	6501	SO:0001583	missense	26278	exon10			GCCGCCTCAAAAT	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.7097A>G	chr13.hg19:g.23910918T>C	ENSP00000371729:p.Glu2366Gly	131.0	0.0		98.0	4.0	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	hg19	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	T	11.46	1.645094	0.29246	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.95342	-3.68;-3.68;-3.68	5.68	5.68	0.88126	.	0.111701	0.64402	D	0.000009	D	0.90342	0.6978	L	0.29908	0.895	0.44539	D	0.997491	B	0.27559	0.181	B	0.24541	0.054	D	0.87717	0.2570	10	0.35671	T	0.21	.	15.9354	0.79698	0.0:0.0:0.0:1.0	.	2366	Q9NZJ4	SACS_HUMAN	G	2366;1616;2366	ENSP00000371729:E2366G;ENSP00000385844:E1616G;ENSP00000371735:E2366G	ENSP00000371729:E2366G	E	-	2	0	SACS	22808918	1.000000	0.71417	0.997000	0.53966	0.170000	0.22686	7.698000	0.84413	2.182000	0.69389	0.533000	0.62120	GAG	.	.		0.348	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		C	23910918	T	C	23910918	3	2	259	1	0	0	0	0	1	0	0	0	13819	1551	54	2	6646	2	SACS	13	23910918	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	12342	23910918	91258960	591	36909										
NBEA	26960	hgsc.bcm.edu	37	chr13	36046654	36046654	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agatgaggatgattctgcctTcaagaagatcgacacgaaag	11	7	2	5			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:36046654T>C	ENST00000400445.3	+	41	7100	c.6566T>C	c.(6565-6567)tTc>tCc	p.F2189S	NBEA_ENST00000540320.1_Missense_Mutation_p.F2189S|NBEA_ENST00000310336.4_Missense_Mutation_p.F2189S|NBEA_ENST00000379939.2_Missense_Mutation_p.F2186S	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	2189					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		GATTCTGCCTTCAAGAAGATC	0.488																																					p.F2189S		Atlas-SNP	.											.	NBEA	340	.	0			c.T6566C						.						91	90	90					13																	36046654		1991	4172	6163	SO:0001583	missense	26960	exon41			CTGCCTTCAAGAA	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.6566T>C	chr13.hg19:g.36046654T>C	ENSP00000383295:p.Phe2189Ser	100.0	0.0		63.0	4.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.160120	0.78226	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336;ENST00000422518	T;T;T;T	0.52295	0.67;0.67;0.67;0.67	5.51	5.51	0.81932	PH-BEACH domain (1);	0.000000	0.85682	D	0.000000	T	0.59238	0.2179	M	0.64997	1.995	0.80722	D	1	B;D	0.58268	0.218;0.982	B;P	0.54312	0.128;0.748	T	0.60535	-0.7244	10	0.45353	T	0.12	.	15.6376	0.76966	0.0:0.0:0.0:1.0	.	2189;2186	Q8NFP9;Q5T321	NBEA_HUMAN;.	S	2189;2189;2186;2189;816	ENSP00000440951:F2189S;ENSP00000383295:F2189S;ENSP00000369271:F2186S;ENSP00000308534:F2189S	ENSP00000308534:F2189S	F	+	2	0	NBEA	34944654	1.000000	0.71417	1.000000	0.80357	0.656000	0.38851	8.040000	0.89188	2.090000	0.63153	0.460000	0.39030	TTC	.	.		0.488	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		C	36046654	T	C	36046654	3	2	259	1	0	0	0	0	1	0	0	0	10196	1783	62	2	6728	2	NBEA	13	36046654	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	12135736	36046654	79123224	592	36910										
FAM48A	55578	hgsc.bcm.edu	37	chr13	37591496	37591496	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttaaaaataagtgaaccaccTggaagctattaagaatttaa	6	5	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:37591496T>C	ENST00000350612.6	-	23	2098	c.1878A>G	c.(1876-1878)ccA>ccG	p.P626P	SUPT20H_ENST00000475892.1_Silent_p.P705P|SUPT20H_ENST00000356185.3_Silent_p.P627P|SUPT20H_ENST00000464744.1_Silent_p.P627P|SUPT20H_ENST00000360252.4_Silent_p.P627P	NM_001014286.2	NP_001014308.2	Q8NEM7	SP20H_HUMAN	suppressor of Ty 20 homolog (S. cerevisiae)	626					autophagy (GO:0006914)|chromatin organization (GO:0006325)|gastrulation (GO:0007369)	SAGA complex (GO:0000124)|SAGA-type complex (GO:0070461)	transcription cofactor activity (GO:0003712)										GTGAACCACCTGGAAGCTATT	0.343																																					p.P627P		Atlas-SNP	.											.	.	.	.	0			c.A1881G						.						80	76	77					13																	37591496		2203	4300	6503	SO:0001819	synonymous_variant	55578	exon23			ACCACCTGGAAGC	AF093250	CCDS9362.1, CCDS31959.1, CCDS61311.1	13q13	2012-11-29	2012-11-29	2012-11-29	ENSG00000102710	ENSG00000102710			20596	protein-coding gene	gene with protein product	"p38 interacting protein", "transcription factor (p38 interacting protein)"	613417	"chromosome 13 open reading frame 19", "family with sequence similarity 48, member A"	C13orf19, FAM48A		12070015 , 16685401	Standard	NM_001278480		Approved	SPT20, bA421P11.4, P38IP	uc001uwg.3	Q8NEM7	OTTHUMG00000016747	ENST00000350612.6:c.1878A>G	chr13.hg19:g.37591496T>C		207.0	0.0		137.0	6.0	NM_017569	E7ER46|Q71RF3|Q9Y6A6	Silent	SNP	ENST00000350612.6	hg19	CCDS31959.1																																																																																			.	.		0.343	SUPT20H-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354766.1	NM_017569		C	37591496	T	C	37591496	2	2	259	1	0	0	0	0	0	0	0	1	5580	1567	55	2		2	FAM48A	13	37591496	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1544842	37591496	77578382	593	36911										
FOXO1	2308	hgsc.bcm.edu	37	chr13	41239792	41239792	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctcttgaccatccactcgtaGatctgcgacagcgtgagccg	10	14	2	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:41239792G>A	ENST00000379561.5	-	1	942	c.558C>T	c.(556-558)atC>atT	p.I186I		NM_002015.3	NP_002006.2	Q12778	FOXO1_HUMAN	forkhead box O1	186					apoptotic process (GO:0006915)|autophagy (GO:0006914)|blood vessel development (GO:0001568)|cellular glucose homeostasis (GO:0001678)|cellular response to cold (GO:0070417)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hyperoxia (GO:0071455)|cellular response to insulin stimulus (GO:0032869)|cellular response to nitric oxide (GO:0071732)|cellular response to oxidative stress (GO:0034599)|cellular response to starvation (GO:0009267)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|fat cell differentiation (GO:0045444)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of apoptotic process (GO:0043065)|positive regulation of autophagy (GO:0010508)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|regulation of cell proliferation (GO:0042127)|regulation of energy homeostasis (GO:2000505)|regulation of gluconeogenesis by regulation of transcription from RNA polymerase II promoter (GO:0035947)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|protein phosphatase 2A binding (GO:0051721)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)		PAX7/FOXO1(197)|PAX3/FOXO1(749)	central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	20		Lung NSC(96;1.18e-05)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;7.32e-09)|Epithelial(112;2.87e-06)|OV - Ovarian serous cystadenocarcinoma(117;6.98e-05)|GBM - Glioblastoma multiforme(144;0.00394)|BRCA - Breast invasive adenocarcinoma(63;0.0815)		TCCACTCGTAGATCTGCGACA	0.652																																					p.I186I		Atlas-SNP	.											.	FOXO1	110	.	0			c.C558T						.						33	27	29					13																	41239792		2203	4300	6503	SO:0001819	synonymous_variant	2308	exon1			CTCGTAGATCTGC		CCDS9371.1	13q14.1	2011-08-01	2007-05-02	2007-05-02	ENSG00000150907	ENSG00000150907		"Forkhead boxes"	3819	protein-coding gene	gene with protein product		136533	"forkhead homolog in rhabdomyosarcoma"	FKHR, FOXO1A		8275086, 15057823	Standard	NM_002015		Approved	FKH1	uc001uxl.4	Q12778	OTTHUMG00000016775	ENST00000379561.5:c.558C>T	chr13.hg19:g.41239792G>A		333.0	1.0		182.0	65.0	NM_002015	O43523|Q5VYC7|Q6NSK6	Silent	SNP	ENST00000379561.5	hg19	CCDS9371.1																																																																																			.	.		0.652	FOXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044634.3	NM_002015		A	41239792	G	A	41239792	2	1	259	1	0	0	0	0	0	0	0	1	6031	932	33	3		3	FOXO1	13	41239792	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	3648296	41239792	73930086	594	36912										
NAA16	79612	hgsc.bcm.edu	37	chr13	41946891	41946891	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agtttctgttaatgctgcagTctgtcaaacgagcttttgcc	9	9	3	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:41946891T>C	ENST00000379406.3	+	17	2404	c.2080T>C	c.(2080-2082)Tct>Cct	p.S694P	NAA16_ENST00000497143.1_3'UTR	NM_024561.4	NP_078837.3	Q6N069	NAA16_HUMAN	N(alpha)-acetyltransferase 16, NatA auxiliary subunit	694					N-terminal protein amino acid acetylation (GO:0006474)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NatA complex (GO:0031415)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ribosome binding (GO:0043022)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|urinary_tract(2)	31						AATGCTGCAGTCTGTCAAACG	0.303																																					p.S694P		Atlas-SNP	.											.	NAA16	74	.	0			c.T2080C						.						84	86	85					13																	41946891		2202	4298	6500	SO:0001583	missense	79612	exon17			CTGCAGTCTGTCA	AL833341	CCDS9379.1, CCDS45044.1	13q14.11	2013-01-10	2010-01-14	2010-01-14	ENSG00000172766	ENSG00000172766		"N(alpha)-acetyltransferase subunits", "Tetratricopeptide (TTC) repeat domain containing"	26164	protein-coding gene	gene with protein product			"NMDA receptor regulated 1-like"	NARG1L		11483580, 19660095	Standard	NM_024561		Approved	FLJ22054, MGC40612, PRO2435	uc001uyf.2	Q6N069	OTTHUMG00000016791	ENST00000379406.3:c.2080T>C	chr13.hg19:g.41946891T>C	ENSP00000368716:p.Ser694Pro	121.0	0.0		89.0	4.0	NM_024561	B0QZ59|Q5VSP9|Q6P2D5|Q8N5J3|Q8N870	Missense_Mutation	SNP	ENST00000379406.3	hg19	CCDS9379.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.454492	0.84209	.	.	ENSG00000172766	ENST00000379406	T	0.46819	0.86	5.3	5.3	0.74995	Tetratricopeptide-like helical (1);	0.000000	0.64402	D	0.000002	T	0.70753	0.3260	M	0.82323	2.585	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.75207	-0.3399	10	0.56958	D	0.05	-12.276	15.23	0.73381	0.0:0.0:0.0:1.0	.	694	Q6N069	NAA16_HUMAN	P	694	ENSP00000368716:S694P	ENSP00000368716:S694P	S	+	1	0	NAA16	40844891	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.127000	0.77210	2.006000	0.58801	0.533000	0.62120	TCT	.	.		0.303	NAA16-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044672.2	NM_018527		C	41946891	T	C	41946891	3	2	259	1	0	0	0	0	1	0	0	0	10128	1667	58	2	2179	2	NAA16	13	41946891	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	707099	41946891	73222987	595	36913										
KCTD4	386618	hgsc.bcm.edu	37	chr13	45768400	45768400	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgattttctcgaaacccttcGggcaatagaagttctccatt	7	10	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:45768400G>T	ENST00000379108.1	-	1	452	c.303C>A	c.(301-303)ccC>ccA	p.P101P	KCTD4_ENST00000405872.1_Silent_p.P101P|GTF2F2_ENST00000340473.6_Intron			Q8WVF5	KCTD4_HUMAN	potassium channel tetramerization domain containing 4	101	BTB.				protein homooligomerization (GO:0051260)					breast(1)|endometrium(1)|large_intestine(2)|lung(4)	8		Lung NSC(96;6.55e-05)|Breast(139;0.00378)|Prostate(109;0.00438)|Lung SC(185;0.0262)|Hepatocellular(98;0.0524)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000249)|BRCA - Breast invasive adenocarcinoma(63;0.207)		GAAACCCTTCGGGCAATAGAA	0.458																																					p.P101P		Atlas-SNP	.											.	KCTD4	18	.	0			c.C303A						.						105	103	104					13																	45768400		2203	4300	6503	SO:0001819	synonymous_variant	386618	exon2			CCCTTCGGGCAAT	BC018063	CCDS9396.1	13q14.12-q14.13	2013-06-20	2013-06-20		ENSG00000180332	ENSG00000180332			23227	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 4"				Standard	NM_198404		Approved	bA321C24.3	uc001uzx.4	Q8WVF5	OTTHUMG00000016844	ENST00000379108.1:c.303C>A	chr13.hg19:g.45768400G>T		133.0	0.0		99.0	4.0	NM_198404	Q5W0P9	Silent	SNP	ENST00000379108.1	hg19	CCDS9396.1																																																																																			.	.		0.458	KCTD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044757.1			T	45768400	G	T	45768400	2	4	259	1	0	0	0	0	0	0	0	1	8120	1103	39	1		1	KCTD4	13	45768400	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	3821509	45768400	69401478	596	36914										
FAM124A	220108	hgsc.bcm.edu	37	chr13	51855022	51855022	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cctgcggctgtcctcatcggAcctgtctgtggtctctgcat	11	14	3	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:51855022A>G	ENST00000322475.8	+	4	1406	c.1271A>G	c.(1270-1272)gAc>gGc	p.D424G	FAM124A_ENST00000280057.6_Missense_Mutation_p.D460G	NM_001242312.1	NP_001229241.1	Q86V42	F124A_HUMAN	family with sequence similarity 124A	424										breast(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|skin(1)	26		Acute lymphoblastic leukemia(7;0.000334)|Breast(56;0.00156)|Prostate(109;0.00538)|Lung NSC(96;0.0216)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;4.25e-07)		TCCTCATCGGACCTGTCTGTG	0.612																																					p.D460G		Atlas-SNP	.											.	FAM124A	61	.	0			c.A1379G						.						53	54	54					13																	51855022		2203	4300	6503	SO:0001583	missense	220108	exon5			CATCGGACCTGTC	AK096364	CCDS9427.1, CCDS55900.1	13q14.3	2006-08-11			ENSG00000150510	ENSG00000150510			26413	protein-coding gene	gene with protein product						12975309	Standard	NM_145019		Approved	FLJ30707	uc001vff.2	Q86V42	OTTHUMG00000016942	ENST00000322475.8:c.1271A>G	chr13.hg19:g.51855022A>G	ENSP00000324625:p.Asp424Gly	77.0	0.0		68.0	4.0	NM_145019	A2A324|Q8N8P9|Q8NE66|Q96NJ9	Missense_Mutation	SNP	ENST00000322475.8	hg19	CCDS55900.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.337995	0.81911	.	.	ENSG00000150510	ENST00000322475;ENST00000280057	T;T	0.60424	0.19;0.21	5.19	5.19	0.71726	.	0.000000	0.64402	D	0.000002	T	0.73690	0.3619	M	0.65498	2.005	0.58432	D	0.999994	D;D	0.89917	1.0;1.0	D;D	0.87578	0.982;0.998	T	0.76852	-0.2806	10	0.72032	D	0.01	-10.6226	14.1985	0.65686	1.0:0.0:0.0:0.0	.	424;460	Q86V42;Q86V42-2	F124A_HUMAN;.	G	424;460	ENSP00000324625:D424G;ENSP00000280057:D460G	ENSP00000280057:D460G	D	+	2	0	FAM124A	50753023	1.000000	0.71417	0.998000	0.56505	0.983000	0.72400	6.735000	0.74806	1.949000	0.56562	0.533000	0.62120	GAC	.	.		0.612	FAM124A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045019.3	NM_145019		G	51855022	A	G	51855022	3	3	259	1	0	0	0	0	1	0	0	0	5430	275	10	2	1397	2	FAM124A	13	51855022	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	6086622	51855022	63314856	597	36915										
THSD1	55901	hgsc.bcm.edu	37	chr13	52971400	52971400	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aattagcatgcactcctcctTtgcagaaaaatggcttctgc	7	11	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:52971400T>A	ENST00000258613.4	-	3	1166	c.988A>T	c.(988-990)Aag>Tag	p.K330*	RNY4P24_ENST00000362735.1_RNA|THSD1_ENST00000544466.1_Intron|THSD1_ENST00000349258.4_Nonsense_Mutation_p.K330*	NM_018676.3	NP_061146.1	Q9NS62	THSD1_HUMAN	thrombospondin, type I, domain containing 1	330					hematopoietic progenitor cell differentiation (GO:0002244)	cell periphery (GO:0071944)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Breast(56;0.000207)|Lung NSC(96;0.00145)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.8e-08)		CACTCCTCCTTTGCAGAAAAA	0.328																																					p.K330X		Atlas-SNP	.											.	THSD1	89	.	0			c.A988T						.						53	55	55					13																	52971400		2203	4300	6503	SO:0001587	stop_gained	55901	exon3			CCTCCTTTGCAGA	AK096289	CCDS9432.1, CCDS9433.1	13q14.13	2010-04-20	2004-03-11		ENSG00000136114	ENSG00000136114			17754	protein-coding gene	gene with protein product			"thrombospondin, type I, domain 1"				Standard	NM_018676		Approved	TMTSP	uc001vgo.3	Q9NS62	OTTHUMG00000016963	ENST00000258613.4:c.988A>T	chr13.hg19:g.52971400T>A	ENSP00000258613:p.Lys330*	139.0	0.0		99.0	4.0	NM_199263	A2A3J3|B2RCF5|Q6P3U1|Q6UXZ2	Nonsense_Mutation	SNP	ENST00000258613.4	hg19	CCDS9432.1	.	.	.	.	.	.	.	.	.	.	T	41	8.929775	0.99006	.	.	ENSG00000136114	ENST00000349258;ENST00000258613;ENST00000378095	.	.	.	5.32	4.12	0.48240	.	0.194119	0.44285	D	0.000466	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-39.6606	8.09	0.30795	0.0:0.1584:0.0:0.8416	.	.	.	.	X	330	.	ENSP00000258613:K330X	K	-	1	0	THSD1	51869401	1.000000	0.71417	0.948000	0.38648	0.996000	0.88848	2.627000	0.46469	2.007000	0.58848	0.459000	0.35465	AAG	.	.		0.328	THSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045058.3			A	52971400	T	A	52971400	4	1	259	1	0	0	0	0	0	1	0	0	15892	1850	64	4	1582	4	THSD1	13	52971400	Nonsense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1116378	52971400	62198478	598	36916										
VPS36	51028	hgsc.bcm.edu	37	chr13	53008984	53008984	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tggcatattctcccatcttcTttgtgtcatttcctctgata	5	11	5	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:53008984T>C	ENST00000378060.4	-	5	412	c.385A>G	c.(385-387)Aga>Gga	p.R129G	VPS36_ENST00000480923.1_5'UTR	NM_001282168.1|NM_001282169.1|NM_016075.2	NP_001269097.1|NP_001269098.1|NP_057159.2	Q86VN1	VPS36_HUMAN	vacuolar protein sorting 36 homolog (S. cerevisiae)	129	GLUE C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00828}.				endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylinositol-3-phosphate binding (GO:0032266)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	17		Breast(56;0.000207)|Lung NSC(96;0.00212)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.14e-08)		TCCCATCTTCTTTGTGTCATT	0.338																																					p.R129G		Atlas-SNP	.											.	VPS36	38	.	0			c.A385G						.						175	186	182					13																	53008984		2203	4300	6503	SO:0001583	missense	51028	exon5			ATCTTCTTTGTGT	AF151903	CCDS9434.1, CCDS73577.1	13q14.13	2008-02-05	2007-01-12	2005-08-02	ENSG00000136100	ENSG00000136100			20312	protein-coding gene	gene with protein product		610903	"chromosome 13 open reading frame 9", "vacuolar protein sorting 36 homolog (yeast)"	C13orf9		11278625, 15755741	Standard	NM_016075		Approved	CGI-145, Eap45	uc001vgs.3	Q86VN1	OTTHUMG00000016964	ENST00000378060.4:c.385A>G	chr13.hg19:g.53008984T>C	ENSP00000367299:p.Arg129Gly	134.0	0.0		98.0	4.0	NM_016075	A8K125|Q3ZCV7|Q5H9S1|Q5VXB6|Q9H8Z5|Q9Y3E3	Missense_Mutation	SNP	ENST00000378060.4	hg19	CCDS9434.1	.	.	.	.	.	.	.	.	.	.	.	16.66	3.186142	0.57909	.	.	ENSG00000136100	ENST00000378060	.	.	.	5.76	4.57	0.56435	.	0.134024	0.64402	D	0.000002	T	0.60431	0.2268	M	0.77616	2.38	0.54753	D	0.99998	B	0.31655	0.334	B	0.20577	0.03	T	0.62215	-0.6901	9	0.66056	D	0.02	-21.5871	12.2152	0.54402	0.0:0.0:0.2677:0.7323	.	129	Q86VN1	VPS36_HUMAN	G	129	.	ENSP00000367299:R129G	R	-	1	2	VPS36	51906985	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.214000	0.51161	0.988000	0.38734	0.460000	0.39030	AGA	.	.		0.338	VPS36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045059.3			C	53008984	T	C	53008984	3	2	259	1	0	0	0	0	1	0	0	0	17219	1617	56	2	815	2	VPS36	13	53008984	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	37584	53008984	62160894	599	36917										
PIBF1	10464	hgsc.bcm.edu	37	chr13	73428292	73428292	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aacacgatcagctcttagacAggtaagcatcataaaaatag	7	8	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:73428292A>G	ENST00000326291.6	+	10	1659	c.1321A>G	c.(1321-1323)Agg>Ggg	p.R441G	AL391384.1_ENST00000408054.1_RNA	NM_006346.2	NP_006337.2	Q8WXW3	PIBF1_HUMAN	progesterone immunomodulatory binding factor 1	441						centrosome (GO:0005813)				breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24		Prostate(6;0.00191)|Breast(118;0.0736)|Acute lymphoblastic leukemia(28;0.0865)		GBM - Glioblastoma multiforme(99;0.000664)		GCTCTTAGACAGGTAAGCATC	0.333																																					p.R441G		Atlas-SNP	.											.	PIBF1	65	.	0			c.A1321G						.						88	90	89					13																	73428292		2203	4300	6503	SO:0001630	splice_region_variant	10464	exon10			TTAGACAGGTAAG	AF330046	CCDS31991.1	13q21.33	2014-02-20	2007-10-17	2007-10-17	ENSG00000083535	ENSG00000083535			23352	protein-coding gene	gene with protein product	"progesterone-induced blocking factor 1"	607532	"chromosome 13 open reading frame 24"	C13orf24		11935316	Standard	NM_006346		Approved	CEP90	uc001vjc.3	Q8WXW3	OTTHUMG00000017071	ENST00000326291.6:c.1322+1A>G	chr13.hg19:g.73428292A>G		100.0	0.0		80.0	4.0	NM_006346	O95664|Q6U9V2|Q6UG50|Q86V07|Q96SF4	Missense_Mutation	SNP	ENST00000326291.6	hg19	CCDS31991.1	.	.	.	.	.	.	.	.	.	.	A	13.82	2.350367	0.41599	.	.	ENSG00000083535	ENST00000326291	T	0.22743	1.94	4.88	3.78	0.43462	.	0.059270	0.64402	D	0.000001	T	0.16811	0.0404	L	0.38175	1.15	0.33061	D	0.534035	B;B	0.24721	0.11;0.11	B;B	0.24848	0.056;0.056	T	0.15037	-1.0451	10	0.72032	D	0.01	-4.0035	9.2173	0.37355	0.5912:0.4088:0.0:0.0	.	441;441	Q8WXW3;Q4G0R1	PIBF1_HUMAN;.	G	441	ENSP00000317144:R441G	ENSP00000317144:R441G	R	+	1	2	PIBF1	72326293	1.000000	0.71417	1.000000	0.80357	0.733000	0.41908	4.148000	0.58085	1.840000	0.53500	0.455000	0.32223	AGG	.	.		0.333	PIBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045255.1	NM_006346	Missense_Mutation	G	73428292	A	G	73428292	5	3	259	1	0	0	0	0	0	0	1	0	11888	202	7	2	1355	2	PIBF1	13	73428292	Splice_Site	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	20419308	73428292	41741586	600	36918										
UCHL3	7347	hgsc.bcm.edu	37	chr13	76135000	76135000	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tctgtgcagtcttacttctcTttcctattacagaaaaggta	6	9	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:76135000T>C	ENST00000377595.3	+	3	196	c.166T>C	c.(166-168)Ttt>Ctt	p.F56L	RP11-29G8.3_ENST00000563635.1_RNA	NM_001270952.1|NM_006002.4	NP_001257881.1|NP_005993.1	P15374	UCHL3_HUMAN	ubiquitin carboxyl-terminal esterase L3 (ubiquitin thiolesterase)	56					protein catabolic process (GO:0030163)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			kidney(1)|large_intestine(2)|lung(3)|skin(1)	7				GBM - Glioblastoma multiforme(99;0.0125)		CTTACTTCTCTTTCCTATTAC	0.348																																					p.F56L		Atlas-SNP	.											.	UCHL3	9	.	0			c.T166C						.						102	92	95					13																	76135000		2203	4300	6503	SO:0001583	missense	7347	exon3			CTTCTCTTTCCTA	M30496	CCDS9453.1, CCDS73586.1	13q21.33	2008-02-05			ENSG00000118939	ENSG00000118939	3.2.1.15		12515	protein-coding gene	gene with protein product		603090				2530630	Standard	NM_001270952		Approved		uc001vjq.4	P15374	OTTHUMG00000017090	ENST00000377595.3:c.166T>C	chr13.hg19:g.76135000T>C	ENSP00000366819:p.Phe56Leu	135.0	0.0		105.0	5.0	NM_006002	B2R970|Q5TBK8|Q6IBE9	Missense_Mutation	SNP	ENST00000377595.3	hg19	CCDS9453.1	.	.	.	.	.	.	.	.	.	.	T	28.3	4.909940	0.92107	.	.	ENSG00000118939	ENST00000377595;ENST00000377589	T	0.69175	-0.38	5.81	5.81	0.92471	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (4);	0.000000	0.85682	D	0.000000	D	0.85630	0.5741	M	0.91872	3.25	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.88762	0.3258	10	0.72032	D	0.01	-11.1154	16.1773	0.81862	0.0:0.0:0.0:1.0	.	56	P15374	UCHL3_HUMAN	L	56;13	ENSP00000366819:F56L	ENSP00000366813:F13L	F	+	1	0	UCHL3	75033001	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	7.698000	0.84413	2.217000	0.71921	0.482000	0.46254	TTT	.	.		0.348	UCHL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045292.2	NM_006002		C	76135000	T	C	76135000	3	2	259	1	0	0	0	0	1	0	0	0	16936	1609	56	2	176	2	UCHL3	13	76135000	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	2706708	76135000	39034878	601	36919										
DCT	1638	hgsc.bcm.edu	37	chr13	95131305	95131305	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gtagggaccactccagggccTtgtgtcggctcgcacctctg	13	14	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:95131305T>C	ENST00000377028.5	-	1	618	c.205A>G	c.(205-207)Agg>Ggg	p.R69G	DCT_ENST00000446125.1_Missense_Mutation_p.R69G	NM_001922.3	NP_001913.2	P40126	TYRP2_HUMAN	dopachrome tautomerase	69					cell development (GO:0048468)|developmental pigmentation (GO:0048066)|epidermis development (GO:0008544)|melanin biosynthetic process from tyrosine (GO:0006583)|positive regulation of neuroblast proliferation (GO:0002052)|ventricular zone neuroblast division (GO:0021847)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)	copper ion binding (GO:0005507)|dopachrome isomerase activity (GO:0004167)|oxidoreductase activity (GO:0016491)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	50	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;3.71e-42)|all_epithelial(2;3.76e-31)|all_lung(2;5.16e-14)|Lung NSC(4;1.33e-13)|Breast(118;0.0013)|Hepatocellular(115;0.00886)|Renal(2;0.00988)		COAD - Colon adenocarcinoma(199;7.07e-05)|GBM - Glioblastoma multiforme(99;0.000472)		CTCCAGGGCCTTGTGTCGGCT	0.607																																					p.R69G		Atlas-SNP	.											.	DCT	186	.	0			c.A205G						.						89	77	81					13																	95131305		2203	4300	6503	SO:0001583	missense	1638	exon1			AGGGCCTTGTGTC	D17547	CCDS9470.1, CCDS45060.1	13q32	2012-09-28	2012-09-28		ENSG00000080166	ENSG00000080166	5.3.3.12		2709	protein-coding gene	gene with protein product	"dopachrome delta-isomerase"	191275	"tyrosine-related protein 2"	TYRP2		8306979	Standard	NM_001922		Approved		uc010afh.3	P40126	OTTHUMG00000017206	ENST00000377028.5:c.205A>G	chr13.hg19:g.95131305T>C	ENSP00000366227:p.Arg69Gly	147.0	0.0		97.0	4.0	NM_001129889	Q09GT4	Missense_Mutation	SNP	ENST00000377028.5	hg19	CCDS9470.1	.	.	.	.	.	.	.	.	.	.	T	14.22	2.470693	0.43942	.	.	ENSG00000080166	ENST00000377028;ENST00000446125	D;D	0.84146	-1.81;-1.81	5.22	2.68	0.31781	.	0.103582	0.64402	D	0.000004	D	0.83580	0.5285	M	0.76574	2.34	0.38912	D	0.957554	P;P	0.47302	0.893;0.835	B;B	0.41813	0.367;0.363	T	0.80730	-0.1252	10	0.24483	T	0.36	-19.6539	13.7089	0.62656	0.0:0.0:0.5326:0.4674	.	69;69	Q09GT4;P40126	.;TYRP2_HUMAN	G	69	ENSP00000366227:R69G;ENSP00000392762:R69G	ENSP00000366227:R69G	R	-	1	2	DCT	93929306	1.000000	0.71417	1.000000	0.80357	0.716000	0.41182	2.493000	0.45320	0.275000	0.22094	-0.299000	0.09455	AGG	.	.		0.607	DCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045461.3			C	95131305	T	C	95131305	3	2	259	1	0	0	0	0	1	0	0	0	4306	1608	56	2	1493	2	DCT	13	95131305	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	18996305	95131305	20038573	602	36920										
HS6ST3	266722	hgsc.bcm.edu	37	chr13	97484904	97484904	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cctgctaccctggggatgacTggtctggggtcagcttgcgg	16	11	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:97484904T>C	ENST00000376705.2	+	2	892	c.868T>C	c.(868-870)Tgg>Cgg	p.W290R		NM_153456.3	NP_703157.2	Q8IZP7	H6ST3_HUMAN	heparan sulfate 6-O-sulfotransferase 3	290					heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)	integral component of membrane (GO:0016021)	heparan sulfate 6-O-sulfotransferase activity (GO:0017095)			NS(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|skin(1)	20	all_neural(89;0.0878)|Medulloblastoma(90;0.163)					TGGGGATGACTGGTCTGGGGT	0.567																																					p.W290R		Atlas-SNP	.											.	HS6ST3	54	.	0			c.T868C						.						64	58	60					13																	97484904		2203	4300	6503	SO:0001583	missense	266722	exon2			GATGACTGGTCTG	AF539426	CCDS9481.1	13q32.2	2007-12-04			ENSG00000185352	ENSG00000185352		"Sulfotransferases, membrane-bound"	19134	protein-coding gene	gene with protein product		609401					Standard	NM_153456		Approved		uc001vmw.4	Q8IZP7	OTTHUMG00000017232	ENST00000376705.2:c.868T>C	chr13.hg19:g.97484904T>C	ENSP00000365895:p.Trp290Arg	105.0	0.0		93.0	4.0	NM_153456	Q5W0L0|Q68CW6	Missense_Mutation	SNP	ENST00000376705.2	hg19	CCDS9481.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.118453	0.77323	.	.	ENSG00000185352	ENST00000376705	T	0.74421	-0.84	5.6	5.6	0.85130	.	0.281587	0.38663	N	0.001619	D	0.88317	0.6404	M	0.89414	3.03	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90578	0.4527	10	0.87932	D	0	-16.9535	15.7645	0.78114	0.0:0.0:0.0:1.0	.	290	Q8IZP7	H6ST3_HUMAN	R	290	ENSP00000365895:W290R	ENSP00000365895:W290R	W	+	1	0	HS6ST3	96282905	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.036000	0.88901	2.108000	0.64289	0.528000	0.53228	TGG	.	.		0.567	HS6ST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045517.2	NM_153456		C	97484904	T	C	97484904	3	2	259	1	0	0	0	0	1	0	0	0	7381	1580	55	2	874	2	HS6ST3	13	97484904	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	2353599	97484904	17684974	603	36921										
DOCK9	23348	hgsc.bcm.edu	37	chr13	99519792	99519792	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acttgtattcaaagagggtcTgcaggaagaagtgtgtagtc	13	5	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:99519792T>C	ENST00000376460.1	-	30	3255		c.e30-2		DOCK9_ENST00000339416.2_Splice_Site|DOCK9_ENST00000442173.1_Splice_Site|DOCK9_ENST00000448493.2_Splice_Site	NM_001130048.1|NM_015296.2	NP_001123520.1|NP_056111.1	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9						blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(18)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					AAAGAGGGTCTGCAGGAAGAA	0.358																																					.		Atlas-SNP	.											.	DOCK9	311	.	0			c.3178-2A>G						.						140	131	134					13																	99519792		1830	4081	5911	SO:0001630	splice_region_variant	23348	exon31			AGGGTCTGCAGGA	AF527605	CCDS45062.1	13q32.3	2013-01-10			ENSG00000088387	ENSG00000088387		"Pleckstrin homology (PH) domain containing"	14132	protein-coding gene	gene with protein product	"zizimin1"	607325				12172552, 12432077	Standard	NM_015296		Approved	KIAA1058, ZIZ1	uc001vnt.2	Q9BZ29	OTTHUMG00000017260	ENST00000376460.1:c.3175-2A>G	chr13.hg19:g.99519792T>C		45.0	0.0		38.0	4.0	NM_015296	B3KX25|E9PFM9|Q5JUD4|Q5JUD6|Q5T2Q1|Q5TAN8|Q9BZ25|Q9BZ26|Q9BZ27|Q9BZ28|Q9UPU4	Splice_Site	SNP	ENST00000376460.1	hg19	CCDS45062.1	.	.	.	.	.	.	.	.	.	.	T	25.1	4.605059	0.87157	.	.	ENSG00000088387	ENST00000376460;ENST00000357329;ENST00000376455;ENST00000400235;ENST00000428223;ENST00000339416;ENST00000448493;ENST00000442173	.	.	.	6.08	6.08	0.98989	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.6438	0.85155	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	DOCK9	98317793	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	7.625000	0.83145	2.333000	0.79357	0.533000	0.62120	.	.	.		0.358	DOCK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045566.1	NM_015296	Intron	C	99519792	T	C	99519792	5	2	259	1	0	0	0	0	0	0	1	0	4696	1594	55	2	3202	2	DOCK9	13	99519792	Splice_Site	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	2034888	99519792	15650086	604	36922										
COL4A1	1282	hgsc.bcm.edu	37	chr13	110822983	110822983	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccggtaaccccggctgtcccTggggccccggaggacccatg	14	17	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:110822983T>C	ENST00000375820.4	-	42	3774	c.3653A>G	c.(3652-3654)cAg>cGg	p.Q1218R		NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	1218	Triple-helical region.				axon guidance (GO:0007411)|basement membrane organization (GO:0071711)|blood vessel morphogenesis (GO:0048514)|brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)|patterning of blood vessels (GO:0001569)|renal tubule morphogenesis (GO:0061333)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)|platelet-derived growth factor binding (GO:0048407)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	105	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			CGGCTGTCCCTGGGGCCCCGG	0.647																																					p.Q1218R		Atlas-SNP	.											.	COL4A1	372	.	0			c.A3653G						.						24	28	27					13																	110822983		2203	4300	6503	SO:0001583	missense	1282	exon42			TGTCCCTGGGGCC	J04217	CCDS9511.1	13q34	2013-09-05			ENSG00000187498	ENSG00000187498		"Collagens"	2202	protein-coding gene	gene with protein product		120130				3691802	Standard	NM_001845		Approved		uc001vqw.4	P02462	OTTHUMG00000017342	ENST00000375820.4:c.3653A>G	chr13.hg19:g.110822983T>C	ENSP00000364979:p.Gln1218Arg	86.0	0.0		50.0	4.0	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Missense_Mutation	SNP	ENST00000375820.4	hg19	CCDS9511.1	.	.	.	.	.	.	.	.	.	.	T	11.51	1.660271	0.29515	.	.	ENSG00000187498	ENST00000375815;ENST00000375820;ENST00000397198	D	0.96073	-3.9	5.21	3.98	0.46160	.	0.191118	0.45867	D	0.000323	D	0.89584	0.6757	N	0.04245	-0.25	0.80722	D	1	P	0.37370	0.592	P	0.44447	0.45	D	0.87795	0.2621	10	0.19590	T	0.45	.	13.314	0.60397	0.0:0.0:0.2064:0.7936	.	1218	P02462	CO4A1_HUMAN	R	861;1218;867	ENSP00000364979:Q1218R	ENSP00000364973:Q861R	Q	-	2	0	COL4A1	109620984	1.000000	0.71417	0.973000	0.42090	0.367000	0.29736	2.304000	0.43655	1.970000	0.57323	0.529000	0.55759	CAG	.	.		0.647	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3			C	110822983	T	C	110822983	3	2	259	1	0	0	0	0	1	0	0	0	3691	1580	55	2	1400	2	COL4A1	13	110822983	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	11303191	110822983	4346895	605	36923										
COL4A1	1282	hgsc.bcm.edu	37	chr13	110833649	110833649	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tggcactcaccttctggcccTgcacacctgggttcccaggt	10	16	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:110833649T>C	ENST00000375820.4	-	29	2304	c.2183A>G	c.(2182-2184)cAg>cGg	p.Q728R		NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	728	Triple-helical region.				axon guidance (GO:0007411)|basement membrane organization (GO:0071711)|blood vessel morphogenesis (GO:0048514)|brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)|patterning of blood vessels (GO:0001569)|renal tubule morphogenesis (GO:0061333)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)|platelet-derived growth factor binding (GO:0048407)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	105	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			CTTCTGGCCCTGCACACCTGG	0.547																																					p.Q728R		Atlas-SNP	.											.	COL4A1	372	.	0			c.A2183G						.						69	66	67					13																	110833649		2203	4300	6503	SO:0001583	missense	1282	exon29			TGGCCCTGCACAC	J04217	CCDS9511.1	13q34	2013-09-05			ENSG00000187498	ENSG00000187498		"Collagens"	2202	protein-coding gene	gene with protein product		120130				3691802	Standard	NM_001845		Approved		uc001vqw.4	P02462	OTTHUMG00000017342	ENST00000375820.4:c.2183A>G	chr13.hg19:g.110833649T>C	ENSP00000364979:p.Gln728Arg	173.0	0.0		85.0	5.0	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Missense_Mutation	SNP	ENST00000375820.4	hg19	CCDS9511.1	.	.	.	.	.	.	.	.	.	.	T	10.64	1.407870	0.25378	.	.	ENSG00000187498	ENST00000375820	D	0.92911	-3.13	4.96	3.1	0.35709	.	0.484707	0.21821	N	0.068614	D	0.87783	0.6264	N	0.16368	0.405	0.80722	D	1	D	0.53462	0.96	P	0.53593	0.73	T	0.82088	-0.0630	10	0.15499	T	0.54	.	10.8468	0.46746	0.0:0.0:0.4054:0.5946	.	728	P02462	CO4A1_HUMAN	R	728	ENSP00000364979:Q728R	ENSP00000364979:Q728R	Q	-	2	0	COL4A1	109631650	0.983000	0.35010	0.056000	0.19401	0.497000	0.33675	1.881000	0.39638	0.587000	0.29643	0.533000	0.62120	CAG	.	.		0.547	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3			C	110833649	T	C	110833649	3	2	259	1	0	0	0	0	1	0	0	0	3691	1580	55	2	2922	2	COL4A1	13	110833649	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	10666	110833649	4336229	606	36924										
TUBGCP3	10426	hgsc.bcm.edu	37	chr13	113242240	113242240	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttcgctcctgcccaggatccTgcagcacaggttctgcagca	10	15	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:113242240T>C	ENST00000261965.3	-	1	241	c.55A>G	c.(55-57)Agg>Ggg	p.R19G	TUBGCP3_ENST00000375669.3_Missense_Mutation_p.R19G	NM_006322.4	NP_006313.1	Q96CW5	GCP3_HUMAN	tubulin, gamma complex associated protein 3	19					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|single fertilization (GO:0007338)	centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|polar microtubule (GO:0005827)|spindle (GO:0005819)	gamma-tubulin binding (GO:0043015)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|prostate(3)|urinary_tract(1)	25	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)					CCCAGGATCCTGCAGCACAGG	0.701																																					p.R19G		Atlas-SNP	.											.	TUBGCP3	74	.	0			c.A55G						.						31	29	30					13																	113242240		2203	4299	6502	SO:0001583	missense	10426	exon1			GGATCCTGCAGCA	AF042378	CCDS9525.1, CCDS66584.1, CCDS73599.1	13q34	2008-07-18			ENSG00000126216	ENSG00000126216			18598	protein-coding gene	gene with protein product	"spindle pole body protein"					9566967, 9566969	Standard	XM_005268293		Approved	GCP3, Spc98p, SPBC98	uc001vse.1	Q96CW5	OTTHUMG00000017367	ENST00000261965.3:c.55A>G	chr13.hg19:g.113242240T>C	ENSP00000261965:p.Arg19Gly	108.0	0.0		94.0	4.0	NM_006322	O43631|O60852|O60853|Q5T8L2|Q7Z4K1|Q96I79	Missense_Mutation	SNP	ENST00000261965.3	hg19	CCDS9525.1	.	.	.	.	.	.	.	.	.	.	t	16.76	3.213535	0.58452	.	.	ENSG00000126216	ENST00000261965;ENST00000375669	T;T	0.24723	1.84;1.84	4.4	3.54	0.40534	.	0.274242	0.35349	N	0.003274	T	0.29423	0.0733	M	0.66939	2.045	0.38890	D	0.957099	B;P;B;B	0.42296	0.02;0.775;0.078;0.02	B;B;B;B	0.39660	0.01;0.306;0.033;0.014	T	0.24297	-1.0164	10	0.59425	D	0.04	-24.9492	13.3616	0.60659	0.0:0.0:0.8348:0.1652	.	19;19;19;19	B4DYP7;Q96CW5-3;Q96CW5-2;Q96CW5	.;.;.;GCP3_HUMAN	G	19	ENSP00000261965:R19G;ENSP00000364821:R19G	ENSP00000261965:R19G	R	-	1	2	TUBGCP3	112290241	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	2.977000	0.49297	0.814000	0.34374	-0.650000	0.03912	AGG	.	.		0.701	TUBGCP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045825.2	NM_006322		C	113242240	T	C	113242240	3	2	259	1	0	0	0	0	1	0	0	0	16782	1579	55	2	2756	2	TUBGCP3	13	113242240	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	2408591	113242240	1927638	607	36925										
TEP1	7011	hgsc.bcm.edu	37	chr14	20874483	20874483	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccagatcctccacctcctccTcctctcccaagctcagacta	3	21	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:20874483T>C	ENST00000262715.5	-	3	684	c.644A>G	c.(643-645)gAg>gGg	p.E215G	TEP1_ENST00000556935.1_Missense_Mutation_p.E215G	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	215					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		CACCTCCTCCTCCTCTCCCAA	0.493																																					p.E215G		Atlas-SNP	.											.	TEP1	224	.	0			c.A644G						.						118	104	109					14																	20874483		2203	4300	6503	SO:0001583	missense	7011	exon3			TCCTCCTCCTCTC		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"WD repeat domain containing"	11726	protein-coding gene	gene with protein product	"TROVE domain family, member 1"	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.644A>G	chr14.hg19:g.20874483T>C	ENSP00000262715:p.Glu215Gly	107.0	0.0		92.0	4.0	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	hg19	CCDS9548.1	.	.	.	.	.	.	.	.	.	.	T	11.45	1.641459	0.29157	.	.	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935	T;T	0.64260	0.47;-0.09	4.94	3.78	0.43462	.	0.239904	0.29293	N	0.012566	T	0.56171	0.1967	L	0.58101	1.795	0.47374	D	0.999405	B;B	0.33612	0.419;0.295	B;B	0.33690	0.168;0.081	T	0.58418	-0.7640	10	0.72032	D	0.01	-6.0532	8.9738	0.35924	0.0:0.0:0.187:0.813	.	215;215	G3V5X7;Q99973	.;TEP1_HUMAN	G	215	ENSP00000262715:E215G;ENSP00000452574:E215G	ENSP00000262715:E215G	E	-	2	0	TEP1	19944323	0.284000	0.24287	0.763000	0.31416	0.397000	0.30659	2.045000	0.41250	0.994000	0.38892	0.533000	0.62120	GAG	.	.		0.493	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		C	20874483	T	C	20874483	3	2	259	1	0	0	0	0	1	0	0	0	15774	1551	54	2	7451	2	TEP1	14	20874483	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10		20874483	86475057	608	36926										
OSGEP	55644	hgsc.bcm.edu	37	chr14	20920172	20920172	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acatacaacacggttgggctGgtggctccagtgatgaggcg	15	9	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:20920172G>T	ENST00000206542.4	-	3	793	c.372C>A	c.(370-372)acC>acA	p.T124T	OSGEP_ENST00000556252.1_5'UTR|RP11-203M5.7_ENST00000555435.1_RNA|OSGEP_ENST00000555656.1_5'Flank|OSGEP_ENST00000554249.1_5'Flank	NM_017807.3	NP_060277.1			O-sialoglycoprotein endopeptidase											endometrium(3)|kidney(1)|large_intestine(1)|liver(1)|lung(4)|stomach(1)	11	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;1.09e-07)|all cancers(55;1.19e-06)	GBM - Glioblastoma multiforme(265;0.0231)|READ - Rectum adenocarcinoma(17;0.196)		CGGTTGGGCTGGTGGCTCCAG	0.512																																					p.T124T		Atlas-SNP	.											.	OSGEP	31	.	0			c.C372A						.						75	67	70					14																	20920172		2203	4300	6503	SO:0001819	synonymous_variant	55644	exon3			TGGGCTGGTGGCT	AB050442	CCDS9549.1	14q12	2010-03-19			ENSG00000092094	ENSG00000092094	3.4.24.57		18028	protein-coding gene	gene with protein product		610107				12039036	Standard	NM_017807		Approved	PRSMG1, GCPL1, OSGEP1, KAE1	uc001vxf.3	Q9NPF4	OTTHUMG00000029543	ENST00000206542.4:c.372C>A	chr14.hg19:g.20920172G>T		159.0	0.0		132.0	6.0	NM_017807		Silent	SNP	ENST00000206542.4	hg19	CCDS9549.1																																																																																			.	.		0.512	OSGEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073635.3	NM_017807		T	20920172	G	T	20920172	2	4	259	1	0	0	0	0	0	0	0	1	11296	1335	47	3		3	OSGEP	14	20920172	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	45689	20920172	86429368	609	36927										
RNASE10	338879	hgsc.bcm.edu	37	chr14	20978863	20978863	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	caacaaagaagtggtgcaacCtggctggccagaagatccca	11	11	0	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:20978863C>A	ENST00000328444.5	+	1	252	c.233C>A	c.(232-234)cCt>cAt	p.P78H	RNASE10_ENST00000430083.1_Missense_Mutation_p.P106H	NM_001012975.1	NP_001012993.1	Q5GAN6	RNS10_HUMAN	ribonuclease, RNase A family, 10 (non-active)	78					epithelial cell morphogenesis (GO:0003382)|heterotypic cell-cell adhesion (GO:0034113)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of sperm motility (GO:1902093)|regulation of fertilization (GO:0080154)|seminiferous tubule development (GO:0072520)|single fertilization (GO:0007338)	extracellular region (GO:0005576)	nucleic acid binding (GO:0003676)			endometrium(1)|large_intestine(2)|lung(8)|urinary_tract(1)	12	all_cancers(95;0.00123)		Epithelial(56;1.81e-07)|all cancers(55;1.86e-06)	GBM - Glioblastoma multiforme(265;0.022)|READ - Rectum adenocarcinoma(17;0.191)		GTGGTGCAACCTGGCTGGCCA	0.532																																					p.P78H		Atlas-SNP	.											.	RNASE10	28	.	0			c.C233A						.						69	69	69					14																	20978863		2203	4300	6503	SO:0001583	missense	338879	exon1			TGCAACCTGGCTG		CCDS32035.1	14q11.1	2004-11-16				ENSG00000182545		"Ribonucleases, RNase A"	19275	protein-coding gene	gene with protein product						12920233	Standard	XM_005267584		Approved	RNASE9	uc010tlj.2	Q5GAN6		ENST00000328444.5:c.233C>A	chr14.hg19:g.20978863C>A	ENSP00000333358:p.Pro78His	72.0	0.0		82.0	4.0	NM_001012975	A2RUQ3|B4DKY4	Missense_Mutation	SNP	ENST00000328444.5	hg19	CCDS32035.1	.	.	.	.	.	.	.	.	.	.	C	11.50	1.655953	0.29425	.	.	ENSG00000182545	ENST00000430083;ENST00000328444	T;T	0.19806	2.12;2.14	4.04	3.15	0.36227	.	0.539632	0.18794	N	0.130971	T	0.28001	0.0690	L	0.34521	1.04	0.09310	N	1	D;D	0.71674	0.996;0.998	P;P	0.61397	0.819;0.888	T	0.02789	-1.1110	10	0.87932	D	0	-11.9476	7.9922	0.30248	0.0:0.8892:0.0:0.1108	.	78;106	Q5GAN6;B4DKY4	RNS10_HUMAN;.	H	106;78	ENSP00000392996:P106H;ENSP00000333358:P78H	ENSP00000333358:P78H	P	+	2	0	RNASE10	20048703	0.002000	0.14202	0.021000	0.16686	0.174000	0.22865	1.496000	0.35638	1.289000	0.44618	0.655000	0.94253	CCT	.	.		0.532	RNASE10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411088.1	XM_292225		A	20978863	C	A	20978863	3	1	259	1	0	0	0	0	1	0	0	0	13415	681	24	3	235	3	RNASE10	14	20978863	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	58691	20978863	86370677	610	36928										
EDDM3B	64184	hgsc.bcm.edu	37	chr14	21238598	21238598	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gaaatgcatatgtatgggtcCagaatcctctcaaagtactc	8	9	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:21238598C>A	ENST00000326783.3	+	2	387	c.289C>A	c.(289-291)Cag>Aag	p.Q97K		NM_022360.4	NP_071755.1	P56851	EP3B_HUMAN	epididymal protein 3B	97						extracellular region (GO:0005576)				central_nervous_system(1)|kidney(1)|lung(3)|ovary(1)|skin(1)	7						TGTATGGGTCCAGAATCCTCT	0.413																																					p.Q97K		Atlas-SNP	.											.	EDDM3B	23	.	0			c.C289A						.						93	87	89					14																	21238598		2203	4300	6503	SO:0001583	missense	64184	exon2			TGGGTCCAGAATC	X76386	CCDS9557.1	14q11.1	2010-03-19	2010-01-27	2010-01-27	ENSG00000181552	ENSG00000181552			19223	protein-coding gene	gene with protein product		611582	"family with sequence similarity 12, member B (epididymal)"	FAM12B		7514008	Standard	NM_022360		Approved	HE3-BETA	uc001vyd.3	P56851	OTTHUMG00000029583	ENST00000326783.3:c.289C>A	chr14.hg19:g.21238598C>A	ENSP00000314810:p.Gln97Lys	109.0	0.0		95.0	4.0	NM_022360	A0PK89	Missense_Mutation	SNP	ENST00000326783.3	hg19	CCDS9557.1	.	.	.	.	.	.	.	.	.	.	C	0.793	-0.758120	0.03019	.	.	ENSG00000181552	ENST00000326783	T	0.71698	-0.59	3.98	-3.23	0.05109	Ribonuclease A, domain (3);	1.083060	0.07192	N	0.855893	T	0.46151	0.1378	N	0.19112	0.55	0.09310	N	1	B	0.18166	0.026	B	0.14023	0.01	T	0.40403	-0.9565	10	0.02654	T	1	.	7.3199	0.26521	0.5156:0.2234:0.261:0.0	.	97	P56851	EP3B_HUMAN	K	97	ENSP00000314810:Q97K	ENSP00000314810:Q97K	Q	+	1	0	EDDM3B	20308438	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.195000	0.09546	-0.285000	0.09089	-0.438000	0.05819	CAG	.	.		0.413	EDDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073745.2			A	21238598	C	A	21238598	3	1	259	1	0	0	0	0	1	0	0	0	4912	595	21	3	291	3	EDDM3B	14	21238598	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	259735	21238598	86110942	611	36929										
OR5AU1	390445	hgsc.bcm.edu	37	chr14	21623682	21623682	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	catagcggtcataggccatgGcagcgatgagatagcactca	12	10	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:21623682G>T	ENST00000304418.3	-	1	540	c.503C>A	c.(502-504)gCc>gAc	p.A168D		NM_001004731.1	NP_001004731.1	Q8NGC0	O5AU1_HUMAN	olfactory receptor, family 5, subfamily AU, member 1	168						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(12)|pancreas(1)	21	all_cancers(95;0.00238)		Epithelial(56;6.88e-07)|all cancers(55;6.02e-06)	GBM - Glioblastoma multiforme(265;0.0192)		ATAGGCCATGGCAGCGATGAG	0.502																																					p.A168D		Atlas-SNP	.											.	OR5AU1	46	.	0			c.C503A						.						68	64	66					14																	21623682		2203	4300	6503	SO:0001583	missense	390445	exon1			GCCATGGCAGCGA	AL157687	CCDS32042.1	14q11.2	2013-09-23			ENSG00000169327	ENSG00000169327		"GPCR / Class A : Olfactory receptors"	15362	protein-coding gene	gene with protein product							Standard	NM_001004731		Approved		uc010tlp.2	Q8NGC0	OTTHUMG00000170753	ENST00000304418.3:c.503C>A	chr14.hg19:g.21623682G>T	ENSP00000302057:p.Ala168Asp	80.0	0.0		81.0	4.0	NM_001004731	B2RP78|Q6IEU2|Q96R10	Missense_Mutation	SNP	ENST00000304418.3	hg19	CCDS32042.1	.	.	.	.	.	.	.	.	.	.	G	14.30	2.492851	0.44352	.	.	ENSG00000169327	ENST00000304418	T	0.03152	4.03	4.22	4.22	0.49857	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.12902	0.0313	M	0.67953	2.075	0.39810	D	0.972689	D	0.71674	0.998	D	0.70487	0.969	T	0.00360	-1.1790	9	0.87932	D	0	.	7.8564	0.29485	0.1107:0.0:0.8893:0.0	.	168	Q8NGC0	O5AU1_HUMAN	D	168	ENSP00000302057:A168D	ENSP00000302057:A168D	A	-	2	0	OR5AU1	20693522	0.000000	0.05858	0.991000	0.47740	0.563000	0.35712	-0.022000	0.12480	2.189000	0.69895	0.313000	0.20887	GCC	.	.		0.502	OR5AU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410213.1			T	21623682	G	T	21623682	3	4	259	1	0	0	0	0	1	0	0	0	11156	1203	42	3	588	3	OR5AU1	14	21623682	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	385084	21623682	85725858	612	36930										
PRMT5	10419	hgsc.bcm.edu	37	chr14	23393528	23393528	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agcatacagctttatccgccGgtcggcctgcttggctgccc	11	15	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:23393528G>T	ENST00000324366.8	-	11	1373	c.1150C>A	c.(1150-1152)Cgg>Agg	p.R384R	PRMT5_ENST00000553897.1_Silent_p.R340R|PRMT5-AS1_ENST00000599580.2_RNA|PRMT5-AS1_ENST00000424245.2_RNA|PRMT5_ENST00000553641.1_5'Flank|PRMT5_ENST00000397440.4_Silent_p.R213R|PRMT5_ENST00000397441.2_Silent_p.R367R|PRMT5-AS1_ENST00000587245.2_RNA|PRMT5_ENST00000216350.8_Silent_p.R323R|PRMT5_ENST00000538452.1_Silent_p.R278R|PRMT5-AS1_ENST00000590290.1_RNA|PRMT5-AS1_ENST00000595662.1_RNA|PRMT5-AS1_ENST00000609885.1_RNA|PRMT5-AS1_ENST00000457443.2_RNA	NM_006109.3	NP_006100.2	O14744	ANM5_HUMAN	protein arginine methyltransferase 5	384	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				cell proliferation (GO:0008283)|circadian regulation of gene expression (GO:0032922)|endothelial cell activation (GO:0042118)|gene expression (GO:0010467)|histone H4-R3 methylation (GO:0043985)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to symmetrical-dimethyl arginine (GO:0019918)|peptidyl-arginine N-methylation (GO:0035246)|regulation of mitosis (GO:0007088)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|methylosome (GO:0034709)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|histone-arginine N-methyltransferase activity (GO:0008469)|methyltransferase activity (GO:0008168)|protein-arginine omega-N symmetric methyltransferase activity (GO:0035243)|ribonucleoprotein complex binding (GO:0043021)|transcription corepressor activity (GO:0003714)			endometrium(4)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	25	all_cancers(95;2.76e-05)			GBM - Glioblastoma multiforme(265;0.0126)		TTTATCCGCCGGTCGGCCTGC	0.552																																					p.R384R		Atlas-SNP	.											PRMT5_ENST00000397441,colon,carcinoma,0,2	PRMT5	101	.	0			c.C1150A						.						84	84	84					14																	23393528		2203	4300	6503	SO:0001819	synonymous_variant	10419	exon11			TCCGCCGGTCGGC	AF015913	CCDS9579.1, CCDS41922.1, CCDS61394.1, CCDS61395.1, CCDS61396.1	14q11.2	2014-06-12	2006-02-16	2006-02-16	ENSG00000100462	ENSG00000100462	2.1.1.125	"Protein arginine methyltransferases"	10894	protein-coding gene	gene with protein product		604045	"skb1 (S. pombe) homolog", "SKB1 homolog (S. pombe)"	HRMT1L5, SKB1		9843966	Standard	NM_001282955		Approved	SKB1Hs	uc001whm.1	O14744	OTTHUMG00000028709	ENST00000324366.8:c.1150C>A	chr14.hg19:g.23393528G>T		63.0	1.0		49.0	2.0	NM_006109	A8MTP3|A8MZ91|B4DX49|B4DY30|B5BU10|D3DS33|E2QRE7|Q6IBR1|Q9UKH1	Silent	SNP	ENST00000324366.8	hg19	CCDS9579.1																																																																																			.	.		0.552	PRMT5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071674.3			T	23393528	G	T	23393528	2	4	259	1	0	0	0	0	0	0	0	1	12551	1115	39	1		1	PRMT5	14	23393528	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1769846	23393528	83956012	613	36931										
PSMB11	122706	hgsc.bcm.edu	37	chr14	23511752	23511752	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gactgtgctacctggtatcgGgtattacagcgggagctgcg	15	9	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:23511752G>T	ENST00000408907.2	+	1	377	c.318G>T	c.(316-318)cgG>cgT	p.R106R		NM_001099780.1	NP_001093250.1	A5LHX3	PSB11_HUMAN	proteasome (prosome, macropain) subunit, beta type, 11	106					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)			endometrium(1)|kidney(2)|lung(4)	7	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.00643)		CCTGGTATCGGGTATTACAGC	0.602																																					p.R106R		Atlas-SNP	.											.	PSMB11	40	.	0			c.G318T						.						64	70	68					14																	23511752		2110	4233	6343	SO:0001819	synonymous_variant	122706	exon1			GTATCGGGTATTA		CCDS41923.1	14q11.2	2008-01-31				ENSG00000222028			31963	protein-coding gene	gene with protein product		611137				17540904	Standard	NM_001099780		Approved	beta5t	uc010ake.1	A5LHX3		ENST00000408907.2:c.318G>T	chr14.hg19:g.23511752G>T		102.0	0.0		78.0	4.0	NM_001099780		Silent	SNP	ENST00000408907.2	hg19	CCDS41923.1																																																																																			.	.		0.602	PSMB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408294.1	NM_001099780		T	23511752	G	T	23511752	2	4	259	1	0	0	0	0	0	0	0	1	12688	1219	43	3		3	PSMB11	14	23511752	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	118224	23511752	83837788	614	36932										
HOMEZ	57594	hgsc.bcm.edu	37	chr14	23745570	23745570	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gccagtacctggaaagaagaAgaggtagaggaagaagaggg	17	4	0	6			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:23745570A>G	ENST00000357460.5	-	2	1031	c.867T>C	c.(865-867)tcT>tcC	p.S289S	HOMEZ_ENST00000431326.2_Silent_p.S291S|HOMEZ_ENST00000561013.1_Silent_p.S291S	NM_020834.2	NP_065885.2	Q8IX15	HOMEZ_HUMAN	homeobox and leucine zipper encoding	289	Poly-Ser.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|lung(7)	12	all_cancers(95;5.54e-06)			GBM - Glioblastoma multiforme(265;0.00643)		GGAAAGAAGAAGAGGTAGAGG	0.512																																					p.S289S		Atlas-SNP	.											.	HOMEZ	80	.	0			c.T867C						.						61	64	63					14																	23745570		2124	4222	6346	SO:0001819	synonymous_variant	57594	exon2			AGAAGAAGAGGTA	AB037864	CCDS45085.1	14q11.2	2011-06-20	2007-02-15	2007-02-15		ENSG00000215271		"Homeoboxes / ZF class"	20164	protein-coding gene	gene with protein product		608119	"KIAA1443"	KIAA1443		12925734	Standard	NM_020834		Approved		uc001wja.2	Q8IX15		ENST00000357460.5:c.867T>C	chr14.hg19:g.23745570A>G		138.0	0.0		132.0	18.0	NM_020834	A1L445|B4DZ80|F8WCA3|Q6P049|Q86XB6|Q9P2A5	Silent	SNP	ENST00000357460.5	hg19	CCDS45085.1																																																																																			.	.		0.512	HOMEZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000416939.2	NM_020834		G	23745570	A	G	23745570	2	3	259	1	0	0	0	0	0	0	0	1	7290	59	3	2		2	HOMEZ	14	23745570	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	233818	23745570	83603970	615	36933										
SLC22A17	51310	hgsc.bcm.edu	37	chr14	23816000	23816000	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gcgcttggtctccggcagcaGcataatgctgagaatgcaga	13	10	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:23816000G>T	ENST00000206544.8	-	9	1810	c.1474C>A	c.(1474-1476)Ctg>Atg	p.L492M	SLC22A17_ENST00000354772.3_Missense_Mutation_p.L474M|SLC22A17_ENST00000474057.1_5'UTR|SLC22A17_ENST00000397267.1_Missense_Mutation_p.L492M|SLC22A17_ENST00000397260.3_Missense_Mutation_p.L363M	NM_020372.2	NP_065105.2	Q8WUG5	S22AH_HUMAN	solute carrier family 22, member 17	492					ion transport (GO:0006811)|iron ion homeostasis (GO:0055072)|siderophore transport (GO:0015891)	integral component of organelle membrane (GO:0031301)|integral component of plasma membrane (GO:0005887)|vacuole (GO:0005773)	transmembrane signaling receptor activity (GO:0004888)|transmembrane transporter activity (GO:0022857)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	15	all_cancers(95;7.12e-06)			GBM - Glioblastoma multiforme(265;0.00643)		TCCGGCAGCAGCATAATGCTG	0.701																																					p.L492M		Atlas-SNP	.											.	SLC22A17	32	.	0			c.C1474A						.						7	9	9					14																	23816000		2131	4217	6348	SO:0001583	missense	51310	exon9			GCAGCAGCATAAT	AJ243653	CCDS9593.1, CCDS9594.2	14q11.2	2013-05-22	2008-01-11		ENSG00000092096	ENSG00000092096		"Solute carriers"	23095	protein-coding gene	gene with protein product	"neutrophil gelatinase-associated lipocalin receptor"	611461				16377569	Standard	NM_016609		Approved	BOCT, BOIT, NGALR	uc001wjl.3	Q8WUG5	OTTHUMG00000028740	ENST00000206544.8:c.1474C>A	chr14.hg19:g.23816000G>T	ENSP00000206544:p.Leu492Met	38.0	0.0		39.0	13.0	NM_020372	A4UA13|A8MUT0|Q2TAB0|Q5BKY8|Q86U04|Q9H1D3|Q9NQD5	Missense_Mutation	SNP	ENST00000206544.8	hg19	CCDS9593.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.239469	0.79800	.	.	ENSG00000092096	ENST00000354772;ENST00000397260;ENST00000206544;ENST00000397267	T;T;T;T	0.74737	-0.87;-0.87;-0.87;-0.87	5.91	5.91	0.95273	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.64402	D	0.000004	D	0.87124	0.6099	M	0.77406	2.37	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.87358	0.2342	10	0.66056	D	0.02	-11.6045	19.0661	0.93110	0.0:0.0:1.0:0.0	.	474;492	Q8WUG5-2;Q8WUG5	.;S22AH_HUMAN	M	474;363;492;492	ENSP00000346824:L474M;ENSP00000380430:L363M;ENSP00000206544:L492M;ENSP00000380437:L492M	ENSP00000206544:L492M	L	-	1	2	SLC22A17	22885840	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	7.332000	0.79203	2.804000	0.96469	0.462000	0.41574	CTG	.	.		0.701	SLC22A17-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157223.3	NM_020372		T	23816000	G	T	23816000	3	4	259	1	0	0	0	0	1	0	0	0	14463	962	34	3	146	3	SLC22A17	14	23816000	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	70430	23816000	83533540	616	36934										
MYH6	4624	hgsc.bcm.edu	37	chr14	23865912	23865912	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tctagactcaccttggtgtgGccaaacttgtactggttgtg	11	9	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:23865912G>T	ENST00000356287.3	-	18	2312	c.2283C>A	c.(2281-2283)ggC>ggA	p.G761G	MYH6_ENST00000405093.3_Silent_p.G761G			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	761	Actin-binding.|Myosin motor.				adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)			breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		CCTTGGTGTGGCCAAACTTGT	0.547																																					p.G761G		Atlas-SNP	.											.	MYH6	274	.	0			c.C2283A						.						116	102	107					14																	23865912		2203	4300	6503	SO:0001819	synonymous_variant	4624	exon19			GGTGTGGCCAAAC	D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"Myosins / Myosin superfamily : Class II"	7576	protein-coding gene	gene with protein product	"cardiomyopathy, hypertrophic 1"	160710	"myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.2283C>A	chr14.hg19:g.23865912G>T		156.0	0.0		124.0	5.0	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Silent	SNP	ENST00000356287.3	hg19	CCDS9600.1																																																																																			.	.		0.547	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3			T	23865912	G	T	23865912	2	4	259	1	0	0	0	0	0	0	0	1	10047	1190	42	3		3	MYH6	14	23865912	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	49912	23865912	83483628	617	36935										
DHRS4L1	728635	hgsc.bcm.edu	37	chr14	24507078	24507078	+	RNA	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gaggggctgagcatgacgggCactgtgtgccatgtggggaa	19	7	0	2	rs373705961		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:24507078C>T	ENST00000558293.1	+	0	176					NR_102693.1																						GCATGACGGGCACTGTGTGCC	0.652													C|||	1	0.000199681	0	0	5008	,	,		17195	0		0.001	False		,,,				2504	0				p.G85G		Atlas-SNP	.											.	.	.	.	0			c.C255T						.	C		0,4406		0,0,2203	32	34	33		255	2.4	1	14		33	1,8599		0,1,4299	no	coding-synonymous	DHRS4L1	NM_001082488.1		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		85/282	24507078	1,13005	2203	4300	6503			728635	exon2			GACGGGCACTGTG																													chr14.hg19:g.24507078C>T		415.0	0.0		306.0	130.0	NM_001082488		Silent	SNP	ENST00000558293.1	hg19																																																																																				.	.		0.652	RP11-468E2.9-005	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417272.1			T	24507078	C	T	24507078	1	4	259	0	1	0	0	0	0	0	0	0	4495	697	25	3		3	DHRS4L1	14	24507078	RNA	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	641166	24507078	82842462	618	36936										
LRRC16B	90668	hgsc.bcm.edu	37	chr14	24523931	24523931	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cttttccaggtgtttgatccGgcgtggaaacgcagacaccc	11	12	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:24523931G>T	ENST00000342740.5	+	6	528	c.374G>T	c.(373-375)cGg>cTg	p.R125L	LRRC16B_ENST00000334420.7_5'UTR	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	125						cytoplasm (GO:0005737)				breast(3)|central_nervous_system(2)|cervix(3)|endometrium(7)|kidney(1)|large_intestine(9)|liver(1)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	52				GBM - Glioblastoma multiforme(265;0.019)		TGTTTGATCCGGCGTGGAAAC	0.552																																					p.R125L		Atlas-SNP	.											LRRC16B,NS,carcinoma,0,1	LRRC16B	120	.	0			c.G374T						.						42	47	45					14																	24523931		2203	4300	6503	SO:0001583	missense	90668	exon6			TGATCCGGCGTGG	AI017934	CCDS32054.1	14q11.2-q12	2010-09-10	2008-02-12	2008-02-12					20272	protein-coding gene	gene with protein product		614716	"chromosome 14 open reading frame 121"	C14orf121		19846667	Standard	NM_138360		Approved	BC008134, crml-1, CARMIL3	uc001wlj.2	Q8ND23		ENST00000342740.5:c.374G>T	chr14.hg19:g.24523931G>T	ENSP00000340467:p.Arg125Leu	36.0	0.0		58.0	3.0	NM_138360	Q8TEF7|Q96HS9	Missense_Mutation	SNP	ENST00000342740.5	hg19	CCDS32054.1	.	.	.	.	.	.	.	.	.	.	G	15.88	2.964994	0.53507	.	.	ENSG00000186648	ENST00000342740	T	0.16743	2.32	4.17	4.17	0.49024	.	0.261098	0.31963	N	0.006800	T	0.19565	0.0470	L	0.58810	1.83	0.80722	D	1	B	0.33135	0.399	B	0.34722	0.188	T	0.03268	-1.1054	10	0.52906	T	0.07	-22.025	12.1519	0.54053	0.0:0.0:1.0:0.0	.	125	Q8ND23	LR16B_HUMAN	L	125	ENSP00000340467:R125L	ENSP00000340467:R125L	R	+	2	0	LRRC16B	23593771	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.072000	0.57563	2.305000	0.77605	0.462000	0.41574	CGG	.	.		0.552	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360		T	24523931	G	T	24523931	3	4	259	1	0	0	0	0	1	0	0	0	8981	1116	39	1	396	1	LRRC16B	14	24523931	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	16853	24523931	82825609	619	36937										
GMPR2	51292	hgsc.bcm.edu	37	chr14	24702442	24702442	+	5'UTR	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cagccctcagattcatcgctAccccgaggctaagcgccatg	9	16	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:24702442A>G	ENST00000355299.4	+	0	444				NEDD8_ENST00000533242.1_5'Flank|NEDD8_ENST00000524927.1_5'Flank|GMPR2_ENST00000559836.1_5'UTR|NEDD8-MDP1_ENST00000604306.1_5'Flank|GMPR2_ENST00000456667.3_5'UTR|NEDD8_ENST00000250495.5_5'Flank|GMPR2_ENST00000559910.1_5'UTR|GMPR2_ENST00000559104.1_Missense_Mutation_p.T13A|GMPR2_ENST00000420554.2_Missense_Mutation_p.T13A|GMPR2_ENST00000557854.1_Missense_Mutation_p.T13A|GMPR2_ENST00000348719.7_5'UTR|GMPR2_ENST00000399440.2_5'UTR|NEDD8-MDP1_ENST00000534348.1_5'Flank	NM_001002000.1	NP_001002000.1	Q9P2T1	GMPR2_HUMAN	guanosine monophosphate reductase 2						GMP metabolic process (GO:0046037)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|GMP reductase complex (GO:1902560)	GMP reductase activity (GO:0003920)|metal ion binding (GO:0046872)			large_intestine(4)|lung(3)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	12				GBM - Glioblastoma multiforme(265;0.0181)		ATTCATCGCTACCCCGAGGCT	0.522																																					p.T13A		Atlas-SNP	.											.	GMPR2	37	.	0			c.A37G						.						270	261	264					14																	24702442		2016	4184	6200	SO:0001623	5_prime_UTR_variant	51292	exon1			ATCGCTACCCCGA		CCDS41935.1, CCDS45087.1, CCDS61419.1, CCDS73624.1	14q11.2	2006-11-24							4377	protein-coding gene	gene with protein product		610781					Standard	XM_005267742		Approved		uc001wnw.3	Q9P2T1		ENST00000355299.4:c.-18A>G	chr14.hg19:g.24702442A>G		132.0	0.0		105.0	5.0	NM_016576	D3DS66|Q567T0|Q6IAJ8|Q86T14	Missense_Mutation	SNP	ENST00000355299.4	hg19	CCDS41935.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.528398	0.85706	.	.	ENSG00000100938	ENST00000420554	T	0.16597	2.33	4.37	3.21	0.36854	.	.	.	.	.	T	0.10165	0.0249	N	0.14661	0.345	0.24973	N	0.991653	B	0.02656	0.0	B	0.04013	0.001	T	0.23547	-1.0185	9	0.72032	D	0.01	.	6.7426	0.23445	0.892:0.0:0.108:0.0	.	13	Q9P2T1-2	.	A	13	ENSP00000392859:T13A	ENSP00000392859:T13A	T	+	1	0	GMPR2	23772282	0.000000	0.05858	0.016000	0.15963	0.951000	0.60555	0.083000	0.14871	0.813000	0.34350	0.460000	0.39030	ACC	.	.		0.522	GMPR2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415821.2	NM_016576		G	24702442	A	G	24702442	1	3	259	0	1	0	0	0	0	0	0	0	6505	391	14	2		2	GMPR2	14	24702442	5'UTR	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	178511	24702442	82647098	620	36938										
HEATR5A	25938	hgsc.bcm.edu	37	chr14	31819853	31819853	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aactgaagaaacaacatgtaActgaaccacttgctgacgag	8	9	0	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:31819853A>G	ENST00000389961.3	-	16	2463	c.2464T>C	c.(2464-2466)Tta>Cta	p.L822L	HEATR5A_ENST00000439348.1_Silent_p.L822L|HEATR5A_ENST00000404677.3_Silent_p.L828L|HEATR5A_ENST00000439727.1_Silent_p.L535L|HEATR5A_ENST00000543095.2_Silent_p.L828L			Q86XA9	HTR5A_HUMAN	HEAT repeat containing 5A	822										breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)	26	Hepatocellular(127;0.0877)|Breast(36;0.137)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.0797)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0059)		ACAACATGTAACTGAACCACT	0.313																																					p.L828L		Atlas-SNP	.											.	HEATR5A	181	.	0			c.T2482C						.						78	74	75					14																	31819853		1818	4074	5892	SO:0001819	synonymous_variant	25938	exon17			CATGTAACTGAAC	AB037737		14q12	2012-04-19	2007-01-02	2007-01-02	ENSG00000129493	ENSG00000129493			20276	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 125"	C14orf125			Standard	NM_015473		Approved	DKFZP434I1735	uc001wrf.4	Q86XA9	OTTHUMG00000169043	ENST00000389961.3:c.2464T>C	chr14.hg19:g.31819853A>G		68.0	0.0		61.0	4.0	NM_015473	Q68DD8|Q6P3S5|Q6P5R9|Q9H8D7|Q9NXB7|Q9P2N0|Q9UFQ3	Silent	SNP	ENST00000389961.3	hg19		.	.	.	.	.	.	.	.	.	.	A	9.185	1.024644	0.19433	.	.	ENSG00000129493	ENST00000550366	.	.	.	5.41	4.26	0.50523	.	.	.	.	.	T	0.59418	0.2192	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55398	-0.8147	4	.	.	.	.	9.1952	0.37224	0.847:0.0:0.153:0.0	.	.	.	.	A	470	.	.	V	-	2	0	HEATR5A	30889604	0.995000	0.38212	1.000000	0.80357	0.998000	0.95712	2.547000	0.45786	0.890000	0.36211	0.533000	0.62120	GTT	.	.		0.313	HEATR5A-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015473		G	31819853	A	G	31819853	2	3	259	1	0	0	0	0	0	0	0	1	7040	40	2	2		2	HEATR5A	14	31819853	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	7117411	31819853	75529687	621	36939										
FANCM	57697	hgsc.bcm.edu	37	chr14	45644488	45644488	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgaaattgttaaacaaactcAtatcaaacctactaaaattg	3	7	2	1	rs113630826		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:45644488A>G	ENST00000267430.5	+	14	2616	c.2531A>G	c.(2530-2532)cAt>cGt	p.H844R	FANCM_ENST00000542564.2_Missense_Mutation_p.H818R	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	844					DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						AAACAAACTCATATCAAACCT	0.274								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.H844R		Atlas-SNP	.											.	FANCM	225	.	0			c.A2531G						.						43	42	42					14																	45644488		2203	4296	6499	SO:0001583	missense	57697	exon14	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AAACTCATATCAA	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"Fanconi anemia, complementation groups"	23168	protein-coding gene	gene with protein product		609644	"KIAA1596"	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.2531A>G	chr14.hg19:g.45644488A>G	ENSP00000267430:p.His844Arg	113.0	0.0		97.0	4.0	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	hg19	CCDS32070.1	.	.	.	.	.	.	.	.	.	.	A	0.016	-1.520158	0.00967	.	.	ENSG00000187790	ENST00000267430;ENST00000542564;ENST00000556250	T;T;T	0.16457	2.93;2.93;2.34	4.8	-4.44	0.03557	.	1.545420	0.03339	N	0.194534	T	0.09642	0.0237	L	0.34521	1.04	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.23762	-1.0179	10	0.15066	T	0.55	.	0.7073	0.00918	0.3496:0.246:0.245:0.1594	.	818;844	B2RTQ9;Q8IYD8	.;FANCM_HUMAN	R	844;818;360	ENSP00000267430:H844R;ENSP00000442493:H818R;ENSP00000452033:H360R	ENSP00000267430:H844R	H	+	2	0	FANCM	44714238	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	-0.438000	0.06905	-0.653000	0.05401	-0.446000	0.05623	CAT	.	A|0.500;G|0.500		0.274	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		G	45644488	A	G	45644488	3	3	259	1	0	0	0	0	1	0	0	0	5679	217	8	2	2585	2	FANCM	14	45644488	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	13824635	45644488	61705052	622	36940										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64630261	64630261	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctctccagagggctgcttatTtggaaaagatgctgcttgtg	12	8	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:64630261T>C	ENST00000344113.4	+	89	16653	c.16441T>C	c.(16441-16443)Ttg>Ctg	p.L5481L	SYNE2_ENST00000394768.2_Silent_p.L1866L|SYNE2_ENST00000357395.3_Silent_p.L1866L|SYNE2_ENST00000358025.3_Silent_p.L5481L|SYNE2_ENST00000555002.1_Silent_p.L2115L|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000554584.1_Silent_p.L5398L	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	5481					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		GGCTGCTTATTTGGAAAAGAT	0.483																																					p.L5481L		Atlas-SNP	.											.	SYNE2	577	.	0			c.T16441C						.						59	59	59					14																	64630261		2203	4300	6503	SO:0001819	synonymous_variant	23224	exon89			GCTTATTTGGAAA	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.16441T>C	chr14.hg19:g.64630261T>C		120.0	0.0		94.0	4.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	hg19	CCDS41963.1																																																																																			.	.		0.483	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		C	64630261	T	C	64630261	2	2	259	1	0	0	0	0	0	0	0	1	15461	1838	64	2		2	SYNE2	14	64630261	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	18985773	64630261	42719279	623	36941										
PLEKHH1	57475	hgsc.bcm.edu	37	chr14	68029351	68029351	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccaaaaggcaccacagccagCcccaggtgggccatgggcac	12	16	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:68029351C>G	ENST00000329153.5	+	7	1135	c.1003C>G	c.(1003-1005)Ccc>Gcc	p.P335A		NM_020715.2	NP_065766.1	Q9ULM0	PKHH1_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 1	335						cytoskeleton (GO:0005856)				endometrium(2)|kidney(4)|lung(12)|urinary_tract(1)	19				all cancers(60;0.000771)|OV - Ovarian serous cystadenocarcinoma(108;0.00502)|BRCA - Breast invasive adenocarcinoma(234;0.011)		CCACAGCCAGCCCCAGGTGGG	0.647																																					p.P335A		Atlas-SNP	.											.	PLEKHH1	118	.	0			c.C1003G						.						20	22	21					14																	68029351		1985	4159	6144	SO:0001583	missense	57475	exon7			AGCCAGCCCCAGG	AB033026	CCDS45128.1	14q24.1	2013-01-10				ENSG00000054690		"Pleckstrin homology (PH) domain containing"	17733	protein-coding gene	gene with protein product						10574462	Standard	NM_020715		Approved	KIAA1200	uc001xjl.1	Q9ULM0		ENST00000329153.5:c.1003C>G	chr14.hg19:g.68029351C>G	ENSP00000330278:p.Pro335Ala	139.0	0.0		97.0	4.0	NM_020715	A6H8X6|Q6PJL4|Q6ZWC7	Missense_Mutation	SNP	ENST00000329153.5	hg19	CCDS45128.1	.	.	.	.	.	.	.	.	.	.	C	19.94	3.920511	0.73213	.	.	ENSG00000054690	ENST00000329153	T	0.21932	1.98	4.78	4.78	0.61160	.	0.000000	0.85682	D	0.000000	T	0.45796	0.1360	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.44667	-0.9313	10	0.72032	D	0.01	.	14.8139	0.70017	0.0:1.0:0.0:0.0	.	335	Q9ULM0	PKHH1_HUMAN	A	335	ENSP00000330278:P335A	ENSP00000330278:P335A	P	+	1	0	PLEKHH1	67099104	1.000000	0.71417	1.000000	0.80357	0.729000	0.41735	6.610000	0.74178	2.467000	0.83353	0.491000	0.48974	CCC	.	.		0.647	PLEKHH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412730.3	XM_031054		G	68029351	C	G	68029351	3	3	259	1	0	0	0	0	1	0	0	0	12085	739	26	4	1025	4	PLEKHH1	14	68029351	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	3399090	68029351	39320189	624	36942										
EXD2	55218	hgsc.bcm.edu	37	chr14	69704317	69704317	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acgtgattccacatgagtacCggaagcacttccccatcgag	9	13	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:69704317C>A	ENST00000409018.3	+	8	1446	c.1318C>A	c.(1318-1320)Cgg>Agg	p.R440R	EXD2_ENST00000409242.1_Silent_p.R315R|EXD2_ENST00000409014.1_Silent_p.R315R|EXD2_ENST00000409675.1_Silent_p.R315R|EXD2_ENST00000492815.1_3'UTR|RP11-363J20.2_ENST00000556316.1_lincRNA|EXD2_ENST00000312994.5_Silent_p.R440R|EXD2_ENST00000409949.1_Silent_p.R315R|EXD2_ENST00000449989.1_Silent_p.R315R	NM_001193361.1	NP_001180290.1	Q9NVH0	EXD2_HUMAN	exonuclease 3'-5' domain containing 2	440							3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(7)|prostate(1)|urinary_tract(1)	14						ACATGAGTACCGGAAGCACTT	0.527																																					p.R440R		Atlas-SNP	.											.	EXD2	43	.	0			c.C1318A						.						77	71	73					14																	69704317		2203	4300	6503	SO:0001819	synonymous_variant	55218	exon8			GAGTACCGGAAGC	AK001600	CCDS9793.1, CCDS53902.1	14q24.1	2009-02-24	2009-02-24	2009-02-24	ENSG00000081177	ENSG00000081177			20217	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 114", "exonuclease 3'-5' domain-like 2"	C14orf114, EXDL2			Standard	NM_018199		Approved	FLJ10738	uc001xkv.3	Q9NVH0	OTTHUMG00000154496	ENST00000409018.3:c.1318C>A	chr14.hg19:g.69704317C>A		92.0	0.0		99.0	4.0	NM_001193361	B4DIH6|G5E947|Q6AWB6|Q8N3D3	Silent	SNP	ENST00000409018.3	hg19	CCDS53902.1																																																																																			.	.		0.527	EXD2-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000335504.1			A	69704317	C	A	69704317	2	1	259	1	0	0	0	0	0	0	0	1	5300	643	23	1		1	EXD2	14	69704317	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	1674966	69704317	37645223	625	36943										
SIPA1L1	26037	hgsc.bcm.edu	37	chr14	72138015	72138015	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aactcggacccgccaggaatAcctgaaagatctggcagaaa	10	11	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:72138015A>G	ENST00000555818.1	+	8	2783	c.2435A>G	c.(2434-2436)tAc>tGc	p.Y812C	SIPA1L1_ENST00000537413.1_Missense_Mutation_p.Y287C|SIPA1L1_ENST00000381232.3_Missense_Mutation_p.Y812C|SIPA1L1_ENST00000358550.2_Missense_Mutation_p.Y812C	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	812	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		CGCCAGGAATACCTGAAAGAT	0.478																																					p.Y812C		Atlas-SNP	.											.	SIPA1L1	219	.	0			c.A2435G						.						92	90	90					14																	72138015		2203	4300	6503	SO:0001583	missense	26037	exon8			AGGAATACCTGAA	AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.2435A>G	chr14.hg19:g.72138015A>G	ENSP00000450832:p.Tyr812Cys	145.0	0.0		149.0	6.0	NM_015556	J3KP19|O95321|Q9UDU4|Q9UNU4	Missense_Mutation	SNP	ENST00000555818.1	hg19	CCDS9807.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.288094	0.80803	.	.	ENSG00000197555	ENST00000381232;ENST00000555818;ENST00000358550;ENST00000537413	T;T;T;T	0.59502	0.26;0.26;0.26;0.26	6.05	6.05	0.98169	Rap/ran-GAP (2);	0.000000	0.85682	D	0.000000	T	0.81083	0.4749	M	0.89840	3.065	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.997;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.988;1.0;1.0;0.998	D	0.84991	0.0894	10	0.87932	D	0	-23.2157	16.5932	0.84781	1.0:0.0:0.0:0.0	.	287;812;287;812;812	F5GYF8;A6H8W6;B4DYX7;O43166-2;O43166	.;.;.;.;SI1L1_HUMAN	C	812;812;812;287	ENSP00000370630:Y812C;ENSP00000450832:Y812C;ENSP00000351352:Y812C;ENSP00000440682:Y287C	ENSP00000351352:Y812C	Y	+	2	0	SIPA1L1	71207768	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.307000	0.96226	2.320000	0.78422	0.528000	0.53228	TAC	.	.		0.478	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556		G	72138015	A	G	72138015	3	3	259	1	0	0	0	0	1	0	0	0	14344	391	14	2	2461	2	SIPA1L1	14	72138015	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2433698	72138015	35211525	626	36944										
ISCA2	122961	hgsc.bcm.edu	37	chr14	74960541	74960541	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gagcggtcactccctggccgAggggcaggtaccaagactag	15	12	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:74960541A>G	ENST00000556816.1	+	1	119	c.64A>G	c.(64-66)Agg>Ggg	p.R22G	NPC2_ENST00000541064.1_5'Flank|NPC2_ENST00000434013.2_5'Flank|ISCA2_ENST00000298818.8_Missense_Mutation_p.R22G|NPC2_ENST00000238633.2_5'Flank|NPC2_ENST00000557510.1_5'Flank|ISCA2_ENST00000554924.1_Missense_Mutation_p.R22G|NPC2_ENST00000555619.1_5'Flank			Q86U28	ISCA2_HUMAN	iron-sulfur cluster assembly 2	22					iron-sulfur cluster assembly (GO:0016226)	mitochondrion (GO:0005739)	iron-sulfur cluster binding (GO:0051536)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			lung(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00146)		TCCCTGGCCGAGGGGCAGGTA	0.632																																					p.R22G		Atlas-SNP	.											.	ISCA2	4	.	0			c.A64G						.						11	13	12					14																	74960541		2174	4251	6425	SO:0001583	missense	122961	exon1			TGGCCGAGGGGCA		CCDS32122.1, CCDS61504.1	14q24.2	2013-08-06	2013-08-06	2007-01-18	ENSG00000165898	ENSG00000165898			19857	protein-coding gene	gene with protein product		615317	"HesB like domain containing 1", "iron-sulfur cluster assembly 2 homolog (S. cerevisiae)"	HBLD1		22323289	Standard	NM_194279		Approved	ISA2	uc001xpz.3	Q86U28		ENST00000556816.1:c.64A>G	chr14.hg19:g.74960541A>G	ENSP00000452007:p.Arg22Gly	94.0	0.0		79.0	5.0	NM_001272007	A6NFF1|A8K3W3|G3V291|Q8IYZ0|Q96BB2	Missense_Mutation	SNP	ENST00000556816.1	hg19	CCDS32122.1	.	.	.	.	.	.	.	.	.	.	A	13.16	2.154748	0.38021	.	.	ENSG00000165898	ENST00000556816;ENST00000298818;ENST00000554924	.	.	.	4.99	1.23	0.21249	.	1.050110	0.07419	N	0.893737	T	0.19327	0.0464	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.27739	-1.0065	9	0.27785	T	0.31	0.0	0.3984	0.00422	0.4127:0.1458:0.1606:0.2809	.	22	Q86U28	ISCA2_HUMAN	G	22	.	ENSP00000298818:R22G	R	+	1	2	ISCA2	74030294	0.005000	0.15991	0.000000	0.03702	0.008000	0.06430	0.209000	0.17435	0.110000	0.17919	0.533000	0.62120	AGG	.	.		0.632	ISCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412354.1	NM_194279		G	74960541	A	G	74960541	3	3	259	1	0	0	0	0	1	0	0	0	7860	295	11	2	66	2	ISCA2	14	74960541	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2822526	74960541	32388999	627	36945										
KIAA0317	9870	hgsc.bcm.edu	37	chr14	75130431	75130431	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acaggagagtggtcagagcaTgccaaagccctcgcaaccct	11	13	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:75130431T>C	ENST00000356357.4	-	20	2979	c.2464A>G	c.(2464-2466)Atg>Gtg	p.M822V	AREL1_ENST00000557401.1_Intron	NM_001039479.1	NP_001034568.1	O15033	AREL1_HUMAN	apoptosis resistant E3 ubiquitin protein ligase 1	822	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										GGTCAGAGCATGCCAAAGCCC	0.522																																					p.M822V		Atlas-SNP	.											.	KIAA0317	68	.	0			c.A2464G						.						133	139	137					14																	75130431		2174	4263	6437	SO:0001583	missense	9870	exon20			AGAGCATGCCAAA	AB002315	CCDS41971.1	14q24.2	2013-04-15	2013-04-15	2013-04-15	ENSG00000119682	ENSG00000119682			20363	protein-coding gene	gene with protein product		615380	"KIAA0317"	KIAA0317		9205841, 23479728	Standard	XM_006720344		Approved		uc001xqb.3	O15033	OTTHUMG00000154499	ENST00000356357.4:c.2464A>G	chr14.hg19:g.75130431T>C	ENSP00000348714:p.Met822Val	71.0	0.0		70.0	5.0	NM_001039479	B4E2C7|Q7LDY1|Q8IYY9	Missense_Mutation	SNP	ENST00000356357.4	hg19	CCDS41971.1	.	.	.	.	.	.	.	.	.	.	T	14.61	2.587795	0.46110	.	.	ENSG00000119682	ENST00000356357	T	0.55413	0.52	5.73	4.57	0.56435	HECT (3);	0.065915	0.85682	D	0.000000	T	0.57989	0.2091	L	0.46819	1.47	0.58432	D	0.999999	P	0.50710	0.938	P	0.53102	0.718	T	0.60449	-0.7261	10	0.72032	D	0.01	.	13.0212	0.58789	0.0:0.0:0.1347:0.8652	.	822	O15033	K0317_HUMAN	V	822	ENSP00000348714:M822V	ENSP00000348714:M822V	M	-	1	0	KIAA0317	74200184	1.000000	0.71417	1.000000	0.80357	0.274000	0.26718	4.967000	0.63722	0.981000	0.38548	-0.323000	0.08544	ATG	.	.		0.522	AREL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335517.2	NM_014821		C	75130431	T	C	75130431	3	2	259	1	0	0	0	0	1	0	0	0	8176	1464	51	2	11	2	KIAA0317	14	75130431	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	169890	75130431	32219109	628	36946										
TGFB3	7043	hgsc.bcm.edu	37	chr14	76437504	76437504	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	actcacgcacagtgtcagtgAcatcaaaggacagccactcg	9	13	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:76437504A>G	ENST00000238682.3	-	3	908	c.611T>C	c.(610-612)gTc>gCc	p.V204A	RP11-270M14.5_ENST00000553732.1_lincRNA|TGFB3_ENST00000556285.1_Missense_Mutation_p.V204A	NM_003239.2	NP_003230.1	P10600	TGFB3_HUMAN	transforming growth factor, beta 3	204					activation of MAPK activity (GO:0000187)|aging (GO:0007568)|blood coagulation (GO:0007596)|cell growth (GO:0016049)|cell-cell junction organization (GO:0045216)|detection of hypoxia (GO:0070483)|digestive tract development (GO:0048565)|embryonic neurocranium morphogenesis (GO:0048702)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|female pregnancy (GO:0007565)|frontal suture morphogenesis (GO:0060364)|in utero embryonic development (GO:0001701)|inner ear development (GO:0048839)|lung alveolus development (GO:0048286)|mammary gland development (GO:0030879)|menstrual cycle phase (GO:0022601)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of macrophage cytokine production (GO:0010936)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|odontogenesis (GO:0042476)|ossification involved in bone remodeling (GO:0043932)|palate development (GO:0060021)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cell division (GO:0051781)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein secretion (GO:0050714)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to laminar fluid shear stress (GO:0034616)|response to progesterone (GO:0032570)|salivary gland morphogenesis (GO:0007435)|SMAD protein import into nucleus (GO:0007184)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|T-tubule (GO:0030315)	identical protein binding (GO:0042802)|transforming growth factor beta binding (GO:0050431)|type I transforming growth factor beta receptor binding (GO:0034713)|type II transforming growth factor beta receptor binding (GO:0005114)			NS(1)|breast(1)|endometrium(4)|kidney(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	11				BRCA - Breast invasive adenocarcinoma(234;0.0169)		AGTGTCAGTGACATCAAAGGA	0.522																																					p.V204A		Atlas-SNP	.											.	TGFB3	25	.	0			c.T611C						.						110	94	99					14																	76437504		2203	4300	6503	SO:0001583	missense	7043	exon3			TCAGTGACATCAA		CCDS9846.1	14q24	2014-09-17				ENSG00000119699		"Endogenous ligands"	11769	protein-coding gene	gene with protein product	"prepro-transforming growth factor beta-3"	190230	"arrhythmogenic right ventricular dysplasia 1"	ARVD1, ARVD		16549496, 15639475	Standard	XM_005268028		Approved		uc001xsc.2	P10600		ENST00000238682.3:c.611T>C	chr14.hg19:g.76437504A>G	ENSP00000238682:p.Val204Ala	62.0	0.0		53.0	4.0	NM_003239	Q8WV88	Missense_Mutation	SNP	ENST00000238682.3	hg19	CCDS9846.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.614681	0.87359	.	.	ENSG00000119699	ENST00000238682;ENST00000556285	T;T	0.74842	-0.88;-0.88	5.55	5.55	0.83447	Transforming growth factor-beta, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.84202	0.5420	M	0.86178	2.8	0.80722	D	1	P	0.52463	0.953	P	0.53593	0.73	D	0.87247	0.2270	10	0.87932	D	0	-11.4624	15.6992	0.77528	1.0:0.0:0.0:0.0	.	204	P10600	TGFB3_HUMAN	A	204	ENSP00000238682:V204A;ENSP00000451110:V204A	ENSP00000238682:V204A	V	-	2	0	TGFB3	75507257	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	8.962000	0.93254	2.122000	0.65172	0.459000	0.35465	GTC	.	.		0.522	TGFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413685.1	NM_003239		G	76437504	A	G	76437504	3	3	259	1	0	0	0	0	1	0	0	0	15834	275	10	2	647	2	TGFB3	14	76437504	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1307073	76437504	30912036	629	36947										
VASH1	22846	hgsc.bcm.edu	37	chr14	77237533	77237533	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cccttaacccgtgcccacagGtacaatcacacagggacaca	7	16	1	0	rs202147705		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:77237533G>A	ENST00000167106.4	+	3	1032	c.399G>A	c.(397-399)caG>caA	p.Q133Q	VASH1_ENST00000554237.1_Splice_Site_p.Q133Q|VASH1_ENST00000556038.1_3'UTR	NM_014909.4	NP_055724.1	Q7L8A9	VASH1_HUMAN	vasohibin 1	133					angiogenesis (GO:0001525)|cell cycle arrest (GO:0007050)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of lymphangiogenesis (GO:1901491)|regulation of cellular senescence (GO:2000772)|response to wounding (GO:0009611)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)		p.Q133H(2)		breast(2)|endometrium(1)|large_intestine(1)|lung(1)|prostate(1)|stomach(1)|urinary_tract(3)	10			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0283)		GTGCCCACAGGTACAATCACA	0.552																																					p.Q133Q		Atlas-SNP	.											VASH1_ENST00000554237,NS,carcinoma,0,2	VASH1	57	.	2	Substitution - Missense(2)	breast(2)	c.G399A						.						119	107	111					14																	77237533		2203	4300	6503	SO:0001630	splice_region_variant	22846	exon3			CCACAGGTACAAT	AB028959	CCDS9851.1	14q24.3	2006-09-25	2005-08-16	2005-08-16		ENSG00000071246			19964	protein-coding gene	gene with protein product		609011	"KIAA1036"	KIAA1036			Standard	NM_014909		Approved		uc001xst.2	Q7L8A9		ENST00000167106.4:c.399-1G>A	chr14.hg19:g.77237533G>A		452.0	0.0		357.0	98.0	NM_014909	Q96H02|Q9UBF4|Q9Y629	Silent	SNP	ENST00000167106.4	hg19	CCDS9851.1																																																																																			.	.		0.552	VASH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413706.1	NM_014909	Silent	A	77237533	G	A	77237533	5	1	259	1	0	0	0	0	0	0	1	0	17140	1275	44	3	409	3	VASH1	14	77237533	Splice_Site	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	800029	77237533	30112007	630	36948										
KIAA1737	85457	hgsc.bcm.edu	37	chr14	77580248	77580248	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gtctgaccttcgcttcccccGccagtcctgtctgcgcatca	8	18	3	1	rs201665496		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:77580248G>T	ENST00000361786.2	+	4	1104	c.787G>T	c.(787-789)Gcc>Tcc	p.A263S	RP11-463C8.4_ENST00000557752.1_Intron	NM_033426.2	NP_219494.2	Q9C0C6	CIPC_HUMAN		263					negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(2)|lung(4)|prostate(3)	9			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0284)		CGCTTCCCCCGCCAGTCCTGT	0.572																																					p.A263S		Atlas-SNP	.											KIAA1737,NS,carcinoma,0,1	KIAA1737	26	.	0			c.G787T						.						86	73	78					14																	77580248		2203	4300	6503	SO:0001583	missense	85457	exon4			TCCCCCGCCAGTC																												ENST00000361786.2:c.787G>T	chr14.hg19:g.77580248G>T	ENSP00000355319:p.Ala263Ser	83.0	0.0		71.0	3.0	NM_033426	B2RCI1|Q8N389|Q8NDZ1	Missense_Mutation	SNP	ENST00000361786.2	hg19	CCDS9855.1	.	.	.	.	.	.	.	.	.	.	G	15.03	2.712699	0.48517	.	.	ENSG00000198894	ENST00000361786	T	0.32023	1.47	5.58	4.63	0.57726	.	0.505693	0.21867	N	0.067941	T	0.32912	0.0845	L	0.51422	1.61	0.40028	D	0.975499	D;D	0.53312	0.959;0.959	P;P	0.51385	0.668;0.668	T	0.01956	-1.1240	10	0.14252	T	0.57	-22.2881	8.9275	0.35650	0.0:0.1491:0.6748:0.1761	.	263;165	Q9C0C6;B3KU75	K1737_HUMAN;.	S	263	ENSP00000355319:A263S	ENSP00000355319:A263S	A	+	1	0	KIAA1737	76650001	0.999000	0.42202	0.996000	0.52242	0.995000	0.86356	2.124000	0.42006	2.792000	0.96026	0.555000	0.69702	GCC	.	G|1.000;C|0.000		0.572	KIAA1737-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414278.1			T	77580248	G	T	77580248	3	4	259	1	0	0	0	0	1	0	0	0	8264	1087	38	1	797	1	KIAA1737	14	77580248	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	342715	77580248	29769292	631	36949										
POMT2	29954	hgsc.bcm.edu	37	chr14	77746806	77746806	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gggtttgaggccactgttccCctgcatgaaggtagcaaaga	13	9	0	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:77746806C>A	ENST00000261534.4	-	16	1856	c.1654G>T	c.(1654-1656)Ggg>Tgg	p.G552W		NM_013382.5	NP_037514.2	Q9UKY4	POMT2_HUMAN	protein-O-mannosyltransferase 2	552						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	dolichyl-phosphate-mannose-protein mannosyltransferase activity (GO:0004169)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|large_intestine(1)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	14			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0292)		CCACTGTTCCCCTGCATGAAG	0.537																																					p.G552W		Atlas-SNP	.											.	POMT2	47	.	0			c.G1654T						.						156	137	143					14																	77746806		2203	4300	6503	SO:0001630	splice_region_variant	29954	exon16			TGTTCCCCTGCAT	AF105020	CCDS9857.1	14q24	2014-09-17			ENSG00000009830	ENSG00000009830	2.4.1.109	"Dolichyl D-mannosyl phosphate dependent mannosyltransferases"	19743	protein-coding gene	gene with protein product		607439				11162531, 12460945	Standard	NM_013382		Approved	LGMD2N	uc001xti.2	Q9UKY4	OTTHUMG00000171556	ENST00000261534.4:c.1654-1G>T	chr14.hg19:g.77746806C>A		256.0	0.0		166.0	83.0	NM_013382	Q9NSG6|Q9P1W0|Q9P1W2	Missense_Mutation	SNP	ENST00000261534.4	hg19	CCDS9857.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.085253	0.76642	.	.	ENSG00000009830	ENST00000261534	D	0.92348	-3.02	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	D	0.95890	0.8662	M	0.74881	2.28	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.94854	0.8016	10	0.38643	T	0.18	-13.1538	19.3746	0.94503	0.0:1.0:0.0:0.0	.	552	Q9UKY4	POMT2_HUMAN	W	552	ENSP00000261534:G552W	ENSP00000261534:G552W	G	-	1	0	POMT2	76816559	1.000000	0.71417	1.000000	0.80357	0.844000	0.47949	4.756000	0.62205	2.584000	0.87258	0.563000	0.77884	GGG	.	.		0.537	POMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414155.1	NM_013382	Missense_Mutation	A	77746806	C	A	77746806	5	1	259	1	0	0	0	0	0	0	1	0	12255	637	22	3	622	3	POMT2	14	77746806	Splice_Site	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	166558	77746806	29602734	632	36950										
STON2	85439	hgsc.bcm.edu	37	chr14	81744156	81744156	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tataggtgacacggtctatcCgcaagctgtggattctgcca	11	10	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:81744156C>A	ENST00000267540.2	-	4	1699	c.1499G>T	c.(1498-1500)cGg>cTg	p.R500L	STON2_ENST00000556280.1_5'Flank|STON2_ENST00000555447.1_Missense_Mutation_p.R500L	NM_033104.3	NP_149095.2	Q8WXE9	STON2_HUMAN	stonin 2	500	SHD. {ECO:0000255|PROSITE- ProRule:PRU00403}.				hematopoietic progenitor cell differentiation (GO:0002244)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleolus (GO:0005730)|synaptic vesicle (GO:0008021)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|pancreas(2)|prostate(1)|skin(5)	34				BRCA - Breast invasive adenocarcinoma(234;0.0348)		ACGGTCTATCCGCAAGCTGTG	0.488																																					p.R500L		Atlas-SNP	.											.	STON2	94	.	0			c.G1499T						.						96	101	99					14																	81744156		2203	4300	6503	SO:0001583	missense	85439	exon6			TCTATCCGCAAGC	AB208948	CCDS9875.1, CCDS58332.1	14q31.1	2007-08-01				ENSG00000140022			30652	protein-coding gene	gene with protein product	"stoned B homolog 2 (Drosophila)"	608467				11381094, 11454741	Standard	NM_033104		Approved	STNB2, STN2	uc001xvk.2	Q8WXE9		ENST00000267540.2:c.1499G>T	chr14.hg19:g.81744156C>A	ENSP00000267540:p.Arg500Leu	131.0	0.0		113.0	5.0	NM_001256430	G3V2T7|Q17R24|Q59H11|Q6NT47|Q96RI7|Q96RU6	Missense_Mutation	SNP	ENST00000267540.2	hg19	CCDS9875.1	.	.	.	.	.	.	.	.	.	.	C	19.88	3.908774	0.72868	.	.	ENSG00000140022	ENST00000555447;ENST00000546306;ENST00000267540	T;T	0.14640	2.49;2.49	6.17	6.17	0.99709	Stonin homology (1);	0.059063	0.64402	D	0.000004	T	0.33760	0.0874	L	0.44542	1.39	0.50313	D	0.999862	D;D	0.76494	0.998;0.999	D;D	0.72075	0.946;0.976	T	0.00380	-1.1776	10	0.87932	D	0	-21.9223	20.8794	0.99867	0.0:1.0:0.0:0.0	.	500;500	Q8WXE9;G3V2T7	STON2_HUMAN;.	L	500;512;500	ENSP00000450857:R500L;ENSP00000267540:R500L	ENSP00000267540:R500L	R	-	2	0	STON2	80813909	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.938000	0.70170	2.941000	0.99782	0.655000	0.94253	CGG	.	.		0.488	STON2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413317.1	NM_033104		A	81744156	C	A	81744156	3	1	259	1	0	0	0	0	1	0	0	0	15333	652	23	1	1224	1	STON2	14	81744156	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	3997350	81744156	25605384	633	36951										
CPSF2	53981	hgsc.bcm.edu	37	chr14	92624221	92624221	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgccactagtgaaactcacaTctaccaggtaaacatgccag	7	12	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:92624221T>C	ENST00000298875.4	+	13	2099	c.1814T>C	c.(1813-1815)aTc>aCc	p.I605T		NM_017437.2	NP_059133.1	Q9P2I0	CPSF2_HUMAN	cleavage and polyadenylation specific factor 2, 100kDa	605					gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)|mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	RNA binding (GO:0003723)			breast(2)|cervix(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	24		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.222)		GAAACTCACATCTACCAGGTA	0.423																																					p.I605T	Ovarian(78;28 1788 18702 44111)	Atlas-SNP	.											.	CPSF2	63	.	0			c.T1814C						.						62	63	62					14																	92624221		2203	4300	6503	SO:0001583	missense	53981	exon13			CTCACATCTACCA	AB037788	CCDS9902.1	14q31.1	2008-07-28	2002-08-29			ENSG00000165934			2325	protein-coding gene	gene with protein product		606028	"cleavage and polyadenylation specific factor 2, 100kD subunit"			7969155, 11124543	Standard	NM_017437		Approved	KIAA1367	uc001yah.2	Q9P2I0		ENST00000298875.4:c.1814T>C	chr14.hg19:g.92624221T>C	ENSP00000298875:p.Ile605Thr	99.0	0.0		87.0	4.0	NM_017437	B3KME1|Q6NSJ1|Q9H3W7	Missense_Mutation	SNP	ENST00000298875.4	hg19	CCDS9902.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.64|19.64	3.865938|3.865938	0.71949|0.71949	.|.	.|.	ENSG00000165934|ENSG00000165934	ENST00000298875|ENST00000555244	T|.	0.46063|.	0.88|.	5.74|5.74	5.74|5.74	0.90152|0.90152	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.75406|0.75406	0.3845|0.3845	M|M	0.74647|0.74647	2.275|2.275	0.80722|0.80722	D|D	1|1	P|.	0.46457|.	0.878|.	P|.	0.51079|.	0.658|.	T|T	0.75693|0.75693	-0.3229|-0.3229	10|5	0.38643|.	T|.	0.18|.	.|.	16.0499|16.0499	0.80749|0.80749	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	605|.	Q9P2I0|.	CPSF2_HUMAN|.	T|P	605|122	ENSP00000298875:I605T|.	ENSP00000298875:I605T|.	I|S	+|+	2|1	0|0	CPSF2|CPSF2	91693974|91693974	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.836000|0.836000	0.47400|0.47400	7.946000|7.946000	0.87746|0.87746	2.193000|2.193000	0.70182|0.70182	0.533000|0.533000	0.62120|0.62120	ATC|TCT	.	.		0.423	CPSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412123.1			C	92624221	T	C	92624221	3	2	259	1	0	0	0	0	1	0	0	0	3827	1435	50	2	1856	2	CPSF2	14	92624221	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	10880065	92624221	14725319	634	36952										
CYP46A1	10858	hgsc.bcm.edu	37	chr14	100192567	100192567	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccttctccctgggccaccgcTcctgcatcgggcagcagttt	10	17	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:100192567T>C	ENST00000261835.3	+	14	1410	c.1306T>C	c.(1306-1308)Tcc>Ccc	p.S436P	CYP46A1_ENST00000423126.2_Missense_Mutation_p.S339P|CYP46A1_ENST00000554176.1_Missense_Mutation_p.S273P	NM_006668.1	NP_006659.1	Q9Y6A2	CP46A_HUMAN	cytochrome P450, family 46, subfamily A, polypeptide 1	436					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cholesterol catabolic process (GO:0006707)|nervous system development (GO:0007399)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	cholesterol 24-hydroxylase activity (GO:0033781)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid hydroxylase activity (GO:0008395)			breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|prostate(1)|skin(1)	25		Melanoma(154;0.0866)|all_epithelial(191;0.179)				GGGCCACCGCTCCTGCATCGG	0.642																																					p.S436P		Atlas-SNP	.											.	CYP46A1	62	.	0			c.T1306C						.						64	60	61					14																	100192567		2203	4300	6503	SO:0001583	missense	10858	exon14			CACCGCTCCTGCA	AF094480	CCDS9954.1	14q32.2	2013-05-03	2003-02-14	2003-02-28	ENSG00000036530	ENSG00000036530		"Cytochrome P450s"	2641	protein-coding gene	gene with protein product		604087	"cytochrome P450, subfamily 46 (cholesterol 24-hydroxylase)"	CYP46		10377398	Standard	NM_006668		Approved		uc001ygo.3	Q9Y6A2	OTTHUMG00000171510	ENST00000261835.3:c.1306T>C	chr14.hg19:g.100192567T>C	ENSP00000261835:p.Ser436Pro	125.0	0.0		74.0	4.0	NM_006668	B4DHP8|E7EQG9|Q8N2B0	Missense_Mutation	SNP	ENST00000261835.3	hg19	CCDS9954.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.00|19.00	3.741777|3.741777	0.69304|0.69304	.|.	.|.	ENSG00000036530|ENSG00000036530	ENST00000380228|ENST00000261835;ENST00000423126;ENST00000554176	.|T;T;T	.|0.69685	.|-0.42;-0.42;-0.42	3.68|3.68	3.68|3.68	0.42216|0.42216	.|Cytochrome P450, conserved site (1);	.|0.127312	.|0.53938	.|D	.|0.000044	T|T	0.79034|0.79034	0.4378|0.4378	M|M	0.78916|0.78916	2.43|2.43	0.44181|0.44181	D|D	0.996997|0.996997	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.79784	.|0.993;0.991	T|T	0.80580|0.80580	-0.1319|-0.1319	5|10	.|0.72032	.|D	.|0.01	.|.	9.2929|9.2929	0.37797|0.37797	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|273;436	.|Q8N2B0;Q9Y6A2	.|.;CP46A_HUMAN	P|P	422|436;339;273	.|ENSP00000261835:S436P;ENSP00000405779:S339P;ENSP00000450553:S273P	.|ENSP00000261835:S436P	L|S	+|+	2|1	0|0	CYP46A1|CYP46A1	99262320|99262320	0.998000|0.998000	0.40836|0.40836	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	1.246000|1.246000	0.32803|0.32803	1.623000|1.623000	0.50342|0.50342	0.459000|0.459000	0.35465|0.35465	CTC|TCC	.	.		0.642	CYP46A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413814.1			C	100192567	T	C	100192567	3	2	259	1	0	0	0	0	1	0	0	0	4184	1551	54	2	1360	2	CYP46A1	14	100192567	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	7568346	100192567	7156973	635	36953										
DLK1	8788	hgsc.bcm.edu	37	chr14	101201179	101201179	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gccgtcaacatcatcttcccCgagaagatcgacatgaccac	7	15	3	3	rs150069528	byFrequency	TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:101201179C>A	ENST00000341267.4	+	5	1340	c.1098C>A	c.(1096-1098)ccC>ccA	p.P366P	RP11-566J3.4_ENST00000608876.1_lincRNA|DLK1_ENST00000331224.6_Silent_p.P293P	NM_003836.5	NP_003827	P80370	DLK1_HUMAN	delta-like 1 homolog (Drosophila)	366					cell differentiation (GO:0030154)|embryonic skeletal system development (GO:0048706)|multicellular organismal development (GO:0007275)|negative regulation of Notch signaling pathway (GO:0045746)|Notch signaling pathway (GO:0007219)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)	external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(16)|ovary(2)|prostate(1)|skin(1)	29		Melanoma(154;0.155)				TCATCTTCCCCGAGAAGATCG	0.577																																					p.P366P		Atlas-SNP	.											DLK1,NS,carcinoma,0,1	DLK1	57	.	0			c.C1098A						.						97	94	95					14																	101201179		2203	4300	6503	SO:0001819	synonymous_variant	8788	exon5			CTTCCCCGAGAAG	U15979	CCDS9963.1	14q32	2011-12-05	2001-12-03			ENSG00000185559			2907	protein-coding gene	gene with protein product		176290	"delta-like homolog (Drosophila)"			8095043, 7925474	Standard	NM_003836		Approved	FA1, pG2, Pref-1, ZOG, Delta1	uc001yhs.4	P80370		ENST00000341267.4:c.1098C>A	chr14.hg19:g.101201179C>A		32.0	0.0		25.0	2.0	NM_003836	P15803|Q96DW5	Silent	SNP	ENST00000341267.4	hg19	CCDS9963.1																																																																																			.	C|0.999;T|0.001		0.577	DLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414389.1			A	101201179	C	A	101201179	2	1	259	1	0	0	0	0	0	0	0	1	4566	639	23	1		1	DLK1	14	101201179	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	1008612	101201179	6148361	636	36954										
DYNC1H1	1778	hgsc.bcm.edu	37	chr14	102452814	102452814	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cacactatccaaagaagtccGgaacctcaaatggcttggtt	8	11	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:102452814G>T	ENST00000360184.4	+	8	2416	c.2252G>T	c.(2251-2253)cGg>cTg	p.R751L		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	751	Interaction with DYNC1LI2. {ECO:0000250}.|Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						AAAGAAGTCCGGAACCTCAAA	0.483																																					p.R751L		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.G2252T						.						94	86	89					14																	102452814		2203	4300	6503	SO:0001583	missense	1778	exon8			AAGTCCGGAACCT	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"Cytoplasmic dyneins"	2961	protein-coding gene	gene with protein product		600112	"dynein, cytoplasmic, heavy polypeptide 1"	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.2252G>T	chr14.hg19:g.102452814G>T	ENSP00000348965:p.Arg751Leu	93.0	0.0		92.0	4.0	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	hg19	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.025019	0.93518	.	.	ENSG00000197102	ENST00000360184	T	0.61742	0.08	5.6	5.6	0.85130	Dynein heavy chain, domain-1 (1);	0.000000	0.85682	D	0.000000	D	0.83248	0.5213	M	0.93720	3.45	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.87242	0.2267	10	0.87932	D	0	.	19.6087	0.95589	0.0:0.0:1.0:0.0	.	751	Q14204	DYHC1_HUMAN	L	751	ENSP00000348965:R751L	ENSP00000348965:R751L	R	+	2	0	DYNC1H1	101522567	1.000000	0.71417	0.984000	0.44739	0.992000	0.81027	9.471000	0.97696	2.639000	0.89480	0.655000	0.94253	CGG	.	.		0.483	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		T	102452814	G	T	102452814	3	4	259	1	0	0	0	0	1	0	0	0	4843	1116	39	1	2282	1	DYNC1H1	14	102452814	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1251635	102452814	4896726	637	36955										
BAG5	9529	hgsc.bcm.edu	37	chr14	104026834	104026834	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gagcatccaggtcagcgatcAgccccgagagcacacaggat	12	13	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:104026834A>G	ENST00000445922.2	-	2	914	c.668T>C	c.(667-669)cTg>cCg	p.L223P	BAG5_ENST00000337322.4_Missense_Mutation_p.L264P|RP11-73M18.2_ENST00000472726.2_5'Flank|APOPT1_ENST00000556253.2_5'Flank|RP11-894P9.2_ENST00000556332.1_RNA|APOPT1_ENST00000247618.4_5'Flank|APOPT1_ENST00000409074.2_5'Flank|BAG5_ENST00000299204.4_Missense_Mutation_p.L223P	NM_004873.3	NP_004864.1	Q9UL15	BAG5_HUMAN	BCL2-associated athanogene 5	223	BAG 3. {ECO:0000255|PROSITE- ProRule:PRU00369}.				negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein refolding (GO:0061084)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|neuron death (GO:0070997)|protein folding (GO:0006457)|regulation of inclusion body assembly (GO:0090083)	inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	chaperone binding (GO:0051087)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)			endometrium(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(2)|skin(2)|urinary_tract(2)	24		Melanoma(154;0.155)	Epithelial(46;0.144)			GTCAGCGATCAGCCCCGAGAG	0.488																																					p.L264P	NSCLC(171;1832 2055 18950 31566 41632)	Atlas-SNP	.											.	BAG5	47	.	0			c.T791C						.						117	109	112					14																	104026834		2203	4300	6503	SO:0001583	missense	9529	exon2			GCGATCAGCCCCG	AF095195	CCDS9982.1, CCDS41995.1	14q32	2008-08-01				ENSG00000166170			941	protein-coding gene	gene with protein product		603885				9873016, 15603737	Standard	NM_001015048		Approved		uc001ynh.2	Q9UL15		ENST00000445922.2:c.668T>C	chr14.hg19:g.104026834A>G	ENSP00000391713:p.Leu223Pro	146.0	0.0		98.0	4.0	NM_001015049	O94950|Q86W59	Missense_Mutation	SNP	ENST00000445922.2	hg19	CCDS9982.1	.	.	.	.	.	.	.	.	.	.	A	14.68	2.608216	0.46527	.	.	ENSG00000166170	ENST00000299204;ENST00000445922;ENST00000337322	D;D;D	0.89485	-2.52;-2.52;-2.52	5.76	5.76	0.90799	BAG domain (3);	0.224733	0.37219	N	0.002186	D	0.90277	0.6959	L	0.27053	0.805	0.80722	D	1	P;D	0.67145	0.921;0.996	P;D	0.65233	0.906;0.933	D	0.91816	0.5463	10	0.87932	D	0	-10.7038	16.0833	0.81020	1.0:0.0:0.0:0.0	.	223;264	Q9UL15;Q9UL15-2	BAG5_HUMAN;.	P	223;223;264	ENSP00000299204:L223P;ENSP00000391713:L223P;ENSP00000338814:L264P	ENSP00000299204:L223P	L	-	2	0	BAG5	103096587	1.000000	0.71417	0.322000	0.25334	0.016000	0.09150	8.158000	0.89649	2.202000	0.70862	0.533000	0.62120	CTG	.	.		0.488	BAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414990.1			G	104026834	A	G	104026834	3	3	259	1	0	0	0	0	1	0	0	0	1290	188	7	2	679	2	BAG5	14	104026834	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1574020	104026834	3322706	638	36956										
THBS1	7057	hgsc.bcm.edu	37	chr15	39886308	39886308	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cttttccttcaggtgcgcacCctgtggcatgaccctcgtca	9	15	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:39886308C>A	ENST00000260356.5	+	20	3441	c.3276C>A	c.(3274-3276)acC>acA	p.T1092T	CTD-2033D15.1_ENST00000560769.1_RNA	NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	1092	TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		AGGTGCGCACCCTGTGGCATG	0.463																																					p.T1092T		Atlas-SNP	.											.	THBS1	106	.	0			c.C3276A						.						56	54	55					15																	39886308		2200	4297	6497	SO:0001819	synonymous_variant	7057	exon20			GCGCACCCTGTGG		CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"thrombospondin-1p180"	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.3276C>A	chr15.hg19:g.39886308C>A		122.0	0.0		103.0	5.0	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Silent	SNP	ENST00000260356.5	hg19	CCDS32194.1																																																																																			.	.		0.463	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246		A	39886308	C	A	39886308	2	1	259	1	0	0	0	0	0	0	0	1	15868	610	22	3		3	THBS1	15	39886308	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10		39886308	62645084	639	36957										
IVD	3712	hgsc.bcm.edu	37	chr15	40700141	40700141	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctccattctgttggcaggaaTtttggaagcagctggggaac	13	8	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:40700141T>C	ENST00000249760.2	+	3	581	c.238T>C	c.(238-240)Ttt>Ctt	p.F80L	IVD_ENST00000479013.2_Missense_Mutation_p.F53L|IVD_ENST00000490194.1_3'UTR|IVD_ENST00000487418.2_Missense_Mutation_p.F83L	NM_002225.3	NP_002216.2	P26440	IVD_HUMAN	isovaleryl-CoA dehydrogenase	80					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	flavin adenine dinucleotide binding (GO:0050660)|isovaleryl-CoA dehydrogenase activity (GO:0008470)			kidney(1)|lung(5)|ovary(2)|prostate(1)	9		all_cancers(109;1.19e-18)|all_epithelial(112;1.52e-15)|Lung NSC(122;5.14e-11)|all_lung(180;1.27e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.65e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0808)	Flavin adenine dinucleotide(DB03147)	TTGGCAGGAATTTTGGAAGCA	0.488																																					p.F83L	GBM(31;293 617 7486 32527 34655)	Atlas-SNP	.											.	IVD	29	.	0			c.T247C						.						98	98	98					15																	40700141		2203	4300	6503	SO:0001583	missense	3712	exon3			CAGGAATTTTGGA	AF038317	CCDS10057.1, CCDS10057.2, CCDS53930.1	15q14-q15	2010-05-11	2010-05-11		ENSG00000128928	ENSG00000128928	1.3.99.10		6186	protein-coding gene	gene with protein product		607036	"isovaleryl Coenzyme A dehydrogenase", "isovaleryl CoA dehydrogenase"			2063866	Standard	NM_002225		Approved	ACAD2	uc001zls.3	P26440	OTTHUMG00000129984	ENST00000249760.2:c.238T>C	chr15.hg19:g.40700141T>C	ENSP00000249760:p.Phe80Leu	81.0	0.0		74.0	4.0	NM_002225	B2RCV5|B3KVI7|J3KR54|Q53XZ9|Q96AF6	Missense_Mutation	SNP	ENST00000249760.2	hg19		.	.	.	.	.	.	.	.	.	.	T	11.87	1.767821	0.31320	.	.	ENSG00000128928	ENST00000249760;ENST00000479013;ENST00000487418	D;D;D	0.98493	-4.96;-4.96;-4.96	5.8	5.8	0.92144	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase, N-terminal (1);Acyl-CoA dehydrogenase/oxidase, N-terminal (1);	0.045148	0.85682	D	0.000000	D	0.97356	0.9135	L	0.28649	0.875	0.80722	D	1	D;B	0.63046	0.992;0.01	D;B	0.68192	0.956;0.03	D	0.95386	0.8477	10	0.02654	T	1	.	16.1549	0.81657	0.0:0.0:0.0:1.0	.	80;53	P26440;B3KVI7	IVD_HUMAN;.	L	80;53;83	ENSP00000249760:F80L;ENSP00000417990:F53L;ENSP00000418397:F83L	ENSP00000249760:F80L	F	+	1	0	IVD	38487433	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.375000	0.79646	2.209000	0.71365	0.533000	0.62120	TTT	.	.		0.488	IVD-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding				C	40700141	T	C	40700141	3	2	259	1	0	0	0	0	1	0	0	0	7937	1493	52	2	257	2	IVD	15	40700141	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	813833	40700141	61831251	640	36958										
GATM	2628	hgsc.bcm.edu	37	chr15	45658625	45658625	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aatgaagtcagcagcatcaaAgcatggctcaaactcagttg	9	9	4	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:45658625A>G	ENST00000396659.3	-	5	1096	c.757T>C	c.(757-759)Ttt>Ctt	p.F253L	GATM_ENST00000558336.1_Missense_Mutation_p.F253L	NM_001482.2	NP_001473.1	P50440	GATM_HUMAN	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	253					cellular nitrogen compound metabolic process (GO:0034641)|creatine biosynthetic process (GO:0006601)|creatine metabolic process (GO:0006600)|embryo development (GO:0009790)|response to mercury ion (GO:0046689)|response to nutrient (GO:0007584)|response to oxidative stress (GO:0006979)|response to peptide hormone (GO:0043434)|small molecule metabolic process (GO:0044281)|tissue regeneration (GO:0042246)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)	glycine amidinotransferase activity (GO:0015068)|hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines (GO:0016813)			biliary_tract(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(6)|prostate(2)|skin(1)|urinary_tract(1)	15		all_cancers(109;1.25e-09)|all_epithelial(112;5.56e-08)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;4.87e-16)|GBM - Glioblastoma multiforme(94;1.97e-06)	Glycine(DB00145)|L-Ornithine(DB00129)	GCAGCATCAAAGCATGGCTCA	0.418																																					p.F253L		Atlas-SNP	.											.	GATM	34	.	0			c.T757C						.						80	75	77					15																	45658625		2198	4298	6496	SO:0001583	missense	2628	exon5			CATCAAAGCATGG	S68805	CCDS10122.1	15q15.1	2007-12-06			ENSG00000171766	ENSG00000171766	2.1.4.1		4175	protein-coding gene	gene with protein product		602360				8313955	Standard	NM_001482		Approved	AGAT	uc001zvc.3	P50440	OTTHUMG00000131427	ENST00000396659.3:c.757T>C	chr15.hg19:g.45658625A>G	ENSP00000379895:p.Phe253Leu	103.0	0.0		86.0	4.0	NM_001482	B4DH99|B4DPI3|Q53EQ4	Missense_Mutation	SNP	ENST00000396659.3	hg19	CCDS10122.1	.	.	.	.	.	.	.	.	.	.	A	32	5.128614	0.94473	.	.	ENSG00000171766	ENST00000396659	T	0.31247	1.5	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.64929	0.2643	M	0.93462	3.42	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.73059	-0.4102	10	0.49607	T	0.09	-13.2515	13.7457	0.62874	1.0:0.0:0.0:0.0	.	253;253	P50440-3;P50440	.;GATM_HUMAN	L	253	ENSP00000379895:F253L	ENSP00000379895:F253L	F	-	1	0	GATM	43445917	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.619000	0.90938	2.126000	0.65437	0.533000	0.62120	TTT	.	.		0.418	GATM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254220.2	NM_001482		G	45658625	A	G	45658625	3	3	259	1	0	0	0	0	1	0	0	0	6271	72	3	2	534	2	GATM	15	45658625	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	4958484	45658625	56872767	641	36959										
GATM	2628	hgsc.bcm.edu	37	chr15	45658705	45658705	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctacagagtggatgggataaTcctaattggaacaagaatga	11	5	0	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:45658705T>C	ENST00000396659.3	-	5	1016	c.677A>G	c.(676-678)gAt>gGt	p.D226G	GATM_ENST00000558336.1_Splice_Site_p.D226G	NM_001482.2	NP_001473.1	P50440	GATM_HUMAN	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	226					cellular nitrogen compound metabolic process (GO:0034641)|creatine biosynthetic process (GO:0006601)|creatine metabolic process (GO:0006600)|embryo development (GO:0009790)|response to mercury ion (GO:0046689)|response to nutrient (GO:0007584)|response to oxidative stress (GO:0006979)|response to peptide hormone (GO:0043434)|small molecule metabolic process (GO:0044281)|tissue regeneration (GO:0042246)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)	glycine amidinotransferase activity (GO:0015068)|hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines (GO:0016813)			biliary_tract(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(6)|prostate(2)|skin(1)|urinary_tract(1)	15		all_cancers(109;1.25e-09)|all_epithelial(112;5.56e-08)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;4.87e-16)|GBM - Glioblastoma multiforme(94;1.97e-06)	Glycine(DB00145)|L-Ornithine(DB00129)	GATGGGATAATCCTAATTGGA	0.378																																					p.D226G		Atlas-SNP	.											.	GATM	34	.	0			c.A677G						.						65	62	63					15																	45658705		2198	4298	6496	SO:0001630	splice_region_variant	2628	exon5			GGATAATCCTAAT	S68805	CCDS10122.1	15q15.1	2007-12-06			ENSG00000171766	ENSG00000171766	2.1.4.1		4175	protein-coding gene	gene with protein product		602360				8313955	Standard	NM_001482		Approved	AGAT	uc001zvc.3	P50440	OTTHUMG00000131427	ENST00000396659.3:c.676-1A>G	chr15.hg19:g.45658705T>C		70.0	0.0		68.0	4.0	NM_001482	B4DH99|B4DPI3|Q53EQ4	Missense_Mutation	SNP	ENST00000396659.3	hg19	CCDS10122.1	.	.	.	.	.	.	.	.	.	.	T	14.32	2.499050	0.44455	.	.	ENSG00000171766	ENST00000396659	T	0.48836	0.8	5.61	4.48	0.54585	.	0.356955	0.35235	N	0.003355	T	0.35799	0.0944	L	0.28344	0.845	0.44085	D	0.996844	B;B	0.14438	0.01;0.0	B;B	0.23419	0.046;0.0	T	0.10474	-1.0628	10	0.42905	T	0.14	-3.9467	11.1585	0.48501	0.0:0.0:0.1546:0.8454	.	226;226	P50440-3;P50440	.;GATM_HUMAN	G	226	ENSP00000379895:D226G	ENSP00000379895:D226G	D	-	2	0	GATM	43445997	1.000000	0.71417	0.980000	0.43619	0.994000	0.84299	4.623000	0.61247	0.941000	0.37499	-0.291000	0.09656	GAT	.	.		0.378	GATM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254220.2	NM_001482	Missense_Mutation	C	45658705	T	C	45658705	5	2	259	1	0	0	0	0	0	0	1	0	6271	1449	50	2	614	2	GATM	15	45658705	Splice_Site	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	80	45658705	56872687	642	36960										
MYEF2	50804	hgsc.bcm.edu	37	chr15	48441407	48441407	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggagcctattctctctctcaTtccgcttcccattggacccg	7	16	3	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:48441407T>C	ENST00000324324.7	-	15	1819	c.1540A>G	c.(1540-1542)Atg>Gtg	p.M514V	MYEF2_ENST00000267836.6_Missense_Mutation_p.M490V	NM_016132.3	NP_057216	Q9P2K5	MYEF2_HUMAN	myelin expression factor 2	514	Gly-rich.				myotube differentiation (GO:0014902)|neuron differentiation (GO:0030182)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(1)|large_intestine(8)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	31		all_lung(180;0.00217)		all cancers(107;3.73e-10)|GBM - Glioblastoma multiforme(94;7.81e-07)		CTCTCTCTCATTCCGCTTCCC	0.373																																					p.M514V		Atlas-SNP	.											.	MYEF2	67	.	0			c.A1540G						.						117	117	117					15																	48441407		2198	4296	6494	SO:0001583	missense	50804	exon15			CTCTCATTCCGCT	AB037762	CCDS32230.1, CCDS73722.1	15q15.1	2013-07-16				ENSG00000104177		"RNA binding motif (RRM) containing"	17940	protein-coding gene	gene with protein product						10718198, 2601707	Standard	XM_005254422		Approved	MEF-2, FLJ11213, KIAA1341, HsT18564	uc001zwi.4	Q9P2K5		ENST00000324324.7:c.1540A>G	chr15.hg19:g.48441407T>C	ENSP00000316950:p.Met514Val	132.0	0.0		121.0	5.0	NM_016132	A7MCZ9|C9J921|C9K0J4|Q6NUM5|Q7L388|Q7Z4B7|Q9H922|Q9NUQ1	Missense_Mutation	SNP	ENST00000324324.7	hg19	CCDS32230.1	.	.	.	.	.	.	.	.	.	.	T	9.310	1.055438	0.19907	.	.	ENSG00000104177	ENST00000324324;ENST00000267836;ENST00000454655	T;T	0.21361	2.62;2.01	4.69	3.53	0.40419	Nucleotide-binding, alpha-beta plait (1);	0.169530	0.64402	D	0.000005	T	0.12732	0.0309	L	0.29908	0.895	0.37790	D	0.927338	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.14309	-1.0477	10	0.16896	T	0.51	-2.7258	7.2769	0.26290	0.1445:0.0:0.1509:0.7046	.	490;514	Q9P2K5-2;Q9P2K5	.;MYEF2_HUMAN	V	514;490;102	ENSP00000316950:M514V;ENSP00000267836:M490V	ENSP00000267836:M490V	M	-	1	0	MYEF2	46228699	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.995000	0.40767	0.861000	0.35504	0.482000	0.46254	ATG	.	.		0.373	MYEF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416909.2	NM_016132		C	48441407	T	C	48441407	3	2	259	1	0	0	0	0	1	0	0	0	10033	1493	52	2	274	2	MYEF2	15	48441407	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	2782702	48441407	54089985	643	36961										
FBN1	2200	hgsc.bcm.edu	37	chr15	48756205	48756205	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccacagattccaggagtctcAcattcattcacatctataat	4	12	4	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:48756205A>T	ENST00000316623.5	-	41	5411	c.4956T>A	c.(4954-4956)tgT>tgA	p.C1652*		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	1652	EGF-like 28; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		CAGGAGTCTCACATTCATTCA	0.408																																					p.C1652X		Atlas-SNP	.											.	FBN1	310	.	0			c.T4956A						.						123	108	113					15																	48756205		2198	4296	6494	SO:0001587	stop_gained	2200	exon41			AGTCTCACATTCA	X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.4956T>A	chr15.hg19:g.48756205A>T	ENSP00000325527:p.Cys1652*	103.0	0.0		98.0	4.0	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Nonsense_Mutation	SNP	ENST00000316623.5	hg19	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	a	28.1	4.887605	0.91814	.	.	ENSG00000166147	ENST00000316623;ENST00000389087;ENST00000544030	.	.	.	5.73	2.17	0.27698	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.4485	0.38712	0.7952:0.0:0.2048:0.0	.	.	.	.	X	1652;220;542	.	ENSP00000325527:C1652X	C	-	3	2	FBN1	46543497	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.187000	0.50950	0.523000	0.28482	-0.378000	0.06908	TGT	.	.		0.408	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			T	48756205	A	T	48756205	4	4	259	1	0	0	0	0	0	1	0	0	5710	157	6	4	3763	4	FBN1	15	48756205	Nonsense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	314798	48756205	53775187	644	36962										
ATP8B4	79895	hgsc.bcm.edu	37	chr15	50190396	50190396	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agcaaattacagtcttacacAtgcaagcaagttctaggaga	8	8	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:50190396A>G	ENST00000284509.6	-	22	2483	c.2342T>C	c.(2341-2343)aTg>aCg	p.M781T	ATP8B4_ENST00000559829.1_Missense_Mutation_p.M781T	NM_024837.2	NP_079113.2	Q8TF62	AT8B4_HUMAN	ATPase, class I, type 8B, member 4	781						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(6)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|urinary_tract(1)	73		all_lung(180;0.00183)		all cancers(107;2.41e-07)|GBM - Glioblastoma multiforme(94;8.28e-05)		AGTCTTACACATGCAAGCAAG	0.403																																					p.M781T		Atlas-SNP	.											.	ATP8B4	173	.	0			c.T2342C						.						131	116	121					15																	50190396		2196	4294	6490	SO:0001583	missense	79895	exon22			TTACACATGCAAG	AB075819	CCDS32238.1	15q21.2	2010-04-20	2007-09-19		ENSG00000104043	ENSG00000104043		"ATPases / P-type"	13536	protein-coding gene	gene with protein product		609123	"ATPase, Class I, type 8B, member 4"			11015572	Standard	NM_024837		Approved	ATPIM, KIAA1939	uc001zxu.3	Q8TF62		ENST00000284509.6:c.2342T>C	chr15.hg19:g.50190396A>G	ENSP00000284509:p.Met781Thr	129.0	0.0		150.0	6.0	NM_024837	Q9H727	Missense_Mutation	SNP	ENST00000284509.6	hg19	CCDS32238.1	.	.	.	.	.	.	.	.	.	.	A	9.964	1.223493	0.22457	.	.	ENSG00000104043	ENST00000284509	D	0.82344	-1.6	5.92	5.92	0.95590	HAD-like domain (1);	0.325157	0.35407	N	0.003227	T	0.78065	0.4225	L	0.33624	1.015	0.34704	D	0.727	B;B	0.33940	0.38;0.433	B;B	0.40901	0.343;0.297	T	0.79077	-0.1951	10	0.15066	T	0.55	.	14.3151	0.66443	1.0:0.0:0.0:0.0	.	1;781	B3KVY8;Q8TF62	.;AT8B4_HUMAN	T	781	ENSP00000284509:M781T	ENSP00000284509:M781T	M	-	2	0	ATP8B4	47977688	0.001000	0.12720	1.000000	0.80357	0.992000	0.81027	0.871000	0.28023	2.266000	0.75297	0.533000	0.62120	ATG	.	.		0.403	ATP8B4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418100.1	NM_024837		G	50190396	A	G	50190396	3	3	259	1	0	0	0	0	1	0	0	0	1197	217	8	2	1264	2	ATP8B4	15	50190396	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1434191	50190396	52340996	645	36963										
UNC13C	440279	hgsc.bcm.edu	37	chr15	54305696	54305696	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atgtgtctcctcagactcagAgttaagcaccatgaaaaaat	7	9	3	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:54305696A>G	ENST00000260323.11	+	1	596	c.596A>G	c.(595-597)gAg>gGg	p.E199G	UNC13C_ENST00000537900.1_Missense_Mutation_p.E199G|UNC13C_ENST00000545554.1_Missense_Mutation_p.E199G	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	199					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		TCAGACTCAGAGTTAAGCACC	0.453																																					p.E199G		Atlas-SNP	.											.	UNC13C	674	.	0			c.A596G						.						96	95	95					15																	54305696		1854	4084	5938	SO:0001583	missense	440279	exon1			ACTCAGAGTTAAG	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.596A>G	chr15.hg19:g.54305696A>G	ENSP00000260323:p.Glu199Gly	141.0	0.0		90.0	4.0	NM_001080534	Q0P613|Q8ND48|Q96NP3	Missense_Mutation	SNP	ENST00000260323.11	hg19	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	A	16.59	3.164540	0.57476	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	D;D;D	0.85258	-1.95;-1.96;-1.95	4.98	4.98	0.66077	.	.	.	.	.	D	0.87237	0.6127	L	0.32530	0.975	0.54753	D	0.999983	D	0.76494	0.999	D	0.80764	0.994	D	0.85496	0.1188	9	0.28530	T	0.3	.	13.8729	0.63631	1.0:0.0:0.0:0.0	.	199	Q8NB66	UN13C_HUMAN	G	199	ENSP00000260323:E199G;ENSP00000438156:E199G;ENSP00000442569:E199G	ENSP00000260323:E199G	E	+	2	0	UNC13C	52092988	1.000000	0.71417	0.998000	0.56505	0.592000	0.36648	9.261000	0.95576	1.854000	0.53819	0.533000	0.62120	GAG	.	.		0.453	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		G	54305696	A	G	54305696	3	3	259	1	0	0	0	0	1	0	0	0	17001	304	11	2	598	2	UNC13C	15	54305696	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	4115300	54305696	48225696	646	36964										
NEDD4	4734	hgsc.bcm.edu	37	chr15	56125247	56125247	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tcataggcacccgagatgtgCcagtgacaaactgaagtaat	10	9	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:56125247C>T	ENST00000508342.1	-	23	4042	c.3743G>A	c.(3742-3744)gGc>gAc	p.G1248D	NEDD4_ENST00000338963.2_Missense_Mutation_p.G1176D|NEDD4_ENST00000506154.1_Missense_Mutation_p.G1232D|NEDD4_ENST00000435532.3_Missense_Mutation_p.G829D	NM_001284338.1	NP_001271267.1	P46934	NEDD4_HUMAN	neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase	1248	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				adaptive immune response (GO:0002250)|blood vessel morphogenesis (GO:0048514)|cellular response to UV (GO:0034644)|cytokine-mediated signaling pathway (GO:0019221)|development involved in symbiotic interaction (GO:0044111)|endocardial cushion development (GO:0003197)|glucocorticoid receptor signaling pathway (GO:0042921)|lysosomal transport (GO:0007041)|negative regulation of sodium ion transport (GO:0010766)|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage (GO:0010768)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|neuromuscular junction development (GO:0007528)|neuron projection development (GO:0031175)|outflow tract morphogenesis (GO:0003151)|positive regulation of nucleocytoplasmic transport (GO:0046824)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|progesterone receptor signaling pathway (GO:0050847)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein targeting to lysosome (GO:0006622)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|receptor internalization (GO:0031623)|regulation of dendrite morphogenesis (GO:0048814)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of synapse organization (GO:0050807)|response to calcium ion (GO:0051592)|T cell activation (GO:0042110)|transmission of virus (GO:0019089)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	apicolateral plasma membrane (GO:0016327)|cell cortex (GO:0005938)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	beta-2 adrenergic receptor binding (GO:0031698)|ligase activity (GO:0016874)|phosphoserine binding (GO:0050815)|phosphothreonine binding (GO:0050816)|proline-rich region binding (GO:0070064)|protein domain specific binding (GO:0019904)|RNA polymerase binding (GO:0070063)|sodium channel inhibitor activity (GO:0019871)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	43				all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113)		CCGAGATGTGCCAGTGACAAA	0.348																																					p.G1176D		Atlas-SNP	.											.	NEDD4	167	.	0			c.G3527A						.						103	103	103					15																	56125247		2193	4292	6485	SO:0001583	missense	4734	exon20			GATGTGCCAGTGA	D42055	CCDS10156.1, CCDS45265.1, CCDS61643.1, CCDS61644.1	15q	2012-02-23	2012-02-23		ENSG00000069869	ENSG00000069869			7727	protein-coding gene	gene with protein product	"receptor-potentiating factor 1"	602278	"neural precursor cell expressed, developmentally down-regulated 4"			9073511, 8649367	Standard	XR_243101		Approved	KIAA0093, MGC176705, NEDD4-1, RPF1	uc002adi.3	P46934	OTTHUMG00000132015	ENST00000508342.1:c.3743G>A	chr15.hg19:g.56125247C>T	ENSP00000424827:p.Gly1248Asp	82.0	0.0		82.0	5.0	NM_198400	A1KY35|A6ND72|A7MD29|B4E2R7|B7ZM59|B7ZM60|B9EGN5|D6RF89	Missense_Mutation	SNP	ENST00000508342.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	33|33	5.263888|5.263888	0.95399|0.95399	.|.	.|.	ENSG00000069869|ENSG00000069869	ENST00000508871|ENST00000508342;ENST00000435532;ENST00000338963;ENST00000506154	.|T;T;T;T	.|0.73681	.|-0.77;-0.77;-0.77;-0.77	5.36|5.36	5.36|5.36	0.76844|0.76844	.|HECT (4);	.|0.049127	.|0.85682	.|D	.|0.000000	D|D	0.92743|0.92743	0.7693|0.7693	H|H	0.99726|0.99726	4.73|4.73	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.76494	.|0.994;0.991;0.998;0.999	.|P;D;D;D	.|0.68353	.|0.759;0.957;0.922;0.957	D|D	0.96066|0.96066	0.9042|0.9042	5|10	.|0.87932	.|D	.|0	.|.	18.0708|18.0708	0.89405|0.89405	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1232;829;1248;1176	.|P46934-2;P46934-4;P46934;P46934-3	.|.;.;NEDD4_HUMAN;.	T|D	839|1248;829;1176;1232	.|ENSP00000424827:G1248D;ENSP00000410613:G829D;ENSP00000345530:G1176D;ENSP00000422705:G1232D	.|ENSP00000345530:G1176D	A|G	-|-	1|2	0|0	NEDD4|NEDD4	53912539|53912539	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	7.754000|7.754000	0.85163|0.85163	2.513000|2.513000	0.84729|0.84729	0.557000|0.557000	0.71058|0.71058	GCA|GGC	.	.		0.348	NEDD4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000359817.1	NM_198400		T	56125247	C	T	56125247	3	4	259	1	0	0	0	0	1	0	0	0	10319	739	26	3	228	3	NEDD4	15	56125247	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	1819551	56125247	46406145	647	36965										
ZNF280D	54816	hgsc.bcm.edu	37	chr15	56924037	56924037	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttcactggagttgtgatcttTaatctgatcagataagatta	8	5	4	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:56924037T>C	ENST00000267807.7	-	22	2815	c.2599A>G	c.(2599-2601)Aaa>Gaa	p.K867E	RP11-1129I3.1_ENST00000562300.1_RNA|ZNF280D_ENST00000559237.1_Missense_Mutation_p.K854E	NM_017661.2	NP_060131.2	Q6N043	Z280D_HUMAN	zinc finger protein 280D	867					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(4)|large_intestine(7)|lung(12)|ovary(1)|skin(1)	30				all cancers(107;0.0399)|GBM - Glioblastoma multiforme(80;0.0787)		TTGTGATCTTTAATCTGATCA	0.323																																					p.K867E		Atlas-SNP	.											.	ZNF280D	82	.	0			c.A2599G						.						135	133	134					15																	56924037		2192	4291	6483	SO:0001583	missense	54816	exon22			GATCTTTAATCTG	AB046804	CCDS32245.1, CCDS42041.1, CCDS58364.1	15q21.2	2008-05-02	2007-09-20	2007-09-20					25953	protein-coding gene	gene with protein product			"suppressor of hairy wing homolog 4 (Drosophila)"	SUHW4		10997877	Standard	XM_005254481		Approved	FLJ20086, ZNF634	uc002adu.3	Q6N043		ENST00000267807.7:c.2599A>G	chr15.hg19:g.56924037T>C	ENSP00000267807:p.Lys867Glu	93.0	0.0		74.0	4.0	NM_017661	A1L495|B2RMT6|Q6MZM6|Q6N085|Q6P2R6|Q7Z6J5|Q9H0U5|Q9HCI8|Q9NXS0	Missense_Mutation	SNP	ENST00000267807.7	hg19	CCDS32245.1	.	.	.	.	.	.	.	.	.	.	T	0.011	-1.732159	0.00687	.	.	ENSG00000137871	ENST00000267807;ENST00000455329	T	0.03065	4.06	5.58	0.757	0.18427	.	.	.	.	.	T	0.01976	0.0062	N	0.12182	0.205	0.09310	N	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.48139	-0.9061	9	0.06236	T	0.91	-1.2374	8.4686	0.32971	0.0:0.3075:0.0:0.6925	.	867	Q6N043	Z280D_HUMAN	E	867;854	ENSP00000267807:K867E	ENSP00000267807:K867E	K	-	1	0	ZNF280D	54711329	0.006000	0.16342	0.002000	0.10522	0.052000	0.14988	-0.140000	0.10342	-0.098000	0.12285	0.460000	0.39030	AAA	.	.		0.323	ZNF280D-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418891.2	XM_370867		C	56924037	T	C	56924037	3	2	259	1	0	0	0	0	1	0	0	0	17832	1763	61	2	344	2	ZNF280D	15	56924037	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	798790	56924037	45607355	648	36966										
CGNL1	84952	hgsc.bcm.edu	37	chr15	57754012	57754012	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gaagaggtttccagccatgaTcaggagatggacaagctgaa	13	7	1	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:57754012T>G	ENST00000281282.5	+	8	2403	c.2325T>G	c.(2323-2325)gaT>gaG	p.D775E		NM_001252335.1|NM_032866.4	NP_001239264.1|NP_116255.2	Q0VF96	CGNL1_HUMAN	cingulin-like 1	775						myosin complex (GO:0016459)|tight junction (GO:0005923)	motor activity (GO:0003774)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(14)|ovary(4)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)	60				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)		CCAGCCATGATCAGGAGATGG	0.532																																					p.D775E		Atlas-SNP	.											.	CGNL1	125	.	0			c.T2325G						.						100	97	98					15																	57754012		2192	4292	6484	SO:0001583	missense	84952	exon8			CCATGATCAGGAG	AY274808	CCDS10161.1	15q21.3	2011-06-10			ENSG00000128849	ENSG00000128849			25931	protein-coding gene	gene with protein product		607856				11214970	Standard	NM_001252335		Approved	FLJ14957, JACOP, KIAA1749, paracingulin	uc002aeg.3	Q0VF96	OTTHUMG00000166485	ENST00000281282.5:c.2325T>G	chr15.hg19:g.57754012T>G	ENSP00000281282:p.Asp775Glu	136.0	0.0		89.0	21.0	NM_032866	Q05BZ4|Q52LR0|Q695C7|Q7Z2L3|Q96JV2|Q96MN6|Q9C0B4	Missense_Mutation	SNP	ENST00000281282.5	hg19	CCDS10161.1	.	.	.	.	.	.	.	.	.	.	T	18.62	3.663587	0.67700	.	.	ENSG00000128849	ENST00000281282	T	0.41065	1.01	5.52	1.63	0.23807	.	0.113301	0.39759	N	0.001278	T	0.41766	0.1173	M	0.79123	2.44	0.38341	D	0.94406	B	0.32731	0.382	B	0.31442	0.13	T	0.48091	-0.9065	10	0.46703	T	0.11	-27.512	11.03	0.47767	0.0:0.7455:0.0:0.2545	.	775	Q0VF96	CGNL1_HUMAN	E	775	ENSP00000281282:D775E	ENSP00000281282:D775E	D	+	3	2	CGNL1	55541304	0.993000	0.37304	1.000000	0.80357	0.687000	0.40016	0.335000	0.19806	0.509000	0.28195	0.368000	0.22195	GAT	.	.		0.532	CGNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255482.2	NM_032866		G	57754012	T	G	57754012	3	3	259	1	0	0	0	0	1	0	0	0	3306	1432	50	5	2351	5	CGNL1	15	57754012	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	829975	57754012	44777380	649	36967										
LIPC	3990	hgsc.bcm.edu	37	chr15	58840664	58840664	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cagccagggcctgtgcctgaGctgcaagaagggccgctgca	15	13	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:58840664G>A	ENST00000356113.6	+	8	1559	c.944G>A	c.(943-945)aGc>aAc	p.S315N	LIPC_ENST00000299022.5_Missense_Mutation_p.S315N|LIPC_ENST00000414170.3_Missense_Mutation_p.S315N|LIPC_ENST00000433326.2_Missense_Mutation_p.S254N			P11150	LIPC_HUMAN	lipase, hepatic	315					cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|chylomicron remnant clearance (GO:0034382)|fatty acid biosynthetic process (GO:0006633)|high-density lipoprotein particle remodeling (GO:0034375)|intermediate-density lipoprotein particle remodeling (GO:0034373)|low-density lipoprotein particle remodeling (GO:0034374)|phosphatidylcholine catabolic process (GO:0034638)|reverse cholesterol transport (GO:0043691)|triglyceride catabolic process (GO:0019433)|triglyceride homeostasis (GO:0070328)|very-low-density lipoprotein particle remodeling (GO:0034372)	extracellular space (GO:0005615)|high-density lipoprotein particle (GO:0034364)	apolipoprotein binding (GO:0034185)|heparin binding (GO:0008201)|low-density lipoprotein particle binding (GO:0030169)|phospholipase activity (GO:0004620)|triglyceride lipase activity (GO:0004806)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		Colorectal(260;0.215)		GBM - Glioblastoma multiforme(80;0.00213)|all cancers(107;0.00548)		CTGTGCCTGAGCTGCAAGAAG	0.642																																					p.S315N		Atlas-SNP	.											.	LIPC	56	.	0			c.G944A						.						39	34	36					15																	58840664		2192	4292	6484	SO:0001583	missense	3990	exon6			GCCTGAGCTGCAA		CCDS10166.1	15q21-q23	2012-10-02			ENSG00000166035	ENSG00000166035	3.1.1.3		6619	protein-coding gene	gene with protein product		151670					Standard	NM_000236		Approved	HL, HTGL	uc002afa.2	P11150	OTTHUMG00000132632	ENST00000356113.6:c.944G>A	chr15.hg19:g.58840664G>A	ENSP00000348425:p.Ser315Asn	172.0	0.0		135.0	64.0	NM_000236	A2RUB4|A8K9B6|O43571|P78529|Q99465	Missense_Mutation	SNP	ENST00000356113.6	hg19	CCDS10166.1	.	.	.	.	.	.	.	.	.	.	G	15.52	2.858592	0.51376	.	.	ENSG00000166035	ENST00000356113;ENST00000414170;ENST00000299022;ENST00000433326	D;D;D;D	0.91351	-2.83;-2.83;-2.83;-2.83	5.18	-0.204	0.13200	Lipase, N-terminal (1);	0.368824	0.34291	N	0.004091	D	0.86041	0.5838	M	0.62209	1.925	0.39169	D	0.96255	B;B	0.20368	0.044;0.005	B;B	0.21151	0.033;0.015	T	0.77882	-0.2422	10	0.54805	T	0.06	.	6.9254	0.24412	0.2676:0.1146:0.6178:0.0	.	254;315	E7EUK6;P11150	.;LIPC_HUMAN	N	315;315;315;254	ENSP00000348425:S315N;ENSP00000395569:S315N;ENSP00000299022:S315N;ENSP00000395002:S254N	ENSP00000299022:S315N	S	+	2	0	LIPC	56627956	1.000000	0.71417	0.979000	0.43373	0.914000	0.54420	1.140000	0.31516	0.047000	0.15862	0.655000	0.94253	AGC	.	.		0.642	LIPC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416209.1			A	58840664	G	A	58840664	3	1	259	1	0	0	0	0	1	0	0	0	8829	971	34	3	966	3	LIPC	15	58840664	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1086652	58840664	43690728	650	36968										
HERC1	8925	hgsc.bcm.edu	37	chr15	63915040	63915040	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctattgtaacccacttctgcGgtggcattgggagagggtat	13	8	1	1	rs560505113		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:63915040G>T	ENST00000443617.2	-	74	13749	c.13662C>A	c.(13660-13662)acC>acA	p.T4554T		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	4554	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						CCACTTCTGCGGTGGCATTGG	0.358																																					p.T4554T		Atlas-SNP	.											.	HERC1	624	.	0			c.C13662A						.						45	44	44					15																	63915040		1834	4087	5921	SO:0001819	synonymous_variant	8925	exon74			TTCTGCGGTGGCA	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.13662C>A	chr15.hg19:g.63915040G>T		77.0	0.0		71.0	4.0	NM_003922	Q8IW65	Silent	SNP	ENST00000443617.2	hg19	CCDS45277.1																																																																																			.	.		0.358	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		T	63915040	G	T	63915040	2	4	259	1	0	0	0	0	0	0	0	1	7066	1103	39	1		1	HERC1	15	63915040	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	5074376	63915040	38616352	651	36969										
HERC1	8925	hgsc.bcm.edu	37	chr15	63920929	63920929	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atgcagcactgtggcagcggCcagccgagatctgccgaaca	13	13	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:63920929C>T	ENST00000443617.2	-	70	13139	c.13052G>A	c.(13051-13053)gGc>gAc	p.G4351D		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	4351					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						GTGGCAGCGGCCAGCCGAGAT	0.522																																					p.G4351D		Atlas-SNP	.											.	HERC1	624	.	0			c.G13052A						.						84	89	87					15																	63920929		1959	4170	6129	SO:0001583	missense	8925	exon70			CAGCGGCCAGCCG	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.13052G>A	chr15.hg19:g.63920929C>T	ENSP00000390158:p.Gly4351Asp	157.0	0.0		130.0	6.0	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	hg19	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	C	32	5.150691	0.94645	.	.	ENSG00000103657	ENST00000443617	D	0.98135	-4.74	5.89	5.89	0.94794	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.85682	D	0.000000	D	0.99254	0.9740	H	0.95982	3.75	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98880	1.0769	10	0.87932	D	0	.	20.2469	0.98398	0.0:1.0:0.0:0.0	.	4351	Q15751	HERC1_HUMAN	D	4351	ENSP00000390158:G4351D	ENSP00000390158:G4351D	G	-	2	0	HERC1	61707982	1.000000	0.71417	1.000000	0.80357	0.778000	0.44026	7.758000	0.85224	2.781000	0.95711	0.555000	0.69702	GGC	.	.		0.522	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		T	63920929	C	T	63920929	3	4	259	1	0	0	0	0	1	0	0	0	7066	739	26	3	1569	3	HERC1	15	63920929	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	5889	63920929	38610463	652	36970										
TRIP4	9325	hgsc.bcm.edu	37	chr15	64689807	64689807	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gatgtctttgtacgataggcAcaagagaacagcaactccgt	10	9	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:64689807A>G	ENST00000261884.3	+	4	468	c.408A>G	c.(406-408)gcA>gcG	p.A136A	RN7SL595P_ENST00000582065.1_RNA|TRIP4_ENST00000559565.1_3'UTR	NM_016213.4	NP_057297.2	Q15650	TRIP4_HUMAN	thyroid hormone receptor interactor 4	136					positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21						TACGATAGGCACAAGAGAACA	0.393																																					p.A136A		Atlas-SNP	.											.	TRIP4	43	.	0			c.A408G						.						64	61	62					15																	64689807		2203	4300	6503	SO:0001819	synonymous_variant	9325	exon4			ATAGGCACAAGAG	L40371	CCDS10194.1	15q22.1	2014-02-17			ENSG00000103671	ENSG00000103671		"-"	12310	protein-coding gene	gene with protein product	"zinc finger, C2HC5-type"	604501				7776974	Standard	NM_016213		Approved	HsT17391, ZC2HC5	uc002anm.3	Q15650	OTTHUMG00000133033	ENST00000261884.3:c.408A>G	chr15.hg19:g.64689807A>G		128.0	0.0		94.0	5.0	NM_016213	B2RAS0|Q96ED7|Q9UKH0	Silent	SNP	ENST00000261884.3	hg19	CCDS10194.1																																																																																			.	.		0.393	TRIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256635.2	NM_016213		G	64689807	A	G	64689807	2	3	259	1	0	0	0	0	0	0	0	1	16573	146	6	2		2	TRIP4	15	64689807	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	768878	64689807	37841585	653	36971										
SPG21	51324	hgsc.bcm.edu	37	chr15	65261687	65261687	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgaagccagttcactctgacCcaaactttctagctgcagga	8	12	3	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:65261687C>A	ENST00000204566.2	-	7	869	c.574G>T	c.(574-576)Ggt>Tgt	p.G192C	SPG21_ENST00000559199.1_Missense_Mutation_p.G38C|SPG21_ENST00000433215.2_Missense_Mutation_p.G192C|SPG21_ENST00000416889.2_Missense_Mutation_p.G165C	NM_016630.3	NP_057714.1	Q9NZD8	SPG21_HUMAN	spastic paraplegia 21 (autosomal recessive, Mast syndrome)	192					antigen receptor-mediated signaling pathway (GO:0050851)|cell death (GO:0008219)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network transport vesicle (GO:0030140)	CD4 receptor binding (GO:0042609)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|urinary_tract(1)	10						TCACTCTGACCCAAACTTTCT	0.333																																					p.G192C		Atlas-SNP	.											.	SPG21	29	.	0			c.G574T						.						97	100	99					15																	65261687		2202	4299	6501	SO:0001583	missense	51324	exon7			TCTGACCCAAACT	AF208861	CCDS10198.1, CCDS45279.1	15q21-q22	2008-02-05	2007-04-23		ENSG00000090487	ENSG00000090487			20373	protein-coding gene	gene with protein product	"maspardin"	608181				11113139, 14564668	Standard	XM_006720564		Approved	ACP33, GL010, BM-019, MAST	uc002aoe.3	Q9NZD8	OTTHUMG00000133098	ENST00000204566.2:c.574G>T	chr15.hg19:g.65261687C>A	ENSP00000204566:p.Gly192Cys	88.0	0.0		94.0	4.0	NM_001127889	B4DW44|Q6ZMB6	Missense_Mutation	SNP	ENST00000204566.2	hg19	CCDS10198.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.259264	0.80246	.	.	ENSG00000090487	ENST00000204566;ENST00000416889;ENST00000433215	T;T;T	0.67345	-0.26;-0.26;-0.26	5.96	5.96	0.96718	.	0.098210	0.85682	D	0.000000	T	0.64305	0.2586	N	0.22421	0.69	0.47584	D	0.999461	P;P	0.45396	0.857;0.808	P;P	0.52758	0.584;0.708	T	0.65393	-0.6179	10	0.52906	T	0.07	-12.482	12.307	0.54908	0.0:0.9226:0.0:0.0774	.	165;192	Q9NZD8-2;Q9NZD8	.;SPG21_HUMAN	C	192;165;192	ENSP00000204566:G192C;ENSP00000394846:G165C;ENSP00000404111:G192C	ENSP00000204566:G192C	G	-	1	0	SPG21	63048740	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.483000	0.60264	2.815000	0.96918	0.650000	0.86243	GGT	.	.		0.333	SPG21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256758.3	NM_016630		A	65261687	C	A	65261687	3	1	259	1	0	0	0	0	1	0	0	0	15058	623	22	3	364	3	SPG21	15	65261687	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	571880	65261687	37269705	654	36972										
IQCH	64799	hgsc.bcm.edu	37	chr15	67664646	67664646	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aactatgctataccagaagtCaaaataaaagggaataattt	6	5	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:67664646C>A	ENST00000335894.4	+	9	1017	c.951C>A	c.(949-951)gtC>gtA	p.V317V	IQCH_ENST00000358767.3_Silent_p.V144V|IQCH_ENST00000546225.1_Silent_p.V65V|IQCH_ENST00000360277.4_Silent_p.V69V	NM_001031715.2	NP_001026885	Q86VS3	IQCH_HUMAN	IQ motif containing H	317										NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(2)|pancreas(2)|skin(5)|upper_aerodigestive_tract(1)	33				Colorectal(3;0.0856)		TACCAGAAGTCAAAATAAAAG	0.418																																					p.V317V		Atlas-SNP	.											.	IQCH	81	.	0			c.C951A						.						114	120	118					15																	67664646		2201	4299	6500	SO:0001819	synonymous_variant	64799	exon9			AGAAGTCAAAATA	AY014282	CCDS10223.1, CCDS32273.1, CCDS10223.2, CCDS61680.1, CCDS61681.1	15q23	2005-10-24			ENSG00000103599	ENSG00000103599			25721	protein-coding gene	gene with protein product		612523				12477932	Standard	NM_022784		Approved	FLJ12476	uc002aqo.2	Q86VS3	OTTHUMG00000133231	ENST00000335894.4:c.951C>A	chr15.hg19:g.67664646C>A		120.0	0.0		139.0	6.0	NM_001031715	A8K8W3|C9JPR6|D6RJ88|Q4G0S6|Q8NEH9|Q9BWX2|Q9H9Y1|Q9UF88	Silent	SNP	ENST00000335894.4	hg19	CCDS32273.1																																																																																			.	.		0.418	IQCH-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256969.1	NM_022784		A	67664646	C	A	67664646	2	1	259	1	0	0	0	0	0	0	0	1	7820	813	29	3		3	IQCH	15	67664646	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	2402959	67664646	34866746	655	36973										
MAP2K5	5607	hgsc.bcm.edu	37	chr15	67835762	67835762	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cccaaatagtggcgcggtggActggacagtgcactccgggc	15	12	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:67835762A>G	ENST00000178640.5	+	1	716	c.89A>G	c.(88-90)gAc>gGc	p.D30G	RP11-502I4.3_ENST00000604760.1_lincRNA|MAP2K5_ENST00000395476.2_Missense_Mutation_p.D30G|MAP2K5_ENST00000560591.1_3'UTR	NM_145160.2	NP_660143.1	Q13163	MP2K5_HUMAN	mitogen-activated protein kinase kinase 5	30	OPR.				activation of MAPK activity (GO:0000187)|cellular response to growth factor stimulus (GO:0071363)|cellular response to laminar fluid shear stress (GO:0071499)|ERK5 cascade (GO:0070375)|heart development (GO:0007507)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000342)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of interleukin-8 biosynthetic process (GO:0045415)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of response to cytokine stimulus (GO:0060761)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|skin(1)	16						GGCGCGGTGGACTGGACAGTG	0.562																																					p.D30G		Atlas-SNP	.											.	MAP2K5	70	.	0			c.A89G						.						122	105	111					15																	67835762		2201	4298	6499	SO:0001583	missense	5607	exon1			CGGTGGACTGGAC	U25265	CCDS10224.1, CCDS42051.1, CCDS55970.1	15q22.31	2011-06-09			ENSG00000137764	ENSG00000137764		"Mitogen-activated protein kinase cascade / Kinase kinases"	6845	protein-coding gene	gene with protein product		602520		PRKMK5		7759517	Standard	NM_002757		Approved	MEK5, MAPKK5, HsT17454	uc002aqu.3	Q13163	OTTHUMG00000133264	ENST00000178640.5:c.89A>G	chr15.hg19:g.67835762A>G	ENSP00000178640:p.Asp30Gly	191.0	0.0		120.0	5.0	NM_145160	B4DE43|Q92961|Q92962	Missense_Mutation	SNP	ENST00000178640.5	hg19	CCDS10224.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.710827	0.89112	.	.	ENSG00000137764	ENST00000541298;ENST00000395476;ENST00000178640	T;T	0.21543	2.0;2.0	4.95	4.95	0.65309	Phox/Bem1p (2);	0.000000	0.85682	D	0.000000	T	0.32010	0.0815	L	0.29908	0.895	0.80722	D	1	D;D;D	0.71674	0.998;0.998;0.998	D;D;D	0.67103	0.915;0.949;0.949	T	0.03231	-1.1058	10	0.36615	T	0.2	-16.0225	14.2868	0.66251	1.0:0.0:0.0:0.0	.	30;30;30	Q13163-2;Q13163;B2RD76	.;MP2K5_HUMAN;.	G	30	ENSP00000378859:D30G;ENSP00000178640:D30G	ENSP00000178640:D30G	D	+	2	0	MAP2K5	65622816	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.066000	0.71185	1.852000	0.53769	0.533000	0.62120	GAC	.	.		0.562	MAP2K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257041.1	NM_145162		G	67835762	A	G	67835762	3	3	259	1	0	0	0	0	1	0	0	0	9249	275	10	2	91	2	MAP2K5	15	67835762	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	171116	67835762	34695630	656	36974										
CLN6	54982	hgsc.bcm.edu	37	chr15	68504132	68504132	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	caccaggtggatgctggcacCcatgatgaagatgatgatgc	13	9	0	5			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:68504132C>T	ENST00000249806.5	-	4	524	c.367G>A	c.(367-369)Ggt>Agt	p.G123S	CLN6_ENST00000418702.2_Intron|CLN6_ENST00000566347.1_Intron|CLN6_ENST00000538696.1_Missense_Mutation_p.G155S|CLN6_ENST00000565471.1_Intron|RP11-315D16.2_ENST00000562767.1_Intron|CLN6_ENST00000564752.1_Missense_Mutation_p.G123S	NM_017882.2	NP_060352.1	Q9NWW5	CLN6_HUMAN	ceroid-lipofuscinosis, neuronal 6, late infantile, variant	123			G -> D (in CLN6; dbSNP:rs28939384). {ECO:0000269|PubMed:11727201}.		cell death (GO:0008219)|cellular macromolecule catabolic process (GO:0044265)|cholesterol metabolic process (GO:0008203)|ganglioside metabolic process (GO:0001573)|glycosaminoglycan metabolic process (GO:0030203)|locomotion involved in locomotory behavior (GO:0031987)|lysosomal lumen acidification (GO:0007042)|positive regulation of proteolysis (GO:0045862)|protein catabolic process (GO:0030163)|visual perception (GO:0007601)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)			large_intestine(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	7						ATGCTGGCACCCATGATGAAG	0.592																																					p.G123S		Atlas-SNP	.											.	CLN6	16	.	0			c.G367A						.						126	117	120					15																	68504132		2200	4298	6498	SO:0001583	missense	54982	exon4			TGGCACCCATGAT	AK000568	CCDS10227.1	15q23	2014-09-17			ENSG00000128973	ENSG00000128973			2077	protein-coding gene	gene with protein product		606725				9097964, 11727201	Standard	NM_017882		Approved	FLJ20561, HsT18960, nclf	uc002arf.3	Q9NWW5	OTTHUMG00000133286	ENST00000249806.5:c.367G>A	chr15.hg19:g.68504132C>T	ENSP00000249806:p.Gly123Ser	136.0	0.0		98.0	4.0	NM_017882	A8K560|B4DDH6|Q6IAB1|Q96SR0	Missense_Mutation	SNP	ENST00000249806.5	hg19	CCDS10227.1	.	.	.	.	.	.	.	.	.	.	C	35	5.510038	0.96386	.	.	ENSG00000128973	ENST00000249806;ENST00000538696	D;D	0.96774	-4.12;-4.12	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	D	0.97801	0.9278	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98784	1.0733	10	0.87932	D	0	-25.7851	18.6234	0.91328	0.0:1.0:0.0:0.0	.	155;123	B4DDH6;Q9NWW5	.;CLN6_HUMAN	S	123;155	ENSP00000249806:G123S;ENSP00000445770:G155S	ENSP00000249806:G123S	G	-	1	0	CLN6	66291186	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.369000	0.79578	2.388000	0.81334	0.511000	0.50034	GGT	.	.		0.592	CLN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257066.1	NM_017882		T	68504132	C	T	68504132	3	4	259	1	0	0	0	0	1	0	0	0	3547	623	22	3	584	3	CLN6	15	68504132	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	668370	68504132	34027260	657	36975										
GLCE	26035	hgsc.bcm.edu	37	chr15	69561466	69561466	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctggctcgctgggactatcaTaccacccacatcaatcagtt	7	14	3	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:69561466T>C	ENST00000261858.2	+	5	1965	c.1737T>C	c.(1735-1737)caT>caC	p.H579H	GLCE_ENST00000559420.2_Silent_p.H515H	NM_015554.1	NP_056369.1	O94923	GLCE_HUMAN	glucuronic acid epimerase	579					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)|small molecule metabolic process (GO:0044281)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	heparosan-N-sulfate-glucuronate 5-epimerase activity (GO:0047464)|racemase and epimerase activity, acting on carbohydrates and derivatives (GO:0016857)|UDP-glucuronate 5'-epimerase activity (GO:0050379)			NS(1)|breast(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	18						GGGACTATCATACCACCCACA	0.493																																					p.H579H		Atlas-SNP	.											.	GLCE	48	.	0			c.T1737C						.						213	207	209					15																	69561466		2200	4298	6498	SO:0001819	synonymous_variant	26035	exon5			CTATCATACCACC	AB020643	CCDS32277.1	15q23	2007-01-30	2007-01-30			ENSG00000138604	5.1.3.12		17855	protein-coding gene	gene with protein product	"heparan sulfate epimerase"	612134	"D-glucuronyl C5-epimerase", "UDP-glucuronic acid epimerase"			15853773	Standard	NM_015554		Approved	KIAA0836, HSEPI	uc002ary.1	O94923		ENST00000261858.2:c.1737T>C	chr15.hg19:g.69561466T>C		100.0	0.0		88.0	4.0	NM_015554	Q6GUQ2	Silent	SNP	ENST00000261858.2	hg19	CCDS32277.1																																																																																			.	.		0.493	GLCE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015554		C	69561466	T	C	69561466	2	2	259	1	0	0	0	0	0	0	0	1	6440	1403	49	2		2	GLCE	15	69561466	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1057334	69561466	32969926	658	36976										
MYO9A	4649	hgsc.bcm.edu	37	chr15	72152137	72152137	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tatggcaagcatacttgcatActgaaaaataggtgaggaat	10	5	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:72152137A>G	ENST00000356056.5	-	34	6564	c.6092T>C	c.(6091-6093)tTa>tCa	p.L2031S	RNA5SP399_ENST00000364003.1_RNA|MYO9A_ENST00000424560.1_Splice_Site_p.L2102S|MYO9A_ENST00000444904.1_Splice_Site_p.L2012S|MYO9A_ENST00000564571.1_Splice_Site_p.L2031S	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	2031	Tail.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)			NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						ATACTTGCATACTGAAAAATA	0.328																																					p.L2031S		Atlas-SNP	.											.	MYO9A	203	.	0			c.T6092C						.						98	95	96					15																	72152137		2199	4297	6496	SO:0001630	splice_region_variant	4649	exon34			TTGCATACTGAAA	AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"Myosins / Myosin superfamily : Class IX"	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.6092-1T>C	chr15.hg19:g.72152137A>G		97.0	0.0		53.0	5.0	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	hg19	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.971708	0.74246	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904	T;T;T	0.14391	2.51;2.51;2.51	5.02	5.02	0.67125	Protein kinase C-like, phorbol ester/diacylglycerol binding (3);	.	.	.	.	T	0.24586	0.0596	L	0.31476	0.935	0.58432	D	0.999997	D	0.76494	0.999	D	0.87578	0.998	T	0.03000	-1.1084	9	0.25106	T	0.35	.	14.7384	0.69434	1.0:0.0:0.0:0.0	.	2031	B2RTY4	MYO9A_HUMAN	S	2031;2102;2012	ENSP00000348349:L2031S;ENSP00000399162:L2102S;ENSP00000398250:L2012S	ENSP00000348349:L2031S	L	-	2	0	MYO9A	69939191	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.060000	0.76692	1.881000	0.54492	0.528000	0.53228	TTA	.	.		0.328	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901	Missense_Mutation	G	72152137	A	G	72152137	5	3	259	1	0	0	0	0	0	0	1	0	10093	405	14	2	1590	2	MYO9A	15	72152137	Splice_Site	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2590671	72152137	30379255	659	36977										
ARIH1	25820	hgsc.bcm.edu	37	chr15	72859489	72859489	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agtgtgatgatgacagtgaaAcctccaattggattgcagcc	11	8	0	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:72859489A>G	ENST00000379887.4	+	9	1311	c.997A>G	c.(997-999)Acc>Gcc	p.T333A		NM_005744.3	NP_005735.2	Q9Y4X5	ARI1_HUMAN	ariadne RBR E3 ubiquitin protein ligase 1	333					cytokine-mediated signaling pathway (GO:0019221)|protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|ubiquitin ligase complex (GO:0000151)	small conjugating protein ligase activity (GO:0019787)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(3)|lung(4)|prostate(1)|skin(1)	14						TGACAGTGAAACCTCCAATTG	0.333																																					p.T333A		Atlas-SNP	.											.	ARIH1	42	.	0			c.A997G						.						130	126	128					15																	72859489		2198	4297	6495	SO:0001583	missense	25820	exon9			AGTGAAACCTCCA	AF072832	CCDS10244.1	15q24	2013-10-03	2013-10-03		ENSG00000166233	ENSG00000166233			689	protein-coding gene	gene with protein product	"ariadne, Drosophila, homolog of"	605624	"ariadne (Drosophila) homolog, ubiquitin-conjugating enzyme E2-binding protein, 1", "ariadne homolog, ubiquitin-conjugating enzyme E2 binding protein, 1 (Drosophila)"			10521492, 24058416	Standard	NM_005744		Approved	HARI, HHARI, UBCH7BP, ARI	uc002aut.4	Q9Y4X5	OTTHUMG00000133474	ENST00000379887.4:c.997A>G	chr15.hg19:g.72859489A>G	ENSP00000369217:p.Thr333Ala	196.0	0.0		149.0	6.0	NM_005744	B2R6U3|O76026|Q9H3T6|Q9UEN0|Q9UP39	Missense_Mutation	SNP	ENST00000379887.4	hg19	CCDS10244.1	.	.	.	.	.	.	.	.	.	.	A	28.1	4.889666	0.91889	.	.	ENSG00000166233	ENST00000379887;ENST00000299305	D	0.87103	-2.21	5.83	5.83	0.93111	Zinc finger, C6HC-type (2);Zinc finger, RING-type (1);	0.000000	0.85682	D	0.000000	D	0.94640	0.8272	M	0.90082	3.085	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	D	0.95540	0.8611	10	0.87932	D	0	.	16.2506	0.82485	1.0:0.0:0.0:0.0	.	333	Q9Y4X5	ARI1_HUMAN	A	333;303	ENSP00000369217:T333A	ENSP00000299305:T303A	T	+	1	0	ARIH1	70646543	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.957000	0.93082	2.237000	0.73441	0.529000	0.55759	ACC	.	.		0.333	ARIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257350.1	NM_005744		G	72859489	A	G	72859489	3	3	259	1	0	0	0	0	1	0	0	0	923	43	2	2	1031	2	ARIH1	15	72859489	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	707352	72859489	29671903	660	36978										
BBS4	585	hgsc.bcm.edu	37	chr15	73028183	73028183	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	caggtgtaaccctttagtaaAcctgaactatgctgtgctgc	9	10	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:73028183A>C	ENST00000268057.4	+	14	1165	c.1124A>C	c.(1123-1125)aAc>aCc	p.N375T	BBS4_ENST00000539603.1_Missense_Mutation_p.N363T|BBS4_ENST00000395205.2_Missense_Mutation_p.N383T|BBS4_ENST00000542334.1_Missense_Mutation_p.N203T	NM_033028.4	NP_149017.2	Q96RK4	BBS4_HUMAN	Bardet-Biedl syndrome 4	375	Required for localization to centrosomes.				adult behavior (GO:0030534)|brain morphogenesis (GO:0048854)|centrosome organization (GO:0051297)|cerebral cortex development (GO:0021987)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|convergent extension involved in gastrulation (GO:0060027)|dendrite development (GO:0016358)|fat cell differentiation (GO:0045444)|heart looping (GO:0001947)|hippocampus development (GO:0021766)|intracellular transport (GO:0046907)|maintenance of protein location in nucleus (GO:0051457)|melanosome transport (GO:0032402)|metabolic process (GO:0008152)|microtubule anchoring at centrosome (GO:0034454)|microtubule cytoskeleton organization (GO:0000226)|mitotic cytokinesis (GO:0000281)|negative regulation of appetite by leptin-mediated signaling pathway (GO:0038108)|negative regulation of gene expression (GO:0010629)|negative regulation of systemic arterial blood pressure (GO:0003085)|neural tube closure (GO:0001843)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|pigment granule aggregation in cell center (GO:0051877)|positive regulation of cilium assembly (GO:0045724)|positive regulation of multicellular organism growth (GO:0040018)|protein localization to centrosome (GO:0071539)|protein localization to organelle (GO:0033365)|protein transport (GO:0015031)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|regulation of cytokinesis (GO:0032465)|regulation of lipid metabolic process (GO:0019216)|retina homeostasis (GO:0001895)|retinal rod cell development (GO:0046548)|sensory perception of smell (GO:0007608)|sensory processing (GO:0050893)|spermatid development (GO:0007286)|striatum development (GO:0021756)|visual perception (GO:0007601)	BBSome (GO:0034464)|centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|ciliary membrane (GO:0060170)|cilium (GO:0005929)|motile cilium (GO:0031514)|nonmotile primary cilium (GO:0031513)|pericentriolar material (GO:0000242)	alpha-tubulin binding (GO:0043014)|beta-tubulin binding (GO:0048487)|dynactin binding (GO:0034452)|microtubule motor activity (GO:0003777)|RNA polymerase II repressing transcription factor binding (GO:0001103)			autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|prostate(2)|urinary_tract(1)	19						CCTTTAGTAAACCTGAACTAT	0.463									Bardet-Biedl syndrome																												p.N375T		Atlas-SNP	.											.	BBS4	34	.	0			c.A1124C						.						156	153	154					15																	73028183		2198	4297	6495	SO:0001583	missense	585	exon14	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	TAGTAAACCTGAA	AF090947	CCDS10246.1, CCDS58377.1	15q22.3-q23	2013-01-10			ENSG00000140463	ENSG00000140463		"Tetratricopeptide (TTC) repeat domain containing"	969	protein-coding gene	gene with protein product		600374				7711739, 11381270	Standard	NM_033028		Approved		uc002avb.3	Q96RK4	OTTHUMG00000133510	ENST00000268057.4:c.1124A>C	chr15.hg19:g.73028183A>C	ENSP00000268057:p.Asn375Thr	115.0	0.0		92.0	4.0	NM_033028	B4E178|Q53DZ5|Q8NHU9|Q96H45	Missense_Mutation	SNP	ENST00000268057.4	hg19	CCDS10246.1	.	.	.	.	.	.	.	.	.	.	A	16.09	3.025248	0.54683	.	.	ENSG00000140463	ENST00000542334;ENST00000268057;ENST00000539603;ENST00000395205	T;T;T;T	0.77750	0.69;-1.12;-1.12;-1.12	5.68	4.57	0.56435	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.045776	0.85682	D	0.000000	T	0.81903	0.4921	M	0.66939	2.045	0.52501	D	0.99995	D;D;D	0.57571	0.979;0.98;0.964	P;P;P	0.57009	0.74;0.811;0.554	T	0.79369	-0.1832	10	0.32370	T	0.25	-16.5762	10.1449	0.42758	0.9247:0.0:0.0753:0.0	.	363;383;375	F5H7I8;Q96RK4-2;Q96RK4	.;.;BBS4_HUMAN	T	203;375;363;383	ENSP00000445964:N203T;ENSP00000268057:N375T;ENSP00000442492:N363T;ENSP00000378631:N383T	ENSP00000268057:N375T	N	+	2	0	BBS4	70815236	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.976000	0.63785	0.999000	0.39023	0.528000	0.53228	AAC	.	.		0.463	BBS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257473.2	NM_033028		C	73028183	A	C	73028183	3	2	259	1	0	0	0	0	1	0	0	0	1339	43	2	5	1178	5	BBS4	15	73028183	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	168694	73028183	29503209	661	36979										
ISLR	3671	hgsc.bcm.edu	37	chr15	74468160	74468160	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tccccgactttggcaagctgGaggaaggcacctacagctgc	12	13	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:74468160G>A	ENST00000249842.3	+	2	1318	c.961G>A	c.(961-963)Gag>Aag	p.E321K	RP11-665J16.1_ENST00000561647.1_RNA|ISLR_ENST00000395118.1_Missense_Mutation_p.E321K	NM_005545.3	NP_005536.1	O14498	ISLR_HUMAN	immunoglobulin superfamily containing leucine-rich repeat	321	Ig-like.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)	20						TGGCAAGCTGGAGGAAGGCAC	0.657																																					p.E321K		Atlas-SNP	.											.	ISLR	49	.	0			c.G961A						.						38	39	39					15																	74468160		2198	4296	6494	SO:0001583	missense	3671	exon2			AAGCTGGAGGAAG	AB003184	CCDS10260.1	15q23-q24	2013-01-11			ENSG00000129009	ENSG00000129009		"Immunoglobulin superfamily / I-set domain containing"	6133	protein-coding gene	gene with protein product		602059				9325048	Standard	NM_005545		Approved	HsT17563	uc002axh.1	O14498	OTTHUMG00000137623	ENST00000249842.3:c.961G>A	chr15.hg19:g.74468160G>A	ENSP00000249842:p.Glu321Lys	67.0	0.0		36.0	16.0	NM_201526		Missense_Mutation	SNP	ENST00000249842.3	hg19	CCDS10260.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.580695	0.86748	.	.	ENSG00000129009	ENST00000249842;ENST00000395118	T;T	0.67698	-0.28;-0.28	4.37	4.37	0.52481	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.152349	0.29410	U	0.012229	T	0.71888	0.3393	M	0.70275	2.135	0.52501	D	0.999956	P	0.47484	0.896	P	0.50934	0.654	T	0.75687	-0.3231	10	0.72032	D	0.01	.	10.5949	0.45331	0.0896:0.0:0.9104:0.0	.	321	O14498	ISLR_HUMAN	K	321	ENSP00000249842:E321K;ENSP00000378550:E321K	ENSP00000249842:E321K	E	+	1	0	ISLR	72255213	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	7.846000	0.86887	1.987000	0.57996	0.313000	0.20887	GAG	.	.		0.657	ISLR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269044.1	NM_005545		A	74468160	G	A	74468160	3	1	259	1	0	0	0	0	1	0	0	0	7867	1175	41	3	963	3	ISLR	15	74468160	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1439977	74468160	28063232	662	36980										
CCDC33	80125	hgsc.bcm.edu	37	chr15	74573035	74573035	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gcagccagccgtggaccctcAaccagcccctgggcatctct	10	18	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:74573035A>G	ENST00000398814.3	+	9	1347	c.916A>G	c.(916-918)Aac>Gac	p.N306D	CCDC33_ENST00000321288.5_Missense_Mutation_p.N509D	NM_025055.3	NP_079331.3	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33	509	C2.									breast(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						GTGGACCCTCAACCAGCCCCT	0.597																																					p.N306D		Atlas-SNP	.											.	CCDC33	160	.	0			c.A916G						.						82	93	90					15																	74573035		1916	4134	6050	SO:0001583	missense	80125	exon9			ACCCTCAACCAGC	BC025689	CCDS42058.1, CCDS42059.1, CCDS73753.1	15q24.1	2009-08-06				ENSG00000140481			26552	protein-coding gene	gene with protein product	"cancer/testis antigen 61"					12477932	Standard	NM_025055		Approved	FLJ32855, CT61	uc002axo.4	Q8N5R6		ENST00000398814.3:c.916A>G	chr15.hg19:g.74573035A>G	ENSP00000381795:p.Asn306Asp	97.0	0.0		87.0	4.0	NM_025055	A8K3U4|A8MPQ6|A8MV61|A8MVU9|B3KQ49|Q8TAX6|Q9H5Q6	Missense_Mutation	SNP	ENST00000398814.3	hg19	CCDS42058.1	.	.	.	.	.	.	.	.	.	.	A	1.459	-0.562826	0.03939	.	.	ENSG00000140481	ENST00000321288;ENST00000398814	T;T	0.23147	1.92;2.25	5.28	-6.73	0.01749	.	1.336340	0.04936	N	0.457774	T	0.15046	0.0363	L	0.47716	1.5	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.06405	0.001;0.002	T	0.31166	-0.9953	10	0.08599	T	0.76	.	3.1067	0.06344	0.4846:0.1094:0.2974:0.1085	.	509;306	C9JFX2;Q8N5R6-6	.;.	D	509;306	ENSP00000325012:N509D;ENSP00000381795:N306D	ENSP00000325012:N509D	N	+	1	0	CCDC33	72360088	0.000000	0.05858	0.002000	0.10522	0.098000	0.18820	-0.360000	0.07622	-0.847000	0.04168	-1.235000	0.01560	AAC	.	.		0.597	CCDC33-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419491.2	NM_182791		G	74573035	A	G	74573035	3	3	259	1	0	0	0	0	1	0	0	0	2808	130	5	2	950	2	CCDC33	15	74573035	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	104875	74573035	27958357	663	36981										
MPI	4351	hgsc.bcm.edu	37	chr15	75183814	75183814	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gtggattgctgagaaccaggAcagcttgggctcaaaggtca	14	8	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:75183814A>G	ENST00000352410.4	+	3	306	c.239A>G	c.(238-240)gAc>gGc	p.D80G	MPI_ENST00000563422.1_Missense_Mutation_p.D80G|MPI_ENST00000323744.6_Missense_Mutation_p.D80G|MPI_ENST00000563786.1_Missense_Mutation_p.D60G|MPI_ENST00000564003.1_Missense_Mutation_p.D30G|MPI_ENST00000535694.1_Missense_Mutation_p.D30G|MPI_ENST00000562606.1_Missense_Mutation_p.D60G|MPI_ENST00000565576.1_Missense_Mutation_p.D80G|MPI_ENST00000566377.1_Missense_Mutation_p.D80G			P34949	MPI_HUMAN	mannose phosphate isomerase	80					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	mannose-6-phosphate isomerase activity (GO:0004476)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|upper_aerodigestive_tract(1)	9						GAGAACCAGGACAGCTTGGGC	0.542																																					p.D80G		Atlas-SNP	.											.	MPI	32	.	0			c.A239G						.						204	172	183					15																	75183814		2197	4295	6492	SO:0001583	missense	4351	exon3			ACCAGGACAGCTT		CCDS10272.1, CCDS73756.1, CCDS73757.1, CCDS73758.1	15q24.1	2013-09-19			ENSG00000178802	ENSG00000178802	5.3.1.8		7216	protein-coding gene	gene with protein product	"mannose-6-phosphate isomerase"	154550					Standard	NM_002435		Approved		uc002azc.1	P34949	OTTHUMG00000142826	ENST00000352410.4:c.239A>G	chr15.hg19:g.75183814A>G	ENSP00000318318:p.Asp80Gly	130.0	0.0		111.0	6.0	NM_002435	A8K8K9|Q96AB0	Missense_Mutation	SNP	ENST00000352410.4	hg19	CCDS10272.1	.	.	.	.	.	.	.	.	.	.	A	10.84	1.464264	0.26335	.	.	ENSG00000178802	ENST00000352410;ENST00000535694;ENST00000379693;ENST00000323744	D;D;D	0.95821	-3.82;-3.82;-3.82	4.86	2.31	0.28768	Cupin, RmlC-type (1);RmlC-like jelly roll fold (1);	0.528034	0.21846	N	0.068258	D	0.88945	0.6575	N	0.26162	0.8	0.24222	N	0.995434	B;B;B;B;B	0.10296	0.003;0.002;0.002;0.0;0.0	B;B;B;B;B	0.15052	0.006;0.012;0.003;0.002;0.005	T	0.77523	-0.2556	10	0.29301	T	0.29	.	6.4655	0.21980	0.6758:0.2345:0.0897:0.0	.	30;80;80;60;80	B4DYB8;B4DFC4;P34949-2;Q8NHZ6;P34949	.;.;.;.;MPI_HUMAN	G	80;30;60;80	ENSP00000318318:D80G;ENSP00000440447:D30G;ENSP00000318192:D80G	ENSP00000318192:D80G	D	+	2	0	MPI	72970867	0.945000	0.32115	0.999000	0.59377	0.965000	0.64279	1.729000	0.38115	1.826000	0.53198	0.379000	0.24179	GAC	.	.		0.542	MPI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286418.4			G	75183814	A	G	75183814	3	3	259	1	0	0	0	0	1	0	0	0	9738	275	10	2	249	2	MPI	15	75183814	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	610779	75183814	27347578	664	36982										
RCN2	5955	hgsc.bcm.edu	37	chr15	77241444	77241444	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttgatgaaatggatttgaatGgtgacaaaaagctctctgaa	10	4	1	5			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:77241444G>T	ENST00000394885.3	+	7	1058	c.835G>T	c.(835-837)Ggt>Tgt	p.G279C	RCN2_ENST00000394883.3_Missense_Mutation_p.G178C|RCN2_ENST00000320963.5_Missense_Mutation_p.G297C	NM_002902.2	NP_002893.1	Q14257	RCN2_HUMAN	reticulocalbin 2, EF-hand calcium binding domain	279	EF-hand 6. {ECO:0000255|PROSITE- ProRule:PRU00448}.					endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)	calcium ion binding (GO:0005509)			endometrium(2)|kidney(2)|large_intestine(2)|lung(1)	7						GGATTTGAATGGTGACAAAAA	0.363																																					p.G297C		Atlas-SNP	.											.	RCN2	16	.	0			c.G889T						.						124	135	131					15																	77241444		2196	4294	6490	SO:0001583	missense	5955	exon8			TTGAATGGTGACA	X78669	CCDS10291.1, CCDS61719.1	15q22.33-q24.1	2013-01-10			ENSG00000117906	ENSG00000117906		"EF-hand domain containing"	9935	protein-coding gene	gene with protein product	"Reticulocalbin 2, EF-hand calcium binding domain (endoplasmic reticulum calcium-binding protein, 55kD)"	602584				9533013, 7624774	Standard	NM_002902		Approved	ERC-55, E6BP, ERC55, TCBP49	uc002bcd.3	Q14257	OTTHUMG00000143730	ENST00000394885.3:c.835G>T	chr15.hg19:g.77241444G>T	ENSP00000378349:p.Gly279Cys	62.0	0.0		74.0	5.0	NM_001271837	A8MTG6|F8WCY5|Q53XN8	Missense_Mutation	SNP	ENST00000394885.3	hg19	CCDS10291.1	.	.	.	.	.	.	.	.	.	.	G	18.03	3.531715	0.64972	.	.	ENSG00000117906	ENST00000394885;ENST00000320963;ENST00000394883	T;T;T	0.75050	-0.9;-0.9;-0.9	6.05	1.74	0.24563	EF-hand-like domain (1);	0.397599	0.32736	N	0.005703	T	0.81173	0.4767	M	0.79614	2.46	0.36877	D	0.889217	D;P;P	0.63880	0.993;0.929;0.78	P;P;P	0.60173	0.87;0.599;0.526	T	0.82360	-0.0496	10	0.72032	D	0.01	-4.3565	8.1976	0.31407	0.3611:0.0:0.6389:0.0	.	178;297;279	A8MXP8;F8WCY5;Q14257	.;.;RCN2_HUMAN	C	279;297;178	ENSP00000378349:G279C;ENSP00000319739:G297C;ENSP00000378347:G178C	ENSP00000319739:G297C	G	+	1	0	RCN2	75028499	1.000000	0.71417	0.433000	0.26760	0.997000	0.91878	4.217000	0.58547	0.324000	0.23333	0.650000	0.86243	GGT	.	.		0.363	RCN2-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289795.1	NM_002902		T	77241444	G	T	77241444	3	4	259	1	0	0	0	0	1	0	0	0	13195	1348	47	3	861	3	RCN2	15	77241444	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	2057630	77241444	25289948	665	36983										
SH2D7	646892	hgsc.bcm.edu	37	chr15	78386536	78386536	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gagccactggctacatcttgTcctacaggtaagaggggaag	13	9	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:78386536T>C	ENST00000328828.5	+	2	259	c.259T>C	c.(259-261)Tcc>Ccc	p.S87P	SNORA63_ENST00000362763.1_RNA|SH2D7_ENST00000409568.2_5'UTR	NM_001101404.1	NP_001094874.1	A6NKC9	SH2D7_HUMAN	SH2 domain containing 7	87	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.									endometrium(2)|kidney(2)|lung(3)	7						CTACATCTTGTCCTACAGGTA	0.557																																					p.S87P		Atlas-SNP	.											.	SH2D7	26	.	0			c.T259C						.						41	45	44					15																	78386536		2003	4172	6175	SO:0001583	missense	646892	exon2			ATCTTGTCCTACA		CCDS45315.1	15q25.1	2013-02-14			ENSG00000183476	ENSG00000183476		"SH2 domain containing"	34549	protein-coding gene	gene with protein product							Standard	NM_001101404		Approved	LOC646892	uc010blb.1	A6NKC9	OTTHUMG00000154271	ENST00000328828.5:c.259T>C	chr15.hg19:g.78386536T>C	ENSP00000327846:p.Ser87Pro	80.0	0.0		63.0	4.0	NM_001101404		Missense_Mutation	SNP	ENST00000328828.5	hg19	CCDS45315.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.373491	0.82573	.	.	ENSG00000183476	ENST00000328828	D	0.93426	-3.22	5.57	5.57	0.84162	SH2 motif (4);	.	.	.	.	D	0.98027	0.9350	H	0.98542	4.26	0.25221	N	0.989907	D	0.89917	1.0	D	0.91635	0.999	D	0.93691	0.7007	9	0.87932	D	0	.	12.1183	0.53878	0.0:0.0:0.0:1.0	.	87	A6NKC9	SH2D7_HUMAN	P	87	ENSP00000327846:S87P	ENSP00000327846:S87P	S	+	1	0	SH2D7	76173591	1.000000	0.71417	0.985000	0.45067	0.984000	0.73092	5.665000	0.68052	2.115000	0.64714	0.454000	0.30748	TCC	.	.		0.557	SH2D7-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000334660.2	NM_001101404		C	78386536	T	C	78386536	3	2	259	1	0	0	0	0	1	0	0	0	14254	1667	58	2	265	2	SH2D7	15	78386536	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1145092	78386536	24144856	666	36984										
AP3B2	8120	hgsc.bcm.edu	37	chr15	83358199	83358199	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tccagcatctccttcaggtcAtcatgcctggtgggaggtac	11	12	4	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:83358199A>G	ENST00000261722.3	-	2	327	c.120T>C	c.(118-120)gaT>gaC	p.D40D	RP11-752G15.3_ENST00000560650.1_RNA|AP3B2_ENST00000542200.1_Silent_p.D40D|AP3B2_ENST00000535359.1_Silent_p.D40D|AP3B2_ENST00000535348.1_Silent_p.D40D|AP3B2_ENST00000561455.1_5'UTR	NM_004644.3	NP_004635.2	Q13367	AP3B2_HUMAN	adaptor-related protein complex 3, beta 2 subunit	40					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|intracellular protein transport (GO:0006886)|post-Golgi vesicle-mediated transport (GO:0006892)	AP-3 adaptor complex (GO:0030123)|COPI-coated vesicle (GO:0030137)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(4)|endometrium(1)|kidney(1)|large_intestine(4)|lung(21)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(2)	41			BRCA - Breast invasive adenocarcinoma(143;0.229)			CCTTCAGGTCATCATGCCTGG	0.572																																					p.D40D		Atlas-SNP	.											.	AP3B2	103	.	0			c.T120C						.						62	58	59					15																	83358199		2029	4191	6220	SO:0001819	synonymous_variant	8120	exon2			CAGGTCATCATGC	U37673	CCDS45331.1, CCDS61736.1, CCDS61737.1	15q	2008-07-07			ENSG00000103723	ENSG00000103723			567	protein-coding gene	gene with protein product		602166				7671305, 1851215	Standard	NM_004644		Approved	NAPTB	uc010uoh.2	Q13367	OTTHUMG00000168009	ENST00000261722.3:c.120T>C	chr15.hg19:g.83358199A>G		136.0	0.0		95.0	4.0	NM_004644	A4Z4T7|B7ZKR7|B7ZKS0|O14808|Q52LY8	Silent	SNP	ENST00000261722.3	hg19	CCDS45331.1																																																																																			.	.		0.572	AP3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397463.1			G	83358199	A	G	83358199	2	3	259	1	0	0	0	0	0	0	0	1	745	214	8	2		2	AP3B2	15	83358199	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	4971663	83358199	19173193	667	36985										
HDGFRP3	50810	hgsc.bcm.edu	37	chr15	83832817	83832817	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gcttcacagcgccctctgggAgttcatcaatctatgaaaga	9	11	5	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:83832817A>G	ENST00000299633.4	-	2	698	c.95T>C	c.(94-96)cTc>cCc	p.L32P		NM_016073.3	NP_057157.1	Q9Y3E1	HDGR3_HUMAN		32	PWWP. {ECO:0000255|PROSITE- ProRule:PRU00162}.				cell proliferation (GO:0008283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.L32P(1)		kidney(1)|large_intestine(1)|lung(4)|prostate(1)	7						GCCCTCTGGGAGTTCATCAAT	0.363																																					p.L32P		Atlas-SNP	.											HDGFRP3,NS,carcinoma,0,1	HDGFRP3	17	.	1	Substitution - Missense(1)	kidney(1)	c.T95C						.						116	111	113					15																	83832817		2203	4300	6503	SO:0001583	missense	0	exon2			TCTGGGAGTTCAT																												ENST00000299633.4:c.95T>C	chr15.hg19:g.83832817A>G	ENSP00000299633:p.Leu32Pro	109.0	0.0		107.0	5.0	NM_016073		Missense_Mutation	SNP	ENST00000299633.4	hg19	CCDS32314.1	.	.	.	.	.	.	.	.	.	.	A	26.9	4.780179	0.90195	.	.	ENSG00000166503	ENST00000299633	T	0.69175	-0.38	5.19	5.19	0.71726	PWWP (3);	0.219879	0.40640	N	0.001060	T	0.69043	0.3067	N	0.25890	0.77	0.80722	D	1	P	0.52463	0.953	P	0.62649	0.905	T	0.65010	-0.6272	10	0.22109	T	0.4	.	15.5098	0.75772	1.0:0.0:0.0:0.0	.	32	Q9Y3E1	HDGR3_HUMAN	P	32	ENSP00000299633:L32P	ENSP00000299633:L32P	L	-	2	0	AC024270.1	81623821	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.010000	0.93611	2.304000	0.77564	0.528000	0.53228	CTC	.	.		0.363	HDGFRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419898.1			G	83832817	A	G	83832817	3	3	259	1	0	0	0	0	1	0	0	0	7030	304	11	2	536	2	HDGFRP3	15	83832817	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	474618	83832817	18698575	668	36986										
ADAMTSL3	57188	hgsc.bcm.edu	37	chr15	84694002	84694002	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gttcctaggtggttcacaagTgtgtggtcacagtgctctgt	13	8	3	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:84694002T>C	ENST00000286744.5	+	27	4694	c.4470T>C	c.(4468-4470)agT>agC	p.S1490S	ADAMTSL3_ENST00000567476.1_Silent_p.S1490S	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	1490	TSP type-1 9. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			GGTTCACAAGTGTGTGGTCAC	0.502																																					p.S1490S		Atlas-SNP	.											.	ADAMTSL3	290	.	0			c.T4470C						.						166	133	144					15																	84694002		2203	4299	6502	SO:0001819	synonymous_variant	57188	exon27			CACAAGTGTGTGG	AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.4470T>C	chr15.hg19:g.84694002T>C		106.0	0.0		54.0	5.0	NM_207517	A1A566|A1A567|Q9ULI7	Silent	SNP	ENST00000286744.5	hg19	CCDS10326.1																																																																																			.	.		0.502	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517		C	84694002	T	C	84694002	2	2	259	1	0	0	0	0	0	0	0	1	276	1693	59	2		2	ADAMTSL3	15	84694002	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	861185	84694002	17837390	669	36987										
ZNF592	9640	hgsc.bcm.edu	37	chr15	85341254	85341254	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acagtgccacccagcaccccAcccagccccacagaccctcc	5	24	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:85341254A>G	ENST00000560079.2	+	6	2842	c.2554A>G	c.(2554-2556)Acc>Gcc	p.T852A	ZNF592_ENST00000299927.3_Missense_Mutation_p.T852A	NM_014630.2	NP_055445.2	Q92610	ZN592_HUMAN	zinc finger protein 592	852					cell death (GO:0008219)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|kidney(1)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(143;0.0587)			CCAGCACCCCACCCAGCCCCA	0.632																																					p.T852A		Atlas-SNP	.											.	ZNF592	95	.	0			c.A2554G						.						49	44	45					15																	85341254		2203	4299	6502	SO:0001583	missense	9640	exon6			CACCCCACCCAGC	D86966	CCDS32317.1	15q25.2	2011-03-15				ENSG00000166716		"Zinc fingers, C2H2-type"	28986	protein-coding gene	gene with protein product		613624	"spinocerebellar ataxia, autosomal recessive 5"	SCAR5		9039502, 12030328, 20531441	Standard	NM_014630		Approved	KIAA0211, CAMOS	uc002bld.3	Q92610		ENST00000560079.2:c.2554A>G	chr15.hg19:g.85341254A>G	ENSP00000452877:p.Thr852Ala	97.0	0.0		76.0	4.0	NM_014630	Q2M1T2|Q504Y9	Missense_Mutation	SNP	ENST00000560079.2	hg19	CCDS32317.1	.	.	.	.	.	.	.	.	.	.	A	3.959	-0.010658	0.07727	.	.	ENSG00000166716	ENST00000299927	T	0.28069	1.63	5.67	-1.31	0.09230	.	0.690424	0.15642	N	0.251852	T	0.11965	0.0291	N	0.12471	0.22	0.21627	N	0.999612	B	0.02656	0.0	B	0.08055	0.003	T	0.32903	-0.9889	10	0.10636	T	0.68	-8.4707	5.714	0.17950	0.5543:0.0:0.3211:0.1246	.	852	Q92610	ZN592_HUMAN	A	852	ENSP00000299927:T852A	ENSP00000299927:T852A	T	+	1	0	ZNF592	83142258	0.008000	0.16893	0.963000	0.40424	0.145000	0.21501	0.403000	0.20982	-0.124000	0.11724	0.459000	0.35465	ACC	.	.		0.632	ZNF592-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418779.2	NM_014630		G	85341254	A	G	85341254	3	3	259	1	0	0	0	0	1	0	0	0	18037	159	6	2	2564	2	ZNF592	15	85341254	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	647252	85341254	17190138	670	36988										
AGBL1	123624	hgsc.bcm.edu	37	chr15	87097688	87097688	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gagcttccacggcccgggtgGtggtgtggagagagatgggg	21	7	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:87097688G>T	ENST00000441037.2	+	20	2871	c.2776G>T	c.(2776-2778)Gtg>Ttg	p.V926L	AGBL1_ENST00000389298.3_Missense_Mutation_p.V657L|AGBL1_ENST00000421325.2_Missense_Mutation_p.V926L	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	926					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						GGCCCGGGTGGTGGTGTGGAG	0.542																																					p.V926L		Atlas-SNP	.											.	AGBL1	151	.	0			c.G2776T						.						29	31	31					15																	87097688		1910	4124	6034	SO:0001583	missense	123624	exon20			CGGGTGGTGGTGT	AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 4"	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.2776G>T	chr15.hg19:g.87097688G>T	ENSP00000413001:p.Val926Leu	133.0	0.0		103.0	5.0	NM_152336	A1A4X5|A6NJH6|C9JHL5	Missense_Mutation	SNP	ENST00000441037.2	hg19	CCDS58398.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.374134	0.82573	.	.	ENSG00000166748	ENST00000441037;ENST00000421325;ENST00000389298	T;T	0.10382	2.88;2.88	4.97	4.05	0.47172	Peptidase M14, carboxypeptidase A (1);	0.199496	0.22238	U	0.062729	T	0.21674	0.0522	M	0.81341	2.54	0.33073	D	0.5356	P	0.41475	0.751	P	0.45167	0.472	T	0.39099	-0.9630	10	0.72032	D	0.01	-10.6475	12.5513	0.56227	0.0799:0.0:0.9201:0.0	.	926	Q96MI9	CBPC4_HUMAN	L	961;926;657	ENSP00000397173:V926L;ENSP00000373949:V657L	ENSP00000373949:V657L	V	+	1	0	AGBL1	84898692	1.000000	0.71417	0.977000	0.42913	0.847000	0.48162	9.477000	0.97925	1.337000	0.45525	-0.145000	0.13849	GTG	.	.		0.542	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336		T	87097688	G	T	87097688	3	4	259	1	0	0	0	0	1	0	0	0	375	1261	44	3	2850	3	AGBL1	15	87097688	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1756434	87097688	15433704	671	36989										
ZNF774	342132	hgsc.bcm.edu	37	chr15	90903883	90903883	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aatgtcacaaaagcttcagtCgaagctcaaatttcatcact	5	10	5	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:90903883C>A	ENST00000354377.3	+	4	1006	c.820C>A	c.(820-822)Cga>Aga	p.R274R	ZNF774_ENST00000379090.5_Intron	NM_001004309.2	NP_001004309.2	Q6NX45	ZN774_HUMAN	zinc finger protein 774	274					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|stomach(1)	14	Melanoma(11;0.00551)|Lung NSC(78;0.0158)|all_lung(78;0.0331)		BRCA - Breast invasive adenocarcinoma(143;0.0224)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			AAGCTTCAGTCGAAGCTCAAA	0.507																																					p.R274R		Atlas-SNP	.											.	ZNF774	35	.	0			c.C820A						.						56	57	56					15																	90903883		2199	4298	6497	SO:0001819	synonymous_variant	342132	exon4			TTCAGTCGAAGCT	BC067279	CCDS32330.1	15q26.1	2013-01-08				ENSG00000196391		"Zinc fingers, C2H2-type"	33108	protein-coding gene	gene with protein product							Standard	NM_001004309		Approved	MGC75360	uc002bpk.4	Q6NX45		ENST00000354377.3:c.820C>A	chr15.hg19:g.90903883C>A		86.0	0.0		84.0	5.0	NM_001004309	A8K020	Silent	SNP	ENST00000354377.3	hg19	CCDS32330.1																																																																																			.	.		0.507	ZNF774-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418048.1	NM_001004309		A	90903883	C	A	90903883	2	1	259	1	0	0	0	0	0	0	0	1	18162	876	31	1		1	ZNF774	15	90903883	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	3806195	90903883	11627509	672	36990										
IQGAP1	8826	hgsc.bcm.edu	37	chr15	90999516	90999516	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggcccagcattaccaagacaCgctgattagagcgaagagag	12	10	0	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:90999516C>T	ENST00000268182.5	+	15	1869	c.1745C>T	c.(1744-1746)aCg>aTg	p.T582M	IQGAP1_ENST00000560738.1_Intron	NM_003870.3	NP_003861.1	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	582					cellular response to calcium ion (GO:0071277)|cellular response to epidermal growth factor stimulus (GO:0071364)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerular visceral epithelial cell development (GO:0072015)|negative regulation of catalytic activity (GO:0043086)|negative regulation of dephosphorylation (GO:0035305)|neuron projection extension (GO:1990138)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|regulation of cytokine production (GO:0001817)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	actin filament (GO:0005884)|axon (GO:0030424)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|midbody (GO:0030496)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activator activity (GO:0043539)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			TACCAAGACACGCTGATTAGA	0.507																																					p.T582M		Atlas-SNP	.											.	IQGAP1	140	.	0			c.C1745T						.						104	93	97					15																	90999516		2198	4298	6496	SO:0001583	missense	8826	exon15			AAGACACGCTGAT	D29640	CCDS10362.1	15q26.1	2008-07-18			ENSG00000140575	ENSG00000140575			6110	protein-coding gene	gene with protein product	"RasGAP-like with IQ motifs"	603379				8051149, 8670801	Standard	XM_005254984		Approved	p195, KIAA0051, SAR1, HUMORFA01	uc002bpl.1	P46940	OTTHUMG00000149832	ENST00000268182.5:c.1745C>T	chr15.hg19:g.90999516C>T	ENSP00000268182:p.Thr582Met	107.0	0.0		90.0	4.0	NM_003870	A7MBM3	Missense_Mutation	SNP	ENST00000268182.5	hg19	CCDS10362.1	.	.	.	.	.	.	.	.	.	.	C	14.01	2.406495	0.42715	.	.	ENSG00000140575	ENST00000268182	T	0.08193	3.12	4.94	4.01	0.46588	.	0.120762	0.56097	D	0.000030	T	0.09598	0.0236	L	0.47716	1.5	0.80722	D	1	P	0.39809	0.689	B	0.37650	0.255	T	0.09228	-1.0684	10	0.52906	T	0.07	-7.9908	12.7561	0.57336	0.0:0.92:0.0:0.08	.	582	P46940	IQGA1_HUMAN	M	582	ENSP00000268182:T582M	ENSP00000268182:T582M	T	+	2	0	IQGAP1	88800520	0.606000	0.26949	0.880000	0.34516	0.955000	0.61496	1.169000	0.31871	1.289000	0.44618	0.650000	0.86243	ACG	.	.		0.507	IQGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313493.1	NM_003870		T	90999516	C	T	90999516	3	4	259	1	0	0	0	0	1	0	0	0	7823	536	19	1	1803	1	IQGAP1	15	90999516	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	95633	90999516	11531876	673	36991										
FURIN	5045	hgsc.bcm.edu	37	chr15	91420416	91420416	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aggaccctgacccccagcctCggtacacacagatgaatgac	9	15	0	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:91420416C>A	ENST00000268171.3	+	6	832	c.553C>A	c.(553-555)Cgg>Agg	p.R185R		NM_002569.2	NP_002560.1	P09958	FURIN_HUMAN	furin (paired basic amino acid cleaving enzyme)	185	Peptidase S8.				cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of low-density lipoprotein particle receptor catabolic process (GO:0032804)|negative regulation of transforming growth factor beta1 production (GO:0032911)|nerve growth factor processing (GO:0032455)|nerve growth factor production (GO:0032902)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|post-translational protein modification (GO:0043687)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)|regulation of protein catabolic process (GO:0042176)|secretion by cell (GO:0032940)|signal peptide processing (GO:0006465)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|nerve growth factor binding (GO:0048406)|peptidase activity (GO:0008233)|peptide binding (GO:0042277)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(4)|endometrium(4)|large_intestine(3)|liver(2)|lung(13)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	36	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			CCCCCAGCCTCGGTACACACA	0.547																																					p.R185R		Atlas-SNP	.											.	FURIN	85	.	0			c.C553A						.						63	64	64					15																	91420416		2198	4298	6496	SO:0001819	synonymous_variant	5045	exon6			CAGCCTCGGTACA	X17094	CCDS10364.1	15q26.1	2007-01-24	2002-12-04	2002-12-06	ENSG00000140564	ENSG00000140564			8568	protein-coding gene	gene with protein product		136950	"paired basic amino acid cleaving enzyme (furin, membrane associated receptor protein)"	PCSK3, FUR, PACE		2251280, 1741956	Standard	NM_002569		Approved	SPC1	uc002bpu.1	P09958	OTTHUMG00000149831	ENST00000268171.3:c.553C>A	chr15.hg19:g.91420416C>A		133.0	0.0		82.0	4.0	NM_002569	Q14336|Q6LBS3|Q9UCZ5	Silent	SNP	ENST00000268171.3	hg19	CCDS10364.1																																																																																			.	.		0.547	FURIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313492.1	NM_002569		A	91420416	C	A	91420416	2	1	259	1	0	0	0	0	0	0	0	1	6107	875	31	1		1	FURIN	15	91420416	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	420900	91420416	11110976	674	36992										
SV2B	9899	hgsc.bcm.edu	37	chr15	91769904	91769904	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tttgccctgcccagtgcagaGaaggacatgtgtctgtccag	12	11	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:91769904G>A	ENST00000394232.1	+	2	881	c.411G>A	c.(409-411)gaG>gaA	p.E137E	SV2B_ENST00000545111.2_Intron|SV2B_ENST00000557291.1_Intron|SV2B_ENST00000330276.4_Silent_p.E137E	NM_014848.4	NP_055663.1	Q7L1I2	SV2B_HUMAN	synaptic vesicle glycoprotein 2B	137					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)			NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(17)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)			CCAGTGCAGAGAAGGACATGT	0.478																																					p.E137E		Atlas-SNP	.											.	SV2B	98	.	0			c.G411A						.						101	77	85					15																	91769904		2198	4298	6496	SO:0001819	synonymous_variant	9899	exon3			TGCAGAGAAGGAC	AB018278	CCDS10370.1, CCDS53972.1	15q26.1	2005-01-10			ENSG00000185518	ENSG00000185518			16874	protein-coding gene	gene with protein product		185861				9872452, 7681585	Standard	NM_014848		Approved	KIAA0735, HsT19680	uc002bqv.3	Q7L1I2	OTTHUMG00000149833	ENST00000394232.1:c.411G>A	chr15.hg19:g.91769904G>A		76.0	0.0		80.0	26.0	NM_014848	B4DH30|C6G489|O94840|Q6IAR8	Silent	SNP	ENST00000394232.1	hg19	CCDS10370.1																																																																																			.	.		0.478	SV2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313494.3	NM_014848		A	91769904	G	A	91769904	2	1	259	1	0	0	0	0	0	0	0	1	15433	933	33	3		3	SV2B	15	91769904	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	349488	91769904	10761488	675	36993										
CHD2	1106	hgsc.bcm.edu	37	chr15	93522390	93522390	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tatttaccgcttagttacaaAggggactgtggaggaggaga	14	5	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:93522390A>G	ENST00000394196.4	+	22	3821	c.2753A>G	c.(2752-2754)aAg>aGg	p.K918R	CHD2_ENST00000557381.1_Missense_Mutation_p.K918R	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	918	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			TTAGTTACAAAGGGGACTGTG	0.478																																					p.K918R		Atlas-SNP	.											.	CHD2	280	.	0			c.A2753G						.						182	183	183					15																	93522390		2197	4298	6495	SO:0001583	missense	1106	exon22			TTACAAAGGGGAC	AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.2753A>G	chr15.hg19:g.93522390A>G	ENSP00000377747:p.Lys918Arg	90.0	0.0		71.0	4.0	NM_001271	C6G482|Q96IP5	Missense_Mutation	SNP	ENST00000394196.4	hg19	CCDS10374.2	.	.	.	.	.	.	.	.	.	.	A	13.70	2.314556	0.40996	.	.	ENSG00000173575	ENST00000394196;ENST00000557381	D;D	0.96232	-3.95;-3.95	5.82	5.82	0.92795	Helicase, C-terminal (1);	0.000000	0.35677	U	0.003046	D	0.91429	0.7295	N	0.10972	0.075	0.80722	D	1	B;B;B	0.30664	0.083;0.005;0.289	B;B;B	0.36845	0.111;0.013;0.234	D	0.89958	0.4084	10	0.52906	T	0.07	-29.9084	10.5235	0.44934	0.9282:0.0:0.0718:0.0	.	918;918;918	A8K9Y5;O14647;O14647-2	.;CHD2_HUMAN;.	R	918	ENSP00000377747:K918R;ENSP00000451366:K918R	ENSP00000377747:K918R	K	+	2	0	CHD2	91323394	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.331000	0.72929	2.227000	0.72691	0.455000	0.32223	AAG	.	.		0.478	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271		G	93522390	A	G	93522390	3	3	259	1	0	0	0	0	1	0	0	0	3327	72	3	2	2839	2	CHD2	15	93522390	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1752486	93522390	9009002	676	36994										
AXIN1	8312	hgsc.bcm.edu	37	chr16	364562	364563	+	Frame_Shift_Del	DEL	AC	AC	-													0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cacgctgctgtccgtgagggAcagggtgtctgcatcgctgg							TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:364562_364563delAC	ENST00000262320.3	-	3	1370_1371	c.999_1000delGT	c.(997-1002)ctgtccfs	p.S334fs	AXIN1_ENST00000481769.1_5'UTR|AXIN1_ENST00000354866.3_Frame_Shift_Del_p.S334fs	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	334	Interaction with TP53. {ECO:0000250}.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)	p.T336fs*17(1)		biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				TCCGTGAGGGACAGGGTGTCTG	0.614																																					p.334_334del		Atlas-Indel,Pindel	.											.	AXIN1	290	.	1	Insertion - Frameshift(1)	liver(1)	c.1000_1001del						.																																			SO:0001589	frameshift_variant	8312	exon3			.	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.999_1000delGT	chr16.hg19:g.364562_364563delAC	ENSP00000262320:p.Ser334fs	135.0	0.0		52.0	23.0	NM_003502	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Frame_Shift_Del	DEL	ENST00000262320.3	hg19	CCDS10405.1																																																																																			.	.		0.614	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3			-	364563	AC	-	364562	7	5	259	1	0	1	0	1	0	0	0	0	1236	275	10	0	1624	0	AXIN1	16	364562	Frame_Shift_Del	DEL	AC	TCGA-ES-A2HS-01A-11D-A183-10		364562	89990191	677	36995										
AXIN1	8312	hgsc.bcm.edu	37	chr16	396448	396448	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agggataggtgttttcctccAtagtggcctggatttcggtc	13	8	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:396448A>T	ENST00000262320.3	-	2	949	c.578T>A	c.(577-579)aTg>aAg	p.M193K	AXIN1_ENST00000481769.1_Intron|AXIN1_ENST00000354866.3_Missense_Mutation_p.M193K	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	193	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				GTTTTCCTCCATAGTGGCCTG	0.502											OREG0003698	type=REGULATORY REGION|Gene=AXIN1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.M193K		Atlas-SNP	.											.	AXIN1	290	.	0			c.T578A						.						96	98	97					16																	396448		2203	4300	6503	SO:0001583	missense	8312	exon2			TCCTCCATAGTGG	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.578T>A	chr16.hg19:g.396448A>T	ENSP00000262320:p.Met193Lys	192.0	0.0	588	114.0	20.0	NM_181050	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Missense_Mutation	SNP	ENST00000262320.3	hg19	CCDS10405.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.579039	0.86645	.	.	ENSG00000103126	ENST00000262320;ENST00000354866	T;T	0.33865	1.39;1.39	5.39	5.39	0.77823	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);	0.038095	0.85682	D	0.000000	T	0.68769	0.3037	H	0.94925	3.6	0.80722	D	1	D;D	0.63880	0.991;0.993	P;D	0.63488	0.861;0.915	T	0.79252	-0.1880	10	0.87932	D	0	-4.3395	15.431	0.75099	1.0:0.0:0.0:0.0	.	193;193	O15169-2;O15169	.;AXIN1_HUMAN	K	193	ENSP00000262320:M193K;ENSP00000346935:M193K	ENSP00000262320:M193K	M	-	2	0	AXIN1	336449	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.206000	0.95056	2.047000	0.60756	0.533000	0.62120	ATG	.	.		0.502	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3			T	396448	A	T	396448	3	4	259	1	0	0	0	0	1	0	0	0	1236	217	8	4	2050	4	AXIN1	16	396448	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	31886	396448	89958305	678	36996										
WDR90	197335	hgsc.bcm.edu	37	chr16	711769	711769	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tggctccttcagcagcgtggGgcagacatcagccttcaggt	13	12	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:711769G>T	ENST00000293879.4	+	31	3846	c.3846G>T	c.(3844-3846)ggG>ggT	p.G1282G	WDR90_ENST00000549091.1_Silent_p.G1282G			Q96KV7	WDR90_HUMAN	WD repeat domain 90	1282										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				AGCAGCGTGGGGCAGACATCA	0.657																																					p.G1282G		Atlas-SNP	.											.	WDR90	107	.	0			c.G3846T						.						44	52	49					16																	711769		2129	4244	6373	SO:0001819	synonymous_variant	197335	exon31			GCGTGGGGCAGAC	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"WD repeat domain containing"	26960	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 17", "chromosome 16 open reading frame 15", "chromosome 16 open reading frame 16", "chromosome 16 open reading frame 19", "chromosome 16 open reading frame 18"	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.3846G>T	chr16.hg19:g.711769G>T		220.0	0.0		87.0	4.0	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Silent	SNP	ENST00000293879.4	hg19	CCDS42092.1																																																																																			.	.		0.657	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294		T	711769	G	T	711769	2	4	259	1	0	0	0	0	0	0	0	1	17352	1219	43	3		3	WDR90	16	711769	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	315321	711769	89642984	679	36997										
MSLN	10232	hgsc.bcm.edu	37	chr16	818713	818713	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tcaccgtcctggcactgctcCtagcctccaccctggcctga	8	19	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:818713C>A	ENST00000382862.3	+	17	1968	c.1873C>A	c.(1873-1875)Cta>Ata	p.L625I	MIR662_ENST00000384847.1_RNA|MSLN_ENST00000545450.2_Missense_Mutation_p.L617I|MSLN_ENST00000566549.1_Missense_Mutation_p.L617I|MSLN_ENST00000563941.1_Missense_Mutation_p.L617I	NM_013404.4	NP_037536.2	Q13421	MSLN_HUMAN	mesothelin	625					cell adhesion (GO:0007155)|pancreas development (GO:0031016)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|kidney(2)|lung(11)|pancreas(1)|prostate(1)|skin(3)	20		Hepatocellular(780;0.00335)				GGCACTGCTCCTAGCCTCCAC	0.697																																					p.L625I		Atlas-SNP	.											.	MSLN	109	.	0			c.C1873A						.						66	55	59					16																	818713		2194	4294	6488	SO:0001583	missense	10232	exon17			CTGCTCCTAGCCT	U40434	CCDS32356.1, CCDS45370.1	16p13.3	2008-04-16			ENSG00000102854	ENSG00000102854			7371	protein-coding gene	gene with protein product		601051				7665620, 8552591	Standard	NM_005823		Approved	CAK1, MPF	uc002cjw.2	Q13421	OTTHUMG00000047992	ENST00000382862.3:c.1873C>A	chr16.hg19:g.818713C>A	ENSP00000372313:p.Leu625Ile	149.0	0.0		59.0	4.0	NM_013404	D3DU65|Q14859|Q4VQD5|Q96GR6|Q96KJ5|Q9BR17|Q9BTR2|Q9UCB2|Q9UK57	Missense_Mutation	SNP	ENST00000382862.3	hg19	CCDS32356.1	.	.	.	.	.	.	.	.	.	.	C	10.26	1.301512	0.23736	.	.	ENSG00000102854	ENST00000446427;ENST00000445361;ENST00000545450;ENST00000382862	T;T	0.12255	2.7;2.7	2.84	-5.01	0.02991	.	0.284179	0.23268	N	0.050054	T	0.07324	0.0185	L	0.38175	1.15	0.09310	N	1	P;P;P	0.39862	0.642;0.692;0.642	B;B;B	0.35510	0.129;0.204;0.129	T	0.09773	-1.0659	10	0.87932	D	0	-2.3097	5.4485	0.16550	0.0:0.2956:0.156:0.5483	.	616;625;617	Q13421-4;Q13421;Q13421-3	.;MSLN_HUMAN;.	I	625;617;617;625	ENSP00000442965:L617I;ENSP00000372313:L625I	ENSP00000372313:L625I	L	+	1	2	MSLN	758714	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-0.840000	0.04363	-1.243000	0.02519	0.407000	0.27541	CTA	.	.		0.697	MSLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109253.2			A	818713	C	A	818713	3	1	259	1	0	0	0	0	1	0	0	0	9890	680	24	3	1935	3	MSLN	16	818713	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	106944	818713	89536040	680	36998										
C16orf73	254528	hgsc.bcm.edu	37	chr16	1884289	1884289	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttgtccagacaagtttctgcTtgcctcagtaggatctgcaa	9	10	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:1884289T>C	ENST00000397344.3	-	13	1491	c.1297A>G	c.(1297-1299)Agc>Ggc	p.S433G	MEIOB_ENST00000452149.2_Missense_Mutation_p.S433G|FAHD1_ENST00000382666.4_Intron|MEIOB_ENST00000470044.1_Missense_Mutation_p.S255G|MEIOB_ENST00000412554.2_Missense_Mutation_p.S462G|FAHD1_ENST00000382668.4_Intron|MEIOB_ENST00000325962.3_Missense_Mutation_p.S462G	NM_152764.2	NP_689977.2	Q8N635	MEIOB_HUMAN	meiosis specific with OB domains	433					double-strand break repair via homologous recombination (GO:0000724)|female meiosis I (GO:0007144)|fertilization (GO:0009566)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|resolution of meiotic recombination intermediates (GO:0000712)|synapsis (GO:0007129)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|single-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008310)|single-stranded DNA binding (GO:0003697)										AAGTTTCTGCTTGCCTCAGTA	0.373																																					p.S462G		Atlas-SNP	.											.	.	.	.	0			c.A1384G						.						105	99	101					16																	1884289		2199	4300	6499	SO:0001583	missense	254528	exon14			TTCTGCTTGCCTC	BC029829	CCDS10449.2, CCDS53983.1	16p13.3	2012-08-13	2012-08-13	2012-08-13	ENSG00000162039	ENSG00000162039			28569	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 73"	C16orf73		12477932	Standard	NM_152764		Approved	MGC35212	uc010uvq.1	Q8N635	OTTHUMG00000128683	ENST00000397344.3:c.1297A>G	chr16.hg19:g.1884289T>C	ENSP00000380504:p.Ser433Gly	173.0	0.0		90.0	4.0	NM_001163560	B1AK39|C9J0S1|Q96RY0	Missense_Mutation	SNP	ENST00000397344.3	hg19	CCDS10449.2	.	.	.	.	.	.	.	.	.	.	T	11.37	1.617258	0.28801	.	.	ENSG00000162039	ENST00000412554;ENST00000452149;ENST00000325962;ENST00000397344	T;T;T;T	0.09817	2.94;2.94;2.94;2.94	5.72	4.56	0.56223	.	0.147993	0.64402	D	0.000009	T	0.15782	0.0380	L	0.54323	1.7	0.21325	N	0.99972	P;P	0.51791	0.948;0.933	P;P	0.48982	0.547;0.597	T	0.07481	-1.0770	10	0.46703	T	0.11	.	9.7866	0.40679	0.1532:0.0:0.0:0.8468	.	462;433	C9J0S1;Q8N635	.;CP073_HUMAN	G	462;433;462;433	ENSP00000390778:S462G;ENSP00000391033:S433G;ENSP00000314484:S462G;ENSP00000380504:S433G	ENSP00000314484:S462G	S	-	1	0	C16orf73	1824290	0.944000	0.32072	0.281000	0.24762	0.077000	0.17291	2.286000	0.43496	2.193000	0.70182	0.477000	0.44152	AGC	.	.		0.373	MEIOB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250580.1	NM_152764		C	1884289	T	C	1884289	3	2	259	1	0	0	0	0	1	0	0	0	1834	1609	56	2	35	2	C16orf73	16	1884289	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1065576	1884289	88470464	681	36999										
SLC9A3R2	9351	hgsc.bcm.edu	37	chr16	2079608	2079608	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gcaaaggatcaaggctgtggAggggcagactcggctgctgg	18	8	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:2079608A>G	ENST00000424542.2	+	2	377	c.239A>G	c.(238-240)gAg>gGg	p.E80G	SLC9A3R2_ENST00000432365.2_Missense_Mutation_p.E80G|SLC9A3R2_ENST00000563587.1_5'UTR	NM_001130012.2|NM_004785.5	NP_001123484.1|NP_004776.3	Q15599	NHRF2_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3 regulator 2	80	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|protein complex assembly (GO:0006461)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatase binding (GO:0019902)|protein C-terminus binding (GO:0008022)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)	2						AAGGCTGTGGAGGGGCAGACT	0.662																																					p.E80G	Ovarian(69;105 1552 17724 23473)	Atlas-SNP	.											.	SLC9A3R2	24	.	0			c.A239G						.						30	41	37					16																	2079608		2105	4209	6314	SO:0001583	missense	9351	exon2			CTGTGGAGGGGCA	AF004900	CCDS45382.1, CCDS45383.1, CCDS58407.1	16p13.3	2014-09-04	2012-03-22		ENSG00000065054	ENSG00000065054			11076	protein-coding gene	gene with protein product		606553	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 3 regulatory factor 2", "solute carrier family 9 (sodium/hydrogen exchanger), isoform 3 regulator 2", "solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 2"			9054412, 9671706	Standard	NM_001130012		Approved	SIP-1, TKA-1, NHERF-2, E3KARP	uc002coi.3	Q15599	OTTHUMG00000176956	ENST00000424542.2:c.239A>G	chr16.hg19:g.2079608A>G	ENSP00000408005:p.Glu80Gly	191.0	0.0		108.0	5.0	NM_004785	D3DU84|D3DU85|H3BSV6|O00272|O00556|Q3KQY7	Missense_Mutation	SNP	ENST00000424542.2	hg19	CCDS45382.1	.	.	.	.	.	.	.	.	.	.	A	11.08	1.534723	0.27475	.	.	ENSG00000065054	ENST00000424542;ENST00000432365	T;T	0.41400	1.0;1.0	4.61	3.52	0.40303	PDZ/DHR/GLGF (4);	0.122780	0.53938	D	0.000045	T	0.13114	0.0318	N	0.00666	-1.275	0.80722	D	1	B;B	0.19935	0.002;0.04	B;B	0.26969	0.006;0.075	T	0.07947	-1.0746	10	0.19590	T	0.45	-17.7268	7.529	0.27672	0.9012:0.0:0.0988:0.0	.	80;80	D3DU85;Q15599	.;NHRF2_HUMAN	G	80	ENSP00000408005:E80G;ENSP00000402857:E80G	ENSP00000408005:E80G	E	+	2	0	SLC9A3R2	2019609	1.000000	0.71417	0.995000	0.50966	0.912000	0.54170	4.297000	0.59061	1.728000	0.51552	0.454000	0.30748	GAG	.	.		0.662	SLC9A3R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434448.1			G	2079608	A	G	2079608	3	3	259	1	0	0	0	0	1	0	0	0	14730	304	11	2	245	2	SLC9A3R2	16	2079608	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	195319	2079608	88275145	682	37000										
AMDHD2	752014	hgsc.bcm.edu	37	chr16	2580390	2580390	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttggccctggcacacacccaTgtggcaaacacgggccgtga	12	14	0	1	rs375591203		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:2580390T>C	ENST00000567119.1	-	1	1019	c.685A>G	c.(685-687)Atg>Gtg	p.M229V	AMDHD2_ENST00000302956.4_3'UTR|CEMP1_ENST00000565480.1_Intron|AMDHD2_ENST00000565570.1_3'UTR|CEMP1_ENST00000382350.1_Missense_Mutation_p.M229V|AMDHD2_ENST00000413459.3_Missense_Mutation_p.M472T|MIR3178_ENST00000581887.1_RNA	NM_001048212.3	NP_001041677.1	Q6PRD7	CEMP1_HUMAN	cementum protein 1	229						cytoplasm (GO:0005737)				lung(1)|skin(1)	2						CACACACCCATGTGGCAAACA	0.627																																					p.M472T		Atlas-SNP	.											.	AMDHD2	33	.	0			c.T1415C						.	T	VAL/MET,THR/MET	1,4111		0,1,2055	55	58	57		685,1415	-3	0	16		57	0,8404		0,0,4202	no	missense,missense	AMDHD2,CEMP1	NM_001048212.3,NM_001145815.1	21,81	0,1,6257	CC,CT,TT		0.0,0.0243,0.0080	benign,benign	229/248,472/595	2580390	1,12515	2056	4202	6258	SO:0001583	missense	51005	exon11			CACCCATGTGGCA	AY584596	CCDS42108.1	16p13.3	2006-09-22							32553	protein-coding gene	gene with protein product	"cementum protein-23"	611113				16263347	Standard	NM_001048212		Approved	CP-23	uc002cqr.3	Q6PRD7		ENST00000567119.1:c.685A>G	chr16.hg19:g.2580390T>C	ENSP00000457380:p.Met229Val	167.0	0.0		78.0	4.0	NM_001145815	B2RUY1	Missense_Mutation	SNP	ENST00000567119.1	hg19	CCDS42108.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	3.146|3.146	-0.175183|-0.175183	0.06421|0.06421	2.43E-4|2.43E-4	0.0|0.0	ENSG00000162066|ENSG00000205923	ENST00000413459|ENST00000382350	.|T	.|0.48522	.|0.81	2.1|2.1	-2.95|-2.95	0.05564|0.05564	.|.	.|.	.|.	.|.	.|.	T|T	0.22399|0.22399	0.0540|0.0540	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B|B	0.02656|0.10296	0.0|0.003	B|B	0.01281|0.13407	0.0|0.009	T|T	0.16012|0.16012	-1.0417|-1.0417	8|9	0.87932|0.87932	D|D	0|0	.|.	3.4838|3.4838	0.07611|0.07611	0.0:0.3012:0.2137:0.485|0.0:0.3012:0.2137:0.485	.|.	472|229	Q9Y303-3|Q6PRD7	.|CEMP1_HUMAN	T|V	472|229	.|ENSP00000371787:M229V	ENSP00000391596:M472T|ENSP00000371787:M229V	M|M	+|-	2|1	0|0	AMDHD2|CEMP1	2520391|2520391	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-0.856000|-0.856000	0.04290|0.04290	-0.752000|-0.752000	0.04728|0.04728	-0.366000|-0.366000	0.07423|0.07423	ATG|ATG	.	.		0.627	CEMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435686.1	NM_001048212		C	2580390	T	C	2580390	3	2	259	1	0	0	0	0	1	0	0	0	568	1464	51	2	1495	2	AMDHD2	16	2580390	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	500782	2580390	87774363	683	37001										
CREBBP	1387	hgsc.bcm.edu	37	chr16	3778015	3778015	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agactggacaggggctggagAccgcacctggttactaaggg	16	9	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:3778015A>G	ENST00000262367.5	-	31	7842	c.7033T>C	c.(7033-7035)Tct>Cct	p.S2345P	CREBBP_ENST00000382070.3_Missense_Mutation_p.S2307P	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	2345					cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		GGGGCTGGAGACCGCACCTGG	0.647			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																														p.S2345P		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP	546	.	0			c.T7033C						.						89	87	88					16																	3778015		2197	4300	6497	SO:0001583	missense	1387	exon31			CTGGAGACCGCAC	U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.7033T>C	chr16.hg19:g.3778015A>G	ENSP00000262367:p.Ser2345Pro	223.0	0.0		108.0	5.0	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	hg19	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	a	12.31	1.900600	0.33535	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070;ENST00000323508	D;D	0.88354	-2.37;-2.31	5.35	5.35	0.76521	.	0.149672	0.47852	D	0.000203	D	0.90827	0.7119	L	0.34521	1.04	0.80722	D	1	D;D	0.65815	0.995;0.995	D;D	0.72982	0.979;0.979	D	0.90892	0.4762	10	0.45353	T	0.12	-8.416	14.8194	0.70059	1.0:0.0:0.0:0.0	.	2375;2345	Q4LE28;Q92793	.;CBP_HUMAN	P	2345;2375;2307;880	ENSP00000262367:S2345P;ENSP00000371502:S2307P	ENSP00000262367:S2345P	S	-	1	0	CREBBP	3718016	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.185000	0.94900	2.156000	0.67533	0.533000	0.62120	TCT	.	.		0.647	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		G	3778015	A	G	3778015	3	3	259	1	0	0	0	0	1	0	0	0	3863	275	10	2	299	2	CREBBP	16	3778015	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1197625	3778015	86576738	684	37002										
ZC3H7A	29066	hgsc.bcm.edu	37	chr16	11862325	11862325	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cttgaaattcccaggaaattCtctgaagcaaacaaactacc	5	11	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:11862325C>A	ENST00000396516.2	-	11	1403	c.1206G>T	c.(1204-1206)gaG>gaT	p.E402D	ZC3H7A_ENST00000355758.4_Missense_Mutation_p.E402D			Q8IWR0	Z3H7A_HUMAN	zinc finger CCCH-type containing 7A	402						nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(3)|kidney(5)|large_intestine(2)|liver(1)|lung(3)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(2)	25						CCAGGAAATTCTCTGAAGCAA	0.368																																					p.E402D		Atlas-SNP	.											ZC3H7A,NS,carcinoma,0,2	ZC3H7A	72	.	0			c.G1206T						.						70	73	72					16																	11862325		2197	4300	6497	SO:0001583	missense	29066	exon12			GAAATTCTCTGAA	AF161540	CCDS10550.1	16p13-p12	2013-01-11	2005-06-02	2005-06-08	ENSG00000122299	ENSG00000122299		"Zinc fingers, CCCH-type domain containing", "Tetratricopeptide (TTC) repeat domain containing"	30959	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 7", "zinc finger CCCH-type containing 7"	ZC3HDC7, ZC3H7		11042152	Standard	NM_014153		Approved	HSPC055, FLJ20318	uc002dbl.3	Q8IWR0	OTTHUMG00000129825	ENST00000396516.2:c.1206G>T	chr16.hg19:g.11862325C>A	ENSP00000379773:p.Glu402Asp	81.0	0.0		60.0	3.0	NM_014153	D3DUG5|Q9NPE9	Missense_Mutation	SNP	ENST00000396516.2	hg19	CCDS10550.1	.	.	.	.	.	.	.	.	.	.	C	10.47	1.358598	0.24598	.	.	ENSG00000122299	ENST00000355758;ENST00000396516	T;T	0.10477	2.87;2.87	5.74	1.54	0.23209	.	0.427763	0.29376	N	0.012323	T	0.04182	0.0116	N	0.11427	0.14	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.09377	0.004;0.002	T	0.44174	-0.9345	10	0.22706	T	0.39	.	2.564	0.04778	0.1315:0.5168:0.1277:0.2241	.	123;402	Q9NXC8;Q8IWR0	.;Z3H7A_HUMAN	D	402	ENSP00000347999:E402D;ENSP00000379773:E402D	ENSP00000347999:E402D	E	-	3	2	ZC3H7A	11769826	0.999000	0.42202	0.811000	0.32455	0.778000	0.44026	0.502000	0.22594	0.064000	0.16427	-0.137000	0.14449	GAG	.	.		0.368	ZC3H7A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437066.1	NM_014153		A	11862325	C	A	11862325	3	1	259	1	0	0	0	0	1	0	0	0	17587	912	32	3	1757	3	ZC3H7A	16	11862325	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	8084310	11862325	78492428	685	37003										
RRN3	54700	hgsc.bcm.edu	37	chr16	15168676	15168676	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	caccatctggtcgagccgttCaggaccagcctttgtttcat	9	13	3	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:15168676C>T	ENST00000198767.6	-	11	984	c.901G>A	c.(901-903)Gaa>Aaa	p.E301K	RRN3_ENST00000540462.1_Missense_Mutation_p.E119K|PDXDC1_ENST00000535621.2_Intron|RRN3_ENST00000563559.1_Missense_Mutation_p.E301K|RRN3_ENST00000429751.2_Missense_Mutation_p.E271K|RRN3_ENST00000327307.7_Missense_Mutation_p.E268K	NM_018427.3	NP_060897.3	Q9NYV6	RRN3_HUMAN	RRN3 RNA polymerase I transcription factor homolog (S. cerevisiae)	301					cell proliferation (GO:0008283)|cytoplasm organization (GO:0007028)|gene expression (GO:0010467)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator (GO:1902254)|nucleolus organization (GO:0007000)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, initiation (GO:2000142)|ribosome biogenesis (GO:0042254)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(2)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)	20						TCGAGCCGTTCAGGACCAGCC	0.408																																					p.E301K		Atlas-SNP	.											.	RRN3	36	.	0			c.G901A						.						117	87	97					16																	15168676		2197	4300	6497	SO:0001583	missense	54700	exon11			GCCGTTCAGGACC	AF227156	CCDS10559.1, CCDS73833.1	16p13.11	2009-10-26	2006-04-04		ENSG00000085721	ENSG00000085721			30346	protein-coding gene	gene with protein product		605121	"RRN3 RNA polymerase I transcription factor homolog (yeast)"			10758157, 11250903	Standard	XM_005255375		Approved	DKFZp566E104	uc002dde.3	Q9NYV6	OTTHUMG00000129847	ENST00000198767.6:c.901G>A	chr16.hg19:g.15168676C>T	ENSP00000198767:p.Glu301Lys	119.0	0.0		71.0	4.0	NM_018427	A2RTY9|B4E0J7|B4E3T2|Q3MHU9|Q6IPL4|Q9H4F0	Missense_Mutation	SNP	ENST00000198767.6	hg19	CCDS10559.1	.	.	.	.	.	.	.	.	.	.	.	0.242	-1.013088	0.02095	.	.	ENSG00000085721	ENST00000198767;ENST00000429751;ENST00000327307;ENST00000540462	T;T;T;T	0.41400	1.0;1.0;1.0;1.0	5.52	-0.359	0.12571	.	1.706890	0.03358	N	0.197154	T	0.33469	0.0864	L	0.46157	1.445	0.09310	N	1	B;B;B	0.12630	0.006;0.001;0.0	B;B;B	0.15870	0.014;0.002;0.001	T	0.09552	-1.0669	10	0.15499	T	0.54	.	5.1958	0.15236	0.1117:0.2372:0.5061:0.145	.	271;202;301	F5H148;B4DZL9;Q9NYV6	.;.;RRN3_HUMAN	K	301;271;268;119	ENSP00000198767:E301K;ENSP00000402027:E271K;ENSP00000318484:E268K;ENSP00000437963:E119K	ENSP00000198767:E301K	E	-	1	0	RRN3	15076177	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.120000	0.15647	0.005000	0.14708	-0.254000	0.11334	GAA	.	.		0.408	RRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252087.2	NM_018427		T	15168676	C	T	15168676	3	4	259	1	0	0	0	0	1	0	0	0	13699	835	29	3	1086	3	RRN3	16	15168676	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	3306351	15168676	75186077	686	37004										
SMG1	23049	hgsc.bcm.edu	37	chr16	18846414	18846414	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atgtctgctgcgtatcgctgCagggtcatttcagtggcagt	13	9	3	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:18846414C>T	ENST00000446231.2	-	49	8542	c.8130G>A	c.(8128-8130)ctG>ctA	p.L2710L	SMG1_ENST00000389467.3_Silent_p.L2710L			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	2710					DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						CGTATCGCTGCAGGGTCATTT	0.453																																					p.L2710L		Atlas-SNP	.											.	SMG1	401	.	0			c.G8130A						.						139	134	135					16																	18846414		1946	4155	6101	SO:0001819	synonymous_variant	23049	exon49			TCGCTGCAGGGTC	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase-related kinase"	607032	"smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.8130G>A	chr16.hg19:g.18846414C>T		243.0	0.0		203.0	116.0	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Silent	SNP	ENST00000446231.2	hg19	CCDS45430.1																																																																																			.	.		0.453	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		T	18846414	C	T	18846414	2	4	259	1	0	0	0	0	0	0	0	1	14810	697	25	3		3	SMG1	16	18846414	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	3677738	18846414	71508339	687	37005										
PALB2	79728	hgsc.bcm.edu	37	chr16	23641766	23641766	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tactccaagaaagggaatccTctttttgatgacgacttttc	7	9	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:23641766T>C	ENST00000261584.4	-	5	1861	c.1709A>G	c.(1708-1710)gAg>gGg	p.E570G		NM_024675.3	NP_078951.2	Q86YC2	PALB2_HUMAN	partner and localizer of BRCA2	570	DNA-binding (with the preference D loop > dsDNA > ssDNA).				DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|inner cell mass cell proliferation (GO:0001833)|mesoderm development (GO:0007498)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|post-anal tail morphogenesis (GO:0036342)|somitogenesis (GO:0001756)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(3)	55				GBM - Glioblastoma multiforme(48;0.0167)		AAGGGAATCCTCTTTTTGATG	0.358			"F, N, Mis"			"Wilms tumor, medulloblastoma, AML ,breast"		Involved in tolerance or repair of DNA crosslinks																													p.E570G		Atlas-SNP	.	yes	Rec		"Fanconi anaemia N, breast cancer susceptibility "	16	16p12.1	79728	partner and localizer of BRCA2		"L, O, E"	.	PALB2	108	.	0			c.A1709G						.						38	34	35					16																	23641766		2197	4300	6497	SO:0001583	missense	79728	exon5			GAATCCTCTTTTT		CCDS32406.1	16p12.1	2014-09-17				ENSG00000083093		"Fanconi anemia, complementation groups"	26144	protein-coding gene	gene with protein product	"Fanconi anemia, complementation group N"	610355				16793542, 17200672	Standard	NM_024675		Approved	FLJ21816, FANCN	uc002dlx.1	Q86YC2		ENST00000261584.4:c.1709A>G	chr16.hg19:g.23641766T>C	ENSP00000261584:p.Glu570Gly	189.0	0.0		93.0	4.0	NM_024675	A6NIE1|Q8N7Y6|Q8ND31|Q9H6W1	Missense_Mutation	SNP	ENST00000261584.4	hg19	CCDS32406.1	.	.	.	.	.	.	.	.	.	.	T	12.53	1.966291	0.34659	.	.	ENSG00000083093	ENST00000261584	T	0.16743	2.32	5.05	3.88	0.44766	.	0.563831	0.17191	N	0.183487	T	0.21227	0.0511	M	0.63428	1.95	0.09310	N	1	P	0.46784	0.884	P	0.46253	0.509	T	0.07252	-1.0782	10	0.30854	T	0.27	-4.9817	8.2211	0.31541	0.0:0.0:0.2023:0.7977	.	570	Q86YC2	PALB2_HUMAN	G	570	ENSP00000261584:E570G	ENSP00000261584:E570G	E	-	2	0	PALB2	23549267	0.000000	0.05858	0.347000	0.25668	0.119000	0.20118	0.136000	0.15974	1.885000	0.54596	0.533000	0.62120	GAG	.	.		0.358	PALB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435287.2	NM_024675		C	23641766	T	C	23641766	3	2	259	1	0	0	0	0	1	0	0	0	11415	1551	54	2	1887	2	PALB2	16	23641766	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	4795352	23641766	66712987	688	37006										
ERN2	10595	hgsc.bcm.edu	37	chr16	23707249	23707249	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cccgcctgccccgcggcccaGcacgtccttgggattgaagg	13	17	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:23707249G>A	ENST00000457008.2	-	13	1458	c.1420C>T	c.(1420-1422)Ctg>Ttg	p.L474L	ERN2_ENST00000256797.4_Silent_p.L574L					endoplasmic reticulum to nucleus signaling 2											large_intestine(2)|lung(2)|ovary(2)	6				GBM - Glioblastoma multiforme(48;0.0156)		CCGCGGCCCAGCACGTCCTTG	0.642																																					p.L574L		Atlas-SNP	.											.	ERN2	131	.	0			c.C1720T						.						45	42	43					16																	23707249		2197	4300	6497	SO:0001819	synonymous_variant	10595	exon14			GGCCCAGCACGTC	AA527544	CCDS32407.1	16p12.2	2008-02-05	2007-08-14			ENSG00000134398			16942	protein-coding gene	gene with protein product		604034	"ER to nucleus signalling 2"			9755171, 11175748	Standard	NM_033266		Approved	IRE1b	uc002dma.4	Q76MJ5		ENST00000457008.2:c.1420C>T	chr16.hg19:g.23707249G>A		96.0	0.0		75.0	22.0	NM_033266		Silent	SNP	ENST00000457008.2	hg19																																																																																				.	.		0.642	ERN2-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000434886.1			A	23707249	G	A	23707249	2	1	259	1	0	0	0	0	0	0	0	1	5240	962	34	3		3	ERN2	16	23707249	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	65483	23707249	66647504	689	37007										
TNRC6A	27327	hgsc.bcm.edu	37	chr16	24834848	24834848	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccagtctctgaccccttctcCcggctggcagtctctcgggt	10	17	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:24834848C>A	ENST00000395799.3	+	25	5738	c.5609C>A	c.(5608-5610)cCc>cAc	p.P1870H	TNRC6A_ENST00000432286.2_Missense_Mutation_p.P348H|TNRC6A_ENST00000315183.7_Missense_Mutation_p.P1821H	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	1870	Sufficient for interaction with AGO2.				cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		ACCCCTTCTCCCGGCTGGCAG	0.557																																					p.P1870H		Atlas-SNP	.											.	TNRC6A	171	.	0			c.C5609A						.						97	103	101					16																	24834848		2197	4300	6497	SO:0001583	missense	27327	exon25			CTTCTCCCGGCTG	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"Trinucleotide (CAG) repeat containing"	11969	protein-coding gene	gene with protein product		610739	"trinucleotide repeat containing 6"	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.5609C>A	chr16.hg19:g.24834848C>A	ENSP00000379144:p.Pro1870His	104.0	0.0		61.0	4.0	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	hg19	CCDS10624.2	.	.	.	.	.	.	.	.	.	.	c	17.76	3.469269	0.63625	.	.	ENSG00000090905	ENST00000315183;ENST00000395799;ENST00000432286	T;T	0.12879	2.65;2.64	5.64	5.64	0.86602	.	0.059955	0.64402	D	0.000002	T	0.32466	0.0830	L	0.44542	1.39	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.70935	0.971;0.956	T	0.01235	-1.1410	10	0.87932	D	0	-4.6991	19.7099	0.96094	0.0:1.0:0.0:0.0	.	1821;1870	Q8NDV7-6;Q8NDV7	.;TNR6A_HUMAN	H	1821;1870;348	ENSP00000326900:P1821H;ENSP00000379144:P1870H	ENSP00000326900:P1821H	P	+	2	0	TNRC6A	24742349	0.999000	0.42202	0.998000	0.56505	0.993000	0.82548	5.619000	0.67729	2.638000	0.89438	0.651000	0.88453	CCC	.	.		0.557	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		A	24834848	C	A	24834848	3	1	259	1	0	0	0	0	1	0	0	0	16355	623	22	3	5707	3	TNRC6A	16	24834848	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	1127599	24834848	65519905	690	37008										
GTF3C1	2975	hgsc.bcm.edu	37	chr16	27499733	27499733	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cccaaatattcaacctgctgTtgcctagacataatcacagg	6	12	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:27499733T>C	ENST00000356183.4	-	23	3530	c.3515A>G	c.(3514-3516)aAc>aGc	p.N1172S	GTF3C1_ENST00000561623.1_Missense_Mutation_p.N1172S	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	1172					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						CAACCTGCTGTTGCCTAGACA	0.542																																					p.N1172S		Atlas-SNP	.											.	GTF3C1	210	.	0			c.A3515G						.						108	109	109					16																	27499733		2197	4300	6497	SO:0001583	missense	2975	exon23			CTGCTGTTGCCTA	U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"General transcription factors"	4664	protein-coding gene	gene with protein product		603246	"general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.3515A>G	chr16.hg19:g.27499733T>C	ENSP00000348510:p.Asn1172Ser	105.0	0.0		60.0	4.0	NM_001520	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Missense_Mutation	SNP	ENST00000356183.4	hg19	CCDS32414.1	.	.	.	.	.	.	.	.	.	.	T	1.419	-0.573316	0.03882	.	.	ENSG00000077235	ENST00000356183;ENST00000388971	T	0.21932	1.98	4.9	-6.65	0.01795	.	0.943286	0.08892	N	0.878477	T	0.08403	0.0209	N	0.16066	0.365	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.09377	0.001;0.004	T	0.43507	-0.9387	10	0.02654	T	1	-19.0721	10.3697	0.44046	0.0:0.5609:0.1161:0.323	.	1172;1172	Q12789;Q12789-3	TF3C1_HUMAN;.	S	1172;1168	ENSP00000348510:N1172S	ENSP00000348510:N1172S	N	-	2	0	GTF3C1	27407234	0.000000	0.05858	0.000000	0.03702	0.895000	0.52256	-0.690000	0.05138	-1.774000	0.01288	0.459000	0.35465	AAC	.	.		0.542	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520		C	27499733	T	C	27499733	3	2	259	1	0	0	0	0	1	0	0	0	6881	1725	60	2	2874	2	GTF3C1	16	27499733	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	2664885	27499733	62855020	691	37009										
SEZ6L2	26470	hgsc.bcm.edu	37	chr16	29891258	29891258	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tcgatggcattggggggcccAgggggctccagggcatatcc	17	11	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:29891258A>G	ENST00000308713.5	-	9	2027	c.1500T>C	c.(1498-1500)ccT>ccC	p.P500P	SEZ6L2_ENST00000350527.3_Silent_p.P430P|SEZ6L2_ENST00000537485.1_Silent_p.P456P|SEZ6L2_ENST00000346932.5_Silent_p.P386P	NM_001114099.2|NM_201575.3	NP_001107571.1|NP_963869.2	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2	500	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TGGGGGGCCCAGGGGGCTCCA	0.612																																					p.P500P		Atlas-SNP	.											.	SEZ6L2	137	.	0			c.T1500C						.						114	114	114					16																	29891258		2197	4300	6497	SO:0001819	synonymous_variant	26470	exon9			GGGCCCAGGGGGC	AY358404	CCDS10658.1, CCDS10659.1, CCDS45458.1, CCDS58447.1, CCDS73865.1	16p12.1	2008-02-05			ENSG00000174938	ENSG00000174938			30844	protein-coding gene	gene with protein product	"type I transmembrane receptor (seizure related protein)"					12975309	Standard	NM_012410		Approved	PSK-1, FLJ90517	uc010vec.2	Q6UXD5	OTTHUMG00000132112	ENST00000308713.5:c.1500T>C	chr16.hg19:g.29891258A>G		95.0	0.0		70.0	4.0	NM_001243332	B7Z1N0|F5H293|H7BXQ6|Q9BW82|Q9UJ45|Q9UJ46|Q9UJ47	Silent	SNP	ENST00000308713.5	hg19	CCDS10659.1																																																																																			.	.		0.612	SEZ6L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255154.2	NM_012410		G	29891258	A	G	29891258	2	3	259	1	0	0	0	0	0	0	0	1	14159	175	7	2		2	SEZ6L2	16	29891258	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2391525	29891258	60463495	692	37010										
ITGAL	3683	hgsc.bcm.edu	37	chr16	30500452	30500452	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aacatggagctgtcctccagCggcatcagtgctgacctcag	11	13	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:30500452C>T	ENST00000356798.6	+	10	1236	c.1056C>T	c.(1054-1056)agC>agT	p.S352S	RP11-297C4.2_ENST00000569459.1_RNA|ITGAL_ENST00000433423.2_Intron|ITGAL_ENST00000358164.5_Silent_p.S269S|ITGAL_ENST00000568012.1_3'UTR	NM_002209.2	NP_002200.2	P20701	ITAL_HUMAN	integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)	352					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell proliferation (GO:0042102)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(10)|kidney(4)|large_intestine(12)|lung(32)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	76					Antithymocyte globulin(DB00098)|Efalizumab(DB00095)|Lovastatin(DB00227)	TGTCCTCCAGCGGCATCAGTG	0.597																																					p.S352S	NSCLC(110;1462 1641 3311 33990 49495)	Atlas-SNP	.											.	ITGAL	149	.	0			c.C1056T						.						68	62	64					16																	30500452		2197	4300	6497	SO:0001819	synonymous_variant	3683	exon10			CTCCAGCGGCATC		CCDS32433.1, CCDS45461.1	16p13.1-p11	2010-03-23				ENSG00000005844		"CD molecules", "Integrins"	6148	protein-coding gene	gene with protein product		153370		CD11A		3284962	Standard	NM_002209		Approved	LFA-1	uc002dyi.4	P20701		ENST00000356798.6:c.1056C>T	chr16.hg19:g.30500452C>T		124.0	0.0		100.0	4.0	NM_002209	O43746|Q45H73|Q96HB1|Q9UBC8	Silent	SNP	ENST00000356798.6	hg19	CCDS32433.1																																																																																			.	.		0.597	ITGAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434508.2			T	30500452	C	T	30500452	2	4	259	1	0	0	0	0	0	0	0	1	7895	767	27	1		1	ITGAL	16	30500452	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	609194	30500452	59854301	693	37011										
ITGAX	3687	hgsc.bcm.edu	37	chr16	31373480	31373480	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	caaatatgagccctaccttcAtcaacatgtctcaggagaat	6	11	3	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:31373480A>T	ENST00000268296.4	+	11	1292	c.1171A>T	c.(1171-1173)Atc>Ttc	p.I391F	ITGAX_ENST00000562522.1_Missense_Mutation_p.I391F	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	391					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						CCCTACCTTCATCAACATGTC	0.582																																					p.I391F		Atlas-SNP	.											.	ITGAX	198	.	0			c.A1171T						.						100	100	100					16																	31373480		2197	4300	6497	SO:0001583	missense	3687	exon11			ACCTTCATCAACA	BC038237	CCDS10711.1, CCDS67014.1	16p11.2	2010-03-23	2006-02-10		ENSG00000140678	ENSG00000140678		"CD molecules", "Complement system", "Integrins"	6152	protein-coding gene	gene with protein product		151510	"integrin, alpha X (antigen CD11C (p150), alpha polypeptide)"	CD11C		3284962, 2303426	Standard	NM_001286375		Approved	CD11c	uc002ebu.1	P20702	OTTHUMG00000132465	ENST00000268296.4:c.1171A>T	chr16.hg19:g.31373480A>T	ENSP00000268296:p.Ile391Phe	170.0	0.0		86.0	4.0	NM_000887	Q8IVA6	Missense_Mutation	SNP	ENST00000268296.4	hg19	CCDS10711.1	.	.	.	.	.	.	.	.	.	.	a	18.06	3.539840	0.65085	.	.	ENSG00000140678	ENST00000268296	T	0.71698	-0.59	4.5	4.5	0.54988	.	.	.	.	.	T	0.79793	0.4507	M	0.68593	2.085	0.34780	D	0.734667	D	0.89917	1.0	D	0.91635	0.999	D	0.84522	0.0628	9	0.72032	D	0.01	.	7.0718	0.25183	0.8953:0.0:0.1047:0.0	.	391	P20702	ITAX_HUMAN	F	391	ENSP00000268296:I391F	ENSP00000268296:I391F	I	+	1	0	ITGAX	31280981	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	1.392000	0.34486	1.798000	0.52647	0.473000	0.43528	ATC	.	.		0.582	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887		T	31373480	A	T	31373480	3	4	259	1	0	0	0	0	1	0	0	0	7898	217	8	4	1213	4	ITGAX	16	31373480	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	873028	31373480	58981273	694	37012										
NETO2	81831	hgsc.bcm.edu	37	chr16	47163230	47163230	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgctggttcgaacccaaatgCcacactgggttgcaggaata	11	10	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:47163230C>T	ENST00000562435.1	-	3	521	c.137G>A	c.(136-138)gGc>gAc	p.G46D	NETO2_ENST00000303155.5_Missense_Mutation_p.G46D	NM_018092.4	NP_060562.3	Q8NC67	NETO2_HUMAN	neuropilin (NRP) and tolloid (TLL)-like 2	46	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				regulation of kainate selective glutamate receptor activity (GO:2000312)	kainate selective glutamate receptor complex (GO:0032983)|postsynaptic density (GO:0014069)				breast(1)|cervix(1)|endometrium(1)|large_intestine(8)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	29		all_cancers(37;0.00114)|all_lung(18;0.00432)|Lung NSC(13;0.0384)|Breast(268;0.174)				AACCCAAATGCCACACTGGGT	0.393										HNSCC(25;0.065)																											p.G46D		Atlas-SNP	.											.	NETO2	67	.	0			c.G137A						.						163	153	156					16																	47163230		2202	4300	6502	SO:0001583	missense	81831	exon3			CAAATGCCACACT	AK001292	CCDS10727.1, CCDS58460.1	16q11.2	2008-08-04			ENSG00000171208	ENSG00000171208			14644	protein-coding gene	gene with protein product		607974				11943477	Standard	NM_018092		Approved	FLJ10430, NEOT2	uc002eer.2	Q8NC67	OTTHUMG00000133101	ENST00000562435.1:c.137G>A	chr16.hg19:g.47163230C>T	ENSP00000455169:p.Gly46Asp	138.0	0.0		79.0	4.0	NM_018092	J3KNF1|Q7Z381|Q8ND51|Q96SP4|Q9NVY8	Missense_Mutation	SNP	ENST00000562435.1	hg19	CCDS10727.1	.	.	.	.	.	.	.	.	.	.	C	19.73	3.882055	0.72294	.	.	ENSG00000171208	ENST00000303155	T	0.37411	1.2	6.03	6.03	0.97812	CUB (5);	0.048111	0.85682	D	0.000000	T	0.56171	0.1967	H	0.96430	3.82	0.54753	D	0.999983	B;B	0.19331	0.035;0.035	B;B	0.26094	0.066;0.066	T	0.61950	-0.6957	10	0.59425	D	0.04	.	14.1385	0.65303	0.0:0.9235:0.0:0.0765	.	46;46	Q32NC3;Q8NC67	.;NETO2_HUMAN	D	46	ENSP00000306726:G46D	ENSP00000306726:G46D	G	-	2	0	NETO2	45720731	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.816000	0.62642	2.854000	0.98071	0.655000	0.94253	GGC	.	.		0.393	NETO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256766.2	NM_018092		T	47163230	C	T	47163230	3	4	259	1	0	0	0	0	1	0	0	0	10349	739	26	3	1468	3	NETO2	16	47163230	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	15789750	47163230	43191523	695	37013										
N4BP1	9683	hgsc.bcm.edu	37	chr16	48596338	48596338	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tcttctagttcaggttcacaGattcctttaatatattcctg	5	9	4	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:48596338G>T	ENST00000262384.3	-	2	452	c.216C>A	c.(214-216)atC>atA	p.I72I	RP11-44I10.3_ENST00000563994.1_RNA	NM_153029.3	NP_694574.3	O75113	N4BP1_HUMAN	NEDD4 binding protein 1	72					cellular response to UV (GO:0034644)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein ubiquitination (GO:0031397)	nucleolus (GO:0005730)|PML body (GO:0016605)				breast(3)|kidney(2)|lung(11)|urinary_tract(1)	17		all_cancers(37;0.179)|all_lung(18;0.11)				CAGGTTCACAGATTCCTTTAA	0.343																																					p.I72I		Atlas-SNP	.											N4BP1_ENST00000262384,NS,carcinoma,0,2	N4BP1	121	.	0			c.C216A						.						37	37	37					16																	48596338		1827	4077	5904	SO:0001819	synonymous_variant	9683	exon2			TTCACAGATTCCT	AK026937	CCDS45479.1	16q12.1	2008-01-18				ENSG00000102921			29850	protein-coding gene	gene with protein product						9734811, 11717310	Standard	NM_153029		Approved		uc002efp.3	O75113		ENST00000262384.3:c.216C>A	chr16.hg19:g.48596338G>T		126.0	0.0		72.0	3.0	NM_153029	A7MD49|Q2YDX1	Silent	SNP	ENST00000262384.3	hg19	CCDS45479.1																																																																																			.	.		0.343	N4BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429920.1	NM_014664		T	48596338	G	T	48596338	2	4	259	1	0	0	0	0	0	0	0	1	10118	932	33	3		3	N4BP1	16	48596338	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1433108	48596338	41758415	696	37014										
SALL1	6299	hgsc.bcm.edu	37	chr16	51175284	51175284	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gataaatgggaacttagcgtGgacaaggggttggcagatgt	16	4	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:51175284G>T	ENST00000251020.4	-	2	882	c.849C>A	c.(847-849)tcC>tcA	p.S283S	SALL1_ENST00000562674.1_5'Flank|SALL1_ENST00000541611.1_Intron|SALL1_ENST00000566102.1_Intron|SALL1_ENST00000440970.1_Silent_p.S186S	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	283					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			AACTTAGCGTGGACAAGGGGT	0.498																																					p.S283S	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											.	SALL1	301	.	0			c.C849A						.						91	91	91					16																	51175284		2198	4300	6498	SO:0001819	synonymous_variant	6299	exon2			TAGCGTGGACAAG	X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"Zinc fingers, C2H2-type"	10524	protein-coding gene	gene with protein product		602218	"sal (Drosophila)-like 1", "sal-like 1 (Drosophila)"	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.849C>A	chr16.hg19:g.51175284G>T		110.0	0.0		69.0	4.0	NM_002968	Q99881|Q9NSC3|Q9P1R0	Silent	SNP	ENST00000251020.4	hg19	CCDS10747.1																																																																																			.	.		0.498	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968		T	51175284	G	T	51175284	2	4	259	1	0	0	0	0	0	0	0	1	13825	1335	47	3		3	SALL1	16	51175284	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	2578946	51175284	39179469	697	37015										
RPGRIP1L	23322	hgsc.bcm.edu	37	chr16	53636067	53636067	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cgactgttaccctgagcttgCcaataccttcaccatctgct	6	15	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:53636067C>T	ENST00000379925.3	-	27	3919	c.3869G>A	c.(3868-3870)gGc>gAc	p.G1290D	RPGRIP1L_ENST00000563746.1_Missense_Mutation_p.G1256D|RPGRIP1L_ENST00000262135.4_Missense_Mutation_p.G1210D	NM_015272.2	NP_056087.2	Q68CZ1	FTM_HUMAN	RPGRIP1-like	1290					camera-type eye development (GO:0043010)|cerebellum development (GO:0021549)|cilium assembly (GO:0042384)|corpus callosum development (GO:0022038)|determination of left/right symmetry (GO:0007368)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|establishment or maintenance of cell polarity (GO:0007163)|head development (GO:0060322)|in utero embryonic development (GO:0001701)|kidney development (GO:0001822)|lateral ventricle development (GO:0021670)|liver development (GO:0001889)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|neural tube patterning (GO:0021532)|nose development (GO:0043584)|olfactory bulb development (GO:0021772)|pericardium development (GO:0060039)|regulation of smoothened signaling pathway (GO:0008589)	axoneme (GO:0005930)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	thromboxane A2 receptor binding (GO:0031870)			endometrium(6)|kidney(3)|large_intestine(9)|lung(19)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(2)	46		all_cancers(37;0.0973)				CCTGAGCTTGCCAATACCTTC	0.453																																					p.G1290D		Atlas-SNP	.											.	RPGRIP1L	118	.	0			c.G3869A						.						118	94	102					16																	53636067		2198	4300	6498	SO:0001583	missense	23322	exon27			AGCTTGCCAATAC		CCDS32447.1, CCDS45486.1	16q12.2	2014-09-17				ENSG00000103494			29168	protein-coding gene	gene with protein product	"fantom homolog", "Meckel syndrome, type 5", "protein phosphatase 1, regulatory subunit 134"	610937				10231032	Standard	NM_015272		Approved	KIAA1005, CORS3, JBTS7, MKS5, NPHP8, FTM, PPP1R134	uc002ehp.3	Q68CZ1		ENST00000379925.3:c.3869G>A	chr16.hg19:g.53636067C>T	ENSP00000369257:p.Gly1290Asp	154.0	0.0		95.0	4.0	NM_015272	A0PJ88|Q9Y2K8	Missense_Mutation	SNP	ENST00000379925.3	hg19	CCDS32447.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.772027	0.90108	.	.	ENSG00000103494	ENST00000379925;ENST00000262135	D;D	0.84442	-1.85;-1.85	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	D	0.91590	0.7343	M	0.72894	2.215	0.80722	D	1	P;D;D	0.62365	0.94;0.991;0.964	P;D;D	0.65233	0.858;0.91;0.933	D	0.91894	0.5526	10	0.87932	D	0	-10.8324	18.3801	0.90448	0.0:1.0:0.0:0.0	.	1244;1290;1210	B7ZKJ9;Q68CZ1;Q68CZ1-2	.;FTM_HUMAN;.	D	1290;1210	ENSP00000369257:G1290D;ENSP00000262135:G1210D	ENSP00000262135:G1210D	G	-	2	0	RPGRIP1L	52193568	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.287000	0.65645	2.776000	0.95493	0.650000	0.86243	GGC	.	.		0.453	RPGRIP1L-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422187.1	NM_015272		T	53636067	C	T	53636067	3	4	259	1	0	0	0	0	1	0	0	0	13565	739	26	3	82	3	RPGRIP1L	16	53636067	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	2460783	53636067	36718686	698	37016										
SLC6A2	6530	hgsc.bcm.edu	37	chr16	55690842	55690842	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cgcagtggacctggccaacgTgtggcgcttcccctacctct	11	16	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:55690842T>C	ENST00000379906.2	+	1	491	c.236T>C	c.(235-237)gTg>gCg	p.V79A	SLC6A2_ENST00000561820.1_Missense_Mutation_p.V79A|SLC6A2_ENST00000414754.3_Missense_Mutation_p.V79A|SLC6A2_ENST00000568943.1_Missense_Mutation_p.V79A|SLC6A2_ENST00000566163.1_Missense_Mutation_p.V79A|SLC6A2_ENST00000219833.8_Missense_Mutation_p.V79A	NM_001043.3	NP_001034.1	P23975	SC6A2_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 2	79					monoamine transport (GO:0015844)|norepinephrine transport (GO:0015874)|response to drug (GO:0042493)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	monoamine transmembrane transporter activity (GO:0008504)|norepinephrine:sodium symporter activity (GO:0005334)			breast(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(20)|ovary(3)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(181;0.01)|Kidney(780;0.0267)	Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Bupropion(DB01156)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Diethylpropion(DB00937)|Dopamine(DB00988)|Doxepin(DB01142)|Droxidopa(DB06262)|Duloxetine(DB00476)|Ephedra(DB01363)|Ephedrine(DB01364)|Ergotamine(DB00696)|Escitalopram(DB01175)|Ginkgo biloba(DB01381)|Guanadrel(DB00226)|Guanethidine(DB01170)|Imipramine(DB00458)|Iobenguane(DB06704)|Ketamine(DB01221)|Levomilnacipran(DB08918)|Levonordefrin(DB06707)|Loxapine(DB00408)|Maprotiline(DB00934)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Milnacipran(DB04896)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Orphenadrine(DB01173)|Paroxetine(DB00715)|Pethidine(DB00454)|Phendimetrazine(DB01579)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Reboxetine(DB00234)|Sibutramine(DB01105)|Tapentadol(DB06204)|Tramadol(DB00193)|Trimipramine(DB00726)|Venlafaxine(DB00285)	CTGGCCAACGTGTGGCGCTTC	0.667																																					p.V79A		Atlas-SNP	.											.	SLC6A2	189	.	0			c.T236C						.						80	85	83					16																	55690842		2198	4300	6498	SO:0001583	missense	6530	exon2			CCAACGTGTGGCG		CCDS10754.1, CCDS54011.1, CCDS58463.1	16q12.2	2013-07-19	2013-07-19		ENSG00000103546	ENSG00000103546		"Solute carriers"	11048	protein-coding gene	gene with protein product	"norepinephrine transporter"	163970	"solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2"	NET1, NAT1, SLC6A5		2008212	Standard	NM_001043		Approved	NET	uc021tio.1	P23975	OTTHUMG00000133208	ENST00000379906.2:c.236T>C	chr16.hg19:g.55690842T>C	ENSP00000369237:p.Val79Ala	178.0	0.0		87.0	5.0	NM_001172501	B2R707|B4DX48|Q96KH8	Missense_Mutation	SNP	ENST00000379906.2	hg19	CCDS10754.1	.	.	.	.	.	.	.	.	.	.	T	16.67	3.187653	0.57909	.	.	ENSG00000103546	ENST00000414754;ENST00000379906;ENST00000219833	T;T;T	0.80480	-1.38;-1.38;-1.38	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	D	0.91885	0.7431	M	0.92169	3.28	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.995;0.996	D	0.93831	0.7128	10	0.87932	D	0	.	15.4969	0.75662	0.0:0.0:0.0:1.0	.	79;79	Q96KH8;P23975	.;SC6A2_HUMAN	A	79	ENSP00000394956:V79A;ENSP00000369237:V79A;ENSP00000219833:V79A	ENSP00000219833:V79A	V	+	2	0	SLC6A2	54248343	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.930000	0.87610	2.117000	0.64856	0.460000	0.39030	GTG	.	.		0.667	SLC6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256922.2			C	55690842	T	C	55690842	3	2	259	1	0	0	0	0	1	0	0	0	14698	1696	59	2	238	2	SLC6A2	16	55690842	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	2054775	55690842	34663911	699	37017										
NUP93	9688	hgsc.bcm.edu	37	chr16	56868679	56868679	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttgggaaactagagaatgacGgaagtagaaaggtgagttaa	14	2	0	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:56868679G>T	ENST00000308159.5	+	16	1892	c.1771G>T	c.(1771-1773)Gga>Tga	p.G591*	NUP93_ENST00000569842.1_Nonsense_Mutation_p.G591*|NUP93_ENST00000542526.1_Nonsense_Mutation_p.G468*|NUP93_ENST00000564887.1_Nonsense_Mutation_p.G468*	NM_014669.4	NP_055484.3	Q8N1F7	NUP93_HUMAN	nucleoporin 93kDa	591					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			breast(2)|endometrium(6)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						AGAGAATGACGGAAGTAGAAA	0.318																																					p.G591X	Colon(33;610 796 1305 1705 38917)	Atlas-SNP	.											.	NUP93	75	.	0			c.G1771T						.						82	82	82					16																	56868679		2198	4300	6498	SO:0001587	stop_gained	9688	exon16			AATGACGGAAGTA	D42085	CCDS10769.1, CCDS55996.1	16q13	2008-02-05			ENSG00000102900	ENSG00000102900			28958	protein-coding gene	gene with protein product		614351				9348540, 9531546	Standard	NM_014669		Approved	KIAA0095	uc002eka.3	Q8N1F7	OTTHUMG00000133278	ENST00000308159.5:c.1771G>T	chr16.hg19:g.56868679G>T	ENSP00000310668:p.Gly591*	171.0	0.0		94.0	5.0	NM_014669	B3KPQ8|Q14705	Nonsense_Mutation	SNP	ENST00000308159.5	hg19	CCDS10769.1	.	.	.	.	.	.	.	.	.	.	G	45	11.378068	0.99554	.	.	ENSG00000102900	ENST00000308159;ENST00000542526	.	.	.	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-15.6325	20.04	0.97581	0.0:0.0:1.0:0.0	.	.	.	.	X	591;468	.	ENSP00000310668:G591X	G	+	1	0	NUP93	55426180	1.000000	0.71417	0.893000	0.35052	0.986000	0.74619	9.312000	0.96287	2.733000	0.93635	0.655000	0.94253	GGA	.	.		0.318	NUP93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257058.4	NM_014669		T	56868679	G	T	56868679	4	4	259	1	0	0	0	0	0	1	0	0	10781	1117	39	1	1829	1	NUP93	16	56868679	Nonsense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1177837	56868679	33486074	700	37018										
CX3CL1	6376	hgsc.bcm.edu	37	chr16	57416825	57416825	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tcttctgcctgggggtggccAtgttcacctaccagagcctc	11	14	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:57416825A>G	ENST00000006053.6	+	3	1186	c.1075A>G	c.(1075-1077)Atg>Gtg	p.M359V	CX3CL1_ENST00000563383.1_Missense_Mutation_p.M365V|CX3CL1_ENST00000565912.1_Missense_Mutation_p.M321V	NM_002996.3	NP_002987.1	P78423	X3CL1_HUMAN	chemokine (C-X3-C motif) ligand 1	359					angiogenesis involved in wound healing (GO:0060055)|cell adhesion (GO:0007155)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|immune response (GO:0006955)|leukocyte adhesive activation (GO:0050902)|leukocyte chemotaxis (GO:0030595)|lymphocyte chemotaxis (GO:0048247)|macrophage chemotaxis (GO:0048246)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|neutrophil chemotaxis (GO:0030593)|positive regulation of angiogenesis (GO:0045766)|positive regulation of calcium-independent cell-cell adhesion (GO:0051041)|positive regulation of inflammatory response (GO:0050729)|positive regulation of transforming growth factor beta1 production (GO:0032914)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	chemokine activity (GO:0008009)|receptor binding (GO:0005102)			breast(1)|endometrium(1)|large_intestine(1)|lung(2)	5						GGGGGTGGCCATGTTCACCTA	0.637																																					p.M359V		Atlas-SNP	.											.	CX3CL1	27	.	0			c.A1075G						.						65	69	67					16																	57416825		2198	4300	6498	SO:0001583	missense	6376	exon3			GTGGCCATGTTCA	U84487	CCDS10779.1	16q13	2013-02-25	2002-08-22	2002-08-23	ENSG00000006210	ENSG00000006210		"Endogenous ligands"	10647	protein-coding gene	gene with protein product		601880	"small inducible cytokine subfamily D (Cys-X3-Cys), member 1 (fractalkine, neurotactin)"	SCYD1		9177350, 9024663	Standard	NM_002996		Approved	NTN, C3Xkine, ABCD-3, CXC3C, CXC3, fractalkine, neurotactin	uc002eli.3	P78423	OTTHUMG00000133469	ENST00000006053.6:c.1075A>G	chr16.hg19:g.57416825A>G	ENSP00000006053:p.Met359Val	93.0	0.0		44.0	4.0	NM_002996	O00672	Missense_Mutation	SNP	ENST00000006053.6	hg19	CCDS10779.1	.	.	.	.	.	.	.	.	.	.	A	18.97	3.735506	0.69189	.	.	ENSG00000006210	ENST00000006053	T	0.09911	2.93	5.19	5.19	0.71726	.	0.585004	0.15417	N	0.263445	T	0.22475	0.0542	L	0.36672	1.1	0.36566	D	0.872705	D	0.63880	0.993	D	0.68192	0.956	T	0.07693	-1.0759	10	0.87932	D	0	-37.3436	11.4823	0.50333	1.0:0.0:0.0:0.0	.	359	P78423	X3CL1_HUMAN	V	359	ENSP00000006053:M359V	ENSP00000006053:M359V	M	+	1	0	CX3CL1	55974326	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	2.655000	0.46707	1.953000	0.56701	0.456000	0.33151	ATG	.	.		0.637	CX3CL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257345.3	NM_002996		G	57416825	A	G	57416825	3	3	259	1	0	0	0	0	1	0	0	0	4076	217	8	2	1085	2	CX3CL1	16	57416825	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	548146	57416825	32937928	701	37019										
GOT2	2806	hgsc.bcm.edu	37	chr16	58743423	58743423	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttgaggttggagaccagttgAgtccgcatgccaatgatgcg	14	8	0	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:58743423A>G	ENST00000245206.5	-	9	1196	c.1068T>C	c.(1066-1068)acT>acC	p.T356T	GOT2_ENST00000434819.2_Silent_p.T313T	NM_002080.2	NP_002071.2	P00505	AATM_HUMAN	glutamic-oxaloacetic transaminase 2, mitochondrial	356					2-oxoglutarate metabolic process (GO:0006103)|4-hydroxyproline catabolic process (GO:0019470)|aspartate biosynthetic process (GO:0006532)|aspartate catabolic process (GO:0006533)|aspartate metabolic process (GO:0006531)|carbohydrate metabolic process (GO:0005975)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|fatty acid transport (GO:0015908)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glutamate catabolic process to 2-oxoglutarate (GO:0019551)|glutamate catabolic process to aspartate (GO:0019550)|glutamate metabolic process (GO:0006536)|oxaloacetate metabolic process (GO:0006107)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	kynurenine-oxoglutarate transaminase activity (GO:0016212)|L-aspartate:2-oxoglutarate aminotransferase activity (GO:0004069)|L-phenylalanine:2-oxoglutarate aminotransferase activity (GO:0080130)|poly(A) RNA binding (GO:0044822)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|prostate(2)|skin(1)	22					L-Aspartic Acid(DB00128)	AGACCAGTTGAGTCCGCATGC	0.498																																					p.T356T		Atlas-SNP	.											.	GOT2	42	.	0			c.T1068C						.						220	205	210					16																	58743423		2198	4300	6498	SO:0001819	synonymous_variant	2806	exon9			CAGTTGAGTCCGC		CCDS10801.1, CCDS67045.1	16q21	2013-05-29	2013-05-29		ENSG00000125166	ENSG00000125166	2.6.1.1		4433	protein-coding gene	gene with protein product	"kynurenine aminotransferase IV", "aspartate aminotransferase 2", "aspartate transaminase 2"	138150	"glutamic-oxaloacetic transaminase 2, mitochondrial (aspartate aminotransferase 2)"			17442055	Standard	NM_002080		Approved	mitAAT, KATIV, KAT4	uc002eof.1	P00505	OTTHUMG00000133769	ENST00000245206.5:c.1068T>C	chr16.hg19:g.58743423A>G		58.0	0.0		34.0	4.0	NM_002080	B4DJA6|E7ERW2|Q53FL3|Q9BWA3	Silent	SNP	ENST00000245206.5	hg19	CCDS10801.1																																																																																			.	.		0.498	GOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258289.3			G	58743423	A	G	58743423	2	3	259	1	0	0	0	0	0	0	0	1	6589	291	11	2		2	GOT2	16	58743423	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1326598	58743423	31611330	702	37020										
CDH5	1003	hgsc.bcm.edu	37	chr16	66426269	66426269	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctggccatggaccctgatgcGgctaggcatagcattgggta	14	10	0	1	rs376087780		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:66426269G>T	ENST00000341529.3	+	7	1348	c.1200G>T	c.(1198-1200)gcG>gcT	p.A400A	CDH5_ENST00000563425.2_Silent_p.A400A	NM_001795.3	NP_001786.2	P33151	CADH5_HUMAN	cadherin 5, type 2 (vascular endothelium)	400	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|blood vessel maturation (GO:0001955)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|negative regulation of cell proliferation (GO:0008285)|regulation of establishment of cell polarity (GO:2000114)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|receptor binding (GO:0005102)	p.A400A(1)		central_nervous_system(1)|endometrium(3)|kidney(18)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	54		Ovarian(137;0.0955)		OV - Ovarian serous cystadenocarcinoma(108;0.107)	Lenalidomide(DB00480)	ACCCTGATGCGGCTAGGCATA	0.552																																					p.A400A		Atlas-SNP	.											CDH5,NS,carcinoma,0,1	CDH5	111	.	1	Substitution - coding silent(1)	endometrium(1)	c.G1200T						.						88	88	88					16																	66426269		2201	4300	6501	SO:0001819	synonymous_variant	1003	exon7			TGATGCGGCTAGG	X79981	CCDS10804.1	16q22.1	2010-01-26	2008-07-25		ENSG00000179776	ENSG00000179776		"CD molecules", "Cadherins / Major cadherins"	1764	protein-coding gene	gene with protein product	"VE-cadherin"	601120	"cadherin 5, type 2, VE-cadherin (vascular epithelium)"			2059658	Standard	NM_001795		Approved	7B4, CD144	uc002eom.4	P33151	OTTHUMG00000137495	ENST00000341529.3:c.1200G>T	chr16.hg19:g.66426269G>T		85.0	0.0		42.0	3.0	NM_001795	Q4VAI5|Q4VAI6	Silent	SNP	ENST00000341529.3	hg19	CCDS10804.1																																																																																			.	.		0.552	CDH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268767.1	NM_001795		T	66426269	G	T	66426269	2	4	259	1	0	0	0	0	0	0	0	1	3115	1103	39	1		1	CDH5	16	66426269	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	7682846	66426269	23928484	703	37021										
CMTM4	146223	hgsc.bcm.edu	37	chr16	66651253	66651253	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttactgttacgtttgtggagTaggaaaaactagaaaggaaa	11	3	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:66651253T>A	ENST00000330687.4	-	5	813	c.632A>T	c.(631-633)tAc>tTc	p.Y211F		NM_178818.2|NM_181521.2	NP_848933.1|NP_852662.1	Q8IZR5	CKLF4_HUMAN	CKLF-like MARVEL transmembrane domain containing 4	211					chemotaxis (GO:0006935)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				cervix(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|pancreas(1)|stomach(1)	9		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0811)|Epithelial(162;0.214)		GTTTGTGGAGTAGGAAAAACT	0.363																																					p.Y211F		Atlas-SNP	.											.	CMTM4	19	.	0			c.A632T						.						82	76	78					16																	66651253		2200	4300	6500	SO:0001583	missense	146223	exon5			GTGGAGTAGGAAA	AF479814	CCDS10817.1, CCDS42170.1	16q22.1-q22.3	2008-02-05	2005-11-08	2005-11-08	ENSG00000183723	ENSG00000183723			19175	protein-coding gene	gene with protein product		607887	"chemokine-like factor super family 4", "chemokine-like factor superfamily 4"	CKLFSF4		12782130	Standard	NM_178818		Approved		uc002epz.3	Q8IZR5	OTTHUMG00000137500	ENST00000330687.4:c.632A>T	chr16.hg19:g.66651253T>A	ENSP00000333833:p.Tyr211Phe	405.0	1.0		287.0	98.0	NM_178818	Q52M40|Q8IZR4|Q8IZV1	Missense_Mutation	SNP	ENST00000330687.4	hg19	CCDS10817.1	.	.	.	.	.	.	.	.	.	.	T	7.873	0.728630	0.15507	.	.	ENSG00000183723	ENST00000330687	T	0.23147	1.92	4.01	4.01	0.46588	.	0.712591	0.12721	N	0.444676	T	0.10165	0.0249	N	0.03608	-0.345	0.35073	D	0.762639	D	0.53885	0.963	B	0.41088	0.347	T	0.03898	-1.0994	10	0.09084	T	0.74	.	9.5874	0.39526	0.0:0.0:0.0:1.0	.	211	Q8IZR5	CKLF4_HUMAN	F	211	ENSP00000333833:Y211F	ENSP00000333833:Y211F	Y	-	2	0	CMTM4	65208754	0.256000	0.24012	0.005000	0.12908	0.003000	0.03518	2.529000	0.45632	2.031000	0.59945	0.459000	0.35465	TAC	.	.		0.363	CMTM4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268807.1			A	66651253	T	A	66651253	3	1	259	1	0	0	0	0	1	0	0	0	3587	1638	57	4	76	4	CMTM4	16	66651253	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	224984	66651253	23703500	704	37022										
PSKH1	5681	hgsc.bcm.edu	37	chr16	67942888	67942888	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gcctccctcagaaccaccacGcagggccagggtagctaagt	11	15	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:67942888G>T	ENST00000291041.5	+	2	406	c.236G>T	c.(235-237)cGc>cTc	p.R79L		NM_006742.2	NP_006733.1	P11801	KPSH1_HUMAN	protein serine kinase H1	79						cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(2)|large_intestine(1)|lung(7)|pancreas(1)	12		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0044)|Epithelial(162;0.0197)|all cancers(182;0.128)		GAACCACCACGCAGGGCCAGG	0.612																																					p.R79L		Atlas-SNP	.											PSKH1,NS,carcinoma,0,1	PSKH1	28	.	0			c.G236T						.						64	58	60					16																	67942888		2198	4300	6498	SO:0001583	missense	5681	exon2			CACCACGCAGGGC	M14504	CCDS10851.1	16q22.1	2008-02-05			ENSG00000159792	ENSG00000159792			9529	protein-coding gene	gene with protein product		177015				8268911	Standard	NM_006742		Approved		uc002euv.3	P11801	OTTHUMG00000137548	ENST00000291041.5:c.236G>T	chr16.hg19:g.67942888G>T	ENSP00000291041:p.Arg79Leu	163.0	0.0		89.0	4.0	NM_006742	Q9NY19	Missense_Mutation	SNP	ENST00000291041.5	hg19	CCDS10851.1	.	.	.	.	.	.	.	.	.	.	G	13.18	2.160033	0.38119	.	.	ENSG00000159792	ENST00000291041	T	0.37752	1.18	4.21	4.21	0.49690	.	0.107588	0.64402	D	0.000006	T	0.31167	0.0788	L	0.56769	1.78	0.49798	D	0.999828	B	0.16396	0.017	B	0.13407	0.009	T	0.10268	-1.0637	10	0.31617	T	0.26	-13.1757	8.1675	0.31235	0.1056:0.0:0.8944:0.0	.	79	P11801	KPSH1_HUMAN	L	79	ENSP00000291041:R79L	ENSP00000291041:R79L	R	+	2	0	PSKH1	66500389	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.920000	0.63390	2.645000	0.89757	0.655000	0.94253	CGC	.	.		0.612	PSKH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268882.3	NM_006742		T	67942888	G	T	67942888	3	4	259	1	0	0	0	0	1	0	0	0	12676	1087	38	1	238	1	PSKH1	16	67942888	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1291635	67942888	22411865	705	37023										
TMCO7	79613	hgsc.bcm.edu	37	chr16	68953121	68953121	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	catgctaggaggagctgttcAggtgagttgtagacatgagg	16	5	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:68953121A>T	ENST00000261778.1	+	12	2138	c.2126A>T	c.(2125-2127)cAg>cTg	p.Q709L		NM_024562.1	NP_078838.1	Q9C0B7	TNG6_HUMAN	transport and golgi organization 6 homolog (Drosophila)	709						integral component of membrane (GO:0016021)											GGAGCTGTTCAGGTGAGTTGT	0.512																																					p.Q709L		Atlas-SNP	.											.	.	.	.	0			c.A2126T						.						59	58	58					16																	68953121		2111	4227	6338	SO:0001630	splice_region_variant	79613	exon12			CTGTTCAGGTGAG		CCDS45516.1	16q22.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000103047	ENSG00000103047			25749	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 7"	TMCO7		11214970	Standard	NM_024562		Approved	FLJ12688, KIAA1746	uc002ewi.4	Q9C0B7	OTTHUMG00000176743	ENST00000261778.1:c.2127+1A>T	chr16.hg19:g.68953121A>T		220.0	0.0		112.0	23.0	NM_024562	Q569F9|Q9H9K1	Missense_Mutation	SNP	ENST00000261778.1	hg19	CCDS45516.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.152870	0.78001	.	.	ENSG00000103047	ENST00000261778	T	0.63580	-0.05	5.36	5.36	0.76844	Armadillo-type fold (1);	0.225081	0.47455	D	0.000229	T	0.54631	0.1870	M	0.64997	1.995	0.44927	D	0.997947	P	0.44090	0.826	B	0.36845	0.234	T	0.57642	-0.7776	10	0.36615	T	0.2	-16.9474	10.2972	0.43631	0.8528:0.0:0.0:0.1472	.	709	Q9C0B7	TMCO7_HUMAN	L	709	ENSP00000261778:Q709L	ENSP00000261778:Q709L	Q	+	2	0	TMCO7	67510622	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.909000	0.56363	2.028000	0.59812	0.533000	0.62120	CAG	.	.		0.512	TANGO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433471.2	XM_928235.2	Missense_Mutation	T	68953121	A	T	68953121	5	4	259	1	0	0	0	0	0	0	1	0	16016	202	7	4	2172	4	TMCO7	16	68953121	Splice_Site	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1010233	68953121	21401632	706	37024										
AARS	16	hgsc.bcm.edu	37	chr16	70292100	70292100	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gctttcgctgctgccaggggGcaatcctgggtatagacggc	15	11	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:70292100G>A	ENST00000261772.8	-	15	2156	c.2013C>T	c.(2011-2013)tgC>tgT	p.C671C	AARS_ENST00000564359.1_Intron	NM_001605.2	NP_001596.2			alanyl-tRNA synthetase											breast(3)|cervix(2)|endometrium(5)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)	27		Ovarian(137;0.0365)		BRCA - Breast invasive adenocarcinoma(221;0.161)		CTGCCAGGGGGCAATCCTGGG	0.597																																					p.C671C		Atlas-SNP	.											.	AARS	62	.	0			c.C2013T						.						32	27	28					16																	70292100		2198	4300	6498	SO:0001819	synonymous_variant	16	exon15			CAGGGGGCAATCC	D32050	CCDS32474.1	16q22.1	2014-09-17			ENSG00000090861	ENSG00000090861	6.1.1.7	"Aminoacyl tRNA synthetases / Class II"	20	protein-coding gene	gene with protein product	"alanine tRNA ligase 1, cytoplasmic"	601065				8595897	Standard	NM_001605		Approved		uc002eyn.1	P49588	OTTHUMG00000177042	ENST00000261772.8:c.2013C>T	chr16.hg19:g.70292100G>A		117.0	0.0		70.0	4.0	NM_001605		Silent	SNP	ENST00000261772.8	hg19	CCDS32474.1																																																																																			.	.		0.597	AARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435021.2	NM_001605		A	70292100	G	A	70292100	2	1	259	1	0	0	0	0	0	0	0	1	19	1195	42	3		3	AARS	16	70292100	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1338979	70292100	20062653	707	37025										
FTSJD1	55783	hgsc.bcm.edu	37	chr16	71319522	71319522	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cattcacagattttctaacaTgagaaatgattttccccgct	5	10	2	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:71319522T>C	ENST00000338099.5	-	3	638	c.302A>G	c.(301-303)cAt>cGt	p.H101R	CMTR2_ENST00000434935.2_Missense_Mutation_p.H101R			Q8IYT2	CMTR2_HUMAN	cap methyltransferase 2	101					7-methylguanosine mRNA capping (GO:0006370)|cap2 mRNA methylation (GO:0097310)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)										TTTTCTAACATGAGAAATGAT	0.388																																					p.H101R		Atlas-SNP	.											.	FTSJD1	70	.	0			c.A302G						.						90	86	88					16																	71319522		2198	4300	6498	SO:0001583	missense	55783	exon3			CTAACATGAGAAA	BC035005	CCDS10898.1	16q22.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000180917	ENSG00000180917			25635	protein-coding gene	gene with protein product	"adrift homolog (Drosophila)"		"FtsJ methyltransferase domain containing 1"	FTSJD1		21310715	Standard	NM_018348		Approved	FLJ11171, AFT, MTr2	uc010cga.3	Q8IYT2	OTTHUMG00000137587	ENST00000338099.5:c.302A>G	chr16.hg19:g.71319522T>C	ENSP00000337512:p.His101Arg	131.0	0.0		79.0	6.0	NM_018348	B2RCD5|D3DWS1|Q8NE77|Q8NFR5|Q9H8Z4|Q9NUS3|Q9NXF5	Missense_Mutation	SNP	ENST00000338099.5	hg19	CCDS10898.1	.	.	.	.	.	.	.	.	.	.	T	0.782	-0.761961	0.02996	.	.	ENSG00000180917	ENST00000338099;ENST00000434935	T;T	0.13901	2.55;2.55	5.56	4.47	0.54385	.	0.255608	0.38217	N	0.001766	T	0.08714	0.0216	L	0.37630	1.12	0.41700	D	0.989398	P	0.43169	0.8	B	0.32289	0.143	T	0.30534	-0.9975	10	0.19147	T	0.46	-28.6195	10.7544	0.46228	0.0:0.0743:0.0:0.9257	.	101	Q8IYT2	FTSJ1_HUMAN	R	101	ENSP00000337512:H101R;ENSP00000411148:H101R	ENSP00000337512:H101R	H	-	2	0	FTSJD1	69877023	1.000000	0.71417	0.977000	0.42913	0.998000	0.95712	6.412000	0.73303	0.941000	0.37499	0.459000	0.35465	CAT	.	.		0.388	CMTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268984.2	NM_018348		C	71319522	T	C	71319522	3	2	259	1	0	0	0	0	1	0	0	0	6098	1464	51	2	2014	2	FTSJD1	16	71319522	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1027422	71319522	19035231	708	37026										
RFWD3	55159	hgsc.bcm.edu	37	chr16	74694849	74694849	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cctggcactgtctgtcctctGagaccctccggctcttgccc	9	18	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:74694849G>A	ENST00000361070.4	-	2	596	c.499C>T	c.(499-501)Cag>Tag	p.Q167*	RFWD3_ENST00000571750.1_Nonsense_Mutation_p.Q167*	NM_018124.3	NP_060594.3	Q6PCD5	RFWD3_HUMAN	ring finger and WD repeat domain 3	167					DNA repair (GO:0006281)|mitotic G1 DNA damage checkpoint (GO:0031571)|protein ubiquitination (GO:0016567)|regulation of DNA damage checkpoint (GO:2000001)|response to ionizing radiation (GO:0010212)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|MDM2/MDM4 family protein binding (GO:0097371)|p53 binding (GO:0002039)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	26						TCTGTCCTCTGAGACCCTCCG	0.468																																					p.Q167X		Atlas-SNP	.											.	RFWD3	49	.	0			c.C499T						.						127	125	126					16																	74694849		2198	4300	6498	SO:0001587	stop_gained	55159	exon2			TCCTCTGAGACCC	AK001382	CCDS32486.1	16q22.3	2013-01-09						"WD repeat domain containing", "RING-type (C3HC4) zinc fingers"	25539	protein-coding gene	gene with protein product		614151				21504906	Standard	XM_005256021		Approved	FLJ10520, RNF201	uc002fda.3	Q6PCD5		ENST00000361070.4:c.499C>T	chr16.hg19:g.74694849G>A	ENSP00000354361:p.Gln167*	154.0	0.0		97.0	4.0	NM_018124	A8K585|B2RE35|D3DUJ8|Q5XKR3|Q9H9Q3|Q9NVT4	Nonsense_Mutation	SNP	ENST00000361070.4	hg19	CCDS32486.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.820351	0.90873	.	.	ENSG00000168411	ENST00000361070	.	.	.	4.64	4.64	0.57946	.	0.345316	0.28114	N	0.016553	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-17.0351	14.7109	0.69232	0.0:0.0:1.0:0.0	.	.	.	.	X	167	.	ENSP00000354361:Q167X	Q	-	1	0	RFWD3	73252350	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	4.082000	0.57635	2.565000	0.86533	0.591000	0.81541	CAG	.	.		0.468	RFWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436506.2	NM_018124		A	74694849	G	A	74694849	4	1	259	1	0	0	0	0	0	1	0	0	13276	1299	45	3	1873	3	RFWD3	16	74694849	Nonsense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	3375327	74694849	15659904	709	37027										
MON1B	22879	hgsc.bcm.edu	37	chr16	77225506	77225506	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acgcggtcccgccggatcccGaagacgagggcctggaggaa	16	13	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:77225506G>T	ENST00000248248.3	+	2	474	c.124G>T	c.(124-126)Gaa>Taa	p.E42*	MON1B_ENST00000545553.1_Intron|MON1B_ENST00000439557.2_Nonsense_Mutation_p.E42*|MON1B_ENST00000320859.6_Nonsense_Mutation_p.E42*	NM_014940.2	NP_055755.1	Q7L1V2	MON1B_HUMAN	MON1 secretory trafficking family member B	42										breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	17						GCCGGATCCCGAAGACGAGGG	0.622																																					p.E42X		Atlas-SNP	.											.	MON1B	55	.	0			c.G124T						.						31	34	33					16																	77225506		2198	4300	6498	SO:0001587	stop_gained	22879	exon2			GATCCCGAAGACG	BC024277	CCDS10925.1, CCDS67082.1, CCDS67083.1	16q23.1	2013-08-21	2013-08-21		ENSG00000103111	ENSG00000103111			25020	protein-coding gene	gene with protein product		608954	"MON1 homolog B (yeast)"			10048485	Standard	NM_014940		Approved	SAND2, HSRG1, KIAA0872	uc002fez.3	Q7L1V2	OTTHUMG00000137618	ENST00000248248.3:c.124G>T	chr16.hg19:g.77225506G>T	ENSP00000248248:p.Glu42*	154.0	0.0		82.0	4.0	NM_014940	B4DDZ0|O94949	Nonsense_Mutation	SNP	ENST00000248248.3	hg19	CCDS10925.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.005079	0.93287	.	.	ENSG00000103111	ENST00000248248;ENST00000320859;ENST00000439557	.	.	.	3.84	0.838	0.18902	.	0.917379	0.08990	N	0.864588	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	.	6.3037	0.21127	0.3107:0.0:0.6893:0.0	.	.	.	.	X	42	.	ENSP00000248248:E42X	E	+	1	0	MON1B	75783007	0.123000	0.22298	0.000000	0.03702	0.004000	0.04260	1.004000	0.29822	0.222000	0.20900	-0.717000	0.03617	GAA	.	.		0.622	MON1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269036.2	NM_014940		T	77225506	G	T	77225506	4	4	259	1	0	0	0	0	0	1	0	0	9708	1059	37	1	126	1	MON1B	16	77225506	Nonsense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	2530657	77225506	13129247	710	37028										
JPH3	57338	hgsc.bcm.edu	37	chr16	87723326	87723326	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgtccaccgggacacccctgCagcaggagagccccgagctg	13	16	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:87723326C>T	ENST00000284262.2	+	4	1602	c.1360C>T	c.(1360-1362)Cag>Tag	p.Q454*	JPH3_ENST00000563609.1_3'UTR	NM_020655.2	NP_065706.2	Q8WXH2	JPH3_HUMAN	junctophilin 3	454					calcium ion transport into cytosol (GO:0060402)|exploration behavior (GO:0035640)|learning (GO:0007612)|locomotion (GO:0040011)|memory (GO:0007613)|neuromuscular process controlling balance (GO:0050885)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)	calcium-release channel activity (GO:0015278)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(80;0.0287)		GACACCCCTGCAGCAGGAGAG	0.677																																					p.Q454X		Atlas-SNP	.											.	JPH3	95	.	0			c.C1360T						.						39	30	33					16																	87723326		2195	4298	6493	SO:0001587	stop_gained	57338	exon4			CCCCTGCAGCAGG	AB042636	CCDS10962.1	16q24.3	2008-02-05	2002-11-13		ENSG00000154118	ENSG00000154118			14203	protein-coding gene	gene with protein product		605268	"trinucleotide repeat containing 22"	TNRC22		10949023, 10891348	Standard	NM_020655		Approved	JP-3, CAGL237, HDL2, JP3	uc002fkd.4	Q8WXH2	OTTHUMG00000137656	ENST00000284262.2:c.1360C>T	chr16.hg19:g.87723326C>T	ENSP00000284262:p.Gln454*	206.0	0.0		71.0	4.0	NM_020655	D3DUN2|Q8N471|Q9HDC3|Q9HDC4	Nonsense_Mutation	SNP	ENST00000284262.2	hg19	CCDS10962.1	.	.	.	.	.	.	.	.	.	.	C	40	8.062469	0.98635	.	.	ENSG00000154118	ENST00000537256;ENST00000284262	.	.	.	4.48	4.48	0.54585	.	0.152719	0.41823	D	0.000819	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	.	16.1715	0.81820	0.0:1.0:0.0:0.0	.	.	.	.	X	317;454	.	ENSP00000284262:Q454X	Q	+	1	0	JPH3	86280827	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	6.073000	0.71245	2.050000	0.60909	0.655000	0.94253	CAG	.	.		0.677	JPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269108.2			T	87723326	C	T	87723326	4	4	259	1	0	0	0	0	0	1	0	0	7971	711	25	3	1374	3	JPH3	16	87723326	Nonsense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	10497820	87723326	2631427	711	37029										
ZNF778	197320	hgsc.bcm.edu	37	chr16	89294364	89294364	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gagcatgtgaaaactcacacAgaggagaagccctttatatg	10	8	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:89294364A>G	ENST00000433976.2	+	6	1916	c.1584A>G	c.(1582-1584)acA>acG	p.T528T	ZNF778_ENST00000306502.6_Silent_p.T486T|RP11-46C24.6_ENST00000563182.1_RNA	NM_001201407.1|NM_182531.3	NP_001188336.1|NP_872337.2	Q96MU6	ZN778_HUMAN	zinc finger protein 778	528					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|skin(2)	24				BRCA - Breast invasive adenocarcinoma(80;0.0269)		AAACTCACACAGAGGAGAAGC	0.438																																					p.T556T		Atlas-SNP	.											.	ZNF778	67	.	0			c.A1668G						.						75	83	80					16																	89294364		2182	4294	6476	SO:0001819	synonymous_variant	197320	exon7			TCACACAGAGGAG	AK056437	CCDS45550.1, CCDS73928.1	16q24.3	2014-09-17			ENSG00000170100	ENSG00000170100		"Zinc fingers, C2H2-type", "-"	26479	protein-coding gene	gene with protein product							Standard	NM_182531		Approved	FLJ31875	uc021tms.1	Q96MU6		ENST00000433976.2:c.1584A>G	chr16.hg19:g.89294364A>G		135.0	0.0		87.0	4.0	NM_001201407	Q08AG0	Silent	SNP	ENST00000433976.2	hg19	CCDS45550.1																																																																																			.	.		0.438	ZNF778-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430383.1	NM_182531		G	89294364	A	G	89294364	2	3	259	1	0	0	0	0	0	0	0	1	18166	175	7	2		2	ZNF778	16	89294364	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1571038	89294364	1060389	712	37030										
VPS53	55275	hgsc.bcm.edu	37	chr17	526908	526908	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gtacgcataatcttggcaagTtctgcccttcaaaacaaaga	7	10	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:526908T>C	ENST00000571805.1	-	11	1117	c.981A>G	c.(979-981)gaA>gaG	p.E327E	VPS53_ENST00000576149.1_5'UTR|VPS53_ENST00000446250.2_Silent_p.E129E|VPS53_ENST00000574029.1_Intron|VPS53_ENST00000401468.3_Intron|VPS53_ENST00000291074.5_Silent_p.E298E|VPS53_ENST00000437048.2_Silent_p.E327E			Q5VIR6	VPS53_HUMAN	vacuolar protein sorting 53 homolog (S. cerevisiae)	327					protein transport (GO:0015031)	endosome (GO:0005768)|GARP complex (GO:0000938)|membrane (GO:0016020)				breast(1)|endometrium(4)|large_intestine(5)|lung(8)|prostate(1)	19				UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)		TCTTGGCAAGTTCTGCCCTTC	0.348																																					p.E327E		Atlas-SNP	.											.	VPS53	109	.	0			c.A981G						.						70	64	66					17																	526908		2203	4300	6503	SO:0001819	synonymous_variant	55275	exon11			GGCAAGTTCTGCC		CCDS10995.1, CCDS45558.1	17p13.3	2007-07-13	2006-12-19			ENSG00000141252			25608	protein-coding gene	gene with protein product		615850	"vacuolar protein sorting 53 (yeast)"			15878329	Standard	NM_018289		Approved	FLJ10979, HCCS1	uc010cjo.2	Q5VIR6		ENST00000571805.1:c.981A>G	chr17.hg19:g.526908T>C		103.0	0.0		94.0	4.0	NM_001128159	A8K2S8|B3FH42|Q8WYW3|Q9BRR2|Q9BY02|Q9NV25	Silent	SNP	ENST00000571805.1	hg19																																																																																				.	.		0.348	VPS53-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000436940.2	NM_018289		C	526908	T	C	526908	2	2	259	1	0	0	0	0	0	0	0	1	17230	1722	60	2		2	VPS53	17	526908	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10		526908	80668302	713	37031										
SMG6	23293	hgsc.bcm.edu	37	chr17	1964865	1964865	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgagcgccttcacacgcaggTtccggtcatccgtcaacagc	10	15	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:1964865T>C	ENST00000263073.6	-	19	4231	c.4181A>G	c.(4180-4182)aAc>aGc	p.N1394S	SMG6_ENST00000354901.4_Missense_Mutation_p.N486S|SMG6_ENST00000544865.1_Missense_Mutation_p.N1363S|SMG6_ENST00000573166.1_5'UTR|SMG6_ENST00000536871.2_Missense_Mutation_p.N486S	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	1394	PINc.				gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|telomere maintenance (GO:0000723)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|telomeric DNA binding (GO:0042162)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(10)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						CACACGCAGGTTCCGGTCATC	0.632																																					p.N1394S	Melanoma(59;28 1088 11621 25887 46638 50814)	Atlas-SNP	.											.	SMG6	97	.	0			c.A4181G						.						93	50	65					17																	1964865		2196	4296	6492	SO:0001583	missense	23293	exon19			CGCAGGTTCCGGT	AB018275	CCDS11016.1, CCDS58498.1	17p13.3	2013-07-02	2013-07-02	2006-02-16	ENSG00000070366	ENSG00000070366			17809	protein-coding gene	gene with protein product	"EST1 telomerase component homolog A (S. cerevisiae)"	610963	"chromosome 17 open reading frame 31", "smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)"	C17orf31		12676087, 12699629	Standard	NM_017575		Approved	KIAA0732, SMG-6, EST1A	uc002fub.1	Q86US8	OTTHUMG00000177578	ENST00000263073.6:c.4181A>G	chr17.hg19:g.1964865T>C	ENSP00000263073:p.Asn1394Ser	100.0	0.0		79.0	4.0	NM_017575	B7Z874|O94837|Q86VH6|Q9UF60	Missense_Mutation	SNP	ENST00000263073.6	hg19	CCDS11016.1	.	.	.	.	.	.	.	.	.	.	T	26.6	4.756121	0.89843	.	.	ENSG00000070366	ENST00000263073;ENST00000544865;ENST00000354901;ENST00000536871	T;T;T	0.28255	2.33;2.32;1.62	4.95	4.95	0.65309	Nucleotide binding protein, PINc (1);	0.000000	0.85682	D	0.000000	T	0.62974	0.2472	M	0.91972	3.26	0.80722	D	1	D	0.71674	0.998	D	0.72338	0.977	T	0.72896	-0.4153	10	0.87932	D	0	-9.1547	14.4404	0.67311	0.0:0.0:0.0:1.0	.	1394	Q86US8	EST1A_HUMAN	S	1394;1363;305;486	ENSP00000263073:N1394S;ENSP00000443920:N1363S;ENSP00000440283:N486S	ENSP00000263073:N1394S	N	-	2	0	SMG6	1911615	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.776000	0.85560	2.078000	0.62432	0.533000	0.62120	AAC	.	.		0.632	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437826.3			C	1964865	T	C	1964865	3	2	259	1	0	0	0	0	1	0	0	0	14812	1725	60	2	82	2	SMG6	17	1964865	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1437957	1964865	79230345	714	37032										
PLD2	5338	hgsc.bcm.edu	37	chr17	4712848	4712848	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acttgggccgcaaaggactgTgagtgtctggcccccttcac	12	13	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:4712848T>C	ENST00000263088.6	+	7	745		c.e7+2		PLD2_ENST00000572940.1_Splice_Site|RP11-81A22.5_ENST00000571067.1_lincRNA	NM_001243108.1|NM_002663.4	NP_001230037.1|NP_002654.3	O14939	PLD2_HUMAN	phospholipase D2						cytoskeleton organization (GO:0007010)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G-protein coupled receptor internalization (GO:0002031)|glycerophospholipid biosynthetic process (GO:0046474)|innate immune response (GO:0045087)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	brush border membrane (GO:0031526)|endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)			autonomic_ganglia(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)	31					Choline(DB00122)	CAAAGGACTGTGAGTGTCTGG	0.572																																					.		Atlas-SNP	.											.	PLD2	138	.	0			c.614+2T>C						.						54	56	56					17																	4712848		2203	4300	6503	SO:0001630	splice_region_variant	5338	exon7			GGACTGTGAGTGT	AF035483	CCDS11057.1, CCDS58507.1	17p13.3	2008-04-14			ENSG00000129219	ENSG00000129219	3.1.4.4		9068	protein-coding gene	gene with protein product	"choline phosphatase 2"	602384				9858823, 9582313	Standard	NM_002663		Approved		uc002fzc.3	O14939	OTTHUMG00000090779	ENST00000263088.6:c.614+2T>C	chr17.hg19:g.4712848T>C		114.0	0.0		110.0	6.0	NM_002663	I3L2C9|O43540|O43579|O43580|Q6PGR0|Q96BY3	Splice_Site	SNP	ENST00000263088.6	hg19	CCDS11057.1	.	.	.	.	.	.	.	.	.	.	T	17.42	3.384349	0.61845	.	.	ENSG00000129219	ENST00000263088	.	.	.	5.1	5.1	0.69264	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.8822	0.58024	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	PLD2	4659812	1.000000	0.71417	1.000000	0.80357	0.757000	0.42996	5.590000	0.67530	2.148000	0.66965	0.459000	0.35465	.	.	.		0.572	PLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207561.3	NM_002663	Intron	C	4712848	T	C	4712848	5	2	259	1	0	0	0	0	0	0	1	0	12055	1710	59	2	638	2	PLD2	17	4712848	Splice_Site	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	2747983	4712848	76482362	715	37033										
DHX33	56919	hgsc.bcm.edu	37	chr17	5365718	5365718	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agagcacatctgtgtggataGtccgttcgtgagcttcatcc	11	10	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:5365718G>T	ENST00000225296.3	-	3	799	c.599C>A	c.(598-600)aCt>aAt	p.T200N	DHX33_ENST00000433302.3_Intron	NM_001199699.1|NM_020162.3	NP_001186628.1|NP_064547.2	Q9H6R0	DHX33_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 33	200	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				positive regulation of transcription from RNA polymerase I promoter (GO:0045943)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|rDNA binding (GO:0000182)			breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						TGTGTGGATAGTCCGTTCGTG	0.463																																					p.T200N		Atlas-SNP	.											.	DHX33	41	.	0			c.C599A						.						96	85	89					17																	5365718		2203	4300	6503	SO:0001583	missense	56919	exon3			TGGATAGTCCGTT	AL359945	CCDS11072.1	17p13	2003-06-13	2003-06-13	2003-06-13	ENSG00000005100	ENSG00000005100		"DEAH-boxes"	16718	protein-coding gene	gene with protein product		614405	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 33"	DDX33			Standard	NM_020162		Approved	FLJ21972, DKFZp762F2011	uc002gca.3	Q9H6R0	OTTHUMG00000102041	ENST00000225296.3:c.599C>A	chr17.hg19:g.5365718G>T	ENSP00000225296:p.Thr200Asn	138.0	0.0		69.0	4.0	NM_020162	B4DHF9|Q4G149|Q5CZ73|Q9H5M9	Missense_Mutation	SNP	ENST00000225296.3	hg19	CCDS11072.1	.	.	.	.	.	.	.	.	.	.	G	34	5.390786	0.95988	.	.	ENSG00000005100	ENST00000225296	T	0.09255	3.0	5.78	5.78	0.91487	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.34978	0.0916	M	0.71036	2.16	0.80722	D	1	D	0.76494	0.999	D	0.74023	0.982	T	0.01643	-1.1305	10	0.87932	D	0	.	19.1701	0.93574	0.0:0.0:1.0:0.0	.	200	Q9H6R0	DHX33_HUMAN	N	200	ENSP00000225296:T200N	ENSP00000225296:T200N	T	-	2	0	DHX33	5306442	1.000000	0.71417	0.982000	0.44146	0.978000	0.69477	7.862000	0.87013	2.769000	0.95229	0.638000	0.83543	ACT	.	.		0.463	DHX33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219826.2	NM_020162		T	5365718	G	T	5365718	3	4	259	1	0	0	0	0	1	0	0	0	4508	1029	36	3	1564	3	DHX33	17	5365718	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	652870	5365718	75829492	716	37034										
POLR2A	5430	hgsc.bcm.edu	37	chr17	7404157	7404157	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttacaagcacatctctcctgGggacaccaaggtagggcttg	11	11	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:7404157G>T	ENST00000322644.6	+	11	2270	c.1871G>T	c.(1870-1872)gGg>gTg	p.G624V		NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	624					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA-directed RNA polymerase activity (GO:0003968)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(17)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	50		Prostate(122;0.173)				ATCTCTCCTGGGGACACCAAG	0.527																																					p.G624V		Atlas-SNP	.											.	POLR2A	157	.	0			c.G1871T						.						135	122	126					17																	7404157		2203	4300	6503	SO:0001583	missense	5430	exon11			CTCCTGGGGACAC			17p13.1	2013-01-21	2002-08-29		ENSG00000181222	ENSG00000181222	2.7.7.6	"RNA polymerase subunits"	9187	protein-coding gene	gene with protein product	"DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit", "RNA polymerase II subunit B1"	180660	"polymerase (RNA) II (DNA directed) polypeptide A (220kD)"	POLR2			Standard	NM_000937		Approved	POLRA, RPB1	uc002ghf.4	P24928	OTTHUMG00000177594	ENST00000322644.6:c.1871G>T	chr17.hg19:g.7404157G>T	ENSP00000314949:p.Gly624Val	172.0	0.0		78.0	4.0	NM_000937	A6NN93|B9EH88|Q6NX41	Missense_Mutation	SNP	ENST00000322644.6	hg19	CCDS32548.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.498307	0.85069	.	.	ENSG00000181222	ENST00000535204;ENST00000322644	T	0.68479	-0.33	5.96	5.96	0.96718	RNA polymerase Rpb1, domain 3 (1);	0.000000	0.85682	D	0.000000	D	0.86230	0.5883	H	0.96080	3.765	0.80722	D	1	D	0.54964	0.969	P	0.56788	0.806	D	0.89892	0.4038	10	0.87932	D	0	.	19.1654	0.93555	0.0:0.0:1.0:0.0	.	624	P24928	RPB1_HUMAN	V	580;624	ENSP00000314949:G624V	ENSP00000314949:G624V	G	+	2	0	SLC35G6	7344881	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	9.075000	0.94004	2.830000	0.97506	0.585000	0.79938	GGG	.	.		0.527	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	NM_000937		T	7404157	G	T	7404157	3	4	259	1	0	0	0	0	1	0	0	0	12223	1232	43	3	1913	3	POLR2A	17	7404157	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	2038439	7404157	73791053	717	37035										
AURKB	9212	hgsc.bcm.edu	37	chr17	8110166	8110166	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aatcaagtagatcctcctccGgtcataaaaatagttgtaga	7	8	2	2	rs148133660	byFrequency	TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:8110166G>T	ENST00000585124.1	-	6	532	c.439C>A	c.(439-441)Cgg>Agg	p.R147R	AURKB_ENST00000578549.1_Silent_p.R115R|AURKB_ENST00000535053.1_Intron|AURKB_ENST00000534871.1_Silent_p.R106R|AURKB_ENST00000316199.6_Silent_p.R148R	NM_004217.3	NP_004208.2	Q96GD4	AURKB_HUMAN	aurora kinase B	147	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				abscission (GO:0009838)|aging (GO:0007568)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|attachment of spindle microtubules to kinetochore (GO:0008608)|cell proliferation (GO:0008283)|cellular response to UV (GO:0034644)|cleavage furrow formation (GO:0036089)|cytokinesis checkpoint (GO:0031565)|histone H3-S28 phosphorylation (GO:0043988)|histone modification (GO:0016570)|mitotic cell cycle (GO:0000278)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cytokinesis (GO:0032467)|protein autophosphorylation (GO:0046777)|protein localization to kinetochore (GO:0034501)|protein phosphorylation (GO:0006468)|regulation of chromosome segregation (GO:0051983)|spindle checkpoint (GO:0031577)|spindle midzone assembly involved in mitosis (GO:0051256)|spindle stabilization (GO:0043146)	chromocenter (GO:0010369)|chromosome passenger complex (GO:0032133)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|histone serine kinase activity (GO:0035174)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)	p.R147W(1)		breast(1)|central_nervous_system(1)|lung(2)	4						ATCCTCCTCCGGTCATAAAAA	0.527																																					p.R147R	NSCLC(134;1161 2470 43664 51568)	Atlas-SNP	.											AURKB_ENST00000316199,NS,haematopoietic_neoplasm,0,1	AURKB	47	.	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C439A						.						37	38	38					17																	8110166		2203	4300	6503	SO:0001819	synonymous_variant	9212	exon6			TCCTCCGGTCATA	AF004022	CCDS11134.1, CCDS58514.1, CCDS67162.1	17p13.1	2013-01-17	2003-07-21	2003-07-23	ENSG00000178999	ENSG00000178999		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	11390	protein-coding gene	gene with protein product	"aurora-B", "aurora-1", "protein phosphatase 1, regulatory subunit 48"	604970	"serine/threonine kinase 12"	STK12		9858806	Standard	NM_001256834		Approved	Aik2, IPL1, AurB, AIM-1, ARK2, STK5, PPP1R48	uc002gkm.4	Q96GD4	OTTHUMG00000108189	ENST00000585124.1:c.439C>A	chr17.hg19:g.8110166G>T		147.0	0.0		48.0	4.0	NM_004217	B4DNM4|C7G533|C7G534|C7G535|D3DTR4|J9JID1|O14630|O60446|O95083|Q96DV5|Q9UQ46	Silent	SNP	ENST00000585124.1	hg19	CCDS11134.1																																																																																			.	G|1.000;A|0.000		0.527	AURKB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000226995.2	NM_004217		T	8110166	G	T	8110166	2	4	259	1	0	0	0	0	0	0	0	1	1223	1115	39	1		1	AURKB	17	8110166	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	706009	8110166	73085044	718	37036										
C17orf68	80169	hgsc.bcm.edu	37	chr17	8131843	8131843	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aatgggacgatcttcgacggTttcctttccagctcaaaaga	9	10	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:8131843T>C	ENST00000315684.8	-	22	3499	c.3492A>G	c.(3490-3492)aaA>aaG	p.K1164K		NM_025099.5	NP_079375.3	Q2NKJ3	CTC1_HUMAN	CTS telomere maintenance complex component 1	1164					bone marrow development (GO:0048539)|cellular response to DNA damage stimulus (GO:0006974)|hematopoietic stem cell proliferation (GO:0071425)|multicellular organism growth (GO:0035264)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|replicative senescence (GO:0090399)|spleen development (GO:0048536)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)|thymus development (GO:0048538)	nuclear chromosome, telomeric region (GO:0000784)|nucleus (GO:0005634)|Stn1-Ten1 complex (GO:0070188)	single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|skin(4)	29						TCTTCGACGGTTTCCTTTCCA	0.527																																					p.K1164K		Atlas-SNP	.											.	CTC1	75	.	0			c.A3492G						.						283	283	283					17																	8131843		1939	4141	6080	SO:0001819	synonymous_variant	80169	exon22			CGACGGTTTCCTT	AL831955	CCDS42259.1	17p13.1	2011-02-21	2011-02-21	2011-02-21	ENSG00000178971	ENSG00000178971			26169	protein-coding gene	gene with protein product	"conserved telomere maintenance component 1", "alpha accessory factor 132", "conserved telomere capping protein 1"	613129	"tmp494178", "chromosome 17 open reading frame 68"	C17orf68		19854130, 19854131	Standard	NM_025099		Approved	FLJ22170, AAF132	uc002gkq.4	Q2NKJ3		ENST00000315684.8:c.3492A>G	chr17.hg19:g.8131843T>C		128.0	0.0		61.0	5.0	NM_025099	B3KR66|C9JEX5|Q1PCD1|Q2TBE3|Q8N3S6|Q9H6L0	Silent	SNP	ENST00000315684.8	hg19	CCDS42259.1																																																																																			.	.		0.527	CTC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442012.1	NM_025099		C	8131843	T	C	8131843	2	2	259	1	0	0	0	0	0	0	0	1	1878	1722	60	2		2	C17orf68	17	8131843	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	21677	8131843	73063367	719	37037										
C17orf68	80169	hgsc.bcm.edu	37	chr17	8133211	8133211	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tggggtctgggcactgacctGatggtggtctcagggggaaa	18	7	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:8133211G>T	ENST00000315684.8	-	18	3016	c.3009C>A	c.(3007-3009)atC>atA	p.I1003I		NM_025099.5	NP_079375.3	Q2NKJ3	CTC1_HUMAN	CTS telomere maintenance complex component 1	1003					bone marrow development (GO:0048539)|cellular response to DNA damage stimulus (GO:0006974)|hematopoietic stem cell proliferation (GO:0071425)|multicellular organism growth (GO:0035264)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|replicative senescence (GO:0090399)|spleen development (GO:0048536)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)|thymus development (GO:0048538)	nuclear chromosome, telomeric region (GO:0000784)|nucleus (GO:0005634)|Stn1-Ten1 complex (GO:0070188)	single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|skin(4)	29						GCACTGACCTGATGGTGGTCT	0.483																																					p.I1003I		Atlas-SNP	.											.	CTC1	75	.	0			c.C3009A						.						115	120	118					17																	8133211		1973	4147	6120	SO:0001819	synonymous_variant	80169	exon18			TGACCTGATGGTG	AL831955	CCDS42259.1	17p13.1	2011-02-21	2011-02-21	2011-02-21	ENSG00000178971	ENSG00000178971			26169	protein-coding gene	gene with protein product	"conserved telomere maintenance component 1", "alpha accessory factor 132", "conserved telomere capping protein 1"	613129	"tmp494178", "chromosome 17 open reading frame 68"	C17orf68		19854130, 19854131	Standard	NM_025099		Approved	FLJ22170, AAF132	uc002gkq.4	Q2NKJ3		ENST00000315684.8:c.3009C>A	chr17.hg19:g.8133211G>T		97.0	0.0		43.0	4.0	NM_025099	B3KR66|C9JEX5|Q1PCD1|Q2TBE3|Q8N3S6|Q9H6L0	Silent	SNP	ENST00000315684.8	hg19	CCDS42259.1																																																																																			.	.		0.483	CTC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442012.1	NM_025099		T	8133211	G	T	8133211	2	4	259	1	0	0	0	0	0	0	0	1	1878	1280	45	3		3	C17orf68	17	8133211	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1368	8133211	73061999	720	37038										
RANGRF	29098	hgsc.bcm.edu	37	chr17	8192743	8192743	+	Intron	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aaaccagcaggtgagggcccGagagtgtgtaatgtcctgga	15	8	0	2	rs370613922		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:8192743G>T	ENST00000226105.6	+	3	643				SLC25A35_ENST00000579192.1_Intron|RANGRF_ENST00000407006.4_Intron|SLC25A35_ENST00000581320.1_5'Flank|SLC25A35_ENST00000396278.1_Intron|RANGRF_ENST00000439238.3_Missense_Mutation_p.R121L|SLC25A35_ENST00000380067.2_3'UTR|RANGRF_ENST00000580434.1_Intron|SLC25A35_ENST00000580340.1_3'UTR	NM_016492.4	NP_057576.2	Q9HD47	MOG1_HUMAN	RAN guanine nucleotide release factor						ER to Golgi vesicle-mediated transport (GO:0006888)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein localization to cell surface (GO:2000010)|protein exit from endoplasmic reticulum (GO:0032527)|regulation of heart rate (GO:0002027)|regulation of membrane depolarization (GO:0003254)|regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900825)|regulation of membrane potential (GO:0042391)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	guanyl-nucleotide exchange factor activity (GO:0005085)|ion channel binding (GO:0044325)|protein transporter activity (GO:0008565)|Ran GTPase binding (GO:0008536)|sodium channel regulator activity (GO:0017080)			endometrium(1)	1						GTGAGGGCCCGAGAGTGTGTA	0.572																																					p.R121L		Atlas-SNP	.											.	RANGRF	5	.	0			c.G362T						.						40	40	40					17																	8192743		2203	4300	6503	SO:0001627	intron_variant	29098	exon3			GGGCCCGAGAGTG	AF151070	CCDS11137.1, CCDS54086.1, CCDS54087.1	17p13	2014-05-09				ENSG00000108961			17679	protein-coding gene	gene with protein product	"MOG1 homolog (S. cerevisiae)"	607954				11290418	Standard	NM_016492		Approved	MOG1, HSPC165, HSPC236, RANGNRF	uc002gkv.3	Q9HD47		ENST00000226105.6:c.351+11G>T	chr17.hg19:g.8192743G>T		248.0	0.0		91.0	4.0	NM_001177802	D3DTR6|Q68DI3|Q9BR68|Q9HD48|Q9NRU9|Q9P001|Q9P0P2	Missense_Mutation	SNP	ENST00000226105.6	hg19	CCDS11137.1	.	.	.	.	.	.	.	.	.	.	G	6.581	0.475506	0.12521	.	.	ENSG00000108961	ENST00000439238	T	0.75821	-0.97	4.93	-3.59	0.04583	.	.	.	.	.	T	0.48892	0.1525	.	.	.	0.09310	N	1	B	0.18863	0.031	B	0.16289	0.015	T	0.25779	-1.0122	7	.	.	.	.	1.0577	0.01593	0.3286:0.262:0.2755:0.1339	.	121	Q9HD47-3	.	L	121	ENSP00000413190:R121L	.	R	+	2	0	RANGRF	8133468	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.541000	0.06099	-0.877000	0.04012	-0.253000	0.11424	CGA	.	.		0.572	RANGRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442127.1	NM_016492		T	8192743	G	T	8192743	1	4	259	0	1	0	0	0	0	0	0	0	13049	1058	37	1		1	RANGRF	17	8192743	Intron	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	59532	8192743	73002467	721	37039										
MYH10	4628	hgsc.bcm.edu	37	chr17	8455422	8455422	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aagatatgaaaagtacgttcAtcttttgcttgacgaacagc	8	7	2	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:8455422A>G	ENST00000269243.4	-	8	969	c.831T>C	c.(829-831)gaT>gaC	p.D277D	MYH10_ENST00000379980.4_Silent_p.D293D|MYH10_ENST00000360416.3_Silent_p.D287D|MYH10_ENST00000396239.1_Silent_p.D277D	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	277	Myosin motor.				actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						AAGTACGTTCATCTTTTGCTT	0.318																																					p.D287D		Atlas-SNP	.											.	MYH10	148	.	0			c.T861C						.						47	48	48					17																	8455422		2203	4300	6503	SO:0001819	synonymous_variant	4628	exon9			ACGTTCATCTTTT	M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026		"Myosins / Myosin superfamily : Class II"	7568	protein-coding gene	gene with protein product		160776	"myosin, heavy polypeptide 10, non-muscle"			1860190	Standard	NM_001256012		Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.831T>C	chr17.hg19:g.8455422A>G		203.0	0.0		83.0	4.0	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Silent	SNP	ENST00000269243.4	hg19	CCDS11144.1																																																																																			.	.		0.318	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2			G	8455422	A	G	8455422	2	3	259	1	0	0	0	0	0	0	0	1	10039	214	8	2		2	MYH10	17	8455422	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	262679	8455422	72739788	722	37040										
HS3ST3A1	9955	hgsc.bcm.edu	37	chr17	13504323	13504323	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggtctggcagcgctcggccaGgcagtagaagacgtaaaggg	17	9	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:13504323G>T	ENST00000284110.1	-	1	921	c.124C>A	c.(124-126)Ctg>Atg	p.L42M		NM_006042.1	NP_006033.1	Q9Y663	HS3SA_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 3A1	42					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 3 activity (GO:0033872)|sulfotransferase activity (GO:0008146)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		all_lung(20;0.114)		UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		CGCTCGGCCAGGCAGTAGAAG	0.716																																					p.L42M		Atlas-SNP	.											.	HS3ST3A1	39	.	0			c.C124A						.						31	28	29					17																	13504323		2183	4291	6474	SO:0001583	missense	9955	exon1			CGGCCAGGCAGTA	AF105376	CCDS11165.1	17p12	2007-04-02			ENSG00000153976	ENSG00000153976	2.8.2.23	"Sulfotransferases, membrane-bound"	5196	protein-coding gene	gene with protein product		604057				9988767	Standard	NM_006042		Approved	3OST3A1, 30ST3A1	uc002gob.1	Q9Y663	OTTHUMG00000058768	ENST00000284110.1:c.124C>A	chr17.hg19:g.13504323G>T	ENSP00000284110:p.Leu42Met	114.0	0.0		56.0	4.0	NM_006042	A8K7N2	Missense_Mutation	SNP	ENST00000284110.1	hg19	CCDS11165.1	.	.	.	.	.	.	.	.	.	.	G	16.76	3.213597	0.58452	.	.	ENSG00000153976	ENST00000284110	T	0.66638	-0.22	3.03	0.926	0.19430	.	.	.	.	.	T	0.50377	0.1612	L	0.34521	1.04	0.80722	D	1	B	0.21905	0.062	B	0.17979	0.02	T	0.42189	-0.9466	9	0.56958	D	0.05	.	6.5802	0.22589	0.1049:0.0:0.7169:0.1782	.	42	Q9Y663	HS3SA_HUMAN	M	42	ENSP00000284110:L42M	ENSP00000284110:L42M	L	-	1	2	HS3ST3A1	13445048	0.979000	0.34478	1.000000	0.80357	0.991000	0.79684	-0.014000	0.12656	0.279000	0.22186	-0.140000	0.14226	CTG	.	.		0.716	HS3ST3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129952.1	NM_006042		T	13504323	G	T	13504323	3	4	259	1	0	0	0	0	1	0	0	0	7374	991	35	3	1104	3	HS3ST3A1	17	13504323	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	5048901	13504323	67690887	723	37041										
PIGL	9487	hgsc.bcm.edu	37	chr17	16137378	16137378	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctccagtgtaatgattattgAcaacaggtaatatatctttt	6	6	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:16137378A>G	ENST00000225609.5	+	2	346	c.329A>G	c.(328-330)gAc>gGc	p.D110G	PIGL_ENST00000395844.4_Missense_Mutation_p.D110G|PIGL_ENST00000498772.2_Missense_Mutation_p.D110G|PIGL_ENST00000581006.1_Missense_Mutation_p.D110G	NM_004278.3	NP_004269.1	Q9Y2B2	PIGL_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class L	110					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	N-acetylglucosaminylphosphatidylinositol deacetylase activity (GO:0000225)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|skin(1)	11				UCEC - Uterine corpus endometrioid carcinoma (92;0.0934)		ATGATTATTGACAACAGGTAA	0.353																																					p.D110G		Atlas-SNP	.											.	PIGL	16	.	0			c.A329G						.						78	81	80					17																	16137378		2203	4300	6503	SO:0001583	missense	9487	exon2			TTATTGACAACAG	AB017165	CCDS11176.1	17p12-p11.2	2013-02-26	2006-06-28		ENSG00000108474	ENSG00000108474	3.5.1.89	"Phosphatidylinositol glycan anchor biosynthesis"	8966	protein-coding gene	gene with protein product	"N-acetylglucosaminylphosphatidylinositol deacetylase"	605947	"phosphatidylinositol glycan, class L"			10085243	Standard	NM_004278		Approved		uc002gpv.3	Q9Y2B2	OTTHUMG00000059346	ENST00000225609.5:c.329A>G	chr17.hg19:g.16137378A>G	ENSP00000225609:p.Asp110Gly	95.0	0.0		54.0	4.0	NM_004278	A8KA67|B4DYN4	Missense_Mutation	SNP	ENST00000225609.5	hg19	CCDS11176.1	.	.	.	.	.	.	.	.	.	.	A	13.60	2.285341	0.40394	.	.	ENSG00000108474	ENST00000225609;ENST00000395844	T;T	0.76448	-1.02;-1.02	5.78	5.78	0.91487	Putative deacetylase LmbE-like domain (2);	0.134522	0.64402	D	0.000003	T	0.80099	0.4561	L	0.47716	1.5	0.49213	D	0.999766	P;P	0.51537	0.946;0.892	P;P	0.53360	0.721;0.724	T	0.80881	-0.1184	10	0.51188	T	0.08	-11.6728	14.11	0.65115	1.0:0.0:0.0:0.0	.	110;110	B4DYN4;Q9Y2B2	.;PIGL_HUMAN	G	110	ENSP00000225609:D110G;ENSP00000379185:D110G	ENSP00000225609:D110G	D	+	2	0	PIGL	16078103	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.741000	0.74837	2.220000	0.72140	0.477000	0.44152	GAC	.	.		0.353	PIGL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131881.1			G	16137378	A	G	16137378	3	3	259	1	0	0	0	0	1	0	0	0	11900	275	10	2	335	2	PIGL	17	16137378	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2633055	16137378	65057832	724	37042										
MYO15A	51168	hgsc.bcm.edu	37	chr17	18047030	18047030	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccatgcactgtccctctaggAgctgagcaagcgggaggtag	14	11	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:18047030A>G	ENST00000205890.5	+	27	6304	c.5966A>G	c.(5965-5967)gAg>gGg	p.E1989G	snoU13_ENST00000459354.1_RNA	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	1989	Neck or regulatory domain.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					TCCCTCTAGGAGCTGAGCAAG	0.677																																					p.E1989G		Atlas-SNP	.											.	MYO15A	268	.	0			c.A5966G						.						31	37	35					17																	18047030		2154	4239	6393	SO:0001630	splice_region_variant	51168	exon26			TCTAGGAGCTGAG	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"Myosins / Myosin superfamily : Class XV"	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.5965-1A>G	chr17.hg19:g.18047030A>G		174.0	0.0		162.0	7.0	NM_016239	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	hg19	CCDS42271.1	.	.	.	.	.	.	.	.	.	.	A	15.22	2.767788	0.49574	.	.	ENSG00000091536	ENST00000205890	D	0.89485	-2.52	5.0	2.7	0.31948	.	.	.	.	.	D	0.83142	0.5190	L	0.47716	1.5	0.80722	D	1	B	0.21753	0.06	B	0.17433	0.018	T	0.78145	-0.2318	9	0.62326	D	0.03	.	7.0293	0.24958	0.7946:0.0:0.0741:0.1313	.	1989	Q9UKN7	MYO15_HUMAN	G	1989	ENSP00000205890:E1989G	ENSP00000205890:E1989G	E	+	2	0	MYO15A	17987755	1.000000	0.71417	1.000000	0.80357	0.672000	0.39443	5.104000	0.64584	0.719000	0.32188	-0.490000	0.04691	GAG	.	.		0.677	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239	Missense_Mutation	G	18047030	A	G	18047030	5	3	259	1	0	0	0	0	0	0	1	0	10072	318	11	2	6064	2	MYO15A	17	18047030	Splice_Site	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1909652	18047030	63148180	725	37043										
SUPT6H	6830	hgsc.bcm.edu	37	chr17	27014158	27014158	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acaggccgtctccctggcccGgcgcatccaggaccctctga	11	18	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:27014158G>T	ENST00000314616.6	+	22	3036	c.2753G>T	c.(2752-2754)cGg>cTg	p.R918L	SUPT6H_ENST00000347486.4_Missense_Mutation_p.R918L	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	918	Interaction with KDM6A. {ECO:0000250}.				chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					TCCCTGGCCCGGCGCATCCAG	0.542																																					p.R918L		Atlas-SNP	.											.	SUPT6H	165	.	0			c.G2753T						.						94	106	102					17																	27014158		2203	4300	6503	SO:0001583	missense	6830	exon22			TGGCCCGGCGCAT	U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"SH2 domain containing"	11470	protein-coding gene	gene with protein product		601333	"suppressor of Ty (S.cerevisiae) 6 homolog"			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85		ENST00000314616.6:c.2753G>T	chr17.hg19:g.27014158G>T	ENSP00000319104:p.Arg918Leu	100.0	0.0		97.0	4.0	NM_003170	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Missense_Mutation	SNP	ENST00000314616.6	hg19	CCDS32596.1	.	.	.	.	.	.	.	.	.	.	G	36	5.642353	0.96704	.	.	ENSG00000109111	ENST00000314616	.	.	.	5.82	5.82	0.92795	YqgF/RNase H-like domain (1);	0.000000	0.85682	D	0.000000	D	0.91164	0.7217	H	0.98446	4.235	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93996	0.7271	9	0.87932	D	0	-18.2791	19.7131	0.96103	0.0:0.0:1.0:0.0	.	918	Q7KZ85	SPT6H_HUMAN	L	918	.	ENSP00000319104:R918L	R	+	2	0	SUPT6H	24038285	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.499000	0.73683	2.760000	0.94817	0.551000	0.68910	CGG	.	.		0.542	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170		T	27014158	G	T	27014158	3	4	259	1	0	0	0	0	1	0	0	0	15415	1116	39	1	2835	1	SUPT6H	17	27014158	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	8967128	27014158	54181052	726	37044										
MYO18A	399687	hgsc.bcm.edu	37	chr17	27437088	27437088	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agcagtgcacaaaatgcagcTttgacttcttgatggtgtcg	11	8	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:27437088T>C	ENST00000527372.1	-	19	3299	c.3119A>G	c.(3118-3120)aAg>aGg	p.K1040R	MYO18A_ENST00000533112.1_Missense_Mutation_p.K1040R|MYO18A_ENST00000354329.4_Missense_Mutation_p.K1040R|MYO18A_ENST00000531253.1_Missense_Mutation_p.K1040R	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	1040	Myosin motor.				actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			AAAATGCAGCTTTGACTTCTT	0.627																																					p.K1040R	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-SNP	.											.	MYO18A	217	.	0			c.A3119G						.						42	53	49					17																	27437088		2186	4279	6465	SO:0001583	missense	399687	exon19			TGCAGCTTTGACT	D86970	CCDS45641.1, CCDS45642.1	17q11.2	2011-09-27			ENSG00000196535	ENSG00000196535		"Myosins / Myosin superfamily : Class XVIII"	31104	protein-coding gene	gene with protein product		610067				12761286	Standard	NM_078471		Approved	KIAA0216, MysPDZ	uc002hdt.1	Q92614	OTTHUMG00000166360	ENST00000527372.1:c.3119A>G	chr17.hg19:g.27437088T>C	ENSP00000437073:p.Lys1040Arg	77.0	0.0		64.0	4.0	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Missense_Mutation	SNP	ENST00000527372.1	hg19	CCDS45642.1	.	.	.	.	.	.	.	.	.	.	T	9.421	1.082964	0.20309	.	.	ENSG00000196535	ENST00000354329;ENST00000359450;ENST00000533112;ENST00000531253;ENST00000527372;ENST00000458428	T;T;T;T	0.71103	-0.54;-0.54;-0.54;-0.54	5.06	5.06	0.68205	Myosin head, motor domain (2);	0.093725	0.64402	D	0.000001	T	0.47432	0.1445	N	0.05306	-0.075	0.34569	D	0.713263	B;B;B;B;B	0.15719	0.001;0.009;0.009;0.009;0.014	B;B;B;B;B	0.16722	0.003;0.016;0.016;0.016;0.014	T	0.51395	-0.8711	10	0.07175	T	0.84	.	14.7537	0.69546	0.0:0.0:0.0:1.0	.	709;652;1040;1040;1040	Q92614-2;F8W6Y3;Q92614-3;Q92614-4;Q92614	.;.;.;.;MY18A_HUMAN	R	1040;1040;1040;1040;1040;652	ENSP00000346291:K1040R;ENSP00000435932:K1040R;ENSP00000434228:K1040R;ENSP00000437073:K1040R	ENSP00000346291:K1040R	K	-	2	0	MYO18A	24461214	1.000000	0.71417	0.997000	0.53966	0.754000	0.42855	3.561000	0.53770	2.029000	0.59856	0.459000	0.35465	AAG	.	.		0.627	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471		C	27437088	T	C	27437088	3	2	259	1	0	0	0	0	1	0	0	0	10074	1609	56	2	3141	2	MYO18A	17	27437088	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	422930	27437088	53758122	727	37045										
RAD51L3	5892	hgsc.bcm.edu	37	chr17	33443890	33443890	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	taatgtaccgtgaagtgctgAccgcagtgcctcgttcatcg	11	11	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:33443890A>G	ENST00000345365.6	-	3	519				RAD51D_ENST00000590380.1_Intron|RAD51D_ENST00000360276.3_Intron|RAD51D_ENST00000335858.7_Intron|RAD51D_ENST00000460118.2_Intron|RAD51D_ENST00000590016.1_Missense_Mutation_p.V104A|RAD51L3-RFFL_ENST00000593039.1_Intron|RAD51D_ENST00000394589.4_Intron	NM_002878.3	NP_002869.3	O75771	RA51D_HUMAN	RAD51 paralog D						ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|reciprocal meiotic recombination (GO:0007131)|strand invasion (GO:0042148)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Rad51B-Rad51C-Rad51D-XRCC2 complex (GO:0033063)|replication fork (GO:0005657)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|gamma-tubulin binding (GO:0043015)|single-stranded DNA binding (GO:0003697)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|liver(1)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						tgaagtgctgaccgcagtgcc	0.502								Direct reversal of damage																													p.V104A		Atlas-SNP	.											.	RAD51D	53	.	0			c.T311C						.						83	76	78					17																	33443890		1559	3559	5118	SO:0001627	intron_variant	5892	exon3			GTGCTGACCGCAG	AF034956	CCDS11287.1, CCDS11288.1, CCDS45646.1	17q11	2014-09-17	2013-07-02	2011-07-01	ENSG00000185379	ENSG00000185379			9823	protein-coding gene	gene with protein product	"recombination repair protein", "DNA repair protein RAD51 homolog 4"	602954	"RAD51 (S. cerevisiae)-like 3", "RAD51-like 3 (S. cerevisiae)", "RAD51 homolog D (S. cerevisiae)"	RAD51L3		9570954	Standard	NM_001142571		Approved	R51H3, Trad, HsTRAD	uc010ctj.2	O75771	OTTHUMG00000132930	ENST00000345365.6:c.263+1629T>C	chr17.hg19:g.33443890A>G		103.0	0.0		114.0	5.0	NM_001142571	B4DJU7|E1P637|O43537|O60355|O75196|O75847|O75848|O76073|O76085|O94908|Q9UFU5	Missense_Mutation	SNP	ENST00000345365.6	hg19	CCDS11287.1	.	.	.	.	.	.	.	.	.	.	A	8.684	0.905906	0.17760	.	.	ENSG00000185379	ENST00000394589	.	.	.	2.38	-0.0313	0.13910	.	.	.	.	.	T	0.27384	0.0672	.	.	.	0.09310	N	1	B	0.19583	0.037	B	0.21151	0.033	T	0.29458	-1.0011	7	0.72032	D	0.01	.	2.7198	0.05197	0.5605:0.2754:0.1641:0.0	.	104	B4DJU7	.	A	104	.	ENSP00000378090:V104A	V	-	2	0	RAD51D	30468003	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.252000	0.18278	-0.044000	0.13491	0.397000	0.26171	GTC	.	.		0.502	RAD51D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256446.1	NM_002878		G	33443890	A	G	33443890	1	3	259	0	1	0	0	0	0	0	0	0	13005	275	10	2		2	RAD51L3	17	33443890	Intron	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	6006802	33443890	47751320	728	37046										
C17orf78	284099	hgsc.bcm.edu	37	chr17	35736083	35736083	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttctccttccagaaactcacAcagaaaccaaaaggacaaca	4	13	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:35736083A>G	ENST00000300618.4	+	3	204	c.154A>G	c.(154-156)Aca>Gca	p.T52A	ACACA_ENST00000353139.5_Intron|ACACA_ENST00000416895.1_Intron|C17orf78_ENST00000586700.1_Missense_Mutation_p.T52A	NM_173625.3	NP_775896.3	Q8N4C9	CQ078_HUMAN	chromosome 17 open reading frame 78	52						integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|large_intestine(1)|lung(2)|stomach(1)	6		Breast(25;0.00295)|Ovarian(249;0.15)				AGAAACTCACACAGAAACCAA	0.418																																					p.T52A		Atlas-SNP	.											.	C17orf78	23	.	0			c.A154G						.						63	64	63					17																	35736083		1851	4087	5938	SO:0001583	missense	284099	exon3			ACTCACACAGAAA	BC034672	CCDS45655.1	17q12	2014-05-06			ENSG00000167230	ENSG00000278505			26831	protein-coding gene	gene with protein product						14702039	Standard	NM_173625		Approved	FLJ39647	uc002hns.3	Q8N4C9	OTTHUMG00000188467	ENST00000300618.4:c.154A>G	chr17.hg19:g.35736083A>G	ENSP00000300618:p.Thr52Ala	99.0	0.0		85.0	4.0	NM_173625	Q8N8D2	Missense_Mutation	SNP	ENST00000300618.4	hg19	CCDS45655.1	.	.	.	.	.	.	.	.	.	.	A	1.738	-0.492534	0.04322	.	.	ENSG00000167230	ENST00000300618;ENST00000321564	T	0.43294	0.95	4.27	2.16	0.27623	.	0.518519	0.16062	N	0.231453	T	0.14960	0.0361	N	0.05124	-0.11	0.23739	N	0.996977	B;B	0.09022	0.002;0.002	B;B	0.08055	0.003;0.003	T	0.31166	-0.9953	10	0.02654	T	1	-3.002	3.9095	0.09197	0.5801:0.0:0.4199:0.0	.	52;52	Q8N4C9-2;Q8N4C9	.;CQ078_HUMAN	A	52	ENSP00000300618:T52A	ENSP00000300618:T52A	T	+	1	0	C17orf78	32810196	0.569000	0.26643	0.998000	0.56505	0.977000	0.68977	0.838000	0.27572	0.298000	0.22638	0.482000	0.46254	ACA	.	.		0.418	C17orf78-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451570.2	NM_173625		G	35736083	A	G	35736083	3	3	259	1	0	0	0	0	1	0	0	0	1885	159	6	2	164	2	C17orf78	17	35736083	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2292193	35736083	45459127	729	37047										
GSDMB	55876	hgsc.bcm.edu	37	chr17	38068744	38068746	+	In_Frame_Del	DEL	TTT	TTT	-													0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccagaatttgaaactcagccTtttgacctggaaagagaatg							TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	TTT	TTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:38068744_38068746delTTT	ENST00000394179.1	-	3	370_372	c.240_242delAAA	c.(238-243)caaaag>cag	p.K81del	GSDMB_ENST00000520542.1_In_Frame_Del_p.K81del|GSDMB_ENST00000418519.1_In_Frame_Del_p.K81del|GSDMB_ENST00000394175.2_In_Frame_Del_p.K81del|GSDMB_ENST00000309481.7_In_Frame_Del_p.K81del|GSDMB_ENST00000360317.3_In_Frame_Del_p.K81del			Q8TAX9	GSDMB_HUMAN	gasdermin B	81						cytoplasm (GO:0005737)				breast(2)|endometrium(3)|large_intestine(6)|lung(6)|pancreas(1)|prostate(1)|stomach(2)	21						AAACTCAGCCTTTTGACCTGGAA	0.478																																					p.81_81del		Atlas-Indel,Pindel	.											.	GSDMB	87	.	0			c.241_243del						.																																			SO:0001651	inframe_deletion	55876	exon3			.	AF119884	CCDS11354.1, CCDS42313.1, CCDS54119.1, CCDS54120.1	17q21.2	2008-07-31	2008-07-31	2008-07-31	ENSG00000073605	ENSG00000073605			23690	protein-coding gene	gene with protein product		611221	"gasdermin-like"	GSDML		12883658, 15010812, 17350798	Standard	NM_001042471		Approved	PRO2521	uc010cwj.3	Q8TAX9	OTTHUMG00000133248	ENST00000394179.1:c.240_242delAAA	chr17.hg19:g.38068744_38068746delTTT	ENSP00000377733:p.Lys81del	216.0	0.0		213.0	104.0	NM_001042471	B4DKK7|Q7Z377|Q8WY76|Q9NX71|Q9P163	In_Frame_Del	DEL	ENST00000394179.1	hg19																																																																																				.	.		0.478	GSDMB-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_018530		-	38068746	TTT	-	38068744	7	5	259	1	0	1	0	1	0	0	0	0	6826	1609	56	0	1044	0	GSDMB	17	38068744	In_Frame_Del	DEL	TTT	TCGA-ES-A2HS-01A-11D-A183-10	2332661	38068744	43126466	730	37048										
TOP2A	7153	hgsc.bcm.edu	37	chr17	38556308	38556308	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttctttaaacagcctacgtgGtcaaaaagcacctgaaaaag	7	9	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:38556308G>A	ENST00000423485.1	-	24	3170	c.3012C>T	c.(3010-3012)gaC>gaT	p.D1004D		NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	1004					apoptotic chromosome condensation (GO:0030263)|ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA ligation (GO:0006266)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|embryonic cleavage (GO:0040016)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|positive regulation of apoptotic process (GO:0043065)|positive regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral genome replication (GO:0045070)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|DNA-dependent ATPase activity (GO:0008094)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(9)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	39		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	AGCCTACGTGGTCAAAAAGCA	0.313																																					p.D1004D		Atlas-SNP	.											.	TOP2A	124	.	0			c.C3012T						.						38	37	37					17																	38556308		1804	4075	5879	SO:0001819	synonymous_variant	7153	exon24			TACGTGGTCAAAA		CCDS45672.1	17q21-q22	2008-08-06	2002-08-29		ENSG00000131747	ENSG00000131747	5.99.1.2		11989	protein-coding gene	gene with protein product		126430	"topoisomerase (DNA) II alpha (170kD)"	TOP2			Standard	NM_001067		Approved		uc002huq.3	P11388	OTTHUMG00000155008	ENST00000423485.1:c.3012C>T	chr17.hg19:g.38556308G>A		57.0	0.0		57.0	4.0	NM_001067	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Silent	SNP	ENST00000423485.1	hg19	CCDS45672.1																																																																																			.	.		0.313	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1			A	38556308	G	A	38556308	2	1	259	1	0	0	0	0	0	0	0	1	16380	1252	44	3		3	TOP2A	17	38556308	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	487564	38556308	42638902	731	37049										
KRTAP1-5	83895	hgsc.bcm.edu	37	chr17	39183240	39183240	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggctggcagcaactggagctGcaggtcccactggttgagaa	15	10	0	1	rs367586882		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:39183240G>A	ENST00000361883.5	-	1	214	c.168C>T	c.(166-168)tgC>tgT	p.C56C		NM_031957.1	NP_114163.1	Q9BYS1	KRA15_HUMAN	keratin associated protein 1-5	56	15 X 5 AA repeats of C-C-[QEPVRC]- [TPIVLE]-[SRHVP].					keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(2)|kidney(1)|lung(9)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	17		Breast(137;0.00043)	STAD - Stomach adenocarcinoma(17;0.000371)			AACTGGAGCTGCAGGTCCCAC	0.622													g|||	1	0.000199681	0	0.0014	5008	,	,		18155	0		0	False		,,,				2504	0				p.C56C		Atlas-SNP	.											.	KRTAP1-5	33	.	0			c.C168T						.	G		0,4046		0,0,2023	41	46	44		168	-3.4	0	17		44	6,8396		0,6,4195	no	coding-synonymous	KRTAP1-5	NM_031957.1		0,6,6218	AA,AG,GG		0.0714,0.0,0.0482		56/175	39183240	6,12442	2023	4201	6224	SO:0001819	synonymous_variant	83895	exon1			GGAGCTGCAGGTC	AJ406928	CCDS42321.1	17q21.2	2013-06-25			ENSG00000221852	ENSG00000221852		"Keratin associated proteins"	16777	protein-coding gene	gene with protein product		608822				11279113	Standard	NM_031957		Approved	KAP1.5	uc002hvu.3	Q9BYS1	OTTHUMG00000133587	ENST00000361883.5:c.168C>T	chr17.hg19:g.39183240G>A		154.0	0.0		132.0	9.0	NM_031957	A6NJW6|A6NLZ6|B6ZDR1|Q52LP6	Silent	SNP	ENST00000361883.5	hg19	CCDS42321.1																																																																																			.	.		0.622	KRTAP1-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257691.1			A	39183240	G	A	39183240	2	1	259	1	0	0	0	0	0	0	0	1	8513	1311	46	3		3	KRTAP1-5	17	39183240	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	626932	39183240	42011970	732	37050										
KRT32	3882	hgsc.bcm.edu	37	chr17	39620667	39620667	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cctcgatgttaaggcggtccCcaagctggcatcgaagggaa	13	11	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:39620667C>A	ENST00000225899.3	-	4	840	c.737G>T	c.(736-738)gGg>gTg	p.G246V		NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	246	Linker 12.|Rod.				epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(137;0.000812)				AAGGCGGTCCCCAAGCTGGCA	0.587																																					p.G246V		Atlas-SNP	.											.	KRT32	57	.	0			c.G737T						.						66	51	56					17																	39620667		2203	4300	6503	SO:0001583	missense	3882	exon4			CGGTCCCCAAGCT	X90761	CCDS11393.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000108759	ENSG00000108759		"-", "Intermediate filaments type I, keratins (acidic)"	6449	protein-coding gene	gene with protein product	"hard keratin type I"	602760	"keratin, hair, acidic, 2"	KRTHA2		7556444, 8823373, 16831889	Standard	NM_002278		Approved	Ha-2	uc002hwr.3	Q14532	OTTHUMG00000133430	ENST00000225899.3:c.737G>T	chr17.hg19:g.39620667C>A	ENSP00000225899:p.Gly246Val	98.0	0.0		96.0	4.0	NM_002278		Missense_Mutation	SNP	ENST00000225899.3	hg19	CCDS11393.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.036808	0.75617	.	.	ENSG00000108759	ENST00000225899	T	0.80123	-1.34	5.13	5.13	0.70059	Filament (1);	0.000000	0.40064	N	0.001184	D	0.91499	0.7316	M	0.91406	3.205	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92786	0.6244	10	0.59425	D	0.04	.	15.6788	0.77352	0.0:1.0:0.0:0.0	.	246	Q14532	K1H2_HUMAN	V	246	ENSP00000225899:G246V	ENSP00000225899:G246V	G	-	2	0	KRT32	36874193	0.122000	0.22280	1.000000	0.80357	0.970000	0.65996	1.883000	0.39658	2.547000	0.85894	0.655000	0.94253	GGG	.	.		0.587	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257293.1	NM_002278		A	39620667	C	A	39620667	3	1	259	1	0	0	0	0	1	0	0	0	8477	623	22	3	625	3	KRT32	17	39620667	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	437427	39620667	41574543	733	37051										
KRT35	3886	hgsc.bcm.edu	37	chr17	39637018	39637018	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gctgacgcaccttctccaggTagccggccaggcggtcgttc	13	15	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:39637018T>A	ENST00000393989.1	-	1	374	c.332A>T	c.(331-333)tAc>tTc	p.Y111F	KRT35_ENST00000246639.2_Missense_Mutation_p.Y81F	NM_002280.4	NP_002271.3	Q92764	KRT35_HUMAN	keratin 35	111	Coil 1A.|Rod.				anatomical structure morphogenesis (GO:0009653)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	29		Breast(137;0.000286)				CTTCTCCAGGTAGCCGGCCAG	0.627																																					p.Y111F		Atlas-SNP	.											.	KRT35	58	.	0			c.A332T						.						68	74	72					17																	39637018		2203	4300	6503	SO:0001583	missense	3886	exon1			TCCAGGTAGCCGG	X90762	CCDS11394.2	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000197079	ENSG00000197079		"-", "Intermediate filaments type I, keratins (acidic)"	6453	protein-coding gene	gene with protein product	"hard keratin type I 5"	602764	"keratin, hair, acidic, 5"	KRTHA5		8823373, 16831889	Standard	NM_002280		Approved	Ha-5	uc002hws.3	Q92764	OTTHUMG00000133425	ENST00000393989.1:c.332A>T	chr17.hg19:g.39637018T>A	ENSP00000377558:p.Tyr111Phe	115.0	0.0		113.0	6.0	NM_002280	O76012|Q92651	Missense_Mutation	SNP	ENST00000393989.1	hg19	CCDS11394.2	.	.	.	.	.	.	.	.	.	.	T	19.49	3.837990	0.71373	.	.	ENSG00000197079	ENST00000246639;ENST00000393989	D;D	0.92446	-3.04;-3.04	5.24	4.16	0.48862	Filament (1);	0.000000	0.53938	D	0.000047	D	0.95468	0.8528	M	0.80028	2.48	0.41674	D	0.989258	D	0.89917	1.0	D	0.97110	1.0	D	0.95310	0.8411	10	0.87932	D	0	.	10.8643	0.46844	0.141:0.0:0.0:0.859	.	111	Q92764	KRT35_HUMAN	F	81;111	ENSP00000246639:Y81F;ENSP00000377558:Y111F	ENSP00000246639:Y81F	Y	-	2	0	KRT35	36890544	1.000000	0.71417	0.999000	0.59377	0.633000	0.38033	7.868000	0.87116	0.988000	0.38734	-0.496000	0.04628	TAC	.	.		0.627	KRT35-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_002280		A	39637018	T	A	39637018	3	1	259	1	0	0	0	0	1	0	0	0	8481	1638	57	4	1063	4	KRT35	17	39637018	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	16351	39637018	41558192	734	37052										
NAGLU	4669	hgsc.bcm.edu	37	chr17	40695160	40695160	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgtgccccgtggccgcctccTggttctggacctgtttgctg	13	14	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:40695160T>C	ENST00000225927.2	+	6	1237	c.1136T>C	c.(1135-1137)cTg>cCg	p.L379P	RP11-400F19.8_ENST00000585572.1_RNA	NM_000263.3	NP_000254.2	P54802	ANAG_HUMAN	N-acetylglucosaminidase, alpha	379					carbohydrate metabolic process (GO:0005975)|cerebellar Purkinje cell layer development (GO:0021680)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|inner ear receptor cell development (GO:0060119)|locomotor rhythm (GO:0045475)|lysosome organization (GO:0007040)|middle ear morphogenesis (GO:0042474)|nervous system development (GO:0007399)|retinal rod cell development (GO:0046548)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	alpha-N-acetylglucosaminidase activity (GO:0004561)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(1)|ovary(2)|skin(1)	12		all_cancers(22;1.58e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344)		BRCA - Breast invasive adenocarcinoma(366;0.13)	N-Acetyl-D-glucosamine(DB00141)	GGCCGCCTCCTGGTTCTGGAC	0.647																																					p.L379P		Atlas-SNP	.											.	NAGLU	36	.	0			c.T1136C						.						52	57	55					17																	40695160		2203	4300	6503	SO:0001583	missense	4669	exon6			GCCTCCTGGTTCT		CCDS11427.1	17q21.2	2010-07-27	2010-07-27		ENSG00000108784	ENSG00000108784	3.2.1.50		7632	protein-coding gene	gene with protein product	"Sanfilippo disease IIIB"	609701					Standard	XM_006721920		Approved	NAG	uc002hzv.3	P54802		ENST00000225927.2:c.1136T>C	chr17.hg19:g.40695160T>C	ENSP00000225927:p.Leu379Pro	88.0	0.0		92.0	4.0	NM_000263		Missense_Mutation	SNP	ENST00000225927.2	hg19	CCDS11427.1	.	.	.	.	.	.	.	.	.	.	T	16.92	3.254197	0.59212	.	.	ENSG00000108784	ENST00000225927;ENST00000377405	D	0.99399	-5.83	4.54	4.54	0.55810	Alpha-N-acetylglucosaminidase, tim-barrel domain (1);	0.069962	0.56097	D	0.000035	D	0.99521	0.9829	M	0.90309	3.105	0.80722	D	1	D	0.76494	0.999	D	0.70716	0.97	D	0.98237	1.0486	10	0.87932	D	0	-14.305	12.8389	0.57790	0.0:0.0:0.0:1.0	.	379	P54802	ANAG_HUMAN	P	379;55	ENSP00000225927:L379P	ENSP00000225927:L379P	L	+	2	0	NAGLU	37948686	1.000000	0.71417	0.998000	0.56505	0.547000	0.35210	7.732000	0.84908	1.906000	0.55180	0.260000	0.18958	CTG	.	.		0.647	NAGLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450385.1	NM_000263		C	40695160	T	C	40695160	3	2	259	1	0	0	0	0	1	0	0	0	10152	1580	55	2	1158	2	NAGLU	17	40695160	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1058142	40695160	40500050	735	37053										
ASB16	92591	hgsc.bcm.edu	37	chr17	42255627	42255627	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tggtgaaccagccaaggcagCtgcagcacctggcccgacta	12	14	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:42255627C>T	ENST00000293414.1	+	5	1315	c.1231C>T	c.(1231-1233)Ctg>Ttg	p.L411L	ASB16-AS1_ENST00000588785.1_RNA|ASB16-AS1_ENST00000585457.1_RNA|ASB16-AS1_ENST00000592897.1_RNA|ASB16-AS1_ENST00000591166.1_RNA	NM_080863.4	NP_543139.4	Q96NS5	ASB16_HUMAN	ankyrin repeat and SOCS box containing 16	411	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|liver(2)|lung(2)|prostate(1)	14		Breast(137;0.00765)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.114)		GCCAAGGCAGCTGCAGCACCT	0.652																																					p.L411L		Atlas-SNP	.											.	ASB16	34	.	0			c.C1231T						.						45	38	40					17																	42255627		2203	4300	6503	SO:0001819	synonymous_variant	92591	exon5			AGGCAGCTGCAGC	AK054727	CCDS11478.1	17q21.31	2013-01-10	2011-01-25		ENSG00000161664	ENSG00000161664		"Ankyrin repeat domain containing"	19768	protein-coding gene	gene with protein product		615056	"ankyrin repeat and SOCS box-containing 16"			12076535	Standard	NM_080863		Approved	FLJ30165	uc002ifl.1	Q96NS5	OTTHUMG00000181809	ENST00000293414.1:c.1231C>T	chr17.hg19:g.42255627C>T		77.0	0.0		54.0	4.0	NM_080863	B2RBC0|Q8WXK0	Silent	SNP	ENST00000293414.1	hg19	CCDS11478.1																																																																																			.	.		0.652	ASB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457703.1			T	42255627	C	T	42255627	2	4	259	1	0	0	0	0	0	0	0	1	1020	796	28	3		3	ASB16	17	42255627	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	1560467	42255627	38939583	736	37054										
GOSR2	9570	hgsc.bcm.edu	37	chr17	45006918	45006918	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gatccagtcttgcatgggacGcctggagacggcagacaagc	14	11	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:45006918G>A	ENST00000393456.2	+	2	119	c.62G>A	c.(61-63)cGc>cAc	p.R21H	RP11-156P1.2_ENST00000571841.1_Missense_Mutation_p.R21H|GOSR2_ENST00000439730.2_Missense_Mutation_p.R21H|GOSR2_ENST00000225567.4_Missense_Mutation_p.R21H|GOSR2_ENST00000576910.2_Missense_Mutation_p.R21H|GOSR2_ENST00000575949.1_Missense_Mutation_p.R21H|GOSR2_ENST00000415811.2_Missense_Mutation_p.R21H	NM_004287.3	NP_004278.2	O14653	GOSR2_HUMAN	golgi SNAP receptor complex member 2	21					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane fusion (GO:0061025)|protein transport (GO:0015031)	Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transporter activity (GO:0005215)			kidney(1)|large_intestine(2)|liver(1)|lung(1)|ovary(1)|skin(1)	7			BRCA - Breast invasive adenocarcinoma(9;0.102)			TGCATGGGACGCCTGGAGACG	0.517																																					p.R21H		Atlas-SNP	.											.	GOSR2	38	.	0			c.G62A						.						100	82	88					17																	45006918		2203	4300	6503	SO:0001583	missense	9570	exon2			TGGGACGCCTGGA	AF007548	CCDS11507.1, CCDS42355.1, CCDS45719.1	17q21	2006-02-10				ENSG00000108433			4431	protein-coding gene	gene with protein product		604027				9349823, 10198168	Standard	XM_005257843		Approved	GS27, Bos1	uc002ikz.3	O14653		ENST00000393456.2:c.62G>A	chr17.hg19:g.45006918G>A	ENSP00000377101:p.Arg21His	70.0	0.0		49.0	23.0	NM_001012511	D3DXJ5|D3DXJ6|Q8N4B8|Q96DA5|Q9BZZ4	Missense_Mutation	SNP	ENST00000393456.2	hg19	CCDS42355.1	.	.	.	.	.	.	.	.	.	.	G	14.75	2.628916	0.46944	.	.	ENSG00000108433	ENST00000225567;ENST00000393456;ENST00000415811;ENST00000439730	T;T;T;T	0.47177	0.85;0.85;0.85;1.85	5.74	5.74	0.90152	.	0.265792	0.45126	D	0.000392	T	0.45034	0.1322	L	0.58810	1.83	0.54753	D	0.999986	B;B;B;B	0.28208	0.01;0.039;0.016;0.203	B;B;B;B	0.19148	0.003;0.003;0.006;0.024	T	0.40924	-0.9537	10	0.62326	D	0.03	-22.8506	14.6945	0.69110	0.0:0.0:0.8548:0.1452	.	21;21;21;21	E7EQ34;O14653;O14653-2;Q8N4B8	.;GOSR2_HUMAN;.;.	H	21	ENSP00000225567:R21H;ENSP00000377101:R21H;ENSP00000394559:R21H;ENSP00000390577:R21H	ENSP00000225567:R21H	R	+	2	0	GOSR2	42361917	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.817000	0.39002	2.873000	0.98535	0.561000	0.74099	CGC	.	.		0.517	GOSR2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440438.1			A	45006918	G	A	45006918	3	1	259	1	0	0	0	0	1	0	0	0	6586	1087	38	1	68	1	GOSR2	17	45006918	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	2751291	45006918	36188292	737	37055										
CDC27	996	hgsc.bcm.edu	37	chr17	45234463	45234463	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	caaggagtactttgaattggAagattctaaattcaatctgt	8	5	3	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:45234463A>C	ENST00000066544.3	-	7	751	c.658T>G	c.(658-660)Tcc>Gcc	p.S220A	CDC27_ENST00000527547.1_Missense_Mutation_p.S220A|CDC27_ENST00000531206.1_Missense_Mutation_p.S220A|CDC27_ENST00000446365.2_Missense_Mutation_p.S159A|CDC27_ENST00000528748.1_5'UTR	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	220					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TTTGAATTGGAAGATTCTAAA	0.323																																					p.S220A		Atlas-SNP	.											CDC27_ENST00000531206,NS,carcinoma,0,2	CDC27	337	.	0			c.T658G						.						25	27	26					17																	45234463		2153	4281	6434	SO:0001583	missense	996	exon7			AATTGGAAGATTC	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1728	protein-coding gene	gene with protein product	"anaphase promoting complex subunit 3"	116946	"cell division cycle 27", "cell division cycle 27 homolog (S. cerevisiae)"	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.658T>G	chr17.hg19:g.45234463A>C	ENSP00000066544:p.Ser220Ala	53.0	0.0		49.0	4.0	NM_001114091	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	hg19	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	A	13.62	2.291146	0.40494	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547;ENST00000526866	T;T;T;T;T	0.68331	-0.32;-0.27;-0.05;-0.32;0.81	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.48150	0.1484	N	0.19112	0.55	0.58432	D	0.999998	B;B;B;B	0.21225	0.013;0.023;0.053;0.031	B;B;B;B	0.15484	0.004;0.004;0.013;0.009	T	0.45086	-0.9285	10	0.07175	T	0.84	-13.9867	13.9377	0.64034	1.0:0.0:0.0:0.0	.	159;220;220;220	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	A	220;220;159;220;220	ENSP00000066544:S220A;ENSP00000434614:S220A;ENSP00000392802:S159A;ENSP00000437339:S220A;ENSP00000432105:S220A	ENSP00000066544:S220A	S	-	1	0	CDC27	42589462	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.754000	0.91642	2.180000	0.69256	0.455000	0.32223	TCC	.	.		0.323	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2			C	45234463	A	C	45234463	3	2	259	1	0	0	0	0	1	0	0	0	3068	246	9	5	1886	5	CDC27	17	45234463	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	227545	45234463	35960747	738	37056										
ITGB3	3690	hgsc.bcm.edu	37	chr17	45363647	45363647	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atgaagaccacctgcttgccCatgtttggctacaaacacgt	8	12	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:45363647C>T	ENST00000559488.1	+	5	652	c.636C>T	c.(634-636)ccC>ccT	p.P212P	ITGB3_ENST00000435993.2_Silent_p.P165P|ITGB3_ENST00000560629.1_Missense_Mutation_p.H201Y|ITGB3_ENST00000571680.1_Silent_p.P212P	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	212	VWFA.				activation of protein kinase activity (GO:0032147)|angiogenesis involved in wound healing (GO:0060055)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|mesodermal cell differentiation (GO:0048333)|negative chemotaxis (GO:0050919)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein folding (GO:0006457)|regulation of bone resorption (GO:0045124)|smooth muscle cell migration (GO:0014909)|substrate adhesion-dependent cell spreading (GO:0034446)|tube development (GO:0035295)|viral entry into host cell (GO:0046718)|wound healing (GO:0042060)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|melanosome (GO:0042470)|microvillus membrane (GO:0031528)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|receptor complex (GO:0043235)|ruffle membrane (GO:0032587)	cell adhesion molecule binding (GO:0050839)|extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|identical protein binding (GO:0042802)|platelet-derived growth factor receptor binding (GO:0005161)|protease binding (GO:0002020)|protein disulfide isomerase activity (GO:0003756)|receptor activity (GO:0004872)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	39					Abciximab(DB00054)|Antithymocyte globulin(DB00098)|Eptifibatide(DB00063)|Tirofiban(DB00775)	CCTGCTTGCCCATGTTTGGCT	0.522																																					p.P212P		Atlas-SNP	.											.	ITGB3	157	.	0			c.C636T						.						163	124	137					17																	45363647		2203	4300	6503	SO:0001819	synonymous_variant	3690	exon5			CTTGCCCATGTTT		CCDS11511.1	17q21.32	2014-09-17			ENSG00000259207	ENSG00000259207		"CD molecules", "Integrins"	6156	protein-coding gene	gene with protein product	"platelet glycoprotein IIIa"	173470		GP3A		2454952	Standard	NM_000212		Approved	CD61, GPIIIa	uc002ilj.3	P05106	OTTHUMG00000171956	ENST00000559488.1:c.636C>T	chr17.hg19:g.45363647C>T		101.0	0.0		86.0	4.0	NM_000212	A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Silent	SNP	ENST00000559488.1	hg19	CCDS11511.1																																																																																			.	.		0.522	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3	NM_000212		T	45363647	C	T	45363647	2	4	259	1	0	0	0	0	0	0	0	1	7904	581	21	3		3	ITGB3	17	45363647	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	129184	45363647	35831563	739	37057										
LUC7L3	51747	hgsc.bcm.edu	37	chr17	48823914	48823914	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	attattaagaagtagagatcGacgaagaagcagaagccatg	11	5	0	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:48823914G>A	ENST00000505658.1	+	9	1178	c.989G>A	c.(988-990)cGa>cAa	p.R330Q	LUC7L3_ENST00000240304.1_Missense_Mutation_p.R330Q|LUC7L3_ENST00000544170.1_Missense_Mutation_p.R254Q|LUC7L3_ENST00000393227.2_Missense_Mutation_p.R330Q			O95232	LC7L3_HUMAN	LUC7-like 3 (S. cerevisiae)	330	Arg/Ser-rich.				mRNA splice site selection (GO:0006376)|RNA splicing (GO:0008380)	focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|U1 snRNP (GO:0005685)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)	12						AGTAGAGATCGACGAAGAAGC	0.388																																					p.R330Q		Atlas-SNP	.											.	LUC7L3	32	.	0			c.G989A						.						78	83	81					17																	48823914		2203	4300	6503	SO:0001583	missense	51747	exon9			GAGATCGACGAAG		CCDS11573.1	17q21.33	2010-02-17			ENSG00000108848	ENSG00000108848			24309	protein-coding gene	gene with protein product	"cisplatin resistance associated overexpressed protein", "CRE-associated protein"	609434				10631324, 12565863	Standard	NM_016424		Approved	LUC7A, CROP, OA48-18, CREAP-1, FLJ11063, CRA, hLuc7A	uc002iss.3	O95232	OTTHUMG00000162257	ENST00000505658.1:c.989G>A	chr17.hg19:g.48823914G>A	ENSP00000425092:p.Arg330Gln	322.0	1.0		336.0	179.0	NM_006107	B3KN54|D3DTY1|Q6PHR9|Q9NUY0|Q9P2S7	Missense_Mutation	SNP	ENST00000505658.1	hg19	CCDS11573.1	.	.	.	.	.	.	.	.	.	.	G	15.67	2.902268	0.52227	.	.	ENSG00000108848	ENST00000505658;ENST00000393227;ENST00000240304;ENST00000544170	T;T;T;T	0.35048	1.33;1.33;1.33;1.43	5.79	4.83	0.62350	.	0.129696	0.51477	D	0.000097	T	0.37732	0.1014	M	0.63843	1.955	0.58432	D	0.999999	B;B;B	0.21147	0.016;0.052;0.029	B;B;B	0.08055	0.002;0.003;0.002	T	0.19224	-1.0312	10	0.48119	T	0.1	-0.5247	15.1117	0.72362	0.0676:0.0:0.9324:0.0	.	254;330;330	B4DJ96;O95232;A8K3C5	.;LC7L3_HUMAN;.	Q	330;330;330;254	ENSP00000425092:R330Q;ENSP00000376919:R330Q;ENSP00000240304:R330Q;ENSP00000444253:R254Q	ENSP00000240304:R330Q	R	+	2	0	LUC7L3	46178913	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	8.950000	0.93019	1.467000	0.48044	-0.119000	0.15052	CGA	.	.		0.388	LUC7L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368205.2	NM_016424		A	48823914	G	A	48823914	3	1	259	1	0	0	0	0	1	0	0	0	9093	1058	37	1	1023	1	LUC7L3	17	48823914	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	3460267	48823914	32371296	740	37058										
NME1	4830	hgsc.bcm.edu	37	chr17	49237415	49237415	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tttgccggcctggtgaaataCatgcactcagggccggtagt	13	10	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:49237415C>T	ENST00000393196.3	+	3	332	c.201C>T	c.(199-201)taC>taT	p.Y67Y	NME1_ENST00000336097.3_Silent_p.Y92Y|NME2_ENST00000555572.1_Silent_p.Y92Y|NME1_ENST00000511355.1_Silent_p.Y67Y|NME1-NME2_ENST00000393198.3_Silent_p.Y67Y|NME1_ENST00000480143.1_Silent_p.Y92Y|NME2_ENST00000393193.2_Silent_p.Y67Y|NME2_ENST00000376392.6_Silent_p.Y67Y|NME1-NME2_ENST00000608447.1_Silent_p.Y92Y|NME1_ENST00000013034.3_Silent_p.Y92Y	NM_000269.2	NP_000260.1	P15531	NDKA_HUMAN	NME/NM23 nucleoside diphosphate kinase 1	67					cellular response to drug (GO:0035690)|cellular response to fatty acid (GO:0071398)|cellular response to glucose stimulus (GO:0071333)|CTP biosynthetic process (GO:0006241)|DNA catabolic process (GO:0006308)|endocytosis (GO:0006897)|GTP biosynthetic process (GO:0006183)|hippocampus development (GO:0021766)|lactation (GO:0007595)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|negative regulation of myeloid leukocyte differentiation (GO:0002762)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of DNA binding (GO:0043388)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amine (GO:0014075)|response to cAMP (GO:0051591)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)|UTP biosynthetic process (GO:0006228)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|deoxyribonuclease activity (GO:0004536)|GTP binding (GO:0005525)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|nucleoside diphosphate kinase activity (GO:0004550)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|single-stranded DNA binding (GO:0003697)			endometrium(1)|large_intestine(1)|lung(1)	3			BRCA - Breast invasive adenocarcinoma(22;1.54e-08)		Adefovir Dipivoxil(DB00718)|Lamivudine(DB00709)|Tenofovir(DB00300)	TGGTGAAATACATGCACTCAG	0.498																																					p.Y92Y	GBM(176;1298 2890 6639 30062)	Atlas-SNP	.											.	NME1	12	.	0			c.C276T						.						163	133	143					17																	49237415		2203	4300	6503	SO:0001819	synonymous_variant	4830	exon4			GAAATACATGCAC	AL360191, X17620	CCDS11578.1, CCDS11579.1	17q21.33	2013-04-29	2012-05-18		ENSG00000239672	ENSG00000239672			7849	protein-coding gene	gene with protein product		156490	"non-metastatic cells 1, protein (NM23A) expressed in"			8270257, 19852809	Standard	NM_000269		Approved	NM23, NM23-H1, NDPKA		P15531	OTTHUMG00000137474	ENST00000393196.3:c.201C>T	chr17.hg19:g.49237415C>T		77.0	0.0		116.0	5.0	NM_198175	Q6FGK3|Q86XQ2|Q9UDJ6	Silent	SNP	ENST00000393196.3	hg19	CCDS11579.1																																																																																			.	.		0.498	NME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268662.2	NM_000269		T	49237415	C	T	49237415	2	4	259	1	0	0	0	0	0	0	0	1	10498	489	17	3		3	NME1	17	49237415	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	413501	49237415	31957795	741	37059										
EPX	8288	hgsc.bcm.edu	37	chr17	56280606	56280606	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccatcgctgagcctcttttgCcgggggctcgagtggggcct	15	13	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:56280606C>T	ENST00000225371.5	+	11	1983	c.1873C>T	c.(1873-1875)Ccg>Tcg	p.P625S		NM_000502.4	NP_000493.1	P11678	PERE_HUMAN	eosinophil peroxidase	625					defense response to nematode (GO:0002215)|eosinophil migration (GO:0072677)|hydrogen peroxide catabolic process (GO:0042744)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-5 production (GO:0032714)|positive regulation of interleukin-4 production (GO:0032753)	extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(2)|endometrium(9)|kidney(1)|large_intestine(9)|liver(2)|lung(20)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	48					Melatonin(DB01065)	GCCTCTTTTGCCGGGGGCTCG	0.517																																					p.P625S		Atlas-SNP	.											.	EPX	95	.	0			c.C1873T						.						67	71	70					17																	56280606		2203	4300	6503	SO:0001583	missense	8288	exon11			CTTTTGCCGGGGG	M26515	CCDS11602.1	17q23.1	2006-09-25				ENSG00000121053	1.11.1.7		3423	protein-coding gene	gene with protein product		131399				2550461, 2541222	Standard	NM_000502		Approved	EPO, EPP, EPX-PEN	uc002ivq.3	P11678		ENST00000225371.5:c.1873C>T	chr17.hg19:g.56280606C>T	ENSP00000225371:p.Pro625Ser	120.0	0.0		84.0	5.0	NM_000502	Q4TVP3	Missense_Mutation	SNP	ENST00000225371.5	hg19	CCDS11602.1	.	.	.	.	.	.	.	.	.	.	C	16.69	3.193243	0.58017	.	.	ENSG00000121053	ENST00000225371	T	0.69806	-0.43	5.96	5.96	0.96718	.	0.271357	0.42964	D	0.000632	T	0.67183	0.2866	M	0.64997	1.995	0.43698	D	0.996156	B	0.12013	0.005	B	0.17433	0.018	T	0.62407	-0.6861	10	0.52906	T	0.07	-3.8105	17.9158	0.88950	0.0:1.0:0.0:0.0	.	625	P11678	PERE_HUMAN	S	625	ENSP00000225371:P625S	ENSP00000225371:P625S	P	+	1	0	EPX	53635605	0.005000	0.15991	0.983000	0.44433	0.862000	0.49288	1.256000	0.32921	2.832000	0.97577	0.655000	0.94253	CCG	.	.		0.517	EPX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443367.1	NM_000502		T	56280606	C	T	56280606	3	4	259	1	0	0	0	0	1	0	0	0	5202	739	26	3	1915	3	EPX	17	56280606	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	7043191	56280606	24914604	742	37060										
LPO	4025	hgsc.bcm.edu	37	chr17	56326538	56326538	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tacgggagactgcaataacaGgtggcggggcttggggtgtg	19	6	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:56326538G>T	ENST00000262290.4	+	5	759	c.443G>T	c.(442-444)aGg>aTg	p.R148M	LPO_ENST00000421678.2_Splice_Site_p.R65M|LPO_ENST00000582328.1_Splice_Site_p.R65M|LPO_ENST00000543544.1_Splice_Site_p.R89M	NM_006151.2	NP_006142.1	P22079	PERL_HUMAN	lactoperoxidase	148					defense response to bacterium (GO:0042742)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|hydrogen peroxide catabolic process (GO:0042744)|response to oxidative stress (GO:0006979)|thiocyanate metabolic process (GO:0018969)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|metal ion binding (GO:0046872)|thiocyanate peroxidase activity (GO:0036393)			breast(5)|cervix(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30						TGCAATAACAGGTGGCGGGGC	0.642																																					p.R148M		Atlas-SNP	.											.	LPO	73	.	0			c.G443T						.						49	43	45					17																	56326538		2203	4300	6503	SO:0001630	splice_region_variant	4025	exon5			ATAACAGGTGGCG	M58151	CCDS32689.1, CCDS54149.1	17q23.1	2008-02-05				ENSG00000167419	1.11.1.7		6678	protein-coding gene	gene with protein product		150205				2222811, 8964511	Standard	NM_006151		Approved	SPO	uc002ivt.3	P22079		ENST00000262290.4:c.443+1G>T	chr17.hg19:g.56326538G>T		95.0	0.0		61.0	4.0	NM_006151	A5JUY4|E7EMJ3|Q13408|Q3KNQ2	Missense_Mutation	SNP	ENST00000262290.4	hg19	CCDS32689.1	.	.	.	.	.	.	.	.	.	.	G	16.11	3.029311	0.54790	.	.	ENSG00000167419	ENST00000262290;ENST00000421678;ENST00000543544	T;T;T	0.69435	-0.4;-0.4;-0.4	5.34	4.37	0.52481	.	0.051265	0.85682	D	0.000000	T	0.79499	0.4456	M	0.77712	2.385	0.51482	D	0.999928	D;D;D;D	0.67145	0.996;0.984;0.992;0.996	D;D;P;D	0.66979	0.934;0.929;0.888;0.948	T	0.79288	-0.1865	10	0.37606	T	0.19	.	13.0866	0.59144	0.0775:0.0:0.9225:0.0	.	65;65;89;148	B4DUH9;E7EMJ3;B4E1M1;P22079	.;.;.;PERL_HUMAN	M	148;65;89	ENSP00000262290:R148M;ENSP00000400245:R65M;ENSP00000445344:R89M	ENSP00000262290:R148M	R	+	2	0	LPO	53681537	1.000000	0.71417	1.000000	0.80357	0.091000	0.18340	4.138000	0.58017	1.245000	0.43885	0.650000	0.86243	AGG	.	.		0.642	LPO-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443961.1		Missense_Mutation	T	56326538	G	T	56326538	5	4	259	1	0	0	0	0	0	0	1	0	8931	1014	35	3	457	3	LPO	17	56326538	Splice_Site	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	45932	56326538	24868672	743	37061										
BCAS3	54828	hgsc.bcm.edu	37	chr17	59152380	59152380	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agatgaagaatggctttcccAggtaaaactctgaaatattg	9	6	1	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:59152380A>G	ENST00000390652.5	+	21	2205	c.2174A>G	c.(2173-2175)cAg>cGg	p.Q725R	BCAS3_ENST00000588874.1_Splice_Site_p.Q481R|BCAS3_ENST00000588462.1_Splice_Site_p.Q725R|BCAS3_ENST00000585744.1_Splice_Site_p.Q496R|BCAS3_ENST00000589222.1_Splice_Site_p.Q710R|BCAS3_ENST00000408905.3_Splice_Site_p.Q710R|BCAS3_ENST00000407086.3_Splice_Site_p.Q710R	NM_001099432.1	NP_001092902.1			breast carcinoma amplified sequence 3											NS(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(24)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)			TGGCTTTCCCAGGTAAAACTC	0.398																																					p.Q725R		Atlas-SNP	.											.	BCAS3	90	.	0			c.A2174G						.						82	76	78					17																	59152380		1813	4081	5894	SO:0001630	splice_region_variant	54828	exon21			TTTCCCAGGTAAA	AF361219	CCDS11626.1, CCDS45749.1	17q23.2	2013-06-25			ENSG00000141376	ENSG00000141376		"WD repeat domain containing"	14347	protein-coding gene	gene with protein product		607470				12378525	Standard	NM_017679		Approved	FLJ20128	uc002iyv.4	Q9H6U6	OTTHUMG00000180064	ENST00000390652.5:c.2175+1A>G	chr17.hg19:g.59152380A>G		84.0	0.0		93.0	4.0	NM_001099432		Missense_Mutation	SNP	ENST00000390652.5	hg19	CCDS45749.1	.	.	.	.	.	.	.	.	.	.	A	26.8	4.775826	0.90195	.	.	ENSG00000141376	ENST00000390652;ENST00000407086;ENST00000408905	T;T;T	0.39056	1.1;1.14;1.12	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.60274	0.2256	M	0.71206	2.165	0.54753	D	0.999987	D;D;B;D;B	0.60575	0.988;0.988;0.135;0.975;0.135	P;P;B;P;B	0.57911	0.794;0.829;0.059;0.819;0.037	T	0.64368	-0.6424	10	0.72032	D	0.01	.	16.1982	0.82046	1.0:0.0:0.0:0.0	.	710;725;710;725;710	Q9H6U6-3;Q9H6U6-8;Q9H6U6-7;Q9H6U6;Q9H6U6-2	.;.;.;BCAS3_HUMAN;.	R	725;710;710	ENSP00000375067:Q725R;ENSP00000385323:Q710R;ENSP00000386173:Q710R	ENSP00000375067:Q725R	Q	+	2	0	BCAS3	56507162	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	8.962000	0.93254	2.226000	0.72624	0.533000	0.62120	CAG	.	.		0.398	BCAS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449578.1	NM_017679	Missense_Mutation	G	59152380	A	G	59152380	5	3	259	1	0	0	0	0	0	0	1	0	1352	202	7	2	2252	2	BCAS3	17	59152380	Splice_Site	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2825842	59152380	22042830	744	37062										
SMARCD2	6603	hgsc.bcm.edu	37	chr17	61914319	61914319	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tggcctcctggatctccatcCgcttgcgagcaatggtctgg	12	13	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:61914319C>T	ENST00000448276.2	-	4	795	c.530G>A	c.(529-531)cGg>cAg	p.R177Q	SMARCD2_ENST00000225742.9_Missense_Mutation_p.R102Q|SMARCD2_ENST00000323347.10_Missense_Mutation_p.R129Q	NM_001098426.1	NP_001091896.1	Q92925	SMRD2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2	177					ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|nucleosome disassembly (GO:0006337)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(1)	8						GATCTCCATCCGCTTGCGAGC	0.547																																					p.R177Q		Atlas-SNP	.											.	SMARCD2	29	.	0			c.G530A						.						110	113	112					17																	61914319		1998	4165	6163	SO:0001583	missense	6603	exon4			TCCATCCGCTTGC	U66618	CCDS45756.1	17q23.3	2014-07-16			ENSG00000108604	ENSG00000108604			11107	protein-coding gene	gene with protein product	"mammalian chromatin remodeling complex BRG1-associated factor 60B", "Swp73-like protein", "chromatin remodeling complex BAF60B subunit", "SWI/SNF complex 60 kDa subunit B"	601736				8804307, 9693044	Standard	NM_001098426		Approved	BAF60B, Rsc6p, CRACD2, PRO2451	uc010deb.1	Q92925	OTTHUMG00000179045	ENST00000448276.2:c.530G>A	chr17.hg19:g.61914319C>T	ENSP00000392617:p.Arg177Gln	103.0	0.0		92.0	4.0	NM_001098426	A5PLL5|A6NNQ7|B4DV56|B4E1R6|Q7L2I6|Q9UHZ1	Missense_Mutation	SNP	ENST00000448276.2	hg19	CCDS45756.1	.	.	.	.	.	.	.	.	.	.	.	22.2	4.261664	0.80358	.	.	ENSG00000108604	ENST00000448276;ENST00000225742;ENST00000450364;ENST00000323347	T;T	0.51817	0.69;0.69	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.71685	0.3369	M	0.83223	2.63	0.80722	D	1	D;D;D	0.71674	0.998;0.998;0.998	D;D;D	0.79108	0.979;0.992;0.992	T	0.75031	-0.3461	10	0.87932	D	0	-12.8855	16.9239	0.86170	0.0:1.0:0.0:0.0	.	129;140;177	Q92925-3;B9EGA3;Q92925	.;.;SMRD2_HUMAN	Q	177;119;140;129	ENSP00000392617:R177Q;ENSP00000318451:R129Q	ENSP00000225742:R119Q	R	-	2	0	SMARCD2	59268051	1.000000	0.71417	1.000000	0.80357	0.029000	0.11900	7.651000	0.83577	2.865000	0.98341	0.655000	0.94253	CGG	.	.		0.547	SMARCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444544.1	NM_001098426		T	61914319	C	T	61914319	3	4	259	1	0	0	0	0	1	0	0	0	14793	652	23	1	1105	1	SMARCD2	17	61914319	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	2761939	61914319	19280891	745	37063										
CACNG5	27091	hgsc.bcm.edu	37	chr17	64875093	64875093	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gattcttgtctccacaggtgAggagcgggggcgttgcttca	15	9	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:64875093A>G	ENST00000533854.1	+	3	437	c.200A>G	c.(199-201)gAg>gGg	p.E67G	CACNG5_ENST00000169565.3_Missense_Mutation_p.E67G|CACNG5_ENST00000307139.3_Missense_Mutation_p.E67G			Q9UF02	CCG5_HUMAN	calcium channel, voltage-dependent, gamma subunit 5	67					regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ion transmembrane transporter activity (GO:0015075)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)|skin(2)	24			BRCA - Breast invasive adenocarcinoma(6;1.61e-08)			TCCACAGGTGAGGAGCGGGGG	0.458																																					p.E67G		Atlas-SNP	.											.	CACNG5	77	.	0			c.A200G						.						105	90	95					17																	64875093		2203	4300	6503	SO:0001583	missense	27091	exon2			CAGGTGAGGAGCG	AF148220	CCDS11665.1	17q24	2004-02-16				ENSG00000075429		"Calcium channel subunits"	1409	protein-coding gene	gene with protein product		606405				10613843	Standard	NM_145811		Approved		uc010wqj.2	Q9UF02		ENST00000533854.1:c.200A>G	chr17.hg19:g.64875093A>G	ENSP00000436836:p.Glu67Gly	83.0	0.0		84.0	4.0	NM_145811	A8K2A6|Q547R3|Q8WXS7|Q9UHM3	Missense_Mutation	SNP	ENST00000533854.1	hg19	CCDS11665.1	.	.	.	.	.	.	.	.	.	.	A	17.63	3.438171	0.62955	.	.	ENSG00000075429	ENST00000533854;ENST00000307139;ENST00000169565	D;D;D	0.88896	-2.44;-2.44;-2.44	4.53	4.53	0.55603	.	0.000000	0.85682	D	0.000000	D	0.84915	0.5578	L	0.46157	1.445	0.80722	D	1	B	0.30542	0.284	B	0.34093	0.175	T	0.81504	-0.0903	10	0.24483	T	0.36	-24.6407	12.3224	0.54991	1.0:0.0:0.0:0.0	.	67	Q9UF02	CCG5_HUMAN	G	67	ENSP00000436836:E67G;ENSP00000303092:E67G;ENSP00000169565:E67G	ENSP00000169565:E67G	E	+	2	0	CACNG5	62305555	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.477000	0.66799	1.996000	0.58369	0.533000	0.62120	GAG	.	.		0.458	CACNG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389882.1	NM_014404, NM_145811		G	64875093	A	G	64875093	3	3	259	1	0	0	0	0	1	0	0	0	2562	304	11	2	206	2	CACNG5	17	64875093	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2960774	64875093	16320117	746	37064										
BPTF	2186	hgsc.bcm.edu	37	chr17	65960451	65960451	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgccagtcaacagaggatgcCatgacagtgctcacgccact	10	13	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:65960451C>T	ENST00000321892.4	+	27	8824	c.8763C>T	c.(8761-8763)gcC>gcT	p.A2921A	BPTF_ENST00000424123.3_Silent_p.A2639A|BPTF_ENST00000306378.6_Silent_p.A2795A|BPTF_ENST00000335221.5_Silent_p.A2778A			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	2921					anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			CAGAGGATGCCATGACAGTGC	0.512																																					p.A2795A		Atlas-SNP	.											.	BPTF	415	.	0			c.C8385T						.						106	95	99					17																	65960451		2203	4300	6503	SO:0001819	synonymous_variant	2186	exon25			GGATGCCATGACA	AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"Zinc fingers, PHD-type"	3581	protein-coding gene	gene with protein product		601819	"fetal Alzheimer antigen"	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.8763C>T	chr17.hg19:g.65960451C>T		179.0	0.0		175.0	7.0	NM_182641	Q6NX67|Q7Z7D6|Q9UIG2	Silent	SNP	ENST00000321892.4	hg19																																																																																				.	.		0.512	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459		T	65960451	C	T	65960451	2	4	259	1	0	0	0	0	0	0	0	1	1497	581	21	3		3	BPTF	17	65960451	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	1085358	65960451	15234759	747	37065										
CDC42EP4	23580	hgsc.bcm.edu	37	chr17	71281766	71281766	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gctgcgggctgagccggggcTgggggccgctgctgcccacc	19	15	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:71281766T>C	ENST00000335793.3	-	2	1268	c.874A>G	c.(874-876)Agc>Ggc	p.S292G	CDC42EP4_ENST00000439510.2_Missense_Mutation_p.S222G|CDC42EP4_ENST00000581014.1_Intron			Q9H3Q1	BORG4_HUMAN	CDC42 effector protein (Rho GTPase binding) 4	292					positive regulation of pseudopodium assembly (GO:0031274)|regulation of cell shape (GO:0008360)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	GTP-Rho binding (GO:0017049)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(3)|large_intestine(1)|lung(7)|urinary_tract(1)	14			LUSC - Lung squamous cell carcinoma(166;0.0352)|Lung(188;0.0711)			GAGCCGGGGCTGGGGGCCGCT	0.706																																					p.S292G		Atlas-SNP	.											.	CDC42EP4	19	.	0			c.A874G						.						14	18	17					17																	71281766		2202	4291	6493	SO:0001583	missense	23580	exon2			CGGGGCTGGGGGC	AB042237	CCDS11695.1	17q24-q25	2008-07-18				ENSG00000179604			17147	protein-coding gene	gene with protein product	"Cdc42 effector protein 4", "binder of Rho GTPases 4"	605468				11035016, 10490598	Standard	NM_012121		Approved	CEP4, KAIA1777, BORG4, MGC3740, MGC17125	uc002jjo.3	Q9H3Q1		ENST00000335793.3:c.874A>G	chr17.hg19:g.71281766T>C	ENSP00000338258:p.Ser292Gly	98.0	0.0		78.0	4.0	NM_012121	B3KUS7|O95828|Q96FT3	Missense_Mutation	SNP	ENST00000335793.3	hg19	CCDS11695.1	.	.	.	.	.	.	.	.	.	.	T	17.17	3.320388	0.60634	.	.	ENSG00000179604	ENST00000335793;ENST00000439510	T;T	0.35236	1.33;1.32	4.91	4.91	0.64330	.	0.225676	0.38492	N	0.001667	T	0.33556	0.0867	M	0.63428	1.95	0.80722	D	1	P;B	0.36599	0.56;0.355	B;B	0.28638	0.092;0.057	T	0.20638	-1.0269	10	0.41790	T	0.15	-20.0915	14.2123	0.65773	0.0:0.0:0.0:1.0	.	222;292	B3KUS7;Q9H3Q1	.;BORG4_HUMAN	G	292;222	ENSP00000338258:S292G;ENSP00000404270:S222G	ENSP00000338258:S292G	S	-	1	0	CDC42EP4	68793361	1.000000	0.71417	0.999000	0.59377	0.600000	0.36913	3.618000	0.54188	1.854000	0.53819	0.397000	0.26171	AGC	.	.		0.706	CDC42EP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441898.1	NM_012121		C	71281766	T	C	71281766	3	2	259	1	0	0	0	0	1	0	0	0	3080	1580	55	2	200	2	CDC42EP4	17	71281766	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	5321315	71281766	9913444	748	37066										
SDK2	54549	hgsc.bcm.edu	37	chr17	71335078	71335078	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cctcgtactcgctgtcacttCcctgggaggacagagaatca	10	13	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:71335078C>T	ENST00000392650.3	-	45	6167	c.6167G>A	c.(6166-6168)gGa>gAa	p.G2056E	SDK2_ENST00000388726.3_Splice_Site_p.G2037E|SDK2_ENST00000410094.1_5'UTR	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	2056					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(15)|lung(31)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	86						GCTGTCACTTCCCTGGGAGGA	0.572																																					p.G2056E		Atlas-SNP	.											.	SDK2	219	.	0			c.G6167A						.						127	119	122					17																	71335078		2203	4300	6503	SO:0001630	splice_region_variant	54549	exon45			TCACTTCCCTGGG	AB040947	CCDS45769.1	17q21.31	2013-02-11	2011-12-09		ENSG00000069188	ENSG00000069188		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19308	protein-coding gene	gene with protein product		607217	"sidekick homolog 2 (chicken)"			12230981, 15213259	Standard	NM_001144952		Approved	FLJ10832, KIAA1514	uc010dfm.3	Q58EX2	OTTHUMG00000152726	ENST00000392650.3:c.6166-1G>A	chr17.hg19:g.71335078C>T		565.0	0.0		537.0	279.0	NM_001144952	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Missense_Mutation	SNP	ENST00000392650.3	hg19	CCDS45769.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.227403	0.79576	.	.	ENSG00000069188	ENST00000409227;ENST00000392650;ENST00000388726;ENST00000424778;ENST00000316893;ENST00000410094	T;T;T	0.60040	0.22;0.24;1.44	4.72	4.72	0.59763	.	0.000000	0.85682	D	0.000000	T	0.64571	0.2610	L	0.40543	1.245	0.58432	D	0.999999	D;P	0.52996	0.957;0.948	P;P	0.56612	0.71;0.802	T	0.68387	-0.5422	10	0.62326	D	0.03	.	17.3228	0.87240	0.0:1.0:0.0:0.0	.	2056;2037	Q58EX2;Q58EX2-3	SDK2_HUMAN;.	E	1680;2056;2037;1213;2056;397	ENSP00000376421:G2056E;ENSP00000373378:G2037E;ENSP00000407098:G1213E	ENSP00000324967:G2056E	G	-	2	0	SDK2	68846673	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	3.777000	0.55364	2.172000	0.68678	0.655000	0.94253	GGA	.	.		0.572	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064	Missense_Mutation	T	71335078	C	T	71335078	5	4	259	1	0	0	0	0	0	0	1	0	13984	869	30	3	355	3	SDK2	17	71335078	Splice_Site	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	53312	71335078	9860132	749	37067										
TMEM104	54868	hgsc.bcm.edu	37	chr17	72786394	72786394	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cagcgatgttctcatccgggAcaactacgagcgggcagaga	13	11	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:72786394A>G	ENST00000335464.5	+	5	467	c.305A>G	c.(304-306)gAc>gGc	p.D102G	TMEM104_ENST00000582773.1_Missense_Mutation_p.D102G|TMEM104_ENST00000417024.2_Missense_Mutation_p.D115G|TMEM104_ENST00000582330.1_Missense_Mutation_p.D102G	NM_017728.3	NP_060198.3	Q8NE00	TM104_HUMAN	transmembrane protein 104	102						integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(5)|ovary(1)	19	all_lung(278;0.23)					CTCATCCGGGACAACTACGAG	0.612																																					p.D102G		Atlas-SNP	.											.	TMEM104	49	.	0			c.A305G						.						116	103	108					17																	72786394		2203	4300	6503	SO:0001583	missense	54868	exon5			TCCGGGACAACTA	AK074029	CCDS32723.1	17q25.1	2005-12-19				ENSG00000109066			25984	protein-coding gene	gene with protein product							Standard	NM_017728		Approved	FLJ20255, FLJ00021	uc002jls.4	Q8NE00		ENST00000335464.5:c.305A>G	chr17.hg19:g.72786394A>G	ENSP00000334849:p.Asp102Gly	61.0	0.0		74.0	4.0	NM_017728	Q8TEU1|Q9NT56|Q9NXH1	Missense_Mutation	SNP	ENST00000335464.5	hg19	CCDS32723.1	.	.	.	.	.	.	.	.	.	.	A	12.20	1.867562	0.32977	.	.	ENSG00000109066	ENST00000335464;ENST00000417024	T;T	0.47177	1.42;0.85	4.97	3.88	0.44766	.	0.395546	0.30329	N	0.009880	T	0.24470	0.0593	N	0.08118	0	0.46701	D	0.999164	B;B;B	0.10296	0.003;0.001;0.0	B;B;B	0.12156	0.007;0.002;0.0	T	0.07558	-1.0766	10	0.21540	T	0.41	-22.2523	9.0102	0.36137	0.9159:0.0:0.0841:0.0	.	115;102;102	B4DKL7;Q8NE00-2;Q8NE00	.;.;TM104_HUMAN	G	102;115	ENSP00000334849:D102G;ENSP00000397676:D115G	ENSP00000334849:D102G	D	+	2	0	TMEM104	70297989	1.000000	0.71417	0.913000	0.36048	0.987000	0.75469	4.636000	0.61339	1.997000	0.58415	0.459000	0.35465	GAC	.	.		0.612	TMEM104-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444442.1	NM_017728		G	72786394	A	G	72786394	3	3	259	1	0	0	0	0	1	0	0	0	16033	275	10	2	319	2	TMEM104	17	72786394	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1451316	72786394	8408816	750	37068										
ITGB4	3691	hgsc.bcm.edu	37	chr17	73738768	73738768	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cgagaagcagctgctggtggAggccatcgacgtgcccgcag	16	12	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:73738768A>G	ENST00000200181.3	+	25	3075	c.2888A>G	c.(2887-2889)gAg>gGg	p.E963G	ITGB4_ENST00000339591.3_Missense_Mutation_p.E963G|ITGB4_ENST00000450894.3_Missense_Mutation_p.E963G|ITGB4_ENST00000579662.1_Missense_Mutation_p.E963G|ITGB4_ENST00000449880.2_Missense_Mutation_p.E963G	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	963					amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			CTGCTGGTGGAGGCCATCGAC	0.652																																					p.E963G		Atlas-SNP	.											.	ITGB4	165	.	0			c.A2888G						.						75	57	63					17																	73738768		2203	4300	6503	SO:0001583	missense	3691	exon25			TGGTGGAGGCCAT		CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"CD molecules", "Integrins", "Fibronectin type III domain containing"	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.2888A>G	chr17.hg19:g.73738768A>G	ENSP00000200181:p.Glu963Gly	117.0	0.0		90.0	5.0	NM_001005731	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Missense_Mutation	SNP	ENST00000200181.3	hg19	CCDS11727.1	.	.	.	.	.	.	.	.	.	.	A	16.83	3.231521	0.58777	.	.	ENSG00000132470	ENST00000200181;ENST00000339591;ENST00000449880	T;T;T	0.76448	-1.02;-0.97;-0.97	5.52	5.52	0.82312	.	0.063637	0.64402	D	0.000008	T	0.81978	0.4937	L	0.29908	0.895	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.74023	0.982;0.959;0.959	D	0.84469	0.0598	10	0.87932	D	0	.	15.6342	0.76937	1.0:0.0:0.0:0.0	.	963;963;963	P16144-3;A0AVL6;P16144	.;.;ITB4_HUMAN	G	963	ENSP00000200181:E963G;ENSP00000344079:E963G;ENSP00000400217:E963G	ENSP00000200181:E963G	E	+	2	0	ITGB4	71250363	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	7.440000	0.80464	2.117000	0.64856	0.533000	0.62120	GAG	.	.		0.652	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1			G	73738768	A	G	73738768	3	3	259	1	0	0	0	0	1	0	0	0	7906	304	11	2	2982	2	ITGB4	17	73738768	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	952374	73738768	7456442	751	37069										
UNC13D	201294	hgsc.bcm.edu	37	chr17	73840396	73840396	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agaagggagggcgctgctgcGgatgggagaggagtgtcgcc	21	7	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:73840396G>T	ENST00000207549.4	-	1	402	c.23C>A	c.(22-24)cCg>cAg	p.P8Q	UNC13D_ENST00000587504.1_5'Flank|UNC13D_ENST00000412096.2_Missense_Mutation_p.P8Q	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	unc-13 homolog D (C. elegans)	8					defense response to virus (GO:0051607)|germinal center formation (GO:0002467)|granuloma formation (GO:0002432)|natural killer cell degranulation (GO:0043320)|phagocytosis (GO:0006909)|positive regulation of exocytosis (GO:0045921)|regulation of mast cell degranulation (GO:0043304)	endosome (GO:0005768)|exocytic vesicle (GO:0070382)|lysosome (GO:0005764)|membrane (GO:0016020)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)			GCGCTGCTGCGGATGGGAGAG	0.622									Familial Hemophagocytic Lymphohistiocytosis																												p.P8Q		Atlas-SNP	.											.	UNC13D	68	.	0			c.C23A						.						46	46	46					17																	73840396		2200	4300	6500	SO:0001583	missense	201294	exon1	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	TGCTGCGGATGGG	AK024474	CCDS11730.1	17q25.3	2014-09-17				ENSG00000092929			23147	protein-coding gene	gene with protein product		608897					Standard	NM_199242		Approved	Munc13-4	uc002jpp.3	Q70J99		ENST00000207549.4:c.23C>A	chr17.hg19:g.73840396G>T	ENSP00000207549:p.Pro8Gln	131.0	0.0		84.0	4.0	NM_199242	B4DWG9|Q9H7K5	Missense_Mutation	SNP	ENST00000207549.4	hg19	CCDS11730.1	.	.	.	.	.	.	.	.	.	.	G	10.50	1.368304	0.24771	.	.	ENSG00000092929	ENST00000207549;ENST00000412096;ENST00000448606	T;T	0.70516	-0.43;-0.49	4.04	3.06	0.35304	.	0.728418	0.11948	N	0.513960	T	0.73426	0.3585	L	0.57536	1.79	0.09310	N	1	P	0.41313	0.745	P	0.47786	0.557	T	0.62651	-0.6809	10	0.72032	D	0.01	4.3639	10.5479	0.45070	0.1046:0.0:0.8954:0.0	.	8	Q70J99	UN13D_HUMAN	Q	8	ENSP00000207549:P8Q;ENSP00000388093:P8Q	ENSP00000207549:P8Q	P	-	2	0	UNC13D	71351991	0.001000	0.12720	0.054000	0.19295	0.018000	0.09664	1.055000	0.30467	0.384000	0.24942	-1.134000	0.01955	CCG	.	.		0.622	UNC13D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448847.2	XM_113950		T	73840396	G	T	73840396	3	4	259	1	0	0	0	0	1	0	0	0	17002	1116	39	1	3377	1	UNC13D	17	73840396	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	101628	73840396	7354814	752	37070										
FBF1	85302	hgsc.bcm.edu	37	chr17	73914288	73914288	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccgcatcgacctctcggtccTtcagcagctttagccgctgc	9	17	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:73914288T>C	ENST00000586717.1	-	20	2432	c.2159A>G	c.(2158-2160)aAg>aGg	p.K720R	FBF1_ENST00000389570.4_Missense_Mutation_p.K720R|FBF1_ENST00000319129.5_Missense_Mutation_p.K719R			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	720					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	4						CTCTCGGTCCTTCAGCAGCTT	0.677																																					p.K719R		Atlas-SNP	.											.	FBF1	48	.	0			c.A2156G						.						29	38	35					17																	73914288		2119	4228	6347	SO:0001583	missense	85302	exon20			CGGTCCTTCAGCA	AK074045	CCDS45779.1	17q25.3	2011-04-21			ENSG00000188878	ENSG00000188878			24674	protein-coding gene	gene with protein product	"albatross"					11347906	Standard	NM_001080542		Approved	FLJ00103, FBF-1, KIAA1863, ALB	uc002jqc.3	Q8TES7		ENST00000586717.1:c.2159A>G	chr17.hg19:g.73914288T>C	ENSP00000465132:p.Lys720Arg	101.0	0.0		98.0	4.0	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000586717.1	hg19		.	.	.	.	.	.	.	.	.	.	T	27.9	4.876701	0.91664	.	.	ENSG00000188878	ENST00000337792;ENST00000389570;ENST00000319129;ENST00000427433	T;T	0.23754	1.89;1.89	5.19	5.19	0.71726	.	.	.	.	.	T	0.46502	0.1396	L	0.60455	1.87	0.51767	D	0.999933	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.997	T	0.32214	-0.9915	9	0.35671	T	0.21	-38.3299	14.7005	0.69152	0.0:0.0:0.0:1.0	.	734;720;719	Q8TES7-6;Q8TES7;A6NLR5	.;FBF1_HUMAN;.	R	720;720;719;733	ENSP00000374221:K720R;ENSP00000324292:K719R	ENSP00000324292:K719R	K	-	2	0	FBF1	71425883	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.735000	0.68587	1.954000	0.56735	0.460000	0.39030	AAG	.	.		0.677	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542		C	73914288	T	C	73914288	3	2	259	1	0	0	0	0	1	0	0	0	5703	1609	56	2	1285	2	FBF1	17	73914288	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	73892	73914288	7280922	753	37071										
ACOX1	51	hgsc.bcm.edu	37	chr17	73944528	73944528	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gtgtaatctgaggctctgtcAtgatgctcccctaaaagaga	10	9	3	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:73944528A>G	ENST00000301608.4	-	13	1799	c.1739T>C	c.(1738-1740)aTg>aCg	p.M580T	ACOX1_ENST00000293217.5_Missense_Mutation_p.M580T|ACOX1_ENST00000537812.1_Missense_Mutation_p.M542T	NM_007292.5	NP_009223.2	Q15067	ACOX1_HUMAN	acyl-CoA oxidase 1, palmitoyl	580					alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|fatty acid oxidation (GO:0019395)|generation of precursor metabolites and energy (GO:0006091)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|peroxisome fission (GO:0016559)|positive regulation of cholesterol homeostasis (GO:2000189)|prostaglandin metabolic process (GO:0006693)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)|FAD binding (GO:0071949)|fatty acid binding (GO:0005504)|flavin adenine dinucleotide binding (GO:0050660)|palmitoyl-CoA oxidase activity (GO:0016401)|PDZ domain binding (GO:0030165)|protein N-terminus binding (GO:0047485)|receptor binding (GO:0005102)			large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(1)	14					Flavin adenine dinucleotide(DB03147)	AGGCTCTGTCATGATGCTCCC	0.353																																					p.M580T		Atlas-SNP	.											.	ACOX1	85	.	0			c.T1739C						.						108	95	100					17																	73944528		2203	4300	6503	SO:0001583	missense	51	exon13			TCTGTCATGATGC	U03254	CCDS11734.1, CCDS11735.1	17q25.1	2012-10-04	2010-04-30		ENSG00000161533	ENSG00000161533	1.3.3.6		119	protein-coding gene	gene with protein product		609751	"acyl-Coenzyme A oxidase 1, palmitoyl"			8159712	Standard	NM_007292		Approved	PALMCOX	uc002jqe.3	Q15067	OTTHUMG00000180027	ENST00000301608.4:c.1739T>C	chr17.hg19:g.73944528A>G	ENSP00000301608:p.Met580Thr	53.0	0.0		69.0	4.0	NM_007292	A8K6X8|A8KAA0|B4DK61|F5GYQ8|Q12863|Q15068|Q15101|Q16131|Q7Z3W5|Q9UD31	Missense_Mutation	SNP	ENST00000301608.4	hg19	CCDS11735.1	.	.	.	.	.	.	.	.	.	.	A	15.93	2.977101	0.53720	.	.	ENSG00000161533	ENST00000301608;ENST00000293217;ENST00000537812;ENST00000539791;ENST00000538781	T;T;T	0.42513	0.97;0.97;0.97	5.25	5.25	0.73442	Acyl-CoA oxidase, C-terminal (1);Acyl-CoA dehydrogenase/oxidase C-terminal (2);	0.324513	0.38005	N	0.001844	T	0.45836	0.1362	L	0.58583	1.82	0.40381	D	0.979449	B;B;B;B	0.26041	0.127;0.127;0.14;0.014	B;B;B;B	0.32583	0.096;0.096;0.148;0.023	T	0.49513	-0.8932	10	0.66056	D	0.02	-10.2759	15.8659	0.79063	1.0:0.0:0.0:0.0	.	512;542;580;580	F5H0M0;F5GYQ8;Q15067;Q15067-2	.;.;ACOX1_HUMAN;.	T	580;580;542;580;512	ENSP00000301608:M580T;ENSP00000293217:M580T;ENSP00000441257:M542T	ENSP00000293217:M580T	M	-	2	0	ACOX1	71456123	1.000000	0.71417	0.985000	0.45067	0.927000	0.56198	8.460000	0.90369	2.289000	0.77006	0.533000	0.62120	ATG	.	.		0.353	ACOX1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439503.1			G	73944528	A	G	73944528	3	3	259	1	0	0	0	0	1	0	0	0	158	217	8	2	251	2	ACOX1	17	73944528	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	30240	73944528	7250682	754	37072										
JMJD6	23210	hgsc.bcm.edu	37	chr17	74716510	74716510	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gctggagctgtcggaagctaTccctgtggactcctgaaggt	14	10	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:74716510T>C	ENST00000397625.4	-	5	1126	c.1012A>G	c.(1012-1014)Ata>Gta	p.I338V	JMJD6_ENST00000445478.2_Missense_Mutation_p.I338V|JMJD6_ENST00000585429.1_Intron	NM_015167.2	NP_055982.2	Q6NYC1	JMJD6_HUMAN	jumonji domain containing 6	338					cell surface receptor signaling pathway (GO:0007166)|erythrocyte development (GO:0048821)|heart development (GO:0007507)|histone H3-R2 demethylation (GO:0070078)|histone H4-R3 demethylation (GO:0070079)|kidney development (GO:0001822)|lung development (GO:0030324)|macrophage activation (GO:0042116)|mRNA processing (GO:0006397)|peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine (GO:0018395)|recognition of apoptotic cell (GO:0043654)|regulation of mRNA splicing, via spliceosome (GO:0048024)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|RNA splicing (GO:0008380)|sprouting angiogenesis (GO:0002040)|T cell differentiation in thymus (GO:0033077)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone demethylase activity (H3-R2 specific) (GO:0033746)|histone demethylase activity (H4-R3 specific) (GO:0033749)|identical protein binding (GO:0042802)|iron ion binding (GO:0005506)|peptidyl-lysine 5-dioxygenase activity (GO:0070815)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			endometrium(2)|kidney(5)|large_intestine(2)|lung(3)|ovary(2)|skin(2)	16						TCGGAAGCTATCCCTGTGGAC	0.572																																					p.I338V		Atlas-SNP	.											.	JMJD6	57	.	0			c.A1012G						.						80	93	88					17																	74716510		2110	4240	6350	SO:0001583	missense	23210	exon5			AAGCTATCCCTGT	AB011157	CCDS42383.1, CCDS42384.1	17q25	2007-11-20	2007-02-16	2007-02-16	ENSG00000070495	ENSG00000070495			19355	protein-coding gene	gene with protein product		604914	"phosphatidylserine receptor"	PTDSR		11877474	Standard	NM_015167		Approved	PTDSR1, KIAA0585	uc002jsn.1	Q6NYC1	OTTHUMG00000169267	ENST00000397625.4:c.1012A>G	chr17.hg19:g.74716510T>C	ENSP00000380750:p.Ile338Val	86.0	0.0		77.0	4.0	NM_001081461	B3KMN8|B4DGX1|Q86VY0|Q8IUM5|Q9Y4E2	Missense_Mutation	SNP	ENST00000397625.4	hg19	CCDS42384.1	.	.	.	.	.	.	.	.	.	.	T	12.60	1.985403	0.35036	.	.	ENSG00000070495	ENST00000445478;ENST00000344991;ENST00000397625	.	.	.	5.61	5.61	0.85477	.	0.045580	0.85682	D	0.000000	T	0.43787	0.1263	N	0.25890	0.77	0.80722	D	1	B;B	0.17268	0.008;0.021	B;B	0.12156	0.006;0.007	T	0.35126	-0.9801	9	0.10902	T	0.67	-17.924	15.8611	0.79021	0.0:0.0:0.0:1.0	.	338;338	Q6NYC1;Q6NYC1-3	JMJD6_HUMAN;.	V	338	.	ENSP00000345857:I338V	I	-	1	0	JMJD6	72228105	1.000000	0.71417	0.855000	0.33649	0.907000	0.53573	5.930000	0.70104	2.145000	0.66743	0.529000	0.55759	ATA	.	.		0.572	JMJD6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403211.1	NM_015167		C	74716510	T	C	74716510	3	2	259	1	0	0	0	0	1	0	0	0	7962	1435	50	2	248	2	JMJD6	17	74716510	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	771982	74716510	6478700	755	37073										
RNF213	57674	hgsc.bcm.edu	37	chr17	78335538	78335538	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggtttcctctctgcaggactGcccaagaagttcgtggacat	11	11	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:78335538G>A	ENST00000582970.1	+	39	11348	c.11205G>A	c.(11203-11205)ctG>ctA	p.L3735L	CTD-2047H16.4_ENST00000572151.1_RNA|RNF213_ENST00000336301.6_Silent_p.L1808L|RNF213_ENST00000508628.2_Silent_p.L3784L|CTD-2047H16.4_ENST00000575034.1_RNA	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	3735					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			CTGCAGGACTGCCCAAGAAGT	0.592																																					p.L3735L		Atlas-SNP	.											.	RNF213	766	.	0			c.G11205A						.						59	57	58					17																	78335538		2203	4300	6503	SO:0001819	synonymous_variant	57674	exon39			AGGACTGCCCAAG	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.11205G>A	chr17.hg19:g.78335538G>A		54.0	0.0		70.0	4.0	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Silent	SNP	ENST00000582970.1	hg19	CCDS58606.1																																																																																			.	.		0.592	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		A	78335538	G	A	78335538	2	1	259	1	0	0	0	0	0	0	0	1	13492	1306	46	3		3	RNF213	17	78335538	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	3619028	78335538	2859672	756	37074										
PDE6G	5148	hgsc.bcm.edu	37	chr17	79618688	79618688	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gtcatacctgttcccaggccTtccattccagggatgtcgtc	9	14	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:79618688T>C	ENST00000331056.5	-	3	317	c.174A>G	c.(172-174)gaA>gaG	p.E58E	PDE6G_ENST00000573076.1_Silent_p.E108E|PDE6G_ENST00000574777.1_5'UTR|TSPAN10_ENST00000328585.4_RNA|PDE6G_ENST00000571224.1_Silent_p.E58E|PDE6G_ENST00000571004.1_Silent_p.E58E	NM_002602.3	NP_002593.1	P18545	CNRG_HUMAN	phosphodiesterase 6G, cGMP-specific, rod, gamma	58					activation of MAPK activity (GO:0000187)|negative regulation of catalytic activity (GO:0043086)|phototransduction, visible light (GO:0007603)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|cGMP binding (GO:0030553)|enzyme inhibitor activity (GO:0004857)			lung(2)|urinary_tract(1)	3	all_neural(118;0.0878)|all_lung(278;0.175)|Lung NSC(278;0.192)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)		Sildenafil(DB00203)|Vardenafil(DB00862)	TTCCCAGGCCTTCCATTCCAG	0.662																																					p.E58E	GBM(189;38 2147 16440 40945 46567)	Atlas-SNP	.											.	PDE6G	9	.	0			c.A174G						.						77	57	64					17																	79618688		2203	4300	6503	SO:0001819	synonymous_variant	5148	exon3			CAGGCCTTCCATT		CCDS11783.1	17q21.1	2014-01-28				ENSG00000185527	3.1.4.17	"Phosphodiesterases"	8789	protein-coding gene	gene with protein product		180073		PDEG		2155175	Standard	NM_002602		Approved	RP57	uc002kay.3	P18545		ENST00000331056.5:c.174A>G	chr17.hg19:g.79618688T>C		102.0	0.0		87.0	4.0	NM_002602	Q3KP63|Q7Z3U8	Silent	SNP	ENST00000331056.5	hg19	CCDS11783.1																																																																																			.	.		0.662	PDE6G-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440314.1			C	79618688	T	C	79618688	2	2	259	1	0	0	0	0	0	0	0	1	11658	1606	56	2		2	PDE6G	17	79618688	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1283150	79618688	1576522	757	37075										
ZNF750	79755	hgsc.bcm.edu	37	chr17	80789773	80789773	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gacacggccttggcagtgggGttgtgtaaagccagtgtctc	15	9	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:80789773G>A	ENST00000269394.3	-	2	1391	c.558C>T	c.(556-558)aaC>aaT	p.N186N	TBCD_ENST00000397466.2_Intron|TBCD_ENST00000355528.4_Intron|ZNF750_ENST00000572562.1_Intron|TBCD_ENST00000539345.2_Intron	NM_024702.2	NP_078978.2	Q32MQ0	ZN750_HUMAN	zinc finger protein 750	186					cell differentiation (GO:0030154)|epidermis development (GO:0008544)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(3)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	31	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0514)|all_epithelial(8;0.0748)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.149)			TGGCAGTGGGGTTGTGTAAAG	0.607																																					p.N186N		Atlas-SNP	.											.	ZNF750	60	.	0			c.C558T						.						57	60	59					17																	80789773		2203	4300	6503	SO:0001819	synonymous_variant	79755	exon2			AGTGGGGTTGTGT	AK023903	CCDS11819.1	17q25.3	2008-05-02				ENSG00000141579			25843	protein-coding gene	gene with protein product		610226				16751772	Standard	NM_024702		Approved	FLJ13841, Zfp750	uc002kga.3	Q32MQ0		ENST00000269394.3:c.558C>T	chr17.hg19:g.80789773G>A		96.0	0.0		86.0	4.0	NM_024702	Q9H899	Silent	SNP	ENST00000269394.3	hg19	CCDS11819.1																																																																																			.	.		0.607	ZNF750-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439074.2	NM_024702		A	80789773	G	A	80789773	2	1	259	1	0	0	0	0	0	0	0	1	18147	1252	44	3		3	ZNF750	17	80789773	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1171085	80789773	405437	758	37076										
SMCHD1	23347	hgsc.bcm.edu	37	chr18	2688459	2688459	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atagtgatatttcctattttGgtgttgggggcaagcaagct	12	5	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:2688459G>T	ENST00000320876.6	+	6	1044	c.706G>T	c.(706-708)Ggt>Tgt	p.G236C	RP11-703M24.5_ENST00000583546.1_RNA|SMCHD1_ENST00000261598.8_Missense_Mutation_p.G236C	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	236					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						TTCCTATTTTGGTGTTGGGGG	0.338																																					p.G236C		Atlas-SNP	.											.	SMCHD1	88	.	0			c.G706T						.						101	96	97					18																	2688459		1866	4099	5965	SO:0001583	missense	23347	exon6			TATTTTGGTGTTG	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.706G>T	chr18.hg19:g.2688459G>T	ENSP00000326603:p.Gly236Cys	145.0	0.0		73.0	4.0	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Missense_Mutation	SNP	ENST00000320876.6	hg19	CCDS45822.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.714519	0.89112	.	.	ENSG00000101596	ENST00000320876;ENST00000261598	D;D	0.99891	-7.56;-7.56	5.08	5.08	0.68730	ATPase-like, ATP-binding domain (2);	0.060687	0.64402	D	0.000003	D	0.99900	0.9952	M	0.88377	2.95	0.50813	D	0.999893	D	0.89917	1.0	D	0.97110	1.0	D	0.96178	0.9128	10	0.87932	D	0	.	18.8289	0.92130	0.0:0.0:1.0:0.0	.	236	A6NHR9	SMHD1_HUMAN	C	236	ENSP00000326603:G236C;ENSP00000261598:G236C	ENSP00000261598:G236C	G	+	1	0	SMCHD1	2678459	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.927000	0.92846	2.502000	0.84385	0.655000	0.94253	GGT	.	.		0.338	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			T	2688459	G	T	2688459	3	4	259	1	0	0	0	0	1	0	0	0	14803	1348	47	3	728	3	SMCHD1	18	2688459	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10		2688459	75388789	759	37077										
SMCHD1	23347	hgsc.bcm.edu	37	chr18	2694533	2694533	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tcactcttgtagccctctgaTtctgttcacattacaaatga	5	11	5	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:2694533T>C	ENST00000320876.6	+	8	1220	c.882T>C	c.(880-882)gaT>gaC	p.D294D	RP11-703M24.5_ENST00000583546.1_RNA|SMCHD1_ENST00000261598.8_Silent_p.D294D	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	294					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						AGCCCTCTGATTCTGTTCACA	0.313																																					p.D294D		Atlas-SNP	.											.	SMCHD1	88	.	0			c.T882C						.						49	42	44					18																	2694533		1844	4076	5920	SO:0001819	synonymous_variant	23347	exon8			CTCTGATTCTGTT	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.882T>C	chr18.hg19:g.2694533T>C		133.0	0.0		89.0	4.0	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Silent	SNP	ENST00000320876.6	hg19	CCDS45822.1																																																																																			.	.		0.313	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			C	2694533	T	C	2694533	2	2	259	1	0	0	0	0	0	0	0	1	14803	1490	52	2		2	SMCHD1	18	2694533	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	6074	2694533	75382715	760	37078										
L3MBTL4	91133	hgsc.bcm.edu	37	chr18	6244510	6244510	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acagaaagcacacagaatacCgatggatgtcggggatcaat	11	8	1	2	rs200697690		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:6244510C>T	ENST00000284898.6	-	6	497	c.297G>A	c.(295-297)tcG>tcA	p.S99S	L3MBTL4_ENST00000400105.2_Silent_p.S99S|L3MBTL4_ENST00000400104.3_Silent_p.S99S|L3MBTL4_ENST00000317931.7_Silent_p.S99S	NM_173464.3	NP_775735.2	Q8NA19	LMBL4_HUMAN	l(3)mbt-like 4 (Drosophila)	99					chromatin modification (GO:0016568)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(17)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		Colorectal(10;0.0249)				CACAGAATACCGATGGATGTC	0.393																																					p.S99S	Esophageal Squamous(41;748 902 17366 28959 43175)	Atlas-SNP	.											.	L3MBTL4	87	.	0			c.G297A						.						207	190	196					18																	6244510		2203	4300	6503	SO:0001819	synonymous_variant	91133	exon6			GAATACCGATGGA	BC039316	CCDS11839.2	18p11.31-p11.23	2013-01-10			ENSG00000154655	ENSG00000154655		"Sterile alpha motif (SAM) domain containing"	26677	protein-coding gene	gene with protein product						14702039	Standard	NM_173464		Approved	FLJ35936, HsT1031	uc010dkt.3	Q8NA19	OTTHUMG00000131573	ENST00000284898.6:c.297G>A	chr18.hg19:g.6244510C>T		148.0	0.0		60.0	4.0	NM_173464	A8MTL8|Q8IXS3	Silent	SNP	ENST00000284898.6	hg19	CCDS11839.2																																																																																			.	C|0.999;T|0.001		0.393	L3MBTL4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254448.2	NM_173464		T	6244510	C	T	6244510	2	4	259	1	0	0	0	0	0	0	0	1	8603	639	23	1		1	L3MBTL4	18	6244510	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	3549977	6244510	71832738	761	37079										
GNAL	2774	hgsc.bcm.edu	37	chr18	11881066	11881066	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccgtggacacagagaacatcCgcagggtgttcaacgactgc	12	12	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:11881066C>A	ENST00000423027.3	+	12	1399	c.1078C>A	c.(1078-1080)Cgc>Agc	p.R360S	GNAL_ENST00000602628.1_Missense_Mutation_p.R153S|GNAL_ENST00000535121.1_Missense_Mutation_p.R360S|GNAL_ENST00000334049.6_Missense_Mutation_p.R437S|GNAL_ENST00000269162.5_Missense_Mutation_p.R360S			P38405	GNAL_HUMAN	guanine nucleotide binding protein (G protein), alpha activating activity polypeptide, olfactory type	360					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|response to amphetamine (GO:0001975)|response to caffeine (GO:0031000)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(4)|ovary(1)	12						AGAGAACATCCGCAGGGTGTT	0.612																																					p.R437S		Atlas-SNP	.											.	GNAL	59	.	0			c.C1309A						.						91	62	72					18																	11881066		2203	4300	6503	SO:0001583	missense	2774	exon12			AACATCCGCAGGG	AF493893	CCDS11851.1, CCDS11852.1, CCDS58614.1	18p11.22-p11.21	2003-12-17			ENSG00000141404	ENSG00000141404			4388	protein-coding gene	gene with protein product		139312				1302014	Standard	NM_182978		Approved		uc002kqc.3	P38405	OTTHUMG00000131660	ENST00000423027.3:c.1078C>A	chr18.hg19:g.11881066C>A	ENSP00000408489:p.Arg360Ser	114.0	0.0		62.0	5.0	NM_182978	B7ZA26|Q86XU3	Missense_Mutation	SNP	ENST00000423027.3	hg19	CCDS11852.1	.	.	.	.	.	.	.	.	.	.	C	36	5.705057	0.96812	.	.	ENSG00000141404	ENST00000540217;ENST00000334049;ENST00000535121;ENST00000269162;ENST00000423027;ENST00000535980	D;D;D;D	0.89123	-2.47;-2.47;-2.47;-2.47	5.55	5.55	0.83447	.	0.046280	0.85682	D	0.000000	D	0.93956	0.8065	M	0.78801	2.425	0.80722	D	1	D;P	0.58620	0.983;0.866	P;P	0.60345	0.873;0.801	D	0.94342	0.7571	10	0.87932	D	0	.	19.4958	0.95072	0.0:1.0:0.0:0.0	.	360;437	P38405;Q86XU3	GNAL_HUMAN;.	S	299;437;360;360;360;153	ENSP00000334051:R437S;ENSP00000439023:R360S;ENSP00000269162:R360S;ENSP00000408489:R360S	ENSP00000269162:R360S	R	+	1	0	GNAL	11871066	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.748000	0.85085	2.591000	0.87537	0.563000	0.77884	CGC	.	.		0.612	GNAL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254561.2	NM_182978, NM_002071		A	11881066	C	A	11881066	3	1	259	1	0	0	0	0	1	0	0	0	6515	652	23	1	1504	1	GNAL	18	11881066	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	5636556	11881066	66196182	762	37080										
RBBP8	5932	hgsc.bcm.edu	37	chr18	20572755	20572755	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tcctcctcaagaagaattacCtactcgagtgtcatctcctg	6	13	3	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:20572755C>A	ENST00000399722.2	+	11	1316	c.965C>A	c.(964-966)cCt>cAt	p.P322H	RBBP8_ENST00000399725.2_Missense_Mutation_p.P322H|RBBP8_ENST00000360790.5_Missense_Mutation_p.P322H|RBBP8_ENST00000327155.5_Missense_Mutation_p.P322H	NM_203291.1	NP_976036.1	Q99708	COM1_HUMAN	retinoblastoma binding protein 8	322					blastocyst hatching (GO:0001835)|cell cycle checkpoint (GO:0000075)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|G1/S transition of mitotic cell cycle (GO:0000082)|G2 DNA damage checkpoint (GO:0031572)|meiotic nuclear division (GO:0007126)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	damaged DNA binding (GO:0003684)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			central_nervous_system(1)|cervix(2)|endometrium(5)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	24	all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19)		OV - Ovarian serous cystadenocarcinoma(1;0.00196)			GAAGAATTACCTACTCGAGTG	0.343								Homologous recombination																													p.P322H		Atlas-SNP	.											.	RBBP8	138	.	0			c.C965A						.						83	87	86					18																	20572755		2194	4299	6493	SO:0001583	missense	5932	exon11			AATTACCTACTCG	AF043431	CCDS11874.1, CCDS11875.1	18q11.2	2012-11-05	2001-11-28		ENSG00000101773	ENSG00000101773			9891	protein-coding gene	gene with protein product	"CTBP-interacting protein"	604124	"retinoblastoma-binding protein 8", "Seckel syndrome 2"	SCKL2		9721205, 17965729, 21998596	Standard	NM_002894		Approved	CtIP, RIM, COM1	uc002ktw.3	Q99708	OTTHUMG00000131769	ENST00000399722.2:c.965C>A	chr18.hg19:g.20572755C>A	ENSP00000382628:p.Pro322His	130.0	0.0		81.0	4.0	NM_203292	A6NKN2|A8K8W6|E7ETY1|O75371|Q8NHQ3	Missense_Mutation	SNP	ENST00000399722.2	hg19	CCDS11875.1	.	.	.	.	.	.	.	.	.	.	C	5.738	0.320620	0.10845	.	.	ENSG00000101773	ENST00000327155;ENST00000399725;ENST00000399722;ENST00000399721;ENST00000360790	T;T;T;T;T	0.28895	1.6;1.59;1.6;1.6;1.6	5.99	2.83	0.33086	.	0.927132	0.09296	N	0.821685	T	0.15912	0.0383	N	0.14661	0.345	0.18873	N	0.999985	B;B;B	0.13145	0.007;0.001;0.007	B;B;B	0.08055	0.003;0.001;0.003	T	0.16867	-1.0388	10	0.33141	T	0.24	-0.2581	3.2437	0.06789	0.3661:0.425:0.1194:0.0895	.	322;322;322	E7ETY1;A6NKN2;Q99708	.;.;COM1_HUMAN	H	322	ENSP00000323050:P322H;ENSP00000382630:P322H;ENSP00000382628:P322H;ENSP00000382627:P322H;ENSP00000354024:P322H	ENSP00000323050:P322H	P	+	2	0	RBBP8	18826753	0.036000	0.19791	0.016000	0.15963	0.197000	0.23852	1.117000	0.31234	1.500000	0.48636	0.655000	0.94253	CCT	.	.		0.343	RBBP8-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446387.1	NM_203291		A	20572755	C	A	20572755	3	1	259	1	0	0	0	0	1	0	0	0	13120	681	24	3	1003	3	RBBP8	18	20572755	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	8691689	20572755	57504493	763	37081										
RBBP8	5932	hgsc.bcm.edu	37	chr18	20573367	20573367	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gactctttatgaggctttgaAgaccattccaaagggctttt	9	8	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:20573367A>G	ENST00000399722.2	+	11	1928	c.1577A>G	c.(1576-1578)aAg>aGg	p.K526R	RBBP8_ENST00000399725.2_Missense_Mutation_p.K526R|RBBP8_ENST00000360790.5_Missense_Mutation_p.K526R|RBBP8_ENST00000327155.5_Missense_Mutation_p.K526R	NM_203291.1	NP_976036.1	Q99708	COM1_HUMAN	retinoblastoma binding protein 8	526	Damage-recruitment motif.				blastocyst hatching (GO:0001835)|cell cycle checkpoint (GO:0000075)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|G1/S transition of mitotic cell cycle (GO:0000082)|G2 DNA damage checkpoint (GO:0031572)|meiotic nuclear division (GO:0007126)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	damaged DNA binding (GO:0003684)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			central_nervous_system(1)|cervix(2)|endometrium(5)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	24	all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19)		OV - Ovarian serous cystadenocarcinoma(1;0.00196)			GAGGCTTTGAAGACCATTCCA	0.468								Homologous recombination																													p.K526R		Atlas-SNP	.											.	RBBP8	138	.	0			c.A1577G						.						43	44	44					18																	20573367		2198	4300	6498	SO:0001583	missense	5932	exon11			CTTTGAAGACCAT	AF043431	CCDS11874.1, CCDS11875.1	18q11.2	2012-11-05	2001-11-28		ENSG00000101773	ENSG00000101773			9891	protein-coding gene	gene with protein product	"CTBP-interacting protein"	604124	"retinoblastoma-binding protein 8", "Seckel syndrome 2"	SCKL2		9721205, 17965729, 21998596	Standard	NM_002894		Approved	CtIP, RIM, COM1	uc002ktw.3	Q99708	OTTHUMG00000131769	ENST00000399722.2:c.1577A>G	chr18.hg19:g.20573367A>G	ENSP00000382628:p.Lys526Arg	123.0	0.0		61.0	4.0	NM_203292	A6NKN2|A8K8W6|E7ETY1|O75371|Q8NHQ3	Missense_Mutation	SNP	ENST00000399722.2	hg19	CCDS11875.1	.	.	.	.	.	.	.	.	.	.	A	19.47	3.833246	0.71258	.	.	ENSG00000101773	ENST00000327155;ENST00000399725;ENST00000399722;ENST00000399721;ENST00000360790	T;T;T;T;T	0.38401	1.21;1.14;1.21;1.2;1.21	5.97	5.97	0.96955	.	0.503154	0.22734	N	0.056284	T	0.59878	0.2226	M	0.72118	2.19	0.80722	D	1	D;D;D	0.89917	0.998;1.0;0.991	D;D;P	0.83275	0.922;0.996;0.79	T	0.62167	-0.6911	10	0.66056	D	0.02	-11.2765	14.2018	0.65710	1.0:0.0:0.0:0.0	.	526;526;526	E7ETY1;A6NKN2;Q99708	.;.;COM1_HUMAN	R	526	ENSP00000323050:K526R;ENSP00000382630:K526R;ENSP00000382628:K526R;ENSP00000382627:K526R;ENSP00000354024:K526R	ENSP00000323050:K526R	K	+	2	0	RBBP8	18827365	0.999000	0.42202	0.997000	0.53966	0.613000	0.37349	4.236000	0.58675	2.288000	0.76882	0.533000	0.62120	AAG	.	.		0.468	RBBP8-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446387.1	NM_203291		G	20573367	A	G	20573367	3	3	259	1	0	0	0	0	1	0	0	0	13120	72	3	2	1615	2	RBBP8	18	20573367	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	612	20573367	57503881	764	37082										
C18orf8	29919	hgsc.bcm.edu	37	chr18	21109173	21109173	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cagggcagagccgaagcagcCcgctcctcaagaggccggtg	15	14	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:21109173C>T	ENST00000269221.3	+	15	1437	c.1327C>T	c.(1327-1329)Ccg>Tcg	p.P443S	C18orf8_ENST00000590868.1_Missense_Mutation_p.P395S	NM_013326.3	NP_037458.3	Q96DM3	MIC1_HUMAN	chromosome 18 open reading frame 8	443						lysosomal membrane (GO:0005765)				endometrium(9)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	21	all_cancers(21;0.000122)|all_epithelial(16;8.08e-07)|Lung NSC(20;0.00206)|all_lung(20;0.00659)|Colorectal(14;0.0202)|Ovarian(20;0.127)					CCGAAGCAGCCCGCTCCTCAA	0.552																																					p.P443S		Atlas-SNP	.											.	C18orf8	58	.	0			c.C1327T						.						69	73	72					18																	21109173		2203	4300	6503	SO:0001583	missense	29919	exon15			AGCAGCCCGCTCC	AK057192	CCDS32803.1, CCDS74199.1	18q11.2	2013-12-13			ENSG00000141452	ENSG00000141452			24326	protein-coding gene	gene with protein product	"colon cancer associated protein Mic1", "macrophage inhibitory cytokine 1"					12477932	Standard	NM_013326		Approved	MIC1, MIC-1, HsT2591	uc021uie.2	Q96DM3		ENST00000269221.3:c.1327C>T	chr18.hg19:g.21109173C>T	ENSP00000269221:p.Pro443Ser	60.0	0.0		35.0	4.0	NM_013326	Q9BU17|Q9Y5M0	Missense_Mutation	SNP	ENST00000269221.3	hg19	CCDS32803.1	.	.	.	.	.	.	.	.	.	.	C	14.34	2.505311	0.44558	.	.	ENSG00000141452	ENST00000269221;ENST00000544799;ENST00000540942;ENST00000542734	.	.	.	5.71	5.71	0.89125	.	0.056544	0.64402	D	0.000001	T	0.43055	0.1230	L	0.29908	0.895	0.80722	D	1	B;B	0.16396	0.017;0.001	B;B	0.15484	0.013;0.001	T	0.32348	-0.9910	9	0.06625	T	0.88	-7.9438	15.3516	0.74393	0.0:0.861:0.139:0.0	.	286;443	B7Z2Y1;Q96DM3	.;MIC1_HUMAN	S	443;286;395;286	.	ENSP00000269221:P443S	P	+	1	0	C18orf8	19363171	0.998000	0.40836	0.637000	0.29366	0.803000	0.45373	3.750000	0.55157	2.698000	0.92095	0.561000	0.74099	CCG	.	.		0.552	C18orf8-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445386.1	NM_013326		T	21109173	C	T	21109173	3	4	259	1	0	0	0	0	1	0	0	0	1909	623	22	3	1385	3	C18orf8	18	21109173	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	535806	21109173	56968075	765	37083										
ANKRD29	147463	hgsc.bcm.edu	37	chr18	21214039	21214039	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agttggtcatggatgtttgcTccgtgcttcagcaaggtctc	12	9	3	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:21214039T>C	ENST00000592179.1	-	5	559	c.405A>G	c.(403-405)ggA>ggG	p.G135G	ANKRD29_ENST00000322980.9_Silent_p.G135G|ANKRD29_ENST00000284207.7_Silent_p.G135G	NM_173505.2	NP_775776.2	Q8N6D5	ANR29_HUMAN	ankyrin repeat domain 29	135										breast(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(3)|prostate(1)|skin(1)	13	all_cancers(21;5.07e-05)|all_epithelial(16;2.49e-07)|Lung NSC(20;0.00211)|all_lung(20;0.00676)|Colorectal(14;0.0202)|Ovarian(20;0.127)					GGATGTTTGCTCCGTGCTTCA	0.483																																					p.G135G		Atlas-SNP	.											.	ANKRD29	24	.	0			c.A405G						.						116	89	98					18																	21214039		2203	4300	6503	SO:0001819	synonymous_variant	147463	exon5			GTTTGCTCCGTGC	AK057782	CCDS11879.1	18q11.2	2013-01-10			ENSG00000154065	ENSG00000154065		"Ankyrin repeat domain containing"	27110	protein-coding gene	gene with protein product							Standard	NM_173505		Approved	FLJ25053	uc002kun.3	Q8N6D5	OTTHUMG00000131875	ENST00000592179.1:c.405A>G	chr18.hg19:g.21214039T>C		169.0	0.0		104.0	5.0	NM_173505	B2R972|Q6ZWE8|Q96LU9	Silent	SNP	ENST00000592179.1	hg19	CCDS11879.1																																																																																			.	.		0.483	ANKRD29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254825.1	NM_173505		C	21214039	T	C	21214039	2	2	259	1	0	0	0	0	0	0	0	1	657	1538	54	2		2	ANKRD29	18	21214039	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	104866	21214039	56863209	766	37084										
TAF4B	6875	hgsc.bcm.edu	37	chr18	23847518	23847518	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atcaagaaagtggcagtgacAcctgttaaaaaattggcaca	9	7	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:23847518A>G	ENST00000269142.5	+	3	1526	c.528A>G	c.(526-528)acA>acG	p.T176T	RP11-25D3.1_ENST00000580975.1_RNA|TAF4B_ENST00000578121.1_Silent_p.T176T|TAF4B_ENST00000400466.2_Silent_p.T176T	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	176					gene expression (GO:0010467)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|NF-kappaB binding (GO:0051059)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|prostate(1)|skin(1)	29	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			TGGCAGTGACACCTGTTAAAA	0.423																																					p.T176T		Atlas-SNP	.											.	TAF4B	71	.	0			c.A528G						.						105	101	102					18																	23847518		1895	4112	6007	SO:0001819	synonymous_variant	6875	exon3			AGTGACACCTGTT	Y09321	CCDS42421.1	18q11.1	2008-08-01	2002-08-29	2001-12-07		ENSG00000141384			11538	protein-coding gene	gene with protein product	"TATA box binding protein (TBP)-associated factor 4B"	601689	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, C2, 105kD"	TAF2C2		8858156, 10849440	Standard	XM_005258339		Approved	TAFII105	uc002kvu.4	Q92750		ENST00000269142.5:c.528A>G	chr18.hg19:g.23847518A>G		126.0	0.0		89.0	4.0	NM_005640	Q29YA4|Q29YA5	Silent	SNP	ENST00000269142.5	hg19	CCDS42421.1																																																																																			.	.		0.423	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000446260.3	NM_005640		G	23847518	A	G	23847518	2	3	259	1	0	0	0	0	0	0	0	1	15542	146	6	2		2	TAF4B	18	23847518	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2633479	23847518	54229730	767	37085										
KIAA1012	22878	hgsc.bcm.edu	37	chr18	29437916	29437916	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tttcggatttctccacagagAagccctgtaggaaaatgtat	9	8	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:29437916A>G	ENST00000283351.4	-	20	3110	c.2775T>C	c.(2773-2775)ctT>ctC	p.L925L	TRAPPC8_ENST00000582539.1_Silent_p.L871L	NM_014939.3	NP_055754	Q9Y2L5	TPPC8_HUMAN	trafficking protein particle complex 8	925					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(7)|liver(2)|lung(13)|ovary(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						CTCCACAGAGAAGCCCTGTAG	0.333																																					p.L925L		Atlas-SNP	.											.	TRAPPC8	126	.	0			c.T2775C						.						95	105	102					18																	29437916		2203	4300	6503	SO:0001819	synonymous_variant	22878	exon20			ACAGAGAAGCCCT	AB023229	CCDS11901.1	18q12.1	2011-10-10	2010-06-29	2010-06-29	ENSG00000153339	ENSG00000153339		"Trafficking protein particle complex"	29169	protein-coding gene	gene with protein product	"general sporulation gene 1 homolog (S. cerevisiae)"	614136	"KIAA1012"	KIAA1012		10231032, 11230166	Standard	NM_014939		Approved	HsT2706, TRS85, GSG1	uc002kxc.4	Q9Y2L5	OTTHUMG00000132267	ENST00000283351.4:c.2775T>C	chr18.hg19:g.29437916A>G		146.0	0.0		82.0	4.0	NM_014939	A0JP15|B3KME5|Q9H0L2	Silent	SNP	ENST00000283351.4	hg19	CCDS11901.1																																																																																			.	.		0.333	TRAPPC8-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255355.1	NM_014939		G	29437916	A	G	29437916	2	3	259	1	0	0	0	0	0	0	0	1	8213	233	9	2		2	KIAA1012	18	29437916	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	5590398	29437916	48639332	768	37086										
KIAA1012	22878	hgsc.bcm.edu	37	chr18	29497605	29497605	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gactgaagaaaggtttctctGtaagactcaaaccatggagt	10	7	2	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:29497605G>T	ENST00000283351.4	-	3	713	c.378C>A	c.(376-378)taC>taA	p.Y126*	TRAPPC8_ENST00000582539.1_Nonsense_Mutation_p.Y72*|TRAPPC8_ENST00000582513.1_Nonsense_Mutation_p.Y126*	NM_014939.3	NP_055754	Q9Y2L5	TPPC8_HUMAN	trafficking protein particle complex 8	126					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(7)|liver(2)|lung(13)|ovary(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						AGGTTTCTCTGTAAGACTCAA	0.328																																					p.Y126X		Atlas-SNP	.											.	TRAPPC8	126	.	0			c.C378A						.						135	143	141					18																	29497605		2203	4300	6503	SO:0001587	stop_gained	22878	exon3			TTCTCTGTAAGAC	AB023229	CCDS11901.1	18q12.1	2011-10-10	2010-06-29	2010-06-29	ENSG00000153339	ENSG00000153339		"Trafficking protein particle complex"	29169	protein-coding gene	gene with protein product	"general sporulation gene 1 homolog (S. cerevisiae)"	614136	"KIAA1012"	KIAA1012		10231032, 11230166	Standard	NM_014939		Approved	HsT2706, TRS85, GSG1	uc002kxc.4	Q9Y2L5	OTTHUMG00000132267	ENST00000283351.4:c.378C>A	chr18.hg19:g.29497605G>T	ENSP00000283351:p.Tyr126*	136.0	0.0		66.0	4.0	NM_014939	A0JP15|B3KME5|Q9H0L2	Nonsense_Mutation	SNP	ENST00000283351.4	hg19	CCDS11901.1	.	.	.	.	.	.	.	.	.	.	G	18.44	3.625505	0.66901	.	.	ENSG00000153339	ENST00000283351	.	.	.	6.05	-8.27	0.01017	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	17.9338	0.89006	0.6614:0.0:0.3386:0.0	.	.	.	.	X	126	.	ENSP00000283351:Y126X	Y	-	3	2	TRAPPC8	27751603	0.993000	0.37304	0.238000	0.24106	0.965000	0.64279	0.221000	0.17680	-1.964000	0.01012	-1.000000	0.02509	TAC	.	.		0.328	TRAPPC8-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255355.1	NM_014939		T	29497605	G	T	29497605	4	4	259	1	0	0	0	0	0	1	0	0	8213	1372	48	3	4037	3	KIAA1012	18	29497605	Nonsense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	59689	29497605	48579643	769	37087										
MEP1B	4225	hgsc.bcm.edu	37	chr18	29788190	29788190	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gcaacgggtttcacaggttcCcagggggccagagagtgatc	15	10	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:29788190C>G	ENST00000269202.6	+	9	922	c.875C>G	c.(874-876)cCc>cGc	p.P292R	MEP1B_ENST00000581447.1_Missense_Mutation_p.P292R	NM_005925.2	NP_005916.2	Q16820	MEP1B_HUMAN	meprin A, beta	292	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				digestion (GO:0007586)|inflammatory response (GO:0006954)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						TCACAGGTTCCCAGGGGGCCA	0.478																																					p.P292R		Atlas-SNP	.											.	MEP1B	54	.	0			c.C875G						.						97	99	98					18																	29788190		1912	4120	6032	SO:0001583	missense	4225	exon9			AGGTTCCCAGGGG	X81333	CCDS45846.1	18q12.2-q12.3	2003-12-17				ENSG00000141434	3.4.24.18		7020	protein-coding gene	gene with protein product		600389				7774936	Standard	NM_005925		Approved		uc002kxj.4	Q16820		ENST00000269202.6:c.875C>G	chr18.hg19:g.29788190C>G	ENSP00000269202:p.Pro292Arg	154.0	0.0		99.0	27.0	NM_005925	B7ZM35|B9EGL6|Q670J1	Missense_Mutation	SNP	ENST00000269202.6	hg19	CCDS45846.1	.	.	.	.	.	.	.	.	.	.	C	8.990	0.977567	0.18812	.	.	ENSG00000141434	ENST00000269202	T	0.02050	4.48	5.48	3.67	0.42095	Concanavalin A-like lectin/glucanase (1);MAM domain (3);	0.773265	0.12702	N	0.446244	T	0.04272	0.0118	L	0.46157	1.445	0.09310	N	1	P	0.34615	0.459	B	0.43103	0.408	T	0.42137	-0.9469	10	0.19147	T	0.46	-0.6288	11.9111	0.52739	0.0:0.8567:0.0:0.1433	.	292	Q16820	MEP1B_HUMAN	R	292	ENSP00000269202:P292R	ENSP00000269202:P292R	P	+	2	0	MEP1B	28042188	0.000000	0.05858	0.001000	0.08648	0.541000	0.35023	1.154000	0.31688	1.308000	0.44962	0.561000	0.74099	CCC	.	.		0.478	MEP1B-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447755.1	NM_005925		G	29788190	C	G	29788190	3	3	259	1	0	0	0	0	1	0	0	0	9485	623	22	4	909	4	MEP1B	18	29788190	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	290585	29788190	48289058	770	37088										
ZNF396	252884	hgsc.bcm.edu	37	chr18	32953458	32953458	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gaagctcccatgatgctcccTggagctgcttcttcacgggc	11	14	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:32953458T>C	ENST00000589332.1	-	3	655	c.524A>G	c.(523-525)cAg>cGg	p.Q175R	ZNF396_ENST00000586687.1_Missense_Mutation_p.Q175R|ZNF396_ENST00000306346.1_Missense_Mutation_p.Q175R			Q96N95	ZN396_HUMAN	zinc finger protein 396	175					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)	7						TGATGCTCCCTGGAGCTGCTT	0.527																																					p.Q175R		Atlas-SNP	.											.	ZNF396	28	.	0			c.A524G						.						114	101	105					18																	32953458		2203	4300	6503	SO:0001583	missense	252884	exon3			GCTCCCTGGAGCT	AK055775	CCDS11913.1	18p12	2013-01-09			ENSG00000186496	ENSG00000186496		"-", "Zinc fingers, C2H2-type"	18824	protein-coding gene	gene with protein product		609600					Standard	NM_145756		Approved	ZSCAN14, FLJ31213	uc010xcf.1	Q96N95	OTTHUMG00000132562	ENST00000589332.1:c.524A>G	chr18.hg19:g.32953458T>C	ENSP00000466500:p.Gln175Arg	275.0	0.0		130.0	6.0	NM_145756	A1L3V0|Q8NF98|Q8TD80	Missense_Mutation	SNP	ENST00000589332.1	hg19		.	.	.	.	.	.	.	.	.	.	T	8.931	0.963336	0.18583	.	.	ENSG00000186496	ENST00000306346;ENST00000399057	T	0.07327	3.2	4.3	-8.6	0.00889	.	.	.	.	.	T	0.03651	0.0104	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.45175	-0.9279	9	0.33141	T	0.24	.	10.9872	0.47528	0.0:0.1576:0.6639:0.1785	.	175	Q96N95-3	.	R	175	ENSP00000302310:Q175R	ENSP00000302310:Q175R	Q	-	2	0	ZNF396	31207456	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-0.565000	0.05929	-2.202000	0.00745	0.459000	0.35465	CAG	.	.		0.527	ZNF396-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255766.1	NM_145756		C	32953458	T	C	32953458	3	2	259	1	0	0	0	0	1	0	0	0	17897	1580	55	2	489	2	ZNF396	18	32953458	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	3165268	32953458	45123790	771	37089										
SLC14A2	8170	hgsc.bcm.edu	37	chr18	43204717	43204717	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cagagtttaccagcccgagcTggccctcgacatccccggat	10	16	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:43204717T>C	ENST00000255226.6	+	2	904	c.88T>C	c.(88-90)Tgg>Cgg	p.W30R	SLC14A2_ENST00000586448.1_Missense_Mutation_p.W30R	NM_007163.3	NP_009094.3	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter), member 2	30					transmembrane transport (GO:0055085)|urea transport (GO:0015840)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|urea transmembrane transporter activity (GO:0015204)			NS(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(35)|ovary(1)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						CAGCCCGAGCTGGCCCTCGAC	0.572																																					p.W30R		Atlas-SNP	.											.	SLC14A2	121	.	0			c.T88C						.						80	75	77					18																	43204717		2203	4300	6503	SO:0001583	missense	8170	exon3			CCGAGCTGGCCCT	X96969	CCDS11924.1	18q12.1-q21.1	2013-05-22			ENSG00000132874	ENSG00000132874		"Solute carriers"	10919	protein-coding gene	gene with protein product		601611				8647271	Standard	NM_007163		Approved	HUT2, UT2	uc010dnj.3	Q15849	OTTHUMG00000132616	ENST00000255226.6:c.88T>C	chr18.hg19:g.43204717T>C	ENSP00000255226:p.Trp30Arg	91.0	0.0		68.0	5.0	NM_001242692	A8K8Q7|Q2TBD6|Q96PH5	Missense_Mutation	SNP	ENST00000255226.6	hg19	CCDS11924.1	.	.	.	.	.	.	.	.	.	.	T	10.11	1.260877	0.23051	.	.	ENSG00000132874	ENST00000255226;ENST00000323329	T;T	0.65178	0.45;-0.14	5.31	5.31	0.75309	.	0.263214	0.32655	N	0.005810	T	0.65595	0.2706	L	0.57536	1.79	0.30059	N	0.811036	P;D	0.55385	0.91;0.971	B;P	0.50440	0.424;0.641	T	0.68750	-0.5326	10	0.52906	T	0.07	-0.4283	11.6475	0.51269	0.0:0.0:0.0:1.0	.	30;30	Q15849;E7EPU1	UT2_HUMAN;.	R	30	ENSP00000255226:W30R;ENSP00000320689:W30R	ENSP00000255226:W30R	W	+	1	0	SLC14A2	41458715	0.989000	0.36119	0.813000	0.32504	0.148000	0.21650	2.448000	0.44926	2.008000	0.58898	0.334000	0.21626	TGG	.	.		0.572	SLC14A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255858.1			C	43204717	T	C	43204717	3	2	259	1	0	0	0	0	1	0	0	0	14412	1580	55	2	90	2	SLC14A2	18	43204717	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	10251259	43204717	34872531	772	37090										
SLC14A1	6563	hgsc.bcm.edu	37	chr18	43329905	43329905	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccaagaaaagaatggtggaaAgccctttgtgagaacaagcc	11	8	0	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:43329905A>G	ENST00000321925.4	+	10	1391	c.1159A>G	c.(1159-1161)Agc>Ggc	p.S387G	SLC14A1_ENST00000402943.2_Missense_Mutation_p.S282G|SLC14A1_ENST00000591541.1_Missense_Mutation_p.S91G|SLC14A1_ENST00000589700.1_3'UTR|SLC14A1_ENST00000586142.1_Missense_Mutation_p.S387G|RP11-116O18.3_ENST00000586213.1_RNA|SLC14A1_ENST00000436407.3_Missense_Mutation_p.S443G|SLC14A1_ENST00000415427.3_Missense_Mutation_p.S443G|SLC14A1_ENST00000502059.2_Missense_Mutation_p.S279G|SLC14A1_ENST00000535474.1_Missense_Mutation_p.S255G	NM_001128588.3|NM_001146036.2|NM_015865.6	NP_001122060.3|NP_001139508.2|NP_056949.4	Q13336	UT1_HUMAN	solute carrier family 14 (urea transporter), member 1 (Kidd blood group)	387					transmembrane transport (GO:0055085)|urea transmembrane transport (GO:0071918)|urea transport (GO:0015840)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	urea channel activity (GO:0015265)|urea transmembrane transporter activity (GO:0015204)|water transmembrane transporter activity (GO:0005372)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(11)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	21						AATGGTGGAAAGCCCTTTGTG	0.453																																					p.S443G		Atlas-SNP	.											.	SLC14A1	84	.	0			c.A1327G						.						118	116	117					18																	43329905		2203	4300	6503	SO:0001583	missense	6563	exon9			GTGGAAAGCCCTT	BC040128	CCDS11925.1, CCDS45860.1	18q11-q12	2014-07-19	2014-01-02		ENSG00000141469	ENSG00000141469		"Blood group antigens", "Solute carriers"	10918	protein-coding gene	gene with protein product		613868	"Kidd blood group", "solute carrier family 14 (urea transporter), member 1"	JK		7797558	Standard	NM_001146037		Approved	HsT1341, RACH1, RACH2	uc010dnk.3	Q13336	OTTHUMG00000132617	ENST00000321925.4:c.1159A>G	chr18.hg19:g.43329905A>G	ENSP00000318546:p.Ser387Gly	143.0	0.0		93.0	4.0	NM_001146037	A8K0P3|B3KR62|B3KVX3|C9EHF2|Q86VM5	Missense_Mutation	SNP	ENST00000321925.4	hg19	CCDS11925.1	.	.	.	.	.	.	.	.	.	.	A	13.18	2.159723	0.38119	.	.	ENSG00000141469	ENST00000321925;ENST00000415427;ENST00000502059;ENST00000402943;ENST00000535474;ENST00000436407	T;T;T;T;T;T	0.53423	0.8;0.66;0.8;0.82;0.62;0.66	5.64	3.28	0.37604	.	0.420374	0.25842	N	0.027948	T	0.36690	0.0976	L	0.42245	1.32	0.28739	N	0.902051	B;B;B	0.14438	0.01;0.002;0.003	B;B;B	0.13407	0.009;0.005;0.005	T	0.29701	-1.0003	10	0.49607	T	0.09	-8.3904	7.1926	0.25834	0.7501:0.0:0.2499:0.0	.	443;279;387	Q13336-2;B3KXJ3;Q13336	.;.;UT1_HUMAN	G	387;443;279;282;255;443	ENSP00000318546:S387G;ENSP00000412309:S443G;ENSP00000442180:S279G;ENSP00000385320:S282G;ENSP00000441998:S255G;ENSP00000390637:S443G	ENSP00000318546:S387G	S	+	1	0	SLC14A1	41583903	0.997000	0.39634	0.124000	0.21820	0.022000	0.10575	2.633000	0.46519	0.510000	0.28216	0.482000	0.46254	AGC	.	.		0.453	SLC14A1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255860.2	NM_015865		G	43329905	A	G	43329905	3	3	259	1	0	0	0	0	1	0	0	0	14411	72	3	2	1361	2	SLC14A1	18	43329905	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	125188	43329905	34747343	773	37091										
MYO5B	4645	hgsc.bcm.edu	37	chr18	47421462	47421462	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tctgctggtagtgcaccagcTccttcttcagccgctctacc	8	16	4	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:47421462T>C	ENST00000285039.7	-	22	3193	c.2894A>G	c.(2893-2895)gAg>gGg	p.E965G	MYO5B_ENST00000324581.6_Missense_Mutation_p.E106G	NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	965					endosome localization (GO:0032439)|metabolic process (GO:0008152)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)|vesicle-mediated transport (GO:0016192)|water transport (GO:0006833)	apical cortex (GO:0045179)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|protein complex (GO:0043234)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|Rab GTPase binding (GO:0017137)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(4)	87				READ - Rectum adenocarcinoma(32;0.103)		GTGCACCAGCTCCTTCTTCAG	0.577																																					p.E965G		Atlas-SNP	.											.	MYO5B	178	.	0			c.A2894G						.						70	70	70					18																	47421462		2033	4187	6220	SO:0001583	missense	4645	exon22			ACCAGCTCCTTCT	AB032945	CCDS42436.1	18q	2011-09-27			ENSG00000167306	ENSG00000167306		"Myosins / Myosin superfamily : Class V"	7603	protein-coding gene	gene with protein product		606540				8884266, 17462998	Standard	NM_001080467		Approved	KIAA1119	uc002leb.2	Q9ULV0		ENST00000285039.7:c.2894A>G	chr18.hg19:g.47421462T>C	ENSP00000285039:p.Glu965Gly	145.0	0.0		78.0	4.0	NM_001080467	B0I1R3|Q0P656|Q9H6Y6	Missense_Mutation	SNP	ENST00000285039.7	hg19	CCDS42436.1	.	.	.	.	.	.	.	.	.	.	T	15.99	2.995585	0.54147	.	.	ENSG00000167306	ENST00000285039;ENST00000324581	T;T	0.21361	2.01;2.01	5.68	5.68	0.88126	.	0.123004	0.53938	D	0.000047	T	0.26882	0.0658	M	0.61703	1.905	0.51482	D	0.999926	B;P	0.36753	0.3;0.568	B;B	0.37387	0.078;0.248	T	0.02533	-1.1145	10	0.46703	T	0.11	.	15.6047	0.76658	0.0:0.0:0.0:1.0	.	965;106	Q9ULV0;Q9H6Y6	MYO5B_HUMAN;.	G	965;106	ENSP00000285039:E965G;ENSP00000315531:E106G	ENSP00000285039:E965G	E	-	2	0	MYO5B	45675460	1.000000	0.71417	1.000000	0.80357	0.630000	0.37929	4.313000	0.59160	2.163000	0.67991	0.402000	0.26972	GAG	.	.		0.577	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2			C	47421462	T	C	47421462	3	2	259	1	0	0	0	0	1	0	0	0	10088	1551	54	2	2728	2	MYO5B	18	47421462	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	4091557	47421462	30655786	774	37092										
TCF4	6925	hgsc.bcm.edu	37	chr18	52937094	52937094	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctgtcccgttggcaggaggcGtacaggaagaggtgctgtaa	16	8	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:52937094G>A	ENST00000356073.4	-	11	1501	c.890C>T	c.(889-891)aCg>aTg	p.T297M	TCF4_ENST00000563760.1_5'UTR|TCF4_ENST00000561831.3_Missense_Mutation_p.T137M|TCF4_ENST00000398339.1_Missense_Mutation_p.T399M|TCF4_ENST00000537578.1_Missense_Mutation_p.T273M|TCF4_ENST00000457482.3_Missense_Mutation_p.T137M|TCF4_ENST00000566286.1_Missense_Mutation_p.T295M|TCF4_ENST00000543082.1_Missense_Mutation_p.T255M|TCF4_ENST00000564228.1_Missense_Mutation_p.T226M|TCF4_ENST00000565018.2_Missense_Mutation_p.T297M|TCF4_ENST00000537856.3_Missense_Mutation_p.T167M|TCF4_ENST00000570287.2_Missense_Mutation_p.T137M|TCF4_ENST00000564403.2_Missense_Mutation_p.T303M|TCF4_ENST00000540999.1_Missense_Mutation_p.T273M|TCF4_ENST00000566279.1_Missense_Mutation_p.T237M|TCF4_ENST00000570177.2_Missense_Mutation_p.T167M|TCF4_ENST00000567880.1_Missense_Mutation_p.T237M|TCF4_ENST00000561992.1_Missense_Mutation_p.T167M|TCF4_ENST00000564999.1_Missense_Mutation_p.T297M|TCF4_ENST00000544241.2_Missense_Mutation_p.T226M|TCF4_ENST00000354452.3_Missense_Mutation_p.T297M|TCF4_ENST00000568673.1_Missense_Mutation_p.T273M|TCF4_ENST00000568740.1_Missense_Mutation_p.T272M	NM_003199.2	NP_003190.1	P15884	ITF2_HUMAN	transcription factor 4	297					DNA-templated transcription, initiation (GO:0006352)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein-DNA complex assembly (GO:0065004)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase recruiting transcription factor activity (GO:0001011)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TFIIB-class binding transcription factor activity (GO:0001087)|TFIIB-class transcription factor binding (GO:0001093)			breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	41				Colorectal(16;0.00108)|READ - Rectum adenocarcinoma(59;0.0649)|COAD - Colon adenocarcinoma(17;0.0718)		GGCAGGAGGCGTACAGGAAGA	0.463																																					p.T399M		Atlas-SNP	.											.	TCF4	178	.	0			c.C1196T						.						167	136	146					18																	52937094		2203	4300	6503	SO:0001583	missense	6925	exon12			GGAGGCGTACAGG	M74719	CCDS11960.1, CCDS42438.1, CCDS58623.1, CCDS58624.1, CCDS58625.1, CCDS58626.1, CCDS58627.1, CCDS58628.1, CCDS58629.1, CCDS58630.1, CCDS58631.1, CCDS59321.1	18q21.1	2013-05-21			ENSG00000196628	ENSG00000196628		"Basic helix-loop-helix proteins"	11634	protein-coding gene	gene with protein product		602272				9302263, 2308860	Standard	NM_001083962		Approved	SEF2-1B, ITF2, bHLHb19, E2-2	uc002lga.3	P15884	OTTHUMG00000132713	ENST00000356073.4:c.890C>T	chr18.hg19:g.52937094G>A	ENSP00000348374:p.Thr297Met	175.0	0.0		96.0	4.0	NM_001243226	B3KT62|B3KUC0|B4DT37|B4DUG3|B7Z5M6|B7Z6Y1|G0LNT9|G0LNU0|G0LNU1|G0LNU2|G0LNU4|G0LNU5|G0LNU8|G0LNU9|G0LNV0|G0LNV1|G0LNV2|H3BPQ1|Q08AP2|Q08AP3|Q15439|Q15440|Q15441	Missense_Mutation	SNP	ENST00000356073.4	hg19	CCDS11960.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.952152	0.92660	.	.	ENSG00000196628	ENST00000354452;ENST00000457482;ENST00000356073;ENST00000543082;ENST00000540999;ENST00000537578;ENST00000544241;ENST00000537856;ENST00000398339	T;T;T;T;T;T;T;T;T	0.53857	0.6;0.6;0.6;0.6;0.6;0.6;0.6;0.6;0.6	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.76385	0.3980	M	0.83603	2.65	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D	0.91635	0.953;0.987;0.97;0.987;0.999;0.911;0.953;0.953;0.949;0.942	T	0.78974	-0.1992	10	0.87932	D	0	-11.1751	18.8159	0.92076	0.0:0.0:1.0:0.0	.	273;297;273;137;399;297;255;226;137;295	B7Z5M6;G0LNT9;B7Z6Y1;G0LNV1;E9PH57;P15884;B3KUC0;B3KT62;G0LNU9;G0LNU5	.;.;.;.;.;ITF2_HUMAN;.;.;.;.	M	297;137;297;255;273;273;226;167;399	ENSP00000346440:T297M;ENSP00000409447:T137M;ENSP00000348374:T297M;ENSP00000439656:T255M;ENSP00000445202:T273M;ENSP00000440731:T273M;ENSP00000441562:T226M;ENSP00000439827:T167M;ENSP00000381382:T399M	ENSP00000346440:T297M	T	-	2	0	TCF4	51088092	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	8.998000	0.93550	2.734000	0.93682	0.460000	0.39030	ACG	.	.		0.463	TCF4-002	KNOWN	upstream_uORF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256014.1	NM_003199		A	52937094	G	A	52937094	3	1	259	1	0	0	0	0	1	0	0	0	15710	1145	40	1	1161	1	TCF4	18	52937094	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	5515632	52937094	25140154	775	37093										
ST8SIA3	51046	hgsc.bcm.edu	37	chr18	55027274	55027274	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aaacggctgagcacaggtatTcttatgtacacccttgcatc	8	11	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:55027274T>C	ENST00000324000.3	+	4	2943	c.909T>C	c.(907-909)atT>atC	p.I303I		NM_015879.2	NP_056963.2	O43173	SIA8C_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	303					cellular protein metabolic process (GO:0044267)|ganglioside biosynthetic process (GO:0001574)|glycoprotein metabolic process (GO:0009100)|glycosphingolipid biosynthetic process (GO:0006688)|N-glycan processing (GO:0006491)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)			breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(16)|prostate(1)|skin(3)	36				READ - Rectum adenocarcinoma(59;0.19)|Colorectal(16;0.205)		GCACAGGTATTCTTATGTACA	0.418																																					p.I303I		Atlas-SNP	.											.	ST8SIA3	73	.	0			c.T909C						.						112	104	107					18																	55027274		2203	4300	6503	SO:0001819	synonymous_variant	51046	exon4			AGGTATTCTTATG	AF004668	CCDS32834.1	18q21.31	2013-03-01	2005-02-07	2005-02-07	ENSG00000177511	ENSG00000177511		"Sialyltransferases"	14269	protein-coding gene	gene with protein product	"ST8Sia III"	609478	"sialyltransferase 8C (alpha2,3Galbeta1,4GlcNAcalpha 2,8-sialyltransferase)"	SIAT8C			Standard	NM_015879		Approved		uc002lgn.3	O43173	OTTHUMG00000180101	ENST00000324000.3:c.909T>C	chr18.hg19:g.55027274T>C		172.0	0.0		79.0	4.0	NM_015879	A8K0F2|Q6B085|Q9NS41	Silent	SNP	ENST00000324000.3	hg19	CCDS32834.1																																																																																			.	.		0.418	ST8SIA3-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449765.1	NM_015879		C	55027274	T	C	55027274	2	2	259	1	0	0	0	0	0	0	0	1	15248	1771	62	2		2	ST8SIA3	18	55027274	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	2090180	55027274	23049974	776	37094										
CDH20	28316	hgsc.bcm.edu	37	chr18	59221741	59221741	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cgacatggacctgtgggcacCgcccttcgactccctccaga	10	17	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:59221741C>A	ENST00000262717.4	+	12	2617	c.2219C>A	c.(2218-2220)cCg>cAg	p.P740Q	CDH20_ENST00000538374.1_Missense_Mutation_p.P740Q|CDH20_ENST00000536675.2_Missense_Mutation_p.P740Q			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2	740					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|skin(3)	61		Colorectal(73;0.186)				CTGTGGGCACCGCCCTTCGAC	0.647																																					p.P740Q		Atlas-SNP	.											CDH20,NS,carcinoma,0,1	CDH20	117	.	0			c.C2219A						.						37	30	33					18																	59221741		2203	4300	6503	SO:0001583	missense	28316	exon11			GGGCACCGCCCTT	AF217289	CCDS11977.1	18q21.33	2010-01-26			ENSG00000101542	ENSG00000101542		"Cadherins / Major cadherins"	1760	protein-coding gene	gene with protein product		605807				10995570	Standard	NM_031891		Approved	CDH7L3, Cdh7	uc010dps.1	Q9HBT6	OTTHUMG00000132768	ENST00000262717.4:c.2219C>A	chr18.hg19:g.59221741C>A	ENSP00000262717:p.Pro740Gln	95.0	0.0		45.0	2.0	NM_031891	Q495S3	Missense_Mutation	SNP	ENST00000262717.4	hg19	CCDS11977.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.637951	0.87760	.	.	ENSG00000101542	ENST00000536675;ENST00000538374;ENST00000262717	T;T;T	0.80033	-1.33;-1.33;-1.33	5.78	5.78	0.91487	Cadherin, cytoplasmic domain (1);	0.000000	0.85682	D	0.000000	D	0.92925	0.7749	M	0.93375	3.41	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93752	0.7059	10	0.87932	D	0	.	20.3668	0.98882	0.0:1.0:0.0:0.0	.	740	Q9HBT6	CAD20_HUMAN	Q	740	ENSP00000444767:P740Q;ENSP00000442226:P740Q;ENSP00000262717:P740Q	ENSP00000262717:P740Q	P	+	2	0	CDH20	57372721	1.000000	0.71417	0.994000	0.49952	0.905000	0.53344	7.756000	0.85195	2.894000	0.99253	0.655000	0.94253	CCG	.	.		0.647	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256141.2	NM_031891		A	59221741	C	A	59221741	3	1	259	1	0	0	0	0	1	0	0	0	3108	652	23	1	2261	1	CDH20	18	59221741	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	4194467	59221741	18855507	777	37095										
SERPINB2	5055	hgsc.bcm.edu	37	chr18	61569075	61569075	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gaaagtggaaaactccatttGagaagaaactaaatgggctt	10	5	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:61569075G>T	ENST00000299502.4	+	6	717	c.637G>T	c.(637-639)Gag>Tag	p.E213*	SERPINB2_ENST00000482254.1_3'UTR|SERPINB2_ENST00000457692.1_Nonsense_Mutation_p.E213*	NM_002575.2	NP_002566.1	P05120	PAI2_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 2	213					blood coagulation (GO:0007596)|fibrinolysis (GO:0042730)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|liver(1)|lung(12)|prostate(2)|skin(2)|stomach(1)	32		Esophageal squamous(42;0.131)			Tenecteplase(DB00031)|Urokinase(DB00013)	AACTCCATTTGAGAAGAAACT	0.388																																					p.E213X		Atlas-SNP	.											.	SERPINB2	63	.	0			c.G637T						.						107	110	109					18																	61569075		2203	4300	6503	SO:0001587	stop_gained	5055	exon6			CCATTTGAGAAGA	Y00630	CCDS11989.1	18q21.3	2014-02-18	2005-08-18		ENSG00000197632	ENSG00000197632		"Serine (or cysteine) peptidase inhibitors"	8584	protein-coding gene	gene with protein product		173390	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2"	PLANH2, PAI2		24172014	Standard	NM_002575		Approved	HsT1201	uc002ljo.3	P05120	OTTHUMG00000060592	ENST00000299502.4:c.637G>T	chr18.hg19:g.61569075G>T	ENSP00000299502:p.Glu213*	101.0	0.0		91.0	4.0	NM_002575	Q96E96	Nonsense_Mutation	SNP	ENST00000299502.4	hg19	CCDS11989.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	38|38	6.690516|6.690516	0.97764|0.97764	.|.	.|.	ENSG00000197632|ENSG00000242550	ENST00000299502;ENST00000457692|ENST00000397996;ENST00000418725	.|.	.|.	.|.	5.79|5.79	0.804|0.804	0.18697|0.18697	.|.	0.424440|.	0.27886|.	N|.	0.017456|.	.|.	.|.	.|.	.|.	.|.	.|.	0.53688|0.53688	D|D	0.999974|0.999974	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.07644|.	T|.	0.81|.	.|.	12.5443|12.5443	0.56190|0.56190	0.1523:0.3234:0.5244:0.0|0.1523:0.3234:0.5244:0.0	.|.	.|.	.|.	.|.	X|L	213|89	.|.	ENSP00000299502:E213X|.	E|X	+|+	1|2	0|2	SERPINB2|SERPINB10	59720055|59720055	0.000000|0.000000	0.05858|0.05858	0.982000|0.982000	0.44146|0.44146	0.992000|0.992000	0.81027|0.81027	-1.608000|-1.608000	0.02068|0.02068	-0.149000|-0.149000	0.11215|0.11215	0.650000|0.650000	0.86243|0.86243	GAG|TGA	.	.		0.388	SERPINB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134009.1	NM_002575		T	61569075	G	T	61569075	4	4	259	1	0	0	0	0	0	1	0	0	14116	1291	45	3	655	3	SERPINB2	18	61569075	Nonsense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	2347334	61569075	16508173	778	37096										
DSEL	92126	hgsc.bcm.edu	37	chr18	65178261	65178261	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atcagagtccagcagatgttTtcaattagtttaatttcatc	6	7	3	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:65178261T>C	ENST00000310045.7	-	2	5088	c.3615A>G	c.(3613-3615)gaA>gaG	p.E1205E	CTD-2541J13.2_ENST00000583493.1_RNA|CTD-2541J13.2_ENST00000581951.1_RNA	NM_032160.2	NP_115536.1	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	1195					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	isomerase activity (GO:0016853)|sulfotransferase activity (GO:0008146)			NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(25)|lung(23)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)				AGCAGATGTTTTCAATTAGTT	0.373																																					p.E1205E		Atlas-SNP	.											.	DSEL	196	.	0			c.A3615G						.						104	101	102					18																	65178261		2203	4300	6503	SO:0001819	synonymous_variant	92126	exon2			GATGTTTTCAATT	AF480435	CCDS11995.1	18q22.1	2007-01-29	2007-01-29	2007-01-29	ENSG00000171451	ENSG00000171451			18144	protein-coding gene	gene with protein product		611125	"chromosome 18 open reading frame 4"	C18orf4		16505484	Standard	NM_032160		Approved	NCAG1, FLJ11477	uc002lke.1	Q8IZU8	OTTHUMG00000132804	ENST00000310045.7:c.3615A>G	chr18.hg19:g.65178261T>C		242.0	0.0		120.0	6.0	NM_032160	Q17RH1|Q6P5Z3	Silent	SNP	ENST00000310045.7	hg19	CCDS11995.1																																																																																			.	.		0.373	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160		C	65178261	T	C	65178261	2	2	259	1	0	0	0	0	0	0	0	1	4777	1838	64	2		2	DSEL	18	65178261	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	3609186	65178261	12898987	779	37097										
ZNF407	55628	hgsc.bcm.edu	37	chr18	72516010	72516010	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tctgaagcccaaagtctttgTgagcacttttcataactgat	7	9	3	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:72516010T>C	ENST00000299687.5	+	3	4877				ZNF407_ENST00000309902.6_Silent_p.C1656C|ZNF407_ENST00000582337.1_Silent_p.C1656C|ZNF407_ENST00000577538.1_Intron	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		AAAGTCTTTGTGAGCACTTTT	0.433																																					p.C1656C		Atlas-SNP	.											.	ZNF407	231	.	0			c.T4968C						.						119	112	114					18																	72516010		692	1591	2283	SO:0001627	intron_variant	55628	exon4			TCTTTGTGAGCAC	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"Zinc fingers, C2H2-type"	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.4877+22552T>C	chr18.hg19:g.72516010T>C		121.0	0.0		96.0	4.0	NM_001146190	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Silent	SNP	ENST00000299687.5	hg19	CCDS45885.1																																																																																			.	.		0.433	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757		C	72516010	T	C	72516010	1	2	259	0	1	0	0	0	0	0	0	0	17902	1702	59	2		2	ZNF407	18	72516010	Intron	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	7337749	72516010	5561238	780	37098										
MIER2	54531	hgsc.bcm.edu	37	chr19	327889	327889	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccagggtcatgtctgggaggTtcggggccacgtcaccaccc	14	14	3	0	rs376851727		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:327889T>C	ENST00000264819.4	-	4	354	c.344A>G	c.(343-345)aAc>aGc	p.N115S	MIER2_ENST00000592722.1_5'UTR	NM_017550.1	NP_060020.1	Q8N344	MIER2_HUMAN	mesoderm induction early response 1, family member 2	115					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(4)|kidney(1)|large_intestine(5)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22		all_cancers(10;1.05e-30)|all_epithelial(18;3.04e-19)|Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;2.49e-05)|all_lung(49;4.36e-05)|Breast(49;0.000304)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GTCTGGGAGGTTCGGGGCCAC	0.617																																					p.N115S		Atlas-SNP	.											.	MIER2	51	.	0			c.A344G						.	T	SER/ASN	0,4406		0,0,2203	105	87	93		344	-4.8	0	19		93	1,8599		0,1,4299	no	missense	MIER2	NM_017550.1	46	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	benign	115/546	327889	1,13005	2203	4300	6503	SO:0001583	missense	54531	exon4			GGGAGGTTCGGGG	AB033019	CCDS32855.1	19p13.3	2008-02-05	2006-04-20	2006-04-20		ENSG00000105556			29210	protein-coding gene	gene with protein product			"KIAA1193"	KIAA1193		10574462	Standard	NM_017550		Approved		uc002lok.1	Q8N344		ENST00000264819.4:c.344A>G	chr19.hg19:g.327889T>C	ENSP00000264819:p.Asn115Ser	146.0	0.0		113.0	5.0	NM_017550	Q9ULM7	Missense_Mutation	SNP	ENST00000264819.4	hg19	CCDS32855.1	.	.	.	.	.	.	.	.	.	.	.	4.151	0.026419	0.08054	0.0	1.16E-4	ENSG00000105556	ENST00000264819	T	0.21361	2.01	5.01	-4.82	0.03171	.	1.871750	0.03258	N	0.182788	T	0.17066	0.0410	L	0.41236	1.265	0.09310	N	1	B	0.12013	0.005	B	0.13407	0.009	T	0.23976	-1.0173	10	0.24483	T	0.36	0.0017	9.8058	0.40792	0.0:0.1465:0.6075:0.246	.	115	Q8N344	MIER2_HUMAN	S	115	ENSP00000264819:N115S	ENSP00000264819:N115S	N	-	2	0	MIER2	278889	0.004000	0.15560	0.001000	0.08648	0.125000	0.20455	0.204000	0.17335	-1.165000	0.02786	-0.376000	0.06991	AAC	.	.		0.617	MIER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451784.1	XM_041843		C	327889	T	C	327889	3	2	259	1	0	0	0	0	1	0	0	0	9590	1725	60	2	1337	2	MIER2	19	327889	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10		327889	58801094	781	37099										
BSG	682	hgsc.bcm.edu	37	chr19	582316	582316	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccttcttcagatgacgacgcCggctctgcacccctgtaagt	9	15	3	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:582316C>A	ENST00000333511.3	+	7	1150	c.1080C>A	c.(1078-1080)gcC>gcA	p.A360A	BSG_ENST00000545507.2_Silent_p.A151A|BSG_ENST00000346916.4_Silent_p.A180A|BSG_ENST00000353555.4_Silent_p.A244A	NM_001728.3	NP_001719.2	P35613	BASI_HUMAN	basigin (Ok blood group)	360					blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cellular metabolic process (GO:0044237)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis of dentin-containing tooth (GO:0042475)|protein targeting to plasma membrane (GO:0072661)|pyruvate metabolic process (GO:0006090)|response to cAMP (GO:0051591)|response to mercury ion (GO:0046689)|response to peptide hormone (GO:0043434)|small molecule metabolic process (GO:0044281)	acrosomal membrane (GO:0002080)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	mannose binding (GO:0005537)			central_nervous_system(1)|endometrium(3)|lung(1)	5		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ATGACGACGCCGGCTCTGCAC	0.642																																					p.A360A		Atlas-SNP	.											.	BSG	48	.	0			c.C1080A						.						27	32	31					19																	582316		2196	4294	6490	SO:0001819	synonymous_variant	682	exon7			CGACGCCGGCTCT	L10240	CCDS12032.1, CCDS12033.1, CCDS12034.1, CCDS58635.1	19p13.3	2014-07-19	2014-01-02		ENSG00000172270	ENSG00000172270		"CD molecules", "Blood group antigens", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1116	protein-coding gene	gene with protein product	"Ok blood group"	109480	"basigin"	OK		8404035, 7812975	Standard	NM_198591		Approved	EMMPRIN, CD147	uc002loz.4	P35613		ENST00000333511.3:c.1080C>A	chr19.hg19:g.582316C>A		118.0	0.0		74.0	4.0	NM_001728	A6NJW1|D3YLG5|Q7Z796|Q8IZL7	Silent	SNP	ENST00000333511.3	hg19	CCDS12033.1																																																																																			.	.		0.642	BSG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438630.2	NM_001728		A	582316	C	A	582316	2	1	259	1	0	0	0	0	0	0	0	1	1531	639	23	1		1	BSG	19	582316	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	254427	582316	58546667	782	37100										
KISS1R	84634	hgsc.bcm.edu	37	chr19	917723	917723	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctgccgccacaagccgatgcGgaccgtgaccaacttctaca	9	16	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:917723G>A	ENST00000234371.5	+	1	374	c.221G>A	c.(220-222)cGg>cAg	p.R74Q	KISS1R_ENST00000606939.1_Missense_Mutation_p.R74Q	NM_032551.4	NP_115940.2	Q969F8	KISSR_HUMAN	KISS1 receptor	74					activation of MAPKK activity (GO:0000186)|arachidonic acid secretion (GO:0050482)|calcium-mediated signaling (GO:0019722)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of cell proliferation (GO:0008285)|neuropeptide signaling pathway (GO:0007218)|positive regulation of hormone secretion (GO:0046887)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of synaptic transmission (GO:0050806)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide binding (GO:0042923)|neuropeptide receptor activity (GO:0008188)			cervix(1)|kidney(1)|ovary(1)|pancreas(1)|skin(1)	5		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AAGCCGATGCGGACCGTGACC	0.706																																					p.R74Q		Atlas-SNP	.											.	KISS1R	10	.	0			c.G221A						.						25	21	22					19																	917723		2198	4296	6494	SO:0001583	missense	84634	exon1			CGATGCGGACCGT	AB051065	CCDS12049.1	19p13.3	2012-08-10	2006-02-15	2006-02-15	ENSG00000116014	ENSG00000116014		"GPCR / Class A : RF amide peptide receptors"	4510	protein-coding gene	gene with protein product		604161	"G protein-coupled receptor 54"	GPR54		10100623	Standard	NM_032551		Approved	HOT7T175, AXOR12	uc002lqk.4	Q969F8		ENST00000234371.5:c.221G>A	chr19.hg19:g.917723G>A	ENSP00000234371:p.Arg74Gln	123.0	0.0		94.0	4.0	NM_032551	A5D8U2|B2RTV1|Q96QG0	Missense_Mutation	SNP	ENST00000234371.5	hg19	CCDS12049.1	.	.	.	.	.	.	.	.	.	.	G	18.91	3.722913	0.68959	.	.	ENSG00000116014	ENST00000234371	T	0.42131	0.98	3.94	1.72	0.24424	GPCR, rhodopsin-like superfamily (1);	0.203848	0.38326	N	0.001727	T	0.37919	0.1021	M	0.66439	2.03	0.40293	D	0.978526	B	0.33637	0.42	B	0.35413	0.202	T	0.12528	-1.0544	10	0.30854	T	0.27	.	8.494	0.33117	0.2055:0.0:0.7945:0.0	.	74	Q969F8	KISSR_HUMAN	Q	74	ENSP00000234371:R74Q	ENSP00000234371:R74Q	R	+	2	0	KISS1R	868723	1.000000	0.71417	0.919000	0.36401	0.960000	0.62799	2.844000	0.48246	0.242000	0.21303	0.400000	0.26472	CGG	.	.		0.706	KISS1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458217.3	NM_032551		A	917723	G	A	917723	3	1	259	1	0	0	0	0	1	0	0	0	8337	1116	39	1	223	1	KISS1R	19	917723	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	335407	917723	58211260	783	37101										
GIPC3	126326	hgsc.bcm.edu	37	chr19	3586866	3586866	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aggcagtgtgcgtgggtgacAgcatcgaagccatcaacgac	14	10	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:3586866A>G	ENST00000322315.5	+	3	511	c.466A>G	c.(466-468)Agc>Ggc	p.S156G		NM_133261.2	NP_573568.1	Q8TF64	GIPC3_HUMAN	GIPC PDZ domain containing family, member 3	156	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.									breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	10				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0025)|STAD - Stomach adenocarcinoma(1328;0.18)		CGTGGGTGACAGCATCGAAGC	0.632											OREG0025154	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S156G		Atlas-SNP	.											.	GIPC3	27	.	0			c.A466G						.						54	50	51					19																	3586866		2202	4300	6502	SO:0001583	missense	126326	exon3			GGTGACAGCATCG	AB073738	CCDS32871.1	19p13.3	2011-11-29				ENSG00000179855			18183	protein-coding gene	gene with protein product		608792	"chromosome 19 open reading frame 64", "deafness, autosomal recessive 72", "deafness, autosomal recessive 15"	C19orf64, DFNB72, DFNB15		11836571, 21326233	Standard	NM_133261		Approved	DFNB95	uc002lyd.4	Q8TF64		ENST00000322315.5:c.466A>G	chr19.hg19:g.3586866A>G	ENSP00000319254:p.Ser156Gly	172.0	0.0	612	113.0	5.0	NM_133261	O75227	Missense_Mutation	SNP	ENST00000322315.5	hg19	CCDS32871.1	.	.	.	.	.	.	.	.	.	.	A	16.72	3.200602	0.58126	.	.	ENSG00000179855	ENST00000322315	T	0.27402	1.67	4.45	4.45	0.53987	PDZ/DHR/GLGF (4);	0.147777	0.64402	D	0.000010	T	0.23410	0.0566	L	0.27053	0.805	0.32532	N	0.534849	P	0.36753	0.568	B	0.36959	0.237	T	0.35076	-0.9803	10	0.52906	T	0.07	-40.31	12.565	0.56304	1.0:0.0:0.0:0.0	.	156	Q8TF64	GIPC3_HUMAN	G	156	ENSP00000319254:S156G	ENSP00000319254:S156G	S	+	1	0	GIPC3	3537866	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	5.989000	0.70587	1.641000	0.50575	0.459000	0.35465	AGC	.	.		0.632	GIPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394577.1	NM_133261		G	3586866	A	G	3586866	3	3	259	1	0	0	0	0	1	0	0	0	6402	188	7	2	476	2	GIPC3	19	3586866	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2669143	3586866	55542117	784	37102										
APBA3	9546	hgsc.bcm.edu	37	chr19	3754233	3754233	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cccgggcctgggccatgcgcGtgctggtgggcgggttccgt	19	13	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:3754233G>A	ENST00000316757.3	-	4	922	c.722C>T	c.(721-723)aCg>aTg	p.T241M	AC005954.3_ENST00000591962.1_RNA|AC005954.4_ENST00000586503.1_RNA	NM_004886.3	NP_004877.1	O96018	APBA3_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 3	241	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				in utero embryonic development (GO:0001701)|negative regulation of catalytic activity (GO:0043086)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	perinuclear region of cytoplasm (GO:0048471)	beta-amyloid binding (GO:0001540)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)			endometrium(1)|large_intestine(1)|skin(1)	3		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00467)|STAD - Stomach adenocarcinoma(1328;0.18)		GGCCATGCGCGTGCTGGTGGG	0.716																																					p.T241M		Atlas-SNP	.											.	APBA3	28	.	0			c.C722T						.																																			SO:0001583	missense	9546	exon4			ATGCGCGTGCTGG	AB021638	CCDS12110.1	19p13.3	2008-07-18	2008-07-18			ENSG00000011132			580	protein-coding gene	gene with protein product	"X11-like 2"	604262				10049767	Standard	NM_004886		Approved	X11L2, mint3	uc002lyp.1	O96018		ENST00000316757.3:c.722C>T	chr19.hg19:g.3754233G>A	ENSP00000315136:p.Thr241Met	76.0	0.0		69.0	4.0	NM_004886	O60483|Q9UPZ2	Missense_Mutation	SNP	ENST00000316757.3	hg19	CCDS12110.1	.	.	.	.	.	.	.	.	.	.	G	9.472	1.095827	0.20552	.	.	ENSG00000011132	ENST00000316757	T	0.23147	1.92	4.63	3.59	0.41128	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.304109	0.29987	N	0.010684	T	0.21062	0.0507	L	0.55743	1.74	0.34727	D	0.729309	P	0.36110	0.537	B	0.30251	0.113	T	0.30822	-0.9965	10	0.59425	D	0.04	.	8.4739	0.33001	0.204:0.0:0.796:0.0	.	241	O96018	APBA3_HUMAN	M	241	ENSP00000315136:T241M	ENSP00000315136:T241M	T	-	2	0	APBA3	3705233	0.015000	0.18098	0.633000	0.29310	0.212000	0.24457	1.436000	0.34980	0.927000	0.37143	0.462000	0.41574	ACG	.	.		0.716	APBA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453634.2			A	3754233	G	A	3754233	3	1	259	1	0	0	0	0	1	0	0	0	758	1145	40	1	1037	1	APBA3	19	3754233	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	167367	3754233	55374750	785	37103										
PLIN5	440503	hgsc.bcm.edu	37	chr19	4531823	4531823	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aggggcagagccaccacacgCtgcaccacgttctgcgggaa	13	14	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:4531823C>T	ENST00000381848.3	-	3	152	c.72G>A	c.(70-72)caG>caA	p.Q24Q	CTB-50L17.14_ENST00000586020.1_Missense_Mutation_p.S42N	NM_001013706.2	NP_001013728.2	Q00G26	PLIN5_HUMAN	perilipin 5	24	Essential for lipid droplet targeting. {ECO:0000250}.|Interaction with LIPE. {ECO:0000250}.				lipid particle organization (GO:0034389)|lipid storage (GO:0019915)|mitochondrion localization (GO:0051646)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of lipase activity (GO:0060192)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of triglyceride catabolic process (GO:0010897)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of lipase activity (GO:0060193)|positive regulation of lipid storage (GO:0010884)|positive regulation of sequestering of triglyceride (GO:0010890)|positive regulation of triglyceride biosynthetic process (GO:0010867)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lipid particle (GO:0005811)|mitochondrion (GO:0005739)				endometrium(4)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	10						CCACCACACGCTGCACCACGT	0.677																																					p.Q24Q		Atlas-SNP	.											.	PLIN5	27	.	0			c.G72A						.						8	11	10					19																	4531823		2038	4140	6178	SO:0001819	synonymous_variant	440503	exon3			CACACGCTGCACC	DQ839131	CCDS42473.1	19p13.3	2009-08-12			ENSG00000214456	ENSG00000214456		"Perilipins"	33196	protein-coding gene	gene with protein product	"lipid storage droplet protein 5"	613248				17234449, 19638644	Standard	NM_001013706		Approved	LSDP5, LSDA5, OXPAT, MLDP	uc002mas.3	Q00G26		ENST00000381848.3:c.72G>A	chr19.hg19:g.4531823C>T		88.0	0.0		80.0	5.0	NM_001013706	A2RRC1|Q6ZS68	Silent	SNP	ENST00000381848.3	hg19	CCDS42473.1																																																																																			.	.		0.677	PLIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458647.1	NM_001013706		T	4531823	C	T	4531823	2	4	259	1	0	0	0	0	0	0	0	1	12102	796	28	3		3	PLIN5	19	4531823	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	777590	4531823	54597160	786	37104										
DPP9	91039	hgsc.bcm.edu	37	chr19	4694679	4694679	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	caggctctgctcaccttcccCggggctgaagggctcactcc	11	17	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:4694679C>A	ENST00000598800.1	-	14	1928	c.1423G>T	c.(1423-1425)Ggg>Tgg	p.G475W	DPP9_ENST00000594671.1_Missense_Mutation_p.G475W|DPP9_ENST00000597849.1_Missense_Mutation_p.G504W|DPP9_ENST00000262960.9_Missense_Mutation_p.G504W			Q86TI2	DPP9_HUMAN	dipeptidyl-peptidase 9	475						cytoplasm (GO:0005737)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|identical protein binding (GO:0042802)|serine-type peptidase activity (GO:0008236)	p.G583W(1)		cervix(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00884)		TCACCTTCCCCGGGGCTGAAG	0.552																																					p.G504W		Atlas-SNP	.											DPP9,NS,carcinoma,0,1	DPP9	59	.	1	Substitution - Missense(1)	lung(1)	c.G1510T						.						26	29	28					19																	4694679		2027	4171	6198	SO:0001583	missense	91039	exon13			CTTCCCCGGGGCT	AF452102	CCDS45928.1	19p13.3	2014-06-11	2006-01-12		ENSG00000142002	ENSG00000142002			18648	protein-coding gene	gene with protein product		608258	"dipeptidylpeptidase 9"				Standard	NM_139159		Approved		uc002mba.3	Q86TI2	OTTHUMG00000182040	ENST00000598800.1:c.1423G>T	chr19.hg19:g.4694679C>A	ENSP00000469603:p.Gly475Trp	73.0	0.0		74.0	3.0	NM_139159	O75273|O75868|Q1ZZB8|Q6AI37|Q6UAL0|Q6ZMT2|Q6ZNJ5|Q8N2J7|Q8N3F5|Q8WXD8|Q96NT8|Q9BVR3	Missense_Mutation	SNP	ENST00000598800.1	hg19		.	.	.	.	.	.	.	.	.	.	C	11.72	1.723574	0.30593	.	.	ENSG00000142002	ENST00000357909;ENST00000381797;ENST00000262960	T	0.34072	1.38	3.76	-1.36	0.09085	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	1.401490	0.04391	N	0.362400	T	0.45196	0.1330	L	0.43152	1.355	0.09310	N	1	D;D	0.71674	0.986;0.998	P;D	0.65573	0.906;0.936	T	0.29912	-0.9996	10	0.72032	D	0.01	-8.9261	2.0833	0.03640	0.1261:0.3911:0.1243:0.3585	.	475;504	Q86TI2;Q1ZZB8	DPP9_HUMAN;.	W	583;445;504	ENSP00000262960:G504W	ENSP00000262960:G504W	G	-	1	0	DPP9	4645679	0.000000	0.05858	0.210000	0.23637	0.595000	0.36748	-0.178000	0.09782	-0.704000	0.05042	-1.134000	0.01955	GGG	.	.		0.552	DPP9-026	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000459343.2			A	4694679	C	A	4694679	3	1	259	1	0	0	0	0	1	0	0	0	4735	652	23	1	1208	1	DPP9	19	4694679	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	162856	4694679	54434304	787	37105										
FEM1A	55527	hgsc.bcm.edu	37	chr19	4792908	4792908	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccccacagctggtcctggccTatgactattccagggaggtc	11	14	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:4792908T>C	ENST00000269856.3	+	1	1181	c.1042T>C	c.(1042-1044)Tat>Cat	p.Y348H	AC005523.2_ENST00000601192.1_RNA|AC005523.3_ENST00000598782.1_lincRNA|AC005523.2_ENST00000596170.1_RNA	NM_018708.2	NP_061178.1	Q9BSK4	FEM1A_HUMAN	fem-1 homolog a (C. elegans)	348					negative regulation of inflammatory response (GO:0050728)|regulation of ubiquitin-protein transferase activity (GO:0051438)	cytoplasm (GO:0005737)	EP4 subtype prostaglandin E2 receptor binding (GO:0031867)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	17		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0139)		GGTCCTGGCCTATGACTATTC	0.642																																					p.Y348H		Atlas-SNP	.											.	FEM1A	41	.	0			c.T1042C						.						36	41	39					19																	4792908		2203	4297	6500	SO:0001583	missense	55527	exon1			CTGGCCTATGACT	BC004988	CCDS12135.1	19p13.3	2013-01-10	2006-11-08		ENSG00000141965	ENSG00000141965		"Ankyrin repeat domain containing"	16934	protein-coding gene	gene with protein product		613538				11441184	Standard	NM_018708		Approved		uc002mbf.3	Q9BSK4		ENST00000269856.3:c.1042T>C	chr19.hg19:g.4792908T>C	ENSP00000269856:p.Tyr348His	81.0	0.0		72.0	5.0	NM_018708	B2RDI3|Q711P8|Q9NPN7|Q9NPW8	Missense_Mutation	SNP	ENST00000269856.3	hg19	CCDS12135.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.943645	0.73672	.	.	ENSG00000141965	ENST00000269856	T	0.74947	-0.89	4.73	4.73	0.59995	.	0.000000	0.64402	U	0.000004	D	0.88362	0.6416	M	0.92923	3.36	0.58432	D	0.999999	D	0.89917	1.0	D	0.83275	0.996	D	0.89148	0.3521	10	0.33940	T	0.23	-6.4772	14.231	0.65892	0.0:0.0:0.0:1.0	.	348	Q9BSK4	FEM1A_HUMAN	H	348	ENSP00000269856:Y348H	ENSP00000269856:Y348H	Y	+	1	0	FEM1A	4743908	1.000000	0.71417	0.988000	0.46212	0.991000	0.79684	7.856000	0.86956	1.768000	0.52137	0.402000	0.26972	TAT	.	.		0.642	FEM1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459000.1			C	4792908	T	C	4792908	3	2	259	1	0	0	0	0	1	0	0	0	5817	1522	53	2	1044	2	FEM1A	19	4792908	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	98229	4792908	54336075	788	37106										
DENND1C	79958	hgsc.bcm.edu	37	chr19	6470311	6470311	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccagctcagcctcaccgagcGgtacatgttcttgacggctg	11	14	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:6470311G>T	ENST00000381480.2	-	18	1469	c.1357C>A	c.(1357-1359)Cgc>Agc	p.R453S	DENND1C_ENST00000543576.1_Missense_Mutation_p.R409S	NM_024898.2	NP_079174.2	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	453					positive regulation of Rab GTPase activity (GO:0032851)	cytoplasmic vesicle (GO:0031410)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(3)|kidney(3)|large_intestine(1)|lung(3)	10						CTCACCGAGCGGTACATGTTC	0.592																																					p.R453S		Atlas-SNP	.											.	DENND1C	93	.	0			c.C1357A						.						43	48	47					19																	6470311		2058	4190	6248	SO:0001583	missense	79958	exon18			CCGAGCGGTACAT	AL713770	CCDS45938.1	19p13.3	2014-02-06	2005-08-17	2005-08-17	ENSG00000205744	ENSG00000205744		"DENN/MADD domain containing"	26225	protein-coding gene	gene with protein product		613634	"family with sequence similarity 31, member C"	FAM31C		12477932	Standard	XM_005259646		Approved	FLJ22757	uc002mfe.3	Q8IV53	OTTHUMG00000180853	ENST00000381480.2:c.1357C>A	chr19.hg19:g.6470311G>T	ENSP00000370889:p.Arg453Ser	143.0	0.0		123.0	5.0	NM_024898	B4E051|D3PFD4|Q8NDB1|Q9H5Z2	Missense_Mutation	SNP	ENST00000381480.2	hg19	CCDS45938.1	.	.	.	.	.	.	.	.	.	.	G	15.12	2.738879	0.49045	.	.	ENSG00000205744	ENST00000381480;ENST00000543576	T;T	0.11277	2.97;2.79	4.99	4.99	0.66335	.	0.192145	0.32703	N	0.005751	T	0.13114	0.0318	L	0.42245	1.32	0.35958	D	0.834372	B	0.33919	0.432	B	0.39379	0.298	T	0.10428	-1.0630	10	0.87932	D	0	-26.9138	10.9417	0.47276	0.0:0.0:0.8125:0.1875	.	453	Q8IV53	DEN1C_HUMAN	S	453;409	ENSP00000370889:R453S;ENSP00000437805:R409S	ENSP00000370889:R453S	R	-	1	0	DENND1C	6421311	1.000000	0.71417	1.000000	0.80357	0.489000	0.33432	2.284000	0.43478	2.313000	0.78055	0.455000	0.32223	CGC	.	.		0.592	DENND1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453332.2	NM_024898		T	6470311	G	T	6470311	3	4	259	1	0	0	0	0	1	0	0	0	4430	1116	39	1	1072	1	DENND1C	19	6470311	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1677403	6470311	52658672	789	37107										
FBN3	84467	hgsc.bcm.edu	37	chr19	8161405	8161405	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agctgccttctgtgtccatgCagtcaccatggctacagaca	9	13	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:8161405C>T	ENST00000600128.1	-	44	5876	c.5462G>A	c.(5461-5463)tGc>tAc	p.C1821Y	FBN3_ENST00000270509.2_Missense_Mutation_p.C1821Y|FBN3_ENST00000601739.1_Missense_Mutation_p.C1821Y			Q75N90	FBN3_HUMAN	fibrillin 3	1821	EGF-like 28. {ECO:0000255|PROSITE- ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						TGTGTCCATGCAGTCACCATG	0.577																																					p.C1821Y		Atlas-SNP	.											.	FBN3	300	.	0			c.G5462A						.						133	91	106					19																	8161405		2203	4300	6503	SO:0001583	missense	84467	exon43			TCCATGCAGTCAC		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.5462G>A	chr19.hg19:g.8161405C>T	ENSP00000470498:p.Cys1821Tyr	77.0	0.0		88.0	4.0	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	hg19	CCDS12196.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.115218	0.77210	.	.	ENSG00000142449	ENST00000270509	D	0.99445	-5.91	3.63	3.63	0.41609	Epidermal growth factor-like (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	U	0.000000	D	0.99722	0.9892	H	0.97783	4.075	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.96980	0.9714	10	0.87932	D	0	.	15.6411	0.77001	0.0:1.0:0.0:0.0	.	1821	Q75N90	FBN3_HUMAN	Y	1821	ENSP00000270509:C1821Y	ENSP00000270509:C1821Y	C	-	2	0	FBN3	8067405	1.000000	0.71417	0.998000	0.56505	0.892000	0.51952	5.339000	0.65953	1.695000	0.51148	0.655000	0.94253	TGC	.	.		0.577	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447		T	8161405	C	T	8161405	3	4	259	1	0	0	0	0	1	0	0	0	5712	710	25	3	3051	3	FBN3	19	8161405	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	1691094	8161405	50967578	790	37108										
OR1M1	125963	hgsc.bcm.edu	37	chr19	9204494	9204494	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tccgactttcgtgcacggacAcctctgtgaataggatcttc	9	12	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:9204494A>G	ENST00000429566.3	+	1	640	c.574A>G	c.(574-576)Acc>Gcc	p.T192A		NM_001004456.1	NP_001004456.1	Q8NGA1	OR1M1_HUMAN	olfactory receptor, family 1, subfamily M, member 1	192						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|large_intestine(3)|lung(17)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32						GTGCACGGACACCTCTGTGAA	0.562																																					p.T192A		Atlas-SNP	.											.	OR1M1	52	.	0			c.A574G						.						147	119	129					19																	9204494		2203	4300	6503	SO:0001583	missense	125963	exon1			ACGGACACCTCTG		CCDS32896.1	19p13.2	2013-09-20			ENSG00000170929	ENSG00000170929		"GPCR / Class A : Olfactory receptors"	8220	protein-coding gene	gene with protein product							Standard	NM_001004456		Approved	OR19-6	uc010xkj.2	Q8NGA1	OTTHUMG00000179930	ENST00000429566.3:c.574A>G	chr19.hg19:g.9204494A>G	ENSP00000401966:p.Thr192Ala	65.0	0.0		61.0	5.0	NM_001004456	B9EHA6|Q6IFJ3|Q96R91	Missense_Mutation	SNP	ENST00000429566.3	hg19	CCDS32896.1	.	.	.	.	.	.	.	.	.	.	g	9.467	1.094709	0.20471	.	.	ENSG00000170929	ENST00000305465;ENST00000429566	T	0.00235	8.48	3.8	1.66	0.24008	GPCR, rhodopsin-like superfamily (1);	0.103104	0.43110	N	0.000603	T	0.00241	0.0007	M	0.87097	2.86	0.09310	N	1	B	0.09022	0.002	B	0.14023	0.01	T	0.49437	-0.8940	10	0.87932	D	0	.	4.2253	0.10577	0.6002:0.0:0.0924:0.3074	.	192	Q8NGA1	OR1M1_HUMAN	A	195;192	ENSP00000401966:T192A	ENSP00000303195:T195A	T	+	1	0	OR1M1	9065494	0.001000	0.12720	0.014000	0.15608	0.002000	0.02628	1.365000	0.34182	0.157000	0.19338	-0.289000	0.09944	ACC	.	.		0.562	OR1M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448993.1			G	9204494	A	G	9204494	3	3	259	1	0	0	0	0	1	0	0	0	10977	159	6	2	576	2	OR1M1	19	9204494	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1043089	9204494	49924489	791	37109										
ZNF317	57693	hgsc.bcm.edu	37	chr19	9271853	9271853	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	taggcagtgtggcaaggcctTcaggaaccagtcaacgctga	13	10	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:9271853T>C	ENST00000247956.6	+	7	1837	c.1532T>C	c.(1531-1533)tTc>tCc	p.F511S	ZNF317_ENST00000360385.3_Missense_Mutation_p.F479S	NM_020933.4	NP_065984.3	Q96PQ6	ZN317_HUMAN	zinc finger protein 317	511					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	27						GGCAAGGCCTTCAGGAACCAG	0.552																																					p.F511S		Atlas-SNP	.											.	ZNF317	61	.	0			c.T1532C						.						81	68	72					19																	9271853		2203	4300	6503	SO:0001583	missense	57693	exon7			AGGCCTTCAGGAA	AF275255	CCDS12210.1, CCDS54213.1	19p13	2013-01-08				ENSG00000130803		"Zinc fingers, C2H2-type", "-"	13507	protein-coding gene	gene with protein product		613864				10997877, 11688974	Standard	NM_020933		Approved		uc002mku.3	Q96PQ6		ENST00000247956.6:c.1532T>C	chr19.hg19:g.9271853T>C	ENSP00000247956:p.Phe511Ser	65.0	0.0		70.0	5.0	NM_020933	Q6DCA9|Q96PM0|Q96PM1|Q96PT2|Q9HCI4	Missense_Mutation	SNP	ENST00000247956.6	hg19	CCDS12210.1	.	.	.	.	.	.	.	.	.	.	T	17.66	3.444134	0.63067	.	.	ENSG00000130803	ENST00000247956;ENST00000360385	T;T	0.44482	0.92;0.92	2.72	2.72	0.32119	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.44285	D	0.000478	T	0.63510	0.2517	M	0.87971	2.92	0.37440	D	0.91439	D;D	0.89917	1.0;1.0	D;D	0.87578	0.986;0.998	T	0.70439	-0.4871	10	0.87932	D	0	-25.5393	7.2844	0.26330	0.0:0.0:0.0:1.0	.	479;511	Q96PQ6-2;Q96PQ6	.;ZN317_HUMAN	S	511;479	ENSP00000247956:F511S;ENSP00000353554:F479S	ENSP00000247956:F511S	F	+	2	0	ZNF317	9132853	0.825000	0.29262	0.386000	0.26170	0.754000	0.42855	2.301000	0.43628	1.502000	0.48669	0.482000	0.46254	TTC	.	.		0.552	ZNF317-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448995.1	NM_020933		C	9271853	T	C	9271853	3	2	259	1	0	0	0	0	1	0	0	0	17850	1783	62	2	1554	2	ZNF317	19	9271853	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	67359	9271853	49857130	792	37110										
OLFM2	93145	hgsc.bcm.edu	37	chr19	9968053	9968053	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggccgccagactgccggagaGattcctcacctcctcccgca	10	18	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:9968053G>T	ENST00000264833.4	-	4	651	c.466C>A	c.(466-468)Ctc>Atc	p.L156I	OLFM2_ENST00000590841.1_Missense_Mutation_p.L78I	NM_058164.2	NP_477512.1	O95897	NOE2_HUMAN	olfactomedin 2	156					protein secretion (GO:0009306)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular region (GO:0005576)|synapse (GO:0045202)				breast(1)|cervix(1)|endometrium(3)|large_intestine(8)|lung(9)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	31						CTGCCGGAGAGATTCCTCACC	0.632																																					p.L156I		Atlas-SNP	.											.	OLFM2	42	.	0			c.C466A						.						104	82	90					19																	9968053		2203	4300	6503	SO:0001583	missense	93145	exon4			CGGAGAGATTCCT	AF131839	CCDS12221.1	19p13.2	2008-07-03				ENSG00000105088			17189	protein-coding gene	gene with protein product	"noelin 2"						Standard	NM_058164		Approved	OlfC, NOE2	uc002mmp.3	O95897		ENST00000264833.4:c.466C>A	chr19.hg19:g.9968053G>T	ENSP00000264833:p.Leu156Ile	89.0	0.0		62.0	4.0	NM_058164	Q6IMJ3|Q96FC2	Missense_Mutation	SNP	ENST00000264833.4	hg19	CCDS12221.1	.	.	.	.	.	.	.	.	.	.	G	16.14	3.039488	0.55003	.	.	ENSG00000105088	ENST00000264833	D	0.90504	-2.68	3.84	3.84	0.44239	.	0.000000	0.64402	D	0.000002	D	0.89192	0.6645	L	0.47016	1.485	0.54753	D	0.999987	P	0.45044	0.849	P	0.47941	0.562	D	0.88086	0.2810	9	.	.	.	.	13.3045	0.60345	0.0:0.0:1.0:0.0	.	156	O95897	NOE2_HUMAN	I	156	ENSP00000264833:L156I	.	L	-	1	0	OLFM2	9829053	1.000000	0.71417	0.979000	0.43373	0.145000	0.21501	6.403000	0.73264	1.988000	0.58038	0.462000	0.41574	CTC	.	.		0.632	OLFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451119.1			T	9968053	G	T	9968053	3	4	259	1	0	0	0	0	1	0	0	0	10862	942	33	3	910	3	OLFM2	19	9968053	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	696200	9968053	49160930	793	37111										
KEAP1	9817	hgsc.bcm.edu	37	chr19	10610159	10610159	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cgaagttggcgatgccgatgGcattgctggggtccagctgc	16	10	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:10610159G>T	ENST00000171111.5	-	2	1098	c.551C>A	c.(550-552)gCc>gAc	p.A184D	KEAP1_ENST00000393623.2_Missense_Mutation_p.A184D|KEAP1_ENST00000588024.1_5'UTR	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	184	BACK.				cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)				breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	GATGCCGATGGCATTGCTGGG	0.582																																					p.A184D		Atlas-SNP	.											.	KEAP1	182	.	0			c.C551A						.						116	93	101					19																	10610159		2203	4300	6503	SO:0001583	missense	9817	exon2			CCGATGGCATTGC	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"Kelch-like", "BTB/POZ domain containing"	23177	protein-coding gene	gene with protein product	"kelch-like family member 19"	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.551C>A	chr19.hg19:g.10610159G>T	ENSP00000171111:p.Ala184Asp	93.0	0.0		88.0	5.0	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Missense_Mutation	SNP	ENST00000171111.5	hg19	CCDS12239.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.586878	0.86851	.	.	ENSG00000079999	ENST00000171111;ENST00000393623	T;T	0.72282	-0.64;-0.64	4.81	4.81	0.61882	BTB/Kelch-associated (1);	0.052992	0.85682	D	0.000000	D	0.82618	0.5076	M	0.71036	2.16	0.80722	D	1	D	0.76494	0.999	D	0.75020	0.985	D	0.85078	0.0944	10	0.87932	D	0	.	15.3825	0.74669	0.0:0.0:1.0:0.0	.	184	Q14145	KEAP1_HUMAN	D	184	ENSP00000171111:A184D;ENSP00000377245:A184D	ENSP00000171111:A184D	A	-	2	0	KEAP1	10471159	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	4.017000	0.57167	2.232000	0.73038	0.561000	0.74099	GCC	.	.		0.582	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289		T	10610159	G	T	10610159	3	4	259	1	0	0	0	0	1	0	0	0	8150	1203	42	3	1343	3	KEAP1	19	10610159	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	642106	10610159	48518824	794	37112										
ZNF653	115950	hgsc.bcm.edu	37	chr19	11606896	11606896	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aagtggggtctagctccgccAggtgcggctcgtacgggcag	17	11	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:11606896A>G	ENST00000293771.5	-	3	564	c.428T>C	c.(427-429)cTg>cCg	p.L143P	ZNF653_ENST00000593191.1_5'UTR|CTC-398G3.6_ENST00000585656.1_Missense_Mutation_p.W114R	NM_138783.3	NP_620138.2	Q96CK0	ZN653_HUMAN	zinc finger protein 653	143					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	17						TAGCTCCGCCAGGTGCGGCTC	0.642																																					p.L143P	Pancreas(83;980 1446 4542 6441 43352)	Atlas-SNP	.											.	ZNF653	48	.	0			c.T428C						.						110	77	88					19																	11606896		2203	4300	6503	SO:0001583	missense	115950	exon3			TCCGCCAGGTGCG	AY072704	CCDS12261.1	19p13.2	2013-01-08						"Zinc fingers, C2H2-type"	25196	protein-coding gene	gene with protein product		611371				12477932	Standard	NM_138783		Approved	Zip67	uc002mrz.2	Q96CK0		ENST00000293771.5:c.428T>C	chr19.hg19:g.11606896A>G	ENSP00000293771:p.Leu143Pro	80.0	0.0		74.0	4.0	NM_138783	Q96AS7	Missense_Mutation	SNP	ENST00000293771.5	hg19	CCDS12261.1	.	.	.	.	.	.	.	.	.	.	A	16.46	3.128368	0.56721	.	.	ENSG00000161914	ENST00000293771	T	0.22336	1.96	4.52	4.52	0.55395	.	0.163743	0.41396	D	0.000889	T	0.27134	0.0665	L	0.29908	0.895	0.80722	D	1	D	0.57899	0.981	P	0.55161	0.77	T	0.03148	-1.1067	10	0.87932	D	0	-19.5122	12.9624	0.58466	1.0:0.0:0.0:0.0	.	143	Q96CK0	ZN653_HUMAN	P	143	ENSP00000293771:L143P	ENSP00000293771:L143P	L	-	2	0	ZNF653	11467896	1.000000	0.71417	0.899000	0.35326	0.133000	0.20885	7.612000	0.82975	1.912000	0.55364	0.459000	0.35465	CTG	.	.		0.642	ZNF653-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458836.2	NM_138783		G	11606896	A	G	11606896	3	3	259	1	0	0	0	0	1	0	0	0	18081	188	7	2	1447	2	ZNF653	19	11606896	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	996737	11606896	47522087	795	37113										
BEST2	54831	hgsc.bcm.edu	37	chr19	12866497	12866497	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cgccagttcctggacccggcTcagggttacaaagaccacga	11	14	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:12866497T>C	ENST00000549706.1	+	7	1107	c.783T>C	c.(781-783)gcT>gcC	p.A261A	BEST2_ENST00000042931.1_Silent_p.A261A|BEST2_ENST00000553030.1_Silent_p.A261A			Q8NFU1	BEST2_HUMAN	bestrophin 2	261					chloride transmembrane transport (GO:1902476)|membrane depolarization (GO:0051899)|sensory perception of smell (GO:0007608)	chloride channel complex (GO:0034707)|cilium (GO:0005929)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			breast(3)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|pancreas(1)	12						TGGACCCGGCTCAGGGTTACA	0.607																																					p.A261A		Atlas-SNP	.											.	BEST2	35	.	0			c.T783C						.						93	98	96					19																	12866497		2048	4227	6275	SO:0001819	synonymous_variant	54831	exon6			CCCGGCTCAGGGT	AF440756	CCDS42506.1	19p13.13	2014-08-12	2006-10-18	2006-10-18	ENSG00000039987	ENSG00000039987		"Ion channels / Chloride channels : Calcium activated : Bestrophins"	17107	protein-coding gene	gene with protein product		607335	"vitelliform macular dystrophy 2-like 1"	VMD2L1		12032738, 16912113	Standard	NM_017682		Approved	FLJ20132	uc002mux.3	Q8NFU1	OTTHUMG00000169293	ENST00000549706.1:c.783T>C	chr19.hg19:g.12866497T>C		168.0	0.0		150.0	7.0	NM_017682	Q53YQ8|Q9NXP0	Silent	SNP	ENST00000549706.1	hg19	CCDS42506.1																																																																																			.	.		0.607	BEST2-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403343.1	NM_017682		C	12866497	T	C	12866497	2	2	259	1	0	0	0	0	0	0	0	1	1405	1538	54	2		2	BEST2	19	12866497	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1259601	12866497	46262486	796	37114										
CC2D1A	54862	hgsc.bcm.edu	37	chr19	14024289	14024289	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cggacatcccgccgccagtgGccataggaaaaggcccggcg	14	15	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:14024289G>A	ENST00000318003.7	+	6	827	c.586G>A	c.(586-588)Gcc>Acc	p.A196T	CC2D1A_ENST00000589606.1_Missense_Mutation_p.A196T	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	196	Pro-rich.				positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	27			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)			GCCGCCAGTGGCCATAGGAAA	0.617																																					p.A196T		Atlas-SNP	.											.	CC2D1A	67	.	0			c.G586A						.						35	44	41					19																	14024289		2009	4157	6166	SO:0001583	missense	54862	exon6			CCAGTGGCCATAG	AF536205	CCDS42512.1	19p13.12	2007-01-08				ENSG00000132024			30237	protein-coding gene	gene with protein product	"mental retardation, nonsyndromic, autosomal recessive, 3"	610055				12761501, 16033914	Standard	NM_017721		Approved	FLJ20241, MRT3	uc002mxo.2	Q6P1N0		ENST00000318003.7:c.586G>A	chr19.hg19:g.14024289G>A	ENSP00000313601:p.Ala196Thr	139.0	0.0		120.0	6.0	NM_017721	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Missense_Mutation	SNP	ENST00000318003.7	hg19	CCDS42512.1	.	.	.	.	.	.	.	.	.	.	G	16.30	3.085832	0.55861	.	.	ENSG00000132024	ENST00000318003;ENST00000254346;ENST00000389233	T	0.26660	1.72	5.2	5.2	0.72013	.	0.058980	0.64402	D	0.000003	T	0.35595	0.0937	M	0.79011	2.435	0.80722	D	1	B;B	0.27351	0.117;0.176	B;B	0.27380	0.043;0.079	T	0.30119	-0.9989	10	0.72032	D	0.01	-15.0001	17.4931	0.87710	0.0:0.0:1.0:0.0	.	196;196	Q6P1N0-2;Q6P1N0	.;C2D1A_HUMAN	T	196;34;171	ENSP00000313601:A196T	ENSP00000254346:A34T	A	+	1	0	CC2D1A	13885289	1.000000	0.71417	0.965000	0.40720	0.096000	0.18686	6.122000	0.71608	2.425000	0.82216	0.462000	0.41574	GCC	.	.		0.617	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721		A	14024289	G	A	14024289	3	1	259	1	0	0	0	0	1	0	0	0	2728	1203	42	3	608	3	CC2D1A	19	14024289	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1157792	14024289	45104694	797	37115										
LPHN1	22859	hgsc.bcm.edu	37	chr19	14274128	14274128	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgcggtcacccgcctgcagcGggtccttgcaccatgcgcca	12	17	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:14274128G>T	ENST00000340736.6	-	6	797	c.500C>A	c.(499-501)cCg>cAg	p.P167Q	LPHN1_ENST00000591528.1_5'UTR|LPHN1_ENST00000361434.3_Missense_Mutation_p.P162Q|CTB-55O6.12_ENST00000592086.1_RNA|CTB-55O6.12_ENST00000588387.1_RNA	NM_001008701.2	NP_001008701.1	O94910	LPHN1_HUMAN	latrophilin 1	167	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|heterophilic cell-cell adhesion (GO:0007157)|neuropeptide signaling pathway (GO:0007218)|positive regulation of synapse maturation (GO:0090129)	axon (GO:0030424)|cell junction (GO:0030054)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)			central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						CGCCTGCAGCGGGTCCTTGCA	0.652																																					p.P167Q		Atlas-SNP	.											.	LPHN1	107	.	0			c.C500A						.						41	34	36					19																	14274128		2202	4300	6502	SO:0001583	missense	22859	exon6			TGCAGCGGGTCCT	AB020628	CCDS12307.1, CCDS32928.1	19p13.2	2014-08-08				ENSG00000072071		"-", "GPCR / Class B : Orphans"	20973	protein-coding gene	gene with protein product						10994649	Standard	NM_014921		Approved	KIAA0821, CIRL1, LEC2	uc010xnn.2	O94910		ENST00000340736.6:c.500C>A	chr19.hg19:g.14274128G>T	ENSP00000340688:p.Pro167Gln	135.0	0.0		77.0	4.0	NM_001008701	Q96IE7|Q9BU07|Q9HAR3	Missense_Mutation	SNP	ENST00000340736.6	hg19	CCDS32928.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.549032	0.86127	.	.	ENSG00000072071	ENST00000340736;ENST00000361434	D;D	0.89810	-2.57;-2.57	5.06	5.06	0.68205	Olfactomedin-like (3);	0.000000	0.85682	D	0.000000	D	0.95698	0.8601	M	0.92738	3.34	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.96704	0.9520	10	0.87932	D	0	.	15.9461	0.79796	0.0:0.0:1.0:0.0	.	162;167	O94910-2;O94910	.;LPHN1_HUMAN	Q	167;162	ENSP00000340688:P167Q;ENSP00000355328:P162Q	ENSP00000340688:P167Q	P	-	2	0	LPHN1	14135128	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	9.783000	0.99037	2.347000	0.79759	0.655000	0.94253	CCG	.	.		0.652	LPHN1-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459696.1	NM_014921		T	14274128	G	T	14274128	3	4	259	1	0	0	0	0	1	0	0	0	8924	1116	39	1	4000	1	LPHN1	19	14274128	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	249839	14274128	44854855	798	37116										
NOTCH3	4854	hgsc.bcm.edu	37	chr19	15297800	15297800	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gttcacttcgcagttcacacCtaggggccaggaacatggca	11	12	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:15297800C>A	ENST00000263388.2	-	12	1916		c.e12-1			NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3						forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			CAGTTCACACCTAGGGGCCAG	0.587																																					.		Atlas-SNP	.											.	NOTCH3	340	.	0			c.1841-1G>T						.						77	55	63					19																	15297800		2203	4300	6503	SO:0001630	splice_region_variant	4854	exon13			TCACACCTAGGGG	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"Ankyrin repeat domain containing"	7883	protein-coding gene	gene with protein product		600276	"Notch (Drosophila) homolog 3", "Notch homolog 3 (Drosophila)"	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.1841-1G>T	chr19.hg19:g.15297800C>A		51.0	0.0		49.0	4.0	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Splice_Site	SNP	ENST00000263388.2	hg19	CCDS12326.1	.	.	.	.	.	.	.	.	.	.	C	16.26	3.072292	0.55646	.	.	ENSG00000074181	ENST00000263388;ENST00000539383	.	.	.	4.52	4.52	0.55395	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3814	0.83462	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NOTCH3	15158800	1.000000	0.71417	0.997000	0.53966	0.545000	0.35147	7.670000	0.83925	2.219000	0.72066	0.655000	0.94253	.	.	.		0.587	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435	Intron	A	15297800	C	A	15297800	5	1	259	1	0	0	0	0	0	0	1	0	10559	695	24	3	5213	3	NOTCH3	19	15297800	Splice_Site	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	1023672	15297800	43831183	799	37117										
SIN3B	23309	hgsc.bcm.edu	37	chr19	16977294	16977294	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccttgaccaccaggctgtgaActtcaagcagaacgacacca	8	14	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:16977294A>G	ENST00000248054.5	+	12	1754	c.1733A>G	c.(1732-1734)aAc>aGc	p.N578S	SIN3B_ENST00000379803.1_Missense_Mutation_p.N610S|SIN3B_ENST00000595541.1_Missense_Mutation_p.N168S					SIN3 transcription regulator family member B											endometrium(4)|kidney(2)|large_intestine(8)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26						CAGGCTGTGAACTTCAAGCAG	0.592																																					p.N610S		Atlas-SNP	.											.	SIN3B	90	.	0			c.A1829G						.						156	111	126					19																	16977294		2203	4300	6503	SO:0001583	missense	23309	exon13			CTGTGAACTTCAA	AB014600	CCDS32946.1, CCDS74308.1	19p13.12	2013-08-21	2013-08-21						19354	protein-coding gene	gene with protein product		607777	"SIN3 homolog B, transcription regulator (yeast)", "SIN3 transcription regulator homolog B (yeast)"			9734811	Standard	XM_005259832		Approved	KIAA0700	uc002ney.2	O75182		ENST00000248054.5:c.1733A>G	chr19.hg19:g.16977294A>G	ENSP00000248054:p.Asn578Ser	74.0	0.0		92.0	4.0	NM_015260		Missense_Mutation	SNP	ENST00000248054.5	hg19		.	.	.	.	.	.	.	.	.	.	A	23.5	4.426872	0.83667	.	.	ENSG00000127511	ENST00000379803;ENST00000248054	T;T	0.43294	0.95;0.95	4.96	4.96	0.65561	.	0.098476	0.64402	D	0.000001	T	0.56499	0.1989	M	0.63169	1.94	0.80722	D	1	D;P;P	0.76494	0.999;0.832;0.938	P;P;P	0.62740	0.906;0.525;0.54	T	0.53063	-0.8491	10	0.20046	T	0.44	-13.1387	14.6166	0.68552	1.0:0.0:0.0:0.0	.	168;578;610	B7Z392;O75182-2;O75182	.;.;SIN3B_HUMAN	S	610;578	ENSP00000369131:N610S;ENSP00000248054:N578S	ENSP00000248054:N578S	N	+	2	0	SIN3B	16838294	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.097000	0.94193	1.850000	0.53721	0.402000	0.26972	AAC	.	.		0.592	SIN3B-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000462846.1	NM_015260		G	16977294	A	G	16977294	3	3	259	1	0	0	0	0	1	0	0	0	14341	43	2	2	1879	2	SIN3B	19	16977294	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1679494	16977294	42151689	800	37118										
C19orf62	29086	hgsc.bcm.edu	37	chr19	17384927	17384927	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tccctgcagctgtctggcctGacctccgacccccgcgagct	10	19	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:17384927G>A	ENST00000359435.4	+	5	670	c.477G>A	c.(475-477)ctG>ctA	p.L159L	CTD-2278I10.6_ENST00000596542.1_Silent_p.L81L|BABAM1_ENST00000598188.1_Silent_p.L159L|BABAM1_ENST00000595632.1_Intron|BABAM1_ENST00000601043.1_Silent_p.L159L|BABAM1_ENST00000447614.2_Silent_p.L159L|BABAM1_ENST00000448635.2_Intron	NM_001033549.1	NP_001028721.1	Q9NWV8	BABA1_HUMAN	BRISC and BRCA1 A complex member 1	159	VWFA-like.				chromatin modification (GO:0016568)|double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|positive regulation of DNA repair (GO:0045739)|protein K63-linked deubiquitination (GO:0070536)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRISC complex (GO:0070552)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	5						TGTCTGGCCTGACCTCCGACC	0.667																																					p.L159L		Atlas-SNP	.											.	BABAM1	14	.	0			c.G477A						.						59	68	65					19																	17384927		2064	4203	6267	SO:0001819	synonymous_variant	29086	exon5			TGGCCTGACCTCC	AK000578	CCDS46012.1, CCDS74310.1	19p13.11	2011-02-21	2011-02-21	2011-01-31	ENSG00000105393	ENSG00000105393			25008	protein-coding gene	gene with protein product	"Mediator of Rap80 Interactions and Targeting 40 kD", "new component of the BRCA1 A complex"	612766	"chromosome 19 open reading frame 62"	C19orf62		11042152	Standard	NM_001288756		Approved	FLJ20571, HSPC142, NBA1, MERIT40	uc002nfv.3	Q9NWV8		ENST00000359435.4:c.477G>A	chr19.hg19:g.17384927G>A		90.0	0.0		82.0	4.0	NM_014173	A8MQT0|B4DRY9|B4DVR1|Q6FIA0|Q9P018	Silent	SNP	ENST00000359435.4	hg19	CCDS46012.1																																																																																			.	.		0.667	BABAM1-005	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463471.1	NM_014173		A	17384927	G	A	17384927	2	1	259	1	0	0	0	0	0	0	0	1	1946	1277	45	3		3	C19orf62	19	17384927	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	407633	17384927	41744056	801	37119										
MAP1S	55201	hgsc.bcm.edu	37	chr19	17837556	17837556	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgcagcacttgaggttcctgCgagagcccgtggtgacgccc	14	13	0	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:17837556C>T	ENST00000324096.4	+	5	1514	c.1363C>T	c.(1363-1365)Cga>Tga	p.R455*	MAP1S_ENST00000544059.2_Nonsense_Mutation_p.R429*|CTD-3149D2.4_ENST00000595363.1_RNA|MAP1S_ENST00000597681.1_Intron	NM_018174.4	NP_060644.4	Q66K74	MAP1S_HUMAN	microtubule-associated protein 1S	455	Necessary for the microtubule-organizing center localization.				apoptotic DNA fragmentation (GO:0006309)|brain development (GO:0007420)|execution phase of apoptosis (GO:0097194)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|nervous system development (GO:0007399)|neuron projection morphogenesis (GO:0048812)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	actin filament binding (GO:0051015)|beta-tubulin binding (GO:0048487)|DNA binding (GO:0003677)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	25						GAGGTTCCTGCGAGAGCCCGT	0.721																																					p.R455X		Atlas-SNP	.											.	MAP1S	74	.	0			c.C1363T						.						4	5	4					19																	17837556		2014	4009	6023	SO:0001587	stop_gained	55201	exon5			TTCCTGCGAGAGC	BC067115	CCDS32954.1	19p13.12	2008-02-05	2006-07-04	2006-07-04		ENSG00000130479			15715	protein-coding gene	gene with protein product		607573	"chromosome 19 open reading frame 5", "VCY2 interacting protein 1", "BPY2 interacting protein 1"	C19orf5, VCY2IP1, BPY2IP1		11827465, 15528209, 16297881, 14627543	Standard	NM_018174		Approved	FLJ10669, MAP8	uc002nhe.1	Q66K74		ENST00000324096.4:c.1363C>T	chr19.hg19:g.17837556C>T	ENSP00000325313:p.Arg455*	49.0	0.0		46.0	10.0	NM_018174	B4DH53|Q27QB1|Q6NXF1|Q8N3L8|Q8N3W5|Q8NI88|Q96H94|Q96IT4|Q96SP8|Q9BRC6|Q9H928|Q9NVK7	Nonsense_Mutation	SNP	ENST00000324096.4	hg19	CCDS32954.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.929511	0.92389	.	.	ENSG00000130479	ENST00000324096;ENST00000544059	.	.	.	3.88	3.88	0.44766	.	0.000000	0.44097	D	0.000494	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.2846	8.9029	0.35505	0.2231:0.7769:0.0:0.0	.	.	.	.	X	455;429	.	ENSP00000325313:R455X	R	+	1	2	MAP1S	17698556	0.890000	0.30428	0.071000	0.20095	0.110000	0.19582	1.758000	0.38410	1.700000	0.51204	0.491000	0.48974	CGA	.	.		0.721	MAP1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466027.1	NM_018174		T	17837556	C	T	17837556	4	4	259	1	0	0	0	0	0	1	0	0	9243	760	27	1	1381	1	MAP1S	19	17837556	Nonsense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	452629	17837556	41291427	802	37120										
SLC5A5	6528	hgsc.bcm.edu	37	chr19	17988801	17988801	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tcatcaaccaggtcggcctgTtcctgatcgtgtccagcgct	10	14	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:17988801T>C	ENST00000222248.3	+	7	1215	c.868T>C	c.(868-870)Ttc>Ctc	p.F290L		NM_000453.2	NP_000444.1	Q92911	SC5A5_HUMAN	solute carrier family 5 (sodium/iodide cotransporter), member 5	290					cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|iodide transport (GO:0015705)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	iodide transmembrane transporter activity (GO:0015111)|sodium:iodide symporter activity (GO:0008507)			NS(2)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|skin(3)	31						GGTCGGCCTGTTCCTGATCGT	0.622																																					p.F290L	Melanoma(65;1008 1708 7910 46650)	Atlas-SNP	.											.	SLC5A5	67	.	0			c.T868C						.						110	78	89					19																	17988801		2203	4300	6503	SO:0001583	missense	6528	exon7			GGCCTGTTCCTGA		CCDS12368.1	19p13.11	2013-07-19	2013-07-19		ENSG00000105641	ENSG00000105641		"Solute carriers"	11040	protein-coding gene	gene with protein product		601843	"solute carrier family 5 (sodium iodide symporter), member 5"			9231811	Standard	NM_000453		Approved	NIS	uc002nhr.4	Q92911		ENST00000222248.3:c.868T>C	chr19.hg19:g.17988801T>C	ENSP00000222248:p.Phe290Leu	82.0	0.0		75.0	4.0	NM_000453	O43702|Q2M335|Q9NYB6	Missense_Mutation	SNP	ENST00000222248.3	hg19	CCDS12368.1	.	.	.	.	.	.	.	.	.	.	T	15.56	2.869649	0.51588	.	.	ENSG00000105641	ENST00000222248	D	0.86497	-2.13	4.87	-1.41	0.08941	.	0.401940	0.29218	N	0.012800	T	0.62085	0.2399	N	0.04373	-0.215	0.27072	N	0.963304	B	0.18166	0.026	B	0.21708	0.036	T	0.53301	-0.8458	10	0.09843	T	0.71	.	1.687	0.02844	0.2579:0.0774:0.2656:0.3991	.	290	Q92911	SC5A5_HUMAN	L	290	ENSP00000222248:F290L	ENSP00000222248:F290L	F	+	1	0	SLC5A5	17849801	0.988000	0.35896	0.963000	0.40424	0.928000	0.56348	0.889000	0.28282	-0.595000	0.05828	0.454000	0.30748	TTC	.	.		0.622	SLC5A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466690.1			C	17988801	T	C	17988801	3	2	259	1	0	0	0	0	1	0	0	0	14683	1725	60	2	894	2	SLC5A5	19	17988801	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	151245	17988801	41140182	803	37121										
COMP	1311	hgsc.bcm.edu	37	chr19	18896349	18896349	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgttcattgtctgcacgatcTcccttccctgatggggtcaa	9	12	4	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:18896349T>C	ENST00000222271.2	-	15	1720	c.1676A>G	c.(1675-1677)gAg>gGg	p.E559G	COMP_ENST00000542601.2_Missense_Mutation_p.E526G|COMP_ENST00000425807.1_Missense_Mutation_p.E506G	NM_000095.2	NP_000086.2	P49747	COMP_HUMAN	cartilage oligomeric matrix protein	559	Mediates cell survival and induction of the IAP family of survival proteins.|TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|limb development (GO:0060173)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|protease binding (GO:0002020)			breast(6)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						CTGCACGATCTCCCTTCCCTG	0.642																																					p.E559G		Atlas-SNP	.											.	COMP	62	.	0			c.A1676G						.						82	84	83					19																	18896349		2203	4300	6503	SO:0001583	missense	1311	exon15			ACGATCTCCCTTC	L32137	CCDS12385.1	19p13.1	2008-02-05				ENSG00000105664			2227	protein-coding gene	gene with protein product	"thrombospondin-5"	600310	"cartilage oligomeric matrix protein (pseudoachondroplasia, epiphyseal dysplasia 1, multiple)"	PSACH, EDM1, EPD1		7713493, 8307576	Standard	NM_000095		Approved	MED, THBS5	uc002nke.3	P49747	OTTHUMG00000169318	ENST00000222271.2:c.1676A>G	chr19.hg19:g.18896349T>C	ENSP00000222271:p.Glu559Gly	136.0	0.0		156.0	7.0	NM_000095	B4DKJ3|O14592|Q16388|Q16389|Q2NL86|Q8N4T2	Missense_Mutation	SNP	ENST00000222271.2	hg19	CCDS12385.1	.	.	.	.	.	.	.	.	.	.	T	29.2	4.984908	0.93044	.	.	ENSG00000105664	ENST00000542601;ENST00000222271;ENST00000425807;ENST00000454701	D;D;D	0.97161	-4.27;-4.27;-4.27	4.6	4.6	0.57074	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Thrombospondin, C-terminal (2);	0.000000	0.85682	U	0.000000	D	0.98585	0.9527	M	0.91717	3.235	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99552	1.0966	10	0.87932	D	0	-47.6512	12.7731	0.57432	0.0:0.0:0.0:1.0	.	506;559	B4DKJ3;P49747	.;COMP_HUMAN	G	526;559;506;546	ENSP00000439156:E526G;ENSP00000222271:E559G;ENSP00000403792:E506G	ENSP00000222271:E559G	E	-	2	0	COMP	18757349	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	7.552000	0.82192	1.705000	0.51264	0.397000	0.26171	GAG	.	.		0.642	COMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403457.1	NM_000095		C	18896349	T	C	18896349	3	2	259	1	0	0	0	0	1	0	0	0	3726	1551	54	2	617	2	COMP	19	18896349	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	907548	18896349	40232634	804	37122										
DDX49	54555	hgsc.bcm.edu	37	chr19	19035101	19035101	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cttccccaccgtggctctgcActccatgatgaagcaggtga	10	14	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:19035101A>G	ENST00000247003.4	+	7	903	c.836A>G	c.(835-837)cAc>cGc	p.H279R	DDX49_ENST00000599156.1_3'UTR|AC002985.3_ENST00000596918.1_Intron|DDX49_ENST00000438170.2_Missense_Mutation_p.H172R	NM_019070.4	NP_061943.2	Q9Y6V7	DDX49_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 49	279	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.						ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	18			Epithelial(12;0.0289)			GTGGCTCTGCACTCCATGATG	0.627																																					p.H279R		Atlas-SNP	.											.	DDX49	37	.	0			c.A836G						.						95	56	69					19																	19035101		2203	4300	6503	SO:0001583	missense	54555	exon7			CTCTGCACTCCAT		CCDS12390.1	19p12	2008-02-05				ENSG00000105671		"DEAD-boxes"	18684	protein-coding gene	gene with protein product							Standard	NM_019070		Approved	FLJ10432	uc002nkq.2	Q9Y6V7		ENST00000247003.4:c.836A>G	chr19.hg19:g.19035101A>G	ENSP00000247003:p.His279Arg	188.0	0.0		145.0	6.0	NM_019070	E7ENA0|Q53FJ1|Q9BVQ8	Missense_Mutation	SNP	ENST00000247003.4	hg19	CCDS12390.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.302383	0.81136	.	.	ENSG00000105671	ENST00000247003;ENST00000438170	T;T	0.08102	3.13;3.13	5.03	5.03	0.67393	Helicase, C-terminal (3);	0.049846	0.85682	D	0.000000	T	0.38746	0.1052	M	0.93978	3.48	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.53041	-0.8494	10	0.87932	D	0	-22.6557	13.9201	0.63926	1.0:0.0:0.0:0.0	.	279;279	A8K7A1;Q9Y6V7	.;DDX49_HUMAN	R	279;172	ENSP00000247003:H279R;ENSP00000395377:H172R	ENSP00000247003:H279R	H	+	2	0	DDX49	18896101	1.000000	0.71417	0.998000	0.56505	0.972000	0.66771	8.927000	0.92846	1.899000	0.54978	0.402000	0.26972	CAC	.	.		0.627	DDX49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464593.1	NM_019070		G	19035101	A	G	19035101	3	3	259	1	0	0	0	0	1	0	0	0	4368	159	6	2	862	2	DDX49	19	19035101	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	138752	19035101	40093882	805	37123										
ZNF682	91120	hgsc.bcm.edu	37	chr19	20117129	20117129	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tcttcacatttgtagggtttCtctccagtgtgaattctctt	7	9	4	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:20117129C>A	ENST00000397165.2	-	4	1342	c.1182G>T	c.(1180-1182)gaG>gaT	p.E394D	ZNF682_ENST00000595736.1_Missense_Mutation_p.E318D|ZNF682_ENST00000596019.1_Intron|ZNF682_ENST00000358523.5_Missense_Mutation_p.E362D|ZNF682_ENST00000397162.1_Missense_Mutation_p.E362D|ZNF682_ENST00000597972.1_Missense_Mutation_p.E400D	NM_033196.2	NP_149973.1	O95780	ZN682_HUMAN	zinc finger protein 682	394					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	14						TGTAGGGTTTCTCTCCAGTGT	0.378																																					p.E394D		Atlas-SNP	.											ZNF682,NS,carcinoma,0,1	ZNF682	51	.	0			c.G1182T						.						62	67	65					19																	20117129		2127	4261	6388	SO:0001583	missense	91120	exon4			GGGTTTCTCTCCA	AC006539	CCDS42533.1, CCDS42534.1	19p12	2014-02-13			ENSG00000197124	ENSG00000197124		"Zinc fingers, C2H2-type", "-"	28857	protein-coding gene	gene with protein product							Standard	NM_033196		Approved	BC39498_3	uc002noq.3	O95780	OTTHUMG00000182650	ENST00000397165.2:c.1182G>T	chr19.hg19:g.20117129C>A	ENSP00000380351:p.Glu394Asp	33.0	0.0		45.0	2.0	NM_033196	B3KU64|E9PFJ5|Q96JV9	Missense_Mutation	SNP	ENST00000397165.2	hg19	CCDS42533.1	.	.	.	.	.	.	.	.	.	.	C	10.56	1.383808	0.25031	.	.	ENSG00000197124	ENST00000397165;ENST00000397162;ENST00000341262;ENST00000358523	T;T;T	0.26810	1.71;1.71;1.71	1.09	-0.0727	0.13738	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.18759	0.0450	L	0.33485	1.01	0.27686	N	0.946271	B	0.21520	0.057	B	0.30179	0.112	T	0.34304	-0.9834	9	0.72032	D	0.01	.	4.8624	0.13590	0.0:0.7293:0.0:0.2707	.	394	O95780	ZN682_HUMAN	D	394;362;63;362	ENSP00000380351:E394D;ENSP00000380348:E362D;ENSP00000351324:E362D	ENSP00000340236:E63D	E	-	3	2	ZNF682	19978129	0.998000	0.40836	0.897000	0.35233	0.885000	0.51271	0.420000	0.21263	0.488000	0.27723	0.491000	0.48974	GAG	.	.		0.378	ZNF682-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462888.1	NM_033196		A	20117129	C	A	20117129	3	1	259	1	0	0	0	0	1	0	0	0	18104	912	32	3	318	3	ZNF682	19	20117129	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	1082028	20117129	39011854	806	37124										
ZNF486	90649	hgsc.bcm.edu	37	chr19	20308359	20308359	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gcctttatgtacccctatacCcttactacacataagataat	3	12	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:20308359C>A	ENST00000335117.8	+	4	897	c.840C>A	c.(838-840)acC>acA	p.T280T	CTC-260E6.6_ENST00000585498.1_RNA|CTC-260E6.6_ENST00000586657.1_RNA|CTC-260E6.6_ENST00000593655.1_RNA	NM_052852.3	NP_443084.2	Q96H40	ZN486_HUMAN	zinc finger protein 486	280					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	11						ACCCCTATACCCTTACTACAC	0.363																																					p.T280T		Atlas-SNP	.											.	ZNF486	74	.	0			c.C840A						.						48	52	51					19																	20308359		2150	4277	6427	SO:0001819	synonymous_variant	90649	exon4			CTATACCCTTACT	BC008936	CCDS46029.1	19p12	2014-02-13	2003-12-16	2003-12-17	ENSG00000256229	ENSG00000256229		"Zinc fingers, C2H2-type", "-"	20807	protein-coding gene	gene with protein product			"KRAB domain only 2"	KRBO2			Standard	NM_052852		Approved	MGC2396	uc002nou.3	Q96H40	OTTHUMG00000179731	ENST00000335117.8:c.840C>A	chr19.hg19:g.20308359C>A		74.0	0.0		76.0	5.0	NM_052852	Q0VG00	Silent	SNP	ENST00000335117.8	hg19	CCDS46029.1																																																																																			.	.		0.363	ZNF486-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447843.2	NM_052852		A	20308359	C	A	20308359	2	1	259	1	0	0	0	0	0	0	0	1	17954	610	22	3		3	ZNF486	19	20308359	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	191230	20308359	38820624	807	37125										
ZNF208	7757	hgsc.bcm.edu	37	chr19	22156027	22156027	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttgtagggtttctcaccagtAtgaattctcttatgtttaat	7	6	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:22156027A>G	ENST00000397126.4	-	4	1957	c.1809T>C	c.(1807-1809)caT>caC	p.H603H	ZNF208_ENST00000601773.1_Intron|ZNF208_ENST00000599916.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	603					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				TCTCACCAGTATGAATTCTCT	0.363																																					p.H603H		Atlas-SNP	.											.	ZNF208	817	.	0			c.T1809C						.						51	54	53					19																	22156027		2088	4235	6323	SO:0001819	synonymous_variant	7757	exon4			ACCAGTATGAATT	BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"Zinc fingers, C2H2-type", "-"	12999	protein-coding gene	gene with protein product	"zinc finger protein 95"	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.1809T>C	chr19.hg19:g.22156027A>G		63.0	0.0		62.0	31.0	NM_007153		Silent	SNP	ENST00000397126.4	hg19	CCDS54240.1																																																																																			.	.		0.363	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		G	22156027	A	G	22156027	2	3	259	1	0	0	0	0	0	0	0	1	17781	446	16	2		2	ZNF208	19	22156027	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1847668	22156027	36972956	808	37126										
ZNF91	7644	hgsc.bcm.edu	37	chr19	23542731	23542731	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atttgtatggtttctctccaGtgtgcatcctcgtatgtcta	8	9	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:23542731G>T	ENST00000300619.7	-	4	3255	c.3050C>A	c.(3049-3051)aCt>aAt	p.T1017N	ZNF91_ENST00000397082.2_Missense_Mutation_p.T985N|ZNF91_ENST00000599743.1_Intron|ZNF91_ENST00000596528.1_5'Flank	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	1017					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				TTTCTCTCCAGTGTGCATCCT	0.383																																					p.T1017N		Atlas-SNP	.											.	ZNF91	349	.	0			c.C3050A						.						95	97	97					19																	23542731		2192	4296	6488	SO:0001583	missense	7644	exon4			TCTCCAGTGTGCA	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"Zinc fingers, C2H2-type", "-"	13166	protein-coding gene	gene with protein product		603971	"zinc finger protein 91 (HPF7, HTF10)"			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.3050C>A	chr19.hg19:g.23542731G>T	ENSP00000300619:p.Thr1017Asn	72.0	0.0		88.0	4.0	NM_003430	A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	hg19	CCDS42541.1	.	.	.	.	.	.	.	.	.	.	G	8.568	0.879416	0.17467	.	.	ENSG00000167232	ENST00000300619;ENST00000397082	T;T	0.26067	1.76;1.76	1.47	-0.478	0.12093	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.36524	0.0970	L	0.39147	1.195	0.27898	N	0.939069	D;D	0.76494	0.958;0.999	B;D	0.81914	0.368;0.995	T	0.25328	-1.0135	9	0.87932	D	0	.	8.2531	0.31739	0.0:0.3106:0.6894:0.0	.	985;1017	Q05481-2;Q05481	.;ZNF91_HUMAN	N	1017;985	ENSP00000300619:T1017N;ENSP00000380272:T985N	ENSP00000300619:T1017N	T	-	2	0	ZNF91	23334571	0.107000	0.21998	0.050000	0.19076	0.089000	0.18198	0.222000	0.17699	-0.184000	0.10567	0.175000	0.17021	ACT	.	.		0.383	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430		T	23542731	G	T	23542731	3	4	259	1	0	0	0	0	1	0	0	0	18215	1029	36	3	529	3	ZNF91	19	23542731	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1386704	23542731	35586252	809	37127										
ZNF675	171392	hgsc.bcm.edu	37	chr19	23836866	23836866	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agaactggttaaaggctttgCcacattcttcacatttgtag	8	8	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:23836866C>T	ENST00000359788.4	-	4	1037	c.869G>A	c.(868-870)gGc>gAc	p.G290D	ZNF675_ENST00000601935.1_Intron|ZNF675_ENST00000596211.1_Intron|ZNF675_ENST00000600313.1_Intron	NM_138330.2	NP_612203.2	Q8TD23	ZN675_HUMAN	zinc finger protein 675	290					bone resorption (GO:0045453)|cytokine-mediated signaling pathway (GO:0019221)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of interleukin-1-mediated signaling pathway (GO:2000660)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	DNA binding (GO:0003677)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				AAAGGCTTTGCCACATTCTTC	0.378																																					p.G290D		Atlas-SNP	.											.,1	ZNF675	88	.	0			c.G869A						.						52	56	55					19																	23836866		2202	4297	6499	SO:0001583	missense	171392	exon4			GCTTTGCCACATT		CCDS32981.1	19p12	2013-01-08						"Zinc fingers, C2H2-type", "-"	30768	protein-coding gene	gene with protein product	"TRAF6 inhibitory zinc finger"					11751921	Standard	NM_138330		Approved	TIZ, TBZF	uc002nri.3	Q8TD23		ENST00000359788.4:c.869G>A	chr19.hg19:g.23836866C>T	ENSP00000352836:p.Gly290Asp	44.0	1.0		64.0	4.0	NM_138330	Q8N211	Missense_Mutation	SNP	ENST00000359788.4	hg19	CCDS32981.1	.	.	.	.	.	.	.	.	.	.	.	8.427	0.847732	0.17034	.	.	ENSG00000197372	ENST00000359788	T	0.07444	3.19	0.916	0.916	0.19373	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12178	0.0296	L	0.43646	1.37	0.31650	N	0.646979	D	0.54772	0.968	P	0.52159	0.691	T	0.15752	-1.0426	9	0.52906	T	0.07	.	8.5828	0.33640	0.0:1.0:0.0:0.0	.	290	Q8TD23	ZN675_HUMAN	D	290	ENSP00000352836:G290D	ENSP00000352836:G290D	G	-	2	0	ZNF675	23628706	0.024000	0.19004	0.307000	0.25127	0.307000	0.27823	-0.013000	0.12678	0.300000	0.22699	0.305000	0.20034	GGC	.	.		0.378	ZNF675-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466433.1	NM_138330		T	23836866	C	T	23836866	3	4	259	1	0	0	0	0	1	0	0	0	18097	739	26	3	841	3	ZNF675	19	23836866	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	294135	23836866	35292117	810	37128										
CCDC123	84902	hgsc.bcm.edu	37	chr19	33370210	33370210	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctgtcctcgtgagtgtgtccTggagaagttctcggattctt	12	9	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:33370210T>C	ENST00000305768.5	-	19	2298	c.2210A>G	c.(2209-2211)cAg>cGg	p.Q737R	CTD-2085J24.4_ENST00000586628.2_lincRNA	NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	737					cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	35						GAGTGTGTCCTGGAGAAGTTC	0.517																																					p.Q737R		Atlas-SNP	.											.	CEP89	82	.	0			c.A2210G						.						170	166	167					19																	33370210		2203	4300	6503	SO:0001583	missense	84902	exon19			GTGTCCTGGAGAA	AL832158	CCDS32987.1	19q13.11	2014-02-20	2011-05-06	2011-05-06		ENSG00000121289			25907	protein-coding gene	gene with protein product		615470	"coiled-coil domain containing 123"	CCDC123		16395595	Standard	NM_032816		Approved	FLJ14640	uc002nty.3	Q96ST8		ENST00000305768.5:c.2210A>G	chr19.hg19:g.33370210T>C	ENSP00000306105:p.Gln737Arg	126.0	0.0		149.0	6.0	NM_032816	B9EGA6|Q8N5J8	Missense_Mutation	SNP	ENST00000305768.5	hg19	CCDS32987.1	.	.	.	.	.	.	.	.	.	.	T	9.127	1.010514	0.19277	.	.	ENSG00000121289	ENST00000305768	T	0.29655	1.56	5.12	1.84	0.25277	.	0.275893	0.30118	N	0.010374	T	0.25005	0.0607	L	0.54323	1.7	0.21473	N	0.999676	B	0.09022	0.002	B	0.11329	0.006	T	0.22487	-1.0215	10	0.20519	T	0.43	-7.482	9.1166	0.36762	0.0:0.2351:0.0:0.7649	.	737	Q96ST8	CEP89_HUMAN	R	737	ENSP00000306105:Q737R	ENSP00000306105:Q737R	Q	-	2	0	CEP89	38062050	0.287000	0.24315	0.492000	0.27490	0.031000	0.12232	0.756000	0.26419	0.369000	0.24510	-0.379000	0.06801	CAG	.	.		0.517	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816		C	33370210	T	C	33370210	3	2	259	1	0	0	0	0	1	0	0	0	2761	1580	55	2	145	2	CCDC123	19	33370210	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	9533344	33370210	25758773	811	37129										
WDR88	126248	hgsc.bcm.edu	37	chr19	33647326	33647326	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccatttcctgtgtacaagctCctgggataaaaacttaaaaa	6	9	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:33647326C>A	ENST00000355868.3	+	7	951	c.875C>A	c.(874-876)tCc>tAc	p.S292Y	WDR88_ENST00000361680.2_Missense_Mutation_p.S292Y	NM_173479.3	NP_775750.3	Q6ZMY6	WDR88_HUMAN	WD repeat domain 88	292										breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	25	Esophageal squamous(110;0.137)					TGTACAAGCTCCTGGGATAAA	0.478																																					p.S292Y		Atlas-SNP	.											.	WDR88	50	.	0			c.C875A						.						124	116	119					19																	33647326		2203	4300	6503	SO:0001583	missense	126248	exon7			CAAGCTCCTGGGA	BC031227	CCDS12429.1	19q13.11	2013-01-09	2007-04-04	2007-04-04		ENSG00000166359		"WD repeat domain containing"	26999	protein-coding gene	gene with protein product			"PQQ repeat and WD repeat domain containing"	PQWD		12477932	Standard	NM_173479		Approved		uc002nui.3	Q6ZMY6		ENST00000355868.3:c.875C>A	chr19.hg19:g.33647326C>A	ENSP00000348129:p.Ser292Tyr	85.0	0.0		91.0	4.0	NM_173479	Q8NEF8	Missense_Mutation	SNP	ENST00000355868.3	hg19	CCDS12429.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.295518	0.81025	.	.	ENSG00000166359	ENST00000355868;ENST00000361680	T;T	0.74421	-0.84;-0.84	5.59	5.59	0.84812	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.636153	0.16440	N	0.214330	D	0.90635	0.7063	H	0.94503	3.545	0.33014	D	0.52796	D	0.89917	1.0	D	0.97110	1.0	D	0.93738	0.7047	10	0.87932	D	0	.	18.2199	0.89898	0.0:1.0:0.0:0.0	.	292	Q6ZMY6	WDR88_HUMAN	Y	292	ENSP00000348129:S292Y;ENSP00000355148:S292Y	ENSP00000348129:S292Y	S	+	2	0	WDR88	38339166	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	5.550000	0.67268	2.639000	0.89480	0.555000	0.69702	TCC	.	.		0.478	WDR88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450840.1	NM_173479		A	33647326	C	A	33647326	3	1	259	1	0	0	0	0	1	0	0	0	17350	855	30	3	901	3	WDR88	19	33647326	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	277116	33647326	25481657	812	37130										
ZNF302	55900	hgsc.bcm.edu	37	chr19	35173713	35173713	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgatgtggctatagacttctCtcatgaagagtgggcatgcc	12	8	2	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:35173713C>G	ENST00000446502.2	+	4	381	c.173C>G	c.(172-174)tCt>tGt	p.S58C	ZNF302_ENST00000507959.1_Missense_Mutation_p.S14C|ZNF302_ENST00000423823.2_Missense_Mutation_p.S14C|ZNF302_ENST00000505365.2_Missense_Mutation_p.S14C|ZNF302_ENST00000509528.1_Intron|ZNF302_ENST00000505242.1_Missense_Mutation_p.S14C|ZNF302_ENST00000457781.2_Missense_Mutation_p.S14C			Q9NR11	ZN302_HUMAN	zinc finger protein 302	14	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(2)|lung(2)|skin(1)	6	all_lung(56;6.16e-07)|Lung NSC(56;9.71e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			ATAGACTTCTCTCATGAAGAG	0.438																																					p.S14C		Atlas-SNP	.											.	ZNF302	27	.	0			c.C41G						.						76	63	67					19																	35173713		1840	4053	5893	SO:0001583	missense	55900	exon3			ACTTCTCTCATGA	AF155656	CCDS46042.1, CCDS74330.1, CCDS74331.1, CCDS74332.1, CCDS74333.1	19q13.2	2013-01-08			ENSG00000089335	ENSG00000089335		"Zinc fingers, C2H2-type", "-"	13848	protein-coding gene	gene with protein product							Standard	NM_018675		Approved	ZNF327, ZNF135L, ZNF140L	uc002nvq.1	Q9NR11	OTTHUMG00000163329	ENST00000446502.2:c.173C>G	chr19.hg19:g.35173713C>G	ENSP00000396379:p.Ser58Cys	296.0	0.0		281.0	89.0	NM_018443	Q658J3|Q9BZD8|Q9P0J4	Missense_Mutation	SNP	ENST00000446502.2	hg19		.	.	.	.	.	.	.	.	.	.	C	12.70	2.015761	0.35606	.	.	ENSG00000089335	ENST00000502743;ENST00000506901;ENST00000457781;ENST00000505242;ENST00000505163;ENST00000423823;ENST00000507959;ENST00000446502;ENST00000505365	T;T;T;T;T;T;T;T;T	0.02944	4.1;4.1;4.1;4.1;4.1;4.1;4.1;4.1;4.1	1.39	1.39	0.22231	.	.	.	.	.	T	0.16471	0.0396	M	0.92122	3.275	0.22112	N	0.999352	D;P;P	0.89917	1.0;0.833;0.895	D;P;P	0.79108	0.992;0.638;0.658	T	0.03175	-1.1064	9	0.87932	D	0	.	6.0849	0.19962	0.0:1.0:0.0:0.0	.	14;58;14	B4DMN2;E7EVR1;Q9NR11-2	.;.;.	C	14;14;14;14;14;14;14;58;14	ENSP00000423460:S14C;ENSP00000424292:S14C;ENSP00000391067:S14C;ENSP00000421028:S14C;ENSP00000421696:S14C;ENSP00000405219:S14C;ENSP00000421201:S14C;ENSP00000396379:S58C;ENSP00000423235:S14C	ENSP00000405219:S14C	S	+	2	0	ZNF302	39865553	0.034000	0.19679	0.998000	0.56505	0.921000	0.55340	0.870000	0.28010	0.737000	0.32582	0.313000	0.20887	TCT	.	.		0.438	ZNF302-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000372731.1			G	35173713	C	G	35173713	3	3	259	1	0	0	0	0	1	0	0	0	17847	913	32	4	47	4	ZNF302	19	35173713	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	1526387	35173713	23955270	813	37131										
CD22	933	hgsc.bcm.edu	37	chr19	35835730	35835730	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggtctctcctttctccacccAgatagcccggagaccatcgg	9	16	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:35835730A>G	ENST00000085219.5	+	10	2101		c.e10-1		CD22_ENST00000544992.2_Splice_Site|CD22_ENST00000270311.6_Splice_Site|CD22_ENST00000341773.6_Splice_Site|MIR5196_ENST00000578146.1_RNA|CD22_ENST00000419549.2_Splice_Site|CD22_ENST00000594250.1_Splice_Site|CD22_ENST00000536635.2_Splice_Site	NM_001771.3	NP_001762.2	P20273	CD22_HUMAN	CD22 molecule						cell adhesion (GO:0007155)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			breast(2)|endometrium(2)|kidney(3)|large_intestine(14)|lung(21)|ovary(5)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	54	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.83e-19)|OV - Ovarian serous cystadenocarcinoma(14;3.19e-18)|all cancers(14;3.41e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			TTCTCCACCCAGATAGCCCGG	0.612																																					.	Ovarian(42;1009 1133 23674 26041)	Atlas-SNP	.											.	CD22	129	.	0			c.2036-2A>G						.						114	119	117					19																	35835730		2203	4300	6503	SO:0001630	splice_region_variant	933	exon10			CCACCCAGATAGC	X52785	CCDS12457.1, CCDS54247.1, CCDS54248.1, CCDS54249.1, CCDS62634.1	19q13.1	2013-01-29	2006-03-28		ENSG00000012124	ENSG00000012124		"CD molecules", "Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1643	protein-coding gene	gene with protein product	"sialic acid binding Ig-like lectin 2"	107266	"CD22 antigen"			8496602, 1691828	Standard	NM_001185099		Approved	SIGLEC-2, SIGLEC2	uc010edt.3	P20273		ENST00000085219.5:c.2036-1A>G	chr19.hg19:g.35835730A>G		82.0	0.0		78.0	4.0	NM_001185100	F5GYU4|F5H7U3|O95699|O95701|O95702|O95703|Q01665|Q32M46|Q92872|Q92873|Q9UQA6|Q9UQA7|Q9UQA8|Q9UQA9|Q9UQB0|Q9Y2A6	Splice_Site	SNP	ENST00000085219.5	hg19	CCDS12457.1	.	.	.	.	.	.	.	.	.	.	A	13.09	2.133854	0.37630	.	.	ENSG00000012124	ENST00000085219;ENST00000536635;ENST00000341773;ENST00000544992;ENST00000270311;ENST00000419549	.	.	.	5.25	5.25	0.73442	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.5374	0.50645	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CD22	40527570	0.996000	0.38824	0.932000	0.37286	0.434000	0.31775	4.138000	0.58017	1.995000	0.58328	0.383000	0.25322	.	.	.		0.612	CD22-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466099.1	NM_001771	Intron	G	35835730	A	G	35835730	5	3	259	1	0	0	0	0	0	0	1	0	2987	202	7	2	2068	2	CD22	19	35835730	Splice_Site	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	662017	35835730	23293253	814	37132										
ZBTB32	27033	hgsc.bcm.edu	37	chr19	36206306	36206306	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cttggttggtggggggccagCctgccctgtggagcatcctg	17	11	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:36206306C>A	ENST00000392197.2	+	3	1096	c.778C>A	c.(778-780)Cct>Act	p.P260T	KMT2B_ENST00000222270.7_5'Flank|KMT2B_ENST00000420124.1_5'Flank|KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000341701.1_5'Flank|ZBTB32_ENST00000262630.3_Missense_Mutation_p.P260T			Q9Y2Y4	ZBT32_HUMAN	zinc finger and BTB domain containing 32	260					DNA repair (GO:0006281)|hemopoiesis (GO:0030097)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of cytokine production (GO:0001817)|T cell proliferation (GO:0042098)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			large_intestine(5)|lung(1)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	14	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GGGGGGCCAGCCTGCCCTGTG	0.672																																					p.P260T		Atlas-SNP	.											.	ZBTB32	33	.	0			c.C778A						.						41	44	43					19																	36206306		2201	4297	6498	SO:0001583	missense	27033	exon2			GGCCAGCCTGCCC	AF130255	CCDS12471.1	19q13.1	2013-01-08			ENSG00000011590	ENSG00000011590		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	16763	protein-coding gene	gene with protein product	"repressor of GATA"	605859				10572087	Standard	XM_005258739		Approved	TZFP, FAZF, FAXF, Rog, ZNF538	uc002oay.3	Q9Y2Y4	OTTHUMG00000048118	ENST00000392197.2:c.778C>A	chr19.hg19:g.36206306C>A	ENSP00000376035:p.Pro260Thr	80.0	0.0		34.0	8.0	NM_014383	Q8WVP2	Missense_Mutation	SNP	ENST00000392197.2	hg19	CCDS12471.1	.	.	.	.	.	.	.	.	.	.	C	15.25	2.779130	0.49891	.	.	ENSG00000011590	ENST00000262630;ENST00000392197	T;T	0.09723	2.95;2.95	5.33	-0.725	0.11174	.	0.314536	0.23405	N	0.048535	T	0.06280	0.0162	L	0.27053	0.805	0.26342	N	0.977351	B	0.34103	0.437	B	0.34590	0.186	T	0.25882	-1.0119	10	0.48119	T	0.1	-0.6659	4.803	0.13307	0.0:0.5096:0.1541:0.3363	.	260	Q9Y2Y4	ZBT32_HUMAN	T	260	ENSP00000262630:P260T;ENSP00000376035:P260T	ENSP00000262630:P260T	P	+	1	0	ZBTB32	40898146	0.001000	0.12720	1.000000	0.80357	0.995000	0.86356	-0.165000	0.09968	0.203000	0.20529	0.655000	0.94253	CCT	.	.		0.672	ZBTB32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109491.3	NM_014383		A	36206306	C	A	36206306	3	1	259	1	0	0	0	0	1	0	0	0	17550	739	26	3	780	3	ZBTB32	19	36206306	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	370576	36206306	22922677	815	37133										
ZNF461	92283	hgsc.bcm.edu	37	chr19	37134755	37134755	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tattgtgaaatccccaagttTtccatgtacctacatggaaa	6	9	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:37134755T>C	ENST00000588268.1	-	5	469	c.242A>G	c.(241-243)aAa>aGa	p.K81R	ZNF461_ENST00000360357.4_Intron|ZNF461_ENST00000540605.2_5'Flank	NM_153257.2	NP_694989.2	Q8TAF7	ZN461_HUMAN	zinc finger protein 461	81					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(4)|lung(17)|prostate(1)|urinary_tract(2)	29	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			tccccaagttttccatgtacc	0.254																																					p.K81R		Atlas-SNP	.											.	ZNF461	73	.	0			c.A242G						.						96	83	87					19																	37134755		915	2073	2988	SO:0001583	missense	92283	exon5			CAAGTTTTCCATG	BX649031	CCDS54257.1, CCDS74348.1	19q13.13	2013-01-08				ENSG00000197808		"Zinc fingers, C2H2-type", "-"	21629	protein-coding gene	gene with protein product		608640				11579202, 15004467	Standard	XM_005259402		Approved	GIOT-1, MGC33911	uc002oem.3	Q8TAF7		ENST00000588268.1:c.242A>G	chr19.hg19:g.37134755T>C	ENSP00000467931:p.Lys81Arg	96.0	0.0		92.0	4.0	NM_153257	A8K9W9|Q6VSF7|Q9ULZ8	Missense_Mutation	SNP	ENST00000588268.1	hg19	CCDS54257.1	.	.	.	.	.	.	.	.	.	.	T	7.933	0.740996	0.15642	.	.	ENSG00000197808	ENST00000396893;ENST00000396892	.	.	.	0.625	0.625	0.17665	.	.	.	.	.	T	0.22003	0.0530	N	0.12961	0.28	0.25117	N	0.990676	P	0.34587	0.458	B	0.39152	0.292	T	0.23655	-1.0182	7	0.33940	T	0.23	.	.	.	.	.	81	Q8TAF7	ZN461_HUMAN	R	81;16	.	ENSP00000380101:K16R	K	-	2	0	ZNF461	41826595	0.568000	0.26635	0.281000	0.24762	0.595000	0.36748	0.533000	0.23082	0.488000	0.27723	0.164000	0.16699	AAA	.	.		0.254	ZNF461-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453202.1	NM_153257		C	37134755	T	C	37134755	3	2	259	1	0	0	0	0	1	0	0	0	17940	1841	64	2	1457	2	ZNF461	19	37134755	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	928449	37134755	21994228	816	37134										
RYR1	6261	hgsc.bcm.edu	37	chr19	39016021	39016021	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gaagaagcgccggggggaccGgtactctgtgcagacgtcac	16	11	2	2	rs369422480		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:39016021G>T	ENST00000359596.3	+	71	10505	c.10505G>T	c.(10504-10506)cGg>cTg	p.R3502L	RYR1_ENST00000355481.4_Missense_Mutation_p.R3497L|AC067969.1_ENST00000597015.1_RNA|RYR1_ENST00000360985.3_Missense_Mutation_p.R3502L			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	3502					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CGGGGGGACCGGTACTCTGTG	0.622																																					p.R3502L		Atlas-SNP	.											.	RYR1	708	.	0			c.G10505T						.						111	115	113					19																	39016021		2203	4300	6503	SO:0001583	missense	6261	exon71			GGGACCGGTACTC	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.10505G>T	chr19.hg19:g.39016021G>T	ENSP00000352608:p.Arg3502Leu	102.0	0.0		98.0	4.0	NM_000540	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	G	10.45	1.355030	0.24512	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985;ENST00000538206	D;D;D	0.96967	-4.18;-4.19;-4.18	4.3	4.3	0.51218	.	0.000000	0.64402	U	0.000003	D	0.91415	0.7291	N	0.26042	0.785	0.46749	D	0.999187	B;B;B	0.25809	0.135;0.135;0.083	B;B;B	0.22753	0.041;0.041;0.018	D	0.88302	0.2950	10	0.18710	T	0.47	.	13.1415	0.59438	0.0:0.0:0.8396:0.1604	.	3502;3497;3502	P21817-3;P21817-2;P21817	.;.;RYR1_HUMAN	L	3502;3497;3502;422	ENSP00000352608:R3502L;ENSP00000347667:R3497L;ENSP00000354254:R3502L	ENSP00000347667:R3497L	R	+	2	0	RYR1	43707861	1.000000	0.71417	1.000000	0.80357	0.324000	0.28378	7.503000	0.81632	2.379000	0.81126	0.655000	0.94253	CGG	.	.		0.622	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			T	39016021	G	T	39016021	3	4	259	1	0	0	0	0	1	0	0	0	13783	1116	39	1	10787	1	RYR1	19	39016021	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1881266	39016021	20112962	817	37135										
IL29	282618	hgsc.bcm.edu	37	chr19	39788656	39788656	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gctggccctgacgctgaaggTcctggaggccgctgctggcc	16	14	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:39788656T>C	ENST00000333625.2	+	3	399	c.302T>C	c.(301-303)gTc>gCc	p.V101A		NM_172140.1	NP_742152.1	Q8IU54	IFNL1_HUMAN	interferon, lambda 1	101					defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|negative regulation of cell proliferation (GO:0008285)|negative regulation of interleukin-13 production (GO:0032696)|negative regulation of interleukin-5 production (GO:0032714)|negative regulation of memory T cell differentiation (GO:0043381)|negative regulation of T cell differentiation (GO:0045581)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of immune response (GO:0050778)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|interleukin-28 receptor complex (GO:0032002)	interleukin-28 receptor binding (GO:0032003)|receptor binding (GO:0005102)										ACGCTGAAGGTCCTGGAGGCC	0.642																																					p.V101A		Atlas-SNP	.											.	.	.	.	0			c.T302C						.						51	53	53					19																	39788656		2203	4300	6503	SO:0001583	missense	282618	exon3			TGAAGGTCCTGGA	AY129150	CCDS12531.1	19q13.13	2014-05-22	2012-11-26	2012-11-26	ENSG00000182393	ENSG00000182393		"Interferons"	18363	protein-coding gene	gene with protein product		607403	"interleukin 29", "interleukin 29 (interferon, lambda 1)"	IL29			Standard	NM_172140		Approved	IL-29	uc002okv.3	Q8IU54		ENST00000333625.2:c.302T>C	chr19.hg19:g.39788656T>C	ENSP00000329991:p.Val101Ala	114.0	0.0		117.0	5.0	NM_172140	A0AV25|Q17R34	Missense_Mutation	SNP	ENST00000333625.2	hg19	CCDS12531.1	.	.	.	.	.	.	.	.	.	.	T	11.92	1.782812	0.31502	.	.	ENSG00000182393	ENST00000333625	T	0.48836	0.8	4.56	4.56	0.56223	.	0.000000	0.56097	D	0.000031	T	0.65739	0.2720	M	0.84326	2.69	0.09310	N	1	D	0.71674	0.998	D	0.66847	0.947	T	0.60439	-0.7263	10	0.87932	D	0	-17.9068	7.8105	0.29228	0.1857:0.0:0.0:0.8143	.	101	Q8IU54	IL29_HUMAN	A	101	ENSP00000329991:V101A	ENSP00000329991:V101A	V	+	2	0	IL29	44480496	0.988000	0.35896	0.219000	0.23793	0.069000	0.16628	1.541000	0.36126	1.843000	0.53566	0.260000	0.18958	GTC	.	.		0.642	IFNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463834.1	NM_172140		C	39788656	T	C	39788656	3	2	259	1	0	0	0	0	1	0	0	0	7694	1667	58	2	312	2	IL29	19	39788656	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	772635	39788656	19340327	818	37136										
FCGBP	8857	hgsc.bcm.edu	37	chr19	40433822	40433822	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acattcctggctgaggtgccGgggggtgtgagcacaaaata	15	8	0	2	rs375117067		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:40433822G>A	ENST00000221347.6	-	2	454	c.447C>T	c.(445-447)ccC>ccT	p.P149P		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	149	IgGFc-binding.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			CTGAGGTGCCGGGGGGTGTGA	0.607													G|||	1	0.000199681	0	0	5008	,	,		19391	0		0	False		,,,				2504	0.001				p.P149P		Atlas-SNP	.											.	FCGBP	416	.	0			c.C447T						.	G		0,4406		0,0,2203	50	49	49		447	-8.3	0	19		49	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	FCGBP	NM_003890.2		0,3,6500	AA,AG,GG		0.0349,0.0,0.0231		149/5406	40433822	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	8857	exon2			GGTGCCGGGGGGT	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.447C>T	chr19.hg19:g.40433822G>A		82.0	0.0		60.0	4.0	NM_003890	O95784	Silent	SNP	ENST00000221347.6	hg19	CCDS12546.1																																																																																			.	.		0.607	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		A	40433822	G	A	40433822	2	1	259	1	0	0	0	0	0	0	0	1	5786	1103	39	1		1	FCGBP	19	40433822	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	645166	40433822	18695161	819	37137										
PSMC4	5704	hgsc.bcm.edu	37	chr19	40480515	40480515	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggaggccgtggagctcccgcTcacgcatttcgagctctaca	12	14	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:40480515T>C	ENST00000157812.2	+	5	752	c.554T>C	c.(553-555)cTc>cCc	p.L185P	PSMC4_ENST00000455878.2_Missense_Mutation_p.L154P	NM_006503.3|NM_153001.2	NP_006494.1|NP_694546.1	P43686	PRS6B_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 4	185				L -> V (in Ref. 4; AAC32612). {ECO:0000305}.	anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|blastocyst development (GO:0001824)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|inclusion body (GO:0016234)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1)	19	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					GAGCTCCCGCTCACGCATTTC	0.627																																					p.L185P	Colon(105;1478 1543 4034 6132 38638)	Atlas-SNP	.											.	PSMC4	48	.	0			c.T554C						.						55	59	58					19																	40480515		2203	4300	6503	SO:0001583	missense	5704	exon5			TCCCGCTCACGCA	U27515	CCDS12547.1, CCDS46076.1	19q13.11-q13.13	2010-04-21			ENSG00000013275	ENSG00000013275		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9551	protein-coding gene	gene with protein product	"protease 26S subunit 6", "Tat-binding protein 7", "MB67 interacting protein"	602707		MIP224		9473509, 8603043	Standard	NM_006503		Approved	TBP7, S6, MGC8570, MGC13687, MGC23214, TBP-7	uc002omq.4	P43686		ENST00000157812.2:c.554T>C	chr19.hg19:g.40480515T>C	ENSP00000157812:p.Leu185Pro	94.0	0.0		62.0	4.0	NM_006503	Q96FV5|Q9UBM3|Q9UEX3	Missense_Mutation	SNP	ENST00000157812.2	hg19	CCDS12547.1	.	.	.	.	.	.	.	.	.	.	t	15.52	2.856524	0.51376	.	.	ENSG00000013275	ENST00000157812;ENST00000455878	D;D	0.95622	-3.76;-3.76	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	D	0.98163	0.9393	M	0.93720	3.45	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.99184	1.0868	10	0.87932	D	0	-5.5019	13.1587	0.59533	0.0:0.0:0.0:1.0	.	154;185	P43686-2;P43686	.;PRS6B_HUMAN	P	185;154	ENSP00000157812:L185P;ENSP00000413869:L154P	ENSP00000157812:L185P	L	+	2	0	PSMC4	45172355	1.000000	0.71417	0.042000	0.18584	0.068000	0.16541	6.066000	0.71185	1.986000	0.57962	0.459000	0.35465	CTC	.	.		0.627	PSMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462485.1	NM_006503		C	40480515	T	C	40480515	3	2	259	1	0	0	0	0	1	0	0	0	12701	1551	54	2	572	2	PSMC4	19	40480515	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	46693	40480515	18648468	820	37138										
CNTD2	79935	hgsc.bcm.edu	37	chr19	40732473	40732473	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agcgagactctgcaaaggagAgggcctgggggcccagcgcc	17	12	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:40732473A>G	ENST00000430325.2	-	1	124	c.76T>C	c.(76-78)Tct>Cct	p.S26P	CNTD2_ENST00000433940.1_Missense_Mutation_p.S26P|CNTD2_ENST00000513948.1_5'Flank	NM_024877.3	NP_079153.2	Q9H8S5	CNTD2_HUMAN	cyclin N-terminal domain containing 2	26					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)					lung(1)|prostate(1)	2						TGCAAAGGAGAGGGCCTGGGG	0.706																																					p.S26P		Atlas-SNP	.											.	CNTD2	22	.	0			c.T76C						.						8	11	10					19																	40732473		2172	4249	6421	SO:0001583	missense	79935	exon1			AAGGAGAGGGCCT	AK023327	CCDS12551.1, CCDS12551.2	19q13.2	2014-07-03				ENSG00000105219			25805	protein-coding gene	gene with protein product	"cyclin P"					11237006	Standard	NM_024877		Approved	FLJ13265, CCNP	uc010xvi.2	Q9H8S5		ENST00000430325.2:c.76T>C	chr19.hg19:g.40732473A>G	ENSP00000396755:p.Ser26Pro	121.0	0.0		112.0	7.0	NM_024877	B4DX65	Missense_Mutation	SNP	ENST00000430325.2	hg19	CCDS12551.2	.	.	.	.	.	.	.	.	.	.	A	13.84	2.358236	0.41801	.	.	ENSG00000105219	ENST00000430325;ENST00000433940	T	0.35236	1.32	4.31	3.21	0.36854	.	0.988702	0.08230	N	0.977802	T	0.33731	0.0873	.	.	.	0.09310	N	1	P	0.50943	0.94	P	0.44860	0.462	T	0.21759	-1.0236	9	0.62326	D	0.03	-25.408	6.5989	0.22689	0.7871:0.0:0.0:0.2129	.	26	B4DX65	.	P	26	ENSP00000396755:S26P	ENSP00000221818:S26P	S	-	1	0	CNTD2	45424313	0.000000	0.05858	0.008000	0.14137	0.093000	0.18481	-0.211000	0.09332	1.938000	0.56188	0.459000	0.35465	TCT	.	.		0.706	CNTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360785.1	NM_024877		G	40732473	A	G	40732473	3	3	259	1	0	0	0	0	1	0	0	0	3638	304	11	2	867	2	CNTD2	19	40732473	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	251958	40732473	18396510	821	37139										
AKT2	208	hgsc.bcm.edu	37	chr19	40761108	40761108	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gaaggtcctctcgatgactgTggtccactgcaggcagcgta	13	11	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:40761108T>C	ENST00000392038.2	-	4	542	c.244A>G	c.(244-246)Aca>Gca	p.T82A	AKT2_ENST00000424901.1_Missense_Mutation_p.T82A|AKT2_ENST00000311278.6_Missense_Mutation_p.T82A|AKT2_ENST00000579047.1_Missense_Mutation_p.T20A	NM_001243027.1|NM_001243028.1|NM_001626.4	NP_001229956.1|NP_001229957.1|NP_001617.1	P31751	AKT2_HUMAN	v-akt murine thymoma viral oncogene homolog 2	82	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				activation of Ral GTPase activity (GO:0032859)|apoptotic process (GO:0006915)|carbohydrate transport (GO:0008643)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|fat cell differentiation (GO:0045444)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|insulin receptor signaling pathway (GO:0008286)|intracellular protein transmembrane transport (GO:0065002)|mammary gland epithelial cell differentiation (GO:0060644)|membrane organization (GO:0061024)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|peripheral nervous system myelin maintenance (GO:0032287)|positive regulation of cell motility (GO:2000147)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)|protein localization to plasma membrane (GO:0072659)|regulation of cell cycle arrest (GO:0071156)|regulation of cell migration (GO:0030334)|regulation of translation (GO:0006417)|signal transduction (GO:0007165)	cell cortex (GO:0005938)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|kidney(3)|large_intestine(9)|lung(10)|prostate(2)|skin(1)	27			Lung(22;0.000499)			TCGATGACTGTGGTCCACTGC	0.602			A		"ovarian, pancreatic "																																p.T82A		Atlas-SNP	.		Dom	yes		19	19q13.1-q13.2	208	v-akt murine thymoma viral oncogene homolog 2		E	.	AKT2	53	.	0			c.A244G						.						135	130	131					19																	40761108		2203	4300	6503	SO:0001583	missense	208	exon4			TGACTGTGGTCCA	M77198	CCDS12552.1	19q13.1-q13.2	2013-01-10			ENSG00000105221	ENSG00000105221	2.7.11.1	"Pleckstrin homology (PH) domain containing"	392	protein-coding gene	gene with protein product		164731				1409633	Standard	NM_001626		Approved		uc002onf.3	P31751	OTTHUMG00000137375	ENST00000392038.2:c.244A>G	chr19.hg19:g.40761108T>C	ENSP00000375892:p.Thr82Ala	138.0	0.0		121.0	6.0	NM_001626	B2RBD8|Q05BV0|Q0VAN0|Q0VAN1|Q68GC0	Missense_Mutation	SNP	ENST00000392038.2	hg19	CCDS12552.1	.	.	.	.	.	.	.	.	.	.	T	13.60	2.284485	0.40394	.	.	ENSG00000105221	ENST00000392038;ENST00000358335;ENST00000424901;ENST00000311278;ENST00000537834;ENST00000452077;ENST00000392037;ENST00000416362;ENST00000423127;ENST00000456441;ENST00000416994	T;T;T;T;T;T;T;T;T	0.46819	0.86;0.86;0.86;0.86;0.86;0.86;0.86;0.86;0.86	4.71	4.71	0.59529	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.107611	0.64402	D	0.000009	T	0.62332	0.2419	M	0.90542	3.125	0.80722	D	1	B;B;P;B	0.39480	0.217;0.403;0.675;0.201	P;B;B;B	0.44772	0.46;0.2;0.345;0.261	T	0.70706	-0.4798	10	0.66056	D	0.02	.	13.152	0.59494	0.0:0.0:0.0:1.0	.	82;20;82;82	B7Z8Z9;B4DG79;Q0VAN0;P31751	.;.;.;AKT2_HUMAN	A	82;81;82;82;82;82;82;82;82;82;82	ENSP00000375892:T82A;ENSP00000399532:T82A;ENSP00000309428:T82A;ENSP00000404083:T82A;ENSP00000375891:T82A;ENSP00000407999:T82A;ENSP00000403842:T82A;ENSP00000396532:T82A;ENSP00000392458:T82A	ENSP00000309428:T82A	T	-	1	0	AKT2	45452948	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	3.106000	0.50322	1.770000	0.52166	0.482000	0.46254	ACA	.	.		0.602	AKT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268029.1	NM_001626		C	40761108	T	C	40761108	3	2	259	1	0	0	0	0	1	0	0	0	480	1696	59	2	1245	2	AKT2	19	40761108	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	28635	40761108	18367875	822	37140										
C19orf47	126526	hgsc.bcm.edu	37	chr19	40832372	40832372	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	caggaacagccaggctctccTcctcccggcgggccagggct	13	17	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:40832372T>C	ENST00000582783.1	-	7	584	c.572A>G	c.(571-573)gAg>gGg	p.E191G	C19orf47_ENST00000392035.2_Missense_Mutation_p.E124G	NM_001256440.1	NP_001243369.1	Q8N9M1	CS047_HUMAN	chromosome 19 open reading frame 47	191						nucleus (GO:0005634)				endometrium(5)|kidney(2)|lung(7)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	20			Lung(22;0.000636)			CAGGCTCTCCTCCTCCCGGCG	0.632																																					p.E191G		Atlas-SNP	.											.	C19orf47	61	.	0			c.A572G						.						53	43	46					19																	40832372		2203	4300	6503	SO:0001583	missense	126526	exon7			CTCTCCTCCTCCC	AL834131	CCDS58662.1	19q13.2	2012-07-20			ENSG00000160392	ENSG00000160392			26723	protein-coding gene	gene with protein product						12477932	Standard	NM_001256440		Approved	FLJ36888	uc002oni.5	Q8N9M1	OTTHUMG00000179028	ENST00000582783.1:c.572A>G	chr19.hg19:g.40832372T>C	ENSP00000463159:p.Glu191Gly	93.0	0.0		76.0	4.0	NM_001256440	Q8IZ33|Q8N0V9	Missense_Mutation	SNP	ENST00000582783.1	hg19	CCDS58662.1	.	.	.	.	.	.	.	.	.	.	T	19.23	3.787564	0.70337	.	.	ENSG00000160392	ENST00000357884;ENST00000392035	D	0.99523	-6.08	5.54	5.54	0.83059	.	0.202588	0.51477	D	0.000097	D	0.98927	0.9636	M	0.67953	2.075	0.49798	D	0.999826	P	0.47545	0.897	P	0.51615	0.675	D	0.98427	1.0580	10	0.34782	T	0.22	-19.27	11.1937	0.48700	0.0:0.0:0.1537:0.8463	.	191	Q8N9M1	CS047_HUMAN	G	191;124	ENSP00000375889:E124G	ENSP00000350556:E191G	E	-	2	0	C19orf47	45524212	0.999000	0.42202	1.000000	0.80357	0.662000	0.39071	1.360000	0.34125	2.115000	0.64714	0.379000	0.24179	GAG	.	.		0.632	C19orf47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444488.1	NM_178830		C	40832372	T	C	40832372	3	2	259	1	0	0	0	0	1	0	0	0	1932	1551	54	2	708	2	C19orf47	19	40832372	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	71264	40832372	18296611	823	37141										
SHKBP1	92799	hgsc.bcm.edu	37	chr19	41094616	41094616	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agcccggctccaccccactcGcttcctttaagatcctggct	7	18	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:41094616G>T	ENST00000291842.5	+	14	1472	c.1423G>T	c.(1423-1425)Gct>Tct	p.A475S	SHKBP1_ENST00000600733.1_Missense_Mutation_p.A450S|SHKBP1_ENST00000597649.1_3'UTR	NM_138392.3	NP_612401.2	Q8TBC3	SHKB1_HUMAN	SH3KBP1 binding protein 1	475					protein homooligomerization (GO:0051260)					breast(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(3)|urinary_tract(1)	29			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			CACCCCACTCGCTTCCTTTAA	0.617																																					p.A475S		Atlas-SNP	.											.	SHKBP1	68	.	0			c.G1423T						.						96	92	93					19																	41094616		2203	4300	6503	SO:0001583	missense	92799	exon14			CCACTCGCTTCCT	AF258553	CCDS12560.1	19q13.2	2013-01-10				ENSG00000160410		"WD repeat domain containing"	19214	protein-coding gene	gene with protein product						11152963	Standard	NM_138392		Approved	PP203, Sb1	uc002oob.3	Q8TBC3		ENST00000291842.5:c.1423G>T	chr19.hg19:g.41094616G>T	ENSP00000291842:p.Ala475Ser	123.0	0.0		88.0	5.0	NM_138392	Q8N2I6|Q8WY93|Q96IB8	Missense_Mutation	SNP	ENST00000291842.5	hg19	CCDS12560.1	.	.	.	.	.	.	.	.	.	.	G	14.36	2.511755	0.44660	.	.	ENSG00000160410	ENST00000291842;ENST00000446701	T	0.45668	0.89	4.21	3.17	0.36434	WD40 repeat-like-containing domain (1);	0.126948	0.52532	D	0.000071	T	0.51041	0.1651	L	0.60845	1.875	0.44136	D	0.996924	D;P;B;B;B;B	0.59767	0.986;0.812;0.084;0.207;0.195;0.086	P;P;B;B;B;B	0.55871	0.786;0.48;0.028;0.05;0.022;0.028	T	0.52779	-0.8530	10	0.56958	D	0.05	-15.8193	11.1437	0.48417	0.0927:0.0:0.9073:0.0	.	353;255;398;312;475;475	B4DLI0;B4DUW2;B4DUV2;B3KVX8;B2R6W9;Q8TBC3	.;.;.;.;.;SHKB1_HUMAN	S	475;255	ENSP00000291842:A475S	ENSP00000291842:A475S	A	+	1	0	SHKBP1	45786456	0.995000	0.38212	0.311000	0.25182	0.870000	0.49936	2.654000	0.46699	0.989000	0.38761	0.462000	0.41574	GCT	.	.		0.617	SHKBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462613.2	NM_138392		T	41094616	G	T	41094616	3	4	259	1	0	0	0	0	1	0	0	0	14299	1087	38	1	1477	1	SHKBP1	19	41094616	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	262244	41094616	18034367	824	37142										
ETHE1	23474	hgsc.bcm.edu	37	chr19	44012185	44012185	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gccgagggttcagagtcctcTcctcctccacggtggacact	11	15	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:44012185T>C	ENST00000292147.2	-	6	689	c.623A>G	c.(622-624)gAg>gGg	p.E208G	ETHE1_ENST00000600651.1_Missense_Mutation_p.E208G	NM_014297.3	NP_055112.2	O95571	ETHE1_HUMAN	ethylmalonic encephalopathy 1	208					cellular nitrogen compound metabolic process (GO:0034641)|glutathione metabolic process (GO:0006749)|hydrogen sulfide metabolic process (GO:0070813)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	iron ion binding (GO:0005506)|sulfur dioxygenase activity (GO:0050313)			central_nervous_system(1)|liver(1)|lung(2)|upper_aerodigestive_tract(1)	5		Prostate(69;0.0153)				CAGAGTCCTCTCCTCCTCCAC	0.557																																					p.E208G		Atlas-SNP	.											.	ETHE1	7	.	0			c.A623G						.						74	59	64					19																	44012185		2203	4300	6503	SO:0001583	missense	23474	exon6			GTCCTCTCCTCCT		CCDS12622.1	19q13.32	2014-06-20				ENSG00000105755	1.13.11.18		23287	protein-coding gene	gene with protein product		608451				19136963	Standard	NM_014297		Approved	YF13H12, HSCO	uc002owp.3	O95571		ENST00000292147.2:c.623A>G	chr19.hg19:g.44012185T>C	ENSP00000292147:p.Glu208Gly	85.0	0.0		79.0	4.0	NM_014297	Q96HR0|Q9H001	Missense_Mutation	SNP	ENST00000292147.2	hg19	CCDS12622.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.608626	0.87258	.	.	ENSG00000105755	ENST00000292147	D	0.97066	-4.23	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	D	0.98820	0.9602	H	0.95365	3.66	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.993;0.997	D	0.99490	1.0950	10	0.87932	D	0	-8.9073	13.0221	0.58794	0.0:0.0:0.0:1.0	.	181;208	B2RCZ7;O95571	.;ETHE1_HUMAN	G	208	ENSP00000292147:E208G	ENSP00000292147:E208G	E	-	2	0	ETHE1	48704025	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.780000	0.68956	2.232000	0.73038	0.524000	0.50904	GAG	.	.		0.557	ETHE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463184.1	NM_014297		C	44012185	T	C	44012185	3	2	259	1	0	0	0	0	1	0	0	0	5274	1551	54	2	149	2	ETHE1	19	44012185	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	2917569	44012185	15116798	825	37143										
IRGC	56269	hgsc.bcm.edu	37	chr19	44223753	44223753	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gactgtcctgcggctctattCccagtcgtccgacggcgcca	11	16	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:44223753C>T	ENST00000244314.5	+	2	1242	c.1043C>T	c.(1042-1044)tCc>tTc	p.S348F		NM_019612.3	NP_062558.1	Q6NXR0	IIGP5_HUMAN	immunity-related GTPase family, cinema	348						membrane (GO:0016020)	GTP binding (GO:0005525)|hydrolase activity, acting on acid anhydrides (GO:0016817)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|skin(2)	25		Prostate(69;0.0435)				CGGCTCTATTCCCAGTCGTCC	0.672																																					p.S348F	Colon(189;350 2037 11447 13433 38914)	Atlas-SNP	.											.	IRGC	67	.	0			c.C1043T						.						40	42	42					19																	44223753		2203	4300	6503	SO:0001583	missense	56269	exon2			TCTATTCCCAGTC	BC066939	CCDS12629.1	19q13.32	2008-02-05	2005-10-31	2005-10-31	ENSG00000124449	ENSG00000124449			28835	protein-coding gene	gene with protein product			"immunity-related GTPase family, cinema 1"	IRGC1		12477932	Standard	NM_019612		Approved	Iigp5, CINEMA	uc002oxh.3	Q6NXR0	OTTHUMG00000154587	ENST00000244314.5:c.1043C>T	chr19.hg19:g.44223753C>T	ENSP00000244314:p.Ser348Phe	93.0	0.0		63.0	4.0	NM_019612	Q05BR8	Missense_Mutation	SNP	ENST00000244314.5	hg19	CCDS12629.1	.	.	.	.	.	.	.	.	.	.	C	7.932	0.740907	0.15642	.	.	ENSG00000124449	ENST00000244314	T	0.25912	1.77	4.67	4.67	0.58626	.	0.713966	0.12326	N	0.478873	T	0.20210	0.0486	L	0.31578	0.945	0.09310	N	1	P	0.44195	0.828	B	0.39935	0.314	T	0.08889	-1.0700	10	0.56958	D	0.05	.	10.3517	0.43939	0.1963:0.8037:0.0:0.0	.	348	Q6NXR0	IIGP5_HUMAN	F	348	ENSP00000244314:S348F	ENSP00000244314:S348F	S	+	2	0	IRGC	48915593	0.001000	0.12720	0.812000	0.32479	0.032000	0.12392	1.187000	0.32090	2.151000	0.67156	0.655000	0.94253	TCC	.	.		0.672	IRGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336191.1	NM_019612		T	44223753	C	T	44223753	3	4	259	1	0	0	0	0	1	0	0	0	7847	855	30	3	1045	3	IRGC	19	44223753	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	211568	44223753	14905230	826	37144										
ZNF284	342909	hgsc.bcm.edu	37	chr19	44590982	44590982	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgcaccagagggtccacacgGgagagagaccttataattgt	12	9	0	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:44590982G>A	ENST00000421176.3	+	5	1567	c.1351G>A	c.(1351-1353)Gga>Aga	p.G451R	RNU6-902P_ENST00000517212.1_RNA|ZNF223_ENST00000591793.1_3'UTR	NM_001037813.2	NP_001032902.1	Q2VY69	ZN284_HUMAN	zinc finger protein 284	451					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|kidney(2)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	15		Prostate(69;0.0435)				GGTCCACACGGGAGAGAGACC	0.423																																					p.G451R		Atlas-SNP	.											.	ZNF284	38	.	0			c.G1351A						.						80	86	84					19																	44590982		2199	4299	6498	SO:0001583	missense	342909	exon5			CACACGGGAGAGA	AY166789	CCDS46099.1	19q13.32	2013-01-08				ENSG00000186026		"Zinc fingers, C2H2-type", "-"	13078	protein-coding gene	gene with protein product						12743021	Standard	NM_001037813		Approved	DKFZp781F1775	uc002oyg.1	Q2VY69		ENST00000421176.3:c.1351G>A	chr19.hg19:g.44590982G>A	ENSP00000411032:p.Gly451Arg	168.0	0.0		154.0	52.0	NM_001037813	Q86WM1	Missense_Mutation	SNP	ENST00000421176.3	hg19	CCDS46099.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.299969	0.81136	.	.	ENSG00000186026	ENST00000421176	T	0.26223	1.75	2.37	1.3	0.21679	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.45657	0.1353	M	0.70787	2.145	0.25856	N	0.983884	D	0.89917	1.0	D	0.91635	0.999	T	0.20605	-1.0270	9	0.72032	D	0.01	.	7.9186	0.29833	0.1366:0.0:0.8634:0.0	.	451	Q2VY69	ZN284_HUMAN	R	451	ENSP00000411032:G451R	ENSP00000411032:G451R	G	+	1	0	ZNF284	49282822	0.279000	0.24239	0.005000	0.12908	0.984000	0.73092	3.147000	0.50639	0.319000	0.23209	0.462000	0.41574	GGA	.	.		0.423	ZNF284-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460473.1	NM_001037813		A	44590982	G	A	44590982	3	1	259	1	0	0	0	0	1	0	0	0	17836	1233	43	3	1365	3	ZNF284	19	44590982	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	367229	44590982	14538001	827	37145										
ZNF227	7770	hgsc.bcm.edu	37	chr19	44740282	44740282	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gttcaaatcttaaactacacCaagtaattcacactggagaa	5	9	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:44740282C>A	ENST00000313040.7	+	6	1904	c.1699C>A	c.(1699-1701)Caa>Aaa	p.Q567K	ZNF235_ENST00000589799.1_3'UTR|ZNF227_ENST00000391961.2_Missense_Mutation_p.Q516K|ZNF227_ENST00000589005.1_Missense_Mutation_p.Q516K	NM_182490.1	NP_872296.1	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	567					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(2)|stomach(1)|urinary_tract(1)	24		Prostate(69;0.0435)				TAAACTACACCAAGTAATTCA	0.403																																					p.Q567K		Atlas-SNP	.											.	ZNF227	62	.	0			c.C1699A						.						67	72	71					19																	44740282		2203	4300	6503	SO:0001583	missense	7770	exon6			CTACACCAAGTAA	AK092253	CCDS12636.1, CCDS74388.1	19q13.32	2013-01-08						"Zinc fingers, C2H2-type", "-"	13020	protein-coding gene	gene with protein product							Standard	XM_005259232		Approved		uc002oyu.3	Q86WZ6		ENST00000313040.7:c.1699C>A	chr19.hg19:g.44740282C>A	ENSP00000321049:p.Gln567Lys	113.0	0.0		142.0	6.0	NM_182490	B3KRU7|B7Z5P9	Missense_Mutation	SNP	ENST00000313040.7	hg19	CCDS12636.1	.	.	.	.	.	.	.	.	.	.	C	17.16	3.318756	0.60524	.	.	ENSG00000131115	ENST00000313040;ENST00000328297;ENST00000391961;ENST00000418980	T;T	0.07216	3.21;3.21	4.36	3.23	0.37069	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07954	0.0199	N	0.24115	0.695	0.80722	D	1	B;B;P;B	0.45126	0.123;0.123;0.851;0.123	B;B;P;B	0.45071	0.074;0.117;0.468;0.117	T	0.38972	-0.9636	9	0.36615	T	0.2	.	12.1839	0.54227	0.1714:0.8286:0.0:0.0	.	488;546;519;567	B7Z6M2;Q658S5;Q9NS43;Q86WZ6	.;.;.;ZN227_HUMAN	K	567;524;516;546	ENSP00000321049:Q567K;ENSP00000375823:Q516K	ENSP00000321049:Q567K	Q	+	1	0	ZNF227	49432122	0.001000	0.12720	0.581000	0.28614	0.818000	0.46254	1.002000	0.29796	2.125000	0.65367	0.563000	0.77884	CAA	.	.		0.403	ZNF227-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460720.1	NM_182490		A	44740282	C	A	44740282	3	1	259	1	0	0	0	0	1	0	0	0	17796	595	21	3	1713	3	ZNF227	19	44740282	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	149300	44740282	14388701	828	37146										
ZNF229	7772	hgsc.bcm.edu	37	chr19	44933201	44933201	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctctggtggctgtgaaggtcTgaattccgccggaagccctt	13	11	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:44933201T>C	ENST00000588931.1	-	6	2188	c.1755A>G	c.(1753-1755)tcA>tcG	p.S585S	ZNF229_ENST00000291187.4_Silent_p.S579S|CTC-512J12.4_ENST00000588655.1_RNA|ZNF229_ENST00000591289.1_Intron	NM_014518.2	NP_055333.2	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	585					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|central_nervous_system(2)|endometrium(6)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	45		Prostate(69;0.0352)				TGTGAAGGTCTGAATTCCGCC	0.572																																					p.S585S		Atlas-SNP	.											.	ZNF229	123	.	0			c.A1755G						.						52	56	55					19																	44933201		2186	4295	6481	SO:0001819	synonymous_variant	7772	exon6			AAGGTCTGAATTC	AF192979	CCDS42574.1, CCDS62706.1	19q13.2	2013-01-08				ENSG00000278318		"Zinc fingers, C2H2-type", "-"	13022	protein-coding gene	gene with protein product							Standard	XM_006723372		Approved		uc002oze.1	Q9UJW7		ENST00000588931.1:c.1755A>G	chr19.hg19:g.44933201T>C		95.0	0.0		85.0	4.0	NM_014518	B2RWN3|Q59FV2|Q86WL9	Silent	SNP	ENST00000588931.1	hg19	CCDS42574.1																																																																																			.	.		0.572	ZNF229-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460833.1	NM_014518		C	44933201	T	C	44933201	2	2	259	1	0	0	0	0	0	0	0	1	17797	1567	55	2		2	ZNF229	19	44933201	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	192919	44933201	14195782	829	37147										
ZNF180	7733	hgsc.bcm.edu	37	chr19	44982061	44982061	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tttatgaaaatggtttcttaTgggtataactggggatgaaa	11	2	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:44982061T>C	ENST00000221327.4	-	5	918	c.637A>G	c.(637-639)Ata>Gta	p.I213V	ZNF180_ENST00000391956.4_Missense_Mutation_p.I188V|ZNF180_ENST00000592529.1_Missense_Mutation_p.I186V|AC069278.4_ENST00000591684.1_lincRNA|ZNF180_ENST00000585514.1_5'Flank|ZNF180_ENST00000586637.1_3'UTR	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	213					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				TGGTTTCTTATGGGTATAACT	0.363																																					p.I213V	Esophageal Squamous(180;1353 2003 32862 46574 49854)	Atlas-SNP	.											.	ZNF180	103	.	0			c.A637G						.						88	87	87					19																	44982061		2203	4300	6503	SO:0001583	missense	7733	exon5			TTCTTATGGGTAT	AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"Zinc fingers, C2H2-type", "-"	12970	protein-coding gene	gene with protein product		606740	"zinc finger protein 180 (HHZ168)"				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8		ENST00000221327.4:c.637A>G	chr19.hg19:g.44982061T>C	ENSP00000221327:p.Ile213Val	96.0	0.0		95.0	4.0	NM_013256	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Missense_Mutation	SNP	ENST00000221327.4	hg19	CCDS12639.1	.	.	.	.	.	.	.	.	.	.	T	0.007	-1.984302	0.00443	.	.	ENSG00000167384	ENST00000221327;ENST00000391956	T;T	0.07021	3.23;3.26	4.89	-3.24	0.05094	.	0.306273	0.23541	N	0.047079	T	0.03178	0.0093	N	0.19112	0.55	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.001	T	0.39482	-0.9612	10	0.15066	T	0.55	-7.4476	1.8481	0.03163	0.1245:0.3207:0.2698:0.2849	.	188;212;213	G5E9B8;Q58F03;Q9UJW8	.;.;ZN180_HUMAN	V	213;188	ENSP00000221327:I213V;ENSP00000375818:I188V	ENSP00000221327:I213V	I	-	1	0	ZNF180	49673901	0.001000	0.12720	0.003000	0.11579	0.029000	0.11900	-0.054000	0.11826	-0.537000	0.06290	0.533000	0.62120	ATA	.	.		0.363	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256		C	44982061	T	C	44982061	3	2	259	1	0	0	0	0	1	0	0	0	17763	1464	51	2	1445	2	ZNF180	19	44982061	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	48860	44982061	14146922	830	37148										
OPA3	7408	hgsc.bcm.edu	37	chr19	46032507	46032507	+	IGR	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cccgcagcgcctccctggcaAcacgtcgctccttttccttg	8	19	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:46032507A>G	ENST00000245932.6	+	0	2305				OPA3_ENST00000323060.3_Missense_Mutation_p.V117A	NM_003370.3	NP_003361.1	P50552	VASP_HUMAN	vasodilator-stimulated phosphoprotein						actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|cell junction assembly (GO:0034329)|neural tube closure (GO:0001843)|positive regulation of actin filament polymerization (GO:0030838)|protein homotetramerization (GO:0051289)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	profilin binding (GO:0005522)			endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|skin(2)	18		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0145)|GBM - Glioblastoma multiforme(486;0.154)		CTCCCTGGCAACACGTCGCTC	0.677																																					p.V117A		Atlas-SNP	.											.	OPA3	19	.	0			c.T350C						.						31	31	31					19																	46032507		2200	4299	6499	SO:0001628	intergenic_variant	80207	exon2			CTGGCAACACGTC		CCDS33051.1	19q13.32	2012-02-22			ENSG00000125753	ENSG00000125753			12652	protein-coding gene	gene with protein product		601703				8812448	Standard	XM_005259199		Approved		uc002pcg.3	P50552			chr19.hg19:g.46032507A>G		82.0	0.0		100.0	4.0	NM_001017989	B2RBT9|Q6PIZ1|Q93035	Missense_Mutation	SNP	ENST00000245932.6	hg19	CCDS33051.1	.	.	.	.	.	.	.	.	.	.	A	1.983	-0.433637	0.04669	.	.	ENSG00000125741	ENST00000323060	D	0.81499	-1.5	3.67	-1.71	0.08133	.	1.518070	0.03623	N	0.236680	T	0.54775	0.1879	.	.	.	0.09310	N	0.999995	B	0.02656	0.0	B	0.01281	0.0	T	0.48281	-0.9049	9	0.07644	T	0.81	-0.1509	0.4545	0.00507	0.2179:0.1594:0.336:0.2867	.	117	Q9H6K4-2	.	A	117	ENSP00000319817:V117A	ENSP00000319817:V117A	V	-	2	0	OPA3	50724347	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.071000	0.14594	0.001000	0.14605	-0.441000	0.05720	GTT	.	.		0.677	VASP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459589.1			G	46032507	A	G	46032507	1	3	259	0	1	0	0	0	0	0	0	0	10881	43	2	2		2	OPA3	19	46032507	IGR	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1050446	46032507	13096476	831	37149										
DMPK	1760	hgsc.bcm.edu	37	chr19	46280628	46280628	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgagcccgtcctccaccaagTcgaagttgcatgtgtcggtg	12	12	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:46280628T>C	ENST00000291270.4	-	8	1228	c.1103A>G	c.(1102-1104)gAc>gGc	p.D368G	DMPK_ENST00000458663.2_Missense_Mutation_p.D368G|DMPK_ENST00000595361.1_5'Flank|DMPK_ENST00000600757.1_Missense_Mutation_p.D378G|DMPK_ENST00000343373.4_Missense_Mutation_p.D378G|DMPK_ENST00000354227.5_Missense_Mutation_p.D368G|DMPK_ENST00000447742.2_Missense_Mutation_p.D368G	NM_004409.3	NP_004400.4	Q09013	DMPK_HUMAN	dystrophia myotonica-protein kinase	368	AGC-kinase C-terminal.				cellular calcium ion homeostasis (GO:0006874)|muscle cell apoptotic process (GO:0010657)|nuclear envelope organization (GO:0006998)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|regulation of excitatory postsynaptic membrane potential involved in skeletal muscle contraction (GO:0014853)|regulation of heart contraction (GO:0008016)|regulation of myotube differentiation (GO:0010830)|regulation of skeletal muscle contraction by calcium ion signaling (GO:0014722)|regulation of sodium ion transport (GO:0002028)|regulation of synapse structural plasticity (GO:0051823)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of mitochondrial outer membrane (GO:0031307)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|myosin phosphatase regulator activity (GO:0017020)|protein serine/threonine kinase activity (GO:0004674)			endometrium(5)|kidney(1)|large_intestine(1)|lung(6)|stomach(1)|urinary_tract(2)	16		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00616)|GBM - Glioblastoma multiforme(486;0.0825)|Epithelial(262;0.24)		CTCCACCAAGTCGAAGTTGCA	0.622																																					p.D378G	Esophageal Squamous(35;307 869 9153 24033 28903)	Atlas-SNP	.											.	DMPK	74	.	0			c.A1133G						.						45	38	40					19																	46280628		2202	4300	6502	SO:0001583	missense	1760	exon7			ACCAAGTCGAAGT	L19268	CCDS12674.1, CCDS46117.1, CCDS46118.1, CCDS46119.1, CCDS74400.1	19q13.3	2014-02-05					2.7.11.1		2933	protein-coding gene	gene with protein product	"dystrophia myotonica 1", "DM protein kinase", "myotonin protein kinase A", "myotonic dystrophy associated protein kinase", "thymopoietin homolog"	605377	"dystrophia myotonica 1 (includes dystrophia myotonia protein kinase)"	DM1, DM		1546325, 1546326	Standard	NM_001288765		Approved	DMK, DM1PK, MDPK, MT-PK	uc002pdf.1	Q09013		ENST00000291270.4:c.1103A>G	chr19.hg19:g.46280628T>C	ENSP00000291270:p.Asp368Gly	101.0	0.0		87.0	4.0	NM_001081563	E5KR08|Q16205|Q6P5Z6	Missense_Mutation	SNP	ENST00000291270.4	hg19	CCDS12674.1	.	.	.	.	.	.	.	.	.	.	t	23.6	4.437347	0.83885	.	.	ENSG00000104936	ENST00000458663;ENST00000342805;ENST00000291270;ENST00000447742;ENST00000377750;ENST00000343373;ENST00000348168;ENST00000354227	T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02	4.63	4.63	0.57726	AGC-kinase, C-terminal (2);Protein kinase-like domain (1);	0.139434	0.32624	N	0.005845	T	0.63873	0.2548	M	0.78456	2.415	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.87578	0.996;0.996;0.997;0.998;0.997;0.992;0.998;0.995	T	0.68708	-0.5337	10	0.87932	D	0	.	12.289	0.54807	0.0:0.0:0.0:1.0	.	368;368;394;368;368;368;415;378	Q09013-12;Q09013-16;G5E982;E5KR07;E5KR05;Q09013;Q59FU6;E5KR08	.;.;.;.;.;DMPK_HUMAN;.;.	G	368;394;368;368;368;378;378;368	ENSP00000401753:D368G;ENSP00000291270:D368G;ENSP00000413417:D368G;ENSP00000345997:D378G;ENSP00000346168:D368G	ENSP00000291270:D368G	D	-	2	0	DMPK	50972468	1.000000	0.71417	0.992000	0.48379	0.719000	0.41307	7.703000	0.84585	2.065000	0.61736	0.459000	0.35465	GAC	.	.		0.622	DMPK-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460572.1	NM_004409		C	46280628	T	C	46280628	3	2	259	1	0	0	0	0	1	0	0	0	4586	1667	58	2	825	2	DMPK	19	46280628	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	248121	46280628	12848355	832	37150										
ARHGAP35	2909	hgsc.bcm.edu	37	chr19	47423542	47423542	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	taaagcattacaaaagctccAagcagagcgtgatgccctta	8	10	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:47423542A>G	ENST00000404338.3	+	1	1610	c.1610A>G	c.(1609-1611)cAa>cGa	p.Q537R		NM_004491.4	NP_004482.4	Q9NRY4	RHG35_HUMAN	Rho GTPase activating protein 35	537	FF 4.				axon guidance (GO:0007411)|camera-type eye development (GO:0043010)|forebrain development (GO:0030900)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular permeability (GO:0043116)|neural tube closure (GO:0001843)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|GTP binding (GO:0005525)|Rho GTPase activator activity (GO:0005100)|transcription corepressor activity (GO:0003714)										CAAAAGCTCCAAGCAGAGCGT	0.473																																					p.Q537R		Atlas-SNP	.											.	.	.	.	0			c.A1610G						.						162	158	159					19																	47423542		1994	4173	6167	SO:0001583	missense	2909	exon1			AGCTCCAAGCAGA	M73077	CCDS46127.1	19q13.32	2011-06-29	2011-06-07	2011-06-07	ENSG00000160007	ENSG00000160007		"Rho GTPase activating proteins"	4591	protein-coding gene	gene with protein product		605277	"glucocorticoid receptor DNA binding factor 1"	GRLF1		1894621, 20675588	Standard	NM_004491		Approved	GRF-1, p190ARhoGAP, P190A, KIAA1722, p190RhoGAP	uc010ekv.3	Q9NRY4		ENST00000404338.3:c.1610A>G	chr19.hg19:g.47423542A>G	ENSP00000385720:p.Gln537Arg	68.0	0.0		92.0	5.0	NM_004491	A7E2A4|Q14452|Q9C0E1	Missense_Mutation	SNP	ENST00000404338.3	hg19	CCDS46127.1	.	.	.	.	.	.	.	.	.	.	A	13.32	2.201121	0.38905	.	.	ENSG00000160007	ENST00000317082;ENST00000501576;ENST00000404338	T	0.29655	1.56	5.82	5.82	0.92795	.	0.102535	0.64402	D	0.000002	T	0.27027	0.0662	N	0.22421	0.69	0.80722	D	1	B	0.32101	0.356	B	0.36922	0.236	T	0.08371	-1.0725	10	0.54805	T	0.06	-26.4002	15.1603	0.72778	1.0:0.0:0.0:0.0	.	537	Q9NRY4-2	.	R	537	ENSP00000385720:Q537R	ENSP00000324820:Q537R	Q	+	2	0	ARHGAP35	52115382	0.999000	0.42202	0.964000	0.40570	0.951000	0.60555	4.477000	0.60223	2.225000	0.72522	0.459000	0.35465	CAA	.	.		0.473	ARHGAP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466652.1	NM_004491		G	47423542	A	G	47423542	3	3	259	1	0	0	0	0	1	0	0	0	6804	130	5	2	1612	2	ARHGAP35	19	47423542	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1142914	47423542	11705441	833	37151										
TULP2	7288	hgsc.bcm.edu	37	chr19	49384335	49384335	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atggaaagcagaagtccatgGtgaatgtgtctgggcccact	13	8	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:49384335G>A	ENST00000221399.3	-	13	1640	c.1496C>T	c.(1495-1497)aCc>aTc	p.T499I		NM_003323.2	NP_003314.2	O00295	TULP2_HUMAN	tubby like protein 2	499					visual perception (GO:0007601)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	protein complex binding (GO:0032403)			NS(1)|breast(2)|central_nervous_system(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	22		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000259)|all cancers(93;0.000435)|Epithelial(262;0.0221)|GBM - Glioblastoma multiforme(486;0.0234)		GAAGTCCATGGTGAATGTGTC	0.488																																					p.T499I		Atlas-SNP	.											.	TULP2	60	.	0			c.C1496T						.						117	116	117					19																	49384335		2203	4300	6503	SO:0001583	missense	7288	exon13			TCCATGGTGAATG	U82469	CCDS12739.1	19q13.1	2009-08-06			ENSG00000104804	ENSG00000104804			12424	protein-coding gene	gene with protein product	"cancer/testis antigen 65"	602309				9096357	Standard	NM_003323		Approved	TUBL2, CT65	uc002pkz.2	O00295	OTTHUMG00000164406	ENST00000221399.3:c.1496C>T	chr19.hg19:g.49384335G>A	ENSP00000221399:p.Thr499Ile	72.0	0.0		82.0	4.0	NM_003323	Q8TC50	Missense_Mutation	SNP	ENST00000221399.3	hg19	CCDS12739.1	.	.	.	.	.	.	.	.	.	.	G	16.46	3.129716	0.56721	.	.	ENSG00000104804	ENST00000221399;ENST00000522341	D;D	0.97941	-4.62;-4.62	4.81	3.78	0.43462	Tubby, C-terminal (4);	0.061993	0.64402	D	0.000004	D	0.98213	0.9409	M	0.73430	2.235	0.53005	D	0.999969	D	0.76494	0.999	D	0.73708	0.981	D	0.98550	1.0636	10	0.87932	D	0	-17.476	11.1381	0.48386	0.0912:0.0:0.9088:0.0	.	499	O00295	TULP2_HUMAN	I	499;59	ENSP00000221399:T499I;ENSP00000429131:T59I	ENSP00000221399:T499I	T	-	2	0	TULP2	54076147	1.000000	0.71417	1.000000	0.80357	0.320000	0.28249	7.205000	0.77881	1.179000	0.42884	-0.136000	0.14681	ACC	.	.		0.488	TULP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378633.1	NM_003323		A	49384335	G	A	49384335	3	1	259	1	0	0	0	0	1	0	0	0	16789	1261	44	3	70	3	TULP2	19	49384335	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1960793	49384335	9744648	834	37152										
PRMT1	3276	hgsc.bcm.edu	37	chr19	50185170	50185170	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgccattcttgccctaggagAtgctgaaggacgaggtgcgc	14	10	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:50185170A>G	ENST00000391851.4	+	3	271	c.142A>G	c.(142-144)Atg>Gtg	p.M48V	MIR5088_ENST00000581740.1_RNA|PRMT1_ENST00000532489.1_Missense_Mutation_p.M20V|PRMT1_ENST00000454376.2_Missense_Mutation_p.M66V	NM_198318.4	NP_938074.2	Q99873	ANM1_HUMAN	protein arginine methyltransferase 1	56	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				cell surface receptor signaling pathway (GO:0007166)|histone H4-R3 methylation (GO:0043985)|histone methylation (GO:0016571)|negative regulation of megakaryocyte differentiation (GO:0045653)|neuron projection development (GO:0031175)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|protein methylation (GO:0006479)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H4-R3 specific) (GO:0044020)|identical protein binding (GO:0042802)|methyltransferase activity (GO:0008168)|N-methyltransferase activity (GO:0008170)|poly(A) RNA binding (GO:0044822)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|ovary(2)	12		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00103)|GBM - Glioblastoma multiforme(134;0.012)		GCCCTAGGAGATGCTGAAGGA	0.617																																					p.M66V		Atlas-SNP	.											.	PRMT1	31	.	0			c.A196G						.						61	48	52					19																	50185170		2203	4300	6503	SO:0001583	missense	3276	exon4			TAGGAGATGCTGA	D66904	CCDS42592.1, CCDS46145.1, CCDS74425.1	19q13	2014-06-12	2006-02-16	2006-02-16	ENSG00000126457	ENSG00000126457	2.1.1.125	"Protein arginine methyltransferases"	5187	protein-coding gene	gene with protein product		602950	"HMT1 (hnRNP methyltransferase, S. cerevisiae)-like 2", "HMT1 hnRNP methyltransferase-like 2 (S. cerevisiae)"	HRMT1L2		9545638	Standard	NM_001207042		Approved	HCP1, ANM1	uc010enf.2	Q99873	OTTHUMG00000167568	ENST00000391851.4:c.142A>G	chr19.hg19:g.50185170A>G	ENSP00000375724:p.Met48Val	94.0	0.0		85.0	4.0	NM_001536	B4E3C3|G5E9B6|Q15529|Q2VP93|Q6LEU5|Q8WUW5|Q99872|Q99874|Q9NZ04|Q9NZ05|Q9NZ06	Missense_Mutation	SNP	ENST00000391851.4	hg19	CCDS42592.1	.	.	.	.	.	.	.	.	.	.	A	11.47	1.649565	0.29336	.	.	ENSG00000126457	ENST00000529284;ENST00000532489;ENST00000527382;ENST00000528623;ENST00000534465;ENST00000391851;ENST00000449059;ENST00000454376;ENST00000529836;ENST00000526224;ENST00000527412	T;T;T;T;T;T;T;T;T	0.23552	1.9;1.9;1.9;1.9;1.9;1.9;1.9;1.9;1.9	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.40067	0.1102	M	0.77712	2.385	0.80722	D	1	D;P;D;P	0.56968	0.962;0.855;0.978;0.91	B;B;P;P	0.49637	0.315;0.288;0.617;0.617	T	0.44847	-0.9301	10	0.87932	D	0	-12.5087	12.7696	0.57412	1.0:0.0:0.0:0.0	.	56;20;48;42	Q99873;E9PKG1;G5E9B6;Q99873-2	ANM1_HUMAN;.;.;.	V	20;20;20;42;20;48;42;66;42;20;45	ENSP00000432349:M20V;ENSP00000433556:M20V;ENSP00000432538:M20V;ENSP00000431957:M20V;ENSP00000375724:M48V;ENSP00000406162:M66V;ENSP00000437273:M42V;ENSP00000432788:M20V;ENSP00000436732:M45V	ENSP00000375724:M48V	M	+	1	0	PRMT1	54876982	1.000000	0.71417	1.000000	0.80357	0.012000	0.07955	8.816000	0.91979	2.124000	0.65301	0.523000	0.50628	ATG	.	.		0.617	PRMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395065.1	NM_001536		G	50185170	A	G	50185170	3	3	259	1	0	0	0	0	1	0	0	0	12547	333	12	2	210	2	PRMT1	19	50185170	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	800835	50185170	8943813	835	37153										
SIGLEC7	27036	hgsc.bcm.edu	37	chr19	51648215	51648215	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gtcttccaaggagaaggcacAggtaggatggagccccctcc	13	12	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:51648215A>G	ENST00000317643.6	+	3	828	c.759A>G	c.(757-759)acA>acG	p.T253T	SIGLEC7_ENST00000600577.1_Intron|SIGLEC7_ENST00000305628.7_Splice_Site_p.T160T	NM_014385.2	NP_055200.1	Q9Y286	SIGL7_HUMAN	sialic acid binding Ig-like lectin 7	253	Ig-like C2-type 2.				cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(11)|skin(2)|stomach(1)	29		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000836)|OV - Ovarian serous cystadenocarcinoma(262;0.00297)		GAGAAGGCACAGGTAGGATGG	0.612																																					p.T253T		Atlas-SNP	.											.	SIGLEC7	74	.	0			c.A759G						.						109	102	104					19																	51648215		2203	4300	6503	SO:0001630	splice_region_variant	27036	exon3			AGGCACAGGTAGG	AF170485	CCDS12826.1, CCDS42601.1, CCDS62771.1	19q13.41	2014-03-20			ENSG00000168995	ENSG00000168995		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10876	protein-coding gene	gene with protein product		604410	"sialic acid binding Ig-like lectin 19, pseudogene", "sialic acid binding Ig-like lectin, pseudogene 2"	SIGLEC19P, SIGLECP2		10567377	Standard	NM_001277201		Approved	SIGLEC-7, p75/AIRM1, QA79, CD328	uc002pvv.1	Q9Y286	OTTHUMG00000182895	ENST00000317643.6:c.760+1A>G	chr19.hg19:g.51648215A>G		73.0	0.0		88.0	4.0	NM_014385	Q9NZQ1|Q9UJ86|Q9UJ87|Q9Y502	Silent	SNP	ENST00000317643.6	hg19	CCDS12826.1																																																																																			.	.		0.612	SIGLEC7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464226.2	NM_016543	Silent	G	51648215	A	G	51648215	5	3	259	1	0	0	0	0	0	0	1	0	14328	202	7	2	769	2	SIGLEC7	19	51648215	Splice_Site	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1463045	51648215	7480768	836	37154										
SIGLEC10	89790	hgsc.bcm.edu	37	chr19	51919307	51919307	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aggagaggactctgttctgcAggacccagctcagtgtggca	14	10	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:51919307A>G	ENST00000339313.5	-	5	985	c.869T>C	c.(868-870)cTg>cCg	p.L290P	SIGLEC10_ENST00000525998.1_Intron|SIGLEC10_ENST00000432469.2_Missense_Mutation_p.L207P|SIGLEC10_ENST00000442846.3_Intron|CTD-2616J11.2_ENST00000526996.1_RNA|SIGLEC10_ENST00000356298.5_Missense_Mutation_p.L290P|CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000439889.2_Missense_Mutation_p.L232P|SIGLEC10_ENST00000353836.5_Missense_Mutation_p.L290P|SIGLEC10_ENST00000441969.3_Missense_Mutation_p.L232P|CTD-2616J11.3_ENST00000532473.1_RNA|SIGLEC10_ENST00000436984.2_Missense_Mutation_p.L242P			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	290	Ig-like C2-type 2.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		TCTGTTCTGCAGGACCCAGCT	0.652																																					p.L290P		Atlas-SNP	.											.	SIGLEC10	112	.	0			c.T869C						.						18	23	21					19																	51919307		2201	4299	6500	SO:0001583	missense	89790	exon5			TTCTGCAGGACCC	AF310233	CCDS12832.1, CCDS54301.1, CCDS54302.1, CCDS54303.1, CCDS54304.1, CCDS54305.1	19q13.3	2013-01-29			ENSG00000142512	ENSG00000142512		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15620	protein-coding gene	gene with protein product	"sialic acid binding Ig-like lectin 10 Ig-like lectin 7", "siglec-like gene 2"	606091				11284738	Standard	NM_033130		Approved	SIGLEC-10, SLG2, PRO940, MGC126774	uc002pwo.3	Q96LC7	OTTHUMG00000165521	ENST00000339313.5:c.869T>C	chr19.hg19:g.51919307A>G	ENSP00000345243:p.Leu290Pro	82.0	0.0		82.0	4.0	NM_001171157	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Missense_Mutation	SNP	ENST00000339313.5	hg19	CCDS12832.1	.	.	.	.	.	.	.	.	.	.	.	8.476	0.858590	0.17178	.	.	ENSG00000142512	ENST00000353836;ENST00000432469;ENST00000356298;ENST00000441969;ENST00000439889;ENST00000436984;ENST00000339313;ENST00000529627	T;T;T;T;T;T;T;T	0.45668	1.46;1.46;1.46;1.46;1.46;1.46;1.46;0.89	4.37	2.1	0.27182	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.498950	0.15393	N	0.264731	T	0.61862	0.2381	M	0.86864	2.845	0.37215	D	0.904993	D;D;D;D;P;D	0.89917	1.0;1.0;1.0;1.0;0.494;0.999	D;D;D;D;B;D	0.91635	0.999;0.999;0.998;0.997;0.221;0.985	T	0.63202	-0.6690	10	0.46703	T	0.11	.	4.2091	0.10503	0.5813:0.1982:0.0:0.2206	.	242;290;290;232;232;290	C9JM10;B7ZL04;Q96LC7-2;Q96LC7-6;Q96LC7-3;Q96LC7	.;.;.;.;.;SIG10_HUMAN	P	290;207;290;232;232;242;290;104	ENSP00000342389:L290P;ENSP00000396742:L207P;ENSP00000348646:L290P;ENSP00000408387:L232P;ENSP00000389132:L232P;ENSP00000414324:L242P;ENSP00000345243:L290P;ENSP00000435281:L104P	ENSP00000345243:L290P	L	-	2	0	SIGLEC10	56611119	0.436000	0.25586	0.716000	0.30569	0.129000	0.20672	0.708000	0.25719	0.710000	0.31997	0.260000	0.18958	CTG	.	.		0.652	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130		G	51919307	A	G	51919307	3	3	259	1	0	0	0	0	1	0	0	0	14321	188	7	2	1252	2	SIGLEC10	19	51919307	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	271092	51919307	7209676	837	37155										
ZNF470	388566	hgsc.bcm.edu	37	chr19	57089654	57089654	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agatgtcatactggtgagaaAccttatgaatgtaatgtttg	10	4	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:57089654A>G	ENST00000330619.8	+	6	2543	c.1857A>G	c.(1855-1857)aaA>aaG	p.K619K	ZNF470_ENST00000391709.3_Silent_p.K619K|ZNF470_ENST00000601902.1_Intron	NM_001001668.3	NP_001001668.3	Q6ECI4	ZN470_HUMAN	zinc finger protein 470	619					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(7)|large_intestine(12)|lung(11)|ovary(1)|pancreas(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	41		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0294)		CTGGTGAGAAACCTTATGAAT	0.428																																					p.K619K		Atlas-SNP	.											.	ZNF470	103	.	0			c.A1857G						.						81	79	80					19																	57089654		2203	4300	6503	SO:0001819	synonymous_variant	388566	exon6			TGAGAAACCTTAT	AK129686	CCDS33122.1	19q13.43	2013-01-08				ENSG00000197016		"Zinc fingers, C2H2-type", "-"	22220	protein-coding gene	gene with protein product						15302581	Standard	NM_001001668		Approved	CZF-1, FLJ26175	uc002qnl.4	Q6ECI4		ENST00000330619.8:c.1857A>G	chr19.hg19:g.57089654A>G		52.0	0.0		90.0	5.0	NM_001001668	A8MTW0|B9EGU1|Q6ZPA1|Q9Y2N9	Silent	SNP	ENST00000330619.8	hg19	CCDS33122.1																																																																																			.	.		0.428	ZNF470-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459707.2	NM_001001668		G	57089654	A	G	57089654	2	3	259	1	0	0	0	0	0	0	0	1	17944	40	2	2		2	ZNF470	19	57089654	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	5170347	57089654	2039329	838	37156										
ZNF304	57343	hgsc.bcm.edu	37	chr19	57867978	57867978	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agccagatgactcatgctgaGgtgagacccttcagatgcct	11	11	2	5			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:57867978G>T	ENST00000282286.5	+	3	914	c.741G>T	c.(739-741)gaG>gaT	p.E247D	ZNF304_ENST00000391705.3_Missense_Mutation_p.E247D|ZNF304_ENST00000598744.1_Missense_Mutation_p.E205D|ZNF304_ENST00000443917.2_Missense_Mutation_p.E294D			Q9HCX3	ZN304_HUMAN	zinc finger protein 304	247					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)	26		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0265)		CTCATGCTGAGGTGAGACCCT	0.438																																					p.E247D		Atlas-SNP	.											.	ZNF304	74	.	0			c.G741T						.						89	85	86					19																	57867978		2203	4300	6503	SO:0001583	missense	57343	exon3			TGCTGAGGTGAGA	AJ276316	CCDS12950.1, CCDS74462.1	19q13.4	2013-01-08				ENSG00000131845		"Zinc fingers, C2H2-type", "-"	13505	protein-coding gene	gene with protein product		613840					Standard	XM_005259090		Approved		uc010ygw.2	Q9HCX3		ENST00000282286.5:c.741G>T	chr19.hg19:g.57867978G>T	ENSP00000282286:p.Glu247Asp	92.0	0.0		94.0	4.0	NM_020657		Missense_Mutation	SNP	ENST00000282286.5	hg19	CCDS12950.1	.	.	.	.	.	.	.	.	.	.	g	11.55	1.671545	0.29693	.	.	ENSG00000131845	ENST00000282286;ENST00000391705;ENST00000443917	T;T;T	0.15256	2.44;2.44;2.44	3.82	-3.28	0.05033	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10937	0.0267	L	0.41079	1.255	0.09310	N	1	B;B	0.09022	0.001;0.002	B;B	0.06405	0.001;0.002	T	0.36720	-0.9736	9	0.66056	D	0.02	.	2.0199	0.03506	0.3923:0.13:0.3494:0.1284	.	247;294	Q9HCX3;E7EQD3	ZN304_HUMAN;.	D	247;247;294	ENSP00000282286:E247D;ENSP00000375586:E247D;ENSP00000401642:E294D	ENSP00000282286:E247D	E	+	3	2	ZNF304	62559790	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.586000	0.23894	-0.595000	0.05828	0.454000	0.30748	GAG	.	.		0.438	ZNF304-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465785.1			T	57867978	G	T	57867978	3	4	259	1	0	0	0	0	1	0	0	0	17848	991	35	3	751	3	ZNF304	19	57867978	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	778324	57867978	1261005	839	37157										
ZNF211	10520	hgsc.bcm.edu	37	chr19	58153448	58153448	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttcaacaccgcagagttcacAcgggaaaaaggccttatcag	9	11	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:58153448A>G	ENST00000347302.3	+	3	1773	c.1594A>G	c.(1594-1596)Acg>Gcg	p.T532A	ZNF211_ENST00000240731.4_Missense_Mutation_p.T545A|ZNF211_ENST00000299871.5_Missense_Mutation_p.T597A|ZNF211_ENST00000544273.1_Missense_Mutation_p.T544A|ZNF211_ENST00000541801.1_Missense_Mutation_p.T523A|ZNF211_ENST00000254182.7_Missense_Mutation_p.T523A|ZNF211_ENST00000420680.1_Missense_Mutation_p.T536A|ZNF211_ENST00000391703.3_Missense_Mutation_p.T471A	NM_198855.2	NP_942152.1	Q13398	ZN211_HUMAN	zinc finger protein 211	532					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		CAGAGTTCACACGGGAAAAAG	0.458																																					p.T597A		Atlas-SNP	.											.	ZNF211	78	.	0			c.A1789G						.						104	101	102					19																	58153448		2203	4300	6503	SO:0001583	missense	10520	exon5			GTTCACACGGGAA	U38904	CCDS12956.1, CCDS12957.1, CCDS58686.1, CCDS58687.1, CCDS58688.1, CCDS74468.1	19q13.4	2013-01-08			ENSG00000121417	ENSG00000121417		"Zinc fingers, C2H2-type", "-"	13003	protein-coding gene	gene with protein product		601856				7633419, 9096115	Standard	NM_006385		Approved	ZNF-25, CH2H2-25	uc031rng.1	Q13398	OTTHUMG00000168012	ENST00000347302.3:c.1594A>G	chr19.hg19:g.58153448A>G	ENSP00000339562:p.Thr532Ala	107.0	0.0		95.0	4.0	NM_001265597	B4DH10|B4DLC9|B4E3C9|B9ZVS7|B9ZVW1|F8WDV2|Q05BQ7|Q2TAL7|Q59EG4|Q59G36|Q5EBL6	Missense_Mutation	SNP	ENST00000347302.3	hg19	CCDS12957.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	a|a	21.0|21.0	4.076156|4.076156	0.76415|0.76415	.|.	.|.	ENSG00000121417|ENSG00000121417	ENST00000407202|ENST00000420680;ENST00000347302;ENST00000254182;ENST00000391703;ENST00000541801;ENST00000299871;ENST00000544273;ENST00000240731	T|T;T;T;T;T;T;T;T	0.67523|0.26518	-0.27|1.73;1.73;1.73;1.73;1.73;1.73;1.73;1.73	3.23|3.23	3.23|3.23	0.37069|0.37069	.|Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.|.	.|.	.|.	.|.	T|T	0.25827|0.25827	0.0629|0.0629	L|L	0.52759|0.52759	1.655|1.655	0.28604|0.28604	N|N	0.908997|0.908997	.|B;B;B;P;B;B	.|0.45768	.|0.384;0.384;0.323;0.866;0.438;0.438	.|B;B;B;B;B;B	.|0.41466	.|0.22;0.22;0.147;0.358;0.328;0.328	T|T	0.13308|0.13308	-1.0514|-1.0514	7|9	0.87932|0.87932	D|D	0|0	.|.	10.8985|10.8985	0.47036|0.47036	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|536;544;597;523;532;545	.|Q13398-4;Q13398-3;F8WDV2;Q13398-2;Q13398;B9ZVW1	.|.;.;.;.;ZN211_HUMAN;.	R|A	535|536;532;523;471;523;597;544;545	ENSP00000384436:H535R|ENSP00000399193:T536A;ENSP00000339562:T532A;ENSP00000254182:T523A;ENSP00000375584:T471A;ENSP00000442601:T523A;ENSP00000299871:T597A;ENSP00000441386:T544A;ENSP00000240731:T545A	ENSP00000384436:H535R|ENSP00000240731:T545A	H|T	+|+	2|1	0|0	ZNF211|ZNF211	62845260|62845260	0.522000|0.522000	0.26266|0.26266	0.223000|0.223000	0.23860|0.23860	0.963000|0.963000	0.63663|0.63663	2.143000|2.143000	0.42187|0.42187	1.467000|1.467000	0.48044|0.48044	0.477000|0.477000	0.44152|0.44152	CAC|ACG	.	.		0.458	ZNF211-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397502.1			G	58153448	A	G	58153448	3	3	259	1	0	0	0	0	1	0	0	0	17782	159	6	2	1647	2	ZNF211	19	58153448	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	285470	58153448	975535	840	37158										
ZSCAN1	284312	hgsc.bcm.edu	37	chr19	58564802	58564802	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cctcgccctccacagggtccCgggcccgcttgcctctgaag	11	19	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:58564802C>A	ENST00000282326.1	+	6	857	c.610C>A	c.(610-612)Cgg>Agg	p.R204R		NM_182572.3	NP_872378.3	Q8NBB4	ZSCA1_HUMAN	zinc finger and SCAN domain containing 1	204					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)		CACAGGGTCCCGGGCCCGCTT	0.652																																					p.R204R		Atlas-SNP	.											.	ZSCAN1	102	.	0			c.C610A						.						45	48	47					19																	58564802		2203	4296	6499	SO:0001819	synonymous_variant	284312	exon6			GGGTCCCGGGCCC	AK091098	CCDS12969.1	19q13.43	2013-06-13	2004-04-21		ENSG00000152467	ENSG00000152467		"-", "Zinc fingers, C2H2-type"	23712	protein-coding gene	gene with protein product			"zinc finger with SCAN domain 1"			12477932	Standard	NM_182572		Approved	FLJ33779, ZNF915	uc002qrc.1	Q8NBB4	OTTHUMG00000183381	ENST00000282326.1:c.610C>A	chr19.hg19:g.58564802C>A		61.0	0.0		65.0	4.0	NM_182572	Q3B798|Q6WLH8|Q86WS8	Silent	SNP	ENST00000282326.1	hg19	CCDS12969.1																																																																																			.	.		0.652	ZSCAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466427.1	NM_182572		A	58564802	C	A	58564802	2	1	259	1	0	0	0	0	0	0	0	1	18241	643	23	1		1	ZSCAN1	19	58564802	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	411354	58564802	564181	841	37159										
ZNF324	25799	hgsc.bcm.edu	37	chr19	58982592	58982592	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aggagccctcgacctgggacGagctgggcgaggctcttcac	15	13	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:58982592G>T	ENST00000536459.2	+	4	1442	c.733G>T	c.(733-735)Gag>Tag	p.E245*	ZNF324_ENST00000535298.1_Nonsense_Mutation_p.E22*|ZNF446_ENST00000596341.1_5'Flank|ZNF324_ENST00000196482.3_Nonsense_Mutation_p.E245*			O75467	Z324A_HUMAN	zinc finger protein 324	245					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E245K(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(2)|prostate(2)|urinary_tract(2)	16		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)		GACCTGGGACGAGCTGGGCGA	0.637																																					p.E245X		Atlas-SNP	.											ZNF324,colon,carcinoma,0,1	ZNF324	46	.	1	Substitution - Missense(1)	large_intestine(1)	c.G733T						.						25	28	27					19																	58982592		2197	4292	6489	SO:0001587	stop_gained	25799	exon4			TGGGACGAGCTGG	AF060503	CCDS12981.1	19q13.43	2013-01-08				ENSG00000083812		"Zinc fingers, C2H2-type", "-"	14096	protein-coding gene	gene with protein product							Standard	NM_014347		Approved	ZF5128, ZNF324A	uc002qsw.2	O75467		ENST00000536459.2:c.733G>T	chr19.hg19:g.58982592G>T	ENSP00000444812:p.Glu245*	170.0	0.0		180.0	52.0	NM_014347	B3KRX1	Nonsense_Mutation	SNP	ENST00000536459.2	hg19	CCDS12981.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.463256	0.84425	.	.	ENSG00000083812	ENST00000378044;ENST00000196482;ENST00000536459;ENST00000539101;ENST00000535298	.	.	.	3.72	1.2	0.21068	.	0.360135	0.20437	N	0.092359	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	3.8068	0.08780	0.1844:0.259:0.5566:0.0	.	.	.	.	X	245;245;245;235;22	.	ENSP00000196482:E245X	E	+	1	0	ZNF324	63674404	0.677000	0.27577	0.021000	0.16686	0.046000	0.14306	0.923000	0.28757	0.356000	0.24157	0.455000	0.32223	GAG	.	.		0.637	ZNF324-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467044.1	NM_014347		T	58982592	G	T	58982592	4	4	259	1	0	0	0	0	0	1	0	0	17859	1059	37	1	743	1	ZNF324	19	58982592	Nonsense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	417790	58982592	146391	842	37160										
SLC27A5	10998	hgsc.bcm.edu	37	chr19	59011753	59011753	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gattgtccctcacaggctccGccgcctccatgtcgaactgc	9	17	1	0	rs371196997		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:59011753G>A	ENST00000263093.2	-	6	1530	c.1421C>T	c.(1420-1422)gCg>gTg	p.A474V	SLC27A5_ENST00000601355.1_Missense_Mutation_p.A390V|SLC27A5_ENST00000594786.1_5'Flank|SLC27A5_ENST00000599700.1_5'Flank	NM_012254.2	NP_036386.1	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid transporter), member 5	474					bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|ketone body biosynthetic process (GO:0046951)|plasma membrane long-chain fatty acid transport (GO:0015911)|small molecule metabolic process (GO:0044281)|triglyceride mobilization (GO:0006642)|very long-chain fatty acid metabolic process (GO:0000038)	basal plasma membrane (GO:0009925)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|protein complex (GO:0043234)	ATP binding (GO:0005524)|cholate-CoA ligase activity (GO:0047747)|fatty acid transporter activity (GO:0015245)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.181)		CACAGGCTCCGCCGCCTCCAT	0.622																																					p.A474V		Atlas-SNP	.											.	SLC27A5	58	.	0			c.C1421T						.	G	VAL/ALA	0,4406		0,0,2203	105	96	99		1421	-5.4	0	19		99	1,8599	1.2+/-3.3	0,1,4299	no	missense	SLC27A5	NM_012254.2	64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	474/691	59011753	1,13005	2203	4300	6503	SO:0001583	missense	10998	exon6			GGCTCCGCCGCCT	AF064255	CCDS12983.1	19q13.43	2013-07-15			ENSG00000083807	ENSG00000083807		"Acyl-CoA synthetase family", "Solute carriers"	10999	protein-coding gene	gene with protein product	"fatty-acid-Coenzyme A ligase, very long-chain 3"	603314				10479480, 10749848	Standard	NM_012254		Approved	FATP5, VLACSR, VLCS-H2, VLCSH2, FACVL3, FLJ22987, ACSVL6, ACSB	uc002qtc.2	Q9Y2P5	OTTHUMG00000183543	ENST00000263093.2:c.1421C>T	chr19.hg19:g.59011753G>A	ENSP00000263093:p.Ala474Val	83.0	0.0		72.0	4.0	NM_012254	B3KVP6|B4DPQ1	Missense_Mutation	SNP	ENST00000263093.2	hg19	CCDS12983.1	.	.	.	.	.	.	.	.	.	.	G	12.22	1.872513	0.33069	0.0	1.16E-4	ENSG00000083807	ENST00000263093	T	0.48522	0.81	5.33	-5.45	0.02616	AMP-dependent synthetase/ligase (1);	0.493199	0.22705	N	0.056644	T	0.29389	0.0732	L	0.27053	0.805	0.09310	N	1	B	0.15930	0.015	B	0.17098	0.017	T	0.05386	-1.0888	10	0.35671	T	0.21	-3.5408	13.4242	0.61015	0.1033:0.0:0.7245:0.1722	.	474	Q9Y2P5	S27A5_HUMAN	V	474	ENSP00000263093:A474V	ENSP00000263093:A474V	A	-	2	0	SLC27A5	63703565	0.189000	0.23263	0.001000	0.08648	0.394000	0.30568	0.697000	0.25556	-1.301000	0.02338	-0.363000	0.07495	GCG	.	.		0.622	SLC27A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467060.1	NM_012254		A	59011753	G	A	59011753	3	1	259	1	0	0	0	0	1	0	0	0	14544	1087	38	1	671	1	SLC27A5	19	59011753	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	29161	59011753	117230	843	37161										
MZF1	7593	hgsc.bcm.edu	37	chr19	59082638	59082638	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aacgcaggcgtgcagcttcaGggcctgggtcccataaggca	14	12	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:59082638G>T	ENST00000215057.2	-	2	679	c.119C>A	c.(118-120)cCt>cAt	p.P40H	MZF1_ENST00000594234.1_Missense_Mutation_p.P40H|MZF1_ENST00000599369.1_Missense_Mutation_p.P40H|AC016629.8_ENST00000593642.1_RNA|AC016629.8_ENST00000600726.1_RNA|AC016629.8_ENST00000600534.1_RNA|MZF1_ENST00000594108.1_Missense_Mutation_p.P40H	NM_001267033.1|NM_198055.1	NP_001253962.1|NP_932172.1	P28698	MZF1_HUMAN	myeloid zinc finger 1	40					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0443)|all cancers(4;7.92e-14)|Epithelial(4;5.57e-11)|OV - Ovarian serous cystadenocarcinoma(4;1.13e-09)|GBM - Glioblastoma multiforme(193;0.0108)|Lung(386;0.182)		TGCAGCTTCAGGGCCTGGGTC	0.657																																					p.P40H		Atlas-SNP	.											.	MZF1	37	.	0			c.C119A						.						26	29	28					19																	59082638		2203	4300	6503	SO:0001583	missense	7593	exon2			GCTTCAGGGCCTG	M58297	CCDS12988.1, CCDS59427.1	19q13.43	2014-08-22	2006-06-15	2006-06-15	ENSG00000099326	ENSG00000099326		"-", "Zinc fingers, C2H2-type"	13108	protein-coding gene	gene with protein product		194550	"zinc finger protein 42 (myeloid-specific retinoic acid-responsive)"	ZNF42		1860835	Standard	NM_198055		Approved	ZSCAN6, MZF1B, MZF-1, Zfp98	uc002qtn.3	P28698	OTTHUMG00000183550	ENST00000215057.2:c.119C>A	chr19.hg19:g.59082638G>T	ENSP00000215057:p.Pro40His	76.0	0.0		90.0	4.0	NM_198055	M0QXU0|Q7Z729|Q96I71|Q9NRY0|Q9UBW2	Missense_Mutation	SNP	ENST00000215057.2	hg19	CCDS12988.1	.	.	.	.	.	.	.	.	.	.	.	11.28	1.592594	0.28357	.	.	ENSG00000099326	ENST00000215057	T	0.06849	3.25	4.35	2.13	0.27403	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (2);	0.390912	0.18930	N	0.127254	T	0.24314	0.0589	M	0.85462	2.755	0.28327	N	0.921974	D;B	0.67145	0.996;0.173	P;B	0.61397	0.888;0.187	T	0.04320	-1.0960	9	.	.	.	-2.5914	7.2443	0.26114	0.2091:0.0:0.7909:0.0	.	40;40	Q7Z729;P28698	.;MZF1_HUMAN	H	40	ENSP00000215057:P40H	.	P	-	2	0	MZF1	63774450	0.000000	0.05858	0.747000	0.31113	0.698000	0.40448	0.333000	0.19768	0.557000	0.29117	0.563000	0.77884	CCT	.	.		0.657	MZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467112.1	NM_198055		T	59082638	G	T	59082638	3	4	259	1	0	0	0	0	1	0	0	0	10117	1000	35	3	2105	3	MZF1	19	59082638	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	70885	59082638	46345	844	37162										
TGM3	7053	hgsc.bcm.edu	37	chr20	2290970	2290970	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctgccagcgcacccataggaCggtacacaatggccctccag	10	16	0	0	rs139117716	byFrequency	TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:2290970C>T	ENST00000381458.5	+	3	391	c.328C>T	c.(328-330)Cgg>Tgg	p.R110W		NM_003245.3	NP_003236.3	Q08188	TGM3_HUMAN	transglutaminase 3	110					cell envelope organization (GO:0043163)|cellular protein modification process (GO:0006464)|hair follicle morphogenesis (GO:0031069)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein tetramerization (GO:0051262)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	calcium ion binding (GO:0005509)|catalytic activity (GO:0003824)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)|transferase activity, transferring acyl groups (GO:0016746)			breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(11)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	39					L-Glutamine(DB00130)	ACCCATAGGACGGTACACAAT	0.552													C|||	2	0.000399361	8e-04	0.0014	5008	,	,		20392	0		0	False		,,,				2504	0				p.R110W		Atlas-SNP	.											.	TGM3	105	.	0			c.C328T						.	C	TRP/ARG	4,4402	8.1+/-20.4	0,4,2199	197	175	183		328	1.7	0	20	dbSNP_134	183	0,8600		0,0,4300	yes	missense	TGM3	NM_003245.3	101	0,4,6499	TT,TC,CC		0.0,0.0908,0.0308	benign	110/694	2290970	4,13002	2203	4300	6503	SO:0001583	missense	7053	exon3			ATAGGACGGTACA	L10386	CCDS33435.1	20q11.2	2013-05-02	2013-05-02		ENSG00000125780	ENSG00000125780	2.3.2.13	"Transglutaminases"	11779	protein-coding gene	gene with protein product	"E polypeptide, protein-glutamine-gamma-glutamyltransferase"	600238	"transglutaminase 3 (E polypeptide, protein-glutamine-gamma-glutamyltransferase)"			7851911, 9452468	Standard	NM_003245		Approved	TGE	uc002wfx.4	Q08188	OTTHUMG00000031690	ENST00000381458.5:c.328C>T	chr20.hg19:g.2290970C>T	ENSP00000370867:p.Arg110Trp	143.0	0.0		131.0	51.0	NM_003245	A8K5N6|B2RCR6|D3DVX1|O95933|Q32ML9|Q32MM0	Missense_Mutation	SNP	ENST00000381458.5	hg19	CCDS33435.1	.	.	.	.	.	.	.	.	.	.	C	7.390	0.630671	0.14322	9.08E-4	0.0	ENSG00000125780	ENST00000381458;ENST00000420960	D	0.86230	-2.09	5.34	1.72	0.24424	Immunoglobulin E-set (1);Transglutaminase, N-terminal (1);Immunoglobulin-like fold (1);	1.329060	0.04642	N	0.405472	D	0.85579	0.5729	M	0.70275	2.135	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.66693	-0.5859	10	0.62326	D	0.03	.	4.5439	0.12071	0.2112:0.5782:0.0:0.2106	.	110	Q08188	TGM3_HUMAN	W	110	ENSP00000370867:R110W	ENSP00000370867:R110W	R	+	1	2	TGM3	2238970	0.000000	0.05858	0.001000	0.08648	0.019000	0.09904	0.748000	0.26305	-0.029000	0.13827	0.462000	0.41574	CGG	.	C|1.000;T|0.000		0.552	TGM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077579.2	NM_003245		T	2290970	C	T	2290970	3	4	259	1	0	0	0	0	1	0	0	0	15846	527	19	1	338	1	TGM3	20	2290970	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10		2290970	60734550	845	37163										
VPS16	64601	hgsc.bcm.edu	37	chr20	2845074	2845074	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agattttttcatgacccttcGgaatcagcccatggccctca	7	13	3	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:2845074G>T	ENST00000380445.3	+	18	1856	c.1784G>T	c.(1783-1785)cGg>cTg	p.R595L	VPS16_ENST00000380443.3_Missense_Mutation_p.R281L|PTPRA_ENST00000380393.3_5'UTR|VPS16_ENST00000380469.3_Missense_Mutation_p.R451L	NM_022575.2	NP_072097.2	Q9H269	VPS16_HUMAN	vacuolar protein sorting 16 homolog (S. cerevisiae)	595					intracellular protein transport (GO:0006886)|viral entry into host cell (GO:0046718)	actin filament (GO:0005884)|axon (GO:0030424)|early endosome (GO:0005769)|HOPS complex (GO:0030897)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|recycling endosome (GO:0055037)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	37						ATGACCCTTCGGAATCAGCCC	0.532																																					p.R595L		Atlas-SNP	.											.	VPS16	76	.	0			c.G1784T						.						117	112	113					20																	2845074		2203	4300	6503	SO:0001583	missense	64601	exon18			CCCTTCGGAATCA	AF308801	CCDS13036.1, CCDS13037.1	20p13	2009-07-07	2009-07-07	2009-07-07	ENSG00000215305	ENSG00000215305			14584	protein-coding gene	gene with protein product		608550					Standard	NM_022575		Approved		uc002whe.3	Q9H269	OTTHUMG00000031714	ENST00000380445.3:c.1784G>T	chr20.hg19:g.2845074G>T	ENSP00000369810:p.Arg595Leu	81.0	0.0		74.0	4.0	NM_022575	Q5JUB1|Q8WU31|Q96EE7|Q96N92|Q9H1Q4|Q9H1Q5	Missense_Mutation	SNP	ENST00000380445.3	hg19	CCDS13036.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.055831	0.76074	.	.	ENSG00000215305	ENST00000380445;ENST00000380469;ENST00000380443	T;T;T	0.46451	0.87;0.87;0.87	5.2	5.2	0.72013	Vps16, C-terminal (1);	0.110998	0.64402	D	0.000011	T	0.49712	0.1573	M	0.67700	2.07	0.80722	D	1	P;P;P;P	0.47409	0.895;0.895;0.683;0.895	P;P;B;P	0.50970	0.655;0.655;0.145;0.655	T	0.47623	-0.9103	10	0.45353	T	0.12	-25.5608	9.6043	0.39624	0.0921:0.0:0.9079:0.0	.	71;281;451;595	A1A4H0;Q5JUA8;Q9H269-2;Q9H269	.;.;.;VPS16_HUMAN	L	595;451;281	ENSP00000369810:R595L;ENSP00000369836:R451L;ENSP00000369808:R281L	ENSP00000369808:R281L	R	+	2	0	VPS16	2793074	1.000000	0.71417	0.999000	0.59377	0.880000	0.50808	5.600000	0.67599	2.706000	0.92434	0.561000	0.74099	CGG	.	.		0.532	VPS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077658.2	NM_022575		T	2845074	G	T	2845074	3	4	259	1	0	0	0	0	1	0	0	0	17208	1116	39	1	1854	1	VPS16	20	2845074	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	554104	2845074	60180446	846	37164										
C20orf103	24141	hgsc.bcm.edu	37	chr20	9496099	9496099	+	Splice_Site	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	attgttttgtttgttccgcaGatacaatggctcaaatcatg	8	7	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:9496099G>T	ENST00000246070.2	+	2	556		c.e2-1		RP5-1119D9.4_ENST00000443469.1_RNA|LAMP5_ENST00000427562.2_Splice_Site	NM_012261.3	NP_036393.1	Q9UJQ1	LAMP5_HUMAN	lysosomal-associated membrane protein family, member 5							cytoplasmic vesicle membrane (GO:0030659)|dendrite membrane (GO:0032590)|early endosome membrane (GO:0031901)|endoplasmic reticulum-Golgi intermediate compartment membrane (GO:0033116)|endosome membrane (GO:0010008)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)											TTGTTCCGCAGATACAATGGC	0.493																																					.		Atlas-SNP	.											.	.	.	.	0			c.65-1G>T						.						89	85	86					20																	9496099		2203	4300	6503	SO:0001630	splice_region_variant	24141	exon2			TCCGCAGATACAA	AL121740	CCDS13106.1, CCDS56177.1	20p12	2013-03-14	2011-11-25	2011-11-25	ENSG00000125869	ENSG00000125869			16097	protein-coding gene	gene with protein product	"brain and dendritic cell associated LAMP"	614641	"chromosome 20 open reading frame 103"	C20orf103		11780052, 21642595	Standard	NM_012261		Approved	dJ1119D9.3, BAD-LAMP, UNC-43	uc002wni.2	Q9UJQ1	OTTHUMG00000031851	ENST00000246070.2:c.65-1G>T	chr20.hg19:g.9496099G>T		73.0	0.0		96.0	5.0	NM_001199897	B4DHZ7|B7Z9Z9	Splice_Site	SNP	ENST00000246070.2	hg19	CCDS13106.1	.	.	.	.	.	.	.	.	.	.	G	19.13	3.766937	0.69878	.	.	ENSG00000125869	ENST00000246070;ENST00000427562	.	.	.	5.65	5.65	0.86999	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.7362	0.96205	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	C20orf103	9444099	1.000000	0.71417	0.997000	0.53966	0.974000	0.67602	7.620000	0.83070	2.678000	0.91216	0.655000	0.94253	.	.	.		0.493	LAMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077946.2	NM_012261	Intron	T	9496099	G	T	9496099	5	4	259	1	0	0	0	0	0	0	1	0	2077	956	33	3	70	3	C20orf103	20	9496099	Splice_Site	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	6651025	9496099	53529421	847	37165										
RRBP1	6238	hgsc.bcm.edu	37	chr20	17596120	17596120	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttctgaagactctagggggcCggctgtgcggagcttctcca	14	11	3	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:17596120C>A	ENST00000377813.1	-	23	4309	c.4006G>T	c.(4006-4008)Ggc>Tgc	p.G1336C	RRBP1_ENST00000377807.2_Missense_Mutation_p.G903C|RRBP1_ENST00000455029.2_Missense_Mutation_p.G677C|RRBP1_ENST00000246043.4_Missense_Mutation_p.G1336C|RRBP1_ENST00000470422.1_5'UTR|RRBP1_ENST00000360807.4_Missense_Mutation_p.G903C			Q9P2E9	RRBP1_HUMAN	ribosome binding protein 1	1336					osteoblast differentiation (GO:0001649)|protein transport (GO:0015031)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(6)	28						TCTAGGGGGCCGGCTGTGCGG	0.617																																					p.G903C		Atlas-SNP	.											.	RRBP1	157	.	0			c.G2707T						.						50	52	51					20																	17596120		2203	4300	6503	SO:0001583	missense	6238	exon23			GGGGGCCGGCTGT	AB037819	CCDS13128.1	20p12	2012-12-07	2012-12-07		ENSG00000125844	ENSG00000125844			10448	protein-coding gene	gene with protein product		601418	"ribosome binding protein 1 (dog 180kD homolog)", "ribosome binding protein 1 homolog 180kDa (dog)"			8812507	Standard	NM_001042576		Approved	ES/130, hES	uc002wpw.1	Q9P2E9	OTTHUMG00000031945	ENST00000377813.1:c.4006G>T	chr20.hg19:g.17596120C>A	ENSP00000367044:p.Gly1336Cys	76.0	0.0		55.0	4.0	NM_004587	A2A2S6|A6NCN6|O75300|O75301|Q5W165|Q96SB2|Q9BWP1|Q9H476	Missense_Mutation	SNP	ENST00000377813.1	hg19		.	.	.	.	.	.	.	.	.	.	C	14.04	2.415869	0.42817	.	.	ENSG00000125844	ENST00000360807;ENST00000377813;ENST00000377807;ENST00000246043;ENST00000455029	T;T;T;T;T	0.30981	1.51;1.51;1.51;1.51;1.51	5.13	-1.17	0.09648	.	1.187640	0.06414	N	0.721149	T	0.37073	0.0990	L	0.36672	1.1	0.09310	N	1	D;D	0.76494	0.999;0.988	P;P	0.60682	0.878;0.488	T	0.33214	-0.9877	10	0.56958	D	0.05	-1.2695	5.4546	0.16584	0.0:0.3958:0.1451:0.459	.	903;1336	Q9P2E9-3;Q9P2E9	.;RRBP1_HUMAN	C	903;1336;903;1336;677	ENSP00000354045:G903C;ENSP00000367044:G1336C;ENSP00000367038:G903C;ENSP00000246043:G1336C;ENSP00000401206:G677C	ENSP00000246043:G1336C	G	-	1	0	RRBP1	17544120	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.005000	0.13129	-0.106000	0.12110	-0.265000	0.10407	GGC	.	.		0.617	RRBP1-002	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000078125.1	NM_001042576		A	17596120	C	A	17596120	3	1	259	1	0	0	0	0	1	0	0	0	13693	652	23	1	238	1	RRBP1	20	17596120	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	8100021	17596120	45429400	848	37166										
GGTLC1	92086	hgsc.bcm.edu	37	chr20	23967085	23967085	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gcccctactagaggttgatgGtgctggtggcggacacagca	15	10	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:23967085G>A	ENST00000335694.4	-	2	368	c.164C>T	c.(163-165)aCc>aTc	p.T55I	GGTLC1_ENST00000278765.4_Missense_Mutation_p.T55I|GGTLC1_ENST00000286890.4_Missense_Mutation_p.T55I	NM_178311.2	NP_842563.1	Q9BX51	GGTL1_HUMAN	gamma-glutamyltransferase light chain 1	55					glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)	gamma-glutamyltransferase activity (GO:0003840)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	15						GAGGTTGATGGTGCTGGTGGC	0.622																																					p.T55I		Atlas-SNP	.											.	GGTLC1	37	.	0			c.C164T						.						18	18	18					20																	23967085		2201	4279	6480	SO:0001583	missense	92086	exon2			TTGATGGTGCTGG	AL133466	CCDS13163.1	20p11.21	2010-07-14	2008-03-10	2008-03-10	ENSG00000149435	ENSG00000149435		"Gamma-glutamyltransferases"	16437	protein-coding gene	gene with protein product		612338	"gamma-glutamyltransferase-like activity 4", "gamma-glutamyltransferase-like activity 3"	GGTLA4, GGTLA3		10843999, 18357469	Standard	NM_178311		Approved	dJ831C21.2, dJ831C21.1	uc002wtu.3	Q9BX51	OTTHUMG00000032095	ENST00000335694.4:c.164C>T	chr20.hg19:g.23967085G>A	ENSP00000337587:p.Thr55Ile	53.0	0.0		54.0	22.0	NM_178311	D3DW43|Q08246	Missense_Mutation	SNP	ENST00000335694.4	hg19	CCDS13163.1	.	.	.	.	.	.	.	.	.	.	g	12.80	2.045074	0.36085	.	.	ENSG00000149435	ENST00000286890;ENST00000278765;ENST00000335694	T;T;T	0.15603	2.41;2.41;2.41	0.844	0.844	0.18943	.	0.000000	0.85682	D	0.000000	T	0.54631	0.1870	H	0.99516	4.605	0.38367	D	0.944774	D	0.76494	0.999	D	0.70935	0.971	T	0.62478	-0.6846	10	0.87932	D	0	-51.049	7.477	0.27382	1.0E-4:0.0:0.9999:0.0	.	55	Q9BX51	GGTL1_HUMAN	I	55	ENSP00000286890:T55I;ENSP00000278765:T55I;ENSP00000337587:T55I	ENSP00000278765:T55I	T	-	2	0	GGTLC1	23915085	1.000000	0.71417	0.028000	0.17463	0.028000	0.11728	4.489000	0.60309	0.088000	0.17205	0.089000	0.15464	ACC	.	.		0.622	GGTLC1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078366.2	NM_178311.2		A	23967085	G	A	23967085	3	1	259	1	0	0	0	0	1	0	0	0	6373	1261	44	3	533	3	GGTLC1	20	23967085	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	6370965	23967085	39058435	849	37167										
C20orf185	359710	hgsc.bcm.edu	37	chr20	31657761	31657761	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	catctccctgtccctggaacGgtaacttgggatcctgggga	12	12	1	0	rs372182848		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:31657761G>T	ENST00000375494.3	+	11	1217	c.1217G>T	c.(1216-1218)cGg>cTg	p.R406L		NM_182658.1	NP_872599.1	P59826	BPIB3_HUMAN	BPI fold containing family B, member 3	406					innate immune response (GO:0045087)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										TCCCTGGAACGGTAACTTGGG	0.562																																					p.R406L		Atlas-SNP	.											.	.	.	.	0			c.G1217T						.						168	151	156					20																	31657761		2203	4300	6503	SO:0001630	splice_region_variant	359710	exon11			TGGAACGGTAACT	AF549189	CCDS13212.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186190	ENSG00000186190		"BPI fold containing"	16178	protein-coding gene	gene with protein product		615717	"chromosome 20 open reading frame 185"	C20orf185		11971875, 21787333	Standard	NM_182658		Approved	dJ726C3.4, LPLUNC3, RYA3	uc002wym.1	P59826	OTTHUMG00000032234	ENST00000375494.3:c.1217+1G>T	chr20.hg19:g.31657761G>T		80.0	0.0		98.0	4.0	NM_182658	Q5TDX7	Missense_Mutation	SNP	ENST00000375494.3	hg19	CCDS13212.1	.	.	.	.	.	.	.	.	.	.	G	12.72	2.021926	0.35701	.	.	ENSG00000186190	ENST00000375494	T	0.10763	2.84	4.43	4.43	0.53597	.	0.000000	0.49916	D	0.000130	T	0.31734	0.0806	M	0.80982	2.52	0.44316	D	0.997196	D	0.69078	0.997	D	0.81914	0.995	T	0.02398	-1.1165	10	0.30078	T	0.28	-19.8272	12.7225	0.57149	0.0:0.0:1.0:0.0	.	406	P59826	BPIB3_HUMAN	L	406	ENSP00000364643:R406L	ENSP00000364643:R406L	R	+	2	0	BPIFB3	31121422	1.000000	0.71417	1.000000	0.80357	0.303000	0.27691	4.189000	0.58358	2.440000	0.82611	0.655000	0.94253	CGG	.	.		0.562	BPIFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078654.2	NM_182658	Missense_Mutation	T	31657761	G	T	31657761	5	4	259	1	0	0	0	0	0	0	1	0	2099	1130	39	1	1259	1	C20orf185	20	31657761	Splice_Site	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	7690676	31657761	31367759	850	37168										
RBM12	10137	hgsc.bcm.edu	37	chr20	34240516	34240516	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agtcaatgacagcagctgtgGcttcatcccgagactcaaag	10	11	3	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:34240516G>A	ENST00000374114.3	-	3	2992	c.2729C>T	c.(2728-2730)gCc>gTc	p.A910V	RBM12_ENST00000359646.1_Missense_Mutation_p.A910V|CPNE1_ENST00000397443.1_Intron|CPNE1_ENST00000317677.5_Intron|RBM12_ENST00000374104.3_Missense_Mutation_p.A910V|CPNE1_ENST00000397446.1_Intron|CPNE1_ENST00000352393.4_Intron|RP1-309K20.6_ENST00000541176.2_Intron|CPNE1_ENST00000397445.1_Intron|CPNE1_ENST00000397442.1_Intron|CPNE1_ENST00000317619.3_Intron	NM_001198838.1|NM_001198840.1|NM_006047.5	NP_001185767.1|NP_001185769.1|NP_006038.2	Q9NTZ6	RBM12_HUMAN	RNA binding motif protein 12	910	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.					nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(7)|kidney(1)|large_intestine(3)|lung(14)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			AGCAGCTGTGGCTTCATCCCG	0.413																																					p.A910V		Atlas-SNP	.											.	RBM12	93	.	0			c.C2729T						.						89	86	87					20																	34240516		2203	4300	6503	SO:0001583	missense	10137	exon2			GCTGTGGCTTCAT	AJ289772	CCDS13261.1	20q11.21	2013-02-12			ENSG00000244462	ENSG00000244462		"RNA binding motif (RRM) containing"	9898	protein-coding gene	gene with protein product		607179				11435693	Standard	NM_006047		Approved	HRIHFB2091, KIAA0765, SWAN	uc021wcq.1	Q9NTZ6	OTTHUMG00000032350	ENST00000374114.3:c.2729C>T	chr20.hg19:g.34240516G>A	ENSP00000363228:p.Ala910Val	131.0	0.0		145.0	6.0	NM_001198840	B3KRU2|E1P5R6|O94865|Q8N3B1|Q9H196	Missense_Mutation	SNP	ENST00000374114.3	hg19	CCDS13261.1	.	.	.	.	.	.	.	.	.	.	G	17.47	3.397344	0.62177	.	.	ENSG00000244462	ENST00000374114;ENST00000359646;ENST00000374104;ENST00000349942	T;T;T	0.18174	2.23;2.23;2.23	5.37	5.37	0.77165	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.49423	0.1556	M	0.84846	2.72	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	T	0.54029	-0.8354	10	0.87932	D	0	-4.4997	19.3135	0.94202	0.0:0.0:1.0:0.0	.	910	Q9NTZ6	RBM12_HUMAN	V	910;910;910;709	ENSP00000363228:A910V;ENSP00000352668:A910V;ENSP00000363217:A910V	ENSP00000339879:A709V	A	-	2	0	RBM12	33703930	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.263000	0.95617	2.798000	0.96311	0.650000	0.86243	GCC	.	.		0.413	RBM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078894.1	NM_006047		A	34240516	G	A	34240516	3	1	259	1	0	0	0	0	1	0	0	0	13128	1203	42	3	73	3	RBM12	20	34240516	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	2582755	34240516	28785004	851	37169										
KIAA1755	85449	hgsc.bcm.edu	37	chr20	36841909	36841909	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gtcagtgccttctccaggagCatccggatctcctcatgcct	9	15	4	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:36841909C>T	ENST00000279024.4	-	14	3409	c.3138G>A	c.(3136-3138)atG>atA	p.M1046I		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	1046										breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				TCTCCAGGAGCATCCGGATCT	0.682																																					p.M1046I		Atlas-SNP	.											.	KIAA1755	145	.	0			c.G3138A						.						38	33	35					20																	36841909		2203	4300	6503	SO:0001583	missense	85449	exon14			CAGGAGCATCCGG	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.3138G>A	chr20.hg19:g.36841909C>T	ENSP00000279024:p.Met1046Ile	81.0	0.0		68.0	4.0	NM_001029864	Q9C0A8	Missense_Mutation	SNP	ENST00000279024.4	hg19	CCDS33467.1	.	.	.	.	.	.	.	.	.	.	C	5.886	0.347533	0.11126	.	.	ENSG00000149633	ENST00000279024	T	0.05319	3.46	5.29	0.843	0.18935	.	1.696560	0.03063	N	0.156110	T	0.07188	0.0182	L	0.36672	1.1	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.38929	-0.9638	10	0.38643	T	0.18	.	7.8512	0.29455	0.0963:0.4943:0.4093:0.0	.	1046	Q5JYT7	K1755_HUMAN	I	1046	ENSP00000279024:M1046I	ENSP00000279024:M1046I	M	-	3	0	KIAA1755	36275323	0.424000	0.25490	0.379000	0.26080	0.169000	0.22640	0.516000	0.22817	0.362000	0.24319	-0.304000	0.09214	ATG	.	.		0.682	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864		T	36841909	C	T	36841909	3	4	259	1	0	0	0	0	1	0	0	0	8266	710	25	3	468	3	KIAA1755	20	36841909	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	2601393	36841909	26183611	852	37170										
L3MBTL	26013	hgsc.bcm.edu	37	chr20	42161426	42161426	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cccctagagtcccccaccccTgggcttccaggtgggcatga	11	17	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:42161426T>C	ENST00000427442.2	+	12	1391	c.1232T>C	c.(1231-1233)cTg>cCg	p.L411P	L3MBTL1_ENST00000373135.3_Missense_Mutation_p.L343P|L3MBTL1_ENST00000373134.1_Missense_Mutation_p.L343P|L3MBTL1_ENST00000444063.1_Missense_Mutation_p.L343P|L3MBTL1_ENST00000418998.1_Missense_Mutation_p.L411P			Q9Y468	LMBL1_HUMAN	l(3)mbt-like 1 (Drosophila)	343					chromatin modification (GO:0016568)|hemopoiesis (GO:0030097)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of megakaryocyte differentiation (GO:0045652)|regulation of mitosis (GO:0007088)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|identical protein binding (GO:0042802)|methylated histone binding (GO:0035064)|nucleosomal histone binding (GO:0031493)|nucleosome binding (GO:0031491)|SAM domain binding (GO:0032093)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(3)|ovary(1)|skin(2)	7						CCCCCACCCCTGGGCTTCCAG	0.602																																					p.L411P		Atlas-SNP	.											.	L3MBTL1	105	.	0			c.T1232C						.						92	97	95					20																	42161426		2203	4300	6503	SO:0001583	missense	26013	exon12			CACCCCTGGGCTT	U89358	CCDS13319.1, CCDS46602.1, CCDS46602.2	20q13.12	2013-01-10	2010-09-03	2010-09-03	ENSG00000185513	ENSG00000185513		"Zinc fingers, C2HC-type containing", "Sterile alpha motif (SAM) domain containing"	15905	protein-coding gene	gene with protein product	"lethal (3) malignant brain tumor l(3)"	608802	"l(3)mbt (Drosophila)-like", "l(3)mbt-like (Drosophila)"	L3MBTL		10445843, 17540172	Standard	NM_032107		Approved	ZC2HC3, dJ138B7.3, DKFZp586P1522, KIAA0681	uc010zwh.2	Q9Y468	OTTHUMG00000032503	ENST00000427442.2:c.1232T>C	chr20.hg19:g.42161426T>C	ENSP00000402107:p.Leu411Pro	159.0	0.0		125.0	5.0	NM_032107	B4DRC9|E1P5W7|Q5H8Y8|Q5H8Y9|Q8IUV7|Q9H1E6|Q9H1G5|Q9UG06|Q9UJB9|Q9Y4C9	Missense_Mutation	SNP	ENST00000427442.2	hg19	CCDS46602.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.18|12.18	1.860769|1.860769	0.32884|0.32884	.|.	.|.	ENSG00000185513|ENSG00000185513	ENST00000427442;ENST00000418998;ENST00000373135;ENST00000444063;ENST00000373134;ENST00000422861|ENST00000445228	T;T;T;T;T;T|.	0.43688|.	0.94;0.94;0.94;0.94;0.94;0.94|.	5.09|5.09	3.96|3.96	0.45880|0.45880	.|.	0.531666|.	0.19869|.	N|.	0.104240|.	T|T	0.36468|0.36468	0.0968|0.0968	N|N	0.19112|0.19112	0.55|0.55	0.43226|0.43226	D|D	0.995113|0.995113	B;B;B|.	0.06786|.	0.001;0.001;0.001|.	B;B;B|.	0.09377|.	0.004;0.003;0.004|.	T|T	0.15954|0.15954	-1.0419|-1.0419	10|5	0.29301|.	T|.	0.29|.	.|.	4.2741|4.2741	0.10800|0.10800	0.0:0.2543:0.0:0.7457|0.0:0.2543:0.0:0.7457	.|.	411;343;343|.	Q9Y468-5;Q9Y468-2;Q9Y468-1|.	.;.;.|.	P|R	411;411;343;343;343;129|34	ENSP00000402107:L411P;ENSP00000398516:L411P;ENSP00000362227:L343P;ENSP00000403316:L343P;ENSP00000362226:L343P;ENSP00000410139:L129P|.	ENSP00000362226:L343P|.	L|W	+|+	2|1	0|0	L3MBTL1|L3MBTL1	41594840|41594840	0.487000|0.487000	0.25988|0.25988	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	1.180000|1.180000	0.32005|0.32005	2.134000|2.134000	0.65973|0.65973	0.482000|0.482000	0.46254|0.46254	CTG|TGG	.	.		0.602	L3MBTL1-007	KNOWN	upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079300.3	NM_032107		C	42161426	T	C	42161426	3	2	259	1	0	0	0	0	1	0	0	0	8600	1580	55	2	1062	2	L3MBTL	20	42161426	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	5319517	42161426	20864094	853	37171										
SLPI	6590	hgsc.bcm.edu	37	chr20	43882355	43882355	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgggcagatttcttaggaggAcagactccagctttgaaggc	13	8	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:43882355A>G	ENST00000338380.2	-	2	125	c.105T>C	c.(103-105)tgT>tgC	p.C35C		NM_003064.2	NP_003055.1	P03973	SLPI_HUMAN	secretory leukocyte peptidase inhibitor	35	Trypsin inhibitory domain.|WAP 1. {ECO:0000255|PROSITE- ProRule:PRU00722}.				negative regulation of protein binding (GO:0032091)|negative regulation of viral genome replication (GO:0045071)	extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|enzyme binding (GO:0019899)|serine-type endopeptidase inhibitor activity (GO:0004867)			lung(3)|ovary(1)	4		Myeloproliferative disorder(115;0.0122)				TCTTAGGAGGACAGACTCCAG	0.498																																					p.C35C	GBM(64;162 1089 31780 33427 34538)	Atlas-SNP	.											.	SLPI	13	.	0			c.T105C						.						81	82	82					20																	43882355		2203	4300	6503	SO:0001819	synonymous_variant	6590	exon2			AGGAGGACAGACT	X04502	CCDS13347.1	20q13.12	2013-01-21	2005-08-17		ENSG00000124107	ENSG00000124107		"WAP four-disulfide core domain containing"	11092	protein-coding gene	gene with protein product	"antileukoproteinase"	107285	"secretory leukocyte protease inhibitor (antileukoproteinase)"			3640338, 12206714	Standard	NM_003064		Approved	HUSI-I, ALK1, ALP, BLPI, HUSI, WAP4, WFDC4	uc002xnm.1	P03973	OTTHUMG00000033075	ENST00000338380.2:c.105T>C	chr20.hg19:g.43882355A>G		102.0	0.0		136.0	6.0	NM_003064	B2R5H8|P07757	Silent	SNP	ENST00000338380.2	hg19	CCDS13347.1																																																																																			.	.		0.498	SLPI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080494.3			G	43882355	A	G	43882355	2	3	259	1	0	0	0	0	0	0	0	1	14768	273	10	2		2	SLPI	20	43882355	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1720929	43882355	19143165	854	37172										
MMP9	4318	hgsc.bcm.edu	37	chr20	44640845	44640845	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccccttcactttcctgggtaAggagtactcgacctgtacca	8	14	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:44640845A>G	ENST00000372330.3	+	7	1086	c.1067A>G	c.(1066-1068)aAg>aGg	p.K356R	RP11-465L10.10_ENST00000535913.1_RNA	NM_004994.2	NP_004985.2	P14780	MMP9_HUMAN	matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)	356	Fibronectin type-II 3. {ECO:0000255|PROSITE-ProRule:PRU00479}.				collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|macrophage differentiation (GO:0030225)|negative regulation of cation channel activity (GO:2001258)|ossification (GO:0001503)|positive regulation of apoptotic process (GO:0043065)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of receptor binding (GO:1900122)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)|identical protein binding (GO:0042802)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|large_intestine(14)|liver(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(3)	46		Myeloproliferative disorder(115;0.0122)			Captopril(DB01197)|Glucosamine(DB01296)|Marimastat(DB00786)|Minocycline(DB01017)	TTCCTGGGTAAGGAGTACTCG	0.632																																					p.K356R		Atlas-SNP	.											.	MMP9	84	.	0			c.A1067G						.						73	83	80					20																	44640845		2203	4300	6503	SO:0001583	missense	4318	exon7			TGGGTAAGGAGTA		CCDS13390.1	20q12-q13	2008-01-07	2005-08-08		ENSG00000100985	ENSG00000100985	3.4.24.35		7176	protein-coding gene	gene with protein product		120361	"matrix metalloproteinase 9 (gelatinase B, 92kD gelatinase, 92kD type IV collagenase)", "matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)"	CLG4B		2158484	Standard	NM_004994		Approved		uc002xqz.3	P14780	OTTHUMG00000033044	ENST00000372330.3:c.1067A>G	chr20.hg19:g.44640845A>G	ENSP00000361405:p.Lys356Arg	82.0	0.0		63.0	4.0	NM_004994	B2R7V9|Q3LR70|Q8N725|Q9H4Z1|Q9UCJ9|Q9UCL1|Q9UDK2	Missense_Mutation	SNP	ENST00000372330.3	hg19	CCDS13390.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.962306	0.74016	.	.	ENSG00000100985	ENST00000372330;ENST00000545925	T	0.53206	0.63	4.89	3.76	0.43208	Peptidase M10, metallopeptidase (1);Fibronectin, type II, collagen-binding (5);Kringle-like fold (1);Peptidase, metallopeptidase (1);	0.161334	0.53938	D	0.000047	T	0.43500	0.1250	M	0.64676	1.99	0.39890	D	0.973758	B	0.11235	0.004	B	0.10450	0.005	T	0.48603	-0.9021	10	0.51188	T	0.08	.	9.8817	0.41238	0.9072:0.0:0.0928:0.0	.	356	P14780	MMP9_HUMAN	R	356;19	ENSP00000361405:K356R	ENSP00000361405:K356R	K	+	2	0	MMP9	44074252	1.000000	0.71417	1.000000	0.80357	0.838000	0.47535	4.847000	0.62867	2.064000	0.61679	0.459000	0.35465	AAG	.	.		0.632	MMP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080337.1			G	44640845	A	G	44640845	3	3	259	1	0	0	0	0	1	0	0	0	9678	72	3	2	1093	2	MMP9	20	44640845	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	758490	44640845	18384675	855	37173										
SLC13A3	64849	hgsc.bcm.edu	37	chr20	45239191	45239191	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agcatcatggcagtggaggcGgtgttgctcagccacatgga	15	9	2	0	rs563338890		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:45239191G>T	ENST00000279027.4	-	3	453	c.435C>A	c.(433-435)acC>acA	p.T145T	SLC13A3_ENST00000372121.1_Silent_p.T145T|SLC13A3_ENST00000435032.1_5'UTR|SLC13A3_ENST00000290317.5_Silent_p.T98T|SLC13A3_ENST00000339636.3_Silent_p.T145T|SLC13A3_ENST00000417157.2_Silent_p.T98T|SLC13A3_ENST00000413164.2_Silent_p.T145T|SLC13A3_ENST00000396360.1_Silent_p.T98T|SLC13A3_ENST00000472148.1_Silent_p.T98T|SLC13A3_ENST00000495082.1_Silent_p.T98T	NM_001193342.1|NM_022829.5	NP_001180271.1|NP_073740.2	Q8WWT9	S13A3_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 3	145					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-affinity sodium:dicarboxylate symporter activity (GO:0015362)	p.T145T(2)		breast(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	CAGTGGAGGCGGTGTTGCTCA	0.552																																					p.T145T		Atlas-SNP	.											SLC13A3_ENST00000339636,NS,carcinoma,0,1	SLC13A3	88	.	2	Substitution - coding silent(2)	endometrium(2)	c.C435A						.						180	161	167					20																	45239191		2203	4300	6503	SO:0001819	synonymous_variant	64849	exon3			GGAGGCGGTGTTG	AF154121	CCDS13400.1, CCDS42886.1, CCDS54469.1, CCDS54470.1	20q13.12	2013-05-22			ENSG00000158296	ENSG00000158296		"Solute carriers"	14430	protein-coding gene	gene with protein product		606411				10794676, 10992006	Standard	NM_001011554		Approved	NADC3, SDCT2	uc002xsf.2	Q8WWT9	OTTHUMG00000033042	ENST00000279027.4:c.435C>A	chr20.hg19:g.45239191G>T		88.0	0.0		68.0	3.0	NM_022829	B4DIR8|E1P5U4|F6WI18|Q5JYC9|Q5JYD0|Q5JYD1|Q5TCQ2|Q8IVB1|Q8N8K4|Q96MM5|Q9BR25|Q9H1G1|Q9H3W4|Q9NQN5|Q9NS04	Silent	SNP	ENST00000279027.4	hg19	CCDS13400.1																																																																																			.	.		0.552	SLC13A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080329.2			T	45239191	G	T	45239191	2	4	259	1	0	0	0	0	0	0	0	1	14408	1103	39	1		1	SLC13A3	20	45239191	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	598346	45239191	17786329	856	37174										
PCK1	5105	hgsc.bcm.edu	37	chr20	56137172	56137172	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gatgtggccaggatcgaaagCaagacggttatcgtcaccca	12	10	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:56137172C>T	ENST00000319441.4	+	3	434	c.270C>T	c.(268-270)agC>agT	p.S90S	PCK1_ENST00000543666.1_Intron|PCK1_ENST00000535860.1_Intron	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	90					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			GGATCGAAAGCAAGACGGTTA	0.557																																					p.S90S		Atlas-SNP	.											.	PCK1	95	.	0			c.C270T						.						101	87	92					20																	56137172		2203	4300	6503	SO:0001819	synonymous_variant	5105	exon3			CGAAAGCAAGACG		CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.270C>T	chr20.hg19:g.56137172C>T		117.0	0.0		95.0	5.0	NM_002591	A8K437|B4DT64|Q8TCA3|Q9UJD2	Silent	SNP	ENST00000319441.4	hg19	CCDS13460.1																																																																																			.	.		0.557	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2			T	56137172	C	T	56137172	2	4	259	1	0	0	0	0	0	0	0	1	11590	709	25	3		3	PCK1	20	56137172	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	10897981	56137172	6888348	857	37175										
PMEPA1	56937	hgsc.bcm.edu	37	chr20	56228121	56228121	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gttgcctgacactgtgctctCcgagggccacaggcatcctt	11	14	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:56228121C>A	ENST00000341744.3	-	3	605	c.286G>T	c.(286-288)Gag>Tag	p.E96*	PMEPA1_ENST00000265626.4_Nonsense_Mutation_p.E46*|PMEPA1_ENST00000395814.1_Nonsense_Mutation_p.E46*|PMEPA1_ENST00000395816.3_Nonsense_Mutation_p.E46*|PMEPA1_ENST00000347215.4_Nonsense_Mutation_p.E61*	NM_020182.4	NP_064567.2	Q969W9	PMEPA_HUMAN	prostate transmembrane protein, androgen induced 1	96					androgen receptor signaling pathway (GO:0030521)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|transforming growth factor beta receptor signaling pathway (GO:0007179)	early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	R-SMAD binding (GO:0070412)|WW domain binding (GO:0050699)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|prostate(1)	16						ACTGTGCTCTCCGAGGGCCAC	0.632																																					p.E96X		Atlas-SNP	.											PMEPA1,NS,carcinoma,0,1	PMEPA1	29	.	0			c.G286T						.						114	69	84					20																	56228121		2203	4300	6503	SO:0001587	stop_gained	56937	exon3			TGCTCTCCGAGGG	AF224278	CCDS13462.1, CCDS13463.1, CCDS13464.1	20q13.31-q13.33	2008-04-03	2008-04-03	2008-04-03	ENSG00000124225	ENSG00000124225			14107	protein-coding gene	gene with protein product	"solid tumor-associated 1"	606564	"transmembrane, prostate androgen induced RNA"	TMEPAI		10873380	Standard	NM_020182		Approved	STAG1	uc002xyq.4	Q969W9	OTTHUMG00000032831	ENST00000341744.3:c.286G>T	chr20.hg19:g.56228121C>A	ENSP00000345826:p.Glu96*	83.0	0.0		109.0	35.0	NM_020182	Q5TDR6|Q8NER4|Q96B72|Q9UJD3	Nonsense_Mutation	SNP	ENST00000341744.3	hg19	CCDS13463.1	.	.	.	.	.	.	.	.	.	.	C	37	5.995370	0.97184	.	.	ENSG00000124225	ENST00000341744;ENST00000347215;ENST00000395816;ENST00000265626;ENST00000395814;ENST00000414037;ENST00000395819	.	.	.	4.51	4.51	0.55191	.	0.168609	0.50627	D	0.000104	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-14.1401	16.852	0.85996	0.0:1.0:0.0:0.0	.	.	.	.	X	96;61;46;46;46;68;153	.	ENSP00000265626:E46X	E	-	1	0	PMEPA1	55661527	1.000000	0.71417	0.880000	0.34516	0.820000	0.46376	6.525000	0.73795	2.055000	0.61198	0.655000	0.94253	GAG	.	.		0.632	PMEPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079858.2	NM_020182		A	56228121	C	A	56228121	4	1	259	1	0	0	0	0	0	1	0	0	12141	864	30	3	585	3	PMEPA1	20	56228121	Nonsense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	90949	56228121	6797399	858	37176										
GNAS	2778	hgsc.bcm.edu	37	chr20	57428565	57428565	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	acccaactttcaggtcctcaAcccggcattcagggaagctg	9	14	3	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:57428565A>G	ENST00000371100.4	+	1	797	c.245A>G	c.(244-246)aAc>aGc	p.N82S	GNAS_ENST00000371102.4_Missense_Mutation_p.N82S|GNAS_ENST00000464624.2_3'UTR|GNAS_ENST00000371099.2_Missense_Mutation_p.N82S|GNAS_ENST00000313949.7_Intron|GNAS_ENST00000371098.2_Intron|GNAS_ENST00000306120.3_Missense_Mutation_p.T19A|GNAS-AS1_ENST00000424094.2_RNA|GNAS_ENST00000371075.3_Intron|GNAS-AS1_ENST00000598163.1_RNA	NM_001077490.1|NM_080425.2	NP_001070958.1|NP_536350.2	P63092	GNAS2_HUMAN	GNAS complex locus	0					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|bone development (GO:0060348)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|cognition (GO:0050890)|developmental growth (GO:0048589)|energy reserve metabolic process (GO:0006112)|hair follicle placode formation (GO:0060789)|intracellular transport (GO:0046907)|platelet aggregation (GO:0070527)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of insulin secretion (GO:0050796)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intrinsic component of membrane (GO:0031224)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	adenylate cyclase activity (GO:0004016)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			adrenal_gland(12)|autonomic_ganglia(1)|biliary_tract(5)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(37)|liver(9)|lung(9)|ovary(16)|pancreas(56)|parathyroid(5)|pituitary(228)|prostate(2)|small_intestine(1)|stomach(1)|testis(2)|thyroid(35)|upper_aerodigestive_tract(3)|urinary_tract(1)	441	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			CAGGTCCTCAACCCGGCATTC	0.612			Mis		pituitary adenoma		"McCune-Albright syndrome; pseudohypoparathyroidism, type IA"			TSP Lung(22;0.16)																											p.N82S	Colon(117;935 1597 6045 8307 46442)	Atlas-SNP	.		Dom	yes		20	20q13.2	2778	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	yes	E	.	GNAS	867	.	0			c.A245G						.						24	27	26					20																	57428565		1926	4132	6058	SO:0001583	missense	2778	exon1			TCCTCAACCCGGC	M21142	CCDS13471.1, CCDS13472.1, CCDS42892.1, CCDS46622.1, CCDS46623.1, CCDS46624.1	20q13.2-q13.3	2010-03-01	2001-12-19	2001-12-20	ENSG00000087460	ENSG00000087460			4392	protein-coding gene	gene with protein product	"secretogranin VI"	139320	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	GNAS1			Standard	NM_000516		Approved	NESP55, NESP, GNASXL, GPSA, SCG6	uc002xzw.3	O95467	OTTHUMG00000033069	ENST00000371100.4:c.245A>G	chr20.hg19:g.57428565A>G	ENSP00000360141:p.Asn82Ser	91.0	0.0		81.0	5.0	NM_080425	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Missense_Mutation	SNP	ENST00000371100.4	hg19	CCDS46622.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	0.014|0.014	-1.575764|-1.575764	0.00887|0.00887	.|.	.|.	ENSG00000087460|ENSG00000087460	ENST00000371099;ENST00000371100;ENST00000371102|ENST00000306120	D;D|.	0.87103|.	-2.21;-2.21|.	4.55|4.55	-6.59|-6.59	0.01830|0.01830	.|.	.|.	.|.	.|.	.|.	T|T	0.08223|0.08223	0.0205|0.0205	N|N	0.02011|0.02011	-0.69|-0.69	0.09310|0.09310	N|N	1|1	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.31806|0.31806	-0.9930|-0.9930	9|6	0.02654|0.22706	T|T	1|0.39	.|.	5.8641|5.8641	0.18765|0.18765	0.4709:0.2422:0.2869:0.0|0.4709:0.2422:0.2869:0.0	.|.	82|.	Q5JWF2|.	GNAS1_HUMAN|.	S|A	82|19	ENSP00000360141:N82S;ENSP00000360143:N82S|.	ENSP00000360140:N82S|ENSP00000302237:T19A	N|T	+|+	2|1	0|0	GNAS|GNAS	56861960|56861960	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.019000|0.019000	0.09904|0.09904	-0.562000|-0.562000	0.05950|0.05950	-0.941000|-0.941000	0.03700|0.03700	-0.410000|-0.410000	0.06199|0.06199	AAC|ACC	.	.		0.612	GNAS-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080417.3	NM_000516		G	57428565	A	G	57428565	3	3	259	1	0	0	0	0	1	0	0	0	6518	43	2	2	989	2	GNAS	20	57428565	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	1200444	57428565	5596955	859	37177										
ZNF831	128611	hgsc.bcm.edu	37	chr20	57768791	57768791	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aagggacaaggctaccccacTgcatcctgcagccccagccc	9	18	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:57768791T>C	ENST00000371030.2	+	1	2717	c.2717T>C	c.(2716-2718)cTg>cCg	p.L906P		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	906							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					GCTACCCCACTGCATCCTGCA	0.662																																					p.L906P		Atlas-SNP	.											.	ZNF831	287	.	0			c.T2717C						.						29	32	31					20																	57768791		1982	4158	6140	SO:0001583	missense	128611	exon1			CCCCACTGCATCC	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 174"	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.2717T>C	chr20.hg19:g.57768791T>C	ENSP00000360069:p.Leu906Pro	91.0	0.0		92.0	4.0	NM_178457	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	hg19	CCDS42894.1	.	.	.	.	.	.	.	.	.	.	T	7.008	0.556245	0.13436	.	.	ENSG00000124203	ENST00000371030	T	0.05258	3.47	4.63	-9.26	0.00662	.	3.549510	0.01228	N	0.008267	T	0.03695	0.0105	N	0.17082	0.46	0.09310	N	0.999996	B	0.09022	0.002	B	0.06405	0.002	T	0.30679	-0.9970	10	0.87932	D	0	3.0326	3.6093	0.08054	0.1793:0.436:0.195:0.1897	.	906	Q5JPB2	ZN831_HUMAN	P	906	ENSP00000360069:L906P	ENSP00000360069:L906P	L	+	2	0	ZNF831	57202186	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-2.690000	0.00831	-3.191000	0.00219	-1.378000	0.01179	CTG	.	.		0.662	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		C	57768791	T	C	57768791	3	2	259	1	0	0	0	0	1	0	0	0	18200	1580	55	2	2719	2	ZNF831	20	57768791	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	340226	57768791	5256729	860	37178										
C20orf20	55257	hgsc.bcm.edu	37	chr20	61428015	61428015	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccacgccatgctgggccacaAgcccgtcggtgagcgcccag	13	17	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:61428015A>G	ENST00000370487.3	+	1	211	c.140A>G	c.(139-141)aAg>aGg	p.K47R		NM_018270.4	NP_060740.1	Q9NV56	MRGBP_HUMAN	MRG/MORF4L binding protein	47					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	H4/H2A histone acetyltransferase complex (GO:0043189)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											CTGGGCCACAAGCCCGTCGGT	0.781																																					p.K47R		Atlas-SNP	.											.	.	.	.	0			c.A140G						.						14	14	14					20																	61428015		2088	4082	6170	SO:0001583	missense	55257	exon1			GCCACAAGCCCGT	AK001776	CCDS13503.1	20q13.33	2012-10-29	2012-10-29	2012-10-29	ENSG00000101189	ENSG00000101189			15866	protein-coding gene	gene with protein product		611157	"chromosome 20 open reading frame 20"	C20orf20		12963728	Standard	NM_018270		Approved	FLJ10914, MRG15BP, Eaf7	uc002ydi.3	Q9NV56	OTTHUMG00000032940	ENST00000370487.3:c.140A>G	chr20.hg19:g.61428015A>G	ENSP00000359518:p.Lys47Arg	51.0	0.0		53.0	4.0	NM_018270	A8C4L5	Missense_Mutation	SNP	ENST00000370487.3	hg19	CCDS13503.1	.	.	.	.	.	.	.	.	.	.	A	12.95	2.092136	0.36952	.	.	ENSG00000101189	ENST00000370487	.	.	.	2.96	2.96	0.34315	.	0.200642	0.43110	N	0.000610	T	0.46619	0.1402	L	0.42529	1.33	0.54753	D	0.999989	B	0.20459	0.045	B	0.21360	0.034	T	0.37731	-0.9693	9	0.26408	T	0.33	-10.9024	11.2412	0.48970	1.0:0.0:0.0:0.0	.	47	Q9NV56	MRGBP_HUMAN	R	47	.	ENSP00000359518:K47R	K	+	2	0	C20orf20	60898460	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.332000	0.59279	1.211000	0.43351	0.323000	0.21402	AAG	.	.		0.781	MRGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080080.1	NM_018270		G	61428015	A	G	61428015	3	3	259	1	0	0	0	0	1	0	0	0	2105	72	3	2	142	2	C20orf20	20	61428015	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	3659224	61428015	1597505	861	37179										
DIDO1	11083	hgsc.bcm.edu	37	chr20	61511261	61511261	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggcccggcttcatcacctgcGgggcctggccctggaagtga	15	14	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:61511261G>T	ENST00000266070.4	-	16	6372	c.6047C>A	c.(6046-6048)cCg>cAg	p.P2016Q	DIDO1_ENST00000395343.1_Missense_Mutation_p.P2016Q	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	2016	Pro-rich.				apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					CATCACCTGCGGGGCCTGGCC	0.687																																					p.P2016Q	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											.	DIDO1	321	.	0			c.C6047A						.						36	47	44					20																	61511261		2177	4264	6441	SO:0001583	missense	11083	exon16			ACCTGCGGGGCCT	AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"Zinc fingers, PHD-type"	2680	protein-coding gene	gene with protein product		604140	"chromosome 20 open reading frame 158", "death associated transcription factor 1"	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.6047C>A	chr20.hg19:g.61511261G>T	ENSP00000266070:p.Pro2016Gln	72.0	0.0		74.0	4.0	NM_001193369	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Missense_Mutation	SNP	ENST00000266070.4	hg19	CCDS33506.1	.	.	.	.	.	.	.	.	.	.	G	1.534	-0.543597	0.04053	.	.	ENSG00000101191	ENST00000266070;ENST00000395343	T;T	0.08546	3.08;3.08	4.94	3.92	0.45320	.	1.080270	0.07312	N	0.876107	T	0.06645	0.0170	N	0.13098	0.295	0.19300	N	0.99998	B	0.24675	0.109	B	0.19391	0.025	T	0.22661	-1.0210	10	0.32370	T	0.25	-1.6771	12.2577	0.54633	0.0:0.0:0.7274:0.2726	.	2016	Q9BTC0	DIDO1_HUMAN	Q	2016	ENSP00000266070:P2016Q;ENSP00000378752:P2016Q	ENSP00000266070:P2016Q	P	-	2	0	DIDO1	60981706	0.822000	0.29219	0.029000	0.17559	0.088000	0.18126	2.359000	0.44142	2.277000	0.76020	0.561000	0.74099	CCG	.	.		0.687	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796		T	61511261	G	T	61511261	3	4	259	1	0	0	0	0	1	0	0	0	4524	1116	39	1	679	1	DIDO1	20	61511261	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	83246	61511261	1514259	862	37180										
SLC17A9	63910	hgsc.bcm.edu	37	chr20	61597040	61597040	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tctgtgagtctgtggtctttGcatcagcctccatcggcctc	10	13	4	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:61597040G>T	ENST00000370351.4	+	10	1155	c.1024G>T	c.(1024-1026)Gca>Tca	p.A342S	SLC17A9_ENST00000370349.3_Missense_Mutation_p.A336S|SLC17A9_ENST00000488738.1_3'UTR	NM_022082.3	NP_071365	Q9BYT1	S17A9_HUMAN	solute carrier family 17 (vesicular nucleotide transporter), member 9	342					exocytosis (GO:0006887)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	23						TGTGGTCTTTGCATCAGCCTC	0.647																																					p.A342S		Atlas-SNP	.											.	SLC17A9	54	.	0			c.G1024T						.						121	132	128					20																	61597040		2110	4231	6341	SO:0001583	missense	63910	exon10			GTCTTTGCATCAG	AK027065	CCDS42901.1	20q13.33	2013-07-18	2013-07-18	2009-01-22	ENSG00000101194	ENSG00000101194		"Solute carriers"	16192	protein-coding gene	gene with protein product		612107	"chromosome 20 open reading frame 59", "solute carrier family 17, member 9"	C20orf59		18375752	Standard	NM_022082		Approved	FLJ23412, VNUT	uc002yea.4	Q9BYT1	OTTHUMG00000032951	ENST00000370351.4:c.1024G>T	chr20.hg19:g.61597040G>T	ENSP00000359376:p.Ala342Ser	98.0	0.0		97.0	4.0	NM_022082	B3KTF2|Q5W198|Q8TB07|Q8TBP4|Q8TEL5|Q9BYT0|Q9BYT2	Missense_Mutation	SNP	ENST00000370351.4	hg19	CCDS42901.1	.	.	.	.	.	.	.	.	.	.	G	18.10	3.547382	0.65311	.	.	ENSG00000101194	ENST00000370351;ENST00000370349	T;T	0.59638	0.25;0.25	4.8	4.8	0.61643	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.053916	0.85682	D	0.000000	T	0.55257	0.1909	N	0.20685	0.6	0.58432	D	0.999991	B;B;B	0.34241	0.444;0.283;0.24	P;B;B	0.45276	0.475;0.326;0.219	T	0.62001	-0.6946	10	0.66056	D	0.02	.	17.8649	0.88793	0.0:0.0:1.0:0.0	.	362;342;336	B4DPU8;Q9BYT1;Q9BYT1-2	.;S17A9_HUMAN;.	S	342;336	ENSP00000359376:A342S;ENSP00000359374:A336S	ENSP00000359374:A336S	A	+	1	0	SLC17A9	61067485	1.000000	0.71417	0.271000	0.24616	0.089000	0.18198	8.533000	0.90617	2.202000	0.70862	0.561000	0.74099	GCA	.	.		0.647	SLC17A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080100.1	NM_022082		T	61597040	G	T	61597040	3	4	259	1	0	0	0	0	1	0	0	0	14439	1319	46	3	1062	3	SLC17A9	20	61597040	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	85779	61597040	1428480	863	37181										
ADAMTS5	11096	hgsc.bcm.edu	37	chr21	28296469	28296469	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttccatcctggcactgcaccGttctggtgtgccaacctgtg	10	14	1	0	rs368781824		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr21:28296469G>A	ENST00000284987.5	-	8	2817	c.2696C>T	c.(2695-2697)aCg>aTg	p.T899M	AP001601.2_ENST00000426771.1_RNA	NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 5	899	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.T899M(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	72						GCACTGCACCGTTCTGGTGTG	0.542																																					p.T899M	Esophageal Squamous(53;683 1080 10100 14424 45938)	Atlas-SNP	.											ADAMTS5,NS,NS,0,1	ADAMTS5	184	.	1	Substitution - Missense(1)	pancreas(1)	c.C2696T						.	G	MET/THR	0,4406		0,0,2203	92	79	83		2696	5.2	1	21		83	2,8598	2.2+/-6.3	0,2,4298	no	missense	ADAMTS5	NM_007038.3	81	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	899/931	28296469	2,13004	2203	4300	6503	SO:0001583	missense	11096	exon8			TGCACCGTTCTGG	AF142099	CCDS13579.1	21q21.3	2008-07-31	2008-07-31		ENSG00000154736	ENSG00000154736		"ADAM metallopeptidases with thrombospondin type 1 motif"	221	protein-coding gene	gene with protein product	"aggrecanase-2"	605007	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"			10438522	Standard	NM_007038		Approved	ADMP-2, ADAMTS11	uc002ymg.3	Q9UNA0	OTTHUMG00000078686	ENST00000284987.5:c.2696C>T	chr21.hg19:g.28296469G>A	ENSP00000284987:p.Thr899Met	45.0	0.0		47.0	2.0	NM_007038	Q52LV4|Q9UKP2	Missense_Mutation	SNP	ENST00000284987.5	hg19	CCDS13579.1	.	.	.	.	.	.	.	.	.	.	G	17.82	3.483244	0.63962	0.0	2.33E-4	ENSG00000154736	ENST00000284987	T	0.54279	0.58	6.07	5.19	0.71726	.	0.000000	0.85682	D	0.000000	T	0.53334	0.1790	L	0.58428	1.81	0.58432	D	0.999998	P	0.44521	0.837	B	0.42593	0.392	T	0.56498	-0.7969	10	0.46703	T	0.11	.	15.649	0.77076	0.0654:0.0:0.9346:0.0	.	899	Q9UNA0	ATS5_HUMAN	M	899	ENSP00000284987:T899M	ENSP00000284987:T899M	T	-	2	0	ADAMTS5	27218340	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	7.398000	0.79919	1.595000	0.50050	-0.119000	0.15052	ACG	.	.		0.542	ADAMTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171648.1			A	28296469	G	A	28296469	3	1	259	1	0	0	0	0	1	0	0	0	269	1145	40	1	100	1	ADAMTS5	21	28296469	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10		28296469	19833426	864	37182										
KCNJ15	3772	hgsc.bcm.edu	37	chr21	39672189	39672189	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agtttgaacagattcggaaaAgcccagattgcacattttac	8	8	0	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr21:39672189A>G	ENST00000328656.4	+	4	1309	c.1006A>G	c.(1006-1008)Agc>Ggc	p.S336G	KCNJ15_ENST00000398930.1_Missense_Mutation_p.S336G|KCNJ15_ENST00000398932.1_Missense_Mutation_p.S336G|KCNJ15_ENST00000398934.1_Missense_Mutation_p.S336G|KCNJ15_ENST00000398938.2_Missense_Mutation_p.S336G	NM_001276437.1|NM_001276438.1|NM_001276439.1|NM_002243.3	NP_001263366.1|NP_001263367.1|NP_001263368.1|NP_002234.2	Q99712	KCJ15_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 15	336					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	24					Yohimbine(DB01392)	GATTCGGAAAAGCCCAGATTG	0.433																																					p.T336A		Atlas-SNP	.											.	KCNJ15	43	.	0			c.A1006G						.						63	63	63					21																	39672189		2203	4300	6503	SO:0001583	missense	3772	exon4			CGGAAAAGCCCAG	Y10745	CCDS13656.1	21q22.2	2011-07-05			ENSG00000157551	ENSG00000157551		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6261	protein-coding gene	gene with protein product		602106				9299242, 8995301, 16382105	Standard	NM_170736		Approved	Kir4.2, Kir1.3, IRKK	uc002ywx.4	Q99712	OTTHUMG00000090609	ENST00000328656.4:c.1006A>G	chr21.hg19:g.39672189A>G	ENSP00000331698:p.Ser336Gly	167.0	0.0		150.0	6.0	NM_002243	D3DSH5|O00564|Q96L28|Q99446	Missense_Mutation	SNP	ENST00000328656.4	hg19	CCDS13656.1	.	.	.	.	.	.	.	.	.	.	A	15.23	2.772990	0.49680	.	.	ENSG00000157551	ENST00000328656;ENST00000398938;ENST00000398932;ENST00000398930;ENST00000398934	D;D;D;D;D	0.94000	-3.33;-3.33;-3.33;-3.33;-3.33	5.83	5.83	0.93111	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (2);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.152159	0.64402	D	0.000020	D	0.90971	0.7161	L	0.46157	1.445	0.38934	D	0.958018	P	0.36086	0.536	B	0.40702	0.338	D	0.89817	0.3986	9	.	.	.	.	11.3152	0.49388	0.8643:0.0:0.0:0.1357	.	336	Q99712	IRK15_HUMAN	G	336	ENSP00000331698:S336G;ENSP00000381911:S336G;ENSP00000381905:S336G;ENSP00000381904:S336G;ENSP00000381907:S336G	.	S	+	1	0	KCNJ15	38594059	1.000000	0.71417	0.994000	0.49952	0.951000	0.60555	4.955000	0.63638	2.236000	0.73375	0.533000	0.62120	AGC	.	.		0.433	KCNJ15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207181.2	NM_002243		G	39672189	A	G	39672189	3	3	259	1	0	0	0	0	1	0	0	0	8058	72	3	2	1008	2	KCNJ15	21	39672189	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	11375720	39672189	8457706	865	37183										
BRWD1	54014	hgsc.bcm.edu	37	chr21	40568902	40568902	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	attttgtgaatattggtatgCctgtgcttgtgttctgaatt	10	4	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr21:40568902C>T	ENST00000333229.2	-	41	6420	c.6093G>A	c.(6091-6093)agG>agA	p.R2031R	BRWD1_ENST00000380800.3_Silent_p.R2031R|BRWD1_ENST00000342449.3_Silent_p.R2031R	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	2031					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				TATTGGTATGCCTGTGCTTGT	0.398																																					p.R2031R	Melanoma(170;988 1986 4794 16843 39731)	Atlas-SNP	.											.	BRWD1	325	.	0			c.G6093A						.						165	155	158					21																	40568902		2203	4300	6503	SO:0001819	synonymous_variant	54014	exon41			GGTATGCCTGTGC	AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"WD repeat domain containing"	12760	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 107", "WD repeat domain 9"	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.6093G>A	chr21.hg19:g.40568902C>T		139.0	0.0		113.0	5.0	NM_018963	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Silent	SNP	ENST00000333229.2	hg19	CCDS13662.1																																																																																			.	.		0.398	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656		T	40568902	C	T	40568902	2	4	259	1	0	0	0	0	0	0	0	1	1527	738	26	3		3	BRWD1	21	40568902	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	896713	40568902	7560993	866	37184										
TFF3	7033	hgsc.bcm.edu	37	chr21	43733711	43733711	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggtagccgcagtccaccctgTccttggctggcacggcacac	12	16	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr21:43733711T>C	ENST00000518498.1	-	2	389	c.155A>G	c.(154-156)gAc>gGc	p.D52G	TFF3_ENST00000489676.1_5'UTR|TFF3_ENST00000291525.10_Missense_Mutation_p.D88G			Q07654	TFF3_HUMAN	trefoil factor 3 (intestinal)	38	P-type. {ECO:0000255|PROSITE- ProRule:PRU00779}.				defense response (GO:0006952)|digestion (GO:0007586)|response to peptide hormone (GO:0043434)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)				cervix(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	6						GTCCACCCTGTCCTTGGCTGG	0.602																																					p.D52G		Atlas-SNP	.											.	TFF3	9	.	0			c.A155G						.						52	46	48					21																	43733711		2203	4300	6503	SO:0001583	missense	7033	exon2			ACCCTGTCCTTGG	AF432265	CCDS33565.1, CCDS33565.2	21q22.3	2006-05-16			ENSG00000160180	ENSG00000160180			11757	protein-coding gene	gene with protein product		600633				7718582, 9043862	Standard	NM_003226		Approved	HITF, ITF	uc002zav.3	Q07654	OTTHUMG00000086798	ENST00000518498.1:c.155A>G	chr21.hg19:g.43733711T>C	ENSP00000430690:p.Asp52Gly	111.0	0.0		70.0	4.0	NM_003226	E9PBB5|Q96NX0|Q9UDA5	Missense_Mutation	SNP	ENST00000518498.1	hg19	CCDS33565.2	.	.	.	.	.	.	.	.	.	.	T	14.08	2.430026	0.43122	.	.	ENSG00000160180	ENST00000518498;ENST00000291525;ENST00000398431	T;T	0.56275	0.47;0.47	4.31	1.61	0.23674	P-type trefoil (5);	0.774326	0.11500	N	0.557742	T	0.41213	0.1149	.	.	.	0.09310	N	1	P	0.39576	0.679	B	0.41946	0.371	T	0.20806	-1.0264	8	.	.	.	-17.236	5.0381	0.14445	0.358:0.0:0.2324:0.4095	.	38	Q07654	TFF3_HUMAN	G	52;88;40	ENSP00000430690:D52G;ENSP00000291525:D88G	.	D	-	2	0	TFF3	42606780	0.187000	0.23238	0.749000	0.31150	0.918000	0.54935	0.383000	0.20651	0.475000	0.27415	0.459000	0.35465	GAC	.	.		0.602	TFF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195358.2	NM_003226		C	43733711	T	C	43733711	3	2	259	1	0	0	0	0	1	0	0	0	15820	1667	58	2	137	2	TFF3	21	43733711	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	3164809	43733711	4396184	867	37185										
SIK1	150094	hgsc.bcm.edu	37	chr21	44839238	44839238	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gctgtgggcactcacccactGcagcgagctctggagctcac	12	15	3	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr21:44839238G>A	ENST00000270162.6	-	10	1372	c.1240C>T	c.(1240-1242)Cag>Tag	p.Q414*		NM_173354.3	NP_775490.2	P57059	SIK1_HUMAN	salt-inducible kinase 1	414					cardiac muscle cell differentiation (GO:0055007)|cell cycle (GO:0007049)|entrainment of circadian clock by photoperiod (GO:0043153)|intracellular signal transduction (GO:0035556)|negative regulation of CREB transcription factor activity (GO:0032792)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of triglyceride biosynthetic process (GO:0010868)|positive regulation of anoikis (GO:2000210)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell differentiation (GO:0045595)|regulation of mitotic cell cycle (GO:0007346)|regulation of myotube differentiation (GO:0010830)|regulation of sodium ion transport (GO:0002028)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|cAMP response element binding protein binding (GO:0008140)|magnesium ion binding (GO:0000287)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|testis(2)|urinary_tract(1)	21					Dabrafenib(DB08912)	CTCACCCACTGCAGCGAGCTC	0.682																																					p.Q414X		Atlas-SNP	.											.	SIK1	65	.	0			c.C1240T						.						33	36	35					21																	44839238		2196	4296	6492	SO:0001587	stop_gained	150094	exon10			CCCACTGCAGCGA	BC038504	CCDS33575.1	21q22.3	2008-12-23	2008-12-23	2008-12-23	ENSG00000142178	ENSG00000142178			11142	protein-coding gene	gene with protein product	"myocardial SNF1-like kinase"	605705	"SNF1-like kinase"	SNF1LK		7893599	Standard	NM_173354		Approved	msk	uc002zdf.2	P57059	OTTHUMG00000086874	ENST00000270162.6:c.1240C>T	chr21.hg19:g.44839238G>A	ENSP00000270162:p.Gln414*	125.0	0.0		100.0	4.0	NM_173354	A6NC84|Q5R2V5|Q6ZNL8|Q86YJ2	Nonsense_Mutation	SNP	ENST00000270162.6	hg19	CCDS33575.1	.	.	.	.	.	.	.	.	.	.	G	37	6.602117	0.97697	.	.	ENSG00000142178	ENST00000270162	.	.	.	4.95	4.95	0.65309	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	.	15.3475	0.74350	0.0:0.0:1.0:0.0	.	.	.	.	X	414	.	ENSP00000270162:Q414X	Q	-	1	0	SIK1	43663666	1.000000	0.71417	0.956000	0.39512	0.410000	0.31052	6.371000	0.73119	2.289000	0.77006	0.561000	0.74099	CAG	.	.		0.682	SIK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195654.1	NM_173354		A	44839238	G	A	44839238	4	1	259	1	0	0	0	0	0	1	0	0	14332	1328	46	3	1131	3	SIK1	21	44839238	Nonsense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1105527	44839238	3290657	868	37186										
MCM3AP	8888	hgsc.bcm.edu	37	chr21	47704423	47704423	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gctagcctggaaaggttcgcCcaaaaccgcagatgatacag	11	11	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr21:47704423C>T	ENST00000397708.1	-	2	1032	c.778G>A	c.(778-780)Ggc>Agc	p.G260S	YBEY_ENST00000397691.1_5'Flank|YBEY_ENST00000329319.3_5'Flank|YBEY_ENST00000397694.1_5'Flank|YBEY_ENST00000397701.4_5'Flank|MCM3AP_ENST00000291688.1_Missense_Mutation_p.G260S|YBEY_ENST00000339195.6_5'Flank|YBEY_ENST00000397692.1_5'Flank			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	260	FG-repeats.				DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					AAAGGTTCGCCCAAAACCGCA	0.463																																					p.G260S		Atlas-SNP	.											.	MCM3AP	146	.	0			c.G778A						.						80	81	80					21																	47704423		2203	4300	6503	SO:0001583	missense	8888	exon1			GTTCGCCCAAAAC	AB005543	CCDS13734.1	21q22.3	2012-12-19	2007-04-04		ENSG00000160294	ENSG00000160294			6946	protein-coding gene	gene with protein product	"germinal-centre associated nuclear protein"	603294	"minichromosome maintenance deficient (S. cerevisiae) 3-associated protein", "MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein"			9712829, 16914116, 21195085	Standard	XM_005261205		Approved	Map80, KIAA0572, GANP, SAC3	uc002zir.1	O60318	OTTHUMG00000090630	ENST00000397708.1:c.778G>A	chr21.hg19:g.47704423C>T	ENSP00000380820:p.Gly260Ser	103.0	0.0		99.0	5.0	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Missense_Mutation	SNP	ENST00000397708.1	hg19	CCDS13734.1	.	.	.	.	.	.	.	.	.	.	C	7.202	0.593703	0.13875	.	.	ENSG00000160294	ENST00000397708;ENST00000291688	T;T	0.16597	2.33;2.33	4.9	4.9	0.64082	.	0.325990	0.32671	N	0.005784	T	0.13670	0.0331	L	0.29908	0.895	0.09310	N	1	B	0.27823	0.19	B	0.27608	0.081	T	0.15435	-1.0437	10	0.35671	T	0.21	-12.7957	13.3539	0.60617	0.0:0.8405:0.1595:0.0	.	260	O60318	MCM3A_HUMAN	S	260	ENSP00000380820:G260S;ENSP00000291688:G260S	ENSP00000291688:G260S	G	-	1	0	MCM3AP	46528851	0.536000	0.26378	0.051000	0.19133	0.041000	0.13682	1.576000	0.36504	2.537000	0.85549	0.563000	0.77884	GGC	.	.		0.463	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906		T	47704423	C	T	47704423	3	4	259	1	0	0	0	0	1	0	0	0	9397	623	22	3	5276	3	MCM3AP	21	47704423	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	2865185	47704423	425472	869	37187										
DIP2A	23181	hgsc.bcm.edu	37	chr21	47983806	47983806	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aaggtcatcatcgcacacacCgagaccaaaggacccttggg	10	13	2	1	rs201790767	byFrequency	TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr21:47983806C>A	ENST00000417564.2	+	35	4146	c.4125C>A	c.(4123-4125)acC>acA	p.T1375T	DIP2A_ENST00000318711.7_Silent_p.T1376T|DIP2A_ENST00000479654.1_3'UTR|DIP2A_ENST00000400274.1_Silent_p.T1371T			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	1375					multicellular organismal development (GO:0007275)|negative regulation of gene expression (GO:0010629)|regulation of apoptotic process (GO:0042981)	cell surface (GO:0009986)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(22)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		TCGCACACACCGAGACCAAAG	0.562																																					p.T1375T		Atlas-SNP	.											.	DIP2A	332	.	0			c.C4125A						.						64	65	65					21																	47983806		1940	4156	6096	SO:0001819	synonymous_variant	23181	exon35			ACACACCGAGACC	AF490768	CCDS46655.1, CCDS46656.1, CCDS46657.1, CCDS54490.1, CCDS54491.1	21q22.3	2010-08-20	2006-01-13	2006-01-13	ENSG00000160305	ENSG00000160305			17217	protein-coding gene	gene with protein product		607711	"chromosome 21 open reading frame 106"	C21orf106			Standard	NM_015151		Approved	Dip2, KIAA0184	uc002zjo.2	Q14689	OTTHUMG00000090717	ENST00000417564.2:c.4125C>A	chr21.hg19:g.47983806C>A		105.0	0.0		85.0	4.0	NM_015151	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Silent	SNP	ENST00000417564.2	hg19	CCDS46655.1																																																																																			.	C|0.996;G|0.004		0.562	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151		A	47983806	C	A	47983806	2	1	259	1	0	0	0	0	0	0	0	1	4529	639	23	1		1	DIP2A	21	47983806	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	279383	47983806	146089	870	37188										
TSSK2	23617	hgsc.bcm.edu	37	chr22	19119730	19119730	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cctcagccactcgtggctgcAgccccccaagcccaaagcca	8	20	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:19119730A>G	ENST00000399635.2	+	1	1410	c.818A>G	c.(817-819)cAg>cGg	p.Q273R	DGCR14_ENST00000252137.6_3'UTR	NM_053006.4	NP_443732.3	Q96PF2	TSSK2_HUMAN	testis-specific serine kinase 2	273					multicellular organismal development (GO:0007275)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			endometrium(2)|large_intestine(2)|lung(2)|prostate(4)|stomach(1)	11	Colorectal(54;0.0993)					TCGTGGCTGCAGCCCCCCAAG	0.617																																					p.Q273R		Atlas-SNP	.											.	TSSK2	29	.	0			c.A818G						.						51	46	48					22																	19119730		2203	4300	6503	SO:0001583	missense	23617	exon1			GGCTGCAGCCCCC	AF362953	CCDS13755.1	22q11.21	2007-01-30	2005-03-10	2005-03-12	ENSG00000206203	ENSG00000206203			11401	protein-coding gene	gene with protein product		610710	"serine/threonine kinase 22B (spermiogenesis associated)"	STK22B		10591208	Standard	NM_053006		Approved	SPOGA2, FLJ38613	uc002zow.2	Q96PF2	OTTHUMG00000150118	ENST00000399635.2:c.818A>G	chr22.hg19:g.19119730A>G	ENSP00000382544:p.Gln273Arg	94.0	0.0		80.0	4.0	NM_053006	Q8IY55	Missense_Mutation	SNP	ENST00000399635.2	hg19	CCDS13755.1	.	.	.	.	.	.	.	.	.	.	A	10.84	1.464904	0.26335	.	.	ENSG00000206203	ENST00000399635	D	0.82433	-1.61	5.7	5.7	0.88788	Protein kinase-like domain (1);	0.000000	0.48767	D	0.000161	T	0.72938	0.3523	N	0.19112	0.55	0.36448	D	0.865923	B	0.11235	0.004	B	0.15870	0.014	T	0.72846	-0.4169	10	0.46703	T	0.11	.	13.4997	0.61447	1.0:0.0:0.0:0.0	.	273	Q96PF2	TSSK2_HUMAN	R	273	ENSP00000382544:Q273R	ENSP00000382544:Q273R	Q	+	2	0	TSSK2	17499730	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.191000	0.72063	2.172000	0.68678	0.533000	0.62120	CAG	.	.		0.617	TSSK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316431.1			G	19119730	A	G	19119730	3	3	259	1	0	0	0	0	1	0	0	0	16684	188	7	2	820	2	TSSK2	22	19119730	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10		19119730	32184836	871	37189										
SLC25A1	6576	hgsc.bcm.edu	37	chr22	19164138	19164138	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aggagtgtttccaaagacacTggctgcgcctgcaatagctc	11	11	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:19164138T>C	ENST00000215882.5	-	7	856	c.700A>G	c.(700-702)Agt>Ggt	p.S234G	SLC25A1_ENST00000461267.1_5'Flank|CLTCL1_ENST00000442042.2_5'Flank|SLC25A1_ENST00000451283.1_Missense_Mutation_p.S131G	NM_005984.3	NP_005975.1	P53007	TXTP_HUMAN	solute carrier family 25 (mitochondrial carrier; citrate transporter), member 1	234					carbohydrate metabolic process (GO:0005975)|cellular lipid metabolic process (GO:0044255)|citrate transport (GO:0015746)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	citrate transmembrane transporter activity (GO:0015137)			cervix(1)|lung(1)	2	Colorectal(54;0.0993)	all_lung(157;9.94e-09)		Lung(27;0.124)		CCAAAGACACTGGCTGCGCCT	0.607																																					p.S241G		Atlas-SNP	.											.	SLC25A1	14	.	0			c.A721G						.						47	53	51					22																	19164138		2203	4299	6502	SO:0001583	missense	6576	exon6			AGACACTGGCTGC	U25147	CCDS13758.1, CCDS74817.1	22q11	2013-05-22			ENSG00000100075	ENSG00000100075		"Solute carriers"	10979	protein-coding gene	gene with protein product		190315	"solute carrier family 20 (mitochondrial citrate transporter), member 3"	SLC20A3		8666394, 9254007	Standard	NM_001256534		Approved	CTP	uc002zoz.4	P53007	OTTHUMG00000150123	ENST00000215882.5:c.700A>G	chr22.hg19:g.19164138T>C	ENSP00000215882:p.Ser234Gly	118.0	0.0		99.0	4.0	NM_001256534	A8K8E8|Q9BSK6	Missense_Mutation	SNP	ENST00000215882.5	hg19	CCDS13758.1	.	.	.	.	.	.	.	.	.	.	T	19.94	3.919203	0.73098	.	.	ENSG00000100075	ENST00000215882;ENST00000451283	T;T	0.80123	-1.34;-1.34	5.48	4.44	0.53790	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.83876	0.5349	L	0.42529	1.33	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.80018	-0.1558	10	0.24483	T	0.36	-12.6986	11.4081	0.49911	0.0:0.0713:0.0:0.9287	.	241;234	D9HTE9;P53007	.;TXTP_HUMAN	G	234;131	ENSP00000215882:S234G;ENSP00000401480:S131G	ENSP00000215882:S234G	S	-	1	0	SLC25A1	17544138	1.000000	0.71417	0.999000	0.59377	0.259000	0.26198	7.983000	0.88140	0.895000	0.36342	0.379000	0.24179	AGT	.	.		0.607	SLC25A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316441.1	NM_005984		C	19164138	T	C	19164138	3	2	259	1	0	0	0	0	1	0	0	0	14486	1580	55	2	247	2	SLC25A1	22	19164138	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	44408	19164138	32140428	872	37190										
C22orf25	128989	hgsc.bcm.edu	37	chr22	20043483	20043483	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cagcacagcaaagggagacgTcatttgctactatgggaacc	11	10	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:20043483T>G	ENST00000327374.4	+	6	576	c.398T>G	c.(397-399)gTc>gGc	p.V133G	TANGO2_ENST00000456048.1_Missense_Mutation_p.V138G|TANGO2_ENST00000434570.2_Missense_Mutation_p.V174G|TANGO2_ENST00000401833.1_Missense_Mutation_p.V174G|TANGO2_ENST00000398042.2_Intron|TANGO2_ENST00000432883.1_Intron|TANGO2_ENST00000420290.2_Missense_Mutation_p.V35G|TANGO2_ENST00000447208.2_Missense_Mutation_p.V133G|TANGO2_ENST00000401886.1_Intron	NM_001283106.1|NM_001283116.1|NM_001283148.1|NM_001283154.1|NM_152906.4	NP_001270035.1|NP_001270045.1|NP_001270077.1|NP_001270083.1|NP_690870.3	Q6ICL3	TNG2_HUMAN	transport and golgi organization 2 homolog (Drosophila)	133																	AAGGGAGACGTCATTTGCTAC	0.587																																					p.V133G		Atlas-SNP	.											C22orf25,colon,carcinoma,0,1	TANGO2	4	.	0			c.T398G						.						141	115	124					22																	20043483		2203	4300	6503	SO:0001583	missense	128989	exon6			GAGACGTCATTTG		CCDS13772.1, CCDS63404.1, CCDS63405.1, CCDS63406.1, CCDS63407.1, CCDS74821.1, CCDS74822.1	22q11.21	2012-12-13	2012-12-13	2012-12-13	ENSG00000183597	ENSG00000183597			25439	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 25"	C22orf25		12477932	Standard	XM_005261222		Approved	DKFZp761P1121	uc002zrc.1	Q6ICL3	OTTHUMG00000150510	ENST00000327374.4:c.398T>G	chr22.hg19:g.20043483T>G	ENSP00000332721:p.Val133Gly	126.0	0.0		118.0	5.0	NM_152906	A8MUE9|B7WNV6|B7Z583|B7Z730|D3DX23|Q8IW05|Q8NAL0|Q8TCS0|Q96M16	Missense_Mutation	SNP	ENST00000327374.4	hg19	CCDS13772.1	.	.	.	.	.	.	.	.	.	.	T	11.50	1.656608	0.29425	.	.	ENSG00000183597	ENST00000447208;ENST00000450664;ENST00000327374;ENST00000401833;ENST00000434168;ENST00000434570;ENST00000420290;ENST00000456048	T;T;T;T;T;T;T;T	0.21932	1.98;1.98;1.98;1.98;1.98;1.98;1.98;1.98	4.52	4.52	0.55395	.	0.475882	0.21803	N	0.068885	T	0.17704	0.0425	N	0.25144	0.715	0.58432	D	0.999999	P;B;P;P;P;B	0.48407	0.709;0.08;0.891;0.91;0.807;0.408	B;B;P;P;B;B	0.48368	0.288;0.036;0.575;0.475;0.215;0.305	T	0.03000	-1.1084	10	0.20519	T	0.43	-21.2036	10.4191	0.44340	0.0:0.0:0.0:1.0	.	133;174;35;174;138;133	B7Z9Q5;B7Z730;B7Z583;B7WNV6;C9JC99;Q6ICL3	.;.;.;.;.;CV025_HUMAN	G	133;133;133;174;133;174;35;138	ENSP00000389797:V133G;ENSP00000415450:V133G;ENSP00000332721:V133G;ENSP00000384827:V174G;ENSP00000411602:V133G;ENSP00000391262:V174G;ENSP00000396182:V35G;ENSP00000403645:V138G	ENSP00000332721:V133G	V	+	2	0	C22orf25	18423483	0.150000	0.22732	0.276000	0.24689	0.919000	0.55068	3.388000	0.52509	2.021000	0.59480	0.460000	0.39030	GTC	.	.		0.587	TANGO2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318689.2	NM_152906		G	20043483	T	G	20043483	3	3	259	1	0	0	0	0	1	0	0	0	2141	1667	58	5	416	5	C22orf25	22	20043483	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	879345	20043483	31261083	873	37191										
KLHL22	84861	hgsc.bcm.edu	37	chr22	20796519	20796519	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	caggccgccaggcctgagatGgagttgtccagctggggccc	16	13	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:20796519G>A	ENST00000328879.4	-	7	1902	c.1746C>T	c.(1744-1746)tcC>tcT	p.S582S	KLHL22_ENST00000440659.2_Silent_p.S439S	NM_032775.3	NP_116164.2	Q53GT1	KLH22_HUMAN	kelch-like family member 22	582					cell division (GO:0051301)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|protein monoubiquitination (GO:0006513)	centrosome (GO:0005813)|Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|mitotic spindle (GO:0072686)|polar microtubule (GO:0005827)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|skin(2)|upper_aerodigestive_tract(1)	20	Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)			GGCCTGAGATGGAGTTGTCCA	0.677																																					p.S582S		Atlas-SNP	.											.	KLHL22	52	.	0			c.C1746T						.						42	43	43					22																	20796519		2202	4300	6502	SO:0001819	synonymous_variant	84861	exon7			TGAGATGGAGTTG		CCDS13780.1	22q11.21	2013-01-30	2013-01-30		ENSG00000099910	ENSG00000099910		"Kelch-like", "BTB/POZ domain containing"	25888	protein-coding gene	gene with protein product			"kelch-like 22 (Drosophila)"			12477932	Standard	NM_032775		Approved	FLJ14360, KELCHL	uc002zsl.2	Q53GT1	OTTHUMG00000150778	ENST00000328879.4:c.1746C>T	chr22.hg19:g.20796519G>A		129.0	0.0		97.0	4.0	NM_032775	A8K3Q4|A8MTV3|B7Z2G1|D3DX30|Q96B68|Q96KC6	Silent	SNP	ENST00000328879.4	hg19	CCDS13780.1																																																																																			.	.		0.677	KLHL22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320045.2	NM_032775		A	20796519	G	A	20796519	2	1	259	1	0	0	0	0	0	0	0	1	8386	1335	47	3		3	KLHL22	22	20796519	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	753036	20796519	30508047	874	37192										
SLC2A11	66035	hgsc.bcm.edu	37	chr22	24217341	24217341	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgaataacatctttgtggtgTcagcagcaatcctgtttgga	10	7	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:24217341T>C	ENST00000345044.6	+	4	587	c.319T>C	c.(319-321)Tca>Cca	p.S107P	AP000350.10_ENST00000433835.3_Missense_Mutation_p.S72P|SLC2A11_ENST00000405847.1_Missense_Mutation_p.S107P|SLC2A11_ENST00000398356.2_Missense_Mutation_p.S114P|SLC2A11_ENST00000467660.1_3'UTR|SLC2A11_ENST00000316185.8_Missense_Mutation_p.S110P			Q9BYW1	GTR11_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 11	107					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|skin(2)	12						CTTTGTGGTGTCAGCAGCAAT	0.532																																					p.S114P		Atlas-SNP	.											.	SLC2A11	32	.	0			c.T340C						.						85	77	80					22																	24217341		2203	4300	6503	SO:0001583	missense	66035	exon5			GTGGTGTCAGCAG	AJ271290	CCDS13818.1, CCDS33616.1, CCDS46673.1, CCDS74828.1	22q11.23	2013-05-22			ENSG00000133460	ENSG00000133460		"Solute carriers"	14239	protein-coding gene	gene with protein product		610367					Standard	NM_001024938		Approved	GLUT11, GLUT10	uc002zyp.4	Q9BYW1	OTTHUMG00000166469	ENST00000345044.6:c.319T>C	chr22.hg19:g.24217341T>C	ENSP00000342542:p.Ser107Pro	76.0	0.0		77.0	4.0	NM_030807	E9PH55|Q542Y4|Q6ICJ5|Q8WXF9|Q8WYM4	Missense_Mutation	SNP	ENST00000345044.6	hg19	CCDS46673.1	.	.	.	.	.	.	.	.	.	.	T	6.890	0.533609	0.13188	.	.	ENSG00000133460;ENSG00000133460;ENSG00000133460;ENSG00000133460;ENSG00000133460;ENSG00000133460;ENSG00000133460;ENSG00000251357	ENST00000345044;ENST00000398356;ENST00000398363;ENST00000398359;ENST00000405847;ENST00000407566;ENST00000316185;ENST00000433835	T;T;T;T	0.74106	-0.81;-0.81;-0.81;-0.81	3.68	0.265	0.15612	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.218800	0.05794	N	0.611008	T	0.68357	0.2992	L	0.49126	1.545	0.09310	N	1	B;P;B;B;P;P	0.42203	0.159;0.507;0.082;0.33;0.507;0.773	B;B;B;B;B;B	0.43838	0.116;0.433;0.104;0.319;0.251;0.433	T	0.57670	-0.7771	10	0.72032	D	0.01	.	1.1429	0.01769	0.2177:0.1702:0.4309:0.1812	.	110;114;110;107;114;114	B4E2T0;E7ENI4;Q9BYW1-3;Q9BYW1;E9PH55;Q6P4C1	.;.;.;GTR11_HUMAN;.;.	P	107;114;107;114;107;114;110;72	ENSP00000342542:S107P;ENSP00000381399:S114P;ENSP00000384987:S107P;ENSP00000326748:S110P	ENSP00000400325:S72P	S	+	1	0	AP000350.10;SLC2A11	22547341	0.000000	0.05858	0.112000	0.21494	0.090000	0.18270	-0.347000	0.07750	0.021000	0.15133	-0.526000	0.04340	TCA	.	.		0.532	SLC2A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319889.3	NM_030807		C	24217341	T	C	24217341	3	2	259	1	0	0	0	0	1	0	0	0	14555	1667	58	2	413	2	SLC2A11	22	24217341	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	3420822	24217341	27087225	875	37193										
UPB1	51733	hgsc.bcm.edu	37	chr22	24896100	24896100	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ttgatctgcccagggaagctTtcgaagctgcctccagagaa	11	11	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:24896100T>C	ENST00000326010.5	+	2	474	c.130T>C	c.(130-132)Ttc>Ctc	p.F44L	UPB1_ENST00000382760.2_Missense_Mutation_p.F44L|UPB1_ENST00000413389.2_Intron	NM_016327.2	NP_057411.1	Q9UBR1	BUP1_HUMAN	ureidopropionase, beta	44					beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	beta-ureidopropionase activity (GO:0003837)|metal ion binding (GO:0046872)			endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	22	Colorectal(2;0.0339)					CAGGGAAGCTTTCGAAGCTGC	0.522																																					p.F44L		Atlas-SNP	.											.	UPB1	60	.	0			c.T130C						.						89	87	87					22																	24896100		2203	4300	6503	SO:0001583	missense	51733	exon2			GAAGCTTTCGAAG	AB013885	CCDS13827.1	22q11.2	2008-04-11			ENSG00000100024	ENSG00000100024			16297	protein-coding gene	gene with protein product		606673				10542323	Standard	XR_244378		Approved	BUP1	uc003aaf.3	Q9UBR1	OTTHUMG00000150749	ENST00000326010.5:c.130T>C	chr22.hg19:g.24896100T>C	ENSP00000324343:p.Phe44Leu	32.0	0.0		36.0	4.0	NM_016327	A3KMF8|Q9UIR3	Missense_Mutation	SNP	ENST00000326010.5	hg19	CCDS13827.1	.	.	.	.	.	.	.	.	.	.	T	4.862	0.160319	0.09287	.	.	ENSG00000100024	ENST00000326010;ENST00000382760;ENST00000426507	T;T	0.74842	-0.88;-0.88	4.73	1.27	0.21489	.	0.877859	0.10274	N	0.694402	T	0.43100	0.1232	N	0.02158	-0.66	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.29305	-1.0016	10	0.11182	T	0.66	-0.4431	7.0302	0.24962	0.0:0.3147:0.0:0.6853	.	44	Q9UBR1	BUP1_HUMAN	L	44	ENSP00000324343:F44L;ENSP00000372208:F44L	ENSP00000324343:F44L	F	+	1	0	UPB1	23226100	0.000000	0.05858	0.015000	0.15790	0.043000	0.13939	-0.175000	0.09825	0.264000	0.21851	0.459000	0.35465	TTC	.	.		0.522	UPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319869.1			C	24896100	T	C	24896100	3	2	259	1	0	0	0	0	1	0	0	0	17017	1841	64	2	136	2	UPB1	22	24896100	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	678759	24896100	26408466	876	37194										
CRYBB1	1414	hgsc.bcm.edu	37	chr22	26997873	26997873	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	agaccttcacgctgcccacgCggtcactgaagccgtagacc	10	16	2	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:26997873C>A	ENST00000215939.2	-	5	675	c.545G>T	c.(544-546)cGc>cTc	p.R182L		NM_001887.3	NP_001878.1	P53674	CRBB1_HUMAN	crystallin, beta B1	182	Beta/gamma crystallin 'Greek key' 3. {ECO:0000255|PROSITE-ProRule:PRU00028}.				visual perception (GO:0007601)		structural constituent of eye lens (GO:0005212)			breast(1)|endometrium(4)|large_intestine(8)|lung(8)|ovary(1)|prostate(3)|skin(2)|urinary_tract(4)	31						GCTGCCCACGCGGTCACTGAA	0.592																																					p.R182L		Atlas-SNP	.											CRYBB1,NS,carcinoma,0,1	CRYBB1	49	.	0			c.G545T						.						84	64	71					22																	26997873		2203	4300	6503	SO:0001583	missense	1414	exon5			CCCACGCGGTCAC		CCDS13840.1	22q12.1	2008-06-10			ENSG00000100122	ENSG00000100122			2397	protein-coding gene	gene with protein product		600929				8575764, 12360425	Standard	NM_001887		Approved		uc003acy.1	P53674	OTTHUMG00000150980	ENST00000215939.2:c.545G>T	chr22.hg19:g.26997873C>A	ENSP00000215939:p.Arg182Leu	48.0	0.0		56.0	3.0	NM_001887		Missense_Mutation	SNP	ENST00000215939.2	hg19	CCDS13840.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.034186	0.93575	.	.	ENSG00000100122	ENST00000215939	T	0.77620	-1.11	4.8	4.8	0.61643	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.000000	0.85682	D	0.000000	D	0.89139	0.6630	H	0.97265	3.97	0.80722	D	1	P	0.52842	0.956	P	0.49887	0.625	D	0.93167	0.6563	10	0.72032	D	0.01	.	17.0174	0.86423	0.0:1.0:0.0:0.0	.	182	P53674	CRBB1_HUMAN	L	182	ENSP00000215939:R182L	ENSP00000215939:R182L	R	-	2	0	CRYBB1	25327873	1.000000	0.71417	0.998000	0.56505	0.950000	0.60333	5.383000	0.66219	2.468000	0.83385	0.591000	0.81541	CGC	.	.		0.592	CRYBB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320767.1	NM_001887		A	26997873	C	A	26997873	3	1	259	1	0	0	0	0	1	0	0	0	3912	768	27	1	221	1	CRYBB1	22	26997873	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	2101773	26997873	24306693	877	37195										
THOC5	8563	hgsc.bcm.edu	37	chr22	29939435	29939435	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tacctcgtgggtctgatctcTtcctttcttcaacctgatgt	7	12	4	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:29939435T>C	ENST00000490103.1	-	4	459	c.337A>G	c.(337-339)Aga>Gga	p.R113G	THOC5_ENST00000397873.2_Missense_Mutation_p.R113G|THOC5_ENST00000397872.1_Missense_Mutation_p.R113G|THOC5_ENST00000397871.1_Missense_Mutation_p.R113G	NM_003678.4	NP_003669.4	Q13769	THOC5_HUMAN	THO complex 5	113	Interaction with CSF1R. {ECO:0000250}.|Interaction with THOC7.				blastocyst development (GO:0001824)|cell morphogenesis (GO:0000902)|monocyte differentiation (GO:0030224)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|negative regulation of DNA damage checkpoint (GO:2000002)|negative regulation of macrophage differentiation (GO:0045650)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|primitive hemopoiesis (GO:0060215)|regulation of mRNA export from nucleus (GO:0010793)|regulation of stem cell division (GO:2000035)|RNA splicing (GO:0008380)|stem cell division (GO:0017145)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	mRNA binding (GO:0003729)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(4)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GTCTGATCTCTTCCTTTCTTC	0.388																																					p.R113G		Atlas-SNP	.											.	THOC5	58	.	0			c.A337G						.						149	150	150					22																	29939435		2203	4300	6503	SO:0001583	missense	8563	exon5			GATCTCTTCCTTT	AB023200	CCDS13859.1	22q12	2013-02-11			ENSG00000100296	ENSG00000100296		"THO complex subunits"	19074	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 79"	612733	"chromosome 22 open reading frame 19"	C22orf19		11979277, 8242058, 10231032, 19015024, 18373705	Standard	NM_003678		Approved	PK1.3, KIAA0983, Fmip, fSAP79	uc003afs.3	Q13769	OTTHUMG00000151291	ENST00000490103.1:c.337A>G	chr22.hg19:g.29939435T>C	ENSP00000420306:p.Arg113Gly	109.0	0.0		182.0	8.0	NM_001002878	O60839|Q9UPZ5	Missense_Mutation	SNP	ENST00000490103.1	hg19	CCDS13859.1	.	.	.	.	.	.	.	.	.	.	T	18.47	3.630526	0.67015	.	.	ENSG00000100296	ENST00000490103;ENST00000397872;ENST00000397871;ENST00000397873;ENST00000440771;ENST00000455450;ENST00000428374	T;T;T;T;T	0.56103	1.35;1.35;1.35;1.35;0.48	5.62	1.83	0.25207	.	0.000000	0.85682	D	0.000000	T	0.73466	0.3590	M	0.85462	2.755	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72982	0.963;0.979	T	0.79105	-0.1940	10	0.87932	D	0	-36.245	15.33	0.74200	0.0:0.0:0.4697:0.5302	.	113;113	F8WCP5;Q13769	.;THOC5_HUMAN	G	113;113;113;113;113;109;113	ENSP00000420306:R113G;ENSP00000380970:R113G;ENSP00000380969:R113G;ENSP00000380971:R113G;ENSP00000415425:R109G	ENSP00000444493:R113G	R	-	1	2	THOC5	28269435	0.344000	0.24827	1.000000	0.80357	0.981000	0.71138	-0.158000	0.10070	0.366000	0.24427	0.455000	0.32223	AGA	.	.		0.388	THOC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322097.1	NM_003678		C	29939435	T	C	29939435	3	2	259	1	0	0	0	0	1	0	0	0	15883	1617	56	2	1782	2	THOC5	22	29939435	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	2941562	29939435	21365131	878	37196										
RBM9	23543	hgsc.bcm.edu	37	chr22	36152191	36152191	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aatccgtcctggtaaaccacActgcagaaaatccacacaaa	5	13	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:36152191A>G	ENST00000438146.2	-	11	1109	c.1110T>C	c.(1108-1110)ggT>ggC	p.G370G	RBFOX2_ENST00000414461.2_Intron|RBFOX2_ENST00000416721.2_Splice_Site_p.G295G|RBFOX2_ENST00000405409.2_Intron|RBFOX2_ENST00000397303.2_Splice_Site_p.G276G|RBFOX2_ENST00000449924.2_Splice_Site_p.G299G|RBFOX2_ENST00000262829.7_Splice_Site_p.G277G|RBFOX2_ENST00000359369.4_Splice_Site_p.G275G	NM_001082578.1|NM_001082579.1	NP_001076047|NP_001076048.1	O43251	RFOX2_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 2	309	Ala-rich.				dendrite morphogenesis (GO:0048813)|intracellular estrogen receptor signaling pathway (GO:0030520)|mRNA processing (GO:0006397)|negative regulation of transcription, DNA-templated (GO:0045892)|neuromuscular process controlling balance (GO:0050885)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of cell proliferation (GO:0042127)|regulation of definitive erythrocyte differentiation (GO:0010724)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			endometrium(4)|large_intestine(7)|lung(7)	18						GGTAAACCACACTGCAGAAAA	0.458																																					p.G370G		Atlas-SNP	.											.	RBFOX2	62	.	0			c.T1110C						.						31	30	31					22																	36152191		1890	4105	5995	SO:0001630	splice_region_variant	23543	exon11			AACCACACTGCAG	AL009266	CCDS13921.1, CCDS43013.1, CCDS46699.1, CCDS46700.1, CCDS46701.1	22q12-q13	2013-02-12	2010-09-10	2010-09-10	ENSG00000100320	ENSG00000100320		"RNA binding motif (RRM) containing"	9906	protein-coding gene	gene with protein product	"hexaribonucleotide binding protein 2"	612149	"RNA binding motif protein 9"	RBM9			Standard	NM_014309		Approved	HNRBP2, FOX-2, HRNBP2	uc003aon.4	O43251	OTTHUMG00000150585	ENST00000438146.2:c.1110-1T>C	chr22.hg19:g.36152191A>G		88.0	0.0		88.0	4.0	NM_001082578	A4F5G8|A8K5Z5|B0QYY8|B0QYY9|Q0PRL5|Q0VH35|Q5TF71|Q6IC09|Q8TD00|Q8WYB1|Q96DZ6|Q96NL7|Q9UGW4|Q9UH33	Silent	SNP	ENST00000438146.2	hg19	CCDS43013.1																																																																																			.	.		0.458	RBFOX2-005	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319299.3		Silent	G	36152191	A	G	36152191	5	3	259	1	0	0	0	0	0	0	1	0	13162	173	6	2	271	2	RBM9	22	36152191	Splice_Site	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	6212756	36152191	15152375	879	37197										
TRIOBP	11078	hgsc.bcm.edu	37	chr22	38165281	38165281	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tctcccaggagctgcatggcCgcctgtcagaggagatagac	13	12	2	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:38165281C>A	ENST00000406386.3	+	21	7003	c.6748C>A	c.(6748-6750)Cgc>Agc	p.R2250S	TRIOBP_ENST00000403663.2_Missense_Mutation_p.R537S	NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	2250					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					GCTGCATGGCCGCCTGTCAGA	0.687																																					p.R2250S		Atlas-SNP	.											.	TRIOBP	262	.	0			c.C6748A						.						15	18	17					22																	38165281		2004	4169	6173	SO:0001583	missense	11078	exon21			CATGGCCGCCTGT	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"Pleckstrin homology (PH) domain containing"	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.6748C>A	chr22.hg19:g.38165281C>A	ENSP00000384312:p.Arg2250Ser	75.0	0.0		70.0	4.0	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	hg19	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	C	17.78	3.474022	0.63737	.	.	ENSG00000100106	ENST00000406386;ENST00000403663	T;T	0.22539	1.97;1.95	4.44	3.42	0.39159	.	.	.	.	.	T	0.25606	0.0623	L	0.52126	1.63	0.48696	D	0.999691	P;P;P;P	0.49559	0.925;0.841;0.712;0.845	B;P;B;B	0.46685	0.446;0.524;0.363;0.325	T	0.04930	-1.0917	9	0.87932	D	0	.	12.5587	0.56269	0.0:0.9186:0.0:0.0814	.	2152;239;537;2250	Q9H2D6-2;Q8TCM3;F8W6V6;Q9H2D6	.;.;.;TARA_HUMAN	S	2250;537	ENSP00000384312:R2250S;ENSP00000386026:R537S	ENSP00000386026:R537S	R	+	1	0	TRIOBP	36495227	0.885000	0.30320	0.559000	0.28332	0.930000	0.56654	1.999000	0.40806	1.101000	0.41535	0.462000	0.41574	CGC	.	.		0.687	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2			A	38165281	C	A	38165281	3	1	259	1	0	0	0	0	1	0	0	0	16568	652	23	1	7124	1	TRIOBP	22	38165281	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	2013090	38165281	13139285	880	37198										
MGAT3	4248	hgsc.bcm.edu	37	chr22	39883658	39883658	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gtggacttggtgctgcccgaGgacaccaccgagtatttcgt	13	11	0	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:39883658G>T	ENST00000341184.6	+	2	521	c.306G>T	c.(304-306)gaG>gaT	p.E102D		NM_001098270.1|NM_002409.4	NP_001091740.1|NP_002400.3	Q09327	MGAT3_HUMAN	mannosyl (beta-1,4-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase	102					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-1,4-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0003830)			endometrium(4)|kidney(1)|large_intestine(5)|lung(12)|prostate(1)|skin(1)	24	Melanoma(58;0.04)					TGCTGCCCGAGGACACCACCG	0.697																																					p.E102D		Atlas-SNP	.											.	MGAT3	65	.	0			c.G306T						.						15	18	17					22																	39883658		2196	4293	6489	SO:0001583	missense	4248	exon2			GCCCGAGGACACC	D13789	CCDS13994.2	22q13.1	2013-02-25			ENSG00000128268	ENSG00000128268	2.4.1.144	"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	7046	protein-coding gene	gene with protein product		604621				8370666	Standard	NM_002409		Approved	GNT-III	uc010gxy.3	Q09327	OTTHUMG00000030185	ENST00000341184.6:c.306G>T	chr22.hg19:g.39883658G>T	ENSP00000345270:p.Glu102Asp	185.0	0.0		152.0	7.0	NM_002409	A6NGD0|Q14CK5|Q6IC49|Q9UH32	Missense_Mutation	SNP	ENST00000341184.6	hg19	CCDS13994.2	.	.	.	.	.	.	.	.	.	.	G	2.247	-0.372506	0.05034	.	.	ENSG00000128268	ENST00000341184;ENST00000429402	.	.	.	4.74	3.72	0.42706	.	0.059458	0.64402	D	0.000004	T	0.24392	0.0591	N	0.11560	0.145	0.34727	D	0.729342	B	0.14438	0.01	B	0.11329	0.006	T	0.19943	-1.0290	9	0.18276	T	0.48	.	7.7287	0.28775	0.2772:0.0:0.7228:0.0	.	102	Q09327	MGAT3_HUMAN	D	102	.	ENSP00000345270:E102D	E	+	3	2	MGAT3	38213604	1.000000	0.71417	1.000000	0.80357	0.190000	0.23558	2.040000	0.41203	0.978000	0.38470	0.467000	0.42956	GAG	.	.		0.697	MGAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075039.2	NM_002409		T	39883658	G	T	39883658	3	4	259	1	0	0	0	0	1	0	0	0	9553	991	35	3	308	3	MGAT3	22	39883658	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1718377	39883658	11420908	881	37199										
MCAT	27349	hgsc.bcm.edu	37	chr22	43529443	43529443	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cactaaccggcaacatcctgGtgcgtctgaaatgaaactta	8	11	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:43529443G>A	ENST00000290429.6	-	4	824	c.779C>T	c.(778-780)aCc>aTc	p.T260I	MCAT_ENST00000327555.5_3'UTR	NM_173467.4	NP_775738.3	Q8IVS2	FABD_HUMAN	malonyl CoA:ACP acyltransferase (mitochondrial)	260					fatty acid biosynthetic process (GO:0006633)|metabolic process (GO:0008152)	mitochondrion (GO:0005739)	[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|poly(A) RNA binding (GO:0044822)|transferase activity (GO:0016740)			breast(1)|endometrium(3)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(1)	11		Ovarian(80;0.0694)				CAACATCCTGGTGCGTCTGAA	0.537																																					p.T260I		Atlas-SNP	.											.	MCAT	26	.	0			c.C779T						.						31	34	33					22																	43529443		2203	4300	6503	SO:0001583	missense	27349	exon4			ATCCTGGTGCGTC	AL359401	CCDS14045.1, CCDS33660.1	22q13.2	2010-04-27			ENSG00000100294	ENSG00000100294	2.3.1.39		29622	protein-coding gene	gene with protein product		614479				12882974	Standard	NM_173467		Approved	MT, MCT, fabD, FASN2C, NET62	uc003bdl.1	Q8IVS2	OTTHUMG00000150704	ENST00000290429.6:c.779C>T	chr22.hg19:g.43529443G>A	ENSP00000290429:p.Thr260Ile	91.0	0.0		69.0	4.0	NM_173467	B0QY72|O95510|O95511	Missense_Mutation	SNP	ENST00000290429.6	hg19	CCDS33660.1	.	.	.	.	.	.	.	.	.	.	G	2.955	-0.215899	0.06101	.	.	ENSG00000100294	ENST00000290429	T	0.42900	0.96	5.26	4.23	0.50019	Acyl transferase/acyl hydrolase/lysophospholipase (1);Malonyl-CoA ACP transacylase, ACP-binding (1);Acyl transferase (1);	0.344834	0.32273	N	0.006335	T	0.34978	0.0916	L	0.52823	1.66	0.43246	D	0.995169	P	0.46020	0.871	B	0.37304	0.246	T	0.18493	-1.0335	10	0.36615	T	0.2	-19.4544	12.2894	0.54810	0.1349:0.0:0.8651:0.0	.	260	Q8IVS2	FABD_HUMAN	I	260	ENSP00000290429:T260I	ENSP00000290429:T260I	T	-	2	0	MCAT	41859387	1.000000	0.71417	1.000000	0.80357	0.138000	0.21146	3.511000	0.53400	2.620000	0.88729	0.655000	0.94253	ACC	.	.		0.537	MCAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319677.2	NM_173467		A	43529443	G	A	43529443	3	1	259	1	0	0	0	0	1	0	0	0	9381	1261	44	3	397	3	MCAT	22	43529443	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	3645785	43529443	7775123	882	37200										
SCUBE1	80274	hgsc.bcm.edu	37	chr22	43610121	43610121	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cattccgacacgttgcgggcAccaggcagaccaagcccgtc	11	16	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:43610121A>G	ENST00000360835.4	-	16	2154	c.2028T>C	c.(2026-2028)ggT>ggC	p.G676G	Z82214.3_ENST00000420269.1_RNA	NM_173050.3	NP_766638.2	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1	676					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|post-embryonic development (GO:0009791)|protein homooligomerization (GO:0051260)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extrinsic component of plasma membrane (GO:0019897)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(4)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_neural(38;0.0414)|Ovarian(80;0.07)				CGTTGCGGGCACCAGGCAGAC	0.647																																					p.G676G		Atlas-SNP	.											.	SCUBE1	105	.	0			c.T2028C						.						58	43	48					22																	43610121		2203	4300	6503	SO:0001819	synonymous_variant	80274	exon16			GCGGGCACCAGGC		CCDS14048.1	22q13	2008-07-01			ENSG00000159307	ENSG00000159307			13441	protein-coding gene	gene with protein product		611746				11087664	Standard	NM_173050		Approved		uc003bdt.2	Q8IWY4	OTTHUMG00000150679	ENST00000360835.4:c.2028T>C	chr22.hg19:g.43610121A>G		123.0	0.0		107.0	5.0	NM_173050	Q5R336	Silent	SNP	ENST00000360835.4	hg19	CCDS14048.1																																																																																			.	.		0.647	SCUBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319582.3	NM_173050		G	43610121	A	G	43610121	2	3	259	1	0	0	0	0	0	0	0	1	13959	146	6	2		2	SCUBE1	22	43610121	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	80678	43610121	7694445	883	37201										
ARHGAP8	23779	hgsc.bcm.edu	37	chr22	45218348	45218348	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tcatccctcccgaagttttgCggtaagtgcctgttagaccc	9	13	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:45218348C>T	ENST00000389774.2	+	7	718	c.577C>T	c.(577-579)Cgg>Tgg	p.R193W	ARHGAP8_ENST00000356099.6_Splice_Site_p.R162W|ARHGAP8_ENST00000517296.3_Splice_Site_p.R372W|PRR5-ARHGAP8_ENST00000352766.7_Splice_Site_p.R372W|PRR5-ARHGAP8_ENST00000361473.5_Splice_Site_p.R293W|ARHGAP8_ENST00000336963.4_Splice_Site_p.R162W|ARHGAP8_ENST00000389773.5_Splice_Site_p.R284W	NM_001017526.1	NP_001017526.1	P85298	RHG08_HUMAN	Rho GTPase activating protein 8	193	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(9)|prostate(1)|skin(7)	29		all_neural(38;0.00409)|Ovarian(80;0.00976)|Glioma(61;0.0649)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0204)		CGAAGTTTTGCGGTAAGTGCC	0.458																																					p.R284W		Atlas-SNP	.											.	PRR5-ARHGAP8	53	.	0			c.C850T						.						101	94	96					22																	45218348		2203	4300	6503	SO:0001630	splice_region_variant	553158	exon9			GTTTTGCGGTAAG	AF177331	CCDS14060.2, CCDS33664.1, CCDS56233.1	22q13.3	2010-05-11			ENSG00000241484	ENSG00000241484		"Rho GTPase activating proteins"	677	protein-coding gene	gene with protein product		609405				10591208	Standard	NM_001198726		Approved	FLJ20185, BPGAP1		P85298	OTTHUMG00000030234	ENST00000389774.2:c.578+1C>T	chr22.hg19:g.45218348C>T		126.0	0.0		112.0	5.0	NM_181334	A6ZJ79|A6ZJ80|O75983|O95695|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Missense_Mutation	SNP	ENST00000389774.2	hg19	CCDS33664.1	.	.	.	.	.	.	.	.	.	.	C	8.164	0.790205	0.16258	.	.	ENSG00000248405;ENSG00000248405;ENSG00000241484;ENSG00000241484;ENSG00000241484;ENSG00000241484;ENSG00000241484	ENST00000361473;ENST00000352766;ENST00000517296;ENST00000389773;ENST00000389774;ENST00000336963;ENST00000356099	T;T;T;T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07	4.12	3.09	0.35607	Cellular retinaldehyde-binding/triple function, C-terminal (2);	0.000000	0.30528	U	0.009431	T	0.50222	0.1603	L	0.52011	1.625	0.33698	D	0.614221	B;B;B;B;B;B;P	0.34909	0.309;0.136;0.32;0.309;0.309;0.073;0.475	B;B;B;B;B;B;B	0.32724	0.087;0.052;0.071;0.087;0.052;0.033;0.151	T	0.60989	-0.7153	10	0.56958	D	0.05	.	5.9787	0.19395	0.2048:0.6954:0.0:0.0998	.	198;162;198;193;203;372;293	B7ZMA4;A6ZJ79;A2RU51;P85298;Q6PCC7;B1AHC4;B1AHC3	.;.;.;RHG08_HUMAN;.;.;.	W	293;372;372;284;193;162;162	ENSP00000354732:R293W;ENSP00000262731:R372W;ENSP00000429240:R372W;ENSP00000374423:R284W;ENSP00000374424:R193W;ENSP00000337287:R162W;ENSP00000348407:R162W	ENSP00000337287:R162W	R	+	1	2	PRR5-ARHGAP8;ARHGAP8	43597012	0.424000	0.25490	0.830000	0.32933	0.054000	0.15201	0.781000	0.26774	0.890000	0.36211	0.313000	0.20887	CGG	.	.		0.458	ARHGAP8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000075088.4	NM_017701	Missense_Mutation	T	45218348	C	T	45218348	5	4	259	1	0	0	0	0	0	0	1	0	888	782	27	1	599	1	ARHGAP8	22	45218348	Splice_Site	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	1608227	45218348	6086218	884	37202										
PKDREJ	10343	hgsc.bcm.edu	37	chr22	46657241	46657241	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cggtggcatgcaaagtcaccTgagaaaaagctcctagagaa	11	9	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:46657241T>C	ENST00000253255.5	-	1	1978	c.1979A>G	c.(1978-1980)cAg>cGg	p.Q660R		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	660	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		CAAAGTCACCTGAGAAAAAGC	0.458																																					p.Q660R		Atlas-SNP	.											.	PKDREJ	195	.	0			c.A1979G						.						73	80	77					22																	46657241		2203	4300	6503	SO:0001583	missense	10343	exon1			GTCACCTGAGAAA	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like", "polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like", "polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.1979A>G	chr22.hg19:g.46657241T>C	ENSP00000253255:p.Gln660Arg	74.0	0.0		70.0	4.0	NM_006071	B1AJY3|O95850	Missense_Mutation	SNP	ENST00000253255.5	hg19	CCDS14073.1	.	.	.	.	.	.	.	.	.	.	T	18.61	3.661362	0.67700	.	.	ENSG00000130943	ENST00000253255	T	0.69926	-0.44	5.27	4.22	0.49857	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	0.107962	0.41396	D	0.000892	T	0.77818	0.4187	M	0.65498	2.005	0.27988	N	0.935773	D	0.89917	1.0	D	0.68943	0.961	T	0.71896	-0.4454	10	0.59425	D	0.04	-15.159	11.9179	0.52776	0.0:0.0:0.1457:0.8543	.	660	Q9NTG1	PKDRE_HUMAN	R	660	ENSP00000253255:Q660R	ENSP00000253255:Q660R	Q	-	2	0	PKDREJ	45035905	1.000000	0.71417	1.000000	0.80357	0.843000	0.47879	2.222000	0.42926	0.929000	0.37192	0.533000	0.62120	CAG	.	.		0.458	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071		C	46657241	T	C	46657241	3	2	259	1	0	0	0	0	1	0	0	0	11979	1580	55	2	4786	2	PKDREJ	22	46657241	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1438893	46657241	4647325	885	37203										
CELSR1	9620	hgsc.bcm.edu	37	chr22	46930936	46930936	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgttggcgtcacggtcgcggGcctgcagggtcagcacgctg	17	12	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:46930936G>T	ENST00000262738.3	-	1	2131	c.2132C>A	c.(2131-2133)gCc>gAc	p.A711D	CELSR1_ENST00000497509.1_5'Flank|CELSR1_ENST00000395964.1_Missense_Mutation_p.A711D	NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	711	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		ACGGTCGCGGGCCTGCAGGGT	0.637																																					p.A711D		Atlas-SNP	.											.	CELSR1	242	.	0			c.C2132A						.						52	34	40					22																	46930936		2202	4297	6499	SO:0001583	missense	9620	exon1			TCGCGGGCCTGCA	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	1850	protein-coding gene	gene with protein product	"flamingo homolog 2 (Drosophila)"	604523	"cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.2132C>A	chr22.hg19:g.46930936G>T	ENSP00000262738:p.Ala711Asp	98.0	0.0		50.0	4.0	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	hg19	CCDS14076.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.75|16.75	3.209567|3.209567	0.58343|0.58343	.|.	.|.	ENSG00000075275|ENSG00000075275	ENST00000262738;ENST00000395964|ENST00000454637	T;T|.	0.61980|.	0.06;0.06|.	4.51|4.51	4.51|4.51	0.55191|0.55191	Cadherin (4);Cadherin-like (1);|.	0.000000|.	0.64402|.	U|.	0.000003|.	D|D	0.90714|0.90714	0.7086|0.7086	H|H	0.98996|0.98996	4.395|4.395	0.51012|0.51012	D|D	0.999902|0.999902	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	D|D	0.94846|0.94846	0.8009|0.8009	10|5	0.87932|.	D|.	0|.	.|.	16.8582|16.8582	0.86011|0.86011	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	711|.	Q9NYQ6|.	CELR1_HUMAN|.	D|T	711|86	ENSP00000262738:A711D;ENSP00000379293:A711D|.	ENSP00000262738:A711D|.	A|P	-|-	2|1	0|0	CELSR1|CELSR1	45309600|45309600	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.608000|0.608000	0.37181|0.37181	7.506000|7.506000	0.81665|0.81665	2.067000|2.067000	0.61834|0.61834	0.305000|0.305000	0.20034|0.20034	GCC|CCC	.	.		0.637	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		T	46930936	G	T	46930936	3	4	259	1	0	0	0	0	1	0	0	0	3223	1203	42	3	7052	3	CELSR1	22	46930936	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	273695	46930936	4373630	886	37204										
IL17REL	400935	hgsc.bcm.edu	37	chr22	50439203	50439203	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ctgctgccccccctgctgccGgtgggaggccctggccaccc	13	20	0	0	rs143091006	byFrequency	TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:50439203G>T	ENST00000389983.2	-	5	463	c.199C>A	c.(199-201)Cgg>Agg	p.R67R	IL17REL_ENST00000341280.5_Silent_p.R67R	NM_001001694.2	NP_001001694.2	Q6ZVW7	I17EL_HUMAN	interleukin 17 receptor E-like	67										endometrium(1)|large_intestine(1)|lung(3)|pancreas(1)	6		all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		CCCTGCTGCCGGTGGGAGGCC	0.706																																					p.R67R		Atlas-SNP	.											.	IL17REL	21	.	0			c.C199A						.						15	18	17					22																	50439203		2198	4291	6489	SO:0001819	synonymous_variant	400935	exon5			GCTGCCGGTGGGA	AK123987	CCDS33679.1	22q13.33	2009-01-13			ENSG00000188263	ENSG00000188263			33808	protein-coding gene	gene with protein product		613414					Standard	NM_001001694		Approved	FLJ41993	uc003bje.1	Q6ZVW7	OTTHUMG00000150242	ENST00000389983.2:c.199C>A	chr22.hg19:g.50439203G>T		99.0	0.0		96.0	5.0	NM_001001694	A6NCN4|A6PVC1	Silent	SNP	ENST00000389983.2	hg19	CCDS33679.1																																																																																			.	G|0.998;A|0.002		0.706	IL17REL-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317011.1	NM_001001694		T	50439203	G	T	50439203	2	4	259	1	0	0	0	0	0	0	0	1	7653	1115	39	1		1	IL17REL	22	50439203	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	3508267	50439203	865363	887	37205										
PANX2	56666	hgsc.bcm.edu	37	chr22	50615968	50615968	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aggtgcggggcccgcggtgcGcgtgagctgcaagctcccgt	18	13	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:50615968G>T	ENST00000395842.2	+	2	827	c.827G>T	c.(826-828)cGc>cTc	p.R276L	PANX2_ENST00000159647.5_Missense_Mutation_p.R276L	NM_052839.3	NP_443071.2	Q96RD6	PANX2_HUMAN	pannexin 2	276					ion transport (GO:0006811)|protein hexamerization (GO:0034214)|response to ischemia (GO:0002931)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gap junction hemi-channel activity (GO:0055077)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(1)|skin(1)	7		all_cancers(38;1.14e-10)|all_epithelial(38;2.12e-09)|all_lung(38;7.01e-05)|Breast(42;0.000523)|Lung NSC(38;0.0018)|Ovarian(80;0.0365)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.105)		CCCGCGGTGCGCGTGAGCTGC	0.667																																					p.R276L		Atlas-SNP	.											PANX2_ENST00000395842,colon,carcinoma,0,2	PANX2	69	.	0			c.G827T						.						43	33	36					22																	50615968		2190	4298	6488	SO:0001583	missense	56666	exon2			CGGTGCGCGTGAG		CCDS14085.2, CCDS54544.1	22q13.33	2011-12-05			ENSG00000073150	ENSG00000073150		"Ion channels / Pannexins"	8600	protein-coding gene	gene with protein product		608421				14702039, 14597722	Standard	NM_052839		Approved	hPANX2, PX2	uc003bjn.4	Q96RD6	OTTHUMG00000044649	ENST00000395842.2:c.827G>T	chr22.hg19:g.50615968G>T	ENSP00000379183:p.Arg276Leu	40.0	0.0		28.0	2.0	NM_052839	B7Z684|Q96RD5|Q9UGX8	Missense_Mutation	SNP	ENST00000395842.2	hg19	CCDS14085.2	.	.	.	.	.	.	.	.	.	.	G	15.61	2.883979	0.51908	.	.	ENSG00000073150	ENST00000159647;ENST00000395842	T;T	0.24350	1.86;1.86	4.42	2.32	0.28847	.	0.286325	0.32134	N	0.006531	T	0.15739	0.0379	N	0.14661	0.345	0.35885	D	0.829212	P;P	0.36354	0.493;0.549	B;B	0.38803	0.185;0.282	T	0.18650	-1.0330	10	0.41790	T	0.15	-20.3256	10.3727	0.44064	0.1617:0.0:0.8383:0.0	.	276;276	Q96RD6-1;Q96RD6	.;PANX2_HUMAN	L	276	ENSP00000159647:R276L;ENSP00000379183:R276L	ENSP00000159647:R276L	R	+	2	0	PANX2	48958095	1.000000	0.71417	0.996000	0.52242	0.491000	0.33493	3.218000	0.51192	0.348000	0.23949	-0.327000	0.08410	CGC	.	.		0.667	PANX2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075010.3	NM_052839		T	50615968	G	T	50615968	3	4	259	1	0	0	0	0	1	0	0	0	11430	1087	38	1	833	1	PANX2	22	50615968	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	176765	50615968	688598	888	37206										
VCX2	51480	hgsc.bcm.edu	37	chrX	8138170	8138171	+	Frame_Shift_Del	DEL	CT	CT	-													0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tcagtggttcttccacctcgCtctcctgactcagggggtcg					rs75657421|rs78723459		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:8138170_8138171delCT	ENST00000317103.4	-	3	628_629	c.322_323delAG	c.(322-324)agcfs	p.S108fs		NM_016378.2	NP_057462.2	Q9H322	VCX2_HUMAN	variable charge, X-linked 2	108	2 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.			S -> A (in Ref. 1; AAG41765, 2; AAF28172 and 4; AAH98113/AAH96715/AAH98163). {ECO:0000305}.						endometrium(1)	1		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				TTCCACCTCGCTCTCCTGACTC	0.644																																					p.108_108del		Pindel	.											.	VCX2	16	.	0			c.323_324del						.																																			SO:0001589	frameshift_variant	51480	exon3			.	AF159127	CCDS35200.1	Xp22.32	2008-02-05			ENSG00000177504	ENSG00000177504			18158	protein-coding gene	gene with protein product		300532				10607842	Standard	NM_016378		Approved	VCX-2r, VCX-2R	uc004csb.3	Q9H322	OTTHUMG00000021105	ENST00000317103.4:c.322_323delAG	chrX.hg19:g.8138172_8138173delCT	ENSP00000321309:p.Ser108fs	186.0	0.0		110.0	12.0	NM_016378	A3KPB6|Q4V9T2|Q9P0H5	Frame_Shift_Del	DEL	ENST00000317103.4	hg19	CCDS35200.1																																																																																			.	.		0.644	VCX2-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055690.1	NM_016378		-	8138171	CT	-	8138170	7	5	259	1	0	1	0	1	0	0	0	0	17158	797	28	0	100	0	VCX2	23	8138170	Frame_Shift_Del	DEL	CT	TCGA-ES-A2HS-01A-11D-A183-10		8138170	147132390	889	37207										
MID1	4281	hgsc.bcm.edu	37	chrX	10437803	10437803	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggagaccacgctgaactcatCatcggaggtccaatgcacag	11	12	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:10437803C>T	ENST00000317552.4	-	7	1619	c.1219G>A	c.(1219-1221)Gat>Aat	p.D407N	MID1_ENST00000380785.1_Missense_Mutation_p.D407N|MID1_ENST00000380782.2_Missense_Mutation_p.D407N|MID1_ENST00000380779.1_Missense_Mutation_p.D407N|MID1_ENST00000380780.1_Missense_Mutation_p.D407N|MID1_ENST00000453318.2_Missense_Mutation_p.D407N|MID1_ENST00000380787.1_Missense_Mutation_p.D407N	NM_000381.3|NM_033289.1	NP_000372.1|NP_150631.1	O15344	TRI18_HUMAN	midline 1	407	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				microtubule cytoskeleton organization (GO:0000226)|negative regulation of microtubule depolymerization (GO:0007026)|pattern specification process (GO:0007389)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein localization to microtubule (GO:0035372)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	ligase activity (GO:0016874)|microtubule binding (GO:0008017)|phosphoprotein binding (GO:0051219)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	26						CTGAACTCATCATCGGAGGTC	0.483																																					p.D458N		Atlas-SNP	.											.	MID1	72	.	0			c.G1372A						.						173	139	150					X																	10437803		2203	4300	6503	SO:0001583	missense	4281	exon7			ACTCATCATCGGA	Y13667	CCDS14138.1, CCDS75952.1, CCDS75953.1	Xp22	2014-06-18	2014-06-18		ENSG00000101871	ENSG00000101871		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Fibronectin type III domain containing"	7095	protein-coding gene	gene with protein product	"Opitz/BBB syndrome"	300552				9354791, 9425238	Standard	NM_001098624		Approved	OS, FXY, TRIM18, RNF59	uc004cti.4	O15344	OTTHUMG00000021127	ENST00000317552.4:c.1219G>A	chrX.hg19:g.10437803C>T	ENSP00000312678:p.Asp407Asn	89.0	0.0		85.0	4.0	NM_001193278	B2RCG2|O75361|Q9BZX5	Missense_Mutation	SNP	ENST00000317552.4	hg19	CCDS14138.1	.	.	.	.	.	.	.	.	.	.	C	35	5.518155	0.96416	.	.	ENSG00000101871	ENST00000453318;ENST00000317552;ENST00000380785;ENST00000380779;ENST00000380787;ENST00000380780;ENST00000380782;ENST00000454373;ENST00000413894	T;T;T;T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91	5.9	5.9	0.94986	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.59649	0.2209	L	0.59436	1.845	0.80722	D	1	D;D;P	0.54397	0.966;0.966;0.847	D;D;P	0.68039	0.955;0.939;0.905	T	0.50457	-0.8826	10	0.14252	T	0.57	.	19.26	0.93964	0.0:1.0:0.0:0.0	.	407;407;357	A8K5A0;O15344;B4DLX8	.;TRI18_HUMAN;.	N	407;407;407;407;407;407;407;357;407	ENSP00000414521:D407N;ENSP00000312678:D407N;ENSP00000370162:D407N;ENSP00000370156:D407N;ENSP00000370164:D407N;ENSP00000370157:D407N;ENSP00000370159:D407N;ENSP00000391154:D407N	ENSP00000312678:D407N	D	-	1	0	MID1	10397803	1.000000	0.71417	0.974000	0.42286	0.980000	0.70556	7.290000	0.78711	2.500000	0.84329	0.600000	0.82982	GAT	.	.		0.483	MID1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055738.1			T	10437803	C	T	10437803	3	4	259	1	0	0	0	0	1	0	0	0	9585	826	29	3	800	3	MID1	23	10437803	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	2299633	10437803	144832757	890	37208										
NHS	4810	hgsc.bcm.edu	37	chrX	17745288	17745288	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gctggctggcttggcatctcCatcaagtggctattcaagcc	11	12	3	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:17745288C>A	ENST00000380060.3	+	6	3337	c.2999C>A	c.(2998-3000)cCa>cAa	p.P1000Q	NHS_ENST00000398097.3_Missense_Mutation_p.P844Q	NM_198270.2	NP_938011.1	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome (congenital cataracts and dental anomalies)	1021					cell differentiation (GO:0030154)|lens development in camera-type eye (GO:0002088)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(5)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(26)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	71	Hepatocellular(33;0.183)					TTGGCATCTCCATCAAGTGGC	0.468																																					p.P1000Q		Atlas-SNP	.											.	NHS	302	.	0			c.C2999A						.						59	54	56					X																	17745288		2202	4299	6501	SO:0001583	missense	4810	exon6			CATCTCCATCAAG		CCDS14181.1, CCDS48087.1	Xp22.3-p21.1	2014-06-18			ENSG00000188158	ENSG00000188158			7820	protein-coding gene	gene with protein product		300457					Standard	NM_001136024		Approved		uc004cxx.3	Q6T4R5	OTTHUMG00000022799	ENST00000380060.3:c.2999C>A	chrX.hg19:g.17745288C>A	ENSP00000369400:p.Pro1000Gln	104.0	0.0		73.0	4.0	NM_198270	B7ZVX8|E2DH69|Q5J7Q0|Q5J7Q1|Q68DR5	Missense_Mutation	SNP	ENST00000380060.3	hg19	CCDS14181.1	.	.	.	.	.	.	.	.	.	.	C	18.15	3.560695	0.65538	.	.	ENSG00000188158	ENST00000380060;ENST00000398097;ENST00000380057	D;D	0.90563	-2.63;-2.69	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	D	0.95726	0.8610	M	0.81802	2.56	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;0.999	D	0.95841	0.8866	10	0.87932	D	0	-14.6637	19.3108	0.94187	0.0:1.0:0.0:0.0	.	1021;842;844;1000	B7ZVX8;C9IYM8;Q6T4R5-2;Q6T4R5	.;.;.;NHS_HUMAN	Q	1000;844;842	ENSP00000369400:P1000Q;ENSP00000381170:P844Q	ENSP00000369397:P842Q	P	+	2	0	NHS	17655209	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.794000	0.85869	2.513000	0.84729	0.544000	0.68410	CCA	.	.		0.468	NHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059120.1	NM_198270		A	17745288	C	A	17745288	3	1	259	1	0	0	0	0	1	0	0	0	10420	594	21	3	3126	3	NHS	23	17745288	Missense_Mutation	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	7307485	17745288	137525272	891	37209										
PPEF1	5475	hgsc.bcm.edu	37	chrX	18797263	18797263	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atgacctgcacttgaacagaGggaaccacgaagattttatg	10	8	0	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:18797263G>T	ENST00000361511.4	+	10	1188	c.694G>T	c.(694-696)Ggg>Tgg	p.G232W	PPEF1_ENST00000349874.5_Missense_Mutation_p.G232W|PPEF1_ENST00000543630.1_Missense_Mutation_p.G232W|PPEF1_ENST00000359763.6_Missense_Mutation_p.G179W|PPEF1_ENST00000544635.1_Missense_Mutation_p.G167W	NM_006240.2|NM_152224.1	NP_006231.2|NP_689410.1	O14829	PPE1_HUMAN	protein phosphatase, EF-hand calcium binding domain 1	232	Catalytic.				detection of stimulus involved in sensory perception (GO:0050906)|phototransduction, visible light (GO:0007603)|protein dephosphorylation (GO:0006470)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|manganese ion binding (GO:0030145)|protein serine/threonine phosphatase activity (GO:0004722)			breast(3)|endometrium(6)|kidney(2)|large_intestine(8)|lung(19)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	43	Hepatocellular(33;0.183)					CTTGAACAGAGGGAACCACGA	0.393																																					p.G232W		Atlas-SNP	.											.	PPEF1	89	.	0			c.G694T						.						120	111	114					X																	18797263		2203	4300	6503	SO:0001583	missense	5475	exon10			AACAGAGGGAACC	BC036026	CCDS14188.1, CCDS43920.1	Xp22	2013-01-10			ENSG00000086717	ENSG00000086717		"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits", "EF-hand domain containing"	9243	protein-coding gene	gene with protein product	"protein phosphatase 7, catalytic subunit, alpha isozyme"	300109		PPEF		9215685, 9326663	Standard	NM_152224		Approved	PPP7CA	uc004cyq.3	O14829	OTTHUMG00000021219	ENST00000361511.4:c.694G>T	chrX.hg19:g.18797263G>T	ENSP00000354871:p.Gly232Trp	84.0	0.0		91.0	4.0	NM_152226	A6NHP4|A8K348|O15253|Q9NU21|Q9UJH0	Missense_Mutation	SNP	ENST00000361511.4	hg19	CCDS14188.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.345829	0.82022	.	.	ENSG00000086717	ENST00000361511;ENST00000359763;ENST00000349874;ENST00000543630;ENST00000544635	D;D;D;D;D	0.85339	-1.97;-1.97;-1.97;-1.97;-1.97	5.19	5.19	0.71726	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (3);Metallophosphoesterase domain (1);	0.000000	0.64402	D	0.000007	D	0.96074	0.8721	H	0.99074	4.42	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.98385	1.0560	10	0.87932	D	0	-11.704	17.8877	0.88862	0.0:0.0:1.0:0.0	.	232;232;232	O14829-5;O14829;O14829-3	.;PPE1_HUMAN;.	W	232;179;232;232;167	ENSP00000354871:G232W;ENSP00000352806:G179W;ENSP00000341892:G232W;ENSP00000437785:G232W;ENSP00000441289:G167W	ENSP00000341892:G232W	G	+	1	0	PPEF1	18707184	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.417000	0.97391	2.156000	0.67533	0.529000	0.55759	GGG	.	.		0.393	PPEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055953.3	NM_006240		T	18797263	G	T	18797263	3	4	259	1	0	0	0	0	1	0	0	0	12316	1000	35	3	720	3	PPEF1	23	18797263	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1051975	18797263	136473297	892	37210										
SMPX	23676	hgsc.bcm.edu	37	chrX	21761892	21761892	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tccacttcaggagtacattcTtttcttctggggggttgacc	10	10	4	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:21761892T>C	ENST00000379494.3	-	3	341	c.108A>G	c.(106-108)aaA>aaG	p.K36K	SMPX_ENST00000494525.1_5'UTR	NM_014332.2	NP_055147.1	Q9UHP9	SMPX_HUMAN	small muscle protein, X-linked	36					striated muscle contraction (GO:0006941)	costamere (GO:0043034)|M band (GO:0031430)|muscle tendon junction (GO:0005927)|nucleus (GO:0005634)				breast(1)|endometrium(1)	2						GAGTACATTCTTTTCTTCTGG	0.463																																					p.K36K		Atlas-SNP	.											.	SMPX	12	.	0			c.A108G						.						100	93	95					X																	21761892		2203	4300	6503	SO:0001819	synonymous_variant	23676	exon3			ACATTCTTTTCTT		CCDS14200.1	Xp22.2-p22.1	2014-01-28			ENSG00000091482	ENSG00000091482			11122	protein-coding gene	gene with protein product		300226	"deafness, X-linked 6, sensorineural"	DFN6		21893181	Standard	NM_014332		Approved	DFNX4	uc004daa.3	Q9UHP9	OTTHUMG00000021235	ENST00000379494.3:c.108A>G	chrX.hg19:g.21761892T>C		60.0	0.0		68.0	4.0	NM_014332	B1AWX2	Silent	SNP	ENST00000379494.3	hg19	CCDS14200.1																																																																																			.	.		0.463	SMPX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056023.1	NM_014332		C	21761892	T	C	21761892	2	2	259	1	0	0	0	0	0	0	0	1	14825	1606	56	2		2	SMPX	23	21761892	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	2964629	21761892	133508668	893	37211										
SMS	6611	hgsc.bcm.edu	37	chrX	22010832	22010832	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tcccttcatacttggaattgTatcctttgaccgtgacattc	6	11	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:22010832T>C	ENST00000404933.2	+	10	1313		c.e10+2		SMS_ENST00000379404.1_Splice_Site|SMS_ENST00000415881.2_Splice_Site	NM_004595.4	NP_004586.2	P52788	SPSY_HUMAN	spermine synthase						cellular nitrogen compound metabolic process (GO:0034641)|methionine metabolic process (GO:0006555)|polyamine metabolic process (GO:0006595)|small molecule metabolic process (GO:0044281)|spermine biosynthetic process (GO:0006597)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	spermidine synthase activity (GO:0004766)|spermine synthase activity (GO:0016768)			endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|skin(2)	14					Spermine(DB00127)	CTTGGAATTGTATCCTTTGAC	0.408																																					.		Atlas-SNP	.											.	SMS	59	.	0			c.1061+2T>C						.						116	87	97					X																	22010832		2203	4300	6503	SO:0001630	splice_region_variant	6611	exon10			GAATTGTATCCTT	AD001528	CCDS14203.1, CCDS59161.1	Xp22.1	2014-05-16			ENSG00000102172	ENSG00000102172			11123	protein-coding gene	gene with protein product		300105	"Snyder-Robinson X-linked mental retardation syndrome"	SRS		7546290, 9299240, 14508504	Standard	NM_004595		Approved	SPMSY, SpS, MRSR	uc004dag.4	P52788	OTTHUMG00000021239	ENST00000404933.2:c.1061+2T>C	chrX.hg19:g.22010832T>C		135.0	0.0		88.0	4.0	NM_004595	A6NHA7|A6NI34|B2R9M0|O00544|Q9UQS1	Splice_Site	SNP	ENST00000404933.2	hg19	CCDS14203.1	.	.	.	.	.	.	.	.	.	.	T	19.82	3.898095	0.72639	.	.	ENSG00000102172	ENST00000404933;ENST00000379404;ENST00000415881	.	.	.	5.19	5.19	0.71726	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.1664	0.65480	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	SMS	21920753	1.000000	0.71417	1.000000	0.80357	0.812000	0.45895	5.408000	0.66368	1.723000	0.51488	0.339000	0.21740	.	.	.		0.408	SMS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056032.1	NM_004595	Intron	C	22010832	T	C	22010832	5	2	259	1	0	0	0	0	0	0	1	0	14828	1652	57	2	1101	2	SMS	23	22010832	Splice_Site	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	248940	22010832	133259728	894	37212										
PCYT1B	9468	hgsc.bcm.edu	37	chrX	24597452	24597452	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	catttataaagctgacattcAgttccttggctgtataccct	6	10	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:24597452A>G	ENST00000379144.2	-	6	819	c.689T>C	c.(688-690)cTg>cCg	p.L230P	PCYT1B_ENST00000356768.4_Missense_Mutation_p.L230P|PCYT1B_ENST00000379145.1_Missense_Mutation_p.L212P	NM_004845.4	NP_004836.2	Q9Y5K3	PCY1B_HUMAN	phosphate cytidylyltransferase 1, choline, beta	230					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|ovarian follicle development (GO:0001541)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)	choline-phosphate cytidylyltransferase activity (GO:0004105)			breast(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)	17					Choline(DB00122)	GCTGACATTCAGTTCCTTGGC	0.463																																					p.L230P		Atlas-SNP	.											.	PCYT1B	88	.	0			c.T689C						.						277	203	228					X																	24597452		2203	4300	6503	SO:0001583	missense	9468	exon6			ACATTCAGTTCCT	AF052510	CCDS14213.1, CCDS55391.1, CCDS55392.1	Xp22	2008-02-05	2005-09-05		ENSG00000102230	ENSG00000102230	2.7.7.15		8755	protein-coding gene	gene with protein product		604926	"phosphate cytidylyltransferase 1, choline, beta isoform"			9593753	Standard	NM_004845		Approved	CCT-beta, CTB	uc004dbi.3	Q9Y5K3	OTTHUMG00000021270	ENST00000379144.2:c.689T>C	chrX.hg19:g.24597452A>G	ENSP00000368439:p.Leu230Pro	185.0	0.0		122.0	5.0	NM_004845	A8IX00|B2RCX8|B4DK10|E9PD84|O60621|Q86XC9	Missense_Mutation	SNP	ENST00000379144.2	hg19	CCDS14213.1	.	.	.	.	.	.	.	.	.	.	a	12.09	1.835092	0.32421	.	.	ENSG00000102230	ENST00000379145;ENST00000379144;ENST00000356768	.	.	.	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	D	0.84866	0.5567	M	0.90870	3.155	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.996;0.996	D	0.88435	0.3038	9	0.87932	D	0	-22.5167	14.0852	0.64951	1.0:0.0:0.0:0.0	.	230;212;230	Q9Y5K3-2;E9PD84;Q9Y5K3	.;.;PCY1B_HUMAN	P	212;230;230	.	ENSP00000349211:L230P	L	-	2	0	PCYT1B	24507373	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	8.753000	0.91637	1.901000	0.55032	0.427000	0.28365	CTG	.	.		0.463	PCYT1B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056103.1	NM_004845		G	24597452	A	G	24597452	3	3	259	1	0	0	0	0	1	0	0	0	11620	188	7	2	469	2	PCYT1B	23	24597452	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2586620	24597452	130673108	895	37213										
MAGEB2	4113	hgsc.bcm.edu	37	chrX	30236769	30236769	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gcccgagatgagacccggggTctcaatgttcctcaggtcac	12	13	3	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:30236769T>C	ENST00000378988.4	+	2	173	c.72T>C	c.(70-72)ggT>ggC	p.G24G		NM_002364.4	NP_002355.2	O15479	MAGB2_HUMAN	melanoma antigen family B, 2	24										breast(1)|large_intestine(3)|lung(17)|ovary(1)|skin(1)	23						AGACCCGGGGTCTCAATGTTC	0.577																																					p.G24G		Atlas-SNP	.											.	MAGEB2	133	.	0			c.T72C						.						38	36	37					X																	30236769		2202	4300	6502	SO:0001819	synonymous_variant	4113	exon2			CCGGGGTCTCAAT	AF015766	CCDS14219.1	Xp21.3	2009-03-17			ENSG00000099399	ENSG00000099399			6809	protein-coding gene	gene with protein product	"DSS/AHC critical interval MAGE superfamily 6", "melanoma-associated antigen B2", "cancer/testis antigen family 3, member 2"	300098				9441743	Standard	NM_002364		Approved	DAM6, MAGE-XP-2, MGC26438, CT3.2	uc004dbz.3	O15479	OTTHUMG00000021319	ENST00000378988.4:c.72T>C	chrX.hg19:g.30236769T>C		125.0	0.0		96.0	4.0	NM_002364	O75860	Silent	SNP	ENST00000378988.4	hg19	CCDS14219.1																																																																																			.	.		0.577	MAGEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056157.1	NM_002364		C	30236769	T	C	30236769	2	2	259	1	0	0	0	0	0	0	0	1	9185	1654	58	2		2	MAGEB2	23	30236769	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	5639317	30236769	125033791	896	37214										
DMD	1756	hgsc.bcm.edu	37	chrX	32328324	32328324	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gatttcagtcaaataagtagAaggcacataagaaatttcca	7	6	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:32328324A>G	ENST00000357033.4	-	42	6198	c.5992T>C	c.(5992-5994)Tct>Cct	p.S1998P	DMD_ENST00000378677.2_Missense_Mutation_p.S1994P	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	1998					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				AAATAAGTAGAAGGCACATAA	0.388																																					p.S1998P		Atlas-SNP	.											.	DMD	2127	.	0			c.T5992C						.						116	95	102					X																	32328324		2202	4300	6502	SO:0001583	missense	1756	exon42			AAGTAGAAGGCAC	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.5992T>C	chrX.hg19:g.32328324A>G	ENSP00000354923:p.Ser1998Pro	223.0	0.0		140.0	6.0	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	hg19	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.296552	0.81025	.	.	ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280	T;T	0.62639	0.01;0.01	6.16	6.16	0.99307	.	0.000000	0.37095	U	0.002258	T	0.76133	0.3945	L	0.61218	1.895	0.80722	D	1	D;D;D;D;D	0.69078	0.997;0.997;0.997;0.997;0.997	D;D;D;D;D	0.81914	0.991;0.995;0.995;0.995;0.995	T	0.76506	-0.2934	10	0.46703	T	0.11	.	14.25	0.66013	1.0:0.0:0.0:0.0	.	1990;1998;1994;657;654	P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6	.;DMD_HUMAN;.;.;.	P	1990;657;654;1994;1998;1998;1875	ENSP00000367948:S1994P;ENSP00000354923:S1998P	ENSP00000354923:S1998P	S	-	1	0	DMD	32238245	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.711000	0.74675	2.085000	0.62840	0.481000	0.45027	TCT	.	.		0.388	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		G	32328324	A	G	32328324	3	3	259	1	0	0	0	0	1	0	0	0	4582	246	9	2	5365	2	DMD	23	32328324	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2091555	32328324	122942236	897	37215										
CXorf59	286464	hgsc.bcm.edu	37	chrX	36156116	36156116	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ggatagtaaattttgacaaaGacctttcagatggtcttgtt	9	5	2	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:36156116G>C	ENST00000313548.4	+	9	1273	c.1087G>C	c.(1087-1089)Gac>Cac	p.D363H		NM_173695.2	NP_775966.1	Q8N9S7	CHDC2_HUMAN	calponin homology domain containing 2	363	CH.					integral component of membrane (GO:0016021)											TTTTGACAAAGACCTTTCAGA	0.323																																					p.D363H		Atlas-SNP	.											.	.	.	.	0			c.G1087C						.						89	78	82					X																	36156116		2202	4298	6500	SO:0001583	missense	286464	exon9			GACAAAGACCTTT	AK093920	CCDS14238.1	Xp21.1	2014-08-07	2012-11-28	2012-11-28	ENSG00000176034	ENSG00000176034			26708	protein-coding gene	gene with protein product			"chromosome X open reading frame 59"	CXorf59			Standard	NM_173695		Approved	FLJ36601, RP13-11B7.1	uc004ddk.1	Q8N9S7	OTTHUMG00000021351	ENST00000313548.4:c.1087G>C	chrX.hg19:g.36156116G>C	ENSP00000324767:p.Asp363His	244.0	0.0		176.0	10.0	NM_173695		Missense_Mutation	SNP	ENST00000313548.4	hg19	CCDS14238.1	.	.	.	.	.	.	.	.	.	.	G	10.80	1.453015	0.26161	.	.	ENSG00000176034	ENST00000378660;ENST00000313548	D;D	0.96745	-4.11;-4.11	5.22	4.34	0.51931	Calponin homology domain (3);	0.093856	0.35585	N	0.003102	D	0.97402	0.9150	M	0.76002	2.32	0.23712	N	0.997049	D	0.65815	0.995	P	0.61397	0.888	D	0.93320	0.6692	10	0.87932	D	0	-6.8663	14.0852	0.64951	0.0:0.1475:0.8525:0.0	.	363	Q8N9S7	CX059_HUMAN	H	363	ENSP00000367929:D363H;ENSP00000324767:D363H	ENSP00000324767:D363H	D	+	1	0	CXorf59	36066037	1.000000	0.71417	0.034000	0.17996	0.068000	0.16541	5.232000	0.65332	0.989000	0.38761	0.529000	0.55759	GAC	.	.		0.323	CHDC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_173695		C	36156116	G	C	36156116	3	2	259	1	0	0	0	0	1	0	0	0	4117	942	33	4	1117	4	CXorf59	23	36156116	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	3827792	36156116	119114444	898	37216										
PRRG1	5638	hgsc.bcm.edu	37	chrX	37312753	37312753	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgaggaagccactggccaagTgaacctgcagaggagtgaaa	14	8	0	4			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:37312753T>C	ENST00000542554.1	+	5	808	c.536T>C	c.(535-537)gTg>gCg	p.V179A	PRRG1_ENST00000378628.4_Missense_Mutation_p.V179A|PRRG1_ENST00000491253.1_3'UTR|PRRG1_ENST00000449135.2_Missense_Mutation_p.V179A|PRRG1_ENST00000543642.1_Missense_Mutation_p.V179A|TM4SF2_ENST00000465127.1_Intron	NM_001173489.1	NP_001166960.1	O14668	TMG1_HUMAN	proline rich Gla (G-carboxyglutamic acid) 1	179						extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	15						ACTGGCCAAGTGAACCTGCAG	0.532																																					p.V179A		Atlas-SNP	.											.	PRRG1	42	.	0			c.T536C						.						76	60	65					X																	37312753		2202	4300	6502	SO:0001583	missense	5638	exon4			GCCAAGTGAACCT	AF009242	CCDS14239.1, CCDS55397.1	Xp21.1	2010-08-13	2004-05-27		ENSG00000130962	ENSG00000130962			9469	protein-coding gene	gene with protein product		604428	"proline-rich Gla (G-carboxyglutamic acid) polypeptide 1"			9256434	Standard	NM_000950		Approved	PRGP1	uc004ddo.3	O14668	OTTHUMG00000021360	ENST00000542554.1:c.536T>C	chrX.hg19:g.37312753T>C	ENSP00000444278:p.Val179Ala	66.0	0.0		55.0	4.0	NM_001173490	B2R7A3|C9JXL7|D3DWA9|Q5JT66	Missense_Mutation	SNP	ENST00000542554.1	hg19	CCDS14239.1	.	.	.	.	.	.	.	.	.	.	T	2.735	-0.263540	0.05754	.	.	ENSG00000130962	ENST00000378628;ENST00000542554;ENST00000543642;ENST00000449135	D;D;D;D	0.98701	-5.08;-5.08;-5.08;-5.08	5.96	1.87	0.25490	.	0.984876	0.08327	N	0.962944	D	0.91975	0.7458	N	0.02539	-0.55	0.20563	N	0.999886	B	0.06786	0.001	B	0.09377	0.004	D	0.86637	0.1889	10	0.07482	T	0.82	-0.158	5.6786	0.17763	0.0:0.2582:0.1376:0.6043	.	179	O14668	TMG1_HUMAN	A	179	ENSP00000367894:V179A;ENSP00000444278:V179A;ENSP00000443271:V179A;ENSP00000390332:V179A	ENSP00000367894:V179A	V	+	2	0	PRRG1	37197674	0.958000	0.32768	1.000000	0.80357	0.996000	0.88848	0.102000	0.15272	0.341000	0.23771	0.486000	0.48141	GTG	.	.		0.532	PRRG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056228.2	NM_000950		C	37312753	T	C	37312753	3	2	259	1	0	0	0	0	1	0	0	0	12617	1696	59	2	628	2	PRRG1	23	37312753	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	1156637	37312753	117957807	899	37217										
BCOR	54880	hgsc.bcm.edu	37	chrX	39913172	39913172	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atacttggatgttataacacGgtaagaggggggtctctgaa	13	5	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:39913172G>T	ENST00000378444.4	-	14	5171	c.4943C>A	c.(4942-4944)cCg>cAg	p.P1648Q	BCOR_ENST00000378463.1_Missense_Mutation_p.P491Q|BCOR_ENST00000342274.4_Missense_Mutation_p.P1614Q|BCOR_ENST00000397354.3_Missense_Mutation_p.P1614Q|BCOR_ENST00000378455.4_Missense_Mutation_p.P1596Q	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	1648	Necessary and sufficient for interaction with PCGF1.				heart development (GO:0007507)|histone H2A monoubiquitination (GO:0035518)|negative regulation of bone mineralization (GO:0030502)|negative regulation of histone H3-K36 methylation (GO:0000415)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|palate development (GO:0060021)|specification of axis polarity (GO:0065001)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	heat shock protein binding (GO:0031072)|histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			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						GTTATAACACGGTAAGAGGGG	0.468			"F, N, S, T"	RARA	"retinoblastoma, AML, APL(translocation)"		oculo-facio-cardio-dental genetic																														p.P1648Q		Atlas-SNP	.		Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	BCOR	351	.	0			c.C4943A						.						47	41	43					X																	39913172		2202	4300	6502	SO:0001583	missense	54880	exon14			TAACACGGTAAGA	AF317391	CCDS14250.1, CCDS48092.1, CCDS48093.1	Xp11.4	2014-09-17	2010-06-10		ENSG00000183337	ENSG00000183337		"Ankyrin repeat domain containing"	20893	protein-coding gene	gene with protein product		300485	"BCL6 co-repressor"			10898795	Standard	NM_017745		Approved	FLJ20285, KIAA1575	uc004den.4	Q6W2J9	OTTHUMG00000024100	ENST00000378444.4:c.4943C>A	chrX.hg19:g.39913172G>T	ENSP00000367705:p.Pro1648Gln	135.0	0.0		86.0	4.0	NM_001123385	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Missense_Mutation	SNP	ENST00000378444.4	hg19	CCDS48093.1	.	.	.	.	.	.	.	.	.	.	G	16.50	3.140948	0.56936	.	.	ENSG00000183337	ENST00000413905;ENST00000378463;ENST00000378455;ENST00000397354;ENST00000378444;ENST00000342274;ENST00000442018	T;T;T;T;T;T;T	0.75260	-0.92;0.36;0.6;0.59;0.49;0.59;-0.83	5.85	5.85	0.93711	.	.	.	.	.	D	0.86356	0.5913	M	0.69823	2.125	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.87140	0.2202	9	0.72032	D	0.01	-10.4304	19.0962	0.93253	0.0:0.0:1.0:0.0	.	1596;1648;1614	Q6W2J9-4;Q6W2J9;Q6W2J9-2	.;BCOR_HUMAN;.	Q	518;491;1596;1614;1648;1614;321	ENSP00000408006:P518Q;ENSP00000367724:P491Q;ENSP00000367716:P1596Q;ENSP00000380512:P1614Q;ENSP00000367705:P1648Q;ENSP00000345923:P1614Q;ENSP00000387552:P321Q	ENSP00000345923:P1614Q	P	-	2	0	BCOR	39798116	1.000000	0.71417	0.092000	0.20876	0.024000	0.10985	9.476000	0.97823	2.459000	0.83118	0.600000	0.82982	CCG	.	.		0.468	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745		T	39913172	G	T	39913172	3	4	259	1	0	0	0	0	1	0	0	0	1386	1116	39	1	332	1	BCOR	23	39913172	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	2600419	39913172	115357388	900	37218										
MED14	9282	hgsc.bcm.edu	37	chrX	40522223	40522223	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gatgtcgtctcatgatgactGatccaaggaatctctcaagt	9	9	3	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:40522223G>A	ENST00000324817.1	-	26	3756	c.3638C>T	c.(3637-3639)tCa>tTa	p.S1213L		NM_004229.3	NP_004220.2	O60244	MED14_HUMAN	mediator complex subunit 14	1213					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(2)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CATGATGACTGATCCAAGGAA	0.443																																					p.S1213L		Atlas-SNP	.											.	MED14	108	.	0			c.C3638T						.						82	66	71					X																	40522223		2203	4300	6503	SO:0001583	missense	9282	exon26			ATGACTGATCCAA	AB006651	CCDS14254.1	Xp11.4	2008-05-14	2007-07-30	2007-07-30	ENSG00000180182	ENSG00000180182			2370	protein-coding gene	gene with protein product		300182	"cofactor required for Sp1 transcriptional activation, subunit 2, 150kDa"	CXorf4, CRSP2		9989412, 9598311	Standard	NM_004229		Approved	EXLM1, CRSP150, TRAP170, RGR1, CSRP	uc004dex.4	O60244	OTTHUMG00000024107	ENST00000324817.1:c.3638C>T	chrX.hg19:g.40522223G>A	ENSP00000323720:p.Ser1213Leu	115.0	0.0		95.0	5.0	NM_004229	Q4KMR7|Q9UNB3	Missense_Mutation	SNP	ENST00000324817.1	hg19	CCDS14254.1	.	.	.	.	.	.	.	.	.	.	G	31	5.086900	0.94100	.	.	ENSG00000180182	ENST00000324817;ENST00000433003	T;T	0.57273	0.41;0.41	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.56963	0.2021	L	0.58101	1.795	0.80722	D	1	P;P	0.47762	0.9;0.9	P;P	0.44518	0.452;0.452	T	0.62534	-0.6834	10	0.66056	D	0.02	.	18.6702	0.91508	0.0:0.0:1.0:0.0	.	1213;1213	A8KAK5;O60244	.;MED14_HUMAN	L	1213;112	ENSP00000323720:S1213L;ENSP00000411357:S112L	ENSP00000323720:S1213L	S	-	2	0	MED14	40407167	1.000000	0.71417	0.977000	0.42913	0.997000	0.91878	9.476000	0.97823	2.353000	0.79882	0.529000	0.55759	TCA	.	.		0.443	MED14-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060692.1	NM_004229		A	40522223	G	A	40522223	3	1	259	1	0	0	0	0	1	0	0	0	9441	1294	45	3	750	3	MED14	23	40522223	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	609051	40522223	114748337	901	37219										
RBM10	8241	hgsc.bcm.edu	37	chrX	47041174	47041185	+	In_Frame_Del	DEL	GCTCAAATCTGA	GCTCAAATCTGA	-													0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	accatcatgtcacccgctgtGctcaaatctgagctccagag					rs150665564		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	GCTCAAATCTGA	GCTCAAATCTGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:47041174_47041185delGCTCAAATCTGA	ENST00000377604.3	+	15	2344_2355	c.1602_1613delGCTCAAATCTGA	c.(1600-1614)gtgctcaaatctgag>gtg	p.LKSE535del	RBM10_ENST00000329236.7_In_Frame_Del_p.LKSE457del|RBM10_ENST00000345781.6_In_Frame_Del_p.LKSE458del	NM_001204467.1|NM_001204468.1|NM_005676.4	NP_001191396.1|NP_001191397.1|NP_005667.2	P98175	RBM10_HUMAN	RNA binding motif protein 10	535					3'-UTR-mediated mRNA stabilization (GO:0070935)|mRNA processing (GO:0006397)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	48						CACCCGCTGTGCTCAAATCTGAGCTCCAGAGC	0.618																																					p.599_603del	Melanoma(171;120 2705 19495 39241)	Atlas-INDEL	.											.	RBM10	117	.	0			c.1796_1807del						.																																			SO:0001651	inframe_deletion	8241	exon15			.	U35373	CCDS14274.1, CCDS56600.1, CCDS75969.1	Xp11.3	2014-06-09			ENSG00000182872	ENSG00000182872		"Zinc fingers, RAN-binding domain containing", "G patch domain containing", "RNA binding motif (RRM) containing"	9896	protein-coding gene	gene with protein product		300080				8590280, 8808293	Standard	NM_005676		Approved	DXS8237E, KIAA0122, GPATC9, ZRANB5, GPATCH9	uc004dhi.3	P98175	OTTHUMG00000021432	ENST00000377604.3:c.1602_1613delGCTCAAATCTGA	chrX.hg19:g.47041174_47041185delGCTCAAATCTGA	ENSP00000366829:p.Leu535_Glu538del	109.0	0.0		31.0	18.0	NM_001204468	C4AM81|Q14136|Q5JRR2|Q9BTE4|Q9BTX0|Q9NTB1	In_Frame_Del	DEL	ENST00000377604.3	hg19	CCDS14274.1																																																																																			.	.		0.618	RBM10-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056381.1	NM_005676		-	47041185	GCTCAAATCTGA	-	47041174	7	5	259	1	0	1	0	1	0	0	0	0	13126	1306	46	0	1656	0	RBM10	23	47041174	In_Frame_Del	DEL	GCTCAAATCTGA	TCGA-ES-A2HS-01A-11D-A183-10	6518951	47041174	108229386	902	37220	185	2								
RBM10	8241	hgsc.bcm.edu	37	chrX	47041175	47041186	+	In_Frame_Del	DEL	CTCAAATCTGAG	CTCAAATCTGAG	-													0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccatcatgtcacccgctgtgCtcaaatctgagctccagagc							TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	CTCAAATCTGAG	CTCAAATCTGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:47041175_47041186delCTCAAATCTGAG	ENST00000377604.3	+	15	2345_2356	c.1603_1614delCTCAAATCTGAG	c.(1603-1614)ctcaaatctgagdel	p.LKSE535del	RBM10_ENST00000329236.7_In_Frame_Del_p.LKSE457del|RBM10_ENST00000345781.6_In_Frame_Del_p.LKSE458del	NM_001204467.1|NM_001204468.1|NM_005676.4	NP_001191396.1|NP_001191397.1|NP_005667.2	P98175	RBM10_HUMAN	RNA binding motif protein 10	535					3'-UTR-mediated mRNA stabilization (GO:0070935)|mRNA processing (GO:0006397)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	48						ACCCGCTGTGCTCAAATCTGAGCTCCAGAGCC	0.618																																					p.599_603del	Melanoma(171;120 2705 19495 39241)	Pindel	.											.	RBM10	117	.	0			c.1797_1808del						.																																			SO:0001651	inframe_deletion	8241	exon15			.	U35373	CCDS14274.1, CCDS56600.1, CCDS75969.1	Xp11.3	2014-06-09			ENSG00000182872	ENSG00000182872		"Zinc fingers, RAN-binding domain containing", "G patch domain containing", "RNA binding motif (RRM) containing"	9896	protein-coding gene	gene with protein product		300080				8590280, 8808293	Standard	NM_005676		Approved	DXS8237E, KIAA0122, GPATC9, ZRANB5, GPATCH9	uc004dhi.3	P98175	OTTHUMG00000021432	ENST00000377604.3:c.1603_1614delCTCAAATCTGAG	chrX.hg19:g.47041175_47041186delCTCAAATCTGAG	ENSP00000366829:p.Leu535_Glu538del	109.0	0.0		31.0	19.0	NM_001204468	C4AM81|Q14136|Q5JRR2|Q9BTE4|Q9BTX0|Q9NTB1	In_Frame_Del	DEL	ENST00000377604.3	hg19	CCDS14274.1																																																																																			.	.		0.618	RBM10-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056381.1	NM_005676		-	47041186	CTCAAATCTGAG	-	47041175	7	5	259	1	0	1	0	1	0	0	0	0	13126	797	28	0	1657	0	RBM10	23	47041175	In_Frame_Del	DEL	CTCAAATCTGAG	TCGA-ES-A2HS-01A-11D-A183-10	1	47041175	108229385	903	37221	185	2								
ZNF182	7569	hgsc.bcm.edu	37	chrX	47836310	47836310	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tctcccgtatgagttctctgGtgtataatgagagttgactt	10	7	2	3	rs376875839		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:47836310G>A	ENST00000396965.1	-	7	1526	c.1176C>T	c.(1174-1176)caC>caT	p.H392H	ZNF182_ENST00000376943.3_Silent_p.H373H|ZNF182_ENST00000305127.6_Silent_p.H392H	NM_001178099.1	NP_001171570.1	P17025	ZN182_HUMAN	zinc finger protein 182	392					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(5)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)	22						GAGTTCTCTGGTGTATAATGA	0.368																																					p.H392H		Atlas-SNP	.											.	ZNF182	117	.	0			c.C1176T						.	G	,,	1,3834		0,0,1,1632,570	106	100	102		1119,1176,1176	1.9	1	X		102	0,6728		0,0,0,2428,1872	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF182	NM_001007088.1,NM_001178099.1,NM_006962.1	,,	0,0,1,4060,2442	AA,AG,A,GG,G		0.0,0.0261,0.0095	,,	373/621,392/640,392/640	47836310	1,10562	2203	4300	6503	SO:0001819	synonymous_variant	7569	exon7			TCTCTGGTGTATA	AK122874, R98366	CCDS35235.1, CCDS35236.1	Xp11.23	2013-01-08	2006-05-10	2006-05-10	ENSG00000147118	ENSG00000147118		"Zinc fingers, C2H2-type", "-"	13001	protein-coding gene	gene with protein product		314993	"zinc finger protein 182 (HHZ150)", "zinc finger protein 21 (KOX 14)"	ZNF21		8088786, 2014798, 8914609	Standard	NM_001178099		Approved	KOX14, HHZ150, Zfp182	uc004dit.3	P17025	OTTHUMG00000021460	ENST00000396965.1:c.1176C>T	chrX.hg19:g.47836310G>A		148.0	0.0		96.0	5.0	NM_006962	A2IDD7|Q3KP67|Q96QH7	Silent	SNP	ENST00000396965.1	hg19	CCDS35236.1																																																																																			.	.		0.368	ZNF182-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277055.1	NM_006962		A	47836310	G	A	47836310	2	1	259	1	0	0	0	0	0	0	0	1	17765	1252	44	3		3	ZNF182	23	47836310	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	795135	47836310	107434250	904	37222										
HDAC6	10013	hgsc.bcm.edu	37	chrX	48661183	48661183	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tcgccccctcaggactccagTgtcacttcggtgaggcccta	10	16	2	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:48661183T>C	ENST00000334136.5	+	2	262	c.84T>C	c.(82-84)agT>agC	p.S28S	HDAC6_ENST00000469223.1_Intron|HDAC6_ENST00000444343.2_Silent_p.S42S|HDAC6_ENST00000376619.2_Silent_p.S28S|HDAC6_ENST00000413163.2_Intron			Q9UBN7	HDAC6_HUMAN	histone deacetylase 6	28					aggresome assembly (GO:0070842)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to misfolded protein (GO:0071218)|cellular response to topologically incorrect protein (GO:0035967)|histone deacetylation (GO:0016575)|Hsp90 deacetylation (GO:0070846)|intracellular protein transport (GO:0006886)|lysosome localization (GO:0032418)|macroautophagy (GO:0016236)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of oxidoreductase activity (GO:0051354)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of proteolysis (GO:0045861)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of chaperone-mediated protein complex assembly (GO:0090035)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of hydrogen peroxide-mediated programmed cell death (GO:1901300)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of signal transduction (GO:0009967)|protein complex disassembly (GO:0043241)|protein deacetylation (GO:0006476)|protein polyubiquitination (GO:0000209)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of establishment of protein localization (GO:0070201)|regulation of gene expression, epigenetic (GO:0040029)|regulation of microtubule-based movement (GO:0060632)|regulation of receptor activity (GO:0010469)|response to growth factor (GO:0070848)|response to misfolded protein (GO:0051788)|response to organic substance (GO:0010033)|response to toxic substance (GO:0009636)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	aggresome (GO:0016235)|axon (GO:0030424)|caveola (GO:0005901)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|dendrite (GO:0030425)|histone deacetylase complex (GO:0000118)|inclusion body (GO:0016234)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)	alpha-tubulin binding (GO:0043014)|beta-catenin binding (GO:0008013)|core promoter binding (GO:0001047)|dynein complex binding (GO:0070840)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|Hsp90 protein binding (GO:0051879)|microtubule binding (GO:0008017)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|polyubiquitin binding (GO:0031593)|tau protein binding (GO:0048156)|tubulin deacetylase activity (GO:0042903)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|kidney(5)|large_intestine(8)|lung(9)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	40					Vorinostat(DB02546)	AGGACTCCAGTGTCACTTCGG	0.597																																					p.S28S	Pancreas(112;205 1675 2305 8976 15959)	Atlas-SNP	.											.	HDAC6	111	.	0			c.T84C						.						45	37	40					X																	48661183		2201	4299	6500	SO:0001819	synonymous_variant	10013	exon2			CTCCAGTGTCACT	AF132609	CCDS14306.1	Xp11.23	2014-06-12			ENSG00000094631	ENSG00000094631			14064	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 90"	300272				10220385, 10048485	Standard	NM_006044		Approved	KIAA0901, JM21, HD6, FLJ16239, PPP1R90	uc004dks.1	Q9UBN7	OTTHUMG00000034496	ENST00000334136.5:c.84T>C	chrX.hg19:g.48661183T>C		168.0	0.0		110.0	5.0	NM_006044	O94975|Q6NT75|Q7L3E5|Q96CY0	Silent	SNP	ENST00000334136.5	hg19	CCDS14306.1																																																																																			.	.		0.597	HDAC6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083394.2	NM_006044		C	48661183	T	C	48661183	2	2	259	1	0	0	0	0	0	0	0	1	7020	1693	59	2		2	HDAC6	23	48661183	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	824873	48661183	106609377	905	37223										
PPP1R3F	89801	hgsc.bcm.edu	37	chrX	49143280	49143280	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atcccaccctcctcagtcccTtgggggccgaagtctgtctc	9	17	3	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:49143280T>C	ENST00000055335.6	+	4	2144	c.2128T>C	c.(2128-2130)Ttg>Ctg	p.L710L	PPP1R3F_ENST00000438316.1_Silent_p.L381L|PPP1R3F_ENST00000466508.1_Silent_p.L364L|PPP1R3F_ENST00000495799.1_Silent_p.L364L|PPP1R3F_ENST00000376188.1_Silent_p.L364L	NM_033215.4	NP_149992.3	Q6ZSY5	PPR3F_HUMAN	protein phosphatase 1, regulatory subunit 3F	710					regulation of glycogen (starch) synthase activity (GO:2000465)|regulation of glycogen biosynthetic process (GO:0005979)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycogen binding (GO:2001069)|protein phosphatase binding (GO:0019903)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(4)	27	Ovarian(276;0.236)					CCTCAGTCCCTTGGGGGCCGA	0.592																																					p.L710L		Atlas-SNP	.											.	PPP1R3F	56	.	0			c.T2128C						.						50	33	38					X																	49143280		2202	4300	6502	SO:0001819	synonymous_variant	89801	exon4			AGTCCCTTGGGGG		CCDS35254.1, CCDS55415.1	Xp11.23	2012-04-17	2011-10-04		ENSG00000049769	ENSG00000049769		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14944	protein-coding gene	gene with protein product			"protein phosphatase 1, regulatory (inhibitor) subunit 3F"			11948623	Standard	NM_033215		Approved	Hb2E	uc004dnh.2	Q6ZSY5	OTTHUMG00000024139	ENST00000055335.6:c.2128T>C	chrX.hg19:g.49143280T>C		140.0	0.0		81.0	4.0	NM_033215	A2VDJ8|B3KPW2|E9PCM3	Silent	SNP	ENST00000055335.6	hg19	CCDS35254.1																																																																																			.	.		0.592	PPP1R3F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060819.2	NM_033215		C	49143280	T	C	49143280	2	2	259	1	0	0	0	0	0	0	0	1	12387	1606	56	2		2	PPP1R3F	23	49143280	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	482097	49143280	106127280	906	37224										
CLCN5	1184	hgsc.bcm.edu	37	chrX	49855056	49855056	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	caggacagtatgactgtggaAgatgtagagaccataatcag	12	6	1	3			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:49855056A>G	ENST00000307367.2	+	10	2109	c.1818A>G	c.(1816-1818)gaA>gaG	p.E606E	CLCN5_ENST00000376091.3_Silent_p.E676E|CLCN5_ENST00000376088.3_Silent_p.E676E|CLCN5_ENST00000376108.3_Silent_p.E606E			P51795	CLCN5_HUMAN	chloride channel, voltage-sensitive 5	606	CBS 1. {ECO:0000255|PROSITE- ProRule:PRU00703}.				chloride transmembrane transport (GO:1902476)|endocytosis (GO:0006897)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(8)|ovary(2)|skin(1)	30	Ovarian(276;0.236)					TGACTGTGGAAGATGTAGAGA	0.478																																					p.E676E		Atlas-SNP	.											.	CLCN5	137	.	0			c.A2028G						.						86	71	76					X																	49855056		2203	4300	6503	SO:0001819	synonymous_variant	1184	exon13			TGTGGAAGATGTA	X91906	CCDS14328.1, CCDS48115.1, CCDS69763.1	Xp11.23-p11.22	2012-09-26	2012-02-23		ENSG00000171365	ENSG00000171365		"Ion channels / Chloride channels : Voltage-sensitive"	2023	protein-coding gene	gene with protein product	"Dent disease"	300008	"nephrolithiasis 2, X-linked", "nephrolithiasis 1 (X-linked)", "chloride channel 5"	NPHL2, NPHL1		7874126, 8111383, 8099916, 8559248, 9602200	Standard	NM_001272102		Approved	DENTS, XLRH, hClC-K2, hCIC-K2, CLC5, XRN, ClC-5	uc004doq.1	P51795	OTTHUMG00000021514	ENST00000307367.2:c.1818A>G	chrX.hg19:g.49855056A>G		115.0	0.0		96.0	4.0	NM_001127898	A1L475|B3KPN6|Q5JQD5|Q7RTN8	Silent	SNP	ENST00000307367.2	hg19	CCDS14328.1																																																																																			.	.		0.478	CLCN5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056544.1			G	49855056	A	G	49855056	2	3	259	1	0	0	0	0	0	0	0	1	3468	69	3	2		2	CLCN5	23	49855056	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	711776	49855056	105415504	907	37225										
AKAP4	8852	hgsc.bcm.edu	37	chrX	49955744	49955744	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cccttctctgctgctttagcTgaaacctgaggaagctgtgg	11	11	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:49955744T>C	ENST00000376056.2	-	6	2547	c.2397A>G	c.(2395-2397)tcA>tcG	p.S799S	AKAP4_ENST00000358526.2_Silent_p.S808S|AKAP4_ENST00000376064.3_Silent_p.S799S|AKAP4_ENST00000481402.1_5'UTR|AKAP4_ENST00000376058.2_Silent_p.S425S					A kinase (PRKA) anchor protein 4											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)					CTGCTTTAGCTGAAACCTGAG	0.512																																					p.S808S		Atlas-SNP	.											.	AKAP4	131	.	0			c.A2424G						.						148	130	136					X																	49955744		2203	4300	6503	SO:0001819	synonymous_variant	8852	exon6			TTTAGCTGAAACC	AF072756	CCDS14329.1, CCDS14330.1	Xp11.2	2009-03-12			ENSG00000147081	ENSG00000147081		"A-kinase anchor proteins"	374	protein-coding gene	gene with protein product	"A-kinase anchor protein 82 kDa", "testis-specific gene HI", "protein kinase A anchoring protein 4", "cancer/testis antigen 99"	300185				9822690, 9514854	Standard	NM_003886		Approved	p82, hAKAP82, AKAP82, Fsc1, HI, CT99	uc004dow.1	Q5JQC9	OTTHUMG00000021517	ENST00000376056.2:c.2397A>G	chrX.hg19:g.49955744T>C		132.0	0.0		83.0	4.0	NM_003886		Silent	SNP	ENST00000376056.2	hg19	CCDS14330.1																																																																																			.	.		0.512	AKAP4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056552.1	NM_003886		C	49955744	T	C	49955744	2	2	259	1	0	0	0	0	0	0	0	1	453	1567	55	2		2	AKAP4	23	49955744	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	100688	49955744	105314816	908	37226										
SMC1A	8243	hgsc.bcm.edu	37	chrX	53432729	53432729	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gtagtcaagaggcaagaaggTctcaggctccccacgctgct	12	12	2	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:53432729T>C	ENST00000322213.4	-	10	1832	c.1705A>G	c.(1705-1707)Acc>Gcc	p.T569A	SMC1A_ENST00000375340.6_Missense_Mutation_p.T335A	NM_006306.2	NP_006297.2	Q14683	SMC1A_HUMAN	structural maintenance of chromosomes 1A	569	Flexible hinge.				DNA repair (GO:0006281)|gene expression (GO:0010467)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic sister chromatid cohesion (GO:0007064)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of DNA endoreduplication (GO:0032876)|response to radiation (GO:0009314)|RNA splicing (GO:0008380)|signal transduction in response to DNA damage (GO:0042770)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin core heterodimer (GO:0008280)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|meiotic cohesin complex (GO:0030893)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(8)|ovary(5)|upper_aerodigestive_tract(2)	49						GGCAAGAAGGTCTCAGGCTCC	0.537																																					p.T569A		Atlas-SNP	.											.	SMC1A	112	.	0			c.A1705G						.						69	53	58					X																	53432729		2203	4300	6503	SO:0001583	missense	8243	exon10			AGAAGGTCTCAGG	S78271	CCDS14352.1, CCDS75985.1	Xp11.22-p11.21	2014-09-17	2006-07-06	2006-07-06	ENSG00000072501	ENSG00000072501		"Structural maintenance of chromosomes proteins"	11111	protein-coding gene	gene with protein product		300040	"SMC1 (structural maintenance of chromosomes 1, yeast)-like 1", "SMC1 structural maintenance of chromosomes 1-like 1 (yeast)"	SMC1L1		7757074	Standard	NM_006306		Approved	DXS423E, KIAA0178, SB1.8, Smcb	uc004dsg.3	Q14683	OTTHUMG00000021614	ENST00000322213.4:c.1705A>G	chrX.hg19:g.53432729T>C	ENSP00000323421:p.Thr569Ala	110.0	0.0		98.0	4.0	NM_006306	O14995|Q16351|Q2M228	Missense_Mutation	SNP	ENST00000322213.4	hg19	CCDS14352.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.289515	0.80914	.	.	ENSG00000072501	ENST00000322213;ENST00000375340	D;D	0.89050	-2.46;-2.46	5.15	5.15	0.70609	SMCs flexible hinge (3);RecF/RecN/SMC (1);	0.000000	0.85682	D	0.000000	D	0.95201	0.8444	M	0.91818	3.245	0.80722	D	1	B;D;D	0.89917	0.301;1.0;0.998	B;D;D	0.73380	0.086;0.98;0.941	D	0.96038	0.9022	10	0.87932	D	0	.	13.4318	0.61059	0.0:0.0:0.0:1.0	.	335;547;569	B7Z709;Q6MZR8;Q14683	.;.;SMC1A_HUMAN	A	569;335	ENSP00000323421:T569A;ENSP00000364489:T335A	ENSP00000323421:T569A	T	-	1	0	SMC1A	53449454	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.704000	0.84595	1.976000	0.57569	0.486000	0.48141	ACC	.	.		0.537	SMC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056756.2	NM_006306		C	53432729	T	C	53432729	3	2	259	1	0	0	0	0	1	0	0	0	14796	1667	58	2	2060	2	SMC1A	23	53432729	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	3476985	53432729	101837831	909	37227										
HUWE1	10075	hgsc.bcm.edu	37	chrX	53579842	53579842	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cagaatcctcagctctctctGgggaaagtgaggctaggaag	13	9	3	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:53579842G>T	ENST00000342160.3	-	61	8964	c.8507C>A	c.(8506-8508)cCa>cAa	p.P2836Q	HUWE1_ENST00000262854.6_Missense_Mutation_p.P2836Q			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	2836					base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						AGCTCTCTCTGGGGAAAGTGA	0.507																																					p.P2836Q		Atlas-SNP	.											.	HUWE1	724	.	0			c.C8507A						.						45	44	44					X																	53579842		2203	4300	6503	SO:0001583	missense	10075	exon62			CTCTCTGGGGAAA	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"HECT, UBA and WWE domain containing 1"			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.8507C>A	chrX.hg19:g.53579842G>T	ENSP00000340648:p.Pro2836Gln	115.0	0.0		83.0	4.0	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	hg19	CCDS35301.1	.	.	.	.	.	.	.	.	.	.	G	17.55	3.418814	0.62622	.	.	ENSG00000086758	ENST00000342160;ENST00000262854	T;T	0.37235	1.21;1.21	5.74	5.74	0.90152	.	0.592639	0.17254	N	0.181031	T	0.48519	0.1504	L	0.27053	0.805	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.83275	0.991;0.996	T	0.31971	-0.9924	10	0.27785	T	0.31	.	17.5784	0.87957	0.0:0.0:1.0:0.0	.	2836;2836	Q7Z6Z7;Q7Z6Z7-2	HUWE1_HUMAN;.	Q	2836	ENSP00000340648:P2836Q;ENSP00000262854:P2836Q	ENSP00000262854:P2836Q	P	-	2	0	HUWE1	53596567	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.813000	0.91963	2.422000	0.82143	0.600000	0.82982	CCA	.	.		0.507	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		T	53579842	G	T	53579842	3	4	259	1	0	0	0	0	1	0	0	0	7470	1348	47	3	4709	3	HUWE1	23	53579842	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	147113	53579842	101690718	910	37228										
KLF8	11279	hgsc.bcm.edu	37	chrX	56291711	56291711	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gccaaccccatggagaacccAgcactgtttaatgacatcaa	7	13	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:56291711A>G	ENST00000468660.1	+	3	468	c.180A>G	c.(178-180)ccA>ccG	p.P60P	KLF8_ENST00000374928.3_Silent_p.P60P	NM_007250.4	NP_009181.2	O95600	KLF8_HUMAN	Kruppel-like factor 8	60					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(4)|large_intestine(6)|lung(5)|ovary(1)	16						TGGAGAACCCAGCACTGTTTA	0.483																																					p.P60P		Atlas-SNP	.											.	KLF8	38	.	0			c.A180G						.						48	42	44					X																	56291711		2203	4300	6503	SO:0001819	synonymous_variant	11279	exon4			GAACCCAGCACTG	U28282	CCDS14373.1, CCDS55428.1	Xp11.21	2013-01-08			ENSG00000102349	ENSG00000102349		"Zinc fingers, C2H2-type", "Kruppel-like transcription factors"	6351	protein-coding gene	gene with protein product		300286					Standard	NM_007250		Approved	BKLF3, ZNF741, DXS741	uc004dur.3	O95600	OTTHUMG00000021666	ENST00000468660.1:c.180A>G	chrX.hg19:g.56291711A>G		138.0	0.0		96.0	4.0	NM_001159296	B4DJN3|E7EQQ8|L0R3U8|L0R4U2|Q2M246|Q59GV5|Q5HYQ5|Q5JXP7|Q6MZJ7|Q9UGC4	Silent	SNP	ENST00000468660.1	hg19	CCDS14373.1																																																																																			.	.		0.483	KLF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056887.2	NM_007250		G	56291711	A	G	56291711	2	3	259	1	0	0	0	0	0	0	0	1	8361	175	7	2		2	KLF8	23	56291711	Silent	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	2711869	56291711	98978849	911	37229										
LAS1L	81887	hgsc.bcm.edu	37	chrX	64744928	64744928	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gaaaagcatccagcacagccTccctggaacaagaggacact	9	13	0	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:64744928T>C	ENST00000374811.3	-	8	999	c.959A>G	c.(958-960)gAg>gGg	p.E320G	LAS1L_ENST00000312391.8_Silent_p.G283G|LAS1L_ENST00000374807.5_Missense_Mutation_p.E320G|LAS1L_ENST00000374804.5_Missense_Mutation_p.E278G	NM_031206.4	NP_112483.1	Q9Y4W2	LAS1L_HUMAN	LAS1-like (S. cerevisiae)	320					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(3)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	33						CAGCACAGCCTCCCTGGAACA	0.512																																					p.E320G		Atlas-SNP	.											.	LAS1L	72	.	0			c.A959G						.						101	77	85					X																	64744928		2203	4300	6503	SO:0001583	missense	81887	exon8			ACAGCCTCCCTGG	BC014545	CCDS14381.1, CCDS55433.1, CCDS55434.1	Xq12	2008-02-05			ENSG00000001497	ENSG00000001497			25726	protein-coding gene	gene with protein product						12477932	Standard	NM_031206		Approved	FLJ12525	uc004dwa.2	Q9Y4W2	OTTHUMG00000021720	ENST00000374811.3:c.959A>G	chrX.hg19:g.64744928T>C	ENSP00000363944:p.Glu320Gly	54.0	0.0		65.0	4.0	NM_031206	A9X410|Q5JXQ0|Q8TEN5|Q9H9V5	Missense_Mutation	SNP	ENST00000374811.3	hg19	CCDS14381.1	.	.	.	.	.	.	.	.	.	.	T	8.332	0.826680	0.16749	.	.	ENSG00000001497	ENST00000374807;ENST00000374811;ENST00000374804	.	.	.	5.35	2.85	0.33270	.	0.742114	0.12835	N	0.435334	T	0.27629	0.0679	L	0.38175	1.15	0.28833	N	0.89703	B;B;B	0.19583	0.001;0.037;0.006	B;B;B	0.15052	0.005;0.012;0.004	T	0.10776	-1.0615	8	.	.	.	.	4.2525	0.10702	0.0:0.1073:0.2042:0.6885	.	278;320;320	Q9Y4W2-3;Q9Y4W2-2;Q9Y4W2	.;.;LAS1L_HUMAN	G	320;320;278	.	.	E	-	2	0	LAS1L	64661653	0.456000	0.25744	0.989000	0.46669	0.953000	0.61014	0.464000	0.21988	1.785000	0.52413	0.486000	0.48141	GAG	.	.		0.512	LAS1L-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056974.1	NM_031206		C	64744928	T	C	64744928	3	2	259	1	0	0	0	0	1	0	0	0	8645	1551	54	2	1273	2	LAS1L	23	64744928	Missense_Mutation	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	8453217	64744928	90525632	912	37230										
SLC7A3	84889	hgsc.bcm.edu	37	chrX	70149744	70149744	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	cacccagggccactaaatccAgggtgcttaggcatctggca	11	13	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:70149744A>G	ENST00000374299.3	-	2	248	c.104T>C	c.(103-105)cTg>cCg	p.L35P	SLC7A3_ENST00000298085.4_Missense_Mutation_p.L35P			Q8WY07	CTR3_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 3	35					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	arginine transmembrane transporter activity (GO:0015181)|L-lysine transmembrane transporter activity (GO:0015189)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|liver(1)|lung(9)|ovary(1)|urinary_tract(1)	31	Renal(35;0.156)				L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	CACTAAATCCAGGGTGCTTAG	0.562																																					p.L35P		Atlas-SNP	.											.	SLC7A3	76	.	0			c.T104C						.						79	62	68					X																	70149744		2203	4300	6503	SO:0001583	missense	84889	exon2			AAATCCAGGGTGC	AF320612	CCDS14404.1	Xq12	2013-05-22			ENSG00000165349	ENSG00000165349		"Solute carriers"	11061	protein-coding gene	gene with protein product		300443				11591158	Standard	NM_001048164		Approved	CAT-3, ATRC3, FLJ14541	uc004dyn.3	Q8WY07	OTTHUMG00000021780	ENST00000374299.3:c.104T>C	chrX.hg19:g.70149744A>G	ENSP00000363417:p.Leu35Pro	89.0	0.0		96.0	4.0	NM_032803	D3DVU7|Q5JQR2|Q8N185|Q8NCA7|Q96SZ7	Missense_Mutation	SNP	ENST00000374299.3	hg19	CCDS14404.1	.	.	.	.	.	.	.	.	.	.	A	16.01	3.002570	0.54254	.	.	ENSG00000165349	ENST00000374299;ENST00000298085	D;D	0.91631	-2.88;-2.88	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	D	0.91825	0.7413	M	0.75777	2.31	0.80722	D	1	B	0.25007	0.116	B	0.32289	0.143	D	0.90740	0.4649	10	0.66056	D	0.02	.	12.6897	0.56968	1.0:0.0:0.0:0.0	.	35	Q8WY07	CTR3_HUMAN	P	35	ENSP00000363417:L35P;ENSP00000298085:L35P	ENSP00000298085:L35P	L	-	2	0	SLC7A3	70066469	1.000000	0.71417	1.000000	0.80357	0.753000	0.42808	8.947000	0.93000	1.787000	0.52448	0.430000	0.28490	CTG	.	.		0.562	SLC7A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057080.1	NM_032803		G	70149744	A	G	70149744	3	3	259	1	0	0	0	0	1	0	0	0	14713	188	7	2	1799	2	SLC7A3	23	70149744	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	5404816	70149744	85120816	913	37231										
MED12	9968	hgsc.bcm.edu	37	chrX	70352238	70352238	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gttctccagctctctagagcGctctggtgtatggctggtgg	14	10	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:70352238G>T	ENST00000374080.3	+	31	4297	c.4265G>T	c.(4264-4266)cGc>cTc	p.R1422L	MED12_ENST00000333646.6_Missense_Mutation_p.R1422L|MED12_ENST00000374102.1_Missense_Mutation_p.R1422L			Q93074	MED12_HUMAN	mediator complex subunit 12	1422					androgen receptor signaling pathway (GO:0030521)|axis elongation involved in somitogenesis (GO:0090245)|canonical Wnt signaling pathway (GO:0060070)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|oligodendrocyte development (GO:0014003)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|Schwann cell development (GO:0014044)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|receptor activity (GO:0004872)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420	Renal(35;0.156)					TCTCTAGAGCGCTCTGGTGTA	0.562			"M, S"		uterine leiomyoma		Opitz-Kaveggia Syndrome																														p.R1422L		Atlas-SNP	.		Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	.	MED12	984	.	0			c.G4265T						.						65	60	62					X																	70352238		2009	4163	6172	SO:0001583	missense	9968	exon31			TAGAGCGCTCTGG	U80742	CCDS43970.1	Xq13	2011-02-14	2007-07-30	2004-11-26	ENSG00000184634	ENSG00000184634			11957	protein-coding gene	gene with protein product		300188	"trinucleotide repeat containing 11 (THR-associated protein, 230kDa subunit)", "mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)", "FG syndrome 1"	TNRC11, FGS1		9225980, 10198638, 17334363, 20507344	Standard	NM_005120		Approved	CAGH45, HOPA, OPA1, TRAP230, KIAA0192, OKS	uc004dyy.3	Q93074	OTTHUMG00000021788	ENST00000374080.3:c.4265G>T	chrX.hg19:g.70352238G>T	ENSP00000363193:p.Arg1422Leu	59.0	0.0		76.0	4.0	NM_005120	O15410|O75557|Q9UHV6|Q9UND7	Missense_Mutation	SNP	ENST00000374080.3	hg19	CCDS43970.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.903756	0.92035	.	.	ENSG00000184634	ENST00000333646;ENST00000536756;ENST00000374102;ENST00000374080;ENST00000430072;ENST00000439750	T;T;T;T;T	0.68479	-0.33;-0.33;-0.33;-0.33;-0.33	4.57	4.57	0.56435	.	0.000000	0.85682	D	0.000000	T	0.71651	0.3365	L	0.60455	1.87	0.80722	D	1	P;D;P;P	0.57571	0.939;0.98;0.78;0.948	P;P;P;P	0.51355	0.643;0.654;0.535;0.667	T	0.73084	-0.4094	10	0.40728	T	0.16	-12.3509	16.9533	0.86251	0.0:0.0:1.0:0.0	.	1422;1269;1422;1422	F5H3Y1;Q7Z3Z5;Q93074-3;Q93074	.;.;.;MED12_HUMAN	L	1422;1422;1422;1422;1390;167	ENSP00000333125:R1422L;ENSP00000363215:R1422L;ENSP00000363193:R1422L;ENSP00000414203:R1390L;ENSP00000408388:R167L	ENSP00000333125:R1422L	R	+	2	0	MED12	70268963	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	8.947000	0.93000	2.267000	0.75376	0.523000	0.50628	CGC	.	.		0.562	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120		T	70352238	G	T	70352238	3	4	259	1	0	0	0	0	1	0	0	0	9437	1087	38	1	4387	1	MED12	23	70352238	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	202494	70352238	84918322	914	37232										
TBX22	50945	hgsc.bcm.edu	37	chrX	79282236	79282236	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccatgcataagtacaaacccCgagtgcacgtgatagagcaa	9	11	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:79282236C>A	ENST00000373294.5	+	5	695	c.667C>A	c.(667-669)Cga>Aga	p.R223R	TBX22_ENST00000373291.1_Silent_p.R103R|TBX22_ENST00000373296.3_Silent_p.R223R|TBX22_ENST00000442340.1_Silent_p.R103R	NM_016954.2	NP_058650.1	Q9Y458	TBX22_HUMAN	T-box 22	223					multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R223*(1)		breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(13)|lung(38)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						GTACAAACCCCGAGTGCACGT	0.453																																					p.R223R		Atlas-SNP	.											.	TBX22	118	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C667A	GRCh37	CD013205	TBX22	D		.						158	128	138					X																	79282236		2203	4300	6503	SO:0001819	synonymous_variant	50945	exon5			AAACCCCGAGTGC	AL031000	CCDS14445.1, CCDS43975.1	Xq21.1	2011-02-11			ENSG00000122145	ENSG00000122145		"T-boxes"	11600	protein-coding gene	gene with protein product		300307	"cleft palate and/or ankyloglossia"	CPX, CLPA		11559848, 14729838	Standard	NM_001109878		Approved		uc004edj.1	Q9Y458	OTTHUMG00000021901	ENST00000373294.5:c.667C>A	chrX.hg19:g.79282236C>A		83.0	0.0		93.0	4.0	NM_016954	Q5JZ06|Q96LC0|Q9HBF1	Silent	SNP	ENST00000373294.5	hg19	CCDS14445.1																																																																																			.	.		0.453	TBX22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057334.1	NM_016954		A	79282236	C	A	79282236	2	1	259	1	0	0	0	0	0	0	0	1	15673	644	23	1		1	TBX22	23	79282236	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	8929998	79282236	75988324	915	37233										
IRS4	8471	hgsc.bcm.edu	37	chrX	107975816	107975816	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	taaaattaccgacctcttttGggagagtcgaactgattatc	8	8	1	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:107975816G>T	ENST00000372129.2	-	1	3835	c.3759C>A	c.(3757-3759)ccC>ccA	p.P1253P	RP6-24A23.6_ENST00000563887.1_Silent_p.P34P	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	1253					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						GACCTCTTTTGGGAGAGTCGA	0.448																																					p.P1253P		Atlas-SNP	.											.	IRS4	253	.	0			c.C3759A						.						96	95	95					X																	107975816		2203	4300	6503	SO:0001819	synonymous_variant	8471	exon1			TCTTTTGGGAGAG	AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.3759C>A	chrX.hg19:g.107975816G>T		77.0	0.0		89.0	4.0	NM_003604		Silent	SNP	ENST00000372129.2	hg19	CCDS14544.1																																																																																			.	.		0.448	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604		T	107975816	G	T	107975816	2	4	259	1	0	0	0	0	0	0	0	1	7851	1335	47	3		3	IRS4	23	107975816	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	28693580	107975816	47294744	916	37234										
NKRF	55922	hgsc.bcm.edu	37	chrX	118725226	118725226	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgtacaggctcaaaacgaggTctcgcatggaatttggaacc	11	9	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:118725226T>C	ENST00000371527.1	-	2	814	c.162A>G	c.(160-162)agA>agG	p.R54R	NKRF_ENST00000487600.1_5'UTR|NKRF_ENST00000542113.1_Silent_p.R69R|NKRF_ENST00000304449.5_Silent_p.R54R	NM_001173488.1	NP_001166959.1	O15226	NKRF_HUMAN	NFKB repressing factor	54	Active repression domain.				negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	30						CAAAACGAGGTCTCGCATGGA	0.363																																					p.R69R		Atlas-SNP	.											.	NKRF	121	.	0			c.A207G						.						90	82	85					X																	118725226		2203	4300	6503	SO:0001819	synonymous_variant	55922	exon4			ACGAGGTCTCGCA	AJ011812	CCDS35375.1, CCDS55486.1	Xq24	2013-01-28	2008-03-26		ENSG00000186416	ENSG00000186416		"G patch domain containing"	19374	protein-coding gene	gene with protein product		300440	"NF-kappaB repressing factor"			10562553	Standard	NM_017544		Approved	ITBA4, NRF	uc022cdk.1	O15226	OTTHUMG00000022277	ENST00000371527.1:c.162A>G	chrX.hg19:g.118725226T>C		60.0	0.0		85.0	4.0	NM_001173487	G3V1N1|Q4VC41|Q9UJ91	Silent	SNP	ENST00000371527.1	hg19	CCDS35375.1																																																																																			.	.		0.363	NKRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058044.1	NM_017544		C	118725226	T	C	118725226	2	2	259	1	0	0	0	0	0	0	0	1	10456	1664	58	2		2	NKRF	23	118725226	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	10749410	118725226	36545334	917	37235										
C1GALT1C1	29071	hgsc.bcm.edu	37	chrX	119760344	119760344	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	aatactccagcatatttcagGcaaactgctagctgtttatc	6	10	1	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:119760344G>A	ENST00000304661.5	-	2	916	c.678C>T	c.(676-678)tgC>tgT	p.C226C	C1GALT1C1_ENST00000371313.2_Silent_p.C226C	NM_001011551.2	NP_001011551.1	Q96EU7	C1GLC_HUMAN	C1GALT1-specific chaperone 1	226					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	11						CATATTTCAGGCAAACTGCTA	0.378																																					p.C226C		Atlas-SNP	.											.	C1GALT1C1	22	.	0			c.C678T						.						113	107	109					X																	119760344		2203	4300	6503	SO:0001819	synonymous_variant	29071	exon3			TTTCAGGCAAACT	AJ238398	CCDS14602.1	Xq24	2008-02-05			ENSG00000171155	ENSG00000171155			24338	protein-coding gene	gene with protein product		300611				11042152, 12361956	Standard	NM_152692		Approved	COSMC, C1GALT2	uc004esz.3	Q96EU7	OTTHUMG00000022305	ENST00000304661.5:c.678C>T	chrX.hg19:g.119760344G>A		93.0	0.0		107.0	6.0	NM_152692	A8K246|Q8WWS3|Q9NZX1	Silent	SNP	ENST00000304661.5	hg19	CCDS14602.1																																																																																			.	.		0.378	C1GALT1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058117.1	NM_152692		A	119760344	G	A	119760344	2	1	259	1	0	0	0	0	0	0	0	1	1955	1195	42	3		3	C1GALT1C1	23	119760344	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1035118	119760344	35510216	918	37236										
STAG2	10735	hgsc.bcm.edu	37	chrX	123190045	123190045	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	atctggtttattcagctcacCggccagtagcagtagcagct	10	11	3	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:123190045C>A	ENST00000371160.1	+	14	1554	c.1264C>A	c.(1264-1266)Cgg>Agg	p.R422R	STAG2_ENST00000371144.3_Silent_p.R422R|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000354548.5_Silent_p.R353R|STAG2_ENST00000371145.3_Silent_p.R422R|STAG2_ENST00000218089.9_Silent_p.R422R|STAG2_ENST00000371157.3_Silent_p.R422R	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	422					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						TTCAGCTCACCGGCCAGTAGC	0.353																																					p.R422R		Atlas-SNP	.											.	STAG2	309	.	0			c.C1264A						.						93	88	89					X																	123190045		2203	4300	6503	SO:0001819	synonymous_variant	10735	exon14			GCTCACCGGCCAG	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.1264C>A	chrX.hg19:g.123190045C>A		79.0	0.0		88.0	4.0	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Silent	SNP	ENST00000371160.1	hg19	CCDS14607.1																																																																																			.	.		0.353	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		A	123190045	C	A	123190045	2	1	259	1	0	0	0	0	0	0	0	1	15258	643	23	1		1	STAG2	23	123190045	Silent	SNP	C	TCGA-ES-A2HS-01A-11D-A183-10	3429701	123190045	32080515	919	37237										
STAG2	10735	hgsc.bcm.edu	37	chrX	123190067	123190067	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gccagtagcagtagcagctgGagaatttctctacaaaaagt	10	8	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:123190067G>T	ENST00000371160.1	+	14	1576	c.1286G>T	c.(1285-1287)gGa>gTa	p.G429V	STAG2_ENST00000371144.3_Missense_Mutation_p.G429V|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000354548.5_Missense_Mutation_p.G360V|STAG2_ENST00000371145.3_Missense_Mutation_p.G429V|STAG2_ENST00000218089.9_Missense_Mutation_p.G429V|STAG2_ENST00000371157.3_Missense_Mutation_p.G429V	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	429					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						GTAGCAGCTGGAGAATTTCTC	0.333																																					p.G429V		Atlas-SNP	.											.	STAG2	309	.	0			c.G1286T						.						74	71	72					X																	123190067		2203	4300	6503	SO:0001583	missense	10735	exon14			CAGCTGGAGAATT	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.1286G>T	chrX.hg19:g.123190067G>T	ENSP00000360202:p.Gly429Val	67.0	0.0		74.0	4.0	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Missense_Mutation	SNP	ENST00000371160.1	hg19	CCDS14607.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.465602	0.84425	.	.	ENSG00000101972	ENST00000218089;ENST00000455404;ENST00000354548;ENST00000371160;ENST00000371157;ENST00000371145;ENST00000371144	T;T;T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58;1.58;1.58	5.2	5.2	0.72013	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.56615	0.1997	M	0.71581	2.175	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.986	T	0.58272	-0.7665	10	0.51188	T	0.08	-17.3276	18.0609	0.89377	0.0:0.0:1.0:0.0	.	429;429	Q8N3U4-2;Q8N3U4	.;STAG2_HUMAN	V	429;429;360;429;429;429;429	ENSP00000218089:G429V;ENSP00000397265:G429V;ENSP00000346555:G360V;ENSP00000360202:G429V;ENSP00000360199:G429V;ENSP00000360187:G429V;ENSP00000360186:G429V	ENSP00000218089:G429V	G	+	2	0	STAG2	123017748	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.809000	0.99208	2.288000	0.76882	0.544000	0.68410	GGA	.	.		0.333	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		T	123190067	G	T	123190067	3	4	259	1	0	0	0	0	1	0	0	0	15258	1174	41	3	1332	3	STAG2	23	123190067	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	22	123190067	32080493	920	37238										
GPR119	139760	hgsc.bcm.edu	37	chrX	129519158	129519158	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gtgaggacagaggcagctgcGgaggaagtgacaaatgccat	16	7	0	3	rs200469524		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:129519158G>T	ENST00000276218.2	-	1	353	c.264C>A	c.(262-264)tcC>tcA	p.S88S		NM_178471.2	NP_848566.1	Q8TDV5	GP119_HUMAN	G protein-coupled receptor 119	88					insulin secretion (GO:0030073)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)|phosphatidylcholine binding (GO:0031210)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(3)|prostate(1)	11						AGGCAGCTGCGGAGGAAGTGA	0.577																																					p.S88S		Atlas-SNP	.											.	GPR119	34	.	0			c.C264A						.						116	111	113					X																	129519158		2203	4300	6503	SO:0001819	synonymous_variant	139760	exon1			AGCTGCGGAGGAA	AY288416	CCDS14625.1	Xq26.1	2014-01-30			ENSG00000147262	ENSG00000147262		"GPCR / Class A : Orphans"	19060	protein-coding gene	gene with protein product		300513				12044878, 14623098	Standard	NM_178471		Approved	hGPCR2, GPCR2	uc011muv.2	Q8TDV5	OTTHUMG00000022397	ENST00000276218.2:c.264C>A	chrX.hg19:g.129519158G>T		80.0	0.0		90.0	5.0	NM_178471	Q495H7|Q4VBN3	Silent	SNP	ENST00000276218.2	hg19	CCDS14625.1																																																																																			.	.		0.577	GPR119-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058270.1	NM_178471		T	129519158	G	T	129519158	2	4	259	1	0	0	0	0	0	0	0	1	6642	1103	39	1		1	GPR119	23	129519158	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	6329091	129519158	25751402	921	37239										
SLC9A6	10479	hgsc.bcm.edu	37	chrX	135067790	135067790	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tttgactgggcaggggcttcGgacggcggcggcggagaggc	21	9	0	2			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:135067790G>A	ENST00000370698.3	+	1	164	c.129G>A	c.(127-129)tcG>tcA	p.S43S	SLC9A6_ENST00000370695.4_Silent_p.S43S|SLC9A6_ENST00000370701.1_5'UTR	NM_006359.2	NP_006350.1	Q92581	SL9A6_HUMAN	solute carrier family 9, subfamily A (NHE6, cation proton antiporter 6), member 6	43					axon extension (GO:0048675)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|dendrite extension (GO:0097484)|dendritic spine development (GO:0060996)|ion transport (GO:0006811)|neuron projection morphogenesis (GO:0048812)|regulation of neurotrophin TRK receptor signaling pathway (GO:0051386)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon terminus (GO:0043679)|axonal spine (GO:0044308)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome membrane (GO:0031901)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)|synapse (GO:0045202)	sodium:proton antiporter activity (GO:0015385)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(18)|ovary(2)|upper_aerodigestive_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					CAGGGGCTTCGGACGGCGGCG	0.687																																					p.S43S		Atlas-SNP	.											.	SLC9A6	64	.	0			c.G129A						.						41	44	43					X																	135067790		2201	4297	6498	SO:0001819	synonymous_variant	10479	exon1			GGCTTCGGACGGC	AF030409	CCDS14654.1, CCDS44003.1, CCDS55504.1	Xq26.3	2013-05-22	2012-03-22		ENSG00000198689	ENSG00000198689		"Solute carriers"	11079	protein-coding gene	gene with protein product		300231	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 6", "solute carrier family 9 (sodium/hydrogen exchanger), member 6"			9507001	Standard	NM_001042537		Approved	NHE6, KIAA0267	uc004ezk.3	Q92581	OTTHUMG00000022498	ENST00000370698.3:c.129G>A	chrX.hg19:g.135067790G>A		63.0	0.0		66.0	4.0	NM_006359	A6NIQ9|A8K160|B4DU30|B7ZAE0|Q3ZCW7|Q5JPP8|Q5JPP9|Q86VS0	Silent	SNP	ENST00000370698.3	hg19	CCDS14654.1																																																																																			.	.		0.687	SLC9A6-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058450.1	NM_006359		A	135067790	G	A	135067790	2	1	259	1	0	0	0	0	0	0	0	1	14733	1103	39	1		1	SLC9A6	23	135067790	Silent	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	5548632	135067790	20202770	922	37240										
AFF2	2334	hgsc.bcm.edu	37	chrX	148062276	148062276	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tctctcttttagcaaaatgcTtcaaaagtcgcacagatacc	5	11	3	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:148062276T>C	ENST00000370460.2	+	19	4058	c.3579T>C	c.(3577-3579)gcT>gcC	p.A1193A	AFF2_ENST00000286437.5_Silent_p.A834A|AFF2_ENST00000342251.3_Silent_p.A1160A|AFF2_ENST00000370457.5_Silent_p.A1158A	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	1193					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)			breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					AGCAAAATGCTTCAAAAGTCG	0.353																																					p.A1193A		Atlas-SNP	.											.	AFF2	679	.	0			c.T3579C						.						82	81	82					X																	148062276		2203	4300	6503	SO:0001819	synonymous_variant	2334	exon19			AAATGCTTCAAAA	U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"fragile X mental retardation 2"	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.3579T>C	chrX.hg19:g.148062276T>C		48.0	0.0		73.0	4.0	NM_002025	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Silent	SNP	ENST00000370460.2	hg19	CCDS14684.1																																																																																			.	.		0.353	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025		C	148062276	T	C	148062276	2	2	259	1	0	0	0	0	0	0	0	1	357	1596	56	2		2	AFF2	23	148062276	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	12994486	148062276	7208284	923	37241										
FATE1	89885	hgsc.bcm.edu	37	chrX	150889973	150889973	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	catacgtttccattatgatcGgtaagagctgagggtctgtg	12	7	1	3	rs149441058		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:150889973G>T	ENST00000370350.3	+	3	426	c.341G>T	c.(340-342)cGc>cTc	p.R114L		NM_033085.2	NP_149076.1	Q969F0	FATE1_HUMAN	fetal and adult testis expressed 1	114						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(2)|lung(6)|ovary(1)	15	Acute lymphoblastic leukemia(192;6.56e-05)					CATTATGATCGGTAAGAGCTG	0.602																																					p.R114L		Atlas-SNP	.											.	FATE1	30	.	0			c.G341T						.						76	60	65					X																	150889973		2203	4300	6503	SO:0001630	splice_region_variant	89885	exon3			ATGATCGGTAAGA	AF249872	CCDS14700.1	Xq28	2009-03-25			ENSG00000147378	ENSG00000147378			24683	protein-coding gene	gene with protein product	"cancer/testis antigen 43"	300450				11694338	Standard	NM_033085		Approved	FATE, CT43	uc004fex.3	Q969F0	OTTHUMG00000024172	ENST00000370350.3:c.341+1G>T	chrX.hg19:g.150889973G>T		66.0	0.0		90.0	4.0	NM_033085		Missense_Mutation	SNP	ENST00000370350.3	hg19	CCDS14700.1	.	.	.	.	.	.	.	.	.	.	G	14.76	2.630216	0.46944	.	.	ENSG00000147378	ENST00000370350	T	0.48836	0.8	3.92	1.14	0.20703	.	1.132520	0.06614	N	0.756234	T	0.40297	0.1111	L	0.29908	0.895	0.80722	D	1	P	0.49090	0.919	P	0.46172	0.506	T	0.20240	-1.0281	10	0.59425	D	0.04	-0.0367	5.8408	0.18633	0.3632:0.0:0.6368:0.0	.	114	Q969F0	FATE1_HUMAN	L	114	ENSP00000359375:R114L	ENSP00000359375:R114L	R	+	2	0	FATE1	150640629	0.516000	0.26218	0.017000	0.16124	0.023000	0.10783	0.465000	0.22004	0.114000	0.18032	0.529000	0.55759	CGC	.	G|1.000;A|0.000		0.602	FATE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060885.1	NM_033085	Missense_Mutation	T	150889973	G	T	150889973	5	4	259	1	0	0	0	0	0	0	1	0	5701	1130	39	1	351	1	FATE1	23	150889973	Splice_Site	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	2827697	150889973	4380587	924	37242										
ATP2B3	492	hgsc.bcm.edu	37	chrX	152821529	152821529	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	ccctgaagctatccgaaaatGccagcgtgctggcatcacag	10	13	1	1			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:152821529G>T	ENST00000349466.2	+	13	2407	c.2081G>T	c.(2080-2082)tGc>tTc	p.C694F	ATP2B3_ENST00000393842.1_Missense_Mutation_p.C680F|ATP2B3_ENST00000359149.3_Missense_Mutation_p.C694F|ATP2B3_ENST00000263519.4_Missense_Mutation_p.C694F|ATP2B3_ENST00000370186.1_Missense_Mutation_p.C680F|ATP2B3_ENST00000370181.2_Missense_Mutation_p.C680F			Q16720	AT2B3_HUMAN	ATPase, Ca++ transporting, plasma membrane 3	694					blood coagulation (GO:0007596)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			NS(2)|breast(5)|endometrium(7)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|skin(3)	50	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					ATCCGAAAATGCCAGCGTGCT	0.597																																					p.C694F		Atlas-SNP	.											.	ATP2B3	552	.	0			c.G2081T						.						129	129	129					X																	152821529		2203	4300	6503	SO:0001583	missense	492	exon12			GAAAATGCCAGCG	U60414	CCDS14722.1, CCDS35440.1	Xq28	2014-07-18			ENSG00000067842	ENSG00000067842	3.6.3.8	"ATPases / P-type"	816	protein-coding gene	gene with protein product	"plasma membrane calcium-transporting ATPase 3", "cilia and flagella associated protein 39"	300014	"spinocerebellar ataxia, X-linked 1", "cerebellar ataxia 2 (X-linked)"	SCAX1, CLA2		8187550, 22912398	Standard	NM_021949		Approved	PMCA3, CFAP39	uc004fht.1	Q16720	OTTHUMG00000024202	ENST00000349466.2:c.2081G>T	chrX.hg19:g.152821529G>T	ENSP00000343886:p.Cys694Phe	72.0	0.0		95.0	4.0	NM_001001344	B7WNR8|B7WNY5|Q12995|Q16858	Missense_Mutation	SNP	ENST00000349466.2	hg19	CCDS35440.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.430579	0.83776	.	.	ENSG00000067842	ENST00000370186;ENST00000349466;ENST00000393842;ENST00000359149;ENST00000263519;ENST00000370181	D;D;D;D;D;D	0.96168	-3.93;-3.93;-3.93;-3.93;-3.93;-3.93	4.87	4.87	0.63330	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.97996	0.9340	M	0.90309	3.105	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.74674	0.984;0.973	D	0.99198	1.0872	10	0.87932	D	0	-27.3007	16.1639	0.81739	0.0:0.0:1.0:0.0	.	694;694	Q16720;Q16720-2	AT2B3_HUMAN;.	F	680;694;680;694;694;680	ENSP00000359205:C680F;ENSP00000343886:C694F;ENSP00000377425:C680F;ENSP00000352062:C694F;ENSP00000263519:C694F;ENSP00000359200:C680F	ENSP00000263519:C694F	C	+	2	0	ATP2B3	152474723	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.721000	0.98766	2.155000	0.67459	0.529000	0.55759	TGC	.	.		0.597	ATP2B3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060957.1	NM_021949		T	152821529	G	T	152821529	3	4	259	1	0	0	0	0	1	0	0	0	1141	1319	46	3	2127	3	ATP2B3	23	152821529	Missense_Mutation	SNP	G	TCGA-ES-A2HS-01A-11D-A183-10	1931556	152821529	2449031	925	37243										
TKTL1	8277	hgsc.bcm.edu	37	chrX	153543546	153543546	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	gctactcggaaagcatgcggTctggctctggctaagctggg	15	10	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:153543546T>C	ENST00000369915.3	+	7	1077	c.888T>C	c.(886-888)ggT>ggC	p.G296G	TKTL1_ENST00000217905.7_Silent_p.G36G|TKTL1_ENST00000369912.2_Silent_p.G240G	NM_001145933.1|NM_012253.3	NP_001139405.1|NP_036385.3	P51854	TKTL1_HUMAN	transketolase-like 1	296					glucose catabolic process (GO:0006007)|thiamine metabolic process (GO:0006772)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|transketolase activity (GO:0004802)			NS(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(5)|prostate(1)|skin(1)|urinary_tract(2)	34	all_cancers(53;5.05e-16)|all_epithelial(53;1.82e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					AAGCATGCGGTCTGGCTCTGG	0.473																																					p.G296G		Atlas-SNP	.											.	TKTL1	61	.	0			c.T888C						.						171	138	149					X																	153543546		2203	4300	6503	SO:0001819	synonymous_variant	8277	exon7			ATGCGGTCTGGCT	X91817	CCDS35448.1, CCDS55541.1	Xq28	2008-02-05			ENSG00000007350	ENSG00000007350			11835	protein-coding gene	gene with protein product		300044				8838793	Standard	NM_012253		Approved	TKR, TKT2	uc004fkg.3	P51854	OTTHUMG00000022707	ENST00000369915.3:c.888T>C	chrX.hg19:g.153543546T>C		84.0	0.0		78.0	4.0	NM_012253	A8K896|Q5TYJ8|Q5TYJ9|Q8TC75	Silent	SNP	ENST00000369915.3	hg19	CCDS35448.1																																																																																			.	.		0.473	TKTL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058923.1	NM_012253		C	153543546	T	C	153543546	2	2	259	1	0	0	0	0	0	0	0	1	15950	1654	58	2		2	TKTL1	23	153543546	Silent	SNP	T	TCGA-ES-A2HS-01A-11D-A183-10	722017	153543546	1727014	926	37244										
DNASE1L1	1774	hgsc.bcm.edu	37	chrX	153631431	153631431	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0237837837837838	22	1	0.859288166473731	2.17946725860155	0.78427799078465	0.000134685372386048	0.00972331562456005	0	tgtcctccccatcggcaatcAcccagtggaagcctggctca	9	16	2	0			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:153631431A>G	ENST00000393638.1	-	7	912	c.626T>C	c.(625-627)gTg>gCg	p.V209A	DNASE1L1_ENST00000369809.1_Missense_Mutation_p.V209A|SNORA70_ENST00000384436.1_RNA	NM_001009934.1	NP_001009934.1	P49184	DNSL1_HUMAN	deoxyribonuclease I-like 1	209					DNA metabolic process (GO:0006259)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)			lung(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					ATCGGCAATCACCCAGTGGAA	0.627																																					p.V209A		Atlas-SNP	.											.	DNASE1L1	20	.	0			c.T626C						.						58	55	56					X																	153631431		2203	4300	6503	SO:0001583	missense	1774	exon7			GCAATCACCCAGT	L40817	CCDS14747.1	Xq28	2008-02-05			ENSG00000013563	ENSG00000013563			2957	protein-coding gene	gene with protein product	"DNase X"	300081		DNL1L		8541839, 8654957	Standard	XM_005277829		Approved	DNAS1L1, XIB, DNASEX	uc004fkw.1	P49184	OTTHUMG00000033188	ENST00000393638.1:c.626T>C	chrX.hg19:g.153631431A>G	ENSP00000377255:p.Val209Ala	73.0	0.0		84.0	5.0	NM_006730	D3DWW7|Q5HY41	Missense_Mutation	SNP	ENST00000393638.1	hg19	CCDS14747.1	.	.	.	.	.	.	.	.	.	.	A	13.86	2.362903	0.41902	.	.	ENSG00000013563	ENST00000369809;ENST00000393638;ENST00000014935;ENST00000369808;ENST00000369807;ENST00000309585	T;T;T;T;T;T	0.50277	0.75;0.75;0.75;0.75;0.75;0.75	4.93	-2.34	0.06704	Endonuclease/exonuclease/phosphatase (2);	0.572650	0.16380	N	0.216952	T	0.27169	0.0666	N	0.17312	0.475	0.26270	N	0.978448	B	0.02656	0.0	B	0.06405	0.002	T	0.13980	-1.0489	10	0.51188	T	0.08	-15.7171	9.5875	0.39526	0.698:0.0:0.302:0.0	.	209	P49184	DNSL1_HUMAN	A	209	ENSP00000358824:V209A;ENSP00000377255:V209A;ENSP00000014935:V209A;ENSP00000358823:V209A;ENSP00000358822:V209A;ENSP00000309168:V209A	ENSP00000014935:V209A	V	-	2	0	DNASE1L1	153284625	0.868000	0.29978	0.129000	0.21949	0.873000	0.50193	1.545000	0.36169	-0.452000	0.07087	-0.327000	0.08410	GTG	.	.		0.627	DNASE1L1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080928.2			G	153631431	A	G	153631431	3	3	259	1	0	0	0	0	1	0	0	0	4663	159	6	2	290	2	DNASE1L1	23	153631431	Missense_Mutation	SNP	A	TCGA-ES-A2HS-01A-11D-A183-10	87885	153631431	1639129	927	37245										
MORN1	79906	hgsc.bcm.edu	37	chr1	2288951	2288951	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctcccctgggcaggggcacgTcggcttctgcccctcccttg	12	18	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:2288951T>C	ENST00000378531.3	-	10	1129	c.956A>G	c.(955-957)gAc>gGc	p.D319G	MORN1_ENST00000378529.3_Missense_Mutation_p.D319G|MORN1_ENST00000606372.1_5'UTR	NM_024848.1	NP_079124.1	Q5T089	MORN1_HUMAN	MORN repeat containing 1	319										breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(1)|ovary(2)	9	all_cancers(77;0.000194)|all_epithelial(69;9.96e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.3e-15)|all_lung(118;1.15e-06)|Lung NSC(185;6.26e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;2.21e-37)|OV - Ovarian serous cystadenocarcinoma(86;5.01e-23)|GBM - Glioblastoma multiforme(42;2.8e-08)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00137)|BRCA - Breast invasive adenocarcinoma(365;0.00488)|STAD - Stomach adenocarcinoma(132;0.00665)|KIRC - Kidney renal clear cell carcinoma(229;0.0203)|Lung(427;0.212)		CAGGGGCACGTCGGCTTCTGC	0.647																																					p.D319G		Atlas-SNP	.											.	MORN1	38	.	0			c.A956G						.						48	53	51					1																	2288951		2203	4299	6502	SO:0001583	missense	79906	exon10			GGCACGTCGGCTT	AK024003	CCDS40.1, CCDS72688.1	1p36.33-p36.32	2008-02-05			ENSG00000116151	ENSG00000116151			25852	protein-coding gene	gene with protein product						12477932	Standard	XM_005244798		Approved	FLJ13941	uc001ajb.1	Q5T089	OTTHUMG00000001402	ENST00000378531.3:c.956A>G	chr1.hg19:g.2288951T>C	ENSP00000367792:p.Asp319Gly	253.0	0.0		174.0	38.0	NM_024848	A6NKZ6|Q8WW30|Q9H852	Missense_Mutation	SNP	ENST00000378531.3	hg19	CCDS40.1	.	.	.	.	.	.	.	.	.	.	T	11.14	1.550902	0.27739	.	.	ENSG00000116151	ENST00000378531;ENST00000378529	T;T	0.57907	0.68;0.37	3.2	3.2	0.36748	.	1.555720	0.04109	N	0.314273	T	0.55609	0.1931	M	0.61703	1.905	0.23581	N	0.997363	P;P	0.40180	0.705;0.483	B;B	0.41510	0.359;0.057	T	0.49351	-0.8949	10	0.56958	D	0.05	.	8.163	0.31209	0.0:0.0:0.0:1.0	.	319;319	Q5T089-2;Q5T089	.;MORN1_HUMAN	G	319	ENSP00000367792:D319G;ENSP00000367790:D319G	ENSP00000367790:D319G	D	-	2	0	MORN1	2278811	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-0.043000	0.12043	1.698000	0.51180	0.460000	0.39030	GAC	.	.		0.647	MORN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004055.1	NM_024848		C	2288951	T	C	2288951	3	2	260	1	0	0	0	0	1	0	0	0	9717	1667	58	2	557	2	MORN1	1	2288951	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10		2288951	246961670	1	37246										
CCDC27	148870	hgsc.bcm.edu	37	chr1	3683876	3683876	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	caccaaggtcagccagctgcAggagcaggtggaactggacc	14	12	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:3683876A>G	ENST00000294600.2	+	10	1694	c.1610A>G	c.(1609-1611)cAg>cGg	p.Q537R		NM_152492.2	NP_689705.2	Q2M243	CCD27_HUMAN	coiled-coil domain containing 27	537										breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(2)|lung(17)|prostate(1)|skin(2)|urinary_tract(2)	36	all_cancers(77;0.0385)|Ovarian(185;0.0634)|Lung NSC(156;0.21)|all_lung(157;0.218)	all_epithelial(116;5.52e-17)|all_lung(118;1.04e-06)|Lung NSC(185;0.000214)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Lung SC(97;0.0367)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)		Epithelial(90;1.11e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.35e-22)|GBM - Glioblastoma multiforme(42;3.46e-16)|Colorectal(212;1.17e-05)|COAD - Colon adenocarcinoma(227;5.76e-05)|Kidney(185;0.00036)|BRCA - Breast invasive adenocarcinoma(365;0.000696)|KIRC - Kidney renal clear cell carcinoma(229;0.00558)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.203)		AGCCAGCTGCAGGAGCAGGTG	0.572																																					p.Q537R		Atlas-SNP	.											.	CCDC27	79	.	0			c.A1610G						.						57	55	56					1																	3683876		2203	4300	6503	SO:0001583	missense	148870	exon10			AGCTGCAGGAGCA		CCDS50.1	1p36.32	2008-02-05			ENSG00000162592	ENSG00000162592			26546	protein-coding gene	gene with protein product							Standard	NM_152492		Approved	FLJ32825	uc001akv.2	Q2M243	OTTHUMG00000003504	ENST00000294600.2:c.1610A>G	chr1.hg19:g.3683876A>G	ENSP00000294600:p.Gln537Arg	204.0	0.0		148.0	7.0	NM_152492	Q5TBV3|Q96M50	Missense_Mutation	SNP	ENST00000294600.2	hg19	CCDS50.1	.	.	.	.	.	.	.	.	.	.	A	16.71	3.197967	0.58126	.	.	ENSG00000162592	ENST00000294600	T	0.20069	2.1	5.24	5.24	0.73138	.	0.465836	0.19916	N	0.103198	T	0.24586	0.0596	L	0.27053	0.805	0.28090	N	0.931854	P	0.52692	0.955	P	0.53401	0.725	T	0.05053	-1.0909	10	0.49607	T	0.09	-27.3492	11.5015	0.50441	1.0:0.0:0.0:0.0	.	537	Q2M243	CCD27_HUMAN	R	537	ENSP00000294600:Q537R	ENSP00000294600:Q537R	Q	+	2	0	CCDC27	3673736	1.000000	0.71417	0.545000	0.28153	0.461000	0.32589	4.661000	0.61518	1.957000	0.56846	0.533000	0.62120	CAG	.	.		0.572	CCDC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009740.1	NM_152492		G	3683876	A	G	3683876	3	3	260	1	0	0	0	0	1	0	0	0	2803	188	7	2	1648	2	CCDC27	1	3683876	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1394925	3683876	245566745	2	37247										
C1orf174	339448	hgsc.bcm.edu	37	chr1	3807353	3807353	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acaggccatctctagtctttGctaagcgagagtcactcaca	8	12	4	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:3807353G>T	ENST00000361605.3	-	3	496	c.398C>A	c.(397-399)gCa>gAa	p.A133E	C1orf174_ENST00000486765.1_5'UTR	NM_207356.2	NP_997239.2	Q8IYL3	CA174_HUMAN	chromosome 1 open reading frame 174	133						nucleus (GO:0005634)				endometrium(1)|large_intestine(5)|lung(4)|prostate(1)	11	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_cancers(23;5.09e-25)|all_epithelial(116;9.35e-17)|all_lung(118;1.09e-06)|Lung NSC(185;0.000139)|all_neural(13;0.00287)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0219)|all_hematologic(16;0.027)|Colorectal(325;0.0276)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.0743)|Ovarian(437;0.127)		Epithelial(90;1.55e-39)|OV - Ovarian serous cystadenocarcinoma(86;5.99e-23)|GBM - Glioblastoma multiforme(42;2.22e-17)|Colorectal(212;1.08e-05)|COAD - Colon adenocarcinoma(227;5.49e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.000365)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.19)		TCTAGTCTTTGCTAAGCGAGA	0.582																																					p.A133E		Atlas-SNP	.											.	C1orf174	20	.	0			c.C398A						.						78	69	72					1																	3807353		2203	4300	6503	SO:0001583	missense	339448	exon3			GTCTTTGCTAAGC	BC035643	CCDS53.1	1p36.32	2012-07-25			ENSG00000198912	ENSG00000198912			27915	protein-coding gene	gene with protein product						12477932	Standard	NM_207356		Approved	RP13-531C17.2	uc001alf.3	Q8IYL3	OTTHUMG00000003739	ENST00000361605.3:c.398C>A	chr1.hg19:g.3807353G>T	ENSP00000355306:p.Ala133Glu	138.0	0.0		99.0	4.0	NM_207356	A8K0C8|A8MUG9|Q5SR20|Q6NX36	Missense_Mutation	SNP	ENST00000361605.3	hg19	CCDS53.1	.	.	.	.	.	.	.	.	.	.	G	16.17	3.048791	0.55110	.	.	ENSG00000198912	ENST00000361605	T	0.06608	3.28	5.56	1.36	0.22044	.	1.823430	0.02225	N	0.064345	T	0.15912	0.0383	L	0.53249	1.67	0.09310	N	1	D	0.63046	0.992	P	0.59948	0.866	T	0.13255	-1.0516	10	0.26408	T	0.33	0.4856	4.7974	0.13279	0.1639:0.0:0.5383:0.2977	.	133	Q8IYL3	CA174_HUMAN	E	133	ENSP00000355306:A133E	ENSP00000355306:A133E	A	-	2	0	C1orf174	3797213	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.346000	0.19997	-0.007000	0.14345	0.563000	0.77884	GCA	.	.		0.582	C1orf174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010539.1	NM_207356		T	3807353	G	T	3807353	3	4	260	1	0	0	0	0	1	0	0	0	2017	1319	46	3	341	3	C1orf174	1	3807353	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	123477	3807353	245443268	3	37248										
TMEM201	199953	hgsc.bcm.edu	37	chr1	9669927	9669927	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	atctgttcagcggtagccgcCcaccatctcaggtgtctcga	10	14	4	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:9669927C>T	ENST00000340381.6	+	8	1432	c.1423C>T	c.(1423-1425)Cca>Tca	p.P475S	TMEM201_ENST00000377376.4_Intron	NM_001130924.2	NP_001124396.2	Q5SNT2	TM201_HUMAN	transmembrane protein 201	475	Ser-rich.				fibroblast migration (GO:0010761)|nuclear migration (GO:0007097)	integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)				lung(3)|upper_aerodigestive_tract(1)	4	all_lung(157;0.222)	all_epithelial(116;2.09e-14)|Renal(390;0.000469)|all_lung(118;0.000521)|Lung NSC(185;0.000744)|Colorectal(325;0.0062)|Breast(348;0.0157)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.5e-08)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|STAD - Stomach adenocarcinoma(132;0.00345)|READ - Rectum adenocarcinoma(331;0.0419)		CGGTAGCCGCCCACCATCTCA	0.602																																					p.P475S		Atlas-SNP	.											.	TMEM201	63	.	0			c.C1423T						.						37	37	37					1																	9669927		692	1591	2283	SO:0001583	missense	199953	exon8			AGCCGCCCACCAT		CCDS30579.1, CCDS44055.1, CCDS44055.2	1p36.22	2009-11-06			ENSG00000188807	ENSG00000188807			33719	protein-coding gene	gene with protein product							Standard	NM_001130924		Approved	RP13-15M17.2, NET5	uc021ofy.1	Q5SNT2	OTTHUMG00000057457	ENST00000340381.6:c.1423C>T	chr1.hg19:g.9669927C>T	ENSP00000344503:p.Pro475Ser	133.0	0.0		80.0	4.0	NM_001130924	B9EH90|Q5SNT3	Missense_Mutation	SNP	ENST00000340381.6	hg19	CCDS44055.2	.	.	.	.	.	.	.	.	.	.	C	23.6	4.436826	0.83885	.	.	ENSG00000188807	ENST00000340381	.	.	.	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.60444	0.2269	L	0.36672	1.1	0.80722	D	1	.	.	.	.	.	.	T	0.54899	-0.8224	7	0.30854	T	0.27	-17.0285	17.7376	0.88399	0.0:1.0:0.0:0.0	.	.	.	.	S	475	.	ENSP00000344503:P475S	P	+	1	0	TMEM201	9592514	1.000000	0.71417	0.989000	0.46669	0.838000	0.47535	6.151000	0.71806	2.630000	0.89119	0.655000	0.94253	CCA	.	.		0.602	TMEM201-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127672.1	NM_001010866		T	9669927	C	T	9669927	3	4	260	1	0	0	0	0	1	0	0	0	16141	623	22	3	1472	3	TMEM201	1	9669927	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	5862574	9669927	239580694	4	37249										
KIF1B	23095	hgsc.bcm.edu	37	chr1	10425293	10425293	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggagctggagaagctggagcTcctacatgaggtatccaggg	16	8	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:10425293T>C	ENST00000377086.1	+	42	4704	c.4502T>C	c.(4501-4503)cTc>cCc	p.L1501P	KIF1B_ENST00000263934.6_Missense_Mutation_p.L1455P|KIF1B_ENST00000377081.1_Missense_Mutation_p.L1501P			O60333	KIF1B_HUMAN	kinesin family member 1B	1501					anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		AAGCTGGAGCTCCTACATGAG	0.557																																					p.L1455P		Atlas-SNP	.											.	KIF1B	242	.	0			c.T4364C						.						42	43	43					1																	10425293		2203	4300	6503	SO:0001583	missense	23095	exon40			TGGAGCTCCTACA	AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"Kinesins", "Pleckstrin homology (PH) domain containing"	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.4502T>C	chr1.hg19:g.10425293T>C	ENSP00000366290:p.Leu1501Pro	185.0	0.0		118.0	5.0	NM_015074	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Missense_Mutation	SNP	ENST00000377086.1	hg19		.	.	.	.	.	.	.	.	.	.	T	14.58	2.578287	0.45902	.	.	ENSG00000054523	ENST00000355249;ENST00000263934;ENST00000377086;ENST00000377081	T;T;T	0.72942	-0.62;-0.7;-0.7	5.29	5.29	0.74685	.	0.072104	0.64402	D	0.000019	T	0.72078	0.3416	L	0.29908	0.895	0.80722	D	1	P;P;P;P;P;B	0.49862	0.863;0.8;0.863;0.929;0.641;0.118	B;B;P;P;B;B	0.59948	0.333;0.188;0.613;0.866;0.188;0.087	T	0.74460	-0.3658	10	0.62326	D	0.03	.	10.5023	0.44813	0.1446:0.0:0.0:0.8554	.	1487;1461;1501;1475;1501;1455	Q4R9M9;Q4R9M7;Q4VXC4;Q4R9M8;O60333;O60333-2	.;.;.;.;KIF1B_HUMAN;.	P	1501;1455;1501;1501	ENSP00000263934:L1455P;ENSP00000366290:L1501P;ENSP00000366284:L1501P	ENSP00000263934:L1455P	L	+	2	0	KIF1B	10347880	1.000000	0.71417	0.990000	0.47175	0.953000	0.61014	2.776000	0.47709	1.991000	0.58162	0.528000	0.53228	CTC	.	.		0.557	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1			C	10425293	T	C	10425293	3	2	260	1	0	0	0	0	1	0	0	0	8293	1551	54	2	6007	2	KIF1B	1	10425293	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	755366	10425293	238825328	5	37250										
C1orf127	148345	hgsc.bcm.edu	37	chr1	11009710	11009710	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgcgtcggaaggccggtgcaGgaggtcccgagaaagccatt	16	10	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:11009710G>A	ENST00000377008.4	-	10	1206	c.760C>T	c.(760-762)Ctg>Ttg	p.L254L	C1orf127_ENST00000377004.4_Silent_p.L421L			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	254	Pro-rich.									NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(5)	32	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)		GGCCGGTGCAGGAGGTCCCGA	0.622																																					p.L421L		Atlas-SNP	.											.	C1orf127	134	.	0			c.C1261T						.						42	36	38					1																	11009710		2199	4300	6499	SO:0001819	synonymous_variant	148345	exon11			GGTGCAGGAGGTC	AK094437	CCDS53267.1	1p36.22	2008-02-05			ENSG00000175262	ENSG00000175262			26730	protein-coding gene	gene with protein product						14702039	Standard	NM_001170754		Approved	FLJ37118	uc010oao.2	Q8N9H9	OTTHUMG00000002032	ENST00000377008.4:c.760C>T	chr1.hg19:g.11009710G>A		133.0	0.0		132.0	26.0	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Silent	SNP	ENST00000377008.4	hg19																																																																																				.	.		0.622	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507		A	11009710	G	A	11009710	2	1	260	1	0	0	0	0	0	0	0	1	1996	991	35	3		3	C1orf127	1	11009710	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	584417	11009710	238240911	6	37251										
MTHFR	4524	hgsc.bcm.edu	37	chr1	11854524	11854524	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcttcagcagctcctccttgGgggacttgctcttcaggtag	11	12	4	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:11854524G>A	ENST00000376592.1	-	7	1366	c.1238C>T	c.(1237-1239)cCc>cTc	p.P413L	MTHFR_ENST00000376585.1_Missense_Mutation_p.P454L|MTHFR_ENST00000376583.3_Missense_Mutation_p.P454L|MTHFR_ENST00000376590.3_Missense_Mutation_p.P413L			P42898	MTHR_HUMAN	methylenetetrahydrofolate reductase (NAD(P)H)	413					blood circulation (GO:0008015)|cellular amino acid metabolic process (GO:0006520)|folic acid metabolic process (GO:0046655)|homocysteine metabolic process (GO:0050667)|methionine biosynthetic process (GO:0009086)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to vitamin B2 (GO:0033274)|S-adenosylmethionine metabolic process (GO:0046500)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|neuron projection (GO:0043005)	flavin adenine dinucleotide binding (GO:0050660)|methylenetetrahydrofolate reductase (NAD(P)H) activity (GO:0004489)|modified amino acid binding (GO:0072341)|NADP binding (GO:0050661)			NS(4)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	33	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Benazepril(DB00542)|Cyanocobalamin(DB00115)|Fluorouracil(DB00544)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Riboflavin(DB00140)|Tetrahydrofolic acid(DB00116)	CTCCTCCTTGGGGGACTTGCT	0.557																																					p.P413L		Atlas-SNP	.											.	MTHFR	65	.	0			c.C1238T						.						84	95	91					1																	11854524		2203	4300	6503	SO:0001583	missense	4524	exon8			TCCTTGGGGGACT	BC053509	CCDS137.1	1p36.3	2014-09-17	2010-05-04		ENSG00000177000	ENSG00000177000	1.5.1.20		7436	protein-coding gene	gene with protein product		607093	"5,10-methylenetetrahydrofolate reductase (NADPH)"			7920641	Standard	NM_005957		Approved		uc001atc.2	P42898	OTTHUMG00000002277	ENST00000376592.1:c.1238C>T	chr1.hg19:g.11854524G>A	ENSP00000365777:p.Pro413Leu	159.0	0.0		125.0	5.0	NM_005957	B2R7A6|Q5SNW6|Q5SNW9|Q7Z6M6|Q8IU73|Q9UQR2	Missense_Mutation	SNP	ENST00000376592.1	hg19	CCDS137.1	.	.	.	.	.	.	.	.	.	.	G	15.27	2.783056	0.49891	.	.	ENSG00000177000	ENST00000376592;ENST00000376583;ENST00000376590;ENST00000376585	D;D;D;D	0.82526	-1.6;-1.62;-1.6;-1.62	4.88	4.88	0.63580	.	0.103268	0.64402	D	0.000002	T	0.79399	0.4439	M	0.64404	1.975	0.80722	D	1	B;P	0.40000	0.029;0.698	B;B	0.32980	0.01;0.156	T	0.79412	-0.1814	10	0.29301	T	0.29	.	17.3796	0.87401	0.0:0.0:1.0:0.0	.	413;454	P42898;Q5SNW6	MTHR_HUMAN;.	L	413;454;413;454	ENSP00000365777:P413L;ENSP00000365767:P454L;ENSP00000365775:P413L;ENSP00000365770:P454L	ENSP00000365767:P454L	P	-	2	0	MTHFR	11777111	1.000000	0.71417	0.919000	0.36401	0.391000	0.30476	9.253000	0.95501	2.395000	0.81488	0.455000	0.32223	CCC	.	.		0.557	MTHFR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000006538.1	NM_005957		A	11854524	G	A	11854524	3	1	260	1	0	0	0	0	1	0	0	0	9940	1232	43	3	752	3	MTHFR	1	11854524	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	844814	11854524	237396097	7	37252										
TNFRSF8	943	hgsc.bcm.edu	37	chr1	12202458	12202458	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cgagttggaggaggagctggAggcggaccataccccccact	15	12	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:12202458A>G	ENST00000263932.2	+	15	1880	c.1658A>G	c.(1657-1659)gAg>gGg	p.E553G	TNFRSF8_ENST00000479933.2_3'UTR|TNFRSF8_ENST00000417814.2_Missense_Mutation_p.E441G|TNFRSF8_ENST00000413146.2_Missense_Mutation_p.E90G	NM_001243.3|NM_001281430.1	NP_001234.2|NP_001268359.1	P28908	TNR8_HUMAN	tumor necrosis factor receptor superfamily, member 8	553					cellular response to mechanical stimulus (GO:0071260)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of TRAIL biosynthetic process (GO:0045556)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	27	Ovarian(185;0.249)	Lung NSC(185;8.71e-05)|all_lung(284;9.89e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Brentuximab vedotin(DB08870)	GAGGAGCTGGAGGCGGACCAT	0.652																																					p.E553G		Atlas-SNP	.											.	TNFRSF8	70	.	0			c.A1658G						.						31	35	34					1																	12202458		2200	4300	6500	SO:0001583	missense	943	exon15			AGCTGGAGGCGGA	M83554	CCDS144.1, CCDS59989.1	1p36	2008-02-05			ENSG00000120949	ENSG00000120949		"Tumor necrosis factor receptor superfamily", "CD molecules"	11923	protein-coding gene	gene with protein product		153243		CD30, D1S166E		1330892, 1310894	Standard	XM_006711049		Approved	KI-1	uc001atq.3	P28908	OTTHUMG00000001827	ENST00000263932.2:c.1658A>G	chr1.hg19:g.12202458A>G	ENSP00000263932:p.Glu553Gly	268.0	0.0		158.0	7.0	NM_001243	B1AN79|B9EGD9|D3YTD8|Q6P4D9	Missense_Mutation	SNP	ENST00000263932.2	hg19	CCDS144.1	.	.	.	.	.	.	.	.	.	.	A	16.12	3.033213	0.54896	.	.	ENSG00000120949	ENST00000263932;ENST00000417814;ENST00000413146	T;T;T	0.34275	1.37;1.37;1.37	5.4	5.4	0.78164	.	0.226584	0.29956	N	0.010772	T	0.54581	0.1867	L	0.59436	1.845	0.38392	D	0.945435	D;D	0.89917	1.0;1.0	D;D	0.80764	0.991;0.994	T	0.60777	-0.7196	10	0.72032	D	0.01	-29.3464	11.8024	0.52135	1.0:0.0:0.0:0.0	.	441;553	D3YTD8;P28908	.;TNR8_HUMAN	G	553;441;90	ENSP00000263932:E553G;ENSP00000390650:E441G;ENSP00000398337:E90G	ENSP00000263932:E553G	E	+	2	0	TNFRSF8	12125045	0.998000	0.40836	0.960000	0.40013	0.067000	0.16453	3.414000	0.52693	2.040000	0.60383	0.533000	0.62120	GAG	.	.		0.652	TNFRSF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005130.1			G	12202458	A	G	12202458	3	3	260	1	0	0	0	0	1	0	0	0	16314	304	11	2	1716	2	TNFRSF8	1	12202458	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	347934	12202458	237048163	8	37253										
HNRNPCL1	343069	hgsc.bcm.edu	37	chr1	12907747	12907747	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gccagagcaatgggaggaggAggaggtacacgtgctgggaa	19	6	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:12907747A>G	ENST00000317869.6	-	2	621	c.396T>C	c.(394-396)ccT>ccC	p.P132P		NM_001013631.1|NM_001136561.2|NM_001146181.1	NP_001013653.1|NP_001130033.2|NP_001139653.1	O60812	HNRC1_HUMAN	heterogeneous nuclear ribonucleoprotein C-like 1	132						nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|stomach(2)	29						TGGGAGGAGGAGGAGGTACAC	0.493																																					p.P132P		Atlas-SNP	.											.	HNRNPCL1	68	.	0			c.T396C						.						94	93	94					1																	12907747		2203	4299	6502	SO:0001819	synonymous_variant	343069	exon2			AGGAGGAGGAGGT	BC002696	CCDS30591.1	1p36.21	2013-02-12		2008-04-18	ENSG00000179172	ENSG00000179172		"RNA binding motif (RRM) containing"	29295	protein-coding gene	gene with protein product				HNRPCL1			Standard	NM_001013631		Approved			O60812	OTTHUMG00000001931	ENST00000317869.6:c.396T>C	chr1.hg19:g.12907747A>G		311.0	0.0		173.0	8.0	NM_001013631	B2RP44	Silent	SNP	ENST00000317869.6	hg19	CCDS30591.1																																																																																			.	.		0.493	HNRNPCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005462.1	NM_001013631		G	12907747	A	G	12907747	2	3	260	1	0	0	0	0	0	0	0	1	7272	291	11	2		2	HNRNPCL1	1	12907747	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	705289	12907747	236342874	9	37254										
PLEKHM2	23207	hgsc.bcm.edu	37	chr1	16051847	16051847	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acacggtcagtggtccccgcTccacagcctccgacctgacc	9	19	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:16051847T>C	ENST00000375799.3	+	8	975	c.748T>C	c.(748-750)Tcc>Ccc	p.S250P	RP11-288I21.1_ENST00000453804.1_RNA|PLEKHM2_ENST00000375793.2_Missense_Mutation_p.S230P	NM_015164.2	NP_055979.2	Q8IWE5	PKHM2_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 2	250	Interaction with KIF5B.				Golgi organization (GO:0007030)	cytoplasm (GO:0005737)	kinesin binding (GO:0019894)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.000259)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00057)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		TGGTCCCCGCTCCACAGCCTC	0.672																																					p.S250P		Atlas-SNP	.											.	PLEKHM2	94	.	0			c.T748C						.						23	32	29					1																	16051847		1902	3836	5738	SO:0001583	missense	23207	exon8			CCCCGCTCCACAG	AB020649	CCDS44063.1	1p36.13	2013-01-10			ENSG00000116786	ENSG00000116786		"Pleckstrin homology (PH) domain containing"	29131	protein-coding gene	gene with protein product		609613				10048485	Standard	NM_015164		Approved	KIAA0842	uc010obo.2	Q8IWE5	OTTHUMG00000003062	ENST00000375799.3:c.748T>C	chr1.hg19:g.16051847T>C	ENSP00000364956:p.Ser250Pro	164.0	0.0		113.0	5.0	NM_015164	O94928|Q5VT65|Q6NUH9|Q7L8G1|Q8IVT7|Q8N2T4|Q96AY0|Q9NTF7	Missense_Mutation	SNP	ENST00000375799.3	hg19	CCDS44063.1	.	.	.	.	.	.	.	.	.	.	T	14.34	2.505231	0.44558	.	.	ENSG00000116786	ENST00000375799;ENST00000375793	T;T	0.58940	0.52;0.3	5.26	5.26	0.73747	.	0.178195	0.49916	D	0.000125	T	0.39733	0.1089	N	0.19112	0.55	0.50313	D	0.999866	B	0.26744	0.158	B	0.25506	0.061	T	0.28427	-1.0044	10	0.27785	T	0.31	-25.5943	9.6654	0.39981	0.0:0.0781:0.0:0.9219	.	250	Q8IWE5	PKHM2_HUMAN	P	250;230	ENSP00000364956:S250P;ENSP00000364950:S230P	ENSP00000364950:S230P	S	+	1	0	PLEKHM2	15924434	1.000000	0.71417	1.000000	0.80357	0.711000	0.40976	4.902000	0.63266	1.991000	0.58162	0.459000	0.35465	TCC	.	.		0.672	PLEKHM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008463.1	NM_015164		C	16051847	T	C	16051847	3	2	260	1	0	0	0	0	1	0	0	0	12090	1551	54	2	778	2	PLEKHM2	1	16051847	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	3144100	16051847	233198774	10	37255										
SPEN	23013	hgsc.bcm.edu	37	chr1	16257506	16257506	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	atagcagatttatggagctcAcacggatgcaacagaaagaa	10	7	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:16257506A>G	ENST00000375759.3	+	11	4975	c.4771A>G	c.(4771-4773)Aca>Gca	p.T1591A		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	1591					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		TATGGAGCTCACACGGATGCA	0.443																																					p.T1591A		Atlas-SNP	.											.	SPEN	374	.	0			c.A4771G						.						55	58	57					1																	16257506		2203	4300	6503	SO:0001583	missense	23013	exon11			GAGCTCACACGGA		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"RNA binding motif (RRM) containing"	17575	protein-coding gene	gene with protein product		613484	"SPEN homolog, transcriptional regulator (Drosophila)", "spen homolog, transcriptional regulator (Drosophila)"			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.4771A>G	chr1.hg19:g.16257506A>G	ENSP00000364912:p.Thr1591Ala	88.0	0.0		68.0	4.0	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	hg19	CCDS164.1	.	.	.	.	.	.	.	.	.	.	A	17.53	3.412046	0.62511	.	.	ENSG00000065526	ENST00000375759	T	0.09911	2.93	4.76	4.76	0.60689	.	.	.	.	.	T	0.16769	0.0403	L	0.36672	1.1	0.46564	D	0.999102	D	0.61080	0.989	P	0.55391	0.775	T	0.05419	-1.0886	9	0.22109	T	0.4	-17.7366	14.4232	0.67198	1.0:0.0:0.0:0.0	.	1591	Q96T58	MINT_HUMAN	A	1591	ENSP00000364912:T1591A	ENSP00000364912:T1591A	T	+	1	0	SPEN	16130093	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.526000	0.81920	1.979000	0.57680	0.383000	0.25322	ACA	.	.		0.443	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		G	16257506	A	G	16257506	3	3	260	1	0	0	0	0	1	0	0	0	15053	159	6	2	4813	2	SPEN	1	16257506	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	205659	16257506	232993115	11	37256										
KLHDC7A	127707	hgsc.bcm.edu	37	chr1	18808601	18808601	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tagcggagaacccagagctgCagctgcagccagatggcttc	13	12	0	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:18808601C>T	ENST00000400664.1	+	1	1178	c.1126C>T	c.(1126-1128)Cag>Tag	p.Q376*		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	376						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		CCCAGAGCTGCAGCTGCAGCC	0.697																																					p.Q376X		Atlas-SNP	.											.	KLHDC7A	60	.	0			c.C1126T						.						12	16	14					1																	18808601		2120	4201	6321	SO:0001587	stop_gained	127707	exon1			GAGCTGCAGCTGC	AK096072	CCDS185.2	1p36.13	2008-02-05			ENSG00000179023	ENSG00000179023			26791	protein-coding gene	gene with protein product							Standard	NM_152375		Approved	FLJ38753	uc001bax.3	Q5VTJ3	OTTHUMG00000002431	ENST00000400664.1:c.1126C>T	chr1.hg19:g.18808601C>T	ENSP00000383505:p.Gln376*	74.0	0.0		42.0	4.0	NM_152375	Q8N8W6	Nonsense_Mutation	SNP	ENST00000400664.1	hg19	CCDS185.2	.	.	.	.	.	.	.	.	.	.	C	21.5	4.154560	0.78114	.	.	ENSG00000179023	ENST00000400664;ENST00000540290	.	.	.	5.16	5.16	0.70880	.	0.280867	0.28748	N	0.014272	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	17.203	0.86911	0.0:1.0:0.0:0.0	.	.	.	.	X	376;313	.	ENSP00000383505:Q376X	Q	+	1	0	KLHDC7A	18681188	0.956000	0.32656	0.791000	0.31998	0.114000	0.19823	3.277000	0.51654	2.400000	0.81607	0.313000	0.20887	CAG	.	.		0.697	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375		T	18808601	C	T	18808601	4	4	260	1	0	0	0	0	0	1	0	0	8369	711	25	3	1128	3	KLHDC7A	1	18808601	Nonsense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	2551095	18808601	230442020	12	37257										
OTUD3	23252	hgsc.bcm.edu	37	chr1	20224100	20224100	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcggtatggagagcactacgAcagtgttcggaggatcaatg	14	7	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:20224100A>G	ENST00000375120.3	+	4	552	c.551A>G	c.(550-552)gAc>gGc	p.D184G	OTUD3_ENST00000466697.1_3'UTR	NM_015207.1	NP_056022.1	Q5T2D3	OTUD3_HUMAN	OTU deubiquitinase 3	184	OTU. {ECO:0000255|PROSITE- ProRule:PRU00139}.				protein K11-linked deubiquitination (GO:0035871)|protein K6-linked deubiquitination (GO:0044313)		ubiquitin-specific protease activity (GO:0004843)			breast(1)|kidney(2)|large_intestine(4)|lung(1)|skin(1)	9		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000276)|Lung NSC(340;0.000338)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.12e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000142)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.000408)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GAGCACTACGACAGTGTTCGG	0.532																																					p.D184G		Atlas-SNP	.											.	OTUD3	25	.	0			c.A551G						.						114	114	114					1																	20224100		2035	4196	6231	SO:0001583	missense	23252	exon4			ACTACGACAGTGT	AB007928	CCDS41279.1	1p36.13	2014-02-24	2014-02-24		ENSG00000169914	ENSG00000169914		"OTU domain containing"	29038	protein-coding gene	gene with protein product		611758	"OTU domain containing 3"			9455484, 23827681	Standard	NM_015207		Approved	KIAA0459, DUBA4	uc001bcs.4	Q5T2D3	OTTHUMG00000002696	ENST00000375120.3:c.551A>G	chr1.hg19:g.20224100A>G	ENSP00000364261:p.Asp184Gly	89.0	0.0		75.0	4.0	NM_015207	O75047	Missense_Mutation	SNP	ENST00000375120.3	hg19	CCDS41279.1	.	.	.	.	.	.	.	.	.	.	A	29.2	4.988821	0.93106	.	.	ENSG00000169914	ENST00000375120	T	0.59638	0.25	5.78	5.78	0.91487	Ovarian tumour, otubain (1);	0.000000	0.85682	D	0.000000	T	0.77968	0.4210	M	0.88310	2.945	0.80722	D	1	D	0.60160	0.987	P	0.62089	0.898	T	0.82559	-0.0397	10	0.72032	D	0.01	.	14.9445	0.71020	1.0:0.0:0.0:0.0	.	184	Q5T2D3	OTUD3_HUMAN	G	184	ENSP00000364261:D184G	ENSP00000364261:D184G	D	+	2	0	OTUD3	20096687	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.501000	0.90501	2.205000	0.71048	0.533000	0.62120	GAC	.	.		0.532	OTUD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007655.1			G	20224100	A	G	20224100	3	3	260	1	0	0	0	0	1	0	0	0	11322	275	10	2	565	2	OTUD3	1	20224100	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1415499	20224100	229026521	13	37258										
HSPG2	3339	hgsc.bcm.edu	37	chr1	22182319	22182319	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cgtggggctccctgtggcgcTgcagcggaactccgccagtt	15	14	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:22182319T>C	ENST00000374695.3	-	45	5741	c.5662A>G	c.(5662-5664)Agc>Ggc	p.S1888G	HSPG2_ENST00000430507.1_5'Flank	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	1888	Ig-like C2-type 4.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	CCTGTGGCGCTGCAGCGGAAC	0.672																																					p.S1888G		Atlas-SNP	.											.	HSPG2	311	.	0			c.A5662G						.						42	42	42					1																	22182319		2203	4300	6503	SO:0001583	missense	3339	exon45			TGGCGCTGCAGCG	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"Proteoglycans / Extracellular Matrix : Other", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5273	protein-coding gene	gene with protein product	"perlecan proteoglycan"	142461	"Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.5662A>G	chr1.hg19:g.22182319T>C	ENSP00000363827:p.Ser1888Gly	151.0	0.0		90.0	5.0	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	hg19	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	t	17.63	3.436349	0.62955	.	.	ENSG00000142798	ENST00000374695	T	0.67865	-0.29	5.37	5.37	0.77165	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.46758	D	0.000262	T	0.55970	0.1954	L	0.29908	0.895	0.39162	D	0.962425	B	0.29378	0.243	B	0.30716	0.119	T	0.59166	-0.7505	10	0.45353	T	0.12	.	13.3338	0.60505	0.0:0.0:0.0:1.0	.	1888	P98160	PGBM_HUMAN	G	1888	ENSP00000363827:S1888G	ENSP00000363827:S1888G	S	-	1	0	HSPG2	22054906	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	2.705000	0.47127	2.049000	0.60858	0.529000	0.55759	AGC	.	.		0.672	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		C	22182319	T	C	22182319	3	2	260	1	0	0	0	0	1	0	0	0	7439	1580	55	2	7725	2	HSPG2	1	22182319	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1958219	22182319	227068302	14	37259										
KDM1A	23028	hgsc.bcm.edu	37	chr1	23403758	23403758	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cactggcagccacctgacagTaaggaatggctactcgtgtg	12	11	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:23403758T>A	ENST00000356634.3	+	14	1849	c.1700T>A	c.(1699-1701)gTa>gAa	p.V567E	KDM1A_ENST00000542151.1_Missense_Mutation_p.V591E|KDM1A_ENST00000400181.4_Missense_Mutation_p.V591E|RP1-184J9.2_ENST00000427154.1_RNA	NM_015013.3	NP_055828.2	O60341	KDM1A_HUMAN	lysine (K)-specific demethylase 1A	567	Demethylase activity.				blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|granulocyte differentiation (GO:0030851)|histone H3-K4 demethylation (GO:0034720)|histone H3-K9 demethylation (GO:0033169)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of DNA binding (GO:0043392)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of protein binding (GO:0032091)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pituitary gland development (GO:0021983)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein demethylation (GO:0006482)|regulation of primitive erythrocyte differentiation (GO:0010725)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|demethylase activity (GO:0032451)|enzyme binding (GO:0019899)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-K4 specific) (GO:0032453)|histone demethylase activity (H3-K9 specific) (GO:0032454)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|MRF binding (GO:0043426)|oxidoreductase activity (GO:0016491)|p53 binding (GO:0002039)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(2)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						CACCTGACAGTAAGGAATGGC	0.448																																					p.V591E		Atlas-SNP	.											.	KDM1A	49	.	0			c.T1772A						.						115	100	105					1																	23403758		2203	4300	6503	SO:0001583	missense	23028	exon16			TGACAGTAAGGAA	AL031428	CCDS30627.1, CCDS53278.1	1p36.12	2011-07-01	2009-09-29	2009-09-29	ENSG00000004487	ENSG00000004487		"Chromatin-modifying enzymes / K-demethylases"	29079	protein-coding gene	gene with protein product		609132	"amine oxidase (flavin containing) domain 2", "lysine (K)-specific demethylase 1"	AOF2, KDM1		9628581, 12493763	Standard	NM_015013		Approved	KIAA0601, BHC110, LSD1	uc001bgj.2	O60341	OTTHUMG00000003220	ENST00000356634.3:c.1700T>A	chr1.hg19:g.23403758T>A	ENSP00000349049:p.Val567Glu	126.0	0.0		79.0	5.0	NM_001009999	A8MWP9|Q5TH94|Q5TH95|Q86VT7|Q8IXK4|Q8NDP6|Q8TAZ3|Q96AW4	Missense_Mutation	SNP	ENST00000356634.3	hg19	CCDS30627.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.421652	0.83559	.	.	ENSG00000004487	ENST00000356634;ENST00000400181;ENST00000542151	T;T;T	0.10960	2.82;2.82;2.82	5.72	4.59	0.56863	Amine oxidase (1);	0.000000	0.85682	D	0.000000	T	0.40546	0.1121	M	0.92317	3.295	0.80722	D	1	D;D	0.89917	0.996;1.0	D;D	0.85130	0.958;0.997	T	0.47661	-0.9100	10	0.87932	D	0	-21.9466	11.0733	0.48016	0.0:0.0723:0.0:0.9277	.	591;567	O60341-2;O60341	.;KDM1A_HUMAN	E	567;591;591	ENSP00000349049:V567E;ENSP00000383042:V591E;ENSP00000439072:V591E	ENSP00000349049:V567E	V	+	2	0	KDM1A	23276345	1.000000	0.71417	0.998000	0.56505	0.964000	0.63967	8.021000	0.88750	0.983000	0.38602	0.533000	0.62120	GTA	.	.		0.448	KDM1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008880.3	NM_015013		A	23403758	T	A	23403758	3	1	260	1	0	0	0	0	1	0	0	0	8131	1638	57	4	1834	4	KDM1A	1	23403758	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1221439	23403758	225846863	15	37260										
ZNF436	80818	hgsc.bcm.edu	37	chr1	23689249	23689249	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggattgtctgatgctgaatcAggtgagaacttcttccaaaa	10	7	3	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:23689249A>G	ENST00000314011.4	-	4	762	c.626T>C	c.(625-627)cTg>cCg	p.L209P	ZNF436_ENST00000374608.3_Missense_Mutation_p.L209P	NM_001077195.1	NP_001070663.1	Q9C0F3	ZN436_HUMAN	zinc finger protein 436	209					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	19		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;5.97e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000977)|KIRC - Kidney renal clear cell carcinoma(1967;0.00336)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		ATGCTGAATCAGGTGAGAACT	0.453																																					p.L209P		Atlas-SNP	.											.	ZNF436	49	.	0			c.T626C						.						128	134	132					1																	23689249		2203	4300	6503	SO:0001583	missense	80818	exon4			TGAATCAGGTGAG	AB051497	CCDS233.1	1p36	2013-01-08			ENSG00000125945	ENSG00000125945		"Zinc fingers, C2H2-type", "-"	20814	protein-coding gene	gene with protein product		611703				11214970	Standard	NM_001077195		Approved	KIAA1710, Zfp46	uc001bgt.3	Q9C0F3	OTTHUMG00000003232	ENST00000314011.4:c.626T>C	chr1.hg19:g.23689249A>G	ENSP00000313582:p.Leu209Pro	241.0	0.0		168.0	8.0	NM_001077195	Q658I9	Missense_Mutation	SNP	ENST00000314011.4	hg19	CCDS233.1	.	.	.	.	.	.	.	.	.	.	A	14.08	2.430000	0.43122	.	.	ENSG00000125945	ENST00000314011;ENST00000374609;ENST00000374608	T;T;T	0.53857	0.6;0.6;0.6	5.79	4.67	0.58626	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.51477	D	0.000083	T	0.62122	0.2402	H	0.94734	3.575	0.58432	D	0.999999	B	0.24651	0.108	B	0.12837	0.008	T	0.64947	-0.6287	10	0.87932	D	0	-30.4376	9.954	0.41655	0.9203:0.0:0.0797:0.0	.	209	Q9C0F3	ZN436_HUMAN	P	209	ENSP00000313582:L209P;ENSP00000363737:L209P;ENSP00000363736:L209P	ENSP00000313582:L209P	L	-	2	0	ZNF436	23561836	1.000000	0.71417	1.000000	0.80357	0.532000	0.34746	9.090000	0.94144	1.031000	0.39867	-0.250000	0.11733	CTG	.	.		0.453	ZNF436-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008908.1	NM_030634		G	23689249	A	G	23689249	3	3	260	1	0	0	0	0	1	0	0	0	17924	188	7	2	790	2	ZNF436	1	23689249	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	285491	23689249	225561372	16	37261										
MAN1C1	57134	hgsc.bcm.edu	37	chr1	26080014	26080014	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcaggctgggagagaagctcCtgccggcgttcaacaccccc	12	15	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:26080014C>T	ENST00000374332.4	+	5	1204	c.874C>T	c.(874-876)Ctg>Ttg	p.L292L	MAN1C1_ENST00000473891.1_3'UTR|MAN1C1_ENST00000374329.1_Silent_p.L63L|MAN1C1_ENST00000263979.3_Silent_p.L112L	NM_020379.2	NP_065112.1	Q9NR34	MA1C1_HUMAN	mannosidase, alpha, class 1C, member 1	292					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(7)|pancreas(1)|prostate(1)|skin(2)	25		Colorectal(325;3.78e-05)|Lung NSC(340;0.000181)|all_lung(284;0.000245)|Renal(390;0.000714)|Ovarian(437;0.00159)|Breast(348;0.0156)|Myeloproliferative disorder(586;0.0257)|all_neural(195;0.0515)|Esophageal squamous(538;0.232)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0574)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.15e-07)|COAD - Colon adenocarcinoma(152;4.31e-06)|STAD - Stomach adenocarcinoma(196;0.00125)|BRCA - Breast invasive adenocarcinoma(304;0.00141)|KIRC - Kidney renal clear cell carcinoma(1967;0.00146)|GBM - Glioblastoma multiforme(114;0.0149)|READ - Rectum adenocarcinoma(331;0.0803)		AGAGAAGCTCCTGCCGGCGTT	0.587																																					p.L292L		Atlas-SNP	.											.	MAN1C1	48	.	0			c.C874T						.						51	48	49					1																	26080014		2203	4300	6503	SO:0001819	synonymous_variant	57134	exon5			AAGCTCCTGCCGG	AF261655	CCDS265.1	1p35	2008-02-05			ENSG00000117643	ENSG00000117643			19080	protein-coding gene	gene with protein product						10915796	Standard	XM_005245945		Approved	HMIC	uc001bkm.2	Q9NR34	OTTHUMG00000004417	ENST00000374332.4:c.874C>T	chr1.hg19:g.26080014C>T		158.0	0.0		102.0	5.0	NM_020379	A6NNE2|B2RNP2|Q9Y545	Silent	SNP	ENST00000374332.4	hg19	CCDS265.1																																																																																			.	.		0.587	MAN1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012828.3	NM_020379		T	26080014	C	T	26080014	2	4	260	1	0	0	0	0	0	0	0	1	9222	680	24	3		3	MAN1C1	1	26080014	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	2390765	26080014	223170607	17	37262										
EXTL1	2134	hgsc.bcm.edu	37	chr1	26356101	26356101	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cgccccccaggccggctgcaTcccagtgcttctcagccccc	9	22	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:26356101T>C	ENST00000374280.3	+	3	1751	c.884T>C	c.(883-885)aTc>aCc	p.I295T	EXTL1_ENST00000484339.1_Intron	NM_004455.2	NP_004446.2	Q92935	EXTL1_HUMAN	exostosin-like glycosyltransferase 1	295					protein glycosylation (GO:0006486)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|stomach(1)|urinary_tract(1)	23		Colorectal(325;3.46e-05)|Lung NSC(340;6.18e-05)|all_lung(284;9.43e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00594)|READ - Rectum adenocarcinoma(331;0.0649)		GCCGGCTGCATCCCAGTGCTT	0.652																																					p.I295T		Atlas-SNP	.											.	EXTL1	61	.	0			c.T884C						.						14	15	15					1																	26356101		2203	4298	6501	SO:0001583	missense	2134	exon3			GCTGCATCCCAGT	U67191	CCDS271.1	1p36.1	2013-03-01	2013-03-01		ENSG00000158008	ENSG00000158008	2.4.1.224	"Exostosin glycosyltransferase family"	3515	protein-coding gene	gene with protein product	"glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase", "alpha-N-acetylglucosaminyltransferase II", "glucuronyl-N-acetylglucosaminylproteoglycan alpha-1,4-N- acetylglucosaminyltransferase", "exostosin-L"	601738	"exostoses (multiple)-like 1"			9037597	Standard	NM_004455		Approved	EXTL, MGC70794	uc001blf.3	Q92935	OTTHUMG00000007509	ENST00000374280.3:c.884T>C	chr1.hg19:g.26356101T>C	ENSP00000363398:p.Ile295Thr	120.0	0.0		95.0	4.0	NM_004455	Q6GSC1	Missense_Mutation	SNP	ENST00000374280.3	hg19	CCDS271.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.308971	0.81247	.	.	ENSG00000158008	ENST00000374280	D	0.99060	-5.38	4.69	4.69	0.59074	.	0.125717	0.52532	D	0.000078	D	0.99248	0.9738	M	0.89214	3.015	0.51012	D	0.999903	D	0.67145	0.996	D	0.72625	0.978	D	0.99226	1.0880	10	0.87932	D	0	-14.8822	11.6295	0.51166	0.0:0.0:0.0:1.0	.	295	Q92935	EXTL1_HUMAN	T	295	ENSP00000363398:I295T	ENSP00000363398:I295T	I	+	2	0	EXTL1	26228688	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.498000	0.81546	1.971000	0.57363	0.459000	0.35465	ATC	.	.		0.652	EXTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019749.1	NM_004455		C	26356101	T	C	26356101	3	2	260	1	0	0	0	0	1	0	0	0	5327	1435	50	2	894	2	EXTL1	1	26356101	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	276087	26356101	222894520	18	37263										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27094372	27094372	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gaagatgtgggtggaccgttAtctggccttcactgaggaga	15	7	2	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:27094372A>G	ENST00000324856.7	+	11	3451	c.3080A>G	c.(3079-3081)tAt>tGt	p.Y1027C	ARID1A_ENST00000374152.2_Missense_Mutation_p.Y644C|ARID1A_ENST00000457599.2_Missense_Mutation_p.Y1027C	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1027	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.				androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		GTGGACCGTTATCTGGCCTTC	0.507			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.Y1027C		Atlas-SNP	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.A3080G						.						216	175	189					1																	27094372		2203	4300	6503	SO:0001583	missense	8289	exon11			ACCGTTATCTGGC	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.3080A>G	chr1.hg19:g.27094372A>G	ENSP00000320485:p.Tyr1027Cys	348.0	0.0		223.0	62.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Missense_Mutation	SNP	ENST00000324856.7	hg19	CCDS285.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.471064	0.84533	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000374152	T;T;T	0.46063	0.88;0.88;0.88	5.17	5.17	0.71159	ARID/BRIGHT DNA-binding domain (5);	0.060291	0.64402	D	0.000002	T	0.62097	0.2400	M	0.63843	1.955	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.997;1.0;1.0	T	0.65496	-0.6154	10	0.72032	D	0.01	-4.6331	15.1717	0.72878	1.0:0.0:0.0:0.0	.	1027;1027;681	O14497;O14497-2;Q4LE49	ARI1A_HUMAN;.;.	C	1027;1027;644	ENSP00000320485:Y1027C;ENSP00000387636:Y1027C;ENSP00000363267:Y644C	ENSP00000320485:Y1027C	Y	+	2	0	ARID1A	26966959	1.000000	0.71417	0.998000	0.56505	0.999000	0.98932	9.139000	0.94554	2.163000	0.67991	0.533000	0.62120	TAT	.	.		0.507	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		G	27094372	A	G	27094372	3	3	260	1	0	0	0	0	1	0	0	0	913	449	16	2	3122	2	ARID1A	1	27094372	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	738271	27094372	222156249	19	37264										
NR0B2	8431	hgsc.bcm.edu	37	chr1	27240242	27240242	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gaggaaggccactgtcttggCcagaacatccaaggcctccc	11	14	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:27240242C>A	ENST00000254227.3	-	1	215	c.190G>T	c.(190-192)Gcc>Tcc	p.A64S		NM_021969.2	NP_068804.1	Q15466	NR0B2_HUMAN	nuclear receptor subfamily 0, group B, member 2	64	Ligand-binding. {ECO:0000250}.				cholesterol metabolic process (GO:0008203)|gene expression (GO:0010467)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ regeneration (GO:0031100)|positive regulation of insulin secretion (GO:0032024)|response to glucose (GO:0009749)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription corepressor activity (GO:0003714)			NS(1)|large_intestine(1)|lung(3)	5		all_cancers(24;1.23e-26)|all_epithelial(13;1.19e-23)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Breast(348;0.00017)|Renal(390;0.0007)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.01e-51)|OV - Ovarian serous cystadenocarcinoma(117;8.22e-30)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419)		ACTGTCTTGGCCAGAACATCC	0.672																																					p.A64S		Atlas-SNP	.											.	NR0B2	14	.	0			c.G190T						.						22	26	24					1																	27240242		2203	4300	6503	SO:0001583	missense	8431	exon1			TCTTGGCCAGAAC	AF044316	CCDS291.1	1p36.1	2013-01-16			ENSG00000131910	ENSG00000131910		"Nuclear hormone receptors"	7961	protein-coding gene	gene with protein product		604630				9603951	Standard	NM_021969		Approved	SHP	uc001bnf.3	Q15466	OTTHUMG00000004231	ENST00000254227.3:c.190G>T	chr1.hg19:g.27240242C>A	ENSP00000254227:p.Ala64Ser	66.0	0.0		41.0	4.0	NM_021969	F1D8P5|Q5QP36	Missense_Mutation	SNP	ENST00000254227.3	hg19	CCDS291.1	.	.	.	.	.	.	.	.	.	.	C	18.32	3.597846	0.66332	.	.	ENSG00000131910	ENST00000254227	D	0.84223	-1.82	5.32	5.32	0.75619	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.329841	0.31636	N	0.007306	T	0.81592	0.4855	L	0.54323	1.7	0.35664	D	0.812785	P	0.35226	0.491	B	0.31946	0.138	D	0.84511	0.0622	10	0.32370	T	0.25	-24.7489	16.0321	0.80585	0.0:0.8657:0.1343:0.0	.	64	Q15466	NR0B2_HUMAN	S	64	ENSP00000254227:A64S	ENSP00000254227:A64S	A	-	1	0	NR0B2	27112829	0.955000	0.32602	1.000000	0.80357	0.994000	0.84299	1.938000	0.40203	2.485000	0.83878	0.561000	0.74099	GCC	.	.		0.672	NR0B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012185.1			A	27240242	C	A	27240242	3	1	260	1	0	0	0	0	1	0	0	0	10623	739	26	3	591	3	NR0B2	1	27240242	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	145870	27240242	222010379	20	37265										
STX12	23673	hgsc.bcm.edu	37	chr1	28136791	28136791	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aagagaggagcagctggtctCatttgacaggtaatagaatt	12	5	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:28136791C>A	ENST00000373943.4	+	5	586	c.461C>A	c.(460-462)tCa>tAa	p.S154*		NM_177424.2	NP_803173.1	Q86Y82	STX12_HUMAN	syntaxin 12	154					cholesterol efflux (GO:0033344)|intracellular protein transport (GO:0006886)|protein stabilization (GO:0050821)|synaptic vesicle exocytosis (GO:0016079)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|phagocytic vesicle (GO:0045335)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)			breast(1)|central_nervous_system(1)|large_intestine(3)|lung(3)	8		Colorectal(325;3.46e-05)|all_lung(284;9.43e-05)|Lung NSC(340;0.000185)|Renal(390;0.00121)|Breast(348;0.0021)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;3.96e-24)|Colorectal(126;3.46e-08)|COAD - Colon adenocarcinoma(152;1.83e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00258)|KIRC - Kidney renal clear cell carcinoma(1967;0.00302)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0649)		CAGCTGGTCTCATTTGACAGG	0.368																																					p.S154X	Ovarian(5;5 342 2097 9488 34083)	Atlas-SNP	.											.	STX12	26	.	0			c.C461A						.						95	94	95					1																	28136791		2203	4300	6503	SO:0001587	stop_gained	23673	exon5			TGGTCTCATTTGA	BC046999	CCDS310.1	1p35.3	2008-05-14			ENSG00000117758	ENSG00000117758			11430	protein-coding gene	gene with protein product		606892				9507000	Standard	NM_177424		Approved	STX13, STX14	uc001bou.4	Q86Y82	OTTHUMG00000003730	ENST00000373943.4:c.461C>A	chr1.hg19:g.28136791C>A	ENSP00000363054:p.Ser154*	132.0	0.0		87.0	4.0	NM_177424	B1AJQ7|O95564	Nonsense_Mutation	SNP	ENST00000373943.4	hg19	CCDS310.1	.	.	.	.	.	.	.	.	.	.	C	38	6.748282	0.97809	.	.	ENSG00000117758	ENST00000373943;ENST00000440806	.	.	.	5.72	5.72	0.89469	.	0.175694	0.52532	D	0.000078	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.6687	18.0594	0.89372	0.0:1.0:0.0:0.0	.	.	.	.	X	154	.	ENSP00000363054:S154X	S	+	2	0	STX12	28009378	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.453000	0.73488	2.704000	0.92352	0.563000	0.77884	TCA	.	.		0.368	STX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010519.1	NM_177424		A	28136791	C	A	28136791	4	1	260	1	0	0	0	0	0	1	0	0	15353	838	29	3	479	3	STX12	1	28136791	Nonsense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	896549	28136791	221113830	21	37266										
COL16A1	1307	hgsc.bcm.edu	37	chr1	32149324	32149324	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcacctggggtccctggactCcccttcctggaggccctggc	12	17	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:32149324C>T	ENST00000373672.3	-	34	2879	c.2363G>A	c.(2362-2364)gGa>gAa	p.G788E	COL16A1_ENST00000373668.3_Missense_Mutation_p.G788E|COL16A1_ENST00000271069.6_Missense_Mutation_p.G787E	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	788	Collagen-like 4.|Triple-helical region 5 (COL5) with 3 imperfections.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female pregnancy (GO:0007565)|integrin-mediated signaling pathway (GO:0007229)	collagen type XVI trimer (GO:0005597)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(15)|ovary(8)|prostate(4)	48		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		TCCCTGGACTCCCCTTCCTGG	0.607																																					p.G788E	Colon(143;498 1786 21362 25193 36625)	Atlas-SNP	.											COL16A1,NS,carcinoma,0,1	COL16A1	137	.	0			c.G2363A						.						74	93	87					1																	32149324		1980	4153	6133	SO:0001583	missense	1307	exon34			TGGACTCCCCTTC	M92642	CCDS41297.1	1p35-p34	2013-01-16			ENSG00000084636	ENSG00000084636		"Collagens"	2193	protein-coding gene	gene with protein product		120326				1631157	Standard	NM_001856		Approved		uc001btk.1	Q07092	OTTHUMG00000003883	ENST00000373672.3:c.2363G>A	chr1.hg19:g.32149324C>T	ENSP00000362776:p.Gly788Glu	111.0	0.0		74.0	4.0	NM_001856	Q16593|Q59F89|Q71RG9	Missense_Mutation	SNP	ENST00000373672.3	hg19	CCDS41297.1	.	.	.	.	.	.	.	.	.	.	C	13.85	2.360954	0.41801	.	.	ENSG00000084636	ENST00000373672;ENST00000271069;ENST00000458715;ENST00000373668	D;D;D;D	0.99353	-5.77;-5.77;-5.52;-5.77	5.17	2.28	0.28536	.	0.126713	0.51477	D	0.000088	D	0.99042	0.9672	H	0.98333	4.205	0.23978	N	0.996285	B;B;B	0.15473	0.013;0.003;0.002	B;B;B	0.23419	0.046;0.013;0.008	D	0.99838	1.1059	10	0.72032	D	0.01	.	7.1895	0.25818	0.0:0.7033:0.1397:0.157	.	788;788;788	A6NCT7;Q07092;Q07092-2	.;COGA1_HUMAN;.	E	788;787;9;788	ENSP00000362776:G788E;ENSP00000271069:G787E;ENSP00000411457:G9E;ENSP00000362772:G788E	ENSP00000271069:G787E	G	-	2	0	COL16A1	31921911	0.001000	0.12720	0.028000	0.17463	0.897000	0.52465	0.032000	0.13732	0.414000	0.25790	-0.191000	0.12829	GGA	.	.		0.607	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856		T	32149324	C	T	32149324	3	4	260	1	0	0	0	0	1	0	0	0	3675	855	30	3	2603	3	COL16A1	1	32149324	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	4012533	32149324	217101297	22	37267										
EIF3I	8668	hgsc.bcm.edu	37	chr1	32696740	32696740	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agcagcggcggcgaagatggTtacgtccgtatccattactt	12	10	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:32696740T>C	ENST00000373586.1	+	11	993	c.921T>C	c.(919-921)ggT>ggC	p.G307G	MTMR9LP_ENST00000441044.1_RNA	NM_003757.2	NP_003748.1			eukaryotic translation initiation factor 3, subunit I											breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.212)				GCGAAGATGGTTACGTCCGTA	0.537																																					p.G307G	Colon(102;1138 2140 2180 17876)	Atlas-SNP	.											.	EIF3I	38	.	0			c.T921C						.						85	85	85					1																	32696740		2203	4300	6503	SO:0001819	synonymous_variant	8668	exon11			AGATGGTTACGTC	U39067	CCDS357.1	1p34.1	2013-01-10	2007-07-27	2007-07-27	ENSG00000084623	ENSG00000084623		"WD repeat domain containing"	3272	protein-coding gene	gene with protein product		603911	"eukaryotic translation initiation factor 3, subunit 2 beta, 36kDa"	EIF3S2		7566156, 8995409	Standard	NM_003757		Approved	TRIP-1, eIF3-beta, eIF3-p36, eIF3i	uc009vuc.3	Q13347	OTTHUMG00000007364	ENST00000373586.1:c.921T>C	chr1.hg19:g.32696740T>C		117.0	0.0		84.0	4.0	NM_003757		Silent	SNP	ENST00000373586.1	hg19	CCDS357.1																																																																																			.	.		0.537	EIF3I-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019282.2	NM_003757		C	32696740	T	C	32696740	2	2	260	1	0	0	0	0	0	0	0	1	5021	1712	60	2		2	EIF3I	1	32696740	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	547416	32696740	216553881	23	37268										
PHC2	1912	hgsc.bcm.edu	37	chr1	33794700	33794700	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctggagtcttcctggctgtgTgttagctgcaaagcagcagt	13	9	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:33794700T>C	ENST00000257118.5	-	13	2246	c.2193A>G	c.(2191-2193)acA>acG	p.T731T	PHC2_ENST00000485928.1_5'UTR|PHC2_ENST00000431992.1_Silent_p.T702T|PHC2_ENST00000373418.3_Silent_p.T196T|PHC2_ENST00000373422.3_Silent_p.T337T|PHC2_ENST00000373416.1_Silent_p.T196T|PHC2_ENST00000419414.2_Silent_p.T732T	NM_198040.2	NP_932157.1	Q8IXK0	PHC2_HUMAN	polyhomeotic homolog 2 (Drosophila)	731					multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				CCTGGCTGTGTGTTAGCTGCA	0.542																																					p.T731T		Atlas-SNP	.											.	PHC2	78	.	0			c.A2193G						.						79	70	73					1																	33794700		2203	4300	6503	SO:0001819	synonymous_variant	1912	exon13			GCTGTGTGTTAGC	AJ419231	CCDS378.1, CCDS379.1	1p34.3	2013-01-10	2006-09-12	2002-11-15	ENSG00000134686	ENSG00000134686		"Sterile alpha motif (SAM) domain containing"	3183	protein-coding gene	gene with protein product		602979	"early development regulator 2 (homolog of polyhomeotic 2)", "polyhomeotic-like 2 (Drosophila)"	EDR2		9121482, 12384788	Standard	NM_198040		Approved	HPH2	uc001bxg.1	Q8IXK0	OTTHUMG00000004133	ENST00000257118.5:c.2193A>G	chr1.hg19:g.33794700T>C		88.0	0.0		78.0	4.0	NM_198040	A1L4Q1|A8KA40|D3DPR2|Q2TAL3|Q5T0C1|Q6NUJ6|Q6ZQR1|Q8N306|Q8TAG8|Q96BL4|Q9Y4Y7	Silent	SNP	ENST00000257118.5	hg19	CCDS378.1																																																																																			.	.		0.542	PHC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000011895.1	NM_198040		C	33794700	T	C	33794700	2	2	260	1	0	0	0	0	0	0	0	1	11826	1683	59	2		2	PHC2	1	33794700	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1097960	33794700	215455921	24	37269										
ZSCAN20	7579	hgsc.bcm.edu	37	chr1	33955141	33955141	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gccctgggccctggcaaacaTgctgagaaggagctctgtaa	13	11	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:33955141T>C	ENST00000361328.3	+	5	858	c.705T>C	c.(703-705)caT>caC	p.H235H	ZSCAN20_ENST00000373413.2_Intron	NM_145238.3	NP_660281	P17040	ZSC20_HUMAN	zinc finger and SCAN domain containing 20	235					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(11)|ovary(2)|pancreas(1)|stomach(1)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				CTGGCAAACATGCTGAGAAGG	0.562																																					p.H235H		Atlas-SNP	.											.	ZSCAN20	107	.	0			c.T705C						.						56	59	58					1																	33955141		1907	4122	6029	SO:0001819	synonymous_variant	7579	exon5			CAAACATGCTGAG	X52360	CCDS41300.1	1p34.3	2013-01-08	2007-02-20	2007-02-20	ENSG00000121903	ENSG00000121903		"-", "Zinc fingers, C2H2-type"	13093	protein-coding gene	gene with protein product		611315	"zinc finger protein 31 (KOX 29)", "zinc finger protein 31"	ZNF360, ZNF31		2288909	Standard	NM_145238		Approved	KOX29	uc001bxj.4	P17040	OTTHUMG00000004173	ENST00000361328.3:c.705T>C	chr1.hg19:g.33955141T>C		82.0	0.0		58.0	4.0	NM_145238	A8K2D0|B1ALI4|B1ALI5|B1ALI6|Q6ZN23|Q96FA9|Q96H84	Silent	SNP	ENST00000361328.3	hg19	CCDS41300.1																																																																																			.	.		0.562	ZSCAN20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277003.2	NM_145238		C	33955141	T	C	33955141	2	2	260	1	0	0	0	0	0	0	0	1	18247	1461	51	2		2	ZSCAN20	1	33955141	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	160441	33955141	215295480	25	37270										
ZMYM4	9202	hgsc.bcm.edu	37	chr1	35846860	35846860	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tatttttttcttatttttagAgacattttaaatccaaagga	4	4	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:35846860A>G	ENST00000314607.6	+	8	1262	c.1182A>G	c.(1180-1182)aaA>aaG	p.K394K	ZMYM4_ENST00000373297.2_Splice_Site_p.K394K	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	394					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(16)|ovary(2)|prostate(3)|skin(2)	54		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TTATTTTTAGAGACATTTTAA	0.308																																					p.K394K		Atlas-SNP	.											.	ZMYM4	143	.	0			c.A1182G						.						68	75	72					1																	35846860		2197	4296	6493	SO:0001630	splice_region_variant	9202	exon8			TTTTAGAGACATT	AB007885	CCDS389.1	1p34-p32	2013-01-08	2005-12-19	2005-12-19	ENSG00000146463	ENSG00000146463		"Zinc fingers, MYM type"	13055	protein-coding gene	gene with protein product		613568	"zinc finger protein 262"	ZNF262		10449923	Standard	NM_005095		Approved	KIAA0425, ZNF198L3, MYM	uc001byt.3	Q5VZL5	OTTHUMG00000004241	ENST00000314607.6:c.1182-1A>G	chr1.hg19:g.35846860A>G		89.0	0.0		82.0	4.0	NM_005095	A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	Silent	SNP	ENST00000314607.6	hg19	CCDS389.1	.	.	.	.	.	.	.	.	.	.	A	11.66	1.703972	0.30232	.	.	ENSG00000146463	ENST00000457946	.	.	.	5.39	3.05	0.35203	.	.	.	.	.	T	0.57315	0.2045	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49588	-0.8924	4	.	.	.	.	8.0777	0.30726	0.7517:0.0:0.2483:0.0	.	.	.	.	G	143	.	.	R	+	1	2	ZMYM4	35619447	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.402000	0.34600	0.347000	0.23924	0.482000	0.46254	AGA	.	.		0.308	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012207.3	NM_005095	Silent	G	35846860	A	G	35846860	5	3	260	1	0	0	0	0	0	0	1	0	17717	318	11	2	1212	2	ZMYM4	1	35846860	Splice_Site	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1891719	35846860	213403761	26	37271										
EIF2C1	26523	hgsc.bcm.edu	37	chr1	36367622	36367622	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agtgaaggatgacatgacggAggtgacagggcgagtgctgc	18	6	0	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:36367622A>G	ENST00000373204.4	+	10	1427	c.1214A>G	c.(1213-1215)gAg>gGg	p.E405G	AGO1_ENST00000373206.1_Missense_Mutation_p.E330G	NM_012199.2	NP_036331.1	Q9UL18	AGO1_HUMAN	argonaute RISC catalytic component 1	405					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|nuclear-transcribed mRNA catabolic process (GO:0000956)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)										GACATGACGGAGGTGACAGGG	0.562																																					p.E405G		Atlas-SNP	.											EIF2C1,colon,carcinoma,0,1	.	.	.	0			c.A1214G						.						82	81	81					1																	36367622		2203	4300	6503	SO:0001583	missense	26523	exon10			TGACGGAGGTGAC	AF093097	CCDS398.1	1p34.3	2013-02-15	2013-02-15	2013-02-15	ENSG00000092847	ENSG00000092847		"Argonaute/PIWI family"	3262	protein-coding gene	gene with protein product	"argonaute 1"	606228	"eukaryotic translation initiation factor 2C, 1"	EIF2C1		10534406, 12906857	Standard	NM_012199		Approved	hAGO1	uc001bzl.3	Q9UL18	OTTHUMG00000007381	ENST00000373204.4:c.1214A>G	chr1.hg19:g.36367622A>G	ENSP00000362300:p.Glu405Gly	204.0	0.0		121.0	5.0	NM_012199	Q5TA57|Q6P4S0	Missense_Mutation	SNP	ENST00000373204.4	hg19	CCDS398.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.194735	0.78902	.	.	ENSG00000092847	ENST00000373206;ENST00000373204	T;T	0.07216	3.21;3.21	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.20577	0.0495	M	0.89904	3.07	0.80722	D	1	P	0.34800	0.469	B	0.35182	0.197	T	0.01786	-1.1274	10	0.51188	T	0.08	-24.6192	16.6093	0.84858	1.0:0.0:0.0:0.0	.	405	Q9UL18	AGO1_HUMAN	G	330;405	ENSP00000362302:E330G;ENSP00000362300:E405G	ENSP00000362300:E405G	E	+	2	0	EIF2C1	36140209	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	9.339000	0.96797	2.324000	0.78689	0.533000	0.62120	GAG	.	.		0.562	AGO1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019337.3			G	36367622	A	G	36367622	3	3	260	1	0	0	0	0	1	0	0	0	5007	304	11	2	1252	2	EIF2C1	1	36367622	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	520762	36367622	212882999	27	37272										
STK40	83931	hgsc.bcm.edu	37	chr1	36814368	36814368	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttcagcaggtccccctcgctCaccagatgcttcccgaggca	9	17	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:36814368C>A	ENST00000373129.3	-	8	1078	c.672G>T	c.(670-672)gtG>gtT	p.V224V	STK40_ENST00000359297.2_Silent_p.V224V|STK40_ENST00000373130.3_Silent_p.V229V|STK40_ENST00000373132.3_Silent_p.V224V	NM_032017.1	NP_114406.1	Q8N2I9	STK40_HUMAN	serine/threonine kinase 40	224	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				glycogen metabolic process (GO:0005977)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|regulation of gene expression (GO:0010468)|regulation of MAPK cascade (GO:0043408)|respiratory system process (GO:0003016)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)|stomach(1)	13		Myeloproliferative disorder(586;0.0393)				CCCCCTCGCTCACCAGATGCT	0.567																																					p.V224V		Atlas-SNP	.											.	STK40	53	.	0			c.G672T						.						103	80	88					1																	36814368		2203	4300	6503	SO:0001819	synonymous_variant	83931	exon8			CTCGCTCACCAGA	BC008344	CCDS407.1, CCDS60089.1	1p34.3	2008-02-05			ENSG00000196182	ENSG00000196182			21373	protein-coding gene	gene with protein product		609437					Standard	NM_032017		Approved	MGC4796, SgK495	uc001cak.1	Q8N2I9	OTTHUMG00000008238	ENST00000373129.3:c.672G>T	chr1.hg19:g.36814368C>A		154.0	0.0		114.0	5.0	NM_032017	D3DPS8|Q5VTK8|Q5VTK9|Q6ZMN1|Q8N2J8|Q8N3I6|Q96HN6|Q96I44|Q9BSA3|Q9H7H6	Silent	SNP	ENST00000373129.3	hg19	CCDS407.1																																																																																			.	.		0.567	STK40-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022592.1	NM_032017		A	36814368	C	A	36814368	2	1	260	1	0	0	0	0	0	0	0	1	15322	813	29	3		3	STK40	1	36814368	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	446746	36814368	212436253	28	37273										
ZC3H12A	80149	hgsc.bcm.edu	37	chr1	37945926	37945926	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggtcttctcctgccggggcaTcctgctggcagtgaactggt	14	12	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:37945926T>C	ENST00000373087.6	+	3	595	c.479T>C	c.(478-480)aTc>aCc	p.I160T		NM_025079.2	NP_079355.2			zinc finger CCCH-type containing 12A											NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				TGCCGGGGCATCCTGCTGGCA	0.632																																					p.I160T		Atlas-SNP	.											.	ZC3H12A	58	.	0			c.T479C						.						84	74	77					1																	37945926		2203	4300	6503	SO:0001583	missense	80149	exon3			GGGGCATCCTGCT		CCDS417.1	1p34.3	2012-07-05			ENSG00000163874	ENSG00000163874		"Zinc fingers, CCCH-type domain containing"	26259	protein-coding gene	gene with protein product	"MCP induced protein 1"	610562				18178554, 22055188	Standard	NM_025079		Approved	FLJ23231, MCPIP1	uc001cbb.4	Q5D1E8	OTTHUMG00000004221	ENST00000373087.6:c.479T>C	chr1.hg19:g.37945926T>C	ENSP00000362179:p.Ile160Thr	202.0	0.0		119.0	5.0	NM_025079		Missense_Mutation	SNP	ENST00000373087.6	hg19	CCDS417.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.548188	0.86022	.	.	ENSG00000163874	ENST00000373087;ENST00000373082	T	0.55588	0.51	4.8	4.8	0.61643	Ribonuclease Zc3h12a-like (1);	0.000000	0.85682	D	0.000000	T	0.79197	0.4405	H	0.94462	3.54	0.80722	D	1	D	0.61080	0.989	D	0.69824	0.966	D	0.85644	0.1278	10	0.87932	D	0	-21.2355	14.6504	0.68792	0.0:0.0:0.0:1.0	.	160	Q5D1E8	ZC12A_HUMAN	T	160	ENSP00000362179:I160T	ENSP00000362174:I160T	I	+	2	0	ZC3H12A	37718513	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.606000	0.82863	1.934000	0.56057	0.460000	0.39030	ATC	.	.		0.632	ZC3H12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012154.2	NM_025079		C	37945926	T	C	37945926	3	2	260	1	0	0	0	0	1	0	0	0	17576	1435	50	2	485	2	ZC3H12A	1	37945926	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1131558	37945926	211304695	29	37274										
MACF1	23499	hgsc.bcm.edu	37	chr1	39757653	39757653	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cagctagaaacacagcagcaCatccatacgagtgtagaaga	9	10	0	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:39757653C>T	ENST00000372915.3	+	15	1959	c.1872C>T	c.(1870-1872)caC>caT	p.H624H	MACF1_ENST00000564288.1_Silent_p.H619H|MACF1_ENST00000567887.1_Silent_p.H656H|MACF1_ENST00000317713.7_Silent_p.H624H|MACF1_ENST00000361689.2_Silent_p.H624H|MACF1_ENST00000545844.1_Silent_p.H624H|MACF1_ENST00000539005.1_Silent_p.H624H			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	624					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			CACAGCAGCACATCCATACGA	0.478																																					p.H624H		Atlas-SNP	.											.	MACF1	909	.	0			c.C1872T						.						129	109	116					1																	39757653		2203	4300	6503	SO:0001819	synonymous_variant	23499	exon17			GCAGCACATCCAT	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.1872C>T	chr1.hg19:g.39757653C>T		109.0	0.0		84.0	4.0	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Silent	SNP	ENST00000372915.3	hg19																																																																																				.	.		0.478	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		T	39757653	C	T	39757653	2	4	260	1	0	0	0	0	0	0	0	1	9153	477	17	3		3	MACF1	1	39757653	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	1811727	39757653	209492968	30	37275										
MACF1	23499	hgsc.bcm.edu	37	chr1	39818713	39818713	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggaactggcagagaacaagaAgaagatcgatgctctcctgg	13	8	1	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:39818713A>G	ENST00000372915.3	+	43	11336	c.11249A>G	c.(11248-11250)aAg>aGg	p.K3750R	MACF1_ENST00000564288.1_Missense_Mutation_p.K3745R|MACF1_ENST00000567887.1_Missense_Mutation_p.K3782R|MACF1_ENST00000317713.7_Missense_Mutation_p.K1683R|MACF1_ENST00000361689.2_Missense_Mutation_p.K1683R|MACF1_ENST00000289893.4_Missense_Mutation_p.K2185R|MACF1_ENST00000545844.1_Missense_Mutation_p.K1683R|MACF1_ENST00000539005.1_Missense_Mutation_p.K1683R|MACF1_ENST00000476350.1_3'UTR			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	3750					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			GAGAACAAGAAGAAGATCGAT	0.488																																					p.K1683R		Atlas-SNP	.											.	MACF1	909	.	0			c.A5048G						.						93	80	85					1																	39818713		2203	4300	6503	SO:0001583	missense	23499	exon40			ACAAGAAGAAGAT	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.11249A>G	chr1.hg19:g.39818713A>G	ENSP00000362006:p.Lys3750Arg	128.0	0.0		80.0	4.0	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	hg19		.	.	.	.	.	.	.	.	.	.	A	1.898	-0.453738	0.04540	.	.	ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000530262;ENST00000289893	T;T;T;T;T;D;T	0.87029	0.11;0.18;0.11;0.08;0.27;-2.2;1.28	5.53	1.54	0.23209	.	0.728003	0.13496	N	0.383654	T	0.62877	0.2464	N	0.00926	-1.1	0.58432	D	0.999999	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.12156	0.002;0.007;0.002;0.002	T	0.46317	-0.9200	10	0.12430	T	0.62	.	8.6482	0.34018	0.5543:0.0:0.4457:0.0	.	3750;1683;1683;1648	Q9UPN3;F8W8Q1;Q9UPN3-2;Q9UPN3-3	MACF1_HUMAN;.;.;.	R	1683;3750;1683;1683;1683;1832;2185	ENSP00000439537:K1683R;ENSP00000362006:K3750R;ENSP00000354573:K1683R;ENSP00000313438:K1683R;ENSP00000444364:K1683R;ENSP00000437059:K1832R;ENSP00000289893:K2185R	ENSP00000289893:K2185R	K	+	2	0	MACF1	39591300	0.011000	0.17503	0.883000	0.34634	0.527000	0.34593	-0.086000	0.11233	0.025000	0.15241	-0.375000	0.07067	AAG	.	.		0.488	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		G	39818713	A	G	39818713	3	3	260	1	0	0	0	0	1	0	0	0	9153	72	3	2	11353	2	MACF1	1	39818713	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	61060	39818713	209431908	31	37276										
PPIE	10450	hgsc.bcm.edu	37	chr1	40218656	40218656	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgacatgtgacaagacagacTggctggatggcaagcatgtg	14	7	0	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:40218656T>C	ENST00000324379.5	+	9	788	c.769T>C	c.(769-771)Tgg>Cgg	p.W257R	PPIE_ENST00000372830.1_Missense_Mutation_p.W257R|PPIE_ENST00000470213.1_3'UTR|PPIE_ENST00000356511.2_Missense_Mutation_p.W257R	NM_006112.3	NP_006103.1	Q9UNP9	PPIE_HUMAN	peptidylprolyl isomerase E (cyclophilin E)	257	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				mRNA splicing, via spliceosome (GO:0000398)|positive regulation of viral genome replication (GO:0045070)|protein folding (GO:0006457)|regulation of transcription, DNA-templated (GO:0006355)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	cyclosporin A binding (GO:0016018)|nucleotide binding (GO:0000166)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			kidney(3)|large_intestine(2)|lung(2)|prostate(1)|urinary_tract(1)	9	all_cancers(7;1.63e-13)|all_lung(5;2.27e-16)|all_epithelial(6;1.35e-15)|Lung NSC(20;1.49e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.87e-18)|Epithelial(16;2.7e-17)|all cancers(16;5.5e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			CAAGACAGACTGGCTGGATGG	0.532																																					p.W257R		Atlas-SNP	.											.	PPIE	33	.	0			c.T769C						.						163	138	147					1																	40218656		2203	4300	6503	SO:0001583	missense	10450	exon9			ACAGACTGGCTGG	AF042385	CCDS442.1, CCDS443.1, CCDS53299.1	1p32	2013-02-12			ENSG00000084072	ENSG00000084072		"RNA binding motif (RRM) containing"	9258	protein-coding gene	gene with protein product	"peptidyl-prolyl cis-trans isomerase E", "cyclophilin 33", "cyclophilin E", "PPIase E", "rotamase E", "peptidylprolyl isomerase E, isoform 1"	602435				9747881	Standard	NM_203456		Approved	CyP-33, MGC3736, MGC111222	uc001cdw.3	Q9UNP9	OTTHUMG00000009248	ENST00000324379.5:c.769T>C	chr1.hg19:g.40218656T>C	ENSP00000312769:p.Trp257Arg	153.0	0.0		99.0	5.0	NM_006112	B2R971|O43634|O43635|Q32Q72|Q3S611|Q5TGA0|Q5TGA2|Q5TGA3|Q9UIZ5	Missense_Mutation	SNP	ENST00000324379.5	hg19	CCDS443.1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.528578	0.85706	.	.	ENSG00000084072	ENST00000324379;ENST00000356511;ENST00000497370;ENST00000372835;ENST00000372830	T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;1.23	5.57	5.57	0.84162	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (4);Cyclophilin-like (1);	0.000000	0.85682	D	0.000000	T	0.73521	0.3597	M	0.93898	3.47	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.997;1.0;0.999;0.997	T	0.81437	-0.0933	10	0.87932	D	0	-9.1456	15.6874	0.77421	0.0:0.0:0.0:1.0	.	178;257;257;257	B4E3F2;Q5TGA3;Q9UNP9-2;Q9UNP9	.;.;.;PPIE_HUMAN	R	257;257;191;206;257	ENSP00000312769:W257R;ENSP00000348904:W257R;ENSP00000433475:W191R;ENSP00000361925:W206R;ENSP00000361918:W257R	ENSP00000312769:W257R	W	+	1	0	PPIE	39991243	1.000000	0.71417	0.997000	0.53966	0.994000	0.84299	5.022000	0.64078	2.243000	0.73865	0.533000	0.62120	TGG	.	.		0.532	PPIE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025642.2	NM_006112		C	40218656	T	C	40218656	3	2	260	1	0	0	0	0	1	0	0	0	12334	1580	55	2	803	2	PPIE	1	40218656	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	399943	40218656	209031965	32	37277										
RLF	6018	hgsc.bcm.edu	37	chr1	40705226	40705226	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agaaagaagaaaatagaagcTgtgaatcagagcgcacagaa	11	5	1	7			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:40705226T>C	ENST00000372771.4	+	8	4879	c.4852T>C	c.(4852-4854)Tgt>Cgt	p.C1618R		NM_012421.3	NP_036553.2	Q13129	RLF_HUMAN	rearranged L-myc fusion	1618					chromosome organization (GO:0051276)|DNA integration (GO:0015074)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(18)|lung(18)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(4)|urinary_tract(2)	68	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)			AAATAGAAGCTGTGAATCAGA	0.458																																					p.C1618R		Atlas-SNP	.											.	RLF	152	.	0			c.T4852C						.						51	52	51					1																	40705226		2203	4300	6503	SO:0001583	missense	6018	exon8			AGAAGCTGTGAAT		CCDS448.1	1p32	2010-05-07	2005-08-16		ENSG00000117000	ENSG00000117000		"Zinc fingers, C2H2-type"	10025	protein-coding gene	gene with protein product		180610	"rearranged L-myc fusion sequence"			1649386	Standard	NM_012421		Approved	ZNF292L, Zn-15L	uc001cfc.4	Q13129	OTTHUMG00000005763	ENST00000372771.4:c.4852T>C	chr1.hg19:g.40705226T>C	ENSP00000361857:p.Cys1618Arg	233.0	0.0		146.0	6.0	NM_012421	Q14CQ1|Q9NU60	Missense_Mutation	SNP	ENST00000372771.4	hg19	CCDS448.1	.	.	.	.	.	.	.	.	.	.	T	5.727	0.318627	0.10845	.	.	ENSG00000117000	ENST00000372771;ENST00000535839	T	0.14893	2.47	6.17	4.99	0.66335	.	0.370221	0.32301	N	0.006290	T	0.14700	0.0355	L	0.40543	1.245	0.54753	D	0.999984	B;B	0.15473	0.013;0.003	B;B	0.12156	0.007;0.002	T	0.03483	-1.1032	10	0.59425	D	0.04	-10.2534	9.2688	0.37659	0.2438:0.0:0.0:0.7562	.	1311;1618	F5H2M5;Q13129	.;RLF_HUMAN	R	1618;1311	ENSP00000361857:C1618R	ENSP00000361857:C1618R	C	+	1	0	RLF	40477813	0.976000	0.34144	1.000000	0.80357	0.502000	0.33828	0.696000	0.25541	2.371000	0.80710	0.533000	0.62120	TGT	.	.		0.458	RLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015767.1	NM_012421		C	40705226	T	C	40705226	3	2	260	1	0	0	0	0	1	0	0	0	13404	1580	55	2	4882	2	RLF	1	40705226	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	486570	40705226	208545395	33	37278										
HIVEP3	59269	hgsc.bcm.edu	37	chr1	42046720	42046720	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggctttccacatcaccagggAgctgaagtgcaaactgggat	12	10	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:42046720A>G	ENST00000372583.1	-	4	4634	c.3749T>C	c.(3748-3750)cTc>cCc	p.L1250P	HIVEP3_ENST00000429157.2_Missense_Mutation_p.L1250P|HIVEP3_ENST00000372584.1_Missense_Mutation_p.L1250P|HIVEP3_ENST00000247584.5_Missense_Mutation_p.L1250P|HIVEP3_ENST00000460604.1_5'Flank	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	1250					positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				ATCACCAGGGAGCTGAAGTGC	0.582																																					p.L1250P		Atlas-SNP	.											.	HIVEP3	235	.	0			c.T3749C						.						56	58	57					1																	42046720		2203	4300	6503	SO:0001583	missense	59269	exon4			CCAGGGAGCTGAA	AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"Zinc fingers, C2H2-type"	13561	protein-coding gene	gene with protein product	"kappabinding protein-1"	606649	"human immunodeficiency virus type I enhancer-binding protein 3"			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.3749T>C	chr1.hg19:g.42046720A>G	ENSP00000361664:p.Leu1250Pro	102.0	0.0		70.0	4.0	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Missense_Mutation	SNP	ENST00000372583.1	hg19	CCDS463.1	.	.	.	.	.	.	.	.	.	.	A	10.27	1.304399	0.23736	.	.	ENSG00000127124	ENST00000372584;ENST00000372583;ENST00000247584;ENST00000429157	T;T;T;T	0.07114	3.23;3.22;3.22;3.23	5.04	3.9	0.45041	.	0.154637	0.30602	N	0.009274	T	0.09905	0.0243	L	0.27053	0.805	0.53005	D	0.999966	D;D	0.59767	0.986;0.976	P;P	0.51135	0.66;0.459	T	0.18085	-1.0348	10	0.36615	T	0.2	-15.1113	10.93	0.47211	0.8593:0.0:0.0:0.1407	.	1250;1250	Q5T1R4-2;Q5T1R4	.;ZEP3_HUMAN	P	1250	ENSP00000361665:L1250P;ENSP00000361664:L1250P;ENSP00000247584:L1250P;ENSP00000410828:L1250P	ENSP00000247584:L1250P	L	-	2	0	HIVEP3	41819307	0.943000	0.32029	1.000000	0.80357	0.813000	0.45954	1.616000	0.36933	0.926000	0.37118	-0.468000	0.05107	CTC	.	.		0.582	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503		G	42046720	A	G	42046720	3	3	260	1	0	0	0	0	1	0	0	0	7197	304	11	2	3495	2	HIVEP3	1	42046720	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1341494	42046720	207203901	34	37279										
FOXJ3	22887	hgsc.bcm.edu	37	chr1	42730811	42730811	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cagggtcatccttagatcgaGgcactttaaggaaacatttg	10	8	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:42730811G>C	ENST00000372572.1	-	6	730	c.419C>G	c.(418-420)cCt>cGt	p.P140R	FOXJ3_ENST00000372573.1_Missense_Mutation_p.P140R|FOXJ3_ENST00000361346.1_Missense_Mutation_p.P140R|FOXJ3_ENST00000361776.1_Missense_Mutation_p.P140R|FOXJ3_ENST00000545068.1_Missense_Mutation_p.P140R	NM_001198851.1	NP_001185780.1	Q9UPW0	FOXJ3_HUMAN	forkhead box J3	140					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	18	Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				CTTAGATCGAGGCACTTTAAG	0.333																																					p.P140R		Atlas-SNP	.											.	FOXJ3	59	.	0			c.C419G						.						142	146	145					1																	42730811		2203	4300	6503	SO:0001583	missense	22887	exon4			GATCGAGGCACTT	AB028964	CCDS30689.1, CCDS55594.1	1p34.2	2008-04-10			ENSG00000198815	ENSG00000198815		"Forkhead boxes"	29178	protein-coding gene	gene with protein product							Standard	NM_014947		Approved	KIAA1041	uc001chf.3	Q9UPW0	OTTHUMG00000007026	ENST00000372572.1:c.419C>G	chr1.hg19:g.42730811G>C	ENSP00000361653:p.Pro140Arg	85.0	0.0		80.0	4.0	NM_001198852	A7MBL7|A7MD18|D3DPW2|Q9NSS7	Missense_Mutation	SNP	ENST00000372572.1	hg19	CCDS30689.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.866291	0.91511	.	.	ENSG00000198815	ENST00000372573;ENST00000372572;ENST00000361346;ENST00000361776;ENST00000545068;ENST00000445886;ENST00000454417	D;D;D;D;D;D;D	0.95724	-3.79;-3.79;-3.79;-3.79;-3.79;-3.79;-3.79	5.65	5.65	0.86999	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.126578	0.51477	D	0.000085	D	0.97707	0.9248	M	0.81179	2.53	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.98283	1.0509	10	0.87932	D	0	.	17.2171	0.86947	0.0:0.0:1.0:0.0	.	140;140	Q9UPW0-2;Q9UPW0	.;FOXJ3_HUMAN	R	140;140;140;140;140;140;97	ENSP00000361654:P140R;ENSP00000361653:P140R;ENSP00000354620:P140R;ENSP00000354449:P140R;ENSP00000439044:P140R;ENSP00000393408:P140R;ENSP00000403060:P97R	ENSP00000354620:P140R	P	-	2	0	FOXJ3	42503398	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.238000	0.95380	2.653000	0.90120	0.563000	0.77884	CCT	.	.		0.333	FOXJ3-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000018310.1	NM_014947		C	42730811	G	C	42730811	3	2	260	1	0	0	0	0	1	0	0	0	6021	1000	35	4	1489	4	FOXJ3	1	42730811	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	684091	42730811	206519810	35	37280										
MPL	4352	hgsc.bcm.edu	37	chr1	43812146	43812146	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgggagaactgcgaagaggaAgagaaaacaaatccaggact	13	6	0	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:43812146A>G	ENST00000372470.3	+	7	1053	c.1011A>G	c.(1009-1011)gaA>gaG	p.E337E	MPL_ENST00000413998.2_Silent_p.E337E	NM_005373.2	NP_005364.1	P40238	TPOR_HUMAN	MPL proto-oncogene, thrombopoietin receptor	337	Poly-Glu.				blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|homeostasis of number of cells (GO:0048872)|platelet activation (GO:0030168)|regulation of chemokine production (GO:0032642)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(551)|large_intestine(3)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	567	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			Eltrombopag(DB06210)|Romiplostim(DB05332)	GCGAAGAGGAAGAGAAAACAA	0.517			Mis		MPD	MPD	congenital amegakaryocytic thrombocytopenia																														p.E337E	NSCLC(52;534 1204 10016 41452 44427)	Atlas-SNP	.	yes	Dom	yes	Familial essential thrombocythemia	1	p34	4352	"myeloproliferative leukemia virus oncogene, thrombopoietin receptor"	yes	L	.	MPL	651	.	0			c.A1011G						.						75	74	74					1																	43812146		2203	4300	6503	SO:0001819	synonymous_variant	4352	exon7			AGAGGAAGAGAAA	M90102	CCDS483.1	1p34	2014-09-17	2014-06-26		ENSG00000117400	ENSG00000117400		"CD molecules", "Fibronectin type III domain containing"	7217	protein-coding gene	gene with protein product		159530	"myeloproliferative leukemia virus oncogene"			1608974	Standard	NM_005373		Approved	CD110, TPOR	uc001ciw.3	P40238	OTTHUMG00000007429	ENST00000372470.3:c.1011A>G	chr1.hg19:g.43812146A>G		156.0	0.0		103.0	5.0	NM_005373	Q5JUZ0	Silent	SNP	ENST00000372470.3	hg19	CCDS483.1																																																																																			.	.		0.517	MPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019522.1	NM_005373		G	43812146	A	G	43812146	2	3	260	1	0	0	0	0	0	0	0	1	9739	69	3	2		2	MPL	1	43812146	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1081335	43812146	205438475	36	37281										
ERI3	79033	hgsc.bcm.edu	37	chr1	44818544	44818544	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctccttacttcgaagatgccAagaccggcagctggggatgc	12	12	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:44818544A>G	ENST00000372257.2	-	2	370	c.189T>C	c.(187-189)ctT>ctC	p.L63L	ERI3_ENST00000495828.1_Intron|ERI3_ENST00000537474.1_5'UTR	NM_024066.1	NP_076971.1	O43414	ERI3_HUMAN	ERI1 exoribonuclease family member 3	63							exonuclease activity (GO:0004527)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(2)|lung(7)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						CGAAGATGCCAAGACCGGCAG	0.493																																					p.L63L		Atlas-SNP	.											.	ERI3	39	.	0			c.T189C						.						137	147	144					1																	44818544		2203	4300	6503	SO:0001819	synonymous_variant	79033	exon2			GATGCCAAGACCG	AF007157	CCDS30696.1	1p34.1	2009-10-07	2009-10-07	2008-12-16	ENSG00000117419	ENSG00000117419		"Enhanced RNAi three prime mRNA exonucleases"	17276	protein-coding gene	gene with protein product	"enhanced RNAi three prime mRNA exonuclease homolog 3 (C.elegans)", "exoribonuclease 3"	609917	"prion protein interacting protein"	PRNPIP			Standard	XM_005271184		Approved	FLJ22943, PINT1	uc001clt.3	O43414	OTTHUMG00000007637	ENST00000372257.2:c.189T>C	chr1.hg19:g.44818544A>G		169.0	0.0		92.0	5.0	NM_024066	B1AK98|Q5T2T7|Q5T2T9|Q5TG35|Q9BQA0|Q9UEB4	Silent	SNP	ENST00000372257.2	hg19	CCDS30696.1																																																																																			.	.		0.493	ERI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020243.1	NM_024066		G	44818544	A	G	44818544	2	3	260	1	0	0	0	0	0	0	0	1	5231	117	5	2		2	ERI3	1	44818544	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1006398	44818544	204432077	37	37282										
PTCH2	8643	hgsc.bcm.edu	37	chr1	45294290	45294290	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgcccgtgcgctgcagacacTcgcccatgcgctcctgccag	11	18	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:45294290T>C	ENST00000372192.3	-	12	1608	c.1478A>G	c.(1477-1479)gAg>gGg	p.E493G	PTCH2_ENST00000447098.2_Missense_Mutation_p.E493G	NM_003738.4	NP_003729.3	Q9Y6C5	PTC2_HUMAN	patched 2	493	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.		E -> K (in dbSNP:rs11573581). {ECO:0000269|Ref.5}.		epidermis development (GO:0008544)|hair cycle (GO:0042633)|negative regulation of smoothened signaling pathway (GO:0045879)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|smoothened binding (GO:0005119)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(19)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	50	Acute lymphoblastic leukemia(166;0.155)					CTGCAGACACTCGCCCATGCG	0.637									Basal Cell Nevus syndrome																												p.E493G		Atlas-SNP	.											.	PTCH2	96	.	0			c.A1478G						.						79	61	67					1																	45294290		2203	4300	6503	SO:0001583	missense	8643	exon12	Familial Cancer Database	Gorlin syndrome, Gorlin-Golz syndrome, Naevoid Basal Cell Carcinoma syndrome, NBCCS	AGACACTCGCCCA	AF091501	CCDS516.1, CCDS53312.1	1p34.1	2010-06-24	2010-06-24		ENSG00000117425	ENSG00000117425			9586	protein-coding gene	gene with protein product		603673	"patched (Drosophila) homolog 2", "patched homolog 2 (Drosophila)"			9811851, 9931336	Standard	NM_003738		Approved		uc010olf.2	Q9Y6C5	OTTHUMG00000008490	ENST00000372192.3:c.1478A>G	chr1.hg19:g.45294290T>C	ENSP00000361266:p.Glu493Gly	135.0	0.0		101.0	5.0	NM_001166292	O95341|O95856|Q53Z57|Q5QP87|Q6UX14	Missense_Mutation	SNP	ENST00000372192.3	hg19	CCDS516.1	.	.	.	.	.	.	.	.	.	.	T	14.32	2.501299	0.44455	.	.	ENSG00000117425	ENST00000447098;ENST00000372192	D;D	0.96300	-3.97;-3.97	4.47	2.0	0.26442	Sterol-sensing domain (1);	0.072962	0.51477	D	0.000083	D	0.94430	0.8208	M	0.72353	2.195	0.38903	D	0.957374	P;P	0.47191	0.647;0.891	B;B	0.43082	0.299;0.407	D	0.90891	0.4761	10	0.22706	T	0.39	-24.1087	10.7276	0.46077	0.0:0.0:0.3054:0.6946	.	493;493	Q9Y6C5-2;Q9Y6C5	.;PTC2_HUMAN	G	493	ENSP00000389703:E493G;ENSP00000361266:E493G	ENSP00000361266:E493G	E	-	2	0	PTCH2	45066877	1.000000	0.71417	0.912000	0.35992	0.961000	0.63080	4.502000	0.60400	0.215000	0.20761	0.379000	0.24179	GAG	.	.		0.637	PTCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023428.4	NM_003738		C	45294290	T	C	45294290	3	2	260	1	0	0	0	0	1	0	0	0	12743	1551	54	2	2197	2	PTCH2	1	45294290	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	475746	45294290	203956331	38	37283										
HECTD3	79654	hgsc.bcm.edu	37	chr1	45473144	45473144	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggggcaggcacggtgttccaTggcaagacggcggttgatgt	18	8	0	2	rs367668335		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:45473144T>C	ENST00000372172.4	-	10	1515	c.1444A>G	c.(1444-1446)Atg>Gtg	p.M482V	HECTD3_ENST00000372168.3_Missense_Mutation_p.M92V|HECTD3_ENST00000486132.1_5'Flank	NM_024602.5	NP_078878.3	Q5T447	HECD3_HUMAN	HECT domain containing E3 ubiquitin protein ligase 3	482					proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|stomach(1)	28	Acute lymphoblastic leukemia(166;0.155)					CGGTGTTCCATGGCAAGACGG	0.612																																					p.M482V		Atlas-SNP	.											.	HECTD3	158	.	0			c.A1444G						.	T	VAL/MET	0,4218		0,0,2109	86	90	89		1444	5.9	1	1		89	1,8445		0,1,4222	no	missense	HECTD3	NM_024602.5	21	0,1,6331	CC,CT,TT		0.0118,0.0,0.0079	benign	482/862	45473144	1,12663	2109	4223	6332	SO:0001583	missense	79654	exon10			GTTCCATGGCAAG	BC019105	CCDS41318.1	1p34.1	2012-02-23	2012-02-23		ENSG00000126107	ENSG00000126107			26117	protein-coding gene	gene with protein product			"HECT domain containing 3"			12477932	Standard	NM_024602		Approved	FLJ21156	uc009vxk.3	Q5T447	OTTHUMG00000008587	ENST00000372172.4:c.1444A>G	chr1.hg19:g.45473144T>C	ENSP00000361245:p.Met482Val	163.0	0.0		119.0	5.0	NM_024602	B3KPV7|B3KRH4|Q5T448|Q9H783	Missense_Mutation	SNP	ENST00000372172.4	hg19	CCDS41318.1	.	.	.	.	.	.	.	.	.	.	T	9.557	1.117427	0.20877	0.0	1.18E-4	ENSG00000126107	ENST00000372172;ENST00000372168	T;T	0.59224	0.28;0.59	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	T	0.42921	0.1224	L	0.27053	0.805	0.52501	D	0.99995	B;B	0.11235	0.004;0.001	B;B	0.04013	0.001;0.001	T	0.31447	-0.9943	10	0.30078	T	0.28	.	10.5681	0.45184	0.0:0.0718:0.0:0.9282	.	482;92	Q5T447;Q5T447-2	HECD3_HUMAN;.	V	482;92	ENSP00000361245:M482V;ENSP00000361241:M92V	ENSP00000361241:M92V	M	-	1	0	HECTD3	45245731	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.714000	0.61902	2.232000	0.73038	0.533000	0.62120	ATG	.	.		0.612	HECTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023734.1	NM_024602		C	45473144	T	C	45473144	3	2	260	1	0	0	0	0	1	0	0	0	7050	1464	51	2	1189	2	HECTD3	1	45473144	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	178854	45473144	203777477	39	37284										
MUTYH	4595	hgsc.bcm.edu	37	chr1	45800076	45800076	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tccttaccatcacaggcagaAggcttggcctgactgttgtt	10	11	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:45800076A>G	ENST00000372098.3	-	2	277	c.144T>C	c.(142-144)ccT>ccC	p.P48P	MUTYH_ENST00000528332.2_Silent_p.P48P|MUTYH_ENST00000354383.6_Silent_p.P34P|MUTYH_ENST00000529984.1_Silent_p.P34P|MUTYH_ENST00000372115.3_Silent_p.P48P|MUTYH_ENST00000372104.1_Silent_p.P34P|MUTYH_ENST00000528013.2_Silent_p.P34P|MUTYH_ENST00000456914.2_Silent_p.P34P|MUTYH_ENST00000355498.2_Silent_p.P34P|MUTYH_ENST00000372100.5_Silent_p.P34P|MUTYH_ENST00000450313.1_Silent_p.P48P|MUTYH_ENST00000448481.1_Silent_p.P34P|MUTYH_ENST00000372110.3_Silent_p.P48P|MUTYH_ENST00000488731.2_Silent_p.P34P|MUTYH_ENST00000531105.1_Silent_p.P34P			Q9UIF7	MUTYH_HUMAN	mutY homolog	48					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depurination (GO:0045007)|DNA repair (GO:0006281)|mismatch repair (GO:0006298)	mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|hydrolase activity, acting on glycosyl bonds (GO:0016798)|metal ion binding (GO:0046872)|MutSalpha complex binding (GO:0032407)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.155)					CACAGGCAGAAGGCTTGGCCT	0.542			Mis			colorectal		Base excision repair (BER), DNA glycosylases	MUTYH-associated polyposis																												p.P48P		Atlas-SNP	.	yes	Rec		Adenomatous polyposis coli	1	1p34.3-1p32.1	4595	mutY homolog (E. coli)		E	.	MUTYH	38	.	0			c.T144C						.						181	137	152					1																	45800076		2203	4300	6503	SO:0001819	synonymous_variant	4595	exon2	Familial Cancer Database	MAP, MYH-associated polyposis	GGCAGAAGGCTTG	U63329	CCDS520.1, CCDS41320.1, CCDS41321.1, CCDS41322.1, CCDS72776.1, CCDS72777.1	1p34.1	2014-09-17	2013-09-12		ENSG00000132781	ENSG00000132781			7527	protein-coding gene	gene with protein product		604933	"mutY (E. coli) homolog", "mutY homolog (E. coli)"			7823963, 10684930	Standard	NM_012222		Approved	MYH	uc009vxp.3	Q9UIF7	OTTHUMG00000007682	ENST00000372098.3:c.144T>C	chr1.hg19:g.45800076A>G		109.0	0.0		80.0	4.0	NM_012222	D3DPZ4|Q15830|Q9UBP2|Q9UBS7|Q9UIF4|Q9UIF5|Q9UIF6	Silent	SNP	ENST00000372098.3	hg19	CCDS520.1																																																																																			.	.		0.542	MUTYH-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000020529.1	NM_012222		G	45800076	A	G	45800076	2	3	260	1	0	0	0	0	0	0	0	1	10002	59	3	2		2	MUTYH	1	45800076	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	326932	45800076	203450545	40	37285										
CC2D1B	200014	hgsc.bcm.edu	37	chr1	52825005	52825005	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctgagggtgctgtgggagccTgagaagcctgctggggcttc	18	9	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:52825005T>C	ENST00000371586.2	-	10	1181	c.1043A>G	c.(1042-1044)cAg>cGg	p.Q348R	CC2D1B_ENST00000284376.3_Missense_Mutation_p.Q348R|CC2D1B_ENST00000438831.1_5'UTR|CC2D1B_ENST00000460261.1_5'UTR	NM_032449.2	NP_115825.1	Q5T0F9	C2D1B_HUMAN	coiled-coil and C2 domain containing 1B	348						nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(1)|large_intestine(6)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	27						TGTGGGAGCCTGAGAAGCCTG	0.667																																					p.Q348R		Atlas-SNP	.											.	CC2D1B	73	.	0			c.A1043G						.						32	31	32					1																	52825005		2203	4300	6503	SO:0001583	missense	200014	exon10			GGAGCCTGAGAAG	AB058739	CCDS30714.1	1p32.3	2008-02-05			ENSG00000154222	ENSG00000154222			29386	protein-coding gene	gene with protein product						11347906	Standard	NM_032449		Approved	KIAA1836	uc001ctq.2	Q5T0F9	OTTHUMG00000008102	ENST00000371586.2:c.1043A>G	chr1.hg19:g.52825005T>C	ENSP00000360642:p.Gln348Arg	157.0	0.0		92.0	4.0	NM_032449	Q49AE8|Q5T0F8|Q5T0G0|Q6ZNQ1|Q96AP3|Q96I04|Q96JJ1	Missense_Mutation	SNP	ENST00000371586.2	hg19	CCDS30714.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.064|0.064	-1.217401|-1.217401	0.01542|0.01542	.|.	.|.	ENSG00000154222|ENSG00000154222	ENST00000371586;ENST00000284376;ENST00000371573|ENST00000438021;ENST00000450942	T;T|.	0.24538|.	1.85;1.85|.	4.43|4.43	2.11|2.11	0.27256|0.27256	.|.	1.648800|.	0.03044|.	N|.	0.153675|.	T|T	0.23370|0.23370	0.0565|0.0565	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	N|N	0.999996|0.999996	B;B|.	0.09022|.	0.0;0.002|.	B;B|.	0.04013|.	0.0;0.001|.	T|T	0.20174|0.20174	-1.0283|-1.0283	10|5	0.17832|.	T|.	0.49|.	-1.5774|-1.5774	5.6345|5.6345	0.17528|0.17528	0.0:0.2183:0.0:0.7817|0.0:0.2183:0.0:0.7817	.|.	134;348|.	Q5T0G1;Q5T0F9|.	.;C2D1B_HUMAN|.	R|G	348;348;262|135;268	ENSP00000360642:Q348R;ENSP00000284376:Q348R|.	ENSP00000284376:Q348R|.	Q|R	-|-	2|1	0|2	CC2D1B|CC2D1B	52597593|52597593	0.001000|0.001000	0.12720|0.12720	0.005000|0.005000	0.12908|0.12908	0.032000|0.032000	0.12392|0.12392	0.800000|0.800000	0.27042|0.27042	0.824000|0.824000	0.34613|0.34613	0.529000|0.529000	0.55759|0.55759	CAG|AGG	.	.		0.667	CC2D1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000022189.1	NM_032449		C	52825005	T	C	52825005	3	2	260	1	0	0	0	0	1	0	0	0	2729	1580	55	2	1593	2	CC2D1B	1	52825005	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	7024929	52825005	196425616	41	37286										
C1orf83	127428	hgsc.bcm.edu	37	chr1	54520126	54520126	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcgtcattcgaacgcctagaAtccagaatagccctcagaag	8	12	2	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:54520126A>G	ENST00000234827.1	+	2	231	c.31A>G	c.(31-33)Atc>Gtc	p.I11V	TCEANC2_ENST00000498272.1_3'UTR|TMEM59_ENST00000234831.5_5'Flank|MIR4781_ENST00000585250.1_RNA|TCEANC2_ENST00000371331.1_Missense_Mutation_p.I41V|TMEM59_ENST00000371337.3_5'Flank|TMEM59_ENST00000371341.1_5'Flank	NM_153035.1	NP_694580.1	Q96MN5	TEAN2_HUMAN	transcription elongation factor A (SII) N-terminal and central domain containing 2	11					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			kidney(1)|lung(3)|pancreas(1)	5						AACGCCTAGAATCCAGAATAG	0.473																																					p.I11V		Atlas-SNP	.											.	TCEANC2	17	.	0			c.A31G						.						78	69	72					1																	54520126		2203	4300	6503	SO:0001583	missense	127428	exon2			CCTAGAATCCAGA	AK056674	CCDS587.1	1p32.3	2011-01-25	2011-01-25	2011-01-25	ENSG00000116205	ENSG00000116205			26494	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 83"	C1orf83		12477932	Standard	NM_153035		Approved	FLJ32112	uc001cwt.1	Q96MN5	OTTHUMG00000008434	ENST00000234827.1:c.31A>G	chr1.hg19:g.54520126A>G	ENSP00000234827:p.Ile11Val	138.0	0.0		112.0	5.0	NM_153035	Q5T702|Q8N8N2	Missense_Mutation	SNP	ENST00000234827.1	hg19	CCDS587.1	.	.	.	.	.	.	.	.	.	.	A	13.03	2.116077	0.37339	.	.	ENSG00000116205	ENST00000234827;ENST00000371331	.	.	.	5.9	-4.89	0.03103	.	1.473130	0.03538	N	0.223471	T	0.30665	0.0772	L	0.36672	1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.27191	-1.0081	9	0.30078	T	0.28	-0.0081	8.667	0.34127	0.2301:0.403:0.3669:0.0	.	11	Q96MN5	TEAN2_HUMAN	V	11;41	.	ENSP00000234827:I11V	I	+	1	0	TCEANC2	54292714	0.221000	0.23642	0.816000	0.32577	0.946000	0.59487	0.463000	0.21972	-0.361000	0.08125	0.533000	0.62120	ATC	.	.		0.473	TCEANC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023245.1	NM_153035		G	54520126	A	G	54520126	3	3	260	1	0	0	0	0	1	0	0	0	2062	101	4	2	33	2	C1orf83	1	54520126	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1695121	54520126	194730495	42	37287										
C8A	731	hgsc.bcm.edu	37	chr1	57378098	57378098	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gcagcctatccacgaggtgcTgcggcacacaagcctggggc	14	14	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:57378098T>C	ENST00000361249.3	+	10	1499	c.1403T>C	c.(1402-1404)cTg>cCg	p.L468P		NM_000562.2	NP_000553.1	P07357	CO8A_HUMAN	complement component 8, alpha polypeptide	468	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane attack complex (GO:0005579)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	43						CACGAGGTGCTGCGGCACACA	0.622																																					p.L468P		Atlas-SNP	.											.	C8A	103	.	0			c.T1403C						.						43	45	44					1																	57378098		2203	4299	6502	SO:0001583	missense	731	exon10			AGGTGCTGCGGCA	M16974	CCDS606.1	1p32.2	2014-09-17			ENSG00000157131	ENSG00000157131		"Complement system"	1352	protein-coding gene	gene with protein product		120950					Standard	NM_000562		Approved		uc001cyo.2	P07357	OTTHUMG00000008306	ENST00000361249.3:c.1403T>C	chr1.hg19:g.57378098T>C	ENSP00000354458:p.Leu468Pro	104.0	0.0		79.0	4.0	NM_000562	A2RUI4|A2RUI5|Q13668|Q9H130	Missense_Mutation	SNP	ENST00000361249.3	hg19	CCDS606.1	.	.	.	.	.	.	.	.	.	.	T	17.67	3.447784	0.63178	.	.	ENSG00000157131	ENST00000361249	D	0.86627	-2.15	5.55	5.55	0.83447	Membrane attack complex component/perforin (MACPF) domain (3);	0.147190	0.46442	D	0.000295	D	0.93552	0.7942	M	0.83118	2.625	0.43688	D	0.996131	D	0.89917	1.0	D	0.85130	0.997	D	0.94384	0.7607	10	0.87932	D	0	-5.9833	14.2624	0.66094	0.0:0.0:0.0:1.0	.	468	P07357	CO8A_HUMAN	P	468	ENSP00000354458:L468P	ENSP00000354458:L468P	L	+	2	0	C8A	57150686	0.523000	0.26274	0.038000	0.18304	0.069000	0.16628	5.494000	0.66905	2.110000	0.64415	0.533000	0.62120	CTG	.	.		0.622	C8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022890.1	NM_000562		C	57378098	T	C	57378098	3	2	260	1	0	0	0	0	1	0	0	0	2418	1580	55	2	1441	2	C8A	1	57378098	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	2857972	57378098	191872523	43	37288										
C1orf87	127795	hgsc.bcm.edu	37	chr1	60491090	60491090	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tactttatttcattttggtaAcccaaatcttgatggttaag	6	6	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:60491090A>G	ENST00000371201.3	-	8	1217	c.1110T>C	c.(1108-1110)ggT>ggC	p.G370G	C1orf87_ENST00000450089.2_Silent_p.G141G	NM_152377.2	NP_689590.1	Q8N0U7	CA087_HUMAN	chromosome 1 open reading frame 87	370							calcium ion binding (GO:0005509)			breast(2)|endometrium(2)|large_intestine(6)|lung(19)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33						CATTTTGGTAACCCAAATCTT	0.363																																					p.G370G	NSCLC(75;811 1386 4923 13371 51772)	Atlas-SNP	.											.	C1orf87	55	.	0			c.T1110C						.						116	119	118					1																	60491090		2203	4300	6503	SO:0001819	synonymous_variant	127795	exon8			TTGGTAACCCAAA	AK124828	CCDS614.1	1p32.1	2014-04-03			ENSG00000162598	ENSG00000162598			28547	protein-coding gene	gene with protein product	"carcinoma-related EF-hand protein"					12477932	Standard	NM_152377		Approved	MGC34837, CREF	uc001czs.2	Q8N0U7	OTTHUMG00000008992	ENST00000371201.3:c.1110T>C	chr1.hg19:g.60491090A>G		156.0	0.0		92.0	5.0	NM_152377	Q6ZU07|Q8IVS0	Silent	SNP	ENST00000371201.3	hg19	CCDS614.1																																																																																			.	.		0.363	C1orf87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024943.1	NM_152377		G	60491090	A	G	60491090	2	3	260	1	0	0	0	0	0	0	0	1	2066	30	2	2		2	C1orf87	1	60491090	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	3112992	60491090	188759531	44	37289										
INADL	10207	hgsc.bcm.edu	37	chr1	62593719	62593719	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gagatatccccgtatttattGccatgattcaggctagcgga	10	9	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:62593719G>T	ENST00000371158.2	+	40	5233	c.5119G>T	c.(5119-5121)Gcc>Tcc	p.A1707S	INADL_ENST00000472512.1_3'UTR	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1707	PDZ 10. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						CGTATTTATTGCCATGATTCA	0.463																																					p.A1707S		Atlas-SNP	.											.	INADL	179	.	0			c.G5119T						.						92	88	89					1																	62593719		1912	4126	6038	SO:0001583	missense	10207	exon40			TTTATTGCCATGA	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.5119G>T	chr1.hg19:g.62593719G>T	ENSP00000360200:p.Ala1707Ser	194.0	0.0		95.0	4.0	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	hg19	CCDS617.2	.	.	.	.	.	.	.	.	.	.	G	29.8	5.032895	0.93575	.	.	ENSG00000132849	ENST00000371158	T	0.23552	1.9	6.06	5.13	0.70059	PDZ/DHR/GLGF (4);	0.238623	0.32244	N	0.006364	T	0.27524	0.0676	N	0.10645	0.015	0.80722	D	1	P	0.50443	0.935	D	0.66196	0.942	T	0.10497	-1.0627	10	0.08837	T	0.75	.	16.5268	0.84333	0.0:0.0:0.8683:0.1317	.	1707	Q8NI35	INADL_HUMAN	S	1707	ENSP00000360200:A1707S	ENSP00000360200:A1707S	A	+	1	0	INADL	62366307	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.400000	0.97290	1.509000	0.48786	0.650000	0.86243	GCC	.	.		0.463	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		T	62593719	G	T	62593719	3	4	260	1	0	0	0	0	1	0	0	0	7740	1319	46	3	5273	3	INADL	1	62593719	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	2102629	62593719	186656902	45	37290										
JAK1	3716	hgsc.bcm.edu	37	chr1	65310560	65310560	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acacacatttccatggaccaGgtctttatcctcctgcagag	7	13	1	1	rs377757935		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:65310560G>T	ENST00000342505.4	-	16	2376	c.2128C>A	c.(2128-2130)Ctg>Atg	p.L710M	JAK1_ENST00000465376.1_5'UTR	NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	710	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	CCATGGACCAGGTCTTTATCC	0.527			Mis		ALL																																p.L710M		Atlas-SNP	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	.	JAK1	209	.	0			c.C2128A						.						86	96	93					1																	65310560		1997	4163	6160	SO:0001583	missense	3716	exon16			GGACCAGGTCTTT	M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.2128C>A	chr1.hg19:g.65310560G>T	ENSP00000343204:p.Leu710Met	197.0	0.0		122.0	5.0	NM_002227	Q59GQ2|Q9UD26	Missense_Mutation	SNP	ENST00000342505.4	hg19	CCDS41346.1	.	.	.	.	.	.	.	.	.	.	G	16.73	3.204452	0.58234	.	.	ENSG00000162434	ENST00000342505	T	0.35973	1.28	5.0	-0.437	0.12272	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.27697	0.0681	M	0.81341	2.54	0.36515	D	0.869802	D	0.53745	0.962	P	0.49451	0.611	T	0.14868	-1.0457	9	0.59425	D	0.04	-4.311	3.8788	0.09069	0.5391:0.0:0.2816:0.1793	.	710	P23458	JAK1_HUMAN	M	710	ENSP00000343204:L710M	ENSP00000343204:L710M	L	-	1	2	JAK1	65083148	1.000000	0.71417	0.998000	0.56505	0.810000	0.45777	1.569000	0.36428	0.043000	0.15746	-0.244000	0.11960	CTG	.	.		0.527	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227		T	65310560	G	T	65310560	3	4	260	1	0	0	0	0	1	0	0	0	7946	991	35	3	1376	3	JAK1	1	65310560	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	2716841	65310560	183940061	46	37291										
LRRC7	57554	hgsc.bcm.edu	37	chr1	70460299	70460299	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gacaatcaacttacaatgctAcccaatacaattggaaagta	5	9	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:70460299A>G	ENST00000035383.5	+	9	903	c.873A>G	c.(871-873)ctA>ctG	p.L291L	LRRC7_ENST00000310961.5_Silent_p.L296L|LRRC7_ENST00000415775.2_5'UTR	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	291						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)				breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						TTACAATGCTACCCAATACAA	0.323																																					p.L291L		Atlas-SNP	.											.	LRRC7	400	.	0			c.A873G						.						107	111	110					1																	70460299		2203	4300	6503	SO:0001819	synonymous_variant	57554	exon9			AATGCTACCCAAT		CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.873A>G	chr1.hg19:g.70460299A>G		109.0	0.0		70.0	4.0	NM_020794	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Silent	SNP	ENST00000035383.5	hg19	CCDS645.1																																																																																			.	.		0.323	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794		G	70460299	A	G	70460299	2	3	260	1	0	0	0	0	0	0	0	1	9029	378	14	2		2	LRRC7	1	70460299	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	5149739	70460299	178790322	47	37292										
LRRC7	57554	hgsc.bcm.edu	37	chr1	70505146	70505146	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aatggcaggtatgaagatgaAcacccttcatatcaagaagt	9	7	2	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:70505146A>G	ENST00000035383.5	+	19	3555	c.3525A>G	c.(3523-3525)gaA>gaG	p.E1175E	LRRC7_ENST00000310961.5_Silent_p.E1180E|LRRC7_ENST00000415775.2_Silent_p.E459E	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	1175						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)				breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						ATGAAGATGAACACCCTTCAT	0.502																																					p.E1175E		Atlas-SNP	.											.	LRRC7	400	.	0			c.A3525G						.						61	61	61					1																	70505146		2203	4300	6503	SO:0001819	synonymous_variant	57554	exon19			AGATGAACACCCT		CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.3525A>G	chr1.hg19:g.70505146A>G		98.0	0.0		93.0	4.0	NM_020794	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Silent	SNP	ENST00000035383.5	hg19	CCDS645.1																																																																																			.	.		0.502	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794		G	70505146	A	G	70505146	2	3	260	1	0	0	0	0	0	0	0	1	9029	40	2	2		2	LRRC7	1	70505146	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	44847	70505146	178745475	48	37293										
LHX8	431707	hgsc.bcm.edu	37	chr1	75602350	75602350	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctggcggccgggaggactcgCaaaggcgccggggaagaggg	21	10	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:75602350C>T	ENST00000294638.5	+	3	745	c.81C>T	c.(79-81)cgC>cgT	p.R27R	LHX8_ENST00000356261.3_Silent_p.R17R	NM_001001933.1	NP_001001933.1	Q68G74	LHX8_HUMAN	LIM homeobox 8	27					female gonad development (GO:0008585)|forebrain neuron development (GO:0021884)|learning or memory (GO:0007611)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	female germ cell nucleus (GO:0001674)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(18)|ovary(3)|urinary_tract(1)	30						GGAGGACTCGCAAAGGCGCCG	0.682																																					p.R27R		Atlas-SNP	.											.	LHX8	73	.	0			c.C81T						.						18	21	20					1																	75602350		1785	3340	5125	SO:0001819	synonymous_variant	431707	exon3			GACTCGCAAAGGC	AB050476	CCDS30756.1, CCDS58008.1	1p31.1	2011-06-20			ENSG00000162624	ENSG00000162624		"Homeoboxes / LIM class"	28838	protein-coding gene	gene with protein product		604425				9598319	Standard	NM_001256114		Approved	Lhx7	uc031pmx.1	Q68G74	OTTHUMG00000009692	ENST00000294638.5:c.81C>T	chr1.hg19:g.75602350C>T		163.0	0.0		93.0	20.0	NM_001001933	E9PGE3	Silent	SNP	ENST00000294638.5	hg19	CCDS30756.1																																																																																			.	.		0.682	LHX8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026700.1	NM_001001933		T	75602350	C	T	75602350	2	4	260	1	0	0	0	0	0	0	0	1	8785	697	25	3		3	LHX8	1	75602350	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	5097204	75602350	173648271	49	37294										
FUBP1	8880	hgsc.bcm.edu	37	chr1	78432758	78432758	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccaaccattccatctggaacTttgtattcttctgtcattac	4	12	4	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:78432758T>C	ENST00000370768.2	-	5	399	c.318A>G	c.(316-318)aaA>aaG	p.K106K	FUBP1_ENST00000436586.2_Silent_p.K127K|FUBP1_ENST00000370767.1_Silent_p.K106K	NM_003902.3	NP_003893.2	Q96AE4	FUBP1_HUMAN	far upstream element (FUSE) binding protein 1	106	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.				positive regulation of gene expression (GO:0010628)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)			central_nervous_system(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(3)	17						CATCTGGAACTTTGTATTCTT	0.269			"F, N"		oligodendroglioma																																p.K106K		Atlas-SNP	.		Rec	yes		1	1p13.1	8880	far upstream element (FUSE) binding protein 1		O	.	FUBP1	112	.	0			c.A318G						.						43	45	44					1																	78432758		2201	4293	6494	SO:0001819	synonymous_variant	8880	exon5			TGGAACTTTGTAT	U05040	CCDS683.1	1p31.1	2008-02-05			ENSG00000162613	ENSG00000162613			4004	protein-coding gene	gene with protein product		603444		FUBP		8125259	Standard	XM_005271309		Approved	FBP	uc001dii.3	Q96AE4	OTTHUMG00000040799	ENST00000370768.2:c.318A>G	chr1.hg19:g.78432758T>C		140.0	0.0		77.0	4.0	NM_003902	Q12828	Silent	SNP	ENST00000370768.2	hg19	CCDS683.1																																																																																			.	.		0.269	FUBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098030.3	NM_003902		C	78432758	T	C	78432758	2	2	260	1	0	0	0	0	0	0	0	1	6100	1606	56	2		2	FUBP1	1	78432758	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	2830408	78432758	170817863	50	37295										
MCOLN2	255231	hgsc.bcm.edu	37	chr1	85431253	85431253	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgtgtggtgaccatgactatCttcaaaatctgcaaacccag	8	10	3	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:85431253C>G	ENST00000370608.3	-	2	283	c.216G>C	c.(214-216)aaG>aaC	p.K72N	MCOLN2_ENST00000284027.5_Missense_Mutation_p.K44N|MCOLN2_ENST00000531325.1_5'UTR	NM_153259.2	NP_694991.2	Q8IZK6	MCLN2_HUMAN	mucolipin 2	72					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)	18				all cancers(265;0.0111)|Epithelial(280;0.0263)|OV - Ovarian serous cystadenocarcinoma(397;0.217)		CCATGACTATCTTCAAAATCT	0.398																																					p.K72N		Atlas-SNP	.											.	MCOLN2	60	.	0			c.G216C						.						114	113	113					1																	85431253		2203	4300	6503	SO:0001583	missense	255231	exon2			GACTATCTTCAAA	AK094010	CCDS30762.1	1p22	2011-12-16			ENSG00000153898	ENSG00000153898		"Voltage-gated ion channels / Transient receptor potential cation channels"	13357	protein-coding gene	gene with protein product		607399				16382100	Standard	XM_005270719		Approved	TRPML2, FLJ36691, TRP-ML2	uc001dkm.3	Q8IZK6	OTTHUMG00000009954	ENST00000370608.3:c.216G>C	chr1.hg19:g.85431253C>G	ENSP00000359640:p.Lys72Asn	186.0	0.0		127.0	23.0	NM_153259	A6NI99|Q2M3I6|Q5TAG5|Q8N9R3	Missense_Mutation	SNP	ENST00000370608.3	hg19	CCDS30762.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.166249	0.78339	.	.	ENSG00000153898	ENST00000370608;ENST00000284027	T;T	0.58358	0.34;0.34	5.87	4.96	0.65561	.	0.000000	0.85682	D	0.000000	T	0.69628	0.3132	M	0.86097	2.795	0.58432	D	0.999999	D	0.89917	1.0	D	0.85130	0.997	T	0.77169	-0.2686	10	0.87932	D	0	-16.8897	15.0754	0.72074	0.0:0.9322:0.0:0.0678	.	72	Q8IZK6	MCLN2_HUMAN	N	72;44	ENSP00000359640:K72N;ENSP00000284027:K44N	ENSP00000284027:K44N	K	-	3	2	MCOLN2	85203841	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.160000	0.42348	1.620000	0.50308	0.655000	0.94253	AAG	.	.		0.398	MCOLN2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027567.2	NM_153259		G	85431253	C	G	85431253	3	3	260	1	0	0	0	0	1	0	0	0	9405	912	32	4	1536	4	MCOLN2	1	85431253	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	6998495	85431253	163819368	51	37296										
BARHL2	343472	hgsc.bcm.edu	37	chr1	91182635	91182635	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctgactcctaaaatccgcggTcctggcctcaccgagcgggc	11	16	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:91182635T>C	ENST00000370445.4	-	1	159	c.118A>G	c.(118-120)Acc>Gcc	p.T40A		NM_020063.1	NP_064447.1	Q9NY43	BARH2_HUMAN	BarH-like homeobox 2	40					cell fate determination (GO:0001709)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|positive regulation of translation (GO:0045727)|regulation of axon extension (GO:0030516)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)			cervix(2)|endometrium(1)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24		all_lung(203;0.0263)|Lung SC(238;0.128)		all cancers(265;0.000897)|Epithelial(280;0.00516)|OV - Ovarian serous cystadenocarcinoma(397;0.211)		AAATCCGCGGTCCTGGCCTCA	0.577																																					p.T40A	GBM(199;3561 4100 22440)	Atlas-SNP	.											.	BARHL2	62	.	0			c.A118G						.						91	100	97					1																	91182635		2203	4300	6503	SO:0001583	missense	343472	exon1			CCGCGGTCCTGGC	AJ251753	CCDS730.1	1p22.2	2011-07-08	2007-07-09		ENSG00000143032	ENSG00000143032		"Homeoboxes / ANTP class : NKL subclass"	954	protein-coding gene	gene with protein product		605212	"BarH (Drosophila)-like 2"				Standard	NM_020063		Approved		uc001dns.3	Q9NY43	OTTHUMG00000010020	ENST00000370445.4:c.118A>G	chr1.hg19:g.91182635T>C	ENSP00000359474:p.Thr40Ala	129.0	0.0		98.0	5.0	NM_020063	A0AVP2|Q7Z4N7	Missense_Mutation	SNP	ENST00000370445.4	hg19	CCDS730.1	.	.	.	.	.	.	.	.	.	.	T	17.62	3.433875	0.62955	.	.	ENSG00000143032	ENST00000370445	D	0.90844	-2.74	5.82	5.82	0.92795	.	0.162260	0.53938	D	0.000052	T	0.64702	0.2622	N	0.08118	0	0.39524	D	0.968553	B	0.02656	0.0	B	0.01281	0.0	T	0.62891	-0.6758	10	0.11794	T	0.64	.	8.6418	0.33981	0.0:0.0846:0.0:0.9154	.	40	Q9NY43	BARH2_HUMAN	A	40	ENSP00000359474:T40A	ENSP00000359474:T40A	T	-	1	0	BARHL2	90955223	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.986000	0.49370	2.222000	0.72286	0.528000	0.53228	ACC	.	.		0.577	BARHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027728.2			C	91182635	T	C	91182635	3	2	260	1	0	0	0	0	1	0	0	0	1314	1667	58	2	1057	2	BARHL2	1	91182635	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	5751382	91182635	158067986	52	37297										
RPAP2	79871	hgsc.bcm.edu	37	chr1	92789692	92789692	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gaagcctctctggttaaagaAgaacttgatgaagatgacat	10	6	1	6			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:92789692A>G	ENST00000610020.1	+	8	1324	c.1215A>G	c.(1213-1215)gaA>gaG	p.E405E		NM_024813.2	NP_079089.2	Q8IXW5	RPAP2_HUMAN	RNA polymerase II associated protein 2	405					dephosphorylation of RNA polymerase II C-terminal domain (GO:0070940)|snRNA transcription (GO:0009301)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|nucleolus (GO:0005730)|nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	22		all_lung(203;0.0565)|Lung NSC(277;0.152)|Glioma(108;0.222)		all cancers(265;0.00647)|GBM - Glioblastoma multiforme(16;0.0234)|Epithelial(280;0.115)		TGGTTAAAGAAGAACTTGATG	0.423																																					p.E405E		Atlas-SNP	.											.	RPAP2	48	.	0			c.A1215G						.						86	88	87					1																	92789692		2203	4300	6503	SO:0001819	synonymous_variant	79871	exon8			TAAAGAAGAACTT	AK023212	CCDS740.1	1p22.1	2014-01-28	2007-07-26	2007-07-26	ENSG00000122484	ENSG00000122484			25791	protein-coding gene	gene with protein product		611476	"chromosome 1 open reading frame 82"	C1orf82		17643375	Standard	NM_024813		Approved	FLJ13150	uc001dot.2	Q8IXW5	OTTHUMG00000010288	ENST00000610020.1:c.1215A>G	chr1.hg19:g.92789692A>G		151.0	0.0		98.0	4.0	NM_024813	C9JKB5|Q49AS7|Q9H8Y2	Silent	SNP	ENST00000610020.1	hg19	CCDS740.1																																																																																			.	.		0.423	RPAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028368.2	NM_024813		G	92789692	A	G	92789692	2	3	260	1	0	0	0	0	0	0	0	1	13557	69	3	2		2	RPAP2	1	92789692	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1607057	92789692	156460929	53	37298										
RPAP2	79871	hgsc.bcm.edu	37	chr1	92789911	92789911	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gttttgggtgaagaaaccacCaaatcacaagactcagaaga	9	8	2	5			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:92789911C>T	ENST00000610020.1	+	8	1543	c.1434C>T	c.(1432-1434)acC>acT	p.T478T		NM_024813.2	NP_079089.2	Q8IXW5	RPAP2_HUMAN	RNA polymerase II associated protein 2	478					dephosphorylation of RNA polymerase II C-terminal domain (GO:0070940)|snRNA transcription (GO:0009301)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|nucleolus (GO:0005730)|nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	22		all_lung(203;0.0565)|Lung NSC(277;0.152)|Glioma(108;0.222)		all cancers(265;0.00647)|GBM - Glioblastoma multiforme(16;0.0234)|Epithelial(280;0.115)		AAGAAACCACCAAATCACAAG	0.398																																					p.T478T		Atlas-SNP	.											.	RPAP2	48	.	0			c.C1434T						.						44	45	45					1																	92789911		2099	4259	6358	SO:0001819	synonymous_variant	79871	exon8			AACCACCAAATCA	AK023212	CCDS740.1	1p22.1	2014-01-28	2007-07-26	2007-07-26	ENSG00000122484	ENSG00000122484			25791	protein-coding gene	gene with protein product		611476	"chromosome 1 open reading frame 82"	C1orf82		17643375	Standard	NM_024813		Approved	FLJ13150	uc001dot.2	Q8IXW5	OTTHUMG00000010288	ENST00000610020.1:c.1434C>T	chr1.hg19:g.92789911C>T		136.0	0.0		89.0	4.0	NM_024813	C9JKB5|Q49AS7|Q9H8Y2	Silent	SNP	ENST00000610020.1	hg19	CCDS740.1																																																																																			.	.		0.398	RPAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028368.2	NM_024813		T	92789911	C	T	92789911	2	4	260	1	0	0	0	0	0	0	0	1	13557	581	21	3		3	RPAP2	1	92789911	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	219	92789911	156460710	54	37299										
FAM69A	388650	hgsc.bcm.edu	37	chr1	93309606	93309606	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgttctttatcttgaagtatCaccatgagaagaaattcatt	6	6	4	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:93309606C>T	ENST00000370310.4	-	5	691	c.621G>A	c.(619-621)gtG>gtA	p.V207V	SNORA51_ENST00000384295.1_RNA	NM_001006605.4|NM_001252269.1|NM_001252271.1	NP_001006606.2|NP_001239198.1|NP_001239200.1	Q5T7M9	FA69A_HUMAN	family with sequence similarity 69, member A	207						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)	4		all_lung(203;0.00265)|Lung NSC(277;0.00562)|all_neural(321;0.185)|Melanoma(281;0.192)|Glioma(108;0.203)		GBM - Glioblastoma multiforme(16;0.000563)|all cancers(265;0.000751)|Epithelial(280;0.127)		CTTGAAGTATCACCATGAGAA	0.428																																					p.V207V		Atlas-SNP	.											.	FAM69A	30	.	0			c.G621A						.						73	59	63					1																	93309606		692	1591	2283	SO:0001819	synonymous_variant	388650	exon5			AAGTATCACCATG	AK027146	CCDS44173.1, CCDS72822.1, CCDS72823.1, CCDS72824.1, CCDS72825.1	1p22	2014-06-25			ENSG00000154511	ENSG00000154511			32213	protein-coding gene	gene with protein product		614542				21334309	Standard	NM_001006605		Approved	FLJ23493	uc001dpg.3	Q5T7M9	OTTHUMG00000010894	ENST00000370310.4:c.621G>A	chr1.hg19:g.93309606C>T		165.0	0.0		97.0	4.0	NM_001006605	Q6IRV2	Silent	SNP	ENST00000370310.4	hg19	CCDS44173.1																																																																																			.	.		0.428	FAM69A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030046.2	NM_001006605		T	93309606	C	T	93309606	2	4	260	1	0	0	0	0	0	0	0	1	5610	813	29	3		3	FAM69A	1	93309606	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	519695	93309606	155941015	55	37300										
DNTTIP2	30836	hgsc.bcm.edu	37	chr1	94342288	94342288	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acacttataactgtggactcTtcttcatcatcactaccacc	3	14	5	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:94342288T>C	ENST00000436063.2	-	2	1260	c.1203A>G	c.(1201-1203)gaA>gaG	p.E401E	DNTTIP2_ENST00000460191.1_5'UTR	NM_014597.4	NP_055412.2	Q5QJE6	TDIF2_HUMAN	deoxynucleotidyltransferase, terminal, interacting protein 2	401					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	38		all_lung(203;0.0111)|Lung NSC(277;0.0347)		all cancers(265;0.00679)|GBM - Glioblastoma multiforme(16;0.0278)|Epithelial(280;0.128)		CTGTGGACTCTTCTTCATCAT	0.413																																					p.E401E		Atlas-SNP	.											.	DNTTIP2	59	.	0			c.A1203G						.						280	268	272					1																	94342288		1968	4144	6112	SO:0001819	synonymous_variant	30836	exon2			GGACTCTTCTTCA	AY394925	CCDS44174.1	1p22.1	2008-02-05			ENSG00000067334	ENSG00000067334			24013	protein-coding gene	gene with protein product	"acidic 82 kDa protein mRNA"	611199				15047147	Standard	NM_014597		Approved	HSU15552, ERBP, TdIF2	uc001dqf.3	Q5QJE6	OTTHUMG00000010268	ENST00000436063.2:c.1203A>G	chr1.hg19:g.94342288T>C		851.0	0.0		547.0	135.0	NM_014597	Q12987|Q53H59|Q5TFJ4|Q6TLI0|Q76MJ8|Q86WX9	Silent	SNP	ENST00000436063.2	hg19	CCDS44174.1																																																																																			.	.		0.413	DNTTIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028317.2	NM_014597		C	94342288	T	C	94342288	2	2	260	1	0	0	0	0	0	0	0	1	4684	1606	56	2		2	DNTTIP2	1	94342288	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1032682	94342288	154908333	56	37301										
ABCA4	24	hgsc.bcm.edu	37	chr1	94520726	94520726	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agacagcagcatcaaggagcAtcatctgcatggacagcagg	12	10	3	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:94520726A>G	ENST00000370225.3	-	16	2614	c.2528T>C	c.(2527-2529)aTg>aCg	p.M843T	ABCA4_ENST00000535735.1_Missense_Mutation_p.M769T	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	843					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			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)		ATCAAGGAGCATCATCTGCAT	0.512																																					p.M843T		Atlas-SNP	.											.	ABCA4	275	.	0			c.T2528C						.						192	141	158					1																	94520726		2203	4300	6503	SO:0001583	missense	24	exon16			AGGAGCATCATCT	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.2528T>C	chr1.hg19:g.94520726A>G	ENSP00000359245:p.Met843Thr	138.0	0.0		102.0	5.0	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	hg19	CCDS747.1	.	.	.	.	.	.	.	.	.	.	A	19.54	3.847014	0.71603	.	.	ENSG00000198691	ENST00000370225;ENST00000535735	D;D	0.88431	-2.38;-2.35	5.41	5.41	0.78517	.	0.079791	0.85682	D	0.000000	D	0.90590	0.7050	M	0.89414	3.03	0.50039	D	0.999849	P;B	0.50272	0.933;0.206	P;B	0.47346	0.544;0.18	D	0.92555	0.6053	10	0.87932	D	0	.	15.1039	0.72306	1.0:0.0:0.0:0.0	.	769;843	F5H6E5;P78363	.;ABCA4_HUMAN	T	843;769	ENSP00000359245:M843T;ENSP00000437682:M769T	ENSP00000359245:M843T	M	-	2	0	ABCA4	94293314	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	9.339000	0.96797	2.067000	0.61834	0.454000	0.30748	ATG	.	.		0.512	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		G	94520726	A	G	94520726	3	3	260	1	0	0	0	0	1	0	0	0	34	217	8	2	4433	2	ABCA4	1	94520726	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	178438	94520726	154729895	57	37302										
EXTL2	2135	hgsc.bcm.edu	37	chr1	101339876	101339876	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agcaccatagagtactggtcAccatttccagaccctggtgc	9	13	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:101339876A>G	ENST00000370114.3	-	5	2051	c.615T>C	c.(613-615)ggT>ggC	p.G205G	EXTL2_ENST00000535414.1_Silent_p.G192G|EXTL2_ENST00000370113.3_Silent_p.G205G	NM_001033025.2|NM_001261440.1	NP_001028197.1|NP_001248369.1	Q9UBQ6	EXTL2_HUMAN	exostosin-like glycosyltransferase 2	205					heparan sulfate proteoglycan biosynthetic process (GO:0015012)|N-acetylglucosamine metabolic process (GO:0006044)|UDP-N-acetylgalactosamine metabolic process (GO:0019276)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	alpha-1,4-N-acetylgalactosaminyltransferase activity (GO:0035248)|glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0001888)|metal ion binding (GO:0046872)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(4)|skin(1)|urinary_tract(1)	14		all_epithelial(167;2.48e-06)|all_lung(203;0.000414)|Lung NSC(277;0.000946)		Epithelial(280;0.0425)|all cancers(265;0.0628)|COAD - Colon adenocarcinoma(174;0.148)|Colorectal(144;0.167)|Lung(183;0.195)		AGTACTGGTCACCATTTCCAG	0.408																																					p.G213G		Atlas-SNP	.											.	EXTL2	57	.	0			c.T639C						.						49	47	48					1																	101339876		2203	4299	6502	SO:0001819	synonymous_variant	2135	exon6			CTGGTCACCATTT	U76189	CCDS775.1, CCDS72831.1	1p21	2013-03-01	2013-03-01		ENSG00000162694	ENSG00000162694	2.4.1.223	"Exostosin glycosyltransferase family"	3516	protein-coding gene	gene with protein product	"alpha-1,4-N-acteylhexosaminyltransferase"	602411	"exostoses (multiple)-like 2"			9450183, 15831490	Standard	NM_001439		Approved		uc001dtk.2	Q9UBQ6	OTTHUMG00000011814	ENST00000370114.3:c.615T>C	chr1.hg19:g.101339876A>G		164.0	0.0		125.0	5.0	NM_001261441	B2R795|D3DT60	Silent	SNP	ENST00000370114.3	hg19	CCDS775.1																																																																																			.	.		0.408	EXTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032705.1	NM_001439		G	101339876	A	G	101339876	2	3	260	1	0	0	0	0	0	0	0	1	5328	146	6	2		2	EXTL2	1	101339876	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	6819150	101339876	147910745	58	37303										
SLC30A7	148867	hgsc.bcm.edu	37	chr1	101379339	101379339	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tagccatgatcatgctcatgGacatggacactttcattctc	7	11	4	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:101379339G>T	ENST00000370112.4	+	6	819	c.632G>T	c.(631-633)gGa>gTa	p.G211V	SLC30A7_ENST00000357650.4_Missense_Mutation_p.G211V	NM_001144884.1|NM_133496.4	NP_001138356.1|NP_598003.2	Q8NEW0	ZNT7_HUMAN	solute carrier family 30 (zinc transporter), member 7	211	His-rich loop.				cellular protein metabolic process (GO:0044267)|sequestering of zinc ion (GO:0032119)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	cation transmembrane transporter activity (GO:0008324)			endometrium(3)|large_intestine(2)|lung(10)	15		all_epithelial(167;0.000445)|all_lung(203;0.00645)|Lung NSC(277;0.0119)		Epithelial(280;0.0437)|all cancers(265;0.0498)|COAD - Colon adenocarcinoma(174;0.162)|Colorectal(144;0.19)|Lung(183;0.201)		CATGCTCATGGACATGGACAC	0.428																																					p.G211V	NSCLC(91;473 1491 3102 16827 21633)	Atlas-SNP	.											.	SLC30A7	33	.	0			c.G632T						.						156	125	135					1																	101379339		2203	4300	6503	SO:0001583	missense	148867	exon6			CTCATGGACATGG	AF233345	CCDS776.1	1p21.1	2013-05-22			ENSG00000162695	ENSG00000162695		"Solute carriers"	19306	protein-coding gene	gene with protein product		611149				12446736	Standard	NM_133496		Approved	ZnTL2, ZNT7	uc001dto.2	Q8NEW0	OTTHUMG00000011815	ENST00000370112.4:c.632G>T	chr1.hg19:g.101379339G>T	ENSP00000359130:p.Gly211Val	123.0	0.0		84.0	4.0	NM_133496	B2R949|D3DT61|Q8TCH2	Missense_Mutation	SNP	ENST00000370112.4	hg19	CCDS776.1	.	.	.	.	.	.	.	.	.	.	G	15.94	2.981306	0.53827	.	.	ENSG00000162695	ENST00000370112;ENST00000357650	T;T	0.66460	-0.21;-0.21	5.53	4.62	0.57501	.	0.208589	0.49916	D	0.000123	T	0.61022	0.2314	M	0.70595	2.14	0.80722	D	1	P	0.46784	0.884	P	0.47528	0.549	T	0.63056	-0.6722	10	0.35671	T	0.21	-0.7518	14.0985	0.65039	0.0724:0.0:0.9276:0.0	.	211	Q8NEW0	ZNT7_HUMAN	V	211	ENSP00000359130:G211V;ENSP00000350278:G211V	ENSP00000350278:G211V	G	+	2	0	SLC30A7	101151927	0.990000	0.36364	0.082000	0.20525	0.850000	0.48378	2.371000	0.44248	1.338000	0.45544	0.585000	0.79938	GGA	.	.		0.428	SLC30A7-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032711.1	NM_133496		T	101379339	G	T	101379339	3	4	260	1	0	0	0	0	1	0	0	0	14575	1174	41	3	654	3	SLC30A7	1	101379339	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	39463	101379339	147871282	59	37304										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103428283	103428283	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aggagggccaggatgcccacGttcccctattggaccagtct	12	13	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:103428283G>A	ENST00000370096.3	-	39	3262	c.2950C>T	c.(2950-2952)Cgt>Tgt	p.R984C	COL11A1_ENST00000512756.1_Missense_Mutation_p.R868C|COL11A1_ENST00000358392.2_Missense_Mutation_p.R996C|COL11A1_ENST00000353414.4_Missense_Mutation_p.R945C	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	984	Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		GGATGCCCACGTTCCCCTATT	0.453																																					p.R996C		Atlas-SNP	.											.	COL11A1	972	.	0			c.C2986T						.						93	91	91					1																	103428283		2203	4300	6503	SO:0001583	missense	1301	exon39			GCCCACGTTCCCC	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.2950C>T	chr1.hg19:g.103428283G>A	ENSP00000359114:p.Arg984Cys	273.0	0.0		166.0	7.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	hg19	CCDS778.1	.	.	.	.	.	.	.	.	.	.	G	17.44	3.390189	0.62066	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000370090;ENST00000512756	D;D;D;D	0.93426	-3.22;-3.22;-3.22;-3.2	5.67	5.67	0.87782	.	0.115539	0.56097	D	0.000025	D	0.96898	0.8987	M	0.91090	3.175	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.85130	0.982;0.996;0.997;0.99;0.992	D	0.97238	0.9889	10	0.72032	D	0.01	.	12.8063	0.57616	0.0:0.0:0.7276:0.2724	.	868;945;996;984;204	E9PCU0;P12107-3;P12107-2;P12107;F5H5Z5	.;.;.;COBA1_HUMAN;.	C	984;996;945;204;868	ENSP00000359114:R984C;ENSP00000351163:R996C;ENSP00000302551:R945C;ENSP00000426533:R868C	ENSP00000302551:R945C	R	-	1	0	COL11A1	103200871	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	2.671000	0.46842	2.673000	0.90976	0.557000	0.71058	CGT	.	.		0.453	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		A	103428283	G	A	103428283	3	1	260	1	0	0	0	0	1	0	0	0	3669	1145	40	1	2586	1	COL11A1	1	103428283	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	2048944	103428283	145822338	60	37305										
C1orf183	55924	hgsc.bcm.edu	37	chr1	112270030	112270030	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccctaacaccagaggctgtcGattccggccccgggacatca	10	16	1	1	rs267597925		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:112270030G>A	ENST00000357260.5	-	2	635	c.454C>T	c.(454-456)Cga>Tga	p.R152*	FAM212B_ENST00000444059.2_Nonsense_Mutation_p.R137*|FAM212B_ENST00000534365.1_Intron	NM_019099.4	NP_061972.1	Q9NTI7	F212B_HUMAN	family with sequence similarity 212, member B	152										cervix(1)|endometrium(1)	2						AGAGGCTGTCGATTCCGGCCC	0.592																																					p.R152X		Atlas-SNP	.											FAM212B,NS,carcinoma,0,2	FAM212B	17	.	0			c.C454T						.						74	66	69					1																	112270030		2203	4300	6503	SO:0001587	stop_gained	55924	exon2			GCTGTCGATTCCG	AK055667	CCDS841.1, CCDS44195.1	1p13.2	2011-11-24	2011-11-24	2011-11-24	ENSG00000197852	ENSG00000197852			28045	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 183"	C1orf183			Standard	NM_019099		Approved	FLJ31105	uc001ebo.2	Q9NTI7	OTTHUMG00000011953	ENST00000357260.5:c.454C>T	chr1.hg19:g.112270030G>A	ENSP00000349805:p.Arg152*	96.0	0.0		57.0	4.0	NM_019099	B3KP38|B4DF94|Q9NTI6	Nonsense_Mutation	SNP	ENST00000357260.5	hg19	CCDS841.1	.	.	.	.	.	.	.	.	.	.	G	19.45	3.830825	0.71258	.	.	ENSG00000197852	ENST00000357260;ENST00000444059;ENST00000527621	.	.	.	5.13	4.21	0.49690	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-30.5002	13.1095	0.59265	0.0795:0.0:0.9205:0.0	.	.	.	.	X	152;137;161	.	ENSP00000349805:R152X	R	-	1	2	C1orf183	112071553	1.000000	0.71417	0.847000	0.33407	0.993000	0.82548	3.042000	0.49815	1.126000	0.42016	0.484000	0.47621	CGA	.	.		0.592	FAM212B-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000033060.2	NM_019099		A	112270030	G	A	112270030	4	1	260	1	0	0	0	0	0	1	0	0	2021	1066	37	1	443	1	C1orf183	1	112270030	Nonsense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	8841747	112270030	136980591	61	37306										
IGSF3	3321	hgsc.bcm.edu	37	chr1	117156433	117156433	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccctcggaacgctttcgggtCatagcataccacgacccatc	8	16	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:117156433C>A	ENST00000369486.3	-	4	1551	c.786G>T	c.(784-786)atG>atT	p.M262I	IGSF3_ENST00000369483.1_Missense_Mutation_p.M262I|IGSF3_ENST00000318837.6_Missense_Mutation_p.M262I	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	262	Ig-like C2-type 2.				lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		GCTTTCGGGTCATAGCATACC	0.592																																					p.M262I		Atlas-SNP	.											.	IGSF3	294	.	0			c.G786T						.						39	35	36					1																	117156433		2203	4299	6502	SO:0001583	missense	3321	exon4			TCGGGTCATAGCA	AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.786G>T	chr1.hg19:g.117156433C>A	ENSP00000358498:p.Met262Ile	180.0	0.0		135.0	32.0	NM_001542	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	hg19	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	C	9.632	1.136666	0.21123	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.01804	4.64;4.63;4.63	4.77	3.86	0.44501	Immunoglobulin subtype (1);	0.043187	0.85682	N	0.000000	T	0.00552	0.0018	N	0.08118	0	0.53005	D	0.999962	B;B	0.25486	0.127;0.0	B;B	0.41174	0.349;0.002	T	0.42207	-0.9465	10	0.02654	T	1	-56.2366	10.7921	0.46438	0.0:0.9073:0.0:0.0927	.	262;262	O75054;A6NJZ6	IGSF3_HUMAN;.	I	262	ENSP00000358498:M262I;ENSP00000358495:M262I;ENSP00000321184:M262I	ENSP00000321184:M262I	M	-	3	0	IGSF3	116957956	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.624000	0.67764	1.236000	0.43740	0.557000	0.71058	ATG	.	.		0.592	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542		A	117156433	C	A	117156433	3	1	260	1	0	0	0	0	1	0	0	0	7610	826	29	3	2894	3	IGSF3	1	117156433	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	4886403	117156433	132094188	62	37307										
HRNR	388697	hgsc.bcm.edu	37	chr1	152192435	152192435	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	catacccatgtgggccatagCtggaagactgcctggaacca	11	12	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:152192435C>G	ENST00000368801.2	-	3	1745	c.1670G>C	c.(1669-1671)aGc>aCc	p.S557T	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	557					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGGGCCATAGCTGGAAGACTG	0.587																																					p.S557T		Atlas-SNP	.											HRNR,right_upper_lobe,carcinoma,0,1	HRNR	403	.	0			c.G1670C						.						148	158	154					1																	152192435		2203	4300	6503	SO:0001583	missense	388697	exon3			CCATAGCTGGAAG	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"EF-hand domain containing"	20846	protein-coding gene	gene with protein product	"filaggrin family member 3"						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.1670G>C	chr1.hg19:g.152192435C>G	ENSP00000357791:p.Ser557Thr	255.0	0.0		291.0	27.0	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	hg19	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	-	5.104	0.204884	0.09704	.	.	ENSG00000197915	ENST00000368801	T	0.02787	4.16	3.92	1.99	0.26369	.	.	.	.	.	T	0.00552	0.0018	N	0.19112	0.55	0.09310	N	1	B	0.19331	0.035	B	0.12156	0.007	T	0.46176	-0.9210	9	0.16896	T	0.51	.	4.1562	0.10261	0.0:0.5902:0.1939:0.2159	.	557	Q86YZ3	HORN_HUMAN	T	557	ENSP00000357791:S557T	ENSP00000357791:S557T	S	-	2	0	HRNR	150459059	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.357000	0.20199	0.322000	0.23283	-0.265000	0.10407	AGC	.	.		0.587	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868		G	152192435	C	G	152192435	3	3	260	1	0	0	0	0	1	0	0	0	7368	797	28	4	6886	4	HRNR	1	152192435	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	35036002	152192435	97058186	63	37308										
TMEM79	84283	hgsc.bcm.edu	37	chr1	156255196	156255196	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tggatctcccacagccatagAgggggctgaggatggtctag	15	9	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:156255196A>G	ENST00000405535.2	+	2	350	c.179A>G	c.(178-180)gAg>gGg	p.E60G	TMEM79_ENST00000295694.5_Missense_Mutation_p.E60G|TMEM79_ENST00000495881.1_3'UTR|SMG5_ENST00000368267.5_5'Flank|SMG5_ENST00000361813.5_5'Flank|TMEM79_ENST00000357501.2_Intron	NM_032323.2	NP_115699.1	Q9BSE2	TMM79_HUMAN	transmembrane protein 79	60					cornification (GO:0070268)|cuticle development (GO:0042335)|epithelial cell maturation (GO:0002070)|establishment of skin barrier (GO:0061436)|hair follicle morphogenesis (GO:0031069)|positive regulation of epidermis development (GO:0045684)|regulated secretory pathway (GO:0045055)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|trans-Golgi network membrane (GO:0032588)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|urinary_tract(1)	21	Hepatocellular(266;0.158)					ACAGCCATAGAGGGGGCTGAG	0.652																																					p.E60G		Atlas-SNP	.											.	TMEM79	43	.	0			c.A179G						.						43	47	45					1																	156255196		2203	4300	6503	SO:0001583	missense	84283	exon2			CCATAGAGGGGGC	BC005094	CCDS1138.1	1q22	2014-04-22			ENSG00000163472	ENSG00000163472			28196	protein-coding gene	gene with protein product	"mattrin"	615531					Standard	NM_032323		Approved	MGC13102, FLJ16057, FLJ32254, MATT	uc009wrw.3	Q9BSE2	OTTHUMG00000019788	ENST00000405535.2:c.179A>G	chr1.hg19:g.156255196A>G	ENSP00000384748:p.Glu60Gly	95.0	0.0		88.0	5.0	NM_032323	B2RE22|D3DVB8	Missense_Mutation	SNP	ENST00000405535.2	hg19	CCDS1138.1	.	.	.	.	.	.	.	.	.	.	A	12.48	1.951545	0.34471	.	.	ENSG00000163472	ENST00000295694;ENST00000405535	T;T	0.50001	0.76;0.76	5.96	4.8	0.61643	.	0.396732	0.28219	N	0.016142	T	0.13200	0.0320	L	0.29908	0.895	0.09310	N	1	B	0.14438	0.01	B	0.11329	0.006	T	0.15809	-1.0424	9	.	.	.	-6.8904	5.3667	0.16117	0.7626:0.0:0.0814:0.156	.	60	Q9BSE2	TMM79_HUMAN	G	60	ENSP00000295694:E60G;ENSP00000384748:E60G	.	E	+	2	0	TMEM79	154521820	0.997000	0.39634	0.730000	0.30809	0.925000	0.55904	0.838000	0.27572	1.013000	0.39391	0.533000	0.62120	GAG	.	.		0.652	TMEM79-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052101.1	NM_032323		G	156255196	A	G	156255196	3	3	260	1	0	0	0	0	1	0	0	0	16218	304	11	2	181	2	TMEM79	1	156255196	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	4062761	156255196	92995425	64	37309										
APOA1BP	128240	hgsc.bcm.edu	37	chr1	156563722	156563722	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agggatccagccagacttgcTcatatccctcacagccccca	7	17	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:156563722T>C	ENST00000368235.3	+	6	756	c.713T>C	c.(712-714)cTc>cCc	p.L238P	GPATCH4_ENST00000497287.1_5'Flank|APOA1BP_ENST00000368234.3_Silent_p.A219A	NM_144772.2	NP_658985.2			apolipoprotein A-I binding protein											central_nervous_system(1)|large_intestine(2)|lung(3)|prostate(2)|urinary_tract(1)	9	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CCAGACTTGCTCATATCCCTC	0.542																																					p.L238P		Atlas-SNP	.											.	APOA1BP	16	.	0			c.T713C						.						115	117	116					1																	156563722		2203	4300	6503	SO:0001583	missense	128240	exon6			ACTTGCTCATATC	AJ315849	CCDS1145.1	1q21	2008-08-14			ENSG00000163382	ENSG00000163382			18453	protein-coding gene	gene with protein product	"apoA-I binding protein"	608862				11991719, 17533573	Standard	NM_144772		Approved	AIBP, MGC119143, MGC119144, MGC119145, YJEFN1	uc001fph.3	Q8NCW5	OTTHUMG00000033206	ENST00000368235.3:c.713T>C	chr1.hg19:g.156563722T>C	ENSP00000357218:p.Leu238Pro	135.0	0.0		143.0	6.0	NM_144772		Missense_Mutation	SNP	ENST00000368235.3	hg19	CCDS1145.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.178412	0.78564	.	.	ENSG00000163382	ENST00000446584;ENST00000368235	T	0.45668	0.89	4.86	4.86	0.63082	YjeF-related protein, N-terminal (5);	0.000000	0.85682	D	0.000000	T	0.69142	0.3078	H	0.96239	3.79	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80096	-0.1525	10	0.72032	D	0.01	.	13.3193	0.60424	0.0:0.0:0.0:1.0	.	238	Q8NCW5	AIBP_HUMAN	P	256;238	ENSP00000357218:L238P	ENSP00000357218:L238P	L	+	2	0	APOA1BP	154830346	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	8.040000	0.89188	1.806000	0.52798	0.460000	0.39030	CTC	.	.		0.542	APOA1BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081044.1	NM_144772		C	156563722	T	C	156563722	3	2	260	1	0	0	0	0	1	0	0	0	781	1551	54	2	735	2	APOA1BP	1	156563722	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	308526	156563722	92686899	65	37310										
ARHGEF11	9826	hgsc.bcm.edu	37	chr1	156954223	156954223	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggataatgacacagcgttgaAcgagacctggaaggcggaga	15	7	0	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:156954223A>G	ENST00000361409.2	-	3	873	c.131T>C	c.(130-132)gTt>gCt	p.V44A	ARHGEF11_ENST00000368194.3_Missense_Mutation_p.V44A|RN7SL612P_ENST00000497704.2_RNA	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	44					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cytokinesis (GO:0000910)|establishment of cell polarity (GO:0030010)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)|striated muscle contraction (GO:0006941)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(27)|ovary(4)|pancreas(2)|pleura(1)|prostate(4)|skin(7)|stomach(1)|urinary_tract(2)	81	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					ACAGCGTTGAACGAGACCTGG	0.552																																					p.V44A		Atlas-SNP	.											.	ARHGEF11	168	.	0			c.T131C						.						112	67	82					1																	156954223		2202	4298	6500	SO:0001583	missense	9826	exon3			CGTTGAACGAGAC	AB002378	CCDS1162.1, CCDS1163.1	1q21	2011-11-16			ENSG00000132694	ENSG00000132694		"Rho guanine nucleotide exchange factors"	14580	protein-coding gene	gene with protein product		605708				10526156, 9205841	Standard	NM_014784		Approved	KIAA0380, GTRAP48, PDZ-RHOGEF	uc001fqn.3	O15085	OTTHUMG00000041292	ENST00000361409.2:c.131T>C	chr1.hg19:g.156954223A>G	ENSP00000354644:p.Val44Ala	87.0	0.0		100.0	4.0	NM_014784	D3DVD0|Q5VY40|Q6PFW2	Missense_Mutation	SNP	ENST00000361409.2	hg19	CCDS1162.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.149915	0.78001	.	.	ENSG00000132694	ENST00000368194;ENST00000361409	T;T	0.16743	2.32;2.32	5.08	5.08	0.68730	PDZ/DHR/GLGF (1);	0.000000	0.50627	D	0.000109	T	0.20618	0.0496	L	0.32530	0.975	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.71184	0.917;0.972	T	0.01920	-1.1247	10	0.72032	D	0.01	-12.6257	13.9783	0.64285	1.0:0.0:0.0:0.0	.	44;44	O15085;O15085-2	ARHGB_HUMAN;.	A	44	ENSP00000357177:V44A;ENSP00000354644:V44A	ENSP00000354644:V44A	V	-	2	0	ARHGEF11	155220847	1.000000	0.71417	0.998000	0.56505	0.816000	0.46133	7.081000	0.76844	2.127000	0.65507	0.533000	0.62120	GTT	.	.		0.552	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236		G	156954223	A	G	156954223	3	3	260	1	0	0	0	0	1	0	0	0	896	43	2	2	4713	2	ARHGEF11	1	156954223	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	390501	156954223	92296398	66	37311										
FCRL5	83416	hgsc.bcm.edu	37	chr1	157497528	157497528	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aaagaagcttctcctccagaGggggctgagctgctccccag	12	13	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:157497528G>A	ENST00000361835.3	-	9	1996	c.1839C>T	c.(1837-1839)ccC>ccT	p.P613P	FCRL5_ENST00000368190.3_Silent_p.P613P|FCRL5_ENST00000356953.4_Silent_p.P613P|FCRL5_ENST00000368191.3_Silent_p.P528P	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	613	Ig-like C2-type 6.				negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(45)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	85	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)				CTCCTCCAGAGGGGGCTGAGC	0.557																																					p.P613P		Atlas-SNP	.											.	FCRL5	177	.	0			c.C1839T						.						80	81	81					1																	157497528		2203	4300	6503	SO:0001819	synonymous_variant	83416	exon9			TCCAGAGGGGGCT	AF369794	CCDS1165.1	1q21	2013-01-11			ENSG00000143297	ENSG00000143297		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18508	protein-coding gene	gene with protein product		605877				11027651, 11290337	Standard	NM_031281		Approved	FCRH5, IRTA2, BXMAS1, CD307e	uc009wsm.3	Q96RD9	OTTHUMG00000017481	ENST00000361835.3:c.1839C>T	chr1.hg19:g.157497528G>A		222.0	0.0		218.0	140.0	NM_031281	A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Silent	SNP	ENST00000361835.3	hg19	CCDS1165.1																																																																																			.	.		0.557	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1	NM_031281		A	157497528	G	A	157497528	2	1	260	1	0	0	0	0	0	0	0	1	5806	987	35	3		3	FCRL5	1	157497528	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	543305	157497528	91753093	67	37312										
DCAF8	50717	hgsc.bcm.edu	37	chr1	160192562	160192562	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcttggggccatagaaattgAcgccttttactgaaatgata	9	7	1	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:160192562A>G	ENST00000368073.3	-	11	1753	c.1319T>C	c.(1318-1320)gTc>gCc	p.V440A	DCAF8_ENST00000326837.2_Missense_Mutation_p.V440A|DCAF8_ENST00000368074.1_Missense_Mutation_p.V440A|DCAF8_ENST00000608310.1_Missense_Mutation_p.V594A|DCAF8_ENST00000556710.1_Missense_Mutation_p.V594A			Q5TAQ9	DCAF8_HUMAN	DDB1 and CUL4 associated factor 8	440					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(16)|skin(3)|upper_aerodigestive_tract(1)	33						ATAGAAATTGACGCCTTTTAC	0.428																																					p.V440A		Atlas-SNP	.											.	DCAF8	64	.	0			c.T1319C						.						76	78	77					1																	160192562		2203	4300	6503	SO:0001583	missense	50717	exon11			AAATTGACGCCTT	AK093176	CCDS1200.1	1q22-q23	2013-01-09	2009-07-17	2009-07-17	ENSG00000132716	ENSG00000132716		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	24891	protein-coding gene	gene with protein product		615820	"WD repeat domain 42A"	WDR42A		11401431	Standard	NM_015726		Approved	H326, FLJ35857	uc010pjb.1	Q5TAQ9	OTTHUMG00000031604	ENST00000368073.3:c.1319T>C	chr1.hg19:g.160192562A>G	ENSP00000357052:p.Val440Ala	99.0	0.0		118.0	5.0	NM_015726	D3DVE6|Q12839|Q4QQI6|Q53F14|Q66K50|Q68CS7|Q96E00	Missense_Mutation	SNP	ENST00000368073.3	hg19	CCDS1200.1	.	.	.	.	.	.	.	.	.	.	A	19.44	3.828457	0.71143	.	.	ENSG00000132716;ENSG00000132716;ENSG00000132716;ENSG00000132716;ENSG00000132716;ENSG00000258465	ENST00000368073;ENST00000326837;ENST00000368074;ENST00000555195;ENST00000540855;ENST00000556710	D;D;D;D;D	0.82711	-1.64;-1.64;-1.64;-1.64;-1.64	5.07	5.07	0.68467	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.181943	0.35349	U	0.003280	D	0.85894	0.5803	L	0.59967	1.855	0.58432	D	0.999994	D;D	0.61697	0.99;0.987	D;P	0.70935	0.971;0.735	D	0.87757	0.2596	10	0.72032	D	0.01	-9.4744	12.4565	0.55708	1.0:0.0:0.0:0.0	.	594;440	G3V3G9;Q5TAQ9	.;DCAF8_HUMAN	A	440;440;440;594;421;594	ENSP00000357052:V440A;ENSP00000318227:V440A;ENSP00000357053:V440A;ENSP00000451989:V594A;ENSP00000451235:V594A	ENSP00000318227:V440A	V	-	2	0	RP11-574F21.3;DCAF8	158459186	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	8.134000	0.89606	2.130000	0.65690	0.528000	0.53228	GTC	.	.		0.428	DCAF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077402.2	NM_015726		G	160192562	A	G	160192562	3	3	260	1	0	0	0	0	1	0	0	0	4278	275	10	2	490	2	DCAF8	1	160192562	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	2695034	160192562	89058059	68	37313										
USP21	27005	hgsc.bcm.edu	37	chr1	161134677	161134677	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	atcaaaaaaagttcagtaggTgtagactttccactgcagcg	9	8	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:161134677T>C	ENST00000289865.8	+	11	1658	c.1437T>C	c.(1435-1437)ggT>ggC	p.G479G	PPOX_ENST00000367999.4_5'Flank|PPOX_ENST00000432542.2_5'Flank|PPOX_ENST00000544598.1_5'Flank|PPOX_ENST00000535223.1_5'Flank|USP21_ENST00000368001.1_Silent_p.G479G|USP21_ENST00000368002.3_Silent_p.G479G|PPOX_ENST00000352210.5_5'Flank|USP21_ENST00000493054.1_3'UTR	NM_012475.4	NP_036607.3	Q9UK80	UBP21_HUMAN	ubiquitin specific peptidase 21	479	USP.				histone deubiquitination (GO:0016578)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	cysteine-type peptidase activity (GO:0008234)|metal ion binding (GO:0046872)|NEDD8-specific protease activity (GO:0019784)|transcription coactivator activity (GO:0003713)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(10)|ovary(3)|prostate(3)	29	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			GTTCAGTAGGTGTAGACTTTC	0.547																																					p.G479G		Atlas-SNP	.											.	USP21	63	.	0			c.T1437C						.						78	79	79					1																	161134677		2203	4300	6503	SO:0001819	synonymous_variant	27005	exon11			AGTAGGTGTAGAC	AF177758	CCDS30920.1	1q22	2008-04-11	2005-08-08		ENSG00000143258	ENSG00000143258		"Ubiquitin-specific peptidases"	12620	protein-coding gene	gene with protein product		604729	"ubiquitin specific protease 21"	USP23		12838346, 10799498	Standard	XM_006711273		Approved	USP16	uc010pkd.2	Q9UK80	OTTHUMG00000033154	ENST00000289865.8:c.1437T>C	chr1.hg19:g.161134677T>C		205.0	0.0		199.0	9.0	NM_012475	Q59H60|Q5BKT5|Q5VTW9|Q5VTX0|Q9BTV1|Q9HBS2|Q9NYN4	Silent	SNP	ENST00000289865.8	hg19	CCDS30920.1																																																																																			.	.		0.547	USP21-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080801.1			C	161134677	T	C	161134677	2	2	260	1	0	0	0	0	0	0	0	1	17068	1683	59	2		2	USP21	1	161134677	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	942115	161134677	88115944	69	37314										
C1orf14	81626	hgsc.bcm.edu	37	chr1	182921997	182921997	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	caggcactggcagcaggggcTcctccgccgccgccgccgcc	14	20	0	0	rs199811188	byFrequency	TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:182921997T>C	ENST00000367547.3	-	1	508	c.272A>G	c.(271-273)gAg>gGg	p.E91G	SHCBP1L_ENST00000423786.1_5'Flank|SHCBP1L_ENST00000488956.1_5'UTR	NM_030933.2	NP_112195.2	Q9BZQ2	SHP1L_HUMAN	SHC SH2-domain binding protein 1-like	163										breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|pancreas(1)|prostate(1)|skin(2)	15						CAGCAGGGGCTCCTccgccgc	0.736													T|||	7	0.00139776	0	0.0014	5008	,	,		11502	0		0.001	False		,,,				2504	0.0051				p.E91G		Atlas-SNP	.											.	SHCBP1L	64	.	0			c.A272G						.	T	GLY/GLU	1,4393		0,1,2196	10	11	11		272	1.8	0.8	1		11	2,8586		0,2,4292	no	missense	SHCBP1L	NM_030933.2	98	0,3,6488	CC,CT,TT		0.0233,0.0228,0.0231	possibly-damaging	91/654	182921997	3,12979	2197	4294	6491	SO:0001583	missense	81626	exon1			AGGGGCTCCTCCG	AF288397	CCDS30955.1	1q25	2011-01-24	2011-01-24	2011-01-24	ENSG00000157060	ENSG00000157060			16788	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 14"	C1orf14		11318611	Standard	NM_030933		Approved		uc001gpu.3	Q9BZQ2	OTTHUMG00000035419	ENST00000367547.3:c.272A>G	chr1.hg19:g.182921997T>C	ENSP00000356518:p.Glu91Gly	32.0	0.0		36.0	4.0	NM_030933	Q4G195|Q9BZQ3|Q9H2B6	Missense_Mutation	SNP	ENST00000367547.3	hg19	CCDS30955.1	.	.	.	.	.	.	.	.	.	.	T	14.83	2.653628	0.47362	2.28E-4	2.33E-4	ENSG00000157060	ENST00000367547;ENST00000287709	T	0.51325	0.71	4.12	1.75	0.24633	.	0.583503	0.13186	N	0.407160	T	0.27933	0.0688	N	0.17082	0.46	0.80722	D	1	B	0.12630	0.006	B	0.14578	0.011	T	0.08330	-1.0727	10	0.46703	T	0.11	-6.046	5.2036	0.15279	0.0:0.2482:0.0:0.7518	.	91	Q9BZQ2-3	.	G	91;160	ENSP00000356518:E91G	ENSP00000287709:E160G	E	-	2	0	SHCBP1L	181188620	0.005000	0.15991	0.800000	0.32199	0.096000	0.18686	-0.056000	0.11787	0.562000	0.29204	0.260000	0.18958	GAG	.	.		0.736	SHCBP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085956.1	NM_030933		C	182921997	T	C	182921997	3	2	260	1	0	0	0	0	1	0	0	0	2002	1551	54	2	1729	2	C1orf14	1	182921997	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	21787320	182921997	66328624	70	37315										
KIF21B	23046	hgsc.bcm.edu	37	chr1	200978024	200978024	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggatgatgccctgctcctccTccgacgttgccatgtcaaag	10	14	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:200978024T>C	ENST00000422435.2	-	3	636	c.320A>G	c.(319-321)gAg>gGg	p.E107G	KIF21B_ENST00000332129.2_Missense_Mutation_p.E107G|KIF21B_ENST00000461742.2_Missense_Mutation_p.E107G|KIF21B_ENST00000360529.5_Missense_Mutation_p.E107G	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	107	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						CTGCTCCTCCTCCGACGTTGC	0.642																																					p.E107G		Atlas-SNP	.											.	KIF21B	208	.	0			c.A320G						.						117	103	108					1																	200978024		2203	4300	6503	SO:0001583	missense	23046	exon3			TCCTCCTCCGACG	BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"Kinesins", "WD repeat domain containing"	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.320A>G	chr1.hg19:g.200978024T>C	ENSP00000411831:p.Glu107Gly	101.0	0.0		100.0	6.0	NM_017596	B2RP62|B7ZMI0|Q5T4J3	Missense_Mutation	SNP	ENST00000422435.2	hg19	CCDS58056.1	.	.	.	.	.	.	.	.	.	.	T	16.47	3.131757	0.56828	.	.	ENSG00000116852	ENST00000332129;ENST00000360529;ENST00000461742;ENST00000422435;ENST00000539858	T;T;T;T	0.76578	-1.03;-1.03;-1.03;-1.03	5.57	5.57	0.84162	Kinesin, motor domain (4);	0.124152	0.53938	D	0.000053	T	0.75671	0.3881	N	0.22421	0.69	0.47905	D	0.999541	P;P;P;P	0.47484	0.896;0.896;0.801;0.873	P;P;P;P	0.51550	0.596;0.596;0.673;0.461	T	0.79485	-0.1784	10	0.72032	D	0.01	.	15.7361	0.77846	0.0:0.0:0.0:1.0	.	107;107;107;107	B7ZMI0;B2RP62;O75037;O75037-2	.;.;KI21B_HUMAN;.	G	107	ENSP00000328494:E107G;ENSP00000353724:E107G;ENSP00000433808:E107G;ENSP00000411831:E107G	ENSP00000328494:E107G	E	-	2	0	KIF21B	199244647	1.000000	0.71417	0.987000	0.45799	0.661000	0.39034	3.609000	0.54117	2.119000	0.64992	0.528000	0.53228	GAG	.	.		0.642	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332		C	200978024	T	C	200978024	3	2	260	1	0	0	0	0	1	0	0	0	8298	1551	54	2	4682	2	KIF21B	1	200978024	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	18056027	200978024	48272597	71	37316										
KLHL12	59349	hgsc.bcm.edu	37	chr1	202887515	202887515	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcacagcaggcttgtttcacAcctaggacagacacaggcag	10	12	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:202887515A>G	ENST00000367261.3	-	4	569	c.351T>C	c.(349-351)ggT>ggC	p.G117G	KLHL12_ENST00000435533.3_Splice_Site_p.G155G	NM_021633.2	NP_067646.1	Q53G59	KLH12_HUMAN	kelch-like family member 12	117					COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|protein monoubiquitination (GO:0006513)|Wnt signaling pathway (GO:0016055)	Cul3-RING ubiquitin ligase complex (GO:0031463)|ER to Golgi transport vesicle (GO:0030134)|Golgi membrane (GO:0000139)				NS(3)|breast(2)|endometrium(1)|large_intestine(1)|lung(6)|stomach(1)	14			BRCA - Breast invasive adenocarcinoma(75;0.166)			CTTGTTTCACACCTAGGACAG	0.418																																					p.G117G		Atlas-SNP	.											.	KLHL12	50	.	0			c.T351C						.						68	63	65					1																	202887515		2203	4300	6503	SO:0001630	splice_region_variant	59349	exon4			TTTCACACCTAGG	AF190900	CCDS1429.1	1q32.1	2013-01-30	2013-01-30		ENSG00000117153	ENSG00000117153		"Kelch-like", "BTB/POZ domain containing"	19360	protein-coding gene	gene with protein product		614522	"kelch-like 12 (Drosophila)"			12477932	Standard	NM_021633		Approved	C3IP1	uc001gyo.1	Q53G59	OTTHUMG00000041385	ENST00000367261.3:c.350-1T>C	chr1.hg19:g.202887515A>G		88.0	0.0		95.0	5.0	NM_021633	A6NEN8|B7Z7B8|Q9HBX5	Silent	SNP	ENST00000367261.3	hg19	CCDS1429.1																																																																																			.	.		0.418	KLHL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099151.1	NM_021633	Silent	G	202887515	A	G	202887515	5	3	260	1	0	0	0	0	0	0	1	0	8377	173	6	2	1391	2	KLHL12	1	202887515	Splice_Site	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1909491	202887515	46363106	72	37317										
ANGEL2	90806	hgsc.bcm.edu	37	chr1	213178764	213178764	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agcacagccatcaggtttccTtcctgtccgcatcttatatt	6	13	2	0	rs144576191		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:213178764T>C	ENST00000366962.3	-	5	899	c.745A>G	c.(745-747)Agg>Ggg	p.R249G	ANGEL2_ENST00000360506.2_Missense_Mutation_p.R80G|ANGEL2_ENST00000535388.1_Missense_Mutation_p.R80G|ANGEL2_ENST00000544555.1_Missense_Mutation_p.R80G|ANGEL2_ENST00000540642.1_Missense_Mutation_p.R123G	NM_144567.3	NP_653168.2	Q5VTE6	ANGE2_HUMAN	angel homolog 2 (Drosophila)	249										central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|skin(1)	24				OV - Ovarian serous cystadenocarcinoma(81;0.00446)|all cancers(67;0.0169)|Epithelial(68;0.0921)|GBM - Glioblastoma multiforme(131;0.185)		TCAGGTTTCCTTCCTGTCCGC	0.373													T|||	1	0.000199681	8e-04	0	5008	,	,		20075	0		0	False		,,,				2504	0				p.R249G		Atlas-SNP	.											.	ANGEL2	45	.	0			c.A745G						.	T	GLY/ARG	5,4391	9.9+/-24.2	0,5,2193	103	110	107		745	1.6	1	1	dbSNP_134	107	0,8598		0,0,4299	yes	missense	ANGEL2	NM_144567.3	125	0,5,6492	CC,CT,TT		0.0,0.1137,0.0385	benign	249/545	213178764	5,12989	2198	4299	6497	SO:0001583	missense	90806	exon5			GTTTCCTTCCTGT	AL079275	CCDS1512.1, CCDS73027.1	1q32.3	2014-06-17			ENSG00000174606	ENSG00000174606			30534	protein-coding gene	gene with protein product						11943475	Standard	XM_005273344		Approved	KIAA0759L, FLJ12793, Ccr4d	uc001hjz.3	Q5VTE6	OTTHUMG00000036927	ENST00000366962.3:c.745A>G	chr1.hg19:g.213178764T>C	ENSP00000355929:p.Arg249Gly	60.0	0.0		91.0	4.0	NM_144567	B7Z2U4|D3DTA3|Q86X13|Q8NHH3	Missense_Mutation	SNP	ENST00000366962.3	hg19	CCDS1512.1	.	.	.	.	.	.	.	.	.	.	T	10.11	1.260633	0.23051	0.001137	0.0	ENSG00000174606	ENST00000366962;ENST00000360506;ENST00000544555;ENST00000540642;ENST00000535388	D;D;D;D;D	0.95137	-3.31;-3.62;-3.62;-3.31;-3.62	5.45	1.62	0.23740	Endonuclease/exonuclease/phosphatase (2);	0.347510	0.36932	N	0.002322	D	0.88455	0.6441	L	0.28649	0.875	0.28520	N	0.913132	B;B	0.22851	0.053;0.076	B;B	0.29440	0.038;0.102	T	0.77062	-0.2727	10	0.23302	T	0.38	-1.7679	7.8676	0.29545	0.0:0.072:0.2227:0.7053	.	123;249	F5H476;Q5VTE6	.;ANGE2_HUMAN	G	249;80;80;123;80	ENSP00000355929:R249G;ENSP00000353696:R80G;ENSP00000443193:R80G;ENSP00000446124:R123G;ENSP00000438141:R80G	ENSP00000353696:R80G	R	-	1	2	ANGEL2	211245387	0.995000	0.38212	0.985000	0.45067	0.997000	0.91878	3.633000	0.54295	0.075000	0.16796	0.528000	0.53228	AGG	.	T|1.000;C|0.000		0.373	ANGEL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089693.1	NM_144567		C	213178764	T	C	213178764	3	2	260	1	0	0	0	0	1	0	0	0	609	1608	56	2	909	2	ANGEL2	1	213178764	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	10291249	213178764	36071857	73	37318										
EXOC8	149371	hgsc.bcm.edu	37	chr1	231472089	231472089	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	caaattctcttgcagtctcgAgaaggctggtaaagaagaca	10	8	2	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:231472089A>G	ENST00000360394.2	-	1	1489	c.1403T>C	c.(1402-1404)cTc>cCc	p.L468P	EXOC8_ENST00000366645.1_Missense_Mutation_p.L464P|SPRTN_ENST00000391858.4_5'Flank|SPRTN_ENST00000295050.7_5'Flank|SPRTN_ENST00000008440.9_5'Flank	NM_175876.3	NP_787072.2	Q8IYI6	EXOC8_HUMAN	exocyst complex component 8	468					cellular protein localization (GO:0034613)|cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|exocyst (GO:0000145)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(2)|endometrium(1)|large_intestine(2)|liver(1)|lung(5)|prostate(1)|skin(1)|stomach(1)	14	Breast(184;0.0871)	all_cancers(173;0.151)|Prostate(94;0.183)				TGCAGTCTCGAGAAGGCTGGT	0.502																																					p.L468P		Atlas-SNP	.											.	EXOC8	42	.	0			c.T1403C						.						44	41	42					1																	231472089		2203	4300	6503	SO:0001583	missense	149371	exon1			GTCTCGAGAAGGC	AL117352	CCDS1593.1	1q42.2	2013-01-22			ENSG00000116903	ENSG00000116903			24659	protein-coding gene	gene with protein product		615283				12477932	Standard	NM_175876		Approved	SEC84, EXO84, Exo84p	uc001huq.3	Q8IYI6	OTTHUMG00000038025	ENST00000360394.2:c.1403T>C	chr1.hg19:g.231472089A>G	ENSP00000353564:p.Leu468Pro	103.0	0.0		93.0	5.0	NM_175876	B3KU33|Q5TE82	Missense_Mutation	SNP	ENST00000360394.2	hg19	CCDS1593.1	.	.	.	.	.	.	.	.	.	.	A	13.94	2.387092	0.42308	.	.	ENSG00000116903	ENST00000360394;ENST00000366645	T;T	0.77229	-1.08;-1.08	5.79	5.79	0.91817	Cullin repeat-like-containing domain (1);	0.069490	0.64402	D	0.000015	D	0.83977	0.5371	M	0.65975	2.015	0.80722	D	1	D	0.64830	0.994	P	0.58721	0.844	T	0.81741	-0.0794	10	0.23891	T	0.37	-12.3418	16.1224	0.81369	1.0:0.0:0.0:0.0	.	468	Q8IYI6	EXOC8_HUMAN	P	468;464	ENSP00000353564:L468P;ENSP00000355605:L464P	ENSP00000353564:L468P	L	-	2	0	EXOC8	229538712	1.000000	0.71417	0.232000	0.24009	0.596000	0.36781	9.297000	0.96120	2.208000	0.71279	0.533000	0.62120	CTC	.	.		0.502	EXOC8-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_175876		G	231472089	A	G	231472089	3	3	260	1	0	0	0	0	1	0	0	0	5313	304	11	2	778	2	EXOC8	1	231472089	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	18293325	231472089	17778532	74	37319										
NID1	4811	hgsc.bcm.edu	37	chr1	236228260	236228260	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tccagctccaggtccccctgTccggggccgaagggaaagag	14	14	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:236228260T>C	ENST00000264187.6	-	1	202	c.120A>G	c.(118-120)ggA>ggG	p.G40G	NID1_ENST00000366595.3_Silent_p.G40G	NM_002508.2	NP_002499.2	P14543	NID1_HUMAN	nidogen 1	40				FGPGQG -> SAPDR (in Ref. 2; CAA57709). {ECO:0000305}.	basement membrane organization (GO:0071711)|cell-matrix adhesion (GO:0007160)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|positive regulation of cell-substrate adhesion (GO:0010811)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|cell periphery (GO:0071944)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|laminin binding (GO:0043236)|proteoglycan binding (GO:0043394)			breast(4)|endometrium(9)|kidney(1)|large_intestine(23)|lung(20)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(1)	66	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Urokinase(DB00013)	GGTCCCCCTGTCCGGGGCCGA	0.701																																					p.G40G		Atlas-SNP	.											.	NID1	196	.	0			c.A120G						.						19	17	18					1																	236228260		2199	4297	6496	SO:0001819	synonymous_variant	4811	exon1			CCCCTGTCCGGGG	BC045606	CCDS1608.1	1q43	2011-05-08	2005-06-02	2005-06-02	ENSG00000116962	ENSG00000116962			7821	protein-coding gene	gene with protein product		131390	"nidogen (enactin)"	NID		2471408, 7557988	Standard	NM_002508		Approved	entactin	uc001hxo.3	P14543	OTTHUMG00000040071	ENST00000264187.6:c.120A>G	chr1.hg19:g.236228260T>C		83.0	0.0		118.0	9.0	NM_002508	Q14942|Q59FL2|Q5TAF2|Q5TAF3|Q86XD7	Silent	SNP	ENST00000264187.6	hg19	CCDS1608.1																																																																																			.	.		0.701	NID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096647.2	NM_002508		C	236228260	T	C	236228260	2	2	260	1	0	0	0	0	0	0	0	1	10423	1654	58	2		2	NID1	1	236228260	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	4756171	236228260	13022361	75	37320										
HEATR1	55127	hgsc.bcm.edu	37	chr1	236715301	236715301	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gaatagtttgggaattacctTccatcaactctgctaagaaa	7	8	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:236715301T>C	ENST00000366582.3	-	44	6458	c.6344A>G	c.(6343-6345)gAa>gGa	p.E2115G	HEATR1_ENST00000366581.2_Missense_Mutation_p.E2034G|RP11-385F5.4_ENST00000433131.1_RNA|LGALS8_ENST00000526589.1_3'UTR	NM_018072.5	NP_060542.4	Q9H583	HEAT1_HUMAN	HEAT repeat containing 1	2115					rRNA processing (GO:0006364)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(18)|lung(28)|ovary(3)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	87	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			GGAATTACCTTCCATCAACTC	0.343																																					p.E2115G		Atlas-SNP	.											.	HEATR1	197	.	0			c.A6344G						.						133	133	133					1																	236715301		2203	4300	6503	SO:0001583	missense	55127	exon44			TTACCTTCCATCA	BC065205	CCDS31066.1	1q43	2011-08-12			ENSG00000119285	ENSG00000119285			25517	protein-coding gene	gene with protein product	"UTP10, small subunit (SSU) processome component, homolog (yeast)"					17699751	Standard	NM_018072		Approved	FLJ10359, BAP28, UTP10	uc001hyd.2	Q9H583	OTTHUMG00000040061	ENST00000366582.3:c.6344A>G	chr1.hg19:g.236715301T>C	ENSP00000355541:p.Glu2115Gly	97.0	0.0		116.0	6.0	NM_018072	Q5T3Q8|Q6P197|Q9NW23	Missense_Mutation	SNP	ENST00000366582.3	hg19	CCDS31066.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.700471	0.88924	.	.	ENSG00000119285	ENST00000366582;ENST00000366581	T;T	0.66280	-0.2;-0.2	4.9	4.9	0.64082	Armadillo-like helical (1);Armadillo-type fold (1);	0.049413	0.85682	D	0.000000	D	0.83839	0.5341	M	0.93507	3.425	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.88377	0.2999	10	0.87932	D	0	.	14.985	0.71342	0.0:0.0:0.0:1.0	.	2034;2115	Q5T3Q7;Q9H583	.;HEAT1_HUMAN	G	2115;2034	ENSP00000355541:E2115G;ENSP00000355540:E2034G	ENSP00000355540:E2034G	E	-	2	0	HEATR1	234781924	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.629000	0.83207	2.181000	0.69327	0.533000	0.62120	GAA	.	.		0.343	HEATR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096635.1	XM_375853		C	236715301	T	C	236715301	3	2	260	1	0	0	0	0	1	0	0	0	7036	1783	62	2	98	2	HEATR1	1	236715301	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	487041	236715301	12535320	76	37321										
RYR2	6262	hgsc.bcm.edu	37	chr1	237666628	237666628	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gggcgacatggagaattcaaAtttcttcctccacctgggta	10	10	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:237666628A>T	ENST00000366574.2	+	22	2753	c.2436A>T	c.(2434-2436)aaA>aaT	p.K812N	RYR2_ENST00000542537.1_Missense_Mutation_p.K796N|RYR2_ENST00000360064.6_Missense_Mutation_p.K810N	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	812					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GAGAATTCAAATTTCTTCCTC	0.408																																					p.K812N		Atlas-SNP	.											.	RYR2	1273	.	0			c.A2436T						.						74	73	73					1																	237666628		1905	4121	6026	SO:0001583	missense	6262	exon22			ATTCAAATTTCTT	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.2436A>T	chr1.hg19:g.237666628A>T	ENSP00000355533:p.Lys812Asn	175.0	0.0		204.0	31.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.033768	0.75504	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	T;T;T	0.61510	0.1;0.1;0.1	5.73	-0.908	0.10517	Concanavalin A-like lectin/glucanase (1);	0.000000	0.64402	D	0.000004	T	0.67748	0.2926	M	0.76574	2.34	0.80722	D	1	D	0.69078	0.997	P	0.60789	0.879	T	0.69154	-0.5220	10	0.56958	D	0.05	.	11.5221	0.50558	0.5216:0.0:0.4784:0.0	.	812	Q92736	RYR2_HUMAN	N	812;810;796	ENSP00000355533:K812N;ENSP00000353174:K810N;ENSP00000443798:K796N	ENSP00000353174:K810N	K	+	3	2	RYR2	235733251	0.977000	0.34250	0.997000	0.53966	0.987000	0.75469	0.153000	0.16323	-0.097000	0.12307	0.533000	0.62120	AAA	.	.		0.408	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		T	237666628	A	T	237666628	3	4	260	1	0	0	0	0	1	0	0	0	13784	98	4	4	2522	4	RYR2	1	237666628	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	951327	237666628	11583993	77	37322										
OR6F1	343169	hgsc.bcm.edu	37	chr1	247875696	247875696	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agcagatggcaagacagcggTcataagccatggctgccagg	14	10	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr1:247875696T>C	ENST00000302084.2	-	1	409	c.362A>G	c.(361-363)gAc>gGc	p.D121G	RP11-634B7.4_ENST00000449298.1_RNA	NM_001005286.1	NP_001005286.1	Q8NGZ6	OR6F1_HUMAN	olfactory receptor, family 6, subfamily F, member 1	121						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(1)|large_intestine(5)|lung(34)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)	47	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.0168)			AAGACAGCGGTCATAAGCCAT	0.507																																					p.D121G		Atlas-SNP	.											OR6F1,NS,carcinoma,0,1	OR6F1	88	.	0			c.A362G						.						83	80	81					1																	247875696		2203	4300	6503	SO:0001583	missense	343169	exon1			CAGCGGTCATAAG	BK004460	CCDS31095.1	1q44	2012-08-09			ENSG00000169214	ENSG00000169214		"GPCR / Class A : Olfactory receptors"	15027	protein-coding gene	gene with protein product							Standard	NM_001005286		Approved	OST731	uc001idj.1	Q8NGZ6	OTTHUMG00000040213	ENST00000302084.2:c.362A>G	chr1.hg19:g.247875696T>C	ENSP00000305640:p.Asp121Gly	101.0	0.0		100.0	4.0	NM_001005286	B2RNV6|Q6IF02|Q96R39	Missense_Mutation	SNP	ENST00000302084.2	hg19	CCDS31095.1	.	.	.	.	.	.	.	.	.	.	T	18.53	3.643734	0.67244	.	.	ENSG00000169214	ENST00000302084	T	0.18174	2.23	3.99	3.99	0.46301	GPCR, rhodopsin-like superfamily (1);	0.147363	0.31177	N	0.008112	T	0.44159	0.1280	H	0.97491	4.015	0.47905	D	0.999546	P	0.52316	0.952	P	0.49477	0.612	T	0.64765	-0.6330	10	0.87932	D	0	-36.9646	12.1482	0.54036	0.0:0.0:0.0:1.0	.	121	Q8NGZ6	OR6F1_HUMAN	G	121	ENSP00000305640:D121G	ENSP00000305640:D121G	D	-	2	0	OR6F1	245942319	1.000000	0.71417	0.455000	0.27031	0.597000	0.36814	6.609000	0.74173	1.793000	0.52555	0.482000	0.46254	GAC	.	.		0.507	OR6F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096870.1	NM_001005286		C	247875696	T	C	247875696	3	2	260	1	0	0	0	0	1	0	0	0	11210	1667	58	2	568	2	OR6F1	1	247875696	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	10209068	247875696	1374925	78	37323										
TPO	7173	hgsc.bcm.edu	37	chr2	1440149	1440149	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggcccatcacaggagcttgcAacaacaggtattgtttgtgg	12	9	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:1440149A>G	ENST00000345913.4	+	5	566	c.475A>G	c.(475-477)Aac>Gac	p.N159D	TPO_ENST00000349624.3_Missense_Mutation_p.N159D|TPO_ENST00000497517.2_Intron|TPO_ENST00000382201.3_Missense_Mutation_p.N159D|TPO_ENST00000346956.3_Missense_Mutation_p.N159D|TPO_ENST00000539820.1_Missense_Mutation_p.N159D|TPO_ENST00000382198.1_Missense_Mutation_p.N159D|TPO_ENST00000337415.3_Missense_Mutation_p.N159D|TPO_ENST00000329066.4_Missense_Mutation_p.N159D|TPO_ENST00000382269.3_Missense_Mutation_p.N159D	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	159					cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	AGGAGCTTGCAACAACAGGTA	0.458																																					p.N159D		Atlas-SNP	.											.	TPO	224	.	0			c.A475G						.						122	119	120					2																	1440149		2203	4300	6503	SO:0001583	missense	7173	exon5			GCTTGCAACAACA		CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.475A>G	chr2.hg19:g.1440149A>G	ENSP00000318820:p.Asn159Asp	195.0	0.0		94.0	4.0	NM_175719	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	hg19	CCDS1643.1	.	.	.	.	.	.	.	.	.	.	A	16.55	3.155631	0.57259	.	.	ENSG00000115705	ENST00000382269;ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000539820;ENST00000329066;ENST00000382201;ENST00000423320;ENST00000382198;ENST00000422464	T;D;D;D;D;T;D;D;D;D;D	0.84730	0.41;-1.89;-1.89;-1.89;-1.89;0.41;-1.89;-1.89;-1.84;-1.89;-1.89	5.14	5.14	0.70334	.	0.042972	0.85682	D	0.000000	D	0.94823	0.8328	H	0.97758	4.07	0.31131	N	0.707749	D;D;D;D;D	0.89917	0.996;0.987;1.0;1.0;0.997	D;P;D;D;D	0.97110	0.913;0.856;1.0;1.0;0.948	D	0.94406	0.7627	10	0.72032	D	0.01	-21.2821	12.4759	0.55814	1.0:0.0:0.0:0.0	.	159;159;159;159;159	P07202-4;P07202-5;E9PFM6;P07202-2;P07202	.;.;.;.;PERT_HUMAN	D	159;159;159;159;159;159;159;159;159;159;88	ENSP00000371704:N159D;ENSP00000337263:N159D;ENSP00000318820:N159D;ENSP00000263886:N159D;ENSP00000332044:N159D;ENSP00000444840:N159D;ENSP00000329869:N159D;ENSP00000371636:N159D;ENSP00000390994:N159D;ENSP00000371633:N159D;ENSP00000405788:N88D	ENSP00000329869:N159D	N	+	1	0	TPO	1419156	1.000000	0.71417	1.000000	0.80357	0.307000	0.27823	5.293000	0.65680	1.935000	0.56089	0.260000	0.18958	AAC	.	.		0.458	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547		G	1440149	A	G	1440149	3	3	260	1	0	0	0	0	1	0	0	0	16425	130	5	2	489	2	TPO	2	1440149	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10		1440149	241759224	79	37324										
MYT1L	23040	hgsc.bcm.edu	37	chr2	1915833	1915833	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctgttgacatgcccgcgcccCgtgcagcccggagtggggca	15	15	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:1915833C>A	ENST00000399161.2	-	12	2415	c.1668G>T	c.(1666-1668)acG>acT	p.T556T	MYT1L_ENST00000428368.2_Silent_p.T554T	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	556					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		GCCCGCGCCCCGTGCAGCCCG	0.597																																					p.T554T		Atlas-SNP	.											.	MYT1L	241	.	0			c.G1662T						.						44	47	46					2																	1915833		2049	4220	6269	SO:0001819	synonymous_variant	23040	exon12			GCGCCCCGTGCAG	AF036943	CCDS46222.1	2p25.3	2013-01-10			ENSG00000186487	ENSG00000186487		"Zinc fingers, C2HC-type containing"	7623	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 1"	613084				9373037	Standard	XM_006711862		Approved	KIAA1106, NZF1, ZC2HC4B	uc002qxd.3	Q9UL68	OTTHUMG00000151407	ENST00000399161.2:c.1668G>T	chr2.hg19:g.1915833C>A		110.0	0.0		75.0	4.0	NM_015025	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Silent	SNP	ENST00000399161.2	hg19																																																																																				.	.		0.597	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025		A	1915833	C	A	1915833	2	1	260	1	0	0	0	0	0	0	0	1	10116	639	23	1		1	MYT1L	2	1915833	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	475684	1915833	241283540	80	37325										
KIDINS220	57498	hgsc.bcm.edu	37	chr2	8931198	8931198	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	caagccctttaccttctagtTtcttgagtaagaaagatttc	6	9	2	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:8931198T>C	ENST00000256707.3	-	13	1614	c.1433A>G	c.(1432-1434)aAa>aGa	p.K478R	KIDINS220_ENST00000427284.1_Missense_Mutation_p.K478R|KIDINS220_ENST00000418530.1_Missense_Mutation_p.K436R|KIDINS220_ENST00000319688.5_Missense_Mutation_p.K479R|KIDINS220_ENST00000473731.1_Missense_Mutation_p.K478R	NM_020738.2	NP_065789.1	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate, 220kDa	478	KAP NTPase.				activation of MAPKK activity (GO:0000186)|cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|dendrite morphogenesis (GO:0048813)|in utero embryonic development (GO:0001701)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of neuron projection development (GO:0010976)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|protein complex (GO:0043234)	PDZ domain binding (GO:0030165)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(25)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	60	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					ACCTTCTAGTTTCTTGAGTAA	0.423																																					p.K478R		Atlas-SNP	.											.	KIDINS220	136	.	0			c.A1433G						.						87	82	84					2																	8931198		1853	4085	5938	SO:0001583	missense	57498	exon13			TCTAGTTTCTTGA	AK025528	CCDS42650.1	2p24	2013-01-10			ENSG00000134313	ENSG00000134313		"Ankyrin repeat domain containing"	29508	protein-coding gene	gene with protein product	"ankyrin repeat-rich membrane-spanning protein"	615759				10998417, 10574462	Standard	NM_020738		Approved	ARMS	uc002qzc.2	Q9ULH0	OTTHUMG00000151658	ENST00000256707.3:c.1433A>G	chr2.hg19:g.8931198T>C	ENSP00000256707:p.Lys478Arg	190.0	0.0		98.0	4.0	NM_020738	A1L4N4|Q4VC08|Q6MZU2|Q9H889|Q9H9E4|Q9NT37|Q9UF42	Missense_Mutation	SNP	ENST00000256707.3	hg19	CCDS42650.1	.	.	.	.	.	.	.	.	.	.	T	28.9	4.959034	0.92726	.	.	ENSG00000134313	ENST00000496383;ENST00000541927;ENST00000256707;ENST00000427284;ENST00000418530;ENST00000473731;ENST00000489024;ENST00000319688	T;T;T;T;T;T;T	0.34275	1.37;1.37;1.37;1.37;1.37;1.37;1.37	5.45	5.45	0.79879	KAP P-loop (1);	0.000000	0.85682	D	0.000000	T	0.60392	0.2265	M	0.71581	2.175	0.80722	D	1	D;D;D;D	0.89917	0.992;1.0;0.999;0.999	D;D;D;D	0.91635	0.987;0.997;0.998;0.999	T	0.64542	-0.6383	10	0.87932	D	0	.	15.8249	0.78690	0.0:0.0:0.0:1.0	.	479;479;436;478	B4DK94;E9PH70;Q9ULH0-2;Q9ULH0	.;.;.;KDIS_HUMAN	R	225;162;478;478;436;478;479;479	ENSP00000420364:K225R;ENSP00000256707:K478R;ENSP00000411849:K478R;ENSP00000414923:K436R;ENSP00000418974:K478R;ENSP00000419964:K479R;ENSP00000319947:K479R	ENSP00000256707:K478R	K	-	2	0	KIDINS220	8848649	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.579000	0.82511	2.194000	0.70268	0.533000	0.62120	AAA	.	.		0.423	KIDINS220-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323408.2	NM_020738		C	8931198	T	C	8931198	3	2	260	1	0	0	0	0	1	0	0	0	8280	1841	64	2	3954	2	KIDINS220	2	8931198	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	7015365	8931198	234268175	81	37326										
ODC1	4953	hgsc.bcm.edu	37	chr2	10582278	10582278	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acggaaagtatttgtccaacGctgggttgattacgccggtg	13	8	0	1	rs375952999		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:10582278G>T	ENST00000234111.4	-	9	1283	c.773C>A	c.(772-774)gCg>gAg	p.A258E	ODC1_ENST00000446285.1_5'Flank|ODC1_ENST00000405333.1_Missense_Mutation_p.A258E	NM_002539.1	NP_002530.1	P11926	DCOR_HUMAN	ornithine decarboxylase 1	258					cellular nitrogen compound metabolic process (GO:0034641)|kidney development (GO:0001822)|polyamine metabolic process (GO:0006595)|positive regulation of cell proliferation (GO:0008284)|putrescine biosynthetic process from ornithine (GO:0033387)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|response to virus (GO:0009615)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ornithine decarboxylase activity (GO:0004586)|protein homodimerization activity (GO:0042803)			NS(1)|central_nervous_system(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|skin(3)	19	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.161)	Spermine(DB00127)	TTTGTCCAACGCTGGGTTGAT	0.458																																					p.A258E		Atlas-SNP	.											ODC1,NS,carcinoma,+1,1	ODC1	40	.	0			c.C773A						.						62	64	64					2																	10582278		2203	4300	6503	SO:0001583	missense	4953	exon9			TCCAACGCTGGGT		CCDS1672.1	2p25	2012-10-02			ENSG00000115758	ENSG00000115758	4.1.1.17		8109	protein-coding gene	gene with protein product		165640					Standard	NM_002539		Approved	ODC	uc002rao.1	P11926	OTTHUMG00000090450	ENST00000234111.4:c.773C>A	chr2.hg19:g.10582278G>T	ENSP00000234111:p.Ala258Glu	177.0	1.0		116.0	5.0	NM_002539	Q53TU3|Q6LDS9	Missense_Mutation	SNP	ENST00000234111.4	hg19	CCDS1672.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.202879	0.79127	.	.	ENSG00000115758	ENST00000234111;ENST00000405333;ENST00000537630	T;T	0.53857	0.6;0.6	5.95	5.95	0.96441	Orn/DAP/Arg decarboxylase 2, N-terminal (1);Alanine racemase/group IV decarboxylase, C-terminal (1);	0.095755	0.64402	D	0.000001	T	0.78585	0.4306	M	0.88570	2.965	0.80722	D	1	D	0.62365	0.991	D	0.70935	0.971	T	0.81031	-0.1117	10	0.72032	D	0.01	.	20.3747	0.98911	0.0:0.0:1.0:0.0	.	258	P11926	DCOR_HUMAN	E	258;258;129	ENSP00000234111:A258E;ENSP00000385333:A258E	ENSP00000234111:A258E	A	-	2	0	ODC1	10499729	1.000000	0.71417	0.939000	0.37840	0.159000	0.22180	7.968000	0.87980	2.817000	0.96982	0.563000	0.77884	GCG	.	.		0.458	ODC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206896.2			T	10582278	G	T	10582278	3	4	260	1	0	0	0	0	1	0	0	0	10834	1087	38	1	628	1	ODC1	2	10582278	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	1651080	10582278	232617095	82	37327										
GREB1	9687	hgsc.bcm.edu	37	chr2	11770126	11770126	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctcttactccatgctaggagAggagatccagctgcacttca	9	12	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:11770126A>G	ENST00000381486.2	+	26	4802	c.4502A>G	c.(4501-4503)gAg>gGg	p.E1501G	GREB1_ENST00000234142.5_Missense_Mutation_p.E1501G|GREB1_ENST00000396123.1_Missense_Mutation_p.E499G	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1501						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		ATGCTAGGAGAGGAGATCCAG	0.587																																					p.E1501G	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											.	GREB1	308	.	0			c.A4502G						.						131	130	131					2																	11770126		2114	4244	6358	SO:0001583	missense	9687	exon26			TAGGAGAGGAGAT		CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"gene regulated by estrogen in breast cancer"	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.4502A>G	chr2.hg19:g.11770126A>G	ENSP00000370896:p.Glu1501Gly	206.0	0.0		116.0	7.0	NM_014668	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	hg19	CCDS42655.1	.	.	.	.	.	.	.	.	.	.	A	25.6	4.659369	0.88154	.	.	ENSG00000196208	ENST00000381486;ENST00000234142;ENST00000396123	T;T;T	0.58652	0.32;0.32;0.32	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.75309	0.3832	M	0.74647	2.275	0.80722	D	1	D	0.76494	0.999	D	0.69824	0.966	T	0.78679	-0.2110	10	0.72032	D	0.01	-36.3023	15.6154	0.76764	1.0:0.0:0.0:0.0	.	1501	Q4ZG55	GREB1_HUMAN	G	1501;1501;499	ENSP00000370896:E1501G;ENSP00000234142:E1501G;ENSP00000379429:E499G	ENSP00000234142:E1501G	E	+	2	0	GREB1	11687577	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	6.993000	0.76245	2.092000	0.63282	0.496000	0.49642	GAG	.	.		0.587	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668		G	11770126	A	G	11770126	3	3	260	1	0	0	0	0	1	0	0	0	6769	304	11	2	4708	2	GREB1	2	11770126	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1187848	11770126	231429247	83	37328										
NBAS	51594	hgsc.bcm.edu	37	chr2	15613387	15613387	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aacgttgaccgctgacttccTccactgcctctgatatacaa	6	14	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:15613387T>C	ENST00000281513.5	-	16	1709	c.1684A>G	c.(1684-1686)Agg>Ggg	p.R562G	NBAS_ENST00000441750.1_Missense_Mutation_p.R562G	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	562					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				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						GCTGACTTCCTCCACTGCCTC	0.368																																					p.R562G		Atlas-SNP	.											.	NBAS	246	.	0			c.A1684G						.						122	112	115					2																	15613387		2203	4300	6503	SO:0001583	missense	51594	exon16			ACTTCCTCCACTG	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.1684A>G	chr2.hg19:g.15613387T>C	ENSP00000281513:p.Arg562Gly	145.0	0.0		90.0	5.0	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	hg19	CCDS1685.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.985401	0.74474	.	.	ENSG00000151779	ENST00000441750;ENST00000281513	T;T	0.12147	2.71;2.86	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.37183	0.0994	M	0.66939	2.045	0.39949	D	0.974519	D	0.76494	0.999	D	0.80764	0.994	T	0.18967	-1.0320	10	0.87932	D	0	.	16.1699	0.81801	0.0:0.0:0.0:1.0	.	562	A2RRP1	NBAS_HUMAN	G	562	ENSP00000413201:R562G;ENSP00000281513:R562G	ENSP00000281513:R562G	R	-	1	2	NBAS	15530838	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.173000	0.58249	2.217000	0.71921	0.533000	0.62120	AGG	.	.		0.368	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		C	15613387	T	C	15613387	3	2	260	1	0	0	0	0	1	0	0	0	10195	1550	54	2	5579	2	NBAS	2	15613387	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	3843261	15613387	227585986	84	37329										
APOB	338	hgsc.bcm.edu	37	chr2	21247880	21247880	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agctggaggtcatggagactGgcaaaaccaagctcctctcc	11	12	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:21247880G>T	ENST00000233242.1	-	16	2488	c.2361C>A	c.(2359-2361)gcC>gcA	p.A787A	APOB_ENST00000399256.4_Silent_p.A787A	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	787					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)	p.A787A(1)		NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CATGGAGACTGGCAAAACCAA	0.552																																					p.A787A		Atlas-SNP	.											APOB,NS,carcinoma,-1,1	APOB	761	.	1	Substitution - coding silent(1)	lung(1)	c.C2361A						.						88	91	90					2																	21247880		2203	4300	6503	SO:0001819	synonymous_variant	338	exon16			GAGACTGGCAAAA	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.2361C>A	chr2.hg19:g.21247880G>T		79.0	0.0		53.0	3.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Silent	SNP	ENST00000233242.1	hg19	CCDS1703.1																																																																																			.	.		0.552	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			T	21247880	G	T	21247880	2	4	260	1	0	0	0	0	0	0	0	1	785	1335	47	3		3	APOB	2	21247880	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	5634493	21247880	221951493	85	37330										
C2orf39	92749	hgsc.bcm.edu	37	chr2	26652560	26652560	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acagtcagatgacatctgccTgcttctggagcggatggaag	13	9	3	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:26652560T>C	ENST00000288710.2	+	5	679	c.605T>C	c.(604-606)cTg>cCg	p.L202P		NM_145038.2	NP_659475.2	Q96MC2	DRC1_HUMAN	dynein regulatory complex subunit 1	202					axonemal dynein complex assembly (GO:0070286)|bacterial-type flagellum-dependent cell motility (GO:0071973)|cilium-dependent cell motility (GO:0060285)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)											GACATCTGCCTGCTTCTGGAG	0.423																																					p.L202P		Atlas-SNP	.											.	CCDC164	84	.	0			c.T605C						.						126	125	126					2																	26652560		2203	4300	6503	SO:0001583	missense	92749	exon5			TCTGCCTGCTTCT	AL833892	CCDS1723.1	2p23.3	2014-07-18	2014-07-18	2013-03-14	ENSG00000157856	ENSG00000157856			24245	protein-coding gene	gene with protein product		615288	"chromosome 2 open reading frame 39", "coiled-coil domain containing 164", "dynein regulatory complex subunit 1 homolog (Chlamydomonas)"	C2orf39, CCDC164		23354437	Standard	NM_145038		Approved	MGC16372, FLJ32660, CILD21	uc002rhg.2	Q96MC2	OTTHUMG00000125531	ENST00000288710.2:c.605T>C	chr2.hg19:g.26652560T>C	ENSP00000288710:p.Leu202Pro	137.0	0.0		94.0	4.0	NM_145038	A8K1N8|Q53R91|Q53TA3|Q8NDI5	Missense_Mutation	SNP	ENST00000288710.2	hg19	CCDS1723.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.206193	0.79127	.	.	ENSG00000157856	ENST00000288710	T	0.16597	2.33	5.35	5.35	0.76521	.	0.152498	0.43919	D	0.000503	T	0.43787	0.1263	M	0.83953	2.67	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.38156	-0.9674	10	0.30854	T	0.27	-5.8978	14.3213	0.66489	0.0:0.0:0.0:1.0	.	202	Q96MC2	CC164_HUMAN	P	202	ENSP00000288710:L202P	ENSP00000288710:L202P	L	+	2	0	CCDC164	26506064	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.379000	0.73154	2.027000	0.59764	0.460000	0.39030	CTG	.	.		0.423	DRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246862.1	NM_145038		C	26652560	T	C	26652560	3	2	260	1	0	0	0	0	1	0	0	0	2166	1580	55	2	623	2	C2orf39	2	26652560	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	5404680	26652560	216546813	86	37331										
AGBL5	60509	hgsc.bcm.edu	37	chr2	27276891	27276891	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggaactgctaaaccagctagAccagcgctttccggagaacc	10	13	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:27276891A>G	ENST00000360131.4	+	4	674	c.515A>G	c.(514-516)gAc>gGc	p.D172G	AGBL5_ENST00000323064.8_Missense_Mutation_p.D172G|RP11-503P10.1_ENST00000607407.1_RNA	NM_021831.5	NP_068603.4	Q8NDL9	CBPC5_HUMAN	ATP/GTP binding protein-like 5	172					protein branching point deglutamylation (GO:0035611)|protein deglutamylation (GO:0035608)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	28	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AACCAGCTAGACCAGCGCTTT	0.567																																					p.D172G		Atlas-SNP	.											.	AGBL5	126	.	0			c.A515G						.						172	168	169					2																	27276891		2203	4300	6503	SO:0001583	missense	60509	exon4			AGCTAGACCAGCG	BC007415	CCDS1732.3, CCDS42665.1	2p23.3	2014-06-23			ENSG00000084693	ENSG00000084693			26147	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 5"	615900				24022482	Standard	NM_001035507		Approved	FLJ21839, CCP5	uc002rie.3	Q8NDL9	OTTHUMG00000128406	ENST00000360131.4:c.515A>G	chr2.hg19:g.27276891A>G	ENSP00000353249:p.Asp172Gly	140.0	0.0		89.0	5.0	NM_021831	A2VDI7|B7WPG9|B7Z7I7|D6W548|Q53SW0|Q53SZ0|Q96IK8|Q9H6V0|Q9H8P8	Missense_Mutation	SNP	ENST00000360131.4	hg19	CCDS1732.3	.	.	.	.	.	.	.	.	.	.	A	20.6	4.018858	0.75275	.	.	ENSG00000084693	ENST00000323064;ENST00000360131	T;T	0.16597	2.37;2.33	5.78	4.62	0.57501	.	0.123176	0.64402	N	0.000001	T	0.39835	0.1093	M	0.76574	2.34	0.53688	D	0.999973	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.999	T	0.15292	-1.0442	9	.	.	.	-5.3169	10.9433	0.47285	0.9254:0.0:0.0746:0.0	.	172;172;172	Q8NDL9;Q8NDL9-3;Q8NDL9-2	CBPC5_HUMAN;.;.	G	172	ENSP00000323681:D172G;ENSP00000353249:D172G	.	D	+	2	0	AGBL5	27130395	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.749000	0.91619	1.020000	0.39573	0.459000	0.35465	GAC	.	.		0.567	AGBL5-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000309033.1	NM_021831		G	27276891	A	G	27276891	3	3	260	1	0	0	0	0	1	0	0	0	378	275	10	2	525	2	AGBL5	2	27276891	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	624331	27276891	215922482	87	37332										
PLB1	151056	hgsc.bcm.edu	37	chr2	28843759	28843759	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tctaaagacattctgaagaaGttcaacccttacctccttgg	6	11	3	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:28843759G>T	ENST00000327757.5	+	49	3485	c.3441G>T	c.(3439-3441)aaG>aaT	p.K1147N	PLB1_ENST00000541605.1_Missense_Mutation_p.K112N|PLB1_ENST00000422425.2_Missense_Mutation_p.K1136N	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	1147	4 X 308-326 AA approximate repeats.				glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(31)|ovary(6)|prostate(1)|skin(7)|stomach(2)	69	Acute lymphoblastic leukemia(172;0.155)					TTCTGAAGAAGTTCAACCCTT	0.562																																					p.K1147N		Atlas-SNP	.											.	PLB1	255	.	0			c.G3441T						.						100	97	98					2																	28843759		2203	4300	6503	SO:0001583	missense	151056	exon49			GAAGAAGTTCAAC		CCDS33168.1, CCDS54340.1	2p23.3	2014-03-14			ENSG00000163803	ENSG00000163803	3.1.1.4, 3.1.1.5		30041	protein-coding gene	gene with protein product		610179				12150957	Standard	NM_153021		Approved	PLB, FLJ30866	uc002rmb.2	Q6P1J6	OTTHUMG00000152014	ENST00000327757.5:c.3441G>T	chr2.hg19:g.28843759G>T	ENSP00000330442:p.Lys1147Asn	124.0	0.0		57.0	4.0	NM_153021	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Missense_Mutation	SNP	ENST00000327757.5	hg19	CCDS33168.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.65|18.65	3.668687|3.668687	0.67814|0.67814	.|.	.|.	ENSG00000163803|ENSG00000163803	ENST00000327757;ENST00000422425;ENST00000541605|ENST00000404858	T;T;T|.	0.14266|.	2.52;2.52;2.52|.	5.65|5.65	3.61|3.61	0.41365|0.41365	Esterase, SGNH hydrolase-type (1);Esterase, SGNH hydrolase-type, subgroup (1);Lipase, GDSL (1);|.	0.062853|.	0.64402|.	D|.	0.000012|.	T|T	0.69333|0.69333	0.3099|0.3099	M|M	0.86573|0.86573	2.825|2.825	0.40556|0.40556	D|D	0.981162|0.981162	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	0.999;1.0|.	T|T	0.71494|0.71494	-0.4576|-0.4576	10|5	0.34782|.	T|.	0.22|.	-27.5428|-27.5428	5.4347|5.4347	0.16474|0.16474	0.2731:0.0:0.7269:0.0|0.2731:0.0:0.7269:0.0	.|.	1136;1147|.	Q6P1J6-3;Q6P1J6|.	.;PLB1_HUMAN|.	N|I	1147;1136;112|1135	ENSP00000330442:K1147N;ENSP00000416440:K1136N;ENSP00000437426:K112N|.	ENSP00000330442:K1147N|.	K|S	+|+	3|2	2|0	PLB1|PLB1	28697263|28697263	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	1.986000|1.986000	0.40677|0.40677	1.410000|1.410000	0.46936|0.46936	0.556000|0.556000	0.70494|0.70494	AAG|AGT	.	.		0.562	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2			T	28843759	G	T	28843759	3	4	260	1	0	0	0	0	1	0	0	0	12033	1020	36	3	3668	3	PLB1	2	28843759	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	1566868	28843759	214355614	88	37333										
CRIM1	51232	hgsc.bcm.edu	37	chr2	36771541	36771541	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	atgtatgtcccagaaccaacCaatatacccattgagaagac	6	11	0	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:36771541C>A	ENST00000280527.2	+	15	3013	c.2646C>A	c.(2644-2646)acC>acA	p.T882T	AC007401.2_ENST00000406220.1_Intron	NM_016441.2	NP_057525.1	Q9NZV1	CRIM1_HUMAN	cysteine rich transmembrane BMP regulator 1 (chordin-like)	882					insulin-like growth factor receptor signaling pathway (GO:0048009)|nervous system development (GO:0007399)|regulation of cell growth (GO:0001558)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	insulin-like growth factor-activated receptor activity (GO:0005010)|PDZ domain binding (GO:0030165)|serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(15)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	45		all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154)				CAGAACCAACCAATATACCCA	0.438																																					p.T882T		Atlas-SNP	.											.	CRIM1	88	.	0			c.C2646A						.						129	128	128					2																	36771541		2203	4300	6503	SO:0001819	synonymous_variant	51232	exon15			ACCAACCAATATA	AF168681	CCDS1783.1	2p21	2010-06-29	2005-07-25		ENSG00000150938	ENSG00000150938			2359	protein-coding gene	gene with protein product		606189	"cysteine-rich motor neuron 1"	S52		10642437	Standard	NM_016441		Approved		uc002rpd.3	Q9NZV1	OTTHUMG00000099419	ENST00000280527.2:c.2646C>A	chr2.hg19:g.36771541C>A		119.0	0.0		90.0	5.0	NM_016441	Q2M2G4|Q59GH0|Q7LCQ5|Q9H318	Silent	SNP	ENST00000280527.2	hg19	CCDS1783.1																																																																																			.	.		0.438	CRIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216878.2	NM_016441		A	36771541	C	A	36771541	2	1	260	1	0	0	0	0	0	0	0	1	3875	581	21	3		3	CRIM1	2	36771541	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	7927782	36771541	206427832	89	37334										
HEATR5B	54497	hgsc.bcm.edu	37	chr2	37227915	37227915	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgctgtgtctttcaatattcTtgcaattaagaacagaattg	7	6	3	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:37227915T>C	ENST00000233099.5	-	33	5454	c.5359A>G	c.(5359-5361)Aga>Gga	p.R1787G	HEATR5B_ENST00000354531.2_Missense_Mutation_p.R1698G	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	1787						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				TTCAATATTCTTGCAATTAAG	0.363																																					p.R1787G		Atlas-SNP	.											.	HEATR5B	185	.	0			c.A5359G						.						92	101	98					2																	37227915		2203	4300	6503	SO:0001583	missense	54497	exon33			ATATTCTTGCAAT	AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.5359A>G	chr2.hg19:g.37227915T>C	ENSP00000233099:p.Arg1787Gly	174.0	0.0		100.0	4.0	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Missense_Mutation	SNP	ENST00000233099.5	hg19	CCDS33181.1	.	.	.	.	.	.	.	.	.	.	T	3.318	-0.139332	0.06669	.	.	ENSG00000008869	ENST00000233099;ENST00000354531	T;T	0.65364	1.18;-0.15	5.03	5.03	0.67393	Armadillo-like helical (1);Armadillo-type fold (1);	0.047823	0.85682	D	0.000000	T	0.21761	0.0524	N	0.00272	-1.73	0.24303	N	0.995111	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.19353	-1.0308	10	0.02654	T	1	-19.8367	11.4357	0.50066	0.0:0.0:0.1508:0.8492	.	1787;1787	Q9P2D3;B9EK47	HTR5B_HUMAN;.	G	1787;1698	ENSP00000233099:R1787G;ENSP00000346531:R1698G	ENSP00000233099:R1787G	R	-	1	2	HEATR5B	37081419	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	2.429000	0.44758	1.887000	0.54652	0.482000	0.46254	AGA	.	.		0.363	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024		C	37227915	T	C	37227915	3	2	260	1	0	0	0	0	1	0	0	0	7041	1617	56	2	872	2	HEATR5B	2	37227915	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	456374	37227915	205971458	90	37335										
DHX57	90957	hgsc.bcm.edu	37	chr2	39042772	39042772	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tatccgataacagttccgtgAattgtcgtttgaggctggcc	11	9	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:39042772A>T	ENST00000295373.6	-	20	3623	c.3497T>A	c.(3496-3498)tTc>tAc	p.F1166Y		NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	1166							ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(20)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	62		all_hematologic(82;0.248)				CAGTTCCGTGAATTGTCGTTT	0.438																																					p.F1166Y	Melanoma(191;1090 2095 4375 23729 47341)	Atlas-SNP	.											.	DHX57	127	.	0			c.T3497A						.						141	133	136					2																	39042772		2203	4300	6503	SO:0001583	missense	90957	exon20			TCCGTGAATTGTC	AF070590	CCDS1800.1	2p22.3	2008-02-05			ENSG00000163214	ENSG00000163214		"DEAH-boxes"	20086	protein-coding gene	gene with protein product							Standard	NM_198963		Approved	DDX57	uc002rrf.3	Q6P158	OTTHUMG00000102103	ENST00000295373.6:c.3497T>A	chr2.hg19:g.39042772A>T	ENSP00000295373:p.Phe1166Tyr	159.0	0.0		95.0	14.0	NM_198963	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	Missense_Mutation	SNP	ENST00000295373.6	hg19	CCDS1800.1	.	.	.	.	.	.	.	.	.	.	A	17.07	3.294992	0.60086	.	.	ENSG00000163214	ENST00000295373	T	0.03035	4.07	5.29	5.29	0.74685	Domain of unknown function DUF1605 (1);	0.000000	0.56097	D	0.000026	T	0.09423	0.0232	L	0.28054	0.825	0.80722	D	1	D;B	0.76494	0.999;0.309	D;B	0.80764	0.994;0.23	T	0.50642	-0.8804	10	0.22109	T	0.4	.	15.5408	0.76043	1.0:0.0:0.0:0.0	.	1166;558	Q6P158;Q59G60	DHX57_HUMAN;.	Y	1166	ENSP00000295373:F1166Y	ENSP00000295373:F1166Y	F	-	2	0	DHX57	38896276	1.000000	0.71417	1.000000	0.80357	0.714000	0.41099	8.843000	0.92142	2.120000	0.65058	0.460000	0.39030	TTC	.	.		0.438	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219940.2	NM_145646		T	39042772	A	T	39042772	3	4	260	1	0	0	0	0	1	0	0	0	4515	246	9	4	683	4	DHX57	2	39042772	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1814857	39042772	204156601	91	37336										
C2orf34	79823	hgsc.bcm.edu	37	chr2	44931461	44931461	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggttttggcttactactgccTcaagcacaataatatattca	6	9	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:44931461T>C	ENST00000378494.3	+	4	460	c.416T>C	c.(415-417)cTc>cCc	p.L139P		NM_024766.4	NP_079042.1	Q7Z624	CMKMT_HUMAN	calmodulin-lysine N-methyltransferase	139						Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	calmodulin-lysine N-methyltransferase activity (GO:0018025)			breast(2)|large_intestine(3)|lung(5)	10						TACTACTGCCTCAAGCACAAT	0.343																																					p.L139P		Atlas-SNP	.											.	CAMKMT	20	.	0			c.T416C						.						97	93	95					2																	44931461		2203	4300	6503	SO:0001583	missense	79823	exon4			ACTGCCTCAAGCA		CCDS1820.1	2p21	2011-06-22	2011-03-10	2011-03-10	ENSG00000143919	ENSG00000143919	2.1.1.60		26276	protein-coding gene	gene with protein product	"CaM KMT"	609559	"chromosome 2 open reading frame 34"	C2orf34		20975703	Standard	NM_024766		Approved	CLNMT	uc002rum.3	Q7Z624	OTTHUMG00000128761	ENST00000378494.3:c.416T>C	chr2.hg19:g.44931461T>C	ENSP00000367755:p.Leu139Pro	104.0	0.0		85.0	4.0	NM_024766	Q4ZG15|Q53SS6|Q8N6P5|Q9H5G8	Missense_Mutation	SNP	ENST00000378494.3	hg19	CCDS1820.1	.	.	.	.	.	.	.	.	.	.	T	18.12	3.553946	0.65425	.	.	ENSG00000143919	ENST00000378494	T	0.07327	3.2	5.08	5.08	0.68730	.	0.070287	0.64402	D	0.000016	T	0.32526	0.0832	M	0.85859	2.78	0.80722	D	1	D	0.76494	0.999	D	0.72982	0.979	T	0.14980	-1.0453	10	0.56958	D	0.05	-1.1434	15.1728	0.72888	0.0:0.0:0.0:1.0	.	139	Q7Z624	CMKMT_HUMAN	P	139	ENSP00000367755:L139P	ENSP00000367755:L139P	L	+	2	0	CAMKMT	44784965	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	6.879000	0.75572	2.040000	0.60383	0.477000	0.44152	CTC	.	.		0.343	CAMKMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250678.2	NM_024766		C	44931461	T	C	44931461	3	2	260	1	0	0	0	0	1	0	0	0	2165	1551	54	2	430	2	C2orf34	2	44931461	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	5888689	44931461	198267912	92	37337										
EPCAM	4072	hgsc.bcm.edu	37	chr2	47600664	47600664	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgaataataatcgtcaatgcCagtgtacttcagttggtgca	9	7	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:47600664C>T	ENST00000263735.4	+	2	497	c.139C>T	c.(139-141)Cag>Tag	p.Q47*	EPCAM_ENST00000405271.1_Nonsense_Mutation_p.Q75*	NM_002354.2	NP_002345.2	P16422	EPCAM_HUMAN	epithelial cell adhesion molecule	47					negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction involved in regulation of gene expression (GO:0023019)|stem cell differentiation (GO:0048863)|ureteric bud development (GO:0001657)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	protein complex binding (GO:0032403)	p.0?(2)|p.?(1)		endometrium(3)|large_intestine(1)|liver(2)|lung(7)|skin(1)|stomach(1)	15						TCGTCAATGCCAGTGTACTTC	0.318																																					p.Q47X		Atlas-SNP	.											.	EPCAM	27	.	3	Whole gene deletion(2)|Unknown(1)	haematopoietic_and_lymphoid_tissue(3)	c.C139T						.						96	90	92					2																	47600664		2203	4300	6503	SO:0001587	stop_gained	4072	exon2			CAATGCCAGTGTA	M33011	CCDS1833.1	2p21	2014-09-17	2008-12-16	2008-12-16	ENSG00000119888	ENSG00000119888		"CD molecules"	11529	protein-coding gene	gene with protein product		185535	"antigen identified by monoclonal antibody AUA1", "tumor-associated calcium signal transducer 1"	M4S1, MIC18, TACSTD1		8382772, 11306819	Standard	NM_002354		Approved	Ly74, TROP1, GA733-2, EGP34, EGP40, EGP-2, KSA, CD326, Ep-CAM, HEA125, KS1/4, MK-1, MH99, MOC31, 323/A3, 17-1A, TACST-1, CO-17A, ESA	uc002rvx.3	P16422	OTTHUMG00000128853	ENST00000263735.4:c.139C>T	chr2.hg19:g.47600664C>T	ENSP00000263735:p.Gln47*	135.0	0.0		94.0	4.0	NM_002354	P18180|Q6FG26|Q6FG49|Q96C47|Q9UCD0	Nonsense_Mutation	SNP	ENST00000263735.4	hg19	CCDS1833.1	.	.	.	.	.	.	.	.	.	.	C	15.45	2.837418	0.50951	.	.	ENSG00000119888	ENST00000405271;ENST00000263735;ENST00000419334	.	.	.	4.93	3.08	0.35506	.	0.809444	0.11817	N	0.526590	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33141	T	0.24	-5.2619	9.6234	0.39734	0.1547:0.6805:0.1648:0.0	.	.	.	.	X	75;47;123	.	ENSP00000263735:Q47X	Q	+	1	0	EPCAM	47454168	0.997000	0.39634	1.000000	0.80357	0.354000	0.29330	0.925000	0.28791	0.635000	0.30488	0.655000	0.94253	CAG	.	.		0.318	EPCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250792.2			T	47600664	C	T	47600664	4	4	260	1	0	0	0	0	0	1	0	0	5164	595	21	3	145	3	EPCAM	2	47600664	Nonsense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	2669203	47600664	195598709	93	37338										
SPTBN1	6711	hgsc.bcm.edu	37	chr2	54871648	54871648	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctagacaaatggctgcacggCctggagagtcagattcagtc	12	10	2	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:54871648C>A	ENST00000356805.4	+	20	4475	c.4194C>A	c.(4192-4194)ggC>ggA	p.G1398G	SPTBN1_ENST00000333896.5_Silent_p.G1385G	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	1398					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			GGCTGCACGGCCTGGAGAGTC	0.498																																					p.G1398G		Atlas-SNP	.											.	SPTBN1	378	.	0			c.C4194A						.						87	84	85					2																	54871648		2203	4300	6503	SO:0001819	synonymous_variant	6711	exon20			GCACGGCCTGGAG		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"Pleckstrin homology (PH) domain containing"	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.4194C>A	chr2.hg19:g.54871648C>A		201.0	0.0		91.0	4.0	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Silent	SNP	ENST00000356805.4	hg19	CCDS33198.1																																																																																			.	.		0.498	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			A	54871648	C	A	54871648	2	1	260	1	0	0	0	0	0	0	0	1	15134	726	26	3		3	SPTBN1	2	54871648	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	7270984	54871648	188327725	94	37339										
SMEK2	57223	hgsc.bcm.edu	37	chr2	55844327	55844327	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acatccccttgagctcctccAcgtaagtggaggagacgtgc	11	13	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:55844327A>G	ENST00000345102.5	-	1	396	c.95T>C	c.(94-96)gTg>gCg	p.V32A	SMEK2_ENST00000477749.1_5'UTR|RP11-554J4.1_ENST00000608113.1_RNA|SMEK2_ENST00000407823.3_Missense_Mutation_p.V32A|SMEK2_ENST00000272313.5_Missense_Mutation_p.V32A	NM_001122964.1	NP_001116436	Q5MIZ7	P4R3B_HUMAN	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	32	WH1.				positive regulation of gluconeogenesis (GO:0045722)|protein dephosphorylation (GO:0006470)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)				kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	16			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			GAGCTCCTCCACGTAAGTGGA	0.602																																					p.V32A		Atlas-SNP	.											.	SMEK2	86	.	0			c.T95C						.						71	66	67					2																	55844327		2203	4300	6503	SO:0001583	missense	57223	exon1			TCCTCCACGTAAG	AB037808	CCDS1855.1, CCDS46289.1, CCDS62913.1	2p16.1	2008-09-15			ENSG00000138041				29267	protein-coding gene	gene with protein product		610352				16085932, 18614045	Standard	NM_001122964		Approved	PSY2, FLFL2, KIAA1387, FLJ31474	uc002rzc.3	Q5MIZ7	OTTHUMG00000129336	ENST00000345102.5:c.95T>C	chr2.hg19:g.55844327A>G	ENSP00000339769:p.Val32Ala	175.0	0.0		122.0	5.0	NM_001122964	Q6P9B0|Q86XB8|Q9BQJ0|Q9BRK2|Q9H913|Q9P2G0	Missense_Mutation	SNP	ENST00000345102.5	hg19	CCDS46289.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.272377	0.80580	.	.	ENSG00000138041	ENST00000272313;ENST00000407823;ENST00000345102	T;T;T	0.41400	1.0;1.0;1.0	5.19	5.19	0.71726	Pleckstrin homology-type (1);	0.056112	0.64402	D	0.000001	T	0.57489	0.2057	L	0.59436	1.845	0.80722	D	1	P;D;P	0.69078	0.845;0.997;0.925	P;D;P	0.68943	0.561;0.961;0.79	T	0.52193	-0.8608	10	0.20519	T	0.43	-6.8952	15.2232	0.73330	1.0:0.0:0.0:0.0	.	32;32;32	Q5MIZ7-2;Q5MIZ7;Q5MIZ7-3	.;P4R3B_HUMAN;.	A	32	ENSP00000272313:V32A;ENSP00000385912:V32A;ENSP00000339769:V32A	ENSP00000272313:V32A	V	-	2	0	SMEK2	55697831	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.761000	0.91691	2.184000	0.69523	0.533000	0.62120	GTG	.	.		0.602	SMEK2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251483.1	NM_020463		G	55844327	A	G	55844327	3	3	260	1	0	0	0	0	1	0	0	0	14809	159	6	2	2522	2	SMEK2	2	55844327	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	972679	55844327	187355046	95	37340										
USP34	9736	hgsc.bcm.edu	37	chr2	61505341	61505341	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aaagggtggtttgtgtttaaCaacacttgttgcaagcctta	10	6	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:61505341C>T	ENST00000398571.2	-	41	5468	c.5392G>A	c.(5392-5394)Gtt>Att	p.V1798I		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	1798					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			TTGTGTTTAACAACACTTGTT	0.338																																					p.V1798I		Atlas-SNP	.											.	USP34	334	.	0			c.G5392A						.						95	84	87					2																	61505341		1874	4100	5974	SO:0001583	missense	9736	exon41			GTTTAACAACACT	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"Ubiquitin-specific peptidases"	20066	protein-coding gene	gene with protein product		615295	"ubiquitin specific protease 34"			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.5392G>A	chr2.hg19:g.61505341C>T	ENSP00000381577:p.Val1798Ile	131.0	0.0		85.0	4.0	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	hg19	CCDS42686.1	.	.	.	.	.	.	.	.	.	.	T	4.121	0.020752	0.08006	.	.	ENSG00000115464	ENST00000263989;ENST00000398569;ENST00000398571;ENST00000453734	T;T	0.03801	4.03;3.8	5.48	4.32	0.51571	.	0.217163	0.45867	N	0.000322	T	0.03348	0.0097	L	0.27053	0.805	0.22552	N	0.998999	B	0.02656	0.0	B	0.01281	0.0	T	0.48281	-0.9049	10	0.08599	T	0.76	.	8.1971	0.31402	0.0:0.2246:0.0:0.7754	.	1798	Q70CQ2	UBP34_HUMAN	I	1646;1646;1798;76	ENSP00000381577:V1798I;ENSP00000410559:V76I	ENSP00000263989:V1646I	V	-	1	0	USP34	61358845	1.000000	0.71417	0.996000	0.52242	0.905000	0.53344	2.722000	0.47269	0.373000	0.24621	-0.360000	0.07572	GTT	.	.		0.338	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			T	61505341	C	T	61505341	3	4	260	1	0	0	0	0	1	0	0	0	17080	478	17	3	5408	3	USP34	2	61505341	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	5661014	61505341	181694032	96	37341										
CYP26B1	56603	hgsc.bcm.edu	37	chr2	72359670	72359670	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	atcggggtcgaacacgttcaCgtctttgaacacgggcgctg	13	11	2	1	rs370211150		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:72359670C>T	ENST00000001146.2	-	6	1428	c.1225G>A	c.(1225-1227)Gtg>Atg	p.V409M	CYP26B1_ENST00000412253.1_Missense_Mutation_p.V218M|CYP26B1_ENST00000546307.1_Missense_Mutation_p.V334M	NM_001277742.1|NM_019885.2	NP_001264671.1|NP_063938.1	Q9NR63	CP26B_HUMAN	cytochrome P450, family 26, subfamily B, polypeptide 1	409					bone morphogenesis (GO:0060349)|cell fate determination (GO:0001709)|cellular response to retinoic acid (GO:0071300)|cornification (GO:0070268)|embryonic limb morphogenesis (GO:0030326)|establishment of skin barrier (GO:0061436)|male meiosis (GO:0007140)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|oxidation-reduction process (GO:0055114)|positive regulation of gene expression (GO:0010628)|positive regulation of tongue muscle cell differentiation (GO:2001037)|proximal/distal pattern formation (GO:0009954)|retinoic acid catabolic process (GO:0034653)|retinoic acid receptor signaling pathway (GO:0048384)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|tongue morphogenesis (GO:0043587)|vitamin metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|retinoic acid 4-hydroxylase activity (GO:0008401)|retinoic acid binding (GO:0001972)			breast(1)|kidney(3)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)	28						AACACGTTCACGTCTTTGAAC	0.617																																					p.V409M		Atlas-SNP	.											.	CYP26B1	73	.	0			c.G1225A						.	C	MET/VAL	0,4406		0,0,2203	49	43	45		1225	5.1	1	2		45	1,8599	1.2+/-3.3	0,1,4299	no	missense	CYP26B1	NM_019885.2	21	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	409/513	72359670	1,13005	2203	4300	6503	SO:0001583	missense	56603	exon6			CGTTCACGTCTTT		CCDS1919.1, CCDS62934.1	2p12	2006-11-24			ENSG00000003137	ENSG00000003137		"Cytochrome P450s"	20581	protein-coding gene	gene with protein product		605207				10545224	Standard	NM_019885		Approved	P450RAI-2	uc002sih.2	Q9NR63	OTTHUMG00000129756	ENST00000001146.2:c.1225G>A	chr2.hg19:g.72359670C>T	ENSP00000001146:p.Val409Met	206.0	0.0		119.0	5.0	NM_019885	B2R8M7|B7Z2K6|B7Z2P4|B7Z3B8|E4W5W7|Q32MC0|Q53TW1|Q9NP41	Missense_Mutation	SNP	ENST00000001146.2	hg19	CCDS1919.1	.	.	.	.	.	.	.	.	.	.	C	19.48	3.835394	0.71373	0.0	1.16E-4	ENSG00000003137	ENST00000001146;ENST00000412253;ENST00000546307	T;T;T	0.68331	-0.32;-0.32;-0.32	5.12	5.12	0.69794	.	0.120924	0.56097	D	0.000034	T	0.60261	0.2255	L	0.28192	0.835	0.80722	D	1	B;B;B	0.32031	0.352;0.304;0.304	B;B;B	0.37047	0.24;0.227;0.227	T	0.64028	-0.6503	10	0.87932	D	0	-14.8495	17.6654	0.88201	0.0:1.0:0.0:0.0	.	334;392;409	B7Z2K6;B7Z2P4;Q9NR63	.;.;CP26B_HUMAN	M	409;218;334	ENSP00000001146:V409M;ENSP00000401465:V218M;ENSP00000443304:V334M	ENSP00000001146:V409M	V	-	1	0	CYP26B1	72213178	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	3.667000	0.54547	2.837000	0.97791	0.655000	0.94253	GTG	.	.		0.617	CYP26B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251969.1	NM_019885		T	72359670	C	T	72359670	3	4	260	1	0	0	0	0	1	0	0	0	4158	536	19	1	317	1	CYP26B1	2	72359670	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	10854329	72359670	170839703	97	37342										
SMYD5	10322	hgsc.bcm.edu	37	chr2	73446019	73446019	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgtttgccacacagctcatcCggaagggggagaccatcttc	11	12	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:73446019C>T	ENST00000389501.4	+	2	172	c.127C>T	c.(127-129)Cgg>Tgg	p.R43W	SMYD5_ENST00000474652.1_3'UTR	NM_006062.2	NP_006053.2	Q6GMV2	SMYD5_HUMAN	SMYD family member 5	43	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.						metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)	13						ACAGCTCATCCGGAAGGGGGA	0.547																																					p.R43W		Atlas-SNP	.											.	SMYD5	58	.	0			c.C127T						.						92	92	92					2																	73446019		1967	4151	6118	SO:0001583	missense	10322	exon2			CTCATCCGGAAGG	U50383	CCDS33221.2	2p12	2007-02-09	2003-05-14	2003-05-16	ENSG00000135632	ENSG00000135632		"Zinc fingers, MYND-type"	16258	protein-coding gene	gene with protein product			"retinoic acid induced 15"	RAI15		8754834	Standard	NM_006062		Approved	RRG1, NN8-4AG, ZMYND23	uc002siw.2	Q6GMV2	OTTHUMG00000150482	ENST00000389501.4:c.127C>T	chr2.hg19:g.73446019C>T	ENSP00000374152:p.Arg43Trp	224.0	0.0		124.0	6.0	NM_006062	D6W5H3|Q13558	Missense_Mutation	SNP	ENST00000389501.4	hg19	CCDS33221.2	.	.	.	.	.	.	.	.	.	.	C	21.0	4.079060	0.76528	.	.	ENSG00000135632	ENST00000389501;ENST00000443900	D;T	0.81908	-1.55;0.9	5.47	3.49	0.39957	SET domain (2);	0.377311	0.28203	N	0.016215	D	0.86142	0.5862	L	0.54323	1.7	0.39477	D	0.967826	D	0.69078	0.997	P	0.57846	0.828	D	0.88311	0.2956	10	0.87932	D	0	-5.499	13.518	0.61551	0.0:0.7017:0.2983:0.0	.	43	Q6GMV2	SMYD5_HUMAN	W	43;16	ENSP00000374152:R43W;ENSP00000412587:R16W	ENSP00000258100:R43W	R	+	1	2	SMYD5	73299527	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.919000	0.40015	1.360000	0.45960	0.650000	0.86243	CGG	.	.		0.547	SMYD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318301.1	NM_006062		T	73446019	C	T	73446019	3	4	260	1	0	0	0	0	1	0	0	0	14840	643	23	1	133	1	SMYD5	2	73446019	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	1086349	73446019	169753354	98	37343										
TET3	200424	hgsc.bcm.edu	37	chr2	74274104	74274104	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccaaggaaaaaaacatcagcTtgcagaccgccattgccatt	7	12	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:74274104T>C	ENST00000409262.3	+	1	655	c.655T>C	c.(655-657)Ttg>Ctg	p.L219L		NM_144993.1	NP_659430.1	O43151	TET3_HUMAN	tet methylcytosine dioxygenase 3	219					DNA demethylation (GO:0080111)|DNA demethylation of male pronucleus (GO:0044727)|histone H3-K4 trimethylation (GO:0080182)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methylcytosine dioxygenase activity (GO:0070579)			NS(1)|breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						AAACATCAGCTTGCAGACCGC	0.617																																					p.L219L		Atlas-SNP	.											.	TET3	101	.	0			c.T655C						.						40	44	43					2																	74274104		2072	4210	6282	SO:0001819	synonymous_variant	200424	exon1			ATCAGCTTGCAGA		CCDS46339.1, CCDS46339.2	2p13.1	2011-09-30	2011-09-30		ENSG00000187605	ENSG00000187605			28313	protein-coding gene	gene with protein product		613555	"tet oncogene family member 3"			9455477	Standard	XM_005264187		Approved	MGC22014, hCG_40738	uc031roi.1	O43151	OTTHUMG00000152823	ENST00000409262.3:c.655T>C	chr2.hg19:g.74274104T>C		157.0	0.0		112.0	5.0	NM_144993	A6NEI3|Q86Z24|Q8TBM9	Silent	SNP	ENST00000409262.3	hg19	CCDS46339.1																																																																																			.	.		0.617	TET3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328141.4			C	74274104	T	C	74274104	2	2	260	1	0	0	0	0	0	0	0	1	15786	1606	56	2		2	TET3	2	74274104	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	828085	74274104	168925269	99	37344										
TET3	200424	hgsc.bcm.edu	37	chr2	74328880	74328880	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gagaacatcggcggcgtggcCgtggccccagcccacggctc	15	16	0	1	rs530313290		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:74328880C>T	ENST00000409262.3	+	9	4560	c.4560C>T	c.(4558-4560)gcC>gcT	p.A1520A		NM_144993.1	NP_659430.1	O43151	TET3_HUMAN	tet methylcytosine dioxygenase 3	1520					DNA demethylation (GO:0080111)|DNA demethylation of male pronucleus (GO:0044727)|histone H3-K4 trimethylation (GO:0080182)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methylcytosine dioxygenase activity (GO:0070579)			NS(1)|breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GCGGCGTGGCCGTGGCCCCAG	0.667																																					p.A1520A		Atlas-SNP	.											TET3,NS,carcinoma,0,1	TET3	101	.	0			c.C4560T						.						36	44	41					2																	74328880		2088	4200	6288	SO:0001819	synonymous_variant	200424	exon9			CGTGGCCGTGGCC		CCDS46339.1, CCDS46339.2	2p13.1	2011-09-30	2011-09-30		ENSG00000187605	ENSG00000187605			28313	protein-coding gene	gene with protein product		613555	"tet oncogene family member 3"			9455477	Standard	XM_005264187		Approved	MGC22014, hCG_40738	uc031roi.1	O43151	OTTHUMG00000152823	ENST00000409262.3:c.4560C>T	chr2.hg19:g.74328880C>T		61.0	0.0		42.0	2.0	NM_144993	A6NEI3|Q86Z24|Q8TBM9	Silent	SNP	ENST00000409262.3	hg19	CCDS46339.1																																																																																			.	.		0.667	TET3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328141.4			T	74328880	C	T	74328880	2	4	260	1	0	0	0	0	0	0	0	1	15786	639	23	1		1	TET3	2	74328880	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	54776	74328880	168870493	100	37345										
TTC31	64427	hgsc.bcm.edu	37	chr2	74719856	74719856	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gcccgagagctccgctcttgCcttctccacctcacactggt	8	18	3	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:74719856C>A	ENST00000233623.5	+	12	1252	c.1245C>A	c.(1243-1245)tgC>tgA	p.C415*	TTC31_ENST00000442235.2_Intron|TTC31_ENST00000410003.1_3'UTR	NM_022492.4	NP_071937.4	Q49AM3	TTC31_HUMAN	tetratricopeptide repeat domain 31	415										breast(1)|endometrium(1)|large_intestine(4)|lung(2)|skin(1)	9						TCCGCTCTTGCCTTCTCCACC	0.602																																					p.C415X		Atlas-SNP	.											.	TTC31	23	.	0			c.C1245A						.						46	49	48					2																	74719856		1966	4149	6115	SO:0001587	stop_gained	64427	exon12			CTCTTGCCTTCTC	AK026819	CCDS42701.1	2p13.1	2013-01-11			ENSG00000115282	ENSG00000115282		"Tetratricopeptide (TTC) repeat domain containing"	25759	protein-coding gene	gene with protein product						12477932	Standard	NM_022492		Approved	FLJ12788	uc002slt.2	Q49AM3	OTTHUMG00000152887	ENST00000233623.5:c.1245C>A	chr2.hg19:g.74719856C>A	ENSP00000233623:p.Cys415*	158.0	0.0		63.0	4.0	NM_022492	Q4KN40|Q53FD4|Q9H9F7	Nonsense_Mutation	SNP	ENST00000233623.5	hg19	CCDS42701.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.97|14.97	2.694982|2.694982	0.48202|0.48202	.|.	.|.	ENSG00000115282|ENSG00000115282	ENST00000414247|ENST00000233623	.|.	.|.	.|.	3.99|3.99	0.862|0.862	0.19056|0.19056	.|.	.|0.403279	.|0.24497	.|N	.|0.038016	T|.	0.24928|.	0.0605|.	.|.	.|.	.|.	0.51767|0.51767	D|D	0.999938|0.999938	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.22521|.	-1.0214|.	4|.	.|0.02654	.|T	.|1	.|.	6.0987|6.0987	0.20035|0.20035	0.0:0.6044:0.0:0.3956|0.0:0.6044:0.0:0.3956	.|.	.|.	.|.	.|.	D|X	143|415	.|.	.|ENSP00000233623:C415X	A|C	+|+	2|3	0|2	TTC31|TTC31	74573364|74573364	0.890000|0.890000	0.30428|0.30428	0.342000|0.342000	0.25602|0.25602	0.986000|0.986000	0.74619|0.74619	0.608000|0.608000	0.24223|0.24223	-0.070000|-0.070000	0.12908|0.12908	0.491000|0.491000	0.48974|0.48974	GCC|TGC	.	.		0.602	TTC31-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328422.1	NM_022492		A	74719856	C	A	74719856	4	1	260	1	0	0	0	0	0	1	0	0	16715	747	26	3	1291	3	TTC31	2	74719856	Nonsense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	390976	74719856	168479517	101	37346										
LOXL3	84695	hgsc.bcm.edu	37	chr2	74761507	74761507	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccctcagccaccttggtgccAtttggggtgaggatatcata	11	11	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:74761507A>G	ENST00000264094.3	-	11	1946	c.1875T>C	c.(1873-1875)aaT>aaC	p.N625N	LOXL3_ENST00000393937.2_Silent_p.N480N|LOXL3_ENST00000409986.1_Silent_p.N480N|LOXL3_ENST00000409249.1_Intron|LOXL3_ENST00000409549.1_Silent_p.N569N	NM_032603.2	NP_115992.1	P58215	LOXL3_HUMAN	lysyl oxidase-like 3	625	Lysyl-oxidase like.				epithelial to mesenchymal transition (GO:0001837)|negative regulation of transcription, DNA-templated (GO:0045892)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|nucleus (GO:0005634)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)			endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30						CCTTGGTGCCATTTGGGGTGA	0.512																																					p.N625N		Atlas-SNP	.											.	LOXL3	73	.	0			c.T1875C						.						201	193	195					2																	74761507		2203	4300	6503	SO:0001819	synonymous_variant	84695	exon11			GGTGCCATTTGGG	AF282619	CCDS1953.1, CCDS74527.1	2p13	2008-05-23			ENSG00000115318	ENSG00000115318			13869	protein-coding gene	gene with protein product		607163				11386757	Standard	NM_032603		Approved		uc002smp.1	P58215	OTTHUMG00000129953	ENST00000264094.3:c.1875T>C	chr2.hg19:g.74761507A>G		435.0	0.0		287.0	64.0	NM_032603	D6W5J1|Q2EHP2|Q6IPL7|Q96RS1	Silent	SNP	ENST00000264094.3	hg19	CCDS1953.1																																																																																			.	.		0.512	LOXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252215.1	NM_032603		G	74761507	A	G	74761507	2	3	260	1	0	0	0	0	0	0	0	1	8910	214	8	2		2	LOXL3	2	74761507	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	41651	74761507	168437866	102	37347										
LRRTM4	80059	hgsc.bcm.edu	37	chr2	77746328	77746328	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gaagagacgtggaaaatgagCaaagttgatcttggaaaact	12	4	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:77746328C>A	ENST00000409093.1	-	3	1003	c.667G>T	c.(667-669)Gct>Tct	p.A223S	LRRTM4_ENST00000409088.3_Missense_Mutation_p.A223S|LRRTM4_ENST00000409282.1_Missense_Mutation_p.A224S|LRRTM4_ENST00000409884.1_Missense_Mutation_p.A223S|LRRTM4_ENST00000409911.1_Missense_Mutation_p.A224S			Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4	223					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|regulation of presynaptic membrane organization (GO:1901629)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				autonomic_ganglia(1)|endometrium(1)|large_intestine(6)|lung(49)|ovary(2)|pancreas(3)|prostate(1)|upper_aerodigestive_tract(1)	64				Colorectal(11;0.059)		GGAAAATGAGCAAAGTTGATC	0.448																																					p.A223S		Atlas-SNP	.											LRRTM4_ENST00000409093,NS,carcinoma,0,2	LRRTM4	334	.	0			c.G667T						.						66	65	65					2																	77746328		1880	4113	5993	SO:0001583	missense	80059	exon3			AATGAGCAAAGTT	AK122612	CCDS46346.1, CCDS46347.1, CCDS74530.1	2p12	2008-02-05			ENSG00000176204	ENSG00000176204			19411	protein-coding gene	gene with protein product		610870				12676565	Standard	NM_024993		Approved	FLJ12568	uc002snr.3	Q86VH4	OTTHUMG00000152842	ENST00000409093.1:c.667G>T	chr2.hg19:g.77746328C>A	ENSP00000386357:p.Ala223Ser	89.0	0.0		76.0	4.0	NM_024993	Q4FZ98|Q6UXJ7	Missense_Mutation	SNP	ENST00000409093.1	hg19	CCDS46346.1	.	.	.	.	.	.	.	.	.	.	C	11.18	1.562264	0.27915	.	.	ENSG00000176204	ENST00000409911;ENST00000409884;ENST00000409093;ENST00000409088;ENST00000409282	T;T;T;T;T	0.04119	3.7;3.7;3.7;3.7;3.7	5.72	5.72	0.89469	.	0.114600	0.64402	D	0.000015	T	0.03959	0.0111	N	0.11255	0.115	0.51767	D	0.999937	B;B;B	0.26512	0.058;0.036;0.151	B;B;B	0.25506	0.028;0.061;0.047	T	0.57201	-0.7852	10	0.23891	T	0.37	.	18.4529	0.90710	0.0:1.0:0.0:0.0	.	224;223;223	Q4KMX1;Q86VH4-2;Q86VH4	.;.;LRRT4_HUMAN	S	224;223;223;223;224	ENSP00000387228:A224S;ENSP00000387297:A223S;ENSP00000386357:A223S;ENSP00000386236:A223S;ENSP00000386286:A224S	ENSP00000386236:A223S	A	-	1	0	LRRTM4	77599836	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.212000	0.42835	2.689000	0.91719	0.655000	0.94253	GCT	.	.		0.448	LRRTM4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328225.1	NM_024993		A	77746328	C	A	77746328	3	1	260	1	0	0	0	0	1	0	0	0	9051	710	25	3	1119	3	LRRTM4	2	77746328	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	2984821	77746328	165453045	103	37348										
TCF7L1	83439	hgsc.bcm.edu	37	chr2	85533589	85533589	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccccagtggcacaacctgtcTcgagaagaacaggccaagta	10	13	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:85533589T>C	ENST00000282111.3	+	10	1439	c.1164T>C	c.(1162-1164)tcT>tcC	p.S388S		NM_031283.2	NP_112573.1	Q9HCS4	TF7L1_HUMAN	transcription factor 7-like 1 (T-cell specific, HMG-box)	388					anterior/posterior axis specification, embryo (GO:0008595)|axial mesoderm morphogenesis (GO:0048319)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|chromatin organization (GO:0006325)|generation of neurons (GO:0048699)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|skin(4)|upper_aerodigestive_tract(1)	18						ACAACCTGTCTCGAGAAGAAC	0.612																																					p.S388S		Atlas-SNP	.											.	TCF7L1	44	.	0			c.T1164C						.						84	77	80					2																	85533589		2203	4300	6503	SO:0001819	synonymous_variant	83439	exon10			CCTGTCTCGAGAA	X62870	CCDS1971.1	2p11.2	2008-02-05			ENSG00000152284	ENSG00000152284			11640	protein-coding gene	gene with protein product		604652		TCF3		1741298, 11085512	Standard	NM_031283		Approved		uc002soy.3	Q9HCS4	OTTHUMG00000130026	ENST00000282111.3:c.1164T>C	chr2.hg19:g.85533589T>C		124.0	0.0		95.0	4.0	NM_031283	Q53R97|Q6PD70|Q9NP00	Silent	SNP	ENST00000282111.3	hg19	CCDS1971.1																																																																																			.	.		0.612	TCF7L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252301.2	NM_031283		C	85533589	T	C	85533589	2	2	260	1	0	0	0	0	0	0	0	1	15712	1538	54	2		2	TCF7L1	2	85533589	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	7787261	85533589	157665784	104	37349										
POLR1A	25885	hgsc.bcm.edu	37	chr2	86332884	86332884	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cagccgccgccagggcatgtTcttggagatcaacatcctcc	10	15	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:86332884T>C	ENST00000263857.6	-	1	394	c.16A>G	c.(16-18)Aac>Gac	p.N6D	POLR1A_ENST00000409681.1_Missense_Mutation_p.N6D|PTCD3_ENST00000409277.3_5'Flank|PTCD3_ENST00000254630.7_5'Flank			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	6					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						CAGGGCATGTTCTTGGAGATC	0.542																																					p.N6D		Atlas-SNP	.											.	POLR1A	137	.	0			c.A16G						.						58	59	59					2																	86332884		1961	4141	6102	SO:0001583	missense	25885	exon1			GCATGTTCTTGGA	AK025568	CCDS42706.1	2p11.2	2013-01-21			ENSG00000068654	ENSG00000068654		"RNA polymerase subunits"	17264	protein-coding gene	gene with protein product						9236775	Standard	NM_015425		Approved	DKFZP586M0122, FLJ21915, RPO1-4, RPA1	uc002sqs.3	O95602	OTTHUMG00000153165	ENST00000263857.6:c.16A>G	chr2.hg19:g.86332884T>C	ENSP00000263857:p.Asn6Asp	140.0	0.0		88.0	4.0	NM_015425	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Missense_Mutation	SNP	ENST00000263857.6	hg19	CCDS42706.1	.	.	.	.	.	.	.	.	.	.	T	16.32	3.090701	0.55968	.	.	ENSG00000068654	ENST00000263857;ENST00000409681	T;T	0.66280	-0.2;-0.2	5.77	2.0	0.26442	.	0.325116	0.36034	N	0.002834	T	0.20577	0.0495	N	0.00538	-1.39	0.25140	N	0.9905	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.23691	-1.0181	10	0.11182	T	0.66	-13.7423	3.8673	0.09021	0.0:0.2032:0.5107:0.2861	.	6;6	B9ZVN9;O95602	.;RPA1_HUMAN	D	6	ENSP00000263857:N6D;ENSP00000386300:N6D	ENSP00000263857:N6D	N	-	1	0	POLR1A	86186395	0.998000	0.40836	0.986000	0.45419	0.990000	0.78478	1.196000	0.32198	0.425000	0.26087	0.455000	0.32223	AAC	.	.		0.542	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425		C	86332884	T	C	86332884	3	2	260	1	0	0	0	0	1	0	0	0	12218	1783	62	2	5282	2	POLR1A	2	86332884	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	799295	86332884	156866489	105	37350										
KIAA1310	55683	hgsc.bcm.edu	37	chr2	97276523	97276523	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tctcagctcgaatcttctccCggaagtcctccatggcttca	7	15	4	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:97276523C>A	ENST00000431828.1	-	11	1335	c.1259G>T	c.(1258-1260)cGg>cTg	p.R420L	KANSL3_ENST00000441706.2_Missense_Mutation_p.R333L|KANSL3_ENST00000487070.1_5'UTR|KANSL3_ENST00000599854.1_Missense_Mutation_p.R333L|KANSL3_ENST00000440133.1_Missense_Mutation_p.R214L			Q9P2N6	KANL3_HUMAN	KAT8 regulatory NSL complex subunit 3	420					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											AATCTTCTCCCGGAAGTCCTC	0.507																																					p.R420L		Atlas-SNP	.											.	.	.	.	0			c.G1259T						.						128	126	126					2																	97276523		1904	4128	6032	SO:0001583	missense	55683	exon11			TTCTCCCGGAAGT	BC063792	CCDS46361.1	2q11.2	2011-10-31	2011-10-31	2011-10-31	ENSG00000114982	ENSG00000114982			25473	protein-coding gene	gene with protein product			"KIAA1310"	KIAA1310			Standard	NM_001115016		Approved	FLJ10081, Rcd1, NSL3	uc002swn.5	Q9P2N6	OTTHUMG00000155249	ENST00000431828.1:c.1259G>T	chr2.hg19:g.97276523C>A	ENSP00000396749:p.Arg420Leu	93.0	0.0		69.0	4.0	NM_001115016	A1L184|D3DXH3|D3DXH4|Q05BU4|Q6P3X2|Q6PJH6|Q86T19|Q96L64|Q9H0C9|Q9H8C9|Q9HAP8|Q9NWE5	Missense_Mutation	SNP	ENST00000431828.1	hg19	CCDS46361.1	.	.	.	.	.	.	.	.	.	.	C	32	5.187828	0.94923	.	.	ENSG00000114982	ENST00000354204;ENST00000447759;ENST00000431828;ENST00000441706;ENST00000440133;ENST00000444759;ENST00000452268	T;T;T	0.20598	2.06;2.06;2.06	5.92	5.05	0.67936	.	0.050741	0.85682	D	0.000000	T	0.41673	0.1169	L	0.59436	1.845	0.80722	D	1	D;P;D;B	0.89917	1.0;0.761;1.0;0.05	D;B;D;B	0.91635	0.999;0.214;0.998;0.09	T	0.20974	-1.0259	10	0.49607	T	0.09	.	12.8512	0.57858	0.0:0.9215:0.0:0.0785	.	214;420;333;308	B4E1W4;Q9P2N6-3;Q9P2N6-5;Q9P2N6-6	.;.;.;.	L	333;308;420;333;214;214;333	ENSP00000396749:R420L;ENSP00000400678:R333L;ENSP00000406207:R214L	ENSP00000346144:R333L	R	-	2	0	KIAA1310	96640250	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.652000	0.83633	1.521000	0.48983	0.557000	0.71058	CGG	.	.		0.507	KANSL3-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339040.2	NM_017991		A	97276523	C	A	97276523	3	1	260	1	0	0	0	0	1	0	0	0	8231	652	23	1	1421	1	KIAA1310	2	97276523	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	10943639	97276523	145922850	106	37351										
COX5B	1329	hgsc.bcm.edu	37	chr2	98262581	98262581	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gttacttcgcggagctggaaCgctggccgcgcaggccctga	15	13	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:98262581C>T	ENST00000258424.2	+	1	79	c.32C>T	c.(31-33)aCg>aTg	p.T11M	COX5B_ENST00000464949.1_3'UTR	NM_001862.2	NP_001853.2	P10606	COX5B_HUMAN	cytochrome c oxidase subunit Vb	11					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|respiratory electron transport chain (GO:0022904)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	cytochrome-c oxidase activity (GO:0004129)|metal ion binding (GO:0046872)			endometrium(1)|lung(1)|urinary_tract(1)	3						GGAGCTGGAACGCTGGCCGCG	0.682																																					p.T11M		Atlas-SNP	.											.	COX5B	9	.	0			c.C32T						.						10	11	10					2																	98262581		2124	4166	6290	SO:0001583	missense	1329	exon1			CTGGAACGCTGGC	BC006229	CCDS2032.1	2q11.2	2011-07-04			ENSG00000135940	ENSG00000135940	1.9.3.1	"Mitochondrial respiratory chain complex / Complex IV"	2269	protein-coding gene	gene with protein product		123866					Standard	NM_001862		Approved		uc002sya.3	P10606	OTTHUMG00000130548	ENST00000258424.2:c.32C>T	chr2.hg19:g.98262581C>T	ENSP00000258424:p.Thr11Met	51.0	0.0		44.0	4.0	NM_001862	Q53YB7|Q96J18|Q99610	Missense_Mutation	SNP	ENST00000258424.2	hg19	CCDS2032.1	.	.	.	.	.	.	.	.	.	.	.	14.43	2.532028	0.45073	.	.	ENSG00000135940	ENST00000258424	.	.	.	4.94	3.07	0.35406	.	0.432105	0.21887	N	0.067660	T	0.17619	0.0423	N	0.24115	0.695	0.09310	N	1	P	0.45672	0.864	B	0.38985	0.287	T	0.08659	-1.0711	9	0.49607	T	0.09	-39.0412	6.8554	0.24038	0.0:0.7274:0.1763:0.0963	.	11	P10606	COX5B_HUMAN	M	11	.	ENSP00000258424:T11M	T	+	2	0	COX5B	97629013	0.153000	0.22777	0.423000	0.26634	0.673000	0.39480	1.477000	0.35431	1.330000	0.45394	0.557000	0.71058	ACG	.	.		0.682	COX5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252972.2	NM_001862		T	98262581	C	T	98262581	3	4	260	1	0	0	0	0	1	0	0	0	3775	536	19	1	34	1	COX5B	2	98262581	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	986058	98262581	144936792	107	37352										
AFF3	3899	hgsc.bcm.edu	37	chr2	100209828	100209828	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aggtcgattttgacccagagAgacctgatctcatcactgtc	9	11	2	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:100209828A>G	ENST00000409236.2	-	13	2407	c.2295T>C	c.(2293-2295)tcT>tcC	p.S765S	AFF3_ENST00000356421.2_Silent_p.S790S|AFF3_ENST00000409579.1_Silent_p.S790S|AFF3_ENST00000317233.4_Silent_p.S765S			P51826	AFF3_HUMAN	AF4/FMR2 family, member 3	765					embryonic hindlimb morphogenesis (GO:0035116)|regulation of transcription, DNA-templated (GO:0006355)|response to tumor necrosis factor (GO:0034612)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)			NS(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(9)|kidney(4)|large_intestine(20)|liver(1)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(3)	86						TGACCCAGAGAGACCTGATCT	0.577																																					p.S790S		Atlas-SNP	.											.	AFF3	164	.	0			c.T2370C						.						70	65	67					2																	100209828		2203	4300	6503	SO:0001819	synonymous_variant	3899	exon14			CCAGAGAGACCTG	U34360	CCDS33258.1, CCDS42723.1	2q11.2-q12	2008-02-05	2005-06-27	2005-06-27	ENSG00000144218	ENSG00000144218			6473	protein-coding gene	gene with protein product		601464	"lymphoid nuclear protein related to AF4"	LAF4		8662235, 8555498	Standard	XM_005263945		Approved	MLLT2-like	uc002taf.3	P51826	OTTHUMG00000153011	ENST00000409236.2:c.2295T>C	chr2.hg19:g.100209828A>G		136.0	0.0		70.0	4.0	NM_001025108	B7ZM46|B9EGL9|D3DVI6|Q53RD6|Q53S47|Q53SI6|Q53TB9|Q59F27|Q8IWJ5	Silent	SNP	ENST00000409236.2	hg19	CCDS42723.1																																																																																			.	.		0.577	AFF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328982.3	NM_002285		G	100209828	A	G	100209828	2	3	260	1	0	0	0	0	0	0	0	1	358	291	11	2		2	AFF3	2	100209828	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1947247	100209828	142989545	108	37353										
SLC9A4	389015	hgsc.bcm.edu	37	chr2	103095346	103095346	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cctcatgccagaaagctgccTcctcatcctggtgggggcgc	12	15	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:103095346T>C	ENST00000295269.4	+	2	762	c.305T>C	c.(304-306)cTc>cCc	p.L102P		NM_001011552.3	NP_001011552.2	Q6AI14	SL9A4_HUMAN	solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4	102					epithelial cell development (GO:0002064)|gastric acid secretion (GO:0001696)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						GAAAGCTGCCTCCTCATCCTG	0.592																																					p.L102P		Atlas-SNP	.											.	SLC9A4	115	.	0			c.T305C						.						57	53	55					2																	103095346		2203	4300	6503	SO:0001583	missense	389015	exon2			GCTGCCTCCTCAT		CCDS33264.1	2q12.1	2013-05-22	2012-03-22		ENSG00000180251	ENSG00000180251		"Solute carriers"	11077	protein-coding gene	gene with protein product		600531	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 4", "solute carrier family 9 (sodium/hydrogen exchanger), member 4"			8199403	Standard	NM_001011552		Approved	NHE4	uc002tbz.4	Q6AI14	OTTHUMG00000153093	ENST00000295269.4:c.305T>C	chr2.hg19:g.103095346T>C	ENSP00000295269:p.Leu102Pro	112.0	0.0		64.0	4.0	NM_001011552	Q69YK0	Missense_Mutation	SNP	ENST00000295269.4	hg19	CCDS33264.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.791271	0.90367	.	.	ENSG00000180251	ENST00000295269	T	0.74947	-0.89	5.6	5.6	0.85130	Cation/H+ exchanger (1);	0.064498	0.64402	D	0.000011	D	0.88919	0.6568	M	0.91872	3.25	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	D	0.91420	0.5158	10	0.87932	D	0	.	15.7878	0.78322	0.0:0.0:0.0:1.0	.	102	Q6AI14	SL9A4_HUMAN	P	102	ENSP00000295269:L102P	ENSP00000295269:L102P	L	+	2	0	SLC9A4	102461778	1.000000	0.71417	0.995000	0.50966	0.907000	0.53573	6.293000	0.72731	2.133000	0.65898	0.533000	0.62120	CTC	.	.		0.592	SLC9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329498.1	NM_001011552.3		C	103095346	T	C	103095346	3	2	260	1	0	0	0	0	1	0	0	0	14731	1551	54	2	311	2	SLC9A4	2	103095346	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	2885518	103095346	140104027	109	37354										
ST6GAL2	84620	hgsc.bcm.edu	37	chr2	107459506	107459506	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cctacctatttcctcgcccaAggaagagttgaggattgcgc	10	12	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:107459506A>G	ENST00000409382.3	-	2	1538	c.928T>C	c.(928-930)Ttg>Ctg	p.L310L	AC016994.2_ENST00000425419.1_RNA|ST6GAL2_ENST00000409087.3_Silent_p.L310L|ST6GAL2_ENST00000361686.4_Silent_p.L310L	NM_001142351.1	NP_001135823.1	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 2	310					growth (GO:0040007)|multicellular organismal development (GO:0007275)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	beta-galactoside alpha-2,6-sialyltransferase activity (GO:0003835)			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						TCCTCGCCCAAGGAAGAGTTG	0.677																																					p.L310L		Atlas-SNP	.											.	ST6GAL2	159	.	0			c.T928C						.						10	12	11					2																	107459506		1747	3700	5447	SO:0001819	synonymous_variant	84620	exon2			CGCCCAAGGAAGA	AB059555	CCDS2073.1, CCDS46380.1	2q11-q12	2008-02-05	2005-02-07	2005-02-07	ENSG00000144057	ENSG00000144057	2.4.99.2		10861	protein-coding gene	gene with protein product		608472	"sialyltransferase 2 (monosialoganglioside sialyltransferase)"	SIAT2			Standard	NM_032528		Approved	KIAA1877, St6gal2, St6GalII	uc002tdr.3	Q96JF0	OTTHUMG00000130923	ENST00000409382.3:c.928T>C	chr2.hg19:g.107459506A>G		176.0	0.0		93.0	4.0	NM_032528	D3DVK3|Q53QP4|Q86Y44|Q8IUG7|Q96HE4	Silent	SNP	ENST00000409382.3	hg19	CCDS2073.1																																																																																			.	.		0.677	ST6GAL2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330065.1	NM_032528		G	107459506	A	G	107459506	2	3	260	1	0	0	0	0	0	0	0	1	15237	69	3	2		2	ST6GAL2	2	107459506	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	4364160	107459506	135739867	110	37355										
SULT1C2	6819	hgsc.bcm.edu	37	chr2	108910710	108910710	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acgtggattcaggaaattgtGgatatgattgaacagaatgg	13	3	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:108910710G>T	ENST00000437390.2	+	3	354	c.177G>T	c.(175-177)gtG>gtT	p.V59V	SULT1C2_ENST00000326853.5_Silent_p.V59V|SULT1C2_ENST00000251481.6_Silent_p.V59V|SULT1C2_ENST00000409880.1_Silent_p.V59V|SULT1C2_ENST00000492554.1_3'UTR			O75897	ST1C4_HUMAN	sulfotransferase family, cytosolic, 1C, member 2	65					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|small molecule metabolic process (GO:0044281)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	sulfotransferase activity (GO:0008146)			NS(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	20						AGGAAATTGTGGATATGATTG	0.502																																					p.V59V		Atlas-SNP	.											.	SULT1C2	82	.	0			c.G177T						.						187	177	180					2																	108910710		2203	4300	6503	SO:0001819	synonymous_variant	6819	exon3			AATTGTGGATATG	U66036, AF186255	CCDS2075.1, CCDS2076.1	2q12.3	2010-09-30	2007-03-16	2007-03-16	ENSG00000198203	ENSG00000198203		"Sulfotransferases, cytosolic"	11456	protein-coding gene	gene with protein product		602385	"sulfotransferase family, cytosolic, 1C, member 1"	SULT1C1		9169148, 10783263	Standard	NM_001056		Approved	ST1C1	uc002tdx.3	O00338	OTTHUMG00000153215	ENST00000437390.2:c.177G>T	chr2.hg19:g.108910710G>T		73.0	0.0		93.0	5.0	NM_001056	Q069I8|Q08AS5|Q53S63	Silent	SNP	ENST00000437390.2	hg19		.	.	.	.	.	.	.	.	.	.	G	9.955	1.221194	0.22457	.	.	ENSG00000198203	ENST00000409067	.	.	.	4.97	-1.31	0.09230	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.2373	0.04011	0.2886:0.1188:0.4707:0.1219	.	.	.	.	X	56	.	.	G	+	1	0	SULT1C2	108277142	0.987000	0.35691	0.993000	0.49108	0.953000	0.61014	-0.107000	0.10873	-0.196000	0.10366	-0.127000	0.14921	GGA	.	.		0.502	SULT1C2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000329969.2	NM_176825		T	108910710	G	T	108910710	2	4	260	1	0	0	0	0	0	0	0	1	15392	1335	47	3		3	SULT1C2	2	108910710	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	1451204	108910710	134288663	111	37356										
SULT1C2	6819	hgsc.bcm.edu	37	chr2	108910807	108910807	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gggctcggccaccccaacctTctggtgagagcacctccctc	10	18	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:108910807T>A	ENST00000437390.2	+	3	451	c.274T>A	c.(274-276)Tct>Act	p.S92T	SULT1C2_ENST00000326853.5_Missense_Mutation_p.S92T|SULT1C2_ENST00000251481.6_Missense_Mutation_p.S92T|SULT1C2_ENST00000409880.1_Missense_Mutation_p.S92T			O75897	ST1C4_HUMAN	sulfotransferase family, cytosolic, 1C, member 2	94					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|small molecule metabolic process (GO:0044281)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	sulfotransferase activity (GO:0008146)			NS(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	20						ACCCCAACCTTCTGGTGAGAG	0.512																																					p.S92T		Atlas-SNP	.											.	SULT1C2	82	.	0			c.T274A						.						118	109	112					2																	108910807		2203	4300	6503	SO:0001583	missense	6819	exon3			CAACCTTCTGGTG	U66036, AF186255	CCDS2075.1, CCDS2076.1	2q12.3	2010-09-30	2007-03-16	2007-03-16	ENSG00000198203	ENSG00000198203		"Sulfotransferases, cytosolic"	11456	protein-coding gene	gene with protein product		602385	"sulfotransferase family, cytosolic, 1C, member 1"	SULT1C1		9169148, 10783263	Standard	NM_001056		Approved	ST1C1	uc002tdx.3	O00338	OTTHUMG00000153215	ENST00000437390.2:c.274T>A	chr2.hg19:g.108910807T>A	ENSP00000399651:p.Ser92Thr	113.0	0.0		92.0	4.0	NM_001056	Q069I8|Q08AS5|Q53S63	Missense_Mutation	SNP	ENST00000437390.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.78|16.78	3.218761|3.218761	0.58560|0.58560	.|.	.|.	ENSG00000198203|ENSG00000198203	ENST00000409067|ENST00000251481;ENST00000326853;ENST00000438339;ENST00000409880;ENST00000437390	.|D;T;T;T;D	.|0.82711	.|-1.64;2.3;4.69;4.69;-1.54	4.97|4.97	4.97|4.97	0.65823|0.65823	.|Sulfotransferase domain (1);	.|0.937080	.|0.08825	.|N	.|0.888210	D|D	0.83115|0.83115	0.5184|0.5184	M|M	0.72624|0.72624	2.21|2.21	0.22754|0.22754	N|N	0.998773|0.998773	.|B;B;B	.|0.23490	.|0.086;0.086;0.07	.|B;B;B	.|0.25759	.|0.063;0.063;0.037	T|T	0.71540|0.71540	-0.4562|-0.4562	5|10	.|0.36615	.|T	.|0.2	.|.	12.6318|12.6318	0.56661|0.56661	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|92;92;92	.|B4DLP0;O00338;O00338-2	.|.;ST1C2_HUMAN;.	Y|T	88|92	.|ENSP00000251481:S92T;ENSP00000319622:S92T;ENSP00000401996:S92T;ENSP00000387054:S92T;ENSP00000399651:S92T	.|ENSP00000251481:S92T	F|S	+|+	2|1	0|0	SULT1C2|SULT1C2	108277239|108277239	0.214000|0.214000	0.23563|0.23563	0.074000|0.074000	0.20217|0.20217	0.308000|0.308000	0.27856|0.27856	2.078000|2.078000	0.41567|0.41567	2.073000|2.073000	0.62155|0.62155	0.533000|0.533000	0.62120|0.62120	TTC|TCT	.	.		0.512	SULT1C2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000329969.2	NM_176825		A	108910807	T	A	108910807	3	1	260	1	0	0	0	0	1	0	0	0	15392	1783	62	4	280	4	SULT1C2	2	108910807	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	97	108910807	134288566	112	37357										
NPHP1	4867	hgsc.bcm.edu	37	chr2	110926056	110926056	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	taggttctgggaacaagaccTtcatttcctttggcatcctt	8	10	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:110926056T>C	ENST00000393272.3	-	6	694	c.597A>G	c.(595-597)gaA>gaG	p.E199E	NPHP1_ENST00000417665.1_Silent_p.E199E|NPHP1_ENST00000316534.4_Silent_p.E199E|NPHP1_ENST00000355301.4_Silent_p.E137E|NPHP1_ENST00000445609.2_Silent_p.E199E	NM_000272.3|NM_207181.2	NP_000263.2|NP_997064.2	O15259	NPHP1_HUMAN	nephronophthisis 1 (juvenile)	199	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin cytoskeleton organization (GO:0030036)|cell projection organization (GO:0030030)|cellular protein localization (GO:0034613)|excretion (GO:0007588)|photoreceptor cell outer segment organization (GO:0035845)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|spermatid differentiation (GO:0048515)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|motile cilium (GO:0031514)|photoreceptor connecting cilium (GO:0032391)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(2)	24						GAACAAGACCTTCATTTCCTT	0.348																																					p.E199E		Atlas-SNP	.											.	NPHP1	68	.	0			c.A597G						.						146	149	148					2																	110926056		2203	4300	6503	SO:0001819	synonymous_variant	4867	exon6			AAGACCTTCATTT	AF023674	CCDS2086.1, CCDS46384.1, CCDS46385.1, CCDS46386.1	2q13	2014-01-28			ENSG00000144061	ENSG00000144061			7905	protein-coding gene	gene with protein product	"nephrocystin-1"	607100		NPH1			Standard	NM_000272		Approved	JBTS4, SLSN1	uc002tfm.4	O15259	OTTHUMG00000131195	ENST00000393272.3:c.597A>G	chr2.hg19:g.110926056T>C		119.0	0.0		68.0	20.0	NM_207181	O14837	Silent	SNP	ENST00000393272.3	hg19	CCDS46385.1																																																																																			.	.		0.348	NPHP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253919.3	NM_000272		C	110926056	T	C	110926056	2	2	260	1	0	0	0	0	0	0	0	1	10588	1606	56	2		2	NPHP1	2	110926056	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	2015249	110926056	132273317	113	37358										
C1QL2	165257	hgsc.bcm.edu	37	chr2	119915747	119915747	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggcgcggcagtgtaagggtcGcagatcatgcggcaggtgcc	18	10	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:119915747G>A	ENST00000272520.3	-	1	718	c.99C>T	c.(97-99)tgC>tgT	p.C33C		NM_182528.3	NP_872334.2	Q7Z5L3	C1QL2_HUMAN	complement component 1, q subcomponent-like 2	33				CD -> WE (in Ref. 1; AAP80787). {ECO:0000305}.	protein oligomerization (GO:0051259)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)		p.C33C(1)		NS(1)|endometrium(1)|large_intestine(3)|pancreas(1)|prostate(1)	7						TGTAAGGGTCGCAGATCATGC	0.726										HNSCC(49;0.14)																											p.C33C		Atlas-SNP	.											C1QL2,colon,carcinoma,0,1	C1QL2	25	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C99T						.						6	7	7					2																	119915747		1677	3758	5435	SO:0001819	synonymous_variant	165257	exon1			AGGGTCGCAGATC	AF525315	CCDS42737.1	2q14.2	2009-05-20			ENSG00000144119	ENSG00000144119			24181	protein-coding gene	gene with protein product	"C1q and tumor necrosis factor related protein 10"	614330				18783346	Standard	NM_182528		Approved	CTRP10, C1QTNF10	uc002tlo.2	Q7Z5L3	OTTHUMG00000153271	ENST00000272520.3:c.99C>T	chr2.hg19:g.119915747G>A		22.0	0.0		33.0	2.0	NM_182528		Silent	SNP	ENST00000272520.3	hg19	CCDS42737.1																																																																																			.	.		0.726	C1QL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330527.2	NM_182528		A	119915747	G	A	119915747	2	1	260	1	0	0	0	0	0	0	0	1	1961	1079	38	1		1	C1QL2	2	119915747	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	8989691	119915747	123283626	114	37359										
MYO7B	4648	hgsc.bcm.edu	37	chr2	128335802	128335802	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccagttctccgactccgagaGctgggacgtcatcaagctgc	11	14	3	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:128335802G>T	ENST00000409816.2	+	8	976	c.944G>T	c.(943-945)aGc>aTc	p.S315I	MYO7B_ENST00000389524.4_Missense_Mutation_p.S315I|MYO7B_ENST00000428314.1_Missense_Mutation_p.S315I			Q6PIF6	MYO7B_HUMAN	myosin VIIB	315	Myosin motor.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		GACTCCGAGAGCTGGGACGTC	0.612																																					p.S315I		Atlas-SNP	.											.	MYO7B	359	.	0			c.G944T						.						55	61	59					2																	128335802		2107	4215	6322	SO:0001583	missense	4648	exon9			CCGAGAGCTGGGA		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"Myosins / Myosin superfamily : Class VII"	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.944G>T	chr2.hg19:g.128335802G>T	ENSP00000386461:p.Ser315Ile	169.0	0.0		116.0	5.0	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	hg19	CCDS46405.1	.	.	.	.	.	.	.	.	.	.	G	4.569	0.105665	0.08780	.	.	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000409816	T;T;T	0.69685	-0.42;-0.42;-0.42	4.25	1.67	0.24075	Myosin head, motor domain (2);	0.382433	0.28031	N	0.016870	T	0.21103	0.0508	N	0.00041	-2.485	0.22675	N	0.998867	B	0.32467	0.372	B	0.35413	0.202	T	0.44034	-0.9354	10	0.15499	T	0.54	.	8.3383	0.32228	0.8334:0.0:0.1666:0.0	.	315	Q6PIF6	MYO7B_HUMAN	I	315	ENSP00000374175:S315I;ENSP00000415090:S315I;ENSP00000386461:S315I	ENSP00000374175:S315I	S	+	2	0	MYO7B	128052272	0.997000	0.39634	0.997000	0.53966	0.309000	0.27889	1.227000	0.32576	0.283000	0.22279	-0.440000	0.05779	AGC	.	.		0.612	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001		T	128335802	G	T	128335802	3	4	260	1	0	0	0	0	1	0	0	0	10092	971	34	3	974	3	MYO7B	2	128335802	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	8420055	128335802	114863571	115	37360										
IMP4	92856	hgsc.bcm.edu	37	chr2	131104030	131104030	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cacgcaagagagtcttcctgAgcaccgagtgagcacactca	10	13	2	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:131104030A>G	ENST00000259239.3	+	9	1573	c.865A>G	c.(865-867)Agc>Ggc	p.S289G	IMP4_ENST00000409935.1_3'UTR	NM_033416.1	NP_219484.1	Q96G21	IMP4_HUMAN	IMP4, U3 small nucleolar ribonucleoprotein	289					rRNA processing (GO:0006364)	nucleolus (GO:0005730)|ribonucleoprotein complex (GO:0030529)				central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|skin(1)|urinary_tract(1)	18	Colorectal(110;0.1)					AGTCTTCCTGAGCACCGAGTG	0.572																																					p.S289G		Atlas-SNP	.											.	IMP4	35	.	0			c.A865G						.						62	50	54					2																	131104030		2183	4256	6439	SO:0001583	missense	92856	exon9			TTCCTGAGCACCG	BC010042	CCDS2160.1	2q21.1	2014-02-19	2014-02-19		ENSG00000136718	ENSG00000136718			30856	protein-coding gene	gene with protein product		612981	"IMP4, U3 small nucleolar ribonucleoprotein, homolog (yeast)"			8619474, 9110174, 12655004	Standard	NM_033416		Approved	MGC19606, BXDC4	uc002tra.1	Q96G21	OTTHUMG00000131627	ENST00000259239.3:c.865A>G	chr2.hg19:g.131104030A>G	ENSP00000259239:p.Ser289Gly	105.0	0.0		74.0	5.0	NM_033416	Q3ZTT3	Missense_Mutation	SNP	ENST00000259239.3	hg19	CCDS2160.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.63|19.63	3.863384|3.863384	0.71949|0.71949	.|.	.|.	ENSG00000136718|ENSG00000136718	ENST00000259239;ENST00000428740|ENST00000452955	T;T|.	0.50548|.	0.74;0.81|.	5.63|5.63	5.63|5.63	0.86233|0.86233	.|.	0.175734|.	0.64402|.	D|.	0.000011|.	T|.	0.63212|.	0.2492|.	L|L	0.54323|0.54323	1.7|1.7	0.80722|0.80722	D|D	1|1	P|.	0.43885|.	0.82|.	P|.	0.50860|.	0.652|.	T|.	0.61589|.	-0.7032|.	10|.	0.32370|.	T|.	0.25|.	-25.5827|-25.5827	12.5231|12.5231	0.56072|0.56072	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	289|.	Q96G21|.	IMP4_HUMAN|.	G|W	289;234|277	ENSP00000259239:S289G;ENSP00000389701:S234G|.	ENSP00000259239:S289G|.	S|X	+|+	1|3	0|0	IMP4|IMP4	130820500|130820500	1.000000|1.000000	0.71417|0.71417	0.989000|0.989000	0.46669|0.46669	0.455000|0.455000	0.32408|0.32408	7.898000|7.898000	0.87363|0.87363	2.279000|2.279000	0.76181|0.76181	0.533000|0.533000	0.62120|0.62120	AGC|TGA	.	.		0.572	IMP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254520.2	NM_033416		G	131104030	A	G	131104030	3	3	260	1	0	0	0	0	1	0	0	0	7729	304	11	2	899	2	IMP4	2	131104030	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	2768228	131104030	112095343	116	37361										
GPR148	344561	hgsc.bcm.edu	37	chr2	131487678	131487678	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccccgtgccatgctcacataCctgtacctgctccgctaccg	7	19	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:131487678C>T	ENST00000309926.4	+	1	1036	c.954C>T	c.(952-954)taC>taT	p.Y318Y		NM_207364.2	NP_997247.2	Q8TDV2	GP148_HUMAN	G protein-coupled receptor 148	318						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(15)|skin(3)|upper_aerodigestive_tract(1)	27	Colorectal(110;0.1)					TGCTCACATACCTGTACCTGC	0.572																																					p.Y318Y		Atlas-SNP	.											.	GPR148	54	.	0			c.C954T						.						79	65	70					2																	131487678		2203	4300	6503	SO:0001819	synonymous_variant	344561	exon1			CACATACCTGTAC	AY255532	CCDS2163.1	2q21.2	2012-08-21			ENSG00000173302	ENSG00000173302		"GPCR / Class A : Orphans"	23623	protein-coding gene	gene with protein product						12679517	Standard	NM_207364		Approved	PGR6	uc002trv.2	Q8TDV2	OTTHUMG00000131655	ENST00000309926.4:c.954C>T	chr2.hg19:g.131487678C>T		91.0	0.0		81.0	5.0	NM_207364	Q2M369|Q86SP7|Q86U87	Silent	SNP	ENST00000309926.4	hg19	CCDS2163.1																																																																																			.	.		0.572	GPR148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254552.3	XM_293092		T	131487678	C	T	131487678	2	4	260	1	0	0	0	0	0	0	0	1	6661	518	18	3		3	GPR148	2	131487678	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	383648	131487678	111711695	117	37362										
MMADHC	27249	hgsc.bcm.edu	37	chr2	150435986	150435986	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgccatcacaaactcatgtcTttcacttgataaaggttctg	6	10	5	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:150435986T>C	ENST00000428879.1	-	3	835	c.331A>G	c.(331-333)Aga>Gga	p.R111G	MMADHC_ENST00000422782.2_Missense_Mutation_p.R111G|MMADHC_ENST00000303319.5_Missense_Mutation_p.R111G			Q9H3L0	MMAD_HUMAN	methylmalonic aciduria (cobalamin deficiency) cblD type, with homocystinuria	111					cobalamin metabolic process (GO:0009235)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrion (GO:0005739)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(4)|skin(2)	11						AACTCATGTCTTTCACTTGAT	0.353																																					p.R111G		Atlas-SNP	.											.	MMADHC	20	.	0			c.A331G						.						93	92	92					2																	150435986		2203	4300	6503	SO:0001583	missense	27249	exon4			CATGTCTTTCACT	BC023995	CCDS2189.1	2q23	2011-05-12	2009-01-08	2009-01-08	ENSG00000168288	ENSG00000168288			25221	protein-coding gene	gene with protein product		611935	"chromosome 2 open reading frame 25"	C2orf25		18385497	Standard	NM_015702		Approved	CL25022, cblD	uc002txc.3	Q9H3L0	OTTHUMG00000155558	ENST00000428879.1:c.331A>G	chr2.hg19:g.150435986T>C	ENSP00000389060:p.Arg111Gly	139.0	0.0		95.0	4.0	NM_015702	B2R895|D3DP91|O95891	Missense_Mutation	SNP	ENST00000428879.1	hg19	CCDS2189.1	.	.	.	.	.	.	.	.	.	.	T	18.90	3.721583	0.68959	.	.	ENSG00000168288	ENST00000303319;ENST00000428879;ENST00000422782	D;D;D	0.89746	-2.56;-2.56;-2.56	5.19	5.19	0.71726	.	0.044848	0.85682	D	0.000000	D	0.94155	0.8125	M	0.85630	2.765	0.49915	D	0.999836	D;D	0.71674	0.998;0.998	D;D	0.71870	0.963;0.975	D	0.94743	0.7920	10	0.87932	D	0	-1.639	11.7879	0.52053	0.0:0.0:0.1464:0.8536	.	111;111	F8WEC0;Q9H3L0	.;MMAD_HUMAN	G	111	ENSP00000301920:R111G;ENSP00000389060:R111G;ENSP00000408331:R111G	ENSP00000301920:R111G	R	-	1	2	MMADHC	150144232	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.895000	0.39778	2.078000	0.62432	0.455000	0.32223	AGA	.	.		0.353	MMADHC-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332312.1	NM_015702		C	150435986	T	C	150435986	3	2	260	1	0	0	0	0	1	0	0	0	9651	1617	56	2	579	2	MMADHC	2	150435986	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	18948308	150435986	92763387	118	37363										
NEB	4703	hgsc.bcm.edu	37	chr2	152402893	152402893	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggtgccgggagcggaccatgTcaggagtgtcatacaggaag	17	8	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:152402893T>C	ENST00000172853.10	-	106	15476	c.15329A>G	c.(15328-15330)gAc>gGc	p.D5110G	NEB_ENST00000409198.1_Missense_Mutation_p.D5110G|NEB_ENST00000604864.1_Missense_Mutation_p.D6811G|NEB_ENST00000603639.1_Missense_Mutation_p.D6811G|NEB_ENST00000427231.2_Missense_Mutation_p.D6811G|NEB_ENST00000397345.3_Missense_Mutation_p.D6811G			P20929	NEBU_HUMAN	nebulin	5110					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		GCGGACCATGTCAGGAGTGTC	0.522																																					p.D6811G		Atlas-SNP	.											.	NEB	1697	.	0			c.A20432G						.						129	138	135					2																	152402893		1996	4188	6184	SO:0001583	missense	4703	exon134			ACCATGTCAGGAG	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.15329A>G	chr2.hg19:g.152402893T>C	ENSP00000172853:p.Asp5110Gly	130.0	0.0		99.0	4.0	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	hg19		.	.	.	.	.	.	.	.	.	.	T	34	5.305732	0.95601	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000397342;ENST00000413693;ENST00000172853	T;T;T;T;T	0.52526	0.66;0.66;0.66;0.66;0.66	6.17	6.17	0.99709	.	0.042414	0.85682	D	0.000000	T	0.67078	0.2855	M	0.64170	1.965	0.80722	D	1	D;D	0.69078	0.997;0.995	D;D	0.78314	0.973;0.991	T	0.67473	-0.5662	10	0.54805	T	0.06	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	5110;1541	P20929;Q14215	NEBU_HUMAN;.	G	5110;6811;6811;1159;1541;5110	ENSP00000386259:D5110G;ENSP00000380505:D6811G;ENSP00000416578:D6811G;ENSP00000410961:D1541G;ENSP00000172853:D5110G	ENSP00000172853:D5110G	D	-	2	0	NEB	152111139	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.633000	0.83260	2.371000	0.80710	0.533000	0.62120	GAC	.	.		0.522	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		C	152402893	T	C	152402893	3	2	260	1	0	0	0	0	1	0	0	0	10311	1667	58	2	5450	2	NEB	2	152402893	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1966907	152402893	90796480	119	37364										
BAZ2B	29994	hgsc.bcm.edu	37	chr2	160242972	160242972	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	atatttagcaatccctcttgAagaacactcaggtttggaac	7	9	2	2	rs532285305		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:160242972A>C	ENST00000392783.2	-	22	3858	c.3363T>G	c.(3361-3363)ctT>ctG	p.L1121L	BAZ2B_ENST00000392782.1_Silent_p.L1085L|BAZ2B_ENST00000355831.2_Silent_p.L1087L|BAZ2B_ENST00000343439.5_Silent_p.L1021L|AC008277.1_ENST00000420020.1_RNA	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	1121	DDT. {ECO:0000255|PROSITE- ProRule:PRU00063}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						ATCCCTCTTGAAGAACACTCA	0.428																																					p.L1121L		Atlas-SNP	.											.	BAZ2B	196	.	0			c.T3363G						.						115	105	108					2																	160242972		1878	4119	5997	SO:0001819	synonymous_variant	29994	exon22			CTCTTGAAGAACA	AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636		"Zinc fingers, PHD-type"	963	protein-coding gene	gene with protein product		605683				10662543	Standard	XM_005246488		Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.3363T>G	chr2.hg19:g.160242972A>C		255.0	0.0		153.0	34.0	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Silent	SNP	ENST00000392783.2	hg19	CCDS2209.2	.	.	.	.	.	.	.	.	.	.	A	15.95	2.984718	0.53934	.	.	ENSG00000123636	ENST00000294905	.	.	.	6.08	4.9	0.64082	.	.	.	.	.	T	0.58807	0.2148	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56117	-0.8032	4	.	.	.	-4.5391	7.8259	0.29315	0.7917:0.14:0.0683:0.0	.	.	.	.	A	182	.	.	S	-	1	0	BAZ2B	159951218	0.997000	0.39634	1.000000	0.80357	0.998000	0.95712	0.722000	0.25925	1.087000	0.41251	0.482000	0.46254	TCA	.	.		0.428	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2			C	160242972	A	C	160242972	2	2	260	1	0	0	0	0	0	0	0	1	1332	233	9	5		5	BAZ2B	2	160242972	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	7840079	160242972	82956401	120	37365										
RBMS1	5937	hgsc.bcm.edu	37	chr2	161133886	161133886	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccttgcatagctgacgttgcAggcatgtactagaaagaaga	11	8	0	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:161133886A>G	ENST00000348849.3	-	12	1501	c.1071T>C	c.(1069-1071)ccT>ccC	p.P357P	RBMS1_ENST00000474820.1_5'UTR|RBMS1_ENST00000409289.2_Silent_p.P321P|RBMS1_ENST00000409972.1_Silent_p.P321P|RBMS1_ENST00000409075.1_Silent_p.P321P|RBMS1_ENST00000392753.3_Silent_p.P370P	NM_002897.4|NM_016836.3	NP_002888.1|NP_058520.1	P29558	RBMS1_HUMAN	RNA binding motif, single stranded interacting protein 1	357					DNA replication (GO:0006260)|RNA processing (GO:0006396)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)		PLA2R1/RBMS1(2)								CTGACGTTGCAGGCATGTACT	0.463																																					p.P357P		Atlas-SNP	.											.	RBMS1	34	.	0			c.T1071C						.						124	93	104					2																	161133886		2203	4300	6503	SO:0001819	synonymous_variant	5937	exon12			CGTTGCAGGCATG	D28482	CCDS2213.1	2q24.2	2013-02-12			ENSG00000153250	ENSG00000153250		"RNA binding motif (RRM) containing"	9907	protein-coding gene	gene with protein product	"suppressor of cdc 2 (cdc13) with RNA binding motif 2", "c-myc gene single strand binding protein 2"	602310	"chromosome 2 open reading frame 12"	C2orf12		8041632, 8134115, 7838710	Standard	NM_016836		Approved	SCR2, MSSP-1, MSSP-2, MSSP-3, YC1, HCC-4, DKFZp564H0764	uc002ubo.3	P29558	OTTHUMG00000132031	ENST00000348849.3:c.1071T>C	chr2.hg19:g.161133886A>G		146.0	0.0		95.0	6.0	NM_016836	Q14869|Q15433|Q53P46|Q53QX8|Q53RG6|Q8WV20	Silent	SNP	ENST00000348849.3	hg19	CCDS2213.1																																																																																			.	.		0.463	RBMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255043.4	NM_016836		G	161133886	A	G	161133886	2	3	260	1	0	0	0	0	0	0	0	1	13163	175	7	2		2	RBMS1	2	161133886	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	890914	161133886	82065487	121	37366										
TBR1	10716	hgsc.bcm.edu	37	chr2	162275531	162275531	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	actttccctgagactcagttCatcgccgtcaccgcctacca	6	17	3	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:162275531C>T	ENST00000389554.3	+	4	1415	c.1098C>T	c.(1096-1098)ttC>ttT	p.F366F	TBR1_ENST00000410035.1_Silent_p.F79F	NM_006593.2	NP_006584.1	Q16650	TBR1_HUMAN	T-box, brain, 1	366					axon guidance (GO:0007411)|brain development (GO:0007420)|hindbrain development (GO:0030902)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of neuron projection development (GO:0010975)|specification of organ identity (GO:0010092)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|prostate(1)|skin(3)	30						AGACTCAGTTCATCGCCGTCA	0.637																																					p.F366F		Atlas-SNP	.											.	TBR1	59	.	0			c.C1098T						.						100	95	97					2																	162275531		2203	4300	6503	SO:0001819	synonymous_variant	10716	exon4			TCAGTTCATCGCC	U49250	CCDS33310.1	2q24.2	2011-06-13			ENSG00000136535	ENSG00000136535		"T-boxes"	11590	protein-coding gene	gene with protein product		604616				7619531	Standard	NM_006593		Approved		uc002ubw.1	Q16650	OTTHUMG00000153888	ENST00000389554.3:c.1098C>T	chr2.hg19:g.162275531C>T		122.0	0.0		89.0	5.0	NM_006593	B0AZS4|B2R6G5|Q14DC5|Q53TH0|Q56A81	Silent	SNP	ENST00000389554.3	hg19	CCDS33310.1																																																																																			.	.		0.637	TBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332845.1	NM_006593		T	162275531	C	T	162275531	2	4	260	1	0	0	0	0	0	0	0	1	15662	825	29	3		3	TBR1	2	162275531	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	1141645	162275531	80923842	122	37367										
LRP2	4036	hgsc.bcm.edu	37	chr2	170136002	170136002	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgaccttggtttccactagaTagattttattattaacccag	6	8	0	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:170136002T>C	ENST00000263816.3	-	12	1730	c.1445A>G	c.(1444-1446)tAt>tGt	p.Y482C	LRP2_ENST00000443831.1_Missense_Mutation_p.Y482C	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	482					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	TTCCACTAGATAGATTTTATT	0.388																																					p.Y482C		Atlas-SNP	.											.	LRP2	751	.	0			c.A1445G						.						104	111	108					2																	170136002		2203	4300	6503	SO:0001583	missense	4036	exon12			ACTAGATAGATTT		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.1445A>G	chr2.hg19:g.170136002T>C	ENSP00000263816:p.Tyr482Cys	201.0	0.0		144.0	45.0	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	hg19	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	T	15.29	2.789002	0.49997	.	.	ENSG00000081479	ENST00000263816;ENST00000443831	D;D	0.99304	-5.72;-5.72	5.58	5.58	0.84498	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	D	0.99654	0.9872	H	0.97340	3.985	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.97459	1.0033	9	.	.	.	.	15.7574	0.78046	0.0:0.0:0.0:1.0	.	482;482	E9PC35;P98164	.;LRP2_HUMAN	C	482	ENSP00000263816:Y482C;ENSP00000409813:Y482C	.	Y	-	2	0	LRP2	169844248	1.000000	0.71417	0.954000	0.39281	0.363000	0.29612	7.971000	0.88012	2.136000	0.66102	0.528000	0.53228	TAT	.	.		0.388	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		C	170136002	T	C	170136002	3	2	260	1	0	0	0	0	1	0	0	0	8965	1406	49	2	12794	2	LRP2	2	170136002	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	7860471	170136002	73063371	123	37368										
UBR3	130507	hgsc.bcm.edu	37	chr2	170806434	170806434	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tggagatggtataactgccgTggaaagaattttactaaaag	11	4	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:170806434T>C	ENST00000272793.5	+	23	3454	c.3404T>C	c.(3403-3405)gTg>gCg	p.V1135A	UBR3_ENST00000418381.1_Missense_Mutation_p.V1135A			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	1135					embryo development (GO:0009790)|in utero embryonic development (GO:0001701)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)|suckling behavior (GO:0001967)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1)	33						ATAACTGCCGTGGAAAGAATT	0.373																																					p.V1135A		Atlas-SNP	.											.	UBR3	182	.	0			c.T3404C						.						50	51	51					2																	170806434		2203	4299	6502	SO:0001583	missense	130507	exon23			CTGCCGTGGAAAG	AL834144	CCDS2238.2	2q31.1	2008-06-23	2008-06-23	2007-11-29	ENSG00000144357	ENSG00000144357		"Ubiquitin protein ligase E3 component n-recognins"	30467	protein-coding gene	gene with protein product		613831	"zinc finger protein 650"	ZNF650		17462990	Standard	NM_172070		Approved	KIAA2024, DKFZp434P117, FLJ37422	uc010zdi.2	Q6ZT12	OTTHUMG00000132229	ENST00000272793.5:c.3404T>C	chr2.hg19:g.170806434T>C	ENSP00000272793:p.Val1135Ala	156.0	0.0		87.0	4.0	NM_172070	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Missense_Mutation	SNP	ENST00000272793.5	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.50|18.50	3.636499|3.636499	0.67130|0.67130	.|.	.|.	ENSG00000144357|ENSG00000144357	ENST00000272793;ENST00000442603;ENST00000418381|ENST00000392632	T;T|.	0.57436|.	0.4;0.4|.	5.71|5.71	5.71|5.71	0.89125|0.89125	.|.	.|.	.|.	.|.	.|.	T|T	0.53270|0.53270	0.1786|0.1786	N|N	0.22421|0.22421	0.69|0.69	0.80722|0.80722	D|D	1|1	B|.	0.34015|.	0.435|.	B|.	0.30401|.	0.115|.	T|T	0.50171|0.50171	-0.8859|-0.8859	9|5	0.48119|.	T|.	0.1|.	.|.	16.0044|16.0044	0.80349|0.80349	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1135|.	Q6ZT12|.	UBR3_HUMAN|.	A|R	1135|193	ENSP00000272793:V1135A;ENSP00000396068:V1135A|.	ENSP00000272793:V1135A|.	V|W	+|+	2|1	0|0	UBR3|UBR3	170514680|170514680	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.893000|0.893000	0.52053|0.52053	7.841000|7.841000	0.86834|0.86834	2.191000|2.191000	0.70037|0.70037	0.528000|0.528000	0.53228|0.53228	GTG|TGG	.	.		0.373	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070		C	170806434	T	C	170806434	3	2	260	1	0	0	0	0	1	0	0	0	16918	1696	59	2	3494	2	UBR3	2	170806434	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	670432	170806434	72392939	124	37369										
UBR3	130507	hgsc.bcm.edu	37	chr2	170897404	170897404	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcttttaggctgggatatgaAgaacaacagcctgaggttcc	11	8	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:170897404A>G	ENST00000272793.5	+	32	4619	c.4569A>G	c.(4567-4569)gaA>gaG	p.E1523E	UBR3_ENST00000418381.1_Silent_p.E1523E|UBR3_ENST00000392631.1_Silent_p.E344E			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	1523					embryo development (GO:0009790)|in utero embryonic development (GO:0001701)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)|suckling behavior (GO:0001967)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1)	33						TGGGATATGAAGAACAACAGC	0.333																																					p.E1523E		Atlas-SNP	.											.	UBR3	182	.	0			c.A4569G						.						112	104	107					2																	170897404		2203	4300	6503	SO:0001819	synonymous_variant	130507	exon32			ATATGAAGAACAA	AL834144	CCDS2238.2	2q31.1	2008-06-23	2008-06-23	2007-11-29	ENSG00000144357	ENSG00000144357		"Ubiquitin protein ligase E3 component n-recognins"	30467	protein-coding gene	gene with protein product		613831	"zinc finger protein 650"	ZNF650		17462990	Standard	NM_172070		Approved	KIAA2024, DKFZp434P117, FLJ37422	uc010zdi.2	Q6ZT12	OTTHUMG00000132229	ENST00000272793.5:c.4569A>G	chr2.hg19:g.170897404A>G		151.0	0.0		93.0	4.0	NM_172070	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Silent	SNP	ENST00000272793.5	hg19		.	.	.	.	.	.	.	.	.	.	A	8.635	0.894600	0.17613	.	.	ENSG00000144357	ENST00000392632	.	.	.	5.27	1.32	0.21799	.	.	.	.	.	T	0.43986	0.1272	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.23762	-1.0179	4	.	.	.	.	3.0354	0.06121	0.5147:0.0:0.2027:0.2826	.	.	.	.	R	585	.	.	K	+	2	0	UBR3	170605650	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	0.865000	0.27940	0.399000	0.25367	0.477000	0.44152	AAG	.	.		0.333	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070		G	170897404	A	G	170897404	2	3	260	1	0	0	0	0	0	0	0	1	16918	69	3	2		2	UBR3	2	170897404	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	90970	170897404	72301969	125	37370										
SCRN3	79634	hgsc.bcm.edu	37	chr2	175269041	175269041	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	caagcttctaaataagcacaAaggtaattttatcatataaa	4	6	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:175269041A>C	ENST00000272732.6	+	5	834	c.752A>C	c.(751-753)aAa>aCa	p.K251T	SCRN3_ENST00000409673.3_Missense_Mutation_p.K244T	NM_001193528.1|NM_024583.4	NP_001180457.1|NP_078859.2	Q0VDG4	SCRN3_HUMAN	secernin 3	251							dipeptidase activity (GO:0016805)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|urinary_tract(3)	13			OV - Ovarian serous cystadenocarcinoma(117;0.229)			AATAAGCACAAAGGTAATTTT	0.333																																					p.K251T		Atlas-SNP	.											.	SCRN3	76	.	0			c.A752C						.						51	48	49					2																	175269041		2203	4300	6503	SO:0001583	missense	79634	exon5			AGCACAAAGGTAA	AF279776	CCDS2258.1, CCDS54420.1	2q31	2008-02-05			ENSG00000144306	ENSG00000144306			30382	protein-coding gene	gene with protein product		614967				12221138	Standard	NM_024583		Approved	FLJ23142	uc002uiq.3	Q0VDG4	OTTHUMG00000132332	ENST00000272732.6:c.752A>C	chr2.hg19:g.175269041A>C	ENSP00000272732:p.Lys251Thr	107.0	0.0		76.0	21.0	NM_024583	B4DI11|C9JPC1|D3DPE0|Q7L1C5|Q9H5R5	Missense_Mutation	SNP	ENST00000272732.6	hg19	CCDS2258.1	.	.	.	.	.	.	.	.	.	.	A	13.06	2.123118	0.37436	.	.	ENSG00000144306	ENST00000409673;ENST00000272732	T;T	0.20738	2.05;2.05	5.82	3.33	0.38152	.	0.446498	0.27640	N	0.018464	T	0.20941	0.0504	L	0.40543	1.245	0.26434	N	0.975891	P;P	0.39920	0.695;0.491	P;B	0.46419	0.516;0.258	T	0.10086	-1.0645	10	0.17832	T	0.49	-16.118	9.0186	0.36186	0.8083:0.126:0.0658:0.0	.	244;251	B4DI11;Q0VDG4	.;SCRN3_HUMAN	T	244;251	ENSP00000387142:K244T;ENSP00000272732:K251T	ENSP00000272732:K251T	K	+	2	0	SCRN3	174977287	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.286000	0.58995	0.409000	0.25649	-0.316000	0.08728	AAA	.	.		0.333	SCRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255451.2	NM_024583		C	175269041	A	C	175269041	3	2	260	1	0	0	0	0	1	0	0	0	13955	14	1	5	766	5	SCRN3	2	175269041	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	4371637	175269041	67930332	126	37371										
TTN	7273	hgsc.bcm.edu	37	chr2	179393915	179393915	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	atttcagaagtcttttgtgtAgagactttctgtgcctcagt	9	7	4	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:179393915A>G	ENST00000591111.1	-	310	101864	c.101640T>C	c.(101638-101640)tcT>tcC	p.S33880S	TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN_ENST00000342992.6_Silent_p.S32953S|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN_ENST00000460472.2_Silent_p.S26456S|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN_ENST00000342175.6_Silent_p.S26648S|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000359218.5_Silent_p.S26581S|TTN-AS1_ENST00000592161.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN_ENST00000589042.1_Silent_p.S35521S|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000587576.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000456053.1_RNA			Q8WZ42	TITIN_HUMAN	titin	33880					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCTTTTGTGTAGAGACTTTCT	0.378																																					p.S35521S		Atlas-SNP	.											.	TTN	18412	.	0			c.T106563C						.						19	18	19					2																	179393915		1799	4058	5857	SO:0001819	synonymous_variant	7273	exon360			TTGTGTAGAGACT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.101640T>C	chr2.hg19:g.179393915A>G		99.0	0.0		63.0	4.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.378	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179393915	A	G	179393915	2	3	260	1	0	0	0	0	0	0	0	1	16750	407	15	2		2	TTN	2	179393915	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	4124874	179393915	63805458	127	37372										
TTN	7273	hgsc.bcm.edu	37	chr2	179396537	179396537	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggggcatggtccagtgtgaaAggctgctgactcaaaacttc	13	9	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:179396537A>G	ENST00000591111.1	-	308	100106	c.99882T>C	c.(99880-99882)ccT>ccC	p.P33294P	TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN_ENST00000342992.6_Silent_p.P32367P|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN_ENST00000460472.2_Silent_p.P25870P|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN_ENST00000342175.6_Silent_p.P26062P|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000359218.5_Silent_p.P25995P|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN_ENST00000589042.1_Silent_p.P34935P|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000456053.1_RNA			Q8WZ42	TITIN_HUMAN	titin	33294					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCAGTGTGAAAGGCTGCTGAC	0.423																																					p.P34935P		Atlas-SNP	.											.	TTN	18412	.	0			c.T104805C						.						64	63	63					2																	179396537		1990	4159	6149	SO:0001819	synonymous_variant	7273	exon358			TGTGAAAGGCTGC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.99882T>C	chr2.hg19:g.179396537A>G		242.0	0.0		144.0	43.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179396537	A	G	179396537	2	3	260	1	0	0	0	0	0	0	0	1	16750	59	3	2		2	TTN	2	179396537	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	2622	179396537	63802836	128	37373										
TTN	7273	hgsc.bcm.edu	37	chr2	179458397	179458397	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ataatcttttccttcaagtaGtttagaaactttgcatgttg	6	6	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:179458397G>T	ENST00000591111.1	-	248	53931	c.53707C>A	c.(53707-53709)Cta>Ata	p.L17903I	TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.L16976I|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.L10479I|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.L10671I|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.L10604I|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.L19544I|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000456053.1_RNA			Q8WZ42	TITIN_HUMAN	titin	17903	Fibronectin type-III 29. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCTTCAAGTAGTTTAGAAACT	0.358																																					p.L19544I		Atlas-SNP	.											.	TTN	18412	.	0			c.C58630A						.						97	92	93					2																	179458397		1853	4089	5942	SO:0001583	missense	7273	exon298			CAAGTAGTTTAGA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.53707C>A	chr2.hg19:g.179458397G>T	ENSP00000465570:p.Leu17903Ile	269.0	0.0		201.0	56.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	9.206	1.029740	0.19512	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	D;D;D;D	0.84516	-1.86;-1.86;-1.86;-1.86	6.02	2.88	0.33553	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.94331	0.8178	H	0.96996	3.92	0.45452	D	0.998423	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.87578	0.998;0.998;0.998;0.998	D	0.94927	0.8079	9	0.87932	D	0	.	12.0732	0.53628	0.2571:0.0:0.7429:0.0	.	10479;10604;10671;17903	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	I	16976;10479;10671;10604;10477	ENSP00000343764:L16976I;ENSP00000434586:L10479I;ENSP00000340554:L10671I;ENSP00000352154:L10604I	ENSP00000340554:L10671I	L	-	1	2	TTN	179166643	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	5.478000	0.66806	0.895000	0.36342	-0.808000	0.03180	CTA	.	.		0.358	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179458397	G	T	179458397	3	4	260	1	0	0	0	0	1	0	0	0	16750	1020	36	3	49609	3	TTN	2	179458397	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	61860	179458397	63740976	129	37374										
TTN	7273	hgsc.bcm.edu	37	chr2	179605820	179605820	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtggaaaatcctcaggagccTctggtgtggactttgctttg	13	8	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:179605820T>C	ENST00000591111.1	-	46	11413	c.11189A>G	c.(11188-11190)gAg>gGg	p.E3730G	TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.E3684G|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.E3876G|TTN_ENST00000359218.5_Missense_Mutation_p.E3809G|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.E4047G			Q8WZ42	TITIN_HUMAN	titin	33770					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTCAGGAGCCTCTGGTGTGGA	0.493																																					p.E4047G		Atlas-SNP	.											.	TTN	18412	.	0			c.A12140G						.						144	142	142					2																	179605820		1871	4110	5981	SO:0001583	missense	7273	exon48			GGAGCCTCTGGTG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.11189A>G	chr2.hg19:g.179605820T>C	ENSP00000465570:p.Glu3730Gly	81.0	0.0		59.0	4.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	11.11	1.542616	0.27563	.	.	ENSG00000155657	ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T	0.60672	0.19;0.18;0.17	5.65	1.71	0.24356	.	.	.	.	.	T	0.32645	0.0836	N	0.11560	0.145	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.24154	-1.0168	9	0.87932	D	0	.	2.1101	0.03701	0.1301:0.1544:0.1346:0.5809	.	3684;3809;3876	D3DPF9;E7EQE6;E7ET18	.;.;.	G	3684;3876;3809;3684	ENSP00000434586:E3684G;ENSP00000340554:E3876G;ENSP00000352154:E3809G	ENSP00000340554:E3876G	E	-	2	0	TTN	179314065	0.000000	0.05858	0.055000	0.19348	0.125000	0.20455	-0.152000	0.10159	0.491000	0.27793	0.533000	0.62120	GAG	.	.		0.493	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179605820	T	C	179605820	3	2	260	1	0	0	0	0	1	0	0	0	16750	1551	54	2	92649	2	TTN	2	179605820	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	147423	179605820	63593553	130	37375										
COL5A2	1290	hgsc.bcm.edu	37	chr2	189950498	189950498	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcctgtaggtcctgcaccacCctacagttgaaaacaaagta	7	12	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:189950498C>T	ENST00000374866.3	-	10	965	c.691G>A	c.(691-693)Ggt>Agt	p.G231S		NM_000393.3	NP_000384.2	P05997	CO5A2_HUMAN	collagen, type V, alpha 2	231					axon guidance (GO:0007411)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|negative regulation of endodermal cell differentiation (GO:1903225)|skeletal system development (GO:0001501)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(53)|ovary(3)|prostate(2)|skin(6)|urinary_tract(3)	95			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			CCTGCACCACCCTACAGTTGA	0.413																																					p.G231S		Atlas-SNP	.											.	COL5A2	230	.	0			c.G691A						.						78	75	76					2																	189950498		2203	4300	6503	SO:0001630	splice_region_variant	1290	exon10			CACCACCCTACAG	Y14690	CCDS33350.1	2q14-q32	2014-09-17			ENSG00000204262	ENSG00000204262		"Collagens"	2210	protein-coding gene	gene with protein product	"AB collagen"	120190				1572660	Standard	NM_000393		Approved		uc002uqk.3	P05997	OTTHUMG00000149842	ENST00000374866.3:c.691-1G>A	chr2.hg19:g.189950498C>T		56.0	0.0		55.0	4.0	NM_000393	P78440|Q13908|Q53WR4|Q59GR4|Q6LDJ5|Q7KZ55|Q86XF6|Q96QB0|Q96QB3	Missense_Mutation	SNP	ENST00000374866.3	hg19	CCDS33350.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.752884	0.89753	.	.	ENSG00000204262	ENST00000374866;ENST00000452536	D	0.99329	-5.75	5.99	5.99	0.97316	.	0.000000	0.56097	D	0.000040	D	0.99722	0.9892	H	0.99026	4.405	0.80722	D	1	D	0.76494	0.999	D	0.97110	1.0	D	0.97362	0.9970	9	.	.	.	.	17.3945	0.87441	0.0:1.0:0.0:0.0	.	231	P05997	CO5A2_HUMAN	S	231;48	ENSP00000364000:G231S	.	G	-	1	0	COL5A2	189658743	1.000000	0.71417	1.000000	0.80357	0.679000	0.39708	3.904000	0.56325	2.840000	0.97914	0.655000	0.94253	GGT	.	.		0.413	COL5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313523.1	NM_000393	Missense_Mutation	T	189950498	C	T	189950498	5	4	260	1	0	0	0	0	0	0	1	0	3699	637	22	3	3988	3	COL5A2	2	189950498	Splice_Site	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	10344678	189950498	53248875	131	37376										
AOX1	316	hgsc.bcm.edu	37	chr2	201502979	201502979	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgttctggaacgaggagaagAcatgttaataactggaggcc	13	6	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:201502979A>G	ENST00000374700.2	+	23	2763	c.2522A>G	c.(2521-2523)gAc>gGc	p.D841G	AOX1_ENST00000485106.1_3'UTR	NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	841					inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)			breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	CGAGGAGAAGACATGTTAATA	0.443																																					p.D841G		Atlas-SNP	.											.	AOX1	152	.	0			c.A2522G						.						150	136	141					2																	201502979		2203	4300	6503	SO:0001583	missense	316	exon23			GAGAAGACATGTT	AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356			553	protein-coding gene	gene with protein product		602841				7570184	Standard	NM_001159		Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	ENST00000374700.2:c.2522A>G	chr2.hg19:g.201502979A>G	ENSP00000363832:p.Asp841Gly	141.0	0.0		91.0	4.0	NM_001159	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	Missense_Mutation	SNP	ENST00000374700.2	hg19	CCDS33360.1	.	.	.	.	.	.	.	.	.	.	A	27.2	4.811773	0.90707	.	.	ENSG00000138356	ENST00000374700	T	0.41758	0.99	5.35	5.35	0.76521	Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding (3);	0.000000	0.85682	D	0.000000	T	0.77831	0.4189	H	0.98612	4.28	0.80722	D	1	D	0.60575	0.988	D	0.71414	0.973	D	0.86836	0.2014	10	0.87932	D	0	-71.5759	15.4951	0.75643	1.0:0.0:0.0:0.0	.	841	Q06278	ADO_HUMAN	G	841	ENSP00000363832:D841G	ENSP00000363832:D841G	D	+	2	0	AOX1	201211224	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.546000	0.90661	2.247000	0.74100	0.482000	0.46254	GAC	.	.		0.443	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335844.1	NM_001159		G	201502979	A	G	201502979	3	3	260	1	0	0	0	0	1	0	0	0	729	275	10	2	2612	2	AOX1	2	201502979	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	11552481	201502979	41696394	132	37377										
ALS2CR8	79800	hgsc.bcm.edu	37	chr2	203817314	203817314	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agcccaacagaaaatggacaGgtacttcgtgtaattccacc	8	11	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:203817314G>T	ENST00000402905.3	+	5	660	c.339G>T	c.(337-339)caG>caT	p.Q113H	CARF_ENST00000434998.1_Missense_Mutation_p.Q11H|CARF_ENST00000545262.1_Missense_Mutation_p.Q37H|CARF_ENST00000320443.8_Missense_Mutation_p.Q113H|CARF_ENST00000444724.1_Missense_Mutation_p.Q113H|CARF_ENST00000438828.2_Missense_Mutation_p.Q113H|CARF_ENST00000456821.2_Missense_Mutation_p.Q101H|CARF_ENST00000428585.1_Missense_Mutation_p.Q37H|CARF_ENST00000471271.1_3'UTR|CARF_ENST00000545253.1_Missense_Mutation_p.Q25H|WDR12_ENST00000477723.1_Intron|CARF_ENST00000414439.1_Missense_Mutation_p.Q11H	NM_001104586.1|NM_001282910.1|NM_001282911.1|NM_001282912.1	NP_001098056.1|NP_001269839.1|NP_001269840.1|NP_001269841.1	Q8N187	CARTF_HUMAN	calcium responsive transcription factor	113					cellular response to calcium ion (GO:0071277)|cellular response to potassium ion (GO:0035865)|positive regulation of transcription from RNA polymerase II promoter in response to calcium ion (GO:0061400)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)										AAAATGGACAGGTACTTCGTG	0.393																																					p.Q113H		Atlas-SNP	.											.	ALS2CR8	56	.	0			c.G339T						.						147	130	136					2																	203817314		1858	4107	5965	SO:0001583	missense	79800	exon6			TGGACAGGTACTT	AB053309	CCDS42801.1, CCDS63091.1	2q33.3	2013-06-12	2013-06-12	2013-06-12	ENSG00000138380	ENSG00000138380			14435	protein-coding gene	gene with protein product	"calcium-response factor"	607586	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 8"	ALS2CR8		11586298, 11832226	Standard	XM_005246858		Approved	FLJ21579, CaRF, NYD-SP24	uc002uzo.2	Q8N187	OTTHUMG00000154528	ENST00000402905.3:c.339G>T	chr2.hg19:g.203817314G>T	ENSP00000384006:p.Gln113His	114.0	0.0		61.0	5.0	NM_024744	B4E1W7|G3V1K7|Q8ND29|Q8WXC0|Q96J78|Q96Q38|Q96Q39|Q9H712	Missense_Mutation	SNP	ENST00000402905.3	hg19	CCDS42801.1	.	.	.	.	.	.	.	.	.	.	G	19.89	3.910357	0.72983	.	.	ENSG00000138380	ENST00000402905;ENST00000431787;ENST00000444724;ENST00000414857;ENST00000414439;ENST00000428585;ENST00000545253;ENST00000545262;ENST00000447539;ENST00000456821;ENST00000434998;ENST00000320443;ENST00000438828	.	.	.	5.46	3.65	0.41850	.	0.116572	0.38492	N	0.001675	T	0.58323	0.2114	M	0.61703	1.905	0.32583	N	0.528232	D;D;D;D;P	0.64830	0.963;0.963;0.994;0.963;0.937	P;P;P;P;P	0.60473	0.81;0.875;0.875;0.81;0.824	T	0.67848	-0.5564	9	0.87932	D	0	-0.078	8.3599	0.32353	0.2388:0.0:0.7612:0.0	.	25;37;113;113;113	B4DIA7;G3V1K7;B4DRP6;Q8N187;F6SXV3	.;.;.;AL2S8_HUMAN;.	H	113;83;113;113;11;37;25;37;37;101;11;113;113	.	ENSP00000316224:Q113H	Q	+	3	2	ALS2CR8	203525559	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	1.484000	0.35508	0.671000	0.31185	0.467000	0.42956	CAG	.	.		0.393	CARF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335768.5	NM_001104586		T	203817314	G	T	203817314	3	4	260	1	0	0	0	0	1	0	0	0	555	991	35	3	349	3	ALS2CR8	2	203817314	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	2314335	203817314	39382059	133	37378										
INO80D	54891	hgsc.bcm.edu	37	chr2	206893049	206893049	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gctcctactctccgcatcatCatcatctgacctggaaagtg	7	14	5	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:206893049C>T	ENST00000403263.1	-	6	1488	c.1084G>A	c.(1084-1086)Gat>Aat	p.D362N	Y_RNA_ENST00000384656.1_RNA	NM_017759.4	NP_060229.3	Q53TQ3	IN80D_HUMAN	INO80 complex subunit D	362	Poly-Asp.				DNA recombination (GO:0006310)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	26						TCCGCATCATCATCATCTGAC	0.458																																					p.D362N		Atlas-SNP	.											.	INO80D	134	.	0			c.G1084A						.						65	64	65					2																	206893049		1933	4152	6085	SO:0001583	missense	54891	exon6			CATCATCATCATC		CCDS46500.1	2q33.3	2011-07-06			ENSG00000114933	ENSG00000114933		"INO80 complex subunits"	25997	protein-coding gene	gene with protein product						16230350	Standard	NM_017759		Approved	FLJ20309	uc002vaz.4	Q53TQ3	OTTHUMG00000154649	ENST00000403263.1:c.1084G>A	chr2.hg19:g.206893049C>T	ENSP00000384198:p.Asp362Asn	61.0	0.0		59.0	4.0	NM_017759	B3KU68|B9EG77|Q6PJC6|Q6PJU1|Q6PKA1|Q9NXD5	Missense_Mutation	SNP	ENST00000403263.1	hg19	CCDS46500.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.431849	0.83776	.	.	ENSG00000114933	ENST00000403263;ENST00000233270;ENST00000424117	T;T	0.52754	0.65;0.65	5.45	5.45	0.79879	.	0.049789	0.85682	D	0.000000	T	0.45013	0.1321	L	0.27053	0.805	0.45528	D	0.998489	P	0.40731	0.728	P	0.46076	0.503	T	0.17806	-1.0357	10	0.22109	T	0.4	.	19.2666	0.93988	0.0:1.0:0.0:0.0	.	362	Q53TQ3-2	.	N	362;362;257	ENSP00000384198:D362N;ENSP00000402369:D257N	ENSP00000233270:D362N	D	-	1	0	INO80D	206601294	1.000000	0.71417	0.788000	0.31933	0.646000	0.38490	6.761000	0.74945	2.555000	0.86185	0.591000	0.81541	GAT	.	.		0.458	INO80D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336459.1	NM_017759		T	206893049	C	T	206893049	3	4	260	1	0	0	0	0	1	0	0	0	7758	826	29	3	2023	3	INO80D	2	206893049	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	3075735	206893049	36306324	134	37379										
ZDBF2	57683	hgsc.bcm.edu	37	chr2	207175357	207175357	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aaaatgaggcaccatagttgGgataatgatattcggtttat	10	4	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:207175357G>A	ENST00000374423.3	+	5	6491	c.6105G>A	c.(6103-6105)tgG>tgA	p.W2035*		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	2035							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						ACCATAGTTGGGATAATGATA	0.358																																					p.W2035X		Atlas-SNP	.											.	ZDBF2	531	.	0			c.G6105A						.						26	24	25					2																	207175357		1828	4074	5902	SO:0001587	stop_gained	57683	exon5			TAGTTGGGATAAT	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"Zinc fingers, DBF-type"	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.6105G>A	chr2.hg19:g.207175357G>A	ENSP00000363545:p.Trp2035*	119.0	0.0		73.0	5.0	NM_020923	Q6ZNP7|Q6ZSN8	Nonsense_Mutation	SNP	ENST00000374423.3	hg19	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	G	46	12.441704	0.99668	.	.	ENSG00000204186	ENST00000374423	.	.	.	5.49	-0.144	0.13440	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	.	1.9505	0.03365	0.1544:0.1464:0.3828:0.3164	.	.	.	.	X	2035	.	ENSP00000363545:W2035X	W	+	3	0	ZDBF2	206883602	0.000000	0.05858	0.001000	0.08648	0.125000	0.20455	-0.476000	0.06591	0.278000	0.22164	0.563000	0.77884	TGG	.	.		0.358	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		A	207175357	G	A	207175357	4	1	260	1	0	0	0	0	0	1	0	0	17614	1241	43	3	6115	3	ZDBF2	2	207175357	Nonsense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	282308	207175357	36024016	135	37380										
ABCA12	26154	hgsc.bcm.edu	37	chr2	215807647	215807647	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aagcaatgcatttgttcttcAcctgctctttatgtgctgca	7	10	3	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:215807647A>G	ENST00000272895.7	-	50	7656		c.e50+1		ABCA12_ENST00000389661.4_Splice_Site|AC072062.1_ENST00000607412.1_RNA	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12						cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		TTTGTTCTTCACCTGCTCTTT	0.393																																					.	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											.	ABCA12	368	.	0			c.6482+2T>C						.						112	99	104					2																	215807647		2203	4300	6503	SO:0001630	splice_region_variant	26154	exon43			TTCTTCACCTGCT	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.7436+1T>C	chr2.hg19:g.215807647A>G		114.0	0.0		85.0	4.0	NM_015657	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Splice_Site	SNP	ENST00000272895.7	hg19	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.574876	0.86542	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	.	.	.	5.65	5.65	0.86999	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.827	0.78718	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ABCA12	215515892	1.000000	0.71417	0.989000	0.46669	0.922000	0.55478	8.971000	0.93419	2.276000	0.75962	0.528000	0.53228	.	.	.		0.393	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076	Intron	G	215807647	A	G	215807647	5	3	260	1	0	0	0	0	0	0	1	0	30	173	6	2	365	2	ABCA12	2	215807647	Splice_Site	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	8632290	215807647	27391726	136	37381										
TNS1	7145	hgsc.bcm.edu	37	chr2	218712293	218712293	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctcctcctctggagtccgggAggggtctgaagtcgcttcct	13	13	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:218712293A>G	ENST00000171887.4	-	17	3024	c.2572T>C	c.(2572-2574)Tcc>Ccc	p.S858P	TNS1_ENST00000430930.1_Missense_Mutation_p.S858P|TNS1_ENST00000480665.1_5'Flank|TNS1_ENST00000419504.1_Missense_Mutation_p.S858P	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	858					cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		GGAGTCCGGGAGGGGTCTGAA	0.597																																					p.S858P		Atlas-SNP	.											.	TNS1	251	.	0			c.T2572C						.						71	80	77					2																	218712293		2203	4300	6503	SO:0001583	missense	7145	exon17			TCCGGGAGGGGTC	AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	11973	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 155"	600076	"tensin", "matrix-remodelling associated 6"	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.2572T>C	chr2.hg19:g.218712293A>G	ENSP00000171887:p.Ser858Pro	135.0	0.0		107.0	5.0	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	hg19	CCDS2407.1	.	.	.	.	.	.	.	.	.	.	A	11.07	1.529497	0.27387	.	.	ENSG00000079308	ENST00000171887;ENST00000419504;ENST00000430930	D;D;D	0.91843	-2.91;-2.92;-2.91	4.31	4.31	0.51392	.	0.331813	0.27258	N	0.020189	D	0.89884	0.6844	L	0.27053	0.805	0.80722	D	1	P;D;D;D;D	0.67145	0.808;0.996;0.996;0.988;0.988	P;P;P;P;P	0.53313	0.461;0.676;0.676;0.723;0.676	D	0.88780	0.3270	10	0.33141	T	0.24	.	13.6499	0.62304	1.0:0.0:0.0:0.0	.	858;912;858;858;858	B2RU35;A1L0S7;Q9HBL0;E9PGF5;E9PF55	.;.;TENS1_HUMAN;.;.	P	858	ENSP00000171887:S858P;ENSP00000408724:S858P;ENSP00000406016:S858P	ENSP00000171887:S858P	S	-	1	0	TNS1	218420538	0.902000	0.30710	0.999000	0.59377	0.781000	0.44180	1.146000	0.31589	1.795000	0.52594	0.379000	0.24179	TCC	.	.		0.597	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		G	218712293	A	G	218712293	3	3	260	1	0	0	0	0	1	0	0	0	16358	304	11	2	2703	2	TNS1	2	218712293	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	2904646	218712293	24487080	137	37382										
ARPC2	10109	hgsc.bcm.edu	37	chr2	219114132	219114132	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cagtgctcgagacaacaccaTcaacctgatccacacgttcc	6	16	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:219114132T>C	ENST00000295685.10	+	8	983	c.722T>C	c.(721-723)aTc>aCc	p.I241T	ARPC2_ENST00000315717.5_Missense_Mutation_p.I241T|ARPC2_ENST00000477992.1_3'UTR	NM_005731.2	NP_005722.1	O15144	ARPC2_HUMAN	actin related protein 2/3 complex, subunit 2, 34kDa	241					Arp2/3 complex-mediated actin nucleation (GO:0034314)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural constituent of cytoskeleton (GO:0005200)			cervix(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)	6		Renal(207;0.0474)		Epithelial(149;1.21e-06)|all cancers(144;0.000212)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0103)		GACAACACCATCAACCTGATC	0.542																																					p.I241T		Atlas-SNP	.											.	ARPC2	25	.	0			c.T722C						.						192	135	154					2																	219114132		2203	4300	6503	SO:0001583	missense	10109	exon8			ACACCATCAACCT	AF006085	CCDS2410.1	2q36.1	2011-07-06	2002-08-29		ENSG00000163466	ENSG00000163466		"Actin related protein 2/3 complex subunits"	705	protein-coding gene	gene with protein product		604224	"actin related protein 2/3 complex, subunit 2 (34 kD)"			9359840, 9230079	Standard	NM_005731		Approved	p34-Arc, ARC34	uc002vhd.4	O15144	OTTHUMG00000133618	ENST00000295685.10:c.722T>C	chr2.hg19:g.219114132T>C	ENSP00000295685:p.Ile241Thr	129.0	0.0		110.0	5.0	NM_005731	Q92801|Q9P1D4	Missense_Mutation	SNP	ENST00000295685.10	hg19	CCDS2410.1	.	.	.	.	.	.	.	.	.	.	T	31	5.065179	0.93898	.	.	ENSG00000163466	ENST00000315717;ENST00000295685;ENST00000456575	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.85741	0.5767	M	0.91300	3.195	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.88443	0.3043	9	0.66056	D	0.02	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	241	O15144	ARPC2_HUMAN	T	241;241;56	.	ENSP00000295685:I241T	I	+	2	0	ARPC2	218822377	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.005000	0.88553	2.371000	0.80710	0.533000	0.62120	ATC	.	.		0.542	ARPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256777.2	NM_005731		C	219114132	T	C	219114132	3	2	260	1	0	0	0	0	1	0	0	0	971	1435	50	2	752	2	ARPC2	2	219114132	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	401839	219114132	24085241	138	37383										
SLC11A1	6556	hgsc.bcm.edu	37	chr2	219251389	219251389	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cgtcctctggctgaccatcgAgctagccattgtgggctccg	12	14	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:219251389A>G	ENST00000233202.6	+	5	765	c.425A>G	c.(424-426)gAg>gGg	p.E142G	SLC11A1_ENST00000539932.1_Missense_Mutation_p.E24G|SLC11A1_ENST00000473367.1_3'UTR	NM_000578.3	NP_000569.3	P49279	NRAM1_HUMAN	solute carrier family 11 (proton-coupled divalent metal ion transporter), member 1	142					activation of protein kinase activity (GO:0032147)|antigen processing and presentation of peptide antigen (GO:0048002)|cadmium ion transmembrane transport (GO:0070574)|cellular cadmium ion homeostasis (GO:0006876)|cellular iron ion homeostasis (GO:0006879)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|defense response to protozoan (GO:0042832)|divalent metal ion export (GO:0070839)|inflammatory response (GO:0006954)|interaction with host (GO:0051701)|interleukin-2 production (GO:0032623)|interleukin-3 production (GO:0032632)|iron ion homeostasis (GO:0055072)|iron ion transport (GO:0006826)|L-arginine import (GO:0043091)|macrophage activation (GO:0042116)|manganese ion transport (GO:0006828)|MHC class II biosynthetic process (GO:0045342)|mRNA stabilization (GO:0048255)|multicellular organismal iron ion homeostasis (GO:0060586)|negative regulation of cytokine production (GO:0001818)|nitrite transport (GO:0015707)|phagocytosis (GO:0006909)|phagosome maturation (GO:0090382)|positive regulation of cytokine production (GO:0001819)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of gene expression (GO:0010628)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of phagocytosis (GO:0050766)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein import into nucleus, translocation (GO:0000060)|respiratory burst (GO:0045730)|response to bacterium (GO:0009617)|response to interferon-gamma (GO:0034341)|response to lipopolysaccharide (GO:0032496)|T cell cytokine production (GO:0002369)|T cell proliferation involved in immune response (GO:0002309)|transmembrane transport (GO:0055085)|vacuolar acidification (GO:0007035)|wound healing (GO:0042060)	cell outer membrane (GO:0009279)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|late endosome membrane (GO:0031902)|lysosome (GO:0005764)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|tertiary granule membrane (GO:0070821)	manganese ion transmembrane transporter activity (GO:0005384)|metal ion:proton antiporter activity (GO:0051139)|protein homodimerization activity (GO:0042803)|transition metal ion transmembrane transporter activity (GO:0046915)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	19		Renal(207;0.0474)		Epithelial(149;1.16e-06)|all cancers(144;0.000195)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CTGACCATCGAGCTAGCCATT	0.567																																					p.E142G		Atlas-SNP	.											.	SLC11A1	41	.	0			c.A425G						.						89	73	78					2																	219251389		2203	4300	6503	SO:0001583	missense	6556	exon5			CCATCGAGCTAGC	D38171	CCDS2415.1	2q35	2013-07-18	2013-07-18		ENSG00000018280	ENSG00000018280		"Solute carriers"	10907	protein-coding gene	gene with protein product	"natural resistance-associated macrophage protein 1"	600266		LSH, NRAMP, NRAMP1		7964458, 7980580	Standard	NM_000578		Approved		uc002vhv.3	P49279	OTTHUMG00000086747	ENST00000233202.6:c.425A>G	chr2.hg19:g.219251389A>G	ENSP00000233202:p.Glu142Gly	43.0	0.0		24.0	4.0	NM_000578	C0H5Y3	Missense_Mutation	SNP	ENST00000233202.6	hg19	CCDS2415.1	.	.	.	.	.	.	.	.	.	.	A	17.55	3.418765	0.62622	.	.	ENSG00000018280	ENST00000233202;ENST00000539932	T;T	0.73258	-0.73;-0.73	5.24	4.1	0.47936	.	0.000000	0.85682	D	0.000000	D	0.88966	0.6581	H	0.97874	4.095	0.58432	D	0.99999	D;D;D	0.89917	0.997;1.0;1.0	D;D;D	0.97110	0.942;1.0;1.0	D	0.91059	0.4884	10	0.87932	D	0	-18.546	11.0891	0.48104	0.9279:0.0:0.0721:0.0	.	142;24;142	B4DQ73;C0H5Y3;P49279	.;.;NRAM1_HUMAN	G	142;24	ENSP00000233202:E142G;ENSP00000443435:E24G	ENSP00000233202:E142G	E	+	2	0	SLC11A1	218959633	1.000000	0.71417	0.992000	0.48379	0.001000	0.01503	6.846000	0.75399	1.128000	0.42052	0.533000	0.62120	GAG	.	.		0.567	SLC11A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195076.2	NM_000578		G	219251389	A	G	219251389	3	3	260	1	0	0	0	0	1	0	0	0	14395	304	11	2	443	2	SLC11A1	2	219251389	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	137257	219251389	23947984	139	37384										
CYP27A1	1593	hgsc.bcm.edu	37	chr2	219674345	219674345	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	caatgtggatgtcctacttaGggcctcagatgcacgtgaac	11	10	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:219674345G>A	ENST00000258415.4	+	2	728	c.301G>A	c.(301-303)Ggg>Agg	p.G101R		NM_000784.3	NP_000775.1	Q02318	CP27A_HUMAN	cytochrome P450, family 27, subfamily A, polypeptide 1	101					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cholesterol metabolic process (GO:0008203)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)	cholestanetriol 26-monooxygenase activity (GO:0047749)|cholesterol 26-hydroxylase activity (GO:0031073)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid hydroxylase activity (GO:0008395)|vitamin D3 25-hydroxylase activity (GO:0030343)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|prostate(3)|urinary_tract(1)	26		Renal(207;0.0474)		Epithelial(149;9.48e-07)|all cancers(144;0.000171)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00981)	Chenodeoxycholic acid(DB06777)|Cholecalciferol(DB00169)|Ergocalciferol(DB00153)|Pegvisomant(DB00082)	GTCCTACTTAGGGCCTCAGAT	0.547																																					p.G101R		Atlas-SNP	.											.	CYP27A1	52	.	0			c.G301A						.						146	130	136					2																	219674345		2203	4300	6503	SO:0001583	missense	1593	exon2			TACTTAGGGCCTC	BC017044	CCDS2423.1	2q35	2013-09-19	2003-01-14		ENSG00000135929	ENSG00000135929		"Cytochrome P450s"	2605	protein-coding gene	gene with protein product	"cerebrotendinous xanthomatosis"	606530	"cytochrome P450, subfamily XXVIIA (steroid 27-hydroxylase, cerebrotendinous xanthomatosis), polypeptide 1"	CYP27		2019602	Standard	NM_000784		Approved	CTX, CP27	uc002viz.4	Q02318	OTTHUMG00000048238	ENST00000258415.4:c.301G>A	chr2.hg19:g.219674345G>A	ENSP00000258415:p.Gly101Arg	70.0	0.0		75.0	20.0	NM_000784	A8K303|Q6LDB4|Q86YQ6	Missense_Mutation	SNP	ENST00000258415.4	hg19	CCDS2423.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.237492	0.79800	.	.	ENSG00000135929	ENST00000258415;ENST00000411688	T;T	0.73789	-0.78;-0.78	5.67	4.76	0.60689	.	0.300622	0.34291	N	0.004081	D	0.85452	0.5700	M	0.82056	2.57	0.58432	D	0.999999	D	0.59357	0.985	D	0.64776	0.929	D	0.86770	0.1972	10	0.59425	D	0.04	-23.2629	15.7687	0.78146	0.0:0.1358:0.8642:0.0	.	101	Q02318	CP27A_HUMAN	R	101;7	ENSP00000258415:G101R;ENSP00000392671:G7R	ENSP00000258415:G101R	G	+	1	0	CYP27A1	219382589	1.000000	0.71417	0.056000	0.19401	0.012000	0.07955	7.895000	0.87343	2.677000	0.91161	0.655000	0.94253	GGG	.	.		0.547	CYP27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109734.4			A	219674345	G	A	219674345	3	1	260	1	0	0	0	0	1	0	0	0	4160	1000	35	3	307	3	CYP27A1	2	219674345	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	422956	219674345	23525028	140	37385										
ATG9A	79065	hgsc.bcm.edu	37	chr2	220088702	220088702	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gcgaggatcacgcggagcagCtgctcagggcagaacaccat	14	12	2	1	rs186498321		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:220088702C>A	ENST00000409618.1	-	9	1747	c.1308G>T	c.(1306-1308)caG>caT	p.Q436H	AC068946.1_ENST00000408417.1_RNA|ATG9A_ENST00000409422.1_Missense_Mutation_p.Q375H|ATG9A_ENST00000488833.1_5'Flank|ATG9A_ENST00000396761.2_Missense_Mutation_p.Q436H|ATG9A_ENST00000361242.4_Missense_Mutation_p.Q436H			Q7Z3C6	ATG9A_HUMAN	autophagy related 9A	436					autophagic vacuole assembly (GO:0000045)|late nucleophagy (GO:0044805)|mitochondrion degradation (GO:0000422)|piecemeal microautophagy of nucleus (GO:0034727)|protein localization to pre-autophagosomal structure (GO:0034497)|protein transport (GO:0015031)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)				endometrium(2)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|stomach(1)	13		Renal(207;0.0474)		Epithelial(149;1.37e-06)|all cancers(144;0.000222)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CGCGGAGCAGCTGCTCAGGGC	0.587																																					p.Q436H		Atlas-SNP	.											.	ATG9A	50	.	0			c.G1308T						.						95	105	102					2																	220088702		2179	4278	6457	SO:0001583	missense	79065	exon9			GAGCAGCTGCTCA	AK021732	CCDS42820.1	2q35	2014-02-12	2012-06-06	2005-09-11	ENSG00000198925	ENSG00000198925			22408	protein-coding gene	gene with protein product		612204	"APG9 autophagy 9-like 1 (S. cerevisiae)", "ATG9 autophagy related 9 homolog A (S. cerevisiae)"	APG9L1			Standard	NM_024085		Approved	FLJ22169	uc002vkf.1	Q7Z3C6	OTTHUMG00000154557	ENST00000409618.1:c.1308G>T	chr2.hg19:g.220088702C>A	ENSP00000386710:p.Gln436His	159.0	0.0		101.0	5.0	NM_001077198	Q3ZAQ6|Q6P0N7|Q7Z317|Q7Z320|Q8NDK6|Q8WU65|Q9BVL5|Q9H6L1|Q9HAG7	Missense_Mutation	SNP	ENST00000409618.1	hg19	CCDS42820.1	.	.	.	.	.	.	.	.	.	.	C	18.54	3.645715	0.67358	.	.	ENSG00000198925	ENST00000396761;ENST00000409618;ENST00000361242;ENST00000409422	T;T;T;T	0.33654	1.81;1.81;1.81;1.4	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.61350	0.2340	M	0.76838	2.35	0.80722	D	1	D	0.69078	0.997	D	0.83275	0.996	T	0.55792	-0.8085	10	0.15952	T	0.53	-12.1268	19.4905	0.95048	0.0:1.0:0.0:0.0	.	436	Q7Z3C6	ATG9A_HUMAN	H	436;436;436;375	ENSP00000379983:Q436H;ENSP00000386710:Q436H;ENSP00000355173:Q436H;ENSP00000386535:Q375H	ENSP00000355173:Q436H	Q	-	3	2	ATG9A	219796946	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.912000	0.69948	2.601000	0.87937	0.585000	0.79938	CAG	.	C|0.999;T|0.001		0.587	ATG9A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335930.1	NM_024085		A	220088702	C	A	220088702	3	1	260	1	0	0	0	0	1	0	0	0	1102	796	28	3	1243	3	ATG9A	2	220088702	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	414357	220088702	23110671	141	37386										
ANKZF1	55139	hgsc.bcm.edu	37	chr2	220097005	220097005	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gaacattataagcttgactgGcatcggtttaacctaaagca	8	8	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:220097005G>A	ENST00000323348.5	+	4	459	c.285G>A	c.(283-285)tgG>tgA	p.W95*	ATG9A_ENST00000409422.1_5'Flank|ATG9A_ENST00000488833.1_5'Flank|ATG9A_ENST00000396761.2_5'Flank|ATG9A_ENST00000361242.4_5'Flank|ANKZF1_ENST00000409849.1_Intron|ANKZF1_ENST00000410034.3_Nonsense_Mutation_p.W95*|ATG9A_ENST00000409618.1_5'Flank	NM_018089.2	NP_060559.2	Q9H8Y5	ANKZ1_HUMAN	ankyrin repeat and zinc finger domain containing 1	95						membrane (GO:0016020)	metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	23		Renal(207;0.0474)		Epithelial(149;1.2e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGCTTGACTGGCATCGGTTTA	0.488																																					p.W95X		Atlas-SNP	.											.	ANKZF1	45	.	0			c.G285A						.						125	119	121					2																	220097005		1921	4122	6043	SO:0001587	stop_gained	55139	exon4			TGACTGGCATCGG	AF364318	CCDS42821.1, CCDS63129.1	2q35	2013-01-10			ENSG00000163516	ENSG00000163516		"Zinc fingers, C2H2-type", "Ankyrin repeat domain containing"	25527	protein-coding gene	gene with protein product						12477932	Standard	NM_018089		Approved	FLJ10415, ZNF744	uc002vkg.3	Q9H8Y5	OTTHUMG00000154533	ENST00000323348.5:c.285G>A	chr2.hg19:g.220097005G>A	ENSP00000321617:p.Trp95*	156.0	0.0		101.0	5.0	NM_001042410	Q9NVZ4	Nonsense_Mutation	SNP	ENST00000323348.5	hg19	CCDS42821.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.393593	0.83011	.	.	ENSG00000163516	ENST00000323348;ENST00000453432;ENST00000410034;ENST00000447157	.	.	.	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.2836	18.8393	0.92176	0.0:0.0:1.0:0.0	.	.	.	.	X	95;30;95;95	.	ENSP00000321617:W95X	W	+	3	0	ANKZF1	219805249	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.841000	0.92131	2.676000	0.91093	0.655000	0.94253	TGG	.	.		0.488	ANKZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335790.1	NM_018089		A	220097005	G	A	220097005	4	1	260	1	0	0	0	0	0	1	0	0	693	1212	42	3	295	3	ANKZF1	2	220097005	Nonsense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	8303	220097005	23102368	142	37387										
DNPEP	23549	hgsc.bcm.edu	37	chr2	220251108	220251108	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cgacttgctggaagcccaccTggctgcggcgagaccgacgt	14	14	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:220251108T>C	ENST00000273075.4	-	5	579	c.359A>G	c.(358-360)cAg>cGg	p.Q120R	DNPEP_ENST00000373972.1_Missense_Mutation_p.Q45R|DNPEP_ENST00000523282.1_Missense_Mutation_p.Q128R|AC053503.4_ENST00000420563.1_RNA	NM_012100.2	NP_036232	Q9ULA0	DNPEP_HUMAN	aspartyl aminopeptidase	110					peptide metabolic process (GO:0006518)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Renal(207;0.0474)		Epithelial(149;1.09e-06)|all cancers(144;0.000179)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GAAGCCCACCTGGCTGCGGCG	0.537																																					p.Q120R		Atlas-SNP	.											.	DNPEP	40	.	0			c.A359G						.						88	95	93					2																	220251108		2102	4223	6325	SO:0001583	missense	23549	exon5			CCCACCTGGCTGC		CCDS42823.1	2q36.1	2008-05-22			ENSG00000123992	ENSG00000123992			2981	protein-coding gene	gene with protein product		611367				9632644	Standard	NM_012100		Approved	DAP, ASPEP	uc002vle.2	Q9ULA0	OTTHUMG00000058919	ENST00000273075.4:c.359A>G	chr2.hg19:g.220251108T>C	ENSP00000273075:p.Gln120Arg	116.0	0.0		66.0	4.0	NM_012100	Q9BW44|Q9NUV5	Missense_Mutation	SNP	ENST00000273075.4	hg19	CCDS42823.1	.	.	.	.	.	.	.	.	.	.	T	16.25	3.071086	0.55646	.	.	ENSG00000123992	ENST00000273075;ENST00000337010;ENST00000373972;ENST00000523282;ENST00000457935;ENST00000429013;ENST00000521459;ENST00000322176;ENST00000434339;ENST00000430206	.	.	.	5.25	5.25	0.73442	Peptidase M18, domain 2 (1);	0.178753	0.49916	D	0.000124	T	0.41650	0.1168	N	0.12569	0.235	0.50039	D	0.999842	B;B;B;B;B	0.09022	0.0;0.001;0.002;0.001;0.0	B;B;B;B;B	0.12156	0.004;0.007;0.004;0.003;0.004	T	0.27468	-1.0073	9	0.45353	T	0.12	-16.7338	15.1664	0.72828	0.0:0.0:0.0:1.0	.	128;120;128;110;120	E7ETB3;B7Z822;B7Z7F0;Q9ULA0;Q53SB6	.;.;.;DNPEP_HUMAN;.	R	120;120;45;128;128;106;120;120;45;45	.	ENSP00000273075:Q120R	Q	-	2	0	DNPEP	219959352	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.087000	0.50167	1.988000	0.58038	0.459000	0.35465	CAG	.	.		0.537	DNPEP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000130212.1	NM_012100		C	220251108	T	C	220251108	3	2	260	1	0	0	0	0	1	0	0	0	4681	1580	55	2	1142	2	DNPEP	2	220251108	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	154103	220251108	22948265	143	37388										
TRIP12	9320	hgsc.bcm.edu	37	chr2	230683119	230683119	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttgacaggaaaccctcccagTgtctcctcatttcccatgac	6	15	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:230683119T>C	ENST00000283943.5	-	8	1594	c.1416A>G	c.(1414-1416)acA>acG	p.T472T	TRIP12_ENST00000389044.4_Silent_p.T520T|TRIP12_ENST00000543084.1_Intron|TRIP12_ENST00000389045.3_Silent_p.T175T	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	472					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		ACCCTCCCAGTGTCTCCTCAT	0.448																																					p.T472T		Atlas-SNP	.											.	TRIP12	207	.	0			c.A1416G						.						152	146	148					2																	230683119		2203	4300	6503	SO:0001819	synonymous_variant	9320	exon8			TCCCAGTGTCTCC	L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.1416A>G	chr2.hg19:g.230683119T>C		285.0	0.0		171.0	7.0	NM_004238	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Silent	SNP	ENST00000283943.5	hg19	CCDS33391.1																																																																																			.	.		0.448	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238		C	230683119	T	C	230683119	2	2	260	1	0	0	0	0	0	0	0	1	16571	1683	59	2		2	TRIP12	2	230683119	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	10432011	230683119	12516254	144	37389										
SP140	11262	hgsc.bcm.edu	37	chr2	231103553	231103553	+	Intron	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gaagtcacgaagagagcctaGcacatactggtacactgagg	12	9	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:231103553G>T	ENST00000392045.3	+	3	520				SP140_ENST00000373645.3_Missense_Mutation_p.A162S|SP140_ENST00000420434.3_Intron|SP140_ENST00000350136.5_Intron|SP140_ENST00000417495.3_Intron|SP140_ENST00000486687.2_Intron|SP140_ENST00000544128.1_3'UTR|SP140_ENST00000343805.6_Intron	NM_007237.4	NP_009168.4	Q13342	SP140_HUMAN	SP140 nuclear body protein						defense response (GO:0006952)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	12		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		AGAGAGCCTAGCACATACTGG	0.438																																					p.A162S		Atlas-SNP	.											SP140,caecum,carcinoma,0,1	SP140	121	.	0			c.G484T						.						48	44	45					2																	231103553		2186	4253	6439	SO:0001627	intron_variant	11262	exon4			AGCCTAGCACATA	U63420	CCDS33392.1, CCDS42831.1, CCDS63149.1, CCDS63150.1, CCDS63151.1	2q37.1	2013-01-28			ENSG00000079263	ENSG00000079263		"Zinc fingers, PHD-type"	17133	protein-coding gene	gene with protein product		608602				8695863, 8910577, 12368356	Standard	NM_001005176		Approved	LYSP100-B, LYSP100-A	uc002vql.3	Q13342	OTTHUMG00000153670	ENST00000392045.3:c.406+457G>T	chr2.hg19:g.231103553G>T		120.0	0.0		80.0	4.0	NM_001005176	E7ESH9|E7EUR5|E9PFJ6|Q0VGE5|Q13341|Q3KR17|Q4ZG66|Q53TG1|Q6NSG4|Q92881|Q96TG3	Missense_Mutation	SNP	ENST00000392045.3	hg19	CCDS42831.1	.	.	.	.	.	.	.	.	.	.	G	9.202	1.028839	0.19512	.	.	ENSG00000079263	ENST00000373645	T	0.50813	0.73	3.24	1.45	0.22620	.	.	.	.	.	T	0.33000	0.0848	.	.	.	0.09310	N	1	B	0.26635	0.155	B	0.23852	0.049	T	0.26643	-1.0097	8	0.59425	D	0.04	.	5.4254	0.16423	0.2599:0.0:0.7401:0.0	.	162	Q6NSG4	.	S	162	ENSP00000362749:A162S	ENSP00000362749:A162S	A	+	1	0	SP140	230811797	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.021000	0.12504	0.404000	0.25506	-0.126000	0.14955	GCA	.	.		0.438	SP140-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000332015.1	NM_007237		T	231103553	G	T	231103553	1	4	260	0	1	0	0	0	0	0	0	0	14977	971	34	3		3	SP140	2	231103553	Intron	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	420434	231103553	12095820	145	37390										
CXCR7	57007	hgsc.bcm.edu	37	chr2	237489260	237489260	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctacacgctctccttcatttAcattttcatcttcgtcatcg	3	14	5	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:237489260A>T	ENST00000272928.3	+	2	462	c.152A>T	c.(151-153)tAc>tTc	p.Y51F		NM_020311.2	NP_064707.1	P25106	ACKR3_HUMAN	atypical chemokine receptor 3	51					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|receptor internalization (GO:0031623)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell surface (GO:0009986)|coated pit (GO:0005905)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C-X-C chemokine binding (GO:0019958)|C-X-C chemokine receptor activity (GO:0016494)|coreceptor activity (GO:0015026)|scavenger receptor activity (GO:0005044)										TCCTTCATTTACATTTTCATC	0.527																																					p.Y51F		Atlas-SNP	.											.	CXCR7	72	.	0			c.A152T						.						224	141	169					2																	237489260		2203	4300	6503	SO:0001583	missense	57007	exon2			TCATTTACATTTT	BC008459	CCDS2516.1	2q37.3	2013-07-17	2013-07-16	2013-07-16	ENSG00000144476	ENSG00000144476		"CD molecules", "GPCR / Class A : Chemokine receptors : Atypical"	23692	protein-coding gene	gene with protein product		610376	"chemokine orphan receptor 1", "chemokine (C-X-C motif) receptor 7"	CMKOR1, CXCR7		16107333, 16148	Standard	NM_020311		Approved	RDC1, GPR159	uc002vwd.3	P25106	OTTHUMG00000133295	ENST00000272928.3:c.152A>T	chr2.hg19:g.237489260A>T	ENSP00000272928:p.Tyr51Phe	140.0	0.0		74.0	5.0	NM_020311	A8K6J4|Q53RV4|Q8NE10|Q92938|Q92986	Missense_Mutation	SNP	ENST00000272928.3	hg19	CCDS2516.1	.	.	.	.	.	.	.	.	.	.	A	15.29	2.789830	0.50102	.	.	ENSG00000144476	ENST00000447924;ENST00000272928	T;T	0.37235	1.21;1.21	5.57	5.57	0.84162	.	0.070524	0.64402	D	0.000016	T	0.27594	0.0678	L	0.27053	0.805	0.38368	D	0.944782	B	0.31383	0.321	B	0.33295	0.161	T	0.24368	-1.0162	10	0.66056	D	0.02	.	10.3839	0.44127	0.9237:0.0:0.0763:0.0	.	51	P25106	CXCR7_HUMAN	F	51	ENSP00000405945:Y51F;ENSP00000272928:Y51F	ENSP00000272928:Y51F	Y	+	2	0	CXCR7	237153999	1.000000	0.71417	0.861000	0.33841	0.726000	0.41606	7.176000	0.77643	2.117000	0.64856	0.460000	0.39030	TAC	.	.		0.527	ACKR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257079.2	NM_020311		T	237489260	A	T	237489260	3	4	260	1	0	0	0	0	1	0	0	0	4098	391	14	4	154	4	CXCR7	2	237489260	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	6385707	237489260	5710113	146	37391										
COL6A3	1293	hgsc.bcm.edu	37	chr2	238270467	238270467	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cacagcaagctttctcggcaAtgttgtcctaccgaaaggaa	9	11	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:238270467A>G	ENST00000295550.4	-	15	6523	c.6071T>C	c.(6070-6072)aTt>aCt	p.I2024T	COL6A3_ENST00000472056.1_Missense_Mutation_p.I1417T|COL6A3_ENST00000409809.1_Missense_Mutation_p.I1818T|COL6A3_ENST00000346358.4_Missense_Mutation_p.I1824T|COL6A3_ENST00000347401.3_Missense_Mutation_p.I1823T|COL6A3_ENST00000353578.4_Missense_Mutation_p.I1818T	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2024	Nonhelical region.|VWFA 10. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		TTTCTCGGCAATGTTGTCCTA	0.522																																					p.I2024T		Atlas-SNP	.											.	COL6A3	608	.	0			c.T6071C						.						69	71	71					2																	238270467		2203	4300	6503	SO:0001583	missense	1293	exon15			TCGGCAATGTTGT	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.6071T>C	chr2.hg19:g.238270467A>G	ENSP00000295550:p.Ile2024Thr	116.0	0.0		73.0	4.0	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	hg19	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	A	13.43	2.234444	0.39498	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	T;T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99;0.99	5.38	5.38	0.77491	von Willebrand factor, type A (2);	0.000000	0.53938	D	0.000055	T	0.65144	0.2663	M	0.80746	2.51	0.58432	D	0.999992	D;D;P	0.65815	0.992;0.995;0.954	P;D;P	0.65987	0.905;0.94;0.476	T	0.69083	-0.5239	10	0.52906	T	0.07	.	15.4187	0.74995	1.0:0.0:0.0:0.0	.	1417;1818;2024	E9PFQ6;P12111-2;P12111	.;.;CO6A3_HUMAN	T	2024;1823;1818;1417;1818;1824	ENSP00000295550:I2024T;ENSP00000315609:I1823T;ENSP00000315873:I1818T;ENSP00000418285:I1417T;ENSP00000386844:I1818T;ENSP00000295546:I1824T	ENSP00000295550:I2024T	I	-	2	0	COL6A3	237935206	1.000000	0.71417	0.965000	0.40720	0.831000	0.47069	8.788000	0.91834	2.034000	0.60081	0.528000	0.53228	ATT	.	.		0.522	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		G	238270467	A	G	238270467	3	3	260	1	0	0	0	0	1	0	0	0	3703	101	4	2	3582	2	COL6A3	2	238270467	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	781207	238270467	4928906	147	37392										
PRLH	51052	hgsc.bcm.edu	37	chr2	238475761	238475761	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtccccaagcctggcctgcgAccccggctgacctgcttccc	10	20	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:238475761A>G	ENST00000165524.1	+	2	207	c.207A>G	c.(205-207)cgA>cgG	p.R69R		NM_015893.1	NP_056977.1	P81277	PRRP_HUMAN	prolactin releasing hormone	69					autonomic nervous system development (GO:0048483)|energy reserve metabolic process (GO:0006112)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|lipid metabolic process (GO:0006629)|reduction of food intake in response to dietary excess (GO:0002023)|response to glucose (GO:0009749)|response to insulin (GO:0032868)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	hormone activity (GO:0005179)			endometrium(1)|large_intestine(1)	2		Lung NSC(271;0.142)|all_lung(227;0.175)		Epithelial(121;8.28e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.03e-10)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.19e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000329)|Lung(119;0.0106)|LUSC - Lung squamous cell carcinoma(224;0.0249)		CTGGCCTGCGACCCCGGCTGA	0.662																																					p.R69R		Atlas-SNP	.											.	PRLH	8	.	0			c.A207G						.						44	42	43					2																	238475761		2203	4300	6503	SO:0001819	synonymous_variant	51052	exon2			CCTGCGACCCCGG	AB015419	CCDS2519.1	2q37.3	2013-02-28			ENSG00000071677	ENSG00000071677		"Endogenous ligands"	17945	protein-coding gene	gene with protein product		602663				9607765	Standard	NM_015893		Approved	PRH	uc010znl.2	P81277	OTTHUMG00000133296	ENST00000165524.1:c.207A>G	chr2.hg19:g.238475761A>G		237.0	0.0		121.0	5.0	NM_015893		Silent	SNP	ENST00000165524.1	hg19	CCDS2519.1																																																																																			.	.		0.662	PRLH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257081.1	NM_015893		G	238475761	A	G	238475761	2	3	260	1	0	0	0	0	0	0	0	1	12541	262	10	2		2	PRLH	2	238475761	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	205294	238475761	4723612	148	37393										
GPR35	2859	hgsc.bcm.edu	37	chr2	241570144	241570144	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agacgatccgtcgcgccctgTacataaccagcaagctctca	8	15	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:241570144T>C	ENST00000319838.5	+	6	1717	c.775T>C	c.(775-777)Tac>Cac	p.Y259H	GPR35_ENST00000407714.1_Missense_Mutation_p.Y259H|GPR35_ENST00000403859.1_Missense_Mutation_p.Y259H|GPR35_ENST00000438013.2_Missense_Mutation_p.Y290H|GPR35_ENST00000430267.1_Missense_Mutation_p.Y259H	NM_001195381.1	NP_001182310.1	Q9HC97	GPR35_HUMAN	G protein-coupled receptor 35	259					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(1)|cervix(1)|endometrium(1)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	17		all_epithelial(40;7.49e-12)|Breast(86;0.000148)|Renal(207;0.00571)|Ovarian(221;0.104)|all_neural(83;0.107)|all_hematologic(139;0.182)|all_lung(227;0.186)|Melanoma(123;0.238)		Epithelial(32;5.29e-32)|all cancers(36;1.38e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.13e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;5.02e-06)|Lung(119;0.00163)|Colorectal(34;0.00463)|LUSC - Lung squamous cell carcinoma(224;0.008)|COAD - Colon adenocarcinoma(134;0.031)		TCGCGCCCTGTACATAACCAG	0.632																																					p.Y290H		Atlas-SNP	.											.	GPR35	43	.	0			c.T868C						.						157	135	143					2																	241570144		2203	4300	6503	SO:0001583	missense	2859	exon6			GCCCTGTACATAA		CCDS2541.1, CCDS56174.1	2q37.3	2012-08-21			ENSG00000178623	ENSG00000178623		"GPCR / Class A : Orphans"	4492	protein-coding gene	gene with protein product		602646				9479505	Standard	NM_005301		Approved		uc021vze.1	Q9HC97	OTTHUMG00000133356	ENST00000319838.5:c.775T>C	chr2.hg19:g.241570144T>C	ENSP00000322731:p.Tyr259His	209.0	0.0		127.0	6.0	NM_001195382	J3KR30|O43495|Q17R58|Q4VBN5|Q4ZFV2|Q6FHI8|Q86UH4	Missense_Mutation	SNP	ENST00000319838.5	hg19	CCDS2541.1	.	.	.	.	.	.	.	.	.	.	T	4.041	0.005171	0.07866	.	.	ENSG00000178623	ENST00000319838;ENST00000403859;ENST00000438013;ENST00000407714;ENST00000430267	T;T;T;T;T	0.37584	1.19;1.19;1.19;1.19;1.19	3.34	-6.69	0.01772	GPCR, rhodopsin-like superfamily (1);	2.219690	0.02422	N	0.082714	T	0.14657	0.0354	N	0.12527	0.23	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.002;0.001	T	0.14755	-1.0461	10	0.15499	T	0.54	-7.1429	0.2604	0.00217	0.2807:0.1949:0.2863:0.2381	.	344;290;259	Q6ZMP9;A8K2J1;Q9HC97	.;.;GPR35_HUMAN	H	259;259;290;259;259	ENSP00000322731:Y259H;ENSP00000385140:Y259H;ENSP00000415890:Y290H;ENSP00000384263:Y259H;ENSP00000411788:Y259H	ENSP00000322731:Y259H	Y	+	1	0	GPR35	241218817	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-5.454000	0.00121	-1.891000	0.01109	0.254000	0.18369	TAC	.	.		0.632	GPR35-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325631.1	NM_001195382		C	241570144	T	C	241570144	3	2	260	1	0	0	0	0	1	0	0	0	6698	1638	57	2	777	2	GPR35	2	241570144	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	3094383	241570144	1629229	149	37394										
PASK	23178	hgsc.bcm.edu	37	chr2	242063478	242063478	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cgttggctgtggaggaggtcTttcaccagccagcagcagaa	14	10	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr2:242063478T>C	ENST00000405260.1	-	11	3488	c.2790A>G	c.(2788-2790)aaA>aaG	p.K930K	PASK_ENST00000358649.4_Silent_p.K930K|PASK_ENST00000234040.4_Silent_p.K930K|PASK_ENST00000403638.3_Silent_p.K930K|PASK_ENST00000539818.1_Silent_p.K714K|PASK_ENST00000544142.1_Silent_p.K744K	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	930					negative regulation of glycogen biosynthetic process (GO:0045719)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of energy homeostasis (GO:2000505)|regulation of glucagon secretion (GO:0070092)|regulation of respiratory gaseous exchange (GO:0043576)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(20)|ovary(4)|prostate(4)|skin(1)|stomach(1)|urinary_tract(2)	53		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		GGAGGAGGTCTTTCACCAGCC	0.632																																					p.K930K		Atlas-SNP	.											.	PASK	230	.	0			c.A2790G						.						43	45	44					2																	242063478		2203	4300	6503	SO:0001819	synonymous_variant	23178	exon11			GAGGTCTTTCACC	U79240	CCDS2545.1, CCDS58758.1, CCDS58759.1	2q37.3	2008-05-23			ENSG00000115687	ENSG00000115687			17270	protein-coding gene	gene with protein product		607505				11688972, 11459942, 15148392	Standard	NM_001252119		Approved	PASKIN, KIAA0135, STK37	uc010fzl.2	Q96RG2	OTTHUMG00000133392	ENST00000405260.1:c.2790A>G	chr2.hg19:g.242063478T>C		165.0	0.0		110.0	5.0	NM_015148	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Silent	SNP	ENST00000405260.1	hg19	CCDS2545.1																																																																																			.	.		0.632	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148		C	242063478	T	C	242063478	2	2	260	1	0	0	0	0	0	0	0	1	11481	1606	56	2		2	PASK	2	242063478	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	493334	242063478	1135895	150	37395										
MTMR14	64419	hgsc.bcm.edu	37	chr3	9714391	9714391	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	taacctcctctgagaaggtgGacaaagcccagcgctatgcc	10	13	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:9714391G>T	ENST00000296003.4	+	7	822	c.700G>T	c.(700-702)Gac>Tac	p.D234Y	MTMR14_ENST00000351233.5_Missense_Mutation_p.D234Y|MTMR14_ENST00000353332.5_Missense_Mutation_p.D234Y|MTMR14_ENST00000420925.1_Intron	NM_001077525.2	NP_001070993.1	Q8NCE2	MTMRE_HUMAN	myotubularin related protein 14	234					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(3)|kidney(2)|lung(10)|skin(3)|upper_aerodigestive_tract(2)	21	Medulloblastoma(99;0.227)					TGAGAAGGTGGACAAAGCCCA	0.512																																					p.D234Y		Atlas-SNP	.											.	MTMR14	43	.	0			c.G700T						.						147	146	146					3																	9714391		2027	4185	6212	SO:0001583	missense	64419	exon7			AAGGTGGACAAAG	BC001674	CCDS43043.1, CCDS43044.1, CCDS43045.1	3p26	2011-06-09	2006-12-18	2006-12-18	ENSG00000163719	ENSG00000163719		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	26190	protein-coding gene	gene with protein product	"egg-derived tyrosine phosphatase homolog (Drosophila)"	611089	"chromosome 3 open reading frame 29"	C3orf29		15186772	Standard	NM_022485		Approved	FLJ22405, FLJ90311, hJumpy, hEDTP	uc003brz.3	Q8NCE2	OTTHUMG00000155111	ENST00000296003.4:c.700G>T	chr3.hg19:g.9714391G>T	ENSP00000296003:p.Asp234Tyr	148.0	0.0		86.0	4.0	NM_022485	Q0JTH5|Q0JU83|Q6PIZ4|Q6QE21|Q86VK9|Q8IYK1|Q8TCM7|Q9H6C0	Missense_Mutation	SNP	ENST00000296003.4	hg19	CCDS43043.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.880163	0.91740	.	.	ENSG00000163719	ENST00000353332;ENST00000296003;ENST00000351233;ENST00000419048	D;D;D	0.90732	-2.72;-2.72;-2.72	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	D	0.95825	0.8641	M	0.83603	2.65	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	D	0.96030	0.9016	10	0.87932	D	0	-4.406	19.216	0.93778	0.0:0.0:1.0:0.0	.	234;234;234	Q8NCE2-3;Q8NCE2-2;Q8NCE2	.;.;MTMRE_HUMAN	Y	234	ENSP00000323462:D234Y;ENSP00000296003:D234Y;ENSP00000334070:D234Y	ENSP00000296003:D234Y	D	+	1	0	MTMR14	9689391	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.893000	0.92498	2.625000	0.88918	0.655000	0.94253	GAC	.	.		0.512	MTMR14-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338435.1	NM_022485		T	9714391	G	T	9714391	3	4	260	1	0	0	0	0	1	0	0	0	9951	1174	41	3	726	3	MTMR14	3	9714391	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10		9714391	188308039	151	37396										
BRPF1	7862	hgsc.bcm.edu	37	chr3	9788027	9788027	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agaaggtatgttccaccatgGggttcccatccctgtgcccc	10	14	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:9788027G>T	ENST00000457855.1	+	12	3361	c.3350G>T	c.(3349-3351)gGg>gTg	p.G1117V	BRPF1_ENST00000433861.2_Missense_Mutation_p.G1022V|BRPF1_ENST00000424362.1_Missense_Mutation_p.G1116V|BRPF1_ENST00000302054.3_Missense_Mutation_p.G1117V|BRPF1_ENST00000383829.2_Missense_Mutation_p.G1123V			P55201	BRPF1_HUMAN	bromodomain and PHD finger containing, 1	1117	PWWP. {ECO:0000255|PROSITE- ProRule:PRU00162}.		G -> E (in dbSNP:rs1042294).		chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	49	Medulloblastoma(99;0.227)					TTCCACCATGGGGTTCCCATC	0.527																																					p.G1123V		Atlas-SNP	.											BRPF1,NS,carcinoma,0,1	BRPF1	104	.	0			c.G3368T						.						97	97	97					3																	9788027		2203	4300	6503	SO:0001583	missense	7862	exon13			ACCATGGGGTTCC	M91585	CCDS2575.1, CCDS33692.1	3p26-p25	2008-07-18			ENSG00000156983	ENSG00000156983			14255	protein-coding gene	gene with protein product	"peregrin", "bromodomain-containing protein, 140kD"	602410				8946209, 7906940	Standard	NM_001003694		Approved	BR140	uc003bsf.3	P55201	OTTHUMG00000097033	ENST00000457855.1:c.3350G>T	chr3.hg19:g.9788027G>T	ENSP00000410210:p.Gly1117Val	105.0	0.0		68.0	3.0	NM_001003694	B4DEZ6|Q7Z6E0|Q8TCM6|Q9UHI0	Missense_Mutation	SNP	ENST00000457855.1	hg19	CCDS2575.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.544594	0.86022	.	.	ENSG00000156983	ENST00000433861;ENST00000424362;ENST00000383829;ENST00000302054;ENST00000457855	T;T;T;T;T	0.39056	1.1;1.1;1.1;1.1;1.1	6.06	6.06	0.98353	PWWP (3);	0.000000	0.85682	D	0.000000	T	0.70500	0.3231	M	0.82323	2.585	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.97110	0.97;1.0;1.0;1.0	T	0.72043	-0.4409	10	0.72032	D	0.01	.	20.6208	0.99490	0.0:0.0:1.0:0.0	.	1022;1116;1123;1117	P55201-4;P55201-3;P55201-2;P55201	.;.;.;BRPF1_HUMAN	V	1022;1116;1123;1117;1117	ENSP00000402485:G1022V;ENSP00000398863:G1116V;ENSP00000373340:G1123V;ENSP00000306297:G1117V;ENSP00000410210:G1117V	ENSP00000306297:G1117V	G	+	2	0	BRPF1	9763027	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	9.869000	0.99810	2.882000	0.98803	0.655000	0.94253	GGG	.	.		0.527	BRPF1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338485.1	NM_001003694		T	9788027	G	T	9788027	3	4	260	1	0	0	0	0	1	0	0	0	1522	1232	43	3	3414	3	BRPF1	3	9788027	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	73636	9788027	188234403	152	37397										
VHL	7428	hgsc.bcm.edu	37	chr3	10191490	10191490	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtgtatactctgaaagagcgAtgcctccaggttgtccggag	13	9	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:10191490A>G	ENST00000256474.2	+	3	1323	c.483A>G	c.(481-483)cgA>cgG	p.R161R	VHL_ENST00000477538.1_3'UTR|VHL_ENST00000345392.2_Silent_p.R120R	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	161	Interaction with Elongin BC complex.		R -> G (in VHLD; type II; dbSNP:rs5030818).|R -> P (in pheochromocytoma and VHLD; type I). {ECO:0000269|PubMed:12000816, ECO:0000269|PubMed:8956040}.|R -> Q (in pheochromocytoma and VHLD; type II). {ECO:0000269|PubMed:12000816, ECO:0000269|PubMed:9829912}.		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.C162fs*12(2)|p.R161del(1)|p.R161fs*12(1)|p.E160fs*9(1)|p.C162fs*9(1)|p.L158fs*6(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TGAAAGAGCGATGCCTCCAGG	0.502		1	"D, Mis, N, F, S"		"renal, hemangioma, pheochromocytoma"	"renal, hemangioma, pheochromocytoma"			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																												p.R161R		Atlas-SNP	.	yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"E, M, O"	VHL,NS,carcinoma,+1,1	VHL	2192	.	7	Deletion - Frameshift(4)|Insertion - Frameshift(2)|Deletion - In frame(1)	kidney(7)	c.A483G						.						94	86	89					3																	10191490		2203	4300	6503	SO:0001819	synonymous_variant	7428	exon3	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	AGAGCGATGCCTC	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"von Hippel-Lindau syndrome", "von Hippel-Lindau tumor suppressor"			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.483A>G	chr3.hg19:g.10191490A>G		66.0	0.0		40.0	2.0	NM_000551	B2RE45|Q13599|Q6PDA9	Silent	SNP	ENST00000256474.2	hg19	CCDS2597.1																																																																																			.	.		0.502	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		G	10191490	A	G	10191490	2	3	260	1	0	0	0	0	0	0	0	1	17177	320	12	2		2	VHL	3	10191490	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	403463	10191490	187830940	153	37398										
FBLN2	2199	hgsc.bcm.edu	37	chr3	13678012	13678012	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acctgccacaacatccagggTagcttccgctgcctgcgctt	9	16	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:13678012T>C	ENST00000295760.7	+	16	3210	c.3141T>C	c.(3139-3141)ggT>ggC	p.G1047G	FBLN2_ENST00000535798.1_Silent_p.G1073G|FBLN2_ENST00000404922.3_Silent_p.G1094G|FBLN2_ENST00000492059.1_Silent_p.G1094G	NM_001998.2	NP_001989.2	P98095	FBLN2_HUMAN	fibulin 2	1047	EGF-like 10; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(3)|prostate(3)|urinary_tract(1)	24			UCEC - Uterine corpus endometrioid carcinoma (1;0.00416)			ACATCCAGGGTAGCTTCCGCT	0.612																																					p.G1094G		Atlas-SNP	.											.	FBLN2	137	.	0			c.T3282C						.						59	71	67					3																	13678012		2185	4285	6470	SO:0001819	synonymous_variant	2199	exon17			CCAGGGTAGCTTC	X82494	CCDS46761.1, CCDS46762.1	3p25-p24	2010-06-15			ENSG00000163520	ENSG00000163520		"Fibulins"	3601	protein-coding gene	gene with protein product		135821				7806230	Standard	NM_001165035		Approved		uc011ava.2	P98095	OTTHUMG00000155437	ENST00000295760.7:c.3141T>C	chr3.hg19:g.13678012T>C		144.0	0.0		122.0	5.0	NM_001004019	B7Z9C5|Q8IUI0|Q8IUI1	Silent	SNP	ENST00000295760.7	hg19	CCDS46762.1	.	.	.	.	.	.	.	.	.	.	T	8.139	0.784705	0.16189	.	.	ENSG00000163520	ENST00000295761;ENST00000421373	.	.	.	4.91	-5.89	0.02282	.	.	.	.	.	T	0.36580	0.0972	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41288	-0.9517	4	.	.	.	.	2.2564	0.04056	0.099:0.2889:0.2911:0.3211	.	.	.	.	A	66;23	.	.	V	+	2	0	FBLN2	13653013	0.000000	0.05858	0.846000	0.33378	0.731000	0.41821	-1.709000	0.01890	-0.774000	0.04590	-1.145000	0.01858	GTA	.	.		0.612	FBLN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000340083.3	NM_001004019		C	13678012	T	C	13678012	2	2	260	1	0	0	0	0	0	0	0	1	5707	1625	57	2		2	FBLN2	3	13678012	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	3486522	13678012	184344418	154	37399										
FGD5	152273	hgsc.bcm.edu	37	chr3	14861366	14861366	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggaggagctggccggggtccAggaggcagagacagccacag	19	10	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:14861366A>G	ENST00000285046.5	+	1	898	c.788A>G	c.(787-789)cAg>cGg	p.Q263R	FGD5_ENST00000543601.1_Missense_Mutation_p.Q22R	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	263	Glu-rich.				actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			NS(2)|breast(2)|endometrium(3)|kidney(5)|large_intestine(10)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(1)	54						GCCGGGGTCCAGGAGGCAGAG	0.617																																					p.Q263R		Atlas-SNP	.											.	FGD5	248	.	0			c.A788G						.						23	28	26					3																	14861366		2097	4222	6319	SO:0001583	missense	152273	exon1			GGGTCCAGGAGGC	AK097276	CCDS46767.1	3p25.1	2013-01-10			ENSG00000154783	ENSG00000154783		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	19117	protein-coding gene	gene with protein product		614788					Standard	NM_152536		Approved	ZFYVE23, FLJ39957, FLJ00274	uc003bzc.3	Q6ZNL6	OTTHUMG00000155556	ENST00000285046.5:c.788A>G	chr3.hg19:g.14861366A>G	ENSP00000285046:p.Gln263Arg	101.0	0.0		90.0	4.0	NM_152536	B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	Missense_Mutation	SNP	ENST00000285046.5	hg19	CCDS46767.1	.	.	.	.	.	.	.	.	.	.	A	15.11	2.737157	0.49045	.	.	ENSG00000154783	ENST00000285046;ENST00000543601	T;T	0.75260	-0.92;-0.81	4.91	2.48	0.30137	.	0.854674	0.10116	N	0.714021	T	0.57110	0.2031	L	0.27053	0.805	0.21020	N	0.99981	B;B	0.30763	0.294;0.294	B;B	0.24974	0.057;0.039	T	0.39522	-0.9610	10	0.20519	T	0.43	-19.0097	7.8196	0.29280	0.7814:0.1446:0.074:0.0	.	22;263	B7ZM68;Q6ZNL6	.;FGD5_HUMAN	R	263;22	ENSP00000285046:Q263R;ENSP00000445949:Q22R	ENSP00000285046:Q263R	Q	+	2	0	FGD5	14836370	0.000000	0.05858	0.986000	0.45419	0.454000	0.32378	-0.186000	0.09670	0.901000	0.36495	0.482000	0.46254	CAG	.	.		0.617	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340628.1	NM_152536		G	14861366	A	G	14861366	3	3	260	1	0	0	0	0	1	0	0	0	5844	188	7	2	790	2	FGD5	3	14861366	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1183354	14861366	183161064	155	37400										
TOP2B	7155	hgsc.bcm.edu	37	chr3	25671863	25671863	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctgagtggaaaaactccgtaTctgtctcgtccaatcacacc	7	13	3	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:25671863T>C	ENST00000264331.4	-	12	1502	c.1503A>G	c.(1501-1503)agA>agG	p.R501R	TOP2B_ENST00000435706.2_Silent_p.R496R	NM_001068.2	NP_001059.2	Q02880	TOP2B_HUMAN	topoisomerase (DNA) II beta 180kDa	501	Toprim. {ECO:0000255|PROSITE- ProRule:PRU00995}.				ATP catabolic process (GO:0006200)|axonogenesis (GO:0007409)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|forebrain development (GO:0030900)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|neuron migration (GO:0001764)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein kinase C binding (GO:0005080)			breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|skin(2)|stomach(1)	36					Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Etoposide(DB00773)	AAACTCCGTATCTGTCTCGTC	0.428																																					p.R496R		Atlas-SNP	.											.	TOP2B	98	.	0			c.A1488G						.						63	60	61					3																	25671863		1802	3946	5748	SO:0001819	synonymous_variant	7155	exon12			TCCGTATCTGTCT	X68060	CCDS46776.1	3p24.2	2012-08-30	2002-08-29		ENSG00000077097	ENSG00000077097	5.99.1.3		11990	protein-coding gene	gene with protein product		126431	"topoisomerase (DNA) II beta (180kD)"			1309226, 1333583	Standard	NM_001068		Approved		uc003cdj.3	Q02880	OTTHUMG00000155596	ENST00000264331.4:c.1503A>G	chr3.hg19:g.25671863T>C		226.0	0.0		121.0	5.0	NM_001068	Q13600|Q9UMG8|Q9UQP8	Silent	SNP	ENST00000264331.4	hg19																																																																																				.	.		0.428	TOP2B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding				C	25671863	T	C	25671863	2	2	260	1	0	0	0	0	0	0	0	1	16381	1432	50	2		2	TOP2B	3	25671863	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	10810497	25671863	172350567	156	37401										
TRANK1	9881	hgsc.bcm.edu	37	chr3	36875346	36875346	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgctgcagcttccaagtaaaActgactggcagaataggaga	11	8	0	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:36875346A>G	ENST00000429976.2	-	21	5843	c.5596T>C	c.(5596-5598)Ttt>Ctt	p.F1866L	TRANK1_ENST00000428977.2_Missense_Mutation_p.F1316L|TRANK1_ENST00000301807.6_Missense_Mutation_p.F1316L	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	1866							ATP binding (GO:0005524)|hydrolase activity (GO:0016787)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(20)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	73						TCCAAGTAAAACTGACTGGCA	0.423																																					p.F1866L		Atlas-SNP	.											.	TRANK1	398	.	0			c.T5596C						.						85	82	83					3																	36875346		1876	4098	5974	SO:0001583	missense	9881	exon21			AGTAAAACTGACT	AK096678	CCDS46789.1, CCDS46789.2	3p22.2	2013-01-11			ENSG00000168016	ENSG00000168016		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29011	protein-coding gene	gene with protein product	"lupus brain antigen 1", "KIAA0342"					9205841	Standard	NM_014831		Approved	LBA1, KIAA0342	uc003cgj.3	O15050	OTTHUMG00000155848	ENST00000429976.2:c.5596T>C	chr3.hg19:g.36875346A>G	ENSP00000416168:p.Phe1866Leu	189.0	0.0		110.0	5.0	NM_014831	Q8N8K0	Missense_Mutation	SNP	ENST00000429976.2	hg19	CCDS46789.2	.	.	.	.	.	.	.	.	.	.	A	7.916	0.737610	0.15574	.	.	ENSG00000168016	ENST00000428977;ENST00000429976;ENST00000301807	T;T;T	0.28454	1.61;2.02;1.61	5.27	4.12	0.48240	.	0.221002	0.31797	N	0.007044	T	0.12689	0.0308	N	0.08118	0	0.32702	N	0.512762	B	0.06786	0.001	B	0.01281	0.0	T	0.25641	-1.0126	10	0.02654	T	1	.	9.7673	0.40567	0.8559:0.0:0.1441:0.0	.	1866	O15050	TRNK1_HUMAN	L	1316;1866;1316	ENSP00000416826:F1316L;ENSP00000416168:F1866L;ENSP00000301807:F1316L	ENSP00000301807:F1316L	F	-	1	0	TRANK1	36850350	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.479000	0.35453	0.966000	0.38159	0.448000	0.29417	TTT	.	.		0.423	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831		G	36875346	A	G	36875346	3	3	260	1	0	0	0	0	1	0	0	0	16469	43	2	2	3193	2	TRANK1	3	36875346	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	11203483	36875346	161147084	157	37402										
CTDSPL	10217	hgsc.bcm.edu	37	chr3	38022326	38022326	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgagccgggaggacgacgtgTacagcatgctgcacagactc	14	11	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:38022326T>C	ENST00000273179.5	+	8	825	c.799T>C	c.(799-801)Tac>Cac	p.Y267H	CTDSPL_ENST00000310189.3_3'UTR|CTDSPL_ENST00000443503.2_Missense_Mutation_p.Y256H	NM_001008392.1	NP_001008393.1	O15194	CTDSL_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase-like	267						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			breast(1)|endometrium(2)|large_intestine(4)|skin(1)	8		Melanoma(1037;0.0122)		KIRC - Kidney renal clear cell carcinoma(284;0.0729)|Kidney(284;0.0902)		GGACGACGTGTACAGCATGCT	0.622																																					p.Y267H		Atlas-SNP	.											.	CTDSPL	17	.	0			c.T799C						.						150	99	116					3																	38022326		2203	4300	6503	SO:0001583	missense	10217	exon8			GACGTGTACAGCA	D88153	CCDS33734.1, CCDS33735.1	3p21.3	2010-06-21	2003-10-27	2003-10-29	ENSG00000144677	ENSG00000144677	3.1.3.16	"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	16890	protein-coding gene	gene with protein product	"small CTD phosphatase 3", "HYA22 protein", "RB protein serine phosphatase from chromosome 3"	608592	"chromosome 3 open reading frame 8"	C3orf8		9179494, 12543795	Standard	NM_005808		Approved	HYA22, SCP3, PSR1, RBSP3	uc003chg.3	O15194	OTTHUMG00000155942	ENST00000273179.5:c.799T>C	chr3.hg19:g.38022326T>C	ENSP00000273179:p.Tyr267His	123.0	0.0		71.0	4.0	NM_001008392	Q3ZTU0|Q70KI4|Q7Z5Q2	Missense_Mutation	SNP	ENST00000273179.5	hg19	CCDS33734.1	.	.	.	.	.	.	.	.	.	.	T	17.53	3.413359	0.62511	.	.	ENSG00000144677	ENST00000443503;ENST00000273179;ENST00000447745	T;T;T	0.17213	2.29;2.29;2.29	5.33	5.33	0.75918	Dullard phosphatase domain, eukaryotic (1);HAD-like domain (2);	0.000000	0.85682	D	0.000000	T	0.45558	0.1348	M	0.87682	2.9	0.80722	D	1	P;P	0.50066	0.716;0.931	P;P	0.62184	0.837;0.899	T	0.49011	-0.8983	10	0.46703	T	0.11	-11.319	15.6002	0.76620	0.0:0.0:0.0:1.0	.	256;267	O15194-2;O15194	.;CTDSL_HUMAN	H	256;267;156	ENSP00000398288:Y256H;ENSP00000273179:Y267H;ENSP00000407443:Y156H	ENSP00000273179:Y267H	Y	+	1	0	CTDSPL	37997330	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.994000	0.88315	2.151000	0.67156	0.533000	0.62120	TAC	.	.		0.622	CTDSPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342392.1	NM_005808		C	38022326	T	C	38022326	3	2	260	1	0	0	0	0	1	0	0	0	4007	1638	57	2	829	2	CTDSPL	3	38022326	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1146980	38022326	160000104	158	37403										
VILL	50853	hgsc.bcm.edu	37	chr3	38038608	38038608	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctttaataagggtgacatctTcctgctggacctaggcaaga	10	9	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:38038608T>C	ENST00000283713.6	+	6	757	c.491T>C	c.(490-492)tTc>tCc	p.F164S	VILL_ENST00000465644.1_Intron|VILL_ENST00000383759.2_Missense_Mutation_p.F164S			O15195	VILL_HUMAN	villin-like	164					actin filament capping (GO:0051693)|cytoskeleton organization (GO:0007010)	actin cytoskeleton (GO:0015629)	structural constituent of cytoskeleton (GO:0005200)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(3)|stomach(3)|urinary_tract(2)	28				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)		GGTGACATCTTCCTGCTGGAC	0.547											OREG0015474	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F164S		Atlas-SNP	.											.	VILL	61	.	0			c.T491C						.						133	126	128					3																	38038608		2203	4300	6503	SO:0001583	missense	50853	exon5			ACATCTTCCTGCT		CCDS2670.2	3p21	2004-07-28			ENSG00000136059	ENSG00000136059			30906	protein-coding gene	gene with protein product						9179494	Standard	XM_005265191		Approved		uc003chl.3	O15195	OTTHUMG00000130814	ENST00000283713.6:c.491T>C	chr3.hg19:g.38038608T>C	ENSP00000283713:p.Phe164Ser	148.0	0.0	875	94.0	4.0	NM_015873	A8MZP1|Q9BT80|Q9BWH7	Missense_Mutation	SNP	ENST00000283713.6	hg19	CCDS2670.2	.	.	.	.	.	.	.	.	.	.	T	23.9	4.466140	0.84425	.	.	ENSG00000136059	ENST00000283713;ENST00000492491;ENST00000383759;ENST00000356246	T;T;T	0.61627	0.91;0.09;0.91	4.69	4.69	0.59074	Gelsolin domain (1);	0.000000	0.85682	D	0.000000	D	0.82848	0.5126	H	0.96015	3.755	0.51012	D	0.999905	D	0.89917	1.0	D	0.83275	0.996	D	0.88456	0.3052	10	0.87932	D	0	-25.7268	14.1256	0.65217	0.0:0.0:0.0:1.0	.	164	O15195	VILL_HUMAN	S	164	ENSP00000283713:F164S;ENSP00000427355:F164S;ENSP00000373266:F164S	ENSP00000283713:F164S	F	+	2	0	VILL	38013612	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.218000	0.72224	1.903000	0.55091	0.482000	0.46254	TTC	.	.		0.547	VILL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253360.3	NM_015873		C	38038608	T	C	38038608	3	2	260	1	0	0	0	0	1	0	0	0	17180	1783	62	2	509	2	VILL	3	38038608	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	16282	38038608	159983822	159	37404										
CSRNP1	64651	hgsc.bcm.edu	37	chr3	39184689	39184689	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gctggcatccccaggtggagAcaggccaggcagggggaagt	18	10	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:39184689A>G	ENST00000273153.5	-	5	1804	c.1627T>C	c.(1627-1629)Tct>Cct	p.S543P	CSRNP1_ENST00000514182.1_Missense_Mutation_p.S543P	NM_033027.3	NP_149016.2	Q96S65	CSRN1_HUMAN	cysteine-serine-rich nuclear protein 1	543					apoptotic process (GO:0006915)|face morphogenesis (GO:0060325)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|skeletal system morphogenesis (GO:0048705)	nucleus (GO:0005634)	RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(5)|lung(3)|ovary(5)|skin(3)	24						CCAGGTGGAGACAGGCCAGGC	0.582																																					p.S543P		Atlas-SNP	.											.	CSRNP1	59	.	0			c.T1627C						.						54	62	59					3																	39184689		2203	4300	6503	SO:0001583	missense	64651	exon5			GTGGAGACAGGCC	AB053121	CCDS2682.1	3p22	2009-04-17	2009-04-17	2009-04-17	ENSG00000144655	ENSG00000144655			14300	protein-coding gene	gene with protein product		606458	"AXIN1 up-regulated 1"	AXUD1		11526492, 17726538	Standard	NM_033027		Approved	URAX1, DKFZp566F164, FAM130B, TAIP-3	uc003cjg.3	Q96S65	OTTHUMG00000131293	ENST00000273153.5:c.1627T>C	chr3.hg19:g.39184689A>G	ENSP00000273153:p.Ser543Pro	130.0	0.0		77.0	4.0	NM_033027	Q69YY5	Missense_Mutation	SNP	ENST00000273153.5	hg19	CCDS2682.1	.	.	.	.	.	.	.	.	.	.	A	8.905	0.957241	0.18507	.	.	ENSG00000144655	ENST00000273153;ENST00000514182;ENST00000318290	T;T	0.41758	0.99;0.99	4.65	3.49	0.39957	.	0.237331	0.34986	N	0.003524	T	0.25158	0.0611	L	0.31207	0.915	0.25613	N	0.986484	B	0.06786	0.001	B	0.08055	0.003	T	0.11470	-1.0586	10	0.29301	T	0.29	-13.9666	3.821	0.08836	0.5753:0.1889:0.2358:0.0	.	543	Q96S65	CSRN1_HUMAN	P	543;543;201	ENSP00000273153:S543P;ENSP00000422532:S543P	ENSP00000273153:S543P	S	-	1	0	CSRNP1	39159693	1.000000	0.71417	0.434000	0.26772	0.291000	0.27294	5.797000	0.69087	0.882000	0.36016	0.533000	0.62120	TCT	.	.		0.582	CSRNP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254061.1	NM_033027		G	39184689	A	G	39184689	3	3	260	1	0	0	0	0	1	0	0	0	3965	275	10	2	146	2	CSRNP1	3	39184689	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1146081	39184689	158837741	160	37405										
MOBP	4336	hgsc.bcm.edu	37	chr3	39554906	39554906	+	3'UTR	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gatcaggccaaccccaaagaAgaagtgaccaaggaggagtt	12	9	1	3	rs369235076		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:39554906A>G	ENST00000420739.1	+	0	843				MOBP_ENST00000447324.1_Missense_Mutation_p.K80R|MOBP_ENST00000428261.1_Missense_Mutation_p.K80R|MOBP_ENST00000415443.1_Missense_Mutation_p.K80R|MOBP_ENST00000383754.3_Missense_Mutation_p.K80R|MOBP_ENST00000311042.6_3'UTR|MOBP_ENST00000396228.1_Missense_Mutation_p.K80R|MOBP_ENST00000479860.1_3'UTR			Q13875	MOBP_HUMAN	myelin-associated oligodendrocyte basic protein						intracellular protein transport (GO:0006886)|nervous system development (GO:0007399)	cytoplasm (GO:0005737)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)	6				KIRC - Kidney renal clear cell carcinoma(284;0.082)|Kidney(284;0.0998)		ACCCCAAAGAAGAAGTGACCA	0.423																																					p.K80R		Atlas-SNP	.											.	MOBP	10	.	0			c.A239G						.	A	ARG/LYS	0,4406		0,0,2203	122	111	115		239	3.9	1	3		115	1,8599	1.2+/-3.3	0,1,4299	no	missense	MOBP	NM_182935.2	26	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign	80/82	39554906	1,13005	2203	4300	6503	SO:0001624	3_prime_UTR_variant	4336	exon4			CAAAGAAGAAGTG	D28113	CCDS2687.1, CCDS63598.1, CCDS2688.1	3p21.33	2004-03-02			ENSG00000168314	ENSG00000168314			7189	protein-coding gene	gene with protein product		600948				7989345	Standard	NM_001278322		Approved		uc031ryw.1	Q13875	OTTHUMG00000131347	ENST00000420739.1:c.*67A>G	chr3.hg19:g.39554906A>G		134.0	0.0		69.0	4.0	NM_182935	A8K2C2|G5E945|Q13874|Q6DHZ6|Q8TBJ1	Missense_Mutation	SNP	ENST00000420739.1	hg19		.	.	.	.	.	.	.	.	.	.	A	7.322	0.617223	0.14129	0.0	1.16E-4	ENSG00000168314	ENST00000428261;ENST00000415443;ENST00000447324;ENST00000383754;ENST00000396228	.	.	.	5.05	3.92	0.45320	.	.	.	.	.	T	0.61590	0.2359	.	.	.	0.80722	D	1	D	0.67145	0.996	D	0.76071	0.987	T	0.57306	-0.7834	7	0.12430	T	0.62	.	6.9665	0.24625	0.9013:0.0:0.0987:0.0	.	80	Q13875-3	.	R	80	.	ENSP00000373261:K80R	K	+	2	0	MOBP	39529910	0.999000	0.42202	0.989000	0.46669	0.044000	0.14063	2.222000	0.42926	2.254000	0.74563	0.533000	0.62120	AAG	.	.		0.423	MOBP-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000343711.1	NM_006501, NM_182934, NM_182935		G	39554906	A	G	39554906	1	3	260	0	1	0	0	0	0	0	0	0	9697	72	3	2		2	MOBP	3	39554906	3'UTR	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	370217	39554906	158467524	161	37406										
MYRIP	25924	hgsc.bcm.edu	37	chr3	40231439	40231439	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttcaggccctggaggtggccTccagtgtggcatctgcctac	13	13	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:40231439T>C	ENST00000302541.6	+	10	1492	c.1150T>C	c.(1150-1152)Tcc>Ccc	p.S384P	MYRIP_ENST00000459828.1_3'UTR|MYRIP_ENST00000539167.1_Missense_Mutation_p.S197P|MYRIP_ENST00000396217.3_Missense_Mutation_p.S295P|MYRIP_ENST00000444716.1_Missense_Mutation_p.S384P|MYRIP_ENST00000425621.1_Missense_Mutation_p.S384P	NM_001284423.1|NM_001284426.1|NM_015460.2	NP_001271352.1|NP_001271355.1|NP_056275.2	Q8NFW9	MYRIP_HUMAN	myosin VIIA and Rab interacting protein	384	Myosin-binding.				intracellular protein transport (GO:0006886)|positive regulation of insulin secretion (GO:0032024)	actin cytoskeleton (GO:0015629)|dense core granule (GO:0031045)|exocyst (GO:0000145)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)|photoreceptor outer segment (GO:0001750)|synapse (GO:0045202)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(2)|lung(10)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				KIRC - Kidney renal clear cell carcinoma(284;0.174)|Kidney(284;0.206)		GGAGGTGGCCTCCAGTGTGGC	0.637																																					p.S384P		Atlas-SNP	.											.	MYRIP	98	.	0			c.T1150C						.						81	73	76					3																	40231439		2203	4300	6503	SO:0001583	missense	25924	exon10			GTGGCCTCCAGTG	AF396687	CCDS2689.1, CCDS68390.1, CCDS68391.1, CCDS68392.1	3p21.33	2010-08-20			ENSG00000170011	ENSG00000170011		"A-kinase anchor proteins"	19156	protein-coding gene	gene with protein product	"synaptotagmin-like protein homologue lacking C2 domains-c", "rab effector MYRIP", "Slp homologue lacking C2 domains"	611790				11964381, 12221080	Standard	NM_001284425		Approved	DKFZp586F1018, exophilin-8, MyRIP, SLAC2-C, SLAC2C	uc003cka.3	Q8NFW9	OTTHUMG00000131392	ENST00000302541.6:c.1150T>C	chr3.hg19:g.40231439T>C	ENSP00000301972:p.Ser384Pro	228.0	0.0		140.0	6.0	NM_015460	B3KWM3|B3KWW4|B7Z2H1|B7Z9V3|G3XAI8|Q32M41|Q32M42|Q569F7|Q8IUF5|Q9Y3V4	Missense_Mutation	SNP	ENST00000302541.6	hg19	CCDS2689.1	.	.	.	.	.	.	.	.	.	.	T	18.21	3.573931	0.65765	.	.	ENSG00000170011	ENST00000444716;ENST00000302541;ENST00000425621;ENST00000396217;ENST00000539167	T;T;T;T;T	0.28255	1.62;1.62;1.62;1.62;1.62	5.94	5.94	0.96194	Myelin-associated oligodendrocytic basic protein (MOBP) (1);	0.000000	0.85682	D	0.000000	T	0.51160	0.1658	L	0.58810	1.83	0.48762	D	0.999702	P;D;D	0.89917	0.494;1.0;1.0	P;D;D	0.77557	0.498;0.984;0.99	T	0.46317	-0.9200	9	.	.	.	.	14.3391	0.66614	0.0:0.0:0.0:1.0	.	295;384;384	Q32M42;G3XAI8;Q8NFW9	.;.;MYRIP_HUMAN	P	384;384;384;295;197	ENSP00000398665:S384P;ENSP00000301972:S384P;ENSP00000389323:S384P;ENSP00000379519:S295P;ENSP00000438297:S197P	.	S	+	1	0	MYRIP	40206443	1.000000	0.71417	0.508000	0.27688	0.990000	0.78478	5.555000	0.67301	2.276000	0.75962	0.533000	0.62120	TCC	.	.		0.637	MYRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254181.2	NM_015460		C	40231439	T	C	40231439	3	2	260	1	0	0	0	0	1	0	0	0	10109	1551	54	2	1184	2	MYRIP	3	40231439	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	676533	40231439	157790991	162	37407										
ENTPD3	956	hgsc.bcm.edu	37	chr3	40433587	40433587	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtgagtattgtggtacttgtGagtatcactgtcatccagat	11	6	2	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:40433587G>A	ENST00000301825.3	+	3	232	c.114G>A	c.(112-114)gtG>gtA	p.V38V	ENTPD3_ENST00000456402.1_Silent_p.V38V|ENTPD3_ENST00000445129.1_Silent_p.V38V|ENTPD3-AS1_ENST00000452768.1_RNA|ENTPD3-AS1_ENST00000439293.1_RNA|ENTPD3-AS1_ENST00000425156.1_RNA	NM_001248.2	NP_001239.2	O75355	ENTP3_HUMAN	ectonucleoside triphosphate diphosphohydrolase 3	38					nucleoside diphosphate catabolic process (GO:0009134)|nucleoside triphosphate catabolic process (GO:0009143)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|nucleoside-diphosphatase activity (GO:0017110)|nucleoside-triphosphatase activity (GO:0017111)			endometrium(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				KIRC - Kidney renal clear cell carcinoma(284;0.0605)|Kidney(284;0.0758)		TGGTACTTGTGAGTATCACTG	0.483																																					p.V38V		Atlas-SNP	.											.	ENTPD3	48	.	0			c.G114A						.						175	160	165					3																	40433587		2203	4300	6503	SO:0001819	synonymous_variant	956	exon3			ACTTGTGAGTATC	AF039917	CCDS2691.1, CCDS74919.1	3p21.3	2004-02-26			ENSG00000168032	ENSG00000168032			3365	protein-coding gene	gene with protein product		603161		CD39L3		9676430	Standard	XM_005265605		Approved	NTPDase-3, HB6	uc003ckd.4	O75355	OTTHUMG00000131390	ENST00000301825.3:c.114G>A	chr3.hg19:g.40433587G>A		158.0	0.0		101.0	5.0	NM_001248	B2R8D0|G5E9N0|O60495|Q8N6K2	Silent	SNP	ENST00000301825.3	hg19	CCDS2691.1																																																																																			.	.		0.483	ENTPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254179.2	NM_001248		A	40433587	G	A	40433587	2	1	260	1	0	0	0	0	0	0	0	1	5142	1277	45	3		3	ENTPD3	3	40433587	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	202148	40433587	157588843	163	37408										
ZDHHC3	51304	hgsc.bcm.edu	37	chr3	44975411	44975411	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cgaagtacttctggttgttcTcgcctacacagttgttgacc	9	11	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:44975411T>C	ENST00000424952.2	-	4	765	c.497A>G	c.(496-498)gAg>gGg	p.E166G	ZDHHC3_ENST00000296127.3_Missense_Mutation_p.E166G|ZDHHC3_ENST00000342790.4_Missense_Mutation_p.E200G	NM_001135179.1	NP_001128651.1	Q9NYG2	ZDHC3_HUMAN	zinc finger, DHHC-type containing 3	166					protein palmitoylation (GO:0018345)|protein targeting (GO:0006605)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(4)	8				BRCA - Breast invasive adenocarcinoma(193;0.00943)|KIRC - Kidney renal clear cell carcinoma(197;0.053)|Kidney(197;0.0665)		CTGGTTGTTCTCGCCTACACA	0.493																																					p.E166G		Atlas-SNP	.											.	ZDHHC3	25	.	0			c.A497G						.						320	279	293					3																	44975411		2203	4300	6503	SO:0001583	missense	51304	exon4			TTGTTCTCGCCTA	AF247703	CCDS2724.1, CCDS46811.1	3p21.31	2010-02-09			ENSG00000163812	ENSG00000163812		"Zinc fingers, DHHC-type"	18470	protein-coding gene	gene with protein product	"golgi-specific DHHC Zinc Finger Protein"					19955568	Standard	NM_016598		Approved	ZNF373, GODZ	uc003cod.3	Q9NYG2	OTTHUMG00000133093	ENST00000424952.2:c.497A>G	chr3.hg19:g.44975411T>C	ENSP00000395502:p.Glu166Gly	147.0	0.0		99.0	4.0	NM_016598	Q53A17|Q96BL0	Missense_Mutation	SNP	ENST00000424952.2	hg19	CCDS46811.1	.	.	.	.	.	.	.	.	.	.	T	31	5.075121	0.94000	.	.	ENSG00000163812	ENST00000339420;ENST00000296127;ENST00000424952;ENST00000342790;ENST00000433512;ENST00000455235	T;T;T;T;T;T	0.25912	1.77;1.86;1.86;1.86;1.77;1.77	5.27	5.27	0.74061	Zinc finger, DHHC-type, palmitoyltransferase (2);	0.000000	0.85682	D	0.000000	T	0.57154	0.2034	M	0.90019	3.08	0.80722	D	1	D;D;D	0.89917	1.0;0.995;1.0	D;D;D	0.85130	0.997;0.965;0.995	T	0.62105	-0.6924	10	0.27785	T	0.31	.	15.1872	0.73012	0.0:0.0:0.0:1.0	.	166;166;166	E9PGS3;Q9NYG2-2;Q9NYG2	.;.;ZDHC3_HUMAN	G	32;166;166;200;14;14	ENSP00000404108:E32G;ENSP00000296127:E166G;ENSP00000395502:E166G;ENSP00000345268:E200G;ENSP00000416132:E14G;ENSP00000408294:E14G	ENSP00000296127:E166G	E	-	2	0	ZDHHC3	44950415	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.928000	0.87587	1.996000	0.58369	0.533000	0.62120	GAG	.	.		0.493	ZDHHC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347004.1	NM_016598		C	44975411	T	C	44975411	3	2	260	1	0	0	0	0	1	0	0	0	17631	1551	54	2	759	2	ZDHHC3	3	44975411	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	4541824	44975411	153047019	164	37409										
ALS2CL	259173	hgsc.bcm.edu	37	chr3	46713386	46713386	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgcctcaccgggcgcgcgacAccacgtagatgagaagtggc	14	13	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:46713386A>G	ENST00000318962.4	-	24	2755	c.2672T>C	c.(2671-2673)gTg>gCg	p.V891A	ALS2CL_ENST00000415953.1_Missense_Mutation_p.V891A|ALS2CL_ENST00000383742.3_Missense_Mutation_p.V238A	NM_147129.3	NP_667340.2	Q60I27	AL2CL_HUMAN	ALS2 C-terminal like	891	VPS9. {ECO:0000255|PROSITE- ProRule:PRU00550}.				endosome organization (GO:0007032)|protein localization (GO:0008104)	cytoplasmic membrane-bounded vesicle (GO:0016023)	GTPase activator activity (GO:0005096)|identical protein binding (GO:0042802)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|skin(3)|stomach(2)	29				BRCA - Breast invasive adenocarcinoma(193;0.000726)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)		GGCGCGCGACACCACGTAGAT	0.627																																					p.V891A		Atlas-SNP	.											ALS2CL,NS,adenocarcinoma,0,1	ALS2CL	78	.	0			c.T2672C						.						71	56	61					3																	46713386		2203	4300	6503	SO:0001583	missense	259173	exon24			CGCGACACCACGT	AK074118	CCDS2743.1, CCDS43080.1	3p21.31	2008-01-30			ENSG00000178038	ENSG00000178038			20605	protein-coding gene	gene with protein product		612402				15388334, 8889548, 17239822	Standard	NM_147129		Approved	FLJ36525, RN49018, DKFZp686I0110	uc003cqb.2	Q60I27	OTTHUMG00000128673	ENST00000318962.4:c.2672T>C	chr3.hg19:g.46713386A>G	ENSP00000313670:p.Val891Ala	104.0	1.0		65.0	4.0	NM_001190707	Q32MA1|Q6AI56|Q6ZNC5|Q6ZNC7|Q6ZTL4|Q86YD2|Q8N9U1|Q8NAL7	Missense_Mutation	SNP	ENST00000318962.4	hg19	CCDS2743.1	.	.	.	.	.	.	.	.	.	.	A	19.87	3.907681	0.72868	.	.	ENSG00000178038	ENST00000318962;ENST00000415953;ENST00000383742	T;T;T	0.38887	1.11;1.11;1.11	4.76	4.76	0.60689	Vacuolar sorting protein 9 (2);	0.000000	0.53938	D	0.000053	T	0.61148	0.2324	M	0.68317	2.08	0.46279	D	0.998961	D	0.89917	1.0	D	0.87578	0.998	T	0.65080	-0.6255	10	0.87932	D	0	.	12.2663	0.54681	1.0:0.0:0.0:0.0	.	891	Q60I27	AL2CL_HUMAN	A	891;891;238	ENSP00000313670:V891A;ENSP00000413223:V891A;ENSP00000373248:V238A	ENSP00000313670:V891A	V	-	2	0	ALS2CL	46688390	1.000000	0.71417	0.996000	0.52242	0.514000	0.34195	7.387000	0.79785	1.995000	0.58328	0.528000	0.53228	GTG	.	.		0.627	ALS2CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250567.3	NM_147129		G	46713386	A	G	46713386	3	3	260	1	0	0	0	0	1	0	0	0	551	159	6	2	201	2	ALS2CL	3	46713386	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1737975	46713386	151309044	165	37410										
NBEAL2	23218	hgsc.bcm.edu	37	chr3	47040568	47040568	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctactggccctgctagtgcgGccagggtcactgcccctgct	12	16	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:47040568G>T	ENST00000450053.3	+	24	3683	c.3504G>T	c.(3502-3504)cgG>cgT	p.R1168R	NBEAL2_ENST00000292309.5_Intron|NBEAL2_ENST00000383740.2_5'UTR	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	1168	Leu-rich.				blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		TGCTAGTGCGGCCAGGGTCAC	0.652											OREG0015546	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R1168R		Atlas-SNP	.											.	NBEAL2	267	.	0			c.G3504T						.						27	31	30					3																	47040568		2102	4206	6308	SO:0001819	synonymous_variant	23218	exon24			AGTGCGGCCAGGG	AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"WD repeat domain containing"	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.3504G>T	chr3.hg19:g.47040568G>T		116.0	0.0	943	69.0	4.0	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Silent	SNP	ENST00000450053.3	hg19	CCDS46817.1																																																																																			.	.		0.652	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064		T	47040568	G	T	47040568	2	4	260	1	0	0	0	0	0	0	0	1	10198	1190	42	3		3	NBEAL2	3	47040568	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	327182	47040568	150981862	166	37411										
QRICH1	54870	hgsc.bcm.edu	37	chr3	49094779	49094779	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cactgtctactgtcagtaagTctggcctcaaagacacataa	7	11	4	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:49094779T>C	ENST00000395443.2	-	3	1326	c.854A>G	c.(853-855)gAc>gGc	p.D285G	QRICH1_ENST00000424300.1_Missense_Mutation_p.D285G|QRICH1_ENST00000479449.1_Intron|QRICH1_ENST00000357496.2_Missense_Mutation_p.D285G	NM_198880.1	NP_942581.1	Q2TAL8	QRIC1_HUMAN	glutamine-rich 1	285	Gln-rich.					nucleus (GO:0005634)				breast(2)|endometrium(5)|large_intestine(8)|lung(8)|ovary(1)|skin(1)	25				BRCA - Breast invasive adenocarcinoma(193;8.88e-05)|Kidney(197;0.00239)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		TGTCAGTAAGTCTGGCCTCAA	0.572																																					p.D285G		Atlas-SNP	.											.	QRICH1	48	.	0			c.A854G						.						66	63	64					3																	49094779		2203	4300	6503	SO:0001583	missense	54870	exon3			AGTAAGTCTGGCC		CCDS2787.1	3p21.31	2011-06-03			ENSG00000198218	ENSG00000198218			24713	protein-coding gene	gene with protein product						12477932	Standard	NM_017730		Approved	FLJ20259	uc003cvv.3	Q2TAL8	OTTHUMG00000156772	ENST00000395443.2:c.854A>G	chr3.hg19:g.49094779T>C	ENSP00000378830:p.Asp285Gly	193.0	0.0		174.0	7.0	NM_198880	Q4G0F7|Q7L621|Q8TEA5	Missense_Mutation	SNP	ENST00000395443.2	hg19	CCDS2787.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.227966	0.79576	.	.	ENSG00000198218	ENST00000395443;ENST00000357496;ENST00000424300	T;T;T	0.24908	1.83;1.83;1.83	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.32164	0.0820	N	0.24115	0.695	0.80722	D	1	D	0.61697	0.99	P	0.54759	0.76	T	0.07309	-1.0779	10	0.87932	D	0	-4.752	16.6277	0.84984	0.0:0.0:0.0:1.0	.	285	Q2TAL8	QRIC1_HUMAN	G	285	ENSP00000378830:D285G;ENSP00000350094:D285G;ENSP00000412890:D285G	ENSP00000350094:D285G	D	-	2	0	QRICH1	49069783	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.698000	0.84413	2.330000	0.79161	0.528000	0.53228	GAC	.	.		0.572	QRICH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345669.1	NM_017730		C	49094779	T	C	49094779	3	2	260	1	0	0	0	0	1	0	0	0	12894	1667	58	2	1508	2	QRICH1	3	49094779	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	2054211	49094779	148927651	167	37412										
LAMB2	3913	hgsc.bcm.edu	37	chr3	49162736	49162736	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cggcagcccaggcaagcgccTgtgtgggtgttgcactcatc	14	13	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:49162736T>C	ENST00000418109.1	-	20	2834	c.2670A>G	c.(2668-2670)acA>acG	p.T890T	LAMB2_ENST00000305544.4_Silent_p.T890T|LAMB2_ENST00000464891.1_5'UTR	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	890	Laminin EGF-like 8. {ECO:0000255|PROSITE- ProRule:PRU00460}.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		GGCAAGCGCCTGTGTGGGTGT	0.617																																					p.T890T		Atlas-SNP	.											.	LAMB2	156	.	0			c.A2670G						.						126	123	124					3																	49162736		2203	4300	6503	SO:0001819	synonymous_variant	3913	exon19			AGCGCCTGTGTGG		CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"Laminins"	6487	protein-coding gene	gene with protein product	"laminin S"	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.2670A>G	chr3.hg19:g.49162736T>C		119.0	0.0		72.0	4.0	NM_002292	Q16321	Silent	SNP	ENST00000418109.1	hg19	CCDS2789.1																																																																																			.	.		0.617	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292		C	49162736	T	C	49162736	2	2	260	1	0	0	0	0	0	0	0	1	8620	1567	55	2		2	LAMB2	3	49162736	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	67957	49162736	148859694	168	37413										
VPRBP	9730	hgsc.bcm.edu	37	chr3	51456190	51456190	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agttatagctggcctcctccTgtccactaaacacattatag	6	12	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:51456190T>C	ENST00000335891.5	-	8	2039	c.2030A>G	c.(2029-2031)cAg>cGg	p.Q677R				Q9Y4B6	VPRBP_HUMAN	Vpr (HIV-1) binding protein	1126					B cell differentiation (GO:0030183)|cell competition in a multicellular organism (GO:0035212)|histone H2A-T120 phosphorylation (GO:1990245)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|transcription, DNA-templated (GO:0006351)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone kinase activity (H2A-T120 specific) (GO:1990244)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(193;0.000272)|Kidney(197;0.000729)|KIRC - Kidney renal clear cell carcinoma(197;0.000875)		GGCCTCCTCCTGTCCACTAAA	0.522																																					p.Q1073R		Atlas-SNP	.											.	VPRBP	107	.	0			c.A3218G						.						121	123	122					3																	51456190		2025	4200	6225	SO:0001583	missense	9730	exon15			TCCTCCTGTCCAC	AB018343	CCDS74943.1, CCDS74944.1	3p21.2	2011-06-17			ENSG00000145041	ENSG00000145041		"DDB1 and CUL4 associated factors"	30911	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 1"					8195203, 11223251	Standard	NM_014703		Approved	KIAA0800, MGC102804, DCAF1	uc003dbe.2	Q9Y4B6	OTTHUMG00000156895	ENST00000335891.5:c.2030A>G	chr3.hg19:g.51456190T>C	ENSP00000338857:p.Gln677Arg	125.0	0.0		74.0	4.0	NM_014703	Q2YD74|Q8TBD9|Q9HCA1|Q9UG37	Missense_Mutation	SNP	ENST00000335891.5	hg19		.	.	.	.	.	.	.	.	.	.	T	17.75	3.465637	0.63513	.	.	ENSG00000145041	ENST00000423656;ENST00000335891	T;T	0.01313	5.02;5.02	5.99	5.99	0.97316	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.01940	0.0061	L	0.31926	0.97	0.58432	D	0.999999	P	0.46512	0.879	B	0.42827	0.399	T	0.74297	-0.3711	10	0.16420	T	0.52	-14.9248	16.4943	0.84223	0.0:0.0:0.0:1.0	.	1126	Q9Y4B6	VPRBP_HUMAN	R	697;677	ENSP00000393183:Q697R;ENSP00000338857:Q677R	ENSP00000338857:Q677R	Q	-	2	0	VPRBP	51431230	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.474000	0.81024	2.291000	0.77112	0.533000	0.62120	CAG	.	.		0.522	VPRBP-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014703		C	51456190	T	C	51456190	3	2	260	1	0	0	0	0	1	0	0	0	17200	1580	55	2	1186	2	VPRBP	3	51456190	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	2293454	51456190	146566240	169	37414										
WDR82	80335	hgsc.bcm.edu	37	chr3	52293863	52293863	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	actcacaagttcgatcatacTgcatcttaaaggtagcaaat	6	9	3	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:52293863T>C	ENST00000296490.3	-	6	850	c.569A>G	c.(568-570)cAg>cGg	p.Q190R		NM_025222.3	NP_079498.2	Q6UXN9	WDR82_HUMAN	WD repeat domain 82	190					histone H3-K4 methylation (GO:0051568)	chromatin (GO:0000785)|histone methyltransferase complex (GO:0035097)|PTW/PP1 phosphatase complex (GO:0072357)|Set1C/COMPASS complex (GO:0048188)	chromatin binding (GO:0003682)								BRCA - Breast invasive adenocarcinoma(193;2.67e-05)|Kidney(197;0.00198)|KIRC - Kidney renal clear cell carcinoma(197;0.00223)|OV - Ovarian serous cystadenocarcinoma(275;0.246)		TCGATCATACTGCATCTTAAA	0.428																																					p.Q190R		Atlas-SNP	.											.	WDR82	19	.	0			c.A569G						.						145	134	137					3																	52293863		1900	4122	6022	SO:0001583	missense	80335	exon6			TCATACTGCATCT	AF132207	CCDS2851.2	3p21.2	2013-01-10	2007-07-04	2007-07-04	ENSG00000164091	ENSG00000164091		"WD repeat domain containing"	28826	protein-coding gene	gene with protein product		611059	"transmembrane protein 113"	TMEM113		17355966	Standard	NM_025222		Approved	PRO2730, MST107, MSTP107, PRO34047, WDR82A, SWD2	uc003ddl.2	Q6UXN9	OTTHUMG00000150391	ENST00000296490.3:c.569A>G	chr3.hg19:g.52293863T>C	ENSP00000296490:p.Gln190Arg	47.0	0.0		35.0	5.0	NM_025222	A8K5R5|Q8TEB2	Missense_Mutation	SNP	ENST00000296490.3	hg19	CCDS2851.2	.	.	.	.	.	.	.	.	.	.	T	17.40	3.380587	0.61845	.	.	ENSG00000164091	ENST00000296490	T	0.17854	2.25	5.88	5.88	0.94601	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.18800	0.0451	L	0.55103	1.725	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.06058	-1.0848	10	0.15952	T	0.53	-26.197	16.259	0.82532	0.0:0.0:0.0:1.0	.	190	Q6UXN9	WDR82_HUMAN	R	190	ENSP00000296490:Q190R	ENSP00000296490:Q190R	Q	-	2	0	WDR82	52268903	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.831000	0.86748	2.245000	0.73994	0.482000	0.46254	CAG	.	.		0.428	WDR82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317919.1	NM_025222		C	52293863	T	C	52293863	3	2	260	1	0	0	0	0	1	0	0	0	17346	1580	55	2	388	2	WDR82	3	52293863	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	837673	52293863	145728567	170	37415										
NEK4	6787	hgsc.bcm.edu	37	chr3	52800369	52800369	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gagttttcagatctcgatgaAggatgtgtttttcatgtaaa	10	4	3	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:52800369A>G	ENST00000233027.5	-	3	585	c.383T>C	c.(382-384)cTt>cCt	p.L128P	NEK4_ENST00000383721.4_Missense_Mutation_p.L128P|NEK4_ENST00000535191.1_Missense_Mutation_p.L39P	NM_001193533.1|NM_003157.4	NP_001180462.1|NP_003148.2	P51957	NEK4_HUMAN	NIMA-related kinase 4	128	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(10)	26				BRCA - Breast invasive adenocarcinoma(193;7.44e-05)|Kidney(197;0.000711)|KIRC - Kidney renal clear cell carcinoma(197;0.00086)|OV - Ovarian serous cystadenocarcinoma(275;0.0513)		ATCTCGATGAAGGATGTGTTT	0.333																																					p.L128P		Atlas-SNP	.											.	NEK4	51	.	0			c.T383C						.						168	149	155					3																	52800369		2203	4300	6503	SO:0001583	missense	6787	exon3			CGATGAAGGATGT	L20321	CCDS2863.1, CCDS54593.1	3p21.1	2012-11-15	2012-11-15	2002-05-10	ENSG00000114904	ENSG00000114904	2.7.11.1		11399	protein-coding gene	gene with protein product	"serine/threonine protein kinase-2"	601959	"serine/threonine kinase 2", "NIMA (never in mitosis gene a)-related kinase 4"	STK2		8208544	Standard	NM_001193533		Approved	NRK2, pp12301	uc003dfq.4	P51957	OTTHUMG00000158836	ENST00000233027.5:c.383T>C	chr3.hg19:g.52800369A>G	ENSP00000233027:p.Leu128Pro	117.0	0.0		97.0	4.0	NM_003157	A5YM70|B2R633|B7Z200|Q6P576	Missense_Mutation	SNP	ENST00000233027.5	hg19	CCDS2863.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.582649	0.86748	.	.	ENSG00000114904	ENST00000233027;ENST00000535191;ENST00000383721;ENST00000461689	T;T;T;T	0.27256	1.68;1.68;1.68;1.68	5.95	5.95	0.96441	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000001	T	0.63977	0.2557	H	0.94462	3.54	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.997;0.998	T	0.75161	-0.3415	10	0.87932	D	0	.	16.4025	0.83647	1.0:0.0:0.0:0.0	.	39;128;128	B7Z200;P51957-2;P51957	.;.;NEK4_HUMAN	P	128;39;128;39	ENSP00000233027:L128P;ENSP00000437703:L39P;ENSP00000373227:L128P;ENSP00000419666:L39P	ENSP00000233027:L128P	L	-	2	0	NEK4	52775409	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.957000	0.93082	2.268000	0.75426	0.533000	0.62120	CTT	.	.		0.333	NEK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352386.2	NM_003157		G	52800369	A	G	52800369	3	3	260	1	0	0	0	0	1	0	0	0	10335	72	3	2	2198	2	NEK4	3	52800369	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	506506	52800369	145222061	171	37416										
ITIH3	3699	hgsc.bcm.edu	37	chr3	52831920	52831920	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acgacctcctgggaagcgccCtcaccaagtccttctcaggg	10	16	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:52831920C>A	ENST00000449956.2	+	6	643	c.637C>A	c.(637-639)Ctc>Atc	p.L213I	ITIH3_ENST00000416872.2_Missense_Mutation_p.L213I	NM_002217.3	NP_002208.3	Q06033	ITIH3_HUMAN	inter-alpha-trypsin inhibitor heavy chain 3	213					hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(6)|ovary(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)		GGGAAGCGCCCTCACCAAGTC	0.552																																					p.L213I		Atlas-SNP	.											.	ITIH3	132	.	0			c.C637A						.						65	66	66					3																	52831920		2059	4218	6277	SO:0001583	missense	3699	exon6			AGCGCCCTCACCA		CCDS46845.1	3p21.1	2011-10-26	2011-10-26		ENSG00000162267	ENSG00000162267			6168	protein-coding gene	gene with protein product	"pre-alpha (globulin) inhibitor, H3 polypeptide", "inter-alpha-trypsin inhibitor heavy chain H3"	146650	"inter-alpha (globulin) inhibitor, H3 polypeptide", "inter-alpha (globulin) inhibitor H3"			2465147, 10100603	Standard	NM_002217		Approved	H3P	uc003dfv.2	Q06033	OTTHUMG00000158956	ENST00000449956.2:c.637C>A	chr3.hg19:g.52831920C>A	ENSP00000415769:p.Leu213Ile	113.0	0.0		75.0	4.0	NM_002217	Q3B7H5|Q53F06|Q6LAM2|Q99085	Missense_Mutation	SNP	ENST00000449956.2	hg19	CCDS46845.1	.	.	.	.	.	.	.	.	.	.	C	7.580	0.668511	0.14776	.	.	ENSG00000162267	ENST00000398670;ENST00000536431;ENST00000273291;ENST00000416872;ENST00000449956	T;T	0.02682	4.2;4.87	5.02	5.02	0.67125	.	0.284466	0.33875	N	0.004463	T	0.02304	0.0071	N	0.04686	-0.185	0.31325	N	0.685504	D;B	0.56968	0.978;0.016	P;B	0.48270	0.572;0.01	T	0.47548	-0.9109	10	0.31617	T	0.26	-28.3717	9.3014	0.37847	0.0:0.9054:0.0:0.0946	.	213;213	E7ET33;Q06033	.;ITIH3_HUMAN	I	213;201;208;213;213	ENSP00000413922:L213I;ENSP00000415769:L213I	ENSP00000273291:L208I	L	+	1	0	ITIH3	52806960	0.495000	0.26051	1.000000	0.80357	0.942000	0.58702	0.833000	0.27504	2.618000	0.88619	0.655000	0.94253	CTC	.	.		0.552	ITIH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352668.2	NM_002217		A	52831920	C	A	52831920	3	1	260	1	0	0	0	0	1	0	0	0	7914	681	24	3	659	3	ITIH3	3	52831920	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	31551	52831920	145190510	172	37417										
TKT	7086	hgsc.bcm.edu	37	chr3	53263137	53263137	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agatcttctagggccatctgGgagggcccgtcttcccctgg	13	13	4	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:53263137G>A	ENST00000462138.1	-	10	1369	c.1281C>T	c.(1279-1281)tcC>tcT	p.S427S	TKT_ENST00000423525.2_Silent_p.S427S|TKT_ENST00000423516.1_Silent_p.S435S|TKT_ENST00000461139.1_5'UTR|TKT_ENST00000296289.6_Silent_p.S380S			P29401	TKT_HUMAN	transketolase	427					carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|glyceraldehyde-3-phosphate biosynthetic process (GO:0046166)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, non-oxidative branch (GO:0009052)|regulation of growth (GO:0040008)|small molecule metabolic process (GO:0044281)|xylulose biosynthetic process (GO:0005999)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|peroxisome (GO:0005777)|vesicle (GO:0031982)	cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|transketolase activity (GO:0004802)			endometrium(5)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17		Prostate(884;0.0959)		BRCA - Breast invasive adenocarcinoma(193;0.000159)|OV - Ovarian serous cystadenocarcinoma(275;0.000314)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)		GGGCCATCTGGGAGGGCCCGT	0.567																																					p.S435S	Colon(133;1506 2347 35238 42177)	Atlas-SNP	.											.	TKT	38	.	0			c.C1305T						.						118	124	122					3																	53263137		2203	4300	6503	SO:0001819	synonymous_variant	7086	exon11			CATCTGGGAGGGC		CCDS2871.1, CCDS58834.1	3p14.3	2008-07-31	2008-07-31		ENSG00000163931	ENSG00000163931	2.2.1.1		11834	protein-coding gene	gene with protein product	"Wernicke-Korsakoff syndrome"	606781				1567394	Standard	NM_001064		Approved		uc011beq.2	P29401	OTTHUMG00000158192	ENST00000462138.1:c.1281C>T	chr3.hg19:g.53263137G>A		111.0	0.0		86.0	4.0	NM_001258028	A8K089|B4DE31|E7EPA7|Q8TBA3|Q96HH3	Silent	SNP	ENST00000462138.1	hg19	CCDS2871.1																																																																																			.	.		0.567	TKT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350356.1			A	53263137	G	A	53263137	2	1	260	1	0	0	0	0	0	0	0	1	15949	1219	43	3		3	TKT	3	53263137	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	431217	53263137	144759293	173	37418										
FAM107A	11170	hgsc.bcm.edu	37	chr3	58553082	58553082	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agctctggcttgctgtccacAccaaggcccctggggtggga	14	13	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:58553082A>G	ENST00000394481.1	-	4	738	c.180T>C	c.(178-180)ggT>ggC	p.G60G	FAM107A_ENST00000447756.2_Silent_p.G88G|FAM107A_ENST00000360997.2_Silent_p.G60G|FAM107A_ENST00000474531.1_Silent_p.G91G|FAM107A_ENST00000464064.1_Silent_p.G60G	NM_001282713.1|NM_007177.2	NP_001269642.1|NP_009108.1	O95990	F107A_HUMAN	family with sequence similarity 107, member A	60					regulation of cell growth (GO:0001558)	neuron projection (GO:0043005)|nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(2)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13				BRCA - Breast invasive adenocarcinoma(55;0.000189)|Kidney(10;0.000536)|KIRC - Kidney renal clear cell carcinoma(10;0.000716)|OV - Ovarian serous cystadenocarcinoma(275;0.154)		TGCTGTCCACACCAAGGCCCC	0.637																																					p.G60G		Atlas-SNP	.											.	FAM107A	33	.	0			c.T180C						.						20	21	21					3																	58553082		2203	4300	6503	SO:0001819	synonymous_variant	11170	exon3			GTCCACACCAAGG	AF089854	CCDS2892.1, CCDS63672.1, CCDS63673.1	3p14.2	2006-02-03			ENSG00000168309	ENSG00000168309			30827	protein-coding gene	gene with protein product		608295				10564580, 10702698	Standard	XM_005264835		Approved	DRR1, TU3A	uc003dkn.3	O95990	OTTHUMG00000159159	ENST00000394481.1:c.180T>C	chr3.hg19:g.58553082A>G		154.0	0.0		112.0	5.0	NM_001076778	B3KNQ4|B7ZAY5|J3KR61|Q96NH4	Silent	SNP	ENST00000394481.1	hg19	CCDS2892.1																																																																																			.	.		0.637	FAM107A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353585.1	NM_007177		G	58553082	A	G	58553082	2	3	260	1	0	0	0	0	0	0	0	1	5394	146	6	2		2	FAM107A	3	58553082	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	5289945	58553082	139469348	174	37419										
PSMD6	9861	hgsc.bcm.edu	37	chr3	64005066	64005066	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tacaatatccaatcggtgacCcagggccacagttttgtcat	8	11	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:64005066C>A	ENST00000295901.4	-	3	543	c.403G>T	c.(403-405)Ggt>Tgt	p.G135C	PSMD6_ENST00000394431.2_Missense_Mutation_p.G97C|PSMD6_ENST00000482510.1_Missense_Mutation_p.G96C|PSMD6_ENST00000492933.1_Missense_Mutation_p.G188C|RP11-245J9.6_ENST00000605919.1_RNA	NM_014814.1	NP_055629.1	Q15008	PSMD6_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 6	135					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATPase activity (GO:0016887)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|pancreas(1)|prostate(1)|skin(1)	13		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000805)|Kidney(15;0.00188)|KIRC - Kidney renal clear cell carcinoma(15;0.00212)		AATCGGTGACCCAGGGCCACA	0.423																																					p.G188C		Atlas-SNP	.											.	PSMD6	30	.	0			c.G562T						.						97	98	97					3																	64005066		2203	4300	6503	SO:0001583	missense	9861	exon4			GGTGACCCAGGGC	AF215935	CCDS2901.1, CCDS63677.1, CCDS63678.1, CCDS63679.1	3p14.1	2008-05-22			ENSG00000163636	ENSG00000163636		"Proteasome (prosome, macropain) subunits"	9564	protein-coding gene	gene with protein product						10723133	Standard	NM_001271779		Approved	S10, p44S10, KIAA0107, Rpn7	uc003dmb.2	Q15008	OTTHUMG00000158765	ENST00000295901.4:c.403G>T	chr3.hg19:g.64005066C>A	ENSP00000295901:p.Gly135Cys	152.0	0.0		94.0	4.0	NM_001271779	A8K2E0|E9PHI9|Q6UV22	Missense_Mutation	SNP	ENST00000295901.4	hg19	CCDS2901.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.959998	0.92791	.	.	ENSG00000163636	ENST00000295901;ENST00000492933;ENST00000394431;ENST00000482510;ENST00000497323	D;D;D;D;D	0.82711	-1.64;-1.64;-1.64;-1.64;-1.64	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	D	0.94473	0.8221	H	0.95917	3.74	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.95722	0.8767	10	0.87932	D	0	.	19.6523	0.95822	0.0:1.0:0.0:0.0	.	97;96;188;135	Q6UV22;E9PHI9;C9IZE4;Q15008	.;.;.;PSMD6_HUMAN	C	135;188;97;96;149	ENSP00000295901:G135C;ENSP00000418695:G188C;ENSP00000377952:G97C;ENSP00000419227:G96C;ENSP00000418887:G149C	ENSP00000295901:G135C	G	-	1	0	PSMD6	63980106	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	7.818000	0.86416	2.650000	0.89964	0.561000	0.74099	GGT	.	.		0.423	PSMD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352082.1	NM_014814		A	64005066	C	A	64005066	3	1	260	1	0	0	0	0	1	0	0	0	12714	623	22	3	790	3	PSMD6	3	64005066	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	5451984	64005066	134017364	175	37420										
ROBO2	6092	hgsc.bcm.edu	37	chr3	77612404	77612404	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aggtcactgatgttactaagAacagtgtcaccttgtcctgg	10	9	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:77612404A>G	ENST00000461745.1	+	11	2506	c.1606A>G	c.(1606-1608)Aac>Gac	p.N536D	ROBO2_ENST00000487694.3_Missense_Mutation_p.N552D|ROBO2_ENST00000332191.8_Missense_Mutation_p.N536D	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	536	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)			NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		TGTTACTAAGAACAGTGTCAC	0.473																																					p.N536D		Atlas-SNP	.											.	ROBO2	527	.	0			c.A1606G						.						98	95	96					3																	77612404		1907	4112	6019	SO:0001583	missense	6092	exon11			ACTAAGAACAGTG	AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10250	protein-coding gene	gene with protein product		602431	"roundabout (axon guidance receptor, Drosophila) homolog 2"			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.1606A>G	chr3.hg19:g.77612404A>G	ENSP00000417164:p.Asn536Asp	179.0	0.0		117.0	6.0	NM_002942	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	hg19	CCDS43109.1	.	.	.	.	.	.	.	.	.	.	A	31	5.060528	0.93846	.	.	ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000343019;ENST00000461745;ENST00000332191;ENST00000398467	T;T;T	0.57436	0.4;0.4;0.4	6.07	6.07	0.98685	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.49916	D	0.000124	T	0.59335	0.2186	L	0.31207	0.915	0.36918	D	0.891261	P;P;P	0.44734	0.842;0.7;0.621	P;P;P	0.56823	0.785;0.807;0.745	T	0.63134	-0.6705	9	0.51188	T	0.08	.	16.6406	0.85098	1.0:0.0:0.0:0.0	.	552;536;536	Q19AB5;F8W703;Q9HCK4	.;.;ROBO2_HUMAN	D	552;552;556;536;536;257	ENSP00000417335:N552D;ENSP00000417164:N536D;ENSP00000327536:N536D	ENSP00000327536:N536D	N	+	1	0	ROBO2	77695094	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.326000	0.78906	0.533000	0.62120	AAC	.	.		0.473	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		G	77612404	A	G	77612404	3	3	260	1	0	0	0	0	1	0	0	0	13529	246	9	2	1650	2	ROBO2	3	77612404	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	13607338	77612404	120410026	176	37421										
EPHA6	285220	hgsc.bcm.edu	37	chr3	96706219	96706219	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aacataataggcccattcacAcataccaggtatgtaatgta	6	9	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:96706219A>G	ENST00000389672.5	+	3	534	c.496A>G	c.(496-498)Aca>Gca	p.T166A	EPHA6_ENST00000542517.1_Missense_Mutation_p.T72A|EPHA6_ENST00000470610.2_Missense_Mutation_p.T166A	NM_001080448.2	NP_001073917.2	Q9UF33	EPHA6_HUMAN	EPH receptor A6	72	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.					integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(2)|lung(60)|ovary(3)|skin(11)|stomach(5)|upper_aerodigestive_tract(2)	101						GCCCATTCACACATACCAGGT	0.378																																					p.T166A		Atlas-SNP	.											EPHA6_ENST00000389672,caecum,carcinoma,0,3	EPHA6	439	.	0			c.A496G						.						108	104	105					3																	96706219		1878	4110	5988	SO:0001583	missense	285220	exon3			ATTCACACATACC	AK092565	CCDS46876.1, CCDS54616.1, CCDS63697.1	3q12.1	2013-02-11	2004-10-28		ENSG00000080224	ENSG00000080224		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	19296	protein-coding gene	gene with protein product		600066				12471243	Standard	NM_001080448		Approved	FLJ35246	uc010how.1	Q9UF33	OTTHUMG00000159208	ENST00000389672.5:c.496A>G	chr3.hg19:g.96706219A>G	ENSP00000374323:p.Thr166Ala	117.0	0.0		91.0	4.0	NM_001080448	D6RAL5	Missense_Mutation	SNP	ENST00000389672.5	hg19	CCDS46876.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	23.0|23.0	4.365329|4.365329	0.82463|0.82463	.|.	.|.	ENSG00000080224|ENSG00000080224	ENST00000506569|ENST00000470610;ENST00000389672;ENST00000542517	T|T;T;T	0.02737|0.10288	4.18|2.89;2.89;2.89	5.74|5.74	5.74|5.74	0.90152|0.90152	.|.	.|0.000000	.|0.64402	.|U	.|0.000002	T|T	0.36908|0.36908	0.0984|0.0984	M|M	0.82056|0.82056	2.57|2.57	0.80722|0.80722	D|D	1|1	.|D;D	.|0.76494	.|0.999;0.999	.|D;D	.|0.85130	.|0.997;0.997	T|T	0.20773|0.20773	-1.0265|-1.0265	7|10	0.02654|0.87932	T|D	1|0	.|.	16.0486|16.0486	0.80740|0.80740	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|166;166	.|B3KS12;E7EU71	.|.;.	R|A	110|166;166;72	ENSP00000425132:H110R|ENSP00000420598:T166A;ENSP00000374323:T166A;ENSP00000439758:T72A	ENSP00000425132:H110R|ENSP00000374323:T166A	H|T	+|+	2|1	0|0	EPHA6|EPHA6	98188909|98188909	1.000000|1.000000	0.71417|0.71417	0.988000|0.988000	0.46212|0.46212	0.953000|0.953000	0.61014|0.61014	9.339000|9.339000	0.96797|0.96797	2.183000|2.183000	0.69458|0.69458	0.533000|0.533000	0.62120|0.62120	CAC|ACA	.	.		0.378	EPHA6-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353845.3	NM_001080448		G	96706219	A	G	96706219	3	3	260	1	0	0	0	0	1	0	0	0	5173	159	6	2	506	2	EPHA6	3	96706219	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	19093815	96706219	101316211	177	37422										
NIT2	56954	hgsc.bcm.edu	37	chr3	100073624	100073624	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	catctttttcaggggggaggTtctagccaaagctggcacag	13	9	3	0	rs17851799		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:100073624T>C	ENST00000394140.4	+	9	783	c.692T>C	c.(691-693)gTt>gCt	p.V231A		NM_020202.4	NP_064587.1	Q9NQR4	NIT2_HUMAN	nitrilase family, member 2	231	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.		V -> A (in dbSNP:rs17851799). {ECO:0000269|PubMed:15489334}.		asparagine metabolic process (GO:0006528)|glutamine metabolic process (GO:0006541)|oxaloacetate metabolic process (GO:0006107)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	omega-amidase activity (GO:0050152)			breast(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(1)	17						AGGGGGGAGGTTCTAGCCAAA	0.458																																					p.V231A		Atlas-SNP	.											.	NIT2	35	.	0			c.T692C						.						132	129	130					3																	100073624		2203	4300	6503	SO:0001583	missense	56954	exon9			GGGAGGTTCTAGC	AF284574	CCDS33806.1	3q12.3	2004-07-12			ENSG00000114021	ENSG00000114021			29878	protein-coding gene	gene with protein product						10959838	Standard	NM_020202		Approved		uc003dtv.3	Q9NQR4	OTTHUMG00000159066	ENST00000394140.4:c.692T>C	chr3.hg19:g.100073624T>C	ENSP00000377696:p.Val231Ala	136.0	0.0		89.0	4.0	NM_020202	B2R9A3|D3DN47|Q8WUF0	Missense_Mutation	SNP	ENST00000394140.4	hg19	CCDS33806.1	.	.	.	.	.	.	.	.	.	.	T	28.8	4.950321	0.92660	.	.	ENSG00000114021	ENST00000394140	T	0.70282	-0.47	5.9	5.9	0.94986	Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (3);	0.000000	0.85682	D	0.000000	D	0.85146	0.5630	M	0.90922	3.16	0.58432	D	0.999999	D	0.57571	0.98	P	0.56916	0.809	D	0.88642	0.3176	10	0.87932	D	0	-34.3945	15.9847	0.80142	0.0:0.0:0.0:1.0	rs17851799	231	Q9NQR4	NIT2_HUMAN	A	231	ENSP00000377696:V231A	ENSP00000377696:V231A	V	+	2	0	NIT2	101556314	1.000000	0.71417	0.994000	0.49952	0.975000	0.68041	6.951000	0.75983	2.254000	0.74563	0.482000	0.46254	GTT	.	T|1.000;|0.000		0.458	NIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353142.2	NM_020202		C	100073624	T	C	100073624	3	2	260	1	0	0	0	0	1	0	0	0	10443	1725	60	2	726	2	NIT2	3	100073624	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	3367405	100073624	97948806	178	37423										
IMPG2	50939	hgsc.bcm.edu	37	chr3	100976517	100976517	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	atcatccagttccacaaggcCatggttttccaccttgttgg	8	12	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:100976517C>T	ENST00000193391.7	-	10	1196	c.1009G>A	c.(1009-1011)Ggc>Agc	p.G337S		NM_016247.3	NP_057331.2	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2	337	SEA 1. {ECO:0000255|PROSITE- ProRule:PRU00188}.				visual perception (GO:0007601)	integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)|receptor complex (GO:0043235)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			NS(1)|breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(14)|lung(32)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64					Hyaluronan(DB08818)	TCCACAAGGCCATGGTTTTCC	0.433																																					p.G337S		Atlas-SNP	.											.	IMPG2	164	.	0			c.G1009A						.						131	125	127					3																	100976517		2203	4300	6503	SO:0001583	missense	50939	exon10			CAAGGCCATGGTT	AF173155	CCDS2940.1	3q12.2-q12.3	2014-01-28			ENSG00000081148	ENSG00000081148			18362	protein-coding gene	gene with protein product		607056				10542133	Standard	NM_016247		Approved	IPM200, RP56	uc003duq.2	Q9BZV3	OTTHUMG00000159091	ENST00000193391.7:c.1009G>A	chr3.hg19:g.100976517C>T	ENSP00000193391:p.Gly337Ser	144.0	0.0		80.0	4.0	NM_016247	A8MWT5|Q9UKD4|Q9UKK5	Missense_Mutation	SNP	ENST00000193391.7	hg19	CCDS2940.1	.	.	.	.	.	.	.	.	.	.	C	17.41	3.383034	0.61845	.	.	ENSG00000081148	ENST00000193391	T	0.31510	1.49	5.38	5.38	0.77491	SEA (1);	0.346876	0.27901	N	0.017394	T	0.34135	0.0887	L	0.43152	1.355	0.32154	N	0.583802	P;P	0.51791	0.948;0.948	P;P	0.50896	0.653;0.526	T	0.25082	-1.0142	10	0.18276	T	0.48	-10.6737	13.2983	0.60311	0.1682:0.8318:0.0:0.0	.	337;337	F1T0J3;Q9BZV3	.;IMPG2_HUMAN	S	337	ENSP00000193391:G337S	ENSP00000193391:G337S	G	-	1	0	IMPG2	102459207	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	2.202000	0.42743	2.522000	0.85027	0.313000	0.20887	GGC	.	.		0.433	IMPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353256.3			T	100976517	C	T	100976517	3	4	260	1	0	0	0	0	1	0	0	0	7738	594	21	3	2756	3	IMPG2	3	100976517	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	902893	100976517	97045913	179	37424										
SIDT1	54847	hgsc.bcm.edu	37	chr3	113300279	113300279	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tccatgaccaagaaagctgcCatcacgctacaggtgaggca	10	12	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:113300279C>A	ENST00000264852.4	+	6	1461	c.735C>A	c.(733-735)gcC>gcA	p.A245A	SIDT1_ENST00000393830.3_Silent_p.A245A	NM_017699.2	NP_060169.2	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1	245					dsRNA transport (GO:0033227)	integral component of membrane (GO:0016021)	RNA transmembrane transporter activity (GO:0051033)			breast(1)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|liver(2)|lung(15)|ovary(3)|pancreas(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50						AGAAAGCTGCCATCACGCTAC	0.468																																					p.A245A		Atlas-SNP	.											.	SIDT1	99	.	0			c.C735A						.						197	154	168					3																	113300279		2203	4300	6503	SO:0001819	synonymous_variant	54847	exon6			AGCTGCCATCACG	AK000181	CCDS2974.1	3q13.31	2009-11-26			ENSG00000072858	ENSG00000072858			25967	protein-coding gene	gene with protein product		606816					Standard	NM_017699		Approved	FLJ20174, SID-1	uc003eak.3	Q9NXL6	OTTHUMG00000159299	ENST00000264852.4:c.735C>A	chr3.hg19:g.113300279C>A		136.0	0.0		89.0	4.0	NM_017699	Q17RR4	Silent	SNP	ENST00000264852.4	hg19	CCDS2974.1																																																																																			.	.		0.468	SIDT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317564.1	NM_017699		A	113300279	C	A	113300279	2	1	260	1	0	0	0	0	0	0	0	1	14317	581	21	3		3	SIDT1	3	113300279	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	12323762	113300279	84722151	180	37425										
ADPRH	141	hgsc.bcm.edu	37	chr3	119301263	119301263	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgactcaactgtattacctcCttgctaagcattaccaagac	5	12	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:119301263C>A	ENST00000478399.1	+	2	1652	c.247C>A	c.(247-249)Ctt>Att	p.L83I	ADPRH_ENST00000357003.3_Missense_Mutation_p.L83I|ADPRH_ENST00000471850.1_Intron|RP11-190C22.9_ENST00000609385.1_RNA|ADPRH_ENST00000465513.1_Missense_Mutation_p.L83I|ADPRH_ENST00000478927.1_Missense_Mutation_p.L83I			P54922	ADPRH_HUMAN	ADP-ribosylarginine hydrolase	83					cellular protein modification process (GO:0006464)|protein de-ADP-ribosylation (GO:0051725)		ADP-ribosylarginine hydrolase activity (GO:0003875)|magnesium ion binding (GO:0000287)			breast(1)|kidney(1)|lung(10)|ovary(1)	13		Lung NSC(201;0.0977)		GBM - Glioblastoma multiforme(114;0.23)		GTATTACCTCCTTGCTAAGCA	0.527																																					p.L83I	GBM(133;579 1804 5989 9967 40052)	Atlas-SNP	.											.	ADPRH	33	.	0			c.C247A						.						82	76	78					3																	119301263		2203	4300	6503	SO:0001583	missense	141	exon3			TACCTCCTTGCTA	L13291	CCDS2990.1	3q13.31-q13.33	2004-02-27			ENSG00000144843	ENSG00000144843			269	protein-coding gene	gene with protein product		603081				8349667, 12070318	Standard	NM_001125		Approved	ARH1	uc003ecs.3	P54922	OTTHUMG00000159420	ENST00000478399.1:c.247C>A	chr3.hg19:g.119301263C>A	ENSP00000420200:p.Leu83Ile	137.0	0.0		72.0	4.0	NM_001125	B2R8H1|D3DN83	Missense_Mutation	SNP	ENST00000478399.1	hg19	CCDS2990.1	.	.	.	.	.	.	.	.	.	.	C	13.07	2.128523	0.37533	.	.	ENSG00000144843	ENST00000478399;ENST00000481816;ENST00000478927;ENST00000357003;ENST00000465513	T;T;T;T;T	0.35236	1.32;1.32;1.32;1.32;1.32	5.85	1.5	0.22942	.	0.423096	0.25732	N	0.028669	T	0.24890	0.0604	L	0.40543	1.245	0.37829	D	0.92866	B	0.09022	0.002	B	0.20767	0.031	T	0.09037	-1.0693	10	0.22109	T	0.4	-27.5155	7.1916	0.25828	0.2543:0.595:0.0:0.1507	.	83	P54922	ADPRH_HUMAN	I	83	ENSP00000420200:L83I;ENSP00000419703:L83I;ENSP00000417528:L83I;ENSP00000349496:L83I;ENSP00000417430:L83I	ENSP00000349496:L83I	L	+	1	0	ADPRH	120783953	0.000000	0.05858	0.981000	0.43875	0.974000	0.67602	-0.469000	0.06648	0.363000	0.24346	0.552000	0.68991	CTT	.	.		0.527	ADPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355199.1	NM_001125		A	119301263	C	A	119301263	3	1	260	1	0	0	0	0	1	0	0	0	331	681	24	3	249	3	ADPRH	3	119301263	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	6000984	119301263	78721167	181	37426										
PLA1A	51365	hgsc.bcm.edu	37	chr3	119334916	119334916	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cttcgtcaacggaggccaagAccaacctggctgccccacct	9	17	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:119334916A>G	ENST00000273371.4	+	6	794	c.722A>G	c.(721-723)gAc>gGc	p.D241G	PLA1A_ENST00000488919.1_Missense_Mutation_p.D68G|PLA1A_ENST00000494440.1_Missense_Mutation_p.D225G|PLA1A_ENST00000495992.1_Missense_Mutation_p.D225G	NM_015900.3	NP_056984.1	Q53H76	PLA1A_HUMAN	phospholipase A1 member A	241					lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)|phosphatidylserine metabolic process (GO:0006658)	extracellular vesicular exosome (GO:0070062)	phosphatidylcholine 1-acylhydrolase activity (GO:0008970)			NS(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						GGAGGCCAAGACCAACCTGGC	0.493																																					p.D241G		Atlas-SNP	.											.	PLA1A	65	.	0			c.A722G						.						119	97	104					3																	119334916		2203	4300	6503	SO:0001583	missense	51365	exon6			GCCAAGACCAACC	AF035268	CCDS2991.1, CCDS56268.1, CCDS56269.1	3q13.13-q13.2	2002-11-28			ENSG00000144837	ENSG00000144837			17661	protein-coding gene	gene with protein product		607460				10196188	Standard	NM_015900		Approved	ps-PLA1	uc003ecu.3	Q53H76	OTTHUMG00000159425	ENST00000273371.4:c.722A>G	chr3.hg19:g.119334916A>G	ENSP00000273371:p.Asp241Gly	128.0	0.0		84.0	4.0	NM_015900	B2R8V2|B4DXA2|O95991|Q86WX6|Q9UPD2	Missense_Mutation	SNP	ENST00000273371.4	hg19	CCDS2991.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.184821	0.78677	.	.	ENSG00000144837	ENST00000273371;ENST00000488919;ENST00000495992;ENST00000494440;ENST00000475963	D;D;D;D;D	0.90620	-2.7;-2.7;-2.7;-2.7;-2.7	5.23	5.23	0.72850	Lipase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.93194	0.7832	L	0.59436	1.845	0.46096	D	0.998868	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.91242	0.5022	10	0.23891	T	0.37	-17.078	12.6803	0.56918	1.0:0.0:0.0:0.0	.	225;241	Q53H76-3;Q53H76	.;PLA1A_HUMAN	G	241;68;225;225;107	ENSP00000273371:D241G;ENSP00000420625:D68G;ENSP00000417326:D225G;ENSP00000418793:D225G;ENSP00000417295:D107G	ENSP00000273371:D241G	D	+	2	0	PLA1A	120817606	1.000000	0.71417	1.000000	0.80357	0.599000	0.36880	8.267000	0.89874	2.223000	0.72356	0.454000	0.30748	GAC	.	.		0.493	PLA1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355252.2			G	119334916	A	G	119334916	3	3	260	1	0	0	0	0	1	0	0	0	11997	275	10	2	744	2	PLA1A	3	119334916	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	33653	119334916	78687514	182	37427										
UROC1	131669	hgsc.bcm.edu	37	chr3	126220121	126220121	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cctccttttttttccttgctTccctggaaggacacaaaagc	6	13	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:126220121T>C	ENST00000290868.2	-	10	958	c.905A>G	c.(904-906)gAa>gGa	p.E302G	UROC1_ENST00000383579.3_Missense_Mutation_p.E362G	NM_144639.2	NP_653240.1	Q96N76	HUTU_HUMAN	urocanate hydratase 1	302					cellular nitrogen compound metabolic process (GO:0034641)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	urocanate hydratase activity (GO:0016153)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(1)|skin(1)	39				GBM - Glioblastoma multiforme(114;0.17)		TTTCCTTGCTTCCCTGGAAGG	0.587																																					p.E362G		Atlas-SNP	.											.	UROC1	150	.	0			c.A1085G						.						182	173	176					3																	126220121		2203	4300	6503	SO:0001583	missense	131669	exon11			CTTGCTTCCCTGG	AK055862	CCDS3038.1, CCDS54636.1	3q21.2	2012-08-21	2012-08-21		ENSG00000159650	ENSG00000159650	4.2.1.49		26444	protein-coding gene	gene with protein product	"urocanase 1"	613012	"urocanase domain containing 1"			19304569	Standard	NM_144639		Approved	FLJ31300, HMFN0320	uc010hsi.2	Q96N76	OTTHUMG00000162753	ENST00000290868.2:c.905A>G	chr3.hg19:g.126220121T>C	ENSP00000290868:p.Glu302Gly	83.0	0.0		50.0	4.0	NM_001165974	E9PE13|Q14C64|Q68CJ7	Missense_Mutation	SNP	ENST00000290868.2	hg19	CCDS3038.1	.	.	.	.	.	.	.	.	.	.	T	14.15	2.449780	0.43531	.	.	ENSG00000159650	ENST00000290868;ENST00000383579	T;T	0.49432	0.78;0.78	4.95	2.37	0.29283	Urocanase domain (2);	0.104250	0.64402	D	0.000004	T	0.54046	0.1834	M	0.77313	2.365	0.48762	D	0.999701	P;B	0.37688	0.605;0.292	P;B	0.45712	0.491;0.232	T	0.53229	-0.8468	10	0.72032	D	0.01	-9.8843	8.2748	0.31866	0.317:0.0:0.0:0.683	.	362;302	E9PE13;Q96N76	.;HUTU_HUMAN	G	302;362	ENSP00000290868:E302G;ENSP00000373073:E362G	ENSP00000290868:E302G	E	-	2	0	UROC1	127702811	1.000000	0.71417	0.994000	0.49952	0.184000	0.23303	5.644000	0.67902	0.183000	0.20059	0.402000	0.26972	GAA	.	.		0.587	UROC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370325.2	NM_144639		C	126220121	T	C	126220121	3	2	260	1	0	0	0	0	1	0	0	0	17043	1783	62	2	1169	2	UROC1	3	126220121	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	6885205	126220121	71802309	183	37428										
KBTBD12	166348	hgsc.bcm.edu	37	chr3	127646843	127646843	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgctgtagtgacagtgaataAtaaactttatgtaattggag	10	3	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:127646843A>G	ENST00000405109.1	+	3	1774	c.1307A>G	c.(1306-1308)aAt>aGt	p.N436S	KBTBD12_ENST00000405256.1_Missense_Mutation_p.N436S|KBTBD12_ENST00000343941.4_Intron|KBTBD12_ENST00000407609.3_Missense_Mutation_p.N43S|KBTBD12_ENST00000492025.1_Intron			Q3ZCT8	KBTBC_HUMAN	kelch repeat and BTB (POZ) domain containing 12	436										endometrium(1)|large_intestine(6)|lung(5)|ovary(1)	13						ACAGTGAATAATAAACTTTAT	0.408																																					p.N436S		Atlas-SNP	.											.	KBTBD12	41	.	0			c.A1307G						.						57	63	61					3																	127646843		2162	4276	6438	SO:0001583	missense	166348	exon2			TGAATAATAAACT		CCDS33848.2	3q21.3	2013-01-08	2009-10-01	2009-10-01	ENSG00000187715	ENSG00000187715		"BTB/POZ domain containing"	25731	protein-coding gene	gene with protein product			"kelch domain containing 6"	KLHDC6			Standard	NM_207335		Approved	FLJ46299	uc010hsr.3	Q3ZCT8	OTTHUMG00000150508	ENST00000405109.1:c.1307A>G	chr3.hg19:g.127646843A>G	ENSP00000385957:p.Asn436Ser	118.0	0.0		68.0	4.0	NM_207335	B5MCC6|Q6ZRK1	Missense_Mutation	SNP	ENST00000405109.1	hg19	CCDS33848.2	.	.	.	.	.	.	.	.	.	.	A	12.47	1.947802	0.34377	.	.	ENSG00000187715	ENST00000405109;ENST00000407609;ENST00000405256	T;T;T	0.80123	-1.34;-1.34;-1.34	5.94	3.55	0.40652	Kelch-type beta propeller (1);	.	.	.	.	T	0.73938	0.3651	L	0.38733	1.17	0.09310	N	1	B	0.20164	0.042	B	0.28385	0.089	T	0.64960	-0.6284	9	0.66056	D	0.02	.	10.1318	0.42682	0.865:0.0:0.135:0.0	.	436	Q3ZCT8	KBTBC_HUMAN	S	436;43;436	ENSP00000385957:N436S;ENSP00000385830:N43S;ENSP00000385879:N436S	ENSP00000385957:N436S	N	+	2	0	KBTBD12	129129533	0.954000	0.32549	0.001000	0.08648	0.894000	0.52154	4.058000	0.57463	0.492000	0.27815	0.482000	0.46254	AAT	.	.		0.408	KBTBD12-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318682.1	NM_207335		G	127646843	A	G	127646843	3	3	260	1	0	0	0	0	1	0	0	0	8000	101	4	2	1313	2	KBTBD12	3	127646843	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1426722	127646843	70375587	184	37429										
NEK11	79858	hgsc.bcm.edu	37	chr3	130881262	130881262	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttatttataggcaaaaaaggAtccacctgcagactctgagg	9	8	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:130881262A>G	ENST00000510769.1	+	7	911	c.658A>G	c.(658-660)Atc>Gtc	p.I220V	NEK11_ENST00000412440.2_Missense_Mutation_p.I177V|NEK11_ENST00000510688.1_Missense_Mutation_p.I325V|NEK11_ENST00000356918.4_Missense_Mutation_p.I325V|NEK11_ENST00000429253.2_Missense_Mutation_p.I325V|NEK11_ENST00000508196.1_Missense_Mutation_p.I325V|NEK11_ENST00000383366.4_Missense_Mutation_p.I325V|NEK11_ENST00000507910.1_Missense_Mutation_p.I325V|NEK11_ENST00000511262.1_Missense_Mutation_p.I325V					NIMA-related kinase 11											breast(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(14)|stomach(1)|urinary_tract(2)	33						GCAAAAAAGGATCCACCTGCA	0.418																																					p.I325V		Atlas-SNP	.											.	NEK11	76	.	0			c.A973G						.						141	164	156					3																	130881262		2203	4300	6503	SO:0001583	missense	79858	exon11			AAAAGGATCCACC	AK027148	CCDS3069.1, CCDS46915.1, CCDS54639.1	3q22.1	2012-11-15	2012-11-15		ENSG00000114670	ENSG00000114670			18593	protein-coding gene	gene with protein product		609779	"NIMA (never in mitosis gene a)- related kinase 11"				Standard	NM_024800		Approved	FLJ23495	uc003eny.3	Q8NG66	OTTHUMG00000159654	ENST00000510769.1:c.658A>G	chr3.hg19:g.130881262A>G	ENSP00000421549:p.Ile220Val	194.0	0.0		146.0	6.0	NM_024800		Missense_Mutation	SNP	ENST00000510769.1	hg19		.	.	.	.	.	.	.	.	.	.	A	8.264	0.811885	0.16537	.	.	ENSG00000114670	ENST00000510769;ENST00000429253;ENST00000356918;ENST00000510688;ENST00000511262;ENST00000383366;ENST00000412440;ENST00000507910;ENST00000508196	T;T;T;T;T;T;T;T;T	0.71461	-0.1;-0.3;-0.43;-0.34;-0.42;-0.3;-0.57;-0.43;-0.3	5.41	0.298	0.15766	.	0.557096	0.16029	N	0.232962	T	0.50769	0.1635	L	0.41710	1.295	0.20403	N	0.999903	B;B;B;B;B;B	0.13594	0.0;0.008;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.12156	0.001;0.007;0.0;0.002;0.001;0.001	T	0.21655	-1.0239	10	0.19147	T	0.46	.	1.1536	0.01791	0.268:0.3471:0.2371:0.1478	.	325;220;177;325;325;325	Q8NG66-3;E9PHI8;B4DDN2;Q8NG66-4;Q8NG66;Q8NG66-2	.;.;.;.;NEK11_HUMAN;.	V	220;325;325;325;325;325;177;325;325	ENSP00000421549:I220V;ENSP00000397180:I325V;ENSP00000349389:I325V;ENSP00000423458:I325V;ENSP00000425114:I325V;ENSP00000372857:I325V;ENSP00000411888:I177V;ENSP00000426662:I325V;ENSP00000421851:I325V	ENSP00000349389:I325V	I	+	1	0	NEK11	132363952	0.993000	0.37304	0.009000	0.14445	0.987000	0.75469	0.654000	0.24918	0.035000	0.15519	0.397000	0.26171	ATC	.	.		0.418	NEK11-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000356757.1	NM_024800		G	130881262	A	G	130881262	3	3	260	1	0	0	0	0	1	0	0	0	10332	333	12	2	1007	2	NEK11	3	130881262	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	3234419	130881262	67141168	185	37430										
PCOLCE2	26577	hgsc.bcm.edu	37	chr3	142607734	142607734	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gcgcccaggcgttcgcgcccCtcatggcagcgtagacgctc	13	17	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:142607734C>T	ENST00000295992.3	-	1	311	c.5G>A	c.(4-6)aGg>aAg	p.R2K	PCOLCE2_ENST00000461818.1_5'UTR|PCOLCE2_ENST00000485766.1_Missense_Mutation_p.R2K	NM_013363.3	NP_037495.1	Q9UKZ9	PCOC2_HUMAN	procollagen C-endopeptidase enhancer 2	2					positive regulation of peptidase activity (GO:0010952)	extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|peptidase activator activity (GO:0016504)			NS(1)|endometrium(1)|large_intestine(11)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	32						GTTCGCGCCCCTCATGGCAGC	0.746																																					p.R2K		Atlas-SNP	.											.	PCOLCE2	63	.	0			c.G5A						.						14	21	18					3																	142607734		2178	4271	6449	SO:0001583	missense	26577	exon1			GCGCCCCTCATGG	AF098269	CCDS3127.1	3q21-q24	2008-07-18			ENSG00000163710	ENSG00000163710			8739	protein-coding gene	gene with protein product		607064				10873381	Standard	NM_013363		Approved	PCPE2	uc003evd.3	Q9UKZ9	OTTHUMG00000159312	ENST00000295992.3:c.5G>A	chr3.hg19:g.142607734C>T	ENSP00000295992:p.Arg2Lys	85.0	0.0		89.0	4.0	NM_013363	B2RCH9|D3DNG4|Q9BRH3	Missense_Mutation	SNP	ENST00000295992.3	hg19	CCDS3127.1	.	.	.	.	.	.	.	.	.	.	C	18.21	3.574063	0.65765	.	.	ENSG00000163710	ENST00000295992;ENST00000485766	T;T	0.21031	2.22;2.03	3.77	2.89	0.33648	.	0.988811	0.08226	N	0.978427	T	0.11410	0.0278	N	0.08118	0	0.19775	N	0.999958	B	0.06786	0.001	B	0.08055	0.003	T	0.27262	-1.0079	10	0.46703	T	0.11	-3.0791	6.8928	0.24238	0.0:0.871:0.0:0.129	.	2	Q9UKZ9	PCOC2_HUMAN	K	2	ENSP00000295992:R2K;ENSP00000419842:R2K	ENSP00000295992:R2K	R	-	2	0	PCOLCE2	144090424	0.996000	0.38824	1.000000	0.80357	0.983000	0.72400	1.709000	0.37909	0.790000	0.33803	0.455000	0.32223	AGG	.	.		0.746	PCOLCE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354509.1	NM_013363		T	142607734	C	T	142607734	3	4	260	1	0	0	0	0	1	0	0	0	11604	681	24	3	1278	3	PCOLCE2	3	142607734	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	11726472	142607734	55414696	186	37431										
HPS3	84343	hgsc.bcm.edu	37	chr3	148847621	148847621	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gacgcgcttttcgtggcggcGggctgcaaggtggaggcgtt	19	9	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:148847621G>T	ENST00000296051.2	+	1	251	c.111G>T	c.(109-111)gcG>gcT	p.A37A	HPS3_ENST00000460120.1_Silent_p.A37A|HPS3_ENST00000494327.1_3'UTR	NM_032383.3	NP_115759.2	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3	37					organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	34			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			TCGTGGCGGCGGGCTGCAAGG	0.716									Hermansky-Pudlak syndrome																												p.A37A		Atlas-SNP	.											.	HPS3	104	.	0			c.G111T						.						13	14	13					3																	148847621		2173	4265	6438	SO:0001819	synonymous_variant	84343	exon1	Familial Cancer Database	HPS, HPS1-8	GGCGGCGGGCTGC	AY033141	CCDS3140.1	3q24	2014-06-18			ENSG00000163755	ENSG00000163755			15597	protein-coding gene	gene with protein product		606118				11455388	Standard	NM_032383		Approved	SUTAL	uc003ewu.1	Q969F9	OTTHUMG00000159548	ENST00000296051.2:c.111G>T	chr3.hg19:g.148847621G>T		92.0	0.0		68.0	4.0	NM_032383	A8K6G6|Q8WTV6|Q96AP1|Q96MR3|Q9H608	Silent	SNP	ENST00000296051.2	hg19	CCDS3140.1																																																																																			.	.		0.716	HPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356151.1	NM_032383		T	148847621	G	T	148847621	2	4	260	1	0	0	0	0	0	0	0	1	7349	1103	39	1		1	HPS3	3	148847621	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	6239887	148847621	49174809	187	37432										
WWTR1	25937	hgsc.bcm.edu	37	chr3	149375035	149375035	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctgtgtctaggtcctgcgtgAcgtggatcacttgctgccca	12	12	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:149375035A>G	ENST00000465804.1	-	3	315	c.59T>C	c.(58-60)gTc>gCc	p.V20A	WWTR1_ENST00000360632.3_Missense_Mutation_p.V20A|WWTR1_ENST00000467467.1_Missense_Mutation_p.V20A|WWTR1-AS1_ENST00000495094.1_RNA|WWTR1-AS1_ENST00000466836.1_RNA|WWTR1-AS1_ENST00000479752.1_RNA	NM_001168278.1	NP_001161750.1	Q9GZV5	WWTR1_HUMAN	WW domain containing transcription regulator 1	20					cilium morphogenesis (GO:0060271)|gene expression (GO:0010467)|glomerulus development (GO:0032835)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast differentiation (GO:0001649)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of SMAD protein import into nucleus (GO:0060390)|regulation of transcription, DNA-templated (GO:0006355)|stem cell division (GO:0017145)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(5)|cervix(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	23			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			GTCCTGCGTGACGTGGATCAC	0.552			T	CAMTA1	epitheliod hemangioendothelioma																																p.V20A		Atlas-SNP	.		Dom	yes		3	3q23-q24	607392	WW domain containing transcription regulator 1		M	.	WWTR1	42	.	0			c.T59C						.						32	33	33					3																	149375035		2201	4300	6501	SO:0001583	missense	25937	exon3			TGCGTGACGTGGA	AK022036	CCDS3144.1	3q23-q24	2004-12-03			ENSG00000018408	ENSG00000018408			24042	protein-coding gene	gene with protein product		607392				11118213, 15096513	Standard	NM_015472		Approved	TAZ, DKFZp586I1419	uc021xfm.1	Q9GZV5	OTTHUMG00000159614	ENST00000465804.1:c.59T>C	chr3.hg19:g.149375035A>G	ENSP00000419465:p.Val20Ala	133.0	0.0		88.0	4.0	NM_001168278	D3DNH7|Q8N3P2|Q9Y3W6	Missense_Mutation	SNP	ENST00000465804.1	hg19	CCDS3144.1	.	.	.	.	.	.	.	.	.	.	A	34	5.411334	0.96072	.	.	ENSG00000018408	ENST00000465804;ENST00000360632;ENST00000467467;ENST00000479238;ENST00000485352;ENST00000475579;ENST00000460517	T;T;T;T	0.63255	-0.03;-0.03;-0.03;0.17	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	T	0.65302	0.2678	N	0.19112	0.55	0.80722	D	1	D	0.58970	0.984	D	0.65443	0.935	T	0.68746	-0.5327	10	0.51188	T	0.08	-22.7957	14.5437	0.68013	1.0:0.0:0.0:0.0	.	20	Q9GZV5	WWTR1_HUMAN	A	20	ENSP00000419465:V20A;ENSP00000353847:V20A;ENSP00000419234:V20A;ENSP00000418580:V20A	ENSP00000353847:V20A	V	-	2	0	WWTR1	150857725	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.792000	0.91856	1.912000	0.55364	0.379000	0.24179	GTC	.	.		0.552	WWTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356498.1	NM_015472		G	149375035	A	G	149375035	3	3	260	1	0	0	0	0	1	0	0	0	17432	275	10	2	1167	2	WWTR1	3	149375035	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	527414	149375035	48647395	188	37433										
MED12L	116931	hgsc.bcm.edu	37	chr3	150834201	150834201	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tggagatgaacatggctcagCcagaaatattgtaattaacc	9	7	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:150834201C>T	ENST00000474524.1	+	2	214	c.176C>T	c.(175-177)gCc>gTc	p.A59V	MED12L_ENST00000309237.4_Missense_Mutation_p.A59V|MED12L_ENST00000422248.2_Missense_Mutation_p.A59V|MED12L_ENST00000273432.4_Missense_Mutation_p.A59V	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	59						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			CATGGCTCAGCCAGAAATATT	0.373																																					p.A59V		Atlas-SNP	.											.	MED12L	271	.	0			c.C176T						.						108	104	105					3																	150834201		2203	4300	6503	SO:0001583	missense	116931	exon2			GCTCAGCCAGAAA	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.176C>T	chr3.hg19:g.150834201C>T	ENSP00000417235:p.Ala59Val	138.0	0.0		93.0	5.0	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Missense_Mutation	SNP	ENST00000474524.1	hg19	CCDS33876.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.167084	0.78339	.	.	ENSG00000144893	ENST00000422248;ENST00000309237;ENST00000474524;ENST00000273432	T;T;T;T	0.62788	0.22;0.22;0.14;-0.0	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	T	0.75510	0.3859	L	0.52126	1.63	0.31001	N	0.72029	B;B;B;D	0.71674	0.288;0.19;0.288;0.998	B;B;B;D	0.76071	0.133;0.063;0.202;0.987	T	0.77135	-0.2699	10	0.87932	D	0	-5.9941	18.204	0.89848	0.0:1.0:0.0:0.0	.	59;59;59;59	F8WAE6;Q86YW9;Q86YW9-2;Q86YW9-3	.;MD12L_HUMAN;.;.	V	59	ENSP00000403308:A59V;ENSP00000310760:A59V;ENSP00000417235:A59V;ENSP00000273432:A59V	ENSP00000273432:A59V	A	+	2	0	MED12L	152316891	1.000000	0.71417	1.000000	0.80357	0.643000	0.38383	5.678000	0.68153	2.383000	0.81215	0.491000	0.48974	GCC	.	.		0.373	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002		T	150834201	C	T	150834201	3	4	260	1	0	0	0	0	1	0	0	0	9438	739	26	3	182	3	MED12L	3	150834201	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	1459166	150834201	47188229	189	37434										
MED12L	116931	hgsc.bcm.edu	37	chr3	150911344	150911344	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gttgggcagaagaatgtcagTtaattgtgagaagttggtga	15	2	1	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:150911344T>C	ENST00000474524.1	+	14	2074	c.2036T>C	c.(2035-2037)gTt>gCt	p.V679A	MED12L_ENST00000309237.4_Missense_Mutation_p.V714A|MED12L_ENST00000422248.2_Missense_Mutation_p.V679A|MED12L_ENST00000273432.4_Missense_Mutation_p.V539A	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	679						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			AGAATGTCAGTTAATTGTGAG	0.388																																					p.V679A		Atlas-SNP	.											.	MED12L	271	.	0			c.T2036C						.						105	102	103					3																	150911344		2203	4300	6503	SO:0001583	missense	116931	exon14			TGTCAGTTAATTG	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.2036T>C	chr3.hg19:g.150911344T>C	ENSP00000417235:p.Val679Ala	148.0	0.0		122.0	5.0	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Missense_Mutation	SNP	ENST00000474524.1	hg19	CCDS33876.1	.	.	.	.	.	.	.	.	.	.	T	1.261	-0.615894	0.03663	.	.	ENSG00000144893	ENST00000422248;ENST00000309237;ENST00000474524;ENST00000273432	T;T;T;T	0.28666	1.6;1.6;1.6;1.6	5.37	4.18	0.49190	Mediator complex, subunit Med12, LCEWAV-domain (1);	0.557908	0.19986	N	0.101662	T	0.20780	0.0500	L	0.27053	0.805	0.09310	N	1	B;B;B;B	0.15930	0.003;0.001;0.0;0.015	B;B;B;B	0.16289	0.01;0.015;0.002;0.013	T	0.18650	-1.0330	10	0.72032	D	0.01	-0.7559	7.2156	0.25957	0.0:0.0745:0.1474:0.7781	.	539;679;679;714	F8WAE6;Q86YW9;Q86YW9-2;Q86YW9-3	.;MD12L_HUMAN;.;.	A	679;714;679;539	ENSP00000403308:V679A;ENSP00000310760:V714A;ENSP00000417235:V679A;ENSP00000273432:V539A	ENSP00000273432:V539A	V	+	2	0	MED12L	152394034	0.263000	0.24083	0.025000	0.17156	0.432000	0.31715	1.849000	0.39318	0.929000	0.37192	0.533000	0.62120	GTT	.	.		0.388	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002		C	150911344	T	C	150911344	3	2	260	1	0	0	0	0	1	0	0	0	9438	1725	60	2	2090	2	MED12L	3	150911344	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	77143	150911344	47111086	190	37435										
SGEF	26084	hgsc.bcm.edu	37	chr3	153840493	153840493	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cttccgtggttttgagtacaAacagccccgccgccctcaaa	8	15	1	1	rs376185280		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:153840493A>G	ENST00000356448.4	+	2	996	c.712A>G	c.(712-714)Aac>Gac	p.N238D	ARHGEF26-AS1_ENST00000467912.1_RNA|ARHGEF26_ENST00000465817.1_Missense_Mutation_p.N238D|ARHGEF26-AS1_ENST00000480639.1_RNA|ARHGEF26-AS1_ENST00000491862.1_RNA|ARHGEF26_ENST00000465093.1_Missense_Mutation_p.N238D|ARHGEF26-AS1_ENST00000479270.1_RNA	NM_001251962.1	NP_001238891.1	Q96DR7	ARHGQ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 26	238					endothelial cell morphogenesis (GO:0001886)|ruffle assembly (GO:0097178)	cell projection (GO:0042995)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	23						TTTGAGTACAAACAGCCCCGC	0.512																																					p.N238D	GBM(163;191 2003 24758 29593 48540)|Ovarian(152;631 1885 20165 22910 51013)	Atlas-SNP	.											.	ARHGEF26	158	.	0			c.A712G						.						15	17	16					3																	153840493		1850	4097	5947	SO:0001583	missense	26084	exon2			AGTACAAACAGCC	BC016628	CCDS46938.1, CCDS58858.1	3q25.2	2013-01-10			ENSG00000114790	ENSG00000114790		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	24490	protein-coding gene	gene with protein product	"Src homology 3 domain-containing guanine nucleotide exchange factor"					15133129, 12697679	Standard	NM_015595		Approved	DKFZP434D146, SGEF	uc021xgc.1	Q96DR7	OTTHUMG00000159098	ENST00000356448.4:c.712A>G	chr3.hg19:g.153840493A>G	ENSP00000348828:p.Asn238Asp	64.0	0.0		56.0	4.0	NM_001251962	B3KVP8|E9PBD0|Q68CL1|Q6AZ96|Q6Q8Q8|Q96AW8|Q96DR6|Q9H9D7|Q9H9R2|Q9UFW5	Missense_Mutation	SNP	ENST00000356448.4	hg19	CCDS46938.1	.	.	.	.	.	.	.	.	.	.	A	17.76	3.469241	0.63625	.	.	ENSG00000114790	ENST00000356448;ENST00000465093;ENST00000465817	T;T;T	0.56611	0.45;0.45;2.27	5.04	2.43	0.29744	.	0.325138	0.36167	N	0.002760	T	0.31949	0.0813	L	0.27053	0.805	0.32654	N	0.51905	P;P	0.43094	0.682;0.799	B;B	0.35413	0.202;0.202	T	0.40776	-0.9545	10	0.12766	T	0.61	-23.0438	12.0788	0.53659	0.5934:0.4066:0.0:0.0	.	238;238	E9PBD0;Q96DR7	.;ARHGQ_HUMAN	D	238	ENSP00000348828:N238D;ENSP00000423418:N238D;ENSP00000423295:N238D	ENSP00000348828:N238D	N	+	1	0	ARHGEF26	155323183	0.004000	0.15560	0.966000	0.40874	0.942000	0.58702	0.098000	0.15189	0.712000	0.32039	0.533000	0.62120	AAC	.	.		0.512	ARHGEF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353287.3	NM_015595		G	153840493	A	G	153840493	3	3	260	1	0	0	0	0	1	0	0	0	14220	14	1	2	714	2	SGEF	3	153840493	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	2929149	153840493	44181937	191	37436										
PLCH1	23007	hgsc.bcm.edu	37	chr3	155200108	155200108	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aggaagacttggattttcccTtgcaaaaaccatgcttgatg	9	8	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:155200108T>C	ENST00000340059.7	-	23	3730	c.3731A>G	c.(3730-3732)aAg>aGg	p.K1244R	PLCH1_ENST00000447496.2_3'UTR|PLCH1_ENST00000460012.1_Missense_Mutation_p.K1206R|PLCH1_ENST00000414191.1_Missense_Mutation_p.K1206R|PLCH1_ENST00000494598.1_Intron|PLCH1_ENST00000334686.6_Missense_Mutation_p.K1206R	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	1244					inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phosphatidylinositol-mediated signaling (GO:0048015)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase C activity (GO:0050429)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			NS(3)|breast(3)|endometrium(9)|kidney(4)|large_intestine(20)|lung(45)|ovary(2)|prostate(5)|skin(8)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	107			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			GGATTTTCCCTTGCAAAAACC	0.463																																					p.K1244R		Atlas-SNP	.											.	PLCH1	406	.	0			c.A3731G						.						87	83	84					3																	155200108		2203	4300	6503	SO:0001583	missense	23007	exon23			TTTCCCTTGCAAA	AB028992	CCDS33881.1, CCDS46939.1, CCDS46940.1	3q25	2013-01-10	2006-03-16	2006-03-16	ENSG00000114805	ENSG00000114805	3.1.4.11	"EF-hand domain containing"	29185	protein-coding gene	gene with protein product		612835	"phospholipase C-like 3"	PLCL3		15702972	Standard	NM_014996		Approved	KIAA1069, MGC117152, DKFZp434C1372, PLCeta1	uc021xge.1	Q4KWH8	OTTHUMG00000158477	ENST00000340059.7:c.3731A>G	chr3.hg19:g.155200108T>C	ENSP00000345988:p.Lys1244Arg	127.0	0.0		83.0	4.0	NM_001130960	Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	Missense_Mutation	SNP	ENST00000340059.7	hg19	CCDS46939.1	.	.	.	.	.	.	.	.	.	.	T	10.39	1.337484	0.24253	.	.	ENSG00000114805	ENST00000460012;ENST00000340059;ENST00000334686;ENST00000414191	T;T;T;T	0.23147	1.92;1.93;1.92;1.92	5.19	-2.05	0.07321	.	8.168240	0.00166	N	0.000000	T	0.13415	0.0325	N	0.14661	0.345	0.09310	N	1	B;B	0.24823	0.078;0.112	B;B	0.21708	0.036;0.016	T	0.08249	-1.0731	10	0.21540	T	0.41	.	2.8848	0.05658	0.0926:0.1611:0.3122:0.4341	.	1206;1244	Q4KWH8-2;Q4KWH8	.;PLCH1_HUMAN	R	1206;1244;1206;1206	ENSP00000417502:K1206R;ENSP00000345988:K1244R;ENSP00000335469:K1206R;ENSP00000412977:K1206R	ENSP00000335469:K1206R	K	-	2	0	PLCH1	156682802	0.000000	0.05858	0.002000	0.10522	0.123000	0.20343	-0.170000	0.09897	-0.687000	0.05162	0.377000	0.23210	AAG	.	.		0.463	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351125.1	NM_014996		C	155200108	T	C	155200108	3	2	260	1	0	0	0	0	1	0	0	0	12046	1609	56	2	1354	2	PLCH1	3	155200108	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1359615	155200108	42822322	192	37437										
CCNL1	57018	hgsc.bcm.edu	37	chr3	156877742	156877742	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gatggtaagtgaaacttccgAgtacaggcgatcgccgatca	12	9	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:156877742A>G	ENST00000295926.3	-	1	260	c.142T>C	c.(142-144)Tcg>Ccg	p.S48P	CCNL1_ENST00000461804.1_Missense_Mutation_p.S48P|CCNL1_ENST00000295925.4_Missense_Mutation_p.S48P	NM_020307.2	NP_064703.1	Q9UK58	CCNL1_HUMAN	cyclin L1	48					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	nuclear speck (GO:0016607)|nucleus (GO:0005634)				NS(1)|breast(1)|cervix(2)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|stomach(1)	18			LUSC - Lung squamous cell carcinoma(72;0.0295)|Lung(72;0.0308)			GAAACTTCCGAGTACAGGCGA	0.657																																					p.S48P		Atlas-SNP	.											.	CCNL1	53	.	0			c.T142C						.						34	30	31					3																	156877742		2203	4300	6503	SO:0001583	missense	57018	exon1			CTTCCGAGTACAG	AF180920	CCDS3178.1	3q25.31	2008-02-05			ENSG00000163660	ENSG00000163660			20569	protein-coding gene	gene with protein product		613384				11980906	Standard	NM_020307		Approved	ania-6a	uc003fbf.3	Q9UK58	OTTHUMG00000158713	ENST00000295926.3:c.142T>C	chr3.hg19:g.156877742A>G	ENSP00000295926:p.Ser48Pro	230.0	0.0		163.0	7.0	NM_020307	B3KMY3|Q6NVY9|Q6UWS7|Q8NI48|Q96QT0|Q9NZF3	Missense_Mutation	SNP	ENST00000295926.3	hg19	CCDS3178.1	.	.	.	.	.	.	.	.	.	.	A	15.53	2.861255	0.51482	.	.	ENSG00000163660	ENST00000461804;ENST00000295926;ENST00000295925	T;T;T	0.50277	1.75;1.74;0.75	4.95	3.79	0.43588	.	0.064498	0.64402	D	0.000006	T	0.53948	0.1828	L	0.55213	1.73	0.53688	D	0.999972	D;P	0.58268	0.982;0.955	P;P	0.58520	0.84;0.616	T	0.53774	-0.8391	10	0.62326	D	0.03	-5.7492	6.5824	0.22602	0.7842:0.0:0.0785:0.1373	.	48;48	Q9UK58;C9JPL0	CCNL1_HUMAN;.	P	48	ENSP00000420277:S48P;ENSP00000295926:S48P;ENSP00000295925:S48P	ENSP00000295925:S48P	S	-	1	0	CCNL1	158360436	1.000000	0.71417	0.990000	0.47175	0.071000	0.16799	6.201000	0.72124	0.832000	0.34804	0.528000	0.53228	TCG	.	.		0.657	CCNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351859.1	NM_020307		G	156877742	A	G	156877742	3	3	260	1	0	0	0	0	1	0	0	0	2933	304	11	2	1482	2	CCNL1	3	156877742	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1677634	156877742	41144688	193	37438										
TRIM59	286827	hgsc.bcm.edu	37	chr3	160156325	160156325	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	caatttgtggagtatattctTgattaattagattgccaaca	7	5	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:160156325T>C	ENST00000309784.4	-	3	832	c.647A>G	c.(646-648)cAa>cGa	p.Q216R	RP11-432B6.3_ENST00000483754.1_Missense_Mutation_p.Q216R|TRIM59_ENST00000543469.1_Missense_Mutation_p.Q216R	NM_173084.2	NP_775107.1	Q8IWR1	TRI59_HUMAN	tripartite motif containing 59	216					innate immune response (GO:0045087)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of viral entry into host cell (GO:0046597)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|urinary_tract(3)	15			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			AGTATATTCTTGATTAATTAG	0.343																																					p.Q216R		Atlas-SNP	.											.	TRIM59	42	.	0			c.A647G						.						76	80	79					3																	160156325		2201	4297	6498	SO:0001583	missense	286827	exon3			TATTCTTGATTAA	AY159379	CCDS3190.1	3q26	2013-01-09	2011-01-25		ENSG00000213186	ENSG00000213186		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	30834	protein-coding gene	gene with protein product			"tripartite motif-containing 57", "tripartite motif-containing 59"	TRIM57		12095697	Standard	NM_173084		Approved	TSBF1, Mrf1, RNF104	uc003fdm.3	Q8IWR1	OTTHUMG00000159034	ENST00000309784.4:c.647A>G	chr3.hg19:g.160156325T>C	ENSP00000311219:p.Gln216Arg	212.0	0.0		122.0	5.0	NM_173084	A8K5G9|D3DNL9	Missense_Mutation	SNP	ENST00000309784.4	hg19	CCDS3190.1	.	.	.	.	.	.	.	.	.	.	T	11.79	1.742840	0.30865	.	.	ENSG00000213186	ENST00000543469;ENST00000309784	T;T	0.25912	1.98;1.77	5.77	3.41	0.39046	.	0.357214	0.29383	N	0.012318	T	0.14313	0.0346	L	0.33485	1.01	0.24928	N	0.991932	B	0.19583	0.037	B	0.11329	0.006	T	0.15065	-1.0450	9	.	.	.	-15.8028	1.8898	0.03246	0.1373:0.1363:0.1435:0.5829	.	216	Q8IWR1	TRI59_HUMAN	R	216	ENSP00000444313:Q216R;ENSP00000311219:Q216R	.	Q	-	2	0	TRIM59	161639019	0.836000	0.29430	1.000000	0.80357	0.977000	0.68977	2.454000	0.44979	0.999000	0.39023	0.459000	0.35465	CAA	.	.		0.343	TRIM59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352963.1	NM_173084		C	160156325	T	C	160156325	3	2	260	1	0	0	0	0	1	0	0	0	16547	1812	63	2	568	2	TRIM59	3	160156325	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	3278583	160156325	37866105	194	37439										
SLC2A2	6514	hgsc.bcm.edu	37	chr3	170732421	170732421	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgggttcattgagtatgagaTtgtgggcagttcatctgtac	13	5	3	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:170732421T>G	ENST00000314251.3	-	3	287	c.208A>C	c.(208-210)Atc>Ctc	p.I70L	SLC2A2_ENST00000382808.4_Intron	NM_000340.1	NP_000331.1	P11168	GTR2_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 2	70					carbohydrate metabolic process (GO:0005975)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transmembrane transport (GO:0035428)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	brush border (GO:0005903)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|hexose transmembrane transporter activity (GO:0015149)			central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)		Streptozocin(DB00428)	GAGTATGAGATTGTGGGCAGT	0.448																																					p.I70L		Atlas-SNP	.											.	SLC2A2	71	.	0			c.A208C						.						221	213	216					3																	170732421		2203	4300	6503	SO:0001583	missense	6514	exon3			ATGAGATTGTGGG	J03810	CCDS3215.1	3q26.2-q27	2013-05-22			ENSG00000163581	ENSG00000163581		"Solute carriers"	11006	protein-coding gene	gene with protein product		138160		GLUT2		1852621	Standard	NM_000340		Approved		uc003fhe.1	P11168	OTTHUMG00000158997	ENST00000314251.3:c.208A>C	chr3.hg19:g.170732421T>G	ENSP00000323568:p.Ile70Leu	698.0	0.0		481.0	135.0	NM_000340	A8K481|B2R936|B7Z547|F8W8V8|Q9UCW9	Missense_Mutation	SNP	ENST00000314251.3	hg19	CCDS3215.1	.	.	.	.	.	.	.	.	.	.	T	3.919	-0.018568	0.07681	.	.	ENSG00000163581	ENST00000314251	D	0.82433	-1.61	5.75	-11.5	0.00074	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	16.683300	0.00166	N	0.000001	T	0.58163	0.2103	N	0.05124	-0.11	0.09310	N	1	B	0.14805	0.011	B	0.14023	0.01	T	0.51252	-0.8729	10	0.10111	T	0.7	.	7.8498	0.29448	0.1769:0.5803:0.0838:0.1591	.	70	P11168	GTR2_HUMAN	L	70	ENSP00000323568:I70L	ENSP00000323568:I70L	I	-	1	0	SLC2A2	172215115	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-5.293000	0.00134	-2.782000	0.00360	-0.438000	0.05819	ATC	.	.		0.448	SLC2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352834.1	NM_000340		G	170732421	T	G	170732421	3	3	260	1	0	0	0	0	1	0	0	0	14559	1493	52	5	1402	5	SLC2A2	3	170732421	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	10576096	170732421	27290009	195	37440										
CHRD	8646	hgsc.bcm.edu	37	chr3	184104453	184104453	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cctgggcggccccgagacccCaacacatgcttcttcgaggg	12	16	1	1	rs35772744		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:184104453C>T	ENST00000204604.1	+	16	2352	c.2106C>T	c.(2104-2106)ccC>ccT	p.P702P	CHRD_ENST00000348986.3_Silent_p.P662P|CHRD_ENST00000450923.1_Silent_p.P702P|CHRD_ENST00000545352.1_Intron|EIF2B5_ENST00000444495.1_Intron	NM_003741.2	NP_003732.2	Q9H2X0	CHRD_HUMAN	chordin	702					BMP signaling pathway involved in spinal cord dorsal/ventral patterning (GO:0021919)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|gastrulation with mouth forming second (GO:0001702)|mesoderm formation (GO:0001707)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell migration (GO:0030336)|negative regulation of osteoblast differentiation (GO:0045668)|osteoblast differentiation (GO:0001649)|positive regulation of cell adhesion (GO:0045785)|positive regulation of mesenchymal cell proliferation (GO:0002053)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)	cytokine binding (GO:0019955)|heparin binding (GO:0008201)			NS(1)|biliary_tract(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(23)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48	all_cancers(143;6.33e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			CCCGAGACCCCAACACATGCT	0.706																																					p.P702P		Atlas-SNP	.											CHRD_ENST00000342610,lower_third,carcinoma,0,2	CHRD	149	.	0			c.C2106T						.						11	13	12					3																	184104453		2138	4212	6350	SO:0001819	synonymous_variant	8646	exon16			AGACCCCAACACA	AF076612	CCDS3266.1	3q27	2008-07-18			ENSG00000090539	ENSG00000090539			1949	protein-coding gene	gene with protein product		603475				9782094, 11472837	Standard	NM_003741		Approved		uc003fov.3	Q9H2X0	OTTHUMG00000141267	ENST00000204604.1:c.2106C>T	chr3.hg19:g.184104453C>T		75.0	0.0		49.0	2.0	NM_003741	O95254|Q2M1I8|Q6UW83|Q9H2D3|Q9H2W8|Q9H2W9|Q9P0Z2|Q9P0Z3|Q9P0Z4|Q9P0Z5	Silent	SNP	ENST00000204604.1	hg19	CCDS3266.1																																																																																			.	.		0.706	CHRD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280432.1	NM_003741		T	184104453	C	T	184104453	2	4	260	1	0	0	0	0	0	0	0	1	3374	581	21	3		3	CHRD	3	184104453	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	13372032	184104453	13917977	196	37441										
DGKG	1608	hgsc.bcm.edu	37	chr3	185970912	185970912	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gcggagacaacgggcaaggtCatttcctgttccaagaggca	13	10	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:185970912C>T	ENST00000265022.3	-	18	2109	c.1570G>A	c.(1570-1572)Gac>Aac	p.D524N	DGKG_ENST00000544847.1_Missense_Mutation_p.D465N|DGKG_ENST00000382164.4_Missense_Mutation_p.D485N|DGKG_ENST00000344484.4_Missense_Mutation_p.D499N	NM_001080744.1|NM_001080745.1|NM_001346.2	NP_001074213.1|NP_001074214.1|NP_001337.2	P49619	DGKG_HUMAN	diacylglycerol kinase, gamma 90kDa	524	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|neuron development (GO:0048666)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	42	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)	CGGGCAAGGTCATTTCCTGTT	0.522																																					p.D524N		Atlas-SNP	.											.	DGKG	98	.	0			c.G1570A						.						173	133	147					3																	185970912		2203	4300	6503	SO:0001583	missense	1608	exon18			CAAGGTCATTTCC	AF020945	CCDS3274.1, CCDS43181.1, CCDS43182.1	3q27-q28	2013-01-10	2002-08-29		ENSG00000058866	ENSG00000058866	2.7.1.107	"EF-hand domain containing"	2853	protein-coding gene	gene with protein product		601854	"diacylglycerol kinase, gamma (90kD)"	DAGK3		8034597	Standard	NM_001080744		Approved		uc003fqa.3	P49619	OTTHUMG00000156617	ENST00000265022.3:c.1570G>A	chr3.hg19:g.185970912C>T	ENSP00000265022:p.Asp524Asn	111.0	0.0		69.0	7.0	NM_001346	B2RAH4|Q2M1H4|Q5FWG1	Missense_Mutation	SNP	ENST00000265022.3	hg19	CCDS3274.1	.	.	.	.	.	.	.	.	.	.	C	35	5.469173	0.96274	.	.	ENSG00000058866	ENST00000265022;ENST00000344484;ENST00000382164;ENST00000544847;ENST00000538691	T;T;T;T	0.53423	0.62;0.64;0.62;0.62	4.97	4.97	0.65823	Diacylglycerol kinase, catalytic domain (3);	0.000000	0.85682	D	0.000000	T	0.73473	0.3591	M	0.86651	2.83	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	T	0.78437	-0.2204	10	0.87932	D	0	.	17.5152	0.87771	0.0:1.0:0.0:0.0	.	465;499;485;524	F5GX27;P49619-2;P49619-3;P49619	.;.;.;DGKG_HUMAN	N	524;499;485;465;488	ENSP00000265022:D524N;ENSP00000339777:D499N;ENSP00000371599:D485N;ENSP00000440507:D465N	ENSP00000265022:D524N	D	-	1	0	DGKG	187453606	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.503000	0.81632	2.742000	0.94016	0.655000	0.94253	GAC	.	.		0.522	DGKG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344800.3			T	185970912	C	T	185970912	3	4	260	1	0	0	0	0	1	0	0	0	4471	826	29	3	837	3	DGKG	3	185970912	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	1866459	185970912	12051518	197	37442										
TBCCD1	55171	hgsc.bcm.edu	37	chr3	186272247	186272247	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cgctgttctctctgcacacaAccattggattatcccaatag	6	13	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:186272247A>G	ENST00000424280.1	-	6	1819	c.1340T>C	c.(1339-1341)gTt>gCt	p.V447A	TBCCD1_ENST00000479590.1_5'UTR|TBCCD1_ENST00000446782.1_Missense_Mutation_p.V351A|TBCCD1_ENST00000338733.5_Missense_Mutation_p.V447A	NM_001134415.1	NP_001127887.1	Q9NVR7	TBCC1_HUMAN	TBCC domain containing 1	447					cell morphogenesis (GO:0000902)|cytoskeleton organization (GO:0007010)|maintenance of centrosome location (GO:0051661)|maintenance of Golgi location (GO:0051684)|regulation of cell migration (GO:0030334)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|spindle pole centrosome (GO:0031616)				breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|skin(1)	17	all_cancers(143;3.75e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.3e-21)	GBM - Glioblastoma multiforme(93;0.0474)		TCTGCACACAACCATTGGATT	0.433																																					p.V447A		Atlas-SNP	.											.	TBCCD1	42	.	0			c.T1340C						.						107	105	106					3																	186272247		2203	4300	6503	SO:0001583	missense	55171	exon6			CACACAACCATTG	BC025748	CCDS3276.1, CCDS75061.1	3q27.3	2006-03-09			ENSG00000113838	ENSG00000113838			25546	protein-coding gene	gene with protein product						12477932	Standard	NM_001134415		Approved	FLJ10560	uc003fqg.3	Q9NVR7	OTTHUMG00000156613	ENST00000424280.1:c.1340T>C	chr3.hg19:g.186272247A>G	ENSP00000411253:p.Val447Ala	159.0	0.0		98.0	4.0	NM_001134415	B3KW69|D3DNU6|G5E9J4	Missense_Mutation	SNP	ENST00000424280.1	hg19	CCDS3276.1	.	.	.	.	.	.	.	.	.	.	A	11.53	1.666953	0.29604	.	.	ENSG00000113838	ENST00000424280;ENST00000338733;ENST00000446782	D;D;D	0.83837	-1.76;-1.76;-1.77	5.81	4.67	0.58626	.	0.419604	0.26210	N	0.025685	T	0.69187	0.3083	N	0.25647	0.755	0.29254	N	0.871812	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.002	T	0.55909	-0.8066	10	0.12430	T	0.62	-4.8466	9.409	0.38480	0.9174:0.0:0.0826:0.0	.	351;447	G5E9J4;Q9NVR7	.;TBCC1_HUMAN	A	447;447;351	ENSP00000411253:V447A;ENSP00000341652:V447A;ENSP00000397091:V351A	ENSP00000341652:V447A	V	-	2	0	TBCCD1	187754941	0.998000	0.40836	0.773000	0.31616	0.923000	0.55619	5.834000	0.69361	2.230000	0.72887	0.451000	0.29950	GTT	.	.		0.433	TBCCD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344774.1	NM_018138		G	186272247	A	G	186272247	3	3	260	1	0	0	0	0	1	0	0	0	15647	43	2	2	341	2	TBCCD1	3	186272247	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	301335	186272247	11750183	198	37443										
APOD	347	hgsc.bcm.edu	37	chr3	195306237	195306237	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acgtcaaaattctcctgcacCggaggattggggcacttccc	10	13	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:195306237C>A	ENST00000343267.3	-	2	457	c.96G>T	c.(94-96)ccG>ccT	p.P32P		NM_001647.3	NP_001638.1	P05090	APOD_HUMAN	apolipoprotein D	32					aging (GO:0007568)|angiogenesis (GO:0001525)|brain development (GO:0007420)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|negative regulation of cytokine production involved in inflammatory response (GO:1900016)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of lipoprotein lipid oxidation (GO:0060588)|negative regulation of monocyte chemotactic protein-1 production (GO:0071638)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein import into nucleus (GO:0042308)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of smooth muscle cell-matrix adhesion (GO:2000098)|negative regulation of T cell migration (GO:2000405)|peripheral nervous system axon regeneration (GO:0014012)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to reactive oxygen species (GO:0000302)|tissue regeneration (GO:0042246)	cytosolic ribosome (GO:0022626)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|lipid transporter activity (GO:0005319)			breast(1)|endometrium(1)|large_intestine(1)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	9	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		TCTCCTGCACCGGAGGATTGG	0.512																																					p.P32P		Atlas-SNP	.											.	APOD	28	.	0			c.G96T						.						120	124	123					3																	195306237		2203	4300	6503	SO:0001819	synonymous_variant	347	exon2			CTGCACCGGAGGA		CCDS33925.1	3q29	2013-09-19			ENSG00000189058	ENSG00000189058		"Lipocalins", "Apolipoproteins"	612	protein-coding gene	gene with protein product		107740				2439269, 3453108	Standard	NM_001647		Approved		uc003fur.2	P05090	OTTHUMG00000155854	ENST00000343267.3:c.96G>T	chr3.hg19:g.195306237C>A		89.0	0.0		45.0	4.0	NM_001647	B2R579|D3DNW6|Q6IBG6	Silent	SNP	ENST00000343267.3	hg19	CCDS33925.1																																																																																			.	.		0.512	APOD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342004.1	NM_001647		A	195306237	C	A	195306237	2	1	260	1	0	0	0	0	0	0	0	1	801	639	23	1		1	APOD	3	195306237	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	9033990	195306237	2716193	199	37444										
MUC20	200958	hgsc.bcm.edu	37	chr3	195453275	195453275	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcgcaaccaaggggcccttcCccaccagcagggaccctctt	9	18	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr3:195453275C>A	ENST00000447234.2	+	2	1927	c.1801C>A	c.(1801-1803)Ccc>Acc	p.P601T	MUC20_ENST00000320736.6_Missense_Mutation_p.P430T|MUC20_ENST00000436408.1_Missense_Mutation_p.P601T|MUC20_ENST00000445522.2_Missense_Mutation_p.P566T	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	601	Involved in oligomerization.|Thr-rich.				activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)				NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		GGGGCCCTTCCCCACCAGCAG	0.597																																					p.P430T		Atlas-SNP	.											.	MUC20	84	.	0			c.C1288A						.						62	63	63					3																	195453275		2081	4200	6281	SO:0001583	missense	200958	exon3			CCCTTCCCCACCA	AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"Mucins"	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.1801C>A	chr3.hg19:g.195453275C>A	ENSP00000414350:p.Pro601Thr	118.0	0.0		86.0	4.0	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Missense_Mutation	SNP	ENST00000447234.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.79|15.79	2.935910|2.935910	0.52972|0.52972	.|.	.|.	ENSG00000176945|ENSG00000176945	ENST00000423938|ENST00000381954;ENST00000447234;ENST00000320736;ENST00000436408;ENST00000445522	.|T;T;T;T	.|0.15372	.|2.86;2.89;3.03;2.43	4.59|4.59	4.59|4.59	0.56863|0.56863	.|.	0.489229|0.489229	0.17483|0.17483	N|N	0.172642|0.172642	T|T	0.30103|0.30103	0.0754|0.0754	L|L	0.36672|0.36672	1.1|1.1	0.09310|0.09310	N|N	1|1	.|D	.|0.71674	.|0.998	.|D	.|0.71656	.|0.974	T|T	0.03840|0.03840	-1.0999|-1.0999	6|10	.|0.46703	.|T	.|0.11	-7.577|-7.577	13.0954|13.0954	0.59188|0.59188	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|430	.|E9PH32	.|.	H|T	12|412;601;430;601;566	.|ENSP00000414350:P601T;ENSP00000325431:P430T;ENSP00000396774:P601T;ENSP00000405629:P566T	.|ENSP00000325431:P430T	P|P	+|+	2|1	0|0	MUC20|MUC20	196938946|196938946	0.000000|0.000000	0.05858|0.05858	0.081000|0.081000	0.20488|0.20488	0.019000|0.019000	0.09904|0.09904	0.014000|0.014000	0.13333|0.13333	2.541000|2.541000	0.85698|0.85698	0.563000|0.563000	0.77884|0.77884	CCC|CCC	.	.		0.597	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673		A	195453275	C	A	195453275	3	1	260	1	0	0	0	0	1	0	0	0	9985	623	22	3	1298	3	MUC20	3	195453275	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	147038	195453275	2569155	200	37445										
SLC26A1	10861	hgsc.bcm.edu	37	chr4	983570	983570	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agcagtggaggaaggcgggtAgcacgttgcagcagcccaca	16	10	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr4:983570A>G	ENST00000361661.2	-	4	1534	c.1157T>C	c.(1156-1158)cTa>cCa	p.L386P	SLC26A1_ENST00000513138.1_5'Flank|IDUA_ENST00000453894.1_Intron|IDUA_ENST00000247933.4_Intron|SLC26A1_ENST00000398520.2_Intron|SLC26A1_ENST00000398516.2_Missense_Mutation_p.L386P	NM_213613.2	NP_998778.1	Q9H2B4	S26A1_HUMAN	solute carrier family 26 (anion exchanger), member 1	386					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|chloride transport (GO:0006821)|glycosaminoglycan metabolic process (GO:0030203)|ion transport (GO:0006811)|oxalate transport (GO:0019532)|small molecule metabolic process (GO:0044281)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|chloride transmembrane transporter activity (GO:0015108)|oxalate transmembrane transporter activity (GO:0019531)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			central_nervous_system(1)|endometrium(4)|pancreas(1)|prostate(1)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GAAGGCGGGTAGCACGTTGCA	0.667																																					p.L386P		Atlas-SNP	.											.	SLC26A1	44	.	0			c.T1157C						.						10	11	11					4																	983570		2143	4251	6394	SO:0001583	missense	10861	exon3			GCGGGTAGCACGT	AF297659	CCDS33933.1, CCDS33934.1	4p16.3	2013-07-18	2013-07-18		ENSG00000145217	ENSG00000145217		"Solute carriers"	10993	protein-coding gene	gene with protein product		610130	"solute carrier family 26 (sulfate transporter), member 1"				Standard	NM_213613		Approved	SAT-1, EDM4	uc003gcc.3	Q9H2B4	OTTHUMG00000160003	ENST00000361661.2:c.1157T>C	chr4.hg19:g.983570A>G	ENSP00000354721:p.Leu386Pro	129.0	0.0		111.0	5.0	NM_022042	A8K9N2|Q7Z5R3|Q96BK0	Missense_Mutation	SNP	ENST00000361661.2	hg19	CCDS33934.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.074494	0.76415	.	.	ENSG00000145217	ENST00000361661;ENST00000398516	D;D	0.94417	-3.42;-3.42	5.14	5.14	0.70334	Sulphate transporter (1);	0.168858	0.50627	D	0.000102	D	0.96321	0.8800	M	0.71206	2.165	0.80722	D	1	D	0.60160	0.987	D	0.65323	0.934	D	0.96671	0.9496	10	0.87932	D	0	.	12.8891	0.58061	1.0:0.0:0.0:0.0	.	386	Q9H2B4	S26A1_HUMAN	P	386	ENSP00000354721:L386P;ENSP00000381528:L386P	ENSP00000354721:L386P	L	-	2	0	SLC26A1	973570	1.000000	0.71417	0.996000	0.52242	0.820000	0.46376	7.248000	0.78268	1.929000	0.55896	0.454000	0.30748	CTA	.	.		0.667	SLC26A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358783.1	NM_022042, NM_134425		G	983570	A	G	983570	3	3	260	1	0	0	0	0	1	0	0	0	14529	420	15	2	1055	2	SLC26A1	4	983570	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10		983570	190170706	201	37446										
SLC26A1	10861	hgsc.bcm.edu	37	chr4	983816	983816	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gctgcccgaagtgcgacacgAgtgtggccaccacgatgacc	13	14	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr4:983816A>G	ENST00000361661.2	-	4	1288	c.911T>C	c.(910-912)cTc>cCc	p.L304P	SLC26A1_ENST00000513138.1_5'Flank|IDUA_ENST00000453894.1_Intron|IDUA_ENST00000247933.4_Intron|SLC26A1_ENST00000398520.2_Intron|SLC26A1_ENST00000398516.2_Missense_Mutation_p.L304P	NM_213613.2	NP_998778.1	Q9H2B4	S26A1_HUMAN	solute carrier family 26 (anion exchanger), member 1	304					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|chloride transport (GO:0006821)|glycosaminoglycan metabolic process (GO:0030203)|ion transport (GO:0006811)|oxalate transport (GO:0019532)|small molecule metabolic process (GO:0044281)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|chloride transmembrane transporter activity (GO:0015108)|oxalate transmembrane transporter activity (GO:0019531)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			central_nervous_system(1)|endometrium(4)|pancreas(1)|prostate(1)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GTGCGACACGAGTGTGGCCAC	0.677																																					p.L304P		Atlas-SNP	.											.	SLC26A1	44	.	0			c.T911C						.						31	24	26					4																	983816		2176	4290	6466	SO:0001583	missense	10861	exon3			GACACGAGTGTGG	AF297659	CCDS33933.1, CCDS33934.1	4p16.3	2013-07-18	2013-07-18		ENSG00000145217	ENSG00000145217		"Solute carriers"	10993	protein-coding gene	gene with protein product		610130	"solute carrier family 26 (sulfate transporter), member 1"				Standard	NM_213613		Approved	SAT-1, EDM4	uc003gcc.3	Q9H2B4	OTTHUMG00000160003	ENST00000361661.2:c.911T>C	chr4.hg19:g.983816A>G	ENSP00000354721:p.Leu304Pro	78.0	0.0		72.0	5.0	NM_022042	A8K9N2|Q7Z5R3|Q96BK0	Missense_Mutation	SNP	ENST00000361661.2	hg19	CCDS33934.1	.	.	.	.	.	.	.	.	.	.	A	12.10	1.835265	0.32421	.	.	ENSG00000145217	ENST00000361661;ENST00000398516	D;D	0.94232	-3.38;-3.38	4.97	3.78	0.43462	Sulphate transporter (1);	0.452720	0.24052	N	0.041997	D	0.96586	0.8886	M	0.89785	3.06	0.58432	D	0.999993	D	0.89917	1.0	D	0.78314	0.991	D	0.95522	0.8595	10	0.59425	D	0.04	.	8.8046	0.34929	0.9091:0.0:0.0909:0.0	.	304	Q9H2B4	S26A1_HUMAN	P	304	ENSP00000354721:L304P;ENSP00000381528:L304P	ENSP00000354721:L304P	L	-	2	0	SLC26A1	973816	0.994000	0.37717	0.001000	0.08648	0.096000	0.18686	7.363000	0.79516	0.746000	0.32786	-0.379000	0.06801	CTC	.	.		0.677	SLC26A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358783.1	NM_022042, NM_134425		G	983816	A	G	983816	3	3	260	1	0	0	0	0	1	0	0	0	14529	304	11	2	1301	2	SLC26A1	4	983816	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	246	983816	190170460	202	37447										
TNIP2	79155	hgsc.bcm.edu	37	chr4	2749527	2749527	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccaaggagcggcacaggacgTcactggcggcccgggcgcgc	17	15	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr4:2749527T>C	ENST00000315423.7	-	2	508	c.422A>G	c.(421-423)gAc>gGc	p.D141G	TNIP2_ENST00000503235.1_Missense_Mutation_p.D141G|TNIP2_ENST00000505186.1_5'Flank|TNIP2_ENST00000510267.1_Missense_Mutation_p.D34G	NM_024309.3	NP_077285.3			TNFAIP3 interacting protein 2											breast(2)|central_nervous_system(1)|large_intestine(4)|lung(6)|prostate(1)	14				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		GCACAGGACGTCACTGGCGGC	0.647																																					p.D141G		Atlas-SNP	.											.	TNIP2	28	.	0			c.A422G						.						109	105	106					4																	2749527		2203	4300	6503	SO:0001583	missense	79155	exon2			AGGACGTCACTGG	BC002740	CCDS3362.1, CCDS54714.1, CCDS75093.1	4p16.3	2008-08-01			ENSG00000168884	ENSG00000168884			19118	protein-coding gene	gene with protein product		610669				11390377, 12933576	Standard	NM_024309		Approved	ABIN-2, MGC4289, KLIP, FLIP1	uc003gfg.2	Q8NFZ5	OTTHUMG00000090267	ENST00000315423.7:c.422A>G	chr4.hg19:g.2749527T>C	ENSP00000321203:p.Asp141Gly	111.0	0.0		87.0	4.0	NM_024309		Missense_Mutation	SNP	ENST00000315423.7	hg19	CCDS3362.1	.	.	.	.	.	.	.	.	.	.	t	10.51	1.371386	0.24771	.	.	ENSG00000168884	ENST00000510267;ENST00000315423;ENST00000503235	T;T;T	0.49432	0.79;0.78;0.78	3.81	1.14	0.20703	.	0.650910	0.15128	N	0.279011	T	0.41488	0.1161	M	0.66939	2.045	0.09310	N	1	B;B	0.25169	0.119;0.118	B;B	0.26770	0.041;0.073	T	0.31586	-0.9938	10	0.33940	T	0.23	-9.8926	6.2697	0.20947	0.1592:0.0:0.1662:0.6746	.	141;141	D6RGJ2;Q8NFZ5	.;TNIP2_HUMAN	G	34;141;141	ENSP00000427613:D34G;ENSP00000321203:D141G;ENSP00000426314:D141G	ENSP00000321203:D141G	D	-	2	0	TNIP2	2719325	0.000000	0.05858	0.000000	0.03702	0.670000	0.39368	0.799000	0.27028	0.136000	0.18733	0.449000	0.29647	GAC	.	.		0.647	TNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206589.5	NM_024309		C	2749527	T	C	2749527	3	2	260	1	0	0	0	0	1	0	0	0	16330	1667	58	2	887	2	TNIP2	4	2749527	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1765711	2749527	188404749	203	37448										
JAKMIP1	152789	hgsc.bcm.edu	37	chr4	6087245	6087245	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctccttgacctgaaccagctGctcatccaaagcctctttct	5	16	3	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr4:6087245G>T	ENST00000282924.5	-	4	1221	c.736C>A	c.(736-738)Cag>Aag	p.Q246K	JAKMIP1_ENST00000409021.3_Missense_Mutation_p.Q246K|JAKMIP1_ENST00000457227.2_5'UTR|JAKMIP1_ENST00000409371.3_Missense_Mutation_p.Q81K|JAKMIP1_ENST00000410077.2_Missense_Mutation_p.Q81K|JAKMIP1_ENST00000409831.1_Missense_Mutation_p.Q246K	NM_144720.3	NP_653321.1	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein 1	246	Mediates association with microtubules.				cognition (GO:0050890)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|microtubule (GO:0005874)|ribonucleoprotein complex (GO:0030529)	GABA receptor binding (GO:0050811)|RNA binding (GO:0003723)			NS(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						TGAACCAGCTGCTCATCCAAA	0.597																																					p.Q246K		Atlas-SNP	.											.	JAKMIP1	250	.	0			c.C736A						.						107	109	108					4																	6087245		2203	4300	6503	SO:0001583	missense	152789	exon4			CCAGCTGCTCATC	AK056126	CCDS3385.1, CCDS47005.1	4p16.1	2013-10-11	2009-08-13		ENSG00000152969	ENSG00000152969			26460	protein-coding gene	gene with protein product		611195				18941173	Standard	NM_144720		Approved	MARLIN1, JAMIP1, Gababrbp, FLJ31564	uc010idb.1	Q96N16	OTTHUMG00000125491	ENST00000282924.5:c.736C>A	chr4.hg19:g.6087245G>T	ENSP00000282924:p.Gln246Lys	151.0	0.0		90.0	5.0	NM_001099433	A6H2J2|A6H2J3|A6H2J4|A6H2J5|A8MTK6|B4DHZ8|B8ZZR7|D3DVT0|Q86Y69|Q8N7G3	Missense_Mutation	SNP	ENST00000282924.5	hg19	CCDS3385.1	.	.	.	.	.	.	.	.	.	.	G	19.09	3.759914	0.69763	.	.	ENSG00000152969	ENST00000409021;ENST00000409371;ENST00000418227;ENST00000425341;ENST00000429819;ENST00000282924;ENST00000409831;ENST00000410077	T;T;T;T;T	0.35048	1.33;1.33;1.33;1.33;1.33	4.1	4.1	0.47936	.	0.251342	0.28883	N	0.013840	T	0.59972	0.2233	M	0.77313	2.365	0.46927	D	0.999257	P;P;P;P;P	0.52577	0.954;0.597;0.954;0.954;0.597	D;B;D;D;B	0.67900	0.932;0.26;0.954;0.932;0.167	T	0.64901	-0.6298	10	0.54805	T	0.06	.	15.5262	0.75910	0.0:0.0:1.0:0.0	.	81;246;81;246;246	B4DHZ8;F2Z2K5;Q96N16-5;Q96N16-2;Q96N16	.;.;.;.;JKIP1_HUMAN	K	246;81;246;246;138;246;246;81	ENSP00000386711:Q246K;ENSP00000387042:Q81K;ENSP00000282924:Q246K;ENSP00000386925:Q246K;ENSP00000386745:Q81K	ENSP00000282924:Q246K	Q	-	1	0	JAKMIP1	6138146	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	8.819000	0.91997	2.135000	0.66039	0.655000	0.94253	CAG	.	.		0.597	JAKMIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246816.2	NM_144720		T	6087245	G	T	6087245	3	4	260	1	0	0	0	0	1	0	0	0	7949	1328	46	3	1906	3	JAKMIP1	4	6087245	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	3337718	6087245	185067031	204	37449										
ACOX3	8310	hgsc.bcm.edu	37	chr4	8375349	8375349	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccgcctgctcaccggagaagTatcctcctgcaagcacagcc	9	17	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr4:8375349T>A	ENST00000356406.5	-	16	1912	c.1835A>T	c.(1834-1836)tAc>tTc	p.Y612F	ACOX3_ENST00000515797.1_5'UTR|ACOX3_ENST00000413009.2_Intron|ACOX3_ENST00000503233.1_Missense_Mutation_p.Y612F	NM_003501.2	NP_003492.2	O15254	ACOX3_HUMAN	acyl-CoA oxidase 3, pristanoyl	612					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|pristanoyl-CoA oxidase activity (GO:0016402)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(17)|prostate(1)|skin(3)|stomach(1)	42						ACCGGAGAAGTATCCTCCTGC	0.582																																					p.Y612F		Atlas-SNP	.											.	ACOX3	70	.	0			c.A1835T						.						89	71	77					4																	8375349		2201	4300	6501	SO:0001583	missense	8310	exon16			GAGAAGTATCCTC	Y11411	CCDS3401.1, CCDS47017.1	4p15.3	2010-04-30	2010-04-30		ENSG00000087008	ENSG00000087008	1.3.3.6		121	protein-coding gene	gene with protein product		603402	"acyl-Coenzyme A oxidase 3, pristanoyl"			9271077	Standard	NM_003501		Approved		uc003glc.4	O15254	OTTHUMG00000090509	ENST00000356406.5:c.1835A>T	chr4.hg19:g.8375349T>A	ENSP00000348775:p.Tyr612Phe	123.0	0.0		84.0	4.0	NM_003501	Q96AJ8	Missense_Mutation	SNP	ENST00000356406.5	hg19	CCDS3401.1	.	.	.	.	.	.	.	.	.	.	T	12.89	2.073756	0.36566	.	.	ENSG00000087008	ENST00000356406;ENST00000503233	T;T	0.42513	0.97;0.97	4.29	4.29	0.51040	Acyl-CoA oxidase, C-terminal (1);Acyl-CoA dehydrogenase/oxidase C-terminal (2);	0.663464	0.14751	N	0.300556	T	0.45155	0.1328	M	0.63428	1.95	0.49299	D	0.999772	B	0.27316	0.175	B	0.37304	0.246	T	0.28490	-1.0042	10	0.22706	T	0.39	-10.2481	11.4611	0.50211	0.0:0.0:0.0:1.0	.	612	O15254	ACOX3_HUMAN	F	612	ENSP00000348775:Y612F;ENSP00000421625:Y612F	ENSP00000348775:Y612F	Y	-	2	0	ACOX3	8426249	1.000000	0.71417	1.000000	0.80357	0.283000	0.27025	4.153000	0.58118	1.820000	0.53075	0.454000	0.30748	TAC	.	.		0.582	ACOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206997.4			A	8375349	T	A	8375349	3	1	260	1	0	0	0	0	1	0	0	0	160	1638	57	4	279	4	ACOX3	4	8375349	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	2288104	8375349	182778927	205	37450										
HS3ST1	9957	hgsc.bcm.edu	37	chr4	11401109	11401109	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cgcgcaccaggaactcctcgAtggacgggtagggcttgtgc	15	12	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr4:11401109A>G	ENST00000002596.5	-	2	1695	c.521T>C	c.(520-522)aTc>aCc	p.I174T		NM_005114.2	NP_005105.1	O14792	HS3S1_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	174					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)|sulfotransferase activity (GO:0008146)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(6)|skin(3)	15						GAACTCCTCGATGGACGGGTA	0.587																																					p.I174T		Atlas-SNP	.											.	HS3ST1	41	.	0			c.T521C						.						87	80	82					4																	11401109		2203	4300	6503	SO:0001583	missense	9957	exon2			TCCTCGATGGACG	AF019386	CCDS3408.1	4p16	2008-02-05			ENSG00000002587	ENSG00000002587	2.8.2.23	"Sulfotransferases, membrane-bound"	5194	protein-coding gene	gene with protein product		603244				9988767	Standard	NM_005114		Approved	3OST1	uc003gmq.3	O14792	OTTHUMG00000090547	ENST00000002596.5:c.521T>C	chr4.hg19:g.11401109A>G	ENSP00000002596:p.Ile174Thr	115.0	0.0		96.0	4.0	NM_005114	B3KUA6|Q6PEY8	Missense_Mutation	SNP	ENST00000002596.5	hg19	CCDS3408.1	.	.	.	.	.	.	.	.	.	.	A	19.05	3.751197	0.69533	.	.	ENSG00000002587	ENST00000002596	D	0.82619	-1.63	5.61	4.39	0.52855	Sulfotransferase domain (1);	0.273444	0.36444	N	0.002589	D	0.83917	0.5358	N	0.22421	0.69	0.47778	D	0.999512	P	0.46457	0.878	D	0.67382	0.951	D	0.84048	0.0368	10	0.54805	T	0.06	.	11.4662	0.50241	0.8653:0.0:0.0:0.1347	.	174	O14792	HS3S1_HUMAN	T	174	ENSP00000002596:I174T	ENSP00000002596:I174T	I	-	2	0	HS3ST1	11010207	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.469000	0.80959	1.016000	0.39470	0.533000	0.62120	ATC	.	.		0.587	HS3ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207073.3	NM_005114		G	11401109	A	G	11401109	3	3	260	1	0	0	0	0	1	0	0	0	7372	333	12	2	406	2	HS3ST1	4	11401109	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	3025760	11401109	179753167	206	37451										
CC2D2A	57545	hgsc.bcm.edu	37	chr4	15572065	15572065	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	atccatactcgtattgagagAcactggctgggatgtgtgaa	12	7	0	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr4:15572065A>G	ENST00000503292.1	+	29	3720	c.3540A>G	c.(3538-3540)agA>agG	p.R1180R	CC2D2A_ENST00000389652.5_Silent_p.R1131R|CC2D2A_ENST00000424120.1_Silent_p.R1180R|CC2D2A_ENST00000413206.1_Silent_p.R1180R	NM_001080522.2	NP_001073991.2	Q9P2K1	C2D2A_HUMAN	coiled-coil and C2 domain containing 2A	1180					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|TCTN-B9D complex (GO:0036038)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|urinary_tract(2)	32						GTATTGAGAGACACTGGCTGG	0.398																																					p.R1180R		Atlas-SNP	.											.	CC2D2A	158	.	0			c.A3540G						.						68	66	67					4																	15572065		1895	4122	6017	SO:0001819	synonymous_variant	57545	exon29			TGAGAGACACTGG	AB037766, EU450799	CCDS47026.1, CCDS47027.1, CCDS47027.2, CCDS54744.1	4p15.33	2014-09-17	2007-10-19		ENSG00000048342	ENSG00000048342			29253	protein-coding gene	gene with protein product	"Meckel syndrome, type 6"	612013				10718198, 18513680	Standard	NM_001080522		Approved	KIAA1345, MKS6, JBTS9	uc010idv.2	Q9P2K1	OTTHUMG00000160255	ENST00000503292.1:c.3540A>G	chr4.hg19:g.15572065A>G		194.0	0.0		99.0	4.0	NM_001080522	A6ND97|B3FW08|D6RB72|E7EP21|E9PEV5|Q3SYP3|Q9H8A7	Silent	SNP	ENST00000503292.1	hg19	CCDS47026.1																																																																																			.	.		0.398	CC2D2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359906.2	NM_001080522		G	15572065	A	G	15572065	2	3	260	1	0	0	0	0	0	0	0	1	2730	272	10	2		2	CC2D2A	4	15572065	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	4170956	15572065	175582211	207	37452										
PCDH7	5099	hgsc.bcm.edu	37	chr4	30725244	30725244	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cagtctcgctttttgtgatgGatgaaaatgacaatgctccc	9	9	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr4:30725244G>T	ENST00000361762.2	+	1	3208	c.2200G>T	c.(2200-2202)Gat>Tat	p.D734Y	PCDH7_ENST00000543491.1_Missense_Mutation_p.D734Y	NM_002589.2	NP_002580.2	O60245	PCDH7_HUMAN	protocadherin 7	734	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(8)|liver(1)|lung(26)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	55						TTTTGTGATGGATGAAAATGA	0.473																																					p.D734Y		Atlas-SNP	.											.	PCDH7	215	.	0			c.G2200T						.						102	97	98					4																	30725244		2203	4300	6503	SO:0001583	missense	5099	exon1			GTGATGGATGAAA	AB006755	CCDS33971.1, CCDS75116.1	4p15	2014-06-13	2007-02-12			ENSG00000169851		"Cadherins / Protocadherins : Non-clustered"	8659	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 120"	602988	"BH-protocadherin (brain-heart)"			9615233	Standard	NM_002589		Approved	BH-Pcdh, PPP1R120	uc021xnd.1	O60245		ENST00000361762.2:c.2200G>T	chr4.hg19:g.30725244G>T	ENSP00000355243:p.Asp734Tyr	238.0	0.0		141.0	35.0	NM_032457	O60246|O60247|Q4W5C4	Missense_Mutation	SNP	ENST00000361762.2	hg19	CCDS33971.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.22|17.22	3.334506|3.334506	0.60853|0.60853	.|.	.|.	ENSG00000169851|ENSG00000169851	ENST00000361762;ENST00000543491;ENST00000333135|ENST00000511884	T;T|.	0.67865|.	-0.29;-0.29|.	5.04|5.04	5.04|5.04	0.67666|0.67666	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);|.	.|.	.|.	.|.	.|.	D|D	0.91092|0.91092	0.7196|0.7196	H|H	0.98901|0.98901	4.365|4.365	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	1.0;1.0;0.999|.	D|D	0.94623|0.94623	0.7815|0.7815	9|5	0.87932|.	D|.	0|.	.|.	18.588|18.588	0.91197|0.91197	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	734;687;734|.	F5GWJ1;O60245-3;O60245|.	.;.;PCDH7_HUMAN|.	Y|V	734;734;687|423	ENSP00000355243:D734Y;ENSP00000441802:D734Y|.	ENSP00000330302:D687Y|.	D|G	+|+	1|2	0|0	PCDH7|PCDH7	30334342|30334342	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.652000|9.652000	0.98499|0.98499	2.612000|2.612000	0.88384|0.88384	0.655000|0.655000	0.94253|0.94253	GAT|GGA	.	.		0.473	PCDH7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360366.1	NM_032457, NM_002589		T	30725244	G	T	30725244	3	4	260	1	0	0	0	0	1	0	0	0	11525	1174	41	3	2202	3	PCDH7	4	30725244	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	15153179	30725244	160429032	208	37453										
PGM2	55276	hgsc.bcm.edu	37	chr4	37831602	37831602	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcagaattccttaactttggAggcagtgaaacgactaatag	9	7	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr4:37831602A>G	ENST00000381967.4	+	2	198	c.98A>G	c.(97-99)gAg>gGg	p.E33G	PGM2_ENST00000544359.1_5'UTR|PGM2_ENST00000537241.1_5'UTR	NM_018290.3	NP_060760.2	Q96G03	PGM2_HUMAN	phosphoglucomutase 2	33					carbohydrate metabolic process (GO:0005975)|deoxyribose phosphate catabolic process (GO:0046386)|galactose catabolic process (GO:0019388)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	magnesium ion binding (GO:0000287)|phosphoglucomutase activity (GO:0004614)|phosphopentomutase activity (GO:0008973)			breast(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(2)|urinary_tract(1)	19						TTAACTTTGGAGGCAGTGAAA	0.378																																					p.E33G		Atlas-SNP	.											.	PGM2	45	.	0			c.A98G						.						56	60	58					4																	37831602		2203	4300	6503	SO:0001583	missense	55276	exon2			CTTTGGAGGCAGT	BC010087	CCDS3443.1	4p14	2012-10-02			ENSG00000169299	ENSG00000169299	5.4.2.2		8906	protein-coding gene	gene with protein product	"phosphopentomutase"	172000				9549096	Standard	NM_018290		Approved	FLJ10983	uc011byb.1	Q96G03	OTTHUMG00000097813	ENST00000381967.4:c.98A>G	chr4.hg19:g.37831602A>G	ENSP00000371393:p.Glu33Gly	161.0	0.0		124.0	5.0	NM_018290	B4E0G8|Q53FP5|Q5QTR0|Q9H0P9|Q9NV22	Missense_Mutation	SNP	ENST00000381967.4	hg19	CCDS3443.1	.	.	.	.	.	.	.	.	.	.	A	4.328	0.060248	0.08339	.	.	ENSG00000169299	ENST00000381967	T	0.53857	0.6	5.64	4.45	0.53987	.	0.481828	0.23129	N	0.051612	T	0.44030	0.1274	L	0.44542	1.39	0.19945	N	0.999946	B	0.02656	0.0	B	0.06405	0.002	T	0.27400	-1.0075	10	0.30078	T	0.28	-9.0177	12.2007	0.54323	0.6049:0.3951:0.0:0.0	.	33	Q96G03	PGM2_HUMAN	G	33	ENSP00000371393:E33G	ENSP00000371393:E33G	E	+	2	0	PGM2	37507997	0.964000	0.33143	0.024000	0.17045	0.125000	0.20455	2.517000	0.45529	0.945000	0.37605	0.528000	0.53228	GAG	.	.		0.378	PGM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215079.2	NM_018290		G	37831602	A	G	37831602	3	3	260	1	0	0	0	0	1	0	0	0	11807	304	11	2	104	2	PGM2	4	37831602	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	7106358	37831602	153322674	209	37454										
KLB	152831	hgsc.bcm.edu	37	chr4	39435941	39435941	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agccaaaccggtcggaaaacAcgatggatatattcaaatgt	9	8	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr4:39435941A>T	ENST00000257408.4	+	2	1034	c.937A>T	c.(937-939)Acg>Tcg	p.T313S		NM_175737.3	NP_783864.1	Q86Z14	KLOTB_HUMAN	klotho beta	313	Glycosyl hydrolase-1 1.				carbohydrate metabolic process (GO:0005975)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fibroblast growth factor binding (GO:0017134)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|skin(6)	29						GTCGGAAAACACGATGGATAT	0.468																																					p.T313S		Atlas-SNP	.											.	KLB	95	.	0			c.A937T						.						122	106	111					4																	39435941		2203	4300	6503	SO:0001583	missense	152831	exon2			GAAAACACGATGG	AB079373	CCDS3451.1	4p14	2008-02-05			ENSG00000134962	ENSG00000134962			15527	protein-coding gene	gene with protein product		611135					Standard	NM_175737		Approved		uc003gua.3	Q86Z14	OTTHUMG00000128577	ENST00000257408.4:c.937A>T	chr4.hg19:g.39435941A>T	ENSP00000257408:p.Thr313Ser	317.0	0.0		197.0	55.0	NM_175737	Q2M3K8	Missense_Mutation	SNP	ENST00000257408.4	hg19	CCDS3451.1	.	.	.	.	.	.	.	.	.	.	A	0.147	-1.095797	0.01858	.	.	ENSG00000134962	ENST00000257408	T	0.30981	1.51	6.17	-3.31	0.04988	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.841312	0.11191	N	0.589895	T	0.13798	0.0334	N	0.16016	0.355	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.10450	0.005;0.005	T	0.37934	-0.9684	10	0.11485	T	0.65	0.1267	9.0259	0.36230	0.3913:0.1226:0.4862:0.0	.	313;313	B7ZL50;Q86Z14	.;KLOTB_HUMAN	S	313	ENSP00000257408:T313S	ENSP00000257408:T313S	T	+	1	0	KLB	39112336	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.460000	0.21924	-0.538000	0.06281	-0.274000	0.10170	ACG	.	.		0.468	KLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250429.1	NM_175737		T	39435941	A	T	39435941	3	4	260	1	0	0	0	0	1	0	0	0	8341	159	6	4	943	4	KLB	4	39435941	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1604339	39435941	151718335	210	37455										
UGT2A2	10941	hgsc.bcm.edu	37	chr4	70504997	70504997	+	Intron	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agaaagtgtctagaagttttCctagttctttgtagaaagcc	9	6	2	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr4:70504997C>T	ENST00000503640.1	-	1	771				UGT2A1_ENST00000286604.4_Intron|UGT2A1_ENST00000514019.1_Missense_Mutation_p.G322E|UGT2A1_ENST00000512704.1_Intron|UGT2A2_ENST00000457664.2_Missense_Mutation_p.G121E	NM_006798.3	NP_006789.2	Q9Y4X1	UD2A1_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide A1, complex locus						cellular glucuronidation (GO:0052695)|detection of chemical stimulus (GO:0009593)|metabolic process (GO:0008152)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(1)|skin(2)	30						TAGAAGTTTTCCTAGTTCTTT	0.363																																					p.G322E		Atlas-SNP	.											.	UGT2A1	131	.	0			c.G965A						.						98	95	96					4																	70504997		1843	4081	5924	SO:0001627	intron_variant	10941	exon3			AGTTTTCCTAGTT	AJ006054	CCDS3529.1, CCDS58901.1, CCDS58902.1	4q13	2013-03-28	2010-12-02					"UDP glucuronosyltransferases"	12542	protein-coding gene	gene with protein product		604716	"UDP glycosyltransferase 2 family, polypeptide A1", "UDP glucuronosyltransferase 2 family, polypeptide A1"			10359671	Standard	NM_001252274		Approved		uc011caq.2	Q9Y4X1	OTTHUMG00000184942	ENST00000503640.1:c.715+7650G>A	chr4.hg19:g.70504997C>T		212.0	0.0		120.0	7.0	NM_001252274	B4E2F4|D3GER1|D3GER2|E9PDM7|J3KNA3	Missense_Mutation	SNP	ENST00000503640.1	hg19	CCDS3529.1	.	.	.	.	.	.	.	.	.	.	C	4.375	0.069181	0.08436	.	.	ENSG00000173610	ENST00000457664;ENST00000514019	T;T	0.61158	0.36;0.13	5.85	5.01	0.66863	.	.	.	.	.	T	0.32041	0.0816	N	0.04508	-0.205	.	.	.	B;P	0.39424	0.032;0.673	B;B	0.36719	0.046;0.231	T	0.41680	-0.9495	8	0.27082	T	0.32	.	8.9764	0.35939	0.0:0.8346:0.0:0.1654	.	322;121	E9PDM7;Q9Y4X1-2	.;.	E	121;322	ENSP00000387888:G121E;ENSP00000425497:G322E	ENSP00000387888:G121E	G	-	2	0	UGT2A1	70539586	0.000000	0.05858	1.000000	0.80357	0.105000	0.19272	0.584000	0.23864	1.495000	0.48549	-0.237000	0.12165	GGA	.	.		0.363	UGT2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251554.3	NM_006798		T	70504997	C	T	70504997	1	4	260	0	1	0	0	0	0	0	0	0	16969	855	30	3		3	UGT2A2	4	70504997	Intron	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	31069056	70504997	120649279	211	37456										
CDKL2	8999	hgsc.bcm.edu	37	chr4	76507088	76507088	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aaatcagcccctgaatcatcTgacaggggaggtcctgatac	10	11	3	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr4:76507088T>C	ENST00000429927.2	-	11	2140	c.1437A>G	c.(1435-1437)tcA>tcG	p.S479S	CDKL2_ENST00000307465.4_Silent_p.S556S	NM_003948.3	NP_003939.1	Q92772	CDKL2_HUMAN	cyclin-dependent kinase-like 2 (CDC2-related kinase)	479					sex differentiation (GO:0007548)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)			breast(3)|endometrium(1)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(2)|stomach(2)	22			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			CTGAATCATCTGACAGGGGAG	0.403																																					p.S479S		Atlas-SNP	.											.	CDKL2	58	.	0			c.A1437G						.						76	74	75					4																	76507088		2203	4299	6502	SO:0001819	synonymous_variant	8999	exon11			ATCATCTGACAGG	U35146	CCDS3570.1	4q21.21	2011-11-04			ENSG00000138769	ENSG00000138769		"Cyclin-dependent kinases"	1782	protein-coding gene	gene with protein product		603442				9000130	Standard	NM_003948		Approved	P56, KKIAMRE	uc003hiq.3	Q92772	OTTHUMG00000130103	ENST00000429927.2:c.1437A>G	chr4.hg19:g.76507088T>C		144.0	0.0		87.0	4.0	NM_003948	B2R695	Silent	SNP	ENST00000429927.2	hg19	CCDS3570.1																																																																																			.	.		0.403	CDKL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252409.2	NM_003948		C	76507088	T	C	76507088	2	2	260	1	0	0	0	0	0	0	0	1	3156	1567	55	2		2	CDKL2	4	76507088	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	6002091	76507088	114647188	212	37457										
SCD5	79966	hgsc.bcm.edu	37	chr4	83602015	83602015	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgggggtcagcatccgtctcTgagtacttgtggtgggctcg	16	9	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr4:83602015T>C	ENST00000319540.4	-	3	733	c.414A>G	c.(412-414)tcA>tcG	p.S138S	SCD5_ENST00000273908.4_Silent_p.S138S	NM_001037582.2	NP_001032671.2	Q86SK9	SCD5_HUMAN	stearoyl-CoA desaturase 5	138					fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	iron ion binding (GO:0005506)|stearoyl-CoA 9-desaturase activity (GO:0004768)			endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)	13		Colorectal(4;0.0323)|Hepatocellular(203;0.115)				CATCCGTCTCTGAGTACTTGT	0.562																																					p.S138S		Atlas-SNP	.											.	SCD5	58	.	0			c.A414G						.						92	99	97					4																	83602015		2203	4300	6503	SO:0001819	synonymous_variant	79966	exon3			CGTCTCTGAGTAC	AF389338	CCDS3595.1, CCDS34024.1	4q21.3	2013-01-25	2005-06-09	2005-06-09	ENSG00000145284	ENSG00000145284		"Fatty acid desaturases"	21088	protein-coding gene	gene with protein product		608370	"stearoyl-CoA desaturase 4"	SCD4		12477932	Standard	NM_024906		Approved	ACOD4, FLJ21032, FADS4, HSCD5	uc003hna.2	Q86SK9	OTTHUMG00000130293	ENST00000319540.4:c.414A>G	chr4.hg19:g.83602015T>C		133.0	0.0		85.0	4.0	NM_024906	B2RPG0|Q4W5Q5|Q8NDS0|Q9H7D1	Silent	SNP	ENST00000319540.4	hg19	CCDS34024.1																																																																																			.	.		0.562	SCD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252635.1	NM_024906		C	83602015	T	C	83602015	2	2	260	1	0	0	0	0	0	0	0	1	13902	1567	55	2		2	SCD5	4	83602015	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	7094927	83602015	107552261	213	37458										
PTPN13	5783	hgsc.bcm.edu	37	chr4	87687669	87687669	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aacactgagaaatacaggacAggtaacagatcattatacca	7	8	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr4:87687669A>G	ENST00000411767.2	+	27	4391	c.4328A>G	c.(4327-4329)cAg>cGg	p.Q1443R	PTPN13_ENST00000316707.6_Splice_Site_p.Q1252R|PTPN13_ENST00000427191.2_Splice_Site_p.Q1424R|PTPN13_ENST00000511467.1_Splice_Site_p.Q1448R|PTPN13_ENST00000436978.1_Splice_Site_p.Q1448R			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	1443	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		AATACAGGACAGGTAACAGAT	0.398																																					p.Q1448R		Atlas-SNP	.											.	PTPN13	203	.	0			c.A4343G						.						110	102	104					4																	87687669		1916	4131	6047	SO:0001630	splice_region_variant	5783	exon27			CAGGACAGGTAAC		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.4329+1A>G	chr4.hg19:g.87687669A>G		119.0	0.0		79.0	4.0	NM_080685	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	hg19	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	A	31	5.058754	0.93846	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T;T	0.27256	1.68;1.68;1.68;1.68;1.68	5.24	5.24	0.73138	PDZ/DHR/GLGF (4);	0.000000	0.45361	D	0.000379	T	0.40040	0.1101	L	0.31420	0.93	0.80722	D	1	D;D;D;D	0.69078	0.984;0.984;0.996;0.997	D;D;D;D	0.91635	0.992;0.993;0.999;0.999	T	0.33497	-0.9866	10	0.87932	D	0	.	15.1489	0.72681	1.0:0.0:0.0:0.0	.	1252;1424;1443;1448	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	R	1424;1448;1252;1443;1448;1392	ENSP00000408368:Q1424R;ENSP00000394794:Q1448R;ENSP00000322675:Q1252R;ENSP00000407249:Q1443R;ENSP00000426626:Q1448R	ENSP00000322675:Q1252R	Q	+	2	0	PTPN13	87906693	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	8.478000	0.90428	1.978000	0.57642	0.377000	0.23210	CAG	.	.		0.398	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1		Missense_Mutation	G	87687669	A	G	87687669	5	3	260	1	0	0	0	0	0	0	1	0	12795	202	7	2	4445	2	PTPN13	4	87687669	Splice_Site	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	4085654	87687669	103466607	214	37459										
HERC5	51191	hgsc.bcm.edu	37	chr4	89397168	89397168	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgtaaaatgagtgaccagtcTtcactggttctgggtaagtt	11	6	3	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr4:89397168T>C	ENST00000264350.3	+	12	1722	c.1569T>C	c.(1567-1569)tcT>tcC	p.S523S	HERC5_ENST00000508159.1_Silent_p.S161S	NM_016323.3	NP_057407.2	Q9UII4	HERC5_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 5	523					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|negative regulation of type I interferon production (GO:0032480)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of defense response to virus (GO:0050688)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ISG15 ligase activity (GO:0042296)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(11)|liver(2)|lung(17)|ovary(4)|prostate(1)|skin(4)	53		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000209)		GTGACCAGTCTTCACTGGTTC	0.393																																					p.S523S	Esophageal Squamous(39;887 1012 34045 50514)	Atlas-SNP	.											.	HERC5	114	.	0			c.T1569C						.						127	124	125					4																	89397168		2203	4300	6503	SO:0001819	synonymous_variant	51191	exon12			CCAGTCTTCACTG	AB027289	CCDS3630.1	4q22.1-q23	2012-02-23	2012-02-23		ENSG00000138646	ENSG00000138646			24368	protein-coding gene	gene with protein product		608242	"hect domain and RLD 5"			10581175	Standard	NM_016323		Approved	CEB1	uc003hrt.4	Q9UII4	OTTHUMG00000130953	ENST00000264350.3:c.1569T>C	chr4.hg19:g.89397168T>C		190.0	0.0		124.0	5.0	NM_016323	B2RTQ1|Q69G20	Silent	SNP	ENST00000264350.3	hg19	CCDS3630.1																																																																																			.	.		0.393	HERC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253554.2	NM_016323		C	89397168	T	C	89397168	2	2	260	1	0	0	0	0	0	0	0	1	7070	1596	56	2		2	HERC5	4	89397168	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1709499	89397168	101757108	215	37460										
RAP1GDS1	5910	hgsc.bcm.edu	37	chr4	99300176	99300176	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tttgttttacagatgagggcAgaagtgcagttgaccaagca	12	6	0	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr4:99300176A>G	ENST00000408927.3	+	5	483	c.370A>G	c.(370-372)Aga>Gga	p.R124G	RAP1GDS1_ENST00000264572.7_Intron|RAP1GDS1_ENST00000380158.4_Intron|RAP1GDS1_ENST00000512857.1_Intron|RAP1GDS1_ENST00000408900.3_Intron|RAP1GDS1_ENST00000453712.2_Missense_Mutation_p.R125G|RAP1GDS1_ENST00000339360.5_Missense_Mutation_p.R125G	NM_001100426.1|NM_001100427.1|NM_021159.4	NP_001093896.1|NP_001093897.1|NP_066982.3	P52306	GDS1_HUMAN	RAP1, GTP-GDP dissociation stimulator 1	124					myosin filament assembly (GO:0031034)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|positive regulation of Rho GTPase activity (GO:0032321)|vascular smooth muscle contraction (GO:0014829)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)	28				OV - Ovarian serous cystadenocarcinoma(123;2.9e-07)|LUSC - Lung squamous cell carcinoma(1;0.0253)|Lung(1;0.0576)		AGATGAGGGCAGAAGTGCAGT	0.343			T	NUP98	T-ALL																																p.R125G		Atlas-SNP	.		Dom	yes		4	4q21-q25	5910	"RAP1, GTP-GDP dissociation stimulator 1"		L	.	RAP1GDS1	61	.	0			c.A373G						.						91	86	88					4																	99300176		1862	4101	5963	SO:0001583	missense	5910	exon5			GAGGGCAGAAGTG		CCDS43253.1, CCDS43254.1, CCDS47105.1, CCDS47106.1, CCDS47107.1, CCDS47108.1	4q23-q25	2013-02-14			ENSG00000138698	ENSG00000138698		"Armadillo repeat containing"	9859	protein-coding gene	gene with protein product		179502				8262526, 17951244	Standard	NM_001100426		Approved	SmgGDS	uc003htw.4	P52306	OTTHUMG00000160987	ENST00000408927.3:c.370A>G	chr4.hg19:g.99300176A>G	ENSP00000386153:p.Arg124Gly	129.0	0.0		65.0	15.0	NM_001100426	E9PH06|G5E9P9|Q499L7|Q4KMV2|Q4QQI8|Q9BUW9|Q9BUX6|Q9NYM2|Q9NZA8	Missense_Mutation	SNP	ENST00000408927.3	hg19	CCDS43253.1	.	.	.	.	.	.	.	.	.	.	A	15.99	2.994822	0.54041	.	.	ENSG00000138698	ENST00000508213;ENST00000408927;ENST00000453712;ENST00000511212;ENST00000339360	T;T;T;T;T	0.55930	0.49;0.63;0.63;0.49;0.63	5.95	4.75	0.60458	Armadillo-like helical (1);Armadillo-type fold (1);	0.145674	0.56097	D	0.000028	T	0.40767	0.1130	N	0.19112	0.55	0.80722	D	1	B;B;B;B	0.23377	0.041;0.084;0.001;0.041	B;B;B;B	0.28139	0.037;0.086;0.003;0.037	T	0.31420	-0.9944	10	0.87932	D	0	-15.4991	12.5273	0.56093	0.875:0.0:0.0:0.125	.	124;125;125;124	P52306;Q4QQI8;G5E9P9;B3KNU0	GDS1_HUMAN;.;.;.	G	83;124;125;83;125	ENSP00000426096:R83G;ENSP00000386153:R124G;ENSP00000407157:R125G;ENSP00000421599:R83G;ENSP00000340454:R125G	ENSP00000340454:R125G	R	+	1	2	RAP1GDS1	99519199	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.900000	0.92551	1.044000	0.40200	0.533000	0.62120	AGA	.	.		0.343	RAP1GDS1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363273.2	NM_001100426		G	99300176	A	G	99300176	3	3	260	1	0	0	0	0	1	0	0	0	13054	180	7	2	391	2	RAP1GDS1	4	99300176	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	9903008	99300176	91854100	216	37461										
CENPE	1062	hgsc.bcm.edu	37	chr4	104116362	104116362	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgtatatttccatgtaagatAcacgtaagagaaattcccta	6	7	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr4:104116362A>G	ENST00000265148.3	-	5	475	c.386T>C	c.(385-387)gTa>gCa	p.V129A	CENPE_ENST00000380026.3_Missense_Mutation_p.V129A	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	129	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)			NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		CATGTAAGATACACGTAAGAG	0.323																																					p.V129A		Atlas-SNP	.											.	CENPE	253	.	0			c.T386C						.						71	71	71					4																	104116362		2203	4292	6495	SO:0001583	missense	1062	exon5			TAAGATACACGTA	Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"Kinesins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1856	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 61"	117143	"centromere protein E (312kD)"			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.386T>C	chr4.hg19:g.104116362A>G	ENSP00000265148:p.Val129Ala	155.0	0.0		128.0	6.0	NM_001813	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	hg19	CCDS34042.1	.	.	.	.	.	.	.	.	.	.	A	29.6	5.017206	0.93404	.	.	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026;ENST00000503705	T;T;T	0.78481	-1.18;-1.18;-1.18	5.94	5.94	0.96194	Kinesin, motor domain (4);	.	.	.	.	D	0.85885	0.5801	L	0.57536	1.79	0.80722	D	1	P;D	0.65815	0.937;0.995	P;D	0.73708	0.812;0.981	D	0.85783	0.1362	9	0.48119	T	0.1	.	16.4075	0.83691	1.0:0.0:0.0:0.0	.	129;129	Q02224-3;Q02224	.;CENPE_HUMAN	A	129	ENSP00000265148:V129A;ENSP00000369365:V129A;ENSP00000423981:V129A	ENSP00000265148:V129A	V	-	2	0	CENPE	104335811	1.000000	0.71417	0.993000	0.49108	0.989000	0.77384	8.489000	0.90461	2.275000	0.75901	0.528000	0.53228	GTA	.	.		0.323	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				G	104116362	A	G	104116362	3	3	260	1	0	0	0	0	1	0	0	0	3232	391	14	2	7899	2	CENPE	4	104116362	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	4816186	104116362	87037914	217	37462										
LRIT3	345193	hgsc.bcm.edu	37	chr4	110791336	110791336	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gagctggcattgttggatcaAacaatgcttacggagacaaa	11	7	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr4:110791336A>G	ENST00000594814.1	+	4	1431	c.1431A>G	c.(1429-1431)caA>caG	p.Q477Q	LRIT3_ENST00000409621.2_Silent_p.Q294Q|LRIT3_ENST00000379920.3_Silent_p.Q432Q|LRIT3_ENST00000327908.3_Silent_p.Q294Q	NM_198506.3	NP_940908.3	Q3SXY7	LRIT3_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 3	477					regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				cervix(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(2)|skin(1)	16				OV - Ovarian serous cystadenocarcinoma(123;0.0011)		TGTTGGATCAAACAATGCTTA	0.443																																					p.Q477Q		Atlas-SNP	.											.	LRIT3	107	.	0			c.A1431G						.						79	78	78					4																	110791336		2203	4300	6503	SO:0001819	synonymous_variant	345193	exon4			GGATCAAACAATG	AK126648	CCDS3688.2, CCDS3688.3	4q25	2014-01-28	2007-06-19		ENSG00000183423	ENSG00000183423		"Immunoglobulin superfamily / I-set domain containing"	24783	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 4"	615004					Standard	NM_198506		Approved	FLJ44691, FIGLER4, CSNB1F	uc031sgv.1	Q3SXY7	OTTHUMG00000132043	ENST00000594814.1:c.1431A>G	chr4.hg19:g.110791336A>G		214.0	0.0		124.0	5.0	NM_198506	C9J1C2|Q6ZTG1	Silent	SNP	ENST00000594814.1	hg19	CCDS3688.3																																																																																			.	.		0.443	LRIT3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335270.2	NM_198506		G	110791336	A	G	110791336	2	3	260	1	0	0	0	0	0	0	0	1	8958	11	1	2		2	LRIT3	4	110791336	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	6674974	110791336	80362940	218	37463										
FAT4	79633	hgsc.bcm.edu	37	chr4	126240414	126240414	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	atgaaaagaatggcactattAgtctgcttgggcccctggat	11	8	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr4:126240414A>G	ENST00000394329.3	+	1	2861	c.2848A>G	c.(2848-2850)Agt>Ggt	p.S950G		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	950	Cadherin 9. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						TGGCACTATTAGTCTGCTTGG	0.473																																					p.S950G		Atlas-SNP	.											.	FAT4	1752	.	0			c.A2848G						.						62	64	64					4																	126240414		1936	4158	6094	SO:0001583	missense	79633	exon1			ACTATTAGTCTGC	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.2848A>G	chr4.hg19:g.126240414A>G	ENSP00000377862:p.Ser950Gly	143.0	0.0		100.0	4.0	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	hg19	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	A	9.167	1.020141	0.19433	.	.	ENSG00000196159	ENST00000394329	T	0.02579	4.24	5.1	3.93	0.45458	Cadherin (4);Cadherin-like (1);	0.000000	0.40064	U	0.001198	T	0.06735	0.0172	M	0.67569	2.06	0.80722	D	1	P	0.36110	0.537	P	0.44921	0.464	T	0.33266	-0.9875	10	0.29301	T	0.29	.	10.6052	0.45390	0.9256:0.0:0.0744:0.0	.	950	Q6V0I7	FAT4_HUMAN	G	950	ENSP00000377862:S950G	ENSP00000377862:S950G	S	+	1	0	FAT4	126459864	1.000000	0.71417	0.881000	0.34555	0.017000	0.09413	4.740000	0.62087	0.981000	0.38548	0.533000	0.62120	AGT	.	.		0.473	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		G	126240414	A	G	126240414	3	3	260	1	0	0	0	0	1	0	0	0	5700	420	15	2	2850	2	FAT4	4	126240414	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	15449078	126240414	64913862	219	37464										
HSPA4L	22824	hgsc.bcm.edu	37	chr4	128716923	128716923	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	caagtgtttactgccaacagAtagtcacgaacgtaagaaat	8	8	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr4:128716923A>G	ENST00000296464.4	+	3	577	c.166A>G	c.(166-168)Ata>Gta	p.I56V	HSPA4L_ENST00000505726.1_Splice_Site_p.I30V|HSPA4L_ENST00000439123.2_Splice_Site_p.I87V|HSPA4L_ENST00000508776.1_Splice_Site_p.I56V	NM_014278.2	NP_055093.2	O95757	HS74L_HUMAN	heat shock 70kDa protein 4-like	56					protein folding (GO:0006457)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)			central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						CTGCCAACAGATAGTCACGAA	0.368																																					p.I56V		Atlas-SNP	.											.	HSPA4L	82	.	0			c.A166G						.						78	76	77					4																	128716923		2203	4300	6503	SO:0001630	splice_region_variant	22824	exon3			CAACAGATAGTCA	AB023421	CCDS3734.1	4q28	2011-09-07			ENSG00000164070	ENSG00000164070		"Heat shock proteins / HSP70"	17041	protein-coding gene	gene with protein product						10524232	Standard	NM_014278		Approved	APG-1, Osp94, HSPH3	uc003ifm.3	O95757	OTTHUMG00000133302	ENST00000296464.4:c.166-1A>G	chr4.hg19:g.128716923A>G		198.0	0.0		117.0	5.0	NM_014278	A2ICT2|Q4W5M5|Q8IWA2	Missense_Mutation	SNP	ENST00000296464.4	hg19	CCDS3734.1	.	.	.	.	.	.	.	.	.	.	A	2.046	-0.418818	0.04766	.	.	ENSG00000164070	ENST00000508776;ENST00000439123;ENST00000296464;ENST00000508549;ENST00000505726	T;T;T;T;T	0.01406	5.62;5.62;5.62;4.93;5.62	4.51	4.51	0.55191	.	0.069562	0.64402	D	0.000007	T	0.00724	0.0024	N	0.01624	-0.795	0.49051	D	0.99974	B;B;B	0.30068	0.019;0.267;0.267	B;B;B	0.33799	0.035;0.17;0.17	T	0.67711	-0.5600	9	.	.	.	.	8.6728	0.34161	0.915:0.0:0.085:0.0	.	30;56;56	E9PDE8;A2ICT2;O95757	.;.;HS74L_HUMAN	V	56;87;56;56;30	ENSP00000422482:I56V;ENSP00000393926:I87V;ENSP00000296464:I56V;ENSP00000427305:I56V;ENSP00000425645:I30V	.	I	+	1	0	HSPA4L	128936373	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	3.199000	0.51043	1.902000	0.55061	0.383000	0.25322	ATA	.	.		0.368	HSPA4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257096.3	NM_014278	Missense_Mutation	G	128716923	A	G	128716923	5	3	260	1	0	0	0	0	0	0	1	0	7422	347	12	2	176	2	HSPA4L	4	128716923	Splice_Site	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	2476509	128716923	62437353	220	37465										
SMARCA5	8467	hgsc.bcm.edu	37	chr4	144464786	144464786	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	actgatgaagatatcgatggTattttggaaagaggtgcaaa	12	3	0	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr4:144464786T>A	ENST00000283131.3	+	15	2490	c.2028T>A	c.(2026-2028)ggT>ggA	p.G676G		NM_003601.3	NP_003592.3	O60264	SMCA5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	676					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA-templated transcription, initiation (GO:0006352)|double-strand break repair (GO:0006302)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin silencing complex (GO:0005677)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NURF complex (GO:0016589)|RSF complex (GO:0031213)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)		EWSR1/SMARCA5(2)	endometrium(2)|kidney(2)|large_intestine(9)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_hematologic(180;0.158)					ATATCGATGGTATTTTGGAAA	0.328																																					p.G676G		Atlas-SNP	.											.	SMARCA5	73	.	0			c.T2028A						.						104	102	103					4																	144464786		2203	4300	6503	SO:0001819	synonymous_variant	8467	exon15			CGATGGTATTTTG	AB010882	CCDS3761.1	4q31.1-q31.2	2011-04-20			ENSG00000153147	ENSG00000153147			11101	protein-coding gene	gene with protein product		603375				9730600	Standard	NM_003601		Approved	hSNF2H, hISWI, ISWI	uc003ijg.3	O60264	OTTHUMG00000161474	ENST00000283131.3:c.2028T>A	chr4.hg19:g.144464786T>A		150.0	0.0		97.0	4.0	NM_003601		Silent	SNP	ENST00000283131.3	hg19	CCDS3761.1																																																																																			.	.		0.328	SMARCA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365077.3			A	144464786	T	A	144464786	2	1	260	1	0	0	0	0	0	0	0	1	14786	1625	57	4		4	SMARCA5	4	144464786	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	15747863	144464786	46689490	221	37466										
PRMT10	90826	hgsc.bcm.edu	37	chr4	148589795	148589795	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aattagcactttcacctttgGtctaaaaaaaataacaataa	3	7	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr4:148589795G>A	ENST00000322396.6	-	6	1090	c.848C>T	c.(847-849)aCc>aTc	p.T283I	TMEM184C_ENST00000508208.1_Intron|PRMT10_ENST00000541232.1_Splice_Site_p.T170I	NM_138364.2	NP_612373.2	Q6P2P2	ANM9_HUMAN		283	SAM-dependent MTase PRMT-type 1. {ECO:0000255|PROSITE-ProRule:PRU01015}.					cytoplasm (GO:0005737)	protein methyltransferase activity (GO:0008276)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28						TTCACCTTTGGTCTAAAAAAA	0.294																																					p.T283I		Atlas-SNP	.											.	PRMT10	68	.	0			c.C848T						.						93	90	91					4																	148589795		2203	4300	6503	SO:0001630	splice_region_variant	90826	exon6			CCTTTGGTCTAAA																												ENST00000322396.6:c.847-1C>T	chr4.hg19:g.148589795G>A		122.0	0.0		98.0	5.0	NM_138364	A8KA39|B3KU92|Q6ZR58|Q8N383|Q9BT55|Q9NT98	Missense_Mutation	SNP	ENST00000322396.6	hg19	CCDS3771.1	.	.	.	.	.	.	.	.	.	.	G	13.52	2.261880	0.39995	.	.	ENSG00000164169	ENST00000322396;ENST00000541232	T;T	0.24723	1.84;1.84	6.03	4.32	0.51571	.	0.587759	0.19804	N	0.105700	T	0.20618	0.0496	L	0.29908	0.895	0.30275	N	0.791883	B	0.02656	0.0	B	0.01281	0.0	T	0.09143	-1.0688	10	0.56958	D	0.05	-8.0681	12.9078	0.58162	0.1311:0.0:0.8689:0.0	.	283	Q6P2P2	ANM10_HUMAN	I	283;170	ENSP00000314396:T283I;ENSP00000439508:T170I	ENSP00000314396:T283I	T	-	2	0	PRMT10	148809245	0.961000	0.32948	0.913000	0.36048	0.900000	0.52787	1.497000	0.35649	0.891000	0.36235	0.551000	0.68910	ACC	.	.		0.294	PRMT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364650.1		Missense_Mutation	A	148589795	G	A	148589795	5	1	260	1	0	0	0	0	0	0	1	0	12548	1275	44	3	1717	3	PRMT10	4	148589795	Splice_Site	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	4125009	148589795	42564481	222	37467										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155180908	155180908	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gttctttcacagtgagttgtCctatttttatttccaaggag	8	7	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr4:155180908C>T	ENST00000357232.4	-	20	5212	c.5213G>A	c.(5212-5214)gGa>gAa	p.G1738E		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1738	Cadherin 15. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		AGTGAGTTGTCCTATTTTTAT	0.313																																					p.G1738E		Atlas-SNP	.											.	DCHS2	594	.	0			c.G5213A						.						52	51	51					4																	155180908		2202	4300	6502	SO:0001630	splice_region_variant	54798	exon20			AGTTGTCCTATTT	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.5213-1G>A	chr4.hg19:g.155180908C>T		98.0	0.0		61.0	4.0	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	hg19	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.193765	0.78902	.	.	ENSG00000197410	ENST00000357232	T	0.57107	0.42	5.52	5.52	0.82312	Cadherin (4);Cadherin-like (1);	0.000000	0.64402	D	0.000002	T	0.81683	0.4874	H	0.95745	3.715	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.86719	0.1941	10	0.87932	D	0	.	18.5738	0.91147	0.0:1.0:0.0:0.0	.	1738	Q6V1P9	PCD23_HUMAN	E	1738	ENSP00000349768:G1738E	ENSP00000349768:G1738E	G	-	2	0	DCHS2	155400358	1.000000	0.71417	1.000000	0.80357	0.839000	0.47603	5.690000	0.68241	2.760000	0.94817	0.655000	0.94253	GGA	.	.		0.313	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	Missense_Mutation	T	155180908	C	T	155180908	5	4	260	1	0	0	0	0	0	0	1	0	4290	869	30	3	3561	3	DCHS2	4	155180908	Splice_Site	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	6591113	155180908	35973368	223	37468										
GUCY1A3	2982	hgsc.bcm.edu	37	chr4	156631936	156631936	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tacatgtttactacttcttcCctaagagaaccacctccctg	4	14	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr4:156631936C>T	ENST00000296518.7	+	6	828	c.619C>T	c.(619-621)Cct>Tct	p.P207S	GUCY1A3_ENST00000511507.1_Missense_Mutation_p.P207S|GUCY1A3_ENST00000511108.1_Missense_Mutation_p.P207S|GUCY1A3_ENST00000455639.2_Missense_Mutation_p.P207S|GUCY1A3_ENST00000513574.1_Missense_Mutation_p.P207S|GUCY1A3_ENST00000506455.1_Missense_Mutation_p.P207S|GUCY1A3_ENST00000393832.3_5'UTR			Q02108	GCYA3_HUMAN	guanylate cyclase 1, soluble, alpha 3	207					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of cGMP biosynthetic process (GO:0030828)|regulation of blood pressure (GO:0008217)|relaxation of vascular smooth muscle (GO:0060087)|response to defense-related host nitric oxide production (GO:0052565)	guanylate cyclase complex, soluble (GO:0008074)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)|receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|liver(2)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.17)		CTACTTCTTCCCTAAGAGAAC	0.478																																					p.P207S		Atlas-SNP	.											.	GUCY1A3	133	.	0			c.C619T						.						77	81	80					4																	156631936		2203	4300	6503	SO:0001583	missense	2982	exon6			TTCTTCCCTAAGA		CCDS34085.1, CCDS54812.1	4q31.3-q33	2008-03-18				ENSG00000164116	4.6.1.2		4685	protein-coding gene	gene with protein product		139396		GUC1A3		1352257	Standard	NM_001130687		Approved	GC-SA3	uc003iow.3	Q02108		ENST00000296518.7:c.619C>T	chr4.hg19:g.156631936C>T	ENSP00000296518:p.Pro207Ser	138.0	0.0		96.0	27.0	NM_001130687	D3DP19|D6RDW3|O43843|Q8TAH3	Missense_Mutation	SNP	ENST00000296518.7	hg19	CCDS34085.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.177777	0.78564	.	.	ENSG00000164116	ENST00000506455;ENST00000511108;ENST00000511507;ENST00000455639;ENST00000296518;ENST00000513574	T;T;T;T;T;T	0.40225	1.04;1.04;1.04;1.04;1.04;1.04	5.64	4.79	0.61399	Heme-NO binding (1);	0.090923	0.48767	N	0.000174	T	0.60663	0.2286	M	0.74881	2.28	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.60591	-0.7233	10	0.09843	T	0.71	.	14.7505	0.69522	0.0:0.9302:0.0:0.0698	.	207;207;207	B3KU69;Q02108;D6RDW3	.;GCYA3_HUMAN;.	S	207	ENSP00000424361:P207S;ENSP00000421493:P207S;ENSP00000426968:P207S;ENSP00000412201:P207S;ENSP00000296518:P207S;ENSP00000426040:P207S	ENSP00000296518:P207S	P	+	1	0	GUCY1A3	156851386	1.000000	0.71417	0.991000	0.47740	0.846000	0.48090	5.524000	0.67105	1.498000	0.48600	0.643000	0.83706	CCT	.	.		0.478	GUCY1A3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365786.2			T	156631936	C	T	156631936	3	4	260	1	0	0	0	0	1	0	0	0	6903	623	22	3	633	3	GUCY1A3	4	156631936	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	1451028	156631936	34522340	224	37469										
ODZ3	55714	hgsc.bcm.edu	37	chr4	183651371	183651371	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agccttgcatctgtcatcagAggccaagtactgactgctga	10	11	3	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr4:183651371A>G	ENST00000511685.1	+	15	2727	c.2604A>G	c.(2602-2604)agA>agG	p.R868R	TENM3_ENST00000502950.1_3'UTR|TENM3_ENST00000406950.2_Silent_p.R868R			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	868					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										CTGTCATCAGAGGCCAAGTAC	0.398																																					p.R868R		Atlas-SNP	.											.	.	.	.	0			c.A2604G						.						116	108	111					4																	183651371		1875	4123	5998	SO:0001819	synonymous_variant	55714	exon14			CATCAGAGGCCAA	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.2604A>G	chr4.hg19:g.183651371A>G		209.0	0.0		142.0	6.0	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Silent	SNP	ENST00000511685.1	hg19	CCDS47165.1																																																																																			.	.		0.398	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			G	183651371	A	G	183651371	2	3	260	1	0	0	0	0	0	0	0	1	10845	301	11	2		2	ODZ3	4	183651371	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	27019435	183651371	7502905	225	37470										
PDLIM3	27295	hgsc.bcm.edu	37	chr4	186446276	186446276	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agccgtcaatagccaggatgAcatctccaggacacaggttg	11	11	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr4:186446276A>G	ENST00000284770.5	-	2	216	c.143T>C	c.(142-144)gTc>gCc	p.V48A	PDLIM3_ENST00000284767.5_Missense_Mutation_p.V48A|PDLIM3_ENST00000284771.6_Missense_Mutation_p.V48A	NM_014476.5	NP_055291.2	Q53GG5	PDLI3_HUMAN	PDZ and LIM domain 3	48	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				actin filament organization (GO:0007015)|heart development (GO:0007507)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	structural constituent of muscle (GO:0008307)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(1)|lung(5)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	17		all_lung(41;1.03e-13)|Lung NSC(41;2.49e-13)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.00996)|Colorectal(36;0.0161)|all_hematologic(60;0.0592)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.4e-10)|BRCA - Breast invasive adenocarcinoma(30;8.64e-05)|GBM - Glioblastoma multiforme(59;0.000167)|STAD - Stomach adenocarcinoma(60;0.000828)|LUSC - Lung squamous cell carcinoma(40;0.00984)|COAD - Colon adenocarcinoma(29;0.0115)|READ - Rectum adenocarcinoma(43;0.171)		AGCCAGGATGACATCTCCAGG	0.493																																					p.V48A		Atlas-SNP	.											.	PDLIM3	49	.	0			c.T143C						.						115	107	109					4																	186446276		2203	4300	6503	SO:0001583	missense	27295	exon2			AGGATGACATCTC	AF002280	CCDS3844.1, CCDS47172.1, CCDS75218.1, CCDS75219.1	4q35	2014-09-17			ENSG00000154553	ENSG00000154553			20767	protein-coding gene	gene with protein product		605889				10063829, 8828038	Standard	NM_014476		Approved	ALP	uc003ixw.4	Q53GG5	OTTHUMG00000160412	ENST00000284770.5:c.143T>C	chr4.hg19:g.186446276A>G	ENSP00000284770:p.Val48Ala	107.0	0.0		75.0	4.0	NM_001257962	B2R866|O43590|O60439|O60440|Q8N6Y6|Q9BVP4	Missense_Mutation	SNP	ENST00000284770.5	hg19	CCDS3844.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.598495	0.87055	.	.	ENSG00000154553	ENST00000284770;ENST00000284771;ENST00000284767	T;T;T	0.28255	1.62;1.62;1.62	5.44	5.44	0.79542	PDZ/DHR/GLGF (4);	0.305950	0.38217	N	0.001771	T	0.36853	0.0982	M	0.70903	2.155	0.58432	D	0.999992	P;B;B	0.38617	0.64;0.099;0.058	B;B;B	0.37198	0.243;0.13;0.102	T	0.37150	-0.9718	10	0.72032	D	0.01	-30.1404	15.7888	0.78332	1.0:0.0:0.0:0.0	.	48;48;48	Q53GG5-3;Q53GG5-2;Q53GG5	.;.;PDLI3_HUMAN	A	48	ENSP00000284770:V48A;ENSP00000284771:V48A;ENSP00000284767:V48A	ENSP00000284767:V48A	V	-	2	0	PDLIM3	186683270	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.885000	0.92439	2.194000	0.70268	0.459000	0.35465	GTC	.	.		0.493	PDLIM3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360499.2	NM_014476		G	186446276	A	G	186446276	3	3	260	1	0	0	0	0	1	0	0	0	11690	275	10	2	1171	2	PDLIM3	4	186446276	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	2794905	186446276	4708000	226	37471										
FAT1	2195	hgsc.bcm.edu	37	chr4	187584675	187584675	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtagatctctatgaacgatgAaagaggcacgacaccctgat	10	9	1	5			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr4:187584675A>G	ENST00000441802.2	-	3	3567	c.3358T>C	c.(3358-3360)Tca>Cca	p.S1120P		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1120	Cadherin 9. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						ATGAACGATGAAAGAGGCACG	0.458										HNSCC(5;0.00058)																											p.S1120P	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.T3358C						.						134	133	133					4																	187584675		1985	4173	6158	SO:0001583	missense	2195	exon3			ACGATGAAAGAGG	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.3358T>C	chr4.hg19:g.187584675A>G	ENSP00000406229:p.Ser1120Pro	144.0	0.0		89.0	5.0	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	hg19	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	A	17.44	3.389748	0.61956	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.55588	0.51	5.12	5.12	0.69794	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.60248	0.2254	M	0.85462	2.755	0.80722	D	1	P	0.38863	0.65	B	0.40782	0.34	T	0.62671	-0.6805	10	0.27785	T	0.31	.	15.0887	0.72177	1.0:0.0:0.0:0.0	.	1120	Q14517	FAT1_HUMAN	P	1120	ENSP00000406229:S1120P	ENSP00000260147:S1120P	S	-	1	0	FAT1	187821669	1.000000	0.71417	0.176000	0.23000	0.237000	0.25408	7.304000	0.78882	2.155000	0.67459	0.482000	0.46254	TCA	.	.		0.458	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		G	187584675	A	G	187584675	3	3	260	1	0	0	0	0	1	0	0	0	5697	246	9	2	10508	2	FAT1	4	187584675	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1138399	187584675	3569601	227	37472										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13820548	13820548	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	atgtcgcactctctgcgtttCgaatagctggatgaccttca	9	11	2	1	rs201285946		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr5:13820548C>A	ENST00000265104.4	-	41	6852	c.6748G>T	c.(6748-6750)Gaa>Taa	p.E2250*		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2250	AAA 2. {ECO:0000250}.			LFE -> QTK (in Ref. 2; AAL06603). {ECO:0000305}.	cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CTCTGCGTTTCGAATAGCTGG	0.493									Kartagener syndrome																												p.E2250X		Atlas-SNP	.											DNAH5,colon,carcinoma,0,1	DNAH5	868	.	0			c.G6748T						.						114	98	103					5																	13820548		2203	4300	6503	SO:0001587	stop_gained	1767	exon41	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GCGTTTCGAATAG	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.6748G>T	chr5.hg19:g.13820548C>A	ENSP00000265104:p.Glu2250*	66.0	0.0		44.0	2.0	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Nonsense_Mutation	SNP	ENST00000265104.4	hg19	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	C	49	15.511972	0.99836	.	.	ENSG00000039139	ENST00000265104	.	.	.	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.1056	0.93293	0.0:1.0:0.0:0.0	.	.	.	.	X	2250	.	ENSP00000265104:E2250X	E	-	1	0	DNAH5	13873548	1.000000	0.71417	0.992000	0.48379	0.898000	0.52572	7.669000	0.83911	2.579000	0.87056	0.650000	0.86243	GAA	.	.		0.493	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		A	13820548	C	A	13820548	4	1	260	1	0	0	0	0	0	1	0	0	4606	893	31	1	7282	1	DNAH5	5	13820548	Nonsense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10		13820548	167094712	228	37473										
PDZD2	23037	hgsc.bcm.edu	37	chr5	32037370	32037370	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	atgaaccccaagatgtgtgcGgtgctgaggaatccaagggg	15	8	0	3	rs529949435		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr5:32037370G>T	ENST00000438447.1	+	7	1829	c.1441G>T	c.(1441-1443)Ggt>Tgt	p.G481C	PDZD2_ENST00000282493.3_Missense_Mutation_p.G481C			O15018	PDZD2_HUMAN	PDZ domain containing 2	481					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)		p.G481S(1)		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						AGATGTGTGCGGTGCTGAGGA	0.537																																					p.G481C		Atlas-SNP	.											PDZD2,caecum,carcinoma,0,1	PDZD2	306	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1441T						.						79	76	77					5																	32037370		2203	4300	6503	SO:0001583	missense	23037	exon6			GTGTGCGGTGCTG	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"PDZ domain containing 3"	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.1441G>T	chr5.hg19:g.32037370G>T	ENSP00000402033:p.Gly481Cys	77.0	1.0		65.0	4.0	NM_178140	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	hg19	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	G	9.197	1.027487	0.19512	.	.	ENSG00000133401	ENST00000438447;ENST00000282493	T;T	0.07327	3.2;3.2	5.37	2.44	0.29823	.	0.123056	0.37623	N	0.002014	T	0.03827	0.0108	N	0.14661	0.345	0.09310	N	1	B;B	0.34161	0.015;0.439	B;B	0.29862	0.006;0.108	T	0.39781	-0.9597	10	0.31617	T	0.26	.	4.9949	0.14233	0.1905:0.0:0.6413:0.1682	.	307;481	B4E3P2;O15018	.;PDZD2_HUMAN	C	481	ENSP00000402033:G481C;ENSP00000282493:G481C	ENSP00000282493:G481C	G	+	1	0	PDZD2	32073127	0.397000	0.25270	0.019000	0.16419	0.087000	0.18053	1.164000	0.31810	0.749000	0.32854	-0.136000	0.14681	GGT	.	.		0.537	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			T	32037370	G	T	32037370	3	4	260	1	0	0	0	0	1	0	0	0	11710	1116	39	1	1463	1	PDZD2	5	32037370	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	18216822	32037370	148877890	229	37474										
C5orf33	133686	hgsc.bcm.edu	37	chr5	36207278	36207278	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cccaagttactcaccaggccTttgatcctgttccagtacac	6	15	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr5:36207278T>C	ENST00000381937.4	-	8	949	c.950A>G	c.(949-951)aAg>aGg	p.K317R	NADK2_ENST00000282512.3_Missense_Mutation_p.K154R|NADK2_ENST00000397338.1_Missense_Mutation_p.K154R|NADK2_ENST00000511613.1_5'UTR|NADK2_ENST00000506945.1_Missense_Mutation_p.K176R|NADK2_ENST00000514504.1_Intron	NM_001085411.1	NP_001078880.1	Q4G0N4	NAKD2_HUMAN	NAD kinase 2, mitochondrial	317					NAD metabolic process (GO:0019674)|NADP biosynthetic process (GO:0006741)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|NAD+ kinase activity (GO:0003951)|protein homodimerization activity (GO:0042803)										TCACCAGGCCTTTGATCCTGT	0.398																																					p.K317R		Atlas-SNP	.											.	NADKD1	47	.	0			c.A950G						.						131	132	132					5																	36207278		2203	4300	6503	SO:0001583	missense	133686	exon8			CAGGCCTTTGATC	BC062567	CCDS3917.1, CCDS47197.1, CCDS75235.1	5p13.2	2013-04-30	2013-04-30	2013-04-30	ENSG00000152620	ENSG00000152620			26404	protein-coding gene	gene with protein product	"mitochondrial NAD kinase"	615787	"chromosome 5 open reading frame 33", "NAD kinase domain containing 1"	C5orf33, NADKD1		23616928	Standard	NM_001085411		Approved	FLJ30596, MNADK	uc003jkf.4	Q4G0N4	OTTHUMG00000131105	ENST00000381937.4:c.950A>G	chr5.hg19:g.36207278T>C	ENSP00000371362:p.Lys317Arg	116.0	0.0		104.0	5.0	NM_001085411	B5MC93|Q6UTX5|Q96NM0	Missense_Mutation	SNP	ENST00000381937.4	hg19	CCDS47197.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.03|19.03	3.748371|3.748371	0.69533|0.69533	.|.	.|.	ENSG00000152620|ENSG00000152620	ENST00000397338;ENST00000282512;ENST00000381937;ENST00000506945|ENST00000502355	T;T;T;T|.	0.41758|.	0.99;0.99;0.99;0.99|.	6.05|6.05	4.86|4.86	0.63082|0.63082	ATP-NAD kinase, PpnK-type, all-beta (1);ATP-NAD kinase, PpnK-type (1);|.	0.043026|.	0.85682|.	D|.	0.000000|.	T|T	0.57446|0.57446	0.2054|0.2054	L|L	0.41236|0.41236	1.265|1.265	0.80722|0.80722	D|D	1|1	D;B|.	0.67145|.	0.996;0.338|.	D;B|.	0.65573|.	0.936;0.239|.	T|T	0.52823|0.52823	-0.8524|-0.8524	10|5	0.72032|.	D|.	0.01|.	-22.1645|-22.1645	13.328|13.328	0.60471|0.60471	0.0:0.0:0.1319:0.8681|0.0:0.0:0.1319:0.8681	.|.	176;317|.	B7Z8V7;Q4G0N4|.	.;NAKD1_HUMAN|.	R|G	154;154;317;176|30	ENSP00000380499:K154R;ENSP00000282512:K154R;ENSP00000371362:K317R;ENSP00000422250:K176R|.	ENSP00000282512:K154R|.	K|R	-|-	2|1	0|2	NADKD1|NADKD1	36243035|36243035	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.883000|0.883000	0.51084|0.51084	7.652000|7.652000	0.83633|0.83633	1.077000|1.077000	0.40990|0.40990	0.528000|0.528000	0.53228|0.53228	AAG|AGG	.	.		0.398	NADK2-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367541.1	NM_153013		C	36207278	T	C	36207278	3	2	260	1	0	0	0	0	1	0	0	0	2294	1609	56	2	398	2	C5orf33	5	36207278	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	4169908	36207278	144707982	230	37475										
IL6ST	3572	hgsc.bcm.edu	37	chr5	55259292	55259292	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttaagatactagacagttccTctgagttgatcactgataaa	7	7	2	5			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr5:55259292T>C	ENST00000381298.2	-	7	1013	c.701A>G	c.(700-702)gAg>gGg	p.E234G	IL6ST_ENST00000522633.2_Missense_Mutation_p.E234G|IL6ST_ENST00000381294.3_Missense_Mutation_p.E234G|IL6ST_ENST00000381287.4_Missense_Mutation_p.E234G|IL6ST_ENST00000381286.3_Intron|IL6ST_ENST00000336909.5_Missense_Mutation_p.E234G|IL6ST_ENST00000577363.1_5'Flank|IL6ST_ENST00000381293.2_Missense_Mutation_p.E68G|IL6ST_ENST00000536319.1_Missense_Mutation_p.E234G|IL6ST_ENST00000502326.3_Missense_Mutation_p.E234G	NM_001190981.1|NM_002184.3|NM_175767.2	NP_001177910.1|NP_002175.2|NP_786943.1	P40189	IL6RB_HUMAN	interleukin 6 signal transducer	234	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|glycogen metabolic process (GO:0005977)|interleukin-27-mediated signaling pathway (GO:0070106)|interleukin-6-mediated signaling pathway (GO:0070102)|leukemia inhibitory factor signaling pathway (GO:0048861)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of Notch signaling pathway (GO:0008593)|response to cytokine (GO:0034097)|viral process (GO:0016032)	ciliary neurotrophic factor receptor complex (GO:0070110)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|interleukin-6 receptor complex (GO:0005896)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|oncostatin-M receptor complex (GO:0005900)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|interleukin-11 receptor activity (GO:0004921)|interleukin-27 receptor activity (GO:0045509)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(5)|kidney(5)|large_intestine(4)|liver(2)|lung(1)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)				AGACAGTTCCTCTGAGTTGAT	0.313			O		hepatocellular ca																																p.E234G		Atlas-SNP	.		Dom	yes		5	5q11	3572	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"		E	.	IL6ST	75	.	0			c.A701G						.						101	103	102					5																	55259292		2203	4300	6503	SO:0001583	missense	3572	exon7			AGTTCCTCTGAGT	M57230	CCDS3971.1, CCDS47209.1, CCDS54856.1	5q11.2	2014-04-04	2014-04-04		ENSG00000134352	ENSG00000134352		"Interleukins and interleukin receptors", "CD molecules", "Fibronectin type III domain containing"	6021	protein-coding gene	gene with protein product	"gp130, oncostatin M receptor"	600694	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"			2261637	Standard	NM_002184		Approved	GP130, CD130	uc003jqq.3	P40189	OTTHUMG00000097043	ENST00000381298.2:c.701A>G	chr5.hg19:g.55259292T>C	ENSP00000370698:p.Glu234Gly	119.0	0.0		95.0	4.0	NM_175767	A0N0L4|Q5FC04|Q9UQ41	Missense_Mutation	SNP	ENST00000381298.2	hg19	CCDS3971.1	.	.	.	.	.	.	.	.	.	.	T	12.39	1.924400	0.34002	.	.	ENSG00000134352	ENST00000381298;ENST00000336909;ENST00000381294;ENST00000381287;ENST00000536319;ENST00000381293;ENST00000522633;ENST00000542298	T;T;T;T;T;T;T	0.40225	1.27;1.27;1.04;1.31;1.31;1.64;1.31	5.91	5.91	0.95273	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.464496	0.23472	N	0.047806	T	0.24812	0.0602	N	0.25144	0.715	0.80722	D	1	B;B;B;B	0.24186	0.099;0.002;0.003;0.001	B;B;B;B	0.19946	0.027;0.003;0.002;0.002	T	0.18555	-1.0333	10	0.27082	T	0.32	.	4.5312	0.12006	0.1627:0.1109:0.0:0.7263	.	68;234;234;234	Q5FC05;Q5FC04;P40189-2;P40189	.;.;.;IL6RB_HUMAN	G	234;234;234;234;234;68;234;234	ENSP00000370698:E234G;ENSP00000338799:E234G;ENSP00000370694:E234G;ENSP00000370687:E234G;ENSP00000444456:E234G;ENSP00000370693:E68G;ENSP00000435399:E234G	ENSP00000338799:E234G	E	-	2	0	IL6ST	55295049	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.519000	0.35888	2.261000	0.74972	0.533000	0.62120	GAG	.	.		0.313	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184		C	55259292	T	C	55259292	3	2	260	1	0	0	0	0	1	0	0	0	7712	1551	54	2	2099	2	IL6ST	5	55259292	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	19052014	55259292	125655968	231	37476										
CRHBP	1393	hgsc.bcm.edu	37	chr5	76249911	76249911	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cttcaccgccgaccggccgcAgctgcactgcgcagccttct	10	19	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr5:76249911A>G	ENST00000274368.4	+	3	655	c.233A>G	c.(232-234)cAg>cGg	p.Q78R	CRHBP_ENST00000506501.1_Missense_Mutation_p.Q78R	NM_001882.3	NP_001873.2	P24387	CRHBP_HUMAN	corticotropin releasing hormone binding protein	78					behavioral response to ethanol (GO:0048149)|cellular response to calcium ion (GO:0071277)|cellular response to cAMP (GO:0071320)|cellular response to cocaine (GO:0071314)|cellular response to drug (GO:0035690)|cellular response to estradiol stimulus (GO:0071392)|cellular response to estrogen stimulus (GO:0071391)|cellular response to gonadotropin-releasing hormone (GO:0097211)|cellular response to potassium ion (GO:0035865)|cellular response to stress (GO:0033554)|cellular response to tumor necrosis factor (GO:0071356)|female pregnancy (GO:0007565)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|inflammatory response (GO:0006954)|learning or memory (GO:0007611)|maternal aggressive behavior (GO:0002125)|negative regulation of corticotropin secretion (GO:0051460)|negative regulation of corticotropin-releasing hormone receptor activity (GO:1900011)|regulated secretory pathway (GO:0045055)|regulation of corticotropin secretion (GO:0051459)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|signal transduction (GO:0007165)|synaptic transmission, dopaminergic (GO:0001963)	axon terminus (GO:0043679)|dendrite (GO:0030425)|dense core granule (GO:0031045)|extracellular space (GO:0005615)|intracellular (GO:0005622)|microtubule (GO:0005874)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|perikaryon (GO:0043204)|secondary lysosome (GO:0005767)|secretory granule (GO:0030141)|varicosity (GO:0043196)	corticotropin-releasing hormone binding (GO:0051424)|peptide binding (GO:0042277)			kidney(3)|large_intestine(4)|lung(6)|prostate(1)|skin(2)	16		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;2.17e-51)|Epithelial(54;8.79e-46)|all cancers(79;2.49e-41)		GACCGGCCGCAGCTGCACTGC	0.642																																					p.Q78R		Atlas-SNP	.											.	CRHBP	46	.	0			c.A233G						.						55	61	59					5																	76249911		2203	4300	6503	SO:0001583	missense	1393	exon3			GGCCGCAGCTGCA	X58022	CCDS4034.1	5q	2008-07-18	2001-11-28		ENSG00000145708	ENSG00000145708			2356	protein-coding gene	gene with protein product		122559	"corticotropin releasing hormone-binding protein"			8198617	Standard	NM_001882		Approved	CRF-BP, CRFBP	uc003ker.3	P24387	OTTHUMG00000102133	ENST00000274368.4:c.233A>G	chr5.hg19:g.76249911A>G	ENSP00000274368:p.Gln78Arg	190.0	0.0		99.0	5.0	NM_001882	Q53F32|Q6FHT5	Missense_Mutation	SNP	ENST00000274368.4	hg19	CCDS4034.1	.	.	.	.	.	.	.	.	.	.	A	15.35	2.807746	0.50421	.	.	ENSG00000145708	ENST00000274368;ENST00000506501	T;T	0.59638	0.25;0.25	4.01	2.84	0.33178	CUB (1);	0.123081	0.56097	N	0.000027	T	0.49029	0.1533	L	0.50919	1.6	0.54753	D	0.999982	B;B	0.15473	0.013;0.004	B;B	0.20955	0.032;0.007	T	0.43702	-0.9375	10	0.44086	T	0.13	-4.3081	9.3649	0.38219	0.9132:0.0:0.0868:0.0	.	78;78	D6RHH7;P24387	.;CRHBP_HUMAN	R	78	ENSP00000274368:Q78R;ENSP00000426097:Q78R	ENSP00000274368:Q78R	Q	+	2	0	CRHBP	76285667	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.803000	0.75180	0.701000	0.31803	0.379000	0.24179	CAG	.	.		0.642	CRHBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219972.2	NM_001882		G	76249911	A	G	76249911	3	3	260	1	0	0	0	0	1	0	0	0	3872	188	7	2	243	2	CRHBP	5	76249911	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	20990619	76249911	104665349	232	37477										
FAM151B	167555	hgsc.bcm.edu	37	chr5	79809580	79809580	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aataaaggcatcaagctggaTttcaaaaggtatttgtataa	8	4	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr5:79809580T>C	ENST00000282226.4	+	3	464	c.309T>C	c.(307-309)gaT>gaC	p.D103D	FAM151B_ENST00000511718.1_3'UTR	NM_205548.2	NP_991111.2	Q6UXP7	F151B_HUMAN	family with sequence similarity 151, member B	103										breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)	7		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;8.21e-47)|Epithelial(54;8.3e-42)|all cancers(79;1.97e-36)		TCAAGCTGGATTTCAAAAGGT	0.373																																					p.D103D		Atlas-SNP	.											.	FAM151B	25	.	0			c.T309C						.						73	70	71					5																	79809580		2203	4300	6503	SO:0001819	synonymous_variant	167555	exon3			GCTGGATTTCAAA		CCDS4051.1	5q14.1	2007-12-18	2007-12-18		ENSG00000152380	ENSG00000152380			33716	protein-coding gene	gene with protein product							Standard	NM_205548		Approved	UNQ9217	uc003kgv.2	Q6UXP7	OTTHUMG00000131303	ENST00000282226.4:c.309T>C	chr5.hg19:g.79809580T>C		108.0	0.0		89.0	4.0	NM_205548	A2RRE4	Silent	SNP	ENST00000282226.4	hg19	CCDS4051.1																																																																																			.	.		0.373	FAM151B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254072.1	NM_205548		C	79809580	T	C	79809580	2	2	260	1	0	0	0	0	0	0	0	1	5464	1490	52	2		2	FAM151B	5	79809580	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	3559669	79809580	101105680	233	37478										
VCAN	1462	hgsc.bcm.edu	37	chr5	82833999	82833999	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgttgaggaaaagaaaaggaAggaggaggagggaactacag	17	2	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr5:82833999A>G	ENST00000265077.3	+	8	5742	c.5177A>G	c.(5176-5178)aAg>aGg	p.K1726R	VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000343200.5_Missense_Mutation_p.K739R|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000512590.2_Intron|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000342785.4_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1726	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	AAGAAAAGGAAGGAGGAGGAG	0.408																																					p.K1726R		Atlas-SNP	.											.	VCAN	498	.	0			c.A5177G						.						83	86	85					5																	82833999		2201	4300	6501	SO:0001583	missense	1462	exon8			AAAGGAAGGAGGA	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.5177A>G	chr5.hg19:g.82833999A>G	ENSP00000265077:p.Lys1726Arg	48.0	0.0		71.0	4.0	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	hg19	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	A	13.65	2.301347	0.40694	.	.	ENSG00000038427	ENST00000265077;ENST00000343200;ENST00000513960	D;D;T	0.85411	-1.95;-1.98;3.17	5.96	4.76	0.60689	.	0.816378	0.11310	N	0.577186	T	0.75817	0.3901	L	0.29908	0.895	0.20307	N	0.999916	P;P	0.41848	0.763;0.651	B;B	0.36608	0.229;0.115	T	0.63501	-0.6623	10	0.19147	T	0.46	.	12.1863	0.54241	0.8583:0.1416:0.0:0.0	.	739;1726	P13611-2;P13611	.;CSPG2_HUMAN	R	1726;739;739	ENSP00000265077:K1726R;ENSP00000340062:K739R;ENSP00000426251:K739R	ENSP00000265077:K1726R	K	+	2	0	VCAN	82869755	0.000000	0.05858	0.004000	0.12327	0.025000	0.11179	0.666000	0.25097	2.285000	0.76669	0.533000	0.62120	AAG	.	.		0.408	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		G	82833999	A	G	82833999	3	3	260	1	0	0	0	0	1	0	0	0	17153	72	3	2	5203	2	VCAN	5	82833999	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	3024419	82833999	98081261	234	37479										
DCP2	167227	hgsc.bcm.edu	37	chr5	112349076	112349076	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttgctagaacatgctgagggAcagcccgtggcatgtaatgg	14	8	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr5:112349076A>G	ENST00000389063.2	+	11	1356	c.1158A>G	c.(1156-1158)ggA>ggG	p.G386G	DCP2_ENST00000543319.1_Silent_p.G175G|DCP2_ENST00000515408.1_Silent_p.G351G	NM_152624.5	NP_689837	Q8IU60	DCP2_HUMAN	decapping mRNA 2	386					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|nucleus (GO:0005634)|RISC complex (GO:0016442)	exoribonuclease activity, producing 5'-phosphomonoesters (GO:0016896)|m7G(5')pppN diphosphatase activity (GO:0050072)|manganese ion binding (GO:0030145)|RNA binding (GO:0003723)			endometrium(3)|large_intestine(6)|lung(1)	10		all_cancers(142;4.41e-05)|all_epithelial(76;3.65e-07)|Colorectal(10;0.00115)|Prostate(80;0.00133)|Ovarian(225;0.0443)		OV - Ovarian serous cystadenocarcinoma(64;6.98e-08)|Epithelial(69;7.87e-08)|all cancers(49;1.06e-05)|COAD - Colon adenocarcinoma(37;0.0123)|Colorectal(14;0.0171)		ATGCTGAGGGACAGCCCGTGG	0.398																																					p.G386G		Atlas-SNP	.											.	DCP2	34	.	0			c.A1158G						.						190	168	176					5																	112349076		2202	4300	6502	SO:0001819	synonymous_variant	167227	exon11			TGAGGGACAGCCC	AY135173	CCDS34210.1, CCDS56377.1	5q22	2013-05-02	2013-05-02		ENSG00000172795	ENSG00000172795	3.6.1.62	"Nudix motif containing"	24452	protein-coding gene	gene with protein product	"nudix (nucleoside diphosphate linked moiety X)-type motif 20", "M(7)GpppN-mRNA hydrolase"	609844	"DCP2 decapping enzyme homolog (S. cerevisiae)"			12218187, 12417715	Standard	NM_152624		Approved	NUDT20	uc003kqh.3	Q8IU60	OTTHUMG00000162853	ENST00000389063.2:c.1158A>G	chr5.hg19:g.112349076A>G		125.0	0.0		71.0	4.0	NM_152624	C9J778|Q6P2D4|Q7Z5W5|Q8NBG5	Silent	SNP	ENST00000389063.2	hg19	CCDS34210.1	.	.	.	.	.	.	.	.	.	.	a	2.568	-0.300291	0.05532	.	.	ENSG00000172795	ENST00000513585	.	.	.	5.83	-0.778	0.10977	.	.	.	.	.	T	0.42607	0.1210	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	T	0.25710	-1.0124	4	.	.	.	0.8466	2.8914	0.05677	0.463:0.1175:0.3154:0.1041	.	.	.	.	A	368	.	.	T	+	1	0	DCP2	112376975	0.988000	0.35896	0.786000	0.31890	0.258000	0.26162	0.288000	0.18939	-0.078000	0.12730	0.451000	0.29950	ACA	.	.		0.398	DCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370765.3	NM_152624		G	112349076	A	G	112349076	2	3	260	1	0	0	0	0	0	0	0	1	4302	262	10	2		2	DCP2	5	112349076	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	29515077	112349076	68566184	235	37480										
PRRC1	133619	hgsc.bcm.edu	37	chr5	126866068	126866068	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	catgattacaacgctggaccCtggcatggctccctatatca	8	13	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr5:126866068C>A	ENST00000296666.8	+	5	925	c.737C>A	c.(736-738)cCt>cAt	p.P246H	PRRC1_ENST00000442138.2_Missense_Mutation_p.P246H|PRRC1_ENST00000512635.2_Missense_Mutation_p.P246H	NM_130809.3	NP_570721.1	Q96M27	PRRC1_HUMAN	proline-rich coiled-coil 1	246						Golgi apparatus (GO:0005794)				endometrium(1)|large_intestine(1)|lung(4)	6		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0851)|Epithelial(69;0.113)		ACGCTGGACCCTGGCATGGCT	0.408																																					p.P246H		Atlas-SNP	.											.	PRRC1	22	.	0			c.C737A						.						108	102	104					5																	126866068		2203	4300	6503	SO:0001583	missense	133619	exon5			TGGACCCTGGCAT	AJ515429	CCDS4143.1, CCDS68943.1	5q23.2	2008-02-05			ENSG00000164244	ENSG00000164244			28164	protein-coding gene	gene with protein product						15541471	Standard	NM_130809		Approved	FLJ32875	uc003kuk.3	Q96M27	OTTHUMG00000128982	ENST00000296666.8:c.737C>A	chr5.hg19:g.126866068C>A	ENSP00000296666:p.Pro246His	79.0	0.0		59.0	4.0	NM_130809	Q69YM8|Q7L2U7|Q86Y42|Q8IVJ4|Q8IVL4|Q8NEZ7|Q96AJ3	Missense_Mutation	SNP	ENST00000296666.8	hg19	CCDS4143.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.757126	0.89843	.	.	ENSG00000164244	ENST00000296666;ENST00000442138;ENST00000330542;ENST00000414018;ENST00000512635;ENST00000512535	.	.	.	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.79621	0.4477	M	0.73962	2.25	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.984;0.998	T	0.81703	-0.0812	9	0.87932	D	0	-18.0015	17.8281	0.88672	0.0:1.0:0.0:0.0	.	246;246	Q96M27;Q96M27-5	PRRC1_HUMAN;.	H	246	.	ENSP00000296666:P246H	P	+	2	0	PRRC1	126893967	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.596000	0.82721	2.683000	0.91414	0.655000	0.94253	CCT	.	.		0.408	PRRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250971.3	NM_130809		A	126866068	C	A	126866068	3	1	260	1	0	0	0	0	1	0	0	0	12616	681	24	3	751	3	PRRC1	5	126866068	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	14516992	126866068	54049192	236	37481										
FBN2	2201	hgsc.bcm.edu	37	chr5	127800501	127800501	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acacatctcacagggatggcCccacgcccgtccaatggtgg	11	15	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr5:127800501C>T	ENST00000508053.1	-	12	1716	c.742G>A	c.(742-744)Ggc>Agc	p.G248S	FBN2_ENST00000508989.1_Missense_Mutation_p.G215S|FBN2_ENST00000262464.4_Missense_Mutation_p.G248S			P35556	FBN2_HUMAN	fibrillin 2	248	TB 1.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		CAGGGATGGCCCCACGCCCGT	0.602																																					p.G248S		Atlas-SNP	.											.	FBN2	858	.	0			c.G742A						.						91	83	86					5																	127800501		2203	4300	6503	SO:0001583	missense	2201	exon6			GATGGCCCCACGC	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.742G>A	chr5.hg19:g.127800501C>T	ENSP00000424571:p.Gly248Ser	110.0	0.0		93.0	4.0	NM_001999	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	hg19	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	C	34	5.357249	0.95854	.	.	ENSG00000138829	ENST00000262464;ENST00000508053;ENST00000508989;ENST00000502468	D;D;D;D	0.97710	-4.5;-4.5;-4.5;-4.5	4.82	4.82	0.62117	Matrix fibril-associated (3);TGF-beta binding (1);	0.000000	0.64402	D	0.000002	D	0.98429	0.9477	M	0.72894	2.215	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;0.999;0.999	D	0.98048	1.0386	10	0.31617	T	0.26	.	18.7725	0.91898	0.0:1.0:0.0:0.0	.	215;248;215;248	P35556-2;E9PHW4;D6RJI3;P35556	.;.;.;FBN2_HUMAN	S	248;248;215;248	ENSP00000262464:G248S;ENSP00000424571:G248S;ENSP00000425596:G215S;ENSP00000424753:G248S	ENSP00000262464:G248S	G	-	1	0	FBN2	127828400	1.000000	0.71417	1.000000	0.80357	0.822000	0.46500	7.729000	0.84864	2.608000	0.88229	0.484000	0.47621	GGC	.	.		0.602	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		T	127800501	C	T	127800501	3	4	260	1	0	0	0	0	1	0	0	0	5711	623	22	3	8236	3	FBN2	5	127800501	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	934433	127800501	53114759	237	37482										
PCDHB2	56133	hgsc.bcm.edu	37	chr5	140475117	140475117	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cccagagtttgcaaagctgcTctatgaggtgcagatcccgg	12	11	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr5:140475117T>C	ENST00000194155.4	+	1	891	c.743T>C	c.(742-744)cTc>cCc	p.L248P		NM_018936.2	NP_061759.1	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2	248					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(22)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GCAAAGCTGCTCTATGAGGTG	0.537																																					p.L248P		Atlas-SNP	.											.	PCDHB2	163	.	0			c.T743C						.						57	59	58					5																	140475117		2203	4300	6503	SO:0001583	missense	56133	exon1			AGCTGCTCTATGA	AF152495	CCDS4244.1	5q31	2010-01-26			ENSG00000112852	ENSG00000112852		"Cadherins / Protocadherins : Clustered"	8687	other	protocadherin		606328				10380929	Standard	NM_018936		Approved	PCDH-BETA2	uc003lil.3	Q9Y5E7	OTTHUMG00000129606	ENST00000194155.4:c.743T>C	chr5.hg19:g.140475117T>C	ENSP00000194155:p.Leu248Pro	82.0	0.0		83.0	4.0	NM_018936	Q4KMU1	Missense_Mutation	SNP	ENST00000194155.4	hg19	CCDS4244.1	.	.	.	.	.	.	.	.	.	.	T	8.394	0.840370	0.16891	.	.	ENSG00000112852	ENST00000194155	T	0.61392	0.11	5.42	-0.518	0.11943	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.41949	0.1181	L	0.37750	1.13	0.09310	N	0.999999	B	0.19817	0.039	B	0.18263	0.021	T	0.27088	-1.0084	9	0.31617	T	0.26	.	6.677	0.23100	0.3262:0.0:0.2217:0.4521	.	248	Q9Y5E7	PCDB2_HUMAN	P	248	ENSP00000194155:L248P	ENSP00000194155:L248P	L	+	2	0	PCDHB2	140455301	0.000000	0.05858	0.499000	0.27577	0.971000	0.66376	0.080000	0.14802	0.059000	0.16252	-0.313000	0.08912	CTC	.	.		0.537	PCDHB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251801.2	NM_018936		C	140475117	T	C	140475117	3	2	260	1	0	0	0	0	1	0	0	0	11551	1551	54	2	745	2	PCDHB2	5	140475117	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	12674616	140475117	40440143	238	37483										
PCDHGA10	56106	hgsc.bcm.edu	37	chr5	140793433	140793433	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctctccgatctggcactgtcCttgtcagtgtgactgtcttc	9	13	4	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr5:140793433C>T	ENST00000398610.2	+	1	691	c.691C>T	c.(691-693)Ctt>Ttt	p.L231F	PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA7_ENST00000518325.1_Intron	NM_018913.2|NM_032090.1	NP_061736.1|NP_114479.1	Q9Y5H3	PCDGA_HUMAN	protocadherin gamma subfamily A, 10	231	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGCACTGTCCTTGTCAGTGT	0.577																																					p.L231F		Atlas-SNP	.											PCDHGA10,colon,carcinoma,0,1	PCDHGA10	114	.	0			c.C691T						.						43	47	46					5																	140793433		2066	4213	6279	SO:0001583	missense	56106	exon1			ACTGTCCTTGTCA		CCDS47292.1, CCDS75343.1	5q31	2010-01-26			ENSG00000253846	ENSG00000253846		"Cadherins / Protocadherins : Clustered"	8697	other	protocadherin		606297				10380929	Standard	NM_018913		Approved	PCDH-GAMMA-A10		Q9Y5H3	OTTHUMG00000163688	ENST00000398610.2:c.691C>T	chr5.hg19:g.140793433C>T	ENSP00000381611:p.Leu231Phe	28.0	0.0		53.0	3.0	NM_032090	Q9Y5E0	Missense_Mutation	SNP	ENST00000398610.2	hg19	CCDS47292.1	.	.	.	.	.	.	.	.	.	.	c	14.44	2.537259	0.45176	.	.	ENSG00000253846	ENST00000398610	T	0.01804	4.63	5.54	5.54	0.83059	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.05593	0.0147	M	0.62209	1.925	0.20074	N	0.999938	B;B	0.30406	0.235;0.278	B;B	0.41917	0.254;0.37	T	0.13415	-1.0510	9	0.62326	D	0.03	.	14.9519	0.71080	0.2084:0.7916:0.0:0.0	.	231;231	Q9Y5H3-2;Q9Y5H3	.;PCDGA_HUMAN	F	231	ENSP00000381611:L231F	ENSP00000381611:L231F	L	+	1	0	PCDHGA10	140773617	0.000000	0.05858	0.975000	0.42487	0.654000	0.38779	-0.137000	0.10389	2.619000	0.88677	0.557000	0.71058	CTT	.	.		0.577	PCDHGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374747.1	NM_018913		T	140793433	C	T	140793433	3	4	260	1	0	0	0	0	1	0	0	0	11560	681	24	3	693	3	PCDHGA10	5	140793433	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	318316	140793433	40121827	239	37484										
DIAPH1	1729	hgsc.bcm.edu	37	chr5	140908052	140908052	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tctccacatgggcaagctcgTctggaaacttgaggacatcg	11	11	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr5:140908052T>C	ENST00000398557.4	-	23	3256	c.3116A>G	c.(3115-3117)gAc>gGc	p.D1039G	DIAPH1_ENST00000494967.1_5'Flank|DIAPH1_ENST00000520569.1_Missense_Mutation_p.D982G|DIAPH1_ENST00000518047.1_Missense_Mutation_p.D1027G|DIAPH1_ENST00000389057.5_Missense_Mutation_p.D1030G|DIAPH1_ENST00000253811.6_Missense_Mutation_p.D1040G|DIAPH1_ENST00000398566.3_Missense_Mutation_p.D1031G|DIAPH1_ENST00000389054.3_Missense_Mutation_p.D1036G|DIAPH1_ENST00000398562.2_Missense_Mutation_p.D1015G	NM_005219.4	NP_005210.3	O60610	DIAP1_HUMAN	diaphanous-related formin 1	1039	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin filament polymerization (GO:0030041)|cellular response to histamine (GO:0071420)|cytoskeleton organization (GO:0007010)|positive regulation of cell migration (GO:0030335)|protein localization to microtubule (GO:0035372)|regulation of cell shape (GO:0008360)|regulation of microtubule-based process (GO:0032886)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|mitotic spindle (GO:0072686)|ruffle membrane (GO:0032587)	ion channel binding (GO:0044325)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(12)|pancreas(1)|skin(2)|stomach(2)	23			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGCAAGCTCGTCTGGAAACTT	0.498																																					p.D1039G		Atlas-SNP	.											.	DIAPH1	64	.	0			c.A3116G						.						86	82	83					5																	140908052		1952	4151	6103	SO:0001583	missense	1729	exon23			AGCTCGTCTGGAA	BC007411		5q31	2013-05-24	2013-05-24		ENSG00000131504	ENSG00000131504			2876	protein-coding gene	gene with protein product		602121	"diaphanous (Drosophila, homolog) 1", "diaphanous homolog 1 (Drosophila)"	DFNA1		9360932, 1350680	Standard	NM_005219		Approved	hDIA1, LFHL1	uc003llb.4	O60610	OTTHUMG00000149893	ENST00000398557.4:c.3116A>G	chr5.hg19:g.140908052T>C	ENSP00000381565:p.Asp1039Gly	134.0	0.0		99.0	4.0	NM_005219	A6NF18|B7ZKW2|E9PEZ2|Q17RN4|Q59FH8|Q9UC76	Missense_Mutation	SNP	ENST00000398557.4	hg19	CCDS43374.1	.	.	.	.	.	.	.	.	.	.	T	19.84	3.902274	0.72754	.	.	ENSG00000131504	ENST00000389054;ENST00000520569;ENST00000398562;ENST00000389057;ENST00000398566;ENST00000398557;ENST00000253811;ENST00000518047	T;T;T;T;T;T;T;T	0.64803	-0.12;-0.12;-0.12;-0.12;-0.12;-0.12;-0.12;-0.12	5.66	5.66	0.87406	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.059479	0.64402	D	0.000006	T	0.77698	0.4169	M	0.78637	2.42	0.80722	D	1	D;P;P	0.59767	0.986;0.953;0.953	D;P;P	0.63381	0.914;0.746;0.746	T	0.80641	-0.1292	10	0.66056	D	0.02	.	14.8844	0.70557	0.0:0.0:0.0:1.0	.	982;1030;1039	E7ERW8;E9PEZ2;O60610	.;.;DIAP1_HUMAN	G	1036;982;1015;1030;1031;1039;1040;1027	ENSP00000373706:D1036G;ENSP00000429282:D982G;ENSP00000381570:D1015G;ENSP00000373709:D1030G;ENSP00000381572:D1031G;ENSP00000381565:D1039G;ENSP00000253811:D1040G;ENSP00000428268:D1027G	ENSP00000253811:D1040G	D	-	2	0	DIAPH1	140888236	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	6.301000	0.72782	2.158000	0.67659	0.383000	0.25322	GAC	.	.		0.498	DIAPH1-203	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_005219		C	140908052	T	C	140908052	3	2	260	1	0	0	0	0	1	0	0	0	4520	1667	58	2	726	2	DIAPH1	5	140908052	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	114619	140908052	40007208	240	37485										
DPYSL3	1809	hgsc.bcm.edu	37	chr5	146773671	146773671	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgctggctgagcgaacccccTcatccacttgggtgcctaca	10	15	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr5:146773671T>C	ENST00000398514.3	-	14	2011	c.1640A>G	c.(1639-1641)gAg>gGg	p.E547G	DPYSL3_ENST00000534907.1_Missense_Mutation_p.E173G|DPYSL3_ENST00000343218.5_Missense_Mutation_p.E661G	NM_001387.2	NP_001378.1	Q14195	DPYL3_HUMAN	dihydropyrimidinase-like 3	547					actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cell migration (GO:0030336)|negative regulation of neuron projection development (GO:0010977)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of neuron projection development (GO:0010976)|protein homooligomerization (GO:0051260)|pyrimidine nucleobase catabolic process (GO:0006208)|response to axon injury (GO:0048678)	cell body (GO:0044297)|cytosol (GO:0005829)|extracellular space (GO:0005615)|filamentous actin (GO:0031941)|growth cone (GO:0030426)|lamellipodium (GO:0030027)	chondroitin sulfate binding (GO:0035374)|hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)|SH3 domain binding (GO:0017124)			breast(2)|endometrium(1)|kidney(4)|large_intestine(6)|liver(1)|lung(9)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGAACCCCCTCATCCACTTG	0.537																																					p.E661G		Atlas-SNP	.											.	DPYSL3	58	.	0			c.A1982G						.						50	52	51					5																	146773671		1831	4086	5917	SO:0001583	missense	1809	exon14			ACCCCCTCATCCA	D78014	CCDS43381.1, CCDS56387.1	5q32	2008-02-05							3015	protein-coding gene	gene with protein product		601168				8973361, 9115293	Standard	NM_001197294		Approved	DRP-3, ULIP, CRMP4	uc003loo.3	Q14195		ENST00000398514.3:c.1640A>G	chr5.hg19:g.146773671T>C	ENSP00000381526:p.Glu547Gly	94.0	0.0		113.0	6.0	NM_001197294	B3SXQ8|Q93012	Missense_Mutation	SNP	ENST00000398514.3	hg19	CCDS43381.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.37|13.37	2.217898|2.217898	0.39201|0.39201	.|.	.|.	ENSG00000113657|ENSG00000113657	ENST00000398514;ENST00000343218;ENST00000534907|ENST00000520473	D;D;T|.	0.86097|.	-2.07;-2.06;-0.87|.	5.42|5.42	5.42|5.42	0.78866|0.78866	.|.	0.095342|.	0.64402|.	D|.	0.000001|.	T|.	0.57080|.	0.2029|.	L|L	0.34521|0.34521	1.04|1.04	0.58432|0.58432	D|D	0.999999|0.999999	B;B|.	0.28350|.	0.208;0.001|.	B;B|.	0.31946|.	0.138;0.002|.	T|.	0.54036|.	-0.8353|.	10|.	0.66056|.	D|.	0.02|.	-3.3678|-3.3678	15.4677|15.4677	0.75416|0.75416	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	661;547|.	B3SXQ8;Q14195|.	.;DPYL3_HUMAN|.	G|W	547;661;173|185	ENSP00000381526:E547G;ENSP00000343690:E661G;ENSP00000441819:E173G|.	ENSP00000343690:E661G|.	E|X	-|-	2|3	0|0	DPYSL3|DPYSL3	146753864|146753864	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.124000|0.124000	0.20399|0.20399	7.562000|7.562000	0.82300|0.82300	2.053000|2.053000	0.61076|0.61076	0.459000|0.459000	0.35465|0.35465	GAG|TGA	.	.		0.537	DPYSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373421.2	NM_001387		C	146773671	T	C	146773671	3	2	260	1	0	0	0	0	1	0	0	0	4750	1551	54	2	76	2	DPYSL3	5	146773671	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	5865619	146773671	34141589	241	37486										
CSF1R	1436	hgsc.bcm.edu	37	chr5	149434853	149434853	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tggtatccatccttcaccagTttatagaacttgctgttcac	6	11	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr5:149434853T>C	ENST00000286301.3	-	20	2892	c.2601A>G	c.(2599-2601)aaA>aaG	p.K867K		NM_005211.3	NP_005202.2	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor	867	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|cell-cell junction maintenance (GO:0045217)|cellular response to cytokine stimulus (GO:0071345)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cytokine-mediated signaling pathway (GO:0019221)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary gland duct morphogenesis (GO:0060603)|monocyte differentiation (GO:0030224)|multicellular organismal development (GO:0007275)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell motility (GO:2000147)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of bone resorption (GO:0045124)|regulation of cell shape (GO:0008360)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|macrophage colony-stimulating factor receptor activity (GO:0005011)|protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(38)|kidney(2)|large_intestine(6)|liver(3)|lung(23)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	93			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Imatinib(DB00619)|Sunitinib(DB01268)	CCTTCACCAGTTTATAGAACT	0.527																																					p.K867K		Atlas-SNP	.											.	CSF1R	250	.	0			c.A2601G						.						127	112	117					5																	149434853		2203	4300	6503	SO:0001819	synonymous_variant	1436	exon20			CACCAGTTTATAG	U63963	CCDS4302.1	5q32	2013-01-11	2008-08-01		ENSG00000182578	ENSG00000182578		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	2433	protein-coding gene	gene with protein product		164770	"McDonough feline sarcoma viral (v-fms) oncogene homolog"	FMS		1611909	Standard	NM_005211		Approved	C-FMS, CSFR, CD115	uc003lrm.3	P07333	OTTHUMG00000130050	ENST00000286301.3:c.2601A>G	chr5.hg19:g.149434853T>C		101.0	0.0		89.0	4.0	NM_005211	B5A955|D3DQG2|Q6LDW5|Q6LDY4|Q86VW7	Silent	SNP	ENST00000286301.3	hg19	CCDS4302.1																																																																																			.	.		0.527	CSF1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252329.2	NM_005211		C	149434853	T	C	149434853	2	2	260	1	0	0	0	0	0	0	0	1	3934	1722	60	2		2	CSF1R	5	149434853	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	2661182	149434853	31480407	242	37487										
CSF1R	1436	hgsc.bcm.edu	37	chr5	149459693	149459693	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	actgcattgatagtcctggcTctgaatgaacttggccctgt	10	10	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr5:149459693T>C	ENST00000286301.3	-	4	805	c.514A>G	c.(514-516)Agc>Ggc	p.S172G	CSF1R_ENST00000543093.1_Missense_Mutation_p.S172G	NM_005211.3	NP_005202.2	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor	172	Ig-like C2-type 2.				cell proliferation (GO:0008283)|cell-cell junction maintenance (GO:0045217)|cellular response to cytokine stimulus (GO:0071345)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cytokine-mediated signaling pathway (GO:0019221)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary gland duct morphogenesis (GO:0060603)|monocyte differentiation (GO:0030224)|multicellular organismal development (GO:0007275)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell motility (GO:2000147)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of bone resorption (GO:0045124)|regulation of cell shape (GO:0008360)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|macrophage colony-stimulating factor receptor activity (GO:0005011)|protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(38)|kidney(2)|large_intestine(6)|liver(3)|lung(23)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	93			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Imatinib(DB00619)|Sunitinib(DB01268)	TAGTCCTGGCTCTGAATGAAC	0.612																																					p.S172G		Atlas-SNP	.											.	CSF1R	250	.	0			c.A514G						.						85	68	74					5																	149459693		2203	4300	6503	SO:0001583	missense	1436	exon4			CCTGGCTCTGAAT	U63963	CCDS4302.1	5q32	2013-01-11	2008-08-01		ENSG00000182578	ENSG00000182578		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	2433	protein-coding gene	gene with protein product		164770	"McDonough feline sarcoma viral (v-fms) oncogene homolog"	FMS		1611909	Standard	NM_005211		Approved	C-FMS, CSFR, CD115	uc003lrm.3	P07333	OTTHUMG00000130050	ENST00000286301.3:c.514A>G	chr5.hg19:g.149459693T>C	ENSP00000286301:p.Ser172Gly	80.0	0.0		80.0	4.0	NM_005211	B5A955|D3DQG2|Q6LDW5|Q6LDY4|Q86VW7	Missense_Mutation	SNP	ENST00000286301.3	hg19	CCDS4302.1	.	.	.	.	.	.	.	.	.	.	T	6.013	0.370777	0.11409	.	.	ENSG00000182578	ENST00000286301;ENST00000394307;ENST00000543093;ENST00000511344	T;T	0.05717	3.4;3.4	4.44	1.82	0.25136	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.664574	0.13886	N	0.355924	T	0.03827	0.0108	N	0.19112	0.55	0.09310	N	1	B;B;B;B	0.23650	0.03;0.004;0.089;0.009	B;B;B;B	0.16722	0.003;0.0;0.016;0.003	T	0.45862	-0.9232	10	0.25106	T	0.35	.	5.8593	0.18736	0.0:0.0996:0.1657:0.7347	.	172;172;24;172	B4DG86;B5A955;B4E2Y8;P07333	.;.;.;CSF1R_HUMAN	G	172;24;172;24	ENSP00000286301:S172G;ENSP00000445282:S172G	ENSP00000286301:S172G	S	-	1	0	CSF1R	149439886	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.044000	0.13992	0.119000	0.18210	-1.447000	0.01057	AGC	.	.		0.612	CSF1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252329.2	NM_005211		C	149459693	T	C	149459693	3	2	260	1	0	0	0	0	1	0	0	0	3934	1551	54	2	2480	2	CSF1R	5	149459693	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	24840	149459693	31455567	243	37488										
SYNPO	11346	hgsc.bcm.edu	37	chr5	150029768	150029768	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gagccctccttacggcggtgAcatctcccccgtgtctccct	9	18	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr5:150029768A>G	ENST00000394243.1	+	3	3037	c.2663A>G	c.(2662-2664)gAc>gGc	p.D888G	SYNPO_ENST00000522122.1_Missense_Mutation_p.D888G|SYNPO_ENST00000307662.4_Missense_Mutation_p.D644G|SYNPO_ENST00000519664.1_Missense_Mutation_p.D644G	NM_001166208.1	NP_001159680.1	Q8N3V7	SYNPO_HUMAN	synaptopodin	888	Pro-rich.				positive regulation of actin filament bundle assembly (GO:0032233)|regulation of stress fiber assembly (GO:0051492)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic membrane (GO:0045211)|stress fiber (GO:0001725)|tight junction (GO:0005923)	actin binding (GO:0003779)			NS(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(4)|prostate(1)|urinary_tract(2)	18		Medulloblastoma(196;0.134)|all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TACGGCGGTGACATCTCCCCC	0.716																																					p.D888G		Atlas-SNP	.											.	SYNPO	147	.	0			c.A2663G						.						47	52	51					5																	150029768		2203	4299	6502	SO:0001583	missense	11346	exon3			GCGGTGACATCTC	AF499137	CCDS4308.1, CCDS54937.1, CCDS54938.1	5q33.1	2008-02-05			ENSG00000171992	ENSG00000171992			30672	protein-coding gene	gene with protein product		608155				9314539, 10470851	Standard	NM_007286		Approved	KIAA1029	uc003lsn.3	Q8N3V7	OTTHUMG00000130078	ENST00000394243.1:c.2663A>G	chr5.hg19:g.150029768A>G	ENSP00000377789:p.Asp888Gly	140.0	0.0		142.0	6.0	NM_001166209	A5PKZ8|D3DQG8|O15271|Q9UPX1	Missense_Mutation	SNP	ENST00000394243.1	hg19	CCDS54937.1	.	.	.	.	.	.	.	.	.	.	A	6.935	0.542262	0.13250	.	.	ENSG00000171992	ENST00000394243;ENST00000522122;ENST00000307662;ENST00000519664	T;T;T	0.23348	1.91;1.91;1.92	5.55	5.55	0.83447	.	0.110951	0.39985	N	0.001216	T	0.23171	0.0560	L	0.51422	1.61	0.09310	N	1	B;B	0.24721	0.11;0.11	B;B	0.17433	0.018;0.018	T	0.16571	-1.0398	10	0.49607	T	0.09	-10.1984	9.4823	0.38908	0.918:0.0:0.082:0.0	.	644;888	Q8N3V7-2;Q8N3V7	.;SYNPO_HUMAN	G	888;888;644;644	ENSP00000377789:D888G;ENSP00000428378:D888G;ENSP00000429268:D644G	ENSP00000302139:D644G	D	+	2	0	SYNPO	150009961	1.000000	0.71417	0.174000	0.22961	0.341000	0.28922	4.596000	0.61055	2.113000	0.64589	0.459000	0.35465	GAC	.	.		0.716	SYNPO-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252371.1	NM_007286		G	150029768	A	G	150029768	3	3	260	1	0	0	0	0	1	0	0	0	15471	275	10	2	2669	2	SYNPO	5	150029768	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	570075	150029768	30885492	244	37489										
FAT2	2196	hgsc.bcm.edu	37	chr5	150946265	150946265	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtttgccattaaaaccagcaTcagggtcagtggctgctagg	12	9	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr5:150946265T>A	ENST00000261800.5	-	1	2240	c.2228A>T	c.(2227-2229)gAt>gTt	p.D743V		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	743	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AAAACCAGCATCAGGGTCAGT	0.532																																					p.D743V		Atlas-SNP	.											.	FAT2	465	.	0			c.A2228T						.						70	75	74					5																	150946265		2203	4300	6503	SO:0001583	missense	2196	exon1			CCAGCATCAGGGT	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.2228A>T	chr5.hg19:g.150946265T>A	ENSP00000261800:p.Asp743Val	121.0	0.0		65.0	6.0	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	hg19	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	T	18.54	3.646074	0.67358	.	.	ENSG00000086570	ENST00000261800	T	0.74737	-0.87	5.78	5.78	0.91487	Cadherin (4);Cadherin-like (1);	0.000000	0.64402	D	0.000002	D	0.92639	0.7661	H	0.99600	4.65	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95758	0.8798	10	0.87932	D	0	.	16.3979	0.83621	0.0:0.0:0.0:1.0	.	743	Q9NYQ8	FAT2_HUMAN	V	743	ENSP00000261800:D743V	ENSP00000261800:D743V	D	-	2	0	FAT2	150926458	1.000000	0.71417	0.595000	0.28798	0.900000	0.52787	7.932000	0.87634	2.333000	0.79357	0.533000	0.62120	GAT	.	.		0.532	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		A	150946265	T	A	150946265	3	1	260	1	0	0	0	0	1	0	0	0	5698	1435	50	4	10913	4	FAT2	5	150946265	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	916497	150946265	29968995	245	37490										
FAM71B	153745	hgsc.bcm.edu	37	chr5	156590132	156590132	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttctgctgcacacttgctggTcgtaatactgcctgcaaacg	9	12	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr5:156590132T>C	ENST00000302938.4	-	2	1239	c.1144A>G	c.(1144-1146)Acc>Gcc	p.T382A		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	382						nucleus (GO:0005634)				NS(3)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(32)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CACTTGCTGGTCGTAATACTG	0.567																																					p.T382A		Atlas-SNP	.											.	FAM71B	145	.	0			c.A1144G						.						46	48	47					5																	156590132		2203	4300	6503	SO:0001583	missense	153745	exon2			TGCTGGTCGTAAT		CCDS4335.1	5q33.3	2005-08-09			ENSG00000170613	ENSG00000170613			28397	protein-coding gene	gene with protein product						12477932	Standard	NM_130899		Approved	MGC26988	uc003lwn.3	Q8TC56	OTTHUMG00000130246	ENST00000302938.4:c.1144A>G	chr5.hg19:g.156590132T>C	ENSP00000305596:p.Thr382Ala	71.0	0.0		67.0	4.0	NM_130899	Q1EDD9|Q8TC64|Q96LY8	Missense_Mutation	SNP	ENST00000302938.4	hg19	CCDS4335.1	.	.	.	.	.	.	.	.	.	.	T	16.21	3.057600	0.55325	.	.	ENSG00000170613	ENST00000302938	T	0.16897	2.31	3.83	3.83	0.44106	.	0.314558	0.23165	N	0.051186	T	0.34919	0.0914	M	0.68317	2.08	0.09310	N	1	D	0.89917	1.0	D	0.71414	0.973	T	0.04229	-1.0967	10	0.51188	T	0.08	-18.4181	9.2849	0.37751	0.0:0.0:0.0:1.0	.	382	Q8TC56	FA71B_HUMAN	A	382	ENSP00000305596:T382A	ENSP00000305596:T382A	T	-	1	0	FAM71B	156522710	0.031000	0.19500	0.012000	0.15200	0.002000	0.02628	0.633000	0.24598	1.959000	0.56917	0.459000	0.35465	ACC	.	.		0.567	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252570.2	NM_130899		C	156590132	T	C	156590132	3	2	260	1	0	0	0	0	1	0	0	0	5616	1667	58	2	677	2	FAM71B	5	156590132	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	5643867	156590132	24325128	246	37491										
FABP6	2172	hgsc.bcm.edu	37	chr5	159626128	159626128	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gaggcgatgaagacagtgacGatgatgatggtggtggagat	18	3	0	6	rs146032989		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr5:159626128G>T	ENST00000393980.4	+	2	161	c.15G>T	c.(13-15)acG>acT	p.T5T	CTB-127C13.1_ENST00000524005.1_RNA|FABP6_ENST00000393982.1_Silent_p.T5T|CTB-127C13.1_ENST00000501818.1_RNA	NM_001130958.1	NP_001124430.1	P51161	FABP6_HUMAN	fatty acid binding protein 6, ileal	0					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|lipid metabolic process (GO:0006629)|negative regulation of cell proliferation (GO:0008285)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			breast(1)|kidney(1)|large_intestine(1)|lung(2)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			AGACAGTGACGATGATGATGG	0.547											OREG0016998	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T5T	Colon(29;562 677 12756 16385 20992)	Atlas-SNP	.											.	FABP6	37	.	0			c.G15T						.						66	76	73					5																	159626128		2195	4283	6478	SO:0001819	synonymous_variant	2172	exon2			AGTGACGATGATG	U19869	CCDS4349.1, CCDS43393.1	5q23-q35	2013-03-01	2008-08-01		ENSG00000170231	ENSG00000170231		"Fatty acid binding protein family"	3561	protein-coding gene	gene with protein product	"illeal lipid-binding protein", "ileal bile acid binding protein", "gastrotropin"	600422				7894165, 7619861	Standard	NM_001130958		Approved	I-15P, ILLBP, I-BAP, ILBP3, I-BABP, ILBP, I-BALB	uc003lxx.1	P51161	OTTHUMG00000130329	ENST00000393980.4:c.15G>T	chr5.hg19:g.159626128G>T		73.0	0.0	1802	45.0	4.0	NM_001130958	Q07DR7|Q8TBI3|Q9UGI7	Silent	SNP	ENST00000393980.4	hg19	CCDS43393.1																																																																																			.	G|1.000;A|0.000		0.547	FABP6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252678.4	NM_001040442		T	159626128	G	T	159626128	2	4	260	1	0	0	0	0	0	0	0	1	5366	1045	37	1		1	FABP6	5	159626128	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	3035996	159626128	21289132	247	37492										
GABRA1	2554	hgsc.bcm.edu	37	chr5	161292754	161292754	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aaccgaagtgaagactgataTcttcgtcaccagtttcggac	9	10	2	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr5:161292754T>A	ENST00000428797.2	+	5	570	c.215T>A	c.(214-216)aTc>aAc	p.I72N	GABRA1_ENST00000393943.4_Missense_Mutation_p.I72N|GABRA1_ENST00000437025.2_Missense_Mutation_p.I72N|GABRA1_ENST00000420560.1_Missense_Mutation_p.I72N|GABRA1_ENST00000023897.6_Missense_Mutation_p.I72N|GABRA1_ENST00000444819.1_Missense_Mutation_p.I72N	NM_001127643.1	NP_001121115.1	P14867	GBRA1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 1	72					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|drug binding (GO:0008144)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|endometrium(2)|kidney(3)|large_intestine(4)|liver(1)|lung(22)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(1)	42	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.228)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethanol(DB00898)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methohexital(DB00474)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Prazepam(DB01588)|Primidone(DB00794)|Progabide(DB00837)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiamylal(DB01154)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zaleplon(DB00962)|Zolpidem(DB00425)|Zopiclone(DB01198)	AAGACTGATATCTTCGTCACC	0.408																																					p.I72N		Atlas-SNP	.											.	GABRA1	132	.	0			c.T215A						.						207	186	193					5																	161292754		2203	4300	6503	SO:0001583	missense	2554	exon5			CTGATATCTTCGT		CCDS4357.1	5q34	2012-06-22			ENSG00000022355	ENSG00000022355		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4075	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 1"	137160				1330891	Standard	NM_000806		Approved	EJM5	uc003lyx.4	P14867	OTTHUMG00000163586	ENST00000428797.2:c.215T>A	chr5.hg19:g.161292754T>A	ENSP00000393097:p.Ile72Asn	225.0	0.0		207.0	12.0	NM_001127643	D3DQK6|Q8N629	Missense_Mutation	SNP	ENST00000428797.2	hg19	CCDS4357.1	.	.	.	.	.	.	.	.	.	.	T	26.9	4.777259	0.90195	.	.	ENSG00000022355	ENST00000023897;ENST00000428797;ENST00000393943;ENST00000437025;ENST00000521339;ENST00000420560;ENST00000522651;ENST00000444819;ENST00000519621	T;T;T;T;T;T;T;T;T	0.81078	-1.45;-1.45;-1.45;-1.45;-1.26;-1.45;-1.26;-1.45;-1.45	5.33	5.33	0.75918	Neurotransmitter-gated ion-channel ligand-binding (3);	0.063724	0.64402	D	0.000006	D	0.91821	0.7412	H	0.94306	3.52	0.80722	D	1	D	0.57257	0.979	D	0.63703	0.917	D	0.94054	0.7320	10	0.87932	D	0	.	15.3028	0.73966	0.0:0.0:0.0:1.0	.	72	P14867	GBRA1_HUMAN	N	72;72;72;72;78;72;72;72;72	ENSP00000023897:I72N;ENSP00000393097:I72N;ENSP00000377517:I72N;ENSP00000415441:I72N;ENSP00000430895:I78N;ENSP00000408041:I72N;ENSP00000430507:I72N;ENSP00000414232:I72N;ENSP00000430435:I72N	ENSP00000023897:I72N	I	+	2	0	GABRA1	161225332	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.946000	0.87746	2.012000	0.59069	0.455000	0.32223	ATC	.	.		0.408	GABRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252702.2	NM_000806.5		A	161292754	T	A	161292754	3	1	260	1	0	0	0	0	1	0	0	0	6168	1435	50	4	225	4	GABRA1	5	161292754	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1666626	161292754	19622506	248	37493										
ODZ2	57451	hgsc.bcm.edu	37	chr5	167489113	167489113	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agacagtggtgaagcagaagTtggtcggcgggtaacacaag	16	6	0	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr5:167489113T>C	ENST00000518659.1	+	7	1397	c.1358T>C	c.(1357-1359)gTt>gCt	p.V453A	TENM2_ENST00000520394.1_Missense_Mutation_p.V221A|TENM2_ENST00000403607.2_Missense_Mutation_p.V286A|TENM2_ENST00000545108.1_Missense_Mutation_p.V453A|TENM2_ENST00000519204.1_Missense_Mutation_p.V332A	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	453					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										GAAGCAGAAGTTGGTCGGCGG	0.453																																					p.V453A		Atlas-SNP	.											.	.	.	.	0			c.T1358C						.						83	84	84					5																	167489113		1857	4096	5953	SO:0001583	missense	57451	exon7			CAGAAGTTGGTCG	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"odz, odd Oz/ten-m homolog 2 (Drosophila)"	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.1358T>C	chr5.hg19:g.167489113T>C	ENSP00000429430:p.Val453Ala	91.0	0.0		89.0	4.0	NM_001122679	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	hg19		.	.	.	.	.	.	.	.	.	.	T	18.26	3.585236	0.66105	.	.	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	T;T;T;T;T	0.27104	1.69;1.69;1.69;1.69;1.69	5.63	5.63	0.86233	.	0.127648	0.52532	D	0.000070	T	0.34571	0.0902	M	0.73962	2.25	0.43160	D	0.994945	B;B;B	0.33883	0.43;0.287;0.391	B;B;B	0.35182	0.129;0.079;0.197	T	0.22941	-1.0202	10	0.59425	D	0.04	.	15.8419	0.78852	0.0:0.0:0.0:1.0	.	453;221;332	Q9NT68;F8VNQ3;G3V106	TEN2_HUMAN;.;.	A	453;453;332;221;286	ENSP00000429430:V453A;ENSP00000438635:V453A;ENSP00000428964:V332A;ENSP00000427874:V221A;ENSP00000384905:V286A	ENSP00000384905:V286A	V	+	2	0	ODZ2	167421691	1.000000	0.71417	0.902000	0.35471	0.845000	0.48019	8.040000	0.89188	2.137000	0.66172	0.533000	0.62120	GTT	.	.		0.453	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		C	167489113	T	C	167489113	3	2	260	1	0	0	0	0	1	0	0	0	10844	1725	60	2	1384	2	ODZ2	5	167489113	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	6196359	167489113	13426147	249	37494										
WWC1	23286	hgsc.bcm.edu	37	chr5	167835651	167835651	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gagctcccagacagacatctCgggaagcgtgagtagacggg	15	10	1	4	rs377343643		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr5:167835651C>A	ENST00000265293.4	+	7	1362	c.860C>A	c.(859-861)tCg>tAg	p.S287*	WWC1_ENST00000521089.1_Nonsense_Mutation_p.S287*	NM_001161661.1|NM_001161662.1|NM_015238.2	NP_001155133.1|NP_001155134.1|NP_056053.1	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1	287					cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|hippo signaling (GO:0035329)|negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of MAPK cascade (GO:0043410)|regulation of hippo signaling (GO:0035330)|regulation of intracellular transport (GO:0032386)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)|transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(2)|prostate(1)|skin(4)	43	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)		ACAGACATCTCGGGAAGCGTG	0.597																																					p.S287X		Atlas-SNP	.											.	WWC1	98	.	0			c.C860A						.						102	101	102					5																	167835651		2203	4300	6503	SO:0001587	stop_gained	23286	exon7			ACATCTCGGGAAG	AF506799	CCDS4366.1, CCDS54945.1	5q34	2014-06-13	2006-11-09		ENSG00000113645	ENSG00000113645		"WW, C2 and coiled-coil domain containing"	29435	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 168"	610533	"WW, C2 and coiled-coil domain containing 1"			10048485, 12559952	Standard	NM_001161661		Approved	KIBRA, KIAA0869, PPP1R168	uc011den.2	Q8IX03	OTTHUMG00000130408	ENST00000265293.4:c.860C>A	chr5.hg19:g.167835651C>A	ENSP00000265293:p.Ser287*	66.0	0.0		66.0	4.0	NM_015238	B4DK05|O94946|Q6MZX4|Q6Y2F8|Q7Z4G8|Q8WVM4|Q9BT29	Nonsense_Mutation	SNP	ENST00000265293.4	hg19	CCDS4366.1	.	.	.	.	.	.	.	.	.	.	C	37	6.056848	0.97241	.	.	ENSG00000113645	ENST00000265293;ENST00000521089	.	.	.	5.22	5.22	0.72569	.	0.070853	0.64402	D	0.000015	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.7966	0.91997	0.0:1.0:0.0:0.0	.	.	.	.	X	287	.	ENSP00000265293:S287X	S	+	2	0	WWC1	167768229	1.000000	0.71417	0.956000	0.39512	0.728000	0.41692	7.291000	0.78721	2.427000	0.82271	0.655000	0.94253	TCG	.	.		0.597	WWC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252791.2	NM_015238		A	167835651	C	A	167835651	4	1	260	1	0	0	0	0	0	1	0	0	17426	893	31	1	886	1	WWC1	5	167835651	Nonsense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	346538	167835651	13079609	250	37495										
DOCK2	1794	hgsc.bcm.edu	37	chr5	169508908	169508908	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccaacacatctccccgcctcAgccagaccttcctccaactc	3	22	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr5:169508908A>G	ENST00000256935.8	+	51	5430	c.5350A>G	c.(5350-5352)Agc>Ggc	p.S1784G	DOCK2_ENST00000540750.1_Missense_Mutation_p.S845G|DOCK2_ENST00000520908.1_Missense_Mutation_p.S1276G|DOCK2_ENST00000523351.1_3'UTR	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1784					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TCCCCGCCTCAGCCAGACCTT	0.562																																					p.S1784G		Atlas-SNP	.											.	DOCK2	389	.	0			c.A5350G						.						106	96	99					5																	169508908		2203	4300	6503	SO:0001583	missense	1794	exon51			CGCCTCAGCCAGA	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.5350A>G	chr5.hg19:g.169508908A>G	ENSP00000256935:p.Ser1784Gly	126.0	0.0		95.0	30.0	NM_004946	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	hg19	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	A	17.68	3.450522	0.63290	.	.	ENSG00000134516	ENST00000256935;ENST00000520908;ENST00000540750	T;T;T	0.10005	3.59;3.22;2.92	4.84	4.84	0.62591	.	0.196350	0.50627	D	0.000120	T	0.17323	0.0416	N	0.19112	0.55	0.29865	N	0.82731	D;D;D	0.69078	0.982;0.997;0.982	D;D;D	0.75020	0.952;0.985;0.952	T	0.04128	-1.0975	10	0.32370	T	0.25	.	12.6806	0.56920	1.0:0.0:0.0:0.0	.	1276;340;1784	E7ERW7;B3KY14;Q92608	.;.;DOCK2_HUMAN	G	1784;1276;845	ENSP00000256935:S1784G;ENSP00000429283:S1276G;ENSP00000438827:S845G	ENSP00000256935:S1784G	S	+	1	0	DOCK2	169441486	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.461000	0.66699	1.919000	0.55581	0.533000	0.62120	AGC	.	.		0.562	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		G	169508908	A	G	169508908	3	3	260	1	0	0	0	0	1	0	0	0	4689	188	7	2	5552	2	DOCK2	5	169508908	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1673257	169508908	11406352	251	37496										
NSD1	64324	hgsc.bcm.edu	37	chr5	176721162	176721162	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccaaccagatgctgtcgctcTccaaaaaagctctggcaggg	10	13	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr5:176721162T>C	ENST00000439151.2	+	23	6838	c.6793T>C	c.(6793-6795)Tcc>Ccc	p.S2265P	NSD1_ENST00000354179.4_Missense_Mutation_p.S1996P|NSD1_ENST00000347982.4_Missense_Mutation_p.S1996P|NSD1_ENST00000361032.4_Missense_Mutation_p.S2162P	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	2265	Pro-rich.				gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		GCTGTCGCTCTCCAAAAAAGC	0.522			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.S2265P		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.T6793C						.						93	97	96					5																	176721162		2203	4300	6503	SO:0001583	missense	64324	exon23	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	TCGCTCTCCAAAA	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	14234	protein-coding gene	gene with protein product		606681	"Sotos syndrome"	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.6793T>C	chr5.hg19:g.176721162T>C	ENSP00000395929:p.Ser2265Pro	92.0	0.0		54.0	4.0	NM_022455	Q96PD8|Q96RN7	Missense_Mutation	SNP	ENST00000439151.2	hg19	CCDS4412.1	.	.	.	.	.	.	.	.	.	.	T	12.09	1.832882	0.32421	.	.	ENSG00000165671	ENST00000354179;ENST00000439151;ENST00000347982;ENST00000361032	D;D;D;D	0.95588	-3.68;-3.68;-3.68;-3.75	5.41	4.21	0.49690	.	0.107272	0.42548	D	0.000698	D	0.90096	0.6906	L	0.27053	0.805	0.35496	D	0.799389	B;B	0.19200	0.021;0.034	B;B	0.19946	0.027;0.012	D	0.87360	0.2343	10	0.49607	T	0.09	.	7.2463	0.26124	0.0:0.0752:0.1461:0.7787	.	1996;2265	Q96L73-2;Q96L73	.;NSD1_HUMAN	P	1996;2265;1996;2162	ENSP00000346111:S1996P;ENSP00000395929:S2265P;ENSP00000343209:S1996P;ENSP00000354310:S2162P	ENSP00000343209:S1996P	S	+	1	0	NSD1	176653768	0.879000	0.30193	0.999000	0.59377	0.949000	0.60115	1.665000	0.37449	1.030000	0.39839	0.533000	0.62120	TCC	.	.		0.522	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349		C	176721162	T	C	176721162	3	2	260	1	0	0	0	0	1	0	0	0	10678	1551	54	2	6879	2	NSD1	5	176721162	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	7212254	176721162	4194098	252	37497										
PDLIM7	9260	hgsc.bcm.edu	37	chr5	176916442	176916442	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cgggagtcttgccgttgttgCtgccccctcctggcacccct	11	17	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr5:176916442C>T	ENST00000355841.2	-	9	887	c.821G>A	c.(820-822)aGc>aAc	p.S274N	PDLIM7_ENST00000356618.4_Silent_p.Q253Q|PDLIM7_ENST00000393551.1_Silent_p.Q253Q|PDLIM7_ENST00000359895.2_Missense_Mutation_p.S240N	NM_005451.3	NP_005442.2	Q9NR12	PDLI7_HUMAN	PDZ and LIM domain 7 (enigma)	274					actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of osteoblast differentiation (GO:0045669)|receptor-mediated endocytosis (GO:0006898)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ruffle (GO:0001726)|stress fiber (GO:0001725)	zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	10	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCCGTTGTTGCTGCCCCCTCC	0.682																																					p.S274N		Atlas-SNP	.											.	PDLIM7	32	.	0			c.G821A						.						24	32	29					5																	176916442		2200	4297	6497	SO:0001583	missense	9260	exon9			TTGTTGCTGCCCC	BC001093	CCDS4422.1, CCDS4423.1, CCDS4424.1	5q35.3	2008-02-05			ENSG00000196923	ENSG00000196923			22958	protein-coding gene	gene with protein product		605903				11874232	Standard	NM_005451		Approved	ENIGMA	uc003mhc.1	Q9NR12	OTTHUMG00000130853	ENST00000355841.2:c.821G>A	chr5.hg19:g.176916442C>T	ENSP00000348099:p.Ser274Asn	149.0	0.0		125.0	5.0	NM_005451	Q14250|Q5XG82|Q6NVZ5|Q96C91|Q9BXB8|Q9BXB9	Missense_Mutation	SNP	ENST00000355841.2	hg19	CCDS4422.1	.	.	.	.	.	.	.	.	.	.	C	0.343	-0.949454	0.02304	.	.	ENSG00000196923	ENST00000359895;ENST00000355841	T;T	0.50813	0.81;0.73	3.53	1.67	0.24075	.	1.006700	0.08008	N	0.989872	T	0.30386	0.0763	L	0.29908	0.895	0.20196	N	0.999924	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.24799	-1.0150	10	0.18710	T	0.47	.	3.1305	0.06421	0.0:0.4855:0.2262:0.2883	.	274;240	Q9NR12;Q9NR12-2	PDLI7_HUMAN;.	N	240;274	ENSP00000352964:S240N;ENSP00000348099:S274N	ENSP00000348099:S274N	S	-	2	0	PDLIM7	176849048	0.001000	0.12720	0.056000	0.19401	0.151000	0.21798	1.005000	0.29834	0.456000	0.26937	0.650000	0.86243	AGC	.	.		0.682	PDLIM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253423.1	NM_005451		T	176916442	C	T	176916442	3	4	260	1	0	0	0	0	1	0	0	0	11693	797	28	3	572	3	PDLIM7	5	176916442	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	195280	176916442	3998818	253	37498										
TBC1D9B	23061	hgsc.bcm.edu	37	chr5	179298474	179298474	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gctgtcaccttaaacaccatGtaaaggtcctccagctcttc	6	14	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr5:179298474G>A	ENST00000356834.3	-	15	2509	c.2472C>T	c.(2470-2472)taC>taT	p.Y824Y	TBC1D9B_ENST00000355235.3_Silent_p.Y824Y|TBC1D9B_ENST00000519746.1_5'UTR|TBC1D9B_ENST00000444477.2_5'UTR	NM_198868.2	NP_942568.2	Q66K14	TBC9B_HUMAN	TBC1 domain family, member 9B (with GRAM domain)	824						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	28	all_cancers(89;0.000197)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0236)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TAAACACCATGTAAAGGTCCT	0.478																																					p.Y824Y		Atlas-SNP	.											.	TBC1D9B	157	.	0			c.C2472T						.						92	73	80					5																	179298474		2203	4300	6503	SO:0001819	synonymous_variant	23061	exon15			CACCATGTAAAGG	AB014576	CCDS4450.1, CCDS43408.1	5q35.3	2013-01-10			ENSG00000197226	ENSG00000197226		"EF-hand domain containing"	29097	protein-coding gene	gene with protein product						9734811	Standard	NM_198868		Approved	KIAA0676	uc003mlh.3	Q66K14	OTTHUMG00000130911	ENST00000356834.3:c.2472C>T	chr5.hg19:g.179298474G>A		159.0	0.0		112.0	18.0	NM_198868	D3DWQ5|D3DWQ6|O75163|Q53EY0|Q6MZI2|Q96H49	Silent	SNP	ENST00000356834.3	hg19	CCDS43408.1																																																																																			.	.		0.478	TBC1D9B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253501.3	NM_015043		A	179298474	G	A	179298474	2	1	260	1	0	0	0	0	0	0	0	1	15643	1372	48	3		3	TBC1D9B	5	179298474	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	2382032	179298474	1616786	254	37499										
TRIM41	90933	hgsc.bcm.edu	37	chr5	180662368	180662368	+	3'UTR	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccatagaccggccagaatttAgcttcacttgagagagatct	9	10	2	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr5:180662368A>G	ENST00000315073.5	+	0	3196				TRIM41_ENST00000351937.5_Missense_Mutation_p.S516G	NM_033549.4	NP_291027.3	Q8WV44	TRI41_HUMAN	tripartite motif containing 41						protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(3)|prostate(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	26	all_cancers(89;9.17e-06)|all_epithelial(37;1.19e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0684)	all_cancers(40;0.000209)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCCAGAATTTAGCTTCACTTG	0.418																																					p.S516G		Atlas-SNP	.											.	TRIM41	96	.	0			c.A1546G						.						82	78	79					5																	180662368		2203	4300	6503	SO:0001624	3_prime_UTR_variant	90933	exon8			GAATTTAGCTTCA	AF258579	CCDS4465.1, CCDS4466.1	5q35.3	2013-01-09	2011-01-25		ENSG00000146063	ENSG00000146063		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19013	protein-coding gene	gene with protein product	"RING-finger protein that interacts with C kinase"	610530	"tripartite motif-containing 41"			16022281	Standard	NM_033549		Approved	MGC1127, RINCK	uc003mne.2	Q8WV44	OTTHUMG00000130965	ENST00000315073.5:c.*593A>G	chr5.hg19:g.180662368A>G		264.0	0.0		254.0	55.0	NM_201627	B3KNJ6|D3DWR9|Q5BKT0|Q7L484|Q96Q10|Q9BSL8	Missense_Mutation	SNP	ENST00000315073.5	hg19	CCDS4466.1	.	.	.	.	.	.	.	.	.	.	A	15.41	2.826614	0.50739	.	.	ENSG00000146063	ENST00000351937	T	0.38240	1.15	4.45	3.29	0.37713	.	.	.	.	.	T	0.18299	0.0439	N	0.08118	0	0.80722	D	1	B	0.10296	0.003	B	0.11329	0.006	T	0.04930	-1.0917	9	0.66056	D	0.02	.	6.6107	0.22749	0.8943:0.0:0.1057:0.0	.	516	Q8WV44-2	.	G	516	ENSP00000336749:S516G	ENSP00000336749:S516G	S	+	1	0	TRIM41	180594974	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.717000	0.37991	1.047000	0.40274	0.459000	0.35465	AGC	.	.		0.418	TRIM41-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253574.3	NM_201627		G	180662368	A	G	180662368	1	3	260	0	1	0	0	0	0	0	0	0	16531	420	15	2		2	TRIM41	5	180662368	3'UTR	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1363894	180662368	252892	255	37500										
CAGE1	285782	hgsc.bcm.edu	37	chr6	7379230	7379230	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tggctgaattagtgcattcgTtgagtaattttcaatgttgt	10	4	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:7379230T>C	ENST00000512086.1	-	4	509	c.307A>G	c.(307-309)Acg>Gcg	p.T103A	CAGE1_ENST00000338150.4_Missense_Mutation_p.T103A|CAGE1_ENST00000379918.4_Missense_Mutation_p.T103A|CAGE1_ENST00000509324.1_Intron|CAGE1_ENST00000502583.1_Missense_Mutation_p.T103A|CAGE1_ENST00000296742.7_5'UTR			Q8TC20	CAGE1_HUMAN	cancer antigen 1	103										breast(1)|cervix(1)|endometrium(3)|kidney(2)|lung(11)|urinary_tract(1)	19	Ovarian(93;0.0418)					AGTGCATTCGTTGAGTAATTT	0.333																																					p.T103A		Atlas-SNP	.											.	CAGE1	165	.	0			c.A307G						.						48	38	41					6																	7379230		692	1591	2283	SO:0001583	missense	285782	exon4			CATTCGTTGAGTA	BC026194	CCDS47367.1, CCDS54964.1, CCDS54965.1	6p24.3	2009-08-06	2005-01-26	2005-01-27	ENSG00000164304	ENSG00000164304			21622	protein-coding gene	gene with protein product	"cancer/testis antigen 95"	608304	"cancer/testis antigen 3"	CTAG3		12531476	Standard	NM_205864		Approved	bA69L16.7, CT95	uc003mxl.2	Q8TC20	OTTHUMG00000014200	ENST00000512086.1:c.307A>G	chr6.hg19:g.7379230T>C	ENSP00000427583:p.Thr103Ala	79.0	0.0		54.0	4.0	NM_001170693	D6RCT9|Q5TAM0|Q86TM4|Q8N7R5	Missense_Mutation	SNP	ENST00000512086.1	hg19		.	.	.	.	.	.	.	.	.	.	T	5.874	0.345456	0.11126	.	.	ENSG00000164304	ENST00000541116;ENST00000379918;ENST00000502583;ENST00000512086;ENST00000338150;ENST00000542431;ENST00000512691	T;T;T;T;T	0.28666	1.6;1.6;1.6;1.6;1.6	5.23	-0.334	0.12666	.	0.927504	0.09101	N	0.848519	T	0.07279	0.0184	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.37197	-0.9716	8	0.49607	T	0.09	0.0131	10.8192	0.46595	0.0:0.5385:0.3205:0.1411	.	.	.	.	A	103;103;103;103;103;103;115	ENSP00000369250:T103A;ENSP00000425493:T103A;ENSP00000427583:T103A;ENSP00000338107:T103A;ENSP00000423789:T115A	ENSP00000338107:T103A	T	-	1	0	CAGE1	7324229	0.015000	0.18098	0.056000	0.19401	0.046000	0.14306	-0.118000	0.10692	0.025000	0.15241	-0.213000	0.12676	ACG	.	.		0.333	CAGE1-008	PUTATIVE	non_canonical_conserved|basic	protein_coding	protein_coding	OTTHUMT00000367136.1	NM_175745		C	7379230	T	C	7379230	3	2	260	1	0	0	0	0	1	0	0	0	2574	1725	60	2	2362	2	CAGE1	6	7379230	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10		7379230	163735837	256	37501										
TFAP2A	7020	hgsc.bcm.edu	37	chr6	10410201	10410201	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cgagtcctgagctgagcgcgTgtgggccgtgcaggaggtcc	18	11	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:10410201T>C	ENST00000482890.1	-	3	765	c.413A>G	c.(412-414)cAc>cGc	p.H138R	TFAP2A_ENST00000379608.3_Missense_Mutation_p.H132R|TFAP2A_ENST00000319516.4_Missense_Mutation_p.H134R|TFAP2A_ENST00000379613.3_Missense_Mutation_p.H140R|TFAP2A_ENST00000379604.2_Missense_Mutation_p.H138R|TFAP2A-AS1_ENST00000420777.1_RNA|TFAP2A_ENST00000497266.1_5'UTR			P05549	AP2A_HUMAN	transcription factor AP-2 alpha (activating enhancer binding protein 2 alpha)	138					anterior neuropore closure (GO:0021506)|basement membrane organization (GO:0071711)|bone morphogenesis (GO:0060349)|cellular response to iron ion (GO:0071281)|cornea development in camera-type eye (GO:0061303)|embryonic body morphogenesis (GO:0010172)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|embryonic pattern specification (GO:0009880)|epidermis morphogenesis (GO:0048730)|eyelid development in camera-type eye (GO:0061029)|face morphogenesis (GO:0060325)|forebrain neuron development (GO:0021884)|inner ear morphogenesis (GO:0042472)|keratinocyte development (GO:0003334)|kidney development (GO:0001822)|lens induction in camera-type eye (GO:0060235)|metanephric nephron development (GO:0072210)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell development (GO:0014032)|oculomotor nerve formation (GO:0021623)|optic cup structural organization (GO:0003409)|optic vesicle morphogenesis (GO:0003404)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cell migration (GO:0030335)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of tooth mineralization (GO:0070172)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell differentiation (GO:0045595)|regulation of neuron differentiation (GO:0045664)|retina layer formation (GO:0010842)|sensory perception of sound (GO:0007605)|sympathetic nervous system development (GO:0048485)|transcription from RNA polymerase II promoter (GO:0006366)|trigeminal nerve development (GO:0021559)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1)	13	Breast(50;0.0427)|Ovarian(93;0.0991)	all_hematologic(90;0.107)				GCTGAGCGCGTGTGGGCCGTG	0.682																																					p.H138R		Atlas-SNP	.											.	TFAP2A	129	.	0			c.A413G						.						19	18	18					6																	10410201		2187	4276	6463	SO:0001583	missense	7020	exon2			AGCGCGTGTGGGC	X52611	CCDS4510.1, CCDS34337.1, CCDS43422.1	6p24.3	2013-09-19	2001-11-28		ENSG00000137203	ENSG00000137203			11742	protein-coding gene	gene with protein product		107580	"transcription factor AP-2 alpha (activating enhancer-binding protein 2 alpha)"	TFAP2, AP2TF		1916817, 3063603	Standard	NM_001032280		Approved	AP-2	uc003myr.3	P05549	OTTHUMG00000014235	ENST00000482890.1:c.413A>G	chr6.hg19:g.10410201T>C	ENSP00000418541:p.His138Arg	153.0	0.0		89.0	4.0	NM_003220	Q13777|Q5TAV5|Q8N1C6	Missense_Mutation	SNP	ENST00000482890.1	hg19	CCDS4510.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	23.7|23.7	4.451234|4.451234	0.84209|0.84209	.|.	.|.	ENSG00000137203|ENSG00000137203	ENST00000379613;ENST00000379604;ENST00000319516;ENST00000379608;ENST00000482890;ENST00000466073|ENST00000475264	T;T;T;T;T;T|.	0.80653|.	-1.4;-1.4;-1.4;-1.4;-1.4;-1.4|.	4.78|4.78	4.78|4.78	0.61160|0.61160	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.69333|0.69333	0.3099|0.3099	M|M	0.82323|0.82323	2.585|2.585	0.80722|0.80722	D|D	1|1	D;D;D;P;D;D;P|.	0.69078|.	0.973;0.973;0.997;0.82;0.973;0.973;0.858|.	D;D;D;B;D;D;P|.	0.79784|.	0.921;0.921;0.993;0.328;0.921;0.921;0.672|.	T|T	0.73398|0.73398	-0.3995|-0.3995	10|5	0.72032|.	D|.	0.01|.	-11.8479|-11.8479	13.1502|13.1502	0.59484|0.59484	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	140;138;138;140;134;138;132|.	Q96SH1;C1K3N0;P05549-2;Q96SH0;Q5TAV5;P05549;Q8N1C6|.	.;.;.;.;.;AP2A_HUMAN;.|.	R|A	140;138;134;132;138;138|43	ENSP00000368933:H140R;ENSP00000368924:H138R;ENSP00000316516:H134R;ENSP00000368928:H132R;ENSP00000418541:H138R;ENSP00000417495:H138R|.	ENSP00000316516:H134R|.	H|T	-|-	2|1	0|0	TFAP2A|TFAP2A	10518187|10518187	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	6.102000|6.102000	0.71486|0.71486	1.780000|1.780000	0.52325|0.52325	0.482000|0.482000	0.46254|0.46254	CAC|ACG	.	.		0.682	TFAP2A-007	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353619.2	NM_003220		C	10410201	T	C	10410201	3	2	260	1	0	0	0	0	1	0	0	0	15802	1696	59	2	924	2	TFAP2A	6	10410201	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	3030971	10410201	160704866	257	37502										
RANBP9	10048	hgsc.bcm.edu	37	chr6	13642722	13642722	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgtccttactttgtctattcTtaatggaagctaattcttct	5	8	4	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:13642722T>C	ENST00000011619.3	-	7	1272	c.1214A>G	c.(1213-1215)aAg>aGg	p.K405R	RANBP9_ENST00000539980.1_Missense_Mutation_p.K176R	NM_005493.2	NP_005484.2	Q96S59	RANB9_HUMAN	RAN binding protein 9	405	CTLH. {ECO:0000255|PROSITE- ProRule:PRU00058}.|Interaction with CALB1. {ECO:0000305}.				axon guidance (GO:0007411)|microtubule nucleation (GO:0007020)|protein complex assembly (GO:0006461)	cytosol (GO:0005829)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|Ran GTPase binding (GO:0008536)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|skin(1)	16	Breast(50;0.00669)|Ovarian(93;0.0634)	all_hematologic(90;0.117)	Epithelial(50;0.223)			TTGTCTATTCTTAATGGAAGC	0.353																																					p.K405R		Atlas-SNP	.											.	RANBP9	42	.	0			c.A1214G						.						92	85	87					6																	13642722		2203	4300	6503	SO:0001583	missense	10048	exon7			CTATTCTTAATGG	AB008515	CCDS4529.1	6p23	2010-05-25			ENSG00000010017	ENSG00000010017			13727	protein-coding gene	gene with protein product	"Ran Binding Protein in the Microtubule organizing center"	603854				9817760	Standard	NM_005493		Approved	RanBPM	uc003nbb.3	Q96S59	OTTHUMG00000015642	ENST00000011619.3:c.1214A>G	chr6.hg19:g.13642722T>C	ENSP00000011619:p.Lys405Arg	76.0	0.0		64.0	4.0	NM_005493	A0PJA2|B2R8E1|O94764|Q6P3T7|Q7LBR2|Q7Z7F9	Missense_Mutation	SNP	ENST00000011619.3	hg19	CCDS4529.1	.	.	.	.	.	.	.	.	.	.	T	18.97	3.735135	0.69189	.	.	ENSG00000010017	ENST00000011619;ENST00000539980	T	0.79749	-1.3	5.75	5.75	0.90469	CTLH, C-terminal LisH motif (2);	0.042023	0.85682	D	0.000000	D	0.86016	0.5832	M	0.70595	2.14	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	D	0.85164	0.0994	10	0.35671	T	0.21	-11.6801	16.0342	0.80612	0.0:0.0:0.0:1.0	.	405	Q96S59	RANB9_HUMAN	R	405;176	ENSP00000011619:K405R	ENSP00000011619:K405R	K	-	2	0	RANBP9	13750701	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.655000	0.83696	2.185000	0.69588	0.460000	0.39030	AAG	.	.		0.353	RANBP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042373.1			C	13642722	T	C	13642722	3	2	260	1	0	0	0	0	1	0	0	0	13047	1609	56	2	1007	2	RANBP9	6	13642722	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	3232521	13642722	157472345	258	37503										
MYLIP	29116	hgsc.bcm.edu	37	chr6	16144041	16144041	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttgtttaaaatgatcagcacCagggcggccagcgggctcta	12	10	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:16144041C>T	ENST00000356840.3	+	5	972	c.774C>T	c.(772-774)acC>acT	p.T258T	MYLIP_ENST00000349606.4_Silent_p.T77T|MIR4639_ENST00000584938.1_RNA	NM_013262.3	NP_037394.2	Q8WY64	MYLIP_HUMAN	myosin regulatory light chain interacting protein	258	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cellular component movement (GO:0006928)|cholesterol homeostasis (GO:0042632)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|nervous system development (GO:0007399)|positive regulation of protein catabolic process (GO:0045732)|protein destabilization (GO:0031648)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	cytoskeletal protein binding (GO:0008092)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28	Breast(50;0.0799)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.241)			TGATCAGCACCAGGGCGGCCA	0.537																																					p.T258T		Atlas-SNP	.											.	MYLIP	44	.	0			c.C774T						.						162	156	158					6																	16144041		2203	4300	6503	SO:0001819	synonymous_variant	29116	exon5			CAGCACCAGGGCG	AF187016	CCDS4536.1	6p23-p22.3	2011-11-17			ENSG00000007944	ENSG00000007944			21155	protein-coding gene	gene with protein product	"E3 ubiquitin ligase-inducible degrader of the low density lipoprotein receptor"	610082				10593918, 11162443, 19688294	Standard	NM_013262		Approved	MIR, IDOL	uc003nbq.3	Q8WY64	OTTHUMG00000016405	ENST00000356840.3:c.774C>T	chr6.hg19:g.16144041C>T		132.0	0.0		90.0	4.0	NM_013262	Q5TIA4|Q9BU73|Q9NRL9|Q9UHE7	Silent	SNP	ENST00000356840.3	hg19	CCDS4536.1																																																																																			.	.		0.537	MYLIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043864.1	NM_013262		T	16144041	C	T	16144041	2	4	260	1	0	0	0	0	0	0	0	1	10064	581	21	3		3	MYLIP	6	16144041	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	2501319	16144041	154971026	259	37504										
KIF13A	63971	hgsc.bcm.edu	37	chr6	17794586	17794586	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtggcagtgtccctgaatgcTgcacaggtttcaccgtgact	12	11	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:17794586T>C	ENST00000259711.6	-	25	3221	c.3116A>G	c.(3115-3117)cAg>cGg	p.Q1039R	KIF13A_ENST00000378816.5_Missense_Mutation_p.Q1039R|KIF13A_ENST00000378843.2_Missense_Mutation_p.Q1039R|KIF13A_ENST00000378814.5_Missense_Mutation_p.Q1039R|KIF13A_ENST00000378826.2_Missense_Mutation_p.Q1039R	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	1039					ATP catabolic process (GO:0006200)|cargo loading into vesicle (GO:0035459)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|Golgi to plasma membrane protein transport (GO:0043001)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)	centrosome (GO:0005813)|endosome membrane (GO:0010008)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|trans-Golgi network membrane (GO:0032588)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	64	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			CCCTGAATGCTGCACAGGTTT	0.512																																					p.Q1039R		Atlas-SNP	.											.	KIF13A	276	.	0			c.A3116G						.						113	105	108					6																	17794586		1928	4148	6076	SO:0001583	missense	63971	exon25			GAATGCTGCACAG	AJ291578	CCDS47380.1, CCDS47381.1, CCDS54967.1, CCDS54968.1, CCDS58998.1	6p23	2008-10-21			ENSG00000137177	ENSG00000137177		"Kinesins"	14566	protein-coding gene	gene with protein product		605433				11106728	Standard	NM_022113		Approved	bA500C11.2	uc003ncg.4	Q9H1H9	OTTHUMG00000014313	ENST00000259711.6:c.3116A>G	chr6.hg19:g.17794586T>C	ENSP00000259711:p.Gln1039Arg	110.0	0.0		95.0	4.0	NM_001105567	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Missense_Mutation	SNP	ENST00000259711.6	hg19	CCDS47381.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	23.4|23.4	4.413348|4.413348	0.83449|0.83449	.|.	.|.	ENSG00000137177|ENSG00000137177	ENST00000378814;ENST00000502297;ENST00000259711;ENST00000378826;ENST00000378843;ENST00000378816|ENST00000358380	T;T;T;T;T;T|.	0.72394|.	-0.64;1.79;-0.65;-0.63;-0.64;-0.63|.	5.43|5.43	5.43|5.43	0.79202|0.79202	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.61048|0.61048	0.2316|0.2316	L|L	0.56280|0.56280	1.765|1.765	0.58432|0.58432	D|D	0.999999|0.999999	B;D;B;D|.	0.63880|.	0.164;0.98;0.197;0.993|.	B;P;B;P|.	0.59115|.	0.142;0.736;0.444;0.852|.	T|T	0.60860|0.60860	-0.7179|-0.7179	10|5	0.44086|.	T|.	0.13|.	.|.	15.7844|15.7844	0.78291|0.78291	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1039;1039;1039;1039|.	Q9H1H9-4;Q9H1H9-2;Q9H1H9;Q9H1H9-3|.	.;.;KI13A_HUMAN;.|.	R|G	1039;56;1039;1039;1039;1039|433	ENSP00000368091:Q1039R;ENSP00000425616:Q56R;ENSP00000259711:Q1039R;ENSP00000368103:Q1039R;ENSP00000368120:Q1039R;ENSP00000368093:Q1039R|.	ENSP00000259711:Q1039R|.	Q|S	-|-	2|1	0|0	KIF13A|KIF13A	17902565|17902565	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.849000|0.849000	0.48306|0.48306	7.608000|7.608000	0.82898|0.82898	2.190000|2.190000	0.69967|0.69967	0.533000|0.533000	0.62120|0.62120	CAG|AGC	.	.		0.512	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4			C	17794586	T	C	17794586	3	2	260	1	0	0	0	0	1	0	0	0	8283	1580	55	2	2386	2	KIF13A	6	17794586	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1650545	17794586	153320481	260	37505										
MRS2	57380	hgsc.bcm.edu	37	chr6	24418379	24418379	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgttggaaaactactaccgaTtggctgacgatctctccaat	8	10	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:24418379T>C	ENST00000378386.3	+	8	997	c.904T>C	c.(904-906)Ttg>Ctg	p.L302L	MRS2_ENST00000483634.1_3'UTR|MRS2_ENST00000535061.1_Silent_p.L252L|MRS2_ENST00000543597.1_Silent_p.L11L|MRS2_ENST00000274747.7_3'UTR|MRS2_ENST00000378353.1_Silent_p.L302L|MRS2_ENST00000443868.2_Silent_p.L305L	NM_020662.2	NP_065713.1	Q9HD23	MRS2_HUMAN	MRS2 magnesium transporter	302						integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	magnesium ion transmembrane transporter activity (GO:0015095)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)|stomach(1)	12						CTACTACCGATTGGCTGACGA	0.388																																					p.L302L		Atlas-SNP	.											.	MRS2	31	.	0			c.T904C						.						139	125	130					6																	24418379		2203	4300	6503	SO:0001819	synonymous_variant	57380	exon8			TACCGATTGGCTG	AF288288	CCDS4552.1, CCDS69055.1, CCDS69056.1, CCDS75408.1	6p22.3-p22.1	2013-05-03	2013-05-03	2008-01-18	ENSG00000124532	ENSG00000124532			13785	protein-coding gene	gene with protein product			"MRS2-like, magnesium homeostasis factor (S. cerevisiae)", "MRS2 magnesium homeostasis factor homolog (S. cerevisiae)"	MRS2L			Standard	XM_005249242		Approved		uc003neb.3	Q9HD23	OTTHUMG00000014355	ENST00000378386.3:c.904T>C	chr6.hg19:g.24418379T>C		234.0	0.0		139.0	6.0	NM_020662	A8K4U3|B3KNN2|B4DQL2|Q5T3Y1|Q6NTG4|Q96KF8|Q9BVP1	Silent	SNP	ENST00000378386.3	hg19	CCDS4552.1																																																																																			.	.		0.388	MRS2-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040002.1			C	24418379	T	C	24418379	2	2	260	1	0	0	0	0	0	0	0	1	9860	1490	52	2		2	MRS2	6	24418379	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	6623793	24418379	146696688	261	37506										
HIST1H3A	8350	hgsc.bcm.edu	37	chr6	26020867	26020867	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccgggcaccgtggctctgcgCgagatccgccgttatcagaa	13	14	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:26020867C>A	ENST00000357647.3	+	1	150	c.150C>A	c.(148-150)cgC>cgA	p.R50R	HIST1H1A_ENST00000244573.3_5'Flank|HIST1H4A_ENST00000359907.3_5'Flank	NM_003529.2	NP_003520.1	P68431	H31_HUMAN	histone cluster 1, H3a	50					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			endometrium(1)|lung(3)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						TGGCTCTGCGCGAGATCCGCC	0.602																																					p.R50R		Atlas-SNP	.											.	HIST1H3A	14	.	0			c.C150A						.						37	43	41					6																	26020867		2203	4300	6503	SO:0001819	synonymous_variant	8350	exon1			TCTGCGCGAGATC	Z46261	CCDS4570.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000198366	ENSG00000275714		"Histones / Replication-dependent"	4766	protein-coding gene	gene with protein product		602810	"H3 histone family, member A", "histone 1, H3a"	H3FA		9119399, 12408966	Standard	NM_003529		Approved	H3/A	uc003nfp.1	P68431	OTTHUMG00000014418	ENST00000357647.3:c.150C>A	chr6.hg19:g.26020867C>A		96.0	0.0		73.0	4.0	NM_003529	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Silent	SNP	ENST00000357647.3	hg19	CCDS4570.1																																																																																			.	.		0.602	HIST1H3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040080.1	NM_003529		A	26020867	C	A	26020867	2	1	260	1	0	0	0	0	0	0	0	1	7164	755	27	1		1	HIST1H3A	6	26020867	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	1602488	26020867	145094200	262	37507										
BTN3A1	11119	hgsc.bcm.edu	37	chr6	26413697	26413697	+	Missense_Mutation	SNP	A	A	C													0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggggctgactgatgggaataAgtatcggactctaactgagc							TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:26413697A>C	ENST00000289361.6	+	10	1687	c.1319A>C	c.(1318-1320)aAg>aCg	p.K440T	BTN3A1_ENST00000414912.2_Missense_Mutation_p.K388T	NM_001145008.1|NM_001145009.1|NM_007048.5	NP_001138480.1|NP_001138481.1|NP_008979.3	O00481	BT3A1_HUMAN	butyrophilin, subfamily 3, member A1	440	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				activated T cell proliferation (GO:0050798)|cytokine secretion (GO:0050663)|interferon-gamma secretion (GO:0072643)|T cell receptor signaling pathway (GO:0050852)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28						GATGGGAATAAGTATCGGACT	0.478																																					p.K440T		Atlas-SNP	.											.	BTN3A1	80	.	0			c.A1319C						.						141	143	142					6																	26413697		2203	4300	6503	SO:0001583	missense	11119	exon10			GGAATAAGTATCG	U90552	CCDS4608.1, CCDS4609.1, CCDS47388.1, CCDS47389.1	6p22.1	2014-01-14			ENSG00000026950	ENSG00000026950		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Butyrophilins"	1138	protein-coding gene	gene with protein product		613593				9149941	Standard	NM_007048		Approved	BT3.1, BTF5, CD277, BTN3.1	uc003nhv.3	O00481	OTTHUMG00000014449	ENST00000289361.6:c.1319A>C	chr6.hg19:g.26413697A>C	ENSP00000289361:p.Lys440Thr	109.0	0.0		60.0	15.0	NM_007048	A2A278|A8K2C8|B4DIQ1|B4DRM2|E9PGB4|E9PHG8|Q0P515|Q147X5|Q53F15|Q99420|Q9HCY1	Missense_Mutation	SNP	ENST00000289361.6	hg19	CCDS4608.1	.	.	.	.	.	.	.	.	.	.	.	8.273	0.813912	0.16537	.	.	ENSG00000026950	ENST00000289361;ENST00000414912	T;T	0.60548	0.18;0.18	2.31	1.12	0.20585	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	.	.	.	.	T	0.17534	0.0421	N	0.12527	0.23	0.09310	N	1	P;P	0.48589	0.802;0.912	B;B	0.41135	0.265;0.348	T	0.03829	-1.1000	9	0.52906	T	0.07	.	5.6531	0.17627	0.8487:0.0:0.1513:0.0	.	388;440	E9PGB4;O00481	.;BT3A1_HUMAN	T	440;388	ENSP00000289361:K440T;ENSP00000406667:K388T	ENSP00000289361:K440T	K	+	2	0	BTN3A1	26521676	0.000000	0.05858	0.001000	0.08648	0.025000	0.11179	-5.592000	0.00111	0.309000	0.22966	0.496000	0.49642	AAG	.	.		0.478	BTN3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040112.3			C	26413697	A	C	26413697	3	2	260	1	0	0	0	0	1	0	0	0	1564	72	3	5	1521	5	BTN3A1	6	26413697	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	392830	26413697	144701370	263	37508	186	2								
BTN3A1	11119	hgsc.bcm.edu	37	chr6	26413707	26413707	+	Silent	SNP	T	T	C													0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gatgggaataagtatcggacTctaactgagcccagaaccaa							TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:26413707T>C	ENST00000289361.6	+	10	1697	c.1329T>C	c.(1327-1329)acT>acC	p.T443T	BTN3A1_ENST00000414912.2_Silent_p.T391T	NM_001145008.1|NM_001145009.1|NM_007048.5	NP_001138480.1|NP_001138481.1|NP_008979.3	O00481	BT3A1_HUMAN	butyrophilin, subfamily 3, member A1	443	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				activated T cell proliferation (GO:0050798)|cytokine secretion (GO:0050663)|interferon-gamma secretion (GO:0072643)|T cell receptor signaling pathway (GO:0050852)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28						AGTATCGGACTCTAACTGAGC	0.478																																					p.T443T		Atlas-SNP	.											.	BTN3A1	80	.	0			c.T1329C						.						140	141	141					6																	26413707		2203	4300	6503	SO:0001819	synonymous_variant	11119	exon10			TCGGACTCTAACT	U90552	CCDS4608.1, CCDS4609.1, CCDS47388.1, CCDS47389.1	6p22.1	2014-01-14			ENSG00000026950	ENSG00000026950		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Butyrophilins"	1138	protein-coding gene	gene with protein product		613593				9149941	Standard	NM_007048		Approved	BT3.1, BTF5, CD277, BTN3.1	uc003nhv.3	O00481	OTTHUMG00000014449	ENST00000289361.6:c.1329T>C	chr6.hg19:g.26413707T>C		132.0	0.0		65.0	4.0	NM_007048	A2A278|A8K2C8|B4DIQ1|B4DRM2|E9PGB4|E9PHG8|Q0P515|Q147X5|Q53F15|Q99420|Q9HCY1	Silent	SNP	ENST00000289361.6	hg19	CCDS4608.1																																																																																			.	.		0.478	BTN3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040112.3			C	26413707	T	C	26413707	2	2	260	1	0	0	0	0	0	0	0	1	1564	1538	54	2		2	BTN3A1	6	26413707	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	10	26413707	144701360	264	37509	186	2								
ZNF165	7718	hgsc.bcm.edu	37	chr6	28057118	28057118	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cttccgagtgagctcacatcTtattcgacactttagaattc	6	11	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:28057118T>A	ENST00000377325.1	+	4	1884	c.1328T>A	c.(1327-1329)cTt>cAt	p.L443H	ZSCAN12P1_ENST00000529104.1_RNA	NM_003447.3	NP_003438.1	P49910	ZN165_HUMAN	zinc finger protein 165	443					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(14)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						AGCTCACATCTTATTCGACAC	0.443																																					p.L443H		Atlas-SNP	.											.	ZNF165	48	.	0			c.T1328A						.						60	61	60					6																	28057118		2203	4300	6503	SO:0001583	missense	7718	exon4			CACATCTTATTCG	U78722	CCDS4643.1	6p21	2013-01-09			ENSG00000197279	ENSG00000197279		"-", "Zinc fingers, C2H2-type"	12953	protein-coding gene	gene with protein product	"cancer/testis antigen 53"	600834				7490084	Standard	NM_003447		Approved	ZSCAN7, CT53	uc021yro.1	P49910	OTTHUMG00000014505	ENST00000377325.1:c.1328T>A	chr6.hg19:g.28057118T>A	ENSP00000366542:p.Leu443His	139.0	0.0		89.0	4.0	NM_003447		Missense_Mutation	SNP	ENST00000377325.1	hg19	CCDS4643.1	.	.	.	.	.	.	.	.	.	.	T	13.87	2.364649	0.41902	.	.	ENSG00000197279	ENST00000377325	T	0.54071	0.59	2.71	2.71	0.32032	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.73753	0.3627	H	0.97465	4.01	0.28928	N	0.89175	D	0.89917	1.0	D	0.97110	1.0	T	0.67673	-0.5610	9	0.87932	D	0	.	10.0209	0.42041	0.0:0.0:0.0:1.0	.	443	P49910	ZN165_HUMAN	H	443	ENSP00000366542:L443H	ENSP00000366542:L443H	L	+	2	0	ZNF165	28165097	0.890000	0.30428	0.937000	0.37676	0.203000	0.24098	6.745000	0.74860	1.268000	0.44264	0.477000	0.44152	CTT	.	.		0.443	ZNF165-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040173.1	NM_003447		A	28057118	T	A	28057118	3	1	260	1	0	0	0	0	1	0	0	0	17755	1609	56	4	1338	4	ZNF165	6	28057118	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1643411	28057118	143057949	265	37510										
SCAND3	114821	hgsc.bcm.edu	37	chr6	28540398	28540398	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cacatctttaaaaagttgggAccacatgggtttcttgcctt	8	9	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:28540398A>G	ENST00000452236.2	-	4	3885	c.3268T>C	c.(3268-3270)Tcc>Ccc	p.S1090P		NM_052923.1	NP_443155.1														NS(3)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(14)|liver(1)|lung(29)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(3)	71						aaaagttgggaccacatgggt	0.378																																					p.S1090P		Atlas-SNP	.											.	SCAND3	156	.	0			c.T3268C						.						60	61	61					6																	28540398		2203	4298	6501	SO:0001583	missense	114821	exon4			GTTGGGACCACAT																												ENST00000452236.2:c.3268T>C	chr6.hg19:g.28540398A>G	ENSP00000395259:p.Ser1090Pro	126.0	0.0		123.0	5.0	NM_052923		Missense_Mutation	SNP	ENST00000452236.2	hg19	CCDS34355.1	.	.	.	.	.	.	.	.	.	.	A	12.97	2.097306	0.37048	.	.	ENSG00000232040	ENST00000452236	T	0.31247	1.5	2.14	2.14	0.27477	Ribonuclease H-like (1);	0.267070	0.21547	N	0.072783	T	0.18087	0.0434	L	0.28192	0.835	0.26251	N	0.978724	P	0.48350	0.909	D	0.63033	0.91	T	0.04593	-1.0940	10	0.29301	T	0.29	.	6.2738	0.20969	1.0:0.0:0.0:0.0	.	1090	Q6R2W3	SCND3_HUMAN	P	1090	ENSP00000395259:S1090P	ENSP00000395259:S1090P	S	-	1	0	SCAND3	28648377	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	2.200000	0.42724	1.237000	0.43756	0.459000	0.35465	TCC	.	.		0.378	SCAND3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000043551.3			G	28540398	A	G	28540398	3	3	260	1	0	0	0	0	1	0	0	0	13891	275	10	2	713	2	SCAND3	6	28540398	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	483280	28540398	142574669	266	37511										
OR2B3	442184	hgsc.bcm.edu	37	chr6	29054341	29054341	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttgccgtccttctgctgaccTgatttttaatactgcttgag	8	10	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:29054341T>C	ENST00000377173.2	-	1	749	c.685A>G	c.(685-687)Agg>Ggg	p.R229G		NM_001005226.2	NP_001005226.1	O76000	OR2B3_HUMAN	olfactory receptor, family 2, subfamily B, member 3	229						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|kidney(2)|lung(17)|prostate(1)|skin(2)	24						TCTGCTGACCTGATTTTTAAT	0.418																																					p.R229G		Atlas-SNP	.											.	OR2B3	44	.	0			c.A685G						.						110	95	100					6																	29054341		2203	4300	6503	SO:0001583	missense	442184	exon1			CTGACCTGATTTT		CCDS34358.1	6p22.2-p21.31	2012-08-09	2008-10-22	2008-10-22	ENSG00000204703	ENSG00000204703		"GPCR / Class A : Olfactory receptors"	8238	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily B, member 3 pseudogene"	OR2B3P			Standard	NM_001005226		Approved	OR6-4	uc003nlx.3	O76000	OTTHUMG00000031226	ENST00000377173.2:c.685A>G	chr6.hg19:g.29054341T>C	ENSP00000366378:p.Arg229Gly	107.0	0.0		84.0	4.0	NM_001005226	B0UYQ1|Q5ST41|Q96R13	Missense_Mutation	SNP	ENST00000377173.2	hg19	CCDS34358.1	.	.	.	.	.	.	.	.	.	.	T	10.70	1.424171	0.25639	.	.	ENSG00000204703	ENST00000377173	T	0.39056	1.1	3.82	2.54	0.30619	GPCR, rhodopsin-like superfamily (1);	1.264610	0.06054	U	0.657133	T	0.25121	0.0610	L	0.58669	1.825	0.09310	N	1	B	0.22080	0.064	B	0.34038	0.174	T	0.45249	-0.9274	10	0.59425	D	0.04	.	5.5155	0.16904	0.1293:0.0:0.3147:0.556	.	229	O76000	OR2B3_HUMAN	G	229	ENSP00000366378:R229G	ENSP00000366378:R229G	R	-	1	2	OR2B3	29162320	0.000000	0.05858	0.808000	0.32385	0.940000	0.58332	0.304000	0.19228	1.352000	0.45808	0.428000	0.28381	AGG	.	.		0.418	OR2B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076469.2			C	29054341	T	C	29054341	3	2	260	1	0	0	0	0	1	0	0	0	10999	1579	55	2	260	2	OR2B3	6	29054341	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	513943	29054341	142060726	267	37512										
SFTA2	389376	hgsc.bcm.edu	37	chr6	30899268	30899268	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acaggcttcaatggctgtcaTgtgttgcagacaacatggtg	12	8	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:30899268T>C	ENST00000359086.3	-	3	312	c.234A>G	c.(232-234)acA>acG	p.T78T	Y_RNA_ENST00000516952.1_RNA	NM_205854.2	NP_995326.1	Q6UW10	SFTA2_HUMAN	surfactant associated 2	78						extracellular region (GO:0005576)				lung(2)	2						ATGGCTGTCATGTGTTGCAGA	0.602																																					p.T78T		Atlas-SNP	.											.	SFTA2	6	.	0			c.A234G						.						92	68	76					6																	30899268		1508	2708	4216	SO:0001819	synonymous_variant	389376	exon3			CTGTCATGTGTTG	AY102070	CCDS4691.1	6p21.3	2008-08-26	2008-08-26	2008-08-26	ENSG00000196260	ENSG00000196260			18386	protein-coding gene	gene with protein product			"surfactant associated protein G"	SFTPG			Standard	NM_205854		Approved		uc003nsf.3	Q6UW10	OTTHUMG00000031183	ENST00000359086.3:c.234A>G	chr6.hg19:g.30899268T>C		137.0	0.0		79.0	4.0	NM_205854	A2ABK7|A2ACH1|B7ZCJ7	Silent	SNP	ENST00000359086.3	hg19	CCDS4691.1																																																																																			.	.		0.602	SFTA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076360.2	NM_205854		C	30899268	T	C	30899268	2	2	260	1	0	0	0	0	0	0	0	1	14202	1451	51	2		2	SFTA2	6	30899268	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1844927	30899268	140215799	268	37513										
CDSN	170679	hgsc.bcm.edu	37	chr6	31084099	31084099	+	Intron	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgggaactggagctgctgctGaaggagccggtgcctggtgg	19	8	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:31084099G>A	ENST00000259881.9	+	1	61				CDSN_ENST00000376288.2_Silent_p.F431F|PSORS1C1_ENST00000467107.1_3'UTR	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1											kidney(1)|ovary(2)|prostate(1)|skin(1)	5						AGCTGCTGCTGAAGGAGCCGG	0.587																																					p.F431F		Atlas-SNP	.											.	CDSN	48	.	0			c.C1293T						.						37	39	38					6																	31084099		2203	4300	6503	SO:0001627	intron_variant	1041	exon2			GCTGCTGAAGGAG	AB031479	CCDS34390.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204540	ENSG00000204540			17202	protein-coding gene	gene with protein product		613525	"chromosome 6 open reading frame 16"	C6orf16			Standard	NM_014068		Approved	SEEK1	uc003nsl.2	Q9UIG5	OTTHUMG00000031077	ENST00000259881.9:c.-229+1431G>A	chr6.hg19:g.31084099G>A		132.0	0.0		82.0	5.0	NM_001264	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Silent	SNP	ENST00000259881.9	hg19	CCDS34390.1																																																																																			.	.		0.587	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068		A	31084099	G	A	31084099	1	1	260	0	1	0	0	0	0	0	0	0	3181	1281	45	3		3	CDSN	6	31084099	Intron	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	184831	31084099	140030968	269	37514										
CCHCR1	54535	hgsc.bcm.edu	37	chr6	31125311	31125311	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	atccagacaccagcaggccaTgactcttgggtccttccctg	9	15	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:31125311T>C	ENST00000376266.5	-	2	72				CCHCR1_ENST00000480060.1_Intron|CCHCR1_ENST00000396268.3_Missense_Mutation_p.M23V|TCF19_ENST00000376255.4_5'Flank|TCF19_ENST00000376257.3_5'Flank|CCHCR1_ENST00000396263.2_Intron|CCHCR1_ENST00000451521.2_Missense_Mutation_p.M23V	NM_019052.3	NP_061925.2	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1						cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein export from nucleus (GO:0006611)	centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(13)|skin(1)	23						CAGCAGGCCATGACTCTTGGG	0.592																																					p.M23V		Atlas-SNP	.											.	CCHCR1	68	.	0			c.A67G						.						46	55	52					6																	31125311		1313	2581	3894	SO:0001627	intron_variant	54535	exon1			AGGCCATGACTCT	AF216493	CCDS4695.1, CCDS43445.1, CCDS47397.1	6p21.3	2007-08-01	2005-02-15	2005-02-16	ENSG00000204536	ENSG00000204536			13930	protein-coding gene	gene with protein product		605310	"chromosome 6 open reading frame 18"	C6orf18		10888604, 10545595	Standard	NM_019052		Approved	HCR	uc003nsp.4	Q8TD31	OTTHUMG00000031112	ENST00000376266.5:c.51-445A>G	chr6.hg19:g.31125311T>C		133.0	0.0		97.0	4.0	NM_001105563	A2ABH6|E9PE84|Q2TB67|Q5SQ82|Q5STE9|Q9NRK8|Q9NWY9|Q9NXJ4|Q9NXK3|Q9Y6W1|Q9Y6W2	Missense_Mutation	SNP	ENST00000376266.5	hg19	CCDS4695.1	.	.	.	.	.	.	.	.	.	.	T	16.15	3.041853	0.55003	.	.	ENSG00000204536	ENST00000396268;ENST00000451521;ENST00000426967	T;T;T	0.25579	3.88;3.52;1.79	5.61	1.74	0.24563	.	.	.	.	.	T	0.03011	0.0089	N	0.08118	0	0.20074	N	0.999932	B;B	0.10296	0.002;0.003	B;B	0.13407	0.004;0.009	T	0.48127	-0.9062	9	0.13853	T	0.58	.	6.1112	0.20102	0.0:0.0854:0.3535:0.5611	.	23;23	E9PE84;Q8TD31-2	.;.	V	23	ENSP00000379566:M23V;ENSP00000401039:M23V;ENSP00000402432:M23V	ENSP00000379566:M23V	M	-	1	0	CCHCR1	31233290	0.963000	0.33076	0.965000	0.40720	0.939000	0.58152	0.404000	0.20999	0.050000	0.15949	0.523000	0.50628	ATG	.	.		0.592	CCHCR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076190.5	NM_019052		C	31125311	T	C	31125311	1	2	260	0	1	0	0	0	0	0	0	0	2879	1464	51	2		2	CCHCR1	6	31125311	Intron	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	41212	31125311	139989756	270	37515										
EHMT2	10919	hgsc.bcm.edu	37	chr6	31848833	31848833	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	taagaatcatcctctctcacAtcagcctcagcatcagagat	5	13	6	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:31848833A>G	ENST00000375537.4	-	26	3240	c.3234T>C	c.(3232-3234)gaT>gaC	p.D1078D	EHMT2_ENST00000375530.4_Silent_p.D1044D|SLC44A4_ENST00000465707.1_5'Flank|EHMT2_ENST00000395728.3_Silent_p.D1135D|SLC44A4_ENST00000229729.6_5'Flank|EHMT2_ENST00000375528.4_Silent_p.D1101D|EHMT2_ENST00000480912.1_5'UTR|SLC44A4_ENST00000375562.4_5'Flank|EHMT2-AS1_ENST00000434689.1_RNA	NM_006709.3	NP_006700.3	Q96KQ7	EHMT2_HUMAN	euchromatic histone-lysine N-methyltransferase 2	1078	Interaction with histone H3. {ECO:0000250}.|SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				DNA methylation (GO:0006306)|DNA methylation on cytosine within a CG sequence (GO:0010424)|fertilization (GO:0009566)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ growth (GO:0035265)|peptidyl-lysine dimethylation (GO:0018027)|regulation of DNA replication (GO:0006275)|spermatid development (GO:0007286)|synaptonemal complex assembly (GO:0007130)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)	21						CCTCTCTCACATCAGCCTCAG	0.557																																					p.D1078D		Atlas-SNP	.											.	EHMT2	45	.	0			c.T3234C						.						139	122	128					6																	31848833		1511	2709	4220	SO:0001819	synonymous_variant	10919	exon26			TCTCACATCAGCC	AF134726	CCDS4725.1, CCDS4726.1, CCDS75425.1	6p21.3	2013-01-10	2004-03-22	2005-06-09	ENSG00000204371	ENSG00000204371	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases", "Ankyrin repeat domain containing"	14129	protein-coding gene	gene with protein product		604599	"chromosome 6 open reading frame 30", "HLA-B associated transcript 8"	C6orf30, BAT8		8457211, 11316813	Standard	XM_005274833		Approved	G9A, Em:AF134726.3, NG36/G9a, KMT1C	uc003nxz.1	Q96KQ7	OTTHUMG00000031180	ENST00000375537.4:c.3234T>C	chr6.hg19:g.31848833A>G		118.0	0.0		90.0	4.0	NM_006709	B0UZY2|Q14349|Q5JP83|Q5JQ92|Q5JQA1|Q5JQG3|Q6PK06|Q96MH5|Q96QD0|Q9UQL8|Q9Y331	Silent	SNP	ENST00000375537.4	hg19	CCDS4725.1																																																																																			.	.		0.557	EHMT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076355.5	NM_006709		G	31848833	A	G	31848833	2	3	260	1	0	0	0	0	0	0	0	1	4986	214	8	2		2	EHMT2	6	31848833	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	723522	31848833	139266234	271	37516										
RXRB	6257	hgsc.bcm.edu	37	chr6	33162736	33162736	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tctcaccgtccctgctgctcAgggtacttctgtttgcagta	9	13	3	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:33162736A>G	ENST00000374680.3	-	9	1651	c.1440T>C	c.(1438-1440)ccT>ccC	p.P480P	RXRB_ENST00000544186.1_Silent_p.P294P|COL11A2_ENST00000374714.1_5'Flank|RXRB_ENST00000374685.4_Silent_p.P484P|COL11A2_ENST00000357486.1_5'Flank|COL11A2_ENST00000374713.1_5'Flank|COL11A2_ENST00000395194.1_5'Flank|COL11A2_ENST00000374712.1_5'Flank|COL11A2_ENST00000361917.1_5'Flank|COL11A2_ENST00000341947.2_5'Flank|COL11A2_ENST00000395197.1_5'Flank|COL11A2_ENST00000374708.4_5'Flank	NM_001270401.1|NM_021976.4	NP_001257330.1|NP_068811.1	P28702	RXRB_HUMAN	retinoid X receptor, beta	480	Ligand-binding. {ECO:0000250}.				cardiac muscle cell proliferation (GO:0060038)|cellular response to retinoic acid (GO:0071300)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|maternal placenta development (GO:0001893)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	9-cis retinoic acid receptor activity (GO:0004886)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(1)|skin(2)	15					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Tazarotene(DB00799)|Tretinoin(DB00755)	CCTGCTGCTCAGGGTACTTCT	0.607																																					p.P484P		Atlas-SNP	.											.	RXRB	34	.	0			c.T1452C						.						70	70	70					6																	33162736		1509	2709	4218	SO:0001819	synonymous_variant	6257	exon9			CTGCTCAGGGTAC	M84820	CCDS4768.1, CCDS59007.1	6p21.3	2013-01-16			ENSG00000204231	ENSG00000204231		"Nuclear hormone receptors"	10478	protein-coding gene	gene with protein product	"nuclear receptor subfamily 2 group B member 2"	180246				8257090	Standard	NM_021976		Approved	NR2B2, H-2RIIBP, RCoR-1	uc003odc.4	P28702	OTTHUMG00000031298	ENST00000374680.3:c.1440T>C	chr6.hg19:g.33162736A>G		294.0	0.0		171.0	8.0	NM_001270401	P28703|Q59G65|Q5JP92|Q5STQ1	Silent	SNP	ENST00000374680.3	hg19	CCDS4768.1																																																																																			.	.		0.607	RXRB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076642.2	NM_021976		G	33162736	A	G	33162736	2	3	260	1	0	0	0	0	0	0	0	1	13779	175	7	2		2	RXRB	6	33162736	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1313903	33162736	137952331	272	37517										
MAPK14	1432	hgsc.bcm.edu	37	chr6	36027094	36027094	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tctgttggacgtttttacacCtgcaaggtctctggaggaat	11	8	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:36027094C>T	ENST00000229794.4	+	3	663	c.275C>T	c.(274-276)cCt>cTt	p.P92L	MAPK14_ENST00000468133.1_Missense_Mutation_p.P15L|MAPK14_ENST00000310795.4_Missense_Mutation_p.P92L|MAPK14_ENST00000229795.3_Missense_Mutation_p.P92L	NM_139012.2|NM_139014.2	NP_620581.1|NP_620583.1	Q16539	MK14_HUMAN	mitogen-activated protein kinase 14	92	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cartilage condensation (GO:0001502)|cell morphogenesis (GO:0000902)|cell surface receptor signaling pathway (GO:0007166)|cellular component movement (GO:0006928)|cellular response to ionizing radiation (GO:0071479)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|chemotaxis (GO:0006935)|chondrocyte differentiation (GO:0002062)|DNA damage checkpoint (GO:0000077)|fatty acid oxidation (GO:0019395)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|mRNA metabolic process (GO:0016071)|muscle cell differentiation (GO:0042692)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|myoblast differentiation involved in skeletal muscle regeneration (GO:0014835)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|neurotrophin TRK receptor signaling pathway (GO:0048011)|osteoclast differentiation (GO:0030316)|p38MAPK cascade (GO:0038066)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of myoblast fusion (GO:1901741)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Ras protein signal transduction (GO:0007265)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to muramyl dipeptide (GO:0032495)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|signal transduction in response to DNA damage (GO:0042770)|skeletal muscle tissue development (GO:0007519)|stress-activated MAPK cascade (GO:0051403)|stress-induced premature senescence (GO:0090400)|striated muscle cell differentiation (GO:0051146)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|MAP kinase kinase activity (GO:0004708)|NFAT protein binding (GO:0051525)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|stomach(1)	16						GTTTTTACACCTGCAAGGTCT	0.338																																					p.P92L	Pancreas(20;8 363 26997 32430 36377 43317 49243 50560 51947)|Colon(176;951 1093 20177 30266 32328 34418 35271 44052 51610)	Atlas-SNP	.											.	MAPK14	75	.	0			c.C275T						.						156	150	152					6																	36027094		2203	4300	6503	SO:0001583	missense	1432	exon3			TTACACCTGCAAG	L35263	CCDS4815.1, CCDS4816.1, CCDS4817.1	6p21.3-p21.2	2011-06-09			ENSG00000112062	ENSG00000112062		"Mitogen-activated protein kinase cascade / Kinases"	6876	protein-coding gene	gene with protein product	"p38 MAP kinase"	600289		CSPB1, CSBP1, CSBP2		7997261	Standard	NM_139012		Approved	PRKM14, p38, Mxi2, PRKM15	uc003olq.3	Q16539	OTTHUMG00000159806	ENST00000229794.4:c.275C>T	chr6.hg19:g.36027094C>T	ENSP00000229794:p.Pro92Leu	162.0	0.0		86.0	4.0	NM_139012	A6ZJ92|A8K6P4|B0LPH0|B5TY32|O60776|Q13083|Q14084|Q8TDX0	Missense_Mutation	SNP	ENST00000229794.4	hg19	CCDS4816.1	.	.	.	.	.	.	.	.	.	.	C	32	5.185270	0.94885	.	.	ENSG00000112062	ENST00000229795;ENST00000229794;ENST00000468133;ENST00000310795;ENST00000472333	T;T;T;T;T	0.64991	-0.13;-0.13;-0.13;-0.13;-0.13	5.7	5.7	0.88788	Serine/threonine-protein kinase-like domain (1);MAP kinase, conserved site (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.70806	0.3266	L	0.52759	1.655	0.80722	D	1	D;D;D;D;D	0.89917	0.998;1.0;0.999;0.998;0.999	D;D;D;D;D	0.80764	0.973;0.994;0.963;0.981;0.989	T	0.72972	-0.4129	10	0.87932	D	0	.	17.6208	0.88080	0.0:1.0:0.0:0.0	.	92;92;92;92;92	B5TY32;Q16539-4;Q16539;Q16539-2;Q16539-3	.;.;MK14_HUMAN;.;.	L	92;92;15;92;15	ENSP00000229795:P92L;ENSP00000229794:P92L;ENSP00000419837:P15L;ENSP00000308669:P92L;ENSP00000419141:P15L	ENSP00000229794:P92L	P	+	2	0	MAPK14	36135072	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.386000	0.79775	2.704000	0.92352	0.650000	0.86243	CCT	.	.		0.338	MAPK14-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000357450.1	NM_001315		T	36027094	C	T	36027094	3	4	260	1	0	0	0	0	1	0	0	0	9285	681	24	3	285	3	MAPK14	6	36027094	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	2864358	36027094	135087973	273	37518										
PXT1	222659	hgsc.bcm.edu	37	chr6	36359651	36359651	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tctgccatcctgttgaagatCctatttgaaaaaagggagac	9	8	1	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:36359651C>T	ENST00000454782.2	-	5	784	c.301G>A	c.(301-303)Gat>Aat	p.D101N	RP1-50J22.4_ENST00000411643.1_RNA	NM_152990.3	NP_694535.2	Q8NFP0	PXT1_HUMAN	peroxisomal, testis specific 1	101					positive regulation of apoptotic process (GO:0043065)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|peroxisome (GO:0005777)											TGTTGAAGATCCTATTTGAAA	0.308																																					p.D101N		Atlas-SNP	.											PXT1,NS,malignant_melanoma,0,1	PXT1	6	.	0			c.G301A						.						81	82	82					6																	36359651		2203	4300	6503	SO:0001630	splice_region_variant	222659	exon5			GAAGATCCTATTT	AF486827	CCDS4820.2	6p21.31	2004-04-30			ENSG00000179165	ENSG00000179165			18312	protein-coding gene	gene with protein product							Standard	NM_152990		Approved	STEPP	uc003omd.2	Q8NFP0	OTTHUMG00000159815	ENST00000454782.2:c.301-1G>A	chr6.hg19:g.36359651C>T		57.0	1.0		35.0	2.0	NM_152990	J3KR74	Missense_Mutation	SNP	ENST00000454782.2	hg19	CCDS4820.2	.	.	.	.	.	.	.	.	.	.	C	9.083	0.999742	0.19121	.	.	ENSG00000179165	ENST00000454782;ENST00000538109	.	.	.	4.84	-1.34	0.09143	.	1.055970	0.07520	N	0.910443	T	0.10078	0.0247	.	.	.	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.32719	-0.9896	8	0.37606	T	0.19	1.4054	5.0904	0.14706	0.0:0.392:0.1566:0.4514	.	18	Q8NFP0	PXT1_HUMAN	N	101;18	.	ENSP00000419944:D101N	D	-	1	0	PXT1	36467629	0.007000	0.16637	0.010000	0.14722	0.037000	0.13140	-0.457000	0.06745	-0.412000	0.07519	0.655000	0.94253	GAT	.	.		0.308	PXT1-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000357516.2	NM_152990	Missense_Mutation	T	36359651	C	T	36359651	5	4	260	1	0	0	0	0	0	0	1	0	12868	869	30	3	107	3	PXT1	6	36359651	Splice_Site	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	332557	36359651	134755416	274	37519										
MTCH1	23787	hgsc.bcm.edu	37	chr6	36946282	36946282	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tggctttgtgtgggctcaccTtcttcatgctaccccgagtc	10	13	3	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:36946282T>C	ENST00000373627.5	-	3	636	c.512A>G	c.(511-513)aAg>aGg	p.K171R	MTCH1_ENST00000538808.1_Splice_Site_p.K15R|MTCH1_ENST00000373616.5_Splice_Site_p.K171R	NM_001271641.1	NP_001258570.1	Q9NZJ7	MTCH1_HUMAN	mitochondrial carrier 1	171					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|neuronal ion channel clustering (GO:0045161)|positive regulation of apoptotic process (GO:0043065)|regulation of signal transduction (GO:0009966)|transport (GO:0006810)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)				endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	6						TGGGCTCACCTTCTTCATGCT	0.587																																					p.K171R		Atlas-SNP	.											.	MTCH1	24	.	0			c.A512G						.						119	98	105					6																	36946282		2203	4300	6503	SO:0001630	splice_region_variant	23787	exon3			CTCACCTTCTTCA	AF151822	CCDS4828.1, CCDS64411.1	6p21.2	2013-05-22	2011-05-19		ENSG00000137409	ENSG00000137409		"Solute carriers"	17586	protein-coding gene	gene with protein product	"solute carrier family 25, member 49"	610449	"mitochondrial carrier homolog 1 (C. elegans)"			12377771	Standard	NM_014341		Approved	CGI-64, PSAP, SLC25A49	uc003ond.2	Q9NZJ7	OTTHUMG00000014614	ENST00000373627.5:c.513+1A>G	chr6.hg19:g.36946282T>C		123.0	0.0		100.0	4.0	NM_014341	A8KAX5|B2RCE3|Q6PK60|Q6UX45|Q7L465|Q9BW23|Q9NZR6|Q9UJZ5	Missense_Mutation	SNP	ENST00000373627.5	hg19		.	.	.	.	.	.	.	.	.	.	T	15.30	2.792815	0.50102	.	.	ENSG00000137409	ENST00000373616;ENST00000373627;ENST00000337855;ENST00000373550;ENST00000460219;ENST00000538808	T;T;T;T	0.63913	1.0;1.0;1.0;-0.07	5.71	5.71	0.89125	Mitochondrial carrier domain (2);	0.000000	0.64402	D	0.000012	T	0.31734	0.0806	N	0.17723	0.515	0.33307	D	0.565577	P;P;B;B	0.49090	0.779;0.919;0.267;0.27	B;B;B;B	0.39339	0.141;0.297;0.086;0.103	T	0.31081	-0.9956	10	0.35671	T	0.21	-3.9503	14.5397	0.67984	0.0:0.0:0.0:1.0	.	15;153;171;171	B4E0C5;Q8IW90;Q9NZJ7;Q9NZJ7-2	.;.;MTCH1_HUMAN;.	R	171;171;107;107;155;15	ENSP00000362718:K171R;ENSP00000362730:K171R;ENSP00000419739:K155R;ENSP00000437660:K15R	ENSP00000338712:K107R	K	-	2	0	MTCH1	37054260	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	4.281000	0.58965	2.179000	0.69175	0.533000	0.62120	AAG	.	.		0.587	MTCH1-008	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040396.1	NM_014341	Missense_Mutation	C	36946282	T	C	36946282	5	2	260	1	0	0	0	0	0	0	1	0	9922	1623	56	2	646	2	MTCH1	6	36946282	Splice_Site	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	586631	36946282	134168785	275	37520										
LRFN2	57497	hgsc.bcm.edu	37	chr6	40360061	40360061	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cctttctctgactcttgaggTccagggaggcgaaggccccc	12	14	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:40360061T>C	ENST00000338305.6	-	3	2533	c.1991A>G	c.(1990-1992)gAc>gGc	p.D664G		NM_020737.1	NP_065788.1	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III domain containing 2	664						cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	58	Ovarian(28;0.0418)|Colorectal(47;0.196)					ACTCTTGAGGTCCAGGGAGGC	0.721																																					p.D664G		Atlas-SNP	.											.	LRFN2	133	.	0			c.A1991G						.						10	12	11					6																	40360061		2174	4234	6408	SO:0001583	missense	57497	exon3			TTGAGGTCCAGGG	AB033072	CCDS34443.1	6p21.2-p21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000156564	ENSG00000156564		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	21226	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 2"	612808	"KIAA1246"	KIAA1246, SALM1		16495444, 16828986	Standard	NM_020737		Approved	FIGLER2	uc003oph.1	Q9ULH4	OTTHUMG00000014662	ENST00000338305.6:c.1991A>G	chr6.hg19:g.40360061T>C	ENSP00000345985:p.Asp664Gly	185.0	0.0		102.0	5.0	NM_020737	A5PKU3|Q5SYP9	Missense_Mutation	SNP	ENST00000338305.6	hg19	CCDS34443.1	.	.	.	.	.	.	.	.	.	.	T	14.06	2.421376	0.42918	.	.	ENSG00000156564	ENST00000338305	T	0.57107	0.42	4.78	4.78	0.61160	.	0.102946	0.64402	D	0.000003	T	0.18341	0.0440	N	0.14661	0.345	0.43637	D	0.996038	P	0.37781	0.608	B	0.32289	0.143	T	0.07731	-1.0757	10	0.29301	T	0.29	.	13.2662	0.60135	0.0:0.0:0.0:1.0	.	664	Q9ULH4	LRFN2_HUMAN	G	664	ENSP00000345985:D664G	ENSP00000345985:D664G	D	-	2	0	LRFN2	40468039	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	4.795000	0.62489	2.012000	0.59069	0.454000	0.30748	GAC	.	.		0.721	LRFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040488.1	XM_166372		C	40360061	T	C	40360061	3	2	260	1	0	0	0	0	1	0	0	0	8947	1667	58	2	382	2	LRFN2	6	40360061	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	3413779	40360061	130755006	276	37521										
TBCC	6903	hgsc.bcm.edu	37	chr6	42713354	42713354	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gggggatgccaggagccgcgTctactttggtagacgaagca	16	9	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:42713354T>C	ENST00000372876.1	-	1	480	c.458A>G	c.(457-459)gAc>gGc	p.D153G	TBCC_ENST00000244625.2_Missense_Mutation_p.D153G	NM_003192.2	NP_003183	Q15814	TBCC_HUMAN	tubulin folding cofactor C	153					'de novo' posttranslational protein folding (GO:0051084)|cell morphogenesis (GO:0000902)|cellular protein metabolic process (GO:0044267)|GTP catabolic process (GO:0006184)|post-chaperonin tubulin folding pathway (GO:0007023)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)	chaperone binding (GO:0051087)|GTPase activity (GO:0003924)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(3)	14	Colorectal(47;0.196)		all cancers(41;0.00122)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.125)			AGGAGCCGCGTCTACTTTGGT	0.652																																					p.D153G		Atlas-SNP	.											.	TBCC	31	.	0			c.A458G						.						14	16	15					6																	42713354		2197	4294	6491	SO:0001583	missense	6903	exon1			GCCGCGTCTACTT	U61234	CCDS4872.1	6p21.1	2008-02-05	2006-11-21		ENSG00000124659	ENSG00000124659			11580	protein-coding gene	gene with protein product		602971	"tubulin-specific chaperone c"			8706133, 11847227	Standard	NM_003192		Approved	CFC	uc003osl.3	Q15814	OTTHUMG00000014704	ENST00000372876.1:c.458A>G	chr6.hg19:g.42713354T>C	ENSP00000361967:p.Asp153Gly	91.0	0.0		94.0	4.0	NM_003192	Q53Y43|Q5T787	Missense_Mutation	SNP	ENST00000372876.1	hg19	CCDS4872.1	.	.	.	.	.	.	.	.	.	.	T	4.451	0.083524	0.08533	.	.	ENSG00000124659	ENST00000372876;ENST00000244625	T;T	0.76709	-1.04;-1.04	5.48	-4.26	0.03755	.	0.958455	0.08599	N	0.921836	T	0.37265	0.0997	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.23655	-1.0182	10	0.24483	T	0.36	-8.6114	7.6599	0.28396	0.0:0.2801:0.3922:0.3277	.	153	Q15814	TBCC_HUMAN	G	153	ENSP00000361967:D153G;ENSP00000244625:D153G	ENSP00000244625:D153G	D	-	2	0	TBCC	42821332	0.000000	0.05858	0.000000	0.03702	0.269000	0.26545	0.155000	0.16362	-0.369000	0.08028	-1.098000	0.02139	GAC	.	.		0.652	TBCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040559.1	NM_003192		C	42713354	T	C	42713354	3	2	260	1	0	0	0	0	1	0	0	0	15646	1667	58	2	586	2	TBCC	6	42713354	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	2353293	42713354	128401713	277	37522										
DLK2	65989	hgsc.bcm.edu	37	chr6	43419708	43419708	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cacagggtccagccttgcgcTcgcagtcacgcccatggaag	12	15	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:43419708T>C	ENST00000357338.3	-	5	1086	c.386A>G	c.(385-387)gAg>gGg	p.E129G	DLK2_ENST00000372485.1_Missense_Mutation_p.E123G|DLK2_ENST00000414245.1_Missense_Mutation_p.E123G|DLK2_ENST00000372488.3_Missense_Mutation_p.E129G	NM_206539.1	NP_996262.1	Q6UY11	DLK2_HUMAN	delta-like 2 homolog (Drosophila)	129	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				negative regulation of Notch signaling pathway (GO:0045746)|regulation of fat cell differentiation (GO:0045598)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	7	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			AGCCTTGCGCTCGCAGTCACG	0.597																																					p.E129G		Atlas-SNP	.											.	DLK2	22	.	0			c.A386G						.						114	81	92					6																	43419708		2203	4300	6503	SO:0001583	missense	65989	exon5			TTGCGCTCGCAGT	AK055380	CCDS4897.1, CCDS75461.1	6p21.1	2008-02-05	2007-07-05	2007-07-05	ENSG00000171462	ENSG00000171462			21113	protein-coding gene	gene with protein product			"EGF-like-domain, multiple 9"	EGFL9			Standard	NM_001286656		Approved	MGC2487	uc003ovb.3	Q6UY11	OTTHUMG00000014735	ENST00000357338.3:c.386A>G	chr6.hg19:g.43419708T>C	ENSP00000349893:p.Glu129Gly	83.0	0.0		49.0	4.0	NM_023932	B3KNZ7|Q5T3T8|Q9BQ54	Missense_Mutation	SNP	ENST00000357338.3	hg19	CCDS4897.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	21.5|21.5	4.163986|4.163986	0.78339|0.78339	.|.	.|.	ENSG00000171462|ENSG00000171462	ENST00000372485;ENST00000372488;ENST00000372496;ENST00000357338;ENST00000414245|ENST00000430324	D;D;D;D|.	0.87729|.	-2.29;-2.29;-2.29;-2.29|.	4.45|4.45	4.45|4.45	0.53987|0.53987	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);|.	0.069823|.	0.64402|.	D|.	0.000012|.	T|T	0.69611|0.69611	0.3130|0.3130	M|M	0.81802|0.81802	2.56|2.56	0.58432|0.58432	D|D	0.999995|0.999995	D|.	0.76494|.	0.999|.	D|.	0.63597|.	0.916|.	T|T	0.73116|0.73116	-0.4084|-0.4084	10|5	0.87932|.	D|.	0|.	.|.	14.1435|14.1435	0.65334|0.65334	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	129|.	Q6UY11|.	DLK2_HUMAN|.	G|G	123;129;129;129;123|35	ENSP00000361563:E123G;ENSP00000361566:E129G;ENSP00000349893:E129G;ENSP00000398906:E123G|.	ENSP00000349893:E129G|.	E|S	-|-	2|1	0|0	DLK2|DLK2	43527686|43527686	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.991000|0.991000	0.79684|0.79684	4.898000|4.898000	0.63238|0.63238	1.990000|1.990000	0.58119|0.58119	0.374000|0.374000	0.22700|0.22700	GAG|AGC	.	.		0.597	DLK2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040618.1	NM_023932		C	43419708	T	C	43419708	3	2	260	1	0	0	0	0	1	0	0	0	4567	1551	54	2	773	2	DLK2	6	43419708	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	706354	43419708	127695359	278	37523										
TDRD6	221400	hgsc.bcm.edu	37	chr6	46657993	46657993	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctggagaaggagagcagaaaGccaagagagagaataaaacc	13	6	0	5			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:46657993G>A	ENST00000316081.6	+	1	2128	c.2128G>A	c.(2128-2130)Gcc>Acc	p.A710T	RP11-446F17.3_ENST00000571590.1_RNA|RP11-446F17.3_ENST00000422284.2_RNA|TDRD6_ENST00000544460.1_Missense_Mutation_p.A710T|RP11-446F17.3_ENST00000434329.2_RNA	NM_001010870.2	NP_001010870.1	O60522	TDRD6_HUMAN	tudor domain containing 6	710					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|P granule (GO:0043186)				NS(1)|breast(9)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80			Lung(136;0.192)			AGAGCAGAAAGCCAAGAGAGA	0.413																																					p.A710T		Atlas-SNP	.											.	TDRD6	205	.	0			c.G2128A						.						40	41	40					6																	46657993		2203	4300	6503	SO:0001583	missense	221400	exon1			CAGAAAGCCAAGA	AF039442	CCDS34470.1, CCDS55017.1	6p12.3	2013-01-23			ENSG00000180113	ENSG00000180113		"Tudor domain containing"	21339	protein-coding gene	gene with protein product	"cancer/testis antigen 41.2", "spermatogenesis associated 36"	611200				9610721	Standard	NM_001010870		Approved	NY-CO-45, bA446F17.4, CT41.2, SPATA36	uc003oyj.3	O60522	OTTHUMG00000014788	ENST00000316081.6:c.2128G>A	chr6.hg19:g.46657993G>A	ENSP00000346065:p.Ala710Thr	272.0	0.0		197.0	60.0	NM_001168359	B3KWU2|F5H5M3|Q5HYB1|Q5VTS4|Q6ZMX5	Missense_Mutation	SNP	ENST00000316081.6	hg19	CCDS34470.1	.	.	.	.	.	.	.	.	.	.	G	13.40	2.226105	0.39300	.	.	ENSG00000180113	ENST00000544460;ENST00000316081	T;T	0.14516	2.5;2.5	5.85	1.51	0.23008	.	1.271800	0.04881	N	0.447652	T	0.02727	0.0082	L	0.44542	1.39	0.09310	N	1	B;B	0.16802	0.019;0.014	B;B	0.12156	0.007;0.004	T	0.40515	-0.9559	10	0.11794	T	0.64	-2.727	1.661	0.02792	0.2038:0.2613:0.3996:0.1354	.	710;710	F5H5M3;O60522	.;TDRD6_HUMAN	T	710	ENSP00000443299:A710T;ENSP00000346065:A710T	ENSP00000346065:A710T	A	+	1	0	TDRD6	46765952	0.000000	0.05858	0.020000	0.16555	0.676000	0.39594	0.398000	0.20899	0.275000	0.22094	0.655000	0.94253	GCC	.	.		0.413	TDRD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040800.1	XM_166443		A	46657993	G	A	46657993	3	1	260	1	0	0	0	0	1	0	0	0	15749	971	34	3	2130	3	TDRD6	6	46657993	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	3238285	46657993	124457074	279	37524										
RIMS1	22999	hgsc.bcm.edu	37	chr6	72968750	72968750	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	caaccagacaccatgatgccTcccgaagtccagttgatcat	7	14	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:72968750T>C	ENST00000521978.1	+	18	2989	c.2989T>C	c.(2989-2991)Tcc>Ccc	p.S997P	RIMS1_ENST00000401910.3_Missense_Mutation_p.S470P|RIMS1_ENST00000538414.1_5'UTR|RIMS1_ENST00000517960.1_Missense_Mutation_p.S996P|RIMS1_ENST00000518273.1_Missense_Mutation_p.S997P|RIMS1_ENST00000520567.1_Missense_Mutation_p.S996P|RIMS1_ENST00000491071.2_Missense_Mutation_p.S997P|RIMS1_ENST00000517827.1_Missense_Mutation_p.S456P|RIMS1_ENST00000522291.1_Missense_Mutation_p.S996P|RIMS1_ENST00000264839.7_Missense_Mutation_p.S997P|RIMS1_ENST00000523963.1_Missense_Mutation_p.S471P|RIMS1_ENST00000348717.5_Missense_Mutation_p.S996P|RIMS1_ENST00000425662.2_Missense_Mutation_p.S390P	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	997					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				CCATGATGCCTCCCGAAGTCC	0.358																																					p.S997P		Atlas-SNP	.											.	RIMS1	278	.	0			c.T2989C						.						131	131	131					6																	72968750		1933	4125	6058	SO:0001583	missense	22999	exon18			GATGCCTCCCGAA	AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"Rab3-interacting molecule"	606629	"RAB3 interacting protein 2"	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.2989T>C	chr6.hg19:g.72968750T>C	ENSP00000428417:p.Ser997Pro	138.0	0.0		80.0	4.0	NM_014989	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Missense_Mutation	SNP	ENST00000521978.1	hg19	CCDS47449.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.2|20.2	3.958303|3.958303	0.73902|0.73902	.|.	.|.	ENSG00000079841|ENSG00000079841	ENST00000517433|ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978;ENST00000401910;ENST00000523963;ENST00000425662;ENST00000453976;ENST00000517827;ENST00000370420	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.19105	.|2.44;2.47;2.55;2.47;2.57;2.57;2.52;2.53;2.6;2.54;2.6;2.28;2.58;2.17	5.41|5.41	5.41|5.41	0.78517|0.78517	.|.	.|0.000000	.|0.64402	.|D	.|0.000005	T|T	0.29355|0.29355	0.0731|0.0731	L|L	0.43152|0.43152	1.355|1.355	0.80722|0.80722	D|D	1|1	.|P;D;D;D;P;D;P;D;D;P;D;D	.|0.76494	.|0.932;0.967;0.999;0.979;0.612;0.962;0.793;0.996;0.987;0.937;0.999;0.997	.|B;D;D;P;B;P;B;P;D;P;D;P	.|0.79784	.|0.296;0.91;0.993;0.627;0.222;0.701;0.119;0.86;0.958;0.579;0.993;0.899	T|T	0.02698|0.02698	-1.1122|-1.1122	5|10	.|0.52906	.|T	.|0.07	-12.7919|-12.7919	15.7332|15.7332	0.77822|0.77822	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|456;471;997;456;470;996;249;997;996;250;997;997	.|B7Z3S3;E9PHF5;E9PHR1;B7Z9Z3;E9PF48;E7EX08;Q5JY22;E7ERQ1;E7ENC2;Q5JY21;C9JNW6;Q86UR5	.|.;.;.;.;.;.;.;.;.;.;.;RIMS1_HUMAN	P|P	570|997;997;997;996;997;996;997;996;997;996;996;997;470;471;390;390;456;222	.|ENSP00000430101:S997P;ENSP00000275037:S996P;ENSP00000264839:S997P;ENSP00000429959:S996P;ENSP00000430408:S997P;ENSP00000430502:S996P;ENSP00000430932:S996P;ENSP00000428417:S997P;ENSP00000385649:S470P;ENSP00000428328:S471P;ENSP00000411235:S390P;ENSP00000389503:S390P;ENSP00000428367:S456P;ENSP00000359448:S222P	.|ENSP00000264839:S997P	L|S	+|+	2|1	0|0	RIMS1|RIMS1	73025471|73025471	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.932000|0.932000	0.56968|0.56968	5.764000|5.764000	0.68826|0.68826	2.182000|2.182000	0.69389|0.69389	0.460000|0.460000	0.39030|0.39030	CTC|TCC	.	.		0.358	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1			C	72968750	T	C	72968750	3	2	260	1	0	0	0	0	1	0	0	0	13382	1551	54	2	3222	2	RIMS1	6	72968750	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	26310757	72968750	98146317	280	37525										
C6orf165	154313	hgsc.bcm.edu	37	chr6	88123541	88123541	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tttctagctttgtatgactcGgctattggatactaaaaatc	7	7	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:88123541G>T	ENST00000507897.1	+	4	289	c.206G>T	c.(205-207)cGg>cTg	p.R69L	C6ORF165_ENST00000369562.4_Missense_Mutation_p.R69L			Q8IYR0	CF165_HUMAN	chromosome 6 open reading frame 165	69										NS(1)|central_nervous_system(1)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0419)		TGTATGACTCGGCTATTGGAT	0.318																																					p.R69L		Atlas-SNP	.											C6orf165_ENST00000369562,caecum,carcinoma,0,2	C6orf165	116	.	0			c.G206T						.						84	82	83					6																	88123541		2203	4296	6499	SO:0001583	missense	154313	exon4			TGACTCGGCTATT	BC035083	CCDS34498.1	6q15	2012-02-07			ENSG00000213204	ENSG00000213204			21405	protein-coding gene	gene with protein product							Standard	NM_001031743		Approved	FLJ25974, dJ382I10.1	uc003plv.3	Q8IYR0	OTTHUMG00000015173	ENST00000507897.1:c.206G>T	chr6.hg19:g.88123541G>T	ENSP00000426769:p.Arg69Leu	135.0	1.0		102.0	5.0	NM_001031743	A8K969|E1P507|Q8N9U4	Missense_Mutation	SNP	ENST00000507897.1	hg19	CCDS34498.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.250606	0.80135	.	.	ENSG00000213204	ENST00000369562;ENST00000480123	T;T	0.34072	1.38;1.39	5.44	4.56	0.56223	.	0.052025	0.85682	D	0.000000	T	0.47728	0.1461	M	0.73319	2.225	0.51233	D	0.99991	D;D	0.76494	0.999;0.976	D;P	0.65874	0.939;0.703	T	0.41305	-0.9516	10	0.42905	T	0.14	.	14.2545	0.66043	0.0741:0.0:0.9259:0.0	.	69;69	Q8IYR0;E1P509	CF165_HUMAN;.	L	69	ENSP00000358575:R69L;ENSP00000422494:R69L	ENSP00000358575:R69L	R	+	2	0	C6orf165	88180260	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.718000	0.61930	2.544000	0.85801	0.484000	0.47621	CGG	.	.		0.318	C6orf165-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000470406.1	NM_178823		T	88123541	G	T	88123541	3	4	260	1	0	0	0	0	1	0	0	0	2343	1116	39	1	216	1	C6orf165	6	88123541	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	15154791	88123541	82991526	281	37526										
CNR1	1268	hgsc.bcm.edu	37	chr6	88854629	88854629	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aggtgcccagcgtgagggacAggactgcaatggccagctgc	16	11	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:88854629A>G	ENST00000537554.1	-	2	3927	c.365T>C	c.(364-366)cTg>cCg	p.L122P	CNR1_ENST00000535130.1_Missense_Mutation_p.L122P|CNR1_ENST00000549716.1_Missense_Mutation_p.L61P|CNR1_ENST00000549890.1_Missense_Mutation_p.L122P|CNR1_ENST00000369501.2_Missense_Mutation_p.L122P|CNR1_ENST00000362094.5_3'UTR|CNR1_ENST00000428600.2_Missense_Mutation_p.L122P|CNR1_ENST00000468898.1_Missense_Mutation_p.L89P|CNR1_ENST00000369499.2_Missense_Mutation_p.L122P	NM_001160226.1|NM_001160258.1	NP_001153698.1|NP_001153730.1	P21554	CNR1_HUMAN	cannabinoid receptor 1 (brain)	122					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|aging (GO:0007568)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose homeostasis (GO:0042593)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|negative regulation of action potential (GO:0045759)|negative regulation of blood pressure (GO:0045776)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of mast cell activation (GO:0033004)|negative regulation of nitric-oxide synthase activity (GO:0051001)|positive regulation of acute inflammatory response to antigenic stimulus (GO:0002866)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood pressure (GO:0045777)|positive regulation of fever generation (GO:0031622)|positive regulation of neuron projection development (GO:0010976)|regulation of feeding behavior (GO:0060259)|regulation of insulin secretion (GO:0050796)|regulation of penile erection (GO:0060405)|regulation of synaptic transmission, GABAergic (GO:0032228)|regulation of synaptic transmission, glutamatergic (GO:0051966)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to morphine (GO:0043278)|response to nicotine (GO:0035094)|response to nutrient (GO:0007584)|sensory perception of pain (GO:0019233)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)|drug binding (GO:0008144)			breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|prostate(1)|skin(10)|urinary_tract(1)	37		all_cancers(76;8.24e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;4.11e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.00011)		BRCA - Breast invasive adenocarcinoma(108;0.15)	Dronabinol(DB00470)|Nabilone(DB00486)|Rimonabant(DB06155)	CGTGAGGGACAGGACTGCAAT	0.582																																					p.L122P		Atlas-SNP	.											.	CNR1	91	.	0			c.T365C						.						60	53	55					6																	88854629		2203	4300	6503	SO:0001583	missense	1268	exon4			AGGGACAGGACTG	AF107262	CCDS5015.1, CCDS5016.1, CCDS5016.2	6q14-q15	2012-08-08			ENSG00000118432	ENSG00000118432		"GPCR / Class A : Cannabinoid receptors"	2159	protein-coding gene	gene with protein product		114610		CNR			Standard	NM_016083		Approved	CB1K5, CB-R, CB1, CANN6, CB1A	uc003pmq.4	P21554	OTTHUMG00000015184	ENST00000537554.1:c.365T>C	chr6.hg19:g.88854629A>G	ENSP00000441046:p.Leu122Pro	107.0	0.0		73.0	5.0	NM_001160258	B2R9T4|E1P512|Q13949|Q495Z0|Q4PLI4|Q4VBM6|Q5JVL5|Q5UB37|Q9UNN0	Missense_Mutation	SNP	ENST00000537554.1	hg19	CCDS5015.1	.	.	.	.	.	.	.	.	.	.	A	17.84	3.487157	0.63962	.	.	ENSG00000118432	ENST00000369501;ENST00000535130;ENST00000537554;ENST00000369499;ENST00000549890;ENST00000468898;ENST00000428600;ENST00000549716	T;T;T;T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92;0.92;0.92;0.92	5.77	5.77	0.91146	.	0.067648	0.64402	D	0.000014	T	0.55513	0.1925	M	0.67397	2.05	0.80722	D	1	D;D	0.89917	0.997;1.0	D;D	0.70487	0.925;0.969	T	0.61153	-0.7120	10	0.87932	D	0	.	16.1022	0.81184	1.0:0.0:0.0:0.0	.	89;122	P21554-3;P21554	.;CNR1_HUMAN	P	122;122;122;122;122;89;122;61	ENSP00000358513:L122P;ENSP00000442689:L122P;ENSP00000441046:L122P;ENSP00000358511:L122P;ENSP00000446819:L122P;ENSP00000420188:L89P;ENSP00000412192:L122P;ENSP00000449549:L61P	ENSP00000358511:L122P	L	-	2	0	CNR1	88911348	1.000000	0.71417	0.996000	0.52242	0.956000	0.61745	9.339000	0.96797	2.205000	0.71048	0.460000	0.39030	CTG	.	.		0.582	CNR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354204.2			G	88854629	A	G	88854629	3	3	260	1	0	0	0	0	1	0	0	0	3633	188	7	2	1057	2	CNR1	6	88854629	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	731088	88854629	82260438	282	37527										
MDN1	23195	hgsc.bcm.edu	37	chr6	90438701	90438701	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtatttcctgaagcctttgcTaatgctcccaccaaacttgt	6	12	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:90438701T>C	ENST00000369393.3	-	36	5413	c.5298A>G	c.(5296-5298)ttA>ttG	p.L1766L	MDN1_ENST00000428876.1_Silent_p.L1766L			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	1766					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		AAGCCTTTGCTAATGCTCCCA	0.458																																					p.L1766L		Atlas-SNP	.											.	MDN1	478	.	0			c.A5298G						.						121	111	115					6																	90438701		2203	4300	6503	SO:0001819	synonymous_variant	23195	exon36			CTTTGCTAATGCT	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.5298A>G	chr6.hg19:g.90438701T>C		170.0	0.0		99.0	4.0	NM_014611	O15019|Q5T794	Silent	SNP	ENST00000369393.3	hg19	CCDS5024.1																																																																																			.	.		0.458	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			C	90438701	T	C	90438701	2	2	260	1	0	0	0	0	0	0	0	1	9424	1519	53	2		2	MDN1	6	90438701	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1584072	90438701	80676366	283	37528										
NR2E1	7101	hgsc.bcm.edu	37	chr6	108497813	108497813	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gccgccgcgcactttccctcGgcggcgctccctgcgccggc	13	21	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:108497813G>A	ENST00000368986.4	+	4	1074	c.366G>A	c.(364-366)tcG>tcA	p.S122S	NR2E1_ENST00000484978.1_3'UTR|NR2E1_ENST00000368983.3_Silent_p.S159S	NM_003269.3	NP_003260.1	Q9Y466	NR2E1_HUMAN	nuclear receptor subfamily 2, group E, member 1	122					aggressive behavior (GO:0002118)|amygdala development (GO:0021764)|anterior commissure morphogenesis (GO:0021960)|behavioral fear response (GO:0001662)|cell fate commitment (GO:0045165)|cerebral cortex neuron differentiation (GO:0021895)|dentate gyrus development (GO:0021542)|extracellular matrix organization (GO:0030198)|forebrain generation of neurons (GO:0021872)|gene expression (GO:0010467)|glial cell migration (GO:0008347)|layer formation in cerebral cortex (GO:0021819)|long-term synaptic potentiation (GO:0060291)|negative regulation of apoptotic process (GO:0043066)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron differentiation (GO:0045665)|nervous system development (GO:0007399)|olfactory bulb development (GO:0021772)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle (GO:0045787)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of stem cell proliferation (GO:2000648)|regulation of cell migration involved in sprouting angiogenesis (GO:0090049)|regulation of dendrite morphogenesis (GO:0048814)|regulation of timing of neuron differentiation (GO:0060164)|retina development in camera-type eye (GO:0060041)|social behavior (GO:0035176)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|visual perception (GO:0007601)	nucleoplasm (GO:0005654)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.S122S(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(4)|liver(1)|lung(16)|prostate(1)|skin(3)	30		all_cancers(87;8.13e-05)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00866)|Colorectal(196;0.0637)		BRCA - Breast invasive adenocarcinoma(108;0.013)|Epithelial(106;0.0521)|all cancers(137;0.068)|OV - Ovarian serous cystadenocarcinoma(136;0.0689)		ACTTTCCCTCGGCGGCGCTCC	0.711																																					p.S122S		Atlas-SNP	.											NR2E1,NS,carcinoma,+1,1	NR2E1	57	.	1	Substitution - coding silent(1)	lung(1)	c.G366A						.						21	22	22					6																	108497813		2201	4297	6498	SO:0001819	synonymous_variant	7101	exon4			TCCCTCGGCGGCG	Y13276	CCDS5063.1, CCDS69165.1	6q21	2013-01-16			ENSG00000112333	ENSG00000112333		"Nuclear hormone receptors"	7973	protein-coding gene	gene with protein product		603849		TLX		9628820	Standard	NM_003269		Approved	TLL, XTLL	uc003psg.3	Q9Y466	OTTHUMG00000015319	ENST00000368986.4:c.366G>A	chr6.hg19:g.108497813G>A		91.0	0.0		52.0	3.0	NM_003269	Q6ZMP8	Silent	SNP	ENST00000368986.4	hg19	CCDS5063.1																																																																																			.	.		0.711	NR2E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041712.2			A	108497813	G	A	108497813	2	1	260	1	0	0	0	0	0	0	0	1	10634	1103	39	1		1	NR2E1	6	108497813	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	18059112	108497813	62617254	284	37529										
AKD1	221264	hgsc.bcm.edu	37	chr6	109837261	109837261	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	atggaaattattggtatcaaAtacctctcaagttcatcctg	6	8	3	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:109837261A>G	ENST00000424296.2	-	31	3940	c.3864T>C	c.(3862-3864)taT>taC	p.Y1288Y		NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9	1288					ADP phosphorylation (GO:0006757)|AMP phosphorylation (GO:0006756)|CDP phosphorylation (GO:0061508)|CMP phosphorylation (GO:0061566)|dADP phosphorylation (GO:0006174)|dAMP phosphorylation (GO:0061565)|dCDP phosphorylation (GO:0061570)|dCMP phosphorylation (GO:0061567)|dGDP phosphorylation (GO:0006186)|GDP phosphorylation (GO:0061568)|TDP phosphorylation (GO:0061571)|UDP phosphorylation (GO:0061569)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside phosphate kinase activity (GO:0050145)										TTGGTATCAAATACCTCTCAA	0.348																																					p.Y1288Y		Atlas-SNP	.											.	AKD1	223	.	0			c.T3864C						.						172	144	153					6																	109837261		692	1591	2283	SO:0001819	synonymous_variant	221264	exon31			TATCAAATACCTC	AK131244, BC146443, BC087860	CCDS5077.1, CCDS55048.1	6q21	2013-04-29	2013-04-29	2013-04-29			2.7.4.3		33814	protein-coding gene	gene with protein product		615358	"chromosome 6 open reading frame 224", "adenylate kinase domain containing 2", "chromosome 6 open reading frame 199", "adenylate kinase domain containing 1"	C6orf224, AKD2, C6orf199, AKD1		23416111	Standard	NM_145025		Approved	FLJ42177, FLJ25791, dJ70A9.1, MGC26954		Q5TCS8		ENST00000424296.2:c.3864T>C	chr6.hg19:g.109837261A>G		184.0	0.0		95.0	4.0	NM_001145128	A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	Silent	SNP	ENST00000424296.2	hg19	CCDS55048.1	.	.	.	.	.	.	.	.	.	.	A	0.010	-1.781282	0.00634	.	.	ENSG00000155085	ENST00000470564	.	.	.	5.94	2.17	0.27698	.	.	.	.	.	T	0.08802	0.0218	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.24657	-1.0154	4	.	.	.	.	1.7344	0.02938	0.5603:0.1056:0.1555:0.1787	.	.	.	.	T	126	.	.	I	-	2	0	AKD1	109943954	0.000000	0.05858	0.035000	0.18076	0.043000	0.13939	0.009000	0.13219	1.081000	0.41110	0.528000	0.53228	ATT	.	.		0.348	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001145128		G	109837261	A	G	109837261	2	3	260	1	0	0	0	0	0	0	0	1	460	108	4	2		2	AKD1	6	109837261	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1339448	109837261	61277806	285	37530										
REV3L	5980	hgsc.bcm.edu	37	chr6	111697828	111697828	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cacttgtgtgtttacactgaAaggtaatcttagcagaagat	9	6	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:111697828A>G	ENST00000358835.3	-	14	2184	c.1730T>C	c.(1729-1731)tTt>tCt	p.F577S	REV3L_ENST00000368802.3_Missense_Mutation_p.F577S|REV3L_ENST00000368805.1_Missense_Mutation_p.F577S|REV3L_ENST00000435970.1_Missense_Mutation_p.F499S			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	577					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		TTTACACTGAAAGGTAATCTT	0.373								DNA polymerases (catalytic subunits)																													p.F577S		Atlas-SNP	.											.	REV3L	386	.	0			c.T1730C						.						116	115	115					6																	111697828		2203	4300	6503	SO:0001583	missense	5980	exon13			CACTGAAAGGTAA	AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"DNA polymerases"	9968	protein-coding gene	gene with protein product	"polymerase, DNA, zeta"	602776	"REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta", "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.1730T>C	chr6.hg19:g.111697828A>G	ENSP00000351697:p.Phe577Ser	96.0	0.0		67.0	4.0	NM_002912	O43214|Q5TC33	Missense_Mutation	SNP	ENST00000358835.3	hg19	CCDS5091.2	.	.	.	.	.	.	.	.	.	.	A	17.00	3.276735	0.59758	.	.	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970	T;T;T;T	0.01527	4.89;4.89;4.89;4.8	5.38	5.38	0.77491	Ribonuclease H-like (1);	0.432027	0.24377	N	0.039055	T	0.02156	0.0067	L	0.27053	0.805	0.39486	D	0.967969	D	0.71674	0.998	P	0.59115	0.852	T	0.66540	-0.5898	10	0.52906	T	0.07	-11.9442	15.3959	0.74794	1.0:0.0:0.0:0.0	.	577	O60673	DPOLZ_HUMAN	S	577;577;577;499	ENSP00000357792:F577S;ENSP00000357795:F577S;ENSP00000351697:F577S;ENSP00000402003:F499S	ENSP00000351697:F577S	F	-	2	0	REV3L	111804521	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.005000	0.63972	2.035000	0.60131	0.460000	0.39030	TTT	.	.		0.373	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		G	111697828	A	G	111697828	3	3	260	1	0	0	0	0	1	0	0	0	13255	14	1	2	7742	2	REV3L	6	111697828	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1860567	111697828	59417239	286	37531										
DSE	29940	hgsc.bcm.edu	37	chr6	116757735	116757735	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccacatacctgtggacaggtGaggccacaggacagtctgcc	12	13	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:116757735G>T	ENST00000331677.3	+	7	2548	c.2104G>T	c.(2104-2106)Gag>Tag	p.E702*	DSE_ENST00000359564.2_Nonsense_Mutation_p.E702*|DSE_ENST00000537543.1_Nonsense_Mutation_p.E721*|DSE_ENST00000452085.3_Nonsense_Mutation_p.E702*			Q9UL01	DSE_HUMAN	dermatan sulfate epimerase	702					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin-glucuronate 5-epimerase activity (GO:0047757)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35		all_cancers(87;0.00019)|all_epithelial(87;0.000416)|Ovarian(999;0.133)|Colorectal(196;0.234)		Epithelial(106;0.00915)|OV - Ovarian serous cystadenocarcinoma(136;0.0149)|GBM - Glioblastoma multiforme(226;0.0189)|all cancers(137;0.0262)		GTGGACAGGTGAGGCCACAGG	0.502																																					p.E702X		Atlas-SNP	.											.	DSE	98	.	0			c.G2104T						.						109	105	106					6																	116757735		2203	4300	6503	SO:0001587	stop_gained	29940	exon6			ACAGGTGAGGCCA	AF098066	CCDS5107.1	6q22	2008-02-05	2007-01-29	2007-01-29	ENSG00000111817	ENSG00000111817	5.1.3.19		21144	protein-coding gene	gene with protein product		605942	"squamous cell carcinoma antigen recognized by T cells 2"	SART2		11920522, 16505484	Standard	NM_001080976		Approved	DSEPI	uc003pws.3	Q9UL01	OTTHUMG00000015434	ENST00000331677.3:c.2104G>T	chr6.hg19:g.116757735G>T	ENSP00000332151:p.Glu702*	56.0	0.0		60.0	4.0	NM_001080976	Q5R3K6	Nonsense_Mutation	SNP	ENST00000331677.3	hg19	CCDS5107.1	.	.	.	.	.	.	.	.	.	.	G	36	5.652632	0.96724	.	.	ENSG00000111817	ENST00000452085;ENST00000537543;ENST00000331677;ENST00000359564	.	.	.	6.06	6.06	0.98353	.	0.096044	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-15.7715	20.6397	0.99537	0.0:0.0:1.0:0.0	.	.	.	.	X	702;721;702;702	.	ENSP00000332151:E702X	E	+	1	0	DSE	116864428	1.000000	0.71417	0.423000	0.26634	0.466000	0.32739	7.512000	0.81728	2.880000	0.98712	0.650000	0.86243	GAG	.	.		0.502	DSE-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041940.2	NM_013352		T	116757735	G	T	116757735	4	4	260	1	0	0	0	0	0	1	0	0	4776	1291	45	3	2122	3	DSE	6	116757735	Nonsense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	5059907	116757735	54357332	287	37532										
GPRC6A	222545	hgsc.bcm.edu	37	chr6	117114093	117114093	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agtaaagctcactccaaacaTtgtctgcctggttttacatg	7	10	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:117114093T>C	ENST00000310357.3	-	6	2014	c.1993A>G	c.(1993-1995)Atg>Gtg	p.M665V	GPRC6A_ENST00000368549.3_Missense_Mutation_p.M594V|GPRC6A_ENST00000530250.1_Missense_Mutation_p.M490V	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	665					calcium-mediated signaling (GO:0019722)|response to amino acid (GO:0043200)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|liver(1)|lung(24)|ovary(5)|pancreas(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)	65		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		ACTCCAAACATTGTCTGCCTG	0.403																																					p.M665V		Atlas-SNP	.											.	GPRC6A	152	.	0			c.A1993G						.						112	100	104					6																	117114093		2203	4300	6503	SO:0001583	missense	222545	exon6			CAAACATTGTCTG	AF502962	CCDS5112.1, CCDS69184.1, CCDS69185.1	6q22.31	2014-01-30	2014-01-30		ENSG00000173612	ENSG00000173612		"GPCR / Class C : Calcium-sensing receptors"	18510	protein-coding gene	gene with protein product			"G protein-coupled receptor, family C, group 6, member A"				Standard	NM_001286354		Approved	bA86F4.3	uc003pxj.1	Q5T6X5	OTTHUMG00000015447	ENST00000310357.3:c.1993A>G	chr6.hg19:g.117114093T>C	ENSP00000309493:p.Met665Val	159.0	0.0		90.0	5.0	NM_148963	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Missense_Mutation	SNP	ENST00000310357.3	hg19	CCDS5112.1	.	.	.	.	.	.	.	.	.	.	t	0.458	-0.890368	0.02491	.	.	ENSG00000173612	ENST00000310357;ENST00000368549;ENST00000530250	D;D;D	0.87103	-2.21;-2.21;-2.21	4.61	1.78	0.24846	GPCR, family 3, C-terminal (2);	0.314743	0.22687	N	0.056865	T	0.38054	0.1026	N	0.01003	-1.06	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.49716	-0.8910	10	0.16420	T	0.52	.	6.639	0.22899	0.0719:0.1283:0.666:0.1339	.	594;490;665	Q5T6X5-3;Q5T6X5-2;Q5T6X5	.;.;GPC6A_HUMAN	V	665;594;490	ENSP00000309493:M665V;ENSP00000357537:M594V;ENSP00000433465:M490V	ENSP00000309493:M665V	M	-	1	0	GPRC6A	117220786	0.000000	0.05858	0.001000	0.08648	0.170000	0.22686	-0.181000	0.09740	0.166000	0.19597	-0.194000	0.12790	ATG	.	.		0.403	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2			C	117114093	T	C	117114093	3	2	260	1	0	0	0	0	1	0	0	0	6737	1493	52	2	791	2	GPRC6A	6	117114093	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	356358	117114093	54000974	288	37533										
RFX6	222546	hgsc.bcm.edu	37	chr6	117198575	117198575	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctatccggaagaaacagtgtAcctggcggccgaagggcagc	14	11	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:117198575A>G	ENST00000332958.2	+	1	153	c.137A>G	c.(136-138)tAc>tGc	p.Y46C		NM_173560.3	NP_775831.2	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	46					endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|pancreatic A cell differentiation (GO:0003310)|pancreatic D cell differentiation (GO:0003311)|pancreatic epsilon cell differentiation (GO:0090104)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of insulin secretion (GO:0050796)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell differentiation (GO:0003309)	nucleus (GO:0005634)	transcription regulatory region DNA binding (GO:0044212)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(29)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	59						GAAACAGTGTACCTGGCGGCC	0.672																																					p.Y46C		Atlas-SNP	.											.	RFX6	141	.	0			c.A137G						.						16	19	18					6																	117198575		2196	4297	6493	SO:0001583	missense	222546	exon1			CAGTGTACCTGGC	BC039248	CCDS5113.1	6q22.31	2008-08-04	2008-08-04	2008-08-04	ENSG00000185002	ENSG00000185002			21478	protein-coding gene	gene with protein product		612659	"regulatory factor X domain containing 1"	RFXDC1			Standard	NM_173560		Approved	MGC33442, dJ955L16.1	uc003pxm.3	Q8HWS3	OTTHUMG00000015449	ENST00000332958.2:c.137A>G	chr6.hg19:g.117198575A>G	ENSP00000332208:p.Tyr46Cys	147.0	0.0		79.0	4.0	NM_173560	Q5T6B3	Missense_Mutation	SNP	ENST00000332958.2	hg19	CCDS5113.1	.	.	.	.	.	.	.	.	.	.	A	12.02	1.813381	0.32053	.	.	ENSG00000185002	ENST00000332958	T	0.56103	0.48	4.27	1.74	0.24563	.	6.084050	0.00166	N	0.000000	T	0.18593	0.0446	N	0.19112	0.55	0.31081	N	0.711958	P	0.40000	0.698	B	0.33295	0.161	T	0.01165	-1.1431	10	0.51188	T	0.08	-5.8337	8.3661	0.32387	0.6029:0.3971:0.0:0.0	.	46	Q8HWS3	RFX6_HUMAN	C	46	ENSP00000332208:Y46C	ENSP00000332208:Y46C	Y	+	2	0	RFX6	117305268	0.935000	0.31712	0.851000	0.33527	0.029000	0.11900	0.705000	0.25675	0.381000	0.24851	-0.435000	0.05868	TAC	.	.		0.672	RFX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041970.2	NM_173560		G	117198575	A	G	117198575	3	3	260	1	0	0	0	0	1	0	0	0	13282	391	14	2	139	2	RFX6	6	117198575	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	84482	117198575	53916492	289	37534										
RNF146	81847	hgsc.bcm.edu	37	chr6	127608496	127608496	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agcacttctctggaagactcTtttgctcatttacaactcag	6	11	4	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:127608496T>C	ENST00000368314.1	+	3	1162	c.738T>C	c.(736-738)tcT>tcC	p.S246S	RNF146_ENST00000356799.2_3'UTR|ECHDC1_ENST00000488087.1_5'Flank|RNF146_ENST00000309649.3_Silent_p.S245S|RNF146_ENST00000610153.1_Silent_p.S246S|RNF146_ENST00000608991.1_Silent_p.S245S	NM_001242850.1|NM_001242851.1	NP_001229779.1|NP_001229780.1	Q9NTX7	RN146_HUMAN	ring finger protein 146	246					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein autoubiquitination (GO:0051865)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly-ADP-D-ribose binding (GO:0072572)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	10				GBM - Glioblastoma multiforme(226;0.0407)|all cancers(137;0.2)		TGGAAGACTCTTTTGCTCATT	0.483																																					p.S246S		Atlas-SNP	.											.	RNF146	31	.	0			c.T738C						.						113	110	111					6																	127608496		2203	4300	6503	SO:0001819	synonymous_variant	81847	exon3			AGACTCTTTTGCT	AK027558	CCDS5136.1, CCDS56449.1	6q22.1-q22.33	2008-02-05			ENSG00000118518	ENSG00000118518		"RING-type (C3HC4) zinc fingers"	21336	protein-coding gene	gene with protein product		612137					Standard	NM_001242844		Approved	DKFZp434O1427, dactylidin, dJ351K20.1	uc021zes.1	Q9NTX7	OTTHUMG00000015522	ENST00000368314.1:c.738T>C	chr6.hg19:g.127608496T>C		142.0	0.0		91.0	4.0	NM_001242850	E1P572|Q6FIB2|Q7L8H4|Q96K03|Q96T06|Q9NTX6	Silent	SNP	ENST00000368314.1	hg19	CCDS56449.1																																																																																			.	.		0.483	RNF146-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042112.1	NM_030963		C	127608496	T	C	127608496	2	2	260	1	0	0	0	0	0	0	0	1	13463	1596	56	2		2	RNF146	6	127608496	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	10409921	127608496	43506571	290	37535										
ARHGAP18	93663	hgsc.bcm.edu	37	chr6	129937450	129937450	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acgcaaaaaagaccagaatcTgcaagaaaaaaaatgaaatt	6	6	1	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:129937450T>C	ENST00000368149.2	-	7	1041		c.e7-2			NM_033515.2	NP_277050.2			Rho GTPase activating protein 18											NS(2)|endometrium(1)|large_intestine(4)|lung(4)|ovary(2)|prostate(2)|skin(3)	18				OV - Ovarian serous cystadenocarcinoma(136;0.0621)|GBM - Glioblastoma multiforme(226;0.0638)|all cancers(137;0.074)		GACCAGAATCTGCAAGAAAAA	0.323																																					.		Atlas-SNP	.											.	ARHGAP18	52	.	0			c.953-2A>G						.						71	65	67					6																	129937450		2203	4300	6503	SO:0001630	splice_region_variant	93663	exon8			AGAATCTGCAAGA	AB053293	CCDS34535.1	6q23.1	2011-06-29			ENSG00000146376	ENSG00000146376		"Rho GTPase activating proteins"	21035	protein-coding gene	gene with protein product		613351					Standard	NM_033515		Approved	MacGAP, bA307O14.2	uc003qbr.3	Q8N392	OTTHUMG00000015547	ENST00000368149.2:c.953-2A>G	chr6.hg19:g.129937450T>C		167.0	0.0		86.0	4.0	NM_033515		Splice_Site	SNP	ENST00000368149.2	hg19	CCDS34535.1	.	.	.	.	.	.	.	.	.	.	T	19.56	3.849916	0.71603	.	.	ENSG00000146376	ENST00000368149;ENST00000275189	.	.	.	5.6	5.6	0.85130	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0773	0.80976	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	ARHGAP18	129979143	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	7.151000	0.77411	2.254000	0.74563	0.482000	0.46254	.	.	.		0.323	ARHGAP18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042185.2	NM_033515	Intron	C	129937450	T	C	129937450	5	2	260	1	0	0	0	0	0	0	1	0	868	1594	55	2	1076	2	ARHGAP18	6	129937450	Splice_Site	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	2328954	129937450	41177617	291	37536										
TMEM200A	114801	hgsc.bcm.edu	37	chr6	130762627	130762627	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggaataattccattggggagTcgttgtcgagtcagtacaag	13	6	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:130762627T>C	ENST00000296978.3	+	3	1931	c.1060T>C	c.(1060-1062)Tcg>Ccg	p.S354P	TMEM200A_ENST00000545622.1_Missense_Mutation_p.S354P|TMEM200A_ENST00000392429.1_Missense_Mutation_p.S354P	NM_001258276.1|NM_001258277.1|NM_001258278.1	NP_001245205.1|NP_001245206.1|NP_001245207.1	Q86VY9	T200A_HUMAN	transmembrane protein 200A	354						integral component of membrane (GO:0016021)				NS(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(30)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52				GBM - Glioblastoma multiforme(226;0.0139)|OV - Ovarian serous cystadenocarcinoma(155;0.12)		CATTGGGGAGTCGTTGTCGAG	0.517																																					p.S354P		Atlas-SNP	.											.	TMEM200A	108	.	0			c.T1060C						.						86	84	85					6																	130762627		2203	4300	6503	SO:0001583	missense	114801	exon3			GGGGAGTCGTTGT	AB067500	CCDS5140.1	6q23.1	2009-09-04	2007-12-18	2007-12-18	ENSG00000164484	ENSG00000164484			21075	protein-coding gene	gene with protein product			"KIAA1913"	KIAA1913		15722956	Standard	NM_001258276		Approved	TTMC	uc010kfh.4	Q86VY9	OTTHUMG00000015557	ENST00000296978.3:c.1060T>C	chr6.hg19:g.130762627T>C	ENSP00000296978:p.Ser354Pro	191.0	0.0		148.0	6.0	NM_001258277	Q96PX5	Missense_Mutation	SNP	ENST00000296978.3	hg19	CCDS5140.1	.	.	.	.	.	.	.	.	.	.	T	6.999	0.554483	0.13374	.	.	ENSG00000164484	ENST00000296978;ENST00000545622;ENST00000392429	.	.	.	5.93	4.74	0.60224	.	0.129722	0.53938	D	0.000057	T	0.16041	0.0386	N	0.19112	0.55	0.45139	D	0.99815	B	0.06786	0.001	B	0.06405	0.002	T	0.10222	-1.0639	9	0.40728	T	0.16	-8.4043	3.5456	0.07827	0.142:0.0714:0.1315:0.6551	.	354	Q86VY9	T200A_HUMAN	P	354	.	ENSP00000296978:S354P	S	+	1	0	TMEM200A	130804320	1.000000	0.71417	0.968000	0.41197	0.093000	0.18481	2.444000	0.44890	1.029000	0.39812	0.533000	0.62120	TCG	.	.		0.517	TMEM200A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042201.1	NM_052913		C	130762627	T	C	130762627	3	2	260	1	0	0	0	0	1	0	0	0	16138	1667	58	2	1062	2	TMEM200A	6	130762627	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	825177	130762627	40352440	292	37537										
EYA4	2070	hgsc.bcm.edu	37	chr6	133767825	133767825	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cttgttggaggtggtgatacTccaggtagctccaaactgga	13	8	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:133767825T>C	ENST00000367895.5	+	4	605	c.141T>C	c.(139-141)acT>acC	p.T47T	EYA4_ENST00000431403.2_Silent_p.T47T|EYA4_ENST00000525849.1_Silent_p.T47T|EYA4_ENST00000430974.2_Silent_p.T47T|EYA4_ENST00000355167.3_Silent_p.T47T|EYA4_ENST00000355286.6_Silent_p.T47T|EYA4_ENST00000531901.1_Silent_p.T47T|EYA4_ENST00000452339.2_Silent_p.T47T	NM_004100.4	NP_004091.3	O95677	EYA4_HUMAN	EYA transcriptional coactivator and phosphatase 4	47					anatomical structure morphogenesis (GO:0009653)|chromatin modification (GO:0016568)|DNA repair (GO:0006281)|inner ear development (GO:0048839)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|skin(1)	48	Colorectal(23;0.221)			GBM - Glioblastoma multiforme(68;0.00457)|OV - Ovarian serous cystadenocarcinoma(155;0.0152)		GTGGTGATACTCCAGGTAGCT	0.448																																					p.T47T	Melanoma(57;398 1237 3528 4702 7415)	Atlas-SNP	.											EYA4_ENST00000355167,right_lower_lobe,carcinoma,0,2	EYA4	196	.	0			c.T141C						.						119	112	115					6																	133767825		2203	4300	6503	SO:0001819	synonymous_variant	2070	exon4			TGATACTCCAGGT	Y17114	CCDS5165.1, CCDS5166.1, CCDS43506.1, CCDS75521.1, CCDS75523.1	6q23	2014-09-17	2014-06-19		ENSG00000112319	ENSG00000112319		"Protein tyrosine phosphatases / Asp-based PTPs"	3522	protein-coding gene	gene with protein product		603550	"eyes absent (Drosophila) homolog 4", "eyes absent homolog 4 (Drosophila)"	DFNA10, CMD1J		9887327, 11159937	Standard	NM_004100		Approved		uc003qed.4	O95677	OTTHUMG00000015602	ENST00000367895.5:c.141T>C	chr6.hg19:g.133767825T>C		115.0	0.0		93.0	4.0	NM_172105	B7Z7F7|O95464|O95679|Q8IW39|Q9NTR7	Silent	SNP	ENST00000367895.5	hg19	CCDS5165.1																																																																																			.	.		0.448	EYA4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042282.2	NM_004100		C	133767825	T	C	133767825	2	2	260	1	0	0	0	0	0	0	0	1	5333	1538	54	2		2	EYA4	6	133767825	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	3005198	133767825	37347242	293	37538										
MYB	4602	hgsc.bcm.edu	37	chr6	135516923	135516923	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cagctaccccgggtggcacaGcaccaccattgccgaccaca	9	18	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:135516923G>A	ENST00000367814.4	+	9	1172	c.986G>A	c.(985-987)aGc>aAc	p.S329N	MYB_ENST00000528774.1_Missense_Mutation_p.S326N|MYB_ENST00000316528.8_Missense_Mutation_p.S329N|MYB_ENST00000525369.1_Intron|MYB_ENST00000442647.2_Missense_Mutation_p.S326N|MYB_ENST00000533624.1_Missense_Mutation_p.S294N|MYB-AS1_ENST00000455534.1_RNA|MYB_ENST00000341911.5_Missense_Mutation_p.S329N|MYB_ENST00000534121.1_Missense_Mutation_p.S329N|MYB_ENST00000531845.1_3'UTR|MYB_ENST00000527615.1_Missense_Mutation_p.S329N|MYB_ENST00000534044.1_Missense_Mutation_p.S329N	NM_001161659.1|NM_005375.2	NP_001155131.1|NP_005366.2	P10242	MYB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog	329	Negative regulatory domain. {ECO:0000250}.				B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|chromatin remodeling (GO:0006338)|embryonic digestive tract development (GO:0048566)|G1/S transition of mitotic cell cycle (GO:0000082)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 methylation (GO:0051574)|positive regulation of T-helper cell differentiation (GO:0045624)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|thymus development (GO:0048538)	nuclear matrix (GO:0016363)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(4)|endometrium(1)|kidney(2)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	all_epithelial(2;0.109)|Breast(56;0.158)|Colorectal(23;0.221)	Lung NSC(302;3.08e-05)|Ovarian(999;0.208)		OV - Ovarian serous cystadenocarcinoma(155;0.0079)|GBM - Glioblastoma multiforme(68;0.0117)		GGGTGGCACAGCACCACCATT	0.547			T	NFIB	adenoid cystic carcinoma																																p.S329N		Atlas-SNP	.		Dom	yes		6	6q22-23	4602	v-myb myeloblastosis viral oncogene homolog		E	.	MYB	137	.	0			c.G986A						.						150	128	135					6																	135516923		2203	4300	6503	SO:0001583	missense	4602	exon9			GGCACAGCACCAC		CCDS5174.1, CCDS47481.1, CCDS47482.1, CCDS55058.1, CCDS55059.1, CCDS55060.1, CCDS55061.1, CCDS55062.1	6q22-q23	2013-07-09	2013-07-09		ENSG00000118513	ENSG00000118513			7545	protein-coding gene	gene with protein product		189990				17599807	Standard	NM_001130172		Approved	c-myb	uc003qfh.3	P10242	OTTHUMG00000015629	ENST00000367814.4:c.986G>A	chr6.hg19:g.135516923G>A	ENSP00000356788:p.Ser329Asn	120.0	0.0		77.0	4.0	NM_001161659	E9PI07|E9PLZ5|E9PNA4|E9PNL6|E9PRS2|P78391|P78392|P78525|P78526|Q14023|Q14024|Q708E4|Q708E7|Q9UE83	Missense_Mutation	SNP	ENST00000367814.4	hg19	CCDS5174.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.346859	0.82022	.	.	ENSG00000118513	ENST00000341911;ENST00000442647;ENST00000316528;ENST00000237302;ENST00000367814;ENST00000527615;ENST00000528774;ENST00000534121;ENST00000534044;ENST00000533624	T;T;T;T;T;T;T;T;T	0.33438	2.66;2.17;2.17;2.18;1.41;2.65;2.61;1.84;2.04	5.7	5.7	0.88788	.	0.074599	0.85682	D	0.000000	T	0.36744	0.0978	L	0.27053	0.805	0.58432	D	0.999998	D;D;D;D;D;D;P;D	0.71674	0.993;0.993;0.996;0.99;0.996;0.998;0.885;0.995	P;D;D;P;P;D;P;P	0.79784	0.777;0.968;0.986;0.841;0.882;0.993;0.521;0.876	T	0.15435	-1.0437	10	0.49607	T	0.09	-11.0642	19.8289	0.96627	0.0:0.0:1.0:0.0	.	294;329;326;326;329;329;329;329	E9PI07;E9PLZ5;P10242-2;E9PNL6;E9PNA4;P10242-4;P10242;Q708E1	.;.;.;.;.;.;MYB_HUMAN;.	N	329;326;329;329;329;329;326;329;329;294	ENSP00000339992:S329N;ENSP00000410825:S326N;ENSP00000326328:S329N;ENSP00000356788:S329N;ENSP00000433227:S329N;ENSP00000434723:S326N;ENSP00000432851:S329N;ENSP00000435055:S329N;ENSP00000436605:S294N	ENSP00000237302:S329N	S	+	2	0	MYB	135558616	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.352000	0.90075	2.692000	0.91855	0.467000	0.42956	AGC	.	.		0.547	MYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042347.4			A	135516923	G	A	135516923	3	1	260	1	0	0	0	0	1	0	0	0	10016	971	34	3	1020	3	MYB	6	135516923	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	1749098	135516923	35598144	294	37539										
KIAA1244	57221	hgsc.bcm.edu	37	chr6	138655204	138655204	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aagagtttgtcaaaggccccTctcctggagaggaaaagacg	12	9	2	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:138655204T>C	ENST00000251691.4	+	33	5387	c.5221T>C	c.(5221-5223)Tct>Cct	p.S1741P		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		CAAAGGCCCCTCTCCTGGAGA	0.473																																					p.S1741P		Atlas-SNP	.											.	KIAA1244	236	.	0			c.T5221C						.						55	57	57					6																	138655204		2203	4300	6503	SO:0001583	missense	57221	exon33			GGCCCCTCTCCTG	AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	21213	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 33"		"chromosome 6 open reading frame 92"	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.5221T>C	chr6.hg19:g.138655204T>C	ENSP00000251691:p.Ser1741Pro	115.0	0.0		70.0	4.0	NM_020340		Missense_Mutation	SNP	ENST00000251691.4	hg19	CCDS5189.2	.	.	.	.	.	.	.	.	.	.	T	14.67	2.603435	0.46423	.	.	ENSG00000112379	ENST00000251691	T	0.19806	2.12	5.02	5.02	0.67125	.	0.643026	0.14731	N	0.301742	T	0.08935	0.0221	N	0.19112	0.55	0.38069	D	0.936325	P	0.37864	0.61	B	0.38803	0.282	T	0.12451	-1.0547	10	0.52906	T	0.07	-22.5281	14.7414	0.69458	0.0:0.0:0.0:1.0	.	1741	Q5TH69	BIG3_HUMAN	P	1741	ENSP00000251691:S1741P	ENSP00000251691:S1741P	S	+	1	0	KIAA1244	138696897	0.999000	0.42202	0.998000	0.56505	0.993000	0.82548	4.530000	0.60595	1.896000	0.54893	0.338000	0.21704	TCT	.	.		0.473	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340		C	138655204	T	C	138655204	3	2	260	1	0	0	0	0	1	0	0	0	8226	1551	54	2	5351	2	KIAA1244	6	138655204	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	3138281	138655204	32459863	295	37540										
TXLNB	167838	hgsc.bcm.edu	37	chr6	139564133	139564133	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtcagcactctcctgagaacTgcctatttcgggttgggttt	11	10	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:139564133T>A	ENST00000358430.3	-	10	1817	c.1585A>T	c.(1585-1587)Agt>Tgt	p.S529C	RP1-225E12.3_ENST00000585874.1_RNA	NM_153235.3	NP_694967.3	Q8N3L3	TXLNB_HUMAN	taxilin beta	529						cytoplasm (GO:0005737)				breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37				OV - Ovarian serous cystadenocarcinoma(155;0.000185)|GBM - Glioblastoma multiforme(68;0.000235)		TCCTGAGAACTGCCTATTTCG	0.547																																					p.S529C		Atlas-SNP	.											.	TXLNB	96	.	0			c.A1585T						.						98	106	103					6																	139564133		2203	4300	6503	SO:0001583	missense	167838	exon10			GAGAACTGCCTAT		CCDS34545.1	6q23.3	2008-02-05	2005-07-29	2005-07-29	ENSG00000164440	ENSG00000164440			21617	protein-coding gene	gene with protein product		611438	"chromosome 6 open reading frame 198"	C6orf198		15184072	Standard	NM_153235		Approved	DKFZp451A175, MDP77, dJ522B19.2	uc021zfy.1	Q8N3L3	OTTHUMG00000015688	ENST00000358430.3:c.1585A>T	chr6.hg19:g.139564133T>A	ENSP00000351206:p.Ser529Cys	267.0	0.0		174.0	47.0	NM_153235	Q5VTF3|Q76L25|Q86T52|Q8N3S2	Missense_Mutation	SNP	ENST00000358430.3	hg19	CCDS34545.1	.	.	.	.	.	.	.	.	.	.	T	11.08	1.533093	0.27387	.	.	ENSG00000164440	ENST00000358430	T	0.16196	2.36	5.54	-0.719	0.11201	.	1.398390	0.04259	N	0.339998	T	0.03220	0.0094	L	0.27053	0.805	0.09310	N	1	B	0.18013	0.025	B	0.12837	0.008	T	0.40365	-0.9567	9	.	.	.	-0.2153	4.6013	0.12354	0.1467:0.3669:0.0:0.4865	.	529	Q8N3L3	TXLNB_HUMAN	C	529	ENSP00000351206:S529C	.	S	-	1	0	TXLNB	139605826	0.000000	0.05858	0.001000	0.08648	0.032000	0.12392	-0.408000	0.07169	0.082000	0.17018	0.460000	0.39030	AGT	.	.		0.547	TXLNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042458.1	NM_153235		A	139564133	T	A	139564133	3	1	260	1	0	0	0	0	1	0	0	0	16803	1580	55	4	473	4	TXLNB	6	139564133	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	908929	139564133	31550934	296	37541										
GPR126	57211	hgsc.bcm.edu	37	chr6	142764487	142764487	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cttgcagacagtgcttccatGgacaagtccttgtcaaaact	8	11	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:142764487G>A	ENST00000230173.6	+	26	4110	c.3634G>A	c.(3634-3636)Gga>Aga	p.G1212R	GPR126_ENST00000367609.3_Missense_Mutation_p.M1196I|GPR126_ENST00000367608.2_Missense_Mutation_p.M1168I|GPR126_ENST00000296932.8_Missense_Mutation_p.G1184R	NM_020455.5	NP_065188	Q86SQ4	GP126_HUMAN	G protein-coupled receptor 126	1212					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(12)|lung(10)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)		GTGCTTCCATGGACAAGTCCT	0.443																																					p.G1212R		Atlas-SNP	.											.	GPR126	192	.	0			c.G3634A						.						193	184	187					6																	142764487		1959	4157	6116	SO:0001583	missense	57211	exon26			TTCCATGGACAAG	AK027843	CCDS47489.1, CCDS47490.1, CCDS47491.1, CCDS55064.1	6q23.1-q24.3	2014-08-08			ENSG00000112414	ENSG00000112414		"-", "GPCR / Class B : Orphans"	13841	protein-coding gene	gene with protein product		612243				12565841	Standard	NM_001032395		Approved	FLJ14937	uc010khe.3	Q86SQ4	OTTHUMG00000015709	ENST00000230173.6:c.3634G>A	chr6.hg19:g.142764487G>A	ENSP00000230173:p.Gly1212Arg	105.0	0.0		82.0	4.0	NM_020455	Q5TGN7|Q6DHZ4|Q6F3F5|Q6F3F6|Q6F3F7|Q6F3F8|Q6MZU7|Q8IXA4|Q8NC14|Q96JW0	Missense_Mutation	SNP	ENST00000230173.6	hg19	CCDS47490.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.41|10.41	1.343525|1.343525	0.24339|0.24339	.|.	.|.	ENSG00000112414|ENSG00000112414	ENST00000230173;ENST00000296932|ENST00000367608;ENST00000367609	T;T|T;T	0.23950|0.22945	1.88;1.88|1.94;1.93	6.07|6.07	4.29|4.29	0.51040|0.51040	.|.	.|0.402565	.|0.24312	.|N	.|0.039625	T|T	0.03305|0.03305	0.0096|0.0096	N|N	0.08118|0.08118	0|0	0.20307|0.20307	N|N	0.999916|0.999916	B;B|B;B;B	0.23249|0.12013	0.082;0.049|0.002;0.005;0.005	B;B|B;B;B	0.17433|0.11329	0.018;0.012|0.001;0.006;0.006	T|T	0.40308|0.40308	-0.9570|-0.9570	9|10	0.45353|0.21540	T|T	0.12|0.41	.|.	5.0134|5.0134	0.14324|0.14324	0.0709:0.1122:0.5039:0.3129|0.0709:0.1122:0.5039:0.3129	.|.	1184;1212|256;1168;1196	Q86SQ4-2;Q86SQ4|B4DSK4;Q86SQ4-4;Q86SQ4-3	.;GP126_HUMAN|.;.;.	R|I	1212;1184|1168;1196	ENSP00000230173:G1212R;ENSP00000296932:G1184R|ENSP00000356580:M1168I;ENSP00000356581:M1196I	ENSP00000230173:G1212R|ENSP00000356580:M1168I	G|M	+|+	1|3	0|0	GPR126|GPR126	142806180|142806180	1.000000|1.000000	0.71417|0.71417	0.943000|0.943000	0.38184|0.38184	0.819000|0.819000	0.46315|0.46315	2.368000|2.368000	0.44222|0.44222	0.888000|0.888000	0.36160|0.36160	0.655000|0.655000	0.94253|0.94253	GGA|ATG	.	.		0.443	GPR126-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042487.2			A	142764487	G	A	142764487	3	1	260	1	0	0	0	0	1	0	0	0	6648	1349	47	3	3736	3	GPR126	6	142764487	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	3200354	142764487	28350580	297	37542										
HIVEP2	3097	hgsc.bcm.edu	37	chr6	143094773	143094773	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctgacagtcttagtgcaagtTtctgtttgactgtgtgcgaa	11	7	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:143094773T>C	ENST00000367604.1	-	4	1742	c.1103A>G	c.(1102-1104)aAa>aGa	p.K368R	HIVEP2_ENST00000012134.2_Missense_Mutation_p.K368R|HIVEP2_ENST00000367603.2_Missense_Mutation_p.K368R			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	368					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		TAGTGCAAGTTTCTGTTTGAC	0.423																																					p.K368R	Esophageal Squamous(107;843 1510 13293 16805 42198)	Atlas-SNP	.											.	HIVEP2	225	.	0			c.A1103G						.						158	154	155					6																	143094773		1931	4144	6075	SO:0001583	missense	3097	exon5			GCAAGTTTCTGTT	M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"Zinc fingers, C2H2-type"	4921	protein-coding gene	gene with protein product	"c-myc intron binding protein 1"	143054	"human immunodeficiency virus type I enhancer-binding protein 2"			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.1103A>G	chr6.hg19:g.143094773T>C	ENSP00000356576:p.Lys368Arg	201.0	0.0		115.0	6.0	NM_006734	Q02646|Q5THT5|Q9NS05	Missense_Mutation	SNP	ENST00000367604.1	hg19	CCDS43510.1	.	.	.	.	.	.	.	.	.	.	T	10.39	1.336682	0.24253	.	.	ENSG00000010818	ENST00000367604;ENST00000367603;ENST00000012134	T;T;T	0.35236	1.32;1.32;1.32	5.62	4.46	0.54185	.	0.050794	0.85682	D	0.000000	T	0.07052	0.0179	N	0.12182	0.205	0.30826	N	0.737199	B	0.09022	0.002	B	0.06405	0.002	T	0.22800	-1.0206	10	0.19147	T	0.46	-16.1119	7.1394	0.25548	0.0:0.1622:0.0:0.8378	.	368	P31629	ZEP2_HUMAN	R	368	ENSP00000356576:K368R;ENSP00000356575:K368R;ENSP00000012134:K368R	ENSP00000012134:K368R	K	-	2	0	HIVEP2	143136466	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.614000	0.46359	2.276000	0.75962	0.529000	0.55759	AAA	.	.		0.423	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042495.1			C	143094773	T	C	143094773	3	2	260	1	0	0	0	0	1	0	0	0	7196	1841	64	2	6261	2	HIVEP2	6	143094773	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	330286	143094773	28020294	298	37543										
UTRN	7402	hgsc.bcm.edu	37	chr6	144801076	144801076	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttggagcgggattttgagtaCaagtcaccagaagagcttga	13	6	1	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:144801076C>T	ENST00000367545.3	+	25	3465	c.3465C>T	c.(3463-3465)taC>taT	p.Y1155Y		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	1155					aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		ATTTTGAGTACAAGTCACCAG	0.507																																					p.Y1155Y		Atlas-SNP	.											.	UTRN	327	.	0			c.C3465T						.						119	118	118					6																	144801076		2203	4300	6503	SO:0001819	synonymous_variant	7402	exon25			TGAGTACAAGTCA	AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"utrophin (homologous to dystrophin)"	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.3465C>T	chr6.hg19:g.144801076C>T		129.0	0.0		97.0	4.0	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Silent	SNP	ENST00000367545.3	hg19	CCDS34547.1																																																																																			.	.		0.507	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1			T	144801076	C	T	144801076	2	4	260	1	0	0	0	0	0	0	0	1	17118	489	17	3		3	UTRN	6	144801076	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	1706303	144801076	26313991	299	37544										
GRM1	2911	hgsc.bcm.edu	37	chr6	146755356	146755356	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gcagaggagacccccctcttCctggccgaaccagccctccc	9	20	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:146755356C>T	ENST00000282753.1	+	8	3244	c.3009C>T	c.(3007-3009)ttC>ttT	p.F1003F	GRM1_ENST00000355289.4_3'UTR|GRM1_ENST00000392299.2_3'UTR|GRM1_ENST00000361719.2_Silent_p.F1003F|GRM1_ENST00000492807.2_3'UTR|GRM1_ENST00000507907.1_3'UTR			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	1003					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		CCCCCCTCTTCCTGGCCGAAC	0.682																																					p.F1003F		Atlas-SNP	.											.	GRM1	419	.	0			c.C3009T						.						55	65	62					6																	146755356		2203	4300	6503	SO:0001819	synonymous_variant	2911	exon9			CCTCTTCCTGGCC	U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4593	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 85"	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	ENST00000282753.1:c.3009C>T	chr6.hg19:g.146755356C>T		148.0	0.0		83.0	4.0	NM_000838	B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Silent	SNP	ENST00000282753.1	hg19	CCDS5209.1																																																																																			.	.		0.682	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838		T	146755356	C	T	146755356	2	4	260	1	0	0	0	0	0	0	0	1	6805	854	30	3		3	GRM1	6	146755356	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	1954280	146755356	24359711	300	37545										
C6orf211	79624	hgsc.bcm.edu	37	chr6	151789989	151789989	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgacttatatgctgaactacAgaaggcacatttaattttat	6	6	0	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:151789989A>G	ENST00000367294.3	+	5	1329	c.1070A>G	c.(1069-1071)cAg>cGg	p.Q357R	C6orf211_ENST00000545879.1_Missense_Mutation_p.Q238R	NM_024573.1	NP_078849.1	Q9H993	CF211_HUMAN	chromosome 6 open reading frame 211	357										breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(7)	15			BRCA - Breast invasive adenocarcinoma(37;0.183)	OV - Ovarian serous cystadenocarcinoma(155;5.27e-11)		GCTGAACTACAGAAGGCACAT	0.388																																					p.Q357R		Atlas-SNP	.											.	C6orf211	30	.	0			c.A1070G						.						96	97	97					6																	151789989		2203	4300	6503	SO:0001583	missense	79624	exon5			AACTACAGAAGGC	AJ420548	CCDS5233.1, CCDS69224.1	6q25.1	2013-01-07			ENSG00000146476	ENSG00000146476			17872	protein-coding gene	gene with protein product							Standard	NM_001286562		Approved	FLJ12910	uc003qok.1	Q9H993	OTTHUMG00000015838	ENST00000367294.3:c.1070A>G	chr6.hg19:g.151789989A>G	ENSP00000356263:p.Gln357Arg	130.0	0.0		79.0	4.0	NM_024573	Q96FC6|Q9UFY5	Missense_Mutation	SNP	ENST00000367294.3	hg19	CCDS5233.1	.	.	.	.	.	.	.	.	.	.	A	27.2	4.810184	0.90707	.	.	ENSG00000146476	ENST00000367294;ENST00000545879	T;T	0.06849	3.25;3.25	6.16	6.16	0.99307	Domain of unknown function DUF89 (2);	0.000000	0.85682	D	0.000000	T	0.08313	0.0207	M	0.61703	1.905	0.80722	D	1	B	0.29270	0.24	B	0.38921	0.285	T	0.15435	-1.0437	10	0.27785	T	0.31	.	16.8061	0.85666	1.0:0.0:0.0:0.0	.	357	Q9H993	CF211_HUMAN	R	357;238	ENSP00000356263:Q357R;ENSP00000444121:Q238R	ENSP00000356263:Q357R	Q	+	2	0	C6orf211	151831682	1.000000	0.71417	0.936000	0.37596	0.991000	0.79684	9.248000	0.95456	2.367000	0.80283	0.528000	0.53228	CAG	.	.		0.388	C6orf211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042724.1	NM_024573		G	151789989	A	G	151789989	3	3	260	1	0	0	0	0	1	0	0	0	2356	188	7	2	1088	2	C6orf211	6	151789989	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	5034633	151789989	19325078	301	37546										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152660387	152660387	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttttcttaccgtttgctctgTttgttgaatgtcttttgctg	8	7	3	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:152660387T>C	ENST00000367255.5	-	75	12941	c.12340A>G	c.(12340-12342)Aca>Gca	p.T4114A	SYNE1_ENST00000265368.4_Missense_Mutation_p.T4114A|SYNE1_ENST00000423061.1_Missense_Mutation_p.T4043A|SYNE1_ENST00000448038.1_Missense_Mutation_p.T4043A|SYNE1_ENST00000341594.5_Missense_Mutation_p.T3979A	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	4114					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GTTTGCTCTGTTTGTTGAATG	0.373										HNSCC(10;0.0054)																											p.T4114A		Atlas-SNP	.											.	SYNE1	3227	.	0			c.A12340G						.						134	127	129					6																	152660387		2203	4300	6503	SO:0001583	missense	23345	exon75			GCTCTGTTTGTTG	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.12340A>G	chr6.hg19:g.152660387T>C	ENSP00000356224:p.Thr4114Ala	136.0	0.0		83.0	4.0	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	T	13.54	2.269136	0.40095	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.35048	1.33;1.33;1.33;1.33;1.33	5.84	5.84	0.93424	.	0.000000	0.64402	D	0.000004	T	0.24851	0.0603	L	0.60455	1.87	0.80722	D	1	P;P;P;P	0.48230	0.495;0.495;0.495;0.907	B;B;B;P	0.48334	0.122;0.122;0.122;0.574	T	0.21484	-1.0244	10	0.02654	T	1	.	16.2169	0.82237	0.0:0.0:0.0:1.0	.	4114;4114;4114;4043	B7ZBC3;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	A	4114;4043;4114;4043;3979	ENSP00000356224:T4114A;ENSP00000396024:T4043A;ENSP00000265368:T4114A;ENSP00000390975:T4043A;ENSP00000341887:T3979A	ENSP00000265368:T4114A	T	-	1	0	SYNE1	152702080	1.000000	0.71417	1.000000	0.80357	0.714000	0.41099	3.093000	0.50217	2.223000	0.72356	0.533000	0.62120	ACA	.	.		0.373	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		C	152660387	T	C	152660387	3	2	260	1	0	0	0	0	1	0	0	0	15460	1725	60	2	14414	2	SYNE1	6	152660387	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	870398	152660387	18454680	302	37547										
CNKSR3	154043	hgsc.bcm.edu	37	chr6	154762454	154762454	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctgtagtggtcaggtccaagCaaagctggataattttgttc	11	7	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:154762454C>T	ENST00000607772.1	-	4	1023	c.479G>A	c.(478-480)tGc>tAc	p.C160Y	CNKSR3_ENST00000479339.1_Missense_Mutation_p.C80Y	NM_173515.2	NP_775786.2	Q6P9H4	CNKR3_HUMAN	CNKSR family member 3	160	CRIC. {ECO:0000255|PROSITE- ProRule:PRU00621}.				negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)	cytoplasm (GO:0005737)|membrane (GO:0016020)				breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)|stomach(1)|urinary_tract(1)	15		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;5.03e-11)|BRCA - Breast invasive adenocarcinoma(81;0.00627)		CAGGTCCAAGCAAAGCTGGAT	0.383																																					p.C160Y		Atlas-SNP	.											.	CNKSR3	56	.	0			c.G479A						.						122	121	122					6																	154762454		2203	4300	6503	SO:0001583	missense	154043	exon4			TCCAAGCAAAGCT	AK055911	CCDS5246.1	6q25.2	2013-01-10	2005-04-11	2005-04-11	ENSG00000153721	ENSG00000153721		"Sterile alpha motif (SAM) domain containing"	23034	protein-coding gene	gene with protein product			"membrane associated guanylate kinase interacting protein-like 1"	MAGI1			Standard	NM_173515		Approved	FLJ31349		Q6P9H4	OTTHUMG00000015873	ENST00000607772.1:c.479G>A	chr6.hg19:g.154762454C>T	ENSP00000475915:p.Cys160Tyr	123.0	0.0		87.0	4.0	NM_173515	Q5SGD5|Q96N65	Missense_Mutation	SNP	ENST00000607772.1	hg19	CCDS5246.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.867628	0.91587	.	.	ENSG00000153721	ENST00000367213;ENST00000479339	T;T	0.57436	1.08;0.4	5.91	5.91	0.95273	CRIC domain (1);CRIC domain, Chordata (1);	0.000000	0.85682	D	0.000000	T	0.71719	0.3373	M	0.78456	2.415	0.58432	D	0.999997	D	0.89917	1.0	D	0.91635	0.999	T	0.73477	-0.3970	10	0.87932	D	0	.	20.2982	0.98569	0.0:1.0:0.0:0.0	.	160	Q6P9H4	CNKR3_HUMAN	Y	160;80	ENSP00000356182:C160Y;ENSP00000418975:C80Y	ENSP00000356182:C160Y	C	-	2	0	CNKSR3	154804146	1.000000	0.71417	0.995000	0.50966	0.990000	0.78478	7.474000	0.81024	2.803000	0.96430	0.655000	0.94253	TGC	.	.		0.383	CNKSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042792.2	NM_173515		T	154762454	C	T	154762454	3	4	260	1	0	0	0	0	1	0	0	0	3610	710	25	3	1228	3	CNKSR3	6	154762454	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	2102067	154762454	16352613	303	37548										
ACAT2	39	hgsc.bcm.edu	37	chr6	160197213	160197213	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gttaaaacagatgagtttccTcgccatgggagcaacataga	10	8	0	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:160197213T>C	ENST00000367048.4	+	6	2426	c.666T>C	c.(664-666)ccT>ccC	p.P222P	ACAT2_ENST00000541436.1_Silent_p.P251P|ACAT2_ENST00000472052.1_3'UTR	NM_005891.2	NP_005882.2	Q9BWD1	THIC_HUMAN	acetyl-CoA acetyltransferase 2	222					lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleus (GO:0005634)	acetyl-CoA C-acetyltransferase activity (GO:0003985)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(1)	9		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.51e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		ATGAGTTTCCTCGCCATGGGA	0.438																																					p.P222P		Atlas-SNP	.											.	ACAT2	32	.	0			c.T666C						.						118	112	114					6																	160197213		2203	4300	6503	SO:0001819	synonymous_variant	39	exon6			GTTTCCTCGCCAT	AF356877	CCDS5268.1	6q25.3	2014-05-19	2010-04-30		ENSG00000120437	ENSG00000120437	2.3.1.9		94	protein-coding gene	gene with protein product	"acetoacetyl Coenzyme A thiolase"	100678	"acetyl-Coenzyme A acetyltransferase 2 (acetoacetyl Coenzyme A thiolase)", "acetyl-Coenzyme A acetyltransferase 2"			2475872	Standard	NM_005891		Approved		uc010kjy.3	Q9BWD1	OTTHUMG00000015935	ENST00000367048.4:c.666T>C	chr6.hg19:g.160197213T>C		160.0	0.0		109.0	7.0	NM_005891	B7Z233|E1P5B1|Q16146|Q5TCL7|Q8TDM4	Silent	SNP	ENST00000367048.4	hg19	CCDS5268.1																																																																																			.	.		0.438	ACAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042912.1	NM_005891		C	160197213	T	C	160197213	2	2	260	1	0	0	0	0	0	0	0	1	122	1538	54	2		2	ACAT2	6	160197213	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	5434759	160197213	10917854	304	37549										
ACAT2	39	hgsc.bcm.edu	37	chr6	160197291	160197291	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggaacgggaacagtcaccccAgccaatgcttcaggttagat	11	11	2	1	rs371174941		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:160197291A>G	ENST00000367048.4	+	6	2504	c.744A>G	c.(742-744)ccA>ccG	p.P248P	ACAT2_ENST00000541436.1_Silent_p.P277P|ACAT2_ENST00000472052.1_3'UTR	NM_005891.2	NP_005882.2	Q9BWD1	THIC_HUMAN	acetyl-CoA acetyltransferase 2	248					lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleus (GO:0005634)	acetyl-CoA C-acetyltransferase activity (GO:0003985)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(1)	9		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.51e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		CAGTCACCCCAGCCAATGCTT	0.393																																					p.P248P		Atlas-SNP	.											.	ACAT2	32	.	0			c.A744G						.						64	63	63					6																	160197291		2203	4300	6503	SO:0001819	synonymous_variant	39	exon6			CACCCCAGCCAAT	AF356877	CCDS5268.1	6q25.3	2014-05-19	2010-04-30		ENSG00000120437	ENSG00000120437	2.3.1.9		94	protein-coding gene	gene with protein product	"acetoacetyl Coenzyme A thiolase"	100678	"acetyl-Coenzyme A acetyltransferase 2 (acetoacetyl Coenzyme A thiolase)", "acetyl-Coenzyme A acetyltransferase 2"			2475872	Standard	NM_005891		Approved		uc010kjy.3	Q9BWD1	OTTHUMG00000015935	ENST00000367048.4:c.744A>G	chr6.hg19:g.160197291A>G		137.0	0.0		98.0	4.0	NM_005891	B7Z233|E1P5B1|Q16146|Q5TCL7|Q8TDM4	Silent	SNP	ENST00000367048.4	hg19	CCDS5268.1																																																																																			.	.		0.393	ACAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042912.1	NM_005891		G	160197291	A	G	160197291	2	3	260	1	0	0	0	0	0	0	0	1	122	175	7	2		2	ACAT2	6	160197291	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	78	160197291	10917776	305	37550										
PDE10A	10846	hgsc.bcm.edu	37	chr6	165801824	165801824	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tctgggagaagtggtgctgcTccatggtggaagtggagtag	18	5	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:165801824T>C	ENST00000366882.1	-	18	1899	c.1745A>G	c.(1744-1746)gAg>gGg	p.E582G	PDE10A_ENST00000539869.2_Missense_Mutation_p.E592G|PDE10A_ENST00000354448.4_Missense_Mutation_p.E582G			Q9Y233	PDE10_HUMAN	phosphodiesterase 10A	582					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of protein kinase A signaling (GO:0010738)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|metal ion binding (GO:0046872)			breast(4)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(39)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	71		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Caffeine(DB00201)|Dipyridamole(DB00975)|Papaverine(DB01113)|Tofisopam(DB08811)|Triflusal(DB08814)	GTGGTGCTGCTCCATGGTGGA	0.572																																					p.E592G	Esophageal Squamous(22;308 615 5753 12038 40624)	Atlas-SNP	.											.	PDE10A	154	.	0			c.A1775G						.						149	122	131					6																	165801824		2203	4300	6503	SO:0001583	missense	10846	exon17			TGCTGCTCCATGG	AB020593	CCDS47513.1	6q26	2008-03-18			ENSG00000112541	ENSG00000112541	3.1.4.17	"Phosphodiesterases"	8772	protein-coding gene	gene with protein product		610652				10373451	Standard	NM_001130690		Approved		uc003quo.3	Q9Y233	OTTHUMG00000015986	ENST00000366882.1:c.1745A>G	chr6.hg19:g.165801824T>C	ENSP00000355847:p.Glu582Gly	119.0	0.0		89.0	5.0	NM_001130690	Q6FHX1|Q9HCP9|Q9NTV4|Q9ULW9|Q9Y5T1	Missense_Mutation	SNP	ENST00000366882.1	hg19		.	.	.	.	.	.	.	.	.	.	T	32	5.183231	0.94885	.	.	ENSG00000112541	ENST00000366882;ENST00000539869;ENST00000343842;ENST00000354448;ENST00000392126	D;D	0.90563	-2.69;-2.69	5.89	5.89	0.94794	Metal-dependent phosphohydrolase, HD domain (1);5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.000000	0.85682	D	0.000000	D	0.96294	0.8791	M	0.94063	3.49	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.97301	0.9931	10	0.87932	D	0	.	16.3109	0.82869	0.0:0.0:0.0:1.0	.	592;582	Q9ULW9;Q9Y233	.;PDE10_HUMAN	G	582;610;592;582;581	ENSP00000355847:E582G;ENSP00000346435:E582G	ENSP00000341187:E592G	E	-	2	0	PDE10A	165721814	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.409000	0.80053	2.257000	0.74773	0.460000	0.39030	GAG	.	.		0.572	PDE10A-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000043031.1			C	165801824	T	C	165801824	3	2	260	1	0	0	0	0	1	0	0	0	11639	1551	54	2	618	2	PDE10A	6	165801824	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	5604533	165801824	5313243	306	37551										
T	6862	hgsc.bcm.edu	37	chr6	166579280	166579280	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gcgctgtggacccccaactcTcactatgtggattcgaggct	11	13	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:166579280T>C	ENST00000296946.2	-	4	988	c.520A>G	c.(520-522)Aga>Gga	p.R174G	T_ENST00000366871.3_Missense_Mutation_p.R174G	NM_003181.3	NP_003172.1	O15178	BRAC_HUMAN	T, brachyury homolog (mouse)	174					anterior/posterior axis specification, embryo (GO:0008595)|BMP signaling pathway (GO:0030509)|bone morphogenesis (GO:0060349)|canonical Wnt signaling pathway (GO:0060070)|determination of heart left/right asymmetry (GO:0061371)|embryonic skeletal system development (GO:0048706)|heart morphogenesis (GO:0003007)|mesoderm development (GO:0007498)|mesoderm migration involved in gastrulation (GO:0007509)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate morphogenesis (GO:0001839)|neural tube closure (GO:0001843)|notochord formation (GO:0014028)|penetration of zona pellucida (GO:0007341)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|signal transduction (GO:0007165)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|somitogenesis (GO:0001756)|transcription from RNA polymerase II promoter (GO:0006366)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(23)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	39		Prostate(117;4.48e-07)|Ovarian(120;1.78e-06)|Breast(66;2.54e-06)|Lung SC(201;0.0225)|Esophageal squamous(34;0.0559)		OV - Ovarian serous cystadenocarcinoma(33;1.09e-113)|GBM - Glioblastoma multiforme(31;1.51e-108)|BRCA - Breast invasive adenocarcinoma(81;8.45e-09)|LUAD - Lung adenocarcinoma(999;0.0407)		CCCCCAACTCTCACTATGTGG	0.512									Chordoma, Familial Clustering of																												p.R174G		Atlas-SNP	.											.	T	77	.	0			c.A520G						.						325	287	300					6																	166579280		2203	4300	6503	SO:0001583	missense	6862	exon4	Familial Cancer Database		CAACTCTCACTAT	AJ001699	CCDS5290.1, CCDS59045.1	6q27	2011-06-13	2001-11-28		ENSG00000164458	ENSG00000164458		"T-boxes"	11515	protein-coding gene	gene with protein product		601397	"T brachyury (mouse) homolog"			8963900	Standard	NM_003181		Approved		uc003quu.2	O15178	OTTHUMG00000015991	ENST00000296946.2:c.520A>G	chr6.hg19:g.166579280T>C	ENSP00000296946:p.Arg174Gly	157.0	0.0		99.0	6.0	NM_003181	E7ERD6|Q4KMP4	Missense_Mutation	SNP	ENST00000296946.2	hg19	CCDS5290.1	.	.	.	.	.	.	.	.	.	.	T	12.24	1.879969	0.33162	.	.	ENSG00000164458	ENST00000366876;ENST00000296946;ENST00000366871	T;T;T	0.80824	-1.42;-1.42;-1.42	4.94	0.963	0.19649	p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.88526	0.6460	M	0.93638	3.44	0.80722	D	1	D;P;D	0.67145	0.996;0.86;0.981	D;P;D	0.68039	0.955;0.573;0.939	D	0.90366	0.4377	10	0.87932	D	0	.	13.6508	0.62310	0.0:0.0:0.5534:0.4466	.	174;174;174	E7ERD6;O15178;Q4KMP4	.;BRAC_HUMAN;.	G	174	ENSP00000355841:R174G;ENSP00000296946:R174G;ENSP00000355836:R174G	ENSP00000296946:R174G	R	-	1	2	T	166499270	1.000000	0.71417	0.939000	0.37840	0.103000	0.19146	2.046000	0.41260	-0.070000	0.12908	-0.488000	0.04728	AGA	.	.		0.512	T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043037.2	NM_003181		C	166579280	T	C	166579280	3	2	260	1	0	0	0	0	1	0	0	0	15503	1559	54	2	811	2	T	6	166579280	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	777456	166579280	4535787	307	37552										
RPS6KA2	6196	hgsc.bcm.edu	37	chr6	166952273	166952273	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tccttcacgacgccttcttcCtgcaagagagcggcacgggt	11	14	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:166952273C>A	ENST00000265678.4	-	2	323		c.e2-1		RPS6KA2_ENST00000481261.2_Splice_Site|RPS6KA2_ENST00000510118.1_Splice_Site|RPS6KA2_ENST00000366863.2_Splice_Site|RPS6KA2_ENST00000503859.1_Splice_Site|RPS6KA2_ENST00000405189.3_Splice_Site	NM_021135.4	NP_066958.2	Q15349	KS6A2_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 2						axon guidance (GO:0007411)|brain renin-angiotensin system (GO:0002035)|cardiac muscle cell apoptotic process (GO:0010659)|cellular response to carbohydrate stimulus (GO:0071322)|heart contraction (GO:0060047)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of meiosis (GO:0045835)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oocyte maturation (GO:0001556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of gene expression (GO:0010628)|regulation of protein processing (GO:0070613)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|ribosomal protein S6 kinase activity (GO:0004711)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	45		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)		CGCCTTCTTCCTGCAAGAGAG	0.552																																					.		Atlas-SNP	.											RPS6KA2_ENST00000503859,NS,carcinoma,0,2	RPS6KA2	212	.	0			c.100-1G>T						.						111	98	102					6																	166952273		2203	4300	6503	SO:0001630	splice_region_variant	6196	exon3			TTCTTCCTGCAAG	L07598	CCDS5294.1, CCDS34570.1	6q27	2011-04-05	2002-08-29		ENSG00000071242	ENSG00000071242			10431	protein-coding gene	gene with protein product		601685	"ribosomal protein S6 kinase, 90kD, polypeptide 2"			8141249	Standard	NM_001006932		Approved	RSK, RSK3, HU-2	uc003qvc.1	Q15349	OTTHUMG00000016007	ENST00000265678.4:c.100-1G>T	chr6.hg19:g.166952273C>A		51.0	0.0		40.0	3.0	NM_021135	B3KTK9|Q15419|Q59GJ3|Q5TI68|Q96J38|Q9UJN5	Splice_Site	SNP	ENST00000265678.4	hg19	CCDS5294.1	.	.	.	.	.	.	.	.	.	.	C	18.72	3.685375	0.68157	.	.	ENSG00000071242	ENST00000265678;ENST00000510118;ENST00000503859;ENST00000507371;ENST00000506565	.	.	.	4.9	4.9	0.64082	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.9986	0.86375	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	RPS6KA2	166872263	1.000000	0.71417	0.907000	0.35723	0.751000	0.42716	5.507000	0.66999	2.434000	0.82447	0.655000	0.94253	.	.	.		0.552	RPS6KA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043075.3	NM_021135	Intron	A	166952273	C	A	166952273	5	1	260	1	0	0	0	0	0	0	1	0	13666	695	24	3	2182	3	RPS6KA2	6	166952273	Splice_Site	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	372993	166952273	4162794	308	37553										
MLLT4	4301	hgsc.bcm.edu	37	chr6	168307929	168307929	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gaatggtgaagccgatgatcAgagtagaacagcagccagat	13	7	1	5			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:168307929A>G	ENST00000447894.2	+	13	1729	c.1729A>G	c.(1729-1731)Aga>Gga	p.R577G	MLLT4_ENST00000351017.4_Missense_Mutation_p.R577G|MLLT4_ENST00000392112.1_Missense_Mutation_p.R561G|MLLT4_ENST00000366806.2_Missense_Mutation_p.R577G|MLLT4_ENST00000400822.3_Missense_Mutation_p.R576G|MLLT4_ENST00000392108.3_Missense_Mutation_p.R577G|MLLT4_ENST00000344191.4_Missense_Mutation_p.R577G			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	577					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(13)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		GCCGATGATCAGAGTAGAACA	0.483			T	MLL	AL																																p.R577G		Atlas-SNP	.		Dom	yes		6	6q27	4301	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"		L	MLLT4_ENST00000392108,NS,carcinoma,0,3	MLLT4	351	.	0			c.A1729G						.						132	122	126					6																	168307929		2203	4300	6503	SO:0001583	missense	4301	exon13			ATGATCAGAGTAG	AB011399	CCDS47517.1, CCDS75553.1	6q27	2008-02-05	2001-11-28		ENSG00000130396	ENSG00000130396			7137	protein-coding gene	gene with protein product		159559	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 4"			8242616	Standard	NM_001040000		Approved	AF-6, AF6	uc021zij.1	P55196	OTTHUMG00000016031	ENST00000447894.2:c.1729A>G	chr6.hg19:g.168307929A>G	ENSP00000404595:p.Arg577Gly	209.0	0.0		140.0	6.0	NM_001040000	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Missense_Mutation	SNP	ENST00000447894.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.38|17.38	3.375781|3.375781	0.61735|0.61735	.|.	.|.	ENSG00000130396|ENSG00000130396	ENST00000423229|ENST00000344191;ENST00000351017;ENST00000392108;ENST00000366806;ENST00000392112;ENST00000341575;ENST00000400822;ENST00000447894	.|T;T;T;T;T;T;T	.|0.04706	.|3.78;3.67;3.78;3.77;3.57;3.67;3.67	5.14|5.14	-0.115|-0.115	0.13560|0.13560	.|.	.|0.060165	.|0.64402	.|D	.|0.000011	T|T	0.03739|0.03739	0.0106|0.0106	M|M	0.68317|0.68317	2.08|2.08	0.43719|0.43719	D|D	0.99619|0.99619	.|B;P;P;P	.|0.51791	.|0.434;0.818;0.948;0.948	.|B;B;B;P	.|0.47430	.|0.13;0.311;0.442;0.547	T|T	0.37596|0.37596	-0.9699|-0.9699	5|10	.|0.20519	.|T	.|0.43	-5.3428|-5.3428	14.6184|14.6184	0.68565|0.68565	0.3337:0.6663:0.0:0.0|0.3337:0.6663:0.0:0.0	.|.	.|275;576;577;561	.|Q96C95;P55196-5;P55196-6;P55196-2	.|.;.;.;.	R|G	275|577;577;577;577;561;577;576;577	.|ENSP00000341118:R577G;ENSP00000252692:R577G;ENSP00000375956:R577G;ENSP00000355771:R577G;ENSP00000375960:R561G;ENSP00000383623:R576G;ENSP00000404595:R577G	.|ENSP00000345834:R577G	Q|R	+|+	2|1	0|2	MLLT4|MLLT4	168050778|168050778	0.362000|0.362000	0.24980|0.24980	0.002000|0.002000	0.10522|0.10522	0.958000|0.958000	0.62258|0.62258	0.965000|0.965000	0.29319|0.29319	-0.261000|-0.261000	0.09405|0.09405	0.528000|0.528000	0.53228|0.53228	CAG|AGA	.	.		0.483	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	NM_005936		G	168307929	A	G	168307929	3	3	260	1	0	0	0	0	1	0	0	0	9638	180	7	2	1779	2	MLLT4	6	168307929	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1355656	168307929	2807138	309	37554										
FAM120B	84498	hgsc.bcm.edu	37	chr6	170657249	170657249	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcttaactagggggaacgccTagtttgaaaatattatggct	10	6	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr6:170657249T>A	ENST00000476287.1	+	5	2136	c.2028T>A	c.(2026-2028)ccT>ccA	p.P676P	FAM120B_ENST00000252510.9_Silent_p.P8P|FAM120B_ENST00000537664.1_Silent_p.P699P|FAM120B_ENST00000540480.1_Silent_p.P688P	NM_032448.1	NP_115824.1	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	676					cell differentiation (GO:0030154)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(2)	44		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)		GGGGAACGCCTAGTTTGAAAA	0.398																																					p.P676P		Atlas-SNP	.											.	FAM120B	108	.	0			c.T2028A						.						50	54	53					6																	170657249		2203	4300	6503	SO:0001819	synonymous_variant	84498	exon5			AACGCCTAGTTTG	AB058741	CCDS5314.1, CCDS75555.1	6q27	2011-04-13	2006-07-04	2006-07-04	ENSG00000112584	ENSG00000112584			21109	protein-coding gene	gene with protein product	"PPARgamma constitutive coactivator 1", "constitutive coactivator of PPAR-gamma"	612266	"KIAA1838"	KIAA1838		14585507	Standard	NM_032448		Approved	PGCC1, CCPG	uc003qxp.3	Q96EK7	OTTHUMG00000016080	ENST00000476287.1:c.2028T>A	chr6.hg19:g.170657249T>A		62.0	0.0		46.0	16.0	NM_032448	B4DL34|Q86V68|Q96JI9	Silent	SNP	ENST00000476287.1	hg19	CCDS5314.1																																																																																			.	.		0.398	FAM120B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000043259.2	NM_032448		A	170657249	T	A	170657249	2	1	260	1	0	0	0	0	0	0	0	1	5422	1509	53	4		4	FAM120B	6	170657249	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	2349320	170657249	457818	310	37555										
INTS1	26173	hgsc.bcm.edu	37	chr7	1534513	1534513	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggtctccggctgctctgtgaAcagcaccttgtgcaggctgg	14	12	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:1534513A>G	ENST00000404767.3	-	14	1934	c.1849T>C	c.(1849-1851)Ttc>Ctc	p.F617L	INTS1_ENST00000389470.4_Missense_Mutation_p.F745L	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1	617					inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	62		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		TGCTCTGTGAACAGCACCTTG	0.642																																					p.F617L		Atlas-SNP	.											.	INTS1	145	.	0			c.T1849C						.						43	49	47					7																	1534513		2094	4186	6280	SO:0001583	missense	26173	exon14			CTGTGAACAGCAC	AB037861	CCDS47526.1	7p22.3	2009-11-06			ENSG00000164880	ENSG00000164880			24555	protein-coding gene	gene with protein product		611345				16239144	Standard	NM_001080453		Approved	DKFZp586J0619, KIAA1440, INT1, NET28	uc003skn.2	Q8N201	OTTHUMG00000151449	ENST00000404767.3:c.1849T>C	chr7.hg19:g.1534513A>G	ENSP00000385722:p.Phe617Leu	116.0	0.0		85.0	4.0	NM_001080453	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Missense_Mutation	SNP	ENST00000404767.3	hg19	CCDS47526.1	.	.	.	.	.	.	.	.	.	.	A	16.73	3.204898	0.58234	.	.	ENSG00000164880	ENST00000404767;ENST00000389470	T;T	0.54279	2.7;0.58	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	T	0.42404	0.1201	L	0.31207	0.915	0.80722	D	1	B	0.29432	0.244	B	0.33254	0.16	T	0.26985	-1.0087	10	0.21014	T	0.42	.	14.3527	0.66713	1.0:0.0:0.0:0.0	.	617	Q8N201	INT1_HUMAN	L	617;745	ENSP00000385722:F617L;ENSP00000374121:F745L	ENSP00000374121:F745L	F	-	1	0	INTS1	1501039	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.274000	0.95731	1.784000	0.52394	0.533000	0.62120	TTC	.	.		0.642	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1			G	1534513	A	G	1534513	3	3	260	1	0	0	0	0	1	0	0	0	7784	43	2	2	4863	2	INTS1	7	1534513	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10		1534513	157604150	311	37556										
HDAC9	9734	hgsc.bcm.edu	37	chr7	18687567	18687567	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acagcagccaccaggctctcCtgcagcatttattattgaaa	7	12	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:18687567C>T	ENST00000432645.2	+	9	1186	c.1186C>T	c.(1186-1188)Ctg>Ttg	p.L396L	HDAC9_ENST00000428307.2_Silent_p.L352L|HDAC9_ENST00000406451.4_Silent_p.L396L|HDAC9_ENST00000401921.1_Silent_p.L355L|HDAC9_ENST00000405010.3_Silent_p.L396L|HDAC9_ENST00000456174.2_Silent_p.L368L|HDAC9_ENST00000417496.2_Silent_p.L394L|HDAC9_ENST00000406072.1_Silent_p.L383L|HDAC9_ENST00000441542.2_Silent_p.L399L|HDAC9_ENST00000524023.1_Silent_p.L319L	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	396					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|regulation of skeletal muscle fiber development (GO:0048742)|regulation of striated muscle cell differentiation (GO:0051153)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|liver(2)|lung(37)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	82	all_lung(11;0.187)				Valproic Acid(DB00313)	CCAGGCTCTCCTGCAGCATTT	0.473																																					p.L399L		Atlas-SNP	.											.	HDAC9	560	.	0			c.C1195T						.						35	36	36					7																	18687567		1974	4164	6138	SO:0001819	synonymous_variant	9734	exon9			GCTCTCCTGCAGC	AF124924	CCDS47553.1, CCDS47554.1, CCDS47555.1, CCDS47557.1, CCDS56465.1, CCDS56466.1, CCDS56467.1, CCDS56468.1, CCDS75565.1	7p21.1	2008-05-15			ENSG00000048052	ENSG00000048052			14065	protein-coding gene	gene with protein product		606543				10523670, 10487760	Standard	NM_178425		Approved	KIAA0744, HDAC, MITR, HD7, HDAC7B	uc003sui.3	Q9UKV0	OTTHUMG00000152487	ENST00000432645.2:c.1186C>T	chr7.hg19:g.18687567C>T		83.0	0.0		57.0	18.0	NM_178425	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Silent	SNP	ENST00000432645.2	hg19	CCDS47555.1																																																																																			.	.		0.473	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1			T	18687567	C	T	18687567	2	4	260	1	0	0	0	0	0	0	0	1	7023	680	24	3		3	HDAC9	7	18687567	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	17153054	18687567	140451096	312	37557										
CDCA7L	55536	hgsc.bcm.edu	37	chr7	21946043	21946043	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tacgccgcgtgatctgtcccTccgagaaggcccgcctcact	10	17	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:21946043T>C	ENST00000406877.3	-	6	1064	c.785A>G	c.(784-786)gAg>gGg	p.E262G	CDCA7L_ENST00000465490.1_5'UTR|CDCA7L_ENST00000356195.5_Missense_Mutation_p.E228G|CDCA7L_ENST00000373934.4_Missense_Mutation_p.E216G	NM_018719.4	NP_061189.2	Q96GN5	CDA7L_HUMAN	cell division cycle associated 7-like	262					positive regulation of cell proliferation (GO:0008284)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(1)|urinary_tract(1)	29						GATCTGTCCCTCCGAGAAGGC	0.542																																					p.E262G		Atlas-SNP	.											.	CDCA7L	56	.	0			c.A785G						.						84	95	91					7																	21946043		2203	4300	6503	SO:0001583	missense	55536	exon6			TGTCCCTCCGAGA		CCDS5374.1, CCDS47558.1, CCDS47559.1	7p15.3	2007-04-27			ENSG00000164649	ENSG00000164649			30777	protein-coding gene	gene with protein product		609685				16829576	Standard	NM_018719		Approved	RAM2, R1, JPO2	uc010kuk.3	Q96GN5	OTTHUMG00000128429	ENST00000406877.3:c.785A>G	chr7.hg19:g.21946043T>C	ENSP00000383986:p.Glu262Gly	78.0	0.0		66.0	4.0	NM_018719	A4D141|A6NF50|B3KTR5|B4DUT3|C9K0Y1|Q6PIL4|Q86YT0|Q8IXN5|Q96C70|Q9H9A2|Q9NPV2	Missense_Mutation	SNP	ENST00000406877.3	hg19	CCDS5374.1	.	.	.	.	.	.	.	.	.	.	T	18.53	3.643896	0.67244	.	.	ENSG00000164649	ENST00000356195;ENST00000406877;ENST00000373934	T;T;T	0.49432	0.8;0.78;0.82	5.82	3.36	0.38483	.	0.245759	0.41712	D	0.000822	T	0.52613	0.1745	L	0.32530	0.975	0.53005	D	0.999966	D;D;D	0.76494	0.998;0.999;0.999	D;D;D	0.70016	0.931;0.922;0.967	T	0.51980	-0.8636	10	0.56958	D	0.05	-2.6127	8.9309	0.35670	0.0:0.0664:0.1256:0.808	.	216;262;261	C9K0Y1;Q96GN5;Q96GN5-2	.;CDA7L_HUMAN;.	G	228;262;216	ENSP00000348523:E228G;ENSP00000383986:E262G;ENSP00000363045:E216G	ENSP00000348523:E228G	E	-	2	0	CDCA7L	21912568	1.000000	0.71417	0.858000	0.33744	0.731000	0.41821	3.394000	0.52551	1.003000	0.39130	0.533000	0.62120	GAG	.	.		0.542	CDCA7L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250218.4	NM_018719		C	21946043	T	C	21946043	3	2	260	1	0	0	0	0	1	0	0	0	3093	1551	54	2	599	2	CDCA7L	7	21946043	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	3258476	21946043	137192620	313	37558										
FAM188B	84182	hgsc.bcm.edu	37	chr7	30921896	30921896	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gcagccggggctcctgcgtgActggaggactgagaggctct	17	11	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:30921896A>G	ENST00000265299.6	+	16	2149	c.2072A>G	c.(2071-2073)gAc>gGc	p.D691G	AQP1_ENST00000509504.1_Missense_Mutation_p.D154G|INMT-FAM188B_ENST00000458257.1_3'UTR|AQP1_ENST00000434909.2_Missense_Mutation_p.D37G	NM_032222.2	NP_115598.2	Q4G0A6	F188B_HUMAN	family with sequence similarity 188, member B	691										endometrium(1)|large_intestine(5)|lung(19)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CTCCTGCGTGACTGGAGGACT	0.612																																					p.D691G		Atlas-SNP	.											.	FAM188B	62	.	0			c.A2072G						.						58	62	61					7																	30921896		1953	4145	6098	SO:0001583	missense	84182	exon16			TGCGTGACTGGAG	AK026027	CCDS43565.1	7p14.3	2010-08-17	2009-07-14	2009-07-14	ENSG00000106125	ENSG00000106125			21916	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 67"	C7orf67			Standard	NM_032222		Approved	FLJ22374	uc003tbt.3	Q4G0A6	OTTHUMG00000152800	ENST00000265299.6:c.2072A>G	chr7.hg19:g.30921896A>G	ENSP00000265299:p.Asp691Gly	192.0	0.0		142.0	6.0	NM_032222	Q71AZ7|Q9H6D2	Missense_Mutation	SNP	ENST00000265299.6	hg19	CCDS43565.1	.	.	.	.	.	.	.	.	.	.	A	12.49	1.955138	0.34471	.	.	ENSG00000106125;ENSG00000106125;ENSG00000240583;ENSG00000250424	ENST00000265299;ENST00000409881;ENST00000434909;ENST00000509504	T;T;T	0.45668	0.89;0.89;0.89	5.38	5.38	0.77491	.	0.235594	0.43747	D	0.000538	T	0.43478	0.1249	L	0.58101	1.795	0.80722	D	1	B;B;B	0.25667	0.001;0.091;0.131	B;B;B	0.30251	0.007;0.058;0.113	T	0.43798	-0.9369	10	0.87932	D	0	-21.8477	13.3461	0.60573	1.0:0.0:0.0:0.0	.	37;211;691	B4E220;B8ZZX1;Q4G0A6	.;.;F188B_HUMAN	G	691;211;37;154	ENSP00000265299:D691G;ENSP00000395059:D37G;ENSP00000421315:D154G	ENSP00000265299:D691G	D	+	2	0	RP5-877J2.1;FAM188B;AQP1	30888421	1.000000	0.71417	0.956000	0.39512	0.349000	0.29174	4.691000	0.61738	2.052000	0.61016	0.533000	0.62120	GAC	.	.		0.612	FAM188B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327962.1	NM_032222		G	30921896	A	G	30921896	3	3	260	1	0	0	0	0	1	0	0	0	5520	275	10	2	2134	2	FAM188B	7	30921896	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	8975853	30921896	128216767	314	37559										
AVL9	23080	hgsc.bcm.edu	37	chr7	32598745	32598745	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgctgccatgaagactgaggAgcctttgttccaagtggaag	13	8	0	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:32598745A>G	ENST00000318709.4	+	10	1105	c.884A>G	c.(883-885)gAg>gGg	p.E295G	AVL9_ENST00000409301.1_Missense_Mutation_p.E295G|AVL9_ENST00000404479.1_Missense_Mutation_p.E295G	NM_015060.1	NP_055875.1	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	295					cell migration (GO:0016477)	integral component of membrane (GO:0016021)|recycling endosome (GO:0055037)				endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						AAGACTGAGGAGCCTTTGTTC	0.463																																					p.E295G		Atlas-SNP	.											.	AVL9	66	.	0			c.A884G						.						85	77	79					7																	32598745		2203	4300	6503	SO:0001583	missense	23080	exon10			CTGAGGAGCCTTT	D87682	CCDS34613.1	7p14.3	2013-05-01	2008-10-03	2008-10-03	ENSG00000105778	ENSG00000105778			28994	protein-coding gene	gene with protein product		612927	"KIAA0241"	KIAA0241		17229886, 22595670	Standard	XM_005249668		Approved		uc003tcv.1	Q8NBF6	OTTHUMG00000152929	ENST00000318709.4:c.884A>G	chr7.hg19:g.32598745A>G	ENSP00000315568:p.Glu295Gly	90.0	0.0		85.0	5.0	NM_015060	Q92573	Missense_Mutation	SNP	ENST00000318709.4	hg19	CCDS34613.1	.	.	.	.	.	.	.	.	.	.	A	1.520	-0.547249	0.04024	.	.	ENSG00000105778	ENST00000318709;ENST00000409301;ENST00000329714;ENST00000404479;ENST00000446718	T;T;T;T	0.47869	0.89;0.89;0.84;0.83	5.31	2.88	0.33553	.	0.581313	0.18634	N	0.135509	T	0.16085	0.0387	N	0.01352	-0.895	0.09310	N	1	B;B;B	0.09022	0.002;0.0;0.001	B;B;B	0.10450	0.005;0.001;0.002	T	0.08932	-1.0698	10	0.45353	T	0.12	-11.9767	1.8924	0.03250	0.4882:0.1248:0.0842:0.3027	.	295;295;295	Q8N6Z3;Q8NBF6-2;Q8NBF6	.;.;AVL9_HUMAN	G	295;295;295;295;226	ENSP00000315568:E295G;ENSP00000387011:E295G;ENSP00000385242:E295G;ENSP00000395134:E226G	ENSP00000315568:E295G	E	+	2	0	AVL9	32565270	0.001000	0.12720	0.010000	0.14722	0.003000	0.03518	1.023000	0.30065	1.004000	0.39156	0.482000	0.46254	GAG	.	.		0.463	AVL9-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328643.1	NM_015060		G	32598745	A	G	32598745	3	3	260	1	0	0	0	0	1	0	0	0	1228	304	11	2	922	2	AVL9	7	32598745	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1676849	32598745	126539918	315	37560										
EEPD1	80820	hgsc.bcm.edu	37	chr7	36194099	36194099	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agctgatgaccctgcctgggGtgacgcgtgccgtggcacgc	16	13	0	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:36194099G>A	ENST00000242108.4	+	2	884	c.166G>A	c.(166-168)Gtg>Atg	p.V56M	EEPD1_ENST00000534978.1_Missense_Mutation_p.V56M	NM_030636.2	NP_085139.2	Q7L9B9	EEPD1_HUMAN	endonuclease/exonuclease/phosphatase family domain containing 1	56	HhH.				DNA repair (GO:0006281)		DNA binding (GO:0003677)			endometrium(2)|large_intestine(3)|lung(10)|ovary(1)|pancreas(1)|skin(1)	18						CCTGCCTGGGGTGACGCGTGC	0.577																																					p.V56M		Atlas-SNP	.											.	EEPD1	47	.	0			c.G166A						.						116	116	116					7																	36194099		2203	4300	6503	SO:0001583	missense	80820	exon2			CCTGGGGTGACGC	AK027386	CCDS34619.1	7p14.2	2007-12-07	2007-12-07		ENSG00000122547	ENSG00000122547			22223	protein-coding gene	gene with protein product							Standard	NM_030636		Approved	KIAA1706	uc003tfa.3	Q7L9B9	OTTHUMG00000154904	ENST00000242108.4:c.166G>A	chr7.hg19:g.36194099G>A	ENSP00000242108:p.Val56Met	103.0	0.0		95.0	4.0	NM_030636	Q96K64|Q9C0F7	Missense_Mutation	SNP	ENST00000242108.4	hg19	CCDS34619.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.291100	0.80914	.	.	ENSG00000122547	ENST00000242108;ENST00000534978	T;T	0.32988	1.43;1.43	5.68	5.68	0.88126	RuvA domain 2-like (1);Competence protein ComEA, helix-hairpin-helix domain (1);Helix-hairpin-helix DNA-binding motif, class 1 (1);	0.000000	0.85682	D	0.000000	T	0.57403	0.2051	M	0.69463	2.115	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.58239	-0.7671	10	0.87932	D	0	-28.3346	19.7989	0.96497	0.0:0.0:1.0:0.0	.	56	Q7L9B9	EEPD1_HUMAN	M	56	ENSP00000242108:V56M;ENSP00000442692:V56M	ENSP00000242108:V56M	V	+	1	0	EEPD1	36160624	1.000000	0.71417	1.000000	0.80357	0.668000	0.39293	7.832000	0.86757	2.683000	0.91414	0.561000	0.74099	GTG	.	.		0.577	EEPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337602.1	NM_030636		A	36194099	G	A	36194099	3	1	260	1	0	0	0	0	1	0	0	0	4934	1261	44	3	168	3	EEPD1	7	36194099	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	3595354	36194099	122944564	316	37561										
AMPH	273	hgsc.bcm.edu	37	chr7	38457492	38457492	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccagaccaacggcaggtgtgAcagcagccagaggctcctct	12	14	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:38457492A>G	ENST00000356264.2	-	17	1546	c.1331T>C	c.(1330-1332)gTc>gCc	p.V444A	AMPH_ENST00000471913.1_Intron|AMPH_ENST00000428293.2_Intron|AMPH_ENST00000325590.5_Intron	NM_001635.3	NP_001626.1	P49418	AMPH_HUMAN	amphiphysin	444					endocytosis (GO:0006897)|learning (GO:0007612)|synaptic transmission (GO:0007268)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|leading edge membrane (GO:0031256)|synaptic vesicle (GO:0008021)	phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|kidney(3)|large_intestine(12)|liver(3)|lung(27)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)	62						GGCAGGTGTGACAGCAGCCAG	0.562																																					p.V444A		Atlas-SNP	.											.	AMPH	157	.	0			c.T1331C						.						92	76	82					7																	38457492		2203	4300	6503	SO:0001583	missense	273	exon17			GGTGTGACAGCAG		CCDS5456.1, CCDS47574.1	7p14-p13	2007-06-19	2007-06-19		ENSG00000078053	ENSG00000078053			471	protein-coding gene	gene with protein product		600418	"amphiphysin (Stiff-Mann syndrome with breast cancer 128kD autoantigen)", "amphiphysin (Stiff-Man syndrome with breast cancer 128kDa autoantigen)"			8245793	Standard	NM_139316		Approved		uc003tgu.3	P49418	OTTHUMG00000023725	ENST00000356264.2:c.1331T>C	chr7.hg19:g.38457492A>G	ENSP00000348602:p.Val444Ala	245.0	0.0		168.0	8.0	NM_001635	A4D1X8|A4D1X9|O43538|Q75MJ8|Q75MK5|Q75MM3|Q8N4G0	Missense_Mutation	SNP	ENST00000356264.2	hg19	CCDS5456.1	.	.	.	.	.	.	.	.	.	.	A	0.013	-1.645723	0.00792	.	.	ENSG00000078053	ENST00000356264	T	0.58210	0.35	4.42	-1.27	0.09347	.	.	.	.	.	T	0.22322	0.0538	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.25187	-1.0139	9	0.05721	T	0.95	0.1344	4.7095	0.12865	0.4084:0.1537:0.4378:0.0	.	444	P49418	AMPH_HUMAN	A	444	ENSP00000348602:V444A	ENSP00000348602:V444A	V	-	2	0	AMPH	38424017	0.039000	0.19947	0.000000	0.03702	0.002000	0.02628	1.090000	0.30902	-0.361000	0.08125	-0.969000	0.02612	GTC	.	.		0.562	AMPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226953.2	NM_001635		G	38457492	A	G	38457492	3	3	260	1	0	0	0	0	1	0	0	0	588	275	10	2	776	2	AMPH	7	38457492	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	2263393	38457492	120681171	317	37562										
POU6F2	11281	hgsc.bcm.edu	37	chr7	39500146	39500146	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttttaaaaacatctccacagAtcctcaaacggcagcgggtg	8	11	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:39500146A>G	ENST00000403058.1	+	10	1557	c.1403A>G	c.(1402-1404)aAt>aGt	p.N468S	POU6F2_ENST00000559001.1_Splice_Site_p.N413S|POU6F2_ENST00000518318.2_Splice_Site_p.N468S	NM_001166018.1|NM_007252.3	NP_001159490.1|NP_009183.3	P78424	PO6F2_HUMAN	POU class 6 homeobox 2	468					central nervous system development (GO:0007417)|ganglion mother cell fate determination (GO:0007402)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	42						ATCTCCACAGATCCTCAAACG	0.458																																					p.N468S		Atlas-SNP	.											.	POU6F2	117	.	0			c.A1403G						.						54	48	50					7																	39500146		2203	4300	6503	SO:0001630	splice_region_variant	11281	exon10			CCACAGATCCTCA	U91934	CCDS34620.2, CCDS55103.1	7p14.1	2011-06-20	2007-07-13		ENSG00000106536	ENSG00000106536		"Homeoboxes / POU class"	21694	protein-coding gene	gene with protein product	"Retina-derived POU-domain factor-1"	609062	"POU domain, class 6, transcription factor 2"			8601806	Standard	NM_007252		Approved	RPF-1	uc003thb.2	P78424	OTTHUMG00000150803	ENST00000403058.1:c.1403-1A>G	chr7.hg19:g.39500146A>G		234.0	0.0		161.0	8.0	NM_007252	A4D1W2|C4AMB9|P78425|Q75ME8|Q86UM6|Q9UDS7	Missense_Mutation	SNP	ENST00000403058.1	hg19	CCDS34620.2	.	.	.	.	.	.	.	.	.	.	A	13.33	2.204127	0.38905	.	.	ENSG00000106536	ENST00000403058;ENST00000518318	T;D	0.85556	1.08;-2.0	5.48	5.48	0.80851	.	2.638820	0.01079	N	0.004942	D	0.87892	0.6292	N	0.12182	0.205	0.50313	D	0.999867	D	0.69078	0.997	D	0.70716	0.97	T	0.75133	-0.3425	9	.	.	.	.	15.5731	0.76354	1.0:0.0:0.0:0.0	.	468	P78424	PO6F2_HUMAN	S	468	ENSP00000384004:N468S;ENSP00000430514:N468S	.	N	+	2	0	POU6F2	39466671	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.293000	0.96082	2.080000	0.62538	0.418000	0.28097	AAT	.	.		0.458	POU6F2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320146.3	NM_007252	Missense_Mutation	G	39500146	A	G	39500146	5	3	260	1	0	0	0	0	0	0	1	0	12294	347	12	2	1437	2	POU6F2	7	39500146	Splice_Site	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1042654	39500146	119638517	318	37563										
NPC1L1	29881	hgsc.bcm.edu	37	chr7	44555532	44555532	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aggcccaggacaaggatgccAggcaggttggtcatggccac	15	11	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:44555532A>G	ENST00000289547.4	-	19	3802	c.3747T>C	c.(3745-3747)ccT>ccC	p.P1249P	NPC1L1_ENST00000546276.1_Silent_p.P1176P|NPC1L1_ENST00000381160.3_Silent_p.P1222P	NM_013389.2	NP_037521.2	Q9UHC9	NPCL1_HUMAN	NPC1-like 1	1249					cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intestinal cholesterol absorption (GO:0030299)|lipoprotein metabolic process (GO:0042157)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)	brush border membrane (GO:0031526)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|hedgehog receptor activity (GO:0008158)|myosin V binding (GO:0031489)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(7)|lung(27)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	57					Ezetimibe(DB00973)	CAAGGATGCCAGGCAGGTTGG	0.622																																					p.P1249P		Atlas-SNP	.											.	NPC1L1	141	.	0			c.T3747C						.						51	52	52					7																	44555532		2203	4300	6503	SO:0001819	synonymous_variant	29881	exon19			GATGCCAGGCAGG		CCDS5491.1, CCDS43575.1, CCDS75587.1	7p13	2012-11-15	2012-11-15		ENSG00000015520	ENSG00000015520			7898	protein-coding gene	gene with protein product		608010	"NPC1 (Niemann-Pick disease, type C1, gene)-like 1"			10783261	Standard	NM_013389		Approved		uc003tlb.3	Q9UHC9	OTTHUMG00000023691	ENST00000289547.4:c.3747T>C	chr7.hg19:g.44555532A>G		111.0	0.0		75.0	4.0	NM_013389	A4D2J7|B7ZLE6|D3DVK9|Q17RV5|Q6R3Q4|Q9UHC8	Silent	SNP	ENST00000289547.4	hg19	CCDS5491.1																																																																																			.	.		0.622	NPC1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251256.1	NM_013389		G	44555532	A	G	44555532	2	3	260	1	0	0	0	0	0	0	0	1	10580	175	7	2		2	NPC1L1	7	44555532	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	5055386	44555532	114583131	319	37564										
COBL	23242	hgsc.bcm.edu	37	chr7	51111115	51111115	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcagagccattcttctcccaCaaggggctcttctggggacc	10	14	5	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:51111115C>T	ENST00000265136.7	-	8	1536	c.1371G>A	c.(1369-1371)ttG>ttA	p.L457L	COBL_ENST00000395542.2_Silent_p.L539L	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	457					actin filament network formation (GO:0051639)|actin filament polymerization (GO:0030041)|collateral sprouting in absence of injury (GO:0048669)|digestive tract development (GO:0048565)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|liver development (GO:0001889)|neural tube closure (GO:0001843)|notochord development (GO:0030903)|positive regulation of dendrite development (GO:1900006)|somite specification (GO:0001757)	actin filament (GO:0005884)|axon (GO:0030424)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic growth cone (GO:0044294)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)			NS(2)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(26)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Glioma(55;0.08)					TCTTCTCCCACAAGGGGCTCT	0.552																																					p.L457L	NSCLC(189;2119 2138 12223 30818 34679)	Atlas-SNP	.											.	COBL	167	.	0			c.G1371A						.						82	81	82					7																	51111115		2203	4300	6503	SO:0001819	synonymous_variant	23242	exon8			CTCCCACAAGGGG	AB014533	CCDS34637.1, CCDS75601.1, CCDS75602.1	7p12.2-p12.1	2012-12-07	2012-12-07		ENSG00000106078	ENSG00000106078			22199	protein-coding gene	gene with protein product		610317	"cordon-bleu homolog (mouse)"				Standard	NM_015198		Approved	KIAA0633	uc003tpr.4	O75128	OTTHUMG00000155999	ENST00000265136.7:c.1371G>A	chr7.hg19:g.51111115C>T		167.0	0.0		87.0	4.0	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Silent	SNP	ENST00000265136.7	hg19	CCDS34637.1	.	.	.	.	.	.	.	.	.	.	C	8.215	0.801172	0.16397	.	.	ENSG00000106078	ENST00000452534	.	.	.	5.5	-8.1	0.01086	.	.	.	.	.	T	0.18509	0.0444	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.27400	-1.0075	4	.	.	.	.	5.2878	0.15710	0.0942:0.1258:0.4968:0.2831	.	.	.	.	M	433	.	.	V	-	1	0	COBL	51078609	0.000000	0.05858	0.000000	0.03702	0.360000	0.29518	-2.273000	0.01164	-1.229000	0.02564	-0.211000	0.12701	GTG	.	.		0.552	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198		T	51111115	C	T	51111115	2	4	260	1	0	0	0	0	0	0	0	1	3655	477	17	3		3	COBL	7	51111115	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	6555583	51111115	108027548	320	37565										
FZD9	8326	hgsc.bcm.edu	37	chr7	72849391	72849391	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aatggggccacgaggccatcGaggcccacggcagctatttc	13	13	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:72849391G>T	ENST00000344575.3	+	1	1283	c.1054G>T	c.(1054-1056)Gag>Tag	p.E352*		NM_003508.2	NP_003499.1	O00144	FZD9_HUMAN	frizzled class receptor 9	352					B cell differentiation (GO:0030183)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|gonad development (GO:0008406)|learning or memory (GO:0007611)|nervous system development (GO:0007399)|neuroblast proliferation (GO:0007405)|vasculature development (GO:0001944)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(4)|prostate(2)|skin(1)	14		Lung NSC(55;0.0659)|all_lung(88;0.152)				CGAGGCCATCGAGGCCCACGG	0.642																																					p.E352X	Pancreas(144;909 1878 36867 38226 39554)	Atlas-SNP	.											.	FZD9	51	.	0			c.G1054T						.						52	51	52					7																	72849391		2203	4300	6503	SO:0001587	stop_gained	8326	exon1			GCCATCGAGGCCC	U82169	CCDS5548.1	7q11.23	2014-01-29	2014-01-29		ENSG00000188763	ENSG00000188763		"GPCR / Class F : Frizzled receptors", "CD molecules"	4047	protein-coding gene	gene with protein product		601766	"frizzled (Drosophila) homolog 9", "frizzled homolog 9 (Drosophila)", "frizzled 9, seven transmembrane spanning receptor", "frizzled family receptor 9"			9147651, 10198163	Standard	NM_003508		Approved	FZD3, CD349	uc003tyb.3	O00144	OTTHUMG00000023051	ENST00000344575.3:c.1054G>T	chr7.hg19:g.72849391G>T	ENSP00000345785:p.Glu352*	126.0	0.0		84.0	4.0	NM_003508		Nonsense_Mutation	SNP	ENST00000344575.3	hg19	CCDS5548.1	.	.	.	.	.	.	.	.	.	.	G	38	7.077418	0.98048	.	.	ENSG00000188763	ENST00000344575	.	.	.	4.3	4.3	0.51218	.	0.127165	0.50627	U	0.000112	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	.	16.0988	0.81152	0.0:0.0:1.0:0.0	.	.	.	.	X	352	.	ENSP00000345785:E352X	E	+	1	0	FZD9	72487327	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.823000	0.99369	2.105000	0.64084	0.563000	0.77884	GAG	.	.		0.642	FZD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252120.1			T	72849391	G	T	72849391	4	4	260	1	0	0	0	0	0	1	0	0	6145	1059	37	1	1056	1	FZD9	7	72849391	Nonsense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	21738276	72849391	86289272	321	37566										
WBSCR22	114049	hgsc.bcm.edu	37	chr7	73108372	73108372	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cccagggagtctgtgttcacCaatgagaggtaaagcaactg	12	9	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:73108372C>A	ENST00000265758.2	+	10	751	c.693C>A	c.(691-693)acC>acA	p.T231T	WBSCR22_ENST00000423166.2_3'UTR|WBSCR22_ENST00000423497.1_Silent_p.T231T	NM_017528.4	NP_059998.2	O43709	WBS22_HUMAN	Williams Beuren syndrome chromosome region 22	231					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|rRNA processing (GO:0006364)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|large_intestine(2)|lung(9)|prostate(1)	13		Lung NSC(55;0.0908)|all_lung(88;0.198)				CTGTGTTCACCAATGAGAGGT	0.542																																					p.T231T		Atlas-SNP	.											.	WBSCR22	27	.	0			c.C693A						.						94	93	93					7																	73108372		2203	4300	6503	SO:0001819	synonymous_variant	114049	exon10			GTTCACCAATGAG	AF420248	CCDS5557.1, CCDS56490.1	7q11.23	2012-06-12			ENSG00000071462	ENSG00000071462			16405	protein-coding gene	gene with protein product	"metastasis-related methyltransferase 1"	615733				12073013, 11978965, 21148752	Standard	NM_001202560		Approved	MGC19709, MGC2022, MGC5140, PP3381, WBMT, MERM1	uc003tyt.3	O43709	OTTHUMG00000023306	ENST00000265758.2:c.693C>A	chr7.hg19:g.73108372C>A		88.0	0.0		52.0	4.0	NM_001202560	A8K501|C9K060|Q96P12|Q9BQ58|Q9HBP9	Silent	SNP	ENST00000265758.2	hg19	CCDS5557.1																																																																																			.	.		0.542	WBSCR22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252303.1			A	73108372	C	A	73108372	2	1	260	1	0	0	0	0	0	0	0	1	17280	581	21	3		3	WBSCR22	7	73108372	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	258981	73108372	86030291	322	37567										
HGF	3082	hgsc.bcm.edu	37	chr7	81335733	81335733	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tccaagccaagcttcataatCtttcaagtctctgttttgaa	5	10	4	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:81335733C>T	ENST00000222390.5	-	15	1853	c.1627G>A	c.(1627-1629)Gat>Aat	p.D543N	HGF_ENST00000457544.2_Missense_Mutation_p.D538N	NM_000601.4	NP_000592.3	P14210	HGF_HUMAN	hepatocyte growth factor (hepapoietin A; scatter factor)	543	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				activation of MAPK activity (GO:0000187)|blood coagulation (GO:0007596)|cell chemotaxis (GO:0060326)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epithelial to mesenchymal transition (GO:0001837)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|hyaluronan metabolic process (GO:0030212)|liver development (GO:0001889)|mitotic nuclear division (GO:0007067)|myoblast proliferation (GO:0051450)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of hydrogen peroxide-mediated programmed cell death (GO:1901299)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|organ regeneration (GO:0031100)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of cell migration (GO:0030335)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	catalytic activity (GO:0003824)|chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|identical protein binding (GO:0042802)			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						GCTTCATAATCTTTCAAGTCT	0.333																																					p.D543N		Atlas-SNP	.											HGF,colon,carcinoma,+2,1	HGF	171	.	0			c.G1627A						.						108	115	112					7																	81335733		2203	4300	6503	SO:0001583	missense	3082	exon15			CATAATCTTTCAA		CCDS5597.1, CCDS47626.1, CCDS47627.1, CCDS47628.1, CCDS47629.1	7q21.1	2009-09-11			ENSG00000019991	ENSG00000019991			4893	protein-coding gene	gene with protein product	"hepatopoietin A", "fibroblast-derived tumor cytotoxic factor", "scatter factor", "lung fibroblast-derived mitogen"	142409	"deafness, autosomal recessive 39"	DFNB39		1837206, 19576567	Standard	XM_006715956		Approved	SF, F-TCF, HGFB, HPTA	uc003uhl.3	P14210	OTTHUMG00000023804	ENST00000222390.5:c.1627G>A	chr7.hg19:g.81335733C>T	ENSP00000222390:p.Asp543Asn	122.0	0.0		80.0	4.0	NM_000601	A1L3U6|Q02935|Q13494|Q14519|Q3KRB2|Q8TCE2|Q9BYL9|Q9BYM0|Q9UDU6	Missense_Mutation	SNP	ENST00000222390.5	hg19	CCDS5597.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.431347	0.83776	.	.	ENSG00000019991	ENST00000222390;ENST00000457544	D;D	0.89050	-2.46;-2.46	5.07	5.07	0.68467	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.098274	0.64402	D	0.000002	D	0.87233	0.6126	N	0.11255	0.115	0.80722	D	1	D;D	0.71674	0.997;0.998	P;P	0.59221	0.772;0.854	D	0.87673	0.2542	10	0.33940	T	0.23	.	18.8012	0.92018	0.0:1.0:0.0:0.0	.	538;543	P14210-3;P14210	.;HGF_HUMAN	N	543;538	ENSP00000222390:D543N;ENSP00000391238:D538N	ENSP00000222390:D543N	D	-	1	0	HGF	81173669	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.926000	0.70070	2.500000	0.84329	0.585000	0.79938	GAT	.	.		0.333	HGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253315.2	NM_000601		T	81335733	C	T	81335733	3	4	260	1	0	0	0	0	1	0	0	0	7094	913	32	3	575	3	HGF	7	81335733	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	8227361	81335733	77802930	323	37568										
PCLO	27445	hgsc.bcm.edu	37	chr7	82390784	82390784	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tccttcttcaatgcaatcttGatttctcccattacctgagt	4	12	4	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:82390784G>T	ENST00000333891.9	-	23	15370	c.15033C>A	c.(15031-15033)atC>atA	p.I5011I		NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						ATGCAATCTTGATTTCTCCCA	0.308																																					p.I5011I		Atlas-SNP	.											PCLO_ENST00000333891,NS,carcinoma,0,2	PCLO	1506	.	0			c.C15033A						.						128	113	118					7																	82390784		1808	4072	5880	SO:0001819	synonymous_variant	27445	exon23			AATCTTGATTTCT	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.15033C>A	chr7.hg19:g.82390784G>T		94.0	0.0		73.0	3.0	NM_033026		Silent	SNP	ENST00000333891.9	hg19	CCDS47630.1																																																																																			.	.		0.308	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		T	82390784	G	T	82390784	2	4	260	1	0	0	0	0	0	0	0	1	11592	1280	45	3		3	PCLO	7	82390784	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	1055051	82390784	76747879	324	37569										
SEMA3A	10371	hgsc.bcm.edu	37	chr7	83640613	83640613	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tctgtgccctccaaagtcatTctgaaagaagggaacaccag	9	11	3	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:83640613T>C	ENST00000265362.4	-	8	1125	c.811A>G	c.(811-813)Aat>Gat	p.N271D	SEMA3A_ENST00000436949.1_Splice_Site_p.N271D	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	271	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				apoptotic process (GO:0006915)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|dendrite morphogenesis (GO:0048813)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of epithelial cell migration (GO:0010633)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neural crest cell migration involved in sympathetic nervous system development (GO:1903045)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of male gonad development (GO:2000020)|positive regulation of neuron migration (GO:2001224)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of heart rate (GO:0002027)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sensory system development (GO:0048880)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular region (GO:0005576)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|neuropilin binding (GO:0038191)|receptor activity (GO:0004872)			breast(3)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						CCAAAGTCATTCTGAAAGAAG	0.378																																					p.N271D		Atlas-SNP	.											.	SEMA3A	121	.	0			c.A811G						.						86	80	82					7																	83640613		2203	4300	6503	SO:0001630	splice_region_variant	10371	exon8			AGTCATTCTGAAA	L26081	CCDS5599.1	7p12.1	2013-01-11			ENSG00000075213	ENSG00000075213		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10723	protein-coding gene	gene with protein product	"sema III"	603961		SEMAD		8269517, 7748561	Standard	NM_006080		Approved	SEMA1, SemD, coll-1, Hsema-I	uc003uhz.3	Q14563	OTTHUMG00000023443	ENST00000265362.4:c.811-1A>G	chr7.hg19:g.83640613T>C		90.0	0.0		63.0	4.0	NM_006080		Missense_Mutation	SNP	ENST00000265362.4	hg19	CCDS5599.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.252180	0.80135	.	.	ENSG00000075213	ENST00000265362;ENST00000436949	T;T	0.25579	1.79;1.79	6.08	6.08	0.98989	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.55273	0.1910	M	0.81802	2.56	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.59268	-0.7486	10	0.66056	D	0.02	.	16.6512	0.85203	0.0:0.0:0.0:1.0	.	271	Q14563	SEM3A_HUMAN	D	271	ENSP00000265362:N271D;ENSP00000415260:N271D	ENSP00000265362:N271D	N	-	1	0	SEMA3A	83478549	1.000000	0.71417	1.000000	0.80357	0.445000	0.32107	8.040000	0.89188	2.333000	0.79357	0.482000	0.46254	AAT	.	.		0.378	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080	Missense_Mutation	C	83640613	T	C	83640613	5	2	260	1	0	0	0	0	0	0	1	0	14039	1797	62	2	1544	2	SEMA3A	7	83640613	Splice_Site	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1249829	83640613	75498050	325	37570										
KIAA1324L	222223	hgsc.bcm.edu	37	chr7	86574222	86574222	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	caaaaggtcttacaaagaacTcaaagaagatgttgttgtcg	9	6	2	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:86574222T>C	ENST00000450689.2	-	4	832	c.647A>G	c.(646-648)gAg>gGg	p.E216G	KIAA1324L_ENST00000416314.1_Missense_Mutation_p.E49G|KIAA1324L_ENST00000444627.1_Missense_Mutation_p.E216G	NM_001142749.2	NP_001136221.1	A8MWY0	K132L_HUMAN	KIAA1324-like	216						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(14)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44	Esophageal squamous(14;0.0058)					TACAAAGAACTCAAAGAAGAT	0.393																																					p.E216G		Atlas-SNP	.											.	KIAA1324L	225	.	0			c.A647G						.						127	111	115					7																	86574222		692	1591	2283	SO:0001583	missense	222223	exon4			AAGAACTCAAAGA	AK055902	CCDS34677.1, CCDS47632.1, CCDS34677.2	7q21.12	2008-09-18			ENSG00000164659	ENSG00000164659			21945	protein-coding gene	gene with protein product	"EIG121-like"	614048					Standard	NM_001142749		Approved	FLJ31340, EIG121L	uc011kha.2	A8MWY0	OTTHUMG00000153995	ENST00000450689.2:c.647A>G	chr7.hg19:g.86574222T>C	ENSP00000413445:p.Glu216Gly	246.0	0.0		134.0	6.0	NM_001142749	A4D1C9|B4DJV3|Q17RI6|Q96DP2	Missense_Mutation	SNP	ENST00000450689.2	hg19	CCDS47632.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	27.1|27.1	4.796900|4.796900	0.90453|0.90453	.|.	.|.	ENSG00000164659|ENSG00000164659	ENST00000450689;ENST00000444627;ENST00000416314;ENST00000398276|ENST00000423294	T;T;T;T|.	0.49432|.	0.78;0.78;0.78;1.46|.	5.42|5.42	5.42|5.42	0.78866|0.78866	.|.	0.000000|.	0.36972|.	U|.	0.002317|.	T|.	0.74520|.	0.3727|.	M|M	0.76328|0.76328	2.33|2.33	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.87578|.	0.991;0.998|.	T|.	0.75411|.	-0.3327|.	10|.	0.72032|.	D|.	0.01|.	.|.	14.9345|14.9345	0.70944|0.70944	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	216;49|.	A8MWY0;B4DJV3|.	K132L_HUMAN;.|.	G|W	216;216;49;102|176	ENSP00000413445:E216G;ENSP00000397377:E216G;ENSP00000402390:E49G;ENSP00000381325:E102G|.	ENSP00000381325:E102G|.	E|X	-|-	2|3	0|0	KIAA1324L|KIAA1324L	86412158|86412158	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	7.951000|7.951000	0.87819|0.87819	2.189000|2.189000	0.69895|0.69895	0.533000|0.533000	0.62120|0.62120	GAG|TGA	.	.		0.393	KIAA1324L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333372.3	NM_152748		C	86574222	T	C	86574222	3	2	260	1	0	0	0	0	1	0	0	0	8233	1551	54	2	2518	2	KIAA1324L	7	86574222	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	2933609	86574222	72564441	326	37571										
HEPACAM2	253012	hgsc.bcm.edu	37	chr7	92825166	92825166	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aaacaccagaaacatctggaAaagcaacaaattcatatatt	4	8	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:92825166A>G	ENST00000394468.2	-	8	1327	c.1250T>C	c.(1249-1251)tTt>tCt	p.F417S	HEPACAM2_ENST00000453812.2_Missense_Mutation_p.F440S|HEPACAM2_ENST00000492616.1_5'UTR|HEPACAM2_ENST00000440868.1_Missense_Mutation_p.F397L|HEPACAM2_ENST00000341723.4_Missense_Mutation_p.F405S	NM_001039372.1	NP_001034461.1	A8MVW5	HECA2_HUMAN	HEPACAM family member 2	417					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|midbody (GO:0030496)|spindle (GO:0005819)				breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|ovary(4)|skin(1)	28						AACATCTGGAAAAGCAACAAA	0.388																																					p.F417S		Atlas-SNP	.											.	HEPACAM2	132	.	0			c.T1250C						.						118	116	116					7																	92825166		2203	4300	6503	SO:0001583	missense	253012	exon8			TCTGGAAAAGCAA	AK096002	CCDS5629.1, CCDS43616.1, CCDS75631.1, CCDS75632.1	7q21.3	2013-01-29	2008-07-11		ENSG00000188175	ENSG00000188175		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	27364	protein-coding gene	gene with protein product		614133				12975309	Standard	NM_001288804		Approved	FLJ38683	uc003umm.3	A8MVW5	OTTHUMG00000131732	ENST00000394468.2:c.1250T>C	chr7.hg19:g.92825166A>G	ENSP00000377980:p.Phe417Ser	113.0	0.0		89.0	5.0	NM_001039372	B3KTT4|B4DPJ1|B9EG93|E9PDV5|Q6UXI0	Missense_Mutation	SNP	ENST00000394468.2	hg19	CCDS43616.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.3|24.3	4.515757|4.515757	0.85495|0.85495	.|.	.|.	ENSG00000188175|ENSG00000188175	ENST00000440868|ENST00000394468;ENST00000341723;ENST00000453812	T|T;T;T	0.57107|0.57107	0.42|0.42;0.44;0.47	4.89|4.89	4.89|4.89	0.63831|0.63831	.|.	0.390165|0.390165	0.28983|0.28983	N|N	0.013514|0.013514	T|T	0.41305|0.41305	0.1153|0.1153	N|N	0.24115|0.24115	0.695|0.695	0.33045|0.33045	D|D	0.532039|0.532039	P|P;B;P	0.34522|0.34909	0.455|0.475;0.337;0.467	B|B;B;B	0.28709|0.38500	0.093|0.142;0.091;0.275	T|T	0.53429|0.53429	-0.8440|-0.8440	10|10	0.27082|0.25751	T|T	0.32|0.34	-14.7831|-14.7831	13.5382|13.5382	0.61657|0.61657	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	397|440;417;405	C9JN07|E9PDV5;A8MVW5;A8MVW5-2	.|.;HECA2_HUMAN;.	L|S	397|417;405;440	ENSP00000389592:F397L|ENSP00000377980:F417S;ENSP00000340532:F405S;ENSP00000390204:F440S	ENSP00000389592:F397L|ENSP00000340532:F405S	F|F	-|-	1|2	0|0	HEPACAM2|HEPACAM2	92663102|92663102	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	5.420000|5.420000	0.66441|0.66441	2.174000|2.174000	0.68829|0.68829	0.528000|0.528000	0.53228|0.53228	TTC|TTT	.	.		0.388	HEPACAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254651.1	NM_198151		G	92825166	A	G	92825166	3	3	260	1	0	0	0	0	1	0	0	0	7062	14	1	2	150	2	HEPACAM2	7	92825166	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	6250944	92825166	66313497	327	37572										
ACN9	57001	hgsc.bcm.edu	37	chr7	96810376	96810376	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cgaaaacagacaaaattcaaCtggaaaagcatgttttggca	8	7	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:96810376C>A	ENST00000432641.2	+	2	1361	c.227C>A	c.(226-228)aCt>aAt	p.T76N	ACN9_ENST00000360382.4_3'UTR|ACN9_ENST00000479853.1_3'UTR	NM_020186.2	NP_064571.1			ACN9 homolog (S. cerevisiae)											large_intestine(1)|lung(4)|ovary(1)|skin(1)|urinary_tract(3)	10	all_cancers(62;2.54e-08)|all_epithelial(64;2.24e-08)|Esophageal squamous(72;0.00507)|all_lung(186;0.154)|Lung NSC(181;0.159)					CAAAATTCAACTGGAAAAGCA	0.363																																					p.T76N		Atlas-SNP	.											.	ACN9	19	.	0			c.C227A						.						79	79	79					7																	96810376		2203	4300	6503	SO:0001583	missense	57001	exon2			ATTCAACTGGAAA	BC028409	CCDS5648.1	7q22.1	2006-02-09			ENSG00000196636	ENSG00000196636			21752	protein-coding gene	gene with protein product		615773					Standard	NM_020186		Approved	DC11	uc003uoo.4	Q9NRP4	OTTHUMG00000154064	ENST00000432641.2:c.227C>A	chr7.hg19:g.96810376C>A	ENSP00000414066:p.Thr76Asn	649.0	0.0		386.0	131.0	NM_020186		Missense_Mutation	SNP	ENST00000432641.2	hg19	CCDS5648.1	.	.	.	.	.	.	.	.	.	.	C	6.924	0.540194	0.13250	.	.	ENSG00000196636	ENST00000432641	.	.	.	4.99	3.12	0.35913	.	1.243490	0.05323	N	0.526843	T	0.37652	0.1011	L	0.46741	1.465	0.19775	N	0.999958	B	0.27316	0.175	B	0.28465	0.09	T	0.30149	-0.9988	9	0.17832	T	0.49	-0.0866	8.3655	0.32385	0.1874:0.6515:0.161:0.0	.	76	Q9NRP4	ACN9_HUMAN	N	76	.	ENSP00000414066:T76N	T	+	2	0	ACN9	96648312	0.350000	0.24878	0.668000	0.29813	0.560000	0.35617	1.221000	0.32503	0.555000	0.29079	0.591000	0.81541	ACT	.	.		0.363	ACN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333685.3	NM_020186		A	96810376	C	A	96810376	3	1	260	1	0	0	0	0	1	0	0	0	145	565	20	3	233	3	ACN9	7	96810376	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	3985210	96810376	62328287	328	37573										
ZNF498	221785	hgsc.bcm.edu	37	chr7	99227239	99227239	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgtgcagcgagtgctggaaaAccttcagccagagacaccac	11	12	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:99227239A>G	ENST00000394152.2	+	8	1558	c.1231A>G	c.(1231-1233)Acc>Gcc	p.T411A	ZSCAN25_ENST00000466948.1_Intron|ZSCAN25_ENST00000262941.6_Missense_Mutation_p.T339A|ZSCAN25_ENST00000334715.3_Missense_Mutation_p.T411A	NM_145115.2	NP_660090.2	Q6NSZ9	ZSC25_HUMAN	zinc finger and SCAN domain containing 25	411					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)										GTGCTGGAAAACCTTCAGCCA	0.592																																					p.T411A		Atlas-SNP	.											.	.	.	.	0			c.A1231G						.						58	56	57					7																	99227239		2203	4300	6503	SO:0001583	missense	221785	exon8			TGGAAAACCTTCA	AK057030	CCDS5671.2	7q22.1	2013-01-09	2013-01-09	2013-01-09	ENSG00000197037	ENSG00000197037		"-", "Zinc fingers, C2H2-type"	21961	protein-coding gene	gene with protein product			"zinc finger protein 498"	ZNF498		11179890	Standard	XM_005250194		Approved	FLJ32468	uc003url.1	Q6NSZ9	OTTHUMG00000074055	ENST00000394152.2:c.1231A>G	chr7.hg19:g.99227239A>G	ENSP00000377708:p.Thr411Ala	73.0	0.0		55.0	4.0	NM_145115	A4D290|D6W5T5|Q14C82|Q14C99|Q5EBM9|Q6DJZ0|Q6N032|Q6ZML3	Missense_Mutation	SNP	ENST00000394152.2	hg19	CCDS5671.2	.	.	.	.	.	.	.	.	.	.	A	8.485	0.860753	0.17178	.	.	ENSG00000197037	ENST00000394152;ENST00000334715;ENST00000262941	T;T;T	0.01126	5.3;5.3;5.3	3.93	3.93	0.45458	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.47093	D	0.000256	T	0.00695	0.0023	N	0.05158	-0.105	0.29414	N	0.86104	B;B	0.21905	0.05;0.062	B;B	0.33196	0.099;0.159	T	0.45440	-0.9261	10	0.02654	T	1	-15.2947	6.1048	0.20067	0.8878:0.0:0.1122:0.0	.	339;411	Q6NSZ9-2;Q6NSZ9	.;ZN498_HUMAN	A	411;411;339	ENSP00000377708:T411A;ENSP00000334800:T411A;ENSP00000262941:T339A	ENSP00000262941:T339A	T	+	1	0	ZNF498	99065175	0.000000	0.05858	0.996000	0.52242	0.994000	0.84299	-0.133000	0.10451	2.001000	0.58596	0.459000	0.35465	ACC	.	.		0.592	ZSCAN25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157203.4	NM_145115		G	99227239	A	G	99227239	3	3	260	1	0	0	0	0	1	0	0	0	17962	43	2	2	1249	2	ZNF498	7	99227239	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	2416863	99227239	59911424	329	37574										
ZSCAN21	7589	hgsc.bcm.edu	37	chr7	99661625	99661625	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agagaatcagttcctactaaAcctaccccaggagagagacg	9	11	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:99661625A>G	ENST00000292450.4	+	4	971	c.807A>G	c.(805-807)aaA>aaG	p.K269K	ZSCAN21_ENST00000456748.2_Intron|ZSCAN21_ENST00000543588.1_Intron|ZSCAN21_ENST00000477297.1_Intron	NM_145914.2	NP_666019.1	Q9Y5A6	ZSC21_HUMAN	zinc finger and SCAN domain containing 21	269					positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|skin(1)	21	Lung NSC(181;0.0211)|all_lung(186;0.0323)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)			TTCCTACTAAACCTACCCCAG	0.448																																					p.K269K		Atlas-SNP	.											.	ZSCAN21	29	.	0			c.A807G						.						83	79	81					7																	99661625		2203	4300	6503	SO:0001819	synonymous_variant	7589	exon4			TACTAAACCTACC	AL136865	CCDS5681.1	7q11.1	2013-01-08	2006-10-06	2006-10-06	ENSG00000166529	ENSG00000166529		"-", "Zinc fingers, C2H2-type"	13104	protein-coding gene	gene with protein product		601261	"zinc finger protein 38 (KOX 25)", "zinc finger protein 38"	ZNF38		2288909, 2014798	Standard	NM_145914		Approved	DKFZp434L134, NY-REN-21, Zipro1	uc003uso.3	Q9Y5A6	OTTHUMG00000154583	ENST00000292450.4:c.807A>G	chr7.hg19:g.99661625A>G		146.0	0.0		100.0	4.0	NM_145914	A4D2A6|D6W5T9|Q9H0B5	Silent	SNP	ENST00000292450.4	hg19	CCDS5681.1																																																																																			.	.		0.448	ZSCAN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336166.1	NM_145914		G	99661625	A	G	99661625	2	3	260	1	0	0	0	0	0	0	0	1	18248	40	2	2		2	ZSCAN21	7	99661625	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	434386	99661625	59477038	330	37575										
AGFG2	3268	hgsc.bcm.edu	37	chr7	100161882	100161882	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gatcagccaagttggggcagAggccactgagccagccagct	14	12	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:100161882A>G	ENST00000300176.4	+	11	1464	c.1342A>G	c.(1342-1344)Agg>Ggg	p.R448G	AGFG2_ENST00000262935.4_3'UTR|AGFG2_ENST00000474713.1_Intron	NM_006076.4	NP_006067.3	O95081	AGFG2_HUMAN	ArfGAP with FG repeats 2	448					regulation of ARF GTPase activity (GO:0032312)	membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GTTGGGGCAGAGGCCACTGAG	0.632											OREG0018204	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R448G		Atlas-SNP	.											.	AGFG2	44	.	0			c.A1342G						.						49	42	44					7																	100161882		2203	4300	6503	SO:0001583	missense	3268	exon11			GGGCAGAGGCCAC	AF015042	CCDS5697.1	7q22.1	2008-09-22	2008-09-22	2008-09-22	ENSG00000106351	ENSG00000106351		"ADP-ribosylation factor GTPase activating proteins"	5177	protein-coding gene	gene with protein product		604019	"HIV-1 Rev binding protein-like"	HRBL		9799793	Standard	XM_005250306		Approved	RABR	uc003uvf.3	O95081	OTTHUMG00000156029	ENST00000300176.4:c.1342A>G	chr7.hg19:g.100161882A>G	ENSP00000300176:p.Arg448Gly	120.0	0.0	1349	81.0	4.0	NM_006076	O75429|Q96AB9|Q96GL4	Missense_Mutation	SNP	ENST00000300176.4	hg19	CCDS5697.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.092622	0.76756	.	.	ENSG00000106351	ENST00000300176	T	0.23754	1.89	4.39	4.39	0.52855	.	0.171076	0.45361	D	0.000379	T	0.43100	0.1232	L	0.57536	1.79	0.80722	D	1	D	0.63880	0.993	D	0.72338	0.977	T	0.25676	-1.0125	10	0.46703	T	0.11	-38.0044	9.9921	0.41877	1.0:0.0:0.0:0.0	.	448	O95081	AGFG2_HUMAN	G	448	ENSP00000300176:R448G	ENSP00000300176:R448G	R	+	1	2	AGFG2	99999818	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.885000	0.56182	1.865000	0.54081	0.454000	0.30748	AGG	.	.		0.632	AGFG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342769.1	NM_006076		G	100161882	A	G	100161882	3	3	260	1	0	0	0	0	1	0	0	0	381	295	11	2	1384	2	AGFG2	7	100161882	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	500257	100161882	58976781	331	37576										
SERPINE1	5054	hgsc.bcm.edu	37	chr7	100773929	100773929	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	atgactgggtgaagacacacAcaaaaggtgagcaggcaggg	15	7	0	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:100773929A>G	ENST00000223095.4	+	3	656	c.499A>G	c.(499-501)Aca>Gca	p.T167A	SERPINE1_ENST00000445463.2_Missense_Mutation_p.T152A	NM_000602.4	NP_000593.1	P05121	PAI1_HUMAN	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1	167					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to lipopolysaccharide (GO:0071222)|chronological cell aging (GO:0001300)|defense response to Gram-negative bacterium (GO:0050829)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|gene expression (GO:0010467)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell migration (GO:0030336)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of plasminogen activation (GO:0010757)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell-matrix adhesion (GO:2000098)|negative regulation of vascular wound healing (GO:0061044)|negative regulation of wound healing (GO:0061045)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of leukotriene production involved in inflammatory response (GO:0035491)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of receptor activity (GO:0010469)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(3)	20	Lung NSC(181;0.136)|all_lung(186;0.182)				Alteplase(DB00009)|Anistreplase(DB00029)|Drotrecogin alfa(DB00055)|Reteplase(DB00015)|Tenecteplase(DB00031)|Urokinase(DB00013)	GAAGACACACACAAAAGGTGA	0.498																																					p.T167A		Atlas-SNP	.											.	SERPINE1	60	.	0			c.A499G						.						133	125	128					7																	100773929		2203	4300	6503	SO:0001583	missense	5054	exon3			ACACACACAAAAG	M16006	CCDS5711.1	7q22.1	2014-02-18	2005-08-18		ENSG00000106366	ENSG00000106366		"Serine (or cysteine) peptidase inhibitors"	8583	protein-coding gene	gene with protein product	"plasminogen activator inhibitor, type I"	173360	"serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1"	PLANH1, PAI1		3097076, 2891140, 24172014	Standard	NM_000602		Approved	PAI	uc003uxt.4	P05121	OTTHUMG00000157107	ENST00000223095.4:c.499A>G	chr7.hg19:g.100773929A>G	ENSP00000223095:p.Thr167Ala	153.0	0.0		91.0	4.0	NM_000602	B7Z4S0|F8WD53	Missense_Mutation	SNP	ENST00000223095.4	hg19	CCDS5711.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.647472	0.87958	.	.	ENSG00000106366	ENST00000223095;ENST00000445463	T;T	0.54866	0.55;0.55	5.33	5.33	0.75918	Serpin domain (3);	0.000000	0.85682	D	0.000000	T	0.80555	0.4645	H	0.95850	3.73	0.58432	D	0.999999	D;D	0.76494	0.999;0.999	D;D	0.85130	0.995;0.997	D	0.86464	0.1781	10	0.87932	D	0	.	13.2518	0.60055	1.0:0.0:0.0:0.0	.	152;167	F8WD53;P05121	.;PAI1_HUMAN	A	167;152	ENSP00000223095:T167A;ENSP00000396766:T152A	ENSP00000223095:T167A	T	+	1	0	SERPINE1	100560649	1.000000	0.71417	0.941000	0.38009	0.958000	0.62258	5.539000	0.67199	2.019000	0.59389	0.459000	0.35465	ACA	.	.		0.498	SERPINE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347458.1	NM_000602		G	100773929	A	G	100773929	3	3	260	1	0	0	0	0	1	0	0	0	14126	159	6	2	505	2	SERPINE1	7	100773929	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	612047	100773929	58364734	332	37577										
LRWD1	222229	hgsc.bcm.edu	37	chr7	102110227	102110227	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	caccacctctatccccctgcGcctctgccctgtcgcctcct	5	23	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:102110227G>A	ENST00000292616.5	+	11	1492	c.1340G>A	c.(1339-1341)cGc>cAc	p.R447H	MIR4467_ENST00000578629.1_RNA	NM_152892.1	NP_690852.1	Q9UFC0	LRWD1_HUMAN	leucine-rich repeats and WD repeat domain containing 1	447					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|DNA replication initiation (GO:0006270)|establishment of protein localization to chromatin (GO:0071169)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nuclear origin of replication recognition complex (GO:0005664)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|telomeric heterochromatin (GO:0031933)	chromatin binding (GO:0003682)|methyl-CpG binding (GO:0008327)|methylated histone binding (GO:0035064)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|skin(1)|stomach(2)	20						ATCCCCCTGCGCCTCTGCCCT	0.701																																					p.R447H		Atlas-SNP	.											.	LRWD1	41	.	0			c.G1340A						.						56	53	54					7																	102110227		2203	4300	6503	SO:0001583	missense	222229	exon11			CCCTGCGCCTCTG	AL133057	CCDS34715.1	7q22.1	2013-01-10			ENSG00000161036	ENSG00000161036		"WD repeat domain containing"	21769	protein-coding gene	gene with protein product	"origin recognition complex associated", "centromere protein 33"	615167				20932478, 20850016, 20180869	Standard	NM_152892		Approved	DKFZp434K1815, ORCA, CENP-33	uc003uzn.3	Q9UFC0	OTTHUMG00000157718	ENST00000292616.5:c.1340G>A	chr7.hg19:g.102110227G>A	ENSP00000292616:p.Arg447His	119.0	0.0		78.0	4.0	NM_152892	A8K4K2|B2R9G2|Q8N0T9|Q8WV43|Q96GJ2	Missense_Mutation	SNP	ENST00000292616.5	hg19	CCDS34715.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.58|11.58	1.682136|1.682136	0.29872|0.29872	.|.	.|.	ENSG00000161036|ENSG00000161036	ENST00000488689;ENST00000468175|ENST00000292616	.|T	.|0.70749	.|-0.51	4.8|4.8	4.8|4.8	0.61643|0.61643	.|WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	.|0.051124	.|0.85682	.|D	.|0.000000	T|T	0.76421|0.76421	0.3985|0.3985	L|L	0.38175|0.38175	1.15|1.15	0.47276|0.47276	D|D	0.999378|0.999378	.|D	.|0.89917	.|1.0	.|D	.|0.85130	.|0.997	T|T	0.70773|0.70773	-0.4781|-0.4781	5|10	.|0.17369	.|T	.|0.5	-32.9076|-32.9076	17.033|17.033	0.86466|0.86466	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|447	.|Q9UFC0	.|LRWD1_HUMAN	T|H	76;33|447	.|ENSP00000292616:R447H	.|ENSP00000292616:R447H	A|R	+|+	1|2	0|0	LRWD1|LRWD1	101897232|101897232	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.107000|0.107000	0.19398|0.19398	5.832000|5.832000	0.69337|0.69337	2.503000|2.503000	0.84419|0.84419	0.561000|0.561000	0.74099|0.74099	GCC|CGC	.	.		0.701	LRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349493.1	NM_152892		A	102110227	G	A	102110227	3	1	260	1	0	0	0	0	1	0	0	0	9056	1087	38	1	1382	1	LRWD1	7	102110227	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	1336298	102110227	57028436	333	37578										
RELN	5649	hgsc.bcm.edu	37	chr7	103180823	103180823	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cgagaggccaccgttgagagAatactgtaggagcacgggtt	15	8	0	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:103180823A>G	ENST00000428762.1	-	44	6910	c.6751T>C	c.(6751-6753)Tct>Cct	p.S2251P	RELN_ENST00000343529.5_Missense_Mutation_p.S2251P|RELN_ENST00000424685.2_Missense_Mutation_p.S2251P	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	2251					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		CCGTTGAGAGAATACTGTAGG	0.493																																					p.S2251P	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.T6751C						.						111	108	109					7																	103180823		2203	4300	6503	SO:0001583	missense	5649	exon44			TGAGAGAATACTG		CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.6751T>C	chr7.hg19:g.103180823A>G	ENSP00000392423:p.Ser2251Pro	83.0	0.0		47.0	4.0	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	hg19	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	A	19.99	3.928203	0.73327	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.65916	-0.18;-0.18;-0.18	5.44	5.44	0.79542	Neuraminidase (2);	0.000000	0.85682	D	0.000000	T	0.80844	0.4701	M	0.82823	2.61	0.58432	D	0.999999	D;D	0.89917	1.0;0.998	D;D	0.97110	1.0;0.994	D	0.84048	0.0368	10	0.87932	D	0	.	15.7924	0.78376	1.0:0.0:0.0:0.0	.	2251;2251	P78509-2;P78509	.;RELN_HUMAN	P	2251	ENSP00000392423:S2251P;ENSP00000345694:S2251P;ENSP00000388446:S2251P	ENSP00000345694:S2251P	S	-	1	0	RELN	102968059	1.000000	0.71417	0.998000	0.56505	0.670000	0.39368	8.678000	0.91211	2.194000	0.70268	0.533000	0.62120	TCT	.	.		0.493	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		G	103180823	A	G	103180823	3	3	260	1	0	0	0	0	1	0	0	0	13235	246	9	2	3719	2	RELN	7	103180823	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1070596	103180823	55957840	334	37579										
ORC5L	5001	hgsc.bcm.edu	37	chr7	103808859	103808859	+	Intron	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgctctttagtattaactttAgtatcttgataattagctga	6	5	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:103808859A>T	ENST00000297431.4	-	9	1020				ORC5_ENST00000545943.1_Intron|ORC5_ENST00000447452.2_Silent_p.T313T	NM_002553.3	NP_002544.1	O43913	ORC5_HUMAN	origin recognition complex, subunit 5						DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)	ATP binding (GO:0005524)|DNA replication origin binding (GO:0003688)|nucleotide binding (GO:0000166)			kidney(1)|large_intestine(2)|lung(9)|pancreas(1)|upper_aerodigestive_tract(1)	14						TATTAACTTTAGTATCTTGAT	0.328																																					p.T313T		Atlas-SNP	.											.	ORC5	48	.	0			c.T939A						.						93	95	94					7																	103808859		1327	2309	3636	SO:0001627	intron_variant	5001	exon9			AACTTTAGTATCT		CCDS5734.1, CCDS47681.1	7q22.1	2014-06-13	2010-10-12	2010-10-12	ENSG00000164815	ENSG00000164815			8491	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 117"	602331	"origin recognition complex, subunit 5 (yeast homolog)-like", "origin recognition complex, subunit 5-like (yeast)", "origin recognition complex, subunit 5 homolog (yeast)"	ORC5L		9417919, 9829972	Standard	NM_002553		Approved	Orc5p, ORC5T, PPP1R117	uc003vcb.3	O43913	OTTHUMG00000157275	ENST00000297431.4:c.877+61T>A	chr7.hg19:g.103808859A>T		102.0	0.0		74.0	4.0	NM_181747	A4D0P8|O60590|O95268	Silent	SNP	ENST00000297431.4	hg19	CCDS5734.1																																																																																			.	.		0.328	ORC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348286.1	NM_002553		T	103808859	A	T	103808859	1	4	260	0	1	0	0	0	0	0	0	0	11274	407	15	4		4	ORC5L	7	103808859	Intron	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	628036	103808859	55329804	335	37580										
MLL5	55904	hgsc.bcm.edu	37	chr7	104681461	104681461	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtcatacttggaaatggctgCaggttcagagtaagtattta	11	5	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:104681461C>T	ENST00000311117.3	+	3	607	c.62C>T	c.(61-63)gCa>gTa	p.A21V	KMT2E_ENST00000334877.4_Missense_Mutation_p.A21V|KMT2E_ENST00000257745.4_Missense_Mutation_p.A21V|KMT2E_ENST00000334914.7_5'UTR|KMT2E_ENST00000476671.1_Missense_Mutation_p.A21V	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	21					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)										GAAATGGCTGCAGGTTCAGAG	0.378																																					p.A21V		Atlas-SNP	.											.	MLL5	173	.	0			c.C62T						.						106	97	100					7																	104681461		2203	4300	6503	SO:0001583	missense	55904	exon2			TGGCTGCAGGTTC	AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	18541	protein-coding gene	gene with protein product		608444	"myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.62C>T	chr7.hg19:g.104681461C>T	ENSP00000312379:p.Ala21Val	112.0	0.0		72.0	4.0	NM_018682	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Missense_Mutation	SNP	ENST00000311117.3	hg19	CCDS34723.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.565884	0.86439	.	.	ENSG00000005483	ENST00000311117;ENST00000393656;ENST00000334877;ENST00000351043;ENST00000257745;ENST00000478990;ENST00000495267;ENST00000476671;ENST00000474203	D;D;D;D;T;D	0.96745	-3.9;-3.19;-3.9;-3.88;0.84;-4.11	5.5	5.5	0.81552	.	0.059107	0.64402	D	0.000002	D	0.97126	0.9061	L	0.41824	1.3	0.80722	D	1	P;D	0.71674	0.457;0.998	B;D	0.76071	0.223;0.987	D	0.97754	1.0216	10	0.62326	D	0.03	.	19.3941	0.94598	0.0:1.0:0.0:0.0	.	21;21	Q8IZD2;Q8IZD2-3	MLL5_HUMAN;.	V	21	ENSP00000312379:A21V;ENSP00000335599:A21V;ENSP00000257745:A21V;ENSP00000419883:A21V;ENSP00000420415:A21V;ENSP00000417888:A21V	ENSP00000257745:A21V	A	+	2	0	MLL5	104468697	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.575000	0.86900	0.585000	0.79938	GCA	.	.		0.378	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1			T	104681461	C	T	104681461	3	4	260	1	0	0	0	0	1	0	0	0	9633	710	25	3	64	3	MLL5	7	104681461	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	872602	104681461	54457202	336	37581										
ATXN7L1	222255	hgsc.bcm.edu	37	chr7	105260739	105260739	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcaaacacatagtaccctcgTcccatgaggcgactcccaaa	6	15	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:105260739T>C	ENST00000419735.3	-	9	1470	c.1425A>G	c.(1423-1425)ggA>ggG	p.G475G	ATXN7L1_ENST00000388807.4_Silent_p.G33G|ATXN7L1_ENST00000472910.1_5'UTR|ATXN7L1_ENST00000477775.1_Silent_p.G351G	NM_020725.1	NP_065776.1	Q9ULK2	AT7L1_HUMAN	ataxin 7-like 1	475										endometrium(1)|large_intestine(4)|lung(5)	10						AGTACCCTCGTCCCATGAGGC	0.353																																					p.G475G		Atlas-SNP	.											.	ATXN7L1	56	.	0			c.A1425G						.						137	103	113					7																	105260739		692	1591	2283	SO:0001819	synonymous_variant	222255	exon9			CCCTCGTCCCATG	AB033044	CCDS34727.1, CCDS47682.1, CCDS47683.1	7q22.1	2007-11-13			ENSG00000146776	ENSG00000146776			22210	protein-coding gene	gene with protein product			"ataxin 7-like 4"	ATXN7L4		15115762	Standard	NM_152749		Approved	KIAA1218, MGC33190	uc003vde.2	Q9ULK2	OTTHUMG00000157521	ENST00000419735.3:c.1425A>G	chr7.hg19:g.105260739T>C		189.0	0.0		86.0	5.0	NM_020725	A4D0Q2|B4DTS1|Q8N2T0	Silent	SNP	ENST00000419735.3	hg19	CCDS47682.1																																																																																			.	.		0.353	ATXN7L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349037.2			C	105260739	T	C	105260739	2	2	260	1	0	0	0	0	0	0	0	1	1216	1654	58	2		2	ATXN7L1	7	105260739	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	579278	105260739	53877924	337	37582										
LRRN3	54674	hgsc.bcm.edu	37	chr7	110764148	110764148	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtagaagctgggagctatgtTtcctttcactgtagagctac	11	8	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:110764148T>C	ENST00000422987.3	+	2	2151	c.1320T>C	c.(1318-1320)gtT>gtC	p.V440V	IMMP2L_ENST00000331762.3_Intron|IMMP2L_ENST00000450877.1_Intron|IMMP2L_ENST00000489381.1_Intron|IMMP2L_ENST00000405709.2_Intron|IMMP2L_ENST00000452895.1_Intron|IMMP2L_ENST00000437687.1_Intron|IMMP2L_ENST00000447215.1_Intron|LRRN3_ENST00000308478.5_Silent_p.V440V|IMMP2L_ENST00000415362.1_Intron|LRRN3_ENST00000451085.1_Silent_p.V440V	NM_018334.4	NP_060804.3	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3	440	Ig-like C2-type.				positive regulation of protein phosphorylation (GO:0001934)	clathrin adaptor complex (GO:0030131)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(15)|lung(20)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)		GGAGCTATGTTTCCTTTCACT	0.433																																					p.V440V		Atlas-SNP	.											.	LRRN3	132	.	0			c.T1320C						.						125	133	130					7																	110764148		2203	4300	6503	SO:0001819	synonymous_variant	54674	exon2			CTATGTTTCCTTT	AB060967	CCDS5754.1	7q31.1	2013-02-11			ENSG00000173114	ENSG00000173114		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	17200	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 5"					11549284	Standard	NM_001099660		Approved	NLRR3, FLJ11129, FIGLER5	uc003vfs.4	Q9H3W5	OTTHUMG00000155039	ENST00000422987.3:c.1320T>C	chr7.hg19:g.110764148T>C		82.0	0.0		50.0	4.0	NM_018334	O43377|Q6I9V8|Q8IYQ6	Silent	SNP	ENST00000422987.3	hg19	CCDS5754.1																																																																																			.	.		0.433	LRRN3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338171.2	NM_018334		C	110764148	T	C	110764148	2	2	260	1	0	0	0	0	0	0	0	1	9045	1828	64	2		2	LRRN3	7	110764148	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	5503409	110764148	48374515	338	37583										
AASS	10157	hgsc.bcm.edu	37	chr7	121721604	121721604	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggcaggaagcgcttctctgtTtataagacctaattttacaa	8	8	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:121721604T>C	ENST00000393376.1	-	19	2325	c.2230A>G	c.(2230-2232)Aac>Gac	p.N744D	AASS_ENST00000473553.1_5'UTR|AASS_ENST00000417368.2_Missense_Mutation_p.N744D|RNU7-154P_ENST00000516194.1_RNA			Q9UDR5	AASS_HUMAN	aminoadipate-semialdehyde synthase	744	Saccharopine dehydrogenase.				cellular nitrogen compound metabolic process (GO:0034641)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity (GO:0047131)|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity (GO:0047130)			autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(6)|large_intestine(12)|lung(27)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	54						GCTTCTCTGTTTATAAGACCT	0.373																																					p.N744D		Atlas-SNP	.											.	AASS	123	.	0			c.A2230G						.						100	107	105					7																	121721604		2203	4300	6503	SO:0001583	missense	10157	exon20			CTCTGTTTATAAG	AF229180	CCDS5783.1	7q31.3	2010-12-14			ENSG00000008311	ENSG00000008311			17366	protein-coding gene	gene with protein product		605113				10775527	Standard	NM_005763		Approved	LORSDH, LKRSDH	uc003vkb.3	Q9UDR5	OTTHUMG00000157058	ENST00000393376.1:c.2230A>G	chr7.hg19:g.121721604T>C	ENSP00000377040:p.Asn744Asp	110.0	0.0		67.0	4.0	NM_005763	O95462	Missense_Mutation	SNP	ENST00000393376.1	hg19	CCDS5783.1	.	.	.	.	.	.	.	.	.	.	T	7.573	0.667111	0.14710	.	.	ENSG00000008311	ENST00000393376;ENST00000417368	T;T	0.40225	1.04;1.04	5.72	5.72	0.89469	.	0.125574	0.64402	D	0.000001	T	0.27205	0.0667	N	0.21097	0.63	0.49483	D	0.999798	B	0.06786	0.001	B	0.15052	0.012	T	0.10706	-1.0618	10	0.02654	T	1	-14.7098	14.8262	0.70113	0.0:0.0:0.0:1.0	.	744	Q9UDR5	AASS_HUMAN	D	744	ENSP00000377040:N744D;ENSP00000403768:N744D	ENSP00000377040:N744D	N	-	1	0	AASS	121508840	1.000000	0.71417	0.963000	0.40424	0.534000	0.34807	3.922000	0.56462	2.184000	0.69523	0.528000	0.53228	AAC	.	.		0.373	AASS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347300.1	NM_005763		C	121721604	T	C	121721604	3	2	260	1	0	0	0	0	1	0	0	0	24	1841	64	2	570	2	AASS	7	121721604	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	10957456	121721604	37417059	339	37584										
KLHDC10	23008	hgsc.bcm.edu	37	chr7	129761948	129761948	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttggaggtacaaccggctatAtttacagcacagacctgcac	9	11	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:129761948A>G	ENST00000335420.5	+	5	819	c.685A>G	c.(685-687)Att>Gtt	p.I229V		NM_014997.3	NP_055812.1	Q6PID8	KLD10_HUMAN	kelch domain containing 10	229						cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|liver(2)|lung(10)|prostate(1)	17						AACCGGCTATATTTACAGCAC	0.443																																					p.I229V		Atlas-SNP	.											.	KLHDC10	36	.	0			c.A685G						.						137	108	118					7																	129761948		2203	4300	6503	SO:0001583	missense	23008	exon5			GGCTATATTTACA		CCDS5815.1	7q32.2	2008-08-20			ENSG00000128607	ENSG00000128607			22194	protein-coding gene	gene with protein product	"scruin like at the midline homolog (Drosophila)"	615152					Standard	NM_014997		Approved	KIAA0265, slim	uc003vpj.2	Q6PID8	OTTHUMG00000157654	ENST00000335420.5:c.685A>G	chr7.hg19:g.129761948A>G	ENSP00000334140:p.Ile229Val	232.0	0.0		184.0	67.0	NM_014997	Q86Y99|Q92554	Missense_Mutation	SNP	ENST00000335420.5	hg19	CCDS5815.1	.	.	.	.	.	.	.	.	.	.	A	12.14	1.847752	0.32606	.	.	ENSG00000128607	ENST00000335420;ENST00000468226	T;T	0.11063	2.81;2.81	5.47	4.11	0.48088	Galactose oxidase, beta-propeller (1);	0.105918	0.64402	D	0.000006	T	0.08133	0.0203	N	0.25789	0.76	0.51012	D	0.999909	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.12156	0.002;0.001;0.007	T	0.21143	-1.0254	10	0.30078	T	0.28	-11.3778	11.1586	0.48501	0.9152:0.0:0.0848:0.0	.	78;86;229	Q96G43;Q6PID8-2;Q6PID8	.;.;KLD10_HUMAN	V	229;86	ENSP00000334140:I229V;ENSP00000420034:I86V	ENSP00000334140:I229V	I	+	1	0	KLHDC10	129549184	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.421000	0.59848	2.064000	0.61679	0.533000	0.62120	ATT	.	.		0.443	KLHDC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349347.2			G	129761948	A	G	129761948	3	3	260	1	0	0	0	0	1	0	0	0	8364	449	16	2	703	2	KLHDC10	7	129761948	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	8040344	129761948	29376715	340	37585										
PLXNA4	91584	hgsc.bcm.edu	37	chr7	131865424	131865424	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cggtcacggtgcacggcttcTccccaaccagcacagtgtag	11	15	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:131865424T>C	ENST00000359827.3	-	19	4522	c.3560A>G	c.(3559-3561)gAg>gGg	p.E1187G	PLXNA4_ENST00000321063.4_Missense_Mutation_p.E1187G			Q9HCM2	PLXA4_HUMAN	plexin A4	1187	IPT/TIG 4.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						GCACGGCTTCTCCCCAACCAG	0.597																																					p.E1187G		Atlas-SNP	.											.	PLXNA4	873	.	0			c.A3560G						.						69	73	72					7																	131865424		2115	4244	6359	SO:0001583	missense	91584	exon19			GGCTTCTCCCCAA	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"Plexins"	9102	protein-coding gene	gene with protein product		604280	"plexin A4, A", "plexin A4, B"	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.3560A>G	chr7.hg19:g.131865424T>C	ENSP00000352882:p.Glu1187Gly	132.0	0.0		87.0	5.0	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	hg19	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	T	15.10	2.733907	0.48939	.	.	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.73681	-0.77;-0.77	5.38	5.38	0.77491	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.096704	0.64402	D	0.000001	T	0.66066	0.2752	L	0.41961	1.31	0.58432	D	0.999999	B	0.12630	0.006	B	0.24006	0.05	T	0.60806	-0.7190	10	0.07644	T	0.81	.	15.3883	0.74723	0.0:0.0:0.0:1.0	.	1187	Q9HCM2	PLXA4_HUMAN	G	1187	ENSP00000323194:E1187G;ENSP00000352882:E1187G	ENSP00000323194:E1187G	E	-	2	0	PLXNA4	131515964	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	8.013000	0.88655	2.062000	0.61559	0.459000	0.35465	GAG	.	.		0.597	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		C	131865424	T	C	131865424	3	2	260	1	0	0	0	0	1	0	0	0	12131	1551	54	2	2180	2	PLXNA4	7	131865424	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	2103476	131865424	27273239	341	37586										
EXOC4	60412	hgsc.bcm.edu	37	chr7	133692446	133692446	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	caggcctgggccacctgatcTcctgcatcctcattaatggt	9	14	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:133692446T>C	ENST00000253861.4	+	17	2574	c.2545T>C	c.(2545-2547)Tcc>Ccc	p.S849P	EXOC4_ENST00000539845.1_Missense_Mutation_p.S748P|EXOC4_ENST00000545148.1_Missense_Mutation_p.S459P|EXOC4_ENST00000541309.1_Missense_Mutation_p.S137P	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	849					cellular protein metabolic process (GO:0044267)|membrane organization (GO:0061024)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)	protein N-terminus binding (GO:0047485)			NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(16)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	50		Esophageal squamous(399;0.129)				CCACCTGATCTCCTGCATCCT	0.488																																					p.S849P		Atlas-SNP	.											.	EXOC4	118	.	0			c.T2545C						.						63	53	56					7																	133692446		2203	4300	6503	SO:0001583	missense	60412	exon17			CTGATCTCCTGCA	AL831989	CCDS5829.1, CCDS43648.1	7q31	2013-01-22	2005-11-01	2005-11-01	ENSG00000131558	ENSG00000131558			30389	protein-coding gene	gene with protein product		608185	"SEC8-like 1 (S. cerevisiae)"	SEC8L1		11214970, 12687004	Standard	XM_005250523		Approved	KIAA1699, MGC27170, SEC8, Sec8p	uc003vrk.3	Q96A65	OTTHUMG00000155259	ENST00000253861.4:c.2545T>C	chr7.hg19:g.133692446T>C	ENSP00000253861:p.Ser849Pro	129.0	0.0		81.0	4.0	NM_021807	E9PED2|Q541U8|Q9C0G4|Q9H9K0|Q9P102	Missense_Mutation	SNP	ENST00000253861.4	hg19	CCDS5829.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.145485	0.77888	.	.	ENSG00000131558	ENST00000253861;ENST00000546185;ENST00000539845;ENST00000545148;ENST00000541309	.	.	.	5.45	4.28	0.50868	.	0.000000	0.85682	D	0.000000	T	0.62889	0.2465	L	0.55481	1.735	0.80722	D	1	P;D;D	0.67145	0.898;0.987;0.996	B;P;P	0.55713	0.434;0.782;0.731	T	0.59279	-0.7484	9	0.30078	T	0.28	.	11.846	0.52385	0.0:0.0:0.1466:0.8534	.	381;459;849	B7Z689;F5GZT1;Q96A65	.;.;EXOC4_HUMAN	P	849;468;748;459;137	.	ENSP00000253861:S849P	S	+	1	0	EXOC4	133342986	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.227000	0.78070	0.894000	0.36317	-0.438000	0.05819	TCC	.	.		0.488	EXOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339182.1	NM_021807		C	133692446	T	C	133692446	3	2	260	1	0	0	0	0	1	0	0	0	5308	1551	54	2	2620	2	EXOC4	7	133692446	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1827022	133692446	25446217	342	37587										
DGKI	9162	hgsc.bcm.edu	37	chr7	137304620	137304620	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gggcgggacaataacagcagCatgagcccccagggagcagg	16	11	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:137304620C>T	ENST00000288490.5	-	8	943	c.943G>A	c.(943-945)Gct>Act	p.A315T	DGKI_ENST00000424189.2_Missense_Mutation_p.A315T|DGKI_ENST00000453654.2_Missense_Mutation_p.A15T|DGKI_ENST00000446122.1_Missense_Mutation_p.A315T	NM_004717.2	NP_004708.1	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	315					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|positive regulation of Ras protein signal transduction (GO:0046579)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of Rap GTPase activity (GO:0032317)	cytoplasm (GO:0005737)|guanyl-nucleotide exchange factor complex (GO:0032045)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(46)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	84						ATAACAGCAGCATGAGCCCCC	0.483																																					p.A315T		Atlas-SNP	.											.	DGKI	335	.	0			c.G943A						.						125	122	123					7																	137304620		2203	4300	6503	SO:0001583	missense	9162	exon8			CAGCAGCATGAGC	AF061936	CCDS5845.1	7q32.3-q33	2013-01-10			ENSG00000157680	ENSG00000157680		"Ankyrin repeat domain containing"	2855	protein-coding gene	gene with protein product		604072				9830018	Standard	NM_004717		Approved	DGK-IOTA	uc003vtt.3	O75912	OTTHUMG00000155697	ENST00000288490.5:c.943G>A	chr7.hg19:g.137304620C>T	ENSP00000288490:p.Ala315Thr	126.0	0.0		80.0	5.0	NM_004717	A4D1Q9|Q9NZ49	Missense_Mutation	SNP	ENST00000288490.5	hg19	CCDS5845.1	.	.	.	.	.	.	.	.	.	.	C	36	5.709426	0.96821	.	.	ENSG00000157680	ENST00000453654;ENST00000540376;ENST00000424189;ENST00000288490;ENST00000446122	T;T;T	0.35973	1.82;1.28;1.47	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.62684	0.2448	M	0.76170	2.325	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.66716	0.945;0.946	T	0.60895	-0.7172	10	0.56958	D	0.05	.	20.6721	0.99693	0.0:1.0:0.0:0.0	.	15;315	E9PFX6;O75912	.;DGKI_HUMAN	T	15;263;315;315;315	ENSP00000392161:A15T;ENSP00000288490:A315T;ENSP00000399131:A315T	ENSP00000288490:A315T	A	-	1	0	DGKI	136955160	1.000000	0.71417	0.975000	0.42487	0.994000	0.84299	7.818000	0.86416	2.894000	0.99253	0.591000	0.81541	GCT	.	.		0.483	DGKI-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341286.3	NM_004717		T	137304620	C	T	137304620	3	4	260	1	0	0	0	0	1	0	0	0	4473	710	25	3	2362	3	DGKI	7	137304620	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	3612174	137304620	21834043	343	37588										
ZC3HAV1	56829	hgsc.bcm.edu	37	chr7	138749685	138749685	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tggcacaactcccctcggacAggattgatagagagactcca	10	12	0	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:138749685A>G	ENST00000242351.5	-	8	2249	c.1933T>C	c.(1933-1935)Tgt>Cgt	p.C645R	ZC3HAV1_ENST00000464606.1_Missense_Mutation_p.C767R|ZC3HAV1_ENST00000471652.1_Missense_Mutation_p.C645R	NM_020119.3	NP_064504.2	Q7Z2W4	ZCCHV_HUMAN	zinc finger CCCH-type, antiviral 1	645	WWE. {ECO:0000255|PROSITE- ProRule:PRU00248}.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of mRNA catabolic process (GO:0061014)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(4)|skin(1)	37						CCCCTCGGACAGGATTGATAG	0.438																																					p.C645R		Atlas-SNP	.											.	ZC3HAV1	75	.	0			c.T1933C						.						125	118	120					7																	138749685		2203	4300	6503	SO:0001583	missense	56829	exon8			TCGGACAGGATTG	BX571742	CCDS5851.1, CCDS55171.1	7q34	2012-07-05			ENSG00000105939	ENSG00000105939		"Zinc fingers, CCCH-type domain containing", "Poly (ADP-ribose) polymerases"	23721	protein-coding gene	gene with protein product	"zinc finger antiviral protein", " CCCH-type zinc finger antiviral protein"	607312				12215647, 12851707	Standard	NM_024625		Approved	ZAP, FLB6421, FLJ13288, MGC48898, ZC3HDC2, ZC3H2, PARP13	uc003vun.3	Q7Z2W4	OTTHUMG00000157471	ENST00000242351.5:c.1933T>C	chr7.hg19:g.138749685A>G	ENSP00000242351:p.Cys645Arg	154.0	0.0		93.0	4.0	NM_024625	A4D1R2|A4D1S4|Q8IW57|Q8TAJ3|Q96N79|Q9H8R9|Q9P0Y7	Missense_Mutation	SNP	ENST00000242351.5	hg19	CCDS5851.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	7.653|7.653	0.683244|0.683244	0.14907|0.14907	.|.	.|.	ENSG00000105939|ENSG00000105939	ENST00000242351;ENST00000464606;ENST00000471652;ENST00000540247|ENST00000460845	T;T;T|.	0.27890|.	1.64;1.64;1.64|.	4.32|4.32	3.13|3.13	0.36017|0.36017	WWE domain (1);|.	1.252960|.	0.05459|.	N|.	0.550944|.	T|T	0.38983|0.38983	0.1061|0.1061	L|L	0.50919|0.50919	1.6|1.6	0.09310|0.09310	N|N	1|1	B;B|.	0.32693|.	0.069;0.38|.	B;B|.	0.30251|.	0.113;0.102|.	T|T	0.27088|0.27088	-1.0084|-1.0084	10|5	0.36615|.	T|.	0.2|.	.|.	5.1171|5.1171	0.14840|0.14840	0.6275:0.1899:0.0:0.1826|0.6275:0.1899:0.0:0.1826	.|.	645;645|.	Q7Z2W4-2;Q7Z2W4|.	.;ZCCHV_HUMAN|.	R|P	645;767;645;405|209	ENSP00000242351:C645R;ENSP00000418385:C767R;ENSP00000419855:C645R|.	ENSP00000242351:C645R|.	C|L	-|-	1|2	0|0	ZC3HAV1|ZC3HAV1	138400225|138400225	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.001000|0.001000	0.01503|0.01503	-0.054000|-0.054000	0.11826|0.11826	0.779000|0.779000	0.33543|0.33543	0.524000|0.524000	0.50904|0.50904	TGT|CTG	.	.		0.438	ZC3HAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348915.1	NM_020119		G	138749685	A	G	138749685	3	3	260	1	0	0	0	0	1	0	0	0	17590	188	7	2	803	2	ZC3HAV1	7	138749685	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1445065	138749685	20388978	344	37589										
TPK1	27010	hgsc.bcm.edu	37	chr7	144288520	144288520	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttcacttttgactcactggtTggagcaggtagatcagcgat	11	8	3	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:144288520T>A	ENST00000360057.3	-	7	599	c.497A>T	c.(496-498)cAa>cTa	p.Q166L	TPK1_ENST00000549981.1_Missense_Mutation_p.Q49L|TPK1_ENST00000378099.3_Intron|TPK1_ENST00000547966.1_5'UTR|TPK1_ENST00000538212.2_Intron	NM_022445.3	NP_071890.2	Q9H3S4	TPK1_HUMAN	thiamin pyrophosphokinase 1	166					small molecule metabolic process (GO:0044281)|thiamine diphosphate biosynthetic process (GO:0009229)|thiamine metabolic process (GO:0006772)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|thiamine binding (GO:0030975)|thiamine diphosphokinase activity (GO:0004788)			large_intestine(3)|lung(12)|ovary(2)|urinary_tract(2)	19					Thiamine(DB00152)	ACTCACTGGTTGGAGCAGGTA	0.428																																					p.Q166L	Ovarian(45;88 1034 2073 5829 28455)	Atlas-SNP	.											.	TPK1	41	.	0			c.A497T						.						138	139	139					7																	144288520		2203	4300	6503	SO:0001583	missense	27010	exon7			ACTGGTTGGAGCA	AB028138	CCDS5888.1, CCDS55178.1	7q34-q35	2008-07-18			ENSG00000196511	ENSG00000196511			17358	protein-coding gene	gene with protein product	"placental protein 20", "thiamine pyrophosphokinase 1", "thiamine kinase", "thiamine diphosphokinase"	606370				11342111	Standard	NM_022445		Approved	HTPK1, PP20	uc003weq.3	Q9H3S4	OTTHUMG00000152774	ENST00000360057.3:c.497A>T	chr7.hg19:g.144288520T>A	ENSP00000353165:p.Gln166Leu	134.0	0.0		83.0	4.0	NM_022445	A8K0T7|D3DWG0|I6L9B8|Q6NUR5|Q9H602	Missense_Mutation	SNP	ENST00000360057.3	hg19	CCDS5888.1	.	.	.	.	.	.	.	.	.	.	T	13.93	2.385254	0.42308	.	.	ENSG00000196511	ENST00000360057;ENST00000549981;ENST00000552881	T;D	0.83075	-1.04;-1.68	5.78	5.78	0.91487	Thiamin pyrophosphokinase, vitamin B1-binding domain (2);	0.110308	0.64402	D	0.000006	T	0.79161	0.4399	M	0.64997	1.995	0.46849	D	0.999227	P	0.40332	0.713	B	0.33568	0.166	T	0.79652	-0.1714	10	0.39692	T	0.17	-13.6891	14.0659	0.64828	0.0:0.0:0.0:1.0	.	166	Q9H3S4	TPK1_HUMAN	L	166;49;166	ENSP00000353165:Q166L;ENSP00000448655:Q166L	ENSP00000353165:Q166L	Q	-	2	0	TPK1	143919453	0.997000	0.39634	0.901000	0.35422	0.512000	0.34134	2.723000	0.47277	2.220000	0.72140	0.533000	0.62120	CAA	.	.		0.428	TPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327777.1	NM_022445		A	144288520	T	A	144288520	3	1	260	1	0	0	0	0	1	0	0	0	16419	1812	63	4	246	4	TPK1	7	144288520	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	5538835	144288520	14850143	345	37590										
SLC4A2	6522	hgsc.bcm.edu	37	chr7	150761997	150761997	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aggaccagtccatcttccccTgcaccactgccccaccagga	7	19	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:150761997T>C	ENST00000485713.1	+	5	1562	c.522T>C	c.(520-522)ccT>ccC	p.P174P	SLC4A2_ENST00000461735.1_Silent_p.P160P|SLC4A2_ENST00000310317.5_Silent_p.P92P|SLC4A2_ENST00000392826.2_Silent_p.P165P|SLC4A2_ENST00000413384.2_Silent_p.P174P	NM_001199692.1	NP_001186621.1	P04920	B3A2_HUMAN	solute carrier family 4 (anion exchanger), member 2	174	Pro-rich.				anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(14)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CATCTTCCCCTGCACCACTGC	0.607																																					p.P174P		Atlas-SNP	.											.	SLC4A2	98	.	0			c.T522C						.						70	71	71					7																	150761997		2203	4300	6503	SO:0001819	synonymous_variant	6522	exon5			TTCCCCTGCACCA		CCDS5917.1, CCDS56520.1, CCDS56521.1	7q36.1	2013-07-19	2013-07-19		ENSG00000164889	ENSG00000164889		"Solute carriers"	11028	protein-coding gene	gene with protein product	"anion exchanger 2 type a", "anion exchanger 2 type b1", "anion exchanger 2 type b2"	109280	"erythrocyte membrane protein band 3-like 1", "solute carrier family 4, anion exchanger, member 2 (erythrocyte membrane protein band 3-like 1)"	EPB3L1, AE2		8434259	Standard	NM_003040		Approved	HKB3, BND3L, NBND3	uc003wit.4	P04920	OTTHUMG00000158443	ENST00000485713.1:c.522T>C	chr7.hg19:g.150761997T>C		104.0	0.0		75.0	4.0	NM_003040	B2R6T0|B4DIT0|D3DX05|F8W682|Q45EY5|Q969L3	Silent	SNP	ENST00000485713.1	hg19	CCDS5917.1																																																																																			.	.		0.607	SLC4A2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351039.1	NM_003040		C	150761997	T	C	150761997	2	2	260	1	0	0	0	0	0	0	0	1	14669	1567	55	2		2	SLC4A2	7	150761997	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	6473477	150761997	8376666	346	37591										
EN2	2020	hgsc.bcm.edu	37	chr7	155255188	155255188	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tccagaccaacaggtacctgAcggagcagcggcgccagagc	13	14	0	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr7:155255188A>G	ENST00000297375.4	+	2	1057	c.808A>G	c.(808-810)Acg>Gcg	p.T270A		NM_001427.3	NP_001418.2	P19622	HME2_HUMAN	engrailed homeobox 2	270					hindbrain development (GO:0030902)|midbrain development (GO:0030901)|multicellular organismal development (GO:0007275)|neuron development (GO:0048666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|large_intestine(1)|lung(2)	4	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CAGGTACCTGACGGAGCAGCG	0.602																																					p.T270A		Atlas-SNP	.											.	EN2	14	.	0			c.A808G						.						71	72	72					7																	155255188		2203	4300	6503	SO:0001583	missense	2020	exon2			TACCTGACGGAGC		CCDS5940.1	7q36.2	2011-06-20	2007-02-15		ENSG00000164778	ENSG00000164778		"Homeoboxes / ANTP class : NKL subclass"	3343	protein-coding gene	gene with protein product		131310					Standard	NM_001427		Approved		uc003wmb.3	P19622	OTTHUMG00000151354	ENST00000297375.4:c.808A>G	chr7.hg19:g.155255188A>G	ENSP00000297375:p.Thr270Ala	138.0	0.0		73.0	4.0	NM_001427	A4D252|Q549U3|Q9UD58	Missense_Mutation	SNP	ENST00000297375.4	hg19	CCDS5940.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.281916	0.80692	.	.	ENSG00000164778	ENST00000297375	D	0.96041	-3.89	5.31	4.14	0.48551	Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.95316	0.8480	M	0.69823	2.125	0.80722	D	1	P	0.37207	0.587	B	0.44224	0.444	D	0.94538	0.7742	10	0.87932	D	0	-25.0126	12.4114	0.55469	0.8593:0.1407:0.0:0.0	.	270	P19622	HME2_HUMAN	A	270	ENSP00000297375:T270A	ENSP00000297375:T270A	T	+	1	0	EN2	154947949	1.000000	0.71417	0.989000	0.46669	0.972000	0.66771	7.125000	0.77193	0.947000	0.37659	-0.313000	0.08912	ACG	.	.		0.602	EN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322337.1	NM_001427		G	155255188	A	G	155255188	3	3	260	1	0	0	0	0	1	0	0	0	5112	275	10	2	814	2	EN2	7	155255188	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	4493191	155255188	3883475	347	37592										
CSMD1	64478	hgsc.bcm.edu	37	chr8	2824171	2824171	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agccctgaggtcttgtagccTtcccagcaggcatagatgac	11	12	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:2824171T>C	ENST00000520002.1	-	59	9579	c.9024A>G	c.(9022-9024)gaA>gaG	p.E3008E	CSMD1_ENST00000400186.3_Intron|CSMD1_ENST00000602723.1_Intron|CSMD1_ENST00000537824.1_Silent_p.E3007E|CSMD1_ENST00000542608.1_Intron|CSMD1_ENST00000602557.1_Silent_p.E3008E			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	3008	Sushi 23. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		TCTTGTAGCCTTCCCAGCAGG	0.557																																					p.E3007E		Atlas-SNP	.											.	CSMD1	1469	.	0			c.A9021G						.						72	76	75					8																	2824171		2066	4220	6286	SO:0001819	synonymous_variant	64478	exon58			GTAGCCTTCCCAG			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.9024A>G	chr8.hg19:g.2824171T>C		138.0	0.0		63.0	4.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	hg19		.	.	.	.	.	.	.	.	.	.	T	5.937	0.356958	0.11239	.	.	ENSG00000183117	ENST00000335551	.	.	.	5.46	-8.95	0.00765	.	.	.	.	.	T	0.36690	0.0976	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42015	-0.9476	4	.	.	.	.	3.7687	0.08633	0.0871:0.3871:0.1864:0.3395	.	.	.	.	G	2425	.	.	R	-	1	2	CSMD1	2811578	0.002000	0.14202	0.486000	0.27416	0.649000	0.38597	-1.551000	0.02178	-2.165000	0.00781	-0.242000	0.12053	AGG	.	.		0.557	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		C	2824171	T	C	2824171	2	2	260	1	0	0	0	0	0	0	0	1	3946	1606	56	2		2	CSMD1	8	2824171	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10		2824171	143539851	348	37593										
CLDN23	137075	hgsc.bcm.edu	37	chr8	8560187	8560187	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcgctggccgccacggtcctGgggcttctgctggcgtcgct	15	15	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:8560187G>T	ENST00000519106.1	+	1	740	c.279G>T	c.(277-279)ctG>ctT	p.L93L		NM_194284.2	NP_919260.2	Q96B33	CLD23_HUMAN	claudin 23	93					calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			endometrium(2)	2		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.071)|READ - Rectum adenocarcinoma(644;0.238)		CCACGGTCCTGGGGCTTCTGC	0.716																																					p.L93L		Atlas-SNP	.											.	CLDN23	5	.	0			c.G279T						.						11	15	14					8																	8560187		2160	4242	6402	SO:0001819	synonymous_variant	137075	exon1			GGTCCTGGGGCTT	AK123547	CCDS55195.1	8p23.1	2006-04-12				ENSG00000253958		"Claudins"	17591	protein-coding gene	gene with protein product		609203				12736707	Standard	NM_194284		Approved	CLDNL	uc003wsi.3	Q96B33		ENST00000519106.1:c.279G>T	chr8.hg19:g.8560187G>T		17.0	0.0		17.0	6.0	NM_194284	Q08AJ3	Silent	SNP	ENST00000519106.1	hg19	CCDS55195.1																																																																																			.	.		0.716	CLDN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374721.1	NM_194284		T	8560187	G	T	8560187	2	4	260	1	0	0	0	0	0	0	0	1	3486	1335	47	3		3	CLDN23	8	8560187	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	5736016	8560187	137803835	349	37594										
LONRF1	91694	hgsc.bcm.edu	37	chr8	12586494	12586494	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	accctaaaccgctttcctccAactgtatcaaccacagacct	3	17	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:12586494A>G	ENST00000398246.3	-	10	1995	c.1926T>C	c.(1924-1926)gtT>gtC	p.V642V	MIR3926-2_ENST00000578598.1_RNA|LONRF1_ENST00000525024.1_Silent_p.V68V|LONRF1_ENST00000533751.1_Silent_p.V285V	NM_152271.3	NP_689484.3	Q17RB8	LONF1_HUMAN	LON peptidase N-terminal domain and ring finger 1	642	Lon.						ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)|upper_aerodigestive_tract(2)	19				READ - Rectum adenocarcinoma(644;0.236)		GCTTTCCTCCAACTGTATCAA	0.363																																					p.V642V		Atlas-SNP	.											.	LONRF1	45	.	0			c.T1926C						.						143	133	136					8																	12586494		1843	4089	5932	SO:0001819	synonymous_variant	91694	exon10			TCCTCCAACTGTA	AK074329	CCDS5987.2	8p23.1	2013-01-09			ENSG00000154359	ENSG00000154359		"RING-type (C3HC4) zinc fingers"	26302	protein-coding gene	gene with protein product						18253036	Standard	XM_005273685		Approved	FLJ23749, RNF191	uc003wwd.1	Q17RB8	OTTHUMG00000165475	ENST00000398246.3:c.1926T>C	chr8.hg19:g.12586494A>G		311.0	0.0		122.0	6.0	NM_152271	B4DM29|B4DU84|Q8TEA0|Q9BSV1	Silent	SNP	ENST00000398246.3	hg19	CCDS5987.2																																																																																			.	.		0.363	LONRF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251693.2	NM_152271		G	12586494	A	G	12586494	2	3	260	1	0	0	0	0	0	0	0	1	8903	117	5	2		2	LONRF1	8	12586494	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	4026307	12586494	133777528	350	37595										
FGF20	26281	hgsc.bcm.edu	37	chr8	16850684	16850684	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gatgcctcttggacctggcgCcatctcttggagttccgtct	11	13	3	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:16850684C>T	ENST00000180166.5	-	3	681	c.533G>A	c.(532-534)gGc>gAc	p.G178D		NM_019851.2	NP_062825.1	Q9NP95	FGF20_HUMAN	fibroblast growth factor 20	178					cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of cardiac muscle cell proliferation (GO:0060043)|signal transduction (GO:0007165)	extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	11				Colorectal(111;0.0511)|COAD - Colon adenocarcinoma(73;0.207)		GGACCTGGCGCCATCTCTTGG	0.428																																					p.G178D		Atlas-SNP	.											.	FGF20	16	.	0			c.G533A						.						184	162	170					8																	16850684		2203	4300	6503	SO:0001583	missense	26281	exon3			CTGGCGCCATCTC	AB030648	CCDS5998.1	8p22	2008-05-15			ENSG00000078579	ENSG00000078579			3677	protein-coding gene	gene with protein product		605558				10913340	Standard	NM_019851		Approved		uc003wxc.1	Q9NP95	OTTHUMG00000096964	ENST00000180166.5:c.533G>A	chr8.hg19:g.16850684C>T	ENSP00000180166:p.Gly178Asp	180.0	0.0		80.0	4.0	NM_019851	B2RPH5	Missense_Mutation	SNP	ENST00000180166.5	hg19	CCDS5998.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.0|25.0	4.591440|4.591440	0.86851|0.86851	.|.	.|.	ENSG00000078579|ENSG00000078579	ENST00000180166|ENST00000519941	D|.	0.84873|.	-1.91|.	5.85|5.85	5.85|5.85	0.93711|0.93711	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|.	0.90106|.	0.6909|.	H|H	0.96430|0.96430	3.82|3.82	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	D|.	0.92071|.	0.5664|.	10|.	0.87932|.	D|.	0|.	.|.	20.5471|20.5471	0.99284|0.99284	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	178|.	Q9NP95|.	FGF20_HUMAN|.	D|X	178|79	ENSP00000180166:G178D|.	ENSP00000180166:G178D|.	G|W	-|-	2|3	0|0	FGF20|FGF20	16895055|16895055	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.757000|0.757000	0.42996|0.42996	7.818000|7.818000	0.86416|0.86416	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	GGC|TGG	.	.		0.428	FGF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214030.1			T	16850684	C	T	16850684	3	4	260	1	0	0	0	0	1	0	0	0	5857	739	26	3	106	3	FGF20	8	16850684	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	4264190	16850684	129513338	351	37596										
MTMR7	9108	hgsc.bcm.edu	37	chr8	17163419	17163419	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aaacacactcaatgaactggTcaataactggagagatttct	7	8	3	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:17163419T>C	ENST00000180173.5	-	11	1233	c.1199A>G	c.(1198-1200)gAc>gGc	p.D400G	MTMR7_ENST00000521857.1_Missense_Mutation_p.D400G|MTMR7_ENST00000398099.3_5'UTR	NM_004686.4	NP_004677.3	Q9Y216	MTMR7_HUMAN	myotubularin related protein 7	400	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				inositol phosphate dephosphorylation (GO:0046855)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|liver(1)|lung(8)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	32				Colorectal(111;0.112)		AATGAACTGGTCAATAACTGG	0.343																																					p.D400G		Atlas-SNP	.											.	MTMR7	75	.	0			c.A1199G						.						99	98	98					8																	17163419		2203	4300	6503	SO:0001583	missense	9108	exon11			AACTGGTCAATAA	AF073482	CCDS34851.1	8p22	2011-06-09			ENSG00000003987	ENSG00000003987		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7454	protein-coding gene	gene with protein product		603562				9736772, 12890864	Standard	NM_004686		Approved		uc003wxm.3	Q9Y216	OTTHUMG00000163771	ENST00000180173.5:c.1199A>G	chr8.hg19:g.17163419T>C	ENSP00000180173:p.Asp400Gly	173.0	0.0		91.0	4.0	NM_004686	A1L4K9|B4DG87|Q68DX4	Missense_Mutation	SNP	ENST00000180173.5	hg19	CCDS34851.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.971386	0.74246	.	.	ENSG00000003987	ENST00000180173;ENST00000521857	D;D	0.89875	-2.58;-2.58	4.87	4.87	0.63330	Myotubularin phosphatase domain (1);	0.000000	0.85682	D	0.000000	D	0.88507	0.6455	L	0.39898	1.24	0.80722	D	1	P;P	0.50528	0.936;0.882	P;P	0.51415	0.669;0.521	D	0.88376	0.2998	10	0.42905	T	0.14	.	14.9478	0.71047	0.0:0.0:0.0:1.0	.	400;400	Q9Y216-2;Q9Y216	.;MTMR7_HUMAN	G	400	ENSP00000180173:D400G;ENSP00000429733:D400G	ENSP00000180173:D400G	D	-	2	0	MTMR7	17207790	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.804000	0.62554	2.180000	0.69256	0.460000	0.39030	GAC	.	.		0.343	MTMR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375311.1	NM_004686		C	17163419	T	C	17163419	3	2	260	1	0	0	0	0	1	0	0	0	9957	1667	58	2	799	2	MTMR7	8	17163419	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	312735	17163419	129200603	352	37597										
MTUS1	57509	hgsc.bcm.edu	37	chr8	17541870	17541870	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgctgaatcacaactgtcaaTgcctcaaacttggtattacc	6	11	3	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:17541870T>C	ENST00000262102.6	-	7	3029	c.2805A>G	c.(2803-2805)gcA>gcG	p.A935A	MTUS1_ENST00000519263.1_Silent_p.A881A|MTUS1_ENST00000381861.3_Silent_p.A182A|MIR548V_ENST00000584165.1_RNA|MTUS1_ENST00000381869.3_Silent_p.A881A|MTUS1_ENST00000518713.1_5'UTR|MTUS1_ENST00000297488.6_Silent_p.A101A|MTUS1_ENST00000544260.1_Silent_p.A80A	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	935					cellular response to peptide hormone stimulus (GO:0071375)|regulation of macrophage chemotaxis (GO:0010758)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(14)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	36				Colorectal(111;0.0778)		CAACTGTCAATGCCTCAAACT	0.468																																					p.A935A		Atlas-SNP	.											.	MTUS1	144	.	0			c.A2805G						.						142	141	141					8																	17541870		2005	4164	6169	SO:0001819	synonymous_variant	57509	exon7			TGTCAATGCCTCA	AL096842	CCDS43716.1, CCDS43717.1, CCDS43718.1, CCDS43719.1, CCDS55204.1	8p22	2013-01-17	2009-10-20		ENSG00000129422	ENSG00000129422			29789	protein-coding gene	gene with protein product	"AT2 receptor-interacting protein", "AT2R binding protein", "mitochondrial tumor suppressor gene 1"	609589	"mitochondrial tumor suppressor 1"			10574462, 12692079	Standard	NM_001001931		Approved	MTSG1, KIAA1288, DKFZp586D1519, FLJ14295, ATIP1, MP44, ATBP, ICIS	uc003wxv.3	Q9ULD2	OTTHUMG00000163756	ENST00000262102.6:c.2805A>G	chr8.hg19:g.17541870T>C		169.0	0.0		79.0	4.0	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Silent	SNP	ENST00000262102.6	hg19	CCDS43717.1																																																																																			.	.		0.468	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031		C	17541870	T	C	17541870	2	2	260	1	0	0	0	0	0	0	0	1	9974	1451	51	2		2	MTUS1	8	17541870	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	378451	17541870	128822152	353	37598										
PCM1	5108	hgsc.bcm.edu	37	chr8	17822267	17822267	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	actcctacaatggaaaggaaActaaaaataggttagtttca	7	6	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:17822267A>G	ENST00000519253.1	+	18	3096	c.2845A>G	c.(2845-2847)Act>Gct	p.T949A	PCM1_ENST00000325083.8_Missense_Mutation_p.T949A|PCM1_ENST00000524226.1_Missense_Mutation_p.T950A			Q15154	PCM1_HUMAN	pericentriolar material 1	949					centrosome organization (GO:0051297)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|interkinetic nuclear migration (GO:0022027)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|microtubule anchoring (GO:0034453)|microtubule anchoring at centrosome (GO:0034454)|mitotic cell cycle (GO:0000278)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|positive regulation of intracellular protein transport (GO:0090316)|protein localization to centrosome (GO:0071539)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|pericentriolar material (GO:0000242)|protein complex (GO:0043234)	identical protein binding (GO:0042802)		PCM1/JAK2(30)	breast(4)|endometrium(8)|kidney(5)|large_intestine(16)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	48				Colorectal(111;0.0789)		TGGAAAGGAAACTAAAAATAG	0.378			T	"RET, JAK2"	"papillary thyroid, CML, MPD"																																p.T949A		Atlas-SNP	.		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"E, L"	.	PCM1	120	.	0			c.A2845G						.						117	114	115					8																	17822267		1868	4101	5969	SO:0001583	missense	5108	exon18			AAGGAAACTAAAA		CCDS47812.1	8p22-p21.3	2008-08-08			ENSG00000078674	ENSG00000078674			8727	protein-coding gene	gene with protein product		600299				8120099, 15659651	Standard	NM_006197		Approved	PTC4	uc003wyi.4	Q15154	OTTHUMG00000163699	ENST00000519253.1:c.2845A>G	chr8.hg19:g.17822267A>G	ENSP00000431099:p.Thr949Ala	183.0	0.0		94.0	4.0	NM_006197	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Missense_Mutation	SNP	ENST00000519253.1	hg19		.	.	.	.	.	.	.	.	.	.	A	17.77	3.471607	0.63737	.	.	ENSG00000078674	ENST00000325083;ENST00000519253;ENST00000524226	T;T;T	0.18502	2.21;2.21;2.21	5.6	0.0601	0.14334	.	0.422521	0.29660	N	0.011525	T	0.12390	0.0301	N	0.22421	0.69	0.80722	D	1	D;B;D	0.61697	0.99;0.001;0.99	P;B;P	0.55999	0.789;0.003;0.789	T	0.44997	-0.9291	10	0.08837	T	0.75	-3.0735	2.3085	0.04180	0.5164:0.2397:0.1288:0.1152	.	949;950;949	E7ETA6;E7EV56;Q15154	.;.;PCM1_HUMAN	A	949;949;950	ENSP00000327077:T949A;ENSP00000431099:T949A;ENSP00000430521:T950A	ENSP00000327077:T949A	T	+	1	0	PCM1	17866547	1.000000	0.71417	0.994000	0.49952	0.991000	0.79684	1.507000	0.35758	-0.135000	0.11495	-0.256000	0.11100	ACT	.	.		0.378	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197		G	17822267	A	G	17822267	3	3	260	1	0	0	0	0	1	0	0	0	11593	43	2	2	2907	2	PCM1	8	17822267	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	280397	17822267	128541755	354	37599										
GFRA2	2675	hgsc.bcm.edu	37	chr8	21562513	21562513	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttacggaggcatgggttctcGgtgaagtccctgaggaactt	14	8	1	2	rs375828964		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:21562513G>T	ENST00000524240.1	-	6	1679	c.1029C>A	c.(1027-1029)acC>acA	p.T343T	GFRA2_ENST00000518077.1_Silent_p.T210T|GFRA2_ENST00000400782.4_Silent_p.T238T|GFRA2_ENST00000517328.1_Silent_p.T343T	NM_001495.4	NP_001486.4	O00451	GFRA2_HUMAN	GDNF family receptor alpha 2	343					negative regulation of protein autophosphorylation (GO:0031953)|nervous system development (GO:0007399)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	anchored component of membrane (GO:0031225)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	glial cell-derived neurotrophic factor receptor activity (GO:0016167)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|prostate(1)|skin(1)	7				Colorectal(74;0.0189)|COAD - Colon adenocarcinoma(73;0.0727)		ATGGGTTCTCGGTGAAGTCCC	0.612																																					p.T343T		Atlas-SNP	.											.	GFRA2	23	.	0			c.C1029A						.						50	54	52					8																	21562513		1993	4176	6169	SO:0001819	synonymous_variant	2675	exon6			GTTCTCGGTGAAG	AF002700	CCDS47816.1, CCDS55207.1	8p21.3	2008-05-02			ENSG00000168546	ENSG00000168546			4244	protein-coding gene	gene with protein product		601956				9177201	Standard	NM_001165038		Approved	RETL2, GDNFRB, NTNRA, TRNR2	uc003wzu.1	O00451	OTTHUMG00000163897	ENST00000524240.1:c.1029C>A	chr8.hg19:g.21562513G>T		160.0	0.0		94.0	4.0	NM_001495	E9PD47|O15316|O15328|Q58J92|Q6GTR9|Q7Z5C2	Silent	SNP	ENST00000524240.1	hg19	CCDS47816.1																																																																																			.	.		0.612	GFRA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376254.3	NM_001495		T	21562513	G	T	21562513	2	4	260	1	0	0	0	0	0	0	0	1	6356	1103	39	1		1	GFRA2	8	21562513	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	3740246	21562513	124801509	355	37600										
FAM160B2	64760	hgsc.bcm.edu	37	chr8	21955610	21955610	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgtaggtaggaagaaagcatGcggagaacccactgccctgc	13	10	0	2	rs556491204		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:21955610G>T	ENST00000289921.7	+	6	603	c.557G>T	c.(556-558)tGc>tTc	p.C186F		NM_022749.5	NP_073586.5	Q86V87	F16B2_HUMAN	family with sequence similarity 160, member B2	186										endometrium(2)|kidney(1)|lung(2)|prostate(3)|urinary_tract(1)	9						AAGAAAGCATGCGGAGAACCC	0.612																																					p.C186F		Atlas-SNP	.											.	FAM160B2	35	.	0			c.G557T						.						27	32	30					8																	21955610		2051	4168	6219	SO:0001583	missense	64760	exon6			AAGCATGCGGAGA	AK025454	CCDS6021.2	8p21.3	2012-11-30	2008-06-05	2008-06-05	ENSG00000158863	ENSG00000158863			16492	protein-coding gene	gene with protein product			"retinoic acid induced 16"	RAI16		22971576, 15626329	Standard	XR_247128		Approved	FLJ21801	uc011kyx.2	Q86V87	OTTHUMG00000097088	ENST00000289921.7:c.557G>T	chr8.hg19:g.21955610G>T	ENSP00000289921:p.Cys186Phe	206.0	0.0		77.0	5.0	NM_022749	B2RDQ5|B3KNX1|Q2M211|Q71JB5|Q7L3J6|Q969T0|Q9H6W4	Missense_Mutation	SNP	ENST00000289921.7	hg19	CCDS6021.2	.	.	.	.	.	.	.	.	.	.	.	7.783	0.710022	0.15239	.	.	ENSG00000158863	ENST00000289921	T	0.13420	2.59	4.71	2.77	0.32553	.	0.878018	0.10183	N	0.705607	T	0.10937	0.0267	N	0.22421	0.69	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.25082	-1.0142	10	0.52906	T	0.07	-7.4293	11.6316	0.51178	0.0:0.6389:0.3611:0.0	.	186	Q86V87	F16B2_HUMAN	F	186	ENSP00000289921:C186F	ENSP00000289921:C186F	C	+	2	0	FAM160B2	22011556	0.047000	0.20315	0.008000	0.14137	0.001000	0.01503	0.606000	0.24194	1.101000	0.41535	-0.311000	0.09066	TGC	.	.		0.612	FAM160B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375334.2			T	21955610	G	T	21955610	3	4	260	1	0	0	0	0	1	0	0	0	5476	1319	46	3	579	3	FAM160B2	8	21955610	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	393097	21955610	124408412	356	37601										
HR	55806	hgsc.bcm.edu	37	chr8	21986470	21986470	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gccctccacaagtgggagcaTgtccttggggccctggggga	16	12	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:21986470T>G	ENST00000381418.4	-	2	1694	c.214A>C	c.(214-216)Atg>Ctg	p.M72L	HR_ENST00000518377.1_5'Flank|HR_ENST00000312841.8_Missense_Mutation_p.M72L	NM_005144.4	NP_005135.2	O43593	HAIR_HUMAN	hair growth associated	72					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	27		Breast(100;0.000162)|Acute lymphoblastic leukemia(644;0.0775)|Prostate(55;0.116)		KIRC - Kidney renal clear cell carcinoma(542;1.19e-05)|BRCA - Breast invasive adenocarcinoma(99;3.56e-05)|Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)		AGTGGGAGCATGTCCTTGGGG	0.662																																					p.M72L		Atlas-SNP	.											.	HR	71	.	0			c.A214C						.						40	43	42					8																	21986470		2203	4300	6503	SO:0001583	missense	55806	exon2			GGAGCATGTCCTT	AF039196	CCDS6022.1, CCDS6023.1	8p12	2012-12-07	2012-12-07		ENSG00000168453	ENSG00000168453			5172	protein-coding gene	gene with protein product		602302	"hairless (mouse) homolog", "hairless homolog (mouse)"	ALUNC		10051399, 9463324	Standard	NM_018411		Approved	AU	uc003xas.3	O43593	OTTHUMG00000097089	ENST00000381418.4:c.214A>C	chr8.hg19:g.21986470T>G	ENSP00000370826:p.Met72Leu	83.0	0.0		60.0	20.0	NM_018411	Q6GS30|Q96H33|Q9NPE1	Missense_Mutation	SNP	ENST00000381418.4	hg19	CCDS6022.1	.	.	.	.	.	.	.	.	.	.	T	11.70	1.716994	0.30413	.	.	ENSG00000168453	ENST00000381418;ENST00000312841	T;T	0.70399	-0.48;-0.48	4.8	-0.255	0.12988	.	1.001710	0.08053	N	0.996871	T	0.46776	0.1410	N	0.08118	0	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.002;0.0	T	0.37407	-0.9707	10	0.72032	D	0.01	1.3083	4.1172	0.10088	0.0:0.3827:0.2242:0.3931	.	72;72;72	A6NCE3;O43593-2;O43593	.;.;HAIR_HUMAN	L	72	ENSP00000370826:M72L;ENSP00000326765:M72L	ENSP00000326765:M72L	M	-	1	0	HR	22042415	0.030000	0.19436	0.361000	0.25849	0.536000	0.34869	-0.139000	0.10358	0.064000	0.16427	0.459000	0.35465	ATG	.	.		0.662	HR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214213.1			G	21986470	T	G	21986470	3	3	260	1	0	0	0	0	1	0	0	0	7356	1464	51	5	3427	5	HR	8	21986470	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	30860	21986470	124377552	357	37602										
CDCA2	157313	hgsc.bcm.edu	37	chr8	25327485	25327485	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcccctttcagagctcacagAgacttcaaatggtaagtaat	7	10	3	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:25327485A>G	ENST00000330560.3	+	7	1286	c.809A>G	c.(808-810)gAg>gGg	p.E270G	CDCA2_ENST00000380665.3_Missense_Mutation_p.E255G	NM_152562.2	NP_689775.2	Q69YH5	CDCA2_HUMAN	cell division cycle associated 2	270					mitotic nuclear division (GO:0007067)|positive regulation of protein dephosphorylation (GO:0035307)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(3)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(7)|lung(10)|ovary(1)|prostate(3)	35		all_cancers(63;0.0378)|Ovarian(32;0.000878)|all_epithelial(46;0.0162)|Breast(100;0.0164)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.022)|Epithelial(17;1.37e-11)|Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0443)		GAGCTCACAGAGACTTCAAAT	0.368																																					p.E270G		Atlas-SNP	.											.	CDCA2	78	.	0			c.A809G						.						81	81	81					8																	25327485		2203	4299	6502	SO:0001583	missense	157313	exon7			TCACAGAGACTTC	BG354575	CCDS6049.1	8p21.2	2014-06-12			ENSG00000184661	ENSG00000184661			14623	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 81"					12188893, 16492807	Standard	NM_152562		Approved	Repo-Man, PPP1R81	uc003xep.1	Q69YH5	OTTHUMG00000099429	ENST00000330560.3:c.809A>G	chr8.hg19:g.25327485A>G	ENSP00000328228:p.Glu270Gly	180.0	0.0		82.0	4.0	NM_152562	Q3SX74|Q4G0W0|Q5RKN0|Q69YI4|Q6P464|Q8N7C1	Missense_Mutation	SNP	ENST00000330560.3	hg19	CCDS6049.1	.	.	.	.	.	.	.	.	.	.	A	17.91	3.503370	0.64298	.	.	ENSG00000184661	ENST00000330560;ENST00000380665	T;T	0.34072	1.38;1.38	5.43	0.956	0.19608	.	0.765052	0.12235	N	0.487047	T	0.29491	0.0735	L	0.57536	1.79	0.20196	N	0.999926	B;B;B	0.13594	0.004;0.008;0.008	B;B;B	0.16289	0.006;0.015;0.015	T	0.35574	-0.9783	10	0.66056	D	0.02	-2.1077	2.5622	0.04774	0.4756:0.0:0.318:0.2064	.	270;255;270	B7Z5Q5;E9PEI0;Q69YH5	.;.;CDCA2_HUMAN	G	270;255	ENSP00000328228:E270G;ENSP00000370040:E255G	ENSP00000328228:E270G	E	+	2	0	CDCA2	25383402	0.510000	0.26171	0.155000	0.22561	0.545000	0.35147	1.291000	0.33330	0.334000	0.23590	0.528000	0.53228	GAG	.	.		0.368	CDCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216891.3	NM_152562		G	25327485	A	G	25327485	3	3	260	1	0	0	0	0	1	0	0	0	3088	304	11	2	831	2	CDCA2	8	25327485	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	3341015	25327485	121036537	358	37603										
ELP3	55140	hgsc.bcm.edu	37	chr8	27964302	27964302	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttacaggaaatatatgtgtgTaagtatggtgattttattaa	9	1	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:27964302T>A	ENST00000256398.8	+	4	706		c.e4+2		ELP3_ENST00000521015.1_Splice_Site|ELP3_ENST00000537665.1_Splice_Site|ELP3_ENST00000380353.4_Splice_Site|ELP3_ENST00000524103.1_Splice_Site|ELP3_ENST00000542181.1_Splice_Site|ELP3_ENST00000523760.1_Splice_Site	NM_001284220.1|NM_001284226.1|NM_018091.5	NP_001271149.1|NP_001271155.1|NP_060561.3	Q9H9T3	ELP3_HUMAN	elongator acetyltransferase complex subunit 3						chromatin organization (GO:0006325)|positive regulation of cell migration (GO:0030335)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	histone acetyltransferase activity (GO:0004402)|iron-sulfur cluster binding (GO:0051536)|metal ion binding (GO:0046872)|phosphorylase kinase regulator activity (GO:0008607)			kidney(2)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.151)|Colorectal(74;0.183)		TATATGTGTGTAAGTATGGTG	0.343																																					.		Atlas-SNP	.											.	ELP3	36	.	0			c.329+2T>A						.						95	91	92					8																	27964302		2203	4300	6503	SO:0001630	splice_region_variant	55140	exon4			TGTGTGTAAGTAT		CCDS6065.1, CCDS64860.1, CCDS64861.1, CCDS75717.1, CCDS75718.1	8p21.1	2012-08-14	2012-08-08		ENSG00000134014	ENSG00000134014		"Chromatin-modifying enzymes / K-acetyltransferases", "Elongator acetyltransferase complex subunits"	20696	protein-coding gene	gene with protein product		612722	"elongation protein 3 homolog (S. cerevisiae)"			11714725	Standard	NM_018091		Approved	FLJ10422, KAT9	uc003xgo.4	Q9H9T3	OTTHUMG00000102124	ENST00000256398.8:c.329+2T>A	chr8.hg19:g.27964302T>A		251.0	0.0		111.0	5.0	NM_018091	B4DE19|B4DIG1|E2QRI5|Q53G84|Q6AWB0|Q9BVF7|Q9NVZ1	Splice_Site	SNP	ENST00000256398.8	hg19	CCDS6065.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.417985	0.83449	.	.	ENSG00000134014	ENST00000520270;ENST00000521015;ENST00000521570;ENST00000256398;ENST00000542181;ENST00000524103;ENST00000524024;ENST00000537665;ENST00000380353;ENST00000520288;ENST00000521099	.	.	.	5.62	5.62	0.85841	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.0608	0.64800	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	ELP3	28020221	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	7.283000	0.78640	2.260000	0.74910	0.528000	0.53228	.	.	.		0.343	ELP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219963.2	NM_018091	Intron	A	27964302	T	A	27964302	5	1	260	1	0	0	0	0	0	0	1	0	5083	1652	57	4	345	4	ELP3	8	27964302	Splice_Site	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	2636817	27964302	118399720	359	37604										
C8orf41	80185	hgsc.bcm.edu	37	chr8	33357923	33357923	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tagcagggcgctcttaacagActcaggtgtaaggtttggat	13	7	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:33357923A>G	ENST00000431156.2	-	7	1963	c.1345T>C	c.(1345-1347)Tct>Cct	p.S449P	TTI2_ENST00000360742.5_Missense_Mutation_p.S449P|MAK16_ENST00000360128.6_3'UTR|TTI2_ENST00000520636.1_Missense_Mutation_p.S418P|TTI2_ENST00000519356.1_5'UTR	NM_001102401.2	NP_001095871.1	Q6NXR4	TTI2_HUMAN	TELO2 interacting protein 2	449																	CTCTTAACAGACTCAGGTGTA	0.498																																					p.S449P		Atlas-SNP	.											.	.	.	.	0			c.T1345C						.						105	91	96					8																	33357923		2203	4300	6503	SO:0001583	missense	80185	exon7			TAACAGACTCAGG	AK026916	CCDS6090.1	8p12	2011-11-10	2011-11-10	2011-09-22		ENSG00000129696			26262	protein-coding gene	gene with protein product		614426	"chromosome 8 open reading frame 41", "Tel2 interacting protein 2 homolog (S. pombe)"	C8orf41		20801936, 20810650	Standard	NM_025115		Approved	FLJ23263	uc003xjm.5	Q6NXR4		ENST00000431156.2:c.1345T>C	chr8.hg19:g.33357923A>G	ENSP00000411169:p.Ser449Pro	93.0	0.0		53.0	5.0	NM_001265581	D3DSV7|Q96IM2|Q9H5N4	Missense_Mutation	SNP	ENST00000431156.2	hg19	CCDS6090.1	.	.	.	.	.	.	.	.	.	.	A	0.005	-2.158687	0.00321	.	.	ENSG00000129696	ENST00000360742;ENST00000431156;ENST00000522668;ENST00000520636	T;T;T	0.55760	0.54;0.54;0.5	5.18	1.08	0.20341	.	0.522635	0.19441	N	0.114163	T	0.11110	0.0271	N	0.00368	-1.59	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.28586	-1.0039	10	0.02654	T	1	-0.0243	0.9793	0.01433	0.2886:0.1622:0.3939:0.1553	.	449;418	Q6NXR4;E5RIH5	TTI2_HUMAN;.	P	449;449;438;418	ENSP00000353971:S449P;ENSP00000411169:S449P;ENSP00000428401:S418P	ENSP00000353971:S449P	S	-	1	0	C8orf41	33477465	0.000000	0.05858	0.001000	0.08648	0.167000	0.22549	-0.104000	0.10923	-0.096000	0.12329	-0.479000	0.04858	TCT	.	.		0.498	TTI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376555.1	NM_025115		G	33357923	A	G	33357923	3	3	260	1	0	0	0	0	1	0	0	0	2429	275	10	2	189	2	C8orf41	8	33357923	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	5393621	33357923	113006099	360	37605										
BAG4	9530	hgsc.bcm.edu	37	chr8	38067825	38067825	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtccagtatcttgaacaagaAgtagaagaatttgtaggaaa	10	4	1	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:38067825A>G	ENST00000287322.4	+	5	1459	c.1188A>G	c.(1186-1188)gaA>gaG	p.E396E	BAG4_ENST00000432471.2_Silent_p.E360E	NM_004874.3	NP_004865.1	O95429	BAG4_HUMAN	BCL2-associated athanogene 4	396	BAG. {ECO:0000255|PROSITE- ProRule:PRU00369}.				cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to tumor necrosis factor (GO:0071356)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mRNA modification (GO:0090367)|negative regulation of phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity (GO:2001145)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell adhesion (GO:0045785)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of stress fiber assembly (GO:0051496)|protein folding (GO:0006457)|protein heterooligomerization (GO:0051291)|protein localization to plasma membrane (GO:0072659)|ruffle assembly (GO:0097178)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)			breast(1)|kidney(2)|large_intestine(2)|liver(2)|lung(2)|ovary(1)|urinary_tract(1)	11	Colorectal(12;0.000442)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.121)				TTGAACAAGAAGTAGAAGAAT	0.398																																					p.E396E		Atlas-SNP	.											.	BAG4	32	.	0			c.A1188G						.						43	46	45					8																	38067825		2203	4300	6503	SO:0001819	synonymous_variant	9530	exon5			ACAAGAAGTAGAA	AF095194	CCDS6104.1, CCDS56533.1	8p11.23	2008-08-07			ENSG00000156735	ENSG00000156735			940	protein-coding gene	gene with protein product	"silencer of death domains"	603884				9873016, 9915703	Standard	NM_004874		Approved	SODD	uc003xky.2	O95429	OTTHUMG00000164064	ENST00000287322.4:c.1188A>G	chr8.hg19:g.38067825A>G		236.0	0.0		93.0	4.0	NM_004874	B4E217|O95818	Silent	SNP	ENST00000287322.4	hg19	CCDS6104.1																																																																																			.	.		0.398	BAG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377038.2	NM_004874		G	38067825	A	G	38067825	2	3	260	1	0	0	0	0	0	0	0	1	1289	69	3	2		2	BAG4	8	38067825	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	4709902	38067825	108296197	361	37606										
IDO1	3620	hgsc.bcm.edu	37	chr8	39781035	39781035	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	caaatgcaagaacgggacacTttgctaaaggcgctgttgga	12	8	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:39781035T>C	ENST00000518237.1	+	7	1224	c.585T>C	c.(583-585)acT>acC	p.T195T	RP11-44K6.3_ENST00000517623.1_RNA|IDO1_ENST00000522495.1_Silent_p.T195T|RP11-44K6.4_ENST00000522970.1_RNA	NM_002164.5	NP_002155.1	P14902	I23O1_HUMAN	indoleamine 2,3-dioxygenase 1	195					cellular nitrogen compound metabolic process (GO:0034641)|cytokine production involved in inflammatory response (GO:0002534)|female pregnancy (GO:0007565)|kynurenic acid biosynthetic process (GO:0034276)|multicellular organismal response to stress (GO:0033555)|negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of T cell apoptotic process (GO:0070233)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chronic inflammatory response (GO:0002678)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of T cell tolerance induction (GO:0002666)|positive regulation of type 2 immune response (GO:0002830)|response to lipopolysaccharide (GO:0032496)|small molecule metabolic process (GO:0044281)|swimming behavior (GO:0036269)|tryptophan catabolic process (GO:0006569)|tryptophan catabolic process to kynurenine (GO:0019441)	cytosol (GO:0005829)|smooth muscle contractile fiber (GO:0030485)|stereocilium bundle (GO:0032421)	electron carrier activity (GO:0009055)|heme binding (GO:0020037)|indoleamine 2,3-dioxygenase activity (GO:0033754)|metal ion binding (GO:0046872)|tryptophan 2,3-dioxygenase activity (GO:0004833)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(2)	12					L-Tryptophan(DB00150)|Melatonin(DB01065)	AACGGGACACTTTGCTAAAGG	0.388																																					p.T195T		Atlas-SNP	.											.	IDO1	43	.	0			c.T585C						.						89	88	88					8																	39781035		1879	4124	6003	SO:0001819	synonymous_variant	3620	exon7			GGACACTTTGCTA	M34455	CCDS47847.1	8p12-p11	2009-01-07	2009-01-07	2009-01-07		ENSG00000131203	1.13.11.52		6059	protein-coding gene	gene with protein product		147435	"indoleamine-pyrrole 2,3 dioxygenase"	IDO, INDO		2109605, 8404046	Standard	NM_002164		Approved		uc003xnm.3	P14902		ENST00000518237.1:c.585T>C	chr8.hg19:g.39781035T>C		152.0	0.0		92.0	4.0	NM_002164	Q540B4	Silent	SNP	ENST00000518237.1	hg19	CCDS47847.1																																																																																			.	.		0.388	IDO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376987.1	NM_002164		C	39781035	T	C	39781035	2	2	260	1	0	0	0	0	0	0	0	1	7510	1596	56	2		2	IDO1	8	39781035	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1713210	39781035	106582987	362	37607										
MYST3	7994	hgsc.bcm.edu	37	chr8	41906387	41906387	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	atccaagccatgggatgaagAcacagcattgcatatccttt	8	10	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:41906387A>G	ENST00000396930.3	-	3	652	c.109T>C	c.(109-111)Tct>Cct	p.S37P	KAT6A_ENST00000406337.1_Missense_Mutation_p.S37P|KAT6A_ENST00000485568.1_Missense_Mutation_p.S37P|KAT6A_ENST00000265713.2_Missense_Mutation_p.S37P	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	37	Required for activation of RUNX1-1.				aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										TGGGATGAAGACACAGCATTG	0.383																																					p.S37P		Atlas-SNP	.											.	.	.	.	0			c.T109C						.						226	214	218					8																	41906387		2203	4300	6503	SO:0001583	missense	7994	exon3			ATGAAGACACAGC	U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	13013	protein-coding gene	gene with protein product	"Monocytic leukemia zinc finger protein"	601408	"runt-related transcription factor binding protein 2", "MYST histone acetyltransferase (monocytic leukemia) 3"	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.109T>C	chr8.hg19:g.41906387A>G	ENSP00000380136:p.Ser37Pro	219.0	0.0		92.0	4.0	NM_001099412	Q76L81	Missense_Mutation	SNP	ENST00000396930.3	hg19	CCDS6124.1	.	.	.	.	.	.	.	.	.	.	A	12.25	1.882968	0.33255	.	.	ENSG00000083168	ENST00000265713;ENST00000406337;ENST00000396930;ENST00000485568	T;T;T;D	0.84800	0.14;0.14;0.14;-1.9	5.66	5.66	0.87406	.	0.000000	0.64402	D	0.000002	D	0.89729	0.6799	L	0.54323	1.7	0.50813	D	0.999894	D;D	0.76494	0.997;0.999	P;D	0.63488	0.897;0.915	D	0.90135	0.4209	10	0.54805	T	0.06	-13.1176	15.8861	0.79251	1.0:0.0:0.0:0.0	.	37;37	A5PLL3;Q92794	.;KAT6A_HUMAN	P	37	ENSP00000265713:S37P;ENSP00000385888:S37P;ENSP00000380136:S37P;ENSP00000430606:S37P	ENSP00000265713:S37P	S	-	1	0	KAT6A	42025544	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	5.594000	0.67557	2.156000	0.67533	0.533000	0.62120	TCT	.	.		0.383	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766		G	41906387	A	G	41906387	3	3	260	1	0	0	0	0	1	0	0	0	10113	275	10	2	5969	2	MYST3	8	41906387	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	2125352	41906387	104457635	363	37608										
SNTG1	54212	hgsc.bcm.edu	37	chr8	51617305	51617305	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aacctttctagaagtagaacGgatacaggtgagagtctgtg	12	6	2	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:51617305G>A	ENST00000522124.1	+	16	1845	c.1184G>A	c.(1183-1185)cGg>cAg	p.R395Q	SNTG1_ENST00000276467.5_Missense_Mutation_p.R395Q|SNTG1_ENST00000517473.1_Missense_Mutation_p.R395Q|SNTG1_ENST00000518864.1_Missense_Mutation_p.R395Q	NM_018967.2	NP_061840.1	Q9NSN8	SNTG1_HUMAN	syntrophin, gamma 1	395					cell communication (GO:0007154)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)|syntrophin complex (GO:0016013)	protein C-terminus binding (GO:0008022)			NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(36)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	66		all_cancers(86;0.00754)|all_epithelial(80;9.76e-05)|Lung NSC(129;0.000865)|all_lung(136;0.00249)|Colorectal(162;0.22)				GAAGTAGAACGGATACAGGTG	0.493																																					p.R395Q		Atlas-SNP	.											.	SNTG1	304	.	0			c.G1184A						.						81	67	72					8																	51617305		2203	4300	6503	SO:0001583	missense	54212	exon16			TAGAACGGATACA	AJ003030	CCDS6147.1, CCDS75737.1	8q11-q12	2008-07-03				ENSG00000147481			13740	protein-coding gene	gene with protein product		608714				10747910	Standard	NM_018967		Approved	SYN4, G1SYN	uc003xqs.1	Q9NSN8		ENST00000522124.1:c.1184G>A	chr8.hg19:g.51617305G>A	ENSP00000429842:p.Arg395Gln	74.0	0.0		88.0	4.0	NM_018967	Q2M3Q0|Q9NY98	Missense_Mutation	SNP	ENST00000522124.1	hg19	CCDS6147.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.756508	0.89843	.	.	ENSG00000147481	ENST00000518864;ENST00000522124;ENST00000517473;ENST00000276467	T;T;T;T	0.78003	-1.14;-1.14;-1.14;-1.14	5.19	5.19	0.71726	.	0.048531	0.85682	D	0.000000	D	0.84871	0.5568	L	0.50333	1.59	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.97110	1.0;0.945	T	0.82271	-0.0540	10	0.30078	T	0.28	.	18.0775	0.89432	0.0:0.0:1.0:0.0	.	395;395	Q9NSN8-2;Q9NSN8	.;SNTG1_HUMAN	Q	395	ENSP00000429276:R395Q;ENSP00000429842:R395Q;ENSP00000431123:R395Q;ENSP00000276467:R395Q	ENSP00000276467:R395Q	R	+	2	0	SNTG1	51779858	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	9.141000	0.94612	2.577000	0.86979	0.643000	0.83706	CGG	.	.		0.493	SNTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377964.1			A	51617305	G	A	51617305	3	1	260	1	0	0	0	0	1	0	0	0	14889	1116	39	1	1238	1	SNTG1	8	51617305	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	9710918	51617305	94746717	364	37609										
PXDNL	137902	hgsc.bcm.edu	37	chr8	52321593	52321593	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tggcacacgcggggctggagCgcgcgaagagcatgcagggc	19	11	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:52321593C>T	ENST00000356297.4	-	17	2691	c.2591G>A	c.(2590-2592)cGc>cAc	p.R864H	PXDNL_ENST00000543296.1_Missense_Mutation_p.R864H	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	864					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.R63L(1)|p.R864L(1)		NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				GGGGCTGGAGCGCGCGAAGAG	0.662																																					p.R864H		Atlas-SNP	.											PXDNL_ENST00000356297,colon,carcinoma,-1,1	PXDNL	414	.	2	Substitution - Missense(2)	lung(2)	c.G2591A						.						23	27	25					8																	52321593		2024	4155	6179	SO:0001583	missense	137902	exon17			CTGGAGCGCGCGA		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"Immunoglobulin superfamily / I-set domain containing"	26359	protein-coding gene	gene with protein product	"polysomal ribonuclease 1 homolog (Xenopus)"	615904	"peroxidasin homolog-like (Drosophila)"			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.2591G>A	chr8.hg19:g.52321593C>T	ENSP00000348645:p.Arg864His	45.0	0.0		65.0	3.0	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	hg19	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	C	14.05	2.420939	0.42918	.	.	ENSG00000147485	ENST00000356297;ENST00000543296	D;D	0.84660	-1.88;-1.88	3.31	2.41	0.29592	.	0.272281	0.26156	N	0.026002	D	0.94991	0.8379	H	0.99286	4.5	0.35901	D	0.830399	D	0.89917	1.0	D	0.87578	0.998	D	0.95258	0.8366	10	0.87932	D	0	.	9.6539	0.39914	0.2105:0.7895:0.0:0.0	.	864	A1KZ92	PXDNL_HUMAN	H	864	ENSP00000348645:R864H;ENSP00000444865:R864H	ENSP00000348645:R864H	R	-	2	0	PXDNL	52484146	1.000000	0.71417	0.249000	0.24280	0.019000	0.09904	5.019000	0.64060	0.487000	0.27698	0.650000	0.86243	CGC	.	.		0.662	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		T	52321593	C	T	52321593	3	4	260	1	0	0	0	0	1	0	0	0	12863	768	27	1	1828	1	PXDNL	8	52321593	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	704288	52321593	94042429	365	37610										
NSMAF	8439	hgsc.bcm.edu	37	chr8	59520364	59520364	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgcctccttttgtagatgcgGcggacatcttggagtgttat	12	8	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:59520364G>T	ENST00000038176.3	-	11	935	c.723C>A	c.(721-723)cgC>cgA	p.R241R	NSMAF_ENST00000519858.1_5'UTR|NSMAF_ENST00000427130.2_Silent_p.R272R	NM_003580.3	NP_003571.2	Q92636	FAN_HUMAN	neutral sphingomyelinase (N-SMase) activation associated factor	241	GRAM.				ceramide metabolic process (GO:0006672)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	receptor signaling protein activity (GO:0005057)|sphingomyelin phosphodiesterase activator activity (GO:0016230)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	38		all_lung(136;0.174)|Lung NSC(129;0.2)				TGTAGATGCGGCGGACATCTT	0.443																																					p.R272R		Atlas-SNP	.											.	NSMAF	156	.	0			c.C816A						.						143	147	146					8																	59520364		2203	4300	6503	SO:0001819	synonymous_variant	8439	exon11			GATGCGGCGGACA	X96586	CCDS6173.1, CCDS47864.1	8q12-q13	2013-01-10			ENSG00000035681	ENSG00000035681		"WD repeat domain containing"	8017	protein-coding gene	gene with protein product		603043				8808629, 10640829	Standard	NM_003580		Approved	FAN	uc011lee.2	Q92636	OTTHUMG00000164352	ENST00000038176.3:c.723C>A	chr8.hg19:g.59520364G>T		88.0	0.0		122.0	5.0	NM_001144772	B4DFB0|E9PCH0|Q8IW26	Silent	SNP	ENST00000038176.3	hg19	CCDS6173.1																																																																																			.	.		0.443	NSMAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378384.1	NM_003580		T	59520364	G	T	59520364	2	4	260	1	0	0	0	0	0	0	0	1	10683	1190	42	3		3	NSMAF	8	59520364	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	7198771	59520364	86843658	366	37611										
CHD7	55636	hgsc.bcm.edu	37	chr8	61765123	61765123	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tttggggttatttttgacccTgtgaaacagcaatttgactg	10	6	0	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:61765123T>C	ENST00000423902.2	+	30	6440	c.5961T>C	c.(5959-5961)ccT>ccC	p.P1987P	CHD7_ENST00000524602.1_Intron	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	1987					adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			TTTTTGACCCTGTGAAACAGC	0.398																																					p.P1987P		Atlas-SNP	.											.	CHD7	534	.	0			c.T5961C						.						64	58	60					8																	61765123		1832	4085	5917	SO:0001819	synonymous_variant	55636	exon30			TGACCCTGTGAAA	AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"CHARGE association"	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.5961T>C	chr8.hg19:g.61765123T>C		92.0	0.0		102.0	5.0	NM_017780	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Silent	SNP	ENST00000423902.2	hg19	CCDS47865.1																																																																																			.	.		0.398	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762		C	61765123	T	C	61765123	2	2	260	1	0	0	0	0	0	0	0	1	3332	1567	55	2		2	CHD7	8	61765123	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	2244759	61765123	84598899	367	37612										
NKAIN3	286183	hgsc.bcm.edu	37	chr8	63492103	63492103	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctttttttgttgtaggtctcAgcattagagaggcagatctt	10	6	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:63492103A>G	ENST00000523211.1	+	2	192	c.60A>G	c.(58-60)tcA>tcG	p.S20S	NKAIN3_ENST00000328472.5_Silent_p.S20S|NKAIN3_ENST00000519049.1_3'UTR	NM_173688.2	NP_775959.1	Q8N8D7	NKAI3_HUMAN	Na+/K+ transporting ATPase interacting 3	20						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				kidney(3)|large_intestine(2)|lung(8)	13	Breast(64;0.127)	Lung NSC(129;0.187)				TGTAGGTCTCAGCATTAGAGA	0.373																																					p.S20S		Atlas-SNP	.											.	NKAIN3	32	.	0			c.A60G						.						160	154	156					8																	63492103		1855	4101	5956	SO:0001819	synonymous_variant	286183	exon2			GGTCTCAGCATTA	AK096949	CCDS55239.1	8q12.3	2014-08-12	2007-10-04	2007-10-04	ENSG00000185942	ENSG00000185942		"Na+/K+ transporting ATPase interacting"	26829	protein-coding gene	gene with protein product		612872	"family with sequence similarity 77, member D"	FAM77D		17606467	Standard	NM_173688		Approved	FLJ39630	uc010lyq.1	Q8N8D7	OTTHUMG00000164361	ENST00000523211.1:c.60A>G	chr8.hg19:g.63492103A>G		112.0	0.0		99.0	5.0	NM_173688		Silent	SNP	ENST00000523211.1	hg19	CCDS55239.1																																																																																			.	.		0.373	NKAIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378447.2	NM_173688		G	63492103	A	G	63492103	2	3	260	1	0	0	0	0	0	0	0	1	10446	175	7	2		2	NKAIN3	8	63492103	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1726980	63492103	82871919	368	37613										
MYBL1	4603	hgsc.bcm.edu	37	chr8	67492490	67492490	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctgagcagacacaggctgatTttcatccatactgtaaaact	7	10	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:67492490T>C	ENST00000522677.3	-	9	1389	c.979A>G	c.(979-981)Aat>Gat	p.N327D	MYBL1_ENST00000517885.1_Intron|MYBL1_ENST00000524176.2_Missense_Mutation_p.N327D	NM_001080416.2|NM_001144755.1	NP_001073885.1|NP_001138227.1	P10243	MYBA_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 1	327	Negative regulatory domain. {ECO:0000250}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|skin(1)	25			Epithelial(68;0.00211)|all cancers(69;0.00726)|OV - Ovarian serous cystadenocarcinoma(28;0.00989)|BRCA - Breast invasive adenocarcinoma(89;0.0938)			ACAGGCTGATTTTCATCCATA	0.443																																					p.N327D		Atlas-SNP	.											.	MYBL1	73	.	0			c.A979G						.						72	72	72					8																	67492490		1941	4140	6081	SO:0001583	missense	4603	exon9			GCTGATTTTCATC	X13294	CCDS47867.1, CCDS55241.1	8q22	2013-07-09	2013-07-09		ENSG00000185697	ENSG00000185697			7547	protein-coding gene	gene with protein product		159405					Standard	XM_005251251		Approved	AMYB, A-myb	uc003xwj.3	P10243	OTTHUMG00000164559	ENST00000522677.3:c.979A>G	chr8.hg19:g.67492490T>C	ENSP00000429633:p.Asn327Asp	88.0	0.0		100.0	4.0	NM_001080416	E7EW29|Q495F9	Missense_Mutation	SNP	ENST00000522677.3	hg19	CCDS47867.1	.	.	.	.	.	.	.	.	.	.	T	11.97	1.798778	0.31777	.	.	ENSG00000185697	ENST00000522677;ENST00000524176	T;T	0.17054	2.79;2.3	5.34	5.34	0.76211	.	0.127826	0.53938	D	0.000049	T	0.12561	0.0305	L	0.44542	1.39	0.26490	N	0.974958	B;B;B	0.34015	0.358;0.435;0.358	B;B;B	0.29598	0.093;0.104;0.093	T	0.18650	-1.0330	10	0.11485	T	0.65	-19.8586	10.5242	0.44938	0.0:0.0759:0.0:0.9241	.	327;326;327	Q495F9;Q495G0;P10243	.;.;MYBA_HUMAN	D	327	ENSP00000429633:N327D;ENSP00000428011:N327D	ENSP00000429633:N327D	N	-	1	0	MYBL1	67655044	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.145000	0.42207	2.007000	0.58848	0.533000	0.62120	AAT	.	.		0.443	MYBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379221.3	XM_034274		C	67492490	T	C	67492490	3	2	260	1	0	0	0	0	1	0	0	0	10018	1841	64	2	1311	2	MYBL1	8	67492490	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	4000387	67492490	78871532	369	37614										
NCOA2	10499	hgsc.bcm.edu	37	chr8	71074948	71074948	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcatttagagatgcttacctTcatgatgatgcctcttagca	7	9	3	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:71074948T>C	ENST00000452400.2	-	9	1155	c.974A>G	c.(973-975)gAa>gGa	p.E325G		NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	325					cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucose metabolic process (GO:0010906)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|signal transducer activity (GO:0004871)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)		PAX3/NCOA2(4)|HEY1/NCOA2(10)	NS(1)|breast(4)|endometrium(7)|kidney(4)|large_intestine(10)|lung(25)|ovary(1)|pancreas(2)|prostate(2)|skin(4)	60	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			ATGCTTACCTTCATGATGATG	0.443			T	"RUNXBP2, HEY1"	"AML, Chondrosarcoma"																																p.E325G		Atlas-SNP	.		Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	.	NCOA2	147	.	0			c.A974G						.						103	99	101					8																	71074948		1938	4137	6075	SO:0001583	missense	10499	exon9			TTACCTTCATGAT	X97674	CCDS47872.1	8q13.3	2011-07-01			ENSG00000140396	ENSG00000140396		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7669	protein-coding gene	gene with protein product		601993				9111344, 8670870	Standard	XM_005251128		Approved	TIF2, GRIP1, NCoA-2, KAT13C, bHLHe75	uc003xyn.1	Q15596	OTTHUMG00000164671	ENST00000452400.2:c.974A>G	chr8.hg19:g.71074948T>C	ENSP00000399968:p.Glu325Gly	95.0	0.0		88.0	4.0	NM_006540	Q14CD2	Missense_Mutation	SNP	ENST00000452400.2	hg19	CCDS47872.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.037192	0.75617	.	.	ENSG00000140396	ENST00000452400	T	0.20463	2.07	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.27454	0.0674	M	0.76170	2.325	0.80722	D	1	P	0.42078	0.77	B	0.36186	0.219	T	0.14309	-1.0477	10	0.87932	D	0	.	16.0238	0.80522	0.0:0.0:0.0:1.0	.	325	Q15596	NCOA2_HUMAN	G	325	ENSP00000399968:E325G	ENSP00000399968:E325G	E	-	2	0	NCOA2	71237502	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.868000	0.87116	2.367000	0.80283	0.528000	0.53228	GAA	.	.		0.443	NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379696.1			C	71074948	T	C	71074948	3	2	260	1	0	0	0	0	1	0	0	0	10238	1783	62	2	3480	2	NCOA2	8	71074948	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	3582458	71074948	75289074	370	37615										
LRRCC1	85444	hgsc.bcm.edu	37	chr8	86039024	86039024	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgatgagctgcataaacatgCaaatgaaaaagaggatattc	9	5	0	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:86039024C>T	ENST00000360375.3	+	9	1522	c.1373C>T	c.(1372-1374)gCa>gTa	p.A458V	LRRCC1_ENST00000414626.2_Missense_Mutation_p.A438V	NM_033402.4	NP_208325.3	Q9C099	LRCC1_HUMAN	leucine rich repeat and coiled-coil centrosomal protein 1	458					mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(4)|kidney(9)|large_intestine(7)|lung(16)|skin(1)|upper_aerodigestive_tract(2)	43						CATAAACATGCAAATGAAAAA	0.368																																					p.A458V		Atlas-SNP	.											.	LRRCC1	212	.	0			c.C1373T						.						91	86	87					8																	86039024		1860	4103	5963	SO:0001583	missense	85444	exon9			AACATGCAAATGA	BC030701	CCDS43750.1	8q21.2	2012-04-10	2012-04-10		ENSG00000133739	ENSG00000133739			29373	protein-coding gene	gene with protein product	"centrosomal leucine-rich repeat and coiled-coil containing protein", "variable number of flagella 1 homolog (Chlamydomonas)"		"leucine rich repeat and coiled-coil domain containing 1"			11214970, 18728398	Standard	NM_033402		Approved	KIAA1764, CLERC, VFL1	uc003ycw.3	Q9C099	OTTHUMG00000164784	ENST00000360375.3:c.1373C>T	chr8.hg19:g.86039024C>T	ENSP00000353538:p.Ala458Val	92.0	0.0		100.0	4.0	NM_033402	B4DYX6|B5RI11|Q8N768|Q96DK7|Q96N01	Missense_Mutation	SNP	ENST00000360375.3	hg19	CCDS43750.1	.	.	.	.	.	.	.	.	.	.	C	13.11	2.138855	0.37728	.	.	ENSG00000133739	ENST00000360375;ENST00000414626	T;T	0.34859	1.34;1.34	5.56	3.75	0.43078	.	0.456574	0.16334	N	0.218994	T	0.38506	0.1043	M	0.71581	2.175	0.45366	D	0.998352	B;P;B;B	0.42908	0.096;0.793;0.096;0.356	B;B;B;B	0.41723	0.028;0.365;0.028;0.073	T	0.18745	-1.0327	10	0.23891	T	0.37	-8.6088	11.775	0.51981	0.0:0.8548:0.0:0.1452	.	365;438;365;458	B4DV06;Q9C099-2;E9PE41;Q9C099	.;.;.;LRCC1_HUMAN	V	458;438	ENSP00000353538:A458V;ENSP00000394695:A438V	ENSP00000353538:A458V	A	+	2	0	LRRCC1	86226276	0.978000	0.34361	0.172000	0.22920	0.823000	0.46562	2.497000	0.45354	1.363000	0.46019	0.655000	0.94253	GCA	.	.		0.368	LRRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380267.1	NM_033402		T	86039024	C	T	86039024	3	4	260	1	0	0	0	0	1	0	0	0	9035	710	25	3	1407	3	LRRCC1	8	86039024	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	14964076	86039024	60324998	371	37616										
OSGIN2	734	hgsc.bcm.edu	37	chr8	90921887	90921887	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gcgaaaagttaaagcgatgcCattagttgaagaaacttctt	9	6	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:90921887C>T	ENST00000297438.2	+	2	360	c.5C>T	c.(4-6)cCa>cTa	p.P2L	OSGIN2_ENST00000520659.1_Missense_Mutation_p.P46L|OSGIN2_ENST00000451899.2_Missense_Mutation_p.P46L	NM_004337.2	NP_004328.1	Q9Y236	OSGI2_HUMAN	oxidative stress induced growth inhibitor family member 2	2					meiotic nuclear division (GO:0007126)					breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|urinary_tract(1)	17			BRCA - Breast invasive adenocarcinoma(11;0.0344)			AAAGCGATGCCATTAGTTGAA	0.313																																					p.P46L		Atlas-SNP	.											.	OSGIN2	73	.	0			c.C137T						.						94	93	93					8																	90921887		2203	4300	6503	SO:0001583	missense	734	exon2			CGATGCCATTAGT	AF061326	CCDS6248.1, CCDS47888.1	8q21	2006-10-05	2006-10-05	2006-10-05	ENSG00000164823	ENSG00000164823			1355	protein-coding gene	gene with protein product		604598	"chromosome 8 open reading frame 1"	C8orf1		9933573	Standard	NM_004337		Approved	hT41	uc003yeh.3	Q9Y236	OTTHUMG00000163811	ENST00000297438.2:c.5C>T	chr8.hg19:g.90921887C>T	ENSP00000297438:p.Pro2Leu	141.0	0.0		121.0	6.0	NM_001126111		Missense_Mutation	SNP	ENST00000297438.2	hg19	CCDS6248.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.627997	0.87560	.	.	ENSG00000164823	ENST00000297438;ENST00000451899;ENST00000520659	T;T;T	0.55052	1.66;1.55;0.54	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.70219	0.3199	M	0.63428	1.95	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.74348	0.983;0.946	T	0.73379	-0.4001	10	0.87932	D	0	-10.7578	16.9813	0.86328	0.0:1.0:0.0:0.0	.	46;2	Q9Y236-2;Q9Y236	.;OSGI2_HUMAN	L	2;46;46	ENSP00000297438:P2L;ENSP00000396445:P46L;ENSP00000431029:P46L	ENSP00000297438:P2L	P	+	2	0	OSGIN2	90991061	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.498000	0.73679	2.430000	0.82344	0.462000	0.41574	CCA	.	.		0.313	OSGIN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375691.1	NM_004337		T	90921887	C	T	90921887	3	4	260	1	0	0	0	0	1	0	0	0	11299	594	21	3	143	3	OSGIN2	8	90921887	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	4882863	90921887	55442135	372	37617										
GEM	2669	hgsc.bcm.edu	37	chr8	95262794	95262794	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cgatgaacttgcagtcaaacAccactgcacaggctctccct	7	15	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:95262794A>G	ENST00000297596.2	-	5	899	c.635T>C	c.(634-636)gTg>gCg	p.V212A	GEM_ENST00000396194.2_Missense_Mutation_p.V212A	NM_005261.3	NP_005252.1	P55040	GEM_HUMAN	GTP binding protein overexpressed in skeletal muscle	212					cell surface receptor signaling pathway (GO:0007166)|chromosome organization (GO:0051276)|immune response (GO:0006955)|metaphase plate congression (GO:0051310)|mitotic nuclear division (GO:0007067)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic side of plasma membrane (GO:0009898)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|spindle midzone (GO:0051233)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)			endometrium(3)|kidney(1)|large_intestine(7)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	22	Breast(36;4.65e-06)	Myeloproliferative disorder(644;0.204)	BRCA - Breast invasive adenocarcinoma(8;0.00691)			GCAGTCAAACACCACTGCACA	0.562																																					p.V212A	GBM(125;80 1653 28655 32188 47338)|Esophageal Squamous(19;97 579 13602 49091 51766)	Atlas-SNP	.											.	GEM	40	.	0			c.T635C						.						45	40	42					8																	95262794		2203	4300	6503	SO:0001583	missense	2669	exon5			TCAAACACCACTG		CCDS6261.1	8q13-q21	2014-05-09	2001-11-28		ENSG00000164949	ENSG00000164949			4234	protein-coding gene	gene with protein product	"kinase-inducible Ras-like protein"	600164	"GTP-binding protein overexpressed in skeletal muscle"			7912851, 11956230	Standard	NM_005261		Approved	KIR	uc003ygj.3	P55040	OTTHUMG00000164392	ENST00000297596.2:c.635T>C	chr8.hg19:g.95262794A>G	ENSP00000297596:p.Val212Ala	76.0	0.0		89.0	4.0	NM_181702	B2RA31	Missense_Mutation	SNP	ENST00000297596.2	hg19	CCDS6261.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.195696	0.78902	.	.	ENSG00000164949	ENST00000396194;ENST00000297596	T;T	0.75589	-0.95;-0.95	5.6	5.6	0.85130	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.79633	0.4479	L	0.28504	0.86	0.80722	D	1	D	0.69078	0.997	D	0.77004	0.989	T	0.80810	-0.1216	10	0.51188	T	0.08	.	16.0697	0.80914	1.0:0.0:0.0:0.0	.	212	P55040	GEM_HUMAN	A	212	ENSP00000379497:V212A;ENSP00000297596:V212A	ENSP00000297596:V212A	V	-	2	0	GEM	95331970	1.000000	0.71417	1.000000	0.80357	0.874000	0.50279	8.910000	0.92685	2.260000	0.74910	0.528000	0.53228	GTG	.	.		0.562	GEM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378566.1	NM_181702		G	95262794	A	G	95262794	3	3	260	1	0	0	0	0	1	0	0	0	6337	159	6	2	259	2	GEM	8	95262794	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	4340907	95262794	51101228	373	37618										
RAD54B	25788	hgsc.bcm.edu	37	chr8	95470643	95470643	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	atcattttgtgacgggagaaAggtgttattaattgcaacac	10	5	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:95470643A>G	ENST00000336148.5	-	3	281	c.157T>C	c.(157-159)Ttt>Ctt	p.F53L	RAD54B_ENST00000297592.5_Missense_Mutation_p.F53L	NM_012415.3	NP_036547.1	Q9Y620	RA54B_HUMAN	RAD54 homolog B (S. cerevisiae)	53					ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|double-strand break repair via homologous recombination (GO:0000724)|mitotic recombination (GO:0006312)|reciprocal meiotic recombination (GO:0007131)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|RNA helicase activity (GO:0003724)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(10)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(36;4.5e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00217)			GACGGGAGAAAGGTGTTATTA	0.284								Direct reversal of damage;Homologous recombination																													p.F53L		Atlas-SNP	.											.	RAD54B	88	.	0			c.T157C						.						81	78	79					8																	95470643		2203	4299	6502	SO:0001583	missense	25788	exon3			GGAGAAAGGTGTT	AF112481	CCDS6262.1, CCDS56546.1, CCDS75768.1	8q22.1	2014-08-08			ENSG00000197275	ENSG00000197275			17228	protein-coding gene	gene with protein product		604289				10362364, 10851248	Standard	NM_012415		Approved	RDH54	uc003ygk.3	Q9Y620	OTTHUMG00000133658	ENST00000336148.5:c.157T>C	chr8.hg19:g.95470643A>G	ENSP00000336606:p.Phe53Leu	92.0	0.0		79.0	5.0	NM_001205262	F6WBS8	Missense_Mutation	SNP	ENST00000336148.5	hg19	CCDS6262.1	.	.	.	.	.	.	.	.	.	.	A	0.972	-0.699822	0.03279	.	.	ENSG00000197275	ENST00000336148;ENST00000523839;ENST00000297592	D;T;T	0.87650	-2.28;1.78;1.89	4.42	0.505	0.16953	.	0.222920	0.28166	N	0.016360	T	0.74854	0.3771	L	0.29908	0.895	0.09310	N	1	B;B	0.17667	0.023;0.0	B;B	0.14023	0.01;0.0	T	0.63269	-0.6675	10	0.62326	D	0.03	-0.8218	3.1298	0.06419	0.6171:0.0:0.2053:0.1776	.	53;53	F6WBS8;Q9Y620	.;RA54B_HUMAN	L	53	ENSP00000336606:F53L;ENSP00000428554:F53L;ENSP00000430153:F53L	ENSP00000430153:F53L	F	-	1	0	RAD54B	95539819	0.001000	0.12720	0.001000	0.08648	0.061000	0.15899	0.299000	0.19138	-0.002000	0.14469	0.528000	0.53228	TTT	.	.		0.284	RAD54B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257806.3	NM_012415		G	95470643	A	G	95470643	3	3	260	1	0	0	0	0	1	0	0	0	13007	72	3	2	2627	2	RAD54B	8	95470643	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	207849	95470643	50893379	374	37619										
STK3	6788	hgsc.bcm.edu	37	chr8	99779493	99779493	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtcacattgctgcattatggAaatttctttgattatttcct	6	7	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:99779493A>G	ENST00000419617.2	-	3	354	c.214T>C	c.(214-216)Tcc>Ccc	p.S72P	STK3_ENST00000523601.1_Missense_Mutation_p.S100P	NM_006281.3	NP_006272.2	Q13188	STK3_HUMAN	serine/threonine kinase 3	72	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell differentiation involved in embryonic placenta development (GO:0060706)|central nervous system development (GO:0007417)|endocardium development (GO:0003157)|hepatocyte apoptotic process (GO:0097284)|hippo signaling (GO:0035329)|intracellular signal transduction (GO:0035556)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of organ growth (GO:0046621)|neural tube formation (GO:0001841)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|primitive hemopoiesis (GO:0060215)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein dimerization activity (GO:0046983)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	17	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)		TGCATTATGGAAATTTCTTTG	0.313																																					p.S100P		Atlas-SNP	.											.	STK3	47	.	0			c.T298C						.						101	97	98					8																	99779493		1884	4156	6040	SO:0001583	missense	6788	exon5			TTATGGAAATTTC	BC010640	CCDS47900.1, CCDS59108.1, CCDS75774.1	8q22.2	2011-05-24	2010-06-25		ENSG00000104375	ENSG00000104375			11406	protein-coding gene	gene with protein product		605030	"serine/threonine kinase 3 (Ste20, yeast homolog)"			8816758	Standard	NM_006281		Approved	MST2, KRS1	uc003yip.4	Q13188	OTTHUMG00000164651	ENST00000419617.2:c.214T>C	chr8.hg19:g.99779493A>G	ENSP00000390500:p.Ser72Pro	85.0	0.0		84.0	4.0	NM_001256312	A8K722|B3KYA7|Q15445|Q15801|Q96FM6	Missense_Mutation	SNP	ENST00000419617.2	hg19	CCDS47900.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.564814	0.86439	.	.	ENSG00000104375	ENST00000419617;ENST00000523601;ENST00000518165	T;T;T	0.66815	-0.23;-0.23;-0.23	5.53	5.53	0.82687	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.81192	0.4771	M	0.77486	2.375	0.80722	D	1	D;D;D	0.69078	0.973;0.974;0.997	P;P;D	0.66497	0.661;0.788;0.944	D	0.84018	0.0352	10	0.87932	D	0	.	15.6641	0.77213	1.0:0.0:0.0:0.0	.	72;72;100	E5RFQ9;Q13188;B3KYA7	.;STK3_HUMAN;.	P	72;100;72	ENSP00000390500:S72P;ENSP00000429744:S100P;ENSP00000428014:S72P	ENSP00000390500:S72P	S	-	1	0	STK3	99848669	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.367000	0.79558	2.086000	0.62901	0.459000	0.35465	TCC	.	.		0.313	STK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379635.1	NM_006281		G	99779493	A	G	99779493	3	3	260	1	0	0	0	0	1	0	0	0	15310	246	9	2	1297	2	STK3	8	99779493	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	4308850	99779493	46584529	375	37620										
MTSS1	9788	hgsc.bcm.edu	37	chr8	125580779	125580779	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggctggatatcacctctcccTgcaaaaaacagagacccaag	8	13	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:125580779T>C	ENST00000518547.1	-	7	934		c.e7-2		MTSS1_ENST00000325064.5_Splice_Site|MTSS1_ENST00000395508.2_5'Flank|MTSS1_ENST00000431961.2_Splice_Site|MTSS1_ENST00000524090.1_Silent_p.A43A|MTSS1_ENST00000354184.4_Splice_Site|MTSS1_ENST00000378017.3_Splice_Site	NM_001282971.1|NM_014751.4	NP_001269900.1|NP_055566.3	O43312	MTSS1_HUMAN	metastasis suppressor 1						actin cytoskeleton organization (GO:0030036)|actin filament polymerization (GO:0030041)|adherens junction maintenance (GO:0034334)|bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|cellular response to fluid shear stress (GO:0071498)|epithelial cell proliferation involved in renal tubule morphogenesis (GO:2001013)|filopodium assembly (GO:0046847)|glomerulus morphogenesis (GO:0072102)|in utero embryonic development (GO:0001701)|magnesium ion homeostasis (GO:0010960)|microspike assembly (GO:0030035)|negative regulation of epithelial cell proliferation (GO:0050680)|nephron tubule epithelial cell differentiation (GO:0072160)|positive regulation of actin filament bundle assembly (GO:0032233)|renal tubule morphogenesis (GO:0061333)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			CACCTCTCCCTGCAAAAAACA	0.488																																					.	Esophageal Squamous(160;622 1893 3862 8546 12509)	Atlas-SNP	.											.	MTSS1	79	.	0			c.461-2A>G						.						54	53	54					8																	125580779		2203	4300	6503	SO:0001630	splice_region_variant	9788	exon8			TCTCCCTGCAAAA	AF086645	CCDS6353.1, CCDS64968.1, CCDS64969.1	8p22	2008-02-05			ENSG00000170873	ENSG00000170873			20443	protein-coding gene	gene with protein product		608486				12482861, 12082544	Standard	XM_005251111		Approved	KIAA0429, MIMA, MIMB, MIM	uc003yrk.2	O43312	OTTHUMG00000048189	ENST00000518547.1:c.461-2A>G	chr8.hg19:g.125580779T>C		89.0	0.0		94.0	6.0	NM_014751	J3KNK6|Q8TCA2|Q96RX2	Splice_Site	SNP	ENST00000518547.1	hg19	CCDS6353.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.17|15.17	2.753676|2.753676	0.49362|0.49362	.|.	.|.	ENSG00000170873|ENSG00000170873	ENST00000378017;ENST00000518547;ENST00000325064;ENST00000522162|ENST00000523179	.|.	.|.	.|.	5.25|5.25	5.25|5.25	0.73442|0.73442	.|.	.|.	.|.	.|.	.|.	.|T	.|0.71533	.|0.3351	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.70920	.|-0.4741	.|4	.|.	.|.	.|.	.|.	15.4446|15.4446	0.75220|0.75220	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|.	.|.	.|.	.|G	-1|1	.|.	.|.	.|R	-|-	.|1	.|2	MTSS1|MTSS1	125649960|125649960	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.670000|0.670000	0.39368|0.39368	7.907000|7.907000	0.87430|0.87430	2.112000|2.112000	0.64535|0.64535	0.533000|0.533000	0.62120|0.62120	.|AGG	.	.		0.488	MTSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109625.3	NM_014751	Intron	C	125580779	T	C	125580779	5	2	260	1	0	0	0	0	0	0	1	0	9971	1594	55	2	1840	2	MTSS1	8	125580779	Splice_Site	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	25801286	125580779	20783243	376	37621										
TG	7038	hgsc.bcm.edu	37	chr8	134125745	134125745	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gaattctctgggtggcgaggActcagatgcccgcgtcgagg	16	10	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:134125745A>G	ENST00000220616.4	+	44	7692	c.7652A>G	c.(7651-7653)gAc>gGc	p.D2551G	TG_ENST00000519543.1_Missense_Mutation_p.D684G|TG_ENST00000377869.1_Missense_Mutation_p.D2494G|TG_ENST00000542445.1_Missense_Mutation_p.D921G	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	2551					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		GGTGGCGAGGACTCAGATGCC	0.527																																					p.D2551G		Atlas-SNP	.											.	TG	416	.	0			c.A7652G						.						78	79	79					8																	134125745		2203	4300	6503	SO:0001583	missense	7038	exon44			GCGAGGACTCAGA	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.7652A>G	chr8.hg19:g.134125745A>G	ENSP00000220616:p.Asp2551Gly	87.0	0.0		100.0	4.0	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	hg19	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	A	6.436	0.448570	0.12223	.	.	ENSG00000042832	ENST00000377869;ENST00000543313;ENST00000220616;ENST00000542445;ENST00000519543	T;T;T;T	0.58358	0.34;0.34;0.34;0.34	4.83	-0.671	0.11381	Carboxylesterase, type B (1);	1.535810	0.03799	N	0.264088	T	0.43277	0.1240	L	0.37630	1.12	0.20764	N	0.999858	B;B;B	0.19200	0.019;0.007;0.034	B;B;B	0.19666	0.026;0.009;0.026	T	0.38394	-0.9663	10	0.72032	D	0.01	.	5.8771	0.18834	0.5795:0.274:0.1465:0.0	.	684;921;2551	E7EVM0;F5GWW5;P01266	.;.;THYG_HUMAN	G	2494;1357;2551;921;684	ENSP00000367100:D2494G;ENSP00000220616:D2551G;ENSP00000441693:D921G;ENSP00000430430:D684G	ENSP00000220616:D2551G	D	+	2	0	TG	134194927	0.727000	0.28069	0.026000	0.17262	0.012000	0.07955	1.387000	0.34430	-0.282000	0.09128	0.533000	0.62120	GAC	.	.		0.527	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		G	134125745	A	G	134125745	3	3	260	1	0	0	0	0	1	0	0	0	15828	275	10	2	7826	2	TG	8	134125745	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	8544966	134125745	12238277	377	37622										
ZFAT	57623	hgsc.bcm.edu	37	chr8	135545138	135545138	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acgttggcatactcctcattAgggtgcttcctgttgtagtg	11	9	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:135545138A>G	ENST00000377838.3	-	12	3228	c.3054T>C	c.(3052-3054)ccT>ccC	p.P1018P	ZFAT_ENST00000429442.2_Silent_p.P1006P|ZFAT_ENST00000520356.1_Silent_p.P1006P|ZFAT_ENST00000523399.1_Silent_p.P956P|ZFAT_ENST00000520214.1_Silent_p.P1006P|ZFAT_ENST00000520727.1_Silent_p.P1006P|ZFAT_ENST00000517307.1_5'UTR	NM_001174157.1|NM_020863.3	NP_001167628.1|NP_065914.2	Q9P243	ZFAT_HUMAN	zinc finger and AT hook domain containing	1018					hematopoietic progenitor cell differentiation (GO:0002244)|spongiotrophoblast layer development (GO:0060712)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(9)|large_intestine(8)|lung(16)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)			ACTCCTCATTAGGGTGCTTCC	0.622																																					p.P1018P		Atlas-SNP	.											.	ZFAT	265	.	0			c.T3054C						.						55	56	56					8																	135545138		2039	4166	6205	SO:0001819	synonymous_variant	57623	exon12			CTCATTAGGGTGC	BC025423	CCDS43768.1, CCDS47924.1, CCDS43768.2, CCDS55275.1, CCDS55276.1	8q24.23	2008-06-05	2008-01-25	2008-01-25	ENSG00000066827	ENSG00000066827		"Zinc fingers, C2H2-type"	19899	protein-coding gene	gene with protein product		610931	"zinc finger protein 406"	ZNF406, ZFAT1		10819331, 18329245	Standard	NM_020863		Approved	KIAA1485	uc003yup.3	Q9P243	OTTHUMG00000164321	ENST00000377838.3:c.3054T>C	chr8.hg19:g.135545138A>G		80.0	0.0		59.0	4.0	NM_020863	B7ZL15|E9PER3|Q3MIM5|Q6PJ01|Q75PJ6|Q75PJ7|Q75PJ9|Q86X64	Silent	SNP	ENST00000377838.3	hg19	CCDS47924.1																																																																																			.	.		0.622	ZFAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378272.1	NM_001029939		G	135545138	A	G	135545138	2	3	260	1	0	0	0	0	0	0	0	1	17647	407	15	2		2	ZFAT	8	135545138	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1419393	135545138	10818884	378	37623										
C8orf73	642475	hgsc.bcm.edu	37	chr8	144652226	144652226	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aggtggtggtcggcatgtgcCaccatagcactggggtgggt	18	8	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:144652226C>A	ENST00000398882.3	-	7	1309	c.1053G>T	c.(1051-1053)gtG>gtT	p.V351V	MROH6_ENST00000524906.1_5'Flank|MROH6_ENST00000532704.1_5'Flank|MROH6_ENST00000534459.1_5'Flank|MROH6_ENST00000533679.1_5'Flank	NM_001100878.1	NP_001094348.1	A6NGR9	MROH6_HUMAN	maestro heat-like repeat family member 6	351	Leu-rich.																CGGCATGTGCCACCATAGCAC	0.642																																					p.V351V		Atlas-SNP	.											.	.	.	.	0			c.G1053T						.						32	40	37					8																	144652226		2064	4190	6254	SO:0001819	synonymous_variant	642475	exon7			ATGTGCCACCATA	AF289596	CCDS47928.1	8q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000204839	ENSG00000204839		"maestro heat-like repeat containing"	27814	protein-coding gene	gene with protein product			"chromosome 8 open reading frame 73"	C8orf73		12477932	Standard	NM_001100878		Approved		uc010mff.3	A6NGR9	OTTHUMG00000165164	ENST00000398882.3:c.1053G>T	chr8.hg19:g.144652226C>A		79.0	0.0		82.0	5.0	NM_001100878	A8MWB1	Silent	SNP	ENST00000398882.3	hg19	CCDS47928.1	.	.	.	.	.	.	.	.	.	.	c	14.34	2.507361	0.44558	.	.	ENSG00000204839	ENST00000529971	T	0.36699	1.24	5.23	3.4	0.38934	.	.	.	.	.	T	0.56307	0.1976	.	.	.	0.80722	D	1	D	0.71674	0.998	D	0.71870	0.975	T	0.57051	-0.7877	8	0.87932	D	0	-49.1988	9.0153	0.36166	0.0:0.7683:0.1483:0.0834	.	364	E9PPP7	.	C	364	ENSP00000436959:G364C	ENSP00000436959:G364C	G	-	1	0	C8orf73	144723369	0.979000	0.34478	0.995000	0.50966	0.825000	0.46686	0.034000	0.13776	0.570000	0.29347	-0.247000	0.11927	GGC	.	.		0.642	MROH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382330.3	NM_001100878		A	144652226	C	A	144652226	2	1	260	1	0	0	0	0	0	0	0	1	2437	581	21	3		3	C8orf73	8	144652226	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	9107088	144652226	1711796	379	37624										
ZNF707	286075	hgsc.bcm.edu	37	chr8	144773301	144773301	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aagggaggagtgggcgtgtcTggaacccagccagagggccc	18	10	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:144773301T>C	ENST00000532205.1	+	6	973	c.74T>C	c.(73-75)cTg>cCg	p.L25P	ZNF707_ENST00000454097.1_Missense_Mutation_p.L25P|ZNF707_ENST00000442058.2_Missense_Mutation_p.L25P|ZNF707_ENST00000358656.4_Missense_Mutation_p.L25P|ZNF707_ENST00000532158.1_Missense_Mutation_p.L25P|ZNF707_ENST00000418203.2_Missense_Mutation_p.L25P			Q96C28	ZN707_HUMAN	zinc finger protein 707	25	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)	1	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;5.6e-41)|Epithelial(56;1.02e-39)|all cancers(56;9.65e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			TGGGCGTGTCTGGAACCCAGC	0.607																																					p.L25P		Atlas-SNP	.											.	ZNF707	21	.	0			c.T74C						.						57	65	62					8																	144773301		2203	4300	6503	SO:0001583	missense	286075	exon4			CGTGTCTGGAACC	AK001126	CCDS47932.1	8q24.3	2013-01-08				ENSG00000181135		"Zinc fingers, C2H2-type", "-"	27815	protein-coding gene	gene with protein product						12477932	Standard	NM_173831		Approved		uc010mfi.3	Q96C28		ENST00000532205.1:c.74T>C	chr8.hg19:g.144773301T>C	ENSP00000436212:p.Leu25Pro	160.0	0.0		143.0	7.0	NM_001100598	A8K317|B3KNY1|D3DWK7	Missense_Mutation	SNP	ENST00000532205.1	hg19	CCDS47932.1	.	.	.	.	.	.	.	.	.	.	T	9.745	1.165852	0.21538	.	.	ENSG00000181135	ENST00000454097;ENST00000534303;ENST00000529833;ENST00000530574;ENST00000358656;ENST00000526970;ENST00000532158;ENST00000532205;ENST00000418203	T;T;T;T;T;T;T;T;T	0.19250	2.16;2.16;2.16;2.16;2.16;2.16;2.16;2.16;2.16	2.46	1.25	0.21368	Krueppel-associated box (4);	.	.	.	.	T	0.51007	0.1649	H	0.94964	3.605	0.19300	N	0.999974	D	0.76494	0.999	D	0.74674	0.984	T	0.35574	-0.9783	9	0.87932	D	0	-22.3826	5.6653	0.17693	0.0:0.1493:0.0:0.8507	.	25	Q96C28	ZN707_HUMAN	P	25	ENSP00000409029:L25P;ENSP00000437134:L25P;ENSP00000434503:L25P;ENSP00000436362:L25P;ENSP00000351482:L25P;ENSP00000436634:L25P;ENSP00000436250:L25P;ENSP00000436212:L25P;ENSP00000413215:L25P	ENSP00000351482:L25P	L	+	2	0	ZNF707	144845289	0.000000	0.05858	0.006000	0.13384	0.182000	0.23217	0.613000	0.24299	0.178000	0.19917	0.460000	0.39030	CTG	.	.		0.607	ZNF707-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382197.1	NM_173831		C	144773301	T	C	144773301	3	2	260	1	0	0	0	0	1	0	0	0	18126	1580	55	2	80	2	ZNF707	8	144773301	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	121075	144773301	1590721	380	37625										
PLEC	5339	hgsc.bcm.edu	37	chr8	144991777	144991777	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cgttcatctcctcatcgaagAggccgcgcttgtaggccacc	10	15	3	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:144991777A>G	ENST00000322810.4	-	32	12792	c.12623T>C	c.(12622-12624)cTc>cCc	p.L4208P	PLEC_ENST00000354589.3_Missense_Mutation_p.L4071P|PLEC_ENST00000357649.2_Missense_Mutation_p.L4075P|PLEC_ENST00000356346.3_Missense_Mutation_p.L4057P|PLEC_ENST00000436759.2_Missense_Mutation_p.L4098P|PLEC_ENST00000354958.2_Missense_Mutation_p.L4049P|PLEC_ENST00000345136.3_Missense_Mutation_p.L4071P|PLEC_ENST00000527096.1_Missense_Mutation_p.L4094P|PLEC_ENST00000398774.2_Missense_Mutation_p.L4039P	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	4208	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						CTCATCGAAGAGGCCGCGCTT	0.637																																					p.L4208P		Atlas-SNP	.											.	PLEC	1144	.	0			c.T12623C						.						52	56	55					8																	144991777		2048	4197	6245	SO:0001583	missense	5339	exon32			TCGAAGAGGCCGC	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"plectin 1, intermediate filament binding protein, 500kD", "epidermolysis bullosa simplex 1 (Ogna)", "plectin 1, intermediate filament binding protein 500kDa"	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.12623T>C	chr8.hg19:g.144991777A>G	ENSP00000323856:p.Leu4208Pro	127.0	0.0		144.0	6.0	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	hg19	CCDS43772.1	.	.	.	.	.	.	.	.	.	.	A	8.976	0.974112	0.18736	.	.	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	D;D;D;D;D;D;D;D;D	0.82433	-1.61;-1.61;-1.61;-1.61;-1.61;-1.61;-1.61;-1.61;-1.61	5.14	3.97	0.46021	.	0.101407	0.39475	U	0.001347	D	0.90693	0.7080	M	0.84773	2.715	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.76071	0.964;0.977;0.977;0.987;0.977;0.977;0.977;0.977	D	0.90929	0.4789	10	0.72032	D	0.01	.	11.1141	0.48249	0.8614:0.0:0.0:0.1386	.	4098;4057;4049;4208;4039;4071;4075;4071	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	P	4071;4075;4071;4039;4208;4049;4057;4098;4094	ENSP00000344848:L4071P;ENSP00000350277:L4075P;ENSP00000346602:L4071P;ENSP00000381756:L4039P;ENSP00000323856:L4208P;ENSP00000347044:L4049P;ENSP00000348702:L4057P;ENSP00000388180:L4098P;ENSP00000434583:L4094P	ENSP00000323856:L4208P	L	-	2	0	PLEC	145063765	1.000000	0.71417	0.993000	0.49108	0.687000	0.40016	7.240000	0.78192	0.949000	0.37715	0.448000	0.29417	CTC	.	.		0.637	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		G	144991777	A	G	144991777	3	3	260	1	0	0	0	0	1	0	0	0	12061	304	11	2	1435	2	PLEC	8	144991777	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	218476	144991777	1372245	381	37626										
GPT	2875	hgsc.bcm.edu	37	chr8	145731975	145731975	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tggcatcagctgcaacccagTgcagggcgccatgtactcct	11	14	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:145731975T>C	ENST00000528431.1	+	10	1380	c.1223T>C	c.(1222-1224)gTg>gCg	p.V408A	MFSD3_ENST00000301327.4_5'Flank|GPT_ENST00000394955.2_Missense_Mutation_p.V408A			P24298	ALAT1_HUMAN	glutamic-pyruvate transaminase (alanine aminotransferase)	408					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-alanine catabolic process (GO:0042853)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	L-alanine:2-oxoglutarate aminotransferase activity (GO:0004021)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|endometrium(1)|lung(2)|ovary(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)		L-Alanine(DB00160)|Phenelzine(DB00780)	TGCAACCCAGTGCAGGGCGCC	0.716																																					p.V408A		Atlas-SNP	.											.	GPT	31	.	0			c.T1223C						.						15	10	11					8																	145731975		2138	4212	6350	SO:0001583	missense	2875	exon9			ACCCAGTGCAGGG		CCDS6430.1	8q24.3	2013-09-19			ENSG00000167701	ENSG00000167701	2.6.1.2		4552	protein-coding gene	gene with protein product		138200					Standard	NM_005309		Approved	ALT1, GPT1	uc003zdh.4	P24298	OTTHUMG00000165176	ENST00000528431.1:c.1223T>C	chr8.hg19:g.145731975T>C	ENSP00000433586:p.Val408Ala	72.0	0.0		89.0	4.0	NM_005309	B0YJ18|D3DWM7|P78398|Q93076	Missense_Mutation	SNP	ENST00000528431.1	hg19	CCDS6430.1	.	.	.	.	.	.	.	.	.	.	T	19.12	3.764966	0.69878	.	.	ENSG00000167701	ENST00000528431;ENST00000394955	T;T	0.21031	2.03;2.03	4.54	4.54	0.55810	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	T	0.20740	0.0499	L	0.46614	1.455	0.80722	D	1	B	0.33919	0.432	B	0.37888	0.26	T	0.03818	-1.1001	10	0.21014	T	0.42	-34.0993	11.8278	0.52278	0.0:0.0:0.0:1.0	.	408	P24298	ALAT1_HUMAN	A	408	ENSP00000433586:V408A;ENSP00000378408:V408A	ENSP00000378408:V408A	V	+	2	0	GPT	145702783	1.000000	0.71417	0.998000	0.56505	0.971000	0.66376	3.230000	0.51286	1.662000	0.50781	0.459000	0.35465	GTG	.	.		0.716	GPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382471.1			C	145731975	T	C	145731975	3	2	260	1	0	0	0	0	1	0	0	0	6746	1696	59	2	1257	2	GPT	8	145731975	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	740198	145731975	632047	382	37627										
COMMD5	28991	hgsc.bcm.edu	37	chr8	146076649	146076649	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tctggaggaagctgggccccCaagaaactcactcggccact	11	14	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr8:146076649C>A	ENST00000305103.3	-	2	327	c.75G>T	c.(73-75)ttG>ttT	p.L25F	AF235103.1_ENST00000578937.1_RNA|COMMD5_ENST00000450361.2_Missense_Mutation_p.L25F|ZNF250_ENST00000543949.1_3'UTR|COMMD5_ENST00000402718.3_Missense_Mutation_p.L25F	NM_014066.3	NP_054785.2	Q9GZQ3	COMD5_HUMAN	COMM domain containing 5	25						nucleus (GO:0005634)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|ovary(1)|pancreas(1)	11	all_cancers(97;1.14e-11)|all_epithelial(106;7.74e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)			GCTGGGCCCCCAAGAAACTCA	0.567																																					p.L25F		Atlas-SNP	.											.	COMMD5	18	.	0			c.G75T						.						72	77	75					8																	146076649		2203	4300	6503	SO:0001583	missense	28991	exon2			GGCCCCCAAGAAA	AK023070	CCDS6436.1	8q24.3	2006-11-06				ENSG00000170619			17902	protein-coding gene	gene with protein product		608216				15799966, 10918053	Standard	NM_014066		Approved	HT002, FLJ13008, HCaRG	uc003zem.3	Q9GZQ3		ENST00000305103.3:c.75G>T	chr8.hg19:g.146076649C>A	ENSP00000304544:p.Leu25Phe	91.0	0.0		69.0	11.0	NM_001081004	D3DWN7|Q9NVN6|Q9UHX5	Missense_Mutation	SNP	ENST00000305103.3	hg19	CCDS6436.1	.	.	.	.	.	.	.	.	.	.	C	14.90	2.672767	0.47781	.	.	ENSG00000170619	ENST00000402718;ENST00000450361;ENST00000305103;ENST00000529143;ENST00000533270	T;T;T;T;T	0.35789	1.3;1.3;1.3;1.29;1.29	4.75	1.76	0.24704	.	0.084765	0.48286	D	0.000196	T	0.33469	0.0864	L	0.54323	1.7	0.80722	D	1	D	0.57571	0.98	P	0.48952	0.596	T	0.08186	-1.0734	10	0.36615	T	0.2	-19.6494	3.7906	0.08718	0.1693:0.5697:0.1647:0.0963	.	25	Q9GZQ3	COMD5_HUMAN	F	25	ENSP00000385793:L25F;ENSP00000394331:L25F;ENSP00000304544:L25F;ENSP00000435552:L25F;ENSP00000433758:L25F	ENSP00000304544:L25F	L	-	3	2	COMMD5	146047453	0.987000	0.35691	0.958000	0.39756	0.896000	0.52359	0.193000	0.17116	0.492000	0.27815	0.557000	0.71058	TTG	.	.		0.567	COMMD5-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000382962.1	NM_014066		A	146076649	C	A	146076649	3	1	260	1	0	0	0	0	1	0	0	0	3721	593	21	3	603	3	COMMD5	8	146076649	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	344674	146076649	287373	383	37628										
GLIS3	169792	hgsc.bcm.edu	37	chr9	4118024	4118024	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccccgtcgtcgtccagggtgGcctggggcaaggccagctgc	16	15	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:4118024G>A	ENST00000324333.10	-	3	1182	c.989C>T	c.(988-990)gCc>gTc	p.A330V	GLIS3_ENST00000381971.3_Missense_Mutation_p.A485V	NM_152629.3	NP_689842.3	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3	330					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(12)|lung(4)|ovary(2)|prostate(1)|skin(1)	26		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)		GTCCAGGGTGGCCTGGGGCAA	0.716																																					p.A485V		Atlas-SNP	.											.	GLIS3	152	.	0			c.C1454T						.						31	33	33					9																	4118024		2203	4299	6502	SO:0001583	missense	169792	exon4			AGGGTGGCCTGGG	BC033899	CCDS6451.1, CCDS43784.1	9p24.2	2008-05-02	2004-07-16	2004-07-16	ENSG00000107249	ENSG00000107249		"Zinc fingers, C2H2-type"	28510	protein-coding gene	gene with protein product		610192	"zinc finger protein 515"	ZNF515		14500813	Standard	NM_152629		Approved	MGC33662	uc003zhx.1	Q8NEA6	OTTHUMG00000019463	ENST00000324333.10:c.989C>T	chr9.hg19:g.4118024G>A	ENSP00000325494:p.Ala330Val	46.0	0.0		31.0	4.0	NM_001042413	B1AL19|Q1PHK5	Missense_Mutation	SNP	ENST00000324333.10	hg19	CCDS6451.1	.	.	.	.	.	.	.	.	.	.	G	10.27	1.305082	0.23736	.	.	ENSG00000107249	ENST00000324333;ENST00000381971	T;T	0.11604	2.78;2.76	5.52	4.63	0.57726	.	0.475283	0.16375	N	0.217180	T	0.08044	0.0201	N	0.24115	0.695	0.30846	N	0.735145	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.001	T	0.14309	-1.0477	10	0.16420	T	0.52	.	12.9123	0.58187	0.0753:0.0:0.9247:0.0	.	485;330	Q8NEA6-2;Q8NEA6	.;GLIS3_HUMAN	V	330;485	ENSP00000325494:A330V;ENSP00000371398:A485V	ENSP00000325494:A330V	A	-	2	0	GLIS3	4108024	0.010000	0.17322	0.342000	0.25602	0.026000	0.11368	1.423000	0.34837	1.334000	0.45468	-0.119000	0.15052	GCC	.	.		0.716	GLIS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051559.1	NM_152629		A	4118024	G	A	4118024	3	1	260	1	0	0	0	0	1	0	0	0	6455	1203	42	3	1370	3	GLIS3	9	4118024	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10		4118024	137095407	384	37629										
KIAA2026	158358	hgsc.bcm.edu	37	chr9	5921962	5921962	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtgtttggctaaaaggtgaaAgactagatgtagtagttgtt	13	2	0	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:5921962A>G	ENST00000399933.3	-	8	4033	c.4034T>C	c.(4033-4035)cTt>cCt	p.L1345P	KIAA2026_ENST00000381461.2_Missense_Mutation_p.L1315P	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	1345	Ser-rich.									breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		AAAAGGTGAAAGACTAGATGT	0.448																																					p.L1345P		Atlas-SNP	.											.	KIAA2026	231	.	0			c.T4034C						.						212	204	207					9																	5921962		1886	4125	6011	SO:0001583	missense	158358	exon8			GGTGAAAGACTAG	AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.4034T>C	chr9.hg19:g.5921962A>G	ENSP00000382815:p.Leu1345Pro	116.0	0.0		92.0	4.0	NM_001017969	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Missense_Mutation	SNP	ENST00000399933.3	hg19		.	.	.	.	.	.	.	.	.	.	A	3.743	-0.053154	0.07362	.	.	ENSG00000183354	ENST00000399933;ENST00000381461	.	.	.	4.38	4.38	0.52667	.	0.520133	0.15422	N	0.263164	T	0.57770	0.2076	L	0.29908	0.895	0.50632	D	0.999883	P	0.51537	0.946	P	0.53809	0.735	T	0.56607	-0.7951	9	0.41790	T	0.15	-0.0406	13.7435	0.62862	1.0:0.0:0.0:0.0	.	1345	Q5HYC2	K2026_HUMAN	P	1345;1315	.	ENSP00000370870:L1315P	L	-	2	0	KIAA2026	5911962	1.000000	0.71417	0.951000	0.38953	0.190000	0.23558	3.522000	0.53480	1.841000	0.53522	0.454000	0.30748	CTT	.	.		0.448	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969		G	5921962	A	G	5921962	3	3	260	1	0	0	0	0	1	0	0	0	8279	72	3	2	2281	2	KIAA2026	9	5921962	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1803938	5921962	135291469	385	37630										
C9orf93	203238	hgsc.bcm.edu	37	chr9	15784674	15784674	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gaagctgacaaaaaccaaacTcttggagaagctgttaaggt	10	7	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:15784674T>C	ENST00000380701.3	+	21	3577	c.3249T>C	c.(3247-3249)acT>acC	p.T1083T	CCDC171_ENST00000297641.3_Silent_p.T1083T	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	1083																	AAAACCAAACTCTTGGAGAAG	0.363																																					p.T1083T		Atlas-SNP	.											.	.	.	.	0			c.T3249C						.						69	64	66					9																	15784674		2203	4300	6503	SO:0001819	synonymous_variant	203238	exon21			CCAAACTCTTGGA	AY422473	CCDS6481.1	9p22.2	2012-03-26	2012-03-26	2012-03-26	ENSG00000164989	ENSG00000164989			29828	protein-coding gene	gene with protein product	"myosin tail domain containing protein"		"chromosome 9 open reading frame 93"	C9orf93		14702039	Standard	NM_173550		Approved	FLJ39267, FLJ46740, Em:AL513423.1, bA778P13.1, bA536D16.1	uc003zmd.3	Q6TFL3	OTTHUMG00000019584	ENST00000380701.3:c.3249T>C	chr9.hg19:g.15784674T>C		149.0	0.0		82.0	4.0	NM_173550	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	Silent	SNP	ENST00000380701.3	hg19	CCDS6481.1	.	.	.	.	.	.	.	.	.	.	T	8.209	0.799914	0.16397	.	.	ENSG00000164989	ENST00000449575;ENST00000432954	.	.	.	5.04	1.31	0.21738	.	.	.	.	.	T	0.44519	0.1297	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.31696	-0.9934	4	.	.	.	-11.0199	3.1827	0.06590	0.1791:0.2726:0.0:0.5484	.	.	.	.	P	323;137	.	.	L	+	2	0	C9orf93	15774674	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.814000	0.38972	0.875000	0.35847	0.533000	0.62120	CTC	.	.		0.363	CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051768.4	NM_173550		C	15784674	T	C	15784674	2	2	260	1	0	0	0	0	0	0	0	1	2508	1538	54	2		2	C9orf93	9	15784674	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	9862712	15784674	125428757	386	37631										
ADAMTSL1	92949	hgsc.bcm.edu	37	chr9	18622358	18622358	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agtataaatcccagctctccGcaaccaaatgtaagacacac	5	13	1	1	rs200455820		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:18622358G>A	ENST00000380548.4	+	5	931	c.592G>A	c.(592-594)Gca>Aca	p.A198T	ADAMTSL1_ENST00000380570.4_Missense_Mutation_p.A198T|ADAMTSL1_ENST00000276935.6_Missense_Mutation_p.A198T|ADAMTSL1_ENST00000327883.7_Missense_Mutation_p.A198T|ADAMTSL1_ENST00000380566.4_Missense_Mutation_p.A198T	NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	198						proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(2)|lung(17)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(50;1.29e-17)		CCAGCTCTCCGCAACCAAATG	0.552																																					p.A198T		Atlas-SNP	.											.	ADAMTSL1	306	.	0			c.G592A						.	G	THR/ALA,THR/ALA	0,4406		0,0,2203	66	66	66		592,592	4.6	0.9	9		66	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	ADAMTSL1	NM_001040272.5,NM_052866.4	58,58	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	198/1763,198/526	18622358	1,13005	2203	4300	6503	SO:0001583	missense	92949	exon5			CTCTCCGCAACCA	AF176313	CCDS6485.1, CCDS47954.1	9p21.3	2013-01-11			ENSG00000178031	ENSG00000178031		"Immunoglobulin superfamily / I-set domain containing"	14632	protein-coding gene	gene with protein product	"punctin"	609198	"chromosome 9 open reading frame 94"	C9orf94		9628581, 11805097	Standard	NM_001040272		Approved	ADAMTSR1, FLJ35283	uc003zne.4	Q8N6G6	OTTHUMG00000019604	ENST00000380548.4:c.592G>A	chr9.hg19:g.18622358G>A	ENSP00000369921:p.Ala198Thr	154.0	0.0		100.0	4.0	NM_052866	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Missense_Mutation	SNP	ENST00000380548.4	hg19	CCDS47954.1	.	.	.	.	.	.	.	.	.	.	G	18.17	3.563446	0.65651	0.0	1.16E-4	ENSG00000178031	ENST00000380548;ENST00000327883;ENST00000380570;ENST00000380566;ENST00000276935	T;T;T;T;T	0.66280	-0.02;0.73;-0.2;0.73;0.73	5.46	4.57	0.56435	.	.	.	.	.	T	0.46171	0.1379	N	0.22421	0.69	0.80722	D	1	B;P	0.42296	0.008;0.775	B;B	0.33890	0.001;0.172	T	0.53899	-0.8373	9	0.66056	D	0.02	.	14.8736	0.70478	0.0698:0.0:0.9302:0.0	.	198;198	Q8N6G6;Q8N6G6-2	ATL1_HUMAN;.	T	198	ENSP00000369921:A198T;ENSP00000327887:A198T;ENSP00000369944:A198T;ENSP00000369940:A198T;ENSP00000276935:A198T	ENSP00000276935:A198T	A	+	1	0	ADAMTSL1	18612358	0.990000	0.36364	0.949000	0.38748	0.998000	0.95712	2.088000	0.41663	1.446000	0.47643	0.655000	0.94253	GCA	.	.		0.552	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1			A	18622358	G	A	18622358	3	1	260	1	0	0	0	0	1	0	0	0	274	1087	38	1	610	1	ADAMTSL1	9	18622358	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	2837684	18622358	122591073	387	37632										
ADAMTSL1	92949	hgsc.bcm.edu	37	chr9	18681884	18681884	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	catcgaggaatgcacacaggAggctgtagcccaaaaacaaa	10	10	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:18681884A>G	ENST00000380548.4	+	12	1755	c.1416A>G	c.(1414-1416)ggA>ggG	p.G472G	ADAMTSL1_ENST00000276935.6_Silent_p.G472G|ADAMTSL1_ENST00000327883.7_Silent_p.G472G	NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	472	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(2)|lung(17)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(50;1.29e-17)		TGCACACAGGAGGCTGTAGCC	0.507																																					p.G472G		Atlas-SNP	.											.	ADAMTSL1	306	.	0			c.A1416G						.						242	220	228					9																	18681884		2203	4300	6503	SO:0001819	synonymous_variant	92949	exon12			CACAGGAGGCTGT	AF176313	CCDS6485.1, CCDS47954.1	9p21.3	2013-01-11			ENSG00000178031	ENSG00000178031		"Immunoglobulin superfamily / I-set domain containing"	14632	protein-coding gene	gene with protein product	"punctin"	609198	"chromosome 9 open reading frame 94"	C9orf94		9628581, 11805097	Standard	NM_001040272		Approved	ADAMTSR1, FLJ35283	uc003zne.4	Q8N6G6	OTTHUMG00000019604	ENST00000380548.4:c.1416A>G	chr9.hg19:g.18681884A>G		192.0	0.0		86.0	4.0	NM_052866	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Silent	SNP	ENST00000380548.4	hg19	CCDS47954.1																																																																																			.	.		0.507	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1			G	18681884	A	G	18681884	2	3	260	1	0	0	0	0	0	0	0	1	274	291	11	2		2	ADAMTSL1	9	18681884	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	59526	18681884	122531547	388	37633										
ACO1	48	hgsc.bcm.edu	37	chr9	32419134	32419134	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggctgatggggaagccccacCctctggtaacatccactgac	11	14	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:32419134C>A	ENST00000309951.6	+	7	895	c.757C>A	c.(757-759)Cct>Act	p.P253T	ACO1_ENST00000541043.1_Missense_Mutation_p.P154T|ACO1_ENST00000379923.1_Missense_Mutation_p.P253T	NM_002197.2	NP_002188.1	P21399	ACOC_HUMAN	aconitase 1, soluble	253					cellular iron ion homeostasis (GO:0006879)|citrate metabolic process (GO:0006101)|intestinal absorption (GO:0050892)|post-embryonic development (GO:0009791)|regulation of translation (GO:0006417)|response to iron(II) ion (GO:0010040)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|endometrium(7)|kidney(5)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	30			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)		GAAGCCCCACCCTCTGGTAAC	0.507																																					p.P253T		Atlas-SNP	.											.	ACO1	149	.	0			c.C757A						.						177	133	148					9																	32419134		2203	4300	6503	SO:0001583	missense	48	exon7			CCCCACCCTCTGG	M58510	CCDS6525.1	9p21.1	2013-05-21			ENSG00000122729	ENSG00000122729	4.2.1.3		117	protein-coding gene	gene with protein product	"aconitate hydratase, cytoplasmic"	100880		IREB1		2172968, 2771641	Standard	NM_002197		Approved	IRP1, IREBP	uc003zqw.4	P21399	OTTHUMG00000019740	ENST00000309951.6:c.757C>A	chr9.hg19:g.32419134C>A	ENSP00000309477:p.Pro253Thr	157.0	0.0		95.0	4.0	NM_002197	D3DRK7|Q14652|Q5VZA7	Missense_Mutation	SNP	ENST00000309951.6	hg19	CCDS6525.1	.	.	.	.	.	.	.	.	.	.	C	13.98	2.399374	0.42512	.	.	ENSG00000122729	ENST00000432017;ENST00000309951;ENST00000379923;ENST00000379921;ENST00000541043	T;T;T	0.19394	2.15;2.15;2.15	5.64	4.73	0.59995	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha (2);Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 2 (1);	0.269447	0.43579	D	0.000546	T	0.34337	0.0894	M	0.84846	2.72	0.51482	D	0.999921	B;B	0.31968	0.349;0.003	B;B	0.35278	0.199;0.024	T	0.28106	-1.0054	10	0.56958	D	0.05	-10.339	15.4486	0.75253	0.0:0.8602:0.1397:0.0	.	289;253	Q59FI0;P21399	.;ACOC_HUMAN	T	289;253;253;253;154	ENSP00000309477:P253T;ENSP00000369255:P253T;ENSP00000438733:P154T	ENSP00000309477:P253T	P	+	1	0	ACO1	32409134	0.872000	0.30054	0.997000	0.53966	0.970000	0.65996	2.093000	0.41710	1.344000	0.45657	0.563000	0.77884	CCT	.	.		0.507	ACO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051998.3	NM_002197		A	32419134	C	A	32419134	3	1	260	1	0	0	0	0	1	0	0	0	146	623	22	3	779	3	ACO1	9	32419134	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	13737250	32419134	108794297	389	37634										
TOPORS	10210	hgsc.bcm.edu	37	chr9	32541494	32541494	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acacaatgttactgggctggTtctccaaatcagaaacaaag	8	9	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:32541494T>C	ENST00000360538.2	-	3	3145	c.3029A>G	c.(3028-3030)aAc>aGc	p.N1010S	TOPORS_ENST00000379858.1_Missense_Mutation_p.N945S	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	1010					cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of apoptotic process (GO:0043066)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein localization to nucleus (GO:0034504)|protein monoubiquitination (GO:0006513)|protein sumoylation (GO:0016925)|regulation of cell proliferation (GO:0042127)|retina layer formation (GO:0010842)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|gamma-tubulin complex (GO:0000930)|midbody (GO:0030496)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|PML body (GO:0016605)|spindle pole (GO:0000922)|ubiquitin ligase complex (GO:0000151)	antigen binding (GO:0003823)|DNA binding (GO:0003677)|DNA topoisomerase binding (GO:0044547)|SUMO ligase activity (GO:0019789)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		ACTGGGCTGGTTCTCCAAATC	0.428																																					p.N1010S		Atlas-SNP	.											.	TOPORS	127	.	0			c.A3029G						.						131	128	129					9																	32541494		2203	4300	6503	SO:0001583	missense	10210	exon3			GGCTGGTTCTCCA	AF098300	CCDS6527.1, CCDS56566.1	9p21	2013-01-09	2010-09-17		ENSG00000197579	ENSG00000197579		"RING-type (C3HC4) zinc fingers"	21653	protein-coding gene	gene with protein product		609507	"retinitis pigmentosa 31 (autosomal dominant)", "topoisomerase I binding, arginine/serine-rich"	RP31		10352183, 12083797, 17924349	Standard	NM_005802		Approved	TP53BPL, LUN	uc003zrb.3	Q9NS56	OTTHUMG00000019743	ENST00000360538.2:c.3029A>G	chr9.hg19:g.32541494T>C	ENSP00000353735:p.Asn1010Ser	173.0	0.0		120.0	5.0	NM_005802	O43273|Q6P987|Q9NS55|Q9UNR9	Missense_Mutation	SNP	ENST00000360538.2	hg19	CCDS6527.1	.	.	.	.	.	.	.	.	.	.	T	7.046	0.563567	0.13498	.	.	ENSG00000197579	ENST00000360538;ENST00000379858	T;T	0.15256	2.44;2.45	5.61	1.93	0.25924	.	0.120219	0.38005	N	0.001847	T	0.06142	0.0159	N	0.03608	-0.345	0.22378	N	0.999153	B	0.06786	0.001	B	0.06405	0.002	T	0.36163	-0.9759	10	0.25751	T	0.34	-3.8034	6.1834	0.20484	0.0:0.1491:0.1356:0.7152	.	1010	Q9NS56	TOPRS_HUMAN	S	1010;945	ENSP00000353735:N1010S;ENSP00000369187:N945S	ENSP00000353735:N1010S	N	-	2	0	TOPORS	32531494	0.998000	0.40836	0.995000	0.50966	0.286000	0.27126	0.285000	0.18883	0.139000	0.18822	0.528000	0.53228	AAC	.	.		0.428	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802		C	32541494	T	C	32541494	3	2	260	1	0	0	0	0	1	0	0	0	16385	1725	60	2	112	2	TOPORS	9	32541494	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	122360	32541494	108671937	390	37635										
IL11RA	3590	hgsc.bcm.edu	37	chr9	34659771	34659771	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cccaggtggagccagctggaCtggaggaggtgatcacagat	16	9	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:34659771C>T	ENST00000555003.1	+	9	2182	c.826C>T	c.(826-828)Ctg>Ttg	p.L276L	IL11RA_ENST00000378817.4_Silent_p.L276L|IL11RA_ENST00000602473.1_Silent_p.L276L|IL11RA_ENST00000441545.2_Silent_p.L276L|IL11RA_ENST00000318041.9_Silent_p.L276L|CCL27_ENST00000557161.1_5'Flank|RP11-195F19.30_ENST00000564224.1_RNA			Q14626	I11RA_HUMAN	interleukin 11 receptor, alpha	276	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				developmental process (GO:0032502)|embryo implantation (GO:0007566)|head development (GO:0060322)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)|signal transducer activity (GO:0004871)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|large_intestine(1)|ovary(1)|skin(1)	4	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.174)	Oprelvekin(DB00038)	GCCAGCTGGACTGGAGGAGGT	0.597																																					p.L276L		Atlas-SNP	.											.	IL11RA	34	.	0			c.C826T						.						100	103	102					9																	34659771		2203	4300	6503	SO:0001819	synonymous_variant	3590	exon9			GCTGGACTGGAGG	Z38102	CCDS6567.1	9p13	2014-05-22			ENSG00000137070	ENSG00000137070		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5967	protein-coding gene	gene with protein product		600939				7670098	Standard	NM_001142784		Approved		uc011loq.3	Q14626	OTTHUMG00000019837	ENST00000555003.1:c.826C>T	chr9.hg19:g.34659771C>T		134.0	0.0		77.0	4.0	NM_001142784	Q16542|Q5VZ80|Q7KYJ7	Silent	SNP	ENST00000555003.1	hg19	CCDS6567.1																																																																																			.	.		0.597	IL11RA-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410625.1	NM_001142784		T	34659771	C	T	34659771	2	4	260	1	0	0	0	0	0	0	0	1	7632	564	20	3		3	IL11RA	9	34659771	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	2118277	34659771	106553660	391	37636										
IL11RA	3590	hgsc.bcm.edu	37	chr9	34659894	34659894	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aggcctggggaactccgagcActggtgagagacaaagccaa	14	10	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:34659894A>G	ENST00000555003.1	+	9	2305	c.949A>G	c.(949-951)Act>Gct	p.T317A	IL11RA_ENST00000378817.4_Missense_Mutation_p.T317A|IL11RA_ENST00000602473.1_Missense_Mutation_p.T317A|IL11RA_ENST00000441545.2_Missense_Mutation_p.T317A|IL11RA_ENST00000318041.9_Missense_Mutation_p.T317A|CCL27_ENST00000557161.1_5'Flank|RP11-195F19.30_ENST00000564224.1_RNA			Q14626	I11RA_HUMAN	interleukin 11 receptor, alpha	317	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				developmental process (GO:0032502)|embryo implantation (GO:0007566)|head development (GO:0060322)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)|signal transducer activity (GO:0004871)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|large_intestine(1)|ovary(1)|skin(1)	4	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.174)	Oprelvekin(DB00038)	AACTCCGAGCACTGGTGAGAG	0.597																																					p.T317A		Atlas-SNP	.											.	IL11RA	34	.	0			c.A949G						.						36	39	38					9																	34659894		2203	4300	6503	SO:0001583	missense	3590	exon9			CCGAGCACTGGTG	Z38102	CCDS6567.1	9p13	2014-05-22			ENSG00000137070	ENSG00000137070		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5967	protein-coding gene	gene with protein product		600939				7670098	Standard	NM_001142784		Approved		uc011loq.3	Q14626	OTTHUMG00000019837	ENST00000555003.1:c.949A>G	chr9.hg19:g.34659894A>G	ENSP00000450565:p.Thr317Ala	94.0	0.0		51.0	4.0	NM_001142784	Q16542|Q5VZ80|Q7KYJ7	Missense_Mutation	SNP	ENST00000555003.1	hg19	CCDS6567.1	.	.	.	.	.	.	.	.	.	.	A	16.97	3.270007	0.59540	.	.	ENSG00000137070	ENST00000555003;ENST00000441545;ENST00000378817;ENST00000318041	T;T;T;T	0.36699	1.4;1.4;1.24;1.4	5.48	1.76	0.24704	.	1.313380	0.05346	N	0.530974	T	0.35595	0.0937	M	0.61703	1.905	0.47374	D	0.999403	B;B	0.14438	0.01;0.01	B;B	0.13407	0.009;0.009	T	0.11036	-1.0604	10	0.23891	T	0.37	-2.1011	7.1989	0.25868	0.5887:0.3248:0.0865:0.0	.	317;317	Q5VZ79;Q14626	.;I11RA_HUMAN	A	317	ENSP00000450565:T317A;ENSP00000394391:T317A;ENSP00000368094:T317A;ENSP00000326500:T317A	ENSP00000326500:T317A	T	+	1	0	IL11RA	34649894	0.035000	0.19736	0.858000	0.33744	0.988000	0.76386	0.791000	0.26915	0.330000	0.23485	0.460000	0.39030	ACT	.	.		0.597	IL11RA-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410625.1	NM_001142784		G	34659894	A	G	34659894	3	3	260	1	0	0	0	0	1	0	0	0	7632	159	6	2	979	2	IL11RA	9	34659894	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	123	34659894	106553537	392	37637										
RECK	8434	hgsc.bcm.edu	37	chr9	36063817	36063817	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tttaagaagtctgatggctgGgttggcttaggctgctgtga	15	5	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:36063817G>A	ENST00000377966.3	+	5	863	c.297G>A	c.(295-297)tgG>tgA	p.W99*	RECK_ENST00000479053.1_3'UTR	NM_021111.2	NP_066934.1	O95980	RECK_HUMAN	reversion-inducing-cysteine-rich protein with kazal motifs	99	5 X Knot repeats.				blood vessel maturation (GO:0001955)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)	anchored component of membrane (GO:0031225)|membrane (GO:0016020)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(7)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|pancreas(1)|skin(2)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(32;0.112)|STAD - Stomach adenocarcinoma(86;0.228)			CTGATGGCTGGGTTGGCTTAG	0.438																																					p.W99X		Atlas-SNP	.											.	RECK	73	.	0			c.G297A						.						129	112	118					9																	36063817		2203	4300	6503	SO:0001587	stop_gained	8434	exon5			TGGCTGGGTTGGC	E13833	CCDS6597.1	9p13.3	2008-05-15			ENSG00000122707	ENSG00000122707			11345	protein-coding gene	gene with protein product		605227		ST15		9789069	Standard	NM_021111		Approved	hRECK	uc003zyv.3	O95980	OTTHUMG00000019898	ENST00000377966.3:c.297G>A	chr9.hg19:g.36063817G>A	ENSP00000367202:p.Trp99*	159.0	0.0		85.0	4.0	NM_021111	B2RNS1|Q5W0K6|Q8WX37	Nonsense_Mutation	SNP	ENST00000377966.3	hg19	CCDS6597.1	.	.	.	.	.	.	.	.	.	.	G	41	9.154406	0.99084	.	.	ENSG00000122707	ENST00000377966	.	.	.	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.7557	17.4988	0.87726	0.0:0.0:1.0:0.0	.	.	.	.	X	99	.	ENSP00000367202:W99X	W	+	3	0	RECK	36053817	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.291000	0.78721	2.726000	0.93360	0.563000	0.77884	TGG	.	.		0.438	RECK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052409.1			A	36063817	G	A	36063817	4	1	260	1	0	0	0	0	0	1	0	0	13215	1241	43	3	315	3	RECK	9	36063817	Nonsense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	1403923	36063817	105149614	393	37638										
DCAF10	79269	hgsc.bcm.edu	37	chr9	37860046	37860046	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcattttcttatatctcaggAgtttcaccacgaaatagtct	5	9	5	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:37860046A>G	ENST00000377724.3	+	6	1532	c.1167A>G	c.(1165-1167)ggA>ggG	p.G389G	DCAF10_ENST00000242323.7_Splice_Site_p.G352G|DCAF10_ENST00000483167.1_3'UTR|RP11-613M10.9_ENST00000540557.1_Intron	NM_024345.3	NP_077321.3	Q5QP82	DCA10_HUMAN	DDB1 and CUL4 associated factor 10	389					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)				central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	12						ATATCTCAGGAGTTTCACCAC	0.443																																					p.G389G		Atlas-SNP	.											.	DCAF10	31	.	0			c.A1167G						.						99	90	93					9																	37860046		2203	4300	6503	SO:0001630	splice_region_variant	79269	exon6			CTCAGGAGTTTCA	BC003520	CCDS6613.2, CCDS75835.1	9p13.2	2013-01-09	2009-07-17	2009-07-17	ENSG00000122741	ENSG00000122741		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	23686	protein-coding gene	gene with protein product			"WD repeat domain 32"	WDR32			Standard	NM_001286810		Approved	MGC10765, FLJ23201	uc004aao.3	Q5QP82	OTTHUMG00000019934	ENST00000377724.3:c.1166-1A>G	chr9.hg19:g.37860046A>G		197.0	0.0		119.0	5.0	NM_024345	A4VCJ5|Q32NE2|Q8N2Q5|Q96ET5|Q9BTQ5|Q9H5P6	Silent	SNP	ENST00000377724.3	hg19	CCDS6613.2																																																																																			.	.		0.443	DCAF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052485.2	NM_024345	Silent	G	37860046	A	G	37860046	5	3	260	1	0	0	0	0	0	0	1	0	4263	318	11	2	1189	2	DCAF10	9	37860046	Splice_Site	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1796229	37860046	103353385	394	37639										
TRPM3	80036	hgsc.bcm.edu	37	chr9	73399114	73399114	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctggcacgggaggggtgtctCgaaggtactccaaaacaatc	13	10	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:73399114C>T	ENST00000377111.2	-	7	1298	c.1055G>A	c.(1054-1056)cGa>cAa	p.R352Q	TRPM3_ENST00000396280.5_Missense_Mutation_p.R199Q|TRPM3_ENST00000396292.4_Missense_Mutation_p.R224Q|TRPM3_ENST00000396283.1_Missense_Mutation_p.R224Q|TRPM3_ENST00000358082.3_Missense_Mutation_p.R224Q|TRPM3_ENST00000377101.1_Missense_Mutation_p.R199Q|TRPM3_ENST00000357533.2_Missense_Mutation_p.R354Q|TRPM3_ENST00000423814.3_Missense_Mutation_p.R379Q|TRPM3_ENST00000361823.5_Missense_Mutation_p.R199Q|TRPM3_ENST00000396285.1_Missense_Mutation_p.R199Q|TRPM3_ENST00000377110.3_Missense_Mutation_p.R352Q|TRPM3_ENST00000377106.1_Missense_Mutation_p.R224Q|TRPM3_ENST00000377105.1_Missense_Mutation_p.R199Q|TRPM3_ENST00000408909.2_Missense_Mutation_p.R199Q|TRPM3_ENST00000360823.2_Missense_Mutation_p.R224Q	NM_001007471.2	NP_001007472.2	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	377					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						AGGGGTGTCTCGAAGGTACTC	0.512																																					p.R352Q		Atlas-SNP	.											TRPM3_ENST00000423814,colon,carcinoma,-1,4	TRPM3	700	.	0			c.G1055A						.						110	90	97					9																	73399114		2203	4300	6503	SO:0001583	missense	80036	exon7			GTGTCTCGAAGGT	AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"Voltage-gated ion channels / Transient receptor potential cation channels"	17992	protein-coding gene	gene with protein product	"melastatin 2"	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377111.2:c.1055G>A	chr9.hg19:g.73399114C>T	ENSP00000366315:p.Arg352Gln	158.0	0.0		125.0	5.0	NM_001007471	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Missense_Mutation	SNP	ENST00000377111.2	hg19		.	.	.	.	.	.	.	.	.	.	C	16.12	3.034044	0.54896	.	.	ENSG00000083067	ENST00000377111;ENST00000377110;ENST00000377106;ENST00000360823;ENST00000377105;ENST00000357533;ENST00000408909;ENST00000396285;ENST00000396292;ENST00000358082;ENST00000423814;ENST00000377101;ENST00000396283;ENST00000361823	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.67865	4.09;4.09;0.55;0.56;4.09;4.09;4.09;4.09;0.55;0.56;0.59;4.09;-0.29;4.09	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.48205	0.1487	N	0.16307	0.4	0.44061	D	0.996805	P;B;B;P;B;B;B;B;P;B	0.42973	0.796;0.04;0.369;0.661;0.086;0.41;0.41;0.086;0.545;0.165	B;B;B;B;B;B;B;B;B;B	0.31101	0.124;0.024;0.057;0.074;0.012;0.015;0.079;0.012;0.074;0.034	T	0.48305	-0.9047	10	0.16896	T	0.51	-7.2457	20.8794	0.99867	0.0:1.0:0.0:0.0	.	377;199;352;352;352;354;224;199;352;199	Q9HCF6;Q504Y1;Q9HCF6-2;Q9HCF6-10;Q9HCF6-4;A2A3F7;A2A3F4;G5E9G1;Q9HCF6-8;A2A3F3	TRPM3_HUMAN;.;.;.;.;.;.;.;.;.	Q	352;352;224;224;199;354;199;199;224;224;379;199;224;199	ENSP00000366315:R352Q;ENSP00000366314:R352Q;ENSP00000366310:R224Q;ENSP00000354066:R224Q;ENSP00000366309:R199Q;ENSP00000350140:R354Q;ENSP00000386127:R199Q;ENSP00000379581:R199Q;ENSP00000379587:R224Q;ENSP00000350791:R224Q;ENSP00000389542:R379Q;ENSP00000366305:R199Q;ENSP00000379579:R224Q;ENSP00000355395:R199Q	ENSP00000350140:R354Q	R	-	2	0	TRPM3	72588934	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	4.780000	0.62382	2.941000	0.99782	0.655000	0.94253	CGA	.	.		0.512	TRPM3-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000214157.5	NM_206945		T	73399114	C	T	73399114	3	4	260	1	0	0	0	0	1	0	0	0	16602	884	31	1	4188	1	TRPM3	9	73399114	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	35539068	73399114	67814317	395	37640										
FAM108B1	51104	hgsc.bcm.edu	37	chr9	74485072	74485072	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cattcccgaagtcagaggagAatgaagaataacagcagcac	10	9	1	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:74485072A>G	ENST00000333421.6	-	3	685	c.574T>C	c.(574-576)Tct>Cct	p.S192P	ABHD17B_ENST00000377041.2_Missense_Mutation_p.S192P	NM_001025780.1	NP_001020951.1	Q5VST6	AB17B_HUMAN	abhydrolase domain containing 17B	192						extracellular region (GO:0005576)|membrane (GO:0016020)	hydrolase activity (GO:0016787)										GTCAGAGGAGAATGAAGAATA	0.413																																					p.S192P		Atlas-SNP	.											.	FAM108B1	24	.	0			c.T574C						.						163	149	153					9																	74485072		2203	4300	6503	SO:0001583	missense	51104	exon3			GAGGAGAATGAAG	AF151825	CCDS35042.1, CCDS35043.1	9q21.2	2013-03-15	2013-03-15	2013-03-15	ENSG00000107362	ENSG00000107362		"Abhydrolase domain containing"	24278	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 77", "family with sequence similarity 108, member B1"	C9orf77, FAM108B1		10810093	Standard	XM_006717134		Approved	CGI-67	uc004ail.3	Q5VST6	OTTHUMG00000020001	ENST00000333421.6:c.574T>C	chr9.hg19:g.74485072A>G	ENSP00000330222:p.Ser192Pro	184.0	0.0		94.0	4.0	NM_016014	A8KAJ5|Q5VST7|Q86YB6|Q8IY03|Q9Y377	Missense_Mutation	SNP	ENST00000333421.6	hg19	CCDS35043.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.634537	0.87660	.	.	ENSG00000107362	ENST00000377041;ENST00000333421	T;T	0.51574	0.7;0.7	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	D	0.82554	0.5062	H	0.99379	4.54	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.994	D	0.90423	0.4418	10	0.87932	D	0	-12.9451	15.6113	0.76721	1.0:0.0:0.0:0.0	.	192;192	Q5VST6;Q5VST6-2	F108B_HUMAN;.	P	192	ENSP00000366240:S192P;ENSP00000330222:S192P	ENSP00000330222:S192P	S	-	1	0	FAM108B1	73674892	1.000000	0.71417	1.000000	0.80357	0.837000	0.47467	9.152000	0.94680	2.151000	0.67156	0.533000	0.62120	TCT	.	.		0.413	ABHD17B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052625.1	NM_016014		G	74485072	A	G	74485072	3	3	260	1	0	0	0	0	1	0	0	0	5397	246	9	2	331	2	FAM108B1	9	74485072	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1085958	74485072	66728359	396	37641										
GDA	9615	hgsc.bcm.edu	37	chr9	74842881	74842881	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agtgatggcacacggctgctAcctctctgcagaagaactga	11	11	1	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:74842881A>G	ENST00000358399.3	+	9	938	c.845A>G	c.(844-846)tAc>tGc	p.Y282C	GDA_ENST00000477618.1_3'UTR|GDA_ENST00000376986.1_Missense_Mutation_p.Y204C|GDA_ENST00000376989.3_Missense_Mutation_p.Y221C|GDA_ENST00000545168.1_Missense_Mutation_p.Y208C|GDA_ENST00000238018.4_Missense_Mutation_p.Y282C	NM_001242505.2|NM_001242506.2|NM_004293.4	NP_001229434.1|NP_001229435.1|NP_004284.1	Q9Y2T3	GUAD_HUMAN	guanine deaminase	282					guanine catabolic process (GO:0006147)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	guanine deaminase activity (GO:0008892)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(1)|kidney(1)|large_intestine(1)|lung(20)|ovary(2)|skin(2)|urinary_tract(1)	32		Myeloproliferative disorder(762;0.0122)		Lung(182;0.0583)		CACGGCTGCTACCTCTCTGCA	0.448																																					p.Y282C		Atlas-SNP	.											.	GDA	113	.	0			c.A845G						.						122	93	103					9																	74842881		2203	4300	6503	SO:0001583	missense	9615	exon9			GCTGCTACCTCTC	AF095286	CCDS6641.1, CCDS56576.1, CCDS56577.1	9q21.13	2008-05-14			ENSG00000119125	ENSG00000119125			4212	protein-coding gene	gene with protein product		139260				10075721, 3966794	Standard	NM_001242507		Approved		uc004air.3	Q9Y2T3	OTTHUMG00000020005	ENST00000358399.3:c.845A>G	chr9.hg19:g.74842881A>G	ENSP00000351170:p.Tyr282Cys	104.0	0.0		65.0	4.0	NM_004293	B4DTY5|Q5SZC7|Q9H335|Q9ULG2	Missense_Mutation	SNP	ENST00000358399.3	hg19	CCDS6641.1	.	.	.	.	.	.	.	.	.	.	A	19.74	3.883957	0.72410	.	.	ENSG00000119125	ENST00000545168;ENST00000238018;ENST00000376989;ENST00000376986;ENST00000358399;ENST00000414671	D;D;D;D;D;D	0.90563	-2.69;-2.69;-2.69;-2.69;-2.69;-2.69	5.51	5.51	0.81932	Amidohydrolase 1 (1);	0.121996	0.64402	D	0.000013	D	0.92381	0.7582	M	0.83483	2.645	0.47659	D	0.999488	P;P;P	0.48503	0.651;0.794;0.911	B;B;P	0.46975	0.432;0.238;0.533	D	0.93283	0.6662	10	0.72032	D	0.01	-14.2477	13.4407	0.61112	1.0:0.0:0.0:0.0	.	204;282;282	Q5SZC6;Q9Y2T3-3;Q9Y2T3	.;.;GUAD_HUMAN	C	208;282;221;204;282;148	ENSP00000437972:Y208C;ENSP00000238018:Y282C;ENSP00000366188:Y221C;ENSP00000366185:Y204C;ENSP00000351170:Y282C;ENSP00000403897:Y148C	ENSP00000238018:Y282C	Y	+	2	0	GDA	74032701	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	6.463000	0.73530	2.210000	0.71456	0.533000	0.62120	TAC	.	.		0.448	GDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052633.1			G	74842881	A	G	74842881	3	3	260	1	0	0	0	0	1	0	0	0	6314	391	14	2	879	2	GDA	9	74842881	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	357809	74842881	66370550	397	37642										
GAS1	2619	hgsc.bcm.edu	37	chr9	89561085	89561085	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	catgtcctcaatgacggtgcGgcattcgtccgtgcagcgca	12	13	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:89561085G>A	ENST00000298743.7	-	1	1019	c.610C>T	c.(610-612)Cgc>Tgc	p.R204C	RP11-276H19.1_ENST00000415801.1_lincRNA	NM_002048.2	NP_002039.2	P54826	GAS1_HUMAN	growth arrest-specific 1	204					axon guidance (GO:0007411)|camera-type eye development (GO:0043010)|cell cycle arrest (GO:0007050)|cell fate commitment (GO:0045165)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cerebellum morphogenesis (GO:0021587)|developmental growth (GO:0048589)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digit morphogenesis (GO:0042733)|eye morphogenesis (GO:0048592)|middle ear morphogenesis (GO:0042474)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein processing (GO:0010955)|negative regulation of smoothened signaling pathway (GO:0045879)|odontogenesis (GO:0042476)|outer ear morphogenesis (GO:0042473)|palate development (GO:0060021)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smoothened signaling pathway (GO:0045880)|programmed cell death (GO:0012501)|regulation of apoptotic process (GO:0042981)|regulation of ER to Golgi vesicle-mediated transport (GO:0060628)|regulation of smoothened signaling pathway (GO:0008589)	anchored component of plasma membrane (GO:0046658)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				kidney(1)|lung(2)|skin(1)	4						ATGACGGTGCGGCATTCGTCC	0.667																																					p.R204C		Atlas-SNP	.											.	GAS1	8	.	0			c.C610T						.						24	22	23					9																	89561085		2201	4297	6498	SO:0001583	missense	2619	exon1			CGGTGCGGCATTC		CCDS6674.1	9q21.3-q22	2008-07-21			ENSG00000180447	ENSG00000180447			4165	protein-coding gene	gene with protein product	"Growth arrest-specific gene-1"	139185				8307588	Standard	NM_002048		Approved		uc004aox.4	P54826	OTTHUMG00000020141	ENST00000298743.7:c.610C>T	chr9.hg19:g.89561085G>A	ENSP00000298743:p.Arg204Cys	63.0	0.0		39.0	4.0	NM_002048	B9EGM4|Q6B086	Missense_Mutation	SNP	ENST00000298743.7	hg19	CCDS6674.1	.	.	.	.	.	.	.	.	.	.	G	13.54	2.268603	0.40095	.	.	ENSG00000180447	ENST00000298743	T	0.65549	-0.16	4.34	4.34	0.51931	GDNF/GAS1 (2);	0.091849	0.44285	U	0.000464	T	0.68522	0.3010	L	0.42245	1.32	0.54753	D	0.999983	D	0.89917	1.0	D	0.79784	0.993	T	0.70539	-0.4844	10	0.87932	D	0	-1.3365	7.6289	0.28228	0.0877:0.0:0.7503:0.162	.	204	P54826	GAS1_HUMAN	C	204	ENSP00000298743:R204C	ENSP00000298743:R204C	R	-	1	0	GAS1	88750905	1.000000	0.71417	1.000000	0.80357	0.007000	0.05969	2.835000	0.48175	1.946000	0.56461	0.555000	0.69702	CGC	.	.		0.667	GAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052928.1	NM_002048		A	89561085	G	A	89561085	3	1	260	1	0	0	0	0	1	0	0	0	6252	1116	39	1	431	1	GAS1	9	89561085	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	14718204	89561085	51652346	398	37643										
IARS	3376	hgsc.bcm.edu	37	chr9	95012165	95012165	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgatatacttctccaaagacTtgatatctttaagagcttct	5	8	3	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:95012165T>C	ENST00000375643.3	-	25	2857	c.2591A>G	c.(2590-2592)aAg>aGg	p.K864R	IARS_ENST00000375629.3_5'UTR|IARS_ENST00000443024.2_Missense_Mutation_p.K864R|IARS_ENST00000447699.2_Missense_Mutation_p.K754R	NM_013417.2	NP_038203.2	P41252	SYIC_HUMAN	isoleucyl-tRNA synthetase	864					gene expression (GO:0010467)|isoleucyl-tRNA aminoacylation (GO:0006428)|osteoblast differentiation (GO:0001649)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|isoleucine-tRNA ligase activity (GO:0004822)			breast(3)|endometrium(2)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	35					L-Isoleucine(DB00167)	CTCCAAAGACTTGATATCTTT	0.368																																					p.K864R		Atlas-SNP	.											.	IARS	74	.	0			c.A2591G						.						130	137	135					9																	95012165		2203	4299	6502	SO:0001583	missense	3376	exon25			AAAGACTTGATAT	AB209234	CCDS6694.1	9q21	2011-07-01	2007-02-26		ENSG00000196305	ENSG00000196305	6.1.1.5	"Aminoacyl tRNA synthetases / Class I"	5330	protein-coding gene	gene with protein product	"isoleucine tRNA ligase 1, cytoplasmic"	600709				8812440	Standard	NM_002161		Approved	ILRS, IARS1	uc004aru.4	P41252	OTTHUMG00000020219	ENST00000375643.3:c.2591A>G	chr9.hg19:g.95012165T>C	ENSP00000364794:p.Lys864Arg	144.0	0.0		78.0	4.0	NM_013417	A8KAE9|Q5TCD0|Q7Z3T4|Q9H588	Missense_Mutation	SNP	ENST00000375643.3	hg19	CCDS6694.1	.	.	.	.	.	.	.	.	.	.	T	10.59	1.391846	0.25118	.	.	ENSG00000196305	ENST00000375643;ENST00000443024;ENST00000447699;ENST00000375660;ENST00000449893	T;T;T	0.56776	0.44;0.44;0.44	5.88	-6.57	0.01842	Aminoacyl-tRNA synthetase, class 1a, anticodon-binding (1);	0.506148	0.25299	N	0.031679	T	0.31544	0.0800	N	0.17248	0.465	0.80722	D	1	B;B;B	0.10296	0.003;0.0;0.0	B;B;B	0.17098	0.017;0.001;0.002	T	0.04565	-1.0942	10	0.19590	T	0.45	-2.3002	18.3501	0.90336	0.0:0.6125:0.0:0.3875	.	374;864;709	F5H1M4;P41252;Q6P0M4	.;SYIC_HUMAN;.	R	864;864;754;864;96	ENSP00000364794:K864R;ENSP00000406448:K864R;ENSP00000415020:K754R	ENSP00000364794:K864R	K	-	2	0	IARS	94051986	0.984000	0.35163	0.060000	0.19600	0.939000	0.58152	0.465000	0.22004	-1.152000	0.02832	-0.326000	0.08463	AAG	.	.		0.368	IARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053059.2	NM_002161		C	95012165	T	C	95012165	3	2	260	1	0	0	0	0	1	0	0	0	7482	1609	56	2	1237	2	IARS	9	95012165	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	5451080	95012165	46201266	399	37644										
IPPK	64768	hgsc.bcm.edu	37	chr9	95411851	95411851	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	atccaggtccttgtcacagcGagactctggaaaacagagca	10	11	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:95411851G>T	ENST00000287996.3	-	5	574	c.298C>A	c.(298-300)Cgc>Agc	p.R100S		NM_022755.5	NP_073592.1	Q9H8X2	IPPK_HUMAN	inositol 1,3,4,5,6-pentakisphosphate 2-kinase	100					inositol phosphate metabolic process (GO:0043647)|inositol phosphorylation (GO:0052746)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|inositol pentakisphosphate 2-kinase activity (GO:0035299)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(2)|urinary_tract(1)	15						TTGTCACAGCGAGACTCTGGA	0.532																																					p.R100S		Atlas-SNP	.											.	IPPK	34	.	0			c.C298A						.						119	94	103					9																	95411851		2203	4300	6503	SO:0001583	missense	64768	exon5			CACAGCGAGACTC	AK023225	CCDS6699.1	9q22.31	2010-12-02	2005-10-20	2005-10-20	ENSG00000127080	ENSG00000127080			14645	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 12"	C9orf12		12084730	Standard	NM_022755		Approved	INSP5K2, FLJ13163, IP5K, IPK1	uc004asl.1	Q9H8X2	OTTHUMG00000020231	ENST00000287996.3:c.298C>A	chr9.hg19:g.95411851G>T	ENSP00000287996:p.Arg100Ser	98.0	0.0		67.0	4.0	NM_022755	Q5T9F7|Q9H7V8	Missense_Mutation	SNP	ENST00000287996.3	hg19	CCDS6699.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.241065	0.79912	.	.	ENSG00000127080	ENST00000287996	T	0.50001	0.76	5.3	4.39	0.52855	.	0.092160	0.85682	N	0.000000	T	0.67887	0.2941	M	0.75615	2.305	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.72984	-0.4125	10	0.87932	D	0	-21.5396	14.609	0.68501	0.0:0.0:0.8527:0.1473	.	100	Q9H8X2	IPPK_HUMAN	S	100	ENSP00000287996:R100S	ENSP00000287996:R100S	R	-	1	0	IPPK	94451672	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	7.402000	0.79972	1.364000	0.46038	0.557000	0.71058	CGC	.	.		0.532	IPPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053101.1	NM_022755		T	95411851	G	T	95411851	3	4	260	1	0	0	0	0	1	0	0	0	7810	1058	37	1	1213	1	IPPK	9	95411851	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	399686	95411851	45801580	400	37645										
WNK2	65268	hgsc.bcm.edu	37	chr9	96024258	96024258	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccagctccctggccacggtgTctgcctctgtgcagagtgtg	13	14	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:96024258T>C	ENST00000297954.4	+	12	3229	c.3229T>C	c.(3229-3231)Tct>Cct	p.S1077P	WNK2_ENST00000427277.2_Missense_Mutation_p.S689P|WNK2_ENST00000349097.3_Missense_Mutation_p.S689P|WNK2_ENST00000356055.3_5'UTR|WNK2_ENST00000395477.2_Missense_Mutation_p.S1077P|WNK2_ENST00000395475.2_3'UTR	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	1077					intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						GGCCACGGTGTCTGCCTCTGT	0.697																																					p.S1077P		Atlas-SNP	.											.	WNK2	277	.	0			c.T3229C						.						32	28	29					9																	96024258		2199	4295	6494	SO:0001583	missense	65268	exon12			ACGGTGTCTGCCT	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"serologically defined colon cancer antigen 43"	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.3229T>C	chr9.hg19:g.96024258T>C	ENSP00000297954:p.Ser1077Pro	123.0	0.0		71.0	4.0	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Missense_Mutation	SNP	ENST00000297954.4	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	8.452|8.452	0.853252|0.853252	0.17106|0.17106	.|.	.|.	ENSG00000165238|ENSG00000165238	ENST00000297954;ENST00000395477;ENST00000349097;ENST00000427277|ENST00000411624	T;T;T;T|T	0.69306|0.61627	-0.36;-0.39;0.23;0.2|0.09	5.3|5.3	-0.198|-0.198	0.13224|0.13224	.|.	2.246780|.	0.01525|.	N|.	0.018559|.	T|T	0.28896|0.28896	0.0717|0.0717	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	0.999999|0.999999	D;B;P;P|.	0.54772|.	0.968;0.396;0.531;0.946|.	P;B;B;B|.	0.46758|.	0.526;0.063;0.095;0.326|.	T|T	0.18209|0.18209	-1.0344|-1.0344	10|7	0.35671|0.08179	T|T	0.21|0.78	.|.	3.5848|3.5848	0.07966|0.07966	0.3304:0.0:0.3828:0.2869|0.3304:0.0:0.3828:0.2869	.|.	1077;680;1077;1077|.	Q9Y3S1-2;A6PVR4;F8W9F9;Q9Y3S1|.	.;.;.;WNK2_HUMAN|.	P|A	1077;1077;689;689|680	ENSP00000297954:S1077P;ENSP00000378860:S1077P;ENSP00000297876:S689P;ENSP00000411181:S689P|ENSP00000414622:V680A	ENSP00000297954:S1077P|ENSP00000414622:V680A	S|V	+|+	1|2	0|0	WNK2|WNK2	95064079|95064079	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	0.071000|0.071000	0.14594|0.14594	-0.031000|-0.031000	0.13781|0.13781	-0.644000|-0.644000	0.03951|0.03951	TCT|GTC	.	.		0.697	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648		C	96024258	T	C	96024258	3	2	260	1	0	0	0	0	1	0	0	0	17393	1667	58	2	3275	2	WNK2	9	96024258	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	612407	96024258	45189173	401	37646										
HSD17B3	3293	hgsc.bcm.edu	37	chr9	99007625	99007625	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tggaagtcatgacatcactcAccttggaagctgagtacatg	10	9	3	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:99007625A>G	ENST00000375263.3	-	8	654		c.e8+1		HSD17B3_ENST00000375262.2_Splice_Site|HSD17B3_ENST00000464104.1_Splice_Site|RP11-240L7.4_ENST00000448857.1_RNA	NM_000197.1	NP_000188.1	P37058	DHB3_HUMAN	hydroxysteroid (17-beta) dehydrogenase 3						androgen biosynthetic process (GO:0006702)|male genitalia development (GO:0030539)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)			breast(1)|endometrium(3)|large_intestine(2)|lung(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13		Acute lymphoblastic leukemia(62;0.0171)|all_hematologic(171;0.214)				GACATCACTCACCTTGGAAGC	0.453																																					.		Atlas-SNP	.											.	HSD17B3	32	.	0			c.606+2T>C						.						151	139	143					9																	99007625		2203	4300	6503	SO:0001630	splice_region_variant	3293	exon9			TCACTCACCTTGG		CCDS6716.1	9q22	2011-09-20			ENSG00000130948	ENSG00000130948	1.1.1.62	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	5212	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 12C, member 2"	605573				8075637, 19027726	Standard	NM_000197		Approved	SDR12C2	uc004awa.1	P37058	OTTHUMG00000020292	ENST00000375263.3:c.606+1T>C	chr9.hg19:g.99007625A>G		153.0	0.0		109.0	5.0	NM_000197	Q5U0Q6	Splice_Site	SNP	ENST00000375263.3	hg19	CCDS6716.1	.	.	.	.	.	.	.	.	.	.	A	18.20	3.570236	0.65765	.	.	ENSG00000130948	ENST00000375263;ENST00000375262	.	.	.	5.01	5.01	0.66863	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.131	0.65253	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	HSD17B3	98047446	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	3.369000	0.52365	2.243000	0.73865	0.533000	0.62120	.	.	.		0.453	HSD17B3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053259.1	NM_000197	Intron	G	99007625	A	G	99007625	5	3	260	1	0	0	0	0	0	0	1	0	7394	173	6	2	340	2	HSD17B3	9	99007625	Splice_Site	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	2983367	99007625	42205806	402	37647										
SLC35D2	11046	hgsc.bcm.edu	37	chr9	99145784	99145784	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggtggtcagcagcgccttgtTgacaagcacgatgaggaagg	16	8	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:99145784T>C	ENST00000253270.7	-	1	195	c.133A>G	c.(133-135)Aac>Gac	p.N45D	SLC35D2_ENST00000375257.1_Missense_Mutation_p.N45D|SLC35D2_ENST00000482643.1_5'UTR|SLC35D2_ENST00000375259.4_Missense_Mutation_p.N45D	NM_007001.2	NP_008932.2	Q76EJ3	S35D2_HUMAN	solute carrier family 35 (UDP-GlcNAc/UDP-glucose transporter), member D2	45					carbohydrate derivative transport (GO:1901264)|carbohydrate metabolic process (GO:0005975)|carbohydrate transport (GO:0008643)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|nucleotide transmembrane transport (GO:1901679)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	nucleotide-sugar transmembrane transporter activity (GO:0005338)			endometrium(3)|large_intestine(3)|lung(4)|skin(2)	12		Acute lymphoblastic leukemia(62;0.0167)				AGCGCCTTGTTGACAAGCACG	0.756																																					p.N45D		Atlas-SNP	.											.	SLC35D2	20	.	0			c.A133G						.						6	6	6					9																	99145784		2014	4024	6038	SO:0001583	missense	11046	exon1			CCTTGTTGACAAG	AB122077	CCDS6717.1, CCDS69625.1	9q22.33	2013-07-17	2013-07-17		ENSG00000130958	ENSG00000130958		"Solute carriers"	20799	protein-coding gene	gene with protein product		609182	"solute carrier family 35, member D2"			15607426	Standard	NM_007001		Approved	UGTrel8, SQV7L	uc004awc.3	Q76EJ3	OTTHUMG00000020293	ENST00000253270.7:c.133A>G	chr9.hg19:g.99145784T>C	ENSP00000253270:p.Asn45Asp	43.0	0.0		26.0	4.0	NM_007001	O95454|Q498C1|Q75W21|Q7Z5X5	Missense_Mutation	SNP	ENST00000253270.7	hg19	CCDS6717.1	.	.	.	.	.	.	.	.	.	.	N	26.9	4.781006	0.90282	.	.	ENSG00000130958	ENST00000253270;ENST00000375259;ENST00000375257	T;D;D	0.87491	-1.43;-2.26;-1.97	4.23	4.23	0.50019	.	0.000000	0.85682	D	0.000000	D	0.92967	0.7762	M	0.83953	2.67	0.41375	D	0.987515	D;D;D	0.89917	0.996;1.0;0.998	D;D;D	0.81914	0.981;0.995;0.964	D	0.93885	0.7174	10	0.87932	D	0	.	12.111	0.53840	0.0:0.0:0.0:1.0	.	45;45;45	Q76EJ3-2;Q5VZJ2;Q76EJ3	.;.;S35D2_HUMAN	D	45	ENSP00000253270:N45D;ENSP00000364408:N45D;ENSP00000364406:N45D	ENSP00000253270:N45D	N	-	1	0	SLC35D2	98185605	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.881000	0.63114	1.785000	0.52413	0.440000	0.28878	AAC	.	.		0.756	SLC35D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053261.1			C	99145784	T	C	99145784	3	2	260	1	0	0	0	0	1	0	0	0	14597	1812	63	2	928	2	SLC35D2	9	99145784	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	138159	99145784	42067647	403	37648										
NCBP1	4686	hgsc.bcm.edu	37	chr9	100410502	100410502	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tttgattacacagatgatccCgaggtaagtgaccgactaaa	9	8	0	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:100410502C>A	ENST00000375147.3	+	8	1150	c.894C>A	c.(892-894)ccC>ccA	p.P298P		NM_002486.4	NP_002477.1	Q09161	NCBP1_HUMAN	nuclear cap binding protein subunit 1, 80kDa	298					7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA cis splicing, via spliceosome (GO:0045292)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of viral transcription (GO:0050434)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|spliceosomal snRNP assembly (GO:0000387)|termination of RNA polymerase II transcription (GO:0006369)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|mRNA cap binding complex (GO:0005845)|nuclear cap binding complex (GO:0005846)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA cap binding (GO:0000339)			NS(1)|central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)	19		Acute lymphoblastic leukemia(62;0.158)				CAGATGATCCCGAGGTAAGTG	0.428																																					p.P298P	Ovarian(36;879 898 2893 44212 50307)	Atlas-SNP	.											.	NCBP1	64	.	0			c.C894A						.						69	56	61					9																	100410502		2203	4300	6503	SO:0001819	synonymous_variant	4686	exon8			TGATCCCGAGGTA	BC001450	CCDS6728.1	9q34.1	2010-01-26	2002-08-29		ENSG00000136937	ENSG00000136937			7658	protein-coding gene	gene with protein product		600469	"nuclear cap binding protein subunit 1, 80kD"	NCBP		7937105, 8812508	Standard	NM_002486		Approved	CBP80, Sto1	uc004axq.3	Q09161	OTTHUMG00000020332	ENST00000375147.3:c.894C>A	chr9.hg19:g.100410502C>A		104.0	0.0		54.0	4.0	NM_002486	B2R718|Q59G76|Q5T1V0|Q5T7X2	Silent	SNP	ENST00000375147.3	hg19	CCDS6728.1																																																																																			.	.		0.428	NCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053337.1	NM_002486		A	100410502	C	A	100410502	2	1	260	1	0	0	0	0	0	0	0	1	10220	639	23	1		1	NCBP1	9	100410502	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	1264718	100410502	40802929	404	37649										
ALG2	85365	hgsc.bcm.edu	37	chr9	101980977	101980978	+	Nonsense_Mutation	DNP	CC	CC	AT													0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgccatgcctgtggtgtattCctctatccagtcaattgggg							TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:101980977_101980978CC>AT	ENST00000476832.1	-	2	550_551	c.489_490GG>AT	c.(487-492)gaGGaa>gaATaa	p.E164*	ALG2_ENST00000319033.6_Nonsense_Mutation_p.E71*	NM_033087.3	NP_149078.1	O75340	PDCD6_HUMAN	ALG2, alpha-1,3/1,6-mannosyltransferase	0	EF-hand 5. {ECO:0000255|PROSITE- ProRule:PRU00448}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|cellular response to heat (GO:0034605)|intracellular protein transport (GO:0006886)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|proteolysis (GO:0006508)|response to calcium ion (GO:0051592)|vascular endothelial growth factor receptor-2 signaling pathway (GO:0036324)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	binding, bridging (GO:0060090)|calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|calcium-dependent protein binding (GO:0048306)|protein dimerization activity (GO:0046983)	p.E164*(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(11)|ovary(2)|prostate(2)	22		Acute lymphoblastic leukemia(62;0.0559)				GTGGTGTATTCCTCTATCCAGT	0.446																																					p.E164X|p.E163E		Atlas-SNP	.											ALG2,NS,carcinoma,0,1|.	ALG2	37	.	1	Substitution - Nonsense(1)	ovary(1)	c.G490T|c.G489A						.																																			SO:0001587	stop_gained	85365	exon2			TGTATTCCTCTAT|GTATTCCTCTATC	AK027417	CCDS6739.1	9q31.1	2013-02-22	2013-02-22		ENSG00000119523	ENSG00000119523	2.4.1.132, 2.4.1.257	"Glycosyltransferase group 1 domain containing"	23159	protein-coding gene	gene with protein product		607905	"asparagine-linked glycosylation 2 homolog (yeast, alpha-1,3-mannosyltransferase)", "asparagine-linked glycosylation 2, alpha-1,3-mannosyltransferase homolog (S. cerevisiae)"			12684507	Standard	NR_024532		Approved	CDGIi, FLJ14511, hALPG2, NET38	uc004azf.3	Q9H553	OTTHUMG00000020355	ENST00000476832.1:c.489_490delinsAT	chr9.hg19:g.101980977_101980978delinsAT	ENSP00000417764:p.Glu164*	79.0	0.0		48.0|47.0	2.0|4.0	NM_033087	B2RD16|E7ESR3|Q2YDC2|Q5TZS0	Nonsense_Mutation|Silent	SNP	ENST00000476832.1	hg19	CCDS6739.1																																																																																			.	.		0.446	ALG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215080.1	NM_033087		AT	101980978	CC	AT	101980977	4	1	260	1	0	0	0	0	0	1	0	0	519	864	30	3	764	3	ALG2	9	101980977	Nonsense_Mutation	DNP	CC	TCGA-ES-A2HT-01A-12D-A183-10	1570475	101980977	39232454	405	37650										
ZNF189	7743	hgsc.bcm.edu	37	chr9	104170939	104170939	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtaccaaatgtaagaagagcTttagtcgaaattcattgctt	8	6	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:104170939T>C	ENST00000339664.2	+	3	1018	c.889T>C	c.(889-891)Ttt>Ctt	p.F297L	ZNF189_ENST00000374861.3_Missense_Mutation_p.F283L|ZNF189_ENST00000259395.4_Missense_Mutation_p.F255L	NM_001278240.1	NP_001265169.1	O75820	ZN189_HUMAN	zinc finger protein 189	297					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	26		Acute lymphoblastic leukemia(62;0.0559)				TAAGAAGAGCTTTAGTCGAAA	0.408																																					p.F297L		Atlas-SNP	.											.	ZNF189	79	.	0			c.T889C						.						142	146	145					9																	104170939		2203	4300	6503	SO:0001583	missense	7743	exon3			AAGAGCTTTAGTC	AF025770	CCDS6754.1, CCDS6755.1, CCDS65096.1, CCDS75867.1	9q22-q31	2013-01-08			ENSG00000136870	ENSG00000136870		"Zinc fingers, C2H2-type", "-"	12980	protein-coding gene	gene with protein product		603132				9653648	Standard	NM_003452		Approved		uc004bbh.2	O75820	OTTHUMG00000020383	ENST00000339664.2:c.889T>C	chr9.hg19:g.104170939T>C	ENSP00000342019:p.Phe297Leu	159.0	0.0		95.0	4.0	NM_003452	O75802|Q5T7D7|Q5T7D8|Q5T7D9|Q9UBL4|Q9UPE9|Q9UPF0|Q9UPF1	Missense_Mutation	SNP	ENST00000339664.2	hg19	CCDS6754.1	.	.	.	.	.	.	.	.	.	.	T	19.23	3.788382	0.70337	.	.	ENSG00000136870	ENST00000374861;ENST00000339664;ENST00000259395	T;T;T	0.46063	0.88;0.88;0.88	4.79	4.79	0.61399	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.49916	D	0.000127	T	0.61438	0.2347	M	0.65975	2.015	0.58432	D	0.999999	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.97110	0.995;1.0;0.999	T	0.64896	-0.6299	10	0.87932	D	0	.	12.9471	0.58379	0.0:0.0:0.0:1.0	.	282;283;297	B7ZLK9;Q5T7D8;O75820	.;.;ZN189_HUMAN	L	283;297;255	ENSP00000363995:F283L;ENSP00000342019:F297L;ENSP00000259395:F255L	ENSP00000259395:F255L	F	+	1	0	ZNF189	103210760	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.868000	0.87116	2.371000	0.80710	0.533000	0.62120	TTT	.	.		0.408	ZNF189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053447.1	NM_003452		C	104170939	T	C	104170939	3	2	260	1	0	0	0	0	1	0	0	0	17769	1609	56	2	899	2	ZNF189	9	104170939	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	2189962	104170939	37042492	406	37651										
ZNF189	7743	hgsc.bcm.edu	37	chr9	104171114	104171114	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtgtggaaaaagtttcagtcGgagctcattccttattgaac	10	7	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:104171114G>T	ENST00000339664.2	+	3	1193	c.1064G>T	c.(1063-1065)cGg>cTg	p.R355L	ZNF189_ENST00000374861.3_Missense_Mutation_p.R341L|ZNF189_ENST00000259395.4_Missense_Mutation_p.R313L	NM_001278240.1	NP_001265169.1	O75820	ZN189_HUMAN	zinc finger protein 189	355					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	26		Acute lymphoblastic leukemia(62;0.0559)				AGTTTCAGTCGGAGCTCATTC	0.408																																					p.R355L		Atlas-SNP	.											.	ZNF189	79	.	0			c.G1064T						.						83	89	87					9																	104171114		2203	4300	6503	SO:0001583	missense	7743	exon3			TCAGTCGGAGCTC	AF025770	CCDS6754.1, CCDS6755.1, CCDS65096.1, CCDS75867.1	9q22-q31	2013-01-08			ENSG00000136870	ENSG00000136870		"Zinc fingers, C2H2-type", "-"	12980	protein-coding gene	gene with protein product		603132				9653648	Standard	NM_003452		Approved		uc004bbh.2	O75820	OTTHUMG00000020383	ENST00000339664.2:c.1064G>T	chr9.hg19:g.104171114G>T	ENSP00000342019:p.Arg355Leu	141.0	0.0		103.0	5.0	NM_003452	O75802|Q5T7D7|Q5T7D8|Q5T7D9|Q9UBL4|Q9UPE9|Q9UPF0|Q9UPF1	Missense_Mutation	SNP	ENST00000339664.2	hg19	CCDS6754.1	.	.	.	.	.	.	.	.	.	.	G	11.38	1.621238	0.28889	.	.	ENSG00000136870	ENST00000374861;ENST00000339664;ENST00000259395	T;T;T	0.19669	2.13;2.13;2.13	4.79	4.79	0.61399	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.44285	D	0.000478	T	0.23410	0.0566	L	0.53780	1.695	0.42701	D	0.993618	P;B;B	0.38129	0.619;0.406;0.432	B;B;B	0.38194	0.064;0.267;0.12	T	0.01630	-1.1308	10	0.27785	T	0.31	.	16.1533	0.81636	0.0:0.0:1.0:0.0	.	340;341;355	B7ZLK9;Q5T7D8;O75820	.;.;ZN189_HUMAN	L	341;355;313	ENSP00000363995:R341L;ENSP00000342019:R355L;ENSP00000259395:R313L	ENSP00000259395:R313L	R	+	2	0	ZNF189	103210935	0.000000	0.05858	1.000000	0.80357	0.978000	0.69477	0.531000	0.23052	2.941000	0.99782	0.655000	0.94253	CGG	.	.		0.408	ZNF189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053447.1	NM_003452		T	104171114	G	T	104171114	3	4	260	1	0	0	0	0	1	0	0	0	17769	1116	39	1	1074	1	ZNF189	9	104171114	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	175	104171114	37042317	407	37652										
CYLC2	1539	hgsc.bcm.edu	37	chr9	105767561	105767561	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aaaggaggtacagagaaagaTagcaaaaaaggtaaaaagga	12	2	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:105767561T>C	ENST00000374798.3	+	5	718	c.648T>C	c.(646-648)gaT>gaC	p.D216D	CYLC2_ENST00000487798.1_Silent_p.D216D	NM_001340.3	NP_001331.1	Q14093	CYLC2_HUMAN	cylicin, basic protein of sperm head cytoskeleton 2	216	3 X approximate tandem repeats.|31 X 3 AA repeats of K-K-X.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(14)|ovary(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)	41		all_hematologic(171;0.125)				CAGAGAAAGATAGCAAAAAAG	0.363																																					p.D216D		Atlas-SNP	.											.	CYLC2	109	.	0			c.T648C						.						83	80	81					9																	105767561		2203	4300	6503	SO:0001819	synonymous_variant	1539	exon5			GAAAGATAGCAAA	Z46788	CCDS35085.1	9q31.2	2008-07-21			ENSG00000155833	ENSG00000155833			2583	protein-coding gene	gene with protein product		604035				7737358	Standard	NM_001340		Approved		uc004bbs.2	Q14093	OTTHUMG00000020396	ENST00000374798.3:c.648T>C	chr9.hg19:g.105767561T>C		1067.0	0.0		724.0	183.0	NM_001340	B2R8F4|Q5VVJ9	Silent	SNP	ENST00000374798.3	hg19	CCDS35085.1																																																																																			.	.		0.363	CYLC2-001	KNOWN	alternative_3_UTR|NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053463.3	NM_001340		C	105767561	T	C	105767561	2	2	260	1	0	0	0	0	0	0	0	1	4144	1403	49	2		2	CYLC2	9	105767561	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1596447	105767561	35445870	408	37653										
ACTL7A	10881	hgsc.bcm.edu	37	chr9	111625693	111625693	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	catcctgctctgcgggggcaGcacgatgctcagtggcttcc	13	14	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:111625693G>T	ENST00000333999.3	+	1	1091	c.1091G>T	c.(1090-1092)aGc>aTc	p.S364I		NM_006687.2	NP_006678.1	Q9Y615	ACL7A_HUMAN	actin-like 7A	364						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|male germ cell nucleus (GO:0001673)|motile cilium (GO:0031514)|nucleus (GO:0005634)|protein complex (GO:0043234)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(2)|large_intestine(4)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						TGCGGGGGCAGCACGATGCTC	0.577																																					p.S364I	Esophageal Squamous(177;1480 3591 17554)	Atlas-SNP	.											.	ACTL7A	34	.	0			c.G1091T						.						122	103	109					9																	111625693		2203	4300	6503	SO:0001583	missense	10881	exon1			GGGGCAGCACGAT	BC014610	CCDS6772.1	9q31	2008-02-05			ENSG00000187003	ENSG00000187003			161	protein-coding gene	gene with protein product		604303				10373328	Standard	NM_006687		Approved		uc004bdj.1	Q9Y615	OTTHUMG00000020461	ENST00000333999.3:c.1091G>T	chr9.hg19:g.111625693G>T	ENSP00000334300:p.Ser364Ile	123.0	0.0		75.0	4.0	NM_006687	B2RC83|Q5JSV0	Missense_Mutation	SNP	ENST00000333999.3	hg19	CCDS6772.1	.	.	.	.	.	.	.	.	.	.	G	13.27	2.186966	0.38609	.	.	ENSG00000187003	ENST00000333999	D	0.95272	-3.66	5.65	3.68	0.42216	.	0.000000	0.56097	D	0.000034	D	0.95915	0.8670	M	0.90019	3.08	0.44531	D	0.99748	P	0.44006	0.824	P	0.46850	0.529	D	0.96526	0.9389	10	0.87932	D	0	.	13.4584	0.61212	0.0:0.428:0.572:0.0	.	364	Q9Y615	ACL7A_HUMAN	I	364	ENSP00000334300:S364I	ENSP00000334300:S364I	S	+	2	0	ACTL7A	110665514	0.996000	0.38824	0.997000	0.53966	0.617000	0.37484	2.178000	0.42519	1.514000	0.48869	0.655000	0.94253	AGC	.	.		0.577	ACTL7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053570.1	NM_006687		T	111625693	G	T	111625693	3	4	260	1	0	0	0	0	1	0	0	0	200	971	34	3	1093	3	ACTL7A	9	111625693	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	5858132	111625693	29587738	409	37654										
SVEP1	79987	hgsc.bcm.edu	37	chr9	113169313	113169313	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acccttcattgcaagtgtatTcaatctctttttggaatgtg	7	8	3	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:113169313T>C	ENST00000401783.2	-	38	8903	c.8567A>G	c.(8566-8568)gAa>gGa	p.E2856G	SVEP1_ENST00000374469.1_Missense_Mutation_p.E2833G|SVEP1_ENST00000297826.5_Missense_Mutation_p.E782G	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2856	Sushi 24. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						GCAAGTGTATTCAATCTCTTT	0.527																																					p.E2856G		Atlas-SNP	.											.	SVEP1	326	.	0			c.A8567G						.						67	71	69					9																	113169313		2039	4186	6225	SO:0001583	missense	79987	exon38			GTGTATTCAATCT	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.8567A>G	chr9.hg19:g.113169313T>C	ENSP00000384917:p.Glu2856Gly	106.0	0.0		78.0	4.0	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	hg19	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	T	9.434	1.086360	0.20390	.	.	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826	T;T;T	0.66995	-0.24;-0.24;-0.24	5.58	1.58	0.23477	Complement control module (2);Sushi/SCR/CCP (3);	0.404899	0.28431	N	0.015362	T	0.64789	0.2630	M	0.80332	2.49	0.58432	D	0.999999	B	0.32653	0.379	B	0.35182	0.197	T	0.60042	-0.7340	10	0.34782	T	0.22	.	8.7548	0.34639	0.1153:0.0:0.2528:0.6319	.	2856	Q4LDE5	SVEP1_HUMAN	G	2856;2833;782	ENSP00000384917:E2856G;ENSP00000363593:E2833G;ENSP00000297826:E782G	ENSP00000297826:E782G	E	-	2	0	SVEP1	112209134	0.281000	0.24258	0.985000	0.45067	0.989000	0.77384	1.525000	0.35953	0.448000	0.26722	0.482000	0.46254	GAA	.	.		0.527	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	113169313	T	C	113169313	3	2	260	1	0	0	0	0	1	0	0	0	15435	1783	62	2	2192	2	SVEP1	9	113169313	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1543620	113169313	28044118	410	37655										
OR2K2	26248	hgsc.bcm.edu	37	chr9	114090233	114090233	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gggtatctgcagggcaaaacTggtttccagcagagcggtca	14	9	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:114090233T>C	ENST00000374428.1	-	1	567	c.568A>G	c.(568-570)Agt>Ggt	p.S190G	OR2K2_ENST00000302681.1_Missense_Mutation_p.S161G			Q8NGT1	OR2K2_HUMAN	olfactory receptor, family 2, subfamily K, member 2	190						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(2)	20						AGGGCAAAACTGGTTTCCAGC	0.527																																					p.S161G		Atlas-SNP	.											.	OR2K2	77	.	0			c.A481G						.						80	71	74					9																	114090233		2203	4300	6503	SO:0001583	missense	26248	exon1			CAAAACTGGTTTC	X64977	CCDS6778.1	9q31.3	2012-08-09			ENSG00000171133	ENSG00000171133		"GPCR / Class A : Olfactory receptors"	8264	protein-coding gene	gene with protein product				OR2AR1P		1370859, 17010214	Standard	NM_205859		Approved	HTPCRH06, HSHTPCRH06	uc011lwp.2	Q8NGT1	OTTHUMG00000020488	ENST00000374428.1:c.568A>G	chr9.hg19:g.114090233T>C	ENSP00000363550:p.Ser190Gly	58.0	0.0		54.0	4.0	NM_205859	Q2TA61|Q5VYK4|Q6IFI5	Missense_Mutation	SNP	ENST00000374428.1	hg19		.	.	.	.	.	.	.	.	.	.	T	1.997	-0.430313	0.04669	.	.	ENSG00000171133	ENST00000302681;ENST00000374428	T;T	0.37411	1.2;1.2	4.92	-1.52	0.08637	GPCR, rhodopsin-like superfamily (1);	0.312298	0.22608	N	0.057879	T	0.21347	0.0514	L	0.28054	0.825	0.09310	N	1	B	0.11235	0.004	B	0.10450	0.005	T	0.17623	-1.0363	10	0.28530	T	0.3	.	10.3269	0.43798	0.0:0.5123:0.0:0.4877	.	190	Q8NGT1	OR2K2_HUMAN	G	161;190	ENSP00000305055:S161G;ENSP00000363550:S190G	ENSP00000305055:S161G	S	-	1	0	OR2K2	113130054	0.000000	0.05858	0.057000	0.19452	0.246000	0.25737	-2.510000	0.00959	-0.337000	0.08426	-0.326000	0.08463	AGT	.	.		0.527	OR2K2-201	KNOWN	basic	protein_coding	protein_coding		NM_205859		C	114090233	T	C	114090233	3	2	260	1	0	0	0	0	1	0	0	0	11014	1580	55	2	472	2	OR2K2	9	114090233	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	920920	114090233	27123198	411	37656										
KIAA1958	158405	hgsc.bcm.edu	37	chr9	115421704	115421704	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttttccatcaccagcagcacCttcagctcctccaccaagaa	4	17	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:115421704C>A	ENST00000337530.6	+	4	1802	c.1506C>A	c.(1504-1506)acC>acA	p.T502T	KIAA1958_ENST00000536272.1_Silent_p.T530T	NM_133465.2	NP_597722.1	Q8N8K9	K1958_HUMAN	KIAA1958	502										endometrium(1)|large_intestine(9)|lung(10)|prostate(2)|skin(3)	25						CCAGCAGCACCTTCAGCTCCT	0.582																																					p.T502T		Atlas-SNP	.											.	KIAA1958	52	.	0			c.C1506A						.						46	43	44					9																	115421704		2203	4300	6503	SO:0001819	synonymous_variant	158405	exon4			CAGCACCTTCAGC	AB075838	CCDS35108.1, CCDS69642.1	9q33.1	2009-09-22			ENSG00000165185	ENSG00000165185			23427	protein-coding gene	gene with protein product							Standard	NM_001287038		Approved	FLJ39294	uc004bgf.1	Q8N8K9	OTTHUMG00000020508	ENST00000337530.6:c.1506C>A	chr9.hg19:g.115421704C>A		82.0	0.0		73.0	4.0	NM_133465	B7ZKW6|Q2M336|Q5T252|Q8TF43|Q96N02	Silent	SNP	ENST00000337530.6	hg19	CCDS35108.1																																																																																			.	.		0.582	KIAA1958-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053690.1	NM_133465		A	115421704	C	A	115421704	2	1	260	1	0	0	0	0	0	0	0	1	8273	668	24	3		3	KIAA1958	9	115421704	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	1331471	115421704	25791727	412	37657										
FKBP15	23307	hgsc.bcm.edu	37	chr9	115932080	115932080	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gcctctccctattcaggggtGcttgaggctgcccagaactg	12	13	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:115932080G>T	ENST00000238256.3	-	26	3026	c.2909C>A	c.(2908-2910)gCa>gAa	p.A970E		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	970					endocytosis (GO:0006897)|negative regulation of phosphatase activity (GO:0010923)|protein folding (GO:0006457)	actin filament (GO:0005884)|axon (GO:0030424)|endosome (GO:0005768)|growth cone (GO:0030426)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(9)|ovary(3)|urinary_tract(1)	26						ATTCAGGGGTGCTTGAGGCTG	0.597																																					p.A970E		Atlas-SNP	.											.	FKBP15	128	.	0			c.C2909A						.						17	20	19					9																	115932080		2051	4191	6242	SO:0001583	missense	23307	exon26			AGGGGTGCTTGAG	AB014574	CCDS48007.1	9q33.1	2014-05-09	2006-10-31	2006-10-31	ENSG00000119321	ENSG00000119321		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	23397	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 76", "WASP and FKBP-like protein"		"KIAA0674"	KIAA0674		16756961, 20376207	Standard	NM_015258		Approved	PPP1R76, FKBP133, WAFL	uc004bgs.2	Q5T1M5	OTTHUMG00000020518	ENST00000238256.3:c.2909C>A	chr9.hg19:g.115932080G>T	ENSP00000238256:p.Ala970Glu	99.0	0.0		93.0	4.0	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Missense_Mutation	SNP	ENST00000238256.3	hg19	CCDS48007.1	.	.	.	.	.	.	.	.	.	.	G	6.645	0.487403	0.12641	.	.	ENSG00000119321	ENST00000446284;ENST00000238256	T;T	0.24151	1.87;1.88	4.53	0.23	0.15372	.	.	.	.	.	T	0.20981	0.0505	L	0.57536	1.79	0.09310	N	1	B;B	0.11235	0.004;0.001	B;B	0.11329	0.006;0.003	T	0.34229	-0.9837	9	0.54805	T	0.06	-0.5965	1.9151	0.03295	0.1113:0.147:0.3304:0.4114	.	551;970	B4DVS2;Q5T1M5	.;FKB15_HUMAN	E	995;970	ENSP00000416158:A995E;ENSP00000238256:A970E	ENSP00000238256:A970E	A	-	2	0	FKBP15	114971901	0.001000	0.12720	0.001000	0.08648	0.116000	0.19942	0.665000	0.25083	0.173000	0.19788	0.491000	0.48974	GCA	.	.		0.597	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258		T	115932080	G	T	115932080	3	4	260	1	0	0	0	0	1	0	0	0	5913	1319	46	3	762	3	FKBP15	9	115932080	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	510376	115932080	25281351	413	37658										
POLE3	54107	hgsc.bcm.edu	37	chr9	116172342	116172342	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctgtcccgctcaccaggatgTggcgtacagcacgaagacgc	12	14	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:116172342T>C	ENST00000374171.4	-	3	315	c.145A>G	c.(145-147)Aca>Gca	p.T49A	C9orf43_ENST00000490544.1_3'UTR|C9orf43_ENST00000374165.1_5'Flank|POLE3_ENST00000479871.1_5'UTR|C9orf43_ENST00000288462.4_5'Flank|POLE3_ENST00000374169.3_Missense_Mutation_p.T49A	NM_001278255.1|NM_017443.4	NP_001265184.1|NP_059139.3	Q9NRF9	DPOE3_HUMAN	polymerase (DNA directed), epsilon 3, accessory subunit	49					DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|histone H3 acetylation (GO:0043966)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|epsilon DNA polymerase complex (GO:0008622)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)|sequence-specific DNA binding (GO:0043565)			large_intestine(2)|lung(1)	3					Cladribine(DB00242)	CACCAGGATGTGGCGTACAGC	0.652																																					p.T49A		Atlas-SNP	.											.	POLE3	8	.	0			c.A145G						.						18	19	18					9																	116172342		2190	4285	6475	SO:0001583	missense	54107	exon3			AGGATGTGGCGTA	AF261689	CCDS6795.1	9q33	2012-05-18	2012-05-18		ENSG00000148229	ENSG00000148229		"DNA polymerases"	13546	protein-coding gene	gene with protein product	"histone fold protein CHRAC17", "DNA polymerase epsilon p17 subunit", "chromatin accessibility complex 17", "arsenic transactivated protein"	607267	"polymerase (DNA directed), epsilon 3 (p17 subunit)"			10801849, 10880450	Standard	NM_017443		Approved	CHRAC17, Ybl1, p17, CHARAC17	uc031tet.1	Q9NRF9	OTTHUMG00000020523	ENST00000374171.4:c.145A>G	chr9.hg19:g.116172342T>C	ENSP00000363286:p.Thr49Ala	67.0	0.0		43.0	4.0	NM_017443	Q5W0U1|Q8N758|Q8NCE5|Q9NR32	Missense_Mutation	SNP	ENST00000374171.4	hg19	CCDS6795.1	.	.	.	.	.	.	.	.	.	.	T	29.5	5.008275	0.93346	.	.	ENSG00000148229	ENST00000374171;ENST00000374169	T;T	0.38077	1.16;1.16	4.88	4.88	0.63580	Histone-fold (2);Transcription factor CBF/NF-Y/archaeal histone (1);	0.000000	0.85682	D	0.000000	T	0.48978	0.1530	L	0.58810	1.83	0.80722	D	1	P	0.50617	0.937	P	0.56216	0.794	T	0.51949	-0.8640	10	0.87932	D	0	-5.2389	11.9833	0.53131	0.0:0.0:0.0:1.0	.	49	Q9NRF9	DPOE3_HUMAN	A	49	ENSP00000363286:T49A;ENSP00000363284:T49A	ENSP00000363284:T49A	T	-	1	0	POLE3	115212163	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	6.718000	0.74713	2.050000	0.60909	0.460000	0.39030	ACA	.	.		0.652	POLE3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053730.1	NM_017443		C	116172342	T	C	116172342	3	2	260	1	0	0	0	0	1	0	0	0	12207	1696	59	2	310	2	POLE3	9	116172342	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	240262	116172342	25041089	414	37659										
COL27A1	85301	hgsc.bcm.edu	37	chr9	116931466	116931466	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tggatcggaagcctcaaagaAagccggacccaagagcagcc	12	12	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:116931466A>G	ENST00000356083.3	+	3	2022	c.1631A>G	c.(1630-1632)aAa>aGa	p.K544R		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	544	Pro-rich.				extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						GCCTCAAAGAAAGCCGGACCC	0.632																																					p.K544R		Atlas-SNP	.											.	COL27A1	200	.	0			c.A1631G						.						76	97	90					9																	116931466		2203	4300	6503	SO:0001583	missense	85301	exon3			CAAAGAAAGCCGG	AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"Collagens"	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.1631A>G	chr9.hg19:g.116931466A>G	ENSP00000348385:p.Lys544Arg	115.0	0.0		87.0	4.0	NM_032888	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	hg19	CCDS6802.1	.	.	.	.	.	.	.	.	.	.	A	9.633	1.136893	0.21123	.	.	ENSG00000196739	ENST00000356083;ENST00000357257;ENST00000374106;ENST00000451716	D;D	0.91945	-2.62;-2.94	5.41	5.41	0.78517	.	.	.	.	.	D	0.92176	0.7519	L	0.36672	1.1	0.28952	N	0.890347	P;D	0.76494	0.9;0.999	P;D	0.66716	0.591;0.946	D	0.84838	0.0806	9	0.12103	T	0.63	.	11.8344	0.52314	1.0:0.0:0.0:0.0	.	544;491	Q8IZC6;Q5T1U7	CORA1_HUMAN;.	R	544;544;491;491	ENSP00000348385:K544R;ENSP00000391328:K491R	ENSP00000348385:K544R	K	+	2	0	COL27A1	115971287	0.920000	0.31207	0.986000	0.45419	0.381000	0.30169	2.713000	0.47194	2.052000	0.61016	0.460000	0.39030	AAA	.	.		0.632	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888		G	116931466	A	G	116931466	3	3	260	1	0	0	0	0	1	0	0	0	3687	14	1	2	1641	2	COL27A1	9	116931466	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	759124	116931466	24281965	415	37660										
ASTN2	23245	hgsc.bcm.edu	37	chr9	119858432	119858432	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctcccaaagctgattcctccTgtgagtaagcacagtctatc	7	13	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:119858432T>A	ENST00000313400.4	-	5	1269		c.e5-2		ASTN2_ENST00000361209.2_Splice_Site|ASTN2_ENST00000361477.3_Splice_Site|AL354981.1_ENST00000583553.1_RNA|ASTN2_ENST00000373996.3_Splice_Site			O75129	ASTN2_HUMAN	astrotactin 2						negative regulation of protein localization to cell surface (GO:2000009)	cell pole (GO:0060187)|endosome (GO:0005768)|integral component of membrane (GO:0016021)				breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1)	102						TGATTCCTCCTGTGAGTAAGC	0.542																																					.		Atlas-SNP	.											.	ASTN2	307	.	0			c.1016-2A>T						.						95	74	81					9																	119858432		2203	4300	6503	SO:0001630	splice_region_variant	23245	exon5			TCCTCCTGTGAGT	AF116574	CCDS6814.1, CCDS6815.1, CCDS48009.1, CCDS48009.2, CCDS55334.1	9q33	2008-02-05			ENSG00000148219	ENSG00000148219			17021	protein-coding gene	gene with protein product		612856				9734811	Standard	NM_014010		Approved	KIAA0634	uc004bjt.2	O75129	OTTHUMG00000021013	ENST00000313400.4:c.1169-2A>T	chr9.hg19:g.119858432T>A		134.0	0.0		81.0	25.0	NM_014010	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Splice_Site	SNP	ENST00000313400.4	hg19		.	.	.	.	.	.	.	.	.	.	T	18.36	3.606103	0.66445	.	.	ENSG00000148219	ENST00000313400;ENST00000373996;ENST00000373986;ENST00000361209	.	.	.	4.98	4.98	0.66077	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.4809	0.55842	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	ASTN2	118898253	1.000000	0.71417	0.985000	0.45067	0.796000	0.44982	4.485000	0.60279	2.013000	0.59113	0.402000	0.26972	.	.	.		0.542	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010	Intron	A	119858432	T	A	119858432	5	1	260	1	0	0	0	0	0	0	1	0	1065	1594	55	4	3160	4	ASTN2	9	119858432	Splice_Site	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	2926966	119858432	21354999	416	37661										
PHF19	26147	hgsc.bcm.edu	37	chr9	123631484	123631484	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cgggcccgccgcagtagcagTagcattgctgctggttggtg	16	11	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:123631484T>C	ENST00000373896.3	-	6	842	c.590A>G	c.(589-591)tAc>tGc	p.Y197C	PHF19_ENST00000419155.1_5'Flank|PHF19_ENST00000487555.1_5'Flank	NM_015651.1	NP_056466.1	Q5T6S3	PHF19_HUMAN	PHD finger protein 19	197					chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K27 methylation (GO:0061087)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)	methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|endometrium(3)|large_intestine(1)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GCAGTAGCAGTAGCATTGCTG	0.682																																					p.Y197C		Atlas-SNP	.											.	PHF19	47	.	0			c.A590G						.						25	22	23					9																	123631484		2203	4300	6503	SO:0001583	missense	26147	exon6			TAGCAGTAGCATT	BX640713	CCDS35116.1, CCDS35117.1, CCDS69648.1, CCDS75889.1	9q34.11	2013-01-28			ENSG00000119403	ENSG00000119403		"Tudor domain containing", "Zinc fingers, PHD-type"	24566	protein-coding gene	gene with protein product	"polycomb-like 3", "tudor domain containing 19B"	609740				15563832	Standard	XM_005251906		Approved	DKFZP727G051, PCL3, MTF2L1, TDRD19B	uc004bks.1	Q5T6S3	OTTHUMG00000020577	ENST00000373896.3:c.590A>G	chr9.hg19:g.123631484T>C	ENSP00000363003:p.Tyr197Cys	118.0	0.0		75.0	4.0	NM_015651	Q32NF2|Q5T6S4|Q6N038|Q8TBL6|Q9UFS9	Missense_Mutation	SNP	ENST00000373896.3	hg19	CCDS35116.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.476806	0.84640	.	.	ENSG00000119403	ENST00000544082;ENST00000373896	T	0.58506	0.33	5.07	5.07	0.68467	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.261651	0.39146	N	0.001456	T	0.74351	0.3705	M	0.84511	2.7	0.80722	D	1	D	0.54772	0.968	P	0.57548	0.823	T	0.79928	-0.1596	10	0.87932	D	0	-12.2448	14.307	0.66391	0.0:0.0:0.0:1.0	.	197	Q5T6S3	PHF19_HUMAN	C	197	ENSP00000363003:Y197C	ENSP00000363003:Y197C	Y	-	2	0	PHF19	122671305	1.000000	0.71417	1.000000	0.80357	0.676000	0.39594	7.894000	0.87336	2.040000	0.60383	0.254000	0.18369	TAC	.	.		0.682	PHF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053838.3	XM_045308		C	123631484	T	C	123631484	3	2	260	1	0	0	0	0	1	0	0	0	11838	1638	57	2	1192	2	PHF19	9	123631484	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	3773052	123631484	17581947	417	37662										
DAB2IP	153090	hgsc.bcm.edu	37	chr9	124522560	124522560	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aggcgcgctaccaaaccatcAccatcctgcccatggagatg	9	15	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:124522560A>G	ENST00000408936.3	+	6	1194	c.1012A>G	c.(1012-1014)Acc>Gcc	p.T338A	DAB2IP_ENST00000309989.1_Missense_Mutation_p.T214A|DAB2IP_ENST00000259371.2_Missense_Mutation_p.T310A			Q5VWQ8	DAB2P_HUMAN	DAB2 interacting protein	338					activation of JUN kinase activity (GO:0007257)|activation of MAPKKK activity (GO:0000185)|angiogenesis (GO:0001525)|cell cycle (GO:0007049)|cell motility involved in cerebral cortex radial glia guided migration (GO:0021814)|cellular protein catabolic process (GO:0044257)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|layer formation in cerebral cortex (GO:0021819)|negative regulation of angiogenesis (GO:0016525)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of G0 to G1 transition (GO:0070317)|negative regulation of GTPase activity (GO:0034260)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphatidylinositol 3-kinase activity (GO:0043553)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of Ras GTPase activity (GO:0034261)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuron projection morphogenesis (GO:0048812)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of dendrite development (GO:1900006)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of synapse maturation (GO:0090129)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of ARF GTPase activity (GO:0032312)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein complex assembly (GO:0043254)|response to unfolded protein (GO:0006986)|transformed cell apoptotic process (GO:0006927)|tube formation (GO:0035148)|vascular endothelial growth factor receptor-2 signaling pathway (GO:0036324)	axon (GO:0030424)|cerebellar mossy fiber (GO:0044300)|climbing fiber (GO:0044301)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|neuronal cell body (GO:0043025)|neuronal cell body membrane (GO:0032809)|parallel fiber (GO:1990032)|plasma membrane (GO:0005886)	14-3-3 protein binding (GO:0071889)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|mitogen-activated protein kinase kinase binding (GO:0031434)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulatory subunit binding (GO:0036312)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein phosphatase 2A binding (GO:0051721)|Ras GTPase activator activity (GO:0005099)|SH3 domain binding (GO:0017124)|signaling adaptor activity (GO:0035591)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(8)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	27						CCAAACCATCACCATCCTGCC	0.607																																					p.T310A		Atlas-SNP	.											.	DAB2IP	150	.	0			c.A928G						.						100	72	81					9																	124522560		2203	4300	6503	SO:0001583	missense	153090	exon6			ACCATCACCATCC	AF367051	CCDS6832.1, CCDS6833.2	9q33.1-q33.3	2008-07-21			ENSG00000136848	ENSG00000136848			17294	protein-coding gene	gene with protein product	"nGAP-like protein", "DOC-2/DAB2 interactive protein", "ASK-interacting protein", "ASK1-interacting protein 1"	609205				11944990, 11812785	Standard	XM_005251721		Approved	AF9Q34, DIP1/2, KIAA1743, AIP1	uc004bln.3	Q5VWQ8	OTTHUMG00000020595	ENST00000408936.3:c.1012A>G	chr9.hg19:g.124522560A>G	ENSP00000386183:p.Thr338Ala	134.0	0.0		81.0	4.0	NM_032552	A6H8V2|A6NHI9|B0QZB1|G3XA90|Q8TDL2|Q96SE1|Q9C0C0	Missense_Mutation	SNP	ENST00000408936.3	hg19		.	.	.	.	.	.	.	.	.	.	A	14.99	2.701458	0.48307	.	.	ENSG00000136848	ENST00000436835;ENST00000259371;ENST00000408936;ENST00000373782;ENST00000309989	T;T;T;T;T	0.54071	0.59;2.3;2.3;2.2;2.2	4.33	4.33	0.51752	.	0.163089	0.64402	D	0.000003	T	0.41419	0.1158	L	0.36672	1.1	0.31871	N	0.619704	B	0.13145	0.007	B	0.15870	0.014	T	0.45086	-0.9285	9	.	.	.	.	12.9856	0.58590	1.0:0.0:0.0:0.0	.	310	G3XA90	.	A	214;310;338;247;214	ENSP00000409327:T214A;ENSP00000259371:T310A;ENSP00000386183:T338A;ENSP00000362887:T247A;ENSP00000310827:T214A	.	T	+	1	0	DAB2IP	123562381	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.471000	0.80985	1.723000	0.51488	0.459000	0.35465	ACC	.	.		0.607	DAB2IP-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317857.1	NM_032552		G	124522560	A	G	124522560	3	3	260	1	0	0	0	0	1	0	0	0	4221	159	6	2	950	2	DAB2IP	9	124522560	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	891076	124522560	16690871	418	37663										
DAB2IP	153090	hgsc.bcm.edu	37	chr9	124528986	124528986	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	accctcatcgccaaggtcacCcagaacctggccaactttgc	7	17	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:124528986C>T	ENST00000408936.3	+	9	1856	c.1674C>T	c.(1672-1674)acC>acT	p.T558T	DAB2IP_ENST00000309989.1_Silent_p.T434T|DAB2IP_ENST00000259371.2_Silent_p.T530T			Q5VWQ8	DAB2P_HUMAN	DAB2 interacting protein	558	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				activation of JUN kinase activity (GO:0007257)|activation of MAPKKK activity (GO:0000185)|angiogenesis (GO:0001525)|cell cycle (GO:0007049)|cell motility involved in cerebral cortex radial glia guided migration (GO:0021814)|cellular protein catabolic process (GO:0044257)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|layer formation in cerebral cortex (GO:0021819)|negative regulation of angiogenesis (GO:0016525)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of G0 to G1 transition (GO:0070317)|negative regulation of GTPase activity (GO:0034260)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphatidylinositol 3-kinase activity (GO:0043553)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of Ras GTPase activity (GO:0034261)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuron projection morphogenesis (GO:0048812)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of dendrite development (GO:1900006)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of synapse maturation (GO:0090129)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of ARF GTPase activity (GO:0032312)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein complex assembly (GO:0043254)|response to unfolded protein (GO:0006986)|transformed cell apoptotic process (GO:0006927)|tube formation (GO:0035148)|vascular endothelial growth factor receptor-2 signaling pathway (GO:0036324)	axon (GO:0030424)|cerebellar mossy fiber (GO:0044300)|climbing fiber (GO:0044301)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|neuronal cell body (GO:0043025)|neuronal cell body membrane (GO:0032809)|parallel fiber (GO:1990032)|plasma membrane (GO:0005886)	14-3-3 protein binding (GO:0071889)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|mitogen-activated protein kinase kinase binding (GO:0031434)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulatory subunit binding (GO:0036312)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein phosphatase 2A binding (GO:0051721)|Ras GTPase activator activity (GO:0005099)|SH3 domain binding (GO:0017124)|signaling adaptor activity (GO:0035591)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(8)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	27						CCAAGGTCACCCAGAACCTGG	0.632																																					p.T530T		Atlas-SNP	.											.	DAB2IP	150	.	0			c.C1590T						.						126	117	120					9																	124528986		2203	4300	6503	SO:0001819	synonymous_variant	153090	exon9			GGTCACCCAGAAC	AF367051	CCDS6832.1, CCDS6833.2	9q33.1-q33.3	2008-07-21			ENSG00000136848	ENSG00000136848			17294	protein-coding gene	gene with protein product	"nGAP-like protein", "DOC-2/DAB2 interactive protein", "ASK-interacting protein", "ASK1-interacting protein 1"	609205				11944990, 11812785	Standard	XM_005251721		Approved	AF9Q34, DIP1/2, KIAA1743, AIP1	uc004bln.3	Q5VWQ8	OTTHUMG00000020595	ENST00000408936.3:c.1674C>T	chr9.hg19:g.124528986C>T		165.0	0.0		97.0	4.0	NM_032552	A6H8V2|A6NHI9|B0QZB1|G3XA90|Q8TDL2|Q96SE1|Q9C0C0	Silent	SNP	ENST00000408936.3	hg19																																																																																				.	.		0.632	DAB2IP-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317857.1	NM_032552		T	124528986	C	T	124528986	2	4	260	1	0	0	0	0	0	0	0	1	4221	610	22	3		3	DAB2IP	9	124528986	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	6426	124528986	16684445	419	37664										
ZNF79	7633	hgsc.bcm.edu	37	chr9	130206630	130206630	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	catcagaagagccacactggAgagaagccctatgagtgcag	12	10	1	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:130206630A>G	ENST00000342483.5	+	5	1057	c.651A>G	c.(649-651)ggA>ggG	p.G217G	ZNF79_ENST00000543471.1_Silent_p.G193G	NM_007135.2	NP_009066.2	Q15937	ZNF79_HUMAN	zinc finger protein 79	217					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|stomach(2)	28						GCCACACTGGAGAGAAGCCCT	0.478																																					p.G217G		Atlas-SNP	.											.	ZNF79	47	.	0			c.A651G						.						89	86	87					9																	130206630		2203	4300	6503	SO:0001819	synonymous_variant	7633	exon5			CACTGGAGAGAAG	X65232	CCDS6871.1, CCDS69664.1, CCDS75904.1	9q34	2013-01-08	2006-05-12		ENSG00000196152	ENSG00000196152		"Zinc fingers, C2H2-type"	13153	protein-coding gene	gene with protein product		194552	"zinc finger protein 79 (pT7)"			8478004	Standard	NM_007135		Approved	pT7	uc004bqw.4	Q15937	OTTHUMG00000020703	ENST00000342483.5:c.651A>G	chr9.hg19:g.130206630A>G		109.0	0.0		66.0	4.0	NM_007135	Q5VVW1|Q96NV1	Silent	SNP	ENST00000342483.5	hg19	CCDS6871.1																																																																																			.	.		0.478	ZNF79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054188.1	NM_007135		G	130206630	A	G	130206630	2	3	260	1	0	0	0	0	0	0	0	1	18176	291	11	2		2	ZNF79	9	130206630	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	5677644	130206630	11006801	420	37665										
FAM129B	64855	hgsc.bcm.edu	37	chr9	130279252	130279252	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tggacagcacctcctcgaagCgcgccttggcctgctcgtac	11	16	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:130279252C>A	ENST00000373312.3	-	8	1070	c.857G>T	c.(856-858)cGc>cTc	p.R286L	FAM129B_ENST00000373314.3_Missense_Mutation_p.R273L|FAM129B_ENST00000468379.1_Intron	NM_022833.2	NP_073744.2	Q96TA1	NIBL1_HUMAN	family with sequence similarity 129, member B	286					negative regulation of apoptotic process (GO:0043066)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R286H(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25						CTCCTCGAAGCGCGCCTTGGC	0.617																																					p.R286L		Atlas-SNP	.											FAM129B_ENST00000373314,NS,carcinoma,0,2	FAM129B	84	.	1	Substitution - Missense(1)	endometrium(1)	c.G857T						.						157	142	147					9																	130279252		2203	4300	6503	SO:0001583	missense	64855	exon8			TCGAAGCGCGCCT	AF151783	CCDS35144.1, CCDS35145.1	9q34.13	2010-02-01	2006-11-23	2006-11-23	ENSG00000136830	ENSG00000136830			25282	protein-coding gene	gene with protein product		614045	"chromosome 9 open reading frame 88"	C9orf88		14702039, 19362540	Standard	XM_005252135		Approved	DKFZP434H0820, FLJ13518, FLJ22151, FLJ22298, bA356B19.6, MINERVA	uc004brh.3	Q96TA1	OTTHUMG00000020705	ENST00000373312.3:c.857G>T	chr9.hg19:g.130279252C>A	ENSP00000362409:p.Arg286Leu	78.0	0.0		68.0	3.0	NM_022833	Q4LE55|Q5VVW6|Q5VVW7|Q9BUS2|Q9NT35	Missense_Mutation	SNP	ENST00000373312.3	hg19	CCDS35145.1	.	.	.	.	.	.	.	.	.	.	C	0.144	-1.099349	0.01843	.	.	ENSG00000136830	ENST00000373314;ENST00000373312	T;T	0.23147	1.92;1.92	4.87	-1.84	0.07809	.	0.626027	0.17484	N	0.172589	T	0.11922	0.0290	L	0.29908	0.895	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.34153	-0.9840	10	0.09084	T	0.74	-6.4907	4.842	0.13494	0.1702:0.2062:0.0:0.6236	.	273;286	Q96TA1-2;Q96TA1	.;NIBL1_HUMAN	L	273;286	ENSP00000362411:R273L;ENSP00000362409:R286L	ENSP00000362409:R286L	R	-	2	0	FAM129B	129319073	0.969000	0.33509	0.014000	0.15608	0.034000	0.12701	0.348000	0.20031	-0.207000	0.10187	-0.140000	0.14226	CGC	.	.		0.617	FAM129B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054196.1	NM_022833		A	130279252	C	A	130279252	3	1	260	1	0	0	0	0	1	0	0	0	5442	768	27	1	1411	1	FAM129B	9	130279252	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	72622	130279252	10934179	421	37666										
SPTAN1	6709	hgsc.bcm.edu	37	chr9	131344805	131344805	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	attcagaacaaccactatgcAatggaagatgtggccactcg	9	10	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:131344805A>G	ENST00000372731.4	+	13	1730	c.1620A>G	c.(1618-1620)gcA>gcG	p.A540A	SPTAN1_ENST00000372739.3_Silent_p.A540A|SPTAN1_ENST00000358161.5_Silent_p.A540A	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	540					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						ACCACTATGCAATGGAAGATG	0.418																																					p.A540A	NSCLC(120;833 1744 2558 35612 37579)	Atlas-SNP	.											.	SPTAN1	266	.	0			c.A1620G						.						178	171	173					9																	131344805		2203	4300	6503	SO:0001819	synonymous_variant	6709	exon13			CTATGCAATGGAA	M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"EF-hand domain containing"	11273	protein-coding gene	gene with protein product	"alpha-fodrin"	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.1620A>G	chr9.hg19:g.131344805A>G		138.0	0.0		93.0	4.0	NM_003127	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Silent	SNP	ENST00000372731.4	hg19	CCDS6905.1																																																																																			.	.		0.418	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127		G	131344805	A	G	131344805	2	3	260	1	0	0	0	0	0	0	0	1	15132	117	5	2		2	SPTAN1	9	131344805	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1065553	131344805	9868626	422	37667										
ZER1	10444	hgsc.bcm.edu	37	chr9	131502396	131502396	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cggccttgctctccaacaggTtgctgccaggagaaagacag	12	12	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:131502396T>C	ENST00000291900.2	-	13	2262	c.1856A>G	c.(1855-1857)aAc>aGc	p.N619S		NM_006336.2	NP_006327.2	Q7Z7L7	ZER1_HUMAN	zyg-11 related, cell cycle regulator	619					protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein transferase activity (GO:0051438)	Cul2-RING ubiquitin ligase complex (GO:0031462)	ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	15						CTCCAACAGGTTGCTGCCAGG	0.557																																					p.N619S		Atlas-SNP	.											.	ZER1	49	.	0			c.A1856G						.						36	32	34					9																	131502396		2203	4300	6503	SO:0001583	missense	10444	exon13			AACAGGTTGCTGC	X99802	CCDS6910.1	9q33.3	2013-01-17	2012-12-10	2007-01-04	ENSG00000160445	ENSG00000160445		"ZYG11 cell cycle regulator family"	30960	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 60", "zyg-11 homolog B (C. elegans)-like", "zer-1 homolog (C. elegans)"	C9orf60, ZYG11BL		11719588	Standard	NM_006336		Approved	ZYG, Hzyg	uc004bwa.2	Q7Z7L7	OTTHUMG00000020759	ENST00000291900.2:c.1856A>G	chr9.hg19:g.131502396T>C	ENSP00000291900:p.Asn619Ser	186.0	0.0		100.0	4.0	NM_006336	O00156|Q5T272|Q5T273	Missense_Mutation	SNP	ENST00000291900.2	hg19	CCDS6910.1	.	.	.	.	.	.	.	.	.	.	T	10.49	1.363733	0.24684	.	.	ENSG00000160445	ENST00000291900	T	0.63913	-0.07	4.78	4.78	0.61160	Armadillo-like helical (1);Armadillo-type fold (1);	0.236047	0.48767	D	0.000162	T	0.38295	0.1035	N	0.08118	0	0.52099	D	0.999941	B	0.14012	0.009	B	0.12837	0.008	T	0.29058	-1.0024	10	0.07325	T	0.83	-44.0297	13.6502	0.62306	0.0:0.0:0.0:1.0	.	619	Q7Z7L7	ZER1_HUMAN	S	619	ENSP00000291900:N619S	ENSP00000291900:N619S	N	-	2	0	ZER1	130542217	1.000000	0.71417	1.000000	0.80357	0.191000	0.23601	5.602000	0.67612	1.995000	0.58328	0.454000	0.30748	AAC	.	.		0.557	ZER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054491.1	NM_006336		C	131502396	T	C	131502396	3	2	260	1	0	0	0	0	1	0	0	0	17640	1725	60	2	460	2	ZER1	9	131502396	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	157591	131502396	9711035	423	37668										
NUP188	23511	hgsc.bcm.edu	37	chr9	131750464	131750464	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gaacaggctctctcacaacaTggtatgtatttctcttccag	7	11	3	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:131750464T>C	ENST00000372577.2	+	24	2553	c.2532T>C	c.(2530-2532)caT>caC	p.H844H		NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	844					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				breast(2)|central_nervous_system(3)|endometrium(6)|kidney(4)|large_intestine(9)|lung(20)|ovary(6)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	60						TCTCACAACATGGTATGTATT	0.423																																					p.H844H		Atlas-SNP	.											.	NUP188	140	.	0			c.T2532C						.						215	203	207					9																	131750464		2203	4300	6503	SO:0001630	splice_region_variant	23511	exon24			ACAACATGGTATG	D79991	CCDS35156.1	9q34.13	2014-01-28	2004-03-19	2004-03-24	ENSG00000095319	ENSG00000095319			17859	protein-coding gene	gene with protein product		615587	"KIAA0169"	KIAA0169		11029043	Standard	NM_015354		Approved		uc004bws.2	Q5SRE5	OTTHUMG00000020768	ENST00000372577.2:c.2533+1T>C	chr9.hg19:g.131750464T>C		155.0	0.0		98.0	4.0	NM_015354	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Silent	SNP	ENST00000372577.2	hg19	CCDS35156.1																																																																																			.	.		0.423	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2		Silent	C	131750464	T	C	131750464	5	2	260	1	0	0	0	0	0	0	1	0	10767	1478	51	2	2626	2	NUP188	9	131750464	Splice_Site	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	248068	131750464	9462967	424	37669										
IER5L	389792	hgsc.bcm.edu	37	chr9	131939318	131939318	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tccgggcagaagtcctcgaaGcgggcgcgcttgcagggggc	18	12	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:131939318G>T	ENST00000372491.2	-	1	1222	c.1014C>A	c.(1012-1014)cgC>cgA	p.R338R	RP11-247A12.2_ENST00000372490.3_RNA|RP11-247A12.8_ENST00000599172.2_RNA	NM_203434.2	NP_982258.2	Q5T953	IER5L_HUMAN	immediate early response 5-like	338													Ovarian(14;0.0448)|Medulloblastoma(224;0.235)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0178)		AGTCCTCGAAGCGGGCGCGCT	0.701																																					p.R338R		Atlas-SNP	.											.	IER5L	4	.	0			c.C1014A						.						9	12	11					9																	131939318		1789	4039	5828	SO:0001819	synonymous_variant	389792	exon1			CTCGAAGCGGGCG	BC013070	CCDS43888.1	9q34.11	2013-09-20			ENSG00000188483	ENSG00000188483			23679	protein-coding gene	gene with protein product							Standard	NM_203434		Approved	bA247A12.2	uc010myt.1	Q5T953	OTTHUMG00000020773	ENST00000372491.2:c.1014C>A	chr9.hg19:g.131939318G>T		84.0	0.0		77.0	4.0	NM_203434	Q6P3E2	Silent	SNP	ENST00000372491.2	hg19	CCDS43888.1																																																																																			.	.		0.701	IER5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054556.2			T	131939318	G	T	131939318	2	4	260	1	0	0	0	0	0	0	0	1	7518	958	34	3		3	IER5L	9	131939318	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	188854	131939318	9274113	425	37670										
ABL1	25	hgsc.bcm.edu	37	chr9	133761037	133761037	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttcagcaagctcctcagttcGgtgaaggaaatcagtgacat	10	9	3	2	rs148391456		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:133761037G>T	ENST00000318560.5	+	11	3741	c.3360G>T	c.(3358-3360)tcG>tcT	p.S1120S		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	1120	F-actin-binding.				actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)			breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	TCCTCAGTTCGGTGAAGGAAA	0.592			"T, Mis"	"BCR, ETV6, NUP214"	"CML, ALL, T-ALL"																																p.S1139S		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.G3417T						.						24	27	26					9																	133761037		2200	4300	6500	SO:0001819	synonymous_variant	25	exon11			CAGTTCGGTGAAG	M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"SH2 domain containing"	76	protein-coding gene	gene with protein product		189980	"v-abl Abelson murine leukemia viral oncogene homolog 1", "c-abl oncogene 1, receptor tyrosine kinase", "c-abl oncogene 1, non-receptor tyrosine kinase"	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.3360G>T	chr9.hg19:g.133761037G>T		121.0	0.0		76.0	4.0	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Silent	SNP	ENST00000318560.5	hg19	CCDS35166.1																																																																																			.	G|1.000;A|0.000		0.592	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313		T	133761037	G	T	133761037	2	4	260	1	0	0	0	0	0	0	0	1	92	1103	39	1		1	ABL1	9	133761037	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	1821719	133761037	7452394	426	37671										
RAPGEF1	2889	hgsc.bcm.edu	37	chr9	134471699	134471699	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccctacctttcctgtcagtcTcagtagcatggaccagtaag	8	13	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:134471699T>C	ENST00000372189.3	-	14	2240	c.2117A>G	c.(2116-2118)gAg>gGg	p.E706G	RAPGEF1_ENST00000372190.3_Missense_Mutation_p.E724G|RAPGEF1_ENST00000372195.1_Missense_Mutation_p.E723G	NM_005312.2	NP_005303.2	Q13905	RPGF1_HUMAN	Rap guanine nucleotide exchange factor (GEF) 1	706	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				activation of MAPKK activity (GO:0000186)|blood vessel development (GO:0001568)|cellular response to cAMP (GO:0071320)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of Ras protein signal transduction (GO:0046580)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of neuron projection development (GO:0010976)|positive regulation of Rap GTPase activity (GO:0032854)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)	Rap guanyl-nucleotide exchange factor activity (GO:0017034)			NS(2)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	39		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.19e-05)|Epithelial(140;0.000364)		CCTGTCAGTCTCAGTAGCATG	0.597																																					p.E724G		Atlas-SNP	.											.	RAPGEF1	126	.	0			c.A2171G						.						90	103	99					9																	134471699		2129	4237	6366	SO:0001583	missense	2889	exon14			TCAGTCTCAGTAG	BC041710	CCDS48047.1	9q34.3	2008-02-05	2004-03-01	2004-03-02	ENSG00000107263	ENSG00000107263			4568	protein-coding gene	gene with protein product		600303	"guanine nucleotide-releasing factor 2 (specific for crk proto-oncogene)"	GRF2		7959692, 7512734	Standard	NM_005312		Approved	C3G	uc022bos.1	Q13905	OTTHUMG00000020829	ENST00000372189.3:c.2117A>G	chr9.hg19:g.134471699T>C	ENSP00000361263:p.Glu706Gly	162.0	0.0		113.0	5.0	NM_198679	Q5JUE4|Q8IV73	Missense_Mutation	SNP	ENST00000372189.3	hg19	CCDS48047.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.37|16.37	3.104034|3.104034	0.56291|0.56291	.|.	.|.	ENSG00000107263|ENSG00000107263	ENST00000266110;ENST00000372195;ENST00000429421;ENST00000372189;ENST00000372190;ENST00000411834;ENST00000337036;ENST00000398415;ENST00000357686|ENST00000414781	T;T;T|.	0.30981|.	1.51;1.51;1.51|.	5.57|5.57	5.57|5.57	0.84162|0.84162	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (3);|.	0.163809|.	0.53938|.	D|.	0.000047|.	T|.	0.52041|.	0.1710|.	N|N	0.22421|0.22421	0.69|0.69	0.58432|0.58432	D|D	0.999996|0.999996	B;B;B|.	0.11235|.	0.003;0.001;0.004|.	B;B;B|.	0.09377|.	0.004;0.004;0.002|.	T|.	0.49224|.	-0.8962|.	10|.	0.72032|.	D|.	0.01|.	.|.	14.9109|14.9109	0.70755|0.70755	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	723;706;724|.	Q68DL3;Q13905;Q13905-3|.	.;RPGF1_HUMAN;.|.	G|W	706;723;652;706;724;686;684;151;723|133	ENSP00000361269:E723G;ENSP00000361263:E706G;ENSP00000361264:E724G|.	ENSP00000266110:E706G|.	E|X	-|-	2|3	0|0	RAPGEF1|RAPGEF1	133461520|133461520	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.845000|0.845000	0.48019|0.48019	7.666000|7.666000	0.83877|0.83877	2.113000|2.113000	0.64589|0.64589	0.459000|0.459000	0.35465|0.35465	GAG|TGA	.	.		0.597	RAPGEF1-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054759.2	NM_005312		C	134471699	T	C	134471699	3	2	260	1	0	0	0	0	1	0	0	0	13058	1551	54	2	1160	2	RAPGEF1	9	134471699	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	710662	134471699	6741732	427	37672										
SETX	23064	hgsc.bcm.edu	37	chr9	135204839	135204839	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgtatatgaagagatctcttTtacagacttctgcttccttg	7	8	2	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:135204839T>C	ENST00000224140.5	-	10	2328	c.2146A>G	c.(2146-2148)Aaa>Gaa	p.K716E	SETX_ENST00000372169.2_Missense_Mutation_p.K716E|SETX_ENST00000393220.1_Missense_Mutation_p.K716E	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	716					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		GAGATCTCTTTTACAGACTTC	0.363																																					p.K716E		Atlas-SNP	.											.	SETX	234	.	0			c.A2146G						.						94	98	97					9																	135204839		2203	4299	6502	SO:0001583	missense	23064	exon10			TCTCTTTTACAGA	AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"amyotrophic lateral sclerosis 4", "spinocerebellar ataxia, recessive, non-Friedreich type 1"	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.2146A>G	chr9.hg19:g.135204839T>C	ENSP00000224140:p.Lys716Glu	99.0	0.0		93.0	4.0	NM_015046	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Missense_Mutation	SNP	ENST00000224140.5	hg19	CCDS6947.1	.	.	.	.	.	.	.	.	.	.	T	11.25	1.584220	0.28268	.	.	ENSG00000107290	ENST00000224140;ENST00000372169;ENST00000393220	D;D;D	0.87103	-2.11;-2.21;-1.82	5.79	0.586	0.17434	.	2.353210	0.01295	N	0.010147	T	0.77592	0.4153	N	0.19112	0.55	0.09310	N	1	B;B;B	0.09022	0.002;0.0;0.002	B;B;B	0.09377	0.004;0.002;0.004	T	0.62144	-0.6916	10	0.27082	T	0.32	.	4.9734	0.14127	0.0:0.2675:0.154:0.5786	.	716;716;716	Q7Z333-3;Q7Z333;Q7Z333-4	.;SETX_HUMAN;.	E	716	ENSP00000224140:K716E;ENSP00000361242:K716E;ENSP00000376913:K716E	ENSP00000224140:K716E	K	-	1	0	SETX	134194660	0.000000	0.05858	0.000000	0.03702	0.097000	0.18754	0.598000	0.24074	0.472000	0.27344	0.533000	0.62120	AAA	.	.		0.363	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046		C	135204839	T	C	135204839	3	2	260	1	0	0	0	0	1	0	0	0	14156	1850	64	2	5955	2	SETX	9	135204839	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	733140	135204839	6008592	428	37673										
RPL7A	6130	hgsc.bcm.edu	37	chr9	136217542	136217542	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gactgggacgtctagtccacAggaagacctgcaccactgtc	11	13	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:136217542A>G	ENST00000323345.6	+	6	616	c.586A>G	c.(586-588)Agg>Ggg	p.R196G	SNORD36A_ENST00000362874.1_RNA|SURF1_ENST00000495952.1_5'Flank|SNORD36B_ENST00000363961.1_RNA|MED22_ENST00000344469.5_5'Flank|MED22_ENST00000491289.1_5'Flank|RPL7A_ENST00000463740.1_3'UTR|SNORD36C_ENST00000516733.1_RNA|MED22_ENST00000471524.1_5'Flank|MED22_ENST00000476080.1_5'Flank|SNORD24_ENST00000383884.1_RNA|MED22_ENST00000371999.1_5'Flank|MED22_ENST00000343730.5_5'Flank|RPL7A_ENST00000315731.4_Missense_Mutation_p.R81G	NM_000972.2	NP_000963.1	P62424	RL7A_HUMAN	ribosomal protein L7a	196					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosome biogenesis (GO:0042254)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			cervix(1)|endometrium(1)|kidney(1)|lung(3)|upper_aerodigestive_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(145;4.93e-07)|Epithelial(140;4.09e-06)|all cancers(34;3.78e-05)		TCTAGTCCACAGGAAGACCTG	0.517																																					p.R196G		Atlas-SNP	.											.	RPL7A	9	.	0			c.A586G						.						60	58	59					9																	136217542		2203	4298	6501	SO:0001583	missense	6130	exon6			GTCCACAGGAAGA	BC005128	CCDS6965.1	9q34	2011-04-06			ENSG00000148303	ENSG00000148303		"L ribosomal proteins"	10364	protein-coding gene	gene with protein product	"surfeit 3", "PLA-X polypeptide", "surfeit locus protein 3", "60S ribosomal protein L7a", ";", "thyroid hormone receptor uncoupling protein"	185640				2403926, 2966065	Standard	NM_000972		Approved	SURF3, TRUP, L7A	uc004cde.1	P62424	OTTHUMG00000020864	ENST00000323345.6:c.586A>G	chr9.hg19:g.136217542A>G	ENSP00000361076:p.Arg196Gly	107.0	0.0		78.0	4.0	NM_000972	P11518|Q5T8U4	Missense_Mutation	SNP	ENST00000323345.6	hg19	CCDS6965.1	.	.	.	.	.	.	.	.	.	.	A	16.74	3.208163	0.58343	.	.	ENSG00000148303	ENST00000323345;ENST00000315731	T;T	0.58506	0.33;0.33	5.73	3.28	0.37604	Ribosomal protein L7Ae/L30e/S12e/Gadd45 (1);	0.000000	0.85682	D	0.000000	T	0.69726	0.3143	M	0.88842	2.985	0.80722	D	1	B	0.19817	0.039	B	0.38683	0.279	T	0.69320	-0.5176	10	0.87932	D	0	.	11.8559	0.52437	0.7219:0.2781:0.0:0.0	.	196	P62424	RL7A_HUMAN	G	196;81	ENSP00000361076:R196G;ENSP00000361071:R81G	ENSP00000361071:R81G	R	+	1	2	RPL7A	135207363	1.000000	0.71417	1.000000	0.80357	0.869000	0.49853	4.469000	0.60169	0.395000	0.25257	-0.313000	0.08912	AGG	.	.		0.517	RPL7A-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054869.1	NM_000972		G	136217542	A	G	136217542	3	3	260	1	0	0	0	0	1	0	0	0	13615	179	7	2	608	2	RPL7A	9	136217542	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1012703	136217542	4995889	429	37674										
SLC2A6	11182	hgsc.bcm.edu	37	chr9	136339170	136339170	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cggcgatcagcacggacaggAgccgcacggccccaacgatg	14	15	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:136339170A>G	ENST00000371899.4	-	7	1045	c.968T>C	c.(967-969)cTc>cCc	p.L323P	SLC2A6_ENST00000371897.4_Missense_Mutation_p.L323P|SLC2A6_ENST00000485978.1_5'UTR	NM_017585.3	NP_060055.2	Q9UGQ3	GTR6_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 6	323					glucose transport (GO:0015758)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glucose transmembrane transporter activity (GO:0005355)			cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(3)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(145;8.47e-08)|Epithelial(140;9.37e-07)|all cancers(34;1.03e-05)		CACGGACAGGAGCCGCACGGC	0.687																																					p.L323P		Atlas-SNP	.											.	SLC2A6	31	.	0			c.T968C						.						32	28	29					9																	136339170		2196	4297	6493	SO:0001583	missense	11182	exon7			GACAGGAGCCGCA	AJ011372	CCDS6975.1, CCDS48052.1	9q34	2013-05-22			ENSG00000160326	ENSG00000160326		"Solute carriers"	11011	protein-coding gene	gene with protein product		606813				10970791	Standard	NM_001145099		Approved	GLUT9, GLUT6, HSA011372	uc004cee.3	Q9UGQ3	OTTHUMG00000020874	ENST00000371899.4:c.968T>C	chr9.hg19:g.136339170A>G	ENSP00000360966:p.Leu323Pro	143.0	0.0		95.0	4.0	NM_017585	A6NNU6|Q5SXD7|Q8NCC2	Missense_Mutation	SNP	ENST00000371899.4	hg19	CCDS6975.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.292352	0.80914	.	.	ENSG00000160326	ENST00000371897;ENST00000371899	T;T	0.75154	-0.91;-0.91	5.48	5.48	0.80851	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.87669	0.6235	M	0.87547	2.89	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.89852	0.4010	10	0.87932	D	0	.	14.7329	0.69397	1.0:0.0:0.0:0.0	.	323;323	Q9UGQ3-2;Q9UGQ3	.;GTR6_HUMAN	P	323	ENSP00000360964:L323P;ENSP00000360966:L323P	ENSP00000360964:L323P	L	-	2	0	SLC2A6	135328991	1.000000	0.71417	0.957000	0.39632	0.763000	0.43281	8.563000	0.90723	2.092000	0.63282	0.459000	0.35465	CTC	.	.		0.687	SLC2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054909.1	NM_017585		G	136339170	A	G	136339170	3	3	260	1	0	0	0	0	1	0	0	0	14564	304	11	2	571	2	SLC2A6	9	136339170	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	121628	136339170	4874261	430	37675										
CAMSAP1	157922	hgsc.bcm.edu	37	chr9	138773507	138773507	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tccagaacaccatggcatccTcgaggtcgtacggaagttct	10	12	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:138773507T>C	ENST00000389532.4	-	3	621	c.557A>G	c.(556-558)gAg>gGg	p.E186G	CAMSAP1_ENST00000312405.6_5'UTR|CAMSAP1_ENST00000409386.3_Missense_Mutation_p.E186G	NM_015447.3	NP_056262.3	Q5T5Y3	CAMP1_HUMAN	calmodulin regulated spectrin-associated protein 1	186	CH.				cytoskeleton organization (GO:0007010)|neuron projection development (GO:0031175)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|spectrin binding (GO:0030507)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(11)|lung(16)|ovary(3)|pancreas(1)|skin(1)	47				OV - Ovarian serous cystadenocarcinoma(145;1.4e-06)|Epithelial(140;1.11e-05)		CATGGCATCCTCGAGGTCGTA	0.537																																					p.E186G		Atlas-SNP	.											.	CAMSAP1	142	.	0			c.A557G						.						229	182	197					9																	138773507		692	1591	2283	SO:0001583	missense	157922	exon3			GCATCCTCGAGGT	AJ519841	CCDS35176.2	9q34.3	2008-02-05			ENSG00000130559	ENSG00000130559			19946	protein-coding gene	gene with protein product		613774				12477932	Standard	NM_015447		Approved	FLJ31228, DKFZp434F195	uc004cgr.4	Q5T5Y3	OTTHUMG00000020918	ENST00000389532.4:c.557A>G	chr9.hg19:g.138773507T>C	ENSP00000374183:p.Glu186Gly	174.0	0.0		99.0	4.0	NM_015447	A1L4L2|B2REB2|B2REB3|Q70W33|Q8NCY0|Q96E80|Q96FM3|Q9UFJ5	Missense_Mutation	SNP	ENST00000389532.4	hg19	CCDS35176.2	.	.	.	.	.	.	.	.	.	.	T	24.2	4.502151	0.85176	.	.	ENSG00000130559	ENST00000389532;ENST00000409386	D;T	0.96651	-4.08;1.47	5.76	5.76	0.90799	Calponin homology domain (1);	0.127583	0.51477	U	0.000090	D	0.97810	0.9281	M	0.72894	2.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.98674	1.0689	10	0.87932	D	0	-26.1351	16.3544	0.83230	0.0:0.0:0.0:1.0	.	186;186	Q5T5Y3;Q5T5Y3-3	CAMP1_HUMAN;.	G	186	ENSP00000374183:E186G;ENSP00000386420:E186G	ENSP00000374183:E186G	E	-	2	0	CAMSAP1	137913328	1.000000	0.71417	0.998000	0.56505	0.510000	0.34073	7.831000	0.86748	2.319000	0.78375	0.533000	0.62120	GAG	.	.		0.537	CAMSAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055024.2	XM_351857		C	138773507	T	C	138773507	3	2	260	1	0	0	0	0	1	0	0	0	2613	1551	54	2	4311	2	CAMSAP1	9	138773507	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	2434337	138773507	2439924	431	37676										
NACC2	138151	hgsc.bcm.edu	37	chr9	138905769	138905769	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttatgcttcacccctgcacaCaggtggcagttcatcagctg	9	13	3	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:138905769C>T	ENST00000371753.1	-	3	1156	c.1098G>A	c.(1096-1098)ctG>ctA	p.L366L	NACC2_ENST00000277554.2_Silent_p.L366L|NACC2_ENST00000467669.1_5'Flank			Q96BF6	NACC2_HUMAN	NACC family member 2, BEN and BTB (POZ) domain containing	366	BEN. {ECO:0000255|PROSITE- ProRule:PRU00784}.				cellular protein complex localization (GO:0034629)|histone deacetylation (GO:0016575)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle by negative regulation of transcription from RNA polymerase II promoter (GO:1900477)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|posttranscriptional regulation of gene expression (GO:0010608)|protein homooligomerization (GO:0051260)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)			endometrium(2)|kidney(1)|lung(1)|urinary_tract(1)	5						CCCCTGCACACAGGTGGCAGT	0.617																																					p.L366L		Atlas-SNP	.											.	NACC2	16	.	0			c.G1098A						.						64	47	53					9																	138905769		2202	4300	6502	SO:0001819	synonymous_variant	138151	exon4			TGCACACAGGTGG	BC015649	CCDS6993.1	9q34.3	2013-01-09	2008-10-03	2008-10-03	ENSG00000148411	ENSG00000148411		"BEN domain containing", "BTB/POZ domain containing"	23846	protein-coding gene	gene with protein product	"BEN domain containing 9"	615786	"BTB (POZ) domain containing 14A"	BTBD14A		12477932	Standard	NM_144653		Approved	MGC23427, BEND9, BTBD31	uc004cgv.4	Q96BF6	OTTHUMG00000020921	ENST00000371753.1:c.1098G>A	chr9.hg19:g.138905769C>T		93.0	0.0		72.0	4.0	NM_144653		Silent	SNP	ENST00000371753.1	hg19	CCDS6993.1																																																																																			.	.		0.617	NACC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055040.1	NM_144653		T	138905769	C	T	138905769	2	4	260	1	0	0	0	0	0	0	0	1	10145	465	17	3		3	NACC2	9	138905769	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	132262	138905769	2307662	432	37677										
INPP5E	56623	hgsc.bcm.edu	37	chr9	139327478	139327478	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctgatgcccaaggcccccttGgtcttgatctgagacacgat	10	13	2	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:139327478G>A	ENST00000371712.3	-	5	1611	c.1209C>T	c.(1207-1209)acC>acT	p.T403T		NM_019892.4	NP_063945.2	Q10713	MPPA_HUMAN	inositol polyphosphate-5-phosphatase, 72 kDa	0					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|endometrium(1)|lung(4)|skin(3)	9		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.36e-06)|Epithelial(140;1.4e-05)		AGGCCCCCTTGGTCTTGATCT	0.597																																					p.T403T		Atlas-SNP	.											.	INPP5E	18	.	0			c.C1209T						.						188	169	175					9																	139327478		2200	4300	6500	SO:0001819	synonymous_variant	56623	exon5			CCCCTTGGTCTTG	AF187891	CCDS7000.1	9q34.3	2011-02-11			ENSG00000148384	ENSG00000148384			21474	protein-coding gene	gene with protein product		613037	"Joubert syndrome 1"	JBTS1		10764818, 10577920, 19668216	Standard	NM_019892		Approved	PPI5PIV, CORS1	uc004cho.3	Q9NRR6	OTTHUMG00000020927	ENST00000371712.3:c.1209C>T	chr9.hg19:g.139327478G>A		206.0	0.0		115.0	5.0	NM_019892	B4DKL3|E7ET61|Q16639|Q5SXM9|Q8N513	Silent	SNP	ENST00000371712.3	hg19	CCDS7000.1																																																																																			.	.		0.597	INPP5E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055058.1	NM_019892		A	139327478	G	A	139327478	2	1	260	1	0	0	0	0	0	0	0	1	7766	1335	47	3		3	INPP5E	9	139327478	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	421709	139327478	1885953	433	37678										
ANAPC2	29882	hgsc.bcm.edu	37	chr9	140082406	140082406	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gagatggcattccagaactcAggggagatgttggcctgcag	15	8	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:140082406A>G	ENST00000323927.2	-	2	271	c.267T>C	c.(265-267)ccT>ccC	p.P89P	SSNA1_ENST00000322310.5_5'Flank	NM_013366.3	NP_037498.1	Q9UJX6	ANC2_HUMAN	anaphase promoting complex subunit 2	89					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of axon extension (GO:0045773)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)				breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	15	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.000858)		TCCAGAACTCAGGGGAGATGT	0.617																																					p.P89P		Atlas-SNP	.											.	ANAPC2	57	.	0			c.T267C						.						84	87	86					9																	140082406		2203	4300	6503	SO:0001819	synonymous_variant	29882	exon2			GAACTCAGGGGAG	AB037827	CCDS7033.1	9q34.3	2011-06-15			ENSG00000176248	ENSG00000176248		"Anaphase promoting complex subunits"	19989	protein-coding gene	gene with protein product		606946				11739784	Standard	NM_013366		Approved	APC2, KIAA1406	uc004clr.1	Q9UJX6	OTTHUMG00000020983	ENST00000323927.2:c.267T>C	chr9.hg19:g.140082406A>G		166.0	0.0		98.0	4.0	NM_013366	Q5VSG1|Q96DG5|Q96GG4|Q9P2E1	Silent	SNP	ENST00000323927.2	hg19	CCDS7033.1																																																																																			.	.		0.617	ANAPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055315.1	NM_013366		G	140082406	A	G	140082406	2	3	260	1	0	0	0	0	0	0	0	1	603	175	7	2		2	ANAPC2	9	140082406	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	754928	140082406	1131025	434	37679										
CACNA1B	774	hgsc.bcm.edu	37	chr9	140777329	140777329	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	catggacttcgtggtcgtccTcacagggtaggcaagctgag	14	10	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr9:140777329T>C	ENST00000371372.1	+	3	669	c.524T>C	c.(523-525)cTc>cCc	p.L175P	CACNA1B_ENST00000371355.4_Missense_Mutation_p.L175P|CACNA1B_ENST00000371363.1_Missense_Mutation_p.L175P|CACNA1B_ENST00000277551.2_Missense_Mutation_p.L175P|RP11-188C12.3_ENST00000371390.1_RNA|CACNA1B_ENST00000371357.1_Missense_Mutation_p.L175P|CACNA1B_ENST00000277549.5_5'UTR	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	175					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	GTGGTCGTCCTCACAGGGTAG	0.617																																					p.L175P		Atlas-SNP	.											.	CACNA1B	266	.	0			c.T524C						.						164	177	173					9																	140777329		2132	4252	6384	SO:0001583	missense	774	exon3			TCGTCCTCACAGG	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.524T>C	chr9.hg19:g.140777329T>C	ENSP00000360423:p.Leu175Pro	155.0	0.0		65.0	4.0	NM_001243812	B1AQK5	Missense_Mutation	SNP	ENST00000371372.1	hg19	CCDS59522.1	.	.	.	.	.	.	.	.	.	.	T	16.44	3.124015	0.56613	.	.	ENSG00000148408	ENST00000371372;ENST00000277551;ENST00000371363;ENST00000371357;ENST00000371355	D;D;D;D;D	0.98926	-5.24;-5.24;-5.24;-5.24;-5.24	4.57	4.57	0.56435	.	0.000000	0.64402	D	0.000009	D	0.99187	0.9718	M	0.90309	3.105	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.99271	1.0893	10	0.72032	D	0.01	.	13.9392	0.64043	0.0:0.0:0.0:1.0	.	175	B1AQK6	.	P	175	ENSP00000360423:L175P;ENSP00000277551:L175P;ENSP00000360414:L175P;ENSP00000360408:L175P;ENSP00000360406:L175P	ENSP00000277551:L175P	L	+	2	0	CACNA1B	139897150	1.000000	0.71417	1.000000	0.80357	0.529000	0.34654	7.854000	0.86942	1.684000	0.51022	0.383000	0.25322	CTC	.	.		0.617	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718		C	140777329	T	C	140777329	3	2	260	1	0	0	0	0	1	0	0	0	2541	1551	54	2	534	2	CACNA1B	9	140777329	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	694923	140777329	436102	435	37680										
PFKFB3	5209	hgsc.bcm.edu	37	chr10	6258145	6258145	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tacctggcgaaagaagggggAcaaattgcggtaagtccagg	15	7	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr10:6258145A>G	ENST00000379775.4	+	4	687	c.357A>G	c.(355-357)ggA>ggG	p.G119G	PFKFB3_ENST00000536985.1_Silent_p.G99G|PFKFB3_ENST00000379785.1_Silent_p.G119G|PFKFB3_ENST00000540253.1_Silent_p.G133G|PFKFB3_ENST00000360521.2_Silent_p.G119G|PFKFB3_ENST00000379789.4_Silent_p.G99G|PFKFB3_ENST00000379782.3_Silent_p.G119G|PFKFB3_ENST00000317350.4_Silent_p.G119G	NM_004566.3	NP_004557.1	Q16875	F263_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	119	6-phosphofructo-2-kinase.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|liver(2)|lung(10)|ovary(3)|upper_aerodigestive_tract(1)	22						AAGAAGGGGGACAAATTGCGG	0.577																																					p.G119G		Atlas-SNP	.											.	PFKFB3	82	.	0			c.A357G						.						155	128	137					10																	6258145		2203	4300	6503	SO:0001819	synonymous_variant	5209	exon4			AGGGGGACAAATT		CCDS7078.1, CCDS44353.1, CCDS60479.1	10p15.1	2008-05-14			ENSG00000170525	ENSG00000170525			8874	protein-coding gene	gene with protein product		605319				9146922, 10072580	Standard	NM_004566		Approved		uc001ije.3	Q16875	OTTHUMG00000017621	ENST00000379775.4:c.357A>G	chr10.hg19:g.6258145A>G		67.0	0.0		60.0	4.0	NM_004566	B7Z955|O43622|O75902|Q5VX15|Q5VX18|Q5VX19	Silent	SNP	ENST00000379775.4	hg19	CCDS7078.1																																																																																			.	.		0.577	PFKFB3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046647.1			G	6258145	A	G	6258145	2	3	260	1	0	0	0	0	0	0	0	1	11771	262	10	2		2	PFKFB3	10	6258145	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10		6258145	129276602	436	37681										
SFMBT2	57713	hgsc.bcm.edu	37	chr10	7247790	7247790	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cacttacagactgttttgtgTggtgcagtcaaaggataaga	11	6	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr10:7247790T>C	ENST00000361972.4	-	12	1521	c.1431A>G	c.(1429-1431)ccA>ccG	p.P477P	SFMBT2_ENST00000397167.1_Silent_p.P477P	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	477					negative regulation of gene expression (GO:0010629)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	histone binding (GO:0042393)			NS(2)|breast(3)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(26)|lung(34)|ovary(5)|pancreas(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	99						CTGTTTTGTGTGGTGCAGTCA	0.463																																					p.P477P		Atlas-SNP	.											.	SFMBT2	209	.	0			c.A1431G						.						108	96	100					10																	7247790		2203	4300	6503	SO:0001819	synonymous_variant	57713	exon12			TTTGTGTGGTGCA	AB046837	CCDS31138.1	10p15.1	2013-01-10	2003-11-14		ENSG00000198879	ENSG00000198879		"Sterile alpha motif (SAM) domain containing"	20256	protein-coding gene	gene with protein product		615392	"Scm-related gene containing four mbt domains 2"			10997877	Standard	NM_001029880		Approved	KIAA1617	uc009xio.2	Q5VUG0	OTTHUMG00000017630	ENST00000361972.4:c.1431A>G	chr10.hg19:g.7247790T>C		189.0	0.0		107.0	5.0	NM_001029880	A7MD09|Q9HCF5	Silent	SNP	ENST00000361972.4	hg19	CCDS31138.1																																																																																			.	.		0.463	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046673.1	NM_001029880		C	7247790	T	C	7247790	2	2	260	1	0	0	0	0	0	0	0	1	14173	1683	59	2		2	SFMBT2	10	7247790	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	989645	7247790	128286957	437	37682										
DHTKD1	55526	hgsc.bcm.edu	37	chr10	12160885	12160885	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cttcccgttggattctttacAgcaagagatgagcaaataca	8	9	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr10:12160885A>G	ENST00000263035.4	+	15	2602	c.2540A>G	c.(2539-2541)cAg>cGg	p.Q847R	U6_ENST00000606801.1_RNA	NM_018706.5	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain containing 1	847					cell death (GO:0008219)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hematopoietic progenitor cell differentiation (GO:0002244)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(1)	44		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)			GATTCTTTACAGCAAGAGATG	0.428																																					p.Q847R		Atlas-SNP	.											.	DHTKD1	104	.	0			c.A2540G						.						137	133	134					10																	12160885		2203	4300	6503	SO:0001583	missense	55526	exon15			CTTTACAGCAAGA	BC002477	CCDS7087.1	10p14	2003-11-24			ENSG00000181192	ENSG00000181192			23537	protein-coding gene	gene with protein product		614984				10997877	Standard	NM_018706		Approved	KIAA1630, MGC3090, DKFZP762M115	uc001ild.5	Q96HY7	OTTHUMG00000017677	ENST00000263035.4:c.2540A>G	chr10.hg19:g.12160885A>G	ENSP00000263035:p.Gln847Arg	106.0	0.0		74.0	4.0	NM_018706	Q68CU5|Q9BUM8|Q9HCE2	Missense_Mutation	SNP	ENST00000263035.4	hg19	CCDS7087.1	.	.	.	.	.	.	.	.	.	.	A	13.27	2.187218	0.38609	.	.	ENSG00000181192	ENST00000263035	T	0.04758	3.56	5.09	3.95	0.45737	.	0.000000	0.85682	D	0.000000	T	0.04272	0.0118	N	0.20574	0.59	0.58432	D	0.999999	B	0.12013	0.005	B	0.22880	0.042	T	0.40794	-0.9544	10	0.59425	D	0.04	-6.0727	10.788	0.46415	0.9246:0.0:0.0754:0.0	.	847	Q96HY7	DHTK1_HUMAN	R	847	ENSP00000263035:Q847R	ENSP00000263035:Q847R	Q	+	2	0	DHTKD1	12200891	1.000000	0.71417	0.125000	0.21846	0.905000	0.53344	8.867000	0.92314	0.889000	0.36185	0.379000	0.24179	CAG	.	.		0.428	DHTKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046777.1	NM_018706		G	12160885	A	G	12160885	3	3	260	1	0	0	0	0	1	0	0	0	4502	188	7	2	2598	2	DHTKD1	10	12160885	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	4913095	12160885	123373862	438	37683										
SPAG6	9576	hgsc.bcm.edu	37	chr10	22680689	22680689	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gttgtcagtctgcttgtcagAagaaccggaagatcatatta	10	7	4	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr10:22680689A>G	ENST00000376624.3	+	8	1179	c.1037A>G	c.(1036-1038)gAa>gGa	p.E346G	SPAG6_ENST00000376603.2_Missense_Mutation_p.E422G|RP11-301N24.3_ENST00000422675.1_RNA|SPAG6_ENST00000538630.1_Missense_Mutation_p.E321G|SPAG6_ENST00000376601.1_Missense_Mutation_p.E107G|SPAG6_ENST00000313311.6_Missense_Mutation_p.E346G	NM_001253855.1|NM_012443.3	NP_001240784.1|NP_036575.1	O75602	SPAG6_HUMAN	sperm associated antigen 6	346					cell projection organization (GO:0030030)|spermatid development (GO:0007286)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|motile cilium (GO:0031514)|nucleus (GO:0005634)				breast(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|prostate(1)|skin(2)	27						TGCTTGTCAGAAGAACCGGAA	0.483																																					p.E346G		Atlas-SNP	.											.	SPAG6	90	.	0			c.A1037G						.						101	97	99					10																	22680689		2203	4300	6503	SO:0001583	missense	9576	exon8			TGTCAGAAGAACC	AF079363	CCDS7139.1, CCDS7140.1, CCDS58071.1, CCDS73072.1	10p12.31	2014-01-21			ENSG00000077327	ENSG00000077327		"Armadillo repeat containing"	11215	protein-coding gene	gene with protein product	"axoneme central apparatus protein"	605730				10493827	Standard	NM_012443		Approved	Repro-SA-1, pf16, CT141	uc001iri.3	O75602	OTTHUMG00000017808	ENST00000376624.3:c.1037A>G	chr10.hg19:g.22680689A>G	ENSP00000365811:p.Glu346Gly	105.0	0.0		72.0	4.0	NM_172242	A8K1I8|B4DXZ4|Q5VUX5|Q5VUX6|Q5VUX7|Q6FI74|Q8NHQ6	Missense_Mutation	SNP	ENST00000376624.3	hg19	CCDS7139.1	.	.	.	.	.	.	.	.	.	.	A	18.40	3.616323	0.66672	.	.	ENSG00000077327	ENST00000376624;ENST00000376603;ENST00000376601;ENST00000538630;ENST00000456231;ENST00000313311	T;T;T;T;T;T	0.65178	-0.14;-0.14;0.67;-0.14;0.67;-0.14	5.56	5.56	0.83823	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.63768	0.2539	M	0.72479	2.2	0.80722	D	1	B;B;B;B	0.23249	0.082;0.033;0.037;0.046	B;B;B;B	0.25291	0.038;0.059;0.022;0.056	T	0.61879	-0.6972	10	0.41790	T	0.15	-32.8842	15.7155	0.77663	1.0:0.0:0.0:0.0	.	321;422;346;346	B4DXZ4;O75602-3;O75602-2;O75602	.;.;.;SPAG6_HUMAN	G	346;422;107;321;107;346	ENSP00000365811:E346G;ENSP00000365788:E422G;ENSP00000365786:E107G;ENSP00000441325:E321G;ENSP00000411111:E107G;ENSP00000323599:E346G	ENSP00000323599:E346G	E	+	2	0	SPAG6	22720695	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.806000	0.91930	2.105000	0.64084	0.477000	0.44152	GAA	.	.		0.483	SPAG6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047187.1			G	22680689	A	G	22680689	3	3	260	1	0	0	0	0	1	0	0	0	14997	246	9	2	1067	2	SPAG6	10	22680689	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	10519804	22680689	112854058	439	37684										
GPR158	57512	hgsc.bcm.edu	37	chr10	25887786	25887786	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtatgcctttgggagagccaAggccagtccattttggaaga	13	8	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr10:25887786A>T	ENST00000376351.3	+	11	3590	c.3231A>T	c.(3229-3231)caA>caT	p.Q1077H	GPR158_ENST00000490549.1_3'UTR	NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	1077					protein localization to plasma membrane (GO:0072659)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|cervix(1)|endometrium(9)|kidney(10)|large_intestine(20)|lung(56)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	119						GGGAGAGCCAAGGCCAGTCCA	0.493																																					p.Q1077H		Atlas-SNP	.											.	GPR158	255	.	0			c.A3231T						.						96	99	98					10																	25887786		2203	4300	6503	SO:0001583	missense	57512	exon11			GAGCCAAGGCCAG	AB032962	CCDS31166.1	10p12.31	2012-08-21			ENSG00000151025	ENSG00000151025		"GPCR / Class C : Orphans"	23689	protein-coding gene	gene with protein product		614573					Standard	NM_020752		Approved	KIAA1136	uc001isj.3	Q5T848	OTTHUMG00000017832	ENST00000376351.3:c.3231A>T	chr10.hg19:g.25887786A>T	ENSP00000365529:p.Gln1077His	175.0	0.0		108.0	5.0	NM_020752	Q6QR81|Q9ULT3	Missense_Mutation	SNP	ENST00000376351.3	hg19	CCDS31166.1	.	.	.	.	.	.	.	.	.	.	A	1.238	-0.622268	0.03636	.	.	ENSG00000151025	ENST00000376351	T	0.31247	1.5	5.37	-1.53	0.08611	.	0.406158	0.25704	N	0.028849	T	0.14700	0.0355	N	0.17082	0.46	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.10268	-1.0637	10	0.44086	T	0.13	.	6.5048	0.22188	0.6473:0.1207:0.2319:0.0	.	1077	Q5T848	GP158_HUMAN	H	1077	ENSP00000365529:Q1077H	ENSP00000365529:Q1077H	Q	+	3	2	GPR158	25927792	1.000000	0.71417	0.001000	0.08648	0.004000	0.04260	3.038000	0.49783	-0.564000	0.06070	-0.408000	0.06270	CAA	.	.		0.493	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	XM_166110		T	25887786	A	T	25887786	3	4	260	1	0	0	0	0	1	0	0	0	6671	69	3	4	3273	4	GPR158	10	25887786	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	3207097	25887786	109646961	440	37685										
SYT15	83849	hgsc.bcm.edu	37	chr10	46968621	46968621	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgaggcagcagctctgatgcCgggcaggggtcccatggggc	18	11	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr10:46968621C>T	ENST00000374321.4	-	3	381	c.315G>A	c.(313-315)ccG>ccA	p.P105P	RP11-38L15.3_ENST00000506914.1_RNA|SYT15_ENST00000503753.1_Silent_p.P105P|SYT15_ENST00000374325.3_Silent_p.P105P|SYT15_ENST00000374323.4_Silent_p.P158P	NM_031912.4	NP_114118.2	Q9BQS2	SYT15_HUMAN	synaptotagmin XV	105						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.P105P(2)|p.P157P(1)		cervix(1)|endometrium(5)|kidney(2)|lung(5)	13						GCTCTGATGCCGGGCAGGGGT	0.672																																					p.P105P	Ovarian(57;1152 1428 19651 37745)	Atlas-SNP	.											SYT15_ENST00000374321,NS,carcinoma,0,2	SYT15	165	.	3	Substitution - coding silent(3)	endometrium(3)	c.G315A						.																																			SO:0001819	synonymous_variant	83849	exon3			TGATGCCGGGCAG	AJ303363	CCDS73103.1, CCDS73104.1	10q11.1	2013-01-21			ENSG00000204176	ENSG00000204176		"Synaptotagmins"	17167	protein-coding gene	gene with protein product		608081				11543631	Standard	NM_031912		Approved	CHR10SYT	uc001jea.3	Q9BQS2	OTTHUMG00000018103	ENST00000374321.4:c.315G>A	chr10.hg19:g.46968621C>T		40.0	0.0		43.0	3.0	NM_031912	A5D6W8|Q5VY53|Q5VY55|Q7Z439|Q7Z440	Silent	SNP	ENST00000374321.4	hg19	CCDS44376.1																																																																																			.	.		0.672	SYT15-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367008.1	NM_031912		T	46968621	C	T	46968621	2	4	260	1	0	0	0	0	0	0	0	1	15486	639	23	1		1	SYT15	10	46968621	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	21080835	46968621	88566126	441	37686										
DKK1	22943	hgsc.bcm.edu	37	chr10	54074421	54074421	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gggcgggaataagtaccagaCcattgacaactaccaggtga	12	9	0	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr10:54074421C>A	ENST00000373970.3	+	1	366	c.227C>A	c.(226-228)aCc>aAc	p.T76N	PRKG1-AS1_ENST00000420193.1_RNA	NM_012242.2	NP_036374.1	O94907	DKK1_HUMAN	dickkopf WNT signaling pathway inhibitor 1	76					cell morphogenesis involved in differentiation (GO:0000904)|embryonic limb morphogenesis (GO:0030326)|endoderm formation (GO:0001706)|extracellular negative regulation of signal transduction (GO:1900116)|face morphogenesis (GO:0060325)|forebrain development (GO:0030900)|hair follicle development (GO:0001942)|mesoderm formation (GO:0001707)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:1901296)|negative regulation of cardiac muscle cell differentiation (GO:2000726)|negative regulation of mesodermal cell fate specification (GO:0042662)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of heart induction by negative regulation of canonical Wnt signaling pathway (GO:0090082)|regulation of endodermal cell fate specification (GO:0042663)|regulation of receptor internalization (GO:0002090)|response to retinoic acid (GO:0032526)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)	growth factor activity (GO:0008083)|low-density lipoprotein particle receptor binding (GO:0050750)|receptor antagonist activity (GO:0048019)|signal transducer activity (GO:0004871)			kidney(2)|large_intestine(4)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	16						AAGTACCAGACCATTGACAAC	0.622											OREG0020191	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T76N		Atlas-SNP	.											.	DKK1	35	.	0			c.C227A						.						26	30	29					10																	54074421		2202	4297	6499	SO:0001583	missense	22943	exon1			ACCAGACCATTGA		CCDS7246.1	10q11.2	2013-05-15	2013-05-15		ENSG00000107984	ENSG00000107984			2891	protein-coding gene	gene with protein product		605189	"dickkopf (Xenopus laevis) homolog 1", "dickkopf 1 homolog (Xenopus laevis)"				Standard	NM_012242		Approved	SK, DKK-1	uc001jjr.3	O94907	OTTHUMG00000018247	ENST00000373970.3:c.227C>A	chr10.hg19:g.54074421C>A	ENSP00000363081:p.Thr76Asn	117.0	0.0	997	52.0	4.0	NM_012242	B2RC19	Missense_Mutation	SNP	ENST00000373970.3	hg19	CCDS7246.1	.	.	.	.	.	.	.	.	.	.	C	6.446	0.450341	0.12223	.	.	ENSG00000107984	ENST00000373970	T	0.44083	0.93	4.49	3.57	0.40892	.	0.767169	0.11791	N	0.529223	T	0.29158	0.0725	N	0.24115	0.695	0.09310	N	1	B	0.16802	0.019	B	0.17098	0.017	T	0.18871	-1.0323	10	0.24483	T	0.36	-12.0254	10.7985	0.46474	0.0:0.8076:0.1924:0.0	.	76	O94907	DKK1_HUMAN	N	76	ENSP00000363081:T76N	ENSP00000363081:T76N	T	+	2	0	DKK1	53744427	0.001000	0.12720	0.251000	0.24312	0.555000	0.35460	0.784000	0.26816	0.992000	0.38840	0.655000	0.94253	ACC	.	.		0.622	DKK1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048100.1			A	54074421	C	A	54074421	3	1	260	1	0	0	0	0	1	0	0	0	4546	507	18	3	229	3	DKK1	10	54074421	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	7105800	54074421	81460326	442	37687										
ZNF365	22891	hgsc.bcm.edu	37	chr10	64415380	64415380	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggcacctccctatgcaggagTttcaattcaaggtcattttt	8	10	3	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr10:64415380T>C	ENST00000395251.1	+	4	714	c.380T>C	c.(379-381)gTt>gCt	p.V127A	ZNF365_ENST00000410046.3_Intron|ZNF365_ENST00000395249.1_Intron|AC067751.1_ENST00000579246.1_RNA	NM_199452.3	NP_955524	Q70YC4	TALAN_HUMAN	zinc finger protein 365	127										breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27	Prostate(12;0.0297)|all_hematologic(501;0.228)					TATGCAGGAGTTTCAATTCAA	0.498																																					p.V127A		Atlas-SNP	.											.	ZNF365	174	.	0			c.T380C						.						75	68	71					10																	64415380		2203	4300	6503	SO:0001583	missense	22891	exon4			CAGGAGTTTCAAT	AB020651	CCDS7264.1, CCDS7265.1, CCDS31209.1, CCDS41531.1	10q21.2	2008-10-28			ENSG00000138311	ENSG00000138311		"Zinc fingers, C2H2-type"	18194	protein-coding gene	gene with protein product	"Talanin"	607818				10048485, 12740763	Standard	NM_199450		Approved	KIAA0844, UAN	uc001jmc.2	Q70YC4	OTTHUMG00000018302	ENST00000395251.1:c.380T>C	chr10.hg19:g.64415380T>C	ENSP00000378672:p.Val127Ala	42.0	0.0		34.0	4.0	NM_199452		Missense_Mutation	SNP	ENST00000395251.1	hg19	CCDS7265.1	.	.	.	.	.	.	.	.	.	.	T	12.23	1.874394	0.33069	.	.	ENSG00000138311	ENST00000395251	T	0.54866	0.55	5.49	4.36	0.52297	.	.	.	.	.	T	0.32704	0.0838	N	0.08118	0	0.80722	D	1	P	0.41393	0.748	B	0.42555	0.391	T	0.10753	-1.0616	9	0.40728	T	0.16	.	7.4638	0.27310	0.0:0.0996:0.0:0.9004	.	127	Q70YC4	TALAN_HUMAN	A	127	ENSP00000378672:V127A	ENSP00000378672:V127A	V	+	2	0	ZNF365	64085386	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.221000	0.42917	0.919000	0.36945	0.482000	0.46254	GTT	.	.		0.498	ZNF365-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277036.1	NM_014951		C	64415380	T	C	64415380	3	2	260	1	0	0	0	0	1	0	0	0	17884	1725	60	2	1868	2	ZNF365	10	64415380	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	10340959	64415380	71119367	443	37688										
EIF4EBP2	1979	hgsc.bcm.edu	37	chr10	72164180	72164180	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtcctcgtcagccggcagcgGccaccagcccagccagagcc	12	19	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr10:72164180G>T	ENST00000373218.4	+	1	46	c.23G>T	c.(22-24)gGc>gTc	p.G8V		NM_004096.4	NP_004087.1	Q13542	4EBP2_HUMAN	eukaryotic translation initiation factor 4E binding protein 2	8					cAMP-mediated signaling (GO:0019933)|insulin receptor signaling pathway (GO:0008286)|negative regulation of translational initiation (GO:0045947)|translation (GO:0006412)					large_intestine(1)	1						GCCGGCAGCGGCCACCAGCCC	0.751																																					p.G8V		Atlas-SNP	.											.	EIF4EBP2	7	.	0			c.G23T						.						11	11	11					10																	72164180		2131	4240	6371	SO:0001583	missense	1979	exon1			GCAGCGGCCACCA		CCDS7303.1	10q21-q22	2008-08-01			ENSG00000148730	ENSG00000148730			3289	protein-coding gene	gene with protein product		602224				7935836, 8975712	Standard	NM_004096		Approved		uc001jrb.3	Q13542	OTTHUMG00000018409	ENST00000373218.4:c.23G>T	chr10.hg19:g.72164180G>T	ENSP00000362314:p.Gly8Val	70.0	0.0		78.0	4.0	NM_004096		Missense_Mutation	SNP	ENST00000373218.4	hg19	CCDS7303.1	.	.	.	.	.	.	.	.	.	.	G	17.81	3.481767	0.63849	.	.	ENSG00000148730	ENST00000373218	.	.	.	3.92	3.01	0.34805	.	0.247007	0.40064	N	0.001191	T	0.42131	0.1189	N	0.22421	0.69	0.58432	D	0.999993	B	0.24963	0.115	B	0.28553	0.091	T	0.27365	-1.0076	9	0.36615	T	0.2	-3.5238	10.7401	0.46147	0.0982:0.0:0.9018:0.0	.	8	Q13542	4EBP2_HUMAN	V	8	.	ENSP00000362314:G8V	G	+	2	0	EIF4EBP2	71834186	1.000000	0.71417	0.937000	0.37676	0.888000	0.51559	6.160000	0.71862	0.965000	0.38133	0.563000	0.77884	GGC	.	.		0.751	EIF4EBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048513.1	NM_004096		T	72164180	G	T	72164180	3	4	260	1	0	0	0	0	1	0	0	0	5035	1203	42	3	25	3	EIF4EBP2	10	72164180	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	7748800	72164180	63370567	444	37689										
C10orf54	64115	hgsc.bcm.edu	37	chr10	73511520	73511520	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cagactcagaaggctgccgcTgggccacataggacaggggg	16	11	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr10:73511520T>C	ENST00000394957.3	-	6	861	c.803A>G	c.(802-804)cAg>cGg	p.Q268R	CDH23_ENST00000224721.6_Intron	NM_022153.1	NP_071436.1	Q9H7M9	GI24_HUMAN	chromosome 10 open reading frame 54	268					BMP signaling pathway (GO:0030509)|negative regulation of CD4-positive, alpha-beta T cell proliferation (GO:2000562)|negative regulation of T cell cytokine production (GO:0002725)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of stem cell differentiation (GO:2000738)|stem cell differentiation (GO:0048863)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|endometrium(1)|lung(1)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	9						AGGCTGCCGCTGGGCCACATA	0.622																																					p.Q268R		Atlas-SNP	.											.	C10orf54	29	.	0			c.A803G						.						41	45	44					10																	73511520		2203	4300	6503	SO:0001583	missense	64115	exon6			TGCCGCTGGGCCA	AF193048	CCDS31218.1	10q22.1	2013-11-28			ENSG00000107738	ENSG00000107738		"Immunoglobulin superfamily / V-set domain containing"	30085	protein-coding gene	gene with protein product	"stress induced secreted protein 1"	615608				12975309	Standard	NM_022153		Approved	SISP1, GI24, B7-H5, B7H5	uc001jsd.3	Q9H7M9	OTTHUMG00000018426	ENST00000394957.3:c.803A>G	chr10.hg19:g.73511520T>C	ENSP00000378409:p.Gln268Arg	88.0	0.0		76.0	4.0	NM_022153	A1L0X9|A4ZYV1|A8MVH5|Q6UXF3|Q8WUG3|Q8WYZ8	Missense_Mutation	SNP	ENST00000394957.3	hg19	CCDS31218.1	.	.	.	.	.	.	.	.	.	.	T	12.24	1.878960	0.33162	.	.	ENSG00000107738	ENST00000394957;ENST00000263569	T	0.43688	0.94	6.08	2.55	0.30701	.	0.499782	0.23284	N	0.049877	T	0.32376	0.0827	L	0.46157	1.445	0.26269	N	0.978458	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.24190	-1.0167	10	0.51188	T	0.08	.	6.8437	0.23977	0.0:0.4254:0.0:0.5746	.	268;268	A4ZYV1;Q9H7M9	.;GI24_HUMAN	R	268;264	ENSP00000378409:Q268R	ENSP00000263569:Q264R	Q	-	2	0	C10orf54	73181526	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	1.555000	0.36277	0.542000	0.28846	0.533000	0.62120	CAG	.	.		0.622	C10orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048548.1	NM_022153		C	73511520	T	C	73511520	3	2	260	1	0	0	0	0	1	0	0	0	1609	1580	55	2	140	2	C10orf54	10	73511520	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1347340	73511520	62023227	445	37690										
ANXA7	310	hgsc.bcm.edu	37	chr10	75156931	75156931	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctggtacctaccaggtagtgGaacctgtgctggaccacctc	11	13	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr10:75156931G>T	ENST00000372921.5	-	4	417	c.361C>A	c.(361-363)Cca>Aca	p.P121T	ANXA7_ENST00000535178.1_Intron|ANXA7_ENST00000492380.1_5'UTR	NM_001156.3	NP_001147.1	P20073	ANXA7_HUMAN	annexin A7	121	Repeat-rich region.				autophagy (GO:0006914)|cell proliferation (GO:0008283)|cellular calcium ion homeostasis (GO:0006874)|cellular water homeostasis (GO:0009992)|epithelial cell differentiation (GO:0030855)|hemostasis (GO:0007599)|membrane fusion (GO:0061025)|negative regulation of gene expression (GO:0010629)|regulation of cell shape (GO:0008360)|response to calcium ion (GO:0051592)|response to organic cyclic compound (GO:0014070)|response to salt stress (GO:0009651)|social behavior (GO:0035176)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|integrin binding (GO:0005178)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	26	Prostate(51;0.0119)					CCAGGTAGTGGAACCTGTGCT	0.448																																					p.P121T		Atlas-SNP	.											.	ANXA7	50	.	0			c.C361A						.						62	53	56					10																	75156931		2203	4300	6503	SO:0001583	missense	310	exon4			GTAGTGGAACCTG	J04543	CCDS7325.1, CCDS7326.1	10q22.2	2005-11-09			ENSG00000138279	ENSG00000138279		"Annexins"	545	protein-coding gene	gene with protein product		186360		ANX7		7515686	Standard	NM_001156		Approved		uc001jtz.2	P20073	OTTHUMG00000018463	ENST00000372921.5:c.361C>A	chr10.hg19:g.75156931G>T	ENSP00000362012:p.Pro121Thr	61.0	0.0		56.0	4.0	NM_004034	Q5F2H3|Q5T0M6|Q5T0M7	Missense_Mutation	SNP	ENST00000372921.5	hg19	CCDS7325.1	.	.	.	.	.	.	.	.	.	.	G	13.84	2.358219	0.41801	.	.	ENSG00000138279	ENST00000372921;ENST00000372919;ENST00000394847	T;T	0.02552	4.25;4.43	5.48	4.57	0.56435	.	1.044460	0.07552	N	0.915625	T	0.08670	0.0215	L	0.32530	0.975	0.80722	D	1	P;D;P	0.69078	0.917;0.997;0.935	P;P;P	0.61397	0.529;0.888;0.476	T	0.26121	-1.0112	10	0.45353	T	0.12	.	12.5497	0.56220	0.0817:0.0:0.9183:0.0	.	48;121;121	B4DWU2;P20073-2;P20073	.;.;ANXA7_HUMAN	T	121	ENSP00000362012:P121T;ENSP00000362010:P121T	ENSP00000362010:P121T	P	-	1	0	ANXA7	74826937	1.000000	0.71417	0.974000	0.42286	0.031000	0.12232	5.304000	0.65744	1.452000	0.47756	-0.300000	0.09419	CCA	.	.		0.448	ANXA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048646.2	NM_001156		T	75156931	G	T	75156931	3	4	260	1	0	0	0	0	1	0	0	0	723	1174	41	3	1149	3	ANXA7	10	75156931	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	1645411	75156931	60377816	446	37691										
MYST4	23522	hgsc.bcm.edu	37	chr10	76739019	76739019	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tggggtggaagactgtggccGgtacccttctgtgattgaat	15	7	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr10:76739019G>A	ENST00000287239.4	+	10	2642	c.2153G>A	c.(2152-2154)cGg>cAg	p.R718Q	KAT6B_ENST00000372714.1_Missense_Mutation_p.R426Q|KAT6B_ENST00000372724.1_Missense_Mutation_p.R426Q|KAT6B_ENST00000372711.1_Missense_Mutation_p.R535Q|KAT6B_ENST00000490365.1_3'UTR|KAT6B_ENST00000372725.1_Missense_Mutation_p.R426Q	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	718	Catalytic.|MYST-type HAT.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										GACTGTGGCCGGTACCCTTCT	0.388																																					p.R718Q		Atlas-SNP	.											.	.	.	.	0			c.G2153A						.						103	101	102					10																	76739019		2203	4300	6503	SO:0001583	missense	23522	exon10			GTGGCCGGTACCC	AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	17582	protein-coding gene	gene with protein product	"MOZ-related factor"	605880	"MYST histone acetyltransferase (monocytic leukemia) 4"	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.2153G>A	chr10.hg19:g.76739019G>A	ENSP00000287239:p.Arg718Gln	143.0	0.0		85.0	4.0	NM_012330	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Missense_Mutation	SNP	ENST00000287239.4	hg19	CCDS7345.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.007120	0.75046	.	.	ENSG00000156650	ENST00000372725;ENST00000372724;ENST00000287239;ENST00000372714;ENST00000372711	T;T;T;T;T	0.80214	-1.28;-1.28;-1.35;-1.28;-1.34	5.98	5.98	0.97165	.	0.000000	0.45361	D	0.000366	D	0.83695	0.5310	L	0.41492	1.28	0.58432	D	0.999991	D;D;P	0.57571	0.98;0.973;0.825	P;B;B	0.54431	0.752;0.314;0.245	D	0.83850	0.0262	10	0.59425	D	0.04	-11.3167	20.4293	0.99080	0.0:0.0:1.0:0.0	.	535;426;718	Q8WYB5-2;Q8WYB5-3;Q8WYB5	.;.;KAT6B_HUMAN	Q	426;426;718;426;535	ENSP00000361810:R426Q;ENSP00000361809:R426Q;ENSP00000287239:R718Q;ENSP00000361799:R426Q;ENSP00000361796:R535Q	ENSP00000287239:R718Q	R	+	2	0	KAT6B	76409025	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.154000	0.71826	2.833000	0.97629	0.655000	0.94253	CGG	.	.		0.388	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330		A	76739019	G	A	76739019	3	1	260	1	0	0	0	0	1	0	0	0	10114	1116	39	1	2183	1	MYST4	10	76739019	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	1582088	76739019	58795728	447	37692										
CDHR1	92211	hgsc.bcm.edu	37	chr10	85968520	85968520	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttcaacttgcagctggtgggAcccaggggcatcttccgagt	13	11	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr10:85968520A>G	ENST00000372117.3	+	12	1306	c.1203A>G	c.(1201-1203)ggA>ggG	p.G401G	CDHR1_ENST00000440770.2_Silent_p.G160G|CDHR1_ENST00000332904.3_Silent_p.G401G	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1	401	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cellular process (GO:0009987)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						AGCTGGTGGGACCCAGGGGCA	0.443																																					p.G401G		Atlas-SNP	.											.	CDHR1	122	.	0			c.A1203G						.						82	80	81					10																	85968520		2203	4300	6503	SO:0001819	synonymous_variant	92211	exon12			GGTGGGACCCAGG	AB053448	CCDS7372.1, CCDS53548.1	10q23.1	2014-01-28	2010-01-25	2010-01-25	ENSG00000148600	ENSG00000148600		"Cadherins / Cadherin-related"	14550	protein-coding gene	gene with protein product		609502	"protocadherin 21"	PCDH21		11597768	Standard	NM_001171971		Approved	KIAA1775, CORD15, RP65	uc001kcv.3	Q96JP9	OTTHUMG00000018634	ENST00000372117.3:c.1203A>G	chr10.hg19:g.85968520A>G		169.0	0.0		100.0	4.0	NM_001171971	Q69YZ8|Q8IXY5	Silent	SNP	ENST00000372117.3	hg19	CCDS7372.1																																																																																			.	.		0.443	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100		G	85968520	A	G	85968520	2	3	260	1	0	0	0	0	0	0	0	1	3120	262	10	2		2	CDHR1	10	85968520	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	9229501	85968520	49566227	448	37693										
ATAD1	84896	hgsc.bcm.edu	37	chr10	89530707	89530707	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aatatcaatcaagaccacctAcaggctggttgatatgaaat	7	8	2	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr10:89530707A>T	ENST00000308448.7	-	7	1159		c.e7+1		ATAD1_ENST00000400215.3_Intron|ATAD1_ENST00000328142.3_Splice_Site|ATAD1_ENST00000541004.1_Splice_Site	NM_032810.2	NP_116199.2	Q8NBU5	ATAD1_HUMAN	ATPase family, AAA domain containing 1						ATP catabolic process (GO:0006200)|learning (GO:0007612)|memory (GO:0007613)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|positive regulation of receptor internalization (GO:0002092)	cell junction (GO:0030054)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			kidney(1)|large_intestine(4)|lung(4)|ovary(1)	10		all_cancers(4;6.78e-12)|Prostate(4;3.56e-12)|all_epithelial(4;5.58e-09)|Melanoma(5;0.0273)|Breast(4;0.0424)|all_hematologic(4;0.0846)|Colorectal(252;0.207)|Glioma(4;0.217)|all_neural(4;0.224)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00131)|GBM - Glioblastoma multiforme(1;1.1e-32)|Lung(2;1.4e-05)|LUSC - Lung squamous cell carcinoma(2;2.69e-05)|Colorectal(12;7.09e-05)|COAD - Colon adenocarcinoma(12;0.000261)|STAD - Stomach adenocarcinoma(243;0.235)		AAGACCACCTACAGGCTGGTT	0.378																																					.		Atlas-SNP	.											.	ATAD1	32	.	0			c.780+2T>A						.						103	95	98					10																	89530707		2203	4300	6503	SO:0001630	splice_region_variant	84896	exon8			CCACCTACAGGCT	AL834370	CCDS7386.1	10q23.31	2010-04-21		2007-02-08	ENSG00000138138	ENSG00000138138		"ATPases / AAA-type"	25903	protein-coding gene	gene with protein product		614452				12477932	Standard	NM_032810		Approved	FLJ14600	uc001kez.1	Q8NBU5	OTTHUMG00000018685	ENST00000308448.7:c.780+1T>A	chr10.hg19:g.89530707A>T		118.0	0.0		98.0	4.0	NM_032810	D3DR26|Q6DKG1|Q6P4B9|Q8N3G1|Q8WYR9|Q969Y3	Splice_Site	SNP	ENST00000308448.7	hg19	CCDS7386.1	.	.	.	.	.	.	.	.	.	.	A	19.47	3.833603	0.71258	.	.	ENSG00000138138	ENST00000308448;ENST00000328142;ENST00000541004	.	.	.	5.03	5.03	0.67393	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.3513	0.60603	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ATAD1	89520687	1.000000	0.71417	0.791000	0.31998	0.772000	0.43724	8.526000	0.90588	2.186000	0.69663	0.528000	0.53228	.	.	.		0.378	ATAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049235.1	NM_032810	Intron	T	89530707	A	T	89530707	5	4	260	1	0	0	0	0	0	0	1	0	1070	405	14	4	319	4	ATAD1	10	89530707	Splice_Site	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	3562187	89530707	46004040	449	37694										
ACTA2	59	hgsc.bcm.edu	37	chr10	90708594	90708594	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcccacaatggatgggaaaaCagccctgggagcatcgtccc	11	13	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr10:90708594C>T	ENST00000458208.1	-	2	568	c.94G>A	c.(94-96)Gtt>Att	p.V32I	ACTA2_ENST00000480297.1_5'UTR|ACTA2_ENST00000224784.6_Missense_Mutation_p.V32I|STAMBPL1_ENST00000371927.3_Intron	NM_001141945.1	NP_001135417.1	P62736	ACTA_HUMAN	actin, alpha 2, smooth muscle, aorta	32					glomerular mesangial cell development (GO:0072144)|muscle contraction (GO:0006936)|regulation of blood pressure (GO:0008217)|response to virus (GO:0009615)|vascular smooth muscle contraction (GO:0014829)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|smooth muscle contractile fiber (GO:0030485)	ATP binding (GO:0005524)|protein kinase binding (GO:0019901)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|skin(1)|urinary_tract(2)	17		Colorectal(252;0.0161)		Colorectal(12;0.000123)|COAD - Colon adenocarcinoma(12;0.00018)		GATGGGAAAACAGCCCTGGGA	0.502																																					p.V32I		Atlas-SNP	.											.	ACTA2	33	.	0			c.G94A						.						124	117	119					10																	90708594		2203	4300	6503	SO:0001583	missense	59	exon2			GGAAAACAGCCCT	X13839	CCDS7392.1	10q23.31	2014-09-17			ENSG00000107796	ENSG00000107796			130	protein-coding gene	gene with protein product		102620				2398629	Standard	NM_001141945		Approved	ACTSA	uc001kfp.3	P62736	OTTHUMG00000018700	ENST00000458208.1:c.94G>A	chr10.hg19:g.90708594C>T	ENSP00000402373:p.Val32Ile	119.0	0.0		78.0	4.0	NM_001141945	B2R8A4|P03996|P04108|Q6FI19	Missense_Mutation	SNP	ENST00000458208.1	hg19	CCDS7392.1	.	.	.	.	.	.	.	.	.	.	C	17.02	3.282013	0.59867	.	.	ENSG00000107796	ENST00000224784;ENST00000458208;ENST00000415557;ENST00000458159	D;D;D;D	0.91740	-2.9;-2.9;-2.9;-2.9	5.7	5.7	0.88788	.	0.000000	0.64402	D	0.000005	D	0.94574	0.8252	L	0.47716	1.5	0.58432	D	0.999994	P;B	0.48503	0.911;0.012	D;B	0.64410	0.925;0.106	D	0.94804	0.7973	10	0.87932	D	0	.	18.4002	0.90514	0.0:1.0:0.0:0.0	.	32;32	B7Z6I1;P62736	.;ACTA_HUMAN	I	32	ENSP00000224784:V32I;ENSP00000402373:V32I;ENSP00000396730:V32I;ENSP00000398239:V32I	ENSP00000224784:V32I	V	-	1	0	ACTA2	90698574	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.818000	0.86416	2.688000	0.91661	0.650000	0.86243	GTT	.	.		0.502	ACTA2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049264.1	NM_001613		T	90708594	C	T	90708594	3	4	260	1	0	0	0	0	1	0	0	0	192	478	17	3	1071	3	ACTA2	10	90708594	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	1177887	90708594	44826153	450	37695										
IFIT1	3434	hgsc.bcm.edu	37	chr10	91163429	91163429	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctatgagcgggccctgagacTggctgctgactttgagaact	13	10	0	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr10:91163429T>C	ENST00000371804.3	+	2	1564	c.1397T>C	c.(1396-1398)cTg>cCg	p.L466P	IFIT1_ENST00000546318.1_Missense_Mutation_p.L435P|LIPA_ENST00000371837.1_Intron	NM_001270927.1|NM_001548.4	NP_001257856.1|NP_001539.3	P09914	IFIT1_HUMAN	interferon-induced protein with tetratricopeptide repeats 1	466					cellular response to exogenous dsRNA (GO:0071360)|cellular response to type I interferon (GO:0071357)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|intracellular transport of viral protein in host cell (GO:0019060)|negative regulation of defense response to virus by host (GO:0050689)|negative regulation of helicase activity (GO:0051097)|negative regulation of protein binding (GO:0032091)|negative regulation of viral genome replication (GO:0045071)|positive regulation of viral genome replication (GO:0045070)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(2)|prostate(2)|upper_aerodigestive_tract(1)	15						GCCCTGAGACTGGCTGCTGAC	0.438																																					p.L466P		Atlas-SNP	.											.	IFIT1	30	.	0			c.T1397C						.						44	46	45					10																	91163429		2203	4300	6503	SO:0001583	missense	3434	exon3			TGAGACTGGCTGC	M24594	CCDS31243.1, CCDS59220.1	10q23.31	2014-05-22			ENSG00000185745	ENSG00000185745		"Tetratricopeptide (TTC) repeat domain containing"	5407	protein-coding gene	gene with protein product		147690		G10P1, IFI56, IFNAI1		1377167, 3360121	Standard	NM_001548		Approved	GARG-16	uc001kgi.4	P09914	OTTHUMG00000018712	ENST00000371804.3:c.1397T>C	chr10.hg19:g.91163429T>C	ENSP00000360869:p.Leu466Pro	118.0	0.0		99.0	5.0	NM_001270927	B3KS50|D3DR31|Q5T7J1|Q96QM5	Missense_Mutation	SNP	ENST00000371804.3	hg19	CCDS31243.1	.	.	.	.	.	.	.	.	.	.	T	14.24	2.476738	0.44044	.	.	ENSG00000185745	ENST00000371804;ENST00000546318	T;T	0.74315	-0.83;-0.83	5.05	3.84	0.44239	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.678072	0.11935	U	0.515315	D	0.85478	0.5706	M	0.81682	2.555	0.09310	N	0.999996	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.73616	-0.3926	10	0.87932	D	0	.	10.0811	0.42391	0.2643:0.0:0.0:0.7357	.	466;466	Q5T7J1;P09914	.;IFIT1_HUMAN	P	466;435	ENSP00000360869:L466P;ENSP00000441968:L435P	ENSP00000360869:L466P	L	+	2	0	IFIT1	91153409	0.003000	0.15002	0.020000	0.16555	0.646000	0.38490	0.809000	0.27168	2.010000	0.58986	0.528000	0.53228	CTG	.	.		0.438	IFIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049302.1	NM_001548		C	91163429	T	C	91163429	3	2	260	1	0	0	0	0	1	0	0	0	7530	1580	55	2	1403	2	IFIT1	10	91163429	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	454835	91163429	44371318	451	37696										
MYOF	26509	hgsc.bcm.edu	37	chr10	95107502	95107502	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgtggtcgatgaccttgatcAccagtgggggcatgtacaat	13	8	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr10:95107502A>G	ENST00000359263.4	-	37	4120	c.4121T>C	c.(4120-4122)gTg>gCg	p.V1374A	MYOF_ENST00000358334.5_Missense_Mutation_p.V1361A|MYOF_ENST00000371501.4_Missense_Mutation_p.V1374A|MYOF_ENST00000371502.4_Missense_Mutation_p.V1374A	NM_013451.3	NP_038479.1	Q9NZM1	MYOF_HUMAN	myoferlin	1374					blood circulation (GO:0008015)|cellular response to heat (GO:0034605)|muscle contraction (GO:0006936)|plasma membrane repair (GO:0001778)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)	caveola (GO:0005901)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)			NS(2)|autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(7)|large_intestine(15)|lung(14)|ovary(4)|prostate(4)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						GACCTTGATCACCAGTGGGGG	0.552																																					p.V1374A		Atlas-SNP	.											.	MYOF	177	.	0			c.T4121C						.						53	55	55					10																	95107502		1962	4159	6121	SO:0001583	missense	26509	exon37			TTGATCACCAGTG	AB033033	CCDS41550.1, CCDS41551.1	10q24	2014-06-27	2008-11-26	2008-11-26	ENSG00000138119	ENSG00000138119			3656	protein-coding gene	gene with protein product	"fer-1-like family member 3"	604603	"fer-1 (C.elegans)-like 3 (myoferlin)", "fer-1-like 3, myoferlin (C. elegans)"	FER1L3		10607832, 10995573, 17702744	Standard	NM_013451		Approved	KIAA1207	uc001kin.3	Q9NZM1	OTTHUMG00000018772	ENST00000359263.4:c.4121T>C	chr10.hg19:g.95107502A>G	ENSP00000352208:p.Val1374Ala	133.0	0.0		85.0	5.0	NM_013451	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	Missense_Mutation	SNP	ENST00000359263.4	hg19	CCDS41551.1	.	.	.	.	.	.	.	.	.	.	A	16.53	3.149672	0.57151	.	.	ENSG00000138119	ENST00000358334;ENST00000359263;ENST00000371501;ENST00000371502	T;T;T;T	0.68181	-0.31;-0.31;-0.31;-0.31	5.68	4.54	0.55810	C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.126462	0.53938	N	0.000057	T	0.77942	0.4206	M	0.79123	2.44	0.52501	D	0.999954	D;D	0.59357	0.963;0.985	P;P	0.60541	0.792;0.876	T	0.77297	-0.2640	10	0.40728	T	0.16	-16.2328	11.5768	0.50866	0.9302:0.0:0.0698:0.0	.	1361;1374	Q9NZM1-6;Q9NZM1	.;MYOF_HUMAN	A	1361;1374;1374;1374	ENSP00000351094:V1361A;ENSP00000352208:V1374A;ENSP00000360556:V1374A;ENSP00000360557:V1374A	ENSP00000351094:V1361A	V	-	2	0	MYOF	95097492	1.000000	0.71417	1.000000	0.80357	0.042000	0.13812	9.339000	0.96797	0.990000	0.38787	-0.388000	0.06559	GTG	.	.		0.552	MYOF-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049423.2	NM_013451		G	95107502	A	G	95107502	3	3	260	1	0	0	0	0	1	0	0	0	10098	159	6	2	2136	2	MYOF	10	95107502	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	3944073	95107502	40427245	452	37697										
RRP12	23223	hgsc.bcm.edu	37	chr10	99148093	99148093	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aagcagggcagcaggtccttCagcagcgtcagcatgtgcag	14	11	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr10:99148093C>A	ENST00000370992.4	-	8	1044	c.933G>T	c.(931-933)ctG>ctT	p.L311L	RRP12_ENST00000414986.1_Silent_p.L250L|RRP12_ENST00000536831.1_Intron|RRP12_ENST00000315563.6_Silent_p.L211L	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	311						integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		GCAGGTCCTTCAGCAGCGTCA	0.612																																					p.L311L		Atlas-SNP	.											.	RRP12	97	.	0			c.G933T						.						70	67	68					10																	99148093		2203	4300	6503	SO:0001819	synonymous_variant	23223	exon8			GTCCTTCAGCAGC		CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"KIAA0690"	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.933G>T	chr10.hg19:g.99148093C>A		93.0	0.0		71.0	4.0	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Silent	SNP	ENST00000370992.4	hg19	CCDS7457.1																																																																																			.	.		0.612	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179		A	99148093	C	A	99148093	2	1	260	1	0	0	0	0	0	0	0	1	13701	813	29	3		3	RRP12	10	99148093	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	4040591	99148093	36386654	453	37698										
CWF19L1	55280	hgsc.bcm.edu	37	chr10	101997942	101997942	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agtgtccaataggcaggatgAggacatggtcatcagataag	13	6	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr10:101997942A>G	ENST00000354105.4	-	11	1177	c.1091T>C	c.(1090-1092)cTc>cCc	p.L364P	CWF19L1_ENST00000370379.1_Missense_Mutation_p.L119P|CWF19L1_ENST00000478047.1_5'UTR|SNORA12_ENST00000391162.1_RNA	NM_018294.4	NP_060764.3	Q69YN2	C19L1_HUMAN	CWF19-like 1, cell cycle control (S. pombe)	364							catalytic activity (GO:0003824)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(4)|pancreas(1)|prostate(1)|stomach(2)	17		Colorectal(252;0.117)		Epithelial(162;3.78e-10)|all cancers(201;3.1e-08)		AGGCAGGATGAGGACATGGTC	0.488																																					p.L364P		Atlas-SNP	.											.	CWF19L1	39	.	0			c.T1091C						.						198	179	186					10																	101997942		2203	4300	6503	SO:0001583	missense	55280	exon11			AGGATGAGGACAT	AK001860	CCDS7489.1	10q24.31	2008-11-24			ENSG00000095485	ENSG00000095485			25613	protein-coding gene	gene with protein product						14702039	Standard	NM_018294		Approved	FLJ10998	uc001kqq.1	Q69YN2	OTTHUMG00000018901	ENST00000354105.4:c.1091T>C	chr10.hg19:g.101997942A>G	ENSP00000326411:p.Leu364Pro	191.0	0.0		125.0	5.0	NM_018294	B4DHX1|D3DR66|Q5W0I3|Q96HC3|Q9H865|Q9NV13	Missense_Mutation	SNP	ENST00000354105.4	hg19	CCDS7489.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.507214	0.85282	.	.	ENSG00000095485	ENST00000354105;ENST00000370379	T;T	0.37235	1.65;1.21	5.57	5.57	0.84162	Histidine triad motif (1);Histidine triad-like motif (1);Cwf19-like, C-terminal domain-1 (1);	0.000000	0.85682	D	0.000000	T	0.70657	0.3249	H	0.95437	3.67	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.998;0.999	T	0.80101	-0.1523	10	0.87932	D	0	-10.8725	13.6919	0.62550	1.0:0.0:0.0:0.0	.	68;227;364	Q69YN2-2;Q69YN2-3;Q69YN2	.;.;C19L1_HUMAN	P	364;119	ENSP00000326411:L364P;ENSP00000359405:L119P	ENSP00000326411:L364P	L	-	2	0	CWF19L1	101987932	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.151000	0.77411	2.127000	0.65507	0.528000	0.53228	CTC	.	.		0.488	CWF19L1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018294		G	101997942	A	G	101997942	3	3	260	1	0	0	0	0	1	0	0	0	4073	304	11	2	541	2	CWF19L1	10	101997942	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	2849849	101997942	33536805	454	37699										
MRPL43	84545	hgsc.bcm.edu	37	chr10	102739042	102739042	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cacagtggtcagtgcagggaCaatcgggaggcaagaaactg	15	8	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr10:102739042C>T	ENST00000318325.2	-	5	669	c.616G>A	c.(616-618)Gtc>Atc	p.V206I	MRPL43_ENST00000370242.4_Missense_Mutation_p.C248Y|SEMA4G_ENST00000517724.1_Intron|SEMA4G_ENST00000370250.4_Intron|SEMA4G_ENST00000210633.3_Intron|MRPL43_ENST00000370241.3_Intron|RP11-108L7.4_ENST00000447344.1_RNA	NM_176792.2	NP_789762.1	Q8N983	RM43_HUMAN	mitochondrial ribosomal protein L43	206					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(1)|skin(2)|upper_aerodigestive_tract(1)	4		Colorectal(252;0.234)		Epithelial(162;6.21e-09)|all cancers(201;3.14e-07)		AGTGCAGGGACAATCGGGAGG	0.562																																					p.V206I		Atlas-SNP	.											.	MRPL43	16	.	0			c.G616A						.						91	77	82					10																	102739042		2203	4300	6503	SO:0001583	missense	84545	exon5			CAGGGACAATCGG	AB049656	CCDS7502.1, CCDS7503.1, CCDS7504.1, CCDS7505.1	10q24.31	2012-09-13			ENSG00000055950	ENSG00000055950		"Mitochondrial ribosomal proteins / large subunits"	14517	protein-coding gene	gene with protein product		611848					Standard	NM_176792		Approved	bMRP36a	uc001ksa.1	Q8N983	OTTHUMG00000018920	ENST00000318325.2:c.616G>A	chr10.hg19:g.102739042C>T	ENSP00000315364:p.Val206Ile	197.0	0.0		120.0	5.0	NM_176792	B1AL06|B1AL07|B1AL09|B1AL10|C9J5Q3|D3DR71|Q5JW06|Q7Z719|Q7Z7H6|Q86XN1|Q9BYC7	Missense_Mutation	SNP	ENST00000318325.2	hg19	CCDS7502.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.96|14.96	2.692255|2.692255	0.48202|0.48202	.|.	.|.	ENSG00000055950|ENSG00000055950	ENST00000370242|ENST00000318325	.|.	.|.	.|.	5.52|5.52	-1.23|-1.23	0.09465|0.09465	.|.	0.596453|.	0.14614|.	N|.	0.308857|.	T|T	0.13798|0.13798	0.0334|0.0334	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B|B	0.02656|0.06786	0.0|0.001	B|B	0.01281|0.06405	0.0|0.002	T|T	0.33599|0.33599	-0.9862|-0.9862	9|8	0.87932|0.06494	D|T	0|0.89	-5.2511|-5.2511	6.807|6.807	0.23782|0.23782	0.0:0.5441:0.1113:0.3447|0.0:0.5441:0.1113:0.3447	.|.	248|206	B1AL06|Q8N983	.|RM43_HUMAN	Y|I	248|206	.|.	ENSP00000359262:C248Y|ENSP00000315364:V206I	C|V	-|-	2|1	0|0	MRPL43|MRPL43	102729032|102729032	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.617000|0.617000	0.37484|0.37484	-0.226000|-0.226000	0.09139|0.09139	-0.097000|-0.097000	0.12307|0.12307	0.479000|0.479000	0.44913|0.44913	TGT|GTC	.	.		0.562	MRPL43-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049902.1			T	102739042	C	T	102739042	3	4	260	1	0	0	0	0	1	0	0	0	9816	478	17	3	35	3	MRPL43	10	102739042	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	741100	102739042	32795705	455	37700										
FBXW4	6468	hgsc.bcm.edu	37	chr10	103372236	103372236	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtgtgtcatcagctgcccacTgggaagggaaggacggagtg	17	8	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr10:103372236T>C	ENST00000331272.7	-	7	1455		c.e7-2		FBXW4_ENST00000470093.1_Splice_Site	NM_022039.3	NP_071322.1	P57775	FBXW4_HUMAN	F-box and WD repeat domain containing 4						cartilage development (GO:0051216)|embryonic digit morphogenesis (GO:0042733)|embryonic limb morphogenesis (GO:0030326)|positive regulation of mesenchymal cell proliferation (GO:0002053)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)	ubiquitin ligase complex (GO:0000151)				breast(3)|endometrium(2)|large_intestine(4)|lung(4)|skin(1)|stomach(1)	15		Colorectal(252;0.123)		Epithelial(162;4.35e-08)|all cancers(201;1.92e-06)		AGCTGCCCACTGGGAAGGGAA	0.557																																					.		Atlas-SNP	.											.	FBXW4	39	.	0			c.837-2A>G						.						141	121	128					10																	103372236		2203	4300	6503	SO:0001630	splice_region_variant	6468	exon8			GCCCACTGGGAAG	AF281859	CCDS31271.1	10q24	2013-01-09	2007-02-08	2005-03-12	ENSG00000107829	ENSG00000107829		"F-boxes / WD-40 domains", "WD repeat domain containing"	10847	protein-coding gene	gene with protein product		608071	"split hand/foot malformation (ectrodactyly) type 3", "F-box and WD-40 domain protein 4"	SHFM3		8723077, 7912888	Standard	XM_005270053		Approved	Fbw4, dactylin	uc001kto.3	P57775	OTTHUMG00000018938	ENST00000331272.7:c.837-2A>G	chr10.hg19:g.103372236T>C		82.0	0.0		61.0	4.0	NM_022039	Q5SVS1|Q96IM6	Splice_Site	SNP	ENST00000331272.7	hg19	CCDS31271.1	.	.	.	.	.	.	.	.	.	.	T	17.16	3.319035	0.60524	.	.	ENSG00000107829	ENST00000331272;ENST00000389046	.	.	.	4.28	4.28	0.50868	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5663	0.61819	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	FBXW4	103362226	1.000000	0.71417	0.997000	0.53966	0.833000	0.47200	6.842000	0.75379	1.791000	0.52520	0.260000	0.18958	.	.	.		0.557	FBXW4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049979.2	NM_022039	Intron	C	103372236	T	C	103372236	5	2	260	1	0	0	0	0	0	0	1	0	5775	1594	55	2	415	2	FBXW4	10	103372236	Splice_Site	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	633194	103372236	32162511	456	37701										
GBF1	8729	hgsc.bcm.edu	37	chr10	104119157	104119157	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	catggattacgtcaatccccGgggcgtgcgctttacacagt	11	12	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr10:104119157G>C	ENST00000369983.3	+	11	1402	c.1142G>C	c.(1141-1143)cGg>cCg	p.R381P	GBF1_ENST00000476019.1_3'UTR	NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	381					COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		GTCAATCCCCGGGGCGTGCGC	0.562																																					p.R382P		Atlas-SNP	.											.	GBF1	142	.	0			c.G1145C						.						145	110	122					10																	104119157		2203	4300	6503	SO:0001583	missense	8729	exon11			ATCCCCGGGGCGT	D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"golgi-specific brefeldin A resistance factor 1"			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.1142G>C	chr10.hg19:g.104119157G>C	ENSP00000359000:p.Arg381Pro	114.0	0.0		76.0	4.0	NM_001199378	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Missense_Mutation	SNP	ENST00000369983.3	hg19	CCDS7533.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.962377	0.92791	.	.	ENSG00000107862	ENST00000369983	T	0.10960	2.82	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.32585	0.0834	M	0.66939	2.045	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.72625	0.962;0.916;0.978	T	0.00567	-1.1667	10	0.30078	T	0.28	-14.2111	19.6846	0.95976	0.0:0.0:1.0:0.0	.	381;381;381	Q149P1;Q149P0;Q92538	.;.;GBF1_HUMAN	P	381	ENSP00000359000:R381P	ENSP00000359000:R381P	R	+	2	0	GBF1	104109147	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.471000	0.97696	2.644000	0.89710	0.655000	0.94253	CGG	.	.		0.562	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1			C	104119157	G	C	104119157	3	2	260	1	0	0	0	0	1	0	0	0	6279	1116	39	4	1180	4	GBF1	10	104119157	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	746921	104119157	31415590	457	37702										
SORCS3	22986	hgsc.bcm.edu	37	chr10	106970970	106970970	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aatccagcatccccatcaaaGgactgcagccttggtcaaag	8	13	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr10:106970970G>T	ENST00000369701.3	+	17	2564	c.2337G>T	c.(2335-2337)aaG>aaT	p.K779N	SORCS3_ENST00000369699.4_Missense_Mutation_p.K65N	NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	779					learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		CCCCATCAAAGGACTGCAGCC	0.463																																					p.K779N	NSCLC(116;1497 1690 7108 13108 14106)	Atlas-SNP	.											.	SORCS3	282	.	0			c.G2337T						.						111	91	97					10																	106970970		2203	4300	6503	SO:0001583	missense	22986	exon17			ATCAAAGGACTGC	AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.2337G>T	chr10.hg19:g.106970970G>T	ENSP00000358715:p.Lys779Asn	205.0	0.0		145.0	32.0	NM_014978	Q5VXF9|Q9NQJ2	Missense_Mutation	SNP	ENST00000369701.3	hg19	CCDS7558.1	.	.	.	.	.	.	.	.	.	.	G	13.19	2.161735	0.38119	.	.	ENSG00000156395	ENST00000369701;ENST00000393176;ENST00000369699	T;T;T	0.32272	2.43;1.46;1.47	5.93	4.09	0.47781	VPS10 (1);	0.055638	0.64402	D	0.000001	T	0.33147	0.0853	L	0.58810	1.83	0.36202	D	0.85081	P	0.47409	0.895	P	0.45071	0.468	T	0.38845	-0.9642	9	.	.	.	.	10.6971	0.45905	0.2032:0.0:0.7968:0.0	.	779	Q9UPU3	SORC3_HUMAN	N	779;140;65	ENSP00000358715:K779N;ENSP00000376876:K140N;ENSP00000358713:K65N	.	K	+	3	2	SORCS3	106960960	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.307000	0.33516	0.858000	0.35431	-0.150000	0.13652	AAG	.	.		0.463	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978		T	106970970	G	T	106970970	3	4	260	1	0	0	0	0	1	0	0	0	14947	991	35	3	2403	3	SORCS3	10	106970970	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	2851813	106970970	28563777	458	37703										
TCF7L2	6934	hgsc.bcm.edu	37	chr10	114849213	114849213	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtcagcacttctacccccccTcagacttcactgtcagcact	5	18	5	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr10:114849213T>C	ENST00000355995.4	+	5	1059				TCF7L2_ENST00000352065.5_Intron|TCF7L2_ENST00000355717.4_Missense_Mutation_p.S180P|TCF7L2_ENST00000349937.2_Intron|TCF7L2_ENST00000534894.1_Intron|TCF7L2_ENST00000369395.1_Missense_Mutation_p.S181P|TCF7L2_ENST00000369397.4_Intron|TCF7L2_ENST00000543371.1_Intron|TCF7L2_ENST00000542695.1_Intron|TCF7L2_ENST00000538897.1_Intron|TCF7L2_ENST00000545257.1_Intron|TCF7L2_ENST00000536810.1_Intron			Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 (T-cell specific, HMG-box)						blood vessel development (GO:0001568)|bone mineralization (GO:0030282)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|catenin import into nucleus (GO:0035411)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cellular response to starvation (GO:0009267)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|generation of neurons (GO:0048699)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen metabolic process (GO:0005977)|insulin metabolic process (GO:1901142)|maintenance of DNA repeat elements (GO:0043570)|multicellular organism growth (GO:0035264)|myoblast fate commitment (GO:0048625)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of organ growth (GO:0046621)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neural tube development (GO:0021915)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of insulin secretion (GO:0032024)|positive regulation of protein binding (GO:0032092)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|post-embryonic development (GO:0009791)|regulation of hormone metabolic process (GO:0032350)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of myelination (GO:0031641)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of skeletal muscle tissue development (GO:0048641)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|secretory granule localization (GO:0032252)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	beta-catenin-TCF7L2 complex (GO:0070369)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|gamma-catenin binding (GO:0045295)|nuclear hormone receptor binding (GO:0035257)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		VTI1A/TCF7L2(8)	central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(24)|liver(2)|lung(8)|ovary(1)|skin(1)	41		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		CTACCCCCCCTCAGACTTCAC	0.562			T	VTI1A	colorectal																																p.S180P		Atlas-SNP	.		Dom	yes		10	10q25.3	6934	transcription factor 7-like 2		E	.	TCF7L2	298	.	0			c.T538C						.						53	49	50					10																	114849213		1568	3582	5150	SO:0001627	intron_variant	6934	exon5			CCCCCCTCAGACT	X62871	CCDS7576.1, CCDS53578.1, CCDS55729.1, CCDS73196.1, CCDS73197.1, CCDS73198.1	10q25.3	2006-11-24			ENSG00000148737	ENSG00000148737			11641	protein-coding gene	gene with protein product		602228		TCF4		1741298	Standard	NM_001146283		Approved	TCF-4	uc001lae.4	Q9NQB0	OTTHUMG00000019070	ENST00000355995.4:c.552+49328T>C	chr10.hg19:g.114849213T>C		96.0	0.0		68.0	4.0	NM_001146283	B4DRJ8|B9X074|C6ZRJ8|C6ZRK0|E2GH14|E2GH19|E2GH20|E2GH24|E2GH25|E9PFH9|F8W742|F8W7T5|O00185|Q9NQB1|Q9NQB2|Q9NQB3|Q9NQB4|Q9NQB5|Q9NQB6|Q9NQB7|Q9ULC2	Missense_Mutation	SNP	ENST00000355995.4	hg19		.	.	.	.	.	.	.	.	.	.	T	15.67	2.902431	0.52227	.	.	ENSG00000148737	ENST00000355717;ENST00000369395;ENST00000346198	D	0.99338	-5.76	4.46	4.46	0.54185	.	0.436448	0.17235	N	0.181790	D	0.98248	0.9420	N	0.14661	0.345	0.80722	D	1	P;D;D	0.59357	0.93;0.985;0.981	P;D;D	0.72075	0.899;0.976;0.972	D	0.96878	0.9644	10	0.39692	T	0.17	.	10.4805	0.44691	0.0:0.0:0.0:1.0	.	50;75;180	B4DWD5;C6ZRJ6;F8W7T5	.;.;.	P	180;181;150	ENSP00000347949:S180P	ENSP00000345640:S150P	S	+	1	0	TCF7L2	114839203	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	1.775000	0.38584	2.242000	0.73789	0.529000	0.55759	TCA	.	.		0.562	TCF7L2-203	KNOWN	basic	protein_coding	protein_coding		NM_030756		C	114849213	T	C	114849213	1	2	260	0	1	0	0	0	0	0	0	0	15713	1551	54	2		2	TCF7L2	10	114849213	Intron	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	7878243	114849213	20685534	459	37704										
C10orf81	79949	hgsc.bcm.edu	37	chr10	115534677	115534677	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggatggggacctccacctgcAagaacaaggctcaggaattg	13	10	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr10:115534677A>G	ENST00000369310.3	+	9	1416	c.854A>G	c.(853-855)cAa>cGa	p.Q285R	PLEKHS1_ENST00000354462.3_Missense_Mutation_p.Q35R|PLEKHS1_ENST00000369312.4_Missense_Mutation_p.Q203R|PLEKHS1_ENST00000369309.1_Missense_Mutation_p.Q105R|PLEKHS1_ENST00000361048.1_Missense_Mutation_p.Q291R	NM_182601.1	NP_872407.1	Q5SXH7	PKHS1_HUMAN	pleckstrin homology domain containing, family S member 1	285																	CTCCACCTGCAAGAACAAGGC	0.512																																					p.Q291R		Atlas-SNP	.											.	PLEKHS1	19	.	0			c.A872G						.						104	93	97					10																	115534677		2203	4300	6503	SO:0001583	missense	79949	exon10			ACCTGCAAGAACA	AK027190	CCDS7583.1, CCDS53580.1, CCDS53581.1	10q26.11	2013-01-11	2012-05-31	2012-05-31	ENSG00000148735	ENSG00000148735		"Pleckstrin homology (PH) domain containing"	26285	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 81"	C10orf81		12477932	Standard	NM_024889		Approved	FLJ23537, bA211N11.2	uc001lat.2	Q5SXH7	OTTHUMG00000019074	ENST00000369310.3:c.854A>G	chr10.hg19:g.115534677A>G	ENSP00000358316:p.Gln285Arg	114.0	0.0		74.0	4.0	NM_024889	A8KA02|B3KX00|B6EDE1|Q5SXH8|Q5SXI0|Q6ZQR5|Q8NE42|Q9H5D9	Missense_Mutation	SNP	ENST00000369310.3	hg19	CCDS53580.1	.	.	.	.	.	.	.	.	.	.	A	14.99	2.699877	0.48307	.	.	ENSG00000148735	ENST00000361048;ENST00000369312;ENST00000369310;ENST00000369309;ENST00000354462	T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5	5.69	5.69	0.88448	.	0.533634	0.20425	N	0.092585	T	0.46210	0.1381	L	0.59436	1.845	0.18873	N	0.999984	P;D;P;D	0.63880	0.921;0.972;0.952;0.993	P;P;P;P	0.59487	0.678;0.742;0.677;0.858	T	0.39210	-0.9625	10	0.39692	T	0.17	-11.0061	12.3346	0.55060	1.0:0.0:0.0:0.0	.	285;285;285;291	Q5SXH7;Q5SXH7-5;Q5SXH7-2;Q5SXH7-4	CJ081_HUMAN;.;.;.	R	291;203;285;105;35	ENSP00000354332:Q291R;ENSP00000358318:Q203R;ENSP00000358316:Q285R;ENSP00000358315:Q105R;ENSP00000346451:Q35R	ENSP00000346451:Q35R	Q	+	2	0	C10orf81	115524667	0.080000	0.21391	0.586000	0.28679	0.183000	0.23260	3.156000	0.50708	2.182000	0.69389	0.482000	0.46254	CAA	.	.		0.512	PLEKHS1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050432.1	NM_024889		G	115534677	A	G	115534677	3	3	260	1	0	0	0	0	1	0	0	0	1621	130	5	2	906	2	C10orf81	10	115534677	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	685464	115534677	20000070	460	37705										
FAM160B1	57700	hgsc.bcm.edu	37	chr10	116605950	116605950	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcagttctgagatgggtattCtcacatccactgctctgctt	8	11	4	1	rs17853717		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr10:116605950C>A	ENST00000369248.4	+	10	1557	c.1222C>A	c.(1222-1224)Ctc>Atc	p.L408I	FAM160B1_ENST00000369250.3_Missense_Mutation_p.L408I	NM_020940.3	NP_065991.3	Q5W0V3	F16B1_HUMAN	family with sequence similarity 160, member B1	408			L -> I (in dbSNP:rs17853717). {ECO:0000269|PubMed:15489334}.							NS(1)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|lung(13)	25						GATGGGTATTCTCACATCCAC	0.433																																					p.L408I		Atlas-SNP	.											.	FAM160B1	107	.	0			c.C1222A						.						211	201	204					10																	116605950		2203	4300	6503	SO:0001583	missense	57700	exon10			GGTATTCTCACAT	AB046820	CCDS31290.1, CCDS44480.1	10q26.11	2008-06-05	2008-06-05	2008-06-05	ENSG00000151553	ENSG00000151553			29320	protein-coding gene	gene with protein product			"KIAA1600"	KIAA1600		10997877	Standard	NM_020940		Approved	bA106M7.3	uc001lcb.3	Q5W0V3	OTTHUMG00000019092	ENST00000369248.4:c.1222C>A	chr10.hg19:g.116605950C>A	ENSP00000358251:p.Leu408Ile	178.0	0.0		119.0	5.0	NM_020940	Q5H9P7|Q5W0V2|Q8IY76|Q9HCH2	Missense_Mutation	SNP	ENST00000369248.4	hg19	CCDS31290.1	.	.	.	.	.	.	.	.	.	.	C	18.24	3.579707	0.65992	.	.	ENSG00000151553	ENST00000369248;ENST00000369250	T;T	0.32023	1.47;1.47	6.17	4.31	0.51392	.	0.000000	0.85682	D	0.000000	T	0.42223	0.1193	L	0.49778	1.585	0.80722	D	1	D;D	0.64830	0.994;0.993	D;P	0.63877	0.919;0.854	T	0.17319	-1.0373	10	0.17832	T	0.49	-13.5125	11.1366	0.48378	0.1298:0.8047:0.0:0.0655	rs17853717	408;408	Q5W0V3-2;Q5W0V3	.;F16B1_HUMAN	I	408	ENSP00000358251:L408I;ENSP00000358253:L408I	ENSP00000358251:L408I	L	+	1	0	FAM160B1	116595940	0.999000	0.42202	0.993000	0.49108	0.979000	0.70002	2.849000	0.48286	1.602000	0.50124	0.655000	0.94253	CTC	.	C|1.000;|0.000		0.433	FAM160B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050499.1	XM_049351		A	116605950	C	A	116605950	3	1	260	1	0	0	0	0	1	0	0	0	5475	913	32	3	1260	3	FAM160B1	10	116605950	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	1071273	116605950	18928797	461	37706										
ATRNL1	26033	hgsc.bcm.edu	37	chr10	117093838	117093838	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgcatcaataataatgtgtgCgaacagtgtaaaaatctcac	7	7	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr10:117093838C>T	ENST00000355044.3	+	19	3210	c.3084C>T	c.(3082-3084)tgC>tgT	p.C1028C	ATRNL1_ENST00000423111.2_Intron|ATRNL1_ENST00000303745.7_Intron	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	1028	Laminin EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00460}.				G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(11)|liver(2)|lung(44)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		ATAATGTGTGCGAACAGTGTA	0.368																																					p.C1028C		Atlas-SNP	.											.	ATRNL1	219	.	0			c.C3084T						.						129	112	118					10																	117093838		2203	4300	6503	SO:0001819	synonymous_variant	26033	exon19			TGTGTGCGAACAG	AB011106	CCDS7592.1, CCDS73204.1	10q26	2004-03-04			ENSG00000107518	ENSG00000107518			29063	protein-coding gene	gene with protein product		612869				9628581	Standard	NM_001276282		Approved	KIAA0534, FLJ45344, ALP	uc001lcg.3	Q5VV63	OTTHUMG00000019096	ENST00000355044.3:c.3084C>T	chr10.hg19:g.117093838C>T		132.0	0.0		100.0	4.0	NM_207303	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Silent	SNP	ENST00000355044.3	hg19	CCDS7592.1																																																																																			.	.		0.368	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349		T	117093838	C	T	117093838	2	4	260	1	0	0	0	0	0	0	0	1	1207	776	27	1		1	ATRNL1	10	117093838	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	487888	117093838	18440909	462	37707										
KIAA1598	57698	hgsc.bcm.edu	37	chr10	118713701	118713701	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aacatgctgattcttttcaaCgttttattttctttatttag	4	6	3	1	rs372967078		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr10:118713701C>T	ENST00000355371.4	-	5	785	c.288G>A	c.(286-288)acG>acA	p.T96T	KIAA1598_ENST00000392903.2_Silent_p.T96T|KIAA1598_ENST00000260777.10_Silent_p.T96T|KIAA1598_ENST00000392901.4_Silent_p.T36T|KIAA1598_ENST00000497044.1_5'UTR	NM_001127211.2|NM_001258298.1|NM_001258299.1	NP_001120683.1|NP_001245227.1|NP_001245228.1	A0MZ66	SHOT1_HUMAN	KIAA1598	96					axon guidance (GO:0007411)|regulation of establishment of cell polarity (GO:2000114)|regulation of neuron migration (GO:2001222)	axonal growth cone (GO:0044295)				endometrium(1)|kidney(1)|large_intestine(5)|lung(3)	10				all cancers(201;0.00494)		TTCTTTTCAACGTTTTATTTT	0.313																																					p.T96T		Atlas-SNP	.											.	KIAA1598	74	.	0			c.G288A						.	C	,	1,4405	2.1+/-5.4	0,1,2202	92	80	84		288,288	-3.7	0.9	10		84	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	KIAA1598	NM_001127211.1,NM_018330.5	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	96/632,96/457	118713701	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	57698	exon5			TTTCAACGTTTTA	BC022348	CCDS31293.1, CCDS44482.1, CCDS58097.1, CCDS73207.1, CCDS73208.1	10q26.12	2007-01-30			ENSG00000187164	ENSG00000187164			29319	protein-coding gene	gene with protein product		611171				10997877, 17030985	Standard	NM_001127211		Approved	shootin1, shootin-1	uc009xyw.4	A0MZ66	OTTHUMG00000019114	ENST00000355371.4:c.288G>A	chr10.hg19:g.118713701C>T		122.0	0.0		89.0	4.0	NM_001258299	A8MYU7|B3KRD3|B3KRH2|B3KTE0|B3KTJ7|B3KTJ8|B4E3U1|B7Z7Z9|Q68DG1|Q6PIM5|Q9HCH4|Q9NUV0	Silent	SNP	ENST00000355371.4	hg19	CCDS44482.1																																																																																			.	.		0.313	KIAA1598-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018330		T	118713701	C	T	118713701	2	4	260	1	0	0	0	0	0	0	0	1	8255	523	19	1		1	KIAA1598	10	118713701	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	1619863	118713701	16821046	463	37708										
EIF3A	8661	hgsc.bcm.edu	37	chr10	120801517	120801517	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gaattttacctggcttgactAatggtctccaaggaccaggt	10	9	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr10:120801517A>T	ENST00000369144.3	-	19	3642	c.3515T>A	c.(3514-3516)tTa>tAa	p.L1172*	EIF3A_ENST00000541549.1_Nonsense_Mutation_p.L1138*	NM_003750.2	NP_003741.1	P56537	IF6_HUMAN	eukaryotic translation initiation factor 3, subunit A	0					mature ribosome assembly (GO:0042256)|ribosomal large subunit biogenesis (GO:0042273)|ribosomal subunit export from nucleus (GO:0000054)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lamin filament (GO:0005638)|nucleus (GO:0005634)	ribosomal large subunit binding (GO:0043023)|ribosome binding (GO:0043022)|translation initiation factor activity (GO:0003743)			endometrium(8)|kidney(4)|large_intestine(14)|lung(22)|prostate(1)|skin(4)|urinary_tract(3)	56		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0236)		TGGCTTGACTAATGGTCTCCA	0.413																																					p.L1172X		Atlas-SNP	.											.	EIF3A	142	.	0			c.T3515A						.						90	77	81					10																	120801517		2203	4300	6503	SO:0001587	stop_gained	8661	exon19			TTGACTAATGGTC	U78311	CCDS7608.1	10q26.11	2007-08-03	2007-07-27	2007-07-27	ENSG00000107581	ENSG00000107581			3271	protein-coding gene	gene with protein product		602039	"eukaryotic translation initiation factor 3, subunit 10 theta, 150/170kDa"	EIF3, EIF3S10		9054404, 8590280	Standard	NM_003750		Approved	eIF3-theta, eIF3-p170, KIAA0139, eIF3a, TIF32	uc001ldu.3	Q14152	OTTHUMG00000019144	ENST00000369144.3:c.3515T>A	chr10.hg19:g.120801517A>T	ENSP00000358140:p.Leu1172*	115.0	0.0		94.0	4.0	NM_003750	B7ZBG9|Q6IBN8|Q96TD5	Nonsense_Mutation	SNP	ENST00000369144.3	hg19	CCDS7608.1	.	.	.	.	.	.	.	.	.	.	A	40	8.112068	0.98659	.	.	ENSG00000107581	ENST00000369144;ENST00000541549	.	.	.	5.79	4.63	0.57726	.	0.178608	0.26578	N	0.023581	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.24483	T	0.36	-10.3137	10.8841	0.46957	0.8598:0.0:0.0:0.1402	.	.	.	.	X	1172;1138	.	ENSP00000358140:L1172X	L	-	2	0	EIF3A	120791507	1.000000	0.71417	0.994000	0.49952	0.984000	0.73092	4.995000	0.63908	0.988000	0.38734	0.533000	0.62120	TTA	.	.		0.413	EIF3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050634.1	NM_003750		T	120801517	A	T	120801517	4	4	260	1	0	0	0	0	0	1	0	0	5014	372	13	4	649	4	EIF3A	10	120801517	Nonsense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	2087816	120801517	14733230	464	37709										
DHX32	55760	hgsc.bcm.edu	37	chr10	127527737	127527737	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acagttgaggaagtaatcacGacaccacttttccacacagt	7	11	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr10:127527737G>A	ENST00000284690.3	-	9	2204	c.1714C>T	c.(1714-1716)Cgt>Tgt	p.R572C	BCCIP_ENST00000429863.2_Intron|DHX32_ENST00000284688.6_Missense_Mutation_p.R491C|BCCIP_ENST00000368759.5_Intron|DHX32_ENST00000368721.1_Missense_Mutation_p.R196C|BCCIP_ENST00000299130.3_Intron	NM_018180.2	NP_060650.2	Q7L7V1	DHX32_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 32	572						mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)	p.R572C(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(2)|stomach(1)	29		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				AAGTAATCACGACACCACTTT	0.453																																					p.R572C		Atlas-SNP	.											DHX32,colon,carcinoma,0,1	DHX32	67	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1714T						.						106	97	100					10																	127527737		2203	4300	6503	SO:0001583	missense	55760	exon9			AATCACGACACCA		CCDS7652.1	10q26.11-q26.2	2008-01-07	2004-01-29	2004-01-30	ENSG00000089876	ENSG00000089876		"DEAH-boxes"	16717	protein-coding gene	gene with protein product		607960	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32"	DDX32			Standard	NM_018180		Approved	FLJ10889, FLJ10694, DHLP1	uc001ljf.1	Q7L7V1	OTTHUMG00000019238	ENST00000284690.3:c.1714C>T	chr10.hg19:g.127527737G>A	ENSP00000284690:p.Arg572Cys	115.0	0.0		75.0	3.0	NM_018180	A8MSV2|D3DRF9|Q49AG5|Q5T3L0|Q5T3L5|Q96NY1|Q9BUN0|Q9H769|Q9NSL5|Q9NV74|Q9NVJ7	Missense_Mutation	SNP	ENST00000284690.3	hg19	CCDS7652.1	.	.	.	.	.	.	.	.	.	.	G	13.95	2.389125	0.42410	.	.	ENSG00000089876	ENST00000368721;ENST00000284690;ENST00000284688	T;T;T	0.19938	2.11;3.89;3.6	5.54	3.59	0.41128	.	0.618446	0.17770	N	0.162612	T	0.08846	0.0219	N	0.08118	0	0.19300	N	0.99998	D	0.56968	0.978	B	0.32805	0.153	T	0.21999	-1.0229	10	0.87932	D	0	-9.6028	12.7102	0.57086	0.0:0.1235:0.7493:0.1272	.	572	Q7L7V1	DHX32_HUMAN	C	196;572;491	ENSP00000357710:R196C;ENSP00000284690:R572C;ENSP00000284688:R491C	ENSP00000284688:R491C	R	-	1	0	DHX32	127517727	0.996000	0.38824	0.880000	0.34516	0.938000	0.57974	3.038000	0.49783	2.592000	0.87571	0.650000	0.86243	CGT	.	.		0.453	DHX32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050945.2	NM_018180		A	127527737	G	A	127527737	3	1	260	1	0	0	0	0	1	0	0	0	4507	1058	37	1	529	1	DHX32	10	127527737	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	6726220	127527737	8007010	465	37710										
ODF3	113746	hgsc.bcm.edu	37	chr11	197590	197590	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agcacacgcccaccaagctgCgtgcaccggcctacagcttc	9	18	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:197590C>A	ENST00000325113.4	+	3	456	c.139C>A	c.(139-141)Cgt>Agt	p.R47S	ODF3_ENST00000525282.1_Missense_Mutation_p.R47S|BET1L_ENST00000410108.1_Intron|ODF3_ENST00000342593.5_Missense_Mutation_p.R47S	NM_053280.3	NP_444510.2	Q96PU9	ODF3A_HUMAN	outer dense fiber of sperm tails 3	47					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	outer dense fiber (GO:0001520)				biliary_tract(1)|breast(1)|kidney(1)|large_intestine(2)|ovary(1)|prostate(2)|skin(1)	9		all_cancers(49;9.23e-07)|all_epithelial(84;0.000315)|Breast(177;0.00122)|Ovarian(85;0.0202)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;3.95e-27)|Epithelial(43;2.66e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.55e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		CACCAAGCTGCGTGCACCGGC	0.637																																					p.R47S		Atlas-SNP	.											.	ODF3	27	.	0			c.C139A						.						41	40	40					11																	197590		2203	4300	6503	SO:0001583	missense	113746	exon3			AAGCTGCGTGCAC	AB067774	CCDS7688.1, CCDS65981.1	11p15.5	2010-04-23			ENSG00000177947	ENSG00000177947			19905	protein-coding gene	gene with protein product	"cancer/testis antigen 135"	608356				11870087	Standard	NM_001286136		Approved	SHIPPO1, hSHIPPO, CT135	uc001lob.3	Q96PU9	OTTHUMG00000119073	ENST00000325113.4:c.139C>A	chr11.hg19:g.197590C>A	ENSP00000325868:p.Arg47Ser	85.0	0.0		71.0	10.0	NM_053280	B7ZLT0|Q69YX0	Missense_Mutation	SNP	ENST00000325113.4	hg19	CCDS7688.1	.	.	.	.	.	.	.	.	.	.	C	10.54	1.377675	0.24944	.	.	ENSG00000177947	ENST00000325113;ENST00000540150;ENST00000342593;ENST00000525282	T;T;T	0.32023	1.49;1.47;1.51	5.02	4.05	0.47172	.	0.000000	0.53938	D	0.000055	T	0.45296	0.1335	L	0.57536	1.79	0.09310	N	0.999999	D;D;D	0.89917	0.98;1.0;0.992	P;D;P	0.81914	0.859;0.995;0.9	T	0.25984	-1.0116	10	0.14656	T	0.56	-8.7064	11.3275	0.49456	0.181:0.819:0.0:0.0	.	47;47;47	B7ZLT0;F8W6Z3;Q96PU9	.;.;ODF3A_HUMAN	S	47	ENSP00000325868:R47S;ENSP00000339623:R47S;ENSP00000436588:R47S	ENSP00000325868:R47S	R	+	1	0	ODF3	187590	0.001000	0.12720	0.112000	0.21494	0.001000	0.01503	0.608000	0.24223	2.497000	0.84241	0.561000	0.74099	CGT	.	.		0.637	ODF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239287.1			A	197590	C	A	197590	3	1	260	1	0	0	0	0	1	0	0	0	10838	768	27	1	145	1	ODF3	11	197590	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10		197590	134808926	466	37711										
BET1L	60626	hgsc.bcm.edu	37	chr11	206034	206034	+	5'Flank	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gaatctcttccacagcgcccGggctctgagctgagaaaaga	11	12	2	3	rs199668338		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:206034G>T	ENST00000526104.1	+	0	0				BET1L_ENST00000529614.2_Missense_Mutation_p.P10Q|BET1L_ENST00000410108.1_Missense_Mutation_p.P10Q|BET1L_ENST00000325147.9_Missense_Mutation_p.P10Q|BET1L_ENST00000486280.1_5'UTR|RP11-304M2.5_ENST00000526963.1_RNA|RIC8A_ENST00000325207.5_5'Flank|BET1L_ENST00000382762.3_Missense_Mutation_p.P10Q|BET1L_ENST00000332865.6_Missense_Mutation_p.P10Q			Q9NPQ8	RIC8A_HUMAN	RIC8 guanine nucleotide exchange factor A						adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|basement membrane organization (GO:0071711)|cell migration involved in gastrulation (GO:0042074)|cell-cell adhesion involved in gastrulation (GO:0070586)|in utero embryonic development (GO:0001701)|vasculature development (GO:0001944)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(3)|kidney(1)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|skin(1)	13		all_cancers(49;9.23e-07)|all_epithelial(84;0.000315)|Breast(177;0.00122)|Ovarian(85;0.0202)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.45e-27)|Epithelial(43;2.94e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.86e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		CACAGCGCCCGGGCTCTGAGC	0.582																																					p.P10Q		Atlas-SNP	.											.	BET1L	7	.	0			c.C29A						.						68	65	66					11																	206034		2203	4300	6503	SO:0001631	upstream_gene_variant	51272	exon2			GCGCCCGGGCTCT	AK022870	CCDS7690.1, CCDS65982.1	11p15.5	2013-08-05	2013-08-05		ENSG00000177963	ENSG00000177963			29550	protein-coding gene	gene with protein product		609146	"resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)"			10985349, 11230166	Standard	XM_005253052		Approved	synembryn, synembryn-A	uc001lof.3	Q9NPQ8	OTTHUMG00000119069		chr11.hg19:g.206034G>T	Exception_encountered	119.0	0.0		70.0	4.0	NM_001098787	Q0P508|Q2T9J1|Q7Z352|Q96EZ1|Q96SZ2|Q9H064|Q9H5H3|Q9H9E7	Missense_Mutation	SNP	ENST00000526104.1	hg19		.	.	.	.	.	.	.	.	.	.	G	12.61	1.990213	0.35131	.	.	ENSG00000177951	ENST00000410108;ENST00000325147;ENST00000382762;ENST00000332865;ENST00000529614	.	.	.	4.17	4.17	0.49024	.	0.641285	0.15582	N	0.254831	T	0.49184	0.1542	N	0.04959	-0.14	0.80722	D	1	B;D	0.57571	0.089;0.98	B;P	0.58391	0.078;0.838	T	0.59364	-0.7468	9	0.52906	T	0.07	.	16.7427	0.85464	0.0:0.0:1.0:0.0	.	10;10	Q9NYM9;B8ZZS0	BET1L_HUMAN;.	Q	10	.	ENSP00000339093:P10Q	P	-	2	0	BET1L	196034	0.777000	0.28628	0.432000	0.26747	0.040000	0.13550	3.621000	0.54210	2.620000	0.88729	0.555000	0.69702	CCG	.	.		0.582	RIC8A-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000384761.1	NM_021932		T	206034	G	T	206034	1	4	260	0	1	0	0	0	0	0	0	0	1409	1116	39	1		1	BET1L	11	206034	5'Flank	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	8444	206034	134800482	467	37712										
ANO9	338440	hgsc.bcm.edu	37	chr11	420547	420547	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gcggatctccacgaggttgcTgaagagcgcgagcagcggcg	17	11	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:420547T>C	ENST00000332826.6	-	19	1786	c.1702A>G	c.(1702-1704)Agc>Ggc	p.S568G		NM_001012302.2	NP_001012302	A1A5B4	ANO9_HUMAN	anoctamin 9	568					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|negative regulation of intracellular calcium activated chloride channel activity (GO:1902939)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)			central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|lung(5)|ovary(1)|prostate(4)|skin(4)	21						ACGAGGTTGCTGAAGAGCGCG	0.692																																					p.S568G		Atlas-SNP	.											.	ANO9	61	.	0			c.A1702G						.						23	20	21					11																	420547		2197	4288	6485	SO:0001583	missense	338440	exon19			GGTTGCTGAAGAG	U33271	CCDS31326.1	11p15.5	2014-04-09	2008-08-28	2008-08-28	ENSG00000185101	ENSG00000185101		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	20679	protein-coding gene	gene with protein product			"tumor protein p53 inducible protein 5", "transmembrane protein 16J"	TP53I5, TMEM16J		9305847, 24692353	Standard	NM_001012302		Approved	PIG5	uc001lpi.2	A1A5B4	OTTHUMG00000165446	ENST00000332826.6:c.1702A>G	chr11.hg19:g.420547T>C	ENSP00000332788:p.Ser568Gly	142.0	0.0		80.0	4.0	NM_001012302	B3KUC4|B4E134|Q8TEN4	Missense_Mutation	SNP	ENST00000332826.6	hg19	CCDS31326.1	.	.	.	.	.	.	.	.	.	.	T	32	5.117698	0.94385	.	.	ENSG00000185101	ENST00000332826	T	0.64618	-0.11	4.05	4.05	0.47172	.	0.198055	0.40385	U	0.001116	T	0.71492	0.3346	M	0.66939	2.045	0.44282	D	0.997149	P;P	0.50710	0.914;0.938	P;P	0.55749	0.528;0.783	T	0.75575	-0.3270	10	0.66056	D	0.02	.	13.3569	0.60633	0.0:0.0:0.0:1.0	.	269;568	A1A5B4-2;A1A5B4	.;ANO9_HUMAN	G	568	ENSP00000332788:S568G	ENSP00000332788:S568G	S	-	1	0	ANO9	410547	1.000000	0.71417	0.998000	0.56505	0.971000	0.66376	5.026000	0.64103	1.611000	0.50210	0.374000	0.22700	AGC	.	.		0.692	ANO9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384116.1	NM_001012302		C	420547	T	C	420547	3	2	260	1	0	0	0	0	1	0	0	0	704	1580	55	2	666	2	ANO9	11	420547	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	214513	420547	134585969	468	37713										
AP2A2	161	hgsc.bcm.edu	37	chr11	1009727	1009727	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cttgaagaagttgatcctaaTcctgcgaatttcgtgggagc	11	8	0	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:1009727T>C	ENST00000448903.2	+	21	2793	c.2652T>C	c.(2650-2652)aaT>aaC	p.N884N	AP2A2_ENST00000534328.1_Intron|AP2A2_ENST00000332231.5_Silent_p.N885N	NM_001242837.1|NM_012305.3	NP_001229766.1|NP_036437.1	O94973	AP2A2_HUMAN	adaptor-related protein complex 2, alpha 2 subunit	884					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(2)	21		all_cancers(49;9.46e-06)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.75e-24)|BRCA - Breast invasive adenocarcinoma(625;5.73e-05)|Lung(200;0.0696)|LUSC - Lung squamous cell carcinoma(625;0.082)		TTGATCCTAATCCTGCGAATT	0.552																																					p.N885N		Atlas-SNP	.											.	AP2A2	50	.	0			c.T2655C						.						45	48	47					11																	1009727		1837	3977	5814	SO:0001819	synonymous_variant	161	exon21			TCCTAATCCTGCG	AB020706	CCDS44512.1, CCDS73234.1	11p15.5	2008-07-18			ENSG00000183020	ENSG00000183020			562	protein-coding gene	gene with protein product	"alpha-adaptin C; Huntingtin interacting protein J", "adaptin, alpha B", "clathrin-associated/assembly/adaptor protein, large, alpha 2"	607242		CLAPA2, ADTAB		9700202, 2564002	Standard	NM_012305		Approved	DKFZP564D1864, HYPJ, KIAA0899, HIP9	uc001lst.2	O94973	OTTHUMG00000165627	ENST00000448903.2:c.2652T>C	chr11.hg19:g.1009727T>C		136.0	0.0		96.0	4.0	NM_001242837	O75403|Q53ET1|Q96SI8	Silent	SNP	ENST00000448903.2	hg19	CCDS44512.1																																																																																			.	.		0.552	AP2A2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385431.2	NM_012305		C	1009727	T	C	1009727	2	2	260	1	0	0	0	0	0	0	0	1	740	1432	50	2		2	AP2A2	11	1009727	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	589180	1009727	133996789	469	37714										
MUC2	4583	hgsc.bcm.edu	37	chr11	1083289	1083289	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cggtctctacctggaggcggGggatgtggtcgtcaggcagg	19	9	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:1083289G>T	ENST00000441003.2	+	16	2216	c.2189G>T	c.(2188-2190)gGg>gTg	p.G730V	MUC2_ENST00000359061.5_Missense_Mutation_p.G730V	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	730					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	CTGGAGGCGGGGGATGTGGTC	0.677																																					p.G730V		Atlas-SNP	.											.	MUC2	614	.	0			c.G2189T						.						25	30	28					11																	1083289		2000	4154	6154	SO:0001583	missense	4583	exon16			AGGCGGGGGATGT	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.2189G>T	chr11.hg19:g.1083289G>T	ENSP00000415183:p.Gly730Val	62.0	0.0		74.0	4.0	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	hg19		.	.	.	.	.	.	.	.	.	.	g	9.329	1.060033	0.19987	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.52057	0.68;0.68	4.27	3.32	0.38043	.	0.196730	0.30565	U	0.009341	T	0.70657	0.3249	M	0.91249	3.19	0.58432	D	0.999995	D	0.76494	0.999	D	0.81914	0.995	T	0.75545	-0.3280	10	0.72032	D	0.01	.	9.1982	0.37242	0.1718:0.0:0.8282:0.0	.	730	E7EUV1	.	V	730	ENSP00000415183:G730V;ENSP00000351956:G730V	ENSP00000351956:G730V	G	+	2	0	MUC2	1073289	0.998000	0.40836	0.043000	0.18650	0.037000	0.13140	2.659000	0.46741	2.212000	0.71576	0.457000	0.33378	GGG	.	.		0.677	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1083289	G	T	1083289	3	4	260	1	0	0	0	0	1	0	0	0	9984	1232	43	3	2251	3	MUC2	11	1083289	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	73562	1083289	133923227	470	37715										
TSPAN32	10077	hgsc.bcm.edu	37	chr11	2337500	2337500	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agcttcctgaggacacaccaGcaggtcgcctccagcctgac	10	16	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:2337500G>A	ENST00000182290.4	+	7	722	c.585G>A	c.(583-585)caG>caA	p.Q195Q	TSPAN32_ENST00000451520.2_Silent_p.Q184Q|TSPAN32_ENST00000381121.3_Silent_p.Q195Q	NM_139022.2	NP_620591.3	Q96QS1	TSN32_HUMAN	tetraspanin 32	195					cell-cell signaling (GO:0007267)|cytoskeleton organization (GO:0007010)|defense response to protozoan (GO:0042832)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of cell proliferation (GO:0008285)|negative regulation of myeloid dendritic cell activation (GO:0030886)|platelet aggregation (GO:0070527)|regulation of defense response to virus (GO:0050688)	cell surface (GO:0009986)|integrin alphaIIb-beta3 complex (GO:0070442)|intracellular (GO:0005622)				breast(1)|central_nervous_system(1)|lung(4)|ovary(1)|skin(1)	8		all_epithelial(84;4.89e-05)|Breast(177;0.000962)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|all_neural(188;0.00791)|Lung NSC(207;0.209)		BRCA - Breast invasive adenocarcinoma(625;0.000533)|LUSC - Lung squamous cell carcinoma(625;0.082)|Lung(200;0.153)		GGACACACCAGCAGGTCGCCT	0.687																																					p.Q195Q		Atlas-SNP	.											.	TSPAN32	19	.	0			c.G585A						.						58	48	51					11																	2337500		2200	4295	6495	SO:0001819	synonymous_variant	10077	exon7			ACACCAGCAGGTC	AF176070	CCDS7733.1	11p15	2013-02-14	2005-08-16	2005-08-16	ENSG00000064201	ENSG00000064201		"Tetraspanins"	13410	protein-coding gene	gene with protein product		603853	"pan-hematopoietic expression"	TSSC6, PHEMX		10072438, 10950922	Standard	NM_139022		Approved		uc001lvy.1	Q96QS1	OTTHUMG00000009762	ENST00000182290.4:c.585G>A	chr11.hg19:g.2337500G>A		203.0	0.0		120.0	6.0	NM_139022	Q96KX4|Q9HC50|Q9HC51|Q9Y5U1	Silent	SNP	ENST00000182290.4	hg19	CCDS7733.1																																																																																			.	.		0.687	TSPAN32-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026912.2	NM_139024		A	2337500	G	A	2337500	2	1	260	1	0	0	0	0	0	0	0	1	16662	962	34	3		3	TSPAN32	11	2337500	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	1254211	2337500	132669016	471	37716										
ZNF195	7748	hgsc.bcm.edu	37	chr11	3392927	3392927	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggccacatccctgaacgtcaAcagagtctgaagaagaaaca	9	11	2	5			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:3392927A>G	ENST00000399602.4	-	2	136	c.10T>C	c.(10-12)Ttg>Ctg	p.L4L	ZNF195_ENST00000005082.9_Silent_p.L4L|ZNF195_ENST00000526601.1_Silent_p.L8L|ZNF195_ENST00000527386.1_5'UTR|AC123788.1_ENST00000581561.1_RNA|ZNF195_ENST00000528796.1_Silent_p.L4L|ZNF195_ENST00000343338.7_Silent_p.L8L|ZNF195_ENST00000429541.2_Silent_p.L8L|ZNF195_ENST00000438262.2_Silent_p.L8L|ZNF195_ENST00000354599.6_Silent_p.L4L	NM_001130520.2	NP_001123992.1	O14628	ZN195_HUMAN	zinc finger protein 195	4	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)	17		Medulloblastoma(188;0.00106)|Breast(177;0.00328)|all_neural(188;0.00681)|Ovarian(85;0.00965)		BRCA - Breast invasive adenocarcinoma(625;0.0361)|LUSC - Lung squamous cell carcinoma(625;0.2)		CTGAACGTCAACAGAGTCTGA	0.438																																					p.L8L		Atlas-SNP	.											.	ZNF195	77	.	0			c.T22C						.						62	67	66					11																	3392927		2193	4297	6490	SO:0001819	synonymous_variant	7748	exon3			ACGTCAACAGAGT		CCDS41604.1, CCDS44521.1, CCDS44522.1, CCDS55736.1, CCDS55737.1, CCDS58111.1	11p15.5	2013-01-08			ENSG00000005801	ENSG00000005801		"Zinc fingers, C2H2-type", "-"	12986	protein-coding gene	gene with protein product		602187				9344677	Standard	NM_001130520		Approved		uc001lxt.3	O14628	OTTHUMG00000011694	ENST00000399602.4:c.10T>C	chr11.hg19:g.3392927A>G		115.0	0.0		79.0	4.0	NM_001256825	A8K234|B3KTK2|B4DEL0|C9JLY9|L7MNK2|Q0VAJ6|Q658N8|Q6ZNA9	Silent	SNP	ENST00000399602.4	hg19	CCDS44522.1																																																																																			.	.		0.438	ZNF195-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000032321.2			G	3392927	A	G	3392927	2	3	260	1	0	0	0	0	0	0	0	1	17773	40	2	2		2	ZNF195	11	3392927	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1055427	3392927	131613589	472	37717										
STIM1	6786	hgsc.bcm.edu	37	chr11	4112725	4112725	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gccaagaaggcattactggcGctgaaccatgggctggacaa	13	10	0	2	rs201902860		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:4112725G>T	ENST00000300737.4	+	12	2324	c.1755G>T	c.(1753-1755)gcG>gcT	p.A585A	STIM1_ENST00000527651.1_3'UTR|STIM1_ENST00000533977.1_Silent_p.A412A	NM_003156.3	NP_003147.2	Q13586	STIM1_HUMAN	stromal interaction molecule 1	585					activation of store-operated calcium channel activity (GO:0032237)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|regulation of calcium ion transport (GO:0051924)|regulation of store-operated calcium entry (GO:2001256)|store-operated calcium entry (GO:0002115)	cortical endoplasmic reticulum (GO:0032541)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|growth cone (GO:0030426)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of plasma membrane (GO:0005887)|microtubule (GO:0005874)	calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|microtubule plus-end binding (GO:0051010)|store-operated calcium channel activity (GO:0015279)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|liver(1)|lung(14)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30		Breast(177;0.00159)|Medulloblastoma(188;0.00258)|all_neural(188;0.0233)		BRCA - Breast invasive adenocarcinoma(625;0.114)|LUSC - Lung squamous cell carcinoma(625;0.141)		CATTACTGGCGCTGAACCATG	0.622																																					p.A585A		Atlas-SNP	.											STIM1,NS,carcinoma,0,1	STIM1	55	.	0			c.G1755T						.						65	70	68					11																	4112725		2201	4298	6499	SO:0001819	synonymous_variant	6786	exon12			ACTGGCGCTGAAC	BC021300, U52426	CCDS7749.1, CCDS60706.1, CCDS73247.1	11p15.5	2014-09-17			ENSG00000167323	ENSG00000167323		"Sterile alpha motif (SAM) domain containing"	11386	protein-coding gene	gene with protein product		605921				8921403, 11463338, 11983428	Standard	NM_003156		Approved	GOK, D11S4896E	uc021qco.1	Q13586	OTTHUMG00000133360	ENST00000300737.4:c.1755G>T	chr11.hg19:g.4112725G>T		92.0	0.0		65.0	3.0	NM_003156	E9PQJ4|Q8N382	Silent	SNP	ENST00000300737.4	hg19	CCDS7749.1	.	.	.	.	.	.	.	.	.	.	G	5.303	0.241362	0.10077	.	.	ENSG00000167323	ENST00000526596	.	.	.	5.44	2.26	0.28386	.	.	.	.	.	T	0.51924	0.1703	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42682	-0.9437	4	.	.	.	-17.1477	4.8331	0.13451	0.2008:0.174:0.6252:0.0	.	.	.	.	L	347	.	.	R	+	2	0	STIM1	4069301	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.584000	0.36589	0.726000	0.32339	0.655000	0.94253	CGC	.	.		0.622	STIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257196.1	NM_003156		T	4112725	G	T	4112725	2	4	260	1	0	0	0	0	0	0	0	1	15298	1074	38	1		1	STIM1	11	4112725	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	719798	4112725	130893791	473	37718										
MMP26	56547	hgsc.bcm.edu	37	chr11	5013445	5013445	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tttttttctgtttccataggAgaaaaatgttcatctgacat	6	6	3	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:5013445A>G	ENST00000380390.1	+	7	975	c.759A>G	c.(757-759)ggA>ggG	p.G253G	MMP26_ENST00000300762.1_Splice_Site_p.G253G			Q9NRE1	MMP26_HUMAN	matrix metallopeptidase 26	253					collagen catabolic process (GO:0030574)|proteolysis (GO:0006508)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(11)|pancreas(1)|skin(3)|stomach(1)	22		Medulloblastoma(188;0.0025)|Breast(177;0.0204)|all_neural(188;0.0227)		Epithelial(150;1.33e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0287)|LUSC - Lung squamous cell carcinoma(625;0.191)	Marimastat(DB00786)	TTTCCATAGGAGAAAAATGTT	0.383																																					p.G253G		Atlas-SNP	.											.	MMP26	49	.	0			c.A759G						.						89	74	79					11																	5013445		2201	4298	6499	SO:0001630	splice_region_variant	56547	exon6			CATAGGAGAAAAA	AF230354	CCDS7752.1	11p15	2008-07-18	2005-08-08		ENSG00000167346	ENSG00000167346	3.4.24.1		14249	protein-coding gene	gene with protein product	"matrilysin 2"	605470	"matrix metalloproteinase 26"			10801841, 10824119	Standard	NM_021801		Approved	endometase, MGC126590, MGC126592	uc001lzv.3	Q9NRE1	OTTHUMG00000066442	ENST00000380390.1:c.758-1A>G	chr11.hg19:g.5013445A>G		187.0	0.0		98.0	4.0	NM_021801	Q3MJ78|Q9GZS2|Q9NR87	Silent	SNP	ENST00000380390.1	hg19	CCDS7752.1																																																																																			.	.		0.383	MMP26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142058.3	NM_021801	Silent	G	5013445	A	G	5013445	5	3	260	1	0	0	0	0	0	0	1	0	9672	318	11	2	781	2	MMP26	11	5013445	Splice_Site	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	900720	5013445	129993071	474	37719										
OR52N5	390075	hgsc.bcm.edu	37	chr11	5799494	5799494	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggtctagagccatgagcatgAgcaccccagactccacacct	9	15	1	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:5799494A>G	ENST00000317093.2	-	1	403	c.371T>C	c.(370-372)cTc>cCc	p.L124P	TRIM5_ENST00000380027.1_Intron	NM_001001922.2	NP_001001922.2	Q8NH56	O52N5_HUMAN	olfactory receptor, family 52, subfamily N, member 5	124						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(3)|liver(1)|lung(17)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.05e-11)|LUSC - Lung squamous cell carcinoma(625;0.112)|BRCA - Breast invasive adenocarcinoma(625;0.135)|Lung(200;0.195)		CATGAGCATGAGCACCCCAGA	0.493																																					p.L124P		Atlas-SNP	.											.	OR52N5	58	.	0			c.T371C						.						112	95	101					11																	5799494		2120	4085	6205	SO:0001583	missense	390075	exon1			AGCATGAGCACCC	AB065535	CCDS31397.1	11p15.4	2012-08-09			ENSG00000181009	ENSG00000181009		"GPCR / Class A : Olfactory receptors"	15231	protein-coding gene	gene with protein product							Standard	NM_001001922		Approved	OR52N5Q	uc010qzn.2	Q8NH56	OTTHUMG00000168799	ENST00000317093.2:c.371T>C	chr11.hg19:g.5799494A>G	ENSP00000322866:p.Leu124Pro	170.0	0.0		107.0	5.0	NM_001001922	B9EH12|Q6IFG2	Missense_Mutation	SNP	ENST00000317093.2	hg19	CCDS31397.1	.	.	.	.	.	.	.	.	.	.	A	18.86	3.713303	0.68730	.	.	ENSG00000181009	ENST00000317093	T	0.07444	3.19	3.7	3.7	0.42460	GPCR, rhodopsin-like superfamily (1);	0.000000	0.28624	U	0.014697	T	0.41581	0.1165	H	0.97758	4.07	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.59402	-0.7461	10	0.87932	D	0	.	11.6494	0.51279	1.0:0.0:0.0:0.0	.	124	Q8NH56	O52N5_HUMAN	P	124	ENSP00000322866:L124P	ENSP00000322866:L124P	L	-	2	0	OR52N5	5756070	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.816000	0.91979	1.679000	0.50963	0.405000	0.27470	CTC	.	.		0.493	OR52N5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401141.1	NM_001001922		G	5799494	A	G	5799494	3	3	260	1	0	0	0	0	1	0	0	0	11139	304	11	2	607	2	OR52N5	11	5799494	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	786049	5799494	129207022	475	37720										
SMPD1	322	hgsc.bcm.edu	37	chr11	6415247	6415247	+	IGR	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccttcctggcacccagtgcaActacctacatcggccttaat	6	16	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:6415247A>G	ENST00000609360.1	-	0	2642				SMPD1_ENST00000299397.3_Missense_Mutation_p.T444A|SMPD1_ENST00000527275.1_Missense_Mutation_p.T487A|SMPD1_ENST00000342245.4_Missense_Mutation_p.T488A|SMPD1_ENST00000356761.2_Missense_Mutation_p.T432A|APBB1_ENST00000526240.1_5'Flank	NM_001164.3	NP_001155.1	O00213	APBB1_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 1 (Fe65)						apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|histone H4 acetylation (GO:0043967)|negative regulation of cell growth (GO:0030308)|negative regulation of thymidylate synthase biosynthetic process (GO:0050760)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|proline-rich region binding (GO:0070064)|transcription factor binding (GO:0008134)			breast(4)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|prostate(2)|skin(1)|urinary_tract(1)	24		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;6.49e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)		ACCCAGTGCAACTACCTACAT	0.552																																					p.T488A	GBM(147;1810 2556 5672 39622)	Atlas-SNP	.											.	SMPD1	108	.	0			c.A1462G						.						54	55	55					11																	6415247		2201	4296	6497	SO:0001628	intergenic_variant	6609	exon5			AGTGCAACTACCT	L77864	CCDS31410.1, CCDS58114.1, CCDS66015.1, CCDS66016.1, CCDS66017.1, CCDS66018.1	11p15	2008-02-01				ENSG00000166313			581	protein-coding gene	gene with protein product		602709		RIR		8955346, 8894693	Standard	NM_001164		Approved	Fe65	uc001mcy.1	O00213			chr11.hg19:g.6415247A>G		158.0	0.0		113.0	5.0	NM_000543	A1E379|A6NH82|A6NL69|B7Z1J5|B7Z1J6|B7Z2Y0|D3DQT2|Q7Z324|Q96A93|V9GYK0|V9GYT4	Missense_Mutation	SNP	ENST00000609360.1	hg19		.	.	.	.	.	.	.	.	.	.	A	23.1	4.380891	0.82792	.	.	ENSG00000166311	ENST00000299397;ENST00000356761;ENST00000342245;ENST00000527275	D;D;D;D	0.98987	-5.3;-5.3;-5.3;-5.3	4.74	4.74	0.60224	.	0.000000	0.85682	D	0.000000	D	0.99330	0.9765	M	0.90425	3.115	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.85130	0.996;0.997;0.975	D	0.98897	1.0775	10	0.87932	D	0	-33.2474	13.2161	0.59861	1.0:0.0:0.0:0.0	.	487;444;486	E9PKS3;G3XAB5;P17405	.;.;ASM_HUMAN	A	444;432;488;487	ENSP00000299397:T444A;ENSP00000349203:T432A;ENSP00000340409:T488A;ENSP00000435350:T487A	ENSP00000299397:T444A	T	+	1	0	SMPD1	6371823	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	8.798000	0.91888	2.006000	0.58801	0.459000	0.35465	ACT	.	.		0.552	APBB1-023	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471831.1	NM_001164		G	6415247	A	G	6415247	1	3	260	0	1	0	0	0	0	0	0	0	14819	43	2	2		2	SMPD1	11	6415247	IGR	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	615753	6415247	128591269	476	37721										
ST5	6764	hgsc.bcm.edu	37	chr11	8717087	8717087	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agtactgctccactcgctgcTcaaaaaggcctgggtaaaag	10	11	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:8717087T>C	ENST00000534127.1	-	22	3687	c.3302A>G	c.(3301-3303)gAg>gGg	p.E1101G	ST5_ENST00000530991.1_Missense_Mutation_p.E573G|ST5_ENST00000526757.1_Missense_Mutation_p.E681G|RPL27A_ENST00000531102.1_Intron|ST5_ENST00000530438.1_Missense_Mutation_p.E681G|ST5_ENST00000534278.1_Missense_Mutation_p.E292G|ST5_ENST00000313726.6_Missense_Mutation_p.E1101G|ST5_ENST00000357665.1_Missense_Mutation_p.E1101G|ST5_ENST00000526099.1_Missense_Mutation_p.E614G|RP11-152H18.3_ENST00000529883.1_RNA	NM_005418.3	NP_005409.3	P78524	ST5_HUMAN	suppression of tumorigenicity 5	1101					positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(13)|liver(1)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	39				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)		CACTCGCTGCTCAAAAAGGCC	0.493																																					p.E1101G		Atlas-SNP	.											.	ST5	85	.	0			c.A3302G						.						117	103	108					11																	8717087		2201	4296	6497	SO:0001583	missense	6764	exon22			CGCTGCTCAAAAA	U15131	CCDS7791.1, CCDS7792.1	11p15	2012-10-04				ENSG00000166444		"DENN/MADD domain containing"	11350	protein-coding gene	gene with protein product	"DENN/MADD domain containing 2B"	140750				1390339	Standard	NM_005418		Approved	HTS1, DENND2B, p126	uc001mgt.3	P78524		ENST00000534127.1:c.3302A>G	chr11.hg19:g.8717087T>C	ENSP00000433528:p.Glu1101Gly	78.0	0.0		60.0	4.0	NM_005418	B2R6X7|B3KXQ6|P78523|Q16492|Q7KYY2|Q7KZ12|Q8NE12|Q9BQQ6	Missense_Mutation	SNP	ENST00000534127.1	hg19	CCDS7791.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.409675	0.83340	.	.	ENSG00000166444	ENST00000526757;ENST00000534127;ENST00000313726;ENST00000530991;ENST00000357665;ENST00000526099;ENST00000534278;ENST00000530438	T;T;T;T;T;T;T;T	0.17528	2.74;2.85;2.85;2.76;2.85;2.73;2.27;2.74	5.76	4.63	0.57726	.	0.000000	0.85682	D	0.000000	T	0.36138	0.0956	L	0.58810	1.83	0.58432	D	0.999998	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.78314	0.979;0.991;0.991	T	0.07271	-1.0781	10	0.87932	D	0	-18.1556	11.2879	0.49232	0.0:0.072:0.0:0.928	.	614;681;1101	B4DDL8;P78524-2;P78524	.;.;ST5_HUMAN	G	681;1101;1101;573;1101;614;292;681	ENSP00000435097:E681G;ENSP00000433528:E1101G;ENSP00000319678:E1101G;ENSP00000432887:E573G;ENSP00000350294:E1101G;ENSP00000436808:E614G;ENSP00000433349:E292G;ENSP00000436802:E681G	ENSP00000319678:E1101G	E	-	2	0	ST5	8673663	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	7.472000	0.80996	1.012000	0.39366	0.454000	0.30748	GAG	.	.		0.493	ST5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386518.1	NM_005418		C	8717087	T	C	8717087	3	2	260	1	0	0	0	0	1	0	0	0	15235	1551	54	2	119	2	ST5	11	8717087	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	2301840	8717087	126289429	477	37722										
SWAP70	23075	hgsc.bcm.edu	37	chr11	9715709	9715709	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gcaggtcctttcccataaccTgtgcacggtgctgaaggttc	11	12	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:9715709T>C	ENST00000318950.6	+	2	219	c.116T>C	c.(115-117)cTg>cCg	p.L39P	SWAP70_ENST00000447399.2_Missense_Mutation_p.L39P	NM_015055.2	NP_055870.2	Q9UH65	SWP70_HUMAN	SWAP switching B-cell complex 70kDa subunit	39					isotype switching (GO:0045190)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|DNA binding (GO:0003677)			NS(1)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(2)|pancreas(1)	11				all cancers(16;1.21e-10)|Epithelial(150;2.81e-09)|BRCA - Breast invasive adenocarcinoma(625;0.00649)		TCCCATAACCTGTGCACGGTG	0.502																																					p.L39P		Atlas-SNP	.											.	SWAP70	40	.	0			c.T116C						.						134	121	125					11																	9715709		2201	4294	6495	SO:0001583	missense	23075	exon2			ATAACCTGTGCAC	AB014540	CCDS31426.1, CCDS73257.1	11p15	2013-01-10			ENSG00000133789	ENSG00000133789		"Pleckstrin homology (PH) domain containing", "EF-hand domain containing"	17070	protein-coding gene	gene with protein product		604762				9734811, 10681448	Standard	XM_005252829		Approved	KIAA0640, SWAP-70	uc001mhw.3	Q9UH65	OTTHUMG00000165865	ENST00000318950.6:c.116T>C	chr11.hg19:g.9715709T>C	ENSP00000315630:p.Leu39Pro	144.0	0.0		108.0	5.0	NM_015055	D3DQV1|O75135|Q7LCY6|Q9P061|Q9P0Z8	Missense_Mutation	SNP	ENST00000318950.6	hg19	CCDS31426.1	.	.	.	.	.	.	.	.	.	.	T	16.19	3.054117	0.55218	.	.	ENSG00000133789	ENST00000447399;ENST00000318950	D;T	0.86956	-2.19;2.6	5.93	5.93	0.95920	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.93677	0.7980	M	0.80982	2.52	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.998	D	0.94345	0.7574	10	0.87932	D	0	-12.0065	16.3943	0.83563	0.0:0.0:0.0:1.0	.	39;39;39	E7EMB1;Q9UH65;B3KUB9	.;SWP70_HUMAN;.	P	39	ENSP00000399056:L39P;ENSP00000315630:L39P	ENSP00000315630:L39P	L	+	2	0	SWAP70	9672285	1.000000	0.71417	1.000000	0.80357	0.575000	0.36095	8.040000	0.89188	2.281000	0.76405	0.533000	0.62120	CTG	.	.		0.502	SWAP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386766.2	NM_015055		C	9715709	T	C	9715709	3	2	260	1	0	0	0	0	1	0	0	0	15440	1580	55	2	122	2	SWAP70	11	9715709	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	998622	9715709	125290807	478	37723										
AMPD3	272	hgsc.bcm.edu	37	chr11	10514945	10514945	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	catgaaccaaaagcatctgcTgcgcttcatcaagcacacat	6	13	3	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:10514945T>C	ENST00000396554.3	+	7	1357	c.1016T>C	c.(1015-1017)cTg>cCg	p.L339P	AMPD3_ENST00000444303.2_Missense_Mutation_p.L171P	NM_000480.2	NP_000471.1	Q01432	AMPD3_HUMAN	adenosine monophosphate deaminase 3	330					ADP metabolic process (GO:0046031)|AMP catabolic process (GO:0006196)|ATP metabolic process (GO:0046034)|energy homeostasis (GO:0097009)|IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(3)|skin(1)	25				all cancers(16;1.14e-08)|Epithelial(150;2.83e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0291)		AAGCATCTGCTGCGCTTCATC	0.617																																					p.L339P		Atlas-SNP	.											.	AMPD3	68	.	0			c.T1016C						.						117	118	117					11																	10514945		2201	4294	6495	SO:0001583	missense	272	exon7			ATCTGCTGCGCTT	M84722	CCDS7802.1, CCDS41617.1, CCDS44537.1, CCDS53601.1	11p15	2010-02-10	2010-02-10			ENSG00000133805	3.5.4.6		470	protein-coding gene	gene with protein product	"erythrocyte-specific AMP deaminase"	102772	"adenosine monophosphate deaminase (isoform E)"			1400401	Standard	NM_001172430		Approved		uc001min.1	Q01432		ENST00000396554.3:c.1016T>C	chr11.hg19:g.10514945T>C	ENSP00000379802:p.Leu339Pro	147.0	0.0		85.0	4.0	NM_000480	A0AUX0|B7Z2S2|B7Z763|B7Z877	Missense_Mutation	SNP	ENST00000396554.3	hg19	CCDS7802.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.585077	0.86748	.	.	ENSG00000133805	ENST00000444303;ENST00000396554;ENST00000396553;ENST00000528723;ENST00000529507	D;D;D;D;D	0.92911	-3.13;-3.13;-3.13;-3.13;-3.13	5.44	5.44	0.79542	Adenosine/AMP deaminase (1);	0.000000	0.85682	D	0.000000	D	0.97167	0.9074	H	0.94264	3.515	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.98306	1.0521	10	0.87932	D	0	-11.9062	15.4924	0.75619	0.0:0.0:0.0:1.0	.	337;330;339	B7Z763;Q01432;A0AUX0	.;AMPD3_HUMAN;.	P	171;339;330;337;330	ENSP00000396000:L171P;ENSP00000379802:L339P;ENSP00000379801:L330P;ENSP00000436987:L337P;ENSP00000431648:L330P	ENSP00000379801:L330P	L	+	2	0	AMPD3	10471521	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	8.040000	0.89188	2.061000	0.61500	0.459000	0.35465	CTG	.	.		0.617	AMPD3-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385783.2	NM_000480		C	10514945	T	C	10514945	3	2	260	1	0	0	0	0	1	0	0	0	587	1580	55	2	1062	2	AMPD3	11	10514945	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	799236	10514945	124491571	479	37724										
DKK3	27122	hgsc.bcm.edu	37	chr11	12020311	12020311	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgaaaagaccatttgtccagTctggttgttggttatctaca	9	7	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:12020311T>C	ENST00000396505.2	-	4	605	c.367A>G	c.(367-369)Act>Gct	p.T123A	DKK3_ENST00000525493.1_Missense_Mutation_p.T123A|DKK3_ENST00000326932.4_Missense_Mutation_p.T123A|DKK3_ENST00000527132.1_Intron|DKK3_ENST00000450094.2_Intron	NM_015881.5	NP_056965.3	Q9UBP4	DKK3_HUMAN	dickkopf WNT signaling pathway inhibitor 3	123					adrenal gland development (GO:0030325)|anatomical structure morphogenesis (GO:0009653)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of transcription, DNA-templated (GO:0045892)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)				breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(1)|pancreas(1)	8				Epithelial(150;0.000502)		ATTTGTCCAGTCTGGTTGTTG	0.403																																					p.T123A		Atlas-SNP	.											.	DKK3	35	.	0			c.A367G						.						180	161	168					11																	12020311		2201	4294	6495	SO:0001583	missense	27122	exon3			GTCCAGTCTGGTT	AF177396	CCDS7808.1	11p15.3	2013-05-15	2013-05-15		ENSG00000050165	ENSG00000050165			2893	protein-coding gene	gene with protein product	"regulated in glioma"	605416	"dickkopf (Xenopus laevis) homolog 3", "dickkopf 3 homolog (Xenopus laevis)"			10570958	Standard	XM_006718177		Approved	REIC, RIG	uc001mjv.3	Q9UBP4	OTTHUMG00000165709	ENST00000396505.2:c.367A>G	chr11.hg19:g.12020311T>C	ENSP00000379762:p.Thr123Ala	159.0	0.0		114.0	5.0	NM_001018057	A8K1I2|D3DQW1|Q9ULB7	Missense_Mutation	SNP	ENST00000396505.2	hg19	CCDS7808.1	.	.	.	.	.	.	.	.	.	.	T	12.68	2.011963	0.35511	.	.	ENSG00000050165	ENST00000396505;ENST00000326932;ENST00000366345;ENST00000525493;ENST00000533813	T;T;T;T	0.27104	1.95;1.95;1.93;1.69	4.99	4.99	0.66335	.	0.048743	0.85682	D	0.000000	T	0.29620	0.0739	M	0.62723	1.935	0.80722	D	1	B;P	0.48294	0.02;0.908	B;B	0.44224	0.016;0.444	T	0.04255	-1.0965	10	0.33141	T	0.24	-16.6146	12.3088	0.54918	0.0:0.0:0.0:1.0	.	123;123	F6SYF8;Q9UBP4	.;DKK3_HUMAN	A	123;123;66;123;123	ENSP00000379762:T123A;ENSP00000314910:T123A;ENSP00000433112:T123A;ENSP00000435269:T123A	ENSP00000314910:T123A	T	-	1	0	DKK3	11976887	1.000000	0.71417	0.983000	0.44433	0.321000	0.28281	4.075000	0.57584	2.106000	0.64143	0.533000	0.62120	ACT	.	.		0.403	DKK3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385863.1	NM_013253		C	12020311	T	C	12020311	3	2	260	1	0	0	0	0	1	0	0	0	4548	1667	58	2	705	2	DKK3	11	12020311	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1505366	12020311	122986205	480	37725										
MICAL2	9645	hgsc.bcm.edu	37	chr11	12278379	12278379	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aacctgggaggcagcgacacGtgttacttctgtaagaaacg	12	9	1	1	rs555210447		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:12278379G>A	ENST00000256194.4	+	24	3291	c.3003G>A	c.(3001-3003)acG>acA	p.T1001T	MICAL2_ENST00000342902.5_Silent_p.T980T|MICAL2_ENST00000537344.1_Silent_p.T811T|MICAL2_ENST00000527546.1_Silent_p.T811T|MICAL2_ENST00000379612.3_Silent_p.T775T	NM_001282663.1|NM_014632.2	NP_001269592.1|NP_055447.1	O94851	MICA2_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 2	1001	LIM zinc-binding. {ECO:0000255|PROSITE- ProRule:PRU00125}.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|heart development (GO:0007507)|heart looping (GO:0001947)|oxidation-reduction process (GO:0055114)|positive regulation of transcription via serum response element binding (GO:0010735)|sulfur oxidation (GO:0019417)	nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|NADPH:sulfur oxidoreductase activity (GO:0043914)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	47				Epithelial(150;0.00552)		GCAGCGACACGTGTTACTTCT	0.542																																					p.T1001T		Atlas-SNP	.											.	MICAL2	114	.	0			c.G3003A						.						134	107	116					11																	12278379		2201	4294	6495	SO:0001819	synonymous_variant	9645	exon24			CGACACGTGTTAC	AB018293	CCDS7809.1, CCDS60726.1, CCDS60727.1, CCDS60728.1	11p15.3	2014-08-12	2013-03-26		ENSG00000133816	ENSG00000133816			24693	protein-coding gene	gene with protein product		608881				12110185	Standard	XM_005253249		Approved	KIAA0750	uc001mjz.3	O94851	OTTHUMG00000165744	ENST00000256194.4:c.3003G>A	chr11.hg19:g.12278379G>A		104.0	0.0		69.0	4.0	NM_014632	B4DGZ0|B7Z849|D3DQW5|G3XAC8|Q5KTR3|Q5KTR4|Q7Z3A8	Silent	SNP	ENST00000256194.4	hg19	CCDS7809.1																																																																																			.	.		0.542	MICAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385993.1	NM_014632		A	12278379	G	A	12278379	2	1	260	1	0	0	0	0	0	0	0	1	9579	1132	40	1		1	MICAL2	11	12278379	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	258068	12278379	122728137	481	37726										
CYP2R1	120227	hgsc.bcm.edu	37	chr11	14902277	14902277	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tttacagctaatcgtctgtgAtcaacccatcctcggccata	6	13	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:14902277A>G	ENST00000334636.5	-	3	451	c.405T>C	c.(403-405)gaT>gaC	p.D135D	CYP2R1_ENST00000526489.1_5'UTR|CYP2R1_ENST00000532378.1_Intron	NM_024514.4	NP_078790.2	Q6VVX0	CP2R1_HUMAN	cytochrome P450, family 2, subfamily R, polypeptide 1	135					small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)|vitamin D3 25-hydroxylase activity (GO:0030343)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14					Cholecalciferol(DB00169)|Ergocalciferol(DB00153)	ATCGTCTGTGATCAACCCATC	0.318																																					p.D135D	NSCLC(173;1584 2058 26117 29365 41534)	Atlas-SNP	.											.	CYP2R1	41	.	0			c.T405C						.						35	36	36					11																	14902277		2197	4292	6489	SO:0001819	synonymous_variant	120227	exon3			TCTGTGATCAACC	AY323817	CCDS7818.1	11p15.2	2008-02-05			ENSG00000186104	ENSG00000186104		"Cytochrome P450s"	20580	protein-coding gene	gene with protein product		608713				12464240, 12867411	Standard	XM_005252788		Approved		uc001mlr.3	Q6VVX0	OTTHUMG00000165900	ENST00000334636.5:c.405T>C	chr11.hg19:g.14902277A>G		167.0	0.0		99.0	4.0	NM_024514	Q2M3H3|Q5RT65	Silent	SNP	ENST00000334636.5	hg19	CCDS7818.1																																																																																			.	.		0.318	CYP2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386985.1	NM_024514		G	14902277	A	G	14902277	2	3	260	1	0	0	0	0	0	0	0	1	4175	330	12	2		2	CYP2R1	11	14902277	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	2623898	14902277	120104239	482	37727										
UEVLD	55293	hgsc.bcm.edu	37	chr11	18557968	18557968	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gttacctgttggacagctgcActtgagaggtatgactcact	11	9	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:18557968A>G	ENST00000396197.3	-	10	1137	c.1109T>C	c.(1108-1110)gTg>gCg	p.V370A	UEVLD_ENST00000543987.1_Missense_Mutation_p.V370A|UEVLD_ENST00000320750.6_Missense_Mutation_p.V348A|UEVLD_ENST00000541984.1_Intron|UEVLD_ENST00000379387.4_Missense_Mutation_p.V348A|UEVLD_ENST00000540666.1_5'UTR|UEVLD_ENST00000535484.1_Missense_Mutation_p.V332A	NM_001040697.2|NM_001261384.1	NP_001035787.1|NP_001248313.1			UEV and lactate/malate dehyrogenase domains											endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						GGACAGCTGCACTTGAGAGGT	0.358																																					p.V370A		Atlas-SNP	.											.	UEVLD	58	.	0			c.T1109C						.						173	159	164					11																	18557968		2199	4293	6492	SO:0001583	missense	55293	exon10			AGCTGCACTTGAG	AF503350	CCDS7843.1, CCDS41624.1, CCDS58122.1, CCDS58123.1, CCDS58124.1, CCDS58125.1, CCDS73266.1	11p15.1	2006-07-14			ENSG00000151116	ENSG00000151116			30866	protein-coding gene	gene with protein product		610985				12427560	Standard	NM_001040697		Approved	Attp, UEV3	uc001mot.4	Q8IX04	OTTHUMG00000167729	ENST00000396197.3:c.1109T>C	chr11.hg19:g.18557968A>G	ENSP00000379500:p.Val370Ala	145.0	0.0		85.0	4.0	NM_001040697		Missense_Mutation	SNP	ENST00000396197.3	hg19	CCDS41624.1	.	.	.	.	.	.	.	.	.	.	A	1.581	-0.531559	0.04112	.	.	ENSG00000151116	ENST00000543987;ENST00000535484;ENST00000396197;ENST00000320750;ENST00000379387;ENST00000540110	D;D;T;D;T	0.82711	-1.64;-1.64;-0.13;-1.64;-0.13	5.38	4.12	0.48240	Lactate/malate dehydrogenase, C-terminal (1);Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal (2);	0.586621	0.17859	N	0.159594	T	0.59155	0.2173	N	0.02539	-0.55	0.80722	D	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.0;0.001	T	0.49716	-0.8910	10	0.30078	T	0.28	-0.7115	6.1795	0.20463	0.8451:0.0:0.1549:0.0	.	348;348;370;370	B4DL43;Q8IX04-3;Q8IX04-2;Q8IX04	.;.;.;UEVLD_HUMAN	A	370;332;370;348;348;147	ENSP00000442974:V370A;ENSP00000441092:V332A;ENSP00000379500:V370A;ENSP00000323353:V348A;ENSP00000368697:V348A	ENSP00000323353:V348A	V	-	2	0	UEVLD	18514544	0.153000	0.22777	0.995000	0.50966	0.206000	0.24218	1.365000	0.34182	0.834000	0.34852	0.374000	0.22700	GTG	.	.		0.358	UEVLD-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395923.2	NM_018314		G	18557968	A	G	18557968	3	3	260	1	0	0	0	0	1	0	0	0	16948	159	6	2	318	2	UEVLD	11	18557968	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	3655691	18557968	116448548	483	37728										
NAV2	89797	hgsc.bcm.edu	37	chr11	20077344	20077344	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccactgtcacccagatgagcTtgtccaacccgaccatgctg	8	16	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:20077344T>C	ENST00000396087.3	+	20	4840	c.4741T>C	c.(4741-4743)Ttg>Ctg	p.L1581L	NAV2_ENST00000527559.2_Silent_p.L1510L|NAV2_ENST00000533917.1_Silent_p.L622L|NAV2_ENST00000349880.4_Silent_p.L1558L|NAV2_ENST00000360655.4_Silent_p.L1494L|NAV2_ENST00000311043.8_Silent_p.L622L|NAV2_ENST00000540292.1_Silent_p.L1512L|NAV2_ENST00000396085.1_Silent_p.L1558L	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	1581	Ser-rich.				glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						CCAGATGAGCTTGTCCAACCC	0.498																																					p.L1581L		Atlas-SNP	.											.	NAV2	255	.	0			c.T4741C						.						119	102	107					11																	20077344		2203	4300	6503	SO:0001819	synonymous_variant	89797	exon20			ATGAGCTTGTCCA	AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 2", "retinoic acid inducible gene in neuroblastoma 1", "helicase, APC down-regulated 1"	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.4741T>C	chr11.hg19:g.20077344T>C		112.0	0.0		73.0	4.0	NM_001244963	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Silent	SNP	ENST00000396087.3	hg19	CCDS58126.1																																																																																			.	.		0.498	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117		C	20077344	T	C	20077344	2	2	260	1	0	0	0	0	0	0	0	1	10193	1606	56	2		2	NAV2	11	20077344	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1519376	20077344	114929172	484	37729										
SLC5A12	159963	hgsc.bcm.edu	37	chr11	26700317	26700317	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cctaagcagcccactgcactGtagtaaaggtaggagatcga	11	10	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:26700317G>A	ENST00000396005.3	-	13	1830	c.1521C>T	c.(1519-1521)taC>taT	p.Y507Y		NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	507					sodium ion transport (GO:0006814)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)	35						CCACTGCACTGTAGTAAAGGT	0.458																																					p.Y507Y		Atlas-SNP	.											.	SLC5A12	134	.	0			c.C1521T						.						134	133	133					11																	26700317		1979	4170	6149	SO:0001819	synonymous_variant	159963	exon13			TGCACTGTAGTAA	BC049207	CCDS7860.2	11p14.2	2013-07-19	2013-07-19		ENSG00000148942	ENSG00000148942		"Solute carriers"	28750	protein-coding gene	gene with protein product		612455	"solute carrier family 5 (sodium/glucose cotransporter), member 12"			12477932	Standard	NM_178498		Approved	MGC52019, SMCT2	uc001mra.2	Q1EHB4	OTTHUMG00000150706	ENST00000396005.3:c.1521C>T	chr11.hg19:g.26700317G>A		139.0	0.0		93.0	4.0	NM_178498	Q86UC7	Silent	SNP	ENST00000396005.3	hg19	CCDS7860.2																																																																																			.	.		0.458	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319681.1	NM_178498		A	26700317	G	A	26700317	2	1	260	1	0	0	0	0	0	0	0	1	14679	1372	48	3		3	SLC5A12	11	26700317	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	6622973	26700317	108306199	485	37730										
QSER1	79832	hgsc.bcm.edu	37	chr11	32956867	32956867	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aacttaaaaacttggaacatTtatcttcattttcttctgat	3	7	4	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:32956867T>C	ENST00000399302.2	+	4	4011	c.3676T>C	c.(3676-3678)Tta>Cta	p.L1226L	QSER1_ENST00000527788.1_Silent_p.L987L	NM_001076786.1	NP_001070254.1	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	1226										breast(5)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	48	Breast(20;0.158)					CTTGGAACATTTATCTTCATT	0.373																																					p.L1226L		Atlas-SNP	.											.	QSER1	153	.	0			c.T3676C						.						142	142	142					11																	32956867		1829	4083	5912	SO:0001819	synonymous_variant	79832	exon4			GAACATTTATCTT	AL834141	CCDS41631.1	11p13	2014-02-12			ENSG00000060749	ENSG00000060749			26154	protein-coding gene	gene with protein product							Standard	XM_006718323		Approved	FLJ21924	uc001mty.3	Q2KHR3		ENST00000399302.2:c.3676T>C	chr11.hg19:g.32956867T>C		52.0	0.0		54.0	4.0	NM_001076786	Q6ZU30|Q6ZUR5	Silent	SNP	ENST00000399302.2	hg19	CCDS41631.1																																																																																			.	.		0.373	QSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388448.1	NM_024774		C	32956867	T	C	32956867	2	2	260	1	0	0	0	0	0	0	0	1	12897	1838	64	2		2	QSER1	11	32956867	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	6256550	32956867	102049649	486	37731										
TSPAN18	90139	hgsc.bcm.edu	37	chr11	44940765	44940765	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcttctccctctgcccccagCtcacccgagaattcttcacc	4	20	6	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:44940765C>T	ENST00000520358.2	+	7	749	c.334C>T	c.(334-336)Ctc>Ttc	p.L112F	TSPAN18_ENST00000340160.3_Splice_Site_p.L112F			Q96SJ8	TSN18_HUMAN	tetraspanin 18	112						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(6)|lung(3)	10						CTGCCCCCAGCTCACCCGAGA	0.577																																					p.L112F		Atlas-SNP	.											.	TSPAN18	38	.	0			c.C334T						.						144	121	129					11																	44940765		2203	4299	6502	SO:0001630	splice_region_variant	90139	exon6			CCCCAGCTCACCC	AY358087	CCDS7910.1	11p11.2	2013-02-14				ENSG00000157570		"Tetraspanins"	20660	protein-coding gene	gene with protein product						11756464	Standard	NM_130783		Approved	TSPAN	uc001mye.4	Q96SJ8		ENST00000520358.2:c.334-1C>T	chr11.hg19:g.44940765C>T		122.0	0.0		92.0	4.0	NM_130783	Q6UY44|Q8NBI9	Missense_Mutation	SNP	ENST00000520358.2	hg19	CCDS7910.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.61|14.61	2.587796|2.587796	0.46110|0.46110	.|.	.|.	ENSG00000157570|ENSG00000157570	ENST00000533786;ENST00000533080;ENST00000520358;ENST00000520999;ENST00000340160|ENST00000518429	T;T;T;T;T|.	0.80824|.	-1.42;-1.42;-1.42;-1.42;-1.42|.	5.15|5.15	5.15|5.15	0.70609|0.70609	Tetraspanin, EC2 domain (1);|.	0.847225|.	0.10765|.	N|.	0.636696|.	T|T	0.65112|0.65112	0.2660|0.2660	M|M	0.63843|0.63843	1.955|1.955	0.80722|0.80722	D|D	1|1	B;P|.	0.51653|.	0.197;0.947|.	B;P|.	0.61275|.	0.068;0.886|.	T|T	0.64149|0.64149	-0.6475|-0.6475	9|5	.|.	.|.	.|.	.|.	11.6434|11.6434	0.51246|0.51246	0.0:0.9133:0.0:0.0867|0.0:0.9133:0.0:0.0867	.|.	112;112|.	Q8WUV1;Q96SJ8|.	.;TSN18_HUMAN|.	F|F	112;47;112;122;112|115	ENSP00000433592:L112F;ENSP00000433362:L47F;ENSP00000429993:L112F;ENSP00000427942:L122F;ENSP00000339820:L112F|.	.|.	L|S	+|+	1|2	0|0	TSPAN18|TSPAN18	44897341|44897341	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.970000|0.970000	0.65996|0.65996	2.879000|2.879000	0.48522|0.48522	2.386000|2.386000	0.81285|0.81285	0.462000|0.462000	0.41574|0.41574	CTC|TCT	.	.		0.577	TSPAN18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376197.3	NM_130783	Missense_Mutation	T	44940765	C	T	44940765	5	4	260	1	0	0	0	0	0	0	1	0	16657	811	28	3	348	3	TSPAN18	11	44940765	Splice_Site	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	11983898	44940765	90065751	487	37732										
CKAP5	9793	hgsc.bcm.edu	37	chr11	46797922	46797922	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acagtcgctagggcagcagcTcgaacattgttctaaatgga	11	9	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:46797922T>C	ENST00000529230.1	-	24	2920	c.2874A>G	c.(2872-2874)cgA>cgG	p.R958R	CKAP5_ENST00000354558.3_Silent_p.R958R|CKAP5_ENST00000415402.1_Silent_p.R958R|CKAP5_ENST00000312055.5_Silent_p.R958R			Q14008	CKAP5_HUMAN	cytoskeleton associated protein 5	958					centrosome organization (GO:0051297)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|RNA transport (GO:0050658)|spindle organization (GO:0007051)	centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|protein complex (GO:0043234)|spindle pole (GO:0000922)				breast(1)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	43						GGGCAGCAGCTCGAACATTGT	0.423																																					p.R958R	Ovarian(4;85 273 2202 4844 13323)	Atlas-SNP	.											.	CKAP5	134	.	0			c.A2874G						.						71	65	67					11																	46797922		2201	4299	6500	SO:0001819	synonymous_variant	9793	exon24			AGCAGCTCGAACA		CCDS7924.1, CCDS31477.1	11p11.2	2006-09-20			ENSG00000175216	ENSG00000175216			28959	protein-coding gene	gene with protein product		611142				7788527, 8536682	Standard	NM_014756		Approved	ch-TOG, KIAA0097, TOG, TOGp	uc001ndi.2	Q14008	OTTHUMG00000166599	ENST00000529230.1:c.2874A>G	chr11.hg19:g.46797922T>C		127.0	0.0		98.0	4.0	NM_001008938	Q05D70|Q0VAX7|Q0VAX8|Q14668|Q2TA89|Q6NSH4	Silent	SNP	ENST00000529230.1	hg19	CCDS31477.1																																																																																			.	.		0.423	CKAP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390679.1	NM_014756		C	46797922	T	C	46797922	2	2	260	1	0	0	0	0	0	0	0	1	3447	1538	54	2		2	CKAP5	11	46797922	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1857157	46797922	88208594	488	37733										
MADD	8567	hgsc.bcm.edu	37	chr11	47298398	47298398	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cccgctgctacccacctgcaTggcatcagcagagcaggtga	11	15	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:47298398T>C	ENST00000311027.5	+	5	1244	c.1079T>C	c.(1078-1080)aTg>aCg	p.M360T	MADD_ENST00000395336.3_Missense_Mutation_p.M360T|MADD_ENST00000406482.1_Missense_Mutation_p.M360T|MADD_ENST00000342922.4_Missense_Mutation_p.M360T|MADD_ENST00000395344.3_Missense_Mutation_p.M360T|MADD_ENST00000489415.1_3'UTR|MADD_ENST00000402192.2_Missense_Mutation_p.M360T|MADD_ENST00000349238.3_Missense_Mutation_p.M360T|MADD_ENST00000402799.1_Missense_Mutation_p.M360T|MADD_ENST00000407859.3_Missense_Mutation_p.M360T	NM_003682.3	NP_003673.3			MAP-kinase activating death domain											breast(7)|central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(19)|lung(26)|ovary(6)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	84				Lung(87;0.182)		CCCACCTGCATGGCATCAGCA	0.512																																					p.M360T		Atlas-SNP	.											.	MADD	172	.	0			c.T1079C						.						176	134	148					11																	47298398		2201	4298	6499	SO:0001583	missense	8567	exon5			CCTGCATGGCATC	AB002356	CCDS7930.1, CCDS7931.1, CCDS7932.1, CCDS41642.1, CCDS44586.1, CCDS44587.1, CCDS44588.1, CCDS44589.1, CCDS44590.1	11p11.2	2012-10-04			ENSG00000110514	ENSG00000110514		"DENN/MADD domain containing"	6766	protein-coding gene	gene with protein product		603584				9115275, 9796103	Standard	NM_130476		Approved	DENN, KIAA0358, RAB3GEP	uc001ner.1	Q8WXG6	OTTHUMG00000150350	ENST00000311027.5:c.1079T>C	chr11.hg19:g.47298398T>C	ENSP00000310933:p.Met360Thr	105.0	0.0		83.0	4.0	NM_130474		Missense_Mutation	SNP	ENST00000311027.5	hg19	CCDS7930.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.377875	0.82682	.	.	ENSG00000110514	ENST00000342922;ENST00000395342;ENST00000428807;ENST00000402799;ENST00000406482;ENST00000349238;ENST00000311027;ENST00000407859;ENST00000395344;ENST00000395336;ENST00000402192	T;T;T;T;T;T;T;T;T;T	0.12569	2.67;2.67;2.67;2.67;2.67;2.67;2.67;2.67;2.67;2.67	5.93	5.93	0.95920	DENN (3);	0.000000	0.85682	D	0.000000	T	0.44993	0.1320	M	0.88450	2.955	0.80722	D	1	D;D;D;P;D;D;P;D;D;D	0.67145	0.992;0.98;0.995;0.935;0.994;0.988;0.862;0.99;0.996;0.995	D;D;D;P;D;P;P;D;D;D	0.71656	0.958;0.929;0.946;0.755;0.941;0.883;0.547;0.974;0.952;0.946	T	0.53258	-0.8464	10	0.87932	D	0	-26.4751	16.3943	0.83563	0.0:0.0:0.0:1.0	.	360;360;360;360;360;360;360;360;360;360	B5MEE5;A8K8S7;Q8WXG6-7;F8W9P9;Q8WXG6-6;Q8WXG6-5;Q8WXG6-2;Q8WXG6-4;Q8WXG6;Q8WXG6-3	.;.;.;.;.;.;.;.;MADD_HUMAN;.	T	360;360;138;360;360;360;360;360;360;360;360	ENSP00000343902:M360T;ENSP00000398167:M138T;ENSP00000385585:M360T;ENSP00000384435:M360T;ENSP00000304505:M360T;ENSP00000310933:M360T;ENSP00000384204:M360T;ENSP00000378753:M360T;ENSP00000378745:M360T;ENSP00000384287:M360T	ENSP00000310933:M360T	M	+	2	0	MADD	47254974	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.698000	0.84413	2.281000	0.76405	0.533000	0.62120	ATG	.	.		0.512	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1			C	47298398	T	C	47298398	3	2	260	1	0	0	0	0	1	0	0	0	9161	1464	51	2	1093	2	MADD	11	47298398	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	500476	47298398	87708118	489	37734										
OR4S1	256148	hgsc.bcm.edu	37	chr11	48328087	48328087	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agctcttttctgcccacttcTttggtggcactgagatcttc	8	12	4	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:48328087T>C	ENST00000319988.1	+	1	313	c.313T>C	c.(313-315)Ttt>Ctt	p.F105L		NM_001004725.1	NP_001004725.1	Q8NGB4	OR4S1_HUMAN	olfactory receptor, family 4, subfamily S, member 1	105						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|skin(3)	21						TGCCCACTTCTTTGGTGGCAC	0.507																																					p.F105L		Atlas-SNP	.											.	OR4S1	52	.	0			c.T313C						.						120	105	110					11																	48328087		2201	4288	6489	SO:0001583	missense	256148	exon1			CACTTCTTTGGTG	AB065908	CCDS31488.1	11p11.2	2012-08-09			ENSG00000176555	ENSG00000176555		"GPCR / Class A : Olfactory receptors"	14705	protein-coding gene	gene with protein product							Standard	NM_001004725		Approved		uc010rhu.2	Q8NGB4	OTTHUMG00000166578	ENST00000319988.1:c.313T>C	chr11.hg19:g.48328087T>C	ENSP00000321447:p.Phe105Leu	135.0	0.0		81.0	4.0	NM_001004725	Q6IFB4	Missense_Mutation	SNP	ENST00000319988.1	hg19	CCDS31488.1	.	.	.	.	.	.	.	.	.	.	T	11.98	1.800804	0.31869	.	.	ENSG00000176555	ENST00000319988	T	0.00381	7.63	5.02	5.02	0.67125	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00271	0.0008	N	0.21240	0.645	0.28779	N	0.899933	B	0.21309	0.054	B	0.20184	0.028	T	0.46119	-0.9214	9	0.48119	T	0.1	.	12.9764	0.58540	0.0:0.0:0.0:1.0	.	105	Q8NGB4	OR4S1_HUMAN	L	105	ENSP00000321447:F105L	ENSP00000321447:F105L	F	+	1	0	OR4S1	48284663	0.001000	0.12720	0.980000	0.43619	0.358000	0.29455	0.312000	0.19397	2.020000	0.59435	0.533000	0.62120	TTT	.	.		0.507	OR4S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390556.1	NM_001004725		C	48328087	T	C	48328087	3	2	260	1	0	0	0	0	1	0	0	0	11091	1609	56	2	315	2	OR4S1	11	48328087	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1029689	48328087	86678429	490	37735										
OR8I2	120586	hgsc.bcm.edu	37	chr11	55861280	55861280	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgtctgggtgataagcagttTggcgttctgtgattccagca	13	7	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:55861280T>C	ENST00000302124.2	+	1	528	c.497T>C	c.(496-498)tTg>tCg	p.L166S		NM_001003750.1	NP_001003750.1	Q8N0Y5	OR8I2_HUMAN	olfactory receptor, family 8, subfamily I, member 2	166						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(24)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	53	Esophageal squamous(21;0.00693)					ATAAGCAGTTTGGCGTTCTGT	0.443																																					p.L166S		Atlas-SNP	.											.,5	OR8I2	119	.	0			c.T497C						.						161	151	154					11																	55861280		2201	4296	6497	SO:0001583	missense	120586	exon1			GCAGTTTGGCGTT	AB065656	CCDS31517.1	11q11	2012-08-09			ENSG00000172154	ENSG00000172154		"GPCR / Class A : Olfactory receptors"	15310	protein-coding gene	gene with protein product							Standard	NM_001003750		Approved		uc010rix.2	Q8N0Y5	OTTHUMG00000166831	ENST00000302124.2:c.497T>C	chr11.hg19:g.55861280T>C	ENSP00000303864:p.Leu166Ser	132.0	0.0		79.0	4.0	NM_001003750	B2RNN4|Q6IFC0|Q96RC5	Missense_Mutation	SNP	ENST00000302124.2	hg19	CCDS31517.1	.	.	.	.	.	.	.	.	.	.	T	12.81	2.048263	0.36181	.	.	ENSG00000172154	ENST00000302124	T	0.00296	8.24	4.33	4.33	0.51752	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33092	U	0.005299	T	0.00815	0.0027	M	0.90369	3.11	0.20307	N	0.999914	D	0.89917	1.0	D	0.97110	1.0	T	0.21109	-1.0255	10	0.72032	D	0.01	-12.1653	12.9964	0.58648	0.0:0.0:0.0:1.0	.	166	Q8N0Y5	OR8I2_HUMAN	S	166	ENSP00000303864:L166S	ENSP00000303864:L166S	L	+	2	0	OR8I2	55617856	0.981000	0.34729	0.116000	0.21606	0.040000	0.13550	7.135000	0.77276	1.717000	0.51406	0.362000	0.22060	TTG	.	.		0.443	OR8I2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001003750		C	55861280	T	C	55861280	3	2	260	1	0	0	0	0	1	0	0	0	11249	1821	63	2	499	2	OR8I2	11	55861280	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	7533193	55861280	79145236	491	37736										
OR5A2	219981	hgsc.bcm.edu	37	chr11	59189652	59189652	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggaactgggtcgcatgtacaTgaagaatccagaaccataga	11	8	0	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:59189652T>C	ENST00000302040.4	-	1	797	c.775A>G	c.(775-777)Atg>Gtg	p.M259V		NM_001001954.1	NP_001001954.1	Q8NGI9	OR5A2_HUMAN	olfactory receptor, family 5, subfamily A, member 2	259						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(3)|liver(1)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	21						CGCATGTACATGAAGAATCCA	0.502																																					p.M259V		Atlas-SNP	.											.	OR5A2	35	.	0			c.A775G						.						94	91	92					11																	59189652		2201	4295	6496	SO:0001583	missense	219981	exon1			TGTACATGAAGAA	AB065805	CCDS31560.1	11q12.1	2012-08-09			ENSG00000172324	ENSG00000172324		"GPCR / Class A : Olfactory receptors"	15249	protein-coding gene	gene with protein product							Standard	NM_001001954		Approved		uc010rkt.2	Q8NGI9	OTTHUMG00000167419	ENST00000302040.4:c.775A>G	chr11.hg19:g.59189652T>C	ENSP00000303834:p.Met259Val	120.0	0.0		89.0	4.0	NM_001001954	B9EH21|Q6IFF4|Q96RB0	Missense_Mutation	SNP	ENST00000302040.4	hg19	CCDS31560.1	.	.	.	.	.	.	.	.	.	.	T	11.35	1.613118	0.28712	.	.	ENSG00000172324	ENST00000302040	T	0.00137	8.68	5.56	-11.1	0.00147	GPCR, rhodopsin-like superfamily (1);	0.175227	0.26792	U	0.022479	T	0.00039	0.0001	N	0.04746	-0.17	0.09310	N	1	B	0.13594	0.008	B	0.15484	0.013	T	0.50030	-0.8875	10	0.52906	T	0.07	.	7.8599	0.29504	0.4591:0.3872:0.0:0.1537	.	259	Q8NGI9	OR5A2_HUMAN	V	259	ENSP00000303834:M259V	ENSP00000303834:M259V	M	-	1	0	OR5A2	58946228	0.000000	0.05858	0.000000	0.03702	0.990000	0.78478	-1.047000	0.03521	-2.295000	0.00662	0.528000	0.53228	ATG	.	.		0.502	OR5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394552.1	NM_001001954		C	59189652	T	C	59189652	3	2	260	1	0	0	0	0	1	0	0	0	11149	1464	51	2	201	2	OR5A2	11	59189652	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	3328372	59189652	75816864	492	37737										
CD5	921	hgsc.bcm.edu	37	chr11	60890419	60890419	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggcctggccgcaggcacggtGgcaagcatcatcctggccct	14	15	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:60890419G>A	ENST00000347785.3	+	7	1306	c.1140G>A	c.(1138-1140)gtG>gtA	p.V380V		NM_014207.3	NP_055022.2	P06127	CD5_HUMAN	CD5 molecule	380					apoptotic signaling pathway (GO:0097190)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|T cell costimulation (GO:0031295)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|scavenger receptor activity (GO:0005044)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_lung(304;5.94e-05)|Lung NSC(402;7.26e-05)		BRCA - Breast invasive adenocarcinoma(625;0.000946)|Lung(977;0.0086)|LUSC - Lung squamous cell carcinoma(625;0.0528)		CAGGCACGGTGGCAAGCATCA	0.622																																					p.V380V		Atlas-SNP	.											.	CD5	52	.	0			c.G1140A						.						80	75	76					11																	60890419		2203	4299	6502	SO:0001819	synonymous_variant	921	exon7			CACGGTGGCAAGC	X04391	CCDS8000.1	11q13	2008-07-18	2006-03-28		ENSG00000110448	ENSG00000110448		"CD molecules"	1685	protein-coding gene	gene with protein product		153340	"CD5 antigen (p56-62)"	LEU1		1711157	Standard	NM_014207		Approved	T1	uc009ynk.3	P06127	OTTHUMG00000167825	ENST00000347785.3:c.1140G>A	chr11.hg19:g.60890419G>A		144.0	0.0		96.0	4.0	NM_014207	A0N0P4|A8K9I3	Silent	SNP	ENST00000347785.3	hg19	CCDS8000.1																																																																																			.	.		0.622	CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396465.2	NM_014207		A	60890419	G	A	60890419	2	1	260	1	0	0	0	0	0	0	0	1	3023	1335	47	3		3	CD5	11	60890419	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	1700767	60890419	74116097	493	37738										
VWCE	220001	hgsc.bcm.edu	37	chr11	61042033	61042033	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cacagccccgtctgcgtaccAccggccgtggaaatagcatc	10	16	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:61042033A>G	ENST00000335613.5	-	12	1905	c.1519T>C	c.(1519-1521)Tgg>Cgg	p.W507R	VWCE_ENST00000535710.1_5'Flank	NM_152718.2	NP_689931.2	Q96DN2	VWCE_HUMAN	von Willebrand factor C and EGF domains	507	VWFC 3. {ECO:0000255|PROSITE- ProRule:PRU00220}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37						TCTGCGTACCACCGGCCGTGG	0.552																																					p.W507R		Atlas-SNP	.											.	VWCE	84	.	0			c.T1519C						.						188	121	144					11																	61042033		2203	4299	6502	SO:0001583	missense	220001	exon12			CGTACCACCGGCC	AK056571	CCDS8002.1	11q12.2	2006-08-04			ENSG00000167992	ENSG00000167992			26487	protein-coding gene	gene with protein product		611115				12869306	Standard	NM_152718		Approved	URG11, FLJ32009, VWC1	uc001nra.3	Q96DN2	OTTHUMG00000168208	ENST00000335613.5:c.1519T>C	chr11.hg19:g.61042033A>G	ENSP00000334186:p.Trp507Arg	96.0	0.0		69.0	4.0	NM_152718	A5PKV0|Q7Z7L6|Q86WK8	Missense_Mutation	SNP	ENST00000335613.5	hg19	CCDS8002.1	.	.	.	.	.	.	.	.	.	.	A	11.73	1.726566	0.30593	.	.	ENSG00000167992	ENST00000335613	T	0.71103	-0.54	4.92	3.71	0.42584	von Willebrand factor, type C (3);	0.337248	0.21989	N	0.066185	T	0.54822	0.1882	N	0.01679	-0.765	0.80722	D	1	D	0.71674	0.998	D	0.68621	0.959	T	0.53041	-0.8494	10	0.15499	T	0.54	.	7.2289	0.26030	0.7046:0.0:0.0:0.2954	.	507	Q96DN2	VWCE_HUMAN	R	507	ENSP00000334186:W507R	ENSP00000334186:W507R	W	-	1	0	VWCE	60798609	0.991000	0.36638	0.993000	0.49108	0.944000	0.59088	2.955000	0.49121	1.847000	0.53656	0.448000	0.29417	TGG	.	.		0.552	VWCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398811.1	NM_152718		G	61042033	A	G	61042033	3	3	260	1	0	0	0	0	1	0	0	0	17260	159	6	2	1384	2	VWCE	11	61042033	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	151614	61042033	73964483	494	37739										
C11orf66	220004	hgsc.bcm.edu	37	chr11	61249330	61249330	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tctccccttatgtgaagatgAgttcggggggctacacggac	13	10	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:61249330A>G	ENST00000338608.2	+	2	174	c.49A>G	c.(49-51)Agt>Ggt	p.S17G	PPP1R32_ENST00000432063.2_Missense_Mutation_p.S17G|RP11-286N22.8_ENST00000543044.1_3'UTR|RP11-286N22.8_ENST00000544880.1_Intron	NM_145017.2	NP_659454.2	Q7Z5V6	PPR32_HUMAN	protein phosphatase 1, regulatory subunit 32	17							phosphatase binding (GO:0019902)										TGTGAAGATGAGTTCGGGGGG	0.627																																					p.S17G		Atlas-SNP	.											.	.	.	.	0			c.A49G						.						33	34	34					11																	61249330		2202	4299	6501	SO:0001583	missense	220004	exon2			AAGATGAGTTCGG	AK057333	CCDS8008.1, CCDS53641.1	11q12.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000162148	ENSG00000162148		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	28869	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 66"	C11orf66		12477932	Standard	NM_145017		Approved	IIIG9, FLJ32771	uc001nru.2	Q7Z5V6	OTTHUMG00000168176	ENST00000338608.2:c.49A>G	chr11.hg19:g.61249330A>G	ENSP00000344140:p.Ser17Gly	50.0	0.0		44.0	4.0	NM_001170753	Q4G0P4|Q96M77	Missense_Mutation	SNP	ENST00000338608.2	hg19	CCDS8008.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.479796	0.84747	.	.	ENSG00000162148	ENST00000432063;ENST00000338608	T;T	0.62105	0.05;0.61	4.9	4.9	0.64082	.	0.000000	0.64402	D	0.000002	T	0.77831	0.4189	M	0.77103	2.36	0.80722	D	1	D;D	0.67145	0.996;0.996	D;D	0.77557	0.99;0.99	T	0.80848	-0.1199	10	0.87932	D	0	-19.0894	12.0411	0.53454	1.0:0.0:0.0:0.0	.	17;17	Q7Z5V6-2;Q7Z5V6	.;PPR32_HUMAN	G	17	ENSP00000391560:S17G;ENSP00000344140:S17G	ENSP00000344140:S17G	S	+	1	0	C11orf66	61005906	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.952000	0.63618	1.848000	0.53677	0.418000	0.28097	AGT	.	.		0.627	PPP1R32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398621.1	NM_145017		G	61249330	A	G	61249330	3	3	260	1	0	0	0	0	1	0	0	0	1658	304	11	2	51	2	C11orf66	11	61249330	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	207297	61249330	73757186	495	37740										
MTA2	9219	hgsc.bcm.edu	37	chr11	62364251	62364251	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtaccagggtcgacatggccTtagccaggtcgtagccgttc	13	12	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:62364251T>C	ENST00000278823.2	-	9	1129	c.740A>G	c.(739-741)aAg>aGg	p.K247R	MTA2_ENST00000527204.1_Missense_Mutation_p.K74R|MTA2_ENST00000524902.1_Missense_Mutation_p.K74R	NM_004739.3	NP_004730.2	O94776	MTA2_HUMAN	metastasis associated 1 family, member 2	247	ELM2. {ECO:0000255|PROSITE- ProRule:PRU00512}.				ATP-dependent chromatin remodeling (GO:0043044)|chromatin assembly or disassembly (GO:0006333)|DNA methylation (GO:0006306)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	histone deacetylase complex (GO:0000118)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|histone deacetylase activity (GO:0004407)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	26						CGACATGGCCTTAGCCAGGTC	0.567																																					p.K247R		Atlas-SNP	.											.	MTA2	54	.	0			c.A740G						.						60	59	60					11																	62364251		2202	4299	6501	SO:0001583	missense	9219	exon9			ATGGCCTTAGCCA	AB016591	CCDS8022.1	11q12-q13.1	2013-01-25	2004-12-15	2003-12-17	ENSG00000149480	ENSG00000149480		"GATA zinc finger domain containing"	7411	protein-coding gene	gene with protein product		603947	"metastasis associated gene family, member 2"	MTA1L1		9929979	Standard	NM_004739		Approved	MTA1-L1	uc001ntq.2	O94776	OTTHUMG00000167684	ENST00000278823.2:c.740A>G	chr11.hg19:g.62364251T>C	ENSP00000278823:p.Lys247Arg	94.0	0.0		66.0	4.0	NM_004739	Q68DB1|Q9UQB5	Missense_Mutation	SNP	ENST00000278823.2	hg19	CCDS8022.1	.	.	.	.	.	.	.	.	.	.	T	13.22	2.171188	0.38315	.	.	ENSG00000149480	ENST00000278823;ENST00000524902;ENST00000527204	T;T;T	0.48836	1.37;0.8;0.8	5.32	5.32	0.75619	ELM2 domain (1);	0.169949	0.49916	D	0.000123	T	0.36936	0.0985	L	0.41356	1.27	0.39544	D	0.968864	B	0.06786	0.001	B	0.04013	0.001	T	0.29912	-0.9996	10	0.46703	T	0.11	-18.0155	8.1559	0.31169	0.0:0.0904:0.0:0.9096	.	247	O94776	MTA2_HUMAN	R	247;74;74	ENSP00000278823:K247R;ENSP00000431346:K74R;ENSP00000431797:K74R	ENSP00000278823:K247R	K	-	2	0	MTA2	62120827	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	2.229000	0.42990	2.135000	0.66039	0.459000	0.35465	AAG	.	.		0.567	MTA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395578.1	NM_004739		C	62364251	T	C	62364251	3	2	260	1	0	0	0	0	1	0	0	0	9918	1609	56	2	1306	2	MTA2	11	62364251	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1114921	62364251	72642265	496	37741										
EML3	256364	hgsc.bcm.edu	37	chr11	62375693	62375693	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cttgatctcagccagcttcaTtccccggctgcagtcccaca	7	17	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:62375693T>C	ENST00000394773.2	-	10	1493	c.1186A>G	c.(1186-1188)Atg>Gtg	p.M396V	EML3_ENST00000494176.2_Missense_Mutation_p.M368V|EML3_ENST00000278845.4_Missense_Mutation_p.M397V|RP11-831H9.3_ENST00000532626.1_RNA|EML3_ENST00000438258.1_5'Flank|EML3_ENST00000531557.1_Missense_Mutation_p.M179V|EML3_ENST00000529309.1_Missense_Mutation_p.M396V	NM_153265.2	NP_694997.2	Q32P44	EMAL3_HUMAN	echinoderm microtubule associated protein like 3	396						cytoplasm (GO:0005737)|microtubule (GO:0005874)				biliary_tract(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						GCCAGCTTCATTCCCCGGCTG	0.577																																					p.M396V		Atlas-SNP	.											.	EML3	61	.	0			c.A1186G						.						226	234	231					11																	62375693		2202	4299	6501	SO:0001583	missense	256364	exon10			GCTTCATTCCCCG	AK093146	CCDS8023.2	11q12.3	2013-01-10			ENSG00000149499	ENSG00000149499		"WD repeat domain containing"	26666	protein-coding gene	gene with protein product						15225882, 14744259	Standard	NM_153265		Approved	FLJ35827, ELP95	uc001ntu.1	Q32P44	OTTHUMG00000149817	ENST00000394773.2:c.1186A>G	chr11.hg19:g.62375693T>C	ENSP00000378254:p.Met396Val	104.0	0.0		59.0	4.0	NM_153265	Q6ZQW7|Q8NA55	Missense_Mutation	SNP	ENST00000394773.2	hg19	CCDS8023.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	5.135|5.135	0.210565|0.210565	0.09757|0.09757	.|.	.|.	ENSG00000149499|ENSG00000149499	ENST00000394773;ENST00000278845;ENST00000531557;ENST00000494176;ENST00000529309|ENST00000394776	T;T;T;T;T|.	0.40756|.	1.11;1.11;1.02;1.02;1.02|.	5.92|5.92	-2.11|-2.11	0.07187|0.07187	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);|.	0.416774|.	0.27219|.	N|.	0.020378|.	T|T	0.10809|0.10809	0.0264|0.0264	N|N	0.00841|0.00841	-1.15|-1.15	0.09310|0.09310	N|N	1|1	B;B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0;0.0|.	B;B;B;B;B|.	0.01281|.	0.0;0.0;0.0;0.0;0.0|.	T|T	0.33904|0.33904	-0.9850|-0.9850	10|5	0.32370|.	T|.	0.25|.	-16.4808|-16.4808	12.8237|12.8237	0.57708|0.57708	0.0:0.4:0.0:0.6|0.0:0.4:0.0:0.6	.|.	396;396;179;397;368|.	Q32P44-2;Q32P44;G3V195;B7WPE2;G3V1D0|.	.;EMAL3_HUMAN;.;.;.|.	V|S	396;397;179;368;396|390	ENSP00000378254:M396V;ENSP00000278845:M397V;ENSP00000433417:M179V;ENSP00000435064:M368V;ENSP00000434513:M396V|.	ENSP00000278845:M397V|.	M|N	-|-	1|2	0|0	EML3|EML3	62132269|62132269	0.000000|0.000000	0.05858|0.05858	0.006000|0.006000	0.13384|0.13384	0.889000|0.889000	0.51656|0.51656	0.119000|0.119000	0.15626|0.15626	-0.640000|-0.640000	0.05495|0.05495	-1.773000|-1.773000	0.00660|0.00660	ATG|AAT	.	.		0.577	EML3-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313432.1	NM_153265		C	62375693	T	C	62375693	3	2	260	1	0	0	0	0	1	0	0	0	5100	1493	52	2	1556	2	EML3	11	62375693	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	11442	62375693	72630823	497	37742										
STIP1	10963	hgsc.bcm.edu	37	chr11	63970927	63970927	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcttctggactgcaggaggcGgcagacggctaccagcgctg	15	12	2	1	rs144539134	byFrequency	TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:63970927G>T	ENST00000305218.4	+	13	1539	c.1392G>T	c.(1390-1392)gcG>gcT	p.A464A	STIP1_ENST00000538945.1_Silent_p.A440A|STIP1_ENST00000358794.5_Silent_p.A511A	NM_006819.2	NP_006810.1	P31948	STIP1_HUMAN	stress-induced phosphoprotein 1	464					response to stress (GO:0006950)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(4)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(1)|skin(1)	27						TGCAGGAGGCGGCAGACGGCT	0.587																																					p.A464A		Atlas-SNP	.											.	STIP1	63	.	0			c.G1392T						.						40	35	37					11																	63970927		2201	4297	6498	SO:0001819	synonymous_variant	10963	exon13			GGAGGCGGCAGAC	BC039299	CCDS8058.1, CCDS60827.1, CCDS60828.1	11q13	2014-01-13	2014-01-13		ENSG00000168439	ENSG00000168439		"Tetratricopeptide (TTC) repeat domain containing"	11387	protein-coding gene	gene with protein product	"Hsp70/Hsp90-organizing protein"	605063	"stress-induced-phosphoprotein 1"			1569099	Standard	NM_006819		Approved	HOP, STI1	uc001nyk.1	P31948	OTTHUMG00000167789	ENST00000305218.4:c.1392G>T	chr11.hg19:g.63970927G>T		94.0	0.0		67.0	4.0	NM_006819	B4DM70|F5H0T1|G3XAD8|Q3ZCU9|Q5TZU9	Silent	SNP	ENST00000305218.4	hg19	CCDS8058.1																																																																																			.	G|1.000;A|0.000		0.587	STIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396289.2	NM_006819		T	63970927	G	T	63970927	2	4	260	1	0	0	0	0	0	0	0	1	15300	1103	39	1		1	STIP1	11	63970927	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	1595234	63970927	71035589	498	37743										
TM7SF2	7108	hgsc.bcm.edu	37	chr11	64880311	64880311	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggggcaggaattgaaggacaAgagtcgcctgcgctatccta	14	9	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:64880311A>G	ENST00000279263.7	+	3	440	c.278A>G	c.(277-279)aAg>aGg	p.K93R	AP003068.9_ENST00000528887.1_RNA|TM7SF2_ENST00000540748.1_Intron|TM7SF2_ENST00000345348.5_Missense_Mutation_p.K93R|TM7SF2_ENST00000531029.1_3'UTR	NM_003273.2	NP_003264.2	O76062	ERG24_HUMAN	transmembrane 7 superfamily member 2	93					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	delta14-sterol reductase activity (GO:0050613)			lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TTGAAGGACAAGAGTCGCCTG	0.672											OREG0021072	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K93R		Atlas-SNP	.											.	TM7SF2	30	.	0			c.A278G						.						4	5	5					11																	64880311		1750	3818	5568	SO:0001583	missense	7108	exon3			AGGACAAGAGTCG	BC012857	CCDS41669.1, CCDS60846.1	11q13.1	2013-05-23			ENSG00000149809	ENSG00000149809	1.3.1.70		11863	protein-coding gene	gene with protein product	"delta(14)-sterol reductase"	603414				9615229, 9286704	Standard	NM_003273		Approved	ANG1, DHCR14A, NET47	uc001oct.4	O76062	OTTHUMG00000165603	ENST00000279263.7:c.278A>G	chr11.hg19:g.64880311A>G	ENSP00000279263:p.Lys93Arg	105.0	0.0	134	75.0	4.0	NM_003273	A8K4H0|O95982|Q8IY06|Q96E64|Q96GZ1	Missense_Mutation	SNP	ENST00000279263.7	hg19	CCDS41669.1	.	.	.	.	.	.	.	.	.	.	A	17.35	3.367871	0.61513	.	.	ENSG00000149809	ENST00000279263;ENST00000524986;ENST00000525385;ENST00000345348;ENST00000531321;ENST00000529414;ENST00000530750	D;D;D;D;D;D;D	0.99005	-4.63;-4.63;-4.63;-4.63;-5.32;-4.63;-4.63	4.77	4.77	0.60923	.	0.280909	0.41396	D	0.000894	D	0.97195	0.9083	L	0.38838	1.175	0.80722	D	1	B;B	0.29552	0.248;0.146	B;B	0.35813	0.211;0.143	D	0.96562	0.9416	10	0.72032	D	0.01	-12.0661	10.6087	0.45408	1.0:0.0:0.0:0.0	.	93;93	O76062-2;O76062	.;ERG24_HUMAN	R	93;64;64;93;64;93;93	ENSP00000279263:K93R;ENSP00000435972:K64R;ENSP00000433325:K64R;ENSP00000329520:K93R;ENSP00000431300:K64R;ENSP00000433275:K93R;ENSP00000432413:K93R	ENSP00000279263:K93R	K	+	2	0	TM7SF2	64636887	1.000000	0.71417	1.000000	0.80357	0.820000	0.46376	3.283000	0.51701	2.013000	0.59113	0.459000	0.35465	AAG	.	.		0.672	TM7SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385234.1	NM_003273		G	64880311	A	G	64880311	3	3	260	1	0	0	0	0	1	0	0	0	15989	72	3	2	288	2	TM7SF2	11	64880311	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	909384	64880311	70126205	499	37744										
EHBP1L1	254102	hgsc.bcm.edu	37	chr11	65349836	65349836	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gaggctgggaggcagaagctGggggttcaggggacctggaa	21	6	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:65349836G>A	ENST00000309295.4	+	9	1958	c.1693G>A	c.(1693-1695)Ggg>Agg	p.G565R		NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	565	Glu-rich.					membrane (GO:0016020)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						GGCAGAAGCTGGGGGTTCAGG	0.607																																					p.G565R		Atlas-SNP	.											.	EHBP1L1	64	.	0			c.G1693A						.						18	20	19					11																	65349836		1862	4086	5948	SO:0001583	missense	254102	exon9			GAAGCTGGGGGTT	AL834433	CCDS44649.1	11q13.1	2008-02-05			ENSG00000173442	ENSG00000173442			30682	protein-coding gene	gene with protein product							Standard	NM_001099409		Approved	DKFZp762C186, TANGERIN	uc001oeo.4	Q8N3D4	OTTHUMG00000166520	ENST00000309295.4:c.1693G>A	chr11.hg19:g.65349836G>A	ENSP00000312671:p.Gly565Arg	50.0	0.0		39.0	9.0	NM_001099409	Q8TB89|Q9H7M7	Missense_Mutation	SNP	ENST00000309295.4	hg19	CCDS44649.1	.	.	.	.	.	.	.	.	.	.	G	15.57	2.872483	0.51695	.	.	ENSG00000173442	ENST00000309295	T	0.68181	-0.31	5.16	2.21	0.28008	.	0.495552	0.17197	N	0.183269	T	0.51075	0.1653	L	0.36672	1.1	0.09310	N	1	B	0.17852	0.024	B	0.12156	0.007	T	0.47898	-0.9081	10	0.87932	D	0	.	4.502	0.11869	0.1709:0.0:0.5245:0.3046	.	565	Q8N3D4	EH1L1_HUMAN	R	565	ENSP00000312671:G565R	ENSP00000312671:G565R	G	+	1	0	EHBP1L1	65106412	0.000000	0.05858	0.029000	0.17559	0.036000	0.12997	0.357000	0.20199	0.559000	0.29153	0.655000	0.94253	GGG	.	.		0.607	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658		A	65349836	G	A	65349836	3	1	260	1	0	0	0	0	1	0	0	0	4978	1348	47	3	1727	3	EHBP1L1	11	65349836	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	469525	65349836	69656680	500	37745										
RELA	5970	hgsc.bcm.edu	37	chr11	65422122	65422122	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gatgccaggtctgtgaacacAgctgggtctgtgctgttgcc	14	10	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:65422122A>G	ENST00000406246.3	-	11	1644	c.1383T>C	c.(1381-1383)gcT>gcC	p.A461A	RELA_ENST00000308639.9_Silent_p.A458A|RELA_ENST00000525693.1_3'UTR	NM_001243984.1|NM_001243985.1|NM_021975.3	NP_001230913.1|NP_001230914.1|NP_068810.3	Q04206	TF65_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog A	461					acetaldehyde metabolic process (GO:0006117)|aging (GO:0007568)|cellular defense response (GO:0006968)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to tumor necrosis factor (GO:0071356)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|Fc-epsilon receptor signaling pathway (GO:0038095)|hair follicle development (GO:0001942)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|liver development (GO:0001889)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of Schwann cell differentiation (GO:0014040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|regulation of inflammatory response (GO:0050727)|response to amino acid (GO:0043200)|response to cAMP (GO:0051591)|response to cobalamin (GO:0033590)|response to drug (GO:0042493)|response to insulin (GO:0032868)|response to interleukin-1 (GO:0070555)|response to mechanical stimulus (GO:0009612)|response to morphine (GO:0043278)|response to muramyl dipeptide (GO:0032495)|response to organic substance (GO:0010033)|response to progesterone (GO:0032570)|response to UV-B (GO:0010224)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|phosphate ion binding (GO:0042301)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|repressing transcription factor binding (GO:0070491)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(11)|ovary(1)|urinary_tract(1)	19						CTGTGAacacagctgggtctg	0.602																																					p.A461A		Atlas-SNP	.											.	RELA	44	.	0			c.T1383C						.						50	49	50					11																	65422122		2201	4297	6498	SO:0001819	synonymous_variant	5970	exon11			GAACACAGCTGGG	Z22951	CCDS31609.1, CCDS44651.1, CCDS73322.1	11q13	2013-07-09	2013-07-09		ENSG00000173039	ENSG00000173039			9955	protein-coding gene	gene with protein product		164014	"nuclear factor of kappa light polypeptide gene enhancer in B-cells 3"	NFKB3		2001591	Standard	NM_021975		Approved	p65	uc001ofg.3	Q04206	OTTHUMG00000166566	ENST00000406246.3:c.1383T>C	chr11.hg19:g.65422122A>G		132.0	0.0		91.0	4.0	NM_021975	Q6GTV1|Q6SLK1	Silent	SNP	ENST00000406246.3	hg19	CCDS31609.1																																																																																			.	.		0.602	RELA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390457.2	NM_021975		G	65422122	A	G	65422122	2	3	260	1	0	0	0	0	0	0	0	1	13231	175	7	2		2	RELA	11	65422122	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	72286	65422122	69584394	501	37746										
RBM14	10432	hgsc.bcm.edu	37	chr11	66392365	66392365	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctcagggttcctcccttgccTcctatggtaaccagccatcc	7	17	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:66392365T>C	ENST00000310137.4	+	2	1157	c.1018T>C	c.(1018-1020)Tcc>Ccc	p.S340P	RBM14-RBM4_ENST00000511114.1_Intron|RBM14_ENST00000409738.4_Intron|RBM14-RBM4_ENST00000412278.2_Intron|RBM4_ENST00000503028.2_Intron|RBM14_ENST00000393979.3_Intron|RBM14-RBM4_ENST00000500635.2_Intron|RBM4_ENST00000514361.3_Intron	NM_006328.3	NP_006319.1	Q96PK6	RBM14_HUMAN	RNA binding motif protein 14	340	Ala-rich.|TRBP-interacting domain.				DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|glucocorticoid receptor signaling pathway (GO:0042921)|histone deacetylation (GO:0016575)|intracellular estrogen receptor signaling pathway (GO:0030520)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to hormone (GO:0009725)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor complex (GO:0005667)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)		RBM14/PACS1(2)	breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17						CTCCCTTGCCTCCTATGGTAA	0.612																																					p.S340P		Atlas-SNP	.											.	RBM14	59	.	0			c.T1018C						.						75	81	79					11																	66392365		2200	4295	6495	SO:0001583	missense	10432	exon2			CTTGCCTCCTATG	AF080561	CCDS8147.1, CCDS55772.1, CCDS55773.1	11q13.2	2013-02-12			ENSG00000239306	ENSG00000239306		"RNA binding motif (RRM) containing"	14219	protein-coding gene	gene with protein product	"coactivator activator", "SYT interacting protein"	612409				9285794	Standard	NM_006328		Approved	SIP, SYTIP1, COAA, DKFZp779J0927	uc001oit.3	Q96PK6	OTTHUMG00000140380	ENST00000310137.4:c.1018T>C	chr11.hg19:g.66392365T>C	ENSP00000311747:p.Ser340Pro	152.0	0.0		90.0	4.0	NM_006328	B0LM41|B3KMN4|D6RGD8|O75932|Q2PYN1|Q53GV1|Q68DQ9|Q96PK5	Missense_Mutation	SNP	ENST00000310137.4	hg19	CCDS8147.1	.	.	.	.	.	.	.	.	.	.	T	15.24	2.775147	0.49786	.	.	ENSG00000239306	ENST00000310137	D	0.84298	-1.83	4.75	4.75	0.60458	.	0.263452	0.38381	N	0.001711	D	0.83050	0.5170	L	0.27053	0.805	0.80722	D	1	P	0.47604	0.898	P	0.52454	0.699	D	0.84795	0.0781	10	0.62326	D	0.03	-6.4028	12.2386	0.54530	0.0:0.0:0.0:1.0	.	340	Q96PK6	RBM14_HUMAN	P	340	ENSP00000311747:S340P	ENSP00000311747:S340P	S	+	1	0	RBM14	66148941	0.837000	0.29446	1.000000	0.80357	0.967000	0.64934	0.558000	0.23469	1.991000	0.58162	0.460000	0.39030	TCC	.	.		0.612	RBM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277128.1	NM_006328		C	66392365	T	C	66392365	3	2	260	1	0	0	0	0	1	0	0	0	13130	1551	54	2	1024	2	RBM14	11	66392365	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	970243	66392365	68614151	502	37747										
ANKRD13D	338692	hgsc.bcm.edu	37	chr11	67068507	67068507	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aagagcacccgctctccctgGgtgaccaggtgacccccatc	10	17	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:67068507G>A	ENST00000447274.2	+	11	2034	c.859G>A	c.(859-861)Ggt>Agt	p.G287S	ANKRD13D_ENST00000514166.1_Missense_Mutation_p.G287S|ANKRD13D_ENST00000308440.6_Missense_Mutation_p.G287S|ANKRD13D_ENST00000511455.2_Missense_Mutation_p.G374S|ANKRD13D_ENST00000515828.1_Missense_Mutation_p.G24S|SSH3_ENST00000308127.4_5'Flank|SSH3_ENST00000376757.5_5'Flank|SSH3_ENST00000308298.7_5'Flank			Q6ZTN6	AN13D_HUMAN	ankyrin repeat domain 13 family, member D	287						endosome (GO:0005768)|plasma membrane (GO:0005886)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|ovary(1)	9			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)			GCTCTCCCTGGGTGACCAGGT	0.612																																					p.G374S		Atlas-SNP	.											.	ANKRD13D	71	.	0			c.G1120A						.						134	108	117					11																	67068507		2200	4295	6495	SO:0001583	missense	338692	exon11			TCCCTGGGTGACC	AK027313	CCDS31616.1, CCDS31616.2	11q13.2	2013-01-11		2005-08-09	ENSG00000172932	ENSG00000172932		"Ankyrin repeat domain containing"	27880	protein-coding gene	gene with protein product		615126					Standard	NM_207354		Approved		uc001okd.2	Q6ZTN6	OTTHUMG00000162929	ENST00000447274.2:c.859G>A	chr11.hg19:g.67068507G>A	ENSP00000402616:p.Gly287Ser	137.0	0.0		100.0	4.0	NM_207354	D6RCN6|Q0VAK0|Q0VGC3|Q6ZVD0|Q86SU1	Missense_Mutation	SNP	ENST00000447274.2	hg19		.	.	.	.	.	.	.	.	.	.	G	13.96	2.392368	0.42410	.	.	ENSG00000172932	ENST00000447274;ENST00000511455;ENST00000308440;ENST00000514166;ENST00000515828	T;T;T;T;T	0.39787	1.06;1.06;1.06;1.06;1.06	4.86	4.86	0.63082	.	0.067094	0.64402	D	0.000010	T	0.27241	0.0668	N	0.08118	0	0.52501	D	0.999958	D;B;B	0.56287	0.975;0.02;0.013	P;B;B	0.45610	0.487;0.036;0.017	T	0.06338	-1.0832	10	0.09338	T	0.73	-20.4443	17.7879	0.88543	0.0:0.0:1.0:0.0	.	24;374;287	Q6ZTN6-2;Q6ZTN6-3;Q6ZTN6	.;.;AN13D_HUMAN	S	287;374;287;287;24	ENSP00000402616:G287S;ENSP00000427130:G374S;ENSP00000310874:G287S;ENSP00000444404:G287S;ENSP00000443977:G24S	ENSP00000310874:G287S	G	+	1	0	ANKRD13D	66825083	1.000000	0.71417	1.000000	0.80357	0.461000	0.32589	3.234000	0.51320	2.517000	0.84864	0.561000	0.74099	GGT	.	.		0.612	ANKRD13D-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000371067.2	NM_207354		A	67068507	G	A	67068507	3	1	260	1	0	0	0	0	1	0	0	0	644	1232	43	3	1162	3	ANKRD13D	11	67068507	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	676142	67068507	67938009	503	37748										
TBX10	347853	hgsc.bcm.edu	37	chr11	67406938	67406938	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gcttcagaacgtagcctaccTgccatggagacagagaggct	12	11	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:67406938T>C	ENST00000335385.3	-	1	93	c.6A>G	c.(4-6)gcA>gcG	p.A2A		NM_005995.4	NP_005986.2	O75333	TBX10_HUMAN	T-box 10	2					anatomical structure morphogenesis (GO:0009653)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|lung(4)|ovary(1)	7						GTAGCCTACCTGCCATGGAGA	0.637																																					p.A2A		Atlas-SNP	.											.	TBX10	25	.	0			c.A6G						.						79	56	64					11																	67406938		2200	4294	6494	SO:0001630	splice_region_variant	347853	exon1			CCTACCTGCCATG	AH006177	CCDS31621.1	11q13.2	2005-10-11	2004-10-05		ENSG00000167800	ENSG00000167800		"T-boxes"	11593	protein-coding gene	gene with protein product		604648	"T-box 7"	TBX7		9545502	Standard	NM_005995		Approved	TBX13	uc001omp.3	O75333	OTTHUMG00000167291	ENST00000335385.3:c.7+1A>G	chr11.hg19:g.67406938T>C		99.0	0.0		66.0	4.0	NM_005995	Q14D64|Q86XS3	Silent	SNP	ENST00000335385.3	hg19	CCDS31621.1																																																																																			.	.		0.637	TBX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394034.1	NM_005995	Silent	C	67406938	T	C	67406938	5	2	260	1	0	0	0	0	0	0	1	0	15666	1594	55	2	1183	2	TBX10	11	67406938	Splice_Site	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	338431	67406938	67599578	504	37749										
IGHMBP2	3508	hgsc.bcm.edu	37	chr11	68682309	68682309	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aggttctgtgctgcgcccccTccaacatcgccgtggacaat	10	15	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:68682309T>C	ENST00000255078.3	+	6	841	c.730T>C	c.(730-732)Tcc>Ccc	p.S244P	IGHMBP2_ENST00000539224.1_3'UTR	NM_002180.2	NP_002171.2	P38935	SMBP2_HUMAN	immunoglobulin mu binding protein 2	244					ATP catabolic process (GO:0006200)|cell death (GO:0008219)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|protein homooligomerization (GO:0051260)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)	axon (GO:0030424)|cytoplasm (GO:0005737)|growth cone (GO:0030426)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|ATP-dependent 5'-3' RNA helicase activity (GO:0032575)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|ribosome binding (GO:0043022)|RNA binding (GO:0003723)|RNA-dependent ATPase activity (GO:0008186)|single-stranded DNA binding (GO:0003697)|transcription factor binding (GO:0008134)|tRNA binding (GO:0000049)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|liver(1)|lung(15)|ovary(2)|prostate(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			CTGCGCCCCCTCCAACATCGC	0.532																																					p.S244P		Atlas-SNP	.											.	IGHMBP2	83	.	0			c.T730C						.						92	92	92					11																	68682309		2200	4294	6494	SO:0001583	missense	3508	exon6			GCCCCCTCCAACA	L14754	CCDS8187.1	11q13.3	2014-09-17			ENSG00000132740	ENSG00000132740		"Zinc fingers, AN1-type domain containing"	5542	protein-coding gene	gene with protein product	"cardiac transcription factor 1", "zinc finger, AN1-type domain 7"	600502				8349627	Standard	NM_002180		Approved	ZFAND7, SMUBP2, CATF1, SMARD1, HCSA, HMN6	uc001ook.1	P38935	OTTHUMG00000167894	ENST00000255078.3:c.730T>C	chr11.hg19:g.68682309T>C	ENSP00000255078:p.Ser244Pro	102.0	0.0		77.0	4.0	NM_002180	A0PJD2|Q00443|Q14177	Missense_Mutation	SNP	ENST00000255078.3	hg19	CCDS8187.1	.	.	.	.	.	.	.	.	.	.	T	19.47	3.834165	0.71373	.	.	ENSG00000132740	ENST00000255078	D	0.83914	-1.78	3.6	3.6	0.41247	DEAD-like helicase (1);Helicase/UvrB domain (1);ATPase, AAA+ type, core (1);	0.266189	0.39020	N	0.001484	D	0.94013	0.8082	H	0.98295	4.195	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95123	0.8248	10	0.87932	D	0	-15.1302	11.6022	0.51010	0.0:0.0:0.0:1.0	.	244	P38935	SMBP2_HUMAN	P	244	ENSP00000255078:S244P	ENSP00000255078:S244P	S	+	1	0	IGHMBP2	68438885	1.000000	0.71417	0.948000	0.38648	0.648000	0.38561	7.265000	0.78442	1.641000	0.50575	0.454000	0.30748	TCC	.	.		0.532	IGHMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396862.1	NM_002180		C	68682309	T	C	68682309	3	2	260	1	0	0	0	0	1	0	0	0	7600	1551	54	2	752	2	IGHMBP2	11	68682309	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1275371	68682309	66324207	505	37750										
NUMA1	4926	hgsc.bcm.edu	37	chr11	71717144	71717144	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agaactgcgagtggtggggcGgtagccaggcaagctgagca	18	8	0	2	rs148430833		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:71717144G>T	ENST00000393695.3	-	22	5960	c.5629C>A	c.(5629-5631)Cgc>Agc	p.R1877S	NUMA1_ENST00000358965.6_Missense_Mutation_p.R1863S|NUMA1_ENST00000351960.6_Missense_Mutation_p.R741S	NM_006185.2	NP_006176.2			nuclear mitotic apparatus protein 1									p.R1877C(1)		central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(12)|lung(20)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	65						GTGGTGGGGCGGTAGCCAGGC	0.612			T	RARA	APL																																p.R1877S		Atlas-SNP	.		Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	NUMA1,NS,carcinoma,0,1	NUMA1	142	.	1	Substitution - Missense(1)	endometrium(1)	c.C5629A						.						79	85	83					11																	71717144		2200	4293	6493	SO:0001583	missense	4926	exon22			TGGGGCGGTAGCC	Z11584	CCDS31633.1, CCDS66156.1	11q13	2008-02-05				ENSG00000137497			8059	protein-coding gene	gene with protein product		164009				8406455	Standard	NM_006185		Approved		uc001orl.1	Q14980		ENST00000393695.3:c.5629C>A	chr11.hg19:g.71717144G>T	ENSP00000377298:p.Arg1877Ser	137.0	1.0		65.0	3.0	NM_006185		Missense_Mutation	SNP	ENST00000393695.3	hg19	CCDS31633.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.952972	0.73902	.	.	ENSG00000137497	ENST00000351960;ENST00000358965;ENST00000393695;ENST00000359652;ENST00000536544	T;T;T	0.29397	1.57;2.01;2.01	5.11	4.14	0.48551	.	0.000000	0.52532	D	0.000080	T	0.42245	0.1194	L	0.27053	0.805	0.38326	D	0.94366	D;D;D;D	0.89917	0.999;1.0;0.999;0.999	D;D;D;D	0.87578	0.983;0.998;0.983;0.937	T	0.48246	-0.9052	10	0.87932	D	0	.	14.8836	0.70550	0.0:0.0:0.847:0.153	.	1883;1863;1877;741	Q4LE64;Q14980-2;Q14980;Q9BTE9	.;.;NUMA1_HUMAN;.	S	741;1863;1877;1426;850	ENSP00000260051:R741S;ENSP00000351851:R1863S;ENSP00000377298:R1877S	ENSP00000260051:R741S	R	-	1	0	NUMA1	71394792	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	2.304000	0.43655	2.652000	0.90054	0.655000	0.94253	CGC	.	G|1.000;A|0.000		0.612	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1			T	71717144	G	T	71717144	3	4	260	1	0	0	0	0	1	0	0	0	10759	1116	39	1	742	1	NUMA1	11	71717144	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	3034835	71717144	63289372	506	37751										
GDPD5	81544	hgsc.bcm.edu	37	chr11	75152777	75152777	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctggcgactgcctccttggaGcctgatgtctgttggaagcc	13	12	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:75152777G>A	ENST00000336898.3	-	13	2076	c.1239C>T	c.(1237-1239)ggC>ggT	p.G413G	GDPD5_ENST00000533784.1_Silent_p.G294G|GDPD5_ENST00000529721.1_Silent_p.G413G|GDPD5_ENST00000443276.2_3'UTR|GDPD5_ENST00000526177.1_Silent_p.G275G|GDPD5_ENST00000376282.3_Silent_p.G294G|GDPD5_ENST00000533805.1_Silent_p.G168G	NM_030792.6	NP_110419.5	Q8WTR4	GDPD5_HUMAN	glycerophosphodiester phosphodiesterase domain containing 5	413	GP-PDE.				cerebral cortex neuron differentiation (GO:0021895)|glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)|negative regulation of Notch signaling pathway (GO:0045746)|neuron projection development (GO:0031175)|positive regulation of neuron differentiation (GO:0045666)|regulation of timing of cell differentiation (GO:0048505)|spinal cord motor neuron differentiation (GO:0021522)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(3)|skin(2)	20						CCTCCTTGGAGCCTGATGTCT	0.662																																					p.G413G		Atlas-SNP	.											.	GDPD5	49	.	0			c.C1239T						.						35	33	34					11																	75152777		2200	4293	6493	SO:0001819	synonymous_variant	81544	exon13			CTTGGAGCCTGAT	AF318377	CCDS8238.1	11q13.4-q13.5	2011-01-25				ENSG00000158555			28804	protein-coding gene	gene with protein product		609632				18667693, 17275818	Standard	NM_030792		Approved	PP1665, GDE2	uc001owp.4	Q8WTR4		ENST00000336898.3:c.1239C>T	chr11.hg19:g.75152777G>A		112.0	0.0		60.0	4.0	NM_030792	Q49AQ5|Q6UX76|Q7Z4S0|Q8N781|Q8NCB7|Q8TB77	Silent	SNP	ENST00000336898.3	hg19	CCDS8238.1																																																																																			.	.		0.662	GDPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384409.1	NM_030792		A	75152777	G	A	75152777	2	1	260	1	0	0	0	0	0	0	0	1	6335	958	34	3		3	GDPD5	11	75152777	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	3435633	75152777	59853739	507	37752										
SERPINH1	871	hgsc.bcm.edu	37	chr11	75279838	75279838	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtggcttcatggtgactcggTcctataccgtgggtgtcatg	14	9	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:75279838T>C	ENST00000524558.1	+	3	2120	c.685T>C	c.(685-687)Tcc>Ccc	p.S229P	SERPINH1_ENST00000358171.3_Missense_Mutation_p.S229P|SERPINH1_ENST00000533603.1_Missense_Mutation_p.S229P|SERPINH1_ENST00000530284.1_Missense_Mutation_p.S229P|SERPINH1_ENST00000525876.1_Missense_Mutation_p.S12P			P50454	SERPH_HUMAN	serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)	229					chondrocyte development involved in endochondral bone morphogenesis (GO:0003433)|collagen biosynthetic process (GO:0032964)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|protein maturation (GO:0051604)|regulation of proteolysis (GO:0030162)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(4)|large_intestine(3)|liver(1)|lung(4)|ovary(2)|stomach(1)	15	Ovarian(111;0.11)					GGTGACTCGGTCCTATACCGT	0.557																																					p.S229P		Atlas-SNP	.											.	SERPINH1	33	.	0			c.T685C						.						153	117	129					11																	75279838		2200	4293	6493	SO:0001583	missense	871	exon3			ACTCGGTCCTATA	X61598	CCDS8239.1	11q13.5	2014-02-18	2005-08-18		ENSG00000149257	ENSG00000149257		"Serine (or cysteine) peptidase inhibitors"	1546	protein-coding gene	gene with protein product		600943	"serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 2", "serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)"	CBP1, CBP2, SERPINH2		7656593, 9533029, 24172014	Standard	NM_001207014		Approved	HSP47, colligen	uc001owr.3	P50454	OTTHUMG00000165362	ENST00000524558.1:c.685T>C	chr11.hg19:g.75279838T>C	ENSP00000434412:p.Ser229Pro	237.0	0.0		121.0	5.0	NM_001235	B3KVJ3|P29043|Q5XPB4|Q6NSJ6|Q8IY96|Q9NP88	Missense_Mutation	SNP	ENST00000524558.1	hg19	CCDS8239.1	.	.	.	.	.	.	.	.	.	.	T	30	5.057440	0.93846	.	.	ENSG00000149257	ENST00000533603;ENST00000358171;ENST00000526397;ENST00000421448;ENST00000530284;ENST00000532356;ENST00000524558;ENST00000525611;ENST00000525876	D;D;D;D;D;D;D;D	0.84800	-1.9;-1.9;-1.9;-1.9;-1.9;-1.9;-1.9;-1.9	5.71	5.71	0.89125	Serpin domain (3);	0.111513	0.64402	D	0.000006	D	0.90410	0.6998	M	0.69823	2.125	0.80722	D	1	D;D	0.65815	0.989;0.995	P;D	0.63283	0.834;0.913	D	0.90193	0.4251	10	0.44086	T	0.13	.	13.9316	0.63998	0.0:0.0:0.0:1.0	.	229;229	E9PPV6;P50454	.;SERPH_HUMAN	P	229;229;229;208;229;229;229;229;12	ENSP00000434657:S229P;ENSP00000350894:S229P;ENSP00000434964:S229P;ENSP00000436305:S229P;ENSP00000436040:S229P;ENSP00000434412:S229P;ENSP00000435452:S229P;ENSP00000433532:S12P	ENSP00000350894:S229P	S	+	1	0	SERPINH1	74957486	1.000000	0.71417	0.989000	0.46669	0.969000	0.65631	6.130000	0.71663	2.169000	0.68431	0.533000	0.62120	TCC	.	.		0.557	SERPINH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383610.1	NM_004353		C	75279838	T	C	75279838	3	2	260	1	0	0	0	0	1	0	0	0	14132	1667	58	2	691	2	SERPINH1	11	75279838	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	127061	75279838	59726678	508	37753										
MYO7A	4647	hgsc.bcm.edu	37	chr11	76922240	76922240	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctaccacaagtgcacgcgggAggaggtgctgcagctggggg	18	10	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:76922240A>G	ENST00000409709.3	+	45	6367	c.6095A>G	c.(6094-6096)gAg>gGg	p.E2032G	MYO7A_ENST00000605744.1_3'UTR|MYO7A_ENST00000409619.2_Missense_Mutation_p.E1983G|MYO7A_ENST00000458637.2_Missense_Mutation_p.E1994G	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	2032	FERM 2. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						TGCACGCGGGAGGAGGTGCTG	0.622																																					p.E2032G		Atlas-SNP	.											.	MYO7A	164	.	0			c.A6095G						.						25	30	28					11																	76922240		2111	4211	6322	SO:0001583	missense	4647	exon45			CGCGGGAGGAGGT	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"A-kinase anchor proteins", "Myosins / Myosin superfamily : Class VII"	7606	protein-coding gene	gene with protein product		276903	"myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.6095A>G	chr11.hg19:g.76922240A>G	ENSP00000386331:p.Glu2032Gly	96.0	0.0		99.0	6.0	NM_000260	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Missense_Mutation	SNP	ENST00000409709.3	hg19	CCDS53683.1	.	.	.	.	.	.	.	.	.	.	A	17.98	3.521904	0.64747	.	.	ENSG00000137474	ENST00000409709;ENST00000458637;ENST00000409619;ENST00000545136;ENST00000358342;ENST00000343356;ENST00000341717;ENST00000458169;ENST00000544424	D;D;D;D	0.83075	-1.68;-1.68;-1.68;-1.68	4.63	4.63	0.57726	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.049395	0.85682	D	0.000000	D	0.89712	0.6794	M	0.69523	2.12	0.80722	D	1	D;B	0.76494	0.999;0.201	D;B	0.72625	0.978;0.14	D	0.91023	0.4858	10	0.87932	D	0	.	14.2037	0.65721	1.0:0.0:0.0:0.0	.	1994;2032	F8VUN5;Q13402	.;MYO7A_HUMAN	G	2032;1994;1983;1205;2031;2001;1908;1174;647	ENSP00000386331:E2032G;ENSP00000392185:E1994G;ENSP00000386635:E1983G;ENSP00000417017:E1174G	ENSP00000345075:E1908G	E	+	2	0	MYO7A	76599888	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.687000	0.91255	1.957000	0.56846	0.454000	0.30748	GAG	.	.		0.622	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260		G	76922240	A	G	76922240	3	3	260	1	0	0	0	0	1	0	0	0	10091	304	11	2	6303	2	MYO7A	11	76922240	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1642402	76922240	58084276	509	37754										
ALG8	79053	hgsc.bcm.edu	37	chr11	77832116	77832116	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gaatatcaaggatacggtccAcaattaataacccgaagttc	7	9	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:77832116A>G	ENST00000299626.5	-	4	544	c.473T>C	c.(472-474)gTg>gCg	p.V158A	ALG8_ENST00000532552.2_Intron|ALG8_ENST00000376156.3_Missense_Mutation_p.V158A	NM_024079.4	NP_076984.2	Q9BVK2	ALG8_HUMAN	ALG8, alpha-1,3-glucosyltransferase	158					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-1,3-mannosyltransferase activity (GO:0000033)			NS(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	30	all_cancers(14;3.62e-19)|all_epithelial(13;1.27e-21)|Breast(9;8.51e-17)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;9.66e-25)			GATACGGTCCACAATTAATAA	0.318																																					p.V158A		Atlas-SNP	.											.	ALG8	54	.	0			c.T473C						.						160	152	155					11																	77832116		2200	4292	6492	SO:0001583	missense	79053	exon4			CGGTCCACAATTA	AJ224875	CCDS8258.1, CCDS41692.1	11q14.1	2013-03-01	2013-03-01		ENSG00000159063	ENSG00000159063	2.4.1.265		23161	protein-coding gene	gene with protein product	"dolichyl-P-Glc:Glc(1)Man(9)GlcNAc(2)-PP-dolichol alpha- 1->3-glucosyltransferase"	608103	"asparagine-linked glycosylation 8 homolog (yeast, alpha-1,3-glucosyltransferase)", "asparagine-linked glycosylation 8, alpha-1,3-glucosyltransferase homolog (S. cerevisiae)"				Standard	XM_005274247		Approved	MGC2840	uc001oza.1	Q9BVK2	OTTHUMG00000166594	ENST00000299626.5:c.473T>C	chr11.hg19:g.77832116A>G	ENSP00000299626:p.Val158Ala	148.0	0.0		98.0	5.0	NM_024079	A6NDW6|O60860	Missense_Mutation	SNP	ENST00000299626.5	hg19	CCDS8258.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	25.8|25.8	4.679874|4.679874	0.88542|0.88542	.|.	.|.	ENSG00000159063|ENSG00000159063	ENST00000299626;ENST00000376156;ENST00000525755;ENST00000530454;ENST00000525870;ENST00000527099|ENST00000532306;ENST00000529139	D;D;D;D;D;D|.	0.85955|.	-2.05;-2.05;-2.05;-2.05;-2.05;-2.05|.	5.81|5.81	5.81|5.81	0.92471|0.92471	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.84938|0.84938	0.5583|0.5583	M|M	0.91872|0.91872	3.25|3.25	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.85130|.	0.997;0.997|.	D|D	0.88331|0.88331	0.2968|0.2968	10|5	0.72032|.	D|.	0.01|.	-12.6418|-12.6418	16.1708|16.1708	0.81812|0.81812	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	158;158|.	Q9BVK2;A6NDW6|.	ALG8_HUMAN;.|.	A|R	158;158;107;159;70;70|32;3	ENSP00000299626:V158A;ENSP00000365326:V158A;ENSP00000435467:V107A;ENSP00000434660:V159A;ENSP00000435417:V70A;ENSP00000436064:V70A|.	ENSP00000299626:V158A|.	V|W	-|-	2|1	0|0	ALG8|ALG8	77509764|77509764	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.971000|0.971000	0.66376|0.66376	8.047000|8.047000	0.89440|0.89440	2.225000|2.225000	0.72522|0.72522	0.533000|0.533000	0.62120|0.62120	GTG|TGG	.	.		0.318	ALG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390637.1	NM_024079		G	77832116	A	G	77832116	3	3	260	1	0	0	0	0	1	0	0	0	523	159	6	2	1206	2	ALG8	11	77832116	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	909876	77832116	57174400	510	37755										
CCDC90B	60492	hgsc.bcm.edu	37	chr11	82985021	82985021	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgttgcttaacttggtctaaTtcaattttcattttctaggt	6	6	4	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:82985021T>C	ENST00000529689.1	-	5	875	c.441A>G	c.(439-441)gaA>gaG	p.E147E	CCDC90B_ENST00000529611.1_Silent_p.E46E|CCDC90B_ENST00000525503.1_Silent_p.E46E|CCDC90B_ENST00000455220.2_Silent_p.E138E|CCDC90B_ENST00000529073.1_Silent_p.E147E			Q9GZT6	CC90B_HUMAN	coiled-coil domain containing 90B	147						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				kidney(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	10		Acute lymphoblastic leukemia(157;0.103)				CTTGGTCTAATTCAATTTTCA	0.264																																					p.E147E		Atlas-SNP	.											.	CCDC90B	20	.	0			c.A441G						.						78	78	78					11																	82985021		2201	4292	6493	SO:0001819	synonymous_variant	60492	exon5			GTCTAATTCAATT	BC048795	CCDS8266.1, CCDS66190.1, CCDS66191.1	11q14.1	2006-10-23			ENSG00000137500	ENSG00000137500			28108	protein-coding gene	gene with protein product						11230166	Standard	XM_005274154		Approved	MDS025, MDS011	uc001pae.3	Q9GZT6	OTTHUMG00000167078	ENST00000529689.1:c.441A>G	chr11.hg19:g.82985021T>C		182.0	0.0		99.0	4.0	NM_021825	A8K8I4|B3KP87|B4E3L2|Q3B781|Q9GZU6	Silent	SNP	ENST00000529689.1	hg19	CCDS8266.1																																																																																			.	.		0.264	CCDC90B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392940.2	NM_021825		C	82985021	T	C	82985021	2	2	260	1	0	0	0	0	0	0	0	1	2871	1490	52	2		2	CCDC90B	11	82985021	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	5152905	82985021	52021495	511	37756										
MRE11A	4361	hgsc.bcm.edu	37	chr11	94180593	94180593	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgagatctgagtgctctggcCctggtcatagcctaagaggg	14	9	3	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:94180593C>T	ENST00000323929.3	-	15	1797	c.1575G>A	c.(1573-1575)agG>agA	p.R525R	MRE11A_ENST00000393241.4_Silent_p.R525R|MRE11A_ENST00000407439.3_Silent_p.R528R|MRE11A_ENST00000323977.3_Silent_p.R525R	NM_005591.3	NP_005582.1	P49959	MRE11_HUMAN	MRE11 meiotic recombination 11 homolog A (S. cerevisiae)	525					base-excision repair (GO:0006284)|cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|innate immune response (GO:0045087)|intra-S DNA damage checkpoint (GO:0031573)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of DNA endoreduplication (GO:0032876)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair (GO:0006289)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of type I interferon production (GO:0032481)|reciprocal meiotic recombination (GO:0007131)|regulation of mitotic recombination (GO:0000019)|sister chromatid cohesion (GO:0007062)|synapsis (GO:0007129)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromatin (GO:0000785)|cytosol (GO:0005829)|Mre11 complex (GO:0030870)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|double-stranded DNA binding (GO:0003690)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|manganese ion binding (GO:0030145)|nuclease activity (GO:0004518)|protein C-terminus binding (GO:0008022)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			breast(5)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	29		Acute lymphoblastic leukemia(157;2.37e-05)|all_hematologic(158;0.00824)				GTGCTCTGGCCCTGGTCATAG	0.418								Homologous recombination	Ataxia-Telangiectasia-Like Disorder																												p.R525R		Atlas-SNP	.											MRE11A_ENST00000323929,right_upper_lobe,carcinoma,0,2	MRE11A	145	.	0			c.G1575A						.						75	69	71					11																	94180593		2201	4298	6499	SO:0001819	synonymous_variant	4361	exon15	Familial Cancer Database	ATLD	TCTGGCCCTGGTC	BC063458	CCDS8298.1, CCDS8299.1	11q21	2014-09-17	2001-11-28		ENSG00000020922	ENSG00000020922			7230	protein-coding gene	gene with protein product	"AT-like disease"	600814	"meiotic recombination (S. cerevisiae) 11 homolog A"	MRE11		8530104	Standard	XM_005274007		Approved	ATLD	uc001peu.2	P49959	OTTHUMG00000167780	ENST00000323929.3:c.1575G>A	chr11.hg19:g.94180593C>T		96.0	0.0		51.0	3.0	NM_005591	O43475	Silent	SNP	ENST00000323929.3	hg19	CCDS8299.1																																																																																			.	.		0.418	MRE11A-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396237.3	NM_005591		T	94180593	C	T	94180593	2	4	260	1	0	0	0	0	0	0	0	1	9768	622	22	3		3	MRE11A	11	94180593	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	11195572	94180593	40825923	512	37757										
FAM76B	143684	hgsc.bcm.edu	37	chr11	95516268	95516268	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gacgatggtgatggtgatgaTggtggtgatgatgttttgga	18	1	0	5			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:95516268T>C	ENST00000358780.5	-	5	836	c.524A>G	c.(523-525)cAt>cGt	p.H175R	FAM76B_ENST00000536839.1_Missense_Mutation_p.H175R	NM_144664.4	NP_653265.3	Q5HYJ3	FA76B_HUMAN	family with sequence similarity 76, member B	175	His-rich.|Poly-His.					nuclear membrane (GO:0031965)|nucleus (GO:0005634)				breast(1)|kidney(1)|lung(1)	3		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				atggtgatgatggtggtgatg	0.378																																					p.H175R		Atlas-SNP	.											.	FAM76B	10	.	0			c.A524G						.						120	116	117					11																	95516268		1984	4162	6146	SO:0001583	missense	143684	exon5			TGATGATGGTGGT		CCDS41700.1	11q21	2008-02-05			ENSG00000077458	ENSG00000077458			28492	protein-coding gene	gene with protein product						12477932	Standard	NM_144664		Approved	MGC33371	uc001pfn.2	Q5HYJ3	OTTHUMG00000167739	ENST00000358780.5:c.524A>G	chr11.hg19:g.95516268T>C	ENSP00000351631:p.His175Arg	443.0	1.0		315.0	80.0	NM_144664	Q6PIU3|Q8TC53	Missense_Mutation	SNP	ENST00000358780.5	hg19	CCDS41700.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.31|14.31	2.498398|2.498398	0.44455|0.44455	.|.	.|.	ENSG00000077458|ENSG00000077458	ENST00000358780;ENST00000536839|ENST00000542135;ENST00000540054	.|.	.|.	.|.	5.6|5.6	5.6|5.6	0.85130|0.85130	.|.	0.149349|.	0.64402|.	D|.	0.000011|.	T|T	0.44850|0.44850	0.1313|0.1313	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	B|.	0.33073|.	0.396|.	B|.	0.34931|.	0.192|.	T|T	0.55515|0.55515	-0.8129|-0.8129	9|6	0.13470|0.87932	T|D	0.59|0	-16.1145|-16.1145	16.0786|16.0786	0.80985|0.80985	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	175|.	Q5HYJ3|.	FA76B_HUMAN|.	R|V	175|79	.|.	ENSP00000351631:H175R|ENSP00000442652:I79V	H|I	-|-	2|1	0|0	FAM76B|FAM76B	95155916|95155916	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.896000|0.896000	0.52359|0.52359	7.356000|7.356000	0.79445|0.79445	2.254000|2.254000	0.74563|0.74563	0.460000|0.460000	0.39030|0.39030	CAT|ATC	.	.		0.378	FAM76B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395969.1	NM_144664		C	95516268	T	C	95516268	3	2	260	1	0	0	0	0	1	0	0	0	5633	1464	51	2	519	2	FAM76B	11	95516268	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1335675	95516268	39490248	513	37758										
YAP1	10413	hgsc.bcm.edu	37	chr11	101984899	101984899	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtactgatgcaggcactgcaGgagccctgactccacagcat	11	13	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:101984899G>T	ENST00000282441.5	+	2	734	c.346G>T	c.(346-348)Gga>Tga	p.G116*	YAP1_ENST00000531439.1_Nonsense_Mutation_p.G116*|YAP1_ENST00000524575.1_5'UTR|YAP1_ENST00000526343.1_Nonsense_Mutation_p.G116*|YAP1_ENST00000345877.2_Nonsense_Mutation_p.G116*|YAP1_ENST00000537274.1_Nonsense_Mutation_p.G116*	NM_001130145.2|NM_001282101.1	NP_001123617.1|NP_001269030.1	P46937	YAP1_HUMAN	Yes-associated protein 1	116					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|contact inhibition (GO:0060242)|embryonic heart tube morphogenesis (GO:0003143)|gene expression (GO:0010467)|hippo signaling (GO:0035329)|keratinocyte differentiation (GO:0030216)|lateral mesoderm development (GO:0048368)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|notochord development (GO:0030903)|paraxial mesoderm development (GO:0048339)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|positive regulation of organ growth (GO:0046622)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of keratinocyte proliferation (GO:0010837)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of stem cell proliferation (GO:0072091)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)	4	all_cancers(8;0.000575)|all_epithelial(12;0.00564)	Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.00936)	Lung(13;0.245)	BRCA - Breast invasive adenocarcinoma(274;0.0189)		AGGCACTGCAGGAGCCCTGAC	0.478																																					p.G116X	Colon(50;247 1103 7861 28956)	Atlas-SNP	.											.	YAP1	45	.	0			c.G346T						.						48	48	48					11																	101984899		2203	4299	6502	SO:0001587	stop_gained	10413	exon2			ACTGCAGGAGCCC		CCDS8314.1, CCDS44716.1, CCDS8314.2, CCDS53699.1, CCDS53700.1, CCDS60944.1, CCDS73373.1, CCDS73374.1	11q13	2010-03-19	2010-03-19		ENSG00000137693	ENSG00000137693			16262	protein-coding gene	gene with protein product		606608	"Yes-associated protein 1, 65kDa"			7782338	Standard	NM_001130145		Approved	YAP65	uc001pgt.3	P46937	OTTHUMG00000167322	ENST00000282441.5:c.346G>T	chr11.hg19:g.101984899G>T	ENSP00000282441:p.Gly116*	132.0	0.0		64.0	4.0	NM_001130145	B4DTY1|B7ZA01|E3WEB5|E3WEB6|E9PRV2|F5H202|K0KQ18|K0KYZ8|K0L195|K0L1G3|Q7Z574|Q8IUY9	Nonsense_Mutation	SNP	ENST00000282441.5	hg19	CCDS44716.1	.	.	.	.	.	.	.	.	.	.	G	41	9.065605	0.99053	.	.	ENSG00000137693	ENST00000526343;ENST00000282441;ENST00000537274;ENST00000345877;ENST00000445250;ENST00000531439	.	.	.	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	.	19.4808	0.95008	0.0:0.0:1.0:0.0	.	.	.	.	X	116;116;116;116;31;116	.	ENSP00000282441:G116X	G	+	1	0	YAP1	101490109	1.000000	0.71417	0.985000	0.45067	0.948000	0.59901	7.564000	0.82326	2.611000	0.88343	0.563000	0.77884	GGA	.	.		0.478	YAP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394151.1	NM_006106		T	101984899	G	T	101984899	4	4	260	1	0	0	0	0	0	1	0	0	17481	1001	35	3	352	3	YAP1	11	101984899	Nonsense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	6468631	101984899	33021617	514	37759										
EXPH5	23086	hgsc.bcm.edu	37	chr11	108409913	108409913	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	atgtaggtaattctatcggaTctagaaaaaaaaattgtaaa	7	3	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:108409913T>C	ENST00000265843.4	-	3	391	c.281A>G	c.(280-282)gAt>gGt	p.D94G	EXPH5_ENST00000428840.1_Splice_Site_p.D18G|EXPH5_ENST00000525344.1_Splice_Site_p.D87G|EXPH5_ENST00000524840.1_5'Flank|EXPH5_ENST00000443411.1_5'Flank	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	94					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		TTCTATCGGATCTAGAAAAAA	0.338																																					p.D94G		Atlas-SNP	.											.	EXPH5	193	.	0			c.A281G						.						59	67	64					11																	108409913		2201	4298	6499	SO:0001630	splice_region_variant	23086	exon3			ATCGGATCTAGAA		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"synaptotagmin-like homologue lacking C2 domains b"	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.281-1A>G	chr11.hg19:g.108409913T>C		144.0	0.0		91.0	4.0	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	hg19	CCDS8341.1	.	.	.	.	.	.	.	.	.	.	T	17.12	3.307583	0.60305	.	.	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000525344;ENST00000526312;ENST00000531386	T;T;T;T;T	0.55052	4.03;3.49;4.04;3.36;0.54	4.97	3.83	0.44106	.	0.000000	0.53938	D	0.000055	T	0.66684	0.2814	M	0.69823	2.125	0.80722	D	1	D	0.76494	0.999	D	0.75484	0.986	T	0.65496	-0.6154	10	0.54805	T	0.06	.	7.56	0.27845	0.0:0.0987:0.0:0.9013	.	94	Q8NEV8	EXPH5_HUMAN	G	94;18;87;18;18	ENSP00000265843:D94G;ENSP00000391966:D18G;ENSP00000432546:D87G;ENSP00000432683:D18G;ENSP00000433909:D18G	ENSP00000265843:D94G	D	-	2	0	EXPH5	107915123	0.995000	0.38212	0.915000	0.36163	0.841000	0.47740	1.208000	0.32345	0.739000	0.32628	0.455000	0.32223	GAT	.	.		0.338	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065	Missense_Mutation	C	108409913	T	C	108409913	5	2	260	1	0	0	0	0	0	0	1	0	5324	1449	50	2	5704	2	EXPH5	11	108409913	Splice_Site	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	6425014	108409913	26596603	515	37760										
ANKK1	255239	hgsc.bcm.edu	37	chr11	113267990	113267990	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgctgtcactgctgcagagtCgtgtggcagtcccagagagc	14	11	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:113267990C>T	ENST00000303941.3	+	6	977	c.883C>T	c.(883-885)Cgt>Tgt	p.R295C		NM_178510.1	NP_848605.1	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1	295							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.R295S(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|stomach(1)	29		all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194)		BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238)		GCTGCAGAGTCGTGTGGCAGT	0.602																																					p.R295C		Atlas-SNP	.											ANKK1,NS,carcinoma,0,1	ANKK1	83	.	1	Substitution - Missense(1)	lung(1)	c.C883T						.						62	68	66					11																	113267990		2158	4246	6404	SO:0001583	missense	255239	exon6			CAGAGTCGTGTGG	AJ541797	CCDS44734.1	11q23.2	2013-01-10			ENSG00000170209	ENSG00000170209		"Ankyrin repeat domain containing"	21027	protein-coding gene	gene with protein product		608774				15146457	Standard	NM_178510		Approved	X-kinase	uc001pny.3	Q8NFD2	OTTHUMG00000167715	ENST00000303941.3:c.883C>T	chr11.hg19:g.113267990C>T	ENSP00000306678:p.Arg295Cys	82.0	0.0		55.0	3.0	NM_178510		Missense_Mutation	SNP	ENST00000303941.3	hg19	CCDS44734.1	.	.	.	.	.	.	.	.	.	.	C	11.26	1.587316	0.28268	.	.	ENSG00000170209	ENST00000303941	T	0.75260	-0.92	4.8	-0.784	0.10954	Protein kinase-like domain (1);	0.868455	0.09547	U	0.787433	T	0.48429	0.1499	N	0.08118	0	0.09310	N	1	P	0.34934	0.476	B	0.30646	0.118	T	0.36065	-0.9763	10	0.51188	T	0.08	-0.3698	5.156	0.15034	0.1416:0.3664:0.413:0.0789	.	295	Q8NFD2	ANKK1_HUMAN	C	295	ENSP00000306678:R295C	ENSP00000306678:R295C	R	+	1	0	ANKK1	112773200	0.000000	0.05858	0.000000	0.03702	0.092000	0.18411	-0.831000	0.04405	-0.315000	0.08703	0.561000	0.74099	CGT	.	.		0.602	ANKK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395830.1	NM_178510		T	113267990	C	T	113267990	3	4	260	1	0	0	0	0	1	0	0	0	631	884	31	1	905	1	ANKK1	11	113267990	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	4858077	113267990	21738526	516	37761										
DDX6	1656	hgsc.bcm.edu	37	chr11	118626140	118626140	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	caatacgatggagataggtcTctgccagctttgggaaatca	11	8	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:118626140T>C	ENST00000526070.2	-	12	1607	c.1247A>G	c.(1246-1248)gAg>gGg	p.E416G	DDX6_ENST00000534980.1_Missense_Mutation_p.E416G|DDX6_ENST00000264018.4_Missense_Mutation_p.E416G	NM_001257191.1	NP_001244120.1	P26196	DDX6_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 6	416	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cytoplasmic mRNA processing body assembly (GO:0033962)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|RISC complex (GO:0016442)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(1)|ovary(1)|prostate(1)	13	all_hematologic(175;0.0839)	Renal(330;0.0183)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)|Hepatocellular(160;0.0893)|Breast(348;0.0979)|all_hematologic(192;0.103)		OV - Ovarian serous cystadenocarcinoma(223;3.39e-06)|BRCA - Breast invasive adenocarcinoma(274;3.4e-05)|Colorectal(284;0.0377)		GAGATAGGTCTCTGCCAGCTT	0.338			T	IGH@	B-NHL																																p.E416G		Atlas-SNP	.		Dom	yes		11	11q23.3	1656	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6		L	.	DDX6	64	.	0			c.A1247G						.						90	86	87					11																	118626140		1821	4082	5903	SO:0001583	missense	1656	exon12			TAGGTCTCTGCCA	D17532	CCDS44751.1	11q23.3	2012-02-23	2012-02-23		ENSG00000110367	ENSG00000110367		"DEAD-boxes"	2747	protein-coding gene	gene with protein product		600326	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 6 (RNA helicase, 54kD)", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 6"	HLR2		1579499, 11839790	Standard	NM_004397		Approved	RCK	uc001pub.2	P26196	OTTHUMG00000166411	ENST00000526070.2:c.1247A>G	chr11.hg19:g.118626140T>C	ENSP00000433704:p.Glu416Gly	142.0	0.0		86.0	5.0	NM_004397	Q5D048	Missense_Mutation	SNP	ENST00000526070.2	hg19	CCDS44751.1	.	.	.	.	.	.	.	.	.	.	T	28.4	4.915438	0.92178	.	.	ENSG00000110367	ENST00000264018;ENST00000534980;ENST00000526070	T;T;T	0.76448	-1.02;-1.02;-1.02	5.46	5.46	0.80206	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.89072	0.6611	M	0.84433	2.695	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90845	0.4726	10	0.87932	D	0	.	15.5001	0.75691	0.0:0.0:0.0:1.0	.	416	P26196	DDX6_HUMAN	G	416	ENSP00000264018:E416G;ENSP00000442266:E416G;ENSP00000433704:E416G	ENSP00000264018:E416G	E	-	2	0	DDX6	118131350	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.950000	0.87804	2.199000	0.70637	0.528000	0.53228	GAG	.	.		0.338	DDX6-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000389647.2	NM_004397		C	118626140	T	C	118626140	3	2	260	1	0	0	0	0	1	0	0	0	4379	1551	54	2	212	2	DDX6	11	118626140	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	5358150	118626140	16380376	517	37762										
HYOU1	10525	hgsc.bcm.edu	37	chr11	118917336	118917336	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cattgaggggtggctctgccCgggtcccattcttgtcctta	12	12	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:118917336C>A	ENST00000404233.3	-	23	2898	c.2774G>T	c.(2773-2775)cGg>cTg	p.R925L	HYOU1_ENST00000529972.1_Missense_Mutation_p.R863L|RP11-110I1.6_ENST00000531886.1_RNA|HYOU1_ENST00000525859.1_Missense_Mutation_p.R863L	NM_001130991.1|NM_006389.3	NP_001124463.1|NP_006380.1	Q9Y4L1	HYOU1_HUMAN	hypoxia up-regulated 1	925					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|response to ischemia (GO:0002931)|response to stress (GO:0006950)	endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(10)|prostate(1)|skin(2)	33	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.78e-05)		TGGCTCTGCCCGGGTCCCATT	0.592																																					p.R925L		Atlas-SNP	.											.	HYOU1	88	.	0			c.G2774T						.						116	117	117					11																	118917336		2200	4295	6495	SO:0001583	missense	10525	exon23			TCTGCCCGGGTCC	U65785	CCDS8408.1	11q23.1-q23.3	2011-09-02			ENSG00000149428	ENSG00000149428		"Heat shock proteins / HSP70"	16931	protein-coding gene	gene with protein product	"glucose-regulated protein 170"	601746				9020069, 10037731	Standard	XM_005271390		Approved	ORP150, HSP12A, Grp170	uc001pux.3	Q9Y4L1	OTTHUMG00000166354	ENST00000404233.3:c.2774G>T	chr11.hg19:g.118917336C>A	ENSP00000384144:p.Arg925Leu	199.0	0.0		94.0	4.0	NM_006389	A8C1Z0|B7Z909|Q2I204|Q53H25	Missense_Mutation	SNP	ENST00000404233.3	hg19	CCDS8408.1	.	.	.	.	.	.	.	.	.	.	C	12.95	2.091328	0.36855	.	.	ENSG00000149428	ENST00000404233;ENST00000353883;ENST00000529972;ENST00000535579;ENST00000525859;ENST00000544701	T;T;T	0.01347	5.0;4.99;4.99	6.04	5.04	0.67666	.	0.178845	0.49305	D	0.000157	T	0.01029	0.0034	N	0.22421	0.69	0.80722	D	1	B;B;B;B	0.31318	0.223;0.319;0.223;0.223	B;B;B;B	0.25506	0.061;0.048;0.061;0.061	T	0.63651	-0.6589	10	0.32370	T	0.25	-25.0421	4.031	0.09710	0.0:0.693:0.0:0.307	.	916;907;925;925	B3KXH0;B7Z2N4;Q9Y4L1;A8C1Z0	.;.;HYOU1_HUMAN;.	L	925;916;863;774;863;906	ENSP00000384144:R925L;ENSP00000437313:R863L;ENSP00000433397:R863L	ENSP00000278752:R916L	R	-	2	0	HYOU1	118422546	0.837000	0.29446	0.993000	0.49108	0.123000	0.20343	1.064000	0.30579	2.873000	0.98535	0.561000	0.74099	CGG	.	.		0.592	HYOU1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389353.1	NM_006389		A	118917336	C	A	118917336	3	1	260	1	0	0	0	0	1	0	0	0	7479	652	23	1	241	1	HYOU1	11	118917336	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	291196	118917336	16089180	518	37763										
FOXRED1	55572	hgsc.bcm.edu	37	chr11	126147548	126147548	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttcctctttacccgcttttaCttgggagagaagatccagga	9	10	1	2	rs150932515		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr11:126147548C>T	ENST00000263578.5	+	11	1499	c.1425C>T	c.(1423-1425)taC>taT	p.Y475Y	FOXRED1_ENST00000534011.1_3'UTR|FOXRED1_ENST00000442061.2_Silent_p.Y305Y|FOXRED1_ENST00000532125.1_Silent_p.Y461Y	NM_017547.3	NP_060017.1	Q96CU9	FXRD1_HUMAN	FAD-dependent oxidoreductase domain containing 1	475						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)			breast(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(1)	15	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0729)		CCCGCTTTTACTTGGGAGAGA	0.552																																					p.Y475Y		Atlas-SNP	.											.	FOXRED1	38	.	0			c.C1425T						.	C		1,4401	2.1+/-5.4	0,1,2200	113	98	103		1425	4.6	1	11	dbSNP_134	103	0,8596		0,0,4298	no	coding-synonymous	FOXRED1	NM_017547.3		0,1,6498	TT,TC,CC		0.0,0.0227,0.0077		475/487	126147548	1,12997	2201	4298	6499	SO:0001819	synonymous_variant	55572	exon11			CTTTTACTTGGGA		CCDS8471.1	11q24.2	2006-02-03			ENSG00000110074	ENSG00000110074			26927	protein-coding gene	gene with protein product		613622				10497265	Standard	NM_017547		Approved	H17	uc001qdi.3	Q96CU9	OTTHUMG00000165827	ENST00000263578.5:c.1425C>T	chr11.hg19:g.126147548C>T		85.0	0.0		64.0	4.0	NM_017547	B3KN84|B4DHU2|Q71MG0|Q9BU39|Q9UKY9	Silent	SNP	ENST00000263578.5	hg19	CCDS8471.1																																																																																			.	C|1.000;T|0.000		0.552	FOXRED1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386434.1	NM_017547		T	126147548	C	T	126147548	2	4	260	1	0	0	0	0	0	0	0	1	6041	576	20	3		3	FOXRED1	11	126147548	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	7230212	126147548	8858968	519	37764										
B4GALNT3	283358	hgsc.bcm.edu	37	chr12	662900	662900	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aggccaggaaggacaagtggAgggagaggaagagggggaag	22	3	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:662900A>G	ENST00000266383.5	+	14	1824	c.1811A>G	c.(1810-1812)gAg>gGg	p.E604G		NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	604					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			GGACAAGTggagggagaggaa	0.612																																					p.E604G		Atlas-SNP	.											.	B4GALNT3	64	.	0			c.A1811G						.						56	48	51					12																	662900		2202	4300	6502	SO:0001583	missense	283358	exon14			AAGTGGAGGGAGA	AB089940	CCDS8504.1	12p13.33	2013-02-19			ENSG00000139044	ENSG00000139044	2.4.1.-	"Beta 4-glycosyltransferases"	24137	protein-coding gene	gene with protein product		612220				12966086	Standard	NM_173593		Approved	B4GalNac-T3, FLJ16224, FLJ40362	uc001qii.1	Q6L9W6	OTTHUMG00000129283	ENST00000266383.5:c.1811A>G	chr12.hg19:g.662900A>G	ENSP00000266383:p.Glu604Gly	147.0	0.0		121.0	5.0	NM_173593	Q6ZNC1|Q8N7T6	Missense_Mutation	SNP	ENST00000266383.5	hg19	CCDS8504.1	.	.	.	.	.	.	.	.	.	.	A	13.94	2.387261	0.42308	.	.	ENSG00000139044	ENST00000266383;ENST00000322843	T;T	0.35048	3.37;1.33	5.44	5.44	0.79542	.	0.506867	0.19338	N	0.116738	T	0.46521	0.1397	L	0.50333	1.59	0.50039	D	0.999844	D;D	0.57257	0.979;0.979	P;P	0.54270	0.747;0.549	T	0.25293	-1.0136	10	0.29301	T	0.29	-26.2211	15.1761	0.72913	1.0:0.0:0.0:0.0	.	507;604	E9PHD9;Q6L9W6	.;B4GN3_HUMAN	G	604;507	ENSP00000266383:E604G;ENSP00000322953:E507G	ENSP00000266383:E604G	E	+	2	0	B4GALNT3	533161	0.214000	0.23563	0.247000	0.24249	0.874000	0.50279	1.360000	0.34125	2.067000	0.61834	0.459000	0.35465	GAG	.	.		0.612	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593		G	662900	A	G	662900	3	3	260	1	0	0	0	0	1	0	0	0	1268	304	11	2	1865	2	B4GALNT3	12	662900	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10		662900	133188995	520	37765										
FBXL14	144699	hgsc.bcm.edu	37	chr12	1702156	1702156	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cagccgtacaggtctatgccGgtgagttggctcaggtgctc	14	11	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:1702156G>A	ENST00000339235.3	-	1	1175	c.1077C>T	c.(1075-1077)acC>acT	p.T359T	WNT5B_ENST00000537031.1_Intron|FBXL14_ENST00000543278.1_5'UTR	NM_152441.2	NP_689654.1	Q8N1E6	FXL14_HUMAN	F-box and leucine-rich repeat protein 14	359					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	8	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00115)			GGTCTATGCCGGTGAGTTGGC	0.627																																					p.T359T		Atlas-SNP	.											.	FBXL14	19	.	0			c.C1077T						.						133	114	120					12																	1702156		2203	4300	6503	SO:0001819	synonymous_variant	144699	exon1			TATGCCGGTGAGT	BC028132	CCDS8509.1	12p13.33	2011-06-09			ENSG00000171823	ENSG00000171823		"F-boxes / Leucine-rich repeats"	28624	protein-coding gene	gene with protein product		609081				12477932	Standard	NM_152441		Approved	MGC40195, Fbl14	uc001qjh.3	Q8N1E6	OTTHUMG00000090369	ENST00000339235.3:c.1077C>T	chr12.hg19:g.1702156G>A		135.0	0.0		68.0	4.0	NM_152441		Silent	SNP	ENST00000339235.3	hg19	CCDS8509.1																																																																																			.	.		0.627	FBXL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206741.1	NM_152441		A	1702156	G	A	1702156	2	1	260	1	0	0	0	0	0	0	0	1	5718	1103	39	1		1	FBXL14	12	1702156	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	1039256	1702156	132149739	521	37766										
TEAD4	7004	hgsc.bcm.edu	37	chr12	3121364	3121364	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccacatccaggtgctggctcGtcgcaaagctcgcgagatcc	11	15	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:3121364G>T	ENST00000359864.2	+	5	510	c.320G>T	c.(319-321)cGt>cTt	p.R107L	TEAD4_ENST00000358409.2_Missense_Mutation_p.R107L|TEAD4_ENST00000397122.2_5'UTR	NM_003213.3	NP_003204	Q15561	TEAD4_HUMAN	TEA domain family member 4	107					gene expression (GO:0010467)|hippo signaling (GO:0035329)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10	Ovarian(42;0.211)		OV - Ovarian serous cystadenocarcinoma(31;0.000563)|COAD - Colon adenocarcinoma(12;0.0831)			GTGCTGGCTCGTCGCAAAGCT	0.592																																					p.R107L		Atlas-SNP	.											.	TEAD4	45	.	0			c.G320T						.						71	60	64					12																	3121364		2203	4300	6503	SO:0001583	missense	7004	exon5			TGGCTCGTCGCAA	X94438	CCDS31729.1, CCDS31730.1, CCDS41737.1	12p13.3-p13.2	2008-05-14				ENSG00000197905			11717	protein-coding gene	gene with protein product		601714		TCF13L1		9889009, 8921372	Standard	NM_003213		Approved	TEF-3, TEFR-1, EFTR-2, RTEF-1	uc010sej.2	Q15561		ENST00000359864.2:c.320G>T	chr12.hg19:g.3121364G>T	ENSP00000352926:p.Arg107Leu	101.0	0.0		82.0	4.0	NM_003213	H0Y308|Q6MZR9|Q8NEV5|Q92883|Q96BK2	Missense_Mutation	SNP	ENST00000359864.2	hg19	CCDS31729.1	.	.	.	.	.	.	.	.	.	.	G	15.99	2.996831	0.54147	.	.	ENSG00000197905	ENST00000358409;ENST00000359864;ENST00000543035	T;T	0.61742	0.28;0.08	4.98	3.13	0.36017	.	0.000000	0.85682	D	0.000000	T	0.80048	0.4552	H	0.94503	3.545	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.81822	-0.0756	10	0.87932	D	0	-8.8362	9.7204	0.40300	0.0776:0.1414:0.781:0.0	.	107	Q15561	TEAD4_HUMAN	L	107	ENSP00000351184:R107L;ENSP00000352926:R107L	ENSP00000351184:R107L	R	+	2	0	TEAD4	2991625	1.000000	0.71417	0.966000	0.40874	0.172000	0.22775	9.068000	0.93961	0.606000	0.29965	-0.175000	0.13238	CGT	.	.		0.592	TEAD4-001	KNOWN	non_ATG_start|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398475.1	NM_003213		T	3121364	G	T	3121364	3	4	260	1	0	0	0	0	1	0	0	0	15756	1145	40	1	330	1	TEAD4	12	3121364	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	1419208	3121364	130730531	522	37767										
KCNA1	3736	hgsc.bcm.edu	37	chr12	5020815	5020815	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gcaaccggcccagcttcgacGccatcctctactactaccag	7	18	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:5020815G>T	ENST00000382545.3	+	2	1378	c.271G>T	c.(271-273)Gcc>Tcc	p.A91S	KCNA1_ENST00000543874.2_Intron	NM_000217.2	NP_000208.2	Q09470	KCNA1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 1 (episodic ataxia with myokymia)	91					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|dendrite (GO:0030425)|juxtaparanode region of axon (GO:0044224)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|potassium ion transmembrane transporter activity (GO:0015079)			NS(1)|breast(3)|cervix(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(23)|ovary(3)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63					Amitriptyline(DB00321)|Dalfampridine(DB06637)|Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Nifedipine(DB01115)|Sevoflurane(DB01236)	CAGCTTCGACGCCATCCTCTA	0.607																																					p.A91S		Atlas-SNP	.											KCNA1,lower_third,carcinoma,0,1	KCNA1	112	.	0			c.G271T						.						53	57	56					12																	5020815		2203	4300	6503	SO:0001583	missense	3736	exon2			TTCGACGCCATCC	L02750	CCDS8535.1	12p13	2012-07-05			ENSG00000111262	ENSG00000111262		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6218	protein-coding gene	gene with protein product		176260		AEMK		1349297, 8821794, 16382104	Standard	NM_000217		Approved	Kv1.1, RBK1, HUK1, MBK1	uc001qnh.3	Q09470	OTTHUMG00000044398	ENST00000382545.3:c.271G>T	chr12.hg19:g.5020815G>T	ENSP00000371985:p.Ala91Ser	94.0	0.0		60.0	3.0	NM_000217	A6NM83|Q3MIQ9	Missense_Mutation	SNP	ENST00000382545.3	hg19	CCDS8535.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.267098	0.80469	.	.	ENSG00000111262	ENST00000382545;ENST00000228858	T	0.76839	-1.05	4.34	4.34	0.51931	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.000000	0.85682	D	0.000000	D	0.83571	0.5283	L	0.45470	1.425	0.80722	D	1	P	0.46220	0.874	D	0.68353	0.957	T	0.80320	-0.1432	10	0.25751	T	0.34	.	16.3898	0.83531	0.0:0.0:1.0:0.0	.	91	Q09470	KCNA1_HUMAN	S	91	ENSP00000371985:A91S	ENSP00000228858:A91S	A	+	1	0	KCNA1	4891076	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.531000	0.98054	2.410000	0.81850	0.650000	0.86243	GCC	.	.		0.607	KCNA1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103343.2	NM_000217		T	5020815	G	T	5020815	3	4	260	1	0	0	0	0	1	0	0	0	8010	1087	38	1	273	1	KCNA1	12	5020815	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	1899451	5020815	128831080	523	37768										
NOP2	4839	hgsc.bcm.edu	37	chr12	6669315	6669315	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tttcttgaacttggcaatgaAgaacccatccatattgtggg	9	8	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:6669315A>G	ENST00000322166.5	-	15	1859	c.1738T>C	c.(1738-1740)Ttc>Ctc	p.F580L	NOP2_ENST00000545200.1_Missense_Mutation_p.F576L|NOP2_ENST00000382421.3_Missense_Mutation_p.F613L|NOP2_ENST00000541778.1_Missense_Mutation_p.F576L|NOP2_ENST00000399466.2_Missense_Mutation_p.F576L|NOP2_ENST00000542015.1_5'UTR|NOP2_ENST00000537442.1_Missense_Mutation_p.F580L	NM_001258308.1|NM_006170.3	NP_001245237.1|NP_006161.2	P46087	NOP2_HUMAN	NOP2 nucleolar protein	580					positive regulation of cell proliferation (GO:0008284)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			breast(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	19						TTGGCAATGAAGAACCCATCC	0.483																																					p.F613L		Atlas-SNP	.											.	NOP2	44	.	0			c.T1837C						.						89	90	90					12																	6669315		1867	4116	5983	SO:0001583	missense	4839	exon16			CAATGAAGAACCC		CCDS44811.1, CCDS58202.1, CCDS58203.1, CCDS58204.1	12p13	2012-12-10	2012-12-10	2008-10-13	ENSG00000111641	ENSG00000111641		"NOP2/Sun domain containing"	7867	protein-coding gene	gene with protein product	"NOP2/Sun domain family, member 1"	164031	"nucleolar protein 1 (120kD)", "nucleolar protein 1, 120kDa", "nucleolar protein 2 homolog (yeast)", "NOP2 nucleolar protein homolog (yeast)"	NOL1		8088812	Standard	NM_006170		Approved	NOP120, NSUN1, p120	uc021qtz.2	P46087	OTTHUMG00000169163	ENST00000322166.5:c.1738T>C	chr12.hg19:g.6669315A>G	ENSP00000313272:p.Phe580Leu	128.0	0.0		67.0	4.0	NM_001258309	A1A4Z3|B3KPD6|Q05BA7|Q0P5S5|Q3KQS4|Q58F30	Missense_Mutation	SNP	ENST00000322166.5	hg19	CCDS58203.1	.	.	.	.	.	.	.	.	.	.	A	31	5.094226	0.94149	.	.	ENSG00000111641	ENST00000537442;ENST00000382421;ENST00000545200;ENST00000399466;ENST00000322166;ENST00000541778	T;T;T;T;T;T	0.29397	1.57;1.57;1.57;1.57;1.57;1.57	4.95	4.95	0.65309	Nop2p (1);Bacterial Fmu (Sun)/eukaryotic nucleolar NOL1/Nop2p (1);	0.140304	0.64402	D	0.000003	T	0.71771	0.3379	H	0.98980	4.39	0.80722	D	1	D;D;D	0.89917	0.997;0.999;1.0	D;D;D	0.76071	0.976;0.973;0.987	D	0.84132	0.0412	10	0.72032	D	0.01	-22.8313	14.7847	0.69793	1.0:0.0:0.0:0.0	.	576;580;576	Q05BA7;P46087;P46087-2	.;NOP2_HUMAN;.	L	580;613;576;576;580;576	ENSP00000444437:F580L;ENSP00000371858:F613L;ENSP00000439422:F576L;ENSP00000382392:F576L;ENSP00000313272:F580L;ENSP00000443150:F576L	ENSP00000313272:F580L	F	-	1	0	NOP2	6539576	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	8.895000	0.92512	2.077000	0.62373	0.533000	0.62120	TTC	.	.		0.483	NOP2-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402614.1	NM_006170		G	6669315	A	G	6669315	3	3	260	1	0	0	0	0	1	0	0	0	10547	72	3	2	708	2	NOP2	12	6669315	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1648500	6669315	127182580	524	37769										
GPR162	27239	hgsc.bcm.edu	37	chr12	6935396	6935396	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	actatgcagagggccgagttTgcaaagttcgctttgatgct	12	8	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:6935396T>C	ENST00000311268.3	+	4	1880	c.1093T>C	c.(1093-1095)Tgc>Cgc	p.C365R	LEPREL2_ENST00000251761.8_RNA|GPR162_ENST00000382315.3_Missense_Mutation_p.C61R|LEPREL2_ENST00000396725.2_RNA|LEPREL2_ENST00000606935.1_RNA|GPR162_ENST00000428545.2_Missense_Mutation_p.C81R	NM_019858.1	NP_062832.1	Q16538	GP162_HUMAN	G protein-coupled receptor 162	365						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(2)|skin(1)	18						GGGCCGAGTTTGCAAAGTTCG	0.602											OREG0021636	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C365R		Atlas-SNP	.											.	GPR162	55	.	0			c.T1093C						.						70	71	71					12																	6935396		2203	4300	6503	SO:0001583	missense	27239	exon4			CGAGTTTGCAAAG	U47928, U47929, U47924, U47925	CCDS8563.1, CCDS44819.1	12p13	2012-08-21						"GPCR / Class A : Orphans"	16693	protein-coding gene	gene with protein product						15777626	Standard	NM_014449		Approved	A-2, GRCA	uc001qqw.1	Q16538		ENST00000311268.3:c.1093T>C	chr12.hg19:g.6935396T>C	ENSP00000311528:p.Cys365Arg	78.0	0.0	637	75.0	4.0	NM_019858	Q16664|Q59EH5|Q66K56	Missense_Mutation	SNP	ENST00000311268.3	hg19	CCDS8563.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.961616	0.74016	.	.	ENSG00000250510	ENST00000311268;ENST00000428545;ENST00000382315	T;T;T	0.47869	2.98;0.84;0.83	4.6	4.6	0.57074	.	.	.	.	.	T	0.60405	0.2266	L	0.44542	1.39	0.80722	D	1	D;D;D	0.76494	0.991;0.999;0.995	D;D;D	0.83275	0.991;0.996;0.979	T	0.62732	-0.6792	9	0.56958	D	0.05	.	14.1388	0.65306	0.0:0.0:0.0:1.0	.	149;81;365	Q13513;Q16538-2;Q16538	.;.;GP162_HUMAN	R	365;81;61	ENSP00000311528:C365R;ENSP00000399670:C81R;ENSP00000371752:C61R	ENSP00000311528:C365R	C	+	1	0	GPR162	6805657	1.000000	0.71417	0.999000	0.59377	0.930000	0.56654	5.308000	0.65768	1.930000	0.55929	0.402000	0.26972	TGC	.	.		0.602	GPR162-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399478.1	NM_019858		C	6935396	T	C	6935396	3	2	260	1	0	0	0	0	1	0	0	0	6674	1812	63	2	1122	2	GPR162	12	6935396	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	266081	6935396	126916499	525	37770										
PZP	5858	hgsc.bcm.edu	37	chr12	9315205	9315205	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	actcttacctgaggcacaggTcatagaactgaaagtctttt	8	9	3	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:9315205T>C	ENST00000261336.2	-	22	2804	c.2776A>G	c.(2776-2778)Acc>Gcc	p.T926A	PZP_ENST00000539983.1_5'UTR|PZP_ENST00000381997.2_Missense_Mutation_p.T712A	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	926					female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						GAGGCACAGGTCATAGAACTG	0.393																																					p.T926A	Melanoma(125;1402 1695 4685 34487 38571)	Atlas-SNP	.											.	PZP	422	.	0			c.A2776G						.						154	136	142					12																	9315205		2203	4300	6503	SO:0001583	missense	5858	exon22			CACAGGTCATAGA	X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.2776A>G	chr12.hg19:g.9315205T>C	ENSP00000261336:p.Thr926Ala	142.0	0.0		73.0	4.0	NM_002864	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	hg19	CCDS8600.1	.	.	.	.	.	.	.	.	.	.	T	10.98	1.504395	0.26949	.	.	ENSG00000126838	ENST00000261336;ENST00000381997	T;T	0.33438	2.35;1.41	2.83	-5.65	0.02459	.	2.832990	0.02197	N	0.061901	T	0.13030	0.0316	N	0.01874	-0.695	0.09310	N	1	B;B	0.29955	0.263;0.0	B;B	0.30316	0.114;0.001	T	0.33007	-0.9885	10	0.87932	D	0	.	8.5109	0.33217	0.0:0.4499:0.3485:0.2016	.	712;926	P20742-2;P20742	.;PZP_HUMAN	A	926;712	ENSP00000261336:T926A;ENSP00000371427:T712A	ENSP00000261336:T926A	T	-	1	0	PZP	9206472	0.000000	0.05858	0.000000	0.03702	0.635000	0.38103	-6.220000	0.00075	-1.935000	0.01049	0.383000	0.25322	ACC	.	.		0.393	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864		C	9315205	T	C	9315205	3	2	260	1	0	0	0	0	1	0	0	0	12884	1667	58	2	1732	2	PZP	12	9315205	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	2379809	9315205	124536690	526	37771										
CSDA	8531	hgsc.bcm.edu	37	chr12	10862602	10862602	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccgctgccggtactgagggcGatactgggggcggcgcagct	18	12	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:10862602G>C	ENST00000228251.4	-	6	885	c.685C>G	c.(685-687)Cgc>Ggc	p.R229G	YBX3_ENST00000279550.7_Intron|YBX3_ENST00000546164.1_5'UTR	NM_003651.4	NP_003642.3	P16989	YBOX3_HUMAN	Y box binding protein 3	229					3'-UTR-mediated mRNA stabilization (GO:0070935)|cellular hyperosmotic response (GO:0071474)|cellular response to tumor necrosis factor (GO:0071356)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress (GO:1902219)|negative regulation of necroptotic process (GO:0060546)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cytoplasmic translation (GO:2000767)|positive regulation of organ growth (GO:0046622)|response to cold (GO:0009409)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|tight junction (GO:0005923)	double-stranded DNA binding (GO:0003690)|mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|Rho GTPase binding (GO:0017048)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)	p.R229C(1)									TACTGAGGGCGATACTGGGGG	0.622																																					p.R229G		Atlas-SNP	.											CSDA,NS,carcinoma,0,1	CSDA	35	.	1	Substitution - Missense(1)	lung(1)	c.C685G						.						31	34	33					12																	10862602		2203	4300	6503	SO:0001583	missense	8531	exon6			GAGGGCGATACTG	L29064	CCDS8630.1, CCDS44831.1	12p13.1	2013-03-13	2013-03-13	2013-03-13	ENSG00000060138	ENSG00000060138			2428	protein-coding gene	gene with protein product	"cold-shock domain containing A1"	603437	"cold shock domain protein A"	CSDA		2977358, 8710501	Standard	NM_003651		Approved	dbpA, ZONAB, CSDA1	uc001qyt.3	P16989	OTTHUMG00000168409	ENST00000228251.4:c.685C>G	chr12.hg19:g.10862602G>C	ENSP00000228251:p.Arg229Gly	100.0	0.0		60.0	3.0	NM_003651	B2RBW6|Q14121|Q969N6|Q96B76	Missense_Mutation	SNP	ENST00000228251.4	hg19	CCDS8630.1	.	.	.	.	.	.	.	.	.	.	G	18.23	3.578112	0.65878	.	.	ENSG00000060138	ENST00000228251	T	0.27104	1.69	4.31	3.42	0.39159	.	0.263447	0.27739	N	0.018047	T	0.21841	0.0526	M	0.62088	1.915	0.31070	N	0.713076	P	0.35033	0.481	B	0.29524	0.103	T	0.17501	-1.0367	10	0.37606	T	0.19	.	8.0823	0.30752	0.1088:0.0:0.8912:0.0	.	229	P16989	DBPA_HUMAN	G	229	ENSP00000228251:R229G	ENSP00000228251:R229G	R	-	1	0	CSDA	10753869	1.000000	0.71417	0.977000	0.42913	0.987000	0.75469	3.090000	0.50191	1.408000	0.46895	0.655000	0.94253	CGC	.	.		0.622	YBX3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399628.1	NM_003651		C	10862602	G	C	10862602	3	2	260	1	0	0	0	0	1	0	0	0	3929	1058	37	4	449	4	CSDA	12	10862602	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	1547397	10862602	122989293	527	37772										
KCNJ8	3764	hgsc.bcm.edu	37	chr12	21918966	21918966	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtcacaatggacacaaagcgGtggccccattggatctcctc	10	13	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:21918966G>T	ENST00000240662.2	-	3	1311	c.966C>A	c.(964-966)caC>caA	p.H322Q	RP11-59N23.1_ENST00000542489.1_RNA	NM_004982.3	NP_004973.1	Q15842	KCNJ8_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 8	322					defense response to virus (GO:0051607)|heart development (GO:0007507)|kidney development (GO:0001822)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|response to exogenous dsRNA (GO:0043330)|response to lipopolysaccharide (GO:0032496)|response to pH (GO:0009268)|synaptic transmission (GO:0007268)|vasodilation (GO:0042311)	ATP-sensitive potassium channel complex (GO:0008282)|mitochondrion (GO:0005739)|myofibril (GO:0030016)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATP-activated inward rectifier potassium channel activity (GO:0015272)|inward rectifier potassium channel activity (GO:0005242)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	28					Gliquidone(DB01251)|Glisoxepide(DB01289)|Glyburide(DB01016)|Levosimendan(DB00922)|Phenformin(DB00914)|Thiamylal(DB01154)|Yohimbine(DB01392)	ACACAAAGCGGTGGCCCCATT	0.488																																					p.H322Q		Atlas-SNP	.											.	KCNJ8	59	.	0			c.C966A						.						96	86	89					12																	21918966		2203	4300	6503	SO:0001583	missense	3764	exon3			AAAGCGGTGGCCC	BC000544	CCDS8692.1	12p12.1	2011-07-05			ENSG00000121361	ENSG00000121361		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6269	protein-coding gene	gene with protein product		600935				8595887, 16382105	Standard	NM_004982		Approved	Kir6.1	uc001rff.4	Q15842	OTTHUMG00000169093	ENST00000240662.2:c.966C>A	chr12.hg19:g.21918966G>T	ENSP00000240662:p.His322Gln	121.0	0.0		98.0	4.0	NM_004982	O00657	Missense_Mutation	SNP	ENST00000240662.2	hg19	CCDS8692.1	.	.	.	.	.	.	.	.	.	.	G	11.93	1.785985	0.31593	.	.	ENSG00000121361	ENST00000240662;ENST00000539350	D	0.94497	-3.44	5.3	3.4	0.38934	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (2);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.000000	0.85682	D	0.000000	D	0.90307	0.6968	L	0.41632	1.29	0.50171	D	0.999851	B	0.25667	0.131	B	0.31390	0.129	D	0.85132	0.0975	10	0.48119	T	0.1	.	6.9663	0.24625	0.388:0.0:0.612:0.0	.	322	Q15842	IRK8_HUMAN	Q	322	ENSP00000240662:H322Q	ENSP00000240662:H322Q	H	-	3	2	KCNJ8	21810233	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.620000	0.46410	0.709000	0.31976	0.563000	0.77884	CAC	.	.		0.488	KCNJ8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402226.1	NM_004982		T	21918966	G	T	21918966	3	4	260	1	0	0	0	0	1	0	0	0	8065	1252	44	3	312	3	KCNJ8	12	21918966	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	11056364	21918966	111932929	528	37773										
TSPAN11	441631	hgsc.bcm.edu	37	chr12	31132605	31132605	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtggaccgactccagcaggaTgtaagccatgccccatatgg	12	12	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:31132605T>C	ENST00000261177.9	+	5	515	c.456T>C	c.(454-456)gaT>gaC	p.D152D	TSPAN11_ENST00000535215.1_Splice_Site_p.D81D|TSPAN11_ENST00000546076.1_Splice_Site_p.D152D|TSPAN11_ENST00000544427.1_Splice_Site_p.D142D	NM_001080509.2	NP_001073978.1	A1L157	TSN11_HUMAN	tetraspanin 11	152						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)	11	all_lung(12;3.11e-10)|Lung NSC(12;5.24e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					TCCAGCAGGATGTAAGCCATG	0.557																																					p.D152D		Atlas-SNP	.											.	TSPAN11	30	.	0			c.T456C						.						70	63	65					12																	31132605		2203	4300	6503	SO:0001630	splice_region_variant	441631	exon5			GCAGGATGTAAGC		CCDS31765.1	12p11.21	2013-02-14				ENSG00000110900		"Tetraspanins"	30795	protein-coding gene	gene with protein product							Standard	NM_001080509		Approved		uc001rjp.3	A1L157		ENST00000261177.9:c.456+1T>C	chr12.hg19:g.31132605T>C		129.0	0.0		97.0	4.0	NM_001080509	A1L158|B2RUX6	Silent	SNP	ENST00000261177.9	hg19	CCDS31765.1																																																																																			.	.		0.557	TSPAN11-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399888.1	XM_497334	Silent	C	31132605	T	C	31132605	5	2	260	1	0	0	0	0	0	0	1	0	16650	1478	51	2	470	2	TSPAN11	12	31132605	Splice_Site	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	9213639	31132605	102719290	529	37774										
ADAMTS20	80070	hgsc.bcm.edu	37	chr12	43846211	43846211	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tttacaacgatcctttgtgcCaactgtaaaaaagaaaaagg	7	7	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:43846211C>G	ENST00000389420.3	-	14	1944	c.1945G>C	c.(1945-1947)Ggc>Cgc	p.G649R	ADAMTS20_ENST00000553158.1_Missense_Mutation_p.G649R	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	649	Cys-rich.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.G649C(2)		breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		TCCTTTGTGCCAACTGTAAAA	0.323																																					p.G649R		Atlas-SNP	.											ADAMTS20_ENST00000389420,NS,carcinoma,0,2	ADAMTS20	635	.	2	Substitution - Missense(2)	lung(2)	c.G1945C						.						69	69	69					12																	43846211		2203	4300	6503	SO:0001583	missense	80070	exon14			TTGTGCCAACTGT	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.1945G>C	chr12.hg19:g.43846211C>G	ENSP00000374071:p.Gly649Arg	72.0	0.0		44.0	3.0	NM_025003	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	hg19	CCDS31778.2	.	.	.	.	.	.	.	.	.	.	C	2.200	-0.383324	0.04966	.	.	ENSG00000173157	ENST00000389420;ENST00000553158;ENST00000389417	T;D	0.85955	3.01;-2.05	4.97	2.07	0.26955	.	0.423664	0.19601	N	0.110384	T	0.70780	0.3263	N	0.16656	0.425	0.58432	D	0.999997	B	0.02656	0.0	B	0.01281	0.0	T	0.55224	-0.8174	10	0.17832	T	0.49	.	10.1208	0.42618	0.2549:0.4565:0.2886:0.0	.	649	P59510	ATS20_HUMAN	R	649	ENSP00000374071:G649R;ENSP00000448341:G649R	ENSP00000374068:G649R	G	-	1	0	ADAMTS20	42132478	0.997000	0.39634	0.169000	0.22859	0.015000	0.08874	0.421000	0.21280	0.059000	0.16252	-1.943000	0.00494	GGC	.	.		0.323	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		G	43846211	C	G	43846211	3	3	260	1	0	0	0	0	1	0	0	0	266	594	21	4	3890	4	ADAMTS20	12	43846211	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	12713606	43846211	90005684	530	37775										
PFKM	5213	hgsc.bcm.edu	37	chr12	48526741	48526741	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acaacctggtgaagcgtgggAtcaccaatctctgtgtcatt	10	10	3	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:48526741A>G	ENST00000312352.7	+	5	367	c.328A>G	c.(328-330)Atc>Gtc	p.I110V	PFKM_ENST00000340802.6_Missense_Mutation_p.I181V|PFKM_ENST00000547587.1_Missense_Mutation_p.I110V|PFKM_ENST00000395233.2_Missense_Mutation_p.I110V|PFKM_ENST00000359794.5_Missense_Mutation_p.I110V|PFKM_ENST00000551804.1_Missense_Mutation_p.I110V	NM_001166687.1	NP_001160159.1	P08237	PFKAM_HUMAN	phosphofructokinase, muscle	110	N-terminal catalytic PFK domain 1.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 6-phosphate metabolic process (GO:0006002)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|muscle cell cellular homeostasis (GO:0046716)|positive regulation of insulin secretion (GO:0032024)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	6-phosphofructokinase complex (GO:0005945)|apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|sperm principal piece (GO:0097228)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|fructose binding (GO:0070061)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			NS(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	35						GAAGCGTGGGATCACCAATCT	0.567																																					p.I181V		Atlas-SNP	.											.	PFKM	117	.	0			c.A541G						.						121	108	112					12																	48526741		2203	4300	6503	SO:0001583	missense	5213	exon7			CGTGGGATCACCA	M26066	CCDS8760.1, CCDS53786.1	12q13.11	2014-06-13					2.7.1.11		8877	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 122"	610681	"phosphofructokinase, polypeptide X"	PFKX			Standard	NM_001166686		Approved	PFK-1, PPP1R122	uc001rrb.2	P08237		ENST00000312352.7:c.328A>G	chr12.hg19:g.48526741A>G	ENSP00000309438:p.Ile110Val	255.0	0.0		143.0	6.0	NM_001166686	J3KNX3|Q16814|Q16815|Q6ZTT1	Missense_Mutation	SNP	ENST00000312352.7	hg19	CCDS8760.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.543348	0.86022	.	.	ENSG00000152556	ENST00000550345;ENST00000549003;ENST00000549941;ENST00000340802;ENST00000359794;ENST00000551339;ENST00000395233;ENST00000548345;ENST00000551804;ENST00000549022;ENST00000547587;ENST00000312352	D;D;D;D;D;D;D;D;D;D;D;D	0.84944	-1.92;-1.92;-1.92;-1.92;-1.92;-1.92;-1.92;-1.92;-1.92;-1.92;-1.92;-1.92	4.67	4.67	0.58626	Phosphofructokinase domain (2);	0.000000	0.85682	D	0.000000	D	0.91405	0.7288	M	0.76574	2.34	0.58432	D	0.999999	D;D;D	0.76494	0.999;0.998;0.997	D;D;D	0.87578	0.998;0.998;0.966	D	0.91963	0.5580	10	0.59425	D	0.04	-22.5436	14.0609	0.64800	1.0:0.0:0.0:0.0	.	110;110;181	P08237-2;P08237;Q6ZTT1	.;K6PF_HUMAN;.	V	110;110;143;181;110;110;110;110;110;110;110;110	ENSP00000450369:I110V;ENSP00000449835:I110V;ENSP00000446829:I143V;ENSP00000345771:I181V;ENSP00000352842:I110V;ENSP00000448253:I110V;ENSP00000378656:I110V;ENSP00000449269:I110V;ENSP00000448177:I110V;ENSP00000446805:I110V;ENSP00000449426:I110V;ENSP00000309438:I110V	ENSP00000309438:I110V	I	+	1	0	PFKM	46813008	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.282000	0.78630	2.322000	0.78497	0.528000	0.53228	ATC	.	.		0.567	PFKM-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406490.1	NM_000289		G	48526741	A	G	48526741	3	3	260	1	0	0	0	0	1	0	0	0	11774	333	12	2	563	2	PFKM	12	48526741	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	4680530	48526741	85325154	531	37776										
RHEBL1	121268	hgsc.bcm.edu	37	chr12	49459212	49459212	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttccttcaactgcctgtaccTctctggaagcaaatttggga	8	11	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:49459212T>C	ENST00000301068.6	-	7	622	c.383A>G	c.(382-384)gAg>gGg	p.E128G		NM_144593.1	NP_653194.1	Q8TAI7	REBL1_HUMAN	Ras homolog enriched in brain like 1	128					GTP catabolic process (GO:0006184)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|small GTPase mediated signal transduction (GO:0007264)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			breast(2)|large_intestine(2)|lung(5)	9						TGCCTGTACCTCTCTGGAAGC	0.483																																					p.E128G		Atlas-SNP	.											.	RHEBL1	12	.	0			c.A383G						.						105	95	98					12																	49459212		2203	4300	6503	SO:0001583	missense	121268	exon7			TGTACCTCTCTGG	AK098663	CCDS8778.1	12q13.12	2014-05-09				ENSG00000167550			21166	protein-coding gene	gene with protein product						12477932	Standard	NM_144593		Approved	MGC34869, FLJ25797	uc001rtc.1	Q8TAI7	OTTHUMG00000170407	ENST00000301068.6:c.383A>G	chr12.hg19:g.49459212T>C	ENSP00000301068:p.Glu128Gly	113.0	0.0		75.0	4.0	NM_144593	Q56VH8	Missense_Mutation	SNP	ENST00000301068.6	hg19	CCDS8778.1	.	.	.	.	.	.	.	.	.	.	T	17.42	3.385429	0.61956	.	.	ENSG00000167550	ENST00000301068	T	0.81078	-1.45	5.77	4.62	0.57501	Small GTP-binding protein domain (1);	0.055457	0.64402	D	0.000001	T	0.81654	0.4868	M	0.83312	2.635	0.44660	D	0.997645	P	0.46395	0.877	B	0.44224	0.444	T	0.82600	-0.0377	10	0.44086	T	0.13	.	9.826	0.40912	0.0:0.0808:0.0:0.9192	.	128	Q8TAI7	REBL1_HUMAN	G	128	ENSP00000301068:E128G	ENSP00000301068:E128G	E	-	2	0	RHEBL1	47745479	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.468000	0.35332	2.205000	0.71048	0.533000	0.62120	GAG	.	.		0.483	RHEBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408969.1	NM_144593		C	49459212	T	C	49459212	3	2	260	1	0	0	0	0	1	0	0	0	13344	1551	54	2	176	2	RHEBL1	12	49459212	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	932471	49459212	84392683	532	37777										
PRPF40B	25766	hgsc.bcm.edu	37	chr12	50029645	50029645	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggaacaggccaagcagctccGgcgccgcaatatccaggccc	12	16	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:50029645G>A	ENST00000380281.1	+	14	1293	c.1229G>A	c.(1228-1230)cGg>cAg	p.R410Q	FMNL3_ENST00000550668.1_5'Flank|PRPF40B_ENST00000548825.2_Missense_Mutation_p.R432Q|PRPF40B_ENST00000261897.1_Missense_Mutation_p.R404Q			Q6NWY9	PR40B_HUMAN	PRP40 pre-mRNA processing factor 40 homolog B (S. cerevisiae)	410	FF 3.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	34						AAGCAGCTCCGGCGCCGCAAT	0.597																																					p.R432Q		Atlas-SNP	.											PRPF40B,colon,carcinoma,0,2	PRPF40B	83	.	0			c.G1295A						.						72	62	65					12																	50029645		2203	4300	6503	SO:0001583	missense	25766	exon15			AGCTCCGGCGCCG	AF049525	CCDS31796.1, CCDS31796.2	12q13.12	2014-09-17	2006-04-04			ENSG00000110844			25031	protein-coding gene	gene with protein product	"Huntingtin interacting protein C"		"PRP40 pre-mRNA processing factor 40 homolog B (yeast)"			9700202	Standard	NM_001031698		Approved	HYPC	uc001rus.2	Q6NWY9		ENST00000380281.1:c.1229G>A	chr12.hg19:g.50029645G>A	ENSP00000369634:p.Arg410Gln	74.0	0.0		49.0	2.0	NM_001031698	O75401|Q6PI09|Q6ZWB3|Q8NCZ1|Q9H5G4|Q9NT95	Missense_Mutation	SNP	ENST00000380281.1	hg19		.	.	.	.	.	.	.	.	.	.	G	35	5.506481	0.96386	.	.	ENSG00000110844	ENST00000261897;ENST00000380281	T;T	0.32023	1.47;1.47	5.0	5.0	0.66597	FF domain (3);	0.000000	0.64402	D	0.000008	T	0.55114	0.1900	M	0.71581	2.175	0.58432	D	0.999998	D;D;D	0.89917	0.998;1.0;1.0	P;D;D	0.74348	0.881;0.977;0.983	T	0.52734	-0.8536	9	.	.	.	-21.7777	17.599	0.88021	0.0:0.0:1.0:0.0	.	410;404;410	Q6NWY9;Q6NWY9-2;Q6NWY9-3	PR40B_HUMAN;.;.	Q	404;410	ENSP00000261897:R404Q;ENSP00000369634:R410Q	.	R	+	2	0	PRPF40B	48315912	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.388000	0.97237	2.775000	0.95449	0.563000	0.77884	CGG	.	.		0.597	PRPF40B-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000404838.1	NM_012272		A	50029645	G	A	50029645	3	1	260	1	0	0	0	0	1	0	0	0	12584	1116	39	1	1283	1	PRPF40B	12	50029645	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	570433	50029645	83822250	533	37778										
FMNL3	91010	hgsc.bcm.edu	37	chr12	50040685	50040685	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccacctgtgatgatgtcctcGatggtaccatccttcccctc	7	16	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:50040685G>T	ENST00000293590.5	-	25	3212	c.2979C>A	c.(2977-2979)atC>atA	p.I993I	FMNL3_ENST00000550488.1_Silent_p.I992I|FMNL3_ENST00000335154.5_Silent_p.I993I|FMNL3_ENST00000352151.5_Silent_p.I942I			Q8IVF7	FMNL3_HUMAN	formin-like 3	993	DAD.				actin cytoskeleton organization (GO:0030036)|cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)	GTPase activating protein binding (GO:0032794)			breast(4)|endometrium(7)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(2)|stomach(1)	39						TGATGTCCTCGATGGTACCAT	0.592																																					p.I993I		Atlas-SNP	.											.	FMNL3	137	.	0			c.C2979A						.						87	89	89					12																	50040685		2042	4187	6229	SO:0001819	synonymous_variant	91010	exon25			GTCCTCGATGGTA	AK128195	CCDS41780.1, CCDS44874.1	12q13.12	2006-04-10							23698	protein-coding gene	gene with protein product						12684686	Standard	NM_198900		Approved	DKFZp762B245, MGC45819, WBP3	uc001ruv.1	Q8IVF7	OTTHUMG00000169651	ENST00000293590.5:c.2979C>A	chr12.hg19:g.50040685G>T		252.0	0.0		150.0	6.0	NM_175736	B0JZA7|Q6ZRJ1	Silent	SNP	ENST00000293590.5	hg19																																																																																				.	.		0.592	FMNL3-201	KNOWN	basic	protein_coding	protein_coding		NM_175736		T	50040685	G	T	50040685	2	4	260	1	0	0	0	0	0	0	0	1	5961	1048	37	1		1	FMNL3	12	50040685	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	11040	50040685	83811210	534	37779										
C12orf44	60673	hgsc.bcm.edu	37	chr12	52470974	52470974	+	Nonstop_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aaagacacccttgccctctgAgcgtcgctggatctctggga	11	13	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:52470974A>G	ENST00000336854.4	+	4	1135	c.657A>G	c.(655-657)tgA>tgG	p.*219W	OR7E47P_ENST00000546390.1_RNA|RP11-1100L3.7_ENST00000550301.1_RNA	NM_001098673.1|NM_021934.4	NP_001092143.1|NP_068753.2	Q9BSB4	ATGA1_HUMAN		0					autophagic vacuole assembly (GO:0000045)	pre-autophagosomal structure (GO:0000407)	identical protein binding (GO:0042802)|protein complex binding (GO:0032403)			endometrium(1)|lung(2)|ovary(1)	4				BRCA - Breast invasive adenocarcinoma(357;0.0978)		TTGCCCTCTGAGCGTCGCTGG	0.567																																					p.X219W		Atlas-SNP	.											.	C12orf44	14	.	0			c.A657G						.						57	57	57					12																	52470974		2203	4300	6503	SO:0001578	stop_lost	60673	exon4			CCTCTGAGCGTCG																												ENST00000336854.4:c.657A>G	chr12.hg19:g.52470974A>G	ENSP00000338990:p.*219Trpext*58	111.0	0.0		71.0	4.0	NM_001098673	Q9HAE2|Q9HBN1	Missense_Mutation	SNP	ENST00000336854.4	hg19	CCDS8820.1	.	.	.	.	.	.	.	.	.	.	A	8.489	0.861581	0.17178	.	.	ENSG00000123395	ENST00000336854;ENST00000550984	.	.	.	4.67	2.62	0.31277	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.2621	0.26209	0.3106:0.0:0.6894:0.0	.	.	.	.	W	219	.	.	X	+	3	0	C12orf44	50757241	1.000000	0.71417	0.907000	0.35723	0.280000	0.26924	5.925000	0.70062	1.139000	0.42245	-0.408000	0.06270	TGA	.	.		0.567	C12orf44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405063.1			G	52470974	A	G	52470974	4	3	260	1	0	0	0	0	0	0	0	0	1692	317	11	2	663	2	C12orf44	12	52470974	Nonstop_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	2430289	52470974	81380921	535	37780										
KRT85	3891	hgsc.bcm.edu	37	chr12	52758122	52758122	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gacaaactcattctctgctgTggctctcagggccacctcct	8	15	3	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:52758122T>C	ENST00000257901.3	-	3	733	c.658A>G	c.(658-660)Aca>Gca	p.T220A	KRT85_ENST00000544265.1_Intron	NM_002283.3	NP_002274.1	P78386	KRT85_HUMAN	keratin 85	220	Coil 1B.|Rod.				epidermis development (GO:0008544)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(6)|kidney(1)|large_intestine(7)|liver(1)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	36	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		TTCTCTGCTGTGGCTCTCAGG	0.572																																					p.T220A		Atlas-SNP	.											.	KRT85	78	.	0			c.A658G						.						95	93	94					12																	52758122		2203	4300	6503	SO:0001583	missense	3891	exon3			CTGCTGTGGCTCT	X99140	CCDS8824.1, CCDS73472.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000135443	ENSG00000135443		"-", "Intermediate filaments type II, keratins (basic)"	6462	protein-coding gene	gene with protein product	"hard keratin type II"	602767	"keratin, hair, basic, 5"	KRTHB5		9084137, 16831889	Standard	NM_002283		Approved	Hb-5	uc001sag.3	P78386	OTTHUMG00000169633	ENST00000257901.3:c.658A>G	chr12.hg19:g.52758122T>C	ENSP00000257901:p.Thr220Ala	193.0	0.0		98.0	4.0	NM_002283	Q9NSB1	Missense_Mutation	SNP	ENST00000257901.3	hg19	CCDS8824.1	.	.	.	.	.	.	.	.	.	.	T	12.78	2.040097	0.35989	.	.	ENSG00000135443	ENST00000257901	D	0.88354	-2.37	4.62	3.44	0.39384	Filament (1);	0.000000	0.64402	D	0.000015	T	0.79257	0.4415	L	0.38175	1.15	0.09310	N	1	B	0.28636	0.218	B	0.35278	0.199	T	0.64266	-0.6448	10	0.05436	T	0.98	.	4.2336	0.10615	0.1614:0.155:0.0:0.6836	.	220	P78386	KRT85_HUMAN	A	220	ENSP00000257901:T220A	ENSP00000257901:T220A	T	-	1	0	KRT85	51044389	0.000000	0.05858	0.991000	0.47740	0.982000	0.71751	0.253000	0.18296	1.953000	0.56701	0.459000	0.35465	ACA	.	.		0.572	KRT85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405184.1	NM_002283		C	52758122	T	C	52758122	3	2	260	1	0	0	0	0	1	0	0	0	8508	1696	59	2	893	2	KRT85	12	52758122	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	287148	52758122	81093773	536	37781										
TENC1	23371	hgsc.bcm.edu	37	chr12	53455989	53455989	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctcatcgagactgggcccaaAggggtgaagatcaagggctg	15	9	2	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:53455989A>G	ENST00000314250.6	+	23	3917	c.3627A>G	c.(3625-3627)aaA>aaG	p.K1209K	TENC1_ENST00000549700.1_Silent_p.K1144K|TENC1_ENST00000314276.3_Silent_p.K1219K|TENC1_ENST00000552570.1_Silent_p.K1209K|TENC1_ENST00000379902.3_Silent_p.K1085K|TENC1_ENST00000451358.1_Silent_p.K1199K|TENC1_ENST00000546602.1_Silent_p.K1112K	NM_170754.2	NP_736610.2	Q63HR2	TENC1_HUMAN	tensin like C1 domain containing phosphatase (tensin 2)	1209	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cellular homeostasis (GO:0019725)|collagen metabolic process (GO:0032963)|intracellular signal transduction (GO:0035556)|kidney development (GO:0001822)|multicellular organism growth (GO:0035264)|multicellular organismal homeostasis (GO:0048871)|negative regulation of cell proliferation (GO:0008285)|response to muscle activity (GO:0014850)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(19)|ovary(1)|pancreas(1)|stomach(3)	34						CTGGGCCCAAAGGGGTGAAGA	0.592																																					p.K1219K		Atlas-SNP	.											.	TENC1	148	.	0			c.A3657G						.						52	56	55					12																	53455989		2203	4300	6503	SO:0001819	synonymous_variant	23371	exon23			GCCCAAAGGGGTG	AF518729	CCDS8842.1, CCDS8843.1, CCDS8844.1	12q13.13	2013-02-14	2004-03-05			ENSG00000111077		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	19737	protein-coding gene	gene with protein product	"tensin 2"	607717	"tensin like C1 domain-containing phosphatase"				Standard	NM_015319		Approved	KIAA1075, C1-TEN, TNS2	uc001sbp.3	Q63HR2	OTTHUMG00000169730	ENST00000314250.6:c.3627A>G	chr12.hg19:g.53455989A>G		103.0	0.0		66.0	5.0	NM_015319	A2VDF2|A2VDF3|A2VDI8|A5PKY4|Q2NL80|Q76MW6|Q7Z5T9|Q8NFF9|Q8NFG0|Q96P25|Q9NT29|Q9UPS7	Silent	SNP	ENST00000314250.6	hg19	CCDS8843.1																																																																																			.	.		0.592	TENC1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405779.1	NM_170754		G	53455989	A	G	53455989	2	3	260	1	0	0	0	0	0	0	0	1	15773	69	3	2		2	TENC1	12	53455989	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	697867	53455989	80395906	537	37782										
ZNF740	283337	hgsc.bcm.edu	37	chr12	53579803	53579803	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aaaaattttgtttgtgaacaCtgctttggagcctttcggag	10	6	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:53579803C>T	ENST00000416904.3	+	5	760	c.315C>T	c.(313-315)caC>caT	p.H105H		NM_001004304.3	NP_001004304.1	Q8NDX6	ZN740_HUMAN	zinc finger protein 740	105					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)	3						TTTGTGAACACTGCTTTGGAG	0.423																																					p.H105H		Atlas-SNP	.											.	ZNF740	15	.	0			c.C315T						.						79	74	76					12																	53579803		1853	4100	5953	SO:0001819	synonymous_variant	283337	exon5			TGAACACTGCTTT	BC053557	CCDS44896.1	12q13.13	2013-01-08				ENSG00000139651		"Zinc fingers, C2H2-type"	27465	protein-coding gene	gene with protein product							Standard	NM_001004304		Approved	Zfp740	uc001scb.4	Q8NDX6		ENST00000416904.3:c.315C>T	chr12.hg19:g.53579803C>T		173.0	0.0		109.0	5.0	NM_001004304	A8K9M9	Silent	SNP	ENST00000416904.3	hg19	CCDS44896.1																																																																																			.	.		0.423	ZNF740-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406890.2	NM_001004304		T	53579803	C	T	53579803	2	4	260	1	0	0	0	0	0	0	0	1	18143	564	20	3		3	ZNF740	12	53579803	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	123814	53579803	80272092	538	37783										
HOXC12	3228	hgsc.bcm.edu	37	chr12	54350171	54350171	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agcgcaagccctattcgaagTtgcaactggcagagctggag	13	10	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:54350171T>C	ENST00000243103.3	+	2	766	c.670T>C	c.(670-672)Ttg>Ctg	p.L224L	AC012531.23_ENST00000603432.1_lincRNA	NM_173860.1	NP_776272.1	P31275	HXC12_HUMAN	homeobox C12	224					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)	12						CTATTCGAAGTTGCAACTGGC	0.577																																					p.L224L		Atlas-SNP	.											.	HOXC12	19	.	0			c.T670C						.						98	102	101					12																	54350171		2203	4300	6503	SO:0001819	synonymous_variant	3228	exon2			TCGAAGTTGCAAC	AF328962	CCDS8866.1	12q13.13	2011-06-20	2005-12-22		ENSG00000123407	ENSG00000123407		"Homeoboxes / ANTP class : HOXL subclass"	5124	protein-coding gene	gene with protein product		142975	"homeo box C12"	HOX3, HOX3F, HOC3F		1973146, 1358459	Standard	NM_173860		Approved		uc010soq.2	P31275	OTTHUMG00000160010	ENST00000243103.3:c.670T>C	chr12.hg19:g.54350171T>C		124.0	0.0		98.0	4.0	NM_173860	Q9BXJ6	Silent	SNP	ENST00000243103.3	hg19	CCDS8866.1																																																																																			.	.		0.577	HOXC12-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358868.2	NM_173860		C	54350171	T	C	54350171	2	2	260	1	0	0	0	0	0	0	0	1	7320	1722	60	2		2	HOXC12	12	54350171	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	770368	54350171	79501724	539	37784										
GPR84	53831	hgsc.bcm.edu	37	chr12	54757018	54757018	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tccagtgcctgtgctgctcgTttgacctggcggtggatgag	15	10	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:54757018T>C	ENST00000551809.1	-	1	1253	c.618A>G	c.(616-618)aaA>aaG	p.K206K	GPR84_ENST00000267015.3_Silent_p.K206K|RP11-753H16.3_ENST00000550474.1_RNA|RP11-753H16.5_ENST00000552785.1_RNA			Q9NQS5	GPR84_HUMAN	G protein-coupled receptor 84	206						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(2)|kidney(2)|large_intestine(6)|lung(5)|skin(1)|urinary_tract(1)	18						GTGCTGCTCGTTTGACCTGGC	0.567																																					p.K206K		Atlas-SNP	.											.	GPR84	38	.	0			c.A618G						.						170	146	154					12																	54757018		2203	4300	6503	SO:0001819	synonymous_variant	53831	exon2			TGCTCGTTTGACC	AF237762	CCDS8878.1	12q13.13	2012-08-20						"GPCR / Class A : Fatty acid receptors"	4535	protein-coding gene	gene with protein product		606383				11273702	Standard	NM_020370		Approved	EX33	uc001sfu.3	Q9NQS5		ENST00000551809.1:c.618A>G	chr12.hg19:g.54757018T>C		76.0	0.0		51.0	5.0	NM_020370	B6V9G7	Silent	SNP	ENST00000551809.1	hg19	CCDS8878.1																																																																																			.	.		0.567	GPR84-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406156.1			C	54757018	T	C	54757018	2	2	260	1	0	0	0	0	0	0	0	1	6722	1722	60	2		2	GPR84	12	54757018	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	406847	54757018	79094877	540	37785										
ITGA5	3678	hgsc.bcm.edu	37	chr12	54797978	54797978	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gctccgctcctctgggttgaAcatggcggggaagatggtga	16	9	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:54797978A>T	ENST00000293379.4	-	15	1777	c.1516T>A	c.(1516-1518)Ttc>Atc	p.F506I	RP11-753H16.3_ENST00000550474.1_RNA|RP11-753H16.5_ENST00000552785.1_RNA	NM_002205.2	NP_002196.2	P08648	ITA5_HUMAN	integrin, alpha 5 (fibronectin receptor, alpha polypeptide)	506					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|memory (GO:0007613)|negative regulation of anoikis (GO:2000811)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|viral process (GO:0016032)|wound healing, spreading of epidermal cells (GO:0035313)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	metal ion binding (GO:0046872)|platelet-derived growth factor receptor binding (GO:0005161)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	34						TCTGGGTTGAACATGGCGGGG	0.602											OREG0021554	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F506I		Atlas-SNP	.											.	ITGA5	99	.	0			c.T1516A						.						71	78	76					12																	54797978		2203	4300	6503	SO:0001583	missense	3678	exon15			GGTTGAACATGGC		CCDS8880.1	12q11-q13	2010-03-23				ENSG00000161638		"CD molecules", "Integrins"	6141	protein-coding gene	gene with protein product		135620		FNRA		2454952	Standard	NM_002205		Approved	CD49e	uc001sga.3	P08648	OTTHUMG00000169841	ENST00000293379.4:c.1516T>A	chr12.hg19:g.54797978A>T	ENSP00000293379:p.Phe506Ile	102.0	0.0	1003	98.0	4.0	NM_002205	Q96HA5	Missense_Mutation	SNP	ENST00000293379.4	hg19	CCDS8880.1	.	.	.	.	.	.	.	.	.	.	A	11.95	1.792335	0.31685	.	.	ENSG00000161638	ENST00000293379	T	0.27890	1.64	3.67	3.67	0.42095	Integrin alpha-2 (1);	0.251469	0.38663	N	0.001610	T	0.15046	0.0363	N	0.05487	-0.04	0.34386	D	0.693696	P	0.38827	0.649	B	0.37692	0.256	T	0.22452	-1.0216	10	0.21540	T	0.41	.	10.9973	0.47585	1.0:0.0:0.0:0.0	.	506	P08648	ITA5_HUMAN	I	506	ENSP00000293379:F506I	ENSP00000293379:F506I	F	-	1	0	ITGA5	53084245	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	3.993000	0.56987	1.926000	0.55796	0.374000	0.22700	TTC	.	.		0.602	ITGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406174.1			T	54797978	A	T	54797978	3	4	260	1	0	0	0	0	1	0	0	0	7888	43	2	4	1697	4	ITGA5	12	54797978	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	40960	54797978	79053917	541	37786										
DCD	117159	hgsc.bcm.edu	37	chr12	55042049	55042049	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	caggcacagaccagggctccTgccagagctgtcaggaagag	14	12	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:55042049T>C	ENST00000293371.6	-	1	228	c.39A>G	c.(37-39)gcA>gcG	p.A13A	DCD_ENST00000456047.2_Silent_p.A13A	NM_053283.2	NP_444513.1	P81605	DCD_HUMAN	dermcidin	13					defense response to bacterium (GO:0042742)|defense response to fungus (GO:0050832)|killing of cells of other organism (GO:0031640)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	peptidase activity (GO:0008233)|poly(A) RNA binding (GO:0044822)			large_intestine(2)|lung(2)|ovary(1)|skin(1)	6		Myeloproliferative disorder(1001;0.0255)				CCAGGGCTCCTGCCAGAGCTG	0.562																																					p.A13A		Atlas-SNP	.											.	DCD	20	.	0			c.A39G						.						108	91	97					12																	55042049		2203	4300	6503	SO:0001819	synonymous_variant	117159	exon1			GGCTCCTGCCAGA	AF144011	CCDS8884.1, CCDS73478.1	12q13.1	2008-08-04				ENSG00000161634			14669	protein-coding gene	gene with protein product	"proteolysis inducing factor", "preproteolysin", "diffusible survival/evasion peptide", "survival promoting peptide"	606634				11694882	Standard	XM_005268627		Approved	AIDD, PIF, DSEP, HCAP, DCD-1	uc001sgj.3	P81605	OTTHUMG00000169937	ENST00000293371.6:c.39A>G	chr12.hg19:g.55042049T>C		109.0	0.0		72.0	4.0	NM_053283	A5JHP2|A5JHP3|P58461|Q53YJ2	Silent	SNP	ENST00000293371.6	hg19	CCDS8884.1																																																																																			.	.		0.562	DCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406617.1	NM_053283		C	55042049	T	C	55042049	2	2	260	1	0	0	0	0	0	0	0	1	4285	1567	55	2		2	DCD	12	55042049	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	244071	55042049	78809846	542	37787										
NEUROD4	58158	hgsc.bcm.edu	37	chr12	55420695	55420695	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggaaaggctttgtggagatgCtgtgtaaagggctctctcag	15	6	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:55420695C>T	ENST00000242994.3	+	2	850	c.472C>T	c.(472-474)Ctg>Ttg	p.L158L		NM_021191.2	NP_067014.2	Q9HD90	NDF4_HUMAN	neuronal differentiation 4	158					amacrine cell differentiation (GO:0035881)|cell fate commitment (GO:0045165)|glial cell differentiation (GO:0010001)|neuroblast proliferation (GO:0007405)|neuron development (GO:0048666)|neuron migration (GO:0001764)|Notch signaling pathway (GO:0007219)|positive regulation of cell differentiation (GO:0045597)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|ovary(3)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	41						TGTGGAGATGCTGTGTAAAGG	0.522																																					p.L158L		Atlas-SNP	.											NEUROD4,caecum,carcinoma,0,1	NEUROD4	87	.	0			c.C472T						.						56	58	57					12																	55420695		2203	4300	6503	SO:0001819	synonymous_variant	58158	exon2			GAGATGCTGTGTA	AF203901	CCDS8886.1	12q13.13	2013-05-21	2012-02-22			ENSG00000123307		"Basic helix-loop-helix proteins"	13802	protein-coding gene	gene with protein product		611635	"neurogenic differentiation 4"				Standard	NM_021191		Approved	Atoh3, ATH-3, MATH-3, bHLHa4	uc001sgp.4	Q9HD90		ENST00000242994.3:c.472C>T	chr12.hg19:g.55420695C>T		62.0	0.0		48.0	2.0	NM_021191	B2RAC9	Silent	SNP	ENST00000242994.3	hg19	CCDS8886.1																																																																																			.	.		0.522	NEUROD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406104.1			T	55420695	C	T	55420695	2	4	260	1	0	0	0	0	0	0	0	1	10359	796	28	3		3	NEUROD4	12	55420695	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	378646	55420695	78431200	543	37788										
SILV	6490	hgsc.bcm.edu	37	chr12	56351868	56351868	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctagaacttgccagtattggCctgaagtttttggaatgaaa	10	6	0	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:56351868C>T	ENST00000548747.1	-	5	1132	c.470G>A	c.(469-471)gGc>gAc	p.G157D	PMEL_ENST00000449260.2_Splice_Site_p.G157D|PMEL_ENST00000536427.1_Splice_Site_p.G157D|PMEL_ENST00000539511.1_Splice_Site_p.G71D|PMEL_ENST00000548493.1_Splice_Site_p.G157D|PMEL_ENST00000552882.1_Splice_Site_p.G157D|PMEL_ENST00000548689.1_5'UTR|PMEL_ENST00000550447.1_Intron|PMEL_ENST00000550464.1_Splice_Site_p.G71D|PMEL_ENST00000360714.4_Splice_Site_p.G157D			P40967	PMEL_HUMAN	premelanosome protein	157					melanin biosynthetic process (GO:0042438)|melanosome organization (GO:0032438)	endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)|multivesicular body membrane (GO:0032585)|plasma membrane (GO:0005886)				NS(1)|breast(2)|endometrium(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						CCAGTATTGGCCTGAAGTTTT	0.532																																					p.G157D		Atlas-SNP	.											.	PMEL	60	.	0			c.G470A						.						48	47	48					12																	56351868		2203	4300	6503	SO:0001630	splice_region_variant	6490	exon5			TATTGGCCTGAAG	AK092881	CCDS8897.1, CCDS55833.1, CCDS55834.1	12q13-q14	2010-12-17	2010-12-17	2010-12-17	ENSG00000185664	ENSG00000185664			10880	protein-coding gene	gene with protein product		155550	"silver (mouse homolog) like", "silver homolog (mouse)"	SIL, SILV		8739560	Standard	NM_001200053		Approved	D12S53E, SI, Pmel17, gp100	uc001siq.3	P40967		ENST00000548747.1:c.470-1G>A	chr12.hg19:g.56351868C>T		62.0	0.0		34.0	4.0	NM_001200054	B3KS57|B7Z6D7|Q12763|Q14448|Q14817|Q16565	Missense_Mutation	SNP	ENST00000548747.1	hg19	CCDS8897.1	.	.	.	.	.	.	.	.	.	.	C	17.25	3.341944	0.61073	.	.	ENSG00000185664	ENST00000449260;ENST00000552882;ENST00000550464;ENST00000548747;ENST00000548493;ENST00000360714;ENST00000536427;ENST00000539511;ENST00000546543	T;T;T;T;T;T;T;T;T	0.30448	1.68;1.71;1.92;1.71;1.71;1.69;1.53;1.92;2.12	4.68	3.8	0.43715	.	0.121832	0.38111	N	0.001806	T	0.34337	0.0894	L	0.56769	1.78	0.80722	D	1	P;P;B	0.46912	0.886;0.608;0.414	P;B;B	0.44422	0.449;0.244;0.064	T	0.30707	-0.9969	10	0.66056	D	0.02	.	12.822	0.57698	0.0:0.918:0.0:0.082	.	71;157;157	P40967-3;P40967-2;P40967	.;.;PMEL_HUMAN	D	157;157;71;157;157;157;157;71;108	ENSP00000402758:G157D;ENSP00000449690:G157D;ENSP00000450036:G71D;ENSP00000448828:G157D;ENSP00000447374:G157D;ENSP00000353940:G157D;ENSP00000438695:G157D;ENSP00000445005:G71D;ENSP00000446662:G108D	ENSP00000353940:G157D	G	-	2	0	PMEL	54638135	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.164000	0.58190	1.581000	0.49865	0.655000	0.94253	GGC	.	.		0.532	PMEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409626.1	NM_006928	Missense_Mutation	T	56351868	C	T	56351868	5	4	260	1	0	0	0	0	0	0	1	0	14337	753	26	3	1543	3	SILV	12	56351868	Splice_Site	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	931173	56351868	77500027	544	37789										
PAN2	9924	hgsc.bcm.edu	37	chr12	56722129	56722129	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	taggagactgtgcatatcctCattctcatccagcctggtgg	10	11	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:56722129C>A	ENST00000425394.2	-	4	842	c.466G>T	c.(466-468)Gag>Tag	p.E156*	PAN2_ENST00000548043.1_Nonsense_Mutation_p.E156*|PAN2_ENST00000257931.5_Nonsense_Mutation_p.E156*|PAN2_ENST00000440411.3_Nonsense_Mutation_p.E156*	NM_001127460.2	NP_001120932	Q9HBH5	RDH14_HUMAN	PAN2 poly(A) specific ribonuclease subunit	0					osteoblast differentiation (GO:0001649)	endoplasmic reticulum (GO:0005783)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	41					Vitamin A(DB00162)	TGCATATCCTCATTCTCATCC	0.527																																					p.E156X		Atlas-SNP	.											.	PAN2	107	.	0			c.G466T						.						132	125	127					12																	56722129		2203	4300	6503	SO:0001587	stop_gained	9924	exon4			TATCCTCATTCTC	AB014610	CCDS8915.1, CCDS44922.1, CCDS53802.1	12q13.2	2014-03-27	2014-03-27	2008-01-08		ENSG00000135473		"Ubiquitin-specific peptidases"	20074	protein-coding gene	gene with protein product	"PAN2 homolog, PABP1 dependent poly A specific ribonuclease subunit (S. cerevisiae)"		"ubiquitin specific protease 52", "ubiquitin specific peptidase 52", "PAN2 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)"	USP52		12838346, 14583602	Standard	NM_014871		Approved	KIAA0710, hPAN2	uc001skx.3	Q504Q3	OTTHUMG00000170412	ENST00000425394.2:c.466G>T	chr12.hg19:g.56722129C>A	ENSP00000401721:p.Glu156*	157.0	0.0		83.0	4.0	NM_014871		Nonsense_Mutation	SNP	ENST00000425394.2	hg19	CCDS44922.1	.	.	.	.	.	.	.	.	.	.	C	37	6.581295	0.97680	.	.	ENSG00000135473	ENST00000425394;ENST00000440411;ENST00000257931;ENST00000548043;ENST00000547572	.	.	.	4.7	4.7	0.59300	.	0.193497	0.46758	D	0.000277	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	-20.7282	10.5273	0.44957	0.0:0.9096:0.0:0.0904	.	.	.	.	X	156;156;156;156;17	.	ENSP00000257931:E156X	E	-	1	0	PAN2	55008396	1.000000	0.71417	0.998000	0.56505	0.904000	0.53231	4.656000	0.61483	2.601000	0.87937	0.655000	0.94253	GAG	.	.		0.527	PAN2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409024.1	NM_014871		A	56722129	C	A	56722129	4	1	260	1	0	0	0	0	0	1	0	0	11423	835	29	3	3234	3	PAN2	12	56722129	Nonsense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	370261	56722129	77129766	545	37790										
BAZ2A	11176	hgsc.bcm.edu	37	chr12	56998513	56998513	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	catatgccataaggaagcagCgcaggatctctgacacattg	10	10	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:56998513C>T	ENST00000551812.1	-	15	3018	c.2825G>A	c.(2824-2826)cGc>cAc	p.R942H	BAZ2A_ENST00000379441.3_Missense_Mutation_p.R912H|BAZ2A_ENST00000549884.1_Missense_Mutation_p.R940H|BAZ2A_ENST00000179765.5_Missense_Mutation_p.R910H	NM_013449.3	NP_038477.2	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	942					chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA methylation (GO:0006306)|heterochromatin assembly involved in chromatin silencing (GO:0070869)|histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|histone H4 deacetylation (GO:0070933)|histone H4-K20 methylation (GO:0034770)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|nucleolus (GO:0005730)|rDNA heterochromatin (GO:0033553)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|lysine-acetylated histone binding (GO:0070577)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(15)|urinary_tract(1)	31						AAGGAAGCAGCGCAGGATCTC	0.572																																					p.R942H		Atlas-SNP	.											.	BAZ2A	263	.	0			c.G2825A						.						77	73	75					12																	56998513		2046	4203	6249	SO:0001583	missense	11176	exon15			AAGCAGCGCAGGA	AB032254	CCDS44924.1, CCDS73483.1	12q13.3	2013-01-28				ENSG00000076108		"Zinc fingers, PHD-type"	962	protein-coding gene	gene with protein product	"TTF-I interacting peptide 5"	605682				10662543, 11532953	Standard	XM_005268596		Approved	KIAA0314, TIP5, WALp3	uc001slq.1	Q9UIF9	OTTHUMG00000170332	ENST00000551812.1:c.2825G>A	chr12.hg19:g.56998513C>T	ENSP00000446880:p.Arg942His	142.0	0.0		85.0	4.0	NM_013449	B3KN66|O00536|O15030|Q68DI8|Q96H26	Missense_Mutation	SNP	ENST00000551812.1	hg19	CCDS44924.1	.	.	.	.	.	.	.	.	.	.	C	35	5.507844	0.96386	.	.	ENSG00000076108	ENST00000379441;ENST00000179765;ENST00000551812;ENST00000549884	T;T;T;T	0.78924	-1.16;-1.16;-1.22;-1.22	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	D	0.88555	0.6468	M	0.78049	2.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	D	0.89494	0.3759	10	0.87932	D	0	.	18.3119	0.90203	0.0:1.0:0.0:0.0	.	940;942	F8VU39;Q9UIF9	.;BAZ2A_HUMAN	H	912;910;942;940	ENSP00000368754:R912H;ENSP00000179765:R910H;ENSP00000446880:R942H;ENSP00000447941:R940H	ENSP00000179765:R910H	R	-	2	0	BAZ2A	55284780	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	2.721000	0.47260	2.687000	0.91594	0.655000	0.94253	CGC	.	.		0.572	BAZ2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408561.1	NM_013449		T	56998513	C	T	56998513	3	4	260	1	0	0	0	0	1	0	0	0	1331	768	27	1	2952	1	BAZ2A	12	56998513	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	276384	56998513	76853382	546	37791										
BAZ2A	11176	hgsc.bcm.edu	37	chr12	56999021	56999021	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aaagcccagcaccttgccaaAgctatgcaggaactccacaa	7	14	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:56999021A>G	ENST00000551812.1	-	14	2783	c.2590T>C	c.(2590-2592)Ttt>Ctt	p.F864L	BAZ2A_ENST00000379441.3_Missense_Mutation_p.F834L|BAZ2A_ENST00000549884.1_Missense_Mutation_p.F862L|BAZ2A_ENST00000179765.5_Missense_Mutation_p.F832L	NM_013449.3	NP_038477.2	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	864	DDT. {ECO:0000255|PROSITE- ProRule:PRU00063}.				chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA methylation (GO:0006306)|heterochromatin assembly involved in chromatin silencing (GO:0070869)|histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|histone H4 deacetylation (GO:0070933)|histone H4-K20 methylation (GO:0034770)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|nucleolus (GO:0005730)|rDNA heterochromatin (GO:0033553)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|lysine-acetylated histone binding (GO:0070577)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(15)|urinary_tract(1)	31						ACCTTGCCAAAGCTATGCAGG	0.572																																					p.F864L		Atlas-SNP	.											.	BAZ2A	263	.	0			c.T2590C						.						57	54	55					12																	56999021		1972	4158	6130	SO:0001583	missense	11176	exon14			TGCCAAAGCTATG	AB032254	CCDS44924.1, CCDS73483.1	12q13.3	2013-01-28				ENSG00000076108		"Zinc fingers, PHD-type"	962	protein-coding gene	gene with protein product	"TTF-I interacting peptide 5"	605682				10662543, 11532953	Standard	XM_005268596		Approved	KIAA0314, TIP5, WALp3	uc001slq.1	Q9UIF9	OTTHUMG00000170332	ENST00000551812.1:c.2590T>C	chr12.hg19:g.56999021A>G	ENSP00000446880:p.Phe864Leu	183.0	0.0		97.0	4.0	NM_013449	B3KN66|O00536|O15030|Q68DI8|Q96H26	Missense_Mutation	SNP	ENST00000551812.1	hg19	CCDS44924.1	.	.	.	.	.	.	.	.	.	.	A	35	5.455615	0.96223	.	.	ENSG00000076108	ENST00000379441;ENST00000179765;ENST00000551812;ENST00000549884	D;D;D;D	0.83837	-1.72;-1.72;-1.77;-1.77	5.03	5.03	0.67393	DDT domain superfamily (1);DDT domain, subgroup (1);DDT domain (1);	0.063541	0.64402	D	0.000004	D	0.86916	0.6048	M	0.72118	2.19	0.50313	D	0.999865	P;P	0.52463	0.942;0.953	P;P	0.52454	0.573;0.699	D	0.88730	0.3236	10	0.87932	D	0	.	14.0748	0.64882	1.0:0.0:0.0:0.0	.	862;864	F8VU39;Q9UIF9	.;BAZ2A_HUMAN	L	834;832;864;862	ENSP00000368754:F834L;ENSP00000179765:F832L;ENSP00000446880:F864L;ENSP00000447941:F862L	ENSP00000179765:F832L	F	-	1	0	BAZ2A	55285288	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.215000	0.95146	2.040000	0.60383	0.533000	0.62120	TTT	.	.		0.572	BAZ2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408561.1	NM_013449		G	56999021	A	G	56999021	3	3	260	1	0	0	0	0	1	0	0	0	1331	72	3	2	3191	2	BAZ2A	12	56999021	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	508	56999021	76852874	547	37792										
BAZ2A	11176	hgsc.bcm.edu	37	chr12	57005366	57005366	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agagcatttacccatgttggAggggaagacgaacttcttct	11	8	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:57005366A>G	ENST00000551812.1	-	7	1860	c.1667T>C	c.(1666-1668)cTc>cCc	p.L556P	BAZ2A_ENST00000379441.3_Missense_Mutation_p.L526P|BAZ2A_ENST00000549884.1_Missense_Mutation_p.L554P|BAZ2A_ENST00000179765.5_Missense_Mutation_p.L524P	NM_013449.3	NP_038477.2	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	556	MBD. {ECO:0000255|PROSITE- ProRule:PRU00338}.				chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA methylation (GO:0006306)|heterochromatin assembly involved in chromatin silencing (GO:0070869)|histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|histone H4 deacetylation (GO:0070933)|histone H4-K20 methylation (GO:0034770)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|nucleolus (GO:0005730)|rDNA heterochromatin (GO:0033553)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|lysine-acetylated histone binding (GO:0070577)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(15)|urinary_tract(1)	31						CCCATGTTGGAGGGGAAGACG	0.423																																					p.L556P		Atlas-SNP	.											.	BAZ2A	263	.	0			c.T1667C						.						89	83	85					12																	57005366		1896	4131	6027	SO:0001583	missense	11176	exon7			TGTTGGAGGGGAA	AB032254	CCDS44924.1, CCDS73483.1	12q13.3	2013-01-28				ENSG00000076108		"Zinc fingers, PHD-type"	962	protein-coding gene	gene with protein product	"TTF-I interacting peptide 5"	605682				10662543, 11532953	Standard	XM_005268596		Approved	KIAA0314, TIP5, WALp3	uc001slq.1	Q9UIF9	OTTHUMG00000170332	ENST00000551812.1:c.1667T>C	chr12.hg19:g.57005366A>G	ENSP00000446880:p.Leu556Pro	209.0	0.0		117.0	5.0	NM_013449	B3KN66|O00536|O15030|Q68DI8|Q96H26	Missense_Mutation	SNP	ENST00000551812.1	hg19	CCDS44924.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.2|20.2	3.949878|3.949878	0.73787|0.73787	.|.	.|.	ENSG00000076108|ENSG00000076108	ENST00000379441;ENST00000179765;ENST00000551812;ENST00000549884|ENST00000551996	D;D;D;D|.	0.99845|.	-7.12;-7.12;-7.12;-7.12|.	4.84|4.84	4.84|4.84	0.62591|0.62591	Methyl-CpG DNA binding (4);DNA-binding, integrase-type (1);|.	0.076866|.	0.51477|.	D|.	0.000097|.	T|T	0.69904|0.69904	0.3163|0.3163	L|L	0.61218|0.61218	1.895|1.895	0.80722|0.80722	D|D	1|1	D;D|.	0.76494|.	0.997;0.999|.	D;D|.	0.91635|.	0.994;0.999|.	T|T	0.69480|0.69480	-0.5134|-0.5134	10|5	0.87932|.	D|.	0|.	.|.	13.8311|13.8311	0.63382|0.63382	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	554;556|.	F8VU39;Q9UIF9|.	.;BAZ2A_HUMAN|.	P|P	526;524;556;554|204	ENSP00000368754:L526P;ENSP00000179765:L524P;ENSP00000446880:L556P;ENSP00000447941:L554P|.	ENSP00000179765:L524P|.	L|S	-|-	2|1	0|0	BAZ2A|BAZ2A	55291633|55291633	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	6.738000|6.738000	0.74822|0.74822	2.170000|2.170000	0.68504|0.68504	0.379000|0.379000	0.24179|0.24179	CTC|TCC	.	.		0.423	BAZ2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408561.1	NM_013449		G	57005366	A	G	57005366	3	3	260	1	0	0	0	0	1	0	0	0	1331	304	11	2	4142	2	BAZ2A	12	57005366	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	6345	57005366	76846529	548	37793										
GPR182	11318	hgsc.bcm.edu	37	chr12	57389925	57389925	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cattgactgcttctccatgcTgcactgtgtcatcaacccca	6	15	3	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:57389925T>C	ENST00000300098.1	+	2	1151	c.932T>C	c.(931-933)cTg>cCg	p.L311P	RP11-474N8.5_ENST00000556850.1_RNA|HBCBP_ENST00000600202.1_5'Flank	NM_007264.3	NP_009195.1	O15218	GP182_HUMAN	G protein-coupled receptor 182	311					cell surface receptor signaling pathway (GO:0007166)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	15						TTCTCCATGCTGCACTGTGTC	0.542																																					p.L311P		Atlas-SNP	.											.	GPR182	35	.	0			c.T932C						.						250	217	228					12																	57389925		2203	4300	6503	SO:0001583	missense	11318	exon2			CCATGCTGCACTG	Y13583	CCDS8927.1	12q13.3	2012-08-21	2007-09-24	2007-09-24		ENSG00000166856		"GPCR / Class A : Orphans"	13708	protein-coding gene	gene with protein product		605307	"adrenomedullin receptor"	ADMR		9367907, 9535752	Standard	NM_007264		Approved	hrhAMR, G10D, AM-R	uc001smk.3	O15218		ENST00000300098.1:c.932T>C	chr12.hg19:g.57389925T>C	ENSP00000300098:p.Leu311Pro	139.0	0.0		83.0	4.0	NM_007264		Missense_Mutation	SNP	ENST00000300098.1	hg19	CCDS8927.1	.	.	.	.	.	.	.	.	.	.	T	19.23	3.786616	0.70337	.	.	ENSG00000166856	ENST00000300098	T	0.44881	0.91	4.31	4.31	0.51392	GPCR, rhodopsin-like superfamily (1);	0.163489	0.41194	D	0.000936	T	0.64011	0.2560	M	0.81802	2.56	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.69289	-0.5184	10	0.87932	D	0	.	11.7228	0.51691	0.0:0.0:0.0:1.0	.	311	O15218	GP182_HUMAN	P	311	ENSP00000300098:L311P	ENSP00000300098:L311P	L	+	2	0	GPR182	55676192	1.000000	0.71417	0.999000	0.59377	0.971000	0.66376	7.821000	0.86641	1.920000	0.55613	0.459000	0.35465	CTG	.	.		0.542	GPR182-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411212.1	NM_007264		C	57389925	T	C	57389925	3	2	260	1	0	0	0	0	1	0	0	0	6685	1580	55	2	934	2	GPR182	12	57389925	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	384559	57389925	76461970	549	37794										
PIP4K2C	79837	hgsc.bcm.edu	37	chr12	57989718	57989718	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gaaagtgaaggcagtgatggTcgcttccttatctcctacga	11	9	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:57989718T>C	ENST00000354947.5	+	4	433	c.417T>C	c.(415-417)ggT>ggC	p.G139G	PIP4K2C_ENST00000540759.2_Silent_p.G139G|PIP4K2C_ENST00000550465.1_Silent_p.G121G|PIP4K2C_ENST00000422156.3_Intron			Q8TBX8	PI42C_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, gamma	139	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	1-phosphatidylinositol-5-phosphate 4-kinase activity (GO:0016309)|ATP binding (GO:0005524)|identical protein binding (GO:0042802)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(13)|pancreas(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	33	Melanoma(17;0.122)					GCAGTGATGGTCGCTTCCTTA	0.502																																					p.G139G		Atlas-SNP	.											.	PIP4K2C	50	.	0			c.T417C						.						155	137	143					12																	57989718		2203	4300	6503	SO:0001819	synonymous_variant	79837	exon4			TGATGGTCGCTTC	AK125526	CCDS8946.1, CCDS53808.1, CCDS55839.1	12q13.3	2014-09-04	2007-08-14	2007-08-14	ENSG00000166908	ENSG00000166908			23786	protein-coding gene	gene with protein product			"phosphatidylinositol-4-phosphate 5-kinase, type II, gamma"	PIP5K2C		9367159	Standard	NM_024779		Approved	FLJ22055	uc001sot.3	Q8TBX8	OTTHUMG00000170144	ENST00000354947.5:c.417T>C	chr12.hg19:g.57989718T>C		146.0	0.0		87.0	4.0	NM_001146258	B2RDL3|B4DM11|B4DY44|Q9H6N2	Silent	SNP	ENST00000354947.5	hg19	CCDS8946.1																																																																																			.	.		0.502	PIP4K2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407644.1	NM_024779		C	57989718	T	C	57989718	2	2	260	1	0	0	0	0	0	0	0	1	11947	1654	58	2		2	PIP4K2C	12	57989718	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	599793	57989718	75862177	550	37795										
AVIL	10677	hgsc.bcm.edu	37	chr12	58191678	58191678	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcttgctttagaaaagccccTtttctttcttcatttggagc	6	10	4	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:58191678T>C	ENST00000257861.3	-	19	2877	c.2447A>G	c.(2446-2448)aAg>aGg	p.K816R	AVIL_ENST00000537081.1_Missense_Mutation_p.K809R|TSFM_ENST00000550559.1_Intron|TSFM_ENST00000543727.1_Intron|TSFM_ENST00000548851.1_Intron	NM_006576.3	NP_006567.3	O75366	AVIL_HUMAN	advillin	816	HP. {ECO:0000255|PROSITE- ProRule:PRU00595}.|Headpiece. {ECO:0000250}.				actin filament capping (GO:0051693)|cilium morphogenesis (GO:0060271)|cytoskeleton organization (GO:0007010)|nervous system development (GO:0007399)|positive regulation of neuron projection development (GO:0010976)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)	actin binding (GO:0003779)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(9)|ovary(1)|prostate(6)	32	Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)					GAAAAGCCCCTTTTCTTTCTT	0.433																																					p.K816R		Atlas-SNP	.											.	AVIL	60	.	0			c.A2447G						.						131	124	127					12																	58191678		2203	4300	6503	SO:0001583	missense	10677	exon19			AGCCCCTTTTCTT	AF041449	CCDS8959.1	12q13.11	2006-03-30				ENSG00000135407			14188	protein-coding gene	gene with protein product		613397				9664034, 12034507	Standard	NM_006576		Approved	p92, FLJ12386, ADVIL, DOC6	uc001sqj.2	O75366	OTTHUMG00000170461	ENST00000257861.3:c.2447A>G	chr12.hg19:g.58191678T>C	ENSP00000257861:p.Lys816Arg	99.0	0.0		84.0	4.0	NM_006576	B2RAU7|Q2NKM9	Missense_Mutation	SNP	ENST00000257861.3	hg19	CCDS8959.1	.	.	.	.	.	.	.	.	.	.	T	7.605	0.673531	0.14776	.	.	ENSG00000135407	ENST00000537081;ENST00000257861	T;T	0.15017	2.46;2.47	4.99	3.16	0.36331	Villin headpiece (5);	0.232479	0.43919	N	0.000508	T	0.10337	0.0253	L	0.34521	1.04	0.32508	N	0.537928	B;B	0.12013	0.001;0.005	B;B	0.21708	0.005;0.036	T	0.18618	-1.0331	10	0.19147	T	0.46	-21.4233	3.1009	0.06325	0.1729:0.2567:0.0:0.5704	.	809;816	O75366-2;O75366	.;AVIL_HUMAN	R	809;816	ENSP00000443207:K809R;ENSP00000257861:K816R	ENSP00000257861:K816R	K	-	2	0	AVIL	56477945	0.007000	0.16637	1.000000	0.80357	0.996000	0.88848	0.211000	0.17474	0.546000	0.28920	0.459000	0.35465	AAG	.	.		0.433	AVIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409276.1	NM_006576		C	58191678	T	C	58191678	3	2	260	1	0	0	0	0	1	0	0	0	1227	1609	56	2	16	2	AVIL	12	58191678	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	201960	58191678	75660217	551	37796										
IL22	50616	hgsc.bcm.edu	37	chr12	68646556	68646556	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tagcttacactgactccgtgGaacagtttctccccaatgag	8	12	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:68646556G>T	ENST00000538666.1	-	3	310	c.240C>A	c.(238-240)ttC>ttA	p.F80L	IL22_ENST00000328087.4_Missense_Mutation_p.F80L			Q9GZX6	IL22_HUMAN	interleukin 22	80					acute-phase response (GO:0006953)|cell-cell signaling (GO:0007267)|inflammatory response (GO:0006954)|response to glucocorticoid (GO:0051384)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	interleukin-22 receptor binding (GO:0045518)			breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)	14		Myeloproliferative disorder(1001;0.0255)	Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;5.06e-05)|BRCA - Breast invasive adenocarcinoma(357;0.00104)		TGACTCCGTGGAACAGTTTCT	0.488																																					p.F80L		Atlas-SNP	.											.	IL22	21	.	0			c.C240A						.						133	115	121					12																	68646556		2203	4300	6503	SO:0001583	missense	50616	exon2			TCCGTGGAACAGT	AF279437	CCDS8982.1	12q15	2014-05-22			ENSG00000127318	ENSG00000127318		"Interleukins and interleukin receptors"	14900	protein-coding gene	gene with protein product	"IL-10-related T-cell-derived inducible factor"	605330				10954742, 10875937	Standard	NM_020525		Approved	ILTIF, IL-21, zcyto18, IL-TIF, IL-D110, TIFa, TIFIL-23, IL-22, MGC79382, MGC79384	uc001sty.1	Q9GZX6	OTTHUMG00000169119	ENST00000538666.1:c.240C>A	chr12.hg19:g.68646556G>T	ENSP00000442424:p.Phe80Leu	119.0	0.0		73.0	4.0	NM_020525		Missense_Mutation	SNP	ENST00000538666.1	hg19	CCDS8982.1	.	.	.	.	.	.	.	.	.	.	g	12.49	1.953102	0.34471	.	.	ENSG00000127318	ENST00000538666;ENST00000328087	T;T	0.52526	0.66;0.66	5.13	2.22	0.28083	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.600755	0.16897	N	0.195059	T	0.39036	0.1063	M	0.72118	2.19	0.09310	N	1	P	0.38250	0.624	B	0.32393	0.145	T	0.27468	-1.0073	9	.	.	.	-4.3059	5.2429	0.15481	0.2531:0.1507:0.5962:0.0	.	80	Q9GZX6	IL22_HUMAN	L	80	ENSP00000442424:F80L;ENSP00000329384:F80L	.	F	-	3	2	IL22	66932823	0.009000	0.17119	0.003000	0.11579	0.138000	0.21146	0.490000	0.22403	0.364000	0.24374	0.558000	0.71614	TTC	.	.		0.488	IL22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402318.1	NM_020525		T	68646556	G	T	68646556	3	4	260	1	0	0	0	0	1	0	0	0	7681	1165	41	3	315	3	IL22	12	68646556	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	10454878	68646556	65205339	552	37797										
NAV3	89795	hgsc.bcm.edu	37	chr12	78401192	78401192	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acagcagcaacatagccaccCgaataccgcgacagtggcac	9	15	0	0	rs573896613	byFrequency	TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:78401192C>A	ENST00000397909.2	+	8	2047	c.1874C>A	c.(1873-1875)cCg>cAg	p.P625Q	NAV3_ENST00000228327.6_Missense_Mutation_p.P625Q|NAV3_ENST00000266692.7_Missense_Mutation_p.P625Q|NAV3_ENST00000536525.2_Missense_Mutation_p.P625Q			Q8IVL0	NAV3_HUMAN	neuron navigator 3	625						membrane (GO:0016020)|nuclear envelope (GO:0005635)		p.P625Q(1)		NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						CATAGCCACCCGAATACCGCG	0.478										HNSCC(70;0.22)																											p.P625Q		Atlas-SNP	.											NAV3,right_lower_lobe,carcinoma,0,1	NAV3	506	.	1	Substitution - Missense(1)	lung(1)	c.C1874A						.						122	120	121					12																	78401192		2068	4200	6268	SO:0001583	missense	89795	exon8			GCCACCCGAATAC	AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.1874C>A	chr12.hg19:g.78401192C>A	ENSP00000381007:p.Pro625Gln	50.0	0.0		36.0	2.0	NM_014903	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	hg19		.	.	.	.	.	.	.	.	.	.	C	18.23	3.577759	0.65878	.	.	ENSG00000067798	ENST00000549464;ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692	T;T;T;T;T	0.15603	2.41;2.41;2.41;2.41;2.41	4.84	4.84	0.62591	.	0.384049	0.18564	U	0.137533	T	0.41834	0.1176	M	0.61703	1.905	0.80722	D	1	D;D	0.89917	0.981;1.0	P;D	0.91635	0.831;0.999	T	0.29731	-1.0002	10	0.62326	D	0.03	-4.6907	17.9357	0.89011	0.0:1.0:0.0:0.0	.	625;625	Q8IVL0;Q8IVL0-2	NAV3_HUMAN;.	Q	625	ENSP00000446628:P625Q;ENSP00000446132:P625Q;ENSP00000381007:P625Q;ENSP00000228327:P625Q;ENSP00000266692:P625Q	ENSP00000228327:P625Q	P	+	2	0	NAV3	76925323	1.000000	0.71417	0.925000	0.36789	0.570000	0.35934	7.625000	0.83145	2.243000	0.73865	0.555000	0.69702	CCG	.	.		0.478	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		A	78401192	C	A	78401192	3	1	260	1	0	0	0	0	1	0	0	0	10194	652	23	1	1904	1	NAV3	12	78401192	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	9754636	78401192	55450703	553	37798										
NAV3	89795	hgsc.bcm.edu	37	chr12	78598913	78598913	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aaactgacacagaaggagatCccctggtaagaatcagatgt	10	8	1	5			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:78598913C>A	ENST00000397909.2	+	39	7206	c.7033C>A	c.(7033-7035)Ccc>Acc	p.P2345T	NAV3_ENST00000228327.6_Missense_Mutation_p.P2323T|NAV3_ENST00000266692.7_Missense_Mutation_p.P2146T|NAV3_ENST00000536525.2_Missense_Mutation_p.P2323T|NAV3_ENST00000541270.1_Missense_Mutation_p.P175T			Q8IVL0	NAV3_HUMAN	neuron navigator 3	2345						membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						AGAAGGAGATCCCCTGGTAAG	0.403										HNSCC(70;0.22)																											p.P2323T		Atlas-SNP	.											.	NAV3	506	.	0			c.C6967A						.						76	83	81					12																	78598913		1986	4167	6153	SO:0001583	missense	89795	exon38			GGAGATCCCCTGG	AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.7033C>A	chr12.hg19:g.78598913C>A	ENSP00000381007:p.Pro2345Thr	69.0	0.0		58.0	4.0	NM_014903	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.92|17.92	3.507327|3.507327	0.64410|0.64410	.|.	.|.	ENSG00000067798|ENSG00000067798	ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692;ENST00000541270|ENST00000552895;ENST00000551162	T;T;T;T;T|.	0.59638|.	0.41;0.44;0.4;0.66;0.25|.	5.14|5.14	5.14|5.14	0.70334|0.70334	.|.	0.000000|.	0.40064|.	U|.	0.001195|.	D|D	0.83514|0.83514	0.5271|0.5271	M|M	0.87758|0.87758	2.905|2.905	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0|.	D;D;D;D|.	0.97110|.	1.0;0.996;0.998;0.998|.	D|D	0.85978|0.85978	0.1481|0.1481	10|5	0.87932|.	D|.	0|.	-13.4514|-13.4514	18.587|18.587	0.91194|0.91194	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	2323;2146;2345;2323|.	E7EUC6;Q8IVL0-3;Q8IVL0;Q8IVL0-2|.	.;.;NAV3_HUMAN;.|.	T|Y	2323;2345;2323;2146;175|1217;212	ENSP00000446132:P2323T;ENSP00000381007:P2345T;ENSP00000228327:P2323T;ENSP00000266692:P2146T;ENSP00000444918:P175T|.	ENSP00000228327:P2323T|.	P|S	+|+	1|2	0|0	NAV3|NAV3	77123044|77123044	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.358000|0.358000	0.29455|0.29455	7.818000|7.818000	0.86416|0.86416	2.389000|2.389000	0.81357|0.81357	0.467000|0.467000	0.42956|0.42956	CCC|TCC	.	.		0.403	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		A	78598913	C	A	78598913	3	1	260	1	0	0	0	0	1	0	0	0	10194	855	30	3	7117	3	NAV3	12	78598913	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	197721	78598913	55252982	554	37799										
TMTC3	160418	hgsc.bcm.edu	37	chr12	88566387	88566387	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tttgtaggcgctttgtttaaTggcattaccatttattcctg	8	7	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:88566387T>A	ENST00000266712.6	+	8	1284	c.1064T>A	c.(1063-1065)aTg>aAg	p.M355K		NM_181783.3	NP_861448.2	Q6ZXV5	TMTC3_HUMAN	transmembrane and tetratricopeptide repeat containing 3	355					bud outgrowth involved in lung branching (GO:0060447)|lung alveolus development (GO:0048286)|muscle fiber development (GO:0048747)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)	integral component of membrane (GO:0016021)				NS(1)|breast(2)|endometrium(1)|kidney(4)|large_intestine(5)|liver(1)|lung(12)|prostate(4)|skin(1)	31						CTTTGTTTAATGGCATTACCA	0.289																																					p.M355K		Atlas-SNP	.											.	TMTC3	75	.	0			c.T1064A						.						108	100	102					12																	88566387		2203	4300	6503	SO:0001583	missense	160418	exon8			GTTTAATGGCATT		CCDS9032.1	12q21.32	2014-09-04			ENSG00000139324	ENSG00000139324		"Tetratricopeptide (TTC) repeat domain containing"	26899	protein-coding gene	gene with protein product							Standard	NM_181783		Approved	FLJ90492, SMILE	uc001tau.3	Q6ZXV5	OTTHUMG00000169887	ENST00000266712.6:c.1064T>A	chr12.hg19:g.88566387T>A	ENSP00000266712:p.Met355Lys	132.0	0.0		76.0	4.0	NM_181783	Q5CZ86|Q5H9T6|Q68DQ6|Q68DX0|Q7Z332|Q8NC50	Missense_Mutation	SNP	ENST00000266712.6	hg19	CCDS9032.1	.	.	.	.	.	.	.	.	.	.	T	18.00	3.524355	0.64747	.	.	ENSG00000139324	ENST00000266712	T	0.43688	0.94	5.73	5.73	0.89815	.	0.137070	0.64402	D	0.000001	T	0.52370	0.1730	M	0.82193	2.58	0.53688	D	0.999977	B	0.28933	0.228	B	0.33454	0.164	T	0.56408	-0.7984	10	0.62326	D	0.03	-9.3112	16.0064	0.80363	0.0:0.0:0.0:1.0	.	355	Q6ZXV5-2	.	K	355	ENSP00000266712:M355K	ENSP00000266712:M355K	M	+	2	0	TMTC3	87090518	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.040000	0.89188	2.171000	0.68590	0.528000	0.53228	ATG	.	.		0.289	TMTC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406421.1	NM_181783		A	88566387	T	A	88566387	3	1	260	1	0	0	0	0	1	0	0	0	16277	1464	51	4	1090	4	TMTC3	12	88566387	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	9967474	88566387	45285508	555	37800										
METAP2	10988	hgsc.bcm.edu	37	chr12	95888769	95888769	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgttcacgcaagttaataaaAgagaatggattaaatgcagg	10	4	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:95888769A>G	ENST00000323666.5	+	6	856	c.627A>G	c.(625-627)aaA>aaG	p.K209K	METAP2_ENST00000261220.9_Silent_p.K186K|METAP2_ENST00000550777.1_Silent_p.K173K|METAP2_ENST00000546753.1_Silent_p.K186K|METAP2_ENST00000551840.1_Silent_p.K208K	NM_006838.3	NP_006829.1			methionyl aminopeptidase 2											endometrium(3)|large_intestine(2)|lung(7)|prostate(1)	13						AGTTAATAAAAGAGAATGGAT	0.353																																					p.K209K		Atlas-SNP	.											.	METAP2	28	.	0			c.A627G						.						93	92	93					12																	95888769		2203	4300	6503	SO:0001819	synonymous_variant	10988	exon6			AATAAAAGAGAAT	U13261	CCDS9052.1	12q22	2014-09-04			ENSG00000111142		3.4.11.18		16672	protein-coding gene	gene with protein product	"Peptidase M"	601870				7644482, 8858118	Standard	NM_006838		Approved	MNPEP, p67, MAP2	uc001tec.3	P50579	OTTHUMG00000170280	ENST00000323666.5:c.627A>G	chr12.hg19:g.95888769A>G		180.0	0.0		91.0	4.0	NM_006838		Silent	SNP	ENST00000323666.5	hg19	CCDS9052.1																																																																																			.	.		0.353	METAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408296.1	NM_006838		G	95888769	A	G	95888769	2	3	260	1	0	0	0	0	0	0	0	1	9496	69	3	2		2	METAP2	12	95888769	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	7322382	95888769	37963126	556	37801										
USP44	84101	hgsc.bcm.edu	37	chr12	95922582	95922582	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gaacacaacgtctttactcaCagttacactggtcacatacg	6	12	3	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:95922582C>T	ENST00000258499.3	-	3	1913		c.e3+1		USP44_ENST00000537435.2_Splice_Site|USP44_ENST00000393091.2_Splice_Site|USP44_ENST00000552440.1_Intron	NM_001278393.1|NM_032147.2	NP_001265322.1|NP_115523.2	Q9H0E7	UBP44_HUMAN	ubiquitin specific peptidase 44						mitotic nuclear division (GO:0007067)|negative regulation of mitotic anaphase-promoting complex activity (GO:0060564)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein deubiquitination (GO:0016579)|regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266)|regulation of spindle checkpoint (GO:0090231)	nucleus (GO:0005634)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(5)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	36						TCTTTACTCACAGTTACACTG	0.383																																					.		Atlas-SNP	.											.	USP44	83	.	0			c.1624+1G>A						.						108	103	105					12																	95922582		2203	4300	6503	SO:0001630	splice_region_variant	84101	exon4			TACTCACAGTTAC	AK027434	CCDS9053.1	12q21.33	2005-08-08	2005-08-08			ENSG00000136014		"Ubiquitin-specific peptidases"	20064	protein-coding gene	gene with protein product		610993	"ubiquitin specific protease 44"			12838346	Standard	NM_001278393		Approved	FLJ14528	uc001teg.3	Q9H0E7		ENST00000258499.3:c.1624+1G>A	chr12.hg19:g.95922582C>T		176.0	0.0		100.0	5.0	NM_032147	B2RDW3	Splice_Site	SNP	ENST00000258499.3	hg19	CCDS9053.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.335778	0.81801	.	.	ENSG00000136014	ENST00000258499;ENST00000393091;ENST00000537435	.	.	.	5.5	5.5	0.81552	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.7538	0.96281	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	USP44	94446713	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	7.750000	0.85110	2.739000	0.93911	0.561000	0.74099	.	.	.		0.383	USP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408312.1	NM_032147	Intron	T	95922582	C	T	95922582	5	4	260	1	0	0	0	0	0	0	1	0	17090	492	17	3	529	3	USP44	12	95922582	Splice_Site	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	33813	95922582	37929313	557	37802										
NR1H4	9971	hgsc.bcm.edu	37	chr12	100955731	100955731	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttggggaactgaaaatgactCaagaggagtatgctctgctt	12	6	2	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:100955731C>A	ENST00000551379.1	+	8	1205	c.1177C>A	c.(1177-1179)Caa>Aaa	p.Q393K	NR1H4_ENST00000392986.3_Missense_Mutation_p.Q383K|NR1H4_ENST00000548884.1_Missense_Mutation_p.Q379K|NR1H4_ENST00000188403.7_Missense_Mutation_p.Q389K|NR1H4_ENST00000549996.1_Missense_Mutation_p.Q332K			Q96RI1	NR1H4_HUMAN	nuclear receptor subfamily 1, group H, member 4	393	Ligand-binding.				bile acid metabolic process (GO:0008206)|cellular response to acid chemical (GO:0071229)|cellular response to organonitrogen compound (GO:0071417)|digestive tract development (GO:0048565)|gene expression (GO:0010467)|intracellular bile acid receptor signaling pathway (GO:0038185)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of bile acid biosynthetic process (GO:0070858)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nitrogen catabolite activation of transcription from RNA polymerase II promoter (GO:0001080)|positive regulation of ammonia assimilation cycle (GO:2001250)|positive regulation of glutamate metabolic process (GO:2000213)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of carbohydrate metabolic process (GO:0006109)|regulation of cholesterol metabolic process (GO:0090181)|regulation of urea metabolic process (GO:0034255)|response to glucose (GO:0009749)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)	bile acid binding (GO:0032052)|bile acid receptor activity (GO:0038181)|chenodeoxycholic acid binding (GO:1902122)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|ligand-dependent nuclear receptor binding (GO:0016922)|peptide binding (GO:0042277)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|thyroid hormone receptor activity (GO:0004887)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	44					Chenodeoxycholic acid(DB06777)	GAAAATGACTCAAGAGGAGTA	0.318																																					p.Q393K		Atlas-SNP	.											.	NR1H4	145	.	0			c.C1177A						.						82	85	84					12																	100955731		2203	4294	6497	SO:0001583	missense	9971	exon8			ATGACTCAAGAGG	U68233	CCDS9078.1, CCDS55873.1, CCDS55874.1, CCDS55875.1, CCDS55876.1	12q23.1	2013-01-16				ENSG00000012504		"Nuclear hormone receptors"	7967	protein-coding gene	gene with protein product		603826				7774010, 9223286	Standard	NM_001206977		Approved	FXR, RIP14, HRR1, HRR-1	uc001tht.2	Q96RI1	OTTHUMG00000170359	ENST00000551379.1:c.1177C>A	chr12.hg19:g.100955731C>A	ENSP00000447149:p.Gln393Lys	181.0	0.0		90.0	5.0	NM_001206993	A1L4K5|B7Z412|B7ZM06|F8VYG8|Q8NFP5|Q8NFP6|Q92943	Missense_Mutation	SNP	ENST00000551379.1	hg19	CCDS55876.1	.	.	.	.	.	.	.	.	.	.	C	17.21	3.330440	0.60743	.	.	ENSG00000012504	ENST00000548884;ENST00000392986;ENST00000549996;ENST00000551379;ENST00000188403	D;D;D;D;D	0.94931	-3.56;-3.56;-3.56;-3.56;-3.56	5.75	5.75	0.90469	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.164580	0.53938	D	0.000044	D	0.88905	0.6564	N	0.12471	0.22	0.50813	D	0.99989	P;P;P;P;B	0.50156	0.932;0.645;0.863;0.765;0.164	B;B;B;B;B	0.41723	0.365;0.291;0.289;0.233;0.094	D	0.90896	0.4765	10	0.72032	D	0.01	.	15.4381	0.75162	0.0:0.8618:0.1382:0.0	.	332;393;389;383;379	F8VYG8;Q96RI1;Q96RI1-4;F1DAL1;B6ZGS9	.;NR1H4_HUMAN;.;.;.	K	379;383;332;393;389	ENSP00000448506:Q379K;ENSP00000376712:Q383K;ENSP00000448978:Q332K;ENSP00000447149:Q393K;ENSP00000188403:Q389K	ENSP00000188403:Q389K	Q	+	1	0	NR1H4	99479862	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.276000	0.58933	2.708000	0.92522	0.650000	0.86243	CAA	.	.		0.318	NR1H4-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409140.1	NM_005123		A	100955731	C	A	100955731	3	1	260	1	0	0	0	0	1	0	0	0	10628	827	29	3	1165	3	NR1H4	12	100955731	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	5033149	100955731	32896164	558	37803										
GAS2L3	283431	hgsc.bcm.edu	37	chr12	101016162	101016162	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	taaaatactctttataagagTaagtccattatttacacttt	3	6	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:101016162T>A	ENST00000539410.1	+	8	1142		c.e8+2		GAS2L3_ENST00000537247.1_Splice_Site|GAS2L3_ENST00000547754.1_Splice_Site|GAS2L3_ENST00000266754.5_Splice_Site			Q86XJ1	GA2L3_HUMAN	growth arrest-specific 2 like 3						actin cytoskeleton organization (GO:0030036)|cell cycle arrest (GO:0007050)|microtubule cytoskeleton organization (GO:0000226)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	actin binding (GO:0003779)|microtubule binding (GO:0008017)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(15)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35						TTTATAAGAGTAAGTCCATTA	0.318																																					.		Atlas-SNP	.											GAS2L3,colon,carcinoma,0,1	GAS2L3	76	.	0			c.756+2T>A						.						79	82	81					12																	101016162		2202	4299	6501	SO:0001630	splice_region_variant	283431	exon9			TAAGAGTAAGTCC	AK095594	CCDS9079.1	12q23.1	2014-09-11			ENSG00000139354	ENSG00000139354			27475	protein-coding gene	gene with protein product							Standard	NM_174942		Approved		uc001thu.3	Q86XJ1	OTTHUMG00000170439	ENST00000539410.1:c.756+2T>A	chr12.hg19:g.101016162T>A		95.0	0.0		59.0	3.0	NM_174942	B2RCN2	Splice_Site	SNP	ENST00000539410.1	hg19	CCDS9079.1	.	.	.	.	.	.	.	.	.	.	T	15.13	2.741239	0.49151	.	.	ENSG00000139354	ENST00000266754;ENST00000547754;ENST00000537247;ENST00000539410	.	.	.	5.9	5.9	0.94986	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3245	0.82970	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	GAS2L3	99540293	1.000000	0.71417	1.000000	0.80357	0.261000	0.26267	7.499000	0.81566	2.254000	0.74563	0.460000	0.39030	.	.	.		0.318	GAS2L3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409143.1	NM_174942	Intron	A	101016162	T	A	101016162	5	1	260	1	0	0	0	0	0	0	1	0	6256	1652	57	4	784	4	GAS2L3	12	101016162	Splice_Site	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	60431	101016162	32835733	559	37804										
SLC5A8	160728	hgsc.bcm.edu	37	chr12	101581168	101581168	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agacatggtactgaacctggTctggtgcagacactttcttg	11	9	2	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:101581168T>C	ENST00000536262.2	-	7	1517	c.959A>G	c.(958-960)gAc>gGc	p.D320G		NM_145913.3	NP_666018.3			solute carrier family 5 (sodium/monocarboxylate cotransporter), member 8											breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(29)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						CTGAACCTGGTCTGGTGCAGA	0.428																																					p.D320G	GBM(60;420 1056 13605 22380 47675)	Atlas-SNP	.											.	SLC5A8	102	.	0			c.A959G						.						109	100	103					12																	101581168		2203	4300	6503	SO:0001583	missense	160728	exon7			ACCTGGTCTGGTG	AY081220	CCDS9080.1	12q23.1	2013-07-19	2013-07-19		ENSG00000256870	ENSG00000256870		"Solute carriers"	19119	protein-coding gene	gene with protein product		608044	"solute carrier family 5 (iodide transporter), member 8"			12107270, 12829793	Standard	NM_145913		Approved	AIT	uc001thz.4	Q8N695	OTTHUMG00000170499	ENST00000536262.2:c.959A>G	chr12.hg19:g.101581168T>C	ENSP00000445340:p.Asp320Gly	109.0	0.0		97.0	4.0	NM_145913		Missense_Mutation	SNP	ENST00000536262.2	hg19	CCDS9080.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.685914	0.88639	.	.	ENSG00000256870	ENST00000536262	D	0.89415	-2.51	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	D	0.96558	0.8877	H	0.97659	4.05	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.98043	1.0383	10	0.87932	D	0	.	15.3279	0.74182	0.0:0.0:0.0:1.0	.	320	Q8N695	SC5A8_HUMAN	G	320	ENSP00000445340:D320G	ENSP00000445340:D320G	D	-	2	0	SLC5A8	100105299	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	8.040000	0.89188	2.019000	0.59389	0.377000	0.23210	GAC	.	.		0.428	SLC5A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409401.1	NM_145913		C	101581168	T	C	101581168	3	2	260	1	0	0	0	0	1	0	0	0	14686	1667	58	2	909	2	SLC5A8	12	101581168	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	565006	101581168	32270727	560	37805										
UTP20	27340	hgsc.bcm.edu	37	chr12	101683948	101683948	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acgcacttttcaatttaatgTttcttgatcttgataaacat	4	7	3	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:101683948T>C	ENST00000261637.4	+	7	805	c.631T>C	c.(631-633)Ttt>Ctt	p.F211L		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	211					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						CAATTTAATGTTTCTTGATCT	0.313																																					p.F211L		Atlas-SNP	.											.	UTP20	222	.	0			c.T631C						.						57	62	60					12																	101683948		2203	4300	6503	SO:0001583	missense	27340	exon7			TTAATGTTTCTTG	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"down regulated in metastasis"	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.631T>C	chr12.hg19:g.101683948T>C	ENSP00000261637:p.Phe211Leu	230.0	0.0		120.0	5.0	NM_014503	Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	hg19	CCDS9081.1	.	.	.	.	.	.	.	.	.	.	T	19.07	3.755732	0.69648	.	.	ENSG00000120800	ENST00000261637	T	0.61158	0.13	5.8	4.66	0.58398	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.68007	0.2954	M	0.69823	2.125	0.54753	D	0.999987	D	0.89917	1.0	D	0.83275	0.996	T	0.69154	-0.5220	10	0.05721	T	0.95	-16.6845	10.2538	0.43385	0.0:0.1365:0.0:0.8635	.	211	O75691	UTP20_HUMAN	L	211	ENSP00000261637:F211L	ENSP00000261637:F211L	F	+	1	0	UTP20	100208079	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.346000	0.52190	1.030000	0.39839	0.477000	0.44152	TTT	.	.		0.313	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		C	101683948	T	C	101683948	3	2	260	1	0	0	0	0	1	0	0	0	17114	1725	60	2	657	2	UTP20	12	101683948	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	102780	101683948	32167947	561	37806										
UTP20	27340	hgsc.bcm.edu	37	chr12	101685546	101685546	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctcttggatctacacacaaaAgtaacaaaaactaactgttg	5	9	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:101685546A>G	ENST00000261637.4	+	9	1092	c.918A>G	c.(916-918)aaA>aaG	p.K306K		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	306					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						TACACACAAAAGTAACAAAAA	0.333																																					p.K306K		Atlas-SNP	.											.	UTP20	222	.	0			c.A918G						.						58	59	58					12																	101685546		2203	4300	6503	SO:0001819	synonymous_variant	27340	exon9			CACAAAAGTAACA	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"down regulated in metastasis"	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.918A>G	chr12.hg19:g.101685546A>G		127.0	0.0		96.0	4.0	NM_014503	Q9H3H4	Silent	SNP	ENST00000261637.4	hg19	CCDS9081.1																																																																																			.	.		0.333	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		G	101685546	A	G	101685546	2	3	260	1	0	0	0	0	0	0	0	1	17114	69	3	2		2	UTP20	12	101685546	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1598	101685546	32166349	562	37807										
GLT8D2	83468	hgsc.bcm.edu	37	chr12	104393207	104393207	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttcaggcctcgatgagtctgGtctgatcttccctttgagga	11	10	4	3	rs199929846		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:104393207G>A	ENST00000360814.4	-	6	775	c.370C>T	c.(370-372)Cca>Tca	p.P124S	GLT8D2_ENST00000546436.1_Missense_Mutation_p.P124S|GLT8D2_ENST00000548660.1_Missense_Mutation_p.P124S	NM_031302.3	NP_112592.1	Q9H1C3	GL8D2_HUMAN	glycosyltransferase 8 domain containing 2	124						integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			kidney(3)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)	16						GATGAGTCTGGTCTGATCTTC	0.448																																					p.P124S		Atlas-SNP	.											.	GLT8D2	40	.	0			c.C370T						.	G	SER/PRO	0,4406		0,0,2203	201	185	191		370	4.9	1	12		191	1,8599	1.2+/-3.3	0,1,4299	yes	missense	GLT8D2	NM_031302.3	74	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	124/350	104393207	1,13005	2203	4300	6503	SO:0001583	missense	83468	exon6			AGTCTGGTCTGAT	BC022343	CCDS9096.1	12q23.3	2013-02-22			ENSG00000120820	ENSG00000120820		"Glycosyltransferase family 8 domain containing"	24890	protein-coding gene	gene with protein product							Standard	NM_031302		Approved	FLJ31494	uc001tkh.1	Q9H1C3	OTTHUMG00000170120	ENST00000360814.4:c.370C>T	chr12.hg19:g.104393207G>A	ENSP00000354053:p.Pro124Ser	190.0	0.0		92.0	4.0	NM_031302	Q96KA2	Missense_Mutation	SNP	ENST00000360814.4	hg19	CCDS9096.1	.	.	.	.	.	.	.	.	.	.	G	15.81	2.942331	0.53079	0.0	1.16E-4	ENSG00000120820	ENST00000360814;ENST00000546436;ENST00000548660;ENST00000546851	T;T;T;T	0.39229	1.09;1.09;1.09;2.03	5.79	4.9	0.64082	.	0.049652	0.85682	D	0.000000	T	0.47619	0.1455	L	0.43152	1.355	0.80722	D	1	D	0.60575	0.988	P	0.55749	0.783	T	0.35301	-0.9794	10	0.09590	T	0.72	.	16.9389	0.86210	0.0:0.1279:0.8721:0.0	.	124	Q9H1C3	GL8D2_HUMAN	S	124;124;124;63	ENSP00000354053:P124S;ENSP00000449750:P124S;ENSP00000447450:P124S;ENSP00000446810:P63S	ENSP00000354053:P124S	P	-	1	0	GLT8D2	102917337	1.000000	0.71417	0.998000	0.56505	0.965000	0.64279	7.065000	0.76727	1.433000	0.47394	0.655000	0.94253	CCA	.	.		0.448	GLT8D2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407371.1	NM_031302		A	104393207	G	A	104393207	3	1	260	1	0	0	0	0	1	0	0	0	6478	1261	44	3	703	3	GLT8D2	12	104393207	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	2707661	104393207	29458688	563	37808										
KIAA1033	23325	hgsc.bcm.edu	37	chr12	105515979	105515979	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	atttgaaaagttcttgctgaAgctagaagggcaattactgg	11	5	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:105515979A>G	ENST00000332180.5	+	10	836	c.749A>G	c.(748-750)aAg>aGg	p.K250R		NM_015275.1	NP_056090.1			KIAA1033											breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(15)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	41						TTCTTGCTGAAGCTAGAAGGG	0.368																																					p.K250R		Atlas-SNP	.											.	KIAA1033	83	.	0			c.A749G						.						103	95	97					12																	105515979		1831	4079	5910	SO:0001583	missense	23325	exon10			TGCTGAAGCTAGA	AB028956	CCDS41826.1, CCDS73514.1	12q24.11	2014-05-09				ENSG00000136051			29174	protein-coding gene	gene with protein product		615748				20376207, 20498093, 21498477	Standard	XM_005268742		Approved	SWIP	uc001tld.3	Q2M389		ENST00000332180.5:c.749A>G	chr12.hg19:g.105515979A>G	ENSP00000328062:p.Lys250Arg	130.0	0.0		99.0	4.0	NM_015275		Missense_Mutation	SNP	ENST00000332180.5	hg19	CCDS41826.1	.	.	.	.	.	.	.	.	.	.	A	11.04	1.522123	0.27211	.	.	ENSG00000136051	ENST00000332180	T	0.30981	1.51	5.72	4.59	0.56863	.	0.136982	0.64402	D	0.000003	T	0.21103	0.0508	L	0.28740	0.885	0.43613	D	0.995988	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.04840	-1.0923	10	0.16420	T	0.52	.	11.483	0.50337	0.93:0.0:0.07:0.0	.	250;250	B7ZKT9;Q2M389	.;WASH7_HUMAN	R	250	ENSP00000328062:K250R	ENSP00000328062:K250R	K	+	2	0	KIAA1033	104040109	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.414000	0.52693	1.018000	0.39521	0.529000	0.55759	AAG	.	.		0.368	KIAA1033-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406138.4	NM_015275		G	105515979	A	G	105515979	3	3	260	1	0	0	0	0	1	0	0	0	8215	72	3	2	787	2	KIAA1033	12	105515979	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1122772	105515979	28335916	564	37809										
PRDM4	11108	hgsc.bcm.edu	37	chr12	108140127	108140127	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccttgctctgctctctattgGagtgtcaggaacaaaagtca	9	10	4	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:108140127G>T	ENST00000228437.5	-	6	1660	c.1201C>A	c.(1201-1203)Cca>Aca	p.P401T	RP11-864J10.4_ENST00000546714.1_RNA	NM_012406.3	NP_036538.3	Q9UKN5	PRDM4_HUMAN	PR domain containing 4	401					cell proliferation (GO:0008283)|negative regulation of cell cycle (GO:0045786)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|methyltransferase activity (GO:0008168)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(2)|skin(2)|urinary_tract(1)	20						CTCTCTATTGGAGTGTCAGGA	0.488																																					p.P401T		Atlas-SNP	.											.	PRDM4	64	.	0			c.C1201A						.						112	103	106					12																	108140127		2203	4300	6503	SO:0001583	missense	11108	exon6			CTATTGGAGTGTC	AF144757	CCDS9115.1	12q23-q24.1	2013-01-08				ENSG00000110851		"Zinc fingers, C2H2-type"	9348	protein-coding gene	gene with protein product		605780				10552934	Standard	NM_012406		Approved	PFM1	uc001tmp.3	Q9UKN5	OTTHUMG00000169914	ENST00000228437.5:c.1201C>A	chr12.hg19:g.108140127G>T	ENSP00000228437:p.Pro401Thr	157.0	0.0		89.0	4.0	NM_012406	Q9UFA6	Missense_Mutation	SNP	ENST00000228437.5	hg19	CCDS9115.1	.	.	.	.	.	.	.	.	.	.	G	32	5.155242	0.94686	.	.	ENSG00000110851	ENST00000228437;ENST00000550659	T;T	0.59772	0.24;0.24	5.83	5.83	0.93111	.	0.052084	0.85682	D	0.000000	T	0.77579	0.4151	M	0.74467	2.265	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	T	0.77432	-0.2590	10	0.56958	D	0.05	.	20.1162	0.97934	0.0:0.0:1.0:0.0	.	401	Q9UKN5	PRDM4_HUMAN	T	401;146	ENSP00000228437:P401T;ENSP00000449295:P146T	ENSP00000228437:P401T	P	-	1	0	PRDM4	106664257	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.267000	0.95665	2.756000	0.94617	0.655000	0.94253	CCA	.	.		0.488	PRDM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406546.1	NM_012406		T	108140127	G	T	108140127	3	4	260	1	0	0	0	0	1	0	0	0	12471	1174	41	3	1232	3	PRDM4	12	108140127	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	2624148	108140127	25711768	565	37810										
CUX2	23316	hgsc.bcm.edu	37	chr12	111655742	111655742	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	taaaaagcttccaagccgagGtaagacccagggcccacagc	10	13	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:111655742G>A	ENST00000261726.6	+	3	376		c.e3+1		CUX2_ENST00000551604.2_Splice_Site	NM_015267.3	NP_056082.2	O14529	CUX2_HUMAN	cut-like homeobox 2						cellular response to organic substance (GO:0071310)|cognition (GO:0050890)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of synapse assembly (GO:0051965)|short-term memory (GO:0007614)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)	p.?(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(24)|ovary(5)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	55						CCAAGCCGAGGTAAGACCCAG	0.562																																					.		Atlas-SNP	.											CUX2,bladder,carcinoma,0,1	CUX2	145	.	1	Unknown(1)	urinary_tract(1)	c.222+1G>A						.						73	79	77					12																	111655742		1883	4103	5986	SO:0001630	splice_region_variant	23316	exon3			GCCGAGGTAAGAC	AB006631	CCDS41837.1	12q24.12	2011-06-20	2007-11-07	2007-11-07	ENSG00000111249	ENSG00000111249		"Homeoboxes / CUT class"	19347	protein-coding gene	gene with protein product		610648	"cut-like 2 (Drosophila)"	CUTL2			Standard	NM_015267		Approved	KIAA0293, CDP2	uc001tsa.2	O14529	OTTHUMG00000169546	ENST00000261726.6:c.222+1G>A	chr12.hg19:g.111655742G>A		113.0	0.0		90.0	4.0	NM_015267	A7E2Y4	Splice_Site	SNP	ENST00000261726.6	hg19	CCDS41837.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.198849	0.79015	.	.	ENSG00000111249	ENST00000261726;ENST00000397643;ENST00000552889	.	.	.	5.3	5.3	0.74995	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.0988	0.89499	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CUX2	110140125	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.285000	0.89914	2.636000	0.89361	0.655000	0.94253	.	.	.		0.562	CUX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404765.1	NM_015267	Intron	A	111655742	G	A	111655742	5	1	260	1	0	0	0	0	0	0	1	0	4067	1275	44	3	233	3	CUX2	12	111655742	Splice_Site	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	3515615	111655742	22196153	566	37811										
CIT	11113	hgsc.bcm.edu	37	chr12	120214542	120214542	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcagcagcaagccgagactcTctcagctcagattcgtagag	10	12	4	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:120214542T>C	ENST00000261833.7	-	14	1822	c.1770A>G	c.(1768-1770)agA>agG	p.R590R	CIT_ENST00000392521.2_Silent_p.R590R|CIT_ENST00000537607.1_5'UTR	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	590					cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		GCCGAGACTCTCTCAGCTCAG	0.483																																					p.R590R		Atlas-SNP	.											.	CIT	535	.	0			c.A1770G						.						122	118	119					12																	120214542		2203	4300	6503	SO:0001819	synonymous_variant	11113	exon14			AGACTCTCTCAGC	AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966			1985	protein-coding gene	gene with protein product	"serine/threonine kinase 21"	605629	"citron (rho-interacting, serine/threonine kinase 21)"			9792683	Standard	NM_001206999		Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000261833.7:c.1770A>G	chr12.hg19:g.120214542T>C		108.0	0.0		69.0	4.0	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Silent	SNP	ENST00000261833.7	hg19	CCDS9192.1	.	.	.	.	.	.	.	.	.	.	T	10.97	1.502567	0.26949	.	.	ENSG00000122966	ENST00000392520	.	.	.	5.48	1.97	0.26223	.	.	.	.	.	T	0.57431	0.2053	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50617	-0.8807	4	.	.	.	.	8.8949	0.35458	0.0:0.2996:0.0:0.7004	.	.	.	.	G	218	.	.	E	-	2	0	CIT	118698925	0.823000	0.29233	1.000000	0.80357	0.989000	0.77384	-0.076000	0.11412	0.419000	0.25927	0.459000	0.35465	GAG	.	.		0.483	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174		C	120214542	T	C	120214542	2	2	260	1	0	0	0	0	0	0	0	1	3440	1548	54	2		2	CIT	12	120214542	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	8558800	120214542	13637353	567	37812										
GCN1L1	10985	hgsc.bcm.edu	37	chr12	120582132	120582132	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gattctccaaaggtcatcaaAgaggccttgctctagctggg	11	10	4	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:120582132A>G	ENST00000300648.6	-	42	5485	c.5473T>C	c.(5473-5475)Ttt>Ctt	p.F1825L		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	1825					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					AGGTCATCAAAGAGGCCTTGC	0.587																																					p.F1825L		Atlas-SNP	.											.	GCN1L1	207	.	0			c.T5473C						.						63	66	65					12																	120582132		2020	4184	6204	SO:0001583	missense	10985	exon42			CATCAAAGAGGCC	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.5473T>C	chr12.hg19:g.120582132A>G	ENSP00000300648:p.Phe1825Leu	190.0	0.0		115.0	6.0	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Missense_Mutation	SNP	ENST00000300648.6	hg19	CCDS41847.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.534285	0.85812	.	.	ENSG00000089154	ENST00000300648	T	0.64085	-0.08	6.16	6.16	0.99307	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.62768	0.2455	L	0.45352	1.415	0.80722	D	1	P	0.41475	0.751	P	0.45794	0.493	T	0.60326	-0.7285	10	0.34782	T	0.22	-17.3737	16.8061	0.85666	1.0:0.0:0.0:0.0	.	1825	Q92616	GCN1L_HUMAN	L	1825	ENSP00000300648:F1825L	ENSP00000300648:F1825L	F	-	1	0	GCN1L1	119066515	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.667000	0.91153	2.367000	0.80283	0.528000	0.53228	TTT	.	.		0.587	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1			G	120582132	A	G	120582132	3	3	260	1	0	0	0	0	1	0	0	0	6307	72	3	2	2610	2	GCN1L1	12	120582132	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	367590	120582132	13269763	568	37813										
GCN1L1	10985	hgsc.bcm.edu	37	chr12	120591048	120591048	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gggtggagagggcagcgatgAgcttggcaacaatgggcttc	18	7	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:120591048A>G	ENST00000300648.6	-	33	4043	c.4031T>C	c.(4030-4032)cTc>cCc	p.L1344P	MIR4498_ENST00000577599.1_RNA	NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	1344					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GGCAGCGATGAGCTTGGCAAC	0.597																																					p.L1344P		Atlas-SNP	.											.	GCN1L1	207	.	0			c.T4031C						.						73	80	77					12																	120591048		2068	4187	6255	SO:0001583	missense	10985	exon33			GCGATGAGCTTGG	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.4031T>C	chr12.hg19:g.120591048A>G	ENSP00000300648:p.Leu1344Pro	188.0	0.0		110.0	5.0	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Missense_Mutation	SNP	ENST00000300648.6	hg19	CCDS41847.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.541144	0.85917	.	.	ENSG00000089154	ENST00000300648	T	0.74632	-0.86	5.7	5.7	0.88788	Armadillo-like helical (1);Armadillo-type fold (2);	0.000000	0.85682	D	0.000000	D	0.90345	0.6979	H	0.95294	3.65	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93147	0.6546	10	0.87932	D	0	-16.188	15.97	0.80008	1.0:0.0:0.0:0.0	.	1344	Q92616	GCN1L_HUMAN	P	1344	ENSP00000300648:L1344P	ENSP00000300648:L1344P	L	-	2	0	GCN1L1	119075431	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	8.997000	0.93544	2.189000	0.69895	0.459000	0.35465	CTC	.	.		0.597	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1			G	120591048	A	G	120591048	3	3	260	1	0	0	0	0	1	0	0	0	6307	304	11	2	4088	2	GCN1L1	12	120591048	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	8916	120591048	13260847	569	37814										
SIRT4	23409	hgsc.bcm.edu	37	chr12	120741675	120741675	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gagtgccccaatccgccagcGgtactgggcgagaaacttcg	13	13	0	1	rs201393186		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:120741675G>T	ENST00000202967.4	+	2	370	c.311G>T	c.(310-312)cGg>cTg	p.R104L		NM_012240.2	NP_036372.1			sirtuin 4											haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)	9	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					ATCCGCCAGCGGTACTGGGCG	0.572																																					p.R104L		Atlas-SNP	.											SIRT4,colon,carcinoma,0,1	SIRT4	29	.	0			c.G311T						.						53	46	48					12																	120741675		2203	4300	6503	SO:0001583	missense	23409	exon2			GCCAGCGGTACTG	AF083109	CCDS9194.1	12q24.31	2010-06-25	2010-06-25		ENSG00000089163	ENSG00000089163			14932	protein-coding gene	gene with protein product		604482	"sirtuin (silent mating type information regulation 2, S. cerevisiae, homolog) 4", "sirtuin (silent mating type information regulation 2 homolog) 4 (S. cerevisiae)"			10381378	Standard	NM_012240		Approved	SIR2L4	uc001tyc.3	Q9Y6E7	OTTHUMG00000169028	ENST00000202967.4:c.311G>T	chr12.hg19:g.120741675G>T	ENSP00000202967:p.Arg104Leu	109.0	0.0		51.0	3.0	NM_012240		Missense_Mutation	SNP	ENST00000202967.4	hg19	CCDS9194.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.359254	0.82353	.	.	ENSG00000089163	ENST00000536460;ENST00000202967	T;T	0.17054	2.3;2.3	5.39	2.58	0.30949	.	0.104417	0.64402	D	0.000007	T	0.36331	0.0963	M	0.72118	2.19	0.58432	D	0.999999	D	0.61080	0.989	D	0.67231	0.95	T	0.07501	-1.0769	10	0.87932	D	0	-21.6834	10.6708	0.45757	0.2078:0.0:0.7922:0.0	.	104	Q9Y6E7	SIRT4_HUMAN	L	45;104	ENSP00000444838:R45L;ENSP00000202967:R104L	ENSP00000202967:R104L	R	+	2	0	SIRT4	119226058	1.000000	0.71417	0.996000	0.52242	0.932000	0.56968	6.503000	0.73699	0.363000	0.24346	0.644000	0.83932	CGG	.	.		0.572	SIRT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402003.1	NM_012240		T	120741675	G	T	120741675	3	4	260	1	0	0	0	0	1	0	0	0	14355	1116	39	1	313	1	SIRT4	12	120741675	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	150627	120741675	13110220	570	37815										
ANAPC5	51433	hgsc.bcm.edu	37	chr12	121746389	121746389	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gggtcttccccagggtatggTagagtctggcctggaagtaa	15	8	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:121746389T>C	ENST00000261819.3	-	17	2283	c.2162A>G	c.(2161-2163)tAc>tGc	p.Y721C	ANAPC5_ENST00000535482.1_Missense_Mutation_p.Y387C|ANAPC5_ENST00000344395.4_Missense_Mutation_p.Y609C|ANAPC5_ENST00000441917.2_Missense_Mutation_p.Y609C|ANAPC5_ENST00000544314.1_5'UTR|ANAPC5_ENST00000541887.1_Missense_Mutation_p.Y708C	NM_016237.4	NP_057321.2	Q9UJX4	APC5_HUMAN	anaphase promoting complex subunit 5	721					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)			breast(6)|endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|prostate(1)|skin(3)	31	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CAGGGTATGGTAGAGTCTGGC	0.542																																					p.Y721C		Atlas-SNP	.											.	ANAPC5	60	.	0			c.A2162G						.						140	126	131					12																	121746389		2203	4300	6503	SO:0001583	missense	51433	exon17			GTATGGTAGAGTC	AF191339	CCDS9220.1, CCDS45000.1	12q24.31	2014-08-12			ENSG00000089053	ENSG00000089053		"Anaphase promoting complex subunits"	15713	protein-coding gene	gene with protein product		606948				9469815	Standard	NM_016237		Approved	APC5	uc001uag.3	Q9UJX4	OTTHUMG00000169157	ENST00000261819.3:c.2162A>G	chr12.hg19:g.121746389T>C	ENSP00000261819:p.Tyr721Cys	131.0	0.0		108.0	5.0	NM_016237	E9PFB2|Q8N4H7|Q9BQD4	Missense_Mutation	SNP	ENST00000261819.3	hg19	CCDS9220.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.956698	0.73902	.	.	ENSG00000089053	ENST00000441917;ENST00000541887;ENST00000261819;ENST00000535482;ENST00000544314;ENST00000344395	T;T;T;T;T	0.80214	-1.35;-1.35;-1.35;-1.35;-1.35	5.61	4.47	0.54385	Tetratricopeptide-like helical (1);	0.224065	0.47093	D	0.000251	D	0.83367	0.5239	L	0.53249	1.67	0.80722	D	1	D;D;D	0.69078	0.997;0.975;0.99	D;P;P	0.63192	0.912;0.498;0.707	T	0.82084	-0.0632	10	0.52906	T	0.07	.	6.5066	0.22198	0.1467:0.0772:0.0:0.7761	.	387;609;721	F5H0N1;E9PFB2;Q9UJX4	.;.;APC5_HUMAN	C	609;708;721;387;323;609	ENSP00000415061:Y609C;ENSP00000439875:Y708C;ENSP00000261819:Y721C;ENSP00000438754:Y387C;ENSP00000343787:Y609C	ENSP00000261819:Y721C	Y	-	2	0	ANAPC5	120230772	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.306000	0.59117	0.966000	0.38159	0.460000	0.39030	TAC	.	.		0.542	ANAPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402582.1			C	121746389	T	C	121746389	3	2	260	1	0	0	0	0	1	0	0	0	605	1638	57	2	109	2	ANAPC5	12	121746389	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1004714	121746389	12105506	571	37816										
KDM2B	84678	hgsc.bcm.edu	37	chr12	121868167	121868167	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acatctcggctatgaactgcTcacagccttccttggtgact	8	13	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:121868167T>C	ENST00000377071.4	-	23	4007	c.3935A>G	c.(3934-3936)gAg>gGg	p.E1312G	RNF34_ENST00000392464.2_Missense_Mutation_p.L465P|KDM2B_ENST00000377069.4_Missense_Mutation_p.E1243G|KDM2B_ENST00000536437.1_3'UTR|KDM2B_ENST00000542973.1_Missense_Mutation_p.E680G	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	1312					embryonic camera-type eye morphogenesis (GO:0048596)|forebrain development (GO:0030900)|fourth ventricle development (GO:0021592)|hindbrain development (GO:0030902)|histone demethylation (GO:0016577)|histone H2A monoubiquitination (GO:0035518)|initiation of neural tube closure (GO:0021993)|lateral ventricle development (GO:0021670)|midbrain development (GO:0030901)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K36 specific) (GO:0051864)|rRNA binding (GO:0019843)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	19						TATGAACTGCTCACAGCCTTC	0.443																																					p.E1312G		Atlas-SNP	.											.	KDM2B	218	.	0			c.A3935G						.						157	151	153					12																	121868167		1973	4164	6137	SO:0001583	missense	84678	exon23			AACTGCTCACAGC	AJ459424	CCDS41849.1, CCDS41850.1	12q24.31	2014-02-18	2009-04-06	2009-04-06	ENSG00000089094	ENSG00000089094		"F-boxes / Leucine-rich repeats", "Chromatin-modifying enzymes / K-demethylases"	13610	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 1B"	609078	"F-box and leucine-rich repeat protein 10"	FBXL10		10799292	Standard	NM_032590		Approved	PCCX2, CXXC2, Fbl10, JHDM1B	uc001uat.3	Q8NHM5	OTTHUMG00000169071	ENST00000377071.4:c.3935A>G	chr12.hg19:g.121868167T>C	ENSP00000366271:p.Glu1312Gly	149.0	0.0		102.0	5.0	NM_032590	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Missense_Mutation	SNP	ENST00000377071.4	hg19	CCDS41850.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	23.3|23.3	4.400707|4.400707	0.83120|0.83120	.|.	.|.	ENSG00000089094|ENSG00000170633	ENST00000397480;ENST00000542973;ENST00000377069;ENST00000377071;ENST00000540043|ENST00000392464	T;T;T|T	0.38560|0.39406	1.13;1.13;1.13|1.08	5.61|5.61	5.61|5.61	0.85477|0.85477	.|.	0.000000|.	0.52532|.	D|.	0.000061|.	T|T	0.58566|0.58566	0.2131|0.2131	M|M	0.70275|0.70275	2.135|2.135	0.80722|0.80722	D|D	1|1	P;P;D;P|.	0.67145|.	0.787;0.953;0.996;0.617|.	B;P;P;B|.	0.62740|.	0.379;0.631;0.906;0.153|.	T|T	0.58194|0.58194	-0.7679|-0.7679	10|6	0.46703|.	T|.	0.11|.	-28.6454|-28.6454	15.7959|15.7959	0.78409|0.78409	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	752;1312;1243;755|.	B7ZB05;Q8NHM5;A8MRS1;B4DSN4|.	.;KDM2B_HUMAN;.;.|.	G|P	1302;680;1243;1312;755|465	ENSP00000437821:E680G;ENSP00000366269:E1243G;ENSP00000366271:E1312G|ENSP00000376257:L465P	ENSP00000366269:E1243G|.	E|L	-|+	2|2	0|0	KDM2B|RNF34	120352550|120352550	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	7.991000|7.991000	0.88244|0.88244	2.134000|2.134000	0.65973|0.65973	0.533000|0.533000	0.62120|0.62120	GAG|CTC	.	.		0.443	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590		C	121868167	T	C	121868167	3	2	260	1	0	0	0	0	1	0	0	0	8134	1551	54	2	131	2	KDM2B	12	121868167	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	121778	121868167	11983728	572	37817										
ZNF664	144348	hgsc.bcm.edu	37	chr12	124497322	124497322	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtgggaaggccttcagtcagAgttcgagcctgtgcatccac	13	11	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:124497322A>G	ENST00000539644.1	+	6	2461	c.631A>G	c.(631-633)Agt>Ggt	p.S211G	ZNF664_ENST00000538932.2_Missense_Mutation_p.S211G|ZNF664_ENST00000337815.4_Missense_Mutation_p.S211G|ZNF664_ENST00000392404.3_Missense_Mutation_p.S211G|FAM101A_ENST00000545615.1_Intron			Q8N3J9	ZN664_HUMAN	zinc finger protein 664	211					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|large_intestine(5)|lung(6)|skin(1)	13	all_neural(191;0.101)|Medulloblastoma(191;0.163)			Epithelial(86;0.000239)|OV - Ovarian serous cystadenocarcinoma(86;0.000247)|all cancers(50;0.00155)|BRCA - Breast invasive adenocarcinoma(302;0.249)		CTTCAGTCAGAGTTCGAGCCT	0.522																																					p.S211G		Atlas-SNP	.											.	ZNF664	27	.	0			c.A631G						.						98	97	97					12																	124497322		2203	4300	6503	SO:0001583	missense	144348	exon5			AGTCAGAGTTCGA		CCDS9257.1	12q24.31	2013-05-10			ENSG00000179195	ENSG00000179195		"Zinc fingers, C2H2-type"	25406	protein-coding gene	gene with protein product			"zinc finger protein 176"	ZNF176		12477932	Standard	NM_001204298		Approved	ZFOC1, DKFZp761B128	uc001uga.3	Q8N3J9	OTTHUMG00000168596	ENST00000539644.1:c.631A>G	chr12.hg19:g.124497322A>G	ENSP00000441405:p.Ser211Gly	95.0	0.0		60.0	4.0	NM_152437	B3KP97|Q15914|Q3ZCQ7	Missense_Mutation	SNP	ENST00000539644.1	hg19	CCDS9257.1	.	.	.	.	.	.	.	.	.	.	A	13.18	2.159304	0.38119	.	.	ENSG00000179195	ENST00000539644;ENST00000392404;ENST00000538932;ENST00000337815;ENST00000535937	T;T;T;T	0.07688	3.17;3.17;3.17;3.17	4.25	4.25	0.50352	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.47852	D	0.000202	T	0.11067	0.0270	M	0.76328	2.33	0.27776	N	0.943303	B	0.33904	0.431	B	0.32289	0.143	T	0.10613	-1.0622	10	0.54805	T	0.06	-34.962	8.1013	0.30859	0.7949:0.2051:0.0:0.0	.	211	Q8N3J9	ZN664_HUMAN	G	211;211;211;211;149	ENSP00000441405:S211G;ENSP00000376205:S211G;ENSP00000440645:S211G;ENSP00000337320:S211G	ENSP00000337320:S211G	S	+	1	0	ZNF664	123063275	0.806000	0.28996	1.000000	0.80357	0.988000	0.76386	3.101000	0.50283	2.142000	0.66516	0.533000	0.62120	AGT	.	.		0.522	ZNF664-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400365.1	NM_152437		G	124497322	A	G	124497322	3	3	260	1	0	0	0	0	1	0	0	0	18087	304	11	2	633	2	ZNF664	12	124497322	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	2629155	124497322	9354573	573	37818										
TMEM132B	114795	hgsc.bcm.edu	37	chr12	126136985	126136985	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agtctcctcgctgacttttcAggtcctctcgccgttgtctg	9	14	4	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:126136985A>G	ENST00000299308.3	+	8	1907		c.e8-1		TMEM132B_ENST00000535886.1_Splice_Site	NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B							integral component of membrane (GO:0016021)				NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		CTGACTTTTCAGGTCCTCTCG	0.567																																					.		Atlas-SNP	.											.	TMEM132B	207	.	0			c.1900-2A>G						.						18	19	19					12																	126136985		2073	4211	6284	SO:0001630	splice_region_variant	114795	exon8			CTTTTCAGGTCCT	AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.1900-1A>G	chr12.hg19:g.126136985A>G		97.0	0.0		69.0	4.0	NM_052907	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Splice_Site	SNP	ENST00000299308.3	hg19	CCDS41859.1	.	.	.	.	.	.	.	.	.	.	A	13.19	2.161848	0.38217	.	.	ENSG00000139364	ENST00000299308;ENST00000535886	.	.	.	5.34	5.34	0.76211	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3203	0.74117	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TMEM132B	124702938	1.000000	0.71417	0.927000	0.36925	0.122000	0.20287	8.936000	0.92931	2.000000	0.58554	0.533000	0.62120	.	.	.		0.567	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907	Intron	G	126136985	A	G	126136985	5	3	260	1	0	0	0	0	0	0	1	0	16061	202	7	2	1928	2	TMEM132B	12	126136985	Splice_Site	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1639663	126136985	7714910	574	37819										
TMEM132D	121256	hgsc.bcm.edu	37	chr12	130184852	130184852	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttctccccggcgctgcggtcGtcccagtctctgcccatgat	10	17	2	1	rs139627769		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:130184852G>A	ENST00000422113.2	-	2	797	c.471C>T	c.(469-471)gaC>gaT	p.D157D	RP11-174M13.2_ENST00000544036.1_lincRNA	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	157					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)		p.D157D(2)		NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		CGCTGCGGTCGTCCCAGTCTC	0.627													g|||	1	0.000199681	0	0	5008	,	,		14894	0		0.001	False		,,,				2504	0				p.D157D		Atlas-SNP	.											TMEM132D,NS,carcinoma,0,2	TMEM132D	299	.	2	Substitution - coding silent(2)	endometrium(2)	c.C471T						.	A		0,4406		0,0,2203	26	27	27		471	-4.8	0	12	dbSNP_134	27	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TMEM132D	NM_133448.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		157/1100	130184852	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	121256	exon2			GCGGTCGTCCCAG	AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 153"	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.471C>T	chr12.hg19:g.130184852G>A		124.0	0.0		108.0	5.0	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Silent	SNP	ENST00000422113.2	hg19	CCDS9266.1																																																																																			.	G|1.000;A|0.000		0.627	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448		A	130184852	G	A	130184852	2	1	260	1	0	0	0	0	0	0	0	1	16062	1136	40	1		1	TMEM132D	12	130184852	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	4047867	130184852	3667043	575	37820										
P2RX2	22953	hgsc.bcm.edu	37	chr12	133197680	133197680	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	actccttccggaggcttgacCccaagcacgtgcctgcctcg	10	17	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr12:133197680C>T	ENST00000389110.3	+	8	905	c.868C>T	c.(868-870)Ccc>Tcc	p.P290S	P2RX2_ENST00000350048.5_Missense_Mutation_p.P266S|P2RX2_ENST00000449132.2_Missense_Mutation_p.P256S|P2RX2_ENST00000343948.4_Missense_Mutation_p.P290S|P2RX2_ENST00000352418.4_Missense_Mutation_p.P218S|P2RX2_ENST00000348800.5_Missense_Mutation_p.P290S|P2RX2_ENST00000351222.4_Missense_Mutation_p.P198S	NM_170682.2|NM_170683.2|NM_174873.1	NP_733782.1|NP_733783.1|NP_777362.1	Q9UBL9	P2RX2_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 2	290					behavioral response to pain (GO:0048266)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of hypoxic conditions in blood by carotid body chemoreceptor signaling (GO:0003029)|ion transmembrane transport (GO:0034220)|neuromuscular junction development (GO:0007528)|neuromuscular synaptic transmission (GO:0007274)|neuronal action potential (GO:0019228)|peristalsis (GO:0030432)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|response to ATP (GO:0033198)|response to carbohydrate (GO:0009743)|response to hypoxia (GO:0001666)|sensory perception of sound (GO:0007605)|sensory perception of taste (GO:0050909)|skeletal muscle fiber development (GO:0048741)|urinary bladder smooth muscle contraction (GO:0014832)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|dendritic spine (GO:0043197)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|cadmium ion binding (GO:0046870)|cobalt ion binding (GO:0050897)|copper ion binding (GO:0005507)|drug binding (GO:0008144)|extracellular ATP-gated cation channel activity (GO:0004931)|identical protein binding (GO:0042802)|ligand-gated ion channel activity (GO:0015276)|mercury ion binding (GO:0045340)|nickel cation binding (GO:0016151)|phosphatidylinositol binding (GO:0035091)|purinergic nucleotide receptor activity (GO:0001614)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|kidney(2)|large_intestine(2)|liver(2)|lung(8)|ovary(1)|prostate(3)	20	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0767)		OV - Ovarian serous cystadenocarcinoma(86;2.32e-08)|Epithelial(86;8.62e-08)|all cancers(50;4.5e-06)		GAGGCTTGACCCCAAGCACGT	0.602																																					p.P290S		Atlas-SNP	.											.	P2RX2	49	.	0			c.C868T						.						112	90	97					12																	133197680		2203	4300	6503	SO:0001583	missense	22953	exon8			CTTGACCCCAAGC	AF109387	CCDS31930.1, CCDS31931.1, CCDS31932.1, CCDS31933.1, CCDS31934.1, CCDS31935.1, CCDS61286.1, CCDS73548.1	12q24.33	2013-03-22			ENSG00000187848	ENSG00000187848		"Purinergic receptors", "Ligand-gated ion channels / Purinergic receptors, ionotropic"	15459	protein-coding gene	gene with protein product		600844	"deafness, autosomal dominant 41"	DFNA41		10570044, 7523952, 23345450	Standard	XM_005266154		Approved	P2X2	uc001ukk.1	Q9UBL9	OTTHUMG00000168018	ENST00000389110.3:c.868C>T	chr12.hg19:g.133197680C>T	ENSP00000373762:p.Pro290Ser	94.0	0.0		80.0	4.0	NM_170683	A6NGB4|A6NH93|A6NHC2|A6NHU3|A6NIG9|Q6V9R6|Q9NR37|Q9NR38|Q9UHD5|Q9UHD6|Q9UHD7|Q9Y637|Q9Y638	Missense_Mutation	SNP	ENST00000389110.3	hg19	CCDS31931.1	.	.	.	.	.	.	.	.	.	.	C	14.45	2.540520	0.45176	.	.	ENSG00000187848	ENST00000389110;ENST00000449132;ENST00000343948;ENST00000352418;ENST00000350048;ENST00000351222;ENST00000348800	T;T;T;T;T;T;T	0.03772	3.81;3.81;3.81;3.81;3.81;3.81;3.81	4.96	4.96	0.65561	.	0.247526	0.35805	N	0.002971	T	0.09555	0.0235	L	0.28014	0.82	0.36111	D	0.844809	D;P;D;D;P;D;D;D	0.63880	0.984;0.754;0.991;0.98;0.849;0.984;0.993;0.98	P;B;P;P;P;P;P;P	0.61940	0.794;0.395;0.894;0.791;0.48;0.833;0.896;0.69	T	0.43589	-0.9382	10	0.11794	T	0.64	-30.6685	16.1502	0.81611	0.0:1.0:0.0:0.0	.	290;256;198;218;266;290;290;290	Q32MC3;Q9UBL9-7;Q9UBL9-5;Q9UBL9-6;Q9UBL9-3;Q9UBL9-4;Q9UBL9;Q9UBL9-2	.;.;.;.;.;.;P2RX2_HUMAN;.	S	290;256;290;218;266;198;290	ENSP00000373762:P290S;ENSP00000405531:P256S;ENSP00000343339:P290S;ENSP00000341419:P218S;ENSP00000343904:P266S;ENSP00000344502:P198S;ENSP00000345095:P290S	ENSP00000343339:P290S	P	+	1	0	P2RX2	131707753	0.952000	0.32445	1.000000	0.80357	0.777000	0.43975	0.742000	0.26216	2.584000	0.87258	0.561000	0.74099	CCC	.	.		0.602	P2RX2-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397542.1			T	133197680	C	T	133197680	3	4	260	1	0	0	0	0	1	0	0	0	11349	623	22	3	898	3	P2RX2	12	133197680	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	3012828	133197680	654215	576	37821										
GJB6	10804	hgsc.bcm.edu	37	chr13	20797362	20797362	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	atggccaccagcagcgctggGgtggagacgaagatcagctg	16	10	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr13:20797362G>T	ENST00000356192.6	-	5	878	c.258C>A	c.(256-258)acC>acA	p.T86T	GJB6_ENST00000400065.3_Silent_p.T86T|GJB6_ENST00000400066.3_Silent_p.T86T|GJB6_ENST00000241124.6_Silent_p.T86T	NM_001110219.2	NP_001103689.1	O95452	CXB6_HUMAN	gap junction protein, beta 6, 30kDa	86					apoptotic process (GO:0006915)|cell communication (GO:0007154)|ear morphogenesis (GO:0042471)|inner ear development (GO:0048839)|negative regulation of cell proliferation (GO:0008285)|sensory perception of sound (GO:0007605)	apical plasma membrane (GO:0016324)|connexon complex (GO:0005922)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)				biliary_tract(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)	9		all_cancers(29;2.04e-22)|all_epithelial(30;1.19e-19)|all_lung(29;2.27e-18)|Lung SC(185;0.0257)|Ovarian(182;0.0822)		all cancers(112;2.17e-05)|Epithelial(112;0.00075)|OV - Ovarian serous cystadenocarcinoma(117;0.00978)|Lung(94;0.0238)|GBM - Glioblastoma multiforme(144;0.0323)|LUSC - Lung squamous cell carcinoma(192;0.0744)		GCAGCGCTGGGGTGGAGACGA	0.552																																					p.T86T		Atlas-SNP	.											.	GJB6	33	.	0			c.C258A						.						56	48	51					13																	20797362		2203	4300	6503	SO:0001819	synonymous_variant	10804	exon4			CGCTGGGGTGGAG	AJ005585	CCDS9291.1	13q12	2010-01-06	2007-11-06		ENSG00000121742	ENSG00000121742		"Ion channels / Gap junction proteins (connexins)"	4288	protein-coding gene	gene with protein product	"connexin 30"	604418	"ectodermal dysplasia 2, hidrotic (Clouston syndrome)", "gap junction protein, beta 6 (connexin 30)", "gap junction protein, beta 6"	DFNA3, ED2		10471490, 8845850	Standard	NM_006783		Approved	EDH, HED, CX30	uc001und.4	O95452	OTTHUMG00000016515	ENST00000356192.6:c.258C>A	chr13.hg19:g.20797362G>T		91.0	0.0		49.0	9.0	NM_001110220	B3KQN2|Q5Q1H9|Q5Q1I0|Q5Q1I1|Q5T5U0|Q8IUP0	Silent	SNP	ENST00000356192.6	hg19	CCDS9291.1																																																																																			.	.		0.552	GJB6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272906.1			T	20797362	G	T	20797362	2	4	260	1	0	0	0	0	0	0	0	1	6420	1219	43	3		3	GJB6	13	20797362	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10		20797362	94372516	577	37822										
XPO4	64328	hgsc.bcm.edu	37	chr13	21442736	21442736	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tttttaagtgaatacttaccCaaaatatgcttgcaaactgc	5	8	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr13:21442736C>T	ENST00000255305.6	-	2	245	c.174G>A	c.(172-174)ttG>ttA	p.L58L	XPO4_ENST00000490513.1_5'UTR|XPO4_ENST00000400602.2_Splice_Site_p.L58L			Q9C0E2	XPO4_HUMAN	exportin 4	58					positive regulation of protein export from nucleus (GO:0046827)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.L31L(1)		breast(1)|endometrium(10)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	41		all_cancers(29;5.05e-24)|all_epithelial(30;5.56e-20)|all_lung(29;2.38e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000521)|Epithelial(112;0.000892)|OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Lung(94;0.0189)|LUSC - Lung squamous cell carcinoma(192;0.0548)		AATACTTACCCAAAATATGCT	0.318																																					p.L58L		Atlas-SNP	.											XPO4_ENST00000255305,NS,carcinoma,0,2	XPO4	153	.	1	Substitution - coding silent(1)	lung(1)	c.G174A						.						118	108	111					13																	21442736		1831	4084	5915	SO:0001630	splice_region_variant	64328	exon2			CTTACCCAAAATA	AB051508	CCDS41872.1	13q11	2011-04-13			ENSG00000132953	ENSG00000132953		"Exportins"	17796	protein-coding gene	gene with protein product		611449				11214970, 10944119	Standard	NM_022459		Approved	FLJ13046, KIAA1721	uc001unq.4	Q9C0E2	OTTHUMG00000016528	ENST00000255305.6:c.175+1G>A	chr13.hg19:g.21442736C>T		146.0	0.0		100.0	4.0	NM_022459	Q5VUZ5|Q8N3V6|Q9H934	Silent	SNP	ENST00000255305.6	hg19	CCDS41872.1																																																																																			.	.		0.318	XPO4-001	KNOWN	non_canonical_conserved|non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044096.1	NM_022459	Silent	T	21442736	C	T	21442736	5	4	260	1	0	0	0	0	0	0	1	0	17461	608	21	3	3369	3	XPO4	13	21442736	Splice_Site	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	645374	21442736	93727142	578	37823										
SPATA13	221178	hgsc.bcm.edu	37	chr13	24797715	24797715	+	Intron	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggccgcatctgcctgctggaTgcgccccagaaccatgcgac	12	16	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr13:24797715T>A	ENST00000382095.4	+	2	185				SPATA13_ENST00000424834.2_Missense_Mutation_p.D216E|RP11-307N16.6_ENST00000382141.4_Missense_Mutation_p.D216E|SPATA13_ENST00000382108.3_Missense_Mutation_p.D216E	NM_153023.2	NP_694568.1	Q96N96	SPT13_HUMAN	spermatogenesis associated 13						cell migration (GO:0016477)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell migration (GO:0030334)	cytoplasm (GO:0005737)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			breast(4)|endometrium(2)|large_intestine(9)|lung(4)|ovary(1)|prostate(1)|skin(2)	23		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)		GCCTGCTGGATGCGCCCCAGA	0.652																																					p.D216E		Atlas-SNP	.											.	SPATA13	92	.	0			c.T648A						.						26	28	27					13																	24797715		692	1591	2283	SO:0001627	intron_variant	221178	exon2			GCTGGATGCGCCC	AK055770	CCDS9305.1, CCDS53857.1, CCDS66517.1, CCDS66518.1, CCDS73553.1	13q12.13	2013-01-10			ENSG00000182957	ENSG00000182957		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	23222	protein-coding gene	gene with protein product		613324					Standard	NM_001286795		Approved	FLJ31208, ARHGEF29	uc021rhg.1	Q96N96	OTTHUMG00000016578	ENST00000382095.4:c.-222-25900T>A	chr13.hg19:g.24797715T>A		49.0	0.0		35.0	4.0	NM_001166271	A2VEA9|A6NF85|B4DQB1|B4DSZ0|B4DVM8|J3KPJ7|J3KQH2|Q5VX68|Q6ZML1|Q8N873|Q8TEK6	Missense_Mutation	SNP	ENST00000382095.4	hg19	CCDS9305.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.65|16.65	3.182552|3.182552	0.57800|0.57800	.|.	.|.	ENSG00000182957|ENSG00000182957	ENST00000424834|ENST00000382108	.|D	.|0.86769	.|-2.17	3.49|3.49	-4.2|-4.2	0.03823|0.03823	.|.	.|0.000000	.|0.39544	.|U	.|0.001328	T|T	0.80059|0.80059	0.4554|0.4554	L|L	0.34521|0.34521	1.04|1.04	0.50039|0.50039	D|D	0.999849|0.999849	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.69401|0.69401	-0.5155|-0.5155	5|8	.|0.72032	.|D	.|0.01	.|.	5.5622|5.5622	0.17150|0.17150	0.0:0.4095:0.1369:0.4536|0.0:0.4095:0.1369:0.4536	.|.	.|.	.|.	.|.	S|E	254|216	.|ENSP00000371542:D216E	.|ENSP00000371542:D216E	C|D	+|+	1|3	0|2	SPATA13|SPATA13	23695715|23695715	0.328000|0.328000	0.24687|0.24687	0.000000|0.000000	0.03702|0.03702	0.096000|0.096000	0.18686|0.18686	-0.294000|-0.294000	0.08309|0.08309	-1.532000|-1.532000	0.01747|0.01747	-0.645000|-0.645000	0.03944|0.03944	TGC|GAT	.	.		0.652	SPATA13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044180.2	NM_153023		A	24797715	T	A	24797715	1	1	260	0	1	0	0	0	0	0	0	0	15015	1461	51	4		4	SPATA13	13	24797715	Intron	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	3354979	24797715	90372163	579	37824										
SPATA13	221178	hgsc.bcm.edu	37	chr13	24798393	24798393	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtccaggatgtgttgagcaaAgactcctgtgacccaaacgc	11	11	0	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr13:24798393A>G	ENST00000382095.4	+	2	185				SPATA13_ENST00000474317.1_3'UTR|SPATA13_ENST00000424834.2_Silent_p.K442K|RP11-307N16.6_ENST00000382141.4_Silent_p.K442K|SPATA13_ENST00000382108.3_Silent_p.K442K	NM_153023.2	NP_694568.1	Q96N96	SPT13_HUMAN	spermatogenesis associated 13						cell migration (GO:0016477)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell migration (GO:0030334)	cytoplasm (GO:0005737)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			breast(4)|endometrium(2)|large_intestine(9)|lung(4)|ovary(1)|prostate(1)|skin(2)	23		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)		TGTTGAGCAAAGACTCCTGTG	0.557																																					p.K442K		Atlas-SNP	.											.	SPATA13	92	.	0			c.A1326G						.						52	58	56					13																	24798393		692	1591	2283	SO:0001627	intron_variant	221178	exon2			GAGCAAAGACTCC	AK055770	CCDS9305.1, CCDS53857.1, CCDS66517.1, CCDS66518.1, CCDS73553.1	13q12.13	2013-01-10			ENSG00000182957	ENSG00000182957		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	23222	protein-coding gene	gene with protein product		613324					Standard	NM_001286795		Approved	FLJ31208, ARHGEF29	uc021rhg.1	Q96N96	OTTHUMG00000016578	ENST00000382095.4:c.-222-25222A>G	chr13.hg19:g.24798393A>G		181.0	0.0		96.0	4.0	NM_001166271	A2VEA9|A6NF85|B4DQB1|B4DSZ0|B4DVM8|J3KPJ7|J3KQH2|Q5VX68|Q6ZML1|Q8N873|Q8TEK6	Silent	SNP	ENST00000382095.4	hg19	CCDS9305.1	.	.	.	.	.	.	.	.	.	.	A	5.476	0.272879	0.10349	.	.	ENSG00000182957	ENST00000424834	.	.	.	4.96	-2.0	0.07433	.	.	.	.	.	T	0.29256	0.0728	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.31166	-0.9953	4	.	.	.	.	7.2172	0.25967	0.4256:0.0:0.4519:0.1225	.	.	.	.	G	480	.	.	R	+	1	2	SPATA13	23696393	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.318000	0.08050	-0.635000	0.05531	-0.361000	0.07541	AGA	.	.		0.557	SPATA13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044180.2	NM_153023		G	24798393	A	G	24798393	1	3	260	0	1	0	0	0	0	0	0	0	15015	69	3	2		2	SPATA13	13	24798393	Intron	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	678	24798393	90371485	580	37825										
RNF17	56163	hgsc.bcm.edu	37	chr13	25442834	25442834	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tctatgctgttcaagttaagCacgttgtctcacctaatgaa	7	9	3	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr13:25442834C>T	ENST00000255324.5	+	31	4310	c.4258C>T	c.(4258-4260)Cac>Tac	p.H1420Y	RNF17_ENST00000339524.3_Missense_Mutation_p.H430Y|RNF17_ENST00000381921.1_Missense_Mutation_p.H1378Y	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	1420					multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(3)|skin(6)	36		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)		TCAAGTTAAGCACGTTGTCTC	0.388																																					p.H1420Y		Atlas-SNP	.											.	RNF17	259	.	0			c.C4258T						.						178	162	168					13																	25442834		2203	4300	6503	SO:0001583	missense	56163	exon31			GTTAAGCACGTTG	AF285602, AK001907	CCDS9308.2	13q12.13	2013-01-23			ENSG00000132972	ENSG00000132972		"RING-type (C3HC4) zinc fingers", "Tudor domain containing"	10060	protein-coding gene	gene with protein product	"spermatogenesis associated 23"	605793	"tudor domain containing 4"	TDRD4		11279525	Standard	NM_001184993		Approved	Mmip-2, SPATA23, FLJ11045	uc001upr.3	Q9BXT8	OTTHUMG00000016589	ENST00000255324.5:c.4258C>T	chr13.hg19:g.25442834C>T	ENSP00000255324:p.His1420Tyr	185.0	0.0		125.0	5.0	NM_031277	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Missense_Mutation	SNP	ENST00000255324.5	hg19	CCDS9308.2	.	.	.	.	.	.	.	.	.	.	C	16.46	3.130255	0.56721	.	.	ENSG00000132972	ENST00000255324;ENST00000381921;ENST00000418120;ENST00000339524	T;T;T;T	0.26223	3.11;2.67;1.87;1.75	5.93	5.93	0.95920	.	0.072543	0.53938	D	0.000042	T	0.41743	0.1172	L	0.46947	1.48	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.998;0.999;0.997;1.0	T	0.07927	-1.0747	10	0.02654	T	1	-11.9309	19.1254	0.93380	0.0:1.0:0.0:0.0	.	1416;430;1414;1420	B7Z7S1;Q5T6R1;Q9BXT8-5;Q9BXT8	.;.;.;RNF17_HUMAN	Y	1420;1378;744;430	ENSP00000255324:H1420Y;ENSP00000371346:H1378Y;ENSP00000388892:H744Y;ENSP00000344776:H430Y	ENSP00000255324:H1420Y	H	+	1	0	RNF17	24340834	1.000000	0.71417	0.722000	0.30670	0.065000	0.16274	5.495000	0.66912	2.826000	0.97356	0.655000	0.94253	CAC	.	.		0.388	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994		T	25442834	C	T	25442834	3	4	260	1	0	0	0	0	1	0	0	0	13476	710	25	3	4380	3	RNF17	13	25442834	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	644441	25442834	89727044	581	37826										
ATP8A2	51761	hgsc.bcm.edu	37	chr13	26273338	26273338	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gggcagccattactcagcacTgcactgaccttgggaatttg	11	11	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr13:26273338T>C	ENST00000381655.2	+	25	2381	c.2239T>C	c.(2239-2241)Tgc>Cgc	p.C747R	ATP8A2_ENST00000255283.8_Missense_Mutation_p.C707R|ATP8A2_ENST00000491840.1_3'UTR	NM_016529.4	NP_057613.4	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8A, member 2	707					aging (GO:0007568)|axonogenesis (GO:0007409)|detection of light stimulus involved in visual perception (GO:0050908)|eating behavior (GO:0042755)|inner ear morphogenesis (GO:0042472)|involuntary skeletal muscle contraction (GO:0003011)|negative regulation of cell proliferation (GO:0008285)|neurofilament cytoskeleton organization (GO:0060052)|neuromuscular process controlling posture (GO:0050884)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phospholipid translocation (GO:0061092)|response to auditory stimulus (GO:0010996)|retina layer formation (GO:0010842)|skin development (GO:0043588)	cell projection (GO:0042995)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.C747S(1)		breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(17)|lung(31)|ovary(4)|skin(3)|stomach(1)|urinary_tract(1)	72		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		TACTCAGCACTGCACTGACCT	0.453																																					p.C747R		Atlas-SNP	.											ATP8A2,bladder,carcinoma,0,1	ATP8A2	181	.	1	Substitution - Missense(1)	urinary_tract(1)	c.T2239C						.						83	78	80					13																	26273338		1964	4136	6100	SO:0001583	missense	51761	exon25			CAGCACTGCACTG	AL137256	CCDS41873.1	13q12	2010-04-20	2010-03-31		ENSG00000132932	ENSG00000132932	3.6.3.1	"ATPases / P-type"	13533	protein-coding gene	gene with protein product		605870	"ATPase, aminophospholipid transporter-like, Class I, type 8A, member 2", "ATPase, aminophospholipid transporter-like, class I, type 8A, member 2"			11015572, 19778899	Standard	NM_016529		Approved	ATPIB, ML-1	uc001uqk.3	Q9NTI2	OTTHUMG00000016611	ENST00000381655.2:c.2239T>C	chr13.hg19:g.26273338T>C	ENSP00000371070:p.Cys747Arg	98.0	0.0		43.0	2.0	NM_016529	Q9H527|Q9NPU6|Q9NTL2|Q9NYM3	Missense_Mutation	SNP	ENST00000381655.2	hg19	CCDS41873.1	.	.	.	.	.	.	.	.	.	.	T	15.29	2.790683	0.50102	.	.	ENSG00000132932	ENST00000381655;ENST00000255283;ENST00000544544	T;T	0.63096	0.41;-0.02	5.88	5.88	0.94601	HAD-like domain (1);	0.000000	0.85682	D	0.000000	T	0.57651	0.2068	L	0.38733	1.17	0.80722	D	1	B;B;B	0.25206	0.12;0.049;0.12	B;B;B	0.31245	0.126;0.082;0.126	T	0.56251	-0.8010	10	0.52906	T	0.07	.	16.2824	0.82697	0.0:0.0:0.0:1.0	.	707;527;707	B7Z880;F5GZN5;Q9NTI2	.;.;AT8A2_HUMAN	R	747;707;527	ENSP00000371070:C747R;ENSP00000255283:C707R	ENSP00000255283:C707R	C	+	1	0	ATP8A2	25171338	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	8.035000	0.88872	2.250000	0.74265	0.533000	0.62120	TGC	.	.		0.453	ATP8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044236.2	NM_016529		C	26273338	T	C	26273338	3	2	260	1	0	0	0	0	1	0	0	0	1193	1580	55	2	2337	2	ATP8A2	13	26273338	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	830504	26273338	88896540	582	37827										
USPL1	10208	hgsc.bcm.edu	37	chr13	31232538	31232538	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttcttttatgccactctgtgTttcagctcataatagaaaca	5	9	4	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr13:31232538T>C	ENST00000255304.4	+	9	2666	c.2324T>C	c.(2323-2325)gTt>gCt	p.V775A		NM_005800.4	NP_005791.3	Q5W0Q7	USPL1_HUMAN	ubiquitin specific peptidase like 1	775					Cajal body organization (GO:0030576)|cell proliferation (GO:0008283)|protein desumoylation (GO:0016926)	Cajal body (GO:0015030)|extracellular space (GO:0005615)	SUMO binding (GO:0032183)|SUMO-specific isopeptidase activity (GO:0070140)			breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(15)|pancreas(3)|skin(3)	34		Lung SC(185;0.0257)|Breast(139;0.203)		all cancers(112;0.0306)|Epithelial(112;0.131)|OV - Ovarian serous cystadenocarcinoma(117;0.134)		CCACTCTGTGTTTCAGCTCAT	0.368																																					p.V775A	Ovarian(60;318 1180 1554 28110 31601)	Atlas-SNP	.											.	USPL1	82	.	0			c.T2324C						.						82	88	86					13																	31232538		2203	4300	6503	SO:0001583	missense	10208	exon9			TCTGTGTTTCAGC	X59131	CCDS9336.1	13q12-q14	2012-11-14	2005-11-24	2005-11-24	ENSG00000132952	ENSG00000132952			20294	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 22"	C13orf22		22878415	Standard	NM_005800		Approved	bA121O19.1, D13S106E	uc001utc.2	Q5W0Q7	OTTHUMG00000016675	ENST00000255304.4:c.2324T>C	chr13.hg19:g.31232538T>C	ENSP00000255304:p.Val775Ala	123.0	0.0		83.0	5.0	NM_005800	Q14109|Q6AI45|Q8IY30|Q8IYE8	Missense_Mutation	SNP	ENST00000255304.4	hg19	CCDS9336.1	.	.	.	.	.	.	.	.	.	.	T	2.735	-0.263449	0.05754	.	.	ENSG00000132952	ENST00000255304	T	0.16073	2.37	5.76	4.62	0.57501	.	0.212421	0.39615	N	0.001313	T	0.11196	0.0273	L	0.38838	1.175	0.29185	N	0.876263	B	0.30563	0.285	B	0.35470	0.203	T	0.24154	-1.0168	10	0.06099	T	0.92	-24.8906	5.3667	0.16117	0.0:0.1944:0.0:0.8056	.	775	Q5W0Q7	USPL1_HUMAN	A	775	ENSP00000255304:V775A	ENSP00000255304:V775A	V	+	2	0	USPL1	30130538	1.000000	0.71417	0.995000	0.50966	0.424000	0.31475	2.390000	0.44416	2.201000	0.70794	0.533000	0.62120	GTT	.	.		0.368	USPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044369.1	NM_005800		C	31232538	T	C	31232538	3	2	260	1	0	0	0	0	1	0	0	0	17107	1725	60	2	2354	2	USPL1	13	31232538	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	4959200	31232538	83937340	583	37828										
STARD13	90627	hgsc.bcm.edu	37	chr13	33700281	33700281	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	atactttgaggcaggggctgTcccgttctttggacgtggac	14	9	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr13:33700281T>C	ENST00000336934.5	-	7	2135	c.2019A>G	c.(2017-2019)ggA>ggG	p.G673G	STARD13_ENST00000399365.3_Silent_p.G555G|STARD13_ENST00000255486.4_Silent_p.G665G	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	673	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	40	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		GCAGGGGCTGTCCCGTTCTTT	0.537																																					p.G673G		Atlas-SNP	.											.	STARD13	100	.	0			c.A2019G						.						174	148	157					13																	33700281		2203	4300	6503	SO:0001819	synonymous_variant	90627	exon7			GGGCTGTCCCGTT	AL049801	CCDS9348.1, CCDS9349.1, CCDS9350.1	13q13.1	2013-08-13	2007-08-16		ENSG00000133121	ENSG00000133121		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	19164	protein-coding gene	gene with protein product		609866	"START domain containing 13", "long intergenic non-protein coding RNA 464"	LINC00464		8812419	Standard	NM_178006		Approved	GT650, DLC2, ARHGAP37	uc001uuw.3	Q9Y3M8	OTTHUMG00000016708	ENST00000336934.5:c.2019A>G	chr13.hg19:g.33700281T>C		182.0	0.0		96.0	5.0	NM_178006	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Silent	SNP	ENST00000336934.5	hg19	CCDS9348.1																																																																																			.	.		0.537	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2	NM_001243466		C	33700281	T	C	33700281	2	2	260	1	0	0	0	0	0	0	0	1	15271	1654	58	2		2	STARD13	13	33700281	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	2467743	33700281	81469597	584	37829										
NBEA	26960	hgsc.bcm.edu	37	chr13	36046571	36046571	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agcacccctgcccagctcatCgctcccgtggtggtggccaa	11	17	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr13:36046571C>A	ENST00000400445.3	+	41	7017	c.6483C>A	c.(6481-6483)atC>atA	p.I2161I	NBEA_ENST00000540320.1_Silent_p.I2161I|NBEA_ENST00000379939.2_Silent_p.I2158I|NBEA_ENST00000310336.4_Silent_p.I2161I	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	2161					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		CCCAGCTCATCGCTCCCGTGG	0.587																																					p.I2161I		Atlas-SNP	.											NBEA,lower_third,carcinoma,0,1	NBEA	340	.	0			c.C6483A						.						64	67	66					13																	36046571		1985	4166	6151	SO:0001819	synonymous_variant	26960	exon41			GCTCATCGCTCCC	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.6483C>A	chr13.hg19:g.36046571C>A		51.0	0.0		40.0	2.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Silent	SNP	ENST00000400445.3	hg19	CCDS45026.1																																																																																			.	.		0.587	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		A	36046571	C	A	36046571	2	1	260	1	0	0	0	0	0	0	0	1	10196	874	31	1		1	NBEA	13	36046571	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	2346290	36046571	79123307	585	37830										
DGKH	160851	hgsc.bcm.edu	37	chr13	42793388	42793388	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gctggaatcgccacatgaagAgcgagtatccaatgccttac	10	11	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr13:42793388A>G	ENST00000337343.4	+	27	3257	c.3236A>G	c.(3235-3237)gAg>gGg	p.E1079G	DGKH_ENST00000498255.2_3'UTR|DGKH_ENST00000538674.1_Missense_Mutation_p.E834G|DGKH_ENST00000261491.5_Missense_Mutation_p.E1079G|DGKH_ENST00000379274.2_Missense_Mutation_p.E943G|DGKH_ENST00000536612.1_Missense_Mutation_p.E943G|DGKH_ENST00000540693.1_Missense_Mutation_p.E1079G	NM_178009.3	NP_821077.1	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta	1079					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(2)|endometrium(3)|kidney(5)|large_intestine(11)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		CCACATGAAGAGCGAGTATCC	0.408																																					p.E1079G		Atlas-SNP	.											.	DGKH	106	.	0			c.A3236G						.						167	175	172					13																	42793388		2203	4300	6503	SO:0001583	missense	160851	exon28			ATGAAGAGCGAGT	AB078967	CCDS9381.1, CCDS9382.1, CCDS55898.1	13q13.3	2013-01-10			ENSG00000102780	ENSG00000102780		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	2854	protein-coding gene	gene with protein product		604071				8702685	Standard	XM_005266271		Approved	DGKeta	uc001uyl.2	Q86XP1	OTTHUMG00000016804	ENST00000337343.4:c.3236A>G	chr13.hg19:g.42793388A>G	ENSP00000337572:p.Glu1079Gly	130.0	0.0		80.0	4.0	NM_001204504	A2A2W7|A6NFX7|B4DZ34|Q5VZW0|Q6PI56|Q86XP2|Q8N3N0|Q8N7J9	Missense_Mutation	SNP	ENST00000337343.4	hg19	CCDS9381.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.172514	0.78452	.	.	ENSG00000102780	ENST00000540693;ENST00000337343;ENST00000261491;ENST00000379274;ENST00000536612;ENST00000538674	D;T;D;D;D;T	0.82619	-1.63;-1.38;-1.63;-1.54;-1.54;1.6	5.29	5.29	0.74685	.	0.101059	0.64402	D	0.000003	T	0.81819	0.4903	M	0.69185	2.1	0.54753	D	0.999987	B;B;B;P	0.37233	0.317;0.317;0.046;0.588	B;B;B;B	0.35607	0.177;0.086;0.087;0.206	D	0.83560	0.0106	10	0.59425	D	0.04	.	15.223	0.73327	1.0:0.0:0.0:0.0	.	834;943;1079;1079	F5GYP2;Q86XP1-3;Q86XP1-2;Q86XP1	.;.;.;DGKH_HUMAN	G	1079;1079;1079;943;943;834	ENSP00000440823:E1079G;ENSP00000337572:E1079G;ENSP00000261491:E1079G;ENSP00000368576:E943G;ENSP00000445114:E943G;ENSP00000441308:E834G	ENSP00000261491:E1079G	E	+	2	0	DGKH	41691388	1.000000	0.71417	1.000000	0.80357	0.727000	0.41649	8.614000	0.90917	1.986000	0.57962	0.528000	0.53228	GAG	.	.		0.408	DGKH-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044699.2	NM_178009		G	42793388	A	G	42793388	3	3	260	1	0	0	0	0	1	0	0	0	4472	304	11	2	3342	2	DGKH	13	42793388	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	6746817	42793388	72376490	586	37831										
AKAP11	11215	hgsc.bcm.edu	37	chr13	42891711	42891711	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	taattacgaatattgacatgGagccatgcacggtagacccc	9	10	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr13:42891711G>T	ENST00000025301.2	+	12	5627	c.5452G>T	c.(5452-5454)Gag>Tag	p.E1818*		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	1818					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2)	56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		TATTGACATGGAGCCATGCAC	0.373																																					p.E1818X		Atlas-SNP	.											.	AKAP11	146	.	0			c.G5452T						.						131	119	123					13																	42891711		2203	4300	6503	SO:0001587	stop_gained	11215	exon12			GACATGGAGCCAT	AB014529	CCDS9383.1	13q	2012-04-17			ENSG00000023516	ENSG00000023516		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	369	protein-coding gene	gene with protein product	"AKAP 220", "A-kinase anchoring protein, 220kDa", "protein kinase A anchoring protein 11", "protein phosphatase 1, regulatory subunit 44"	604696				9734811, 8621616	Standard	NM_016248		Approved	KIAA0629, AKAP220, PRKA11, FLJ11304, DKFZp781I12161, PPP1R44	uc001uys.2	Q9UKA4	OTTHUMG00000016805	ENST00000025301.2:c.5452G>T	chr13.hg19:g.42891711G>T	ENSP00000025301:p.Glu1818*	153.0	0.0		85.0	4.0	NM_016248	O75124|Q9NUK7	Nonsense_Mutation	SNP	ENST00000025301.2	hg19	CCDS9383.1	.	.	.	.	.	.	.	.	.	.	G	46	12.221437	0.99647	.	.	ENSG00000023516	ENST00000025301	.	.	.	5.79	4.77	0.60923	.	0.456574	0.21608	N	0.071827	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	15.7494	0.77972	0.076:0.0:0.924:0.0	.	.	.	.	X	1818	.	ENSP00000025301:E1818X	E	+	1	0	AKAP11	41789711	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.404000	0.52623	2.725000	0.93324	0.557000	0.71058	GAG	.	.		0.373	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248		T	42891711	G	T	42891711	4	4	260	1	0	0	0	0	0	1	0	0	447	1175	41	3	5490	3	AKAP11	13	42891711	Nonsense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	98323	42891711	72278167	587	37832										
KIAA1704	55425	hgsc.bcm.edu	37	chr13	45589705	45589705	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gatcaatctggacagatactCcagctgatagggaaaggaaa	11	7	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr13:45589705C>T	ENST00000379151.4	+	6	782	c.679C>T	c.(679-681)Cca>Tca	p.P227S	RP11-321C24.1_ENST00000437748.2_lincRNA|GPALPP1_ENST00000361121.2_Missense_Mutation_p.P227S|GPALPP1_ENST00000357537.3_Missense_Mutation_p.P57S	NM_018559.2	NP_061029.2	Q8IXQ4	GPAM1_HUMAN	GPALPP motifs containing 1	227																	GACAGATACTCCAGCTGATAG	0.393																																					p.P227S		Atlas-SNP	.											.	KIAA1704	36	.	0			c.C679T						.						103	98	100					13																	45589705		2203	4300	6503	SO:0001583	missense	55425	exon6			GATACTCCAGCTG	AB051491	CCDS9394.1	13q14.12	2013-08-13	2013-08-12	2013-08-12	ENSG00000133114	ENSG00000133114			20298	protein-coding gene	gene with protein product			"KIAA1704"	KIAA1704		11214970	Standard	NM_018559		Approved	bA245H20.2, AD029, LSR7	uc001uzq.3	Q8IXQ4	OTTHUMG00000016841	ENST00000379151.4:c.679C>T	chr13.hg19:g.45589705C>T	ENSP00000368447:p.Pro227Ser	136.0	0.0		98.0	4.0	NM_018559	A8K8X8|Q05BX8|Q05D87|Q5T3Z3|Q5T3Z5|Q9C0F9|Q9H2R0|Q9P0W6	Missense_Mutation	SNP	ENST00000379151.4	hg19	CCDS9394.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.901295	0.92035	.	.	ENSG00000133114	ENST00000379151;ENST00000361121;ENST00000357537	.	.	.	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	D	0.84889	0.5572	M	0.87180	2.865	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.86599	0.1865	9	0.72032	D	0.01	1.6417	18.9896	0.92786	0.0:1.0:0.0:0.0	.	78;227	Q8IXQ4-2;Q8IXQ4	.;K1704_HUMAN	S	227;227;57	.	ENSP00000350145:P57S	P	+	1	0	KIAA1704	44487705	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	7.192000	0.77771	2.793000	0.96121	0.655000	0.94253	CCA	.	.		0.393	GPALPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044749.2	NM_018559		T	45589705	C	T	45589705	3	4	260	1	0	0	0	0	1	0	0	0	8261	855	30	3	701	3	KIAA1704	13	45589705	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	2697994	45589705	69580173	588	37833										
FAM124A	220108	hgsc.bcm.edu	37	chr13	51825706	51825706	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gcaggaggccatcgacaacgTcctggcgtggatccaccccg	13	15	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr13:51825706T>C	ENST00000322475.8	+	3	338	c.203T>C	c.(202-204)gTc>gCc	p.V68A	FAM124A_ENST00000280057.6_Missense_Mutation_p.V104A	NM_001242312.1	NP_001229241.1	Q86V42	F124A_HUMAN	family with sequence similarity 124A	68										breast(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|skin(1)	26		Acute lymphoblastic leukemia(7;0.000334)|Breast(56;0.00156)|Prostate(109;0.00538)|Lung NSC(96;0.0216)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;4.25e-07)		ATCGACAACGTCCTGGCGTGG	0.687																																					p.V104A		Atlas-SNP	.											.	FAM124A	61	.	0			c.T311C						.						26	23	24					13																	51825706		2203	4300	6503	SO:0001583	missense	220108	exon4			ACAACGTCCTGGC	AK096364	CCDS9427.1, CCDS55900.1	13q14.3	2006-08-11			ENSG00000150510	ENSG00000150510			26413	protein-coding gene	gene with protein product						12975309	Standard	NM_145019		Approved	FLJ30707	uc001vff.2	Q86V42	OTTHUMG00000016942	ENST00000322475.8:c.203T>C	chr13.hg19:g.51825706T>C	ENSP00000324625:p.Val68Ala	124.0	0.0		84.0	4.0	NM_145019	A2A324|Q8N8P9|Q8NE66|Q96NJ9	Missense_Mutation	SNP	ENST00000322475.8	hg19	CCDS55900.1	.	.	.	.	.	.	.	.	.	.	T	29.3	4.997865	0.93227	.	.	ENSG00000150510	ENST00000322475;ENST00000280057	T;T	0.47869	0.83;0.83	5.79	5.79	0.91817	.	0.149802	0.45126	D	0.000390	T	0.62551	0.2437	L	0.59436	1.845	0.45087	D	0.998101	D;D;P	0.63880	0.993;0.993;0.571	P;P;B	0.60789	0.826;0.879;0.288	T	0.65450	-0.6165	10	0.72032	D	0.01	-21.3215	15.3036	0.73976	0.0:0.0:0.0:1.0	.	68;104;68	Q86V42;Q86V42-2;Q86V42-3	F124A_HUMAN;.;.	A	68;104	ENSP00000324625:V68A;ENSP00000280057:V104A	ENSP00000280057:V104A	V	+	2	0	FAM124A	50723707	1.000000	0.71417	0.936000	0.37596	0.981000	0.71138	7.466000	0.80914	2.208000	0.71279	0.533000	0.62120	GTC	.	.		0.687	FAM124A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045019.3	NM_145019		C	51825706	T	C	51825706	3	2	260	1	0	0	0	0	1	0	0	0	5430	1667	58	2	325	2	FAM124A	13	51825706	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	6236001	51825706	63344172	589	37834										
PCDH17	27253	hgsc.bcm.edu	37	chr13	58209048	58209048	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgaacgtggtgagcagccccTccctggccacctcccccatg	10	18	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr13:58209048T>C	ENST00000377918.3	+	1	2394	c.2368T>C	c.(2368-2370)Tcc>Ccc	p.S790P		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	790					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(30)|liver(2)|lung(54)|ovary(4)|pancreas(2)|prostate(5)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		GAGCAGCCCCTCCCTGGCCAC	0.572																																					p.S790P	Melanoma(72;952 1291 1619 12849 33676)	Atlas-SNP	.											.	PCDH17	304	.	0			c.T2368C						.						88	83	85					13																	58209048		2203	4300	6503	SO:0001583	missense	27253	exon1			AGCCCCTCCCTGG	AF029343	CCDS31986.1	13q21.1	2010-01-26			ENSG00000118946	ENSG00000118946		"Cadherins / Protocadherins : Non-clustered"	14267	protein-coding gene	gene with protein product		611760				10835267	Standard	NM_001040429		Approved	PCDH68, PCH68	uc001vhq.1	O14917	OTTHUMG00000016992	ENST00000377918.3:c.2368T>C	chr13.hg19:g.58209048T>C	ENSP00000367151:p.Ser790Pro	108.0	0.0		67.0	7.0	NM_001040429	A8K1R5|Q5VVW9|Q5VVX0	Missense_Mutation	SNP	ENST00000377918.3	hg19	CCDS31986.1	.	.	.	.	.	.	.	.	.	.	T	17.81	3.480352	0.63849	.	.	ENSG00000118946	ENST00000377918	T	0.55052	0.54	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.66208	0.2766	L	0.52573	1.65	0.58432	D	0.999999	D;D	0.71674	0.992;0.998	D;D	0.69142	0.962;0.942	T	0.64841	-0.6312	9	.	.	.	.	15.8379	0.78814	0.0:0.0:0.0:1.0	.	790;790	O14917-2;O14917	.;PCD17_HUMAN	P	790	ENSP00000367151:S790P	.	S	+	1	0	PCDH17	57107049	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.698000	0.84413	2.141000	0.66446	0.383000	0.25322	TCC	.	.		0.572	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429		C	58209048	T	C	58209048	3	2	260	1	0	0	0	0	1	0	0	0	11521	1551	54	2	2370	2	PCDH17	13	58209048	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	6383342	58209048	56960830	590	37835										
MYCBP2	23077	hgsc.bcm.edu	37	chr13	77672359	77672359	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctctcatttcctgttcatctTtcagtggtgcttttccaatg	6	11	4	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr13:77672359T>C	ENST00000544440.2	-	56	8833	c.8816A>G	c.(8815-8817)aAa>aGa	p.K2939R	MYCBP2_ENST00000407578.2_Missense_Mutation_p.K2977R|MYCBP2_ENST00000482517.1_5'UTR|MYCBP2-AS1_ENST00000593933.1_RNA|MYCBP2_ENST00000360084.5_Missense_Mutation_p.K462R|MYCBP2_ENST00000357337.6_Missense_Mutation_p.K2939R					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		CTGTTCATCTTTCAGTGGTGC	0.378																																					p.K2977R		Atlas-SNP	.											.	MYCBP2	1029	.	0			c.A8930G						.						148	143	145					13																	77672359		2203	4300	6503	SO:0001583	missense	23077	exon56			TCATCTTTCAGTG	AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"MYC binding protein 2"			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.8816A>G	chr13.hg19:g.77672359T>C	ENSP00000444596:p.Lys2939Arg	188.0	0.0		96.0	4.0	NM_015057		Missense_Mutation	SNP	ENST00000544440.2	hg19		.	.	.	.	.	.	.	.	.	.	T	9.716	1.158446	0.21454	.	.	ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440;ENST00000360084	T;T;T;T	0.53640	1.47;1.46;1.47;0.61	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.37999	0.1024	L	0.41710	1.295	0.49213	D	0.999762	B;B;B	0.14805	0.011;0.0;0.001	B;B;B	0.17722	0.019;0.001;0.001	T	0.18618	-1.0331	10	0.26408	T	0.33	.	10.8639	0.46842	0.0:0.0733:0.0:0.9267	.	325;2939;2939	Q9UG08;O75592-2;O75592	.;.;MYCB2_HUMAN	R	2939;2977;2939;462	ENSP00000349892:K2939R;ENSP00000384288:K2977R;ENSP00000444596:K2939R;ENSP00000353197:K462R	ENSP00000349892:K2939R	K	-	2	0	MYCBP2	76570360	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.968000	0.70413	2.117000	0.64856	0.477000	0.44152	AAA	.	.		0.378	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057		C	77672359	T	C	77672359	3	2	260	1	0	0	0	0	1	0	0	0	10027	1841	64	2	5218	2	MYCBP2	13	77672359	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	19463311	77672359	37497519	591	37836										
SPRY2	10253	hgsc.bcm.edu	37	chr13	80911489	80911489	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgtcctcgtactgctccgcgAccctgagctgaccgtgctta	10	15	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr13:80911489A>G	ENST00000377102.1	-	2	1329	c.352T>C	c.(352-354)Tcg>Ccg	p.S118P	SPRY2_ENST00000540649.1_Missense_Mutation_p.S118P|SPRY2_ENST00000377104.3_Missense_Mutation_p.S118P			O43597	SPY2_HUMAN	sprouty homolog 2 (Drosophila)	118					bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment of mitotic spindle orientation (GO:0000132)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inner ear morphogenesis (GO:0042472)|lung growth (GO:0060437)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of Ras GTPase activity (GO:0034261)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|sensory perception of sound (GO:0007605)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase inhibitor activity (GO:0030291)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)	12	Medulloblastoma(90;0.18)	Acute lymphoblastic leukemia(28;0.218)|Breast(118;0.244)		GBM - Glioblastoma multiforme(99;0.0318)		CTGCTCCGCGACCCTGAGCTG	0.592																																					p.S118P		Atlas-SNP	.											.	SPRY2	28	.	0			c.T352C						.						102	94	97					13																	80911489		2203	4300	6503	SO:0001583	missense	10253	exon2			TCCGCGACCCTGA	AF039843	CCDS9463.1	13q31.1	2008-05-14	2001-11-28		ENSG00000136158	ENSG00000136158			11270	protein-coding gene	gene with protein product		602466	"sprouty (Drosophila) homolog 2"			9458049	Standard	NM_005842		Approved	hSPRY2	uc001vlj.3	O43597	OTTHUMG00000017140	ENST00000377102.1:c.352T>C	chr13.hg19:g.80911489A>G	ENSP00000366306:p.Ser118Pro	103.0	0.0		71.0	4.0	NM_005842	B2R9J9|Q5T6Z7	Missense_Mutation	SNP	ENST00000377102.1	hg19	CCDS9463.1	.	.	.	.	.	.	.	.	.	.	A	12.74	2.029843	0.35797	.	.	ENSG00000136158	ENST00000377104;ENST00000377102;ENST00000541655;ENST00000540649	T;T;T	0.57907	0.37;0.37;0.37	4.89	4.89	0.63831	.	0.292074	0.33477	N	0.004872	T	0.55832	0.1945	M	0.78456	2.415	0.39573	D	0.969314	B	0.09022	0.002	B	0.06405	0.002	T	0.60449	-0.7261	10	0.72032	D	0.01	.	14.5419	0.68002	1.0:0.0:0.0:0.0	.	118	O43597	SPY2_HUMAN	P	118	ENSP00000366308:S118P;ENSP00000366306:S118P;ENSP00000439027:S118P	ENSP00000366306:S118P	S	-	1	0	SPRY2	79809490	1.000000	0.71417	0.968000	0.41197	0.992000	0.81027	5.770000	0.68873	1.849000	0.53698	0.459000	0.35465	TCG	.	.		0.592	SPRY2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045387.1			G	80911489	A	G	80911489	3	3	260	1	0	0	0	0	1	0	0	0	15121	275	10	2	599	2	SPRY2	13	80911489	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	3239130	80911489	34258389	592	37837										
GPC6	10082	hgsc.bcm.edu	37	chr13	94482742	94482742	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cccgcgccttcattgctgccAggacctttgtccaggggctg	12	15	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr13:94482742A>G	ENST00000377047.4	+	3	1270	c.655A>G	c.(655-657)Agg>Ggg	p.R219G	GPC6-AS2_ENST00000445540.1_RNA	NM_005708.3	NP_005699.1	Q9Y625	GPC6_HUMAN	glypican 6	219					carbohydrate metabolic process (GO:0005975)|cell migration (GO:0016477)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	38	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				CATTGCTGCCAGGACCTTTGT	0.493																																					p.R219G		Atlas-SNP	.											.	GPC6	102	.	0			c.A655G						.						50	48	49					13																	94482742		2203	4300	6503	SO:0001583	missense	10082	exon3			GCTGCCAGGACCT	AF111178	CCDS9469.1	13q32	2008-02-05			ENSG00000183098	ENSG00000183098		"Proteoglycans / Cell Surface : Glypicans"	4454	protein-coding gene	gene with protein product	"glypican proteoglycan 6"	604404				10329016	Standard	NM_005708		Approved		uc001vlt.3	Q9Y625	OTTHUMG00000017205	ENST00000377047.4:c.655A>G	chr13.hg19:g.94482742A>G	ENSP00000366246:p.Arg219Gly	175.0	0.0		92.0	4.0	NM_005708	A8K279|Q96SG5|Q96SG8|Q9H1P4	Missense_Mutation	SNP	ENST00000377047.4	hg19	CCDS9469.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.044259	0.75732	.	.	ENSG00000183098	ENST00000377047	T	0.61980	0.06	5.49	3.71	0.42584	.	0.000000	0.85682	D	0.000000	D	0.83644	0.5299	M	0.93550	3.43	0.47949	D	0.999558	D;D	0.89917	0.988;1.0	D;D	0.87578	0.954;0.998	D	0.87786	0.2615	10	0.87932	D	0	.	14.9491	0.71057	0.2644:0.7356:0.0:0.0	.	219;219	B4E2M1;Q9Y625	.;GPC6_HUMAN	G	219	ENSP00000366246:R219G	ENSP00000366246:R219G	R	+	1	2	GPC6	93280743	0.877000	0.30153	0.167000	0.22817	0.928000	0.56348	1.738000	0.38207	0.784000	0.33661	-0.178000	0.13098	AGG	.	.		0.493	GPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045460.4	NM_005708		G	94482742	A	G	94482742	3	3	260	1	0	0	0	0	1	0	0	0	6610	179	7	2	665	2	GPC6	13	94482742	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	13571253	94482742	20687136	593	37838										
UGGT2	55757	hgsc.bcm.edu	37	chr13	96530059	96530059	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cactttatcaaagcattgtcCttccagtagtaagtattcta	5	9	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr13:96530059C>A	ENST00000376747.3	-	28	3350	c.3280G>T	c.(3280-3282)Gga>Tga	p.G1094*		NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	1094					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-glucosylation (GO:0097359)	endoplasmic reticulum lumen (GO:0005788)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(17)|lung(20)|ovary(3)|pancreas(1)|prostate(4)|urinary_tract(2)	60						AAGCATTGTCCTTCCAGTAGT	0.393																																					p.G1094X		Atlas-SNP	.											.	UGGT2	127	.	0			c.G3280T						.						161	155	157					13																	96530059		2203	4300	6503	SO:0001587	stop_gained	55757	exon28			ATTGTCCTTCCAG	AF227906	CCDS9480.1	13q32.1	2009-07-23	2009-07-23	2009-07-23	ENSG00000102595	ENSG00000102595			15664	protein-coding gene	gene with protein product	"UDP-glucose:glycoprotein glucosyltransferase 2"	605898	"UDP-glucose ceramide glucosyltransferase-like 2"	UGCGL2		10694380	Standard	NM_020121		Approved	FLJ11485, HUGT2, FLJ10873, MGC150689, MGC87276, MGC117360	uc001vmt.3	Q9NYU1	OTTHUMG00000017230	ENST00000376747.3:c.3280G>T	chr13.hg19:g.96530059C>A	ENSP00000365938:p.Gly1094*	82.0	0.0		62.0	4.0	NM_020121	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Nonsense_Mutation	SNP	ENST00000376747.3	hg19	CCDS9480.1	.	.	.	.	.	.	.	.	.	.	C	39	7.494992	0.98319	.	.	ENSG00000102595	ENST00000376747	.	.	.	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-18.3445	18.6161	0.91303	0.0:1.0:0.0:0.0	.	.	.	.	X	1094	.	ENSP00000365938:G1094X	G	-	1	0	UGGT2	95328060	1.000000	0.71417	1.000000	0.80357	0.087000	0.18053	7.084000	0.76866	2.387000	0.81309	0.467000	0.42956	GGA	.	.		0.393	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121		A	96530059	C	A	96530059	4	1	260	1	0	0	0	0	0	1	0	0	16957	690	24	3	1318	3	UGGT2	13	96530059	Nonsense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	2047317	96530059	18639819	594	37839										
OR4K13	390433	hgsc.bcm.edu	37	chr14	20502875	20502875	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttgagatttggaaagtcccaAcaaaataaattccgatacca	6	8	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr14:20502875A>G	ENST00000315693.2	-	1	44	c.43T>C	c.(43-45)Ttg>Ctg	p.L15L	AL359218.1_ENST00000580563.1_RNA	NM_001004714.1	NP_001004714.1	Q8NH42	OR4KD_HUMAN	olfactory receptor, family 4, subfamily K, member 13	15						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|ovary(3)|skin(4)	24	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)		GAAAGTCCCAACAAAATAAAT	0.383																																					p.L15L		Atlas-SNP	.											OR4K13,NS,carcinoma,0,1	OR4K13	68	.	0			c.T43C						.						53	55	54					14																	20502875		2200	4299	6499	SO:0001819	synonymous_variant	390433	exon1			GTCCCAACAAAAT		CCDS32028.1	14q11.2	2013-09-23			ENSG00000176253	ENSG00000176253		"GPCR / Class A : Olfactory receptors"	15351	protein-coding gene	gene with protein product							Standard	NM_001004714		Approved		uc010tkz.2	Q8NH42	OTTHUMG00000170781	ENST00000315693.2:c.43T>C	chr14.hg19:g.20502875A>G		139.0	0.0		98.0	4.0	NM_001004714	Q6IF13	Silent	SNP	ENST00000315693.2	hg19	CCDS32028.1																																																																																			.	.		0.383	OR4K13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410344.1			G	20502875	A	G	20502875	2	3	260	1	0	0	0	0	0	0	0	1	11077	40	2	2		2	OR4K13	14	20502875	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10		20502875	86846665	595	37840										
OR10G2	26534	hgsc.bcm.edu	37	chr14	22102803	22102803	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgagagcactcccagaagaaTgtacatggggcgagcacaga	13	9	0	4	rs370971403		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr14:22102803T>C	ENST00000542433.1	-	1	293	c.196A>G	c.(196-198)Att>Gtt	p.I66V		NM_001005466.1	NP_001005466.1	Q8NGC3	O10G2_HUMAN	olfactory receptor, family 10, subfamily G, member 2	66						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|prostate(1)|skin(2)|stomach(2)	22	all_cancers(95;0.00113)	Acute lymphoblastic leukemia(2;0.0279)		GBM - Glioblastoma multiforme(265;0.0142)		CCCAGAAGAATGTACATGGGG	0.517																																					p.I66V		Atlas-SNP	.											.	OR10G2	35	.	0			c.A196G						.						60	60	60					14																	22102803		2203	4300	6503	SO:0001583	missense	26534	exon1			GAAGAATGTACAT		CCDS32047.1	14q11.2	2013-09-24			ENSG00000255582	ENSG00000255582		"GPCR / Class A : Olfactory receptors"	8170	protein-coding gene	gene with protein product						8188290	Standard	NM_001005466		Approved		uc010tmc.2	Q8NGC3	OTTHUMG00000168890	ENST00000542433.1:c.196A>G	chr14.hg19:g.22102803T>C	ENSP00000445383:p.Ile66Val	447.0	0.0		290.0	71.0	NM_001005466	B2RPD0	Missense_Mutation	SNP	ENST00000542433.1	hg19	CCDS32047.1	.	.	.	.	.	.	.	.	.	.	T	10.06	1.247993	0.22880	.	.	ENSG00000255582	ENST00000542433	T	0.00463	7.25	3.79	2.6	0.31112	GPCR, rhodopsin-like superfamily (1);	0.156674	0.28549	N	0.014944	T	0.00328	0.0010	L	0.35414	1.06	0.23903	N	0.996517	B	0.12013	0.005	B	0.06405	0.002	T	0.49184	-0.8966	10	0.87932	D	0	-2.1043	4.4135	0.11445	0.1987:0.0:0.2057:0.5955	.	66	Q8NGC3	O10G2_HUMAN	V	66	ENSP00000445383:I66V	ENSP00000445383:I66V	I	-	1	0	OR10G2	21172643	0.967000	0.33354	0.998000	0.56505	0.956000	0.61745	0.488000	0.22371	0.482000	0.27582	0.460000	0.39030	ATT	.	.		0.517	OR10G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401525.1			C	22102803	T	C	22102803	3	2	260	1	0	0	0	0	1	0	0	0	10908	1464	51	2	739	2	OR10G2	14	22102803	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1599928	22102803	85246737	596	37841										
ACIN1	22985	hgsc.bcm.edu	37	chr14	23540644	23540644	+	Intron	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttaagtcctcacggcaaaccCcgagttcggctggattggtc	11	12	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr14:23540644C>A	ENST00000262710.1	-	9	2625				ACIN1_ENST00000397341.3_5'UTR|ACIN1_ENST00000555352.1_Intron|ACIN1_ENST00000555053.1_Intron|ACIN1_ENST00000457657.1_Intron|ACIN1_ENST00000338631.6_Silent_p.R36R|ACIN1_ENST00000605057.1_Intron|ACIN1_ENST00000557515.1_5'UTR|ACIN1_ENST00000357481.2_5'UTR	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1						apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		ACGGCAAACCCCGAGTTCGGC	0.547																																					p.R36R		Atlas-SNP	.											.	ACIN1	147	.	0			c.G108T						.						48	47	47					14																	23540644		692	1591	2283	SO:0001627	intron_variant	22985	exon1			CAAACCCCGAGTT	AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 152"	604562	"apoptotic chromatin condensation inducer in the nucleus"	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.2298-1818G>T	chr14.hg19:g.23540644C>A		138.0	0.0		78.0	4.0	NM_001164816	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Silent	SNP	ENST00000262710.1	hg19	CCDS9587.1																																																																																			.	.		0.547	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977		A	23540644	C	A	23540644	1	1	260	0	1	0	0	0	0	0	0	0	142	610	22	3		3	ACIN1	14	23540644	Intron	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	1437841	23540644	83808896	597	37842										
AP1G2	8906	hgsc.bcm.edu	37	chr14	24035857	24035857	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aggtagcccaccctcttgtcTgtgaatctggaggaggcgat	13	10	3	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr14:24035857T>A	ENST00000308724.5	-	2	998	c.243A>T	c.(241-243)acA>acT	p.T81T	RP11-66N24.3_ENST00000555968.1_RNA|AP1G2_ENST00000556277.1_5'UTR|AP1G2_ENST00000397120.3_Silent_p.T81T	NM_003917.2	NP_003908.1	O75843	AP1G2_HUMAN	adaptor-related protein complex 1, gamma 2 subunit	81					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	AP-1 adaptor complex (GO:0030121)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle (GO:0005798)|membrane (GO:0016020)|transport vesicle (GO:0030133)	protein transporter activity (GO:0008565)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	28	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00672)		CCCTCTTGTCTGTGAATCTGG	0.542																																					p.T81T		Atlas-SNP	.											.	AP1G2	75	.	0			c.A243T						.						156	145	149					14																	24035857		2203	4300	6503	SO:0001819	synonymous_variant	8906	exon3			CTTGTCTGTGAAT	AB015318	CCDS9602.1	14q11.2	2008-07-03			ENSG00000213983	ENSG00000213983			556	protein-coding gene	gene with protein product		603534				9733768, 9762922	Standard	XM_005268167		Approved	G2AD	uc001wkl.2	O75843	OTTHUMG00000028760	ENST00000308724.5:c.243A>T	chr14.hg19:g.24035857T>A		97.0	0.0		77.0	4.0	NM_003917	D3DS51|O75504	Silent	SNP	ENST00000308724.5	hg19	CCDS9602.1																																																																																			.	.		0.542	AP1G2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071812.4	NM_003917		A	24035857	T	A	24035857	2	1	260	1	0	0	0	0	0	0	0	1	733	1567	55	4		4	AP1G2	14	24035857	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	495213	24035857	83313683	598	37843										
RNF31	55072	hgsc.bcm.edu	37	chr14	24617329	24617329	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gcagcacggtggatgctgtgCaggtgaatcccctggcctta	14	11	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr14:24617329C>A	ENST00000324103.6	+	2	657	c.337C>A	c.(337-339)Cag>Aag	p.Q113K	RNF31_ENST00000557878.1_3'UTR|PSME2_ENST00000560410.1_5'Flank|PSME2_ENST00000471700.2_5'Flank|RNF31_ENST00000382687.3_5'Flank|RNF31_ENST00000559275.1_5'UTR|PSME2_ENST00000216802.5_5'Flank	NM_017999.4	NP_060469.4	Q96EP0	RNF31_HUMAN	ring finger protein 31	113	Polyubiquitin-binding.				CD40 signaling pathway (GO:0023035)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein linear polyubiquitination (GO:0097039)|protein polyubiquitination (GO:0000209)|T cell receptor signaling pathway (GO:0050852)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|LUBAC complex (GO:0071797)	ligase activity (GO:0016874)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|prostate(4)|skin(2)|soft_tissue(1)	39				GBM - Glioblastoma multiforme(265;0.00861)		GGATGCTGTGCAGGTGAATCC	0.582																																					p.Q113K		Atlas-SNP	.											.	RNF31	95	.	0			c.C337A						.						92	93	92					14																	24617329		2015	4182	6197	SO:0001583	missense	55072	exon2			GCTGTGCAGGTGA	AK000973	CCDS41931.1	14q11.2	2012-09-20			ENSG00000092098	ENSG00000092098		"RING-type (C3HC4) zinc fingers"	16031	protein-coding gene	gene with protein product	"HOIL-1-interacting protein"	612487				10422847	Standard	NM_017999		Approved	ZIBRA, FLJ10111, FLJ23501, HOIP	uc001wmn.1	Q96EP0	OTTHUMG00000028798	ENST00000324103.6:c.337C>A	chr14.hg19:g.24617329C>A	ENSP00000315112:p.Gln113Lys	82.0	0.0		83.0	5.0	NM_017999	A0A962|Q86VI2|Q8TEI0|Q96GB4|Q96NF1|Q9H5F1|Q9NWD2	Missense_Mutation	SNP	ENST00000324103.6	hg19	CCDS41931.1	.	.	.	.	.	.	.	.	.	.	C	16.11	3.030337	0.54790	.	.	ENSG00000092098	ENST00000324103	T	0.41400	1.0	5.31	5.31	0.75309	PUB domain (1);	0.137675	0.49305	D	0.000147	T	0.36880	0.0983	N	0.12746	0.255	0.80722	D	1	P	0.52463	0.953	P	0.54174	0.744	T	0.07751	-1.0756	9	.	.	.	-20.8993	13.6085	0.62061	0.0:0.8442:0.1558:0.0	.	113	Q96EP0	RNF31_HUMAN	K	113	ENSP00000315112:Q113K	.	Q	+	1	0	RNF31	23687169	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	2.959000	0.49153	2.779000	0.95612	0.655000	0.94253	CAG	.	.		0.582	RNF31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071921.3	NM_017999		A	24617329	C	A	24617329	3	1	260	1	0	0	0	0	1	0	0	0	13502	711	25	3	343	3	RNF31	14	24617329	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	581472	24617329	82732211	599	37844										
ADCY4	196883	hgsc.bcm.edu	37	chr14	24791372	24791372	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tctccatcgtctctgtctccTccctctcctgcctcagcttc	4	20	5	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr14:24791372T>C	ENST00000310677.4	-	21	2599	c.2486A>G	c.(2485-2487)gAg>gGg	p.E829G	ADCY4_ENST00000418030.2_Missense_Mutation_p.E829G|ADCY4_ENST00000554068.2_Missense_Mutation_p.E829G	NM_001198568.1|NM_001198592.1|NM_139247.3	NP_001185497.1|NP_001185521.1|NP_640340.2	Q8NFM4	ADCY4_HUMAN	adenylate cyclase 4	829					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(265;0.0192)		CTCTGTCTCCTCCCTCTCCTG	0.617																																					p.E829G		Atlas-SNP	.											.	ADCY4	86	.	0			c.A2486G						.						115	102	106					14																	24791372		2203	4300	6503	SO:0001583	missense	196883	exon21			GTCTCCTCCCTCT	AF497516	CCDS9627.1	14q11.2	2013-02-04			ENSG00000129467	ENSG00000129467	4.6.1.1	"Adenylate cyclases"	235	protein-coding gene	gene with protein product		600292				7766992	Standard	NM_001198592		Approved	AC4	uc001woy.3	Q8NFM4	OTTHUMG00000029347	ENST00000310677.4:c.2486A>G	chr14.hg19:g.24791372T>C	ENSP00000312126:p.Glu829Gly	115.0	0.0		93.0	5.0	NM_001198592	B3KV74|D3DS75|Q17R40|Q6ZTM6|Q96ML7	Missense_Mutation	SNP	ENST00000310677.4	hg19	CCDS9627.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.501330	0.85176	.	.	ENSG00000129467	ENST00000310677;ENST00000554068;ENST00000418030	T;T;T	0.80480	-1.38;-1.38;-1.38	5.16	4.0	0.46444	.	0.000000	0.50627	D	0.000111	D	0.82342	0.5016	M	0.90870	3.155	0.80722	D	1	B	0.30211	0.273	B	0.26969	0.075	T	0.81621	-0.0850	10	0.72032	D	0.01	.	9.6287	0.39765	0.1562:0.0:0.0:0.8438	.	829	Q8NFM4	ADCY4_HUMAN	G	829	ENSP00000312126:E829G;ENSP00000452250:E829G;ENSP00000393177:E829G	ENSP00000312126:E829G	E	-	2	0	ADCY4	23861212	1.000000	0.71417	0.997000	0.53966	0.994000	0.84299	6.088000	0.71371	0.964000	0.38108	0.533000	0.62120	GAG	.	.		0.617	ADCY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073200.4			C	24791372	T	C	24791372	3	2	260	1	0	0	0	0	1	0	0	0	296	1551	54	2	771	2	ADCY4	14	24791372	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	174043	24791372	82558168	600	37845										
NYNRIN	57523	hgsc.bcm.edu	37	chr14	24868547	24868547	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gcggcagcggctgcaagtgcAgcgcatctttagggtcaagc	15	11	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr14:24868547A>G	ENST00000382554.3	+	2	413	c.95A>G	c.(94-96)cAg>cGg	p.Q32R		NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	32					DNA integration (GO:0015074)	integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(8)|lung(21)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	56						CTGCAAGTGCAGCGCATCTTT	0.632																																					p.Q32R		Atlas-SNP	.											.	NYNRIN	120	.	0			c.A95G						.						31	41	38					14																	24868547		1965	4144	6109	SO:0001583	missense	57523	exon2			AAGTGCAGCGCAT	AB037726	CCDS45090.1	14q11.2	2009-10-14	2009-10-14	2009-10-14		ENSG00000205978			20165	protein-coding gene	gene with protein product	"Cousin of GIN1"		"KIAA1305"	KIAA1305		19561090, 17114934	Standard	NM_025081		Approved	FLJ11811, CGIN1	uc001wpf.4	Q9P2P1		ENST00000382554.3:c.95A>G	chr14.hg19:g.24868547A>G	ENSP00000371994:p.Gln32Arg	137.0	0.0		105.0	6.0	NM_025081	Q6P153|Q86TR3|Q9HAC4	Missense_Mutation	SNP	ENST00000382554.3	hg19	CCDS45090.1	.	.	.	.	.	.	.	.	.	.	A	19.97	3.924383	0.73213	.	.	ENSG00000205978	ENST00000382554	T	0.11169	2.8	4.46	4.46	0.54185	.	0.560572	0.13040	U	0.418623	T	0.08179	0.0204	N	0.24115	0.695	0.25307	N	0.98923	B	0.33694	0.421	B	0.27608	0.081	T	0.21177	-1.0253	10	0.87932	D	0	.	11.7195	0.51675	1.0:0.0:0.0:0.0	.	32	Q9P2P1	NYNRI_HUMAN	R	32	ENSP00000371994:Q32R	ENSP00000371994:Q32R	Q	+	2	0	NYNRIN	23938387	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.745000	0.62125	1.864000	0.54056	0.402000	0.26972	CAG	.	.		0.632	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412939.1			G	24868547	A	G	24868547	3	3	260	1	0	0	0	0	1	0	0	0	10805	188	7	2	97	2	NYNRIN	14	24868547	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	77175	24868547	82480993	601	37846										
FOXG1	2290	hgsc.bcm.edu	37	chr14	29237531	29237531	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctccgtgttgactcagaactCgctgggcaacaaccactcct	8	15	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr14:29237531C>A	ENST00000313071.4	+	1	1245	c.1046C>A	c.(1045-1047)tCg>tAg	p.S349*	FOXG1_ENST00000382535.3_Nonsense_Mutation_p.S349*	NM_005249.4	NP_005240.3	P55316	FOXG1_HUMAN	forkhead box G1	349					aging (GO:0007568)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|dorsal/ventral pattern formation (GO:0009953)|inner ear morphogenesis (GO:0042472)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron fate determination (GO:0048664)|positive regulation of cell cycle (GO:0045787)|positive regulation of neuroblast proliferation (GO:0002052)|pyramidal neuron migration (GO:0021852)|regulation of mitotic cell cycle (GO:0007346)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(23)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(2)	43			LUAD - Lung adenocarcinoma(48;0.011)|Lung(238;0.0575)	GBM - Glioblastoma multiforme(265;0.00413)		ACTCAGAACTCGCTGGGCAAC	0.662																																					p.S349X		Atlas-SNP	.											FOXG1,NS,carcinoma,0,1	FOXG1	92	.	0			c.C1046A						.						101	93	96					14																	29237531		2203	4300	6503	SO:0001587	stop_gained	2290	exon1			AGAACTCGCTGGG		CCDS9636.1	14q11-q13	2007-10-05	2007-05-16	2007-05-16	ENSG00000176165	ENSG00000176165		"Forkhead boxes"	3811	protein-coding gene	gene with protein product		164874	"forkhead box G1B", "forkhead box G1C", "forkhead box G1A"	FKHL2, FOXG1B, FKHL4, FKH2, FKHL1, FOXG1C, FKHL3, FOXG1A		7959731, 17260156	Standard	NM_005249		Approved	HFK2, QIN, BF1, HFK1, HFK3, HBF-3	uc001wqe.4	P55316	OTTHUMG00000140187	ENST00000313071.4:c.1046C>A	chr14.hg19:g.29237531C>A	ENSP00000339004:p.Ser349*	98.0	0.0		67.0	3.0	NM_005249	A6NFY2|P55315|Q14488|Q86XT7	Nonsense_Mutation	SNP	ENST00000313071.4	hg19	CCDS9636.1	.	.	.	.	.	.	.	.	.	.	C	38	7.195950	0.98129	.	.	ENSG00000176165	ENST00000382535;ENST00000313071	.	.	.	4.21	4.21	0.49690	.	0.802151	0.10077	U	0.718940	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.5401	0.61668	0.1563:0.8437:0.0:0.0	.	.	.	.	X	349	.	ENSP00000339004:S349X	S	+	2	0	FOXG1	28307282	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.128000	0.57951	2.042000	0.60477	0.491000	0.48974	TCG	.	.		0.662	FOXG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276559.3			A	29237531	C	A	29237531	4	1	260	1	0	0	0	0	0	1	0	0	6015	893	31	1	1048	1	FOXG1	14	29237531	Nonsense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	4368984	29237531	78112009	602	37847										
AKAP6	9472	hgsc.bcm.edu	37	chr14	33014622	33014622	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcaaaaccaaaccctttgacTcttggagctacagtgagatg	8	10	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr14:33014622T>C	ENST00000280979.4	+	4	933	c.763T>C	c.(763-765)Tct>Cct	p.S255P	AKAP6_ENST00000557272.1_Missense_Mutation_p.S255P|AKAP6_ENST00000557354.1_Missense_Mutation_p.S255P	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	255					action potential (GO:0001508)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cAMP biosynthetic process (GO:0030818)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell growth (GO:0030307)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of delayed rectifier potassium channel activity (GO:1902261)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of potassium ion transmembrane transport (GO:1901381)|positive regulation of protein phosphatase type 2B activity (GO:0032514)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|protein targeting (GO:0006605)|regulation of membrane repolarization (GO:0060306)|regulation of protein kinase A signaling (GO:0010738)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	calcium channel complex (GO:0034704)|caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|junctional sarcoplasmic reticulum membrane (GO:0014701)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	adenylate cyclase binding (GO:0008179)|ion channel binding (GO:0044325)|protein anchor (GO:0043495)|protein complex scaffold (GO:0032947)|protein kinase A binding (GO:0051018)|protein kinase A regulatory subunit binding (GO:0034237)			NS(2)|breast(10)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(25)|lung(42)|ovary(5)|pancreas(2)|prostate(3)|skin(9)|urinary_tract(2)	122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		ACCCTTTGACTCTTGGAGCTA	0.463																																					p.S255P	Melanoma(49;821 1200 7288 13647 42351)	Atlas-SNP	.											.	AKAP6	308	.	0			c.T763C						.						149	126	134					14																	33014622		2203	4300	6503	SO:0001583	missense	9472	exon4			TTTGACTCTTGGA	AB002309	CCDS9644.1	14q12	2008-08-11			ENSG00000151320	ENSG00000151320		"A-kinase anchor proteins"	376	protein-coding gene	gene with protein product	"protein kinase A anchoring protein 6"	604691				7721854, 9205841	Standard	NM_004274		Approved	KIAA0311, mAKAP, AKAP100, PRKA6, ADAP6	uc001wrq.3	Q13023	OTTHUMG00000140207	ENST00000280979.4:c.763T>C	chr14.hg19:g.33014622T>C	ENSP00000280979:p.Ser255Pro	173.0	0.0		100.0	4.0	NM_004274	A7E242|A7E2D4|O15028	Missense_Mutation	SNP	ENST00000280979.4	hg19	CCDS9644.1	.	.	.	.	.	.	.	.	.	.	T	17.65	3.441316	0.63067	.	.	ENSG00000151320	ENST00000280979;ENST00000557354;ENST00000557272;ENST00000553547;ENST00000554410;ENST00000556638	T;T;T;T	0.35789	3.09;1.84;1.84;1.29	5.91	5.91	0.95273	.	0.072118	0.64402	D	0.000014	T	0.56187	0.1968	M	0.62723	1.935	0.40613	D	0.981696	D;D	0.76494	0.999;0.999	D;D	0.75484	0.941;0.986	T	0.60732	-0.7205	10	0.87932	D	0	-9.6006	12.2242	0.54451	0.0:0.0:0.1419:0.8581	.	255;255	A7E242;Q13023	.;AKAP6_HUMAN	P	255;255;255;13;13;13	ENSP00000280979:S255P;ENSP00000450531:S255P;ENSP00000451247:S255P;ENSP00000451239:S13P	ENSP00000280979:S255P	S	+	1	0	AKAP6	32084373	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.878000	0.39608	2.269000	0.75478	0.533000	0.62120	TCT	.	.		0.463	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274		C	33014622	T	C	33014622	3	2	260	1	0	0	0	0	1	0	0	0	455	1551	54	2	773	2	AKAP6	14	33014622	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	3777091	33014622	74334918	603	37848										
AKAP6	9472	hgsc.bcm.edu	37	chr14	33201661	33201661	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttttctcttttcattttagcGatacagtgtggaaatgtcca	7	7	2	0	rs541213739		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr14:33201661G>T	ENST00000280979.4	+	10	3172	c.3002G>T	c.(3001-3003)cGa>cTa	p.R1001L	AKAP6_ENST00000557272.1_Splice_Site_p.R1001L|AKAP6_ENST00000557354.1_Splice_Site_p.R1001L	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	1001					action potential (GO:0001508)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cAMP biosynthetic process (GO:0030818)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell growth (GO:0030307)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of delayed rectifier potassium channel activity (GO:1902261)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of potassium ion transmembrane transport (GO:1901381)|positive regulation of protein phosphatase type 2B activity (GO:0032514)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|protein targeting (GO:0006605)|regulation of membrane repolarization (GO:0060306)|regulation of protein kinase A signaling (GO:0010738)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	calcium channel complex (GO:0034704)|caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|junctional sarcoplasmic reticulum membrane (GO:0014701)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	adenylate cyclase binding (GO:0008179)|ion channel binding (GO:0044325)|protein anchor (GO:0043495)|protein complex scaffold (GO:0032947)|protein kinase A binding (GO:0051018)|protein kinase A regulatory subunit binding (GO:0034237)			NS(2)|breast(10)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(25)|lung(42)|ovary(5)|pancreas(2)|prostate(3)|skin(9)|urinary_tract(2)	122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		TCATTTTAGCGATACAGTGTG	0.373																																					p.R1001L	Melanoma(49;821 1200 7288 13647 42351)	Atlas-SNP	.											.	AKAP6	308	.	0			c.G3002T						.						97	99	98					14																	33201661		2203	4299	6502	SO:0001630	splice_region_variant	9472	exon10			TTTAGCGATACAG	AB002309	CCDS9644.1	14q12	2008-08-11			ENSG00000151320	ENSG00000151320		"A-kinase anchor proteins"	376	protein-coding gene	gene with protein product	"protein kinase A anchoring protein 6"	604691				7721854, 9205841	Standard	NM_004274		Approved	KIAA0311, mAKAP, AKAP100, PRKA6, ADAP6	uc001wrq.3	Q13023	OTTHUMG00000140207	ENST00000280979.4:c.3001-1G>T	chr14.hg19:g.33201661G>T		89.0	0.0		83.0	4.0	NM_004274	A7E242|A7E2D4|O15028	Missense_Mutation	SNP	ENST00000280979.4	hg19	CCDS9644.1	.	.	.	.	.	.	.	.	.	.	G	16.01	3.000231	0.54147	.	.	ENSG00000151320	ENST00000280979;ENST00000557354;ENST00000557272	T;T;T	0.18960	3.45;2.18;2.2	5.49	4.6	0.57074	.	0.100021	0.39909	N	0.001225	T	0.11707	0.0285	N	0.14661	0.345	0.39303	D	0.964943	P;P	0.44090	0.678;0.826	B;B	0.35039	0.194;0.194	T	0.10154	-1.0642	10	0.52906	T	0.07	-6.442	13.7021	0.62616	0.0742:0.0:0.9258:0.0	.	1001;1001	A7E242;Q13023	.;AKAP6_HUMAN	L	1001	ENSP00000280979:R1001L;ENSP00000450531:R1001L;ENSP00000451247:R1001L	ENSP00000280979:R1001L	R	+	2	0	AKAP6	32271412	1.000000	0.71417	0.987000	0.45799	0.731000	0.41821	6.092000	0.71414	2.565000	0.86533	0.585000	0.79938	CGA	.	.		0.373	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274	Missense_Mutation	T	33201661	G	T	33201661	5	4	260	1	0	0	0	0	0	0	1	0	455	1072	37	1	3036	1	AKAP6	14	33201661	Splice_Site	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	187039	33201661	74147879	604	37849										
LRFN5	145581	hgsc.bcm.edu	37	chr14	42356737	42356737	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agagtcctggagggacaaagGgcaacactgaggtgcaaagc	15	8	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr14:42356737G>A	ENST00000298119.4	+	3	2098	c.909G>A	c.(907-909)agG>agA	p.R303R	LRFN5_ENST00000554171.1_Silent_p.R303R|LRFN5_ENST00000554120.1_Silent_p.R303R	NM_152447.3	NP_689660.2	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III domain containing 5	303	Ig-like.					integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(67)|ovary(5)|pancreas(3)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(2)	120			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		AGGGACAAAGGGCAACACTGA	0.483										HNSCC(30;0.082)																											p.R303R		Atlas-SNP	.											.	LRFN5	269	.	0			c.G909A						.						114	109	111					14																	42356737		2203	4300	6503	SO:0001819	synonymous_variant	145581	exon3			ACAAAGGGCAACA	AK055365	CCDS9678.1	14q21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000165379	ENSG00000165379		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	20360	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 8"	612811	"chromosome 14 open reading frame 146"	C14orf146		16828986	Standard	NM_152447		Approved	FIGLER8, SALM5	uc001wvm.3	Q96NI6	OTTHUMG00000140261	ENST00000298119.4:c.909G>A	chr14.hg19:g.42356737G>A		140.0	0.0		93.0	4.0	NM_152447	B3KU78|Q86XL2	Silent	SNP	ENST00000298119.4	hg19	CCDS9678.1																																																																																			.	.		0.483	LRFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276786.1	NM_152447		A	42356737	G	A	42356737	2	1	260	1	0	0	0	0	0	0	0	1	8950	1223	43	3		3	LRFN5	14	42356737	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	9155076	42356737	64992803	605	37850										
KLHL28	54813	hgsc.bcm.edu	37	chr14	45414503	45414503	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agtatttctggcgttcttgtAcatcatacttgatccaagac	7	9	3	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr14:45414503A>T	ENST00000396128.4	-	2	748	c.629T>A	c.(628-630)gTa>gAa	p.V210E	KLHL28_ENST00000355081.2_Missense_Mutation_p.V224E	NM_017658.3	NP_060128.2	Q9NXS3	KLH28_HUMAN	kelch-like family member 28	210										breast(2)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						GCGTTCTTGTACATCATACTT	0.358																																					p.V210E		Atlas-SNP	.											.	KLHL28	53	.	0			c.T629A						.						116	109	111					14																	45414503		2203	4300	6503	SO:0001583	missense	54813	exon2			TCTTGTACATCAT	AK000088	CCDS9680.1	14q21.1	2013-02-22	2013-02-22	2007-01-09	ENSG00000179454	ENSG00000179454		"Kelch-like", "BTB/POZ domain containing"	19741	protein-coding gene	gene with protein product			"BTB (POZ) domain containing 5", "kelch-like 28 (Drosophila)"	BTBD5			Standard	NM_017658		Approved	FLJ20081	uc001wvr.3	Q9NXS3	OTTHUMG00000140263	ENST00000396128.4:c.629T>A	chr14.hg19:g.45414503A>T	ENSP00000379434:p.Val210Glu	186.0	0.0		148.0	6.0	NM_017658	Q0VAL5	Missense_Mutation	SNP	ENST00000396128.4	hg19	CCDS9680.1	.	.	.	.	.	.	.	.	.	.	A	15.15	2.747629	0.49257	.	.	ENSG00000179454	ENST00000396128;ENST00000355081	T;T	0.68181	-0.31;-0.31	5.75	5.75	0.90469	BTB/Kelch-associated (2);	0.051465	0.85682	D	0.000000	T	0.53286	0.1787	N	0.21324	0.655	0.53688	D	0.999975	B;P	0.44946	0.01;0.846	B;B	0.41332	0.015;0.354	T	0.60525	-0.7246	10	0.87932	D	0	.	10.8718	0.46887	0.926:0.0:0.074:0.0	.	210;210	Q9NXS3-2;Q9NXS3	.;KLH28_HUMAN	E	210;224	ENSP00000379434:V210E;ENSP00000347193:V224E	ENSP00000347193:V224E	V	-	2	0	KLHL28	44484253	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.101000	0.76997	2.193000	0.70182	0.533000	0.62120	GTA	.	.		0.358	KLHL28-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276790.3			T	45414503	A	T	45414503	3	4	260	1	0	0	0	0	1	0	0	0	8391	391	14	4	1102	4	KLHL28	14	45414503	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	3057766	45414503	61935037	606	37851										
FAM179B	23116	hgsc.bcm.edu	37	chr14	45464958	45464958	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgttcttatagttttcaacaTatgatttcatcccatctgca	4	9	4	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr14:45464958T>C	ENST00000361577.3	+	2	2270	c.2056T>C	c.(2056-2058)Tat>Cat	p.Y686H	KLHL28_ENST00000553817.1_Intron|FAM179B_ENST00000361462.2_Missense_Mutation_p.Y686H|FAM179B_ENST00000382233.2_Missense_Mutation_p.Y686H	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	686										endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						GTTTTCAACATATGATTTCAT	0.274																																					p.Y686H		Atlas-SNP	.											.	FAM179B	115	.	0			c.T2056C						.						58	58	58					14																	45464958		2201	4297	6498	SO:0001583	missense	23116	exon2			TCAACATATGATT	AB007883	CCDS9681.1	14q21.3	2008-07-21	2008-07-21	2008-07-21	ENSG00000198718	ENSG00000198718			19959	protein-coding gene	gene with protein product			"KIAA0423"	KIAA0423			Standard	XM_005267451		Approved		uc001wvv.3	Q9Y4F4	OTTHUMG00000140264	ENST00000361577.3:c.2056T>C	chr14.hg19:g.45464958T>C	ENSP00000355045:p.Tyr686His	107.0	0.0		65.0	4.0	NM_015091	Q68D66|Q6PG27	Missense_Mutation	SNP	ENST00000361577.3	hg19	CCDS9681.1	.	.	.	.	.	.	.	.	.	.	T	12.36	1.914015	0.33815	.	.	ENSG00000198718	ENST00000429476;ENST00000361577;ENST00000361462;ENST00000382233;ENST00000555874	T;T;T;T	0.03496	3.91;3.91;3.91;3.91	5.42	0.0567	0.14320	Armadillo-type fold (1);	0.620543	0.15421	N	0.263241	T	0.01765	0.0056	N	0.12182	0.205	0.09310	N	0.999999	B;B;B;B	0.06786	0.001;0.0;0.0;0.001	B;B;B;B	0.04013	0.001;0.0;0.001;0.001	T	0.47787	-0.9090	10	0.17832	T	0.49	-0.5589	3.2262	0.06732	0.2763:0.2429:0.0:0.4808	.	686;686;686;686	Q9Y4F4-3;G3XAE9;Q9Y4F4;Q9Y4F4-2	.;.;F179B_HUMAN;.	H	686;686;686;686;5	ENSP00000355045:Y686H;ENSP00000354917:Y686H;ENSP00000371668:Y686H;ENSP00000451141:Y5H	ENSP00000354917:Y686H	Y	+	1	0	FAM179B	44534708	0.020000	0.18652	0.783000	0.31826	0.814000	0.46013	0.378000	0.20569	0.059000	0.16252	0.477000	0.44152	TAT	.	.		0.274	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781		C	45464958	T	C	45464958	3	2	260	1	0	0	0	0	1	0	0	0	5511	1406	49	2	2062	2	FAM179B	14	45464958	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	50455	45464958	61884582	607	37852										
FAM179B	23116	hgsc.bcm.edu	37	chr14	45535808	45535808	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	actgaagttcgtgaagtcacCagaaaatcagtccctcgtaa	8	10	2	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr14:45535808C>T	ENST00000361577.3	+	16	4642	c.4428C>T	c.(4426-4428)acC>acT	p.T1476T	FAM179B_ENST00000361462.2_Silent_p.T1529T|FAM179B_ENST00000382233.2_3'UTR	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	1476										endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						GTGAAGTCACCAGAAAATCAG	0.328																																					p.T1476T		Atlas-SNP	.											.	FAM179B	115	.	0			c.C4428T						.						115	116	116					14																	45535808		2203	4300	6503	SO:0001819	synonymous_variant	23116	exon16			AGTCACCAGAAAA	AB007883	CCDS9681.1	14q21.3	2008-07-21	2008-07-21	2008-07-21	ENSG00000198718	ENSG00000198718			19959	protein-coding gene	gene with protein product			"KIAA0423"	KIAA0423			Standard	XM_005267451		Approved		uc001wvv.3	Q9Y4F4	OTTHUMG00000140264	ENST00000361577.3:c.4428C>T	chr14.hg19:g.45535808C>T		167.0	0.0		81.0	4.0	NM_015091	Q68D66|Q6PG27	Silent	SNP	ENST00000361577.3	hg19	CCDS9681.1																																																																																			.	.		0.328	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781		T	45535808	C	T	45535808	2	4	260	1	0	0	0	0	0	0	0	1	5511	581	21	3		3	FAM179B	14	45535808	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	70850	45535808	61813732	608	37853										
LGALS3	3958	hgsc.bcm.edu	37	chr14	55611952	55611952	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	caaactgggaatttctggtgAcatagacctcaccagtgctt	9	10	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr14:55611952A>G	ENST00000254301.9	+	6	977	c.716A>G	c.(715-717)gAc>gGc	p.D239G		NM_002306.3	NP_002297.2	P17931	LEG3_HUMAN	lectin, galactoside-binding, soluble, 3	239	Galectin. {ECO:0000255|PROSITE- ProRule:PRU00639}.				eosinophil chemotaxis (GO:0048245)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|macrophage chemotaxis (GO:0048246)|monocyte chemotaxis (GO:0002548)|mononuclear cell migration (GO:0071674)|mRNA processing (GO:0006397)|negative regulation of endocytosis (GO:0045806)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of immunological synapse formation (GO:2000521)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell receptor signaling pathway (GO:0050860)|neutrophil chemotaxis (GO:0030593)|positive chemotaxis (GO:0050918)|positive regulation of calcium ion import (GO:0090280)|positive regulation of mononuclear cell migration (GO:0071677)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|regulation of T cell apoptotic process (GO:0070232)|regulation of T cell proliferation (GO:0042129)|RNA splicing (GO:0008380)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|spliceosomal complex (GO:0005681)	carbohydrate binding (GO:0030246)|chemoattractant activity (GO:0042056)|IgE binding (GO:0019863)|laminin binding (GO:0043236)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(1)|prostate(1)	3						ATTTCTGGTGACATAGACCTC	0.373																																					p.D239G		Atlas-SNP	.											.	LGALS3	10	.	0			c.A716G						.						99	95	96					14																	55611952		1845	4092	5937	SO:0001583	missense	3958	exon6			CTGGTGACATAGA	M64303	CCDS41956.1	14q22.3	2014-03-19	2007-02-01		ENSG00000131981	ENSG00000131981		"Lectins, galactoside-binding", "Endogenous ligands"	6563	protein-coding gene	gene with protein product	"galectin 3"	153619		LGALS2		2009535, 8063692	Standard	NR_003225		Approved	MAC-2, GALIG	uc001xbr.3	P17931	OTTHUMG00000171030	ENST00000254301.9:c.716A>G	chr14.hg19:g.55611952A>G	ENSP00000254301:p.Asp239Gly	185.0	0.0		93.0	4.0	NM_002306	B2RC38|Q16005|Q6IBA7|Q96J47	Missense_Mutation	SNP	ENST00000254301.9	hg19	CCDS41956.1	.	.	.	.	.	.	.	.	.	.	A	16.73	3.204113	0.58234	.	.	ENSG00000131981	ENST00000254301	T	0.53857	0.6	5.9	5.9	0.94986	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	0.045023	0.85682	N	0.000000	T	0.74230	0.3689	M	0.81942	2.565	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.78074	-0.2346	10	0.87932	D	0	-21.6848	15.3143	0.74062	1.0:0.0:0.0:0.0	.	239	P17931	LEG3_HUMAN	G	239	ENSP00000254301:D239G	ENSP00000254301:D239G	D	+	2	0	LGALS3	54681705	1.000000	0.71417	1.000000	0.80357	0.199000	0.23934	6.722000	0.74735	2.264000	0.75181	0.533000	0.62120	GAC	.	.		0.373	LGALS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411309.1	NM_002306		G	55611952	A	G	55611952	3	3	260	1	0	0	0	0	1	0	0	0	8752	275	10	2	734	2	LGALS3	14	55611952	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	10076144	55611952	51737588	609	37854										
SPTB	6710	hgsc.bcm.edu	37	chr14	65241212	65241212	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cgcacgctgctgccgcaaatGtcgcttcagcatcacaatgg	10	14	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr14:65241212G>A	ENST00000389721.5	-	23	4908	c.4876C>T	c.(4876-4878)Cat>Tat	p.H1626Y	SPTB_ENST00000389720.3_Missense_Mutation_p.H1626Y|SPTB_ENST00000542895.1_Missense_Mutation_p.H1626Y|SPTB_ENST00000389722.3_Missense_Mutation_p.H1626Y|SPTB_ENST00000556626.1_Missense_Mutation_p.H1626Y	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	1626					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		TGCCGCAAATGTCGCTTCAGC	0.642																																					p.H1626Y		Atlas-SNP	.											.	SPTB	378	.	0			c.C4876T						.						19	17	18					14																	65241212		2183	4268	6451	SO:0001583	missense	6710	exon23			GCAAATGTCGCTT		CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"Pleckstrin homology (PH) domain containing"	11274	protein-coding gene	gene with protein product	"spherocytosis, clinical type I"	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.4876C>T	chr14.hg19:g.65241212G>A	ENSP00000374371:p.His1626Tyr	129.0	0.0		81.0	4.0	NM_001024858	Q15510|Q15519	Missense_Mutation	SNP	ENST00000389721.5	hg19	CCDS32100.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.620484	0.87460	.	.	ENSG00000070182	ENST00000389723;ENST00000389722;ENST00000335612;ENST00000553938;ENST00000556626;ENST00000389721;ENST00000542895;ENST00000389720	T;T;T;T;T;T	0.60040	0.22;0.22;0.22;0.22;0.22;0.22	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.81578	0.4852	M	0.91920	3.255	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.999	D	0.86040	0.1519	10	0.87932	D	0	.	17.6185	0.88074	0.0:0.0:1.0:0.0	.	410;1626;1630	E7EV95;P11277;Q59FP5	.;SPTB1_HUMAN;.	Y	1630;1626;410;291;1626;1626;1626;1626	ENSP00000374372:H1626Y;ENSP00000451324:H291Y;ENSP00000451752:H1626Y;ENSP00000374371:H1626Y;ENSP00000443882:H1626Y;ENSP00000374370:H1626Y	ENSP00000334218:H410Y	H	-	1	0	SPTB	64310965	1.000000	0.71417	0.994000	0.49952	0.743000	0.42351	9.833000	0.99426	2.428000	0.82296	0.542000	0.68232	CAT	.	.		0.642	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1			A	65241212	G	A	65241212	3	1	260	1	0	0	0	0	1	0	0	0	15133	1377	48	3	2231	3	SPTB	14	65241212	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	9629260	65241212	42108328	610	37855										
SPTB	6710	hgsc.bcm.edu	37	chr14	65249225	65249225	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gggcttccagcttttgggacAccagggctgtaaactggggc	15	10	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr14:65249225A>G	ENST00000389721.5	-	19	4081	c.4049T>C	c.(4048-4050)gTg>gCg	p.V1350A	SPTB_ENST00000389720.3_Missense_Mutation_p.V1350A|SPTB_ENST00000542895.1_Missense_Mutation_p.V1350A|SPTB_ENST00000389722.3_Missense_Mutation_p.V1350A|SPTB_ENST00000556626.1_Missense_Mutation_p.V1350A	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	1350					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		CTTTTGGGACACCAGGGCTGT	0.602																																					p.V1350A		Atlas-SNP	.											.	SPTB	378	.	0			c.T4049C						.						115	124	121					14																	65249225		2203	4300	6503	SO:0001583	missense	6710	exon19			TGGGACACCAGGG		CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"Pleckstrin homology (PH) domain containing"	11274	protein-coding gene	gene with protein product	"spherocytosis, clinical type I"	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.4049T>C	chr14.hg19:g.65249225A>G	ENSP00000374371:p.Val1350Ala	81.0	0.0		48.0	4.0	NM_001024858	Q15510|Q15519	Missense_Mutation	SNP	ENST00000389721.5	hg19	CCDS32100.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.428396	0.83667	.	.	ENSG00000070182	ENST00000389723;ENST00000389722;ENST00000335612;ENST00000553938;ENST00000556626;ENST00000389721;ENST00000542895;ENST00000389720	T;T;T;T;T;T	0.54866	0.55;1.18;0.55;0.55;0.55;0.55	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.78168	0.4241	M	0.93283	3.4	0.80722	D	1	D;P;D	0.60160	0.987;0.742;0.985	D;P;P	0.66351	0.943;0.479;0.861	D	0.84399	0.0559	10	0.87932	D	0	.	14.6216	0.68588	1.0:0.0:0.0:0.0	.	134;1350;1354	E7EV95;P11277;Q59FP5	.;SPTB1_HUMAN;.	A	1354;1350;134;15;1350;1350;1350;1350	ENSP00000374372:V1350A;ENSP00000451324:V15A;ENSP00000451752:V1350A;ENSP00000374371:V1350A;ENSP00000443882:V1350A;ENSP00000374370:V1350A	ENSP00000334218:V134A	V	-	2	0	SPTB	64318978	1.000000	0.71417	0.940000	0.37924	0.745000	0.42441	9.324000	0.96373	2.165000	0.68154	0.379000	0.24179	GTG	.	.		0.602	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1			G	65249225	A	G	65249225	3	3	260	1	0	0	0	0	1	0	0	0	15133	159	6	2	3074	2	SPTB	14	65249225	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	8013	65249225	42100315	611	37856										
ARG2	384	hgsc.bcm.edu	37	chr14	68086759	68086759	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gcattccatcctgaagaaatCcgtccactccgtggctgtga	9	13	0	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr14:68086759C>A	ENST00000261783.3	+	1	245	c.65C>A	c.(64-66)tCc>tAc	p.S22Y	ARG2_ENST00000556491.1_3'UTR|Y_RNA_ENST00000364659.1_RNA	NM_001172.3	NP_001163.1	P78540	ARGI2_HUMAN	arginase 2	22					arginine metabolic process (GO:0006525)|cellular nitrogen compound metabolic process (GO:0034641)|nitric oxide biosynthetic process (GO:0006809)|small molecule metabolic process (GO:0044281)|striated muscle contraction (GO:0006941)|urea cycle (GO:0000050)|ureteric bud development (GO:0001657)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	arginase activity (GO:0004053)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|ovary(1)|prostate(1)	11				all cancers(60;0.000582)|OV - Ovarian serous cystadenocarcinoma(108;0.00392)|BRCA - Breast invasive adenocarcinoma(234;0.00928)	L-Arginine(DB00125)|L-Ornithine(DB00129)	CTGAAGAAATCCGTCCACTCC	0.612																																					p.S22Y		Atlas-SNP	.											.	ARG2	20	.	0			c.C65A						.						32	32	32					14																	68086759		2202	4300	6502	SO:0001583	missense	384	exon1			AGAAATCCGTCCA	D86724	CCDS9785.1	14q24.1	2013-05-01	2013-05-01			ENSG00000081181			664	protein-coding gene	gene with protein product		107830	"arginase, type II"			8954792, 8898077	Standard	NM_001172		Approved		uc001xjs.3	P78540		ENST00000261783.3:c.65C>A	chr14.hg19:g.68086759C>A	ENSP00000261783:p.Ser22Tyr	103.0	0.0		86.0	4.0	NM_001172	B2R690|Q6FHY8	Missense_Mutation	SNP	ENST00000261783.3	hg19	CCDS9785.1	.	.	.	.	.	.	.	.	.	.	C	14.95	2.689700	0.48097	.	.	ENSG00000081181	ENST00000261783	D	0.86562	-2.14	4.48	4.48	0.54585	.	0.273225	0.38326	N	0.001737	T	0.80380	0.4612	L	0.29908	0.895	0.35330	D	0.785522	B	0.21753	0.06	B	0.17098	0.017	T	0.81543	-0.0885	10	0.42905	T	0.14	.	14.16	0.65441	0.0:1.0:0.0:0.0	.	22	P78540	ARGI2_HUMAN	Y	22	ENSP00000261783:S22Y	ENSP00000261783:S22Y	S	+	2	0	ARG2	67156512	0.627000	0.27129	0.997000	0.53966	0.373000	0.29922	2.505000	0.45424	2.321000	0.78463	0.561000	0.74099	TCC	.	.		0.612	ARG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415190.2	NM_001172		A	68086759	C	A	68086759	3	1	260	1	0	0	0	0	1	0	0	0	858	855	30	3	67	3	ARG2	14	68086759	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	2837534	68086759	39262781	612	37857										
SIPA1L1	26037	hgsc.bcm.edu	37	chr14	72090842	72090842	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcgacagccagaggcctgccTctcaaagaagtgctggagca	12	12	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr14:72090842T>C	ENST00000555818.1	+	4	2055	c.1707T>C	c.(1705-1707)ccT>ccC	p.P569P	SIPA1L1_ENST00000381232.3_Silent_p.P569P|SIPA1L1_ENST00000358550.2_Silent_p.P569P|SIPA1L1_ENST00000537413.1_Silent_p.P44P	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	569					actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		GAGGCCTGCCTCTCAAAGAAG	0.577																																					p.P569P		Atlas-SNP	.											.	SIPA1L1	219	.	0			c.T1707C						.						165	148	154					14																	72090842		2203	4300	6503	SO:0001819	synonymous_variant	26037	exon4			CCTGCCTCTCAAA	AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.1707T>C	chr14.hg19:g.72090842T>C		90.0	0.0		75.0	4.0	NM_015556	J3KP19|O95321|Q9UDU4|Q9UNU4	Silent	SNP	ENST00000555818.1	hg19	CCDS9807.1																																																																																			.	.		0.577	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556		C	72090842	T	C	72090842	2	2	260	1	0	0	0	0	0	0	0	1	14344	1538	54	2		2	SIPA1L1	14	72090842	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	4004083	72090842	35258698	613	37858										
VSX2	338917	hgsc.bcm.edu	37	chr14	74706312	74706312	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agcaagcccaaatccgagacAgtggccaagagtacctcggg	12	12	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr14:74706312A>G	ENST00000261980.2	+	1	138	c.48A>G	c.(46-48)acA>acG	p.T16T		NM_182894.2	NP_878314.1	P58304	VSX2_HUMAN	visual system homeobox 2	16	Pro-rich.				cell fate commitment (GO:0045165)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to stimulus (GO:0050896)|retinal bipolar neuron differentiation (GO:0060040)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	7				BRCA - Breast invasive adenocarcinoma(234;0.00154)		AATCCGAGACAGTGGCCAAGA	0.662																																					p.T16T		Atlas-SNP	.											.	VSX2	32	.	0			c.A48G						.						18	24	22					14																	74706312		1928	3683	5611	SO:0001819	synonymous_variant	338917	exon1			CGAGACAGTGGCC	AC005519	CCDS9827.1	14q24.3	2011-06-20	2007-08-21	2007-08-21		ENSG00000119614		"Homeoboxes / PRD class"	1975	protein-coding gene	gene with protein product		142993	"C elegans ceh-10 homeo domain-containing homolog", "ceh-10 homeo domain containing homolog (C. elegans)", "ceh-10 homeodomain containing homolog (C. elegans)"	HOX10, CHX10		1973146	Standard	NM_182894		Approved	RET1	uc001xpq.3	P58304		ENST00000261980.2:c.48A>G	chr14.hg19:g.74706312A>G		143.0	0.0		96.0	4.0	NM_182894	A1A4X6	Silent	SNP	ENST00000261980.2	hg19	CCDS9827.1																																																																																			.	.		0.662	VSX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412323.1	NM_182894		G	74706312	A	G	74706312	2	3	260	1	0	0	0	0	0	0	0	1	17247	175	7	2		2	VSX2	14	74706312	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	2615470	74706312	32643228	614	37859										
PROX2	283571	hgsc.bcm.edu	37	chr14	75330181	75330181	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctgttgccctggtcccaggcAggggctggcatcaggaggcc	16	13	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr14:75330181A>G	ENST00000445876.1	-	1	356	c.357T>C	c.(355-357)ccT>ccC	p.P119P	PROX2_ENST00000556084.2_Silent_p.P119P|PROX2_ENST00000556489.2_Silent_p.P119P			Q3B8N5	PROX2_HUMAN	prospero homeobox 2	119					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			kidney(1)|large_intestine(2)|lung(3)	6			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00652)		GGTCCCAGGCAGGGGCTGGCA	0.597																																					p.P119P		Atlas-SNP	.											.	PROX2	44	.	0			c.T357C						.						38	38	38					14																	75330181		1939	4145	6084	SO:0001819	synonymous_variant	283571	exon1			CCAGGCAGGGGCT		CCDS45136.1, CCDS45136.2, CCDS73663.1	14q24.3	2012-10-02			ENSG00000119608	ENSG00000119608		"Homeoboxes / PROS class"	26715	protein-coding gene	gene with protein product		615094					Standard	NM_001080408		Approved	FLJ36749	uc031qpi.1	Q3B8N5	OTTHUMG00000171481	ENST00000445876.1:c.357T>C	chr14.hg19:g.75330181A>G		118.0	0.0		89.0	5.0	NM_001080408	C9J5W1|Q8N9Q3	Silent	SNP	ENST00000445876.1	hg19	CCDS45136.2	.	.	.	.	.	.	.	.	.	.	A	0.541	-0.853675	0.02630	.	.	ENSG00000119608	ENST00000556084	.	.	.	5.35	1.61	0.23674	.	.	.	.	.	T	0.22244	0.0536	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.19386	-1.0307	4	.	.	.	.	2.3149	0.04196	0.5451:0.1293:0.2122:0.1133	.	.	.	.	P	119	.	.	L	-	2	0	PROX2	74399934	0.000000	0.05858	0.950000	0.38849	0.041000	0.13682	-0.196000	0.09532	0.869000	0.35703	0.454000	0.30748	CTG	.	.		0.597	PROX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				G	75330181	A	G	75330181	2	3	260	1	0	0	0	0	0	0	0	1	12573	175	7	2		2	PROX2	14	75330181	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	623869	75330181	32019359	615	37860										
TTLL5	23093	hgsc.bcm.edu	37	chr14	76156612	76156612	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tacacatggattcaaggcttTtcacatcctcccccagacct	5	15	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr14:76156612T>C	ENST00000298832.9	+	6	654	c.449T>C	c.(448-450)tTt>tCt	p.F150S	TTLL5_ENST00000557636.1_Missense_Mutation_p.F150S|TTLL5_ENST00000286650.5_Missense_Mutation_p.F150S	NM_015072.4	NP_055887.3	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5	150	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				fertilization (GO:0009566)|protein polyglutamylation (GO:0018095)|sperm axoneme assembly (GO:0007288)|sperm motility (GO:0030317)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)			NS(2)|breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(3)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	50				BRCA - Breast invasive adenocarcinoma(234;0.029)		TTCAAGGCTTTTCACATCCTC	0.458																																					p.F150S		Atlas-SNP	.											.	TTLL5	102	.	0			c.T449C						.						157	125	136					14																	76156612		2203	4300	6503	SO:0001583	missense	23093	exon6			AGGCTTTTCACAT	AF107885	CCDS32124.1	14q24.3	2014-09-09	2005-07-29	2005-07-29	ENSG00000119685	ENSG00000119685		"Tubulin tyrosine ligase-like family"	19963	protein-coding gene	gene with protein product		612268	"KIAA0998"	KIAA0998		15890843	Standard	NM_015072		Approved		uc001xrx.3	Q6EMB2	OTTHUMG00000171611	ENST00000298832.9:c.449T>C	chr14.hg19:g.76156612T>C	ENSP00000298832:p.Phe150Ser	157.0	0.0		124.0	5.0	NM_015072	B9EGH8|B9EGH9|Q9BUB0|Q9H0G4|Q9H7W2|Q9P1V5|Q9UPZ4	Missense_Mutation	SNP	ENST00000298832.9	hg19	CCDS32124.1	.	.	.	.	.	.	.	.	.	.	T	26.6	4.757129	0.89843	.	.	ENSG00000119685	ENST00000557003;ENST00000557636;ENST00000286650;ENST00000298832	T;T;T	0.05996	3.36;3.36;3.36	5.26	5.26	0.73747	.	0.094170	0.85682	D	0.000000	T	0.16599	0.0399	M	0.71871	2.18	0.80722	D	1	P;P;P	0.50369	0.511;0.89;0.934	B;P;P	0.51193	0.381;0.596;0.662	T	0.00329	-1.1813	10	0.87932	D	0	.	14.1532	0.65401	0.0:0.0:0.0:1.0	.	150;150;150	G3V2J9;Q6EMB2;Q6EMB2-3	.;TTLL5_HUMAN;.	S	150	ENSP00000450713:F150S;ENSP00000286650:F150S;ENSP00000298832:F150S	ENSP00000286650:F150S	F	+	2	0	TTLL5	75226365	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	7.680000	0.84062	1.977000	0.57605	0.533000	0.62120	TTT	.	.		0.458	TTLL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414453.1	NM_015072		C	76156612	T	C	76156612	3	2	260	1	0	0	0	0	1	0	0	0	16745	1841	64	2	467	2	TTLL5	14	76156612	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	826431	76156612	31192928	616	37861										
C14orf159	80017	hgsc.bcm.edu	37	chr14	91639751	91639751	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctgctgctccctcggaggtgAgcaggggcaacctgttcaca	13	13	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr14:91639751A>G	ENST00000523771.1	+	6	1163	c.560A>G	c.(559-561)gAg>gGg	p.E187G	C14orf159_ENST00000520328.1_Intron|C14orf159_ENST00000523816.1_Missense_Mutation_p.E187G|C14orf159_ENST00000412671.2_Missense_Mutation_p.E192G|C14orf159_ENST00000518868.1_Missense_Mutation_p.E192G|C14orf159_ENST00000256324.10_Missense_Mutation_p.E192G|C14orf159_ENST00000428926.2_Missense_Mutation_p.E187G|C14orf159_ENST00000522322.1_Missense_Mutation_p.E187G|C14orf159_ENST00000521077.2_Missense_Mutation_p.E192G|C14orf159_ENST00000525393.2_Missense_Mutation_p.E63G			Q7Z3D6	CN159_HUMAN	chromosome 14 open reading frame 159	187						mitochondrion (GO:0005739)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	21		all_cancers(154;0.0191)|all_epithelial(191;0.241)		Epithelial(152;0.141)|OV - Ovarian serous cystadenocarcinoma(161;0.207)		CTCGGAGGTGAGCAGGGGCAA	0.622											OREG0022869	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E192G		Atlas-SNP	.											.	C14orf159	57	.	0			c.A575G						.						48	41	43					14																	91639751		2203	4300	6503	SO:0001583	missense	80017	exon6			GAGGTGAGCAGGG	AK097294	CCDS32141.1, CCDS41979.1, CCDS45150.1, CCDS66693.1, CCDS73677.1	14q32.11	2012-09-26			ENSG00000133943	ENSG00000133943			20498	protein-coding gene	gene with protein product							Standard	NM_001102367		Approved	FLJ39975	uc001xze.2	Q7Z3D6	OTTHUMG00000164980	ENST00000523771.1:c.560A>G	chr14.hg19:g.91639751A>G	ENSP00000429655:p.Glu187Gly	96.0	0.0	1284	90.0	4.0	NM_001102368	B3KUI7|Q86SW3|Q86SX8|Q86SX9|Q86T08|Q86TV5|Q96GW5|Q9H7G0|Q9H8Y9|Q9H9W6	Missense_Mutation	SNP	ENST00000523771.1	hg19	CCDS32141.1	.	.	.	.	.	.	.	.	.	.	A	7.709	0.694650	0.15039	.	.	ENSG00000133943	ENST00000256324;ENST00000522170;ENST00000519950;ENST00000521077;ENST00000518868;ENST00000523816;ENST00000517518;ENST00000525393;ENST00000428926;ENST00000522322;ENST00000523771;ENST00000412671	T;T;T;T;T;T;T;T;T;T;T;T	0.29397	1.57;1.57;1.57;1.57;1.57;1.57;1.57;1.57;1.57;1.57;1.57;1.57	4.29	-1.36	0.09085	.	0.856909	0.09901	N	0.741077	T	0.10852	0.0265	N	0.03608	-0.345	0.09310	N	1	B;B;B;B;B	0.25563	0.002;0.129;0.002;0.002;0.002	B;B;B;B;B	0.27887	0.007;0.084;0.007;0.004;0.004	T	0.27088	-1.0084	10	0.33141	T	0.24	.	1.471	0.02416	0.3253:0.3577:0.1833:0.1337	.	187;63;192;192;192	Q7Z3D6;Q8NB88;B3KVU6;Q7Z3D6-2;Q7Z3D6-3	CN159_HUMAN;.;.;.;.	G	192;192;192;192;192;187;192;63;187;187;187;192	ENSP00000256324:E192G;ENSP00000430666:E192G;ENSP00000428296:E192G;ENSP00000430137:E192G;ENSP00000428263:E192G;ENSP00000428974:E187G;ENSP00000428652:E192G;ENSP00000435459:E63G;ENSP00000404343:E187G;ENSP00000427953:E187G;ENSP00000429655:E187G;ENSP00000404196:E192G	ENSP00000256324:E192G	E	+	2	0	C14orf159	90709504	0.001000	0.12720	0.004000	0.12327	0.003000	0.03518	0.195000	0.17155	-0.016000	0.14127	-0.678000	0.03780	GAG	.	.		0.622	C14orf159-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381273.1	NM_024952		G	91639751	A	G	91639751	3	3	260	1	0	0	0	0	1	0	0	0	1757	304	11	2	589	2	C14orf159	14	91639751	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	15483139	91639751	15709789	617	37862										
IFI27L1	122509	hgsc.bcm.edu	37	chr14	94568204	94568204	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tggcgctcagtgccatgggcTtcacctcagtaggaatcgcc	12	13	3	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr14:94568204T>C	ENST00000555523.1	+	4	325	c.106T>C	c.(106-108)Ttc>Ctc	p.F36L	IFI27L1_ENST00000556381.1_Missense_Mutation_p.F35L|IFI27L1_ENST00000553350.1_Intron|IFI27L1_ENST00000557218.1_Intron|IFI27L1_ENST00000393115.3_Missense_Mutation_p.F36L|IFI27L1_ENST00000553664.1_Missense_Mutation_p.L58P|IFI27L1_ENST00000554562.1_Missense_Mutation_p.F36L|IFI27L1_ENST00000554544.1_Intron|IFI27L1_ENST00000557066.1_Intron	NM_206949.2	NP_996832.1	Q96BM0	I27L1_HUMAN	interferon, alpha-inducible protein 27-like 1	36						integral component of membrane (GO:0016021)				lung(2)	2						TGCCATGGGCTTCACCTCAGT	0.617																																					p.F36L		Atlas-SNP	.											.	IFI27L1	11	.	0			c.T106C						.						103	84	91					14																	94568204		2203	4300	6503	SO:0001583	missense	122509	exon4			ATGGGCTTCACCT	BC015423	CCDS9919.1	14q32.13	2008-10-08	2008-10-08	2008-10-08		ENSG00000165948			19754	protein-coding gene	gene with protein product		611320	"family with sequence similarity 14, member B"	FAM14B			Standard	NM_145249		Approved		uc001yck.3	Q96BM0		ENST00000555523.1:c.106T>C	chr14.hg19:g.94568204T>C	ENSP00000451851:p.Phe36Leu	157.0	0.0		99.0	6.0	NM_145249		Missense_Mutation	SNP	ENST00000555523.1	hg19	CCDS9919.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.69|17.69	3.452746|3.452746	0.63290|0.63290	.|.	.|.	ENSG00000165948|ENSG00000165948	ENST00000555523;ENST00000393115;ENST00000554166;ENST00000556381;ENST00000555341;ENST00000554562|ENST00000553664	T;T;T;T;T;T|.	0.53206|.	0.63;0.63;0.63;0.63;0.63;0.63|.	3.48|3.48	3.48|3.48	0.39840|0.39840	.|.	0.000000|.	0.64402|.	U|.	0.000001|.	T|T	0.78136|0.78136	0.4236|0.4236	M|M	0.91406|0.91406	3.205|3.205	0.42249|0.42249	D|D	0.991967|0.991967	D|.	0.61697|.	0.99|.	P|.	0.60682|.	0.878|.	T|T	0.81333|0.81333	-0.0980|-0.0980	10|5	0.87932|.	D|.	0|.	.|.	8.6431|8.6431	0.33989|0.33989	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	36|.	Q96BM0|.	I27L1_HUMAN|.	L|P	36;36;35;35;35;36|58	ENSP00000451851:F36L;ENSP00000376824:F36L;ENSP00000452226:F35L;ENSP00000451459:F35L;ENSP00000451608:F35L;ENSP00000450620:F36L|.	ENSP00000376824:F36L|.	F|L	+|+	1|2	0|0	IFI27L1|IFI27L1	93637957|93637957	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.012000|0.012000	0.07955|0.07955	6.638000|6.638000	0.74309|0.74309	1.836000|1.836000	0.53414|0.53414	0.482000|0.482000	0.46254|0.46254	TTC|CTT	.	.		0.617	IFI27L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412868.1	NM_206949		C	94568204	T	C	94568204	3	2	260	1	0	0	0	0	1	0	0	0	7522	1609	56	2	116	2	IFI27L1	14	94568204	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	2928453	94568204	12781336	618	37863										
PPP4R4	57718	hgsc.bcm.edu	37	chr14	94716580	94716580	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cgttataatcgtaaacaagaAcagagacatgaggtcattca	8	7	2	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr14:94716580A>G	ENST00000304338.3	+	15	1837	c.1683A>G	c.(1681-1683)gaA>gaG	p.E561E		NM_058237.1	NP_478144.1	Q6NUP7	PP4R4_HUMAN	protein phosphatase 4, regulatory subunit 4	561					negative regulation of phosphoprotein phosphatase activity (GO:0032515)|regulation of protein serine/threonine phosphatase activity (GO:0080163)	cytoplasm (GO:0005737)|protein serine/threonine phosphatase complex (GO:0008287)	protein phosphatase regulator activity (GO:0019888)			NS(1)|breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(15)|lung(10)|skin(7)|upper_aerodigestive_tract(2)	40						GTAAACAAGAACAGAGACATG	0.333																																					p.E561E		Atlas-SNP	.											PPP4R4,NS,carcinoma,0,1	PPP4R4	107	.	0			c.A1683G						.						127	113	118					14																	94716580		2203	4300	6503	SO:0001819	synonymous_variant	57718	exon15			ACAAGAACAGAGA	AB046842, BC068491	CCDS9921.1, CCDS9922.1	14q32.2	2014-07-18	2008-09-16	2008-09-16	ENSG00000119698	ENSG00000119698		"Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits"	23788	protein-coding gene	gene with protein product	"cilia and flagella associated protein 14"		"KIAA1622"	KIAA1622		18715871	Standard	NM_020958		Approved	PP4R4, CFAP14	uc001ycs.1	Q6NUP7		ENST00000304338.3:c.1683A>G	chr14.hg19:g.94716580A>G		118.0	0.0		66.0	4.0	NM_058237	Q9BUF8|Q9HCF0	Silent	SNP	ENST00000304338.3	hg19	CCDS9921.1																																																																																			.	.		0.333	PPP4R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413056.1	NM_058237		G	94716580	A	G	94716580	2	3	260	1	0	0	0	0	0	0	0	1	12417	40	2	2		2	PPP4R4	14	94716580	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	148376	94716580	12632960	619	37864										
SERPINA10	51156	hgsc.bcm.edu	37	chr14	94750485	94750485	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcaacttcaatcactgttctTtgtaaaacctggaaaaagga	6	8	4	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr14:94750485T>C	ENST00000393096.1	-	5	1617	c.1152A>G	c.(1150-1152)caA>caG	p.Q384Q	SERPINA10_ENST00000554173.1_Silent_p.Q384Q|SERPINA10_ENST00000261994.4_Silent_p.Q384Q|SERPINA10_ENST00000554723.1_Silent_p.Q424Q	NM_016186.2	NP_057270.1	Q9UK55	ZPI_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10	384			Q -> P. {ECO:0000269|Ref.4}.|Q -> R (in dbSNP:rs2232710). {ECO:0000269|PubMed:12975309}.		blood coagulation (GO:0007596)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)			haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	33		all_cancers(154;0.105)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)		TCACTGTTCTTTGTAAAACCT	0.423																																					p.Q384Q		Atlas-SNP	.											.	SERPINA10	83	.	0			c.A1152G						.						74	66	69					14																	94750485		2203	4300	6503	SO:0001819	synonymous_variant	51156	exon5			TGTTCTTTGTAAA	AF181467	CCDS9923.1	14q32.13	2014-02-18	2005-08-18		ENSG00000140093	ENSG00000140093		"Serine (or cysteine) peptidase inhibitors"	15996	protein-coding gene	gene with protein product		605271	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10"			10460162, 9689066, 24172014	Standard	NM_016186		Approved	PZI, ZPI	uc001yct.3	Q9UK55	OTTHUMG00000171345	ENST00000393096.1:c.1152A>G	chr14.hg19:g.94750485T>C		91.0	0.0		62.0	4.0	NM_001100607	A5Z2A5|Q6UWX9|Q86U20	Silent	SNP	ENST00000393096.1	hg19	CCDS9923.1																																																																																			.	.		0.423	SERPINA10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413061.1	NM_016186		C	94750485	T	C	94750485	2	2	260	1	0	0	0	0	0	0	0	1	14102	1838	64	2		2	SERPINA10	14	94750485	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	33905	94750485	12599055	620	37865										
SERPINA1	5265	hgsc.bcm.edu	37	chr14	94845816	94845816	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctcaccttggagagcttcagGggtgcctcctctgtgacccc	11	15	3	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr14:94845816G>A	ENST00000448921.1	-	6	1622	c.1050C>T	c.(1048-1050)ccC>ccT	p.P350P	SERPINA1_ENST00000393088.4_Silent_p.P350P|SERPINA1_ENST00000449399.3_Silent_p.P350P|SERPINA1_ENST00000393087.4_Silent_p.P350P|SERPINA1_ENST00000440909.1_Silent_p.P350P|SERPINA1_ENST00000437397.1_Silent_p.P350P|SERPINA1_ENST00000402629.1_Silent_p.P350P|SERPINA1_ENST00000404814.4_Silent_p.P350P|SERPINA1_ENST00000355814.4_Silent_p.P350P	NM_001002236.2|NM_001127701.1|NM_001127703.1|NM_001127704.1|NM_001127705.1	NP_001002236.1|NP_001121173.1|NP_001121175.1|NP_001121176.1|NP_001121177.1	P01009	A1AT_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1	350					acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of proteolysis (GO:0030162)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)	glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|skin(6)|stomach(1)	24		all_cancers(154;0.0649)|all_epithelial(191;0.223)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)		AGAGCTTCAGGGGTGCCTCCT	0.567																																					p.P350P		Atlas-SNP	.											.	SERPINA1	51	.	0			c.C1050T						.						113	106	109					14																	94845816		2203	4300	6503	SO:0001819	synonymous_variant	5265	exon6			CTTCAGGGGTGCC	X01683	CCDS9925.1	14q32.1	2014-02-18	2005-08-18		ENSG00000197249	ENSG00000197249		"Serine (or cysteine) peptidase inhibitors"	8941	protein-coding gene	gene with protein product	"protease inhibitor 1 (anti-elastase), alpha-1-antitrypsin"	107400	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1"	PI		24172014	Standard	NM_000295		Approved	AAT, A1A, PI1, alpha-1-antitrypsin, A1AT, alpha1AT	uc010aux.3	P01009	OTTHUMG00000150355	ENST00000448921.1:c.1050C>T	chr14.hg19:g.94845816G>A		79.0	0.0		53.0	6.0	NM_001127701	A6PX14|B2RDQ8|Q0PVP5|Q13672|Q53XB8|Q5U0M1|Q7M4R2|Q86U18|Q86U19|Q96BF9|Q96ES1|Q9P1P0|Q9UCE6|Q9UCM3	Silent	SNP	ENST00000448921.1	hg19	CCDS9925.1																																																																																			.	.		0.567	SERPINA1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317768.2	NM_001002235		A	94845816	G	A	94845816	2	1	260	1	0	0	0	0	0	0	0	1	14101	1219	43	3		3	SERPINA1	14	94845816	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	95331	94845816	12503724	621	37866										
AK7	122481	hgsc.bcm.edu	37	chr14	96917876	96917876	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggaaaatatcaacactatccTcaaggagtacaagcaaagca	7	9	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr14:96917876T>C	ENST00000267584.4	+	10	1111	c.1067T>C	c.(1066-1068)cTc>cCc	p.L356P		NM_152327.3	NP_689540.2	Q96M32	KAD7_HUMAN	adenylate kinase 7	356					axoneme assembly (GO:0035082)|brain development (GO:0007420)|epithelial cilium movement (GO:0003351)|inflammatory response to antigenic stimulus (GO:0002437)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)			breast(2)|cervix(2)|endometrium(3)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)		AACACTATCCTCAAGGAGTAC	0.383																																					p.L356P		Atlas-SNP	.											.	AK7	69	.	0			c.T1067C						.						91	86	88					14																	96917876		2203	4300	6503	SO:0001583	missense	122481	exon10			CTATCCTCAAGGA	AK057426	CCDS9945.1	14q32.31	2012-08-15			ENSG00000140057	ENSG00000140057		"Adenylate kinases"	20091	protein-coding gene	gene with protein product		615364					Standard	NM_152327		Approved	FLJ32864	uc001yfn.3	Q96M32	OTTHUMG00000171421	ENST00000267584.4:c.1067T>C	chr14.hg19:g.96917876T>C	ENSP00000267584:p.Leu356Pro	105.0	0.0		88.0	4.0	NM_152327	Q8IYP6	Missense_Mutation	SNP	ENST00000267584.4	hg19	CCDS9945.1	.	.	.	.	.	.	.	.	.	.	T	14.95	2.687379	0.48097	.	.	ENSG00000140057	ENST00000267584	T	0.62498	0.02	5.72	5.72	0.89469	.	0.125602	0.53938	D	0.000047	T	0.67021	0.2849	L	0.60455	1.87	0.80722	D	1	D	0.56968	0.978	P	0.49421	0.61	T	0.71206	-0.4661	10	0.66056	D	0.02	-26.691	14.9982	0.71449	0.0:0.0:0.0:1.0	.	356	Q96M32	KAD7_HUMAN	P	356	ENSP00000267584:L356P	ENSP00000267584:L356P	L	+	2	0	AK7	95987629	1.000000	0.71417	1.000000	0.80357	0.047000	0.14425	4.584000	0.60971	2.189000	0.69895	0.533000	0.62120	CTC	.	.		0.383	AK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413340.1			C	96917876	T	C	96917876	3	2	260	1	0	0	0	0	1	0	0	0	444	1551	54	2	1105	2	AK7	14	96917876	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	2072060	96917876	10431664	622	37867										
C14orf177	283598	hgsc.bcm.edu	37	chr14	99183503	99183503	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	catgaagaaacttctccaggGtcatgtaatcaccaaataat	6	9	3	2	rs149397774	byFrequency	TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr14:99183503G>T	ENST00000325812.2	+	4	689	c.270G>T	c.(268-270)ggG>ggT	p.G90G		NM_182560.2	NP_872366.2	Q52M58	CN177_HUMAN	chromosome 14 open reading frame 177	90										endometrium(1)|kidney(1)|large_intestine(1)|lung(10)	13		Melanoma(154;0.128)				CTTCTCCAGGGTCATGTAATC	0.438																																					p.G90G		Atlas-SNP	.											.	C14orf177	37	.	0			c.G270T						.						134	109	117					14																	99183503		2203	4300	6503	SO:0001819	synonymous_variant	283598	exon4			TCCAGGGTCATGT	AK098639	CCDS9948.1	14q32.2	2012-05-30			ENSG00000176605	ENSG00000176605			26375	protein-coding gene	gene with protein product						12477932	Standard	NM_182560		Approved	FLJ25773	uc001yfz.2	Q52M58	OTTHUMG00000167745	ENST00000325812.2:c.270G>T	chr14.hg19:g.99183503G>T		198.0	0.0		112.0	5.0	NM_182560	Q8N7D2	Silent	SNP	ENST00000325812.2	hg19	CCDS9948.1																																																																																			.	G|1.000;A|0.000		0.438	C14orf177-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396078.1	NM_182560		T	99183503	G	T	99183503	2	4	260	1	0	0	0	0	0	0	0	1	1762	1248	44	3		3	C14orf177	14	99183503	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	2265627	99183503	8166037	623	37868										
HSP90AA1	3320	hgsc.bcm.edu	37	chr14	102548723	102548723	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tctccatgtttgctgtccagCcatatgtgcttgtgacaata	8	10	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr14:102548723C>A	ENST00000216281.8	-	10	2019	c.1814G>T	c.(1813-1815)gGc>gTc	p.G605V	HSP90AA1_ENST00000334701.7_Missense_Mutation_p.G727V	NM_005348.3	NP_005339.3	P07900	HS90A_HUMAN	heat shock protein 90kDa alpha (cytosolic), class A member 1	605					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone-mediated protein complex assembly (GO:0051131)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|mitochondrial transport (GO:0006839)|mitotic cell cycle (GO:0000278)|nitric oxide metabolic process (GO:0046209)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|protein import into mitochondrial outer membrane (GO:0045040)|protein refolding (GO:0042026)|regulation of nitric-oxide synthase activity (GO:0050999)|response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|identical protein binding (GO:0042802)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|TPR domain binding (GO:0030911)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(6)|large_intestine(3)|liver(1)|lung(10)|ovary(2)|prostate(1)	28					Nedocromil(DB00716)|Rifabutin(DB00615)	TGCTGTCCAGCCATATGTGCT	0.423																																					p.G727V		Atlas-SNP	.											.	HSP90AA1	65	.	0			c.G2180T						.						70	69	70					14																	102548723		2203	4300	6503	SO:0001583	missense	3320	exon11			GTCCAGCCATATG	M27024	CCDS9967.1, CCDS32160.1	14q32.33	2011-09-02	2006-02-24	2006-02-24	ENSG00000080824	ENSG00000080824		"Heat shock proteins / HSPC"	5253	protein-coding gene	gene with protein product		140571	"heat shock 90kD protein 1, alpha", "heat shock 90kDa protein 1, alpha"	HSPC1, HSPCA		2527334, 16269234	Standard	NM_001017963		Approved	Hsp89, Hsp90, FLJ31884, HSP90N	uc001ykv.4	P07900		ENST00000216281.8:c.1814G>T	chr14.hg19:g.102548723C>A	ENSP00000216281:p.Gly605Val	136.0	0.0		99.0	5.0	NM_001017963	A8K500|B3KPJ9|Q2PP14|Q5CAQ6|Q5CAQ7|Q9BVQ5	Missense_Mutation	SNP	ENST00000216281.8	hg19	CCDS9967.1	.	.	.	.	.	.	.	.	.	.	c	23.8	4.459420	0.84317	.	.	ENSG00000080824	ENST00000216281;ENST00000334701	T;T	0.26067	1.76;1.76	4.51	4.51	0.55191	.	0.000000	0.85682	U	0.000000	T	0.73497	0.3594	H	0.99927	4.965	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.994;0.997	D	0.88014	0.2764	10	0.87932	D	0	-22.548	17.5881	0.87988	0.0:1.0:0.0:0.0	.	727;605	P07900-2;P07900	.;HS90A_HUMAN	V	605;727	ENSP00000216281:G605V;ENSP00000335153:G727V	ENSP00000216281:G605V	G	-	2	0	HSP90AA1	101618476	1.000000	0.71417	0.994000	0.49952	0.965000	0.64279	7.497000	0.81536	2.228000	0.72767	0.585000	0.79938	GGC	.	.		0.423	HSP90AA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414952.2	NM_005348		A	102548723	C	A	102548723	3	1	260	1	0	0	0	0	1	0	0	0	7410	739	26	3	392	3	HSP90AA1	14	102548723	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	3365220	102548723	4800817	624	37869										
BAG5	9529	hgsc.bcm.edu	37	chr14	104026246	104026246	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtttcctggcagccttacacTtctcttctccctgcggatca	7	15	3	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr14:104026246T>C	ENST00000445922.2	-	2	1502	c.1256A>G	c.(1255-1257)aAg>aGg	p.K419R	BAG5_ENST00000299204.4_Missense_Mutation_p.K419R|BAG5_ENST00000337322.4_Missense_Mutation_p.K460R|RP11-894P9.2_ENST00000556332.1_RNA	NM_004873.3	NP_004864.1	Q9UL15	BAG5_HUMAN	BCL2-associated athanogene 5	419	BAG 5. {ECO:0000255|PROSITE- ProRule:PRU00369}.				negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein refolding (GO:0061084)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|neuron death (GO:0070997)|protein folding (GO:0006457)|regulation of inclusion body assembly (GO:0090083)	inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	chaperone binding (GO:0051087)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)			endometrium(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(2)|skin(2)|urinary_tract(2)	24		Melanoma(154;0.155)	Epithelial(46;0.144)			AGCCTTACACTTCTCTTCTCC	0.488																																					p.K460R	NSCLC(171;1832 2055 18950 31566 41632)	Atlas-SNP	.											.	BAG5	47	.	0			c.A1379G						.						100	95	96					14																	104026246		2203	4300	6503	SO:0001583	missense	9529	exon2			TTACACTTCTCTT	AF095195	CCDS9982.1, CCDS41995.1	14q32	2008-08-01				ENSG00000166170			941	protein-coding gene	gene with protein product		603885				9873016, 15603737	Standard	NM_001015048		Approved		uc001ynh.2	Q9UL15		ENST00000445922.2:c.1256A>G	chr14.hg19:g.104026246T>C	ENSP00000391713:p.Lys419Arg	148.0	0.0		88.0	4.0	NM_001015049	O94950|Q86W59	Missense_Mutation	SNP	ENST00000445922.2	hg19	CCDS9982.1	.	.	.	.	.	.	.	.	.	.	T	4.163	0.028833	0.08054	.	.	ENSG00000166170	ENST00000299204;ENST00000445922;ENST00000337322	D;D;D	0.87966	-2.32;-2.32;-2.32	5.74	-0.934	0.10428	BAG domain (3);	0.700611	0.12922	N	0.428111	T	0.55625	0.1932	N	0.00707	-1.245	0.09310	N	0.999997	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.53968	-0.8363	10	0.11794	T	0.64	-14.8627	3.4516	0.07501	0.1268:0.4304:0.1306:0.3123	.	419;460	Q9UL15;Q9UL15-2	BAG5_HUMAN;.	R	419;419;460	ENSP00000299204:K419R;ENSP00000391713:K419R;ENSP00000338814:K460R	ENSP00000299204:K419R	K	-	2	0	BAG5	103095999	0.001000	0.12720	0.068000	0.19968	0.756000	0.42949	0.064000	0.14437	-0.298000	0.08921	-0.371000	0.07208	AAG	.	.		0.488	BAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414990.1			C	104026246	T	C	104026246	3	2	260	1	0	0	0	0	1	0	0	0	1290	1609	56	2	91	2	BAG5	14	104026246	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1477523	104026246	3323294	625	37870										
KIAA0284	283638	hgsc.bcm.edu	37	chr14	105349493	105349493	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gagatccccacgaaggagacCccgcagccgtcgcagccccc	11	19	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr14:105349493C>T	ENST00000414716.3	+	8	927	c.699C>T	c.(697-699)acC>acT	p.T233T	CEP170B_ENST00000418279.1_Silent_p.T163T|CEP170B_ENST00000453495.1_Silent_p.T234T|CEP170B_ENST00000556508.1_Silent_p.T163T	NM_001112726.2	NP_001106197.1	Q9Y4F5	C170B_HUMAN	centrosomal protein 170B	233						cytoplasm (GO:0005737)|microtubule (GO:0005874)											CGAAGGAGACCCCGCAGCCGT	0.716																																					p.T233T		Atlas-SNP	.											.	.	.	.	0			c.C699T						.						16	21	19					14																	105349493		1944	4118	6062	SO:0001819	synonymous_variant	283638	exon8			GGAGACCCCGCAG	AB006622	CCDS45175.1, CCDS45176.1, CCDS45176.2	14q32.33	2014-02-20	2012-11-30	2012-11-30	ENSG00000099814	ENSG00000099814			20362	protein-coding gene	gene with protein product	"Cep170-related"		"KIAA0284"	KIAA0284		23087211	Standard	NM_015005		Approved	FAM68C, Cep170R	uc010axb.4	Q9Y4F5	OTTHUMG00000170763	ENST00000414716.3:c.699C>T	chr14.hg19:g.105349493C>T		105.0	0.0		70.0	4.0	NM_001112726	Q2KHR7|Q86TI7	Silent	SNP	ENST00000414716.3	hg19	CCDS45175.1																																																																																			.	.		0.716	CEP170B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000410289.2	NM_001112726		T	105349493	C	T	105349493	2	4	260	1	0	0	0	0	0	0	0	1	8175	610	22	3		3	KIAA0284	14	105349493	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	1323247	105349493	2000047	626	37871										
MTMR15	22909	hgsc.bcm.edu	37	chr15	31221547	31221547	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cgtggcatgagcaggaaggcAgagtggcttcccttgtcagc	15	10	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:31221547A>G	ENST00000362065.4	+	12	3025	c.2734A>G	c.(2734-2736)Aga>Gga	p.R912G	FAN1_ENST00000568145.1_3'UTR|RP11-540B6.6_ENST00000602886.1_RNA	NM_014967.4	NP_055782.3	Q9Y2M0	FAN1_HUMAN	FANCD2/FANCI-associated nuclease 1	912	VRR-NUC.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA incision (GO:0033683)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|5'-flap endonuclease activity (GO:0017108)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|phosphodiesterase I activity (GO:0004528)|ubiquitin binding (GO:0043130)			autonomic_ganglia(2)|breast(2)|cervix(2)|endometrium(7)|kidney(1)|large_intestine(6)|lung(8)|skin(1)	29						GCAGGAAGGCAGAGTGGCTTC	0.597								Direct reversal of damage																													p.R912G		Atlas-SNP	.											.	FAN1	77	.	0			c.A2734G						.						130	127	128					15																	31221547		2202	4300	6502	SO:0001583	missense	22909	exon12			GAAGGCAGAGTGG		CCDS32186.1, CCDS58344.1	15q13.2-q13.3	2010-08-04	2010-08-04	2010-08-04		ENSG00000198690			29170	protein-coding gene	gene with protein product		613534	"KIAA1018", "myotubularin related protein 15"	KIAA1018, MTMR15		20603015, 20603016, 20603073	Standard	NM_014967		Approved		uc001zff.3	Q9Y2M0		ENST00000362065.4:c.2734A>G	chr15.hg19:g.31221547A>G	ENSP00000354497:p.Arg912Gly	133.0	0.0		100.0	26.0	NM_014967	A8K4M2|Q86WU8	Missense_Mutation	SNP	ENST00000362065.4	hg19	CCDS32186.1	.	.	.	.	.	.	.	.	.	.	A	18.10	3.548380	0.65311	.	.	ENSG00000198690	ENST00000362065	D	0.85484	-1.99	5.39	-1.59	0.08453	VRR-NUC (1);	0.111885	0.64402	D	0.000012	T	0.81153	0.4763	M	0.62723	1.935	0.80722	D	1	P;P	0.44344	0.833;0.737	B;B	0.42959	0.403;0.403	T	0.77480	-0.2572	10	0.56958	D	0.05	-23.1458	10.0175	0.42022	0.4853:0.4507:0.0639:0.0	.	912;912	Q9Y2M0;D9MXF4	FAN1_HUMAN;.	G	912	ENSP00000354497:R912G	ENSP00000354497:R912G	R	+	1	2	FAN1	29008839	0.832000	0.29368	0.639000	0.29394	0.798000	0.45092	1.308000	0.33528	-0.182000	0.10602	0.528000	0.53228	AGA	.	.		0.597	FAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430740.1	NM_014967		G	31221547	A	G	31221547	3	3	260	1	0	0	0	0	1	0	0	0	9952	180	7	2	2801	2	MTMR15	15	31221547	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10		31221547	71309845	627	37872										
RYR3	6263	hgsc.bcm.edu	37	chr15	34040731	34040731	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtgctctccagagagctccaGgtcagtgccccaggtccagc	12	15	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:34040731G>T	ENST00000389232.4	+	55	8269	c.8199G>T	c.(8197-8199)caG>caT	p.Q2733H	RYR3_ENST00000415757.3_Splice_Site_p.Q2733H	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	2733	4 X approximate repeats.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			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)		GAGAGCTCCAGGTCAGTGCCC	0.507																																					p.Q2733H		Atlas-SNP	.											.	RYR3	760	.	0			c.G8199T						.						61	60	60					15																	34040731		1943	4139	6082	SO:0001630	splice_region_variant	6263	exon55			GCTCCAGGTCAGT		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.8199+1G>T	chr15.hg19:g.34040731G>T		71.0	0.0		75.0	4.0	NM_001243996	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	hg19	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.124196	0.77436	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D;D	0.91894	-2.93;-2.93	5.04	5.04	0.67666	Ryanodine receptor Ryr (1);	0.000000	0.85682	D	0.000000	D	0.94404	0.8200	L	0.53780	1.695	0.80722	D	1	D;B	0.69078	0.997;0.046	D;B	0.68483	0.958;0.056	D	0.92968	0.6395	10	0.31617	T	0.26	.	17.3179	0.87228	0.0:0.0:1.0:0.0	.	2733;2733	Q15413-2;Q15413	.;RYR3_HUMAN	H	2733	ENSP00000373884:Q2733H;ENSP00000399610:Q2733H	ENSP00000354735:Q2733H	Q	+	3	2	RYR3	31828023	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	8.577000	0.90773	2.610000	0.88304	0.561000	0.74099	CAG	.	.		0.507	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		Missense_Mutation	T	34040731	G	T	34040731	5	4	260	1	0	0	0	0	0	0	1	0	13785	1014	35	3	8417	3	RYR3	15	34040731	Splice_Site	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	2819184	34040731	68490661	628	37873										
SLC12A6	9990	hgsc.bcm.edu	37	chr15	34547554	34547554	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	caacagccccaccaaactctGggcccagtgcccgggaaatc	9	17	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:34547554G>T	ENST00000354181.3	-	8	1277	c.785C>A	c.(784-786)cCa>cAa	p.P262Q	SLC12A6_ENST00000397702.2_Missense_Mutation_p.P203Q|SLC12A6_ENST00000558589.1_Missense_Mutation_p.P253Q|SLC12A6_ENST00000560164.1_Missense_Mutation_p.P74Q|SLC12A6_ENST00000458406.2_Missense_Mutation_p.P203Q|SLC12A6_ENST00000558667.1_Missense_Mutation_p.P262Q|SLC12A6_ENST00000560611.1_Missense_Mutation_p.P262Q|SLC12A6_ENST00000451844.2_Missense_Mutation_p.P74Q|SLC12A6_ENST00000290209.5_Missense_Mutation_p.P211Q|RP11-1084A12.2_ENST00000559867.1_RNA|SLC12A6_ENST00000397707.2_Missense_Mutation_p.P247Q			Q9UHW9	S12A6_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 6	262					angiogenesis (GO:0001525)|cellular hypotonic response (GO:0071476)|cellular hypotonic salinity response (GO:0071477)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|rubidium ion transport (GO:0035826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium ion transmembrane transporter activity (GO:0015079)|potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)|rubidium ion transmembrane transporter activity (GO:0035827)			central_nervous_system(5)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|skin(3)	45		all_lung(180;2.78e-08)		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	Potassium Chloride(DB00761)	ACCAAACTCTGGGCCCAGTGC	0.443																																					p.P262Q		Atlas-SNP	.											.	SLC12A6	205	.	0			c.C785A						.						64	66	65					15																	34547554		2201	4298	6499	SO:0001583	missense	9990	exon7			AACTCTGGGCCCA	AF108831	CCDS10036.1, CCDS42010.1, CCDS42011.1, CCDS42012.1, CCDS58352.1	15q13	2014-09-17	2013-07-18		ENSG00000140199	ENSG00000140199		"Solute carriers"	10914	protein-coding gene	gene with protein product		604878	"agenesis of corpus callosum and peripheral neuropathy (Andermann syndrome)"	KCC3, ACCPN		10187864, 10347194	Standard	NM_133647		Approved		uc001zhw.3	Q9UHW9	OTTHUMG00000129441	ENST00000354181.3:c.785C>A	chr15.hg19:g.34547554G>T	ENSP00000346112:p.Pro262Gln	108.0	0.0		69.0	4.0	NM_133647	A0AV76|Q2VI00|Q7Z2E7|Q7Z4G5|Q8TDD4|Q9UFR2|Q9Y642|Q9Y665	Missense_Mutation	SNP	ENST00000354181.3	hg19	CCDS58352.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.992616	0.93167	.	.	ENSG00000140199	ENST00000290209;ENST00000397707;ENST00000354181;ENST00000397702;ENST00000458406;ENST00000451844	D;D;D;D;D	0.99089	-5.41;-5.41;-5.41;-5.41;-5.41	5.43	5.43	0.79202	Amino acid permease domain (1);	0.066377	0.64402	D	0.000012	D	0.99573	0.9846	H	0.96720	3.87	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.993;0.999;0.997;1.0	D	0.98018	1.0369	10	0.87932	D	0	.	18.1759	0.89761	0.0:0.0:1.0:0.0	.	247;262;211;74	Q9UHW9-3;Q9UHW9;A0AV76;B3KXX3	.;S12A6_HUMAN;.;.	Q	211;247;253;203;203;74	ENSP00000290209:P211Q;ENSP00000380819:P247Q;ENSP00000380814:P203Q;ENSP00000387725:P203Q;ENSP00000390199:P74Q	ENSP00000290209:P211Q	P	-	2	0	SLC12A6	32334846	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.657000	0.98554	2.826000	0.97356	0.655000	0.94253	CCA	.	.		0.443	SLC12A6-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000417991.1	NM_005135		T	34547554	G	T	34547554	3	4	260	1	0	0	0	0	1	0	0	0	14402	1348	47	3	2743	3	SLC12A6	15	34547554	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	506823	34547554	67983838	629	37874										
RPUSD2	27079	hgsc.bcm.edu	37	chr15	40865856	40865856	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tccccggggcaagccctgtgAgacagtgttccagaggctaa	13	12	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:40865856A>G	ENST00000315616.7	+	3	1072	c.1034A>G	c.(1033-1035)gAg>gGg	p.E345G	RPUSD2_ENST00000559271.1_Missense_Mutation_p.E284G	NM_152260.1	NP_689473.1	Q8IZ73	RUSD2_HUMAN	RNA pseudouridylate synthase domain containing 2	345					pseudouridine synthesis (GO:0001522)		poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)			kidney(4)|lung(4)|skin(3)	11		all_cancers(109;2.74e-14)|all_epithelial(112;1.64e-11)|Lung NSC(122;6.69e-09)|all_lung(180;1.22e-07)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;3.1e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0786)		AAGCCCTGTGAGACAGTGTTC	0.567																																					p.E345G		Atlas-SNP	.											.	RPUSD2	28	.	0			c.A1034G						.						90	69	76					15																	40865856		2203	4300	6503	SO:0001583	missense	27079	exon3			CCTGTGAGACAGT	AK055971	CCDS10061.1, CCDS66737.1	15q13.3	2013-02-11	2005-01-31	2005-02-07	ENSG00000166133	ENSG00000166133		"RNA pseudouridylate synthase domain containing"	24180	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 19"	C15orf19		12477932	Standard	NM_001286407		Approved	C18B11, FLJ31409	uc001zmd.1	Q8IZ73	OTTHUMG00000130031	ENST00000315616.7:c.1034A>G	chr15.hg19:g.40865856A>G	ENSP00000323288:p.Glu345Gly	118.0	0.0		92.0	4.0	NM_152260	B4DDD1|Q7L989|Q92939|Q96IA7|Q96N50	Missense_Mutation	SNP	ENST00000315616.7	hg19	CCDS10061.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.279287	0.80692	.	.	ENSG00000166133	ENST00000315616;ENST00000417769	T	0.22743	1.94	5.94	4.83	0.62350	Pseudouridine synthase, RsuA and RluB/C/D/E/F (1);Pseudouridine synthase, catalytic domain (1);	0.223555	0.46145	D	0.000320	T	0.34716	0.0907	M	0.82716	2.605	0.36113	D	0.844958	P	0.39665	0.682	P	0.45538	0.484	T	0.48948	-0.8989	10	0.46703	T	0.11	-27.6584	11.2092	0.48788	0.9282:0.0:0.0718:0.0	.	345	Q8IZ73	RUSD2_HUMAN	G	345;324	ENSP00000323288:E345G	ENSP00000323288:E345G	E	+	2	0	RPUSD2	38653148	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.078000	0.71282	2.265000	0.75225	0.482000	0.46254	GAG	.	.		0.567	RPUSD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252308.2	NM_152260		G	40865856	A	G	40865856	3	3	260	1	0	0	0	0	1	0	0	0	13682	304	11	2	1044	2	RPUSD2	15	40865856	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	6318302	40865856	61665536	630	37875										
CASC5	57082	hgsc.bcm.edu	37	chr15	40914165	40914165	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tagaaagactgaactcttatCaggtgaaaatatggatttga	9	4	2	5			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:40914165C>T	ENST00000346991.5	+	11	2171	c.1781C>T	c.(1780-1782)tCa>tTa	p.S594L	CASC5_ENST00000527044.1_3'UTR|CASC5_ENST00000399668.2_Missense_Mutation_p.S568L			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	594	Interaction with BUB1 and BUB1B.				acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		GAACTCTTATCAGGTGAAAAT	0.383																																					p.S594L		Atlas-SNP	.											.	CASC5	269	.	0			c.C1781T						.						56	52	53					15																	40914165		1863	4106	5969	SO:0001583	missense	57082	exon11			TCTTATCAGGTGA	AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	24054	protein-coding gene	gene with protein product	"cancer/testis antigen 29", "kinetochore null 1 homolog (C. elegans)", "blinkin, bub-linking kinetochore protein", "protein phosphatase 1, regulatory subunit 55"	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.1781C>T	chr15.hg19:g.40914165C>T	ENSP00000335463:p.Ser594Leu	130.0	0.0		95.0	5.0	NM_170589	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Missense_Mutation	SNP	ENST00000346991.5	hg19	CCDS42023.1	.	.	.	.	.	.	.	.	.	.	C	9.287	1.049751	0.19827	.	.	ENSG00000137812	ENST00000346991;ENST00000260369;ENST00000399668	T;T	0.06849	3.25;3.26	4.7	1.72	0.24424	.	2.059420	0.02153	N	0.058167	T	0.08802	0.0218	L	0.39898	1.24	0.09310	N	1	B;B;B	0.15141	0.012;0.001;0.005	B;B;B	0.16289	0.013;0.003;0.015	T	0.33189	-0.9878	10	0.39692	T	0.17	.	3.7933	0.08730	0.2913:0.4722:0.0:0.2365	.	568;594;568	Q8NG31-2;Q8NG31;Q8NG31-4	.;CASC5_HUMAN;.	L	594;568;568	ENSP00000335463:S594L;ENSP00000382576:S568L	ENSP00000260369:S568L	S	+	2	0	CASC5	38701457	0.000000	0.05858	0.018000	0.16275	0.567000	0.35839	0.206000	0.17375	0.199000	0.20427	0.455000	0.32223	TCA	.	.		0.383	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508		T	40914165	C	T	40914165	3	4	260	1	0	0	0	0	1	0	0	0	2665	838	29	3	1819	3	CASC5	15	40914165	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	48309	40914165	61617227	631	37876										
VPS18	57617	hgsc.bcm.edu	37	chr15	41191112	41191112	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cttgtccccacagcattgacTtgggcaaggcaaatgagccc	10	13	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:41191112T>C	ENST00000220509.5	+	3	580	c.241T>C	c.(241-243)Ttg>Ctg	p.L81L	VPS18_ENST00000558474.1_Silent_p.L81L	NM_020857.2	NP_065908.1	Q9P253	VPS18_HUMAN	vacuolar protein sorting 18 homolog (S. cerevisiae)	81					endosome organization (GO:0007032)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|vesicle-mediated transport (GO:0016192)|viral entry into host cell (GO:0046718)	actin filament (GO:0005884)|early endosome (GO:0005769)|HOPS complex (GO:0030897)|lysosomal membrane (GO:0005765)	metal ion binding (GO:0046872)			autonomic_ganglia(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	28		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;1.07e-05)|COAD - Colon adenocarcinoma(120;0.15)|BRCA - Breast invasive adenocarcinoma(123;0.164)		CAGCATTGACTTGGGCAAGGC	0.443																																					p.L81L		Atlas-SNP	.											.	VPS18	67	.	0			c.T241C						.						97	80	86					15																	41191112		2203	4300	6503	SO:0001819	synonymous_variant	57617	exon3			ATTGACTTGGGCA	AF308802	CCDS10069.1	15q14-q15	2006-12-19	2006-12-19		ENSG00000104142	ENSG00000104142			15972	protein-coding gene	gene with protein product		608551	"vacuolar protein sorting protein 18"			11250079, 16203730	Standard	NM_020857		Approved	KIAA1475, PEP3	uc001zne.3	Q9P253	OTTHUMG00000130135	ENST00000220509.5:c.241T>C	chr15.hg19:g.41191112T>C		100.0	0.0		75.0	4.0	NM_020857	Q8TCG0|Q96DI3|Q9H268	Silent	SNP	ENST00000220509.5	hg19	CCDS10069.1																																																																																			.	.		0.443	VPS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252443.2			C	41191112	T	C	41191112	2	2	260	1	0	0	0	0	0	0	0	1	17209	1606	56	2		2	VPS18	15	41191112	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	276947	41191112	61340280	632	37877										
INO80	54617	hgsc.bcm.edu	37	chr15	41339666	41339666	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctggagatatatcaataaagCgaaggaaagagaaacagctt	10	5	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:41339666C>A	ENST00000361937.3	-	23	3099	c.2675G>T	c.(2674-2676)cGc>cTc	p.R892L	INO80_ENST00000401393.3_Missense_Mutation_p.R892L			Q9ULG1	INO80_HUMAN	INO80 complex subunit	892	Assembles INO80 complex module consisting of conserved components INO80B, INO80C, ACTR5, RVBL1, RVBL2.				ATP catabolic process (GO:0006200)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of cell growth (GO:0030307)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|spindle assembly (GO:0051225)|UV-damage excision repair (GO:0070914)	Ino80 complex (GO:0031011)|microtubule (GO:0005874)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			NS(1)|breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						ATCAATAAAGCGAAGGAAAGA	0.403																																					p.R892L		Atlas-SNP	.											.	INO80	122	.	0			c.G2675T						.						66	68	67					15																	41339666		2203	4300	6503	SO:0001583	missense	54617	exon23			ATAAAGCGAAGGA	AB033085	CCDS10071.1	15q15.1	2013-08-21	2013-08-21	2008-08-07	ENSG00000128908	ENSG00000128908	3.6.1.3	"INO80 complex subunits"	26956	protein-coding gene	gene with protein product	"INO80 complex subunit A"	610169	"INO80 complex homolog 1 (S. cerevisiae)", "INO80 homolog (S. cerevisiae)"	INOC1		16298340, 16230350, 20237820	Standard	NM_017553		Approved	KIAA1259, Ino80, hINO80, INO80A	uc001zni.3	Q9ULG1	OTTHUMG00000130209	ENST00000361937.3:c.2675G>T	chr15.hg19:g.41339666C>A	ENSP00000355205:p.Arg892Leu	89.0	0.0		60.0	4.0	NM_017553	A6H8X4|Q9NTG6	Missense_Mutation	SNP	ENST00000361937.3	hg19	CCDS10071.1	.	.	.	.	.	.	.	.	.	.	C	32	5.139513	0.94560	.	.	ENSG00000128908	ENST00000361937;ENST00000401393	D;D	0.93247	-3.19;-3.19	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	D	0.96658	0.8909	M	0.78344	2.41	0.80722	D	1	D	0.63880	0.993	D	0.74023	0.982	D	0.96806	0.9593	10	0.87932	D	0	.	19.1067	0.93299	0.0:1.0:0.0:0.0	.	892	Q9ULG1	INO80_HUMAN	L	892	ENSP00000355205:R892L;ENSP00000384686:R892L	ENSP00000355205:R892L	R	-	2	0	INO80	39126958	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.674000	0.74487	2.826000	0.97356	0.491000	0.48974	CGC	.	.		0.403	INO80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252527.2	NM_017553		A	41339666	C	A	41339666	3	1	260	1	0	0	0	0	1	0	0	0	7755	768	27	1	2051	1	INO80	15	41339666	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	148554	41339666	61191726	633	37878										
MAPKBP1	23005	hgsc.bcm.edu	37	chr15	42104835	42104835	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	caaattctggtatctcgatgAcagcaagacctcaaaggtga	9	9	3	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:42104835A>G	ENST00000456763.2	+	7	816	c.620A>G	c.(619-621)gAc>gGc	p.D207G	MAPKBP1_ENST00000457542.2_Missense_Mutation_p.D207G|MAPKBP1_ENST00000221214.6_Missense_Mutation_p.D207G|MAPKBP1_ENST00000260357.7_Missense_Mutation_p.D95G|MAPKBP1_ENST00000514566.1_Missense_Mutation_p.D207G	NM_001128608.1	NP_001122080.1	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein 1	207										breast(6)|central_nervous_system(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)		TATCTCGATGACAGCAAGACC	0.572																																					p.D207G		Atlas-SNP	.											.	MAPKBP1	120	.	0			c.A620G						.						71	65	67					15																	42104835		2203	4300	6503	SO:0001583	missense	23005	exon7			TCGATGACAGCAA	AB011168	CCDS32201.1, CCDS45239.1, CCDS58359.1	15q15.1	2013-01-10	2008-01-30		ENSG00000137802	ENSG00000137802		"WD repeat domain containing"	29536	protein-coding gene	gene with protein product			"mitogen activated protein kinase binding protein 1"			9628581, 10471813	Standard	NM_014994		Approved	KIAA0596	uc001zok.4	O60336	OTTHUMG00000160227	ENST00000456763.2:c.620A>G	chr15.hg19:g.42104835A>G	ENSP00000393099:p.Asp207Gly	110.0	0.0		61.0	4.0	NM_001128608	A6NM93|A8K8P9|Q14CB5|Q14CD8|Q49AJ8|Q5W9G9	Missense_Mutation	SNP	ENST00000456763.2	hg19	CCDS45239.1	.	.	.	.	.	.	.	.	.	.	a	19.15	3.771653	0.69992	.	.	ENSG00000137802	ENST00000457542;ENST00000221214;ENST00000260357;ENST00000456763;ENST00000514566	T;T;T;T;T	0.57436	1.18;0.4;0.93;1.23;1.33	5.95	5.95	0.96441	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.088446	0.85682	D	0.000000	T	0.53753	0.1816	L	0.29908	0.895	0.45594	D	0.998539	D;P;P;B	0.60575	0.988;0.726;0.629;0.038	P;B;B;B	0.53861	0.736;0.399;0.444;0.12	T	0.48736	-0.9009	10	0.27082	T	0.32	-24.1512	16.4101	0.83708	1.0:0.0:0.0:0.0	.	95;207;207;207	F8WC21;O60336-2;O60336;O60336-6	.;.;MABP1_HUMAN;.	G	207;207;95;207;207	ENSP00000397570:D207G;ENSP00000221214:D207G;ENSP00000260357:D95G;ENSP00000393099:D207G;ENSP00000426154:D207G	ENSP00000221214:D207G	D	+	2	0	MAPKBP1	39892127	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	5.975000	0.70475	2.280000	0.76307	0.460000	0.39030	GAC	.	.		0.572	MAPKBP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359745.1	NM_014994		G	42104835	A	G	42104835	3	3	260	1	0	0	0	0	1	0	0	0	9301	275	10	2	642	2	MAPKBP1	15	42104835	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	765169	42104835	60426557	634	37879										
MAPKBP1	23005	hgsc.bcm.edu	37	chr15	42107824	42107824	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tctaacctgttccactaggaCctcattaaaatcatctatgt	4	11	4	0	rs200313290		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:42107824C>T	ENST00000456763.2	+	13	1534	c.1338C>T	c.(1336-1338)gaC>gaT	p.D446D	MAPKBP1_ENST00000457542.2_Silent_p.D440D|MAPKBP1_ENST00000221214.6_Silent_p.D323D|MAPKBP1_ENST00000260357.7_Silent_p.D279D|MAPKBP1_ENST00000514566.1_Silent_p.D440D	NM_001128608.1	NP_001122080.1	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein 1	446								p.D440D(1)		breast(6)|central_nervous_system(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)		TCCACTAGGACCTCATTAAAA	0.537																																					p.D446D		Atlas-SNP	.											MAPKBP1,brain,glioma,0,1	MAPKBP1	120	.	1	Substitution - coding silent(1)	central_nervous_system(1)	c.C1338T						.						47	43	44					15																	42107824		2203	4300	6503	SO:0001819	synonymous_variant	23005	exon13			CTAGGACCTCATT	AB011168	CCDS32201.1, CCDS45239.1, CCDS58359.1	15q15.1	2013-01-10	2008-01-30		ENSG00000137802	ENSG00000137802		"WD repeat domain containing"	29536	protein-coding gene	gene with protein product			"mitogen activated protein kinase binding protein 1"			9628581, 10471813	Standard	NM_014994		Approved	KIAA0596	uc001zok.4	O60336	OTTHUMG00000160227	ENST00000456763.2:c.1338C>T	chr15.hg19:g.42107824C>T		47.0	0.0		25.0	2.0	NM_001128608	A6NM93|A8K8P9|Q14CB5|Q14CD8|Q49AJ8|Q5W9G9	Silent	SNP	ENST00000456763.2	hg19	CCDS45239.1																																																																																			.	C|1.000;A|0.000		0.537	MAPKBP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359745.1	NM_014994		T	42107824	C	T	42107824	2	4	260	1	0	0	0	0	0	0	0	1	9301	506	18	3		3	MAPKBP1	15	42107824	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	2989	42107824	60423568	635	37880										
GANC	2595	hgsc.bcm.edu	37	chr15	42621587	42621587	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gagcaaaccatgcagaagaaTgccattcatcatggcaattg	9	9	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:42621587T>C	ENST00000318010.8	+	14	1824	c.1584T>C	c.(1582-1584)aaT>aaC	p.N528N		NM_198141.2	NP_937784.2	Q8TET4	GANC_HUMAN	glucosidase, alpha; neutral C	528					carbohydrate metabolic process (GO:0005975)		alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|maltose alpha-glucosidase activity (GO:0032450)			breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		all_cancers(109;3.08e-16)|all_epithelial(112;7.48e-15)|Lung NSC(122;3.08e-09)|all_lung(180;1.48e-08)|Melanoma(134;0.0574)|Colorectal(260;0.153)		GBM - Glioblastoma multiforme(94;1.06e-06)	Miglitol(DB00491)	TGCAGAAGAATGCCATTCATC	0.443																																					p.N528N		Atlas-SNP	.											.	GANC	57	.	0			c.T1584C						.						119	101	107					15																	42621587		2203	4299	6502	SO:0001819	synonymous_variant	2595	exon14			GAAGAATGCCATT	AF545045	CCDS10084.1	15q15.2	2012-10-02			ENSG00000214013	ENSG00000214013	3.2.1.20		4139	protein-coding gene	gene with protein product		104180				6995030, 12370436	Standard	NM_198141		Approved		uc001zpi.3	Q8TET4	OTTHUMG00000130487	ENST00000318010.8:c.1584T>C	chr15.hg19:g.42621587T>C		69.0	0.0		46.0	4.0	NM_198141	Q52LQ4|Q8IWZ0|Q8IZM4|Q8IZM5	Silent	SNP	ENST00000318010.8	hg19	CCDS10084.1																																																																																			.	.		0.443	GANC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252887.2	NM_198141		C	42621587	T	C	42621587	2	2	260	1	0	0	0	0	0	0	0	1	6242	1461	51	2		2	GANC	15	42621587	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	513763	42621587	59909805	636	37881										
LRRC57	255252	hgsc.bcm.edu	37	chr15	42839716	42839716	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tttcagattgcatatctcatCaggcagaacagctggcaaag	9	9	3	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:42839716C>A	ENST00000323443.2	-	3	602	c.235G>T	c.(235-237)Gat>Tat	p.D79Y	HAUS2_ENST00000568876.1_5'Flank|HAUS2_ENST00000260372.3_5'Flank|HAUS2_ENST00000568846.2_5'Flank|LRRC57_ENST00000563454.1_Missense_Mutation_p.D79Y|LRRC57_ENST00000397130.3_Missense_Mutation_p.D79Y			Q8N9N7	LRC57_HUMAN	leucine rich repeat containing 57	79						extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|lung(5)|prostate(1)	8		all_cancers(109;1.99e-12)|all_epithelial(112;5.11e-11)|Lung NSC(122;4.53e-07)|all_lung(180;1.64e-06)|Melanoma(134;0.0262)		GBM - Glioblastoma multiforme(94;6.87e-07)		CATATCTCATCAGGCAGAACA	0.403																																					p.D79Y		Atlas-SNP	.											.	LRRC57	20	.	0			c.G235T						.						70	71	70					15																	42839716		2203	4299	6502	SO:0001583	missense	255252	exon4			TCTCATCAGGCAG	AK094891	CCDS10089.1	15q15.1	2006-02-13			ENSG00000180979	ENSG00000180979			26719	protein-coding gene	gene with protein product							Standard	NM_153260		Approved	FLJ36812	uc001zqc.3	Q8N9N7	OTTHUMG00000130679	ENST00000323443.2:c.235G>T	chr15.hg19:g.42839716C>A	ENSP00000326817:p.Asp79Tyr	207.0	0.0		115.0	5.0	NM_153260	Q7Z2Z6|Q8N1T6	Missense_Mutation	SNP	ENST00000323443.2	hg19	CCDS10089.1	.	.	.	.	.	.	.	.	.	.	C	14.53	2.563885	0.45694	.	.	ENSG00000180979	ENST00000323443;ENST00000397130	T;T	0.55052	0.54;0.54	5.63	5.63	0.86233	.	0.918363	0.09517	N	0.791423	T	0.59905	0.2228	L	0.60904	1.88	0.43263	D	0.995207	P	0.36599	0.56	B	0.39217	0.294	T	0.60702	-0.7211	10	0.72032	D	0.01	.	20.0572	0.97657	0.0:1.0:0.0:0.0	.	79	Q8N9N7	LRC57_HUMAN	Y	79	ENSP00000326817:D79Y;ENSP00000380319:D79Y	ENSP00000326817:D79Y	D	-	1	0	LRRC57	40627008	0.943000	0.32029	1.000000	0.80357	0.995000	0.86356	3.032000	0.49736	2.826000	0.97356	0.655000	0.94253	GAT	.	.		0.403	LRRC57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253174.1	NM_153260		A	42839716	C	A	42839716	3	1	260	1	0	0	0	0	1	0	0	0	9022	826	29	3	496	3	LRRC57	15	42839716	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	218129	42839716	59691676	637	37882										
TGM5	9333	hgsc.bcm.edu	37	chr15	43548802	43548802	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggacatgggcggatccagttCttgctgccttggtagatgaa	14	8	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:43548802C>T	ENST00000220420.5	-	4	526	c.519G>A	c.(517-519)aaG>aaA	p.K173K	TGM5_ENST00000349114.4_Silent_p.K91K	NM_201631.3	NP_963925.2	O43548	TGM5_HUMAN	transglutaminase 5	173					cellular protein modification process (GO:0006464)|epidermis development (GO:0008544)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(11)|lung(15)|skin(6)|urinary_tract(1)	44		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;4e-07)	L-Glutamine(DB00130)	GGATCCAGTTCTTGCTGCCTT	0.562																																					p.K173K		Atlas-SNP	.											.	TGM5	88	.	0			c.G519A						.						229	190	203					15																	43548802		2202	4299	6501	SO:0001819	synonymous_variant	9333	exon4			CCAGTTCTTGCTG	AF035960	CCDS32211.1, CCDS32212.1	15q15	2004-07-07				ENSG00000104055		"Transglutaminases"	11781	protein-coding gene	gene with protein product		603805				9452468, 11390390	Standard	NM_201631		Approved	TGX	uc001zrd.2	O43548		ENST00000220420.5:c.519G>A	chr15.hg19:g.43548802C>T		163.0	0.0		119.0	6.0	NM_201631	O43549|Q0VF40|Q9UEZ4	Silent	SNP	ENST00000220420.5	hg19	CCDS32212.1																																																																																			.	.		0.562	TGM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432257.1	NM_004245		T	43548802	C	T	43548802	2	4	260	1	0	0	0	0	0	0	0	1	15848	912	32	3		3	TGM5	15	43548802	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	709086	43548802	58982590	638	37883										
TUBGCP4	27229	hgsc.bcm.edu	37	chr15	43689513	43689513	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcgagtatcacggaaaggagCacaaaggtttgccattcctc	10	10	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:43689513C>T	ENST00000260383.7	+	12	1527	c.1273C>T	c.(1273-1275)Cac>Tac	p.H425Y	TUBGCP4_ENST00000399460.3_Missense_Mutation_p.H289Y|TUBGCP4_ENST00000564079.1_Missense_Mutation_p.H425Y			Q9UGJ1	GCP4_HUMAN	tubulin, gamma complex associated protein 4	425					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|protein complex assembly (GO:0006461)	centrosome (GO:0005813)|cytosol (GO:0005829)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|spindle pole (GO:0000922)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(4)|prostate(2)|upper_aerodigestive_tract(2)	21		all_cancers(109;1.27e-10)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.72e-06)|all_lung(180;1.59e-05)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;3.53e-07)		CGGAAAGGAGCACAAAGGTTT	0.483																																					p.H425Y		Atlas-SNP	.											.	TUBGCP4	48	.	0			c.C1273T						.						139	136	137					15																	43689513		2063	4209	6272	SO:0001583	missense	27229	exon12			AAGGAGCACAAAG	AJ249677	CCDS42030.1, CCDS66745.1	15q15.3	2014-08-12			ENSG00000137822	ENSG00000137822			16691	protein-coding gene	gene with protein product		609610				10562286	Standard	NM_001286414		Approved	76P, FLJ14797	uc001zrn.3	Q9UGJ1	OTTHUMG00000176647	ENST00000260383.7:c.1273C>T	chr15.hg19:g.43689513C>T	ENSP00000260383:p.His425Tyr	134.0	0.0		70.0	4.0	NM_014444	B3KNK6|Q969X3|Q9NVF0	Missense_Mutation	SNP	ENST00000260383.7	hg19		.	.	.	.	.	.	.	.	.	.	C	11.97	1.797389	0.31777	.	.	ENSG00000137822	ENST00000260383;ENST00000399460	T;T	0.08193	3.12;3.12	5.11	5.11	0.69529	.	1.086800	0.06898	N	0.805435	T	0.06508	0.0167	N	0.03608	-0.345	0.35280	D	0.781275	B;B	0.22541	0.071;0.0	B;B	0.21708	0.036;0.001	T	0.43393	-0.9394	10	0.33940	T	0.23	-14.8412	18.0692	0.89400	0.0:1.0:0.0:0.0	.	425;425	Q9UGJ1;Q9UGJ1-2	GCP4_HUMAN;.	Y	425;289	ENSP00000260383:H425Y;ENSP00000382387:H289Y	ENSP00000260383:H425Y	H	+	1	0	TUBGCP4	41476805	0.999000	0.42202	0.670000	0.29842	0.968000	0.65278	2.319000	0.43788	2.816000	0.96949	0.563000	0.77884	CAC	.	.		0.483	TUBGCP4-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000432970.1	NM_014444		T	43689513	C	T	43689513	3	4	260	1	0	0	0	0	1	0	0	0	16783	710	25	3	1319	3	TUBGCP4	15	43689513	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	140711	43689513	58841879	639	37884										
SPG11	80208	hgsc.bcm.edu	37	chr15	44859730	44859730	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggcaatcatattgtgcttttCactgtctccaggacggcagc	10	11	3	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:44859730C>T	ENST00000261866.7	-	36	6662	c.6646G>A	c.(6646-6648)Gaa>Aaa	p.E2216K	SPG11_ENST00000535302.2_Missense_Mutation_p.E2103K|SPG11_ENST00000427534.2_Missense_Mutation_p.E2216K	NM_025137.3	NP_079413.3	Q96JI7	SPTCS_HUMAN	spastic paraplegia 11 (autosomal recessive)	2216					cell death (GO:0008219)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	72		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		TTGTGCTTTTCACTGTCTCCA	0.517																																					p.E2216K		Atlas-SNP	.											.	SPG11	207	.	0			c.G6646A						.						90	79	82					15																	44859730		2198	4298	6496	SO:0001583	missense	80208	exon36			GCTTTTCACTGTC		CCDS10112.1, CCDS53939.1	15q13-q15	2007-11-13			ENSG00000104133	ENSG00000104133			11226	protein-coding gene	gene with protein product	"spatacsin"	610844	"KIAA1840"	KIAA1840		10408536, 17322883	Standard	NM_001160227		Approved	FLJ21439	uc001ztx.3	Q96JI7	OTTHUMG00000131199	ENST00000261866.7:c.6646G>A	chr15.hg19:g.44859730C>T	ENSP00000261866:p.Glu2216Lys	142.0	0.0		73.0	4.0	NM_025137	A8KAX9|B9EK60|F5H3N6|Q4VC11|Q58G86|Q69YG6|Q6NW01|Q8N270|Q8TBU9|Q9H734	Missense_Mutation	SNP	ENST00000261866.7	hg19	CCDS10112.1	.	.	.	.	.	.	.	.	.	.	C	37	6.269070	0.97431	.	.	ENSG00000104133	ENST00000261866;ENST00000535302;ENST00000427534	D;T;D	0.82984	-1.67;-1.26;-1.52	6.14	6.14	0.99180	.	0.000000	0.85682	D	0.000000	D	0.91633	0.7356	M	0.76002	2.32	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.998;0.999;0.999	D	0.91082	0.4900	10	0.72032	D	0.01	.	20.819	0.99723	0.0:1.0:0.0:0.0	.	2216;2103;2216;2216	C4B7M2;F5H3N6;C4B7M4;Q96JI7	.;.;.;SPTCS_HUMAN	K	2216;2103;2216	ENSP00000261866:E2216K;ENSP00000445278:E2103K;ENSP00000396110:E2216K	ENSP00000261866:E2216K	E	-	1	0	SPG11	42647022	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.773000	0.85462	2.927000	0.99377	0.637000	0.83480	GAA	.	.		0.517	SPG11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253927.1			T	44859730	C	T	44859730	3	4	260	1	0	0	0	0	1	0	0	0	15056	835	29	3	705	3	SPG11	15	44859730	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	1170217	44859730	57671662	640	37885										
SPG11	80208	hgsc.bcm.edu	37	chr15	44903081	44903081	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acattgtagtagcaagggccAggagggtatgtccttccaat	12	8	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:44903081A>G	ENST00000261866.7	-	18	3264	c.3248T>C	c.(3247-3249)cTg>cCg	p.L1083P	SPG11_ENST00000535302.2_Missense_Mutation_p.L1083P|SPG11_ENST00000558319.1_Missense_Mutation_p.L1083P|SPG11_ENST00000427534.2_Missense_Mutation_p.L1083P	NM_025137.3	NP_079413.3	Q96JI7	SPTCS_HUMAN	spastic paraplegia 11 (autosomal recessive)	1083					cell death (GO:0008219)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	72		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		AGCAAGGGCCAGGAGGGTATG	0.433																																					p.L1083P		Atlas-SNP	.											.	SPG11	207	.	0			c.T3248C						.						126	109	114					15																	44903081		2198	4298	6496	SO:0001583	missense	80208	exon18			AGGGCCAGGAGGG		CCDS10112.1, CCDS53939.1	15q13-q15	2007-11-13			ENSG00000104133	ENSG00000104133			11226	protein-coding gene	gene with protein product	"spatacsin"	610844	"KIAA1840"	KIAA1840		10408536, 17322883	Standard	NM_001160227		Approved	FLJ21439	uc001ztx.3	Q96JI7	OTTHUMG00000131199	ENST00000261866.7:c.3248T>C	chr15.hg19:g.44903081A>G	ENSP00000261866:p.Leu1083Pro	116.0	0.0		95.0	5.0	NM_025137	A8KAX9|B9EK60|F5H3N6|Q4VC11|Q58G86|Q69YG6|Q6NW01|Q8N270|Q8TBU9|Q9H734	Missense_Mutation	SNP	ENST00000261866.7	hg19	CCDS10112.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.119956	0.77323	.	.	ENSG00000104133	ENST00000261866;ENST00000535302;ENST00000427534	T;T;T	0.35789	1.29;1.29;1.29	5.58	5.58	0.84498	.	0.000000	0.64402	D	0.000009	T	0.60301	0.2258	M	0.74881	2.28	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	T	0.64516	-0.6389	10	0.72032	D	0.01	.	13.9677	0.64218	1.0:0.0:0.0:0.0	.	1083;1083;1083	C4B7M2;F5H3N6;Q96JI7	.;.;SPTCS_HUMAN	P	1083	ENSP00000261866:L1083P;ENSP00000445278:L1083P;ENSP00000396110:L1083P	ENSP00000261866:L1083P	L	-	2	0	SPG11	42690373	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.799000	0.85936	2.115000	0.64714	0.397000	0.26171	CTG	.	.		0.433	SPG11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253927.1			G	44903081	A	G	44903081	3	3	260	1	0	0	0	0	1	0	0	0	15056	188	7	2	4175	2	SPG11	15	44903081	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	43351	44903081	57628311	641	37886										
DUOXA2	405753	hgsc.bcm.edu	37	chr15	45408394	45408394	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctacaaagccttcagcgcagCgcgcgttacagcccgtgtcc	10	16	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:45408394C>T	ENST00000323030.5	+	3	563	c.278C>T	c.(277-279)gCg>gTg	p.A93V	DUOX2_ENST00000389039.6_5'Flank|DUOX2_ENST00000603300.1_5'Flank	NM_207581.3	NP_997464.2	Q1HG44	DOXA2_HUMAN	dual oxidase maturation factor 2	93					hydrogen peroxide metabolic process (GO:0042743)|protein transport (GO:0015031)|regulation of inflammatory response (GO:0050727)|regulation of thyroid hormone generation (GO:2000609)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)							all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;2.88e-18)|GBM - Glioblastoma multiforme(94;3.95e-07)|COAD - Colon adenocarcinoma(120;0.0652)|Colorectal(133;0.0659)		TTCAGCGCAGCGCGCGTTACA	0.577																																					p.A93V		Atlas-SNP	.											.	DUOXA2	38	.	0			c.C278T						.						137	129	132					15																	45408394		2003	4152	6155	SO:0001583	missense	405753	exon3			GCGCAGCGCGCGT	BX537581	CCDS10118.2	15q21.1	2008-10-30		2006-07-25	ENSG00000140274	ENSG00000140274			32698	protein-coding gene	gene with protein product		612772				16651268	Standard	NM_207581		Approved		uc001zuo.3	Q1HG44	OTTHUMG00000131354	ENST00000323030.5:c.278C>T	chr15.hg19:g.45408394C>T	ENSP00000319705:p.Ala93Val	97.0	0.0		76.0	4.0	NM_207581	B2RPI9|H0YNQ6	Missense_Mutation	SNP	ENST00000323030.5	hg19	CCDS10118.2	.	.	.	.	.	.	.	.	.	.	C	8.786	0.929456	0.18131	.	.	ENSG00000140274	ENST00000323030	T	0.56611	0.45	5.38	-3.84	0.04256	.	0.412635	0.28262	N	0.015999	T	0.62208	0.2409	M	0.74258	2.255	0.09310	N	1	D	0.69078	0.997	P	0.55222	0.771	T	0.64495	-0.6394	10	0.38643	T	0.18	-1.2827	18.2262	0.89917	0.7357:0.2643:0.0:0.0	.	93	Q1HG44	DOXA2_HUMAN	V	93	ENSP00000319705:A93V	ENSP00000319705:A93V	A	+	2	0	DUOXA2	43195686	0.005000	0.15991	0.000000	0.03702	0.063000	0.16089	0.130000	0.15850	-1.136000	0.02892	-0.521000	0.04368	GCG	.	.		0.577	DUOXA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254142.1	NM_207581		T	45408394	C	T	45408394	3	4	260	1	0	0	0	0	1	0	0	0	4805	768	27	1	288	1	DUOXA2	15	45408394	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	505313	45408394	57122998	642	37887										
SLC24A5	283652	hgsc.bcm.edu	37	chr15	48413333	48413333	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tctgcctctctcagggacctCcctgccccaacgtctcccaa	6	20	4	0	rs201294244	byFrequency	TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:48413333C>A	ENST00000341459.3	+	1	165	c.92C>A	c.(91-93)tCc>tAc	p.S31Y	SLC24A5_ENST00000449382.2_Missense_Mutation_p.S31Y|SLC24A5_ENST00000482911.2_Missense_Mutation_p.S31Y	NM_205850.2	NP_995322.1	Q71RS6	NCKX5_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 5	31					ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|negative regulation of melanin biosynthetic process (GO:0048022)|response to stimulus (GO:0050896)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(17)|skin(1)|upper_aerodigestive_tract(1)	27		all_lung(180;0.00217)		all cancers(107;3.29e-10)|GBM - Glioblastoma multiforme(94;7.32e-07)		TCAGGGACCTCCCTGCCCCAA	0.587																																					p.S31Y		Atlas-SNP	.											.	SLC24A5	64	.	0			c.C92A						.						59	51	54					15																	48413333		2198	4297	6495	SO:0001583	missense	283652	exon1			GGACCTCCCTGCC	AF348468	CCDS10128.1	15q21.1	2014-01-28	2013-07-18		ENSG00000188467	ENSG00000188467		"Solute carriers"	20611	protein-coding gene	gene with protein product	"oculocutaneous albinism 6 (autosomal recessive)"	609802	"solute carrier family 24, member 5"			23364476	Standard	XM_005254308		Approved	JSX, OCA6	uc001zwe.3	Q71RS6	OTTHUMG00000131494	ENST00000341459.3:c.92C>A	chr15.hg19:g.48413333C>A	ENSP00000341550:p.Ser31Tyr	60.0	0.0		55.0	4.0	NM_205850	A5X8Z8|A5X8Z9|Q14CT4|Q6DKH3	Missense_Mutation	SNP	ENST00000341459.3	hg19	CCDS10128.1	.	.	.	.	.	.	.	.	.	.	C	13.33	2.205027	0.38905	.	.	ENSG00000188467	ENST00000341459;ENST00000449382	T;T	0.75477	-0.93;-0.94	5.38	4.46	0.54185	.	0.255835	0.28393	N	0.015509	T	0.61726	0.2370	N	0.14661	0.345	0.09310	N	1	P;B;P	0.46277	0.454;0.278;0.875	B;B;P	0.44647	0.276;0.088;0.456	T	0.58429	-0.7638	10	0.62326	D	0.03	.	11.5957	0.50972	0.0:0.9164:0.0:0.0836	.	31;31;31	A5X8Z9;Q71RS6;A5X8Z8	.;NCKX5_HUMAN;.	Y	31	ENSP00000341550:S31Y;ENSP00000389966:S31Y	ENSP00000341550:S31Y	S	+	2	0	SLC24A5	46200625	0.036000	0.19791	0.895000	0.35142	0.097000	0.18754	2.171000	0.42453	1.488000	0.48433	0.655000	0.94253	TCC	.	C|0.999;T|0.001		0.587	SLC24A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254340.2	NM_205850		A	48413333	C	A	48413333	3	1	260	1	0	0	0	0	1	0	0	0	14484	855	30	3	94	3	SLC24A5	15	48413333	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	3004939	48413333	54118059	643	37888										
DMXL2	23312	hgsc.bcm.edu	37	chr15	51766616	51766616	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aaaaacagcagcccacattcGattatttaatgggtgggctg	10	8	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:51766616G>T	ENST00000251076.5	-	28	7422	c.7135C>A	c.(7135-7137)Cga>Aga	p.R2379R	RP11-707P17.1_ENST00000561007.1_RNA|DMXL2_ENST00000449909.3_Silent_p.R1743R|DMXL2_ENST00000543779.2_Silent_p.R2380R	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	2379						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)	p.R2379*(1)		breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		GCCCACATTCGATTATTTAAT	0.388																																					p.R2380R		Atlas-SNP	.											DMXL2,colon,carcinoma,+1,1	DMXL2	262	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C7138A						.						54	56	55					15																	51766616		2196	4293	6489	SO:0001819	synonymous_variant	23312	exon28			ACATTCGATTATT	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"WD repeat domain containing"	2938	protein-coding gene	gene with protein product	"rabconnectin 3"	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.7135C>A	chr15.hg19:g.51766616G>T		125.0	2.0		84.0	4.0	NM_001174116	B2RTR3|B7ZMH3|F5GWF1|O94938	Silent	SNP	ENST00000251076.5	hg19	CCDS10141.1																																																																																			.	.		0.388	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263		T	51766616	G	T	51766616	2	4	260	1	0	0	0	0	0	0	0	1	4597	1066	37	1		1	DMXL2	15	51766616	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	3353283	51766616	50764776	644	37889										
MYO5C	55930	hgsc.bcm.edu	37	chr15	52540902	52540902	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	taggactttacagaccttgcTtgctctcaggatttcaacca	7	11	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:52540902T>C	ENST00000261839.7	-	14	1902	c.1741A>G	c.(1741-1743)Agc>Ggc	p.S581G	MYO5C_ENST00000443683.2_3'UTR	NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	581	Myosin motor.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(7)|large_intestine(15)|lung(12)|ovary(7)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66				all cancers(107;0.0137)		CAGACCTTGCTTGCTCTCAGG	0.378																																					p.S581G		Atlas-SNP	.											.	MYO5C	162	.	0			c.A1741G						.						111	105	107					15																	52540902		1854	4089	5943	SO:0001583	missense	55930	exon14			CCTTGCTTGCTCT	AF272390	CCDS42036.1	15q21	2011-09-27				ENSG00000128833		"Myosins / Myosin superfamily : Class V"	7604	protein-coding gene	gene with protein product	"myosin 5C"	610022				11870218	Standard	NM_018728		Approved	MGC74969	uc010bff.3	Q9NQX4		ENST00000261839.7:c.1741A>G	chr15.hg19:g.52540902T>C	ENSP00000261839:p.Ser581Gly	179.0	0.0		94.0	6.0	NM_018728	Q6P1W8	Missense_Mutation	SNP	ENST00000261839.7	hg19	CCDS42036.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.617376	0.87359	.	.	ENSG00000128833	ENST00000261839	D	0.97455	-4.39	5.48	5.48	0.80851	Myosin head, motor domain (2);	0.083812	0.85682	D	0.000000	D	0.98311	0.9440	M	0.93106	3.38	0.80722	D	1	D	0.54207	0.965	P	0.53912	0.737	D	0.99097	1.0842	10	0.66056	D	0.02	.	15.6198	0.76796	0.0:0.0:0.0:1.0	.	581	Q9NQX4	MYO5C_HUMAN	G	581	ENSP00000261839:S581G	ENSP00000261839:S581G	S	-	1	0	MYO5C	50328194	1.000000	0.71417	0.994000	0.49952	0.979000	0.70002	5.983000	0.70540	2.097000	0.63578	0.454000	0.30748	AGC	.	.		0.378	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728		C	52540902	T	C	52540902	3	2	260	1	0	0	0	0	1	0	0	0	10089	1609	56	2	3599	2	MYO5C	15	52540902	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	774286	52540902	49990490	645	37890										
WDR72	256764	hgsc.bcm.edu	37	chr15	54003136	54003136	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttccatcagcagggtatatgCtttttgaaagcccactgcgt	9	10	1	1	rs374482757		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:54003136C>T	ENST00000396328.1	-	9	1111	c.872G>A	c.(871-873)aGc>aAc	p.S291N	WDR72_ENST00000360509.5_Missense_Mutation_p.S291N|WDR72_ENST00000559418.1_Missense_Mutation_p.S303N|WDR72_ENST00000557913.1_Missense_Mutation_p.S290N	NM_001277176.1|NM_182758.2	NP_001264105.1|NP_877435.3	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	291										NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(18)|lung(29)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	71				all cancers(107;0.0511)		AGGGTATATGCTTTTTGAAAG	0.388																																					p.S291N		Atlas-SNP	.											.	WDR72	177	.	0			c.G872A						.	C	ASN/SER	2,4386	4.2+/-10.8	0,2,2192	110	100	104		872	5.6	1	15		104	0,8586		0,0,4293	no	missense	WDR72	NM_182758.2	46	0,2,6485	TT,TC,CC		0.0,0.0456,0.0154	benign	291/1103	54003136	2,12972	2194	4293	6487	SO:0001583	missense	256764	exon9			TATATGCTTTTTG	BX537884	CCDS10151.1, CCDS73730.1	15q21.3	2013-01-09			ENSG00000166415	ENSG00000166415		"WD repeat domain containing"	26790	protein-coding gene	gene with protein product		613214					Standard	NM_182758		Approved	FLJ38736	uc002acj.2	Q3MJ13	OTTHUMG00000131939	ENST00000396328.1:c.872G>A	chr15.hg19:g.54003136C>T	ENSP00000379619:p.Ser291Asn	47.0	0.0		52.0	4.0	NM_182758	Q7Z3I3|Q8N8X2	Missense_Mutation	SNP	ENST00000396328.1	hg19	CCDS10151.1	.	.	.	.	.	.	.	.	.	.	C	12.54	1.969668	0.34754	4.56E-4	0.0	ENSG00000166415	ENST00000396328;ENST00000360509	T;T	0.55052	0.54;0.54	5.58	5.58	0.84498	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.108147	0.64402	D	0.000004	T	0.45617	0.1351	L	0.44542	1.39	0.31561	N	0.657464	P	0.47106	0.89	B	0.37943	0.261	T	0.53019	-0.8497	10	0.27785	T	0.31	.	18.9191	0.92518	0.0:1.0:0.0:0.0	.	291	Q3MJ13	WDR72_HUMAN	N	291	ENSP00000379619:S291N;ENSP00000353699:S291N	ENSP00000353699:S291N	S	-	2	0	WDR72	51790428	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	5.017000	0.64047	2.778000	0.95560	0.655000	0.94253	AGC	.	.		0.388	WDR72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254893.2	NM_182758		T	54003136	C	T	54003136	3	4	260	1	0	0	0	0	1	0	0	0	17337	797	28	3	2484	3	WDR72	15	54003136	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	1462234	54003136	48528256	646	37891										
CCNB2	9133	hgsc.bcm.edu	37	chr15	59409529	59409529	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctaaggtagcagcagctgctTcctgcttgtctcagaaggtt	11	10	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:59409529T>C	ENST00000288207.2	+	7	1128	c.937T>C	c.(937-939)Tcc>Ccc	p.S313P	CCNB2_ENST00000559622.1_Intron	NM_004701.3	NP_004692.1	O95067	CCNB2_HUMAN	cyclin B2	313					G2/M transition of mitotic cell cycle (GO:0000086)|growth (GO:0040007)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)	centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)				kidney(4)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	9						AGCAGCTGCTTCCTGCTTGTC	0.403																																					p.S313P		Atlas-SNP	.											.	CCNB2	23	.	0			c.T937C						.						111	101	105					15																	59409529		2191	4291	6482	SO:0001583	missense	9133	exon7			GCTGCTTCCTGCT	AF002822	CCDS10170.1	15q21.3	2004-01-19			ENSG00000157456	ENSG00000157456			1580	protein-coding gene	gene with protein product		602755					Standard	NM_004701		Approved	HsT17299	uc002afz.3	O95067	OTTHUMG00000132715	ENST00000288207.2:c.937T>C	chr15.hg19:g.59409529T>C	ENSP00000288207:p.Ser313Pro	111.0	0.0		64.0	4.0	NM_004701	B3KM93|Q6FI99	Missense_Mutation	SNP	ENST00000288207.2	hg19	CCDS10170.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.272716	0.80580	.	.	ENSG00000157456	ENST00000288207	T	0.21932	1.98	5.45	5.45	0.79879	Cyclin, C-terminal (1);Cyclin-like (3);	0.094304	0.56097	D	0.000021	T	0.31358	0.0794	L	0.55481	1.735	0.80722	D	1	P	0.51537	0.946	P	0.56163	0.793	T	0.08973	-1.0696	10	0.72032	D	0.01	.	6.4997	0.22162	0.0:0.1734:0.0:0.8266	.	313	O95067	CCNB2_HUMAN	P	313	ENSP00000288207:S313P	ENSP00000288207:S313P	S	+	1	0	CCNB2	57196821	0.996000	0.38824	0.845000	0.33349	0.995000	0.86356	3.038000	0.49783	2.065000	0.61736	0.533000	0.62120	TCC	.	.		0.403	CCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256016.1	NM_004701		C	59409529	T	C	59409529	3	2	260	1	0	0	0	0	1	0	0	0	2915	1783	62	2	963	2	CCNB2	15	59409529	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	5406393	59409529	43121863	647	37892										
NARG2	79664	hgsc.bcm.edu	37	chr15	60720770	60720770	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aaggtacaccaggaaggccgCaatgtgttttatacaaattg	10	7	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:60720770C>T	ENST00000261520.4	-	15	2912	c.2678G>A	c.(2677-2679)tGc>tAc	p.C893Y	NARG2_ENST00000439632.1_Missense_Mutation_p.C756Y	NM_024611.4	NP_078887.2														breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	32						AGGAAGGCCGCAATGTGTTTT	0.418																																					p.C893Y		Atlas-SNP	.											.	NARG2	82	.	0			c.G2678A						.						84	81	82					15																	60720770		2203	4300	6503	SO:0001583	missense	79664	exon15			AGGCCGCAATGTG																												ENST00000261520.4:c.2678G>A	chr15.hg19:g.60720770C>T	ENSP00000261520:p.Cys893Tyr	155.0	0.0		96.0	4.0	NM_024611		Missense_Mutation	SNP	ENST00000261520.4	hg19	CCDS10176.1	.	.	.	.	.	.	.	.	.	.	C	15.02	2.709978	0.48517	.	.	ENSG00000128915	ENST00000261520;ENST00000439632	.	.	.	5.96	4.06	0.47325	NMDA receptor-regulated gene protein 2 (1);	0.420659	0.29551	N	0.011823	T	0.42787	0.1218	L	0.53249	1.67	0.09310	N	1	B	0.18461	0.028	B	0.19666	0.026	T	0.42882	-0.9425	9	0.72032	D	0.01	-0.1891	9.7395	0.40409	0.0:0.6664:0.2634:0.0701	.	893	Q659A1	NARG2_HUMAN	Y	893;756	.	ENSP00000261520:C893Y	C	-	2	0	NARG2	58508062	0.007000	0.16637	0.001000	0.08648	0.826000	0.46750	1.194000	0.32174	0.834000	0.34852	0.650000	0.86243	TGC	.	.		0.418	NARG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256136.1			T	60720770	C	T	60720770	3	4	260	1	0	0	0	0	1	0	0	0	10178	710	25	3	278	3	NARG2	15	60720770	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	1311241	60720770	41810622	648	37893										
VPS13C	54832	hgsc.bcm.edu	37	chr15	62352482	62352482	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cctctcgcttaccgccccagAtgcccagcttcagctgggac	9	18	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:62352482A>C	ENST00000261517.5	-	1	165	c.92T>G	c.(91-93)aTc>aGc	p.I31S	VPS13C_ENST00000249837.3_Missense_Mutation_p.I31S|RP11-643M14.1_ENST00000560813.2_RNA|VPS13C_ENST00000395898.3_Missense_Mutation_p.I31S|VPS13C_ENST00000395896.4_Missense_Mutation_p.I31S|RP11-643M14.1_ENST00000558368.2_RNA	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						ACCGCCCCAGATGCCCAGCTT	0.687																																					p.I31S		Atlas-SNP	.											.	VPS13C	506	.	0			c.T92G						.						28	27	28					15																	62352482		2203	4300	6503	SO:0001583	missense	54832	exon1			CCCCAGATGCCCA	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"vacuolar protein sorting 13C (yeast)"				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.92T>G	chr15.hg19:g.62352482A>C	ENSP00000261517:p.Ile31Ser	84.0	0.0		50.0	15.0	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	hg19	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.159036	0.78226	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	D;D;D;D	0.84800	-1.9;-1.9;-1.9;-1.9	4.7	4.7	0.59300	.	0.000000	0.85682	D	0.000000	D	0.91633	0.7356	M	0.84082	2.675	0.80722	D	1	P;P;P;P	0.48503	0.821;0.891;0.821;0.911	P;P;P;D	0.63793	0.697;0.867;0.697;0.918	D	0.92630	0.6115	10	0.87932	D	0	.	12.1476	0.54031	1.0:0.0:0.0:0.0	.	31;31;31;31	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	S	31	ENSP00000249837:I31S;ENSP00000261517:I31S;ENSP00000379233:I31S;ENSP00000379235:I31S	ENSP00000249837:I31S	I	-	2	0	VPS13C	60139774	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.620000	0.67736	1.965000	0.57142	0.533000	0.62120	ATC	.	.		0.687	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		C	62352482	A	C	62352482	3	2	260	1	0	0	0	0	1	0	0	0	17206	333	12	5	11537	5	VPS13C	15	62352482	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1631712	62352482	40178910	649	37894										
USP3	9960	hgsc.bcm.edu	37	chr15	63850378	63850378	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tttcatgaatgccatccttcAgtcactcaggtaacgctaca	6	12	4	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:63850378A>G	ENST00000380324.3	+	6	653	c.524A>G	c.(523-525)cAg>cGg	p.Q175R	USP3_ENST00000536001.1_Intron|USP3-AS1_ENST00000559357.1_RNA|USP3_ENST00000559711.1_Missense_Mutation_p.Q86R|USP3-AS1_ENST00000559861.1_RNA|USP3_ENST00000540797.1_Missense_Mutation_p.Q131R|USP3_ENST00000558285.1_Missense_Mutation_p.Q158R|USP3-AS1_ENST00000560067.1_RNA|USP3_ENST00000268049.7_Missense_Mutation_p.Q153R|USP3_ENST00000539772.1_Intron|USP3-AS1_ENST00000560350.1_RNA	NM_006537.3	NP_006528.2	Q9Y6I4	UBP3_HUMAN	ubiquitin specific peptidase 3	175	USP.				DNA repair (GO:0006281)|histone deubiquitination (GO:0016578)|mitotic cell cycle (GO:0000278)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	nuclear chromatin (GO:0000790)	histone binding (GO:0042393)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(7)|lung(4)	14				GBM - Glioblastoma multiforme(80;0.0187)		GCCATCCTTCAGTCACTCAGG	0.498																																					p.Q175R		Atlas-SNP	.											.	USP3	37	.	0			c.A524G						.						140	113	122					15																	63850378		2203	4300	6503	SO:0001583	missense	9960	exon6			TCCTTCAGTCACT	AF073344	CCDS32265.1, CCDS58370.1	15q22.3	2008-04-11	2005-08-08			ENSG00000140455		"Ubiquitin-specific peptidases"	12626	protein-coding gene	gene with protein product		604728	"ubiquitin specific protease 3"			12838346	Standard	NM_006537		Approved		uc002amf.4	Q9Y6I4		ENST00000380324.3:c.524A>G	chr15.hg19:g.63850378A>G	ENSP00000369681:p.Gln175Arg	119.0	0.0		56.0	4.0	NM_006537	B4DVU5|F5H1A6|Q8WVD0	Missense_Mutation	SNP	ENST00000380324.3	hg19	CCDS32265.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.708253	0.89018	.	.	ENSG00000140455	ENST00000540797;ENST00000380324;ENST00000268049;ENST00000536848;ENST00000538686	T;T;T	0.09723	2.95;2.95;2.95	5.79	5.79	0.91817	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site (1);Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.48696	0.1514	H	0.98068	4.14	0.80722	D	1	D;D;D;D	0.69078	0.996;0.997;0.997;0.994	D;D;D;D	0.66979	0.913;0.948;0.948;0.948	T	0.68394	-0.5420	10	0.87932	D	0	.	14.6892	0.69072	1.0:0.0:0.0:0.0	.	131;131;153;175	F5H1A6;B4DVU5;Q6JHV3;Q9Y6I4	.;.;.;UBP3_HUMAN	R	131;175;153;90;6	ENSP00000445828:Q131R;ENSP00000369681:Q175R;ENSP00000268049:Q153R	ENSP00000268049:Q153R	Q	+	2	0	USP3	61637431	1.000000	0.71417	1.000000	0.80357	0.732000	0.41865	9.331000	0.96430	2.205000	0.71048	0.528000	0.53228	CAG	.	.		0.498	USP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417773.1			G	63850378	A	G	63850378	3	3	260	1	0	0	0	0	1	0	0	0	17075	188	7	2	546	2	USP3	15	63850378	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1497896	63850378	38681014	650	37895										
HERC1	8925	hgsc.bcm.edu	37	chr15	64047472	64047472	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cccatgtgtataattccccaTcctctgtgacagcagcacta	6	14	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:64047472T>C	ENST00000443617.2	-	6	1673	c.1586A>G	c.(1585-1587)gAt>gGt	p.D529G		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	529					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						TAATTCCCCATCCTCTGTGAC	0.353																																					p.D529G		Atlas-SNP	.											.	HERC1	624	.	0			c.A1586G						.						97	90	92					15																	64047472		1959	4138	6097	SO:0001583	missense	8925	exon6			TCCCCATCCTCTG	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.1586A>G	chr15.hg19:g.64047472T>C	ENSP00000390158:p.Asp529Gly	149.0	0.0		75.0	4.0	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	hg19	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	T	29.9	5.044435	0.93685	.	.	ENSG00000103657	ENST00000443617	D	0.89196	-2.48	5.97	5.97	0.96955	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.85682	U	0.000000	D	0.93657	0.7974	M	0.69463	2.115	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.79784	0.993;0.993	D	0.94023	0.7294	10	0.66056	D	0.02	.	16.1343	0.81471	0.0:0.0:0.0:1.0	.	529;529	C9JUT5;Q15751	.;HERC1_HUMAN	G	529	ENSP00000390158:D529G	ENSP00000390158:D529G	D	-	2	0	HERC1	61834525	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.276000	0.72601	2.288000	0.76882	0.533000	0.62120	GAT	.	.		0.353	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		C	64047472	T	C	64047472	3	2	260	1	0	0	0	0	1	0	0	0	7066	1435	50	2	13291	2	HERC1	15	64047472	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	197094	64047472	38483920	651	37896										
CILP	8483	hgsc.bcm.edu	37	chr15	65490900	65490900	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tggcttccaaagtgatgggcTttttccgacgaagcatcttg	11	9	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:65490900T>C	ENST00000261883.4	-	9	1890	c.1724A>G	c.(1723-1725)aAg>aGg	p.K575R		NM_003613.3	NP_003604	O75339	CILP1_HUMAN	cartilage intermediate layer protein, nucleotide pyrophosphohydrolase	575			K -> E (in dbSNP:rs2679118). {ECO:0000269|PubMed:10319588, ECO:0000269|PubMed:10601732, ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9722584}.		negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(17)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(1)	55						AGTGATGGGCTTTTTCCGACG	0.512																																					p.K575R		Atlas-SNP	.											.	CILP	124	.	0			c.A1724G						.						72	65	67					15																	65490900		2202	4299	6501	SO:0001583	missense	8483	exon9			ATGGGCTTTTTCC	AY358904	CCDS10203.1	15q22	2013-01-14			ENSG00000138615	ENSG00000138615		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1980	protein-coding gene	gene with protein product		603489				9722584, 9722583	Standard	NM_003613		Approved	HsT18872	uc002aon.2	O75339	OTTHUMG00000133140	ENST00000261883.4:c.1724A>G	chr15.hg19:g.65490900T>C	ENSP00000261883:p.Lys575Arg	126.0	0.0		77.0	4.0	NM_003613	B2R8F7|Q6UW99|Q8IYI5	Missense_Mutation	SNP	ENST00000261883.4	hg19	CCDS10203.1	.	.	.	.	.	.	.	.	.	.	T	0.378	-0.930194	0.02359	.	.	ENSG00000138615	ENST00000261883	T	0.40756	1.02	5.63	3.13	0.36017	.	0.653399	0.16048	N	0.232119	T	0.24122	0.0584	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.19811	-1.0294	10	0.51188	T	0.08	-12.4177	12.5426	0.56179	0.0:0.0:0.2165:0.7835	.	575	O75339	CILP1_HUMAN	R	575	ENSP00000261883:K575R	ENSP00000261883:K575R	K	-	2	0	CILP	63277953	0.646000	0.27295	1.000000	0.80357	0.093000	0.18481	1.662000	0.37418	2.145000	0.66743	0.533000	0.62120	AAG	.	.		0.512	CILP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256829.1	NM_003613		C	65490900	T	C	65490900	3	2	260	1	0	0	0	0	1	0	0	0	3431	1609	56	2	1834	2	CILP	15	65490900	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1443428	65490900	37040492	652	37897										
ZWILCH	55055	hgsc.bcm.edu	37	chr15	66820213	66820213	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agacttaaataagctggatgGatttggtgattctacaaaaa	9	4	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:66820213G>T	ENST00000307897.5	+	10	1312	c.932G>T	c.(931-933)gGa>gTa	p.G311V	ZWILCH_ENST00000535141.2_Missense_Mutation_p.G197V|ZWILCH_ENST00000565627.1_Missense_Mutation_p.G197V|ZWILCH_ENST00000446801.2_Missense_Mutation_p.G197V	NM_017975.3	NP_060445.3	Q9H900	ZWILC_HUMAN	zwilch kinetochore protein	311					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)	cytosol (GO:0005829)|kinetochore (GO:0000776)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|liver(1)|lung(6)|ovary(1)	18						AAGCTGGATGGATTTGGTGAT	0.308																																					p.G311V		Atlas-SNP	.											.	ZWILCH	46	.	0			c.G932T						.						81	81	81					15																	66820213		2201	4299	6500	SO:0001583	missense	55055	exon10			TGGATGGATTTGG	AK023175	CCDS10219.1, CCDS73746.1	15q22.31	2013-01-17	2012-12-13		ENSG00000174442	ENSG00000174442			25468	protein-coding gene	gene with protein product		609984	"Zwilch, kinetochore associated, homolog (Drosophila)"			12686595	Standard	NM_017975		Approved	FLJ10036, KNTC1AP	uc002aqb.3	Q9H900	OTTHUMG00000133194	ENST00000307897.5:c.932G>T	chr15.hg19:g.66820213G>T	ENSP00000311429:p.Gly311Val	183.0	0.0		122.0	5.0	NM_017975	B3KVB8|Q6N049|Q8N404|Q96SY7|Q9NWG7	Missense_Mutation	SNP	ENST00000307897.5	hg19	CCDS10219.1	.	.	.	.	.	.	.	.	.	.	G	17.55	3.416844	0.62511	.	.	ENSG00000174442	ENST00000307897;ENST00000446801;ENST00000535141	T;T;T	0.44482	0.92;0.92;0.92	5.96	0.645	0.17782	.	0.422728	0.27739	N	0.018057	T	0.48484	0.1502	L	0.50333	1.59	0.58432	D	0.999999	D	0.67145	0.996	D	0.67725	0.953	T	0.41378	-0.9512	10	0.62326	D	0.03	-4.5524	4.5931	0.12317	0.3601:0.1525:0.4873:0.0	.	311	Q9H900	ZWILC_HUMAN	V	311;197;197	ENSP00000311429:G311V;ENSP00000402217:G197V;ENSP00000437749:G197V	ENSP00000311429:G311V	G	+	2	0	ZWILCH	64607267	0.999000	0.42202	0.994000	0.49952	0.998000	0.95712	0.207000	0.17395	-0.121000	0.11787	0.655000	0.94253	GGA	.	.		0.308	ZWILCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256904.4	NM_017975		T	66820213	G	T	66820213	3	4	260	1	0	0	0	0	1	0	0	0	18263	1174	41	3	970	3	ZWILCH	15	66820213	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	1329313	66820213	35711179	653	37898										
HEXA	3073	hgsc.bcm.edu	37	chr15	72643538	72643538	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aaggatcatctaccagatgcCagtggaacacgttcaattta	8	9	3	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:72643538C>T	ENST00000268097.5	-	6	1111	c.608G>A	c.(607-609)tGg>tAg	p.W203*	RP11-106M3.3_ENST00000570175.1_RNA|HEXA_ENST00000567159.1_Nonsense_Mutation_p.W203*|HEXA_ENST00000457859.2_Nonsense_Mutation_p.W11*|HEXA_ENST00000429918.2_Nonsense_Mutation_p.W30*|RP11-106M3.2_ENST00000379915.4_RNA|HEXA_ENST00000566304.1_Nonsense_Mutation_p.W214*	NM_000520.4	NP_000511.2	P06865	HEXA_HUMAN	hexosaminidase A (alpha polypeptide)	203					carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|glycosphingolipid metabolic process (GO:0006687)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-N-acetylhexosaminidase activity (GO:0004563)|protein heterodimerization activity (GO:0046982)			breast(2)|cervix(1)|endometrium(3)|kidney(3)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	24						TACCAGATGCCAGTGGAACAC	0.458																																					p.W203X		Atlas-SNP	.											.	HEXA	48	.	0			c.G608A						.						172	143	153					15																	72643538		2199	4297	6496	SO:0001587	stop_gained	3073	exon6			AGATGCCAGTGGA	M13520	CCDS10243.1	15q24.1	2012-10-02			ENSG00000213614	ENSG00000213614	3.2.1.52		4878	protein-coding gene	gene with protein product	"Tay Sachs disease", "GM2 gangliosidosis"	606869				2952641, 3013851	Standard	NM_000520		Approved		uc002aun.4	P06865	OTTHUMG00000133445	ENST00000268097.5:c.608G>A	chr15.hg19:g.72643538C>T	ENSP00000268097:p.Trp203*	108.0	0.0		82.0	4.0	NM_000520	B4DKE7|E7ENH7|Q53HS8|Q6AI32	Nonsense_Mutation	SNP	ENST00000268097.5	hg19	CCDS10243.1	.	.	.	.	.	.	.	.	.	.	C	30	5.056859	0.93793	.	.	ENSG00000213614	ENST00000268097;ENST00000457859;ENST00000429918	.	.	.	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.7567	20.0119	0.97458	0.0:1.0:0.0:0.0	.	.	.	.	X	203;11;30	.	ENSP00000268097:W203X	W	-	2	0	HEXA	70430592	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.721000	0.84768	2.706000	0.92434	0.655000	0.94253	TGG	.	.		0.458	HEXA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257317.2	NM_000520		T	72643538	C	T	72643538	4	4	260	1	0	0	0	0	0	1	0	0	7082	595	21	3	1017	3	HEXA	15	72643538	Nonsense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	5823325	72643538	29887854	654	37899										
NEO1	4756	hgsc.bcm.edu	37	chr15	73418904	73418904	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aaaatgaggaggcacttgacAcagaaaggtaagtgttgtct	12	5	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:73418904A>G	ENST00000339362.5	+	5	1318	c.871A>G	c.(871-873)Aca>Gca	p.T291A	NEO1_ENST00000261908.6_Missense_Mutation_p.T291A|NEO1_ENST00000558964.1_Missense_Mutation_p.T291A|NEO1_ENST00000560262.1_Missense_Mutation_p.T291A			Q92859	NEO1_HUMAN	neogenin 1	291	Ig-like C2-type 3.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|iron ion homeostasis (GO:0055072)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of transcription, DNA-templated (GO:0006355)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(9)|lung(26)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	57						GGCACTTGACACAGAAAGGTA	0.403																																					p.T291A		Atlas-SNP	.											.	NEO1	102	.	0			c.A871G						.						124	95	104					15																	73418904		2198	4297	6495	SO:0001583	missense	4756	exon4			CTTGACACAGAAA	U61262	CCDS10247.1, CCDS53957.1, CCDS58378.1	15q22.3-q23	2014-06-20	2010-06-24		ENSG00000067141	ENSG00000067141		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7754	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 2"	601907	"neogenin (chicken) homolog 1"			9121761	Standard	NM_002499		Approved	NGN, HsT17534, IGDCC2, NTN1R2	uc002avm.4	Q92859	OTTHUMG00000133509	ENST00000339362.5:c.871A>G	chr15.hg19:g.73418904A>G	ENSP00000341198:p.Thr291Ala	128.0	0.0		96.0	4.0	NM_001172623	B7ZKM9|B7ZKN0|O00340|Q17RX1	Missense_Mutation	SNP	ENST00000339362.5	hg19	CCDS10247.1	.	.	.	.	.	.	.	.	.	.	A	3.455	-0.111268	0.06881	.	.	ENSG00000067141	ENST00000339362;ENST00000379842;ENST00000261908	T;T	0.66460	-0.21;-0.21	5.37	1.41	0.22369	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.265014	0.31797	N	0.007052	T	0.44052	0.1275	L	0.28274	0.84	0.36560	D	0.872346	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.001;0.002;0.002	T	0.28713	-1.0035	10	0.08599	T	0.76	0.4203	7.0283	0.24952	0.6083:0.249:0.1427:0.0	.	291;291;291	B7ZKM9;B7ZKN0;Q92859	.;.;NEO1_HUMAN	A	291;9;291	ENSP00000341198:T291A;ENSP00000261908:T291A	ENSP00000261908:T291A	T	+	1	0	NEO1	71205957	0.546000	0.26457	0.949000	0.38748	0.311000	0.27955	1.527000	0.35975	0.346000	0.23899	0.383000	0.25322	ACA	.	.		0.403	NEO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257472.2	NM_002499		G	73418904	A	G	73418904	3	3	260	1	0	0	0	0	1	0	0	0	10345	159	6	2	885	2	NEO1	15	73418904	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	775366	73418904	29112488	655	37900										
LOXL1	4016	hgsc.bcm.edu	37	chr15	74239486	74239486	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aagaaggtggccgagggccaCaaggccagtttctgcctgga	15	10	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:74239486C>T	ENST00000261921.7	+	4	1754	c.1428C>T	c.(1426-1428)caC>caT	p.H476H		NM_005576.2	NP_005567.2	Q08397	LOXL1_HUMAN	lysyl oxidase-like 1	476	Lysyl-oxidase like.				extracellular matrix organization (GO:0030198)|oxidation-reduction process (GO:0055114)|protein deamination (GO:0018277)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	copper ion binding (GO:0005507)|oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor (GO:0016641)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10						CCGAGGGCCACAAGGCCAGTT	0.582																																					p.H476H		Atlas-SNP	.											.	LOXL1	25	.	0			c.C1428T						.						81	71	75					15																	74239486		2198	4297	6495	SO:0001819	synonymous_variant	4016	exon4			GGGCCACAAGGCC	L21186	CCDS10253.1	15q24-q25	2008-07-18			ENSG00000129038	ENSG00000129038			6665	protein-coding gene	gene with protein product		153456				7689553	Standard	NM_005576		Approved	LOXL, LOL	uc002awc.1	Q08397	OTTHUMG00000137595	ENST00000261921.7:c.1428C>T	chr15.hg19:g.74239486C>T		128.0	0.0		81.0	4.0	NM_005576	Q6NUL3|Q96BW7	Silent	SNP	ENST00000261921.7	hg19	CCDS10253.1																																																																																			.	.		0.582	LOXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268995.2	NM_005576		T	74239486	C	T	74239486	2	4	260	1	0	0	0	0	0	0	0	1	8908	477	17	3		3	LOXL1	15	74239486	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	820582	74239486	28291906	656	37901										
ISLR	3671	hgsc.bcm.edu	37	chr15	74467702	74467702	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggccgagggcaccttcacccCgctcaccgcgctgtcccacc	10	21	2	0	rs371808969		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:74467702C>T	ENST00000249842.3	+	2	860	c.503C>T	c.(502-504)cCg>cTg	p.P168L	ISLR_ENST00000395118.1_Missense_Mutation_p.P168L|RP11-665J16.1_ENST00000561647.1_RNA	NM_005545.3	NP_005536.1	O14498	ISLR_HUMAN	immunoglobulin superfamily containing leucine-rich repeat	168					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)	20						ACCTTCACCCCGCTCACCGCG	0.652																																					p.P168L		Atlas-SNP	.											ISLR,colon,carcinoma,0,1	ISLR	49	.	0			c.C503T						.						65	61	62					15																	74467702		2198	4297	6495	SO:0001583	missense	3671	exon2			TCACCCCGCTCAC	AB003184	CCDS10260.1	15q23-q24	2013-01-11			ENSG00000129009	ENSG00000129009		"Immunoglobulin superfamily / I-set domain containing"	6133	protein-coding gene	gene with protein product		602059				9325048	Standard	NM_005545		Approved	HsT17563	uc002axh.1	O14498	OTTHUMG00000137623	ENST00000249842.3:c.503C>T	chr15.hg19:g.74467702C>T	ENSP00000249842:p.Pro168Leu	52.0	0.0		40.0	3.0	NM_201526		Missense_Mutation	SNP	ENST00000249842.3	hg19	CCDS10260.1	.	.	.	.	.	.	.	.	.	.	C	8.265	0.812003	0.16537	.	.	ENSG00000129009	ENST00000249842;ENST00000395118	T;T	0.57107	0.42;0.42	4.05	3.05	0.35203	.	0.419473	0.18821	U	0.130246	T	0.40595	0.1123	L	0.28556	0.865	0.09310	N	0.999998	D	0.53151	0.958	B	0.41299	0.353	T	0.31724	-0.9933	10	0.30078	T	0.28	.	15.6641	0.77213	0.0:0.7645:0.2355:0.0	.	168	O14498	ISLR_HUMAN	L	168	ENSP00000249842:P168L;ENSP00000378550:P168L	ENSP00000249842:P168L	P	+	2	0	ISLR	72254755	0.000000	0.05858	0.093000	0.20910	0.108000	0.19459	0.756000	0.26419	1.822000	0.53115	0.313000	0.20887	CCG	.	.		0.652	ISLR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269044.1	NM_005545		T	74467702	C	T	74467702	3	4	260	1	0	0	0	0	1	0	0	0	7867	652	23	1	505	1	ISLR	15	74467702	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	228216	74467702	28063690	657	37902										
SEMA7A	8482	hgsc.bcm.edu	37	chr15	74710280	74710280	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cagcagcccctcactccgccTctccaggagagtgatgtagt	10	15	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:74710280T>C	ENST00000261918.4	-	4	951	c.403A>G	c.(403-405)Agg>Ggg	p.R135G	SEMA7A_ENST00000542748.1_5'UTR|SEMA7A_ENST00000543145.2_Missense_Mutation_p.R121G	NM_003612.3	NP_003603.1	O75326	SEM7A_HUMAN	semaphorin 7A, GPI membrane anchor (John Milton Hagen blood group)	135	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon extension (GO:0048675)|axon guidance (GO:0007411)|immune response (GO:0006955)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|olfactory lobe development (GO:0021988)|osteoblast differentiation (GO:0001649)|positive regulation of axon extension (GO:0045773)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of protein phosphorylation (GO:0001934)|regulation of inflammatory response (GO:0050727)	anchored component of membrane (GO:0031225)|external side of plasma membrane (GO:0009897)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(3)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(3)|lung(12)|upper_aerodigestive_tract(1)	30						TCACTCCGCCTCTCCAGGAGA	0.622																																					p.R135G		Atlas-SNP	.											.	SEMA7A	58	.	0			c.A403G						.						44	54	50					15																	74710280		2197	4296	6493	SO:0001583	missense	8482	exon4			TCCGCCTCTCCAG	AF069493	CCDS10262.1, CCDS53958.1, CCDS53959.1	15q22.3-q23	2014-07-18	2006-02-23		ENSG00000138623	ENSG00000138623		"Semaphorins", "CD molecules", "Blood group antigens", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10741	protein-coding gene	gene with protein product	"John Milton Hagen blood group", "H-Sema K1"	607961	"sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A", "sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A (JMH blood group)"	SEMAL		9721204	Standard	NM_003612		Approved	H-Sema-L, CD108	uc002axv.3	O75326	OTTHUMG00000139000	ENST00000261918.4:c.403A>G	chr15.hg19:g.74710280T>C	ENSP00000261918:p.Arg135Gly	110.0	0.0		74.0	4.0	NM_003612	B4DDP7|F5H1S0|Q1XE81|Q1XE82|Q1XE83|Q1XE84|Q3MIY5	Missense_Mutation	SNP	ENST00000261918.4	hg19	CCDS10262.1	.	.	.	.	.	.	.	.	.	.	T	12.00	1.805385	0.31961	.	.	ENSG00000138623	ENST00000261918;ENST00000543145	T;T	0.11063	2.81;2.81	4.84	2.35	0.29111	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.748097	0.12308	N	0.480519	T	0.09423	0.0232	L	0.35542	1.07	0.46564	D	0.999102	B;B	0.11235	0.004;0.002	B;B	0.09377	0.003;0.004	T	0.09640	-1.0665	10	0.49607	T	0.09	-2.5475	9.9496	0.41631	0.0:0.0:0.3307:0.6693	.	121;135	F5H1S0;O75326	.;SEM7A_HUMAN	G	135;121	ENSP00000261918:R135G;ENSP00000438966:R121G	ENSP00000261918:R135G	R	-	1	2	SEMA7A	72497333	0.096000	0.21769	0.301000	0.25044	0.993000	0.82548	1.889000	0.39718	0.283000	0.22279	0.402000	0.26972	AGG	.	.		0.622	SEMA7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272904.3	NM_003612		C	74710280	T	C	74710280	3	2	260	1	0	0	0	0	1	0	0	0	14058	1550	54	2	1641	2	SEMA7A	15	74710280	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	242578	74710280	27821112	658	37903										
FBXO22	26263	hgsc.bcm.edu	37	chr15	76206465	76206465	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttacagcaaggaaaagaactAgtatggaaacagcacttgcc	9	8	0	1	rs375440844		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:76206465A>G	ENST00000308275.3	+	4	487	c.382A>G	c.(382-384)Agt>Ggt	p.S128G	FBXO22_ENST00000453211.2_Missense_Mutation_p.S128G|FBXO22_ENST00000540507.1_Missense_Mutation_p.S24G	NM_147188.2	NP_671717.1	Q8NEZ5	FBX22_HUMAN	F-box protein 22	128					cellular protein modification process (GO:0006464)|cellular response to starvation (GO:0009267)|nucleocytoplasmic transport (GO:0006913)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein polyubiquitination (GO:0000209)|regulation of skeletal muscle fiber development (GO:0048742)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21						GAAAAGAACTAGTATGGAAAC	0.358																																					p.S128G		Atlas-SNP	.											.	FBXO22	60	.	0			c.A382G						.	A	GLY/SER,GLY/SER	0,4394		0,0,2197	105	94	98		382,382	4.2	1	15		98	1,8587	1.2+/-3.3	0,1,4293	no	missense,missense	FBXO22	NM_012170.3,NM_147188.2	56,56	0,1,6490	GG,GA,AA		0.0116,0.0,0.0077	benign,benign	128/277,128/404	76206465	1,12981	2197	4294	6491	SO:0001583	missense	26263	exon4			AGAACTAGTATGG	AF174602	CCDS10287.1, CCDS45310.1	15q23	2008-10-03	2004-06-15		ENSG00000167196	ENSG00000167196		"F-boxes /  "other""	13593	protein-coding gene	gene with protein product	"FIST domain containing 1"	609096	"F-box only protein 22"			10531035, 10531037, 17855421	Standard	NM_147188		Approved	FBX22, FISTC1	uc002bbk.3	Q8NEZ5	OTTHUMG00000142841	ENST00000308275.3:c.382A>G	chr15.hg19:g.76206465A>G	ENSP00000307833:p.Ser128Gly	154.0	0.0		92.0	4.0	NM_012170	Q0D2P8|Q6PIL5|Q8IXW3|Q9H824|Q9UKC0	Missense_Mutation	SNP	ENST00000308275.3	hg19	CCDS10287.1	.	.	.	.	.	.	.	.	.	.	A	13.71	2.317409	0.40996	0.0	1.16E-4	ENSG00000167196	ENST00000308275;ENST00000453211;ENST00000540507	.	.	.	5.44	4.25	0.50352	.	0.375999	0.32548	N	0.005955	T	0.26991	0.0661	N	0.19112	0.55	0.22629	N	0.998916	B;B	0.27559	0.181;0.058	B;B	0.21917	0.014;0.037	T	0.18241	-1.0343	9	0.44086	T	0.13	-12.1549	11.4063	0.49900	0.8381:0.1619:0.0:0.0	.	128;128	Q8NEZ5;Q8NEZ5-3	FBX22_HUMAN;.	G	128;128;24	.	ENSP00000307833:S128G	S	+	1	0	FBXO22	73993520	0.558000	0.26554	0.996000	0.52242	0.997000	0.91878	1.897000	0.39799	2.055000	0.61198	0.528000	0.53228	AGT	.	.		0.358	FBXO22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286477.2	NM_147188		G	76206465	A	G	76206465	3	3	260	1	0	0	0	0	1	0	0	0	5742	420	15	2	396	2	FBXO22	15	76206465	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1496185	76206465	26324927	659	37904										
TBC1D2B	23102	hgsc.bcm.edu	37	chr15	78301403	78301403	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aaacttccactatggtaacgAgacaccagaaagcatcttct	6	11	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:78301403A>G	ENST00000300584.3	-	10	2323	c.2324T>C	c.(2323-2325)cTc>cCc	p.L775P	TBC1D2B_ENST00000409931.3_Missense_Mutation_p.L775P	NM_015079.5|NM_144572.1	NP_055894.6|NP_653173.1	Q9UPU7	TBD2B_HUMAN	TBC1 domain family, member 2B	775	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						Rab GTPase activator activity (GO:0005097)			breast(3)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(2)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	26						TATGGTAACGAGACACCAGAA	0.463																																					p.L775P		Atlas-SNP	.											.	TBC1D2B	104	.	0			c.T2324C						.						68	56	60					15																	78301403		2196	4293	6489	SO:0001583	missense	23102	exon10			GTAACGAGACACC	AB028978	CCDS32301.2, CCDS45314.1	15q24.3-q25.1	2005-11-29			ENSG00000167202	ENSG00000167202			29183	protein-coding gene	gene with protein product						10470851	Standard	NM_015079		Approved	KIAA1055	uc002bcy.4	Q9UPU7	OTTHUMG00000152885	ENST00000300584.3:c.2324T>C	chr15.hg19:g.78301403A>G	ENSP00000300584:p.Leu775Pro	95.0	0.0		36.0	4.0	NM_144572	A7MD42|Q8N1F9|Q9NXM0	Missense_Mutation	SNP	ENST00000300584.3	hg19	CCDS45314.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.0|22.0	4.226687|4.226687	0.79576|0.79576	.|.	.|.	ENSG00000167202|ENSG00000167202	ENST00000409931;ENST00000300584|ENST00000418039	T;T|.	0.16324|.	2.35;2.35|.	4.78|4.78	4.78|4.78	0.61160|0.61160	Rab-GAP/TBC domain (4);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.88422|0.88422	0.6432|0.6432	H|H	0.98507|0.98507	4.25|4.25	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	0.999;1.0;1.0|.	D|D	0.92549|0.92549	0.6048|0.6048	10|5	0.87932|.	D|.	0|.	.|.	13.7935|13.7935	0.63157|0.63157	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	775;227;775|.	Q9UPU7-2;Q9UPU7-3;Q9UPU7|.	.;.;TBD2B_HUMAN|.	P|P	775|657	ENSP00000387165:L775P;ENSP00000300584:L775P|.	ENSP00000300584:L775P|.	L|S	-|-	2|1	0|0	TBC1D2B|TBC1D2B	76088458|76088458	1.000000|1.000000	0.71417|0.71417	0.909000|0.909000	0.35828|0.35828	0.956000|0.956000	0.61745|0.61745	9.120000|9.120000	0.94369|0.94369	1.914000|1.914000	0.55421|0.55421	0.533000|0.533000	0.62120|0.62120	CTC|TCG	.	.		0.463	TBC1D2B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328369.3	NM_015079		G	78301403	A	G	78301403	3	3	260	1	0	0	0	0	1	0	0	0	15634	304	11	2	583	2	TBC1D2B	15	78301403	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	2094938	78301403	24229989	660	37905										
TBC1D2B	23102	hgsc.bcm.edu	37	chr15	78308988	78308988	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tatgacctcccgggtgggccCctggtcttctgagcacactg	12	14	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:78308988C>T	ENST00000300584.3	-	8	1674	c.1675G>A	c.(1675-1677)Ggg>Agg	p.G559R	TBC1D2B_ENST00000409931.3_Missense_Mutation_p.G559R	NM_015079.5|NM_144572.1	NP_055894.6|NP_653173.1	Q9UPU7	TBD2B_HUMAN	TBC1 domain family, member 2B	559							Rab GTPase activator activity (GO:0005097)			breast(3)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(2)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	26						CGGGTGGGCCCCTGGTCTTCT	0.512																																					p.G559R		Atlas-SNP	.											.	TBC1D2B	104	.	0			c.G1675A						.						74	58	63					15																	78308988		2196	4293	6489	SO:0001583	missense	23102	exon8			TGGGCCCCTGGTC	AB028978	CCDS32301.2, CCDS45314.1	15q24.3-q25.1	2005-11-29			ENSG00000167202	ENSG00000167202			29183	protein-coding gene	gene with protein product						10470851	Standard	NM_015079		Approved	KIAA1055	uc002bcy.4	Q9UPU7	OTTHUMG00000152885	ENST00000300584.3:c.1675G>A	chr15.hg19:g.78308988C>T	ENSP00000300584:p.Gly559Arg	105.0	0.0		75.0	4.0	NM_144572	A7MD42|Q8N1F9|Q9NXM0	Missense_Mutation	SNP	ENST00000300584.3	hg19	CCDS45314.1	.	.	.	.	.	.	.	.	.	.	C	19.73	3.881857	0.72294	.	.	ENSG00000167202	ENST00000409931;ENST00000300584	T;T	0.08546	3.08;3.08	5.46	5.46	0.80206	.	0.263668	0.42420	D	0.000716	T	0.19327	0.0464	M	0.70595	2.14	0.44995	D	0.998011	D;P;P	0.53462	0.96;0.773;0.933	P;B;P	0.54312	0.748;0.219;0.564	T	0.00403	-1.1761	10	0.33141	T	0.24	.	11.6469	0.51265	0.0:0.91:0.0:0.09	.	559;11;559	Q9UPU7-2;Q9UPU7-3;Q9UPU7	.;.;TBD2B_HUMAN	R	559	ENSP00000387165:G559R;ENSP00000300584:G559R	ENSP00000300584:G559R	G	-	1	0	TBC1D2B	76096043	1.000000	0.71417	0.907000	0.35723	0.930000	0.56654	2.912000	0.48782	2.572000	0.86782	0.591000	0.81541	GGG	.	.		0.512	TBC1D2B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328369.3	NM_015079		T	78308988	C	T	78308988	3	4	260	1	0	0	0	0	1	0	0	0	15634	623	22	3	1240	3	TBC1D2B	15	78308988	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	7585	78308988	24222404	661	37906										
ACSBG1	23205	hgsc.bcm.edu	37	chr15	78485849	78485849	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cactgcctcttccccaaaccTtcaggatcttttccagctgc	5	17	3	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:78485849T>C	ENST00000258873.4	-	5	867	c.662A>G	c.(661-663)aAg>aGg	p.K221R	ACSBG1_ENST00000541759.1_Intron|ACSBG1_ENST00000560817.1_Intron|ACSBG1_ENST00000558828.1_5'Flank	NM_001199377.1|NM_015162.4	NP_001186306.1|NP_055977.3	Q96GR2	ACBG1_HUMAN	acyl-CoA synthetase bubblegum family member 1	221					long-chain fatty acid metabolic process (GO:0001676)|myelination (GO:0042552)|ovarian follicle atresia (GO:0001552)|response to glucocorticoid (GO:0051384)|very long-chain fatty acid metabolic process (GO:0000038)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			endometrium(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	37						TCCCCAAACCTTCAGGATCTT	0.577																																					p.K221R		Atlas-SNP	.											.	ACSBG1	79	.	0			c.A662G						.						111	109	110					15																	78485849		2196	4293	6489	SO:0001630	splice_region_variant	23205	exon5			CAAACCTTCAGGA	AB014531	CCDS10298.1	15q23-q24	2006-02-09			ENSG00000103740	ENSG00000103740		"Acyl-CoA synthetase family"	29567	protein-coding gene	gene with protein product	"bubblegum", "very long-chain acyl-CoA synthetase", "lipidosin"	614362				9734811, 10954726	Standard	NM_015162		Approved	BGM, FLJ30320, MGC14352, BG1, KIAA0631, hBG1, hsBG	uc002bdh.3	Q96GR2	OTTHUMG00000143734	ENST00000258873.4:c.663+1A>G	chr15.hg19:g.78485849T>C		134.0	0.0		76.0	5.0	NM_015162	B2RB61|O75126|Q76N27|Q9HC26	Missense_Mutation	SNP	ENST00000258873.4	hg19	CCDS10298.1	.	.	.	.	.	.	.	.	.	.	T	16.95	3.262436	0.59431	.	.	ENSG00000103740	ENST00000258873	T	0.44083	0.93	4.49	3.3	0.37823	AMP-dependent synthetase/ligase (1);	0.217249	0.38217	N	0.001761	T	0.39009	0.1062	N	0.25332	0.735	0.80722	D	1	P;B	0.47910	0.902;0.261	P;B	0.53035	0.716;0.149	T	0.12889	-1.0530	10	0.39692	T	0.17	-30.5462	9.3622	0.38203	0.1591:0.0:0.0:0.8409	.	217;221	B7Z2Y6;Q96GR2	.;ACBG1_HUMAN	R	221	ENSP00000258873:K221R	ENSP00000258873:K221R	K	-	2	0	ACSBG1	76272904	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	5.288000	0.65651	1.663000	0.50791	0.533000	0.62120	AAG	.	.		0.577	ACSBG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289802.2	NM_015162	Missense_Mutation	C	78485849	T	C	78485849	5	2	260	1	0	0	0	0	0	0	1	0	173	1623	56	2	1552	2	ACSBG1	15	78485849	Splice_Site	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	176861	78485849	24045543	662	37907										
RASGRF1	5923	hgsc.bcm.edu	37	chr15	79339198	79339198	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acaaggatgtgcagctgctgCacgtactcagcctcagcctc	10	14	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:79339198C>A	ENST00000419573.3	-	5	1042	c.768G>T	c.(766-768)gtG>gtT	p.V256V	RASGRF1_ENST00000558480.2_Silent_p.V256V|RASGRF1_ENST00000560334.1_5'UTR	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	256	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						GCAGCTGCTGCACGTACTCAG	0.587																																					p.V256V		Atlas-SNP	.											.	RASGRF1	168	.	0			c.G768T						.						138	105	116					15																	79339198		2196	4293	6489	SO:0001819	synonymous_variant	5923	exon5			CTGCTGCACGTAC	M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.768G>T	chr15.hg19:g.79339198C>A		133.0	0.0		74.0	4.0	NM_001145648	F8VPA5|H0YKF2|J3KQP9|Q16027	Silent	SNP	ENST00000419573.3	hg19	CCDS10309.1																																																																																			.	.		0.587	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891		A	79339198	C	A	79339198	2	1	260	1	0	0	0	0	0	0	0	1	13087	697	25	3		3	RASGRF1	15	79339198	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	853349	79339198	23192194	663	37908										
KIAA1024	23251	hgsc.bcm.edu	37	chr15	79748703	79748703	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcaaagacaagatgaaatgcActgtgaataaccagcaatca	7	8	2	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:79748703A>G	ENST00000305428.3	+	2	289	c.214A>G	c.(214-216)Act>Gct	p.T72A		NM_015206.2	NP_056021.1	Q9UPX6	K1024_HUMAN	KIAA1024	72						integral component of membrane (GO:0016021)				central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(2)|pancreas(2)|prostate(1)	49						GATGAAATGCACTGTGAATAA	0.463																																					p.T72A		Atlas-SNP	.											.	KIAA1024	146	.	0			c.A214G						.						90	87	88					15																	79748703		2196	4293	6489	SO:0001583	missense	23251	exon2			AAATGCACTGTGA	AB028947	CCDS32306.1	15q25.1	2007-12-12				ENSG00000169330			29172	protein-coding gene	gene with protein product						10470851	Standard	NM_015206		Approved		uc002bew.1	Q9UPX6		ENST00000305428.3:c.214A>G	chr15.hg19:g.79748703A>G	ENSP00000307461:p.Thr72Ala	165.0	0.0		130.0	6.0	NM_015206	A7MD43	Missense_Mutation	SNP	ENST00000305428.3	hg19	CCDS32306.1	.	.	.	.	.	.	.	.	.	.	A	8.552	0.875863	0.17395	.	.	ENSG00000169330	ENST00000305428	T	0.34072	1.38	5.88	-1.1	0.09872	.	0.687597	0.15573	N	0.255338	T	0.15262	0.0368	N	0.17474	0.49	0.18873	N	0.999988	B	0.02656	0.0	B	0.01281	0.0	T	0.16012	-1.0417	9	.	.	.	.	1.4896	0.02454	0.3948:0.2864:0.2005:0.1182	.	72	Q9UPX6	K1024_HUMAN	A	72	ENSP00000307461:T72A	.	T	+	1	0	KIAA1024	77535758	0.896000	0.30565	0.170000	0.22879	0.992000	0.81027	0.457000	0.21875	-0.473000	0.06871	0.482000	0.46254	ACT	.	.		0.463	KIAA1024-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416718.1	NM_015206		G	79748703	A	G	79748703	3	3	260	1	0	0	0	0	1	0	0	0	8214	159	6	2	216	2	KIAA1024	15	79748703	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	409505	79748703	22782689	664	37909										
AP3B2	8120	hgsc.bcm.edu	37	chr15	83331514	83331514	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgcccacatgcaggcccttgAtgggggtatcagagctgttg	14	10	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:83331514A>G	ENST00000261722.3	-	22	2915	c.2708T>C	c.(2707-2709)aTc>aCc	p.I903T	AP3B2_ENST00000535348.1_Missense_Mutation_p.I871T|AP3B2_ENST00000535359.1_Missense_Mutation_p.I922T|RP11-752G15.3_ENST00000560650.1_RNA	NM_004644.3	NP_004635.2	Q13367	AP3B2_HUMAN	adaptor-related protein complex 3, beta 2 subunit	903					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|intracellular protein transport (GO:0006886)|post-Golgi vesicle-mediated transport (GO:0006892)	AP-3 adaptor complex (GO:0030123)|COPI-coated vesicle (GO:0030137)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(4)|endometrium(1)|kidney(1)|large_intestine(4)|lung(21)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(2)	41			BRCA - Breast invasive adenocarcinoma(143;0.229)			CAGGCCCTTGATGGGGGTATC	0.582																																					p.I903T		Atlas-SNP	.											.	AP3B2	103	.	0			c.T2708C						.						38	42	40					15																	83331514		1988	4157	6145	SO:0001583	missense	8120	exon22			CCCTTGATGGGGG	U37673	CCDS45331.1, CCDS61736.1, CCDS61737.1	15q	2008-07-07			ENSG00000103723	ENSG00000103723			567	protein-coding gene	gene with protein product		602166				7671305, 1851215	Standard	NM_004644		Approved	NAPTB	uc010uoh.2	Q13367	OTTHUMG00000168009	ENST00000261722.3:c.2708T>C	chr15.hg19:g.83331514A>G	ENSP00000261722:p.Ile903Thr	156.0	0.0		69.0	4.0	NM_004644	A4Z4T7|B7ZKR7|B7ZKS0|O14808|Q52LY8	Missense_Mutation	SNP	ENST00000261722.3	hg19	CCDS45331.1	.	.	.	.	.	.	.	.	.	.	A	19.91	3.914232	0.72983	.	.	ENSG00000103723	ENST00000261722;ENST00000535348;ENST00000535359	T;T;T	0.35973	1.28;1.28;1.28	6.04	4.92	0.64577	Coatomer/clathrin adaptor appendage, Ig-like subdomain (1);Clathrin adaptor, gamma-adaptin, appendage (1);	0.245199	0.42294	D	0.000740	T	0.25005	0.0607	N	0.16833	0.445	0.80722	D	1	B;B;B	0.21905	0.062;0.0;0.0	B;B;B	0.20184	0.028;0.001;0.001	T	0.04229	-1.0967	10	0.72032	D	0.01	-25.8165	12.2488	0.54587	0.9339:0.0:0.0661:0.0	.	871;922;903	B7ZKR7;B7ZKS0;Q13367	.;.;AP3B2_HUMAN	T	903;871;922	ENSP00000261722:I903T;ENSP00000438721:I871T;ENSP00000440984:I922T	ENSP00000261722:I903T	I	-	2	0	AP3B2	81128569	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	6.836000	0.75349	1.101000	0.41535	0.460000	0.39030	ATC	.	.		0.582	AP3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397463.1			G	83331514	A	G	83331514	3	3	260	1	0	0	0	0	1	0	0	0	745	333	12	2	560	2	AP3B2	15	83331514	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	3582811	83331514	19199878	665	37910										
AKAP13	11214	hgsc.bcm.edu	37	chr15	86273745	86273745	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cattttctccttcctgcagaAcaacttcaccagaaggacca	5	14	2	2	rs116261620	byFrequency	TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:86273745A>G	ENST00000394518.2	+	30	7184	c.7089A>G	c.(7087-7089)gaA>gaG	p.E2363E	AKAP13_ENST00000361243.2_Splice_Site_p.E2367E|AKAP13_ENST00000394510.2_Splice_Site_p.E608E|AKAP13_ENST00000560579.1_3'UTR	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	2363	Interaction with ESR1.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						TTCCTGCAGAACAACTTCACC	0.438											OREG0023425	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E2367E	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.A7101G						.						119	112	114					15																	86273745		2202	4299	6501	SO:0001630	splice_region_variant	11214	exon30			TGCAGAACAACTT	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"A-kinase anchor proteins", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	371	protein-coding gene	gene with protein product		604686	"lymphoid blast crisis oncogene"	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.7088-1A>G	chr15.hg19:g.86273745A>G		60.0	0.0	1243	56.0	4.0	NM_006738	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Silent	SNP	ENST00000394518.2	hg19	CCDS32319.1																																																																																			.	A|0.998;C|0.002		0.438	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200	Silent	G	86273745	A	G	86273745	5	3	260	1	0	0	0	0	0	0	1	0	449	57	2	2	7273	2	AKAP13	15	86273745	Splice_Site	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	2942231	86273745	16257647	666	37911										
AKAP13	11214	hgsc.bcm.edu	37	chr15	86273922	86273922	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aaaggaggacctttaatgaaAagtgcaataaatgagggtaa	11	3	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:86273922A>G	ENST00000394518.2	+	30	7361	c.7266A>G	c.(7264-7266)aaA>aaG	p.K2422K	AKAP13_ENST00000361243.2_Silent_p.K2426K|AKAP13_ENST00000394510.2_Silent_p.K667K|AKAP13_ENST00000560579.1_3'UTR	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	2422	Interaction with ESR1.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)	p.K2426K(1)		NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						CTTTAATGAAAAGTGCAATAA	0.453											OREG0023425	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K2426K	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											AKAP13,colon,carcinoma,0,1	AKAP13	394	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A7278G						.						82	77	79					15																	86273922		2202	4299	6501	SO:0001819	synonymous_variant	11214	exon30			AATGAAAAGTGCA	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"A-kinase anchor proteins", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	371	protein-coding gene	gene with protein product		604686	"lymphoid blast crisis oncogene"	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.7266A>G	chr15.hg19:g.86273922A>G		68.0	1.0	1243	40.0	2.0	NM_006738	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Silent	SNP	ENST00000394518.2	hg19	CCDS32319.1																																																																																			.	.		0.453	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200		G	86273922	A	G	86273922	2	3	260	1	0	0	0	0	0	0	0	1	449	11	1	2		2	AKAP13	15	86273922	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	177	86273922	16257470	667	37912										
RHCG	51458	hgsc.bcm.edu	37	chr15	90023578	90023578	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtcggtagaggatccgggtcActgtgagcccaaagtaggcg	16	9	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:90023578A>G	ENST00000268122.4	-	4	652	c.584T>C	c.(583-585)gTg>gCg	p.V195A	RHCG_ENST00000544600.1_Missense_Mutation_p.V195A	NM_016321.1	NP_057405.1	Q9UBD6	RHCG_HUMAN	Rh family, C glycoprotein	195					amine transport (GO:0015837)|ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|cellular ion homeostasis (GO:0006873)|epithelial cell differentiation (GO:0030855)|homeostatic process (GO:0042592)|regulation of pH (GO:0006885)|transepithelial ammonium transport (GO:0070634)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ammonium transmembrane transporter activity (GO:0008519)|ankyrin binding (GO:0030506)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Lung NSC(78;0.0237)|all_lung(78;0.0478)					GATCCGGGTCACTGTGAGCCC	0.557																																					p.V195A		Atlas-SNP	.											.	RHCG	49	.	0			c.T584C						.						222	203	209					15																	90023578		2200	4299	6499	SO:0001583	missense	51458	exon4			CGGGTCACTGTGA	AF081497	CCDS10351.1	15q25	2013-05-22	2006-02-23		ENSG00000140519	ENSG00000140519		"Solute carriers"	18140	protein-coding gene	gene with protein product		605381	"chromosome 15 open reading frame 6", "Rhesus blood group, C glycoprotein"	C15orf6		10852913	Standard	NM_016321		Approved	RHGK, PDRC2, SLC42A3	uc002bnz.2	Q9UBD6	OTTHUMG00000149647	ENST00000268122.4:c.584T>C	chr15.hg19:g.90023578A>G	ENSP00000268122:p.Val195Ala	177.0	0.0		125.0	5.0	NM_016321	A8K4D4|Q6X3Y4	Missense_Mutation	SNP	ENST00000268122.4	hg19	CCDS10351.1	.	.	.	.	.	.	.	.	.	.	A	18.91	3.724379	0.68959	.	.	ENSG00000140519	ENST00000544600;ENST00000268122;ENST00000536247	T;T	0.20881	2.04;2.04	5.45	5.45	0.79879	Ammonium transporter AmtB-like (3);	0.113799	0.64402	D	0.000014	T	0.25975	0.0633	L	0.60904	1.88	0.58432	D	0.999999	B;B	0.22480	0.07;0.07	B;B	0.29785	0.107;0.107	T	0.03514	-1.1029	9	.	.	.	-18.5972	15.5559	0.76192	1.0:0.0:0.0:0.0	.	195;195	A8K4D4;Q9UBD6	.;RHCG_HUMAN	A	195;195;186	ENSP00000438123:V195A;ENSP00000268122:V195A	.	V	-	2	0	RHCG	87824582	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	7.487000	0.81328	2.084000	0.62774	0.374000	0.22700	GTG	.	.		0.557	RHCG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000312855.2	NM_016321		G	90023578	A	G	90023578	3	3	260	1	0	0	0	0	1	0	0	0	13341	159	6	2	883	2	RHCG	15	90023578	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	3749656	90023578	12507814	668	37913										
TTLL13	440307	hgsc.bcm.edu	37	chr15	90793872	90793872	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aatctgagagaatggagccgAgtacctgtaggaccatggaa	13	7	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:90793872A>G	ENST00000561573.1	+	2	274	c.10A>G	c.(10-12)Agt>Ggt	p.S4G	TTLL13_ENST00000339615.5_Missense_Mutation_p.S4G|TTLL13_ENST00000438251.1_Missense_Mutation_p.S4G																							AATGGAGCCGAGTACCTGTAG	0.493																																					p.S4G		Atlas-SNP	.											.	TTLL13	44	.	0			c.A10G						.						75	75	75					15																	90793872		2199	4298	6497	SO:0001583	missense	440307	exon2			GAGCCGAGTACCT																												ENST00000561573.1:c.10A>G	chr15.hg19:g.90793872A>G	ENSP00000456615:p.Ser4Gly	170.0	0.0		97.0	4.0	NM_001029964		Missense_Mutation	SNP	ENST00000561573.1	hg19		.	.	.	.	.	.	.	.	.	.	A	8.884	0.952418	0.18431	.	.	ENSG00000213471	ENST00000438251;ENST00000339615	T;T	0.04083	3.71;3.77	5.16	2.83	0.33086	.	.	.	.	.	T	0.02727	0.0082	N	0.08118	0	0.09310	N	1	B	0.19200	0.034	B	0.21917	0.037	T	0.46707	-0.9172	9	0.28530	T	0.3	.	6.3432	0.21335	0.8044:0.0:0.1956:0.0	.	4	A6NNM8-2	.	G	4	ENSP00000413362:S4G;ENSP00000345294:S4G	ENSP00000345294:S4G	S	+	1	0	TTLL13	88594876	0.005000	0.15991	0.016000	0.15963	0.122000	0.20287	1.285000	0.33261	0.910000	0.36722	0.402000	0.26972	AGT	.	.		0.493	RP11-697E2.6-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	protein_coding	OTTHUMT00000435855.1			G	90793872	A	G	90793872	3	3	260	1	0	0	0	0	1	0	0	0	16741	304	11	2	12	2	TTLL13	15	90793872	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	770294	90793872	11737520	669	37914										
SV2B	9899	hgsc.bcm.edu	37	chr15	91809826	91809826	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tttcaggtttccaacatcaaAactcccaagcaaatggatga	6	10	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr15:91809826A>G	ENST00000394232.1	+	7	1493	c.1023A>G	c.(1021-1023)aaA>aaG	p.K341K	SV2B_ENST00000330276.4_Silent_p.K341K|SV2B_ENST00000545111.2_Silent_p.K190K	NM_014848.4	NP_055663.1	Q7L1I2	SV2B_HUMAN	synaptic vesicle glycoprotein 2B	341					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)			NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(17)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)			CCAACATCAAAACTCCCAAGC	0.373																																					p.K341K		Atlas-SNP	.											.	SV2B	98	.	0			c.A1023G						.						74	76	76					15																	91809826		2198	4298	6496	SO:0001819	synonymous_variant	9899	exon8			CATCAAAACTCCC	AB018278	CCDS10370.1, CCDS53972.1	15q26.1	2005-01-10			ENSG00000185518	ENSG00000185518			16874	protein-coding gene	gene with protein product		185861				9872452, 7681585	Standard	NM_014848		Approved	KIAA0735, HsT19680	uc002bqv.3	Q7L1I2	OTTHUMG00000149833	ENST00000394232.1:c.1023A>G	chr15.hg19:g.91809826A>G		75.0	0.0		78.0	4.0	NM_014848	B4DH30|C6G489|O94840|Q6IAR8	Silent	SNP	ENST00000394232.1	hg19	CCDS10370.1																																																																																			.	.		0.373	SV2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313494.3	NM_014848		G	91809826	A	G	91809826	2	3	260	1	0	0	0	0	0	0	0	1	15433	11	1	2		2	SV2B	15	91809826	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1015954	91809826	10721566	670	37915										
LUC7L	55692	hgsc.bcm.edu	37	chr16	242959	242959	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gctcctcccgttccctctccTctctcctcctcaagcgatcc	4	22	3	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:242959T>C	ENST00000293872.8	-	7	853	c.743A>G	c.(742-744)gAg>gGg	p.E248G	LUC7L_ENST00000397780.1_Missense_Mutation_p.E195G|LUC7L_ENST00000397783.1_Missense_Mutation_p.E248G|LUC7L_ENST00000337351.4_Missense_Mutation_p.E248G	NM_201412.1	NP_958815.1	Q9NQ29	LUC7L_HUMAN	LUC7-like (S. cerevisiae)	248	Arg/Ser-rich.				mRNA splice site selection (GO:0006376)|negative regulation of striated muscle tissue development (GO:0045843)	U1 snRNP (GO:0005685)	identical protein binding (GO:0042802)|mRNA binding (GO:0003729)			NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	11		all_cancers(16;1.1e-06)|all_epithelial(16;2.71e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.0138)|all_lung(18;0.0306)				TTCCCTCTCCTCTCTCCTCCT	0.517																																					p.E248G		Atlas-SNP	.											.	LUC7L	46	.	0			c.A743G						.						272	249	257					16																	242959		2203	4300	6503	SO:0001583	missense	55692	exon7			CTCTCCTCTCTCC	AY005111	CCDS10401.1, CCDS32348.1	16p13.3	2010-01-25	2001-11-28		ENSG00000007392	ENSG00000007392			6723	protein-coding gene	gene with protein product		607782	"LUC7 (S. cerevisiae)-like"				Standard	NM_201412		Approved	LUC7B1, hLuc7B1, Luc7	uc002cgc.1	Q9NQ29	OTTHUMG00000060730	ENST00000293872.8:c.743A>G	chr16.hg19:g.242959T>C	ENSP00000293872:p.Glu248Gly	111.0	0.0		76.0	5.0	NM_201412	B8ZZ13|Q96S32|Q9NPH4	Missense_Mutation	SNP	ENST00000293872.8	hg19	CCDS32348.1	.	.	.	.	.	.	.	.	.	.	T	18.45	3.625639	0.66901	.	.	ENSG00000007392	ENST00000337351;ENST00000293872;ENST00000397783;ENST00000429378;ENST00000397780;ENST00000430864	T;T;T;T	0.64991	0.96;0.96;-0.13;0.96	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.67316	0.2880	M	0.74881	2.28	0.80722	D	1	P	0.48089	0.905	P	0.47118	0.538	T	0.68345	-0.5433	10	0.33141	T	0.24	.	14.0517	0.64742	0.0:0.0:0.0:1.0	.	248	Q9NQ29	LUC7L_HUMAN	G	248;248;248;47;195;162	ENSP00000337507:E248G;ENSP00000380885:E248G;ENSP00000413033:E47G;ENSP00000380882:E195G	ENSP00000293872:E248G	E	-	2	0	LUC7L	182960	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.827000	0.69300	2.061000	0.61500	0.379000	0.24179	GAG	.	.		0.517	LUC7L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134239.1			C	242959	T	C	242959	3	2	260	1	0	0	0	0	1	0	0	0	9091	1551	54	2	392	2	LUC7L	16	242959	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10		242959	90111794	671	37916										
MSLN	10232	hgsc.bcm.edu	37	chr16	815776	815776	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	catcctccggccgcggttccGgcgggaagtggagagtgagt	17	11	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:815776G>T	ENST00000382862.3	+	10	976	c.881G>T	c.(880-882)cGg>cTg	p.R294L	MSLN_ENST00000563941.1_Missense_Mutation_p.R294L|MSLN_ENST00000545450.2_Missense_Mutation_p.R294L|MSLN_ENST00000566549.1_Missense_Mutation_p.R294L	NM_013404.4	NP_037536.2	Q13421	MSLN_HUMAN	mesothelin	294					cell adhesion (GO:0007155)|pancreas development (GO:0031016)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|kidney(2)|lung(11)|pancreas(1)|prostate(1)|skin(3)	20		Hepatocellular(780;0.00335)				CCGCGGTTCCGGCGGGAAGTG	0.701																																					p.R294L		Atlas-SNP	.											.	MSLN	109	.	0			c.G881T						.						16	19	18					16																	815776		2170	4277	6447	SO:0001583	missense	10232	exon11			GGTTCCGGCGGGA	U40434	CCDS32356.1, CCDS45370.1	16p13.3	2008-04-16			ENSG00000102854	ENSG00000102854			7371	protein-coding gene	gene with protein product		601051				7665620, 8552591	Standard	NM_005823		Approved	CAK1, MPF	uc002cjw.2	Q13421	OTTHUMG00000047992	ENST00000382862.3:c.881G>T	chr16.hg19:g.815776G>T	ENSP00000372313:p.Arg294Leu	88.0	0.0		60.0	4.0	NM_005823	D3DU65|Q14859|Q4VQD5|Q96GR6|Q96KJ5|Q9BR17|Q9BTR2|Q9UCB2|Q9UK57	Missense_Mutation	SNP	ENST00000382862.3	hg19	CCDS32356.1	.	.	.	.	.	.	.	.	.	.	G	12.71	2.018308	0.35606	.	.	ENSG00000102854	ENST00000446427;ENST00000445361;ENST00000545450;ENST00000382862	T;T	0.18657	2.2;2.2	4.73	-1.06	0.10002	.	1.363720	0.05188	N	0.502529	T	0.17534	0.0421	M	0.61703	1.905	0.09310	N	1	P;P;P;P	0.43542	0.678;0.725;0.81;0.678	B;B;B;B	0.33690	0.098;0.158;0.168;0.098	T	0.25882	-1.0119	10	0.41790	T	0.15	-4.6104	4.0101	0.09619	0.3418:0.0:0.4902:0.168	.	293;294;294;294	Q13421-4;Q13421;Q13421-2;Q13421-3	.;MSLN_HUMAN;.;.	L	294	ENSP00000442965:R294L;ENSP00000372313:R294L	ENSP00000372313:R294L	R	+	2	0	MSLN	755777	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-0.396000	0.07278	-0.372000	0.07992	0.551000	0.68910	CGG	.	.		0.701	MSLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109253.2			T	815776	G	T	815776	3	4	260	1	0	0	0	0	1	0	0	0	9890	1116	39	1	915	1	MSLN	16	815776	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	572817	815776	89538977	672	37917										
CHTF18	63922	hgsc.bcm.edu	37	chr16	843038	843038	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtgagaaaactgacaatgacAtccgggcctgcatcaacacc	9	12	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:843038A>G	ENST00000262315.9	+	13	1708	c.1645A>G	c.(1645-1647)Atc>Gtc	p.I549V	CHTF18_ENST00000317063.6_Missense_Mutation_p.I739V|CHTF18_ENST00000455171.2_Missense_Mutation_p.I577V	NM_022092.2	NP_071375.1	Q8WVB6	CTF18_HUMAN	CTF18, chromosome transmission fidelity factor 18 homolog (S. cerevisiae)	549					cell cycle (GO:0007049)|DNA replication (GO:0006260)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(1)|kidney(3)|liver(2)|lung(4)|prostate(1)	11		Hepatocellular(780;0.00335)				TGACAATGACATCCGGGCCTG	0.692																																					p.I549V		Atlas-SNP	.											.	CHTF18	52	.	0			c.A1645G						.						18	21	20					16																	843038		1863	4066	5929	SO:0001583	missense	63922	exon13			AATGACATCCGGG	BC018184	CCDS45371.1	16p13.3	2010-04-21	2003-12-09		ENSG00000127586	ENSG00000127586		"ATPases / AAA-type"	18435	protein-coding gene	gene with protein product		613201	"chromosome 16 open reading frame 41"	C16orf41		12171929	Standard	NM_022092		Approved	CHL12, C321D2.4, Ctf18	uc002cke.4	Q8WVB6	OTTHUMG00000047838	ENST00000262315.9:c.1645A>G	chr16.hg19:g.843038A>G	ENSP00000262315:p.Ile549Val	97.0	0.0		103.0	5.0	NM_022092	B7ZBA2|D3DU68|Q7Z6Y4|Q7Z6Y6|Q9BR83|Q9BRG5|Q9H7K3	Missense_Mutation	SNP	ENST00000262315.9	hg19	CCDS45371.1	.	.	.	.	.	.	.	.	.	.	a	15.67	2.900812	0.52227	.	.	ENSG00000127586	ENST00000317063;ENST00000455171;ENST00000262315	T;T;T	0.16743	2.32;2.32;2.32	4.9	4.9	0.64082	.	0.000000	0.85682	D	0.000000	T	0.32793	0.0841	L	0.55103	1.725	0.80722	D	1	D;P	0.54207	0.965;0.941	P;P	0.61201	0.885;0.77	T	0.01966	-1.1238	10	0.40728	T	0.16	-33.9346	13.3686	0.60701	1.0:0.0:0.0:0.0	.	577;549	Q8WVB6-2;Q8WVB6	.;CTF18_HUMAN	V	739;577;549	ENSP00000313029:I739V;ENSP00000406252:I577V;ENSP00000262315:I549V	ENSP00000262315:I549V	I	+	1	0	CHTF18	783039	1.000000	0.71417	1.000000	0.80357	0.088000	0.18126	5.085000	0.64468	1.843000	0.53566	0.454000	0.30748	ATC	.	.		0.692	CHTF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109061.3	NM_022092		G	843038	A	G	843038	3	3	260	1	0	0	0	0	1	0	0	0	3416	217	8	2	1695	2	CHTF18	16	843038	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	27262	843038	89511715	673	37918										
BAIAP3	8938	hgsc.bcm.edu	37	chr16	1388575	1388575	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cgaccttgctggacattaagAgcagcgtgctcaggcaggtg	14	10	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:1388575A>G	ENST00000324385.5	+	2	288	c.130A>G	c.(130-132)Agc>Ggc	p.S44G	BAIAP3_ENST00000397488.2_Missense_Mutation_p.S9G|BAIAP3_ENST00000397489.1_Missense_Mutation_p.S9G|BAIAP3_ENST00000421665.2_Missense_Mutation_p.S9G|BAIAP3_ENST00000426824.3_Missense_Mutation_p.S9G|BAIAP3_ENST00000562208.1_Missense_Mutation_p.S9G|BAIAP3_ENST00000568887.1_Missense_Mutation_p.S9G	NM_003933.4	NP_003924.2	O94812	BAIP3_HUMAN	BAI1-associated protein 3	44					G-protein coupled receptor signaling pathway (GO:0007186)|neurotransmitter secretion (GO:0007269)		protein C-terminus binding (GO:0008022)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(25)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42		Hepatocellular(780;0.0893)				GGACATTAAGAGCAGCGTGCT	0.672																																					p.S44G		Atlas-SNP	.											.	BAIAP3	88	.	0			c.A130G						.						44	34	38					16																	1388575		2194	4296	6490	SO:0001583	missense	8938	exon2			ATTAAGAGCAGCG	AB017111	CCDS10434.1, CCDS55978.1, CCDS55979.1, CCDS58402.1, CCDS58403.1, CCDS66894.1	16p13.3	2008-07-04			ENSG00000007516	ENSG00000007516			948	protein-coding gene	gene with protein product		604009				9790924	Standard	NM_003933		Approved	BAP3, KIAA0734	uc002clk.2	O94812	OTTHUMG00000047833	ENST00000324385.5:c.130A>G	chr16.hg19:g.1388575A>G	ENSP00000324510:p.Ser44Gly	286.0	0.0		178.0	8.0	NM_003933	A2A2B2|B2RCD7|B4DGS5|B4DIK3|B4DRK9|B4DRP1|E7EUB9|H3BUH8|H3BVI3|H7C2Q1|O94839|Q2M226|Q658J2|Q76N05|Q96RZ3|Q9UJK1	Missense_Mutation	SNP	ENST00000324385.5	hg19	CCDS10434.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.165555	0.78339	.	.	ENSG00000007516	ENST00000426824;ENST00000397488;ENST00000324385;ENST00000397489;ENST00000421665	T;T;T;T;T	0.78924	-0.86;-0.86;-0.91;-0.86;-1.22	4.01	4.01	0.46588	.	0.000000	0.85682	D	0.000000	D	0.82889	0.5135	L	0.56769	1.78	0.33056	D	0.53339	D;D;D;D;D	0.71674	0.997;0.998;0.997;0.997;0.997	D;D;D;D;D	0.77004	0.985;0.989;0.985;0.985;0.985	D	0.84228	0.0465	10	0.32370	T	0.25	-32.4674	9.4946	0.38980	1.0:0.0:0.0:0.0	.	9;44;9;44;9	E7EUB9;B4DGA2;B4DIK3;O94812;A2A2B2	.;.;.;BAIP3_HUMAN;.	G	9;9;44;9;9	ENSP00000407242:S9G;ENSP00000380625:S9G;ENSP00000324510:S44G;ENSP00000380626:S9G;ENSP00000409533:S9G	ENSP00000324510:S44G	S	+	1	0	BAIAP3	1328576	1.000000	0.71417	1.000000	0.80357	0.864000	0.49448	2.079000	0.41577	1.819000	0.53055	0.402000	0.26972	AGC	.	.		0.672	BAIAP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109056.3			G	1388575	A	G	1388575	3	3	260	1	0	0	0	0	1	0	0	0	1304	304	11	2	136	2	BAIAP3	16	1388575	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	545537	1388575	88966178	674	37919										
GFER	2671	hgsc.bcm.edu	37	chr16	2034924	2034924	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttttacccctgtgaggagtgTgctgaagacctaagaaaaag	11	7	0	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:2034924T>C	ENST00000248114.6	+	2	441	c.435T>C	c.(433-435)tgT>tgC	p.C145C	GFER_ENST00000567719.1_Silent_p.C70C|GFER_ENST00000569451.1_Intron|AC005606.14_ENST00000564438.1_lincRNA	NM_005262.2	NP_005253.3	P55789	ALR_HUMAN	growth factor, augmenter of liver regeneration	145	ERV/ALR sulfhydryl oxidase. {ECO:0000255|PROSITE-ProRule:PRU00654}.				cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|protein disulfide oxidoreductase activity (GO:0015035)|thiol oxidase activity (GO:0016972)			endometrium(1)|large_intestine(1)|lung(3)	5					Flavin adenine dinucleotide(DB03147)	GTGAGGAGTGTGCTGAAGACC	0.547																																					p.C145C		Atlas-SNP	.											.	GFER	8	.	0			c.T435C						.						85	83	84					16																	2034924		2198	4300	6498	SO:0001819	synonymous_variant	2671	exon2			GGAGTGTGCTGAA	BC002429	CCDS32368.1	16p13.3-p13.12	2011-06-22	2008-08-01		ENSG00000127554	ENSG00000127554			4236	protein-coding gene	gene with protein product	"ERV1 homolog (S. cerevisiae)"	600924	"growth factor, erv1 (S. cerevisiae)-like (augmenter of liver regeneration)"			8575761	Standard	NM_005262		Approved	HSS, ERV1, ALR, HERV1, HPO1, HPO2	uc002cob.3	P55789		ENST00000248114.6:c.435T>C	chr16.hg19:g.2034924T>C		118.0	0.0		89.0	4.0	NM_005262	Q53YM6|Q8TAH6|Q9H290|Q9UK40	Silent	SNP	ENST00000248114.6	hg19	CCDS32368.1																																																																																			.	.		0.547	GFER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434243.1	NM_005262		C	2034924	T	C	2034924	2	2	260	1	0	0	0	0	0	0	0	1	6346	1702	59	2		2	GFER	16	2034924	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	646349	2034924	88319829	675	37920										
RAB26	25837	hgsc.bcm.edu	37	chr16	2203391	2203391	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gcatgattacgttaagagggAgggtcgaggggcctcctgct	16	8	0	2	rs199768285		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:2203391A>G	ENST00000210187.6	+	9	900	c.740A>G	c.(739-741)gAg>gGg	p.E247G	RP11-304L19.5_ENST00000563192.1_lincRNA|SNORD60_ENST00000383903.1_RNA|TRAF7_ENST00000326181.6_5'Flank|RAB26_ENST00000541451.1_Missense_Mutation_p.E181G	NM_014353.4	NP_055168.2	Q9ULW5	RAB26_HUMAN	RAB26, member RAS oncogene family	247					exocrine system development (GO:0035272)|Golgi to plasma membrane protein transport (GO:0043001)|regulated secretory pathway (GO:0045055)|regulation of exocytosis (GO:0017157)|small GTPase mediated signal transduction (GO:0007264)	Golgi membrane (GO:0000139)|intrinsic component of plasma membrane (GO:0031226)|secretory granule membrane (GO:0030667)	GMP binding (GO:0019002)|GTP binding (GO:0005525)			kidney(1)|large_intestine(1)|lung(3)	5						GTTAAGAGGGAGGGTCGAGGG	0.642																																					p.E247G		Atlas-SNP	.											.	RAB26	9	.	0			c.A740G						.						40	45	43					16																	2203391		2198	4299	6497	SO:0001583	missense	25837	exon9			AGAGGGAGGGTCG	AB027137	CCDS10460.1	16p13.3	2008-07-28			ENSG00000167964	ENSG00000167964		"RAB, member RAS oncogene"	14259	protein-coding gene	gene with protein product		605455				11043516	Standard	NM_014353		Approved		uc002cou.3	Q9ULW5	OTTHUMG00000128829	ENST00000210187.6:c.740A>G	chr16.hg19:g.2203391A>G	ENSP00000210187:p.Glu247Gly	115.0	0.0		78.0	5.0	NM_014353	B2RAA6|Q3L6K5|Q6NXS7	Missense_Mutation	SNP	ENST00000210187.6	hg19	CCDS10460.1	.	.	.	.	.	.	.	.	.	.	A	14.54	2.564699	0.45694	.	.	ENSG00000167964	ENST00000541451;ENST00000210187	T;T	0.64991	-0.13;0.02	4.42	4.42	0.53409	.	0.000000	0.64402	U	0.000002	T	0.51618	0.1685	N	0.20807	0.61	0.45295	D	0.998294	P	0.34892	0.474	B	0.41088	0.347	T	0.55049	-0.8201	10	0.44086	T	0.13	.	12.6103	0.56547	1.0:0.0:0.0:0.0	.	247	Q9ULW5	RAB26_HUMAN	G	181;247	ENSP00000441580:E181G;ENSP00000210187:E247G	ENSP00000210187:E247G	E	+	2	0	RAB26	2143392	1.000000	0.71417	0.975000	0.42487	0.014000	0.08584	6.433000	0.73404	1.860000	0.53959	0.260000	0.18958	GAG	.	A|0.999;C|0.001		0.642	RAB26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250767.2			G	2203391	A	G	2203391	3	3	260	1	0	0	0	0	1	0	0	0	12928	304	11	2	774	2	RAB26	16	2203391	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	168467	2203391	88151362	676	37921										
CASKIN1	57524	hgsc.bcm.edu	37	chr16	2233896	2233896	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgatgaagttgggggcgtagAgctgcagctggaacgcggtg	19	6	0	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:2233896A>G	ENST00000343516.6	-	15	1555	c.1463T>C	c.(1462-1464)cTc>cCc	p.L488P	CASKIN1_ENST00000564289.1_Intron	NM_020764.3	NP_065815.1	Q8WXD9	CSKI1_HUMAN	CASK interacting protein 1	488	SAM 1. {ECO:0000255|PROSITE- ProRule:PRU00184}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|liver(1)|lung(7)|ovary(4)|prostate(5)|skin(3)	28						GGGGGCGTAGAGCTGCAGCTG	0.682																																					p.L488P		Atlas-SNP	.											.	CASKIN1	130	.	0			c.T1463C						.						38	48	44					16																	2233896		2149	4265	6414	SO:0001583	missense	57524	exon15			GCGTAGAGCTGCA	AF451977	CCDS42103.1	16p13.3	2013-01-10				ENSG00000167971		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	20879	protein-coding gene	gene with protein product		612184				12040031	Standard	NM_020764		Approved	KIAA1306, ANKS5A	uc010bsg.1	Q8WXD9		ENST00000343516.6:c.1463T>C	chr16.hg19:g.2233896A>G	ENSP00000345436:p.Leu488Pro	103.0	0.0		72.0	5.0	NM_020764	Q9P2P0	Missense_Mutation	SNP	ENST00000343516.6	hg19	CCDS42103.1	.	.	.	.	.	.	.	.	.	.	A	11.55	1.672436	0.29693	.	.	ENSG00000167971	ENST00000343516;ENST00000382453	T	0.45276	0.9	4.01	2.81	0.32909	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	.	.	.	.	T	0.46151	0.1378	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	T	0.21586	-1.0241	9	0.25751	T	0.34	-24.315	9.463	0.38796	0.8414:0.0:0.0:0.1585	.	488	Q8WXD9	CSKI1_HUMAN	P	488;317	ENSP00000345436:L488P	ENSP00000345436:L488P	L	-	2	0	CASKIN1	2173897	1.000000	0.71417	1.000000	0.80357	0.289000	0.27227	3.887000	0.56197	1.805000	0.52779	0.247000	0.18012	CTC	.	.		0.682	CASKIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435055.1	NM_020764		G	2233896	A	G	2233896	3	3	260	1	0	0	0	0	1	0	0	0	2668	304	11	2	2856	2	CASKIN1	16	2233896	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	30505	2233896	88120857	677	37922										
RNPS1	10921	hgsc.bcm.edu	37	chr16	2305610	2305610	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcctcatccgtgggggagacCtgcgccacataggcggtggt	15	12	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:2305610C>A	ENST00000565678.1	-	7	1339	c.794G>T	c.(793-795)aGg>aTg	p.R265M	RNPS1_ENST00000301730.8_Missense_Mutation_p.R265M|RNPS1_ENST00000397086.2_Missense_Mutation_p.R265M|RNPS1_ENST00000567147.1_Intron|RNPS1_ENST00000320225.5_Missense_Mutation_p.R265M|AC009065.1_ENST00000454671.1_Missense_Mutation_p.L118M|RNPS1_ENST00000566458.1_Missense_Mutation_p.R242M|RNPS1_ENST00000568631.1_Missense_Mutation_p.R265M|RNPS1_ENST00000569598.2_Missense_Mutation_p.R171M|RNPS1_ENST00000566397.1_Missense_Mutation_p.R88M|RNPS1_ENST00000561718.1_Missense_Mutation_p.R88M			Q15287	RNPS1_HUMAN	RNA binding protein S1, serine-rich domain	265	Arg/Pro-rich.|Necessary for interaction with TRA2B, nuclear localization and exon-skipping.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of apoptotic process (GO:0043065)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(1)|large_intestine(1)|lung(4)|ovary(2)|urinary_tract(1)	9						TGGGGGAGACCTGCGCCACAT	0.577																																					p.R265M		Atlas-SNP	.											.	RNPS1	18	.	0			c.G794T						.						54	57	56					16																	2305610		2198	4300	6498	SO:0001583	missense	10921	exon7			GGAGACCTGCGCC	AF015608	CCDS10465.1, CCDS66907.1, CCDS73811.1	16p13.3	2013-02-12	2001-11-28		ENSG00000205937	ENSG00000205937		"RNA binding motif (RRM) containing"	10080	protein-coding gene	gene with protein product		606447	"RNA-binding protein S1, serine-rich domain"			9580558, 8543184	Standard	XM_005255048		Approved		uc002cpu.3	Q15287	OTTHUMG00000128828	ENST00000565678.1:c.794G>T	chr16.hg19:g.2305610C>A	ENSP00000457723:p.Arg265Met	175.0	0.0		91.0	4.0	NM_006711	A8K1P0|B4DDU8|B4DZU7|B7ZA17|O75308|Q32P25|Q8WY42|Q9NYG3	Missense_Mutation	SNP	ENST00000565678.1	hg19	CCDS10465.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.65|17.65	3.441055|3.441055	0.63067|0.63067	.|.	.|.	ENSG00000167970|ENSG00000205937	ENST00000454671|ENST00000320225;ENST00000397086;ENST00000301730	.|T;T;T	.|0.09630	.|2.96;2.96;2.96	5.08|5.08	5.08|5.08	0.68730|0.68730	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.31389|0.31389	0.0795|0.0795	M|M	0.73962|0.73962	2.25|2.25	0.80722|0.80722	D|D	1|1	.|D;D	.|0.58970	.|0.984;0.972	.|D;P	.|0.63877	.|0.919;0.831	T|T	0.00961|0.00961	-1.1499|-1.1499	5|10	.|0.46703	.|T	.|0.11	.|.	16.024|16.024	0.80528|0.80528	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|242;265	.|Q15287-2;Q15287	.|.;RNPS1_HUMAN	M|M	118|265	.|ENSP00000315859:R265M;ENSP00000380275:R265M;ENSP00000301730:R265M	.|ENSP00000301730:R265M	L|R	+|-	1|2	2|0	AC009065.1|RNPS1	2245611|2245611	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.936000|0.936000	0.57629|0.57629	7.006000|7.006000	0.76329|0.76329	2.623000|2.623000	0.88846|0.88846	0.544000|0.544000	0.68410|0.68410	CTG|AGG	.	.		0.577	RNPS1-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435415.1	NM_080594		A	2305610	C	A	2305610	3	1	260	1	0	0	0	0	1	0	0	0	13526	681	24	3	131	3	RNPS1	16	2305610	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	71714	2305610	88049143	678	37923										
ABCA3	21	hgsc.bcm.edu	37	chr16	2358552	2358552	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcagagtcatccagttgtacCgaggggccacgaagaagtag	13	9	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:2358552C>A	ENST00000301732.5	-	11	1884	c.1184G>T	c.(1183-1185)cGg>cTg	p.R395L	ABCA3_ENST00000382381.3_Intron	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	395					response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	alveolar lamellar body (GO:0097208)|alveolar lamellar body membrane (GO:0097233)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(7)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(7)|prostate(5)|skin(6)|upper_aerodigestive_tract(1)	70		Ovarian(90;0.17)			Imatinib(DB00619)	CCAGTTGTACCGAGGGGCCAC	0.572																																					p.R395L		Atlas-SNP	.											.	ABCA3	176	.	0			c.G1184T						.						125	104	111					16																	2358552		2198	4300	6498	SO:0001583	missense	21	exon11			TTGTACCGAGGGG	U78735	CCDS10466.1	16p13.3	2012-03-14			ENSG00000167972	ENSG00000167972		"ATP binding cassette transporters / subfamily A"	33	protein-coding gene	gene with protein product		601615		ABC3		8706931	Standard	NM_001089		Approved	ABC-C, EST111653, LBM180	uc002cpy.1	Q99758	OTTHUMG00000128845	ENST00000301732.5:c.1184G>T	chr16.hg19:g.2358552C>A	ENSP00000301732:p.Arg395Leu	153.0	0.0		85.0	4.0	NM_001089	B2RU09|Q54A95|Q6P5P9|Q92473	Missense_Mutation	SNP	ENST00000301732.5	hg19	CCDS10466.1	.	.	.	.	.	.	.	.	.	.	C	3.904	-0.021369	0.07634	.	.	ENSG00000167972	ENST00000301732	T	0.73469	-0.75	5.65	2.64	0.31445	.	.	.	.	.	T	0.63803	0.2542	L	0.54323	1.7	0.43137	D	0.99488	B;B	0.16802	0.019;0.019	B;B	0.20577	0.03;0.03	T	0.49952	-0.8884	9	0.12430	T	0.62	.	7.4918	0.27466	0.1353:0.7204:0.0:0.1443	.	395;395	A7MBM9;Q99758	.;ABCA3_HUMAN	L	395	ENSP00000301732:R395L	ENSP00000301732:R395L	R	-	2	0	ABCA3	2298553	1.000000	0.71417	0.000000	0.03702	0.004000	0.04260	5.856000	0.69518	0.324000	0.23333	0.650000	0.86243	CGG	.	.		0.572	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089		A	2358552	C	A	2358552	3	1	260	1	0	0	0	0	1	0	0	0	33	652	23	1	4022	1	ABCA3	16	2358552	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	52942	2358552	87996201	679	37924										
PRSS33	260429	hgsc.bcm.edu	37	chr16	2834720	2834720	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acccctggacggttgggcagGgcacaacccttgccccagct	12	16	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:2834720G>T	ENST00000293851.5	-	6	927	c.768C>A	c.(766-768)gcC>gcA	p.A256A	PRSS33_ENST00000576886.1_3'UTR|PRSS33_ENST00000570702.1_Silent_p.A256A	NM_152891.2	NP_690851.2	Q8NF86	PRS33_HUMAN	protease, serine, 33	256	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular space (GO:0005615)	serine-type endopeptidase activity (GO:0004252)			prostate(1)	1						GGTTGGGCAGGGCACAACCCT	0.622																																					p.A256A	NSCLC(194;489 2153 16702 19171 27758)	Atlas-SNP	.											.	PRSS33	7	.	0			c.C768A						.						26	31	29					16																	2834720		2074	4219	6293	SO:0001819	synonymous_variant	260429	exon6			GGGCAGGGCACAA	AF536382	CCDS42110.1	16p13.3	2014-09-04			ENSG00000103355	ENSG00000103355		"Serine peptidases / Serine peptidases"	30405	protein-coding gene	gene with protein product		613797				12795636	Standard	NM_152891		Approved	EOS	uc002cro.1	Q8NF86	OTTHUMG00000177360	ENST00000293851.5:c.768C>A	chr16.hg19:g.2834720G>T		143.0	0.0		99.0	4.0	NM_152891	A6NNQ3|Q8N171	Silent	SNP	ENST00000293851.5	hg19	CCDS42110.1																																																																																			.	.		0.622	PRSS33-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436446.1	NM_152891		T	2834720	G	T	2834720	2	4	260	1	0	0	0	0	0	0	0	1	12635	1219	43	3		3	PRSS33	16	2834720	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	476168	2834720	87520033	680	37925										
CREBBP	1387	hgsc.bcm.edu	37	chr16	3788625	3788625	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	taaacggctgtgcggaggcaAcgtggccggaagaaatgaat	15	7	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:3788625A>G	ENST00000262367.5	-	26	5138	c.4329T>C	c.(4327-4329)cgT>cgC	p.R1443R	CREBBP_ENST00000382070.3_Silent_p.R1405R	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1443	CBP/p300-type HAT. {ECO:0000255|PROSITE- ProRule:PRU01065}.|Cys/His-rich.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		TGCGGAGGCAACGTGGCCGGA	0.408			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																														p.R1443R		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP	546	.	0			c.T4329C						.						78	70	72					16																	3788625		2197	4300	6497	SO:0001819	synonymous_variant	1387	exon26			GAGGCAACGTGGC	U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.4329T>C	chr16.hg19:g.3788625A>G		102.0	0.0		89.0	4.0	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Silent	SNP	ENST00000262367.5	hg19	CCDS10509.1																																																																																			.	.		0.408	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		G	3788625	A	G	3788625	2	3	260	1	0	0	0	0	0	0	0	1	3863	30	2	2		2	CREBBP	16	3788625	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	953905	3788625	86566128	681	37926										
C16orf71	146562	hgsc.bcm.edu	37	chr16	4793096	4793096	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcagagtctggcgggacaagAagacaaccagggaaatcgtg	14	8	2	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:4793096A>G	ENST00000299320.5	+	5	1314	c.836A>G	c.(835-837)gAa>gGa	p.E279G	C16orf71_ENST00000590191.1_Missense_Mutation_p.E293G|RP11-127I20.7_ENST00000588099.1_RNA	NM_139170.2	NP_631909.2	Q8IYS4	CP071_HUMAN	chromosome 16 open reading frame 71	279										breast(1)|central_nervous_system(1)|large_intestine(4)|lung(4)|ovary(1)	11						GCGGGACAAGAAGACAACCAG	0.522																																					p.E279G		Atlas-SNP	.											.	C16orf71	46	.	0			c.A836G						.						165	140	149					16																	4793096		2197	4300	6497	SO:0001583	missense	146562	exon5			GACAAGAAGACAA	AF447587	CCDS10521.1	16p13.3	2008-02-05			ENSG00000166246	ENSG00000166246			25081	protein-coding gene	gene with protein product						12477932	Standard	XM_005255144		Approved	FLJ43261, DKFZp686H2240	uc002cxn.3	Q8IYS4	OTTHUMG00000129480	ENST00000299320.5:c.836A>G	chr16.hg19:g.4793096A>G	ENSP00000299320:p.Glu279Gly	126.0	0.0		86.0	4.0	NM_139170	Q8NCV0	Missense_Mutation	SNP	ENST00000299320.5	hg19	CCDS10521.1	.	.	.	.	.	.	.	.	.	.	A	16.02	3.004898	0.54254	.	.	ENSG00000166246	ENST00000299320;ENST00000411541	T	0.18016	2.24	4.65	2.32	0.28847	.	0.168881	0.28425	N	0.015399	T	0.15652	0.0377	L	0.52573	1.65	0.09310	N	1	P	0.46142	0.873	B	0.43575	0.424	T	0.12811	-1.0533	10	0.72032	D	0.01	-16.3339	4.6167	0.12430	0.7036:0.1955:0.1008:0.0	.	279	Q8IYS4	CP071_HUMAN	G	279;34	ENSP00000299320:E279G	ENSP00000299320:E279G	E	+	2	0	C16orf71	4733097	0.084000	0.21492	0.002000	0.10522	0.824000	0.46624	1.737000	0.38197	0.359000	0.24239	0.524000	0.50904	GAA	.	.		0.522	C16orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251644.1	NM_139170		G	4793096	A	G	4793096	3	3	260	1	0	0	0	0	1	0	0	0	1832	246	9	2	850	2	C16orf71	16	4793096	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1004471	4793096	85561657	682	37927										
C16orf71	146562	hgsc.bcm.edu	37	chr16	4793141	4793141	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tggaactgtgtggtgggcagCtgaccaccgccaagttcaag	14	10	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:4793141C>A	ENST00000299320.5	+	5	1359	c.881C>A	c.(880-882)gCt>gAt	p.A294D	C16orf71_ENST00000590191.1_Missense_Mutation_p.A308D|RP11-127I20.7_ENST00000588099.1_RNA	NM_139170.2	NP_631909.2	Q8IYS4	CP071_HUMAN	chromosome 16 open reading frame 71	294										breast(1)|central_nervous_system(1)|large_intestine(4)|lung(4)|ovary(1)	11						TGGTGGGCAGCTGACCACCGC	0.572																																					p.A294D		Atlas-SNP	.											C16orf71,mucosal,malignant_melanoma,0,1	C16orf71	46	.	0			c.C881A						.						118	96	104					16																	4793141		2197	4300	6497	SO:0001583	missense	146562	exon5			GGGCAGCTGACCA	AF447587	CCDS10521.1	16p13.3	2008-02-05			ENSG00000166246	ENSG00000166246			25081	protein-coding gene	gene with protein product						12477932	Standard	XM_005255144		Approved	FLJ43261, DKFZp686H2240	uc002cxn.3	Q8IYS4	OTTHUMG00000129480	ENST00000299320.5:c.881C>A	chr16.hg19:g.4793141C>A	ENSP00000299320:p.Ala294Asp	65.0	0.0		49.0	4.0	NM_139170	Q8NCV0	Missense_Mutation	SNP	ENST00000299320.5	hg19	CCDS10521.1	.	.	.	.	.	.	.	.	.	.	C	12.85	2.062193	0.36373	.	.	ENSG00000166246	ENST00000299320;ENST00000411541	T	0.19806	2.12	4.92	2.9	0.33743	.	0.000000	0.41712	D	0.000821	T	0.35653	0.0939	L	0.59436	1.845	0.09310	N	0.99999	D	0.76494	0.999	D	0.76575	0.988	T	0.03608	-1.1020	10	0.66056	D	0.02	-12.4457	6.0551	0.19807	0.0:0.7056:0.1938:0.1006	.	294	Q8IYS4	CP071_HUMAN	D	294;49	ENSP00000299320:A294D	ENSP00000299320:A294D	A	+	2	0	C16orf71	4733142	0.349000	0.24870	0.501000	0.27601	0.078000	0.17371	0.516000	0.22817	1.382000	0.46385	0.644000	0.83932	GCT	.	.		0.572	C16orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251644.1	NM_139170		A	4793141	C	A	4793141	3	1	260	1	0	0	0	0	1	0	0	0	1832	797	28	3	895	3	C16orf71	16	4793141	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	45	4793141	85561612	683	37928										
ZNF500	26048	hgsc.bcm.edu	37	chr16	4802991	4802991	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gcatcgtgccgagagcactcGgtaccactccattctcaacg	9	15	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:4802991G>T	ENST00000219478.6	-	6	1128	c.829C>A	c.(829-831)Cga>Aga	p.R277R	ZNF500_ENST00000591026.1_5'UTR|RP11-127I20.7_ENST00000588099.1_RNA|ZNF500_ENST00000545009.1_Silent_p.R277R			O60304	ZN500_HUMAN	zinc finger protein 500	277					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	21						GAGAGCACTCGGTACCACTCC	0.637																																					p.R277R		Atlas-SNP	.											.	ZNF500	45	.	0			c.C829A						.						49	58	55					16																	4802991		2197	4299	6496	SO:0001819	synonymous_variant	26048	exon6			GCACTCGGTACCA	AB011129	CCDS32383.1	16p13.3	2013-01-09				ENSG00000103199		"Zinc fingers, C2H2-type", "-", "-", "-"	23716	protein-coding gene	gene with protein product						9628581	Standard	XM_005255243		Approved	ZKSCAN18, KIAA0557, ZSCAN50	uc002cxp.1	O60304		ENST00000219478.6:c.829C>A	chr16.hg19:g.4802991G>T		57.0	0.0		40.0	4.0	NM_021646	A8K6X7|B4DNN9|Q0VAL2|Q96CQ8|Q9BTG0	Silent	SNP	ENST00000219478.6	hg19	CCDS32383.1																																																																																			.	.		0.637	ZNF500-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432461.1	XM_085507		T	4802991	G	T	4802991	2	4	260	1	0	0	0	0	0	0	0	1	17963	1124	39	1		1	ZNF500	16	4802991	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	9850	4802991	85551762	684	37929										
CLEC16A	23274	hgsc.bcm.edu	37	chr16	11114058	11114058	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tttggcttccagagatcgagAtggtgatcatggagcgtagc	14	7	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:11114058A>G	ENST00000409790.1	+	12	1542	c.1312A>G	c.(1312-1314)Atg>Gtg	p.M438V	CLEC16A_ENST00000409552.3_Missense_Mutation_p.M420V	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A									p.0?(1)		breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						AGAGATCGAGATGGTGATCAT	0.527																																					p.M438V		Atlas-SNP	.											.	CLEC16A	101	.	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.A1312G						.						43	45	44					16																	11114058		1970	4163	6133	SO:0001583	missense	23274	exon11			ATCGAGATGGTGA	AB002348	CCDS45409.1, CCDS58423.1	16p13.13	2010-04-27	2007-07-17	2007-07-17	ENSG00000038532	ENSG00000038532		"C-type lectin domain containing"	29013	protein-coding gene	gene with protein product		611303	"KIAA0350"	KIAA0350		9205841, 17632545	Standard	NM_015226		Approved	Gop-1	uc002dao.3	Q2KHT3	OTTHUMG00000152915	ENST00000409790.1:c.1312A>G	chr16.hg19:g.11114058A>G	ENSP00000387122:p.Met438Val	137.0	0.0		85.0	4.0	NM_015226		Missense_Mutation	SNP	ENST00000409790.1	hg19	CCDS45409.1	.	.	.	.	.	.	.	.	.	.	A	18.38	3.610525	0.66558	.	.	ENSG00000038532	ENST00000409790;ENST00000542102;ENST00000409552	T	0.44083	0.93	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.52613	0.1745	L	0.57536	1.79	0.80722	D	1	P;P	0.47191	0.891;0.811	P;P	0.60789	0.867;0.879	T	0.48375	-0.9041	10	0.10636	T	0.68	-32.3322	11.5584	0.50761	1.0:0.0:0.0:0.0	.	438;420	Q2KHT3;Q2KHT3-2	CL16A_HUMAN;.	V	438;438;420	ENSP00000387122:M438V	ENSP00000386495:M420V	M	+	1	0	CLEC16A	11021559	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.884000	0.75600	1.980000	0.57719	0.459000	0.35465	ATG	.	.		0.527	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226		G	11114058	A	G	11114058	3	3	260	1	0	0	0	0	1	0	0	0	3502	333	12	2	1354	2	CLEC16A	16	11114058	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	6311067	11114058	79240695	685	37930										
PDXDC1	23042	hgsc.bcm.edu	37	chr16	15128199	15128199	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	attcaggaagctcaagtggaGctgcagaaggcaagtgaaga	14	6	2	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:15128199G>T	ENST00000396410.4	+	20	1966	c.1869G>T	c.(1867-1869)gaG>gaT	p.E623D	PDXDC1_ENST00000535621.2_Intron|PDXDC1_ENST00000450288.2_Missense_Mutation_p.E595D|PDXDC1_ENST00000447912.2_Missense_Mutation_p.E532D|PDXDC1_ENST00000569715.1_Missense_Mutation_p.E596D|PDXDC1_ENST00000563679.1_Missense_Mutation_p.E641D|PDXDC1_ENST00000325823.7_Missense_Mutation_p.E608D	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	623					carboxylic acid metabolic process (GO:0019752)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(10)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CTCAAGTGGAGCTGCAGAAGG	0.552																																					p.E623D		Atlas-SNP	.											.	PDXDC1	59	.	0			c.G1869T						.						66	63	64					16																	15128199		2197	4300	6497	SO:0001583	missense	23042	exon20			AGTGGAGCTGCAG	AK025504, BX647809	CCDS32393.1, CCDS66954.1, CCDS66957.1, CCDS73830.1, CCDS73831.1	16p13.11	2008-02-05							28995	protein-coding gene	gene with protein product		614244					Standard	XM_005255173		Approved	KIAA0251	uc002dda.4	Q6P996	OTTHUMG00000166304	ENST00000396410.4:c.1869G>T	chr16.hg19:g.15128199G>T	ENSP00000379691:p.Glu623Asp	97.0	0.0		73.0	4.0	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Missense_Mutation	SNP	ENST00000396410.4	hg19	CCDS32393.1	.	.	.	.	.	.	.	.	.	.	G	7.010	0.556575	0.13436	.	.	ENSG00000179889	ENST00000325823;ENST00000447912;ENST00000396410;ENST00000450288	T;T;T;T	0.71461	-0.57;-0.57;-0.57;-0.57	5.76	-2.86	0.05717	.	0.099987	0.64402	D	0.000001	T	0.30230	0.0758	N	0.01761	-0.735	0.24003	N	0.996208	B;B;B;B	0.28208	0.06;0.203;0.06;0.102	B;B;B;B	0.24006	0.05;0.05;0.05;0.05	T	0.47235	-0.9133	10	0.05833	T	0.94	-9.0895	6.6986	0.23213	0.4758:0.0:0.4124:0.1118	.	595;532;595;623	E7EPL4;E7EMH5;B4DR55;Q6P996	.;.;.;PDXD1_HUMAN	D	608;532;623;595	ENSP00000322807:E608D;ENSP00000400310:E532D;ENSP00000379691:E623D;ENSP00000391147:E595D	ENSP00000322807:E608D	E	+	3	2	PDXDC1	15035700	1.000000	0.71417	0.932000	0.37286	0.882000	0.50991	0.559000	0.23485	-0.420000	0.07427	-0.140000	0.14226	GAG	.	.		0.552	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027		T	15128199	G	T	15128199	3	4	260	1	0	0	0	0	1	0	0	0	11705	962	34	3	1947	3	PDXDC1	16	15128199	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	4014141	15128199	75226554	686	37931										
XYLT1	64131	hgsc.bcm.edu	37	chr16	17235219	17235219	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccgatccaggccctgcttccGaatgaacctgggagggagaa	13	12	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:17235219G>T	ENST00000261381.6	-	7	1462	c.1378C>A	c.(1378-1380)Cgg>Agg	p.R460R	CTD-2576D5.4_ENST00000567344.1_RNA	NM_022166.3	NP_071449.1	Q86Y38	XYLT1_HUMAN	xylosyltransferase I	460					cellular response to heat (GO:0034605)|chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						CCCTGCTTCCGAATGAACCTG	0.572																																					p.R460R		Atlas-SNP	.											XYLT1,NS,carcinoma,0,1	XYLT1	147	.	0			c.C1378A						.						40	39	40					16																	17235219		2197	4300	6497	SO:0001819	synonymous_variant	64131	exon7			GCTTCCGAATGAA	AJ277441	CCDS10569.1	16p12	2013-02-25			ENSG00000103489	ENSG00000103489	2.4.2.26	"Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	15516	protein-coding gene	gene with protein product	"protein xylosyltransferase 1"	608124				11099377	Standard	NM_022166		Approved	XT-I, PXYLT1	uc002dfa.3	Q86Y38	OTTHUMG00000129975	ENST00000261381.6:c.1378C>A	chr16.hg19:g.17235219G>T		39.0	0.0		27.0	2.0	NM_022166	Q9H1B6	Silent	SNP	ENST00000261381.6	hg19	CCDS10569.1																																																																																			.	.		0.572	XYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252241.2	NM_022166		T	17235219	G	T	17235219	2	4	260	1	0	0	0	0	0	0	0	1	17478	1057	37	1		1	XYLT1	16	17235219	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	2107020	17235219	73119534	687	37932										
DNAH3	55567	hgsc.bcm.edu	37	chr16	20974803	20974803	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcaccatcttctccaatcctTgagagaacttccaagaccca	4	15	3	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:20974803T>C	ENST00000261383.3	-	53	10402	c.10403A>G	c.(10402-10404)cAa>cGa	p.Q3468R	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	3468					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			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)		CTCCAATCCTTGAGAGAACTT	0.512																																					p.Q3468R		Atlas-SNP	.											.	DNAH3	1142	.	0			c.A10403G						.						89	73	78					16																	20974803		2201	4300	6501	SO:0001583	missense	55567	exon53			AATCCTTGAGAGA	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"Axonemal dyneins"	2949	protein-coding gene	gene with protein product		603334	"dynein, axonemal, heavy polypeptide 3"			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.10403A>G	chr16.hg19:g.20974803T>C	ENSP00000261383:p.Gln3468Arg	99.0	0.0		78.0	4.0	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	hg19	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	T	0.015	-1.559554	0.00910	.	.	ENSG00000158486	ENST00000261383	T	0.08193	3.12	5.39	3.08	0.35506	Dynein heavy chain (1);	1.297190	0.04812	N	0.435494	T	0.07954	0.0199	N	0.11927	0.2	0.09310	N	1	B	0.16603	0.018	B	0.23716	0.048	T	0.48328	-0.9045	10	0.42905	T	0.14	.	13.395	0.60846	0.0:0.0:0.4622:0.5378	.	3468	Q8TD57	DYH3_HUMAN	R	3468	ENSP00000261383:Q3468R	ENSP00000261383:Q3468R	Q	-	2	0	DNAH3	20882304	0.000000	0.05858	0.000000	0.03702	0.097000	0.18754	0.078000	0.14761	0.327000	0.23409	0.460000	0.39030	CAA	.	.		0.512	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		C	20974803	T	C	20974803	3	2	260	1	0	0	0	0	1	0	0	0	4605	1812	63	2	1986	2	DNAH3	16	20974803	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	3739584	20974803	69379950	688	37933										
DNAH3	55567	hgsc.bcm.edu	37	chr16	21008757	21008757	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgggtggctgggccccatacAcctctttggctggcatgttg	14	11	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:21008757A>G	ENST00000261383.3	-	44	6448	c.6449T>C	c.(6448-6450)gTg>gCg	p.V2150A	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	2150	AAA 3. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			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)		GGCCCCATACACCTCTTTGGC	0.507																																					p.V2150A		Atlas-SNP	.											.	DNAH3	1142	.	0			c.T6449C						.						101	95	97					16																	21008757		2201	4300	6501	SO:0001583	missense	55567	exon44			CCATACACCTCTT	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"Axonemal dyneins"	2949	protein-coding gene	gene with protein product		603334	"dynein, axonemal, heavy polypeptide 3"			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.6449T>C	chr16.hg19:g.21008757A>G	ENSP00000261383:p.Val2150Ala	150.0	0.0		104.0	5.0	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	hg19	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	A	7.686	0.690021	0.15039	.	.	ENSG00000158486	ENST00000261383	T	0.32753	1.44	5.16	4.06	0.47325	ATPase, AAA+ type, core (1);	0.721979	0.13122	N	0.412103	T	0.17662	0.0424	N	0.17564	0.495	0.46701	D	0.999162	B	0.19200	0.034	B	0.16289	0.015	T	0.04307	-1.0961	10	0.12430	T	0.62	.	9.608	0.39645	0.8516:0.0:0.1484:0.0	.	2150	Q8TD57	DYH3_HUMAN	A	2150	ENSP00000261383:V2150A	ENSP00000261383:V2150A	V	-	2	0	DNAH3	20916258	0.014000	0.17966	0.967000	0.41034	0.942000	0.58702	2.796000	0.47869	0.810000	0.34279	0.528000	0.53228	GTG	.	.		0.507	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		G	21008757	A	G	21008757	3	3	260	1	0	0	0	0	1	0	0	0	4605	159	6	2	5976	2	DNAH3	16	21008757	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	33954	21008757	69345996	689	37934										
GGA2	23062	hgsc.bcm.edu	37	chr16	23489698	23489698	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agaagactcacagagggcacGgagctggctgtgctgagagg	17	8	1	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:23489698G>T	ENST00000309859.4	-	13	1365	c.1283C>A	c.(1282-1284)cCg>cAg	p.P428Q	GGA2_ENST00000567468.1_Intron|GGA2_ENST00000569182.1_5'UTR	NM_015044.4	NP_055859.1	Q9UJY4	GGA2_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 2	428	Unstructured hinge.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(48;0.0386)		CAGAGGGCACGGAGCTGGCTG	0.582																																					p.P428Q		Atlas-SNP	.											.	GGA2	49	.	0			c.C1283A						.						94	86	89					16																	23489698		2197	4300	6497	SO:0001583	missense	23062	exon13			GGGCACGGAGCTG	AF190863	CCDS10611.1	16p12	2010-02-12	2010-02-12		ENSG00000103365	ENSG00000103365			16064	protein-coding gene	gene with protein product		606005				10747088, 10749927	Standard	NM_015044		Approved	VEAR, KIAA1080	uc002dlq.3	Q9UJY4	OTTHUMG00000096957	ENST00000309859.4:c.1283C>A	chr16.hg19:g.23489698G>T	ENSP00000311962:p.Pro428Gln	146.0	0.0		87.0	4.0	NM_015044	D3DWF0|O14564|Q9NYN2|Q9UPS2	Missense_Mutation	SNP	ENST00000309859.4	hg19	CCDS10611.1	.	.	.	.	.	.	.	.	.	.	G	6.743	0.505926	0.12883	.	.	ENSG00000103365	ENST00000309859	T	0.16597	2.33	4.15	1.15	0.20763	.	1.116690	0.07031	N	0.828502	T	0.16128	0.0388	L	0.51422	1.61	0.09310	N	1	B	0.19445	0.036	B	0.14023	0.01	T	0.31696	-0.9934	10	0.44086	T	0.13	-4.3035	5.9296	0.19132	0.3299:0.0:0.6701:0.0	.	428	Q9UJY4	GGA2_HUMAN	Q	428	ENSP00000311962:P428Q	ENSP00000311962:P428Q	P	-	2	0	GGA2	23397199	0.001000	0.12720	0.001000	0.08648	0.000000	0.00434	0.414000	0.21164	0.519000	0.28406	-0.751000	0.03497	CCG	.	.		0.582	GGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214019.1			T	23489698	G	T	23489698	3	4	260	1	0	0	0	0	1	0	0	0	6361	1116	39	1	578	1	GGA2	16	23489698	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	2480941	23489698	66865055	690	37935										
KIAA0556	23247	hgsc.bcm.edu	37	chr16	27640026	27640026	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggaccccgtgcaattgaggcTggagcacttggagcaaggtt	15	9	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:27640026T>C	ENST00000261588.4	+	4	204	c.185T>C	c.(184-186)cTg>cCg	p.L62P		NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	62						extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						CAATTGAGGCTGGAGCACTTG	0.478																																					p.L62P		Atlas-SNP	.											.	KIAA0556	348	.	0			c.T185C						.						150	139	143					16																	27640026		2197	4300	6497	SO:0001583	missense	23247	exon4			TGAGGCTGGAGCA	AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.185T>C	chr16.hg19:g.27640026T>C	ENSP00000261588:p.Leu62Pro	159.0	0.0		91.0	4.0	NM_015202	A7E2C2	Missense_Mutation	SNP	ENST00000261588.4	hg19	CCDS32415.1	.	.	.	.	.	.	.	.	.	.	T	19.54	3.847667	0.71603	.	.	ENSG00000047578	ENST00000261588	T	0.56103	0.48	5.21	5.21	0.72293	.	0.105307	0.39020	N	0.001498	T	0.70254	0.3203	M	0.72894	2.215	0.58432	D	0.99999	D	0.89917	1.0	D	0.91635	0.999	T	0.74022	-0.3798	10	0.87932	D	0	-4.1322	12.6144	0.56567	0.0:0.0:0.0:1.0	.	62	O60303	K0556_HUMAN	P	62	ENSP00000261588:L62P	ENSP00000261588:L62P	L	+	2	0	KIAA0556	27547527	1.000000	0.71417	0.960000	0.40013	0.987000	0.75469	4.806000	0.62569	1.973000	0.57446	0.454000	0.30748	CTG	.	.		0.478	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202		C	27640026	T	C	27640026	3	2	260	1	0	0	0	0	1	0	0	0	8192	1580	55	2	199	2	KIAA0556	16	27640026	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	4150328	27640026	62714727	691	37936										
CLN3	1201	hgsc.bcm.edu	37	chr16	28489132	28489132	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctcatacagaatgatcaggaAgacgaggtagatgcttggca	12	7	2	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:28489132A>G	ENST00000569430.1	-	16	1942	c.1123T>C	c.(1123-1125)Ttc>Ctc	p.F375L	CLN3_ENST00000357857.9_Missense_Mutation_p.F321L|CLN3_ENST00000568224.1_Missense_Mutation_p.F297L|CLN3_ENST00000354630.5_Missense_Mutation_p.F358L|CLN3_ENST00000360019.2_Missense_Mutation_p.F375L|CLN3_ENST00000355477.5_Missense_Mutation_p.F327L|CLN3_ENST00000333496.9_Missense_Mutation_p.F351L|CLN3_ENST00000567963.1_Intron|CLN3_ENST00000395653.4_Missense_Mutation_p.F275L|CLN3_ENST00000565316.1_Missense_Mutation_p.F358L|CLN3_ENST00000357806.7_Missense_Mutation_p.F276L|CLN3_ENST00000359984.7_Missense_Mutation_p.F375L|CLN3_ENST00000535392.1_Missense_Mutation_p.F297L			Q13286	CLN3_HUMAN	ceroid-lipofuscinosis, neuronal 3	375					action potential (GO:0001508)|amyloid precursor protein catabolic process (GO:0042987)|arginine transport (GO:0015809)|associative learning (GO:0008306)|autophagic vacuole fusion (GO:0000046)|cell death (GO:0008219)|cellular amino acid metabolic process (GO:0006520)|ceramide metabolic process (GO:0006672)|cytosolic calcium ion homeostasis (GO:0051480)|galactosylceramide metabolic process (GO:0006681)|globoside metabolic process (GO:0001575)|glucosylceramide metabolic process (GO:0006678)|ionotropic glutamate receptor signaling pathway (GO:0035235)|lysosomal lumen acidification (GO:0007042)|lysosomal lumen pH elevation (GO:0035752)|lysosome organization (GO:0007040)|macroautophagy (GO:0016236)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of catalytic activity (GO:0043086)|negative regulation of macroautophagy (GO:0016242)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of proteolysis (GO:0045861)|neuromuscular process controlling balance (GO:0050885)|neurotransmitter metabolic process (GO:0042133)|protein catabolic process (GO:0030163)|protein processing (GO:0016485)|receptor-mediated endocytosis (GO:0006898)|sphingomyelin metabolic process (GO:0006684)|vacuolar transport (GO:0007034)|vesicle transport along microtubule (GO:0047496)	autophagic vacuole (GO:0005776)|caveola (GO:0005901)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|trans-Golgi network (GO:0005802)	unfolded protein binding (GO:0051082)			breast(1)|large_intestine(2)|lung(11)|upper_aerodigestive_tract(1)	15						ATGATCAGGAAGACGAGGTAG	0.597																																					p.F375L		Atlas-SNP	.											.	CLN3	33	.	0			c.T1123C						.						78	77	77					16																	28489132		2197	4300	6497	SO:0001583	missense	1201	exon15			TCAGGAAGACGAG	U32680	CCDS10632.1, CCDS73852.1, CCDS73853.1, CCDS73854.1, CCDS73855.1	16p12	2014-09-17	2008-07-29		ENSG00000188603	ENSG00000188603			2074	protein-coding gene	gene with protein product	"juvenile neuronal ceroid lipofuscinosis"	607042	"Batten, Spielmeyer-Vogt disease"	BTS		18317235	Standard	NM_001042432		Approved	JNCL	uc002dpp.3	Q13286	OTTHUMG00000097024	ENST00000569430.1:c.1123T>C	chr16.hg19:g.28489132A>G	ENSP00000454229:p.Phe375Leu	113.0	0.0		71.0	4.0	NM_001042432	B2R7J1|O00668|O95089|Q549S9|Q9UP09|Q9UP11|Q9UP12|Q9UP13|Q9UP14	Missense_Mutation	SNP	ENST00000569430.1	hg19	CCDS10632.1	.	.	.	.	.	.	.	.	.	.	a	22.8	4.336462	0.81801	.	.	ENSG00000188603	ENST00000535392;ENST00000359984;ENST00000360019;ENST00000354630;ENST00000355477;ENST00000357857;ENST00000395653;ENST00000357806	D;D;D;D;D;D;D;D	0.95821	-3.82;-3.82;-3.82;-3.82;-3.82;-3.82;-3.82;-3.82	5.29	5.29	0.74685	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	D	0.96719	0.8929	M	0.63428	1.95	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	0.999;0.998;0.999;0.999;0.997;0.999;0.999;1.0	D;D;D;D;D;D;D;D	0.87578	0.994;0.987;0.998;0.998;0.969;0.99;0.969;0.998	D	0.95735	0.8778	10	0.30078	T	0.28	-23.8521	13.1832	0.59666	1.0:0.0:0.0:0.0	.	351;358;273;275;321;327;375;276	B4DXL3;Q13286-3;O95086;B4DMY6;B4DFF3;Q13286-2;Q13286;O95089	.;.;.;.;.;.;CLN3_HUMAN;.	L	297;375;375;358;327;321;275;276	ENSP00000443221:F297L;ENSP00000353073:F375L;ENSP00000353116:F375L;ENSP00000346650:F358L;ENSP00000347660:F327L;ENSP00000350523:F321L;ENSP00000379014:F275L;ENSP00000350457:F276L	ENSP00000346650:F358L	F	-	1	0	CLN3	28396633	1.000000	0.71417	0.994000	0.49952	0.792000	0.44763	5.026000	0.64103	2.013000	0.59113	0.454000	0.30748	TTC	.	.		0.597	CLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214115.2			G	28489132	A	G	28489132	3	3	260	1	0	0	0	0	1	0	0	0	3545	72	3	2	201	2	CLN3	16	28489132	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	849106	28489132	61865621	692	37937										
SH2B1	25970	hgsc.bcm.edu	37	chr16	28883910	28883910	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccgggtccagcacctgtggtTccagtccattttcgatatgc	10	13	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:28883910T>C	ENST00000322610.8	+	10	2220	c.1781T>C	c.(1780-1782)tTc>tCc	p.F594S	SH2B1_ENST00000337120.5_Missense_Mutation_p.F594S|SH2B1_ENST00000395532.4_Missense_Mutation_p.F594S|SH2B1_ENST00000359285.5_Missense_Mutation_p.F594S|SH2B1_ENST00000563674.1_Intron|SH2B1_ENST00000545570.1_Missense_Mutation_p.F284S|SH2B1_ENST00000538342.1_Missense_Mutation_p.F258S			Q9NRF2	SH2B1_HUMAN	SH2B adaptor protein 1	594	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|intracellular signal transduction (GO:0035556)|lamellipodium assembly (GO:0030032)|positive regulation of mitosis (GO:0045840)|regulation of DNA biosynthetic process (GO:2000278)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25						CACCTGTGGTTCCAGTCCATT	0.607																																					p.F594S		Atlas-SNP	.											.	SH2B1	160	.	0			c.T1781C						.						151	131	138					16																	28883910		2197	4300	6497	SO:0001583	missense	25970	exon8			TGTGGTTCCAGTC	AK055104	CCDS32424.1, CCDS53996.1, CCDS53997.1	16p11.2	2013-02-14						"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	30417	protein-coding gene	gene with protein product	"SH2-B homolog"	608937				11827956, 10594240	Standard	NM_001145812		Approved	FLJ30542, SH2B	uc002drl.3	Q9NRF2		ENST00000322610.8:c.1781T>C	chr16.hg19:g.28883910T>C	ENSP00000321221:p.Phe594Ser	219.0	0.0		161.0	7.0	NM_001145796	A8K2R7|Q96FK3|Q96SX3|Q9NRF1|Q9NRF3|Q9P2P7|Q9Y3Y3	Missense_Mutation	SNP	ENST00000322610.8	hg19	CCDS53996.1	.	.	.	.	.	.	.	.	.	.	t	20.7	4.032473	0.75504	.	.	ENSG00000178188	ENST00000322610;ENST00000545570;ENST00000359285;ENST00000538342;ENST00000395532;ENST00000337120	D;D;D;D;D;D	0.98362	-4.89;-4.89;-4.89;-4.89;-4.89;-4.89	5.23	5.23	0.72850	SH2 motif (5);	0.000000	0.85682	D	0.000000	D	0.99293	0.9753	H	0.97131	3.945	0.58432	D	0.999996	D;D;D;D;D	0.89917	0.998;1.0;0.997;0.999;1.0	D;D;D;D;D	0.91635	0.982;0.999;0.99;0.99;0.999	D	0.98805	1.0741	10	0.62326	D	0.03	-17.4899	14.1061	0.65091	0.0:0.0:0.0:1.0	.	258;284;594;594;594	B4DLN5;F5GXU7;Q9NRF2-2;Q9NRF2-3;Q9NRF2	.;.;.;.;SH2B1_HUMAN	S	594;284;594;258;594;594	ENSP00000321221:F594S;ENSP00000440354:F284S;ENSP00000352232:F594S;ENSP00000438784:F258S;ENSP00000378903:F594S;ENSP00000337163:F594S	ENSP00000321221:F594S	F	+	2	0	SH2B1	28791411	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.577000	0.82486	1.970000	0.57323	0.529000	0.55759	TTC	.	.		0.607	SH2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000432666.1	NM_015503		C	28883910	T	C	28883910	3	2	260	1	0	0	0	0	1	0	0	0	14242	1783	62	2	1807	2	SH2B1	16	28883910	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	394778	28883910	61470843	693	37938										
ZNF688	146542	hgsc.bcm.edu	37	chr16	30582420	30582420	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cctgttccatccaagagatgAgggctggtttggggcctggg	16	9	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:30582420A>G	ENST00000223459.6	-	2	1325	c.221T>C	c.(220-222)cTc>cCc	p.L74P	ZNF688_ENST00000395219.1_Missense_Mutation_p.L60P|ZNF688_ENST00000567855.1_Missense_Mutation_p.L74P|AC002310.7_ENST00000492040.1_RNA|ZNF688_ENST00000563707.1_Intron|AC002310.7_ENST00000486926.1_RNA	NM_145271.3	NP_660314.1	P0C7X2	ZN688_HUMAN	zinc finger protein 688	74	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(2)|lung(2)|ovary(1)	8						CCAAGAGATGAGGGCTGGTTT	0.627																																					p.L74P		Atlas-SNP	.											.	ZNF688	37	.	0			c.T221C						.						35	37	36					16																	30582420		2197	4300	6497	SO:0001583	missense	146542	exon2			GAGATGAGGGCTG	AK122680	CCDS10684.1	16p11.2	2013-01-08			ENSG00000229809	ENSG00000229809		"Zinc fingers, C2H2-type", "-"	30489	protein-coding gene	gene with protein product						10493829	Standard	XM_005255139		Approved		uc002dys.2	P0C7X2	OTTHUMG00000132408	ENST00000223459.6:c.221T>C	chr16.hg19:g.30582420A>G	ENSP00000223459:p.Leu74Pro	94.0	0.0		64.0	4.0	NM_145271	A8MV39|B3KV51|O75701|Q8IW91|Q8WV14|Q96MN0	Missense_Mutation	SNP	ENST00000223459.6	hg19	CCDS10684.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.333769	0.81801	.	.	ENSG00000229809	ENST00000395219;ENST00000223459	T;T	0.05447	3.44;5.48	5.2	5.2	0.72013	Krueppel-associated box (3);	.	.	.	.	T	0.22589	0.0545	M	0.73217	2.22	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.00202	-1.1925	9	0.87932	D	0	.	11.636	0.51204	1.0:0.0:0.0:0.0	.	74;60	P0C7X2;A8MV39	ZN688_HUMAN;.	P	60;74	ENSP00000378645:L60P;ENSP00000223459:L74P	ENSP00000223459:L74P	L	-	2	0	ZNF688	30489921	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.527000	0.60573	2.308000	0.77769	0.533000	0.62120	CTC	.	.		0.627	ZNF688-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255544.2	NM_145271		G	30582420	A	G	30582420	3	3	260	1	0	0	0	0	1	0	0	0	18108	304	11	2	617	2	ZNF688	16	30582420	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1698510	30582420	59772333	694	37939										
PRSS8	5652	hgsc.bcm.edu	37	chr16	31143805	31143805	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cacacaccatgtcctcttggAcaaagtgcggctcctcaggc	9	15	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:31143805A>G	ENST00000317508.6	-	5	913	c.650T>C	c.(649-651)gTc>gCc	p.V217A	PRSS8_ENST00000568261.1_Missense_Mutation_p.V163A|RP11-388M20.2_ENST00000563605.1_RNA	NM_002773.3	NP_002764.1	Q16651	PRSS8_HUMAN	protease, serine, 8	217	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				positive regulation of sodium ion transport (GO:0010765)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|skin(1)|upper_aerodigestive_tract(1)	8						GTCCTCTTGGACAAAGTGCGG	0.597																																					p.V217A		Atlas-SNP	.											.	PRSS8	24	.	0			c.T650C						.						100	105	104					16																	31143805		2101	4219	6320	SO:0001583	missense	5652	exon5			TCTTGGACAAAGT	U33446	CCDS45469.1	16p11.2	2010-05-07	2007-02-21			ENSG00000052344		"Serine peptidases / Serine peptidases"	9491	protein-coding gene	gene with protein product	"prostasin"	600823				8838796, 7768952	Standard	NM_002773		Approved		uc002ebc.4	Q16651		ENST00000317508.6:c.650T>C	chr16.hg19:g.31143805A>G	ENSP00000319730:p.Val217Ala	121.0	0.0		92.0	7.0	NM_002773	B4DWP2|Q9UCA3	Missense_Mutation	SNP	ENST00000317508.6	hg19	CCDS45469.1	.	.	.	.	.	.	.	.	.	.	A	16.61	3.169861	0.57584	.	.	ENSG00000052344	ENST00000317508;ENST00000419768	D	0.90900	-2.75	5.51	5.51	0.81932	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.207589	0.33753	N	0.004582	D	0.86239	0.5885	N	0.20445	0.575	0.20638	N	0.999877	P;P	0.46142	0.873;0.873	P;P	0.44946	0.465;0.465	T	0.81895	-0.0723	10	0.87932	D	0	.	14.6064	0.68481	1.0:0.0:0.0:0.0	.	163;217	B4DWP2;Q16651	.;PRSS8_HUMAN	A	217;135	ENSP00000319730:V217A	ENSP00000319730:V217A	V	-	2	0	PRSS8	31051306	1.000000	0.71417	0.159000	0.22649	0.791000	0.44710	3.278000	0.51662	2.098000	0.63641	0.459000	0.35465	GTC	.	.		0.597	PRSS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433536.1	NM_002773		G	31143805	A	G	31143805	3	3	260	1	0	0	0	0	1	0	0	0	12647	275	10	2	389	2	PRSS8	16	31143805	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	561385	31143805	59210948	695	37940										
PRSS36	146547	hgsc.bcm.edu	37	chr16	31151659	31151659	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgcatacaggacacagagggTtccagggggcaggatgccct	15	10	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:31151659T>C	ENST00000268281.4	-	14	2303	c.2245A>G	c.(2245-2247)Acc>Gcc	p.T749A	PRSS36_ENST00000569305.1_Missense_Mutation_p.T744A|PRSS36_ENST00000418068.2_Intron	NM_001258290.1|NM_173502.4	NP_001245219.1|NP_775773.2	Q5K4E3	POLS2_HUMAN	protease, serine, 36	749	Peptidase S1 3. {ECO:0000255|PROSITE- ProRule:PRU00274}.					cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)	serine-type endopeptidase activity (GO:0004252)			kidney(2)|large_intestine(4)|lung(8)|ovary(3)	17						ACACAGAGGGTTCCAGGGGGC	0.587																																					p.T749A		Atlas-SNP	.											.	PRSS36	50	.	0			c.A2245G						.						73	71	72					16																	31151659		2197	4300	6497	SO:0001583	missense	146547	exon14			AGAGGGTTCCAGG	AK075142	CCDS32436.1, CCDS58452.1, CCDS58453.1	16p11.2	2014-09-04			ENSG00000178226			"Serine peptidases / Serine peptidases"	26906	protein-coding gene	gene with protein product	"polyserase 2"	610560				15536082	Standard	NM_173502		Approved	FLJ90661	uc002ebd.4	Q5K4E3	OTTHUMG00000176751	ENST00000268281.4:c.2245A>G	chr16.hg19:g.31151659T>C	ENSP00000268281:p.Thr749Ala	162.0	0.0		98.0	4.0	NM_173502	A8K2P5|B4DW80|B7ZMK8|E7EX56|Q8NBY4	Missense_Mutation	SNP	ENST00000268281.4	hg19	CCDS32436.1	.	.	.	.	.	.	.	.	.	.	T	11.37	1.617719	0.28801	.	.	ENSG00000178226	ENST00000268281	T	0.59502	0.26	4.92	2.47	0.30058	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.56673	0.2001	N	0.20807	0.61	0.09310	N	1	D;D	0.69078	0.997;0.997	D;D	0.79108	0.992;0.992	T	0.40701	-0.9549	9	0.72032	D	0.01	.	4.6071	0.12383	0.0:0.1024:0.1956:0.702	.	744;749	B7ZMK8;Q5K4E3	.;POLS2_HUMAN	A	749	ENSP00000268281:T749A	ENSP00000268281:T749A	T	-	1	0	PRSS36	31059160	0.128000	0.22383	0.108000	0.21378	0.223000	0.24884	1.260000	0.32968	0.829000	0.34733	0.454000	0.30748	ACC	.	.		0.587	PRSS36-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000433542.1	NM_173502		C	31151659	T	C	31151659	3	2	260	1	0	0	0	0	1	0	0	0	12637	1725	60	2	330	2	PRSS36	16	31151659	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	7854	31151659	59203094	696	37941										
ZNF267	10308	hgsc.bcm.edu	37	chr16	31926790	31926790	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aattcacactggagagaaacCatacaaatgtaaagaatgtg	8	6	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:31926790C>A	ENST00000300870.10	+	4	1429	c.1220C>A	c.(1219-1221)cCa>cAa	p.P407Q		NM_001265588.1|NM_003414.5	NP_001252517.1|NP_003405	Q14586	ZN267_HUMAN	zinc finger protein 267	407					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(5)|kidney(1)|large_intestine(14)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	41						GGAGAGAAACCATACAAATGT	0.353																																					p.P407Q		Atlas-SNP	.											.	ZNF267	94	.	0			c.C1220A						.						45	50	49					16																	31926790		2197	4298	6495	SO:0001583	missense	10308	exon4			AGAAACCATACAA	X78925	CCDS32440.1	16p11.2	2013-01-08			ENSG00000185947	ENSG00000185947		"Zinc fingers, C2H2-type", "-"	13060	protein-coding gene	gene with protein product		604752				7865130	Standard	NM_003414		Approved	HZF2	uc002ecs.5	Q14586		ENST00000300870.10:c.1220C>A	chr16.hg19:g.31926790C>A	ENSP00000300870:p.Pro407Gln	100.0	0.0		49.0	4.0	NM_003414	A0JNZ9|Q8NE41|Q9NRJ0	Missense_Mutation	SNP	ENST00000300870.10	hg19	CCDS32440.1	.	.	.	.	.	.	.	.	.	.	.	21.3	4.123892	0.77436	.	.	ENSG00000185947	ENST00000300870	T	0.28454	1.61	0.458	0.458	0.16670	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.50394	0.1613	M	0.80508	2.5	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	T	0.51529	-0.8694	9	0.87932	D	0	.	6.6931	0.23183	0.0:0.9999:0.0:1.0E-4	.	407	Q14586	ZN267_HUMAN	Q	407	ENSP00000300870:P407Q	ENSP00000300870:P407Q	P	+	2	0	ZNF267	31834291	0.995000	0.38212	0.945000	0.38365	0.936000	0.57629	5.363000	0.66104	0.482000	0.27582	0.484000	0.47621	CCA	.	.		0.353	ZNF267-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432446.2	NM_003414		A	31926790	C	A	31926790	3	1	260	1	0	0	0	0	1	0	0	0	17821	594	21	3	1234	3	ZNF267	16	31926790	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	775131	31926790	58427963	697	37942										
PHKB	5257	hgsc.bcm.edu	37	chr16	47698853	47698853	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttttcttcctctatagccccAcacattactacttttctggt	3	13	3	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:47698853A>G	ENST00000323584.5	+	25	2418	c.2394A>G	c.(2392-2394)ccA>ccG	p.P798P	PHKB_ENST00000455779.1_Silent_p.P791P|PHKB_ENST00000566044.1_Intron|PHKB_ENST00000299167.8_Intron	NM_000293.2	NP_000284.1	Q93100	KPBB_HUMAN	phosphorylase kinase, beta	798					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|liver(1)|lung(18)|ovary(1)|skin(1)	41		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				CTATAGCCCCACACATTACTA	0.448																																					p.P798P		Atlas-SNP	.											.	PHKB	298	.	0			c.A2394G						.						79	70	73					16																	47698853		2201	4300	6501	SO:0001819	synonymous_variant	5257	exon25			AGCCCCACACATT		CCDS10729.1, CCDS42161.1	16q12-q13	2009-07-10			ENSG00000102893	ENSG00000102893	2.7.11.19		8927	protein-coding gene	gene with protein product		172490					Standard	NM_000293		Approved		uc002eev.4	Q93100	OTTHUMG00000133102	ENST00000323584.5:c.2394A>G	chr16.hg19:g.47698853A>G		124.0	0.0		88.0	4.0	NM_000293	Q8N4T5	Silent	SNP	ENST00000323584.5	hg19	CCDS10729.1																																																																																			.	.		0.448	PHKB-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000430413.1			G	47698853	A	G	47698853	2	3	260	1	0	0	0	0	0	0	0	1	11854	146	6	2		2	PHKB	16	47698853	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	15772063	47698853	42655900	698	37943										
N4BP1	9683	hgsc.bcm.edu	37	chr16	48595790	48595790	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gcacatctggtgagctagaaAggactgtgtccatttgtttt	11	7	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:48595790A>G	ENST00000262384.3	-	2	1000	c.764T>C	c.(763-765)cTt>cCt	p.L255P	RP11-44I10.3_ENST00000563994.1_RNA	NM_153029.3	NP_694574.3	O75113	N4BP1_HUMAN	NEDD4 binding protein 1	255					cellular response to UV (GO:0034644)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein ubiquitination (GO:0031397)	nucleolus (GO:0005730)|PML body (GO:0016605)				breast(3)|kidney(2)|lung(11)|urinary_tract(1)	17		all_cancers(37;0.179)|all_lung(18;0.11)				TGAGCTAGAAAGGACTGTGTC	0.403																																					p.L255P		Atlas-SNP	.											.	N4BP1	121	.	0			c.T764C						.						68	64	65					16																	48595790		1876	4085	5961	SO:0001583	missense	9683	exon2			CTAGAAAGGACTG	AK026937	CCDS45479.1	16q12.1	2008-01-18				ENSG00000102921			29850	protein-coding gene	gene with protein product						9734811, 11717310	Standard	NM_153029		Approved		uc002efp.3	O75113		ENST00000262384.3:c.764T>C	chr16.hg19:g.48595790A>G	ENSP00000262384:p.Leu255Pro	227.0	0.0		137.0	6.0	NM_153029	A7MD49|Q2YDX1	Missense_Mutation	SNP	ENST00000262384.3	hg19	CCDS45479.1	.	.	.	.	.	.	.	.	.	.	A	7.468	0.646153	0.14451	.	.	ENSG00000102921	ENST00000262384	T	0.47869	0.83	5.75	4.67	0.58626	.	0.147156	0.43747	D	0.000525	T	0.30070	0.0753	N	0.08118	0	0.41511	D	0.98834	B	0.33448	0.412	B	0.35353	0.201	T	0.24440	-1.0160	10	0.72032	D	0.01	-7.5536	11.6399	0.51227	0.9309:0.0:0.0691:0.0	.	255	O75113	N4BP1_HUMAN	P	255	ENSP00000262384:L255P	ENSP00000262384:L255P	L	-	2	0	N4BP1	47153291	1.000000	0.71417	0.016000	0.15963	0.070000	0.16714	6.831000	0.75324	1.016000	0.39470	-0.250000	0.11733	CTT	.	.		0.403	N4BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429920.1	NM_014664		G	48595790	A	G	48595790	3	3	260	1	0	0	0	0	1	0	0	0	10118	72	3	2	1950	2	N4BP1	16	48595790	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	896937	48595790	41758963	699	37944										
ZNF423	23090	hgsc.bcm.edu	37	chr16	49671524	49671524	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttgcagaagaaagcattattAccgtcagaggggttggcgtt	13	6	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:49671524A>T	ENST00000561648.1	-	4	1592	c.1539T>A	c.(1537-1539)ggT>ggA	p.G513G	ZNF423_ENST00000562871.1_Silent_p.G453G|ZNF423_ENST00000567169.1_Silent_p.G396G|ZNF423_ENST00000562520.1_Silent_p.G453G|ZNF423_ENST00000535559.1_Silent_p.G396G|ZNF423_ENST00000262383.2_Silent_p.G513G|ZNF423_ENST00000563137.2_Silent_p.G453G	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	513					cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				AAGCATTATTACCGTCAGAGG	0.587																																					p.G513G		Atlas-SNP	.											.	ZNF423	463	.	0			c.T1539A						.						86	85	85					16																	49671524		2198	4300	6498	SO:0001819	synonymous_variant	23090	exon4			ATTATTACCGTCA	AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"Zinc fingers, C2H2-type"	16762	protein-coding gene	gene with protein product	"OLF-1/EBF associated zinc finger gene", " Smad- and Olf-interacting zinc finger protein", "early B-cell factor associated zinc finger protein"	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.1539T>A	chr16.hg19:g.49671524A>T		80.0	0.0		54.0	4.0	NM_015069	O94860|Q76N04|Q9NZ13	Silent	SNP	ENST00000561648.1	hg19	CCDS32445.1																																																																																			.	.		0.587	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069		T	49671524	A	T	49671524	2	4	260	1	0	0	0	0	0	0	0	1	17913	378	14	4		4	ZNF423	16	49671524	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1075734	49671524	40683229	700	37945										
HEATR3	55027	hgsc.bcm.edu	37	chr16	50120179	50120179	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tctccagagtcttgtgtcccTcctggatgtggagcacctgg	12	12	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:50120179T>C	ENST00000299192.7	+	11	1618	c.1427T>C	c.(1426-1428)cTc>cCc	p.L476P	HEATR3_ENST00000285767.4_Missense_Mutation_p.L390P|HEATR3_ENST00000564942.1_3'UTR	NM_182922.2	NP_891552.1	Q7Z4Q2	HEAT3_HUMAN	HEAT repeat containing 3	476										cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	28						CTTGTGTCCCTCCTGGATGTG	0.498																																					p.L476P		Atlas-SNP	.											.	HEATR3	59	.	0			c.T1427C						.						43	36	39					16																	50120179		2198	4298	6496	SO:0001583	missense	55027	exon11			TGTCCCTCCTGGA	BC018730	CCDS10739.1	16q12.1	2008-02-05			ENSG00000155393	ENSG00000155393			26087	protein-coding gene	gene with protein product		614951				12477932	Standard	XM_005256013		Approved	FLJ20718	uc002efw.3	Q7Z4Q2	OTTHUMG00000133174	ENST00000299192.7:c.1427T>C	chr16.hg19:g.50120179T>C	ENSP00000299192:p.Leu476Pro	180.0	0.0		108.0	5.0	NM_182922	A8K1N4|Q8N525|Q8WV56|Q96CC9|Q9NWN7	Missense_Mutation	SNP	ENST00000299192.7	hg19	CCDS10739.1	.	.	.	.	.	.	.	.	.	.	T	13.76	2.333597	0.41297	.	.	ENSG00000155393	ENST00000285767;ENST00000299192	T;T	0.66099	-0.19;-0.19	5.68	5.68	0.88126	Armadillo-type fold (1);	0.369118	0.30704	N	0.009045	T	0.57021	0.2025	L	0.47716	1.5	0.58432	D	0.999997	B;P	0.52842	0.01;0.956	B;B	0.41619	0.008;0.361	T	0.59590	-0.7426	10	0.39692	T	0.17	.	15.9267	0.79624	0.0:0.0:0.0:1.0	.	390;476	B7WNW7;Q7Z4Q2	.;HEAT3_HUMAN	P	390;476	ENSP00000285767:L390P;ENSP00000299192:L476P	ENSP00000285767:L390P	L	+	2	0	HEATR3	48677680	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	3.937000	0.56575	2.144000	0.66660	0.528000	0.53228	CTC	.	.		0.498	HEATR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256880.2	NM_182922		C	50120179	T	C	50120179	3	2	260	1	0	0	0	0	1	0	0	0	7038	1551	54	2	1469	2	HEATR3	16	50120179	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	448655	50120179	40234574	701	37946										
ADCY7	113	hgsc.bcm.edu	37	chr16	50346835	50346835	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtcctatgactgcgtctgtgTcatgtttgcctccgtgccgg	12	12	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:50346835T>C	ENST00000394697.2	+	22	2979	c.2639T>C	c.(2638-2640)gTc>gCc	p.V880A	ADCY7_ENST00000254235.3_Missense_Mutation_p.V880A			P51828	ADCY7_HUMAN	adenylate cyclase 7	880	Guanylate cyclase 2. {ECO:0000255|PROSITE-ProRule:PRU00099}.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to ethanol (GO:0071361)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|maternal process involved in female pregnancy (GO:0060135)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cAMP biosynthetic process (GO:0030819)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(5)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	35		all_cancers(37;0.0127)		GBM - Glioblastoma multiforme(240;0.195)		TGCGTCTGTGTCATGTTTGCC	0.532																																					p.V880A		Atlas-SNP	.											.	ADCY7	90	.	0			c.T2639C						.						256	195	215					16																	50346835		2198	4300	6498	SO:0001583	missense	113	exon21			TCTGTGTCATGTT	D25538	CCDS10741.1, CCDS73882.1	16q12.1	2013-02-04			ENSG00000121281	ENSG00000121281	4.6.1.1	"Adenylate cyclases"	238	protein-coding gene	gene with protein product		600385				7860067	Standard	NM_001286057		Approved	KIAA0037, AC7	uc002egd.1	P51828	OTTHUMG00000133172	ENST00000394697.2:c.2639T>C	chr16.hg19:g.50346835T>C	ENSP00000378187:p.Val880Ala	83.0	0.0		51.0	4.0	NM_001114	A0AVA6	Missense_Mutation	SNP	ENST00000394697.2	hg19	CCDS10741.1	.	.	.	.	.	.	.	.	.	.	T	31	5.079819	0.94050	.	.	ENSG00000121281	ENST00000394697;ENST00000254235	D;D	0.84442	-1.85;-1.85	5.47	5.47	0.80525	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.000000	0.39985	U	0.001212	D	0.95579	0.8563	H	0.98577	4.27	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97429	1.0014	10	0.87932	D	0	.	15.5676	0.76306	0.0:0.0:0.0:1.0	.	880	P51828	ADCY7_HUMAN	A	880	ENSP00000378187:V880A;ENSP00000254235:V880A	ENSP00000254235:V880A	V	+	2	0	ADCY7	48904336	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.036000	0.88901	2.063000	0.61619	0.459000	0.35465	GTC	.	.		0.532	ADCY7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256877.3			C	50346835	T	C	50346835	3	2	260	1	0	0	0	0	1	0	0	0	299	1667	58	2	2721	2	ADCY7	16	50346835	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	226656	50346835	40007918	702	37947										
NOD2	64127	hgsc.bcm.edu	37	chr16	50745876	50745876	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggcagggctgttgtcccgggAgcactggggcctgctggctg	19	11	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:50745876A>G	ENST00000300589.2	+	4	2159	c.2054A>G	c.(2053-2055)gAg>gGg	p.E685G	RP11-327F22.6_ENST00000602304.1_RNA	NM_022162.1	NP_071445.1	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain containing 2	685					activation of MAPK activity (GO:0000187)|activation of MAPK activity involved in innate immune response (GO:0035419)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to peptidoglycan (GO:0071224)|cytokine production involved in immune response (GO:0002367)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|detection of biotic stimulus (GO:0009595)|detection of muramyl dipeptide (GO:0032498)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|innate immune response (GO:0045087)|innate immune response in mucosa (GO:0002227)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|macrophage inflammatory protein-1 alpha production (GO:0071608)|maintenance of gastrointestinal epithelium (GO:0030277)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-18 production (GO:0032701)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of macrophage apoptotic process (GO:2000110)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell mediated immunity (GO:0002710)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of tumor necrosis factor production (GO:0032720)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of B cell activation (GO:0050871)|positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria (GO:0006965)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell cytokine production (GO:0002732)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gamma-delta T cell activation (GO:0046645)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of prostaglandin-E synthase activity (GO:2000363)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type 2 immune response (GO:0002830)|protein oligomerization (GO:0051259)|regulation of inflammatory response (GO:0050727)|regulation of neutrophil chemotaxis (GO:0090022)|response to exogenous dsRNA (GO:0043330)|response to lipopolysaccharide (GO:0032496)|response to muramyl dipeptide (GO:0032495)|response to nutrient (GO:0007584)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|enzyme binding (GO:0019899)|muramyl dipeptide binding (GO:0032500)|peptidoglycan binding (GO:0042834)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(30)|ovary(3)|skin(3)	52		all_cancers(37;0.0156)				TTGTCCCGGGAGCACTGGGGC	0.667																																					p.E685G		Atlas-SNP	.											.	NOD2	118	.	0			c.A2054G						.						32	35	34					16																	50745876		2198	4299	6497	SO:0001583	missense	64127	exon4			CCCGGGAGCACTG	AF178930	CCDS10746.1	16q12	2014-09-17	2006-12-08	2006-12-08	ENSG00000167207	ENSG00000167207		"Nucleotide-binding domain and leucine rich repeat containing"	5331	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 2", "NOD-like receptor C2", "NLR family, CARD domain containing 2"	605956	"caspase recruitment domain family, member 15"	IBD1, CARD15		7809109, 8587604	Standard	XM_005256084		Approved	BLAU, CD, PSORAS1, CLR16.3, NLRC2	uc002egm.1	Q9HC29	OTTHUMG00000133171	ENST00000300589.2:c.2054A>G	chr16.hg19:g.50745876A>G	ENSP00000300589:p.Glu685Gly	113.0	0.0		90.0	4.0	NM_022162	E2JEQ6|Q96RH5|Q96RH6|Q96RH8	Missense_Mutation	SNP	ENST00000300589.2	hg19	CCDS10746.1	.	.	.	.	.	.	.	.	.	.	A	8.557	0.876958	0.17395	.	.	ENSG00000167207	ENST00000526417;ENST00000300589	T	0.70045	-0.45	5.74	4.58	0.56647	.	0.512739	0.19747	N	0.106998	T	0.59998	0.2235	L	0.55834	1.745	0.24788	N	0.992775	P;P;P	0.44429	0.732;0.835;0.835	B;B;B	0.40825	0.204;0.302;0.341	T	0.57323	-0.7831	10	0.40728	T	0.16	.	9.727	0.40337	0.7062:0.2938:0.0:0.0	.	469;658;685	D6CHF9;Q9HC29-2;Q9HC29	.;.;NOD2_HUMAN	G	658;685	ENSP00000300589:E685G	ENSP00000300589:E685G	E	+	2	0	NOD2	49303377	1.000000	0.71417	0.995000	0.50966	0.408000	0.30992	3.053000	0.49901	2.189000	0.69895	0.459000	0.35465	GAG	.	.		0.667	NOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256876.2	NM_022162		G	50745876	A	G	50745876	3	3	260	1	0	0	0	0	1	0	0	0	10526	304	11	2	2068	2	NOD2	16	50745876	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	399041	50745876	39608877	703	37948										
SLC12A3	6559	hgsc.bcm.edu	37	chr16	56906359	56906359	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aggacaaggcctccaaaggcTtcttcagctaccggggtatg	12	11	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:56906359T>C	ENST00000563236.1	+	7	974	c.949T>C	c.(949-951)Ttc>Ctc	p.F317L	SLC12A3_ENST00000566786.1_Missense_Mutation_p.F316L|SLC12A3_ENST00000438926.2_Missense_Mutation_p.F317L|SLC12A3_ENST00000262502.5_Missense_Mutation_p.F316L			P55017	S12A3_HUMAN	solute carrier family 12 (sodium/chloride transporter), member 3	317					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:chloride symporter activity (GO:0015378)|transporter activity (GO:0005215)	p.F317I(1)		breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(28)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50					Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325)	CTCCAAAGGCTTCTTCAGCTA	0.567																																					p.F317L		Atlas-SNP	.											SLC12A3,NS,carcinoma,0,1	SLC12A3	99	.	1	Substitution - Missense(1)	lung(1)	c.T949C						.						81	73	76					16																	56906359		2198	4300	6498	SO:0001583	missense	6559	exon7			AAAGGCTTCTTCA		CCDS10770.1, CCDS45491.1, CCDS58464.1	16q13	2013-07-18	2013-07-18		ENSG00000070915	ENSG00000070915		"Solute carriers"	10912	protein-coding gene	gene with protein product		600968				8812482	Standard	NM_000339		Approved	NCCT	uc002ekd.4	P55017	OTTHUMG00000133284	ENST00000563236.1:c.949T>C	chr16.hg19:g.56906359T>C	ENSP00000456149:p.Phe317Leu	68.0	0.0		51.0	3.0	NM_001126108	A8MSJ2|C9JNN9	Missense_Mutation	SNP	ENST00000563236.1	hg19	CCDS58464.1	.	.	.	.	.	.	.	.	.	.	T	28.0	4.882274	0.91740	.	.	ENSG00000070915	ENST00000438926;ENST00000262502	D	0.98313	-4.86	5.72	5.72	0.89469	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.98102	0.9374	M	0.87180	2.865	0.80722	D	1	B;B;B	0.26318	0.146;0.028;0.022	B;B;B	0.33339	0.162;0.084;0.05	D	0.97750	1.0214	10	0.87932	D	0	.	15.9826	0.80125	0.0:0.0:0.0:1.0	.	316;317;317	P55017-3;P55017;P55017-2	.;S12A3_HUMAN;.	L	316;317	ENSP00000262502:F317L	ENSP00000262502:F317L	F	+	1	0	SLC12A3	55463860	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.152000	0.71812	2.182000	0.69389	0.459000	0.35465	TTC	.	.		0.567	SLC12A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432337.1			C	56906359	T	C	56906359	3	2	260	1	0	0	0	0	1	0	0	0	14399	1609	56	2	975	2	SLC12A3	16	56906359	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	6160483	56906359	33448394	704	37949										
CPNE2	221184	hgsc.bcm.edu	37	chr16	57153527	57153527	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cattcacagtgcccttggtgTccctgtgtgatggggacatg	13	10	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:57153527T>C	ENST00000535318.2	+	8	1007	c.646T>C	c.(646-648)Tcc>Ccc	p.S216P	CPNE2_ENST00000290776.8_Missense_Mutation_p.S216P|CPNE2_ENST00000565874.1_Missense_Mutation_p.S216P|CPNE2_ENST00000537605.1_Missense_Mutation_p.S114P			Q96FN4	CPNE2_HUMAN	copine II	216	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.					extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|endometrium(4)|large_intestine(4)|lung(5)|ovary(1)|skin(5)	21		all_neural(199;0.224)				GCCCTTGGTGTCCCTGTGTGA	0.622																																					p.S216P		Atlas-SNP	.											.	CPNE2	48	.	0			c.T646C						.						80	67	72					16																	57153527		2198	4300	6498	SO:0001583	missense	221184	exon7			TTGGTGTCCCTGT		CCDS10774.1	16q13	2008-02-05			ENSG00000140848	ENSG00000140848			2315	protein-coding gene	gene with protein product		604206				9430674	Standard	NM_152727		Approved	CPN2	uc002eks.2	Q96FN4	OTTHUMG00000133471	ENST00000535318.2:c.646T>C	chr16.hg19:g.57153527T>C	ENSP00000439018:p.Ser216Pro	213.0	0.0		123.0	5.0	NM_152727	Q68D19|Q719H8|Q86XP9	Missense_Mutation	SNP	ENST00000535318.2	hg19	CCDS10774.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.035567	0.75617	.	.	ENSG00000140848	ENST00000290776;ENST00000537605;ENST00000535318	T;T;T	0.39592	1.07;1.07;1.07	5.1	5.1	0.69264	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.52837	0.1759	L	0.41710	1.295	0.49798	D	0.999828	D;D	0.67145	0.996;0.984	P;P	0.62089	0.898;0.884	T	0.55642	-0.8109	10	0.62326	D	0.03	-19.1259	14.8933	0.70625	0.0:0.0:0.0:1.0	.	216;216	A8K8A4;Q96FN4	.;CPNE2_HUMAN	P	216;114;216	ENSP00000290776:S216P;ENSP00000445468:S114P;ENSP00000439018:S216P	ENSP00000290776:S216P	S	+	1	0	CPNE2	55711028	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	4.993000	0.63895	1.920000	0.55613	0.459000	0.35465	TCC	.	.		0.622	CPNE2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432986.2	NM_152727		C	57153527	T	C	57153527	3	2	260	1	0	0	0	0	1	0	0	0	3814	1667	58	2	668	2	CPNE2	16	57153527	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	247168	57153527	33201226	705	37950										
CNGB1	1258	hgsc.bcm.edu	37	chr16	57954321	57954321	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gctctcctcatcagaggtgaCgtcagggtcaatgagtttct	11	10	6	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:57954321C>A	ENST00000251102.8	-	19	1831	c.1771G>T	c.(1771-1773)Gtc>Ttc	p.V591F	CNGB1_ENST00000564448.1_Missense_Mutation_p.V585F	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	591					cation transport (GO:0006812)|cytosolic calcium ion homeostasis (GO:0051480)|detection of light stimulus involved in visual perception (GO:0050908)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|protein heterotetramerization (GO:0051290)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina homeostasis (GO:0001895)|rhodopsin mediated signaling pathway (GO:0016056)|sensory perception of smell (GO:0007608)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|intracellular cyclic nucleotide activated cation channel complex (GO:0017071)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)|transmembrane transporter complex (GO:1902495)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(7)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(11)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	54						TCAGAGGTGACGTCAGGGTCA	0.572																																					p.V591F	Colon(156;1293 1853 16336 28962 38659)	Atlas-SNP	.											.	CNGB1	105	.	0			c.G1771T						.						84	87	86					16																	57954321		1957	4147	6104	SO:0001583	missense	1258	exon19			AGGTGACGTCAGG	AF042498	CCDS42169.1, CCDS45495.1, CCDS67042.1	16q13	2013-02-14			ENSG00000070729	ENSG00000070729		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2151	protein-coding gene	gene with protein product	"glutamic acid-rich protein"	600724		CNCG2, CNCG3L		8766832, 7590744, 16382102	Standard	NM_001297		Approved	RCNC2, RCNCb, GARP, GAR1, CNGB1B, RP45	uc002emt.2	Q14028	OTTHUMG00000154810	ENST00000251102.8:c.1771G>T	chr16.hg19:g.57954321C>A	ENSP00000251102:p.Val591Phe	111.0	0.0		77.0	4.0	NM_001297	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Missense_Mutation	SNP	ENST00000251102.8	hg19	CCDS42169.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.124121	0.77436	.	.	ENSG00000070729	ENST00000251102	T	0.76709	-1.04	5.42	5.42	0.78866	.	0.000000	0.47455	D	0.000228	D	0.85982	0.5824	M	0.73598	2.24	0.80722	D	1	D	0.64830	0.994	P	0.62813	0.907	D	0.87018	0.2127	10	0.62326	D	0.03	.	13.9072	0.63843	0.0:0.8479:0.1521:0.0	.	591	Q14028	CNGB1_HUMAN	F	591	ENSP00000251102:V591F	ENSP00000251102:V591F	V	-	1	0	CNGB1	56511822	0.883000	0.30277	0.986000	0.45419	0.974000	0.67602	1.595000	0.36708	2.557000	0.86248	0.555000	0.69702	GTC	.	.		0.572	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297		A	57954321	C	A	57954321	3	1	260	1	0	0	0	0	1	0	0	0	3602	536	19	1	2044	1	CNGB1	16	57954321	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	800794	57954321	32400432	706	37951										
C16orf80	29105	hgsc.bcm.edu	37	chr16	58148804	58148804	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tctgagaagtaaacccgtcgGatgcgacaatttgcatggat	11	8	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:58148804G>T	ENST00000262498.3	-	5	820	c.486C>A	c.(484-486)atC>atA	p.I162I	CTB-134F13.1_ENST00000564672.1_RNA|C16orf80_ENST00000562443.1_5'Flank	NM_013242.2	NP_037374.1														kidney(1)|large_intestine(1)|lung(1)|prostate(1)	4						AAACCCGTCGGATGCGACAAT	0.483																																					p.I162I	Pancreas(103;1212 1612 18629 30162 52390)	Atlas-SNP	.											.	C16orf80	17	.	0			c.C486A						.						104	102	102					16																	58148804		2198	4300	6498	SO:0001819	synonymous_variant	29105	exon5			CCGTCGGATGCGA																												ENST00000262498.3:c.486C>A	chr16.hg19:g.58148804G>T		110.0	0.0		70.0	4.0	NM_013242		Silent	SNP	ENST00000262498.3	hg19	CCDS10793.1																																																																																			.	.		0.483	C16orf80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257388.2			T	58148804	G	T	58148804	2	4	260	1	0	0	0	0	0	0	0	1	1839	1164	41	3		3	C16orf80	16	58148804	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	194483	58148804	32205949	707	37952										
CSNK2A2	1459	hgsc.bcm.edu	37	chr16	58198047	58198047	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgggactgctccttcaccacAgggtctgcaagaaagcagga	12	11	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:58198047A>G	ENST00000262506.3	-	11	1164	c.981T>C	c.(979-981)ccT>ccC	p.P327P	CSNK2A2_ENST00000566813.1_5'UTR	NM_001896.2	NP_001887.1	P19784	CSK22_HUMAN	casein kinase 2, alpha prime polypeptide	327					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|mitotic cell cycle (GO:0000278)|mitotic spindle checkpoint (GO:0071174)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)	1						CCTTCACCACAGGGTCTGCAA	0.552																																					p.P327P	Melanoma(54;119 1219 18349 35700 39738)	Atlas-SNP	.											.	CSNK2A2	25	.	0			c.T981C						.						96	79	85					16																	58198047		2198	4300	6498	SO:0001819	synonymous_variant	1459	exon11			CACCACAGGGTCT	M55268	CCDS10794.1	16q21	2013-01-17			ENSG00000070770	ENSG00000070770			2459	protein-coding gene	gene with protein product		115442				2174700, 1766873	Standard	NM_001896		Approved	CSNK2A1	uc002enc.3	P19784	OTTHUMG00000133488	ENST00000262506.3:c.981T>C	chr16.hg19:g.58198047A>G		87.0	0.0		71.0	4.0	NM_001896		Silent	SNP	ENST00000262506.3	hg19	CCDS10794.1																																																																																			.	.		0.552	CSNK2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257386.2	NM_001896		G	58198047	A	G	58198047	2	3	260	1	0	0	0	0	0	0	0	1	3960	175	7	2		2	CSNK2A2	16	58198047	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	49243	58198047	32156706	708	37953										
CNOT1	23019	hgsc.bcm.edu	37	chr16	58620483	58620483	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttaagaaaagcgtctatctgTtcttgtccaactccaaaggc	7	10	3	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:58620483T>C	ENST00000317147.5	-	7	935	c.603A>G	c.(601-603)gaA>gaG	p.E201E	CNOT1_ENST00000569240.1_Silent_p.E201E|CNOT1_ENST00000441024.2_Silent_p.E201E	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	201					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		CGTCTATCTGTTCTTGTCCAA	0.488																																					p.E201E		Atlas-SNP	.											.	CNOT1	359	.	0			c.A603G						.						246	246	246					16																	58620483		2198	4300	6498	SO:0001819	synonymous_variant	23019	exon7			TATCTGTTCTTGT	AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.603A>G	chr16.hg19:g.58620483T>C		194.0	0.0		95.0	4.0	NM_206999	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Silent	SNP	ENST00000317147.5	hg19	CCDS10799.1																																																																																			.	.		0.488	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284		C	58620483	T	C	58620483	2	2	260	1	0	0	0	0	0	0	0	1	3619	1722	60	2		2	CNOT1	16	58620483	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	422436	58620483	31734270	709	37954										
B3GNT9	80262	hgsc.bcm.edu	37	chr16	67183637	67183637	+	IGR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttacgtcaccagcaagcaggTcttgcgccgggtcccgcggc	13	15	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:67183637T>C	ENST00000219139.3	+	0	2865				B3GNT9_ENST00000449549.3_Missense_Mutation_p.D251G	NM_025187.3	NP_079463.2	Q9BSU1	CP070_HUMAN	chromosome 16 open reading frame 70											cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(3)|skin(1)	17		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0017)|Epithelial(162;0.00655)|all cancers(182;0.0579)		AGCAAGCAGGTCTTGCGCCGG	0.632																																					p.D251G		Atlas-SNP	.											.	B3GNT9	25	.	0			c.A752G						.						21	23	22					16																	67183637		1986	4132	6118	SO:0001628	intergenic_variant	84752	exon2			AGCAGGTCTTGCG	AK022138	CCDS10828.1	16q22.1	2011-01-25	2006-04-12	2006-04-12	ENSG00000125149	ENSG00000125149			29564	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 6"	C16orf6, LIN10		12477932	Standard	NM_025187		Approved	lin-10, FLJ12076	uc002erd.3	Q9BSU1	OTTHUMG00000137510		chr16.hg19:g.67183637T>C		147.0	0.0		86.0	4.0	NM_033309	Q9HA86	Missense_Mutation	SNP	ENST00000219139.3	hg19	CCDS10828.1	.	.	.	.	.	.	.	.	.	.	t	21.1	4.090436	0.76756	.	.	ENSG00000237172	ENST00000449549	T	0.43688	0.94	5.02	3.85	0.44370	.	.	.	.	.	T	0.54255	0.1847	M	0.61703	1.905	0.40236	D	0.9779	D	0.60575	0.988	P	0.60541	0.876	T	0.56044	-0.8044	9	0.45353	T	0.12	-16.6784	10.4738	0.44652	0.0:0.0:0.1629:0.837	.	251	Q6UX72	B3GN9_HUMAN	G	251	ENSP00000400157:D251G	ENSP00000400157:D251G	D	-	2	0	B3GNT9	65741138	1.000000	0.71417	0.805000	0.32314	0.508000	0.34012	6.234000	0.72326	1.885000	0.54596	0.454000	0.30748	GAC	.	.		0.632	C16orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268829.2	NM_025187		C	67183637	T	C	67183637	1	2	260	0	1	0	0	0	0	0	0	0	1264	1667	58	2		2	B3GNT9	16	67183637	IGR	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	8563154	67183637	23171116	710	37955										
ELMO3	1874	hgsc.bcm.edu	37	chr16	67235697	67235697	+	IGR	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggctgccttcgaggtggaggGggagtcctcgggtgccgggc	21	10	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:67235697G>T	ENST00000379378.3	+	0	2096				ELMO3_ENST00000477898.1_Missense_Mutation_p.G211V|MIR328_ENST00000385213.1_RNA|ELMO3_ENST00000393997.2_Missense_Mutation_p.G377V|ELMO3_ENST00000360833.1_Missense_Mutation_p.G360V	NM_001950.3	NP_001941.2	Q16254	E2F4_HUMAN	E2F transcription factor 4, p107/p130-binding						blood circulation (GO:0008015)|cell volume homeostasis (GO:0006884)|cilium assembly (GO:0042384)|epithelial cell development (GO:0002064)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of cell size (GO:0008361)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(4)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)	11		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000697)|Epithelial(162;0.00303)|all cancers(182;0.0325)		GAGGTGGAGGGGGAGTCCTCG	0.622																																					p.G377V		Atlas-SNP	.											.	ELMO3	41	.	0			c.G1130T						.						46	55	52					16																	67235697		2066	4207	6273	SO:0001628	intergenic_variant	79767	exon11			TGGAGGGGGAGTC	BC021050	CCDS32464.1	16q22.1	2014-05-06			ENSG00000205250	ENSG00000205250			3118	protein-coding gene	gene with protein product		600659				7958924, 7892279	Standard	NM_001950		Approved	E2F-4	uc002erz.3	Q16254	OTTHUMG00000172975		chr16.hg19:g.67235697G>T		113.0	0.0		100.0	4.0	NM_024712	A6NGR8|B5BU56|Q12991|Q15328	Missense_Mutation	SNP	ENST00000379378.3	hg19	CCDS32464.1	.	.	.	.	.	.	.	.	.	.	G	14.21	2.468709	0.43839	.	.	ENSG00000102890	ENST00000360833;ENST00000393997	T;T	0.15372	2.43;2.43	5.55	5.55	0.83447	Engulfment/cell motility, ELMO (2);	0.084362	0.52532	D	0.000062	T	0.16685	0.0401	N	0.25647	0.755	0.80722	D	1	B;P;P	0.38440	0.371;0.631;0.631	B;B;B	0.39531	0.302;0.296;0.296	T	0.01966	-1.1238	10	0.46703	T	0.11	-27.5198	18.0933	0.89480	0.0:0.0:1.0:0.0	.	324;360;377	Q96BJ8;F8W9E7;Q96BJ8-3	ELMO3_HUMAN;.;.	V	360;377	ENSP00000354077:G360V;ENSP00000377566:G377V	ENSP00000354077:G360V	G	+	2	0	ELMO3	65793198	0.992000	0.36948	0.993000	0.49108	0.138000	0.21146	3.680000	0.54641	2.630000	0.89119	0.561000	0.74099	GGG	.	.		0.622	E2F4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421565.1	NM_001950		T	67235697	G	T	67235697	1	4	260	0	1	0	0	0	0	0	0	0	5069	1232	43	3		3	ELMO3	16	67235697	IGR	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	52060	67235697	23119056	711	37956										
KCTD19	146212	hgsc.bcm.edu	37	chr16	67331487	67331487	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tggctcgtaggtgatgtcccTtttgtctaggaaggcacaga	13	8	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:67331487T>C	ENST00000304372.5	-	7	1121	c.1066A>G	c.(1066-1068)Agg>Ggg	p.R356G	KCTD19_ENST00000562860.1_5'Flank	NM_001100915.1	NP_001094385.1	Q17RG1	KCD19_HUMAN	potassium channel tetramerization domain containing 19	356					protein homooligomerization (GO:0051260)					endometrium(3)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)	23		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0311)|Epithelial(162;0.0906)		GTGATGTCCCTTTTGTCTAGG	0.517																																					p.R356G		Atlas-SNP	.											.	KCTD19	82	.	0			c.A1066G						.						114	114	114					16																	67331487		1913	4125	6038	SO:0001583	missense	146212	exon7			TGTCCCTTTTGTC	AK097481	CCDS42179.1	16q22.1	2013-06-20	2013-06-20			ENSG00000168676			24753	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 19"				Standard	NM_001100915		Approved	FLJ40162	uc002esu.2	Q17RG1		ENST00000304372.5:c.1066A>G	chr16.hg19:g.67331487T>C	ENSP00000305702:p.Arg356Gly	148.0	0.0		126.0	6.0	NM_001100915	B4DZ49|Q8N804	Missense_Mutation	SNP	ENST00000304372.5	hg19	CCDS42179.1	.	.	.	.	.	.	.	.	.	.	T	10.38	1.335147	0.24253	.	.	ENSG00000168676	ENST00000304372	T	0.58060	0.36	5.97	4.89	0.63831	.	0.072732	0.64402	D	0.000014	T	0.22205	0.0535	N	0.02011	-0.69	0.32528	N	0.535309	B	0.09022	0.002	B	0.08055	0.003	T	0.19484	-1.0304	10	0.22109	T	0.4	-24.3638	6.716	0.23304	0.0:0.1482:0.0:0.8518	.	356	Q17RG1	KCD19_HUMAN	G	356	ENSP00000305702:R356G	ENSP00000305702:R356G	R	-	1	2	KCTD19	65888988	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.733000	0.38156	2.288000	0.76882	0.533000	0.62120	AGG	.	.		0.517	KCTD19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422061.1	XM_085367		C	67331487	T	C	67331487	3	2	260	1	0	0	0	0	1	0	0	0	8115	1608	56	2	1754	2	KCTD19	16	67331487	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	95790	67331487	23023266	712	37957										
NFATC3	4775	hgsc.bcm.edu	37	chr16	68156472	68156472	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agaaacttggcatcaacagtAtggacttggacactcattat	8	8	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:68156472A>G	ENST00000346183.3	+	2	710	c.686A>G	c.(685-687)tAt>tGt	p.Y229C	NFATC3_ENST00000535127.2_3'UTR|NFATC3_ENST00000575270.1_Missense_Mutation_p.Y229C|RP11-67A1.2_ENST00000548144.1_RNA|NFATC3_ENST00000329524.4_Missense_Mutation_p.Y229C|NFATC3_ENST00000349223.5_Missense_Mutation_p.Y229C	NM_173165.2	NP_775188.1	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3	229	3 X SP repeats.				cellular respiration (GO:0045333)|cellular response to calcium ion (GO:0071277)|cellular response to lithium ion (GO:0071285)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	44		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0452)|all cancers(182;0.24)		CATCAACAGTATGGACTTGGA	0.542																																					p.Y229C		Atlas-SNP	.											.	NFATC3	190	.	0			c.A686G						.						102	101	101					16																	68156472		2198	4300	6498	SO:0001583	missense	4775	exon2			AACAGTATGGACT	L41067	CCDS10860.1, CCDS10861.1, CCDS10862.1	16q22	2009-11-24			ENSG00000072736	ENSG00000072736		"Nuclear factor of activated T-cells"	7777	protein-coding gene	gene with protein product		602698				7749981	Standard	NM_004555		Approved	NFAT4, NFATX	uc002evo.2	Q12968	OTTHUMG00000137555	ENST00000346183.3:c.686A>G	chr16.hg19:g.68156472A>G	ENSP00000300659:p.Tyr229Cys	106.0	0.0		74.0	4.0	NM_173163	O75211|Q14516|Q99840|Q99841|Q99842	Missense_Mutation	SNP	ENST00000346183.3	hg19	CCDS10860.1	.	.	.	.	.	.	.	.	.	.	A	15.98	2.991958	0.54041	.	.	ENSG00000072736	ENST00000349223;ENST00000346183;ENST00000329524	T;T;T	0.08896	3.04;3.04;3.04	5.28	5.28	0.74379	.	0.116888	0.64402	D	0.000013	T	0.21347	0.0514	L	0.50333	1.59	0.45791	D	0.998672	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.996;0.936;0.996;0.996	T	0.00492	-1.1707	9	.	.	.	-14.2683	11.4951	0.50404	0.85:0.15:0.0:0.0	.	229;229;229;229	Q12968;Q12968-3;B5B2S0;B5B2S2	NFAC3_HUMAN;.;.;.	C	229	ENSP00000264008:Y229C;ENSP00000300659:Y229C;ENSP00000331324:Y229C	.	Y	+	2	0	NFATC3	66713973	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.700000	0.68318	2.111000	0.64477	0.460000	0.39030	TAT	.	.		0.542	NFATC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268890.2	NM_004555		G	68156472	A	G	68156472	3	3	260	1	0	0	0	0	1	0	0	0	10373	449	16	2	692	2	NFATC3	16	68156472	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	824985	68156472	22198281	713	37958										
HAS3	3038	hgsc.bcm.edu	37	chr16	69143389	69143389	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gcatcctggcagcctatgtgAcgggctaccagttcatccac	10	14	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:69143389A>G	ENST00000306560.1	+	2	247	c.91A>G	c.(91-93)Acg>Gcg	p.T31A	HAS3_ENST00000569188.1_Missense_Mutation_p.T31A|HAS3_ENST00000219322.3_Missense_Mutation_p.T31A	NM_005329.2	NP_005320.2	O00219	HYAS3_HUMAN	hyaluronan synthase 3	31					carbohydrate metabolic process (GO:0005975)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|positive regulation of hyaluranon cable assembly (GO:1900106)|positive regulation of transcription, DNA-templated (GO:0045893)|small molecule metabolic process (GO:0044281)	hyaluranon cable (GO:0036117)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronan synthase activity (GO:0050501)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|urinary_tract(2)	16		Ovarian(137;0.101)		OV - Ovarian serous cystadenocarcinoma(108;0.0694)		AGCCTATGTGACGGGCTACCA	0.617																																					p.T31A		Atlas-SNP	.											.	HAS3	61	.	0			c.A91G						.						112	82	93					16																	69143389		2198	4300	6498	SO:0001583	missense	3038	exon2			TATGTGACGGGCT	BC021853	CCDS10870.1, CCDS10871.1	16q22.1	2013-02-22			ENSG00000103044	ENSG00000103044	2.4.1.212	"Glycosyltransferase family 2 domain containing"	4820	protein-coding gene	gene with protein product		602428				9169154, 9083017	Standard	NM_005329		Approved		uc010cfh.3	O00219	OTTHUMG00000137562	ENST00000306560.1:c.91A>G	chr16.hg19:g.69143389A>G	ENSP00000304440:p.Thr31Ala	114.0	0.0		86.0	4.0	NM_138612	A8K5T5|Q8WTZ0|Q9NYP0	Missense_Mutation	SNP	ENST00000306560.1	hg19	CCDS10871.1	.	.	.	.	.	.	.	.	.	.	A	11.69	1.714959	0.30413	.	.	ENSG00000103044	ENST00000219322;ENST00000306560	T;T	0.44083	0.93;0.94	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.32102	0.0818	L	0.32530	0.975	0.51767	D	0.999937	B;B	0.30146	0.212;0.27	B;B	0.28139	0.079;0.086	T	0.09729	-1.0661	10	0.14656	T	0.56	2.2485	15.4219	0.75018	1.0:0.0:0.0:0.0	.	31;31	O00219;O00219-2	HAS3_HUMAN;.	A	31	ENSP00000219322:T31A;ENSP00000304440:T31A	ENSP00000219322:T31A	T	+	1	0	HAS3	67700890	0.437000	0.25593	1.000000	0.80357	0.979000	0.70002	2.102000	0.41796	2.140000	0.66376	0.454000	0.30748	ACG	.	.		0.617	HAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268898.2	NM_138612		G	69143389	A	G	69143389	3	3	260	1	0	0	0	0	1	0	0	0	6972	275	10	2	93	2	HAS3	16	69143389	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	986917	69143389	21211364	714	37959										
FUK	197258	hgsc.bcm.edu	37	chr16	70502753	70502753	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cttttggggtcccttccaggTctctggggttgtcttcttct	11	11	4	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:70502753T>C	ENST00000288078.6	+	9	897	c.665T>C	c.(664-666)gTc>gCc	p.V222A	FUK_ENST00000571514.1_5'UTR|FUK_ENST00000378912.2_Splice_Site_p.V254A	NM_145059.2	NP_659496.2	Q8N0W3	FUK_HUMAN	fucokinase	222						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|fucokinase activity (GO:0050201)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(11)|ovary(2)|prostate(2)	23		Ovarian(137;0.0694)				CCCTTCCAGGTCTCTGGGGTT	0.617																																					p.V222A		Atlas-SNP	.											.	FUK	72	.	0			c.T665C						.						124	122	122					16																	70502753		1958	4135	6093	SO:0001630	splice_region_variant	197258	exon9			TCCAGGTCTCTGG		CCDS10891.2	16q22.1	2008-02-05			ENSG00000157353	ENSG00000157353	2.7.1.52		29500	protein-coding gene	gene with protein product	"L-fucose kinase"	608675				12056818	Standard	XM_006721161		Approved	FLJ39408	uc002eyy.3	Q8N0W3	OTTHUMG00000074085	ENST00000288078.6:c.664-1T>C	chr16.hg19:g.70502753T>C		170.0	0.0		85.0	5.0	NM_145059	Q5PSM3|Q5XKL6|Q6ZRA0|Q96MT9	Missense_Mutation	SNP	ENST00000288078.6	hg19	CCDS10891.2	.	.	.	.	.	.	.	.	.	.	T	36	5.849913	0.97023	.	.	ENSG00000157353	ENST00000288078;ENST00000378912	T;T	0.31769	1.48;1.48	5.2	4.07	0.47477	L-fucokinase (1);	0.150517	0.43747	D	0.000532	T	0.46889	0.1416	M	0.70275	2.135	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.69142	0.962;0.952	T	0.49143	-0.8970	10	0.08381	T	0.77	-28.1242	11.4442	0.50114	0.1352:0.0:0.0:0.8648	.	254;222	Q8N0W3-2;Q8N0W3	.;FUK_HUMAN	A	222;254	ENSP00000288078:V222A;ENSP00000368192:V254A	ENSP00000288078:V222A	V	+	2	0	FUK	69060254	1.000000	0.71417	0.887000	0.34795	0.973000	0.67179	7.062000	0.76706	0.892000	0.36259	0.454000	0.30748	GTC	.	.		0.617	FUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157291.2	NM_145059	Missense_Mutation	C	70502753	T	C	70502753	5	2	260	1	0	0	0	0	0	0	1	0	6104	1681	58	2	695	2	FUK	16	70502753	Splice_Site	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1359364	70502753	19852000	715	37960										
HYDIN	54768	hgsc.bcm.edu	37	chr16	71163592	71163592	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agaacagcttgctgtctcccTgcaccagcctcctctgattc	7	16	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:71163592T>C	ENST00000393567.2	-	9	1328	c.1178A>G	c.(1177-1179)cAg>cGg	p.Q393R	HYDIN_ENST00000288168.10_Missense_Mutation_p.Q410R|HYDIN_ENST00000321489.5_Missense_Mutation_p.Q393R|HYDIN_ENST00000448089.2_Missense_Mutation_p.Q393R|HYDIN_ENST00000448691.1_Missense_Mutation_p.Q393R|HYDIN_ENST00000538248.1_Missense_Mutation_p.Q420R|HYDIN_ENST00000393550.2_Missense_Mutation_p.Q393R|HYDIN_ENST00000541601.1_Missense_Mutation_p.Q410R	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	393					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				GCTGTCTCCCTGCACCAGCCT	0.453																																					p.Q420R		Atlas-SNP	.											.	HYDIN	788	.	0			c.A1259G						.						66	65	65					16																	71163592		2198	4300	6498	SO:0001583	missense	54768	exon9			TCTCCCTGCACCA	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.1178A>G	chr16.hg19:g.71163592T>C	ENSP00000377197:p.Gln393Arg	121.0	0.0		80.0	4.0	NM_001198542	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	hg19	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	T	5.299	0.240472	0.10023	.	.	ENSG00000157423	ENST00000393567;ENST00000316490;ENST00000448089;ENST00000448691;ENST00000321489;ENST00000538248;ENST00000541601;ENST00000288168;ENST00000393550	T;T;T;T;T;T;T;T	0.14766	5.59;3.73;3.74;3.74;3.7;3.71;3.37;2.48	4.97	1.19	0.21007	.	0.000000	0.30193	U	0.010183	T	0.12603	0.0306	M	0.69823	2.125	0.23325	N	0.997903	B;B;B;B;B	0.23058	0.079;0.079;0.049;0.079;0.004	B;B;B;B;B	0.23018	0.043;0.025;0.021;0.043;0.007	T	0.29701	-1.0003	10	0.17832	T	0.49	.	5.4306	0.16450	0.1292:0.1524:0.0:0.7184	.	420;410;410;393;393	B4DRN4;F5H6V3;F8WD03;Q4G0P3-5;F8WD23	.;.;.;.;.	R	393;393;393;393;393;420;410;410;393	ENSP00000377197:Q393R;ENSP00000398544:Q393R;ENSP00000394826:Q393R;ENSP00000314736:Q393R;ENSP00000444970:Q420R;ENSP00000437341:Q410R;ENSP00000288168:Q410R;ENSP00000377181:Q393R	ENSP00000288168:Q410R	Q	-	2	0	HYDIN	69721093	0.837000	0.29446	0.836000	0.33094	0.062000	0.15995	0.809000	0.27168	0.341000	0.23771	0.409000	0.27619	CAG	.	.		0.453	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			C	71163592	T	C	71163592	3	2	260	1	0	0	0	0	1	0	0	0	7476	1580	55	2	14508	2	HYDIN	16	71163592	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	660839	71163592	19191161	716	37961										
MARVELD3	91862	hgsc.bcm.edu	37	chr16	71660407	71660407	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggaccgaggcccccgccgggAcacacacagggacgcgggcc	16	17	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:71660407A>G	ENST00000268485.3	+	1	319	c.275A>G	c.(274-276)gAc>gGc	p.D92G	MARVELD3_ENST00000299952.4_Missense_Mutation_p.D92G|RP11-432I5.2_ENST00000562763.1_RNA|MARVELD3_ENST00000567566.1_Missense_Mutation_p.D92G|MARVELD3_ENST00000565261.1_Missense_Mutation_p.D92G|MARVELD3_ENST00000567501.1_5'Flank	NM_052858.4	NP_443090.4	Q96A59	MALD3_HUMAN	MARVEL domain containing 3	92	Arg-rich.				cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|tight junction (GO:0005923)				NS(1)|endometrium(3)|large_intestine(5)|lung(6)|skin(2)	17		Ovarian(137;0.125)				CCCCGCCGGGACACACACAGG	0.701																																					p.D92G		Atlas-SNP	.											.,2	MARVELD3	63	.	0			c.A275G						.						15	24	21					16																	71660407		1959	3836	5795	SO:0001583	missense	91862	exon1			GCCGGGACACACA	BC013376	CCDS10904.1, CCDS32478.1, CCDS59270.1	16q22.2	2008-02-05	2004-07-12	2004-07-14	ENSG00000140832	ENSG00000140832			30525	protein-coding gene	gene with protein product		614094	"MARVEL (membrane-associating) domain containing 3"	MRVLDC3			Standard	NM_001017967		Approved		uc002fat.4	Q96A59	OTTHUMG00000137591	ENST00000268485.3:c.275A>G	chr16.hg19:g.71660407A>G	ENSP00000268485:p.Asp92Gly	86.0	0.0		65.0	3.0	NM_001017967	A8K820|H3BQM5|Q96MJ4	Missense_Mutation	SNP	ENST00000268485.3	hg19	CCDS10904.1	.	.	.	.	.	.	.	.	.	.	A	13.48	2.249927	0.39797	.	.	ENSG00000140832	ENST00000268485;ENST00000299952	T;T	0.52526	0.66;0.66	3.96	3.96	0.45880	.	0.670440	0.13213	N	0.404984	T	0.60881	0.2303	M	0.66939	2.045	0.80722	D	1	D;P;D	0.71674	0.965;0.939;0.998	P;P;D	0.64321	0.638;0.457;0.924	T	0.60010	-0.7346	10	0.54805	T	0.06	-45.2508	7.422	0.27077	0.778:0.222:0.0:0.0	.	92;92;115	Q96A59-2;Q96A59;Q9BSH2	.;MALD3_HUMAN;.	G	92	ENSP00000268485:D92G;ENSP00000299952:D92G	ENSP00000268485:D92G	D	+	2	0	MARVELD3	70217908	0.820000	0.29190	0.040000	0.18447	0.219000	0.24729	1.563000	0.36364	1.649000	0.50652	0.362000	0.22060	GAC	.	.		0.701	MARVELD3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268991.2	NM_052858		G	71660407	A	G	71660407	3	3	260	1	0	0	0	0	1	0	0	0	9328	275	10	2	277	2	MARVELD3	16	71660407	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	496815	71660407	18694346	717	37962										
ZNF821	55565	hgsc.bcm.edu	37	chr16	71895749	71895749	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agatcgctggtcctccgagtGgattaagaggtggcgaccca	14	10	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:71895749G>T	ENST00000565601.1	-	6	921	c.514C>A	c.(514-516)Cac>Aac	p.H172N	ZNF821_ENST00000313565.6_Missense_Mutation_p.H130N|ZNF821_ENST00000425432.1_Missense_Mutation_p.H172N|ATXN1L_ENST00000569119.1_Intron|ZNF821_ENST00000564943.1_5'Flank|ZNF821_ENST00000564134.1_Intron|ZNF821_ENST00000446827.2_Missense_Mutation_p.H130N	NM_001201553.1	NP_001188482.1	O75541	ZN821_HUMAN	zinc finger protein 821	172					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|ovary(2)	13						TCCTCCGAGTGGATTAAGAGG	0.587																																					p.H172N		Atlas-SNP	.											.	ZNF821	25	.	0			c.C514A						.						96	84	88					16																	71895749		2198	4300	6498	SO:0001583	missense	55565	exon6			CCGAGTGGATTAA	AF070588	CCDS32481.1, CCDS56006.1, CCDS73911.1	16q22.3	2008-05-02				ENSG00000102984		"Zinc fingers, C2H2-type"	28043	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_017530		Approved		uc021tlb.1	O75541		ENST00000565601.1:c.514C>A	chr16.hg19:g.71895749G>T	ENSP00000455648:p.His172Asn	137.0	0.0		67.0	4.0	NM_001201553	A6NK48|B4DKK4|D3DWS3	Missense_Mutation	SNP	ENST00000565601.1	hg19	CCDS56006.1	.	.	.	.	.	.	.	.	.	.	G	34	5.296284	0.95574	.	.	ENSG00000102984	ENST00000425432;ENST00000313565;ENST00000446827	T;T;T	0.28895	1.59;1.59;1.59	6.08	6.08	0.98989	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.72087	0.3417	H	0.97158	3.95	0.80722	D	1	D;D;D	0.62365	0.991;0.989;0.991	D;D;D	0.76575	0.988;0.969;0.988	T	0.80596	-0.1312	10	0.87932	D	0	-16.4098	20.6721	0.99693	0.0:0.0:1.0:0.0	.	172;130;172	B4DKK4;O75541-2;O75541	.;.;ZN821_HUMAN	N	172;130;130	ENSP00000398089:H172N;ENSP00000313822:H130N;ENSP00000405908:H130N	ENSP00000313822:H130N	H	-	1	0	ZNF821	70453250	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.476000	0.97823	2.894000	0.99253	0.591000	0.81541	CAC	.	.		0.587	ZNF821-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434180.1	NM_017530		T	71895749	G	T	71895749	3	4	260	1	0	0	0	0	1	0	0	0	18193	1348	47	3	732	3	ZNF821	16	71895749	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	235342	71895749	18459004	718	37963										
MON1B	22879	hgsc.bcm.edu	37	chr16	77227387	77227387	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gccacccagcccatcaccacCgccccagtcagaggccctgt	8	21	2	1	rs374424902		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:77227387C>A	ENST00000248248.3	+	3	538	c.188C>A	c.(187-189)cCg>cAg	p.P63Q	MON1B_ENST00000439557.2_Intron|MON1B_ENST00000545553.1_Intron|MON1B_ENST00000320859.6_Missense_Mutation_p.P63Q	NM_014940.2	NP_055755.1	Q7L1V2	MON1B_HUMAN	MON1 secretory trafficking family member B	63								p.P63L(1)		breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	17						CCATCACCACCGCCCCAGTCA	0.597																																					p.P63Q		Atlas-SNP	.											MON1B,NS,carcinoma,0,1	MON1B	55	.	1	Substitution - Missense(1)	breast(1)	c.C188A						.						54	58	56					16																	77227387		2198	4300	6498	SO:0001583	missense	22879	exon3			CACCACCGCCCCA	BC024277	CCDS10925.1, CCDS67082.1, CCDS67083.1	16q23.1	2013-08-21	2013-08-21		ENSG00000103111	ENSG00000103111			25020	protein-coding gene	gene with protein product		608954	"MON1 homolog B (yeast)"			10048485	Standard	NM_014940		Approved	SAND2, HSRG1, KIAA0872	uc002fez.3	Q7L1V2	OTTHUMG00000137618	ENST00000248248.3:c.188C>A	chr16.hg19:g.77227387C>A	ENSP00000248248:p.Pro63Gln	157.0	0.0		95.0	4.0	NM_014940	B4DDZ0|O94949	Missense_Mutation	SNP	ENST00000248248.3	hg19	CCDS10925.1	.	.	.	.	.	.	.	.	.	.	C	13.67	2.306668	0.40795	.	.	ENSG00000103111	ENST00000248248;ENST00000320859	.	.	.	3.42	1.17	0.20885	.	2.304150	0.02406	N	0.081149	T	0.17408	0.0418	N	0.08118	0	0.21652	N	0.999604	B	0.32573	0.376	B	0.25884	0.064	T	0.14980	-1.0453	9	0.13470	T	0.59	.	6.1628	0.20373	0.0:0.2449:0.0:0.7551	.	63	Q7L1V2	MON1B_HUMAN	Q	63	.	ENSP00000248248:P63Q	P	+	2	0	MON1B	75784888	0.000000	0.05858	0.735000	0.30896	0.648000	0.38561	0.044000	0.13992	0.208000	0.20626	-0.471000	0.05019	CCG	.	.		0.597	MON1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269036.2	NM_014940		A	77227387	C	A	77227387	3	1	260	1	0	0	0	0	1	0	0	0	9708	652	23	1	194	1	MON1B	16	77227387	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	5331638	77227387	13127366	719	37964										
PKD1L2	114780	hgsc.bcm.edu	37	chr16	81219117	81219117	+	RNA	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctgactcgaggcctgagttcCcagggcgcagacacgtagag	14	12	0	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:81219117C>T	ENST00000525539.1	-	0	1976				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						GCCTGAGTTCCCAGGGCGCAG	0.627																																					p.W659X		Atlas-SNP	.											.	PKD1L2	361	.	0			c.G1977A						.						32	39	37					16																	81219117		2051	4210	6261			114780	exon11			GAGTTCCCAGGGC	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		chr16.hg19:g.81219117C>T		87.0	0.0		96.0	5.0	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Nonsense_Mutation	SNP	ENST00000525539.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.19|14.19	2.460889|2.460889	0.43736|0.43736	.|.	.|.	ENSG00000166473|ENSG00000166473	ENST00000526632|ENST00000337114	.|.	.|.	.|.	4.38|4.38	3.41|3.41	0.39046|0.39046	.|.	.|1.062830	.|0.07438	.|N	.|0.896808	T|.	0.45236|.	0.1332|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.49093|.	-0.8975|.	3|.	.|0.44086	.|T	.|0.13	1.1622|1.1622	6.8802|6.8802	0.24168|0.24168	0.0:0.7388:0.0:0.2612|0.0:0.7388:0.0:0.2612	.|.	.|.	.|.	.|.	R|X	187|659	.|.	.|ENSP00000337397:W659X	G|W	-|-	1|3	0|0	PKD1L2|PKD1L2	79776618|79776618	0.004000|0.004000	0.15560|0.15560	0.329000|0.329000	0.25429|0.25429	0.097000|0.097000	0.18754|0.18754	1.533000|1.533000	0.36040|0.36040	0.955000|0.955000	0.37878|0.37878	0.551000|0.551000	0.68910|0.68910	GGA|TGG	.	.		0.627	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2			T	81219117	C	T	81219117	1	4	260	0	1	0	0	0	0	0	0	0	11974	624	22	3		3	PKD1L2	16	81219117	RNA	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	3991730	81219117	9135636	720	37965										
TAF1C	9013	hgsc.bcm.edu	37	chr16	84214784	84214784	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aaaagcaacagaccacagccCggcgggccctggaagataaa	11	12	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:84214784C>T	ENST00000567759.1	-	11	1433	c.1251G>A	c.(1249-1251)ccG>ccA	p.P417P	TAF1C_ENST00000566732.1_Silent_p.P391P|TAF1C_ENST00000341690.6_Silent_p.P324P|TAF1C_ENST00000541676.1_Silent_p.P324P|TAF1C_ENST00000378541.4_Silent_p.P417P|TAF1C_ENST00000570117.1_Silent_p.P85P	NM_005679.3	NP_005670	Q15572	TAF1C_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kDa	417					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	26						GACCACAGCCCGGCGGGCCCT	0.642																																					p.P417P		Atlas-SNP	.											.	TAF1C	60	.	0			c.G1251A						.						72	83	79					16																	84214784		2200	4300	6500	SO:0001819	synonymous_variant	9013	exon11			ACAGCCCGGCGGG	L39059	CCDS32496.1, CCDS45535.1, CCDS58488.1, CCDS58489.1	16q24	2008-02-05	2002-08-29			ENSG00000103168			11534	protein-coding gene	gene with protein product		604905	"TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kD"			7801123	Standard	NM_005679		Approved	TAFI110, TAFI95, SL1, MGC:39976	uc010vnx.2	Q15572		ENST00000567759.1:c.1251G>A	chr16.hg19:g.84214784C>T		190.0	0.0		99.0	4.0	NM_005679	B7Z5K5|B7Z5S4|B7Z908|B7Z9L7|Q59F67|Q8N6V3	Silent	SNP	ENST00000567759.1	hg19	CCDS32496.1																																																																																			.	.		0.642	TAF1C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000433045.2	NM_139353		T	84214784	C	T	84214784	2	4	260	1	0	0	0	0	0	0	0	1	15536	639	23	1		1	TAF1C	16	84214784	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	2995667	84214784	6139969	721	37966										
MVD	4597	hgsc.bcm.edu	37	chr16	88724396	88724396	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttcagccaaatccggtcctcGgtgaagtccttgctgatgac	10	12	1	3	rs568814170	byFrequency	TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:88724396G>T	ENST00000301012.3	-	3	212	c.183C>A	c.(181-183)acC>acA	p.T61T	MVD_ENST00000568709.1_5'UTR	NM_002461.1	NP_002452.1	P53602	MVD1_HUMAN	mevalonate (diphospho) decarboxylase	61					cellular protein metabolic process (GO:0044267)|cholesterol biosynthetic process (GO:0006695)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|dolichyl diphosphate biosynthetic process (GO:0006489)|isopentenyl diphosphate biosynthetic process, mevalonate pathway (GO:0019287)|isoprenoid biosynthetic process (GO:0008299)|positive regulation of cell proliferation (GO:0008284)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|diphosphomevalonate decarboxylase activity (GO:0004163)|Hsp70 protein binding (GO:0030544)|protein homodimerization activity (GO:0042803)			endometrium(3)|large_intestine(1)|lung(7)|ovary(1)	12				BRCA - Breast invasive adenocarcinoma(80;0.0478)		TCCGGTCCTCGGTGAAGTCCT	0.617																																					p.T61T		Atlas-SNP	.											.	MVD	27	.	0			c.C183A						.						73	79	77					16																	88724396		2198	4300	6498	SO:0001819	synonymous_variant	4597	exon3			GTCCTCGGTGAAG	U49260	CCDS10968.1	16q24.3	2010-04-29			ENSG00000167508	ENSG00000167508	4.1.1.33		7529	protein-coding gene	gene with protein product	"mevalonate pyrophosphate decarboxylase"	603236				8626466	Standard	NM_002461		Approved	MPD	uc002flg.1	P53602	OTTHUMG00000137865	ENST00000301012.3:c.183C>A	chr16.hg19:g.88724396G>T		169.0	0.0		115.0	5.0	NM_002461	Q53Y65	Silent	SNP	ENST00000301012.3	hg19	CCDS10968.1																																																																																			.	.		0.617	MVD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269547.2	NM_002461		T	88724396	G	T	88724396	2	4	260	1	0	0	0	0	0	0	0	1	10003	1103	39	1		1	MVD	16	88724396	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	4509612	88724396	1630357	722	37967										
CBFA2T3	863	hgsc.bcm.edu	37	chr16	88958364	88958364	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cttggaatgaaactcctcgaTcgtcaatgtcgagttctgca	9	10	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:88958364T>C	ENST00000268679.4	-	5	1033	c.637A>G	c.(637-639)Atc>Gtc	p.I213V	CBFA2T3_ENST00000448839.1_Missense_Mutation_p.I137V|CBFA2T3_ENST00000327483.5_Missense_Mutation_p.I127V|CBFA2T3_ENST00000360302.2_Missense_Mutation_p.I127V|CBFA2T3_ENST00000436887.2_Missense_Mutation_p.I188V	NM_005187.5	NP_005178.4	O75081	MTG16_HUMAN	core-binding factor, runt domain, alpha subunit 2; translocated to, 3	213	Mediates interaction with PDE7A (in isoform 2).|Mediates localization to the nucleus. {ECO:0000250}.|TAFH. {ECO:0000255|PROSITE- ProRule:PRU00440}.				cell proliferation (GO:0008283)|granulocyte differentiation (GO:0030851)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	17				BRCA - Breast invasive adenocarcinoma(80;0.0275)		AACTCCTCGATCGTCAATGTC	0.587			T	RUNX1	AML																																p.I213V		Atlas-SNP	.		Dom	yes		16	16q24	863	"core-binding factor, runt domain, alpha subunit 2; translocated to, 3 (MTG-16)"		L	.	CBFA2T3	47	.	0			c.A637G						.						100	80	87					16																	88958364		2196	4300	6496	SO:0001583	missense	863	exon5			CCTCGATCGTCAA	AF052213	CCDS10972.1, CCDS10973.1	16q24	2013-10-16			ENSG00000129993	ENSG00000129993		"Zinc fingers, MYND-type", "A-kinase anchor proteins"	1537	protein-coding gene	gene with protein product	"myeloid translocation gene 8 and 16b"	603870				9790752, 20150326	Standard	NM_005187		Approved	MTGR2, ZMYND4, MTG16	uc002fmm.2	O75081	OTTHUMG00000137864	ENST00000268679.4:c.637A>G	chr16.hg19:g.88958364T>C	ENSP00000268679:p.Ile213Val	77.0	0.0		63.0	4.0	NM_005187	D3DX78|O60615|O60616|O60617|O75082|O75107|O75108|Q0P5Z6|Q6P5W6	Missense_Mutation	SNP	ENST00000268679.4	hg19	CCDS10972.1	.	.	.	.	.	.	.	.	.	.	t	12.34	1.909887	0.33721	.	.	ENSG00000129993	ENST00000327483;ENST00000268679;ENST00000436887;ENST00000448839;ENST00000360302	T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02	4.44	4.44	0.53790	TAFH/NHR1 (3);	0.054514	0.64402	D	0.000001	T	0.35189	0.0923	L	0.36672	1.1	0.80722	D	1	B;B;B;B	0.09022	0.001;0.002;0.0;0.001	B;B;B;B	0.21708	0.008;0.036;0.013;0.012	T	0.13791	-1.0496	10	0.36615	T	0.2	-6.0078	14.1299	0.65247	0.0:0.0:0.0:1.0	.	188;213;213;127	E7EU24;B2RBQ7;O75081;O75081-2	.;.;MTG16_HUMAN;.	V	127;213;188;137;127	ENSP00000332122:I127V;ENSP00000268679:I213V;ENSP00000395739:I188V;ENSP00000401254:I137V;ENSP00000353449:I127V	ENSP00000268679:I213V	I	-	1	0	CBFA2T3	87485865	1.000000	0.71417	0.998000	0.56505	0.383000	0.30230	7.260000	0.78391	1.980000	0.57719	0.454000	0.30748	ATC	.	.		0.587	CBFA2T3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269545.2	NM_005187		C	88958364	T	C	88958364	3	2	260	1	0	0	0	0	1	0	0	0	2700	1435	50	2	1356	2	CBFA2T3	16	88958364	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	233968	88958364	1396389	723	37968										
ANKRD11	29123	hgsc.bcm.edu	37	chr16	89346917	89346917	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggggcggggtacggcgcctcCgaggcgctgaagggccctgg	21	12	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:89346917C>T	ENST00000301030.4	-	9	6493	c.6033G>A	c.(6031-6033)tcG>tcA	p.S2011S	ANKRD11_ENST00000378330.2_Silent_p.S2011S	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	2011	Pro-rich.				bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		ACGGCGCCTCCGAGGCGCTGA	0.711																																					p.S2011S		Atlas-SNP	.											.	ANKRD11	195	.	0			c.G6033A						.						6	7	7					16																	89346917		1733	3603	5336	SO:0001819	synonymous_variant	29123	exon9			CGCCTCCGAGGCG	AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"Ankyrin repeat domain containing"	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.6033G>A	chr16.hg19:g.89346917C>T		58.0	0.0		44.0	4.0	NM_001256183	Q6NTG1|Q6QMF8	Silent	SNP	ENST00000301030.4	hg19	CCDS32513.1																																																																																			.	.		0.711	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		T	89346917	C	T	89346917	2	4	260	1	0	0	0	0	0	0	0	1	639	639	23	1		1	ANKRD11	16	89346917	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	388553	89346917	1007836	724	37969										
CPNE7	27132	hgsc.bcm.edu	37	chr16	89651220	89651220	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gaccccttcctggagctctaCagggtcaacgacgaccaggg	12	14	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr16:89651220C>T	ENST00000268720.5	+	7	901	c.771C>T	c.(769-771)taC>taT	p.Y257Y	CPNE7_ENST00000319518.8_Silent_p.Y182Y	NM_014427.4	NP_055242.1	Q9UBL6	CPNE7_HUMAN	copine VII	257	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				lipid metabolic process (GO:0006629)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)	transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(2)	17		all_hematologic(23;0.0748)		all cancers(4;3.63e-08)|OV - Ovarian serous cystadenocarcinoma(4;1.7e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0147)		TGGAGCTCTACAGGGTCAACG	0.647																																					p.Y257Y		Atlas-SNP	.											.	CPNE7	56	.	0			c.C771T						.						78	66	70					16																	89651220		2198	4300	6498	SO:0001819	synonymous_variant	27132	exon7			GCTCTACAGGGTC	AJ133798	CCDS10980.1, CCDS10981.1	16q24.3	2008-07-03			ENSG00000178773	ENSG00000178773			2320	protein-coding gene	gene with protein product		605689					Standard	NM_014427		Approved		uc002fnq.3	Q9UBL6	OTTHUMG00000138051	ENST00000268720.5:c.771C>T	chr16.hg19:g.89651220C>T		69.0	0.0		54.0	5.0	NM_014427		Silent	SNP	ENST00000268720.5	hg19	CCDS10980.1																																																																																			.	.		0.647	CPNE7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269929.2			T	89651220	C	T	89651220	2	4	260	1	0	0	0	0	0	0	0	1	3819	489	17	3		3	CPNE7	16	89651220	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	304303	89651220	703533	725	37970										
KIAA0664	23277	hgsc.bcm.edu	37	chr17	2605026	2605026	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	caagcccttcttccgcttccCgctgtctgagggacccgagg	11	16	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:2605026C>T	ENST00000570628.2	-	5	616	c.511G>A	c.(511-513)Ggg>Agg	p.G171R	CLUH_ENST00000435359.1_Missense_Mutation_p.G171R|CLUH_ENST00000538975.1_Missense_Mutation_p.G171R			O75153	CLU_HUMAN	clustered mitochondria (cluA/CLU1) homolog	171					intracellular distribution of mitochondria (GO:0048312)	cytoplasm (GO:0005737)											TTCCGCTTCCCGCTGTCTGAG	0.682																																					p.G171R		Atlas-SNP	.											.	.	.	.	0			c.G511A						.						38	46	43					17																	2605026		2003	4153	6156	SO:0001583	missense	23277	exon5			GCTTCCCGCTGTC	AB014564	CCDS45572.1	17p13.3	2012-12-18	2012-11-30	2012-11-30	ENSG00000132361	ENSG00000132361			29094	protein-coding gene	gene with protein product			"KIAA0664"	KIAA0664			Standard	XM_005256567		Approved	CLU1	uc002fuy.1	O75153	OTTHUMG00000177575	ENST00000570628.2:c.511G>A	chr17.hg19:g.2605026C>T	ENSP00000458986:p.Gly171Arg	95.0	0.0		79.0	4.0	NM_015229	Q6AHY2|Q6P3X7|Q6ZUG8|Q8N4U7|Q9BTA3|Q9H979	Missense_Mutation	SNP	ENST00000570628.2	hg19	CCDS45572.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.001285	0.74818	.	.	ENSG00000132361	ENST00000435359;ENST00000322335;ENST00000538975	T;T	0.80653	-1.4;-1.4	5.42	5.42	0.78866	GSKIP/TIF31 domain (1);	0.046466	0.85682	D	0.000000	T	0.78515	0.4295	L	0.38531	1.155	0.80722	D	1	D;D	0.67145	0.972;0.996	B;P	0.47102	0.39;0.537	T	0.79878	-0.1617	10	0.48119	T	0.1	.	18.1971	0.89826	0.0:1.0:0.0:0.0	.	171;171	O75153;C9J6D7	K0664_HUMAN;.	R	171	ENSP00000388872:G171R;ENSP00000439628:G171R	ENSP00000320468:G171R	G	-	1	0	KIAA0664	2551776	1.000000	0.71417	0.995000	0.50966	0.675000	0.39556	7.473000	0.81007	2.557000	0.86248	0.591000	0.81541	GGG	.	.		0.682	CLUH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437807.2	NM_015229		T	2605026	C	T	2605026	3	4	260	1	0	0	0	0	1	0	0	0	8198	652	23	1	3506	1	KIAA0664	17	2605026	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10		2605026	78590184	726	37971										
PELP1	27043	hgsc.bcm.edu	37	chr17	4607242	4607242	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gagcggtttgggggatgcacCggagcaacggcagaccccgt	17	11	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:4607242C>T	ENST00000574876.1	-	1	182	c.165G>A	c.(163-165)ccG>ccA	p.P55P	PELP1_ENST00000301396.4_Silent_p.P55P|PELP1_ENST00000436683.2_5'UTR|RP11-314A20.2_ENST00000497885.1_RNA|PELP1_ENST00000269230.7_Silent_p.P55P|PELP1_ENST00000570823.1_5'UTR|PELP1_ENST00000572293.1_Silent_p.P105P			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	55					cellular response to estrogen stimulus (GO:0071391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	15						GGGGATGCACCGGAGCAACGG	0.687																																					p.P55P		Atlas-SNP	.											.	PELP1	102	.	0			c.G165A						.						23	30	28					17																	4607242		1987	4127	6114	SO:0001819	synonymous_variant	27043	exon1			ATGCACCGGAGCA		CCDS58503.1, CCDS58503.2, CCDS62038.1	17p13.2	2012-05-02	2008-02-21			ENSG00000141456			30134	protein-coding gene	gene with protein product		609455	"proline, glutamic acid and leucine rich protein 1"			11481323, 12682072	Standard	NM_014389		Approved	MNAR	uc002fyi.4	Q8IZL8		ENST00000574876.1:c.165G>A	chr17.hg19:g.4607242C>T		138.0	0.0		80.0	4.0	NM_014389	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	Silent	SNP	ENST00000574876.1	hg19	CCDS58503.1																																																																																			.	.		0.687	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389		T	4607242	C	T	4607242	2	4	260	1	0	0	0	0	0	0	0	1	11734	639	23	1		1	PELP1	17	4607242	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	2002216	4607242	76587968	727	37972										
NLRP1	22861	hgsc.bcm.edu	37	chr17	5425083	5425083	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tttaaagtgggccatttggaAcagggatgtgtccacatggc	13	7	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:5425083A>G	ENST00000572272.1	-	13	3543	c.3544T>C	c.(3544-3546)Ttc>Ctc	p.F1182L	NLRP1_ENST00000354411.3_Missense_Mutation_p.F1152L|NLRP1_ENST00000577119.1_Missense_Mutation_p.F1152L|NLRP1_ENST00000345221.3_Missense_Mutation_p.F1182L|NLRP1_ENST00000262467.5_Missense_Mutation_p.F1186L|NLRP1_ENST00000269280.4_Missense_Mutation_p.F1182L			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	1182					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of inflammatory response (GO:0050727)|response to muramyl dipeptide (GO:0032495)	cytosol (GO:0005829)|intracellular (GO:0005622)|NLRP1 inflammasome complex (GO:0072558)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(17)|liver(5)|lung(17)|ovary(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Colorectal(1115;3.48e-05)				GCCATTTGGAACAGGGATGTG	0.473																																					p.F1186L		Atlas-SNP	.											.	NLRP1	358	.	0			c.T3556C						.						51	55	54					17																	5425083		2203	4300	6503	SO:0001583	missense	22861	exon13			TTTGGAACAGGGA	AB023143	CCDS32537.1, CCDS42244.1, CCDS42245.1, CCDS42246.1, CCDS58508.1	17p13	2014-01-29	2006-12-08	2006-12-08	ENSG00000091592	ENSG00000091592		"Nucleotide-binding domain and leucine rich repeat containing"	14374	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 1"	606636	"NACHT, leucine rich repeat and PYD (pyrin domain) containing 1", "systemic lupus erythematosus, vitiligo-related 1"	NALP1, SLEV1		8781126, 12563287, 17377159	Standard	NM_033006		Approved	KIAA0926, DKFZp586O1822, CARD7, NAC, CLR17.1, DEFCAP, VAMAS1	uc002gci.3	Q9C000		ENST00000572272.1:c.3544T>C	chr17.hg19:g.5425083A>G	ENSP00000460475:p.Phe1182Leu	61.0	0.0		51.0	4.0	NM_001033053	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Missense_Mutation	SNP	ENST00000572272.1	hg19	CCDS42246.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.066079	0.76187	.	.	ENSG00000091592	ENST00000544378;ENST00000262467;ENST00000269280;ENST00000354411;ENST00000345221;ENST00000537069	T;T;T;T;T	0.30714	1.52;1.52;1.52;1.52;1.52	4.3	4.3	0.51218	.	0.000000	0.40469	N	0.001090	T	0.56558	0.1993	M	0.83953	2.67	0.31012	N	0.719143	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.999	D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.983	T	0.64711	-0.6343	10	0.87932	D	0	.	11.7714	0.51960	1.0:0.0:0.0:0.0	.	1152;1152;1182;1182;1186	Q9C000-3;Q9C000-4;Q9C000;Q9C000-2;E9PE50	.;.;NALP1_HUMAN;.;.	L	1186;1186;1182;1152;1182;448	ENSP00000442029:F1186L;ENSP00000262467:F1186L;ENSP00000269280:F1182L;ENSP00000346390:F1152L;ENSP00000324366:F1182L	ENSP00000262467:F1186L	F	-	1	0	NLRP1	5365807	0.962000	0.33011	0.203000	0.23512	0.946000	0.59487	2.073000	0.41519	1.945000	0.56424	0.529000	0.55759	TTC	.	.		0.473	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004		G	5425083	A	G	5425083	3	3	260	1	0	0	0	0	1	0	0	0	10480	43	2	2	960	2	NLRP1	17	5425083	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	817841	5425083	75770127	728	37973										
FBXO39	162517	hgsc.bcm.edu	37	chr17	6683348	6683348	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccagatgatgtattctgctgAgctctggcggtacagaacca	11	10	2	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:6683348A>G	ENST00000321535.4	+	2	291	c.161A>G	c.(160-162)gAg>gGg	p.E54G		NM_153230.2	NP_694962.1	Q8N4B4	FBX39_HUMAN	F-box protein 39	54	F-box.									NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	26						TATTCTGCTGAGCTCTGGCGG	0.507																																					p.E54G		Atlas-SNP	.											.	FBXO39	50	.	0			c.A161G						.						109	103	105					17																	6683348		2203	4300	6503	SO:0001583	missense	162517	exon2			CTGCTGAGCTCTG	BC034782	CCDS11082.1	17p13.2	2014-01-21			ENSG00000177294	ENSG00000177294		"F-boxes /  "other""	28565	protein-coding gene	gene with protein product		609106				12477932	Standard	NM_153230		Approved	MGC35179, Fbx39, CT144	uc010vtg.2	Q8N4B4	OTTHUMG00000102062	ENST00000321535.4:c.161A>G	chr17.hg19:g.6683348A>G	ENSP00000321386:p.Glu54Gly	225.0	0.0		137.0	6.0	NM_153230		Missense_Mutation	SNP	ENST00000321535.4	hg19	CCDS11082.1	.	.	.	.	.	.	.	.	.	.	A	11.02	1.516258	0.27123	.	.	ENSG00000177294	ENST00000321535	T	0.45668	0.89	5.56	5.56	0.83823	F-box domain, cyclin-like (1);	0.358632	0.27210	N	0.020412	T	0.32071	0.0817	L	0.29908	0.895	0.21652	N	0.999606	B	0.15141	0.012	B	0.21917	0.037	T	0.15435	-1.0437	10	0.27082	T	0.32	-32.2557	12.406	0.55441	1.0:0.0:0.0:0.0	.	54	Q8N4B4	FBX39_HUMAN	G	54	ENSP00000321386:E54G	ENSP00000321386:E54G	E	+	2	0	FBXO39	6624072	0.995000	0.38212	1.000000	0.80357	0.862000	0.49288	2.220000	0.42908	2.257000	0.74773	0.459000	0.35465	GAG	.	.		0.507	FBXO39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219866.2	NM_153230		G	6683348	A	G	6683348	3	3	260	1	0	0	0	0	1	0	0	0	5755	304	11	2	163	2	FBXO39	17	6683348	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1258265	6683348	74511862	729	37974										
ACAP1	9744	hgsc.bcm.edu	37	chr17	7249578	7249578	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tacagacgctggttcaccatTcagagcaaccaactggttta	8	11	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:7249578T>C	ENST00000158762.3	+	11	1076	c.870T>C	c.(868-870)atT>atC	p.I290I		NM_014716.3	NP_055531.1	Q15027	ACAP1_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 1	290	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.|Required for formation of endosomal tubules when overexpressed with PIP5K1C.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)	endosome (GO:0005768)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(3)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|prostate(3)|skin(1)|urinary_tract(1)	33						GGTTCACCATTCAGAGCAACC	0.527											OREG0024135	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I290I		Atlas-SNP	.											.	ACAP1	66	.	0			c.T870C						.						148	143	145					17																	7249578		2203	4300	6503	SO:0001819	synonymous_variant	9744	exon11			CACCATTCAGAGC	D30758	CCDS11101.1	17p13.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000072818	ENSG00000072818		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16467	protein-coding gene	gene with protein product		607763	"centaurin, beta 1"	CENTB1		11050434, 11062263	Standard	NM_014716		Approved	KIAA0050	uc002ggd.2	Q15027	OTTHUMG00000102199	ENST00000158762.3:c.870T>C	chr17.hg19:g.7249578T>C		189.0	0.0	640	109.0	5.0	NM_014716	Q53XN9	Silent	SNP	ENST00000158762.3	hg19	CCDS11101.1																																																																																			.	.		0.527	ACAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220049.4	NM_014716		C	7249578	T	C	7249578	2	2	260	1	0	0	0	0	0	0	0	1	118	1771	62	2		2	ACAP1	17	7249578	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	566230	7249578	73945632	730	37975										
CHRNB1	1140	hgsc.bcm.edu	37	chr17	7359909	7359909	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgcctacccacagctgaaggAggactggcagtttgtggcca	13	11	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:7359909A>G	ENST00000306071.2	+	11	1440	c.1373A>G	c.(1372-1374)gAg>gGg	p.E458G	CHRNB1_ENST00000536404.2_Missense_Mutation_p.E386G|CHRNB1_ENST00000576360.1_Missense_Mutation_p.E337G|CHRNB1_ENST00000575379.1_5'UTR	NM_000747.2	NP_000738.2	P11230	ACHB_HUMAN	cholinergic receptor, nicotinic, beta 1 (muscle)	458					behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|muscle fiber development (GO:0048747)|neurological system process (GO:0050877)|neuromuscular synaptic transmission (GO:0007274)|postsynaptic membrane organization (GO:0001941)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)|ligand-gated ion channel activity (GO:0015276)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|ovary(3)	23		Prostate(122;0.157)			Galantamine(DB00674)	CAGCTGAAGGAGGACTGGCAG	0.602																																					p.E458G		Atlas-SNP	.											.	CHRNB1	46	.	0			c.A1373G						.						178	143	155					17																	7359909		2203	4300	6503	SO:0001583	missense	1140	exon11			TGAAGGAGGACTG	X14830	CCDS11106.1	17p13.1	2012-02-11	2006-02-01		ENSG00000170175	ENSG00000170175		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1961	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, beta 1 (muscle)"	100710	"cholinergic receptor, nicotinic, beta polypeptide 1 (muscle)"	CHRNB			Standard	NM_000747		Approved		uc002ghb.3	P11230	OTTHUMG00000108139	ENST00000306071.2:c.1373A>G	chr17.hg19:g.7359909A>G	ENSP00000304290:p.Glu458Gly	121.0	0.0		78.0	4.0	NM_000747	B7Z5H1|Q8IZ46|Q96FB8	Missense_Mutation	SNP	ENST00000306071.2	hg19	CCDS11106.1	.	.	.	.	.	.	.	.	.	.	a	16.00	2.997207	0.54147	.	.	ENSG00000170175	ENST00000306071;ENST00000536404	T;T	0.25912	1.77;1.77	5.51	5.51	0.81932	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.222920	0.44902	D	0.000401	T	0.34048	0.0884	M	0.75150	2.29	0.80722	D	1	B	0.34015	0.435	B	0.36608	0.229	T	0.20075	-1.0286	10	0.62326	D	0.03	.	13.584	0.61919	1.0:0.0:0.0:0.0	.	458	P11230	ACHB_HUMAN	G	458;386	ENSP00000304290:E458G;ENSP00000439209:E386G	ENSP00000304290:E458G	E	+	2	0	CHRNB1	7300633	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	5.074000	0.64401	2.093000	0.63338	0.449000	0.29647	GAG	.	.		0.602	CHRNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226942.3			G	7359909	A	G	7359909	3	3	260	1	0	0	0	0	1	0	0	0	3392	304	11	2	1415	2	CHRNB1	17	7359909	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	110331	7359909	73835301	731	37976										
TP53	7157	hgsc.bcm.edu	37	chr17	7577602	7577602	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtggatggtggtacagtcagAgccaacctaggagataacac	13	8	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:7577602A>G	ENST00000269305.4	-	7	868	c.679T>C	c.(679-681)Tct>Cct	p.S227P	TP53_ENST00000413465.2_Missense_Mutation_p.S227P|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000445888.2_Missense_Mutation_p.S227P|TP53_ENST00000455263.2_Missense_Mutation_p.S227P|TP53_ENST00000359597.4_Missense_Mutation_p.S227P|TP53_ENST00000420246.2_Missense_Mutation_p.S227P	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	227	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		S -> C (in sporadic cancers; somatic mutation).|S -> F (in sporadic cancers; somatic mutation).|S -> P (in a sporadic cancer; somatic mutation).|S -> T (in LFS; germline mutation and in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.?(5)|p.S227fs*20(3)|p.S227fs*1(2)|p.V225_S227delVGS(2)|p.G226_D228delGSD(1)|p.S134fs*20(1)|p.V225fs*23(1)|p.S227fs*14(1)|p.S227_I232delSDCTTI(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GTACAGTCAGAGCCAACCTAG	0.522		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.S227P	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,colon,carcinoma,0,1	TP53	33396	.	25	Whole gene deletion(8)|Deletion - Frameshift(7)|Unknown(5)|Deletion - In frame(4)|Insertion - Frameshift(1)	biliary_tract(5)|liver(5)|bone(4)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(3)|breast(2)|stomach(1)|oesophagus(1)|lung(1)	c.T679C	GRCh37	CM951228	TP53	M		.						97	81	86					17																	7577602		2203	4300	6503	SO:0001583	missense	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AGTCAGAGCCAAC	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.679T>C	chr17.hg19:g.7577602A>G	ENSP00000269305:p.Ser227Pro	208.0	2.0		149.0	6.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	A	16.39	3.110765	0.56398	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99816	-6.91;-6.91;-6.91;-6.91;-6.91;-6.91;-6.91;-6.91	4.48	0.868	0.19090	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.331184	0.32459	N	0.006067	D	0.99354	0.9773	M	0.62723	1.935	0.42369	D	0.992447	B;D;B;B;B;B	0.59357	0.02;0.985;0.005;0.056;0.012;0.02	B;P;B;B;B;B	0.52957	0.047;0.714;0.004;0.105;0.039;0.017	D	0.98216	1.0475	10	0.87932	D	0	-0.1971	4.9977	0.14247	0.3814:0.3136:0.0:0.305	.	227;227;134;227;227;227	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	P	227;227;227;227;227;227;216;134;95;134	ENSP00000410739:S227P;ENSP00000352610:S227P;ENSP00000269305:S227P;ENSP00000398846:S227P;ENSP00000391127:S227P;ENSP00000391478:S227P;ENSP00000425104:S95P;ENSP00000423862:S134P	ENSP00000269305:S227P	S	-	1	0	TP53	7518327	0.014000	0.17966	0.130000	0.21974	0.841000	0.47740	0.255000	0.18333	0.012000	0.14892	0.379000	0.24179	TCT	.	.		0.522	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		G	7577602	A	G	7577602	3	3	260	1	0	0	0	0	1	0	0	0	16396	304	11	2	611	2	TP53	17	7577602	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	217693	7577602	73617608	732	37977										
WDR16	146845	hgsc.bcm.edu	37	chr17	9490134	9490134	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttgtacttggtatcactaggAggcccagatgacggaaggta	13	7	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:9490134A>G	ENST00000352665.5	+	3	459	c.390A>G	c.(388-390)ggA>ggG	p.G130G	WDR16_ENST00000396219.3_Silent_p.G62G|WDR16_ENST00000576499.1_3'UTR|WDR16_ENST00000299764.5_Silent_p.G140G	NM_145054.4	NP_659491.4			WD repeat domain 16											NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	31						TATCACTAGGAGGCCCAGATG	0.378																																					p.G130G		Atlas-SNP	.											.	WDR16	67	.	0			c.A390G						.						77	74	75					17																	9490134		2203	4300	6503	SO:0001819	synonymous_variant	146845	exon3			ACTAGGAGGCCCA	AB065281	CCDS11149.2, CCDS42262.1	17p13.1	2014-08-01			ENSG00000166596	ENSG00000166596		"WD repeat domain containing"	16053	protein-coding gene	gene with protein product	"WD40-repeat protein upregulated in HCC"	609804				15967112	Standard	NM_001080556		Approved	WDRPUH, FLJ37528	uc002gly.3	Q8N1V2	OTTHUMG00000150149	ENST00000352665.5:c.390A>G	chr17.hg19:g.9490134A>G		175.0	0.0		80.0	4.0	NM_145054		Silent	SNP	ENST00000352665.5	hg19	CCDS11149.2																																																																																			.	.		0.378	WDR16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316569.2	NM_145054		G	9490134	A	G	9490134	2	3	260	1	0	0	0	0	0	0	0	1	17291	291	11	2		2	WDR16	17	9490134	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1912532	9490134	71705076	733	37978										
CDRT4	284040	hgsc.bcm.edu	37	chr17	15341250	15341250	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccgaataagcgccccacattGataacgtggattctgacagc	9	12	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:15341250G>T	ENST00000312177.6	-	4	576	c.296C>A	c.(295-297)tCa>tAa	p.S99*	TVP23C-CDRT4_ENST00000522212.2_3'UTR|TVP23C_ENST00000519970.1_3'UTR|CDRT4_ENST00000519354.1_5'UTR	NM_001204477.1	NP_001191406.1	Q8N9R6	CDRT4_HUMAN	CMT1A duplicated region transcript 4	99										endometrium(3)|skin(1)	4				UCEC - Uterine corpus endometrioid carcinoma (92;0.0874)		GCCCCACATTGATAACGTGGA	0.488																																					p.S100X		Atlas-SNP	.											.	CDRT4	11	.	0			c.C299A						.						179	157	164					17																	15341250		2203	4300	6503	SO:0001587	stop_gained	284040	exon4			CACATTGATAACG	BC029542	CCDS73995.1	17p12	2011-09-28			ENSG00000239704	ENSG00000239704			14383	protein-coding gene	gene with protein product						11381029	Standard	NM_001204477		Approved	FLJ36674	uc002gop.2	Q8N9R6	OTTHUMG00000059070	ENST00000312177.6:c.296C>A	chr17.hg19:g.15341250G>T	ENSP00000310031:p.Ser99*	172.0	0.0		121.0	5.0	NM_001204477	A8MSL9|Q8IZ19	Nonsense_Mutation	SNP	ENST00000312177.6	hg19		.	.	.	.	.	.	.	.	.	.	G	20.2	3.957308	0.73902	.	.	ENSG00000239704	ENST00000520956;ENST00000312177	.	.	.	4.9	4.9	0.64082	.	0.486635	0.17540	N	0.170575	.	.	.	.	.	.	0.58432	D	0.999992	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	3.42	13.4329	0.61066	0.0:0.0:1.0:0.0	.	.	.	.	X	100;99	.	ENSP00000310031:S99X	S	-	2	0	CDRT4	15281975	0.166000	0.22962	0.010000	0.14722	0.008000	0.06430	4.195000	0.58400	2.545000	0.85829	0.591000	0.81541	TCA	.	.		0.488	CDRT4-001	KNOWN	non_canonical_conserved|non_canonical_other|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000130383.7	NM_173622		T	15341250	G	T	15341250	4	4	260	1	0	0	0	0	0	1	0	0	3178	1294	45	3	163	3	CDRT4	17	15341250	Nonsense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	5851116	15341250	65853960	734	37979										
MYO15A	51168	hgsc.bcm.edu	37	chr17	18024955	18024955	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tccccctggccaggaggtgcAggcagccgccgaggcttttc	14	15	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:18024955A>G	ENST00000205890.5	+	2	3179	c.2841A>G	c.(2839-2841)gcA>gcG	p.A947A		NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	947					inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					CAGGAGGTGCAGGCAGCCGCC	0.692																																					p.A947A		Atlas-SNP	.											.	MYO15A	268	.	0			c.A2841G						.						7	9	9					17																	18024955		1771	3949	5720	SO:0001819	synonymous_variant	51168	exon2			AGGTGCAGGCAGC	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"Myosins / Myosin superfamily : Class XV"	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.2841A>G	chr17.hg19:g.18024955A>G		167.0	0.0		105.0	5.0	NM_016239	B4DFC7	Silent	SNP	ENST00000205890.5	hg19	CCDS42271.1																																																																																			.	.		0.692	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239		G	18024955	A	G	18024955	2	3	260	1	0	0	0	0	0	0	0	1	10072	175	7	2		2	MYO15A	17	18024955	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	2683705	18024955	63170255	735	37980										
MYO15A	51168	hgsc.bcm.edu	37	chr17	18055165	18055165	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctccaatgcccacaggaaggAtggcgggaaagtgttcatga	13	9	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:18055165A>G	ENST00000205890.5	+	41	8131	c.7793A>G	c.(7792-7794)gAt>gGt	p.D2598G	MYO15A_ENST00000585180.1_5'Flank|MYO15A_ENST00000418233.3_5'Flank	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	2598	Tail.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					CACAGGAAGGATGGCGGGAAA	0.567																																					p.D2598G		Atlas-SNP	.											.	MYO15A	268	.	0			c.A7793G						.						40	45	44					17																	18055165		2034	4176	6210	SO:0001583	missense	51168	exon40			GGAAGGATGGCGG	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"Myosins / Myosin superfamily : Class XV"	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.7793A>G	chr17.hg19:g.18055165A>G	ENSP00000205890:p.Asp2598Gly	137.0	0.0		85.0	4.0	NM_016239	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	hg19	CCDS42271.1	.	.	.	.	.	.	.	.	.	.	A	11.39	1.624496	0.28889	.	.	ENSG00000091536	ENST00000205890	D	0.87887	-2.31	5.11	4.03	0.46877	.	.	.	.	.	T	0.81460	0.4827	L	0.47716	1.5	0.58432	D	0.999998	B	0.02656	0.0	B	0.01281	0.0	T	0.73717	-0.3895	9	0.27785	T	0.31	.	10.2996	0.43644	0.9194:0.0:0.0806:0.0	.	2598	Q9UKN7	MYO15_HUMAN	G	2598	ENSP00000205890:D2598G	ENSP00000205890:D2598G	D	+	2	0	MYO15A	17995890	0.998000	0.40836	0.971000	0.41717	0.671000	0.39405	3.610000	0.54125	0.881000	0.35993	-0.609000	0.04063	GAT	.	.		0.567	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239		G	18055165	A	G	18055165	3	3	260	1	0	0	0	0	1	0	0	0	10072	333	12	2	7947	2	MYO15A	17	18055165	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	30210	18055165	63140045	736	37981										
USP22	23326	hgsc.bcm.edu	37	chr17	20914512	20914512	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttcccgacacgtggctttccCcgtttaccacgttgccctcg	8	17	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:20914512C>A	ENST00000261497.4	-	8	1258	c.1055G>T	c.(1054-1056)gGg>gTg	p.G352V	USP22_ENST00000455117.2_Intron|USP22_ENST00000537526.2_Missense_Mutation_p.G340V	NM_015276.1	NP_056091.1	Q9UPT9	UBP22_HUMAN	ubiquitin specific peptidase 22	352	USP.				cell cycle (GO:0007049)|chromatin organization (GO:0006325)|embryo development (GO:0009790)|histone deubiquitination (GO:0016578)|histone H4 acetylation (GO:0043967)|histone ubiquitination (GO:0016574)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|protein deubiquitination (GO:0016579)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	SAGA complex (GO:0000124)	enzyme binding (GO:0019899)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|transcription coactivator activity (GO:0003713)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)	15						GTGGCTTTCCCCGTTTACCAC	0.662																																					p.G352V		Atlas-SNP	.											.	USP22	45	.	0			c.G1055T						.						37	42	40					17																	20914512		2083	4216	6299	SO:0001583	missense	23326	exon8			CTTTCCCCGTTTA	AB028986	CCDS42285.1	17p11.2	2006-11-24	2005-08-08		ENSG00000124422	ENSG00000124422		"Ubiquitin-specific peptidases"	12621	protein-coding gene	gene with protein product		612116	"ubiquitin specific protease 22", "ubiquitin specific peptidase 3-like"	USP3L		12838346	Standard	NM_015276		Approved	KIAA1063	uc002gym.4	Q9UPT9	OTTHUMG00000133621	ENST00000261497.4:c.1055G>T	chr17.hg19:g.20914512C>A	ENSP00000261497:p.Gly352Val	95.0	0.0		92.0	4.0	NM_015276	A0JNS3|Q2NLE2|Q6MZY4|Q8TBS8|Q96IW5	Missense_Mutation	SNP	ENST00000261497.4	hg19	CCDS42285.1	.	.	.	.	.	.	.	.	.	.	C	16.79	3.221600	0.58560	.	.	ENSG00000124422	ENST00000455117;ENST00000537526;ENST00000261497	T;T	0.10382	2.88;2.88	4.05	4.05	0.47172	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.064498	0.64402	D	0.000012	T	0.32912	0.0845	M	0.81802	2.56	0.80722	D	1	P;D	0.61697	0.829;0.99	P;D	0.63033	0.743;0.91	T	0.25012	-1.0144	10	0.51188	T	0.08	.	16.6186	0.84924	0.0:1.0:0.0:0.0	.	340;352	Q9UPT9-2;Q9UPT9	.;UBP22_HUMAN	V	420;340;352	ENSP00000440950:G340V;ENSP00000261497:G352V	ENSP00000261497:G352V	G	-	2	0	USP22	20855104	1.000000	0.71417	0.917000	0.36280	0.344000	0.29017	6.973000	0.76116	1.978000	0.57642	0.558000	0.71614	GGG	.	.		0.662	USP22-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444169.1			A	20914512	C	A	20914512	3	1	260	1	0	0	0	0	1	0	0	0	17069	623	22	3	546	3	USP22	17	20914512	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	2859347	20914512	60280698	737	37982										
PIGS	94005	hgsc.bcm.edu	37	chr17	26888474	26888474	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agaggccgcctcttctcagcGctccacttgtcctctggaag	10	15	3	1	rs116094938		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:26888474G>T	ENST00000308360.7	-	6	1017	c.642C>A	c.(640-642)agC>agA	p.S214R	PIGS_ENST00000543734.1_Missense_Mutation_p.S153R|PIGS_ENST00000465444.1_5'UTR|PIGS_ENST00000395346.2_Missense_Mutation_p.S206R	NM_033198.3	NP_149975.1	Q96S52	PIGS_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class S	214					attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)	endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|membrane (GO:0016020)	GPI-anchor transamidase activity (GO:0003923)			breast(3)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	Lung NSC(42;0.00431)					TCTTCTCAGCGCTCCACTTGT	0.577																																					p.S214R		Atlas-SNP	.											.	PIGS	42	.	0			c.C642A						.						71	58	63					17																	26888474		2203	4300	6503	SO:0001583	missense	94005	exon6			CTCAGCGCTCCAC		CCDS11235.1	17p13.2	2013-02-26	2006-06-28		ENSG00000087111	ENSG00000087111		"Phosphatidylinositol glycan anchor biosynthesis"	14937	protein-coding gene	gene with protein product	"GPI transamidase subunit"	610271	"phosphatidylinositol glycan, class S"				Standard	NM_033198		Approved		uc002hbo.2	Q96S52	OTTHUMG00000132604	ENST00000308360.7:c.642C>A	chr17.hg19:g.26888474G>T	ENSP00000309430:p.Ser214Arg	141.0	0.0		82.0	5.0	NM_033198	Q6UVX6	Missense_Mutation	SNP	ENST00000308360.7	hg19	CCDS11235.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.306199	0.81247	.	.	ENSG00000087111	ENST00000395346;ENST00000308360;ENST00000543734	T;T;T	0.47869	0.85;0.85;0.83	5.68	3.69	0.42338	.	0.150347	0.85682	D	0.000000	T	0.57799	0.2078	L	0.49126	1.545	0.38285	D	0.942535	D;D	0.89917	1.0;1.0	D;D	0.77004	0.989;0.982	T	0.56637	-0.7946	10	0.17832	T	0.49	-16.7225	12.2614	0.54652	0.1406:0.0:0.8594:0.0	.	214;206	Q96S52;Q96S52-2	PIGS_HUMAN;.	R	206;214;153	ENSP00000378755:S206R;ENSP00000309430:S214R;ENSP00000438447:S153R	ENSP00000309430:S214R	S	-	3	2	PIGS	23912601	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	2.504000	0.45416	1.411000	0.46957	0.655000	0.94253	AGC	.	G|1.000;A|0.000		0.577	PIGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255833.3	NM_033198		T	26888474	G	T	26888474	3	4	260	1	0	0	0	0	1	0	0	0	11907	1078	38	1	1053	1	PIGS	17	26888474	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	5973962	26888474	54306736	738	37983										
PHF12	57649	hgsc.bcm.edu	37	chr17	27251158	27251158	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgtgggtgtgccaggcctgcTggctctcctttccaggatcc	13	13	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:27251158T>C	ENST00000332830.4	-	4	1294	c.484A>G	c.(484-486)Agc>Ggc	p.S162G	PHF12_ENST00000582655.1_5'UTR|RP11-20B24.5_ENST00000582631.1_RNA|PHF12_ENST00000577226.1_Missense_Mutation_p.S162G|PHF12_ENST00000268756.3_Missense_Mutation_p.S162G|RP11-20B24.5_ENST00000580782.1_RNA	NM_001033561.1	NP_001028733.1			PHD finger protein 12											breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30	all_cancers(5;1.95e-14)|all_epithelial(6;5e-18)|Lung NSC(42;0.01)		Epithelial(11;1.64e-05)|all cancers(11;7.47e-05)|BRCA - Breast invasive adenocarcinoma(11;9.79e-05)			CCAGGCCTGCTGGCTCTCCTT	0.557																																					p.S162G		Atlas-SNP	.											.	PHF12	69	.	0			c.A484G						.						91	74	79					17																	27251158		2203	4300	6503	SO:0001583	missense	57649	exon4			GCCTGCTGGCTCT	AB040956	CCDS11247.1, CCDS32598.1	17q11.2	2013-01-28			ENSG00000109118	ENSG00000109118		"Zinc fingers, PHD-type"	20816	protein-coding gene	gene with protein product						11390640	Standard	XM_005258015		Approved	PF1, KIAA1523	uc002hdg.1	Q96QT6	OTTHUMG00000132676	ENST00000332830.4:c.484A>G	chr17.hg19:g.27251158T>C	ENSP00000329933:p.Ser162Gly	275.0	0.0		186.0	8.0	NM_020889		Missense_Mutation	SNP	ENST00000332830.4	hg19	CCDS32598.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.575786	0.86645	.	.	ENSG00000109118	ENST00000332830;ENST00000378879;ENST00000268756	D;D;D	0.96491	-3.71;-4.03;-4.03	5.69	5.69	0.88448	.	0.077767	0.85682	D	0.000000	D	0.97158	0.9071	L	0.53249	1.67	0.80722	D	1	D;D;D;D	0.69078	0.993;0.996;0.997;0.993	D;D;D;D	0.73380	0.956;0.98;0.97;0.956	D	0.96850	0.9624	10	0.39692	T	0.17	-11.6092	14.7509	0.69525	0.0:0.0:0.0:1.0	.	144;162;162;162	B4DFE2;Q96QT6-2;Q2TAK2;Q96QT6	.;.;.;PHF12_HUMAN	G	162	ENSP00000329933:S162G;ENSP00000368157:S162G;ENSP00000268756:S162G	ENSP00000268756:S162G	S	-	1	0	PHF12	24275284	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.866000	0.69590	2.163000	0.67991	0.533000	0.62120	AGC	.	.		0.557	PHF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255941.1	NM_020889		C	27251158	T	C	27251158	3	2	260	1	0	0	0	0	1	0	0	0	11832	1580	55	2	2604	2	PHF12	17	27251158	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	362684	27251158	53944052	739	37984										
NF1	4763	hgsc.bcm.edu	37	chr17	29490211	29490211	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	atttctattttagcaaccaaAggacacaatgagattagatg	7	6	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:29490211A>G	ENST00000358273.4	+	4	679	c.296A>G	c.(295-297)aAg>aGg	p.K99R	NF1_ENST00000431387.4_Missense_Mutation_p.K99R|NF1_ENST00000356175.3_Missense_Mutation_p.K99R	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	99					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TAGCAACCAAAGGACACAATG	0.343			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																											p.K99R		Atlas-SNP	.	yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	.	NF1	1586	.	12	Whole gene deletion(8)|Unknown(4)	soft_tissue(7)|autonomic_ganglia(3)|central_nervous_system(2)	c.A296G						.						62	64	63					17																	29490211		2203	4300	6503	SO:0001583	missense	4763	exon4	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	AACCAAAGGACAC		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.296A>G	chr17.hg19:g.29490211A>G	ENSP00000351015:p.Lys99Arg	111.0	0.0		100.0	4.0	NM_001128147	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	hg19	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	A	15.23	2.772791	0.49680	.	.	ENSG00000196712	ENST00000431387;ENST00000358273;ENST00000356175	T;T;T	0.81415	-1.49;-1.49;-1.49	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	D	0.88753	0.6522	M	0.74881	2.28	0.80722	D	1	D;D;D;D	0.63046	0.974;0.992;0.974;0.974	D;P;D;D	0.70487	0.969;0.784;0.969;0.969	D	0.87679	0.2546	10	0.34782	T	0.22	.	16.2055	0.82126	1.0:0.0:0.0:0.0	.	99;99;99;99	P21359-2;P21359;Q14931;P21359-3	.;NF1_HUMAN;.;.	R	99	ENSP00000412921:K99R;ENSP00000351015:K99R;ENSP00000348498:K99R	ENSP00000348498:K99R	K	+	2	0	NF1	26514337	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.565000	0.90730	2.226000	0.72624	0.482000	0.46254	AAG	.	.		0.343	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		G	29490211	A	G	29490211	3	3	260	1	0	0	0	0	1	0	0	0	10365	72	3	2	310	2	NF1	17	29490211	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	2239053	29490211	51704999	740	37985										
MYO19	80179	hgsc.bcm.edu	37	chr17	34884035	34884035	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccggattgtggccattgaccTggaagagataacgtgaaggt	14	7	0	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:34884035T>C	ENST00000431794.3	-	4	535		c.e4-2		MYO19_ENST00000586007.1_Splice_Site|MYO19_ENST00000544606.1_Intron|MYO19_ENST00000268852.9_Splice_Site	NM_001163735.1	NP_001157207.1	Q96H55	MYO19_HUMAN	myosin XIX							cytoplasm (GO:0005737)|mitochondrial outer membrane (GO:0005741)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|urinary_tract(1)	20		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		GCCATTGACCTGGAAGAGATA	0.577																																					.		Atlas-SNP	.											.	MYO19	130	.	0			c.13-2A>G						.						30	31	30					17																	34884035		1950	4137	6087	SO:0001630	splice_region_variant	80179	exon6			TTGACCTGGAAGA	BC008900	CCDS45654.1, CCDS54112.1, CCDS59283.1	17q12	2014-08-12	2007-09-26	2007-09-26	ENSG00000278259	ENSG00000278259		"Myosins / Myosin superfamily : Class XIX"	26234	protein-coding gene	gene with protein product			"myosin head domain containing 1"	MYOHD1		17877792, 19932026	Standard	NM_001033580		Approved	FLJ22865	uc010wcy.2	Q96H55	OTTHUMG00000188437	ENST00000431794.3:c.13-2A>G	chr17.hg19:g.34884035T>C		75.0	0.0		50.0	4.0	NM_025109	Q59GS4|Q9H5X2	Splice_Site	SNP	ENST00000431794.3	hg19	CCDS54112.1	.	.	.	.	.	.	.	.	.	.	T	17.88	3.497112	0.64186	.	.	ENSG00000141140	ENST00000431794;ENST00000268852	.	.	.	5.46	5.46	0.80206	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.161	0.42851	0.1485:0.0:0.0:0.8515	.	.	.	.	.	-1	.	.	.	-	.	.	MYO19	31958148	1.000000	0.71417	0.629000	0.29254	0.965000	0.64279	4.143000	0.58051	2.291000	0.77112	0.533000	0.62120	.	.	.		0.577	MYO19-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451074.1	NM_025109	Intron	C	34884035	T	C	34884035	5	2	260	1	0	0	0	0	0	0	1	0	10076	1594	55	2	3053	2	MYO19	17	34884035	Splice_Site	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	5393824	34884035	46311175	741	37986										
ACACA	31	hgsc.bcm.edu	37	chr17	35598872	35598872	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gagttacaagttactacctcTgtaccagctgaacaatgctc	7	11	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:35598872T>C	ENST00000394406.2	-	23	3108	c.2918A>G	c.(2917-2919)cAg>cGg	p.Q973R	ACACA_ENST00000353139.5_Missense_Mutation_p.Q1010R|ACACA_ENST00000335166.5_Missense_Mutation_p.Q895R|ACACA_ENST00000360679.3_Missense_Mutation_p.Q915R	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	973					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	TTACTACCTCTGTACCAGCTG	0.403																																					p.Q1010R	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)	Atlas-SNP	.											.	ACACA	395	.	0			c.A3029G						.						116	102	107					17																	35598872		2203	4300	6503	SO:0001583	missense	31	exon23			TACCTCTGTACCA	U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 1"	200350	"acetyl-Coenzyme A carboxylase alpha"	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.2918A>G	chr17.hg19:g.35598872T>C	ENSP00000377928:p.Gln973Arg	224.0	0.0		121.0	5.0	NM_198834	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Missense_Mutation	SNP	ENST00000394406.2	hg19	CCDS11317.1	.	.	.	.	.	.	.	.	.	.	T	14.16	2.451271	0.43531	.	.	ENSG00000132142	ENST00000353139;ENST00000360679;ENST00000394406;ENST00000452074;ENST00000335166	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	4.89	4.89	0.63831	Acetyl-CoA carboxylase, central domain (1);	0.059531	0.64402	D	0.000001	T	0.43211	0.1237	L	0.56340	1.77	0.80722	D	1	P;B;B	0.38978	0.652;0.059;0.048	B;B;B	0.42827	0.399;0.036;0.021	T	0.26950	-1.0088	10	0.26408	T	0.33	.	13.8335	0.63395	0.0:0.0:0.0:1.0	.	1010;973;915	Q13085-4;Q13085;Q13085-2	.;ACACA_HUMAN;.	R	1010;915;973;997;895	ENSP00000344789:Q1010R;ENSP00000353898:Q915R;ENSP00000377928:Q973R;ENSP00000335323:Q895R	ENSP00000335323:Q895R	Q	-	2	0	ACACA	32672985	1.000000	0.71417	0.994000	0.49952	0.584000	0.36387	7.868000	0.87116	2.049000	0.60858	0.482000	0.46254	CAG	.	.		0.403	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836		C	35598872	T	C	35598872	3	2	260	1	0	0	0	0	1	0	0	0	106	1580	55	2	4258	2	ACACA	17	35598872	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	714837	35598872	45596338	742	37987										
PIP4K2B	8396	hgsc.bcm.edu	37	chr17	36934625	36934625	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttctctggcaaccgtagaacCctgaaaggataagagccatc	9	11	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:36934625C>T	ENST00000269554.3	-	6	1135	c.655G>A	c.(655-657)Ggt>Agt	p.G219S	PIP4K2B_ENST00000311500.6_5'UTR	NM_003559.4	NP_003550.1	P78356	PI42B_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, beta	219	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				cell surface receptor signaling pathway (GO:0007166)|intracellular signal transduction (GO:0035556)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|1-phosphatidylinositol-5-phosphate 4-kinase activity (GO:0016309)|ATP binding (GO:0005524)|receptor signaling protein activity (GO:0005057)			endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(8)|ovary(1)	19						ACCGTAGAACCCTGAAAGGAT	0.532																																					p.G219S		Atlas-SNP	.											.	PIP4K2B	35	.	0			c.G655A						.						159	153	155					17																	36934625		2203	4300	6503	SO:0001630	splice_region_variant	8396	exon6			TAGAACCCTGAAA	U85245	CCDS11329.1	17q21.2	2007-08-14	2007-08-14	2007-08-14		ENSG00000276293	2.7.1.149		8998	protein-coding gene	gene with protein product		603261	"phosphatidylinositol-4-phosphate 5-kinase, type II, beta"	PIP5K2B		9038203, 14691457, 9367159	Standard	NM_003559		Approved	PIP5KIIB, PIP5KIIbeta	uc002hqs.3	P78356		ENST00000269554.3:c.655-1G>A	chr17.hg19:g.36934625C>T		71.0	0.0		55.0	4.0	NM_003559	Q5U0E8|Q8TBP2	Missense_Mutation	SNP	ENST00000269554.3	hg19	CCDS11329.1	.	.	.	.	.	.	.	.	.	.	C	35	5.475791	0.96291	.	.	ENSG00000141720	ENST00000269554;ENST00000311500	T	0.79454	-1.27	4.82	4.82	0.62117	Phosphatidylinositol-4-phosphate 5-kinase, core (2);Phosphatidylinositol-4-phosphate 5-kinase, core, subgroup (1);	0.052327	0.85682	D	0.000000	D	0.93067	0.7793	H	0.98883	4.36	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.997;0.999	D	0.95751	0.8792	10	0.87932	D	0	-13.5437	16.6288	0.85011	0.0:1.0:0.0:0.0	.	219;219;219	C9JMM2;P78356-2;P78356	.;.;PI42B_HUMAN	S	219	ENSP00000269554:G219S	ENSP00000269554:G219S	G	-	1	0	PIP4K2B	34188151	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.110000	0.77069	2.516000	0.84829	0.561000	0.74099	GGT	.	.		0.532	PIP4K2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256791.1	NM_003559	Missense_Mutation	T	36934625	C	T	36934625	5	4	260	1	0	0	0	0	0	0	1	0	11946	637	22	3	615	3	PIP4K2B	17	36934625	Splice_Site	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	1335753	36934625	44260585	743	37988										
MED24	9862	hgsc.bcm.edu	37	chr17	38187435	38187435	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttagccataaggttgttgacGctggcctcagacagaagccc	11	11	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:38187435G>T	ENST00000394128.2	-	12	1212	c.1131C>A	c.(1129-1131)agC>agA	p.S377R	MED24_ENST00000394127.2_Missense_Mutation_p.S364R|MED24_ENST00000394126.1_Missense_Mutation_p.S402R|MED24_ENST00000356271.3_Missense_Mutation_p.S364R|MED24_ENST00000501516.3_Missense_Mutation_p.S396R|MED24_ENST00000479829.1_5'Flank	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	377					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	41	Colorectal(19;0.000442)					GGTTGTTGACGCTGGCCTCAG	0.557																																					p.S377R		Atlas-SNP	.											.	MED24	89	.	0			c.C1131A						.						83	64	70					17																	38187435		2202	4298	6500	SO:0001583	missense	9862	exon12			GTTGACGCTGGCC	AF055995	CCDS11359.1, CCDS42315.1	17q21.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000008838	ENSG00000008838			22963	protein-coding gene	gene with protein product		607000	"thyroid hormone receptor associated protein 4", "cofactor required for Sp1 transcriptional activation, subunit 4, 100kDa"	THRAP4, CRSP4			Standard	NM_001079518		Approved	TRAP100, KIAA0130, DRIP100, CRSP100	uc002htt.3	O75448	OTTHUMG00000133329	ENST00000394128.2:c.1131C>A	chr17.hg19:g.38187435G>T	ENSP00000377686:p.Ser377Arg	163.0	0.0		107.0	5.0	NM_014815	A8K4S5|B3KMR9|Q14143|Q9NNY5	Missense_Mutation	SNP	ENST00000394128.2	hg19	CCDS11359.1	.	.	.	.	.	.	.	.	.	.	G	11.58	1.681603	0.29872	.	.	ENSG00000008838	ENST00000394126;ENST00000356271;ENST00000394128;ENST00000535071;ENST00000394127;ENST00000536318;ENST00000431269	T;T;T	0.41758	0.99;0.99;0.99	6.11	-9.51	0.00581	Mediator complex, subunit Med24, N-terminal (1);	0.257624	0.43110	D	0.000601	T	0.24928	0.0605	N	0.08118	0	0.09310	N	1	B;B;B;B;B;B	0.27286	0.116;0.044;0.107;0.144;0.174;0.107	B;B;B;B;B;B	0.26416	0.069;0.041;0.059;0.041;0.069;0.059	T	0.11203	-1.0597	10	0.51188	T	0.08	-0.609	28.2319	0.99998	0.117:0.0:0.883:0.0	.	318;327;287;364;377;319	B4DSQ6;F5H5K2;F8W9R9;O75448-2;O75448;F5H0K1	.;.;.;.;MED24_HUMAN;.	R	377;377;377;327;364;319;287	ENSP00000377686:S377R;ENSP00000443344:S327R;ENSP00000377685:S364R	ENSP00000348610:S377R	S	-	3	2	MED24	35440961	0.841000	0.29509	0.000000	0.03702	0.016000	0.09150	0.241000	0.18065	-2.201000	0.00746	-1.851000	0.00568	AGC	.	.		0.557	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815		T	38187435	G	T	38187435	3	4	260	1	0	0	0	0	1	0	0	0	9451	1078	38	1	1898	1	MED24	17	38187435	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	1252810	38187435	43007775	744	37989										
KRTAP4-9	100132386	hgsc.bcm.edu	37	chr17	39261994	39261994	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acgacctgctgccaccctagGtgctgcatctccagctgctg	10	16	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:39261994G>A	ENST00000391415.1	+	1	411	c.354G>A	c.(352-354)agG>agA	p.R118R		NM_001146041.1	NP_001139513.1	Q9BYQ8	KRA49_HUMAN	keratin associated protein 4-9	118	29 X 5 AA repeats of C-C-[RQVHIEK]- [SPTR]-[VSTQCRNP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|urinary_tract(3)	14						GCCACCCTAGGtgctgcatct	0.667																																					p.R118R		Atlas-SNP	.											KRTAP4-9_ENST00000377734,NS,carcinoma,0,2	KRTAP4-9	110	.	0			c.G354A						.						26	30	29					17																	39261994		692	1591	2283	SO:0001819	synonymous_variant	100132386	exon1			CCCTAGGTGCTGC	AJ406941	CCDS54124.1	17q21.2	2013-06-25			ENSG00000212722	ENSG00000212722		"Keratin associated proteins"	18910	protein-coding gene	gene with protein product							Standard	NM_001146041		Approved	KAP4.9	uc010wfp.2	Q9BYQ8	OTTHUMG00000133584	ENST00000391415.1:c.354G>A	chr17.hg19:g.39261994G>A		86.0	1.0		56.0	3.0	NM_001146041		Silent	SNP	ENST00000391415.1	hg19	CCDS54124.1																																																																																			.	.		0.667	KRTAP4-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257688.1	NM_001146041		A	39261994	G	A	39261994	2	1	260	1	0	0	0	0	0	0	0	1	8566	1252	44	3		3	KRTAP4-9	17	39261994	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	1074559	39261994	41933216	745	37990										
KRTAP4-11	653240	hgsc.bcm.edu	37	chr17	39274140	39274140	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agcaagaggggcggcagcagCtggagatgctgcagctgggg	20	8	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:39274140C>A	ENST00000391413.2	-	1	466	c.428G>T	c.(427-429)aGc>aTc	p.S143I		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	143	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament (GO:0045095)				endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			gcggcagcagctggagatgct	0.662																																					p.S143I		Atlas-SNP	.											.	KRTAP4-11	94	.	0			c.G428T						.						7	12	11					17																	39274140		688	1586	2274	SO:0001583	missense	653240	exon1			CAGCAGCTGGAGA	AC025904	CCDS45675.1	17q21.2	2013-06-25			ENSG00000212721	ENSG00000212721		"Keratin associated proteins"	18911	protein-coding gene	gene with protein product			"keratin associated protein 4-14"	KRTAP4-14			Standard	NM_033059		Approved	KAP4.11, KAP4.14	uc002hvz.3	Q9BYQ6	OTTHUMG00000133586	ENST00000391413.2:c.428G>T	chr17.hg19:g.39274140C>A	ENSP00000375232:p.Ser143Ile	148.0	0.0		97.0	18.0	NM_033059	A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	hg19	CCDS45675.1	.	.	.	.	.	.	.	.	.	.	.	15.59	2.878322	0.51801	.	.	ENSG00000212721	ENST00000391413	T	0.01516	4.81	4.29	1.58	0.23477	.	.	.	.	.	T	0.03053	0.0090	M	0.83384	2.64	0.09310	N	1	B	0.25850	0.136	B	0.23716	0.048	T	0.39440	-0.9614	9	0.51188	T	0.08	.	2.2044	0.03932	0.1862:0.3472:0.3494:0.1172	.	143	Q9BYQ6	KR411_HUMAN	I	143	ENSP00000375232:S143I	ENSP00000375232:S143I	S	-	2	0	KRTAP4-11	36527666	0.019000	0.18553	0.968000	0.41197	0.759000	0.43091	0.449000	0.21744	0.775000	0.33450	0.397000	0.26171	AGC	.	.		0.662	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1			A	39274140	C	A	39274140	3	1	260	1	0	0	0	0	1	0	0	0	8558	797	28	3	163	3	KRTAP4-11	17	39274140	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	12146	39274140	41921070	746	37991										
KRT15	3866	hgsc.bcm.edu	37	chr17	39673092	39673092	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cttcttcaggtaggctagctCctcattcaggccctcgatct	8	14	5	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:39673092C>T	ENST00000254043.3	-	3	4291	c.706G>A	c.(706-708)Gag>Aag	p.E236K	KRT15_ENST00000393974.3_Missense_Mutation_p.E71K|KRT15_ENST00000393981.3_Missense_Mutation_p.E71K|KRT15_ENST00000393976.2_Missense_Mutation_p.E236K	NM_002275.3	NP_002266	P19012	K1C15_HUMAN	keratin 15	236	Coil 1B.|Rod.				epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16		Breast(137;0.000286)				TAGGCTAGCTCCTCATTCAGG	0.587																																					p.E236K		Atlas-SNP	.											.	KRT15	60	.	0			c.G706A						.						98	86	90					17																	39673092		2203	4300	6503	SO:0001583	missense	3866	exon3			CTAGCTCCTCATT		CCDS11398.1	17q21.2	2013-06-20			ENSG00000171346	ENSG00000171346		"-", "Intermediate filaments type I, keratins (acidic)"	6421	protein-coding gene	gene with protein product	"keratin-15, basic", "keratin-15, beta", "type I cytoskeletal 15", "cytokeratin 15"	148030				16831889	Standard	NM_002275		Approved	K15, CK15, K1CO	uc002hwy.3	P19012	OTTHUMG00000133435	ENST00000254043.3:c.706G>A	chr17.hg19:g.39673092C>T	ENSP00000254043:p.Glu236Lys	198.0	0.0		98.0	4.0	NM_002275	B3KQY1|B3KRA2|E0CX14|Q53XV8|Q9BUG4	Missense_Mutation	SNP	ENST00000254043.3	hg19	CCDS11398.1	.	.	.	.	.	.	.	.	.	.	C	36	5.749084	0.96882	.	.	ENSG00000171346	ENST00000254043;ENST00000393974;ENST00000393976;ENST00000393981;ENST00000458290	D;D;D;D;D	0.93019	-3.15;-3.15;-3.15;-3.15;-3.15	4.67	4.67	0.58626	Filament (1);	0.140060	0.32231	N	0.006400	D	0.97980	0.9335	H	0.97564	4.03	0.80722	D	1	D;D;D	0.76494	0.971;0.999;0.999	P;D;D	0.74674	0.868;0.984;0.984	D	0.99651	1.0991	10	0.87932	D	0	.	17.7614	0.88465	0.0:1.0:0.0:0.0	.	71;236;236	A8MT21;B3KVF5;P19012	.;.;K1C15_HUMAN	K	236;71;236;71;71	ENSP00000254043:E236K;ENSP00000377544:E71K;ENSP00000377546:E236K;ENSP00000377550:E71K;ENSP00000409282:E71K	ENSP00000254043:E236K	E	-	1	0	KRT15	36926618	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	5.920000	0.70017	2.412000	0.81896	0.655000	0.94253	GAG	.	.		0.587	KRT15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257301.1	NM_002275		T	39673092	C	T	39673092	3	4	260	1	0	0	0	0	1	0	0	0	8461	864	30	3	688	3	KRT15	17	39673092	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	398952	39673092	41522118	747	37992										
HAP1	9001	hgsc.bcm.edu	37	chr17	39889015	39889015	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tttgacgtcttcctgggtgaTctttttgactggcggaggta	13	7	2	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:39889015T>C	ENST00000310778.5	-	2	514	c.505A>G	c.(505-507)Atc>Gtc	p.I169V	RN7SL399P_ENST00000471648.2_RNA|HAP1_ENST00000393939.2_Missense_Mutation_p.I169V|JUP_ENST00000540235.1_Intron|HAP1_ENST00000347901.4_Missense_Mutation_p.I169V|HAP1_ENST00000341193.5_Missense_Mutation_p.I169V			P54257	HAP1_HUMAN	huntingtin-associated protein 1	169	HAP1 N-terminal.				anterograde axon cargo transport (GO:0008089)|autophagy (GO:0006914)|brain development (GO:0007420)|cell projection organization (GO:0030030)|exocytosis (GO:0006887)|negative regulation of beta-amyloid formation (GO:1902430)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|positive regulation of neurotrophin production (GO:0032901)|positive regulation of nonmotile primary cilium assembly (GO:1902857)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|protein localization (GO:0008104)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|regulation of organelle transport along microtubule (GO:1902513)|retrograde axon cargo transport (GO:0008090)|synaptic transmission (GO:0007268)|vesicle transport along microtubule (GO:0047496)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|inclusion body (GO:0016234)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|synapse (GO:0045202)	brain-derived neurotrophic factor binding (GO:0048403)|ion channel binding (GO:0044325)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(4)|skin(1)	21		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.0677)			TCCTGGGTGATCTTTTTGACT	0.527																																					p.I169V		Atlas-SNP	.											.	HAP1	48	.	0			c.A505G						.						145	125	132					17																	39889015		2203	4300	6503	SO:0001583	missense	9001	exon2			GGGTGATCTTTTT	AF040723	CCDS11406.1, CCDS42338.1, CCDS42339.1	17q21.2-q21.3	2008-04-23	2008-04-23		ENSG00000173805	ENSG00000173805			4812	protein-coding gene	gene with protein product	"neuroan 1"	600947		HAP2		7477378, 9668110	Standard	NM_177977		Approved	HLP, hHLP1, HIP5	uc002hxn.1	P54257	OTTHUMG00000133498	ENST00000310778.5:c.505A>G	chr17.hg19:g.39889015T>C	ENSP00000309392:p.Ile169Val	250.0	0.0		130.0	6.0	NM_177977	A8MQB5|O75358|Q59GK4|Q9H4G3|Q9HA98|Q9NY90	Missense_Mutation	SNP	ENST00000310778.5	hg19		.	.	.	.	.	.	.	.	.	.	T	9.774	1.173555	0.21704	.	.	ENSG00000173805	ENST00000393939;ENST00000310778;ENST00000347901;ENST00000341193	T;T;T;T	0.08102	3.15;3.31;3.29;3.13	2.75	1.66	0.24008	.	0.190363	0.26038	N	0.026706	T	0.18173	0.0436	L	0.57536	1.79	0.23589	N	0.997341	P;P;P;P	0.47604	0.876;0.876;0.876;0.898	P;P;D;D	0.68192	0.894;0.894;0.927;0.956	T	0.02813	-1.1107	10	0.49607	T	0.09	-7.7441	4.6019	0.12357	0.0:0.1545:0.0:0.8455	.	169;169;169;169	P54257-3;P54257-4;P54257-2;P54257	.;.;.;HAP1_HUMAN	V	169	ENSP00000377513:I169V;ENSP00000309392:I169V;ENSP00000334002:I169V;ENSP00000343170:I169V	ENSP00000309392:I169V	I	-	1	0	HAP1	37142541	0.998000	0.40836	0.995000	0.50966	0.011000	0.07611	1.365000	0.34182	0.464000	0.27142	0.374000	0.22700	ATC	.	.		0.527	HAP1-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000389619.1	NM_003949		C	39889015	T	C	39889015	3	2	260	1	0	0	0	0	1	0	0	0	6962	1435	50	2	1418	2	HAP1	17	39889015	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	215923	39889015	41306195	748	37993										
FKBP10	60681	hgsc.bcm.edu	37	chr17	39976640	39976640	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	catctgagacctgcaatgagAccaccaagcttggggacttt	10	11	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:39976640A>G	ENST00000321562.4	+	7	1287	c.1183A>G	c.(1183-1185)Acc>Gcc	p.T395A	FKBP10_ENST00000544340.1_Missense_Mutation_p.T168A	NM_021939.3	NP_068758.3	Q96AY3	FKB10_HUMAN	FK506 binding protein 10, 65 kDa	395					chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			cervix(1)|endometrium(3)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	14		Breast(137;0.00122)		BRCA - Breast invasive adenocarcinoma(366;0.148)		CTGCAATGAGACCACCAAGCT	0.567																																					p.T395A		Atlas-SNP	.											.	FKBP10	57	.	0			c.A1183G						.						168	159	162					17																	39976640		2203	4300	6503	SO:0001583	missense	60681	exon7			AATGAGACCACCA	AB045981	CCDS11409.1	17q21.2	2014-09-17	2002-08-29		ENSG00000141756	ENSG00000141756		"EF-hand domain containing"	18169	protein-coding gene	gene with protein product		607063	"FK506 binding protein 10 (65 kDa)"			11071917, 18786928	Standard	NM_021939		Approved	hFKBP65, FLJ22041, FKBP6, FLJ20683, FLJ23833	uc002hxv.2	Q96AY3	OTTHUMG00000133497	ENST00000321562.4:c.1183A>G	chr17.hg19:g.39976640A>G	ENSP00000317232:p.Thr395Ala	221.0	0.0		140.0	6.0	NM_021939	Q7Z3R4|Q9H3N3|Q9H6J3|Q9H6N5|Q9UF89	Missense_Mutation	SNP	ENST00000321562.4	hg19	CCDS11409.1	.	.	.	.	.	.	.	.	.	.	A	15.28	2.785597	0.49997	.	.	ENSG00000141756	ENST00000269598;ENST00000321562;ENST00000414352;ENST00000544340	D;D	0.85702	-2.02;-2.02	5.38	5.38	0.77491	Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain (1);	0.000000	0.49916	D	0.000126	D	0.85195	0.5641	L	0.37800	1.135	0.53688	D	0.999977	P;P	0.50443	0.872;0.935	P;P	0.57620	0.688;0.824	T	0.81182	-0.1049	10	0.10111	T	0.7	-11.6624	15.3508	0.74384	1.0:0.0:0.0:0.0	.	168;395	Q9H6J3;Q96AY3	.;FKB10_HUMAN	A	283;395;395;168	ENSP00000317232:T395A;ENSP00000442009:T168A	ENSP00000269598:T283A	T	+	1	0	FKBP10	37230166	1.000000	0.71417	0.991000	0.47740	0.393000	0.30537	5.885000	0.69736	2.182000	0.69389	0.533000	0.62120	ACC	.	.		0.567	FKBP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257410.2	NM_021939		G	39976640	A	G	39976640	3	3	260	1	0	0	0	0	1	0	0	0	5910	275	10	2	1209	2	FKBP10	17	39976640	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	87625	39976640	41218570	749	37994										
KAT2A	2648	hgsc.bcm.edu	37	chr17	40266531	40266531	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgccaggaacgctctccacaGggatctgcctcacgccctcc	9	18	3	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:40266531G>T	ENST00000225916.5	-	14	2164	c.2111C>A	c.(2110-2112)cCt>cAt	p.P704H	DHX58_ENST00000251642.3_5'Flank	NM_021078.2	NP_066564.2	Q92830	KAT2A_HUMAN	K(lysine) acetyltransferase 2A	704					cell proliferation (GO:0008283)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|histone deubiquitination (GO:0016578)|histone H3 acetylation (GO:0043966)|histone H3-K14 acetylation (GO:0044154)|in utero embryonic development (GO:0001701)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|positive regulation of gluconeogenesis (GO:0045722)|regulation of protein stability (GO:0031647)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|somitogenesis (GO:0001756)|telencephalon development (GO:0021537)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|extracellular space (GO:0005615)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|STAGA complex (GO:0030914)|transcription factor TFTC complex (GO:0033276)	chromatin binding (GO:0003682)|H3 histone acetyltransferase activity (GO:0010484)|histone acetyltransferase activity (GO:0004402)|histone acetyltransferase activity (H4-K12 specific) (GO:0043997)|histone deacetylase binding (GO:0042826)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						GCTCTCCACAGGGATCTGCCT	0.572																																					p.P704H		Atlas-SNP	.											.	KAT2A	54	.	0			c.C2111A						.						169	160	163					17																	40266531		2203	4300	6503	SO:0001583	missense	2648	exon14			TCCACAGGGATCT	AF029777	CCDS11417.1	17q12-q21	2011-07-01	2008-07-04	2008-07-04	ENSG00000108773	ENSG00000108773		"Chromatin-modifying enzymes / K-acetyltransferases"	4201	protein-coding gene	gene with protein product		602301	"GCN5 general control of amino-acid synthesis 5-like 2 (yeast)"	GCN5L2		8552087	Standard	NM_021078		Approved	GCN5, PCAF-b	uc002hyx.2	Q92830	OTTHUMG00000133504	ENST00000225916.5:c.2111C>A	chr17.hg19:g.40266531G>T	ENSP00000225916:p.Pro704His	104.0	0.0		68.0	4.0	NM_021078	Q8N1A2|Q9UCW1	Missense_Mutation	SNP	ENST00000225916.5	hg19	CCDS11417.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.886894	0.91814	.	.	ENSG00000108773	ENST00000225916	T	0.05855	3.38	4.96	4.96	0.65561	Bromodomain (1);	0.051637	0.85682	D	0.000000	T	0.27384	0.0672	M	0.79123	2.44	0.80722	D	1	D	0.89917	1.0	D	0.72338	0.977	T	0.02805	-1.1108	10	0.87932	D	0	-8.5427	18.2093	0.89865	0.0:0.0:1.0:0.0	.	704	Q92830	KAT2A_HUMAN	H	704	ENSP00000225916:P704H	ENSP00000225916:P704H	P	-	2	0	KAT2A	37520057	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	9.813000	0.99286	2.296000	0.77279	0.462000	0.41574	CCT	.	.		0.572	KAT2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257458.1	NM_021078		T	40266531	G	T	40266531	3	4	260	1	0	0	0	0	1	0	0	0	7990	1000	35	3	422	3	KAT2A	17	40266531	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	289891	40266531	40928679	750	37995										
EZH1	2145	hgsc.bcm.edu	37	chr17	40870506	40870506	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcgtatttaaagcagcgccgGcaaaaaagtgtgtggaagga	13	6	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:40870506G>T	ENST00000428826.2	-	9	1018	c.897C>A	c.(895-897)tgC>tgA	p.C299*	EZH1_ENST00000590078.1_Nonsense_Mutation_p.C229*|EZH1_ENST00000585893.1_Nonsense_Mutation_p.C259*|EZH1_ENST00000592743.1_Nonsense_Mutation_p.C299*|EZH1_ENST00000415827.2_Nonsense_Mutation_p.C290*|EZH1_ENST00000435174.1_Nonsense_Mutation_p.C160*			Q92800	EZH1_HUMAN	enhancer of zeste 1 polycomb repressive complex 2 subunit	299					anatomical structure morphogenesis (GO:0009653)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)			breast(1)|endometrium(4)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	27		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0784)		AGCAGCGCCGGCAAAAAAGTG	0.537																																					p.C299X		Atlas-SNP	.											.	EZH1	62	.	0			c.C897A						.						88	82	84					17																	40870506		2203	4300	6503	SO:0001587	stop_gained	2145	exon9			GCGCCGGCAAAAA		CCDS32659.1	17q21.1-q21.3	2014-05-28	2014-05-28			ENSG00000108799		"Chromatin-modifying enzymes / K-methyltransferases"	3526	protein-coding gene	gene with protein product		601674	"enhancer of zeste (Drosophila) homolog 1", "enhancer of zeste homolog 1 (Drosophila)"			8921387	Standard	NM_001991		Approved	KIAA0388, KMT6B	uc002iaz.3	Q92800		ENST00000428826.2:c.897C>A	chr17.hg19:g.40870506G>T	ENSP00000404658:p.Cys299*	130.0	0.0		72.0	4.0	NM_001991	A6NCH6|B4DIJ1|B4DIZ7|B4DSS2|B4E3R7|O43287|Q14459|Q53XP3	Nonsense_Mutation	SNP	ENST00000428826.2	hg19	CCDS32659.1	.	.	.	.	.	.	.	.	.	.	G	37	6.333478	0.97480	.	.	ENSG00000108799	ENST00000264646;ENST00000428826;ENST00000415827;ENST00000435174	.	.	.	4.71	0.385	0.16249	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.6419	0.33983	0.3721:0.0:0.6279:0.0	.	.	.	.	X	302;299;259;160	.	ENSP00000264646:C302X	C	-	3	2	EZH1	38124032	1.000000	0.71417	0.980000	0.43619	0.998000	0.95712	1.558000	0.36309	0.035000	0.15519	0.655000	0.94253	TGC	.	.		0.537	EZH1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452347.1	NM_001991		T	40870506	G	T	40870506	4	4	260	1	0	0	0	0	0	1	0	0	5335	1195	42	3	1398	3	EZH1	17	40870506	Nonsense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	603975	40870506	40324704	751	37996										
RUNDC1	146923	hgsc.bcm.edu	37	chr17	41142394	41142394	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgagtgcaaggccggtgggaAgacaggaaatggctgcagca	17	7	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:41142394A>G	ENST00000361677.1	+	4	929	c.917A>G	c.(916-918)aAg>aGg	p.K306R		NM_173079.2	NP_775102	Q96C34	RUND1_HUMAN	RUN domain containing 1	306										breast(1)|large_intestine(2)|lung(4)|prostate(1)	8		Breast(137;0.00499)		BRCA - Breast invasive adenocarcinoma(366;0.161)		GCCGGTGGGAAGACAGGAAAT	0.498																																					p.K306R		Atlas-SNP	.											.	RUNDC1	25	.	0			c.A917G						.						93	96	95					17																	41142394		2203	4300	6503	SO:0001583	missense	146923	exon4			GTGGGAAGACAGG	AL831813	CCDS11448.1	17q21.31	2004-02-27				ENSG00000198863			25418	protein-coding gene	gene with protein product						12477932	Standard	NM_173079		Approved	DKFZp761H0421	uc002ici.1	Q96C34		ENST00000361677.1:c.917A>G	chr17.hg19:g.41142394A>G	ENSP00000354622:p.Lys306Arg	155.0	0.0		98.0	4.0	NM_173079	Q6Y2K8|Q8IXT9|Q8N3W1	Missense_Mutation	SNP	ENST00000361677.1	hg19	CCDS11448.1	.	.	.	.	.	.	.	.	.	.	A	8.683	0.905695	0.17760	.	.	ENSG00000198863	ENST00000361677	T	0.18338	2.22	4.88	2.7	0.31948	.	0.464831	0.23165	N	0.051183	T	0.08492	0.0211	N	0.14661	0.345	0.34613	D	0.717808	B	0.10296	0.003	B	0.06405	0.002	T	0.20672	-1.0268	10	0.21540	T	0.41	-27.4736	7.3035	0.26434	0.8152:0.0:0.1848:0.0	.	306	Q96C34	RUND1_HUMAN	R	306	ENSP00000354622:K306R	ENSP00000354622:K306R	K	+	2	0	RUNDC1	38395920	0.998000	0.40836	0.999000	0.59377	0.396000	0.30629	2.109000	0.41863	1.006000	0.39211	0.460000	0.39030	AAG	.	.		0.498	RUNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452464.1	NM_173079		G	41142394	A	G	41142394	3	3	260	1	0	0	0	0	1	0	0	0	13757	72	3	2	931	2	RUNDC1	17	41142394	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	271888	41142394	40052816	752	37997										
BRCA1	672	hgsc.bcm.edu	37	chr17	41246557	41246557	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttctgtgctgggagtccgccTatcattacatgtttccttac	8	11	2	0	rs80359872		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:41246557T>C	ENST00000357654.3	-	10	1109	c.991A>G	c.(991-993)Agg>Ggg	p.R331G	BRCA1_ENST00000471181.2_Missense_Mutation_p.R331G|BRCA1_ENST00000491747.2_Intron|BRCA1_ENST00000309486.4_Missense_Mutation_p.R35G|BRCA1_ENST00000468300.1_Intron|BRCA1_ENST00000352993.3_Intron|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000493795.1_Missense_Mutation_p.R284G|BRCA1_ENST00000351666.3_Intron|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000354071.3_Missense_Mutation_p.R331G|BRCA1_ENST00000346315.3_Missense_Mutation_p.R331G	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	331					androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		GGAGTCCGCCTATCATTACAT	0.433			"D, Mis, N, F, S"		ovarian	"breast, ovarian"		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																											p.R331G		Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	.	BRCA1	304	.	0			c.A991G						.						199	185	190					17																	41246557		2203	4300	6503	SO:0001583	missense	672	exon10	Familial Cancer Database		TCCGCCTATCATT	U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1100	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 1", "protein phosphatase 1, regulatory subunit 53"	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.991A>G	chr17.hg19:g.41246557T>C	ENSP00000350283:p.Arg331Gly	154.0	0.0		116.0	5.0	NM_007300	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Missense_Mutation	SNP	ENST00000357654.3	hg19	CCDS11453.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.242|9.242	1.038477|1.038477	0.19669|0.19669	.|.	.|.	ENSG00000012048|ENSG00000012048	ENST00000473961|ENST00000357654;ENST00000412061;ENST00000354071;ENST00000346315;ENST00000309486;ENST00000471181;ENST00000493795;ENST00000470026;ENST00000477152;ENST00000497488;ENST00000494123	.|D;D;D;D;D;D;D;D;D;D	.|0.88509	.|-2.11;-2.23;-2.22;-2.04;-2.11;-2.24;-1.8;-1.8;-2.39;-1.8	4.95|4.95	2.78|2.78	0.32641|0.32641	.|.	.|0.188754	.|0.38605	.|N	.|0.001635	D|D	0.83751|0.83751	0.5322|0.5322	L|L	0.49640|0.49640	1.575|1.575	0.09310|0.09310	N|N	1|1	.|B;B;B;B;P;B	.|0.44986	.|0.016;0.016;0.211;0.191;0.847;0.421	.|B;B;B;B;B;B	.|0.43194	.|0.007;0.007;0.143;0.084;0.411;0.283	T|T	0.73388|0.73388	-0.3998|-0.3998	5|10	.|0.29301	.|T	.|0.29	.|.	6.6838|6.6838	0.23134|0.23134	0.0:0.2505:0.0:0.7495|0.0:0.2505:0.0:0.7495	.|.	.|331;290;331;331;331;331	.|E7EMP0;E7ERL4;Q5YLB2;E9PFC7;P38398;P38398-2	.|.;.;.;.;BRCA1_HUMAN;.	M|G	196|331;331;331;331;35;331;284;331;305;35;331	.|ENSP00000350283:R331G;ENSP00000326002:R331G;ENSP00000246907:R331G;ENSP00000310938:R35G;ENSP00000418960:R331G;ENSP00000418775:R284G;ENSP00000419274:R331G;ENSP00000419988:R305G;ENSP00000418986:R35G;ENSP00000419103:R331G	.|ENSP00000310938:R35G	I|R	-|-	3|1	3|2	BRCA1|BRCA1	38500083|38500083	0.003000|0.003000	0.15002|0.15002	0.980000|0.980000	0.43619|0.43619	0.604000|0.604000	0.37047|0.37047	0.380000|0.380000	0.20602|0.20602	1.027000|1.027000	0.39758|0.39758	0.533000|0.533000	0.62120|0.62120	ATA|AGG	.	.		0.433	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294		C	41246557	T	C	41246557	3	2	260	1	0	0	0	0	1	0	0	0	1500	1521	53	2	4726	2	BRCA1	17	41246557	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	104163	41246557	39948653	753	37998										
TMEM106A	113277	hgsc.bcm.edu	37	chr17	41365155	41365155	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cattggcagcaaggctgtcaActactccagcaccggtagca	10	13	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:41365155A>G	ENST00000331615.3	+	3	332	c.95A>G	c.(94-96)aAc>aGc	p.N32S	TMEM106A_ENST00000541594.1_Intron|TMEM106A_ENST00000536052.1_Missense_Mutation_p.N32S|TMEM106A_ENST00000592564.1_3'UTR|TMEM106A_ENST00000588659.1_Missense_Mutation_p.N32S	NM_145041.1	NP_659478.1	Q96A25	T106A_HUMAN	transmembrane protein 106A	32						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|endometrium(2)|large_intestine(1)|lung(6)|prostate(1)	11		Breast(137;0.0164)		BRCA - Breast invasive adenocarcinoma(366;0.0917)		AAGGCTGTCAACTACTCCAGC	0.537																																					p.N32S		Atlas-SNP	.											.	TMEM106A	20	.	0			c.A95G						.						110	97	101					17																	41365155		2203	4296	6499	SO:0001583	missense	113277	exon3			CTGTCAACTACTC	AK056132	CCDS11462.1, CCDS74073.1	17q21.31	2012-01-23			ENSG00000184988	ENSG00000184988			28288	protein-coding gene	gene with protein product							Standard	XM_006721658		Approved	MGC20235	uc002idn.1	Q96A25		ENST00000331615.3:c.95A>G	chr17.hg19:g.41365155A>G	ENSP00000330774:p.Asn32Ser	109.0	0.0		86.0	4.0	NM_145041	A8K2X2|B7Z698	Missense_Mutation	SNP	ENST00000331615.3	hg19	CCDS11462.1	.	.	.	.	.	.	.	.	.	.	G	4.958	0.177897	0.09443	.	.	ENSG00000184988	ENST00000331615;ENST00000536052	T;T	0.20332	2.08;2.08	4.81	2.81	0.32909	.	0.407137	0.27096	N	0.020958	T	0.06781	0.0173	N	0.02736	-0.51	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.40156	-0.9578	10	0.09843	T	0.71	-24.5471	6.3126	0.21173	0.4068:0.0:0.5932:0.0	.	32;32	B7Z779;Q96A25	.;T106A_HUMAN	S	32	ENSP00000330774:N32S;ENSP00000439835:N32S	ENSP00000330774:N32S	N	+	2	0	TMEM106A	38720681	0.085000	0.21516	0.683000	0.30040	0.055000	0.15305	0.169000	0.16641	0.241000	0.21283	-0.119000	0.15052	AAC	.	.		0.537	TMEM106A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453470.2	NM_145041		G	41365155	A	G	41365155	3	3	260	1	0	0	0	0	1	0	0	0	16035	43	2	2	97	2	TMEM106A	17	41365155	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	118598	41365155	39830055	754	37999										
ITGA2B	3674	hgsc.bcm.edu	37	chr17	42461045	42461045	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gcccggctctccatatacagTggagcgcccaccagcagatc	10	16	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:42461045T>C	ENST00000262407.5	-	12	1057	c.1026A>G	c.(1024-1026)ccA>ccG	p.P342P	ITGA2B_ENST00000353281.4_Silent_p.P342P|ITGA2B_ENST00000377068.3_Silent_p.P27P	NM_000419.3	NP_000410.2	P08514	ITA2B_HUMAN	integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41)	342					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of leukocyte migration (GO:0002687)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)	extracellular matrix binding (GO:0050840)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			biliary_tract(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.191)	Abciximab(DB00054)|Tirofiban(DB00775)	CCATATACAGTGGAGCGCCCA	0.627																																					p.P342P		Atlas-SNP	.											.	ITGA2B	88	.	0			c.A1026G						.						19	18	18					17																	42461045		2201	4297	6498	SO:0001819	synonymous_variant	3674	exon12			ATACAGTGGAGCG		CCDS32665.1	17q21.32	2014-09-17	2006-02-22			ENSG00000005961		"CD molecules", "Integrins"	6138	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 93"	607759	"integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41B)"	GP2B			Standard	NM_000419		Approved	CD41B, CD41, PPP1R93	uc002igt.1	P08514		ENST00000262407.5:c.1026A>G	chr17.hg19:g.42461045T>C		146.0	0.0		94.0	4.0	NM_000419	B2RCY8|O95366|Q14443|Q17R67	Silent	SNP	ENST00000262407.5	hg19	CCDS32665.1																																																																																			.	.		0.627	ITGA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439823.1			C	42461045	T	C	42461045	2	2	260	1	0	0	0	0	0	0	0	1	7885	1683	59	2		2	ITGA2B	17	42461045	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1095890	42461045	38734165	755	38000										
MAPT	4137	hgsc.bcm.edu	37	chr17	44049223	44049223	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gggctcactgtatgtgttccAgaatctcccctgcagacccc	9	15	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:44049223A>G	ENST00000571987.1	+	2	133		c.e2-1		MAPT_ENST00000535772.1_Splice_Site|MAPT_ENST00000344290.5_Splice_Site|MAPT_ENST00000420682.2_Splice_Site|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000340799.5_Splice_Site|MAPT_ENST00000415613.2_Splice_Site|MAPT_ENST00000574436.1_Splice_Site|MAPT_ENST00000347967.5_Splice_Site|MAPT_ENST00000576518.1_5'Flank|MAPT_ENST00000446361.3_Intron|MAPT_ENST00000262410.5_Splice_Site|MAPT_ENST00000334239.8_Intron|MAPT_ENST00000351559.5_Splice_Site|MAPT_ENST00000431008.3_Splice_Site			P10636	TAU_HUMAN	microtubule-associated protein tau						adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	TATGTGTTCCAGAATCTCCCC	0.592																																					.		Atlas-SNP	.											.	MAPT	135	.	0			c.134-2A>G						.						62	58	59					17																	44049223		2203	4300	6503	SO:0001630	splice_region_variant	4137	exon3			TGTTCCAGAATCT	J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"G protein beta1/gamma2 subunit-interacting factor 1", "microtubule-associated protein tau, isoform 4", "protein phosphatase 1, regulatory subunit 103"	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.134-1A>G	chr17.hg19:g.44049223A>G		85.0	0.0		57.0	4.0	NM_001123066	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Splice_Site	SNP	ENST00000571987.1	hg19	CCDS11501.1	.	.	.	.	.	.	.	.	.	.	A	13.21	2.170024	0.38315	.	.	ENSG00000186868	ENST00000344290;ENST00000262410;ENST00000351559;ENST00000340799;ENST00000535772;ENST00000354326;ENST00000420682;ENST00000415613	.	.	.	5.67	5.67	0.87782	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.3055	0.54900	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MAPT	41405059	1.000000	0.71417	1.000000	0.80357	0.358000	0.29455	5.293000	0.65680	2.161000	0.67846	0.459000	0.35465	.	.	.		0.592	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835	Intron	G	44049223	A	G	44049223	5	3	260	1	0	0	0	0	0	0	1	0	9306	202	7	2	138	2	MAPT	17	44049223	Splice_Site	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1588178	44049223	37145987	756	38001										
C17orf57	124989	hgsc.bcm.edu	37	chr17	45451912	45451912	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtgtagcaggatgctatctaAaatataagaagaaaaatagt	9	3	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:45451912A>C	ENST00000331493.2	+	12	1363	c.952A>C	c.(952-954)Aaa>Caa	p.K318Q	EFCAB13_ENST00000517484.1_Missense_Mutation_p.K222Q	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	318						cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)										ATGCTATCTAAAATATAAGAA	0.279																																					p.K318Q		Atlas-SNP	.											.	.	.	.	0			c.A952C						.						29	33	32					17																	45451912		2184	4253	6437	SO:0001583	missense	124989	exon12			TATCTAAAATATA	BC036407	CCDS11512.1, CCDS56034.1	17q21.32	2013-01-11	2012-07-20	2012-07-20	ENSG00000178852	ENSG00000178852		"EF-hand domain containing"	26864	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 57"	C17orf57			Standard	NM_152347		Approved	FLJ40342	uc002iln.3	Q8IY85	OTTHUMG00000164767	ENST00000331493.2:c.952A>C	chr17.hg19:g.45451912A>C	ENSP00000332111:p.Lys318Gln	303.0	0.0		160.0	45.0	NM_152347	G3V128|Q49AG9	Missense_Mutation	SNP	ENST00000331493.2	hg19	CCDS11512.1	.	.	.	.	.	.	.	.	.	.	A	1.988	-0.432530	0.04669	.	.	ENSG00000178852	ENST00000331493;ENST00000517484;ENST00000344176	T;T	0.62105	0.41;0.05	3.09	0.885	0.19188	.	0.652062	0.13910	N	0.354315	T	0.27205	0.0667	N	0.00841	-1.15	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.24190	-1.0167	10	0.31617	T	0.26	-18.3861	7.802	0.29180	0.4552:0.5448:0.0:0.0	.	270;318;222	Q8N7U2;Q8IY85;G3V128	.;CQ057_HUMAN;.	Q	318;222;270	ENSP00000332111:K318Q;ENSP00000430048:K222Q	ENSP00000332111:K318Q	K	+	1	0	C17orf57	42806911	0.001000	0.12720	0.001000	0.08648	0.118000	0.20060	0.460000	0.21924	0.113000	0.18004	-0.261000	0.10672	AAA	.	.		0.279	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4	NM_152347		C	45451912	A	C	45451912	3	2	260	1	0	0	0	0	1	0	0	0	1867	15	1	5	986	5	C17orf57	17	45451912	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1402689	45451912	35743298	757	38002										
KPNB1	3837	hgsc.bcm.edu	37	chr17	45742517	45742517	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aatcctcacacagacactaaCtaaacaggtgagttaccttc	5	12	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:45742517C>T	ENST00000290158.4	+	9	1399	c.992C>T	c.(991-993)aCt>aTt	p.T331I	KPNB1_ENST00000540627.1_Missense_Mutation_p.T186I|KPNB1_ENST00000537679.1_Intron|KPNB1_ENST00000535458.2_Missense_Mutation_p.T186I	NM_001276453.1|NM_002265.4	NP_001263382.1|NP_002256.2	Q14974	IMB1_HUMAN	karyopherin (importin) beta 1	331	IAB-binding.				apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cytokine-mediated signaling pathway (GO:0019221)|intracellular transport of virus (GO:0075733)|NLS-bearing protein import into nucleus (GO:0006607)|protein import into nucleus (GO:0006606)|protein import into nucleus, translocation (GO:0000060)|ribosomal protein import into nucleus (GO:0006610)|small molecule metabolic process (GO:0044281)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum tubular network (GO:0071782)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(1)|ovary(1)|pancreas(1)|skin(1)	4						CAGACACTAACTAAACAGGTG	0.478																																					p.S331F		Atlas-SNP	.											.	KPNB1	58	.	0			c.C992T						.						79	71	74					17																	45742517		2203	4300	6503	SO:0001583	missense	3837	exon9			CACTAACTAAACA	L39793	CCDS11513.1, CCDS62228.1	17q21.32	2013-02-14			ENSG00000108424	ENSG00000108424		"Importins", "Armadillo repeat containing"	6400	protein-coding gene	gene with protein product	"importin 1"	602738				7615630, 7627554	Standard	NM_002265		Approved	NTF97, IPOB, MGC2155, MGC2156, MGC2157, IMB1, Impnb, IPO1	uc002ilt.2	Q14974	OTTHUMG00000036957	ENST00000290158.4:c.992C>T	chr17.hg19:g.45742517C>T	ENSP00000290158:p.Thr331Ile	64.0	0.0		67.0	4.0	NM_002265	B7ZAV6|D3DTT3|Q14637|Q53XN2|Q96J27	Missense_Mutation	SNP	ENST00000290158.4	hg19	CCDS11513.1	.	.	.	.	.	.	.	.	.	.	C	18.20	3.571751	0.65765	.	.	ENSG00000108424	ENST00000535458;ENST00000290158;ENST00000540627	T;T;T	0.68765	-0.35;-0.35;-0.35	5.76	4.74	0.60224	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.65523	0.2699	M	0.79926	2.475	0.37709	D	0.924496	P	0.48230	0.907	B	0.35971	0.215	T	0.78360	-0.2234	9	0.42905	T	0.14	-7.9905	16.2841	0.82710	0.0:0.8676:0.1324:0.0	.	331	Q14974	IMB1_HUMAN	I	186;331;186	ENSP00000438253:T186I;ENSP00000290158:T331I;ENSP00000438964:T186I	ENSP00000290158:T331I	T	+	2	0	KPNB1	43097516	1.000000	0.71417	0.984000	0.44739	0.981000	0.71138	4.891000	0.63185	2.730000	0.93505	0.591000	0.81541	ACT	.	.		0.478	KPNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089755.2	NM_002265		T	45742517	C	T	45742517	3	4	260	1	0	0	0	0	1	0	0	0	8444	565	20	3	1026	3	KPNB1	17	45742517	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	290605	45742517	35452693	758	38003										
OSBPL7	114881	hgsc.bcm.edu	37	chr17	45894019	45894019	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cgaggagtcccgagactccaGgtagcgagacaggttgggaa	16	9	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:45894019G>T	ENST00000007414.3	-	10	1029	c.838C>A	c.(838-840)Ctg>Atg	p.L280M	OSBPL7_ENST00000392507.3_Missense_Mutation_p.L280M	NM_145798.2	NP_665741.1	Q9BZF2	OSBL7_HUMAN	oxysterol binding protein-like 7	280					cellular response to cholesterol (GO:0071397)|lipid transport (GO:0006869)|positive regulation of proteasomal protein catabolic process (GO:1901800)	autophagic vacuole (GO:0005776)|cytosol (GO:0005829)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			autonomic_ganglia(1)|endometrium(6)|kidney(2)|large_intestine(5)|liver(2)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32						CGAGACTCCAGGTAGCGAGAC	0.647																																					p.L280M		Atlas-SNP	.											.	OSBPL7	65	.	0			c.C838A						.						38	41	40					17																	45894019		2203	4300	6503	SO:0001583	missense	114881	exon10			ACTCCAGGTAGCG	AF392446	CCDS11515.1	17q21	2013-01-10				ENSG00000006025		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16387	protein-coding gene	gene with protein product		606735				14593528, 11735225	Standard	NM_145798		Approved	ORP7, MGC71150	uc002ilx.1	Q9BZF2		ENST00000007414.3:c.838C>A	chr17.hg19:g.45894019G>T	ENSP00000007414:p.Leu280Met	94.0	0.0		63.0	14.0	NM_145798	D3DTT6|Q6PIV6	Missense_Mutation	SNP	ENST00000007414.3	hg19	CCDS11515.1	.	.	.	.	.	.	.	.	.	.	G	11.56	1.675705	0.29783	.	.	ENSG00000006025	ENST00000007414;ENST00000392507	T;T	0.19532	2.14;2.14	5.44	1.16	0.20824	.	0.477084	0.19318	N	0.117209	T	0.25827	0.0629	N	0.19112	0.55	0.35967	D	0.835019	D	0.71674	0.998	D	0.83275	0.996	T	0.14531	-1.0469	10	0.41790	T	0.15	-15.9654	8.4614	0.32929	0.3944:0.0:0.6056:0.0	.	280	Q9BZF2	OSBL7_HUMAN	M	280	ENSP00000007414:L280M;ENSP00000376295:L280M	ENSP00000007414:L280M	L	-	1	2	OSBPL7	43249018	1.000000	0.71417	0.999000	0.59377	0.962000	0.63368	1.464000	0.35288	0.087000	0.17167	-0.137000	0.14449	CTG	.	.		0.647	OSBPL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441367.1	NM_017731		T	45894019	G	T	45894019	3	4	260	1	0	0	0	0	1	0	0	0	11291	991	35	3	1746	3	OSBPL7	17	45894019	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	151502	45894019	35301191	759	38004										
SNF8	11267	hgsc.bcm.edu	37	chr17	47022064	47022064	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tctgcaagtttcttcttggcGatggcgccagctcccacccc	9	16	3	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:47022064G>T	ENST00000502492.1	-	1	415	c.33C>A	c.(31-33)atC>atA	p.I11I	SNF8_ENST00000290330.3_Silent_p.I11I			Q96H20	SNF8_HUMAN	SNF8, ESCRT-II complex subunit	11					endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|lung(1)	3						TCTTCTTGGCGATGGCGCCAG	0.711																																					p.I11I		Atlas-SNP	.											.	SNF8	15	.	0			c.C33A						.						101	109	107					17																	47022064		2203	4300	6503	SO:0001819	synonymous_variant	11267	exon1			CTTGGCGATGGCG	AF156102	CCDS11541.1	17q21.32	2013-06-05	2013-06-05		ENSG00000159210	ENSG00000159210			17028	protein-coding gene	gene with protein product		610904	"SNF8, ESCRT-II complex subunit, homolog (S. cerevisiae)"			10419521, 15329733	Standard	NM_007241		Approved	EAP30, VPS22, Dot3	uc002ioj.3	Q96H20	OTTHUMG00000160569	ENST00000502492.1:c.33C>A	chr17.hg19:g.47022064G>T		58.0	0.0		41.0	4.0	NM_007241	Q8IXY3|Q9UN50	Silent	SNP	ENST00000502492.1	hg19	CCDS11541.1																																																																																			.	.		0.711	SNF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000361172.1	NM_007241		T	47022064	G	T	47022064	2	4	260	1	0	0	0	0	0	0	0	1	14861	1048	37	1		1	SNF8	17	47022064	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	1128045	47022064	34173146	760	38005										
TOB1	10140	hgsc.bcm.edu	37	chr17	48941375	48941375	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgctacttggatttcaagctGcatagctgctacgccacaaa	8	11	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:48941375G>A	ENST00000268957.3	-	3	432	c.4C>T	c.(4-6)Cag>Tag	p.Q2*	TOB1_ENST00000499247.2_Nonsense_Mutation_p.Q2*|TOB1_ENST00000509385.1_Intron|TOB1-AS1_ENST00000523470.1_RNA|TOB1-AS1_ENST00000416263.3_RNA	NM_001243877.1	NP_001230806.1	P50616	TOB1_HUMAN	transducer of ERBB2, 1	2					negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell proliferation (GO:0008285)|negative regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060212)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of translation (GO:0017148)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of signal transduction (GO:0009967)|SMAD protein import into nucleus (GO:0007184)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	receptor tyrosine kinase binding (GO:0030971)|SH3/SH2 adaptor activity (GO:0005070)|transcription corepressor activity (GO:0003714)			breast(1)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13			BRCA - Breast invasive adenocarcinoma(22;1.09e-08)			ATTTCAAGCTGCATAGCTGCT	0.338																																					p.Q2X	NSCLC(144;643 1919 24513 29423 40686)	Atlas-SNP	.											.	TOB1	40	.	0			c.C4T						.						31	32	32					17																	48941375		2184	4293	6477	SO:0001587	stop_gained	10140	exon2			CAAGCTGCATAGC	D38305	CCDS11576.1	17q21.33	2012-08-14			ENSG00000141232	ENSG00000141232			11979	protein-coding gene	gene with protein product		605523		TROB1		8632892, 17785442	Standard	NM_005749		Approved	TOB, TROB	uc002isw.3	P50616	OTTHUMG00000162277	ENST00000268957.3:c.4C>T	chr17.hg19:g.48941375G>A	ENSP00000268957:p.Gln2*	68.0	0.0		45.0	4.0	NM_005749	B2R9T0|D3DTY3|Q4KMQ0	Nonsense_Mutation	SNP	ENST00000268957.3	hg19	CCDS11576.1	.	.	.	.	.	.	.	.	.	.	G	37	5.991335	0.97179	.	.	ENSG00000141232	ENST00000499247;ENST00000268957	.	.	.	5.76	4.79	0.61399	.	0.054585	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.22109	T	0.4	.	16.1971	0.82040	0.0:0.0:0.8658:0.1342	.	.	.	.	X	2	.	ENSP00000268957:Q2X	Q	-	1	0	TOB1	46296374	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.476000	0.97823	1.405000	0.46838	-0.182000	0.12963	CAG	.	.		0.338	TOB1-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000368364.1			A	48941375	G	A	48941375	4	1	260	1	0	0	0	0	0	1	0	0	16362	1328	46	3	1037	3	TOB1	17	48941375	Nonsense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	1919311	48941375	32253835	761	38006										
ERN1	2081	hgsc.bcm.edu	37	chr17	62132159	62132159	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cttgggacagaaggaaatttTcccaactatcaccacgctgg	9	11	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:62132159T>C	ENST00000433197.3	-	14	1797	c.1702A>G	c.(1702-1704)Aaa>Gaa	p.K568E		NM_001433.3	NP_001424.3			endoplasmic reticulum to nucleus signaling 1											central_nervous_system(4)|kidney(1)|lung(2)|ovary(1)|stomach(1)	9						AAGGAAATTTTCCCAACTATC	0.488																																					p.K568E		Atlas-SNP	.											ERN1_ENST00000433197,NS,carcinoma,0,2	ERN1	102	.	0			c.A1702G						.						52	54	53					17																	62132159		2009	4174	6183	SO:0001583	missense	2081	exon14			AAATTTTCCCAAC	AF059198	CCDS45762.1	17q23	2011-08-12	2007-08-14			ENSG00000178607			3449	protein-coding gene	gene with protein product	"inositol-requiring enzyme 1"	604033	"ER to nucleus signalling 1"			9637683	Standard	NM_001433		Approved	IRE1, IRE1P	uc002jdz.2	O75460		ENST00000433197.3:c.1702A>G	chr17.hg19:g.62132159T>C	ENSP00000401445:p.Lys568Glu	72.0	0.0		44.0	3.0	NM_001433		Missense_Mutation	SNP	ENST00000433197.3	hg19	CCDS45762.1	.	.	.	.	.	.	.	.	.	.	T	14.65	2.598332	0.46318	.	.	ENSG00000178607	ENST00000433197	T	0.61040	0.14	4.36	3.28	0.37604	Protein kinase-like domain (1);	0.155618	0.56097	N	0.000027	T	0.35595	0.0937	N	0.08118	0	0.48975	D	0.999731	B	0.15719	0.014	B	0.12837	0.008	T	0.14896	-1.0456	10	0.56958	D	0.05	-17.6224	10.1931	0.43039	0.0:0.0806:0.0:0.9194	.	568	O75460	ERN1_HUMAN	E	568	ENSP00000401445:K568E	ENSP00000401445:K568E	K	-	1	0	ERN1	59485891	1.000000	0.71417	0.923000	0.36655	0.624000	0.37722	7.651000	0.83577	0.784000	0.33661	0.533000	0.62120	AAA	.	.		0.488	ERN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443734.2	NM_001433		C	62132159	T	C	62132159	3	2	260	1	0	0	0	0	1	0	0	0	5239	1792	62	2	1267	2	ERN1	17	62132159	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	13190784	62132159	19063051	762	38007										
AXIN2	8313	hgsc.bcm.edu	37	chr17	63534322	63534322	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aaggcctaggccgcattaccTctcggatctgctgcaggcgc	12	14	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:63534322T>C	ENST00000375702.5	-	4	1307	c.1199A>G	c.(1198-1200)gAg>gGg	p.E400G	CTD-2535L24.2_ENST00000577662.1_3'UTR|AXIN2_ENST00000307078.5_Splice_Site_p.E400G			Q9Y2T1	AXIN2_HUMAN	axin 2	400	Interaction with GSK3B. {ECO:0000250}.				bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to organic cyclic compound (GO:0071407)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|dorsal/ventral axis specification (GO:0009950)|intramembranous ossification (GO:0001957)|maintenance of DNA repeat elements (GO:0043570)|mRNA stabilization (GO:0048255)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell proliferation (GO:0008285)|negative regulation of osteoblast differentiation (GO:0045668)|odontogenesis (GO:0042476)|positive regulation of cell death (GO:0010942)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein phosphorylation (GO:0001934)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of chondrocyte development (GO:0061181)|regulation of mismatch repair (GO:0032423)|secondary heart field specification (GO:0003139)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)			NS(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	34						CCGCATTACCTCTCGGATCTG	0.617									Oligodontia, Ectodermal Dysplasia and Colorectal Polyp syndrome																												p.E400G		Atlas-SNP	.											.	AXIN2	92	.	0			c.A1199G						.						69	56	60					17																	63534322		2203	4300	6503	SO:0001630	splice_region_variant	8313	exon5	Familial Cancer Database	Oligodontia-Colorectal Cancer syndrome, Tooth Agenesis-Colorectal Cancer Syndrome	ATTACCTCTCGGA	AF078165	CCDS11662.1	17q24.1	2014-09-17	2008-08-01		ENSG00000168646				904	protein-coding gene	gene with protein product	"conductin", "axil"	604025				10049590	Standard	NM_004655		Approved	MGC126582, DKFZp781B0869	uc002jfi.3	Q9Y2T1	OTTHUMG00000179353	ENST00000375702.5:c.1200+1A>G	chr17.hg19:g.63534322T>C		132.0	0.0		99.0	4.0	NM_004655	Q3MJ88|Q9H3M6|Q9UH84	Missense_Mutation	SNP	ENST00000375702.5	hg19		.	.	.	.	.	.	.	.	.	.	T	12.11	1.838963	0.32513	.	.	ENSG00000168646	ENST00000307078;ENST00000375702	D;D	0.84298	-1.83;-1.83	4.68	4.68	0.58851	.	0.161055	0.53938	D	0.000043	T	0.69557	0.3124	N	0.08118	0	0.51482	D	0.999929	B;B;P	0.39665	0.008;0.228;0.682	B;B;B	0.35550	0.005;0.098;0.205	T	0.71189	-0.4666	10	0.25106	T	0.35	-23.052	14.2791	0.66199	0.0:0.0:0.0:1.0	.	400;400;400	B7ZKL5;Q9Y2T1;E7ES00	.;AXIN2_HUMAN;.	G	400	ENSP00000302625:E400G;ENSP00000364854:E400G	ENSP00000302625:E400G	E	-	2	0	AXIN2	60964784	1.000000	0.71417	1.000000	0.80357	0.773000	0.43773	3.710000	0.54860	1.962000	0.57031	0.454000	0.30748	GAG	.	.		0.617	AXIN2-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000445901.1	NM_004655	Missense_Mutation	C	63534322	T	C	63534322	5	2	260	1	0	0	0	0	0	0	1	0	1237	1565	54	2	1360	2	AXIN2	17	63534322	Splice_Site	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1402163	63534322	17660888	763	38008										
BPTF	2186	hgsc.bcm.edu	37	chr17	65850816	65850816	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aataaaccatatattcgacaTgaacctattggatatgatag	6	6	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:65850816T>C	ENST00000321892.4	+	2	1435	c.1374T>C	c.(1372-1374)caT>caC	p.H458H	BPTF_ENST00000306378.6_Silent_p.H458H|BPTF_ENST00000335221.5_Silent_p.H458H|BPTF_ENST00000424123.3_Silent_p.H319H			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	458					anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			ATATTCGACATGAACCTATTG	0.388																																					p.H458H		Atlas-SNP	.											.	BPTF	415	.	0			c.T1374C						.						87	79	81					17																	65850816		2203	4300	6503	SO:0001819	synonymous_variant	2186	exon2			TCGACATGAACCT	AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"Zinc fingers, PHD-type"	3581	protein-coding gene	gene with protein product		601819	"fetal Alzheimer antigen"	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.1374T>C	chr17.hg19:g.65850816T>C		134.0	0.0		94.0	4.0	NM_004459	Q6NX67|Q7Z7D6|Q9UIG2	Silent	SNP	ENST00000321892.4	hg19																																																																																				.	.		0.388	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459		C	65850816	T	C	65850816	2	2	260	1	0	0	0	0	0	0	0	1	1497	1461	51	2		2	BPTF	17	65850816	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	2316494	65850816	15344394	764	38009										
BPTF	2186	hgsc.bcm.edu	37	chr17	65942113	65942113	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acaaatacagcagccacagcCccaagtcattgctgtgcctc	7	15	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:65942113C>T	ENST00000321892.4	+	23	7728	c.7667C>T	c.(7666-7668)cCc>cTc	p.P2556L	BPTF_ENST00000306378.6_Missense_Mutation_p.P2430L|BPTF_ENST00000335221.5_Intron|BPTF_ENST00000424123.3_Intron			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	2556					anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			CAGCCACAGCCCCAAGTCATT	0.478																																					p.P2430L		Atlas-SNP	.											.	BPTF	415	.	0			c.C7289T						.						117	104	108					17																	65942113		2203	4300	6503	SO:0001583	missense	2186	exon21			CACAGCCCCAAGT	AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"Zinc fingers, PHD-type"	3581	protein-coding gene	gene with protein product		601819	"fetal Alzheimer antigen"	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.7667C>T	chr17.hg19:g.65942113C>T	ENSP00000315454:p.Pro2556Leu	198.0	0.0		149.0	31.0	NM_182641	Q6NX67|Q7Z7D6|Q9UIG2	Missense_Mutation	SNP	ENST00000321892.4	hg19		.	.	.	.	.	.	.	.	.	.	C	16.26	3.074271	0.55646	.	.	ENSG00000171634	ENST00000306378;ENST00000321892	T;T	0.63417	-0.04;2.02	6.1	6.1	0.99115	.	.	.	.	.	T	0.54062	0.1835	L	0.34521	1.04	0.80722	D	1	P	0.38078	0.617	B	0.33960	0.173	T	0.52215	-0.8605	9	0.38643	T	0.18	-8.4007	20.7146	0.99709	0.0:1.0:0.0:0.0	.	2430	Q12830-2	.	L	2430;2556	ENSP00000307208:P2430L;ENSP00000315454:P2556L	ENSP00000307208:P2430L	P	+	2	0	BPTF	63372575	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.492000	0.60334	2.902000	0.99343	0.650000	0.86243	CCC	.	.		0.478	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459		T	65942113	C	T	65942113	3	4	260	1	0	0	0	0	1	0	0	0	1497	623	22	3	7757	3	BPTF	17	65942113	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	91297	65942113	15253097	765	38010										
ABCA6	23460	hgsc.bcm.edu	37	chr17	67111077	67111077	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttattatagatggtaactgaTcctaagaatagaagttaaaa	7	3	0	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:67111077T>C	ENST00000284425.2	-	13	1782	c.1608A>G	c.(1606-1608)ggA>ggG	p.G536G		NM_080284.2	NP_525023.2	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 6	536	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(6)|endometrium(5)|kidney(17)|large_intestine(18)|lung(20)|ovary(3)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	82	Breast(10;5.65e-12)					TGGTAACTGATCCTAAGAATA	0.294																																					p.G536G		Atlas-SNP	.											.	ABCA6	210	.	0			c.A1608G						.						46	45	45					17																	67111077		2203	4300	6503	SO:0001630	splice_region_variant	23460	exon13			AACTGATCCTAAG	U66680	CCDS11683.1	17q21	2012-03-14			ENSG00000154262	ENSG00000154262		"ATP binding cassette transporters / subfamily A"	36	protein-coding gene	gene with protein product		612504				8894702	Standard	NM_080284		Approved	EST155051	uc002jhw.1	Q8N139		ENST00000284425.2:c.1607-1A>G	chr17.hg19:g.67111077T>C		52.0	0.0		46.0	5.0	NM_080284	Q6NSH9|Q8N856|Q8WWZ6	Silent	SNP	ENST00000284425.2	hg19	CCDS11683.1																																																																																			.	.		0.294	ABCA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450463.1	NM_080284	Silent	C	67111077	T	C	67111077	5	2	260	1	0	0	0	0	0	0	1	0	36	1449	50	2	3353	2	ABCA6	17	67111077	Splice_Site	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1168964	67111077	14084133	766	38011										
TMEM104	54868	hgsc.bcm.edu	37	chr17	72784959	72784959	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccacctttgtgatagaggccAtggctgcagccaacgcgcag	12	13	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:72784959A>G	ENST00000335464.5	+	4	361	c.199A>G	c.(199-201)Atg>Gtg	p.M67V	TMEM104_ENST00000417024.2_Missense_Mutation_p.M80V|TMEM104_ENST00000582773.1_Missense_Mutation_p.M67V|TMEM104_ENST00000582330.1_Missense_Mutation_p.M67V	NM_017728.3	NP_060198.3	Q8NE00	TM104_HUMAN	transmembrane protein 104	67						integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(5)|ovary(1)	19	all_lung(278;0.23)					GATAGAGGCCATGGCTGCAGC	0.602																																					p.M67V		Atlas-SNP	.											.	TMEM104	49	.	0			c.A199G						.						80	66	71					17																	72784959		2203	4300	6503	SO:0001583	missense	54868	exon4			GAGGCCATGGCTG	AK074029	CCDS32723.1	17q25.1	2005-12-19				ENSG00000109066			25984	protein-coding gene	gene with protein product							Standard	NM_017728		Approved	FLJ20255, FLJ00021	uc002jls.4	Q8NE00		ENST00000335464.5:c.199A>G	chr17.hg19:g.72784959A>G	ENSP00000334849:p.Met67Val	48.0	0.0		42.0	4.0	NM_017728	Q8TEU1|Q9NT56|Q9NXH1	Missense_Mutation	SNP	ENST00000335464.5	hg19	CCDS32723.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.712411	0.89112	.	.	ENSG00000109066	ENST00000335464;ENST00000417024	T;T	0.52754	1.32;0.65	4.55	4.55	0.56014	.	0.000000	0.85682	D	0.000000	T	0.65428	0.2690	M	0.78049	2.395	0.80722	D	1	D;D;D	0.63046	0.962;0.988;0.992	P;P;P	0.60117	0.843;0.793;0.869	T	0.71210	-0.4660	10	0.66056	D	0.02	-41.044	14.2094	0.65755	1.0:0.0:0.0:0.0	.	80;67;67	B4DKL7;Q8NE00-2;Q8NE00	.;.;TM104_HUMAN	V	67;80	ENSP00000334849:M67V;ENSP00000397676:M80V	ENSP00000334849:M67V	M	+	1	0	TMEM104	70296554	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	8.928000	0.92853	1.816000	0.52996	0.459000	0.35465	ATG	.	.		0.602	TMEM104-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444442.1	NM_017728		G	72784959	A	G	72784959	3	3	260	1	0	0	0	0	1	0	0	0	16033	217	8	2	209	2	TMEM104	17	72784959	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	5673882	72784959	8410251	767	38012										
SLC25A19	60386	hgsc.bcm.edu	37	chr17	73279599	73279599	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agccaggccaccacatacaaAgtgcactgagaattcccggg	10	13	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:73279599A>G	ENST00000402418.3	-	3	1273	c.364T>C	c.(364-366)Ttt>Ctt	p.F122L	SLC25A19_ENST00000580994.1_Missense_Mutation_p.F122L|SLC25A19_ENST00000320362.3_Missense_Mutation_p.F122L|SLC25A19_ENST00000442286.2_Missense_Mutation_p.F122L|SLC25A19_ENST00000375261.4_Intron|SLC25A19_ENST00000416858.2_Missense_Mutation_p.F122L			Q9HC21	TPC_HUMAN	solute carrier family 25 (mitochondrial thiamine pyrophosphate carrier), member 19	122					deoxynucleotide transport (GO:0030302)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	deoxynucleotide transmembrane transporter activity (GO:0030233)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	9	all_cancers(13;5.98e-08)|all_epithelial(9;1.16e-08)|Breast(9;3.1e-08)		all cancers(21;6.82e-07)|Epithelial(20;6.86e-06)			CCACATACAAAGTGCACTGAG	0.562																																					p.F122L		Atlas-SNP	.											.	SLC25A19	25	.	0			c.T364C						.						55	44	48					17																	73279599		2203	4300	6503	SO:0001583	missense	60386	exon4			ATACAAAGTGCAC		CCDS11720.1	17q25.1	2013-05-22	2007-03-08		ENSG00000125454	ENSG00000125454		"Solute carriers"	14409	protein-coding gene	gene with protein product		606521	"solute carrier family 25 (mitochondrial deoxynucleotide carrier), member 19", "microcephaly, Amish"	MCPHA		11474176, 11226231, 19798730	Standard	NM_021734		Approved	DNC, MUP1, TPC	uc002jnw.4	Q9HC21		ENST00000402418.3:c.364T>C	chr17.hg19:g.73279599A>G	ENSP00000385312:p.Phe122Leu	105.0	0.0		80.0	4.0	NM_001126122	E9PF74|Q6V9R7	Missense_Mutation	SNP	ENST00000402418.3	hg19	CCDS11720.1	.	.	.	.	.	.	.	.	.	.	A	10.40	1.339462	0.24339	.	.	ENSG00000125454	ENST00000416858;ENST00000442286;ENST00000320362;ENST00000402418	T;T;T;T	0.75821	-0.97;-0.97;-0.97;-0.97	5.2	5.2	0.72013	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	T	0.70413	0.3221	L	0.43554	1.36	0.80722	D	1	D	0.56287	0.975	P	0.50825	0.651	T	0.66232	-0.5975	10	0.14252	T	0.57	-19.8534	10.3055	0.43678	0.9205:0.0:0.0795:0.0	.	122	Q9HC21	TPC_HUMAN	L	122	ENSP00000397818:F122L;ENSP00000402202:F122L;ENSP00000319574:F122L;ENSP00000385312:F122L	ENSP00000319574:F122L	F	-	1	0	SLC25A19	70791194	1.000000	0.71417	0.829000	0.32907	0.032000	0.12392	7.126000	0.77201	1.958000	0.56883	0.448000	0.29417	TTT	.	.		0.562	SLC25A19-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447282.1	NM_021734		G	73279599	A	G	73279599	3	3	260	1	0	0	0	0	1	0	0	0	14496	72	3	2	614	2	SLC25A19	17	73279599	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	494640	73279599	7915611	768	38013										
FBF1	85302	hgsc.bcm.edu	37	chr17	73926112	73926112	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gcagagcctgtgggtctgccTctgagatacctgaaacctaa	11	11	2	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:73926112T>C	ENST00000586717.1	-	6	476	c.203A>G	c.(202-204)gAg>gGg	p.E68G	FBF1_ENST00000319129.5_Missense_Mutation_p.E68G|FBF1_ENST00000389570.4_Missense_Mutation_p.E68G			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	68					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	4						TGGGTCTGCCTCTGAGATACC	0.522																																					p.E68G		Atlas-SNP	.											.	FBF1	48	.	0			c.A203G						.						28	26	27					17																	73926112		1933	4110	6043	SO:0001583	missense	85302	exon6			TCTGCCTCTGAGA	AK074045	CCDS45779.1	17q25.3	2011-04-21			ENSG00000188878	ENSG00000188878			24674	protein-coding gene	gene with protein product	"albatross"					11347906	Standard	NM_001080542		Approved	FLJ00103, FBF-1, KIAA1863, ALB	uc002jqc.3	Q8TES7		ENST00000586717.1:c.203A>G	chr17.hg19:g.73926112T>C	ENSP00000465132:p.Glu68Gly	58.0	0.0		40.0	4.0	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000586717.1	hg19		.	.	.	.	.	.	.	.	.	.	T	14.79	2.641295	0.47153	.	.	ENSG00000188878	ENST00000337792;ENST00000389570;ENST00000319129;ENST00000427433	T;T	0.21191	2.02;2.02	4.97	4.97	0.65823	.	.	.	.	.	T	0.20210	0.0486	L	0.29908	0.895	0.23991	N	0.99624	P;P;P	0.46142	0.763;0.804;0.873	B;B;B	0.42625	0.167;0.393;0.298	T	0.08889	-1.0700	9	0.87932	D	0	-1.8461	14.318	0.66465	0.0:0.0:0.0:1.0	.	82;68;68	Q8TES7-6;Q8TES7;A6NLR5	.;FBF1_HUMAN;.	G	68;68;68;81	ENSP00000374221:E68G;ENSP00000324292:E68G	ENSP00000324292:E68G	E	-	2	0	FBF1	71437707	0.998000	0.40836	0.044000	0.18714	0.571000	0.35966	5.511000	0.67024	1.850000	0.53721	0.533000	0.62120	GAG	.	.		0.522	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542		C	73926112	T	C	73926112	3	2	260	1	0	0	0	0	1	0	0	0	5703	1551	54	2	3294	2	FBF1	17	73926112	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	646513	73926112	7269098	769	38014										
EVPL	2125	hgsc.bcm.edu	37	chr17	74014678	74014678	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccgctcaccctgcagcagctGcacctgggggcacagaaagg	13	15	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:74014678G>T	ENST00000301607.3	-	12	1541	c.1288C>A	c.(1288-1290)Cag>Aag	p.Q430K	EVPL_ENST00000586740.1_Missense_Mutation_p.Q430K	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	430	Globular 1.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						TGCAGCAGCTGCACCTGGGGG	0.672																																					p.Q430K		Atlas-SNP	.											.	EVPL	155	.	0			c.C1288A						.						18	21	20					17																	74014678		2201	4293	6494	SO:0001583	missense	2125	exon12			GCAGCTGCACCTG	U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.1288C>A	chr17.hg19:g.74014678G>T	ENSP00000301607:p.Gln430Lys	199.0	0.0		140.0	41.0	NM_001988	A0AUV5	Missense_Mutation	SNP	ENST00000301607.3	hg19	CCDS11737.1	.	.	.	.	.	.	.	.	.	.	G	14.32	2.498783	0.44455	.	.	ENSG00000167880	ENST00000301607	T	0.75938	-0.98	5.12	5.12	0.69794	.	0.133205	0.53938	D	0.000050	T	0.78553	0.4301	M	0.66939	2.045	0.36532	D	0.870778	P;P	0.52842	0.836;0.956	B;P	0.47528	0.346;0.549	D	0.83484	0.0066	10	0.48119	T	0.1	-45.9129	18.9474	0.92627	0.0:0.0:1.0:0.0	.	430;430	B7ZLH8;Q92817	.;EVPL_HUMAN	K	430	ENSP00000301607:Q430K	ENSP00000301607:Q430K	Q	-	1	0	EVPL	71526273	1.000000	0.71417	1.000000	0.80357	0.686000	0.39977	6.470000	0.73558	2.573000	0.86826	0.561000	0.74099	CAG	.	.		0.672	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988		T	74014678	G	T	74014678	3	4	260	1	0	0	0	0	1	0	0	0	5294	1328	46	3	4857	3	EVPL	17	74014678	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	88566	74014678	7180532	770	38015										
MGAT5B	146664	hgsc.bcm.edu	37	chr17	74898718	74898718	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	atcgctgtgaaggtggaccaGatcctgcgccacagtctgct	12	12	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:74898718G>T	ENST00000569840.2	+	4	985	c.411G>T	c.(409-411)caG>caT	p.Q137H	MGAT5B_ENST00000428789.2_Missense_Mutation_p.Q148H|MGAT5B_ENST00000374998.3_3'UTR|MGAT5B_ENST00000301618.4_Missense_Mutation_p.Q137H	NM_001199172.1	NP_001186101.1	Q3V5L5	MGT5B_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B	137					protein N-linked glycosylation (GO:0006487)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(15)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						AGGTGGACCAGATCCTGCGCC	0.647																																					p.Q148H		Atlas-SNP	.											.	MGAT5B	98	.	0			c.G444T						.						26	22	24					17																	74898718		2201	4300	6501	SO:0001583	missense	146664	exon3			GGACCAGATCCTG	AB109185	CCDS11751.1, CCDS45788.1, CCDS59299.1	17q25.3	2013-02-25	2005-11-16		ENSG00000167889	ENSG00000167889		"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	24140	protein-coding gene	gene with protein product		612441	"mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isoenzyme B"			14617637, 14623122	Standard	NM_001199172		Approved	GnT-IX, FLJ25132, GnT-VB	uc002jth.3	Q3V5L5	OTTHUMG00000177278	ENST00000569840.2:c.411G>T	chr17.hg19:g.74898718G>T	ENSP00000456037:p.Gln137His	207.0	0.0		117.0	23.0	NM_198955	Q6P3S8|Q6P6B3|Q766X5|Q76D04|Q96LS2	Missense_Mutation	SNP	ENST00000569840.2	hg19	CCDS59299.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.049578	0.75846	.	.	ENSG00000167889	ENST00000374998;ENST00000301618;ENST00000428789	T;T	0.52295	0.68;0.67	5.55	3.21	0.36854	.	0.000000	0.85682	D	0.000000	T	0.61388	0.2343	L	0.53249	1.67	0.47737	D	0.999508	D;D	0.76494	0.999;0.999	D;D	0.85130	0.997;0.997	T	0.63866	-0.6540	10	0.59425	D	0.04	-29.5481	12.2441	0.54560	0.1644:0.0:0.8356:0.0	.	148;137	Q3V5L5-2;Q3V5L5-5	.;.	H	137;137;148	ENSP00000301618:Q137H;ENSP00000391227:Q148H	ENSP00000301618:Q137H	Q	+	3	2	MGAT5B	72410313	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.444000	0.73452	1.337000	0.45525	0.655000	0.94253	CAG	.	.		0.647	MGAT5B-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460624.2	NM_144677		T	74898718	G	T	74898718	3	4	260	1	0	0	0	0	1	0	0	0	9558	933	33	3	526	3	MGAT5B	17	74898718	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	884040	74898718	6296492	771	38016										
MGAT5B	146664	hgsc.bcm.edu	37	chr17	74944796	74944796	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gttcgcccagcctggccaggAgtgctacctgcagaaggagc	14	13	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:74944796A>G	ENST00000569840.2	+	18	2829	c.2255A>G	c.(2254-2256)gAg>gGg	p.E752G	RP11-87G24.3_ENST00000564292.1_RNA|MGAT5B_ENST00000428789.2_Missense_Mutation_p.E761G|MGAT5B_ENST00000301618.4_Missense_Mutation_p.E750G	NM_001199172.1	NP_001186101.1	Q3V5L5	MGT5B_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B	752					protein N-linked glycosylation (GO:0006487)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(15)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CCTGGCCAGGAGTGCTACCTG	0.667																																					p.E761G		Atlas-SNP	.											.	MGAT5B	98	.	0			c.A2282G						.						44	42	43					17																	74944796		2203	4300	6503	SO:0001583	missense	146664	exon16			GCCAGGAGTGCTA	AB109185	CCDS11751.1, CCDS45788.1, CCDS59299.1	17q25.3	2013-02-25	2005-11-16		ENSG00000167889	ENSG00000167889		"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	24140	protein-coding gene	gene with protein product		612441	"mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isoenzyme B"			14617637, 14623122	Standard	NM_001199172		Approved	GnT-IX, FLJ25132, GnT-VB	uc002jth.3	Q3V5L5	OTTHUMG00000177278	ENST00000569840.2:c.2255A>G	chr17.hg19:g.74944796A>G	ENSP00000456037:p.Glu752Gly	147.0	0.0		107.0	5.0	NM_198955	Q6P3S8|Q6P6B3|Q766X5|Q76D04|Q96LS2	Missense_Mutation	SNP	ENST00000569840.2	hg19	CCDS59299.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.727511	0.89390	.	.	ENSG00000167889	ENST00000301618;ENST00000428789	T;T	0.48522	0.81;0.81	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.62913	0.2467	L	0.59436	1.845	0.80722	D	1	D;D;D	0.89917	1.0;0.998;0.998	D;D;D	0.85130	0.997;0.91;0.91	T	0.59461	-0.7450	10	0.25106	T	0.35	-34.2044	14.1613	0.65448	1.0:0.0:0.0:0.0	.	157;761;750	Q3V5L5-4;Q3V5L5-2;Q3V5L5-5	.;.;.	G	750;761	ENSP00000301618:E750G;ENSP00000391227:E761G	ENSP00000301618:E750G	E	+	2	0	MGAT5B	72456391	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.309000	0.78937	1.942000	0.56320	0.379000	0.24179	GAG	.	.		0.667	MGAT5B-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460624.2	NM_144677		G	74944796	A	G	74944796	3	3	260	1	0	0	0	0	1	0	0	0	9558	304	11	2	2416	2	MGAT5B	17	74944796	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	46078	74944796	6250414	772	38017										
SEPT9	10801	hgsc.bcm.edu	37	chr17	75471676	75471676	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gctggccccagggtctggatTcaggggagcctgcagaggga	18	10	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:75471676T>C	ENST00000427177.1	+	4	847				SEPT9_ENST00000592951.1_Intron|SEPT9_ENST00000591198.1_Intron|RP11-75C10.9_ENST00000591110.1_RNA|SEPT9_ENST00000585930.1_Intron|SEPT9_ENST00000423034.2_Intron|SEPT9_ENST00000590917.1_Intron|SEPT9_ENST00000588690.1_Intron|SEPT9_ENST00000427180.1_Missense_Mutation_p.S26P|SEPT9_ENST00000449803.2_Intron|SEPT9_ENST00000590294.1_Intron|SEPT9_ENST00000591088.1_Intron|SEPT9_ENST00000541152.2_Intron|SEPT9_ENST00000592481.1_Intron|SEPT9_ENST00000427674.2_Intron|SEPT9_ENST00000592420.1_Intron|SEPT9_ENST00000431235.2_Intron|SEPT9_ENST00000329047.8_Intron	NM_001113491.1	NP_001106963.1	Q9UHD8	SEPT9_HUMAN	septin 9						cell cycle (GO:0007049)|cell division (GO:0051301)|GTP catabolic process (GO:0006184)|protein heterooligomerization (GO:0051291)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|perinuclear region of cytoplasm (GO:0048471)|stress fiber (GO:0001725)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			autonomic_ganglia(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|prostate(2)	16			BRCA - Breast invasive adenocarcinoma(99;0.153)			GGGTCTGGATTCAGGGGAGCC	0.642																																					p.S26P		Atlas-SNP	.											.	SEPT9	105	.	0			c.T76C						.						22	24	24					17																	75471676		1567	3582	5149	SO:0001627	intron_variant	10801	exon1			CTGGATTCAGGGG	AB023208	CCDS45790.1, CCDS45791.1, CCDS45792.1, CCDS45793.1, CCDS45794.1, CCDS45795.1, CCDS74166.1	17q25.3	2014-09-17	2005-01-11	2005-01-12	ENSG00000184640	ENSG00000184640		"Septins"	7323	protein-coding gene	gene with protein product	"Ov/Br septin"	604061	"MLL septin-like fusion"	MSF		10339604, 10485469	Standard	NM_006640		Approved	MSF1, KIAA0991, PNUTL4, AF17q25, SeptD1	uc002jts.4	Q9UHD8		ENST00000427177.1:c.722-6550T>C	chr17.hg19:g.75471676T>C		153.0	0.0		81.0	4.0	NM_001113495	A8K2V3|B3KPM0|B4DTL9|B4E0N2|B4E274|B7Z654|Q96QF3|Q96QF4|Q96QF5|Q9HA04|Q9UG40|Q9Y5W4	Missense_Mutation	SNP	ENST00000427177.1	hg19	CCDS45790.1	.	.	.	.	.	.	.	.	.	.	T	10.18	1.278473	0.23307	.	.	ENSG00000184640	ENST00000427180	T	0.52983	0.64	1.48	1.48	0.22813	.	.	.	.	.	T	0.27900	0.0687	.	.	.	0.19775	N	0.999958	P	0.44309	0.832	B	0.29440	0.102	T	0.18209	-1.0344	8	0.87932	D	0	.	6.6406	0.22906	0.0:0.0:0.0:1.0	.	26	Q9UHD8-8	.	P	26	ENSP00000415624:S26P	ENSP00000415624:S26P	S	+	1	0	SEPT9	72983271	0.000000	0.05858	0.002000	0.10522	0.017000	0.09413	-0.192000	0.09587	0.939000	0.37446	0.368000	0.22195	TCA	.	.		0.642	SEPT9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000436304.2	NM_006640		C	75471676	T	C	75471676	1	2	260	0	1	0	0	0	0	0	0	0	14086	1783	62	2		2	SEPT9	17	75471676	Intron	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	526880	75471676	5723534	773	38018										
DNAH17	8632	hgsc.bcm.edu	37	chr17	76450568	76450568	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acacctcttctgtcccaggcGgatggctttcagttcactcc	8	15	4	0	rs371338775		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:76450568G>T	ENST00000585328.1	-	64	10499	c.10375C>A	c.(10375-10377)Cgc>Agc	p.R3459S	DNAH17_ENST00000389840.5_Missense_Mutation_p.R3450S|DNAH17_ENST00000586052.1_5'UTR	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	3450	AAA 5. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			TGTCCCAGGCGGATGGCTTTC	0.577																																					p.R3464S		Atlas-SNP	.											.	DNAH17	347	.	0			c.C10390A						.						114	85	95					17																	76450568		2203	4300	6503	SO:0001583	missense	8632	exon64			CCAGGCGGATGGC	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"Axonemal dyneins"	2946	protein-coding gene	gene with protein product		610063	"dynein, axonemal, heavy polypeptide 17", "dynein, axonemal, heavy chain like 1", "dynein, axonemal, heavy like 1"	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.10375C>A	chr17.hg19:g.76450568G>T	ENSP00000465516:p.Arg3459Ser	150.0	0.0		101.0	5.0	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Missense_Mutation	SNP	ENST00000585328.1	hg19		.	.	.	.	.	.	.	.	.	.	G	19.32	3.805501	0.70682	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.26067	1.76	5.11	5.11	0.69529	.	0.099873	0.44688	D	0.000427	T	0.31263	0.0791	L	0.40543	1.245	0.33747	D	0.620105	P	0.47604	0.898	P	0.51742	0.678	T	0.34329	-0.9833	10	0.28530	T	0.3	.	13.4947	0.61419	0.0:0.0:0.8437:0.1563	.	3459	E7EUM8	.	S	3459;3450	ENSP00000374490:R3450S	ENSP00000300671:R3459S	R	-	1	0	DNAH17	73962163	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.466000	0.53071	2.343000	0.79666	0.650000	0.86243	CGC	.	.		0.577	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		T	76450568	G	T	76450568	3	4	260	1	0	0	0	0	1	0	0	0	4603	1116	39	1	3070	1	DNAH17	17	76450568	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	978892	76450568	4744642	774	38019										
CYTH1	9267	hgsc.bcm.edu	37	chr17	76695035	76695035	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acatgatgatggcaaaggagAggacgtaacaagtatctaaa	11	5	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:76695035A>G	ENST00000446868.3	-	8	636	c.566T>C	c.(565-567)cTc>cCc	p.L189P	CYTH1_ENST00000585509.1_Missense_Mutation_p.L130P|RNU6-638P_ENST00000516582.1_RNA|CYTH1_ENST00000589297.1_Missense_Mutation_p.L130P|CYTH1_ENST00000361101.4_Missense_Mutation_p.L189P|CYTH1_ENST00000591455.1_Missense_Mutation_p.L189P|CYTH1_ENST00000589296.1_Intron			Q15438	CYH1_HUMAN	cytohesin 1	189	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				establishment of epithelial cell polarity (GO:0090162)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|regulation of cell adhesion (GO:0030155)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|lipid binding (GO:0008289)			endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	19						GGCAAAGGAGAGGACGTAACA	0.473																																					p.L189P		Atlas-SNP	.											.	CYTH1	36	.	0			c.T566C						.						210	204	206					17																	76695035		2203	4300	6503	SO:0001583	missense	9267	exon8			AAGGAGAGGACGT	M85169	CCDS32754.1, CCDS42392.2	17q25	2014-05-02	2008-08-14	2008-08-14	ENSG00000108669	ENSG00000108669		"Pleckstrin homology (PH) domain containing"	9501	protein-coding gene	gene with protein product		182115	"pleckstrin homology, Sec7 and coiled-coil domains 1"	PSCD1		1511013, 8449036, 21628335, 20018626	Standard	XM_006722180		Approved	B2-1, D17S811E, cytohesin-1	uc002jvw.3	Q15438	OTTHUMG00000150253	ENST00000446868.3:c.566T>C	chr17.hg19:g.76695035A>G	ENSP00000389095:p.Leu189Pro	220.0	0.0		157.0	7.0	NM_017456	A6NFW7|B7Z1T4|Q9P123|Q9P124	Missense_Mutation	SNP	ENST00000446868.3	hg19		.	.	.	.	.	.	.	.	.	.	A	22.4	4.288528	0.80914	.	.	ENSG00000108669	ENST00000446868;ENST00000361101;ENST00000539525;ENST00000537048;ENST00000262763;ENST00000392453	T;T	0.55234	0.53;0.53	5.24	5.24	0.73138	SEC7-like, alpha orthogonal bundle (1);SEC7-like (4);	0.000000	0.85682	D	0.000000	D	0.85031	0.5604	H	0.99770	4.765	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.91869	0.5506	10	0.87932	D	0	.	15.1351	0.72558	1.0:0.0:0.0:0.0	.	189;189	Q15438;Q15438-2	CYH1_HUMAN;.	P	189;189;130;130;189;26	ENSP00000389095:L189P;ENSP00000354398:L189P	ENSP00000262763:L189P	L	-	2	0	CYTH1	74206630	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.205000	0.95048	1.958000	0.56883	0.482000	0.46254	CTC	.	.		0.473	CYTH1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317099.1	NM_004762		G	76695035	A	G	76695035	3	3	260	1	0	0	0	0	1	0	0	0	4205	304	11	2	654	2	CYTH1	17	76695035	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	244467	76695035	4500175	775	38020										
USP36	57602	hgsc.bcm.edu	37	chr17	76799931	76799931	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcgttgacctgaggcagcgcCgtcgagatggaggagcagct	16	10	0	3	rs577284191	byFrequency	TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:76799931C>A	ENST00000542802.3	-	16	2789	c.2346G>T	c.(2344-2346)acG>acT	p.T782T	USP36_ENST00000312010.6_Silent_p.T782T|USP36_ENST00000449938.2_Intron			Q9P275	UBP36_HUMAN	ubiquitin specific peptidase 36	782					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	34			BRCA - Breast invasive adenocarcinoma(99;0.000842)|OV - Ovarian serous cystadenocarcinoma(97;0.151)			GAGGCAGCGCCGTCGAGATGG	0.637																																					p.T782T		Atlas-SNP	.											.	USP36	243	.	0			c.G2346T						.						37	41	40					17																	76799931		2177	4243	6420	SO:0001819	synonymous_variant	57602	exon16			CAGCGCCGTCGAG	AB040886	CCDS32755.1	17q25.3	2008-02-05	2005-08-08			ENSG00000055483		"Ubiquitin-specific peptidases"	20062	protein-coding gene	gene with protein product		612543	"ubiquitin specific protease 36"			12838346	Standard	NM_025090		Approved	KIAA1453, FLJ12851	uc002jvz.1	Q9P275		ENST00000542802.3:c.2346G>T	chr17.hg19:g.76799931C>A		107.0	0.0		68.0	19.0	NM_025090	Q05C98|Q05DD0|Q6IQ38|Q8NDM8|Q9NVC8	Silent	SNP	ENST00000542802.3	hg19	CCDS32755.1																																																																																			.	.		0.637	USP36-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437472.3	NM_025090		A	76799931	C	A	76799931	2	1	260	1	0	0	0	0	0	0	0	1	17082	639	23	1		1	USP36	17	76799931	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	104896	76799931	4395279	776	38021										
C1QTNF1	114897	hgsc.bcm.edu	37	chr17	77043987	77043987	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gaggaggaggtggtgatcttGttcgcgcaggtgggcgaccg	20	7	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:77043987G>A	ENST00000339142.2	+	5	1218	c.663G>A	c.(661-663)ttG>ttA	p.L221L	C1QTNF1_ENST00000583904.1_Silent_p.L221L|C1QTNF1_ENST00000580474.1_Silent_p.L221L|C1QTNF1_ENST00000579760.1_Silent_p.L221L|C1QTNF1_ENST00000392445.2_Silent_p.L221L|C1QTNF1_ENST00000582625.1_3'UTR|C1QTNF1_ENST00000581774.1_Silent_p.L221L|C1QTNF1_ENST00000580454.1_Silent_p.L221L|C1QTNF1_ENST00000578229.1_Silent_p.L139L|C1QTNF1_ENST00000311661.4_Silent_p.L139L|C1QTNF1_ENST00000354124.3_Silent_p.L231L	NM_198593.3	NP_940995.1	Q9BXJ1	C1QT1_HUMAN	C1q and tumor necrosis factor related protein 1	221	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				negative regulation of platelet activation (GO:0010544)|negative regulation of platelet aggregation (GO:0090331)|positive regulation of aldosterone secretion (GO:2000860)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase B signaling (GO:0051897)|protein heterotrimerization (GO:0070208)|protein homooligomerization (GO:0051260)|regulation of glucose metabolic process (GO:0010906)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	collagen binding (GO:0005518)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|ovary(2)	14			BRCA - Breast invasive adenocarcinoma(99;0.0294)|OV - Ovarian serous cystadenocarcinoma(97;0.201)			TGGTGATCTTGTTCGCGCAGG	0.592																																					p.L221L		Atlas-SNP	.											.	C1QTNF1	62	.	0			c.G663A						.						160	127	138					17																	77043987		2203	4300	6503	SO:0001819	synonymous_variant	114897	exon4			GATCTTGTTCGCG	AF329840	CCDS11761.1, CCDS11762.1	17q25	2012-07-02			ENSG00000173918	ENSG00000173918			14324	protein-coding gene	gene with protein product	"G protein coupled receptor interacting protein"	610365				12409230	Standard	NM_198593		Approved	CTRP1, ZSIG37, GIP, FLJ90694	uc002jwp.4	Q9BXJ1	OTTHUMG00000177533	ENST00000339142.2:c.663G>A	chr17.hg19:g.77043987G>A		155.0	0.0		95.0	4.0	NM_030968	Q6ZMH6|Q96NF2|Q9GZR4	Silent	SNP	ENST00000339142.2	hg19	CCDS11761.1																																																																																			.	.		0.592	C1QTNF1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437388.2	NM_030968		A	77043987	G	A	77043987	2	1	260	1	0	0	0	0	0	0	0	1	1964	1368	48	3		3	C1QTNF1	17	77043987	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	244056	77043987	4151223	777	38022										
PYCR1	5831	hgsc.bcm.edu	37	chr17	79892251	79892251	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gttgatgagcagggagcggaAgcccccactctccagcacat	12	13	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:79892251A>G	ENST00000329875.8	-	6	812	c.748T>C	c.(748-750)Ttc>Ctc	p.F250L	PYCR1_ENST00000577756.1_Intron|PYCR1_ENST00000402252.2_Missense_Mutation_p.F277L|PYCR1_ENST00000337943.5_Missense_Mutation_p.F250L|PYCR1_ENST00000403172.4_Missense_Mutation_p.F219L|RP11-498C9.13_ENST00000583521.1_RNA	NM_001282280.1|NM_001282281.1|NM_006907.2	NP_001269209.1|NP_001269210.1|NP_008838.2	P32322	P5CR1_HUMAN	pyrroline-5-carboxylate reductase 1	250					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to oxidative stress (GO:0034599)|L-proline biosynthetic process (GO:0055129)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|proline biosynthetic process (GO:0006561)|regulation of mitochondrial membrane potential (GO:0051881)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	identical protein binding (GO:0042802)|pyrroline-5-carboxylate reductase activity (GO:0004735)			endometrium(2)|kidney(1)|lung(1)|prostate(1)	5	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.0165)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)		L-Proline(DB00172)	AGGGAGCGGAAGCCCCCACTC	0.652																																					p.F250L		Atlas-SNP	.											.	PYCR1	44	.	0			c.T748C						.						54	47	49					17																	79892251		2202	4298	6500	SO:0001583	missense	5831	exon6			AGCGGAAGCCCCC		CCDS11794.1, CCDS11795.1, CCDS62365.1, CCDS62366.1	17q25.3	2013-09-23			ENSG00000183010	ENSG00000183010	1.5.1.2		9721	protein-coding gene	gene with protein product		179035				1730675	Standard	XM_005256381		Approved	P5C	uc002kcr.1	P32322	OTTHUMG00000178436	ENST00000329875.8:c.748T>C	chr17.hg19:g.79892251A>G	ENSP00000328858:p.Phe250Leu	127.0	0.0		56.0	4.0	NM_153824	A6NFM2|B4DMU0|Q6FHI4|Q96DI6|Q9HBQ4	Missense_Mutation	SNP	ENST00000329875.8	hg19	CCDS11795.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.01|17.01	3.280060|3.280060	0.59758|0.59758	.|.	.|.	ENSG00000183010|ENSG00000183010	ENST00000337943;ENST00000329875;ENST00000402252;ENST00000405481|ENST00000403172	D;D;D|.	0.82711|.	-1.64;-1.64;-1.64|.	3.47|3.47	3.47|3.47	0.39725|0.39725	6-phosphogluconate dehydrogenase, C-terminal-like (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.46092|0.46092	0.1375|0.1375	N|N	0.26092|0.26092	0.79|0.79	0.58432|0.58432	D|D	0.999996|0.999996	P;D;D;D;D|.	0.89917|.	0.849;0.97;0.97;0.97;1.0|.	B;P;P;P;D|.	0.69307|.	0.318;0.705;0.66;0.66;0.963|.	T|T	0.48103|0.48103	-0.9064|-0.9064	10|6	0.16896|0.66056	T|D	0.51|0.02	.|.	8.7107|8.7107	0.34382|0.34382	0.9041:0.0:0.0959:0.0|0.9041:0.0:0.0959:0.0	.|.	191;277;250;250;250|.	B7Z8T1;B4DMU0;E7D7X9;P32322;A6NFM2|.	.;.;.;P5CR1_HUMAN;.|.	L|P	250;250;277;191|250	ENSP00000336579:F250L;ENSP00000328858:F250L;ENSP00000384949:F277L|.	ENSP00000328858:F250L|ENSP00000385483:L250P	F|L	-|-	1|2	0|0	PYCR1|PYCR1	77485542|77485542	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.906000|0.906000	0.53458|0.53458	7.019000|7.019000	0.76412|0.76412	1.454000|1.454000	0.47793|0.47793	0.459000|0.459000	0.35465|0.35465	TTC|CTT	.	.		0.652	PYCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441953.1			G	79892251	A	G	79892251	3	3	260	1	0	0	0	0	1	0	0	0	12870	72	3	2	307	2	PYCR1	17	79892251	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	2848264	79892251	1302959	778	38023										
FASN	2194	hgsc.bcm.edu	37	chr17	80041462	80041462	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	accgtgcgtagccaagcaccTcacgctggcctgcagcttct	10	16	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:80041462T>C	ENST00000306749.2	-	31	5490	c.5272A>G	c.(5272-5274)Agg>Ggg	p.R1758G	FASN_ENST00000579758.1_5'Flank	NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	1758	Enoyl reductase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	GCCAAGCACCTCACGCTGGCC	0.637																																					p.R1758G	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.A5272G						.						37	36	36					17																	80041462		2193	4293	6486	SO:0001583	missense	2194	exon31			AGCACCTCACGCT	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.5272A>G	chr17.hg19:g.80041462T>C	ENSP00000304592:p.Arg1758Gly	83.0	0.0		64.0	5.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	hg19	CCDS11801.1	.	.	.	.	.	.	.	.	.	.	T	17.46	3.394659	0.62066	.	.	ENSG00000169710	ENST00000306749;ENST00000545909	T	0.04551	3.6	4.57	-0.218	0.13142	Alcohol dehydrogenase, C-terminal (1);Polyketide synthase, enoylreductase (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.17831	0.0428	M	0.72894	2.215	0.58432	D	0.999995	D	0.89917	1.0	D	0.97110	1.0	T	0.00071	-1.2132	10	0.72032	D	0.01	-46.6612	14.3605	0.66768	0.0:0.0:0.7353:0.2647	.	1758	P49327	FAS_HUMAN	G	1758;723	ENSP00000304592:R1758G	ENSP00000304592:R1758G	R	-	1	2	FASN	77634751	1.000000	0.71417	0.890000	0.34922	0.625000	0.37756	4.412000	0.59787	-0.306000	0.08818	-0.488000	0.04728	AGG	.	.		0.637	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		C	80041462	T	C	80041462	3	2	260	1	0	0	0	0	1	0	0	0	5691	1550	54	2	2315	2	FASN	17	80041462	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	149211	80041462	1153748	779	38024										
HEXDC	284004	hgsc.bcm.edu	37	chr17	80399134	80399134	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tctgtggatgcgctgctggaGggcaacaggtgagcgtgtgg	19	7	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:80399134G>T	ENST00000327949.9	+	10	1166	c.1155G>T	c.(1153-1155)gaG>gaT	p.E385D	HEXDC_ENST00000577944.1_Missense_Mutation_p.G388W|HEXDC_ENST00000337014.6_Missense_Mutation_p.R415M			Q8WVB3	HEXDC_HUMAN	hexosaminidase (glycosyl hydrolase family 20, catalytic domain) containing	385					carbohydrate metabolic process (GO:0005975)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	beta-N-acetylhexosaminidase activity (GO:0004563)			breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	16	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)			CGCTGCTGGAGGGCAACAGGT	0.677																																					p.R415M		Atlas-SNP	.											.	HEXDC	43	.	0			c.G1244T						.						29	31	30					17																	80399134		2003	4155	6158	SO:0001583	missense	284004	exon10			GCTGGAGGGCAAC	AK074405	CCDS42402.1	17q25.3	2011-12-19			ENSG00000169660	ENSG00000169660			26307	protein-coding gene	gene with protein product						12477932	Standard	NM_173620		Approved	FLJ23825	uc002kev.4	Q8WVB3		ENST00000327949.9:c.1155G>T	chr17.hg19:g.80399134G>T	ENSP00000332634:p.Glu385Asp	208.0	0.0		101.0	5.0	NM_173620	B7UUP6|Q8IYN4|Q8TE81	Missense_Mutation	SNP	ENST00000327949.9	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	3.569|3.569	-0.088046|-0.088046	0.07097|0.07097	.|.	.|.	ENSG00000169660|ENSG00000169660	ENST00000327949|ENST00000337014	T|T	0.33438|0.40756	1.41|1.02	4.58|4.58	-0.822|-0.822	0.10819|0.10819	.|.	.|3.090850	.|0.01037	.|N	.|0.004244	T|T	0.27629|0.27629	0.0679|0.0679	.|.	.|.	.|.	0.21967|0.21967	N|N	0.999442|0.999442	P|B	0.34934|0.33807	0.476|0.426	B|B	0.31547|0.28011	0.132|0.085	T|T	0.23655|0.23655	-1.0182|-1.0182	8|9	0.17832|0.87932	T|D	0.49|0	.|.	1.2809|1.2809	0.02040|0.02040	0.2911:0.1927:0.3743:0.1419|0.2911:0.1927:0.3743:0.1419	.|.	385|415	Q8WVB3|Q8WVB3-2	HEXDC_HUMAN|.	D|M	385|415	ENSP00000332634:E385D|ENSP00000337854:R415M	ENSP00000332634:E385D|ENSP00000337854:R415M	E|R	+|+	3|2	2|0	HEXDC|HEXDC	77992423|77992423	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.074000|0.074000	0.17049|0.17049	0.706000|0.706000	0.25690|0.25690	0.066000|0.066000	0.16515|0.16515	0.563000|0.563000	0.77884|0.77884	GAG|AGG	.	.		0.677	HEXDC-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000443513.1	NM_173620		T	80399134	G	T	80399134	3	4	260	1	0	0	0	0	1	0	0	0	7084	1000	35	3	1278	3	HEXDC	17	80399134	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	357672	80399134	796076	780	38025										
FN3K	64122	hgsc.bcm.edu	37	chr17	80699230	80699230	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cctcagtatgtggacaagttCggcttccacacggtgacgtg	12	11	1	1	rs566893191		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr17:80699230C>A	ENST00000300784.7	+	4	491	c.429C>A	c.(427-429)ttC>ttA	p.F143L		NM_022158.3	NP_071441.1	Q9H479	FN3K_HUMAN	fructosamine 3 kinase	143					epithelial cell differentiation (GO:0030855)|fructoselysine metabolic process (GO:0030393)		fructosamine-3-kinase activity (GO:0030387)			central_nervous_system(1)|kidney(1)|lung(1)|urinary_tract(1)	4	Breast(20;0.000523)|all_neural(118;0.0952)		BRCA - Breast invasive adenocarcinoma(99;0.0344)|OV - Ovarian serous cystadenocarcinoma(97;0.061)			TGGACAAGTTCGGCTTCCACA	0.547																																					p.F143L	Melanoma(10;391 597 14592 32548 32749)	Atlas-SNP	.											.	FN3K	17	.	0			c.C429A						.						106	78	87					17																	80699230		2203	4300	6503	SO:0001583	missense	64122	exon4			CAAGTTCGGCTTC	AJ404615	CCDS11818.1	17q25	2008-02-05				ENSG00000167363			24822	protein-coding gene	gene with protein product		608425				11522682, 14641062	Standard	NM_022158		Approved		uc010wvs.1	Q9H479		ENST00000300784.7:c.429C>A	chr17.hg19:g.80699230C>A	ENSP00000300784:p.Phe143Leu	114.0	0.0		87.0	4.0	NM_022158		Missense_Mutation	SNP	ENST00000300784.7	hg19	CCDS11818.1	.	.	.	.	.	.	.	.	.	.	C	18.44	3.625028	0.66901	.	.	ENSG00000167363	ENST00000300784;ENST00000457624;ENST00000536165	T	0.61158	0.13	4.1	-3.47	0.04753	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.79684	0.4488	H	0.96861	3.895	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.81590	-0.0863	9	.	.	.	-26.7469	11.3834	0.49771	0.0:0.2443:0.0:0.7557	.	143;98	Q9H479;B3KNR9	FN3K_HUMAN;.	L	143;143;98	ENSP00000300784:F143L	.	F	+	3	2	FN3K	78292519	0.644000	0.27277	0.972000	0.41901	0.638000	0.38207	-0.989000	0.03736	-0.607000	0.05738	0.586000	0.80456	TTC	.	.		0.547	FN3K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439229.1	NM_022158		A	80699230	C	A	80699230	3	1	260	1	0	0	0	0	1	0	0	0	5971	883	31	1	443	1	FN3K	17	80699230	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	300096	80699230	495980	781	38026										
SMCHD1	23347	hgsc.bcm.edu	37	chr18	2726476	2726476	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aatctgaaggttactctgccTggcttaaaagaagactcaca	8	9	3	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr18:2726476T>C	ENST00000320876.6	+	22	3065	c.2727T>C	c.(2725-2727)ccT>ccC	p.P909P	RP11-703M24.5_ENST00000583546.1_RNA|SMCHD1_ENST00000261598.8_Silent_p.P909P	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	909					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						TTACTCTGCCTGGCTTAAAAG	0.259																																					p.P909P		Atlas-SNP	.											.	SMCHD1	88	.	0			c.T2727C						.						23	23	23					18																	2726476		1746	3924	5670	SO:0001819	synonymous_variant	23347	exon22			TCTGCCTGGCTTA	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.2727T>C	chr18.hg19:g.2726476T>C		118.0	0.0		67.0	4.0	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Silent	SNP	ENST00000320876.6	hg19	CCDS45822.1																																																																																			.	.		0.259	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			C	2726476	T	C	2726476	2	2	260	1	0	0	0	0	0	0	0	1	14803	1567	55	2		2	SMCHD1	18	2726476	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10		2726476	75350772	782	38027										
L3MBTL4	91133	hgsc.bcm.edu	37	chr18	6138235	6138235	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gaccacggatatggcctattCctcggcacccgggagtagga	13	12	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr18:6138235C>T	ENST00000284898.6	-	14	1357	c.1157G>A	c.(1156-1158)gGa>gAa	p.G386E	L3MBTL4_ENST00000535782.1_Missense_Mutation_p.G199E|L3MBTL4_ENST00000317931.7_Missense_Mutation_p.G386E|L3MBTL4_ENST00000400105.2_Missense_Mutation_p.G386E|L3MBTL4_ENST00000400104.3_Missense_Mutation_p.G386E	NM_173464.3	NP_775735.2	Q8NA19	LMBL4_HUMAN	l(3)mbt-like 4 (Drosophila)	386					chromatin modification (GO:0016568)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(17)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		Colorectal(10;0.0249)				ATGGCCTATTCCTCGGCACCC	0.443																																					p.G386E	Esophageal Squamous(41;748 902 17366 28959 43175)	Atlas-SNP	.											.	L3MBTL4	87	.	0			c.G1157A						.						73	62	66					18																	6138235		2203	4300	6503	SO:0001583	missense	91133	exon14			CCTATTCCTCGGC	BC039316	CCDS11839.2	18p11.31-p11.23	2013-01-10			ENSG00000154655	ENSG00000154655		"Sterile alpha motif (SAM) domain containing"	26677	protein-coding gene	gene with protein product						14702039	Standard	NM_173464		Approved	FLJ35936, HsT1031	uc010dkt.3	Q8NA19	OTTHUMG00000131573	ENST00000284898.6:c.1157G>A	chr18.hg19:g.6138235C>T	ENSP00000284898:p.Gly386Glu	67.0	0.0		66.0	4.0	NM_173464	A8MTL8|Q8IXS3	Missense_Mutation	SNP	ENST00000284898.6	hg19	CCDS11839.2	.	.	.	.	.	.	.	.	.	.	C	20.7	4.035719	0.75617	.	.	ENSG00000154655	ENST00000400105;ENST00000317931;ENST00000284898;ENST00000535782;ENST00000400104	T;T;T;T;T	0.47177	0.85;0.89;0.85;0.93;1.11	4.82	4.82	0.62117	.	0.000000	0.64402	D	0.000004	T	0.71558	0.3354	M	0.86864	2.845	0.45979	D	0.998791	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.77360	-0.2617	10	0.87932	D	0	.	13.4011	0.60883	0.0:1.0:0.0:0.0	.	386;386	Q8NA19;F8W9S8	LMBL4_HUMAN;.	E	386;386;386;199;386	ENSP00000382976:G386E;ENSP00000318543:G386E;ENSP00000284898:G386E;ENSP00000444774:G199E;ENSP00000382975:G386E	ENSP00000284898:G386E	G	-	2	0	L3MBTL4	6128235	0.997000	0.39634	0.998000	0.56505	0.992000	0.81027	3.569000	0.53827	2.242000	0.73789	0.650000	0.86243	GGA	.	.		0.443	L3MBTL4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254448.2	NM_173464		T	6138235	C	T	6138235	3	4	260	1	0	0	0	0	1	0	0	0	8603	855	30	3	742	3	L3MBTL4	18	6138235	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	3411759	6138235	71939013	783	38028										
LAMA1	284217	hgsc.bcm.edu	37	chr18	6955406	6955406	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgaaatggctgttttgtgtgAgaccaaactggtgagcgccg	14	7	0	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr18:6955406A>G	ENST00000389658.3	-	57	8246	c.8153T>C	c.(8152-8154)cTc>cCc	p.L2718P	RP11-781P6.1_ENST00000584722.1_RNA	NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2718	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				GTTTTGTGTGAGACCAAACTG	0.512																																					p.L2718P		Atlas-SNP	.											.	LAMA1	458	.	0			c.T8153C						.						94	72	79					18																	6955406		2203	4300	6503	SO:0001583	missense	284217	exon57			TGTGTGAGACCAA	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.8153T>C	chr18.hg19:g.6955406A>G	ENSP00000374309:p.Leu2718Pro	178.0	0.0		142.0	6.0	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	hg19	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	A	15.84	2.951497	0.53186	.	.	ENSG00000101680	ENST00000389658	T	0.70749	-0.51	5.32	5.32	0.75619	Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	0.000000	0.64402	D	0.000003	D	0.84284	0.5438	M	0.82517	2.595	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.994;0.998	D	0.83992	0.0338	10	0.31617	T	0.26	.	15.2633	0.73640	1.0:0.0:0.0:0.0	.	2718;48	P25391;B3KSD8	LAMA1_HUMAN;.	P	2718	ENSP00000374309:L2718P	ENSP00000374309:L2718P	L	-	2	0	LAMA1	6945406	1.000000	0.71417	0.942000	0.38095	0.231000	0.25187	5.057000	0.64294	2.014000	0.59158	0.460000	0.39030	CTC	.	.		0.512	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		G	6955406	A	G	6955406	3	3	260	1	0	0	0	0	1	0	0	0	8614	304	11	2	1102	2	LAMA1	18	6955406	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	817171	6955406	71121842	784	38029										
SPIRE1	56907	hgsc.bcm.edu	37	chr18	12535544	12535544	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tctgcaaacagtgcacgacaTactgcctgataatgatttgg	9	9	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr18:12535544T>C	ENST00000409402.4	-	4	927	c.660A>G	c.(658-660)gtA>gtG	p.V220V	SPIRE1_ENST00000453447.2_Silent_p.V100V|SPIRE1_ENST00000383356.2_Silent_p.V61V|SPIRE1_ENST00000309836.5_Silent_p.V23V|SPIRE1_ENST00000410092.3_Silent_p.V220V|snoU13_ENST00000459256.1_RNA	NM_001128626.1	NP_001122098.1			spire-type actin nucleation factor 1											breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)	28						GTGCACGACATACTGCCTGAT	0.393																																					p.V220V		Atlas-SNP	.											.	SPIRE1	120	.	0			c.A660G						.						177	162	167					18																	12535544		2203	4300	6503	SO:0001819	synonymous_variant	56907	exon4			ACGACATACTGCC	AL833817	CCDS32790.2, CCDS45829.1, CCDS45830.1	18p11.21	2013-08-27	2013-08-27		ENSG00000134278	ENSG00000134278			30622	protein-coding gene	gene with protein product		609216	"spire homolog 1 (Drosophila)", "spire family actin nucleation factor 1"			10574461, 11747823	Standard	NM_001128626		Approved	spir-1, KIAA1135	uc002kre.3	Q08AE8	OTTHUMG00000153940	ENST00000409402.4:c.660A>G	chr18.hg19:g.12535544T>C		183.0	0.0		94.0	4.0	NM_020148		Silent	SNP	ENST00000409402.4	hg19	CCDS45829.1																																																																																			.	.		0.393	SPIRE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333109.2	XM_290818		C	12535544	T	C	12535544	2	2	260	1	0	0	0	0	0	0	0	1	15086	1393	49	2		2	SPIRE1	18	12535544	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	5580138	12535544	65541704	785	38030										
CABLES1	91768	hgsc.bcm.edu	37	chr18	20774473	20774473	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agaagattcattttatcaagAacatgcggcaacacgatacc	7	9	2	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr18:20774473A>G	ENST00000256925.7	+	3	979	c.979A>G	c.(979-981)Aac>Gac	p.N327D	CABLES1_ENST00000420687.2_Missense_Mutation_p.N62D|CABLES1_ENST00000585061.1_Intron|CABLES1_ENST00000400473.2_5'UTR	NM_001100619.2	NP_001094089.1	Q8TDN4	CABL1_HUMAN	Cdk5 and Abl enzyme substrate 1	327	Interacts with CDK3. {ECO:0000250}.				blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|nervous system development (GO:0007399)|regulation of cell cycle (GO:0051726)|regulation of cell division (GO:0051302)	cytosol (GO:0005829)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			breast(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|stomach(1)	11	all_cancers(21;0.000102)|all_epithelial(16;2.48e-06)|Lung NSC(20;0.00696)|all_lung(20;0.0197)|Colorectal(14;0.0202)|Ovarian(20;0.127)					TTTTATCAAGAACATGCGGCA	0.463																																					p.N327D		Atlas-SNP	.											.	CABLES1	32	.	0			c.A979G						.						81	76	77					18																	20774473		1905	4132	6037	SO:0001583	missense	91768	exon3			ATCAAGAACATGC	BC037218	CCDS42417.1, CCDS42418.1, CCDS58615.1	18q11.2	2005-08-16				ENSG00000134508			25097	protein-coding gene	gene with protein product		609194				12477932	Standard	NM_138375		Approved	HsT2563, FLJ35924	uc002kuc.2	Q8TDN4		ENST00000256925.7:c.979A>G	chr18.hg19:g.20774473A>G	ENSP00000256925:p.Asn327Asp	146.0	0.0		94.0	4.0	NM_001100619	B4DK60|Q8N3Y8|Q8NA22|Q9BTG1	Missense_Mutation	SNP	ENST00000256925.7	hg19	CCDS42417.1	.	.	.	.	.	.	.	.	.	.	A	19.45	3.829565	0.71258	.	.	ENSG00000134508	ENST00000256925;ENST00000420687	T;T	0.47869	0.83;0.89	5.77	5.77	0.91146	.	0.042490	0.85682	D	0.000000	T	0.58337	0.2115	M	0.68317	2.08	0.58432	D	0.999995	P;D	0.67145	0.461;0.996	B;P	0.52343	0.164;0.696	T	0.57940	-0.7724	10	0.34782	T	0.22	-21.7396	16.1024	0.81184	1.0:0.0:0.0:0.0	.	62;327	Q8TDN4-2;Q8TDN4	.;CABL1_HUMAN	D	327;62	ENSP00000256925:N327D;ENSP00000413851:N62D	ENSP00000256925:N327D	N	+	1	0	CABLES1	19028471	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.924000	0.92827	2.200000	0.70718	0.459000	0.35465	AAC	.	.		0.463	CABLES1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445198.2	NM_138375		G	20774473	A	G	20774473	3	3	260	1	0	0	0	0	1	0	0	0	2531	246	9	2	1043	2	CABLES1	18	20774473	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	8238929	20774473	57302775	786	38031										
ANKRD29	147463	hgsc.bcm.edu	37	chr18	21218861	21218861	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aatccaaagagaaatctcacGacatcattatggccttgctg	7	10	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr18:21218861G>T	ENST00000592179.1	-	4	436	c.282C>A	c.(280-282)gtC>gtA	p.V94V	ANKRD29_ENST00000322980.9_Silent_p.V94V|ANKRD29_ENST00000284207.7_Silent_p.V94V	NM_173505.2	NP_775776.2	Q8N6D5	ANR29_HUMAN	ankyrin repeat domain 29	94										breast(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(3)|prostate(1)|skin(1)	13	all_cancers(21;5.07e-05)|all_epithelial(16;2.49e-07)|Lung NSC(20;0.00211)|all_lung(20;0.00676)|Colorectal(14;0.0202)|Ovarian(20;0.127)					GAAATCTCACGACATCATTAT	0.413																																					p.V94V		Atlas-SNP	.											.	ANKRD29	24	.	0			c.C282A						.						111	106	108					18																	21218861		2203	4300	6503	SO:0001819	synonymous_variant	147463	exon4			TCTCACGACATCA	AK057782	CCDS11879.1	18q11.2	2013-01-10			ENSG00000154065	ENSG00000154065		"Ankyrin repeat domain containing"	27110	protein-coding gene	gene with protein product							Standard	NM_173505		Approved	FLJ25053	uc002kun.3	Q8N6D5	OTTHUMG00000131875	ENST00000592179.1:c.282C>A	chr18.hg19:g.21218861G>T		145.0	0.0		98.0	4.0	NM_173505	B2R972|Q6ZWE8|Q96LU9	Silent	SNP	ENST00000592179.1	hg19	CCDS11879.1																																																																																			.	.		0.413	ANKRD29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254825.1	NM_173505		T	21218861	G	T	21218861	2	4	260	1	0	0	0	0	0	0	0	1	657	1045	37	1		1	ANKRD29	18	21218861	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	444388	21218861	56858387	787	38032										
LAMA3	3909	hgsc.bcm.edu	37	chr18	21451567	21451567	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgacacaggaagtgggcgcaTagcacttgctgtggaaatct	13	8	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr18:21451567T>C	ENST00000313654.9	+	38	5181	c.4940T>C	c.(4939-4941)aTa>aCa	p.I1647T	LAMA3_ENST00000399516.3_Missense_Mutation_p.I1647T|LAMA3_ENST00000269217.6_5'Flank|LAMA3_ENST00000587184.1_5'Flank	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	1647	Laminin IV type A. {ECO:0000255|PROSITE- ProRule:PRU00458}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					AGTGGGCGCATAGCACTTGCT	0.572																																					p.I1647T		Atlas-SNP	.											.	LAMA3	397	.	0			c.T4940C						.						63	73	70					18																	21451567		2068	4206	6274	SO:0001583	missense	3909	exon38			GGCGCATAGCACT	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"Laminins"	6483	protein-coding gene	gene with protein product		600805	"laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.4940T>C	chr18.hg19:g.21451567T>C	ENSP00000324532:p.Ile1647Thr	144.0	0.0		99.0	4.0	NM_001127717	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	hg19	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	T	0.649	-0.810335	0.02798	.	.	ENSG00000053747	ENST00000313654;ENST00000399516	T;T	0.33865	1.39;1.39	5.21	-0.868	0.10652	Laminin B type IV (2);Growth factor, receptor (1);	.	.	.	.	T	0.17238	0.0414	N	0.17312	0.475	0.09310	N	0.999999	B;B	0.30563	0.285;0.285	B;B	0.28916	0.062;0.096	T	0.23511	-1.0186	9	0.22706	T	0.39	.	3.8927	0.09125	0.0866:0.1534:0.4506:0.3093	.	1647;1647	Q6VU67;Q16787	.;LAMA3_HUMAN	T	1647	ENSP00000324532:I1647T;ENSP00000382432:I1647T	ENSP00000324532:I1647T	I	+	2	0	LAMA3	19705565	0.000000	0.05858	0.001000	0.08648	0.030000	0.12068	0.238000	0.18004	-0.030000	0.13804	-0.256000	0.11100	ATA	.	.		0.572	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		C	21451567	T	C	21451567	3	2	260	1	0	0	0	0	1	0	0	0	8616	1406	49	2	5090	2	LAMA3	18	21451567	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	232706	21451567	56625681	788	38033										
PSMA8	143471	hgsc.bcm.edu	37	chr18	23713973	23713973	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gatcactgtcttctccccagAcggacacctttttcaagttg	7	13	4	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr18:23713973A>G	ENST00000308268.6	+	1	133	c.44A>G	c.(43-45)gAc>gGc	p.D15G	PSMA8_ENST00000415576.2_Missense_Mutation_p.D15G|PSMA8_ENST00000343848.6_Missense_Mutation_p.D15G	NM_001025096.1|NM_144662.2	NP_001020267.1|NP_653263.2	Q8TAA3	PSA7L_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 8	15					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|proteasome core complex, alpha-subunit complex (GO:0019773)|spermatoproteasome complex (GO:1990111)	threonine-type endopeptidase activity (GO:0004298)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|skin(2)	16	all_cancers(21;0.000585)|Lung NSC(5;0.00148)|all_lung(6;0.0038)|Ovarian(20;0.124)		OV - Ovarian serous cystadenocarcinoma(3;0.000324)|all cancers(3;0.000954)|LUSC - Lung squamous cell carcinoma(2;0.181)			TTCTCCCCAGACGGACACCTT	0.562																																					p.D15G		Atlas-SNP	.											.	PSMA8	36	.	0			c.A44G						.						122	110	114					18																	23713973		2203	4300	6503	SO:0001583	missense	143471	exon1			CCCCAGACGGACA	BC047355	CCDS32808.1, CCDS45842.1, CCDS45843.1	18q11.2	2006-12-18				ENSG00000154611		"Proteasome (prosome, macropain) subunits"	22985	protein-coding gene	gene with protein product							Standard	XM_005258199		Approved	MGC26605, PSMA7L	uc002kvq.3	Q8TAA3		ENST00000308268.6:c.44A>G	chr18.hg19:g.23713973A>G	ENSP00000311121:p.Asp15Gly	200.0	0.0		122.0	5.0	NM_001025096	B0YJ75|Q8IVP4|Q8TA98|Q8TAA2	Missense_Mutation	SNP	ENST00000308268.6	hg19	CCDS32808.1	.	.	.	.	.	.	.	.	.	.	A	14.46	2.542708	0.45280	.	.	ENSG00000154611	ENST00000308268;ENST00000415576;ENST00000343848;ENST00000536423	T;T;T	0.50277	0.75;0.75;0.75	5.08	5.08	0.68730	Proteasome, alpha-subunit, conserved site (3);	0.000000	0.85682	D	0.000000	T	0.75079	0.3801	H	0.97732	4.065	0.80722	D	1	B;B;B	0.31026	0.304;0.259;0.245	P;B;B	0.47915	0.561;0.425;0.222	T	0.80471	-0.1368	10	0.87932	D	0	-17.7597	12.8545	0.57878	1.0:0.0:0.0:0.0	.	15;15;15	Q8TAA3;Q8TAA3-5;Q8TAA3-2	PSA7L_HUMAN;.;.	G	15	ENSP00000311121:D15G;ENSP00000409284:D15G;ENSP00000345584:D15G	ENSP00000311121:D15G	D	+	2	0	PSMA8	21967971	1.000000	0.71417	0.423000	0.26634	0.990000	0.78478	8.097000	0.89539	2.131000	0.65755	0.533000	0.62120	GAC	.	.		0.562	PSMA8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000446255.1	NM_144662		G	23713973	A	G	23713973	3	3	260	1	0	0	0	0	1	0	0	0	12685	275	10	2	46	2	PSMA8	18	23713973	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	2262406	23713973	54363275	789	38034										
DSG4	147409	hgsc.bcm.edu	37	chr18	28968861	28968861	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	attgccgggctctgaattcaCggggtgaagatttagaaagg	14	6	2	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr18:28968861C>T	ENST00000308128.4	+	5	532	c.397C>T	c.(397-399)Cgg>Tgg	p.R133W	RP11-534N16.1_ENST00000581856.1_RNA|RP11-534N16.1_ENST00000581452.1_RNA|RP11-534N16.1_ENST00000578477.1_RNA|DSG4_ENST00000359747.4_Missense_Mutation_p.R133W	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4	133	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.		Missing (in HYPT6). {ECO:0000269|PubMed:12705872, ECO:0000269|PubMed:15191570}.		anagen (GO:0042640)|BMP signaling pathway (GO:0030509)|homophilic cell adhesion (GO:0007156)|keratinocyte differentiation (GO:0030216)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(6)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(11)|liver(2)|lung(35)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			TCTGAATTCACGGGGTGAAGA	0.383																																					p.R133W		Atlas-SNP	.											.	DSG4	343	.	0			c.C397T						.						100	106	104					18																	28968861		2203	4299	6502	SO:0001583	missense	147409	exon5			AATTCACGGGGTG	AY177664, AY168788	CCDS11897.1, CCDS45845.1	18q12.1	2010-01-26			ENSG00000175065	ENSG00000175065		"Cadherins / Major cadherins"	21307	protein-coding gene	gene with protein product		607892				12648213	Standard	NM_001134453		Approved	CDHF13, LAH	uc002kwq.2	Q86SJ6	OTTHUMG00000131979	ENST00000308128.4:c.397C>T	chr18.hg19:g.28968861C>T	ENSP00000311859:p.Arg133Trp	160.0	0.0		117.0	5.0	NM_001134453	A2RUI1|Q6Y9L9|Q8IXV4	Missense_Mutation	SNP	ENST00000308128.4	hg19	CCDS11897.1	.	.	.	.	.	.	.	.	.	.	C	17.64	3.439580	0.63067	.	.	ENSG00000175065	ENST00000308128;ENST00000359747	T;T	0.61274	0.12;0.12	6.11	0.799	0.18667	Cadherin (4);Cadherin-like (1);	0.000000	0.31438	N	0.007654	T	0.56934	0.2019	N	0.16266	0.395	0.28224	N	0.926408	D;B	0.89917	1.0;0.244	D;B	0.74023	0.982;0.098	T	0.56577	-0.7956	10	0.51188	T	0.08	.	12.0318	0.53401	0.6393:0.2499:0.1108:0.0	.	133;133	Q86SJ6-2;Q86SJ6	.;DSG4_HUMAN	W	133	ENSP00000311859:R133W;ENSP00000352785:R133W	ENSP00000311859:R133W	R	+	1	2	DSG4	27222859	0.079000	0.21365	0.982000	0.44146	0.932000	0.56968	-0.211000	0.09332	0.109000	0.17891	-0.262000	0.10625	CGG	.	.		0.383	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254941.1	NM_177986		T	28968861	C	T	28968861	3	4	260	1	0	0	0	0	1	0	0	0	4781	527	19	1	415	1	DSG4	18	28968861	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	5254888	28968861	49108387	790	38035										
B4GALT6	9331	hgsc.bcm.edu	37	chr18	29207086	29207086	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aaattctttatatggaagacTagaaaagaaagacacagtat	7	4	1	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr18:29207086T>C	ENST00000306851.5	-	7	1073		c.e7-2		B4GALT6_ENST00000237019.7_Splice_Site|B4GALT6_ENST00000383131.3_Splice_Site	NM_004775.3	NP_004766.2	Q9UBX8	B4GT6_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 6						carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)|metal ion binding (GO:0046872)	p.?(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(6)|pancreas(1)	20			OV - Ovarian serous cystadenocarcinoma(10;0.00791)			TATGGAAGACTAGAAAAGAAA	0.353																																					.		Atlas-SNP	.											B4GALT6,NS,carcinoma,0,1	B4GALT6	44	.	1	Unknown(1)	kidney(1)	c.777-2A>G						.						46	46	46					18																	29207086		2203	4300	6503	SO:0001630	splice_region_variant	9331	exon8			GAAGACTAGAAAA	AF038664	CCDS11900.1	18q11	2013-02-19			ENSG00000118276	ENSG00000118276		"Beta 4-glycosyltransferases"	929	protein-coding gene	gene with protein product	"UDP-Gal:glucosylceramide beta-1,4-galactosyltransferase"	604017				9597550, 12180132	Standard	NM_004775		Approved	beta4GalT-VI	uc002kwz.4	Q9UBX8	OTTHUMG00000131980	ENST00000306851.5:c.777-2A>G	chr18.hg19:g.29207086T>C		83.0	1.0		50.0	4.0	NM_004775	O60514|Q6NT09	Splice_Site	SNP	ENST00000306851.5	hg19	CCDS11900.1	.	.	.	.	.	.	.	.	.	.	T	19.67	3.871803	0.72180	.	.	ENSG00000118276	ENST00000306851;ENST00000237019;ENST00000383131	.	.	.	5.74	5.74	0.90152	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7112	0.77629	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	B4GALT6	27461084	1.000000	0.71417	0.923000	0.36655	0.793000	0.44817	8.040000	0.89188	2.190000	0.69967	0.528000	0.53228	.	.	.		0.353	B4GALT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254942.2	NM_004775	Intron	C	29207086	T	C	29207086	5	2	260	1	0	0	0	0	0	0	1	0	1275	1536	53	2	385	2	B4GALT6	18	29207086	Splice_Site	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	238225	29207086	48870162	791	38036										
MEP1B	4225	hgsc.bcm.edu	37	chr18	29800206	29800206	+	Nonstop_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccttttagcagcatgcttttTgaagattaactcgacaatat	6	8	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr18:29800206T>C	ENST00000269202.6	+	15	2151	c.2104T>C	c.(2104-2106)Tga>Cga	p.*702R	MEP1B_ENST00000581447.1_Nonstop_Mutation_p.*701R	NM_005925.2	NP_005916.2	Q16820	MEP1B_HUMAN	meprin A, beta	0					digestion (GO:0007586)|inflammatory response (GO:0006954)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						GCATGCTTTTTGAAGATTAAC	0.299																																					p.X702R		Atlas-SNP	.											.	MEP1B	54	.	0			c.T2104C						.						76	66	69					18																	29800206		1815	4079	5894	SO:0001578	stop_lost	4225	exon15			GCTTTTTGAAGAT	X81333	CCDS45846.1	18q12.2-q12.3	2003-12-17				ENSG00000141434	3.4.24.18		7020	protein-coding gene	gene with protein product		600389				7774936	Standard	NM_005925		Approved		uc002kxj.4	Q16820		ENST00000269202.6:c.2104T>C	chr18.hg19:g.29800206T>C	ENSP00000269202:p.*702Argext*32	122.0	0.0		86.0	4.0	NM_005925	B7ZM35|B9EGL6|Q670J1	Missense_Mutation	SNP	ENST00000269202.6	hg19	CCDS45846.1	.	.	.	.	.	.	.	.	.	.	T	14.52	2.560962	0.45590	.	.	ENSG00000141434	ENST00000269202	.	.	.	5.74	5.74	0.90152	.	.	.	.	.	.	.	.	.	.	.	0.58432	D	0.999996	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.4093	0.55457	0.0:0.0:0.0:1.0	.	.	.	.	R	702	.	.	X	+	1	0	MEP1B	28054204	1.000000	0.71417	1.000000	0.80357	0.698000	0.40448	3.550000	0.53691	2.183000	0.69458	0.533000	0.62120	TGA	.	.		0.299	MEP1B-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447755.1	NM_005925		C	29800206	T	C	29800206	4	2	260	1	0	0	0	0	0	0	0	0	9485	1825	63	2	2162	2	MEP1B	18	29800206	Nonstop_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	593120	29800206	48277042	792	38037										
NOL4	8715	hgsc.bcm.edu	37	chr18	31673528	31673528	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	catccgtgttgaatcactcaTgtcaaattcatcactttcta	4	11	6	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr18:31673528T>C	ENST00000261592.5	-	5	970	c.673A>G	c.(673-675)Atg>Gtg	p.M225V	NOL4_ENST00000269185.4_Missense_Mutation_p.M111V|NOL4_ENST00000535475.1_Missense_Mutation_p.M70V|NOL4_ENST00000589544.1_Missense_Mutation_p.M225V|NOL4_ENST00000538587.1_Missense_Mutation_p.M151V	NM_001198546.1|NM_003787.4	NP_001185475.1|NP_003778.2	O94818	NOL4_HUMAN	nucleolar protein 4	225						nucleolus (GO:0005730)	RNA binding (GO:0003723)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	51						GAATCACTCATGTCAAATTCA	0.338																																					p.M225V		Atlas-SNP	.											.	NOL4	139	.	0			c.A673G						.						99	93	95					18																	31673528		2203	4300	6503	SO:0001583	missense	8715	exon5			CACTCATGTCAAA	AB017800	CCDS11907.2, CCDS56058.1, CCDS56059.1, CCDS59308.1	18q12	2010-05-04			ENSG00000101746	ENSG00000101746			7870	protein-coding gene	gene with protein product	"cancer/testis antigen 125"	603577				9813152	Standard	NM_003787		Approved	NOLP, HRIHFB2255, CT125	uc010dmi.3	O94818	OTTHUMG00000132291	ENST00000261592.5:c.673A>G	chr18.hg19:g.31673528T>C	ENSP00000261592:p.Met225Val	103.0	0.0		72.0	4.0	NM_003787	B4DSQ0|B7Z3Z7|F5H1E3|Q6IBS2|Q9BWF1	Missense_Mutation	SNP	ENST00000261592.5	hg19	CCDS11907.2	.	.	.	.	.	.	.	.	.	.	T	14.64	2.596418	0.46318	.	.	ENSG00000101746	ENST00000261592;ENST00000269185;ENST00000535475;ENST00000538587	.	.	.	5.5	5.5	0.81552	.	0.000000	0.64402	D	0.000001	T	0.67382	0.2887	L	0.58101	1.795	0.43444	D	0.995628	D;B;B;B;B	0.63046	0.992;0.007;0.007;0.452;0.007	P;B;B;P;B	0.59012	0.85;0.01;0.015;0.455;0.01	T	0.64360	-0.6426	9	0.25106	T	0.35	-13.2683	14.7793	0.69754	0.0:0.0:0.0:1.0	.	111;151;225;225;70	B4DLW2;B4DSQ0;O94818;O94818-2;B3KRF4	.;.;NOL4_HUMAN;.;.	V	225;111;70;151	.	ENSP00000261592:M225V	M	-	1	0	NOL4	29927526	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.418000	0.59828	2.088000	0.63022	0.402000	0.26972	ATG	.	.		0.338	NOL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255386.1	NM_003787		C	31673528	T	C	31673528	3	2	260	1	0	0	0	0	1	0	0	0	10533	1464	51	2	1271	2	NOL4	18	31673528	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1873322	31673528	46403720	793	38038										
SIGLEC15	284266	hgsc.bcm.edu	37	chr18	43417043	43417043	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acggagaacttgctcaacacAgaggtgcacagtaagtgctt	11	9	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr18:43417043A>G	ENST00000389474.3	+	2	319	c.102A>G	c.(100-102)acA>acG	p.T34T	SIGLEC15_ENST00000587418.1_5'Flank|SIGLEC15_ENST00000546268.1_5'UTR|SIGLEC15_ENST00000602118.2_3'UTR	NM_213602.2	NP_998767.1	Q6ZMC9	SIG15_HUMAN	sialic acid binding Ig-like lectin 15	34					cellular response to lipoprotein particle stimulus (GO:0071402)|innate immune response (GO:0045087)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of bone resorption (GO:0045124)|regulation of osteoclast development (GO:2001204)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)				endometrium(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	4						tgctcaacacagaggtgcaca	0.438																																					p.T34T		Atlas-SNP	.											.	SIGLEC15	10	.	0			c.A102G						.						98	98	98					18																	43417043		2203	4300	6503	SO:0001819	synonymous_variant	284266	exon2			CAACACAGAGGTG	AK095432	CCDS32819.1	18q21.1	2014-01-28	2007-05-31	2007-05-31	ENSG00000197046	ENSG00000197046		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	27596	protein-coding gene	gene with protein product			"CD33 antigen-like 3", "CD33 molecule-like 3"	CD33L3		17483134	Standard	NM_213602		Approved	HsT1361	uc002lbl.1	Q6ZMC9		ENST00000389474.3:c.102A>G	chr18.hg19:g.43417043A>G		77.0	0.0		71.0	4.0	NM_213602	A8K2Y5|B4DVQ9	Silent	SNP	ENST00000389474.3	hg19	CCDS32819.1																																																																																			.	.		0.438	SIGLEC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410768.2	NM_213602		G	43417043	A	G	43417043	2	3	260	1	0	0	0	0	0	0	0	1	14325	175	7	2		2	SIGLEC15	18	43417043	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	11743515	43417043	34660205	794	38039										
KIAA1632	57724	hgsc.bcm.edu	37	chr18	43528527	43528527	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	atgaaagacccctgatgggtTatgcaacactttgatctgaa	9	8	1	5			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr18:43528527T>C	ENST00000282041.5	-	6	1547	c.1513A>G	c.(1513-1515)Aac>Gac	p.N505D		NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	505					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)					NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						CCTGATGGGTTATGCAACACT	0.393																																					p.N505D		Atlas-SNP	.											.	EPG5	199	.	0			c.A1513G						.						78	71	73					18																	43528527		1828	4103	5931	SO:0001583	missense	57724	exon6			ATGGGTTATGCAA	AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"KIAA1632"	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.1513A>G	chr18.hg19:g.43528527T>C	ENSP00000282041:p.Asn505Asp	75.0	0.0		46.0	10.0	NM_020964	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	hg19	CCDS11926.2	.	.	.	.	.	.	.	.	.	.	T	17.76	3.469695	0.63625	.	.	ENSG00000152223	ENST00000282041	T	0.80653	-1.4	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.81088	0.4750	L	0.47716	1.5	0.45621	D	0.998559	P;P	0.52316	0.952;0.873	P;B	0.49085	0.6;0.385	T	0.83339	-0.0009	10	0.66056	D	0.02	-17.2537	15.4578	0.75330	0.0:0.0:0.0:1.0	.	505;505	Q9HCE0-2;Q9HCE0	.;EPG5_HUMAN	D	505	ENSP00000282041:N505D	ENSP00000282041:N505D	N	-	1	0	EPG5	41782525	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	5.934000	0.70138	2.053000	0.61076	0.460000	0.39030	AAC	.	.		0.393	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		C	43528527	T	C	43528527	3	2	260	1	0	0	0	0	1	0	0	0	8258	1754	61	2	6382	2	KIAA1632	18	43528527	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	111484	43528527	34548721	795	38040										
MBD2	8932	hgsc.bcm.edu	37	chr18	51690975	51690975	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agcagggttcttttccacagCagcggagacttgccctgtga	12	11	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr18:51690975C>T	ENST00000256429.3	-	5	1255	c.1027G>A	c.(1027-1029)Gct>Act	p.A343T		NM_003927.4	NP_003918.1	Q9UBB5	MBD2_HUMAN	methyl-CpG binding domain protein 2	343					ATP-dependent chromatin remodeling (GO:0043044)|cellular protein complex assembly (GO:0043623)|maternal behavior (GO:0042711)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of cell proliferation (GO:0042127)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|histone deacetylase complex (GO:0000118)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	C2H2 zinc finger domain binding (GO:0070742)|chromatin binding (GO:0003682)|methyl-CpG binding (GO:0008327)|mRNA binding (GO:0003729)|protein domain specific binding (GO:0019904)|satellite DNA binding (GO:0003696)|siRNA binding (GO:0035197)			breast(1)|large_intestine(3)|lung(2)|prostate(1)|urinary_tract(1)	8				Colorectal(16;0.0212)|READ - Rectum adenocarcinoma(32;0.188)		TTTTCCACAGCAGCGGAGACT	0.478																																					p.A343T		Atlas-SNP	.											.	MBD2	28	.	0			c.G1027A						.						125	112	116					18																	51690975		2203	4300	6503	SO:0001583	missense	8932	exon5			CCACAGCAGCGGA	AF072242	CCDS11953.1, CCDS45871.1	18q21	2008-08-01			ENSG00000134046	ENSG00000134046			6917	protein-coding gene	gene with protein product		603547				9774669, 10441743	Standard	NM_003927		Approved		uc002lfg.2	Q9UBB5	OTTHUMG00000132705	ENST00000256429.3:c.1027G>A	chr18.hg19:g.51690975C>T	ENSP00000256429:p.Ala343Thr	132.0	0.0		94.0	4.0	NM_003927	O95242|Q9UIS8	Missense_Mutation	SNP	ENST00000256429.3	hg19	CCDS11953.1	.	.	.	.	.	.	.	.	.	.	C	36	5.777034	0.96929	.	.	ENSG00000134046	ENST00000256429	D	0.98792	-5.14	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	D	0.97770	0.9268	L	0.37630	1.12	0.80722	D	1	P	0.42908	0.793	P	0.48654	0.585	D	0.98323	1.0529	10	0.54805	T	0.06	-1.6072	18.7633	0.91862	0.0:1.0:0.0:0.0	.	343	Q9UBB5	MBD2_HUMAN	T	343	ENSP00000256429:A343T	ENSP00000256429:A343T	A	-	1	0	MBD2	49944973	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	7.818000	0.86416	2.728000	0.93425	0.585000	0.79938	GCT	.	.		0.478	MBD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256003.2	NM_003927		T	51690975	C	T	51690975	3	4	260	1	0	0	0	0	1	0	0	0	9352	710	25	3	216	3	MBD2	18	51690975	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	8162448	51690975	26386273	796	38041										
SERPINB8	5271	hgsc.bcm.edu	37	chr18	61654208	61654208	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccttcccagattaaagctggAggagagttatgacttggagc	12	8	0	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr18:61654208A>G	ENST00000397985.2	+	7	1077	c.821A>G	c.(820-822)gAg>gGg	p.E274G	SERPINB8_ENST00000493661.1_Intron|SERPINB8_ENST00000542677.1_Missense_Mutation_p.E92G|SERPINB8_ENST00000353706.2_Missense_Mutation_p.E274G	NM_001276490.1	NP_001263419.1	P50452	SPB8_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 8	274					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.E274V(1)		breast(2)|kidney(1)|large_intestine(4)|lung(9)|skin(1)	17		Esophageal squamous(42;0.129)				TTAAAGCTGGAGGAGAGTTAT	0.393																																					p.E274G		Atlas-SNP	.											SERPINB8,NS,carcinoma,0,1	SERPINB8	42	.	1	Substitution - Missense(1)	lung(1)	c.A821G						.						100	100	100					18																	61654208		2203	4300	6503	SO:0001583	missense	5271	exon7			AGCTGGAGGAGAG	L40377	CCDS11991.1, CCDS42442.1, CCDS62460.1	18q22.1	2014-02-18	2005-08-18		ENSG00000166401	ENSG00000166401		"Serine (or cysteine) peptidase inhibitors"	8952	protein-coding gene	gene with protein product	"cytoplasmic antiproteinase 2"	601697	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 8"	PI8		8530382, 9268635, 24172014	Standard	NM_198833		Approved	CAP2	uc002lju.3	P50452	OTTHUMG00000060596	ENST00000397985.2:c.821A>G	chr18.hg19:g.61654208A>G	ENSP00000381072:p.Glu274Gly	155.0	0.0		96.0	5.0	NM_198833	B4DTW2|Q7Z2V6|Q8N178	Missense_Mutation	SNP	ENST00000397985.2	hg19	CCDS11991.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.080559	0.76528	.	.	ENSG00000166401	ENST00000397985;ENST00000353706;ENST00000542677;ENST00000295211	D;D;T	0.85484	-1.99;-1.99;2.42	5.65	1.64	0.23874	Serpin domain (3);	0.088259	0.85682	D	0.000000	D	0.87799	0.6268	M	0.84433	2.695	0.58432	D	0.999997	P	0.36733	0.567	B	0.44224	0.444	D	0.86202	0.1619	9	.	.	.	.	12.8737	0.57978	0.6121:0.3879:0.0:0.0	.	274	P50452	SPB8_HUMAN	G	274;274;92;186	ENSP00000381072:E274G;ENSP00000331368:E274G;ENSP00000438328:E92G	.	E	+	2	0	SERPINB8	59805188	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.211000	0.58507	0.521000	0.28445	0.533000	0.62120	GAG	.	.		0.393	SERPINB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134014.1	NM_001031848		G	61654208	A	G	61654208	3	3	260	1	0	0	0	0	1	0	0	0	14122	304	11	2	856	2	SERPINB8	18	61654208	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	9963233	61654208	16423040	797	38042										
TXNL4A	10907	hgsc.bcm.edu	37	chr18	77748286	77748286	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cgtccatcttcatgcacgtaGgatcccagtcgtggccgaag	11	13	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr18:77748286G>T	ENST00000269601.5	-	1	307	c.107C>A	c.(106-108)cCt>cAt	p.P36H	TXNL4A_ENST00000592957.1_Intron|TXNL4A_ENST00000588162.1_Missense_Mutation_p.P36H|TXNL4A_ENST00000585474.1_Intron|TXNL4A_ENST00000591711.1_Missense_Mutation_p.P36H	NM_006701.2	NP_006692.1	P83876	TXN4A_HUMAN	thioredoxin-like 4A	36					gene expression (GO:0010467)|mitotic nuclear division (GO:0007067)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|spliceosomal complex assembly (GO:0000245)	nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)				breast(1)|large_intestine(1)|lung(3)	5		all_cancers(4;1.15e-12)|all_epithelial(4;8.61e-09)|all_lung(4;0.00366)|Lung NSC(4;0.00683)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0646)|Melanoma(33;0.2)		OV - Ovarian serous cystadenocarcinoma(15;7.36e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0249)		CATGCACGTAGGATCCCAGTC	0.657																																					p.P36H	Ovarian(160;2333 2597 11821 36245)	Atlas-SNP	.											.	TXNL4A	6	.	0			c.C107A						.						75	50	59					18																	77748286		2203	4300	6503	SO:0001583	missense	10907	exon1			CACGTAGGATCCC	AF023612	CCDS32852.1	18q23	2013-07-16	2004-08-11	2004-08-12		ENSG00000141759			30551	protein-coding gene	gene with protein product	"similar to S. pombe dim1+"	611595	"thioredoxin-like 4"	TXNL4		11015569	Standard	NM_006701		Approved	U5-15kD, DIM1, HsT161, DIB1, SNRNP15	uc002lnp.3	P83876		ENST00000269601.5:c.107C>A	chr18.hg19:g.77748286G>T	ENSP00000269601:p.Pro36His	122.0	0.0		67.0	5.0	NM_006701	B2RC18|O14834	Missense_Mutation	SNP	ENST00000269601.5	hg19	CCDS32852.1	.	.	.	.	.	.	.	.	.	.	G	16.85	3.236384	0.58886	.	.	ENSG00000141759	ENST00000269601;ENST00000355491	.	.	.	4.45	3.57	0.40892	Thioredoxin-like fold (2);	0.000000	0.85682	U	0.000000	T	0.80380	0.4612	M	0.90252	3.1	0.58432	D	0.999999	D;B	0.69078	0.997;0.09	D;B	0.66979	0.948;0.099	D	0.83531	0.0091	9	0.66056	D	0.02	-26.0171	12.2191	0.54423	0.0849:0.0:0.9151:0.0	.	36;36	O14835;P83876	.;TXN4A_HUMAN	H	36	.	ENSP00000269601:P36H	P	-	2	0	TXNL4A	75849274	1.000000	0.71417	0.869000	0.34112	0.070000	0.16714	8.375000	0.90135	0.994000	0.38892	0.655000	0.94253	CCT	.	.		0.657	TXNL4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451036.1	NM_006701		T	77748286	G	T	77748286	3	4	260	1	0	0	0	0	1	0	0	0	16820	1000	35	3	333	3	TXNL4A	18	77748286	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	16094078	77748286	328962	798	38043										
MIER2	54531	hgsc.bcm.edu	37	chr19	311933	311933	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cctcttcactccaagcacagAgcccatctgcaaacacggcc	6	18	3	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:311933A>G	ENST00000264819.4	-	10	906	c.896T>C	c.(895-897)cTc>cCc	p.L299P		NM_017550.1	NP_060020.1	Q8N344	MIER2_HUMAN	mesoderm induction early response 1, family member 2	299	SANT. {ECO:0000255|PROSITE- ProRule:PRU00624}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(4)|kidney(1)|large_intestine(5)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22		all_cancers(10;1.05e-30)|all_epithelial(18;3.04e-19)|Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;2.49e-05)|all_lung(49;4.36e-05)|Breast(49;0.000304)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCAAGCACAGAGCCCATCTGC	0.632																																					p.L299P		Atlas-SNP	.											.	MIER2	51	.	0			c.T896C						.						93	68	77					19																	311933		2203	4300	6503	SO:0001583	missense	54531	exon10			GCACAGAGCCCAT	AB033019	CCDS32855.1	19p13.3	2008-02-05	2006-04-20	2006-04-20		ENSG00000105556			29210	protein-coding gene	gene with protein product			"KIAA1193"	KIAA1193		10574462	Standard	NM_017550		Approved		uc002lok.1	Q8N344		ENST00000264819.4:c.896T>C	chr19.hg19:g.311933A>G	ENSP00000264819:p.Leu299Pro	163.0	0.0		89.0	4.0	NM_017550	Q9ULM7	Missense_Mutation	SNP	ENST00000264819.4	hg19	CCDS32855.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.208023	0.79240	.	.	ENSG00000105556	ENST00000264819	T	0.46063	0.88	4.67	4.67	0.58626	SANT domain, DNA binding (1);Homeodomain-like (1);SANT, eukarya (1);	0.501047	0.16424	N	0.215033	T	0.61937	0.2387	M	0.81497	2.545	0.80722	D	1	D	0.52996	0.957	P	0.57846	0.828	T	0.66964	-0.5790	10	0.87932	D	0	-16.3468	13.3114	0.60382	1.0:0.0:0.0:0.0	.	299	Q8N344	MIER2_HUMAN	P	299	ENSP00000264819:L299P	ENSP00000264819:L299P	L	-	2	0	MIER2	262933	1.000000	0.71417	0.820000	0.32676	0.892000	0.51952	5.980000	0.70516	1.757000	0.51966	0.379000	0.24179	CTC	.	.		0.632	MIER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451784.1	XM_041843		G	311933	A	G	311933	3	3	260	1	0	0	0	0	1	0	0	0	9590	304	11	2	761	2	MIER2	19	311933	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10		311933	58817050	799	38044										
C19orf20	91978	hgsc.bcm.edu	37	chr19	507710	507710	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gagccgatcgccttcctggcTcactacttcgagaacatggg	11	13	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:507710T>C	ENST00000359315.5	+	1	412	c.204T>C	c.(202-204)gcT>gcC	p.A68A	AC005775.2_ENST00000592413.1_RNA	NM_033513.2	NP_277048.2	Q6ZTW0	TPGS1_HUMAN	tubulin polyglutamylase complex subunit 1	68					adult behavior (GO:0030534)|multicellular organismal development (GO:0007275)|protein polyglutamylation (GO:0018095)|sperm axoneme assembly (GO:0007288)|synaptic transmission (GO:0007268)|vesicle localization (GO:0051648)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)	tubulin-glutamic acid ligase activity (GO:0070740)										CCTTCCTGGCTCACTACTTCG	0.711																																					p.A68A		Atlas-SNP	.											.	.	.	.	0			c.T204C						.						7	10	9					19																	507710		1855	4030	5885	SO:0001819	synonymous_variant	91978	exon1			CCTGGCTCACTAC	BC009520	CCDS42454.1	19p13.3	2011-11-23	2011-11-23	2011-11-23	ENSG00000141933	ENSG00000141933			25058	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 20"	C19orf20		11441184, 12972506	Standard	NM_033513		Approved	GTRGEO22, PGs1	uc002lou.3	Q6ZTW0		ENST00000359315.5:c.204T>C	chr19.hg19:g.507710T>C		136.0	0.0		111.0	6.0	NM_033513	Q96GE2	Silent	SNP	ENST00000359315.5	hg19	CCDS42454.1																																																																																			.	.		0.711	TPGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451887.2	NM_033513		C	507710	T	C	507710	2	2	260	1	0	0	0	0	0	0	0	1	1914	1538	54	2		2	C19orf20	19	507710	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	195777	507710	58621273	800	38045										
ELANE	1991	hgsc.bcm.edu	37	chr19	855736	855736	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cgtgacggtggtgacgtcccTctgccgtcgcagcaacgtct	13	14	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:855736T>C	ENST00000590230.1	+	5	680	c.539T>C	c.(538-540)cTc>cCc	p.L180P	ELANE_ENST00000263621.1_Missense_Mutation_p.L180P			P08246	ELNE_HUMAN	elastase, neutrophil expressed	180	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				acute inflammatory response to antigenic stimulus (GO:0002438)|cellular calcium ion homeostasis (GO:0006874)|collagen catabolic process (GO:0030574)|defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|negative regulation of chemokine biosynthetic process (GO:0045079)|negative regulation of chemotaxis (GO:0050922)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-8 biosynthetic process (GO:0045415)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neutrophil mediated killing of fungus (GO:0070947)|phagocytosis (GO:0006909)|positive regulation of immune response (GO:0050778)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein catabolic process (GO:0030163)|proteolysis (GO:0006508)|response to lipopolysaccharide (GO:0032496)|response to UV (GO:0009411)|response to yeast (GO:0001878)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|secretory granule (GO:0030141)|transcriptional repressor complex (GO:0017053)	cytokine binding (GO:0019955)|endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|peptidase activity (GO:0008233)|protease binding (GO:0002020)|RNA polymerase II transcription corepressor activity (GO:0001106)|serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(1)|lung(4)|pancreas(1)	13					Alpha-1-proteinase inhibitor(DB00058)|Filgrastim(DB00099)|Pegfilgrastim(DB00019)	GTGACGTCCCTCTGCCGTCGC	0.687																																					p.L180P		Atlas-SNP	.											.	ELANE	27	.	0			c.T539C						.						70	63	66					19																	855736		2203	4297	6500	SO:0001583	missense	1991	exon4			CGTCCCTCTGCCG		CCDS12045.1	19p13.3	2014-09-17	2009-05-05	2009-05-05	ENSG00000197561	ENSG00000197561	3.4.21.37		3309	protein-coding gene	gene with protein product	"neutrophil elastase", "leukocyte elastase", "medullasin"	130130	"elastase 2, neutrophil"	ELA2		2902087	Standard	XM_005259517		Approved	NE, HNE, HLE	uc002lqb.3	P08246		ENST00000590230.1:c.539T>C	chr19.hg19:g.855736T>C	ENSP00000466090:p.Leu180Pro	126.0	0.0		87.0	4.0	NM_001972	P09649|Q6B0D9|Q6LDP5	Missense_Mutation	SNP	ENST00000590230.1	hg19	CCDS12045.1	.	.	.	.	.	.	.	.	.	.	T	5.993	0.367050	0.11352	.	.	ENSG00000197561	ENST00000263621	D	0.88818	-2.43	4.57	-5.52	0.02560	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	1.042500	0.07743	U	0.947196	D	0.83184	0.5199	L	0.60455	1.87	0.19945	N	0.999949	B	0.27679	0.185	B	0.31191	0.125	T	0.69610	-0.5099	10	0.33940	T	0.23	.	5.3476	0.16018	0.4468:0.0:0.3617:0.1916	.	180	P08246	ELNE_HUMAN	P	180	ENSP00000263621:L180P	ENSP00000263621:L180P	L	+	2	0	ELANE	806736	0.000000	0.05858	0.000000	0.03702	0.267000	0.26476	-1.617000	0.02051	-0.792000	0.04480	-0.689000	0.03729	CTC	.	.		0.687	ELANE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457890.2	NM_001972		C	855736	T	C	855736	3	2	260	1	0	0	0	0	1	0	0	0	5050	1551	54	2	553	2	ELANE	19	855736	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	348026	855736	58273247	801	38046										
MED16	10025	hgsc.bcm.edu	37	chr19	890977	890977	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acgcaccctggtcatcgctgCgcaggtccatggtgaaggcg	14	13	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:890977C>T	ENST00000589119.1	-	1	154	c.155G>A	c.(154-156)cGc>cAc	p.R52H	MED16_ENST00000395808.3_Missense_Mutation_p.R52H|MED16_ENST00000269814.4_Missense_Mutation_p.R52H|RNU6-9_ENST00000384776.1_RNA|MED16_ENST00000325464.1_Missense_Mutation_p.R52H|MED16_ENST00000606828.1_Intron|MED16_ENST00000312090.6_Missense_Mutation_p.R52H			Q9Y2X0	MED16_HUMAN	mediator complex subunit 16	52					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|receptor activity (GO:0004872)|thyroid hormone receptor binding (GO:0046966)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GTCATCGCTGCGCAGGTCCAT	0.672																																					p.R52H		Atlas-SNP	.											.	MED16	61	.	0			c.G155A						.						93	76	82					19																	890977		2203	4300	6503	SO:0001583	missense	10025	exon2			TCGCTGCGCAGGT	AF121228	CCDS12047.1	19p13.3	2013-01-10	2007-07-30	2007-07-30		ENSG00000175221		"WD repeat domain containing"	17556	protein-coding gene	gene with protein product		604062	"thyroid hormone receptor associated protein 5"	THRAP5		10235266, 10198638	Standard	NM_005481		Approved	DRIP92, TRAP95	uc002lqd.1	Q9Y2X0		ENST00000589119.1:c.155G>A	chr19.hg19:g.890977C>T	ENSP00000464810:p.Arg52His	82.0	0.0		52.0	12.0	NM_005481	Q6PJT2|Q96AD4|Q96I35|Q9Y652	Missense_Mutation	SNP	ENST00000589119.1	hg19	CCDS12047.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.829072	0.90955	.	.	ENSG00000175221	ENST00000325464;ENST00000312090;ENST00000395808;ENST00000269814;ENST00000534906;ENST00000537596;ENST00000540679;ENST00000538572;ENST00000541440;ENST00000424039	T;T;T	0.44482	1.49;0.92;0.92	4.24	3.12	0.35913	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.359113	0.26418	N	0.024497	T	0.35799	0.0944	N	0.19112	0.55	0.38973	D	0.958795	D;P;P;P;P	0.69078	0.997;0.871;0.606;0.871;0.874	P;B;B;P;B	0.52554	0.702;0.365;0.143;0.487;0.293	T	0.29305	-1.0016	10	0.54805	T	0.06	-14.7818	9.5904	0.39543	0.0:0.8454:0.0:0.1546	.	52;52;52;52;52	B9TX03;Q9Y2X0-2;E7ETV0;Q9Y2X0-3;Q9Y2X0	.;.;.;.;MED16_HUMAN	H	52	ENSP00000325612:R52H;ENSP00000308528:R52H;ENSP00000379153:R52H	ENSP00000269814:R52H	R	-	2	0	MED16	841977	0.994000	0.37717	0.616000	0.29078	0.926000	0.56050	3.319000	0.51983	1.923000	0.55706	0.561000	0.74099	CGC	.	.		0.672	MED16-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457902.3	NM_005481		T	890977	C	T	890977	3	4	260	1	0	0	0	0	1	0	0	0	9443	768	27	1	2538	1	MED16	19	890977	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	35241	890977	58238006	802	38047										
MIDN	90007	hgsc.bcm.edu	37	chr19	1255586	1255586	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccagtgctccccggcctcacCggcccccgacctggccccca	9	24	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:1255586C>G	ENST00000591446.2	+	6	1431	c.1022C>G	c.(1021-1023)cCg>cGg	p.P341R	MIDN_ENST00000300952.2_Missense_Mutation_p.P341R			Q504T8	MIDN_HUMAN	midnolin	341						cytosol (GO:0005829)|nucleolus (GO:0005730)				NS(1)|endometrium(3)|kidney(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCGGCCTCACCGGCCCCCGAC	0.701																																					p.P341R		Atlas-SNP	.											MIDN,NS,carcinoma,0,1	MIDN	34	.	0			c.C1022G						.						23	27	26					19																	1255586		2196	4292	6488	SO:0001583	missense	90007	exon7			CCTCACCGGCCCC	AC004221	CCDS32864.1	19p13.3	2013-09-20			ENSG00000167470	ENSG00000167470			16298	protein-coding gene	gene with protein product		606700				10974535	Standard	XM_005259671		Approved		uc002lrp.3	Q504T8	OTTHUMG00000180144	ENST00000591446.2:c.1022C>G	chr19.hg19:g.1255586C>G	ENSP00000467679:p.Pro341Arg	63.0	0.0		66.0	3.0	NM_177401	Q96BW8	Missense_Mutation	SNP	ENST00000591446.2	hg19	CCDS32864.1	.	.	.	.	.	.	.	.	.	.	C	4.743	0.138217	0.09083	.	.	ENSG00000167470	ENST00000300952	.	.	.	3.25	3.25	0.37280	.	0.228749	0.36101	N	0.002788	T	0.11922	0.0290	N	0.08118	0	0.21064	N	0.999794	P	0.37276	0.589	B	0.33196	0.159	T	0.12344	-1.0551	9	0.22706	T	0.39	-10.6683	6.2323	0.20742	0.0:0.8584:0.0:0.1416	.	341	Q504T8	MIDN_HUMAN	R	341	.	ENSP00000300952:P341R	P	+	2	0	MIDN	1206586	0.027000	0.19231	0.004000	0.12327	0.010000	0.07245	2.755000	0.47540	1.651000	0.50673	0.462000	0.41574	CCG	.	.		0.701	MIDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449965.2			G	1255586	C	G	1255586	3	3	260	1	0	0	0	0	1	0	0	0	9588	652	23	4	1044	4	MIDN	19	1255586	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	364609	1255586	57873397	803	38048										
C19orf25	148223	hgsc.bcm.edu	37	chr19	1478838	1478838	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cccgcacatcctccaggatcTgctccaccgtggggggcgct	12	17	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:1478838T>C	ENST00000436106.2	-	2	460	c.65A>G	c.(64-66)cAg>cGg	p.Q22R	C19orf25_ENST00000591027.1_5'UTR|C19orf25_ENST00000586564.1_Missense_Mutation_p.Q22R|C19orf25_ENST00000588427.1_Missense_Mutation_p.Q22R|C19orf25_ENST00000588849.1_Missense_Mutation_p.Q22R|C19orf25_ENST00000427685.2_Missense_Mutation_p.Q22R|C19orf25_ENST00000585675.1_Missense_Mutation_p.Q22R|C19orf25_ENST00000588871.1_Missense_Mutation_p.Q22R|C19orf25_ENST00000592872.1_Missense_Mutation_p.Q22R			Q9UFG5	CS025_HUMAN	chromosome 19 open reading frame 25	22													Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTCCAGGATCTGCTCCACCGT	0.701																																					p.Q22R		Atlas-SNP	.											.	C19orf25	3	.	0			c.A65G						.						8	10	9					19																	1478838		1868	4066	5934	SO:0001583	missense	148223	exon2			AGGATCTGCTCCA	AK075267	CCDS45898.1	19p13.3	2012-10-24			ENSG00000119559	ENSG00000119559			26711	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_152482		Approved	FLJ36666	uc010dsk.3	Q9UFG5	OTTHUMG00000180092	ENST00000436106.2:c.65A>G	chr19.hg19:g.1478838T>C	ENSP00000397394:p.Gln22Arg	157.0	0.0		79.0	4.0	NM_152482	B3KQN6|Q8N9R7|Q8WV94	Missense_Mutation	SNP	ENST00000436106.2	hg19	CCDS45898.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.077514	0.76528	.	.	ENSG00000119559	ENST00000436106;ENST00000427685;ENST00000335104	.	.	.	4.77	4.77	0.60923	.	0.066848	0.64402	D	0.000011	T	0.67420	0.2891	M	0.63843	1.955	0.45227	D	0.998238	D;P;P	0.67145	0.996;0.932;0.879	P;P;P	0.59424	0.857;0.66;0.58	T	0.70085	-0.4969	9	0.59425	D	0.04	.	10.6844	0.45835	0.0:0.0:0.0:1.0	.	22;22;22	E7EP72;Q9UFG5;B4DNJ8	.;CS025_HUMAN;.	R	22	.	ENSP00000335309:Q22R	Q	-	2	0	C19orf25	1429838	1.000000	0.71417	1.000000	0.80357	0.298000	0.27526	2.976000	0.49289	1.793000	0.52555	0.459000	0.35465	CAG	.	.		0.701	C19orf25-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449694.1	NM_152482		C	1478838	T	C	1478838	3	2	260	1	0	0	0	0	1	0	0	0	1917	1580	55	2	299	2	C19orf25	19	1478838	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	223252	1478838	57650145	804	38049										
TMPRSS9	360200	hgsc.bcm.edu	37	chr19	2396594	2396594	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggccgagctgcggggaatccGgtggaccagcagtttgcggc	18	11	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:2396594G>T	ENST00000332578.3	+	2	200	c.200G>T	c.(199-201)cGg>cTg	p.R67L	TMPRSS9_ENST00000592650.1_3'UTR	NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	67					plasminogen activation (GO:0031639)	integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CGGGGAATCCGGTGGACCAGC	0.672																																					p.R67L		Atlas-SNP	.											.	TMPRSS9	79	.	0			c.G200T						.						30	25	27					19																	2396594		2203	4300	6503	SO:0001583	missense	360200	exon2			GAATCCGGTGGAC	AJ488946	CCDS12088.1	19p13.3	2010-04-13						"Serine peptidases / Transmembrane"	30079	protein-coding gene	gene with protein product	"polyserase 1"	610477				12886014	Standard	NM_182973		Approved		uc010xgx.2	Q7Z410		ENST00000332578.3:c.200G>T	chr19.hg19:g.2396594G>T	ENSP00000330264:p.Arg67Leu	131.0	0.0		89.0	5.0	NM_182973	Q6ZND6|Q7Z411	Missense_Mutation	SNP	ENST00000332578.3	hg19	CCDS12088.1	.	.	.	.	.	.	.	.	.	.	G	9.892	1.204588	0.22205	.	.	ENSG00000178297	ENST00000395264;ENST00000332578	D	0.88124	-2.34	3.98	0.292	0.15737	.	1.008230	0.07982	N	0.985760	T	0.80308	0.4599	L	0.45581	1.43	0.09310	N	1	B;B	0.13594	0.007;0.008	B;B	0.17979	0.003;0.02	T	0.65076	-0.6256	10	0.34782	T	0.22	.	3.8038	0.08768	0.0967:0.2911:0.4637:0.1484	.	67;67	Q7Z410;E7EMP4	TMPS9_HUMAN;.	L	67	ENSP00000330264:R67L	ENSP00000330264:R67L	R	+	2	0	TMPRSS9	2347594	0.000000	0.05858	0.028000	0.17463	0.005000	0.04900	-0.952000	0.03881	0.783000	0.33636	-0.314000	0.08810	CGG	.	.		0.672	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973		T	2396594	G	T	2396594	3	4	260	1	0	0	0	0	1	0	0	0	16268	1116	39	1	206	1	TMPRSS9	19	2396594	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	917756	2396594	56732389	805	38050										
SLC39A3	29985	hgsc.bcm.edu	37	chr19	2733301	2733301	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	atgaaggggctctcatactcCgagtcgctgcccacgtccga	11	14	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:2733301C>G	ENST00000269740.4	-	3	722	c.393G>C	c.(391-393)tcG>tcC	p.S131S	SLC39A3_ENST00000545664.1_Silent_p.S131S|AC006538.4_ENST00000586572.1_Intron	NM_144564.4	NP_653165.2	Q9BRY0	S39A3_HUMAN	solute carrier family 39 (zinc transporter), member 3	131					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	10		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCTCATACTCCGAGTCGCTGC	0.687																																					p.S131S		Atlas-SNP	.											.	SLC39A3	20	.	0			c.G393C						.						40	41	41					19																	2733301		2201	4300	6501	SO:0001819	synonymous_variant	29985	exon3			ATACTCCGAGTCG	AF052125	CCDS12093.1, CCDS45909.1	19p13.3	2013-05-22			ENSG00000141873	ENSG00000141873		"Solute carriers"	17128	protein-coding gene	gene with protein product		612168				10681536	Standard	NM_144564		Approved	ZIP3	uc002lwg.3	Q9BRY0		ENST00000269740.4:c.393G>C	chr19.hg19:g.2733301C>G		110.0	0.0		68.0	4.0	NM_144564	B3KMJ3|Q8WUG1	Silent	SNP	ENST00000269740.4	hg19	CCDS12093.1																																																																																			.	.		0.687	SLC39A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451354.2			G	2733301	C	G	2733301	2	3	260	1	0	0	0	0	0	0	0	1	14634	639	23	4		4	SLC39A3	19	2733301	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	336707	2733301	56395682	806	38051										
ZNF77	58492	hgsc.bcm.edu	37	chr19	2933802	2933802	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgacagctgaaggctttcccAcaatgcttacactcaaaggg	9	11	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:2933802A>G	ENST00000314531.4	-	4	1415	c.1323T>C	c.(1321-1323)tgT>tgC	p.C441C		NM_021217.2	NP_067040.1	Q15935	ZNF77_HUMAN	zinc finger protein 77	441					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(5)|ovary(1)	17				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|GBM - Glioblastoma multiforme(1328;2.11e-07)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.174)|STAD - Stomach adenocarcinoma(1328;0.18)		AGGCTTTCCCACAATGCTTAC	0.502																																					p.C441C		Atlas-SNP	.											.	ZNF77	47	.	0			c.T1323C						.						90	78	82					19																	2933802		2203	4300	6503	SO:0001819	synonymous_variant	58492	exon4			TTTCCCACAATGC	X65230	CCDS12099.1	19p13.3	2013-01-08	2006-05-12					"Zinc fingers, C2H2-type", "-"	13150	protein-coding gene	gene with protein product		194551	"zinc finger protein 77 (pT1)"			8478004	Standard	NM_021217		Approved	pT1	uc002lws.4	Q15935		ENST00000314531.4:c.1323T>C	chr19.hg19:g.2933802A>G		117.0	0.0		65.0	4.0	NM_021217	Q86XJ3|Q9NPP0	Silent	SNP	ENST00000314531.4	hg19	CCDS12099.1																																																																																			.	.		0.502	ZNF77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451924.1	NM_021217		G	2933802	A	G	2933802	2	3	260	1	0	0	0	0	0	0	0	1	18157	157	6	2		2	ZNF77	19	2933802	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	200501	2933802	56195181	807	38052										
TLE2	7089	hgsc.bcm.edu	37	chr19	3006425	3006425	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	accccgccctcaccaggcagTcgagctgggccacgggcgtc	13	18	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:3006425T>C	ENST00000262953.6	-	15	1755	c.1493A>G	c.(1492-1494)gAc>gGc	p.D498G	TLE2_ENST00000447365.2_Missense_Mutation_p.D165G|TLE2_ENST00000426948.2_Missense_Mutation_p.D512G|TLE2_ENST00000455444.2_Missense_Mutation_p.D376G|TLE2_ENST00000590536.1_Missense_Mutation_p.D499G|TLE2_ENST00000586422.1_Intron|TLE2_ENST00000443826.3_Missense_Mutation_p.D376G|TLE2_ENST00000591529.1_Missense_Mutation_p.D512G	NM_003260.4	NP_003251.2	Q04725	TLE2_HUMAN	transducin-like enhancer of split 2	498					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|prostate(1)	13				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CACCAGGCAGTCGAGCTGGGC	0.682																																					p.D512G		Atlas-SNP	.											.	TLE2	35	.	0			c.A1535G						.						12	14	13					19																	3006425		1945	4117	6062	SO:0001583	missense	7089	exon16			AGGCAGTCGAGCT	M99436	CCDS45911.1, CCDS45912.1, CCDS45913.1, CCDS74255.1	19p13.3	2014-03-07	2014-03-07					"WD repeat domain containing"	11838	protein-coding gene	gene with protein product	"enhancer of split groucho 2"	601041	"transducin-like enhancer of split 2, homolog of Drosophila E(sp1)", "transducin-like enhancer of split 2 (E(sp1) homolog, Drosophila)"			8808280	Standard	NM_003260		Approved	ESG2, GRG2, ESG, FLJ41188	uc002lww.3	Q04725		ENST00000262953.6:c.1493A>G	chr19.hg19:g.3006425T>C	ENSP00000262953:p.Asp498Gly	113.0	0.0		110.0	5.0	NM_001144761	B4DE03|E9PEV7|F8WCH2|Q8WVY0|Q9Y6S0	Missense_Mutation	SNP	ENST00000262953.6	hg19	CCDS45911.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.32|17.32	3.360851|3.360851	0.61403|0.61403	.|.	.|.	ENSG00000065717|ENSG00000065717	ENST00000262953;ENST00000455444;ENST00000450017;ENST00000447365;ENST00000443826;ENST00000426948|ENST00000439015	T;T;T;T;T|.	0.11169|.	2.8;2.8;2.8;2.8;2.8|.	3.33|3.33	3.33|3.33	0.38152|0.38152	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);|.	0.050469|.	0.85682|.	D|.	0.000000|.	T|T	0.72882|0.72882	0.3516|0.3516	M|M	0.77103|0.77103	2.36|2.36	0.50313|0.50313	D|D	0.999861|0.999861	D;B;B;D;D|.	0.56035|.	0.974;0.054;0.113;0.974;0.974|.	D;B;B;D;D|.	0.68765|.	0.96;0.028;0.069;0.96;0.96|.	T|T	0.76683|0.76683	-0.2869|-0.2869	10|6	0.87932|0.87932	D|D	0|0	-15.5278|-15.5278	11.0158|11.0158	0.47687|0.47687	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	376;165;512;376;498|.	E9PEV7;B4DE62;F8WCH2;B4DE03;Q04725|.	.;.;.;.;TLE2_HUMAN|.	G|A	498;376;492;165;376;512|359	ENSP00000262953:D498G;ENSP00000413107:D376G;ENSP00000406523:D165G;ENSP00000392427:D376G;ENSP00000392869:D512G|.	ENSP00000262953:D498G|ENSP00000398351:T359A	D|T	-|-	2|1	0|0	TLE2|TLE2	2957425|2957425	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.943000|0.943000	0.58893|0.58893	7.682000|7.682000	0.84083|0.84083	1.537000|1.537000	0.49254|0.49254	0.254000|0.254000	0.18369|0.18369	GAC|ACT	.	.		0.682	TLE2-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000452194.2	NM_003260		C	3006425	T	C	3006425	3	2	260	1	0	0	0	0	1	0	0	0	15954	1667	58	2	762	2	TLE2	19	3006425	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	72623	3006425	56122558	808	38053										
NFIC	4782	hgsc.bcm.edu	37	chr19	3381967	3381967	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gaggacttcgtgctgagcatCaccggcaagaaggcgccggg	16	11	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:3381967C>T	ENST00000443272.2	+	2	339	c.288C>T	c.(286-288)atC>atT	p.I96I	NFIC_ENST00000341919.3_Silent_p.I96I|NFIC_ENST00000346156.5_Silent_p.I87I|NFIC_ENST00000395111.3_Silent_p.I87I|NFIC_ENST00000590282.1_Silent_p.I96I|NFIC_ENST00000589123.1_Silent_p.I87I|NFIC_ENST00000586919.1_Silent_p.I87I	NM_001245002.1	NP_001231931.1	P08651	NFIC_HUMAN	nuclear factor I/C (CCAAT-binding transcription factor)	96					DNA replication (GO:0006260)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleolus (GO:0005730)|nucleus (GO:0005634)	core promoter proximal region DNA binding (GO:0001159)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;7.8e-05)|Epithelial(107;2.94e-108)|BRCA - Breast invasive adenocarcinoma(158;0.00154)|STAD - Stomach adenocarcinoma(1328;0.191)		TGCTGAGCATCACCGGCAAGA	0.682																																					p.I96I		Atlas-SNP	.											.	NFIC	36	.	0			c.C288T						.						74	80	78					19																	3381967		2203	4299	6502	SO:0001819	synonymous_variant	4782	exon2			GAGCATCACCGGC	X12492	CCDS12107.1, CCDS45914.1, CCDS58640.1, CCDS59330.1, CCDS59331.1	19p13.3	2008-02-05				ENSG00000141905			7786	protein-coding gene	gene with protein product		600729		NFI		3398920, 7590749	Standard	NM_205843		Approved	CTF, NF-I, CTF5	uc010xhi.2	P08651		ENST00000443272.2:c.288C>T	chr19.hg19:g.3381967C>T		89.0	0.0		74.0	4.0	NM_001245004	A8K1H0|B7Z4U5|B7Z9C3|K7EMU1|P08652|Q14932|Q9UPJ3|Q9UPJ9|Q9UPK0|Q9UPK1	Silent	SNP	ENST00000443272.2	hg19	CCDS59330.1																																																																																			.	.		0.682	NFIC-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452834.1	NM_005597		T	3381967	C	T	3381967	2	4	260	1	0	0	0	0	0	0	0	1	10381	816	29	3		3	NFIC	19	3381967	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	375542	3381967	55747016	809	38054										
FSD1	79187	hgsc.bcm.edu	37	chr19	4323608	4323608	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gcctgcaaaagcgaggcagtGctaccagcagctccaacacc	10	15	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:4323608G>A	ENST00000221856.6	+	13	1606	c.1459G>A	c.(1459-1461)Gct>Act	p.A487T	STAP2_ENST00000597593.1_5'Flank|FSD1_ENST00000597590.1_3'UTR	NM_024333.2	NP_077309.1	Q9BTV5	FSD1_HUMAN	fibronectin type III and SPRY domain containing 1	487					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.034)|STAD - Stomach adenocarcinoma(1328;0.18)		GCGAGGCAGTGCTACCAGCAG	0.672																																					p.A487T		Atlas-SNP	.											.	FSD1	51	.	0			c.G1459A						.						27	30	29					19																	4323608		2203	4300	6503	SO:0001583	missense	79187	exon13			GGCAGTGCTACCA	AF316829	CCDS12127.1	19p13.3	2013-02-11	2005-03-01			ENSG00000105255		"Fibronectin type III domain containing"	13745	protein-coding gene	gene with protein product		609828	"fibronectin type 3 and SPRY domain containing 1"			11267680	Standard	NM_024333		Approved	MGC3213, MIR1	uc002lzy.2	Q9BTV5		ENST00000221856.6:c.1459G>A	chr19.hg19:g.4323608G>A	ENSP00000221856:p.Ala487Thr	197.0	0.0		111.0	5.0	NM_024333	B2RDT0|Q9BXN0|Q9HAG4	Missense_Mutation	SNP	ENST00000221856.6	hg19	CCDS12127.1	.	.	.	.	.	.	.	.	.	.	G	17.69	3.453067	0.63290	.	.	ENSG00000105255	ENST00000221856	T	0.28666	1.6	4.97	3.93	0.45458	.	0.279039	0.36268	N	0.002698	T	0.22975	0.0555	L	0.36672	1.1	0.34036	D	0.654465	P	0.36683	0.565	B	0.32928	0.155	T	0.38178	-0.9673	10	0.62326	D	0.03	.	11.0405	0.47827	0.093:0.0:0.907:0.0	.	487	Q9BTV5	FSD1_HUMAN	T	487	ENSP00000221856:A487T	ENSP00000221856:A487T	A	+	1	0	FSD1	4274608	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.410000	0.52664	1.095000	0.41419	0.478000	0.44815	GCT	.	.		0.672	FSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458091.1	NM_024333		A	4323608	G	A	4323608	3	1	260	1	0	0	0	0	1	0	0	0	6078	1319	46	3	1509	3	FSD1	19	4323608	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	941641	4323608	54805375	810	38055										
VAV1	7409	hgsc.bcm.edu	37	chr19	6828673	6828673	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cgaggtcaagcgagacaacgAgacactgcgacagatcacca	11	12	2	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:6828673A>G	ENST00000602142.1	+	12	1215	c.1133A>G	c.(1132-1134)gAg>gGg	p.E378G	VAV1_ENST00000596764.1_Missense_Mutation_p.E346G|VAV1_ENST00000304076.2_Missense_Mutation_p.E378G|VAV1_ENST00000599806.1_Missense_Mutation_p.E323G|VAV1_ENST00000539284.1_Missense_Mutation_p.E281G	NM_005428.3	NP_005419.2	P15498	VAV_HUMAN	vav 1 guanine nucleotide exchange factor	378					apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|reactive oxygen species metabolic process (GO:0072593)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(16)|lung(18)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	62						CGAGACAACGAGACACTGCGA	0.632																																					p.E378G		Atlas-SNP	.											.	VAV1	140	.	0			c.A1133G						.						133	131	132					19																	6828673		2203	4300	6503	SO:0001583	missense	7409	exon12			ACAACGAGACACT		CCDS12174.1, CCDS59341.1, CCDS59342.1	19p13.2	2013-02-14	2007-07-25			ENSG00000141968		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "SH2 domain containing"	12657	protein-coding gene	gene with protein product		164875	"vav 1 oncogene"	VAV		9438848	Standard	NM_005428		Approved		uc010xjh.2	P15498		ENST00000602142.1:c.1133A>G	chr19.hg19:g.6828673A>G	ENSP00000472929:p.Glu378Gly	144.0	0.0		98.0	4.0	NM_005428	B4DVK9|M0QXX6|Q15860	Missense_Mutation	SNP	ENST00000602142.1	hg19	CCDS12174.1	.	.	.	.	.	.	.	.	.	.	A	29.8	5.033448	0.93575	.	.	ENSG00000141968	ENST00000304076;ENST00000539284	T;T	0.75704	-0.67;-0.96	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	D	0.84311	0.5444	M	0.85299	2.745	0.80722	D	1	D;D;D;D	0.63046	0.992;0.981;0.987;0.989	P;P;P;P	0.57009	0.746;0.64;0.811;0.811	D	0.87177	0.2225	10	0.87932	D	0	.	13.1651	0.59567	1.0:0.0:0.0:0.0	.	281;378;323;378	F5H5P4;B2R8B5;Q96D37;P15498	.;.;.;VAV_HUMAN	G	378;281	ENSP00000302269:E378G;ENSP00000443242:E281G	ENSP00000302269:E378G	E	+	2	0	VAV1	6779673	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	6.471000	0.73562	2.010000	0.58986	0.482000	0.46254	GAG	.	.		0.632	VAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458475.1			G	6828673	A	G	6828673	3	3	260	1	0	0	0	0	1	0	0	0	17146	304	11	2	1179	2	VAV1	19	6828673	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	2505065	6828673	52300310	811	38056										
INSR	3643	hgsc.bcm.edu	37	chr19	7132201	7132201	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cgtagaaataggtgggttccGtccaagagccgttgcccgca	13	11	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:7132201G>A	ENST00000302850.5	-	14	2952	c.2810C>T	c.(2809-2811)aCg>aTg	p.T937M	INSR_ENST00000341500.5_Missense_Mutation_p.T925M	NM_000208.2	NP_000199.2	P06213	INSR_HUMAN	insulin receptor	937	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.		T -> M (in LEPRCH; impaired receptor processing).		activation of MAPK activity (GO:0000187)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|carbohydrate metabolic process (GO:0005975)|cellular response to growth factor stimulus (GO:0071363)|cellular response to insulin stimulus (GO:0032869)|epidermis development (GO:0008544)|exocrine pancreas development (GO:0031017)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|insulin receptor signaling pathway (GO:0008286)|male sex determination (GO:0030238)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of developmental growth (GO:0048639)|positive regulation of DNA replication (GO:0045740)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of respiratory burst (GO:0060267)|protein autophosphorylation (GO:0046777)|protein heterotetramerization (GO:0051290)|regulation of embryonic development (GO:0045995)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction by phosphorylation (GO:0023014)|transformation of host cell by virus (GO:0019087)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|insulin receptor complex (GO:0005899)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|insulin binding (GO:0043559)|insulin receptor substrate binding (GO:0043560)|insulin-activated receptor activity (GO:0005009)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor II binding (GO:0031995)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|PTB domain binding (GO:0051425)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(1)|central_nervous_system(4)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(4)|prostate(4)|skin(3)|stomach(2)|urinary_tract(2)	66					"""Insulin(DB00071)|""Insulin(DB08914)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"	GGTGGGTTCCGTCCAAGAGCC	0.602																																					p.T937M		Atlas-SNP	.											.	INSR	265	.	0			c.C2810T	GRCh37	CM970787	INSR	M		.						92	75	81					19																	7132201		2203	4300	6503	SO:0001583	missense	3643	exon14			GGTTCCGTCCAAG	M10051	CCDS12176.1, CCDS42487.1	19p13.3-p13.2	2013-02-11				ENSG00000171105		"CD molecules", "Fibronectin type III domain containing"	6091	protein-coding gene	gene with protein product		147670				2983222	Standard	NM_000208		Approved	CD220	uc002mgd.1	P06213		ENST00000302850.5:c.2810C>T	chr19.hg19:g.7132201G>A	ENSP00000303830:p.Thr937Met	120.0	0.0		87.0	4.0	NM_000208	Q17RW0|Q59H98|Q9UCB7|Q9UCB8|Q9UCB9	Missense_Mutation	SNP	ENST00000302850.5	hg19	CCDS12176.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.486413	0.84854	.	.	ENSG00000171105	ENST00000302850;ENST00000341500	T;T	0.54479	0.57;0.57	6.07	6.07	0.98685	Fibronectin, type III (2);	0.000000	0.43110	U	0.000604	T	0.80717	0.4676	M	0.93638	3.44	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.84668	0.0710	10	0.87932	D	0	.	18.1531	0.89682	0.0:0.0:1.0:0.0	.	925;937	P06213-2;P06213	.;INSR_HUMAN	M	937;925	ENSP00000303830:T937M;ENSP00000342838:T925M	ENSP00000303830:T937M	T	-	2	0	INSR	7083201	1.000000	0.71417	0.972000	0.41901	0.623000	0.37688	9.047000	0.93823	2.885000	0.99019	0.655000	0.94253	ACG	.	.		0.602	INSR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458544.1			A	7132201	G	A	7132201	3	1	260	1	0	0	0	0	1	0	0	0	7782	1145	40	1	1374	1	INSR	19	7132201	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	303528	7132201	51996782	812	38057										
ZNF558	148156	hgsc.bcm.edu	37	chr19	8922642	8922642	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agtcatagggtttttctccaGtatgaattctcttgtgctga	9	7	3	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:8922642G>C	ENST00000601372.1	-	10	1235	c.524C>G	c.(523-525)aCt>aGt	p.T175S	ZNF558_ENST00000301475.1_Missense_Mutation_p.T175S|ZNF558_ENST00000444186.2_Missense_Mutation_p.T104S			Q96NG5	ZN558_HUMAN	zinc finger protein 558	175					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	15						TTTTTCTCCAGTATGAATTCT	0.388																																					p.T175S		Atlas-SNP	.											.	ZNF558	43	.	0			c.C524G						.						55	53	54					19																	8922642		2203	4300	6503	SO:0001583	missense	148156	exon6			TCTCCAGTATGAA	AK055494	CCDS12208.1	19p13.2	2013-09-20			ENSG00000167785	ENSG00000167785		"Zinc fingers, C2H2-type", "-"	26422	protein-coding gene	gene with protein product							Standard	NM_144693		Approved	FLJ30932	uc002mkn.1	Q96NG5	OTTHUMG00000182196	ENST00000601372.1:c.524C>G	chr19.hg19:g.8922642G>C	ENSP00000471277:p.Thr175Ser	134.0	0.0		79.0	4.0	NM_144693	A8K5F0|B7Z798	Missense_Mutation	SNP	ENST00000601372.1	hg19	CCDS12208.1	.	.	.	.	.	.	.	.	.	.	G	19.98	3.927872	0.73327	.	.	ENSG00000167785	ENST00000301475;ENST00000444186	T;T	0.24151	1.87;1.87	4.77	4.77	0.60923	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.42821	D	0.000641	T	0.27313	0.0670	L	0.31065	0.9	0.34944	D	0.750559	B	0.26744	0.158	B	0.38655	0.278	T	0.41324	-0.9515	10	0.56958	D	0.05	-12.2029	15.3356	0.74250	0.0:0.0:1.0:0.0	.	175	Q96NG5	ZN558_HUMAN	S	175;104	ENSP00000301475:T175S;ENSP00000410703:T104S	ENSP00000301475:T175S	T	-	2	0	ZNF558	8783642	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	4.834000	0.62774	2.485000	0.83878	0.591000	0.81541	ACT	.	.		0.388	ZNF558-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459955.2	NM_144693		C	8922642	G	C	8922642	3	2	260	1	0	0	0	0	1	0	0	0	18004	1029	36	4	688	4	ZNF558	19	8922642	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	1790441	8922642	50206341	813	38058										
MUC16	94025	hgsc.bcm.edu	37	chr19	8976277	8976277	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	caccattgatgaagaggctaTccctgtccaggacatagaag	10	10	0	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:8976277T>C	ENST00000397910.4	-	75	42754	c.42551A>G	c.(42550-42552)gAt>gGt	p.D14184G	MUC16_ENST00000596956.1_Intron|MUC16_ENST00000380951.5_Missense_Mutation_p.D825G	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	14215	SEA 14. {ECO:0000255|PROSITE- ProRule:PRU00188}.			Missing (in Ref. 3; AAK74120). {ECO:0000305}.	cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GAAGAGGCTATCCCTGTCCAG	0.512																																					p.D14184G		Atlas-SNP	.											.	MUC16	4315	.	0			c.A42551G						.						62	59	60					19																	8976277		2003	4160	6163	SO:0001583	missense	94025	exon75			AGGCTATCCCTGT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.42551A>G	chr19.hg19:g.8976277T>C	ENSP00000381008:p.Asp14184Gly	95.0	0.0		98.0	5.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	5.507|5.507	0.278471|0.278471	0.10403|0.10403	.|.	.|.	ENSG00000181143|ENSG00000181143	ENST00000397910;ENST00000380951|ENST00000542240	T;T|.	0.39229|.	1.09;1.09|.	4.07|4.07	-0.594|-0.594	0.11664|0.11664	.|.	0.515438|.	0.15762|.	N|.	0.245871|.	T|T	0.37865|0.37865	0.1019|0.1019	L|L	0.38531|0.38531	1.155|1.155	.|.	.|.	.|.	B;D|.	0.60575|.	0.006;0.988|.	B;D|.	0.75020|.	0.007;0.985|.	T|T	0.45366|0.45366	-0.9266|-0.9266	9|4	0.52906|.	T|.	0.07|.	.|.	7.4395|7.4395	0.27174|0.27174	0.0:0.4042:0.0:0.5958|0.0:0.4042:0.0:0.5958	.|.	21829;14184|.	Q8WXI7;B5ME49|.	MUC16_HUMAN;.|.	G|V	14184;825|1007	ENSP00000381008:D14184G;ENSP00000370338:D825G|.	ENSP00000370338:D825G|.	D|I	-|-	2|1	0|0	MUC16|MUC16	8837277|8837277	0.000000|0.000000	0.05858|0.05858	0.010000|0.010000	0.14722|0.14722	0.032000|0.032000	0.12392|0.12392	-0.901000|-0.901000	0.04093|0.04093	-0.281000|-0.281000	0.09141|0.09141	0.456000|0.456000	0.33151|0.33151	GAT|ATA	.	.		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	8976277	T	C	8976277	3	2	260	1	0	0	0	0	1	0	0	0	9982	1435	50	2	1012	2	MUC16	19	8976277	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	53635	8976277	50152706	814	38059										
ZNF177	7730	hgsc.bcm.edu	37	chr19	9491942	9491942	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcatactggagagaagccttAtgagtgtgatcactgtggaa	12	6	2	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:9491942A>G	ENST00000589262.1	+	6	1001	c.935A>G	c.(934-936)tAt>tGt	p.Y312C	ZNF177_ENST00000602738.1_Missense_Mutation_p.Y152C|ZNF177_ENST00000590616.1_Intron|ZNF177_ENST00000602856.1_3'UTR|ZNF177_ENST00000434737.2_Missense_Mutation_p.Y312C|ZNF177_ENST00000541595.2_Missense_Mutation_p.Y152C|ZNF177_ENST00000343499.4_Missense_Mutation_p.Y152C|ZNF177_ENST00000446085.4_3'UTR	NM_001172651.1	NP_001166122.1	Q13360	ZN177_HUMAN	zinc finger protein 177	312					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	blood microparticle (GO:0072562)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|stomach(2)	13						GAGAAGCCTTATGAGTGTGAT	0.433																																					p.Y312C		Atlas-SNP	.											.	ZNF177	57	.	0			c.A935G						.						100	93	95					19																	9491942		2203	4300	6503	SO:0001583	missense	7730	exon6			AGCCTTATGAGTG	U37263, BC012012	CCDS12212.1, CCDS54214.1	19p13.2	2013-01-08						"Zinc fingers, C2H2-type", "-"	12966	protein-coding gene	gene with protein product		601276					Standard	NM_003451		Approved		uc021uon.1	Q13360		ENST00000589262.1:c.935A>G	chr19.hg19:g.9491942A>G	ENSP00000468531:p.Tyr312Cys	165.0	0.0		91.0	4.0	NM_001172651	B4DY57|E9PDG0|I3L0I4|Q96ER2	Missense_Mutation	SNP	ENST00000589262.1	hg19	CCDS54214.1	.	.	.	.	.	.	.	.	.	.	A	10.86	1.469232	0.26423	.	.	ENSG00000188629	ENST00000541595;ENST00000343499;ENST00000434737	T;T;T	0.25414	1.8;1.8;1.8	2.64	0.345	0.16011	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.44953	0.1318	M	0.79614	2.46	0.26986	N	0.965257	D;D	0.76494	0.999;0.999	D;D	0.70487	0.926;0.969	T	0.53690	-0.8403	8	0.87932	D	0	.	6.4667	0.21985	0.3798:0.0:0.0:0.6202	.	312;152	B4DY57;Q13360	.;ZN177_HUMAN	C	152;152;312	ENSP00000445323:Y152C;ENSP00000341497:Y152C;ENSP00000415070:Y312C	ENSP00000341497:Y152C	Y	+	2	0	ZNF177	9352942	0.000000	0.05858	0.043000	0.18650	0.873000	0.50193	0.001000	0.13038	0.001000	0.14605	-0.490000	0.04691	TAT	.	.		0.433	ZNF177-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449028.1	NM_003451		G	9491942	A	G	9491942	3	3	260	1	0	0	0	0	1	0	0	0	17761	449	16	2	953	2	ZNF177	19	9491942	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	515665	9491942	49637041	815	38060										
S1PR5	53637	hgsc.bcm.edu	37	chr19	10624905	10624905	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aagagggggccccaacatgcCacaaaggccaggagcaccac	12	14	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:10624905C>A	ENST00000439028.3	-	2	908	c.783G>T	c.(781-783)gtG>gtT	p.V261V	S1PR5_ENST00000333430.4_Silent_p.V261V	NM_001166215.1	NP_001159687.1	Q9H228	S1PR5_HUMAN	sphingosine-1-phosphate receptor 5	261					regulation of neuron differentiation (GO:0045664)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sphingosine-1-phosphate receptor activity (GO:0038036)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	12					Fingolimod(DB08868)	CCCAACATGCCACAAAGGCCA	0.711																																					p.V261V		Atlas-SNP	.											.	S1PR5	33	.	0			c.G783T						.						21	21	21					19																	10624905		2188	4291	6479	SO:0001819	synonymous_variant	53637	exon2			ACATGCCACAAAG	AK074661	CCDS12240.1	19p13.2	2012-08-08	2008-04-30	2008-04-30		ENSG00000180739		"GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"	14299	protein-coding gene	gene with protein product		605146	"endothelial differentiation, sphingolipid G-protein-coupled receptor, 8"	EDG8		10799507	Standard	NM_030760		Approved	Edg-8	uc002mou.2	Q9H228		ENST00000439028.3:c.783G>T	chr19.hg19:g.10624905C>A		96.0	0.0		78.0	5.0	NM_030760	Q6NW11	Silent	SNP	ENST00000439028.3	hg19	CCDS12240.1	.	.	.	.	.	.	.	.	.	.	C	8.536	0.872195	0.17322	.	.	ENSG00000180739	ENST00000359134	.	.	.	4.37	-0.479	0.12089	.	.	.	.	.	T	0.54013	0.1832	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	T	0.55755	-0.8091	5	0.62326	D	0.03	.	3.1024	0.06330	0.2363:0.2835:0.386:0.0942	.	.	.	.	C	230	.	ENSP00000352045:G230C	G	-	1	0	S1PR5	10485905	0.035000	0.19736	0.145000	0.22337	0.824000	0.46624	0.215000	0.17562	0.462000	0.27095	0.491000	0.48974	GGC	.	.		0.711	S1PR5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452015.1	NM_030760		A	10624905	C	A	10624905	2	1	260	1	0	0	0	0	0	0	0	1	13812	581	21	3		3	S1PR5	19	10624905	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	1132963	10624905	48504078	816	38061										
LOC55908	55908	hgsc.bcm.edu	37	chr19	11352157	11352157	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agagccacatcctatgggccCtcacaggccacgtgcagcgg	12	15	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:11352157C>T	ENST00000252453.8	+	3	515	c.496C>T	c.(496-498)Ctc>Ttc	p.L166F	C19orf80_ENST00000591200.1_Missense_Mutation_p.L67F|DOCK6_ENST00000294618.7_Intron	NM_018687.6	NP_061157.3	Q6UXH0	BETAT_HUMAN	chromosome 19 open reading frame 80	166					cellular lipid metabolic process (GO:0044255)|glucose metabolic process (GO:0006006)|positive regulation of protein processing (GO:0010954)|regulation of lipoprotein metabolic process (GO:0050746)|triglyceride homeostasis (GO:0070328)|type B pancreatic cell proliferation (GO:0044342)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(1)|breast(1)|endometrium(2)	4						CCTATGGGCCCTCACAGGCCA	0.642																																					p.L166F		Atlas-SNP	.											.	C19orf80	8	.	0			c.C496T						.						9	12	11					19																	11352157		2091	4114	6205	SO:0001583	missense	55908	exon3			TGGGCCCTCACAG		CCDS54220.1	19p13.2	2014-02-13			ENSG00000130173	ENSG00000130173			24933	protein-coding gene	gene with protein product	"lipasin", "betatrophin"					22809513, 23150577, 24262987	Standard	NM_018687		Approved	TD26, RIFL, ANGPTL8	uc021upg.1	Q6UXH0		ENST00000252453.8:c.496C>T	chr19.hg19:g.11352157C>T	ENSP00000252453:p.Leu166Phe	130.0	0.0		72.0	18.0	NM_018687	Q9NQZ1	Missense_Mutation	SNP	ENST00000252453.8	hg19	CCDS54220.1	.	.	.	.	.	.	.	.	.	.	C	13.56	2.274373	0.40194	.	.	ENSG00000130173	ENST00000397785;ENST00000252453	T	0.59364	0.27	4.17	3.09	0.35607	.	0.000000	0.42821	D	0.000658	T	0.67711	0.2922	L	0.59436	1.845	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.55244	-0.8171	10	0.87932	D	0	-6.3913	8.1266	0.31003	0.0:0.8834:0.0:0.1166	.	166	Q6UXH0	TD26_HUMAN	F	91;166	ENSP00000252453:L166F	ENSP00000252453:L166F	L	+	1	0	C19orf80	11213157	0.385000	0.25172	0.042000	0.18584	0.473000	0.32948	1.533000	0.36040	2.174000	0.68829	0.306000	0.20318	CTC	.	.		0.642	C19orf80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453175.1	NM_018687		T	11352157	C	T	11352157	3	4	260	1	0	0	0	0	1	0	0	0	8890	681	24	3	506	3	LOC55908	19	11352157	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	727252	11352157	47776826	817	38062										
FBXW9	84261	hgsc.bcm.edu	37	chr19	12805705	12805705	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	atcctctgcccagcgggacaGgtgctgctccagcgcaatgc	12	15	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:12805705G>T	ENST00000380339.3	-	2	493	c.457C>A	c.(457-459)Ctg>Atg	p.L153M	FBXW9_ENST00000393261.3_Missense_Mutation_p.L153M|FBXW9_ENST00000587955.1_Missense_Mutation_p.L143M|FBXW9_ENST00000544494.1_Intron			Q5XUX1	FBXW9_HUMAN	F-box and WD repeat domain containing 9	153					SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)					cervix(1)|lung(4)|ovary(1)|prostate(1)	7						CAGCGGGACAGGTGCTGCTCC	0.632																																					p.L153M		Atlas-SNP	.											.	FBXW9	30	.	0			c.C457A						.						33	39	37					19																	12805705		2081	4227	6308	SO:0001583	missense	84261	exon2			GGGACAGGTGCTG	BC004290	CCDS12278.2	19p13.2	2013-01-09	2007-02-08		ENSG00000132004	ENSG00000132004		"F-boxes / WD-40 domains", "WD repeat domain containing"	28136	protein-coding gene	gene with protein product		609074	"F-box and WD-40 domain protein 9"			12477932	Standard	NM_032301		Approved	MGC10870, Fbw9	uc002mum.1	Q5XUX1	OTTHUMG00000150152	ENST00000380339.3:c.457C>A	chr19.hg19:g.12805705G>T	ENSP00000369696:p.Leu153Met	118.0	0.0		82.0	4.0	NM_032301	B3KVP7|Q9BT89	Missense_Mutation	SNP	ENST00000380339.3	hg19		.	.	.	.	.	.	.	.	.	.	G	14.74	2.626573	0.46840	.	.	ENSG00000132004	ENST00000393261;ENST00000380339	T;T	0.48836	1.8;0.8	5.01	2.72	0.32119	.	0.252675	0.31636	N	0.007317	T	0.51041	0.1651	L	0.32530	0.975	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.70716	0.935;0.97	T	0.42699	-0.9436	10	0.33940	T	0.23	-12.9353	9.015	0.36164	0.2464:0.0:0.7536:0.0	.	143;153	Q5XUX1-2;Q5XUX1-3	.;.	M	153	ENSP00000376945:L153M;ENSP00000369696:L153M	ENSP00000369696:L153M	L	-	1	2	FBXW9	12666705	0.989000	0.36119	1.000000	0.80357	0.792000	0.44763	0.727000	0.25999	1.127000	0.42034	0.456000	0.33151	CTG	.	.		0.632	FBXW9-201	KNOWN	basic	protein_coding	protein_coding		NM_032301		T	12805705	G	T	12805705	3	4	260	1	0	0	0	0	1	0	0	0	5779	991	35	3	955	3	FBXW9	19	12805705	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	1453548	12805705	46323278	818	38063										
NDUFB7	4713	hgsc.bcm.edu	37	chr19	14677715	14677715	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gctggagcctcagctgcgcgTccatcatctcctgctgtgtg	12	14	3	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:14677715T>C	ENST00000215565.2	-	2	204	c.143A>G	c.(142-144)gAc>gGc	p.D48G		NM_004146.5	NP_004137.2	P17568	NDUB7_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7, 18kDa	48					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			endometrium(3)|large_intestine(2)|lung(2)|ovary(1)	8						CAGCTGCGCGTCCATCATCTC	0.657																																					p.D48G		Atlas-SNP	.											.	NDUFB7	14	.	0			c.A143G						.						42	34	37					19																	14677715		2194	4294	6488	SO:0001583	missense	4713	exon2			TGCGCGTCCATCA		CCDS12314.1	19p13.12	2011-07-04	2002-08-29		ENSG00000099795	ENSG00000099795		"Mitochondrial respiratory chain complex / Complex I"	7702	protein-coding gene	gene with protein product	"NADH-ubiquinone oxidoreductase B18 subunit", "complex I B18 subunit"	603842	"NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7 (18kD, B18)"			9763677, 10830904	Standard	NM_004146		Approved	B18, CI-B18, MGC2480	uc002mzg.3	P17568		ENST00000215565.2:c.143A>G	chr19.hg19:g.14677715T>C	ENSP00000215565:p.Asp48Gly	113.0	0.0		79.0	4.0	NM_004146	Q6ICN9|Q9UI16	Missense_Mutation	SNP	ENST00000215565.2	hg19	CCDS12314.1	.	.	.	.	.	.	.	.	.	.	T	1.256	-0.617205	0.03663	.	.	ENSG00000099795	ENST00000215565	T	0.47528	0.84	4.76	4.76	0.60689	.	0.214881	0.39210	N	0.001422	T	0.46444	0.1393	M	0.79693	2.465	0.21290	N	0.999733	B	0.17852	0.024	B	0.19666	0.026	T	0.35895	-0.9770	10	0.23302	T	0.38	-2.7662	7.7478	0.28879	0.1866:0.0:0.0:0.8134	.	48	P17568	NDUB7_HUMAN	G	48	ENSP00000215565:D48G	ENSP00000215565:D48G	D	-	2	0	NDUFB7	14538715	0.411000	0.25384	0.133000	0.22050	0.045000	0.14185	3.456000	0.53000	2.003000	0.58678	0.477000	0.44152	GAC	.	.		0.657	NDUFB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466025.1	NM_004146		C	14677715	T	C	14677715	3	2	260	1	0	0	0	0	1	0	0	0	10295	1667	58	2	278	2	NDUFB7	19	14677715	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1872010	14677715	44451268	819	38064										
AKAP8	10270	hgsc.bcm.edu	37	chr19	15485443	15485443	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tggccacaccagttccatatGcaccttaggggaaacagaaa	9	11	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:15485443G>A	ENST00000269701.2	-	3	122	c.62C>T	c.(61-63)gCa>gTa	p.A21V		NM_005858.3	NP_005849.1	O43823	AKAP8_HUMAN	A kinase (PRKA) anchor protein 8	21					mitotic chromosome condensation (GO:0007076)|mitotic nuclear division (GO:0007067)|signal transduction (GO:0007165)	condensed chromosome (GO:0000793)|female pronucleus (GO:0001939)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)	26						AGTTCCATATGCACCTTAGGG	0.617																																					p.A21V	GBM(190;1671 2163 3274 27186 30476)	Atlas-SNP	.											.	AKAP8	68	.	0			c.C62T						.						100	89	93					19																	15485443		2203	4300	6503	SO:0001583	missense	10270	exon3			CCATATGCACCTT	Y11997	CCDS12329.1	19p13.12	2012-05-16			ENSG00000105127	ENSG00000105127		"A-kinase anchor proteins"	378	protein-coding gene	gene with protein product	"A-kinase anchor protein, 95kDa"	604692				9473338	Standard	NM_005858		Approved	AKAP95, DKFZp586B1222	uc002nav.3	O43823		ENST00000269701.2:c.62C>T	chr19.hg19:g.15485443G>A	ENSP00000269701:p.Ala21Val	177.0	0.0		94.0	5.0	NM_005858		Missense_Mutation	SNP	ENST00000269701.2	hg19	CCDS12329.1	.	.	.	.	.	.	.	.	.	.	G	14.74	2.626450	0.46840	.	.	ENSG00000105127	ENST00000269701	T	0.47869	0.83	5.42	5.42	0.78866	.	0.392722	0.21585	N	0.072187	T	0.42517	0.1206	L	0.44542	1.39	0.80722	D	1	B	0.32573	0.376	B	0.30401	0.115	T	0.35151	-0.9800	10	0.45353	T	0.12	-8.3054	16.1296	0.81418	0.0:0.0:1.0:0.0	.	21	O43823	AKAP8_HUMAN	V	21	ENSP00000269701:A21V	ENSP00000269701:A21V	A	-	2	0	AKAP8	15346443	0.977000	0.34250	0.974000	0.42286	0.350000	0.29205	5.244000	0.65400	2.537000	0.85549	0.563000	0.77884	GCA	.	.		0.617	AKAP8-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461293.3	NM_005858		A	15485443	G	A	15485443	3	1	260	1	0	0	0	0	1	0	0	0	457	1319	46	3	2064	3	AKAP8	19	15485443	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	807728	15485443	43643540	820	38065										
MRPL34	64981	hgsc.bcm.edu	37	chr19	17416718	17416718	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggatatggctgtcttggctgGatccctgttgggccccacga	14	11	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:17416718G>T	ENST00000252602.1	+	1	242	c.17G>T	c.(16-18)gGa>gTa	p.G6V	MRPL34_ENST00000595444.1_Missense_Mutation_p.G98V|MRPL34_ENST00000600434.1_Missense_Mutation_p.G6V|ABHD8_ENST00000247706.3_5'Flank|MRPL34_ENST00000594999.1_Missense_Mutation_p.G6V|MRPL34_ENST00000602206.1_Missense_Mutation_p.G6V	NM_023937.3	NP_076426.1	Q9BQ48	RM34_HUMAN	mitochondrial ribosomal protein L34	6					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)	structural constituent of ribosome (GO:0003735)			endometrium(1)|lung(1)	2						GTCTTGGCTGGATCCCTGTTG	0.632																																					p.G6V		Atlas-SNP	.											.	MRPL34	5	.	0			c.G17T						.						52	56	55					19																	17416718		2203	4300	6503	SO:0001583	missense	64981	exon1			TGGCTGGATCCCT	AB049652	CCDS12356.1	19p13.1	2012-09-13						"Mitochondrial ribosomal proteins / large subunits"	14488	protein-coding gene	gene with protein product		611840				11543634	Standard	NM_023937		Approved	L34mt, MGC2633, MGC24974	uc002ngc.1	Q9BQ48		ENST00000252602.1:c.17G>T	chr19.hg19:g.17416718G>T	ENSP00000252602:p.Gly6Val	169.0	0.0		93.0	4.0	NM_023937		Missense_Mutation	SNP	ENST00000252602.1	hg19	CCDS12356.1	.	.	.	.	.	.	.	.	.	.	G	13.65	2.301430	0.40694	.	.	ENSG00000130312	ENST00000252602	.	.	.	3.22	3.22	0.36961	.	0.552270	0.17337	N	0.177898	T	0.41351	0.1155	.	.	.	0.09310	N	0.999996	P	0.47106	0.89	P	0.47299	0.543	T	0.24799	-1.0150	8	0.54805	T	0.06	-15.7287	10.2199	0.43190	0.0:0.0:1.0:0.0	.	6	Q9BQ48	RM34_HUMAN	V	6	.	ENSP00000252602:G6V	G	+	2	0	MRPL34	17277718	0.004000	0.15560	0.005000	0.12908	0.028000	0.11728	1.490000	0.35573	2.117000	0.64856	0.561000	0.74099	GGA	.	.		0.632	MRPL34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463516.1	NM_023937		T	17416718	G	T	17416718	3	4	260	1	0	0	0	0	1	0	0	0	9806	1174	41	3	19	3	MRPL34	19	17416718	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	1931275	17416718	41712265	821	38066										
KIAA1683	80726	hgsc.bcm.edu	37	chr19	18376583	18376583	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gcagccctggggaccccagtTcccggatgtggttgagccag	15	13	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:18376583T>C	ENST00000600328.3	-	3	1960	c.1767A>G	c.(1765-1767)ggA>ggG	p.G589G	KIAA1683_ENST00000392413.4_Silent_p.G589G|KIAA1683_ENST00000600359.3_Silent_p.G543G			Q9H0B3	K1683_HUMAN	KIAA1683	589						mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						GGACCCCAGTTCCCGGATGTG	0.552																																					p.G589G		Atlas-SNP	.											.	KIAA1683	190	.	0			c.A1767G						.						42	42	42					19																	18376583		2203	4299	6502	SO:0001819	synonymous_variant	80726	exon3			CCCAGTTCCCGGA	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.1767A>G	chr19.hg19:g.18376583T>C		101.0	0.0		79.0	5.0	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Silent	SNP	ENST00000600328.3	hg19	CCDS32958.1																																																																																			.	.		0.552	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3			C	18376583	T	C	18376583	2	2	260	1	0	0	0	0	0	0	0	1	8260	1770	62	2		2	KIAA1683	19	18376583	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	959865	18376583	40752400	822	38067										
SFRS14	10147	hgsc.bcm.edu	37	chr19	19129923	19129923	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	catttaaagacctaccagtaAgcagggtcctctttgagaag	9	9	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:19129923A>G	ENST00000601879.1	-	4	2142	c.1845T>C	c.(1843-1845)gcT>gcC	p.A615A	SUGP2_ENST00000600377.1_Silent_p.A629A|SUGP2_ENST00000337018.6_Silent_p.A615A|SUGP2_ENST00000456085.2_Silent_p.A384A|SUGP2_ENST00000452918.2_Silent_p.A615A			Q8IX01	SUGP2_HUMAN	SURP and G patch domain containing 2	615					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						CCTACCAGTAAGCAGGGTCCT	0.488																																					p.A615A		Atlas-SNP	.											.	SUGP2	107	.	0			c.T1845C						.						103	94	97					19																	19129923		2203	4300	6503	SO:0001819	synonymous_variant	10147	exon4			CCAGTAAGCAGGG	AB002363	CCDS12392.1	19p13	2013-01-28	2010-08-10	2010-08-10	ENSG00000064607	ENSG00000064607		"G patch domain containing"	18641	protein-coding gene	gene with protein product		607993	"splicing factor, arginine/serine-rich 14"	SFRS14		12594045	Standard	NM_014884		Approved	KIAA0365	uc002nkx.2	Q8IX01		ENST00000601879.1:c.1845T>C	chr19.hg19:g.19129923A>G		139.0	0.0		83.0	4.0	NM_014884	C9JI71|O15071|O60369|Q5JPH7|Q8WUF7	Silent	SNP	ENST00000601879.1	hg19	CCDS12392.1																																																																																			.	.		0.488	SUGP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464627.1	NM_001017392		G	19129923	A	G	19129923	2	3	260	1	0	0	0	0	0	0	0	1	14185	59	3	2		2	SFRS14	19	19129923	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	753340	19129923	39999060	823	38068										
ZNF90	7643	hgsc.bcm.edu	37	chr19	20229869	20229869	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cttagcacacataagataatTcacagtggagagaatcccta	7	9	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:20229869T>C	ENST00000418063.2	+	4	1618	c.1506T>C	c.(1504-1506)atT>atC	p.I502I	ZNF90_ENST00000474284.1_Intron	NM_007138.1	NP_009069.1	Q03938	ZNF90_HUMAN	zinc finger protein 90	502					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.I502I(1)		breast(1)|lung(2)|ovary(1)|skin(1)	5						ATAAGATAATTCACAGTGGAG	0.398																																					p.I502I		Atlas-SNP	.											ZNF90_ENST00000418063,NS,carcinoma,0,1	ZNF90	93	.	1	Substitution - coding silent(1)	endometrium(1)	c.T1506C						.						61	58	59					19																	20229869		692	1591	2283	SO:0001819	synonymous_variant	7643	exon4			GATAATTCACAGT	M61870	CCDS46028.1	19p12	2013-01-08	2006-02-01		ENSG00000213988	ENSG00000213988		"Zinc fingers, C2H2-type", "-"	13165	protein-coding gene	gene with protein product		603973	"zinc finger protein 90 (HTF9)"			8467795	Standard	NM_007138		Approved	HTF9	uc002nor.2	Q03938	OTTHUMG00000158057	ENST00000418063.2:c.1506T>C	chr19.hg19:g.20229869T>C		74.0	0.0		56.0	4.0	NM_007138	B9EH87	Silent	SNP	ENST00000418063.2	hg19	CCDS46028.1																																																																																			.	.		0.398	ZNF90-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350101.1	NM_007138		C	20229869	T	C	20229869	2	2	260	1	0	0	0	0	0	0	0	1	18214	1771	62	2		2	ZNF90	19	20229869	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1099946	20229869	38899114	824	38069										
ZNF208	7757	hgsc.bcm.edu	37	chr19	22157552	22157552	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttctcaatatcactttttggAaagaatcttctatgccctgc	5	10	4	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:22157552A>G	ENST00000397126.4	-	4	432	c.284T>C	c.(283-285)tTc>tCc	p.F95S	ZNF208_ENST00000601773.1_Intron|ZNF208_ENST00000599916.1_Missense_Mutation_p.F95S	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	95					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				CACTTTTTGGAAAGAATCTTC	0.328																																					p.F95S		Atlas-SNP	.											.	ZNF208	817	.	0			c.T284C						.						41	40	40					19																	22157552		2042	4240	6282	SO:0001583	missense	7757	exon4			TTTTGGAAAGAAT	BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"Zinc fingers, C2H2-type", "-"	12999	protein-coding gene	gene with protein product	"zinc finger protein 95"	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.284T>C	chr19.hg19:g.22157552A>G	ENSP00000380315:p.Phe95Ser	198.0	0.0		123.0	6.0	NM_007153		Missense_Mutation	SNP	ENST00000397126.4	hg19	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	A	9.324	1.058833	0.19987	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.07444	3.19	0.77	0.77	0.18497	.	.	.	.	.	T	0.10766	0.0263	.	.	.	0.09310	N	1	D;P	0.71674	0.998;0.729	P;B	0.59115	0.852;0.439	T	0.29458	-1.0011	8	0.16420	T	0.52	.	3.9499	0.09364	1.0:0.0:0.0:0.0	.	95;95	O43345;F8WEA0	ZN208_HUMAN;.	S	95	ENSP00000380315:F95S	ENSP00000380315:F95S	F	-	2	0	ZNF208	21949392	0.000000	0.05858	0.018000	0.16275	0.530000	0.34684	0.035000	0.13797	0.647000	0.30713	0.246000	0.17985	TTC	.	.		0.328	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		G	22157552	A	G	22157552	3	3	260	1	0	0	0	0	1	0	0	0	17781	246	9	2	3562	2	ZNF208	19	22157552	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1927683	22157552	36971431	825	38070										
WDR88	126248	hgsc.bcm.edu	37	chr19	33623281	33623281	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cttggacagggaaccaccacCgcatctgttgcctgagaagc	11	13	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:33623281C>T	ENST00000355868.3	+	1	282	c.206C>T	c.(205-207)cCg>cTg	p.P69L	WDR88_ENST00000361680.2_Missense_Mutation_p.P69L|WDR88_ENST00000592765.1_Missense_Mutation_p.P69L	NM_173479.3	NP_775750.3	Q6ZMY6	WDR88_HUMAN	WD repeat domain 88	69										breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	25	Esophageal squamous(110;0.137)					GAACCACCACCGCATCTGTTG	0.657																																					p.P69L		Atlas-SNP	.											.	WDR88	50	.	0			c.C206T						.						77	77	77					19																	33623281		2203	4300	6503	SO:0001583	missense	126248	exon1			CACCACCGCATCT	BC031227	CCDS12429.1	19q13.11	2013-01-09	2007-04-04	2007-04-04		ENSG00000166359		"WD repeat domain containing"	26999	protein-coding gene	gene with protein product			"PQQ repeat and WD repeat domain containing"	PQWD		12477932	Standard	NM_173479		Approved		uc002nui.3	Q6ZMY6		ENST00000355868.3:c.206C>T	chr19.hg19:g.33623281C>T	ENSP00000348129:p.Pro69Leu	105.0	0.0		82.0	4.0	NM_173479	Q8NEF8	Missense_Mutation	SNP	ENST00000355868.3	hg19	CCDS12429.1	.	.	.	.	.	.	.	.	.	.	C	0.019	-1.457517	0.01071	.	.	ENSG00000166359	ENST00000355868;ENST00000361680	T;T	0.60548	0.49;0.18	1.21	-2.42	0.06542	.	3.784440	0.00859	N	0.001911	T	0.36054	0.0953	L	0.27053	0.805	0.09310	N	1	D	0.57571	0.98	B	0.34873	0.191	T	0.39702	-0.9601	10	0.56958	D	0.05	.	2.5246	0.04688	0.2239:0.4276:0.0:0.3485	.	69	Q6ZMY6	WDR88_HUMAN	L	69	ENSP00000348129:P69L;ENSP00000355148:P69L	ENSP00000348129:P69L	P	+	2	0	WDR88	38315121	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.544000	0.00933	-1.063000	0.03177	-2.210000	0.00300	CCG	.	.		0.657	WDR88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450840.1	NM_173479		T	33623281	C	T	33623281	3	4	260	1	0	0	0	0	1	0	0	0	17350	652	23	1	208	1	WDR88	19	33623281	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	11465729	33623281	25505702	826	38071										
LSR	51599	hgsc.bcm.edu	37	chr19	35758316	35758316	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cccccgcggagccgcagccgGgacgacctctatgaccaaga	12	17	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:35758316G>A	ENST00000361790.3	+	9	1752	c.1593G>A	c.(1591-1593)cgG>cgA	p.R531R	LSR_ENST00000347609.4_Silent_p.R473R|LSR_ENST00000602122.1_Silent_p.R511R|LSR_ENST00000354900.3_Silent_p.R512R|USF2_ENST00000343550.5_5'Flank|USF2_ENST00000595068.1_5'Flank|LSR_ENST00000427250.1_Silent_p.R375R|USF2_ENST00000379134.3_5'Flank|USF2_ENST00000222305.3_5'Flank|LSR_ENST00000360798.3_Silent_p.R463R|AD000684.2_ENST00000602262.1_RNA|USF2_ENST00000594064.1_5'Flank	NM_205834.3	NP_991403.1	Q86X29	LSR_HUMAN	lipolysis stimulated lipoprotein receptor	531					embryo development (GO:0009790)|liver development (GO:0001889)	chylomicron (GO:0042627)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|low-density lipoprotein particle (GO:0034362)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	13	all_lung(56;3.91e-09)|Lung NSC(56;5.64e-09)|Esophageal squamous(110;0.162)		Epithelial(14;1.33e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.29e-18)|all cancers(14;7.11e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			GCCGCAGCCGGGACGACCTCT	0.687																																					p.R531R		Atlas-SNP	.											.	LSR	60	.	0			c.G1593A						.						14	21	19					19																	35758316		2169	4240	6409	SO:0001819	synonymous_variant	51599	exon9			CAGCCGGGACGAC	AF130366	CCDS12449.1, CCDS12450.1, CCDS12451.1, CCDS59376.1	19q13.12	2013-01-11			ENSG00000105699	ENSG00000105699		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29572	protein-coding gene	gene with protein product	"lipolysis-stimulated remnant", "immunoglobulin-like domain containing receptor 3"					10224102	Standard	NM_015925		Approved	LISCH7, ILDR3	uc002nyl.3	Q86X29		ENST00000361790.3:c.1593G>A	chr19.hg19:g.35758316G>A		55.0	0.0		44.0	4.0	NM_205834	A6NDW3|B4DKL4|E9PHD4|O00112|O00426|Q6ZT80|Q8NBM0|Q9BT33|Q9UQL3	Silent	SNP	ENST00000361790.3	hg19	CCDS12450.1																																																																																			.	.		0.687	LSR-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465513.2	NM_015925		A	35758316	G	A	35758316	2	1	260	1	0	0	0	0	0	0	0	1	9073	1219	43	3		3	LSR	19	35758316	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	2135035	35758316	23370667	827	38072										
DMKN	93099	hgsc.bcm.edu	37	chr19	36002356	36002356	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cacctctgctgccaccactgTtgccactgctgccaccactg	7	19	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:36002356T>C	ENST00000339686.3	-	5	1051	c.875A>G	c.(874-876)aAc>aGc	p.N292S	DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000418261.1_Missense_Mutation_p.N292S|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000424570.2_Missense_Mutation_p.N292S|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000447113.2_Missense_Mutation_p.N292S|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000440396.1_Missense_Mutation_p.N292S|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000451297.2_Missense_Mutation_p.N292S|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000402589.2_5'Flank	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	292	Gly-rich.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			gccaccactgttgccactgct	0.627																																					p.N292S		Atlas-SNP	.											.,2	DMKN	116	.	0			c.A875G						.						33	27	29					19																	36002356		2199	4293	6492	SO:0001583	missense	93099	exon5			CCACTGTTGCCAC	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.875A>G	chr19.hg19:g.36002356T>C	ENSP00000342012:p.Asn292Ser	92.0	1.0		73.0	4.0	NM_001126058	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Missense_Mutation	SNP	ENST00000339686.3	hg19	CCDS12463.1	.	.	.	.	.	.	.	.	.	.	T	0.299	-0.974956	0.02215	.	.	ENSG00000161249	ENST00000339686;ENST00000392207;ENST00000447113;ENST00000440396;ENST00000418261;ENST00000424570;ENST00000451297	T;T;T;T;T;T	0.22336	2.35;1.96;1.99;2.03;1.98;2.29	3.3	-1.48	0.08745	.	1.889910	0.02733	N	0.115301	T	0.07143	0.0181	N	0.01576	-0.805	0.09310	N	1	B;B;B;B;B	0.10296	0.003;0.003;0.003;0.003;0.001	B;B;B;B;B	0.10450	0.005;0.005;0.005;0.005;0.003	T	0.30327	-0.9982	10	0.07990	T	0.79	13.9526	6.6897	0.23163	0.0:0.478:0.0:0.522	.	292;292;292;292;292	E7EUS0;Q6E0U4-7;Q6E0U4-3;Q6E0U4-5;Q6E0U4	.;.;.;.;DMKN_HUMAN	S	292	ENSP00000342012:N292S;ENSP00000394908:N292S;ENSP00000415277:N292S;ENSP00000414743:N292S;ENSP00000388404:N292S;ENSP00000409513:N292S	ENSP00000342012:N292S	N	-	2	0	DMKN	40694196	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-0.842000	0.04354	-0.247000	0.09597	0.260000	0.18958	AAC	.	.		0.627	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317		C	36002356	T	C	36002356	3	2	260	1	0	0	0	0	1	0	0	0	4584	1725	60	2	920	2	DMKN	19	36002356	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	244040	36002356	23126627	828	38073										
MLL4	9757	hgsc.bcm.edu	37	chr19	36222960	36222960	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccccgttctttttcgggggcTcgaatcaaagtgcccaacta	9	13	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:36222960T>C	ENST00000222270.7	+	27	5589	c.5589T>C	c.(5587-5589)gcT>gcC	p.A1863A	KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000420124.1_Silent_p.A1863A	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	1863					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										TTTCGGGGGCTCGAATCAAAG	0.662																																					p.A1863A		Atlas-SNP	.											.	MLL4	229	.	0			c.T5589C						.						20	22	21					19																	36222960		1889	4097	5986	SO:0001819	synonymous_variant	8085	exon27			GGGGGCTCGAATC	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"Chromatin-modifying enzymes / K-methyltransferases"	15840	protein-coding gene	gene with protein product	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.5589T>C	chr19.hg19:g.36222960T>C		59.0	0.0		45.0	4.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Silent	SNP	ENST00000222270.7	hg19	CCDS46055.1																																																																																			.	.		0.662	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727		C	36222960	T	C	36222960	2	2	260	1	0	0	0	0	0	0	0	1	9632	1538	54	2		2	MLL4	19	36222960	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	220604	36222960	22906023	829	38074										
APLP1	333	hgsc.bcm.edu	37	chr19	36368656	36368656	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgaacacctgggtcccagtgAattggaagcccctgcccctg	11	14	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:36368656A>T	ENST00000221891.4	+	12	1673	c.1481A>T	c.(1480-1482)gAa>gTa	p.E494V	APLP1_ENST00000589298.2_3'UTR|APLP1_ENST00000586861.1_Missense_Mutation_p.E488V|APLP1_ENST00000537454.2_Missense_Mutation_p.E455V	NM_001024807.1|NM_005166.3	NP_001019978.1|NP_005157.1	P51693	APLP1_HUMAN	amyloid beta (A4) precursor-like protein 1	494					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular response to norepinephrine stimulus (GO:0071874)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|mRNA polyadenylation (GO:0006378)|negative regulation of cAMP biosynthetic process (GO:0030818)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|regulation of translation (GO:0006417)	basement membrane (GO:0005604)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|alpha-2B adrenergic receptor binding (GO:0031695)|alpha-2C adrenergic receptor binding (GO:0031696)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|transition metal ion binding (GO:0046914)			breast(4)|endometrium(2)|kidney(2)|large_intestine(12)|liver(1)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	33	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GGTCCCAGTGAATTGGAAGCC	0.597																																					p.E494V		Atlas-SNP	.											.	APLP1	77	.	0			c.A1481T						.						80	74	76					19																	36368656		2203	4300	6503	SO:0001583	missense	333	exon12			CCAGTGAATTGGA	U48437	CCDS32997.1	19q	2008-07-15							597	protein-coding gene	gene with protein product	"amyloid-like protein 1", "amyloid precursor-like protein 1"	104775				8432545	Standard	NM_001024807		Approved	APLP	uc002ocf.3	P51693		ENST00000221891.4:c.1481A>T	chr19.hg19:g.36368656A>T	ENSP00000221891:p.Glu494Val	68.0	0.0		75.0	4.0	NM_005166	O00113|Q96A92	Missense_Mutation	SNP	ENST00000221891.4	hg19	CCDS32997.1	.	.	.	.	.	.	.	.	.	.	A	12.64	1.999663	0.35320	.	.	ENSG00000105290	ENST00000537454;ENST00000221891	D;D	0.94862	-3.45;-3.54	5.3	4.22	0.49857	.	0.853808	0.09831	N	0.750239	D	0.89121	0.6625	N	0.14661	0.345	0.28750	N	0.901508	B;B;P;B	0.35844	0.005;0.448;0.524;0.221	B;B;B;B	0.39379	0.002;0.298;0.094;0.043	D	0.83712	0.0188	10	0.48119	T	0.1	-0.4882	8.0386	0.30508	0.8193:0.0:0.0:0.1806	.	488;455;494;494	B7Z4G8;F5GZ08;P51693-2;P51693	.;.;.;APLP1_HUMAN	V	455;494	ENSP00000441501:E455V;ENSP00000221891:E494V	ENSP00000221891:E494V	E	+	2	0	APLP1	41060496	0.994000	0.37717	0.832000	0.32986	0.852000	0.48524	2.459000	0.45023	2.157000	0.67596	0.533000	0.62120	GAA	.	.		0.597	APLP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452564.1	NM_001024807		T	36368656	A	T	36368656	3	4	260	1	0	0	0	0	1	0	0	0	778	246	9	4	1527	4	APLP1	19	36368656	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	145696	36368656	22760327	830	38075										
ZFP14	57677	hgsc.bcm.edu	37	chr19	36853129	36853129	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tctatggccacatccctgaaTgtcactgaaccctgaaaaaa	6	12	2	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:36853129T>C	ENST00000270001.7	-	3	136	c.21A>G	c.(19-21)acA>acG	p.T7T	ZFP14_ENST00000589280.1_Silent_p.T7T	NM_020917.2	NP_065968.1	Q9HCL3	ZFP14_HUMAN	ZFP14 zinc finger protein	7	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T7T(1)		NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	26	Esophageal squamous(110;0.162)					CATCCCTGAATGTCACTGAAC	0.403																																					p.T7T		Atlas-SNP	.											ZFP14,NS,carcinoma,0,1	ZFP14	68	.	1	Substitution - coding silent(1)	lung(1)	c.A21G						.						86	82	83					19																	36853129		2203	4300	6503	SO:0001819	synonymous_variant	57677	exon3			CCTGAATGTCACT	AB046779	CCDS33002.1	19q13.13	2013-01-08	2012-11-27			ENSG00000142065		"Zinc fingers, C2H2-type", "-"	29312	protein-coding gene	gene with protein product			"zinc finger protein 14 homolog (mouse)"			10997877	Standard	NM_020917		Approved	KIAA1559, ZNF531	uc010eex.2	Q9HCL3		ENST00000270001.7:c.21A>G	chr19.hg19:g.36853129T>C		123.0	0.0		66.0	4.0	NM_020917	A7MD23	Silent	SNP	ENST00000270001.7	hg19	CCDS33002.1																																																																																			.	.		0.403	ZFP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452528.1	NM_020917		C	36853129	T	C	36853129	2	2	260	1	0	0	0	0	0	0	0	1	17654	1451	51	2		2	ZFP14	19	36853129	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	484473	36853129	22275854	831	38076										
ZNF567	163081	hgsc.bcm.edu	37	chr19	37210227	37210227	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	atgaagttcttatgcagtatCagaaaacggaaactccagca	8	8	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:37210227C>T	ENST00000536254.2	+	6	823	c.601C>T	c.(601-603)Cag>Tag	p.Q201*	ZNF567_ENST00000360729.4_Nonsense_Mutation_p.Q170*|ZNF850_ENST00000589390.1_Intron|ZNF567_ENST00000588311.1_Nonsense_Mutation_p.Q170*|ZNF567_ENST00000392163.2_Nonsense_Mutation_p.Q170*|ZNF567_ENST00000585696.1_Nonsense_Mutation_p.Q170*			Q8N184	ZN567_HUMAN	zinc finger protein 567	201					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			TATGCAGTATCAGAAAACGGA	0.398																																					p.Q170X		Atlas-SNP	.											.	ZNF567	61	.	0			c.C508T						.						47	46	46					19																	37210227		2203	4300	6503	SO:0001587	stop_gained	163081	exon4			CAGTATCAGAAAA	AK093034	CCDS12495.1, CCDS74349.1	19q13.12	2013-10-08				ENSG00000189042		"Zinc fingers, C2H2-type", "-"	28696	protein-coding gene	gene with protein product						12477932	Standard	XM_006723064		Approved	MGC45586	uc002oep.4	Q8N184		ENST00000536254.2:c.601C>T	chr19.hg19:g.37210227C>T	ENSP00000441838:p.Gln201*	136.0	0.0		78.0	4.0	NM_152603	B3KX49|Q6N044	Nonsense_Mutation	SNP	ENST00000536254.2	hg19		.	.	.	.	.	.	.	.	.	.	C	16.98	3.270836	0.59540	.	.	ENSG00000189042	ENST00000536254;ENST00000378686;ENST00000360729;ENST00000423498;ENST00000392163	.	.	.	4.16	3.1	0.35709	.	0.324668	0.22594	N	0.058050	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	.	12.4841	0.55861	0.0:0.8306:0.1694:0.0	.	.	.	.	X	201;201;170;200;170	.	ENSP00000353957:Q170X	Q	+	1	0	ZNF567	41902067	0.001000	0.12720	0.873000	0.34254	0.619000	0.37552	0.105000	0.15333	1.315000	0.45114	0.462000	0.41574	CAG	.	.		0.398	ZNF567-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000453549.1	NM_152603		T	37210227	C	T	37210227	4	4	260	1	0	0	0	0	0	1	0	0	18013	827	29	3	518	3	ZNF567	19	37210227	Nonsense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	357098	37210227	21918756	832	38077										
ZNF790	388536	hgsc.bcm.edu	37	chr19	37309733	37309733	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acattcttcacattcatatgGcctctttccagtatgaattt	4	10	4	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:37309733G>T	ENST00000356725.4	-	5	1633	c.1513C>A	c.(1513-1515)Cca>Aca	p.P505T	CTD-2162K18.5_ENST00000587278.1_RNA|CTD-2162K18.5_ENST00000588906.1_RNA	NM_001242802.1|NM_206894.3	NP_001229731.1|NP_996777.2	Q6PG37	ZN790_HUMAN	zinc finger protein 790	505					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			biliary_tract(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	32	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			CATTCATATGGCCTCTTTCCA	0.398																																					p.P505T		Atlas-SNP	.											.	ZNF790	89	.	0			c.C1513A						.						109	102	104					19																	37309733		2203	4300	6503	SO:0001583	missense	388536	exon5			CATATGGCCTCTT	BC057245	CCDS12496.1	19q13.12	2013-01-08			ENSG00000197863	ENSG00000197863		"Zinc fingers, C2H2-type", "-"	33114	protein-coding gene	gene with protein product							Standard	NM_206894		Approved	MGC62100, FLJ20350	uc021utm.1	Q6PG37	OTTHUMG00000165616	ENST00000356725.4:c.1513C>A	chr19.hg19:g.37309733G>T	ENSP00000349161:p.Pro505Thr	125.0	0.0		71.0	4.0	NM_206894		Missense_Mutation	SNP	ENST00000356725.4	hg19	CCDS12496.1	.	.	.	.	.	.	.	.	.	.	G	12.01	1.808396	0.31961	.	.	ENSG00000197863	ENST00000356725	T	0.16897	2.31	3.04	-0.911	0.10507	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.22551	0.0544	M	0.82056	2.57	0.29696	N	0.840516	B	0.26041	0.14	B	0.34180	0.177	T	0.36311	-0.9753	9	0.87932	D	0	.	4.88	0.13674	0.1151:0.0:0.5212:0.3638	.	505	Q6PG37	ZN790_HUMAN	T	505	ENSP00000349161:P505T	ENSP00000349161:P505T	P	-	1	0	ZNF790	42001573	1.000000	0.71417	0.004000	0.12327	0.433000	0.31745	4.187000	0.58344	-0.218000	0.10018	-0.500000	0.04577	CCA	.	.		0.398	ZNF790-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385341.2	NM_206894		T	37309733	G	T	37309733	3	4	260	1	0	0	0	0	1	0	0	0	18177	1203	42	3	401	3	ZNF790	19	37309733	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	99506	37309733	21819250	833	38078										
ZNF420	147923	hgsc.bcm.edu	37	chr19	37619072	37619072	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aatgaaaagccctatgaatgTaaggaatgtggaaagatgtt	11	3	0	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:37619072T>A	ENST00000337995.3	+	5	1394	c.1179T>A	c.(1177-1179)tgT>tgA	p.C393*	ZNF585A_ENST00000588723.1_Intron|ZNF420_ENST00000304239.7_Nonsense_Mutation_p.C393*|CTC-454I21.4_ENST00000587645.1_RNA	NM_144689.3	NP_653290.2	Q8TAQ5	ZN420_HUMAN	zinc finger protein 420	393					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(2)|large_intestine(9)|lung(10)|prostate(1)|skin(3)	27			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CCTATGAATGTAAGGAATGTG	0.398																																					p.C393X		Atlas-SNP	.											.	ZNF420	71	.	0			c.T1179A						.						87	89	88					19																	37619072		2203	4300	6503	SO:0001587	stop_gained	147923	exon5			TGAATGTAAGGAA	AK056695	CCDS12498.1	19q13.12	2013-01-08			ENSG00000197050	ENSG00000197050		"Zinc fingers, C2H2-type", "-"	20649	protein-coding gene	gene with protein product							Standard	NM_144689		Approved	FLJ32191	uc002ofl.3	Q8TAQ5	OTTHUMG00000048168	ENST00000337995.3:c.1179T>A	chr19.hg19:g.37619072T>A	ENSP00000338770:p.Cys393*	146.0	0.0		98.0	4.0	NM_144689	B2RDY6|Q96ML5	Nonsense_Mutation	SNP	ENST00000337995.3	hg19	CCDS12498.1	.	.	.	.	.	.	.	.	.	.	T	36	5.828513	0.96996	.	.	ENSG00000197050	ENST00000304239;ENST00000337995	.	.	.	4.24	3.19	0.36642	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.2498	0.26142	0.0:0.1807:0.0:0.8193	.	.	.	.	X	393	.	ENSP00000306102:C393X	C	+	3	2	ZNF420	42310912	0.001000	0.12720	1.000000	0.80357	0.995000	0.86356	-0.186000	0.09670	1.780000	0.52325	0.533000	0.62120	TGT	.	.		0.398	ZNF420-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109587.3	NM_144689		A	37619072	T	A	37619072	4	1	260	1	0	0	0	0	0	1	0	0	17912	1644	57	4	1189	4	ZNF420	19	37619072	Nonsense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	309339	37619072	21509911	834	38079										
ZNF569	148266	hgsc.bcm.edu	37	chr19	37905051	37905051	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tattaccatatgatttcacaGgttcattatattcacaatgc	4	8	3	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:37905051G>T	ENST00000316950.6	-	6	1066	c.509C>A	c.(508-510)cCt>cAt	p.P170H	ZNF569_ENST00000392150.2_Missense_Mutation_p.P11H|ZNF569_ENST00000392149.2_Missense_Mutation_p.P170H	NM_152484.2	NP_689697.2	Q5MCW4	ZN569_HUMAN	zinc finger protein 569	170					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(5)|endometrium(4)|large_intestine(16)|lung(11)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	40			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TGATTTCACAGGTTCATTATA	0.338																																					p.P170H		Atlas-SNP	.											.	ZNF569	101	.	0			c.C509A						.						86	84	85					19																	37905051		2203	4300	6503	SO:0001583	missense	148266	exon6			TTCACAGGTTCAT	AL833408	CCDS12503.1	19q13.12	2013-09-20			ENSG00000196437	ENSG00000196437		"Zinc fingers, C2H2-type", "-"	24737	protein-coding gene	gene with protein product		613904				12477932	Standard	NM_152484		Approved	FLJ32053, ZAP1	uc002ogi.3	Q5MCW4	OTTHUMG00000048172	ENST00000316950.6:c.509C>A	chr19.hg19:g.37905051G>T	ENSP00000325018:p.Pro170His	130.0	0.0		82.0	4.0	NM_152484	A8K1S2|Q15925|Q17RR6|Q96MQ2	Missense_Mutation	SNP	ENST00000316950.6	hg19	CCDS12503.1	.	.	.	.	.	.	.	.	.	.	G	0.029	-1.344691	0.01277	.	.	ENSG00000196437	ENST00000316950;ENST00000392150	T;T	0.09163	3.24;3.01	3.11	2.06	0.26882	.	0.573207	0.13626	N	0.374075	T	0.06280	0.0162	N	0.14661	0.345	0.09310	N	1	B;B	0.31519	0.327;0.118	B;B	0.28232	0.087;0.053	T	0.32613	-0.9900	10	0.66056	D	0.02	.	8.3047	0.32036	0.1259:0.0:0.8741:0.0	.	11;170	Q17RR6;Q5MCW4	.;ZN569_HUMAN	H	170;11	ENSP00000325018:P170H;ENSP00000375993:P11H	ENSP00000325018:P170H	P	-	2	0	ZNF569	42596891	0.000000	0.05858	0.002000	0.10522	0.712000	0.41017	0.380000	0.20602	0.874000	0.35823	0.591000	0.81541	CCT	.	.		0.338	ZNF569-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109594.2	NM_152484		T	37905051	G	T	37905051	3	4	260	1	0	0	0	0	1	0	0	0	18015	1000	35	3	1555	3	ZNF569	19	37905051	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	285979	37905051	21223932	835	38080										
SIPA1L3	23094	hgsc.bcm.edu	37	chr19	38633306	38633306	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccttctgggagcttctccacCcccggttcggccacctacgt	9	18	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:38633306C>T	ENST00000222345.6	+	12	3998	c.3489C>T	c.(3487-3489)acC>acT	p.T1163T		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	1163					hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			GCTTCTCCACCCCCGGTTCGG	0.557											OREG0025445	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T1163T		Atlas-SNP	.											.	SIPA1L3	150	.	0			c.C3489T						.						185	179	181					19																	38633306		2203	4300	6503	SO:0001819	synonymous_variant	23094	exon12			CTCCACCCCCGGT	AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738			23801	protein-coding gene	gene with protein product							Standard	XM_005258671		Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.3489C>T	chr19.hg19:g.38633306C>T		87.0	0.0	879	69.0	4.0	NM_015073	Q2TV87	Silent	SNP	ENST00000222345.6	hg19	CCDS33007.1																																																																																			.	.		0.557	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278		T	38633306	C	T	38633306	2	4	260	1	0	0	0	0	0	0	0	1	14346	610	22	3		3	SIPA1L3	19	38633306	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	728255	38633306	20495677	836	38081										
EIF3K	11184	hgsc.bcm.edu	37	chr19	39111009	39111009	+	5'Flank	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gaacctggccaccctggagcGctatgtagagacgcaggcca	13	13	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:39111009G>T	ENST00000591517.1	-	0	0				EIF3K_ENST00000593062.1_3'UTR|EIF3K_ENST00000538434.1_Intron|MAP4K1_ENST00000589130.1_5'Flank|EIF3K_ENST00000545173.2_Missense_Mutation_p.R31L|EIF3K_ENST00000248342.4_Missense_Mutation_p.R31L|MAP4K1_ENST00000586296.1_5'Flank|EIF3K_ENST00000592558.1_Missense_Mutation_p.R31L|EIF3K_ENST00000593149.1_5'UTR|MAP4K1_ENST00000396857.2_5'Flank|EIF3K_ENST00000588934.1_Missense_Mutation_p.R31L	NM_007181.4	NP_009112.1	Q92918	M4K1_HUMAN	mitogen-activated protein kinase kinase kinase kinase 1						activation of JUN kinase activity (GO:0007257)|activation of MAPKKK activity (GO:0000185)|cell proliferation (GO:0008283)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to stress (GO:0006950)	membrane (GO:0016020)	ATP binding (GO:0005524)|MAP kinase kinase kinase kinase activity (GO:0008349)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(24)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	44	all_cancers(60;6.42e-06)|Ovarian(47;0.103)		Lung(45;0.000751)|LUSC - Lung squamous cell carcinoma(53;0.00272)			ACCCTGGAGCGCTATGTAGAG	0.517																																					p.R31L		Atlas-SNP	.											.	EIF3K	22	.	0			c.G92T						.						112	84	93					19																	39111009		2203	4300	6503	SO:0001631	upstream_gene_variant	27335	exon2			TGGAGCGCTATGT	U66464	CCDS42564.1, CCDS59385.1	19q13.1-q13.4	2011-06-09				ENSG00000104814	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6863	protein-coding gene	gene with protein product	"hematopoietic progenitor kinase 1"	601983				8824585	Standard	NM_001042600		Approved	HPK1	uc002oix.1	Q92918			chr19.hg19:g.39111009G>T	Exception_encountered	113.0	0.0		83.0	4.0	NM_013234		Missense_Mutation	SNP	ENST00000591517.1	hg19	CCDS59385.1	.	.	.	.	.	.	.	.	.	.	G	13.88	2.370098	0.42003	.	.	ENSG00000178982	ENST00000248342;ENST00000545173	.	.	.	4.45	4.45	0.53987	Translation initiation factor 3, subunit 12, N-terminal, eukaryotic (1);Armadillo-type fold (1);	0.062115	0.64402	D	0.000005	T	0.45856	0.1363	L	0.32530	0.975	0.58432	D	0.999997	B;B	0.16166	0.016;0.016	B;B	0.15484	0.013;0.008	T	0.48222	-0.9054	9	0.87932	D	0	-12.3368	11.1129	0.48243	0.0937:0.0:0.9063:0.0	.	31;31	B7ZAM9;Q9UBQ5	.;EIF3K_HUMAN	L	31	.	ENSP00000248342:R31L	R	+	2	0	EIF3K	43802849	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	6.017000	0.70805	2.386000	0.81285	0.563000	0.77884	CGC	.	.		0.517	MAP4K1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000453390.1	NM_001042600		T	39111009	G	T	39111009	1	4	260	0	1	0	0	0	0	0	0	0	5023	1087	38	1		1	EIF3K	19	39111009	5'Flank	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	477703	39111009	20017974	837	38082										
ADCK4	79934	hgsc.bcm.edu	37	chr19	41220243	41220243	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctgcgaatgtcctcctcaccCaggcctctcccaggcccatc	7	20	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:41220243C>T	ENST00000324464.3	-	3	463	c.162G>A	c.(160-162)ctG>ctA	p.L54L	ADCK4_ENST00000450541.1_Silent_p.L54L|ADCK4_ENST00000243583.6_Silent_p.L54L|ITPKC_ENST00000263370.2_5'Flank	NM_024876.3	NP_079152.3	Q96D53	ADCK4_HUMAN	aarF domain containing kinase 4	54						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(6)|stomach(2)|urinary_tract(1)	17			Lung(22;9.49e-05)|LUSC - Lung squamous cell carcinoma(20;0.000219)			CCTCCTCACCCAGGCCTCTCC	0.592																																					p.L54L		Atlas-SNP	.											.	ADCK4	92	.	0			c.G162A						.						63	67	66					19																	41220243		2203	4300	6503	SO:0001819	synonymous_variant	79934	exon3			CTCACCCAGGCCT	AK022291	CCDS12562.1, CCDS46081.1	19q13.2	2008-02-05				ENSG00000123815			19041	protein-coding gene	gene with protein product		615567					Standard	NM_024876		Approved	FLJ12229, COQ8	uc002oor.2	Q96D53		ENST00000324464.3:c.162G>A	chr19.hg19:g.41220243C>T		126.0	0.0		84.0	4.0	NM_001142555	Q8TAJ1|Q9HA52	Silent	SNP	ENST00000324464.3	hg19	CCDS12562.1																																																																																			.	.		0.592	ADCK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462731.1	NM_024876		T	41220243	C	T	41220243	2	4	260	1	0	0	0	0	0	0	0	1	290	581	21	3		3	ADCK4	19	41220243	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	2109234	41220243	17908740	838	38083										
AXL	558	hgsc.bcm.edu	37	chr19	41762466	41762466	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccaagatgccagtcaagtggAttgccattgagagtctagct	11	9	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:41762466A>G	ENST00000301178.4	+	18	2336	c.2146A>G	c.(2146-2148)Att>Gtt	p.I716V	AXL_ENST00000593513.1_Missense_Mutation_p.I448V|AXL_ENST00000359092.3_Missense_Mutation_p.I707V	NM_001278599.1|NM_021913.3	NP_001265528.1|NP_068713	P30530	UFO_HUMAN	AXL receptor tyrosine kinase	716	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic cell clearance (GO:0043277)|blood vessel remodeling (GO:0001974)|cell maturation (GO:0048469)|cellular response to extracellular stimulus (GO:0031668)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interferon-alpha (GO:0035457)|cellular response to lipopolysaccharide (GO:0071222)|dendritic cell differentiation (GO:0097028)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte homeostasis (GO:0034101)|forebrain cell migration (GO:0021885)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|natural killer cell differentiation (GO:0001779)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of tumor necrosis factor production (GO:0032720)|neuron migration (GO:0001764)|organ regeneration (GO:0031100)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of protein kinase B signaling (GO:0051897)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|phosphatidylserine binding (GO:0001786)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(9)|lung(12)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	48						AGTCAAGTGGATTGCCATTGA	0.567																																					p.I716V		Atlas-SNP	.											.	AXL	126	.	0			c.A2146G						.						235	170	192					19																	41762466		2203	4300	6503	SO:0001583	missense	558	exon18			AAGTGGATTGCCA	M76125	CCDS12574.1, CCDS12575.1, CCDS62677.1	19q13.1	2013-02-11				ENSG00000167601	2.7.10.1	"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	905	protein-coding gene	gene with protein product		109135				1656220	Standard	NM_021913		Approved	UFO, JTK11	uc010ehj.3	P30530		ENST00000301178.4:c.2146A>G	chr19.hg19:g.41762466A>G	ENSP00000301178:p.Ile716Val	192.0	0.0		121.0	5.0	NM_021913	Q8N5L2|Q9UD27	Missense_Mutation	SNP	ENST00000301178.4	hg19	CCDS12575.1	.	.	.	.	.	.	.	.	.	.	A	19.72	3.880464	0.72294	.	.	ENSG00000167601	ENST00000301178;ENST00000359092	T;T	0.61980	0.06;0.06	4.49	4.49	0.54785	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.53610	0.1807	N	0.11154	0.105	0.34945	D	0.750694	D;P	0.54207	0.965;0.941	P;P	0.52646	0.662;0.705	T	0.69514	-0.5125	10	0.72032	D	0.01	-17.9022	13.1778	0.59637	1.0:0.0:0.0:0.0	.	707;716	P30530-2;P30530	.;UFO_HUMAN	V	716;707	ENSP00000301178:I716V;ENSP00000351995:I707V	ENSP00000301178:I716V	I	+	1	0	AXL	46454306	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.154000	0.77437	2.004000	0.58718	0.482000	0.46254	ATT	.	.		0.567	AXL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463323.2			G	41762466	A	G	41762466	3	3	260	1	0	0	0	0	1	0	0	0	1238	333	12	2	2216	2	AXL	19	41762466	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	542223	41762466	17366517	839	38084										
DEDD2	162989	hgsc.bcm.edu	37	chr19	42703669	42703669	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggccagcctcatagtcagccTcatccacactgaccagcagg	9	16	3	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:42703669T>C	ENST00000595337.1	-	5	989	c.902A>G	c.(901-903)gAg>gGg	p.E301G	DEDD2_ENST00000593804.1_5'UTR|DEDD2_ENST00000336034.4_Missense_Mutation_p.E296G|DEDD2_ENST00000596251.1_Missense_Mutation_p.E301G	NM_001270614.1	NP_001257543.1	Q8WXF8	DEDD2_HUMAN	death effector domain containing 2	301					apoptotic nuclear changes (GO:0030262)|cellular homeostasis (GO:0019725)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|RNA processing (GO:0006396)|rRNA catabolic process (GO:0016075)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)	DNA binding (GO:0003677)|receptor signaling complex scaffold activity (GO:0030159)			endometrium(1)|large_intestine(1)|ovary(1)|prostate(2)	5		Prostate(69;0.0704)				ATAGTCAGCCTCATCCACACT	0.682																																					p.E301G		Atlas-SNP	.											.	DEDD2	16	.	0			c.A902G						.						31	31	31					19																	42703669		2203	4297	6500	SO:0001583	missense	162989	exon5			TCAGCCTCATCCA	AY125488	CCDS12597.1, CCDS59391.1	19q13.31	2008-02-05				ENSG00000160570			24450	protein-coding gene	gene with protein product						11965497, 12235123	Standard	NM_133328		Approved	FLAME-3	uc031rkv.1	Q8WXF8		ENST00000595337.1:c.902A>G	chr19.hg19:g.42703669T>C	ENSP00000470082:p.Glu301Gly	182.0	0.0		101.0	5.0	NM_133328	Q8NBR2|Q8NES1|Q8TAA8|Q96D35	Missense_Mutation	SNP	ENST00000595337.1	hg19	CCDS12597.1	.	.	.	.	.	.	.	.	.	.	T	28.3	4.906655	0.92107	.	.	ENSG00000160570	ENST00000336034	.	.	.	4.03	4.03	0.46877	.	0.068636	0.56097	D	0.000024	T	0.54287	0.1849	N	0.24115	0.695	0.42321	D	0.992256	D;D	0.65815	0.995;0.991	P;P	0.61003	0.882;0.766	T	0.60910	-0.7169	9	0.87932	D	0	-21.3874	12.6309	0.56657	0.0:0.0:0.0:1.0	.	296;301	Q8WXF8-2;Q8WXF8	.;DEDD2_HUMAN	G	301	.	ENSP00000336972:E301G	E	-	2	0	DEDD2	47395509	1.000000	0.71417	0.964000	0.40570	0.978000	0.69477	7.997000	0.88414	1.764000	0.52075	0.460000	0.39030	GAG	.	.		0.682	DEDD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463508.1	NM_133328		C	42703669	T	C	42703669	3	2	260	1	0	0	0	0	1	0	0	0	4387	1551	54	2	82	2	DEDD2	19	42703669	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	941203	42703669	16425314	840	38085										
XRCC1	7515	hgsc.bcm.edu	37	chr19	44048332	44048332	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cgtatcggatgagtttccgcCgctcgtccccagggaactcc	11	15	0	1	rs2307167	byFrequency	TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:44048332C>A	ENST00000262887.5	-	15	2223	c.1676G>T	c.(1675-1677)cGg>cTg	p.R559L	XRCC1_ENST00000543982.1_Missense_Mutation_p.R528L			P18887	XRCC1_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 1	559	BRCT 2. {ECO:0000255|PROSITE- ProRule:PRU00033}.		R -> Q (in dbSNP:rs2307167).		base-excision repair (GO:0006284)|DNA repair (GO:0006281)|hippocampus development (GO:0021766)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to organic substance (GO:0010033)|single strand break repair (GO:0000012)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)			breast(2)|endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Prostate(69;0.0153)				GAGTTTCCGCCGCTCGTCCCC	0.582								Other BER factors																													p.R559L		Atlas-SNP	.											.	XRCC1	47	.	0			c.G1676T						.						63	55	58					19																	44048332		2203	4300	6503	SO:0001583	missense	7515	exon15			TTCCGCCGCTCGT	M36089	CCDS12624.1	19q13.2	2014-09-17				ENSG00000073050			12828	protein-coding gene	gene with protein product		194360		RCC		2247054	Standard	NM_006297		Approved		uc002owt.2	P18887		ENST00000262887.5:c.1676G>T	chr19.hg19:g.44048332C>A	ENSP00000262887:p.Arg559Leu	104.0	0.0		92.0	4.0	NM_006297	Q6IBS4|Q9HCB1	Missense_Mutation	SNP	ENST00000262887.5	hg19	CCDS12624.1	.	.	.	.	.	.	.	.	.	.	C	11.55	1.671996	0.29693	.	.	ENSG00000073050	ENST00000458471;ENST00000262887;ENST00000543982	D;D	0.84800	-1.9;-1.9	4.75	2.58	0.30949	BRCT (4);	0.000000	0.64402	D	0.000001	T	0.78039	0.4221	L	0.45581	1.43	0.39517	D	0.968455	B;P	0.44734	0.001;0.842	B;B	0.41271	0.001;0.352	T	0.73040	-0.4108	10	0.29301	T	0.29	-23.3026	8.3823	0.32479	0.154:0.7608:0.0:0.0852	.	528;559	F5H8D7;P18887	.;XRCC1_HUMAN	L	573;559;528	ENSP00000262887:R559L;ENSP00000443671:R528L	ENSP00000262887:R559L	R	-	2	0	XRCC1	48740172	1.000000	0.71417	0.974000	0.42286	0.169000	0.22640	2.406000	0.44557	0.682000	0.31407	-0.464000	0.05259	CGG	.	C|0.999;T|0.001		0.582	XRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463194.1	NM_006297		A	44048332	C	A	44048332	3	1	260	1	0	0	0	0	1	0	0	0	17467	652	23	1	237	1	XRCC1	19	44048332	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	1344663	44048332	15080651	841	38086										
ZNF227	7770	hgsc.bcm.edu	37	chr19	44739253	44739253	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttaaaactgacacagaaccaAaaccctgcaaaggtaatgaa	6	9	0	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:44739253A>C	ENST00000313040.7	+	6	875	c.670A>C	c.(670-672)Aaa>Caa	p.K224Q	ZNF227_ENST00000391961.2_Missense_Mutation_p.K173Q|ZNF227_ENST00000589005.1_Missense_Mutation_p.K173Q	NM_182490.1	NP_872296.1	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	224					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(2)|stomach(1)|urinary_tract(1)	24		Prostate(69;0.0435)				CACAGAACCAAAACCCTGCAA	0.378																																					p.K224Q		Atlas-SNP	.											.	ZNF227	62	.	0			c.A670C						.						62	62	62					19																	44739253		2203	4300	6503	SO:0001583	missense	7770	exon6			GAACCAAAACCCT	AK092253	CCDS12636.1, CCDS74388.1	19q13.32	2013-01-08						"Zinc fingers, C2H2-type", "-"	13020	protein-coding gene	gene with protein product							Standard	XM_005259232		Approved		uc002oyu.3	Q86WZ6		ENST00000313040.7:c.670A>C	chr19.hg19:g.44739253A>C	ENSP00000321049:p.Lys224Gln	122.0	0.0		81.0	24.0	NM_182490	B3KRU7|B7Z5P9	Missense_Mutation	SNP	ENST00000313040.7	hg19	CCDS12636.1	.	.	.	.	.	.	.	.	.	.	A	10.27	1.303731	0.23736	.	.	ENSG00000131115	ENST00000313040;ENST00000328297;ENST00000391961;ENST00000418980	T;T	0.02103	4.45;4.45	4.27	3.24	0.37175	.	.	.	.	.	T	0.04634	0.0126	M	0.81614	2.55	0.09310	N	0.999998	B;B;B;B	0.12013	0.005;0.005;0.005;0.005	B;B;B;B	0.08055	0.003;0.003;0.003;0.003	T	0.21143	-1.0254	9	0.66056	D	0.02	.	7.7259	0.28759	0.7438:0.2562:0.0:0.0	.	145;203;176;224	B7Z6M2;Q658S5;Q9NS43;Q86WZ6	.;.;.;ZN227_HUMAN	Q	224;181;173;203	ENSP00000321049:K224Q;ENSP00000375823:K173Q	ENSP00000321049:K224Q	K	+	1	0	ZNF227	49431093	0.001000	0.12720	0.130000	0.21974	0.042000	0.13812	0.751000	0.26348	0.814000	0.34374	0.460000	0.39030	AAA	.	.		0.378	ZNF227-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460720.1	NM_182490		C	44739253	A	C	44739253	3	2	260	1	0	0	0	0	1	0	0	0	17796	15	1	5	684	5	ZNF227	19	44739253	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	690921	44739253	14389730	842	38087										
ZNF227	7770	hgsc.bcm.edu	37	chr19	44740046	44740046	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcatttcagagttcacacggGagagaaaccctataaatgta	8	8	3	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:44740046G>T	ENST00000313040.7	+	6	1668	c.1463G>T	c.(1462-1464)gGa>gTa	p.G488V	ZNF227_ENST00000391961.2_Missense_Mutation_p.G437V|ZNF227_ENST00000589005.1_Missense_Mutation_p.G437V	NM_182490.1	NP_872296.1	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	488					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(2)|stomach(1)|urinary_tract(1)	24		Prostate(69;0.0435)				GTTCACACGGGAGAGAAACCC	0.468																																					p.G488V		Atlas-SNP	.											.	ZNF227	62	.	0			c.G1463T						.						70	69	69					19																	44740046		2203	4300	6503	SO:0001583	missense	7770	exon6			ACACGGGAGAGAA	AK092253	CCDS12636.1, CCDS74388.1	19q13.32	2013-01-08						"Zinc fingers, C2H2-type", "-"	13020	protein-coding gene	gene with protein product							Standard	XM_005259232		Approved		uc002oyu.3	Q86WZ6		ENST00000313040.7:c.1463G>T	chr19.hg19:g.44740046G>T	ENSP00000321049:p.Gly488Val	134.0	0.0		83.0	4.0	NM_182490	B3KRU7|B7Z5P9	Missense_Mutation	SNP	ENST00000313040.7	hg19	CCDS12636.1	.	.	.	.	.	.	.	.	.	.	G	19.62	3.862029	0.71949	.	.	ENSG00000131115	ENST00000313040;ENST00000328297;ENST00000391961;ENST00000418980;ENST00000377916	T;T	0.23552	1.9;1.9	3.93	3.93	0.45458	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.55289	0.1911	M	0.86740	2.835	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.996;1.0;1.0;0.996	T	0.65022	-0.6269	9	0.72032	D	0.01	.	14.2892	0.66265	0.0:0.0:1.0:0.0	.	409;467;440;488	B7Z6M2;Q658S5;Q9NS43;Q86WZ6	.;.;.;ZN227_HUMAN	V	488;445;437;467;189	ENSP00000321049:G488V;ENSP00000375823:G437V	ENSP00000321049:G488V	G	+	2	0	ZNF227	49431886	0.992000	0.36948	0.989000	0.46669	0.994000	0.84299	2.054000	0.41335	2.125000	0.65367	0.563000	0.77884	GGA	.	.		0.468	ZNF227-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460720.1	NM_182490		T	44740046	G	T	44740046	3	4	260	1	0	0	0	0	1	0	0	0	17796	1174	41	3	1477	3	ZNF227	19	44740046	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	793	44740046	14388937	843	38088										
BCAM	4059	hgsc.bcm.edu	37	chr19	45322317	45322317	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tccccaccacccacaggctcGccagagctaaagacagcgga	9	17	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:45322317G>T	ENST00000270233.6	+	11	1363	c.1341G>T	c.(1339-1341)tcG>tcT	p.S447S	BCAM_ENST00000589651.1_Silent_p.S447S	NM_001013257.2|NM_005581.4	NP_001013275.1|NP_005572.2	P50895	BCAM_HUMAN	basal cell adhesion molecule (Lutheran blood group)	447					cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	laminin binding (GO:0043236)|laminin receptor activity (GO:0005055)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)				CCACAGGCTCGCCAGAGCTAA	0.587																																					p.S447S		Atlas-SNP	.											BCAM,NS,carcinoma,0,1	BCAM	53	.	0			c.G1341T						.						136	158	150					19																	45322317		2203	4300	6503	SO:0001819	synonymous_variant	4059	exon11			AGGCTCGCCAGAG	X83425	CCDS12644.1, CCDS42575.1	19q12-q13	2014-07-18	2006-02-23	2006-01-12		ENSG00000187244		"CD molecules", "Blood group antigens", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6722	protein-coding gene	gene with protein product		612773	"Lutheran blood group (Auberger b antigen included)", "basal cell adhesion molecule (Lu and Au blood groups)"	LU			Standard	NM_005581		Approved	CD239	uc002ozu.4	P50895		ENST00000270233.6:c.1341G>T	chr19.hg19:g.45322317G>T		130.0	1.0		59.0	4.0	NM_001013257	A8MYF9|A9YWT5|A9YWT6|Q86VC7	Silent	SNP	ENST00000270233.6	hg19	CCDS12644.1																																																																																			.	.		0.587	BCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453220.1	NM_005581		T	45322317	G	T	45322317	2	4	260	1	0	0	0	0	0	0	0	1	1344	1074	38	1		1	BCAM	19	45322317	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	582271	45322317	13806666	844	38089										
VASP	7408	hgsc.bcm.edu	37	chr19	46021235	46021235	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtgtcaagtataaccaggccAcccccaacttccatcagtgg	8	14	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:46021235A>G	ENST00000245932.6	+	3	582	c.226A>G	c.(226-228)Acc>Gcc	p.T76A	VASP_ENST00000586619.1_3'UTR	NM_003370.3	NP_003361.1	P50552	VASP_HUMAN	vasodilator-stimulated phosphoprotein	76	WH1. {ECO:0000255|PROSITE- ProRule:PRU00410}.				actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|cell junction assembly (GO:0034329)|neural tube closure (GO:0001843)|positive regulation of actin filament polymerization (GO:0030838)|protein homotetramerization (GO:0051289)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	profilin binding (GO:0005522)			endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|skin(2)	18		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0145)|GBM - Glioblastoma multiforme(486;0.154)		TAACCAGGCCACCCCCAACTT	0.682																																					p.T76A		Atlas-SNP	.											.	VASP	26	.	0			c.A226G						.						39	40	39					19																	46021235		2203	4300	6503	SO:0001583	missense	7408	exon3			CAGGCCACCCCCA		CCDS33051.1	19q13.32	2012-02-22			ENSG00000125753	ENSG00000125753			12652	protein-coding gene	gene with protein product		601703				8812448	Standard	XM_005259199		Approved		uc002pcg.3	P50552		ENST00000245932.6:c.226A>G	chr19.hg19:g.46021235A>G	ENSP00000245932:p.Thr76Ala	260.0	0.0		191.0	10.0	NM_003370	B2RBT9|Q6PIZ1|Q93035	Missense_Mutation	SNP	ENST00000245932.6	hg19	CCDS33051.1	.	.	.	.	.	.	.	.	.	.	A	13.23	2.175095	0.38413	.	.	ENSG00000125753	ENST00000245932	D	0.98807	-5.15	4.56	4.56	0.56223	EVH1 (3);Pleckstrin homology-type (1);	0.122937	0.51477	D	0.000089	D	0.98099	0.9373	M	0.77313	2.365	0.80722	D	1	P	0.36222	0.544	B	0.42827	0.399	D	0.98874	1.0767	10	0.66056	D	0.02	-24.2521	12.1609	0.54103	1.0:0.0:0.0:0.0	.	76	P50552	VASP_HUMAN	A	76	ENSP00000245932:T76A	ENSP00000245932:T76A	T	+	1	0	VASP	50713075	1.000000	0.71417	0.999000	0.59377	0.003000	0.03518	8.866000	0.92307	1.812000	0.52913	0.533000	0.62120	ACC	.	.		0.682	VASP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459589.1			G	46021235	A	G	46021235	3	3	260	1	0	0	0	0	1	0	0	0	17143	159	6	2	236	2	VASP	19	46021235	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	698918	46021235	13107748	845	38090										
NOVA2	4858	hgsc.bcm.edu	37	chr19	46444042	46444042	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acggccttgtgcacctgctcGggctcgccgctgaccgtcac	12	17	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:46444042G>A	ENST00000263257.5	-	4	752	c.558C>T	c.(556-558)ccC>ccT	p.P186P		NM_002516.2	NP_002507.1	Q9UNW9	NOVA2_HUMAN	neuro-oncological ventral antigen 2	186	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.				regulation of RNA metabolic process (GO:0051252)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(3)|large_intestine(5)|lung(13)	21		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00245)|GBM - Glioblastoma multiforme(486;0.0782)|Epithelial(262;0.179)		GCACCTGCTCGGGCTCGCCGC	0.632																																					p.P186P		Atlas-SNP	.											NOVA2,colon,carcinoma,0,1	NOVA2	38	.	0			c.C558T						.						57	34	42					19																	46444042		2203	4300	6503	SO:0001819	synonymous_variant	4858	exon4			CTGCTCGGGCTCG	U70477	CCDS12679.1	19q13.3	2008-07-17				ENSG00000104967			7887	protein-coding gene	gene with protein product	"neuro-oncological ventral antigen 3"	601991		NOVA3		9344654, 10368286	Standard	NM_002516		Approved	ANOVA	uc002pdv.2	Q9UNW9		ENST00000263257.5:c.558C>T	chr19.hg19:g.46444042G>A		97.0	0.0		49.0	2.0	NM_002516	O43267|Q9UEA1	Silent	SNP	ENST00000263257.5	hg19	CCDS12679.1																																																																																			.	.		0.632	NOVA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437210.2	NM_002516		A	46444042	G	A	46444042	2	1	260	1	0	0	0	0	0	0	0	1	10564	1103	39	1		1	NOVA2	19	46444042	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	422807	46444042	12684941	846	38091										
EHD2	30846	hgsc.bcm.edu	37	chr19	48219955	48219955	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctcggccctcaaggagctgtAccgcacgaagctgctgccgc	12	16	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:48219955A>G	ENST00000263277.3	+	2	337	c.86A>G	c.(85-87)tAc>tGc	p.Y29C	CTD-2571L23.8_ENST00000599924.1_lincRNA|EHD2_ENST00000538399.1_Intron	NM_014601.3	NP_055416.2	Q9NZN4	EHD2_HUMAN	EH-domain containing 2	29					blood coagulation (GO:0007596)|cortical actin cytoskeleton organization (GO:0030866)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of myoblast fusion (GO:1901741)|protein localization to plasma membrane (GO:0072659)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|nucleic acid binding (GO:0003676)			endometrium(3)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	19		all_cancers(25;6.74e-07)|all_lung(116;2.02e-05)|Lung NSC(112;3.77e-05)|all_epithelial(76;4.89e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		OV - Ovarian serous cystadenocarcinoma(262;0.000336)|all cancers(93;0.000415)|Epithelial(262;0.0132)|GBM - Glioblastoma multiforme(486;0.0537)		AAGGAGCTGTACCGCACGAAG	0.692																																					p.Y29C		Atlas-SNP	.											.	EHD2	59	.	0			c.A86G						.						26	22	23					19																	48219955		2201	4298	6499	SO:0001583	missense	30846	exon2			AGCTGTACCGCAC	AF181263	CCDS12704.1	19q13.3	2014-08-12			ENSG00000024422	ENSG00000024422		"EF-hand domain containing"	3243	protein-coding gene	gene with protein product		605890		PAST2		10673336	Standard	NM_014601		Approved		uc002phj.4	Q9NZN4	OTTHUMG00000183266	ENST00000263277.3:c.86A>G	chr19.hg19:g.48219955A>G	ENSP00000263277:p.Tyr29Cys	118.0	0.0		80.0	4.0	NM_014601	B2RDH9|B4DNU6|Q96CB6	Missense_Mutation	SNP	ENST00000263277.3	hg19	CCDS12704.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.133329	0.77662	.	.	ENSG00000024422	ENST00000263277;ENST00000539439;ENST00000540364	T	0.40476	1.03	3.88	3.88	0.44766	.	0.000000	0.85682	D	0.000000	T	0.70325	0.3211	M	0.93720	3.45	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.77627	-0.2517	10	0.87932	D	0	-33.2545	10.947	0.47306	1.0:0.0:0.0:0.0	.	29	Q9NZN4	EHD2_HUMAN	C	29	ENSP00000263277:Y29C	ENSP00000263277:Y29C	Y	+	2	0	EHD2	52911767	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	8.943000	0.92975	1.772000	0.52199	0.418000	0.28097	TAC	.	.		0.692	EHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465851.1			G	48219955	A	G	48219955	3	3	260	1	0	0	0	0	1	0	0	0	4980	391	14	2	88	2	EHD2	19	48219955	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1775913	48219955	10909028	847	38092										
LIG1	3978	hgsc.bcm.edu	37	chr19	48636262	48636262	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgccctctgcccgtcatattTgtattcgcaggtgaaagctg	10	11	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:48636262T>C	ENST00000263274.7	-	18	2121	c.1702A>G	c.(1702-1704)Aaa>Gaa	p.K568E	LIG1_ENST00000427526.2_Missense_Mutation_p.K537E|LIG1_ENST00000536218.1_Missense_Mutation_p.K500E	NM_000234.1	NP_000225.1	P18858	DNLI1_HUMAN	ligase I, DNA, ATP-dependent	568					anatomical structure morphogenesis (GO:0009653)|base-excision repair (GO:0006284)|cell division (GO:0051301)|DNA biosynthetic process (GO:0071897)|DNA ligation involved in DNA repair (GO:0051103)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|response to hydrogen peroxide (GO:0042542)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(22)|prostate(2)|skin(1)	44		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)	CCGTCATATTTGTATTCGCAG	0.567								Nucleotide excision repair (NER)																													p.K568E		Atlas-SNP	.											.	LIG1	151	.	0			c.A1702G						.						182	168	172					19																	48636262		2203	4300	6503	SO:0001583	missense	3978	exon18			CATATTTGTATTC		CCDS12711.1, CCDS74409.1, CCDS74410.1	19q13.2-q13.3	2014-09-17				ENSG00000105486	6.5.1.1		6598	protein-coding gene	gene with protein product		126391					Standard	XM_005258934		Approved		uc002pia.1	P18858		ENST00000263274.7:c.1702A>G	chr19.hg19:g.48636262T>C	ENSP00000263274:p.Lys568Glu	145.0	0.0		96.0	4.0	NM_000234	B2RAI8|Q2TB12|Q32P23	Missense_Mutation	SNP	ENST00000263274.7	hg19	CCDS12711.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.843632	0.91197	.	.	ENSG00000105486	ENST00000263274;ENST00000544761;ENST00000427526;ENST00000536218	D;D;D	0.97731	-4.51;-4.51;-4.51	5.48	5.48	0.80851	DNA ligase, ATP-dependent, central (1);DNA ligase, ATP-dependent, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.99447	0.9804	H	0.99952	5.035	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.97673	1.0168	10	0.87932	D	0	-20.0359	13.8169	0.63297	0.0:0.0:0.0:1.0	.	537;500;568	B4DTU4;F5GZ28;P18858	.;.;DNLI1_HUMAN	E	568;599;537;500	ENSP00000263274:K568E;ENSP00000442841:K537E;ENSP00000441531:K500E	ENSP00000263274:K568E	K	-	1	0	LIG1	53328074	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	6.890000	0.75633	2.215000	0.71742	0.533000	0.62120	AAA	.	.		0.567	LIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465575.1	NM_000234		C	48636262	T	C	48636262	3	2	260	1	0	0	0	0	1	0	0	0	8790	1821	63	2	1101	2	LIG1	19	48636262	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	416307	48636262	10492721	848	38093										
PIH1D1	55011	hgsc.bcm.edu	37	chr19	49950318	49950318	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cttcggccaagaggaggtcgGgggcttccagccacaggttc	15	12	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:49950318G>T	ENST00000262265.5	-	7	885	c.650C>A	c.(649-651)cCc>cAc	p.P217H	PIH1D1_ENST00000602226.1_5'Flank|PIH1D1_ENST00000596049.1_Missense_Mutation_p.P217H	NM_017916.2	NP_060386.1	Q9NWS0	PIHD1_HUMAN	PIH1 domain containing 1	217					box C/D snoRNP assembly (GO:0000492)|epithelial cell differentiation (GO:0030855)	pre-snoRNP complex (GO:0070761)				NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(5)|urinary_tract(1)	11		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00152)|GBM - Glioblastoma multiforme(486;0.0244)		GAGGAGGTCGGGGGCTTCCAG	0.602																																					p.P217H		Atlas-SNP	.											.	PIH1D1	23	.	0			c.C650A						.						102	104	103					19																	49950318		2203	4300	6503	SO:0001583	missense	55011	exon7			AGGTCGGGGGCTT	AK000650	CCDS12765.1	19q13.33	2012-07-18	2007-01-31	2007-01-31	ENSG00000104872	ENSG00000104872			26075	protein-coding gene	gene with protein product		611480		NOP17		12477932	Standard	NM_017916		Approved	FLJ20643	uc002pns.2	Q9NWS0		ENST00000262265.5:c.650C>A	chr19.hg19:g.49950318G>T	ENSP00000262265:p.Pro217His	117.0	0.0		63.0	4.0	NM_017916	B4DGN7|B4E2X7|Q9BVL0	Missense_Mutation	SNP	ENST00000262265.5	hg19	CCDS12765.1	.	.	.	.	.	.	.	.	.	.	G	15.60	2.881966	0.51908	.	.	ENSG00000104872	ENST00000262265	T	0.30981	1.51	4.98	3.92	0.45320	.	0.060806	0.64402	D	0.000003	T	0.34395	0.0896	M	0.67397	2.05	0.38583	D	0.950234	B	0.28552	0.215	B	0.33196	0.159	T	0.40059	-0.9583	10	0.87932	D	0	-12.6748	10.7926	0.46443	0.0:0.0:0.8109:0.1891	.	217	Q9NWS0	PIHD1_HUMAN	H	217	ENSP00000262265:P217H	ENSP00000262265:P217H	P	-	2	0	PIH1D1	54642130	1.000000	0.71417	0.996000	0.52242	0.420000	0.31355	4.575000	0.60908	1.443000	0.47586	0.655000	0.94253	CCC	.	.		0.602	PIH1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465389.2	NM_017916		T	49950318	G	T	49950318	3	4	260	1	0	0	0	0	1	0	0	0	11915	1232	43	3	234	3	PIH1D1	19	49950318	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	1314056	49950318	9178665	849	38094										
AP2A1	160	hgsc.bcm.edu	37	chr19	50303262	50303262	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cctggccgagaagtacgccgTggactacagctggtacgtgg	15	11	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:50303262T>C	ENST00000359032.5	+	11	1310	c.1310T>C	c.(1309-1311)gTg>gCg	p.V437A	AP2A1_ENST00000354293.5_Missense_Mutation_p.V437A	NM_014203.2	NP_055018.2	O95782	AP2A1_HUMAN	adaptor-related protein complex 2, alpha 1 subunit	437					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Golgi to endosome transport (GO:0006895)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	AP-2 adaptor complex (GO:0030122)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)	19		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.0023)|GBM - Glioblastoma multiforme(134;0.0157)		AAGTACGCCGTGGACTACAGC	0.617																																					p.V437A		Atlas-SNP	.											.	AP2A1	108	.	0			c.T1310C						.						90	97	95					19																	50303262		2134	4233	6367	SO:0001583	missense	160	exon11			ACGCCGTGGACTA	AA993745	CCDS46148.1, CCDS46149.1	19q13.3	2008-05-23				ENSG00000196961			561	protein-coding gene	gene with protein product		601026		CLAPA1, ADTAA		2564002	Standard	NM_014203		Approved		uc002ppn.3	O95782		ENST00000359032.5:c.1310T>C	chr19.hg19:g.50303262T>C	ENSP00000351926:p.Val437Ala	163.0	0.0		98.0	4.0	NM_130787	Q96CI7|Q96PP6|Q96PP7|Q9H070	Missense_Mutation	SNP	ENST00000359032.5	hg19	CCDS46148.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.411492	0.83340	.	.	ENSG00000196961	ENST00000354293;ENST00000359032	T;T	0.35973	1.28;1.28	4.65	4.65	0.58169	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.39172	0.1068	L	0.33485	1.01	0.54753	D	0.999987	P;P	0.40211	0.459;0.707	B;P	0.49361	0.352;0.608	T	0.23297	-1.0192	10	0.48119	T	0.1	.	13.1876	0.59691	0.0:0.0:0.0:1.0	.	437;437	O95782-2;O95782	.;AP2A1_HUMAN	A	437	ENSP00000346246:V437A;ENSP00000351926:V437A	ENSP00000346246:V437A	V	+	2	0	AP2A1	54995074	1.000000	0.71417	0.991000	0.47740	0.938000	0.57974	7.370000	0.79589	1.944000	0.56390	0.379000	0.24179	GTG	.	.		0.617	AP2A1-008	NOVEL	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465809.1			C	50303262	T	C	50303262	3	2	260	1	0	0	0	0	1	0	0	0	739	1696	59	2	1352	2	AP2A1	19	50303262	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	352944	50303262	8825721	850	38095										
POLD1	5424	hgsc.bcm.edu	37	chr19	50921165	50921165	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctggaagaccaggagcagctCctgcggcgcttcggaccccc	13	16	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:50921165C>T	ENST00000440232.2	+	27	3338	c.3285C>T	c.(3283-3285)ctC>ctT	p.L1095L	SPIB_ENST00000270632.7_5'Flank|CTD-2545M3.6_ENST00000599632.1_Intron|SPIB_ENST00000439922.2_5'Flank|SPIB_ENST00000597855.1_5'Flank|POLD1_ENST00000599857.1_Silent_p.L1095L|SPIB_ENST00000596074.1_5'Flank|POLD1_ENST00000595904.1_Silent_p.L1121L|SPIB_ENST00000595883.1_5'Flank	NM_001256849.1|NM_002691.3	NP_001243778.1|NP_002682.2	P28340	DPOD1_HUMAN	polymerase (DNA directed), delta 1, catalytic subunit	1095					base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|fatty acid homeostasis (GO:0055089)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)|response to UV (GO:0009411)|small molecule metabolic process (GO:0044281)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|delta DNA polymerase complex (GO:0043625)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		AGGAGCAGCTCCTGCGGCGCT	0.642								DNA polymerases (catalytic subunits)																													p.L1095L		Atlas-SNP	.											.	POLD1	174	.	0			c.C3285T						.						31	32	32					19																	50921165		2199	4298	6497	SO:0001819	synonymous_variant	5424	exon27			GCAGCTCCTGCGG		CCDS12795.1	19q13.3	2014-09-17	2012-05-18		ENSG00000062822	ENSG00000062822		"DNA polymerases"	9175	protein-coding gene	gene with protein product	"CDC2 homolog (S. cerevisiae)"	174761	"polymerase (DNA directed), delta 1, catalytic subunit (125kD)"	POLD		1722322	Standard	NM_001256849		Approved	CDC2	uc002psc.5	P28340		ENST00000440232.2:c.3285C>T	chr19.hg19:g.50921165C>T		255.0	0.0		174.0	52.0	NM_002691	Q8NER3|Q96H98	Silent	SNP	ENST00000440232.2	hg19	CCDS12795.1																																																																																			.	.		0.642	POLD1-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464732.1			T	50921165	C	T	50921165	2	4	260	1	0	0	0	0	0	0	0	1	12199	842	30	3		3	POLD1	19	50921165	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	617903	50921165	8207818	851	38096										
ZNF808	388558	hgsc.bcm.edu	37	chr19	53057390	53057390	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgtaatgagtgtggtaaggcTtttaatcatcaatcaagcct	9	6	3	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:53057390T>C	ENST00000359798.4	+	5	1401	c.1221T>C	c.(1219-1221)gcT>gcC	p.A407A		NM_001039886.3	NP_001034975.2	Q8N4W9	ZN808_HUMAN	zinc finger protein 808	407					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(8)|kidney(3)|lung(12)|urinary_tract(1)	24				OV - Ovarian serous cystadenocarcinoma(262;0.00501)|GBM - Glioblastoma multiforme(134;0.0213)		GTGGTAAGGCTTTTAATCATC	0.368																																					p.A407A		Atlas-SNP	.											.	ZNF808	81	.	0			c.T1221C						.						78	84	82					19																	53057390		2196	4290	6486	SO:0001819	synonymous_variant	388558	exon5			TAAGGCTTTTAAT	CR749856	CCDS46167.1	19q13.41	2013-01-08			ENSG00000198482	ENSG00000198482		"Zinc fingers, C2H2-type", "-"	33230	protein-coding gene	gene with protein product							Standard	NM_001039886		Approved		uc010epq.1	Q8N4W9	OTTHUMG00000158230	ENST00000359798.4:c.1221T>C	chr19.hg19:g.53057390T>C		156.0	0.0		92.0	4.0	NM_001039886	Q68CN7	Silent	SNP	ENST00000359798.4	hg19	CCDS46167.1																																																																																			.	.		0.368	ZNF808-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350447.3	NM_001039886		C	53057390	T	C	53057390	2	2	260	1	0	0	0	0	0	0	0	1	18188	1596	56	2		2	ZNF808	19	53057390	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	2136225	53057390	6071593	852	38097										
ZNF611	81856	hgsc.bcm.edu	37	chr19	53208496	53208496	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	caatgaagggatgacctgcgActgaaggtcttgctgcactc	12	10	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:53208496A>G	ENST00000319783.1	-	7	2128	c.1812T>C	c.(1810-1812)agT>agC	p.S604S	ZNF611_ENST00000453741.2_Silent_p.S535S|ZNF611_ENST00000602162.1_Silent_p.S535S|ZNF611_ENST00000595798.1_Silent_p.S535S|ZNF611_ENST00000543227.1_Silent_p.S604S|ZNF611_ENST00000540744.1_Silent_p.S604S|ZNF611_ENST00000602046.1_5'Flank	NM_030972.3	NP_112234.3	Q8N823	ZN611_HUMAN	zinc finger protein 611	604					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(262;0.0233)|GBM - Glioblastoma multiforme(134;0.04)		ATGACCTGCGACTGAAGGTCT	0.458																																					p.S604S		Atlas-SNP	.											.	ZNF611	72	.	0			c.T1812C						.						249	226	234					19																	53208496		2203	4300	6503	SO:0001819	synonymous_variant	81856	exon7			CCTGCGACTGAAG	AK091389	CCDS12855.1, CCDS54312.1	19q13.42	2013-01-08			ENSG00000213020	ENSG00000213020		"Zinc fingers, C2H2-type", "-"	28766	protein-coding gene	gene with protein product						12477932	Standard	NM_030972		Approved	MGC5384	uc010ydq.2	Q8N823	OTTHUMG00000154908	ENST00000319783.1:c.1812T>C	chr19.hg19:g.53208496A>G		145.0	0.0		88.0	4.0	NM_030972	B3KRD5|Q69YG9	Silent	SNP	ENST00000319783.1	hg19	CCDS12855.1																																																																																			.	.		0.458	ZNF611-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337612.1	NM_030972		G	53208496	A	G	53208496	2	3	260	1	0	0	0	0	0	0	0	1	18052	272	10	2		2	ZNF611	19	53208496	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	151106	53208496	5920487	853	38098										
ZNF665	79788	hgsc.bcm.edu	37	chr19	53667902	53667902	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgtgaattcttctatgatttGcaagatgtgaattttgagtg	10	3	2	5			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:53667902G>A	ENST00000600412.1	-	2	1761	c.1646C>T	c.(1645-1647)gCa>gTa	p.A549V	ZNF665_ENST00000396424.3_Missense_Mutation_p.A614V|CTD-2245F17.2_ENST00000600257.1_RNA			Q9H7R5	ZN665_HUMAN	zinc finger protein 665	549					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	35				GBM - Glioblastoma multiforme(134;0.0196)		TCTATGATTTGCAAGATGTGA	0.403																																					p.A614V		Atlas-SNP	.											.	ZNF665	136	.	0			c.C1841T						.						106	111	110					19																	53667902		2203	4300	6503	SO:0001583	missense	79788	exon4			TGATTTGCAAGAT		CCDS46169.1	19q13.42	2013-01-08				ENSG00000197497		"Zinc fingers, C2H2-type", "-"	25885	protein-coding gene	gene with protein product							Standard	NM_024733		Approved	FLJ14345	uc010eqm.1	Q9H7R5		ENST00000600412.1:c.1646C>T	chr19.hg19:g.53667902G>A	ENSP00000469154:p.Ala549Val	139.0	0.0		98.0	6.0	NM_024733	A8K5T8	Missense_Mutation	SNP	ENST00000600412.1	hg19		.	.	.	.	.	.	.	.	.	.	G	6.014	0.370892	0.11409	.	.	ENSG00000197497	ENST00000396424	T	0.36520	1.25	2.55	-3.83	0.04269	.	.	.	.	.	T	0.17365	0.0417	N	0.16903	0.455	0.09310	N	1	B	0.29671	0.254	B	0.32022	0.139	T	0.25222	-1.0138	9	0.25751	T	0.34	.	3.5311	0.07777	0.229:0.0:0.3005:0.4706	.	614	Q9H7R5-2	.	V	614	ENSP00000379702:A614V	ENSP00000379702:A614V	A	-	2	0	ZNF665	58359714	0.000000	0.05858	0.000000	0.03702	0.039000	0.13416	-6.420000	0.00066	-0.912000	0.03837	-0.399000	0.06403	GCA	.	.		0.403	ZNF665-002	PUTATIVE	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000464179.1	NM_024733		A	53667902	G	A	53667902	3	1	260	1	0	0	0	0	1	0	0	0	18088	1319	46	3	199	3	ZNF665	19	53667902	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	459406	53667902	5461081	854	38099										
ZNF845	91664	hgsc.bcm.edu	37	chr19	53854926	53854926	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttacaagtgtaatgaatgtgGcaagaccttcagtcaaacgt	9	7	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:53854926G>A	ENST00000595091.1	+	5	1217	c.998G>A	c.(997-999)gGc>gAc	p.G333D	ZNF845_ENST00000458035.1_Missense_Mutation_p.G333D			Q96IR2	ZN845_HUMAN	zinc finger protein 845	333					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						AATGAATGTGGCAAGACCTTC	0.403																																					p.G333D		Atlas-SNP	.											.	ZNF845	101	.	0			c.G998A						.						64	57	59					19																	53854926		692	1591	2283	SO:0001583	missense	91664	exon4			AATGTGGCAAGAC	BC007307	CCDS46170.1	19q13.42	2013-01-08			ENSG00000213799	ENSG00000213799		"Zinc fingers, C2H2-type", "-"	25112	protein-coding gene	gene with protein product							Standard	NM_138374		Approved		uc010ydv.1	Q96IR2		ENST00000595091.1:c.998G>A	chr19.hg19:g.53854926G>A	ENSP00000470005:p.Gly333Asp	156.0	0.0		67.0	4.0	NM_138374		Missense_Mutation	SNP	ENST00000595091.1	hg19	CCDS46170.1	.	.	.	.	.	.	.	.	.	.	G	16.04	3.011452	0.54468	.	.	ENSG00000213799	ENST00000458035;ENST00000427984	T	0.01430	4.9	2.05	-0.511	0.11970	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01320	0.0043	N	0.25890	0.77	0.09310	N	0.99999	B	0.22604	0.072	B	0.23716	0.048	T	0.45702	-0.9243	9	0.52906	T	0.07	.	6.8118	0.23809	0.2693:0.0:0.7307:0.0	.	333	Q96IR2	ZN845_HUMAN	D	333	ENSP00000388311:G333D	ENSP00000412086:G333D	G	+	2	0	ZNF845	58546738	0.800000	0.28916	0.000000	0.03702	0.680000	0.39746	0.921000	0.28718	-0.210000	0.10140	0.205000	0.17691	GGC	.	.		0.403	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908		A	53854926	G	A	53854926	3	1	260	1	0	0	0	0	1	0	0	0	18206	1203	42	3	1008	3	ZNF845	19	53854926	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	187024	53854926	5274057	855	38100										
ZNF845	91664	hgsc.bcm.edu	37	chr19	53855322	53855322	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gagaattcatactggagagaAaccttacaagtgtaatgatt	9	5	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:53855322A>G	ENST00000595091.1	+	5	1613	c.1394A>G	c.(1393-1395)aAa>aGa	p.K465R	ZNF845_ENST00000458035.1_Missense_Mutation_p.K465R			Q96IR2	ZN845_HUMAN	zinc finger protein 845	465					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						ACTGGAGAGAAACCTTACAAG	0.383																																					p.K465R		Atlas-SNP	.											ZNF845,NS,carcinoma,0,1	ZNF845	101	.	0			c.A1394G						.						27	26	26					19																	53855322		692	1590	2282	SO:0001583	missense	91664	exon4			GAGAGAAACCTTA	BC007307	CCDS46170.1	19q13.42	2013-01-08			ENSG00000213799	ENSG00000213799		"Zinc fingers, C2H2-type", "-"	25112	protein-coding gene	gene with protein product							Standard	NM_138374		Approved		uc010ydv.1	Q96IR2		ENST00000595091.1:c.1394A>G	chr19.hg19:g.53855322A>G	ENSP00000470005:p.Lys465Arg	120.0	0.0		68.0	4.0	NM_138374		Missense_Mutation	SNP	ENST00000595091.1	hg19	CCDS46170.1	.	.	.	.	.	.	.	.	.	.	A	14.82	2.650087	0.47362	.	.	ENSG00000213799	ENST00000458035;ENST00000427984	T	0.24908	1.83	2.08	2.08	0.27032	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.27866	0.0686	N	0.11698	0.16	0.22317	N	0.999202	P	0.49961	0.93	D	0.66196	0.942	T	0.13548	-1.0505	9	0.40728	T	0.16	.	8.8735	0.35332	1.0:0.0:0.0:0.0	.	465	Q96IR2	ZN845_HUMAN	R	465	ENSP00000388311:K465R	ENSP00000412086:K465R	K	+	2	0	ZNF845	58547134	0.154000	0.22792	0.015000	0.15790	0.041000	0.13682	0.683000	0.25349	0.942000	0.37525	0.338000	0.21704	AAA	.	.		0.383	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908		G	53855322	A	G	53855322	3	3	260	1	0	0	0	0	1	0	0	0	18206	14	1	2	1404	2	ZNF845	19	53855322	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	396	53855322	5273661	856	38101										
NLRP2	55655	hgsc.bcm.edu	37	chr19	55496563	55496563	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtgaacaaatagcctctgacAcctgtcatctccagagagtg	9	11	3	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:55496563A>G	ENST00000543010.1	+	7	2322	c.2179A>G	c.(2179-2181)Acc>Gcc	p.T727A	NLRP2_ENST00000391721.4_Missense_Mutation_p.T703A|NLRP2_ENST00000538819.1_Missense_Mutation_p.T703A|NLRP2_ENST00000427260.2_Missense_Mutation_p.T704A|NLRP2_ENST00000263437.6_Missense_Mutation_p.T724A|NLRP2_ENST00000448584.2_Missense_Mutation_p.T727A|NLRP2_ENST00000339757.7_Missense_Mutation_p.T705A|NLRP2_ENST00000537859.1_Missense_Mutation_p.T705A	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	727					positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|Pyrin domain binding (GO:0032090)			large_intestine(4)|liver(1)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	11			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		AGCCTCTGACACCTGTCATCT	0.398																																					p.T727A		Atlas-SNP	.											.	NLRP2	161	.	0			c.A2179G						.						144	128	133					19																	55496563		2203	4300	6503	SO:0001583	missense	55655	exon7			TCTGACACCTGTC	AK000517	CCDS12913.1, CCDS54318.1, CCDS54319.1	19q13.42	2008-02-05	2006-12-08	2006-12-08	ENSG00000022556	ENSG00000022556		"Nucleotide-binding domain and leucine rich repeat containing"	22948	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2"	609364	"NACHT, leucine rich repeat and PYD containing 2"	NALP2		12563287, 11270363	Standard	NM_001174081		Approved	FLJ20510, PYPAF2, NBS1, PAN1, CLR19.9	uc021vbq.1	Q9NX02	OTTHUMG00000167763	ENST00000543010.1:c.2179A>G	chr19.hg19:g.55496563A>G	ENSP00000445135:p.Thr727Ala	72.0	0.0		68.0	4.0	NM_017852	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Missense_Mutation	SNP	ENST00000543010.1	hg19	CCDS12913.1	.	.	.	.	.	.	.	.	.	.	a	6.975	0.549806	0.13374	.	.	ENSG00000022556	ENST00000543010;ENST00000391721;ENST00000339757;ENST00000448584;ENST00000537859;ENST00000427260;ENST00000538819;ENST00000263437	T;T;T;T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67	2.45	-2.83	0.05769	.	1.117520	0.07063	N	0.834022	T	0.33933	0.0880	M	0.62723	1.935	0.09310	N	1	B;B;B;B;B	0.12630	0.006;0.004;0.006;0.004;0.006	B;B;B;B;B	0.15052	0.005;0.012;0.005;0.012;0.005	T	0.31475	-0.9942	10	0.08381	T	0.77	.	1.113	0.01708	0.2911:0.387:0.1318:0.1901	.	704;705;724;703;727	B4DZL7;Q9NX02-2;A8K9G6;Q9NX02-4;Q9NX02	.;.;.;.;NALP2_HUMAN	A	727;703;705;727;705;704;703;724	ENSP00000445135:T727A;ENSP00000375601:T703A;ENSP00000344074:T705A;ENSP00000409370:T727A;ENSP00000440601:T705A;ENSP00000402474:T704A;ENSP00000441133:T703A;ENSP00000263437:T724A	ENSP00000263437:T724A	T	+	1	0	NLRP2	60188375	0.000000	0.05858	0.000000	0.03702	0.222000	0.24845	-0.532000	0.06164	-0.853000	0.04136	0.449000	0.29647	ACC	.	.		0.398	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852		G	55496563	A	G	55496563	3	3	260	1	0	0	0	0	1	0	0	0	10486	159	6	2	2201	2	NLRP2	19	55496563	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1641241	55496563	3632420	857	38102										
NLRP2	55655	hgsc.bcm.edu	37	chr19	55497649	55497649	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttcccgcattgtgtgaggtcTtgagacatccagaatgtaac	10	9	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:55497649T>C	ENST00000543010.1	+	8	2475	c.2332T>C	c.(2332-2334)Ttg>Ctg	p.L778L	NLRP2_ENST00000391721.4_Silent_p.L754L|NLRP2_ENST00000538819.1_Silent_p.L754L|NLRP2_ENST00000427260.2_Silent_p.L755L|NLRP2_ENST00000263437.6_Silent_p.L775L|NLRP2_ENST00000448584.2_Silent_p.L778L|NLRP2_ENST00000339757.7_Silent_p.L756L|NLRP2_ENST00000537859.1_Silent_p.L756L	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	778					positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|Pyrin domain binding (GO:0032090)			large_intestine(4)|liver(1)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	11			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		GTGTGAGGTCTTGAGACATCC	0.433																																					p.L778L		Atlas-SNP	.											.	NLRP2	161	.	0			c.T2332C						.						156	127	137					19																	55497649		2203	4300	6503	SO:0001819	synonymous_variant	55655	exon8			GAGGTCTTGAGAC	AK000517	CCDS12913.1, CCDS54318.1, CCDS54319.1	19q13.42	2008-02-05	2006-12-08	2006-12-08	ENSG00000022556	ENSG00000022556		"Nucleotide-binding domain and leucine rich repeat containing"	22948	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2"	609364	"NACHT, leucine rich repeat and PYD containing 2"	NALP2		12563287, 11270363	Standard	NM_001174081		Approved	FLJ20510, PYPAF2, NBS1, PAN1, CLR19.9	uc021vbq.1	Q9NX02	OTTHUMG00000167763	ENST00000543010.1:c.2332T>C	chr19.hg19:g.55497649T>C		157.0	0.0		97.0	4.0	NM_017852	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Silent	SNP	ENST00000543010.1	hg19	CCDS12913.1																																																																																			.	.		0.433	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852		C	55497649	T	C	55497649	2	2	260	1	0	0	0	0	0	0	0	1	10486	1606	56	2		2	NLRP2	19	55497649	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1086	55497649	3631334	858	38103										
PTPRH	5794	hgsc.bcm.edu	37	chr19	55708079	55708079	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aaaggcctcgtagcctccctGggggcaggaccagatcaagt	13	12	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:55708079G>T	ENST00000376350.3	-	10	2090	c.2068C>A	c.(2068-2070)Cag>Aag	p.Q690K	PTPRH_ENST00000588559.1_5'UTR|PTPRH_ENST00000263434.5_Missense_Mutation_p.Q512K	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	690	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic process (GO:0006915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		TAGCCTCCCTGGGGGCAGGAC	0.602																																					p.Q690K		Atlas-SNP	.											.	PTPRH	139	.	0			c.C2068A						.						70	65	67					19																	55708079		2203	4300	6503	SO:0001583	missense	5794	exon10			CTCCCTGGGGGCA		CCDS33110.1, CCDS54321.1	19q13.4	2013-02-11				ENSG00000080031		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9672	protein-coding gene	gene with protein product		602510				8294459	Standard	XM_006723312		Approved	SAP-1	uc002qjq.3	Q9HD43		ENST00000376350.3:c.2068C>A	chr19.hg19:g.55708079G>T	ENSP00000365528:p.Gln690Lys	110.0	0.0		75.0	4.0	NM_002842	C9JCH2|Q15426|Q2NKN9|Q2NKP0	Missense_Mutation	SNP	ENST00000376350.3	hg19	CCDS33110.1	.	.	.	.	.	.	.	.	.	.	G	11.55	1.671381	0.29693	.	.	ENSG00000080031	ENST00000376350;ENST00000263434	T;T	0.05717	3.4;4.42	5.33	-10.7	0.00240	Fibronectin, type III (1);	4.765710	0.00702	N	0.000787	T	0.02970	0.0088	N	0.24115	0.695	0.09310	N	1	P;P;B	0.37781	0.473;0.608;0.448	B;B;B	0.39119	0.152;0.291;0.127	T	0.46205	-0.9208	10	0.05959	T	0.93	.	2.4582	0.04535	0.0902:0.2809:0.3478:0.2811	.	512;512;690	C9JCH2;Q9HD43-2;Q9HD43	.;.;PTPRH_HUMAN	K	690;512	ENSP00000365528:Q690K;ENSP00000263434:Q512K	ENSP00000263434:Q512K	Q	-	1	0	PTPRH	60399891	0.000000	0.05858	0.000000	0.03702	0.342000	0.28953	-2.581000	0.00906	-1.739000	0.01347	-0.322000	0.08575	CAG	.	.		0.602	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1			T	55708079	G	T	55708079	3	4	260	1	0	0	0	0	1	0	0	0	12818	1357	47	3	1323	3	PTPRH	19	55708079	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	210430	55708079	3420904	859	38104										
NLRP11	204801	hgsc.bcm.edu	37	chr19	56320276	56320276	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	attgaaggtaaactgtaaccTccatgagagcatccacaatc	7	10	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:56320276T>C	ENST00000589093.1	-	3	1793	c.1700A>G	c.(1699-1701)gAg>gGg	p.E567G	NLRP11_ENST00000360133.3_Missense_Mutation_p.E567G|NLRP11_ENST00000589824.2_Missense_Mutation_p.E567G|NLRP11_ENST00000592953.1_Missense_Mutation_p.E468G|NLRP11_ENST00000443188.1_Missense_Mutation_p.E567G			P59045	NAL11_HUMAN	NLR family, pyrin domain containing 11	567							ATP binding (GO:0005524)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	66		Colorectal(82;0.0002)		GBM - Glioblastoma multiforme(193;0.0325)		AACTGTAACCTCCATGAGAGC	0.438																																					p.E567G		Atlas-SNP	.											.	NLRP11	139	.	0			c.A1700G						.						133	118	123					19																	56320276		2203	4300	6503	SO:0001583	missense	204801	exon5			GTAACCTCCATGA	AY095145	CCDS12935.1, CCDS74458.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179873		"Nucleotide-binding domain and leucine rich repeat containing"	22945	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 11"	609664	"NACHT, leucine rich repeat and PYD containing 11"	NALP11		12563287, 12019269	Standard	NM_145007		Approved	PYPAF6, NOD17, PAN10, CLR19.6	uc010ygf.2	P59045		ENST00000589093.1:c.1700A>G	chr19.hg19:g.56320276T>C	ENSP00000466285:p.Glu567Gly	212.0	0.0		100.0	4.0	NM_145007	C9JSF5|Q2TV85|Q2TV86|Q53ZZ0|Q8NBF5	Missense_Mutation	SNP	ENST00000589093.1	hg19	CCDS12935.1	.	.	.	.	.	.	.	.	.	.	T	13.02	2.113774	0.37339	.	.	ENSG00000179873	ENST00000443188;ENST00000360133	T;T	0.55413	0.52;0.52	2.39	1.3	0.21679	.	.	.	.	.	T	0.54271	0.1848	L	0.52573	1.65	0.09310	N	1	D;D	0.58620	0.971;0.983	P;P	0.54759	0.58;0.76	T	0.43015	-0.9417	9	0.72032	D	0.01	.	5.3109	0.15829	0.0:0.0:0.2989:0.7011	.	567;567	P59045;P59045-2	NAL11_HUMAN;.	G	567	ENSP00000409898:E567G;ENSP00000353251:E567G	ENSP00000353251:E567G	E	-	2	0	NLRP11	61012088	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	0.710000	0.25748	0.320000	0.23234	0.533000	0.62120	GAG	.	.		0.438	NLRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453657.1	NM_145007		C	56320276	T	C	56320276	3	2	260	1	0	0	0	0	1	0	0	0	10482	1551	54	2	1433	2	NLRP11	19	56320276	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	612197	56320276	2808707	860	38105										
NLRP5	126206	hgsc.bcm.edu	37	chr19	56565058	56565058	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gagagtctgtcctgtgtgatCtcgaggagcagacacctgaa	13	9	2	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:56565058C>A	ENST00000390649.3	+	13	3183	c.3183C>A	c.(3181-3183)atC>atA	p.I1061I		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	1061					cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|ovary(5)|skin(2)|stomach(4)|upper_aerodigestive_tract(2)	25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		CCTGTGTGATCTCGAGGAGCA	0.572																																					p.I1061I		Atlas-SNP	.											NLRP5_ENST00000390649,NS,carcinoma,0,1	NLRP5	217	.	0			c.C3183A						.						83	84	84					19																	56565058		2097	4218	6315	SO:0001819	synonymous_variant	126206	exon13			TGTGATCTCGAGG	AY154460	CCDS12938.1	19q13.43	2008-10-30	2006-12-08	2006-12-08	ENSG00000171487	ENSG00000171487		"Nucleotide-binding domain and leucine rich repeat containing"	21269	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 5"	609658	"NACHT, leucine rich repeat and PYD containing 5"	NALP5		12563287, 11925379	Standard	NM_153447		Approved	PYPAF8, MATER, PAN11, CLR19.8	uc002qmj.3	P59047	OTTHUMG00000149887	ENST00000390649.3:c.3183C>A	chr19.hg19:g.56565058C>A		148.0	0.0		89.0	20.0	NM_153447	A8MTY4|Q86W29	Silent	SNP	ENST00000390649.3	hg19	CCDS12938.1																																																																																			.	.		0.572	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447		A	56565058	C	A	56565058	2	1	260	1	0	0	0	0	0	0	0	1	10489	903	32	3		3	NLRP5	19	56565058	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	244782	56565058	2563925	861	38106										
ZNF582	147948	hgsc.bcm.edu	37	chr19	56895790	56895790	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tagagtttcctgccagtatgAacagtctgatgttgaatcaa	9	7	2	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:56895790A>G	ENST00000301310.4	-	5	1154	c.996T>C	c.(994-996)gtT>gtC	p.V332V	AC006116.12_ENST00000589671.1_RNA|ZNF582_ENST00000586929.1_Silent_p.V332V	NM_144690.1	NP_653291.1	Q96NG8	ZN582_HUMAN	zinc finger protein 582	332					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0547)		TGCCAGTATGAACAGTCTGAT	0.388																																					p.V332V	Ovarian(183;1887 2032 4349 30507 51343)	Atlas-SNP	.											.	ZNF582	56	.	0			c.T996C						.						91	91	91					19																	56895790		2203	4300	6503	SO:0001819	synonymous_variant	147948	exon5			AGTATGAACAGTC	AK055489	CCDS33121.1	19q13.43	2013-07-15			ENSG00000018869	ENSG00000018869		"Zinc fingers, C2H2-type", "-"	26421	protein-coding gene	gene with protein product		615600				12477932	Standard	NM_144690		Approved	FLJ30927	uc002qmz.1	Q96NG8	OTTHUMG00000181939	ENST00000301310.4:c.996T>C	chr19.hg19:g.56895790A>G		126.0	0.0		84.0	4.0	NM_144690	B4DQZ9|B7Z9R3|Q6PJT6	Silent	SNP	ENST00000301310.4	hg19	CCDS33121.1																																																																																			.	.		0.388	ZNF582-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458387.2	NM_144690		G	56895790	A	G	56895790	2	3	260	1	0	0	0	0	0	0	0	1	18029	233	9	2		2	ZNF582	19	56895790	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	330732	56895790	2233193	862	38107										
ZNF667	63934	hgsc.bcm.edu	37	chr19	56953574	56953574	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aagtaaaagggatgacatctGattgaaggcttttccgcact	10	7	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:56953574G>A	ENST00000504904.3	-	7	1509	c.790C>T	c.(790-792)Cag>Tag	p.Q264*	ZNF667_ENST00000342634.3_Nonsense_Mutation_p.Q392*|ZNF667_ENST00000292069.6_Nonsense_Mutation_p.Q264*|ZNF667_ENST00000591790.1_3'UTR			Q5HYK9	ZN667_HUMAN	zinc finger protein 667	264					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	38		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0615)		GATGACATCTGATTGAAGGCT	0.363																																					p.Q264X		Atlas-SNP	.											.	ZNF667	95	.	0			c.C790T						.						87	91	89					19																	56953574		2203	4300	6503	SO:0001587	stop_gained	63934	exon5			ACATCTGATTGAA		CCDS12944.1	19q13.43	2013-01-08				ENSG00000198046		"Zinc fingers, C2H2-type", "-"	28854	protein-coding gene	gene with protein product		611024					Standard	NM_022103		Approved	FLJ14011	uc002qnd.3	Q5HYK9		ENST00000504904.3:c.790C>T	chr19.hg19:g.56953574G>A	ENSP00000439402:p.Gln264*	180.0	0.0		104.0	5.0	NM_022103	B2RMS6|B9EK36|Q6B093|Q9H807	Nonsense_Mutation	SNP	ENST00000504904.3	hg19	CCDS12944.1	.	.	.	.	.	.	.	.	.	.	G	13.61	2.289890	0.40494	.	.	ENSG00000198046	ENST00000342634;ENST00000504904;ENST00000292069;ENST00000452518	.	.	.	5.05	1.54	0.23209	.	1.254260	0.05897	N	0.629368	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	0.8174	5.5581	0.17127	0.099:0.0:0.3978:0.5032	.	.	.	.	X	392;264;264;46	.	ENSP00000292069:Q264X	Q	-	1	0	ZNF667	61645386	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.088000	0.11198	0.221000	0.20879	-0.282000	0.10007	CAG	.	.		0.363	ZNF667-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458394.1	NM_022103		A	56953574	G	A	56953574	4	1	260	1	0	0	0	0	0	1	0	0	18089	1299	45	3	1046	3	ZNF667	19	56953574	Nonsense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	57784	56953574	2175409	863	38108										
ZIK1	284307	hgsc.bcm.edu	37	chr19	58102154	58102154	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggagcaaggccttatgagtgTagccagtgtgggaaatcctt	14	7	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:58102154T>C	ENST00000597850.1	+	4	1190	c.975T>C	c.(973-975)tgT>tgC	p.C325C	ZIK1_ENST00000307468.4_3'UTR|ZIK1_ENST00000599456.1_Silent_p.C270C|ZIK1_ENST00000536878.2_Silent_p.C312C	NM_001010879.2	NP_001010879.2	Q3SY52	ZIK1_HUMAN	zinc finger protein interacting with K protein 1	325					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	34		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		CTTATGAGTGTAGCCAGTGTG	0.433																																					p.C325C		Atlas-SNP	.											.	ZIK1	94	.	0			c.T975C						.						66	64	65					19																	58102154		2203	4300	6503	SO:0001819	synonymous_variant	284307	exon4			TGAGTGTAGCCAG	AK092538	CCDS33135.1	19q13.43	2013-01-08	2012-12-07		ENSG00000171649	ENSG00000171649		"Zinc fingers, C2H2-type", "-"	33104	protein-coding gene	gene with protein product			"zinc finger protein interacting with K protein 1 homolog (mouse)"				Standard	XM_005258769		Approved	ZNF762	uc002qpg.3	Q3SY52		ENST00000597850.1:c.975T>C	chr19.hg19:g.58102154T>C		115.0	0.0		76.0	4.0	NM_001010879	O43339|Q3SY51|Q3SY53	Silent	SNP	ENST00000597850.1	hg19	CCDS33135.1																																																																																			.	.		0.433	ZIK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466791.1	NM_001010879		C	58102154	T	C	58102154	2	2	260	1	0	0	0	0	0	0	0	1	17698	1644	57	2		2	ZIK1	19	58102154	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1148580	58102154	1026829	864	38109										
ZNF418	147686	hgsc.bcm.edu	37	chr19	58438293	58438293	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aaggtctttctccagtgtgaCctcgctgatggttcctaagg	11	10	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:58438293C>T	ENST00000396147.1	-	4	1547	c.1256G>A	c.(1255-1257)gGt>gAt	p.G419D	ZNF418_ENST00000425570.3_Missense_Mutation_p.G440D|ZNF418_ENST00000599852.1_Missense_Mutation_p.G334D|ZNF418_ENST00000595830.1_Missense_Mutation_p.G419D|ZNF418_ENST00000599086.1_5'Flank|ZNF418_ENST00000600989.1_Intron	NM_133460.1	NP_597717.1	Q8TF45	ZN418_HUMAN	zinc finger protein 418	419					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	31		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0158)		TCCAGTGTGACCTCGCTGATG	0.468																																					p.G419D		Atlas-SNP	.											.	ZNF418	76	.	0			c.G1256A						.						159	162	161					19																	58438293		2203	4300	6503	SO:0001583	missense	147686	exon4			GTGTGACCTCGCT	AB075836, AY695825	CCDS42642.1	19q13.43	2013-01-08				ENSG00000196724		"Zinc fingers, C2H2-type", "-"	20647	protein-coding gene	gene with protein product						11853319	Standard	NM_133460		Approved	KIAA1956, FLJ31551	uc002qqs.1	Q8TF45		ENST00000396147.1:c.1256G>A	chr19.hg19:g.58438293C>T	ENSP00000379451:p.Gly419Asp	152.0	0.0		97.0	4.0	NM_133460	Q2M1S2|Q670L5|Q96N18	Missense_Mutation	SNP	ENST00000396147.1	hg19	CCDS42642.1	.	.	.	.	.	.	.	.	.	.	.	16.13	3.035615	0.54896	.	.	ENSG00000196724	ENST00000396147;ENST00000425570;ENST00000545403	T;T	0.07688	3.17;3.17	2.36	-0.124	0.13523	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06096	0.0158	N	0.17838	0.53	0.21020	N	0.999804	B	0.30211	0.273	B	0.32211	0.142	T	0.38308	-0.9667	9	0.87932	D	0	.	8.3196	0.32121	0.5942:0.4058:0.0:0.0	.	419	Q8TF45	ZN418_HUMAN	D	419;440;385	ENSP00000379451:G419D;ENSP00000407039:G440D	ENSP00000379451:G419D	G	-	2	0	ZNF418	63130105	.	.	0.059000	0.19551	0.883000	0.51084	.	.	-0.241000	0.09681	0.298000	0.19748	GGT	.	.		0.468	ZNF418-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466693.1	NM_133460		T	58438293	C	T	58438293	3	4	260	1	0	0	0	0	1	0	0	0	17910	507	18	3	778	3	ZNF418	19	58438293	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	336139	58438293	690690	865	38110										
ZNF418	147686	hgsc.bcm.edu	37	chr19	58438372	58438372	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctcataaggtcgttctctagTgtgaactcgatgatgttcag	10	8	3	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:58438372T>C	ENST00000396147.1	-	4	1468	c.1177A>G	c.(1177-1179)Act>Gct	p.T393A	ZNF418_ENST00000425570.3_Missense_Mutation_p.T414A|ZNF418_ENST00000599852.1_Missense_Mutation_p.T308A|ZNF418_ENST00000595830.1_Missense_Mutation_p.T393A|ZNF418_ENST00000599086.1_5'Flank|ZNF418_ENST00000600989.1_Intron	NM_133460.1	NP_597717.1	Q8TF45	ZN418_HUMAN	zinc finger protein 418	393					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	31		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0158)		CGTTCTCTAGTGTGAACTCGA	0.433																																					p.T393A		Atlas-SNP	.											.	ZNF418	76	.	0			c.A1177G						.						145	148	147					19																	58438372		2194	4295	6489	SO:0001583	missense	147686	exon4			CTCTAGTGTGAAC	AB075836, AY695825	CCDS42642.1	19q13.43	2013-01-08				ENSG00000196724		"Zinc fingers, C2H2-type", "-"	20647	protein-coding gene	gene with protein product						11853319	Standard	NM_133460		Approved	KIAA1956, FLJ31551	uc002qqs.1	Q8TF45		ENST00000396147.1:c.1177A>G	chr19.hg19:g.58438372T>C	ENSP00000379451:p.Thr393Ala	155.0	0.0		103.0	8.0	NM_133460	Q2M1S2|Q670L5|Q96N18	Missense_Mutation	SNP	ENST00000396147.1	hg19	CCDS42642.1	.	.	.	.	.	.	.	.	.	.	.	16.57	3.161337	0.57368	.	.	ENSG00000196724	ENST00000396147;ENST00000425570;ENST00000545403	T;T	0.35605	1.3;1.3	2.26	2.26	0.28386	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.49525	0.1562	M	0.70108	2.13	0.25789	N	0.984646	P	0.36660	0.564	P	0.50109	0.631	T	0.45366	-0.9266	9	0.66056	D	0.02	.	9.2268	0.37412	0.0:0.0:0.0:1.0	.	393	Q8TF45	ZN418_HUMAN	A	393;414;359	ENSP00000379451:T393A;ENSP00000407039:T414A	ENSP00000379451:T393A	T	-	1	0	ZNF418	63130184	1.000000	0.71417	0.005000	0.12908	0.662000	0.39071	3.915000	0.56409	1.051000	0.40369	0.234000	0.17832	ACT	.	.		0.433	ZNF418-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466693.1	NM_133460		C	58438372	T	C	58438372	3	2	260	1	0	0	0	0	1	0	0	0	17910	1696	59	2	857	2	ZNF418	19	58438372	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	79	58438372	690611	866	38111										
ZNF606	80095	hgsc.bcm.edu	37	chr19	58491239	58491239	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	taggttgaatggactgataaAcagttttgtcataatcatta	8	4	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:58491239A>G	ENST00000341164.4	-	7	1429	c.809T>C	c.(808-810)gTt>gCt	p.V270A	ZNF606_ENST00000536132.1_Missense_Mutation_p.V180A	NM_025027.3	NP_079303.2	Q8WXB4	ZN606_HUMAN	zinc finger protein 606	270					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)		GGACTGATAAACAGTTTTGTC	0.328																																					p.V270A		Atlas-SNP	.											.	ZNF606	155	.	0			c.T809C						.						87	88	87					19																	58491239		2203	4300	6503	SO:0001583	missense	80095	exon7			TGATAAACAGTTT	AB058755	CCDS12968.1	19q13.43	2013-01-08			ENSG00000166704	ENSG00000166704		"Zinc fingers, C2H2-type", "-"	25879	protein-coding gene	gene with protein product		613905		ZNF328		11347906	Standard	XM_005259276		Approved	FLJ14260, KIAA1852	uc002qqw.3	Q8WXB4	OTTHUMG00000169804	ENST00000341164.4:c.809T>C	chr19.hg19:g.58491239A>G	ENSP00000343617:p.Val270Ala	104.0	0.0		57.0	4.0	NM_025027	A8KAN2|Q8NE04|Q96JH5	Missense_Mutation	SNP	ENST00000341164.4	hg19	CCDS12968.1	.	.	.	.	.	.	.	.	.	.	A	1.326	-0.598126	0.03744	.	.	ENSG00000166704	ENST00000341164;ENST00000536132;ENST00000551380	T;T;T	0.08193	3.26;3.12;3.69	4.19	3.18	0.36537	.	0.504108	0.16866	N	0.196337	T	0.04815	0.0130	N	0.08118	0	0.19300	N	0.99997	B	0.09022	0.002	B	0.06405	0.002	T	0.34775	-0.9815	10	0.72032	D	0.01	.	9.4919	0.38965	0.9119:0.0:0.0881:0.0	.	270	Q8WXB4	ZN606_HUMAN	A	270;180;270	ENSP00000343617:V270A;ENSP00000445624:V180A;ENSP00000446972:V270A	ENSP00000343617:V270A	V	-	2	0	ZNF606	63183051	0.065000	0.20965	0.010000	0.14722	0.008000	0.06430	2.563000	0.45922	0.939000	0.37446	-0.274000	0.10170	GTT	.	.		0.328	ZNF606-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405961.1	NM_025027		G	58491239	A	G	58491239	3	3	260	1	0	0	0	0	1	0	0	0	18047	43	2	2	1573	2	ZNF606	19	58491239	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	52867	58491239	637744	867	38112										
ZNF544	27300	hgsc.bcm.edu	37	chr19	58773098	58773098	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tacaccagagaacacacactGgagaaaagcccttcgaatgt	8	11	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr19:58773098G>T	ENST00000596652.1	+	6	1360	c.1126G>T	c.(1126-1128)Gga>Tga	p.G376*	ZNF544_ENST00000596929.1_Intron|CTD-3138B18.5_ENST00000597230.1_RNA|ZNF544_ENST00000599953.1_Nonsense_Mutation_p.G234*|ZNF544_ENST00000600044.1_Nonsense_Mutation_p.G348*|ZNF544_ENST00000415203.2_Nonsense_Mutation_p.G348*|CTD-3138B18.4_ENST00000600029.1_Intron|ZNF544_ENST00000596825.1_3'UTR|ZNF544_ENST00000600220.1_Nonsense_Mutation_p.G348*|ZNF544_ENST00000595981.1_Intron|ZNF544_ENST00000269829.4_Nonsense_Mutation_p.G376*|ZNF544_ENST00000599227.1_3'UTR			Q6NX49	ZN544_HUMAN	zinc finger protein 544	376					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|skin(1)|urinary_tract(1)	18		all_cancers(17;4.17e-12)|all_epithelial(17;1.25e-08)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.17)|GBM - Glioblastoma multiforme(193;0.018)		AACACACACTGGAGAAAAGCC	0.438																																					p.G376X		Atlas-SNP	.											.	ZNF544	57	.	0			c.G1126T						.						83	80	81					19																	58773098		2203	4300	6503	SO:0001587	stop_gained	27300	exon7			CACACTGGAGAAA	AF020591	CCDS12973.1	19q13.43	2013-01-08				ENSG00000198131		"Zinc fingers, C2H2-type", "-"	16759	protein-coding gene	gene with protein product	"zinc finger protein AF020591"						Standard	NM_014480		Approved	AF020591	uc010euo.3	Q6NX49		ENST00000596652.1:c.1126G>T	chr19.hg19:g.58773098G>T	ENSP00000469635:p.Gly376*	69.0	0.0		48.0	4.0	NM_014480	A8K6J1|Q9UEX4	Nonsense_Mutation	SNP	ENST00000596652.1	hg19	CCDS12973.1	.	.	.	.	.	.	.	.	.	.	G	38	6.961201	0.97964	.	.	ENSG00000198131	ENST00000269829;ENST00000415203;ENST00000441758	.	.	.	2.9	0.64	0.17752	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	6.0361	0.19708	0.2927:0.0:0.7073:0.0	.	.	.	.	X	376;348;40	.	ENSP00000269829:G376X	G	+	1	0	ZNF544	63464910	0.047000	0.20315	0.028000	0.17463	0.580000	0.36256	1.013000	0.29937	0.102000	0.17638	0.491000	0.48974	GGA	.	.		0.438	ZNF544-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466754.1	NM_014480		T	58773098	G	T	58773098	4	4	260	1	0	0	0	0	0	1	0	0	17992	1349	47	3	1140	3	ZNF544	19	58773098	Nonsense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	281859	58773098	355885	868	38113										
C20orf96	140680	hgsc.bcm.edu	37	chr20	259904	259904	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tctcgatcagctcccggttgAgcttgctgaggaagttctca	11	11	3	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr20:259904A>G	ENST00000360321.2	-	5	512	c.374T>C	c.(373-375)cTc>cCc	p.L125P	C20orf96_ENST00000382369.5_Missense_Mutation_p.L90P|C20orf96_ENST00000400269.3_Missense_Mutation_p.L67P	NM_080571.1|NM_153269.2	NP_542138.1|NP_695001.2	Q9NUD7	CT096_HUMAN	chromosome 20 open reading frame 96	125										endometrium(3)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	12		all_cancers(10;0.00959)|Lung NSC(37;0.227)	OV - Ovarian serous cystadenocarcinoma(29;0.149)			CTCCCGGTTGAGCTTGCTGAG	0.672																																					p.L125P		Atlas-SNP	.											.	C20orf96	28	.	0			c.T374C						.						111	80	90					20																	259904		2203	4300	6503	SO:0001583	missense	140680	exon5			CGGTTGAGCTTGC	AL034548	CCDS12994.1, CCDS74685.1	20p13	2012-10-30			ENSG00000196476	ENSG00000196476			16227	protein-coding gene	gene with protein product							Standard	NM_153269		Approved	dJ1103G7.2	uc002wde.2	Q9NUD7	OTTHUMG00000031626	ENST00000360321.2:c.374T>C	chr20.hg19:g.259904A>G	ENSP00000353470:p.Leu125Pro	121.0	0.0		86.0	4.0	NM_153269	A3KPE0|B2RPH9|Q8N840|Q8NAX5	Missense_Mutation	SNP	ENST00000360321.2	hg19	CCDS12994.1	.	.	.	.	.	.	.	.	.	.	A	14.56	2.571013	0.45798	.	.	ENSG00000196476	ENST00000382369;ENST00000360321;ENST00000400269	T;T;T	0.46451	0.87;0.87;0.87	4.92	-0.136	0.13473	.	1.088790	0.07072	N	0.835671	T	0.42245	0.1194	L	0.50333	1.59	0.19775	N	0.999954	D;D;D;D	0.59767	0.986;0.986;0.986;0.986	P;P;P;P	0.54100	0.742;0.742;0.66;0.656	T	0.27606	-1.0069	10	0.30854	T	0.27	0.6675	1.006	0.01487	0.4052:0.1712:0.0932:0.3304	.	67;90;125;90	F5GZA9;B7Z971;Q9NUD7;Q5JYC3	.;.;CT096_HUMAN;.	P	90;125;67	ENSP00000371806:L90P;ENSP00000353470:L125P;ENSP00000383128:L67P	ENSP00000353470:L125P	L	-	2	0	C20orf96	207904	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.048000	0.11944	0.062000	0.16340	0.460000	0.39030	CTC	.	.		0.672	C20orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077439.2	NM_153269		G	259904	A	G	259904	3	3	260	1	0	0	0	0	1	0	0	0	2124	304	11	2	745	2	C20orf96	20	259904	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10		259904	62765616	869	38114										
TMC2	117532	hgsc.bcm.edu	37	chr20	2593953	2593953	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aactactgctggtgctgggaCttggaggctggatttgtagg	16	6	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr20:2593953C>G	ENST00000358864.1	+	14	1872	c.1857C>G	c.(1855-1857)gaC>gaG	p.D619E	TMC2_ENST00000496948.1_3'UTR	NM_080751.2	NP_542789.2	Q8TDI7	TMC2_HUMAN	transmembrane channel-like 2	619					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						GGTGCTGGGACTTGGAGGCTG	0.483																																					p.D619E		Atlas-SNP	.											.	TMC2	121	.	0			c.C1857G						.						210	166	181					20																	2593953		2203	4300	6503	SO:0001583	missense	117532	exon14			CTGGGACTTGGAG	AF417580	CCDS13029.2	20p13	2010-08-05	2003-02-23		ENSG00000149488	ENSG00000149488			16527	protein-coding gene	gene with protein product		606707	"transmembrane, cochlear expressed, 2"	C20orf145		11850618, 12906855	Standard	XM_005260660		Approved	dJ686C3.3	uc002wgf.1	Q8TDI7	OTTHUMG00000031698	ENST00000358864.1:c.1857C>G	chr20.hg19:g.2593953C>G	ENSP00000351732:p.Asp619Glu	513.0	0.0		313.0	68.0	NM_080751	Q5JXT0|Q5JXT1|Q6UWW4|Q6ZS41|Q8N9F3|Q9BYN2|Q9BYN3|Q9BYN4|Q9BYN5	Missense_Mutation	SNP	ENST00000358864.1	hg19	CCDS13029.2	.	.	.	.	.	.	.	.	.	.	C	18.40	3.615110	0.66672	.	.	ENSG00000149488	ENST00000358864	T	0.62941	-0.01	4.93	1.94	0.25998	.	0.000000	0.85682	D	0.000000	T	0.76169	0.3950	M	0.82323	2.585	0.43819	D	0.996384	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.999;0.999;1.0	T	0.74262	-0.3722	10	0.87932	D	0	-26.7544	7.2386	0.26084	0.0:0.645:0.0:0.355	.	450;451;619;619	B4DFB3;B7ZAE6;Q8TDI7-3;Q8TDI7	.;.;.;TMC2_HUMAN	E	619	ENSP00000351732:D619E	ENSP00000351732:D619E	D	+	3	2	TMC2	2541953	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.052000	0.41316	0.235000	0.21160	0.655000	0.94253	GAC	.	.		0.483	TMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077601.2			G	2593953	C	G	2593953	3	3	260	1	0	0	0	0	1	0	0	0	16000	564	20	4	1911	4	TMC2	20	2593953	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	2334049	2593953	60431567	870	38115										
SIGLEC1	6614	hgsc.bcm.edu	37	chr20	3677238	3677238	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aagactgacactcacctcggAcctggaagaagagtgaggtg	13	9	1	5			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr20:3677238A>G	ENST00000344754.4	-	10	2677	c.2678T>C	c.(2677-2679)gTc>gCc	p.V893A	SIGLEC1_ENST00000202578.4_Missense_Mutation_p.V893A	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	893	Ig-like C2-type 8.				cell-matrix adhesion (GO:0007160)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of T cell apoptotic process (GO:0070234)|single organismal cell-cell adhesion (GO:0016337)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|liver(2)|lung(24)|ovary(3)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)	70						CTCACCTCGGACCTGGAAGAA	0.522																																					p.V893A		Atlas-SNP	.											.	SIGLEC1	210	.	0			c.T2678C						.						61	62	62					20																	3677238		2203	4300	6503	SO:0001583	missense	6614	exon10			CCTCGGACCTGGA	AF230073	CCDS13060.1	20p13	2013-01-29	2006-01-19	2006-01-19	ENSG00000088827	ENSG00000088827		"CD molecules", "Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	11127	protein-coding gene	gene with protein product		600751	"sialoadhesin"	SN		8530048	Standard	XM_006723610		Approved	SIGLEC-1, CD169, FLJ00051, FLJ00055, FLJ00073, FLJ32150, dJ1009E24.1, sialoadhesin	uc002wja.3	Q9BZZ2	OTTHUMG00000031757	ENST00000344754.4:c.2678T>C	chr20.hg19:g.3677238A>G	ENSP00000341141:p.Val893Ala	155.0	0.0		89.0	4.0	NM_023068	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Missense_Mutation	SNP	ENST00000344754.4	hg19	CCDS13060.1	.	.	.	.	.	.	.	.	.	.	A	16.95	3.263835	0.59431	.	.	ENSG00000088827	ENST00000344754;ENST00000202578	D;D	0.87491	-2.26;-2.26	5.03	3.95	0.45737	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.37809	N	0.001940	D	0.90532	0.7033	L	0.60455	1.87	0.33325	D	0.567862	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.91646	0.5331	10	0.54805	T	0.06	.	8.8391	0.35131	0.9118:0.0:0.0882:0.0	.	893;893	Q9BZZ2;Q9BZZ2-3	SN_HUMAN;.	A	893	ENSP00000341141:V893A;ENSP00000202578:V893A	ENSP00000202578:V893A	V	-	2	0	SIGLEC1	3625238	0.999000	0.42202	0.998000	0.56505	0.969000	0.65631	2.845000	0.48254	0.956000	0.37904	0.533000	0.62120	GTC	.	.		0.522	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068		G	3677238	A	G	3677238	3	3	260	1	0	0	0	0	1	0	0	0	14320	275	10	2	2499	2	SIGLEC1	20	3677238	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1083285	3677238	59348282	871	38116										
SIGLEC1	6614	hgsc.bcm.edu	37	chr20	3678483	3678483	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctgaggtggaggcgttgcccAgggcattgctggcctcacag	16	11	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr20:3678483A>G	ENST00000344754.4	-	8	2083	c.2084T>C	c.(2083-2085)cTg>cCg	p.L695P	SIGLEC1_ENST00000202578.4_Missense_Mutation_p.L695P	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	695	Ig-like C2-type 6.				cell-matrix adhesion (GO:0007160)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of T cell apoptotic process (GO:0070234)|single organismal cell-cell adhesion (GO:0016337)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|liver(2)|lung(24)|ovary(3)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)	70						GGCGTTGCCCAGGGCATTGCT	0.612																																					p.L695P		Atlas-SNP	.											.	SIGLEC1	210	.	0			c.T2084C						.						63	44	51					20																	3678483		2203	4300	6503	SO:0001583	missense	6614	exon8			TTGCCCAGGGCAT	AF230073	CCDS13060.1	20p13	2013-01-29	2006-01-19	2006-01-19	ENSG00000088827	ENSG00000088827		"CD molecules", "Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	11127	protein-coding gene	gene with protein product		600751	"sialoadhesin"	SN		8530048	Standard	XM_006723610		Approved	SIGLEC-1, CD169, FLJ00051, FLJ00055, FLJ00073, FLJ32150, dJ1009E24.1, sialoadhesin	uc002wja.3	Q9BZZ2	OTTHUMG00000031757	ENST00000344754.4:c.2084T>C	chr20.hg19:g.3678483A>G	ENSP00000341141:p.Leu695Pro	101.0	0.0		69.0	4.0	NM_023068	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Missense_Mutation	SNP	ENST00000344754.4	hg19	CCDS13060.1	.	.	.	.	.	.	.	.	.	.	A	18.71	3.682218	0.68042	.	.	ENSG00000088827	ENST00000344754;ENST00000202578	T;T	0.76060	-0.99;-0.99	5.54	5.54	0.83059	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.278833	0.19350	N	0.116415	D	0.87208	0.6120	M	0.89785	3.06	0.58432	D	0.999999	D;D	0.69078	0.997;0.992	D;D	0.69824	0.966;0.942	D	0.87372	0.2351	10	0.40728	T	0.16	.	11.9958	0.53201	1.0:0.0:0.0:0.0	.	695;695	Q9BZZ2;Q9BZZ2-3	SN_HUMAN;.	P	695	ENSP00000341141:L695P;ENSP00000202578:L695P	ENSP00000202578:L695P	L	-	2	0	SIGLEC1	3626483	0.305000	0.24481	0.993000	0.49108	0.824000	0.46624	2.044000	0.41241	2.326000	0.78906	0.533000	0.62120	CTG	.	.		0.612	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068		G	3678483	A	G	3678483	3	3	260	1	0	0	0	0	1	0	0	0	14320	188	7	2	3101	2	SIGLEC1	20	3678483	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1245	3678483	59347037	872	38117										
PLCB4	5332	hgsc.bcm.edu	37	chr20	9438138	9438138	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	atcagatcacaaatctaaggTaagaaaatgcccatttttac	5	8	3	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr20:9438138T>A	ENST00000378493.1	+	30	3051		c.e30+2		PLCB4_ENST00000278655.4_Splice_Site|PLCB4_ENST00000378473.3_Splice_Site|PLCB4_ENST00000334005.3_Splice_Site|PLCB4_ENST00000378501.2_Splice_Site|PLCB4_ENST00000414679.2_Splice_Site|PLCB4_ENST00000492632.1_Splice_Site			Q15147	PLCB4_HUMAN	phospholipase C, beta 4						inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|smooth endoplasmic reticulum (GO:0005790)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(2)|breast(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(11)|liver(4)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(19)|upper_aerodigestive_tract(1)	87						AAATCTAAGGTAAGAAAATGC	0.353																																					.		Atlas-SNP	.											.	PLCB4	204	.	0			c.3072+2T>A						.						60	61	61					20																	9438138		2203	4300	6503	SO:0001630	splice_region_variant	5332	exon33			CTAAGGTAAGAAA		CCDS13104.1, CCDS13105.1, CCDS54447.1	20p12	2008-03-18			ENSG00000101333	ENSG00000101333	3.1.4.11		9059	protein-coding gene	gene with protein product		600810				8530101	Standard	NM_000933		Approved		uc021wam.1	Q15147	OTTHUMG00000031853	ENST00000378493.1:c.3036+2T>A	chr20.hg19:g.9438138T>A		314.0	0.0		195.0	8.0	NM_001172646	B7ZLK6|E2QRH8|Q17R56|Q5JYS8|Q5JYS9|Q5JYT0|Q5JYT3|Q5JYT4|Q9BQW5|Q9BQW6|Q9BQW8|Q9UJQ2	Splice_Site	SNP	ENST00000378493.1	hg19	CCDS13105.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.177343	0.78564	.	.	ENSG00000101333	ENST00000334005;ENST00000378473;ENST00000278655;ENST00000378493;ENST00000378501;ENST00000414679	.	.	.	5.01	5.01	0.66863	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0161	0.71584	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	PLCB4	9386138	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.026000	0.76455	2.019000	0.59389	0.533000	0.62120	.	.	.		0.353	PLCB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077948.2		Intron	A	9438138	T	A	9438138	5	1	260	1	0	0	0	0	0	0	1	0	12039	1652	57	4	3196	4	PLCB4	20	9438138	Splice_Site	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	5759655	9438138	53587382	873	38118										
C20orf72	92667	hgsc.bcm.edu	37	chr20	17968897	17968897	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acaacccactgcaagttgtgGcatacatgggtgccatgaac	10	11	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr20:17968897G>A	ENST00000377710.5	+	4	1108	c.820G>A	c.(820-822)Gca>Aca	p.A274T	MGME1_ENST00000467391.1_3'UTR|MGME1_ENST00000377709.1_Missense_Mutation_p.A194T|MGME1_ENST00000377704.4_Intron	NM_052865.2	NP_443097.1			mitochondrial genome maintenance exonuclease 1																		GCAAGTTGTGGCATACATGGG	0.408																																					p.A274T		Atlas-SNP	.											.	.	.	.	0			c.G820A						.						107	95	99					20																	17968897		2203	4300	6503	SO:0001583	missense	92667	exon4			GTTGTGGCATACA		CCDS13131.1	20p11.23	2013-08-29	2013-01-11	2013-01-11	ENSG00000125871	ENSG00000125871			16205	protein-coding gene	gene with protein product		615076	"chromosome 20 open reading frame 72"	C20orf72		23313956, 23358826, 23434322	Standard	NM_052865		Approved	bA504H3.4, DDK1	uc002wqh.3	Q9BQP7	OTTHUMG00000031955	ENST00000377710.5:c.820G>A	chr20.hg19:g.17968897G>A	ENSP00000366939:p.Ala274Thr	151.0	0.0		97.0	4.0	NM_052865		Missense_Mutation	SNP	ENST00000377710.5	hg19	CCDS13131.1	.	.	.	.	.	.	.	.	.	.	G	35	5.521357	0.96416	.	.	ENSG00000125871	ENST00000377710;ENST00000377709	T;T	0.73897	-0.79;-0.43	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	D	0.89343	0.6688	M	0.89601	3.045	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90977	0.4824	10	0.87932	D	0	-21.1275	19.2525	0.93930	0.0:0.0:1.0:0.0	.	274	Q9BQP7	CT072_HUMAN	T	274;194	ENSP00000366939:A274T;ENSP00000366938:A194T	ENSP00000366938:A194T	A	+	1	0	C20orf72	17916897	1.000000	0.71417	0.975000	0.42487	0.991000	0.79684	9.134000	0.94467	2.645000	0.89757	0.462000	0.41574	GCA	.	.		0.408	MGME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078139.1	NM_052865		A	17968897	G	A	17968897	3	1	260	1	0	0	0	0	1	0	0	0	2120	1203	42	3	830	3	C20orf72	20	17968897	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	8530759	17968897	45056623	874	38119										
C20orf12	55184	hgsc.bcm.edu	37	chr20	18407716	18407716	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	atgcaatcaacctacctcttGtgatgaaggcagggccccct	9	13	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr20:18407716G>A	ENST00000358866.6	-	9	971	c.949C>T	c.(949-951)Caa>Taa	p.Q317*	DZANK1_ENST00000487128.1_5'UTR|DZANK1_ENST00000329494.5_Nonsense_Mutation_p.Q319*|DZANK1_ENST00000262547.5_Nonsense_Mutation_p.Q317*|DZANK1_ENST00000357236.4_Nonsense_Mutation_p.Q203*			Q9NVP4	DZAN1_HUMAN	double zinc ribbon and ankyrin repeat domains 1	317							zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(10)	19						CCTACCTCTTGTGATGAAGGC	0.468																																					p.Q317X		Atlas-SNP	.											.	DZANK1	65	.	0			c.C949T						.						64	66	65					20																	18407716		1893	4116	6009	SO:0001587	stop_gained	55184	exon10			CCTCTTGTGATGA	AK001462	CCDS46582.1	20p11.23	2013-01-11	2011-10-03	2011-10-03	ENSG00000089091	ENSG00000089091		"Ankyrin repeat domain containing"	15858	protein-coding gene	gene with protein product	"ankyrin repeat domain 64"		"chromosome 20 open reading frame 12"	C20orf84, C20orf12			Standard	NM_001099407		Approved	FLJ10600, dJ568F9.2, FLJ30892, bA189K21.8, ANKRD64	uc002wqq.4	Q9NVP4	OTTHUMG00000031968	ENST00000358866.6:c.949C>T	chr20.hg19:g.18407716G>A	ENSP00000351734:p.Gln317*	98.0	0.0		75.0	18.0	NM_001099407	B7ZLZ4|Q4F7X1|Q5QPD9|Q5QPE0|Q68DN8|Q6ZMX9|Q96NF0|Q9H1E0|Q9H442	Nonsense_Mutation	SNP	ENST00000358866.6	hg19	CCDS46582.1	.	.	.	.	.	.	.	.	.	.	G	37	6.180095	0.97352	.	.	ENSG00000089091	ENST00000377630;ENST00000262547;ENST00000329494;ENST00000414623;ENST00000377637;ENST00000357236	.	.	.	5.63	0.645	0.17782	.	1.457470	0.03627	N	0.237380	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	0.4985	6.7012	0.23227	0.0899:0.0:0.4749:0.4352	.	.	.	.	X	144;317;319;143;143;203	.	ENSP00000262547:Q317X	Q	-	1	0	C20orf12	18355716	0.806000	0.28996	0.012000	0.15200	0.376000	0.30014	1.083000	0.30815	0.259000	0.21709	0.655000	0.94253	CAA	.	.		0.468	DZANK1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471926.1	NM_001099407		A	18407716	G	A	18407716	4	1	260	1	0	0	0	0	0	1	0	0	2087	1386	48	3	1357	3	C20orf12	20	18407716	Nonsense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	438819	18407716	44617804	875	38120										
C20orf12	55184	hgsc.bcm.edu	37	chr20	18414338	18414338	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggctgcagctgtagagcaagAggggcctcacacaccacaca	12	13	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr20:18414338A>G	ENST00000358866.6	-	8	841	c.819T>C	c.(817-819)ccT>ccC	p.P273P	DZANK1_ENST00000487128.1_5'UTR|DZANK1_ENST00000329494.5_Silent_p.P275P|DZANK1_ENST00000262547.5_Silent_p.P273P|DZANK1_ENST00000357236.4_Silent_p.P159P|RNA5SP476_ENST00000516613.1_RNA			Q9NVP4	DZAN1_HUMAN	double zinc ribbon and ankyrin repeat domains 1	273							zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(10)	19						GTAGAGCAAGAGGGGCCTCAC	0.453																																					p.P273P		Atlas-SNP	.											.	DZANK1	65	.	0			c.T819C						.						84	87	86					20																	18414338		2007	4171	6178	SO:0001819	synonymous_variant	55184	exon9			AGCAAGAGGGGCC	AK001462	CCDS46582.1	20p11.23	2013-01-11	2011-10-03	2011-10-03	ENSG00000089091	ENSG00000089091		"Ankyrin repeat domain containing"	15858	protein-coding gene	gene with protein product	"ankyrin repeat domain 64"		"chromosome 20 open reading frame 12"	C20orf84, C20orf12			Standard	NM_001099407		Approved	FLJ10600, dJ568F9.2, FLJ30892, bA189K21.8, ANKRD64	uc002wqq.4	Q9NVP4	OTTHUMG00000031968	ENST00000358866.6:c.819T>C	chr20.hg19:g.18414338A>G		142.0	0.0		87.0	4.0	NM_001099407	B7ZLZ4|Q4F7X1|Q5QPD9|Q5QPE0|Q68DN8|Q6ZMX9|Q96NF0|Q9H1E0|Q9H442	Silent	SNP	ENST00000358866.6	hg19	CCDS46582.1	.	.	.	.	.	.	.	.	.	.	A	3.159	-0.172490	0.06421	.	.	ENSG00000089091	ENST00000358866	.	.	.	4.97	-9.01	0.00744	.	.	.	.	.	T	0.27205	0.0667	.	.	.	0.20074	N	0.999938	.	.	.	.	.	.	T	0.31806	-0.9930	4	.	.	.	-1.1565	9.8516	0.41059	0.1698:0.5189:0.3114:0.0	.	.	.	.	P	72	.	.	L	-	2	0	C20orf12	18362338	0.083000	0.21467	0.001000	0.08648	0.377000	0.30045	-0.957000	0.03861	-1.547000	0.01715	-0.313000	0.08912	CTC	.	.		0.453	DZANK1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471926.1	NM_001099407		G	18414338	A	G	18414338	2	3	260	1	0	0	0	0	0	0	0	1	2087	291	11	2		2	C20orf12	20	18414338	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	6622	18414338	44611182	876	38121										
ABHD12	26090	hgsc.bcm.edu	37	chr20	25284191	25284191	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gaggccaggacccacctttcTgccaagctggaagggcacca	12	14	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr20:25284191T>C	ENST00000339157.5	-	11	1296	c.1024A>G	c.(1024-1026)Aga>Gga	p.R342G	ABHD12_ENST00000376542.3_Missense_Mutation_p.R342G	NM_001042472.2	NP_001035937.1	Q8N2K0	ABD12_HUMAN	abhydrolase domain containing 12	342					adult walking behavior (GO:0007628)|phosphatidylserine catabolic process (GO:0006660)|response to auditory stimulus (GO:0010996)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)	acylglycerol lipase activity (GO:0047372)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|liver(1)|lung(1)|skin(1)|urinary_tract(1)	12						CCCACCTTTCTGCCAAGCTGG	0.637																																					p.R342G		Atlas-SNP	.											.	ABHD12	46	.	0			c.A1024G						.						95	65	75					20																	25284191		2203	4300	6503	SO:0001583	missense	26090	exon11			CCTTTCTGCCAAG	AL117442	CCDS13172.1, CCDS42857.1	20p11.21	2007-04-24	2006-03-10	2006-03-10	ENSG00000100997	ENSG00000100997		"Abhydrolase domain containing"	15868	protein-coding gene	gene with protein product		613599	"chromosome 20 open reading frame 22"	C20orf22			Standard	NM_015600		Approved	DKFZP434P106, dJ965G21.2, BEM46L2, ABHD12A	uc002wuq.3	Q8N2K0	OTTHUMG00000032121	ENST00000339157.5:c.1024A>G	chr20.hg19:g.25284191T>C	ENSP00000341408:p.Arg342Gly	38.0	0.0		35.0	4.0	NM_001042472	A6NED4|A6NJ90|A8K450|B4DE71|Q5T710|Q5T711|Q96CR1|Q9BX05|Q9NPX7|Q9UFV6	Missense_Mutation	SNP	ENST00000339157.5	hg19	CCDS42857.1	.	.	.	.	.	.	.	.	.	.	T	17.10	3.303914	0.60305	.	.	ENSG00000100997	ENST00000376542;ENST00000339157;ENST00000526543	T;T	0.24350	1.86;1.86	5.23	5.23	0.72850	.	0.088799	0.85682	D	0.000000	T	0.29588	0.0738	M	0.73372	2.23	0.45648	D	0.998579	B;P;P	0.39717	0.038;0.684;0.646	B;B;B	0.34536	0.03;0.185;0.164	T	0.19063	-1.0317	10	0.62326	D	0.03	-21.1429	15.2379	0.73447	0.0:0.0:0.0:1.0	.	304;342;342	Q8N2K0-3;Q8N2K0;Q8N2K0-2	.;ABD12_HUMAN;.	G	342;342;304	ENSP00000365725:R342G;ENSP00000341408:R342G	ENSP00000341408:R342G	R	-	1	2	ABHD12	25232191	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	2.945000	0.49043	2.319000	0.78375	0.533000	0.62120	AGA	.	.		0.637	ABHD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078423.2	NM_015600		C	25284191	T	C	25284191	3	2	260	1	0	0	0	0	1	0	0	0	76	1588	55	2	246	2	ABHD12	20	25284191	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	6869853	25284191	37741329	877	38122										
CPNE1	8904	hgsc.bcm.edu	37	chr20	34215233	34215233	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cctgatgtgcagcctgggctGcaaacctggccacatggttg	13	12	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr20:34215233G>A	ENST00000317619.3	-	16	1599	c.1205C>T	c.(1204-1206)gCa>gTa	p.A402V	CPNE1_ENST00000397445.1_Missense_Mutation_p.A402V|CPNE1_ENST00000352393.4_Missense_Mutation_p.A402V|CPNE1_ENST00000397446.1_Missense_Mutation_p.A402V|CPNE1_ENST00000397443.1_Missense_Mutation_p.A402V|CPNE1_ENST00000317677.5_Missense_Mutation_p.A407V|CPNE1_ENST00000397442.1_Missense_Mutation_p.A402V			Q99829	CPNE1_HUMAN	copine I	402	VWFA.				lipid metabolic process (GO:0006629)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)	calcium-dependent phospholipid binding (GO:0005544)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	21	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			AGCCTGGGCTGCAAACCTGGC	0.582																																					p.A407V		Atlas-SNP	.											.	CPNE1	44	.	0			c.C1220T						.						101	87	92					20																	34215233		2203	4300	6503	SO:0001583	missense	8904	exon14			TGGGCTGCAAACC	U83246	CCDS13260.1, CCDS46595.1	20q11.22	2009-06-01			ENSG00000214078	ENSG00000214078			2314	protein-coding gene	gene with protein product		604205				9430674	Standard	NM_152925		Approved	CPN1	uc002xdm.3	Q99829	OTTHUMG00000032356	ENST00000317619.3:c.1205C>T	chr20.hg19:g.34215233G>A	ENSP00000326126:p.Ala402Val	141.0	0.0		120.0	5.0	NM_003915	E1P5Q4|Q6IBL3|Q9H243|Q9NTZ7	Missense_Mutation	SNP	ENST00000317619.3	hg19	CCDS13260.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	35|35	5.555230|5.555230	0.96514|0.96514	.|.	.|.	ENSG00000214078|ENSG00000214078	ENST00000352393;ENST00000317677;ENST00000317619;ENST00000397446;ENST00000397445;ENST00000397443;ENST00000397442;ENST00000437340;ENST00000430570|ENST00000415920	T;T;T;T;T;T;T;T;T|.	0.24350|.	1.86;1.86;1.86;1.86;1.86;1.86;1.86;1.86;1.86|.	5.06|5.06	5.06|5.06	0.68205|0.68205	von Willebrand factor, type A (1);Copine (1);|.	0.000000|.	0.85682|.	U|.	0.000000|.	T|.	0.74627|.	0.3741|.	M|M	0.70903|0.70903	2.155|2.155	0.80722|0.80722	D|D	1|1	D;D;D;D;D|.	0.89917|.	0.988;1.0;0.999;1.0;1.0|.	D;D;D;D;D|.	0.91635|.	0.936;0.993;0.996;0.999;0.999|.	T|.	0.74093|.	-0.3776|.	10|.	0.72032|.	D|.	0.01|.	-17.6519|-17.6519	17.3695|17.3695	0.87372|0.87372	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	407;402;402;382;402|.	B0QZ18;A6PVH9;Q99829;Q59EI4;F2Z2V0|.	.;.;CPNE1_HUMAN;.;.|.	V|X	402;407;402;402;402;402;402;402;378|41	ENSP00000336945:A402V;ENSP00000317257:A407V;ENSP00000326126:A402V;ENSP00000380588:A402V;ENSP00000380587:A402V;ENSP00000380585:A402V;ENSP00000380584:A402V;ENSP00000415597:A402V;ENSP00000390626:A378V|.	ENSP00000326126:A402V|.	A|Q	-|-	2|1	0|0	CPNE1|CPNE1	33678647|33678647	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	9.629000|9.629000	0.98417|0.98417	2.627000|2.627000	0.88993|0.88993	0.563000|0.563000	0.77884|0.77884	GCA|CAG	.	.		0.582	CPNE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078909.3	NM_152930		A	34215233	G	A	34215233	3	1	260	1	0	0	0	0	1	0	0	0	3813	1319	46	3	420	3	CPNE1	20	34215233	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	8931042	34215233	28810287	878	38123										
EPB41L1	2036	hgsc.bcm.edu	37	chr20	34765929	34765929	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctgtgaacacctcaacctccTagagaaggactacttcggcc	8	14	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr20:34765929T>C	ENST00000338074.2	+	4	559	c.398T>C	c.(397-399)cTa>cCa	p.L133P	EPB41L1_ENST00000373941.1_Missense_Mutation_p.L133P|EPB41L1_ENST00000441639.1_Missense_Mutation_p.L71P|EPB41L1_ENST00000373950.2_Intron|EPB41L1_ENST00000202028.5_Missense_Mutation_p.L71P|EPB41L1_ENST00000373946.3_Missense_Mutation_p.L102P	NM_001258329.1|NM_012156.2	NP_001245258.1|NP_036288.2	Q9H4G0	E41L1_HUMAN	erythrocyte membrane protein band 4.1-like 1	133	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cortical actin cytoskeleton organization (GO:0030866)|synaptic transmission (GO:0007268)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(10)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	37	Breast(12;0.0239)					CTCAACCTCCTAGAGAAGGAC	0.582																																					p.L133P		Atlas-SNP	.											.	EPB41L1	111	.	0			c.T398C						.						126	102	110					20																	34765929		2203	4300	6503	SO:0001583	missense	2036	exon5			ACCTCCTAGAGAA	AB002336	CCDS13271.1, CCDS13272.1, CCDS58771.1	20q11.2-q12	2003-03-17			ENSG00000088367	ENSG00000088367			3378	protein-coding gene	gene with protein product		602879				9570967, 9828140	Standard	NM_012156		Approved	KIAA0338	uc002xfb.3	Q9H4G0	OTTHUMG00000032378	ENST00000338074.2:c.398T>C	chr20.hg19:g.34765929T>C	ENSP00000337168:p.Leu133Pro	102.0	0.0		94.0	4.0	NM_001258329	O15046|Q4VXM6|Q4VXM7|Q4VXM8|Q4VXN4|Q6ZT61|Q8IUU7|Q96CV5|Q96L65	Missense_Mutation	SNP	ENST00000338074.2	hg19	CCDS13271.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.415320	0.83449	.	.	ENSG00000088367	ENST00000202028;ENST00000406771;ENST00000430276;ENST00000397315;ENST00000452261;ENST00000397307;ENST00000441639;ENST00000373946;ENST00000373945;ENST00000338074;ENST00000373941	T;T;T;T;T;T;T;T;T	0.76839	-1.05;-1.05;-1.05;-1.05;-1.05;-1.05;-1.05;-1.05;-1.05	5.4	5.4	0.78164	FERM, N-terminal (1);Band 4.1 domain (1);FERM domain (1);	.	.	.	.	D	0.88145	0.6358	M	0.80746	2.51	0.80722	D	1	D;D;D;D;D	0.89917	0.999;1.0;1.0;0.999;1.0	D;D;D;D;D	0.97110	0.988;1.0;0.999;0.969;0.992	D	0.89753	0.3941	9	0.87932	D	0	.	14.5515	0.68070	0.0:0.0:0.0:1.0	.	133;133;133;102;71	B7Z653;Q9H4G0;Q4VXN5;Q9H4G0-4;Q9H4G0-2	.;E41L1_HUMAN;.;.;.	P	71;133;71;133;133;71;71;102;71;133;133	ENSP00000202028:L71P;ENSP00000385244:L133P;ENSP00000404341:L71P;ENSP00000413262:L133P;ENSP00000399214:L71P;ENSP00000363057:L102P;ENSP00000363056:L71P;ENSP00000337168:L133P;ENSP00000363052:L133P	ENSP00000202028:L71P	L	+	2	0	EPB41L1	34229343	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.997000	0.88414	2.168000	0.68352	0.533000	0.62120	CTA	.	.		0.582	EPB41L1-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078978.3	NM_012156		C	34765929	T	C	34765929	3	2	260	1	0	0	0	0	1	0	0	0	5154	1522	53	2	408	2	EPB41L1	20	34765929	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	550696	34765929	28259591	879	38124										
MAFB	9935	hgsc.bcm.edu	37	chr20	39316659	39316659	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cacctcctgcttaagctgctCcacctgctgaatgagctgcg	9	15	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr20:39316659C>T	ENST00000373313.2	-	1	1221	c.832G>A	c.(832-834)Gag>Aag	p.E278K	MAFB_ENST00000396967.1_Missense_Mutation_p.E278K	NM_005461.3	NP_005452.2	Q9Y5Q3	MAFB_HUMAN	v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog B	278	Leucine-zipper. {ECO:0000255|PROSITE- ProRule:PRU00978}.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				brain segmentation (GO:0035284)|inner ear morphogenesis (GO:0042472)|negative regulation of erythrocyte differentiation (GO:0045647)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|respiratory gaseous exchange (GO:0007585)|rhombomere 5 development (GO:0021571)|rhombomere 6 development (GO:0021572)|segment specification (GO:0007379)|sensory organ development (GO:0007423)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			kidney(1)|large_intestine(1)	2		Myeloproliferative disorder(115;0.00878)				TTAAGCTGCTCCACCTGCTGA	0.607			T	IGH@	MM																																p.E278K		Atlas-SNP	.		Dom	yes		20	20q11.2-q13.1	9935	v-maf musculoaponeurotic fibrosarcoma oncogene homolog B (avian)		L	.	MAFB	13	.	0			c.G832A						.						77	79	78					20																	39316659		2203	4300	6503	SO:0001583	missense	9935	exon1			GCTGCTCCACCTG	AF134157	CCDS13311.1	20q11.1-q13.1	2013-07-09	2013-07-09	2001-11-30	ENSG00000204103	ENSG00000204103			6408	protein-coding gene	gene with protein product		608968	"Kreisler (mouse) maf-related leucine zipper homolog"	KRML		10444328	Standard	NM_005461		Approved		uc002xji.3	Q9Y5Q3	OTTHUMG00000033052	ENST00000373313.2:c.832G>A	chr20.hg19:g.39316659C>T	ENSP00000362410:p.Glu278Lys	124.0	0.0		94.0	4.0	NM_005461	B3KNE1|Q9H1F1	Missense_Mutation	SNP	ENST00000373313.2	hg19	CCDS13311.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.188441	0.78789	.	.	ENSG00000204103	ENST00000373313;ENST00000396967	D;D	0.91686	-2.89;-2.89	4.36	3.42	0.39159	Basic-leucine zipper (bZIP) transcription factor (2);Maf transcription factor (1);	0.000000	0.85682	D	0.000000	D	0.94499	0.8229	M	0.68317	2.08	0.80722	D	1	D	0.69078	0.997	D	0.69307	0.963	D	0.94172	0.7424	10	0.59425	D	0.04	.	12.1756	0.54184	0.0:0.9165:0.0:0.0835	.	278	Q9Y5Q3	MAFB_HUMAN	K	278	ENSP00000362410:E278K;ENSP00000380167:E278K	ENSP00000362410:E278K	E	-	1	0	MAFB	38750073	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.606000	0.82863	1.077000	0.40990	0.456000	0.33151	GAG	.	.		0.607	MAFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080375.2			T	39316659	C	T	39316659	3	4	260	1	0	0	0	0	1	0	0	0	9167	864	30	3	143	3	MAFB	20	39316659	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	4550730	39316659	23708861	880	38125										
ADA	100	hgsc.bcm.edu	37	chr20	43257689	43257689	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgggttgggggcaactcacgCgatagcaggcatgtagtagt	16	7	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr20:43257689C>T	ENST00000372874.4	-	3	351	c.217G>A	c.(217-219)Gcg>Acg	p.A73T	ADA_ENST00000464097.1_5'Flank|ADA_ENST00000537820.1_Splice_Site_p.A73T	NM_000022.2	NP_000013.2	P00813	ADA_HUMAN	adenosine deaminase	73					adenosine catabolic process (GO:0006154)|aging (GO:0007568)|cell adhesion (GO:0007155)|dATP catabolic process (GO:0046061)|deoxyadenosine catabolic process (GO:0006157)|embryonic digestive tract development (GO:0048566)|germinal center B cell differentiation (GO:0002314)|histamine secretion (GO:0001821)|hypoxanthine salvage (GO:0043103)|inosine biosynthetic process (GO:0046103)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|negative regulation of adenosine receptor signaling pathway (GO:0060169)|negative regulation of circadian sleep/wake cycle, non-REM sleep (GO:0042323)|negative regulation of inflammatory response (GO:0050728)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of mature B cell apoptotic process (GO:0002906)|negative regulation of mucus secretion (GO:0070256)|negative regulation of penile erection (GO:0060407)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleobase-containing small molecule metabolic process (GO:0055086)|Peyer's patch development (GO:0048541)|placenta development (GO:0001890)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of germinal center formation (GO:0002636)|positive regulation of heart rate (GO:0010460)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of T cell receptor signaling pathway (GO:0050862)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide salvage (GO:0032261)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|purine-containing compound salvage (GO:0043101)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to morphine (GO:0043278)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|trophectodermal cell differentiation (GO:0001829)|xanthine biosynthetic process (GO:0046111)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|lysosome (GO:0005764)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenosine deaminase activity (GO:0004000)|purine nucleoside binding (GO:0001883)|zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|pancreas(2)|prostate(3)|skin(2)|urinary_tract(1)	18		all_lung(126;1.24e-07)|Lung NSC(126;1.94e-07)|Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)		Adenosine(DB00640)|Dipyridamole(DB00975)|Edetic Acid(DB00974)|Nelarabine(DB01280)|Pentostatin(DB00552)|Theophylline(DB00277)|Vidarabine(DB00194)	GCAACTCACGCGATAGCAGGC	0.577									Adenosine Deaminase Deficiency																												p.A73T		Atlas-SNP	.											ADA,NS,carcinoma,0,1	ADA	42	.	0			c.G217A						.						164	119	134					20																	43257689		2203	4300	6503	SO:0001630	splice_region_variant	100	exon3	Familial Cancer Database	Severe Combined Immunodeficiency (SCID) due to ADA-deficiency	CTCACGCGATAGC	X02994	CCDS13335.1	20q13.12	2014-09-17			ENSG00000196839	ENSG00000196839	3.5.4.4		186	protein-coding gene	gene with protein product		608958				6198240, 6090454	Standard	NM_000022		Approved		uc002xmj.3	P00813	OTTHUMG00000033081	ENST00000372874.4:c.218+1G>A	chr20.hg19:g.43257689C>T		93.0	0.0		48.0	3.0	NM_000022	Q53F92|Q6LA59	Missense_Mutation	SNP	ENST00000372874.4	hg19	CCDS13335.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.685211	0.88639	.	.	ENSG00000196839	ENST00000372874;ENST00000537820	D;D	0.95412	-3.7;-3.7	5.84	5.84	0.93424	Adenosine/AMP deaminase (1);	0.049571	0.85682	D	0.000000	D	0.94751	0.8306	M	0.68728	2.09	0.80722	D	1	D	0.56521	0.976	P	0.44447	0.45	D	0.93126	0.6529	10	0.21014	T	0.42	-0.9005	18.8993	0.92435	0.0:1.0:0.0:0.0	.	73	P00813	ADA_HUMAN	T	73	ENSP00000361965:A73T;ENSP00000441818:A73T	ENSP00000361965:A73T	A	-	1	0	ADA	42691103	1.000000	0.71417	0.965000	0.40720	0.698000	0.40448	6.505000	0.73708	2.768000	0.95171	0.561000	0.74099	GCG	.	.		0.577	ADA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080509.2	NM_000022	Missense_Mutation	T	43257689	C	T	43257689	5	4	260	1	0	0	0	0	0	0	1	0	230	782	27	1	914	1	ADA	20	43257689	Splice_Site	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	3941030	43257689	19767831	881	38126										
PABPC1L	80336	hgsc.bcm.edu	37	chr20	43552887	43552887	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctctccctatggagtaattaCcagtgcgaaggtgaggactg	12	9	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr20:43552887C>T	ENST00000217073.2	+	7	962	c.962C>T	c.(961-963)aCc>aTc	p.T321I	PABPC1L_ENST00000255136.3_Missense_Mutation_p.T321I|PABPC1L_ENST00000537323.1_Missense_Mutation_p.T321I|PABPC1L_ENST00000490798.1_3'UTR|PABPC1L_ENST00000217074.4_Missense_Mutation_p.T321I			Q4VXU2	PAP1L_HUMAN	poly(A) binding protein, cytoplasmic 1-like	321	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA polyadenylation (GO:0006378)|oocyte maturation (GO:0001556)	extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	20						GGAGTAATTACCAGTGCGAAG	0.572																																					p.T321I		Atlas-SNP	.											.	PABPC1L	59	.	0			c.C962T						.						106	97	100					20																	43552887		1568	3582	5150	SO:0001583	missense	80336	exon7			TAATTACCAGTGC	AK026760	CCDS42878.1	20q12-q13.1	2013-02-12	2007-11-21	2007-11-21	ENSG00000101104	ENSG00000101104		"RNA binding motif (RRM) containing"	15797	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 119"	C20orf119		11549316	Standard	NM_001124756		Approved	dJ1069P2.3, PABPC1L1, ePAB	uc010ggv.1	Q4VXU2	OTTHUMG00000032553	ENST00000217073.2:c.962C>T	chr20.hg19:g.43552887C>T	ENSP00000217073:p.Thr321Ile	63.0	0.0		44.0	4.0	NM_001124756	Q4VY17	Missense_Mutation	SNP	ENST00000217073.2	hg19	CCDS42878.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.732363	0.89482	.	.	ENSG00000101104	ENST00000217074;ENST00000255136;ENST00000537323;ENST00000217073	T;T;T;T	0.16073	2.37;2.37;2.37;2.37	5.32	5.32	0.75619	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.29620	0.0739	L	0.31065	0.9	0.80722	D	1	D	0.58268	0.982	P	0.60949	0.881	T	0.02498	-1.1150	10	0.72032	D	0.01	.	18.5905	0.91210	0.0:1.0:0.0:0.0	.	321	Q4VXU2	PAP1L_HUMAN	I	321	ENSP00000217074:T321I;ENSP00000255136:T321I;ENSP00000445661:T321I;ENSP00000217073:T321I	ENSP00000217073:T321I	T	+	2	0	PABPC1L	42986301	1.000000	0.71417	1.000000	0.80357	0.847000	0.48162	7.723000	0.84788	2.496000	0.84212	0.655000	0.94253	ACC	.	.		0.572	PABPC1L-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127816.2			T	43552887	C	T	43552887	3	4	260	1	0	0	0	0	1	0	0	0	11373	507	18	3	988	3	PABPC1L	20	43552887	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	295198	43552887	19472633	882	38127										
SPINLW1	57119	hgsc.bcm.edu	37	chr20	44171499	44171499	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccagtttcttttggcatttcGcatacatctgcagagagact	8	10	2	2	rs570448304		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr20:44171499G>T	ENST00000354280.4	-	3	297	c.231C>A	c.(229-231)tgC>tgA	p.C77*	EPPIN_ENST00000336443.3_Nonsense_Mutation_p.C61*|EPPIN_ENST00000409554.1_Intron|EPPIN_ENST00000555685.1_Nonsense_Mutation_p.C77*|EPPIN-WFDC6_ENST00000504988.1_Nonsense_Mutation_p.C77*	NM_020398.3	NP_065131.1	O95925	EPPI_HUMAN	epididymal peptidase inhibitor	77	BPTI/Kunitz inhibitor. {ECO:0000255|PROSITE-ProRule:PRU00031}.				defense response to bacterium (GO:0042742)|negative regulation of peptidase activity (GO:0010466)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.C61C(2)									TTGGCATTTCGCATACATCTG	0.433																																					p.C77X		Atlas-SNP	.											SPINLW1_ENST00000336443,NS,carcinoma,0,5	.	.	.	2	Substitution - coding silent(2)	prostate(2)	c.C231A						.						80	79	79					20																	44171499		2203	4300	6503	SO:0001587	stop_gained	100526773	exon3			CATTTCGCATACA	AF286370	CCDS13359.1	20q13.12	2014-01-21	2012-08-22	2012-08-22	ENSG00000101448	ENSG00000101448		"WAP four-disulfide core domain containing"	15932	protein-coding gene	gene with protein product	"epididymal protease inhibitor", "cancer/testis antigen 72"	609031	"serine protease inhibitor-like, with Kunitz and WAP domains 1 (eppin)", "serine peptidase inhibitor-like, with Kunitz and WAP domains 1 (eppin)"	SPINLW1		11404006, 12206714	Standard	NM_020398		Approved	EPPIN1, EPPIN2, EPPIN3, dJ461P17.2, WAP7, WFDC7, CT71		O95925	OTTHUMG00000032588	ENST00000354280.4:c.231C>A	chr20.hg19:g.44171499G>T	ENSP00000361746:p.Cys77*	162.0	1.0		125.0	0.0	NM_001198986	A6PVD6|Q86TP9|Q96SD7|Q9HD30	Nonsense_Mutation	SNP	ENST00000354280.4	hg19	CCDS13359.1	.	.	.	.	.	.	.	.	.	.	G	31	5.059737	0.93846	.	.	ENSG00000101448;ENSG00000101448;ENSG00000101448;ENSG00000249139	ENST00000555685;ENST00000354280;ENST00000336443;ENST00000504988	.	.	.	4.41	0.197	0.15164	.	0.414326	0.23296	N	0.049738	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.4015	0.38435	0.331:0.0:0.669:0.0	.	.	.	.	X	77;77;61;77	.	ENSP00000338114:C61X	C	-	3	2	SPINLW1;SPINLW1-WFDC6	43604913	0.876000	0.30132	0.002000	0.10522	0.000000	0.00434	1.041000	0.30291	-0.220000	0.09988	-2.317000	0.00253	TGC	.	.		0.433	EPPIN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079467.4			T	44171499	G	T	44171499	4	4	260	1	0	0	0	0	0	1	0	0	15082	1079	38	1	178	1	SPINLW1	20	44171499	Nonsense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	618612	44171499	18854021	883	38128										
STAU1	6780	hgsc.bcm.edu	37	chr20	47739657	47739657	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	caaactccctgcggcgcgggAggcctcgctctgtgaggagc	15	14	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr20:47739657A>G	ENST00000371856.2	-	8	1348	c.938T>C	c.(937-939)cTc>cCc	p.L313P	STAU1_ENST00000371802.1_Missense_Mutation_p.L238P|STAU1_ENST00000371828.3_Missense_Mutation_p.L238P|STAU1_ENST00000347458.5_Missense_Mutation_p.L232P|STAU1_ENST00000371792.1_Missense_Mutation_p.L230P|STAU1_ENST00000340954.7_Missense_Mutation_p.L232P|STAU1_ENST00000360426.4_Missense_Mutation_p.L232P	NM_017453.2	NP_059347.2	O95793	STAU1_HUMAN	staufen double-stranded RNA binding protein 1	313	DRBM 3. {ECO:0000255|PROSITE- ProRule:PRU00266}.				intracellular mRNA localization (GO:0008298)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|rough endoplasmic reticulum (GO:0005791)	double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|liver(1)|lung(6)|ovary(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	23			BRCA - Breast invasive adenocarcinoma(12;0.000644)|Colorectal(8;0.198)			GCGGCGCGGGAGGCCTCGCTC	0.612																																					p.L313P		Atlas-SNP	.											.	STAU1	54	.	0			c.T938C						.						77	60	66					20																	47739657		2203	4300	6503	SO:0001583	missense	6780	exon8			CGCGGGAGGCCTC		CCDS13414.1, CCDS13415.1, CCDS33481.1	20q13.1	2014-06-13	2013-06-05	2005-11-04	ENSG00000124214	ENSG00000124214			11370	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 150"	601716	"staufen (Drosophila, RNA-binding protein)", "staufen, RNA binding protein (Drosophila)", "staufen, RNA binding protein, homolog 1 (Drosophila)"	STAU		8884277, 15680326	Standard	XM_005260524		Approved	PPP1R150	uc002xud.3	O95793	OTTHUMG00000032691	ENST00000371856.2:c.938T>C	chr20.hg19:g.47739657A>G	ENSP00000360922:p.Leu313Pro	166.0	0.0		92.0	4.0	NM_017453	A8K9Z4|E1P5Y1|E1P608|Q5JW29|Q6GTM4|Q9H5B4|Q9H5B5|Q9Y3Q2	Missense_Mutation	SNP	ENST00000371856.2	hg19	CCDS13414.1	.	.	.	.	.	.	.	.	.	.	A	26.9	4.785054	0.90282	.	.	ENSG00000124214	ENST00000371828;ENST00000340954;ENST00000371856;ENST00000360426;ENST00000347458;ENST00000371805;ENST00000371802;ENST00000371792	T;T;T;T;T;T;T	0.72167	-0.63;-0.63;-0.63;-0.63;-0.63;-0.63;-0.63	5.19	5.19	0.71726	Double-stranded RNA-binding (3);Double-stranded RNA-binding-like (1);	0.000000	0.85682	D	0.000000	T	0.65606	0.2707	N	0.02296	-0.605	0.80722	D	1	D;D	0.76494	0.994;0.999	D;D	0.70227	0.953;0.968	T	0.77259	-0.2654	10	0.66056	D	0.02	-11.1605	15.0426	0.71803	1.0:0.0:0.0:0.0	.	313;238	O95793;Q5JW29	STAU1_HUMAN;.	P	238;232;313;232;232;232;238;230	ENSP00000360893:L238P;ENSP00000345425:L232P;ENSP00000360922:L313P;ENSP00000353604:L232P;ENSP00000323443:L232P;ENSP00000360867:L238P;ENSP00000360857:L230P	ENSP00000345425:L232P	L	-	2	0	STAU1	47173064	1.000000	0.71417	0.987000	0.45799	0.990000	0.78478	9.339000	0.96797	1.939000	0.56221	0.528000	0.53228	CTC	.	.		0.612	STAU1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079633.1	NM_017453		G	47739657	A	G	47739657	3	3	260	1	0	0	0	0	1	0	0	0	15287	304	11	2	823	2	STAU1	20	47739657	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	3568158	47739657	15285863	884	38129										
NFATC2	4773	hgsc.bcm.edu	37	chr20	50071199	50071199	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgtgtcttgtctttcaaccaTgggcagctcgtgagcagatc	11	10	3	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr20:50071199T>C	ENST00000396009.3	-	6	1954	c.1735A>G	c.(1735-1737)Atg>Gtg	p.M579V	NFATC2_ENST00000609507.1_Missense_Mutation_p.M360V|NFATC2_ENST00000371564.3_Missense_Mutation_p.M579V|NFATC2_ENST00000609943.1_Missense_Mutation_p.M559V|NFATC2_ENST00000610033.1_Missense_Mutation_p.M360V|MIR3194_ENST00000582236.1_RNA|NFATC2_ENST00000414705.1_Missense_Mutation_p.M559V	NM_001258297.1|NM_173091.3	NP_001245226.1|NP_775114.1	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	579					B cell receptor signaling pathway (GO:0050853)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear transcription factor complex (GO:0044798)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)		EWSR1/NFATC2(9)	breast(2)|endometrium(7)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	53	Hepatocellular(150;0.248)					CTTTCAACCATGGGCAGCTCG	0.507																																					p.M579V		Atlas-SNP	.											.	NFATC2	112	.	0			c.A1735G						.						152	149	150					20																	50071199		2203	4300	6503	SO:0001583	missense	4773	exon6			CAACCATGGGCAG	U43342, U43341	CCDS13437.1, CCDS33488.1, CCDS46614.1, CCDS68156.1, CCDS68157.1	20q13.2	2009-11-24			ENSG00000101096	ENSG00000101096		"Nuclear factor of activated T-cells"	7776	protein-coding gene	gene with protein product		600490				8202141	Standard	NM_012340		Approved	NF-ATP, NFATp, NFAT1	uc002xwd.4	Q13469	OTTHUMG00000032747	ENST00000396009.3:c.1735A>G	chr20.hg19:g.50071199T>C	ENSP00000379330:p.Met579Val	120.0	0.0		98.0	5.0	NM_012340	B5B2N8|B5B2N9|B5B2P0|B5B2P2|B5B2P3|Q13468|Q5TFW7|Q5TFW8|Q9NPX6|Q9NQH3|Q9UJR2	Missense_Mutation	SNP	ENST00000396009.3	hg19	CCDS13437.1	.	.	.	.	.	.	.	.	.	.	T	14.48	2.547800	0.45383	.	.	ENSG00000101096	ENST00000371564;ENST00000396009;ENST00000414705	T;T;T	0.13657	2.57;2.57;2.58	5.8	3.45	0.39498	Cell surface receptor IPT/TIG (1);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.041569	0.85682	D	0.000000	T	0.10165	0.0249	N	0.19112	0.55	0.42017	D	0.990964	P;B;P;P	0.48230	0.907;0.399;0.846;0.907	P;B;P;P	0.44860	0.462;0.097;0.462;0.462	T	0.12218	-1.0556	10	0.52906	T	0.07	-25.9878	7.9868	0.30216	0.1284:0.0:0.2685:0.603	.	559;559;579;579	B5B2N9;B5B2P2;Q13469;B5B2N8	.;.;NFAC2_HUMAN;.	V	579;579;559	ENSP00000360619:M579V;ENSP00000379330:M579V;ENSP00000396471:M559V	ENSP00000360619:M579V	M	-	1	0	NFATC2	49504606	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	4.603000	0.61105	0.410000	0.25675	0.528000	0.53228	ATG	.	.		0.507	NFATC2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079730.2	NM_012340		C	50071199	T	C	50071199	3	2	260	1	0	0	0	0	1	0	0	0	10371	1464	51	2	1110	2	NFATC2	20	50071199	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	2331542	50071199	12954321	885	38130										
CASS4	57091	hgsc.bcm.edu	37	chr20	55027971	55027971	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	caagaggtttgcctccattgTcattgccaatggaaggctcc	10	11	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr20:55027971T>C	ENST00000360314.3	+	6	1964	c.1739T>C	c.(1738-1740)gTc>gCc	p.V580A	CASS4_ENST00000371336.3_Missense_Mutation_p.V580A|CASS4_ENST00000434344.1_Intron	NM_001164116.1	NP_001157588.1	Q9NQ75	CASS4_HUMAN	Cas scaffolding protein family member 4	580					cell adhesion (GO:0007155)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)			breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(4)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	54						GCCTCCATTGTCATTGCCAAT	0.463																																					p.V580A		Atlas-SNP	.											.	CASS4	121	.	0			c.T1739C						.						78	76	77					20																	55027971		2203	4300	6503	SO:0001583	missense	57091	exon5			CCATTGTCATTGC	AJ276678	CCDS33492.1, CCDS54475.1	20q13.31	2011-04-13	2008-04-14	2008-04-15	ENSG00000087589	ENSG00000087589		"Cas scaffolding proteins"	15878	protein-coding gene	gene with protein product	"HEF-like protein", "HEF1-Efs-p130Cas-like"		"chromosome 20 open reading frame 32"	C20orf32			Standard	NM_020356		Approved	HEFL, HEPL	uc002xxr.2	Q9NQ75	OTTHUMG00000032788	ENST00000360314.3:c.1739T>C	chr20.hg19:g.55027971T>C	ENSP00000353462:p.Val580Ala	163.0	0.0		111.0	7.0	NM_020356	E1P5Z8|Q5QPD6|Q96K09|Q9BYL5	Missense_Mutation	SNP	ENST00000360314.3	hg19	CCDS33492.1	.	.	.	.	.	.	.	.	.	.	T	29.8	5.038168	0.93630	.	.	ENSG00000087589	ENST00000360314;ENST00000371336	T;T	0.28069	1.63;1.63	6.17	6.17	0.99709	Serine rich protein interaction (1);	0.328819	0.32548	N	0.005950	T	0.47469	0.1447	M	0.63428	1.95	0.47245	D	0.999361	D;P;P	0.58268	0.982;0.925;0.939	P;P;P	0.53954	0.738;0.54;0.67	T	0.46843	-0.9162	10	0.87932	D	0	-25.8264	16.8222	0.85835	0.0:0.0:0.0:1.0	.	526;580;580	B4DII4;Q9NQ75-2;Q9NQ75	.;.;CASS4_HUMAN	A	580	ENSP00000353462:V580A;ENSP00000360387:V580A	ENSP00000353462:V580A	V	+	2	0	CASS4	54461378	1.000000	0.71417	0.950000	0.38849	0.921000	0.55340	7.251000	0.78297	2.371000	0.80710	0.533000	0.62120	GTC	.	.		0.463	CASS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079789.2	NM_020356		C	55027971	T	C	55027971	3	2	260	1	0	0	0	0	1	0	0	0	2685	1667	58	2	1757	2	CASS4	20	55027971	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	4956772	55027971	7997549	886	38131										
BMP7	655	hgsc.bcm.edu	37	chr20	55758796	55758796	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acctgccacgttggccatccGcagggcttcctggttcttgg	12	14	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr20:55758796G>T	ENST00000395863.3	-	4	1445	c.940C>A	c.(940-942)Cgg>Agg	p.R314R	BMP7_ENST00000395864.3_Intron|BMP7_ENST00000450594.2_Silent_p.R314R|BMP7_ENST00000460817.1_5'UTR	NM_001719.2	NP_001710.1	P18075	BMP7_HUMAN	bone morphogenetic protein 7	314					axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of an epithelial tube (GO:0048754)|cartilage development (GO:0051216)|cellular response to hypoxia (GO:0071456)|dendrite development (GO:0016358)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic skeletal joint morphogenesis (GO:0060272)|epithelial cell differentiation (GO:0030855)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|growth (GO:0040007)|mesenchymal cell differentiation (GO:0048762)|mesenchyme development (GO:0060485)|mesoderm formation (GO:0001707)|mesonephros development (GO:0001823)|metanephric mesenchymal cell proliferation involved in metanephros development (GO:0072136)|metanephric mesenchyme morphogenesis (GO:0072133)|metanephros development (GO:0001656)|monocyte aggregation (GO:0070487)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell death (GO:0060548)|negative regulation of glomerular mesangial cell proliferation (GO:0072125)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of mesenchymal cell apoptotic process involved in nephron morphogenesis (GO:0072040)|negative regulation of mitosis (GO:0045839)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of phosphorylation (GO:0042326)|negative regulation of prostatic bud formation (GO:0060686)|negative regulation of striated muscle cell apoptotic process (GO:0010664)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neuron projection morphogenesis (GO:0048812)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone mineralization (GO:0030501)|positive regulation of dendrite development (GO:1900006)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of hyaluranon cable assembly (GO:1900106)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to nucleus (GO:0034504)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|regulation of removal of superoxide radicals (GO:2000121)|response to estradiol (GO:0032355)|response to peptide hormone (GO:0043434)|response to vitamin D (GO:0033280)|skeletal system development (GO:0001501)|SMAD protein signal transduction (GO:0060395)|steroid hormone mediated signaling pathway (GO:0043401)|ureteric bud development (GO:0001657)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane-bounded vesicle (GO:0031988)	heparin binding (GO:0008201)			endometrium(4)|kidney(1)|large_intestine(7)|lung(6)|prostate(1)|skin(1)	20	all_lung(29;0.0133)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;2.49e-13)|Epithelial(14;1.74e-08)|all cancers(14;2.05e-07)			TTGGCCATCCGCAGGGCTTCC	0.647																																					p.R314R		Atlas-SNP	.											.	BMP7	60	.	0			c.C940A						.						79	70	73					20																	55758796		2203	4300	6503	SO:0001819	synonymous_variant	655	exon4			CCATCCGCAGGGC		CCDS13455.1	20q13	2014-01-30	2008-05-22		ENSG00000101144	ENSG00000101144		"Bone morphogenetic proteins", "Endogenous ligands"	1074	protein-coding gene	gene with protein product	"osteogenic protein 1"	112267				1427904	Standard	NM_001719		Approved	OP-1	uc010gip.1	P18075	OTTHUMG00000032812	ENST00000395863.3:c.940C>A	chr20.hg19:g.55758796G>T		70.0	0.0		48.0	4.0	NM_001719	Q9H512|Q9NTQ7	Silent	SNP	ENST00000395863.3	hg19	CCDS13455.1	.	.	.	.	.	.	.	.	.	.	G	9.629	1.135813	0.21123	.	.	ENSG00000101144	ENST00000433911	.	.	.	5.48	-1.19	0.09585	.	.	.	.	.	T	0.69287	0.3094	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.70382	-0.4887	4	.	.	.	.	17.5893	0.87991	0.0:0.0:0.3681:0.6319	.	.	.	.	E	235	.	.	A	-	2	0	BMP7	55192203	1.000000	0.71417	0.997000	0.53966	0.920000	0.55202	1.486000	0.35530	-0.116000	0.11893	-0.196000	0.12772	GCG	.	.		0.647	BMP7-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079831.2			T	55758796	G	T	55758796	2	4	260	1	0	0	0	0	0	0	0	1	1465	1086	38	1		1	BMP7	20	55758796	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	730825	55758796	7266724	887	38132										
LAMA5	3911	hgsc.bcm.edu	37	chr20	60891820	60891820	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcggtccaccaggccctgccGcaccaccgtctgtggatgcc	11	18	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr20:60891820G>A	ENST00000252999.3	-	57	7729	c.7663C>T	c.(7663-7665)Cgg>Tgg	p.R2555W		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2555	Domain II and I.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			AGGCCCTGCCGCACCACCGTC	0.692																																					p.R2555W		Atlas-SNP	.											.	LAMA5	268	.	0			c.C7663T						.						20	16	17					20																	60891820		2174	4272	6446	SO:0001583	missense	3911	exon57			CCTGCCGCACCAC	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"Laminins"	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.7663C>T	chr20.hg19:g.60891820G>A	ENSP00000252999:p.Arg2555Trp	69.0	0.0		60.0	5.0	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	hg19	CCDS33502.1	.	.	.	.	.	.	.	.	.	.	g	11.89	1.773911	0.31411	.	.	ENSG00000130702	ENST00000252999	T	0.19532	2.14	3.79	2.8	0.32819	.	0.931382	0.09110	U	0.847230	T	0.10208	0.0250	N	0.14661	0.345	0.24721	N	0.993147	P	0.48589	0.912	B	0.30782	0.12	T	0.14476	-1.0471	10	0.72032	D	0.01	.	8.876	0.35345	0.0:0.2302:0.7698:0.0	.	2555	O15230	LAMA5_HUMAN	W	2555	ENSP00000252999:R2555W	ENSP00000252999:R2555W	R	-	1	2	LAMA5	60325215	0.258000	0.24033	0.950000	0.38849	0.259000	0.26198	1.406000	0.34646	0.755000	0.32990	0.306000	0.20318	CGG	.	.		0.692	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		A	60891820	G	A	60891820	3	1	260	1	0	0	0	0	1	0	0	0	8618	1086	38	1	3520	1	LAMA5	20	60891820	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	5133024	60891820	2133700	888	38133										
YTHDF1	54915	hgsc.bcm.edu	37	chr20	61835053	61835053	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgaggtatggaatcggagggTcccctgcagtagaccacgga	15	9	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr20:61835053T>C	ENST00000370339.3	-	4	580	c.239A>G	c.(238-240)gAc>gGc	p.D80G	YTHDF1_ENST00000370334.4_Intron|YTHDF1_ENST00000370333.4_Missense_Mutation_p.D30G	NM_017798.3	NP_060268.2	Q9BYJ9	YTHD1_HUMAN	YTH domain family, member 1	80							N6-methyladenosine-containing RNA binding (GO:1990247)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)	24						AATCGGAGGGTCCCCTGCAGT	0.557																																					p.D80G		Atlas-SNP	.											.	YTHDF1	66	.	0			c.A239G						.						103	109	107					20																	61835053		2203	4300	6503	SO:0001583	missense	54915	exon4			GGAGGGTCCCCTG	AK000398	CCDS13511.1	20q13.33	2010-03-15	2004-11-16	2004-06-04	ENSG00000149658	ENSG00000149658			15867	protein-coding gene	gene with protein product			"YTH domain family 1"	C20orf21			Standard	NM_017798		Approved	FLJ20391	uc002yeh.3	Q9BYJ9	OTTHUMG00000032955	ENST00000370339.3:c.239A>G	chr20.hg19:g.61835053T>C	ENSP00000359364:p.Asp80Gly	170.0	0.0		115.0	5.0	NM_017798	Q8N3G5|Q8TBT1|Q96AN4|Q96S57|Q9BTI7|Q9NX79	Missense_Mutation	SNP	ENST00000370339.3	hg19	CCDS13511.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.048398	0.75846	.	.	ENSG00000149658	ENST00000370339;ENST00000370333	T;T	0.68765	-0.35;-0.35	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.79661	0.4484	M	0.72118	2.19	0.80722	D	1	D	0.63880	0.993	D	0.64506	0.926	T	0.82285	-0.0533	10	0.72032	D	0.01	-35.703	15.1531	0.72717	0.0:0.0:0.0:1.0	.	80	Q9BYJ9	YTHD1_HUMAN	G	80;30	ENSP00000359364:D80G;ENSP00000359358:D30G	ENSP00000359358:D30G	D	-	2	0	YTHDF1	61305498	1.000000	0.71417	1.000000	0.80357	0.836000	0.47400	7.927000	0.87577	1.983000	0.57843	0.459000	0.35465	GAC	.	.		0.557	YTHDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080110.2	NM_017798		C	61835053	T	C	61835053	3	2	260	1	0	0	0	0	1	0	0	0	17513	1667	58	2	1448	2	YTHDF1	20	61835053	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	943233	61835053	1190467	889	38134										
CHRNA4	1137	hgsc.bcm.edu	37	chr20	61981085	61981085	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccgggtcagggccggcgacaGgggcaggtgcgggggcggcg	24	11	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr20:61981085G>T	ENST00000370263.4	-	5	1899	c.1678C>A	c.(1678-1680)Ctg>Atg	p.L560M	CHRNA4_ENST00000463705.1_5'UTR	NM_000744.6|NM_001256573.1	NP_000735.1|NP_001243502.1	P43681	ACHA4_HUMAN	cholinergic receptor, nicotinic, alpha 4 (neuronal)	560					action potential (GO:0001508)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cognition (GO:0050890)|DNA repair (GO:0006281)|exploration behavior (GO:0035640)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|neurological system process (GO:0050877)|regulation of dopamine secretion (GO:0014059)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of membrane potential (GO:0042391)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(19)|prostate(3)|skin(3)|soft_tissue(1)	33	all_cancers(38;1.71e-10)				Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273)	GCCGGCGACAGGGGCAGGTGC	0.662																																					p.L560M		Atlas-SNP	.											.	CHRNA4	98	.	0			c.C1678A						.						33	41	38					20																	61981085		2201	4296	6497	SO:0001583	missense	1137	exon5			GCGACAGGGGCAG		CCDS13517.1	20q13.33	2013-09-20	2012-02-07		ENSG00000101204	ENSG00000101204		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1958	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 4 (neuronal)"	118504	"cholinergic receptor, nicotinic, alpha polypeptide 4"	EBN, EBN1		1505988	Standard	NM_000744		Approved	BFNC	uc002yes.3	P43681	OTTHUMG00000033080	ENST00000370263.4:c.1678C>A	chr20.hg19:g.61981085G>T	ENSP00000359285:p.Leu560Met	61.0	0.0		87.0	4.0	NM_000744	Q4JGR7|Q4VAQ5|Q4VAQ6	Missense_Mutation	SNP	ENST00000370263.4	hg19	CCDS13517.1	.	.	.	.	.	.	.	.	.	.	G	8.285	0.816399	0.16607	.	.	ENSG00000101204	ENST00000370258;ENST00000370263;ENST00000539366	D	0.86297	-2.1	4.72	2.58	0.30949	Neurotransmitter-gated ion-channel transmembrane domain (2);	26.139000	0.00166	N	0.000000	D	0.84101	0.5398	L	0.39633	1.23	0.35505	D	0.800125	B;B	0.27068	0.167;0.136	B;B	0.30646	0.118;0.081	T	0.71892	-0.4455	10	0.48119	T	0.1	.	7.2309	0.26043	0.1025:0.0:0.6363:0.2612	.	489;560	Q4VAQ5;P43681	.;ACHA4_HUMAN	M	466;560;489	ENSP00000359285:L560M	ENSP00000359280:L466M	L	-	1	2	CHRNA4	61451529	0.991000	0.36638	0.482000	0.27366	0.364000	0.29643	0.830000	0.27462	0.988000	0.38734	0.491000	0.48974	CTG	.	.		0.662	CHRNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080508.3			T	61981085	G	T	61981085	3	4	260	1	0	0	0	0	1	0	0	0	3387	991	35	3	213	3	CHRNA4	20	61981085	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	146032	61981085	1044435	890	38135										
NRIP1	8204	hgsc.bcm.edu	37	chr21	16337049	16337049	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggtacattttattctgattcTttctttatcgttagcacgct	6	8	3	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr21:16337049T>C	ENST00000400202.1	-	3	4177	c.3465A>G	c.(3463-3465)aaA>aaG	p.K1155K	NRIP1_ENST00000400199.1_Silent_p.K1155K|NRIP1_ENST00000318948.4_Silent_p.K1155K|AF127577.10_ENST00000446301.1_RNA			P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	1155	Interaction with ZNF366.|Repression domain 4.				androgen receptor signaling pathway (GO:0030521)|lipid storage (GO:0019915)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|ovarian follicle rupture (GO:0001543)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|estrogen receptor binding (GO:0030331)|glucocorticoid receptor binding (GO:0035259)|nuclear hormone receptor binding (GO:0035257)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			cervix(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(13)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	39				Epithelial(23;1.19e-05)|all cancers(11;4.64e-05)|COAD - Colon adenocarcinoma(22;0.000232)|Colorectal(24;0.0006)|OV - Ovarian serous cystadenocarcinoma(11;0.00418)|Lung(58;0.199)|LUSC - Lung squamous cell carcinoma(23;0.24)		ATTCTGATTCTTTCTTTATCG	0.368																																					p.K1155K		Atlas-SNP	.											.	NRIP1	103	.	0			c.A3465G						.						94	97	96					21																	16337049		2203	4299	6502	SO:0001819	synonymous_variant	8204	exon4			TGATTCTTTCTTT	X84373	CCDS13568.1	21q11.2	2008-07-31			ENSG00000180530	ENSG00000180530			8001	protein-coding gene	gene with protein product	"receptor interacting protein 140", "nuclear factor RIP140"	602490				7641693, 9521594	Standard	NM_003489		Approved	RIP140	uc002yjx.2	P48552	OTTHUMG00000074323	ENST00000400202.1:c.3465A>G	chr21.hg19:g.16337049T>C		110.0	0.0		85.0	4.0	NM_003489	Q8IWE8	Silent	SNP	ENST00000400202.1	hg19	CCDS13568.1																																																																																			.	.		0.368	NRIP1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157926.1	NM_003489		C	16337049	T	C	16337049	2	2	260	1	0	0	0	0	0	0	0	1	10661	1606	56	2		2	NRIP1	21	16337049	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10		16337049	31792846	891	38136										
TIAM1	7074	hgsc.bcm.edu	37	chr21	32639207	32639207	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtgcgagaggcgcagggagcGggaagtgtgcttgcgcccca	19	10	0	1	rs371962651		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr21:32639207G>T	ENST00000286827.3	-	5	553	c.82C>A	c.(82-84)Cgc>Agc	p.R28S	TIAM1_ENST00000469412.1_Intron|TIAM1_ENST00000541036.1_Missense_Mutation_p.R28S	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	28					apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						CGCAGGGAGCGGGAAGTGTGC	0.577																																					p.R28S		Atlas-SNP	.											.	TIAM1	522	.	0			c.C82A						.						46	48	47					21																	32639207		2203	4300	6503	SO:0001583	missense	7074	exon5			GGGAGCGGGAAGT		CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.82C>A	chr21.hg19:g.32639207G>T	ENSP00000286827:p.Arg28Ser	91.0	0.0		70.0	4.0	NM_003253	B7ZLR6|F5GZ53|Q17RT7	Missense_Mutation	SNP	ENST00000286827.3	hg19	CCDS13609.1	.	.	.	.	.	.	.	.	.	.	G	16.55	3.154923	0.57259	.	.	ENSG00000156299	ENST00000286827;ENST00000541036;ENST00000455508	T;T	0.55760	0.57;0.5	5.12	4.22	0.49857	.	0.058320	0.64402	D	0.000003	T	0.54334	0.1852	L	0.48642	1.525	0.51233	D	0.999918	P;P;P	0.48016	0.904;0.845;0.845	P;B;B	0.47744	0.556;0.354;0.354	T	0.59606	-0.7423	10	0.87932	D	0	.	14.7325	0.69393	0.0:0.0:0.854:0.146	.	28;28;28	F5GZ53;B7ZLR6;Q13009	.;.;TIAM1_HUMAN	S	28	ENSP00000286827:R28S;ENSP00000441570:R28S	ENSP00000286827:R28S	R	-	1	0	TIAM1	31561078	0.991000	0.36638	0.824000	0.32777	0.926000	0.56050	3.981000	0.56902	1.112000	0.41740	0.411000	0.27672	CGC	.	.		0.577	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253		T	32639207	G	T	32639207	3	4	260	1	0	0	0	0	1	0	0	0	15905	1116	39	1	4793	1	TIAM1	21	32639207	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	16302158	32639207	15490688	892	38137										
SYNJ1	8867	hgsc.bcm.edu	37	chr21	34056410	34056410	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acaatccaagcagtttgttcGaactgtaccactctggcatc	7	12	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr21:34056410G>A	ENST00000322229.7	-	9	1137	c.1138C>T	c.(1138-1140)Cga>Tga	p.R380*	SYNJ1_ENST00000382491.3_Nonsense_Mutation_p.R380*|SYNJ1_ENST00000382499.2_Nonsense_Mutation_p.R419*|SYNJ1_ENST00000433931.2_Nonsense_Mutation_p.R419*|SYNJ1_ENST00000357345.3_Nonsense_Mutation_p.R380*			O43426	SYNJ1_HUMAN	synaptojanin 1	380	SAC. {ECO:0000255|PROSITE- ProRule:PRU00183}.				cell death (GO:0008219)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of synaptic vesicle uncoating (GO:1903390)|regulation of synaptic vesicle membrane organization (GO:1901632)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)	cytosol (GO:0005829)	inositol-polyphosphate 5-phosphatase activity (GO:0004445)|nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|lung(11)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	57						CAGTTTGTTCGAACTGTACCA	0.318																																					p.R419X		Atlas-SNP	.											.	SYNJ1	253	.	0			c.C1255T						.						134	118	123					21																	34056410		2203	4300	6503	SO:0001587	stop_gained	8867	exon10			TTGTTCGAACTGT	AF009040	CCDS33539.1, CCDS33540.1, CCDS33539.2, CCDS33540.2, CCDS54483.1	21q22.2	2008-06-23			ENSG00000159082	ENSG00000159082			11503	protein-coding gene	gene with protein product		604297				9428629, 10773674	Standard	NM_203446		Approved	INPP5G	uc002yqh.2	O43426	OTTHUMG00000064926	ENST00000322229.7:c.1138C>T	chr21.hg19:g.34056410G>A	ENSP00000322234:p.Arg380*	158.0	0.0		95.0	4.0	NM_203446	O43425|O94984|Q4KMR1	Nonsense_Mutation	SNP	ENST00000322229.7	hg19	CCDS54484.1	.	.	.	.	.	.	.	.	.	.	G	36	5.951296	0.97139	.	.	ENSG00000159082	ENST00000382491;ENST00000357345;ENST00000382499;ENST00000433931;ENST00000322229;ENST00000429236	.	.	.	5.78	2.73	0.32206	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.9927	0.64376	0.0:0.0:0.3348:0.6652	.	.	.	.	X	380;380;419;419;380;380	.	ENSP00000322234:R380X	R	-	1	2	SYNJ1	32978281	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	3.967000	0.56802	0.720000	0.32209	0.585000	0.79938	CGA	.	.		0.318	SYNJ1-201	KNOWN	basic|CCDS	protein_coding	protein_coding				A	34056410	G	A	34056410	4	1	260	1	0	0	0	0	0	1	0	0	15467	1066	37	1	3709	1	SYNJ1	21	34056410	Nonsense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	1417203	34056410	14073485	893	38138										
ITSN1	6453	hgsc.bcm.edu	37	chr21	35140133	35140133	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	attagaaaagaaattacctgGtaaggcagcctttatgttga	9	5	0	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr21:35140133G>T	ENST00000381318.3	+	11	1330		c.e11+1		ITSN1_ENST00000381285.4_Splice_Site|ITSN1_ENST00000399338.4_Splice_Site|ITSN1_ENST00000381291.4_Splice_Site|ITSN1_ENST00000399353.1_Splice_Site|AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000399349.1_Splice_Site|ITSN1_ENST00000488166.1_Splice_Site|ITSN1_ENST00000437442.2_Splice_Site|ITSN1_ENST00000399367.3_Splice_Site|ITSN1_ENST00000399355.2_Splice_Site|ITSN1_ENST00000399326.3_Splice_Site|ITSN1_ENST00000379960.5_Splice_Site|ITSN1_ENST00000399352.1_Splice_Site	NM_003024.2	NP_003015.2	Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)						apoptotic signaling pathway (GO:0097190)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|kinase activator activity (GO:0019209)|proline-rich region binding (GO:0070064)|protein complex scaffold (GO:0032947)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(26)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	67						AAATTACCTGGTAAGGCAGCC	0.323																																					.		Atlas-SNP	.											.	ITSN1	166	.	0			c.1042+1G>T						.						52	50	51					21																	35140133		2203	4300	6503	SO:0001630	splice_region_variant	6453	exon11			TACCTGGTAAGGC	AF064244	CCDS33545.1, CCDS33546.1	21q22.1-q22.2	2013-01-10			ENSG00000205726	ENSG00000205726		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "EF-hand domain containing"	6183	protein-coding gene	gene with protein product	"SH3 domain protein-1A", "human intersectin-SH3 domain-containing protein SH3P17", "Src homology 3 domain-containing protein", "intersectin 1 short form variant, 11", "intersectin 1 short form variant 3", "intersectin short variant 12"	602442		SH3D1A, ITSN		9799604, 9813051	Standard	NM_003024		Approved	SH3P17, MGC134948, MGC134949	uc002yta.1	Q15811	OTTHUMG00000065284	ENST00000381318.3:c.1042+1G>T	chr21.hg19:g.35140133G>T		153.0	0.0		81.0	4.0	NM_003024	A7Y322|A8CTX8|A8CTY3|A8CTY7|A8D7D0|A8DCP3|B4DTM2|E7ERJ1|E9PE44|E9PG01|E9PHV2|O95216|Q0PW94|Q0PW95|Q0PW97|Q14BD3|Q1ED40|Q20BK3|Q9UET5|Q9UK60|Q9UNK1|Q9UNK2|Q9UQ92	Splice_Site	SNP	ENST00000381318.3	hg19	CCDS33545.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.268166	0.80469	.	.	ENSG00000205726	ENST00000399353;ENST00000381318;ENST00000381291;ENST00000381285;ENST00000381288;ENST00000381289;ENST00000399367;ENST00000399352;ENST00000399355;ENST00000399349;ENST00000381283;ENST00000399338;ENST00000437442;ENST00000399326;ENST00000379960	.	.	.	5.83	5.83	0.93111	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.119	0.97953	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ITSN1	34062003	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	7.479000	0.81095	2.763000	0.94921	0.555000	0.69702	.	.	.		0.323	ITSN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000140070.4	NM_003024	Intron	T	35140133	G	T	35140133	5	4	260	1	0	0	0	0	0	0	1	0	7935	1275	44	3	1081	3	ITSN1	21	35140133	Splice_Site	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	1083723	35140133	12989762	894	38139										
ITSN1	6453	hgsc.bcm.edu	37	chr21	35255856	35255856	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctgtgtgttactttccagccTattttcctaaatgaggttct	7	9	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr21:35255856T>C	ENST00000381318.3	+	36	4845	c.4557T>C	c.(4555-4557)ccT>ccC	p.P1519P	ITSN1_ENST00000381285.4_Silent_p.P1519P|AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000437442.2_Silent_p.P1458P|ITSN1_ENST00000399367.3_Silent_p.P1514P|ITSN1_ENST00000399326.3_3'UTR	NM_003024.2	NP_003015.2	Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)	1519	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|kinase activator activity (GO:0019209)|proline-rich region binding (GO:0070064)|protein complex scaffold (GO:0032947)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(26)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	67						CTTTCCAGCCTATTTTCCTAA	0.498																																					p.P1519P		Atlas-SNP	.											.	ITSN1	166	.	0			c.T4557C						.						134	142	139					21																	35255856		2203	4300	6503	SO:0001819	synonymous_variant	6453	exon36			CCAGCCTATTTTC	AF064244	CCDS33545.1, CCDS33546.1	21q22.1-q22.2	2013-01-10			ENSG00000205726	ENSG00000205726		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "EF-hand domain containing"	6183	protein-coding gene	gene with protein product	"SH3 domain protein-1A", "human intersectin-SH3 domain-containing protein SH3P17", "Src homology 3 domain-containing protein", "intersectin 1 short form variant, 11", "intersectin 1 short form variant 3", "intersectin short variant 12"	602442		SH3D1A, ITSN		9799604, 9813051	Standard	NM_003024		Approved	SH3P17, MGC134948, MGC134949	uc002yta.1	Q15811	OTTHUMG00000065284	ENST00000381318.3:c.4557T>C	chr21.hg19:g.35255856T>C		161.0	0.0		100.0	4.0	NM_003024	A7Y322|A8CTX8|A8CTY3|A8CTY7|A8D7D0|A8DCP3|B4DTM2|E7ERJ1|E9PE44|E9PG01|E9PHV2|O95216|Q0PW94|Q0PW95|Q0PW97|Q14BD3|Q1ED40|Q20BK3|Q9UET5|Q9UK60|Q9UNK1|Q9UNK2|Q9UQ92	Silent	SNP	ENST00000381318.3	hg19	CCDS33545.1	.	.	.	.	.	.	.	.	.	.	T	10.65	1.411007	0.25465	.	.	ENSG00000205726	ENST00000381284	.	.	.	5.75	-0.817	0.10836	.	.	.	.	.	T	0.43743	0.1261	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.23226	-1.0194	4	.	.	.	.	4.0636	0.09849	0.1366:0.5421:0.1384:0.183	.	.	.	.	H	199	.	.	Y	+	1	0	ITSN1	34177726	0.006000	0.16342	0.991000	0.47740	0.860000	0.49131	-1.212000	0.02994	-0.375000	0.07955	0.528000	0.53228	TAT	.	.		0.498	ITSN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000140070.4	NM_003024		C	35255856	T	C	35255856	2	2	260	1	0	0	0	0	0	0	0	1	7935	1509	53	2		2	ITSN1	21	35255856	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	115723	35255856	12874039	895	38140										
PWP2	5822	hgsc.bcm.edu	37	chr21	45548277	45548277	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	acggacagaagctgaagtccAggtagagggtctcccccgca	13	12	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr21:45548277A>G	ENST00000291576.7	+	19	2636	c.2509A>G	c.(2509-2511)Aga>Gga	p.R837G	PWP2_ENST00000494310.1_3'UTR	NM_005049.2	NP_005040.2	Q15269	PWP2_HUMAN	PWP2 periodic tryptophan protein homolog (yeast)	837					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(6)|large_intestine(6)|lung(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	21				STAD - Stomach adenocarcinoma(101;0.172)|Colorectal(79;0.2)		GCTGAAGTCCAGGTAGAGGGT	0.522																																					p.R837G		Atlas-SNP	.											.	PWP2	64	.	0			c.A2509G						.						61	60	61					21																	45548277		2203	4300	6503	SO:0001630	splice_region_variant	5822	exon19			AAGTCCAGGTAGA		CCDS33579.1	21q22.3	2013-01-10	2001-11-28	2006-11-24	ENSG00000241945	ENSG00000241945		"WD repeat domain containing"	9711	protein-coding gene	gene with protein product		601475	"PWP2 (periodic tryptophan protein, yeast) homolog"	PWP2H		8893822	Standard	NM_005049		Approved	EHOC-17, UTP1	uc002zeb.3	Q15269	OTTHUMG00000086893	ENST00000291576.7:c.2510+1A>G	chr21.hg19:g.45548277A>G		120.0	0.0		89.0	4.0	NM_005049	B2RAG8|Q96A77	Missense_Mutation	SNP	ENST00000291576.7	hg19	CCDS33579.1	.	.	.	.	.	.	.	.	.	.	A	13.68	2.309538	0.40895	.	.	ENSG00000241945;ENSG00000248354	ENST00000291576;ENST00000433711	T	0.59502	0.26	4.05	4.05	0.47172	.	0.000000	0.85682	D	0.000000	T	0.61677	0.2366	M	0.76170	2.325	0.53688	D	0.999976	B	0.34103	0.437	B	0.41666	0.363	T	0.67110	-0.5753	10	0.87932	D	0	-8.7499	9.9907	0.41870	0.8298:0.1701:0.0:0.0	.	837	Q15269	PWP2_HUMAN	G	837;19	ENSP00000291576:R837G	ENSP00000415634:R19G	R	+	1	2	AP001055.7;PWP2	44372705	1.000000	0.71417	0.994000	0.49952	0.700000	0.40528	2.861000	0.48380	1.784000	0.52394	0.460000	0.39030	AGA	.	.		0.522	PWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195736.3	NM_005049	Missense_Mutation	G	45548277	A	G	45548277	5	3	260	1	0	0	0	0	0	0	1	0	12859	202	7	2	2583	2	PWP2	21	45548277	Splice_Site	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	10292421	45548277	2581618	896	38141										
PFKL	5211	hgsc.bcm.edu	37	chr21	45744485	45744485	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccgtgactggcattgctgtgGgggccgacgccgcctacgtc	15	14	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr21:45744485G>T	ENST00000349048.4	+	17	1817	c.1762G>T	c.(1762-1764)Ggg>Tgg	p.G588W	PFKL_ENST00000403390.1_Missense_Mutation_p.G635W	NM_002626.4	NP_002617.3	P17858	PFKAL_HUMAN	phosphofructokinase, liver	588	C-terminal regulatory PFK domain 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 1,6-bisphosphate metabolic process (GO:0030388)|fructose 6-phosphate metabolic process (GO:0006002)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|negative regulation of insulin secretion (GO:0046676)|protein homotetramerization (GO:0051289)|protein oligomerization (GO:0051259)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	6-phosphofructokinase complex (GO:0005945)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|fructose binding (GO:0070061)|fructose-6-phosphate binding (GO:0070095)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	23				Colorectal(79;0.0811)		CATTGCTGTGGGGGCCGACGC	0.632																																					p.G588W		Atlas-SNP	.											.	PFKL	65	.	0			c.G1762T						.						81	73	76					21																	45744485		2202	4300	6502	SO:0001583	missense	5211	exon17			GCTGTGGGGGCCG		CCDS33582.1	21q22.3	1992-12-17			ENSG00000141959	ENSG00000141959	2.7.1.11		8876	protein-coding gene	gene with protein product		171860					Standard	NR_024108		Approved		uc002zel.3	P17858	OTTHUMG00000086910	ENST00000349048.4:c.1762G>T	chr21.hg19:g.45744485G>T	ENSP00000269848:p.Gly588Trp	148.0	0.0		95.0	5.0	NM_002626	Q96A64|Q96IH4|Q9BR91	Missense_Mutation	SNP	ENST00000349048.4	hg19	CCDS33582.1	.	.	.	.	.	.	.	.	.	.	G	17.62	3.433650	0.62955	.	.	ENSG00000141959	ENST00000349048;ENST00000534847;ENST00000403390	D;D	0.83837	-1.77;-1.77	4.1	4.1	0.47936	Phosphofructokinase domain (2);	0.000000	0.85682	D	0.000000	D	0.94928	0.8360	H	0.99169	4.455	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97171	0.9844	10	0.87932	D	0	-38.7407	15.126	0.72483	0.0:0.0:1.0:0.0	.	588;635	P17858;P17858-2	K6PL_HUMAN;.	W	588;381;635	ENSP00000269848:G588W;ENSP00000384038:G635W	ENSP00000269848:G588W	G	+	1	0	PFKL	44568913	1.000000	0.71417	0.813000	0.32504	0.238000	0.25445	9.323000	0.96364	1.852000	0.53769	0.467000	0.42956	GGG	.	.		0.632	PFKL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195805.1			T	45744485	G	T	45744485	3	4	260	1	0	0	0	0	1	0	0	0	11773	1232	43	3	1828	3	PFKL	21	45744485	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	196208	45744485	2385410	897	38142										
MCM3AP	8888	hgsc.bcm.edu	37	chr21	47704014	47704014	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctctactttcagtttcttccTctttattcacacctggaatc	3	13	5	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr21:47704014T>C	ENST00000397708.1	-	2	1441	c.1187A>G	c.(1186-1188)gAg>gGg	p.E396G	YBEY_ENST00000397701.4_5'Flank|MCM3AP_ENST00000291688.1_Missense_Mutation_p.E396G|YBEY_ENST00000397692.1_5'Flank|YBEY_ENST00000339195.6_5'Flank|YBEY_ENST00000329319.3_5'Flank|YBEY_ENST00000397691.1_5'Flank|YBEY_ENST00000397694.1_5'Flank			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	396					DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					AGTTTCTTCCTCTTTATTCAC	0.463																																					p.E396G		Atlas-SNP	.											.	MCM3AP	146	.	0			c.A1187G						.						86	90	88					21																	47704014		2203	4300	6503	SO:0001583	missense	8888	exon1			TCTTCCTCTTTAT	AB005543	CCDS13734.1	21q22.3	2012-12-19	2007-04-04		ENSG00000160294	ENSG00000160294			6946	protein-coding gene	gene with protein product	"germinal-centre associated nuclear protein"	603294	"minichromosome maintenance deficient (S. cerevisiae) 3-associated protein", "MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein"			9712829, 16914116, 21195085	Standard	XM_005261205		Approved	Map80, KIAA0572, GANP, SAC3	uc002zir.1	O60318	OTTHUMG00000090630	ENST00000397708.1:c.1187A>G	chr21.hg19:g.47704014T>C	ENSP00000380820:p.Glu396Gly	165.0	0.0		91.0	4.0	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Missense_Mutation	SNP	ENST00000397708.1	hg19	CCDS13734.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.976562	0.74360	.	.	ENSG00000160294	ENST00000397708;ENST00000291688	T;T	0.03889	3.77;3.77	5.33	5.33	0.75918	.	0.328893	0.31601	N	0.007368	T	0.08670	0.0215	L	0.32530	0.975	0.36077	D	0.842545	D	0.57257	0.979	P	0.52554	0.702	T	0.23332	-1.0191	10	0.52906	T	0.07	-28.6181	12.8246	0.57712	0.0:0.0:0.0:1.0	.	396	O60318	MCM3A_HUMAN	G	396	ENSP00000380820:E396G;ENSP00000291688:E396G	ENSP00000291688:E396G	E	-	2	0	MCM3AP	46528442	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	4.960000	0.63673	2.015000	0.59207	0.460000	0.39030	GAG	.	.		0.463	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906		C	47704014	T	C	47704014	3	2	260	1	0	0	0	0	1	0	0	0	9397	1551	54	2	4867	2	MCM3AP	21	47704014	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1959529	47704014	425881	898	38143										
MRPL40	64976	hgsc.bcm.edu	37	chr22	19423190	19423190	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcaggtggagctcacctttgAggagactgagaggagagctc	15	8	2	4			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr22:19423190A>G	ENST00000333130.3	+	4	979	c.326A>G	c.(325-327)gAg>gGg	p.E109G	MRPL40_ENST00000443660.1_3'UTR|HIRA_ENST00000541063.1_Intron|HIRA_ENST00000546308.1_Intron	NM_003776.2	NP_003767.2	Q9NQ50	RM40_HUMAN	mitochondrial ribosomal protein L40	109					anatomical structure morphogenesis (GO:0009653)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|upper_aerodigestive_tract(1)	2	Colorectal(54;0.0993)					CTCACCTTTGAGGAGACTGAG	0.512																																					p.E109G		Atlas-SNP	.											.	MRPL40	13	.	0			c.A326G						.						214	222	220					22																	19423190		2203	4300	6503	SO:0001583	missense	64976	exon4			CCTTTGAGGAGAC	AB051624	CCDS13760.1	22q11.2	2012-09-13	2002-11-13		ENSG00000185608	ENSG00000185608		"Mitochondrial ribosomal proteins / large subunits"	14491	protein-coding gene	gene with protein product		605089	"nuclear localization signal deleted in velocardiofacial syndrome"	NLVCF		9790763, 11543634	Standard	NM_003776		Approved	MRP-L22	uc002zpg.3	Q9NQ50	OTTHUMG00000150136	ENST00000333130.3:c.326A>G	chr22.hg19:g.19423190A>G	ENSP00000333401:p.Glu109Gly	123.0	0.0		99.0	5.0	NM_003776	B3KVZ7|O95134	Missense_Mutation	SNP	ENST00000333130.3	hg19	CCDS13760.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.297018	0.81025	.	.	ENSG00000185608	ENST00000333130	T	0.58506	0.33	5.33	4.3	0.51218	.	0.103877	0.64402	D	0.000005	T	0.77718	0.4172	M	0.88842	2.985	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.80788	-0.1226	10	0.87932	D	0	-28.0143	11.1553	0.48484	0.9283:0.0:0.0717:0.0	.	109	Q9NQ50	RM40_HUMAN	G	109	ENSP00000333401:E109G	ENSP00000333401:E109G	E	+	2	0	MRPL40	17803190	1.000000	0.71417	0.729000	0.30791	0.963000	0.63663	6.389000	0.73199	1.044000	0.40200	0.460000	0.39030	GAG	.	.		0.512	MRPL40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316491.2	NM_003776		G	19423190	A	G	19423190	3	3	260	1	0	0	0	0	1	0	0	0	9813	304	11	2	340	2	MRPL40	22	19423190	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10		19423190	31881376	899	38144										
PI4KA	5297	hgsc.bcm.edu	37	chr22	21159287	21159287	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcgtccttcacagcccacacCatgaggtccacacaggcagc	8	17	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr22:21159287C>A	ENST00000572273.1	-	11	1391	c.1161G>T	c.(1159-1161)atG>atT	p.M387I	PI4KA_ENST00000255882.6_Missense_Mutation_p.M445I			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	387					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi-associated vesicle membrane (GO:0030660)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			breast(3)|endometrium(8)|kidney(9)|large_intestine(19)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|salivary_gland(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	79	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			CAGCCCACACCATGAGGTCCA	0.572																																					p.M445I	GBM(136;1332 1831 3115 23601 50806)	Atlas-SNP	.											.	PI4KA	313	.	0			c.G1335T						.						140	124	130					22																	21159287		2203	4300	6503	SO:0001583	missense	5297	exon11			CCACACCATGAGG	L36151	CCDS33603.1, CCDS33603.2	22q11.21	2011-05-25	2007-08-14	2007-08-02	ENSG00000241973	ENSG00000241973			8983	protein-coding gene	gene with protein product		600286		PIK4CA		7961848, 8662589	Standard	NM_002650		Approved	PI4K-ALPHA, pi4K230	uc002zsz.5	P42356	OTTHUMG00000167440	ENST00000572273.1:c.1161G>T	chr22.hg19:g.21159287C>A	ENSP00000458238:p.Met387Ile	135.0	0.0		94.0	4.0	NM_058004	Q7Z625|Q9UPG2	Missense_Mutation	SNP	ENST00000572273.1	hg19		.	.	.	.	.	.	.	.	.	.	C	17.23	3.337749	0.60963	.	.	ENSG00000241973	ENST00000255882	.	.	.	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.61825	0.2378	L	0.60455	1.87	0.80722	D	1	B;B	0.27316	0.175;0.039	B;B	0.25987	0.065;0.011	T	0.55866	-0.8073	9	0.25106	T	0.35	-39.3336	20.3214	0.98679	0.0:1.0:0.0:0.0	.	445;387	D3DX33;P42356	.;PI4KA_HUMAN	I	387	.	ENSP00000255882:M387I	M	-	3	0	PI4KA	19489287	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.813000	0.86123	2.804000	0.96469	0.655000	0.94253	ATG	.	.		0.572	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004		A	21159287	C	A	21159287	3	1	260	1	0	0	0	0	1	0	0	0	11882	594	21	3	5153	3	PI4KA	22	21159287	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	1736097	21159287	30145279	900	38145										
IGLL1	3543	hgsc.bcm.edu	37	chr22	23922198	23922198	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	caccggctcctcaggctggaCcggctgcttcctccaggggc	13	17	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr22:23922198C>T	ENST00000330377.2	-	1	297	c.180G>A	c.(178-180)cgG>cgA	p.R60R	IGLL1_ENST00000249053.3_Silent_p.R60R|KB-208E9.1_ENST00000608615.1_lincRNA	NM_020070.3	NP_064455.1	P15814	IGLL1_HUMAN	immunoglobulin lambda-like polypeptide 1	60					immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				kidney(1)|large_intestine(1)|lung(5)|skin(4)|stomach(1)	12						TCAGGCTGGACCGGCTGCTTC	0.677																																					p.R60R		Atlas-SNP	.											.	IGLL1	27	.	0			c.G180A						.						6	7	7					22																	23922198		1893	3906	5799	SO:0001819	synonymous_variant	3543	exon1			GCTGGACCGGCTG	X52204	CCDS13809.1, CCDS13810.1	22q11.23	2014-09-17			ENSG00000128322	ENSG00000128322		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	5870	protein-coding gene	gene with protein product		146770		IGLL		3139558, 2511029	Standard	NM_020070		Approved	IGVPB, IGL5, 14.1, CD179B	uc002zxd.3	P15814	OTTHUMG00000150673	ENST00000330377.2:c.180G>A	chr22.hg19:g.23922198C>T		83.0	0.0		60.0	4.0	NM_020070	Q0P681	Silent	SNP	ENST00000330377.2	hg19	CCDS13809.1																																																																																			.	.		0.677	IGLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319569.1	NM_020070		T	23922198	C	T	23922198	2	4	260	1	0	0	0	0	0	0	0	1	7602	494	18	3		3	IGLL1	22	23922198	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	2762911	23922198	27382368	901	38146										
CABIN1	23523	hgsc.bcm.edu	37	chr22	24455827	24455827	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agccacattcatggaatctgGtaggaatcgagcagtgtgac	12	8	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr22:24455827G>A	ENST00000398319.2	+	11	1784		c.e11+1		CABIN1_ENST00000405822.2_Splice_Site|CABIN1_ENST00000263119.5_Splice_Site	NM_001199281.1	NP_001186210.1	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1						cell surface receptor signaling pathway (GO:0007166)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of catalytic activity (GO:0043086)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)			breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(13)|liver(1)|lung(18)|ovary(5)|pancreas(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						ATGGAATCTGGTAGGAATCGA	0.438																																					.		Atlas-SNP	.											.	CABIN1	153	.	0			c.1249+1G>A						.						63	59	61					22																	24455827		2203	4300	6503	SO:0001630	splice_region_variant	23523	exon10			AATCTGGTAGGAA	AF072441	CCDS13823.1, CCDS74830.1	22q11.23	2008-09-16			ENSG00000099991	ENSG00000099991			24187	protein-coding gene	gene with protein product		604251				9655484, 9205841	Standard	NM_001199281		Approved	KIAA0330, PPP3IN	uc002zzi.1	Q9Y6J0	OTTHUMG00000150797	ENST00000398319.2:c.1399+1G>A	chr22.hg19:g.24455827G>A		132.0	0.0		72.0	4.0	NM_001201429	G5E9F3|Q6PHY0|Q9Y460	Splice_Site	SNP	ENST00000398319.2	hg19	CCDS13823.1	.	.	.	.	.	.	.	.	.	.	G	18.94	3.729955	0.69074	.	.	ENSG00000099991	ENST00000263119;ENST00000405822;ENST00000398319	.	.	.	5.3	5.3	0.74995	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.3775	0.90440	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CABIN1	22785827	1.000000	0.71417	1.000000	0.80357	0.722000	0.41435	7.737000	0.84957	2.662000	0.90505	0.558000	0.71614	.	.	.		0.438	CABIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320161.2	NM_012295	Intron	A	24455827	G	A	24455827	5	1	260	1	0	0	0	0	0	0	1	0	2530	1275	44	3	1438	3	CABIN1	22	24455827	Splice_Site	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	533629	24455827	26848739	902	38147										
C22orf36	2678	hgsc.bcm.edu	37	chr22	24981864	24981864	+	Intron	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gggtggtgggtcacctggcaCagcaggcctggggctcgggt	20	10	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr22:24981864C>A	ENST00000248923.4	+	1	59				FAM211B_ENST00000318753.8_Missense_Mutation_p.C313F|FAM211B_ENST00000495297.1_5'Flank	NM_013430.2	NP_038347.2	P19440	GGT1_HUMAN	gamma-glutamyltransferase 1						arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|cysteine biosynthetic process (GO:0019344)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione catabolic process (GO:0006751)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|regulation of immune system process (GO:0002682)|regulation of inflammatory response (GO:0050727)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|xenobiotic metabolic process (GO:0006805)|zymogen activation (GO:0031638)	anchored component of external side of plasma membrane (GO:0031362)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			breast(1)|endometrium(2)|kidney(14)|large_intestine(2)|lung(6)|pancreas(1)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	40					Glutathione(DB00143)	TCACCTGGCACAGCAGGCCTG	0.647																																					p.C313F		Atlas-SNP	.											.	.	.	.	0			c.G938T						.						7	10	9					22																	24981864		1940	4104	6044	SO:0001627	intron_variant	388886	exon4			CTGGCACAGCAGG	M24903	CCDS42992.1	22q11.23	2008-08-15			ENSG00000100031	ENSG00000100031	2.3.2.2	"CD molecules", "Gamma-glutamyltransferases"	4250	protein-coding gene	gene with protein product		612346		GGT		8104871, 18357469	Standard	NM_001288833		Approved	D22S672, D22S732, CD224	uc003aan.1	P19440	OTTHUMG00000030859	ENST00000248923.4:c.-429+2088C>A	chr22.hg19:g.24981864C>A		59.0	0.0		64.0	4.0	NM_207644	Q08247|Q14404|Q8TBS1|Q9UMK1	Missense_Mutation	SNP	ENST00000248923.4	hg19	CCDS42992.1	.	.	.	.	.	.	.	.	.	.	C	11.30	1.598675	0.28445	.	.	ENSG00000178026	ENST00000318753	T	0.54479	0.57	4.36	3.33	0.38152	.	0.000000	0.39985	U	0.001217	T	0.63343	0.2503	L	0.57536	1.79	0.36028	D	0.839187	D	0.64830	0.994	D	0.65443	0.935	T	0.71318	-0.4629	10	0.87932	D	0	-8.0036	8.8651	0.35280	0.0:0.891:0.0:0.109	.	313	Q2VPJ9	LRC6X_HUMAN	F	313	ENSP00000320520:C313F	ENSP00000320520:C313F	C	-	2	0	C22orf36	23311864	0.926000	0.31397	0.761000	0.31378	0.023000	0.10783	1.949000	0.40313	1.128000	0.42052	0.655000	0.94253	TGT	.	.		0.647	GGT1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319110.1	NM_013430		A	24981864	C	A	24981864	1	1	260	0	1	0	0	0	0	0	0	0	2148	478	17	3		3	C22orf36	22	24981864	Intron	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	526037	24981864	26322702	903	38148										
HORMAD2	150280	hgsc.bcm.edu	37	chr22	30517682	30517682	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aagatattaagaaagccagtGttctactgatccgtaaattg	8	6	1	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr22:30517682G>T	ENST00000336726.6	+	9	827	c.472G>T	c.(472-474)Gtt>Ttt	p.V158F	HORMAD2_ENST00000403975.1_Missense_Mutation_p.V158F	NM_152510.2	NP_689723.1	Q8N7B1	HORM2_HUMAN	HORMA domain containing 2	158	HORMA. {ECO:0000255|PROSITE- ProRule:PRU00109}.				meiotic nuclear division (GO:0007126)|meiotic sister chromatid cohesion (GO:0051177)	chromosome (GO:0005694)|nucleus (GO:0005634)				large_intestine(1)|lung(1)	2			Epithelial(10;0.125)			GAAAGCCAGTGTTCTACTGAT	0.348																																					p.V158F		Atlas-SNP	.											.	HORMAD2	12	.	0			c.G472T						.						88	77	81					22																	30517682		1853	4104	5957	SO:0001583	missense	150280	exon9			GCCAGTGTTCTAC	AK098703	CCDS46683.1	22q12.2	2014-01-21			ENSG00000176635	ENSG00000176635			28383	protein-coding gene	gene with protein product						12477932	Standard	NM_152510		Approved	MGC26710, CT46.2	uc003agy.3	Q8N7B1	OTTHUMG00000150881	ENST00000336726.6:c.472G>T	chr22.hg19:g.30517682G>T	ENSP00000336984:p.Val158Phe	301.0	0.0		225.0	60.0	NM_152510	B5MEB2|Q8NHR2	Missense_Mutation	SNP	ENST00000336726.6	hg19	CCDS46683.1	.	.	.	.	.	.	.	.	.	.	G	14.93	2.682200	0.47991	.	.	ENSG00000176635	ENST00000336726;ENST00000403975	T;T	0.32515	1.45;1.45	4.87	-4.25	0.03766	DNA-binding HORMA (4);	0.581117	0.17993	N	0.155158	T	0.25344	0.0616	L	0.54323	1.7	0.21386	N	0.999703	P	0.48016	0.904	P	0.46940	0.532	T	0.22173	-1.0224	10	0.25751	T	0.34	-0.824	6.3177	0.21200	0.6383:0.0:0.2103:0.1515	.	158	Q8N7B1	HORM2_HUMAN	F	158	ENSP00000336984:V158F;ENSP00000385055:V158F	ENSP00000336984:V158F	V	+	1	0	HORMAD2	28847682	0.537000	0.26386	0.609000	0.28983	0.990000	0.78478	0.650000	0.24858	-0.549000	0.06191	0.655000	0.94253	GTT	.	.		0.348	HORMAD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320416.2	NM_152510		T	30517682	G	T	30517682	3	4	260	1	0	0	0	0	1	0	0	0	7296	1377	48	3	502	3	HORMAD2	22	30517682	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	5535818	30517682	20786884	904	38149										
TBC1D10A	83874	hgsc.bcm.edu	37	chr22	30688656	30688656	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggaggggggcatctaggggcAggcggatggatggtgaaggt	23	4	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr22:30688656A>G	ENST00000215790.7	-	9	1399	c.1235T>C	c.(1234-1236)cTg>cCg	p.L412P	TBC1D10A_ENST00000403477.3_Missense_Mutation_p.L419P|TBC1D10A_ENST00000403362.1_Missense_Mutation_p.L324P|RP1-130H16.18_ENST00000447976.1_Intron	NM_031937.2	NP_114143.1	Q9BXI6	TB10A_HUMAN	TBC1 domain family, member 10A	412					activation of cysteine-type endopeptidase activity (GO:0097202)|positive regulation of proteolysis (GO:0045862)|retrograde transport, endosome to Golgi (GO:0042147)	extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rab GTPase activator activity (GO:0005097)			cervix(2)|endometrium(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	23						ATCTAGGGGCAGGCGGATGGA	0.647																																					p.L419P		Atlas-SNP	.											.	TBC1D10A	49	.	0			c.T1256C						.						47	54	52					22																	30688656		2203	4300	6503	SO:0001583	missense	83874	exon9			AGGGGCAGGCGGA	AF331038	CCDS13874.1, CCDS56227.1	22q12.2	2013-07-09	2005-03-10	2005-03-10	ENSG00000099992	ENSG00000099992			23609	protein-coding gene	gene with protein product	"EBP50-PDZ interactor of 64 kD"	610020	"TBC1 domain family, member 10"	TBC1D10		11285285, 20404108	Standard	NM_001204240		Approved	EPI64, AC004997.C22.2	uc010gvu.3	Q9BXI6	OTTHUMG00000150924	ENST00000215790.7:c.1235T>C	chr22.hg19:g.30688656A>G	ENSP00000215790:p.Leu412Pro	94.0	0.0		76.0	4.0	NM_001204240	B3KXT8|O76053|Q20WK7|Q543A2	Missense_Mutation	SNP	ENST00000215790.7	hg19	CCDS13874.1	.	.	.	.	.	.	.	.	.	.	A	15.55	2.866805	0.51588	.	.	ENSG00000099992	ENST00000215790;ENST00000403477;ENST00000403362	T;T;T	0.09723	3.14;3.12;2.95	5.51	5.51	0.81932	.	0.234223	0.35677	N	0.003045	T	0.23886	0.0578	L	0.56769	1.78	0.80722	D	1	D;D;D	0.64830	0.994;0.994;0.994	P;P;P	0.58077	0.832;0.832;0.832	T	0.00735	-1.1588	10	0.30854	T	0.27	.	14.753	0.69543	1.0:0.0:0.0:0.0	.	412;419;412	Q20WK7;B3KXT8;Q9BXI6	.;.;TB10A_HUMAN	P	412;419;324	ENSP00000215790:L412P;ENSP00000384996:L419P;ENSP00000385050:L324P	ENSP00000215790:L412P	L	-	2	0	TBC1D10A	29018656	1.000000	0.71417	0.982000	0.44146	0.149000	0.21700	3.610000	0.54125	2.234000	0.73211	0.459000	0.35465	CTG	.	.		0.647	TBC1D10A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320550.1	NM_031937		G	30688656	A	G	30688656	3	3	260	1	0	0	0	0	1	0	0	0	15613	188	7	2	295	2	TBC1D10A	22	30688656	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	170974	30688656	20615910	905	38150										
EIF4ENIF1	56478	hgsc.bcm.edu	37	chr22	31851919	31851919	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tctgctcgggttagagaaccAcctactgaaccgactggcag	11	12	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr22:31851919A>G	ENST00000397525.1	-	8	1241	c.1018T>C	c.(1018-1020)Tgg>Cgg	p.W340R	EIF4ENIF1_ENST00000382180.2_Missense_Mutation_p.W19R|RP11-247I13.11_ENST00000464523.1_RNA|EIF4ENIF1_ENST00000397523.1_Missense_Mutation_p.W340R|EIF4ENIF1_ENST00000344710.5_Missense_Mutation_p.W177R|EIF4ENIF1_ENST00000330125.5_Missense_Mutation_p.W340R	NM_001164501.1	NP_001157973.1	Q9NRA8	4ET_HUMAN	eukaryotic translation initiation factor 4E nuclear import factor 1	340						cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						TTAGAGAACCACCTACTGAAC	0.438											OREG0003517	type=REGULATORY REGION|Gene=LOC486366|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.W340R		Atlas-SNP	.											.	EIF4ENIF1	80	.	0			c.T1018C						.						101	93	96					22																	31851919		2203	4300	6503	SO:0001583	missense	56478	exon8			AGAACCACCTACT	AF240775	CCDS13898.1, CCDS54520.1	22q11.2	2007-01-16			ENSG00000184708	ENSG00000184708			16687	protein-coding gene	gene with protein product		607445				10856257	Standard	NM_019843		Approved	4E-T, FLJ21601, Clast4, 2610509L04Rik	uc003akz.2	Q9NRA8	OTTHUMG00000030793	ENST00000397525.1:c.1018T>C	chr22.hg19:g.31851919A>G	ENSP00000380659:p.Trp340Arg	129.0	0.0	828	104.0	5.0	NM_019843	B1AKL2|B1AKL3|B2RBF1|Q8NCF2|Q9H708	Missense_Mutation	SNP	ENST00000397525.1	hg19	CCDS13898.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.501269	0.85176	.	.	ENSG00000184708	ENST00000344710;ENST00000397525;ENST00000330125;ENST00000397523;ENST00000382180;ENST00000420671	.	.	.	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.77745	0.4176	M	0.71036	2.16	0.80722	D	1	D;D;D;D	0.89917	1.0;0.998;1.0;0.999	D;D;D;D	0.91635	0.999;0.996;0.999;0.999	T	0.78209	-0.2293	9	0.48119	T	0.1	-7.6038	14.3816	0.66914	1.0:0.0:0.0:0.0	.	177;340;177;340	B1AKL3;Q9NRA8;Q9NRA8-2;B1AKL4	.;4ET_HUMAN;.;.	R	177;340;340;340;19;340	.	ENSP00000328103:W340R	W	-	1	0	EIF4ENIF1	30181919	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.561000	0.90715	2.326000	0.78906	0.533000	0.62120	TGG	.	.		0.438	EIF4ENIF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127926.1	NM_019843		G	31851919	A	G	31851919	3	3	260	1	0	0	0	0	1	0	0	0	5037	159	6	2	1990	2	EIF4ENIF1	22	31851919	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1163263	31851919	19452647	906	38151										
SFI1	9814	hgsc.bcm.edu	37	chr22	31927044	31927044	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gctttttttccttctttcagAtgcgtggccagaaagttctt	8	9	3	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr22:31927044A>G	ENST00000400288.2	+	4	372	c.267A>G	c.(265-267)agA>agG	p.R89R	SFI1_ENST00000443326.1_Intron|SFI1_ENST00000400289.1_Intron|SFI1_ENST00000443011.1_Intron|SFI1_ENST00000414585.1_Intron|SFI1_ENST00000432498.1_Splice_Site_p.R89R|SFI1_ENST00000540643.1_Intron	NM_001007467.2	NP_001007468.1	A8K8P3	SFI1_HUMAN	Sfi1 homolog, spindle assembly associated (yeast)	89					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(2)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)	38						CTTCTTTCAGATGCGTGGCCA	0.358																																					p.R89R		Atlas-SNP	.											.	SFI1	78	.	0			c.A267G						.						113	103	106					22																	31927044		1830	4087	5917	SO:0001630	splice_region_variant	9814	exon4			TTTCAGATGCGTG	AB011114	CCDS43004.1, CCDS43005.1, CCDS58803.1, CCDS58804.1	22q12.2	2014-06-13			ENSG00000198089	ENSG00000198089			29064	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 139"	612765				14504268	Standard	NM_001007467		Approved	KIAA0542, PISD, PPP1R139	uc003ale.4	A8K8P3	OTTHUMG00000030249	ENST00000400288.2:c.267-1A>G	chr22.hg19:g.31927044A>G		139.0	0.0		93.0	4.0	NM_001007467	A1L373|A1L387|A2A2L2|B1AKL9|B5MDB7|B7Z1V6|B7Z8G3|B7ZBE2|B7ZBE3|O60289|Q2TAN8|Q5W1B5|Q86TK0|Q8N4U8|Q8N8C1|Q8WU14	Silent	SNP	ENST00000400288.2	hg19	CCDS43004.1																																																																																			.	.		0.358	SFI1-023	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337180.3	NM_014775	Silent	G	31927044	A	G	31927044	5	3	260	1	0	0	0	0	0	0	1	0	14171	347	12	2	277	2	SFI1	22	31927044	Splice_Site	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	75125	31927044	19377522	907	38152										
MYH9	4627	hgsc.bcm.edu	37	chr22	36684860	36684860	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgggccttcatggcctgcagGttgacctccaaccgcagctt	11	14	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr22:36684860G>A	ENST00000216181.5	-	33	4913	c.4683C>T	c.(4681-4683)aaC>aaT	p.N1561N	MYH9_ENST00000475726.1_5'Flank	NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	1561					actin cytoskeleton reorganization (GO:0031532)|actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|angiogenesis (GO:0001525)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood vessel endothelial cell migration (GO:0043534)|cytokinesis (GO:0000910)|establishment of meiotic spindle localization (GO:0051295)|establishment of T cell polarity (GO:0001768)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|meiotic spindle organization (GO:0000212)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte differentiation (GO:0030224)|myoblast fusion (GO:0007520)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of cell shape (GO:0008360)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|uropod organization (GO:0032796)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|actomyosin contractile ring (GO:0005826)|cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|cleavage furrow (GO:0032154)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|spindle (GO:0005819)|stress fiber (GO:0001725)|uropod (GO:0001931)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3)	86						TGGCCTGCAGGTTGACCTCCA	0.632			T	ALK	ALCL		"Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"		Hereditary Macrothrombocytopenia, MYH9-associated																												p.N1561N		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"myosin, heavy polypeptide 9, non-muscle"	yes	L	.	MYH9	225	.	0			c.C4683T						.						127	113	118					22																	36684860		2203	4300	6503	SO:0001819	synonymous_variant	4627	exon33	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	CTGCAGGTTGACC		CCDS13927.1	22q13.1	2014-09-17	2006-09-29		ENSG00000100345	ENSG00000100345		"Myosins / Myosin superfamily : Class II"	7579	protein-coding gene	gene with protein product	"nonmuscle myosin heavy chain II-A"	160775	"myosin, heavy polypeptide 9, non-muscle"	DFNA17		1860190, 11023810	Standard	NM_002473		Approved	NMMHCA, NMHC-II-A, MHA, FTNS, EPSTS	uc003apg.3	P35579	OTTHUMG00000030429	ENST00000216181.5:c.4683C>T	chr22.hg19:g.36684860G>A		136.0	0.0		81.0	4.0	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Silent	SNP	ENST00000216181.5	hg19	CCDS13927.1																																																																																			.	.		0.632	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473		A	36684860	G	A	36684860	2	1	260	1	0	0	0	0	0	0	0	1	10051	1252	44	3		3	MYH9	22	36684860	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	4757816	36684860	14619706	908	38153										
SUN2	25777	hgsc.bcm.edu	37	chr22	39136284	39136284	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccactcacgtcgtcccgcacGgcctggatctgctggggcag	13	16	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr22:39136284G>T	ENST00000405510.1	-	13	1702	c.1344C>A	c.(1342-1344)gcC>gcA	p.A448A	RP3-508I15.18_ENST00000420118.1_RNA|SUN2_ENST00000216064.4_Silent_p.A448A|RP3-508I15.14_ENST00000416406.1_RNA|SUN2_ENST00000406622.1_Silent_p.A448A|SUN2_ENST00000405018.1_Silent_p.A469A|SUN2_ENST00000411587.2_Silent_p.A437A|RP3-508I15.21_ENST00000609212.1_RNA|RP3-508I15.19_ENST00000418803.1_RNA	NM_001199580.1	NP_001186509.1	Q9UH99	SUN2_HUMAN	Sad1 and UNC84 domain containing 2	448					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|mitotic spindle organization (GO:0007052)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)	condensed nuclear chromosome (GO:0000794)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nuclear inner membrane (GO:0005637)|nuclear membrane (GO:0031965)|SUN-KASH complex (GO:0034993)	identical protein binding (GO:0042802)|lamin binding (GO:0005521)|microtubule binding (GO:0008017)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(2)|stomach(1)	15						CGTCCCGCACGGCCTGGATCT	0.677																																					p.A469A		Atlas-SNP	.											.	SUN2	59	.	0			c.C1407A						.						12	14	13					22																	39136284		2193	4296	6489	SO:0001819	synonymous_variant	25777	exon12			CCGCACGGCCTGG	AF202723	CCDS13978.1, CCDS56231.1	22q12-q13	2010-05-18	2010-05-18	2010-01-27	ENSG00000100242	ENSG00000100242			14210	protein-coding gene	gene with protein product		613569	"unc-84 homolog B (C. elegans)"	UNC84B		10508607, 10375507	Standard	NM_015374		Approved		uc010gxq.2	Q9UH99	OTTHUMG00000151031	ENST00000405510.1:c.1344C>A	chr22.hg19:g.39136284G>T		140.0	0.0		87.0	4.0	NM_001199579	B0QY62|O75156|Q2NKN8|Q2T9F7|Q504T5|Q6B4H1|Q7Z3E3	Silent	SNP	ENST00000405510.1	hg19	CCDS13978.1																																																																																			.	.		0.677	SUN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321057.1	XM_039332		T	39136284	G	T	39136284	2	4	260	1	0	0	0	0	0	0	0	1	15407	1103	39	1		1	SUN2	22	39136284	Silent	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	2451424	39136284	12168282	909	38154										
CBX6	23466	hgsc.bcm.edu	37	chr22	39268185	39268185	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agacccgctcgcccactgcaGacagctccatcttgctcagc	8	18	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr22:39268185G>T	ENST00000407418.3	-	1	134	c.11C>A	c.(10-12)tCt>tAt	p.S4Y	CBX6_ENST00000216083.6_Missense_Mutation_p.S4Y			O95503	CBX6_HUMAN	chromobox homolog 6	4					chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)	single-stranded RNA binding (GO:0003727)			large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6	Melanoma(58;0.04)					GCCCACTGCAGACAGCTCCAT	0.736																																					p.S4Y		Atlas-SNP	.											.	CBX6	26	.	0			c.C11A						.						20	19	19					22																	39268185		2193	4275	6468	SO:0001583	missense	23466	exon1			ACTGCAGACAGCT		CCDS13980.1	22q13.1	2013-04-23			ENSG00000183741	ENSG00000183741			1556	protein-coding gene	gene with protein product							Standard	NM_014292		Approved		uc003awl.3	O95503	OTTHUMG00000150456	ENST00000407418.3:c.11C>A	chr22.hg19:g.39268185G>T	ENSP00000384490:p.Ser4Tyr	102.0	0.0		78.0	4.0	NM_014292	A8KAH0|Q96EM5	Missense_Mutation	SNP	ENST00000407418.3	hg19	CCDS13980.1	.	.	.	.	.	.	.	.	.	.	g	18.83	3.706279	0.68615	.	.	ENSG00000183741	ENST00000407418;ENST00000216083	.	.	.	4.58	3.56	0.40772	Chromo domain-like (1);	2.001140	0.02767	N	0.119287	D	0.82628	0.5078	M	0.83223	2.63	0.37471	D	0.915621	D;D	0.89917	1.0;0.997	D;D	0.87578	0.998;0.987	T	0.65726	-0.6098	9	0.87932	D	0	.	11.5557	0.50745	0.0894:0.0:0.9106:0.0	.	4;4	B3KT27;O95503	.;CBX6_HUMAN	Y	4	.	ENSP00000216083:S4Y	S	-	2	0	CBX6	37598131	1.000000	0.71417	1.000000	0.80357	0.461000	0.32589	6.356000	0.73046	1.143000	0.42306	0.543000	0.68304	TCT	.	.		0.736	CBX6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318190.1	NM_014292		T	39268185	G	T	39268185	3	4	260	1	0	0	0	0	1	0	0	0	2724	942	33	3	1247	3	CBX6	22	39268185	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	131901	39268185	12036381	910	38155										
SYNGR1	9145	hgsc.bcm.edu	37	chr22	39760240	39760240	+	Intron	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gattctggaattcgatccttCatggataggcagctggacac	11	9	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr22:39760240C>T	ENST00000328933.5	+	2	114				SYNGR1_ENST00000406293.3_Intron|SYNGR1_ENST00000216155.7_Intron|SYNGR1_ENST00000318801.4_Intron|SYNGR1_ENST00000381535.4_Missense_Mutation_p.S14L	NM_004711.4	NP_004702.2	O43759	SNG1_HUMAN	synaptogyrin 1						protein targeting (GO:0006605)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle membrane (GO:0030672)				endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(1)	7	Melanoma(58;0.04)					TTCGATCCTTCATGGATAGGC	0.592																																					p.S14L		Atlas-SNP	.											.	SYNGR1	19	.	0			c.C41T						.						166	143	151					22																	39760240		2203	4300	6503	SO:0001627	intron_variant	9145	exon1			ATCCTTCATGGAT	AJ002303	CCDS13989.1, CCDS13990.1, CCDS13991.1	22q13	2008-06-10			ENSG00000100321	ENSG00000100321			11498	protein-coding gene	gene with protein product		603925				9760194, 10595519	Standard	NM_004711		Approved			O43759	OTTHUMG00000030978	ENST00000328933.5:c.100-10081C>T	chr22.hg19:g.39760240C>T		183.0	0.0		97.0	4.0	NM_145738	A6NP69|A8K0E2|O43757|O43758|Q53Y02|Q96J56|Q9UGZ4	Missense_Mutation	SNP	ENST00000328933.5	hg19	CCDS13989.1	.	.	.	.	.	.	.	.	.	.	C	6.932	0.541712	0.13250	.	.	ENSG00000100321	ENST00000381535	.	.	.	1.3	1.3	0.21679	.	.	.	.	.	T	0.37598	0.1009	.	.	.	0.09310	N	1	P	0.51449	0.945	P	0.54965	0.765	T	0.17018	-1.0383	7	0.22706	T	0.39	.	6.0176	0.19611	0.0:1.0:0.0:0.0	.	14	O43759-3	.	L	14	.	ENSP00000370946:S14L	S	+	2	0	SYNGR1	38090186	0.000000	0.05858	0.071000	0.20095	0.048000	0.14542	-0.226000	0.09139	1.043000	0.40175	0.563000	0.77884	TCA	.	.		0.592	SYNGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075866.2	NM_004711		T	39760240	C	T	39760240	1	4	260	0	1	0	0	0	0	0	0	0	15463	838	29	3		3	SYNGR1	22	39760240	Intron	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	492055	39760240	11544326	911	38156										
SYNGR1	9145	hgsc.bcm.edu	37	chr22	39772194	39772194	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccttctcctttttctccatcTtcacctgggtgagtacagcc	6	15	4	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr22:39772194T>C	ENST00000328933.5	+	3	490	c.475T>C	c.(475-477)Ttc>Ctc	p.F159L	SYNGR1_ENST00000406293.3_Missense_Mutation_p.F159L|SYNGR1_ENST00000318801.4_Missense_Mutation_p.F159L|SYNGR1_ENST00000381535.4_Missense_Mutation_p.F160L	NM_004711.4	NP_004702.2	O43759	SNG1_HUMAN	synaptogyrin 1	159	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				protein targeting (GO:0006605)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle membrane (GO:0030672)				endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(1)	7	Melanoma(58;0.04)					TTTCTCCATCTTCACCTGGGT	0.647																																					p.F160L		Atlas-SNP	.											.	SYNGR1	19	.	0			c.T478C						.						94	101	99					22																	39772194		2203	4300	6503	SO:0001583	missense	9145	exon3			TCCATCTTCACCT	AJ002303	CCDS13989.1, CCDS13990.1, CCDS13991.1	22q13	2008-06-10			ENSG00000100321	ENSG00000100321			11498	protein-coding gene	gene with protein product		603925				9760194, 10595519	Standard	NM_004711		Approved			O43759	OTTHUMG00000030978	ENST00000328933.5:c.475T>C	chr22.hg19:g.39772194T>C	ENSP00000332287:p.Phe159Leu	199.0	0.0		115.0	5.0	NM_145738	A6NP69|A8K0E2|O43757|O43758|Q53Y02|Q96J56|Q9UGZ4	Missense_Mutation	SNP	ENST00000328933.5	hg19	CCDS13989.1	.	.	.	.	.	.	.	.	.	.	T	18.17	3.563669	0.65651	.	.	ENSG00000100321	ENST00000318801;ENST00000406293;ENST00000328933;ENST00000381535	T;T;T;T	0.21932	1.98;1.98;1.98;1.98	5.21	5.21	0.72293	Marvel (1);MARVEL-like domain (1);	0.000000	0.85682	D	0.000000	T	0.34424	0.0897	L	0.48877	1.53	0.58432	D	0.999998	D;P;D;D	0.76494	0.999;0.951;0.999;0.999	D;P;D;D	0.83275	0.996;0.703;0.978;0.995	T	0.09729	-1.0661	10	0.02654	T	1	.	15.3829	0.74673	0.0:0.0:0.0:1.0	.	160;153;159;159	O43759-3;Q59FT7;O43759;O43759-2	.;.;SNG1_HUMAN;.	L	159;159;159;160	ENSP00000318845:F159L;ENSP00000385447:F159L;ENSP00000332287:F159L;ENSP00000370946:F160L	ENSP00000318845:F159L	F	+	1	0	SYNGR1	38102140	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.986000	0.63851	2.088000	0.63022	0.454000	0.30748	TTC	.	.		0.647	SYNGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075866.2	NM_004711		C	39772194	T	C	39772194	3	2	260	1	0	0	0	0	1	0	0	0	15463	1609	56	2	591	2	SYNGR1	22	39772194	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	11954	39772194	11532372	912	38157										
MGAT3	4248	hgsc.bcm.edu	37	chr22	39883578	39883578	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgctgcgtaccccactctacTcccactcgcccctgctgcag	7	20	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr22:39883578T>C	ENST00000341184.6	+	2	441	c.226T>C	c.(226-228)Tcc>Ccc	p.S76P		NM_001098270.1|NM_002409.4	NP_001091740.1|NP_002400.3	Q09327	MGAT3_HUMAN	mannosyl (beta-1,4-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase	76	Pro-rich.				cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-1,4-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0003830)			endometrium(4)|kidney(1)|large_intestine(5)|lung(12)|prostate(1)|skin(1)	24	Melanoma(58;0.04)					CCCACTCTACTCCCACTCGCC	0.672																																					p.S76P		Atlas-SNP	.											.	MGAT3	65	.	0			c.T226C						.						38	45	42					22																	39883578		2203	4299	6502	SO:0001583	missense	4248	exon2			CTCTACTCCCACT	D13789	CCDS13994.2	22q13.1	2013-02-25			ENSG00000128268	ENSG00000128268	2.4.1.144	"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	7046	protein-coding gene	gene with protein product		604621				8370666	Standard	NM_002409		Approved	GNT-III	uc010gxy.3	Q09327	OTTHUMG00000030185	ENST00000341184.6:c.226T>C	chr22.hg19:g.39883578T>C	ENSP00000345270:p.Ser76Pro	53.0	0.0		50.0	4.0	NM_002409	A6NGD0|Q14CK5|Q6IC49|Q9UH32	Missense_Mutation	SNP	ENST00000341184.6	hg19	CCDS13994.2	.	.	.	.	.	.	.	.	.	.	T	5.092	0.202533	0.09652	.	.	ENSG00000128268	ENST00000341184;ENST00000429402;ENST00000418314	.	.	.	4.93	4.93	0.64822	.	0.425233	0.22894	N	0.054343	T	0.24353	0.0590	L	0.27053	0.805	0.29464	N	0.85752	P	0.43826	0.818	B	0.34722	0.188	T	0.11084	-1.0602	9	0.40728	T	0.16	.	14.2384	0.65941	0.0:0.0:0.0:1.0	.	76	Q09327	MGAT3_HUMAN	P	76;76;104	.	ENSP00000345270:S76P	S	+	1	0	MGAT3	38213524	1.000000	0.71417	0.999000	0.59377	0.148000	0.21650	2.658000	0.46733	1.849000	0.53698	0.383000	0.25322	TCC	.	.		0.672	MGAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075039.2	NM_002409		C	39883578	T	C	39883578	3	2	260	1	0	0	0	0	1	0	0	0	9553	1551	54	2	228	2	MGAT3	22	39883578	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	111384	39883578	11420988	913	38158										
CACNA1I	8911	hgsc.bcm.edu	37	chr22	40068952	40068952	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cctcccatgcacggctgagcAgatggaaccagctggacctg	12	14	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr22:40068952A>G	ENST00000402142.3	+	28	4649		c.e28-1		CACNA1I_ENST00000407673.1_Splice_Site|CACNA1I_ENST00000404898.1_Splice_Site|CACNA1I_ENST00000336649.4_Splice_Site|CACNA1I_ENST00000400164.3_Splice_Site|CACNA1I_ENST00000401624.1_Splice_Site	NM_021096.3	NP_066919.2	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type, alpha 1I subunit						axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|signal transduction (GO:0007165)|sleep (GO:0030431)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(2)|lung(27)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Melanoma(58;0.0749)				Cinnarizine(DB00568)|Flunarizine(DB04841)|Paramethadione(DB00617)|Spironolactone(DB00421)|Verapamil(DB00661)|Zonisamide(DB00909)	ACGGCTGAGCAGATGGAACCA	0.592																																					.		Atlas-SNP	.											.	CACNA1I	264	.	0			c.4650-2A>G						.						58	60	59					22																	40068952		2141	4243	6384	SO:0001630	splice_region_variant	8911	exon28			CTGAGCAGATGGA	AF129133	CCDS46710.1, CCDS46711.1	22q13.1	2012-03-07	2007-02-16		ENSG00000100346	ENSG00000100346		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1396	protein-coding gene	gene with protein product		608230				10454147, 16382099	Standard	NM_021096		Approved	Cav3.3	uc003ayd.3	Q9P0X4	OTTHUMG00000151096	ENST00000402142.3:c.4650-1A>G	chr22.hg19:g.40068952A>G		160.0	0.0		91.0	4.0	NM_021096	B0QY12|B0QY13|B0QY14|O95504|Q5JZ88|Q7Z6S9|Q8NFX6|Q9NZC8|Q9UH15|Q9UH30|Q9ULU9|Q9UNE6	Splice_Site	SNP	ENST00000402142.3	hg19	CCDS46710.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.954069	0.73902	.	.	ENSG00000100346	ENST00000402142;ENST00000404898;ENST00000401624;ENST00000407673;ENST00000336649;ENST00000400164	.	.	.	4.73	4.73	0.59995	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.2158	0.65792	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CACNA1I	38398898	1.000000	0.71417	0.961000	0.40146	0.819000	0.46315	9.275000	0.95738	1.754000	0.51921	0.454000	0.30748	.	.	.		0.592	CACNA1I-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321290.1	NM_001003406	Intron	G	40068952	A	G	40068952	5	3	260	1	0	0	0	0	0	0	1	0	2548	202	7	2	4758	2	CACNA1I	22	40068952	Splice_Site	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	185374	40068952	11235614	914	38159										
FAM83F	113828	hgsc.bcm.edu	37	chr22	40417619	40417619	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccagcggtggcgagtcggccTggcgcctggagagcttcctg	17	13	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr22:40417619T>C	ENST00000333407.6	+	4	1199	c.1105T>C	c.(1105-1107)Tgg>Cgg	p.W369R	FAM83F_ENST00000473717.1_Missense_Mutation_p.W201R	NM_138435.2	NP_612444.2	Q8NEG4	FA83F_HUMAN	family with sequence similarity 83, member F	369										breast(1)|endometrium(2)|large_intestine(1)|lung(4)|skin(4)|urinary_tract(2)	14						CGAGTCGGCCTGGCGCCTGGA	0.711																																					p.W369R		Atlas-SNP	.											.	FAM83F	29	.	0			c.T1105C						.						27	24	25					22																	40417619		2203	4300	6503	SO:0001583	missense	113828	exon4			TCGGCCTGGCGCC		CCDS14000.2	22q13.1	2006-03-22			ENSG00000133477	ENSG00000133477			25148	protein-coding gene	gene with protein product						12477932	Standard	NM_138435		Approved		uc003ayk.1	Q8NEG4	OTTHUMG00000150688	ENST00000333407.6:c.1105T>C	chr22.hg19:g.40417619T>C	ENSP00000330432:p.Trp369Arg	36.0	0.0		29.0	4.0	NM_138435	Q96FD6	Missense_Mutation	SNP	ENST00000333407.6	hg19	CCDS14000.2	.	.	.	.	.	.	.	.	.	.	C	0.012	-1.674767	0.00758	.	.	ENSG00000133477	ENST00000333407	T	0.05996	3.36	4.65	3.64	0.41730	.	0.879723	0.09934	N	0.736796	T	0.01765	0.0056	N	0.01048	-1.04	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45381	-0.9265	10	0.02654	T	1	-4.3881	4.4001	0.11383	0.2253:0.588:0.0:0.1867	.	369	Q8NEG4	FA83F_HUMAN	R	369	ENSP00000330432:W369R	ENSP00000330432:W369R	W	+	1	0	FAM83F	38747565	0.001000	0.12720	0.951000	0.38953	0.426000	0.31534	0.312000	0.19397	0.592000	0.29728	-0.374000	0.07098	TGG	.	.		0.711	FAM83F-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319624.3	NM_138435		C	40417619	T	C	40417619	3	2	260	1	0	0	0	0	1	0	0	0	5646	1580	55	2	1119	2	FAM83F	22	40417619	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	348667	40417619	10886947	915	38160										
FAM83F	113828	hgsc.bcm.edu	37	chr22	40417665	40417665	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cctggttacggtggagcaggTgctgccccccgtggagccca	15	14	0	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr22:40417665T>C	ENST00000333407.6	+	4	1245	c.1151T>C	c.(1150-1152)gTg>gCg	p.V384A	FAM83F_ENST00000473717.1_Missense_Mutation_p.V216A	NM_138435.2	NP_612444.2	Q8NEG4	FA83F_HUMAN	family with sequence similarity 83, member F	384										breast(1)|endometrium(2)|large_intestine(1)|lung(4)|skin(4)|urinary_tract(2)	14						GTGGAGCAGGTGCTGCCCCCC	0.667																																					p.V384A		Atlas-SNP	.											.	FAM83F	29	.	0			c.T1151C						.						37	31	33					22																	40417665		2203	4300	6503	SO:0001583	missense	113828	exon4			AGCAGGTGCTGCC		CCDS14000.2	22q13.1	2006-03-22			ENSG00000133477	ENSG00000133477			25148	protein-coding gene	gene with protein product						12477932	Standard	NM_138435		Approved		uc003ayk.1	Q8NEG4	OTTHUMG00000150688	ENST00000333407.6:c.1151T>C	chr22.hg19:g.40417665T>C	ENSP00000330432:p.Val384Ala	118.0	0.0		88.0	5.0	NM_138435	Q96FD6	Missense_Mutation	SNP	ENST00000333407.6	hg19	CCDS14000.2	.	.	.	.	.	.	.	.	.	.	T	7.621	0.676738	0.14841	.	.	ENSG00000133477	ENST00000333407	T	0.09723	2.95	4.74	3.71	0.42584	.	0.841667	0.10433	N	0.675298	T	0.07369	0.0186	L	0.29908	0.895	0.09310	N	1	B	0.12630	0.006	B	0.09377	0.004	T	0.44034	-0.9354	10	0.15952	T	0.53	-7.1522	4.9879	0.14200	0.2722:0.079:0.0:0.6487	.	384	Q8NEG4	FA83F_HUMAN	A	384	ENSP00000330432:V384A	ENSP00000330432:V384A	V	+	2	0	FAM83F	38747611	0.029000	0.19370	0.945000	0.38365	0.422000	0.31414	-0.044000	0.12023	0.860000	0.35481	0.379000	0.24179	GTG	.	.		0.667	FAM83F-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319624.3	NM_138435		C	40417665	T	C	40417665	3	2	260	1	0	0	0	0	1	0	0	0	5646	1696	59	2	1165	2	FAM83F	22	40417665	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	46	40417665	10886901	916	38161										
SLC25A17	10478	hgsc.bcm.edu	37	chr22	41173121	41173121	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggctactgcaccaatgatgaAcacatccaaggaagaaagct	9	10	0	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr22:41173121A>G	ENST00000435456.2	-	7	749	c.616T>C	c.(616-618)Ttc>Ctc	p.F206L	SLC25A17_ENST00000402844.3_Missense_Mutation_p.F124L|SLC25A17_ENST00000544408.1_Missense_Mutation_p.F169L|SLC25A17_ENST00000491545.1_5'UTR|SLC25A17_ENST00000542412.1_Missense_Mutation_p.F133L	NM_006358.2	NP_006349.1	O43808	PM34_HUMAN	solute carrier family 25 (mitochondrial carrier; peroxisomal membrane protein, 34kDa), member 17	206					ADP transport (GO:0015866)|AMP transport (GO:0080121)|ATP transport (GO:0015867)|cellular lipid metabolic process (GO:0044255)|coenzyme A transmembrane transport (GO:0035349)|FAD transmembrane transport (GO:0035350)|fatty acid alpha-oxidation (GO:0001561)|fatty acid beta-oxidation (GO:0006635)|fatty acid transport (GO:0015908)|NAD transport (GO:0043132)|nucleotide transmembrane transport (GO:1901679)|small molecule metabolic process (GO:0044281)	integral component of peroxisomal membrane (GO:0005779)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ADP transmembrane transporter activity (GO:0015217)|AMP transmembrane transporter activity (GO:0080122)|ATP transmembrane transporter activity (GO:0005347)|chaperone binding (GO:0051087)|coenzyme A transmembrane transporter activity (GO:0015228)|FAD transmembrane transporter activity (GO:0015230)|FMN transmembrane transporter activity (GO:0044610)|NAD transporter activity (GO:0051724)			central_nervous_system(1)|large_intestine(4)|lung(2)|skin(1)	8						CCAATGATGAACACATCCAAG	0.448																																					p.F206L		Atlas-SNP	.											.	SLC25A17	25	.	0			c.T616C						.						94	80	85					22																	41173121		2203	4300	6503	SO:0001583	missense	10478	exon7			TGATGAACACATC	Y12860	CCDS14005.1, CCDS74868.1	22q13.2	2013-05-22	2002-08-29		ENSG00000100372	ENSG00000100372		"Solute carriers"	10987	protein-coding gene	gene with protein product	"peroxisomal membrane protein (34kD)"	606795	"solute carrier family 25 (mitochondrial carrier; peroxisomal membrane protein, 34kD), member 17"			9874197	Standard	NM_006358		Approved	PMP34	uc003azc.3	O43808	OTTHUMG00000151139	ENST00000435456.2:c.616T>C	chr22.hg19:g.41173121A>G	ENSP00000390722:p.Phe206Leu	103.0	0.0		63.0	5.0	NM_006358	A8KA59|Q5TFL0|Q9UGW8|Q9UGY7	Missense_Mutation	SNP	ENST00000435456.2	hg19	CCDS14005.1	.	.	.	.	.	.	.	.	.	.	A	35	5.509637	0.96386	.	.	ENSG00000100372	ENST00000435456;ENST00000402844;ENST00000544408;ENST00000542412	T;T;T;T	0.75821	-0.97;-0.97;-0.97;-0.97	5.65	5.65	0.86999	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	T	0.81531	0.4842	L	0.50847	1.595	0.80722	D	1	D;D;D	0.71674	0.994;0.998;0.998	D;D;D	0.80764	0.944;0.994;0.991	T	0.77067	-0.2725	10	0.16420	T	0.52	-14.2959	16.1864	0.81955	1.0:0.0:0.0:0.0	.	133;169;206	F5GYD1;B4DU97;O43808	.;.;PM34_HUMAN	L	206;124;169;133	ENSP00000390722:F206L;ENSP00000385303:F124L;ENSP00000438355:F169L;ENSP00000446471:F133L	ENSP00000385303:F124L	F	-	1	0	SLC25A17	39503067	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.988000	0.93501	2.281000	0.76405	0.528000	0.53228	TTC	.	.		0.448	SLC25A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321487.1	NM_006358		G	41173121	A	G	41173121	3	3	260	1	0	0	0	0	1	0	0	0	14494	43	2	2	319	2	SLC25A17	22	41173121	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	755456	41173121	10131445	917	38162										
PKDREJ	10343	hgsc.bcm.edu	37	chr22	46656423	46656423	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gttatctgcaactcctgtcaTtctgaatccagacacctcca	5	14	3	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr22:46656423T>C	ENST00000253255.5	-	1	2796	c.2797A>G	c.(2797-2799)Atg>Gtg	p.M933V		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	933					acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		ACTCCTGTCATTCTGAATCCA	0.413																																					p.M933V		Atlas-SNP	.											.	PKDREJ	195	.	0			c.A2797G						.						160	169	166					22																	46656423		2203	4300	6503	SO:0001583	missense	10343	exon1			CTGTCATTCTGAA	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like", "polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like", "polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.2797A>G	chr22.hg19:g.46656423T>C	ENSP00000253255:p.Met933Val	114.0	0.0		84.0	6.0	NM_006071	B1AJY3|O95850	Missense_Mutation	SNP	ENST00000253255.5	hg19	CCDS14073.1	.	.	.	.	.	.	.	.	.	.	T	14.53	2.563031	0.45694	.	.	ENSG00000130943	ENST00000253255	T	0.40756	1.02	5.33	3.17	0.36434	.	0.439248	0.23442	N	0.048134	T	0.33265	0.0857	L	0.59436	1.845	0.30837	N	0.736037	P	0.38788	0.647	B	0.32465	0.146	T	0.40813	-0.9543	10	0.72032	D	0.01	-25.1043	6.6959	0.23199	0.1365:0.0746:0.0:0.7889	.	933	Q9NTG1	PKDRE_HUMAN	V	933	ENSP00000253255:M933V	ENSP00000253255:M933V	M	-	1	0	PKDREJ	45035087	0.995000	0.38212	0.860000	0.33809	0.577000	0.36160	1.704000	0.37857	0.407000	0.25591	0.533000	0.62120	ATG	.	.		0.413	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071		C	46656423	T	C	46656423	3	2	260	1	0	0	0	0	1	0	0	0	11979	1493	52	2	3968	2	PKDREJ	22	46656423	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	5483302	46656423	4648143	918	38163										
GTSE1	51512	hgsc.bcm.edu	37	chr22	46704325	46704325	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccgaacagcctccgttgcccAcatctgagagtccctttgcc	8	17	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr22:46704325A>G	ENST00000454366.1	+	4	459	c.247A>G	c.(247-249)Aca>Gca	p.T83A		NM_016426.6	NP_057510	Q9NYZ3	GTSE1_HUMAN	G-2 and S-phase expressed 1	64					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|microtubule-based process (GO:0007017)	cytoplasmic microtubule (GO:0005881)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	27		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)		TCCGTTGCCCACATCTGAGAG	0.498																																					p.T83A	GBM(153;542 1915 12487 29016 50495)	Atlas-SNP	.											.	GTSE1	100	.	0			c.A247G						.						105	116	112					22																	46704325		2203	4300	6503	SO:0001583	missense	51512	exon4			TTGCCCACATCTG	AF223408	CCDS14074.2	22q13.2-q13.3	2008-06-10			ENSG00000075218	ENSG00000075218			13698	protein-coding gene	gene with protein product		607477				10974554, 10984615, 12750368	Standard	NM_016426		Approved	GTSE-1, B99	uc011aqy.2	Q9NYZ3	OTTHUMG00000150486	ENST00000454366.1:c.247A>G	chr22.hg19:g.46704325A>G	ENSP00000415430:p.Thr83Ala	128.0	0.0		80.0	4.0	NM_016426	B0QYM3|Q20WK2|Q53GX5|Q5R3I6|Q6DHX4|Q9BRE0|Q9UGZ9|Q9Y557	Missense_Mutation	SNP	ENST00000454366.1	hg19	CCDS14074.2	.	.	.	.	.	.	.	.	.	.	G	0.690	-0.794801	0.02862	.	.	ENSG00000075218	ENST00000454366;ENST00000361934	T	0.06294	3.32	4.88	3.77	0.43336	.	0.791236	0.10885	N	0.623396	T	0.01353	0.0044	N	0.00347	-1.61	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45585	-0.9251	10	0.06625	T	0.88	-0.5449	3.2106	0.06681	0.0897:0.129:0.4894:0.2919	.	64	Q9NYZ3	GTSE1_HUMAN	A	83;43	ENSP00000415430:T83A	ENSP00000354634:T43A	T	+	1	0	GTSE1	45082989	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	0.168000	0.16622	1.379000	0.46325	-0.213000	0.12676	ACA	.	.		0.498	GTSE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318360.2	NM_016426		G	46704325	A	G	46704325	3	3	260	1	0	0	0	0	1	0	0	0	6894	159	6	2	257	2	GTSE1	22	46704325	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	47902	46704325	4600241	919	38164										
CELSR1	9620	hgsc.bcm.edu	37	chr22	46860155	46860155	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tctcctgggacatgttctccAggcggacagtgatgctgttg	13	10	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr22:46860155A>G	ENST00000262738.3	-	2	3631	c.3632T>C	c.(3631-3633)cTg>cCg	p.L1211P	CELSR1_ENST00000395964.1_Missense_Mutation_p.L1211P	NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	1211	Cadherin 9. {ECO:0000255|PROSITE- ProRule:PRU00043}.				anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		CATGTTCTCCAGGCGGACAGT	0.617																																					p.L1211P		Atlas-SNP	.											.	CELSR1	242	.	0			c.T3632C						.						100	83	88					22																	46860155		2203	4300	6503	SO:0001583	missense	9620	exon2			TTCTCCAGGCGGA	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	1850	protein-coding gene	gene with protein product	"flamingo homolog 2 (Drosophila)"	604523	"cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.3632T>C	chr22.hg19:g.46860155A>G	ENSP00000262738:p.Leu1211Pro	149.0	0.0		100.0	4.0	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	hg19	CCDS14076.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.8|21.8	4.199213|4.199213	0.79015|0.79015	.|.	.|.	ENSG00000075275|ENSG00000075275	ENST00000262738;ENST00000395964|ENST00000454637	T;T|.	0.74002|.	-0.8;-0.33|.	4.68|4.68	4.68|4.68	0.58851|0.58851	Cadherin (1);|.	0.000000|.	0.52532|.	U|.	0.000069|.	T|T	0.78451|0.78451	0.4285|0.4285	M|M	0.86343|0.86343	2.81|2.81	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	T|T	0.81786|0.81786	-0.0773|-0.0773	10|5	0.87932|.	D|.	0|.	.|.	13.8213|13.8213	0.63322|0.63322	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	1211|.	Q9NYQ6|.	CELR1_HUMAN|.	P|R	1211|586	ENSP00000262738:L1211P;ENSP00000379293:L1211P|.	ENSP00000262738:L1211P|.	L|W	-|-	2|1	0|0	CELSR1|CELSR1	45238819|45238819	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	8.568000|8.568000	0.90741|0.90741	1.743000|1.743000	0.51761|0.51761	0.533000|0.533000	0.62120|0.62120	CTG|TGG	.	.		0.617	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		G	46860155	A	G	46860155	3	3	260	1	0	0	0	0	1	0	0	0	3223	188	7	2	5548	2	CELSR1	22	46860155	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	155830	46860155	4444411	920	38165										
BRD1	23774	hgsc.bcm.edu	37	chr22	50181097	50181097	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cggagtctccgcatgtgctcCgcgaccttttccttggctgc	11	15	1	0	rs140147452		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr22:50181097C>A	ENST00000216267.8	-	7	2891	c.2405G>T	c.(2404-2406)cGg>cTg	p.R802L	BRD1_ENST00000404760.1_Missense_Mutation_p.R933L|BRD1_ENST00000404034.1_Missense_Mutation_p.R802L|BRD1_ENST00000457780.2_Nonsense_Mutation_p.G906*|BRD1_ENST00000342989.5_Missense_Mutation_p.R528L|BRD1_ENST00000542442.1_Missense_Mutation_p.R490L	NM_014577.1	NP_055392.1	O95696	BRD1_HUMAN	bromodomain containing 1	802					histone H3 acetylation (GO:0043966)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleus (GO:0005634)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(3)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	37		all_cancers(38;6.11e-10)|all_epithelial(38;8.06e-09)|all_lung(38;6.64e-05)|Lung NSC(38;0.0011)|Breast(42;0.00235)|Ovarian(80;0.0139)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0369)|BRCA - Breast invasive adenocarcinoma(115;0.21)		GCATGTGCTCCGCGACCTTTT	0.602																																					p.R802L		Atlas-SNP	.											BRD1_ENST00000342989,colon,carcinoma,-1,2	BRD1	144	.	0			c.G2405T						.						60	62	61					22																	50181097		2203	4300	6503	SO:0001583	missense	23774	exon7			GTGCTCCGCGACC	AF005067	CCDS14080.1	22q13.33	2008-07-01	2002-01-14		ENSG00000100425	ENSG00000100425			1102	protein-coding gene	gene with protein product	"BR140-like"	604589	"bromodomain-containing 1"			10591208, 10602503	Standard	NM_014577		Approved	BRL, BRPF2	uc003biv.3	O95696	OTTHUMG00000150288	ENST00000216267.8:c.2405G>T	chr22.hg19:g.50181097C>A	ENSP00000216267:p.Arg802Leu	81.0	0.0		59.0	4.0	NM_014577	A6ZJA4	Missense_Mutation	SNP	ENST00000216267.8	hg19	CCDS14080.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	40|40	8.169614|8.169614	0.98688|0.98688	.|.	.|.	ENSG00000100425|ENSG00000100425	ENST00000457780|ENST00000216267;ENST00000404034;ENST00000404760;ENST00000542442;ENST00000342989;ENST00000419212	.|T;T;T;T;T	.|0.34472	.|2.34;2.34;2.34;1.36;1.76	5.39|5.39	5.39|5.39	0.77823|0.77823	.|.	.|0.173334	.|0.49305	.|D	.|0.000153	.|T	.|0.53110	.|0.1776	L|L	0.58428|0.58428	1.81|1.81	0.80722|0.80722	A|A	1|1	.|D;D;D;D	.|0.63046	.|0.983;0.992;0.983;0.99	.|P;P;P;P	.|0.60236	.|0.746;0.846;0.629;0.871	.|T	.|0.40059	.|-0.9583	.|9	0.15952|0.23302	T|T	0.53|0.38	.|.	19.1506|19.1506	0.93487|0.93487	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|933;528;802;933	.|Q86X06;B7Z926;O95696;O95696-2	.|.;.;BRD1_HUMAN;.	X|L	906|802;802;933;490;528;393	.|ENSP00000216267:R802L;ENSP00000384076:R802L;ENSP00000385858:R933L;ENSP00000437514:R490L;ENSP00000345886:R528L	ENSP00000410042:G906X|ENSP00000216267:R802L	G|R	-|-	1|2	0|0	BRD1|BRD1	48567101|48567101	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	3.063000|3.063000	0.49978|0.49978	2.527000|2.527000	0.85204|0.85204	0.655000|0.655000	0.94253|0.94253	GGA|CGG	.	C|1.000;T|0.000		0.602	BRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317402.1	NM_014577		A	50181097	C	A	50181097	3	1	260	1	0	0	0	0	1	0	0	0	1503	652	23	1	795	1	BRD1	22	50181097	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	3320942	50181097	1123469	921	38166										
TYMP	1890	hgsc.bcm.edu	37	chr22	50966131	50966131	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gatacagcagcccgcctggtCcagcagcacttgcatctggt	11	14	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr22:50966131C>A	ENST00000252029.3	-	5	694	c.532G>T	c.(532-534)Gac>Tac	p.D178Y	SCO2_ENST00000252785.3_5'Flank|SCO2_ENST00000543927.1_5'Flank|TYMP_ENST00000395680.1_Missense_Mutation_p.D178Y|TYMP_ENST00000395678.3_Missense_Mutation_p.D178Y|SCO2_ENST00000395693.3_5'Flank|TYMP_ENST00000395681.1_Missense_Mutation_p.D178Y|CTA-384D8.36_ENST00000608319.1_RNA|SCO2_ENST00000535425.1_5'Flank	NM_001113755.2|NM_001113756.2|NM_001257988.1|NM_001257989.1|NM_001953.4	NP_001107227.1|NP_001107228.1|NP_001244917.1|NP_001244918.1|NP_001944.1	P19971	TYPH_HUMAN	thymidine phosphorylase	178					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|chemotaxis (GO:0006935)|DNA replication (GO:0006260)|mitochondrial genome maintenance (GO:0000002)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside salvage (GO:0043097)|pyrimidine nucleotide metabolic process (GO:0006220)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	phosphorylase activity (GO:0004645)|platelet-derived growth factor receptor binding (GO:0005161)|pyrimidine-nucleoside phosphorylase activity (GO:0016154)|thymidine phosphorylase activity (GO:0009032)|transferase activity, transferring pentosyl groups (GO:0016763)			large_intestine(1)|lung(2)|ovary(1)|prostate(1)	5		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;0.206)|LUAD - Lung adenocarcinoma(64;0.247)	Capecitabine(DB01101)|Cidofovir(DB00369)|Floxuridine(DB00322)|Fluorouracil(DB00544)|Trifluridine(DB00432)	CCCGCCTGGTCCAGCAGCACT	0.488																																					p.D178Y		Atlas-SNP	.											.	TYMP	25	.	0			c.G532T						.						78	77	77					22																	50966131		2203	4300	6503	SO:0001583	missense	1890	exon5			CCTGGTCCAGCAG	M63193	CCDS14096.1, CCDS58811.1	22q13	2014-09-17	2008-01-21	2008-01-21	ENSG00000025708	ENSG00000025708	2.4.2.4		3148	protein-coding gene	gene with protein product	"gliostatin"	131222	"endothelial cell growth factor 1 (platelet-derived)"	MNGIE, ECGF1		1590793, 11733540	Standard	NM_001113755		Approved		uc003bme.5	P19971	OTTHUMG00000150249	ENST00000252029.3:c.532G>T	chr22.hg19:g.50966131C>A	ENSP00000252029:p.Asp178Tyr	119.0	0.0		96.0	4.0	NM_001257989	A8MW15|H9KVA0|Q13390|Q8WVB7	Missense_Mutation	SNP	ENST00000252029.3	hg19	CCDS14096.1	.	.	.	.	.	.	.	.	.	.	C	8.105	0.777440	0.16120	.	.	ENSG00000025708	ENST00000395680;ENST00000395681;ENST00000252029;ENST00000395678;ENST00000425169	D;D;D;D;D	0.98512	-4.97;-4.97;-4.97;-4.97;-4.97	4.99	4.99	0.66335	Glycosyl transferase, family 3 (3);	0.791796	0.11523	N	0.555539	D	0.96275	0.8785	L	0.43923	1.385	0.24730	N	0.99309	B;B;B;B	0.30326	0.276;0.136;0.136;0.136	B;B;B;B	0.30105	0.111;0.059;0.059;0.059	D	0.93217	0.6605	10	0.87932	D	0	-10.8425	11.6426	0.51242	0.0:0.8204:0.1796:0.0	.	178;178;178;178	B4DVR2;B2RBL3;E5KRG5;P19971	.;.;.;TYPH_HUMAN	Y	178;178;178;178;145	ENSP00000379037:D178Y;ENSP00000379038:D178Y;ENSP00000252029:D178Y;ENSP00000379036:D178Y;ENSP00000395875:D145Y	ENSP00000252029:D178Y	D	-	1	0	TYMP	49312997	0.969000	0.33509	0.094000	0.20943	0.066000	0.16364	2.004000	0.40854	2.323000	0.78572	0.462000	0.41574	GAC	.	.		0.488	TYMP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317081.1	NM_001953		A	50966131	C	A	50966131	3	1	260	1	0	0	0	0	1	0	0	0	16826	855	30	3	940	3	TYMP	22	50966131	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	785034	50966131	338435	922	38167										
TYMP	1890	hgsc.bcm.edu	37	chr22	50968110	50968110	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	caccaggcgcgggtggggccCcggttcccggggtcatcaag	17	14	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr22:50968110C>A	ENST00000252029.3	-	2	191	c.29G>T	c.(28-30)gGg>gTg	p.G10V	TYMP_ENST00000395680.1_Missense_Mutation_p.G10V|TYMP_ENST00000395678.3_Missense_Mutation_p.G10V|TYMP_ENST00000395681.1_Missense_Mutation_p.G10V	NM_001113755.2|NM_001113756.2|NM_001257988.1|NM_001257989.1|NM_001953.4	NP_001107227.1|NP_001107228.1|NP_001244917.1|NP_001244918.1|NP_001944.1	P19971	TYPH_HUMAN	thymidine phosphorylase	10					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|chemotaxis (GO:0006935)|DNA replication (GO:0006260)|mitochondrial genome maintenance (GO:0000002)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside salvage (GO:0043097)|pyrimidine nucleotide metabolic process (GO:0006220)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	phosphorylase activity (GO:0004645)|platelet-derived growth factor receptor binding (GO:0005161)|pyrimidine-nucleoside phosphorylase activity (GO:0016154)|thymidine phosphorylase activity (GO:0009032)|transferase activity, transferring pentosyl groups (GO:0016763)			large_intestine(1)|lung(2)|ovary(1)|prostate(1)	5		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;0.206)|LUAD - Lung adenocarcinoma(64;0.247)	Capecitabine(DB01101)|Cidofovir(DB00369)|Floxuridine(DB00322)|Fluorouracil(DB00544)|Trifluridine(DB00432)	GGGTGGGGCCCCGGTTCCCGG	0.706																																					p.G10V		Atlas-SNP	.											.	TYMP	25	.	0			c.G29T						.						11	15	14					22																	50968110		2187	4288	6475	SO:0001583	missense	1890	exon2			GGGGCCCCGGTTC	M63193	CCDS14096.1, CCDS58811.1	22q13	2014-09-17	2008-01-21	2008-01-21	ENSG00000025708	ENSG00000025708	2.4.2.4		3148	protein-coding gene	gene with protein product	"gliostatin"	131222	"endothelial cell growth factor 1 (platelet-derived)"	MNGIE, ECGF1		1590793, 11733540	Standard	NM_001113755		Approved		uc003bme.5	P19971	OTTHUMG00000150249	ENST00000252029.3:c.29G>T	chr22.hg19:g.50968110C>A	ENSP00000252029:p.Gly10Val	174.0	0.0		99.0	4.0	NM_001257989	A8MW15|H9KVA0|Q13390|Q8WVB7	Missense_Mutation	SNP	ENST00000252029.3	hg19	CCDS14096.1	.	.	.	.	.	.	.	.	.	.	C	9.324	1.058845	0.19987	.	.	ENSG00000025708	ENST00000395680;ENST00000395681;ENST00000252029;ENST00000395678;ENST00000425169	D;D;D;D;D	0.97505	-4.41;-4.4;-4.41;-4.41;-4.37	3.51	-3.9	0.04181	.	.	.	.	.	D	0.88599	0.6480	N	0.08118	0	0.09310	N	1	B;B;B;B	0.11235	0.004;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.0;0.0	T	0.78971	-0.1993	9	0.87932	D	0	1.3718	0.9455	0.01365	0.2724:0.3466:0.2204:0.1605	.	10;10;10;10	B4DVR2;B2RBL3;E5KRG5;P19971	.;.;.;TYPH_HUMAN	V	10	ENSP00000379037:G10V;ENSP00000379038:G10V;ENSP00000252029:G10V;ENSP00000379036:G10V;ENSP00000395875:G10V	ENSP00000252029:G10V	G	-	2	0	TYMP	49314976	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.550000	0.00434	-0.221000	0.09973	-0.379000	0.06801	GGG	.	.		0.706	TYMP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317081.1	NM_001953		A	50968110	C	A	50968110	3	1	260	1	0	0	0	0	1	0	0	0	16826	623	22	3	1455	3	TYMP	22	50968110	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	1979	50968110	336456	923	38168										
CPT1B	1375	hgsc.bcm.edu	37	chr22	51011460	51011460	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tattctttccagagctaaagAaggcctggcgtgcctgcgcc	11	12	1	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr22:51011460A>G	ENST00000360719.2	-	11	1333	c.1196T>C	c.(1195-1197)tTc>tCc	p.F399S	CPT1B_ENST00000405237.3_Missense_Mutation_p.F399S|CPT1B_ENST00000440709.1_Intron|CPT1B_ENST00000457250.1_Missense_Mutation_p.F365S|CPT1B_ENST00000395650.2_Missense_Mutation_p.F399S|CHKB-CPT1B_ENST00000453634.1_3'UTR|CPT1B_ENST00000434492.2_Missense_Mutation_p.F196S|CPT1B_ENST00000312108.7_Missense_Mutation_p.F399S	NM_001145135.1|NM_152245.2	NP_001138607.1|NP_689451.1	Q92523	CPT1B_HUMAN	carnitine palmitoyltransferase 1B (muscle)	399					carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	carnitine O-palmitoyltransferase activity (GO:0004095)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22		all_cancers(38;8.8e-15)|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)		all cancers(3;3.56e-77)|OV - Ovarian serous cystadenocarcinoma(4;5.39e-74)|Epithelial(4;5.58e-70)|GBM - Glioblastoma multiforme(4;5.59e-08)|LUAD - Lung adenocarcinoma(64;0.0016)|Lung(4;0.00942)|BRCA - Breast invasive adenocarcinoma(115;0.207)		AGAGCTAAAGAAGGCCTGGCG	0.607																																					p.F399S	Esophageal Squamous(170;988 1933 25577 30295 48163)	Atlas-SNP	.											.	CPT1B	61	.	0			c.T1196C						.						47	45	45					22																	51011460		2203	4300	6503	SO:0001583	missense	1375	exon11			CTAAAGAAGGCCT	U62733	CCDS14098.1, CCDS46734.1	22q13.33	2007-07-26			ENSG00000205560	ENSG00000205560			2329	protein-coding gene	gene with protein product		601987				9070950	Standard	NM_152245		Approved	M-CPT1, CPT1-M	uc003bmm.3	Q92523	OTTHUMG00000137390	ENST00000360719.2:c.1196T>C	chr22.hg19:g.51011460A>G	ENSP00000353945:p.Phe399Ser	62.0	0.0		42.0	4.0	NM_001145135	B7Z4U4|B7Z5T8|E9PCP2|Q13389|Q99655|Q9BY90	Missense_Mutation	SNP	ENST00000360719.2	hg19	CCDS14098.1	.	.	.	.	.	.	.	.	.	.	A	15.40	2.823721	0.50739	.	.	ENSG00000205560	ENST00000405237;ENST00000312108;ENST00000360719;ENST00000457250;ENST00000434492;ENST00000395650	D;D;D;D;D;D	0.89552	-2.53;-2.53;-2.53;-2.53;-2.53;-2.53	4.98	2.69	0.31865	.	0.233858	0.45126	D	0.000392	D	0.90253	0.6952	M	0.83118	2.625	0.47621	D	0.999472	B;P;P	0.39131	0.293;0.661;0.661	B;P;B	0.45794	0.392;0.493;0.371	D	0.89351	0.3661	10	0.72032	D	0.01	-25.3512	8.4875	0.33080	0.6487:0.0:0.0:0.3513	.	365;196;399	B7Z4U4;A2RRE8;Q92523	.;.;CPT1B_HUMAN	S	399;399;399;365;196;399	ENSP00000385486:F399S;ENSP00000312189:F399S;ENSP00000353945:F399S;ENSP00000409342:F365S;ENSP00000410966:F196S;ENSP00000379011:F399S	ENSP00000312189:F399S	F	-	2	0	CPT1B	49358326	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	1.417000	0.34770	0.879000	0.35944	0.459000	0.35465	TTC	.	.		0.607	CPT1B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317264.5	NM_152246		G	51011460	A	G	51011460	3	3	260	1	0	0	0	0	1	0	0	0	3834	246	9	2	1158	2	CPT1B	22	51011460	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	43350	51011460	293106	924	38169										
ARSA	410	hgsc.bcm.edu	37	chr22	51063861	51063861	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gagctggaggcgtggcaggcAgggtctgcagtggtatcact	18	8	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chr22:51063861A>G	ENST00000547307.1	-	8	1641	c.1236T>C	c.(1234-1236)ccT>ccC	p.P412P	ARSA_ENST00000453344.2_Silent_p.P328P|ARSA_ENST00000610191.1_5'Flank|ARSA_ENST00000216124.5_Silent_p.P414P|ARSA_ENST00000395619.3_Silent_p.P414P|ARSA_ENST00000547805.1_Silent_p.P412P|ARSA_ENST00000356098.5_Silent_p.P414P|ARSA_ENST00000395621.3_Silent_p.P414P			P15289	ARSA_HUMAN	arylsulfatase A	412					autophagy (GO:0006914)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|central nervous system development (GO:0007417)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to methylmercury (GO:0051597)|response to nutrient (GO:0007584)|response to pH (GO:0009268)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum lumen (GO:0005788)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|cerebroside-sulfatase activity (GO:0004098)|sulfuric ester hydrolase activity (GO:0008484)			endometrium(1)|large_intestine(1)|lung(5)|pancreas(1)|skin(1)	9		all_cancers(38;8.8e-15)|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)	Micafungin(DB01141)|Suramin(DB04786)	CGTGGCAGGCAGGGTCTGCAG	0.647																																					p.P414P		Atlas-SNP	.											.	ARSA	19	.	0			c.T1242C						.						47	58	54					22																	51063861		2202	4295	6497	SO:0001819	synonymous_variant	410	exon9			GCAGGCAGGGTCT	X52150	CCDS14100.1, CCDS46736.1, CCDS14100.2	22q13.33	2013-09-19			ENSG00000100299	ENSG00000100299	3.1.6.8	"Arylsulfatase family"	713	protein-coding gene	gene with protein product	"metachromatic leucodystrophy"	607574				15772092	Standard	NM_000487		Approved		uc003bmz.5	P15289	OTTHUMG00000150180	ENST00000547307.1:c.1236T>C	chr22.hg19:g.51063861A>G		147.0	0.0		91.0	5.0	NM_001085426	B2RCA6|B7XD04|F8WCC8|Q6ICI5|Q96CJ0	Silent	SNP	ENST00000547307.1	hg19																																																																																				.	.		0.647	ARSA-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000487		G	51063861	A	G	51063861	2	3	260	1	0	0	0	0	0	0	0	1	987	175	7	2		2	ARSA	22	51063861	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	52401	51063861	240705	925	38170										
P2RY8	286530	hgsc.bcm.edu	37	chrX	1585322	1585322	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccggcacagcacccacagagAgaagaggttgcccgggatgc	14	13	0	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chrX:1585322A>G	ENST00000381297.4	-	2	340	c.130T>C	c.(130-132)Tct>Cct	p.S44P	P2RY8_ENST00000460672.1_5'Flank	NM_178129.4	NP_835230.1	Q86VZ1	P2RY8_HUMAN	purinergic receptor P2Y, G-protein coupled, 8	44						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|lung(13)|prostate(1)	23		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				ACCCACAGAGAGAAGAGGTTG	0.667			T	CRLF2	"B-ALL, Downs associated ALL"																																p.S44P		Atlas-SNP	.		Dom	yes		"X,Y"	Xp22.3; Yp11.3	286530	"purinergic receptor P2Y, G-protein coupled, 8"		L	.	P2RY8	53	.	0			c.T130C						.						49	50	50					X																	1585322		2203	4296	6499	SO:0001583	missense	286530	exon2			ACAGAGAGAAGAG	AA804531	CCDS14115.1	Xp22.33 and Yp11.3	2012-08-08			ENSG00000182162	ENSG00000182162		"Pseudoautosomal regions / PAR1", "Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	15524	protein-coding gene	gene with protein product		300525				11004484	Standard	NM_178129		Approved	P2Y8	uc004cpz.2	Q86VZ1	OTTHUMG00000021060	ENST00000381297.4:c.130T>C	chrX.hg19:g.1585322A>G	ENSP00000370697:p.Ser44Pro	94.0	0.0		100.0	4.0	NM_178129		Missense_Mutation	SNP	ENST00000381297.4	hg19	CCDS14115.1	.	.	.	.	.	.	.	.	.	.	a	11.50	1.658548	0.29515	.	.	ENSG00000182162	ENST00000381297	T	0.71817	-0.6	2.1	2.1	0.27182	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	U	0.000001	T	0.80691	0.4671	M	0.74881	2.28	0.19300	N	0.99998	D	0.89917	1.0	D	0.81914	0.995	T	0.70539	-0.4844	10	0.72032	D	0.01	.	9.6627	0.39965	1.0:0.0:0.0:0.0	.	44	Q86VZ1	P2RY8_HUMAN	P	44	ENSP00000370697:S44P	ENSP00000370697:S44P	S	-	1	0	P2RY8	1545322	1.000000	0.71417	0.059000	0.19551	0.016000	0.09150	5.199000	0.65152	0.528000	0.28580	0.230000	0.17803	TCT	.	.		0.667	P2RY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055602.1	NM_178129		G	1585322	A	G	1585322	3	3	260	1	0	0	0	0	1	0	0	0	11364	304	11	2	953	2	P2RY8	23	1585322	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10		1585322	153685238	926	38171										
ARSD	414	hgsc.bcm.edu	37	chrX	2825611	2825611	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gcagacgcctcggccgtagcAggcccccgctccctcggggt	14	18	0	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chrX:2825611A>G	ENST00000381154.1	-	10	1558	c.1483T>C	c.(1483-1485)Tgc>Cgc	p.C495R	ARSD-AS1_ENST00000414053.1_RNA	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D	495					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			large_intestine(3)|lung(3)	6		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				CGGCCGTAGCAGGCCCCCGCT	0.647																																					p.C495R		Atlas-SNP	.											.	ARSD	47	.	0			c.T1483C						.						13	14	14					X																	2825611		2180	4257	6437	SO:0001583	missense	414	exon10			CGTAGCAGGCCCC	X83572	CCDS35196.1	Xp22.3	2013-02-14			ENSG00000006756	ENSG00000006756		"Arylsulfatase family"	717	protein-coding gene	gene with protein product		300002				7720070	Standard	NM_001669		Approved		uc004cqy.3	P51689	OTTHUMG00000021077	ENST00000381154.1:c.1483T>C	chrX.hg19:g.2825611A>G	ENSP00000370546:p.Cys495Arg	73.0	0.0		99.0	5.0	NM_001669	Q9UHJ8	Missense_Mutation	SNP	ENST00000381154.1	hg19	CCDS35196.1	.	.	.	.	.	.	.	.	.	.	a	12.82	2.052932	0.36181	.	.	ENSG00000006756	ENST00000381154;ENST00000458014	D;D	0.91407	-2.84;-2.84	3.03	3.03	0.35002	Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	U	0.000000	D	0.96188	0.8757	H	0.95224	3.64	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96008	0.8999	10	0.87932	D	0	.	10.7922	0.46440	1.0:0.0:0.0:0.0	.	495	P51689	ARSD_HUMAN	R	495;97	ENSP00000370546:C495R;ENSP00000409180:C97R	ENSP00000370546:C495R	C	-	1	0	ARSD	2835611	1.000000	0.71417	0.153000	0.22517	0.058000	0.15608	7.550000	0.82173	0.951000	0.37770	0.424000	0.28305	TGC	.	.		0.647	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1			G	2825611	A	G	2825611	3	3	260	1	0	0	0	0	1	0	0	0	989	188	7	2	302	2	ARSD	23	2825611	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1240289	2825611	152444949	927	38172										
AMELX	265	hgsc.bcm.edu	37	chrX	11316394	11316394	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tggtaccagagcataaggccAccggtatgtagacattttgt	11	8	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chrX:11316394A>G	ENST00000380714.3	+	4	209	c.141A>G	c.(139-141)ccA>ccG	p.P47P	ARHGAP6_ENST00000380732.3_Intron|ARHGAP6_ENST00000380736.1_Intron|AMELX_ENST00000380712.3_Silent_p.P61P|ARHGAP6_ENST00000337414.4_Intron|AMELX_ENST00000348912.4_Silent_p.P31P|ARHGAP6_ENST00000380718.1_Intron|ARHGAP6_ENST00000413512.3_Intron	NM_001142.2	NP_001133.1	Q99217	AMELX_HUMAN	amelogenin, X-linked	47					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|chondrocyte differentiation (GO:0002062)|enamel mineralization (GO:0070166)|epithelial to mesenchymal transition (GO:0001837)|ion homeostasis (GO:0050801)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of tooth mineralization (GO:0070172)|signal transduction (GO:0007165)|tooth mineralization (GO:0034505)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	growth factor activity (GO:0008083)|hydroxyapatite binding (GO:0046848)|identical protein binding (GO:0042802)|structural constituent of tooth enamel (GO:0030345)			endometrium(3)|kidney(2)|large_intestine(1)|lung(9)	15						GCATAAGGCCACCGGTATGTA	0.348																																					p.P61P		Atlas-SNP	.											.	AMELX	31	.	0			c.A183G						.						191	191	191					X																	11316394		2203	4300	6503	SO:0001819	synonymous_variant	265	exon5			AAGGCCACCGGTA		CCDS14144.1, CCDS14145.1, CCDS14146.1	Xp22.31-p22.1	2010-04-20	2010-04-20		ENSG00000125363	ENSG00000125363			461	protein-coding gene	gene with protein product	"amelogenesis imperfecta 1"	300391	"amelogenin (X chromosome, amelogenesis imperfecta 1)"	AMG, AIH1		1734713	Standard	NM_182680		Approved		uc004cus.3	Q99217	OTTHUMG00000021130	ENST00000380714.3:c.141A>G	chrX.hg19:g.11316394A>G		103.0	0.0		77.0	4.0	NM_182680	Q96NW6|Q9UCA7	Silent	SNP	ENST00000380714.3	hg19	CCDS14144.1																																																																																			.	.		0.348	AMELX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055746.1	NM_001142		G	11316394	A	G	11316394	2	3	260	1	0	0	0	0	0	0	0	1	569	146	6	2		2	AMELX	23	11316394	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	8490783	11316394	143954166	928	38173										
PCYT1B	9468	hgsc.bcm.edu	37	chrX	24605380	24605380	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gcttcctttatgtgcttgtaAacatcatcagagccagcaga	8	10	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chrX:24605380A>G	ENST00000379144.2	-	5	673	c.543T>C	c.(541-543)gtT>gtC	p.V181V	PCYT1B_ENST00000356768.4_Silent_p.V181V|PCYT1B_ENST00000379145.1_Silent_p.V163V	NM_004845.4	NP_004836.2	Q9Y5K3	PCY1B_HUMAN	phosphate cytidylyltransferase 1, choline, beta	181					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|ovarian follicle development (GO:0001541)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)	choline-phosphate cytidylyltransferase activity (GO:0004105)			breast(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)	17					Choline(DB00122)	TGTGCTTGTAAACATCATCAG	0.473																																					p.V181V		Atlas-SNP	.											.	PCYT1B	88	.	0			c.T543C						.						161	109	127					X																	24605380		2203	4300	6503	SO:0001819	synonymous_variant	9468	exon5			CTTGTAAACATCA	AF052510	CCDS14213.1, CCDS55391.1, CCDS55392.1	Xp22	2008-02-05	2005-09-05		ENSG00000102230	ENSG00000102230	2.7.7.15		8755	protein-coding gene	gene with protein product		604926	"phosphate cytidylyltransferase 1, choline, beta isoform"			9593753	Standard	NM_004845		Approved	CCT-beta, CTB	uc004dbi.3	Q9Y5K3	OTTHUMG00000021270	ENST00000379144.2:c.543T>C	chrX.hg19:g.24605380A>G		101.0	0.0		90.0	4.0	NM_004845	A8IX00|B2RCX8|B4DK10|E9PD84|O60621|Q86XC9	Silent	SNP	ENST00000379144.2	hg19	CCDS14213.1																																																																																			.	.		0.473	PCYT1B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056103.1	NM_004845		G	24605380	A	G	24605380	2	3	260	1	0	0	0	0	0	0	0	1	11620	1	1	2		2	PCYT1B	23	24605380	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	13288986	24605380	130665180	929	38174										
DMD	1756	hgsc.bcm.edu	37	chrX	32509552	32509552	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	atactccagccagttaagtcTctcacttagcaactggcaga	7	12	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chrX:32509552T>C	ENST00000357033.4	-	20	2670	c.2464A>G	c.(2464-2466)Aga>Gga	p.R822G	DMD_ENST00000378677.2_Missense_Mutation_p.R818G	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	822					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				CAGTTAAGTCTCTCACTTAGC	0.403																																					p.R822G		Atlas-SNP	.											.	DMD	2127	.	0			c.A2464G						.						104	81	89					X																	32509552		2202	4300	6502	SO:0001583	missense	1756	exon20			TAAGTCTCTCACT	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.2464A>G	chrX.hg19:g.32509552T>C	ENSP00000354923:p.Arg822Gly	89.0	0.0		84.0	4.0	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	hg19	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	T	18.75	3.691215	0.68271	.	.	ENSG00000198947	ENST00000534884;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280	T;T	0.61392	0.11;0.11	4.84	4.84	0.62591	.	0.000000	0.40554	U	0.001063	T	0.71702	0.3371	M	0.68317	2.08	0.80722	D	1	D;D;D	0.62365	0.989;0.984;0.991	D;P;D	0.76071	0.978;0.867;0.987	T	0.69525	-0.5122	10	0.25751	T	0.34	.	13.8307	0.63380	0.0:0.0:0.0:1.0	.	814;822;818	P11532-4;P11532;E9PDN5	.;DMD_HUMAN;.	G	814;818;822;822;699	ENSP00000367948:R818G;ENSP00000354923:R822G	ENSP00000354923:R822G	R	-	1	2	DMD	32419473	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.789000	0.69029	1.710000	0.51325	0.350000	0.21858	AGA	.	.		0.403	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		C	32509552	T	C	32509552	3	2	260	1	0	0	0	0	1	0	0	0	4582	1559	54	2	9076	2	DMD	23	32509552	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	7904172	32509552	122761008	930	38175										
USP11	8237	hgsc.bcm.edu	37	chrX	47098823	47098823	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ctgctcccagcagctgcttgGcattacctggtcagctggta	11	13	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chrX:47098823G>A	ENST00000218348.3	+	3	489	c.489G>A	c.(487-489)tgG>tgA	p.W163*	USP11_ENST00000377107.2_Nonsense_Mutation_p.W120*	NM_004651.3	NP_004642.2	P51784	UBP11_HUMAN	ubiquitin specific peptidase 11	163	DUSP. {ECO:0000255|PROSITE- ProRule:PRU00613}.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|ovary(3)|pancreas(1)|stomach(1)	40						CAGCTGCTTGGCATTACCTGG	0.582																																					p.W163X		Atlas-SNP	.											.	USP11	93	.	0			c.G489A						.						61	50	54					X																	47098823		2203	4300	6503	SO:0001587	stop_gained	8237	exon3			TGCTTGGCATTAC	U44839	CCDS14277.1	Xp11.23	2008-02-05	2005-08-08		ENSG00000102226	ENSG00000102226		"Ubiquitin-specific peptidases"	12609	protein-coding gene	gene with protein product		300050	"ubiquitin specific protease 11"			12838346	Standard	XM_005272674		Approved	UHX1	uc004dhp.3	P51784	OTTHUMG00000021437	ENST00000218348.3:c.489G>A	chrX.hg19:g.47098823G>A	ENSP00000218348:p.Trp163*	61.0	0.0		90.0	4.0	NM_004651	B2RTX1|Q8IUG6|Q9BWE1	Nonsense_Mutation	SNP	ENST00000218348.3	hg19	CCDS14277.1	.	.	.	.	.	.	.	.	.	.	g	36	5.765725	0.96906	.	.	ENSG00000102226	ENST00000377107;ENST00000218348	.	.	.	5.84	4.97	0.65823	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.812	12.8433	0.57815	0.0815:0.0:0.9185:0.0	.	.	.	.	X	120;163	.	ENSP00000218348:W163X	W	+	3	0	USP11	46983767	1.000000	0.71417	0.994000	0.49952	0.983000	0.72400	7.048000	0.76606	1.216000	0.43427	0.597000	0.82753	TGG	.	.		0.582	USP11-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_004651		A	47098823	G	A	47098823	4	1	260	1	0	0	0	0	0	1	0	0	17057	1212	42	3	499	3	USP11	23	47098823	Nonsense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	14589271	47098823	108171737	931	38176										
ARAF	369	hgsc.bcm.edu	37	chrX	47426698	47426698	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtgaggtgcagctgctgaagAggatcgggacgggctcgttt	18	7	0	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chrX:47426698A>G	ENST00000377045.4	+	10	1137	c.943A>G	c.(943-945)Agg>Ggg	p.R315G	ARAF_ENST00000290277.6_3'UTR	NM_001256196.1|NM_001654.4	NP_001243125.1|NP_001645.1	P10398	ARAF_HUMAN	A-Raf proto-oncogene, serine/threonine kinase	315	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular protein modification process (GO:0006464)|negative regulation of apoptotic process (GO:0043066)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|regulation of TOR signaling (GO:0032006)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)			biliary_tract(1)|endometrium(4)|large_intestine(7)|liver(2)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	29					Adenosine triphosphate(DB00171)	GCTGCTGAAGAGGATCGGGAC	0.622																																					p.R318G		Atlas-SNP	.											.	ARAF	67	.	0			c.A952G						.						96	66	76					X																	47426698		2203	4300	6503	SO:0001583	missense	369	exon10			CTGAAGAGGATCG	X04790	CCDS35232.1, CCDS59164.1, CCDS75970.1	Xp11.3-p11.23	2014-06-26	2014-06-26	2005-01-19	ENSG00000078061	ENSG00000078061			646	protein-coding gene	gene with protein product		311010	"v-raf murine sarcoma 3611 viral oncogene homolog 1"	ARAF1			Standard	NM_001654		Approved		uc004dic.2	P10398	OTTHUMG00000021446	ENST00000377045.4:c.943A>G	chrX.hg19:g.47426698A>G	ENSP00000366244:p.Arg315Gly	116.0	0.0		125.0	5.0	NM_001256196	P07557|Q5H9B2|Q5H9B3	Missense_Mutation	SNP	ENST00000377045.4	hg19	CCDS35232.1	.	.	.	.	.	.	.	.	.	.	A	19.08	3.758836	0.69763	.	.	ENSG00000078061	ENST00000377045	T	0.62639	0.01	5.71	3.12	0.35913	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.71651	0.3365	L	0.58510	1.815	0.80722	D	1	D;B	0.89917	1.0;0.359	D;B	0.71870	0.975;0.216	T	0.74103	-0.3773	10	0.87932	D	0	.	9.8988	0.41335	0.6478:0.3522:0.0:0.0	.	315;181	P10398;B4DV85	ARAF_HUMAN;.	G	315	ENSP00000366244:R315G	ENSP00000366244:R315G	R	+	1	2	ARAF	47311642	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	1.626000	0.37039	1.905000	0.55150	0.345000	0.21793	AGG	.	.		0.622	ARAF-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056418.1			G	47426698	A	G	47426698	3	3	260	1	0	0	0	0	1	0	0	0	837	295	11	2	977	2	ARAF	23	47426698	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	327875	47426698	107843862	932	38177										
SYN1	6853	hgsc.bcm.edu	37	chrX	47434132	47434132	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cgggggccctgcgggctgctGggaggtctggcggcccaagg	21	12	1	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chrX:47434132G>A	ENST00000295987.7	-	11	1472	c.1348C>T	c.(1348-1350)Cag>Tag	p.Q450*	SYN1_ENST00000340666.4_Nonsense_Mutation_p.Q450*	NM_006950.3	NP_008881.2	P17600	SYN1_HUMAN	synapsin I	450	D; Pro-rich linker.				neurotransmitter secretion (GO:0007269)|regulation of neurotransmitter secretion (GO:0046928)|regulation of synaptic vesicle exocytosis (GO:2000300)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|protein kinase binding (GO:0019901)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(6)|lung(6)|ovary(1)	21						GCGGGCTGCTGGGAGGTCTGG	0.672																																					p.Q450X		Atlas-SNP	.											.	SYN1	84	.	0			c.C1348T						.						5	7	6					X																	47434132		2050	4054	6104	SO:0001587	stop_gained	6853	exon11			GCTGCTGGGAGGT		CCDS14280.1, CCDS35233.1	Xp11.2	2012-10-02			ENSG00000008056	ENSG00000008056			11494	protein-coding gene	gene with protein product		313440					Standard	NM_133499		Approved		uc004die.3	P17600	OTTHUMG00000021454	ENST00000295987.7:c.1348C>T	chrX.hg19:g.47434132G>A	ENSP00000295987:p.Gln450*	71.0	0.0		64.0	4.0	NM_006950	B1AJQ1|O75825|Q5H9A9	Nonsense_Mutation	SNP	ENST00000295987.7	hg19	CCDS14280.1	.	.	.	.	.	.	.	.	.	.	G	37	6.107674	0.97291	.	.	ENSG00000008056	ENST00000295987;ENST00000340666	.	.	.	4.64	4.64	0.57946	.	0.374286	0.20871	N	0.084179	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08837	T	0.75	-8.5999	10.6076	0.45402	0.0:0.1917:0.8083:0.0	.	.	.	.	X	450	.	ENSP00000295987:Q450X	Q	-	1	0	SYN1	47319076	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	1.869000	0.39519	2.257000	0.74773	0.529000	0.55759	CAG	.	.		0.672	SYN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056445.1	NM_006950		A	47434132	G	A	47434132	4	1	260	1	0	0	0	0	0	1	0	0	15455	1357	47	3	781	3	SYN1	23	47434132	Nonsense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	7434	47434132	107836428	933	38178										
GATA1	2623	hgsc.bcm.edu	37	chrX	48650745	48650745	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	accagaggccagggagtgtgTgaactgcggagcaacagcca	15	10	0	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chrX:48650745T>C	ENST00000376670.3	+	4	725	c.614T>C	c.(613-615)gTg>gCg	p.V205A	GATA1_ENST00000376665.3_Missense_Mutation_p.V205A	NM_002049.3	NP_002040.1	P15976	GATA1_HUMAN	GATA binding protein 1 (globin transcription factor 1)	205	Required for interaction with ZFPM1.		V -> M (in XDAT; severe impairment of ZFPM1 binding and erythroid differentiation in vitro). {ECO:0000269|PubMed:10700180}.		basophil differentiation (GO:0030221)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cellular response to thyroid hormone stimulus (GO:0097067)|dendritic cell differentiation (GO:0097028)|embryonic hemopoiesis (GO:0035162)|eosinophil differentiation (GO:0030222)|eosinophil fate commitment (GO:0035854)|erythrocyte development (GO:0048821)|erythrocyte differentiation (GO:0030218)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|megakaryocyte differentiation (GO:0030219)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of definitive erythrocyte differentiation (GO:0010724)|regulation of glycoprotein biosynthetic process (GO:0010559)|transcription from RNA polymerase II promoter (GO:0006366)|transcriptional activation by promoter-enhancer looping (GO:0071733)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	C2H2 zinc finger domain binding (GO:0070742)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|enhancer sequence-specific DNA binding (GO:0001158)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(259)|large_intestine(8)|lung(9)|prostate(1)	283						AGGGAGTGTGTGAACTGCGGA	0.597			"Mis, F"		megakaryoblastic leukemia of Downs Syndrome																																p.V205A	Pancreas(9;429 505 11287 29617)	Atlas-SNP	.		Dom	yes		X	Xp11.23	2623	GATA binding protein 1 (globin transcription factor 1)		L	.	GATA1	342	.	0			c.T614C						.						55	46	49					X																	48650745		2203	4299	6502	SO:0001583	missense	2623	exon4			AGTGTGTGAACTG	X17254	CCDS14305.1	Xp11.23	2014-09-17	2001-11-28		ENSG00000102145	ENSG00000102145		"GATA zinc finger domain containing"	4170	protein-coding gene	gene with protein product	"nuclear factor, erythroid 1"	305371	"GATA-binding protein 1 (globin transcription factor 1)"	GF1		1999341	Standard	NM_002049		Approved	ERYF1, NFE1, GATA-1, NF-E1	uc004dkq.4	P15976	OTTHUMG00000021504	ENST00000376670.3:c.614T>C	chrX.hg19:g.48650745T>C	ENSP00000365858:p.Val205Ala	113.0	0.0		113.0	5.0	NM_002049	Q96GB8	Missense_Mutation	SNP	ENST00000376670.3	hg19	CCDS14305.1	.	.	.	.	.	.	.	.	.	.	T	19.89	3.911362	0.72983	.	.	ENSG00000102145	ENST00000376670;ENST00000376665	D;D	0.99445	-5.91;-5.91	4.8	3.6	0.41247	Zinc finger, NHR/GATA-type (1);Zinc finger, GATA-type (5);	0.135916	0.48767	D	0.000178	D	0.97711	0.9249	N	0.05012	-0.13	0.54753	D	0.999987	B	0.33379	0.41	P	0.47528	0.549	D	0.95772	0.8809	10	0.87932	D	0	-2.6325	9.0396	0.36309	0.0:0.0:0.1839:0.8161	.	205	P15976	GATA1_HUMAN	A	205	ENSP00000365858:V205A;ENSP00000365853:V205A	ENSP00000365853:V205A	V	+	2	0	GATA1	48535689	1.000000	0.71417	0.977000	0.42913	0.911000	0.54048	6.101000	0.71479	0.504000	0.28082	0.400000	0.26472	GTG	.	.		0.597	GATA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056517.1	NM_002049		C	48650745	T	C	48650745	3	2	260	1	0	0	0	0	1	0	0	0	6261	1696	59	2	624	2	GATA1	23	48650745	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1216613	48650745	106619815	934	38179										
TFE3	7030	hgsc.bcm.edu	37	chrX	48896668	48896668	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggcacctgagcagggggtggAcggctcaatgtgtggccccc	17	12	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chrX:48896668A>G	ENST00000315869.7	-	3	757	c.498T>C	c.(496-498)cgT>cgC	p.R166R	TFE3_ENST00000487451.1_5'UTR	NM_006521.4	NP_006512.2	P19532	TFE3_HUMAN	transcription factor binding to IGHM enhancer 3	166					humoral immune response (GO:0006959)|positive regulation of cell adhesion (GO:0045785)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of osteoclast differentiation (GO:0045670)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)		NONO/TFE3(2)|PRCC/TFE3(25)|SFPQ/TFE3(6)|CLTC/TFE3(2)|ASPSCR1/TFE3(167)	central_nervous_system(1)	1						CAGGGGGTGGACGGCTCAATG	0.657			T	"SFPQ, ASPSCR1, PRCC, NONO, CLTC"	"papillary renal, alveolar soft part sarcoma, renal"																																p.R166R		Atlas-SNP	.		Dom	yes		X	Xp11.22	7030	transcription factor binding to IGHM enhancer 3		E	.	TFE3	93	.	0			c.T498C						.						27	29	28					X																	48896668		2201	4300	6501	SO:0001819	synonymous_variant	7030	exon3			GGGTGGACGGCTC	X96717	CCDS14315.3	Xp11.22	2013-05-21			ENSG00000068323	ENSG00000068323		"Basic helix-loop-helix proteins"	11752	protein-coding gene	gene with protein product	transcription factor E family, member A	314310				1672758, 1685140	Standard	NM_006521		Approved	TFEA, bHLHe33	uc004dmb.3	P19532	OTTHUMG00000022690	ENST00000315869.7:c.498T>C	chrX.hg19:g.48896668A>G		181.0	0.0		147.0	6.0	NM_006521	A8MZL6|Q5JU74|Q92757|Q92758|Q99964	Silent	SNP	ENST00000315869.7	hg19	CCDS14315.3																																																																																			.	.		0.657	TFE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058872.2	NM_006521		G	48896668	A	G	48896668	2	3	260	1	0	0	0	0	0	0	0	1	15815	262	10	2		2	TFE3	23	48896668	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	245923	48896668	106373892	935	38180										
CACNA1F	778	hgsc.bcm.edu	37	chrX	49061725	49061725	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtcactggcagcattgtccaTctcatccagcgtcaggcgac	10	14	3	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chrX:49061725T>C	ENST00000376265.2	-	48	5867	c.5806A>G	c.(5806-5808)Atg>Gtg	p.M1936V	SYP-AS1_ENST00000433499.1_RNA|CACNA1F_ENST00000323022.5_Missense_Mutation_p.M1925V|CACNA1F_ENST00000376251.1_Missense_Mutation_p.M1871V|AF196779.1_ENST00000583131.1_RNA	NM_005183.2	NP_005174.2	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type, alpha 1F subunit	1936					axonogenesis (GO:0007409)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|dendrite morphogenesis (GO:0048813)|detection of light stimulus involved in visual perception (GO:0050908)|membrane depolarization during action potential (GO:0086010)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|perikaryon (GO:0043204)|photoreceptor outer segment (GO:0001750)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			autonomic_ganglia(1)|breast(8)|central_nervous_system(3)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(4)|urinary_tract(1)	85					Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	GCATTGTCCATCTCATCCAGC	0.587																																					p.M1936V		Atlas-SNP	.											.	CACNA1F	218	.	0			c.A5806G						.						96	56	70					X																	49061725		2203	4300	6503	SO:0001583	missense	778	exon48			TGTCCATCTCATC	AA019975	CCDS35253.1, CCDS59166.1, CCDS59167.1	Xp11.23	2013-01-23	2007-02-16		ENSG00000102001	ENSG00000102001		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1393	protein-coding gene	gene with protein product		300110	"Aland island eye disease (Forsius-Eriksson ocular albinism, ocular albinism type 2)"	CSNB2, AIED		9344658, 9662400, 16382099, 12111638, 17525176	Standard	NM_005183		Approved	Cav1.4, JM8, JMC8, CSNBX2, CORDX3, CSNB2A, OA2	uc010nip.3	O60840	OTTHUMG00000022703	ENST00000376265.2:c.5806A>G	chrX.hg19:g.49061725T>C	ENSP00000365441:p.Met1936Val	90.0	0.0		88.0	5.0	NM_005183	A6NI29|F5CIQ9|O43901|O95226|Q9UHB1	Missense_Mutation	SNP	ENST00000376265.2	hg19	CCDS35253.1	.	.	.	.	.	.	.	.	.	.	T	15.22	2.768170	0.49680	.	.	ENSG00000102001	ENST00000376251;ENST00000323022;ENST00000376265	T;T;T	0.68025	-0.3;-0.3;-0.3	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	T	0.79269	0.4417	M	0.76170	2.325	0.50171	D	0.999852	D;D	0.58268	0.982;0.969	D;D	0.68943	0.961;0.914	T	0.78615	-0.2135	10	0.34782	T	0.22	.	13.0076	0.58715	0.0:0.0:0.0:1.0	.	1925;1936	F5CIQ9;O60840	.;CAC1F_HUMAN	V	1871;1925;1936	ENSP00000365427:M1871V;ENSP00000321618:M1925V;ENSP00000365441:M1936V	ENSP00000321618:M1925V	M	-	1	0	CACNA1F	48948669	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	4.837000	0.62796	1.780000	0.52325	0.430000	0.28490	ATG	.	.		0.587	CACNA1F-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358157.1	NM_005183		C	49061725	T	C	49061725	3	2	260	1	0	0	0	0	1	0	0	0	2545	1435	50	2	131	2	CACNA1F	23	49061725	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	165057	49061725	106208835	936	38181										
TSPYL2	64061	hgsc.bcm.edu	37	chrX	53114011	53114011	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	actaacccctacttcacaaaCatggtgattgtcaaggagtt	7	10	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chrX:53114011C>T	ENST00000375442.4	+	3	1092	c.960C>T	c.(958-960)aaC>aaT	p.N320N		NM_022117.3	NP_071400.1	Q9H2G4	TSYL2_HUMAN	TSPY-like 2	320					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell cycle (GO:0007049)|cellular protein metabolic process (GO:0044267)|chromatin modification (GO:0016568)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA replication (GO:0008156)|nucleosome assembly (GO:0006334)|regulation of protein kinase activity (GO:0045859)|regulation of signal transduction (GO:0009966)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	rDNA binding (GO:0000182)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(1)	19						ACTTCACAAACATGGTGATTG	0.498																																					p.N320N		Atlas-SNP	.											.	TSPYL2	53	.	0			c.C960T						.						122	97	106					X																	53114011		2203	4300	6503	SO:0001819	synonymous_variant	64061	exon3			CACAAACATGGTG	AF273046	CCDS14350.1	Xp11	2014-06-09			ENSG00000184205	ENSG00000184205			24358	protein-coding gene	gene with protein product		300564				11318608, 11395479	Standard	NM_022117		Approved	SE20-4, HRIHFB2216, CTCL, DENTT, CDA1, CINAP, TSPX	uc004drw.3	Q9H2G4	OTTHUMG00000021597	ENST00000375442.4:c.960C>T	chrX.hg19:g.53114011C>T		128.0	0.0		91.0	4.0	NM_022117	O94799|Q96DG7|Q9BZW6	Silent	SNP	ENST00000375442.4	hg19	CCDS14350.1																																																																																			.	.		0.498	TSPYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056718.1	NM_022117		T	53114011	C	T	53114011	2	4	260	1	0	0	0	0	0	0	0	1	16675	477	17	3		3	TSPYL2	23	53114011	Silent	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	4052286	53114011	102156549	937	38182										
ARHGEF9	23229	hgsc.bcm.edu	37	chrX	62917040	62917040	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gggtcctatctcgctgaggtGggggtcatcattgttatact	13	8	3	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chrX:62917040G>T	ENST00000253401.6	-	4	1326	c.526C>A	c.(526-528)Cac>Aac	p.H176N	ARHGEF9_ENST00000437457.2_Missense_Mutation_p.H123N|ARHGEF9_ENST00000495564.1_5'UTR|ARHGEF9_ENST00000374872.1_Missense_Mutation_p.H155N|ARHGEF9_ENST00000374870.4_Missense_Mutation_p.H74N|ARHGEF9_ENST00000374878.1_Missense_Mutation_p.H174N	NM_015185.2	NP_056000.1	O43307	ARHG9_HUMAN	Cdc42 guanine nucleotide exchange factor (GEF) 9	176	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|ion transmembrane transport (GO:0034220)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(14)|ovary(5)|pancreas(1)|skin(1)	35						TCGCTGAGGTGGGGGTCATCA	0.453																																					p.H176N		Atlas-SNP	.											.	ARHGEF9	117	.	0			c.C526A						.						131	94	106					X																	62917040		2203	4300	6503	SO:0001583	missense	23229	exon4			TGAGGTGGGGGTC	AB007884	CCDS35315.1, CCDS55429.1, CCDS55430.1	Xq11.1	2013-01-10			ENSG00000131089	ENSG00000131089		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	14561	protein-coding gene	gene with protein product	"collybistin"	300429				10559246, 9455477	Standard	NM_015185		Approved	KIAA0424, PEM-2	uc011mot.2	O43307	OTTHUMG00000021700	ENST00000253401.6:c.526C>A	chrX.hg19:g.62917040G>T	ENSP00000253401:p.His176Asn	117.0	0.0		129.0	6.0	NM_015185	A8K1S8|B4DHC7|F8W7P8|Q5JSL6	Missense_Mutation	SNP	ENST00000253401.6	hg19	CCDS35315.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.718849	0.89205	.	.	ENSG00000131089	ENST00000253401;ENST00000374878;ENST00000437457;ENST00000374870;ENST00000374872	T;T;T;T;T	0.62364	0.03;0.03;0.03;0.03;0.03	5.65	5.65	0.86999	Dbl homology (DH) domain (5);	0.000000	0.85682	D	0.000000	T	0.70692	0.3253	L	0.48362	1.52	0.80722	D	1	D;P;D;D	0.55172	0.97;0.916;0.97;0.97	P;P;P;P	0.58331	0.837;0.837;0.837;0.837	T	0.69702	-0.5074	10	0.41790	T	0.15	.	17.1464	0.86767	0.0:0.0:1.0:0.0	.	123;174;176;176	B4DHC7;B1AMR4;O43307;A8K1S8	.;.;ARHG9_HUMAN;.	N	176;174;123;74;155	ENSP00000253401:H176N;ENSP00000364012:H174N;ENSP00000399994:H123N;ENSP00000364004:H74N;ENSP00000364006:H155N	ENSP00000253401:H176N	H	-	1	0	ARHGEF9	62833765	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	9.229000	0.95273	2.364000	0.80123	0.513000	0.50165	CAC	.	.		0.453	ARHGEF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056937.1			T	62917040	G	T	62917040	3	4	260	1	0	0	0	0	1	0	0	0	912	1348	47	3	1052	3	ARHGEF9	23	62917040	Missense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	9803029	62917040	92353520	938	38183										
STARD8	9754	hgsc.bcm.edu	37	chrX	67938076	67938076	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtcaaatgccaagctgaggcTctcagccagatggaggttcc	12	11	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chrX:67938076T>C	ENST00000252336.6	+	5	1452	c.1080T>C	c.(1078-1080)gcT>gcC	p.A360A	STARD8_ENST00000374597.3_Silent_p.A360A|STARD8_ENST00000374599.3_Silent_p.A440A	NM_014725.4	NP_055540.2	Q92502	STAR8_HUMAN	StAR-related lipid transfer (START) domain containing 8	360					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)			NS(2)|breast(5)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(2)	50						AAGCTGAGGCTCTCAGCCAGA	0.617																																					p.A440A		Atlas-SNP	.											.	STARD8	282	.	0			c.T1320C						.						50	46	48					X																	67938076		2203	4300	6503	SO:0001819	synonymous_variant	9754	exon6			TGAGGCTCTCAGC	D80011	CCDS14390.1, CCDS48134.1	Xq13.1	2011-09-13	2007-08-16		ENSG00000130052	ENSG00000130052		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	19161	protein-coding gene	gene with protein product		300689	"START domain containing 8"			8724849	Standard	NM_001142504		Approved	KIAA0189, ARHGAP38	uc004dxb.3	Q92502	OTTHUMG00000021748	ENST00000252336.6:c.1080T>C	chrX.hg19:g.67938076T>C		143.0	0.0		118.0	5.0	NM_001142503	A8K6T2|D3DVT9|Q5JST0|Q68DG7	Silent	SNP	ENST00000252336.6	hg19	CCDS14390.1																																																																																			.	.		0.617	STARD8-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057026.2	NM_014725		C	67938076	T	C	67938076	2	2	260	1	0	0	0	0	0	0	0	1	15278	1538	54	2		2	STARD8	23	67938076	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	5021036	67938076	87332484	939	38184										
EDA	1896	hgsc.bcm.edu	37	chrX	69247861	69247861	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ggtcctcctggtcctcaaggAccccctggcctccagggacc	11	18	1	0	rs397516670		TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chrX:69247861A>G	ENST00000374552.4	+	4	923	c.681A>G	c.(679-681)ggA>ggG	p.G227G	EDA_ENST00000374553.2_Silent_p.G227G|EDA_ENST00000524573.1_Silent_p.G227G	NM_001399.4	NP_001390.1	Q92838	EDA_HUMAN	ectodysplasin A	227	Collagen-like.				cell differentiation (GO:0030154)|cell-matrix adhesion (GO:0007160)|ectoderm development (GO:0007398)|gene expression (GO:0010467)|hair follicle placode formation (GO:0060789)|immune response (GO:0006955)|odontogenesis of dentin-containing tooth (GO:0042475)|pigmentation (GO:0043473)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|salivary gland cavitation (GO:0060662)|signal transduction (GO:0007165)|trachea gland development (GO:0061153)	apical part of cell (GO:0045177)|collagen trimer (GO:0005581)|cytoskeleton (GO:0005856)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(2)|urinary_tract(1)	14						GTCCTCAAGGACCCCCTGGCC	0.587																																					p.G227G		Atlas-SNP	.											.	EDA	61	.	0			c.A681G						.						21	19	20					X																	69247861		2202	4298	6500	SO:0001819	synonymous_variant	1896	exon4			TCAAGGACCCCCT	U59227	CCDS14394.1, CCDS35318.1, CCDS35319.1, CCDS43966.1, CCDS35318.2, CCDS35319.2, CCDS55436.1	Xq12-q13.1	2013-05-22	2004-08-09	2004-08-12	ENSG00000158813	ENSG00000158813		"Tumor necrosis factor (ligand) superfamily"	3157	protein-coding gene	gene with protein product		300451	"ectodermal dysplasia 1, anhidrotic", "oligodontia 1"	ED1, EDA2, ODT1		8696334, 18657636, 16583127	Standard	NM_001005612		Approved	EDA1, XLHED, HED, XHED, ED1-A1, ED1-A2, EDA-A1, EDA-A2	uc004dxs.3	Q92838	OTTHUMG00000021764	ENST00000374552.4:c.681A>G	chrX.hg19:g.69247861A>G		66.0	0.0		82.0	4.0	NM_001399	A0AUZ2|A2A337|B7ZLU2|B7ZLU4|O75910|Q5JS00|Q5JUM7|Q9UP77|Q9Y6L0|Q9Y6L1|Q9Y6L2|Q9Y6L3|Q9Y6L4	Silent	SNP	ENST00000374552.4	hg19	CCDS14394.1																																																																																			.	.		0.587	EDA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057048.2	NM_001399		G	69247861	A	G	69247861	2	3	260	1	0	0	0	0	0	0	0	1	4905	262	10	2		2	EDA	23	69247861	Silent	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	1309785	69247861	86022699	940	38185										
ERCC6L	54821	hgsc.bcm.edu	37	chrX	71426582	71426582	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tttaacagacagatcacatgTgtacatcaaatcatggtctg	7	8	4	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chrX:71426582T>C	ENST00000334463.3	-	2	2170	c.2035A>G	c.(2035-2037)Aca>Gca	p.T679A	PIN4_ENST00000423432.2_Intron|ERCC6L_ENST00000373657.1_Missense_Mutation_p.T556A	NM_017669.2	NP_060139.2	Q2NKX8	ERC6L_HUMAN	excision repair cross-complementation group 6-like	679					mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			breast(2)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(9)|lung(9)|ovary(3)|skin(1)	38	Renal(35;0.156)					AGATCACATGTGTACATCAAA	0.403																																					p.T679A		Atlas-SNP	.											.	ERCC6L	98	.	0			c.A2035G						.						90	84	86					X																	71426582		2203	4300	6503	SO:0001583	missense	54821	exon2			CACATGTGTACAT	AK000112	CCDS35329.1	Xq13.1	2014-03-07	2014-03-07		ENSG00000186871	ENSG00000186871			20794	protein-coding gene	gene with protein product	"PLK1-interacting checkpoint helicase"	300687	"excision repair cross-complementing rodent repair deficiency, complementation group 6-like"			17218258	Standard	NM_017669		Approved	FLJ20105, PICH, RAD26L	uc004eaq.1	Q2NKX8	OTTHUMG00000021810	ENST00000334463.3:c.2035A>G	chrX.hg19:g.71426582T>C	ENSP00000334675:p.Thr679Ala	79.0	0.0		85.0	4.0	NM_017669	Q8NCI1|Q96H93|Q9NXQ8	Missense_Mutation	SNP	ENST00000334463.3	hg19	CCDS35329.1	.	.	.	.	.	.	.	.	.	.	T	7.848	0.723288	0.15439	.	.	ENSG00000186871	ENST00000373657;ENST00000334463	T;T	0.21932	1.98;1.98	5.24	4.05	0.47172	.	.	.	.	.	T	0.15565	0.0375	L	0.45698	1.435	0.34522	D	0.708222	P	0.36599	0.56	B	0.33121	0.158	T	0.22836	-1.0205	9	0.44086	T	0.13	-12.6927	3.9878	0.09524	0.1874:0.0987:0.0:0.7139	.	679	Q2NKX8	ERC6L_HUMAN	A	556;679	ENSP00000362761:T556A;ENSP00000334675:T679A	ENSP00000334675:T679A	T	-	1	0	ERCC6L	71343307	1.000000	0.71417	0.489000	0.27452	0.871000	0.50021	2.836000	0.48183	0.623000	0.30267	-0.400000	0.06385	ACA	.	.		0.403	ERCC6L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057174.2	NM_017669		C	71426582	T	C	71426582	3	2	260	1	0	0	0	0	1	0	0	0	5220	1696	59	2	1721	2	ERCC6L	23	71426582	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	2178721	71426582	83843978	941	38186										
PHKA1	5255	hgsc.bcm.edu	37	chrX	71822975	71822975	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ttattcaatctcaccgcttcGttccactccaaactccttgc	3	16	2	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chrX:71822975G>A	ENST00000373542.4	-	26	3070	c.2911C>T	c.(2911-2913)Cga>Tga	p.R971*	PHKA1_ENST00000541944.1_Nonsense_Mutation_p.R912*|PHKA1_ENST00000339490.3_Nonsense_Mutation_p.R971*|PHKA1_ENST00000373539.3_Nonsense_Mutation_p.R971*|PHKA1_ENST00000373545.3_Nonsense_Mutation_p.R912*	NM_002637.3	NP_002628.2	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle)	971					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)	p.R971*(2)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(2)|lung(18)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	52	Renal(35;0.156)					TCACCGCTTCGTTCCACTCCA	0.423																																					p.R971X		Atlas-SNP	.											.	PHKA1	129	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C2911T						.						127	98	107					X																	71822975		2203	4300	6503	SO:0001587	stop_gained	5255	exon26			CGCTTCGTTCCAC		CCDS14421.1, CCDS48137.1, CCDS55453.1	Xq12-q13	2009-07-10			ENSG00000067177	ENSG00000067177	2.7.11.19		8925	protein-coding gene	gene with protein product		311870		PHKA			Standard	NM_002637		Approved		uc004eax.4	P46020	OTTHUMG00000022696	ENST00000373542.4:c.2911C>T	chrX.hg19:g.71822975G>A	ENSP00000362643:p.Arg971*	79.0	0.0		71.0	4.0	NM_002637	B7ZL05|B7ZL07|Q2M3D7	Nonsense_Mutation	SNP	ENST00000373542.4	hg19	CCDS14421.1	.	.	.	.	.	.	.	.	.	.	G	43	10.468460	0.99411	.	.	ENSG00000067177	ENST00000373545;ENST00000373542;ENST00000541944;ENST00000339490;ENST00000373539	.	.	.	5.64	2.62	0.31277	.	0.053778	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.0938	11.4523	0.50160	0.0:0.0:0.4858:0.5142	.	.	.	.	X	912;971;912;971;971	.	ENSP00000342469:R971X	R	-	1	2	PHKA1	71739700	1.000000	0.71417	1.000000	0.80357	0.779000	0.44077	1.545000	0.36169	1.138000	0.42230	-0.222000	0.12452	CGA	.	.		0.423	PHKA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058896.1			A	71822975	G	A	71822975	4	1	260	1	0	0	0	0	0	1	0	0	11852	1153	40	1	788	1	PHKA1	23	71822975	Nonsense_Mutation	SNP	G	TCGA-ES-A2HT-01A-12D-A183-10	396393	71822975	83447585	942	38187										
ATP7A	538	hgsc.bcm.edu	37	chrX	77258577	77258577	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcaatgctcttaggaatataTtctatacttgtggccctgat	7	8	3	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chrX:77258577T>C	ENST00000341514.6	+	6	1706	c.1551T>C	c.(1549-1551)taT>taC	p.Y517Y	ATP7A_ENST00000350425.4_Intron|ATP7A_ENST00000343533.5_Silent_p.Y517Y	NM_000052.5	NP_000043.4	Q04656	ATP7A_HUMAN	ATPase, Cu++ transporting, alpha polypeptide	517	HMA 5. {ECO:0000255|PROSITE- ProRule:PRU00280}.				blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|cartilage development (GO:0051216)|catecholamine metabolic process (GO:0006584)|cellular copper ion homeostasis (GO:0006878)|central nervous system neuron development (GO:0021954)|cerebellar Purkinje cell differentiation (GO:0021702)|collagen fibril organization (GO:0030199)|copper ion export (GO:0060003)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detoxification of copper ion (GO:0010273)|dopamine metabolic process (GO:0042417)|elastic fiber assembly (GO:0048251)|elastin biosynthetic process (GO:0051542)|epinephrine metabolic process (GO:0042414)|extracellular matrix organization (GO:0030198)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|lung alveolus development (GO:0048286)|mitochondrion organization (GO:0007005)|negative regulation of metalloenzyme activity (GO:0048553)|negative regulation of neuron apoptotic process (GO:0043524)|neuron projection morphogenesis (GO:0048812)|norepinephrine biosynthetic process (GO:0042421)|norepinephrine metabolic process (GO:0042415)|peptidyl-lysine modification (GO:0018205)|pigmentation (GO:0043473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of oxidoreductase activity (GO:0051353)|pyramidal neuron development (GO:0021860)|regulation of gene expression (GO:0010468)|regulation of oxidative phosphorylation (GO:0002082)|release of cytochrome c from mitochondria (GO:0001836)|removal of superoxide radicals (GO:0019430)|response to iron(III) ion (GO:0010041)|response to zinc ion (GO:0010043)|serotonin metabolic process (GO:0042428)|skin development (GO:0043588)|T-helper cell differentiation (GO:0042093)|transmembrane transport (GO:0055085)|tryptophan metabolic process (GO:0006568)|tyrosine metabolic process (GO:0006570)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|copper-dependent protein binding (GO:0032767)|copper-exporting ATPase activity (GO:0004008)|superoxide dismutase copper chaperone activity (GO:0016532)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(26)|pancreas(1)|prostate(1)|urinary_tract(1)	53					Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	TAGGAATATATTCTATACTTG	0.343																																					p.Y517Y		Atlas-SNP	.											.	ATP7A	248	.	0			c.T1551C						.						111	104	106					X																	77258577		2203	4295	6498	SO:0001819	synonymous_variant	538	exon6			AATATATTCTATA	L06133	CCDS35339.1, CCDS75997.1	Xq21.1	2012-10-22	2008-07-31		ENSG00000165240	ENSG00000165240	3.6.3.4	"ATPases / P-type"	869	protein-coding gene	gene with protein product	"copper pump 1", "copper-transporting ATPase 1"	300011	"Menkes syndrome"	MNK		10079817	Standard	NM_000052		Approved		uc004ecx.4	Q04656	OTTHUMG00000021885	ENST00000341514.6:c.1551T>C	chrX.hg19:g.77258577T>C		113.0	0.0		82.0	4.0	NM_000052	B1AT72|O00227|O00745|Q9BYY8	Silent	SNP	ENST00000341514.6	hg19	CCDS35339.1																																																																																			.	.		0.343	ATP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057306.1	NM_000052		C	77258577	T	C	77258577	2	2	260	1	0	0	0	0	0	0	0	1	1190	1500	52	2		2	ATP7A	23	77258577	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	5435602	77258577	78011983	943	38188										
SRPX2	27286	hgsc.bcm.edu	37	chrX	99901349	99901349	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cagctaactcaaagaggagcTctctttctgctgttcttcct	7	12	4	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chrX:99901349T>C	ENST00000373004.3	+	2	458	c.30T>C	c.(28-30)gcT>gcC	p.A10A	SRPX2_ENST00000481988.1_3'UTR	NM_014467.2	NP_055282.1	O60687	SRPX2_HUMAN	sushi-repeat containing protein, X-linked 2	10					angiogenesis (GO:0001525)|cell motility (GO:0048870)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|positive regulation of synapse assembly (GO:0051965)|regulation of phosphorylation (GO:0042325)|single organismal cell-cell adhesion (GO:0016337)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|excitatory synapse (GO:0060076)|extracellular space (GO:0005615)|synaptic membrane (GO:0097060)	hepatocyte growth factor binding (GO:0036458)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(10)|ovary(2)|upper_aerodigestive_tract(1)	19						AAAGAGGAGCTCTCTTTCTGC	0.463																																					p.A10A		Atlas-SNP	.											.	SRPX2	41	.	0			c.T30C						.						155	133	140					X																	99901349		2203	4300	6503	SO:0001819	synonymous_variant	27286	exon2			AGGAGCTCTCTTT	AF393649	CCDS14471.1	Xq21.33-q23	2011-01-25	2011-01-25		ENSG00000102359	ENSG00000102359			30668	protein-coding gene	gene with protein product		300642	"sushi-repeat-containing protein, X-linked 2"			9864177	Standard	NM_014467		Approved	SRPUL	uc004egb.3	O60687	OTTHUMG00000022003	ENST00000373004.3:c.30T>C	chrX.hg19:g.99901349T>C		49.0	0.0		71.0	4.0	NM_014467	B3KQT3|Q8WW85	Silent	SNP	ENST00000373004.3	hg19	CCDS14471.1																																																																																			.	.		0.463	SRPX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057486.1	NM_014467		C	99901349	T	C	99901349	2	2	260	1	0	0	0	0	0	0	0	1	15180	1538	54	2		2	SRPX2	23	99901349	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	22642772	99901349	55369211	944	38189										
PLS3	5358	hgsc.bcm.edu	37	chrX	114883870	114883870	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gtttgatgggcaggggaatgAagagagtgtaaaataaccaa	14	3	0	3			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chrX:114883870A>G	ENST00000420625.2	+	16	2016	c.1882A>G	c.(1882-1884)Aag>Gag	p.K628E	PLS3_ENST00000355899.3_Missense_Mutation_p.K628E|PLS3_ENST00000537301.1_Missense_Mutation_p.K615E|PLS3_ENST00000543070.1_Missense_Mutation_p.K222E|PLS3_ENST00000289290.3_Missense_Mutation_p.K592E|PLS3_ENST00000539310.1_Missense_Mutation_p.K583E	NM_001136025.3|NM_001172335.1|NM_001282338.1	NP_001129497.1|NP_001165806.1|NP_001269267.1	P13797	PLST_HUMAN	plastin 3	628					bone development (GO:0060348)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(11)	26						CAGGGGAATGAAGAGAGTGTA	0.458																																					p.K628E	Colon(160;1047 1864 8490 12969 29601)	Atlas-SNP	.											.	PLS3	60	.	0			c.A1882G						.						162	144	150					X																	114883870		2203	4300	6503	SO:0001583	missense	5358	exon16			GGAATGAAGAGAG	L05491	CCDS14568.1, CCDS65312.1	Xq23	2013-01-10	2010-02-10		ENSG00000102024	ENSG00000102024		"EF-hand domain containing"	9091	protein-coding gene	gene with protein product		300131	"plastin 3 (T isoform)"			8428952	Standard	NM_005032		Approved	T-plastin	uc004eqe.3	P13797	OTTHUMG00000022237	ENST00000420625.2:c.1882A>G	chrX.hg19:g.114883870A>G	ENSP00000398945:p.Lys628Glu	103.0	0.0		100.0	4.0	NM_005032	A8K579|B1AQ09|B4DGB4|B7Z6M1|Q86YI6	Missense_Mutation	SNP	ENST00000420625.2	hg19	CCDS14568.1	.	.	.	.	.	.	.	.	.	.	a	16.20	3.055431	0.55325	.	.	ENSG00000102024	ENST00000355899;ENST00000537301;ENST00000289290;ENST00000420625;ENST00000539310;ENST00000543070	T;D;D;T;D;D	0.87650	-0.51;-1.84;-2.05;-0.51;-2.04;-2.28	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.82263	0.4999	L	0.31526	0.94	0.80722	D	1	B;B;B	0.21753	0.06;0.002;0.002	B;B;B	0.29942	0.109;0.007;0.012	T	0.78074	-0.2346	10	0.39692	T	0.17	-19.7374	14.0035	0.64449	1.0:0.0:0.0:0.0	.	601;615;628	B4DPW9;B4DGB4;P13797	.;.;PLST_HUMAN	E	628;615;592;628;583;222	ENSP00000348163:K628E;ENSP00000445105:K615E;ENSP00000289290:K592E;ENSP00000398945:K628E;ENSP00000445339:K583E;ENSP00000439260:K222E	ENSP00000289290:K592E	K	+	1	0	PLS3	114790126	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.160000	0.94734	1.989000	0.58080	0.478000	0.44815	AAG	.	.		0.458	PLS3-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057976.2			G	114883870	A	G	114883870	3	3	260	1	0	0	0	0	1	0	0	0	12117	247	9	2	1940	2	PLS3	23	114883870	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	14982521	114883870	40386690	945	38190										
KLHL13	90293	hgsc.bcm.edu	37	chrX	117053530	117053536	+	Frame_Shift_Del	DEL	TGTAGGA	TGTAGGA	-													0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	agtccaaaactggcagaatcTgtaggaaactggcagcttcc							TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	TGTAGGA	TGTAGGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chrX:117053530_117053536delTGTAGGA	ENST00000262820.3	-	4	1427_1433	c.518_524delTCCTACA	c.(517-525)ttcctacagfs	p.FLQ173fs	KLHL13_ENST00000371876.1_Frame_Shift_Del_p.FLQ122fs|KLHL13_ENST00000539496.1_Frame_Shift_Del_p.FLQ176fs|KLHL13_ENST00000541812.1_Frame_Shift_Del_p.FLQ157fs|KLHL13_ENST00000371878.1_Frame_Shift_Del_p.FLQ122fs|KLHL13_ENST00000469946.1_Frame_Shift_Del_p.FLQ122fs|KLHL13_ENST00000540167.1_Frame_Shift_Del_p.FLQ157fs|KLHL13_ENST00000545703.1_Frame_Shift_Del_p.FLQ131fs|KLHL13_ENST00000371882.1_Frame_Shift_Del_p.FLQ122fs	NM_033495.3	NP_277030.2	Q9P2N7	KLH13_HUMAN	kelch-like family member 13	173					cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)				NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(9)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	34						TGGCAGAATCTGTAGGAAACTGGCAGC	0.386																																					p.176_178del		Atlas-Indel,Pindel	.											.	KLHL13	87	.	0			c.528_534del						.																																			SO:0001589	frameshift_variant	90293	exon5			.	AB037730	CCDS14571.1, CCDS55479.1, CCDS55480.1, CCDS55481.1	Xq23-q24	2013-01-30	2013-01-30	2004-02-18	ENSG00000003096	ENSG00000003096		"Kelch-like", "BTB/POZ domain containing"	22931	protein-coding gene	gene with protein product		300655	"BTB and kelch domain containing 2, KIAA1309", "kelch-like 13 (Drosophila)"	BKLHD2, KIAA1309		10718198	Standard	NM_033495		Approved	FLJ10262	uc011mtp.2	Q9P2N7	OTTHUMG00000022252	ENST00000262820.3:c.518_524delTCCTACA	chrX.hg19:g.117053530_117053536delTGTAGGA	ENSP00000262820:p.Phe173fs	342.0	0.0		165.0	69.0	NM_001168299	B3KV78|B3KWM7|B7Z3S9|B7Z5P2|B7Z802|D3DWH6|Q6P2E3|Q96QI7|Q9UDN9	Frame_Shift_Del	DEL	ENST00000262820.3	hg19	CCDS14571.1																																																																																			.	.		0.386	KLHL13-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_033495		-	117053536	TGTAGGA	-	117053530	7	5	260	1	0	1	0	1	0	0	0	0	8378	1580	55	0	1459	0	KLHL13	23	117053530	Frame_Shift_Del	DEL	TGTAGGA	TCGA-ES-A2HT-01A-12D-A183-10	2169660	117053530	38217030	946	38191	187	2								
KLHL13	90293	hgsc.bcm.edu	37	chrX	117053532	117053532	+	Silent	SNP	T	T	C													0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tccaaaactggcagaatctgTaggaaactggcagcttccag							TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chrX:117053532T>C	ENST00000262820.3	-	4	1431	c.522A>G	c.(520-522)ctA>ctG	p.L174L	KLHL13_ENST00000371876.1_Silent_p.L123L|KLHL13_ENST00000539496.1_Silent_p.L177L|KLHL13_ENST00000541812.1_Silent_p.L158L|KLHL13_ENST00000371878.1_Silent_p.L123L|KLHL13_ENST00000469946.1_Silent_p.L123L|KLHL13_ENST00000540167.1_Silent_p.L158L|KLHL13_ENST00000545703.1_Silent_p.L132L|KLHL13_ENST00000371882.1_Silent_p.L123L	NM_033495.3	NP_277030.2	Q9P2N7	KLH13_HUMAN	kelch-like family member 13	174					cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)				NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(9)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	34						GCAGAATCTGTAGGAAACTGG	0.388																																					p.L177L		Atlas-SNP	.											.	KLHL13	87	.	0			c.A531G						.						76	85	82					X																	117053532		2203	4300	6503	SO:0001819	synonymous_variant	90293	exon5			AATCTGTAGGAAA	AB037730	CCDS14571.1, CCDS55479.1, CCDS55480.1, CCDS55481.1	Xq23-q24	2013-01-30	2013-01-30	2004-02-18	ENSG00000003096	ENSG00000003096		"Kelch-like", "BTB/POZ domain containing"	22931	protein-coding gene	gene with protein product		300655	"BTB and kelch domain containing 2, KIAA1309", "kelch-like 13 (Drosophila)"	BKLHD2, KIAA1309		10718198	Standard	NM_033495		Approved	FLJ10262	uc011mtp.2	Q9P2N7	OTTHUMG00000022252	ENST00000262820.3:c.522A>G	chrX.hg19:g.117053532T>C		345.0	0.0		94.0	6.0	NM_001168299	B3KV78|B3KWM7|B7Z3S9|B7Z5P2|B7Z802|D3DWH6|Q6P2E3|Q96QI7|Q9UDN9	Silent	SNP	ENST00000262820.3	hg19	CCDS14571.1																																																																																			.	.		0.388	KLHL13-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_033495		C	117053532	T	C	117053532	2	2	260	1	0	0	0	0	0	0	0	1	8378	1625	57	2		2	KLHL13	23	117053532	Silent	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	2	117053532	38217028	947	38192	187	2								
THOC2	57187	hgsc.bcm.edu	37	chrX	122760485	122760485	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	cctgaagggcagtacagcgcTccttctcttttttcttttta	7	11	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chrX:122760485T>C	ENST00000245838.8	-	24	2817	c.2786A>G	c.(2785-2787)gAg>gGg	p.E929G	THOC2_ENST00000355725.4_Missense_Mutation_p.E929G|THOC2_ENST00000491737.1_Missense_Mutation_p.E814G	NM_001081550.1	NP_001075019.1	Q8NI27	THOC2_HUMAN	THO complex 2	929					mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						AGTACAGCGCTCCTTCTCTTT	0.353																																					p.E929G		Atlas-SNP	.											.	THOC2	310	.	0			c.A2786G						.						116	98	104					X																	122760485		1813	4060	5873	SO:0001583	missense	57187	exon24			CAGCGCTCCTTCT	AF441770	CCDS43988.1	Xq25-q26.3	2013-02-11	2004-08-09		ENSG00000125676	ENSG00000125676		"THO complex subunits"	19073	protein-coding gene	gene with protein product		300395	"chromosome X open reading frame 3"	CXorf3		11979277	Standard	NM_001081550		Approved	THO2, dJ506G2.1	uc004etu.3	Q8NI27	OTTHUMG00000022334	ENST00000245838.8:c.2786A>G	chrX.hg19:g.122760485T>C	ENSP00000245838:p.Glu929Gly	90.0	0.0		98.0	4.0	NM_001081550	A6NM50|Q5JZ12|Q6IN92|Q9H8I6	Missense_Mutation	SNP	ENST00000245838.8	hg19	CCDS43988.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.318645	0.81469	.	.	ENSG00000125676	ENST00000245838;ENST00000355725;ENST00000491737	T;T;T	0.42900	0.96;0.96;0.96	5.83	5.83	0.93111	THO complex, subunitTHOC2, C-terminal (1);	0.000000	0.64402	D	0.000002	T	0.70988	0.3287	M	0.89601	3.045	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.77286	-0.2644	10	0.59425	D	0.04	-14.0537	15.1686	0.72850	0.0:0.0:0.0:1.0	.	929	Q8NI27	THOC2_HUMAN	G	929;929;814	ENSP00000245838:E929G;ENSP00000347959:E929G;ENSP00000419795:E814G	ENSP00000245838:E929G	E	-	2	0	THOC2	122588166	1.000000	0.71417	0.996000	0.52242	0.995000	0.86356	8.040000	0.89188	1.965000	0.57142	0.486000	0.48141	GAG	.	.		0.353	THOC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058153.3			C	122760485	T	C	122760485	3	2	260	1	0	0	0	0	1	0	0	0	15880	1551	54	2	2055	2	THOC2	23	122760485	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	5706953	122760485	32510075	948	38193										
ZDHHC9	51114	hgsc.bcm.edu	37	chrX	128947657	128947657	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tgccagcggaggatatgttcCaggagtttctttcaatgtct	11	8	3	0			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chrX:128947657C>T	ENST00000357166.6	-	7	1061	c.670G>A	c.(670-672)Gga>Aga	p.G224R	ZDHHC9_ENST00000371064.3_Missense_Mutation_p.G224R	NM_016032.3	NP_057116.2	Q9Y397	ZDHC9_HUMAN	zinc finger, DHHC-type containing 9	224					peptidyl-L-cysteine S-palmitoylation (GO:0018230)|protein palmitoylation (GO:0018345)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)|palmitoyltransferase complex (GO:0002178)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|Ras palmitoyltransferase activity (GO:0043849)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)	19						GGATATGTTCCAGGAGTTTCT	0.408																																					p.G224R		Atlas-SNP	.											.	ZDHHC9	41	.	0			c.G670A						.						93	85	87					X																	128947657		2203	4300	6503	SO:0001583	missense	51114	exon6			ATGTTCCAGGAGT	AF151847	CCDS35395.1	Xq26.1	2008-02-05			ENSG00000188706	ENSG00000188706		"Zinc fingers, DHHC-type"	18475	protein-coding gene	gene with protein product		300646	"zinc finger, DHHC-type containing 10", "chromosome X open reading frame 11"	ZDHHC10, CXorf11		10810093	Standard	NM_001008222		Approved	ZNF379, CGI-89, ZNF380	uc004euw.3	Q9Y397	OTTHUMG00000022375	ENST00000357166.6:c.670G>A	chrX.hg19:g.128947657C>T	ENSP00000349689:p.Gly224Arg	62.0	0.0		72.0	4.0	NM_001008222	B4F6G2|D3DTF9|Q59EK4|Q5JSW5|Q8WWS7|Q9BPY4|Q9NSP0|Q9NVL0|Q9NVR6	Missense_Mutation	SNP	ENST00000357166.6	hg19	CCDS35395.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.371114	0.82573	.	.	ENSG00000188706	ENST00000357166;ENST00000371064	T;T	0.23754	1.89;1.89	5.95	5.07	0.68467	.	0.267654	0.42682	D	0.000675	T	0.29126	0.0724	L	0.58583	1.82	0.53688	D	0.999972	B	0.10296	0.003	B	0.21151	0.033	T	0.02885	-1.1098	10	0.36615	T	0.2	.	15.1376	0.72579	0.1425:0.8575:0.0:0.0	.	224	Q9Y397	ZDHC9_HUMAN	R	224	ENSP00000349689:G224R;ENSP00000360103:G224R	ENSP00000349689:G224R	G	-	1	0	ZDHHC9	128775338	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.471000	0.80985	1.239000	0.43787	0.596000	0.82720	GGA	.	.		0.408	ZDHHC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058213.1	NM_016032		T	128947657	C	T	128947657	3	4	260	1	0	0	0	0	1	0	0	0	17637	603	21	3	444	3	ZDHHC9	23	128947657	Missense_Mutation	SNP	C	TCGA-ES-A2HT-01A-12D-A183-10	6187172	128947657	26322903	949	38194										
IGSF1	3547	hgsc.bcm.edu	37	chrX	130408626	130408626	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	gctctgaccagatatcagggTaggcctggaggcggtagctg	16	9	2	2			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chrX:130408626T>A	ENST00000361420.3	-	18	3777	c.3698A>T	c.(3697-3699)tAc>tTc	p.Y1233F	IGSF1_ENST00000370910.1_Missense_Mutation_p.Y1224F|IGSF1_ENST00000467244.1_5'Flank|IGSF1_ENST00000370904.1_Missense_Mutation_p.Y1224F|IGSF1_ENST00000370903.3_Missense_Mutation_p.Y1238F			Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1	1233	Ig-like C2-type 12.				regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	coreceptor activity (GO:0015026)|inhibin binding (GO:0034711)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|liver(1)|lung(37)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)	78						GATATCAGGGTAGGCCTGGAG	0.527																																					p.Y1238F		Atlas-SNP	.											.	IGSF1	231	.	0			c.A3713T						.						169	157	161					X																	130408626		2203	4300	6503	SO:0001583	missense	3547	exon18			TCAGGGTAGGCCT	AF034198	CCDS14629.1, CCDS14630.1, CCDS55490.1, CCDS55491.1	Xq25	2013-01-11			ENSG00000147255	ENSG00000147255		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5948	protein-coding gene	gene with protein product		300137				9521868, 9729118	Standard	NM_001555		Approved	KIAA0364, IGDC1, IGCD1, INHBP, MGC75490, PGSF2	uc004ewe.4	Q8N6C5	OTTHUMG00000022406	ENST00000361420.3:c.3698A>T	chrX.hg19:g.130408626T>A	ENSP00000355010:p.Tyr1233Phe	187.0	0.0		140.0	11.0	NM_001170961	B5MEG2|H9KV64|O15070|Q9NTC8	Missense_Mutation	SNP	ENST00000361420.3	hg19	CCDS14629.1	.	.	.	.	.	.	.	.	.	.	T	10.89	1.477748	0.26511	.	.	ENSG00000147255	ENST00000370910;ENST00000361420;ENST00000370904;ENST00000370903	T;T;T;T	0.00730	5.77;5.77;5.77;5.77	5.42	1.24	0.21308	Immunoglobulin-like fold (1);	1.128570	0.06730	N	0.776543	T	0.00608	0.0020	N	0.13235	0.315	0.09310	N	1	B;B;P	0.35821	0.273;0.288;0.523	B;B;B	0.36808	0.118;0.233;0.209	T	0.44667	-0.9313	10	0.12103	T	0.63	.	5.3586	0.16075	0.1726:0.0:0.3511:0.4763	.	1224;677;1233	Q8N6C5-2;C9JP68;Q8N6C5	.;.;IGSF1_HUMAN	F	1224;1233;1224;1238	ENSP00000359947:Y1224F;ENSP00000355010:Y1233F;ENSP00000359941:Y1224F;ENSP00000359940:Y1238F	ENSP00000355010:Y1233F	Y	-	2	0	IGSF1	130236307	0.766000	0.28496	0.988000	0.46212	0.992000	0.81027	0.734000	0.26101	0.251000	0.21505	0.481000	0.45027	TAC	.	.		0.527	IGSF1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058288.1			A	130408626	T	A	130408626	3	1	260	1	0	0	0	0	1	0	0	0	7605	1638	57	4	324	4	IGSF1	23	130408626	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1460969	130408626	24861934	950	38195										
HS6ST2	90161	hgsc.bcm.edu	37	chrX	131763092	131763092	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	tcaagtaccgggacactgggTctcggaggatggtgatgtag	16	7	2	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chrX:131763092T>C	ENST00000370836.2	-	4	1392	c.977A>G	c.(976-978)gAc>gGc	p.D326G	HS6ST2_ENST00000521489.1_Missense_Mutation_p.D366G|HS6ST2_ENST00000406696.3_Missense_Mutation_p.D52G|HS6ST2_ENST00000370833.2_Missense_Mutation_p.D220G	NM_147175.3	NP_671704.3	Q96MM7	H6ST2_HUMAN	heparan sulfate 6-O-sulfotransferase 2	326	3'-phosphate binding. {ECO:0000255}.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	heparan sulfate 6-O-sulfotransferase activity (GO:0017095)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(2)	9	Acute lymphoblastic leukemia(192;0.000127)					GGACACTGGGTCTCGGAGGAT	0.522																																					p.D366G		Atlas-SNP	.											.	HS6ST2	89	.	0			c.A1097G						.						35	32	33					X																	131763092		2051	4196	6247	SO:0001583	missense	90161	exon6			ACTGGGTCTCGGA	AB067776	CCDS48169.1, CCDS48170.1	Xq26.2	2008-02-05			ENSG00000171004	ENSG00000171004		"Sulfotransferases, membrane-bound"	19133	protein-coding gene	gene with protein product		300545				10644753	Standard	NM_147175		Approved		uc011mvd.1	Q96MM7	OTTHUMG00000022430	ENST00000370836.2:c.977A>G	chrX.hg19:g.131763092T>C	ENSP00000359873:p.Asp326Gly	98.0	0.0		103.0	5.0	NM_001077188	B9WRT4|B9WRT5|E9PDY5|Q2TB13|Q4VC07|Q6PIC4|Q86SM9|Q8N3T4|Q8NBN4|Q96SJ4	Missense_Mutation	SNP	ENST00000370836.2	hg19	CCDS48169.1	.	.	.	.	.	.	.	.	.	.	t	18.78	3.695987	0.68386	.	.	ENSG00000171004	ENST00000370837;ENST00000370836;ENST00000521489;ENST00000406696;ENST00000370833;ENST00000319809	T;T;T;T;T	0.79247	0.27;0.27;0.27;-1.25;0.27	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	D	0.89037	0.6601	M	0.85197	2.74	0.51767	D	0.999936	D;D;D	0.89917	1.0;0.994;1.0	D;D;D	0.91635	0.999;0.955;0.999	D	0.90661	0.4590	10	0.87932	D	0	-4.2728	14.5424	0.68005	0.0:0.0:0.0:1.0	.	326;366;52	Q96MM7;E9PDY5;B7Z5H6	H6ST2_HUMAN;.;.	G	180;326;366;52;220;207	ENSP00000359874:D180G;ENSP00000359873:D326G;ENSP00000429473:D366G;ENSP00000384013:D52G;ENSP00000359870:D220G	ENSP00000324617:D207G	D	-	2	0	HS6ST2	131590773	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.037000	0.88933	2.034000	0.60081	0.483000	0.47432	GAC	.	.		0.522	HS6ST2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058332.3	NM_147174		C	131763092	T	C	131763092	3	2	260	1	0	0	0	0	1	0	0	0	7380	1667	58	2	844	2	HS6ST2	23	131763092	Missense_Mutation	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	1354466	131763092	23507468	951	38196										
PLXNA3	55558	hgsc.bcm.edu	37	chrX	153699869	153699869	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	aaagatggcatccatcagcgAccaggacatggatgcctacc	10	12	1	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chrX:153699869A>G	ENST00000369682.3	+	32	5583	c.5408A>G	c.(5407-5409)gAc>gGc	p.D1803G		NM_017514.3	NP_059984.3	P51805	PLXA3_HUMAN	plexin A3	1803					axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|hippocampus development (GO:0021766)|multicellular organismal development (GO:0007275)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|positive regulation of cytoskeleton organization (GO:0051495)|pyramidal neuron development (GO:0021860)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|trigeminal nerve structural organization (GO:0021637)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	48	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TCCATCAGCGACCAGGACATG	0.542																																					p.D1803G		Atlas-SNP	.											.	PLXNA3	156	.	0			c.A5408G						.						105	86	92					X																	153699869		2203	4300	6503	SO:0001583	missense	55558	exon32			TCAGCGACCAGGA	X74609	CCDS14752.1	Xq28	2008-02-05			ENSG00000130827	ENSG00000130827		"Plexins"	9101	protein-coding gene	gene with protein product		300022		PLXN4		8248200, 8733135	Standard	NM_017514		Approved	SEX, XAP-6, 6.3, Plxn3	uc004flm.3	P51805	OTTHUMG00000033290	ENST00000369682.3:c.5408A>G	chrX.hg19:g.153699869A>G	ENSP00000358696:p.Asp1803Gly	92.0	0.0		78.0	4.0	NM_017514	Q5HY36	Missense_Mutation	SNP	ENST00000369682.3	hg19	CCDS14752.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.643616	0.87859	.	.	ENSG00000130827	ENST00000369682	T	0.19938	2.11	4.93	4.93	0.64822	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.50188	0.1601	M	0.87900	2.915	0.80722	D	1	D	0.69078	0.997	D	0.73708	0.981	T	0.58578	-0.7612	10	0.72032	D	0.01	.	12.718	0.57125	1.0:0.0:0.0:0.0	.	1803	P51805	PLXA3_HUMAN	G	1803	ENSP00000358696:D1803G	ENSP00000358696:D1803G	D	+	2	0	PLXNA3	153353063	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	9.332000	0.96446	1.641000	0.50575	0.356000	0.21956	GAC	.	.		0.542	PLXNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081634.1	NM_017514		G	153699869	A	G	153699869	3	3	260	1	0	0	0	0	1	0	0	0	12130	275	10	2	5530	2	PLXNA3	23	153699869	Missense_Mutation	SNP	A	TCGA-ES-A2HT-01A-12D-A183-10	21936777	153699869	1570691	952	38197										
IKBKG	8517	hgsc.bcm.edu	37	chrX	153770550	153770550	+	5'UTR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0157728706624606	15	1	0.624561489137133	0.761965016747302	0.616619088697238	0.000156407221842789	0.00972331562456005	0	ccgcagactatcaatcccagTctcttcccctcactccctgt	4	19	3	1			TCGA-ES-A2HT-01A-12D-A183-10	TCGA-ES-A2HT-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6ccfd6f-2ea9-499d-a25d-4ba9d4a9258e	1a9dd052-17c3-4a9d-a566-ad9f88b85428	g.chrX:153770550T>C	ENST00000369607.1	+	0	73				G6PD_ENST00000393564.2_Intron|G6PD_ENST00000497281.1_Intron|G6PD_ENST00000393562.2_Intron|G6PD_ENST00000369620.2_Intron|IKBKG_ENST00000369609.5_Silent_p.S24S			Q9Y6K9	NEMO_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma						activation of MAPK activity (GO:0000187)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|B cell homeostasis (GO:0001782)|cellular response to DNA damage stimulus (GO:0006974)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of neuron death (GO:1901215)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|response to virus (GO:0009615)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|intracellular (GO:0005622)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	linear polyubiquitin binding (GO:1990450)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)|ubiquitin protein ligase binding (GO:0031625)			endometrium(1)|lung(1)	2	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TCAATCCCAGTCTCTTCCCCT	0.577																																					p.S24S		Atlas-SNP	.											.	IKBKG	17	.	0			c.T72C						.						54	44	47					X																	153770550		1568	3578	5146	SO:0001623	5_prime_UTR_variant	8517	exon1			TCCCAGTCTCTTC	AF074382	CCDS14757.1, CCDS48196.1, CCDS48197.1	Xq28	2014-09-17			ENSG00000073009	ENSG00000269335		"Zinc fingers, C2HC-type containing"	5961	protein-coding gene	gene with protein product		300248	"incontinentia pigmenti"	IP2, IP1		9751060, 10087442, 11590134	Standard	NM_001099857		Approved	IKK-gamma, NEMO, Fip3p, FIP-3, FIP3, ZC2HC9	uc011mzr.2	Q9Y6K9	OTTHUMG00000024234	ENST00000369607.1:c.-68T>C	chrX.hg19:g.153770550T>C		112.0	0.0		79.0	5.0	NM_001099856	Q7LBY6|Q7Z7F1	Silent	SNP	ENST00000369607.1	hg19	CCDS14757.1																																																																																			.	.		0.577	IKBKG-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000061155.2	NM_003639		C	153770550	T	C	153770550	1	2	260	0	1	0	0	0	0	0	0	0	7622	1664	58	2		2	IKBKG	23	153770550	5'UTR	SNP	T	TCGA-ES-A2HT-01A-12D-A183-10	70681	153770550	1500010	953	38198										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27101342	27101342	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	cagatcagagggccaaccacGaaggctcgtggccttcccat	11	14	1	2			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr1:27101342G>T	ENST00000324856.7	+	18	4995	c.4624G>T	c.(4624-4626)Gaa>Taa	p.E1542*	ARID1A_ENST00000540690.1_Intron|ARID1A_ENST00000374152.2_Nonsense_Mutation_p.E1159*|ARID1A_ENST00000457599.2_Intron	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1542					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)	p.E1542*(1)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		GGCCAACCACGAAGGCTCGTG	0.642			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.E1542X		Atlas-SNP	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	ARID1A,caecum,carcinoma,-2,1	ARID1A	842	.	1	Substitution - Nonsense(1)	ovary(1)	c.G4624T						.						60	63	62					1																	27101342		2203	4300	6503	SO:0001587	stop_gained	8289	exon18			AACCACGAAGGCT	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.4624G>T	chr1.hg19:g.27101342G>T	ENSP00000320485:p.Glu1542*	79.0	0.0		50.0	36.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Nonsense_Mutation	SNP	ENST00000324856.7	hg19	CCDS285.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	43|43	10.343878|10.343878	0.99388|0.99388	.|.	.|.	ENSG00000117713|ENSG00000117713	ENST00000324856;ENST00000374152|ENST00000430799	.|.	.|.	.|.	5.41|5.41	5.41|5.41	0.78517|0.78517	.|.	0.045702|.	0.85682|.	D|.	0.000000|.	.|T	.|0.75287	.|0.3829	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.72743	.|-0.4201	.|4	0.42905|.	T|.	0.14|.	-7.5866|-7.5866	19.3941|19.3941	0.94598|0.94598	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|L	1542;1159|438	.|.	ENSP00000320485:E1542X|.	E|R	+|+	1|2	0|0	ARID1A|ARID1A	26973929|26973929	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.479000|0.479000	0.33129|0.33129	9.144000|9.144000	0.94629|0.94629	2.822000|2.822000	0.97130|0.97130	0.557000|0.557000	0.71058|0.71058	GAA|CGA	.	.		0.642	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		T	27101342	G	T	27101342	4	4	261	1	0	0	0	0	0	1	0	0	913	1059	37	1	4694	1	ARID1A	1	27101342	Nonsense_Mutation	SNP	G	TCGA-FV-A23B-01A-11D-A16V-10		27101342	222149279	1	38199										
AKIRIN1	79647	hgsc.bcm.edu	37	chr1	39463936	39463936	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	tcagagtgaagcttgtgcttCggaaagtcaacctcactcct	9	11	3	2			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr1:39463936C>T	ENST00000432648.3	+	2	472	c.314C>T	c.(313-315)tCg>tTg	p.S105L	AKIRIN1_ENST00000372984.4_Intron|AKIRIN1_ENST00000446189.2_Missense_Mutation_p.S105L	NM_024595.2	NP_078871.1	Q9H9L7	AKIR1_HUMAN	akirin 1	105						nuclear membrane (GO:0031965)|nucleus (GO:0005634)				lung(1)|prostate(1)|skin(1)	3						GCTTGTGCTTCGGAAAGTCAA	0.388																																					p.S105L		Atlas-SNP	.											.	AKIRIN1	7	.	0			c.C314T						.						85	83	84					1																	39463936		2203	4300	6503	SO:0001583	missense	79647	exon2			GTGCTTCGGAAAG	AK022728	CCDS433.1, CCDS44113.1	1p34.3	2013-10-11	2008-06-23	2008-06-23	ENSG00000174574	ENSG00000174574			25744	protein-coding gene	gene with protein product		615164	"chromosome 1 open reading frame 108"	C1orf108		19200367	Standard	NM_024595		Approved	FLJ12666	uc001ccw.3	Q9H9L7	OTTHUMG00000007496	ENST00000432648.3:c.314C>T	chr1.hg19:g.39463936C>T	ENSP00000392678:p.Ser105Leu	68.0	0.0		38.0	24.0	NM_024595	B4DZU6|Q0VDB3|Q53FK8	Missense_Mutation	SNP	ENST00000432648.3	hg19	CCDS433.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.4|20.4	3.982818|3.982818	0.74474|0.74474	.|.	.|.	ENSG00000174574|ENSG00000174574	ENST00000531822|ENST00000432648;ENST00000446189	.|T;T	.|0.64260	.|-0.09;-0.09	5.14|5.14	5.14|5.14	0.70334|0.70334	.|.	.|0.274240	.|0.34777	.|N	.|0.003686	T|T	0.61714|0.61714	0.2369|0.2369	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	D|D	1|1	.|D;P	.|0.56521	.|0.976;0.948	.|P;B	.|0.51385	.|0.668;0.254	T|T	0.65841|0.65841	-0.6070|-0.6070	5|10	.|0.62326	.|D	.|0.03	-6.9641|-6.9641	16.4569|16.4569	0.84021|0.84021	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|105;105	.|B4DZU6;Q9H9L7	.|.;AKIR1_HUMAN	W|L	67|105	.|ENSP00000392678:S105L;ENSP00000389866:S105L	.|ENSP00000392678:S105L	R|S	+|+	1|2	2|0	AKIRIN1|AKIRIN1	39236523|39236523	0.988000|0.988000	0.35896|0.35896	0.966000|0.966000	0.40874|0.40874	0.982000|0.982000	0.71751|0.71751	2.292000|2.292000	0.43549|0.43549	2.534000|2.534000	0.85438|0.85438	0.563000|0.563000	0.77884|0.77884	CGG|TCG	.	.		0.388	AKIRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019687.2	NM_024595		T	39463936	C	T	39463936	3	4	261	1	0	0	0	0	1	0	0	0	461	893	31	1	320	1	AKIRIN1	1	39463936	Missense_Mutation	SNP	C	TCGA-FV-A23B-01A-11D-A16V-10	12362594	39463936	209786685	2	38200										
PRMT6	55170	hgsc.bcm.edu	37	chr1	107599362	107599362	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	cgcagcccaagaaaagaaagCttgagtcggggggcggcggc	17	10	0	3	rs539124873	byFrequency	TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr1:107599362C>T	ENST00000370078.1	+	1	62	c.25C>T	c.(25-27)Ctt>Ttt	p.L9F	PRMT6_ENST00000361318.5_5'UTR			Q96LA8	ANM6_HUMAN	protein arginine methyltransferase 6	9					base-excision repair (GO:0006284)|histone H3-R2 methylation (GO:0034970)|histone H4-R3 methylation (GO:0043985)|histone methylation (GO:0016571)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	histone binding (GO:0042393)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H2A-R3 specific) (GO:0070612)|histone methyltransferase activity (H3-R2 specific) (GO:0070611)|histone methyltransferase activity (H4-R3 specific) (GO:0044020)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)			biliary_tract(1)|breast(2)|kidney(1)|large_intestine(4)|lung(5)|urinary_tract(1)	14		all_epithelial(167;0.000429)|all_lung(203;0.00122)|Lung NSC(277;0.00185)		Lung(183;0.0305)|Epithelial(280;0.0765)|Colorectal(144;0.0998)|all cancers(265;0.14)|LUSC - Lung squamous cell carcinoma(189;0.173)|BRCA - Breast invasive adenocarcinoma(282;0.242)		GAAAAGAAAGCTTGAGTCGGG	0.706																																					p.L9F		Atlas-SNP	.											.	PRMT6	55	.	0			c.C25T						.						8	12	11					1																	107599362		683	1578	2261	SO:0001583	missense	55170	exon1			AGAAAGCTTGAGT	AK001421	CCDS41360.1, CCDS41360.2	1p13.2	2008-02-05	2006-02-16	2006-02-16	ENSG00000198890	ENSG00000198890		"Protein arginine methyltransferases"	18241	protein-coding gene	gene with protein product		608274	"HMT1 hnRNP methyltransferase-like 6 (S. cerevisiae)"	HRMT1L6		11724789	Standard	NM_018137		Approved	FLJ10559	uc010ous.2	Q96LA8	OTTHUMG00000010964	ENST00000370078.1:c.25C>T	chr1.hg19:g.107599362C>T	ENSP00000359095:p.Leu9Phe	37.0	0.0		34.0	14.0	NM_018137	A3KME1|B4DID8|Q5T5Y5|Q6DKI4|Q9NVR8	Missense_Mutation	SNP	ENST00000370078.1	hg19	CCDS41360.2	.	.	.	.	.	.	.	.	.	.	C	15.87	2.961994	0.53400	.	.	ENSG00000198890	ENST00000370078	T	0.26810	1.71	4.85	0.326	0.15908	.	3.494140	0.01036	N	0.004231	T	0.03739	0.0106	N	0.08118	0	0.80722	D	1	B	0.34015	0.435	B	0.24269	0.052	T	0.35226	-0.9797	10	0.38643	T	0.18	-9.5259	2.4087	0.04419	0.3624:0.3819:0.1583:0.0973	.	9	Q96LA8	ANM6_HUMAN	F	9	ENSP00000359095:L9F	ENSP00000359095:L9F	L	+	1	0	PRMT6	107400885	0.999000	0.42202	0.992000	0.48379	0.871000	0.50021	0.653000	0.24902	0.214000	0.20742	-0.332000	0.08345	CTT	.	.		0.706	PRMT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030185.1	NM_018137		T	107599362	C	T	107599362	3	4	261	1	0	0	0	0	1	0	0	0	12552	797	28	3	27	3	PRMT6	1	107599362	Missense_Mutation	SNP	C	TCGA-FV-A23B-01A-11D-A16V-10	68135426	107599362	141651259	3	38201										
PRPF38B	55119	hgsc.bcm.edu	37	chr1	109242492	109242492	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	agtcccagcaaagaaaaatcTagaaagcgtagtagaagcaa	9	7	1	3			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr1:109242492T>C	ENST00000370025.4	+	6	1760	c.1491T>C	c.(1489-1491)tcT>tcC	p.S497S	PRPF38B_ENST00000370021.1_Silent_p.S386S	NM_018061.2	NP_060531.2	Q5VTL8	PR38B_HUMAN	pre-mRNA processing factor 38B	497					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			NS(1)|kidney(3)|large_intestine(5)|lung(8)|prostate(1)|skin(1)	19		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0149)|Lung(183;0.0888)|COAD - Colon adenocarcinoma(174;0.113)|Epithelial(280;0.161)		AAGAAAAATCTAGAAAGCGTA	0.398																																					p.S497S		Atlas-SNP	.											.	PRPF38B	55	.	0			c.T1491C						.						115	115	115					1																	109242492		2203	4300	6503	SO:0001819	synonymous_variant	55119	exon6			AAAATCTAGAAAG	AL833950	CCDS788.1	1p13.3	2013-10-03	2013-10-03		ENSG00000134186	ENSG00000134186			25512	protein-coding gene	gene with protein product			"PRP38 pre-mRNA processing factor 38 (yeast) domain containing B"				Standard	NM_018061		Approved	FLJ10330, NET1	uc001dvv.4	Q5VTL8	OTTHUMG00000010991	ENST00000370025.4:c.1491T>C	chr1.hg19:g.109242492T>C		183.0	0.0		206.0	75.0	NM_018061	Q05DD6|Q32Q58|Q5VTL9|Q6PK39|Q7Z6E2|Q86WF3|Q8IWG9|Q9NW40	Silent	SNP	ENST00000370025.4	hg19	CCDS788.1																																																																																			.	.		0.398	PRPF38B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030231.1	NM_018061		C	109242492	T	C	109242492	2	2	261	1	0	0	0	0	0	0	0	1	12580	1509	53	2		2	PRPF38B	1	109242492	Silent	SNP	T	TCGA-FV-A23B-01A-11D-A16V-10	1643130	109242492	140008129	4	38202										
C1orf103	55791	hgsc.bcm.edu	37	chr1	111494007	111494007	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	tgctctggaggacacttcctTttctagcataaatgacggct	9	10	2	1			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr1:111494007T>C	ENST00000369763.4	-	2	1889	c.1499A>G	c.(1498-1500)aAa>aGa	p.K500R	RP11-96K19.2_ENST00000440689.1_RNA|LRIF1_ENST00000494675.1_Intron|LRIF1_ENST00000485275.2_Intron	NM_018372.3	NP_060842.3	Q5T3J3	LRIF1_HUMAN	ligand dependent nuclear receptor interacting factor 1	500					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)				endometrium(2)|kidney(2)|large_intestine(7)|lung(12)|ovary(2)|skin(1)|urinary_tract(2)	28						GACACTTCCTTTTCTAGCATA	0.393																																					p.K500R		Atlas-SNP	.											.	LRIF1	65	.	0			c.A1499G						.						166	156	160					1																	111494007		2203	4300	6503	SO:0001583	missense	55791	exon2			CTTCCTTTTCTAG	AY190122	CCDS30800.1, CCDS41366.1	1p13.3	2011-04-15	2011-04-15	2011-04-15	ENSG00000121931	ENSG00000121931			30299	protein-coding gene	gene with protein product	"receptor interacting factor 1"	615354	"chromosome 1 open reading frame 103"	C1orf103		17455211	Standard	NM_018372		Approved	RIF1, FLJ11269	uc001eaa.3	Q5T3J3	OTTHUMG00000011913	ENST00000369763.4:c.1499A>G	chr1.hg19:g.111494007T>C	ENSP00000358778:p.Lys500Arg	135.0	0.0		128.0	44.0	NM_018372	Q86XS4|Q8N3B6|Q96HT4|Q9NUM5|Q9NV32	Missense_Mutation	SNP	ENST00000369763.4	hg19	CCDS30800.1	.	.	.	.	.	.	.	.	.	.	T	1.571	-0.534080	0.04082	.	.	ENSG00000121931	ENST00000369763	T	0.39406	1.08	1.06	1.06	0.20224	.	.	.	.	.	T	0.14356	0.0347	L	0.51422	1.61	0.09310	N	1	B	0.30281	0.275	B	0.25405	0.06	T	0.21861	-1.0233	9	0.66056	D	0.02	-4.0474	4.0121	0.09627	0.0:0.0:0.0:1.0	.	500	Q5T3J3	LRIF1_HUMAN	R	500	ENSP00000358778:K500R	ENSP00000358778:K500R	K	-	2	0	LRIF1	111295530	0.935000	0.31712	0.697000	0.30258	0.646000	0.38490	0.147000	0.16202	0.115000	0.18071	0.113000	0.15668	AAA	.	.		0.393	LRIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000032932.2	NM_018372		C	111494007	T	C	111494007	3	2	261	1	0	0	0	0	1	0	0	0	1979	1841	64	2	822	2	C1orf103	1	111494007	Missense_Mutation	SNP	T	TCGA-FV-A23B-01A-11D-A16V-10	2251515	111494007	137756614	5	38203										
NUP210L	91181	hgsc.bcm.edu	37	chr1	154042865	154042865	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	attctagcattagtgaactgAaattatcaaactttctccta	4	8	3	2			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr1:154042865A>G	ENST00000368559.3	-	17	2509	c.2438T>C	c.(2437-2439)tTc>tCc	p.F813S	NUP210L_ENST00000271854.3_Missense_Mutation_p.F813S	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	813					Sertoli cell development (GO:0060009)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|lung(34)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|urinary_tract(2)	80	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			TAGTGAACTGAAATTATCAAA	0.368																																					p.F813S		Atlas-SNP	.											.	NUP210L	181	.	0			c.T2438C						.						119	107	111					1																	154042865		1862	4089	5951	SO:0001583	missense	91181	exon17			GAACTGAAATTAT	AK125924	CCDS41399.1, CCDS53370.1	1q21.3	2008-02-05			ENSG00000143552	ENSG00000143552			29915	protein-coding gene	gene with protein product							Standard	NM_207308		Approved		uc001fdw.3	Q5VU65	OTTHUMG00000035852	ENST00000368559.3:c.2438T>C	chr1.hg19:g.154042865A>G	ENSP00000357547:p.Phe813Ser	121.0	0.0		142.0	47.0	NM_001159484	E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	Missense_Mutation	SNP	ENST00000368559.3	hg19	CCDS41399.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.985650	0.74589	.	.	ENSG00000143552	ENST00000368559;ENST00000271854	T;T	0.24151	1.87;1.87	5.0	5.0	0.66597	.	0.109676	0.40908	D	0.000981	T	0.22085	0.0532	M	0.69358	2.11	0.31685	N	0.64267	D;D	0.57899	0.981;0.981	P;P	0.52109	0.69;0.69	T	0.08472	-1.0720	10	0.20046	T	0.44	-29.4441	12.3464	0.55124	1.0:0.0:0.0:0.0	.	813;813	E7EP56;Q5VU65	.;P210L_HUMAN	S	813	ENSP00000357547:F813S;ENSP00000271854:F813S	ENSP00000271854:F813S	F	-	2	0	NUP210L	152309489	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.731000	0.74785	1.910000	0.55303	0.321000	0.21382	TTC	.	.		0.368	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308		G	154042865	A	G	154042865	3	3	261	1	0	0	0	0	1	0	0	0	10770	246	9	2	3324	2	NUP210L	1	154042865	Missense_Mutation	SNP	A	TCGA-FV-A23B-01A-11D-A16V-10	42548858	154042865	95207756	6	38204										
LMNA	4000	hgsc.bcm.edu	37	chr1	156106182	156106183	+	Missense_Mutation	DNP	GG	GG	TA													0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	cgcgtggccgtggaggaggtGgatgaggagggcaagtttgt							TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr1:156106182_156106183GG>TA	ENST00000368300.4	+	7	1547_1548	c.1335_1336GG>TA	c.(1333-1338)gtGGat>gtTAat	p.D446N	LMNA_ENST00000448611.2_Missense_Mutation_p.D334N|LMNA_ENST00000368297.1_Missense_Mutation_p.D365N|LMNA_ENST00000368301.2_Missense_Mutation_p.D446N|LMNA_ENST00000368299.3_Missense_Mutation_p.D446N|LMNA_ENST00000392353.3_Missense_Mutation_p.D365N|LMNA_ENST00000361308.4_Missense_Mutation_p.D446N|LMNA_ENST00000496738.1_3'UTR|LMNA_ENST00000473598.2_Missense_Mutation_p.D347N|LMNA_ENST00000347559.2_Missense_Mutation_p.D446N	NM_170707.3	NP_733821.1	P02545	LMNA_HUMAN	lamin A/C	446	LTD.|Tail.		D -> V (in EDMD2). {ECO:0000269|PubMed:14684700}.		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to hypoxia (GO:0071456)|endoplasmic reticulum unfolded protein response (GO:0030968)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|muscle organ development (GO:0007517)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|positive regulation of cell aging (GO:0090343)|protein localization to nucleus (GO:0034504)|regulation of cell migration (GO:0030334)|regulation of protein localization to nucleus (GO:1900180)|sterol regulatory element binding protein import into nucleus (GO:0035105)|ventricular cardiac muscle cell development (GO:0055015)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|lamin filament (GO:0005638)|nuclear envelope (GO:0005635)|nuclear lamina (GO:0005652)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	structural molecule activity (GO:0005198)			NS(1)|endometrium(1)|kidney(1)|lung(3)|ovary(4)	10	Hepatocellular(266;0.158)					TGGAGGAGGTGGATGAGGAGGG	0.609									Werner syndrome;Hutchinson-Gilford Progeria Syndrome																												p.V445V|p.D446N		Atlas-SNP	.											.	LMNA	31	.	0			c.G1335T|c.G1336A						.																																			SO:0001583	missense	4000	exon7	Familial Cancer Database	WS, Adult Progeria;HGPS, Progeria	GGAGGTGGATGAG|GAGGTGGATGAGG	BC014507	CCDS1129.1, CCDS1131.1, CCDS58038.1, CCDS72941.1, CCDS72942.1	1q22	2014-09-17			ENSG00000160789	ENSG00000160789		"Intermediate filaments type V, lamins"	6636	protein-coding gene	gene with protein product		150330	"cardiomyopathy, dilated 1A (autosomal dominant)", "limb girdle muscular dystrophy 1B (autosomal dominant)", "progeria 1 (Hutchinson-Gilford type)", "lamin A/C-like 1"	LMN1, CMD1A, LGMD1B, PRO1, LMNL1		8511676, 8838815, 12702809	Standard	NM_005572		Approved	HGPS	uc001fni.3	P02545	OTTHUMG00000013961	Exception_encountered	chr1.hg19:g.156106182_156106183delinsTA	ENSP00000357283:p.Asp446Asn	53.0	0.0		69.0|68.0	35.0	NM_170707	B4DI32|D3DVB0|D6RAQ3|E7EUI9|P02546|Q5I6Y4|Q5I6Y6|Q5TCJ2|Q5TCJ3|Q6UYC3|Q969I8|Q96JA2	Silent|Missense_Mutation	SNP	ENST00000368300.4	hg19	CCDS1129.1																																																																																			.	.		0.609	LMNA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039200.2	NM_170707		TA	156106183	GG	TA	156106182	3	4	261	1	0	0	0	0	1	0	0	0	8857	1335	47	3	1361	3	LMNA	1	156106182	Missense_Mutation	DNP	GG	TCGA-FV-A23B-01A-11D-A16V-10	2063317	156106182	93144439	7	38205										
NUF2	83540	hgsc.bcm.edu	37	chr1	163325198	163325198	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	aaaggcagcagaggactcctAtgctaagatagatgagaaga	12	6	0	5			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr1:163325198A>G	ENST00000271452.3	+	14	1613	c.1334A>G	c.(1333-1335)tAt>tGt	p.Y445C	NUF2_ENST00000524800.1_Missense_Mutation_p.Y398C|NUF2_ENST00000367900.3_Missense_Mutation_p.Y445C	NM_145697.2	NP_663735.2	Q9BZD4	NUF2_HUMAN	NUF2, NDC80 kinetochore complex component	445	Interaction with the C-terminus of NDC80 and the SPBC24-SPBC25 subcomplex.				chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35	all_hematologic(923;0.101)					GAGGACTCCTATGCTAAGATA	0.348																																					p.Y445C		Atlas-SNP	.											.	NUF2	138	.	0			c.A1334G						.						84	88	86					1																	163325198		2203	4300	6503	SO:0001583	missense	83540	exon14			ACTCCTATGCTAA	BG354574	CCDS1245.1	1q23.3	2013-07-03	2013-07-03	2006-11-07	ENSG00000143228	ENSG00000143228			14621	protein-coding gene	gene with protein product	"cancer/testis antigen 106"	611772	"cell division cycle associated 1", "NUF2, NDC80 kinetochore complex component, homolog (S. cerevisiae)"	CDCA1		11266451, 11685532	Standard	NM_031423		Approved	NUF2R, CT106	uc001gcr.1	Q9BZD4	OTTHUMG00000034275	ENST00000271452.3:c.1334A>G	chr1.hg19:g.163325198A>G	ENSP00000271452:p.Tyr445Cys	207.0	0.0		272.0	65.0	NM_145697	Q8WU69|Q96HJ4|Q96Q78	Missense_Mutation	SNP	ENST00000271452.3	hg19	CCDS1245.1	.	.	.	.	.	.	.	.	.	.	A	15.05	2.717779	0.48622	.	.	ENSG00000143228	ENST00000524800;ENST00000367900;ENST00000271452	T;T;T	0.29655	1.56;1.56;1.56	5.11	-10.2	0.00374	.	2.319440	0.01322	N	0.010962	T	0.03305	0.0096	N	0.02011	-0.69	0.22961	N	0.998509	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.25117	-1.0141	9	0.45353	T	0.12	8.6129	10.061	0.42275	0.2144:0.3045:0.4811:0.0	.	398;445	E9PQC4;Q9BZD4	.;NUF2_HUMAN	C	398;445;445	ENSP00000436888:Y398C;ENSP00000356875:Y445C;ENSP00000271452:Y445C	ENSP00000271452:Y445C	Y	+	2	0	NUF2	161591822	0.000000	0.05858	0.000000	0.03702	0.962000	0.63368	-0.478000	0.06575	-1.513000	0.01789	0.482000	0.46254	TAT	.	.		0.348	NUF2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000082812.1	NM_145697		G	163325198	A	G	163325198	3	3	261	1	0	0	0	0	1	0	0	0	10756	449	16	2	1384	2	NUF2	1	163325198	Missense_Mutation	SNP	A	TCGA-FV-A23B-01A-11D-A16V-10	7219016	163325198	85925423	8	38206										
ADCY10	55811	hgsc.bcm.edu	37	chr1	167802265	167802267	+	In_Frame_Del	DEL	GAA	GAA	-													0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	ggcctgccgattcacataatGaaagtgtctgtttttctcga					rs369038387		TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr1:167802265_167802267delGAA	ENST00000367851.4	-	25	3735_3737	c.3551_3553delTTC	c.(3550-3555)tttcat>tat	p.1184_1185FH>Y	ADCY10_ENST00000367848.1_In_Frame_Del_p.1092_1093FH>Y|ADCY10_ENST00000545172.1_In_Frame_Del_p.1031_1032FH>Y	NM_018417.4	NP_060887.2	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10 (soluble)	1184					cAMP biosynthetic process (GO:0006171)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|spermatogenesis (GO:0007283)	apical part of cell (GO:0045177)|axon (GO:0030424)|basal part of cell (GO:0045178)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)			autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(26)|ovary(2)|prostate(4)|skin(6)|stomach(1)|urinary_tract(1)	63						TTCACATAATGAAAGTGTCTGTT	0.488																																					p.1184_1185del		Atlas-Indel,Pindel	.											.	ADCY10	175	.	0			c.3552_3554del						.																																			SO:0001651	inframe_deletion	55811	exon25			.	AF271058	CCDS1265.1, CCDS53426.1, CCDS72977.1	1q24	2013-02-04			ENSG00000143199	ENSG00000143199	4.6.1.1	"Adenylate cyclases"	21285	protein-coding gene	gene with protein product	"soluble adenylyl cyclase", "Hypercalciuria, absorptive, 2"	605205					Standard	XM_006711449		Approved	SAC, Sacy, SACI, HCA2, RP1-313L4.2	uc001ger.3	Q96PN6	OTTHUMG00000034573	ENST00000367851.4:c.3551_3553delTTC	chr1.hg19:g.167802265_167802267delGAA	ENSP00000356825:p.Phe1184_His1185delinsTyr	101.0	0.0		121.0	28.0	NM_018417	B4DZF0|F5GWS5|O95558|Q5R329|Q5R330|Q8WXV4|Q9NNX0	In_Frame_Del	DEL	ENST00000367851.4	hg19	CCDS1265.1																																																																																			.	.		0.488	ADCY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083663.1	NM_018417		-	167802267	GAA	-	167802265	7	5	261	1	0	1	0	1	0	0	0	0	293	1290	45	0	1315	0	ADCY10	1	167802265	In_Frame_Del	DEL	GAA	TCGA-FV-A23B-01A-11D-A16V-10	4477067	167802265	81448356	9	38207										
IL18R1	8809	hgsc.bcm.edu	37	chr2	102988510	102988510	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	gtaaaattgtggaagttaaaAaattttttcagataacctgt	7	3	1	1			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr2:102988510A>C	ENST00000409599.1	+	5	756	c.400A>C	c.(400-402)Aaa>Caa	p.K134Q	IL18R1_ENST00000334376.3_Missense_Mutation_p.K134Q|IL18R1_ENST00000233957.1_Missense_Mutation_p.K134Q			Q13478	IL18R_HUMAN	interleukin 18 receptor 1	134	Ig-like C2-type 2.				immune response (GO:0006955)|natural killer cell activation (GO:0030101)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|signal transduction (GO:0007165)|T-helper 1 cell differentiation (GO:0045063)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-18 receptor activity (GO:0042008)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34						GGAAGTTAAAAAATTTTTTCA	0.279																																					p.K134Q		Atlas-SNP	.											.	IL18R1	72	.	0			c.A400C						.						38	41	40					2																	102988510		2201	4295	6496	SO:0001583	missense	8809	exon3			GTTAAAAAATTTT	U43672	CCDS2060.1	2q12	2013-01-29			ENSG00000115604	ENSG00000115604		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5988	protein-coding gene	gene with protein product		604494				8626725, 10191101	Standard	NM_003855		Approved	IL1RRP, IL-1Rrp, CD218a	uc010fiy.3	Q13478	OTTHUMG00000130780	ENST00000409599.1:c.400A>C	chr2.hg19:g.102988510A>C	ENSP00000387211:p.Lys134Gln	190.0	0.0		178.0	65.0	NM_003855	B2R9Y5|Q52LC9	Missense_Mutation	SNP	ENST00000409599.1	hg19	CCDS2060.1	.	.	.	.	.	.	.	.	.	.	A	13.68	2.309550	0.40895	.	.	ENSG00000115604	ENST00000410040;ENST00000409599;ENST00000233957;ENST00000334376	T;T;T	0.10573	2.86;2.86;2.86	5.15	4.0	0.46444	.	0.355112	0.25552	N	0.029887	T	0.18383	0.0441	L	0.49778	1.585	0.09310	N	1	P;D;P	0.57257	0.901;0.979;0.901	P;P;P	0.59546	0.692;0.859;0.692	T	0.07385	-1.0775	10	0.23891	T	0.37	.	7.5431	0.27751	0.9023:0.0:0.0977:0.0	.	134;134;134	B7ZKV7;Q86YL8;Q13478	.;.;IL18R_HUMAN	Q	134	ENSP00000386663:K134Q;ENSP00000387211:K134Q;ENSP00000233957:K134Q	ENSP00000233957:K134Q	K	+	1	0	IL18R1	102354942	0.037000	0.19845	0.001000	0.08648	0.003000	0.03518	2.614000	0.46359	0.932000	0.37266	0.459000	0.35465	AAA	.	.		0.279	IL18R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253294.2	NM_003855		C	102988510	A	C	102988510	3	2	261	1	0	0	0	0	1	0	0	0	7656	15	1	5	410	5	IL18R1	2	102988510	Missense_Mutation	SNP	A	TCGA-FV-A23B-01A-11D-A16V-10		102988510	140210863	10	38208										
ZNF804A	91752	hgsc.bcm.edu	37	chr2	185800964	185800964	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	aaactaactcttttcatccaCcagaggcaatgtgcagagac	7	11	2	2			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr2:185800964C>T	ENST00000302277.6	+	4	1435	c.841C>T	c.(841-843)Cca>Tca	p.P281S		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	281							metal ion binding (GO:0046872)			NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						TTTTCATCCACCAGAGGCAAT	0.368																																					p.P281S		Atlas-SNP	.											.	ZNF804A	322	.	0			c.C841T						.						62	59	60					2																	185800964		2203	4299	6502	SO:0001583	missense	91752	exon4			CATCCACCAGAGG	AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.841C>T	chr2.hg19:g.185800964C>T	ENSP00000303252:p.Pro281Ser	24.0	0.0		46.0	16.0	NM_194250	A7E253|Q6ZN26	Missense_Mutation	SNP	ENST00000302277.6	hg19	CCDS2291.1	.	.	.	.	.	.	.	.	.	.	C	1.718	-0.497322	0.04291	.	.	ENSG00000170396	ENST00000302277	T	0.65364	-0.15	5.57	0.304	0.15796	.	0.359593	0.24083	N	0.041715	T	0.36220	0.0959	N	0.22421	0.69	0.09310	N	1	B	0.26195	0.144	B	0.15870	0.014	T	0.20672	-1.0268	10	0.08599	T	0.76	-0.3547	6.7364	0.23411	0.1192:0.4811:0.3323:0.0675	.	281	Q7Z570	Z804A_HUMAN	S	281	ENSP00000303252:P281S	ENSP00000303252:P281S	P	+	1	0	ZNF804A	185509209	0.282000	0.24268	0.345000	0.25642	0.849000	0.48306	1.301000	0.33447	-0.017000	0.14103	0.591000	0.81541	CCA	.	.		0.368	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250		T	185800964	C	T	185800964	3	4	261	1	0	0	0	0	1	0	0	0	18185	507	18	3	855	3	ZNF804A	2	185800964	Missense_Mutation	SNP	C	TCGA-FV-A23B-01A-11D-A16V-10	82812454	185800964	57398409	11	38209										
STXBP5L	9515	hgsc.bcm.edu	37	chr3	120876465	120876465	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	gtcgccctttccagaccacaAttccacatggtaagatgtat	7	12	0	2	rs371884493		TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr3:120876465A>G	ENST00000273666.6	+	9	1139	c.868A>G	c.(868-870)Att>Gtt	p.I290V	STXBP5L_ENST00000492541.1_Missense_Mutation_p.I290V|STXBP5L_ENST00000472879.1_Missense_Mutation_p.I290V|STXBP5L_ENST00000497029.1_Missense_Mutation_p.I290V|STXBP5L_ENST00000471454.1_Missense_Mutation_p.I290V	NM_014980.2	NP_055795.1	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	290					exocytosis (GO:0006887)|glucose homeostasis (GO:0042593)|negative regulation of insulin secretion (GO:0046676)|positive regulation of protein secretion (GO:0050714)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(12)|lung(28)|ovary(7)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				GBM - Glioblastoma multiforme(114;0.0694)		CCAGACCACAATTCCACATGG	0.418																																					p.I290V		Atlas-SNP	.											.	STXBP5L	159	.	0			c.A868G						.	A	VAL/ILE	2,3800		0,2,1899	97	88	91		868	-1.1	1	3		91	0,8226		0,0,4113	no	missense	STXBP5L	NM_014980.2	29	0,2,6012	GG,GA,AA		0.0,0.0526,0.0166	benign	290/1187	120876465	2,12026	1901	4113	6014	SO:0001583	missense	9515	exon9			ACCACAATTCCAC	AB023223	CCDS43137.1	3q13.33-q21.1	2013-01-10			ENSG00000145087	ENSG00000145087		"WD repeat domain containing"	30757	protein-coding gene	gene with protein product		609381				10231032, 14767561	Standard	NM_014980		Approved	KIAA1006, LLGL4	uc003eec.4	Q9Y2K9	OTTHUMG00000159426	ENST00000273666.6:c.868A>G	chr3.hg19:g.120876465A>G	ENSP00000273666:p.Ile290Val	70.0	0.0		51.0	12.0	NM_014980	Q4G1B4|Q6PIC3	Missense_Mutation	SNP	ENST00000273666.6	hg19	CCDS43137.1	.	.	.	.	.	.	.	.	.	.	A	7.892	0.732435	0.15507	5.26E-4	0.0	ENSG00000145087	ENST00000273666;ENST00000471454;ENST00000472879;ENST00000497029;ENST00000492541;ENST00000471262	T;T;T;T;T;T	0.54071	0.59;1.63;0.59;0.59;1.63;1.63	5.26	-1.14	0.09741	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);Lethal giant larvae homologue 2 (1);	0.344395	0.34314	N	0.004078	T	0.19208	0.0461	N	0.02539	-0.55	0.26059	N	0.981373	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.34403	-0.9830	10	0.02654	T	1	-31.9659	11.0024	0.47614	0.4002:0.0:0.5998:0.0	.	290;290	E9PFI2;Q9Y2K9	.;STB5L_HUMAN	V	290	ENSP00000273666:I290V;ENSP00000420019:I290V;ENSP00000419627:I290V;ENSP00000420287:I290V;ENSP00000420666:I290V;ENSP00000420167:I290V	ENSP00000273666:I290V	I	+	1	0	STXBP5L	122359155	1.000000	0.71417	0.997000	0.53966	0.980000	0.70556	0.923000	0.28757	-0.119000	0.11830	-0.385000	0.06624	ATT	.	.		0.418	STXBP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355256.3			G	120876465	A	G	120876465	3	3	261	1	0	0	0	0	1	0	0	0	15372	101	4	2	898	2	STXBP5L	3	120876465	Missense_Mutation	SNP	A	TCGA-FV-A23B-01A-11D-A16V-10		120876465	77145965	12	38210										
COL6A6	131873	hgsc.bcm.edu	37	chr3	130282231	130282231	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	cccgcaaatgggagagacaaGaaacagtttcccccaattct	8	12	1	2			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr3:130282231G>T	ENST00000358511.6	+	2	415	c.384G>T	c.(382-384)aaG>aaT	p.K128N	COL6A6_ENST00000453409.2_Missense_Mutation_p.K128N	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	128	Nonhelical region.|VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						GGAGAGACAAGAAACAGTTTC	0.498																																					p.K128N		Atlas-SNP	.											.	COL6A6	497	.	0			c.G384T						.						42	42	42					3																	130282231		1886	4112	5998	SO:0001583	missense	131873	exon2			AGACAAGAAACAG	AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.384G>T	chr3.hg19:g.130282231G>T	ENSP00000351310:p.Lys128Asn	86.0	0.0		75.0	36.0	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	hg19	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	G	8.613	0.889623	0.17540	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	D;D	0.82984	-1.67;-1.67	5.21	3.29	0.37713	von Willebrand factor, type A (3);	0.460721	0.20698	N	0.087328	T	0.70456	0.3226	L	0.31476	0.935	0.22050	N	0.999394	B	0.06786	0.001	B	0.13407	0.009	T	0.57499	-0.7801	10	0.34782	T	0.22	.	6.782	0.23650	0.165:0.1489:0.6862:0.0	.	128	A6NMZ7	CO6A6_HUMAN	N	128	ENSP00000351310:K128N;ENSP00000399236:K128N	ENSP00000351310:K128N	K	+	3	2	COL6A6	131764921	0.047000	0.20315	0.873000	0.34254	0.315000	0.28087	0.440000	0.21592	1.334000	0.45468	0.561000	0.74099	AAG	.	.		0.498	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		T	130282231	G	T	130282231	3	4	261	1	0	0	0	0	1	0	0	0	3705	933	33	3	390	3	COL6A6	3	130282231	Missense_Mutation	SNP	G	TCGA-FV-A23B-01A-11D-A16V-10	9405766	130282231	67740199	13	38211										
PIK3R4	30849	hgsc.bcm.edu	37	chr3	130427320	130427320	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	gtgccagaagtttgtcttccTcttcctctgtcattccctaa	6	13	4	1			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr3:130427320T>A	ENST00000356763.3	-	10	2905	c.2348A>T	c.(2347-2349)gAg>gTg	p.E783V		NM_014602.2	NP_055417.1	Q99570	PI3R4_HUMAN	phosphoinositide-3-kinase, regulatory subunit 4	783	Poly-Glu.				innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	axoneme (GO:0005930)|cytosol (GO:0005829)|late endosome (GO:0005770)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(6)|large_intestine(16)|lung(28)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	77						TTTGTCTTCCTCTTCCTCTGT	0.358																																					p.E783V		Atlas-SNP	.											.	PIK3R4	145	.	0			c.A2348T						.						158	146	150					3																	130427320		2202	4300	6502	SO:0001583	missense	30849	exon10			TCTTCCTCTTCCT	Y08991	CCDS3067.1	3q22.1	2013-01-10	2008-02-04		ENSG00000196455	ENSG00000196455		"WD repeat domain containing"	8982	protein-coding gene	gene with protein product		602610				8999962	Standard	NM_014602		Approved	VPS15, p150	uc003enj.3	Q99570	OTTHUMG00000159645	ENST00000356763.3:c.2348A>T	chr3.hg19:g.130427320T>A	ENSP00000349205:p.Glu783Val	163.0	0.0		200.0	78.0	NM_014602	Q2TBF4	Missense_Mutation	SNP	ENST00000356763.3	hg19	CCDS3067.1	.	.	.	.	.	.	.	.	.	.	T	12.99	2.103191	0.37145	.	.	ENSG00000196455	ENST00000356763;ENST00000508273	T;T	0.46451	0.87;0.89	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.38665	0.1049	L	0.51422	1.61	0.80722	D	1	B	0.19331	0.035	B	0.11329	0.006	T	0.15235	-1.0444	10	0.25751	T	0.34	-30.3496	15.4838	0.75548	0.0:0.0:0.0:1.0	.	783	Q99570	PI3R4_HUMAN	V	783;142	ENSP00000349205:E783V;ENSP00000427302:E142V	ENSP00000349205:E783V	E	-	2	0	PIK3R4	131910010	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.615000	0.83006	2.058000	0.61347	0.460000	0.39030	GAG	.	.		0.358	PIK3R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356668.1	NM_014602		A	130427320	T	A	130427320	3	1	261	1	0	0	0	0	1	0	0	0	11930	1551	54	4	1772	4	PIK3R4	3	130427320	Missense_Mutation	SNP	T	TCGA-FV-A23B-01A-11D-A16V-10	145089	130427320	67595110	14	38212										
EXOC1	55763	hgsc.bcm.edu	37	chr4	56744128	56744128	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	cccaacactctgttgaactgActttacccaatcatcatcca	3	15	3	2			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr4:56744128A>G	ENST00000381295.2	+	9	1468	c.1120A>G	c.(1120-1122)Act>Gct	p.T374A	EXOC1_ENST00000346134.7_Missense_Mutation_p.T374A|EXOC1_ENST00000349598.6_Missense_Mutation_p.T374A	NM_001024924.1	NP_001020095.1	Q9NV70	EXOC1_HUMAN	exocyst complex component 1	374					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	35	Glioma(25;0.08)|all_neural(26;0.101)					TGTTGAACTGACTTTACCCAA	0.373																																					p.T374A		Atlas-SNP	.											.	EXOC1	103	.	0			c.A1120G						.						154	134	141					4																	56744128		2203	4300	6503	SO:0001583	missense	55763	exon9			GAACTGACTTTAC	AK027047	CCDS3502.1, CCDS3503.1	4q12	2013-01-22	2005-11-01	2005-11-01	ENSG00000090989	ENSG00000090989			30380	protein-coding gene	gene with protein product		607879	"SEC3-like 1 (S. cerevisiae)"	SEC3L1		11042152, 11406615	Standard	XM_005265747		Approved	SEC3, FLJ10893, BM-102, Sec3p	uc003hbf.1	Q9NV70	OTTHUMG00000102165	ENST00000381295.2:c.1120A>G	chr4.hg19:g.56744128A>G	ENSP00000370695:p.Thr374Ala	60.0	0.0		71.0	24.0	NM_018261	Q504V4|Q8WUE7|Q96T15|Q9NZE4	Missense_Mutation	SNP	ENST00000381295.2	hg19	CCDS3502.1	.	.	.	.	.	.	.	.	.	.	A	16.34	3.096395	0.56075	.	.	ENSG00000090989	ENST00000381295;ENST00000346134;ENST00000349598	.	.	.	5.65	4.46	0.54185	.	0.089605	0.85682	N	0.000000	T	0.45856	0.1363	L	0.41236	1.265	0.80722	D	1	B;B	0.22683	0.073;0.008	B;B	0.28305	0.088;0.042	T	0.22765	-1.0207	9	0.09843	T	0.71	.	10.8708	0.46883	0.9236:0.0:0.0764:0.0	.	374;374	Q9NV70-2;Q9NV70	.;EXOC1_HUMAN	A	374	.	ENSP00000326514:T374A	T	+	1	0	EXOC1	56438885	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.867000	0.69597	0.962000	0.38057	0.455000	0.32223	ACT	.	.		0.373	EXOC1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361799.1	NM_018261		G	56744128	A	G	56744128	3	3	261	1	0	0	0	0	1	0	0	0	5303	275	10	2	1150	2	EXOC1	4	56744128	Missense_Mutation	SNP	A	TCGA-FV-A23B-01A-11D-A16V-10		56744128	134410148	15	38213										
CENPC1	1060	hgsc.bcm.edu	37	chr4	68396566	68396566	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	ggcttcacttggttctacaaCaaactgtagagaggcttctt	9	9	3	1			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr4:68396566C>A	ENST00000273853.6	-	5	548	c.298G>T	c.(298-300)Gtt>Ttt	p.V100F		NM_001812.2	NP_001803.2	Q03188	CENPC_HUMAN	centromere protein C	100					chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	centromeric DNA binding (GO:0019237)|DNA binding (GO:0003677)										GGTTCTACAACAAACTGTAGA	0.388																																					p.V100F		Atlas-SNP	.											.	CENPC1	66	.	0			c.G298T						.						68	67	67					4																	68396566		1826	4082	5908	SO:0001583	missense	1060	exon5			CTACAACAAACTG	M95724	CCDS47063.1	4q13.2	2013-11-05	2013-07-03	2013-07-03	ENSG00000145241	ENSG00000145241			1854	protein-coding gene	gene with protein product		117141	"centromere protein C 1"	CENPC1		7959789	Standard	XR_245245		Approved	CENP-C, hcp-4, MIF2	uc003hdd.1	Q03188	OTTHUMG00000160735	ENST00000273853.6:c.298G>T	chr4.hg19:g.68396566C>A	ENSP00000273853:p.Val100Phe	57.0	0.0		66.0	18.0	NM_001812	Q8IW27|Q9P0M5	Missense_Mutation	SNP	ENST00000273853.6	hg19	CCDS47063.1	.	.	.	.	.	.	.	.	.	.	C	6.723	0.502156	0.12822	.	.	ENSG00000145241	ENST00000273853	.	.	.	4.22	-8.44	0.00950	.	2.868950	0.01019	N	0.003950	T	0.13200	0.0320	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.24225	-1.0166	9	0.10902	T	0.67	2.1738	1.7234	0.02916	0.2099:0.3068:0.3181:0.1651	.	100;100	Q8IW27;Q03188	.;CENPC_HUMAN	F	100	.	ENSP00000273853:V100F	V	-	1	0	CENPC1	68079161	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-3.781000	0.00368	-2.873000	0.00322	-0.982000	0.02568	GTT	.	.		0.388	CENPC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362001.2			A	68396566	C	A	68396566	3	1	261	1	0	0	0	0	1	0	0	0	3231	478	17	3	2593	3	CENPC1	4	68396566	Missense_Mutation	SNP	C	TCGA-FV-A23B-01A-11D-A16V-10	11652438	68396566	122757710	16	38214										
PF4V1	5197	hgsc.bcm.edu	37	chr4	74719566	74719566	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	cacctcccaggtccgtcccaGgcacatcaccagcctggagg	10	18	1	0			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr4:74719566G>A	ENST00000226524.3	+	2	341	c.167G>A	c.(166-168)aGg>aAg	p.R56K		NM_002620.2	NP_002611.1	P10720	PF4V_HUMAN	platelet factor 4 variant 1	56					cell chemotaxis (GO:0060326)|immune response (GO:0006955)	extracellular space (GO:0005615)	heparin binding (GO:0008201)			endometrium(1)|liver(2)	3	Breast(15;0.00102)		all cancers(17;0.00176)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)			GTCCGTCCCAGGCACATCACC	0.607																																					p.R56K		Atlas-SNP	.											.	PF4V1	8	.	0			c.G167A						.						56	60	59					4																	74719566		2202	4296	6498	SO:0001583	missense	5197	exon2			GTCCCAGGCACAT	M26167	CCDS3561.1	4q12-q21	2008-08-15			ENSG00000109272	ENSG00000109272			8862	protein-coding gene	gene with protein product		173461				2725510	Standard	NM_002620		Approved	SCYB4V1, CXCL4V1, CXCL4L1	uc003hhg.1	P10720	OTTHUMG00000130177	ENST00000226524.3:c.167G>A	chr4.hg19:g.74719566G>A	ENSP00000226524:p.Arg56Lys	58.0	0.0		62.0	23.0	NM_002620	A1L4S0	Missense_Mutation	SNP	ENST00000226524.3	hg19	CCDS3561.1	.	.	.	.	.	.	.	.	.	.	G	0.799	-0.756074	0.03019	.	.	ENSG00000109272	ENST00000226524	T	0.04862	3.54	4.12	-4.36	0.03645	CXC chemokine, conserved site (1);Chemokine interleukin-8-like domain (3);	0.802256	0.11866	N	0.521853	T	0.02418	0.0074	N	0.04132	-0.27	0.09310	N	1	B	0.24651	0.108	B	0.28991	0.097	T	0.42515	-0.9447	10	0.02654	T	1	.	11.6031	0.51015	0.348:0.0:0.652:0.0	.	56	P10720	PF4V_HUMAN	K	56	ENSP00000226524:R56K	ENSP00000226524:R56K	R	+	2	0	PF4V1	74938430	0.000000	0.05858	0.000000	0.03702	0.048000	0.14542	0.038000	0.13862	-0.820000	0.04318	-0.768000	0.03414	AGG	.	.		0.607	PF4V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252495.1			A	74719566	G	A	74719566	3	1	261	1	0	0	0	0	1	0	0	0	11762	1000	35	3	173	3	PF4V1	4	74719566	Missense_Mutation	SNP	G	TCGA-FV-A23B-01A-11D-A16V-10	6323000	74719566	116434710	17	38215										
CDKL2	8999	hgsc.bcm.edu	37	chr4	76551045	76551045	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	gcattgcaatctttttaaccAttttgtcatcgtcactttct	4	10	4	0			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr4:76551045A>G	ENST00000429927.2	-	2	831	c.128T>C	c.(127-129)aTg>aCg	p.M43T	CDKL2_ENST00000307465.4_Missense_Mutation_p.M43T	NM_003948.3	NP_003939.1	Q92772	CDKL2_HUMAN	cyclin-dependent kinase-like 2 (CDC2-related kinase)	43	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				sex differentiation (GO:0007548)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)			breast(3)|endometrium(1)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(2)|stomach(2)	22			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			CTTTTTAACCATTTTGTCATC	0.323																																					p.M43T		Atlas-SNP	.											.	CDKL2	58	.	0			c.T128C						.						174	166	169					4																	76551045		2202	4300	6502	SO:0001583	missense	8999	exon2			TTAACCATTTTGT	U35146	CCDS3570.1	4q21.21	2011-11-04			ENSG00000138769	ENSG00000138769		"Cyclin-dependent kinases"	1782	protein-coding gene	gene with protein product		603442				9000130	Standard	NM_003948		Approved	P56, KKIAMRE	uc003hiq.3	Q92772	OTTHUMG00000130103	ENST00000429927.2:c.128T>C	chr4.hg19:g.76551045A>G	ENSP00000412365:p.Met43Thr	104.0	0.0		133.0	54.0	NM_003948	B2R695	Missense_Mutation	SNP	ENST00000429927.2	hg19	CCDS3570.1	.	.	.	.	.	.	.	.	.	.	A	4.164	0.028925	0.08054	.	.	ENSG00000138769	ENST00000429927;ENST00000307465	T;T	0.63744	-0.06;-0.06	5.04	2.68	0.31781	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.38348	0.1037	N	0.11845	0.185	0.30427	N	0.777591	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.30416	-0.9979	9	0.10902	T	0.67	-19.8366	8.963	0.35858	0.8371:0.0:0.1629:0.0	.	43;43	B4DH08;Q92772	.;CDKL2_HUMAN	T	43	ENSP00000412365:M43T;ENSP00000306340:M43T	ENSP00000306340:M43T	M	-	2	0	CDKL2	76770069	0.986000	0.35501	1.000000	0.80357	0.998000	0.95712	1.208000	0.32345	1.055000	0.40461	0.533000	0.62120	ATG	.	.		0.323	CDKL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252409.2	NM_003948		G	76551045	A	G	76551045	3	3	261	1	0	0	0	0	1	0	0	0	3156	217	8	2	1393	2	CDKL2	4	76551045	Missense_Mutation	SNP	A	TCGA-FV-A23B-01A-11D-A16V-10	1831479	76551045	114603231	18	38216										
WDFY3	23001	hgsc.bcm.edu	37	chr4	85663040	85663040	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	ttcaccaatacctggtagctTcctccactggtaataggcag	8	12	1	0			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr4:85663040T>C	ENST00000295888.4	-	38	6515	c.6108A>G	c.(6106-6108)ggA>ggG	p.G2036G	WDFY3_ENST00000322366.6_Silent_p.G2036G	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	2036					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		CCTGGTAGCTTCCTCCACTGG	0.403																																					p.G2036G		Atlas-SNP	.											.	WDFY3	314	.	0			c.A6108G						.						73	72	73					4																	85663040		2203	4300	6503	SO:0001819	synonymous_variant	23001	exon38			GTAGCTTCCTCCA	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.6108A>G	chr4.hg19:g.85663040T>C		86.0	0.0		93.0	38.0	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Silent	SNP	ENST00000295888.4	hg19	CCDS3609.1																																																																																			.	.		0.403	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		C	85663040	T	C	85663040	2	2	261	1	0	0	0	0	0	0	0	1	17285	1770	62	2		2	WDFY3	4	85663040	Silent	SNP	T	TCGA-FV-A23B-01A-11D-A16V-10	9111995	85663040	105491236	19	38217										
NDST3	9348	hgsc.bcm.edu	37	chr4	118975959	118975959	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	ttatcagggaagaggctgacAttgtccttggacaggtacat	12	7	1	2	rs372361471		TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr4:118975959A>G	ENST00000296499.5	+	2	1297	c.894A>G	c.(892-894)acA>acG	p.T298T	NDST3_ENST00000433996.2_Silent_p.T298T	NM_004784.2	NP_004775.1	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	298	Heparan sulfate N-deacetylase 3.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			NS(1)|breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	54						AGAGGCTGACATTGTCCTTGG	0.398																																					p.T298T		Atlas-SNP	.											.	NDST3	107	.	0			c.A894G						.	A		0,4406		0,0,2203	155	144	148		894	-10.5	0	4		148	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	NDST3	NM_004784.2		0,1,6501	GG,GA,AA		0.0116,0.0,0.0077		298/874	118975959	1,13003	2203	4299	6502	SO:0001819	synonymous_variant	9348	exon2			GCTGACATTGTCC	AF074924	CCDS3708.1	4q26	2008-08-04			ENSG00000164100	ENSG00000164100		"Sulfotransferases, membrane-bound"	7682	protein-coding gene	gene with protein product		603950				9915799	Standard	NM_004784		Approved	HSST3	uc003ibx.3	O95803	OTTHUMG00000132959	ENST00000296499.5:c.894A>G	chr4.hg19:g.118975959A>G		69.0	0.0		60.0	23.0	NM_004784	B4DI67|Q4W5C1|Q4W5D0|Q6UWC5|Q9UP21	Silent	SNP	ENST00000296499.5	hg19	CCDS3708.1																																																																																			.	.		0.398	NDST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256517.4	NM_004784		G	118975959	A	G	118975959	2	3	261	1	0	0	0	0	0	0	0	1	10266	204	8	2		2	NDST3	4	118975959	Silent	SNP	A	TCGA-FV-A23B-01A-11D-A16V-10	33312919	118975959	72178317	20	38218										
IL31RA	133396	hgsc.bcm.edu	37	chr5	55202077	55202077	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	agcccaccaccctttcctggGaatctgtgtctcaggccacg	9	16	2	0			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr5:55202077G>C	ENST00000447346.2	+	9	1278	c.1213G>C	c.(1213-1215)Gaa>Caa	p.E405Q	IL31RA_ENST00000297015.3_Missense_Mutation_p.E263Q|IL31RA_ENST00000396834.1_Missense_Mutation_p.E386Q|IL31RA_ENST00000359040.5_Missense_Mutation_p.E405Q|IL31RA_ENST00000354961.4_Missense_Mutation_p.E386Q|IL31RA_ENST00000396836.2_Missense_Mutation_p.E405Q|IL31RA_ENST00000490985.1_Missense_Mutation_p.E263Q	NM_001242636.1|NM_139017.5	NP_001229565.1|NP_620586.3	Q8NI17	IL31R_HUMAN	interleukin 31 receptor A	373	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|homeostatic process (GO:0042592)|JAK-STAT cascade (GO:0007259)|macrophage differentiation (GO:0030225)|MAPK cascade (GO:0000165)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of macrophage activation (GO:0043031)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cytokine binding (GO:0019955)|cytokine receptor activity (GO:0004896)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)	21		Lung NSC(810;6.93e-05)|Prostate(74;0.00741)|Breast(144;0.0544)|Ovarian(174;0.223)				CCTTTCCTGGGAATCTGTGTC	0.527																																					p.E405Q		Atlas-SNP	.											.	IL31RA	84	.	0			c.G1213C						.						111	104	106					5																	55202077		2203	4300	6503	SO:0001583	missense	133396	exon9			TCCTGGGAATCTG	AY499339	CCDS3970.2, CCDS56365.1, CCDS56366.1, CCDS56367.1, CCDS75244.1, CCDS75245.1	5q11.2	2013-02-11			ENSG00000164509	ENSG00000164509		"Interleukins and interleukin receptors", "Fibronectin type III domain containing"	18969	protein-coding gene	gene with protein product		609510				15184896, 11877449	Standard	NM_139017		Approved	CRL3, GLM-R, CRL, Glmr, IL-31RA	uc003jql.3	Q8NI17	OTTHUMG00000097045	ENST00000447346.2:c.1213G>C	chr5.hg19:g.55202077G>C	ENSP00000415900:p.Glu405Gln	57.0	0.0		54.0	25.0	NM_001242637	A6NIF8|Q2TBA1|Q6EBC3|Q6EBC4|Q6EBC5|Q6EBC6|Q6UWL8|Q8WYJ0	Missense_Mutation	SNP	ENST00000447346.2	hg19	CCDS3970.2	.	.	.	.	.	.	.	.	.	.	G	12.69	2.014725	0.35511	.	.	ENSG00000164509	ENST00000396836;ENST00000396834;ENST00000447346;ENST00000359040;ENST00000297015;ENST00000490985;ENST00000354961	T;T;T;T;T;T;T	0.44083	1.52;1.17;1.14;1.16;1.33;0.93;1.17	4.95	4.95	0.65309	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.903970	0.09722	N	0.764265	T	0.42449	0.1203	L	0.42581	1.335	0.29837	N	0.829572	P;P;P;P;P	0.51537	0.911;0.884;0.884;0.946;0.607	P;P;B;P;B	0.49665	0.532;0.54;0.421;0.618;0.419	T	0.06285	-1.0835	10	0.10377	T	0.69	-7.9589	11.4193	0.49971	0.0:0.1821:0.8179:0.0	.	373;405;386;405;405	Q8NI17;Q8NI17-5;Q8NI17-3;Q8NI17-2;Q8NI17-8	IL31R_HUMAN;.;.;.;.	Q	405;386;405;405;263;263;386	ENSP00000380048:E405Q;ENSP00000380046:E386Q;ENSP00000415900:E405Q;ENSP00000351935:E405Q;ENSP00000297015:E263Q;ENSP00000427533:E263Q;ENSP00000347047:E386Q	ENSP00000297015:E263Q	E	+	1	0	IL31RA	55237834	1.000000	0.71417	0.997000	0.53966	0.813000	0.45954	3.262000	0.51538	2.586000	0.87340	0.655000	0.94253	GAA	.	.		0.527	IL31RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214148.1	NM_139017		C	55202077	G	C	55202077	3	2	261	1	0	0	0	0	1	0	0	0	7700	1175	41	4	1247	4	IL31RA	5	55202077	Missense_Mutation	SNP	G	TCGA-FV-A23B-01A-11D-A16V-10		55202077	125713183	21	38219										
HTR1A	3350	hgsc.bcm.edu	37	chr5	63256420	63256420	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	cgcccaacagggtgggcatgTggcagctgctctcgcagaag	15	12	1	1			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr5:63256420T>A	ENST00000323865.3	-	1	1360	c.1127A>T	c.(1126-1128)cAc>cTc	p.H376L	RP11-158J3.2_ENST00000502882.1_RNA	NM_000524.3	NP_000515.2	P08908	5HT1A_HUMAN	5-hydroxytryptamine (serotonin) receptor 1A, G protein-coupled	376					adenylate cyclase-inhibiting serotonin receptor signaling pathway (GO:0007198)|behavioral fear response (GO:0001662)|cell proliferation (GO:0008283)|exploration behavior (GO:0035640)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cell proliferation (GO:0008284)|regulation of behavior (GO:0050795)|regulation of dopamine metabolic process (GO:0042053)|regulation of hormone secretion (GO:0046883)|regulation of serotonin secretion (GO:0014062)|serotonin metabolic process (GO:0042428)|serotonin receptor signaling pathway (GO:0007210)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin receptor activity (GO:0004993)			cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(29)|ovary(2)|pancreas(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	56		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0575)|Colorectal(97;0.234)		Lung(70;0.105)	Acepromazine(DB01614)|Alprenolol(DB00866)|Alverine(DB01616)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bopindolol(DB08807)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinitapride(DB08810)|Clozapine(DB00363)|Desipramine(DB01151)|Dopamine(DB00988)|Doxepin(DB01142)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Methysergide(DB00247)|Mianserin(DB06148)|Molindone(DB01618)|Naratriptan(DB00952)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Ondansetron(DB00904)|Paliperidone(DB01267)|Penbutolol(DB01359)|Pergolide(DB01186)|Pindolol(DB00960)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Propranolol(DB00571)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sumatriptan(DB00669)|Thioproperazine(DB01622)|Trazodone(DB00656)|Trimipramine(DB00726)|Vilazodone(DB06684)|Yohimbine(DB01392)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)	GGTGGGCATGTGGCAGCTGCT	0.532																																					p.H376L		Atlas-SNP	.											.	HTR1A	128	.	0			c.A1127T						.						139	145	143					5																	63256420		2203	4300	6503	SO:0001583	missense	3350	exon1			GGCATGTGGCAGC	AF498978	CCDS34168.1	5q11.2-q13	2012-08-08	2012-02-03			ENSG00000178394		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5286	protein-coding gene	gene with protein product		109760	"5-hydroxytryptamine (serotonin) receptor 1A"	ADRB2RL1, ADRBRL1		2591972, 12969265	Standard	NM_000524		Approved	5-HT1A	uc011cqt.3	P08908		ENST00000323865.3:c.1127A>T	chr5.hg19:g.63256420T>A	ENSP00000316244:p.His376Leu	61.0	0.0		63.0	24.0	NM_000524	Q6LAE7	Missense_Mutation	SNP	ENST00000323865.3	hg19	CCDS34168.1	.	.	.	.	.	.	.	.	.	.	T	8.267	0.812444	0.16537	.	.	ENSG00000178394	ENST00000323865	T	0.69435	-0.4	5.7	3.19	0.36642	GPCR, rhodopsin-like superfamily (1);	0.510690	0.22553	N	0.058571	T	0.44871	0.1314	N	0.21240	0.645	0.38590	D	0.950406	B	0.30146	0.27	B	0.28916	0.096	T	0.27971	-1.0058	10	0.09843	T	0.71	.	7.4116	0.27021	0.0:0.0747:0.1441:0.7812	.	376	P08908	5HT1A_HUMAN	L	376	ENSP00000316244:H376L	ENSP00000316244:H376L	H	-	2	0	HTR1A	63292176	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	2.751000	0.47508	0.998000	0.38996	0.533000	0.62120	CAC	.	.		0.532	HTR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368397.1	NM_000524		A	63256420	T	A	63256420	3	1	261	1	0	0	0	0	1	0	0	0	7445	1696	59	4	144	4	HTR1A	5	63256420	Missense_Mutation	SNP	T	TCGA-FV-A23B-01A-11D-A16V-10	8054343	63256420	117658840	22	38220										
MTX3	345778	hgsc.bcm.edu	37	chr5	79287047	79287047	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	cctccccagcaactgagttcCaagggggccgccatcttgcg	11	16	1	1			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr5:79287047C>A	ENST00000512528.1	-	1	35	c.15G>T	c.(13-15)ttG>ttT	p.L5F	MTX3_ENST00000509852.1_Missense_Mutation_p.L5F|MTX3_ENST00000512560.1_5'UTR			Q5HYI7	MTX3_HUMAN	metaxin 3	5					protein targeting to mitochondrion (GO:0006626)	mitochondrial outer membrane (GO:0005741)				endometrium(1)|large_intestine(3)|lung(2)|urinary_tract(1)	7		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.63e-45)|Epithelial(54;2.9e-40)|all cancers(79;4.68e-35)		AACTGAGTTCCAAGGGGGCCG	0.652																																					p.L5F		Atlas-SNP	.											.	MTX3	29	.	0			c.G15T						.						5	7	6					5																	79287047		1640	3567	5207	SO:0001583	missense	345778	exon1			GAGTTCCAAGGGG	BX538064	CCDS47239.1, CCDS47239.2, CCDS54872.1	5q14.1	2004-08-18				ENSG00000177034			24812	protein-coding gene	gene with protein product						15087125	Standard	NM_001010891		Approved		uc010jah.3	Q5HYI7		ENST00000512528.1:c.15G>T	chr5.hg19:g.79287047C>A	ENSP00000424798:p.Leu5Phe	27.0	0.0		26.0	14.0	NM_001010891	B4DL65|E9PB57|Q7Z380|Q8NB92	Missense_Mutation	SNP	ENST00000512528.1	hg19		.	.	.	.	.	.	.	.	.	.	C	15.99	2.996853	0.54147	.	.	ENSG00000177034	ENST00000328496;ENST00000509852;ENST00000512528;ENST00000418095	T;T	0.54675	0.56;0.59	5.1	3.32	0.38043	.	0.167153	0.48286	D	0.000187	T	0.45816	0.1361	L	0.49126	1.545	0.28350	N	0.920937	B;B	0.31859	0.343;0.006	B;B	0.33799	0.17;0.011	T	0.46775	-0.9167	10	0.44086	T	0.13	-0.8557	10.5593	0.45135	0.0:0.8425:0.0:0.1575	.	5;5	Q5HYI7-4;Q5HYI7	.;MTX3_HUMAN	F	5	ENSP00000423302:L5F;ENSP00000424798:L5F	ENSP00000331672:L5F	L	-	3	2	MTX3	79322803	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.687000	0.46976	1.511000	0.48818	0.655000	0.94253	TTG	.	.		0.652	MTX3-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372567.1	XM_293971		A	79287047	C	A	79287047	3	1	261	1	0	0	0	0	1	0	0	0	9978	593	21	3	959	3	MTX3	5	79287047	Missense_Mutation	SNP	C	TCGA-FV-A23B-01A-11D-A16V-10	16030627	79287047	101628213	23	38221										
ANKHD1	54882	hgsc.bcm.edu	37	chr5	139903797	139903798	+	Frame_Shift_Ins	INS	-	-	G													0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	attcggaactaccagaggatINSgaagatgaagaggagaatga							TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr5:139903797_139903798insG	ENST00000360839.2	+	25	4618_4619	c.4464_4465insG	c.(4465-4467)gaafs	p.E1489fs	ANKHD1_ENST00000297183.6_Frame_Shift_Ins_p.E1489fs|ANKHD1-EIF4EBP3_ENST00000532219.1_Frame_Shift_Ins_p.E1489fs|ANKHD1_ENST00000544120.1_5'Flank	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	1489						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TACCAGAGGATGAAGATGAAGA	0.342																																					p.D1488fs		Atlas-INDEL	.											.	ANKHD1	233	.	0			c.4464_4465insG						.																																			SO:0001589	frameshift_variant	54882	exon25			.	AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503		"Ankyrin repeat domain containing"	24714	protein-coding gene	gene with protein product		610500				10470851, 11230166, 16098192	Standard	NM_017747		Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.4465dupG	chr5.hg19:g.139903798_139903798dupG	ENSP00000354085:p.Glu1489fs	410.0	0.0		479.0	160.0	NM_017747	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Frame_Shift_Ins	INS	ENST00000360839.2	hg19	CCDS4225.1																																																																																			.	.		0.342	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747		G	139903798	-	G	139903797	7	5	261	1	0	1	1	0	0	0	0	0	628	1461	51	0	4668	0	ANKHD1	5	139903797	Frame_Shift_Ins	INS	-	TCGA-FV-A23B-01A-11D-A16V-10	60616750	139903797	41011463	24	38222										
FBXW11	23291	hgsc.bcm.edu	37	chr5	171296743	171296743	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	gatcacataccaccaatgtgCgcaaacacaatgtgcttgct	7	12	1	0			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr5:171296743C>T	ENST00000265094.5	-	11	1594	c.1457G>A	c.(1456-1458)cGc>cAc	p.R486H	FBXW11_ENST00000393802.2_Missense_Mutation_p.R452H|FBXW11_ENST00000296933.6_Missense_Mutation_p.R473H|FBXW11_ENST00000425623.2_Missense_Mutation_p.R454H	NM_012300.2	NP_036432.2	Q9UKB1	FBW1B_HUMAN	F-box and WD repeat domain containing 11	486					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of proteolysis (GO:0045862)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein dephosphorylation (GO:0006470)|protein destabilization (GO:0031648)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|rhythmic process (GO:0048511)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|prostate(2)|urinary_tract(2)	21	Renal(175;0.000159)|Lung NSC(126;0.00384)|all_lung(126;0.00659)	Medulloblastoma(196;0.00853)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CACCAATGTGCGCAAACACAA	0.468																																					p.R486H		Atlas-SNP	.											.	FBXW11	72	.	0			c.G1457A						.						66	50	55					5																	171296743		2203	4300	6503	SO:0001583	missense	23291	exon11			AATGTGCGCAAAC	AB014596	CCDS34289.1, CCDS47340.1, CCDS47341.1	5q35.1	2013-01-09	2007-02-08	2004-06-16	ENSG00000072803	ENSG00000072803		"F-boxes / WD-40 domains", "WD repeat domain containing"	13607	protein-coding gene	gene with protein product		605651	"F-box and WD-40 domain protein 1B", "F-box and WD-40 domain protein 11"	FBXW1B		10531035, 10694485	Standard	NM_033644		Approved	KIAA0696, Fbw1b, BTRCP2, BTRC2, Hos, Fbw11	uc003mbm.1	Q9UKB1	OTTHUMG00000163267	ENST00000265094.5:c.1457G>A	chr5.hg19:g.171296743C>T	ENSP00000265094:p.Arg486His	48.0	0.0		46.0	22.0	NM_012300	B2RC98|Q9P2S8|Q9P2S9|Q9Y4C6	Missense_Mutation	SNP	ENST00000265094.5	hg19	CCDS34289.1	.	.	.	.	.	.	.	.	.	.	C	17.80	3.478284	0.63849	.	.	ENSG00000072803	ENST00000296933;ENST00000265094;ENST00000393802;ENST00000425623	T;T;T;T	0.60424	0.19;0.19;0.19;0.19	5.48	5.48	0.80851	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.40570	0.1122	N	0.13198	0.31	0.80722	D	1	P;B;P;P	0.36392	0.551;0.346;0.551;0.496	B;B;B;B	0.26202	0.046;0.027;0.067;0.04	T	0.42413	-0.9453	10	0.48119	T	0.1	-10.3967	18.9821	0.92758	0.0:1.0:0.0:0.0	.	454;452;486;473	B4DH70;Q9UKB1-2;Q9UKB1;Q9UKB1-3	.;.;FBW1B_HUMAN;.	H	473;486;452;454	ENSP00000296933:R473H;ENSP00000265094:R486H;ENSP00000377391:R452H;ENSP00000444929:R454H	ENSP00000265094:R486H	R	-	2	0	FBXW11	171229348	1.000000	0.71417	1.000000	0.80357	0.635000	0.38103	7.770000	0.85390	2.572000	0.86782	0.655000	0.94253	CGC	.	.		0.468	FBXW11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000372382.1	NM_012300		T	171296743	C	T	171296743	3	4	261	1	0	0	0	0	1	0	0	0	5772	768	27	1	179	1	FBXW11	5	171296743	Missense_Mutation	SNP	C	TCGA-FV-A23B-01A-11D-A16V-10	31392946	171296743	9618517	25	38223										
HLA-B	3106	hgsc.bcm.edu	37	chr6	31324160	31324161	+	Frame_Shift_Ins	INS	-	-	A													0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	gcgtactggtcatgcccgcgINSgaggaggcgcccgtccggcc					rs45532737|rs137854719		TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr6:31324160_31324161insA	ENST00000412585.2	-	3	430_431	c.402_403insT	c.(400-405)ctccgcfs	p.R135fs		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	135	Alpha-2.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						TCATGCCCGCGGAGGAGGCGCC	0.718									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.R135fs		Atlas-INDEL	.											.,1	HLA-B	54	.	0			c.403_404insT						.																																			SO:0001589	frameshift_variant	3106	exon3	Familial Cancer Database	;Lichen Sclerosis, Familial	.	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4932	protein-coding gene	gene with protein product		142830	"ankylosing spondylitis"	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.402_403insT	chr6.hg19:g.31324160_31324161insA	ENSP00000399168:p.Arg135fs	46.0	0.0		40.0	13.0	NM_005514	Q29764	Frame_Shift_Ins	INS	ENST00000412585.2	hg19	CCDS34394.1																																																																																			.	.		0.718	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514		A	31324161	-	A	31324160	7	5	261	1	0	1	1	0	0	0	0	0	7205	1116	39	0	705	0	HLA-B	6	31324160	Frame_Shift_Ins	INS	-	TCGA-FV-A23B-01A-11D-A16V-10		31324160	139790907	26	38224										
COL12A1	1303	hgsc.bcm.edu	37	chr6	75855116	75855116	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	ggactgtgactgcatactccGtgttgggaacaaggtcagtc	13	9	1	1	rs373216375		TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr6:75855116G>A	ENST00000322507.8	-	25	4925	c.4616C>T	c.(4615-4617)aCg>aTg	p.T1539M	COL12A1_ENST00000416123.2_Missense_Mutation_p.T1539M|COL12A1_ENST00000483888.2_Missense_Mutation_p.T1539M|COL12A1_ENST00000345356.6_Missense_Mutation_p.T375M	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	1539	Fibronectin type-III 10. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						TGCATACTCCGTGTTGGGAAC	0.478																																					p.T1539M		Atlas-SNP	.											.	COL12A1	385	.	0			c.C4616T						.						98	104	102					6																	75855116		2089	4232	6321	SO:0001583	missense	1303	exon25			TACTCCGTGTTGG	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.4616C>T	chr6.hg19:g.75855116G>A	ENSP00000325146:p.Thr1539Met	34.0	0.0		24.0	17.0	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	hg19	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	G	15.40	2.823489	0.50739	.	.	ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000345356;ENST00000416123;ENST00000483888	T;T;T;T	0.62232	0.04;0.04;0.04;0.04	5.34	4.46	0.54185	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.064401	0.64402	D	0.000009	T	0.78457	0.4286	M	0.89715	3.055	0.51233	D	0.999917	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.83526	0.0088	10	0.56958	D	0.05	.	15.3834	0.74679	0.0:0.0:0.8594:0.1406	.	375;1539	Q99715-2;Q99715	.;COCA1_HUMAN	M	1539;1539;375;1539;1539	ENSP00000325146:T1539M;ENSP00000305147:T375M;ENSP00000412864:T1539M;ENSP00000421216:T1539M	ENSP00000325146:T1539M	T	-	2	0	COL12A1	75911836	1.000000	0.71417	0.663000	0.29738	0.024000	0.10985	9.395000	0.97266	1.226000	0.43582	0.655000	0.94253	ACG	.	.		0.478	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		A	75855116	G	A	75855116	3	1	261	1	0	0	0	0	1	0	0	0	3671	1145	40	1	4743	1	COL12A1	6	75855116	Missense_Mutation	SNP	G	TCGA-FV-A23B-01A-11D-A16V-10	44530956	75855116	95259951	27	38225										
FGFR1OP	11116	hgsc.bcm.edu	37	chr6	167438330	167438330	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	ctctcggatgcaccccccttAaaaagtggactcagctccct	7	16	2	0			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr6:167438330A>G	ENST00000366847.4	+	9	1098	c.867A>G	c.(865-867)ttA>ttG	p.L289L	RP11-517H2.6_ENST00000609590.1_RNA|FGFR1OP_ENST00000349556.4_Silent_p.L269L	NM_007045.2	NP_008976.1	O95684	FR1OP_HUMAN	FGFR1 oncogene partner	289					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|mitotic cell cycle (GO:0000278)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein tyrosine kinase activity (GO:0061099)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|protein tyrosine kinase inhibitor activity (GO:0030292)			large_intestine(2)|ovary(1)|stomach(1)	4		Breast(66;1.48e-05)|Ovarian(120;0.0607)		OV - Ovarian serous cystadenocarcinoma(33;1.73e-19)|BRCA - Breast invasive adenocarcinoma(81;5.1e-06)|GBM - Glioblastoma multiforme(31;0.00231)		CACCCCCCTTAAAAAGTGGAC	0.483			T	FGFR1	"MPD, NHL"																																p.L289L		Atlas-SNP	.		Dom	yes		6	6q27	11116	FGFR1 oncogene partner (FOP)		L	.	FGFR1OP	24	.	0			c.A867G						.						113	128	123					6																	167438330		2203	4300	6503	SO:0001819	synonymous_variant	11116	exon9			CCCCTTAAAAAGT	Y18046	CCDS5296.1, CCDS5297.1, CCDS75550.1	6q27	2008-02-05			ENSG00000213066	ENSG00000213066			17012	protein-coding gene	gene with protein product		605392				9949182, 10373756	Standard	NM_007045		Approved	FOP	uc003qvj.3	O95684	OTTHUMG00000016011	ENST00000366847.4:c.867A>G	chr6.hg19:g.167438330A>G		80.0	0.0		30.0	23.0	NM_007045	A8K1D1|B2R705|Q49AI0|Q5R3F6|Q96EW1	Silent	SNP	ENST00000366847.4	hg19	CCDS5296.1																																																																																			.	.		0.483	FGFR1OP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043099.2	NM_007045		G	167438330	A	G	167438330	2	3	261	1	0	0	0	0	0	0	0	1	5872	359	13	2		2	FGFR1OP	6	167438330	Silent	SNP	A	TCGA-FV-A23B-01A-11D-A16V-10	91583214	167438330	3676737	28	38226										
C7orf70	84792	hgsc.bcm.edu	37	chr7	6370386	6370386	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	gccgtcagtggccctgggccCtcctcccagccagtctcgcc	11	20	2	0			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr7:6370386C>T	ENST00000313324.4	-	2	867	c.400G>A	c.(400-402)Ggg>Agg	p.G134R	FAM220A_ENST00000533877.1_5'Flank	NM_001037163.1	NP_001032240.1	Q7Z4H9	F220A_HUMAN	family with sequence similarity 220, member A	134						nucleus (GO:0005634)											GCCCTGGGCCCTCCTCCCAGC	0.612																																					p.G134R		Atlas-SNP	.											.	.	.	.	0			c.G400A						.						33	36	35					7																	6370386		2203	4300	6503	SO:0001583	missense	84792	exon2			TGGGCCCTCCTCC	BC006110	CCDS34599.1	7p22.1	2012-03-19	2012-03-19	2012-03-19	ENSG00000178397	ENSG00000178397			22422	protein-coding gene	gene with protein product	"STAT3-interacting protein as a repressor"		"chromosome 7 open reading frame 70"	C7orf70			Standard	NM_001037163		Approved	SIPAR, MGC12966	uc003spu.3	Q7Z4H9	OTTHUMG00000122091	ENST00000313324.4:c.400G>A	chr7.hg19:g.6370386C>T	ENSP00000317289:p.Gly134Arg	32.0	0.0		45.0	14.0	NM_001037163	Q75ML2|Q8NA52|Q9BRR7	Missense_Mutation	SNP	ENST00000313324.4	hg19	CCDS34599.1	.	.	.	.	.	.	.	.	.	.	C	12.88	2.069454	0.36470	.	.	ENSG00000178397	ENST00000313324	T	0.08370	3.1	5.29	2.44	0.29823	.	1.072050	0.07395	U	0.889859	T	0.17577	0.0422	L	0.50333	1.59	0.09310	N	0.999999	D	0.59357	0.985	P	0.58820	0.846	T	0.17776	-1.0358	10	0.51188	T	0.08	-0.2748	5.3453	0.16006	0.1483:0.632:0.1429:0.0768	.	134	Q7Z4H9	SIPAR_HUMAN	R	134	ENSP00000317289:G134R	ENSP00000317289:G134R	G	-	1	0	C7orf70	6336911	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	0.603000	0.24149	0.216000	0.20781	-0.175000	0.13238	GGG	.	.		0.612	FAM220A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000242853.2	NM_001037163		T	6370386	C	T	6370386	3	4	261	1	0	0	0	0	1	0	0	0	2417	681	24	3	383	3	C7orf70	7	6370386	Missense_Mutation	SNP	C	TCGA-FV-A23B-01A-11D-A16V-10		6370386	152768277	29	38227										
GRM8	2918	hgsc.bcm.edu	37	chr7	126542649	126542649	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	catgtgatcctaacttgcagCcaaaattctcctcccagaat	5	13	1	2	rs78947184		TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr7:126542649C>A	ENST00000339582.2	-	6	1911	c.1103G>T	c.(1102-1104)gGc>gTc	p.G368V	GRM8_ENST00000444921.2_Missense_Mutation_p.G368V|GRM8_ENST00000358373.3_Missense_Mutation_p.G368V|GRM8_ENST00000480995.1_5'UTR|GRM8_ENST00000405249.1_Missense_Mutation_p.G368V			O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8	368			G -> D. {ECO:0000269|Ref.6}.		adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of cAMP biosynthetic process (GO:0030818)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(16)|lung(62)|ovary(5)|pancreas(1)|prostate(1)|skin(14)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(4)	125		Prostate(267;0.186)				TAACTTGCAGCCAAAATTCTC	0.373										HNSCC(24;0.065)																											p.G368V		Atlas-SNP	.											.	GRM8	377	.	0			c.G1103T						.						87	86	86					7																	126542649		2203	4300	6503	SO:0001583	missense	2918	exon5			TTGCAGCCAAAAT		CCDS5794.1, CCDS47696.1	7q31.3-q32.1	2012-08-29			ENSG00000179603	ENSG00000179603		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4600	protein-coding gene	gene with protein product		601116				8824806	Standard	NM_000845		Approved	GLUR8, GPRC1H, mGlu8, MGLUR8	uc003vlr.2	O00222	OTTHUMG00000022888	ENST00000339582.2:c.1103G>T	chr7.hg19:g.126542649C>A	ENSP00000344173:p.Gly368Val	77.0	0.0		66.0	28.0	NM_000845	A4D0Y3|B0FZ74|B0M0L0|O15493|O95945|O95946|Q3MIV9|Q52M02|Q6J165	Missense_Mutation	SNP	ENST00000339582.2	hg19	CCDS5794.1	.	.	.	.	.	.	.	.	.	.	C	12.29	1.893439	0.33442	.	.	ENSG00000179603	ENST00000339582;ENST00000444921;ENST00000358373;ENST00000405249	D;D;D;D	0.87029	-2.2;-2.2;-2.2;-2.2	4.88	4.88	0.63580	Extracellular ligand-binding receptor (1);	0.266832	0.38111	N	0.001801	D	0.84624	0.5513	L	0.47716	1.5	0.80722	D	1	B;B;B	0.18013	0.009;0.002;0.025	B;B;B	0.21151	0.021;0.003;0.033	T	0.82510	-0.0421	10	0.72032	D	0.01	.	17.0297	0.86457	0.0:1.0:0.0:0.0	.	368;368;368	O00222-3;O00222-2;O00222	.;.;GRM8_HUMAN	V	368	ENSP00000344173:G368V;ENSP00000409790:G368V;ENSP00000351142:G368V;ENSP00000385731:G368V	ENSP00000344173:G368V	G	-	2	0	GRM8	126329885	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	2.385000	0.44371	2.251000	0.74343	0.511000	0.50034	GGC	.	C|0.995;T|0.005		0.373	GRM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059209.4			A	126542649	C	A	126542649	3	1	261	1	0	0	0	0	1	0	0	0	6812	739	26	3	1697	3	GRM8	7	126542649	Missense_Mutation	SNP	C	TCGA-FV-A23B-01A-11D-A16V-10	120172263	126542649	32596014	30	38228										
XKR5	389610	hgsc.bcm.edu	37	chr8	6681084	6681084	+	RNA	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	agtggtaggctttgtagaacAgaaccagactcagcacgcgg	13	9	1	3			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr8:6681084A>T	ENST00000518724.1	-	0	746							Q6UX68	XKR5_HUMAN	XK, Kell blood group complex subunit-related family, member 5							integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(1)	3			STAD - Stomach adenocarcinoma(24;0.0984)	READ - Rectum adenocarcinoma(644;0.137)|COAD - Colon adenocarcinoma(149;0.166)		TTTGTAGAACAGAACCAGACT	0.532																																					p.L199Q		Atlas-SNP	.											.	XKR5	20	.	0			c.T596A						.						42	48	46					8																	6681084		2009	4167	6176			389610	exon4			TAGAACAGAACCA	AY358489		8p23.1	2006-01-12	2006-01-12		ENSG00000186530	ENSG00000275591			20782	protein-coding gene	gene with protein product			"X Kell blood group precursor-related family, member 5"				Standard	NM_207411		Approved		uc022aqv.1	Q6UX68	OTTHUMG00000153652		chr8.hg19:g.6681084A>T		82.0	0.0		85.0	36.0	NM_207411	Q5GH74	Missense_Mutation	SNP	ENST00000518724.1	hg19																																																																																				.	.		0.532	XKR5-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000331969.2	NM_207411		T	6681084	A	T	6681084	1	4	261	0	1	0	0	0	0	0	0	0	17449	188	7	4		4	XKR5	8	6681084	RNA	SNP	A	TCGA-FV-A23B-01A-11D-A16V-10		6681084	139682938	31	38229										
OPLAH	26873	hgsc.bcm.edu	37	chr8	145112593	145112593	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	gcgacccaggaccagattagCatccgtcactgtcacagggc	11	14	2	1			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr8:145112593C>T	ENST00000426825.1	-	10	1261	c.1180G>A	c.(1180-1182)Gct>Act	p.A394T	OPLAH_ENST00000534424.1_5'UTR	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	394					glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	5-oxoprolinase (ATP-hydrolyzing) activity (GO:0017168)|ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			ACCAGATTAGCATCCGTCACT	0.647																																					p.A394T		Atlas-SNP	.											.	OPLAH	78	.	0			c.G1180A						.						18	22	21					8																	145112593		2015	4154	6169	SO:0001583	missense	26873	exon10			GATTAGCATCCGT	AF024672, AB122018	CCDS75802.1	8q24.3	2010-11-23			ENSG00000178814	ENSG00000178814	3.5.2.9		8149	protein-coding gene	gene with protein product		614243				14993790	Standard	NM_017570		Approved	OPLA, 5-Opase	uc003zar.3	O14841		ENST00000426825.1:c.1180G>A	chr8.hg19:g.145112593C>T	ENSP00000475943:p.Ala394Thr	58.0	0.0		48.0	22.0	NM_017570	A5PKY8|Q75W65|Q9Y4Q0	Missense_Mutation	SNP	ENST00000426825.1	hg19		.	.	.	.	.	.	.	.	.	.	C	14.55	2.567423	0.45694	.	.	ENSG00000178814	ENST00000426825	.	.	.	4.31	4.31	0.51392	.	0.054782	0.64402	D	0.000001	T	0.77922	0.4203	.	.	.	0.44908	D	0.997921	D	0.69078	0.997	D	0.69654	0.965	D	0.84442	0.0583	7	0.87932	D	0	.	14.6309	0.68655	0.0:1.0:0.0:0.0	.	394	O14841	OPLA_HUMAN	T	394	.	ENSP00000412071:A394T	A	-	1	0	OPLAH	145184581	0.998000	0.40836	1.000000	0.80357	0.995000	0.86356	3.592000	0.53993	2.103000	0.63969	0.467000	0.42956	GCT	.	.		0.647	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017570		T	145112593	C	T	145112593	3	4	261	1	0	0	0	0	1	0	0	0	10885	710	25	3	2760	3	OPLAH	8	145112593	Missense_Mutation	SNP	C	TCGA-FV-A23B-01A-11D-A16V-10	138431509	145112593	1251429	32	38230										
FAM108B1	51104	hgsc.bcm.edu	37	chr9	74481719	74481719	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	tattttacaaatttaccagtTcctgtgacacaaactgtttc	4	9	0	1			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr9:74481719T>G	ENST00000333421.6	-	4	962	c.851A>C	c.(850-852)gAa>gCa	p.E284A	ABHD17B_ENST00000377041.2_Missense_Mutation_p.E284A	NM_001025780.1	NP_001020951.1	Q5VST6	AB17B_HUMAN	abhydrolase domain containing 17B	284						extracellular region (GO:0005576)|membrane (GO:0016020)	hydrolase activity (GO:0016787)										ATTTACCAGTTCCTGTGACAC	0.388																																					p.E284A		Atlas-SNP	.											.	FAM108B1	24	.	0			c.A851C						.						55	52	53					9																	74481719		2203	4300	6503	SO:0001583	missense	51104	exon4			ACCAGTTCCTGTG	AF151825	CCDS35042.1, CCDS35043.1	9q21.2	2013-03-15	2013-03-15	2013-03-15	ENSG00000107362	ENSG00000107362		"Abhydrolase domain containing"	24278	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 77", "family with sequence similarity 108, member B1"	C9orf77, FAM108B1		10810093	Standard	XM_006717134		Approved	CGI-67	uc004ail.3	Q5VST6	OTTHUMG00000020001	ENST00000333421.6:c.851A>C	chr9.hg19:g.74481719T>G	ENSP00000330222:p.Glu284Ala	40.0	0.0		31.0	12.0	NM_016014	A8KAJ5|Q5VST7|Q86YB6|Q8IY03|Q9Y377	Missense_Mutation	SNP	ENST00000333421.6	hg19	CCDS35043.1	.	.	.	.	.	.	.	.	.	.	T	19.47	3.833591	0.71258	.	.	ENSG00000107362	ENST00000377041;ENST00000333421	T;T	0.40476	1.03;1.4	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.65585	0.2705	M	0.77616	2.38	0.80722	D	1	D;D	0.65815	0.991;0.995	P;D	0.68621	0.881;0.959	T	0.70193	-0.4939	10	0.87932	D	0	-15.1162	16.07	0.80919	0.0:0.0:0.0:1.0	.	284;284	Q5VST6;Q5VST6-2	F108B_HUMAN;.	A	284	ENSP00000366240:E284A;ENSP00000330222:E284A	ENSP00000330222:E284A	E	-	2	0	FAM108B1	73671539	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.844000	0.86867	2.254000	0.74563	0.533000	0.62120	GAA	.	.		0.388	ABHD17B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052625.1	NM_016014		G	74481719	T	G	74481719	3	3	261	1	0	0	0	0	1	0	0	0	5397	1783	62	5	50	5	FAM108B1	9	74481719	Missense_Mutation	SNP	T	TCGA-FV-A23B-01A-11D-A16V-10		74481719	66731712	33	38231										
CDK5RAP2	55755	hgsc.bcm.edu	37	chr9	123199606	123199606	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	cttttccaatttctccagcaGctcagcacattgattcagct	5	13	3	1			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr9:123199606G>A	ENST00000349780.4	-	25	4101	c.3922C>T	c.(3922-3924)Ctg>Ttg	p.L1308L	CDK5RAP2_ENST00000360822.3_Silent_p.L1276L|CDK5RAP2_ENST00000360190.4_Silent_p.L1308L|CDK5RAP2_ENST00000359309.3_Silent_p.L1267L	NM_018249.4	NP_060719.4	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	1308					brain development (GO:0007420)|centrosome organization (GO:0051297)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of centriole replication (GO:0046600)|negative regulation of neuron differentiation (GO:0045665)|neurogenesis (GO:0022008)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of spindle checkpoint (GO:0090231)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)			breast(6)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	58						TTCTCCAGCAGCTCAGCACAT	0.493																																					p.L1308L		Atlas-SNP	.											.	CDK5RAP2	157	.	0			c.C3922T						.						158	119	132					9																	123199606		2203	4300	6503	SO:0001819	synonymous_variant	55755	exon25			CCAGCAGCTCAGC	BK005504	CCDS6823.1, CCDS43871.1, CCDS75888.1	9q33.3	2014-02-21			ENSG00000136861	ENSG00000136861			18672	protein-coding gene	gene with protein product	"centrosomin"	608201	"microcephaly, primary autosomal recessive 3"	MCPH3		10721722, 17764569, 24466316	Standard	NM_018249		Approved	C48, FLJ10867, CEP215	uc004bkf.4	Q96SN8	OTTHUMG00000021043	ENST00000349780.4:c.3922C>T	chr9.hg19:g.123199606G>A		89.0	0.0		67.0	33.0	NM_018249	Q5JV18|Q7Z3L4|Q7Z3U1|Q7Z7I6|Q9BSW0|Q9H6J6|Q9HCD9|Q9NV90|Q9UIW9	Silent	SNP	ENST00000349780.4	hg19	CCDS6823.1																																																																																			.	.		0.493	CDK5RAP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055535.1	NM_018249		A	123199606	G	A	123199606	2	1	261	1	0	0	0	0	0	0	0	1	3148	962	34	3		3	CDK5RAP2	9	123199606	Silent	SNP	G	TCGA-FV-A23B-01A-11D-A16V-10	48717887	123199606	18013825	34	38232										
ABCC8	6833	hgsc.bcm.edu	37	chr11	17418528	17418528	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	cttcagggagctgtcgtagcGcacgctcaggttctggatct	13	11	4	0			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr11:17418528G>A	ENST00000389817.3	-	33	4122	c.4054C>T	c.(4054-4056)Cgc>Tgc	p.R1352C	ABCC8_ENST00000302539.4_Missense_Mutation_p.R1353C			Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 8	1352	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.		R -> H (in LIH; partially impairs ATP- dependent potassium channel function). {ECO:0000269|PubMed:15356046}.|R -> P (in HHF1; dbSNP:rs28936370). {ECO:0000269|PubMed:9769320}.		carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium ion transmembrane transporter activity (GO:0015079)|sulfonylurea receptor activity (GO:0008281)			NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(38)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	67				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Chlorpropamide(DB00672)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Gliquidone(DB01251)|Glyburide(DB01016)|Glycodiazine(DB01382)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)|Tolbutamide(DB01124)	CTGTCGTAGCGCACGCTCAGG	0.627																																					p.R1352C		Atlas-SNP	.											ABCC8,NS,carcinoma,0,1	ABCC8	170	.	0			c.C4054T						.						134	107	116					11																	17418528		2200	4293	6493	SO:0001583	missense	6833	exon33			CGTAGCGCACGCT	L78207	CCDS31437.1, CCDS73264.1	11p15.1	2014-09-17			ENSG00000006071	ENSG00000006071		"ATP binding cassette transporters / subfamily C"	59	protein-coding gene	gene with protein product	"sulfonylurea receptor (hyperinsulinemia)"	600509		SUR, HRINS		7920639, 7716548	Standard	NM_000352		Approved	HI, PHHI, SUR1, MRP8, ABC36, HHF1, TNDM2	uc001mnc.3	Q09428	OTTHUMG00000166316	ENST00000389817.3:c.4054C>T	chr11.hg19:g.17418528G>A	ENSP00000374467:p.Arg1352Cys	99.0	0.0		81.0	26.0	NM_000352	A6NMX8|E3UYX6|O75948|Q16583	Missense_Mutation	SNP	ENST00000389817.3	hg19	CCDS31437.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.3|25.3	4.626477|4.626477	0.87560|0.87560	.|.	.|.	ENSG00000006071|ENSG00000006071	ENST00000528374|ENST00000389817;ENST00000302539	.|D;D	.|0.90955	.|-2.76;-2.76	4.83|4.83	4.83|4.83	0.62350|0.62350	.|ABC transporter-like (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.94162|0.94162	0.8127|0.8127	L|L	0.53561|0.53561	1.675|1.675	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.87578	.|0.998	D|D	0.94829|0.94829	0.7994|0.7994	5|10	.|0.87932	.|D	.|0	.|.	18.2867|18.2867	0.90117|0.90117	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1352	.|Q09428	.|ABCC8_HUMAN	V|C	179|1352;1353	.|ENSP00000374467:R1352C;ENSP00000303960:R1353C	.|ENSP00000303960:R1353C	A|R	-|-	2|1	0|0	ABCC8|ABCC8	17375104|17375104	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.979000|0.979000	0.70002|0.70002	7.637000|7.637000	0.83313|0.83313	2.386000|2.386000	0.81285|0.81285	0.555000|0.555000	0.69702|0.69702	GCG|CGC	.	.		0.627	ABCC8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389093.1	NM_000352		A	17418528	G	A	17418528	3	1	261	1	0	0	0	0	1	0	0	0	58	1087	38	1	719	1	ABCC8	11	17418528	Missense_Mutation	SNP	G	TCGA-FV-A23B-01A-11D-A16V-10		17418528	117587988	35	38233										
CTTN	2017	hgsc.bcm.edu	37	chr11	70260723	70260723	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	actcggtccgtggcttcggaGgcaagtttggtgtccagatg	15	9	0	1			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr11:70260723G>A	ENST00000301843.8	+	6	573	c.367G>A	c.(367-369)Ggc>Agc	p.G123S	CTTN_ENST00000346329.3_Missense_Mutation_p.G123S|CTTN_ENST00000376561.3_Missense_Mutation_p.G123S	NM_005231.3	NP_005222.2	Q14247	SRC8_HUMAN	cortactin	123					negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|mitotic spindle midzone (GO:1990023)|ruffle (GO:0001726)				breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	31			BRCA - Breast invasive adenocarcinoma(2;4.34e-41)|LUSC - Lung squamous cell carcinoma(11;1.51e-13)|STAD - Stomach adenocarcinoma(18;0.0513)	Lung(977;0.0234)|LUSC - Lung squamous cell carcinoma(976;0.133)		TGGCTTCGGAGGCAAGTTTGG	0.572																																					p.G123S		Atlas-SNP	.											.	CTTN	162	.	0			c.G367A						.						143	128	133					11																	70260723		2200	4294	6494	SO:0001583	missense	2017	exon6			TTCGGAGGCAAGT	AJ288897	CCDS8197.1, CCDS41680.1, CCDS53676.1	11q13	2008-02-05	2004-06-08	2004-06-09	ENSG00000085733	ENSG00000085733			3338	protein-coding gene	gene with protein product		164765	"ems1 sequence (mammary tumor and squamous cell carcinoma-associated (p80/85 src substrate)"	EMS1		7685625	Standard	NM_005231		Approved		uc001opu.3	Q14247	OTTHUMG00000134307	ENST00000301843.8:c.367G>A	chr11.hg19:g.70260723G>A	ENSP00000301843:p.Gly123Ser	100.0	0.0		100.0	34.0	NM_001184740	Q8N707|Q96H99	Missense_Mutation	SNP	ENST00000301843.8	hg19	CCDS41680.1	.	.	.	.	.	.	.	.	.	.	G	36	5.623738	0.96660	.	.	ENSG00000085733	ENST00000346329;ENST00000301843;ENST00000376561	T;T;T	0.53423	0.77;0.78;0.62	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.77850	0.4192	M	0.92691	3.335	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	T	0.82808	-0.0274	10	0.87932	D	0	-52.3417	19.812	0.96551	0.0:0.0:1.0:0.0	.	123;123;123	Q96H99;Q14247;Q8N707	.;SRC8_HUMAN;.	S	123	ENSP00000317189:G123S;ENSP00000301843:G123S;ENSP00000365745:G123S	ENSP00000301843:G123S	G	+	1	0	CTTN	69938371	1.000000	0.71417	1.000000	0.80357	0.783000	0.44284	9.434000	0.97515	2.685000	0.91497	0.655000	0.94253	GGC	.	.		0.572	CTTN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259233.2	NM_138565		A	70260723	G	A	70260723	3	1	261	1	0	0	0	0	1	0	0	0	4046	1000	35	3	381	3	CTTN	11	70260723	Missense_Mutation	SNP	G	TCGA-FV-A23B-01A-11D-A16V-10	52842195	70260723	64745793	36	38234										
PPM1H	57460	hgsc.bcm.edu	37	chr12	63083509	63083509	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	gaagacaggaatggtttaatGtagatgttggagtcatgcac	13	4	1	2			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr12:63083509G>A	ENST00000228705.6	-	8	1515	c.1215C>T	c.(1213-1215)taC>taT	p.Y405Y	PPM1H_ENST00000551214.1_5'UTR	NM_020700.1	NP_065751.1	Q9ULR3	PPM1H_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1H	405	PP2C-like.						phosphoprotein phosphatase activity (GO:0004721)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)	18			GBM - Glioblastoma multiforme(1;0.000443)|BRCA - Breast invasive adenocarcinoma(9;0.209)	GBM - Glioblastoma multiforme(28;0.0126)		ATGGTTTAATGTAGATGTTGG	0.463																																					p.Y405Y		Atlas-SNP	.											.	PPM1H	42	.	0			c.C1215T						.						97	96	96					12																	63083509		1898	4149	6047	SO:0001819	synonymous_variant	57460	exon8			TTTAATGTAGATG	AB032983	CCDS44934.1	12q14.1	2012-04-17	2010-03-05	2004-03-26	ENSG00000111110	ENSG00000111110	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	18583	protein-coding gene	gene with protein product	"neurite extension-related protein phosphatase related to PP2C"		"ras homolog gene family, member C like 1", "protein phosphatase 1H (PP2C domain containing)"	ARHCL1			Standard	NM_020700		Approved	KIAA1157, FLJ13253, NERPP-2C	uc001srk.3	Q9ULR3	OTTHUMG00000169990	ENST00000228705.6:c.1215C>T	chr12.hg19:g.63083509G>A		45.0	0.0		40.0	15.0	NM_020700	B1Q2A9|B2RXG4|Q6PI86	Silent	SNP	ENST00000228705.6	hg19	CCDS44934.1																																																																																			.	.		0.463	PPM1H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406760.2	NM_020700		A	63083509	G	A	63083509	2	1	261	1	0	0	0	0	0	0	0	1	12353	1372	48	3		3	PPM1H	12	63083509	Silent	SNP	G	TCGA-FV-A23B-01A-11D-A16V-10		63083509	70768386	37	38235										
STAB2	55576	hgsc.bcm.edu	37	chr12	104118857	104118857	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	ggagatggatttacctgccgCggcagcatttatcaggtaac	12	9	1	1			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr12:104118857C>T	ENST00000388887.2	+	45	4992	c.4788C>T	c.(4786-4788)cgC>cgT	p.R1596R		NM_017564.9	NP_060034.9			stabilin 2									p.R1596R(1)		NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						TTACCTGCCGCGGCAGCATTT	0.448																																					p.R1596R		Atlas-SNP	.											STAB2,colon,carcinoma,0,2	STAB2	370	.	1	Substitution - coding silent(1)	ovary(1)	c.C4788T						.						120	116	118					12																	104118857		2203	4300	6503	SO:0001819	synonymous_variant	55576	exon45			CTGCCGCGGCAGC	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"hyaluronic acid receptor for endocytosis"	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.4788C>T	chr12.hg19:g.104118857C>T		52.0	0.0		32.0	18.0	NM_017564		Silent	SNP	ENST00000388887.2	hg19	CCDS31888.1																																																																																			.	.		0.448	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			T	104118857	C	T	104118857	2	4	261	1	0	0	0	0	0	0	0	1	15253	755	27	1		1	STAB2	12	104118857	Silent	SNP	C	TCGA-FV-A23B-01A-11D-A16V-10	41035348	104118857	29733038	38	38236										
TRPC4	7223	hgsc.bcm.edu	37	chr13	38248410	38248410	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	gagattgttgctaaatataaGgagttcattacaaagtccat	8	5	1	1			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr13:38248410G>A	ENST00000379705.3	-	5	2186	c.1329C>T	c.(1327-1329)tcC>tcT	p.S443S	TRPC4_ENST00000426868.2_Silent_p.S443S|TRPC4_ENST00000379673.2_Silent_p.S443S|TRPC4_ENST00000358477.2_Silent_p.S443S|TRPC4_ENST00000355779.2_Silent_p.S443S|TRPC4_ENST00000379679.1_Silent_p.S270S|TRPC4_ENST00000494529.1_5'UTR|TRPC4_ENST00000338947.5_Silent_p.S270S|TRPC4_ENST00000379681.3_Silent_p.S443S|TRPC4_ENST00000447043.1_Silent_p.S443S			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	443					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|gamma-aminobutyric acid secretion (GO:0014051)|ion transmembrane transport (GO:0034220)|oligodendrocyte differentiation (GO:0048709)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|calcium channel complex (GO:0034704)|caveola (GO:0005901)|cell surface (GO:0009986)|cortical cytoskeleton (GO:0030863)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			NS(2)|breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(26)|lung(30)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	83				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		CTAAATATAAGGAGTTCATTA	0.343																																					p.S443S		Atlas-SNP	.											.	TRPC4	389	.	0			c.C1329T						.						74	72	73					13																	38248410		2203	4300	6503	SO:0001819	synonymous_variant	7223	exon5			ATATAAGGAGTTC	U40983	CCDS9365.1, CCDS45035.1, CCDS45036.1, CCDS45038.1, CCDS45039.1	13q13.3	2013-01-10			ENSG00000133107	ENSG00000133107		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	12336	protein-coding gene	gene with protein product		603651				8646775, 16382100	Standard	NM_016179		Approved	HTRP4, TRP4	uc010abx.3	Q9UBN4	OTTHUMG00000016752	ENST00000379705.3:c.1329C>T	chr13.hg19:g.38248410G>A		106.0	0.0		106.0	40.0	NM_003306	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Silent	SNP	ENST00000379705.3	hg19	CCDS9365.1																																																																																			.	.		0.343	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306		A	38248410	G	A	38248410	2	1	261	1	0	0	0	0	0	0	0	1	16595	987	35	3		3	TRPC4	13	38248410	Silent	SNP	G	TCGA-FV-A23B-01A-11D-A16V-10		38248410	76921468	39	38237										
SYT16	83851	hgsc.bcm.edu	37	chr14	62550927	62550927	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	cctccagagtggagggtctcCgctcagcccatctgcggttt	12	14	3	1			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr14:62550927C>T	ENST00000430451.2	+	5	1645	c.1448C>T	c.(1447-1449)cCg>cTg	p.P483L		NM_031914.2	NP_114120.2	Q17RD7	SYT16_HUMAN	synaptotagmin XVI	483					exocytosis (GO:0006887)					central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	35				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)		GGAGGGTCTCCGCTCAGCCCA	0.517																																					p.P483L		Atlas-SNP	.											.	SYT16	144	.	0			c.C1448T						.						99	97	97					14																	62550927		1982	4148	6130	SO:0001583	missense	83851	exon5			GGTCTCCGCTCAG	BC040924	CCDS45121.1	14q23.2	2014-07-02	2005-07-15	2005-07-15	ENSG00000139973	ENSG00000139973		"Synaptotagmins"	23142	protein-coding gene	gene with protein product	"synaptotagmin XIV-related", " chr14 synaptotagmin"	610950	"synaptotagmin XIV-like"	SYT14L		11543631	Standard	NM_031914		Approved	yt14r, CHR14SYT, Strep14	uc001xfu.1	Q17RD7	OTTHUMG00000171106	ENST00000430451.2:c.1448C>T	chr14.hg19:g.62550927C>T	ENSP00000394700:p.Pro483Leu	54.0	0.0		57.0	27.0	NM_031914	B4DZH2|B7ZL60|C9J8I3|Q707N2|Q7Z441|Q8IUU0|Q9BQR8	Missense_Mutation	SNP	ENST00000430451.2	hg19	CCDS45121.1	.	.	.	.	.	.	.	.	.	.	C	10.49	1.365415	0.24684	.	.	ENSG00000139973	ENST00000430451	T	0.04083	3.71	5.44	2.45	0.29901	.	0.438877	0.25948	N	0.027265	T	0.02230	0.0069	N	0.14661	0.345	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.42682	-0.9437	10	0.06099	T	0.92	-3.8934	5.2381	0.15458	0.4366:0.3745:0.0:0.1889	.	483	Q17RD7	SYT16_HUMAN	L	483	ENSP00000394700:P483L	ENSP00000394700:P483L	P	+	2	0	SYT16	61620680	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.294000	0.43567	0.381000	0.24851	0.643000	0.83706	CCG	.	.		0.517	SYT16-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000411700.1	NM_031914		T	62550927	C	T	62550927	3	4	261	1	0	0	0	0	1	0	0	0	15487	652	23	1	1466	1	SYT16	14	62550927	Missense_Mutation	SNP	C	TCGA-FV-A23B-01A-11D-A16V-10		62550927	44798613	40	38238										
FLRT2	23768	hgsc.bcm.edu	37	chr14	86089513	86089513	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	cttgatcgggggcgcggtgaTatttgtgctggtggtcttgc	17	7	1	2			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr14:86089513T>C	ENST00000330753.4	+	2	2422	c.1655T>C	c.(1654-1656)aTa>aCa	p.I552T	FLRT2_ENST00000554746.1_Missense_Mutation_p.I552T	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	552					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		GGCGCGGTGATATTTGTGCTG	0.592																																					p.I552T		Atlas-SNP	.											.	FLRT2	168	.	0			c.T1655C						.						76	81	79					14																	86089513		2203	4300	6503	SO:0001583	missense	23768	exon2			CGGTGATATTTGT	AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070		"Fibronectin type III domain containing"	3761	protein-coding gene	gene with protein product		604807				10644439, 16872596	Standard	XM_005267490		Approved		uc001xvr.3	O43155		ENST00000330753.4:c.1655T>C	chr14.hg19:g.86089513T>C	ENSP00000332879:p.Ile552Thr	88.0	0.0		73.0	25.0	NM_013231	A0AV84|B7ZLP3	Missense_Mutation	SNP	ENST00000330753.4	hg19	CCDS9877.1	.	.	.	.	.	.	.	.	.	.	T	11.30	1.597853	0.28445	.	.	ENSG00000185070	ENST00000330753;ENST00000554746;ENST00000535800	T;T	0.58060	0.36;0.36	6.17	6.17	0.99709	.	0.047672	0.85682	D	0.000000	T	0.39989	0.1099	N	0.19112	0.55	0.51482	D	0.999921	B	0.27498	0.18	B	0.22753	0.041	T	0.19257	-1.0311	10	0.34782	T	0.22	-17.0787	16.8222	0.85835	0.0:0.0:0.0:1.0	.	552	O43155	FLRT2_HUMAN	T	552;552;205	ENSP00000332879:I552T;ENSP00000451050:I552T	ENSP00000332879:I552T	I	+	2	0	FLRT2	85159266	1.000000	0.71417	0.997000	0.53966	0.926000	0.56050	6.295000	0.72744	2.371000	0.80710	0.533000	0.62120	ATA	.	.		0.592	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1			C	86089513	T	C	86089513	3	2	261	1	0	0	0	0	1	0	0	0	5947	1406	49	2	1657	2	FLRT2	14	86089513	Missense_Mutation	SNP	T	TCGA-FV-A23B-01A-11D-A16V-10	23538586	86089513	21260027	41	38239										
C15orf39	56905	hgsc.bcm.edu	37	chr15	75498804	75498804	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	ctgtctaccgcaaccctctgTgctatgggctctcaacttgt	8	14	3	0			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr15:75498804T>C	ENST00000360639.2	+	2	735	c.415T>C	c.(415-417)Tgc>Cgc	p.C139R	C15orf39_ENST00000567617.1_Missense_Mutation_p.C139R|C15orf39_ENST00000394987.4_Missense_Mutation_p.C139R			Q6ZRI6	CO039_HUMAN	chromosome 15 open reading frame 39	139						cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(2)|endometrium(3)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	16						CAACCCTCTGTGCTATGGGCT	0.622																																					p.C139R		Atlas-SNP	.											.	C15orf39	64	.	0			c.T415C						.						54	51	52					15																	75498804		2197	4295	6492	SO:0001583	missense	56905	exon2			CCTCTGTGCTATG	AK128205	CCDS10276.1	15q23	2013-03-14	2005-10-24		ENSG00000167173	ENSG00000167173			24497	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 38~Name Same As HGNC:28782"				Standard	NM_015492		Approved	DKFZP434H132, FLJ46337	uc002azq.4	Q6ZRI6	OTTHUMG00000142820	ENST00000360639.2:c.415T>C	chr15.hg19:g.75498804T>C	ENSP00000353854:p.Cys139Arg	55.0	0.0		53.0	22.0	NM_015492	B3KWI3|C9J888|Q71JB1|Q7L3S0|Q8N3F2|Q96FB6|Q9NTU5	Missense_Mutation	SNP	ENST00000360639.2	hg19	CCDS10276.1	.	.	.	.	.	.	.	.	.	.	T	13.31	2.199280	0.38806	.	.	ENSG00000167173	ENST00000360639;ENST00000394987	T;T	0.71698	-0.59;-0.59	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.78748	0.4332	L	0.60455	1.87	0.58432	D	0.99999	D	0.71674	0.998	D	0.78314	0.991	T	0.80174	-0.1492	10	0.87932	D	0	-12.1195	7.7302	0.28783	0.0:0.0949:0.0:0.9051	.	139	Q6ZRI6	CO039_HUMAN	R	139	ENSP00000353854:C139R;ENSP00000378438:C139R	ENSP00000353854:C139R	C	+	1	0	C15orf39	73285857	0.998000	0.40836	0.999000	0.59377	0.929000	0.56500	4.534000	0.60622	1.938000	0.56188	0.459000	0.35465	TGC	.	.		0.622	C15orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286410.1	NM_015492		C	75498804	T	C	75498804	3	2	261	1	0	0	0	0	1	0	0	0	1795	1696	59	2	417	2	C15orf39	15	75498804	Missense_Mutation	SNP	T	TCGA-FV-A23B-01A-11D-A16V-10		75498804	27032588	42	38240										
SCNN1B	6338	hgsc.bcm.edu	37	chr16	23366664	23366664	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	accttccggaacttcaccagTgctacccaggcattgacaga	8	14	1	2			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr16:23366664T>C	ENST00000343070.2	+	4	806	c.630T>C	c.(628-630)agT>agC	p.S210S	SCNN1B_ENST00000568085.1_Silent_p.S210S|SCNN1B_ENST00000568923.1_Intron|SCNN1B_ENST00000307331.5_Silent_p.S255S	NM_000336.2	NP_000327.2	P51168	SCNNB_HUMAN	sodium channel, non-voltage-gated 1, beta subunit	210					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|WW domain binding (GO:0050699)			breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	32				GBM - Glioblastoma multiforme(48;0.0465)	Amiloride(DB00594)|Triamterene(DB00384)	ACTTCACCAGTGCTACCCAGG	0.587																																					p.S210S		Atlas-SNP	.											.	SCNN1B	81	.	0			c.T630C						.						146	105	119					16																	23366664		2197	4300	6497	SO:0001819	synonymous_variant	6338	exon4			CACCAGTGCTACC	X87159	CCDS10609.1	16p12.2-p12.1	2012-02-28	2012-02-28		ENSG00000168447	ENSG00000168447		"Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels"	10600	protein-coding gene	gene with protein product	"Liddle syndrome"	600760	"sodium channel, nonvoltage-gated 1, beta", "sodium channel, non-voltage-gated 1, beta"				Standard	NM_000336		Approved	ENaCbeta	uc002dln.3	P51168	OTTHUMG00000131608	ENST00000343070.2:c.630T>C	chr16.hg19:g.23366664T>C		74.0	0.0		34.0	29.0	NM_000336	C5HTZ2|O60891|Q96KG2|Q9UJ32|Q9UMU5	Silent	SNP	ENST00000343070.2	hg19	CCDS10609.1																																																																																			.	.		0.587	SCNN1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254495.2			C	23366664	T	C	23366664	2	2	261	1	0	0	0	0	0	0	0	1	13943	1693	59	2		2	SCNN1B	16	23366664	Silent	SNP	T	TCGA-FV-A23B-01A-11D-A16V-10		23366664	66988089	43	38241										
MYH4	4622	hgsc.bcm.edu	37	chr17	10353951	10353951	+	Frame_Shift_Del	DEL	C	C	-													0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	ggctgactgcagggcatgggCcagagtgctcttggcctaga							TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr17:10353951delC	ENST00000255381.2	-	30	4110	c.4000delG	c.(4000-4002)gccfs	p.A1334fs	RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	1334					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						AGGGCATGGGCCAGAGTGCTC	0.483																																					p.A1334fs		Atlas-Indel,Pindel	.											.	MYH4	349	.	0			c.4001delC						.						84	74	77					17																	10353951		2203	4300	6503	SO:0001589	frameshift_variant	4622	exon30			.		CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"Myosins / Myosin superfamily : Class II"	7574	protein-coding gene	gene with protein product		160742	"myosin, heavy polypeptide 4, skeletal muscle"			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.4000delG	chr17.hg19:g.10353951delC	ENSP00000255381:p.Ala1334fs	49.0	0.0		31.0	18.0	NM_017533		Frame_Shift_Del	DEL	ENST00000255381.2	hg19	CCDS11154.1																																																																																			.	.		0.483	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533		-	10353951	C	-	10353951	7	5	261	1	0	1	0	1	0	0	0	0	10046	739	26	0	1863	0	MYH4	17	10353951	Frame_Shift_Del	DEL	C	TCGA-FV-A23B-01A-11D-A16V-10		10353951	70841259	44	38242										
MYH1	4619	hgsc.bcm.edu	37	chr17	10404676	10404676	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	ttcttgttcatctcaatctgGgctgaggtggccccaccggc	11	13	4	1			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr17:10404676G>T	ENST00000226207.5	-	27	3583	c.3489C>A	c.(3487-3489)gcC>gcA	p.A1163A	RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	1163				A -> T (in Ref. 4; CAA27380). {ECO:0000305}.	muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						TCTCAATCTGGGCTGAGGTGG	0.632																																					p.A1163A		Atlas-SNP	.											.	MYH1	403	.	0			c.C3489A						.						89	98	95					17																	10404676		2203	4300	6503	SO:0001819	synonymous_variant	4619	exon27			AATCTGGGCTGAG		CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"Myosins / Myosin superfamily : Class II"	7567	protein-coding gene	gene with protein product	"myosin heavy chain IIx/d"	160730	"myosin, heavy polypeptide 1, skeletal muscle, adult"			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.3489C>A	chr17.hg19:g.10404676G>T		100.0	0.0		40.0	26.0	NM_005963	Q14CA4|Q9Y622	Silent	SNP	ENST00000226207.5	hg19	CCDS11155.1																																																																																			.	.		0.632	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963		T	10404676	G	T	10404676	2	4	261	1	0	0	0	0	0	0	0	1	10038	1219	43	3		3	MYH1	17	10404676	Silent	SNP	G	TCGA-FV-A23B-01A-11D-A16V-10	50725	10404676	70790534	45	38243										
PSMD11	5717	hgsc.bcm.edu	37	chr17	30806343	30806343	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	ttggccaagttgtatgataaCttactagaacagaatctgat	8	6	1	4			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr17:30806343C>T	ENST00000261712.3	+	10	1250	c.987C>T	c.(985-987)aaC>aaT	p.N329N	PSMD11_ENST00000457654.2_Silent_p.N329N	NM_001270482.1|NM_002815.3	NP_001257411.1|NP_002806.2	O00231	PSD11_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 11	329	PCI.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome assembly (GO:0043248)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stem cell differentiation (GO:0048863)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	19		Breast(31;0.159)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.109)			TGTATGATAACTTACTAGAAC	0.498																																					p.N329N	Ovarian(130;1038 1716 9294 11987 19279)	Atlas-SNP	.											.	PSMD11	41	.	0			c.C987T						.						151	143	146					17																	30806343		2203	4300	6503	SO:0001819	synonymous_variant	5717	exon10			TGATAACTTACTA	AB003102	CCDS11272.1	17q12	2008-05-22			ENSG00000108671	ENSG00000108671		"Proteasome (prosome, macropain) subunits"	9556	protein-coding gene	gene with protein product		604449				9426256, 9119060	Standard	NM_001270482		Approved	S9, p44.5, MGC3844, Rpn6	uc010cta.2	O00231	OTTHUMG00000132811	ENST00000261712.3:c.987C>T	chr17.hg19:g.30806343C>T		63.0	0.0		106.0	21.0	NM_002815	A8K3I7|E1P663|O00495|Q53FT5	Silent	SNP	ENST00000261712.3	hg19	CCDS11272.1	.	.	.	.	.	.	.	.	.	.	C	9.790	1.177547	0.21787	.	.	ENSG00000108671	ENST00000457654	.	.	.	5.41	5.41	0.78517	.	.	.	.	.	T	0.72447	0.3461	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.69822	-0.5041	4	.	.	.	-12.4301	16.7464	0.85473	0.0:1.0:0.0:0.0	.	.	.	.	F	67	.	.	L	+	1	0	PSMD11	27830456	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	3.803000	0.55560	2.826000	0.97356	0.561000	0.74099	CTT	.	.		0.498	PSMD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256252.2	NM_002815		T	30806343	C	T	30806343	2	4	261	1	0	0	0	0	0	0	0	1	12706	564	20	3		3	PSMD11	17	30806343	Silent	SNP	C	TCGA-FV-A23B-01A-11D-A16V-10	20401667	30806343	50388867	46	38244										
BRCA1	672	hgsc.bcm.edu	37	chr17	41228578	41228578	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	aaacttgtcagcagaaaggcCttctggattctggcttatag	10	8	3	1			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr17:41228578C>G	ENST00000357654.3	-	13	4529	c.4411G>C	c.(4411-4413)Ggc>Cgc	p.G1471R	BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000493795.1_Missense_Mutation_p.G1424R|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000471181.2_Missense_Mutation_p.G1492R|BRCA1_ENST00000491747.2_Missense_Mutation_p.G367R|BRCA1_ENST00000354071.3_Intron|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000468300.1_Missense_Mutation_p.G367R|BRCA1_ENST00000346315.3_Intron|BRCA1_ENST00000309486.4_Missense_Mutation_p.G1175R|BRCA1_ENST00000352993.3_Missense_Mutation_p.G329R|BRCA1_ENST00000351666.3_Missense_Mutation_p.G288R	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	1471					androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		GCAGAAAGGCCTTCTGGATTC	0.368			"D, Mis, N, F, S"		ovarian	"breast, ovarian"		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																											p.G1492R		Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	.	BRCA1	304	.	0			c.G4474C						.						145	138	140					17																	41228578		2202	4300	6502	SO:0001583	missense	672	exon14	Familial Cancer Database		AAAGGCCTTCTGG	U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1100	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 1", "protein phosphatase 1, regulatory subunit 53"	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.4411G>C	chr17.hg19:g.41228578C>G	ENSP00000350283:p.Gly1471Arg	81.0	0.0		75.0	29.0	NM_007300	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Missense_Mutation	SNP	ENST00000357654.3	hg19	CCDS11453.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.836|8.836	0.941068|0.941068	0.18281|0.18281	.|.	.|.	ENSG00000012048|ENSG00000012048	ENST00000357654;ENST00000412061;ENST00000352993;ENST00000351666;ENST00000309486;ENST00000468300;ENST00000393691;ENST00000471181;ENST00000493795;ENST00000491747;ENST00000478531;ENST00000484087;ENST00000493919;ENST00000487825|ENST00000461574	T;T;T;T;T;T;T;T;T;T;T|.	0.56444|.	0.46;0.46;0.46;0.46;0.46;0.46;0.46;0.46;0.46;0.46;0.46|.	4.97|4.97	-3.6|-3.6	0.04570|0.04570	.|.	1.054980|.	0.07355|.	N|.	0.883009|.	T|T	0.14874|0.14874	0.0359|0.0359	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B;P;B;B;B;B;B;B|.	0.46706|.	0.002;0.883;0.001;0.037;0.001;0.004;0.201;0.007|.	B;B;B;B;B;B;B;B|.	0.39419|.	0.004;0.299;0.001;0.03;0.001;0.002;0.055;0.005|.	T|T	0.29397|0.29397	-1.0013|-1.0013	10|5	0.39692|.	T|.	0.17|.	.|.	6.6577|6.6577	0.22996|0.22996	0.0:0.4305:0.1377:0.4318|0.0:0.4305:0.1377:0.4318	.|.	367;320;366;368;367;1493;1471;1471|.	E7EUM2;B4DES0;E7ETR2;P38398-3;Q6IN79;E9PFC7;P38398;P38398-2|.	.;.;.;.;.;.;BRCA1_HUMAN;.|.	R|N	1471;1492;329;288;1175;367;320;1493;1424;366;367;242;321;243|234	ENSP00000350283:G1471R;ENSP00000312236:G329R;ENSP00000338007:G288R;ENSP00000310938:G1175R;ENSP00000417148:G367R;ENSP00000377294:G320R;ENSP00000418775:G1424R;ENSP00000420412:G367R;ENSP00000419481:G242R;ENSP00000418819:G321R;ENSP00000418212:G243R|.	ENSP00000310938:G1175R|.	G|K	-|-	1|3	0|2	BRCA1|BRCA1	38482104|38482104	0.000000|0.000000	0.05858|0.05858	0.007000|0.007000	0.13788|0.13788	0.960000|0.960000	0.62799|0.62799	-0.366000|-0.366000	0.07563|0.07563	-0.901000|-0.901000	0.03891|0.03891	-0.291000|-0.291000	0.09656|0.09656	GGC|AAG	.	.		0.368	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294		G	41228578	C	G	41228578	3	3	261	1	0	0	0	0	1	0	0	0	1500	681	24	4	1224	4	BRCA1	17	41228578	Missense_Mutation	SNP	C	TCGA-FV-A23B-01A-11D-A16V-10	10422235	41228578	39966632	47	38245										
MUC16	94025	hgsc.bcm.edu	37	chr19	9057886	9057886	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	ggcaggatttgatgtgaaaaCagtggtatcgtccacagcgg	14	7	0	2			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr19:9057886C>G	ENST00000397910.4	-	3	29763	c.29560G>C	c.(29560-29562)Gtt>Ctt	p.V9854L		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9856	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GATGTGAAAACAGTGGTATCG	0.468																																					p.V9854L		Atlas-SNP	.											.	MUC16	4315	.	0			c.G29560C						.						154	145	148					19																	9057886		2010	4183	6193	SO:0001583	missense	94025	exon3			TGAAAACAGTGGT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.29560G>C	chr19.hg19:g.9057886C>G	ENSP00000381008:p.Val9854Leu	92.0	0.0		91.0	40.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	5.579	0.291676	0.10567	.	.	ENSG00000181143	ENST00000397910	T	0.35605	1.3	2.43	-4.75	0.03239	.	.	.	.	.	T	0.18551	0.0445	N	0.19112	0.55	.	.	.	B	0.02656	0.0	B	0.06405	0.002	T	0.23261	-1.0193	8	0.87932	D	0	.	4.0956	0.09990	0.0:0.2634:0.3471:0.3895	.	9854	B5ME49	.	L	9854	ENSP00000381008:V9854L	ENSP00000381008:V9854L	V	-	1	0	MUC16	8918886	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-5.919000	0.00090	-1.056000	0.03205	-0.232000	0.12228	GTT	.	.		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	9057886	C	G	9057886	3	3	261	1	0	0	0	0	1	0	0	0	9982	478	17	4	14291	4	MUC16	19	9057886	Missense_Mutation	SNP	C	TCGA-FV-A23B-01A-11D-A16V-10		9057886	50071097	48	38246										
ELAVL3	1995	hgsc.bcm.edu	37	chr19	11577475	11577475	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	tcgatgtcgccaatgctgccGaagagactcttgaactcatc	9	12	2	2	rs201270169	byFrequency	TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr19:11577475G>A	ENST00000359227.3	-	2	601	c.177C>T	c.(175-177)ttC>ttT	p.F59F	CTC-398G3.6_ENST00000585656.1_3'UTR|ELAVL3_ENST00000438662.2_Silent_p.F59F|RN7SL669P_ENST00000581926.1_RNA	NM_001420.3|NM_032281.2	NP_001411.2|NP_115657.2	Q14576	ELAV3_HUMAN	ELAV like neuron-specific RNA binding protein 3	59	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)		AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)			breast(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	15						CAATGCTGCCGAAGAGACTCT	0.547													g|||	3	0.000599042	0	0.0029	5008	,	,		20239	0		0	False		,,,				2504	0.001				p.F59F		Atlas-SNP	.											.	ELAVL3	58	.	0			c.C177T						.	A	,	0,4406		0,0,2203	163	143	150		177,177	-2.6	1	19		150	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous,coding-synonymous	ELAVL3	NM_001420.3,NM_032281.2	,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,	59/368,59/361	11577475	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	1995	exon2			GCTGCCGAAGAGA		CCDS32912.1, CCDS45978.1	19p13.2	2013-10-03	2013-10-03			ENSG00000196361		"RNA binding motif (RRM) containing"	3314	protein-coding gene	gene with protein product	"Hu antigen C", "paraneoplastic limbic encephalitis antigen 21", "paraneoplastic cerebellar degeneration-associated antigen", "ELAV-like protein 3"	603458	"ELAV (embryonic lethal, abnormal vision, Drosophila)-like 3 (Hu antigen C)"			9799595	Standard	NM_001420		Approved	HUC, PLE21, DKFZp547J036, HUCL, MGC20653	uc002mry.1	Q14576		ENST00000359227.3:c.177C>T	chr19.hg19:g.11577475G>A		123.0	0.0		90.0	50.0	NM_032281	Q16135|Q96CL8|Q96QS9	Silent	SNP	ENST00000359227.3	hg19	CCDS32912.1																																																																																			.	G|0.999;A|0.001		0.547	ELAVL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458827.2	NM_001420		A	11577475	G	A	11577475	2	1	261	1	0	0	0	0	0	0	0	1	5053	1049	37	1		1	ELAVL3	19	11577475	Silent	SNP	G	TCGA-FV-A23B-01A-11D-A16V-10	2519589	11577475	47551508	49	38247										
CYP4F3	4051	hgsc.bcm.edu	37	chr19	15758035	15758046	+	In_Frame_Del	DEL	AAAGTGGAGCCG	AAAGTGGAGCCG	-													0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	ctcctgctgagtgctggtgaAaagtggagccgccaccgtcg							TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	AAAGTGGAGCCG	AAAGTGGAGCCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr19:15758035_15758046delAAAGTGGAGCCG	ENST00000221307.8	+	5	473_484	c.426_437delAAAGTGGAGCCG	c.(424-438)gaaaagtggagccgc>gac	p.142_146EKWSR>D	CYP4F3_ENST00000585846.1_In_Frame_Del_p.142_146EKWSR>D|CYP4F3_ENST00000591058.1_In_Frame_Del_p.142_146EKWSR>D|CYP4F3_ENST00000586182.2_In_Frame_Del_p.142_146EKWSR>D	NM_000896.2	NP_000887.2	Q08477	CP4F3_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 3	142					arachidonic acid metabolic process (GO:0019369)|icosanoid metabolic process (GO:0006690)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-tocopherol omega-hydroxylase activity (GO:0052871)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|monooxygenase activity (GO:0004497)			endometrium(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|stomach(1)	34						GTGCTGGTGAAAAGTGGAGCCGCCACCGTCGG	0.566																																					p.142_146del		Atlas-INDEL	.											.	CYP4F3	69	.	0			c.425_436del						.																																			SO:0001651	inframe_deletion	4051	exon5			.	AB002454	CCDS12332.1, CCDS59362.1	19p13.12	2013-02-21	2003-01-14		ENSG00000186529	ENSG00000186529		"Cytochrome P450s"	2646	protein-coding gene	gene with protein product		601270	"cytochrome P450, subfamily IVF, polypeptide 3 (leukotriene B4 omega hydroxylase)"	LTB4H		8486631, 9539102	Standard	NM_000896		Approved	CYP4F	uc010xol.2	Q08477	OTTHUMG00000182374	ENST00000221307.8:c.426_437delAAAGTGGAGCCG	chr19.hg19:g.15758035_15758046delAAAGTGGAGCCG	ENSP00000221307:p.Glu142_Arg146delinsAsp	67.0	0.0		48.0	12.0	NM_001199209	B7Z8Z3|O60634|Q5U740	In_Frame_Del	DEL	ENST00000221307.8	hg19	CCDS12332.1																																																																																			.	.		0.566	CYP4F3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460819.3	NM_000896		-	15758046	AAAGTGGAGCCG	-	15758035	7	5	261	1	0	1	0	1	0	0	0	0	4192	11	1	0	440	0	CYP4F3	19	15758035	In_Frame_Del	DEL	AAAGTGGAGCCG	TCGA-FV-A23B-01A-11D-A16V-10	4180560	15758035	43370948	50	38248										
CRLF1	9244	hgsc.bcm.edu	37	chr19	18707746	18707746	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	tcggtagcggatctggtattTggcttgaaagaggaaatcct	13	6	1	2			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr19:18707746T>A	ENST00000392386.3	-	5	1004	c.811A>T	c.(811-813)Aaa>Taa	p.K271*	CRLF1_ENST00000594325.1_5'Flank	NM_004750.4	NP_004741.1	O75462	CRLF1_HUMAN	cytokine receptor-like factor 1	271	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				negative regulation of motor neuron apoptotic process (GO:2000672)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of cell proliferation (GO:0008284)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|ureteric bud development (GO:0001657)	CRLF-CLCF1 complex (GO:0097058)|extracellular space (GO:0005615)	cytokine binding (GO:0019955)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)	9						ATCTGGTATTTGGCTTGAAAG	0.672																																					p.K271X		Atlas-SNP	.											.	CRLF1	32	.	0			c.A811T						.						78	63	68					19																	18707746		2203	4300	6503	SO:0001587	stop_gained	9244	exon5			GGTATTTGGCTTG	AF059293	CCDS32962.1	19p12	2013-02-11				ENSG00000006016		"Fibronectin type III domain containing"	2364	protein-coding gene	gene with protein product	"cold-induced sweating syndrome"	604237				9686600	Standard	NM_004750		Approved	CLF-1, CLF, CISS, CISS1	uc010ebt.2	O75462		ENST00000392386.3:c.811A>T	chr19.hg19:g.18707746T>A	ENSP00000376188:p.Lys271*	88.0	0.0		51.0	16.0	NM_004750	Q9UHH5	Nonsense_Mutation	SNP	ENST00000392386.3	hg19	CCDS32962.1	.	.	.	.	.	.	.	.	.	.	T	39	7.711627	0.98447	.	.	ENSG00000006016	ENST00000392386	.	.	.	4.7	4.7	0.59300	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-28.6245	12.3848	0.55327	0.0:0.0:0.0:1.0	.	.	.	.	X	271	.	ENSP00000376188:K271X	K	-	1	0	CRLF1	18568746	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.235000	0.78143	1.894000	0.54839	0.402000	0.26972	AAA	.	.		0.672	CRLF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465129.1			A	18707746	T	A	18707746	4	1	261	1	0	0	0	0	0	1	0	0	3888	1821	63	4	477	4	CRLF1	19	18707746	Nonsense_Mutation	SNP	T	TCGA-FV-A23B-01A-11D-A16V-10	2949711	18707746	40421237	51	38249										
ZNF419	79744	hgsc.bcm.edu	37	chr19	58004285	58004285	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	attgcttctgtaggactgctCagttcaaacattcagcaaca	7	10	4	0			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr19:58004285C>T	ENST00000221735.7	+	5	546	c.360C>T	c.(358-360)ctC>ctT	p.L120L	ZNF419_ENST00000426954.2_Silent_p.L108L|ZNF419_ENST00000354197.4_Silent_p.L108L|ZNF419_ENST00000347466.6_Silent_p.L88L|AC003005.4_ENST00000601674.1_Intron|ZNF419_ENST00000415379.2_Silent_p.L74L|ZNF419_ENST00000424930.2_Silent_p.L121L|ZNF419_ENST00000442920.2_Silent_p.L107L			Q96HQ0	ZN419_HUMAN	zinc finger protein 419	120					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Breast(46;0.0848)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0252)|Lung(386;0.171)		TAGGACTGCTCAGTTCAAACA	0.473																																					p.L121L		Atlas-SNP	.											.	ZNF419	134	.	0			c.C363T						.						75	76	76					19																	58004285		2203	4300	6503	SO:0001819	synonymous_variant	79744	exon5			ACTGCTCAGTTCA	AK026886	CCDS42637.1, CCDS46211.1, CCDS54325.1, CCDS54326.1, CCDS54327.1, CCDS54328.1	19q13.43	2013-01-08	2006-12-15	2006-12-15	ENSG00000105136	ENSG00000105136		"Zinc fingers, C2H2-type", "-"	20648	protein-coding gene	gene with protein product			"zinc finger protein 419A"	ZNF419A			Standard	NM_001098492		Approved		uc010ety.1	Q96HQ0	OTTHUMG00000037073	ENST00000221735.7:c.360C>T	chr19.hg19:g.58004285C>T		77.0	0.0		122.0	41.0	NM_001098491	B4DXU7|B4E348|B7ZA41|E9PCP4|E9PED0|E9PET3|E9PFX9|Q9H5P0	Silent	SNP	ENST00000221735.7	hg19	CCDS54326.1	.	.	.	.	.	.	.	.	.	.	C	1.470	-0.560106	0.03967	.	.	ENSG00000105136	ENST00000427558	.	.	.	1.45	-1.07	0.09968	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.6393	0.04966	0.4876:0.3333:0.0:0.1791	.	.	.	.	.	-1	.	.	.	+	.	.	ZNF419	62696097	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-1.061000	0.03472	-0.229000	0.09854	0.205000	0.17691	.	.	.		0.473	ZNF419-006	KNOWN	NAGNAG_splice_site|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378506.1	NM_024691		T	58004285	C	T	58004285	2	4	261	1	0	0	0	0	0	0	0	1	17911	813	29	3		3	ZNF419	19	58004285	Silent	SNP	C	TCGA-FV-A23B-01A-11D-A16V-10	39296539	58004285	1124698	52	38250										
ZNF134	7693	hgsc.bcm.edu	37	chr19	58132394	58132399	+	In_Frame_Del	DEL	CTTGTT	CTTGTT	-													0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	tcttcagacacaaatctacaCttgttcagcatgagagtatt							TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	CTTGTT	CTTGTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr19:58132394_58132399delCTTGTT	ENST00000396161.5	+	3	1217_1222	c.907_912delCTTGTT	c.(907-912)cttgttdel	p.LV303del		NM_003435.3	NP_003426.3	P52741	ZN134_HUMAN	zinc finger protein 134	303					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(3)|prostate(1)	11		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0265)		CAAATCTACACTTGTTCAGCATGAGA	0.413																																					p.302_304del		Atlas-INDEL	.											.	ZNF134	34	.	0			c.906_911del						.																																			SO:0001651	inframe_deletion	7693	exon3			.	U09412	CCDS42638.1	19q13.4	2013-01-08	2006-06-13			ENSG00000213762		"Zinc fingers, C2H2-type"	12918	protein-coding gene	gene with protein product		604076	"zinc finger protein 134 (clone pHZ-15)"			7557990	Standard	NM_003435		Approved	pHZ-15	uc002qpn.2	P52741		ENST00000396161.5:c.907_912delCTTGTT	chr19.hg19:g.58132394_58132399delCTTGTT	ENSP00000379464:p.Leu303_Val304del	34.0	0.0		50.0	10.0	NM_003435	Q9Y4B2	In_Frame_Del	DEL	ENST00000396161.5	hg19	CCDS42638.1																																																																																			.	.		0.413	ZNF134-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466808.1	NM_003435		-	58132399	CTTGTT	-	58132394	7	5	261	1	0	1	0	1	0	0	0	0	17739	565	20	0	913	0	ZNF134	19	58132394	In_Frame_Del	DEL	CTTGTT	TCGA-FV-A23B-01A-11D-A16V-10	128109	58132394	996589	53	38251										
ZNF256	10172	hgsc.bcm.edu	37	chr19	58453498	58453498	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	aggtctccctggtgctgaacAcgtacatgtttgtagctgaa	11	9	1	2			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr19:58453498A>G	ENST00000282308.3	-	3	874	c.678T>C	c.(676-678)cgT>cgC	p.R226R	ZNF256_ENST00000598928.1_3'UTR	NM_005773.2	NP_005764.2	Q9Y2P7	ZN256_HUMAN	zinc finger protein 256	226					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0155)		GGTGCTGAACACGTACATGTT	0.428																																					p.R226R	NSCLC(55;1313 1552 8040 11996)	Atlas-SNP	.											.	ZNF256	117	.	0			c.T678C						.						198	176	184					19																	58453498		2203	4300	6503	SO:0001819	synonymous_variant	10172	exon3			CTGAACACGTACA	AF067165	CCDS12966.1	19q13	2013-01-08				ENSG00000152454		"Zinc fingers, C2H2-type", "-"	13049	protein-coding gene	gene with protein product		606956					Standard	NM_005773		Approved	BMZF-3	uc002qqu.3	Q9Y2P7		ENST00000282308.3:c.678T>C	chr19.hg19:g.58453498A>G		68.0	0.0		115.0	35.0	NM_005773	B2RA92|Q53Y85|Q9BV71	Silent	SNP	ENST00000282308.3	hg19	CCDS12966.1																																																																																			.	.		0.428	ZNF256-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466702.1			G	58453498	A	G	58453498	2	3	261	1	0	0	0	0	0	0	0	1	17814	146	6	2		2	ZNF256	19	58453498	Silent	SNP	A	TCGA-FV-A23B-01A-11D-A16V-10	321104	58453498	675485	54	38252										
GPCPD1	56261	hgsc.bcm.edu	37	chr20	5579378	5579378	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	tttccatactcacctttcacCtgtgtcattctctggaagaa	5	12	4	1			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr20:5579378C>T	ENST00000379019.4	-	3	351	c.139G>A	c.(139-141)Ggt>Agt	p.G47S		NM_019593.3	NP_062539.1	Q9NPB8	GPCP1_HUMAN	glycerophosphocholine phosphodiesterase GDE1 homolog (S. cerevisiae)	47	CBM20. {ECO:0000255|PROSITE- ProRule:PRU00594}.				glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)	glycerophosphocholine phosphodiesterase activity (GO:0047389)|starch binding (GO:2001070)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|skin(1)	16						CACCTTTCACCTGTGTCATTC	0.378																																					p.G47S		Atlas-SNP	.											.	GPCPD1	52	.	0			c.G139A						.						82	68	73					20																	5579378		2203	4300	6503	SO:0001583	missense	56261	exon3			TTTCACCTGTGTC		CCDS13090.1	20p12.3	2011-01-25			ENSG00000125772	ENSG00000125772			26957	protein-coding gene	gene with protein product		614124				10718198, 20576599	Standard	NM_019593		Approved	KIAA1434, GDE5, GDPD6	uc002wme.4	Q9NPB8	OTTHUMG00000031806	ENST00000379019.4:c.139G>A	chr20.hg19:g.5579378C>T	ENSP00000368305:p.Gly47Ser	73.0	0.0		82.0	30.0	NM_019593	D3DW06|Q9BQL8|Q9NUX0	Missense_Mutation	SNP	ENST00000379019.4	hg19	CCDS13090.1	.	.	.	.	.	.	.	.	.	.	C	11.83	1.754585	0.31046	.	.	ENSG00000125772	ENST00000379019	D	0.92446	-3.04	5.09	4.04	0.47022	Carbohydrate-binding-like fold (1);Glycoside hydrolase, carbohydrate-binding (2);Immunoglobulin-like fold (1);	0.595328	0.17773	N	0.162505	T	0.79627	0.4478	N	0.05441	-0.05	0.34433	D	0.698748	B	0.12013	0.005	B	0.17979	0.02	T	0.74618	-0.3605	10	0.08381	T	0.77	-7.2896	8.1899	0.31361	0.0:0.8484:0.0:0.1516	.	47	Q9NPB8	GPCP1_HUMAN	S	47	ENSP00000368305:G47S	ENSP00000368305:G47S	G	-	1	0	GPCPD1	5527378	1.000000	0.71417	1.000000	0.80357	0.490000	0.33462	1.368000	0.34216	2.356000	0.79943	0.561000	0.74099	GGT	.	.		0.378	GPCPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077869.1	NM_019593		T	5579378	C	T	5579378	3	4	261	1	0	0	0	0	1	0	0	0	6611	681	24	3	1951	3	GPCPD1	20	5579378	Missense_Mutation	SNP	C	TCGA-FV-A23B-01A-11D-A16V-10		5579378	57446142	55	38253										
CLTCL1	8218	hgsc.bcm.edu	37	chr22	19168279	19168279	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	caggctctgtcacatgctccTcttgcttgcgcagactctcc	8	16	4	1			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chr22:19168279T>A	ENST00000263200.10	-	31	4940	c.4868A>T	c.(4867-4869)gAg>gTg	p.E1623V	CLTCL1_ENST00000442042.2_5'UTR|SLC25A1_ENST00000215882.5_5'Flank|CLTCL1_ENST00000353891.5_Missense_Mutation_p.E1566V|CLTCL1_ENST00000427926.1_Missense_Mutation_p.E1623V|SLC25A1_ENST00000451283.1_5'Flank|SLC25A1_ENST00000461267.1_5'Flank	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	1623	Heavy chain arm.|Proximal segment.|Trimerization. {ECO:0000250}.			RKQEEHVTEPAPLVFDFDGHE -> PPSKRSM (in Ref. 3; AAB40908/AAB40909). {ECO:0000305}.	anatomical structure morphogenesis (GO:0009653)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|positive regulation of glucose import (GO:0046326)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|spindle (GO:0005819)|trans-Golgi network (GO:0005802)	signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					CACATGCTCCTCTTGCTTGCG	0.607			T	?	ALCL																																p.E1623V		Atlas-SNP	.		Dom	yes		22	22q11.21	8218	"clathrin, heavy polypeptide-like 1"		L	.	CLTCL1	115	.	0			c.A4868T						.						86	93	91					22																	19168279		2132	4251	6383	SO:0001583	missense	8218	exon31			TGCTCCTCTTGCT		CCDS46662.1, CCDS54497.1, CCDS46662.2, CCDS54497.2	22q11.2	2008-06-10	2006-09-29		ENSG00000070371	ENSG00000070371			2093	protein-coding gene	gene with protein product		601273	"clathrin, heavy polypeptide-like 1"	CLTCL		8844170, 15133132	Standard	NM_007098		Approved	CLTD, CLH22, CHC22	uc021wle.1	P53675	OTTHUMG00000150109	ENST00000263200.10:c.4868A>T	chr22.hg19:g.19168279T>A	ENSP00000445677:p.Glu1623Val	58.0	0.0		55.0	26.0	NM_007098	B7Z7U5|Q14017|Q15808|Q15809	Missense_Mutation	SNP	ENST00000263200.10	hg19	CCDS46662.1	.	.	.	.	.	.	.	.	.	.	T	10.91	1.484759	0.26598	.	.	ENSG00000070371	ENST00000353891;ENST00000263200;ENST00000427926	T;T;T	0.32988	1.43;1.43;1.43	4.69	2.52	0.30459	.	0.224775	0.36002	N	0.002851	T	0.27349	0.0671	L	0.50993	1.605	0.45005	D	0.998021	B;B;B	0.31680	0.005;0.335;0.081	B;B;B	0.36567	0.012;0.086;0.228	T	0.04165	-1.0972	10	0.48119	T	0.1	-2.4268	6.2511	0.20845	0.0:0.0809:0.3076:0.6115	.	1566;352;1623	P53675-2;B7Z1Z7;P53675	.;.;CLH2_HUMAN	V	1566;1623;1623	ENSP00000439662:E1566V;ENSP00000445677:E1623V;ENSP00000441158:E1623V	ENSP00000445677:E1623V	E	-	2	0	CLTCL1	17548279	0.999000	0.42202	0.000000	0.03702	0.001000	0.01503	3.028000	0.49705	0.302000	0.22762	-0.313000	0.08912	GAG	.	.		0.607	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098		A	19168279	T	A	19168279	3	1	261	1	0	0	0	0	1	0	0	0	3569	1551	54	4	62	4	CLTCL1	22	19168279	Missense_Mutation	SNP	T	TCGA-FV-A23B-01A-11D-A16V-10		19168279	32136287	56	38254										
RPS6KA3	6197	hgsc.bcm.edu	37	chrX	20206011	20206011	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	tcgacgattaactacttctgGagccatatactccacagttc	6	12	1	0			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chrX:20206011G>A	ENST00000379565.3	-	9	916	c.709C>T	c.(709-711)Cca>Tca	p.P237S	RPS6KA3_ENST00000540702.1_Missense_Mutation_p.P209S|RPS6KA3_ENST00000544447.1_Missense_Mutation_p.P209S|RPS6KA3_ENST00000379548.4_Missense_Mutation_p.P208S	NM_004586.2	NP_004577.1	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 3	237	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|central nervous system development (GO:0007417)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(14)|lung(7)|ovary(1)|stomach(1)	41					Acetylsalicylic acid(DB00945)	ACTACTTCTGGAGCCATATAC	0.388																																					p.P237S		Atlas-SNP	.											.	RPS6KA3	110	.	0			c.C709T						.						159	143	148					X																	20206011		2203	4300	6503	SO:0001583	missense	6197	exon9			CTTCTGGAGCCAT	U08316	CCDS14197.1	Xp22.2-p22.1	2013-06-03	2002-08-29		ENSG00000177189	ENSG00000177189			10432	protein-coding gene	gene with protein product		300075	"ribosomal protein S6 kinase, 90kD, polypeptide 3", "mental retardation, X-linked 19", "Coffin-Lowry syndrome"	MRX19, CLS		8141249, 11896450, 16879200	Standard	XM_005274573		Approved	RSK, RSK2, HU-3	uc004czu.3	P51812	OTTHUMG00000021231	ENST00000379565.3:c.709C>T	chrX.hg19:g.20206011G>A	ENSP00000368884:p.Pro237Ser	202.0	0.0		177.0	71.0	NM_004586	B2R9V4|Q4VAP3|Q59H26|Q5JPK8|Q7Z3Z7	Missense_Mutation	SNP	ENST00000379565.3	hg19	CCDS14197.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.958932	0.92726	.	.	ENSG00000177189	ENST00000379565;ENST00000544447;ENST00000379548;ENST00000540702;ENST00000457145	T;T;T;T;T	0.75154	-0.91;-0.91;-0.91;-0.91;-0.91	5.08	5.08	0.68730	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.91673	0.7368	H	0.98133	4.155	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.95028	0.8166	10	0.87932	D	0	.	17.5586	0.87900	0.0:0.0:1.0:0.0	.	209;208;209;237	B4DG22;F5GYC4;B7ZB17;P51812	.;.;.;KS6A3_HUMAN	S	237;209;208;209;208	ENSP00000368884:P237S;ENSP00000440220:P209S;ENSP00000368865:P208S;ENSP00000444837:P209S;ENSP00000407655:P208S	ENSP00000368865:P208S	P	-	1	0	RPS6KA3	20115932	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.813000	0.99286	2.074000	0.62210	0.513000	0.50165	CCA	.	.		0.388	RPS6KA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056011.3	NM_004586		A	20206011	G	A	20206011	3	1	261	1	0	0	0	0	1	0	0	0	13667	1174	41	3	1569	3	RPS6KA3	23	20206011	Missense_Mutation	SNP	G	TCGA-FV-A23B-01A-11D-A16V-10		20206011	135064549	57	38255										
TSPAN7	7102	hgsc.bcm.edu	37	chrX	38525510	38525510	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	gcaccactattgttgtctttGgcctgtttggatgctttgct	10	9	1	0			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chrX:38525510G>C	ENST00000378482.2	+	2	394	c.217G>C	c.(217-219)Ggc>Cgc	p.G73R	TM4SF2_ENST00000465127.1_Missense_Mutation_p.G103R|TSPAN7_ENST00000545599.1_Missense_Mutation_p.G47R|TSPAN7_ENST00000488893.1_3'UTR|TSPAN7_ENST00000422612.2_Missense_Mutation_p.G99R|TSPAN7_ENST00000286824.6_Missense_Mutation_p.G90R	NM_004615.3	NP_004606.2	P41732	TSN7_HUMAN	tetraspanin 7	73					viral process (GO:0016032)	integral component of plasma membrane (GO:0005887)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	11						TGTTGTCTTTGGCCTGTTTGG	0.448																																					p.G73R		Atlas-SNP	.											.	TSPAN7	33	.	0			c.G217C						.						245	165	192					X																	38525510		2202	4300	6502	SO:0001583	missense	7102	exon2			GTCTTTGGCCTGT	D29808	CCDS14248.1	Xp11.4	2013-02-14	2005-03-21	2005-03-21	ENSG00000156298	ENSG00000156298		"CD molecules", "Tetraspanins"	11854	protein-coding gene	gene with protein product		300096	"transmembrane 4 superfamily member 2", "mental retardation, X-linked 58"	MXS1, TM4SF2, MRX58		12070254	Standard	NM_004615		Approved	DXS1692E, TALLA-1, A15, CD231	uc004deg.4	P41732	OTTHUMG00000024090	ENST00000378482.2:c.217G>C	chrX.hg19:g.38525510G>C	ENSP00000367743:p.Gly73Arg	92.0	0.0		121.0	43.0	NM_004615	B2R5W7|D3DWB1|Q8WVG5|Q9UEY9	Missense_Mutation	SNP	ENST00000378482.2	hg19	CCDS14248.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.582598	0.86748	.	.	ENSG00000250349;ENSG00000156298;ENSG00000156298;ENSG00000156298;ENSG00000156298	ENST00000465127;ENST00000378482;ENST00000422612;ENST00000286824;ENST00000545599	D;D;D;D;D	0.81908	-1.55;-1.55;-1.55;-1.55;-1.55	5.96	5.1	0.69264	Tetraspanin, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.93360	0.7883	M	0.94142	3.5	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.94750	0.7926	9	.	.	.	.	14.4266	0.67220	0.0722:0.0:0.9278:0.0	.	90;99;73	B4DDG0;B4DEA5;P41732	.;.;TSN7_HUMAN	R	103;73;99;90;47	ENSP00000417050:G103R;ENSP00000367743:G73R;ENSP00000388954:G99R;ENSP00000286824:G90R;ENSP00000441540:G47R	.	G	+	1	0	RP5-972B16.2;TSPAN7	38410454	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	9.476000	0.97823	1.274000	0.44362	0.594000	0.82650	GGC	.	.		0.448	TSPAN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356412.1			C	38525510	G	C	38525510	3	2	261	1	0	0	0	0	1	0	0	0	16667	1348	47	4	223	4	TSPAN7	23	38525510	Missense_Mutation	SNP	G	TCGA-FV-A23B-01A-11D-A16V-10	18319499	38525510	116745050	58	38256										
BCOR	54880	hgsc.bcm.edu	37	chrX	39922119	39922119	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	gatggcttctcgctgttgtcGgtgtatttctgcagcaggga	14	8	2	0			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chrX:39922119G>T	ENST00000378444.4	-	9	4281	c.4053C>A	c.(4051-4053)acC>acA	p.T1351T	BCOR_ENST00000397354.3_Silent_p.T1317T|BCOR_ENST00000378455.4_Silent_p.T1299T|BCOR_ENST00000342274.4_Silent_p.T1317T|BCOR_ENST00000378463.1_Silent_p.T194T	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	1351					heart development (GO:0007507)|histone H2A monoubiquitination (GO:0035518)|negative regulation of bone mineralization (GO:0030502)|negative regulation of histone H3-K36 methylation (GO:0000415)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|palate development (GO:0060021)|specification of axis polarity (GO:0065001)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	heat shock protein binding (GO:0031072)|histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			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						CGCTGTTGTCGGTGTATTTCT	0.517			"F, N, S, T"	RARA	"retinoblastoma, AML, APL(translocation)"		oculo-facio-cardio-dental genetic																														p.T1351T		Atlas-SNP	.		Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	BCOR	351	.	0			c.C4053A						.						126	98	108					X																	39922119		2202	4300	6502	SO:0001819	synonymous_variant	54880	exon9			GTTGTCGGTGTAT	AF317391	CCDS14250.1, CCDS48092.1, CCDS48093.1	Xp11.4	2014-09-17	2010-06-10		ENSG00000183337	ENSG00000183337		"Ankyrin repeat domain containing"	20893	protein-coding gene	gene with protein product		300485	"BCL6 co-repressor"			10898795	Standard	NM_017745		Approved	FLJ20285, KIAA1575	uc004den.4	Q6W2J9	OTTHUMG00000024100	ENST00000378444.4:c.4053C>A	chrX.hg19:g.39922119G>T		183.0	0.0		184.0	8.0	NM_001123385	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Silent	SNP	ENST00000378444.4	hg19	CCDS48093.1	.	.	.	.	.	.	.	.	.	.	G	7.436	0.639723	0.14386	.	.	ENSG00000183337	ENST00000427012	.	.	.	5.67	3.81	0.43845	.	.	.	.	.	T	0.59582	0.2204	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53592	-0.8417	4	.	.	.	-8.1494	9.5913	0.39548	0.0:0.1328:0.5743:0.2929	.	.	.	.	Q	46	.	.	P	-	2	0	BCOR	39807063	0.883000	0.30277	0.951000	0.38953	0.926000	0.56050	-0.084000	0.11268	0.497000	0.27926	0.600000	0.82982	CCG	.	.		0.517	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745		T	39922119	G	T	39922119	2	4	261	1	0	0	0	0	0	0	0	1	1386	1103	39	1		1	BCOR	23	39922119	Silent	SNP	G	TCGA-FV-A23B-01A-11D-A16V-10	1396609	39922119	115348441	59	38257										
HTR2C	3358	hgsc.bcm.edu	37	chrX	114141874	114141874	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0166666666666667	1	1	0.273373983739837	0	0.328048780487805	1	1	0	ataccaatgaaccggtgatcGagaaagccagtgacaatgag	11	8	0	5			TCGA-FV-A23B-01A-11D-A16V-10	TCGA-FV-A23B-11A-11D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63adc09c-e1b1-40dd-9c35-2f8276b656fc	6c3072b0-3eb6-4a43-8a18-74e5a5869d4c	g.chrX:114141874G>T	ENST00000276198.1	+	6	2001	c.1273G>T	c.(1273-1275)Gag>Tag	p.E425*	HTR2C_ENST00000371950.3_3'UTR|HTR2C_ENST00000371951.1_Nonsense_Mutation_p.E425*	NM_000868.2	NP_000859.1	P28335	5HT2C_HUMAN	5-hydroxytryptamine (serotonin) receptor 2C, G protein-coupled	425					behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|cGMP biosynthetic process (GO:0006182)|feeding behavior (GO:0007631)|locomotory behavior (GO:0007626)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|phospholipase C-activating serotonin receptor signaling pathway (GO:0007208)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|regulation of appetite (GO:0032098)|regulation of corticotropin-releasing hormone secretion (GO:0043397)|regulation of neurological system process (GO:0031644)|release of sequestered calcium ion into cytosol (GO:0051209)|response to drug (GO:0042493)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding (GO:0071886)|drug binding (GO:0008144)|Gq/11-coupled serotonin receptor activity (GO:0001587)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(15)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	50					Agomelatine(DB06594)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Clomipramine(DB01242)|Clozapine(DB00363)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Dexfenfluramine(DB01191)|Doxepin(DB01142)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Lorcaserin(DB04871)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Pramipexole(DB00413)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Sertindole(DB06144)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)	ACCGGTGATCGAGAAAGCCAG	0.468																																					p.E425X		Atlas-SNP	.											.	HTR2C	117	.	0			c.G1273T						.						144	141	142					X																	114141874		2203	4300	6503	SO:0001587	stop_gained	3358	exon6			GTGATCGAGAAAG		CCDS14564.1, CCDS59174.1	Xq23	2013-12-19	2012-02-03		ENSG00000147246	ENSG00000147246		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5295	protein-coding gene	gene with protein product		312861	"5-hydroxytryptamine (serotonin) receptor 2C"	HTR1C		7895773	Standard	NM_000868		Approved	5-HT2C, 5HTR2C	uc004epu.1	P28335	OTTHUMG00000022226	ENST00000276198.1:c.1273G>T	chrX.hg19:g.114141874G>T	ENSP00000276198:p.Glu425*	216.0	0.0		196.0	74.0	NM_000868	B1AMW4|Q5VUF8|Q9NP28	Nonsense_Mutation	SNP	ENST00000276198.1	hg19	CCDS14564.1	.	.	.	.	.	.	.	.	.	.	G	33	5.200961	0.94997	.	.	ENSG00000147246	ENST00000276198;ENST00000371951	.	.	.	4.89	-3.99	0.04069	.	0.580762	0.17675	N	0.165808	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.06236	T	0.91	.	6.367	0.21461	0.2236:0.4318:0.3446:0.0	.	.	.	.	X	425	.	ENSP00000276198:E425X	E	+	1	0	HTR2C	114048130	0.766000	0.28496	0.001000	0.08648	0.001000	0.01503	1.423000	0.34837	-0.371000	0.08004	-2.142000	0.00338	GAG	.	.		0.468	HTR2C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057962.1	NM_000868		T	114141874	G	T	114141874	4	4	261	1	0	0	0	0	0	1	0	0	7452	1059	37	1	1287	1	HTR2C	23	114141874	Nonsense_Mutation	SNP	G	TCGA-FV-A23B-01A-11D-A16V-10	74219755	114141874	41128686	60	38258										
ZMYND12	84217	hgsc.bcm.edu	37	chr1	42914268	42914268	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	tcgtgtttcccttcaaagagGtatttctgggctatggtgta	11	7	2	1			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr1:42914268G>T	ENST00000372565.3	-	3	563	c.294C>A	c.(292-294)taC>taA	p.Y98*	ZMYND12_ENST00000433602.2_Intron	NM_032257.4	NP_115633.3	Q9H0C1	ZMY12_HUMAN	zinc finger, MYND-type containing 12	98						intracellular (GO:0005622)	metal ion binding (GO:0046872)			NS(1)|endometrium(2)|large_intestine(3)|lung(5)|ovary(2)|prostate(2)|skin(2)	17	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				CTTCAAAGAGGTATTTCTGGG	0.468																																					p.Y98X		Atlas-SNP	.											.	ZMYND12	35	.	0			c.C294A						.						112	100	104					1																	42914268		2203	4300	6503	SO:0001587	stop_gained	84217	exon3			AAAGAGGTATTTC	AK057384	CCDS467.1	1p34.1	2008-02-05			ENSG00000066185	ENSG00000066185		"Zinc fingers, MYND-type"	21192	protein-coding gene	gene with protein product						11230166	Standard	NM_032257		Approved	DKFZp434N2435	uc001chj.3	Q9H0C1	OTTHUMG00000007333	ENST00000372565.3:c.294C>A	chr1.hg19:g.42914268G>T	ENSP00000361646:p.Tyr98*	119.0	0.0		88.0	38.0	NM_032257	Q5VUS6|Q8TC87|Q96M51	Nonsense_Mutation	SNP	ENST00000372565.3	hg19	CCDS467.1	.	.	.	.	.	.	.	.	.	.	G	36	5.809436	0.96975	.	.	ENSG00000066185	ENST00000372565	.	.	.	5.58	-0.793	0.10922	.	0.470389	0.24671	N	0.036550	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.825	10.7948	0.46453	0.4596:0.0:0.5404:0.0	.	.	.	.	X	98	.	ENSP00000361646:Y98X	Y	-	3	2	ZMYND12	42686855	0.869000	0.29996	0.966000	0.40874	0.946000	0.59487	-0.109000	0.10840	-0.404000	0.07610	-0.367000	0.07326	TAC	.	.		0.468	ZMYND12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019170.1	NM_032257		T	42914268	G	T	42914268	4	4	262	1	0	0	0	0	0	1	0	0	17722	1256	44	3	827	3	ZMYND12	1	42914268	Nonsense_Mutation	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10		42914268	206336353	1	38259										
ATXN7L2	127002	hgsc.bcm.edu	37	chr1	110029743	110029743	+	Frame_Shift_Del	DEL	C	C	-													0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	gcagggcccagcttgtagggCcccaggttccacgaaaacct							TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr1:110029743delC	ENST00000369870.3	+	4	428	c.413delC	c.(412-414)gccfs	p.A138fs		NM_153340.4	NP_699171.3	Q5T6C5	AT7L2_HUMAN	ataxin 7-like 2	138										breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)	17		all_epithelial(167;0.00197)|all_lung(203;0.00291)|Lung NSC(277;0.00453)		Colorectal(144;0.0129)|Lung(183;0.0426)|Epithelial(280;0.0675)|READ - Rectum adenocarcinoma(129;0.0693)|all cancers(265;0.071)|LUSC - Lung squamous cell carcinoma(189;0.228)		GCTTGTAGGGCCCCAGGTTCC	0.637																																					p.A138fs		Atlas-Indel,Pindel	.											.	ATXN7L2	60	.	0			c.412delG						.						22	26	24					1																	110029743		2202	4300	6502	SO:0001589	frameshift_variant	127002	exon4			.	BC037582	CCDS30794.1	1p13.2	2008-02-05			ENSG00000162650	ENSG00000162650			28713	protein-coding gene	gene with protein product						12477932	Standard	NM_153340		Approved	MGC46534, FLJ00381	uc001dxr.3	Q5T6C5	OTTHUMG00000011027	ENST00000369870.3:c.413delC	chr1.hg19:g.110029743delC	ENSP00000358886:p.Ala138fs	111.0	0.0		114.0	33.0	NM_153340		Frame_Shift_Del	DEL	ENST00000369870.3	hg19	CCDS30794.1																																																																																			.	.		0.637	ATXN7L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030331.1	NM_153340		-	110029743	C	-	110029743	7	5	262	1	0	1	0	1	0	0	0	0	1217	739	26	0	427	0	ATXN7L2	1	110029743	Frame_Shift_Del	DEL	C	TCGA-FV-A2QQ-01A-11D-A22F-10	67115475	110029743	139220878	2	38260										
DENND2D	79961	hgsc.bcm.edu	37	chr1	111738547	111738547	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	tgctaacccacctcagtgccTgagtcggggatgaagctctt	11	12	2	2			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr1:111738547T>A	ENST00000357640.4	-	6	865	c.636A>T	c.(634-636)tcA>tcT	p.S212S	DENND2D_ENST00000369752.5_Silent_p.S209S|DENND2D_ENST00000473682.1_5'UTR	NM_024901.3	NP_079177.2	Q9H6A0	DEN2D_HUMAN	DENN/MADD domain containing 2D	212	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of Rab GTPase activity (GO:0032851)	cytoplasm (GO:0005737)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(1)|kidney(7)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	25		all_cancers(81;0.00198)|all_epithelial(167;0.000686)|all_lung(203;0.00318)|Lung NSC(277;0.00499)		Lung(183;0.0162)|Colorectal(144;0.069)|all cancers(265;0.0757)|LUSC - Lung squamous cell carcinoma(189;0.0845)|Epithelial(280;0.114)|COAD - Colon adenocarcinoma(174;0.14)		CCTCAGTGCCTGAGTCGGGGA	0.557																																					p.S212S		Atlas-SNP	.											.	DENND2D	50	.	0			c.A636T						.						142	137	139					1																	111738547		2203	4300	6503	SO:0001819	synonymous_variant	79961	exon6			AGTGCCTGAGTCG		CCDS831.1, CCDS60219.1	1p13.3	2014-02-12	2005-08-17		ENSG00000162777	ENSG00000162777		"DENN/MADD domain containing"	26192	protein-coding gene	gene with protein product		615111				12477932	Standard	NM_024901		Approved	FLJ22457, RP5-1180E21.2	uc001eal.2	Q9H6A0	OTTHUMG00000012356	ENST00000357640.4:c.636A>T	chr1.hg19:g.111738547T>A		27.0	0.0		29.0	7.0	NM_024901	Q5T5V6|Q9BSU0	Silent	SNP	ENST00000357640.4	hg19	CCDS831.1																																																																																			.	.		0.557	DENND2D-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000034456.1	NM_024901		A	111738547	T	A	111738547	2	1	262	1	0	0	0	0	0	0	0	1	4433	1567	55	4		4	DENND2D	1	111738547	Silent	SNP	T	TCGA-FV-A2QQ-01A-11D-A22F-10	1708804	111738547	137512074	3	38261										
ANKRD34A	284615	hgsc.bcm.edu	37	chr1	145474461	145474461	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	ccctccagccggctcggctcCctctccgcgccagtcccagg	10	22	1	0			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr1:145474461C>T	ENST00000323397.4	+	4	2426	c.1133C>T	c.(1132-1134)cCc>cTc	p.P378L	LIX1L_ENST00000369308.3_5'Flank|RP11-315I20.1_ENST00000600340.1_RNA	NM_001039888.2	NP_001034977.1	Q69YU3	AN34A_HUMAN	ankyrin repeat domain 34A	378	Pro-rich.					cytoplasm (GO:0005737)				endometrium(2)|kidney(2)|large_intestine(2)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	20	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GGCTCGGCTCCCTCTCCGCGC	0.711																																					p.P378L		Atlas-SNP	.											.	ANKRD34A	52	.	0			c.C1133T						.						17	19	18					1																	145474461		2202	4296	6498	SO:0001583	missense	284615	exon4			CGGCTCCCTCTCC	AK128050	CCDS72874.1	1q21.1	2013-01-10	2007-11-20	2007-11-20	ENSG00000181039	ENSG00000272031		"Ankyrin repeat domain containing"	27639	protein-coding gene	gene with protein product			"ankyrin repeat domain 34"	ANKRD34			Standard	NM_001039888		Approved		uc001enq.1	Q69YU3	OTTHUMG00000013740	ENST00000323397.4:c.1133C>T	chr1.hg19:g.145474461C>T	ENSP00000314103:p.Pro378Leu	68.0	0.0		67.0	11.0	NM_001039888	B3KSU3	Missense_Mutation	SNP	ENST00000323397.4	hg19	CCDS30829.1	.	.	.	.	.	.	.	.	.	.	C	12.76	2.035425	0.35893	.	.	ENSG00000181039	ENST00000323397	T	0.17213	2.29	5.11	4.17	0.49024	.	1.222920	0.05731	N	0.599596	T	0.04137	0.0115	N	0.08118	0	0.30567	N	0.763884	B	0.10296	0.003	B	0.12156	0.007	T	0.29274	-1.0017	10	0.87932	D	0	-4.7809	10.6339	0.45554	0.191:0.809:0.0:0.0	.	378	Q69YU3	AN34A_HUMAN	L	378	ENSP00000314103:P378L	ENSP00000314103:P378L	P	+	2	0	ANKRD34A	144185818	0.185000	0.23213	0.915000	0.36163	0.915000	0.54546	1.603000	0.36794	1.322000	0.45245	0.650000	0.86243	CCC	.	.		0.711	ANKRD34A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038512.1			T	145474461	C	T	145474461	3	4	262	1	0	0	0	0	1	0	0	0	662	623	22	3	1135	3	ANKRD34A	1	145474461	Missense_Mutation	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10	33735914	145474461	103776160	4	38262										
BCAN	63827	hgsc.bcm.edu	37	chr1	156628362	156628362	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	tgggccgccaccggagctgcCcctggctcaagtgttcggcc	14	16	1	0			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr1:156628362C>A	ENST00000329117.5	+	13	2801	c.2465C>A	c.(2464-2466)cCc>cAc	p.P822H	RP11-284F21.7_ENST00000448869.1_RNA	NM_021948.4	NP_068767.3	Q96GW7	PGCB_HUMAN	brevican	822	Sushi. {ECO:0000255|PROSITE- ProRule:PRU00302}.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hippocampus development (GO:0021766)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	55	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CCGGAGCTGCCCCTGGCTCAA	0.632																																					p.P822H		Atlas-SNP	.											.	BCAN	174	.	0			c.C2465A						.						36	41	39					1																	156628362		2203	4300	6503	SO:0001583	missense	63827	exon13			AGCTGCCCCTGGC	BC027971	CCDS1149.1, CCDS1150.1	1q31	2013-05-07			ENSG00000132692	ENSG00000132692		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	23059	protein-coding gene	gene with protein product	"chondroitin sulfate proteoglycan 7", "brevican proteoglycan"	600347				11054543, 11873941	Standard	NM_021948		Approved	BEHAB, MGC13038, CSPG7	uc001fpp.3	Q96GW7	OTTHUMG00000033322	ENST00000329117.5:c.2465C>A	chr1.hg19:g.156628362C>A	ENSP00000331210:p.Pro822His	58.0	0.0		63.0	6.0	NM_021948	D3DVC2|Q5SZ10|Q5T3I5|Q8TBB9|Q9HBK1|Q9HBK4	Missense_Mutation	SNP	ENST00000329117.5	hg19	CCDS1149.1	.	.	.	.	.	.	.	.	.	.	C	17.72	3.458108	0.63401	.	.	ENSG00000132692	ENST00000329117	T	0.68624	-0.34	5.4	4.46	0.54185	Complement control module (2);Sushi/SCR/CCP (3);	0.112919	0.37012	N	0.002285	T	0.52837	0.1759	L	0.58669	1.825	0.80722	D	1	B	0.33637	0.42	B	0.36186	0.219	T	0.62315	-0.6880	10	0.66056	D	0.02	-18.4459	13.7094	0.62659	0.0:0.8444:0.1556:0.0	.	822	Q96GW7	PGCB_HUMAN	H	822	ENSP00000331210:P822H	ENSP00000331210:P822H	P	+	2	0	BCAN	154894986	0.000000	0.05858	0.999000	0.59377	0.982000	0.71751	0.373000	0.20484	1.474000	0.48178	0.555000	0.69702	CCC	.	.		0.632	BCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081844.2	NM_021948		A	156628362	C	A	156628362	3	1	262	1	0	0	0	0	1	0	0	0	1345	623	22	3	2585	3	BCAN	1	156628362	Missense_Mutation	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10	11153901	156628362	92622259	5	38263										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158655029	158655029	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	atcctcaagcttctgaccccTctcagcgacccgctccttga	6	18	3	2			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr1:158655029T>C	ENST00000368147.4	-	2	313	c.133A>G	c.(133-135)Agg>Ggg	p.R45G		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	45			R -> S (in EL2; Clichy). {ECO:0000269|PubMed:2568862}.|R -> T (in EL2; Anastasia). {ECO:0000269|PubMed:7772539}.		actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					ttctgaccccTCTCAGCGACC	0.483																																					p.R45G		Atlas-SNP	.											.	SPTA1	720	.	0			c.A133G						.						116	118	117					1																	158655029		1935	4138	6073	SO:0001583	missense	6708	exon2			GACCCCTCTCAGC	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.133A>G	chr1.hg19:g.158655029T>C	ENSP00000357129:p.Arg45Gly	102.0	0.0		154.0	74.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	T	17.50	3.404231	0.62288	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.50277	0.75;0.75	5.18	2.75	0.32379	.	0.000000	0.35805	N	0.002974	T	0.53610	0.1807	M	0.68593	2.085	0.43598	D	0.995951	D	0.60575	0.988	D	0.68765	0.96	T	0.60454	-0.7260	10	0.87932	D	0	.	11.8885	0.52616	0.0:0.0:0.2859:0.714	.	45	P02549	SPTA1_HUMAN	G	45	ENSP00000357130:R45G;ENSP00000357129:R45G	ENSP00000357129:R45G	R	-	1	2	SPTA1	156921653	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.626000	0.54245	0.961000	0.38030	0.383000	0.25322	AGG	.	.		0.483	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		C	158655029	T	C	158655029	3	2	262	1	0	0	0	0	1	0	0	0	15131	1550	54	2	7330	2	SPTA1	1	158655029	Missense_Mutation	SNP	T	TCGA-FV-A2QQ-01A-11D-A22F-10	2026667	158655029	90595592	6	38264										
SELE	6401	hgsc.bcm.edu	37	chr1	169702100	169702100	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	aagtcatagcttccgtggagGtgttgtaagaccaggctcca	12	9	1	1			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr1:169702100G>T	ENST00000333360.7	-	3	216	c.77C>A	c.(76-78)aCc>aAc	p.T26N	SELE_ENST00000367777.1_Missense_Mutation_p.T26N|SELE_ENST00000367779.4_Missense_Mutation_p.T26N|C1orf112_ENST00000498289.1_Intron|SELE_ENST00000367774.1_Missense_Mutation_p.T26N|SELE_ENST00000367781.4_Missense_Mutation_p.T26N|SELE_ENST00000367776.1_Missense_Mutation_p.T26N|SELE_ENST00000367775.1_Missense_Mutation_p.T26N|SELE_ENST00000367780.4_Missense_Mutation_p.T26N|SELE_ENST00000367782.4_Missense_Mutation_p.T26N	NM_000450.2	NP_000441.2	P16581	LYAM2_HUMAN	selectin E	26	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				actin filament-based process (GO:0030029)|activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of receptor internalization (GO:0002092)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)	caveola (GO:0005901)|coated pit (GO:0005905)|cortical cytoskeleton (GO:0030863)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	oligosaccharide binding (GO:0070492)|phospholipase binding (GO:0043274)|sialic acid binding (GO:0033691)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(3)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	all_hematologic(923;0.208)				Carvedilol(DB01136)	TTCCGTGGAGGTGTTGTAAGA	0.418																																					p.T26N		Atlas-SNP	.											.	SELE	84	.	0			c.C77A						.						111	104	106					1																	169702100		2203	4300	6503	SO:0001583	missense	6401	exon3			GTGGAGGTGTTGT	M30640	CCDS1283.1	1q22-q25	2008-07-31	2008-07-31		ENSG00000007908	ENSG00000007908		"CD molecules"	10718	protein-coding gene	gene with protein product		131210	"endothelial adhesion molecule 1"	ELAM1, ELAM		1375831	Standard	NM_000450		Approved	ESEL, CD62E	uc001ggm.4	P16581	OTTHUMG00000034851	ENST00000333360.7:c.77C>A	chr1.hg19:g.169702100G>T	ENSP00000331736:p.Thr26Asn	82.0	0.0		130.0	17.0	NM_000450	A2RRD6|P16111	Missense_Mutation	SNP	ENST00000333360.7	hg19	CCDS1283.1	.	.	.	.	.	.	.	.	.	.	G	15.27	2.783198	0.49891	.	.	ENSG00000007908	ENST00000367781;ENST00000367782;ENST00000367780;ENST00000367779;ENST00000333360;ENST00000367777;ENST00000367775;ENST00000367776;ENST00000367774	T;T;T;T;T;T;T;T;T	0.22539	1.95;1.95;1.95;1.95;1.95;1.95;1.95;1.95;1.95	5.58	0.174	0.15040	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (2);	1.218260	0.06047	N	0.655883	T	0.04048	0.0113	L	0.37561	1.115	0.09310	N	1	B	0.30584	0.286	B	0.25506	0.061	T	0.40515	-0.9559	10	0.31617	T	0.26	-0.9604	0.8401	0.01148	0.2939:0.1191:0.3771:0.2099	.	26	P16581	LYAM2_HUMAN	N	26	ENSP00000356755:T26N;ENSP00000356756:T26N;ENSP00000356754:T26N;ENSP00000356753:T26N;ENSP00000331736:T26N;ENSP00000356751:T26N;ENSP00000356749:T26N;ENSP00000356750:T26N;ENSP00000356748:T26N	ENSP00000331736:T26N	T	-	2	0	SELE	167968724	0.051000	0.20477	0.001000	0.08648	0.765000	0.43378	1.664000	0.37439	0.031000	0.15407	0.655000	0.94253	ACC	.	.		0.418	SELE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084333.1	NM_000450		T	169702100	G	T	169702100	3	4	262	1	0	0	0	0	1	0	0	0	14028	1261	44	3	1799	3	SELE	1	169702100	Missense_Mutation	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10	11047071	169702100	79548521	7	38265										
HHAT	55733	hgsc.bcm.edu	37	chr1	210637950	210637950	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	tggatggactcactccacccGccctcccccgctgcgtgagc	10	19	1	1	rs143700139		TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr1:210637950G>A	ENST00000367010.1	+	8	1185	c.958G>A	c.(958-960)Gcc>Acc	p.A320T	HHAT_ENST00000545781.1_Missense_Mutation_p.A257T|HHAT_ENST00000308852.6_Missense_Mutation_p.A275T|HHAT_ENST00000413764.2_Missense_Mutation_p.A320T|HHAT_ENST00000367009.1_Missense_Mutation_p.A10T|HHAT_ENST00000545154.1_Missense_Mutation_p.A321T|HHAT_ENST00000537898.1_Missense_Mutation_p.A255T|HHAT_ENST00000391905.3_Missense_Mutation_p.A320T|HHAT_ENST00000261458.3_Missense_Mutation_p.A320T|HHAT_ENST00000541565.1_Missense_Mutation_p.A183T	NM_001170580.1	NP_001164051.1	Q5VTY9	HHAT_HUMAN	hedgehog acyltransferase	320					multicellular organismal development (GO:0007275)|protein palmitoylation (GO:0018345)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|palmitoyltransferase activity (GO:0016409)			breast(3)|central_nervous_system(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	27				OV - Ovarian serous cystadenocarcinoma(81;0.0136)|all cancers(67;0.161)|KIRC - Kidney renal clear cell carcinoma(1967;0.215)		CACTCCACCCGCCCTCCCCCG	0.592																																					p.A321T		Atlas-SNP	.											HHAT,colon,carcinoma,0,1	HHAT	66	.	0			c.G961A						.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	1,4405	2.1+/-5.4	0,1,2202	120	110	114		958,547,958,961,763,958	3.5	0.1	1	dbSNP_134	114	0,8600		0,0,4300	no	missense,missense,missense,missense,missense,missense	HHAT	NM_001122834.2,NM_001170564.1,NM_001170580.1,NM_001170587.1,NM_001170588.1,NM_018194.4	58,58,58,58,58,58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign,benign,benign,benign,benign	320/494,183/357,320/494,321/495,255/429,320/494	210637950	1,13005	2203	4300	6503	SO:0001583	missense	55733	exon7			CCACCCGCCCTCC	AK001586	CCDS1495.1, CCDS53471.1, CCDS53472.1, CCDS53473.1	1q32	2008-02-05			ENSG00000054392	ENSG00000054392			18270	protein-coding gene	gene with protein product		605743				11160356	Standard	NM_001170587		Approved	FLJ10724, MART-2, MART2, Skn, ski, rasp, sit, GUP2	uc009xcx.3	Q5VTY9	OTTHUMG00000036447	ENST00000367010.1:c.958G>A	chr1.hg19:g.210637950G>A	ENSP00000355977:p.Ala320Thr	133.0	1.0		172.0	68.0	NM_001170587	B7Z4D5|B7Z5I1|B7Z868|B7ZA75|D3DT91|F5H444|Q17RZ7|Q4G0K3|Q5CZ95|Q5TGI2|Q9NVH9|Q9Y3N8	Missense_Mutation	SNP	ENST00000367010.1	hg19	CCDS1495.1	.	.	.	.	.	.	.	.	.	.	G	12.13	1.846171	0.32606	2.27E-4	0.0	ENSG00000054392	ENST00000413764;ENST00000541565;ENST00000545154;ENST00000537898;ENST00000391905;ENST00000545781;ENST00000261458;ENST00000308852;ENST00000367010;ENST00000426968;ENST00000367009	T;T;T;T;T;T;T;T;T;T;T	0.72725	-0.68;-0.68;-0.68;-0.68;-0.68;-0.68;-0.68;-0.68;-0.68;-0.68;-0.68	5.42	3.49	0.39957	.	0.301734	0.36893	N	0.002341	T	0.55847	0.1946	L	0.34521	1.04	0.09310	N	1	B;B;B;B;B	0.29671	0.226;0.177;0.254;0.115;0.226	B;B;B;B;B	0.25405	0.051;0.021;0.06;0.019;0.051	T	0.37502	-0.9703	10	0.15066	T	0.55	-21.4242	13.6214	0.62138	0.0:0.4157:0.5843:0.0	.	275;321;183;255;320	B7Z2U8;F5H444;B7Z4D5;B7Z5I1;Q5VTY9	.;.;.;.;HHAT_HUMAN	T	320;183;321;255;320;257;320;275;320;192;10	ENSP00000416845:A320T;ENSP00000444995:A183T;ENSP00000438468:A321T;ENSP00000442625:A255T;ENSP00000375773:A320T;ENSP00000439229:A257T;ENSP00000261458:A320T;ENSP00000308628:A275T;ENSP00000355977:A320T;ENSP00000413399:A192T;ENSP00000355976:A10T	ENSP00000261458:A320T	A	+	1	0	HHAT	208704573	0.152000	0.22762	0.065000	0.19835	0.166000	0.22503	1.291000	0.33330	1.276000	0.44395	-0.321000	0.08615	GCC	.	G|1.000;A|0.000		0.592	HHAT-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088662.1	NM_018194		A	210637950	G	A	210637950	3	1	262	1	0	0	0	0	1	0	0	0	7098	1087	38	1	1082	1	HHAT	1	210637950	Missense_Mutation	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10	40935850	210637950	38612671	8	38266										
APOB	338	hgsc.bcm.edu	37	chr2	21232125	21232125	+	Frame_Shift_Del	DEL	C	C	-													0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	tgtgctataaacctggcctaCcagagacaggtatcgttgaa					rs148170480	byFrequency	TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr2:21232125delC	ENST00000233242.1	-	26	7742	c.7615delG	c.(7615-7617)gtafs	p.V2539fs		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	2539					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ACCTGGCCTACCAGAGACAGG	0.448																																					p.V2539fs		Atlas-Indel,Pindel	.											.	APOB	761	.	0			c.7616delT						.						122	102	108					2																	21232125		2203	4299	6502	SO:0001589	frameshift_variant	338	exon26			.	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.7615delG	chr2.hg19:g.21232125delC	ENSP00000233242:p.Val2539fs	105.0	0.0		137.0	18.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Frame_Shift_Del	DEL	ENST00000233242.1	hg19	CCDS1703.1																																																																																			.	.		0.448	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			-	21232125	C	-	21232125	7	5	262	1	0	1	0	1	0	0	0	0	785	507	18	0	6092	0	APOB	2	21232125	Frame_Shift_Del	DEL	C	TCGA-FV-A2QQ-01A-11D-A22F-10		21232125	221967248	9	38267										
PSD4	23550	hgsc.bcm.edu	37	chr2	113940279	113940279	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	gggagctgggtccatcaggaCgggctggagccttgccagga	18	10	1	0	rs147089589		TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr2:113940279C>T	ENST00000245796.6	+	2	441	c.246C>T	c.(244-246)gaC>gaT	p.D82D	PSD4_ENST00000441564.3_Silent_p.D82D|PSD4_ENST00000465917.1_3'UTR	NM_012455.2	NP_036587.2	Q8NDX1	PSD4_HUMAN	pleckstrin and Sec7 domain containing 4	82					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			cervix(1)|endometrium(2)|large_intestine(4)|lung(13)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TCCATCAGGACGGGCTGGAGC	0.622																																					p.D82D		Atlas-SNP	.											PSD4,NS,carcinoma,0,1	PSD4	74	.	0			c.C246T						.	T		1,4405	2.1+/-5.4	0,1,2202	51	52	52		246	-1.1	0	2	dbSNP_134	52	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PSD4	NM_012455.2		0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154		82/1057	113940279	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	23550	exon2			TCAGGACGGGCTG	U63127	CCDS33276.1	2q13	2013-01-10			ENSG00000125637	ENSG00000125637		"Pleckstrin homology (PH) domain containing"	19096	protein-coding gene	gene with protein product		614442				12082148	Standard	XM_005263634		Approved	TIC, EFA6B	uc002tjc.3	Q8NDX1	OTTHUMG00000153339	ENST00000245796.6:c.246C>T	chr2.hg19:g.113940279C>T		71.0	1.0		87.0	29.0	NM_012455	A6NEG7|A8K1Y0|O95621|Q4ZG34|Q6GPH8|Q8IYP4	Silent	SNP	ENST00000245796.6	hg19	CCDS33276.1																																																																																			.	C|1.000;T|0.000		0.622	PSD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330789.1	NM_012455		T	113940279	C	T	113940279	2	4	262	1	0	0	0	0	0	0	0	1	12661	535	19	1		1	PSD4	2	113940279	Silent	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10	92708154	113940279	129259094	10	38268										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141806729	141806729	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	agctatcttggtattcaagtCcattcctctaacaattcctg	5	11	3	0			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr2:141806729C>A	ENST00000389484.3	-	11	2586	c.1615G>T	c.(1615-1617)Gac>Tac	p.D539Y		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	539					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		GTATTCAAGTCCATTCCTCTA	0.403										TSP Lung(27;0.18)																											p.D539Y	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											LRP1B,NS,carcinoma,0,2	LRP1B	1315	.	0			c.G1615T						.						141	141	141					2																	141806729		2203	4300	6503	SO:0001583	missense	53353	exon11			TCAAGTCCATTCC	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.1615G>T	chr2.hg19:g.141806729C>A	ENSP00000374135:p.Asp539Tyr	182.0	0.0		220.0	67.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	15.60	2.880652	0.51801	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.93712	-3.27	5.49	5.49	0.81192	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.000000	0.85682	U	0.000000	D	0.93112	0.7807	L	0.48642	1.525	0.80722	D	1	D	0.57899	0.981	P	0.48425	0.577	D	0.93477	0.6824	10	0.59425	D	0.04	.	19.3798	0.94527	0.0:1.0:0.0:0.0	.	539	Q9NZR2	LRP1B_HUMAN	Y	539;477	ENSP00000374135:D539Y	ENSP00000374135:D539Y	D	-	1	0	LRP1B	141523199	1.000000	0.71417	1.000000	0.80357	0.025000	0.11179	7.710000	0.84655	2.565000	0.86533	0.563000	0.77884	GAC	.	.		0.403	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		A	141806729	C	A	141806729	3	1	262	1	0	0	0	0	1	0	0	0	8964	855	30	3	12508	3	LRP1B	2	141806729	Missense_Mutation	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10	27866450	141806729	101392644	11	38269										
FMNL2	114793	hgsc.bcm.edu	37	chr2	153471433	153471433	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	tacctggacaatgtttttgaTgtaggagctctactggaaga	11	6	1	2			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr2:153471433T>C	ENST00000288670.9	+	12	1498	c.1131T>C	c.(1129-1131)gaT>gaC	p.D377D		NM_052905.3	NP_443137.2	Q96PY5	FMNL2_HUMAN	formin-like 2	377	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				cortical actin cytoskeleton organization (GO:0030866)|cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)				central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(2)|lung(3)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	23						ATGTTTTTGATGTAGGAGCTC	0.418																																					p.D377D		Atlas-SNP	.											.	FMNL2	75	.	0			c.T1131C						.						96	98	97					2																	153471433		1992	4199	6191	SO:0001819	synonymous_variant	114793	exon12			TTTTGATGTAGGA	AB067489	CCDS46429.1	2q23.3	2008-02-05	2003-12-02	2003-12-03	ENSG00000157827	ENSG00000157827			18267	protein-coding gene	gene with protein product			"formin homology 2 domain containing 2"	FHOD2			Standard	XM_005246263		Approved	KIAA1902	uc002tye.3	Q96PY5	OTTHUMG00000154035	ENST00000288670.9:c.1131T>C	chr2.hg19:g.153471433T>C		149.0	0.0		127.0	47.0	NM_052905	B2RZH5|Q14CC9|Q4ZG52|Q8N3E0	Silent	SNP	ENST00000288670.9	hg19	CCDS46429.1																																																																																			.	.		0.418	FMNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333582.2	NM_052905		C	153471433	T	C	153471433	2	2	262	1	0	0	0	0	0	0	0	1	5960	1461	51	2		2	FMNL2	2	153471433	Silent	SNP	T	TCGA-FV-A2QQ-01A-11D-A22F-10	11664704	153471433	89727940	12	38270										
RPRM	56475	hgsc.bcm.edu	37	chr2	154334986	154334986	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	gtcggtcaccacggacgcctGggtgcagcagcgcacggctc	15	15	1	0			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr2:154334986G>T	ENST00000325926.3	-	1	336	c.94C>A	c.(94-96)Cag>Aag	p.Q32K	AC012501.2_ENST00000424322.1_RNA	NM_019845.2	NP_062819.1	Q9NS64	RPRM_HUMAN	reprimo, TP53 dependent G2 arrest mediator candidate	32					cell cycle arrest (GO:0007050)|regulation of mitotic cell cycle (GO:0007346)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				large_intestine(2)|lung(1)|prostate(1)	4						ACGGACGCCTGGGTGCAGCAG	0.677																																					p.Q32K		Atlas-SNP	.											.	RPRM	12	.	0			c.C94A						.						53	38	43					2																	154334986		2203	4299	6502	SO:0001583	missense	56475	exon1			ACGCCTGGGTGCA	AK074808	CCDS2198.1	2q24.1	2011-01-26	2005-12-01		ENSG00000177519	ENSG00000177519			24201	protein-coding gene	gene with protein product	"candidate mediator of the p53 dependent G2 arrest", "REPRIMO"	612171	"reprimo, TP53 dependant G2 arrest mediator candidate"			10930422	Standard	NM_019845		Approved	FLJ90327, REPRIMO	uc002tyq.1	Q9NS64	OTTHUMG00000131905	ENST00000325926.3:c.94C>A	chr2.hg19:g.154334986G>T	ENSP00000314946:p.Gln32Lys	28.0	0.0		30.0	9.0	NM_019845	B2R4V1	Missense_Mutation	SNP	ENST00000325926.3	hg19	CCDS2198.1	.	.	.	.	.	.	.	.	.	.	G	6.363	0.435014	0.12045	.	.	ENSG00000177519	ENST00000325926	.	.	.	4.92	4.92	0.64577	.	0.313337	0.30809	N	0.008838	T	0.48804	0.1520	L	0.39898	1.24	0.35027	D	0.758377	B	0.17268	0.021	B	0.17098	0.017	T	0.54384	-0.8302	9	0.21540	T	0.41	3.7537	15.5916	0.76534	0.0:0.0:1.0:0.0	.	32	Q9NS64	RPRM_HUMAN	K	32	.	ENSP00000314946:Q32K	Q	-	1	0	RPRM	154043232	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.825000	0.69286	2.260000	0.74910	0.591000	0.81541	CAG	.	.		0.677	RPRM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254856.1	NM_019845		T	154334986	G	T	154334986	3	4	262	1	0	0	0	0	1	0	0	0	13633	1357	47	3	239	3	RPRM	2	154334986	Missense_Mutation	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10	863553	154334986	88864387	13	38271										
FIGN	55137	hgsc.bcm.edu	37	chr2	164467480	164467481	+	Frame_Shift_Ins	INS	-	-	G													0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	gtgtagccaggaacagtggtINSggggggtaggggggtgggag					rs376830180	byFrequency	TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr2:164467480_164467481insG	ENST00000333129.3	-	3	1175_1176	c.861_862insC	c.(859-864)cccaccfs	p.T288fs	FIGN_ENST00000482917.1_5'Flank|FIGN_ENST00000409634.1_Intron	NM_018086.2	NP_060556.2	Q5HY92	FIGN_HUMAN	fidgetin	288	Pro-rich.				mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)			breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(1)|prostate(2)|skin(1)	47						GGAACAGTGGTGGGGGGTAGGG	0.589																																					p.T288fs		Atlas-INDEL	.											.	FIGN	106	.	0			c.862_863insC						.																																			SO:0001589	frameshift_variant	55137	exon3			.	AK001267	CCDS2221.2	2q24	2010-04-21			ENSG00000182263	ENSG00000182263		"ATPases / AAA-type"	13285	protein-coding gene	gene with protein product		605295				11017077	Standard	XM_005246661		Approved		uc002uck.1	Q5HY92	OTTHUMG00000074059	ENST00000333129.3:c.862dupC	chr2.hg19:g.164467486_164467486dupG	ENSP00000333836:p.Thr288fs	70.0	0.0		67.0	12.0	NM_018086	B3KWM0|Q9H6M5|Q9NVZ9	Frame_Shift_Ins	INS	ENST00000333129.3	hg19	CCDS2221.2																																																																																			.	.		0.589	FIGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157220.2	NM_018086		G	164467481	-	G	164467480	7	5	262	1	0	1	1	0	0	0	0	0	5899	1696	59	0	1421	0	FIGN	2	164467480	Frame_Shift_Ins	INS	-	TCGA-FV-A2QQ-01A-11D-A22F-10	10132494	164467480	78731893	14	38272										
TTN	7273	hgsc.bcm.edu	37	chr2	179436094	179436094	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	attgtacttccatgctgtccCtggaggacagtgtgacaact	10	10	0	1			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr2:179436094C>G	ENST00000591111.1	-	276	70066	c.69842G>C	c.(69841-69843)aGg>aCg	p.R23281T	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R22354T|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R16049T|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R15982T|TTN_ENST00000589042.1_Missense_Mutation_p.R24922T|TTN_ENST00000460472.2_Missense_Mutation_p.R15857T|TTN-AS1_ENST00000456053.1_RNA			Q8WZ42	TITIN_HUMAN	titin	23281	Fibronectin type-III 69. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CATGCTGTCCCTGGAGGACAG	0.473																																					p.R24922T		Atlas-SNP	.											TTN_ENST00000359218,rectum,carcinoma,0,5	TTN	18412	.	0			c.G74765C						.						116	110	112					2																	179436094		1935	4166	6101	SO:0001583	missense	7273	exon326			CTGTCCCTGGAGG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.69842G>C	chr2.hg19:g.179436094C>G	ENSP00000465570:p.Arg23281Thr	142.0	0.0		170.0	47.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	4.684	0.127205	0.08981	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.55413	0.52;0.52;0.52;0.52	5.39	0.177	0.15054	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.33933	0.0880	N	0.20357	0.565	0.26028	N	0.98178	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.08055	0.002;0.002;0.003;0.003	T	0.25813	-1.0121	9	0.87932	D	0	.	6.3835	0.21548	0.0:0.3952:0.138:0.4668	.	15857;15982;16049;23281	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	T	22354;15857;16049;15982;15855	ENSP00000343764:R22354T;ENSP00000434586:R15857T;ENSP00000340554:R16049T;ENSP00000352154:R15982T	ENSP00000340554:R16049T	R	-	2	0	TTN	179144340	1.000000	0.71417	0.232000	0.24009	0.479000	0.33129	2.271000	0.43364	-0.130000	0.11599	-0.312000	0.09012	AGG	.	.		0.473	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179436094	C	G	179436094	3	3	262	1	0	0	0	0	1	0	0	0	16750	681	24	4	33362	4	TTN	2	179436094	Missense_Mutation	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10	14968614	179436094	63763279	15	38273										
TTN	7273	hgsc.bcm.edu	37	chr2	179636192	179636192	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	ctgtgagtggcttggagatgGccccacctttggaacaagag	14	9	0	3			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr2:179636192G>T	ENST00000591111.1	-	34	8086	c.7862C>A	c.(7861-7863)gCc>gAc	p.A2621D	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.A2621D|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.A2575D|TTN_ENST00000360870.5_Missense_Mutation_p.A2621D|TTN-AS1_ENST00000584485.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.A2575D|TTN_ENST00000589042.1_Missense_Mutation_p.A2621D|TTN_ENST00000460472.2_Missense_Mutation_p.A2575D			Q8WZ42	TITIN_HUMAN	titin	12946	Ig-like 15.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTTGGAGATGGCCCCACCTTT	0.413																																					p.A2621D		Atlas-SNP	.											TTN_ENST00000360870,colon,carcinoma,0,6	TTN	18412	.	0			c.C7862A						.						95	84	88					2																	179636192		2203	4300	6503	SO:0001583	missense	7273	exon34			GAGATGGCCCCAC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.7862C>A	chr2.hg19:g.179636192G>T	ENSP00000465570:p.Ala2621Asp	102.0	0.0		119.0	17.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	17.81	3.480766	0.63849	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.66099	-0.19;-0.03;-0.03;-0.04;0.25	6.17	6.17	0.99709	Immunoglobulin-like (1);Ribonuclease H-like (1);	.	.	.	.	T	0.77398	0.4124	L	0.52364	1.645	0.49798	D	0.999823	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.999	T	0.76564	-0.2913	9	0.87932	D	0	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	2575;2575;2575;2621;2621	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	D	2621;2575;2575;2575;2575;2621	ENSP00000343764:A2621D;ENSP00000434586:A2575D;ENSP00000340554:A2575D;ENSP00000352154:A2575D;ENSP00000354117:A2621D	ENSP00000340554:A2575D	A	-	2	0	TTN	179344437	1.000000	0.71417	0.997000	0.53966	0.926000	0.56050	8.025000	0.88777	2.941000	0.99782	0.655000	0.94253	GCC	.	.		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179636192	G	T	179636192	3	4	262	1	0	0	0	0	1	0	0	0	16750	1203	42	3	103442	3	TTN	2	179636192	Missense_Mutation	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10	200098	179636192	63563181	16	38274										
ITGA4	3676	hgsc.bcm.edu	37	chr2	182358113	182358113	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	gctatttatatttacaatggCcgtgcagatgggatctcgtc	10	8	1	1			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr2:182358113C>T	ENST00000397033.2	+	11	1645	c.1215C>T	c.(1213-1215)ggC>ggT	p.G405G		NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	405					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|chorio-allantoic fusion (GO:0060710)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|face development (GO:0060324)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|negative regulation of protein homodimerization activity (GO:0090074)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha4-beta7 complex (GO:0034669)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)|Tinzaparin(DB06822)	TTTACAATGGCCGTGCAGATG	0.363																																					p.G405G		Atlas-SNP	.											.	ITGA4	142	.	0			c.C1215T						.						111	105	107					2																	182358113		1870	4104	5974	SO:0001819	synonymous_variant	3676	exon11			CAATGGCCGTGCA		CCDS42788.1	2q31-q32	2010-03-23			ENSG00000115232	ENSG00000115232		"CD molecules", "Integrins"	6140	protein-coding gene	gene with protein product		192975		CD49D		1537388	Standard	NM_000885		Approved	CD49d	uc002unu.3	P13612	OTTHUMG00000154212	ENST00000397033.2:c.1215C>T	chr2.hg19:g.182358113C>T		106.0	0.0		115.0	28.0	NM_000885	D3DPG4|Q7Z4L6	Silent	SNP	ENST00000397033.2	hg19	CCDS42788.1																																																																																			.	.		0.363	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1			T	182358113	C	T	182358113	2	4	262	1	0	0	0	0	0	0	0	1	7887	726	26	3		3	ITGA4	2	182358113	Silent	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10	2721921	182358113	60841260	17	38275										
STAT4	6775	hgsc.bcm.edu	37	chr2	191927489	191927489	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	ttgatagcacttcacttactTcttgaaaaggttgtagatca	7	7	3	3			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr2:191927489T>C	ENST00000392320.2	-	9	1254	c.940A>G	c.(940-942)Aac>Gac	p.N314D	STAT4_ENST00000358470.4_Splice_Site_p.N314D	NM_003151.3	NP_003142.1	Q14765	STAT4_HUMAN	signal transducer and activator of transcription 4	314					cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|JAK-STAT cascade (GO:0007259)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(4)|endometrium(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.0864)|all cancers(119;0.204)			TTCACTTACTTCTTGAAAAGG	0.418																																					p.N314D		Atlas-SNP	.											.	STAT4	85	.	0			c.A940G						.						163	139	147					2																	191927489		2203	4300	6503	SO:0001630	splice_region_variant	6775	exon9			CTTACTTCTTGAA		CCDS2310.1	2q32.2-q32.3	2013-02-14			ENSG00000138378	ENSG00000138378		"SH2 domain containing"	11365	protein-coding gene	gene with protein product		600558				8007943, 8700208	Standard	NM_003151		Approved		uc002usn.2	Q14765	OTTHUMG00000132700	ENST00000392320.2:c.941+1A>G	chr2.hg19:g.191927489T>C		119.0	0.0		149.0	43.0	NM_001243835	Q96NZ6	Missense_Mutation	SNP	ENST00000392320.2	hg19	CCDS2310.1	.	.	.	.	.	.	.	.	.	.	T	18.63	3.664338	0.67700	.	.	ENSG00000138378	ENST00000358470;ENST00000392320	T;T	0.59906	0.23;0.23	5.33	5.33	0.75918	STAT transcription factor, all-alpha (2);STAT transcription factor, coiled coil (1);	0.043287	0.85682	D	0.000000	T	0.51278	0.1665	L	0.42245	1.32	0.80722	D	1	B;B;B	0.33777	0.425;0.285;0.285	B;B;B	0.31946	0.138;0.138;0.138	T	0.56025	-0.8047	10	0.62326	D	0.03	-20.6434	15.452	0.75279	0.0:0.0:0.0:1.0	.	223;314;314	Q53S87;B4DV04;Q14765	.;.;STAT4_HUMAN	D	314	ENSP00000351255:N314D;ENSP00000376134:N314D	ENSP00000351255:N314D	N	-	1	0	STAT4	191635734	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.760000	0.74939	2.234000	0.73211	0.533000	0.62120	AAC	.	.		0.418	STAT4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335586.1	NM_003151	Missense_Mutation	C	191927489	T	C	191927489	5	2	262	1	0	0	0	0	0	0	1	0	15282	1797	62	2	1370	2	STAT4	2	191927489	Splice_Site	SNP	T	TCGA-FV-A2QQ-01A-11D-A22F-10	9569376	191927489	51271884	18	38276										
TRIP12	9320	hgsc.bcm.edu	37	chr2	230724096	230724096	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	ttgtttctgagggagattcaGtatgctgaagtgcttttggt	13	4	2	3	rs532583604	byFrequency	TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr2:230724096G>A	ENST00000283943.5	-	3	471	c.293C>T	c.(292-294)aCt>aTt	p.T98I	TRIP12_ENST00000389044.4_Missense_Mutation_p.T140I|TRIP12_ENST00000409677.1_Missense_Mutation_p.T140I|TRIP12_ENST00000543084.1_Missense_Mutation_p.T140I|TRIP12_ENST00000389045.3_Intron	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	98					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		GGGAGATTCAGTATGCTGAAG	0.423																																					p.T98I		Atlas-SNP	.											.	TRIP12	207	.	0			c.C293T						.						186	180	182					2																	230724096		2203	4300	6503	SO:0001583	missense	9320	exon3			GATTCAGTATGCT	L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.293C>T	chr2.hg19:g.230724096G>A	ENSP00000283943:p.Thr98Ile	156.0	0.0		201.0	70.0	NM_004238	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Missense_Mutation	SNP	ENST00000283943.5	hg19	CCDS33391.1	.	.	.	.	.	.	.	.	.	.	G	13.97	2.394617	0.42512	.	.	ENSG00000153827	ENST00000283943;ENST00000389044;ENST00000543084;ENST00000409677;ENST00000435716;ENST00000428959;ENST00000430954;ENST00000343290	T;T	0.43688	0.94;0.94	5.85	4.96	0.65561	.	0.561680	0.20856	N	0.084450	T	0.25306	0.0615	N	0.08118	0	0.28841	N	0.89662	B;B;B	0.19583	0.037;0.0;0.01	B;B;B	0.21360	0.034;0.0;0.005	T	0.12451	-1.0547	10	0.30854	T	0.27	.	13.995	0.64390	0.0732:0.0:0.9268:0.0	.	98;140;98	D4HL82;Q14CA3;Q14669	.;.;TRIPC_HUMAN	I	98;140;140;140;98;98;140;98	ENSP00000283943:T98I;ENSP00000373696:T140I	ENSP00000283943:T98I	T	-	2	0	TRIP12	230432340	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	4.166000	0.58203	1.457000	0.47850	0.655000	0.94253	ACT	.	.		0.423	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238		A	230724096	G	A	230724096	3	1	262	1	0	0	0	0	1	0	0	0	16571	1029	36	3	5841	3	TRIP12	2	230724096	Missense_Mutation	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10	38796607	230724096	12475277	19	38277										
IQCA1	79781	hgsc.bcm.edu	37	chr2	237406078	237406078	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	catcttctgaggctctttatCgagtaaagcaccgagggctt	10	10	3	1	rs200469019	byFrequency	TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr2:237406078C>T	ENST00000409907.3	-	2	338	c.64G>A	c.(64-66)Gat>Aat	p.D22N	IQCA1_ENST00000309507.5_Missense_Mutation_p.D18N|IQCA1_ENST00000431676.2_Missense_Mutation_p.D22N	NM_024726.4	NP_079002.3	Q86XH1	IQCA1_HUMAN	IQ motif containing with AAA domain 1	22							ATP binding (GO:0005524)	p.D22Y(1)|p.D29Y(1)		cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)	26						GGCTCTTTATCGAGTAAAGCA	0.373													C|||	3	0.000599042	0.0015	0	5008	,	,		18768	0		0	False		,,,				2504	0.001				p.D29N		Atlas-SNP	.											.	IQCA1	170	.	2	Substitution - Missense(2)	lung(2)	c.G85A						.	C	ASN/ASP	1,3673		0,1,1836	48	47	47		64	2.8	1	2		47	3,8173		0,3,4085	yes	missense	IQCA1	NM_024726.3	23	0,4,5921	TT,TC,CC		0.0367,0.0272,0.0338	benign	22/823	237406078	4,11846	1837	4088	5925	SO:0001583	missense	79781	exon2			CTTTATCGAGTAA	AK026180	CCDS46549.1, CCDS59441.1, CCDS74677.1	2q37.3	2014-07-18	2008-07-02	2008-07-02	ENSG00000132321	ENSG00000132321		"ATPases / AAA-type"	26195	protein-coding gene	gene with protein product	"dynein regulatory complex subunit 11"		"IQ motif containing with AAA domain"	IQCA		23427265	Standard	NM_024726		Approved	FLJ22527, DRC11	uc002vwb.3	Q86XH1	OTTHUMG00000153058	ENST00000409907.3:c.64G>A	chr2.hg19:g.237406078C>T	ENSP00000387347:p.Asp22Asn	125.0	0.0		157.0	36.0	NM_001270585	B4DFH9|E7EWQ0|Q4G164|Q53R37|Q53RV3|Q96NS7|Q9H680	Missense_Mutation	SNP	ENST00000409907.3	hg19	CCDS46549.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.00|11.00	1.511138|1.511138	0.27036|0.27036	2.72E-4|2.72E-4	3.67E-4|3.67E-4	ENSG00000132321|ENSG00000132321	ENST00000409907;ENST00000457693;ENST00000309507;ENST00000431676;ENST00000412437|ENST00000418802	D;D;D|.	0.94092|.	-3.22;-3.2;-3.35|.	5.52|5.52	2.75|2.75	0.32379|0.32379	.|.	0.514224|.	0.19401|.	N|.	0.115166|.	T|T	0.45256|0.45256	0.1333|0.1333	L|L	0.61387|0.61387	1.9|1.9	0.09310|0.09310	N|N	0.999999|0.999999	P;P;P|.	0.46656|.	0.882;0.8;0.882|.	B;B;B|.	0.35470|.	0.071;0.155;0.203|.	T|T	0.31110|0.31110	-0.9955|-0.9955	10|5	0.18276|.	T|.	0.48|.	.|.	7.8701|7.8701	0.29561|0.29561	0.0:0.4337:0.4111:0.1552|0.0:0.4337:0.4111:0.1552	.|.	22;29;22|.	E7EWQ0;E9PH78;Q86XH1|.	.;.;IQCA1_HUMAN|.	N|Q	22;29;18;22;18|40	ENSP00000387347:D22N;ENSP00000311951:D18N;ENSP00000407213:D22N|.	ENSP00000254653:D22N|.	D|R	-|-	1|2	0|0	IQCA1|IQCA1	237070817|237070817	0.000000|0.000000	0.05858|0.05858	0.973000|0.973000	0.42090|0.42090	0.597000|0.597000	0.36814|0.36814	0.995000|0.995000	0.29706|0.29706	0.293000|0.293000	0.22520|0.22520	0.655000|0.655000	0.94253|0.94253	GAT|CGA	.	.		0.373	IQCA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000329266.1	NM_024726		T	237406078	C	T	237406078	3	4	262	1	0	0	0	0	1	0	0	0	7811	884	31	1	2476	1	IQCA1	2	237406078	Missense_Mutation	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10	6681982	237406078	5793295	20	38278										
CHL1	10752	hgsc.bcm.edu	37	chr3	361529	361529	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	tcctgttaaaattctcaaaaGcaattgaaataccatcttca	3	9	3	1			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr3:361529G>T	ENST00000256509.2	+	3	712	c.70G>T	c.(70-72)Gca>Tca	p.A24S	CHL1_ENST00000397491.2_Missense_Mutation_p.A24S	NM_001253387.1|NM_001253388.1|NM_006614.3	NP_001240316.1|NP_001240317.1|NP_006605.2	Q96FC9	DDX11_HUMAN	cell adhesion molecule L1-like	0	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			NS(1)|central_nervous_system(5)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|lung(31)|ovary(1)|prostate(4)|skin(10)|stomach(1)	93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		ATTCTCAAAAGCAATTGAAAT	0.338																																					p.A24S		Atlas-SNP	.											CHL1,NS,carcinoma,0,1	CHL1	242	.	0			c.G70T						.						56	58	58					3																	361529		2202	4300	6502	SO:0001583	missense	10752	exon1			TCAAAAGCAATTG	AF002246	CCDS2556.1, CCDS58812.1, CCDS74887.1	3p26	2013-05-01	2013-05-01		ENSG00000134121	ENSG00000134121		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	1939	protein-coding gene	gene with protein product	"neural cell adhesion molecule", "close homolog of L1"	607416	"cell adhesion molecule with homology to L1CAM (close homologue of L1)", "cell adhesion molecule with homology to L1CAM (close homolog of L1)"			9799093	Standard	NM_006614		Approved	CALL, L1CAM2, FLJ44930, MGC132578	uc003bot.3	O00533	OTTHUMG00000090601	ENST00000256509.2:c.70G>T	chr3.hg19:g.361529G>T	ENSP00000256509:p.Ala24Ser	26.0	0.0		46.0	15.0	NM_001253388	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000256509.2	hg19	CCDS2556.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.247105	0.80024	.	.	ENSG00000134121	ENST00000256509;ENST00000397491;ENST00000427688;ENST00000421198;ENST00000435603;ENST00000449294	T;T;T;T;T;T	0.68181	0.16;0.18;0.63;0.12;0.11;-0.31	4.91	4.91	0.64330	.	0.070339	0.56097	D	0.000031	T	0.53948	0.1828	N	0.08118	0	0.35902	D	0.83045	B;P;P	0.44006	0.014;0.525;0.824	B;B;P	0.45232	0.085;0.425;0.474	T	0.69723	-0.5068	10	0.87932	D	0	.	16.4499	0.83976	0.0:0.0:1.0:0.0	.	24;24;24	B3KX75;O00533;O00533-2	.;CHL1_HUMAN;.	S	24	ENSP00000256509:A24S;ENSP00000380628:A24S;ENSP00000403311:A24S;ENSP00000413628:A24S;ENSP00000397445:A24S;ENSP00000390440:A24S	ENSP00000256509:A24S	A	+	1	0	CHL1	336529	0.983000	0.35010	0.119000	0.21687	0.622000	0.37654	5.364000	0.66110	2.535000	0.85469	0.655000	0.94253	GCA	.	.		0.338	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614		T	361529	G	T	361529	3	4	262	1	0	0	0	0	1	0	0	0	3351	971	34	3	72	3	CHL1	3	361529	Missense_Mutation	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10		361529	197660901	21	38279										
GOLGA4	2803	hgsc.bcm.edu	37	chr3	37367438	37367438	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	gttatctgaaaacatcaatgCtgtcacattgatgaaagaag	8	6	3	4			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr3:37367438C>A	ENST00000361924.2	+	14	4435	c.4061C>A	c.(4060-4062)gCt>gAt	p.A1354D	GOLGA4_ENST00000356847.4_Missense_Mutation_p.A1376D|GOLGA4_ENST00000444882.1_Intron	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	1354	Glu-rich.				Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						AACATCAATGCTGTCACATTG	0.363																																					p.A1376D		Atlas-SNP	.											.	GOLGA4	173	.	0			c.C4127A						.						31	31	31					3																	37367438		2203	4298	6501	SO:0001583	missense	2803	exon15			TCAATGCTGTCAC	U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"golgin 245"	602509	"golgi autoantigen, golgin subfamily a, 4"			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.4061C>A	chr3.hg19:g.37367438C>A	ENSP00000354486:p.Ala1354Asp	106.0	0.0		125.0	44.0	NM_001172713	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Missense_Mutation	SNP	ENST00000361924.2	hg19	CCDS2666.1	.	.	.	.	.	.	.	.	.	.	C	15.14	2.745203	0.49151	.	.	ENSG00000144674	ENST00000361924;ENST00000356847;ENST00000437131	T;T;T	0.31510	1.5;1.49;1.51	5.53	2.81	0.32909	.	0.451006	0.16518	N	0.210933	T	0.42200	0.1192	M	0.64997	1.995	0.33935	D	0.642502	D;D;D;D	0.63046	0.988;0.978;0.978;0.992	P;P;P;P	0.61201	0.885;0.628;0.628;0.69	T	0.49360	-0.8948	10	0.12766	T	0.61	.	8.6708	0.34149	0.0:0.6477:0.0:0.3523	.	1354;1354;1376;1354	Q13439-3;Q13439-4;F8W8Q7;Q13439	.;.;.;GOGA4_HUMAN	D	1354;1376;1225	ENSP00000354486:A1354D;ENSP00000349305:A1376D;ENSP00000405842:A1225D	ENSP00000349305:A1376D	A	+	2	0	GOLGA4	37342442	0.959000	0.32827	0.980000	0.43619	0.972000	0.66771	0.862000	0.27899	0.315000	0.23110	-0.251000	0.11542	GCT	.	.		0.363	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078		A	37367438	C	A	37367438	3	1	262	1	0	0	0	0	1	0	0	0	6563	797	28	3	4185	3	GOLGA4	3	37367438	Missense_Mutation	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10	37005909	37367438	160654992	22	38280										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41274911	41274911	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	tgtctttggactctcaggaaTctttcagatgctgcaactaa	8	9	4	1			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr3:41274911T>G	ENST00000349496.5	+	8	1441	c.1161T>G	c.(1159-1161)aaT>aaG	p.N387K	CTNNB1_ENST00000396183.3_Missense_Mutation_p.N387K|CTNNB1_ENST00000405570.1_Missense_Mutation_p.N387K|CTNNB1_ENST00000396185.3_Missense_Mutation_p.N387K|CTNNB1_ENST00000453024.1_Missense_Mutation_p.N380K	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	387					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.N387K(4)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CTCTCAGGAATCTTTCAGATG	0.393		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.N387K	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,carcinoma,0,5	CTNNB1	4904	.	4	Substitution - Missense(4)	large_intestine(1)|prostate(1)|liver(1)|kidney(1)	c.T1161G						.						102	93	96					3																	41274911		2203	4300	6503	SO:0001583	missense	1499	exon8	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	CAGGAATCTTTCA	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.1161T>G	chr3.hg19:g.41274911T>G	ENSP00000344456:p.Asn387Lys	112.0	0.0		130.0	45.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	18.91	3.723022	0.68959	.	.	ENSG00000168036	ENST00000405570;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185	D;D;D;D;D	0.83992	-1.79;-1.79;-1.79;-1.79;-1.79	5.72	1.33	0.21861	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.90263	0.6955	M	0.89478	3.035	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	D	0.88091	0.2813	10	0.54805	T	0.06	-10.1444	8.463	0.32938	0.0:0.3714:0.0:0.6286	.	315;387	B4DSW9;P35222	.;CTNB1_HUMAN	K	387;387;387;380;387	ENSP00000385604:N387K;ENSP00000379486:N387K;ENSP00000344456:N387K;ENSP00000411226:N380K;ENSP00000379488:N387K	ENSP00000344456:N387K	N	+	3	2	CTNNB1	41249915	0.995000	0.38212	0.998000	0.56505	0.998000	0.95712	0.358000	0.20216	0.227000	0.20999	0.533000	0.62120	AAT	.	.		0.393	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41274911	T	G	41274911	3	3	262	1	0	0	0	0	1	0	0	0	4018	1432	50	5	1187	5	CTNNB1	3	41274911	Missense_Mutation	SNP	T	TCGA-FV-A2QQ-01A-11D-A22F-10	3907473	41274911	156747519	23	38281										
CCDC71	64925	hgsc.bcm.edu	37	chr3	49200370	49200370	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	acctttatggcacggaacttCagcagctttgctgttccagg	10	11	1	0			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr3:49200370C>A	ENST00000321895.6	-	2	1378	c.1272G>T	c.(1270-1272)ctG>ctT	p.L424L		NM_022903.3	NP_075054.3	Q8IV32	CCD71_HUMAN	coiled-coil domain containing 71	424										endometrium(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)	10				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00217)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		CACGGAACTTCAGCAGCTTTG	0.577																																					p.L424L		Atlas-SNP	.											.	CCDC71	33	.	0			c.G1272T						.						95	89	91					3																	49200370		2203	4300	6503	SO:0001819	synonymous_variant	64925	exon2			GAACTTCAGCAGC	AK022862	CCDS2790.1	3p21.31	2014-02-12			ENSG00000177352	ENSG00000177352			25760	protein-coding gene	gene with protein product						12477932	Standard	NM_022903		Approved	FLJ12800	uc003cwg.4	Q8IV32	OTTHUMG00000156815	ENST00000321895.6:c.1272G>T	chr3.hg19:g.49200370C>A		130.0	0.0		139.0	23.0	NM_022903	Q6IPE2|Q9H8H4|Q9H9F1	Silent	SNP	ENST00000321895.6	hg19	CCDS2790.1																																																																																			.	.		0.577	CCDC71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345980.1	NM_022903		A	49200370	C	A	49200370	2	1	262	1	0	0	0	0	0	0	0	1	2846	813	29	3		3	CCDC71	3	49200370	Silent	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10	7925459	49200370	148822060	24	38282										
CCDC66	285331	hgsc.bcm.edu	37	chr3	56597778	56597778	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	ctgggcacattctaaaatcaAcacaagatacttgtattggg	8	8	2	1			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr3:56597778A>G	ENST00000394672.3	+	4	239	c.169A>G	c.(169-171)Aca>Gca	p.T57A	CCDC66_ENST00000442522.2_3'UTR|CCDC66_ENST00000436465.2_Missense_Mutation_p.T57A|CCDC66_ENST00000326595.7_Missense_Mutation_p.T23A|CCDC66_ENST00000538560.1_Missense_Mutation_p.T57A	NM_001012506.4|NM_001141947.1	NP_001012524.4|NP_001135419.1	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66	57					post-embryonic retina morphogenesis in camera-type eye (GO:0060060)|retinal rod cell development (GO:0046548)					breast(1)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(2)|urinary_tract(1)	12				KIRC - Kidney renal clear cell carcinoma(284;0.0478)|Kidney(284;0.0597)|OV - Ovarian serous cystadenocarcinoma(275;0.233)		TCTAAAATCAACACAAGATAC	0.343																																					p.T57A		Atlas-SNP	.											.	CCDC66	145	.	0			c.A169G						.						87	73	77					3																	56597778		692	1591	2283	SO:0001583	missense	285331	exon4			AAATCAACACAAG	AL832692	CCDS33770.2, CCDS46852.1	3p14.3	2006-03-27			ENSG00000180376	ENSG00000180376			27709	protein-coding gene	gene with protein product						14702039	Standard	NR_024460		Approved	DKFZp686C0433	uc003dhz.3	A2RUB6	OTTHUMG00000155748	ENST00000394672.3:c.169A>G	chr3.hg19:g.56597778A>G	ENSP00000378167:p.Thr57Ala	119.0	0.0		104.0	14.0	NM_001141947	B3KWL8|Q4VC34|Q8N949	Missense_Mutation	SNP	ENST00000394672.3	hg19	CCDS46852.1	.	.	.	.	.	.	.	.	.	.	A	15.74	2.921548	0.52653	.	.	ENSG00000180376	ENST00000422222;ENST00000394672;ENST00000326595;ENST00000436465;ENST00000538560	D;D;D;D;D	0.99660	-6.32;-6.32;-6.32;-6.32;-6.32	5.53	5.53	0.82687	.	.	.	.	.	D	0.99354	0.9773	M	0.62723	1.935	0.28916	N	0.892418	D;D	0.65815	0.987;0.995	P;D	0.67548	0.907;0.952	D	0.98327	1.0531	9	0.59425	D	0.04	.	9.5103	0.39074	0.9201:0.0:0.0799:0.0	.	57;57	A2RUB6;A2RUB6-2	CCD66_HUMAN;.	A	57;57;23;57;57	ENSP00000401451:T57A;ENSP00000378167:T57A;ENSP00000326050:T23A;ENSP00000404320:T57A;ENSP00000444919:T57A	ENSP00000326050:T23A	T	+	1	0	CCDC66	56572818	1.000000	0.71417	1.000000	0.80357	0.664000	0.39144	2.439000	0.44846	2.097000	0.63578	0.496000	0.49642	ACA	.	.		0.343	CCDC66-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341473.1	NM_001012506		G	56597778	A	G	56597778	3	3	262	1	0	0	0	0	1	0	0	0	2840	43	2	2	183	2	CCDC66	3	56597778	Missense_Mutation	SNP	A	TCGA-FV-A2QQ-01A-11D-A22F-10	7397408	56597778	141424652	25	38283										
SPATA18	132671	hgsc.bcm.edu	37	chr4	52948586	52948586	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	tacgactcggatttcactgcTcccttagtcctctatcacgt	6	14	3	0			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr4:52948586T>C	ENST00000295213.4	+	10	1763	c.1389T>C	c.(1387-1389)gcT>gcC	p.A463A	SPATA18_ENST00000419395.2_Silent_p.A431A	NM_145263.2	NP_660306.1	Q8TC71	MIEAP_HUMAN	spermatogenesis associated 18	463					cellular response to DNA damage stimulus (GO:0006974)|mitochondrial protein catabolic process (GO:0035694)|mitochondrion degradation by induced vacuole formation (GO:0035695)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial outer membrane (GO:0005741)				breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(4;1.77e-13)|LUSC - Lung squamous cell carcinoma(32;0.00204)			ATTTCACTGCTCCCTTAGTCC	0.458																																					p.A463A		Atlas-SNP	.											.	SPATA18	222	.	0			c.T1389C						.						178	160	166					4																	52948586		2203	4300	6503	SO:0001819	synonymous_variant	132671	exon10			CACTGCTCCCTTA	BC025396	CCDS3489.1, CCDS75124.1	4q11	2012-01-23	2012-01-23		ENSG00000163071	ENSG00000163071			29579	protein-coding gene	gene with protein product		612814	"spermatogenesis associated 18 homolog (rat)"			21300779	Standard	XR_245253		Approved	FLJ32906	uc003gzl.3	Q8TC71	OTTHUMG00000128698	ENST00000295213.4:c.1389T>C	chr4.hg19:g.52948586T>C		76.0	0.0		63.0	21.0	NM_145263	B4E2R0|E5RLK1|Q8IY48|Q8N7D7	Silent	SNP	ENST00000295213.4	hg19	CCDS3489.1																																																																																			.	.		0.458	SPATA18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250597.2	NM_145263		C	52948586	T	C	52948586	2	2	262	1	0	0	0	0	0	0	0	1	15018	1538	54	2		2	SPATA18	4	52948586	Silent	SNP	T	TCGA-FV-A2QQ-01A-11D-A22F-10		52948586	138205690	26	38284										
ALB	213	hgsc.bcm.edu	37	chr4	74270860	74270860	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	tgaggttgctcatcggtttaAagatttgggagaagaaaatt	12	3	1	4			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr4:74270860A>G	ENST00000295897.4	+	2	196	c.107A>G	c.(106-108)aAa>aGa	p.K36R	ALB_ENST00000509063.1_Missense_Mutation_p.K36R|ALB_ENST00000415165.2_Missense_Mutation_p.K36R|ALB_ENST00000503124.1_Intron|ALB_ENST00000401494.3_Missense_Mutation_p.K36R	NM_000477.5	NP_000468.1	Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CATCGGTTTAAAGATTTGGGA	0.279																																					p.K36R		Atlas-SNP	.											.	ALB	132	.	0			c.A107G						.						74	78	77					4																	74270860		2203	4299	6502	SO:0001583	missense	213	exon2			GGTTTAAAGATTT	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000295897.4:c.107A>G	chr4.hg19:g.74270860A>G	ENSP00000295897:p.Lys36Arg	201.0	0.0		223.0	48.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000295897.4	hg19	CCDS3555.1	.	.	.	.	.	.	.	.	.	.	A	8.865	0.947970	0.18356	.	.	ENSG00000163631	ENST00000441319;ENST00000295897;ENST00000415165;ENST00000329326;ENST00000509063;ENST00000401494;ENST00000430202	T;T;T;T;T	0.74106	-0.81;-0.81;-0.81;-0.81;-0.74	5.65	1.74	0.24563	Serum albumin-like (1);Serum albumin, N-terminal (3);	0.872881	0.10228	N	0.700042	T	0.64843	0.2635	L	0.41824	1.3	0.09310	N	1	P;B;B;B	0.48911	0.917;0.2;0.003;0.003	B;B;B;B	0.42319	0.383;0.224;0.007;0.013	T	0.54125	-0.8340	10	0.54805	T	0.06	-1.7265	7.5821	0.27972	0.6673:0.0:0.3327:0.0	.	36;36;36;36	B7WNR0;C9JKR2;A6NBZ8;P02768	.;.;.;ALBU_HUMAN	R	38;36;36;36;36;36;45	ENSP00000392541:K38R;ENSP00000295897:K36R;ENSP00000401820:K36R;ENSP00000422784:K36R;ENSP00000384695:K36R	ENSP00000295897:K36R	K	+	2	0	ALB	74489724	0.003000	0.15002	0.008000	0.14137	0.622000	0.37654	0.161000	0.16481	0.473000	0.27368	0.533000	0.62120	AAA	.	.		0.279	ALB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252173.3	NM_000477		G	74270860	A	G	74270860	3	3	262	1	0	0	0	0	1	0	0	0	486	14	1	2	113	2	ALB	4	74270860	Missense_Mutation	SNP	A	TCGA-FV-A2QQ-01A-11D-A22F-10	21322274	74270860	116883416	27	38285										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79396668	79396668	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	acctgaaccaatatgccatcGtcctgtgtcgcaccgagcaa	8	14	0	1	rs373757948		TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr4:79396668G>T	ENST00000264895.6	+	54	8199	c.7759G>T	c.(7759-7761)Gtc>Ttc	p.V2587F		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	2587	Calx-beta 1.				cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						ATATGCCATCGTCCTGTGTCG	0.567																																					p.V2587F		Atlas-SNP	.											.	FRAS1	779	.	0			c.G7759T						.						116	127	123					4																	79396668		2109	4241	6350	SO:0001583	missense	80144	exon54			GCCATCGTCCTGT	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.7759G>T	chr4.hg19:g.79396668G>T	ENSP00000264895:p.Val2587Phe	100.0	0.0		83.0	30.0	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000264895.6	hg19	CCDS54771.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	33|33	5.257995|5.257995	0.95368|0.95368	.|.	.|.	ENSG00000138759|ENSG00000138759	ENST00000512123|ENST00000264895	.|T	.|0.57436	.|0.4	5.44|5.44	5.44|5.44	0.79542|0.79542	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.80352|0.80352	0.4607|0.4607	M|M	0.92507|0.92507	3.315|3.315	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.97110	.|1.0	D|D	0.85097|0.85097	0.0955|0.0955	5|10	.|0.87932	.|D	.|0	.|.	19.2863|19.2863	0.94072|0.94072	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|2587	.|E9PHH6	.|.	L|F	815|2587	.|ENSP00000264895:V2587F	.|ENSP00000264895:V2587F	R|V	+|+	2|1	0|0	FRAS1|FRAS1	79615692|79615692	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.980000|0.980000	0.70556|0.70556	9.727000|9.727000	0.98787|0.98787	2.558000|2.558000	0.86282|0.86282	0.591000|0.591000	0.81541|0.81541	CGT|GTC	.	.		0.567	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	79396668	G	T	79396668	3	4	262	1	0	0	0	0	1	0	0	0	6050	1145	40	1	8048	1	FRAS1	4	79396668	Missense_Mutation	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10	5125808	79396668	111757608	28	38286										
DSPP	1834	hgsc.bcm.edu	37	chr4	88536020	88536020	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	gcaacagcagcgatagcagtGacagcagcaacagcagtgac	12	11	0	2	rs201263760		TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr4:88536020G>A	ENST00000282478.7	+	4	2239	c.2206G>A	c.(2206-2208)Gac>Aac	p.D736N	DSPP_ENST00000399271.1_Missense_Mutation_p.D736N|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	736	Asp/Ser-rich.			Missing (in Ref. 1; AAF42472). {ECO:0000305}.	biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			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)		cgatagcagtgacagcagcaa	0.498																																					p.D736N		Atlas-SNP	.											.	DSPP	174	.	0			c.G2206A						.						63	72	69					4																	88536020		1656	2933	4589	SO:0001583	missense	1834	exon5			AGCAGTGACAGCA	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2206G>A	chr4.hg19:g.88536020G>A	ENSP00000282478:p.Asp736Asn	111.0	0.0		147.0	17.0	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	hg19	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	g	9.288	1.049894	0.19827	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.89485	-2.52;-2.52	1.33	1.33	0.21861	.	.	.	.	.	D	0.86372	0.5917	N	0.20986	0.625	0.22081	N	0.999371	D	0.76494	0.999	D	0.74023	0.982	T	0.75393	-0.3333	9	0.11485	T	0.65	.	6.0839	0.19956	0.0:0.0:1.0:0.0	.	736	Q9NZW4	DSPP_HUMAN	N	736	ENSP00000382213:D736N;ENSP00000282478:D736N	ENSP00000282478:D736N	D	+	1	0	DSPP	88755044	0.000000	0.05858	0.660000	0.29694	0.008000	0.06430	-0.322000	0.08007	1.047000	0.40274	0.165000	0.16767	GAC	.	.		0.498	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		A	88536020	G	A	88536020	3	1	262	1	0	0	0	0	1	0	0	0	4784	1290	45	3	2220	3	DSPP	4	88536020	Missense_Mutation	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10	9139352	88536020	102618256	29	38287										
FAM13A	10144	hgsc.bcm.edu	37	chr4	89772242	89772242	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	aagcaggcttttctataactTagccgcaagctgagctgagg	11	9	1	2			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr4:89772242T>C	ENST00000264344.5	-	7	1143	c.936A>G	c.(934-936)ctA>ctG	p.L312L	FAM13A_ENST00000511976.1_Intron|FAM13A_ENST00000502459.1_5'UTR	NM_014883.3	NP_055698.2	O94988	FA13A_HUMAN	family with sequence similarity 13, member A	312					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	55						TTCTATAACTTAGCCGCAAGC	0.463																																					p.L312L		Atlas-SNP	.											.	FAM13A	181	.	0			c.A936G						.						147	149	148					4																	89772242		2203	4300	6503	SO:0001819	synonymous_variant	10144	exon7			ATAACTTAGCCGC	AB020721	CCDS34029.1, CCDS43251.1, CCDS58911.1, CCDS58912.1, CCDS58913.1	4q22.1	2011-09-07	2009-01-20	2009-01-20	ENSG00000138640	ENSG00000138640		"Rho GTPase activating proteins"	19367	protein-coding gene	gene with protein product		613299	"family with sequence similarity 13, member A1"	FAM13A1			Standard	NM_014883		Approved	KIAA0914, ARHGAP48	uc003hse.2	O94988	OTTHUMG00000161006	ENST00000264344.5:c.936A>G	chr4.hg19:g.89772242T>C		57.0	0.0		62.0	13.0	NM_014883	B4DLC1|Q24JP0|Q5PR21|Q8NBA3	Silent	SNP	ENST00000264344.5	hg19	CCDS34029.1																																																																																			.	.		0.463	FAM13A-022	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363371.1			C	89772242	T	C	89772242	2	2	262	1	0	0	0	0	0	0	0	1	5457	1741	61	2		2	FAM13A	4	89772242	Silent	SNP	T	TCGA-FV-A2QQ-01A-11D-A22F-10	1236222	89772242	101382034	30	38288										
UNC5C	8633	hgsc.bcm.edu	37	chr4	96141185	96141185	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	tgaaagcccccattgagtgcCgaagagtcaataatatctga	9	9	2	4	rs555624855		TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr4:96141185C>A	ENST00000453304.1	-	8	1599	c.1251G>T	c.(1249-1251)tcG>tcT	p.S417S	UNC5C_ENST00000506749.1_Silent_p.S436S	NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	417					anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|brain development (GO:0007420)|positive regulation of apoptotic process (GO:0043065)|regulation of cell migration (GO:0030334)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(14)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	55		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)		CATTGAGTGCCGAAGAGTCAA	0.453																																					p.S417S		Atlas-SNP	.											.	UNC5C	141	.	0			c.G1251T						.						140	127	132					4																	96141185		2203	4300	6503	SO:0001819	synonymous_variant	8633	exon8			GAGTGCCGAAGAG	AF055634	CCDS3643.1	4q21-q23	2013-01-11	2001-11-28		ENSG00000182168	ENSG00000182168		"Immunoglobulin superfamily / I-set domain containing"	12569	protein-coding gene	gene with protein product		603610	"unc5 (C.elegans homolog) c"			9126742, 9782087	Standard	NM_003728		Approved		uc003hto.3	O95185	OTTHUMG00000130989	ENST00000453304.1:c.1251G>T	chr4.hg19:g.96141185C>A		189.0	0.0		196.0	73.0	NM_003728	Q8IUT0	Silent	SNP	ENST00000453304.1	hg19	CCDS3643.1																																																																																			.	.		0.453	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728		A	96141185	C	A	96141185	2	1	262	1	0	0	0	0	0	0	0	1	17008	639	23	1		1	UNC5C	4	96141185	Silent	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10	6368943	96141185	95013091	31	38289										
ZNF827	152485	hgsc.bcm.edu	37	chr4	146696966	146696966	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	ataataaggatgtttcttccCatcactgccttcagaggtga	8	9	3	2			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr4:146696966C>T	ENST00000508784.1	-	10	2895	c.2668G>A	c.(2668-2670)Ggg>Agg	p.G890R	ZNF827_ENST00000379448.4_Missense_Mutation_p.G890R|ZNF827_ENST00000513320.1_Missense_Mutation_p.G540R			Q17R98	ZN827_HUMAN	zinc finger protein 827	890					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	all_hematologic(180;0.151)					TGTTTCTTCCCATCACTGCCT	0.502																																					p.G890R		Atlas-SNP	.											.	ZNF827	102	.	0			c.G2668A						.						146	131	136					4																	146696966		2203	4300	6503	SO:0001583	missense	152485	exon10			TCTTCCCATCACT	AK091130	CCDS34072.1	4q31.22	2013-01-08			ENSG00000151612	ENSG00000151612		"Zinc fingers, C2H2-type"	27193	protein-coding gene	gene with protein product						12477932	Standard	NM_178835		Approved		uc003ikm.3	Q17R98	OTTHUMG00000161362	ENST00000508784.1:c.2668G>A	chr4.hg19:g.146696966C>T	ENSP00000421863:p.Gly890Arg	59.0	0.0		59.0	21.0	NM_178835	B7ZL52|Q7Z4S7|Q8N279	Missense_Mutation	SNP	ENST00000508784.1	hg19		.	.	.	.	.	.	.	.	.	.	C	13.33	2.205115	0.39003	.	.	ENSG00000151612	ENST00000508784;ENST00000513320;ENST00000379448;ENST00000281318;ENST00000440280	T;T;T	0.06933	3.34;3.24;3.37	5.82	5.82	0.92795	.	0.169058	0.56097	D	0.000025	T	0.03915	0.0110	N	0.03608	-0.345	0.41632	D	0.989023	B;B;B	0.20052	0.017;0.024;0.041	B;B;B	0.16722	0.011;0.007;0.016	T	0.47849	-0.9085	10	0.10111	T	0.7	-21.658	13.3128	0.60390	0.0:0.9281:0.0:0.0719	.	540;890;890	G5E9Z1;Q17R98;Q17R98-2	.;ZN827_HUMAN;.	R	890;540;890;889;540	ENSP00000421863:G890R;ENSP00000423130:G540R;ENSP00000368761:G890R	ENSP00000281318:G889R	G	-	1	0	ZNF827	146916416	1.000000	0.71417	0.973000	0.42090	0.907000	0.53573	4.858000	0.62947	2.752000	0.94435	0.655000	0.94253	GGG	.	.		0.502	ZNF827-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000364654.2	NM_178835		T	146696966	C	T	146696966	3	4	262	1	0	0	0	0	1	0	0	0	18195	594	21	3	581	3	ZNF827	4	146696966	Missense_Mutation	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10	50555781	146696966	44457310	32	38290										
LRBA	987	hgsc.bcm.edu	37	chr4	151770044	151770044	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	caatttcagtaaagccaagaGaacttgcaaatataagcaca	6	8	1	1			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr4:151770044G>A	ENST00000357115.3	-	26	4508	c.4265C>T	c.(4264-4266)tCt>tTt	p.S1422F	LRBA_ENST00000510413.1_Missense_Mutation_p.S1422F|LRBA_ENST00000535741.1_Missense_Mutation_p.S1422F|LRBA_ENST00000507224.1_Missense_Mutation_p.S1422F	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	1422						cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					AAAGCCAAGAGAACTTGCAAA	0.413																																					p.S1422F		Atlas-SNP	.											.	LRBA	253	.	0			c.C4265T						.						107	110	109					4																	151770044		2203	4300	6503	SO:0001583	missense	987	exon26			CCAAGAGAACTTG	AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"WD repeat domain containing"	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.4265C>T	chr4.hg19:g.151770044G>A	ENSP00000349629:p.Ser1422Phe	164.0	0.0		192.0	77.0	NM_006726	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Missense_Mutation	SNP	ENST00000357115.3	hg19	CCDS3773.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.5|25.5	4.649316|4.649316	0.87958|0.87958	.|.	.|.	ENSG00000198589|ENSG00000198589	ENST00000509835|ENST00000535741;ENST00000510413;ENST00000357115;ENST00000507224	.|T;T;T;T	.|0.60797	.|0.59;0.74;0.59;0.16	5.9|5.9	5.9|5.9	0.94986|0.94986	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.77791|0.77791	0.4183|0.4183	M|M	0.80183|0.80183	2.485|2.485	0.80722|0.80722	D|D	1|1	.|D;D	.|0.67145	.|0.994;0.996	.|P;D	.|0.63877	.|0.832;0.919	T|T	0.79429|0.79429	-0.1807|-0.1807	5|10	.|0.87932	.|D	.|0	.|.	20.2768|20.2768	0.98488|0.98488	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1422;1422	.|P50851;P50851-2	.|LRBA_HUMAN;.	F|F	75|1422	.|ENSP00000446299:S1422F;ENSP00000421552:S1422F;ENSP00000349629:S1422F;ENSP00000422180:S1422F	.|ENSP00000349629:S1422F	L|S	-|-	1|2	0|0	LRBA|LRBA	151989494|151989494	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.902000|7.902000	0.87389|0.87389	2.808000|2.808000	0.96608|0.96608	0.650000|0.650000	0.86243|0.86243	CTC|TCT	.	.		0.413	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			A	151770044	G	A	151770044	3	1	262	1	0	0	0	0	1	0	0	0	8940	942	33	3	4458	3	LRBA	4	151770044	Missense_Mutation	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10	5073078	151770044	39384232	33	38291										
TAS2R1	50834	hgsc.bcm.edu	37	chr5	9629277	9629277	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	cttactgtggaggaggaactTttttgcattttgtttcaatt	9	5	1	0			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr5:9629277T>A	ENST00000382492.2	-	1	1186	c.868A>T	c.(868-870)Aag>Tag	p.K290*	CTD-2001E22.1_ENST00000504182.2_RNA	NM_019599.2	NP_062545.1	Q9NYW7	TA2R1_HUMAN	taste receptor, type 2, member 1	290					chemosensory behavior (GO:0007635)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(19)|ovary(3)|prostate(1)|skin(1)|stomach(1)	39						AGGAGGAACTTTTTTGCATTT	0.398																																					p.K290X		Atlas-SNP	.											.	TAS2R1	84	.	0			c.A868T						.						94	96	95					5																	9629277		2203	4300	6503	SO:0001587	stop_gained	50834	exon1			GGAACTTTTTTGC	AF227129	CCDS3876.1	5p15	2012-08-22			ENSG00000169777	ENSG00000169777		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14909	protein-coding gene	gene with protein product		604796				10761934, 10766242	Standard	NM_019599		Approved	T2R1, TRB7	uc003jem.1	Q9NYW7	OTTHUMG00000090500	ENST00000382492.2:c.868A>T	chr5.hg19:g.9629277T>A	ENSP00000371932:p.Lys290*	74.0	0.0		107.0	30.0	NM_019599	Q646G8	Nonsense_Mutation	SNP	ENST00000382492.2	hg19	CCDS3876.1	.	.	.	.	.	.	.	.	.	.	T	29.3	4.998377	0.93227	.	.	ENSG00000169777	ENST00000382492	.	.	.	5.55	-1.09	0.09904	.	1.630680	0.03126	N	0.164526	.	.	.	.	.	.	0.29641	N	0.844734	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.7256	0.18010	0.0:0.2975:0.1337:0.5688	.	.	.	.	X	290	.	.	K	-	1	0	TAS2R1	9682277	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	0.451000	0.21779	-0.288000	0.09051	-0.261000	0.10672	AAG	.	.		0.398	TAS2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206988.2			A	9629277	T	A	9629277	4	1	262	1	0	0	0	0	0	1	0	0	15580	1850	64	4	35	4	TAS2R1	5	9629277	Nonsense_Mutation	SNP	T	TCGA-FV-A2QQ-01A-11D-A22F-10		9629277	171285983	34	38292										
CDH9	1007	hgsc.bcm.edu	37	chr5	26881520	26881521	+	Frame_Shift_Ins	INS	-	-	A													0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	ggcacagtcctccttatctgINSaaaaatagtttcaggcatta							TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr5:26881520_26881521insA	ENST00000231021.4	-	12	2266_2267	c.2094_2095insT	c.(2092-2097)tttcagfs	p.Q699fs		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	699					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						CTCCTTATCTGAAAAATAGTTT	0.411																																					p.Q699fs	Melanoma(8;187 585 15745 40864 52829)	Atlas-INDEL	.											.	CDH9	305	.	0			c.2095_2096insT						.																																			SO:0001589	frameshift_variant	1007	exon12			.	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"Cadherins / Major cadherins"	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.2095dupT	chr5.hg19:g.26881525_26881525dupA	ENSP00000231021:p.Gln699fs	149.0	0.0		166.0	46.0	NM_016279	Q3B7I5	Frame_Shift_Ins	INS	ENST00000231021.4	hg19	CCDS3893.1																																																																																			.	.		0.411	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		A	26881521	-	A	26881520	7	5	262	1	0	1	1	0	0	0	0	0	3119	1299	45	0	278	0	CDH9	5	26881520	Frame_Shift_Ins	INS	-	TCGA-FV-A2QQ-01A-11D-A22F-10	17252243	26881520	154033740	35	38293										
EGFLAM	133584	hgsc.bcm.edu	37	chr5	38451432	38451432	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	tccagggtgtcaggatcaagAtcaaatgtgttcatgaggtt	12	6	4	2			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr5:38451432A>G	ENST00000354891.3	+	20	2929	c.2583A>G	c.(2581-2583)agA>agG	p.R861R	EGFLAM_ENST00000397202.2_Silent_p.R219R|EGFLAM_ENST00000336740.6_Silent_p.R619R|EGFLAM_ENST00000322350.5_Silent_p.R853R|EGFLAM_ENST00000506135.1_5'UTR|EGFLAM_ENST00000514476.1_5'UTR|EGFLAM_ENST00000397210.3_5'UTR	NM_001205301.1	NP_001192230.1	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G domains	861	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				extracellular matrix organization (GO:0030198)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|cell junction (GO:0030054)|interstitial matrix (GO:0005614)|synapse (GO:0045202)	glycosaminoglycan binding (GO:0005539)			NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(43)|ovary(1)|pancreas(3)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	85	all_lung(31;0.000385)					CAGGATCAAGATCAAATGTGT	0.473																																					p.R861R	Colon(62;485 1295 3347 17454)	Atlas-SNP	.											.	EGFLAM	302	.	0			c.A2583G						.						231	210	217					5																	38451432		2203	4300	6503	SO:0001819	synonymous_variant	133584	exon20			ATCAAGATCAAAT	AK097549	CCDS3924.1, CCDS3925.1, CCDS47199.1, CCDS56363.1	5p13.2-p13.1	2014-04-03			ENSG00000164318	ENSG00000164318		"Fibronectin type III domain containing"	26810	protein-coding gene	gene with protein product	"pikachurin", "agrin-like"					18641643, 20078962, 22760553	Standard	NM_182801		Approved	FLJ39155, AGRINL, AGRNL, PIKA	uc003jlc.2	Q63HQ2	OTTHUMG00000131139	ENST00000354891.3:c.2583A>G	chr5.hg19:g.38451432A>G		48.0	0.0		52.0	13.0	NM_001205301	A8K6D7|Q5U643|Q6P3V1|Q8N124|Q8N197|Q8N7Y0|Q8N8N5|Q8NAL2	Silent	SNP	ENST00000354891.3	hg19	CCDS56363.1																																																																																			.	.		0.473	EGFLAM-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367323.1	NM_152403		G	38451432	A	G	38451432	2	3	262	1	0	0	0	0	0	0	0	1	4968	330	12	2		2	EGFLAM	5	38451432	Silent	SNP	A	TCGA-FV-A2QQ-01A-11D-A22F-10	11569912	38451432	142463828	36	38294										
HCN1	348980	hgsc.bcm.edu	37	chr5	45353238	45353238	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	ttgagttcattgagaatattTtcctcatcaaagattttgcc	6	7	3	3			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr5:45353238T>A	ENST00000303230.4	-	5	1398	c.1341A>T	c.(1339-1341)gaA>gaT	p.E447D		NM_021072.3	NP_066550.2	O60741	HCN1_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 1	447					apical protein localization (GO:0045176)|cellular response to cAMP (GO:0071320)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|retinal cone cell development (GO:0046549)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|intracellular cAMP activated cation channel activity (GO:0005222)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(3)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(21)|liver(1)|lung(98)|ovary(1)|prostate(7)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(5)	156						TGAGAATATTTTCCTCATCAA	0.343																																					p.E447D		Atlas-SNP	.											.	HCN1	298	.	0			c.A1341T						.						136	125	129					5																	45353238		2203	4297	6500	SO:0001583	missense	348980	exon5			AATATTTTCCTCA	AF064876	CCDS3952.1	5p12	2011-07-05			ENSG00000164588	ENSG00000164588		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	4845	protein-coding gene	gene with protein product		602780		BCNG1		9405696, 9630217, 16382102	Standard	NM_021072		Approved	BCNG-1, HAC-2	uc003jok.3	O60741	OTTHUMG00000131155	ENST00000303230.4:c.1341A>T	chr5.hg19:g.45353238T>A	ENSP00000307342:p.Glu447Asp	103.0	0.0		124.0	15.0	NM_021072		Missense_Mutation	SNP	ENST00000303230.4	hg19	CCDS3952.1	.	.	.	.	.	.	.	.	.	.	T	13.89	2.370935	0.42003	.	.	ENSG00000164588	ENST00000303230	D	0.96774	-4.12	5.97	4.75	0.60458	Cyclic nucleotide-binding-like (1);	0.158012	0.43579	D	0.000558	D	0.92021	0.7472	L	0.28649	0.875	0.39107	D	0.961405	B	0.02656	0.0	B	0.01281	0.0	D	0.89005	0.3424	10	0.27082	T	0.32	.	12.3987	0.55399	0.0:0.0:0.3193:0.6807	.	447	O60741	HCN1_HUMAN	D	447	ENSP00000307342:E447D	ENSP00000307342:E447D	E	-	3	2	HCN1	45388995	0.993000	0.37304	1.000000	0.80357	0.997000	0.91878	0.116000	0.15561	2.281000	0.76405	0.533000	0.62120	GAA	.	.		0.343	HCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253847.1	NM_021072		A	45353238	T	A	45353238	3	1	262	1	0	0	0	0	1	0	0	0	7005	1838	64	4	1347	4	HCN1	5	45353238	Missense_Mutation	SNP	T	TCGA-FV-A2QQ-01A-11D-A22F-10	6901806	45353238	135562022	37	38295										
CDC20B	166979	hgsc.bcm.edu	37	chr5	54468477	54468477	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	agagcacacgcatgatacttTcctttgaaaacacagataac	6	10	0	4			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr5:54468477T>C	ENST00000381375.2	-	2	210	c.65A>G	c.(64-66)gAa>gGa	p.E22G	CDC20B_ENST00000296733.1_Splice_Site_p.E22G|MIR449A_ENST00000362113.1_RNA|MIR449C_ENST00000516047.1_RNA|CDC20B_ENST00000334206.5_Splice_Site_p.E22G|CDC20B_ENST00000331730.3_Intron|CDC20B_ENST00000322374.6_Splice_Site_p.E22G|MIR449B_ENST00000384995.1_RNA			Q86Y33	CD20B_HUMAN	cell division cycle 20B	22										kidney(1)|large_intestine(5)|lung(7)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	19		Lung NSC(810;0.000744)|Breast(144;0.159)|Prostate(74;0.194)	LUSC - Lung squamous cell carcinoma(15;0.225)			CATGATACTTTCCTTTGAAAA	0.383																																					p.E22G		Atlas-SNP	.											.	CDC20B	61	.	0			c.A65G						.						123	127	125					5																	54468477		2203	4300	6503	SO:0001630	splice_region_variant	166979	exon2			ATACTTTCCTTTG	AB086378	CCDS3966.1, CCDS47207.1, CCDS54852.1	5q11.2	2013-01-17	2013-01-17		ENSG00000164287	ENSG00000164287		"WD repeat domain containing"	24222	protein-coding gene	gene with protein product			"CDC20 cell division cycle 20 homolog B (S. cerevisiae)", "cell division cycle 20 homolog B (S. cerevisiae)"				Standard	NM_152623		Approved	FLJ37927	uc003jpo.2	Q86Y33	OTTHUMG00000131185	ENST00000381375.2:c.64-1A>G	chr5.hg19:g.54468477T>C		53.0	0.0		54.0	10.0	NM_001170402	B7WNV8|B9EGL8|C9J6X8|C9JHE9|C9JKL5|Q86Y31|Q86Y32|Q8IUZ8|Q8N1S1|Q8NG56	Missense_Mutation	SNP	ENST00000381375.2	hg19	CCDS54852.1	.	.	.	.	.	.	.	.	.	.	T	16.69	3.193905	0.58017	.	.	ENSG00000164287	ENST00000334206;ENST00000296733;ENST00000381375;ENST00000322374	T;T;T;T	0.34275	1.37;1.37;1.37;1.37	5.3	4.11	0.48088	.	0.157480	0.30020	N	0.010618	T	0.46560	0.1399	L	0.54323	1.7	0.80722	D	1	D;D;P;D	0.59357	0.985;0.959;0.931;0.959	P;P;P;P	0.58130	0.833;0.675;0.476;0.675	T	0.40365	-0.9567	10	0.56958	D	0.05	-20.3119	9.0417	0.36322	0.0:0.0:0.186:0.814	.	22;22;22;22	Q86Y33-4;Q86Y33-3;Q86Y33;Q86Y33-2	.;.;CD20B_HUMAN;.	G	22	ENSP00000335664:E22G;ENSP00000296733:E22G;ENSP00000370781:E22G;ENSP00000315720:E22G	ENSP00000296733:E22G	E	-	2	0	CDC20B	54504234	0.953000	0.32496	0.960000	0.40013	0.486000	0.33341	1.381000	0.34362	0.993000	0.38866	0.528000	0.53228	GAA	.	.		0.383	CDC20B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369715.1	NM_152623	Missense_Mutation	C	54468477	T	C	54468477	5	2	262	1	0	0	0	0	0	0	1	0	3062	1797	62	2	1538	2	CDC20B	5	54468477	Splice_Site	SNP	T	TCGA-FV-A2QQ-01A-11D-A22F-10	9115239	54468477	126446783	38	38296										
MAP3K1	4214	hgsc.bcm.edu	37	chr5	56178151	56178151	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	aaaacaaagactcagataaaCtttccccagtctttactcag	4	11	3	2			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr5:56178151C>G	ENST00000399503.3	+	14	3124	c.3124C>G	c.(3124-3126)Ctt>Gtt	p.L1042V		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	1042					activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		CTCAGATAAACTTTCCCCAGT	0.443																																					p.L1042V		Atlas-SNP	.											.	MAP3K1	355	.	0			c.C3124G						.						68	68	68					5																	56178151		1869	4093	5962	SO:0001583	missense	4214	exon14			GATAAACTTTCCC	U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6848	protein-coding gene	gene with protein product		600982	"mitogen-activated protein kinase kinase kinase 1"	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.3124C>G	chr5.hg19:g.56178151C>G	ENSP00000382423:p.Leu1042Val	100.0	0.0		96.0	28.0	NM_005921		Missense_Mutation	SNP	ENST00000399503.3	hg19	CCDS43318.1	.	.	.	.	.	.	.	.	.	.	C	16.44	3.122964	0.56613	.	.	ENSG00000095015	ENST00000399503	T	0.72725	-0.68	5.71	4.83	0.62350	.	0.069806	0.64402	N	0.000019	T	0.68128	0.2967	L	0.54323	1.7	0.48632	D	0.999686	B	0.15141	0.012	B	0.12156	0.007	T	0.65340	-0.6192	10	0.54805	T	0.06	.	16.7333	0.85440	0.0:0.8706:0.1294:0.0	.	1042	Q13233	M3K1_HUMAN	V	1042	ENSP00000382423:L1042V	ENSP00000382423:L1042V	L	+	1	0	MAP3K1	56213908	1.000000	0.71417	0.998000	0.56505	0.983000	0.72400	2.711000	0.47177	1.399000	0.46721	-0.176000	0.13171	CTT	.	.		0.443	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066		G	56178151	C	G	56178151	3	3	262	1	0	0	0	0	1	0	0	0	9252	565	20	4	3178	4	MAP3K1	5	56178151	Missense_Mutation	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10	1709674	56178151	124737109	39	38297										
TRIM36	55521	hgsc.bcm.edu	37	chr5	114506845	114506845	+	Intron	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	ttatttcctgtttgggagaaGtctgtcgctgtggcaagttc	12	7	1	1			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr5:114506845G>T	ENST00000282369.3	-	2	185				TRIM36_ENST00000515104.1_5'Flank|TRIM36_ENST00000379618.2_Missense_Mutation_p.D46E|TRIM36_ENST00000513154.1_5'Flank|TRIM36_ENST00000514154.1_Intron	NM_018700.3	NP_061170.2	Q9NQ86	TRI36_HUMAN	tripartite motif containing 36						acrosome reaction (GO:0007340)|regulation of cell cycle (GO:0051726)	acrosomal vesicle (GO:0001669)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	37		all_cancers(142;0.00133)|all_epithelial(76;2.41e-05)|Prostate(80;0.00955)|Ovarian(225;0.0443)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;3.62e-08)|Epithelial(69;7.69e-08)|all cancers(49;9.33e-06)		TTTGGGAGAAGTCTGTCGCTG	0.468																																					p.D46E		Atlas-SNP	.											.	TRIM36	126	.	0			c.C138A						.						172	183	180					5																	114506845		2202	4300	6502	SO:0001627	intron_variant	55521	exon2			GGAGAAGTCTGTC	AJ272269	CCDS4115.1, CCDS34211.1, CCDS34212.1, CCDS75287.1	5q22	2013-02-11	2011-01-25		ENSG00000152503	ENSG00000152503		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Fibronectin type III domain containing"	16280	protein-coding gene	gene with protein product	"zinc-binding protein Rbcc728", "tripartite motif protein 36", "RING finger protein 98"	609317	"tripartite motif-containing 36"			11331580	Standard	XM_005272031		Approved	RBCC728, RNF98, HAPRIN	uc003kqs.3	Q9NQ86	OTTHUMG00000128892	ENST00000282369.3:c.64-7396C>A	chr5.hg19:g.114506845G>T		108.0	0.0		129.0	15.0	NM_001017397	A1L3Z1|A6NDD0|B7Z3V4|B7ZAV7|E9PFI8|Q0P5Z9	Missense_Mutation	SNP	ENST00000282369.3	hg19	CCDS4115.1	.	.	.	.	.	.	.	.	.	.	G	12.90	2.076378	0.36662	.	.	ENSG00000152503	ENST00000379618	.	.	.	2.46	-1.91	0.07641	.	.	.	.	.	T	0.25901	0.0631	.	.	.	0.09310	N	1	B	0.12630	0.006	B	0.12156	0.007	T	0.28396	-1.0045	7	0.87932	D	0	.	1.8813	0.03228	0.1372:0.41:0.2677:0.1851	.	46	Q0P5Z9	.	E	46	.	ENSP00000368938:D46E	D	-	3	2	TRIM36	114534744	0.000000	0.05858	0.000000	0.03702	0.566000	0.35808	-0.525000	0.06214	-0.523000	0.06409	-0.238000	0.12139	GAC	.	.		0.468	TRIM36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250854.2	NM_018700		T	114506845	G	T	114506845	1	4	262	0	1	0	0	0	0	0	0	0	16525	1020	36	3		3	TRIM36	5	114506845	Intron	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10	58328694	114506845	66408415	40	38298										
CHSY3	337876	hgsc.bcm.edu	37	chr5	129241310	129241310	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	gttcatgcgcgccgacgacgAtgtctacatcaaaggtgacc	11	12	3	1			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr5:129241310A>T	ENST00000305031.4	+	1	1146	c.788A>T	c.(787-789)gAt>gTt	p.D263V	CTC-575N7.1_ENST00000515569.1_RNA|CTC-575N7.1_ENST00000503616.1_RNA	NM_175856.4	NP_787052.3	Q70JA7	CHSS3_HUMAN	chondroitin sulfate synthase 3	263					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.136)		GCCGACGACGATGTCTACATC	0.572																																					p.D263V		Atlas-SNP	.											.	CHSY3	92	.	0			c.A788T						.						95	97	96					5																	129241310		2203	4300	6503	SO:0001583	missense	337876	exon1			ACGACGATGTCTA	AB086062	CCDS34223.1	5q13	2013-02-19			ENSG00000198108	ENSG00000198108	2.4.1.175, 2.4.1.226	"Beta 3-glycosyltransferases", "Beta 4-glycosyltransferases"	24293	protein-coding gene	gene with protein product		609963				12907687	Standard	XM_005271982		Approved	CSS3, CHSY-2	uc003kvd.3	Q70JA7	OTTHUMG00000163043	ENST00000305031.4:c.788A>T	chr5.hg19:g.129241310A>T	ENSP00000302629:p.Asp263Val	49.0	0.0		62.0	22.0	NM_175856	B2RP97|Q76L22|Q86Y52	Missense_Mutation	SNP	ENST00000305031.4	hg19	CCDS34223.1	.	.	.	.	.	.	.	.	.	.	A	19.84	3.902331	0.72754	.	.	ENSG00000198108	ENST00000305031	D	0.98135	-4.74	3.59	3.59	0.41128	.	0.000000	0.36591	U	0.002502	D	0.99193	0.9720	H	0.98446	4.235	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98501	1.0614	9	.	.	.	.	13.2228	0.59899	1.0:0.0:0.0:0.0	.	263	Q70JA7	CHSS3_HUMAN	V	263	ENSP00000302629:D263V	.	D	+	2	0	CHSY3	129269209	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	8.995000	0.93534	1.862000	0.54008	0.260000	0.18958	GAT	.	.		0.572	CHSY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371453.1	NM_175856		T	129241310	A	T	129241310	3	4	262	1	0	0	0	0	1	0	0	0	3415	333	12	4	790	4	CHSY3	5	129241310	Missense_Mutation	SNP	A	TCGA-FV-A2QQ-01A-11D-A22F-10	14734465	129241310	51673950	41	38299										
GLRA1	2741	hgsc.bcm.edu	37	chr5	151304062	151304062	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	gaaaattgcatacctgaagaAtacaatggtctcccaaaggt	8	8	1	2			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr5:151304062A>G	ENST00000455880.2	-	1	335	c.49T>C	c.(49-51)Ttc>Ctc	p.F17L	GLRA1_ENST00000274576.4_Missense_Mutation_p.F17L|GLRA1_ENST00000471351.2_5'UTR|GLRA1_ENST00000545569.1_5'UTR			P23415	GLRA1_HUMAN	glycine receptor, alpha 1	17					acrosome reaction (GO:0007340)|action potential (GO:0001508)|adult walking behavior (GO:0007628)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|muscle contraction (GO:0006936)|negative regulation of transmission of nerve impulse (GO:0051970)|neuromuscular process controlling posture (GO:0050884)|neuropeptide signaling pathway (GO:0007218)|positive regulation of acrosome reaction (GO:2000344)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of membrane potential (GO:0042391)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|righting reflex (GO:0060013)|startle response (GO:0001964)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|external side of plasma membrane (GO:0009897)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glycine-gated chloride channel activity (GO:0016934)|glycine binding (GO:0016594)|taurine binding (GO:0030977)|transmitter-gated ion channel activity (GO:0022824)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	23		all_hematologic(541;0.0341)|Medulloblastoma(196;0.0912)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Ethanol(DB00898)|Ginkgo biloba(DB01381)|Glycine(DB00145)|Halothane(DB01159)|Isoflurane(DB00753)|Lindane(DB00431)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	TACCTGAAGAATACAATGGTC	0.458																																					p.F17L		Atlas-SNP	.											.	GLRA1	61	.	0			c.T49C						.						219	193	202					5																	151304062		2203	4300	6503	SO:0001583	missense	2741	exon1			TGAAGAATACAAT		CCDS4320.1, CCDS54942.1	5q33.1	2012-02-07	2008-01-24		ENSG00000145888	ENSG00000145888		"Ligand-gated ion channels / Glycine receptors"	4326	protein-coding gene	gene with protein product	"startle disease/hyperekplexia", "stiff person syndrome"	138491	"glycine receptor, alpha 1 (startle disease/hyperekplexia)"	STHE		1355335, 8298642	Standard	NM_000171		Approved		uc003lut.3	P23415	OTTHUMG00000130121	ENST00000455880.2:c.49T>C	chr5.hg19:g.151304062A>G	ENSP00000411593:p.Phe17Leu	81.0	0.0		90.0	30.0	NM_000171	B2R6T3|Q14C77|Q6DJV9	Missense_Mutation	SNP	ENST00000455880.2	hg19	CCDS54942.1	.	.	.	.	.	.	.	.	.	.	A	9.666	1.145336	0.21288	.	.	ENSG00000145888	ENST00000274576;ENST00000455880	T;T	0.70516	-0.33;-0.49	5.13	5.13	0.70059	.	0.296801	0.32687	N	0.005765	T	0.47116	0.1428	N	0.08118	0	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.45249	-0.9274	10	0.06757	T	0.87	.	13.5239	0.61584	1.0:0.0:0.0:0.0	.	17;17	P23415;P23415-2	GLRA1_HUMAN;.	L	17	ENSP00000274576:F17L;ENSP00000411593:F17L	ENSP00000274576:F17L	F	-	1	0	GLRA1	151284255	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.709000	0.68384	1.939000	0.56221	0.460000	0.39030	TTC	.	.		0.458	GLRA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000373959.1			G	151304062	A	G	151304062	3	3	262	1	0	0	0	0	1	0	0	0	6462	101	4	2	1360	2	GLRA1	5	151304062	Missense_Mutation	SNP	A	TCGA-FV-A2QQ-01A-11D-A22F-10	22062752	151304062	29611198	42	38300										
ERGIC1	57222	hgsc.bcm.edu	37	chr5	172359509	172359509	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	gacaagagtggcaagcagcgGtactcctaccagtacacggt	12	11	0	1	rs144844076	byFrequency	TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr5:172359509G>A	ENST00000393784.3	+	8	751	c.612G>A	c.(610-612)cgG>cgA	p.R204R		NM_001031711.2	NP_001026881.1	Q969X5	ERGI1_HUMAN	endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1	204					ER to Golgi vesicle-mediated transport (GO:0006888)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(2)	9	Renal(175;0.000159)|Lung NSC(126;0.00344)|all_lung(126;0.00594)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			GCAAGCAGCGGTACTCCTACC	0.622											OREG0017050	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R204R		Atlas-SNP	.											.	ERGIC1	35	.	0			c.G612A						.						74	58	63					5																	172359509		2203	4300	6503	SO:0001819	synonymous_variant	57222	exon8			GCAGCGGTACTCC	AF267855	CCDS34292.1	5q35.1	2009-11-06			ENSG00000113719	ENSG00000113719			29205	protein-coding gene	gene with protein product						10574461, 15308636	Standard	NM_001031711		Approved	ERGIC32, ERGIC-32, KIAA1181, NET24	uc003mbw.4	Q969X5	OTTHUMG00000130520	ENST00000393784.3:c.612G>A	chr5.hg19:g.172359509G>A		47.0	0.0	237	50.0	5.0	NM_001031711	Q9H0L0|Q9H2J2|Q9ULN9	Silent	SNP	ENST00000393784.3	hg19	CCDS34292.1																																																																																			.	G|0.993;T|0.007		0.622	ERGIC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252938.3	NM_020462		A	172359509	G	A	172359509	2	1	262	1	0	0	0	0	0	0	0	1	5225	1248	44	3		3	ERGIC1	5	172359509	Silent	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10	21055447	172359509	8555751	43	38301										
RUFY1	80230	hgsc.bcm.edu	37	chr5	179023595	179023595	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	ggagcgggcgaggcagggggCtgaggagcggagccacaagc	22	9	0	1			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr5:179023595C>T	ENST00000319449.4	+	13	1556	c.1544C>T	c.(1543-1545)gCt>gTt	p.A515V	RUFY1_ENST00000393438.2_Missense_Mutation_p.A407V|RP11-1379J22.2_ENST00000500262.1_RNA|RUFY1_ENST00000437570.2_Missense_Mutation_p.A407V|RUFY1_ENST00000377001.2_3'UTR	NM_025158.4	NP_079434.3	Q96T51	RUFY1_HUMAN	RUN and FYVE domain containing 1	515					endocytosis (GO:0006897)|regulation of endocytosis (GO:0030100)	cytoplasm (GO:0005737)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	lipid binding (GO:0008289)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	26	all_cancers(89;0.00018)|all_epithelial(37;8.37e-05)|Renal(175;0.000159)|Lung NSC(126;0.00108)|all_lung(126;0.00195)	all_cancers(40;0.0322)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGGCAGGGGGCTGAGGAGCGG	0.622										HNSCC(44;0.11)																											p.A515V		Atlas-SNP	.											.	RUFY1	101	.	0			c.C1544T						.						75	90	85					5																	179023595		2188	4266	6454	SO:0001583	missense	80230	exon13			AGGGGGCTGAGGA	AF361055	CCDS4445.2, CCDS34312.1	5q35.3	2008-02-05			ENSG00000176783	ENSG00000176783		"Zinc fingers, FYVE domain containing"	19760	protein-coding gene	gene with protein product		610327				11877430	Standard	NM_001040451		Approved	FLJ22251, ZFYVE12, RABIP4	uc003mka.2	Q96T51	OTTHUMG00000130913	ENST00000319449.4:c.1544C>T	chr5.hg19:g.179023595C>T	ENSP00000325594:p.Ala515Val	36.0	0.0		39.0	13.0	NM_025158	Q59FF3|Q71S93|Q9H6I3	Missense_Mutation	SNP	ENST00000319449.4	hg19	CCDS4445.2	.	.	.	.	.	.	.	.	.	.	C	14.09	2.432322	0.43122	.	.	ENSG00000176783	ENST00000319449;ENST00000437570;ENST00000393438;ENST00000360569	T;T;T	0.56275	0.47;0.53;0.53	5.3	5.3	0.74995	.	0.101230	0.64402	D	0.000002	T	0.62792	0.2457	M	0.83483	2.645	0.80722	D	1	P	0.44260	0.83	P	0.45681	0.49	T	0.65228	-0.6219	10	0.36615	T	0.2	-16.0844	16.0344	0.80612	0.0:1.0:0.0:0.0	.	515	Q96T51	RUFY1_HUMAN	V	515;407;407;117	ENSP00000325594:A515V;ENSP00000390025:A407V;ENSP00000377087:A407V	ENSP00000325594:A515V	A	+	2	0	RUFY1	178956201	0.888000	0.30383	0.156000	0.22583	0.034000	0.12701	1.704000	0.37857	2.631000	0.89168	0.561000	0.74099	GCT	.	.		0.622	RUFY1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253505.2	NM_001040451		T	179023595	C	T	179023595	3	4	262	1	0	0	0	0	1	0	0	0	13753	797	28	3	1594	3	RUFY1	5	179023595	Missense_Mutation	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10	6664086	179023595	1891665	44	38302										
DSP	1832	hgsc.bcm.edu	37	chr6	7585457	7585457	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	cagaggcttctggaggctcaGgcctgcacaggtggcatcat	14	11	3	1			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr6:7585457G>A	ENST00000379802.3	+	24	8303	c.7962G>A	c.(7960-7962)caG>caA	p.Q2654Q	DSP_ENST00000418664.2_Silent_p.Q2055Q	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	2654	4.5 X 38 AA tandem repeats (Domain C).|Globular 2.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		TGGAGGCTCAGGCCTGCACAG	0.557																																					p.Q2654Q		Atlas-SNP	.											.	DSP	306	.	0			c.G7962A						.						81	81	81					6																	7585457		2203	4300	6503	SO:0001819	synonymous_variant	1832	exon24			GGCTCAGGCCTGC	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"desmoplakin (DPI, DPII)"			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.7962G>A	chr6.hg19:g.7585457G>A		77.0	0.0		86.0	17.0	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Silent	SNP	ENST00000379802.3	hg19	CCDS4501.1																																																																																			.	.		0.557	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		A	7585457	G	A	7585457	2	1	262	1	0	0	0	0	0	0	0	1	4783	991	35	3		3	DSP	6	7585457	Silent	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10		7585457	163529610	45	38303										
UHRF1BP1	54887	hgsc.bcm.edu	37	chr6	34827055	34827055	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	ggccatgaggcagtagagtcCctacaggccaagaaactgag	13	10	0	4			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr6:34827055C>G	ENST00000192788.5	+	14	3093	c.2922C>G	c.(2920-2922)tcC>tcG	p.S974S	UHRF1BP1_ENST00000452449.2_Silent_p.S974S	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	974							histone deacetylase binding (GO:0042826)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(24)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	54						CAGTAGAGTCCCTACAGGCCA	0.587																																					p.S974S		Atlas-SNP	.											.	UHRF1BP1	102	.	0			c.C2922G						.						41	44	43					6																	34827055		2043	4190	6233	SO:0001819	synonymous_variant	54887	exon14			AGAGTCCCTACAG	AB126777	CCDS43455.1	6p21.31	2008-10-28	2008-08-15	2007-11-27	ENSG00000065060	ENSG00000065060			21216	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 107"	C6orf107			Standard	NM_017754		Approved	FLJ20302, dJ349A12.1, ICBP90	uc003oju.4	Q6BDS2	OTTHUMG00000014557	ENST00000192788.5:c.2922C>G	chr6.hg19:g.34827055C>G		52.0	0.0		70.0	27.0	NM_017754	Q9NXE0	Silent	SNP	ENST00000192788.5	hg19	CCDS43455.1																																																																																			.	.		0.587	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754		G	34827055	C	G	34827055	2	3	262	1	0	0	0	0	0	0	0	1	16983	610	22	4		4	UHRF1BP1	6	34827055	Silent	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10	27241598	34827055	136288012	46	38304										
EFHC1	114327	hgsc.bcm.edu	37	chr6	52334232	52334232	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	aaagacgttattaaaatgctGgtgaatgataacaaggtgct	10	4	0	3			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr6:52334232G>A	ENST00000371068.5	+	7	1342	c.1239G>A	c.(1237-1239)ctG>ctA	p.L413L	EFHC1_ENST00000433625.2_Silent_p.L322L|EFHC1_ENST00000538167.1_Silent_p.L394L	NM_018100.3	NP_060570.2	Q5JVL4	EFHC1_HUMAN	EF-hand domain (C-terminal) containing 1	413						axoneme (GO:0005930)|neuronal cell body (GO:0043025)	calcium ion binding (GO:0005509)|protein C-terminus binding (GO:0008022)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(8)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	27	Lung NSC(77;0.109)					TTAAAATGCTGGTGAATGATA	0.358																																					p.L413L		Atlas-SNP	.											.	EFHC1	68	.	0			c.G1239A						.						134	134	134					6																	52334232		2203	4300	6503	SO:0001819	synonymous_variant	114327	exon7			AATGCTGGTGAAT	AK001328	CCDS4942.1, CCDS55021.1	6p12.3	2014-02-04			ENSG00000096093	ENSG00000096093		"EF-hand domain containing"	16406	protein-coding gene	gene with protein product	"myoclonin-1"	608815	"epilepsy, juvenile myoclonic 1"	EJM1, EJM		15258581	Standard	NM_018100		Approved	FLJ10466	uc003pap.4	Q5JVL4	OTTHUMG00000014848	ENST00000371068.5:c.1239G>A	chr6.hg19:g.52334232G>A		64.0	0.0		61.0	19.0	NM_018100	B4DMU3|F5GZD8|Q5XKM4|Q6E1U7|Q6E1U8|Q8WUL2|Q9NVW6	Silent	SNP	ENST00000371068.5	hg19	CCDS4942.1																																																																																			.	.		0.358	EFHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040905.2	NM_018100		A	52334232	G	A	52334232	2	1	262	1	0	0	0	0	0	0	0	1	4948	1335	47	3		3	EFHC1	6	52334232	Silent	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10	17507177	52334232	118780835	47	38305										
RAB23	51715	hgsc.bcm.edu	37	chr6	57055398	57055398	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	caccagatgtattaaagacaCctgtataaattgagggaaaa	8	6	0	3			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr6:57055398C>A	ENST00000317483.3	-	7	1194	c.575G>T	c.(574-576)gGt>gTt	p.G192V	RAB23_ENST00000468148.1_Splice_Site_p.G192V	NM_016277.3	NP_057361.3	Q9ULC3	RAB23_HUMAN	RAB23, member RAS oncogene family	192					autophagic vacuole assembly (GO:0000045)|cellular defense response (GO:0006968)|cilium assembly (GO:0042384)|craniofacial suture morphogenesis (GO:0097094)|embryonic digit morphogenesis (GO:0042733)|GTP catabolic process (GO:0006184)|negative regulation of proteolysis (GO:0045861)|negative regulation of transcription factor import into nucleus (GO:0042992)|protein transport (GO:0015031)|regulation of smoothened signaling pathway (GO:0008589)|small GTPase mediated signal transduction (GO:0007264)|spinal cord dorsal/ventral patterning (GO:0021513)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	8	Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			ATTAAAGACACCTGTATAAAT	0.408																																					p.G192V		Atlas-SNP	.											.	RAB23	22	.	0			c.G575T						.						127	120	123					6																	57055398		2203	4300	6503	SO:0001630	splice_region_variant	51715	exon7			AAGACACCTGTAT	AB034244	CCDS4962.1	6p12.1	2008-05-15			ENSG00000112210	ENSG00000112210		"RAB, member RAS oncogene"	14263	protein-coding gene	gene with protein product		606144					Standard	NM_016277		Approved		uc003pdt.3	Q9ULC3	OTTHUMG00000014918	ENST00000317483.3:c.575-1G>T	chr6.hg19:g.57055398C>A		95.0	0.0		93.0	34.0	NM_016277	B2R9I5|Q68DJ6|Q8NI06|Q9P023	Missense_Mutation	SNP	ENST00000317483.3	hg19	CCDS4962.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.062151	0.76187	.	.	ENSG00000112210	ENST00000317483;ENST00000468148	T;T	0.65364	-0.15;-0.15	5.69	4.81	0.61882	.	0.000000	0.85682	D	0.000000	T	0.60495	0.2273	M	0.66939	2.045	0.80722	D	1	D	0.57899	0.981	P	0.50136	0.632	T	0.63079	-0.6717	10	0.46703	T	0.11	.	15.0545	0.71904	0.0:0.9305:0.0:0.0695	.	192	Q9ULC3	RAB23_HUMAN	V	192	ENSP00000320413:G192V;ENSP00000417610:G192V	ENSP00000320413:G192V	G	-	2	0	RAB23	57163357	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	7.384000	0.79751	2.687000	0.91594	0.462000	0.41574	GGT	.	.		0.408	RAB23-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041042.1		Missense_Mutation	A	57055398	C	A	57055398	5	1	262	1	0	0	0	0	0	0	1	0	12925	521	18	3	142	3	RAB23	6	57055398	Splice_Site	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10	4721166	57055398	114059669	48	38306										
FILIP1	27145	hgsc.bcm.edu	37	chr6	76024199	76024199	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	ccagatttaaatgtagctggGtgcactcagatttactcttg	9	8	2	2			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr6:76024199G>A	ENST00000237172.7	-	5	1679	c.1349C>T	c.(1348-1350)aCc>aTc	p.T450I	FILIP1_ENST00000498523.1_5'UTR|FILIP1_ENST00000370020.1_Missense_Mutation_p.T351I|FILIP1_ENST00000393004.2_Missense_Mutation_p.T450I	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	450										breast(3)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)	80						ATGTAGCTGGGTGCACTCAGA	0.383																																					p.T450I		Atlas-SNP	.											.	FILIP1	173	.	0			c.C1349T						.						139	140	140					6																	76024199		2203	4300	6503	SO:0001583	missense	27145	exon5			AGCTGGGTGCACT	AB033101	CCDS4984.1, CCDS75480.1	6q14.1	2008-02-05			ENSG00000118407	ENSG00000118407			21015	protein-coding gene	gene with protein product		607307				10574462	Standard	XM_005248713		Approved	FILIP, KIAA1275	uc003pia.3	Q7Z7B0	OTTHUMG00000015056	ENST00000237172.7:c.1349C>T	chr6.hg19:g.76024199G>A	ENSP00000237172:p.Thr450Ile	201.0	0.0		227.0	70.0	NM_015687	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Missense_Mutation	SNP	ENST00000237172.7	hg19	CCDS4984.1	.	.	.	.	.	.	.	.	.	.	G	8.453	0.853420	0.17106	.	.	ENSG00000118407	ENST00000393004;ENST00000237172;ENST00000370020	T;T;T	0.19938	2.11;2.11;2.11	5.65	4.75	0.60458	.	0.375966	0.30979	N	0.008488	T	0.11067	0.0270	L	0.50333	1.59	0.31760	N	0.633495	B;B;B	0.23735	0.09;0.047;0.078	B;B;B	0.26614	0.057;0.032;0.071	T	0.08391	-1.0724	10	0.35671	T	0.21	-4.7858	15.9068	0.79436	0.0:0.0:0.8636:0.1364	.	450;450;450	A8K2G7;Q7Z7B0;Q7Z7B0-2	.;FLIP1_HUMAN;.	I	450;450;351	ENSP00000376728:T450I;ENSP00000237172:T450I;ENSP00000359037:T351I	ENSP00000237172:T450I	T	-	2	0	FILIP1	76080919	0.890000	0.30428	0.966000	0.40874	0.988000	0.76386	4.651000	0.61447	1.454000	0.47793	0.655000	0.94253	ACC	.	.		0.383	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179		A	76024199	G	A	76024199	3	1	262	1	0	0	0	0	1	0	0	0	5902	1261	44	3	2300	3	FILIP1	6	76024199	Missense_Mutation	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10	18968801	76024199	95090868	49	38307										
ARMC2	84071	hgsc.bcm.edu	37	chr6	109190048	109190048	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	aaccgaaagttccagcatctCccaccagagaggaggattcc	9	13	1	1			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr6:109190048C>G	ENST00000392644.4	+	4	481	c.313C>G	c.(313-315)Ccc>Gcc	p.P105A	ARMC2_ENST00000368972.3_5'UTR	NM_032131.4	NP_115507.4	Q8NEN0	ARMC2_HUMAN	armadillo repeat containing 2	105										endometrium(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(1)|skin(1)	24		all_cancers(87;1.14e-07)|Acute lymphoblastic leukemia(125;2.3e-10)|all_hematologic(75;3.3e-08)|all_epithelial(87;0.000111)|Colorectal(196;0.03)|all_lung(197;0.11)		Epithelial(106;0.000197)|BRCA - Breast invasive adenocarcinoma(108;0.000236)|all cancers(137;0.000279)|OV - Ovarian serous cystadenocarcinoma(136;0.00434)		TCCAGCATCTCCCACCAGAGA	0.483																																					p.P105A		Atlas-SNP	.											.	ARMC2	56	.	0			c.C313G						.						48	50	49					6																	109190048		2203	4300	6503	SO:0001583	missense	84071	exon4			GCATCTCCCACCA	BC030603	CCDS5069.2, CCDS69168.1	6q21	2013-02-14			ENSG00000118690	ENSG00000118690		"Armadillo repeat containing"	23045	protein-coding gene	gene with protein product							Standard	XM_005267154		Approved	DKFZp434P0714, bA787I22.1	uc003pss.4	Q8NEN0	OTTHUMG00000015335	ENST00000392644.4:c.313C>G	chr6.hg19:g.109190048C>G	ENSP00000376417:p.Pro105Ala	56.0	0.0		49.0	16.0	NM_032131	A8K8Y4|B4DGF5|G5E993|Q5VVY8|Q9H0K9	Missense_Mutation	SNP	ENST00000392644.4	hg19	CCDS5069.2	.	.	.	.	.	.	.	.	.	.	C	0.513	-0.865466	0.02590	.	.	ENSG00000118690	ENST00000392644;ENST00000237512	T;T	0.41758	0.99;0.99	5.41	3.61	0.41365	.	0.434509	0.25352	N	0.031300	T	0.13841	0.0335	M	0.63428	1.95	0.80722	D	1	B	0.12013	0.005	B	0.10450	0.005	T	0.23119	-1.0197	10	0.02654	T	1	.	5.282	0.15680	0.0:0.6513:0.1699:0.1788	.	105	Q8NEN0	ARMC2_HUMAN	A	105	ENSP00000376417:P105A;ENSP00000237512:P105A	ENSP00000237512:P105A	P	+	1	0	ARMC2	109296741	0.994000	0.37717	0.991000	0.47740	0.409000	0.31022	1.102000	0.31050	1.411000	0.46957	0.655000	0.94253	CCC	.	.		0.483	ARMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041732.2	NM_032131		G	109190048	C	G	109190048	3	3	262	1	0	0	0	0	1	0	0	0	951	855	30	4	323	4	ARMC2	6	109190048	Missense_Mutation	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10	33165849	109190048	61925019	50	38308										
ACAT2	39	hgsc.bcm.edu	37	chr6	160196295	160196295	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	gacagagaatgcacagaaagCtggccattttgacaaagaga	11	7	0	4			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr6:160196295C>T	ENST00000367048.4	+	5	2344	c.584C>T	c.(583-585)gCt>gTt	p.A195V	ACAT2_ENST00000541436.1_Missense_Mutation_p.A224V	NM_005891.2	NP_005882.2	Q9BWD1	THIC_HUMAN	acetyl-CoA acetyltransferase 2	195					lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleus (GO:0005634)	acetyl-CoA C-acetyltransferase activity (GO:0003985)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(1)	9		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.51e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		GCACAGAAAGCTGGCCATTTT	0.398																																					p.A195V		Atlas-SNP	.											.	ACAT2	32	.	0			c.C584T						.						107	96	100					6																	160196295		2203	4300	6503	SO:0001583	missense	39	exon5			AGAAAGCTGGCCA	AF356877	CCDS5268.1	6q25.3	2014-05-19	2010-04-30		ENSG00000120437	ENSG00000120437	2.3.1.9		94	protein-coding gene	gene with protein product	"acetoacetyl Coenzyme A thiolase"	100678	"acetyl-Coenzyme A acetyltransferase 2 (acetoacetyl Coenzyme A thiolase)", "acetyl-Coenzyme A acetyltransferase 2"			2475872	Standard	NM_005891		Approved		uc010kjy.3	Q9BWD1	OTTHUMG00000015935	ENST00000367048.4:c.584C>T	chr6.hg19:g.160196295C>T	ENSP00000356015:p.Ala195Val	67.0	0.0		70.0	18.0	NM_005891	B7Z233|E1P5B1|Q16146|Q5TCL7|Q8TDM4	Missense_Mutation	SNP	ENST00000367048.4	hg19	CCDS5268.1	.	.	.	.	.	.	.	.	.	.	C	32	5.155988	0.94686	.	.	ENSG00000120437	ENST00000367048;ENST00000541436	T;T	0.53206	0.63;0.63	5.65	5.65	0.86999	Thiolase-like, subgroup (1);Thiolase, N-terminal (1);Thiolase-like (1);	0.049163	0.85682	D	0.000000	T	0.60663	0.2286	M	0.90542	3.125	0.53688	D	0.999974	P;P	0.51449	0.945;0.858	P;P	0.48677	0.586;0.586	T	0.71041	-0.4707	10	0.72032	D	0.01	-0.049	19.7278	0.96172	0.0:1.0:0.0:0.0	.	224;195	B7Z233;Q9BWD1	.;THIC_HUMAN	V	195;224	ENSP00000356015:A195V;ENSP00000437850:A224V	ENSP00000356015:A195V	A	+	2	0	ACAT2	160116285	1.000000	0.71417	0.970000	0.41538	0.995000	0.86356	5.504000	0.66968	2.681000	0.91329	0.563000	0.77884	GCT	.	.		0.398	ACAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042912.1	NM_005891		T	160196295	C	T	160196295	3	4	262	1	0	0	0	0	1	0	0	0	122	797	28	3	602	3	ACAT2	6	160196295	Missense_Mutation	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10	51006247	160196295	10918772	51	38309										
STEAP2	261729	hgsc.bcm.edu	37	chr7	89854507	89854507	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	gtcactgtaggtgtgattggAagtggagattttgccaaatc	13	5	1	2			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr7:89854507A>G	ENST00000287908.3	+	2	504	c.111A>G	c.(109-111)ggA>ggG	p.G37G	STEAP2_ENST00000394621.2_Silent_p.G37G|STEAP2_ENST00000394632.1_Silent_p.G37G|STEAP2_ENST00000394626.1_Silent_p.G37G|STEAP2_ENST00000394622.2_Silent_p.G37G|STEAP2_ENST00000402625.2_Silent_p.G37G|STEAP2_ENST00000394629.2_Silent_p.G37G	NM_001244944.1|NM_152999.3	NP_001231873.1|NP_694544.2	Q8NFT2	STEA2_HUMAN	STEAP family member 2, metalloreductase	37					copper ion import (GO:0015677)|endocytosis (GO:0006897)|ferric iron import into cell (GO:0097461)|Golgi to plasma membrane transport (GO:0006893)|iron ion homeostasis (GO:0055072)|regulated secretory pathway (GO:0045055)|response to hormone (GO:0009725)	cytosol (GO:0005829)|early endosome (GO:0005769)|integral component of Golgi membrane (GO:0030173)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|trans-Golgi network transport vesicle (GO:0030140)	cupric reductase activity (GO:0008823)|ferric-chelate reductase (NADPH) activity (GO:0052851)|metal ion binding (GO:0046872)|transporter activity (GO:0005215)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(1)	15	all_hematologic(106;0.112)					GTGTGATTGGAAGTGGAGATT	0.393																																					p.G37G		Atlas-SNP	.											.	STEAP2	78	.	0			c.A111G						.						213	184	194					7																	89854507		2203	4300	6503	SO:0001819	synonymous_variant	261729	exon3			GATTGGAAGTGGA	AF455138	CCDS5615.1, CCDS43612.1, CCDS59064.1	7q21.13	2011-09-30	2011-09-30		ENSG00000157214	ENSG00000157214			17885	protein-coding gene	gene with protein product		605094	"prostate cancer associated protein 1", "six transmembrane epithelial antigen of the prostate 2"	PCANAP1		10613842, 12095985	Standard	NM_001040665		Approved	IPCA-1, STAMP1, STMP	uc003ujz.3	Q8NFT2	OTTHUMG00000023341	ENST00000287908.3:c.111A>G	chr7.hg19:g.89854507A>G		177.0	0.0		191.0	50.0	NM_001244946	A4D1F1|G5E9C6|Q6UXN6|Q6YPB1|Q8IUE7	Silent	SNP	ENST00000287908.3	hg19	CCDS5615.1																																																																																			.	.		0.393	STEAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059662.4	NM_152999		G	89854507	A	G	89854507	2	3	262	1	0	0	0	0	0	0	0	1	15293	233	9	2		2	STEAP2	7	89854507	Silent	SNP	A	TCGA-FV-A2QQ-01A-11D-A22F-10		89854507	69284156	52	38310										
RELN	5649	hgsc.bcm.edu	37	chr7	103159876	103159876	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	ttggttacggttgtttggtgTaatcaggcacccatacatga	11	7	1	1			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr7:103159876T>A	ENST00000428762.1	-	49	7915	c.7756A>T	c.(7756-7758)Aca>Tca	p.T2586S	RELN_ENST00000424685.2_Missense_Mutation_p.T2586S|RELN_ENST00000343529.5_Missense_Mutation_p.T2586S	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	2586					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		TTGTTTGGTGTAATCAGGCAC	0.398																																					p.T2586S	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.A7756T						.						143	117	126					7																	103159876		2203	4300	6503	SO:0001583	missense	5649	exon49			TTGGTGTAATCAG		CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.7756A>T	chr7.hg19:g.103159876T>A	ENSP00000392423:p.Thr2586Ser	95.0	0.0		121.0	16.0	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	hg19	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	T	12.61	1.991048	0.35131	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000424828;ENST00000448171	T;T;T	0.19532	2.14;2.14;2.14	5.87	1.95	0.26073	Neuraminidase (2);	0.252057	0.46758	N	0.000271	T	0.10121	0.0248	N	0.11427	0.14	0.28758	N	0.901063	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.19778	-1.0295	10	0.32370	T	0.25	.	8.8871	0.35409	0.1175:0.0:0.246:0.6365	.	2586;2586	P78509-2;P78509	.;RELN_HUMAN	S	2586;2586;2586;103;2586	ENSP00000392423:T2586S;ENSP00000345694:T2586S;ENSP00000388446:T2586S	ENSP00000345694:T2586S	T	-	1	0	RELN	102947112	0.995000	0.38212	0.992000	0.48379	0.994000	0.84299	0.967000	0.29344	0.075000	0.16796	0.533000	0.62120	ACA	.	.		0.398	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		A	103159876	T	A	103159876	3	1	262	1	0	0	0	0	1	0	0	0	13235	1638	57	4	2694	4	RELN	7	103159876	Missense_Mutation	SNP	T	TCGA-FV-A2QQ-01A-11D-A22F-10	13305369	103159876	55978787	53	38311										
OR2A12	346525	hgsc.bcm.edu	37	chr7	143792372	143792372	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	actctagactgcacacacccAtgtatgtcttcctgtcacac	5	15	3	1			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr7:143792372A>G	ENST00000408949.2	+	1	232	c.172A>G	c.(172-174)Atg>Gtg	p.M58V		NM_001004135.1	NP_001004135.1	Q8NGT7	O2A12_HUMAN	olfactory receptor, family 2, subfamily A, member 12	58						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(14)|ovary(2)	25	Melanoma(164;0.0783)					GCACACACCCATGTATGTCTT	0.458																																					p.M58V		Atlas-SNP	.											.	OR2A12	56	.	0			c.A172G						.						169	163	165					7																	143792372		2074	4239	6313	SO:0001583	missense	346525	exon1			ACACCCATGTATG		CCDS43670.1	7q35	2013-09-20	2002-11-13	2002-11-13	ENSG00000221858	ENSG00000221858		"GPCR / Class A : Olfactory receptors"	15082	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily A, member 12 pseudogene"	OR2A12P			Standard	NM_001004135		Approved		uc011kty.2	Q8NGT7	OTTHUMG00000157996	ENST00000408949.2:c.172A>G	chr7.hg19:g.143792372A>G	ENSP00000386174:p.Met58Val	131.0	0.0		131.0	44.0	NM_001004135	Q6IF43	Missense_Mutation	SNP	ENST00000408949.2	hg19	CCDS43670.1	.	.	.	.	.	.	.	.	.	.	A	12.86	2.065236	0.36470	.	.	ENSG00000221858	ENST00000408949	T	0.09350	2.99	4.27	4.27	0.50696	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.26376	0.0644	M	0.92649	3.33	0.37891	D	0.930715	P	0.46706	0.883	P	0.45856	0.495	T	0.44159	-0.9346	9	0.87932	D	0	-32.7291	11.3678	0.49681	1.0:0.0:0.0:0.0	.	58	Q8NGT7	O2A12_HUMAN	V	58	ENSP00000386174:M58V	ENSP00000386174:M58V	M	+	1	0	OR2A12	143423305	1.000000	0.71417	0.997000	0.53966	0.040000	0.13550	5.914000	0.69964	1.788000	0.52465	0.413000	0.27773	ATG	.	.		0.458	OR2A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349969.1			G	143792372	A	G	143792372	3	3	262	1	0	0	0	0	1	0	0	0	10984	217	8	2	174	2	OR2A12	7	143792372	Missense_Mutation	SNP	A	TCGA-FV-A2QQ-01A-11D-A22F-10	40632496	143792372	15346291	54	38312										
PTPRN2	5799	hgsc.bcm.edu	37	chr7	157369433	157369433	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	agatagaagctcctcaccagGaagtcctcacaccagatgtg	9	12	2	3			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr7:157369433G>C	ENST00000389418.4	-	19	2664	c.2655C>G	c.(2653-2655)ttC>ttG	p.F885L	PTPRN2_ENST00000409483.1_Missense_Mutation_p.F847L|PTPRN2_ENST00000389413.3_Missense_Mutation_p.F856L|PTPRN2_ENST00000389416.4_Missense_Mutation_p.F868L|MIR153-2_ENST00000385225.1_RNA|PTPRN2_ENST00000404321.2_Missense_Mutation_p.F908L	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	885	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		TCCTCACCAGGAAGTCCTCAC	0.577																																					p.F885L		Atlas-SNP	.											.	PTPRN2	243	.	0			c.C2655G						.						75	57	63					7																	157369433		2203	4300	6503	SO:0001583	missense	5799	exon19			CACCAGGAAGTCC	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9677	protein-coding gene	gene with protein product	"IAR PTPRP"	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.2655C>G	chr7.hg19:g.157369433G>C	ENSP00000374069:p.Phe885Leu	40.0	0.0		41.0	9.0	NM_002847	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Missense_Mutation	SNP	ENST00000389418.4	hg19	CCDS5947.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.511035	0.85389	.	.	ENSG00000155093	ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321	T;T;T;T;T	0.14022	2.54;2.54;2.54;2.54;2.54	5.44	3.63	0.41609	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	D	0.000000	T	0.31857	0.0810	L	0.58969	1.84	0.52501	D	0.999955	D;D;D;D;D	0.89917	0.999;0.999;0.999;1.0;0.994	D;D;D;D;D	0.91635	0.971;0.974;0.956;0.999;0.947	T	0.00849	-1.1541	10	0.87932	D	0	.	11.8231	0.52250	0.2035:0.0:0.7965:0.0	.	908;847;856;868;885	Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932	.;.;.;.;PTPR2_HUMAN	L	847;856;868;885;908	ENSP00000387114:F847L;ENSP00000374064:F856L;ENSP00000374067:F868L;ENSP00000374069:F885L;ENSP00000385464:F908L	ENSP00000374064:F856L	F	-	3	2	PTPRN2	157062194	1.000000	0.71417	0.999000	0.59377	0.945000	0.59286	3.898000	0.56281	0.288000	0.22398	-0.813000	0.03139	TTC	.	.		0.577	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1			C	157369433	G	C	157369433	3	2	262	1	0	0	0	0	1	0	0	0	12823	1165	41	4	412	4	PTPRN2	7	157369433	Missense_Mutation	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10	13577061	157369433	1769230	55	38313										
CSMD1	64478	hgsc.bcm.edu	37	chr8	3063095	3063095	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	gtaattatgggggtagtttgGtgataaaactaccccttctg	11	6	1	1			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr8:3063095G>T	ENST00000520002.1	-	32	5473	c.4918C>A	c.(4918-4920)Cca>Aca	p.P1640T	CSMD1_ENST00000539096.1_Missense_Mutation_p.P1639T|CSMD1_ENST00000537824.1_Missense_Mutation_p.P1639T|CSMD1_ENST00000542608.1_Missense_Mutation_p.P1639T|CSMD1_ENST00000602723.1_Missense_Mutation_p.P1640T|CSMD1_ENST00000523387.1_5'UTR|CSMD1_ENST00000400186.3_Missense_Mutation_p.P1640T|CSMD1_ENST00000602557.1_Missense_Mutation_p.P1640T			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1640	CUB 10. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		GGGTAGTTTGGTGATAAAACT	0.428																																					p.P1639T		Atlas-SNP	.											.	CSMD1	1469	.	0			c.C4915A						.						68	66	67					8																	3063095		1858	4091	5949	SO:0001583	missense	64478	exon31			AGTTTGGTGATAA			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.4918C>A	chr8.hg19:g.3063095G>T	ENSP00000430733:p.Pro1640Thr	31.0	0.0		26.0	18.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.9|20.9	4.058554|4.058554	0.76074|0.76074	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096|ENST00000335551	T;T;T;T;T|.	0.68181|.	-0.31;-0.31;-0.31;-0.31;-0.31|.	5.28|5.28	5.28|5.28	0.74379|0.74379	CUB (5);|.	0.000000|.	0.64402|.	D|.	0.000001|.	D|D	0.88247|0.88247	0.6385|0.6385	H|H	0.95917|0.95917	3.74|3.74	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	0.999;1.0;1.0|.	D|D	0.91737|0.91737	0.5401|0.5401	10|5	0.51188|.	T|.	0.08|.	.|.	19.2736|19.2736	0.94021|0.94021	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1640;1640;1640|.	E5RIG2;Q96PZ7;Q96PZ7-4|.	.;CSMD1_HUMAN;.|.	T|N	1640;1640;1502;1639;1639;1639|1119	ENSP00000383047:P1640T;ENSP00000430733:P1640T;ENSP00000441462:P1639T;ENSP00000446243:P1639T;ENSP00000441675:P1639T|.	ENSP00000320445:P1502T|.	P|T	-|-	1|2	0|0	CSMD1|CSMD1	3050502|3050502	1.000000|1.000000	0.71417|0.71417	0.195000|0.195000	0.23364|0.23364	0.568000|0.568000	0.35870|0.35870	9.576000|9.576000	0.98192|0.98192	2.617000|2.617000	0.88574|0.88574	0.655000|0.655000	0.94253|0.94253	CCA|ACC	.	.		0.428	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		T	3063095	G	T	3063095	3	4	262	1	0	0	0	0	1	0	0	0	3946	1261	44	3	5939	3	CSMD1	8	3063095	Missense_Mutation	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10		3063095	143300927	56	38314										
CTSB	1508	hgsc.bcm.edu	37	chr8	11705274	11705274	+	Frame_Shift_Del	DEL	G	G	-													0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	tatctccctcccccgtgcatGggggccgggagccgttgacg							TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr8:11705274delG	ENST00000353047.6	-	7	843	c.590delC	c.(589-591)ccafs	p.P197fs	CTSB_ENST00000415599.2_3'UTR|RP11-589N15.2_ENST00000602711.1_RNA|CTSB_ENST00000533455.1_Frame_Shift_Del_p.P197fs|CTSB_ENST00000531089.1_Frame_Shift_Del_p.P197fs|CTSB_ENST00000345125.3_Frame_Shift_Del_p.P197fs|CTSB_ENST00000534510.1_Frame_Shift_Del_p.P197fs|CTSB_ENST00000530640.2_Frame_Shift_Del_p.P197fs|CTSB_ENST00000525076.1_5'Flank|CTSB_ENST00000453527.2_Frame_Shift_Del_p.P197fs|CTSB_ENST00000434271.1_Frame_Shift_Del_p.P197fs	NM_001908.3	NP_001899.1	P07858	CATB_HUMAN	cathepsin B	197					cellular response to thyroid hormone stimulus (GO:0097067)|collagen catabolic process (GO:0030574)|decidualization (GO:0046697)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of apoptotic process (GO:0042981)|regulation of catalytic activity (GO:0050790)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|perinuclear region of cytoplasm (GO:0048471)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|proteoglycan binding (GO:0043394)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(1)	16	all_epithelial(15;0.205)		STAD - Stomach adenocarcinoma(15;0.00546)	COAD - Colon adenocarcinoma(149;0.184)		CCCCGTGCATGGGGGCCGGGA	0.627																																					p.P197fs		Atlas-INDEL	.											.	CTSB	24	.	0			c.591delA						.						76	76	76					8																	11705274		2203	4300	6503	SO:0001589	frameshift_variant	1508	exon8			.	M14221	CCDS5986.1	8p23.1	2012-10-02			ENSG00000164733	ENSG00000164733	3.4.22.1	"Cathepsins"	2527	protein-coding gene	gene with protein product		116810				8112600, 3463996	Standard	XM_006716244		Approved		uc003wuq.3	P07858	OTTHUMG00000090799	ENST00000353047.6:c.590delC	chr8.hg19:g.11705274delG	ENSP00000345672:p.Pro197fs	60.0	0.0		51.0	15.0	NM_147782	B3KQR5|B3KRR5|Q503A6|Q96D87	Frame_Shift_Del	DEL	ENST00000353047.6	hg19	CCDS5986.1																																																																																			.	.		0.627	CTSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207586.3	NM_147780		-	11705274	G	-	11705274	7	5	262	1	0	1	0	1	0	0	0	0	4032	1348	47	0	445	0	CTSB	8	11705274	Frame_Shift_Del	DEL	G	TCGA-FV-A2QQ-01A-11D-A22F-10	8642179	11705274	134658748	57	38315										
CNGB3	54714	hgsc.bcm.edu	37	chr8	87645119	87645119	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	cccaataataacatctcagaTacctgtgaaaacagaagata	5	9	1	4			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr8:87645119T>G	ENST00000320005.5	-	11	1228	c.1181A>C	c.(1180-1182)tAt>tCt	p.Y394S		NM_019098.4	NP_061971.3	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	394					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(15)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	80						ACATCTCAGATACCTGTGAAA	0.299																																					p.Y394S		Atlas-SNP	.											.	CNGB3	176	.	0			c.A1181C						.						56	56	56					8																	87645119		2203	4299	6502	SO:0001583	missense	54714	exon11			CTCAGATACCTGT	AF228520	CCDS6244.1	8q21.3	2013-01-23	2003-06-25		ENSG00000170289	ENSG00000170289		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2153	protein-coding gene	gene with protein product		605080	"achromatopsia (rod monochromacy) 3", "achromatopsia (rod monochromacy) 1"	ACHM3, ACHM1, RMCH		10888875, 10958649, 16382102	Standard	NM_019098		Approved		uc003ydx.3	Q9NQW8	OTTHUMG00000163738	ENST00000320005.5:c.1181A>C	chr8.hg19:g.87645119T>G	ENSP00000316605:p.Tyr394Ser	172.0	0.0		243.0	77.0	NM_019098	C9JA51|Q9NRE9	Missense_Mutation	SNP	ENST00000320005.5	hg19	CCDS6244.1	.	.	.	.	.	.	.	.	.	.	T	18.81	3.703202	0.68501	.	.	ENSG00000170289	ENST00000320005	D	0.97941	-4.62	5.12	5.12	0.69794	.	0.069289	0.64402	D	0.000016	D	0.98720	0.9570	M	0.87971	2.92	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.70016	0.945;0.967	D	0.99795	1.1033	10	0.87932	D	0	.	15.1974	0.73104	0.0:0.0:0.0:1.0	.	394;394	Q9NQW8-2;Q9NQW8	.;CNGB3_HUMAN	S	394	ENSP00000316605:Y394S	ENSP00000316605:Y394S	Y	-	2	0	CNGB3	87714235	1.000000	0.71417	1.000000	0.80357	0.718000	0.41266	6.260000	0.72502	2.052000	0.61016	0.477000	0.44152	TAT	.	.		0.299	CNGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375107.1	NM_019098		G	87645119	T	G	87645119	3	3	262	1	0	0	0	0	1	0	0	0	3603	1406	49	5	1280	5	CNGB3	8	87645119	Missense_Mutation	SNP	T	TCGA-FV-A2QQ-01A-11D-A22F-10	75939845	87645119	58718903	58	38316										
RRM2B	50484	hgsc.bcm.edu	37	chr8	103237178	103237178	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	atctctgagtgaacattctcGatgagaatttgaaagccata	8	7	2	4			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr8:103237178G>T	ENST00000251810.3	-	4	633	c.390C>A	c.(388-390)atC>atA	p.I130I	RRM2B_ENST00000519962.1_Intron|RRM2B_ENST00000519317.1_Intron|RRM2B_ENST00000395912.2_Silent_p.I78I	NM_001172478.1|NM_015713.4	NP_001165949.1|NP_056528.2	Q7LG56	RIR2B_HUMAN	ribonucleotide reductase M2 B (TP53 inducible)	130					deoxyribonucleoside diphosphate metabolic process (GO:0009186)|deoxyribonucleoside triphosphate metabolic process (GO:0009200)|deoxyribonucleotide biosynthetic process (GO:0009263)|DNA repair (GO:0006281)|kidney development (GO:0001822)|mitochondrial DNA replication (GO:0006264)|negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator (GO:1902254)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|renal system process (GO:0003014)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor (GO:0004748)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	9	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000728)		Cladribine(DB00242)	GAACATTCTCGATGAGAATTT	0.388								Modulation of nucleotide pools																													p.I202I		Atlas-SNP	.											.	RRM2B	31	.	0			c.C606A						.						85	82	83					8																	103237178		2203	4300	6503	SO:0001819	synonymous_variant	50484	exon4			ATTCTCGATGAGA	AB036532	CCDS34932.1, CCDS55267.1	8q23.1	2014-09-17			ENSG00000048392	ENSG00000048392			17296	protein-coding gene	gene with protein product		604712				10716435, 10980602, 17486094	Standard	NM_015713		Approved	p53R2	uc022azl.1	Q7LG56	OTTHUMG00000164776	ENST00000251810.3:c.390C>A	chr8.hg19:g.103237178G>T		71.0	0.0		162.0	33.0	NM_001172477	B4E2N4|Q17R22|Q75PQ6|Q75PQ7|Q75PY8|Q75PY9|Q86YE3|Q9NPD6|Q9NTD8|Q9NUW3	Silent	SNP	ENST00000251810.3	hg19	CCDS34932.1																																																																																			.	.		0.388	RRM2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380191.3			T	103237178	G	T	103237178	2	4	262	1	0	0	0	0	0	0	0	1	13698	1048	37	1		1	RRM2B	8	103237178	Silent	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10	15592059	103237178	43126844	59	38317										
FAM84B	157638	hgsc.bcm.edu	37	chr8	127568717	127568717	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	gcccatcagtgtgccactgcCtctccgtcctcctcctcgga	8	19	2	0			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr8:127568717C>G	ENST00000304916.3	-	2	1373	c.918G>C	c.(916-918)gaG>gaC	p.E306D	RP11-89K10.1_ENST00000519880.1_RNA|RP11-103H7.5_ENST00000524320.1_RNA|RP11-89K10.1_ENST00000517773.1_RNA|FAM84B_ENST00000517458.1_5'Flank|RP11-89K10.1_ENST00000520512.1_RNA	NM_174911.4	NP_777571.1	Q96KN1	FA84B_HUMAN	family with sequence similarity 84, member B	306						cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				lung(2)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	5	Ovarian(5;9.43e-05)|Esophageal squamous(12;0.0012)|Hepatocellular(40;0.128)|Myeloproliferative disorder(2;0.135)		STAD - Stomach adenocarcinoma(47;0.000556)|Colorectal(2;0.0102)|Lung(2;0.0136)|READ - Rectum adenocarcinoma(2;0.0723)			GTGCCACTGCCTCTCCGTCCT	0.687																																					p.E306D		Atlas-SNP	.											.	FAM84B	19	.	0			c.G918C						.						11	11	11					8																	127568717		2190	4276	6466	SO:0001583	missense	157638	exon2			CACTGCCTCTCCG	AJ417849	CCDS6358.1	8q24.13	2006-02-09				ENSG00000168672			24166	protein-coding gene	gene with protein product	"breast cancer membrane-associated protein 101", "neurological/sensory 2"	609483				12477722	Standard	NM_174911		Approved	BCMP101, NSE2	uc003yrz.2	Q96KN1		ENST00000304916.3:c.918G>C	chr8.hg19:g.127568717C>G	ENSP00000302578:p.Glu306Asp	49.0	0.0		70.0	7.0	NM_174911		Missense_Mutation	SNP	ENST00000304916.3	hg19	CCDS6358.1	.	.	.	.	.	.	.	.	.	.	C	5.018	0.188932	0.09547	.	.	ENSG00000168672	ENST00000304916	T	0.44482	0.92	4.2	1.27	0.21489	.	1.206040	0.06305	N	0.701618	T	0.17023	0.0409	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.17684	-1.0361	10	0.42905	T	0.14	-1.678	2.9417	0.05833	0.1832:0.5381:0.1776:0.1011	.	306	Q96KN1	FA84B_HUMAN	D	306	ENSP00000302578:E306D	ENSP00000302578:E306D	E	-	3	2	FAM84B	127637899	0.001000	0.12720	0.001000	0.08648	0.408000	0.30992	-0.235000	0.09016	0.145000	0.18977	0.558000	0.71614	GAG	.	.		0.687	FAM84B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381487.1	NM_174911		G	127568717	C	G	127568717	3	3	262	1	0	0	0	0	1	0	0	0	5650	680	24	4	18	4	FAM84B	8	127568717	Missense_Mutation	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10	24331539	127568717	18795305	60	38318										
ADCY8	114	hgsc.bcm.edu	37	chr8	132051783	132051783	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	agcctatgccgtcgcccaggAgcccgtagccgaggcctgct	13	16	0	0			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr8:132051783A>C	ENST00000286355.5	-	1	2889	c.797T>G	c.(796-798)cTc>cGc	p.L266R	ADCY8_ENST00000377928.3_Missense_Mutation_p.L266R	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	266					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			GTCGCCCAGGAGCCCGTAGCC	0.667										HNSCC(32;0.087)																											p.L266R		Atlas-SNP	.											.	ADCY8	291	.	0			c.T797G						.						46	41	43					8																	132051783		2203	4299	6502	SO:0001583	missense	114	exon1			CCCAGGAGCCCGT	Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"Adenylate cyclases"	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.797T>G	chr8.hg19:g.132051783A>C	ENSP00000286355:p.Leu266Arg	53.0	0.0		95.0	20.0	NM_001115		Missense_Mutation	SNP	ENST00000286355.5	hg19	CCDS6363.1	.	.	.	.	.	.	.	.	.	.	A	14.15	2.448196	0.43429	.	.	ENSG00000155897	ENST00000286355;ENST00000377928	T;T	0.44482	0.92;0.92	5.46	5.46	0.80206	.	0.000000	0.64402	D	0.000003	T	0.48696	0.1514	L	0.54323	1.7	0.47778	D	0.99951	D;D	0.64830	0.994;0.984	P;P	0.52109	0.69;0.69	T	0.38845	-0.9642	10	0.23302	T	0.38	.	14.7078	0.69203	1.0:0.0:0.0:0.0	.	266;266	E7EVL1;P40145	.;ADCY8_HUMAN	R	266	ENSP00000286355:L266R;ENSP00000367161:L266R	ENSP00000286355:L266R	L	-	2	0	ADCY8	132120965	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	8.932000	0.92897	2.085000	0.62840	0.374000	0.22700	CTC	.	.		0.667	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			C	132051783	A	C	132051783	3	2	262	1	0	0	0	0	1	0	0	0	300	304	11	5	3030	5	ADCY8	8	132051783	Missense_Mutation	SNP	A	TCGA-FV-A2QQ-01A-11D-A22F-10	4483066	132051783	14312239	61	38319										
CA9	768	hgsc.bcm.edu	37	chr9	35674288	35674288	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	agagggctccctgaagttagAggatctacctactgttgagg	13	8	1	4			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr9:35674288A>C	ENST00000378357.4	+	1	436	c.332A>C	c.(331-333)gAg>gCg	p.E111A	RN7SL22P_ENST00000471800.2_RNA	NM_001216.2	NP_001207.2	Q16790	CAH9_HUMAN	carbonic anhydrase IX	111	Proteoglycan-like (PG).				bicarbonate transport (GO:0015701)|cellular response to hypoxia (GO:0071456)|morphogenesis of an epithelium (GO:0002009)|one-carbon metabolic process (GO:0006730)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to drug (GO:0042493)|response to testosterone (GO:0033574)|secretion (GO:0046903)|small molecule metabolic process (GO:0044281)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(3)|lung(5)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	17	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)		Benzthiazide(DB00562)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Zonisamide(DB00909)	CTGAAGTTAGAGGATCTACCT	0.502																																					p.E111A		Atlas-SNP	.											.	CA9	48	.	0			c.A332C						.						64	56	59					9																	35674288		2203	4300	6503	SO:0001583	missense	768	exon1			AGTTAGAGGATCT	X66839	CCDS6585.1	9p13.3	2012-08-21			ENSG00000107159	ENSG00000107159		"Carbonic anhydrases"	1383	protein-coding gene	gene with protein product	"carbonic dehydratase", "RCC-associated protein G250"	603179				8661007, 9787087	Standard	NM_001216		Approved	MN, CAIX	uc003zxo.4	Q16790	OTTHUMG00000021029	ENST00000378357.4:c.332A>C	chr9.hg19:g.35674288A>C	ENSP00000367608:p.Glu111Ala	68.0	0.0		67.0	19.0	NM_001216	Q5T4R1	Missense_Mutation	SNP	ENST00000378357.4	hg19	CCDS6585.1	.	.	.	.	.	.	.	.	.	.	A	33	5.211180	0.95069	.	.	ENSG00000107159	ENST00000378357;ENST00000544074	T	0.68765	-0.35	4.68	4.68	0.58851	.	2.002980	0.02927	N	0.138752	T	0.76835	0.4043	L	0.34521	1.04	0.40649	D	0.982014	D;D	0.67145	0.996;0.993	D;D	0.76071	0.987;0.984	T	0.63444	-0.6636	10	0.87932	D	0	.	10.7273	0.46077	1.0:0.0:0.0:0.0	.	111;111	F5H404;Q16790	.;CAH9_HUMAN	A	111	ENSP00000367608:E111A	ENSP00000367608:E111A	E	+	2	0	CA9	35664288	1.000000	0.71417	0.986000	0.45419	0.953000	0.61014	3.996000	0.57009	2.107000	0.64212	0.533000	0.62120	GAG	.	.		0.502	CA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055479.1	NM_001216		C	35674288	A	C	35674288	3	2	262	1	0	0	0	0	1	0	0	0	2526	304	11	5	334	5	CA9	9	35674288	Missense_Mutation	SNP	A	TCGA-FV-A2QQ-01A-11D-A22F-10		35674288	105539143	62	38320										
STXBP1	6812	hgsc.bcm.edu	37	chr9	130428513	130428513	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	gaccccagctcccctgtgctCcatgaattgacttttcaggc	8	15	1	2			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr9:130428513C>A	ENST00000373299.1	+	9	847	c.732C>A	c.(730-732)ctC>ctA	p.L244L	STXBP1_ENST00000373302.3_Silent_p.L244L	NM_001032221.3	NP_001027392.1	P61764	STXB1_HUMAN	syntaxin binding protein 1	244					axon target recognition (GO:0007412)|energy reserve metabolic process (GO:0006112)|glutamate secretion (GO:0014047)|long term synaptic depression (GO:0060292)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter secretion (GO:0007269)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|protein stabilization (GO:0050821)|protein transport (GO:0015031)|regulation of insulin secretion (GO:0050796)|regulation of SNARE complex assembly (GO:0035542)|regulation of synaptic vesicle fusion to presynaptic membrane (GO:0031630)|regulation of synaptic vesicle priming (GO:0010807)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|synaptic vesicle maturation (GO:0016188)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|protein complex (GO:0043234)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|SNARE binding (GO:0000149)|syntaxin binding (GO:0019905)|syntaxin-1 binding (GO:0017075)			breast(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(7)|skin(2)	23						CCCCTGTGCTCCATGAATTGA	0.507																																					p.L244L		Atlas-SNP	.											.	STXBP1	99	.	0			c.C732A						.						110	94	99					9																	130428513		2203	4300	6503	SO:0001819	synonymous_variant	6812	exon9			TGTGCTCCATGAA	AF004563	CCDS6874.1, CCDS35146.1	9q34.1	2008-07-21			ENSG00000136854	ENSG00000136854			11444	protein-coding gene	gene with protein product	"syntaxin-binding protein 1"	602926				9545644	Standard	NM_001032221		Approved	hUNC18, MUNC18-1, UNC18, rbSec1	uc004brk.2	P61764	OTTHUMG00000020713	ENST00000373299.1:c.732C>A	chr9.hg19:g.130428513C>A		53.0	0.0		54.0	17.0	NM_001032221	B1AM97|Q28208|Q62759|Q64320|Q96TG8	Silent	SNP	ENST00000373299.1	hg19	CCDS35146.1																																																																																			.	.		0.507	STXBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054229.1	NM_003165		A	130428513	C	A	130428513	2	1	262	1	0	0	0	0	0	0	0	1	15367	842	30	3		3	STXBP1	9	130428513	Silent	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10	94754225	130428513	10784918	63	38321										
SLC39A12	221074	hgsc.bcm.edu	37	chr10	18292223	18292223	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	ttccgtgtcagctgatccatGtgttcaagactggatcttca	9	10	4	2			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr10:18292223G>A	ENST00000377369.2	+	12	2156	c.1883G>A	c.(1882-1884)tGt>tAt	p.C628Y	SLC39A12_ENST00000377374.4_Missense_Mutation_p.C591Y|SLC39A12_ENST00000539911.1_Missense_Mutation_p.C494Y|SLC39A12_ENST00000377371.3_Missense_Mutation_p.C627Y|SLC39A12-AS1_ENST00000445287.1_RNA|SLC39A12-AS1_ENST00000439319.1_RNA	NM_001145195.1|NM_001282733.1|NM_001282734.1	NP_001138667.1|NP_001269662.1|NP_001269663.1	Q504Y0	S39AC_HUMAN	solute carrier family 39 (zinc transporter), member 12	628					regulation of microtubule polymerization (GO:0031113)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)|zinc ion transmembrane import (GO:0071578)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	zinc ion transmembrane transporter activity (GO:0005385)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(5)|lung(38)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	60						GCTGATCCATGTGTTCAAGAC	0.403																																					p.C628Y		Atlas-SNP	.											SLC39A12,NS,carcinoma,0,3	SLC39A12	181	.	0			c.G1883A						.						190	170	177					10																	18292223		2203	4300	6503	SO:0001583	missense	221074	exon12			ATCCATGTGTTCA		CCDS7124.1, CCDS44362.1, CCDS60493.1, CCDS60494.1	10p12.33	2013-05-22			ENSG00000148482	ENSG00000148482		"Solute carriers"	20860	protein-coding gene	gene with protein product		608734	"solute carrier family 39 (metal ion transporter), member 12"			12659941	Standard	NM_152725		Approved	FLJ30499	uc001ipo.2	Q504Y0	OTTHUMG00000017759	ENST00000377369.2:c.1883G>A	chr10.hg19:g.18292223G>A	ENSP00000366586:p.Cys628Tyr	123.0	0.0		163.0	65.0	NM_001145195	B7ZL35|C9JJL4|Q49AN8|Q4G0L3|Q5VWV8|Q5VWV9|Q6NZY5|Q96NN4	Missense_Mutation	SNP	ENST00000377369.2	hg19	CCDS44362.1	.	.	.	.	.	.	.	.	.	.	G	4.923	0.171439	0.09391	.	.	ENSG00000148482	ENST00000377369;ENST00000377374;ENST00000377371;ENST00000539911;ENST00000425219	T;T;T;T	0.46819	0.86;0.86;0.86;0.86	5.48	2.55	0.30701	.	0.564365	0.20942	N	0.082903	T	0.48786	0.1519	L	0.43152	1.355	0.09310	N	1	D;P;D	0.61080	0.98;0.829;0.989	P;P;P	0.56700	0.627;0.699;0.804	T	0.33854	-0.9852	10	0.56958	D	0.05	-0.9601	6.163	0.20373	0.2061:0.2502:0.5437:0.0	.	627;628;591	Q504Y0-4;Q504Y0;Q504Y0-3	.;S39AC_HUMAN;.	Y	628;591;627;494;548	ENSP00000366586:C628Y;ENSP00000366591:C591Y;ENSP00000366588:C627Y;ENSP00000440445:C494Y	ENSP00000366586:C628Y	C	+	2	0	SLC39A12	18332229	0.027000	0.19231	0.035000	0.18076	0.092000	0.18411	1.629000	0.37071	0.342000	0.23796	0.655000	0.94253	TGT	.	.		0.403	SLC39A12-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_152725		A	18292223	G	A	18292223	3	1	262	1	0	0	0	0	1	0	0	0	14630	1377	48	3	1925	3	SLC39A12	10	18292223	Missense_Mutation	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10		18292223	117242524	64	38322										
MYO3A	53904	hgsc.bcm.edu	37	chr10	26436361	26436361	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	agcatactgtatcaacaggtCctctataatgcaagtggatt	8	8	2	0			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr10:26436361C>A	ENST00000265944.5	+	23	2674	c.2508C>A	c.(2506-2508)gtC>gtA	p.V836V	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	836	Myosin motor.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V836V(1)		NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						ATCAACAGGTCCTCTATAATG	0.398																																					p.V836V		Atlas-SNP	.											MYO3A,NS,carcinoma,0,1	MYO3A	371	.	1	Substitution - coding silent(1)	lung(1)	c.C2508A						.						172	145	154					10																	26436361		2203	4300	6503	SO:0001819	synonymous_variant	53904	exon23			ACAGGTCCTCTAT	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.2508C>A	chr10.hg19:g.26436361C>A		92.0	0.0		106.0	14.0	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Silent	SNP	ENST00000265944.5	hg19	CCDS7148.1																																																																																			.	.		0.398	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		A	26436361	C	A	26436361	2	1	262	1	0	0	0	0	0	0	0	1	10085	842	30	3		3	MYO3A	10	26436361	Silent	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10	8144138	26436361	109098386	65	38323										
MYO3A	53904	hgsc.bcm.edu	37	chr10	26465727	26465727	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	actttatctgggtgtctcgcAccataagccaattaatagac	7	10	2	1			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr10:26465727A>G	ENST00000265944.5	+	31	4557	c.4391A>G	c.(4390-4392)cAc>cGc	p.H1464R	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	1464					ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						GGTGTCTCGCACCATAAGCCA	0.368																																					p.H1464R		Atlas-SNP	.											.	MYO3A	371	.	0			c.A4391G						.						94	89	91					10																	26465727		2203	4300	6503	SO:0001583	missense	53904	exon31			TCTCGCACCATAA	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.4391A>G	chr10.hg19:g.26465727A>G	ENSP00000265944:p.His1464Arg	102.0	0.0		85.0	21.0	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	hg19	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	A	4.844	0.156822	0.09236	.	.	ENSG00000095777	ENST00000265944	T	0.75704	-0.96	5.91	0.231	0.15377	.	0.659750	0.16573	N	0.208532	T	0.37544	0.1007	N	0.02011	-0.69	0.25573	N	0.986879	B	0.02656	0.0	B	0.01281	0.0	T	0.29610	-1.0006	10	0.07990	T	0.79	.	3.8862	0.09099	0.4889:0.2294:0.2066:0.0751	.	1464	Q8NEV4	MYO3A_HUMAN	R	1464	ENSP00000265944:H1464R	ENSP00000265944:H1464R	H	+	2	0	MYO3A	26505733	0.096000	0.21769	0.417000	0.26559	0.897000	0.52465	0.106000	0.15354	0.036000	0.15547	-0.219000	0.12488	CAC	.	.		0.368	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		G	26465727	A	G	26465727	3	3	262	1	0	0	0	0	1	0	0	0	10085	159	6	2	4505	2	MYO3A	10	26465727	Missense_Mutation	SNP	A	TCGA-FV-A2QQ-01A-11D-A22F-10	29366	26465727	109069020	66	38324										
ZNF488	118738	hgsc.bcm.edu	37	chr10	48371172	48371172	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	tttcaactcccaagcttttgGttggtgatttgtggaacttg	10	7	1	1			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr10:48371172G>A	ENST00000395702.2	+	2	867	c.640G>A	c.(640-642)Gtt>Att	p.V214I	ZNF488_ENST00000586537.1_Missense_Mutation_p.V107I|ZNF488_ENST00000494156.1_3'UTR			Q96MN9	ZN488_HUMAN	zinc finger protein 488	214					negative regulation of transcription, DNA-templated (GO:0045892)|oligodendrocyte development (GO:0014003)|positive regulation of oligodendrocyte differentiation (GO:0048714)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|ovary(2)	14						CAAGCTTTTGGTTGGTGATTT	0.552																																					p.V214I		Atlas-SNP	.											.	ZNF488	38	.	0			c.G640A						.						134	128	130					10																	48371172		2203	4300	6503	SO:0001583	missense	118738	exon2			CTTTTGGTTGGTG	AK056666	CCDS73120.1	10q11.22	2014-04-10			ENSG00000165388	ENSG00000265763		"Zinc fingers, C2H2-type"	23535	protein-coding gene	gene with protein product							Standard	NM_153034		Approved	FLJ32104	uc001jex.3	Q96MN9	OTTHUMG00000188322	ENST00000395702.2:c.640G>A	chr10.hg19:g.48371172G>A	ENSP00000379054:p.Val214Ile	57.0	0.0		47.0	13.0	NM_153034	Q05CE0	Missense_Mutation	SNP	ENST00000395702.2	hg19	CCDS7217.1	.	.	.	.	.	.	.	.	.	.	G	11.24	1.580886	0.28180	.	.	ENSG00000165388	ENST00000395702	T	0.24151	1.87	5.55	-0.402	0.12404	.	0.639568	0.15979	U	0.235386	T	0.15046	0.0363	L	0.40543	1.245	0.09310	N	1	B	0.12630	0.006	B	0.10450	0.005	T	0.20874	-1.0262	10	0.24483	T	0.36	.	2.8536	0.05565	0.3046:0.1136:0.466:0.1158	.	214	Q96MN9	ZN488_HUMAN	I	214	ENSP00000379054:V214I	ENSP00000379054:V214I	V	+	1	0	ZNF488	47991178	0.063000	0.20901	0.000000	0.03702	0.693000	0.40251	1.285000	0.33261	0.015000	0.14971	-0.291000	0.09656	GTT	.	.		0.552	ZNF488-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314632.1	NM_153034		A	48371172	G	A	48371172	3	1	262	1	0	0	0	0	1	0	0	0	17955	1261	44	3	642	3	ZNF488	10	48371172	Missense_Mutation	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10	21905445	48371172	87163575	67	38325										
DNA2	1763	hgsc.bcm.edu	37	chr10	70192040	70192040	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	aggatataaactgaggttcaCgaaagtcaataattaaatct	7	5	3	1	rs201999986		TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr10:70192040C>G	ENST00000358410.3	-	12	1846	c.1796G>C	c.(1795-1797)cGt>cCt	p.R599P	DNA2_ENST00000399179.2_Missense_Mutation_p.R599P|DNA2_ENST00000399180.2_Missense_Mutation_p.R685P	NM_001080449.2	NP_001073918.2	P51530	DNA2_HUMAN	DNA replication helicase/nuclease 2	599	Helicase activity. {ECO:0000250}.				ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|DNA replication, Okazaki fragment processing (GO:0033567)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|mitochondrial DNA repair (GO:0043504)|mitochondrial DNA replication (GO:0006264)|mitotic cell cycle (GO:0000278)|positive regulation of DNA replication (GO:0045740)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	mitochondrial nucleoid (GO:0042645)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|5'-flap endonuclease activity (GO:0017108)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|nuclease activity (GO:0004518)|single-stranded DNA-dependent ATPase activity (GO:0043142)|site-specific endodeoxyribonuclease activity, specific for altered base (GO:0016890)	p.R599H(1)|p.R685H(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(7)|prostate(1)	20						CTGAGGTTCACGAAAGTCAAT	0.343																																					p.R599P		Atlas-SNP	.											.	DNA2	76	.	2	Substitution - Missense(2)	lung(2)	c.G1796C						.						130	125	126					10																	70192040		1830	4082	5912	SO:0001583	missense	1763	exon12			GGTTCACGAAAGT	D42046	CCDS44415.1, CCDS44415.2	10q21.3-q22.1	2013-05-13	2013-05-13	2008-01-08	ENSG00000138346	ENSG00000138346			2939	protein-coding gene	gene with protein product		601810	"DNA2 DNA replication helicase 2-like (yeast)", "DNA replication helicase 2 homolog (yeast)"	DNA2L		8938459, 17032657, 23352259	Standard	NM_001080449		Approved	KIAA0083	uc031pvh.1	P51530	OTTHUMG00000018352	ENST00000358410.3:c.1796G>C	chr10.hg19:g.70192040C>G	ENSP00000351185:p.Arg599Pro	209.0	0.0		171.0	23.0	NM_001080449	Q2NKM1|Q5TC49|Q5TC50|Q6P455|Q6PI80|Q7Z6H9|Q8N346	Missense_Mutation	SNP	ENST00000358410.3	hg19		.	.	.	.	.	.	.	.	.	.	C	17.86	3.492094	0.64074	.	.	ENSG00000138346	ENST00000551118;ENST00000399180;ENST00000399179;ENST00000358410	D;T;D	0.91996	-2.95;0.55;-2.92	5.9	1.58	0.23477	.	0.347519	0.32624	N	0.005850	D	0.93380	0.7889	M	0.69823	2.125	0.24915	N	0.992015	P;D	0.58970	0.946;0.984	P;P	0.57911	0.619;0.829	D	0.87323	0.2319	10	0.54805	T	0.06	.	10.2132	0.43154	0.0:0.5826:0.0:0.4174	.	599;599	F8VR31;P51530	.;DNA2L_HUMAN	P	599;685;599;599	ENSP00000382133:R685P;ENSP00000382132:R599P;ENSP00000351185:R599P	ENSP00000351185:R599P	R	-	2	0	DNA2	69862046	0.002000	0.14202	0.750000	0.31169	0.992000	0.81027	0.144000	0.16135	0.010000	0.14839	0.558000	0.71614	CGT	.	.		0.343	DNA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048334.2			G	70192040	C	G	70192040	3	3	262	1	0	0	0	0	1	0	0	0	4598	536	19	4	1426	4	DNA2	10	70192040	Missense_Mutation	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10	21820868	70192040	65342707	68	38326										
VAX1	11023	hgsc.bcm.edu	37	chr10	118896162	118896163	+	Missense_Mutation	DNP	CC	CC	TT													0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	gatgatctctcggatggaccCcttggcatctggggaagggg					rs567659626		TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr10:118896162_118896163CC>TT	ENST00000369206.5	-	2	248_249	c.249_250GG>AA	c.(247-252)aaGGgg>aaAAgg	p.G84R	VAX1_ENST00000277905.2_Missense_Mutation_p.G84R	NM_001112704.1	NP_001106175.1	Q5SQQ9	VAX1_HUMAN	ventral anterior homeobox 1	84					axon guidance (GO:0007411)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|palate development (GO:0060021)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(1)|lung(8)|ovary(2)	12				all cancers(201;0.0108)		CGGATGGACCCCTTGGCATCTG	0.644																																					p.G84R|p.K83K		Atlas-SNP	.											.	VAX1	50	.	0			c.G250A|c.G249A						.																																			SO:0001583	missense	11023	exon2			TGGACCCCTTGGC|GGACCCCTTGGCA	AK127095	CCDS7597.1, CCDS44483.1	10q26.11	2011-06-20			ENSG00000148704	ENSG00000148704		"Homeoboxes / ANTP class : NKL subclass"	12660	protein-coding gene	gene with protein product		604294				9636075, 10485894	Standard	NM_199131		Approved		uc009xyx.3	Q5SQQ9	OTTHUMG00000019117	ENST00000369206.5:c.249_250delinsTT	chr10.hg19:g.118896162_118896163delinsTT	ENSP00000358207:p.Gly84Arg	41.0|42.0	0.0		50.0	15.0	NM_001112704	B1AVW5|Q6ZSX0	Missense_Mutation|Silent	SNP	ENST00000369206.5	hg19	CCDS44483.1																																																																																			.	.		0.644	VAX1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050559.3	XM_301242		TT	118896163	CC	TT	118896162	3	4	262	1	0	0	0	0	1	0	0	0	17149	623	22	3	902	3	VAX1	10	118896162	Missense_Mutation	DNP	CC	TCGA-FV-A2QQ-01A-11D-A22F-10	48704122	118896162	16638585	69	38327										
CD81	975	hgsc.bcm.edu	37	chr11	2417938	2417938	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	gctgccatcgtggtcgctgtGatcatggtgagcgggcgggg	19	9	1	2			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr11:2417938G>T	ENST00000263645.5	+	7	898	c.642G>T	c.(640-642)gtG>gtT	p.V214V	CD81_ENST00000381036.3_Silent_p.V252V|CD81_ENST00000492627.1_Silent_p.V143V|CD81_ENST00000526072.1_Silent_p.V143V|CD81_ENST00000481687.1_Silent_p.V220V	NM_004356.3	NP_004347.1	P60033	CD81_HUMAN	CD81 molecule	214					activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of 1-phosphatidylinositol 4-kinase activity (GO:0043128)|positive regulation of cell proliferation (GO:0008284)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein localization (GO:0008104)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of immune response (GO:0050776)|viral entry into host cell (GO:0046718)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	MHC class II protein complex binding (GO:0023026)			endometrium(1)|lung(3)|skin(1)	5		all_epithelial(84;0.000161)|Breast(177;0.000962)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|all_neural(188;0.0137)|Lung NSC(207;0.209)		BRCA - Breast invasive adenocarcinoma(625;0.000338)|LUSC - Lung squamous cell carcinoma(625;0.191)		TGGTCGCTGTGATCATGGTGA	0.662																																					p.V214V		Atlas-SNP	.											.	CD81	11	.	0			c.G642T						.						69	68	68					11																	2417938		2202	4299	6501	SO:0001819	synonymous_variant	975	exon7			CGCTGTGATCATG		CCDS7734.1, CCDS73240.1	11p15.5	2014-09-17	2006-03-28		ENSG00000110651	ENSG00000110651		"CD molecules", "Tetraspanins"	1701	protein-coding gene	gene with protein product		186845	"CD81 antigen (target of antiproliferative antibody 1)"	TAPA1		1650385	Standard	XM_005253260		Approved	TAPA-1, TSPAN28	uc001lwf.1	P60033	OTTHUMG00000009892	ENST00000263645.5:c.642G>T	chr11.hg19:g.2417938G>T		47.0	0.0		38.0	4.0	NM_004356	P18582|Q5U0J6	Silent	SNP	ENST00000263645.5	hg19	CCDS7734.1	.	.	.	.	.	.	.	.	.	.	G	9.401	1.078002	0.20227	.	.	ENSG00000110651	ENST00000464784	.	.	.	3.39	1.29	0.21616	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.0626	0.19846	0.0:0.5072:0.3267:0.1661	.	.	.	.	L	199	.	.	X	+	2	2	CD81	2374514	0.433000	0.25562	0.999000	0.59377	0.891000	0.51852	-0.655000	0.05348	0.780000	0.33566	0.462000	0.41574	TGA	.	.		0.662	CD81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027357.4	NM_004356		T	2417938	G	T	2417938	2	4	262	1	0	0	0	0	0	0	0	1	3041	1277	45	3		3	CD81	11	2417938	Silent	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10		2417938	132588578	70	38328										
KCNE3	10008	hgsc.bcm.edu	37	chr11	74168404	74168404	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	gaggctgcccacagttacagCaaatagaaacatgacaaaga	9	9	0	3			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr11:74168404C>G	ENST00000310128.4	-	3	624	c.205G>C	c.(205-207)Gct>Cct	p.A69P	RP11-702H23.4_ENST00000533008.1_RNA|RP11-702H23.6_ENST00000530510.1_RNA|KCNE3_ENST00000525550.1_Missense_Mutation_p.A69P	NM_005472.4	NP_005463.1	Q9Y6H6	KCNE3_HUMAN	potassium voltage-gated channel, Isk-related family, member 3	69					regulation of potassium ion transport (GO:0043266)	integral component of membrane (GO:0016021)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)			cervix(1)|large_intestine(1)|lung(1)|ovary(1)	4	Breast(11;2.86e-06)					ACAGTTACAGCAAATAGAAAC	0.522																																					p.A69P		Atlas-SNP	.											.	KCNE3	7	.	0			c.G205C						.						74	65	68					11																	74168404		2200	4293	6493	SO:0001583	missense	10008	exon3			TTACAGCAAATAG	AF076531	CCDS8232.1	11q13.4	2014-09-17				ENSG00000175538		"Potassium channels"	6243	protein-coding gene	gene with protein product		604433				10219239	Standard	NM_005472		Approved	MiRP2, HOKPP	uc001ovc.3	Q9Y6H6		ENST00000310128.4:c.205G>C	chr11.hg19:g.74168404C>G	ENSP00000310557:p.Ala69Pro	105.0	0.0		98.0	18.0	NM_005472		Missense_Mutation	SNP	ENST00000310128.4	hg19	CCDS8232.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.669970	0.88348	.	.	ENSG00000175538	ENST00000310128;ENST00000525550;ENST00000532569	D;D;D	0.92446	-3.04;-3.04;-3.04	5.33	5.33	0.75918	.	0.000000	0.64402	D	0.000001	D	0.95245	0.8458	M	0.62723	1.935	0.53005	D	0.999963	D	0.89917	1.0	D	0.91635	0.999	D	0.95282	0.8387	10	0.72032	D	0.01	-17.7987	16.5607	0.84565	0.0:1.0:0.0:0.0	.	69	Q9Y6H6	KCNE3_HUMAN	P	69	ENSP00000310557:A69P;ENSP00000433633:A69P;ENSP00000431739:A69P	ENSP00000310557:A69P	A	-	1	0	KCNE3	73846052	1.000000	0.71417	0.998000	0.56505	0.914000	0.54420	4.879000	0.63100	2.771000	0.95319	0.561000	0.74099	GCT	.	.		0.522	KCNE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385531.1	NM_005472		G	74168404	C	G	74168404	3	3	262	1	0	0	0	0	1	0	0	0	8033	710	25	4	110	4	KCNE3	11	74168404	Missense_Mutation	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10	71750466	74168404	60838112	71	38329										
PGR	5241	hgsc.bcm.edu	37	chr11	100999292	100999292	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	ccggagctgtctccaaccttGcacccggaccggctcatgag	11	16	2	1			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr11:100999292G>C	ENST00000325455.5	-	1	1963	c.510C>G	c.(508-510)tgC>tgG	p.C170W	PGR_ENST00000534013.1_Intron|PGR_ENST00000263463.5_Missense_Mutation_p.C170W	NM_000926.4|NM_001202474.1|NM_001271162.1	NP_000917.3|NP_001189403.1|NP_001258091.1	P06401	PRGR_HUMAN	progesterone receptor	170	Modulating, Pro-Rich.				cell-cell signaling (GO:0007267)|epithelial cell maturation (GO:0002070)|gene expression (GO:0010467)|negative regulation of gene expression (GO:0010629)|ovulation from ovarian follicle (GO:0001542)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone receptor signaling pathway (GO:0050847)|regulation of epithelial cell proliferation (GO:0050678)|signal transduction (GO:0007165)|tertiary branching involved in mammary gland duct morphogenesis (GO:0060748)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mitochondrial outer membrane (GO:0005741)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|liver(1)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	36		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Allylestrenol(DB01431)|Danazol(DB01406)|Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluticasone Propionate(DB00588)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Megestrol acetate(DB00351)|Mifepristone(DB00834)|Norelgestromin(DB06713)|Norethindrone(DB00717)|Norgestimate(DB00957)|Progesterone(DB00396)|Spironolactone(DB00421)	CTCCAACCTTGCACCCGGACC	0.692																																					p.C170W	Pancreas(124;2271 2354 21954 22882)	Atlas-SNP	.											.	PGR	115	.	0			c.C510G						.						7	8	8					11																	100999292		2155	4253	6408	SO:0001583	missense	5241	exon1			AACCTTGCACCCG	M15716	CCDS8310.1, CCDS59229.1	11q22-q23	2013-01-16			ENSG00000082175	ENSG00000082175		"Nuclear hormone receptors"	8910	protein-coding gene	gene with protein product		607311					Standard	NM_000926		Approved	PR, NR3C3	uc001pgh.2	P06401	OTTHUMG00000167531	ENST00000325455.5:c.510C>G	chr11.hg19:g.100999292G>C	ENSP00000325120:p.Cys170Trp	15.0	0.0		13.0	5.0	NM_000926	A7LQ08|A7X8B0|B4E3T0|Q8TDS3|Q9UPF7	Missense_Mutation	SNP	ENST00000325455.5	hg19	CCDS8310.1	.	.	.	.	.	.	.	.	.	.	G	10.02	1.235275	0.22626	.	.	ENSG00000082175	ENST00000325455;ENST00000263463;ENST00000537623	T;T	0.06371	3.31;3.31	4.35	4.35	0.52113	.	2.200960	0.02042	N	0.049354	T	0.07369	0.0186	N	0.08118	0	0.29907	N	0.823906	B;B	0.25169	0.119;0.119	B;B	0.34452	0.183;0.183	T	0.31392	-0.9945	10	0.72032	D	0.01	.	12.3745	0.55273	0.0:0.0:1.0:0.0	.	170;170	Q8TDS3;P06401	.;PRGR_HUMAN	W	170	ENSP00000325120:C170W;ENSP00000263463:C170W	ENSP00000263463:C170W	C	-	3	2	PGR	100504502	0.911000	0.30947	0.726000	0.30738	0.282000	0.26991	2.091000	0.41691	1.964000	0.57103	0.462000	0.41574	TGC	.	.		0.692	PGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394934.1			C	100999292	G	C	100999292	3	2	262	1	0	0	0	0	1	0	0	0	11814	1311	46	4	2323	4	PGR	11	100999292	Missense_Mutation	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10	26830888	100999292	34007224	72	38330										
CARD18	59082	hgsc.bcm.edu	37	chr11	105009742	105009742	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	ctaataggcaatccagcaagGcatttattgtgcctgcaccc	8	12	0	0			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr11:105009742G>T	ENST00000530950.1	-	2	70	c.71C>A	c.(70-72)gCc>gAc	p.A24D	CARD18_ENST00000532895.1_5'UTR|CARD18_ENST00000526823.1_5'UTR	NM_021571.3	NP_067546.1	P57730	CAR18_HUMAN	caspase recruitment domain family, member 18	24	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				inflammatory response (GO:0006954)|regulation of apoptotic process (GO:0042981)		cysteine-type endopeptidase inhibitor activity (GO:0004869)	p.A24>?(1)		central_nervous_system(1)|ovary(1)	2						ATCCAGCAAGGCATTTATTGT	0.398																																					p.A24D		Atlas-SNP	.											.,1	CARD18	18	.	1	Complex(1)	large_intestine(1)	c.C71A						.						146	132	136					11																	105009742		1892	4125	6017	SO:0001583	missense	59082	exon2			AGCAAGGCATTTA	AY358231	CCDS53705.1	11q22.3	2008-09-02				ENSG00000255501			28861	protein-coding gene	gene with protein product		605354				11051551	Standard	NM_021571		Approved	UNQ5804, ICEBERG, pseudo-ICE	uc021qpy.1	P57730		ENST00000530950.1:c.71C>A	chr11.hg19:g.105009742G>T	ENSP00000436691:p.Ala24Asp	118.0	1.0		126.0	59.0	NM_021571	A2RRF8	Missense_Mutation	SNP	ENST00000530950.1	hg19	CCDS53705.1	.	.	.	.	.	.	.	.	.	.	.	10.52	1.373714	0.24857	.	.	ENSG00000255501	ENST00000530950	T	0.19669	2.13	2.49	-4.25	0.03766	DEATH-like (2);Caspase Recruitment (3);	0.474595	0.21820	U	0.068635	T	0.19046	0.0457	.	.	.	0.09310	N	0.999999	P	0.35656	0.514	B	0.43082	0.407	T	0.17930	-1.0353	9	0.62326	D	0.03	.	7.8111	0.29232	0.1279:0.4337:0.4384:0.0	.	24	P57730	CAR18_HUMAN	D	24	ENSP00000436691:A24D	ENSP00000436691:A24D	A	-	2	0	CARD18	104514952	0.000000	0.05858	0.001000	0.08648	0.199000	0.23934	-2.733000	0.00803	-1.037000	0.03283	-0.267000	0.10333	GCC	.	.		0.398	CARD18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388183.2	NM_021571		T	105009742	G	T	105009742	3	4	262	1	0	0	0	0	1	0	0	0	2651	1203	42	3	205	3	CARD18	11	105009742	Missense_Mutation	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10	4010450	105009742	29996774	73	38331										
DDX10	1662	hgsc.bcm.edu	37	chr11	108712068	108712068	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	cagcagtggccacaaatgcaGaaatctgccatcaaggatgc	10	11	2	1			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr11:108712068G>T	ENST00000322536.3	+	15	2241	c.2112G>T	c.(2110-2112)caG>caT	p.Q704H	DDX10_ENST00000526794.1_Missense_Mutation_p.Q704H	NM_004398.2	NP_004389.2	Q13206	DDX10_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10	704					metabolic process (GO:0008152)		ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)	p.Q704H(1)		breast(2)|endometrium(5)|kidney(2)|large_intestine(4)|lung(11)|pancreas(1)|prostate(2)	27		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)		CACAAATGCAGAAATCTGCCA	0.418			T	NUP98	AML*																																p.Q704H		Atlas-SNP	.		Dom	yes		11	11q22-q23	1662	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10		L	DDX10,NS,carcinoma,0,1	DDX10	70	.	1	Substitution - Missense(1)	lung(1)	c.G2112T						.						80	76	77					11																	108712068		2201	4298	6499	SO:0001583	missense	1662	exon15			AATGCAGAAATCT	U28042	CCDS8342.1	11q22-q23	2005-10-11	2003-06-13		ENSG00000178105	ENSG00000178105		"DEAD-boxes"	2735	protein-coding gene	gene with protein product		601235	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 10 (RNA helicase)"			8660968	Standard	NM_004398		Approved	HRH-J8	uc001pkm.3	Q13206	OTTHUMG00000166540	ENST00000322536.3:c.2112G>T	chr11.hg19:g.108712068G>T	ENSP00000314348:p.Gln704His	217.0	0.0		230.0	85.0	NM_004398	B2RCQ3|Q5BJD8	Missense_Mutation	SNP	ENST00000322536.3	hg19	CCDS8342.1	.	.	.	.	.	.	.	.	.	.	G	16.03	3.006128	0.54361	.	.	ENSG00000178105	ENST00000322536;ENST00000456020;ENST00000526794	T;T	0.45276	0.9;0.92	5.11	5.11	0.69529	.	0.000000	0.64402	D	0.000001	T	0.59702	0.2213	L	0.61218	1.895	0.48571	D	0.999675	D;D	0.89917	1.0;0.998	D;D	0.83275	0.996;0.936	T	0.61436	-0.7063	10	0.66056	D	0.02	-12.9617	11.5624	0.50785	0.0856:0.0:0.9144:0.0	.	704;704	Q13206;E9PIF2	DDX10_HUMAN;.	H	704;610;704	ENSP00000314348:Q704H;ENSP00000432032:Q704H	ENSP00000314348:Q704H	Q	+	3	2	DDX10	108217278	1.000000	0.71417	0.999000	0.59377	0.588000	0.36517	1.435000	0.34969	2.536000	0.85505	0.650000	0.86243	CAG	.	.		0.418	DDX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390343.1	NM_004398		T	108712068	G	T	108712068	3	4	262	1	0	0	0	0	1	0	0	0	4344	933	33	3	2170	3	DDX10	11	108712068	Missense_Mutation	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10	3702326	108712068	26294448	74	38332										
TMPRSS13	84000	hgsc.bcm.edu	37	chr11	117784524	117784524	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	agctgctggcaggtcttctcTgagtaggagtcattccagtt	12	9	3	1			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr11:117784524T>C	ENST00000430170.2	-	5	864	c.777A>G	c.(775-777)tcA>tcG	p.S259S	TMPRSS13_ENST00000528626.1_Silent_p.S224S|TMPRSS13_ENST00000526090.1_Silent_p.S259S|TMPRSS13_ENST00000524993.1_Silent_p.S259S|TMPRSS13_ENST00000445164.2_Silent_p.S259S	NM_001244995.1	NP_001231924.1	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	259	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.					blood microparticle (GO:0072562)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|pancreas(1)|prostate(1)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.00106)		AGGTCTTCTCTGAGTAGGAGT	0.537																																					p.S259S		Atlas-SNP	.											.	TMPRSS13	75	.	0			c.A777G						.						74	77	76					11																	117784524		1892	4110	6002	SO:0001819	synonymous_variant	84000	exon5			CTTCTCTGAGTAG	AB048796	CCDS41721.1, CCDS55788.1, CCDS55789.1, CCDS58185.1	11q23	2010-04-13	2005-03-11	2005-03-12	ENSG00000137747	ENSG00000137747		"Serine peptidases / Transmembrane"	29808	protein-coding gene	gene with protein product		610050	"transmembrane protease, serine 11"	TMPRSS11		11267681	Standard	NM_001077263		Approved	MSPL	uc001prs.2	Q9BYE2	OTTHUMG00000166992	ENST00000430170.2:c.777A>G	chr11.hg19:g.117784524T>C		42.0	0.0		60.0	12.0	NM_001206790	B4DTM9|E9PIJ5|F8WAJ3|Q86YM4|Q96JY8|Q9BYE1	Silent	SNP	ENST00000430170.2	hg19	CCDS58185.1																																																																																			.	.		0.537	TMPRSS13-006	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000392318.1	NM_032046		C	117784524	T	C	117784524	2	2	262	1	0	0	0	0	0	0	0	1	16260	1567	55	2		2	TMPRSS13	11	117784524	Silent	SNP	T	TCGA-FV-A2QQ-01A-11D-A22F-10	9072456	117784524	17221992	75	38333										
ATN1	1822	hgsc.bcm.edu	37	chr12	7047886	7047886	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	gggctcctgggttacaatgtCccggccctgtacagcagtga	13	12	0	1			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr12:7047886C>T	ENST00000356654.4	+	7	2997	c.2760C>T	c.(2758-2760)gtC>gtT	p.V920V	ATN1_ENST00000396684.2_Silent_p.V920V	NM_001007026.1	NP_001007027.1	P54259	ATN1_HUMAN	atrophin 1	920					cell migration (GO:0016477)|central nervous system development (GO:0007417)|maintenance of cell polarity (GO:0030011)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron apoptotic process (GO:0051402)|toxin metabolic process (GO:0009404)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	40						GTTACAATGTCCCGGCCCTGT	0.622																																					p.V920V		Atlas-SNP	.											.	ATN1	95	.	0			c.C2760T						.						64	73	70					12																	7047886		2203	4300	6503	SO:0001819	synonymous_variant	1822	exon7			CAATGTCCCGGCC	U23851	CCDS31734.1	12p	2007-08-01	2005-03-15	2005-03-17		ENSG00000111676			3033	protein-coding gene	gene with protein product		607462	"dentatorubral-pallidoluysian atrophy (atrophin-1)"	D12S755E, DRPLA		8136826	Standard	NM_001940		Approved	B37	uc001qrw.1	P54259		ENST00000356654.4:c.2760C>T	chr12.hg19:g.7047886C>T		45.0	0.0		43.0	14.0	NM_001007026	Q99495|Q99621|Q9UEK7	Silent	SNP	ENST00000356654.4	hg19	CCDS31734.1																																																																																			.	.		0.622	ATN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401948.2	NM_001940		T	7047886	C	T	7047886	2	4	262	1	0	0	0	0	0	0	0	1	1111	842	30	3		3	ATN1	12	7047886	Silent	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10		7047886	126804009	76	38334										
CLEC9A	283420	hgsc.bcm.edu	37	chr12	10205339	10205339	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	gtgggatagcccagcaccagAcacttaccagaaatgtctgt	10	11	1	2			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr12:10205339A>T	ENST00000355819.1	+	4	666	c.53A>T	c.(52-54)gAc>gTc	p.D18V	CLEC9A_ENST00000544751.1_3'UTR	NM_207345.2	NP_997228.1	Q6UXN8	CLC9A_HUMAN	C-type lectin domain family 9, member A	18					positive regulation of cytokine secretion (GO:0050715)|receptor-mediated endocytosis (GO:0006898)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|urinary_tract(1)	22						CCAGCACCAGACACTTACCAG	0.413																																					p.D18V		Atlas-SNP	.											.	CLEC9A	41	.	0			c.A53T						.						115	107	110					12																	10205339		2203	4300	6503	SO:0001583	missense	283420	exon4			CACCAGACACTTA		CCDS8611.1	12p13.31	2010-04-27				ENSG00000197992		"C-type lectin domain containing"	26705	protein-coding gene	gene with protein product		612252					Standard	NM_207345		Approved	UNQ9341, HEEE9341	uc001qxa.3	Q6UXN8		ENST00000355819.1:c.53A>T	chr12.hg19:g.10205339A>T	ENSP00000348074:p.Asp18Val	83.0	0.0		88.0	23.0	NM_207345	B0ZBM2	Missense_Mutation	SNP	ENST00000355819.1	hg19	CCDS8611.1	.	.	.	.	.	.	.	.	.	.	A	3.602	-0.081293	0.07141	.	.	ENSG00000197992	ENST00000355819	T	0.01422	4.91	4.2	1.87	0.25490	.	0.676729	0.12890	N	0.430656	T	0.00906	0.0030	N	0.08118	0	0.09310	N	1	B	0.12630	0.006	B	0.12837	0.008	T	0.48822	-0.9001	10	0.30854	T	0.27	.	5.7809	0.18306	0.7871:0.0:0.2129:0.0	.	18	Q6UXN8	CLC9A_HUMAN	V	18	ENSP00000348074:D18V	ENSP00000348074:D18V	D	+	2	0	CLEC9A	10096606	0.000000	0.05858	0.004000	0.12327	0.052000	0.14988	0.830000	0.27462	0.418000	0.25898	0.533000	0.62120	GAC	.	.		0.413	CLEC9A-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000399564.1	NM_207345		T	10205339	A	T	10205339	3	4	262	1	0	0	0	0	1	0	0	0	3524	275	10	4	55	4	CLEC9A	12	10205339	Missense_Mutation	SNP	A	TCGA-FV-A2QQ-01A-11D-A22F-10	3157453	10205339	123646556	77	38335										
KLRC2	3823	hgsc.bcm.edu	37	chr12	10587104	10587104	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	cctttctgcgttcttgtattCggggaaaaattgttctgctc	9	9	3	0			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr12:10587104C>T	ENST00000539033.1	-	3	326	c.312G>A	c.(310-312)ccG>ccA	p.P104P	KLRC2_ENST00000536833.2_Silent_p.P45P|KLRC2_ENST00000381902.2_Silent_p.P104P|KLRC2_ENST00000381901.1_Intron																							TTCTTGTATTCGGGGAAAAAT	0.284																																					p.P104P		Atlas-SNP	.											.	KLRC2	29	.	0			c.G312A						.						79	90	86					12																	10587104		2203	4294	6497	SO:0001819	synonymous_variant	3822	exon3			TGTATTCGGGGAA																												ENST00000539033.1:c.312G>A	chr12.hg19:g.10587104C>T		562.0	0.0		590.0	104.0	NM_002260		Silent	SNP	ENST00000539033.1	hg19																																																																																				.	.		0.284	NKG2-E-001	KNOWN	basic|appris_principal|readthrough_transcript	protein_coding	protein_coding	OTTHUMT00000400274.1			T	10587104	C	T	10587104	2	4	262	1	0	0	0	0	0	0	0	1	8425	871	31	1		1	KLRC2	12	10587104	Silent	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10	381765	10587104	123264791	78	38336										
TMEM106C	79022	hgsc.bcm.edu	37	chr12	48359775	48359775	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	actcccttgtaattctcaccAtcatggtaagccttagggtt	7	11	2	0			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr12:48359775A>G	ENST00000429772.2	+	4	519	c.406A>G	c.(406-408)Atc>Gtc	p.I136V	TMEM106C_ENST00000552561.1_Missense_Mutation_p.I136V|TMEM106C_ENST00000256686.6_Missense_Mutation_p.I136V|TMEM106C_ENST00000449758.2_Missense_Mutation_p.I136V|TMEM106C_ENST00000549288.1_Intron|TMEM106C_ENST00000550552.1_Missense_Mutation_p.I136V|TMEM106C_ENST00000552546.1_Missense_Mutation_p.I65V	NM_001143842.1	NP_001137314.1	Q9BVX2	T106C_HUMAN	transmembrane protein 106C	136						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|skin(3)|upper_aerodigestive_tract(1)	14		Acute lymphoblastic leukemia(13;0.11)		GBM - Glioblastoma multiforme(48;0.241)		AATTCTCACCATCATGGTAAG	0.483																																					p.I136V		Atlas-SNP	.											.	TMEM106C	24	.	0			c.A406G						.						172	155	161					12																	48359775		2203	4300	6503	SO:0001583	missense	79022	exon4			CTCACCATCATGG	BC000854	CCDS8758.1, CCDS44867.1	12q13.1	2005-12-19				ENSG00000134291			28775	protein-coding gene	gene with protein product							Standard	NM_024056		Approved	MGC5576	uc001rqr.3	Q9BVX2	OTTHUMG00000169892	ENST00000429772.2:c.406A>G	chr12.hg19:g.48359775A>G	ENSP00000400471:p.Ile136Val	127.0	0.0		145.0	40.0	NM_001143843	B2R998|B7Z5M4|Q3B761	Missense_Mutation	SNP	ENST00000429772.2	hg19	CCDS8758.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	6.506|6.506	0.461633|0.461633	0.12342|0.12342	.|.	.|.	ENSG00000134291|ENSG00000134291	ENST00000547682|ENST00000256686;ENST00000552561;ENST00000552546;ENST00000550552;ENST00000429772;ENST00000449758;ENST00000548640	.|T;T;T;T;T;T;T	.|0.22945	.|1.93;1.93;1.93;1.93;1.93;1.93;1.93	4.68|4.68	2.3|2.3	0.28687|0.28687	.|.	.|0.105308	.|0.64402	.|N	.|0.000006	T|T	0.14098|0.14098	0.0341|0.0341	N|N	0.21545|0.21545	0.675|0.675	0.32497|0.32497	N|N	0.539331|0.539331	.|B;B	.|0.10296	.|0.003;0.002	.|B;B	.|0.14578	.|0.011;0.006	T|T	0.14144|0.14144	-1.0483|-1.0483	5|10	.|0.25106	.|T	.|0.35	-0.167|-0.167	6.5115|6.5115	0.22224|0.22224	0.7563:0.1575:0.0862:0.0|0.7563:0.1575:0.0862:0.0	.|.	.|136;136	.|Q9BVX2;Q9BVX2-2	.|T106C_HUMAN;.	R|V	22|136;136;65;136;136;136;65	.|ENSP00000256686:I136V;ENSP00000446657:I136V;ENSP00000448268:I65V;ENSP00000449737:I136V;ENSP00000400471:I136V;ENSP00000402705:I136V;ENSP00000447254:I65V	.|ENSP00000256686:I136V	H|I	+|+	2|1	0|0	TMEM106C|TMEM106C	46646042|46646042	1.000000|1.000000	0.71417|0.71417	0.882000|0.882000	0.34594|0.34594	0.037000|0.037000	0.13140|0.13140	3.535000|3.535000	0.53575|0.53575	0.518000|0.518000	0.28383|0.28383	0.533000|0.533000	0.62120|0.62120	CAT|ATC	.	.		0.483	TMEM106C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406452.1	NM_024056		G	48359775	A	G	48359775	3	3	262	1	0	0	0	0	1	0	0	0	16037	217	8	2	416	2	TMEM106C	12	48359775	Missense_Mutation	SNP	A	TCGA-FV-A2QQ-01A-11D-A22F-10	37772671	48359775	85492120	79	38337										
TROAP	10024	hgsc.bcm.edu	37	chr12	49724529	49724529	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	ggggcagtctggacccccagGgccctgccctagggtagagc	16	14	1	1			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr12:49724529G>A	ENST00000257909.3	+	13	1977	c.1901G>A	c.(1900-1902)gGg>gAg	p.G634E	TROAP_ENST00000547923.1_Missense_Mutation_p.G313E|TROAP_ENST00000551245.1_Missense_Mutation_p.G634E	NM_005480.3	NP_005471.3	Q12815	TROAP_HUMAN	trophinin associated protein	634	4 X 33 AA approximate tandem repeats.|Cys-rich.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	32						GGACCCCCAGGGCCCTGCCCT	0.647																																					p.G634E		Atlas-SNP	.											.	TROAP	80	.	0			c.G1901A						.						49	52	51					12																	49724529		2203	4300	6503	SO:0001583	missense	10024	exon13			CCCCAGGGCCCTG	U04810	CCDS8784.1, CCDS41779.1, CCDS61117.1	12q13.12	2012-10-17	2012-10-17		ENSG00000135451	ENSG00000135451			12327	protein-coding gene	gene with protein product	"tastin"	603872				7758945	Standard	NM_005480		Approved	TASTIN	uc001rtx.4	Q12815	OTTHUMG00000169486	ENST00000257909.3:c.1901G>A	chr12.hg19:g.49724529G>A	ENSP00000257909:p.Gly634Glu	36.0	0.0		39.0	15.0	NM_005480	F8VSF9|Q6PJU7|Q8N5B2	Missense_Mutation	SNP	ENST00000257909.3	hg19	CCDS8784.1	.	.	.	.	.	.	.	.	.	.	G	2.209	-0.381034	0.05000	.	.	ENSG00000135451	ENST00000551245;ENST00000257909;ENST00000547923	.	.	.	4.28	-0.898	0.10550	.	0.898969	0.09538	N	0.788605	T	0.11665	0.0284	N	0.04090	-0.28	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.31223	-0.9951	9	0.02654	T	1	0.2159	3.3988	0.07316	0.5478:0.0:0.2864:0.1659	.	634;313;634	F8W130;F8W1U0;Q12815	.;.;TROAP_HUMAN	E	634;634;313	.	ENSP00000257909:G634E	G	+	2	0	TROAP	48010796	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.390000	0.20768	-0.144000	0.11314	-1.267000	0.01435	GGG	.	.		0.647	TROAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404300.1	NM_005480		A	49724529	G	A	49724529	3	1	262	1	0	0	0	0	1	0	0	0	16590	1232	43	3	2049	3	TROAP	12	49724529	Missense_Mutation	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10	1364754	49724529	84127366	80	38338										
DCD	117159	hgsc.bcm.edu	37	chr12	55040929	55040929	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	ccccgatcctggggcagaggCggcctctggatcatctgcaa	13	14	3	1			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr12:55040929C>A	ENST00000293371.6	-	2	262	c.73G>T	c.(73-75)Gcc>Tcc	p.A25S	DCD_ENST00000456047.2_Missense_Mutation_p.A25S	NM_053283.2	NP_444513.1	P81605	DCD_HUMAN	dermcidin	25					defense response to bacterium (GO:0042742)|defense response to fungus (GO:0050832)|killing of cells of other organism (GO:0031640)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	peptidase activity (GO:0008233)|poly(A) RNA binding (GO:0044822)			large_intestine(2)|lung(2)|ovary(1)|skin(1)	6		Myeloproliferative disorder(1001;0.0255)				GGGGCAGAGGCGGCCTCTGGA	0.572																																					p.A25S		Atlas-SNP	.											.	DCD	20	.	0			c.G73T						.						61	40	47					12																	55040929		2196	4286	6482	SO:0001583	missense	117159	exon2			CAGAGGCGGCCTC	AF144011	CCDS8884.1, CCDS73478.1	12q13.1	2008-08-04				ENSG00000161634			14669	protein-coding gene	gene with protein product	"proteolysis inducing factor", "preproteolysin", "diffusible survival/evasion peptide", "survival promoting peptide"	606634				11694882	Standard	XM_005268627		Approved	AIDD, PIF, DSEP, HCAP, DCD-1	uc001sgj.3	P81605	OTTHUMG00000169937	ENST00000293371.6:c.73G>T	chr12.hg19:g.55040929C>A	ENSP00000293371:p.Ala25Ser	48.0	0.0		57.0	18.0	NM_053283	A5JHP2|A5JHP3|P58461|Q53YJ2	Missense_Mutation	SNP	ENST00000293371.6	hg19	CCDS8884.1	.	.	.	.	.	.	.	.	.	.	C	10.30	1.311679	0.23821	.	.	ENSG00000161634	ENST00000293371;ENST00000456047	.	.	.	2.64	1.73	0.24493	.	.	.	.	.	T	0.34048	0.0884	N	0.08118	0	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.10800	-1.0614	8	0.87932	D	0	.	5.0764	0.14634	0.0:0.8321:0.0:0.1679	.	25;25	A5JHP3;P81605	.;DCD_HUMAN	S	25	.	ENSP00000293371:A25S	A	-	1	0	DCD	53327196	0.002000	0.14202	0.083000	0.20561	0.009000	0.06853	0.015000	0.13355	0.678000	0.31325	0.563000	0.77884	GCC	.	.		0.572	DCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406617.1	NM_053283		A	55040929	C	A	55040929	3	1	262	1	0	0	0	0	1	0	0	0	4285	768	27	1	275	1	DCD	12	55040929	Missense_Mutation	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10	5316400	55040929	78810966	81	38339										
NAV3	89795	hgsc.bcm.edu	37	chr12	78400495	78400495	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	agaaattcaagctagtcaatGcccggactgctttacgcccc	8	13	2	1	rs34682552		TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr12:78400495G>A	ENST00000397909.2	+	8	1350	c.1177G>A	c.(1177-1179)Gcc>Acc	p.A393T	NAV3_ENST00000536525.2_Missense_Mutation_p.A393T|NAV3_ENST00000228327.6_Missense_Mutation_p.A393T|NAV3_ENST00000266692.7_Missense_Mutation_p.A393T			Q8IVL0	NAV3_HUMAN	neuron navigator 3	393						membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						GCTAGTCAATGCCCGGACTGC	0.507										HNSCC(70;0.22)																											p.A393T		Atlas-SNP	.											.	NAV3	506	.	0			c.G1177A						.						79	83	81					12																	78400495		1991	4150	6141	SO:0001583	missense	89795	exon8			GTCAATGCCCGGA	AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.1177G>A	chr12.hg19:g.78400495G>A	ENSP00000381007:p.Ala393Thr	107.0	0.0		121.0	28.0	NM_014903	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.23|19.23	3.787642|3.787642	0.70337|0.70337	.|.	.|.	ENSG00000067798|ENSG00000067798	ENST00000549464;ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692|ENST00000550503	T;T;T;T;T|.	0.60548|.	0.18;1.67;1.67;1.67;1.6|.	5.74|5.74	3.92|3.92	0.45320|0.45320	.|.	0.000000|.	0.39834|.	U|.	0.001245|.	T|T	0.51329|0.51329	0.1668|0.1668	L|L	0.36672|0.36672	1.1|1.1	0.80722|0.80722	D|D	1|1	P;B|.	0.44734|.	0.842;0.041|.	B;B|.	0.31946|.	0.138;0.011|.	T|T	0.40346|0.40346	-0.9568|-0.9568	10|5	0.29301|.	T|.	0.29|.	-10.5837|-10.5837	8.6761|8.6761	0.34181|0.34181	0.0685:0.0:0.6605:0.271|0.0685:0.0:0.6605:0.271	.|.	393;393|.	Q8IVL0;Q8IVL0-2|.	NAV3_HUMAN;.|.	T|Y	393|216	ENSP00000446628:A393T;ENSP00000446132:A393T;ENSP00000381007:A393T;ENSP00000228327:A393T;ENSP00000266692:A393T|.	ENSP00000228327:A393T|.	A|C	+|+	1|2	0|0	NAV3|NAV3	76924626|76924626	0.999000|0.999000	0.42202|0.42202	1.000000|1.000000	0.80357|0.80357	0.912000|0.912000	0.54170|0.54170	1.547000|1.547000	0.36190|0.36190	0.780000|0.780000	0.33566|0.33566	0.655000|0.655000	0.94253|0.94253	GCC|TGC	.	.		0.507	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		A	78400495	G	A	78400495	3	1	262	1	0	0	0	0	1	0	0	0	10194	1319	46	3	1207	3	NAV3	12	78400495	Missense_Mutation	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10	23359566	78400495	55451400	82	38340										
DAOA	267012	hgsc.bcm.edu	37	chr13	106142291	106142291	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	tgttggaaaagtcttcatggCaagaaactatgagttccttg	10	6	2	2			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr13:106142291C>A	ENST00000375936.3	+	4	369	c.323C>A	c.(322-324)gCa>gAa	p.A108E	DAOA_ENST00000329625.5_Missense_Mutation_p.A37E|DAOA-AS1_ENST00000448407.1_RNA	NM_001161812.1|NM_172370.3	NP_001155284.1|NP_758958.3	P59103	DAOA_HUMAN	D-amino acid oxidase activator	108					negative regulation of D-amino-acid oxidase activity (GO:1900758)|positive regulation of catalytic activity (GO:0043085)	Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)	enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|skin(1)	13	Lung NSC(43;0.01)|all_neural(89;0.0741)|Lung SC(71;0.14)|Medulloblastoma(90;0.169)					gtcttcatggcaagaaactat	0.493																																					p.A108E		Atlas-SNP	.											.	DAOA	26	.	0			c.C323A						.						65	70	69					13																	106142291		2120	4249	6369	SO:0001583	missense	267012	exon4			TCATGGCAAGAAA	AY138547	CCDS41905.1, CCDS53880.1, CCDS59242.1	13q33.2	2011-08-01			ENSG00000182346	ENSG00000182346			21191	protein-coding gene	gene with protein product	"G72 transcript"	607408				12364586, 15057823	Standard	NM_001161814		Approved	G72	uc010tjg.2	P59103	OTTHUMG00000041333	ENST00000375936.3:c.323C>A	chr13.hg19:g.106142291C>A	ENSP00000365103:p.Ala108Glu	64.0	0.0		91.0	26.0	NM_172370	A6NKG7|Q0VAE6|Q5VX59|Q86Y17|Q8IWM4	Missense_Mutation	SNP	ENST00000375936.3	hg19	CCDS41905.1	.	.	.	.	.	.	.	.	.	.	C	8.871	0.949352	0.18356	.	.	ENSG00000182346	ENST00000375936;ENST00000329625	T	0.27402	1.67	2.44	-1.89	0.07689	.	.	.	.	.	T	0.13884	0.0336	N	0.08118	0	0.09310	N	1	P;P	0.52061	0.95;0.95	P;P	0.47573	0.55;0.55	T	0.07443	-1.0772	9	0.02654	T	1	.	6.7879	0.23683	0.0:0.3562:0.0:0.6438	.	80;108	A2T115;P59103	.;DAOA_HUMAN	E	108;37	ENSP00000365103:A108E	ENSP00000329951:A37E	A	+	2	0	DAOA	104940292	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.483000	0.06536	-0.592000	0.05851	-0.137000	0.14449	GCA	.	.		0.493	DAOA-005	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000099040.2	NM_172370		A	106142291	C	A	106142291	3	1	262	1	0	0	0	0	1	0	0	0	4234	710	25	3	446	3	DAOA	13	106142291	Missense_Mutation	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10		106142291	9027587	83	38341										
PARP2	10038	hgsc.bcm.edu	37	chr14	20822996	20822996	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	acagtggcacaaatcaaggcAggttaccagtctcttaagaa	9	9	2	1			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr14:20822996A>C	ENST00000250416.5	+	9	858	c.831A>C	c.(829-831)gcA>gcC	p.A277A	PARP2_ENST00000429687.3_Silent_p.A264A|PARP2_ENST00000527915.1_Silent_p.A277A	NM_001042618.1|NM_005484.3	NP_001036083.1|NP_005475.2	Q9UGN5	PARP2_HUMAN	poly (ADP-ribose) polymerase 2	277	PARP alpha-helical. {ECO:0000255|PROSITE- ProRule:PRU00398}.				base-excision repair (GO:0006284)|DNA repair (GO:0006281)|extrinsic apoptotic signaling pathway (GO:0097191)|protein ADP-ribosylation (GO:0006471)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			central_nervous_system(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)	15	all_cancers(95;0.00092)	all_lung(585;0.235)	Epithelial(56;5.34e-07)|all cancers(55;3.7e-06)	GBM - Glioblastoma multiforme(265;0.00888)|READ - Rectum adenocarcinoma(17;0.0649)		AAATCAAGGCAGGTTACCAGT	0.498								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA																													p.A277A		Atlas-SNP	.											.	PARP2	92	.	0			c.A831C						.						138	138	138					14																	20822996		1973	4171	6144	SO:0001819	synonymous_variant	10038	exon9			CAAGGCAGGTTAC	AF085734	CCDS41910.1, CCDS45077.1	14q11.2-q12	2010-02-16	2008-07-28	2004-08-26	ENSG00000129484	ENSG00000129484		"Poly (ADP-ribose) polymerases"	272	protein-coding gene	gene with protein product		607725	"ADP-ribosyltransferase (NAD+; poly(ADP-ribose) polymerase)-like 2", "poly (ADP-ribose) polymerase family, member 2"	ADPRTL2		10329013, 18353725	Standard	NM_005484		Approved		uc001vxc.3	Q9UGN5	OTTHUMG00000166106	ENST00000250416.5:c.831A>C	chr14.hg19:g.20822996A>C		100.0	0.0		91.0	30.0	NM_005484	Q8TEU4|Q9NUV2|Q9UMR4|Q9Y6C8	Silent	SNP	ENST00000250416.5	hg19	CCDS41910.1																																																																																			.	.		0.498	PARP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000387847.2			C	20822996	A	C	20822996	2	2	262	1	0	0	0	0	0	0	0	1	11470	175	7	5		5	PARP2	14	20822996	Silent	SNP	A	TCGA-FV-A2QQ-01A-11D-A22F-10		20822996	86526544	84	38342										
LRFN5	145581	hgsc.bcm.edu	37	chr14	42356953	42356953	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	atagtggatcttcatataatTaagctccctcacttactaaa	4	9	3	0			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr14:42356953T>G	ENST00000298119.4	+	3	2314	c.1125T>G	c.(1123-1125)atT>atG	p.I375M	LRFN5_ENST00000554120.1_Missense_Mutation_p.I375M|LRFN5_ENST00000554171.1_Missense_Mutation_p.I375M	NM_152447.3	NP_689660.2	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III domain containing 5	375						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(67)|ovary(5)|pancreas(3)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(2)	120			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		TTCATATAATTAAGCTCCCTC	0.393										HNSCC(30;0.082)																											p.I375M		Atlas-SNP	.											.	LRFN5	269	.	0			c.T1125G						.						77	79	78					14																	42356953		2203	4300	6503	SO:0001583	missense	145581	exon3			TATAATTAAGCTC	AK055365	CCDS9678.1	14q21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000165379	ENSG00000165379		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	20360	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 8"	612811	"chromosome 14 open reading frame 146"	C14orf146		16828986	Standard	NM_152447		Approved	FIGLER8, SALM5	uc001wvm.3	Q96NI6	OTTHUMG00000140261	ENST00000298119.4:c.1125T>G	chr14.hg19:g.42356953T>G	ENSP00000298119:p.Ile375Met	88.0	0.0		94.0	34.0	NM_152447	B3KU78|Q86XL2	Missense_Mutation	SNP	ENST00000298119.4	hg19	CCDS9678.1	.	.	.	.	.	.	.	.	.	.	T	12.93	2.085524	0.36758	.	.	ENSG00000165379	ENST00000298119;ENST00000554120;ENST00000554171	T;T;T	0.53423	0.77;0.62;0.62	5.4	4.1	0.47936	.	0.000000	0.56097	D	0.000022	T	0.48095	0.1481	L	0.49778	1.585	0.43683	D	0.996125	P;P	0.49783	0.886;0.928	P;P	0.53401	0.725;0.634	T	0.48080	-0.9066	10	0.46703	T	0.11	.	4.7262	0.12941	0.0:0.2312:0.0:0.7688	.	375;375	G3V364;Q96NI6	.;LRFN5_HUMAN	M	375	ENSP00000298119:I375M;ENSP00000451897:I375M;ENSP00000451067:I375M	ENSP00000298119:I375M	I	+	3	3	LRFN5	41426703	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.413000	0.34725	2.165000	0.68154	0.460000	0.39030	ATT	.	.		0.393	LRFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276786.1	NM_152447		G	42356953	T	G	42356953	3	3	262	1	0	0	0	0	1	0	0	0	8950	1742	61	5	1127	5	LRFN5	14	42356953	Missense_Mutation	SNP	T	TCGA-FV-A2QQ-01A-11D-A22F-10	21533957	42356953	64992587	85	38343										
LTBP2	4053	hgsc.bcm.edu	37	chr14	74989512	74989512	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	cctgtgcagtaggcctggctGgggtgcagctggtagccagg	18	10	0	0			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr14:74989512G>T	ENST00000261978.4	-	16	3026	c.2640C>A	c.(2638-2640)ccC>ccA	p.P880P	LTBP2_ENST00000556690.1_Silent_p.P880P	NM_000428.2	NP_000419.1	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding protein 2	880	Cys-rich.|EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				protein secretion (GO:0009306)|protein targeting (GO:0006605)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|liver(1)|lung(29)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)		AGGCCTGGCTGGGGTGCAGCT	0.622																																					p.P880P		Atlas-SNP	.											.	LTBP2	158	.	0			c.C2640A						.						46	33	38					14																	74989512		2203	4300	6503	SO:0001819	synonymous_variant	4053	exon16			CTGGCTGGGGTGC		CCDS9831.1	14q24.3	2011-10-20	2001-12-04			ENSG00000119681		"Latent transforming growth factor, beta binding proteins"	6715	protein-coding gene	gene with protein product		602091	"chromosome 14 open reading frame 141"	LTBP3, C14orf141		7798248	Standard	NM_000428		Approved		uc001xqa.3	Q14767		ENST00000261978.4:c.2640C>A	chr14.hg19:g.74989512G>T		26.0	0.0		42.0	17.0	NM_000428	Q99907|Q9NS51	Silent	SNP	ENST00000261978.4	hg19	CCDS9831.1																																																																																			.	.		0.622	LTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413595.1	NM_000428		T	74989512	G	T	74989512	2	4	262	1	0	0	0	0	0	0	0	1	9083	1335	47	3		3	LTBP2	14	74989512	Silent	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10	32632559	74989512	32360028	86	38344										
TDRD9	122402	hgsc.bcm.edu	37	chr14	104506642	104506642	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	acatggagcttgcgtttgacGttcaattcagcgtggaggat	13	7	2	1	rs182776644	byFrequency	TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr14:104506642G>A	ENST00000409874.4	+	33	3874	c.3826G>A	c.(3826-3828)Gtt>Att	p.V1276I	TDRD9_ENST00000339063.5_Intron	NM_153046.2	NP_694591.2	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	1276				V -> F (in Ref. 3; BAC05144). {ECO:0000305}.	cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|piP-body (GO:0071547)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				TGCGTTTGACGTTCAATTCAG	0.532																																					p.V1276I		Atlas-SNP	.											.	TDRD9	175	.	0			c.G3826A						.						163	133	142					14																	104506642		692	1591	2283	SO:0001583	missense	122402	exon33			TTTGACGTTCAAT	AK093483	CCDS9987.2	14q32.33	2013-01-23	2004-04-01	2004-04-02	ENSG00000156414	ENSG00000156414		"Tudor domain containing"	20122	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 75"	C14orf75			Standard	NM_153046		Approved	DKFZp434N0820, FLJ36164, NET54	uc001yom.4	Q8NDG6	OTTHUMG00000152876	ENST00000409874.4:c.3826G>A	chr14.hg19:g.104506642G>A	ENSP00000387303:p.Val1276Ile	93.0	0.0		90.0	25.0	NM_153046	A1A4S7|Q6ZU54|Q8N7T3|Q8N827|Q8N9V5|Q96AS9	Missense_Mutation	SNP	ENST00000409874.4	hg19	CCDS9987.2	.	.	.	.	.	.	.	.	.	.	G	14.66	2.601080	0.46423	.	.	ENSG00000156414	ENST00000409874	T	0.03831	3.79	5.24	5.24	0.73138	.	.	.	.	.	T	0.07728	0.0194	L	0.56769	1.78	0.80722	D	1	D	0.55172	0.97	B	0.38712	0.28	T	0.09796	-1.0658	9	0.66056	D	0.02	.	17.598	0.88017	0.0:0.0:1.0:0.0	.	1276	Q8NDG6	TDRD9_HUMAN	I	1276	ENSP00000387303:V1276I	ENSP00000387303:V1276I	V	+	1	0	TDRD9	103576395	1.000000	0.71417	0.022000	0.16811	0.003000	0.03518	5.942000	0.70203	2.450000	0.82876	0.650000	0.86243	GTT	.	G|1.000;T|0.000		0.532	TDRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328325.3	NM_153046		A	104506642	G	A	104506642	3	1	262	1	0	0	0	0	1	0	0	0	15751	1145	40	1	3956	1	TDRD9	14	104506642	Missense_Mutation	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10	29517130	104506642	2842898	87	38345										
PLCB2	5330	hgsc.bcm.edu	37	chr15	40585896	40585896	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	tctacataggtgcgcacgctGcgttctgacaggaactgccc	11	13	2	1			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr15:40585896G>A	ENST00000260402.3	-	20	2340	c.2091C>T	c.(2089-2091)cgC>cgT	p.R697R	PLCB2_ENST00000557821.1_Silent_p.R693R|PLCB2_ENST00000456256.2_Silent_p.R697R	NM_001284297.1|NM_004573.2	NP_001271226.1|NP_004564.2	Q00722	PLCB2_HUMAN	phospholipase C, beta 2	697	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				activation of phospholipase C activity (GO:0007202)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|sensory perception of bitter taste (GO:0050913)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(3)	39		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0508)		TGCGCACGCTGCGTTCTGACA	0.582																																					p.R697R		Atlas-SNP	.											.	PLCB2	177	.	0			c.C2091T						.						75	79	78					15																	40585896		2008	4204	6212	SO:0001819	synonymous_variant	5330	exon20			CACGCTGCGTTCT		CCDS42020.1, CCDS61591.1, CCDS61592.1, CCDS73704.1	15q15.1	2012-01-23			ENSG00000137841	ENSG00000137841	3.1.4.11		9055	protein-coding gene	gene with protein product		604114				1644792, 9925923	Standard	XM_005254448		Approved	FLJ38135	uc001zld.3	Q00722	OTTHUMG00000172412	ENST00000260402.3:c.2091C>T	chr15.hg19:g.40585896G>A		91.0	0.0		98.0	23.0	NM_004573	A8K6J2|B9EGH5	Silent	SNP	ENST00000260402.3	hg19	CCDS42020.1																																																																																			.	.		0.582	PLCB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418430.1			A	40585896	G	A	40585896	2	1	262	1	0	0	0	0	0	0	0	1	12037	1306	46	3		3	PLCB2	15	40585896	Silent	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10		40585896	61945496	88	38346										
PLA2G4F	255189	hgsc.bcm.edu	37	chr15	42436338	42436338	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	ttggggaaggcgtccgggtgTgtgtctgcaaggaacccatg	17	8	1	0			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr15:42436338T>A	ENST00000382396.4	-	18	2066	c.1980A>T	c.(1978-1980)acA>acT	p.T660T	PLA2G4F_ENST00000397272.3_Silent_p.T662T			Q68DD2	PA24F_HUMAN	phospholipase A2, group IVF	660	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid secretion (GO:0050482)|cellular response to antibiotic (GO:0071236)|cellular response to organic cyclic compound (GO:0071407)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	calcium-dependent phospholipase A2 activity (GO:0047498)|lysophospholipase activity (GO:0004622)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32		all_cancers(109;4.82e-12)|all_epithelial(112;5.64e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(94;8.97e-07)		CGTCCGGGTGTGTGTCTGCAA	0.567																																					p.T660T		Atlas-SNP	.											.	PLA2G4F	75	.	0			c.A1980T						.						83	69	74					15																	42436338		2203	4299	6502	SO:0001819	synonymous_variant	255189	exon18			CGGGTGTGTGTCT		CCDS32204.1	15q15.1	2008-09-19				ENSG00000168907	3.1.1.4		27396	protein-coding gene	gene with protein product						14702039, 15866882	Standard	NM_213600		Approved	PLA2G4F/Z	uc001zoz.3	Q68DD2		ENST00000382396.4:c.1980A>T	chr15.hg19:g.42436338T>A		26.0	0.0		34.0	10.0	NM_213600	Q6ZMC8	Silent	SNP	ENST00000382396.4	hg19	CCDS32204.1																																																																																			.	.		0.567	PLA2G4F-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000420463.1	NM_213600		A	42436338	T	A	42436338	2	1	262	1	0	0	0	0	0	0	0	1	12015	1683	59	4		4	PLA2G4F	15	42436338	Silent	SNP	T	TCGA-FV-A2QQ-01A-11D-A22F-10	1850442	42436338	60095054	89	38347										
CSPG4	1464	hgsc.bcm.edu	37	chr15	75969717	75969717	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	ggcccgctggccctcggggaCccagagacctgggggtggga	19	13	0	1			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr15:75969717C>T	ENST00000308508.5	-	10	5235	c.5143G>A	c.(5143-5145)Gtc>Atc	p.V1715I	AC105020.1_ENST00000435356.1_5'Flank|CTD-2026K11.1_ENST00000569467.1_RNA	NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	1715	Cysteine-containing.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						CCCTCGGGGACCCAGAGACCT	0.642																																					p.V1715I		Atlas-SNP	.											.	CSPG4	175	.	0			c.G5143A						.						9	8	8					15																	75969717		2142	4222	6364	SO:0001583	missense	1464	exon10			CGGGGACCCAGAG	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"Proteoglycans / Cell surface : Other"	2466	protein-coding gene	gene with protein product	"melanoma-associated chondroitin sulfate proteoglycan"	601172	"chondroitin sulfate proteoglycan 4 (melanoma-associated)"			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.5143G>A	chr15.hg19:g.75969717C>T	ENSP00000312506:p.Val1715Ile	41.0	0.0		38.0	18.0	NM_001897	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	hg19	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	C	15.98	2.993270	0.54041	.	.	ENSG00000173546	ENST00000308508	T	0.27720	1.65	5.39	5.39	0.77823	.	0.092925	0.45126	D	0.000399	T	0.28300	0.0699	M	0.64567	1.98	0.44188	D	0.997009	P	0.38020	0.615	B	0.29267	0.1	T	0.08046	-1.0741	10	0.42905	T	0.14	.	12.6639	0.56830	0.0:0.8209:0.1791:0.0	.	1715	Q6UVK1	CSPG4_HUMAN	I	1715	ENSP00000312506:V1715I	ENSP00000312506:V1715I	V	-	1	0	CSPG4	73756772	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.823000	0.39062	2.517000	0.84864	0.561000	0.74099	GTC	.	.		0.642	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897		T	75969717	C	T	75969717	3	4	262	1	0	0	0	0	1	0	0	0	3962	507	18	3	1829	3	CSPG4	15	75969717	Missense_Mutation	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10	33533379	75969717	26561675	90	38348										
RASGRF1	5923	hgsc.bcm.edu	37	chr15	79298691	79298691	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	cagcagccgctccacactggCgtagcggatctgcagcactt	11	15	1	0			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr15:79298691C>T	ENST00000419573.3	-	15	2225	c.1951G>A	c.(1951-1953)Gcc>Acc	p.A651T	RASGRF1_ENST00000394745.3_5'Flank|RASGRF1_ENST00000558480.2_Missense_Mutation_p.A638T|RASGRF1_ENST00000560334.1_5'UTR	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	651	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						TCCACACTGGCGTAGCGGATC	0.567																																					p.A651T		Atlas-SNP	.											RASGRF1,NS,carcinoma,+2,1	RASGRF1	168	.	0			c.G1951A						.						107	90	96					15																	79298691		2196	4293	6489	SO:0001583	missense	5923	exon15			CACTGGCGTAGCG	M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.1951G>A	chr15.hg19:g.79298691C>T	ENSP00000405963:p.Ala651Thr	57.0	0.0		74.0	20.0	NM_002891	F8VPA5|H0YKF2|J3KQP9|Q16027	Missense_Mutation	SNP	ENST00000419573.3	hg19	CCDS10309.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.500016	0.85176	.	.	ENSG00000058335	ENST00000419573;ENST00000394741	T	0.56611	0.45	4.63	4.63	0.57726	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (3);	0.000000	0.85682	D	0.000000	T	0.73305	0.3570	M	0.80183	2.485	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.998;0.997;0.999;0.998	T	0.77861	-0.2430	10	0.87932	D	0	.	15.0277	0.71682	0.0:1.0:0.0:0.0	.	47;651;638;651;638	B7Z6Z6;A8K270;Q8IUU5;Q13972;F8VPA5	.;.;.;RGRF1_HUMAN;.	T	651;638	ENSP00000405963:A651T	ENSP00000378224:A638T	A	-	1	0	RASGRF1	77085746	1.000000	0.71417	0.991000	0.47740	0.898000	0.52572	7.429000	0.80309	2.413000	0.81919	0.591000	0.81541	GCC	.	.		0.567	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891		T	79298691	C	T	79298691	3	4	262	1	0	0	0	0	1	0	0	0	13087	768	27	1	1926	1	RASGRF1	15	79298691	Missense_Mutation	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10	3328974	79298691	23232701	91	38349										
IFT140	9742	hgsc.bcm.edu	37	chr16	1634278	1634278	+	Frame_Shift_Del	DEL	G	G	-													0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	aggctgtgtgcgacccccgtGgacaggaagcacacattcag					rs377217453		TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr16:1634278delG	ENST00000426508.2	-	11	1662	c.1299delC	c.(1297-1299)tccfs	p.S433fs	LA16c-395F10.2_ENST00000563162.1_RNA|IFT140_ENST00000439987.2_5'UTR	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	433					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)|protein localization to cilium (GO:0061512)|regulation of cilium assembly (GO:1902017)|renal system development (GO:0072001)|retina development in camera-type eye (GO:0060041)|skeletal system morphogenesis (GO:0048705)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)|photoreceptor connecting cilium (GO:0032391)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(12)|lung(10)|ovary(5)|pancreas(1)|prostate(4)|skin(4)|stomach(2)|urinary_tract(1)	53		Hepatocellular(780;0.219)				CGACCCCCGTGGACAGGAAGC	0.632																																					p.T434fs		Atlas-INDEL	.											.	IFT140	128	.	0			c.1300delA						.						48	39	42					16																	1634278		2199	4300	6499	SO:0001589	frameshift_variant	9742	exon11			.	AB011162	CCDS10439.1	16p13.3	2014-07-03	2014-07-03	2005-11-02	ENSG00000187535	ENSG00000187535		"Intraflagellar transport homologs", "WD repeat domain containing"	29077	protein-coding gene	gene with protein product		614620	"WD and tetratricopeptide repeats 2", "intraflagellar transport 140 homolog (Chlamydomonas)"	WDTC2		9628581	Standard	NM_014714		Approved	gs114, KIAA0590	uc002cmb.3	Q96RY7	OTTHUMG00000128585	ENST00000426508.2:c.1299delC	chr16.hg19:g.1634278delG	ENSP00000406012:p.Ser433fs	18.0	0.0		33.0	11.0	NM_014714	A2A2A8|D3DU75|O60332|Q9UG52	Frame_Shift_Del	DEL	ENST00000426508.2	hg19	CCDS10439.1																																																																																			.	.		0.632	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714		-	1634278	G	-	1634278	7	5	262	1	0	1	0	1	0	0	0	0	7565	1335	47	0	3173	0	IFT140	16	1634278	Frame_Shift_Del	DEL	G	TCGA-FV-A2QQ-01A-11D-A22F-10		1634278	88720475	92	38350										
TPPP3	51673	hgsc.bcm.edu	37	chr16	67424387	67424387	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	cagcagggcacttacagtgaCgcccacattggctggctctt	11	13	1	1	rs146906089		TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr16:67424387C>T	ENST00000564104.1	-	2	1178	c.337G>A	c.(337-339)Gtc>Atc	p.V113I	TPPP3_ENST00000393957.2_Missense_Mutation_p.V113I|TPPP3_ENST00000562206.1_Missense_Mutation_p.V113I|RNU1-123P_ENST00000458950.1_RNA|TPPP3_ENST00000290942.5_Missense_Mutation_p.V113I			Q9BW30	TPPP3_HUMAN	tubulin polymerization-promoting protein family member 3	113					microtubule bundle formation (GO:0001578)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	tubulin binding (GO:0015631)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(2)|prostate(1)	7		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0336)|Epithelial(162;0.0781)		CTTACAGTGACGCCCACATTG	0.627																																					p.V113I		Atlas-SNP	.											.	TPPP3	13	.	0			c.G337A						.		ILE/VAL,ILE/VAL	3,4393	6.2+/-15.9	0,3,2195	82	86	85		337,337	3.7	0.8	16	dbSNP_134	85	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	TPPP3	NM_015964.2,NM_016140.2	29,29	0,4,6494	TT,TC,CC		0.0116,0.0682,0.0308	benign,benign	113/177,113/177	67424387	4,12992	2198	4300	6498	SO:0001583	missense	51673	exon4			CAGTGACGCCCAC	BC000691	CCDS10835.1	16q22.1	2008-02-05			ENSG00000159713	ENSG00000159713			24162	protein-coding gene	gene with protein product						15590652, 17105200	Standard	XM_005255979		Approved	CGI-38, p25gamma, p20	uc002etb.3	Q9BW30	OTTHUMG00000137516	ENST00000564104.1:c.337G>A	chr16.hg19:g.67424387C>T	ENSP00000462435:p.Val113Ile	55.0	0.0		65.0	16.0	NM_016140	Q49AH9|Q9Y326|Q9Y6H0	Missense_Mutation	SNP	ENST00000564104.1	hg19	CCDS10835.1	.	.	.	.	.	.	.	.	.	.	c	12.80	2.046815	0.36085	6.82E-4	1.16E-4	ENSG00000159713	ENST00000393957;ENST00000290942	T;T	0.42900	0.96;0.96	3.74	3.74	0.42951	.	0.068946	0.56097	D	0.000021	T	0.33177	0.0854	L	0.48260	1.515	0.47276	D	0.999379	B	0.06786	0.001	B	0.11329	0.006	T	0.16012	-1.0417	10	0.36615	T	0.2	-11.7503	8.3276	0.32167	0.0:0.8891:0.0:0.1109	.	113	Q9BW30	TPPP3_HUMAN	I	113	ENSP00000377529:V113I;ENSP00000290942:V113I	ENSP00000290942:V113I	V	-	1	0	TPPP3	65981888	1.000000	0.71417	0.794000	0.32065	0.563000	0.35712	4.597000	0.61062	1.910000	0.55303	0.457000	0.33378	GTC	.	C|1.000;T|0.000		0.627	TPPP3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421787.2	NM_015964		T	67424387	C	T	67424387	3	4	262	1	0	0	0	0	1	0	0	0	16430	536	19	1	201	1	TPPP3	16	67424387	Missense_Mutation	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10	65790109	67424387	22930366	93	38351										
CDRT1	374286	hgsc.bcm.edu	37	chr17	15510886	15510886	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	agattctgaccccagtacctAcgtgtcagagagaatgcgaa	10	10	2	4			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr17:15510886A>T	ENST00000395906.3	-	6	1232		c.e6+1		RP11-385D13.1_ENST00000455584.2_Splice_Site	NM_006382.3	NP_006373.2	O95170	CDRT1_HUMAN	CMT1A duplicated region transcript 1											endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	10				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(2;1.36e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0541)		CCCAGTACCTACGTGTCAGAG	0.498																																					.		Atlas-SNP	.											.	CDRT1	83	.	0			c.1232+2T>A						.						67	64	65					17																	15510886		2203	4300	6503	SO:0001630	splice_region_variant	374286	exon7			GTACCTACGTGTC	U65652	CCDS45619.1, CCDS73996.1	17p11	2013-01-10			ENSG00000241322	ENSG00000241322		"F-boxes / WD-40 domains", "WD repeat domain containing"	14379	protein-coding gene	gene with protein product		604596	"F-box and WD repeat domain containing 10 pseudogene 1", "F-box and WD-40 domain protein 10 pseudogene 1"	FBXW10P1		9787083, 11381029	Standard	NM_006382		Approved	HREP, SM25H2, FBXW10B		O95170	OTTHUMG00000059074	ENST00000395906.3:c.1232+1T>A	chr17.hg19:g.15510886A>T		123.0	0.0		139.0	57.0	NM_006382	O43848|O95611	Splice_Site	SNP	ENST00000395906.3	hg19	CCDS45619.1	.	.	.	.	.	.	.	.	.	.	A	9.805	1.181633	0.21787	.	.	ENSG00000251537	ENST00000455584;ENST00000261644;ENST00000395906	.	.	.	4.99	4.99	0.66335	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.3649	0.49666	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	RP11-385D13.1	15451611	1.000000	0.71417	0.908000	0.35775	0.014000	0.08584	5.923000	0.70045	2.015000	0.59207	0.459000	0.35465	.	.	.		0.498	CDRT1-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448127.1	NM_006382	Intron	T	15510886	A	T	15510886	5	4	262	1	0	0	0	0	0	0	1	0	3176	405	14	4	1052	4	CDRT1	17	15510886	Splice_Site	SNP	A	TCGA-FV-A2QQ-01A-11D-A22F-10		15510886	65684324	94	38352										
CCDC144NL	339184	hgsc.bcm.edu	37	chr17	20769875	20769875	+	Frame_Shift_Del	DEL	G	G	-													0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	tcctacctccaggcccccgtGggtgccctcctaccgctcca							TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr17:20769875delG	ENST00000327925.5	-	3	676	c.557delC	c.(556-558)ccafs	p.P186fs	RP11-344E13.3_ENST00000439794.2_RNA|RP11-344E13.3_ENST00000583962.1_RNA|RP11-344E13.3_ENST00000577537.1_RNA|RP11-344E13.3_ENST00000577860.1_RNA|RP11-344E13.3_ENST00000417232.2_RNA|CCDC144NL_ENST00000539484.1_Intron|RP11-344E13.3_ENST00000582324.1_RNA	NM_001004306.1	NP_001004306.1	Q6NUI1	C144L_HUMAN	coiled-coil domain containing 144 family, N-terminal like	186										large_intestine(3)|lung(3)|skin(1)	7						aggcccccgtgggtgccctcc	0.602																																					p.P186fs		Atlas-INDEL	.											.	CCDC144NL	34	.	0			c.558delA						.						44	32	36					17																	20769875		2200	4297	6497	SO:0001589	frameshift_variant	339184	exon3			.		CCDS32591.1	17p11.2	2009-01-15			ENSG00000205212	ENSG00000205212			33735	protein-coding gene	gene with protein product							Standard	NM_001004306		Approved	MGC87631	uc002gyf.3	Q6NUI1	OTTHUMG00000132271	ENST00000327925.5:c.557delC	chr17.hg19:g.20769875delG	ENSP00000328054:p.Pro186fs	71.0	0.0		82.0	13.0	NM_001004306		Frame_Shift_Del	DEL	ENST00000327925.5	hg19	CCDS32591.1																																																																																			.	.		0.602	CCDC144NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255361.2	NM_001004306		-	20769875	G	-	20769875	7	5	262	1	0	1	0	1	0	0	0	0	2781	1348	47	0	116	0	CCDC144NL	17	20769875	Frame_Shift_Del	DEL	G	TCGA-FV-A2QQ-01A-11D-A22F-10	5258989	20769875	60425335	95	38353										
CORO6	84940	hgsc.bcm.edu	37	chr17	27943827	27943828	+	Frame_Shift_Del	DEL	CT	CT	-													0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	aggtagtgcacgaaaggcggCtcgtcggtaatctcaaagta							TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr17:27943827_27943828delCT	ENST00000445145.2	-	7	897_898	c.896_897delAG	c.(895-897)gagfs	p.E299fs	RP11-68I3.2_ENST00000581474.1_RNA|CORO6_ENST00000577909.1_5'UTR|CORO6_ENST00000345068.5_Frame_Shift_Del_p.E299fs|CORO6_ENST00000580212.1_Frame_Shift_Del_p.E259fs|CORO6_ENST00000456796.3_Frame_Shift_Del_p.E65fs|CORO6_ENST00000584969.1_Frame_Shift_Del_p.E299fs|CORO6_ENST00000388767.3_Frame_Shift_Del_p.E299fs			Q6QEF8	CORO6_HUMAN	coronin 6	299					actin cytoskeleton organization (GO:0030036)	actin cytoskeleton (GO:0015629)	actin filament binding (GO:0051015)			breast(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(4)|prostate(1)|urinary_tract(2)	14						CGAAAGGCGGCTCGTCGGTAAT	0.584																																					p.299_300del		Atlas-Indel,Pindel	.											.	CORO6	34	.	0			c.897_898del						.																																			SO:0001589	frameshift_variant	84940	exon7			.	AF193039	CCDS11252.2	17q11.2	2013-01-10			ENSG00000167549	ENSG00000167549		"Coronins", "WD repeat domain containing"	21356	protein-coding gene	gene with protein product							Standard	NM_032854		Approved	FLJ14871	uc002hel.2	Q6QEF8	OTTHUMG00000132732	ENST00000445145.2:c.896_897delAG	chr17.hg19:g.27943827_27943828delCT	ENSP00000393624:p.Glu299fs	61.0	0.0		66.0	20.0	NM_032854	B3KU26|Q71MF3|Q8WYH7|Q96K02	Frame_Shift_Del	DEL	ENST00000445145.2	hg19																																																																																				.	.		0.584	CORO6-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000447831.1	NM_032854		-	27943828	CT	-	27943827	7	5	262	1	0	1	0	1	0	0	0	0	3760	796	28	0	537	0	CORO6	17	27943827	Frame_Shift_Del	DEL	CT	TCGA-FV-A2QQ-01A-11D-A22F-10	7173952	27943827	53251383	96	38354										
MRC2	9902	hgsc.bcm.edu	37	chr17	60766320	60766320	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	ttcatctgccagaagggcacGggtatgtgtcaccagtcacc	11	12	4	1	rs144406119	byFrequency	TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr17:60766320G>T	ENST00000303375.5	+	23	3735	c.3333G>T	c.(3331-3333)acG>acT	p.T1111T	MRC2_ENST00000580916.1_3'UTR|MRC2_ENST00000446119.2_Splice_Site_p.R57L	NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	1111					collagen catabolic process (GO:0030574)|endocytosis (GO:0006897)|osteoblast differentiation (GO:0001649)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|collagen binding (GO:0005518)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(11)|lung(28)|ovary(2)|prostate(1)|skin(3)	53						AGAAGGGCACGGGTATGTGTC	0.642																																					p.T1111T		Atlas-SNP	.											.	MRC2	126	.	0			c.G3333T						.						43	36	38					17																	60766320		2203	4300	6503	SO:0001630	splice_region_variant	9902	exon23			GGGCACGGGTATG	AB014609	CCDS11634.1	17q23	2011-08-30				ENSG00000011028		"CD molecules", "C-type lectin domain containing"	16875	protein-coding gene	gene with protein product		612264				9734811, 8702911	Standard	NM_006039		Approved	KIAA0709, ENDO180, CLEC13E, CD280	uc002jad.4	Q9UBG0		ENST00000303375.5:c.3334+1G>T	chr17.hg19:g.60766320G>T		80.0	0.0		67.0	25.0	NM_006039	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	Silent	SNP	ENST00000303375.5	hg19	CCDS11634.1	.	.	.	.	.	.	.	.	.	.	G	19.30	3.800347	0.70567	.	.	ENSG00000011028	ENST00000446119	T	0.03035	4.07	4.73	-9.46	0.00597	.	.	.	.	.	T	0.01800	0.0057	.	.	.	0.20307	N	0.999914	B	0.02656	0.0	B	0.01281	0.0	T	0.39396	-0.9616	8	0.29301	T	0.29	-11.2449	2.3556	0.04294	0.2657:0.1763:0.3749:0.1832	.	57	E7EME3	.	L	57	ENSP00000400445:R57L	ENSP00000400445:R57L	R	+	2	0	MRC2	58120052	0.864000	0.29904	0.200000	0.23457	0.553000	0.35397	0.005000	0.13129	-3.470000	0.00157	-1.069000	0.02264	CGG	.	G|0.993;A|0.007		0.642	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1		Silent	T	60766320	G	T	60766320	5	4	262	1	0	0	0	0	0	0	1	0	9767	1130	39	1	3423	1	MRC2	17	60766320	Splice_Site	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10	32822493	60766320	20428890	97	38355										
AFMID	7083	hgsc.bcm.edu	37	chr17	76183452	76183452	+	5'Flank	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	cccatgcggctgtagacgccAtgatggatgtgtctggtgtg	15	9	1	2			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr17:76183452A>G	ENST00000301634.7	-	0	0				TK1_ENST00000588734.1_5'Flank|AFMID_ENST00000586731.1_5'Flank|TK1_ENST00000590430.1_5'Flank|AFMID_ENST00000591952.1_Start_Codon_SNP_p.M1V|AFMID_ENST00000589256.1_Start_Codon_SNP_p.M1V|AFMID_ENST00000327898.5_Start_Codon_SNP_p.M1V|TK1_ENST00000590862.1_5'Flank|AFMID_ENST00000409257.5_Start_Codon_SNP_p.M1V|TK1_ENST00000405273.1_5'Flank|AFMID_ENST00000588800.1_Start_Codon_SNP_p.M1V	NM_003258.4	NP_003249.3	P04183	KITH_HUMAN	thymidine kinase 1, soluble						deoxyribonucleoside monophosphate biosynthetic process (GO:0009157)|digestive tract development (GO:0048565)|DNA replication (GO:0006260)|fetal process involved in parturition (GO:0060138)|liver development (GO:0001889)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide biosynthetic process (GO:0009165)|protein homotetramerization (GO:0051289)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|response to copper ion (GO:0046688)|response to cortisol (GO:0051414)|response to nutrient levels (GO:0031667)|response to toxic substance (GO:0009636)|skeletal muscle cell proliferation (GO:0014856)|small molecule metabolic process (GO:0044281)|thymidine metabolic process (GO:0046104)	cytosol (GO:0005829)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|nucleoside kinase activity (GO:0019206)|thymidine kinase activity (GO:0004797)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|urinary_tract(2)	4			BRCA - Breast invasive adenocarcinoma(99;0.00269)|OV - Ovarian serous cystadenocarcinoma(97;0.0804)|Lung(188;0.23)		Trifluridine(DB00432)|Zidovudine(DB00495)	TGTAGACGCCATGATGGATGT	0.612																																					p.M1V		Atlas-SNP	.											.	AFMID	38	.	0			c.A1G						.						127	115	119					17																	76183452		2203	4300	6503	SO:0001631	upstream_gene_variant	125061	exon1			GACGCCATGATGG		CCDS11754.1	17q23.2-q25.3	2012-10-02			ENSG00000167900	ENSG00000167900	2.7.1.21		11830	protein-coding gene	gene with protein product		188300					Standard	NM_003258		Approved		uc002juw.2	P04183	OTTHUMG00000150674		chr17.hg19:g.76183452A>G	Exception_encountered	48.0	0.0		43.0	12.0	NM_001145526	B2RC58|Q969V0|Q9UMG9	Missense_Mutation	SNP	ENST00000301634.7	hg19	CCDS11754.1	.	.	.	.	.	.	.	.	.	.	A	0.033	-1.323974	0.01309	.	.	ENSG00000183077	ENST00000409257;ENST00000409431;ENST00000409722;ENST00000392388;ENST00000327898	.	.	.	2.98	-1.46	0.08800	.	.	.	.	.	T	0.26810	0.0656	.	.	.	0.18873	N	0.999987	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.27905	-1.0060	7	0.87932	D	0	.	3.5092	0.07701	0.3903:0.221:0.3888:0.0	.	1;1;1;1	A5PLM3;B8ZZB1;Q63HM1;Q63HM1-2	.;.;AFMID_HUMAN;.	V	1	.	ENSP00000328938:M1V	M	+	1	0	AFMID	73695047	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.803000	0.04540	-0.226000	0.09899	-0.971000	0.02607	ATG	.	.		0.612	TK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319577.1	NM_003258		G	76183452	A	G	76183452	1	3	262	0	1	0	0	0	0	0	0	0	362	217	8	2		2	AFMID	17	76183452	5'Flank	SNP	A	TCGA-FV-A2QQ-01A-11D-A22F-10	15417132	76183452	5011758	98	38356										
DNAH17	8632	hgsc.bcm.edu	37	chr17	76565546	76565546	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	agccagggagatgccactcaGgacttcctcgatttcacctt	9	13	2	1	rs563501310		TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr17:76565546G>A	ENST00000585328.1	-	8	1232	c.1108C>T	c.(1108-1110)Ctg>Ttg	p.L370L	DNAH17_ENST00000389840.5_Silent_p.L370L	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	370	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			ATGCCACTCAGGACTTCCTCG	0.522																																					p.L370L		Atlas-SNP	.											.	DNAH17	347	.	0			c.C1108T						.						82	63	69					17																	76565546		2203	4299	6502	SO:0001819	synonymous_variant	8632	exon8			CACTCAGGACTTC	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"Axonemal dyneins"	2946	protein-coding gene	gene with protein product		610063	"dynein, axonemal, heavy polypeptide 17", "dynein, axonemal, heavy chain like 1", "dynein, axonemal, heavy like 1"	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.1108C>T	chr17.hg19:g.76565546G>A		84.0	0.0		77.0	27.0	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	hg19																																																																																				.	.		0.522	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		A	76565546	G	A	76565546	2	1	262	1	0	0	0	0	0	0	0	1	4603	991	35	3		3	DNAH17	17	76565546	Silent	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10	382094	76565546	4629664	99	38357										
ME2	4200	hgsc.bcm.edu	37	chr18	48450496	48450496	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	agcaaaaatagatagttatcAggaaccatttactcactcag	6	8	3	1			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr18:48450496A>T	ENST00000321341.5	+	11	1357	c.1085A>T	c.(1084-1086)cAg>cTg	p.Q362L	ME2_ENST00000382927.3_Missense_Mutation_p.Q362L	NM_002396.4	NP_002387.1	P23368	MAOM_HUMAN	malic enzyme 2, NAD(+)-dependent, mitochondrial	362					malate metabolic process (GO:0006108)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|malate dehydrogenase (decarboxylating) (NAD+) activity (GO:0004471)|metal ion binding (GO:0046872)|NAD binding (GO:0051287)|oxaloacetate decarboxylase activity (GO:0008948)			breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(11)|upper_aerodigestive_tract(3)	23		Colorectal(6;0.0273)|all_epithelial(6;0.118)		Colorectal(21;0.0313)|READ - Rectum adenocarcinoma(32;0.105)|STAD - Stomach adenocarcinoma(97;0.184)		GATAGTTATCAGGAACCATTT	0.313																																					p.Q362L		Atlas-SNP	.											.	ME2	49	.	0			c.A1085T						.						107	107	107					18																	48450496		2203	4300	6503	SO:0001583	missense	4200	exon11			GTTATCAGGAACC	M55905	CCDS11948.1, CCDS54187.1	18q21	2012-10-02			ENSG00000082212	ENSG00000082212	1.1.1.40		6984	protein-coding gene	gene with protein product		154270				1993674	Standard	NM_002396		Approved		uc002ley.3	P23368	OTTHUMG00000132694	ENST00000321341.5:c.1085A>T	chr18.hg19:g.48450496A>T	ENSP00000321070:p.Gln362Leu	164.0	0.0		197.0	27.0	NM_001168335	B2R8J2|Q9BWL6|Q9BYG1|Q9H4B2	Missense_Mutation	SNP	ENST00000321341.5	hg19	CCDS11948.1	.	.	.	.	.	.	.	.	.	.	A	12.06	1.824846	0.32237	.	.	ENSG00000082212	ENST00000321341;ENST00000382927	T;T	0.32753	1.44;1.44	5.56	5.56	0.83823	Malic enzyme, NAD-binding (2);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.37293	0.0998	L	0.60957	1.885	0.54753	D	0.999987	B;P	0.34837	0.048;0.472	B;B	0.40285	0.016;0.325	T	0.28996	-1.0026	10	0.87932	D	0	-13.9313	13.5384	0.61659	1.0:0.0:0.0:0.0	.	362;362	Q9BWL6;P23368	.;MAOM_HUMAN	L	362	ENSP00000321070:Q362L;ENSP00000372384:Q362L	ENSP00000321070:Q362L	Q	+	2	0	ME2	46704494	1.000000	0.71417	1.000000	0.80357	0.118000	0.20060	6.601000	0.74136	2.244000	0.73946	0.528000	0.53228	CAG	.	.		0.313	ME2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255991.1	NM_002396		T	48450496	A	T	48450496	3	4	262	1	0	0	0	0	1	0	0	0	9427	188	7	4	1123	4	ME2	18	48450496	Missense_Mutation	SNP	A	TCGA-FV-A2QQ-01A-11D-A22F-10		48450496	29626752	100	38358										
CNDP2	55748	hgsc.bcm.edu	37	chr18	72183571	72183572	+	Missense_Mutation	DNP	GG	GG	TT													0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	tgattcccaggaaggtggttGgcaagttctccatcaggctc							TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr18:72183571_72183572GG>TT	ENST00000324262.4	+	9	1328_1329	c.1012_1013GG>TT	c.(1012-1014)GGc>TTc	p.G338F	CNDP2_ENST00000324301.8_Missense_Mutation_p.G254F|CNDP2_ENST00000579847.1_Missense_Mutation_p.G338F	NM_018235.2	NP_060705.2	Q96KP4	CNDP2_HUMAN	CNDP dipeptidase 2 (metallopeptidase M20 family)	338					cellular nitrogen compound metabolic process (GO:0034641)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)	p.G338S(1)		breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(5)|ovary(2)|skin(2)|stomach(3)	24		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.22)		GAAGGTGGTTGGCAAGTTCTCC	0.624																																					p.G338C|p.G338V		Atlas-SNP	.											CNDP2,caecum,carcinoma,-1,1|CNDP2,caecum,carcinoma,0,1	CNDP2	55	.	1	Substitution - Missense(1)	ovary(1)	c.G1012T|c.G1013T						.																																			SO:0001583	missense	55748	exon9			GTGGTTGGCAAGT|TGGTTGGCAAGTT	AK001692	CCDS12006.1, CCDS54190.1	18q22.3	2014-07-14	2004-07-12		ENSG00000133313	ENSG00000133313	3.4.13.18		24437	protein-coding gene	gene with protein product	"cytosolic nonspecific dipeptidase"	169800	"peptidase A"	PEPA		12473676	Standard	NM_018235		Approved	FLJ10830, CN2, HsT2298, CPGL	uc002llm.2	Q96KP4	OTTHUMG00000132853	Exception_encountered	chr18.hg19:g.72183571_72183572delinsTT	ENSP00000325548:p.Gly338Phe	57.0|56.0	0.0		65.0|63.0	24.0|22.0	NM_018235	B3KUG4|Q8WY59|Q9BQ94|Q9NVB4	Missense_Mutation	SNP	ENST00000324262.4	hg19	CCDS12006.1																																																																																			.	.		0.624	CNDP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256327.1	NM_018235		TT	72183572	GG	TT	72183571	3	4	262	1	0	0	0	0	1	0	0	0	3596	1348	47	3	1042	3	CNDP2	18	72183571	Missense_Mutation	DNP	GG	TCGA-FV-A2QQ-01A-11D-A22F-10	23733075	72183571	5893677	101	38359										
FEM1A	55527	hgsc.bcm.edu	37	chr19	4792915	4792915	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	gctggtcctggcctatgactAttccagggaggtcaacacca	11	12	1	1			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr19:4792915A>C	ENST00000269856.3	+	1	1188	c.1049A>C	c.(1048-1050)tAt>tCt	p.Y350S	AC005523.3_ENST00000598782.1_lincRNA|AC005523.2_ENST00000601192.1_RNA|AC005523.2_ENST00000596170.1_RNA	NM_018708.2	NP_061178.1	Q9BSK4	FEM1A_HUMAN	fem-1 homolog a (C. elegans)	350					negative regulation of inflammatory response (GO:0050728)|regulation of ubiquitin-protein transferase activity (GO:0051438)	cytoplasm (GO:0005737)	EP4 subtype prostaglandin E2 receptor binding (GO:0031867)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	17		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0139)		GCCTATGACTATTCCAGGGAG	0.652																																					p.Y350S		Atlas-SNP	.											.	FEM1A	41	.	0			c.A1049C						.						37	42	40					19																	4792915		2203	4294	6497	SO:0001583	missense	55527	exon1			ATGACTATTCCAG	BC004988	CCDS12135.1	19p13.3	2013-01-10	2006-11-08		ENSG00000141965	ENSG00000141965		"Ankyrin repeat domain containing"	16934	protein-coding gene	gene with protein product		613538				11441184	Standard	NM_018708		Approved		uc002mbf.3	Q9BSK4		ENST00000269856.3:c.1049A>C	chr19.hg19:g.4792915A>C	ENSP00000269856:p.Tyr350Ser	26.0	0.0		44.0	13.0	NM_018708	B2RDI3|Q711P8|Q9NPN7|Q9NPW8	Missense_Mutation	SNP	ENST00000269856.3	hg19	CCDS12135.1	.	.	.	.	.	.	.	.	.	.	A	8.208	0.799671	0.16397	.	.	ENSG00000141965	ENST00000269856	T	0.66280	-0.2	4.73	3.57	0.40892	.	0.075028	0.56097	U	0.000031	T	0.50939	0.1645	L	0.45352	1.415	0.42105	D	0.991357	B	0.22983	0.078	B	0.25405	0.06	T	0.36311	-0.9753	10	0.22109	T	0.4	-0.1881	10.0274	0.42079	0.9118:0.0:0.0882:0.0	.	350	Q9BSK4	FEM1A_HUMAN	S	350	ENSP00000269856:Y350S	ENSP00000269856:Y350S	Y	+	2	0	FEM1A	4743915	1.000000	0.71417	0.224000	0.23877	0.991000	0.79684	4.214000	0.58527	0.523000	0.28482	0.402000	0.26972	TAT	.	.		0.652	FEM1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459000.1			C	4792915	A	C	4792915	3	2	262	1	0	0	0	0	1	0	0	0	5817	449	16	5	1051	5	FEM1A	19	4792915	Missense_Mutation	SNP	A	TCGA-FV-A2QQ-01A-11D-A22F-10		4792915	54336068	102	38360										
ZNF626	199777	hgsc.bcm.edu	37	chr19	20807980	20807980	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	ggagtgcttaaaggctttgcCacattcttcacatttgtagg	10	8	2	0			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr19:20807980C>A	ENST00000601440.1	-	4	849	c.703G>T	c.(703-705)Ggc>Tgc	p.G235C	CTC-513N18.7_ENST00000595094.1_lincRNA	NM_001076675.2	NP_001070143.1	Q68DY1	ZN626_HUMAN	zinc finger protein 626	235					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|lung(3)|skin(1)	6						AAGGCTTTGCCACATTCTTCA	0.393																																					p.G235C		Atlas-SNP	.											.	ZNF626	121	.	0			c.G703T						.						54	58	56					19																	20807980		2181	4287	6468	SO:0001583	missense	199777	exon4			CTTTGCCACATTC	BC007116	CCDS32976.1, CCDS42535.1	19p13.11	2013-01-08				ENSG00000188171		"Zinc fingers, C2H2-type", "-"	30461	protein-coding gene	gene with protein product						12477932	Standard	NM_145297		Approved		uc002npb.1	Q68DY1		ENST00000601440.1:c.703G>T	chr19.hg19:g.20807980C>A	ENSP00000469958:p.Gly235Cys	29.0	0.0		39.0	8.0	NM_001076675	Q8N8T4|Q96QM1	Missense_Mutation	SNP	ENST00000601440.1	hg19	CCDS42535.1	.	.	.	.	.	.	.	.	.	.	N	12.67	2.006714	0.35415	.	.	ENSG00000188171	ENST00000392298;ENST00000453075;ENST00000305570	.	.	.	0.798	0.798	0.18660	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.85457	0.5701	H	0.98218	4.175	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.83154	-0.0102	8	0.87932	D	0	.	6.9412	0.24494	0.0:0.9999:0.0:1.0E-4	.	235	Q68DY1	ZN626_HUMAN	C	235;159;235	.	ENSP00000445201:G235C	G	-	1	0	ZNF626	20599820	0.000000	0.05858	0.582000	0.28627	0.581000	0.36288	0.651000	0.24873	0.162000	0.19483	0.165000	0.16767	GGC	.	.		0.393	ZNF626-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447845.2	NM_145297		A	20807980	C	A	20807980	3	1	262	1	0	0	0	0	1	0	0	0	18065	594	21	3	887	3	ZNF626	19	20807980	Missense_Mutation	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10	16015065	20807980	38321003	103	38361										
PPP5C	5536	hgsc.bcm.edu	37	chr19	46857048	46857048	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	aagttctacagccaggccatCgagctgaaccccagcaatgc	9	14	1	1	rs374930457		TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr19:46857048C>T	ENST00000012443.4	+	2	268	c.165C>T	c.(163-165)atC>atT	p.I55I	PPP5C_ENST00000391919.1_5'UTR	NM_006247.3	NP_006238.1	P53041	PPP5_HUMAN	protein phosphatase 5, catalytic subunit	55					cell death (GO:0008219)|DNA repair (GO:0006281)|mitotic nuclear division (GO:0007067)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein dephosphorylation (GO:0006470)|protein heterooligomerization (GO:0051291)|response to morphine (GO:0043278)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|RNA binding (GO:0003723)|signal transducer activity (GO:0004871)			endometrium(4)|kidney(1)|large_intestine(5)|liver(2)|lung(4)|ovary(1)|pancreas(1)	18		Ovarian(192;0.0731)|all_neural(266;0.196)		OV - Ovarian serous cystadenocarcinoma(262;0.000196)|all cancers(93;0.00192)|GBM - Glioblastoma multiforme(486;0.0499)|Epithelial(262;0.0504)		GCCAGGCCATCGAGCTGAACC	0.617																																					p.I55I		Atlas-SNP	.											.	PPP5C	44	.	0			c.C165T						.	C	,	1,4405	2.1+/-5.4	0,1,2202	81	59	67		165,165	1.8	1	19		67	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PPP5C	NM_001204284.1,NM_006247.3	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	55/478,55/500	46857048	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	5536	exon2			GGCCATCGAGCTG		CCDS12684.1	19q13.3	2013-01-10			ENSG00000011485	ENSG00000011485	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits", "Tetratricopeptide (TTC) repeat domain containing"	9322	protein-coding gene	gene with protein product		600658		PPP5		8666404	Standard	NM_006247		Approved	PP5	uc002pem.3	P53041	OTTHUMG00000134287	ENST00000012443.4:c.165C>T	chr19.hg19:g.46857048C>T		77.0	0.0		78.0	23.0	NM_006247	Q16722|Q53XV2	Silent	SNP	ENST00000012443.4	hg19	CCDS12684.1																																																																																			.	.		0.617	PPP5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258969.2	NM_006247		T	46857048	C	T	46857048	2	4	262	1	0	0	0	0	0	0	0	1	12418	874	31	1		1	PPP5C	19	46857048	Silent	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10	26049068	46857048	12271935	104	38362										
NKG7	4818	hgsc.bcm.edu	37	chr19	51875422	51875422	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	ccagagtccttacctgcagcAaaggctgcggtggttgagac	13	11	0	2			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr19:51875422A>G	ENST00000221978.5	-	2	476	c.297T>C	c.(295-297)ttT>ttC	p.F99F	NKG7_ENST00000600427.1_Silent_p.F64F|NKG7_ENST00000595217.1_Silent_p.F64F	NM_005601.3	NP_005592.1	Q16617	NKG7_HUMAN	natural killer cell granule protein 7	99						integral component of plasma membrane (GO:0005887)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	10		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000211)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		TACCTGCAGCAAAGGCTGCGG	0.627																																					p.F99F		Atlas-SNP	.											.	NKG7	20	.	0			c.T297C						.						74	83	80					19																	51875422		2203	4300	6503	SO:0001819	synonymous_variant	4818	exon2			TGCAGCAAAGGCT		CCDS12830.1	19q13.41	2014-03-07	2014-03-07		ENSG00000105374	ENSG00000105374			7830	protein-coding gene	gene with protein product	"granule membrane protein 17"	606008	"natural killer cell group 7 sequence"			8458737	Standard	NM_005601		Approved	GIG1, GMP-17	uc002pwj.3	Q16617	OTTHUMG00000182898	ENST00000221978.5:c.297T>C	chr19.hg19:g.51875422A>G		37.0	0.0		44.0	9.0	NM_005601		Silent	SNP	ENST00000221978.5	hg19	CCDS12830.1																																																																																			.	.		0.627	NKG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464260.2	NM_005601		G	51875422	A	G	51875422	2	3	262	1	0	0	0	0	0	0	0	1	10452	127	5	2		2	NKG7	19	51875422	Silent	SNP	A	TCGA-FV-A2QQ-01A-11D-A22F-10	5018374	51875422	7253561	105	38363										
ZNF350	59348	hgsc.bcm.edu	37	chr19	52468795	52468795	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	ttcgctggtgtacaatgagaTttcctttctggatgaagcct	10	8	1	2			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr19:52468795T>G	ENST00000243644.4	-	5	1138	c.911A>C	c.(910-912)aAt>aCt	p.N304T	HCCAT3_ENST00000600253.1_RNA|ZNF350_ENST00000600703.1_5'Flank|HCCAT3_ENST00000595010.1_RNA	NM_021632.3	NP_067645.3	Q9GZX5	ZN350_HUMAN	zinc finger protein 350	304					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(3)|kidney(3)|large_intestine(7)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		all_neural(266;0.0505)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0179)		TACAATGAGATTTCCTTTCTG	0.398																																					p.N304T		Atlas-SNP	.											.	ZNF350	48	.	0			c.A911C						.						116	109	111					19																	52468795		2203	4300	6503	SO:0001583	missense	59348	exon5			ATGAGATTTCCTT	AF295096	CCDS12845.1	19q13.41	2013-05-23			ENSG00000256683	ENSG00000256683		"Zinc fingers, C2H2-type", "-"	16656	protein-coding gene	gene with protein product		605422				11090615, 11161714	Standard	NM_021632		Approved	ZBRK1, ZFQR	uc002pyd.3	Q9GZX5	OTTHUMG00000182538	ENST00000243644.4:c.911A>C	chr19.hg19:g.52468795T>G	ENSP00000243644:p.Asn304Thr	152.0	0.0		183.0	57.0	NM_021632	Q96G73|Q9HAQ4	Missense_Mutation	SNP	ENST00000243644.4	hg19	CCDS12845.1	.	.	.	.	.	.	.	.	.	.	T	5.803	0.332392	0.10956	.	.	ENSG00000256683	ENST00000243644	T	0.07021	3.23	3.41	-0.00732	0.14009	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.39407	N	0.001364	T	0.11067	0.0270	L	0.48642	1.525	0.09310	N	1	D	0.67145	0.996	P	0.59221	0.854	T	0.23940	-1.0174	10	0.17832	T	0.49	.	3.2949	0.06963	0.1748:0.3117:0.0:0.5135	.	304	Q9GZX5	ZN350_HUMAN	T	304	ENSP00000243644:N304T	ENSP00000243644:N304T	N	-	2	0	ZNF350	57160607	0.000000	0.05858	0.001000	0.08648	0.092000	0.18411	-1.186000	0.03070	-0.308000	0.08792	-0.468000	0.05107	AAT	.	.		0.398	ZNF350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462278.1	NM_021632		G	52468795	T	G	52468795	3	3	262	1	0	0	0	0	1	0	0	0	17878	1493	52	5	691	5	ZNF350	19	52468795	Missense_Mutation	SNP	T	TCGA-FV-A2QQ-01A-11D-A22F-10	593373	52468795	6660188	106	38364										
ZNF665	79788	hgsc.bcm.edu	37	chr19	53668481	53668481	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	tctctccagtatgaattcttCgatgatttgctaagtgtgaa	8	7	2	3	rs375603672	byFrequency	TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr19:53668481C>A	ENST00000600412.1	-	2	1182	c.1067G>T	c.(1066-1068)cGa>cTa	p.R356L	CTD-2245F17.2_ENST00000600257.1_RNA|ZNF665_ENST00000396424.3_Missense_Mutation_p.R421L			Q9H7R5	ZN665_HUMAN	zinc finger protein 665	356					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	35				GBM - Glioblastoma multiforme(134;0.0196)		ATGAATTCTTCGATGATTTGC	0.408																																					p.R421L		Atlas-SNP	.											.,2	ZNF665	136	.	0			c.G1262T						.						82	88	86					19																	53668481		2202	4298	6500	SO:0001583	missense	79788	exon4			ATTCTTCGATGAT		CCDS46169.1	19q13.42	2013-01-08				ENSG00000197497		"Zinc fingers, C2H2-type", "-"	25885	protein-coding gene	gene with protein product							Standard	NM_024733		Approved	FLJ14345	uc010eqm.1	Q9H7R5		ENST00000600412.1:c.1067G>T	chr19.hg19:g.53668481C>A	ENSP00000469154:p.Arg356Leu	74.0	0.0		94.0	29.0	NM_024733	A8K5T8	Missense_Mutation	SNP	ENST00000600412.1	hg19		.	.	.	.	.	.	.	.	.	.	C	12.09	1.834024	0.32421	.	.	ENSG00000197497	ENST00000396424	T	0.05649	3.41	2.26	-4.52	0.03472	.	.	.	.	.	T	0.02727	0.0082	N	0.05280	-0.08	0.09310	N	0.999995	P	0.40197	0.706	B	0.40285	0.325	T	0.30149	-0.9988	9	0.49607	T	0.09	.	2.7641	0.05315	0.3174:0.2193:0.0:0.4633	.	421	Q9H7R5-2	.	L	421	ENSP00000379702:R421L	ENSP00000379702:R421L	R	-	2	0	ZNF665	58360293	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.574000	0.05868	-1.554000	0.01700	-1.951000	0.00486	CGA	.	.		0.408	ZNF665-002	PUTATIVE	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000464179.1	NM_024733		A	53668481	C	A	53668481	3	1	262	1	0	0	0	0	1	0	0	0	18088	884	31	1	778	1	ZNF665	19	53668481	Missense_Mutation	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10	1199686	53668481	5460502	107	38365										
CACNG7	59284	hgsc.bcm.edu	37	chr19	54445427	54445427	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	cagttcctgcagcccgaggcGtggcgccgcggccggagccc	16	17	0	0			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr19:54445427G>A	ENST00000391767.1	+	6	920	c.708G>A	c.(706-708)gcG>gcA	p.A236A	CACNG7_ENST00000222212.2_Silent_p.A236A			P62955	CCG7_HUMAN	calcium channel, voltage-dependent, gamma subunit 7	236				GAGVMSVYLFTKRYAEEEMYRPHPAFYRPRLSDCSDYSGQF LQPEAWRRGRSPSDISSDVSIQMTQNYPPAIKYPDHLHIST SPC -> VTSVGPRL (in Ref. 1; AAK20030). {ECO:0000305}.	calcium ion transport (GO:0006816)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0711)		AGCCCGAGGCGTGGCGCCGCG	0.667																																					p.A236A		Atlas-SNP	.											.	CACNG7	58	.	0			c.G708A						.						85	86	86					19																	54445427		2203	4300	6503	SO:0001819	synonymous_variant	59284	exon5			CGAGGCGTGGCGC	AF288387	CCDS12868.1	19q13.4	2008-05-02			ENSG00000105605	ENSG00000105605		"Calcium channel subunits"	13626	protein-coding gene	gene with protein product		606899				11170751	Standard	NM_031896		Approved		uc002qcr.2	P62955	OTTHUMG00000064852	ENST00000391767.1:c.708G>A	chr19.hg19:g.54445427G>A		59.0	0.0		47.0	19.0	NM_031896	Q52LL8|Q8VBX3|Q8WXS6|Q9BXT1	Silent	SNP	ENST00000391767.1	hg19	CCDS12868.1																																																																																			.	.		0.667	CACNG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139240.2			A	54445427	G	A	54445427	2	1	262	1	0	0	0	0	0	0	0	1	2564	1132	40	1		1	CACNG7	19	54445427	Silent	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10	776946	54445427	4683556	108	38366										
NLRP7	199713	hgsc.bcm.edu	37	chr19	55453049	55453049	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	cagctgctccagaagggtctGcagagtccactctagctggg	13	12	2	2			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr19:55453049G>C	ENST00000590030.1	-	1	71	c.31C>G	c.(31-33)Cag>Gag	p.Q11E	NLRP7_ENST00000340844.2_Missense_Mutation_p.Q11E|NLRP7_ENST00000592784.1_Missense_Mutation_p.Q11E|NLRP7_ENST00000588756.1_Missense_Mutation_p.Q11E|NLRP7_ENST00000448121.2_Missense_Mutation_p.Q11E|NLRP7_ENST00000446217.1_Missense_Mutation_p.Q39E|NLRP7_ENST00000328092.5_Missense_Mutation_p.Q11E			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	11	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.						ATP binding (GO:0005524)			autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		AGAAGGGTCTGCAGAGTCCAC	0.488																																					p.Q11E		Atlas-SNP	.											.	NLRP7	411	.	0			c.C31G						.						39	39	39					19																	55453049		2203	4300	6503	SO:0001583	missense	199713	exon2			GGGTCTGCAGAGT	AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"Nucleotide-binding domain and leucine rich repeat containing"	22947	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"	609661	"NACHT, leucine rich repeat and PYD containing 7"	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.31C>G	chr19.hg19:g.55453049G>C	ENSP00000465520:p.Gln11Glu	93.0	0.0		93.0	24.0	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Missense_Mutation	SNP	ENST00000590030.1	hg19	CCDS33109.1	.	.	.	.	.	.	.	.	.	.	G	5.997	0.367782	0.11352	.	.	ENSG00000167634	ENST00000328092;ENST00000448121;ENST00000340844;ENST00000446217;ENST00000399724	T;T;T;T	0.49720	0.77;0.77;0.77;0.77	1.53	0.337	0.15966	Pyrin (2);DEATH-like (2);	.	.	.	.	T	0.37652	0.1011	M	0.64404	1.975	0.09310	N	1	P;P;P;P	0.44946	0.846;0.846;0.846;0.815	B;B;B;B	0.43386	0.418;0.418;0.418;0.293	T	0.29518	-1.0009	9	0.06236	T	0.91	.	4.6364	0.12527	0.0:0.0:0.6273:0.3727	.	39;11;11;11	E7EPM2;Q32MH9;Q8WX94;Q8WX94-2	.;.;NALP7_HUMAN;.	E	11;11;11;39;11	ENSP00000329568:Q11E;ENSP00000409137:Q11E;ENSP00000339491:Q11E;ENSP00000414273:Q39E	ENSP00000329568:Q11E	Q	-	1	0	NLRP7	60144861	0.031000	0.19500	0.020000	0.16555	0.204000	0.24138	-0.174000	0.09839	0.144000	0.18951	0.313000	0.20887	CAG	.	.		0.488	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176		C	55453049	G	C	55453049	3	2	262	1	0	0	0	0	1	0	0	0	10491	1328	46	4	3122	4	NLRP7	19	55453049	Missense_Mutation	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10	1007622	55453049	3675934	109	38367										
PEG3	5178	hgsc.bcm.edu	37	chr19	57326459	57326459	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	tctgtgaggtctgtgagatcCacaaagcccaggccacagtc	11	12	2	2			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr19:57326459C>T	ENST00000326441.9	-	10	3714	c.3351G>A	c.(3349-3351)gtG>gtA	p.V1117V	ZIM2_ENST00000599935.1_Intron|ZIM2_ENST00000221722.5_Intron|ZIM2_ENST00000593711.1_Intron|ZIM2_ENST00000601070.1_Intron|PEG3_ENST00000423103.2_Silent_p.V1117V|ZIM2_ENST00000391708.3_Intron|PEG3_ENST00000598410.1_Silent_p.V993V|PEG3_ENST00000593695.1_Silent_p.V991V	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	1117				V -> M (in Ref. 7; BAB85588). {ECO:0000305}.	apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		CTGTGAGATCCACAAAGCCCA	0.488																																					p.V1117V		Atlas-SNP	.											.	PEG3	414	.	0			c.G3351A						.						130	121	124					19																	57326459		2203	4300	6503	SO:0001819	synonymous_variant	5178	exon9			GAGATCCACAAAG	AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"Zinc fingers, C2H2-type", "-", "-", "-"	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.3351G>A	chr19.hg19:g.57326459C>T		72.0	0.0		64.0	23.0	NM_001146184	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Silent	SNP	ENST00000326441.9	hg19	CCDS12948.1																																																																																			.	.		0.488	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2			T	57326459	C	T	57326459	2	4	262	1	0	0	0	0	0	0	0	1	11729	581	21	3		3	PEG3	19	57326459	Silent	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10	1873410	57326459	1802524	110	38368										
SNTA1	6640	hgsc.bcm.edu	37	chr20	32000381	32000381	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	gtcccaggcccagcaggtacCtgctcagttagccagccaat	10	15	1	0			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr20:32000381C>T	ENST00000217381.2	-	4	1180	c.909G>A	c.(907-909)caG>caA	p.Q303Q		NM_003098.2	NP_003089.1	Q13424	SNTA1_HUMAN	syntrophin, alpha 1	303	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				muscle contraction (GO:0006936)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|neuromuscular junction development (GO:0007528)|regulation of heart rate (GO:0002027)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of vasoconstriction by circulating norepinephrine (GO:0003117)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|ventricular cardiac muscle cell action potential (GO:0086005)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular (GO:0005622)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	ATPase binding (GO:0051117)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)			breast(1)|large_intestine(4)|liver(1)|lung(4)|skin(1)|stomach(1)|urinary_tract(1)	13						CAGCAGGTACCTGCTCAGTTA	0.642																																					p.Q303Q		Atlas-SNP	.											.	SNTA1	35	.	0			c.G909A						.						86	68	74					20																	32000381		2203	4300	6503	SO:0001630	splice_region_variant	6640	exon4			AGGTACCTGCTCA	U40571	CCDS13220.1	20q11.2	2014-09-17	2012-06-15		ENSG00000101400	ENSG00000101400			11167	protein-coding gene	gene with protein product	"pro-TGF-alpha cytoplasmic domain-interacting protein 1", "dystrophin-associated protein A1, 59kDa, acidic component"	601017	"syntrophin, alpha 1 (dystrophin-associated protein A1, 59kD, acidic component)"	SNT1		8576247, 8612778	Standard	NM_003098		Approved	TACIP1, LQT12	uc002wzd.1	Q13424	OTTHUMG00000032259	ENST00000217381.2:c.909+1G>A	chr20.hg19:g.32000381C>T		44.0	0.0		42.0	14.0	NM_003098	A8K7H9|B4DX40|E1P5N1|Q16438	Silent	SNP	ENST00000217381.2	hg19	CCDS13220.1																																																																																			.	.		0.642	SNTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078704.2	NM_003098	Silent	T	32000381	C	T	32000381	5	4	262	1	0	0	0	0	0	0	1	0	14886	695	24	3	628	3	SNTA1	20	32000381	Splice_Site	SNP	C	TCGA-FV-A2QQ-01A-11D-A22F-10		32000381	31025139	111	38369										
CDH4	1002	hgsc.bcm.edu	37	chr20	60348088	60348088	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	ggaaagaaggtcgtggctctGgacccctctccgcctccgaa	12	14	2	1			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr20:60348088G>T	ENST00000360469.5	+	4	514	c.426G>T	c.(424-426)ctG>ctT	p.L142L	CDH4_ENST00000543233.1_Silent_p.L68L	NM_001794.3	NP_001785.2	P55283	CADH4_HUMAN	cadherin 4, type 1, R-cadherin (retinal)	142					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(2)|lung(25)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			TCGTGGCTCTGGACCCCTCTC	0.597																																					p.L142L		Atlas-SNP	.											.	CDH4	172	.	0			c.G426T						.						41	40	40					20																	60348088		2203	4300	6503	SO:0001819	synonymous_variant	1002	exon4			GGCTCTGGACCCC	L34059	CCDS13488.1, CCDS58784.1	20q13.3	2010-01-26			ENSG00000179242	ENSG00000179242		"Cadherins / Major cadherins"	1763	protein-coding gene	gene with protein product	"R-Cadherin"	603006				10191097, 10516427	Standard	NM_001794		Approved		uc002ybn.2	P55283	OTTHUMG00000032890	ENST00000360469.5:c.426G>T	chr20.hg19:g.60348088G>T		49.0	0.0		49.0	9.0	NM_001794	B3KWB8|G3V1P8|Q2M208|Q5VZ44|Q9BZ05	Silent	SNP	ENST00000360469.5	hg19	CCDS13488.1																																																																																			.	.		0.597	CDH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079965.2	NM_001794		T	60348088	G	T	60348088	2	4	262	1	0	0	0	0	0	0	0	1	3114	1335	47	3		3	CDH4	20	60348088	Silent	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10	28347707	60348088	2677432	112	38370										
BIRC7	79444	hgsc.bcm.edu	37	chr20	61867529	61867529	+	Frame_Shift_Del	DEL	G	G	-													0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	gccggtgatggtcccacgcaGgagcgctgtggaccccgctc							TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr20:61867529delG	ENST00000217169.3	+	1	295	c.81delG	c.(79-81)cagfs	p.Q27fs	BIRC7_ENST00000395306.1_5'Flank|BIRC7_ENST00000342412.6_Frame_Shift_Del_p.Q27fs|MIR3196_ENST00000579556.1_RNA	NM_139317.1	NP_647478.1	Q96CA5	BIRC7_HUMAN	baculoviral IAP repeat containing 7	27					activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of natural killer cell apoptotic process (GO:0070247)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|lung(9)|ovary(1)	12	all_cancers(38;2.72e-09)					GTCCCACGCAGGAGCGCTGTG	0.667																																					p.Q27fs		Atlas-Indel,Pindel	.											.	BIRC7	25	.	0			c.80delA						.						16	15	15					20																	61867529		2182	4287	6469	SO:0001589	frameshift_variant	79444	exon1			.	AF301009	CCDS13512.1, CCDS13513.1	20q13.3	2011-01-25	2011-01-25		ENSG00000101197	ENSG00000101197		"Baculoviral IAP repeat containing", "RING-type (C3HC4) zinc fingers"	13702	protein-coding gene	gene with protein product	"melanoma inhibitor of apoptosis protein", "kidney inhibitor of apoptosis protein", "livin inhibitor-of-apoptosis", "livin"	605737	"baculoviral IAP repeat-containing 7"			11024045, 11162435	Standard	NM_139317		Approved	mliap, ML-IAP, KIAP, RNF50	uc002yej.3	Q96CA5	OTTHUMG00000032957	ENST00000217169.3:c.81delG	chr20.hg19:g.61867529delG	ENSP00000217169:p.Gln27fs	96.0	0.0		79.0	14.0	NM_139317	Q9BQV0|Q9H2A8|Q9HAP7	Frame_Shift_Del	DEL	ENST00000217169.3	hg19	CCDS13513.1																																																																																			.	.		0.667	BIRC7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080114.2	NM_139317		-	61867529	G	-	61867529	7	5	262	1	0	1	0	1	0	0	0	0	1439	991	35	0	83	0	BIRC7	20	61867529	Frame_Shift_Del	DEL	G	TCGA-FV-A2QQ-01A-11D-A22F-10	1519441	61867529	1157991	113	38371										
ZNRF3	84133	hgsc.bcm.edu	37	chr22	29445870	29445871	+	Frame_Shift_Del	DEL	TG	TG	-													0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	cactgttcctccagtgactcTgtggtagactgcactgaggt							TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr22:29445870_29445871delTG	ENST00000544604.2	+	8	1876_1877	c.1701_1702delTG	c.(1699-1704)tctgtgfs	p.V569fs	ZNRF3_ENST00000406323.3_Frame_Shift_Del_p.V469fs|ZNRF3_ENST00000402174.1_Frame_Shift_Del_p.V469fs|ZNRF3_ENST00000332811.4_Frame_Shift_Del_p.V469fs	NM_001206998.1	NP_001193927.1	Q9ULT6	ZNRF3_HUMAN	zinc and ring finger 3	569					canonical Wnt signaling pathway (GO:0060070)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of non-canonical Wnt signaling pathway (GO:2000051)|protein ubiquitination (GO:0016567)|stem cell proliferation (GO:0072089)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	integral component of plasma membrane (GO:0005887)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(4)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	28						CCAGTGACTCTGTGGTAGACTG	0.644																																					p.567_567del		Atlas-INDEL	.											.	ZNRF3	75	.	0			c.1700_1701del						.																																			SO:0001589	frameshift_variant	84133	exon8			.	AB051436	CCDS42999.1, CCDS56225.1	22q12.1	2013-01-09			ENSG00000183579	ENSG00000183579		"RING-type (C3HC4) zinc fingers"	18126	protein-coding gene	gene with protein product		612062				10574461	Standard	NM_032173		Approved	KIAA1133, BK747E2.3, FLJ22057, RNF203	uc003aeg.3	Q9ULT6	OTTHUMG00000151009	ENST00000544604.2:c.1701_1702delTG	chr22.hg19:g.29445872_29445873delTG	ENSP00000443824:p.Val569fs	42.0	0.0		42.0	10.0	NM_001206998	B3KU18|Q6ICH1|Q6NTF8|Q8WU18	Frame_Shift_Del	DEL	ENST00000544604.2	hg19	CCDS56225.1																																																																																			.	.		0.644	ZNRF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320943.2	XM_290972		-	29445871	TG	-	29445870	7	5	262	1	0	1	0	1	0	0	0	0	18228	1567	55	0	1427	0	ZNRF3	22	29445870	Frame_Shift_Del	DEL	TG	TCGA-FV-A2QQ-01A-11D-A22F-10		29445870	21858696	114	38372										
FBLN1	2192	hgsc.bcm.edu	37	chr22	45946402	45946402	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	gtgtgtgactggcatccacaActgctccatcaacgagacct	9	13	1	2			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chr22:45946402A>G	ENST00000327858.6	+	14	1699	c.1604A>G	c.(1603-1605)aAc>aGc	p.N535S	FBLN1_ENST00000476366.1_3'UTR|FBLN1_ENST00000262722.7_Missense_Mutation_p.N535S|FBLN1_ENST00000340923.5_Missense_Mutation_p.N535S|FBLN1_ENST00000442170.2_Missense_Mutation_p.N535S|FBLN1_ENST00000348697.2_Missense_Mutation_p.N535S|FBLN1_ENST00000402984.3_Missense_Mutation_p.N573S	NM_006486.2	NP_006477	P23142	FBLN1_HUMAN	fibulin 1	535	EGF-like 9; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|viral process (GO:0016032)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)|peptidase activator activity (GO:0016504)			biliary_tract(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)	30		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		GGCATCCACAACTGCTCCATC	0.597																																					p.N535S		Atlas-SNP	.											.	FBLN1	143	.	0			c.A1604G						.						92	72	79					22																	45946402		2203	4300	6503	SO:0001583	missense	2192	exon14			TCCACAACTGCTC		CCDS14067.1, CCDS14068.1, CCDS14069.1, CCDS43028.1	22q13.31	2010-06-15			ENSG00000077942	ENSG00000077942		"Fibulins"	3600	protein-coding gene	gene with protein product		135820				2269669, 1400330	Standard	NM_006485		Approved	FBLN	uc003bgj.1	P23142	OTTHUMG00000151340	ENST00000327858.6:c.1604A>G	chr22.hg19:g.45946402A>G	ENSP00000331544:p.Asn535Ser	38.0	0.0		46.0	9.0	NM_006487	B0QY42|B1AHL4|P23143|P23144|P37888|Q5TIC4|Q8TBH8|Q9HBQ5|Q9UC21|Q9UGR4|Q9UH41	Missense_Mutation	SNP	ENST00000327858.6	hg19	CCDS14067.1	.	.	.	.	.	.	.	.	.	.	A	14.40	2.523637	0.44866	.	.	ENSG00000077942	ENST00000348697;ENST00000402984;ENST00000262722;ENST00000327858;ENST00000442170;ENST00000340923	D;D;D;D;D;D	0.92199	-2.99;-2.26;-2.26;-2.99;-2.99;-2.26	4.97	4.97	0.65823	EGF-like calcium-binding, conserved site (1);Epidermal growth factor-like (1);EGF-like calcium-binding (1);	0.060794	0.64402	D	0.000003	D	0.90363	0.6984	L	0.37850	1.14	0.39020	D	0.95973	P;P;B;B	0.48834	0.757;0.916;0.094;0.359	B;P;B;B	0.51582	0.214;0.674;0.068;0.234	D	0.90038	0.4140	10	0.38643	T	0.18	.	11.077	0.48038	0.8449:0.1551:0.0:0.0	.	573;535;535;535	B1AHL2;P23142;B1AHL4;P23142-4	.;FBLN1_HUMAN;.;.	S	535;573;535;535;535;535	ENSP00000262723:N535S;ENSP00000385521:N573S;ENSP00000262722:N535S;ENSP00000331544:N535S;ENSP00000393812:N535S;ENSP00000342212:N535S	ENSP00000262722:N535S	N	+	2	0	FBLN1	44325066	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.093000	0.57714	1.874000	0.54306	0.459000	0.35465	AAC	.	.		0.597	FBLN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322287.1	NM_006486		G	45946402	A	G	45946402	3	3	262	1	0	0	0	0	1	0	0	0	5706	43	2	2	1658	2	FBLN1	22	45946402	Missense_Mutation	SNP	A	TCGA-FV-A2QQ-01A-11D-A22F-10	16500532	45946402	5358164	115	38373										
TEX11	56159	hgsc.bcm.edu	37	chrX	69942515	69942515	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0172413793103448	2	1	0.321802935010482	0	0.422366352201258	0.444444444444444	1	0	atgttcagacagaagtctaaGggcatgtcaagatgtagtat	11	5	3	3			TCGA-FV-A2QQ-01A-11D-A22F-10	TCGA-FV-A2QQ-10B-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4904d56f-0fe7-4482-8f6d-9e54d261f399	e31c3b51-9a28-4191-b67f-21ac68e47c1e	g.chrX:69942515G>A	ENST00000395889.2	-	14	1157	c.1002C>T	c.(1000-1002)ccC>ccT	p.P334P	TEX11_ENST00000374333.2_Silent_p.P319P|TEX11_ENST00000374320.2_Silent_p.P9P|TEX11_ENST00000344304.3_Silent_p.P334P	NM_001003811.1	NP_001003811.1	Q8IYF3	TEX11_HUMAN	testis expressed 11	334					chiasma assembly (GO:0051026)|fertilization (GO:0009566)|male gonad development (GO:0008584)|male meiosis chromosome segregation (GO:0007060)|meiotic gene conversion (GO:0006311)|negative regulation of apoptotic process (GO:0043066)|reciprocal meiotic recombination (GO:0007131)|resolution of meiotic recombination intermediates (GO:0000712)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)				breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(13)|ovary(3)|prostate(3)|skin(3)	48	Renal(35;0.156)					AGAAGTCTAAGGGCATGTCAA	0.338																																					p.P334P		Atlas-SNP	.											.	TEX11	132	.	0			c.C1002T						.						121	97	105					X																	69942515		2203	4300	6503	SO:0001819	synonymous_variant	56159	exon14			GTCTAAGGGCATG	AF285594	CCDS35323.1, CCDS43968.1	Xp11	2008-02-05	2007-03-13		ENSG00000120498	ENSG00000120498			11733	protein-coding gene	gene with protein product		300311	"testis expressed sequence 11"			11279525	Standard	NM_001003811		Approved	TSGA3, TGC1	uc004dyl.3	Q8IYF3	OTTHUMG00000021782	ENST00000395889.2:c.1002C>T	chrX.hg19:g.69942515G>A		55.0	0.0		63.0	43.0	NM_001003811	A8K8V6|Q5JQQ8|Q96LZ4|Q96M47|Q9BXU6	Silent	SNP	ENST00000395889.2	hg19	CCDS35323.1																																																																																			.	.		0.338	TEX11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359072.1			A	69942515	G	A	69942515	2	1	262	1	0	0	0	0	0	0	0	1	15789	987	35	3		3	TEX11	23	69942515	Silent	SNP	G	TCGA-FV-A2QQ-01A-11D-A22F-10		69942515	85328045	116	38374										
SSU72	29101	hgsc.bcm.edu	37	chr1	1509930	1509930	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ccgccacccgcagcggggacGacggcatggcggcggccgca	17	17	0	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:1509930G>A	ENST00000291386.3	-	1	319	c.8C>T	c.(7-9)tCg>tTg	p.S3L	SSU72_ENST00000359060.4_Missense_Mutation_p.S3L|AL645728.1_ENST00000366221.2_5'Flank	NM_014188.2	NP_054907.1	Q9NP77	SSU72_HUMAN	SSU72 RNA polymerase II CTD phosphatase homolog (S. cerevisiae)	3					dephosphorylation of RNA polymerase II C-terminal domain (GO:0070940)|mRNA polyadenylation (GO:0006378)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)	p.S3L(1)		large_intestine(2)|lung(5)	7	all_cancers(77;0.00125)|all_epithelial(69;0.000703)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.03e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;5.04e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.72e-23)|GBM - Glioblastoma multiforme(42;1.2e-07)|Colorectal(212;0.000188)|COAD - Colon adenocarcinoma(227;0.000214)|Kidney(185;0.00254)|STAD - Stomach adenocarcinoma(132;0.00645)|BRCA - Breast invasive adenocarcinoma(365;0.00837)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)		CAGCGGGGACGACGGCATGGC	0.706																																					p.S3L		Atlas-SNP	.											SSU72_ENST00000359060,NS,carcinoma,0,2	SSU72	15	.	1	Substitution - Missense(1)	lung(1)	c.C8T						.						37	25	29					1																	1509930		2195	4299	6494	SO:0001583	missense	29101	exon1			GGGGACGACGGCA	AJ276409	CCDS32.1	1p36	2010-03-24	2006-04-04		ENSG00000160075	ENSG00000160075			25016	protein-coding gene	gene with protein product			"Ssu72 RNA polymerase II CTD phosphatase homolog (yeast)"			15125841, 15659578	Standard	NM_014188		Approved	HSPC182	uc001agd.3	Q9NP77	OTTHUMG00000000576	ENST00000291386.3:c.8C>T	chr1.hg19:g.1509930G>A	ENSP00000291386:p.Ser3Leu	184.0	0.0		60.0	3.0	NM_014188	Q9BZS6|Q9H933	Missense_Mutation	SNP	ENST00000291386.3	hg19	CCDS32.1	.	.	.	.	.	.	.	.	.	.	G	18.00	3.526432	0.64860	.	.	ENSG00000160075	ENST00000291386;ENST00000378725;ENST00000359060	T;T	0.16897	2.31;2.31	3.95	3.95	0.45737	.	0.350330	0.27294	N	0.020022	T	0.11452	0.0279	N	0.19112	0.55	0.45837	D	0.9987	B;B;B	0.26935	0.004;0.164;0.0	B;B;B	0.18263	0.009;0.021;0.001	T	0.12837	-1.0532	10	0.32370	T	0.25	-3.9771	14.7173	0.69280	0.0:0.0:1.0:0.0	.	3;3;3	B4DMK6;Q9NP77-2;Q9NP77	.;.;SSU72_HUMAN	L	3	ENSP00000291386:S3L;ENSP00000351955:S3L	ENSP00000291386:S3L	S	-	2	0	SSU72	1499793	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	2.977000	0.49297	2.051000	0.60960	0.313000	0.20887	TCG	.	.		0.706	SSU72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001366.1	NM_014188		A	1509930	G	A	1509930	3	1	263	1	0	0	0	0	1	0	0	0	15217	1059	37	1	596	1	SSU72	1	1509930	Missense_Mutation	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10		1509930	247740691	1	38375										
DFFB	1677	hgsc.bcm.edu	37	chr1	3775365	3775365	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ttccccagtgttcccgacaaCgccgagctggtgctgctcac	10	16	1	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:3775365C>T	ENST00000378209.3	+	2	521	c.198C>T	c.(196-198)aaC>aaT	p.N66N	DFFB_ENST00000378212.2_Silent_p.N66N|DFFB_ENST00000341385.3_Silent_p.N66N|CEP104_ENST00000378230.3_5'Flank|DFFB_ENST00000338895.3_Silent_p.N66N|CEP104_ENST00000378223.3_5'Flank	NM_004402.2	NP_004393.1	O76075	DFFB_HUMAN	DNA fragmentation factor, 40kDa, beta polypeptide (caspase-activated DNase)	66	CIDE-N. {ECO:0000255|PROSITE- ProRule:PRU00447}.				apoptotic chromosome condensation (GO:0030263)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)	p.N66N(1)		endometrium(1)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_cancers(23;2.05e-30)|all_epithelial(116;6.22e-21)|all_lung(118;2.65e-08)|Lung NSC(185;6.25e-06)|Breast(487;0.000659)|Renal(390;0.00121)|all_neural(13;0.0019)|Hepatocellular(190;0.00705)|Colorectal(325;0.0113)|all_hematologic(16;0.0194)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0548)|Medulloblastoma(700;0.211)		Epithelial(90;1.18e-39)|OV - Ovarian serous cystadenocarcinoma(86;7.28e-23)|GBM - Glioblastoma multiforme(42;2.95e-17)|Colorectal(212;1.23e-05)|COAD - Colon adenocarcinoma(227;5.94e-05)|Kidney(185;0.000371)|BRCA - Breast invasive adenocarcinoma(365;0.00038)|KIRC - Kidney renal clear cell carcinoma(229;0.00571)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.124)		TTCCCGACAACGCCGAGCTGG	0.652																																					p.N66N		Atlas-SNP	.											DFFB,NS,carcinoma,0,2	DFFB	30	.	1	Substitution - coding silent(1)	endometrium(1)	c.C198T						.						63	58	60					1																	3775365		2203	4300	6503	SO:0001819	synonymous_variant	1677	exon2			CGACAACGCCGAG		CCDS52.1, CCDS72693.1	1p36.3	2014-03-06	2002-08-29		ENSG00000169598	ENSG00000169598			2773	protein-coding gene	gene with protein product		601883				9108473, 9560346	Standard	NM_004402		Approved	CAD, CPAN, DFF-40, DFF40	uc001alc.3	O76075	OTTHUMG00000003525	ENST00000378209.3:c.198C>T	chr1.hg19:g.3775365C>T		104.0	0.0		94.0	4.0	NM_004402	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Silent	SNP	ENST00000378209.3	hg19	CCDS52.1																																																																																			.	.		0.652	DFFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009821.2	NM_001282669		T	3775365	C	T	3775365	2	4	263	1	0	0	0	0	0	0	0	1	4455	535	19	1		1	DFFB	1	3775365	Silent	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	2265435	3775365	245475256	2	38376										
TAS1R1	80835	hgsc.bcm.edu	37	chr1	6638906	6638906	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tggcacctagacacccctgtGgtgaggtcagcagggggccg	16	12	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:6638906G>A	ENST00000333172.6	+	6	1981	c.1788G>A	c.(1786-1788)gtG>gtA	p.V596V	TAS1R1_ENST00000351136.3_Silent_p.V342V|ZBTB48_ENST00000377674.4_5'Flank|TAS1R1_ENST00000328191.4_3'UTR	NM_138697.3	NP_619642.2	Q7RTX1	TS1R1_HUMAN	taste receptor, type 1, member 1	596					detection of chemical stimulus involved in sensory perception of taste (GO:0050912)|sensory perception of umami taste (GO:0050917)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(13)|ovary(1)|skin(1)|urinary_tract(2)	29	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;8.73e-34)|all_epithelial(116;9.26e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Breast(487;0.000353)|Renal(390;0.0007)|Colorectal(325;0.00104)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443)		Colorectal(212;1.29e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00108)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0642)		ACACCCCTGTGGTGAGGTCAG	0.622																																					p.V596V		Atlas-SNP	.											.	TAS1R1	76	.	0			c.G1788A						.						41	39	40					1																	6638906		2203	4300	6503	SO:0001819	synonymous_variant	80835	exon6			CCCTGTGGTGAGG		CCDS81.1, CCDS82.1	1p36.23	2012-08-22	2003-03-24		ENSG00000173662	ENSG00000173662		"Taste receptors / Type 1", "GPCR / Unclassified : Taste receptors"	14448	protein-coding gene	gene with protein product		606225	"G protein-coupled receptor 70"	GPR70			Standard	NM_138697		Approved	T1R1, TR1	uc001ant.3	Q7RTX1	OTTHUMG00000001441	ENST00000333172.6:c.1788G>A	chr1.hg19:g.6638906G>A		107.0	0.0		100.0	5.0	NM_138697	B2RMX0|Q5SY22|Q5SY24|Q8NGZ7|Q8TDJ7|Q8TDJ8|Q8TDJ9|Q8TDK0	Silent	SNP	ENST00000333172.6	hg19	CCDS81.1																																																																																			.	.		0.622	TAS1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004211.1			A	6638906	G	A	6638906	2	1	263	1	0	0	0	0	0	0	0	1	15577	1335	47	3		3	TAS1R1	1	6638906	Silent	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	2863541	6638906	242611715	3	38377										
UBE4B	10277	hgsc.bcm.edu	37	chr1	10166449	10166449	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gcggtatcgcccctacactgTcactcacccatgggcgtcct	9	17	2	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:10166449T>C	ENST00000343090.6	+	7	1079	c.1004T>C	c.(1003-1005)gTc>gCc	p.V335A	UBE4B_ENST00000253251.8_Intron|UBE4B_ENST00000377157.3_Intron	NM_001105562.2	NP_001099032.1			ubiquitination factor E4B									p.V335A(1)		NS(3)|breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(14)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	48		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		CCCTACACTGTCACTCACCCA	0.647																																					p.V335A		Atlas-SNP	.											UBE4B_ENST00000343090,NS,carcinoma,0,1	UBE4B	233	.	1	Substitution - Missense(1)	endometrium(1)	c.T1004C						.						78	87	84					1																	10166449		2089	4204	6293	SO:0001583	missense	10277	exon7			ACACTGTCACTCA	AF091093	CCDS110.1, CCDS41245.1	1p36.1	2013-01-28	2011-05-19		ENSG00000130939	ENSG00000130939		"U-box domain containing"	12500	protein-coding gene	gene with protein product		613565	"ubiquitination factor E4B (homologous to yeast UFD2)", "ubiquitination factor E4B (UFD2 homolog, yeast)"			9734811, 10089879	Standard	NM_006048		Approved	UBOX3, E4, UFD2, KIAA0684	uc001aqs.4	O95155	OTTHUMG00000001797	ENST00000343090.6:c.1004T>C	chr1.hg19:g.10166449T>C	ENSP00000343001:p.Val335Ala	102.0	0.0		60.0	3.0	NM_001105562		Missense_Mutation	SNP	ENST00000343090.6	hg19	CCDS41245.1	.	.	.	.	.	.	.	.	.	.	T	17.18	3.324437	0.60634	.	.	ENSG00000130939	ENST00000343090	T	0.53857	0.6	5.49	5.49	0.81192	.	0.357378	0.25405	N	0.030915	T	0.39545	0.1082	N	0.22421	0.69	0.80722	D	1	B	0.14438	0.01	B	0.14023	0.01	T	0.20042	-1.0287	10	0.18276	T	0.48	-4.8631	15.9029	0.79397	0.0:0.0:0.0:1.0	.	335	O95155	UBE4B_HUMAN	A	335	ENSP00000343001:V335A	ENSP00000343001:V335A	V	+	2	0	UBE4B	10089036	0.997000	0.39634	0.992000	0.48379	0.631000	0.37964	6.385000	0.73182	2.217000	0.71921	0.482000	0.46254	GTC	.	.		0.647	UBE4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000005016.1	NM_006048		C	10166449	T	C	10166449	3	2	263	1	0	0	0	0	1	0	0	0	16898	1667	58	2	1030	2	UBE4B	1	10166449	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	3527543	10166449	239084172	4	38378										
SPEN	23013	hgsc.bcm.edu	37	chr1	16263967	16263967	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tgaagcctgaccttccagtcTctcttcccactcagactgcc	6	17	3	3			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:16263967T>C	ENST00000375759.3	+	12	10540	c.10336T>C	c.(10336-10338)Tct>Cct	p.S3446P		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	3446	Pro-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		CCTTCCAGTCTCTCTTCCCAC	0.577																																					p.S3446P		Atlas-SNP	.											.	SPEN	374	.	0			c.T10336C						.						87	79	81					1																	16263967		2203	4300	6503	SO:0001583	missense	23013	exon12			CCAGTCTCTCTTC		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"RNA binding motif (RRM) containing"	17575	protein-coding gene	gene with protein product		613484	"SPEN homolog, transcriptional regulator (Drosophila)", "spen homolog, transcriptional regulator (Drosophila)"			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.10336T>C	chr1.hg19:g.16263967T>C	ENSP00000364912:p.Ser3446Pro	50.0	0.0		74.0	6.0	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	hg19	CCDS164.1	.	.	.	.	.	.	.	.	.	.	T	6.856	0.527276	0.13066	.	.	ENSG00000065526	ENST00000375759	T	0.07908	3.15	5.23	4.32	0.51571	.	.	.	.	.	T	0.02494	0.0076	N	0.00926	-1.1	0.22479	N	0.999069	B	0.02656	0.0	B	0.01281	0.0	T	0.35674	-0.9779	9	0.02654	T	1	-9.4211	10.649	0.45636	0.0:0.8513:0.0:0.1487	.	3446	Q96T58	MINT_HUMAN	P	3446	ENSP00000364912:S3446P	ENSP00000364912:S3446P	S	+	1	0	SPEN	16136554	0.397000	0.25270	0.890000	0.34922	0.338000	0.28826	1.080000	0.30779	1.318000	0.45170	-0.146000	0.13790	TCT	.	.		0.577	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		C	16263967	T	C	16263967	3	2	263	1	0	0	0	0	1	0	0	0	15053	1551	54	2	10382	2	SPEN	1	16263967	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	6097518	16263967	232986654	5	38379										
EPHB2	2048	hgsc.bcm.edu	37	chr1	23232489	23232489	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ttgtcccccagtgaccccagGcatgaagatctacatcgatc	8	14	1	3			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:23232489G>T	ENST00000400191.3	+	10	1793	c.1775G>T	c.(1774-1776)gGc>gTc	p.G592V	EPHB2_ENST00000374627.1_Missense_Mutation_p.G587V|EPHB2_ENST00000374630.3_Missense_Mutation_p.G592V|EPHB2_ENST00000374632.3_Missense_Mutation_p.G593V	NM_004442.6|NM_017449.3	NP_004433.2|NP_059145.2	P29323	EPHB2_HUMAN	EPH receptor B2	592					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|camera-type eye morphogenesis (GO:0048593)|central nervous system projection neuron axonogenesis (GO:0021952)|commissural neuron axon guidance (GO:0071679)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|ephrin receptor signaling pathway (GO:0048013)|inner ear morphogenesis (GO:0042472)|learning (GO:0007612)|negative regulation of axonogenesis (GO:0050771)|nervous system development (GO:0007399)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse assembly (GO:0051965)|regulation of body fluid levels (GO:0050878)|retinal ganglion cell axon guidance (GO:0031290)|urogenital system development (GO:0001655)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|protein tyrosine kinase activity (GO:0004713)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(8)|stomach(1)|urinary_tract(1)	56		Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153)		GTGACCCCAGGCATGAAGATC	0.522																																					p.G593V		Atlas-SNP	.											.	EPHB2	257	.	0			c.G1778T						.						85	79	81					1																	23232489		2203	4300	6503	SO:0001583	missense	2048	exon10			CCCCAGGCATGAA	AF025304	CCDS229.2, CCDS230.1	1p36.1-p35	2014-09-17	2004-10-28		ENSG00000133216	ENSG00000133216	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3393	protein-coding gene	gene with protein product		600997	"EphB2"	DRT, ERK, EPHT3		1648701	Standard	NM_017449		Approved	Hek5, Tyro5	uc001bge.3	P29323	OTTHUMG00000002881	ENST00000400191.3:c.1775G>T	chr1.hg19:g.23232489G>T	ENSP00000383053:p.Gly592Val	99.0	0.0		89.0	38.0	NM_004442	O43477|Q5T0U6|Q5T0U7|Q5T0U8	Missense_Mutation	SNP	ENST00000400191.3	hg19		.	.	.	.	.	.	.	.	.	.	G	21.6	4.180541	0.78677	.	.	ENSG00000133216	ENST00000374625;ENST00000374630;ENST00000400191;ENST00000374632;ENST00000374627	T;T;T;T	0.12465	2.68;2.68;2.68;2.68	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	T	0.46229	0.1382	M	0.90542	3.125	0.80722	D	1	B;D;D;D	0.76494	0.035;0.999;0.998;0.995	B;D;D;D	0.76575	0.026;0.988;0.98;0.985	T	0.54417	-0.8297	10	0.66056	D	0.02	.	17.4757	0.87658	0.0:0.0:1.0:0.0	.	534;592;610;593	A6NJM0;P29323;Q4LE53;P29323-3	.;EPHB2_HUMAN;.;.	V	534;592;592;593;587	ENSP00000363761:G592V;ENSP00000383053:G592V;ENSP00000363763:G593V;ENSP00000363758:G587V	ENSP00000363755:G534V	G	+	2	0	EPHB2	23105076	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.601000	0.98297	2.774000	0.95407	0.644000	0.83932	GGC	.	.		0.522	EPHB2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000008060.2	NM_017449		T	23232489	G	T	23232489	3	4	263	1	0	0	0	0	1	0	0	0	5177	1203	42	3	1816	3	EPHB2	1	23232489	Missense_Mutation	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	6968522	23232489	226018132	6	38380										
ASAP3	55616	hgsc.bcm.edu	37	chr1	23759640	23759640	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ttgactggcaagggcgggggAcagtcctcactctcgccctg	14	13	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:23759640A>G	ENST00000336689.3	-	22	2297	c.2253T>C	c.(2251-2253)tgT>tgC	p.C751C	ASAP3_ENST00000495646.1_Silent_p.C255C|ASAP3_ENST00000437606.2_Silent_p.C742C	NM_017707.3	NP_060177.2	Q8TDY4	ASAP3_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 3	751					cell migration (GO:0016477)|positive regulation of ARF GTPase activity (GO:0032850)|regulation of stress fiber assembly (GO:0051492)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	24						AGGGCGGGGGACAGTCCTCAC	0.582																																					p.C751C		Atlas-SNP	.											.	ASAP3	65	.	0			c.T2253C						.						98	102	100					1																	23759640		2203	4300	6503	SO:0001819	synonymous_variant	55616	exon22			CGGGGGACAGTCC	AK000206	CCDS235.1, CCDS44087.1	1p36.13	2013-01-10	2008-10-09	2008-09-22	ENSG00000088280	ENSG00000088280		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	14987	protein-coding gene	gene with protein product	"centaurin, beta 6"		"development and differentiation enhancing factor-like 1"	DDEFL1		14654939	Standard	NM_017707		Approved	FLJ20199, UPLC1, CENTB6	uc001bha.2	Q8TDY4	OTTHUMG00000003234	ENST00000336689.3:c.2253T>C	chr1.hg19:g.23759640A>G		118.0	0.0		164.0	7.0	NM_017707	B3KRW0|B4DHH4|Q6P9F4|Q86UY1|Q9NXK2	Silent	SNP	ENST00000336689.3	hg19	CCDS235.1																																																																																			.	.		0.582	ASAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008916.2	NM_017707		G	23759640	A	G	23759640	2	3	263	1	0	0	0	0	0	0	0	1	1012	273	10	2		2	ASAP3	1	23759640	Silent	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	527151	23759640	225490981	7	38381										
GMEB1	10691	hgsc.bcm.edu	37	chr1	29040628	29040628	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cagaagaagcaaggccaggaTcacaggctgaaatctcagac	11	10	2	4			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:29040628T>C	ENST00000294409.2	+	10	1155	c.1065T>C	c.(1063-1065)gaT>gaC	p.D355D	GMEB1_ENST00000373816.1_Silent_p.D345D|GMEB1_ENST00000480454.1_3'UTR|GMEB1_ENST00000361872.4_Silent_p.D345D	NM_006582.3	NP_006573.2	Q9Y692	GMEB1_HUMAN	glucocorticoid modulatory element binding protein 1	355					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(4)	11		Colorectal(325;3.46e-05)|Lung NSC(340;0.000451)|all_lung(284;0.00063)|Breast(348;0.00502)|Renal(390;0.00555)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0221)|KIRC - Kidney renal clear cell carcinoma(1967;0.0296)|READ - Rectum adenocarcinoma(331;0.0649)		AAGGCCAGGATCACAGGCTGA	0.493																																					p.D355D		Atlas-SNP	.											.	GMEB1	28	.	0			c.T1065C						.						89	96	94					1																	29040628		2203	4300	6503	SO:0001819	synonymous_variant	10691	exon10			CCAGGATCACAGG	AF099013	CCDS327.1, CCDS328.1	1p35	2008-02-05			ENSG00000162419	ENSG00000162419			4370	protein-coding gene	gene with protein product		604409				10386584, 10523663	Standard	NM_006582		Approved	P96PIF, PIF96	uc001bra.3	Q9Y692	OTTHUMG00000003647	ENST00000294409.2:c.1065T>C	chr1.hg19:g.29040628T>C		88.0	0.0		89.0	4.0	NM_006582	B1AT48|Q9NWH1|Q9UKD0	Silent	SNP	ENST00000294409.2	hg19	CCDS327.1																																																																																			.	.		0.493	GMEB1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000010333.1	NM_006582		C	29040628	T	C	29040628	2	2	263	1	0	0	0	0	0	0	0	1	6495	1432	50	2		2	GMEB1	1	29040628	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	5280988	29040628	220209993	8	38382										
SFPQ	6421	hgsc.bcm.edu	37	chr1	35656352	35656352	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	atgcctttcttgctgctggcTtagaagcaaattcaacaatg	8	9	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:35656352T>G	ENST00000357214.5	-	3	1360	c.1262A>C	c.(1261-1263)aAg>aCg	p.K421T		NM_005066.2	NP_005057.1	P23246	SFPQ_HUMAN	splicing factor proline/glutamine-rich	421	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H3 deacetylation (GO:0070932)|mRNA processing (GO:0006397)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902177)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|histone deacetylase binding (GO:0042826)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)		SFPQ/TFE3(6)	NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(4)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	25		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.196)				TGCTGCTGGCTTAGAAGCAAA	0.383			T	TFE3	papillary renal cell																																p.K421T		Atlas-SNP	.		Dom	yes		1	1p34.3	6421	splicing factor proline/glutamine rich(polypyrimidine tract binding protein associated)		E	.	SFPQ	51	.	0			c.A1262C						.						139	135	137					1																	35656352		2203	4300	6503	SO:0001583	missense	6421	exon3			GCTGGCTTAGAAG	X70944	CCDS388.1	1p34.3	2014-06-13	2010-05-04		ENSG00000116560	ENSG00000116560		"RNA binding motif (RRM) containing"	10774	protein-coding gene	gene with protein product	"polypyrimidine tract binding protein associated", "protein phosphatase 1, regulatory subunit 140"	605199	"splicing factor proline/glutamine rich (polypyrimidine tract-binding protein-associated)"			8449401	Standard	NM_005066		Approved	PSF, PPP1R140	uc001bys.3	P23246	OTTHUMG00000004157	ENST00000357214.5:c.1262A>C	chr1.hg19:g.35656352T>G	ENSP00000349748:p.Lys421Thr	137.0	0.0		155.0	57.0	NM_005066	P30808|Q5SZ71	Missense_Mutation	SNP	ENST00000357214.5	hg19	CCDS388.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.481314	0.84747	.	.	ENSG00000116560	ENST00000357214	T	0.18016	2.24	5.52	5.52	0.82312	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.138027	0.64402	D	0.000004	T	0.35158	0.0922	L	0.45698	1.435	0.80722	D	1	D	0.76494	0.999	D	0.69307	0.963	T	0.05468	-1.0883	10	0.72032	D	0.01	-13.1554	15.6879	0.77426	0.0:0.0:0.0:1.0	.	421	P23246	SFPQ_HUMAN	T	421	ENSP00000349748:K421T	ENSP00000349748:K421T	K	-	2	0	SFPQ	35428939	1.000000	0.71417	0.986000	0.45419	0.986000	0.74619	4.867000	0.63013	2.102000	0.63906	0.451000	0.29950	AAG	.	.		0.383	SFPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011984.4	NM_005066		G	35656352	T	G	35656352	3	3	263	1	0	0	0	0	1	0	0	0	14175	1609	56	5	893	5	SFPQ	1	35656352	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	6615724	35656352	213594269	9	38383										
KIAA0319L	79932	hgsc.bcm.edu	37	chr1	35928258	35928258	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tgtagaagtggttggcaaagAgatctcctggaactgaggtg	15	5	1	3			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:35928258A>G	ENST00000325722.3	-	8	1492	c.1258T>C	c.(1258-1260)Tct>Cct	p.S420P	KIAA0319L_ENST00000485551.1_5'UTR	NM_024874.4	NP_079150.3	Q8IZA0	K319L_HUMAN	KIAA0319-like	420	PKD 2. {ECO:0000255|PROSITE- ProRule:PRU00151}.					cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(12)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	34		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				GTTGGCAAAGAGATCTCCTGG	0.448																																					p.S420P		Atlas-SNP	.											.	KIAA0319L	156	.	0			c.T1258C						.						89	82	84					1																	35928258		2203	4300	6503	SO:0001583	missense	79932	exon8			GCAAAGAGATCTC	AY163234	CCDS390.1	1p34.3	2008-10-24			ENSG00000142687	ENSG00000142687			30071	protein-coding gene	gene with protein product		613535				11347906	Standard	NM_024874		Approved	KIAA1837	uc001byx.3	Q8IZA0	OTTHUMG00000004370	ENST00000325722.3:c.1258T>C	chr1.hg19:g.35928258A>G	ENSP00000318406:p.Ser420Pro	54.0	0.0		63.0	4.0	NM_024874	B1AN13|D3DPR8|O95010|Q6PJJ7|Q7L1C9|Q8N2B3|Q8NDA0|Q8WY39|Q8WYZ5|Q96IC3|Q96JJ0|Q9BUW6|Q9H7V0	Missense_Mutation	SNP	ENST00000325722.3	hg19	CCDS390.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.9|22.9	4.349505|4.349505	0.82132|0.82132	.|.	.|.	ENSG00000142687|ENSG00000142687	ENST00000431916|ENST00000325722;ENST00000426982;ENST00000440579	.|T;T;T	.|0.13657	.|2.57;2.57;2.57	5.54|5.54	4.38|4.38	0.52667|0.52667	.|PKD/Chitinase domain (1);Fibronectin, type III (1);PKD/REJ-like protein (1);PKD domain (1);	.|0.183165	.|0.48767	.|D	.|0.000163	T|T	0.36608|0.36608	0.0973|0.0973	M|M	0.78223|0.78223	2.4|2.4	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;0.999	.|D;D	.|0.76575	.|0.988;0.972	T|T	0.10894|0.10894	-1.0610|-1.0610	5|10	.|0.59425	.|D	.|0.04	-6.7581|-6.7581	11.7978|11.7978	0.52110|0.52110	0.853:0.147:0.0:0.0|0.853:0.147:0.0:0.0	.|.	.|420;420	.|Q8IZA0-2;Q8IZA0	.|.;K319L_HUMAN	P|P	249|420	.|ENSP00000318406:S420P;ENSP00000395883:S420P;ENSP00000407576:S420P	.|ENSP00000318406:S420P	L|S	-|-	2|1	0|0	KIAA0319L|KIAA0319L	35700845|35700845	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	5.869000|5.869000	0.69613|0.69613	0.893000|0.893000	0.36288|0.36288	0.533000|0.533000	0.62120|0.62120	CTC|TCT	.	.		0.448	KIAA0319L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012684.2	NM_024874		G	35928258	A	G	35928258	3	3	263	1	0	0	0	0	1	0	0	0	8178	304	11	2	1947	2	KIAA0319L	1	35928258	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	271906	35928258	213322363	10	38384										
MYCL1	4610	hgsc.bcm.edu	37	chr1	40363211	40363211	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cttggagcagctggccagggTgggcacctggtccctcagcg	16	13	1	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:40363211T>C	ENST00000372816.2	-	2	1375	c.928A>G	c.(928-930)Acc>Gcc	p.T310A	RP1-118J21.5_ENST00000418255.1_RNA|MYCL_ENST00000397332.2_Missense_Mutation_p.T340A			P12524	MYCL_HUMAN	v-myc avian myelocytomatosis viral oncogene lung carcinoma derived homolog	310	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.					nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)										CTGGCCAGGGTGGGCACCTGG	0.572																																					p.T340A		Atlas-SNP	.											MYCL1_ENST00000397332,NS,carcinoma,0,1	MYCL1	36	.	0			c.A1018G						.						59	61	61					1																	40363211		2203	4300	6503	SO:0001583	missense	4610	exon3			CCAGGGTGGGCAC		CCDS30682.1, CCDS44117.1, CCDS44117.2, CCDS53300.1	1p34.3	2013-07-09	2013-07-09	2013-07-09	ENSG00000116990	ENSG00000116990		"Basic helix-loop-helix proteins"	7555	protein-coding gene	gene with protein product	"l-myc protein", "myc-related gene from lung cancer", "oncogene lmyc"	164850	"v-myc avian myelocytomatosis viral oncogene homolog 1, lung carcinoma derived"	MYCL1		8978772	Standard	NM_001033082		Approved	LMYC, bHLHe38	uc001cer.2	P12524	OTTHUMG00000009243	ENST00000372816.2:c.928A>G	chr1.hg19:g.40363211T>C	ENSP00000361903:p.Thr310Ala	101.0	0.0		108.0	5.0	NM_001033082	A2A2C9|B4DJH2|Q14897|Q5QPL0|Q5QPL1|Q9NUE9	Missense_Mutation	SNP	ENST00000372816.2	hg19	CCDS30682.1	.	.	.	.	.	.	.	.	.	.	T	1.501	-0.552160	0.03996	.	.	ENSG00000116990	ENST00000397332;ENST00000372816	D;D	0.98012	-4.66;-4.66	5.75	3.43	0.39272	Helix-loop-helix DNA-binding (5);	0.276577	0.41194	N	0.000926	D	0.90448	0.7009	N	0.05031	-0.125	0.80722	D	1	B	0.10296	0.003	B	0.12156	0.007	D	0.83398	0.0021	10	0.18276	T	0.48	-28.1252	5.5714	0.17198	0.0:0.3228:0.0:0.6772	.	310	P12524	MYCL1_HUMAN	A	340;310	ENSP00000380494:T340A;ENSP00000361903:T310A	ENSP00000361903:T310A	T	-	1	0	MYCL1	40135798	0.996000	0.38824	1.000000	0.80357	0.994000	0.84299	2.211000	0.42825	1.017000	0.39495	0.533000	0.62120	ACC	.	.		0.572	MYCL-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277004.1	NM_001033082		C	40363211	T	C	40363211	3	2	263	1	0	0	0	0	1	0	0	0	10029	1696	59	2	170	2	MYCL1	1	40363211	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	4434953	40363211	208887410	11	38385										
ZNF691	51058	hgsc.bcm.edu	37	chr1	43316763	43316763	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ggagcatgggcaagagagccTgtcggatgaactgcaagaaa	15	7	0	3			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:43316763T>C	ENST00000372506.1	+	4	474	c.134T>C	c.(133-135)cTg>cCg	p.L45P	ZNF691_ENST00000372508.3_Missense_Mutation_p.L45P|ZNF691_ENST00000372504.1_Missense_Mutation_p.L67P|ZNF691_ENST00000372507.1_Missense_Mutation_p.L45P|ZNF691_ENST00000397044.3_Missense_Mutation_p.L76P|ZNF691_ENST00000372502.1_Missense_Mutation_p.L67P	NM_001242739.1	NP_001229668.1	Q5VV52	ZN691_HUMAN	zinc finger protein 691	76						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(2)|lung(2)|ovary(2)|prostate(1)	7	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				CAAGAGAGCCTGTCGGATGAA	0.562																																					p.L76P		Atlas-SNP	.											.	ZNF691	30	.	0			c.T227C						.						99	100	100					1																	43316763		2203	4300	6503	SO:0001583	missense	51058	exon4			AGAGCCTGTCGGA		CCDS476.1, CCDS55595.1	1p34.2	2013-01-08			ENSG00000164011	ENSG00000164011		"Zinc fingers, C2H2-type"	28028	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_001242739		Approved	Zfp691	uc021omh.1	Q5VV52	OTTHUMG00000007623	ENST00000372506.1:c.134T>C	chr1.hg19:g.43316763T>C	ENSP00000361584:p.Leu45Pro	67.0	0.0		95.0	4.0	NM_001242739	A8MXP6|B4DJR7|O95878|Q9NWE8	Missense_Mutation	SNP	ENST00000372506.1	hg19	CCDS476.1	.	.	.	.	.	.	.	.	.	.	T	6.624	0.483629	0.12581	.	.	ENSG00000164011	ENST00000372508;ENST00000372507;ENST00000372506;ENST00000397044;ENST00000372504;ENST00000397034;ENST00000372503;ENST00000372502	T;T;T;T;T;T;T	0.09817	2.97;2.97;2.97;2.98;2.94;4.43;2.94	5.21	-5.05	0.02955	.	0.712288	0.12256	N	0.485209	T	0.03564	0.0102	N	0.08118	0	0.38060	D	0.936037	B;B	0.06786	0.001;0.001	B;B	0.06405	0.001;0.002	T	0.33650	-0.9860	10	0.56958	D	0.05	0.1626	1.018	0.01512	0.2198:0.2679:0.1125:0.3998	.	76;76	B4DJR7;Q5VV52	.;ZN691_HUMAN	P	45;45;45;76;67;76;76;67	ENSP00000361586:L45P;ENSP00000361585:L45P;ENSP00000361584:L45P;ENSP00000380237:L76P;ENSP00000361582:L67P;ENSP00000380228:L76P;ENSP00000361580:L67P	ENSP00000361580:L67P	L	+	2	0	ZNF691	43089350	0.000000	0.05858	0.031000	0.17742	0.546000	0.35178	-0.661000	0.05311	-0.648000	0.05437	0.533000	0.62120	CTG	.	.		0.562	ZNF691-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020192.1	NM_015911		C	43316763	T	C	43316763	3	2	263	1	0	0	0	0	1	0	0	0	18111	1580	55	2	136	2	ZNF691	1	43316763	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	2953552	43316763	205933858	12	38386										
ERI3	79033	hgsc.bcm.edu	37	chr1	44778868	44778868	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	acttgctgcaggcttggctgAccatccaccatggcttgaat	10	12	0	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:44778868A>G	ENST00000372257.2	-	5	820	c.639T>C	c.(637-639)ggT>ggC	p.G213G	ERI3_ENST00000495828.1_5'UTR|ERI3_ENST00000537474.1_Silent_p.G36G|ERI3_ENST00000372259.5_Silent_p.G98G	NM_024066.1	NP_076971.1	O43414	ERI3_HUMAN	ERI1 exoribonuclease family member 3	213	Exonuclease.						exonuclease activity (GO:0004527)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(2)|lung(7)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						GGCTTGGCTGACCATCCACCA	0.532																																					p.G213G		Atlas-SNP	.											.	ERI3	39	.	0			c.T639C						.						91	89	90					1																	44778868		2203	4300	6503	SO:0001819	synonymous_variant	79033	exon5			TGGCTGACCATCC	AF007157	CCDS30696.1	1p34.1	2009-10-07	2009-10-07	2008-12-16	ENSG00000117419	ENSG00000117419		"Enhanced RNAi three prime mRNA exonucleases"	17276	protein-coding gene	gene with protein product	"enhanced RNAi three prime mRNA exonuclease homolog 3 (C.elegans)", "exoribonuclease 3"	609917	"prion protein interacting protein"	PRNPIP			Standard	XM_005271184		Approved	FLJ22943, PINT1	uc001clt.3	O43414	OTTHUMG00000007637	ENST00000372257.2:c.639T>C	chr1.hg19:g.44778868A>G		126.0	0.0		154.0	7.0	NM_024066	B1AK98|Q5T2T7|Q5T2T9|Q5TG35|Q9BQA0|Q9UEB4	Silent	SNP	ENST00000372257.2	hg19	CCDS30696.1																																																																																			.	.		0.532	ERI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020243.1	NM_024066		G	44778868	A	G	44778868	2	3	263	1	0	0	0	0	0	0	0	1	5231	262	10	2		2	ERI3	1	44778868	Silent	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	1462105	44778868	204471753	13	38387										
NRD1	4898	hgsc.bcm.edu	37	chr1	52306079	52306079	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	catcatcttcttcttcttccTccacctcctcttcttcttca	0	18	9	0	rs62648104		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:52306079T>A	ENST00000354831.7	-	2	638	c.449A>T	c.(448-450)gAg>gTg	p.E150V	NRD1_ENST00000544028.1_Missense_Mutation_p.E18V|NRD1_ENST00000485608.1_5'UTR|NRD1_ENST00000539524.1_Missense_Mutation_p.E18V|NRD1_ENST00000352171.7_Missense_Mutation_p.E150V	NM_002525.2	NP_002516.2	O43847	NRDC_HUMAN	nardilysin (N-arginine dibasic convertase)	0	Asp/Glu-rich (highly acidic).|Poly-Glu.				cell migration (GO:0016477)|cell proliferation (GO:0008283)|neuromuscular junction development (GO:0007528)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)	cell surface (GO:0009986)|cytosol (GO:0005829)	epidermal growth factor binding (GO:0048408)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)	27						ttcttcttcctccacctcctc	0.378																																					p.E150V		Atlas-SNP	.											.	NRD1	89	.	0			c.A449T						.						163	138	146					1																	52306079		2203	4300	6503	SO:0001583	missense	4898	exon2			TCTTCCTCCACCT	X93207	CCDS559.1, CCDS41335.1, CCDS55599.1	1p32.2-p32.1	2008-07-18			ENSG00000078618	ENSG00000078618			7995	protein-coding gene	gene with protein product		602651				9581555, 9479496	Standard	NM_002525		Approved	hNRD1, hNRD2	uc001ctc.4	O43847	OTTHUMG00000008278	ENST00000354831.7:c.449A>T	chr1.hg19:g.52306079T>A	ENSP00000346890:p.Glu150Val	239.0	0.0		261.0	44.0	NM_001101662	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	Missense_Mutation	SNP	ENST00000354831.7	hg19	CCDS559.1	.	.	.	.	.	.	.	.	.	.	T	3.056	-0.194350	0.06259	.	.	ENSG00000078618	ENST00000352171;ENST00000354831;ENST00000539524;ENST00000546169;ENST00000544028	T;T;T;T	0.38240	1.31;3.15;1.15;1.22	5.25	2.92	0.33932	Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.525899	0.19688	N	0.108344	T	0.18341	0.0440	N	0.14661	0.345	0.09310	N	1	B;B;B	0.23650	0.062;0.089;0.01	B;B;B	0.17098	0.017;0.007;0.007	T	0.14755	-1.0461	10	0.38643	T	0.18	-0.0317	5.1939	0.15225	0.0:0.1704:0.2022:0.6274	rs62648104	150;150;150	F5H6R2;O43847;B1AKJ5	.;NRDC_HUMAN;.	V	150;150;18;150;18	ENSP00000262679:E150V;ENSP00000346890:E150V;ENSP00000444416:E18V;ENSP00000442262:E18V	ENSP00000262679:E150V	E	-	2	0	NRD1	52078667	0.129000	0.22400	0.012000	0.15200	0.145000	0.21501	0.870000	0.28010	0.317000	0.23160	0.454000	0.30748	GAG	.	T|0.024;A|0.976		0.378	NRD1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023045.1	NM_002525		A	52306079	T	A	52306079	3	1	263	1	0	0	0	0	1	0	0	0	10654	1551	54	4	3338	4	NRD1	1	52306079	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	7527211	52306079	196944542	14	38388										
AK3L1	205	hgsc.bcm.edu	37	chr1	65690526	65690526	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gctaagacagtacaaagacgTggcaaagccagtcattgaat	10	8	1	3			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:65690526T>C	ENST00000327299.7	+	4	735	c.530T>C	c.(529-531)gTg>gCg	p.V177A	AK4_ENST00000545314.1_Missense_Mutation_p.V177A|AK4_ENST00000546702.1_Missense_Mutation_p.V125A|AK4_ENST00000395334.2_Missense_Mutation_p.V177A	NM_013410.3	NP_037542.1			adenylate kinase 4											breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|pancreas(1)|skin(1)	9						TACAAAGACGTGGCAAAGCCA	0.473																																					p.V177A		Atlas-SNP	.											.	AK4	22	.	0			c.T530C						.						87	85	85					1																	65690526		2203	4300	6503	SO:0001583	missense	205	exon5			AAGACGTGGCAAA	AK025926	CCDS629.1	1p31.3	2012-10-02	2010-06-15	2010-06-15	ENSG00000162433	ENSG00000162433	2.7.4.3	"Adenylate kinases"	363	protein-coding gene	gene with protein product		103030	"adenylate kinase 3", "adenylate kinase 3-like 1"	AK3, AK3L1		11485571	Standard	NM_203464		Approved		uc001dby.3	P27144	OTTHUMG00000009033	ENST00000327299.7:c.530T>C	chr1.hg19:g.65690526T>C	ENSP00000322175:p.Val177Ala	108.0	0.0		122.0	6.0	NM_203464		Missense_Mutation	SNP	ENST00000327299.7	hg19	CCDS629.1	.	.	.	.	.	.	.	.	.	.	T	1.968	-0.437108	0.04636	.	.	ENSG00000162433	ENST00000545314;ENST00000546702;ENST00000395334;ENST00000327299	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	5.15	2.75	0.32379	.	0.253398	0.39146	N	0.001454	T	0.10035	0.0246	N	0.17631	0.505	0.38865	D	0.956569	B	0.06786	0.001	B	0.09377	0.004	T	0.08086	-1.0739	10	0.46703	T	0.11	-10.7039	3.1857	0.06599	0.1777:0.3235:0.0:0.4989	.	177	P27144	KAD4_HUMAN	A	177;125;177;177	ENSP00000445912:V177A;ENSP00000448458:V125A;ENSP00000378743:V177A;ENSP00000322175:V177A	ENSP00000322175:V177A	V	+	2	0	AK4	65463114	0.999000	0.42202	0.063000	0.19743	0.402000	0.30811	3.429000	0.52800	0.374000	0.24650	0.528000	0.53228	GTG	.	.		0.473	AK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025040.2	NM_013410		C	65690526	T	C	65690526	3	2	263	1	0	0	0	0	1	0	0	0	442	1696	59	2	544	2	AK3L1	1	65690526	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	13384447	65690526	183560095	15	38389										
TCTEX1D1	200132	hgsc.bcm.edu	37	chr1	67241997	67241997	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ttcctgtggtcaccgtcaatCatattttgaaagatgtagta	8	7	3	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:67241997C>G	ENST00000282670.2	+	4	375	c.247C>G	c.(247-249)Cat>Gat	p.H83D		NM_152665.2	NP_689878.2	Q8N7M0	TC1D1_HUMAN	Tctex1 domain containing 1	83										large_intestine(2)|lung(10)|skin(1)	13						CACCGTCAATCATATTTTGAA	0.378																																					p.H83D		Atlas-SNP	.											.	TCTEX1D1	27	.	0			c.C247G						.						104	102	103					1																	67241997		2203	4300	6503	SO:0001583	missense	200132	exon4			GTCAATCATATTT	AK098192	CCDS633.1	1p31.2	2008-02-05			ENSG00000152760	ENSG00000152760			26882	protein-coding gene	gene with protein product							Standard	NM_152665		Approved	FLJ40873	uc001dcv.3	Q8N7M0	OTTHUMG00000009162	ENST00000282670.2:c.247C>G	chr1.hg19:g.67241997C>G	ENSP00000282670:p.His83Asp	174.0	0.0		231.0	95.0	NM_152665	Q06YR9|Q5VYE1	Missense_Mutation	SNP	ENST00000282670.2	hg19	CCDS633.1	.	.	.	.	.	.	.	.	.	.	C	5.556	0.287404	0.10513	.	.	ENSG00000152760	ENST00000282670	T	0.27890	1.64	5.92	4.99	0.66335	.	0.452764	0.25971	N	0.027123	T	0.04497	0.0123	N	0.04787	-0.16	0.24258	N	0.99529	B	0.02656	0.0	B	0.04013	0.001	T	0.36504	-0.9745	10	0.13853	T	0.58	-18.0728	9.3461	0.38109	0.2651:0.5979:0.137:0.0	.	83	Q8N7M0	TC1D1_HUMAN	D	83	ENSP00000282670:H83D	ENSP00000282670:H83D	H	+	1	0	TCTEX1D1	67014585	0.714000	0.27936	0.988000	0.46212	0.894000	0.52154	2.053000	0.41326	1.452000	0.47756	0.655000	0.94253	CAT	.	.		0.378	TCTEX1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025399.2	NM_152665		G	67241997	C	G	67241997	3	3	263	1	0	0	0	0	1	0	0	0	15734	826	29	4	257	4	TCTEX1D1	1	67241997	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	1551471	67241997	182008624	16	38390										
SLC35D1	23169	hgsc.bcm.edu	37	chr1	67512974	67512974	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	atctaatttttgttttacgtAtgcaccatttgctgctgtta	6	7	1	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:67512974A>G	ENST00000235345.5	-	7	695	c.610T>C	c.(610-612)Tac>Cac	p.Y204H	SLC35D1_ENST00000506472.2_Missense_Mutation_p.Y125H	NM_015139.2	NP_055954.1	Q9NTN3	S35D1_HUMAN	solute carrier family 35 (UDP-GlcA/UDP-GalNAc transporter), member D1	204					carbohydrate transport (GO:0008643)|cellular glucuronidation (GO:0052695)|chondroitin sulfate biosynthetic process (GO:0030206)|embryonic skeletal system development (GO:0048706)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|UDP-glucuronate biosynthetic process (GO:0006065)|UDP-glucuronic acid transport (GO:0015787)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	UDP-glucuronic acid transmembrane transporter activity (GO:0005461)			endometrium(2)|kidney(1)|large_intestine(3)|lung(4)	10						TGTTTTACGTATGCACCATTT	0.358																																					p.Y204H		Atlas-SNP	.											.	SLC35D1	22	.	0			c.T610C						.						170	156	161					1																	67512974		2203	4300	6503	SO:0001583	missense	23169	exon7			TTACGTATGCACC	AB044343	CCDS636.1	1p32-p31	2013-07-17	2013-07-17		ENSG00000116704	ENSG00000116704		"Solute carriers"	20800	protein-coding gene	gene with protein product		610804	"solute carrier family 35 (UDP-glucuronic acid/UDP-N-acetylgalactosamine dual transporter), member D1"			11322953	Standard	NM_015139		Approved	UGTREL7, KIAA0260	uc001ddk.2	Q9NTN3	OTTHUMG00000009360	ENST00000235345.5:c.610T>C	chr1.hg19:g.67512974A>G	ENSP00000235345:p.Tyr204His	61.0	0.0		75.0	4.0	NM_015139	A8K185|B7Z3X2|Q52LU5|Q92548	Missense_Mutation	SNP	ENST00000235345.5	hg19	CCDS636.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.336122	0.81801	.	.	ENSG00000116704	ENST00000235345;ENST00000506472	T;T	0.68624	-0.34;0.13	5.15	5.15	0.70609	Domain of unknown function DUF250 (1);	0.293349	0.39544	N	0.001333	T	0.75428	0.3848	M	0.76574	2.34	0.80722	D	1	D;D	0.71674	0.998;0.996	D;D	0.70016	0.967;0.928	T	0.77525	-0.2555	10	0.48119	T	0.1	-7.5711	14.2723	0.66159	1.0:0.0:0.0:0.0	.	125;204	B7Z3X2;Q9NTN3	.;S35D1_HUMAN	H	204;125	ENSP00000235345:Y204H;ENSP00000445189:Y125H	ENSP00000235345:Y204H	Y	-	1	0	SLC35D1	67285562	1.000000	0.71417	0.994000	0.49952	0.990000	0.78478	8.864000	0.92294	2.076000	0.62316	0.533000	0.62120	TAC	.	.		0.358	SLC35D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025948.1	NM_015139		G	67512974	A	G	67512974	3	3	263	1	0	0	0	0	1	0	0	0	14596	449	16	2	481	2	SLC35D1	1	67512974	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	270977	67512974	181737647	17	38391										
PTGER3	5733	hgsc.bcm.edu	37	chr1	71478142	71478142	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	agtgctcaactgatgtctgaTtgaagatcattttcaacatc	7	8	4	4			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:71478142T>A	ENST00000306666.5	-	2	1133	c.923A>T	c.(922-924)aAt>aTt	p.N308I	PTGER3_ENST00000370932.2_Missense_Mutation_p.N308I|PTGER3_ENST00000370924.4_Missense_Mutation_p.N308I|PTGER3_ENST00000370931.3_Missense_Mutation_p.N308I|PTGER3_ENST00000356595.4_Missense_Mutation_p.N308I|PTGER3_ENST00000351052.5_Missense_Mutation_p.N308I|PTGER3_ENST00000414819.1_Missense_Mutation_p.N308I|PTGER3_ENST00000460330.1_Missense_Mutation_p.N308I|PTGER3_ENST00000354608.5_Missense_Mutation_p.N308I	NM_198719.1	NP_942012.1	P43115	PE2R3_HUMAN	prostaglandin E receptor 3 (subtype EP3)	308					cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of fever generation (GO:0031622)|transcription, DNA-templated (GO:0006351)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|prostaglandin E receptor activity (GO:0004957)			endometrium(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	25					Bimatoprost(DB00905)|Dinoprostone(DB00917)|Misoprostol(DB00929)	TGATGTCTGATTGAAGATCAT	0.393																																					p.N308I		Atlas-SNP	.											.	PTGER3	246	.	0			c.A923T						.						103	98	100					1																	71478142		2203	4300	6503	SO:0001583	missense	5733	exon2			GTCTGATTGAAGA	X83863	CCDS652.1, CCDS655.1, CCDS656.1, CCDS657.1, CCDS658.1	1p31.2	2012-08-08			ENSG00000050628	ENSG00000050628		"GPCR / Class A : Prostanoid receptors"	9595	protein-coding gene	gene with protein product		176806				7759114, 9073510	Standard	NM_001126044		Approved	EP3	uc001dfo.3	P43115	OTTHUMG00000009399	ENST00000306666.5:c.923A>T	chr1.hg19:g.71478142T>A	ENSP00000302313:p.Asn308Ile	65.0	0.0		99.0	35.0	NM_001126044	B0AZN4|B1AK19|B5BUP5|O00326|Q12943|Q12944|Q12945|Q16546|Q5CZ59|Q5CZ61|Q5CZ62|Q5CZ63|Q5CZ64	Missense_Mutation	SNP	ENST00000306666.5	hg19	CCDS657.1	.	.	.	.	.	.	.	.	.	.	T	15.59	2.877568	0.51801	.	.	ENSG00000050628	ENST00000370931;ENST00000370932;ENST00000351052;ENST00000460330;ENST00000370934;ENST00000354608;ENST00000356595;ENST00000414819;ENST00000306666;ENST00000370924	T;T;T;T;T;T;T;T;T	0.72051	-0.62;-0.62;-0.62;-0.62;-0.62;-0.62;-0.62;-0.62;-0.62	5.64	3.31	0.37934	GPCR, rhodopsin-like superfamily (1);	0.309163	0.32134	N	0.006525	T	0.70360	0.3215	M	0.72353	2.195	0.36597	D	0.874467	D;D;D;D;D;D;D;D	0.71674	0.996;0.991;0.995;0.996;0.998;0.989;0.995;0.996	D;P;D;D;D;P;D;D	0.66602	0.945;0.903;0.909;0.945;0.945;0.843;0.909;0.945	T	0.69064	-0.5244	10	0.23302	T	0.38	-12.724	9.8856	0.41260	0.0:0.1424:0.0:0.8576	.	308;308;308;308;308;308;308;308	Q147U0;Q6TTN3;F5H821;B1AK19;Q147X8;P43115-3;P43115-4;P43115	.;.;.;.;.;.;.;PE2R3_HUMAN	I	308	ENSP00000359969:N308I;ENSP00000359970:N308I;ENSP00000280208:N308I;ENSP00000418073:N308I;ENSP00000346624:N308I;ENSP00000349003:N308I;ENSP00000401423:N308I;ENSP00000302313:N308I;ENSP00000359962:N308I	ENSP00000302313:N308I	N	-	2	0	PTGER3	71250730	0.997000	0.39634	1.000000	0.80357	0.764000	0.43329	0.270000	0.18607	0.982000	0.38575	-0.425000	0.05940	AAT	.	.		0.393	PTGER3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026076.1	NM_000957		A	71478142	T	A	71478142	3	1	263	1	0	0	0	0	1	0	0	0	12757	1493	52	4	564	4	PTGER3	1	71478142	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	3965168	71478142	177772479	18	38392										
FAM73A	374986	hgsc.bcm.edu	37	chr1	78309009	78309009	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	aagataaagatacagatatcAccatgaagggtaatgtggaa	10	4	1	4			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:78309009A>G	ENST00000370791.3	+	8	945	c.913A>G	c.(913-915)Acc>Gcc	p.T305A	FAM73A_ENST00000443751.2_Missense_Mutation_p.T267A	NM_001270384.1|NM_198549.3	NP_001257313.1|NP_940951.1	Q8NAN2	FA73A_HUMAN	family with sequence similarity 73, member A	305						integral component of membrane (GO:0016021)				breast(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	19				Colorectal(170;0.226)		TACAGATATCACCATGAAGGG	0.398																																					p.T305A		Atlas-SNP	.											.	FAM73A	56	.	0			c.A913G						.						115	112	113					1																	78309009		2203	4300	6503	SO:0001583	missense	374986	exon8			GATATCACCATGA		CCDS681.1, CCDS72809.1	1p31.1	2008-02-05			ENSG00000180488	ENSG00000180488			24741	protein-coding gene	gene with protein product							Standard	NM_001270384		Approved	FLJ35093	uc010ork.3	Q8NAN2	OTTHUMG00000009766	ENST00000370791.3:c.913A>G	chr1.hg19:g.78309009A>G	ENSP00000359827:p.Thr305Ala	47.0	0.0		63.0	4.0	NM_001270384	Q6MZG0	Missense_Mutation	SNP	ENST00000370791.3	hg19	CCDS681.1	.	.	.	.	.	.	.	.	.	.	A	0.371	-0.934047	0.02340	.	.	ENSG00000180488	ENST00000370791;ENST00000443751	T;T	0.22336	1.96;1.96	5.98	5.98	0.97165	.	0.236711	0.44097	D	0.000493	T	0.08980	0.0222	L	0.50333	1.59	0.28238	N	0.925799	B;B;P;B	0.37207	0.167;0.201;0.587;0.201	B;B;B;B	0.38156	0.077;0.197;0.266;0.197	T	0.26292	-1.0107	10	0.07990	T	0.79	-11.2822	15.0333	0.71725	1.0:0.0:0.0:0.0	.	267;305;305;305	F8W7S1;B7ZLZ8;Q8NAN2-2;Q8NAN2	.;.;.;FA73A_HUMAN	A	305;267	ENSP00000359827:T305A;ENSP00000393675:T267A	ENSP00000359827:T305A	T	+	1	0	FAM73A	78081597	0.998000	0.40836	0.041000	0.18516	0.293000	0.27360	4.990000	0.63876	2.289000	0.77006	0.533000	0.62120	ACC	.	.		0.398	FAM73A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000026931.1	NM_198549		G	78309009	A	G	78309009	3	3	263	1	0	0	0	0	1	0	0	0	5625	159	6	2	943	2	FAM73A	1	78309009	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	6830867	78309009	170941612	19	38393										
RPAP2	79871	hgsc.bcm.edu	37	chr1	92789250	92789250	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	agctggtcacaaagctaactCcaaacacaaagacaaagaac	6	11	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:92789250C>G	ENST00000610020.1	+	8	882	c.773C>G	c.(772-774)tCc>tGc	p.S258C	RPAP2_ENST00000484158.1_3'UTR	NM_024813.2	NP_079089.2	Q8IXW5	RPAP2_HUMAN	RNA polymerase II associated protein 2	258					dephosphorylation of RNA polymerase II C-terminal domain (GO:0070940)|snRNA transcription (GO:0009301)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|nucleolus (GO:0005730)|nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	22		all_lung(203;0.0565)|Lung NSC(277;0.152)|Glioma(108;0.222)		all cancers(265;0.00647)|GBM - Glioblastoma multiforme(16;0.0234)|Epithelial(280;0.115)		AAAGCTAACTCCAAACACAAA	0.393																																					p.S258C		Atlas-SNP	.											.	RPAP2	48	.	0			c.C773G						.						117	111	113					1																	92789250		2203	4300	6503	SO:0001583	missense	79871	exon8			CTAACTCCAAACA	AK023212	CCDS740.1	1p22.1	2014-01-28	2007-07-26	2007-07-26	ENSG00000122484	ENSG00000122484			25791	protein-coding gene	gene with protein product		611476	"chromosome 1 open reading frame 82"	C1orf82		17643375	Standard	NM_024813		Approved	FLJ13150	uc001dot.2	Q8IXW5	OTTHUMG00000010288	ENST00000610020.1:c.773C>G	chr1.hg19:g.92789250C>G	ENSP00000476948:p.Ser258Cys	125.0	0.0		149.0	73.0	NM_024813	C9JKB5|Q49AS7|Q9H8Y2	Missense_Mutation	SNP	ENST00000610020.1	hg19	CCDS740.1	.	.	.	.	.	.	.	.	.	.	C	16.10	3.026453	0.54683	.	.	ENSG00000122484	ENST00000370343;ENST00000394482	.	.	.	6.07	5.11	0.69529	.	0.457271	0.24613	N	0.037021	T	0.60637	0.2284	M	0.69823	2.125	0.31756	N	0.633972	D	0.64830	0.994	P	0.57371	0.819	T	0.64740	-0.6336	8	0.39692	T	0.17	-2.6866	14.1725	0.65519	0.0:0.923:0.0:0.077	.	258	Q8IXW5	RPAP2_HUMAN	C	258	.	ENSP00000359368:S258C	S	+	2	0	RPAP2	92561838	0.729000	0.28090	0.430000	0.26722	0.397000	0.30659	2.250000	0.43178	1.443000	0.47586	0.655000	0.94253	TCC	.	.		0.393	RPAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028368.2	NM_024813		G	92789250	C	G	92789250	3	3	263	1	0	0	0	0	1	0	0	0	13557	855	30	4	803	4	RPAP2	1	92789250	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	14480241	92789250	156461371	20	38394										
MTF2	22823	hgsc.bcm.edu	37	chr1	93575851	93575851	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ctttacgtcgaaaccaaaagAccccaacatccttgaccaag	5	14	0	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:93575851A>G	ENST00000370298.4	+	2	359	c.70A>G	c.(70-72)Acc>Gcc	p.T24A	MTF2_ENST00000370303.4_Missense_Mutation_p.T24A|MTF2_ENST00000471953.1_3'UTR|MTF2_ENST00000545708.1_Intron|MTF2_ENST00000540243.1_Intron	NM_001164392.1|NM_007358.3	NP_001157864.1|NP_031384	Q9Y483	MTF2_HUMAN	metal response element binding transcription factor 2	24					chromatin modification (GO:0016568)|negative regulation of histone H3-K27 methylation (GO:0061086)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K27 methylation (GO:0061087)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|segment specification (GO:0007379)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_lung(203;0.00196)|Lung NSC(277;0.00902)|Melanoma(281;0.099)|Ovarian(761;0.109)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00076)|GBM - Glioblastoma multiforme(16;0.00157)|Epithelial(280;0.0886)		AAACCAAAAGACCCCAACATC	0.443																																					p.T24A		Atlas-SNP	.											.	MTF2	51	.	0			c.A70G						.						129	126	127					1																	93575851		2203	4300	6503	SO:0001583	missense	22823	exon2			CAAAAGACCCCAA	AJ010014	CCDS742.1, CCDS53340.1, CCDS53341.1	1p22.1	2013-01-28			ENSG00000143033	ENSG00000143033		"Tudor domain containing", "Zinc fingers, PHD-type"	29535	protein-coding gene	gene with protein product	"polycomb-like 2", "tudor domain containing 19A"	609882				15563832	Standard	NM_007358		Approved	M96, PCL2, TDRD19A	uc009wdj.3	Q9Y483	OTTHUMG00000010161	ENST00000370298.4:c.70A>G	chr1.hg19:g.93575851A>G	ENSP00000359321:p.Thr24Ala	120.0	0.0		140.0	8.0	NM_001164392	A6NGQ9|A8K2Q3|B1AKT5|B1AKT6|Q9UES9|Q9UP40	Missense_Mutation	SNP	ENST00000370298.4	hg19	CCDS742.1	.	.	.	.	.	.	.	.	.	.	A	9.529	1.110349	0.20714	.	.	ENSG00000143033	ENST00000370298;ENST00000370303	T;T	0.21191	2.02;2.02	5.44	1.77	0.24775	.	0.480152	0.25183	N	0.032512	T	0.02230	0.0069	N	0.03115	-0.41	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40346	-0.9568	10	0.15499	T	0.54	1.5123	6.5706	0.22537	0.5173:0.1268:0.3559:0.0	.	24;24	B1AKT6;Q9Y483	.;MTF2_HUMAN	A	24	ENSP00000359321:T24A;ENSP00000359326:T24A	ENSP00000359321:T24A	T	+	1	0	MTF2	93348439	0.999000	0.42202	1.000000	0.80357	0.997000	0.91878	0.961000	0.29267	0.065000	0.16485	0.455000	0.32223	ACC	.	.		0.443	MTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028075.3	NM_007358		G	93575851	A	G	93575851	3	3	263	1	0	0	0	0	1	0	0	0	9932	275	10	2	76	2	MTF2	1	93575851	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	786601	93575851	155674770	21	38395										
F3	2152	hgsc.bcm.edu	37	chr1	95001634	95001634	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cccgtgccaagtacgtctgcTtcacatccttcacaatctcg	6	16	4	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:95001634T>C	ENST00000334047.7	-	3	462	c.299A>G	c.(298-300)aAg>aGg	p.K100R	F3_ENST00000480356.1_5'UTR|F3_ENST00000370207.4_Missense_Mutation_p.K100R	NM_001993.4	NP_001984.1	P13726	TF_HUMAN	coagulation factor III (thromboplastin, tissue factor)	100					activation of blood coagulation via clotting cascade (GO:0002543)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of plasma proteins involved in acute inflammatory response (GO:0002541)|blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of platelet-derived growth factor receptor signaling pathway (GO:0010641)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein kinase B signaling (GO:0051897)	cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intrinsic component of external side of plasma membrane (GO:0031233)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)|protease binding (GO:0002020)			NS(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(7)	14		all_lung(203;0.00106)|Lung NSC(277;0.00475)		all cancers(265;0.0232)|Epithelial(280;0.121)	Coagulation factor VIIa(DB00036)	GTACGTCTGCTTCACATCCTT	0.493																																					p.K100R	Melanoma(40;358 1339 15970 39161)	Atlas-SNP	.											.	F3	21	.	0			c.A299G						.						257	229	239					1																	95001634		2203	4300	6503	SO:0001583	missense	2152	exon3			GTCTGCTTCACAT	BC011029	CCDS750.1, CCDS53345.1	1p22-p21	2012-10-02			ENSG00000117525	ENSG00000117525		"CD molecules"	3541	protein-coding gene	gene with protein product		134390					Standard	NM_001993		Approved	CD142	uc001dqr.3	P13726	OTTHUMG00000010716	ENST00000334047.7:c.299A>G	chr1.hg19:g.95001634T>C	ENSP00000334145:p.Lys100Arg	108.0	0.0		121.0	5.0	NM_001993	D3DT47|Q6FHG2|Q86WH4	Missense_Mutation	SNP	ENST00000334047.7	hg19	CCDS750.1	.	.	.	.	.	.	.	.	.	.	T	8.932	0.963624	0.18583	.	.	ENSG00000117525	ENST00000334047;ENST00000370207	T;T	0.74737	-0.87;-0.87	5.48	-5.38	0.02673	Fibronectin, type III (1);Immunoglobulin-like fold (1);	1.429860	0.04043	N	0.303347	T	0.28830	0.0715	N	0.21097	0.63	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.08055	0.001;0.003	T	0.05767	-1.0865	10	0.23302	T	0.38	.	1.8111	0.03090	0.128:0.3306:0.2626:0.2788	.	100;100	P13726-2;P13726	.;TF_HUMAN	R	100	ENSP00000334145:K100R;ENSP00000359226:K100R	ENSP00000334145:K100R	K	-	2	0	F3	94774222	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-0.596000	0.05720	-0.867000	0.04063	-0.479000	0.04858	AAG	.	.		0.493	F3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029593.1	NM_001993		C	95001634	T	C	95001634	3	2	263	1	0	0	0	0	1	0	0	0	5349	1609	56	2	604	2	F3	1	95001634	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	1425783	95001634	154248987	22	38396										
GPSM2	29899	hgsc.bcm.edu	37	chr1	109465167	109465168	+	Missense_Mutation	DNP	TT	TT	AA													0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	catacagcttcaacaacaacTtcttccactccccctaaaat					rs374875864|rs79761186|rs35029887|rs201481482	byFrequency	TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:109465167_109465168TT>AA	ENST00000406462.2	+	14	2342_2343	c.1569_1570TT>AA	c.(1567-1572)acTTct>acAAct	p.S524T	GPSM2_ENST00000264126.3_Missense_Mutation_p.S524T|AKNAD1_ENST00000357393.4_Intron			P81274	GPSM2_HUMAN	G-protein signaling modulator 2	524					establishment of mitotic spindle orientation (GO:0000132)|G-protein coupled receptor signaling pathway (GO:0007186)|lung epithelial cell differentiation (GO:0060487)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTPase regulator activity (GO:0030695)|identical protein binding (GO:0042802)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)	14		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0353)|Lung(183;0.0984)|COAD - Colon adenocarcinoma(174;0.129)|Epithelial(280;0.175)|all cancers(265;0.209)		CAACAACAACTTCTTCCACTCC	0.371																																					p.T523T|p.S524T		Atlas-SNP	.											.	GPSM2	56	.	0			c.T1569A|c.T1570A						.																																			SO:0001583	missense	29899	exon13			AACAACTTCTTCC|ACAACTTCTTCCA	AY136740	CCDS792.2	1p13.3	2013-10-11	2010-06-24		ENSG00000121957	ENSG00000121957		"Tetratricopeptide (TTC) repeat domain containing"	29501	protein-coding gene	gene with protein product		609245	"G-protein signalling modulator 2 (AGS3-like, C. elegans)", "deafness, autosomal recessive 82"	DFNB82		11832491, 8973305, 19888295, 20602914, 21348867	Standard	NM_013296		Approved	LGN, Pins	uc010ovc.2	P81274	OTTHUMG00000011730	Exception_encountered	chr1.hg19:g.109465167_109465168delinsAA	ENSP00000385510:p.Ser524Thr	10.0|7.0	0.0		25.0	8.0	NM_013296	Q5T1N8|Q6IBL7|Q8N0Z5	Silent|Missense_Mutation	SNP	ENST00000406462.2	hg19	CCDS792.2																																																																																			.	.		0.371	GPSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032400.3	NM_013296		AA	109465168	TT	AA	109465167	3	1	263	1	0	0	0	0	1	0	0	0	6744	1596	56	4	1615	4	GPSM2	1	109465167	Missense_Mutation	DNP	TT	TCGA-FV-A2QR-01A-11D-A20W-10	14463533	109465167	139785454	23	38397										
RSBN1	54665	hgsc.bcm.edu	37	chr1	114354478	114354478	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tgtgccgctccttgtggcccTtatgcttgggcccggccgcg	14	15	0	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:114354478T>C	ENST00000261441.5	-	1	620	c.557A>G	c.(556-558)aAg>aGg	p.K186R	RP5-1073O3.2_ENST00000429398.1_RNA|RP5-1073O3.2_ENST00000418238.1_RNA	NM_018364.3	NP_060834.2	Q5VWQ0	RSBN1_HUMAN	round spermatid basic protein 1	186	His-rich.					nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(3)|urinary_tract(2)	29	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CTTGTGGCCCTTATGCTTGGG	0.677																																					p.K186R		Atlas-SNP	.											.	RSBN1	71	.	0			c.A557G						.						57	49	52					1																	114354478		2203	4300	6503	SO:0001583	missense	54665	exon1			TGGCCCTTATGCT	AK002082	CCDS862.1	1p13.1	2008-02-05			ENSG00000081019	ENSG00000081019			25642	protein-coding gene	gene with protein product		615858				12477932	Standard	NM_018364		Approved	FLJ11220, ROSBIN	uc001edq.3	Q5VWQ0	OTTHUMG00000011938	ENST00000261441.5:c.557A>G	chr1.hg19:g.114354478T>C	ENSP00000261441:p.Lys186Arg	77.0	0.0		74.0	4.0	NM_018364	A8K937|Q6AI21|Q8TC33|Q9HA80|Q9NUP6	Missense_Mutation	SNP	ENST00000261441.5	hg19	CCDS862.1	.	.	.	.	.	.	.	.	.	.	T	17.49	3.403479	0.62288	.	.	ENSG00000081019	ENST00000261441	.	.	.	4.23	4.23	0.50019	.	0.172694	0.37483	N	0.002073	T	0.16214	0.0390	N	0.08118	0	0.25420	N	0.988274	P	0.49696	0.927	P	0.56563	0.801	T	0.05582	-1.0876	9	0.33940	T	0.23	-7.2464	9.6322	0.39787	0.0:0.0:0.0:1.0	.	186	Q5VWQ0	RSBN1_HUMAN	R	186	.	ENSP00000261441:K186R	K	-	2	0	RSBN1	114156001	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.294000	0.51787	1.775000	0.52247	0.533000	0.62120	AAG	.	.		0.677	RSBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033022.2	NM_018364		C	114354478	T	C	114354478	3	2	263	1	0	0	0	0	1	0	0	0	13711	1609	56	2	1879	2	RSBN1	1	114354478	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	4889311	114354478	134896143	24	38398										
PTPN22	26191	hgsc.bcm.edu	37	chr1	114380814	114380814	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gaagaggctccccaactattGgaaatgcctttgtctgccat	9	11	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:114380814G>A	ENST00000359785.5	-	13	1343	c.1208C>T	c.(1207-1209)cCa>cTa	p.P403L	PTPN22_ENST00000538253.1_Missense_Mutation_p.P159L|PTPN22_ENST00000525799.1_Missense_Mutation_p.P276L|PTPN22_ENST00000460620.1_Intron|PTPN22_ENST00000528414.1_Missense_Mutation_p.P348L|PTPN22_ENST00000420377.2_Missense_Mutation_p.P403L	NM_001193431.1|NM_015967.5	NP_001180360.1|NP_057051	Q9Y2R2	PTN22_HUMAN	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	403					negative regulation of T cell activation (GO:0050868)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphoanandamide dephosphorylation (GO:0035644)|protein dephosphorylation (GO:0006470)|regulation of B cell receptor signaling pathway (GO:0050855)|regulation of innate immune response (GO:0045088)|regulation of natural killer cell proliferation (GO:0032817)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	kinase binding (GO:0019900)|protein tyrosine phosphatase activity (GO:0004725)|SH3 domain binding (GO:0017124)			NS(1)|breast(1)|kidney(3)|large_intestine(4)|lung(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CCCAACTATTGGAAATGCCTT	0.403																																					p.P403L		Atlas-SNP	.											.	PTPN22	90	.	0			c.C1208T						.						86	88	87					1																	114380814		2203	4300	6503	SO:0001583	missense	26191	exon13			ACTATTGGAAATG	AF001846	CCDS863.1, CCDS864.1, CCDS864.2	1p13.2	2011-06-09	2005-02-02		ENSG00000134242	ENSG00000134242		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9652	protein-coding gene	gene with protein product		600716	"protein tyrosine phosphatase, non-receptor type 8"	PTPN8		10068674, 1373816	Standard	NM_015967		Approved	Lyp, Lyp1, Lyp2	uc001eds.3	Q9Y2R2	OTTHUMG00000011936	ENST00000359785.5:c.1208C>T	chr1.hg19:g.114380814G>A	ENSP00000352833:p.Pro403Leu	126.0	0.0		124.0	45.0	NM_015967	A0N0K6|B1ALC8|D4NZ71|E9PLD8|E9PPI1|O95063|O95064|Q6IPX8|Q8WVM1	Missense_Mutation	SNP	ENST00000359785.5	hg19	CCDS863.1	.	.	.	.	.	.	.	.	.	.	G	7.931	0.740675	0.15642	.	.	ENSG00000134242	ENST00000359785;ENST00000528414;ENST00000538253;ENST00000420377;ENST00000525799;ENST00000354605	T;T;T;T;T	0.36520	1.25;1.25;1.25;1.25;1.25	5.58	2.66	0.31614	.	0.342816	0.25546	N	0.029933	T	0.13286	0.0322	L	0.55103	1.725	0.09310	N	0.999998	B;B;B;B;B;B	0.24043	0.096;0.034;0.004;0.005;0.008;0.004	B;B;B;B;B;B	0.27608	0.081;0.012;0.005;0.005;0.008;0.005	T	0.17806	-1.0357	10	0.38643	T	0.18	.	4.8974	0.13757	0.2456:0.1581:0.5963:0.0	.	159;276;403;348;403;403	F5H2S8;E9PPI1;E9PMT0;E9PLD8;G5E984;Q9Y2R2	.;.;.;.;.;PTN22_HUMAN	L	403;348;159;403;276;403	ENSP00000352833:P403L;ENSP00000435176:P348L;ENSP00000439372:P159L;ENSP00000388229:P403L;ENSP00000432674:P276L	ENSP00000346621:P403L	P	-	2	0	PTPN22	114182337	0.026000	0.19158	0.011000	0.14972	0.413000	0.31143	1.052000	0.30429	0.702000	0.31825	0.655000	0.94253	CCA	.	.		0.403	PTPN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033015.1	NM_015967		A	114380814	G	A	114380814	3	1	263	1	0	0	0	0	1	0	0	0	12802	1348	47	3	1274	3	PTPN22	1	114380814	Missense_Mutation	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	26336	114380814	134869807	25	38399										
AMPD1	270	hgsc.bcm.edu	37	chr1	115215782	115215782	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	aattaaattgagttcataacAccaggtttcatagcgatagg	8	6	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:115215782A>G	ENST00000520113.2	-	16	2311	c.2296T>C	c.(2296-2298)Tgt>Cgt	p.C766R	AMPD1_ENST00000369538.3_Missense_Mutation_p.C762R|AMPD1_ENST00000353928.6_Missense_Mutation_p.C733R			P23109	AMPD1_HUMAN	adenosine monophosphate deaminase 1	766					IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(3)|pancreas(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	45	all_epithelial(7;7.83e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	Adenosine monophosphate(DB00131)	AGTTCATAACACCAGGTTTCA	0.383																																					p.C766R		Atlas-SNP	.											.	AMPD1	223	.	0			c.T2296C						.						82	77	79					1																	115215782		2203	4300	6503	SO:0001583	missense	270	exon16			CATAACACCAGGT	M60092	CCDS876.1, CCDS876.2, CCDS53349.1	1p13	2010-02-10	2010-02-10		ENSG00000116748	ENSG00000116748	3.5.4.6		468	protein-coding gene	gene with protein product	"AMPD isoform M", "skeletal muscle AMPD"	102770	"adenosine monophosphate deaminase 1 (isoform M)"			1400401	Standard	NM_001172626		Approved	MAD, MADA	uc001efe.2	P23109	OTTHUMG00000011892	ENST00000520113.2:c.2296T>C	chr1.hg19:g.115215782A>G	ENSP00000430075:p.Cys766Arg	164.0	0.0		149.0	6.0	NM_000036	A8K5N4|B2RAM1|F2Z3B3|Q5TF00|Q5TF02	Missense_Mutation	SNP	ENST00000520113.2	hg19	CCDS876.2	.	.	.	.	.	.	.	.	.	.	A	17.54	3.414061	0.62511	.	.	ENSG00000116748	ENST00000520113;ENST00000369538;ENST00000353928	D;D;D	0.82081	-1.57;-1.57;-1.57	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	D	0.83871	0.5348	L	0.48362	1.52	0.80722	D	1	D;D	0.76494	0.999;0.992	D;D	0.83275	0.996;0.923	T	0.81123	-0.1076	10	0.18710	T	0.47	-18.2802	15.9461	0.79796	1.0:0.0:0.0:0.0	.	762;733	Q5TF02;P23109	.;AMPD1_HUMAN	R	766;762;733	ENSP00000430075:C766R;ENSP00000358551:C762R;ENSP00000316520:C733R	ENSP00000316520:C733R	C	-	1	0	AMPD1	115017305	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.287000	0.95975	2.229000	0.72834	0.482000	0.46254	TGT	.	.		0.383	AMPD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032860.4			G	115215782	A	G	115215782	3	3	263	1	0	0	0	0	1	0	0	0	585	159	6	2	50	2	AMPD1	1	115215782	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	834968	115215782	134034839	26	38400										
IGSF3	3321	hgsc.bcm.edu	37	chr1	117122269	117122269	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cagggccgtccgctctgttgGgtcgtcgtcgtcgtcgtcgt	15	13	1	0	rs531457319|rs562520690	byFrequency	TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:117122269G>C	ENST00000369486.3	-	10	3844	c.3079C>G	c.(3079-3081)Cca>Gca	p.P1027A	IGSF3_ENST00000369483.1_Missense_Mutation_p.P1047A|IGSF3_ENST00000318837.6_Missense_Mutation_p.P1047A	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	1027	Ig-like C2-type 8.				lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		CGCTCTGTTGGgtcgtcgtcg	0.642																																					p.P1047A		Atlas-SNP	.											.	IGSF3	294	.	0			c.C3139G						.						31	31	31					1																	117122269		2202	4300	6502	SO:0001583	missense	3321	exon11			CTGTTGGGTCGTC	AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.3079C>G	chr1.hg19:g.117122269G>C	ENSP00000358498:p.Pro1027Ala	93.0	0.0		89.0	5.0	NM_001542	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	hg19	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	G	2.924	-0.222631	0.06061	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.21031	2.03;2.03;2.03	3.81	2.91	0.33838	Immunoglobulin subtype (1);Immunoglobulin-like (1);	1.010950	0.07921	N	0.975860	T	0.04003	0.0112	N	0.08118	0	0.09310	N	1	B;B	0.15141	0.012;0.001	B;B	0.15870	0.014;0.004	T	0.41680	-0.9495	10	0.35671	T	0.21	-3.6628	9.9136	0.41421	0.1033:0.0:0.8967:0.0	.	1027;1047	O75054;A6NJZ6	IGSF3_HUMAN;.	A	1027;1047;1047	ENSP00000358498:P1027A;ENSP00000358495:P1047A;ENSP00000321184:P1047A	ENSP00000321184:P1047A	P	-	1	0	IGSF3	116923792	0.000000	0.05858	0.013000	0.15412	0.133000	0.20885	0.089000	0.15002	1.190000	0.43042	-0.448000	0.05591	CCA	.	.		0.642	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542		C	117122269	G	C	117122269	3	2	263	1	0	0	0	0	1	0	0	0	7610	1232	43	4	513	4	IGSF3	1	117122269	Missense_Mutation	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	1906487	117122269	132128352	27	38401										
TTF2	8458	hgsc.bcm.edu	37	chr1	117634026	117634026	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gaagccctaataatccattcAgtagaggtaagctgtaggac	10	8	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:117634026A>G	ENST00000369466.4	+	16	2709	c.2665A>G	c.(2665-2667)Agt>Ggt	p.S889G		NM_003594.3	NP_003585.3	Q9UNY4	TTF2_HUMAN	transcription termination factor, RNA polymerase II	889					ATP catabolic process (GO:0006200)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(24)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	50	Lung SC(450;0.225)	all_cancers(81;4.23e-06)|all_epithelial(167;3.65e-07)|all_lung(203;2.81e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0553)|Colorectal(144;0.179)|LUSC - Lung squamous cell carcinoma(189;0.19)		TAATCCATTCAGTAGAGGTAA	0.378																																					p.S889G		Atlas-SNP	.											.	TTF2	92	.	0			c.A2665G						.						120	124	123					1																	117634026		2203	4300	6503	SO:0001583	missense	8458	exon16			CCATTCAGTAGAG	AF073771	CCDS892.1	1p13.1	2014-02-18			ENSG00000116830	ENSG00000116830			12398	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 6"	604718				9748214	Standard	NM_003594		Approved	HuF2, ZGRF6	uc001egy.3	Q9UNY4	OTTHUMG00000012030	ENST00000369466.4:c.2665A>G	chr1.hg19:g.117634026A>G	ENSP00000358478:p.Ser889Gly	46.0	0.0		71.0	4.0	NM_003594	A8K4Q2|O75921|Q5T2K7|Q5VVU8|Q8N6I8	Missense_Mutation	SNP	ENST00000369466.4	hg19	CCDS892.1	.	.	.	.	.	.	.	.	.	.	A	14.20	2.465640	0.43839	.	.	ENSG00000116830	ENST00000369466	D	0.87412	-2.25	5.74	2.05	0.26809	SNF2-related (1);	0.646821	0.13731	N	0.366662	T	0.66752	0.2821	L	0.38175	1.15	0.27843	N	0.941049	P	0.35527	0.507	B	0.40702	0.338	T	0.56505	-0.7968	10	0.24483	T	0.36	0.2758	4.4553	0.11640	0.5082:0.3358:0.156:0.0	.	889	Q9UNY4	TTF2_HUMAN	G	889	ENSP00000358478:S889G	ENSP00000358478:S889G	S	+	1	0	TTF2	117435549	0.914000	0.31030	0.678000	0.29963	0.767000	0.43475	1.130000	0.31393	0.400000	0.25396	0.496000	0.49642	AGT	.	.		0.378	TTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033277.3			G	117634026	A	G	117634026	3	3	263	1	0	0	0	0	1	0	0	0	16734	188	7	2	2727	2	TTF2	1	117634026	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	511757	117634026	131616595	28	38402										
CHD1L	9557	hgsc.bcm.edu	37	chr1	146737617	146737617	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	aactgcacaaactcttgcagCcatttctgctgaggcgagtg	10	11	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:146737617C>G	ENST00000369258.4	+	8	786	c.766C>G	c.(766-768)Cca>Gca	p.P256A	CHD1L_ENST00000431239.1_Missense_Mutation_p.P256A|CHD1L_ENST00000361293.5_5'UTR|CHD1L_ENST00000369259.3_Missense_Mutation_p.P52A|CHD1L_ENST00000467213.1_3'UTR	NM_001256336.1|NM_004284.4|NM_024568.2	NP_001243265.1|NP_004275.4|NP_078844.2	Q86WJ1	CHD1L_HUMAN	chromodomain helicase DNA binding protein 1-like	256					ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|nucleotide binding (GO:0000166)			breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(923;0.0487)					ACTCTTGCAGCCATTTCTGCT	0.413																																					p.P256A		Atlas-SNP	.											.	CHD1L	72	.	0			c.C766G						.						74	69	71					1																	146737617		2203	4300	6503	SO:0001583	missense	9557	exon8			TTGCAGCCATTTC	AF054177	CCDS927.1, CCDS58021.1, CCDS58022.1, CCDS72882.1	1q21.1	2008-02-05			ENSG00000131778	ENSG00000131778			1916	protein-coding gene	gene with protein product		613039				9653160	Standard	NM_004284		Approved	ALC1	uc001epm.5	Q86WJ1	OTTHUMG00000150271	ENST00000369258.4:c.766C>G	chr1.hg19:g.146737617C>G	ENSP00000358262:p.Pro256Ala	109.0	0.0		94.0	4.0	NM_004284	A5YM64|B4DDE1|B5MDZ7|Q53EZ3|Q5VXX7|Q6DD94|Q6PK83|Q86XH3|Q96HF7|Q96SP3|Q9BVJ1|Q9NVV8	Missense_Mutation	SNP	ENST00000369258.4	hg19	CCDS927.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.8|20.8	4.043725|4.043725	0.75732|0.75732	.|.	.|.	ENSG00000131778|ENSG00000131778	ENST00000431239;ENST00000369259;ENST00000369258;ENST00000436230|ENST00000254086	D;D;D|.	0.94687|.	-3.49;-3.21;-3.49|.	5.48|5.48	5.48|5.48	0.80851|0.80851	SNF2-related (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.75539|0.75539	0.3863|0.3863	M|M	0.84511|0.84511	2.7|2.7	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	0.997;1.0;0.996|.	T|T	0.78283|0.78283	-0.2264|-0.2264	10|6	0.25106|0.54805	T|T	0.35|0.06	.|.	16.8472|16.8472	0.85984|0.85984	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	256;52;256|.	Q86WJ1-2;Q86WJ1-3;Q86WJ1|.	.;.;CHD1L_HUMAN|.	A|R	256;52;256;156|216	ENSP00000389031:P256A;ENSP00000358263:P52A;ENSP00000358262:P256A|.	ENSP00000358262:P256A|ENSP00000254086:S216R	P|S	+|+	1|3	0|2	CHD1L|CHD1L	145204241|145204241	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.951000|0.951000	0.60555|0.60555	7.302000|7.302000	0.78861|0.78861	2.588000|2.588000	0.87417|0.87417	0.563000|0.563000	0.77884|0.77884	CCA|AGC	.	.		0.413	CHD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040377.1	NM_004284		G	146737617	C	G	146737617	3	3	263	1	0	0	0	0	1	0	0	0	3326	739	26	4	796	4	CHD1L	1	146737617	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	29103591	146737617	102513004	29	38403										
MCL1	4170	hgsc.bcm.edu	37	chr1	150551951	150551951	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cgctgccggcccccaagccgGcccccccacagtagaggttg	12	19	0	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:150551951G>A	ENST00000369026.2	-	1	115	c.56C>T	c.(55-57)gCc>gTc	p.A19V	MCL1_ENST00000464132.1_5'Flank|MCL1_ENST00000307940.3_Missense_Mutation_p.A19V	NM_001197320.1|NM_021960.4	NP_001184249.1|NP_068779.1	Q07820	MCL1_HUMAN	myeloid cell leukemia 1	19					apoptotic mitochondrial changes (GO:0008637)|cell fate determination (GO:0001709)|cellular homeostasis (GO:0019725)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organismal development (GO:0007275)|negative regulation of anoikis (GO:2000811)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|protein transmembrane transport (GO:0071806)|regulation of response to DNA damage stimulus (GO:2001020)|response to cytokine (GO:0034097)	Bcl-2 family protein complex (GO:0097136)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	BH3 domain binding (GO:0051434)|protein channel activity (GO:0015266)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(2)|large_intestine(1)|lung(4)|prostate(1)	8	all_cancers(9;1.69e-53)|all_epithelial(9;1.95e-43)|all_lung(15;1.09e-34)|Lung NSC(24;4.04e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			CCCCAAGCCGGCCCCCCCACA	0.682																																					p.A19V		Atlas-SNP	.											.	MCL1	27	.	0			c.C56T						.						9	13	12					1																	150551951		1246	2578	3824	SO:0001583	missense	4170	exon1			AAGCCGGCCCCCC	BC017197	CCDS956.1, CCDS957.1, CCDS72909.1	1q21	2014-03-07	2014-03-07		ENSG00000143384	ENSG00000143384			6943	protein-coding gene	gene with protein product		159552	"myeloid cell leukemia sequence 1 (BCL2-related)"			7682708, 7835896	Standard	NM_021960		Approved	BCL2L3, Mcl-1	uc001euz.3	Q07820	OTTHUMG00000034867	ENST00000369026.2:c.56C>T	chr1.hg19:g.150551951G>A	ENSP00000358022:p.Ala19Val	82.0	0.0		138.0	33.0	NM_182763	B2R6B2|D3DV03|D3DV04|Q9HD91|Q9NRQ3|Q9NRQ4|Q9UHR7|Q9UHR8|Q9UHR9|Q9UNJ1	Missense_Mutation	SNP	ENST00000369026.2	hg19	CCDS957.1	.	.	.	.	.	.	.	.	.	.	g	17.64	3.440387	0.63067	.	.	ENSG00000143384	ENST00000369026;ENST00000307940;ENST00000439749	T;T	0.35421	2.42;1.31	4.72	4.72	0.59763	.	0.633271	0.13115	N	0.412699	T	0.26448	0.0646	L	0.29908	0.895	0.09310	N	0.999999	D;P	0.53619	0.961;0.476	P;B	0.52909	0.713;0.225	T	0.08576	-1.0715	10	0.66056	D	0.02	-4.2208	13.0603	0.59003	0.0:0.0:1.0:0.0	.	19;19	Q07820-2;Q07820	.;MCL1_HUMAN	V	19	ENSP00000358022:A19V;ENSP00000309973:A19V	ENSP00000309973:A19V	A	-	2	0	MCL1	148818575	0.744000	0.28250	0.162000	0.22713	0.008000	0.06430	3.040000	0.49799	2.459000	0.83118	0.556000	0.70494	GCC	.	.		0.682	MCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084402.1	NM_021960		A	150551951	G	A	150551951	3	1	263	1	0	0	0	0	1	0	0	0	9393	1203	42	3	1019	3	MCL1	1	150551951	Missense_Mutation	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	3814334	150551951	98698670	30	38404										
THEM4	117145	hgsc.bcm.edu	37	chr1	151867506	151867506	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	agaaaatgggttttgaagtcTtgaatccattcagtaggtgt	11	4	2	3			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:151867506T>G	ENST00000368814.3	-	2	613	c.264A>C	c.(262-264)caA>caC	p.Q88H	THEM4_ENST00000489410.1_Missense_Mutation_p.Q88H	NM_053055.4	NP_444283.2	Q5T1C6	THEM4_HUMAN	thioesterase superfamily member 4	88					epidermal growth factor receptor signaling pathway (GO:0007173)|fatty acid metabolic process (GO:0006631)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|protein kinase B signaling (GO:0043491)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)	cell projection (GO:0042995)|cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	palmitoyl-CoA hydrolase activity (GO:0016290)			endometrium(1)|large_intestine(4)|lung(3)|urinary_tract(1)	9	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			TTTTGAAGTCTTGAATCCATT	0.373																																					p.Q88H		Atlas-SNP	.											.	THEM4	19	.	0			c.A264C						.						119	119	119					1																	151867506		2203	4300	6503	SO:0001583	missense	117145	exon2			GAAGTCTTGAATC	AJ313515	CCDS1006.1	1q21.3	2008-02-05			ENSG00000159445	ENSG00000159445			17947	protein-coding gene	gene with protein product	"C-terminal modulator protein"	606388				11598301	Standard	NM_053055		Approved	CTMP	uc001ezj.2	Q5T1C6	OTTHUMG00000013049	ENST00000368814.3:c.264A>C	chr1.hg19:g.151867506T>G	ENSP00000357804:p.Gln88His	97.0	0.0		241.0	11.0	NM_053055	B2RBX2|Q96KR2	Missense_Mutation	SNP	ENST00000368814.3	hg19	CCDS1006.1	.	.	.	.	.	.	.	.	.	.	T	13.76	2.332748	0.41297	.	.	ENSG00000159445	ENST00000368814;ENST00000489410	T;T	0.36340	2.4;1.26	3.67	0.0402	0.14208	.	0.876505	0.10037	N	0.723986	T	0.13628	0.0330	L	0.59436	1.845	0.09310	N	1	P	0.41041	0.736	B	0.38712	0.28	T	0.15723	-1.0427	10	0.51188	T	0.08	0.114	3.3509	0.07151	0.0:0.2256:0.2073:0.5671	.	88	Q5T1C6	THEM4_HUMAN	H	88	ENSP00000357804:Q88H;ENSP00000433304:Q88H	ENSP00000357804:Q88H	Q	-	3	2	THEM4	150134130	0.002000	0.14202	0.000000	0.03702	0.015000	0.08874	0.470000	0.22084	-0.013000	0.14199	-0.280000	0.10049	CAA	.	.		0.373	THEM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036615.1	NM_053055		G	151867506	T	G	151867506	3	3	263	1	0	0	0	0	1	0	0	0	15873	1606	56	5	478	5	THEM4	1	151867506	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	1315555	151867506	97383115	31	38405										
DENND4B	9909	hgsc.bcm.edu	37	chr1	153907287	153907287	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tgacacctgctcctgctgctGctgctgctgctgctgctgtt	11	14	0	1	rs3835302|rs199597671		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:153907287G>C	ENST00000361217.4	-	18	3140	c.2722C>G	c.(2722-2724)Cag>Gag	p.Q908E	DENND4B_ENST00000474386.1_5'Flank	NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	908	Gln-rich.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab protein signal transduction (GO:0032483)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	36	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			tcctgctgctgctgctgctgc	0.632																																					p.Q908E		Atlas-SNP	.											.	DENND4B	210	.	0			c.C2722G						.						23	27	26					1																	153907287		2184	4281	6465	SO:0001583	missense	9909	exon18			GCTGCTGCTGCTG	AB007945	CCDS44228.1	1q21.3	2012-10-03	2006-01-27	2006-01-27	ENSG00000198837	ENSG00000198837		"DENN/MADD domain containing"	29044	protein-coding gene	gene with protein product			"KIAA0476"	KIAA0476		9455484, 12906859	Standard	NM_014856		Approved		uc001fdd.1	O75064	OTTHUMG00000037157	ENST00000361217.4:c.2722C>G	chr1.hg19:g.153907287G>C	ENSP00000354597:p.Gln908Glu	14.0	0.0		143.0	48.0	NM_014856	Q5T4K0	Missense_Mutation	SNP	ENST00000361217.4	hg19	CCDS44228.1	.	.	.	.	.	.	.	.	.	.	G	1.785	-0.481073	0.04383	.	.	ENSG00000198837	ENST00000361217;ENST00000368646	T;T	0.06294	3.33;3.32	2.67	0.673	0.17941	.	5.053470	0.00166	N	0.000001	T	0.00815	0.0027	N	0.14661	0.345	0.19300	N	0.999977	B	0.02656	0.0	B	0.04013	0.001	T	0.26573	-1.0099	10	0.02654	T	1	-2.4288	3.3651	0.07201	0.1454:0.0:0.5849:0.2697	.	908	O75064	DEN4B_HUMAN	E	908;919	ENSP00000354597:Q908E;ENSP00000357635:Q919E	ENSP00000354597:Q908E	Q	-	1	0	DENND4B	152173911	0.943000	0.32029	0.986000	0.45419	0.760000	0.43138	0.537000	0.23144	0.194000	0.20326	0.271000	0.19318	CAG	.	.		0.632	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806		C	153907287	G	C	153907287	3	2	263	1	0	0	0	0	1	0	0	0	4436	1328	46	4	1812	4	DENND4B	1	153907287	Missense_Mutation	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	2039781	153907287	95343334	32	38406										
DENND4B	9909	hgsc.bcm.edu	37	chr1	153907315	153907315	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tgctgctgctgttgctgctgCtgctgctgttgccgttctct	12	12	1	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:153907315C>T	ENST00000361217.4	-	18	3112	c.2694G>A	c.(2692-2694)caG>caA	p.Q898Q	DENND4B_ENST00000474386.1_5'Flank	NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	898	Gln-rich.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab protein signal transduction (GO:0032483)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	36	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			gttgctgctgctgctgctgtt	0.647																																					p.Q898Q		Atlas-SNP	.											.	DENND4B	210	.	0			c.G2694A						.						37	46	43					1																	153907315		2194	4286	6480	SO:0001819	synonymous_variant	9909	exon18			CTGCTGCTGCTGC	AB007945	CCDS44228.1	1q21.3	2012-10-03	2006-01-27	2006-01-27	ENSG00000198837	ENSG00000198837		"DENN/MADD domain containing"	29044	protein-coding gene	gene with protein product			"KIAA0476"	KIAA0476		9455484, 12906859	Standard	NM_014856		Approved		uc001fdd.1	O75064	OTTHUMG00000037157	ENST00000361217.4:c.2694G>A	chr1.hg19:g.153907315C>T		86.0	0.0		182.0	14.0	NM_014856	Q5T4K0	Silent	SNP	ENST00000361217.4	hg19	CCDS44228.1																																																																																			.	.		0.647	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806		T	153907315	C	T	153907315	2	4	263	1	0	0	0	0	0	0	0	1	4436	796	28	3		3	DENND4B	1	153907315	Silent	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	28	153907315	95343306	33	38407										
ASH1L	55870	hgsc.bcm.edu	37	chr1	155448559	155448559	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	agaaagaggaaaactaaggcTgtgcataaaaggcatttcag	11	5	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:155448559T>C	ENST00000368346.3	-	3	4741	c.4102A>G	c.(4102-4104)Agc>Ggc	p.S1368G	ASH1L_ENST00000392403.3_Missense_Mutation_p.S1368G			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	1368					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			AAACTAAGGCTGTGCATAAAA	0.433																																					p.S1368G		Atlas-SNP	.											.	ASH1L	279	.	0			c.A4102G						.						79	71	74					1																	155448559		2203	4300	6503	SO:0001583	missense	55870	exon3			TAAGGCTGTGCAT	AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.4102A>G	chr1.hg19:g.155448559T>C	ENSP00000357330:p.Ser1368Gly	50.0	0.0		146.0	6.0	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	hg19		.	.	.	.	.	.	.	.	.	.	T	7.800	0.713437	0.15306	.	.	ENSG00000116539	ENST00000368346;ENST00000392403	D;D	0.92752	-3.1;-3.1	4.92	4.92	0.64577	.	0.053086	0.85682	D	0.000000	T	0.56834	0.2012	N	0.01352	-0.895	0.80722	D	1	B;B	0.10296	0.002;0.003	B;B	0.13407	0.004;0.009	T	0.61501	-0.7050	10	0.02654	T	1	.	9.007	0.36117	0.0:0.0834:0.0:0.9166	.	1368;1368	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	G	1368	ENSP00000357330:S1368G;ENSP00000376204:S1368G	ENSP00000357330:S1368G	S	-	1	0	ASH1L	153715183	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.843000	0.62838	2.061000	0.61500	0.482000	0.46254	AGC	.	.		0.433	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		C	155448559	T	C	155448559	3	2	263	1	0	0	0	0	1	0	0	0	1041	1580	55	2	4896	2	ASH1L	1	155448559	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	1541244	155448559	93802062	34	38408										
YY1AP1	55249	hgsc.bcm.edu	37	chr1	155630158	155630158	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	aaacatggaagaggcaggggAgggcatcattaccttgggca	15	7	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:155630158A>G	ENST00000295566.4	-	11	1704	c.1681T>C	c.(1681-1683)Tcc>Ccc	p.S561P	YY1AP1_ENST00000368340.5_Missense_Mutation_p.S633P|YY1AP1_ENST00000359205.5_Missense_Mutation_p.S504P|YY1AP1_ENST00000368339.5_Missense_Mutation_p.S653P|YY1AP1_ENST00000404643.1_Missense_Mutation_p.S495P|YY1AP1_ENST00000535662.1_Missense_Mutation_p.S361P|YY1AP1_ENST00000368330.2_Missense_Mutation_p.S515P|YY1AP1_ENST00000361831.5_Missense_Mutation_p.S504P|MSTO1_ENST00000452804.2_Intron|YY1AP1_ENST00000355499.4_Missense_Mutation_p.S515P|YY1AP1_ENST00000407221.1_Missense_Mutation_p.S484P|YY1AP1_ENST00000311573.5_Missense_Mutation_p.S484P|MSTO1_ENST00000538143.1_Intron|YY1AP1_ENST00000347088.5_Missense_Mutation_p.S515P	NM_001198906.1|NM_139118.2	NP_001185835.1|NP_620829.1	Q9H869	YYAP1_HUMAN	YY1 associated protein 1	561					regulation of cell cycle (GO:0051726)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(7)|ovary(2)|skin(2)|urinary_tract(2)	31	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)					GAGGCAGGGGAGGGCATCATT	0.557																																					p.S653P		Atlas-SNP	.											.	YY1AP1	104	.	0			c.T1957C						.						73	70	71					1																	155630158		2203	4300	6503	SO:0001583	missense	55249	exon10			CAGGGGAGGGCAT	BC008766	CCDS1115.1, CCDS1116.1, CCDS55643.1, CCDS55644.1, CCDS55645.1	1q22	2009-05-07			ENSG00000163374	ENSG00000163374			30935	protein-coding gene	gene with protein product		607860				11710830	Standard	NM_139119		Approved	YY1AP, HCCA2, YAP		Q9H869	OTTHUMG00000035437	ENST00000295566.4:c.1681T>C	chr1.hg19:g.155630158A>G	ENSP00000295566:p.Ser561Pro	82.0	0.0		247.0	14.0	NM_001198903	B0QZ54|B4DMP2|B4E0I0|D3DV96|D3DV98|H7BY62|Q5VYZ1|Q5VYZ4|Q5VYZ7|Q7L4C3|Q7L5E2|Q8IXA6|Q8TEW5|Q8TF04|Q96HB6|Q9BQ64|Q9NV84	Missense_Mutation	SNP	ENST00000295566.4	hg19	CCDS1115.1	.	.	.	.	.	.	.	.	.	.	a	11.77	1.739015	0.30774	.	.	ENSG00000163374	ENST00000359205;ENST00000355499;ENST00000311573;ENST00000347088;ENST00000361831;ENST00000368340;ENST00000295566;ENST00000368330;ENST00000407221;ENST00000404643;ENST00000368339;ENST00000535662	T;T;T;T;T;T;T;T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68	2.53	2.53	0.30540	.	0.420404	0.20424	N	0.092611	T	0.44286	0.1286	L	0.51422	1.61	0.27856	N	0.940571	D;D;P;D;D	0.76494	0.982;0.999;0.914;0.998;0.999	P;D;P;D;D	0.80764	0.737;0.994;0.838;0.917;0.994	T	0.16867	-1.0388	10	0.62326	D	0.03	.	7.4814	0.27406	0.5407:0.4593:0.0:0.0	.	653;495;561;515;633	B4DMP2;Q9H869-4;Q9H869;Q9H869-2;Q5VYZ1	.;.;YYAP1_HUMAN;.;.	P	504;515;484;515;504;633;561;515;484;495;653;361	ENSP00000352134:S504P;ENSP00000347686:S515P;ENSP00000311138:S484P;ENSP00000316079:S515P;ENSP00000355298:S504P;ENSP00000357324:S633P;ENSP00000295566:S561P;ENSP00000357314:S515P;ENSP00000385791:S484P;ENSP00000385390:S495P;ENSP00000357323:S653P;ENSP00000437926:S361P	ENSP00000295566:S561P	S	-	1	0	YY1AP1	153896782	0.732000	0.28121	0.958000	0.39756	0.373000	0.29922	0.986000	0.29590	1.165000	0.42670	0.254000	0.18369	TCC	.	.		0.557	YY1AP1-043	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000086027.1	NM_139118		G	155630158	A	G	155630158	3	3	263	1	0	0	0	0	1	0	0	0	17523	304	11	2	713	2	YY1AP1	1	155630158	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	181599	155630158	93620463	35	38409										
IFI16	3428	hgsc.bcm.edu	37	chr1	158988074	158988074	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cagaagaaatgttctccaaaAacgcccagtgatagtgaagg	10	8	1	4			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:158988074A>T	ENST00000295809.7	+	5	860	c.605A>T	c.(604-606)aAa>aTa	p.K202I	IFI16_ENST00000368131.4_Missense_Mutation_p.K202I|IFI16_ENST00000368132.3_Missense_Mutation_p.K202I|IFI16_ENST00000448393.2_Missense_Mutation_p.K202I|IFI16_ENST00000340979.6_Missense_Mutation_p.K202I|IFI16_ENST00000430894.2_Missense_Mutation_p.K150I|IFI16_ENST00000359709.3_Missense_Mutation_p.K146I			Q16666	IF16_HUMAN	interferon, gamma-inducible protein 16	202	HIN-200 1. {ECO:0000255|PROSITE- ProRule:PRU00106}.|Interaction with TP53 C-terminus.		K -> E (in dbSNP:rs11585341).		activation of cysteine-type endopeptidase activity (GO:0097202)|activation of innate immune response (GO:0002218)|autophagy (GO:0006914)|cell proliferation (GO:0008283)|cellular response to glucose starvation (GO:0042149)|cellular response to ionizing radiation (GO:0071479)|defense response to virus (GO:0051607)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|monocyte differentiation (GO:0030224)|myeloid cell differentiation (GO:0030099)|negative regulation of cysteine-type endopeptidase activity (GO:2000117)|negative regulation of DNA binding (GO:0043392)|negative regulation of innate immune response (GO:0045824)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|positive regulation of cytokine production (GO:0001819)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of autophagy (GO:0010506)|regulation of gene expression, epigenetic (GO:0040029)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_hematologic(112;0.0429)					GTTCTCCAAAAACGCCCAGTG	0.398																																					p.K202I		Atlas-SNP	.											.	IFI16	111	.	0			c.A605T						.						86	81	82					1																	158988074		2203	4300	6503	SO:0001583	missense	3428	exon5			TCCAAAAACGCCC	M63838	CCDS1180.3, CCDS58039.1	1q22	2008-02-05			ENSG00000163565	ENSG00000163565			5395	protein-coding gene	gene with protein product		147586				1526658, 7959953	Standard	NM_005531		Approved	IFNGIP1, PYHIN2	uc010pis.2	Q16666	OTTHUMG00000037108	ENST00000295809.7:c.605A>T	chr1.hg19:g.158988074A>T	ENSP00000295809:p.Lys202Ile	128.0	0.0		364.0	120.0	NM_005531	B4DJT8|H3BLV7|Q59GX0|Q5T3W7|Q5T3W8|Q5T3X0|Q5T3X1|Q5T3X2|Q8N9E5|Q8NEQ7|Q96AJ5|Q9UH78	Missense_Mutation	SNP	ENST00000295809.7	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	13.97|13.97	2.396697|2.396697	0.42512|0.42512	.|.	.|.	ENSG00000163565|ENSG00000163565	ENST00000359709;ENST00000295809;ENST00000340979;ENST00000368131;ENST00000368132;ENST00000430894|ENST00000448393	T;T;T;T;T|.	0.15952|.	2.38;2.38;2.38;2.38;2.38|.	2.78|2.78	-4.66|-4.66	0.03329|0.03329	HIN-200/IF120x (2);Nucleic acid-binding, OB-fold (1);|.	.|.	.|.	.|.	.|.	T|T	0.22936|0.22936	0.0554|0.0554	M|M	0.69358|0.69358	2.11|2.11	0.09310|0.09310	N|N	1|1	B;B;B|.	0.29508|.	0.139;0.114;0.246|.	P;B;P|.	0.45428|.	0.48;0.348;0.48|.	T|T	0.42682|0.42682	-0.9437|-0.9437	9|5	0.72032|.	D|.	0.01|.	.|.	5.6331|5.6331	0.17522|0.17522	0.2787:0.5828:0.1384:0.0|0.2787:0.5828:0.1384:0.0	.|.	150;202;202|.	E7EPR3;Q16666-2;Q16666|.	.;.;IF16_HUMAN|.	I|Y	202;202;202;202;202;150|23	ENSP00000295809:K202I;ENSP00000342741:K202I;ENSP00000357113:K202I;ENSP00000357114:K202I;ENSP00000394935:K150I|.	ENSP00000295809:K202I|.	K|N	+|+	2|1	0|0	IFI16|IFI16	157254698|157254698	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.003000|0.003000	0.03518|0.03518	-0.797000|-0.797000	0.04570|0.04570	-0.568000|-0.568000	0.06038|0.06038	0.379000|0.379000	0.24179|0.24179	AAA|AAC	.	.		0.398	IFI16-013	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000421720.1	NM_005531		T	158988074	A	T	158988074	3	4	263	1	0	0	0	0	1	0	0	0	7520	14	1	4	619	4	IFI16	1	158988074	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	3357916	158988074	90262547	36	38410										
ATP1A4	480	hgsc.bcm.edu	37	chr1	160151564	160151564	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	agtgggcggatctcatcatcTccaagactcgccgcaactca	9	14	4	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:160151564T>C	ENST00000368081.4	+	19	3298	c.2827T>C	c.(2827-2829)Tcc>Ccc	p.S943P	ATP1A4_ENST00000470705.1_Missense_Mutation_p.S79P|ATP1A4_ENST00000418334.1_3'UTR	NM_144699.3	NP_653300.2	Q13733	AT1A4_HUMAN	ATPase, Na+/K+ transporting, alpha 4 polypeptide	943					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|fertilization (GO:0009566)|ion transmembrane transport (GO:0034220)|potassium ion transport (GO:0006813)|regulation of cellular pH (GO:0030641)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(34)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	75	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			TCTCATCATCTCCAAGACTCG	0.522																																					p.S943P		Atlas-SNP	.											.	ATP1A4	167	.	0			c.T2827C						.						164	166	165					1																	160151564		2203	4300	6503	SO:0001583	missense	480	exon19			ATCATCTCCAAGA	BC028297	CCDS1197.1, CCDS44255.1	1q23.2	2012-10-22	2002-02-25		ENSG00000132681	ENSG00000132681		"ATPases / P-type"	14073	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-4", "sodium pump subunit alpha-4", "sodium-potassium ATPase catalytic subunit alpha-4"	607321	"ATPase, Na+/K+ transporting, alpha polypeptide-like 2"	ATP1AL2		1981991, 3035563	Standard	NM_144699		Approved		uc001fve.4	Q13733	OTTHUMG00000031609	ENST00000368081.4:c.2827T>C	chr1.hg19:g.160151564T>C	ENSP00000357060:p.Ser943Pro	175.0	0.0		447.0	18.0	NM_144699	Q504T2|Q7Z4I9|Q8TBN8|Q8WXA7|Q8WXH7|Q8WY13	Missense_Mutation	SNP	ENST00000368081.4	hg19	CCDS1197.1	.	.	.	.	.	.	.	.	.	.	T	13.59	2.283604	0.40394	.	.	ENSG00000132681	ENST00000368081;ENST00000470705	D;D	0.96104	-3.91;-3.91	4.16	4.16	0.48862	ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type,  transmembrane domain (1);	0.050605	0.85682	D	0.000000	D	0.94255	0.8155	M	0.83483	2.645	0.32463	N	0.543875	P	0.44659	0.84	P	0.49477	0.612	D	0.93747	0.7055	10	0.87932	D	0	.	6.3642	0.21445	0.0:0.11:0.0:0.89	.	943	Q13733	AT1A4_HUMAN	P	943;79	ENSP00000357060:S943P;ENSP00000433094:S79P	ENSP00000357060:S943P	S	+	1	0	ATP1A4	158418188	1.000000	0.71417	1.000000	0.80357	0.085000	0.17905	4.947000	0.63583	1.877000	0.54381	0.374000	0.22700	TCC	.	.		0.522	ATP1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077415.1	NM_144699		C	160151564	T	C	160151564	3	2	263	1	0	0	0	0	1	0	0	0	1131	1551	54	2	2901	2	ATP1A4	1	160151564	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	1163490	160151564	89099057	37	38411										
F5	2153	hgsc.bcm.edu	37	chr1	169555549	169555549	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ccttagctgtgccgcttctgTcccttggctcccccagccta	8	18	1	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:169555549T>C	ENST00000367797.3	-	1	277	c.76A>G	c.(76-78)Aca>Gca	p.T26A	F5_ENST00000367796.3_Missense_Mutation_p.T26A|F5_ENST00000546081.1_5'UTR	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	26					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	GCCGCTTCTGTCCCTTGGCTC	0.612																																					p.T26A		Atlas-SNP	.											.	F5	301	.	0			c.A76G						.						73	55	61					1																	169555549		2203	4300	6503	SO:0001583	missense	2153	exon1			CTTCTGTCCCTTG	M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.76A>G	chr1.hg19:g.169555549T>C	ENSP00000356771:p.Thr26Ala	96.0	0.0		220.0	10.0	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	hg19	CCDS1281.1	.	.	.	.	.	.	.	.	.	.	T	0.006	-2.109576	0.00353	.	.	ENSG00000198734	ENST00000367797;ENST00000367796	D;D	0.97959	-4.63;-4.63	5.38	3.43	0.39272	Cupredoxin (1);	1.249000	0.05648	N	0.584627	T	0.82056	0.4954	N	0.02916	-0.46	0.27738	N	0.944598	B	0.02656	0.0	B	0.01281	0.0	T	0.77713	-0.2485	10	0.09084	T	0.74	-0.9191	6.8045	0.23770	0.0:0.7709:0.0:0.2291	.	26	P12259	FA5_HUMAN	A	26	ENSP00000356771:T26A;ENSP00000356770:T26A	ENSP00000356770:T26A	T	-	1	0	F5	167822173	0.025000	0.19082	0.026000	0.17262	0.059000	0.15707	0.509000	0.22707	0.563000	0.29222	-0.366000	0.07423	ACA	.	.		0.612	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130		C	169555549	T	C	169555549	3	2	263	1	0	0	0	0	1	0	0	0	5350	1667	58	2	6698	2	F5	1	169555549	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	9403985	169555549	79695072	38	38412										
BAT2L2	23215	hgsc.bcm.edu	37	chr1	171510373	171510373	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	agctctgattttgaagttgtCcccaaaagaagacgacagcg	10	9	1	4			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:171510373C>T	ENST00000338920.4	+	16	3999	c.3762C>T	c.(3760-3762)gtC>gtT	p.V1254V	PRRC2C_ENST00000426496.2_Silent_p.V1254V|PRRC2C_ENST00000367742.3_Silent_p.V1256V|PRRC2C_ENST00000392078.3_Silent_p.V1256V	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	1254					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										TTGAAGTTGTCCCCAAAAGAA	0.458																																					p.V1254V		Atlas-SNP	.											.	.	.	.	0			c.C3762T						.						51	51	51					1																	171510373		2203	4300	6503	SO:0001819	synonymous_variant	23215	exon16			AGTTGTCCCCAAA	AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"BAT2 domain containing 1", "HLA-B associated transcript 2-like 2"	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.3762C>T	chr1.hg19:g.171510373C>T		157.0	0.0		431.0	29.0	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Silent	SNP	ENST00000338920.4	hg19	CCDS1296.2																																																																																			.	.		0.458	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172		T	171510373	C	T	171510373	2	4	263	1	0	0	0	0	0	0	0	1	1321	842	30	3		3	BAT2L2	1	171510373	Silent	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	1954824	171510373	77740248	39	38413										
TDRD5	163589	hgsc.bcm.edu	37	chr1	179564922	179564922	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gttaaatgtagtggagacttCaagactgaatcacactgaaa	9	6	2	4			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:179564922C>G	ENST00000367614.1	+	4	1159	c.800C>G	c.(799-801)tCa>tGa	p.S267*	TDRD5_ENST00000444136.1_Nonsense_Mutation_p.S267*|TDRD5_ENST00000294848.8_Nonsense_Mutation_p.S267*	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	267					DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)				NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						GTGGAGACTTCAAGACTGAAT	0.358																																					p.S267X		Atlas-SNP	.											.	TDRD5	149	.	0			c.C800G						.						75	77	76					1																	179564922		2203	4300	6503	SO:0001587	stop_gained	163589	exon4			AGACTTCAAGACT	AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"Tudor domain containing"	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.800C>G	chr1.hg19:g.179564922C>G	ENSP00000356586:p.Ser267*	102.0	0.0		259.0	42.0	NM_173533	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Nonsense_Mutation	SNP	ENST00000367614.1	hg19	CCDS1332.1	.	.	.	.	.	.	.	.	.	.	C	40	8.082449	0.98646	.	.	ENSG00000162782	ENST00000367614;ENST00000294848;ENST00000444136	.	.	.	5.69	4.78	0.61160	.	0.232509	0.30126	N	0.010349	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	-14.4089	10.5493	0.45079	0.0:0.9112:0.0:0.0888	.	.	.	.	X	267	.	ENSP00000294848:S267X	S	+	2	0	TDRD5	177831545	0.998000	0.40836	0.982000	0.44146	0.711000	0.40976	1.278000	0.33179	1.404000	0.46819	0.585000	0.79938	TCA	.	.		0.358	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533		G	179564922	C	G	179564922	4	3	263	1	0	0	0	0	0	1	0	0	15748	838	29	4	810	4	TDRD5	1	179564922	Nonsense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	8054549	179564922	69685699	40	38414										
NVL	4931	hgsc.bcm.edu	37	chr1	224514099	224514099	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ctatatttatttacctgtacActctttgtaaatcagacgct	4	9	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:224514099A>G	ENST00000281701.6	-	2	384	c.125T>C	c.(124-126)gTg>gCg	p.V42A	NVL_ENST00000391875.2_Intron|NVL_ENST00000361463.3_Intron|NVL_ENST00000340871.4_Intron|NVL_ENST00000468673.1_5'UTR|NVL_ENST00000482491.1_Intron|NVL_ENST00000469075.1_Missense_Mutation_p.V42A	NM_002533.3	NP_002524.2	O15381	NVL_HUMAN	nuclear VCP-like	42						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|prostate(1)|skin(4)|soft_tissue(1)|urinary_tract(1)	42				GBM - Glioblastoma multiforme(131;0.00501)		TTACCTGTACACTCTTTGTAA	0.323																																					p.V42A		Atlas-SNP	.											.	NVL	74	.	0			c.T125C						.						98	100	99					1																	224514099		2203	4300	6503	SO:0001583	missense	4931	exon2			CTGTACACTCTTT	U78772	CCDS1541.1, CCDS1542.1, CCDS58062.1, CCDS58063.1	1q41-q42.2	2010-04-21			ENSG00000143748	ENSG00000143748		"ATPases / AAA-type"	8070	protein-coding gene	gene with protein product	"Nuclear valosin-containing protein-like", "nuclear VCP-like protein"	602426				9286697	Standard	NM_002533		Approved		uc001hok.3	O15381	OTTHUMG00000037536	ENST00000281701.6:c.125T>C	chr1.hg19:g.224514099A>G	ENSP00000281701:p.Val42Ala	50.0	0.0		110.0	5.0	NM_001243147	B4DMC4|B4DP98|Q96EM7	Missense_Mutation	SNP	ENST00000281701.6	hg19	CCDS1541.1	.	.	.	.	.	.	.	.	.	.	A	15.13	2.743239	0.49151	.	.	ENSG00000143748	ENST00000281701;ENST00000469075;ENST00000488718;ENST00000461546	D;D	0.94497	-3.38;-3.44	5.91	5.91	0.95273	.	0.394021	0.28176	N	0.016315	D	0.87605	0.6219	N	0.22421	0.69	0.80722	D	1	B;B;B	0.11235	0.004;0.002;0.0	B;B;B	0.11329	0.006;0.006;0.0	T	0.81037	-0.1114	10	0.17369	T	0.5	-11.8838	7.2743	0.26275	0.8794:0.0:0.1206:0.0	.	42;42;42	B4DF43;B4DP98;O15381	.;.;NVL_HUMAN	A	42	ENSP00000281701:V42A;ENSP00000417826:V42A	ENSP00000281701:V42A	V	-	2	0	NVL	222580722	1.000000	0.71417	1.000000	0.80357	0.855000	0.48748	2.943000	0.49026	2.261000	0.74972	0.533000	0.62120	GTG	.	.		0.323	NVL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091453.2	NM_002533		G	224514099	A	G	224514099	3	3	263	1	0	0	0	0	1	0	0	0	10789	159	6	2	2533	2	NVL	1	224514099	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	44949177	224514099	24736522	41	38415										
JMJD4	65094	hgsc.bcm.edu	37	chr1	227922402	227922402	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cagcccctgggagaggagtaGcccgcctgtatgtactcttt	12	12	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:227922402G>A	ENST00000366758.3	-	2	515	c.516C>T	c.(514-516)ggC>ggT	p.G172G	JMJD4_ENST00000485807.1_5'Flank|SNAP47_ENST00000366760.1_Intron|JMJD4_ENST00000438896.2_Silent_p.G172G|SNAP47_ENST00000366759.4_5'Flank|SNAP47_ENST00000315781.5_5'Flank	NM_023007.2	NP_075383.2	Q9H9V9	JMJD4_HUMAN	jumonji domain containing 4	172										endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	9		Prostate(94;0.0885)				GAGAGGAGTAGCCCGCCTGTA	0.562																																					p.G172G		Atlas-SNP	.											.	JMJD4	28	.	0			c.C516T						.						221	184	197					1																	227922402		2203	4300	6503	SO:0001819	synonymous_variant	65094	exon2			GGAGTAGCCCGCC	AK022579	CCDS1561.1, CCDS59203.1	1q42.13	2008-02-05			ENSG00000081692	ENSG00000081692			25724	protein-coding gene	gene with protein product						12477932	Standard	NM_023007		Approved	FLJ12517	uc001hrb.3	Q9H9V9	OTTHUMG00000037698	ENST00000366758.3:c.516C>T	chr1.hg19:g.227922402G>A		287.0	0.0		562.0	285.0	NM_023007	Q5TBZ1|Q5TBZ6|Q9H970	Silent	SNP	ENST00000366758.3	hg19	CCDS1561.1	.	.	.	.	.	.	.	.	.	.	.	11.00	1.509531	0.27036	.	.	ENSG00000081692	ENST00000438896	.	.	.	4.55	2.44	0.29823	.	.	.	.	.	T	0.56077	0.1961	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50898	-0.8773	4	.	.	.	-12.0369	7.9626	0.30081	0.0945:0.1617:0.7439:0.0	.	.	.	.	V	165	.	.	A	-	2	0	JMJD4	225989025	0.720000	0.27996	0.755000	0.31263	0.903000	0.53119	0.932000	0.28884	0.991000	0.38814	0.555000	0.69702	GCT	.	.		0.562	JMJD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091970.1	NM_023007		A	227922402	G	A	227922402	2	1	263	1	0	0	0	0	0	0	0	1	7960	958	34	3		3	JMJD4	1	227922402	Silent	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	3408303	227922402	21328219	42	38416										
HEATR1	55127	hgsc.bcm.edu	37	chr1	236749177	236749177	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ttatcagccaacaactcaatCatcttctgatttgctacacc	3	13	5	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:236749177C>G	ENST00000366582.3	-	16	2106	c.1992G>C	c.(1990-1992)atG>atC	p.M664I	HEATR1_ENST00000366581.2_Missense_Mutation_p.M664I	NM_018072.5	NP_060542.4	Q9H583	HEAT1_HUMAN	HEAT repeat containing 1	664					rRNA processing (GO:0006364)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(18)|lung(28)|ovary(3)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	87	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			ACAACTCAATCATCTTCTGAT	0.353																																					p.M664I		Atlas-SNP	.											.	HEATR1	197	.	0			c.G1992C						.						104	96	99					1																	236749177		2203	4300	6503	SO:0001583	missense	55127	exon16			CTCAATCATCTTC	BC065205	CCDS31066.1	1q43	2011-08-12			ENSG00000119285	ENSG00000119285			25517	protein-coding gene	gene with protein product	"UTP10, small subunit (SSU) processome component, homolog (yeast)"					17699751	Standard	NM_018072		Approved	FLJ10359, BAP28, UTP10	uc001hyd.2	Q9H583	OTTHUMG00000040061	ENST00000366582.3:c.1992G>C	chr1.hg19:g.236749177C>G	ENSP00000355541:p.Met664Ile	149.0	0.0		274.0	17.0	NM_018072	Q5T3Q8|Q6P197|Q9NW23	Missense_Mutation	SNP	ENST00000366582.3	hg19	CCDS31066.1	.	.	.	.	.	.	.	.	.	.	C	18.13	3.554774	0.65425	.	.	ENSG00000119285	ENST00000366582;ENST00000366581	T;T	0.61510	0.1;0.72	5.76	5.76	0.90799	Armadillo-type fold (1);	0.049130	0.85682	D	0.000000	T	0.55386	0.1917	M	0.64997	1.995	0.80722	D	1	B	0.16396	0.017	B	0.08055	0.003	T	0.49380	-0.8946	10	0.25106	T	0.35	.	16.2348	0.82365	0.1333:0.8667:0.0:0.0	.	664	Q9H583	HEAT1_HUMAN	I	664	ENSP00000355541:M664I;ENSP00000355540:M664I	ENSP00000355540:M664I	M	-	3	0	HEATR1	234815800	1.000000	0.71417	1.000000	0.80357	0.744000	0.42396	1.585000	0.36600	2.721000	0.93114	0.591000	0.81541	ATG	.	.		0.353	HEATR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096635.1	XM_375853		G	236749177	C	G	236749177	3	3	263	1	0	0	0	0	1	0	0	0	7036	826	29	4	4562	4	HEATR1	1	236749177	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	8826775	236749177	12501444	43	38417										
MTR	4548	hgsc.bcm.edu	37	chr1	237038042	237038042	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	atagatataattggcctgtcAggactcatcactccttccct	6	12	3	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr1:237038042A>G	ENST00000366577.5	+	24	2884	c.2490A>G	c.(2488-2490)tcA>tcG	p.S830S	MTR_ENST00000535889.1_Silent_p.S779S	NM_000254.2	NP_000245.2	Q99707	METH_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase	830	B12-binding. {ECO:0000255|PROSITE- ProRule:PRU00666}.				cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|methylation (GO:0032259)|nervous system development (GO:0007399)|pteridine-containing compound metabolic process (GO:0042558)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	cobalamin binding (GO:0031419)|methionine synthase activity (GO:0008705)|S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	67	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)	ttGGCCTGTCAGGACTCATCA	0.348																																					p.S830S		Atlas-SNP	.											.	MTR	127	.	0			c.A2490G						.						91	82	85					1																	237038042		2203	4300	6503	SO:0001819	synonymous_variant	4548	exon24			CCTGTCAGGACTC	U73338	CCDS1614.1, CCDS73054.1	1q43	2011-05-12			ENSG00000116984	ENSG00000116984	2.1.1.13		7468	protein-coding gene	gene with protein product		156570				8968735	Standard	NM_000254		Approved	cblG	uc001hyi.4	Q99707	OTTHUMG00000040060	ENST00000366577.5:c.2490A>G	chr1.hg19:g.237038042A>G		31.0	0.0		75.0	4.0	NM_000254	A1L4N8|A9Z1W4|B9EGF7|Q99713|Q99723	Silent	SNP	ENST00000366577.5	hg19	CCDS1614.1																																																																																			.	.		0.348	MTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096632.2	NM_000254		G	237038042	A	G	237038042	2	3	263	1	0	0	0	0	0	0	0	1	9967	175	7	2		2	MTR	1	237038042	Silent	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	288865	237038042	12212579	44	38418										
PXDN	7837	hgsc.bcm.edu	37	chr2	1677567	1677567	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	agtttaggcgggaatctgtcTtcatgctcagctcattacta	9	9	5	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr2:1677567T>C	ENST00000252804.4	-	9	916	c.866A>G	c.(865-867)aAg>aGg	p.K289R	PXDN_ENST00000483018.1_5'UTR	NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	289	Ig-like C2-type 1.				extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		GGAATCTGTCTTCATGCTCAG	0.502																																					p.K289R		Atlas-SNP	.											.	PXDN	255	.	0			c.A866G						.						111	113	112					2																	1677567		2053	4195	6248	SO:0001583	missense	7837	exon9			TCTGTCTTCATGC	AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"Immunoglobulin superfamily / I-set domain containing"	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.866A>G	chr2.hg19:g.1677567T>C	ENSP00000252804:p.Lys289Arg	108.0	0.0		121.0	5.0	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Missense_Mutation	SNP	ENST00000252804.4	hg19	CCDS46221.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	10.02|10.02	1.235324|1.235324	0.22626|0.22626	.|.	.|.	ENSG00000130508|ENSG00000130508	ENST00000252804|ENST00000433670	T|.	0.60672|.	0.17|.	5.25|5.25	4.07|4.07	0.47477|0.47477	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	0.349867|.	0.31051|.	N|.	0.008342|.	T|T	0.28896|0.28896	0.0717|0.0717	N|N	0.16098|0.16098	0.37|0.37	0.26878|0.26878	N|N	0.967596|0.967596	B;B|.	0.06786|.	0.0;0.001|.	B;B|.	0.11329|.	0.002;0.006|.	T|T	0.18681|0.18681	-1.0329|-1.0329	10|5	0.19147|.	T|.	0.46|.	-33.4981|-33.4981	11.3246|11.3246	0.49442|0.49442	0.0:0.0:0.1522:0.8478|0.0:0.0:0.1522:0.8478	.|.	289;289|.	Q92626-2;Q92626|.	.;PXDN_HUMAN|.	R|G	289|285	ENSP00000252804:K289R|.	ENSP00000252804:K289R|.	K|R	-|-	2|1	0|2	PXDN|PXDN	1656574|1656574	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.760000|0.760000	0.43138|0.43138	3.210000|3.210000	0.51129|0.51129	0.902000|0.902000	0.36520|0.36520	-0.488000|-0.488000	0.04728|0.04728	AAG|AGA	.	.		0.502	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455		C	1677567	T	C	1677567	3	2	263	1	0	0	0	0	1	0	0	0	12862	1609	56	2	3633	2	PXDN	2	1677567	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10		1677567	241521806	45	38419										
ALLC	55821	hgsc.bcm.edu	37	chr2	3729256	3729256	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	aaatcccagaaagaggaaccAggacaggagctgcagccact	11	11	0	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr2:3729256A>G	ENST00000252505.3	+	6	493	c.331A>G	c.(331-333)Agg>Ggg	p.R111G		NM_018436.3	NP_060906.3	Q8N6M5	ALLC_HUMAN	allantoicase	130					allantoin catabolic process (GO:0000256)		allantoicase activity (GO:0004037)			breast(4)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	30	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.088)	all_cancers(51;0.24)		OV - Ovarian serous cystadenocarcinoma(76;0.088)|all cancers(51;0.151)|Epithelial(75;0.206)		AAGAGGAACCAGGACAGGAGC	0.443										HNSCC(21;0.051)																											p.R111G		Atlas-SNP	.											.	ALLC	61	.	0			c.A331G						.						52	56	55					2																	3729256		1897	4116	6013	SO:0001583	missense	55821	exon6			GGAACCAGGACAG	AF215924	CCDS46223.1	2p25.3	2008-02-05			ENSG00000151360	ENSG00000151360			17377	protein-coding gene	gene with protein product		612396				11054555	Standard	NM_018436		Approved	ALC	uc010ewt.3	Q8N6M5	OTTHUMG00000151485	ENST00000252505.3:c.331A>G	chr2.hg19:g.3729256A>G	ENSP00000252505:p.Arg111Gly	79.0	0.0		79.0	4.0	NM_018436	Q53T95|Q5RL81|Q96RE6|Q9NZA7	Missense_Mutation	SNP	ENST00000252505.3	hg19	CCDS46223.1	.	.	.	.	.	.	.	.	.	.	A	8.448	0.852473	0.17106	.	.	ENSG00000151360	ENST00000252505	.	.	.	4.98	3.8	0.43715	Allantoicase domain (1);Galactose-binding domain-like (1);	0.215393	0.49305	D	0.000158	T	0.40015	0.1100	M	0.61703	1.905	0.09310	N	1	P	0.37594	0.601	B	0.40506	0.331	T	0.19745	-1.0296	9	0.26408	T	0.33	-5.3742	8.8671	0.35294	0.8105:0.1895:0.0:0.0	.	130	Q8N6M5	ALLC_HUMAN	G	111	.	ENSP00000252505:R111G	R	+	1	2	ALLC	3707131	0.735000	0.28153	0.215000	0.23724	0.016000	0.09150	1.735000	0.38176	0.994000	0.38892	0.528000	0.53228	AGG	.	.		0.443	ALLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322855.1			G	3729256	A	G	3729256	3	3	263	1	0	0	0	0	1	0	0	0	534	179	7	2	349	2	ALLC	2	3729256	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	2051689	3729256	239470117	46	38420										
HS1BP3	64342	hgsc.bcm.edu	37	chr2	20823705	20823705	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gctgaggctgggtgtgggccCtccactctcacaggcggctg	16	13	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr2:20823705C>A	ENST00000304031.3	-	6	896	c.871G>T	c.(871-873)Ggg>Tgg	p.G291W		NM_022460.3	NP_071905.3	Q53T59	H1BP3_HUMAN	HCLS1 binding protein 3	291							phosphatidylinositol binding (GO:0035091)			endometrium(4)|large_intestine(1)|lung(7)|ovary(1)|skin(2)	15	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGTGTGGGCCCTCCACTCTCA	0.642																																					p.G291W		Atlas-SNP	.											.	HS1BP3	33	.	0			c.G871T						.						29	31	31					2																	20823705		2203	4299	6502	SO:0001583	missense	64342	exon6			TGGGCCCTCCACT		CCDS1700.1	2p24.1	2006-08-15			ENSG00000118960	ENSG00000118960			24979	protein-coding gene	gene with protein product		609359				10590261, 15699368	Standard	NM_022460		Approved	HS1-BP3,FLJ14249	uc002rdw.1	Q53T59	OTTHUMG00000122099	ENST00000304031.3:c.871G>T	chr2.hg19:g.20823705C>A	ENSP00000305193:p.Gly291Trp	84.0	0.0		103.0	33.0	NM_022460	B2RAW2|D6W529|Q86VC2|Q8N367	Missense_Mutation	SNP	ENST00000304031.3	hg19	CCDS1700.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	13.96|13.96|13.96	2.391889|2.391889|2.391889	0.42410|0.42410|0.42410	.|.|.	.|.|.	ENSG00000118960|ENSG00000118960|ENSG00000118960	ENST00000415264|ENST00000304031;ENST00000458740|ENST00000445102	.|T;T|.	.|0.34072|.	.|2.16;1.38|.	4.16|4.16|4.16	-0.339|-0.339|-0.339	0.12647|0.12647|0.12647	.|.|.	.|0.574784|.	.|0.17430|.	.|N|.	.|0.174509|.	T|T|T	0.39253|0.39253|0.39253	0.1071|0.1071|0.1071	L|L|L	0.60455|0.60455|0.60455	1.87|1.87|1.87	0.09310|0.09310|0.09310	N|N|N	0.99999|0.99999|0.99999	.|D|.	.|0.63046|.	.|0.992|.	.|P|.	.|0.54499|.	.|0.754|.	T|T|T	0.35201|0.35201|0.35201	-0.9798|-0.9798|-0.9798	5|10|5	.|0.72032|.	.|D|.	.|0.01|.	-4.5709|-4.5709|-4.5709	4.1741|4.1741|4.1741	0.10343|0.10343|0.10343	0.0:0.468:0.2176:0.3144|0.0:0.468:0.2176:0.3144|0.0:0.468:0.2176:0.3144	.|.|.	.|291|.	.|Q53T59|.	.|H1BP3_HUMAN|.	D|W|M	43|291;110|83	.|ENSP00000305193:G291W;ENSP00000392203:G110W|.	.|ENSP00000305193:G291W|.	E|G|R	-|-|-	3|1|2	2|0|0	HS1BP3|HS1BP3|HS1BP3	20687186|20687186|20687186	0.000000|0.000000|0.000000	0.05858|0.05858|0.05858	0.000000|0.000000|0.000000	0.03702|0.03702|0.03702	0.039000|0.039000|0.039000	0.13416|0.13416|0.13416	-0.176000|-0.176000|-0.176000	0.09811|0.09811|0.09811	-0.155000|-0.155000|-0.155000	0.11098|0.11098|0.11098	0.561000|0.561000|0.561000	0.74099|0.74099|0.74099	GAG|GGG|AGG	.	.		0.642	HS1BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242863.1	NM_022460		A	20823705	C	A	20823705	3	1	263	1	0	0	0	0	1	0	0	0	7370	681	24	3	315	3	HS1BP3	2	20823705	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	17094449	20823705	222375668	47	38421										
ALK	238	hgsc.bcm.edu	37	chr2	29451807	29451807	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ccctccaccccctccgaaacCccctcttgtctcccaccccc	2	27	2	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr2:29451807C>A	ENST00000389048.3	-	16	3664	c.2758G>T	c.(2758-2760)Ggt>Tgt	p.G920C	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	920	Gly-rich.				activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	CCTCCGAAACCCCCTCTTGTC	0.587			"T, Mis, A"	"NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"	"ALCL, NSCLC, Neuroblastoma"	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																												p.G920C		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"L, E, M"	.	ALK	533	.	0			c.G2758T						.						34	35	35					2																	29451807		2203	4300	6503	SO:0001583	missense	238	exon16	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	CGAAACCCCCTCT	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"CD molecules"	427	protein-coding gene	gene with protein product		105590	"anaplastic lymphoma kinase (Ki-1)"			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.2758G>T	chr2.hg19:g.29451807C>A	ENSP00000373700:p.Gly920Cys	331.0	1.0		385.0	164.0	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Missense_Mutation	SNP	ENST00000389048.3	hg19	CCDS33172.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.691038	0.88735	.	.	ENSG00000171094	ENST00000389048	T	0.72835	-0.69	5.22	5.22	0.72569	.	0.000000	0.49305	D	0.000158	D	0.87904	0.6295	M	0.91920	3.255	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90362	0.4374	9	.	.	.	.	18.7875	0.91961	0.0:1.0:0.0:0.0	.	920	Q9UM73	ALK_HUMAN	C	920	ENSP00000373700:G920C	.	G	-	1	0	ALK	29305311	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.263000	0.78421	2.420000	0.82092	0.561000	0.74099	GGT	.	.		0.587	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		A	29451807	C	A	29451807	3	1	263	1	0	0	0	0	1	0	0	0	525	623	22	3	2160	3	ALK	2	29451807	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	8628102	29451807	213747566	48	38422										
CEP68	23177	hgsc.bcm.edu	37	chr2	65296913	65296913	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	caccatggggtctggagaccTtctgctctccggggaaagcc	13	13	3	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr2:65296913T>C	ENST00000377990.2	+	2	538	c.335T>C	c.(334-336)cTt>cCt	p.L112P	CEP68_ENST00000546106.1_Missense_Mutation_p.L112P|CEP68_ENST00000260569.4_Missense_Mutation_p.L112P|RAB1A_ENST00000494188.1_5'Flank|CEP68_ENST00000537589.1_Intron	NM_015147.2	NP_055962.2	Q76N32	CEP68_HUMAN	centrosomal protein 68kDa	112					centriole-centriole cohesion (GO:0010457)|centrosome organization (GO:0051297)|protein localization to organelle (GO:0033365)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|endometrium(6)|kidney(8)|large_intestine(5)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32						TCTGGAGACCTTCTGCTCTCC	0.572																																					p.L112P		Atlas-SNP	.											.	CEP68	69	.	0			c.T335C						.						61	66	64					2																	65296913		2203	4300	6503	SO:0001583	missense	23177	exon2			GAGACCTTCTGCT	BC004873	CCDS1880.2	2p14	2014-02-20	2005-12-01	2005-12-01	ENSG00000011523	ENSG00000011523			29076	protein-coding gene	gene with protein product			"KIAA0582"	KIAA0582		9628581, 9847074, 14654843	Standard	NM_015147		Approved		uc002sdl.4	Q76N32	OTTHUMG00000129538	ENST00000377990.2:c.335T>C	chr2.hg19:g.65296913T>C	ENSP00000367229:p.Leu112Pro	54.0	0.0		57.0	4.0	NM_015147	B4DRQ1|D6W5F1|D6W5F2|O60326|Q9BQ18|Q9UDM9	Missense_Mutation	SNP	ENST00000377990.2	hg19	CCDS1880.2	.	.	.	.	.	.	.	.	.	.	T	9.975	1.226460	0.22542	.	.	ENSG00000011523	ENST00000377990;ENST00000546106;ENST00000260569;ENST00000545501	T;T;T	0.36340	1.26;1.26;1.26	4.04	0.163	0.14986	.	1.507680	0.03866	N	0.274817	T	0.28499	0.0705	L	0.34521	1.04	0.09310	N	1	B;B;B;B;B	0.27013	0.02;0.02;0.087;0.166;0.02	B;B;B;B;B	0.27796	0.022;0.014;0.063;0.083;0.022	T	0.24190	-1.0167	10	0.38643	T	0.18	0.0386	6.3232	0.21229	0.0:0.3242:0.0:0.6758	.	100;112;112;112;112	F5H3N9;F5H2Y2;Q76N32;Q76N32-2;Q05C09	.;.;CEP68_HUMAN;.;.	P	112;112;112;100	ENSP00000367229:L112P;ENSP00000438306:L112P;ENSP00000260569:L112P	ENSP00000260569:L112P	L	+	2	0	CEP68	65150417	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.494000	0.22467	0.034000	0.15491	0.533000	0.62120	CTT	.	.		0.572	CEP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251727.2	NM_015147		C	65296913	T	C	65296913	3	2	263	1	0	0	0	0	1	0	0	0	3260	1609	56	2	337	2	CEP68	2	65296913	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	35845106	65296913	177902460	49	38423										
REV1	51455	hgsc.bcm.edu	37	chr2	100029414	100029414	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ttccattgaatgtccaactcCtaggaaagggaatatagtta	8	7	0	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr2:100029414C>T	ENST00000258428.3	-	13	2180		c.e13-1		REV1_ENST00000393445.3_Splice_Site|REV1_ENST00000465835.1_Splice_Site	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)						DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|error-prone translesion synthesis (GO:0042276)|response to UV (GO:0009411)	nucleoplasm (GO:0005654)	damaged DNA binding (GO:0003684)|deoxycytidyl transferase activity (GO:0017125)|DNA-directed DNA polymerase activity (GO:0003887)|magnesium ion binding (GO:0000287)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(12)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TGTCCAACTCCTAGGAAAGGG	0.333								Direct reversal of damage																													.		Atlas-SNP	.											.	REV1	100	.	0			c.1952-1G>A						.						56	56	56					2																	100029414		2203	4300	6503	SO:0001630	splice_region_variant	51455	exon14			CAACTCCTAGGAA	AF206019	CCDS2045.1, CCDS42722.1	2q11.1-q11.2	2012-05-18	2012-05-18	2006-11-07	ENSG00000135945	ENSG00000135945		"DNA polymerases"	14060	protein-coding gene	gene with protein product		606134	"REV1 (yeast homolog)- like", "REV1-like (yeast)", "REV1 homolog (S. cerevisiae)"	REV1L		10536157	Standard	XM_005263968		Approved		uc002tad.3	Q9UBZ9	OTTHUMG00000130636	ENST00000258428.3:c.1952-1G>A	chr2.hg19:g.100029414C>T		120.0	0.0		117.0	46.0	NM_016316	O95941|Q53SI7|Q9C0J4|Q9NUP2	Splice_Site	SNP	ENST00000258428.3	hg19	CCDS2045.1	.	.	.	.	.	.	.	.	.	.	C	9.216	1.032067	0.19590	.	.	ENSG00000135945	ENST00000393445;ENST00000258428	.	.	.	5.21	4.33	0.51752	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.806	0.63233	0.0:0.9256:0.0:0.0744	.	.	.	.	.	-1	.	.	.	-	.	.	REV1	99395846	1.000000	0.71417	0.979000	0.43373	0.171000	0.22731	7.107000	0.77047	1.317000	0.45149	0.563000	0.77884	.	.	.		0.333	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253123.2	NM_016316	Intron	T	100029414	C	T	100029414	5	4	263	1	0	0	0	0	0	0	1	0	13254	695	24	3	1848	3	REV1	2	100029414	Splice_Site	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	34732501	100029414	143169959	50	38424										
ARHGEF4	50649	hgsc.bcm.edu	37	chr2	131801915	131801915	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gtactacaagggccggctggAcatggacggcctggaggtgg	18	9	0	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr2:131801915A>G	ENST00000326016.5	+	12	2162	c.1643A>G	c.(1642-1644)gAc>gGc	p.D548G	ARHGEF4_ENST00000355771.3_Missense_Mutation_p.D477G|ARHGEF4_ENST00000428230.2_Intron|ARHGEF4_ENST00000409303.1_Missense_Mutation_p.D488G|ARHGEF4_ENST00000525839.1_Missense_Mutation_p.D548G|ARHGEF4_ENST00000392953.3_Missense_Mutation_p.D548G	NM_015320.2	NP_056135.2	Q9NR80	ARHG4_HUMAN	Rho guanine nucleotide exchange factor (GEF) 4	548	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein domain specific binding (GO:0019904)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(4)	29		Prostate(154;0.055)		BRCA - Breast invasive adenocarcinoma(221;0.097)		GGCCGGCTGGACATGGACGGC	0.652																																					p.D548G		Atlas-SNP	.											.	ARHGEF4	89	.	0			c.A1643G						.						58	46	50					2																	131801915		2199	4300	6499	SO:0001583	missense	50649	exon12			GGCTGGACATGGA	AL137289	CCDS2165.1, CCDS42754.1	2q22	2013-01-10			ENSG00000136002	ENSG00000136002		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	684	protein-coding gene	gene with protein product	"APC-stimulated guanine nucleotide exchange factor"	605216				10873612	Standard	NM_015320		Approved	STM6, KIAA1112, ASEF	uc002tsa.1	Q9NR80	OTTHUMG00000131657	ENST00000326016.5:c.1643A>G	chr2.hg19:g.131801915A>G	ENSP00000316845:p.Asp548Gly	162.0	0.0		209.0	9.0	NM_032995	Q9HDC6|Q9UPP0	Missense_Mutation	SNP	ENST00000326016.5	hg19	CCDS2165.1	.	.	.	.	.	.	.	.	.	.	A	19.72	3.880876	0.72294	.	.	ENSG00000136002	ENST00000326016;ENST00000392953;ENST00000525839;ENST00000409303;ENST00000355771	T;T;T;T;T	0.76578	-1.03;-1.03;-1.03;-1.03;-1.03	5.2	2.77	0.32553	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.283692	0.37577	N	0.002021	D	0.83580	0.5285	M	0.83603	2.65	0.49051	D	0.99974	P;P;P	0.50943	0.94;0.854;0.94	P;P;P	0.60173	0.87;0.735;0.87	T	0.79087	-0.1947	10	0.36615	T	0.2	.	5.3104	0.15828	0.756:0.0:0.0871:0.1569	.	488;548;548	E9PEM0;Q9NR80-4;Q9NR80	.;.;ARHG4_HUMAN	G	548;548;548;488;477	ENSP00000316845:D548G;ENSP00000376680:D548G;ENSP00000432267:D548G;ENSP00000387285:D488G;ENSP00000348017:D477G	ENSP00000316845:D548G	D	+	2	0	ARHGEF4	131518385	1.000000	0.71417	0.997000	0.53966	0.867000	0.49689	3.424000	0.52764	0.295000	0.22570	0.459000	0.35465	GAC	.	.		0.652	ARHGEF4-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254554.4			G	131801915	A	G	131801915	3	3	263	1	0	0	0	0	1	0	0	0	908	275	10	2	1681	2	ARHGEF4	2	131801915	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	31772501	131801915	111397458	51	38425										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141819744	141819744	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ctagtgccagtgcagctggcTgctctgtctttgaatcaatt	10	10	3	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr2:141819744T>G	ENST00000389484.3	-	8	2083	c.1112A>C	c.(1111-1113)cAg>cCg	p.Q371P		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	371					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TGCAGCTGGCTGCTCTGTCTT	0.423										TSP Lung(27;0.18)																											p.Q371P	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.A1112C						.						174	153	160					2																	141819744		2203	4300	6503	SO:0001583	missense	53353	exon8			GCTGGCTGCTCTG	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.1112A>C	chr2.hg19:g.141819744T>G	ENSP00000374135:p.Gln371Pro	163.0	0.0		173.0	62.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	T	12.14	1.847611	0.32606	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.94184	-3.37	5.63	5.63	0.86233	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.153604	0.44688	D	0.000436	D	0.92535	0.7629	M	0.71036	2.16	0.34714	D	0.728065	P	0.51653	0.947	B	0.41374	0.355	D	0.96039	0.9023	10	0.62326	D	0.03	.	16.1307	0.81436	0.0:0.0:0.0:1.0	.	371	Q9NZR2	LRP1B_HUMAN	P	371;309	ENSP00000374135:Q371P	ENSP00000374135:Q371P	Q	-	2	0	LRP1B	141536214	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.529000	0.45632	2.263000	0.75096	0.533000	0.62120	CAG	.	.		0.423	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		G	141819744	T	G	141819744	3	3	263	1	0	0	0	0	1	0	0	0	8964	1580	55	5	13023	5	LRP1B	2	141819744	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	10017829	141819744	101379629	52	38426										
LY75	4065	hgsc.bcm.edu	37	chr2	160676430	160676430	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tcaaaccacataagagacttAtctagagaagaaacattttt	5	7	2	3	rs386652068		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr2:160676430A>G	ENST00000263636.4	-	29	3987	c.3960T>C	c.(3958-3960)aaT>aaC	p.N1320N	LY75-CD302_ENST00000505052.1_Splice_Site_p.N1320N|LY75-CD302_ENST00000504764.1_Splice_Site_p.N1320N|LY75_ENST00000554112.1_Splice_Site_p.N1320N|LY75_ENST00000553424.1_Splice_Site_p.N1320N	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	1320	C-type lectin 8. {ECO:0000255|PROSITE- ProRule:PRU00040}.				endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		TAAGAGACTTATCTAGAGAAG	0.318																																					p.N1320N		Atlas-SNP	.											.	LY75	151	.	0			c.T3960C						.						47	49	49					2																	160676430		2200	4300	6500	SO:0001630	splice_region_variant	4065	exon29			AGACTTATCTAGA	AF011333	CCDS2211.1	2q24	2011-08-30			ENSG00000054219	ENSG00000054219		"CD molecules", "C-type lectin domain containing"	6729	protein-coding gene	gene with protein product		604524				9553150	Standard	NM_002349		Approved	DEC-205, CLEC13B, CD205		O60449	OTTHUMG00000132025	ENST00000263636.4:c.3959-1T>C	chr2.hg19:g.160676430A>G		64.0	0.0		98.0	4.0	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Silent	SNP	ENST00000263636.4	hg19	CCDS2211.1																																																																																			.	.		0.318	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		Silent	G	160676430	A	G	160676430	5	3	263	1	0	0	0	0	0	0	1	0	9108	463	16	2	1236	2	LY75	2	160676430	Splice_Site	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	18856686	160676430	82522943	53	38427										
SCN3A	6328	hgsc.bcm.edu	37	chr2	166032778	166032779	+	Missense_Mutation	DNP	TA	TA	CT													0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tggtttgttctcatcatcatTatcttgttcctttttgggct					rs34236036|rs72471101	byFrequency	TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T|A	T|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr2:166032778_166032779TA>CT	ENST00000360093.3	-	3	617_618	c.126_127TA>AG	c.(124-129)gaTAat>gaAGat	p.42_43DN>ED	SCN3A_ENST00000283254.7_Missense_Mutation_p.42_43DN>ED|SCN3A_ENST00000409101.3_Missense_Mutation_p.42_43DN>ED	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	42			Missing. {ECO:0000269|PubMed:12610651}.		membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TCATCATCATTATCTTGTTCCT	0.431																																					p.N43D|p.D42E		Atlas-SNP	.											.	SCN3A	544	.	0			c.A127G|c.T126A						.																																			SO:0001583	missense	6328	exon3			CATCATTATCTTG|ATCATTATCTTGT	AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10590	protein-coding gene	gene with protein product		182391	"sodium channel, voltage-gated, type III, alpha polypeptide"			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.126_127delinsCT	chr2.hg19:g.166032778_166032779delinsCT	ENSP00000353206:p.D42_N43delinsED	119.0|121.0	0.0		170.0	22.0|9.0	NM_001081676	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Missense_Mutation	SNP	ENST00000360093.3	hg19																																																																																				.	.		0.431	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922		CT	166032779	TA	CT	166032778	3	2	263	1	0	0	0	0	1	0	0	0	13933	1754	61	2	6075	2	SCN3A	2	166032778	Missense_Mutation	DNP	TA	TCGA-FV-A2QR-01A-11D-A20W-10	5356348	166032778	77166595	54	38428										
PDE11A	50940	hgsc.bcm.edu	37	chr2	178545631	178545631	+	Splice_Site	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tcaaagaattcagttctcctCctgcaggaaaatcaaatgaa	6	9	4	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr2:178545631C>A	ENST00000286063.6	-	16	2663	c.2346G>T	c.(2344-2346)gaG>gaT	p.E782D	PDE11A_ENST00000449286.2_Splice_Site_p.E424D|PDE11A_ENST00000358450.4_Splice_Site_p.E532D|PDE11A_ENST00000409504.1_Splice_Site_p.E424D|PDE11A_ENST00000389683.3_Splice_Site_p.E338D	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	782	Catalytic. {ECO:0000250}.				blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|signal transduction (GO:0007165)	cytosol (GO:0005829)|perikaryon (GO:0043204)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)		Caffeine(DB00201)|Tadalafil(DB00820)	CAGTTCTCCTCCTGCAGGAAA	0.348									Primary Pigmented Nodular Adrenocortical Disease, Familial																												p.E782D		Atlas-SNP	.											PDE11A_ENST00000358450,NS,carcinoma,0,2	PDE11A	283	.	0			c.G2346T						.						86	83	84					2																	178545631		2201	4297	6498	SO:0001630	splice_region_variant	50940	exon16	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	TCTCCTCCTGCAG	AJ251509	CCDS33334.1, CCDS42785.1, CCDS42786.1, CCDS46459.1	2q31.3	2010-06-22			ENSG00000128655	ENSG00000128655	3.1.4.17	"Phosphodiesterases"	8773	protein-coding gene	gene with protein product		604961				10725373	Standard	NM_001077196		Approved		uc002ulq.3	Q9HCR9	OTTHUMG00000154188	ENST00000286063.6:c.2346-1G>T	chr2.hg19:g.178545631C>A		38.0	0.0		24.0	10.0	NM_016953	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	Missense_Mutation	SNP	ENST00000286063.6	hg19	CCDS33334.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.72|14.72	2.618248|2.618248	0.46736|0.46736	.|.	.|.	ENSG00000128655|ENSG00000128655	ENST00000286063;ENST00000358450;ENST00000409504;ENST00000389683;ENST00000449286|ENST00000433879	T;T;T;T;T|.	0.78246|.	-1.16;-1.16;-1.16;-1.16;-1.16|.	5.61|5.61	3.8|3.8	0.43715|0.43715	Metal-dependent phosphohydrolase, HD domain (1);5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);|.	0.143299|.	0.64402|.	D|.	0.000008|.	T|T	0.53948|0.53948	0.1828|0.1828	L|L	0.41492|0.41492	1.28|1.28	0.80722|0.80722	D|D	1|1	B;B|.	0.16166|.	0.004;0.016|.	B;B|.	0.16722|.	0.004;0.016|.	T|T	0.49753|0.49753	-0.8906|-0.8906	10|5	0.87932|.	D|.	0|.	.|.	9.3756|9.3756	0.38281|0.38281	0.0:0.7845:0.0:0.2155|0.0:0.7845:0.0:0.2155	.|.	532;782|.	Q9HCR9-2;Q9HCR9|.	.;PDE11_HUMAN|.	D|I	782;532;424;338;424|390	ENSP00000286063:E782D;ENSP00000351232:E532D;ENSP00000386539:E424D;ENSP00000374333:E338D;ENSP00000390599:E424D|.	ENSP00000286063:E782D|.	E|R	-|-	3|2	2|0	PDE11A|PDE11A	178253877|178253877	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.659000|1.659000	0.37387|0.37387	1.516000|1.516000	0.48900|0.48900	0.655000|0.655000	0.94253|0.94253	GAG|AGA	.	.		0.348	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2		Missense_Mutation	A	178545631	C	A	178545631	5	1	263	1	0	0	0	0	0	0	1	0	11640	869	30	3	475	3	PDE11A	2	178545631	Splice_Site	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	12512853	178545631	64653742	55	38429										
TTN	7273	hgsc.bcm.edu	37	chr2	179659759	179659759	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ttgctcctggacaccgtatcTcccttcccatctctcttctg	5	17	4	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr2:179659759T>C	ENST00000591111.1	-	7	1359	c.1135A>G	c.(1135-1137)Aga>Gga	p.R379G	TTN_ENST00000460472.2_Missense_Mutation_p.R379G|TTN_ENST00000359218.5_Missense_Mutation_p.R379G|TTN_ENST00000360870.5_Missense_Mutation_p.R379G|TTN_ENST00000342175.6_Missense_Mutation_p.R379G|TTN_ENST00000342992.6_Missense_Mutation_p.R379G|TTN_ENST00000589042.1_Missense_Mutation_p.R379G			Q8WZ42	TITIN_HUMAN	titin	0					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACACCGTATCTCCCTTCCCAT	0.582																																					p.R379G		Atlas-SNP	.											.	TTN	18412	.	0			c.A1135G						.						142	127	132					2																	179659759		2203	4300	6503	SO:0001583	missense	7273	exon7			CGTATCTCCCTTC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.1135A>G	chr2.hg19:g.179659759T>C	ENSP00000465570:p.Arg379Gly	31.0	0.0		57.0	4.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	13.33	2.204673	0.38905	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.67698	-0.28;-0.06;-0.07;-0.08;0.06	5.96	4.78	0.61160	.	.	.	.	.	T	0.61899	0.2384	L	0.47716	1.5	0.22975	N	0.998481	B;B;B;B;P	0.42296	0.1;0.1;0.1;0.1;0.775	B;B;B;B;B	0.39660	0.036;0.036;0.036;0.036;0.306	T	0.55995	-0.8052	9	0.87932	D	0	.	12.9235	0.58245	0.0:0.0:0.2543:0.7457	.	379;379;379;379;379	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	G	379	ENSP00000343764:R379G;ENSP00000434586:R379G;ENSP00000340554:R379G;ENSP00000352154:R379G;ENSP00000354117:R379G	ENSP00000340554:R379G	R	-	1	2	TTN	179368004	0.977000	0.34250	1.000000	0.80357	0.985000	0.73830	1.142000	0.31540	1.047000	0.40274	0.528000	0.53228	AGA	.	.		0.582	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179659759	T	C	179659759	3	2	263	1	0	0	0	0	1	0	0	0	16750	1559	54	2	110277	2	TTN	2	179659759	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	1114128	179659759	63539614	56	38430										
SSFA2	6744	hgsc.bcm.edu	37	chr2	182781149	182781149	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gaaactcactgcagaatcttTcacaggtatgagaaaaagta	8	7	3	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr2:182781149T>C	ENST00000431877.2	+	11	2961	c.2782T>C	c.(2782-2784)Tca>Cca	p.S928P	SSFA2_ENST00000409001.1_Missense_Mutation_p.S928P|SSFA2_ENST00000320370.7_Missense_Mutation_p.S928P|SSFA2_ENST00000428267.2_Missense_Mutation_p.S775P|SSFA2_ENST00000409136.1_Missense_Mutation_p.S437P	NM_001130445.1	NP_001123917.1	P28290	SSFA2_HUMAN	sperm specific antigen 2	928						cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.S928A(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(18)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	38			OV - Ovarian serous cystadenocarcinoma(117;0.0856)			GCAGAATCTTTCACAGGTATG	0.383																																					p.S928P		Atlas-SNP	.											SSFA2,NS,carcinoma,0,1	SSFA2	130	.	1	Substitution - Missense(1)	lung(1)	c.T2782C						.						62	62	62					2																	182781149		2203	4300	6503	SO:0001583	missense	6744	exon11			AATCTTTCACAGG	M61199	CCDS2284.1, CCDS46467.1, CCDS74611.1	2q32.1	2012-02-01			ENSG00000138434	ENSG00000138434			11319	protein-coding gene	gene with protein product	"cleavage signal-1 protein", "KRAS-induced actin-interacting protein", "sperm associated antigen 13"	118990				1555770	Standard	XM_005246812		Approved	CS-1, SPAG13, KRAP, KIAA1927	uc002uoh.3	P28290	OTTHUMG00000132584	ENST00000431877.2:c.2782T>C	chr2.hg19:g.182781149T>C	ENSP00000388731:p.Ser928Pro	65.0	0.0		70.0	3.0	NM_001130445	A8K6T0|Q68DA6|Q7Z7L2|Q8N1L3|Q8N263|Q8N7H2|Q8NEN5|Q96E36|Q96PW1	Missense_Mutation	SNP	ENST00000431877.2	hg19	CCDS46467.1	.	.	.	.	.	.	.	.	.	.	T	17.59	3.428048	0.62844	.	.	ENSG00000138434	ENST00000431877;ENST00000320370;ENST00000409001;ENST00000428267;ENST00000409136	T;T;T;T;T	0.36878	1.23;1.23;1.23;1.23;1.23	5.95	4.78	0.61160	.	0.376195	0.30159	N	0.010279	T	0.59824	0.2222	M	0.73598	2.24	0.45541	D	0.998499	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.87578	0.998;0.997;0.997;0.997;0.997	T	0.63314	-0.6665	10	0.72032	D	0.01	-6.451	13.3688	0.60701	0.0:0.0:0.1316:0.8684	.	775;437;928;928;928	E7END2;E7EUL7;E9PHV5;P28290;P28290-3	.;.;.;SSFA2_HUMAN;.	P	928;928;928;775;437	ENSP00000388731:S928P;ENSP00000314669:S928P;ENSP00000387319:S928P;ENSP00000409867:S775P;ENSP00000386916:S437P	ENSP00000314669:S928P	S	+	1	0	SSFA2	182489394	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	3.233000	0.51311	1.055000	0.40461	-0.316000	0.08728	TCA	.	.		0.383	SSFA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255793.2	NM_006751		C	182781149	T	C	182781149	3	2	263	1	0	0	0	0	1	0	0	0	15198	1783	62	2	2824	2	SSFA2	2	182781149	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	3121390	182781149	60418224	57	38431										
COL5A2	1290	hgsc.bcm.edu	37	chr2	189922082	189922082	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ccaggagttcctgcaattccTctttctcccggcataccttg	7	15	2	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr2:189922082T>C	ENST00000374866.3	-	34	2575	c.2301A>G	c.(2299-2301)agA>agG	p.R767R		NM_000393.3	NP_000384.2	P05997	CO5A2_HUMAN	collagen, type V, alpha 2	767					axon guidance (GO:0007411)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|negative regulation of endodermal cell differentiation (GO:1903225)|skeletal system development (GO:0001501)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(53)|ovary(3)|prostate(2)|skin(6)|urinary_tract(3)	95			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			CTGCAATTCCTCTTTCTCCCG	0.438																																					p.R767R		Atlas-SNP	.											.	COL5A2	230	.	0			c.A2301G						.						70	69	69					2																	189922082		2203	4300	6503	SO:0001819	synonymous_variant	1290	exon34			AATTCCTCTTTCT	Y14690	CCDS33350.1	2q14-q32	2014-09-17			ENSG00000204262	ENSG00000204262		"Collagens"	2210	protein-coding gene	gene with protein product	"AB collagen"	120190				1572660	Standard	NM_000393		Approved		uc002uqk.3	P05997	OTTHUMG00000149842	ENST00000374866.3:c.2301A>G	chr2.hg19:g.189922082T>C		86.0	0.0		90.0	5.0	NM_000393	P78440|Q13908|Q53WR4|Q59GR4|Q6LDJ5|Q7KZ55|Q86XF6|Q96QB0|Q96QB3	Silent	SNP	ENST00000374866.3	hg19	CCDS33350.1																																																																																			.	.		0.438	COL5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313523.1	NM_000393		C	189922082	T	C	189922082	2	2	263	1	0	0	0	0	0	0	0	1	3699	1548	54	2		2	COL5A2	2	189922082	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	7140933	189922082	53277291	58	38432										
FN1	2335	hgsc.bcm.edu	37	chr2	216239959	216239959	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gtaatagtagcctctgtgacAccagggcggggccgagggac	16	10	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr2:216239959A>G	ENST00000359671.1	-	37	6127	c.5862T>C	c.(5860-5862)ggT>ggC	p.G1954G	FN1_ENST00000421182.1_Silent_p.G1864G|FN1_ENST00000323926.6_Silent_p.G2045G|FN1_ENST00000345488.5_Silent_p.G1954G|FN1_ENST00000357867.4_Silent_p.G1864G|FN1_ENST00000446046.1_Silent_p.G1954G|FN1_ENST00000443816.1_Silent_p.G1864G|FN1_ENST00000356005.4_Silent_p.G1864G|FN1_ENST00000336916.4_Silent_p.G1954G|FN1_ENST00000354785.4_Silent_p.G2045G|FN1_ENST00000432072.2_Silent_p.G1955G|FN1_ENST00000346544.3_Silent_p.G1954G|FN1_ENST00000357009.2_Silent_p.G1954G			P02751	FINC_HUMAN	fibronectin 1	1954	Binds to FBLN1.|Fibronectin type-III 15. {ECO:0000255|PROSITE-ProRule:PRU00316}.|Heparin-binding 2.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	CCTCTGTGACACCAGGGCGGG	0.532																																					p.G2045G		Atlas-SNP	.											.	FN1	521	.	0			c.T6135C						.						82	87	85					2																	216239959		2203	4300	6503	SO:0001819	synonymous_variant	2335	exon38			TGTGACACCAGGG		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"Fibronectin type III domain containing", "Endogenous ligands"	3778	protein-coding gene	gene with protein product	"migration-stimulating factor", "cold-insoluble globulin"	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.5862T>C	chr2.hg19:g.216239959A>G		110.0	0.0		116.0	5.0	NM_212482	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Silent	SNP	ENST00000359671.1	hg19																																																																																				.	.		0.532	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		G	216239959	A	G	216239959	2	3	263	1	0	0	0	0	0	0	0	1	5970	146	6	2		2	FN1	2	216239959	Silent	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	26317877	216239959	26959414	59	38433										
CCDC108	255101	hgsc.bcm.edu	37	chr2	219892384	219892384	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gcacacaccttatagatggcGaaggcttcgagctccaccgt	10	13	0	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr2:219892384G>A	ENST00000341552.5	-	13	2282	c.2199C>T	c.(2197-2199)ttC>ttT	p.F733F	CCDC108_ENST00000410037.1_Silent_p.F668F|CCDC108_ENST00000453220.1_Silent_p.F733F|CCDC108_ENST00000441968.1_Silent_p.F733F|CCDC108_ENST00000409865.3_Silent_p.F722F	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108	733						integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(1)|lung(34)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TATAGATGGCGAAGGCTTCGA	0.617																																					p.F733F		Atlas-SNP	.											.	CCDC108	208	.	0			c.C2199T						.						82	84	84					2																	219892384		2203	4300	6503	SO:0001819	synonymous_variant	255101	exon13			GATGGCGAAGGCT	NM_194302, AL833882, AK127189	CCDS2430.2, CCDS2431.2, CCDS63125.1, CCDS63126.1	2q35	2008-02-05			ENSG00000181378	ENSG00000181378			25325	protein-coding gene	gene with protein product		614270				12477932	Standard	NM_194302		Approved	DKFZp434O0527, MGC35338	uc002vjl.2	Q6ZU64	OTTHUMG00000133013	ENST00000341552.5:c.2199C>T	chr2.hg19:g.219892384G>A		185.0	0.0		255.0	84.0	NM_194302	A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Silent	SNP	ENST00000341552.5	hg19	CCDS2430.2																																																																																			.	.		0.617	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4	NM_194302		A	219892384	G	A	219892384	2	1	263	1	0	0	0	0	0	0	0	1	2745	1049	37	1		1	CCDC108	2	219892384	Silent	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	3652425	219892384	23306989	60	38434										
COL6A3	1293	hgsc.bcm.edu	37	chr2	238244875	238244875	+	Silent	SNP	A	A	G													0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	actggttttgcagcagcagcAgcggggggtcttacagctgc					rs398102314		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr2:238244875A>G	ENST00000295550.4	-	40	9320	c.8868T>C	c.(8866-8868)gcT>gcC	p.A2956A	COL6A3_ENST00000347401.3_Silent_p.A2755A|COL6A3_ENST00000353578.4_Silent_p.A2750A|COL6A3_ENST00000472056.1_Silent_p.A2349A|COL6A3_ENST00000409809.1_Silent_p.A2750A|COL6A3_ENST00000346358.4_Silent_p.A2756A	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2956	Ala-rich.|Nonhelical region.			Missing (in Ref. 1; CAA36267). {ECO:0000305}.	axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		CAGCAGCAGCAGCGGGGGGTC	0.617																																					p.A2956A		Atlas-SNP	.											.,7	COL6A3	608	.	0			c.T8868C						.						37	41	40					2																	238244875		2199	4298	6497	SO:0001819	synonymous_variant	1293	exon40			AGCAGCAGCGGGG	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.8868T>C	chr2.hg19:g.238244875A>G		39.0	1.0		47.0	5.0	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	hg19	CCDS33412.1																																																																																			.	.		0.617	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		G	238244875	A	G	238244875	2	3	263	1	0	0	0	0	0	0	0	1	3703	175	7	2		2	COL6A3	2	238244875	Silent	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	18352491	238244875	4954498	61	38435	188	2								
COL6A3	1293	hgsc.bcm.edu	37	chr2	238244877	238244877	+	Missense_Mutation	SNP	C	C	G													0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tggttttgcagcagcagcagCggggggtcttacagctgctg							TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr2:238244877C>G	ENST00000295550.4	-	40	9318	c.8866G>C	c.(8866-8868)Gct>Cct	p.A2956P	COL6A3_ENST00000347401.3_Missense_Mutation_p.A2755P|COL6A3_ENST00000353578.4_Missense_Mutation_p.A2750P|COL6A3_ENST00000472056.1_Missense_Mutation_p.A2349P|COL6A3_ENST00000409809.1_Missense_Mutation_p.A2750P|COL6A3_ENST00000346358.4_Missense_Mutation_p.A2756P	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2956	Ala-rich.|Nonhelical region.			Missing (in Ref. 1; CAA36267). {ECO:0000305}.	axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		GCAGCAGCAGCGGGGGGTCTT	0.622																																					p.A2956P		Atlas-SNP	.											.	COL6A3	608	.	0			c.G8866C						.						37	41	40					2																	238244877		2199	4299	6498	SO:0001583	missense	1293	exon40			CAGCAGCGGGGGG	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.8866G>C	chr2.hg19:g.238244877C>G	ENSP00000295550:p.Ala2956Pro	40.0	0.0		46.0	4.0	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	hg19	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	3.672	-0.067344	0.07273	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	D;D;D;D;D;D	0.90844	-2.74;-2.71;-2.7;-2.69;-2.7;-2.68	0.158	0.158	0.14942	.	2.351570	0.03169	U	0.170515	D	0.90899	0.7140	L	0.36672	1.1	0.09310	N	1	D;D;D	0.56968	0.962;0.978;0.962	P;P;P	0.61800	0.787;0.894;0.787	T	0.79799	-0.1651	9	0.25751	T	0.34	.	.	.	.	.	2349;2750;2956	E9PFQ6;P12111-2;P12111	.;.;CO6A3_HUMAN	P	2956;2755;2750;2349;2750;2756	ENSP00000295550:A2956P;ENSP00000315609:A2755P;ENSP00000315873:A2750P;ENSP00000418285:A2349P;ENSP00000386844:A2750P;ENSP00000295546:A2756P	ENSP00000295550:A2956P	A	-	1	0	COL6A3	237909616	0.002000	0.14202	0.017000	0.16124	0.231000	0.25187	0.465000	0.22004	0.202000	0.20498	0.205000	0.17691	GCT	.	.		0.622	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		G	238244877	C	G	238244877	3	3	263	1	0	0	0	0	1	0	0	0	3703	768	27	4	687	4	COL6A3	2	238244877	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	2	238244877	4954496	62	38436	188	2								
PER2	8864	hgsc.bcm.edu	37	chr2	239165617	239165617	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gacgatggtgctgctgtagcTgcactggctggtgagcgacg	17	9	0	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr2:239165617T>C	ENST00000254657.3	-	17	2290	c.2011A>G	c.(2011-2013)Agc>Ggc	p.S671G	PER2_ENST00000254658.3_3'UTR|AC096574.4_ENST00000456601.1_RNA	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN	period circadian clock 2	671	CSNK1E binding domain. {ECO:0000250}.				circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|fatty acid metabolic process (GO:0006631)|gluconeogenesis (GO:0006094)|glycogen biosynthetic process (GO:0005978)|histone H3 deacetylation (GO:0070932)|lactate biosynthetic process (GO:0019249)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of DNA-templated transcription, termination (GO:0060567)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of glutamate uptake involved in transmission of nerve impulse (GO:0051946)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of vasoconstriction (GO:0019229)|response to ischemia (GO:0002931)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	pre-mRNA binding (GO:0036002)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|ubiquitin binding (GO:0043130)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)		CTGCTGTAGCTGCACTGGCTG	0.592											OREG0015336	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S671G		Atlas-SNP	.											.	PER2	85	.	0			c.A2011G						.						90	91	90					2																	239165617		2203	4300	6503	SO:0001583	missense	8864	exon17			TGTAGCTGCACTG	AB002345	CCDS2528.1	2q37.3	2012-12-13	2012-12-13		ENSG00000132326	ENSG00000132326			8846	protein-coding gene	gene with protein product		603426	"period (Drosophila) homolog 2", "period homolog 2 (Drosophila)"			9427249, 17218255	Standard	NM_022817		Approved	KIAA0347	uc002vyc.3	O15055	OTTHUMG00000152884	ENST00000254657.3:c.2011A>G	chr2.hg19:g.239165617T>C	ENSP00000254657:p.Ser671Gly	78.0	0.0	2409	113.0	6.0	NM_022817	A2I2P7|Q4ZG49|Q6DT41|Q9UQ45	Missense_Mutation	SNP	ENST00000254657.3	hg19	CCDS2528.1	.	.	.	.	.	.	.	.	.	.	T	28.6	4.932103	0.92389	.	.	ENSG00000132326	ENST00000254657	T	0.24908	1.83	4.75	4.75	0.60458	.	0.082585	0.85682	D	0.000000	T	0.52869	0.1761	M	0.83852	2.665	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.994;0.998	T	0.59573	-0.7429	10	0.72032	D	0.01	-29.9714	12.5438	0.56186	0.0:0.0:0.0:1.0	.	671;671	B4DH14;O15055	.;PER2_HUMAN	G	671	ENSP00000254657:S671G	ENSP00000254657:S671G	S	-	1	0	PER2	238830356	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.404000	0.79996	1.907000	0.55213	0.533000	0.62120	AGC	.	.		0.592	PER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257167.1	NM_022817		C	239165617	T	C	239165617	3	2	263	1	0	0	0	0	1	0	0	0	11739	1580	55	2	1784	2	PER2	2	239165617	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	920740	239165617	4033756	63	38437										
TMEM43	79188	hgsc.bcm.edu	37	chr3	14180787	14180787	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	aaccttatgacacggatcctCtacaccttgggtaggtgttg	10	10	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr3:14180787C>T	ENST00000306077.4	+	11	1244	c.990C>T	c.(988-990)ctC>ctT	p.L330L	RP11-434D12.1_ENST00000601399.1_3'UTR|RP11-434D12.1_ENST00000608606.1_Silent_p.L76L	NM_024334.2	NP_077310.1	Q9BTV4	TMM43_HUMAN	transmembrane protein 43	330					nuclear membrane organization (GO:0071763)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|cervix(3)|endometrium(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(2)	19						CACGGATCCTCTACACCTTGG	0.582																																					p.L330L		Atlas-SNP	.											.	TMEM43	33	.	0			c.C990T						.						125	109	114					3																	14180787		2203	4300	6503	SO:0001819	synonymous_variant	79188	exon11			GATCCTCTACACC	BC008054	CCDS2618.1	3p25.1	2014-09-17			ENSG00000170876	ENSG00000170876			28472	protein-coding gene	gene with protein product		612048	"arrhythmogenic right ventricular dysplasia 5"	ARVD5		11230166, 18313022	Standard	NM_024334		Approved	MGC3222, DKFZp586G1919, LUMA	uc003byk.2	Q9BTV4	OTTHUMG00000129802	ENST00000306077.4:c.990C>T	chr3.hg19:g.14180787C>T		109.0	0.0		174.0	72.0	NM_024334	Q7L4N5|Q8NC30|Q96A63|Q96F19|Q96JX0|Q9H076	Silent	SNP	ENST00000306077.4	hg19	CCDS2618.1																																																																																			.	.		0.582	TMEM43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252030.2	NM_024334		T	14180787	C	T	14180787	2	4	263	1	0	0	0	0	0	0	0	1	16182	900	32	3		3	TMEM43	3	14180787	Silent	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10		14180787	183841643	64	38438										
GOLGA4	2803	hgsc.bcm.edu	37	chr3	37367411	37367411	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gtcttgtataacacagttgaAgaaagagttatctgaaaaca	8	5	2	4			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr3:37367411A>G	ENST00000361924.2	+	14	4408	c.4034A>G	c.(4033-4035)aAg>aGg	p.K1345R	GOLGA4_ENST00000444882.1_Intron|GOLGA4_ENST00000356847.4_Missense_Mutation_p.K1367R	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	1345	Glu-rich.				Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						ACACAGTTGAAGAAAGAGTTA	0.353																																					p.K1367R		Atlas-SNP	.											.	GOLGA4	173	.	0			c.A4100G						.						36	35	36					3																	37367411		2203	4299	6502	SO:0001583	missense	2803	exon15			AGTTGAAGAAAGA	U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"golgin 245"	602509	"golgi autoantigen, golgin subfamily a, 4"			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.4034A>G	chr3.hg19:g.37367411A>G	ENSP00000354486:p.Lys1345Arg	54.0	0.0		76.0	4.0	NM_001172713	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Missense_Mutation	SNP	ENST00000361924.2	hg19	CCDS2666.1	.	.	.	.	.	.	.	.	.	.	A	10.56	1.385287	0.25031	.	.	ENSG00000144674	ENST00000361924;ENST00000356847;ENST00000437131	T;T;T	0.26067	1.76;1.76;1.76	5.53	3.12	0.35913	.	0.000000	0.38217	N	0.001765	T	0.20047	0.0482	L	0.52266	1.64	0.23920	N	0.996462	B;B;B;B	0.17465	0.01;0.01;0.01;0.022	B;B;B;B	0.14578	0.009;0.006;0.006;0.011	T	0.21759	-1.0236	10	0.16420	T	0.52	.	8.6536	0.34049	0.7766:0.0:0.2234:0.0	.	1345;1345;1367;1345	Q13439-3;Q13439-4;F8W8Q7;Q13439	.;.;.;GOGA4_HUMAN	R	1345;1367;1216	ENSP00000354486:K1345R;ENSP00000349305:K1367R;ENSP00000405842:K1216R	ENSP00000349305:K1367R	K	+	2	0	GOLGA4	37342415	1.000000	0.71417	0.999000	0.59377	0.987000	0.75469	1.195000	0.32186	0.899000	0.36444	0.460000	0.39030	AAG	.	.		0.353	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078		G	37367411	A	G	37367411	3	3	263	1	0	0	0	0	1	0	0	0	6563	72	3	2	4158	2	GOLGA4	3	37367411	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	23186624	37367411	160655019	65	38439										
DHX30	22907	hgsc.bcm.edu	37	chr3	47882442	47882442	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tgctagctgatcgctttggcTcccctgccgacagctggtgg	13	13	0	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr3:47882442T>C	ENST00000445061.1	+	7	849	c.442T>C	c.(442-444)Tcc>Ccc	p.S148P	DHX30_ENST00000348968.4_Missense_Mutation_p.S120P|DHX30_ENST00000457607.1_Missense_Mutation_p.S176P|DHX30_ENST00000446256.2_Missense_Mutation_p.S109P	NM_138615.2	NP_619520.1	Q7L2E3	DHX30_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 30	148						cytoplasm (GO:0005737)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(1)|large_intestine(11)|lung(13)|ovary(4)|pancreas(1)|prostate(1)|skin(3)	37				BRCA - Breast invasive adenocarcinoma(193;0.000696)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)		TCGCTTTGGCTCCCCTGCCGA	0.602																																					p.S148P		Atlas-SNP	.											.	DHX30	101	.	0			c.T442C						.						53	48	50					3																	47882442		2203	4300	6503	SO:0001583	missense	22907	exon7			TTTGGCTCCCCTG	AB020697	CCDS2759.1	3p24.3-p22.1	2013-07-16	2013-07-16	2003-06-13	ENSG00000132153	ENSG00000132153		"DEAH-boxes"	16716	protein-coding gene	gene with protein product			"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 30", "DEAH (Asp-Glu-Ala-His) box polypeptide 30"	DDX30		10048485, 18022663	Standard	NM_138615		Approved	KIAA0890, FLJ11214	uc003cru.3	Q7L2E3	OTTHUMG00000133522	ENST00000445061.1:c.442T>C	chr3.hg19:g.47882442T>C	ENSP00000405620:p.Ser148Pro	112.0	0.0		161.0	8.0	NM_138615	A8K5F1|O94965|Q7Z753|Q96CH4|Q9NUQ0	Missense_Mutation	SNP	ENST00000445061.1	hg19	CCDS2759.1	.	.	.	.	.	.	.	.	.	.	T	16.03	3.007590	0.54361	.	.	ENSG00000132153	ENST00000446256;ENST00000445061;ENST00000348968;ENST00000457607	T;T;T;T	0.03635	3.9;3.87;3.89;3.86	4.89	4.89	0.63831	.	0.410909	0.25222	N	0.032224	T	0.04497	0.0123	L	0.36672	1.1	0.44227	D	0.997066	B;B;B	0.28933	0.228;0.148;0.148	B;B;B	0.30316	0.106;0.114;0.114	T	0.46952	-0.9154	10	0.44086	T	0.13	.	12.2716	0.54710	0.0:0.0:0.0:1.0	.	148;109;176	Q7L2E3;Q7L2E3-3;Q7L2E3-2	DHX30_HUMAN;.;.	P	109;148;120;176	ENSP00000392601:S109P;ENSP00000405620:S148P;ENSP00000343442:S120P;ENSP00000394682:S176P	ENSP00000343442:S120P	S	+	1	0	DHX30	47857446	1.000000	0.71417	0.997000	0.53966	0.911000	0.54048	4.753000	0.62183	1.821000	0.53095	0.533000	0.62120	TCC	.	.		0.602	DHX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257495.2	NM_138615		C	47882442	T	C	47882442	3	2	263	1	0	0	0	0	1	0	0	0	4506	1551	54	2	471	2	DHX30	3	47882442	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	10515031	47882442	150139988	66	38440										
CELSR3	1951	hgsc.bcm.edu	37	chr3	48697030	48697030	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ggacaattccagaggtgggcTcaatggtaaaatctccatcc	10	10	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr3:48697030T>C	ENST00000164024.4	-	1	3318	c.3038A>G	c.(3037-3039)gAg>gGg	p.E1013G	CELSR3_ENST00000544264.1_Missense_Mutation_p.E1013G	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	1013	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		AGAGGTGGGCTCAATGGTAAA	0.552																																					p.E1013G		Atlas-SNP	.											.	CELSR3	237	.	0			c.A3038G						.						75	72	73					3																	48697030		2203	4300	6503	SO:0001583	missense	1951	exon1			GTGGGCTCAATGG	AF231023	CCDS2775.1	3p21.31	2014-08-08	2013-02-18		ENSG00000008300	ENSG00000008300		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3230	protein-coding gene	gene with protein product	"flamingo homolog 1 (Drosophila)"	604264	"cadherin EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog"	EGFL1		9693030	Standard	NM_001407		Approved	MEGF2, HFMI1, FMI1, CDHF11	uc003cuf.1	Q9NYQ7	OTTHUMG00000133544	ENST00000164024.4:c.3038A>G	chr3.hg19:g.48697030T>C	ENSP00000164024:p.Glu1013Gly	68.0	0.0		86.0	4.0	NM_001407	O75092	Missense_Mutation	SNP	ENST00000164024.4	hg19	CCDS2775.1	.	.	.	.	.	.	.	.	.	.	T	17.14	3.314376	0.60414	.	.	ENSG00000008300	ENST00000164024;ENST00000544264	T;T	0.61040	0.14;0.14	5.78	5.78	0.91487	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.66944	0.2841	L	0.28694	0.88	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.986	T	0.70454	-0.4867	9	0.72032	D	0.01	.	16.0993	0.81158	0.0:0.0:0.0:1.0	.	1013;1083	Q9NYQ7;Q5Y190	CELR3_HUMAN;.	G	1013	ENSP00000164024:E1013G;ENSP00000445694:E1013G	ENSP00000164024:E1013G	E	-	2	0	CELSR3	48672034	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.186000	0.72026	2.207000	0.71202	0.459000	0.35465	GAG	.	.		0.552	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407		C	48697030	T	C	48697030	3	2	263	1	0	0	0	0	1	0	0	0	3225	1551	54	2	7040	2	CELSR3	3	48697030	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	814588	48697030	149325400	67	38441										
RBM6	10180	hgsc.bcm.edu	37	chr3	50103698	50103698	+	Frame_Shift_Del	DEL	C	C	-													0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	aaagtggtaaacccactgatCggcctcttgggtgaatatgg					rs150609021		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr3:50103698delC	ENST00000266022.4	+	17	2965	c.2706delC	c.(2704-2706)atcfs	p.I902fs	RBM6_ENST00000539992.1_Frame_Shift_Del_p.I244fs|RBM6_ENST00000422955.1_Frame_Shift_Del_p.I380fs|RBM6_ENST00000443081.1_Frame_Shift_Del_p.I770fs|RBM6_ENST00000441115.1_3'UTR|RBM6_ENST00000442092.1_Frame_Shift_Del_p.I380fs|RBM6_ENST00000421682.1_5'Flank	NM_005777.2	NP_005768.1	P78332	RBM6_HUMAN	RNA binding motif protein 6	902					RNA processing (GO:0006396)	nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(3)|prostate(1)|skin(4)|urinary_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)		ACCCACTGATCGGCCTCTTGG	0.498																																					p.I902fs		Atlas-Indel,Pindel	.											.	RBM6	85	.	0			c.2705delT						.						38	42	41					3																	50103698		2203	4300	6503	SO:0001589	frameshift_variant	10180	exon17			.	AF069517	CCDS2809.1, CCDS54586.1	3p21.3	2013-01-28			ENSG00000004534	ENSG00000004534		"RNA binding motif (RRM) containing", "G patch domain containing"	9903	protein-coding gene	gene with protein product		606886				10352938	Standard	NM_001167582		Approved	DEF-3, 3G2, NY-LU-12, g16, DEF3	uc003cyc.3	P78332	OTTHUMG00000156736	ENST00000266022.4:c.2706delC	chr3.hg19:g.50103698delC	ENSP00000266022:p.Ile902fs	44.0	0.0		52.0	16.0	NM_005777	O60549|O75524|Q86SS3	Frame_Shift_Del	DEL	ENST00000266022.4	hg19	CCDS2809.1																																																																																			.	.		0.498	RBM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345528.4	NM_005777		-	50103698	C	-	50103698	7	5	263	1	0	1	0	1	0	0	0	0	13159	874	31	0	2768	0	RBM6	3	50103698	Frame_Shift_Del	DEL	C	TCGA-FV-A2QR-01A-11D-A20W-10	1406668	50103698	147918732	68	38442										
CCDC66	285331	hgsc.bcm.edu	37	chr3	56650051	56650051	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	atacatatatgaattctacgActtctaagaaggatactggt	7	6	2	2	rs77152637|rs74463118	byFrequency	TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr3:56650051A>T	ENST00000394672.3	+	13	1883	c.1813A>T	c.(1813-1815)Act>Tct	p.T605S	CCDC66_ENST00000436465.2_Missense_Mutation_p.T605S|CCDC66_ENST00000326595.7_Missense_Mutation_p.T571S	NM_001012506.4|NM_001141947.1	NP_001012524.4|NP_001135419.1	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66	605				T -> TS (in Ref. 3; AAI32828). {ECO:0000305}.	post-embryonic retina morphogenesis in camera-type eye (GO:0060060)|retinal rod cell development (GO:0046548)					breast(1)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(2)|urinary_tract(1)	12				KIRC - Kidney renal clear cell carcinoma(284;0.0478)|Kidney(284;0.0597)|OV - Ovarian serous cystadenocarcinoma(275;0.233)		GAATTCTACGACTTCTAAGAA	0.289																																					p.T605S		Atlas-SNP	.											.	CCDC66	145	.	0			c.A1813T						.						83	96	92					3																	56650051		2203	4291	6494	SO:0001583	missense	285331	exon13			TCTACGACTTCTA	AL832692	CCDS33770.2, CCDS46852.1	3p14.3	2006-03-27			ENSG00000180376	ENSG00000180376			27709	protein-coding gene	gene with protein product						14702039	Standard	NR_024460		Approved	DKFZp686C0433	uc003dhz.3	A2RUB6	OTTHUMG00000155748	ENST00000394672.3:c.1813A>T	chr3.hg19:g.56650051A>T	ENSP00000378167:p.Thr605Ser	96.0	0.0		99.0	5.0	NM_001141947	B3KWL8|Q4VC34|Q8N949	Missense_Mutation	SNP	ENST00000394672.3	hg19	CCDS46852.1	.	.	.	.	.	.	.	.	.	.	A	0.012	-1.687010	0.00738	.	.	ENSG00000180376	ENST00000422222;ENST00000394672;ENST00000326595;ENST00000436465	T;T;T;T	0.17370	2.28;2.31;2.3;2.31	5.59	1.92	0.25849	.	0.882722	0.10049	N	0.722482	T	0.12774	0.0310	L	0.54323	1.7	0.09310	N	1	B	0.25272	0.122	B	0.25291	0.059	T	0.42816	-0.9429	10	0.02654	T	1	0.5859	4.5617	0.12163	0.5839:0.1576:0.2585:0.0	.	605	A2RUB6	CCD66_HUMAN	S	561;605;571;605	ENSP00000401451:T561S;ENSP00000378167:T605S;ENSP00000326050:T571S;ENSP00000404320:T605S	ENSP00000326050:T571S	T	+	1	0	CCDC66	56625091	0.000000	0.05858	0.003000	0.11579	0.045000	0.14185	-0.099000	0.11007	0.161000	0.19458	0.482000	0.46254	ACT	.	.		0.289	CCDC66-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341473.1	NM_001012506		T	56650051	A	T	56650051	3	4	263	1	0	0	0	0	1	0	0	0	2840	275	10	4	1863	4	CCDC66	3	56650051	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	6546353	56650051	141372379	69	38443										
PDHB	5162	hgsc.bcm.edu	37	chr3	58415861	58415861	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cttagttttcttaccttgccTttctattttggcttttccaa	4	10	2	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr3:58415861T>C	ENST00000302746.6	-	7	736	c.694A>G	c.(694-696)Agg>Ggg	p.R232G	PDHB_ENST00000474765.1_Missense_Mutation_p.R214G|PDHB_ENST00000485460.1_Missense_Mutation_p.R214G|RP11-802O23.3_ENST00000607214.1_RNA	NM_000925.3|NM_001173468.1	NP_000916.2|NP_001166939.1	P11177	ODPB_HUMAN	pyruvate dehydrogenase (lipoamide) beta	232					acetyl-CoA biosynthetic process from pyruvate (GO:0006086)|cellular metabolic process (GO:0044237)|glucose metabolic process (GO:0006006)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|pyruvate dehydrogenase complex (GO:0045254)	pyruvate dehydrogenase (acetyl-transferring) activity (GO:0004739)|pyruvate dehydrogenase activity (GO:0004738)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)	9				BRCA - Breast invasive adenocarcinoma(55;0.000179)|Kidney(10;0.00231)|KIRC - Kidney renal clear cell carcinoma(10;0.00258)|OV - Ovarian serous cystadenocarcinoma(275;0.187)	Pyruvic acid(DB00119)	TTACCTTGCCTTTCTATTTTG	0.338																																					p.R232G		Atlas-SNP	.											.	PDHB	19	.	0			c.A694G						.						108	110	109					3																	58415861		2203	4300	6503	SO:0001583	missense	5162	exon7			CTTGCCTTTCTAT		CCDS2890.1, CCDS54602.1	3p21.1-p14.2	1995-12-20			ENSG00000168291	ENSG00000168291	1.2.4.1		8808	protein-coding gene	gene with protein product		179060					Standard	NR_033384		Approved		uc003dkf.4	P11177	OTTHUMG00000159157	ENST00000302746.6:c.694A>G	chr3.hg19:g.58415861T>C	ENSP00000307241:p.Arg232Gly	79.0	0.0		98.0	4.0	NM_000925	B2R7L0|B4DDD7|Q6FH45|Q9BQ27|Q9UFK3	Missense_Mutation	SNP	ENST00000302746.6	hg19	CCDS2890.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.039994	0.75732	.	.	ENSG00000168291	ENST00000302746;ENST00000383714;ENST00000485460;ENST00000474765	D;D;D;D	0.92099	-2.97;-2.97;-2.97;-2.97	6.17	4.98	0.66077	Transketolase, C-terminal (1);Transketolase, C-terminal/Pyruvate-ferredoxin oxidoreductase, domain II (1);Transketolase-like, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.97579	0.9207	H	0.98754	4.32	0.80722	D	1	P;D;D;D	0.76494	0.727;0.999;0.996;0.996	P;D;D;D	0.72075	0.622;0.976;0.97;0.958	D	0.98298	1.0517	10	0.87932	D	0	-21.8434	12.4693	0.55777	0.0:0.0:0.261:0.739	.	214;214;214;232	B4DDD7;C9J634;P11177-2;P11177	.;.;.;ODPB_HUMAN	G	232;214;214;214	ENSP00000307241:R232G;ENSP00000373220:R214G;ENSP00000417267:R214G;ENSP00000418448:R214G	ENSP00000307241:R232G	R	-	1	2	PDHB	58390901	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.961000	0.49168	2.371000	0.80710	0.533000	0.62120	AGG	.	.		0.338	PDHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353558.1			C	58415861	T	C	58415861	3	2	263	1	0	0	0	0	1	0	0	0	11675	1608	56	2	401	2	PDHB	3	58415861	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	1765810	58415861	139606569	70	38444										
MITF	4286	hgsc.bcm.edu	37	chr3	69813025	69813025	+	Intron	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gaaaatacttcagtggttttCccacgagctattttctctct	6	10	3	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr3:69813025C>T	ENST00000448226.2	+	1	231				MITF_ENST00000352241.4_Intron|MITF_ENST00000472437.1_Intron|MITF_ENST00000328528.6_Silent_p.F11F			O75030	MITF_HUMAN	microphthalmia-associated transcription factor						bone remodeling (GO:0046849)|camera-type eye development (GO:0043010)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|cell fate commitment (GO:0045165)|melanocyte differentiation (GO:0030318)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)|regulation of osteoclast differentiation (GO:0045670)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)			NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|skin(6)|stomach(1)|urinary_tract(2)	30		Lung NSC(201;0.0384)|Prostate(884;0.0526)		BRCA - Breast invasive adenocarcinoma(55;3.07e-05)|Epithelial(33;0.000138)|LUSC - Lung squamous cell carcinoma(21;0.008)|Lung(16;0.0107)|KIRC - Kidney renal clear cell carcinoma(39;0.204)|Kidney(39;0.239)		CAGTGGTTTTCCCACGAGCTA	0.398			A		melanoma		"Waardenburg syndrome type 2, Tietz syndrome"																														p.F11F	Melanoma(29;269 969 31479 41502 42961)	Atlas-SNP	.		Dom	yes		3	3p14.1	4286	microphthalmia-associated transcription factor	yes	E	.	MITF	156	.	0			c.C33T						.						53	51	51					3																	69813025		1824	4083	5907	SO:0001627	intron_variant	4286	exon1			GGTTTTCCCACGA		CCDS2913.1, CCDS43106.1, CCDS43107.1, CCDS46865.1, CCDS46866.1, CCDS46866.2, CCDS54607.1, CCDS74962.1	3p14.1-p12.3	2014-09-17			ENSG00000187098	ENSG00000187098		"Basic helix-loop-helix proteins"	7105	protein-coding gene	gene with protein product	"homolog of mouse microphthalmia"	156845	"Waardenburg syndrome, type 2A"	WS2A, WS2		8069297, 7874167, 7951321	Standard	NM_198159		Approved	MI, bHLHe32	uc003dnz.3	O75030	OTTHUMG00000149921	ENST00000448226.2:c.104+24173C>T	chr3.hg19:g.69813025C>T		81.0	0.0		94.0	37.0	NM_006722	B4DJL2|D3K197|E9PFN0|Q14841|Q9P2V0|Q9P2V1|Q9P2V2|Q9P2Y8	Silent	SNP	ENST00000448226.2	hg19																																																																																				.	.		0.398	MITF-007	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000313947.1	NM_198159		T	69813025	C	T	69813025	1	4	263	0	1	0	0	0	0	0	0	0	9605	854	30	3		3	MITF	3	69813025	Intron	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	11397164	69813025	128209405	71	38445										
DRD3	1814	hgsc.bcm.edu	37	chr3	113850192	113850192	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gtccacccaaggcagtgtccTggcagatgctgtagtaacgc	12	12	0	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr3:113850192T>G	ENST00000460779.1	-	7	1068	c.779A>C	c.(778-780)cAg>cCg	p.Q260P	DRD3_ENST00000295881.7_Missense_Mutation_p.Q260P|DRD3_ENST00000467632.1_Missense_Mutation_p.Q260P|DRD3_ENST00000383673.2_Missense_Mutation_p.Q260P	NM_001282563.1	NP_001269492.1	P35462	DRD3_HUMAN	dopamine receptor D3	260					acid secretion (GO:0046717)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|arachidonic acid secretion (GO:0050482)|behavioral response to cocaine (GO:0048148)|cellular calcium ion homeostasis (GO:0006874)|circadian regulation of gene expression (GO:0032922)|dopamine metabolic process (GO:0042417)|G-protein coupled receptor internalization (GO:0002031)|G-protein coupled receptor signaling pathway (GO:0007186)|gastric emptying (GO:0035483)|learning (GO:0007612)|learning or memory (GO:0007611)|locomotory behavior (GO:0007626)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of blood pressure (GO:0045776)|negative regulation of dopamine receptor signaling pathway (GO:0060160)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein secretion (GO:0050709)|negative regulation of sodium:proton antiporter activity (GO:0032416)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of mitosis (GO:0045840)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prepulse inhibition (GO:0060134)|regulation of blood volume by renin-angiotensin (GO:0002016)|regulation of cAMP metabolic process (GO:0030814)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|regulation of dopamine secretion (GO:0014059)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of lipid metabolic process (GO:0019216)|regulation of locomotion involved in locomotory behavior (GO:0090325)|regulation of multicellular organism growth (GO:0040014)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to histamine (GO:0034776)|response to morphine (GO:0043278)|social behavior (GO:0035176)|synaptic transmission, dopaminergic (GO:0001963)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|cell projection (GO:0042995)|endocytic vesicle (GO:0030139)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity, coupled via Gi/Go (GO:0001591)|drug binding (GO:0008144)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(23)|ovary(1)|pancreas(1)|skin(1)	36					Amisulpride(DB06288)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Clozapine(DB00363)|Domperidone(DB01184)|Dopamine(DB00988)|Haloperidol(DB00502)|Iloperidone(DB04946)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Pimozide(DB01100)|Pramipexole(DB00413)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sulpiride(DB00391)|Yohimbine(DB01392)|Ziprasidone(DB00246)	GGCAGTGTCCTGGCAGATGCT	0.542																																					p.Q260P		Atlas-SNP	.											.	DRD3	76	.	0			c.A779C						.						136	139	138					3																	113850192		2203	4300	6503	SO:0001583	missense	1814	exon6			GTGTCCTGGCAGA		CCDS2978.1, CCDS33829.1	3q13.3	2012-08-08			ENSG00000151577	ENSG00000151577		"GPCR / Class A : Dopamine receptors"	3024	protein-coding gene	gene with protein product		126451				1916765	Standard	XM_005247171		Approved		uc003ebc.1	P35462	OTTHUMG00000159334	ENST00000460779.1:c.779A>C	chr3.hg19:g.113850192T>G	ENSP00000419402:p.Gln260Pro	120.0	0.0		195.0	67.0	NM_033663	A1A4V5|Q4VBM8	Missense_Mutation	SNP	ENST00000460779.1	hg19	CCDS2978.1	.	.	.	.	.	.	.	.	.	.	T	11.89	1.772316	0.31411	.	.	ENSG00000151577	ENST00000460779;ENST00000467632;ENST00000383673;ENST00000281274;ENST00000295881	T;T;T;T	0.72942	-0.7;-0.7;-0.7;-0.65	5.64	5.64	0.86602	GPCR, rhodopsin-like superfamily (1);	0.229185	0.41605	D	0.000856	T	0.58133	0.2101	L	0.33668	1.02	0.47153	D	0.999332	B;B;B;B	0.12630	0.006;0.0;0.0;0.001	B;B;B;B	0.15870	0.014;0.004;0.004;0.009	T	0.53690	-0.8403	10	0.27785	T	0.31	.	10.8001	0.46483	0.0:0.0736:0.0:0.9264	.	260;260;260;260	A1A4V4;A8K8E4;P35462;E9PCM4	.;.;DRD3_HUMAN;.	P	260	ENSP00000419402:Q260P;ENSP00000420662:Q260P;ENSP00000373169:Q260P;ENSP00000295881:Q260P	ENSP00000281274:Q260P	Q	-	2	0	DRD3	115332882	1.000000	0.71417	0.999000	0.59377	0.913000	0.54294	5.399000	0.66314	2.367000	0.80283	0.528000	0.53228	CAG	.	.		0.542	DRD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354699.1	NM_000796.3		G	113850192	T	G	113850192	3	3	263	1	0	0	0	0	1	0	0	0	4760	1580	55	5	431	5	DRD3	3	113850192	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	44037167	113850192	84172238	72	38446										
POLQ	10721	hgsc.bcm.edu	37	chr3	121186373	121186373	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tcagccaccttacctgggaaAggcacaaaggcatgtcgcat	10	12	1	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr3:121186373A>G	ENST00000264233.5	-	24	7088	c.6960T>C	c.(6958-6960)ccT>ccC	p.P2320P		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	2320					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		TACCTGGGAAAGGCACAAAGG	0.458								DNA polymerases (catalytic subunits)																													p.P2320P	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.T6960C						.						160	143	149					3																	121186373		2203	4300	6503	SO:0001819	synonymous_variant	10721	exon24			TGGGAAAGGCACA	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.6960T>C	chr3.hg19:g.121186373A>G		84.0	0.0		89.0	4.0	NM_199420	O95160|Q6VMB5	Silent	SNP	ENST00000264233.5	hg19	CCDS33833.1																																																																																			.	.		0.458	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		G	121186373	A	G	121186373	2	3	263	1	0	0	0	0	0	0	0	1	12217	59	3	2		2	POLQ	3	121186373	Silent	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	7336181	121186373	76836057	73	38447										
PARP14	54625	hgsc.bcm.edu	37	chr3	122419294	122419294	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	caaaattcctccccaaacacTgtaatcatcaatgagttaac	3	12	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr3:122419294T>C	ENST00000474629.2	+	6	2159	c.1893T>C	c.(1891-1893)acT>acC	p.T631T		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	631					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		CCCCAAACACTGTAATCATCA	0.358																																					p.T631T		Atlas-SNP	.											.	PARP14	242	.	0			c.T1893C						.						31	30	30					3																	122419294		1841	4102	5943	SO:0001819	synonymous_variant	54625	exon6			AAACACTGTAATC	AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"Poly (ADP-ribose) polymerases"	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.1893T>C	chr3.hg19:g.122419294T>C		85.0	0.0		77.0	4.0	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Silent	SNP	ENST00000474629.2	hg19	CCDS46894.1																																																																																			.	.		0.358	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554		C	122419294	T	C	122419294	2	2	263	1	0	0	0	0	0	0	0	1	11467	1567	55	2		2	PARP14	3	122419294	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	1232921	122419294	75603136	74	38448										
ITGB5	3693	hgsc.bcm.edu	37	chr3	124515576	124515576	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tgacccccacctccaggctgTcccggaatcccaccggccgc	9	21	0	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr3:124515576T>C	ENST00000296181.4	-	10	1648	c.1352A>G	c.(1351-1353)gAc>gGc	p.D451G		NM_002213.3	NP_002204.2	P18084	ITB5_HUMAN	integrin, beta 5	451					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|epithelial cell-cell adhesion (GO:0090136)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|stress fiber assembly (GO:0043149)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alphav-beta5 complex (GO:0034684)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	30				GBM - Glioblastoma multiforme(114;0.163)		CTCCAGGCTGTCCCGGAATCC	0.632																																					p.D451G		Atlas-SNP	.											.	ITGB5	66	.	0			c.A1352G						.						29	30	30					3																	124515576		2203	4300	6503	SO:0001583	missense	3693	exon10			AGGCTGTCCCGGA	J05633	CCDS3030.1	3q21.2	2010-03-23			ENSG00000082781	ENSG00000082781		"Integrins"	6160	protein-coding gene	gene with protein product		147561				2211615	Standard	NM_002213		Approved		uc003eho.3	P18084	OTTHUMG00000159432	ENST00000296181.4:c.1352A>G	chr3.hg19:g.124515576T>C	ENSP00000296181:p.Asp451Gly	119.0	0.0		106.0	6.0	NM_002213	B0LPF8|B2RD70	Missense_Mutation	SNP	ENST00000296181.4	hg19	CCDS3030.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	28.0|28.0	4.882517|4.882517	0.91740|0.91740	.|.	.|.	ENSG00000082781|ENSG00000082781	ENST00000296181|ENST00000481591	T|.	0.69685|.	-0.42|.	5.26|5.26	5.26|5.26	0.73747|0.73747	Integrin beta subunit, N-terminal (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.71221|0.71221	0.3314|0.3314	M|M	0.63169|0.63169	1.94|1.94	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	T|T	0.70502|0.70502	-0.4854|-0.4854	10|5	0.87932|.	D|.	0|.	.|.	15.3487|15.3487	0.74363|0.74363	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	451|.	P18084|.	ITB5_HUMAN|.	G|A	451|141	ENSP00000296181:D451G|.	ENSP00000296181:D451G|.	D|T	-|-	2|1	0|0	ITGB5|ITGB5	125998266|125998266	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	7.792000|7.792000	0.85828|0.85828	2.208000|2.208000	0.71279|0.71279	0.460000|0.460000	0.39030|0.39030	GAC|ACA	.	.		0.632	ITGB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355286.3	NM_002213		C	124515576	T	C	124515576	3	2	263	1	0	0	0	0	1	0	0	0	7907	1667	58	2	1071	2	ITGB5	3	124515576	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	2096282	124515576	73506854	75	38449										
SEC61A1	29927	hgsc.bcm.edu	37	chr3	127775642	127775642	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	caagataattgaagttggtgAcaccccaaaagaccgagctc	9	10	0	4			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr3:127775642A>G	ENST00000243253.3	+	5	495	c.311A>G	c.(310-312)gAc>gGc	p.D104G	SEC61A1_ENST00000464451.1_Missense_Mutation_p.D110G|SEC61A1_ENST00000424880.2_Intron	NM_013336.3	NP_037468.1	P61619	S61A1_HUMAN	Sec61 alpha 1 subunit (S. cerevisiae)	104					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell growth (GO:0016049)|endoplasmic reticulum organization (GO:0007029)|posttranslational protein targeting to membrane (GO:0006620)|protein targeting to ER (GO:0045047)|response to interferon-gamma (GO:0034341)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)	integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	ribosome binding (GO:0043022)			central_nervous_system(1)|kidney(1)|large_intestine(5)|liver(1)|lung(8)|ovary(1)|prostate(4)	21						GAAGTTGGTGACACCCCAAAA	0.423																																					p.D104G		Atlas-SNP	.											.	SEC61A1	39	.	0			c.A311G						.						82	80	81					3																	127775642		2203	4300	6503	SO:0001583	missense	29927	exon5			TTGGTGACACCCC	AF077032	CCDS3046.1	3q21.3	2008-02-05			ENSG00000058262	ENSG00000058262			18276	protein-coding gene	gene with protein product		609213					Standard	NM_013336		Approved		uc003ekb.3	P61619	OTTHUMG00000159624	ENST00000243253.3:c.311A>G	chr3.hg19:g.127775642A>G	ENSP00000243253:p.Asp104Gly	82.0	0.0		105.0	6.0	NM_013336	P38378|P57726|Q5JPF8|Q8N0Z4|Q8N3U3|Q8NC71|Q9BU16|Q9Y2R3	Missense_Mutation	SNP	ENST00000243253.3	hg19	CCDS3046.1	.	.	.	.	.	.	.	.	.	.	A	17.00	3.275904	0.59649	.	.	ENSG00000058262	ENST00000464451;ENST00000243253;ENST00000481210	.	.	.	5.79	5.79	0.91817	SecY subunit domain (2);	0.000000	0.85682	D	0.000000	T	0.68970	0.3059	M	0.65975	2.015	0.80722	D	1	B	0.17038	0.02	B	0.30646	0.118	T	0.65162	-0.6235	9	0.37606	T	0.19	.	16.1388	0.81509	1.0:0.0:0.0:0.0	.	104	P61619	S61A1_HUMAN	G	110;104;51	.	ENSP00000243253:D104G	D	+	2	0	SEC61A1	129258332	1.000000	0.71417	0.967000	0.41034	0.554000	0.35429	9.339000	0.96797	2.205000	0.71048	0.528000	0.53228	GAC	.	.		0.423	SEC61A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356541.2	NM_013336		G	127775642	A	G	127775642	3	3	263	1	0	0	0	0	1	0	0	0	14015	275	10	2	329	2	SEC61A1	3	127775642	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	3260066	127775642	70246788	76	38450										
KIAA1257	57501	hgsc.bcm.edu	37	chr3	128694728	128694728	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cctgccaaagaaatggttggTgttcttgaaacactccatct	8	10	2	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr3:128694728T>C	ENST00000265068.5	-	7	1082	c.915A>G	c.(913-915)acA>acG	p.T305T	KIAA1257_ENST00000510149.1_5'Flank|KIAA1257_ENST00000515659.1_Silent_p.T193T|KIAA1257_ENST00000511438.1_Silent_p.T305T	NM_020741.2	NP_065792.1	Q9ULG3	K1257_HUMAN	KIAA1257	305										breast(1)|endometrium(2)|large_intestine(3)|lung(6)|skin(2)	14						AAATGGTTGGTGTTCTTGAAA	0.363																																					p.T305T		Atlas-SNP	.											.	KIAA1257	33	.	0			c.A915G						.						92	79	83					3																	128694728		1834	4094	5928	SO:0001819	synonymous_variant	57501	exon7			GGTTGGTGTTCTT	AB033083	CCDS46905.1	3q21.3	2011-11-07			ENSG00000114656	ENSG00000114656			29231	protein-coding gene	gene with protein product						10574462	Standard	NM_020741		Approved		uc003elj.4	Q9ULG3	OTTHUMG00000159946	ENST00000265068.5:c.915A>G	chr3.hg19:g.128694728T>C		64.0	0.0		90.0	4.0	NM_020741	Q8IXY7|Q8N5T4	Silent	SNP	ENST00000265068.5	hg19	CCDS46905.1																																																																																			.	.		0.363	KIAA1257-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000358430.1	NM_020741		C	128694728	T	C	128694728	2	2	263	1	0	0	0	0	0	0	0	1	8227	1683	59	2		2	KIAA1257	3	128694728	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	919086	128694728	69327702	77	38451										
TMCC1	23023	hgsc.bcm.edu	37	chr3	129547013	129547013	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gatctgcctgaatttgctgcAcatcatgtggagacactgat	10	9	2	3			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr3:129547013A>G	ENST00000393238.3	-	3	549	c.209T>C	c.(208-210)gTg>gCg	p.V70A	TMCC1_ENST00000426664.2_Intron	NM_001017395.3	NP_001017395.2	O94876	TMCC1_HUMAN	transmembrane and coiled-coil domain family 1	70						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)			PLXND1/TMCC1(4)	breast(1)|endometrium(3)|large_intestine(8)|lung(12)|skin(1)	25						AATTTGCTGCACATCATGTGG	0.507																																					p.V70A		Atlas-SNP	.											.	TMCC1	105	.	0			c.T209C						.						88	73	78					3																	129547013		2203	4300	6503	SO:0001583	missense	23023	exon3			TGCTGCACATCAT	AB018322	CCDS33855.1	3q21.3	2010-04-19	2005-07-13		ENSG00000172765	ENSG00000172765		"Transmembrane and coiled-coil domain containing"	29116	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 1"			9872452	Standard	NR_033361		Approved	KIAA0779	uc021xdy.1	O94876	OTTHUMG00000159579	ENST00000393238.3:c.209T>C	chr3.hg19:g.129547013A>G	ENSP00000376930:p.Val70Ala	69.0	0.0		93.0	4.0	NM_001017395	A8K5Y3|B4DE04|Q68E06|Q8IXM8	Missense_Mutation	SNP	ENST00000393238.3	hg19	CCDS33855.1	.	.	.	.	.	.	.	.	.	.	A	6.728	0.503118	0.12822	.	.	ENSG00000172765	ENST00000393238	T	0.32023	1.47	5.68	4.53	0.55603	.	0.419391	0.23977	N	0.042709	T	0.15912	0.0383	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.06058	-1.0848	10	0.22109	T	0.4	-9.5469	11.7828	0.52023	0.9312:0.0:0.0688:0.0	.	70	O94876	TMCC1_HUMAN	A	70	ENSP00000376930:V70A	ENSP00000376930:V70A	V	-	2	0	TMCC1	131029703	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.550000	0.67268	1.094000	0.41399	0.482000	0.46254	GTG	.	.		0.507	TMCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356418.2	NM_015008		G	129547013	A	G	129547013	3	3	263	1	0	0	0	0	1	0	0	0	16007	159	6	2	1768	2	TMCC1	3	129547013	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	852285	129547013	68475417	78	38452										
ZIC1	7545	hgsc.bcm.edu	37	chr3	147128512	147128526	+	In_Frame_Del	DEL	GCCGCGCATCACGGC	GCCGCGCATCACGGC	-													0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ggcccatgaacgtgaacatgGccgcgcatcacggcgccggc					rs370404401		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	GCCGCGCATCACGGC	GCCGCGCATCACGGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr3:147128512_147128526delGCCGCGCATCACGGC	ENST00000282928.4	+	1	1342_1356	c.613_627delGCCGCGCATCACGGC	c.(613-627)gccgcgcatcacggcdel	p.AAHHG205del		NM_003412.3	NP_003403.2	Q15915	ZIC1_HUMAN	Zic family member 1	205					adult walking behavior (GO:0007628)|brain development (GO:0007420)|cell differentiation (GO:0030154)|inner ear morphogenesis (GO:0042472)|pattern specification process (GO:0007389)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord development (GO:0021510)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G209C(1)|p.H208N(1)		central_nervous_system(4)|cervix(1)|endometrium(2)|large_intestine(8)|lung(38)|ovary(1)|prostate(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	63						CGTGAACATGGCCGCGCATCACGGCGCCGGCGCCT	0.647																																					p.204_209del		Atlas-Indel,Pindel	.											.	ZIC1	141	.	2	Substitution - Missense(2)	lung(1)|prostate(1)	c.612_626del						.																																			SO:0001651	inframe_deletion	7545	exon1			.	D76435	CCDS3136.1	3q24	2013-01-08	2011-05-19		ENSG00000152977	ENSG00000152977		"Zinc fingers, C2H2-type"	12872	protein-coding gene	gene with protein product		600470	"Zic family member 1 (odd-paired Drosophila homolog)", "Zic family member 1 (odd-paired homolog, Drosophila)"			8542595	Standard	NM_003412		Approved	ZIC, ZNF201	uc003ewe.3	Q15915	OTTHUMG00000159456	ENST00000282928.4:c.613_627delGCCGCGCATCACGGC	chr3.hg19:g.147128512_147128526delGCCGCGCATCACGGC	ENSP00000282928:p.Ala205_Gly209del	116.0	0.0		49.0	15.0	NM_003412	Q2M3N1	In_Frame_Del	DEL	ENST00000282928.4	hg19	CCDS3136.1																																																																																			.	.		0.647	ZIC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355497.1	NM_003412		-	147128526	GCCGCGCATCACGGC	-	147128512	7	5	263	1	0	1	0	1	0	0	0	0	17693	1203	42	0	615	0	ZIC1	3	147128512	In_Frame_Del	DEL	GCCGCGCATCACGGC	TCGA-FV-A2QR-01A-11D-A20W-10	17581499	147128512	50893918	79	38453										
P2RY12	64805	hgsc.bcm.edu	37	chr3	151055763	151055763	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gatgaacggatccaggcatgCatttaaggaagttaaccaca	10	8	0	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr3:151055763C>A	ENST00000302632.3	-	3	1170	c.871G>T	c.(871-873)Gca>Tca	p.A291S	MED12L_ENST00000474524.1_Intron|MED12L_ENST00000491549.1_Intron|MED12L_ENST00000273432.4_Intron	NM_022788.4|NM_176876.2	NP_073625.1|NP_795345.1	Q9H244	P2Y12_HUMAN	purinergic receptor P2Y, G-protein coupled, 12	291					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell projection organization (GO:0030030)|G-protein coupled purinergic nucleotide receptor signaling pathway (GO:0035589)|G-protein coupled receptor signaling pathway (GO:0007186)|hemostasis (GO:0007599)|negative regulation of cell differentiation (GO:0045596)|negative regulation of norepinephrine secretion (GO:0010700)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of GTPase activity (GO:0043547)|positive regulation of ion transport (GO:0043270)|potassium ion transmembrane transport (GO:0071805)|protein kinase B signaling (GO:0043491)|regulation of calcium ion transport (GO:0051924)	basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	ADP receptor activity (GO:0001621)|G-protein coupled adenosine receptor activity (GO:0001609)|guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)	17			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)		Clopidogrel(DB00758)|Epoprostenol(DB01240)|Prasugrel(DB06209)|Ticagrelor(DB08816)|Ticlopidine(DB00208)|Treprostinil(DB00374)	TCCAGGCATGCATTTAAGGAA	0.438																																					p.A291S		Atlas-SNP	.											.	P2RY12	36	.	0			c.G871T						.						116	113	114					3																	151055763		2203	4300	6503	SO:0001583	missense	64805	exon3			GGCATGCATTTAA	AJ320495	CCDS3159.1	3q24-q25	2014-09-17			ENSG00000169313	ENSG00000169313		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	18124	protein-coding gene	gene with protein product		600515				11502873, 11104774	Standard	NM_022788		Approved	P2Y12, SP1999, HORK3	uc003eyw.1	Q9H244	OTTHUMG00000159863	ENST00000302632.3:c.871G>T	chr3.hg19:g.151055763C>A	ENSP00000307259:p.Ala291Ser	111.0	0.0		66.0	46.0	NM_022788	D3DNJ5|Q546J7	Missense_Mutation	SNP	ENST00000302632.3	hg19	CCDS3159.1	.	.	.	.	.	.	.	.	.	.	C	13.83	2.355428	0.41700	.	.	ENSG00000169313	ENST00000302632;ENST00000455408	T	0.62788	-0.0	5.33	5.33	0.75918	GPCR, rhodopsin-like superfamily (1);	0.158495	0.56097	D	0.000028	T	0.26011	0.0634	N	0.00382	-1.575	0.49213	D	0.999766	B	0.24258	0.1	B	0.25405	0.06	T	0.49031	-0.8981	10	0.02654	T	1	-20.4475	16.3945	0.83586	0.0:0.8686:0.1314:0.0	.	291	Q9H244	P2Y12_HUMAN	S	291;194	ENSP00000307259:A291S	ENSP00000307259:A291S	A	-	1	0	P2RY12	152538453	1.000000	0.71417	0.330000	0.25442	0.972000	0.66771	4.726000	0.61986	2.654000	0.90174	0.655000	0.94253	GCA	.	.		0.438	P2RY12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357796.1			A	151055763	C	A	151055763	3	1	263	1	0	0	0	0	1	0	0	0	11358	710	25	3	161	3	P2RY12	3	151055763	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	3927251	151055763	46966667	80	38454										
SGEF	26084	hgsc.bcm.edu	37	chr3	153847474	153847474	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	aaaaattgtgattcaccataAgccattgagatccacatgga	7	8	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr3:153847474A>G	ENST00000356448.4	+	4	1519	c.1235A>G	c.(1234-1236)aAg>aGg	p.K412R	ARHGEF26_ENST00000465817.1_Missense_Mutation_p.K412R|ARHGEF26_ENST00000465093.1_Missense_Mutation_p.K412R	NM_001251962.1	NP_001238891.1	Q96DR7	ARHGQ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 26	412					endothelial cell morphogenesis (GO:0001886)|ruffle assembly (GO:0097178)	cell projection (GO:0042995)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	23						ATTCACCATAAGCCATTGAGA	0.388																																					p.K412R	GBM(163;191 2003 24758 29593 48540)|Ovarian(152;631 1885 20165 22910 51013)	Atlas-SNP	.											.	ARHGEF26	158	.	0			c.A1235G						.						105	96	99					3																	153847474		1855	4126	5981	SO:0001583	missense	26084	exon4			ACCATAAGCCATT	BC016628	CCDS46938.1, CCDS58858.1	3q25.2	2013-01-10			ENSG00000114790	ENSG00000114790		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	24490	protein-coding gene	gene with protein product	"Src homology 3 domain-containing guanine nucleotide exchange factor"					15133129, 12697679	Standard	NM_015595		Approved	DKFZP434D146, SGEF	uc021xgc.1	Q96DR7	OTTHUMG00000159098	ENST00000356448.4:c.1235A>G	chr3.hg19:g.153847474A>G	ENSP00000348828:p.Lys412Arg	198.0	0.0		93.0	4.0	NM_001251962	B3KVP8|E9PBD0|Q68CL1|Q6AZ96|Q6Q8Q8|Q96AW8|Q96DR6|Q9H9D7|Q9H9R2|Q9UFW5	Missense_Mutation	SNP	ENST00000356448.4	hg19	CCDS46938.1	.	.	.	.	.	.	.	.	.	.	A	13.30	2.196935	0.38806	.	.	ENSG00000114790	ENST00000356448;ENST00000465093;ENST00000465817	T;T;T	0.55760	0.5;0.5;2.68	5.91	5.91	0.95273	.	0.045615	0.85682	D	0.000000	T	0.29716	0.0742	N	0.10809	0.05	0.44547	D	0.9975	B;B	0.32071	0.355;0.355	B;B	0.24974	0.057;0.057	T	0.28396	-1.0045	10	0.05620	T	0.96	-29.7627	16.3483	0.83171	1.0:0.0:0.0:0.0	.	412;412	E9PBD0;Q96DR7	.;ARHGQ_HUMAN	R	412	ENSP00000348828:K412R;ENSP00000423418:K412R;ENSP00000423295:K412R	ENSP00000348828:K412R	K	+	2	0	ARHGEF26	155330164	1.000000	0.71417	0.998000	0.56505	0.985000	0.73830	4.183000	0.58317	2.254000	0.74563	0.533000	0.62120	AAG	.	.		0.388	ARHGEF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353287.3	NM_015595		G	153847474	A	G	153847474	3	3	263	1	0	0	0	0	1	0	0	0	14220	72	3	2	1245	2	SGEF	3	153847474	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	2791711	153847474	44174956	81	38455										
KCNAB1	7881	hgsc.bcm.edu	37	chr3	156183439	156183439	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tttttcttggcagagctgaaAcagaaagagggctgtcaaga	12	6	2	5			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr3:156183439A>G	ENST00000490337.1	+	7	599	c.535A>G	c.(535-537)Aca>Gca	p.T179A	KCNAB1_ENST00000471742.1_Missense_Mutation_p.T168A|KCNAB1_ENST00000389636.5_Missense_Mutation_p.T179A|KCNAB1_ENST00000497291.1_3'UTR|KCNAB1_ENST00000389634.5_Missense_Mutation_p.T161A|KCNAB1_ENST00000302490.8_Missense_Mutation_p.T161A	NM_172160.2	NP_751892.1	Q14722	KCAB1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, beta member 1	179					learning or memory (GO:0007611)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	28			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			CAGAGCTGAAACAGAAAGAGG	0.388																																					p.T179A		Atlas-SNP	.											.	KCNAB1	176	.	0			c.A535G						.						105	103	104					3																	156183439		2203	4300	6503	SO:0001583	missense	7881	exon7			GCTGAAACAGAAA	U33428	CCDS3174.1, CCDS3175.1, CCDS33882.1	3q26.1	2006-11-29			ENSG00000169282	ENSG00000169282		"Potassium channels", "Aldo-keto reductases"	6228	protein-coding gene	gene with protein product		601141				8838324, 7499366	Standard	NM_172160		Approved	AKR6A3, KCNA1B, hKvBeta3, Kvb1.3, hKvb3	uc003far.2	Q14722	OTTHUMG00000158552	ENST00000490337.1:c.535A>G	chr3.hg19:g.156183439A>G	ENSP00000419952:p.Thr179Ala	86.0	0.0		100.0	4.0	NM_172160	A8K9H8|A8KAD4|B3KPZ4|Q13031|Q13302|Q16547|Q6PI60|Q99869	Missense_Mutation	SNP	ENST00000490337.1	hg19	CCDS3174.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.555449	0.86231	.	.	ENSG00000169282	ENST00000472028;ENST00000490337;ENST00000389636;ENST00000471742;ENST00000475456;ENST00000302490;ENST00000389634	T;T;T;T;T;T;T	0.23147	1.92;1.92;1.92;1.92;1.92;1.92;1.92	5.66	5.66	0.87406	NADP-dependent oxidoreductase domain (3);	0.000000	0.85682	D	0.000000	T	0.45836	0.1362	L	0.54323	1.7	0.58432	D	0.999999	D;D;P;P;P	0.71674	0.979;0.998;0.887;0.862;0.887	D;D;P;P;P	0.68192	0.956;0.956;0.808;0.709;0.808	T	0.40496	-0.9560	10	0.66056	D	0.02	-7.6788	14.8633	0.70397	1.0:0.0:0.0:0.0	.	179;161;161;168;179	B7Z8E5;F8W6W4;B3KPZ4;Q14722-3;Q14722	.;.;.;.;KCAB1_HUMAN	A	97;179;179;168;122;161;161	ENSP00000420755:T97A;ENSP00000419952:T179A;ENSP00000374287:T179A;ENSP00000418956:T168A;ENSP00000420221:T122A;ENSP00000305858:T161A;ENSP00000374285:T161A	ENSP00000305858:T161A	T	+	1	0	KCNAB1	157666133	1.000000	0.71417	0.990000	0.47175	0.923000	0.55619	7.767000	0.85331	2.151000	0.67156	0.533000	0.62120	ACA	.	.		0.388	KCNAB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351411.1	NM_003471		G	156183439	A	G	156183439	3	3	263	1	0	0	0	0	1	0	0	0	8018	43	2	2	1032	2	KCNAB1	3	156183439	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	2335965	156183439	41838991	82	38456										
MFSD1	64747	hgsc.bcm.edu	37	chr3	158527010	158527010	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gttgcccagaatacatatgcTgtgagctggtttaaaggcaa	11	7	0	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr3:158527010T>C	ENST00000264266.8	+	6	545	c.483T>C	c.(481-483)gcT>gcC	p.A161A	MFSD1_ENST00000415822.2_Silent_p.A210A|MFSD1_ENST00000392813.4_Silent_p.A171A			Q9H3U5	MFSD1_HUMAN	major facilitator superfamily domain containing 1	161					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	26			Lung(72;0.00372)|LUSC - Lung squamous cell carcinoma(72;0.00523)			ATACATATGCTGTGAGCTGGT	0.358																																					p.A210A	Pancreas(62;1186 1654 36636 37908)	Atlas-SNP	.											.	MFSD1	88	.	0			c.T630C						.						119	120	120					3																	158527010		2203	4300	6503	SO:0001819	synonymous_variant	64747	exon6			ATATGCTGTGAGC	BC017661	CCDS3185.1, CCDS3185.2, CCDS54666.1	3q25.32	2005-11-17			ENSG00000118855	ENSG00000118855			25874	protein-coding gene	gene with protein product							Standard	NM_022736		Approved	FLJ14153, UG0581B09	uc003fcl.2	Q9H3U5	OTTHUMG00000158835	ENST00000264266.8:c.483T>C	chr3.hg19:g.158527010T>C		58.0	0.0		74.0	4.0	NM_022736	B4DGJ8|B4DMR8|B4DU49|B4DWU1|C9JS94|J3KQL7|Q05C07|Q5XKJ1|Q8IVS1|Q8IXG4|Q9H7X1	Silent	SNP	ENST00000264266.8	hg19																																																																																				.	.		0.358	MFSD1-018	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470730.1	NM_022736		C	158527010	T	C	158527010	2	2	263	1	0	0	0	0	0	0	0	1	9536	1567	55	2		2	MFSD1	3	158527010	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	2343571	158527010	39495420	83	38457										
ABCF3	55324	hgsc.bcm.edu	37	chr3	183907370	183907370	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gccctccaccatcctagtcgTctcccacgaccgcaacttct	5	20	2	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr3:183907370T>C	ENST00000429586.2	+	13	1324	c.1139T>C	c.(1138-1140)gTc>gCc	p.V380A	ABCF3_ENST00000292808.5_Missense_Mutation_p.V374A|EIF2B5_ENST00000444495.1_Intron	NM_018358.2	NP_060828.2	Q9NUQ8	ABCF3_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 3	380	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				defense response to virus (GO:0051607)	membrane (GO:0016020)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|cervix(1)|endometrium(2)|large_intestine(5)|lung(20)|ovary(3)|prostate(5)|upper_aerodigestive_tract(1)	39	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.35e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			ATCCTAGTCGTCTCCCACGAC	0.602																																					p.V380A		Atlas-SNP	.											.	ABCF3	72	.	0			c.T1139C						.						74	64	68					3																	183907370		2203	4300	6503	SO:0001583	missense	55324	exon13			TAGTCGTCTCCCA	U66685	CCDS3254.1	3q27.1	2012-05-16			ENSG00000161204	ENSG00000161204		"ATP binding cassette transporters / subfamily F"	72	protein-coding gene	gene with protein product						8894702	Standard	NM_018358		Approved	EST201864	uc003fmz.2	Q9NUQ8	OTTHUMG00000156824	ENST00000429586.2:c.1139T>C	chr3.hg19:g.183907370T>C	ENSP00000411471:p.Val380Ala	124.0	0.0		151.0	8.0	NM_018358	A8K241|Q86UA2|Q8NAN1|Q96GS8|Q9H7A8	Missense_Mutation	SNP	ENST00000429586.2	hg19	CCDS3254.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.076336	0.76415	.	.	ENSG00000161204	ENST00000429586;ENST00000292808	D;D	0.95724	-3.79;-3.78	4.2	4.2	0.49525	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.000000	0.85682	D	0.000000	D	0.97424	0.9157	M	0.82716	2.605	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.78314	0.991;0.979	D	0.97957	1.0335	10	0.87932	D	0	-21.3595	12.6127	0.56560	0.0:0.0:0.0:1.0	.	374;380	Q9NUQ8-2;Q9NUQ8	.;ABCF3_HUMAN	A	380;374	ENSP00000411471:V380A;ENSP00000292808:V374A	ENSP00000292808:V374A	V	+	2	0	ABCF3	185390064	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.283000	0.78640	1.775000	0.52247	0.460000	0.39030	GTC	.	.		0.602	ABCF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346047.1	NM_018358		C	183907370	T	C	183907370	3	2	263	1	0	0	0	0	1	0	0	0	67	1667	58	2	1189	2	ABCF3	3	183907370	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	25380360	183907370	14115060	84	38458										
SST	6750	hgsc.bcm.edu	37	chr3	187388043	187388043	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cagggccaggacgatggacaGcgcagccagcgcgcactgga	16	13	0	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr3:187388043G>A	ENST00000287641.3	-	1	144	c.37C>T	c.(37-39)Ctg>Ttg	p.L13L		NM_001048.3	NP_001039.1	P61278	SMS_HUMAN	somatostatin	13					cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|digestion (GO:0007586)|G-protein coupled receptor signaling pathway (GO:0007186)|hormone-mediated apoptotic signaling pathway (GO:0008628)|hyperosmotic response (GO:0006972)|negative regulation of cell proliferation (GO:0008285)|regulation of cell migration (GO:0030334)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to heat (GO:0009408)|response to nutrient (GO:0007584)|response to steroid hormone (GO:0048545)|synaptic transmission (GO:0007268)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)	hormone activity (GO:0005179)			kidney(1)|large_intestine(1)|lung(6)|pancreas(1)	9	all_cancers(143;4.06e-12)|Ovarian(172;0.0418)		OV - Ovarian serous cystadenocarcinoma(80;1.76e-18)	GBM - Glioblastoma multiforme(93;0.00444)	Cysteamine(DB00847)	ACGATGGACAGCGCAGCCAGC	0.677											OREG0004470	type=TRANSCRIPTION FACTOR BINDING SITE|Gene=SST|TFbs=REST|Dataset=NRSF/REST ChIPSeq sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.L13L		Atlas-SNP	.											.	SST	20	.	0			c.C37T						.						18	17	17					3																	187388043		2194	4294	6488	SO:0001819	synonymous_variant	6750	exon1			TGGACAGCGCAGC		CCDS3288.1	3q28	2013-02-28			ENSG00000157005	ENSG00000157005		"Endogenous ligands"	11329	protein-coding gene	gene with protein product	"somatostatin-14", "somatostatin-28", "prepro-somatostatin"	182450				6126875, 6142531	Standard	NM_001048		Approved	SMST	uc003frn.3	P61278	OTTHUMG00000156462	ENST00000287641.3:c.37C>T	chr3.hg19:g.187388043G>A		131.0	0.0	2014	108.0	50.0	NM_001048	B2R5G3|P01166	Silent	SNP	ENST00000287641.3	hg19	CCDS3288.1																																																																																			.	.		0.677	SST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344278.1	NM_001048		A	187388043	G	A	187388043	2	1	263	1	0	0	0	0	0	0	0	1	15211	962	34	3		3	SST	3	187388043	Silent	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	3480673	187388043	10634387	85	38459										
KIAA1530	57654	hgsc.bcm.edu	37	chr4	1377635	1377635	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	atccaggtacagcgggaaagGcagggggaagaagaggaggt	19	5	0	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr4:1377635G>A	ENST00000389851.4	+	13	2390	c.1943G>A	c.(1942-1944)gGc>gAc	p.G648D	UVSSA_ENST00000512728.1_Missense_Mutation_p.G199D|UVSSA_ENST00000511563.1_Missense_Mutation_p.G199D|UVSSA_ENST00000507531.1_Missense_Mutation_p.G648D|UVSSA_ENST00000511216.1_Missense_Mutation_p.G648D	NM_020894.2	NP_065945.2	Q2YD98	UVSSA_HUMAN	UV-stimulated scaffold protein A	648					protein ubiquitination (GO:0016567)|response to UV (GO:0009411)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)	RNA polymerase II core binding (GO:0000993)	p.G648V(1)									AGCGGGAAAGGCAGGGGGAAG	0.572																																					p.G648D		Atlas-SNP	.											KIAA1530,NS,carcinoma,0,1	.	.	.	1	Substitution - Missense(1)	endometrium(1)	c.G1943A						.						113	98	103					4																	1377635		2203	4300	6503	SO:0001583	missense	57654	exon13			GGAAAGGCAGGGG	BC021930	CCDS33938.1	4p16.3	2012-04-27	2012-04-27	2012-04-27		ENSG00000163945			29304	protein-coding gene	gene with protein product		614632	"KIAA1530"	KIAA1530		10819331, 22466610, 22466611, 22466612	Standard	NM_020894		Approved		uc003gde.4	Q2YD98		ENST00000389851.4:c.1943G>A	chr4.hg19:g.1377635G>A	ENSP00000374501:p.Gly648Asp	64.0	0.0		48.0	24.0	NM_020894	A8K9E6|B2RU11|Q8WTX4|Q9P1Z8	Missense_Mutation	SNP	ENST00000389851.4	hg19	CCDS33938.1	.	.	.	.	.	.	.	.	.	.	G	10.14	1.268830	0.23136	.	.	ENSG00000163945	ENST00000511216;ENST00000389851;ENST00000507531;ENST00000511563;ENST00000512728	T;T;T;T;T	0.48201	1.38;1.38;1.38;0.82;0.82	5.04	4.2	0.49525	.	0.259729	0.43110	D	0.000620	T	0.44286	0.1286	L	0.52905	1.665	0.48975	D	0.999737	B	0.24768	0.111	B	0.22386	0.039	T	0.40251	-0.9573	10	0.48119	T	0.1	.	14.0277	0.64594	0.0743:0.0:0.9257:0.0	.	648	Q2YD98	K1530_HUMAN	D	648;648;648;199;199	ENSP00000425130:G648D;ENSP00000374501:G648D;ENSP00000421741:G648D;ENSP00000423340:G199D;ENSP00000427701:G199D	ENSP00000374501:G648D	G	+	2	0	KIAA1530	1367635	1.000000	0.71417	0.351000	0.25721	0.057000	0.15508	4.383000	0.59600	1.255000	0.44051	-0.272000	0.10252	GGC	.	.		0.572	UVSSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359480.1	NM_020894		A	1377635	G	A	1377635	3	1	263	1	0	0	0	0	1	0	0	0	8250	1203	42	3	1989	3	KIAA1530	4	1377635	Missense_Mutation	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10		1377635	189776641	86	38460										
RAB28	9364	hgsc.bcm.edu	37	chr4	13462450	13462450	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	atatcatataccaagaggacTccctgtcacaaaagagttac	6	10	2	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr4:13462450T>C	ENST00000330852.5	-	4	478	c.264A>G	c.(262-264)ggA>ggG	p.G88G	RAB28_ENST00000288723.4_Silent_p.G88G|RAB28_ENST00000338176.4_Silent_p.G88G	NM_001017979.2	NP_001017979.1	P51157	RAB28_HUMAN	RAB28, member RAS oncogene family	88					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	ciliary basal body (GO:0036064)|ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	8						CCAAGAGGACTCCCTGTCACA	0.333																																					p.G88G		Atlas-SNP	.											.	RAB28	56	.	0			c.A264G						.						50	53	52					4																	13462450		2203	4299	6502	SO:0001819	synonymous_variant	9364	exon4			GAGGACTCCCTGT	X94703	CCDS3409.1, CCDS33961.1, CCDS54741.1	4p16.1	2014-04-24			ENSG00000157869	ENSG00000157869		"RAB, member RAS oncogene"	9768	protein-coding gene	gene with protein product		612994				8647132	Standard	NM_004249		Approved		uc003gmu.2	P51157	OTTHUMG00000090543	ENST00000330852.5:c.264A>G	chr4.hg19:g.13462450T>C		63.0	0.0		104.0	5.0	NM_004249	G8JLC5|Q8IYR8|Q8NI05	Silent	SNP	ENST00000330852.5	hg19	CCDS33961.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	10.96|10.96	1.498836|1.498836	0.26861|0.26861	.|.	.|.	ENSG00000157869|ENSG00000157869	ENST00000510528|ENST00000511649	.|.	.|.	.|.	6.01|6.01	0.932|0.932	0.19466|0.19466	.|.	.|.	.|.	.|.	.|.	T|T	0.51193|0.51193	0.1660|0.1660	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.34625|0.34625	-0.9821|-0.9821	4|4	.|.	.|.	.|.	.|.	5.2801|5.2801	0.15670|0.15670	0.1447:0.278:0.0:0.5773|0.1447:0.278:0.0:0.5773	.|.	.|.	.|.	.|.	G|G	3|11	.|.	.|.	E|S	-|-	2|1	0|0	RAB28|RAB28	13071548|13071548	0.935000|0.935000	0.31712|0.31712	0.846000|0.846000	0.33378|0.33378	0.939000|0.939000	0.58152|0.58152	0.234000|0.234000	0.17930|0.17930	-0.037000|-0.037000	0.13646|0.13646	-0.263000|-0.263000	0.10527|0.10527	GAG|AGT	.	.		0.333	RAB28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207068.2	NM_001017979		C	13462450	T	C	13462450	2	2	263	1	0	0	0	0	0	0	0	1	12931	1538	54	2		2	RAB28	4	13462450	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	12084815	13462450	177691826	87	38461										
RBM47	54502	hgsc.bcm.edu	37	chr4	40440472	40440472	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gaggcggcagttgtccacgcTgcagcacacgccgagcaggc	15	14	0	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr4:40440472T>C	ENST00000381793.2	-	3	835	c.439A>G	c.(439-441)Agc>Ggc	p.S147G	RBM47_ENST00000381795.6_Missense_Mutation_p.S147G|RBM47_ENST00000514014.1_Missense_Mutation_p.S109G|RBM47_ENST00000295971.7_Missense_Mutation_p.S147G|RBM47_ENST00000319592.4_Missense_Mutation_p.S147G|RBM47_ENST00000515809.1_Intron			A0AV96	RBM47_HUMAN	RNA binding motif protein 47	147	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				hematopoietic progenitor cell differentiation (GO:0002244)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(5)|endometrium(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	29						TTGTCCACGCTGCAGCACACG	0.632																																					p.S147G		Atlas-SNP	.											.	RBM47	146	.	0			c.A439G						.						43	39	40					4																	40440472		2203	4298	6501	SO:0001583	missense	54502	exon4			CCACGCTGCAGCA	AK000280	CCDS3460.1, CCDS43223.1	4p14	2013-02-12			ENSG00000163694	ENSG00000163694		"RNA binding motif (RRM) containing"	30358	protein-coding gene	gene with protein product							Standard	NM_019027		Approved	FLJ20273, NET18	uc003gvc.2	A0AV96	OTTHUMG00000128598	ENST00000381793.2:c.439A>G	chr4.hg19:g.40440472T>C	ENSP00000371212:p.Ser147Gly	96.0	0.0		95.0	4.0	NM_001098634	A0PJK2|B5MED4|Q8NI52|Q8NI53|Q9NXG3	Missense_Mutation	SNP	ENST00000381793.2	hg19	CCDS43223.1	.	.	.	.	.	.	.	.	.	.	T	16.19	3.052161	0.55218	.	.	ENSG00000163694	ENST00000319592;ENST00000381793;ENST00000381795;ENST00000295971;ENST00000514014;ENST00000515053;ENST00000513473;ENST00000505414	T;T;T;T;T;T;T;T	0.29397	3.25;1.86;3.25;1.86;1.9;3.25;1.57;1.66	5.47	5.47	0.80525	.	0.079254	0.85682	D	0.000000	T	0.59155	0.2173	M	0.82323	2.585	0.80722	D	1	P;D	0.58268	0.937;0.982	D;D	0.70227	0.931;0.968	T	0.65734	-0.6096	10	0.87932	D	0	-29.2544	15.5455	0.76097	0.0:0.0:0.0:1.0	.	147;147	A0AV96-2;A0AV96	.;RBM47_HUMAN	G	147;147;147;147;109;147;147;147	ENSP00000320108:S147G;ENSP00000371212:S147G;ENSP00000371214:S147G;ENSP00000295971:S147G;ENSP00000423243:S109G;ENSP00000422564:S147G;ENSP00000421589:S147G;ENSP00000423527:S147G	ENSP00000295971:S147G	S	-	1	0	RBM47	40135229	1.000000	0.71417	1.000000	0.80357	0.348000	0.29142	4.286000	0.58995	2.080000	0.62538	0.260000	0.18958	AGC	.	.		0.632	RBM47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250456.2	NM_019027		C	40440472	T	C	40440472	3	2	263	1	0	0	0	0	1	0	0	0	13156	1580	55	2	1358	2	RBM47	4	40440472	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	26978022	40440472	150713804	88	38462										
NFXL1	152518	hgsc.bcm.edu	37	chr4	47916121	47916121	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ccccttctctcgccctcctcCggcgccgcggagatggactc	10	20	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr4:47916121C>T	ENST00000507489.1	-	2	276	c.100G>A	c.(100-102)Gga>Aga	p.G34R	NFXL1_ENST00000381538.3_Missense_Mutation_p.G34R|NFXL1_ENST00000329043.3_Missense_Mutation_p.G34R	NM_001278624.1	NP_001265553.1	Q6ZNB6	NFXL1_HUMAN	nuclear transcription factor, X-box binding-like 1	34						integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(4)	27						CGCCCTCCTCCGGCGCCGCGG	0.726																																					p.G34R		Atlas-SNP	.											.	NFXL1	79	.	0			c.G100A						.						7	10	9					4																	47916121		2141	4184	6325	SO:0001583	missense	152518	exon2			CTCCTCCGGCGCC	AY134856	CCDS3478.2	4p12	2008-02-05			ENSG00000170448	ENSG00000170448			18726	protein-coding gene	gene with protein product	"ovarian zinc finger protein"						Standard	NM_152995		Approved	HOZFP	uc003gxp.3	Q6ZNB6	OTTHUMG00000128621	ENST00000507489.1:c.100G>A	chr4.hg19:g.47916121C>T	ENSP00000422037:p.Gly34Arg	89.0	0.0		37.0	15.0	NM_152995	B1Q2K1|Q86VG1|Q8WVH1	Missense_Mutation	SNP	ENST00000507489.1	hg19	CCDS3478.2	.	.	.	.	.	.	.	.	.	.	C	26.1	4.705928	0.89018	.	.	ENSG00000170448	ENST00000381538;ENST00000507489;ENST00000329043	T;T;T	0.23950	1.9;1.9;1.88	4.32	4.32	0.51571	.	0.382466	0.19009	N	0.125132	T	0.29684	0.0741	L	0.50333	1.59	0.39457	D	0.967506	P	0.49862	0.929	P	0.45971	0.499	T	0.10917	-1.0609	10	0.45353	T	0.12	-13.028	13.5399	0.61668	0.0:1.0:0.0:0.0	.	34	Q6ZNB6	NFXL1_HUMAN	R	34	ENSP00000370949:G34R;ENSP00000422037:G34R;ENSP00000333113:G34R	ENSP00000333113:G34R	G	-	1	0	NFXL1	47610878	0.903000	0.30736	0.988000	0.46212	0.969000	0.65631	1.368000	0.34216	1.949000	0.56562	0.484000	0.47621	GGA	.	.		0.726	NFXL1-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361636.1	NM_152995		T	47916121	C	T	47916121	3	4	263	1	0	0	0	0	1	0	0	0	10397	661	23	1	2723	1	NFXL1	4	47916121	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	7475649	47916121	143238155	89	38463										
SRP72	6731	hgsc.bcm.edu	37	chr4	57340266	57340277	+	In_Frame_Del	DEL	ATCTCGTCCGAA	ATCTCGTCCGAA	-													0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	atgcttagcagtgtatagagAtctcgtccgaaactcccaag					rs201653221|rs145817936		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	ATCTCGTCCGAA	ATCTCGTCCGAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr4:57340266_57340277delATCTCGTCCGAA	ENST00000342756.5	+	4	1122_1133	c.401_412delATCTCGTCCGAA	c.(400-414)gatctcgtccgaaac>gac	p.LVRN135del	SRP72_ENST00000510663.1_In_Frame_Del_p.LVRN135del|SRP72_ENST00000504757.1_In_Frame_Del_p.LVRN135del	NM_006947.3	NP_008878.3	O76094	SRP72_HUMAN	signal recognition particle 72kDa	135					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)			breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|liver(2)|lung(7)|ovary(2)	22	Glioma(25;0.08)|all_neural(26;0.101)					GTGTATAGAGATCTCGTCCGAAACTCCCAAGA	0.377																																					p.134_137del		Atlas-Indel,Pindel	.											.	SRP72	59	.	0			c.400_411del						.																																			SO:0001651	inframe_deletion	6731	exon4			.	AF069765	CCDS3506.1, CCDS58898.1	4q11	2013-01-10	2002-08-29		ENSG00000174780	ENSG00000174780		"Tetratricopeptide (TTC) repeat domain containing"	11303	protein-coding gene	gene with protein product		602122	"signal recognition particle 72kD"			9224693, 9857079	Standard	NM_006947		Approved		uc003hbv.3	O76094	OTTHUMG00000128843	ENST00000342756.5:c.401_412delATCTCGTCCGAA	chr4.hg19:g.57340266_57340277delATCTCGTCCGAA	ENSP00000342181:p.Leu135_Asn138del	124.0	0.0		122.0	20.0	NM_001267722	G5E9Z8|Q7Z3C0	In_Frame_Del	DEL	ENST00000342756.5	hg19	CCDS3506.1																																																																																			.	.		0.377	SRP72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250782.7			-	57340277	ATCTCGTCCGAA	-	57340266	7	5	263	1	0	1	0	1	0	0	0	0	15172	333	12	0	415	0	SRP72	4	57340266	In_Frame_Del	DEL	ATCTCGTCCGAA	TCGA-FV-A2QR-01A-11D-A20W-10	9424145	57340266	133814010	90	38464										
SRP72	6731	hgsc.bcm.edu	37	chr4	57340277	57340277	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tgtatagagatctcgtccgaAactcccaagatgattatgat	8	8	1	4			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr4:57340277A>G	ENST00000342756.5	+	4	1133	c.412A>G	c.(412-414)Aac>Gac	p.N138D	SRP72_ENST00000510663.1_Missense_Mutation_p.N138D|SRP72_ENST00000504757.1_Missense_Mutation_p.N138D	NM_006947.3	NP_008878.3	O76094	SRP72_HUMAN	signal recognition particle 72kDa	138					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)			breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|liver(2)|lung(7)|ovary(2)	22	Glioma(25;0.08)|all_neural(26;0.101)					TCTCGTCCGAAACTCCCAAGA	0.383																																					p.N138D		Atlas-SNP	.											.	SRP72	59	.	0			c.A412G						.						96	92	93					4																	57340277		2203	4300	6503	SO:0001583	missense	6731	exon4			GTCCGAAACTCCC	AF069765	CCDS3506.1, CCDS58898.1	4q11	2013-01-10	2002-08-29		ENSG00000174780	ENSG00000174780		"Tetratricopeptide (TTC) repeat domain containing"	11303	protein-coding gene	gene with protein product		602122	"signal recognition particle 72kD"			9224693, 9857079	Standard	NM_006947		Approved		uc003hbv.3	O76094	OTTHUMG00000128843	ENST00000342756.5:c.412A>G	chr4.hg19:g.57340277A>G	ENSP00000342181:p.Asn138Asp	128.0	0.0		106.0	13.0	NM_006947	G5E9Z8|Q7Z3C0	Missense_Mutation	SNP	ENST00000342756.5	hg19	CCDS3506.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.687896	0.88639	.	.	ENSG00000174780	ENST00000342756;ENST00000537129;ENST00000510663	T;T	0.37584	1.19;1.19	5.35	5.35	0.76521	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.50684	0.1630	L	0.55017	1.72	0.80722	D	1	D;D	0.76494	0.999;0.997	D;P	0.76071	0.987;0.89	T	0.43212	-0.9405	10	0.12103	T	0.63	.	13.2961	0.60298	1.0:0.0:0.0:0.0	.	138;138	G5E9Z8;O76094	.;SRP72_HUMAN	D	138;144;138	ENSP00000342181:N138D;ENSP00000424576:N138D	ENSP00000342181:N138D	N	+	1	0	SRP72	57035034	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.339000	0.96797	2.023000	0.59567	0.528000	0.53228	AAC	.	.		0.383	SRP72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250782.7			G	57340277	A	G	57340277	3	3	263	1	0	0	0	0	1	0	0	0	15172	14	1	2	426	2	SRP72	4	57340277	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	11	57340277	133813999	91	38465										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79367953	79367953	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tgagctcgggagtggtgataAgcaattcttctttgagcctg	13	7	2	3			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr4:79367953A>C	ENST00000264895.6	+	43	6369	c.5929A>C	c.(5929-5931)Agc>Cgc	p.S1977R		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	1977					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						AGTGGTGATAAGCAATTCTTC	0.478																																					p.S1977R		Atlas-SNP	.											.	FRAS1	779	.	0			c.A5929C						.						69	72	71					4																	79367953		1972	4174	6146	SO:0001583	missense	80144	exon43			GTGATAAGCAATT	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.5929A>C	chr4.hg19:g.79367953A>C	ENSP00000264895:p.Ser1977Arg	108.0	0.0		125.0	5.0	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000264895.6	hg19	CCDS54771.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.38|10.38	1.334963|1.334963	0.24253|0.24253	.|.	.|.	ENSG00000138759|ENSG00000138759	ENST00000512123|ENST00000264895	.|T	.|0.30182	.|1.54	5.57|5.57	4.32|4.32	0.51571|0.51571	.|.	.|0.182279	.|0.49916	.|D	.|0.000121	T|T	0.20047|0.20047	0.0482|0.0482	N|N	0.22421|0.22421	0.69|0.69	0.80722|0.80722	D|D	1|1	.|B	.|0.13145	.|0.007	.|B	.|0.09377	.|0.004	T|T	0.04579|0.04579	-1.0941|-1.0941	5|10	.|0.31617	.|T	.|0.26	.|.	11.306|11.306	0.49336|0.49336	0.7198:0.2802:0.0:0.0|0.7198:0.2802:0.0:0.0	.|.	.|1977	.|E9PHH6	.|.	T|R	205|1977	.|ENSP00000264895:S1977R	.|ENSP00000264895:S1977R	K|S	+|+	2|1	0|0	FRAS1|FRAS1	79586977|79586977	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.049000|0.049000	0.14656|0.14656	4.511000|4.511000	0.60462|0.60462	2.133000|2.133000	0.65898|0.65898	0.528000|0.528000	0.53228|0.53228	AAG|AGC	.	.		0.478	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	79367953	A	C	79367953	3	2	263	1	0	0	0	0	1	0	0	0	6050	72	3	5	6174	5	FRAS1	4	79367953	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	22027676	79367953	111786323	92	38466										
PKD2	5311	hgsc.bcm.edu	37	chr4	88940628	88940628	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	aggtctctggggaacaagacTcatggaggaaagcagcacta	13	8	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr4:88940628T>C	ENST00000237596.2	+	2	680	c.614T>C	c.(613-615)cTc>cCc	p.L205P		NM_000297.3	NP_000288.1	Q9BZL6	KPCD2_HUMAN	polycystic kidney disease 2 (autosomal dominant)	0					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial tube morphogenesis (GO:0061154)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(2)|lung(15)|skin(4)|upper_aerodigestive_tract(1)	36		Hepatocellular(203;0.114)|Acute lymphoblastic leukemia(40;0.221)		OV - Ovarian serous cystadenocarcinoma(123;9.98e-10)|COAD - Colon adenocarcinoma(81;0.0237)		GGAACAAGACTCATGGAGGAA	0.353																																					p.L205P		Atlas-SNP	.											.	PKD2	82	.	0			c.T614C						.						85	82	83					4																	88940628		2203	4300	6503	SO:0001583	missense	5311	exon2			CAAGACTCATGGA	U50928	CCDS3627.1	4q22.1	2014-01-28			ENSG00000118762	ENSG00000118762		"Voltage-gated ion channels / Transient receptor potential cation channels", "EF-hand domain containing"	9009	protein-coding gene	gene with protein product	"transient receptor potential cation channel, subfamily P, member 2"	173910				8298643	Standard	NM_000297		Approved	PKD4, PC2, Pc-2, TRPP2	uc003hre.3	Q13563	OTTHUMG00000160982	ENST00000237596.2:c.614T>C	chr4.hg19:g.88940628T>C	ENSP00000237596:p.Leu205Pro	44.0	0.0		61.0	4.0	NM_000297	Q8TB08|Q9P0T6|Q9Y3X8	Missense_Mutation	SNP	ENST00000237596.2	hg19	CCDS3627.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.175702	0.78564	.	.	ENSG00000118762	ENST00000237596	T	0.71103	-0.54	5.9	5.9	0.94986	.	0.146176	0.47852	D	0.000220	T	0.79299	0.4422	M	0.77103	2.36	0.80722	D	1	D	0.60575	0.988	P	0.52514	0.701	T	0.82123	-0.0613	10	0.62326	D	0.03	-12.3317	14.562	0.68148	0.0:0.0:0.0:1.0	.	205	Q13563	PKD2_HUMAN	P	205	ENSP00000237596:L205P	ENSP00000237596:L205P	L	+	2	0	PKD2	89159652	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.669000	0.68081	2.251000	0.74343	0.528000	0.53228	CTC	.	.		0.353	PKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253042.4	NM_000297		C	88940628	T	C	88940628	3	2	263	1	0	0	0	0	1	0	0	0	11975	1551	54	2	620	2	PKD2	4	88940628	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	9572675	88940628	102213648	93	38467										
GPRIN3	285513	hgsc.bcm.edu	37	chr4	90170576	90170576	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tacaggacctcatttcagagTcacagatggctccctgcctt	8	13	3	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr4:90170576T>C	ENST00000609438.1	-	2	1204	c.686A>G	c.(685-687)gAc>gGc	p.D229G	GPRIN3_ENST00000333209.4_Missense_Mutation_p.D229G	NM_198281.2	NP_938022.2	Q6ZVF9	GRIN3_HUMAN	GPRIN family member 3	229										breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|prostate(2)|skin(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;5.67e-05)		CATTTCAGAGTCACAGATGGC	0.547																																					p.D229G		Atlas-SNP	.											.	GPRIN3	90	.	0			c.A686G						.						50	53	52					4																	90170576		2203	4300	6503	SO:0001583	missense	285513	exon2			TCAGAGTCACAGA	AK124616	CCDS34030.1	4q22.1	2006-08-24				ENSG00000185477			27733	protein-coding gene	gene with protein product		611241				15488195	Standard	NM_198281		Approved	GRIN3, FLJ42625	uc003hsm.1	Q6ZVF9		ENST00000609438.1:c.686A>G	chr4.hg19:g.90170576T>C	ENSP00000476603:p.Asp229Gly	65.0	0.0		78.0	4.0	NM_198281	Q8IVE4	Missense_Mutation	SNP	ENST00000609438.1	hg19	CCDS34030.1	.	.	.	.	.	.	.	.	.	.	T	10.75	1.438998	0.25900	.	.	ENSG00000185477	ENST00000333209	T	0.12147	2.71	4.93	-0.481	0.12082	.	1.634920	0.04032	N	0.301571	T	0.06826	0.0174	N	0.14661	0.345	0.09310	N	1	B	0.11235	0.004	B	0.11329	0.006	T	0.31724	-0.9933	10	0.13108	T	0.6	-5.0277	1.5259	0.02525	0.129:0.2131:0.1336:0.5243	.	229	Q6ZVF9	GRIN3_HUMAN	G	229	ENSP00000328672:D229G	ENSP00000328672:D229G	D	-	2	0	GPRIN3	90389599	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	0.156000	0.16382	-0.119000	0.11830	0.528000	0.53228	GAC	.	.		0.547	GPRIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363540.2	NM_198281		C	90170576	T	C	90170576	3	2	263	1	0	0	0	0	1	0	0	0	6740	1667	58	2	1648	2	GPRIN3	4	90170576	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	1229948	90170576	100983700	94	38468										
PPP3CA	5530	hgsc.bcm.edu	37	chr4	101982264	101982264	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	catcaaatccatcttcttctGaccctagttcatcatctgag	4	13	7	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr4:101982264G>A	ENST00000394854.3	-	10	1819	c.1136C>T	c.(1135-1137)tCa>tTa	p.S379L	PPP3CA_ENST00000323055.6_Missense_Mutation_p.S337L|PPP3CA_ENST00000523694.2_Missense_Mutation_p.S312L|PPP3CA_ENST00000507176.1_Missense_Mutation_p.S281L|PPP3CA_ENST00000394853.4_Missense_Mutation_p.S379L|PPP3CA_ENST00000512215.1_Missense_Mutation_p.S147L	NM_000944.4	NP_000935.1	Q08209	PP2BA_HUMAN	protein phosphatase 3, catalytic subunit, alpha isozyme	379					calcineurin-NFAT signaling cascade (GO:0033173)|calcium ion transport (GO:0006816)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|dephosphorylation (GO:0016311)|Fc-epsilon receptor signaling pathway (GO:0038095)|G1/S transition of mitotic cell cycle (GO:0000082)|innate immune response (GO:0045087)|multicellular organismal response to stress (GO:0033555)|negative regulation of insulin secretion (GO:0046676)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein dephosphorylation (GO:0006470)|protein import into nucleus (GO:0006606)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic transmission (GO:0050804)|response to amphetamine (GO:0001975)|response to calcium ion (GO:0051592)|skeletal muscle fiber development (GO:0048741)|T cell activation (GO:0042110)|transition between fast and slow fiber (GO:0014883)	calcineurin complex (GO:0005955)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|calmodulin-dependent protein phosphatase activity (GO:0033192)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|protein dimerization activity (GO:0046983)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	20				OV - Ovarian serous cystadenocarcinoma(123;6.79e-08)		ATCTTCTTCTGACCCTAGTTC	0.368																																					p.S379L		Atlas-SNP	.											.	PPP3CA	51	.	0			c.C1136T						.						128	121	123					4																	101982264		2203	4300	6503	SO:0001583	missense	5530	exon10			TCTTCTGACCCTA		CCDS34037.1, CCDS47113.1, CCDS47114.1	4q24	2010-03-17	2010-03-05		ENSG00000138814	ENSG00000138814	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9314	protein-coding gene	gene with protein product	"calcineurin A alpha", "protein phosphatase 2B, catalytic subunit, alpha isoform"	114105	"protein phosphatase 3 (formerly 2B), catalytic subunit, alpha isoform (calcineurin A alpha)", "protein phosphatase 3 (formerly 2B), catalytic subunit, alpha isoform"	CALN, CALNA		2848250, 1659808	Standard	NM_000944		Approved	CNA1, PPP2B	uc011cen.1	Q08209	OTTHUMG00000133839	ENST00000394854.3:c.1136C>T	chr4.hg19:g.101982264G>A	ENSP00000378323:p.Ser379Leu	424.0	0.0		405.0	86.0	NM_000944	A1A441|A8K3B7|A8W6Z7|A8W6Z8|B5BUA2|Q8TAW9	Missense_Mutation	SNP	ENST00000394854.3	hg19	CCDS34037.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.222758	0.79464	.	.	ENSG00000138814	ENST00000512215;ENST00000394854;ENST00000323055;ENST00000394853;ENST00000507176;ENST00000523694	T;T;T;T;T;T	0.05717	3.4;3.4;3.4;3.4;3.4;3.4	5.34	5.34	0.76211	.	0.312988	0.31031	N	0.008391	T	0.06005	0.0156	N	0.17474	0.49	0.58432	D	0.999998	B;B;B;B;B;B	0.23058	0.0;0.079;0.001;0.001;0.0;0.0	B;B;B;B;B;B	0.18263	0.001;0.021;0.002;0.005;0.001;0.001	T	0.44329	-0.9335	10	0.38643	T	0.18	-10.1385	19.0616	0.93095	0.0:0.0:1.0:0.0	.	379;147;337;379;281;312	Q08209;A8W6Z8;A8W6Z7;Q08209-2;E7ETC2;A1A441	PP2BA_HUMAN;.;.;.;.;.	L	147;379;337;379;281;312	ENSP00000422781:S147L;ENSP00000378323:S379L;ENSP00000320580:S337L;ENSP00000378322:S379L;ENSP00000422990:S281L;ENSP00000429350:S312L	ENSP00000320580:S337L	S	-	2	0	PPP3CA	102201287	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.327000	0.72910	2.499000	0.84300	0.591000	0.81541	TCA	.	.		0.368	PPP3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258379.2	NM_000944		A	101982264	G	A	101982264	3	1	263	1	0	0	0	0	1	0	0	0	12409	1294	45	3	449	3	PPP3CA	4	101982264	Missense_Mutation	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	11811688	101982264	89172012	95	38469										
PPP3CA	5530	hgsc.bcm.edu	37	chr4	102030182	102030182	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	agtgttggcaggagatccccCgacttcaaagagcttcatca	10	11	3	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr4:102030182C>T	ENST00000394854.3	-	3	996	c.313G>A	c.(313-315)Ggg>Agg	p.G105R	PPP3CA_ENST00000323055.6_Missense_Mutation_p.G105R|PPP3CA_ENST00000523694.2_Missense_Mutation_p.G38R|PPP3CA_ENST00000507176.1_Missense_Mutation_p.G7R|PPP3CA_ENST00000394853.4_Missense_Mutation_p.G105R|PPP3CA_ENST00000512215.1_Intron|PPP3CA_ENST00000510292.1_5'UTR	NM_000944.4	NP_000935.1	Q08209	PP2BA_HUMAN	protein phosphatase 3, catalytic subunit, alpha isozyme	105	Catalytic.				calcineurin-NFAT signaling cascade (GO:0033173)|calcium ion transport (GO:0006816)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|dephosphorylation (GO:0016311)|Fc-epsilon receptor signaling pathway (GO:0038095)|G1/S transition of mitotic cell cycle (GO:0000082)|innate immune response (GO:0045087)|multicellular organismal response to stress (GO:0033555)|negative regulation of insulin secretion (GO:0046676)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein dephosphorylation (GO:0006470)|protein import into nucleus (GO:0006606)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic transmission (GO:0050804)|response to amphetamine (GO:0001975)|response to calcium ion (GO:0051592)|skeletal muscle fiber development (GO:0048741)|T cell activation (GO:0042110)|transition between fast and slow fiber (GO:0014883)	calcineurin complex (GO:0005955)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|calmodulin-dependent protein phosphatase activity (GO:0033192)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|protein dimerization activity (GO:0046983)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	20				OV - Ovarian serous cystadenocarcinoma(123;6.79e-08)		GGAGATCCCCCGACTTCAAAG	0.393																																					p.G105R		Atlas-SNP	.											.	PPP3CA	51	.	0			c.G313A						.						87	82	83					4																	102030182		2203	4300	6503	SO:0001583	missense	5530	exon3			ATCCCCCGACTTC		CCDS34037.1, CCDS47113.1, CCDS47114.1	4q24	2010-03-17	2010-03-05		ENSG00000138814	ENSG00000138814	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9314	protein-coding gene	gene with protein product	"calcineurin A alpha", "protein phosphatase 2B, catalytic subunit, alpha isoform"	114105	"protein phosphatase 3 (formerly 2B), catalytic subunit, alpha isoform (calcineurin A alpha)", "protein phosphatase 3 (formerly 2B), catalytic subunit, alpha isoform"	CALN, CALNA		2848250, 1659808	Standard	NM_000944		Approved	CNA1, PPP2B	uc011cen.1	Q08209	OTTHUMG00000133839	ENST00000394854.3:c.313G>A	chr4.hg19:g.102030182C>T	ENSP00000378323:p.Gly105Arg	76.0	0.0		86.0	4.0	NM_000944	A1A441|A8K3B7|A8W6Z7|A8W6Z8|B5BUA2|Q8TAW9	Missense_Mutation	SNP	ENST00000394854.3	hg19	CCDS34037.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.935218	0.92458	.	.	ENSG00000138814	ENST00000394854;ENST00000323055;ENST00000394853;ENST00000507176;ENST00000523694;ENST00000529324;ENST00000525819	T;T;T;T;T;T;T	0.68765	-0.35;-0.35;-0.35;3.39;3.39;-0.35;-0.35	4.93	4.93	0.64822	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (2);Metallophosphoesterase domain (1);	0.000000	0.85682	D	0.000000	D	0.88009	0.6322	H	0.96460	3.825	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;0.998;1.0;1.0	D;D;P;D;D	0.97110	0.999;1.0;0.825;1.0;0.998	D	0.92027	0.5630	10	0.87932	D	0	-13.7346	18.5379	0.91017	0.0:1.0:0.0:0.0	.	105;105;105;7;38	Q08209;A8W6Z7;Q08209-2;E7ETC2;A1A441	PP2BA_HUMAN;.;.;.;.	R	105;105;105;7;38;55;55	ENSP00000378323:G105R;ENSP00000320580:G105R;ENSP00000378322:G105R;ENSP00000422990:G7R;ENSP00000429350:G38R;ENSP00000431619:G55R;ENSP00000434599:G55R	ENSP00000320580:G105R	G	-	1	0	PPP3CA	102249205	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.538000	0.82048	2.423000	0.82170	0.650000	0.86243	GGG	.	.		0.393	PPP3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258379.2	NM_000944		T	102030182	C	T	102030182	3	4	263	1	0	0	0	0	1	0	0	0	12409	652	23	1	1300	1	PPP3CA	4	102030182	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	47918	102030182	89124094	96	38470										
BANK1	55024	hgsc.bcm.edu	37	chr4	102783739	102783739	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gtaattggtgatactgtagaGgttgaatttacatcaagtaa	10	3	1	3			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr4:102783739G>T	ENST00000322953.4	+	4	955	c.681G>T	c.(679-681)gaG>gaT	p.E227D	BANK1_ENST00000444316.2_Missense_Mutation_p.E197D|BANK1_ENST00000428908.1_Missense_Mutation_p.E94D|BANK1_ENST00000508653.1_Missense_Mutation_p.E94D|BANK1_ENST00000504592.1_Missense_Mutation_p.E212D	NM_017935.4	NP_060405	Q8NDB2	BANK1_HUMAN	B-cell scaffold protein with ankyrin repeats 1	227	DBB. {ECO:0000255|PROSITE- ProRule:PRU00707}.				B cell activation (GO:0042113)					NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|liver(2)|lung(16)|ovary(2)|skin(2)|urinary_tract(1)	44		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)		ATACTGTAGAGGTTGAATTTA	0.338																																					p.E227D		Atlas-SNP	.											.	BANK1	95	.	0			c.G681T						.						80	80	80					4																	102783739		2203	4299	6502	SO:0001583	missense	55024	exon4			TGTAGAGGTTGAA	AB063170	CCDS34038.1, CCDS47115.1, CCDS47116.1	4q23	2013-01-11						"Ankyrin repeat domain containing"	18233	protein-coding gene	gene with protein product		610292				11782428, 21208380, 21480188	Standard	NM_017935		Approved	BANK, FLJ20706	uc003hvy.4	Q8NDB2		ENST00000322953.4:c.681G>T	chr4.hg19:g.102783739G>T	ENSP00000320509:p.Glu227Asp	144.0	0.0		187.0	73.0	NM_017935	A8K7W8|B0F3S2|Q8N5K8|Q8NB56|Q8WYN5|Q9NWP2	Missense_Mutation	SNP	ENST00000322953.4	hg19	CCDS34038.1	.	.	.	.	.	.	.	.	.	.	G	15.94	2.980235	0.53827	.	.	ENSG00000153064	ENST00000504592;ENST00000322953;ENST00000428908;ENST00000508653;ENST00000444316	T;T;T;T;T	0.27104	2.41;2.41;1.69;1.69;2.42	5.14	1.94	0.25998	DBB domain (1);	0.000000	0.64402	D	0.000005	T	0.42291	0.1196	M	0.65975	2.015	0.25299	N	0.989295	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.80764	0.994;0.991;0.991	T	0.11397	-1.0589	10	0.49607	T	0.09	.	7.3529	0.26703	0.3815:0.0:0.6185:0.0	.	94;227;212	Q8NDB2-4;Q8NDB2;Q8NDB2-2	.;BANK1_HUMAN;.	D	212;227;94;94;197	ENSP00000421443:E212D;ENSP00000320509:E227D;ENSP00000412748:E94D;ENSP00000422314:E94D;ENSP00000388817:E197D	ENSP00000320509:E227D	E	+	3	2	BANK1	103002762	0.926000	0.31397	0.984000	0.44739	0.689000	0.40095	-0.093000	0.11111	0.527000	0.28560	0.585000	0.79938	GAG	.	.		0.338	BANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363161.1	NM_017935		T	102783739	G	T	102783739	3	4	263	1	0	0	0	0	1	0	0	0	1309	991	35	3	695	3	BANK1	4	102783739	Missense_Mutation	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	753557	102783739	88370537	97	38471										
SYNPO2	171024	hgsc.bcm.edu	37	chr4	119947966	119947966	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ccctagctgagaaccaaagaAgtggtcccgactgtgcaggc	12	12	0	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr4:119947966A>G	ENST00000429713.2	+	3	624	c.442A>G	c.(442-444)Agt>Ggt	p.S148G	SYNPO2_ENST00000307142.4_Missense_Mutation_p.S148G|SYNPO2_ENST00000448416.2_Intron|SYNPO2_ENST00000434046.2_Missense_Mutation_p.S148G	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	148						actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|Z disc (GO:0030018)	14-3-3 protein binding (GO:0071889)|muscle alpha-actinin binding (GO:0051371)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						GAACCAAAGAAGTGGTCCCGA	0.552																																					p.S148G		Atlas-SNP	.											.	SYNPO2	353	.	0			c.A442G						.						42	43	43					4																	119947966		2203	4300	6503	SO:0001583	missense	171024	exon3			CAAAGAAGTGGTC	AJ010482	CCDS34054.1, CCDS47128.1, CCDS47129.1, CCDS75185.1, CCDS75186.1	4q26	2008-08-29			ENSG00000172403	ENSG00000172403			17732	protein-coding gene	gene with protein product						11673475, 17828378	Standard	NM_133477		Approved	MYOPODIN	uc010inb.3	Q9UMS6	OTTHUMG00000161165	ENST00000429713.2:c.442A>G	chr4.hg19:g.119947966A>G	ENSP00000395143:p.Ser148Gly	77.0	0.0		77.0	6.0	NM_001128934	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Missense_Mutation	SNP	ENST00000429713.2	hg19	CCDS47129.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.306|9.306	1.054287|1.054287	0.19907|0.19907	.|.	.|.	ENSG00000172403|ENSG00000172403	ENST00000504178|ENST00000307142;ENST00000429713;ENST00000434046	.|T;T;T	.|0.09538	.|2.97;2.99;2.98	5.51|5.51	4.31|4.31	0.51392|0.51392	.|.	.|0.197914	.|0.35349	.|N	.|0.003278	T|T	0.12561|0.12561	0.0305|0.0305	L|L	0.54323|0.54323	1.7|1.7	0.25522|0.25522	N|N	0.987354|0.987354	.|B;B;B;B	.|0.20261	.|0.043;0.003;0.043;0.043	.|B;B;B;B	.|0.19391	.|0.025;0.006;0.025;0.025	T|T	0.13176|0.13176	-1.0519|-1.0519	5|10	.|0.49607	.|T	.|0.09	-0.5522|-0.5522	11.3767|11.3767	0.49733|0.49733	0.8483:0.1517:0.0:0.0|0.8483:0.1517:0.0:0.0	.|.	.|148;148;148;148	.|B9EG60;Q9UMS6-2;E9PEM2;Q9UMS6	.|.;.;.;SYNP2_HUMAN	R|G	99|148	.|ENSP00000306015:S148G;ENSP00000395143:S148G;ENSP00000390965:S148G	.|ENSP00000306015:S148G	K|S	+|+	2|1	0|0	SYNPO2|SYNPO2	120167414|120167414	0.005000|0.005000	0.15991|0.15991	0.001000|0.001000	0.08648|0.08648	0.328000|0.328000	0.28507|0.28507	0.963000|0.963000	0.29293|0.29293	0.897000|0.897000	0.36392|0.36392	0.455000|0.455000	0.32223|0.32223	AAG|AGT	.	.		0.552	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1			G	119947966	A	G	119947966	3	3	263	1	0	0	0	0	1	0	0	0	15472	72	3	2	452	2	SYNPO2	4	119947966	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	17164227	119947966	71206310	98	38472										
HSPA4L	22824	hgsc.bcm.edu	37	chr4	128724944	128724944	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ggaatgtgaaaaactaaagaAgctaatgagtgcaaatgcat	10	4	0	3			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr4:128724944A>G	ENST00000296464.4	+	7	1235	c.824A>G	c.(823-825)aAg>aGg	p.K275R	HSPA4L_ENST00000505726.1_Missense_Mutation_p.K249R|HSPA4L_ENST00000508776.1_Missense_Mutation_p.K275R|HSPA4L_ENST00000439123.2_Missense_Mutation_p.K306R	NM_014278.2	NP_055093.2	O95757	HS74L_HUMAN	heat shock 70kDa protein 4-like	275					protein folding (GO:0006457)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)			central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						AAACTAAAGAAGCTAATGAGT	0.353																																					p.K275R		Atlas-SNP	.											.	HSPA4L	82	.	0			c.A824G						.						82	85	84					4																	128724944		2203	4300	6503	SO:0001583	missense	22824	exon7			TAAAGAAGCTAAT	AB023421	CCDS3734.1	4q28	2011-09-07			ENSG00000164070	ENSG00000164070		"Heat shock proteins / HSP70"	17041	protein-coding gene	gene with protein product						10524232	Standard	NM_014278		Approved	APG-1, Osp94, HSPH3	uc003ifm.3	O95757	OTTHUMG00000133302	ENST00000296464.4:c.824A>G	chr4.hg19:g.128724944A>G	ENSP00000296464:p.Lys275Arg	111.0	0.0		99.0	4.0	NM_014278	A2ICT2|Q4W5M5|Q8IWA2	Missense_Mutation	SNP	ENST00000296464.4	hg19	CCDS3734.1	.	.	.	.	.	.	.	.	.	.	A	27.9	4.869552	0.91587	.	.	ENSG00000164070	ENST00000508776;ENST00000439123;ENST00000296464;ENST00000508549;ENST00000505726	T;T;T;T;T	0.28895	1.59;1.59;1.59;1.59;1.59	4.87	4.87	0.63330	.	0.000000	0.85682	D	0.000000	T	0.36441	0.0967	N	0.12422	0.21	0.58432	D	0.999999	P;D;D	0.76494	0.584;0.999;0.999	P;D;D	0.81914	0.539;0.995;0.995	T	0.32079	-0.9920	10	0.40728	T	0.16	.	14.6317	0.68660	1.0:0.0:0.0:0.0	.	249;275;275	E9PDE8;A2ICT2;O95757	.;.;HS74L_HUMAN	R	275;306;275;234;249	ENSP00000422482:K275R;ENSP00000393926:K306R;ENSP00000296464:K275R;ENSP00000427305:K234R;ENSP00000425645:K249R	ENSP00000296464:K275R	K	+	2	0	HSPA4L	128944394	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.313000	0.89978	2.055000	0.61198	0.477000	0.44152	AAG	.	.		0.353	HSPA4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257096.3	NM_014278		G	128724944	A	G	128724944	3	3	263	1	0	0	0	0	1	0	0	0	7422	72	3	2	850	2	HSPA4L	4	128724944	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	8776978	128724944	62429332	99	38473										
INPP4B	8821	hgsc.bcm.edu	37	chr4	143029265	143029265	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	caatcaggaggcatcttttcCataaatatcttgtaatattc	5	8	3	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr4:143029265C>T	ENST00000513000.1	-	24	2788	c.2355G>A	c.(2353-2355)atG>atA	p.M785I	INPP4B_ENST00000508116.1_Missense_Mutation_p.M785I|INPP4B_ENST00000509777.1_Missense_Mutation_p.M785I|INPP4B_ENST00000262992.4_Missense_Mutation_p.M785I|INPP4B_ENST00000308502.4_Missense_Mutation_p.M785I	NM_003866.2	NP_003857.2	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II, 105kDa	785					cellular calcium ion homeostasis (GO:0006874)|inositol phosphate metabolic process (GO:0043647)|negative regulation of osteoclast differentiation (GO:0045671)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of bone remodeling (GO:0046850)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of protein kinase B signaling (GO:0051896)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	lipid binding (GO:0008289)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)	p.M785I(1)		breast(3)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(29)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58	all_hematologic(180;0.158)					GCATCTTTTCCATAAATATCT	0.328																																					p.M785I		Atlas-SNP	.											INPP4B,NS,carcinoma,0,1	INPP4B	132	.	1	Substitution - Missense(1)	lung(1)	c.G2355A						.						80	83	82					4																	143029265		2201	4299	6500	SO:0001583	missense	8821	exon24			CTTTTCCATAAAT	U96922	CCDS3757.1	4q31.1	2008-02-05	2002-08-29			ENSG00000109452			6075	protein-coding gene	gene with protein product		607494	"inositol polyphosphate-4-phosphatase, type II, 105kD"			9295334	Standard	NM_003866		Approved		uc003iiw.4	O15327		ENST00000513000.1:c.2355G>A	chr4.hg19:g.143029265C>T	ENSP00000425487:p.Met785Ile	80.0	0.0		70.0	3.0	NM_003866	Q2TAI2|Q5XLE7|Q6IN59|Q6PJB4	Missense_Mutation	SNP	ENST00000513000.1	hg19	CCDS3757.1	.	.	.	.	.	.	.	.	.	.	C	12.58	1.980441	0.34942	.	.	ENSG00000109452	ENST00000513000;ENST00000262992;ENST00000308502;ENST00000543161;ENST00000508116;ENST00000509777;ENST00000511838;ENST00000542702;ENST00000510812;ENST00000514525	T;T;T;T;T;T;T;T	0.29397	2.0;2.0;2.0;2.0;2.0;1.99;1.57;1.57	5.63	3.75	0.43078	.	0.160134	0.53938	D	0.000053	T	0.14356	0.0347	N	0.12182	0.205	0.31020	N	0.718235	B	0.13145	0.007	B	0.08055	0.003	T	0.03463	-1.1034	10	0.34782	T	0.22	.	5.4425	0.16517	0.2198:0.5893:0.1137:0.0772	.	785	O15327	INP4B_HUMAN	I	785;785;785;656;785;785;600;600;785;656	ENSP00000425487:M785I;ENSP00000262992:M785I;ENSP00000308441:M785I;ENSP00000423954:M785I;ENSP00000422793:M785I;ENSP00000426207:M600I;ENSP00000427250:M785I;ENSP00000421065:M656I	ENSP00000262992:M785I	M	-	3	0	INPP4B	143248715	0.995000	0.38212	1.000000	0.80357	0.987000	0.75469	0.432000	0.21461	2.641000	0.89580	0.650000	0.86243	ATG	.	.		0.328	INPP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364587.1	NM_003866		T	143029265	C	T	143029265	3	4	263	1	0	0	0	0	1	0	0	0	7762	594	21	3	435	3	INPP4B	4	143029265	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	14304321	143029265	48125011	100	38474										
SH3D19	152503	hgsc.bcm.edu	37	chr4	152095911	152095911	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	caaagctgatgagatcgatgTccaccaagggcttgctctgc	11	11	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr4:152095911T>C	ENST00000409252.2	-	6	1312	c.605A>G	c.(604-606)gAc>gGc	p.D202G	SH3D19_ENST00000604030.1_5'Flank|SH3D19_ENST00000455740.1_Missense_Mutation_p.D202G|SH3D19_ENST00000427414.2_Missense_Mutation_p.D202G|SH3D19_ENST00000514152.1_Missense_Mutation_p.D202G|SH3D19_ENST00000409598.4_Missense_Mutation_p.D202G|SH3D19_ENST00000304527.4_Missense_Mutation_p.D202G|SH3D19_ENST00000424281.1_Missense_Mutation_p.D202G			Q5HYK7	SH319_HUMAN	SH3 domain containing 19	202	Pro-rich.				cytoskeleton organization (GO:0007010)|membrane organization (GO:0061024)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of cell morphogenesis (GO:0022604)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)			autonomic_ganglia(1)|endometrium(1)|large_intestine(3)|lung(10)|ovary(1)|skin(3)|urinary_tract(1)	20	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)				GAGATCGATGTCCACCAAGGG	0.537																																					p.D202G		Atlas-SNP	.											.	SH3D19	54	.	0			c.A605G						.						160	176	171					4																	152095911		2203	4300	6503	SO:0001583	missense	152503	exon1			TCGATGTCCACCA	BX647422	CCDS34077.2, CCDS47143.1, CCDS47144.1	4q31.3	2009-03-05	2009-03-05	2009-03-05	ENSG00000109686	ENSG00000109686			30418	protein-coding gene	gene with protein product	"EEN binding protein"	608674				12477932	Standard	NM_001009555		Approved	DKFZp434D0215, EVE1, EBP, Kryn, SH3P19	uc010ipl.1	Q5HYK7	OTTHUMG00000154051	ENST00000409252.2:c.605A>G	chr4.hg19:g.152095911T>C	ENSP00000386848:p.Asp202Gly	96.0	0.0		125.0	5.0	NM_001128924	B7Z296|Q08EK1|Q32N10|Q5U3B8|Q86XB3|Q8N5E7|Q9UFC8	Missense_Mutation	SNP	ENST00000409252.2	hg19	CCDS34077.2	.	.	.	.	.	.	.	.	.	.	T	7.098	0.573582	0.13623	.	.	ENSG00000109686	ENST00000409598;ENST00000304527;ENST00000455740;ENST00000424281;ENST00000427414;ENST00000409252;ENST00000514152	T;T;T;T;T;T;T	0.71579	-0.55;0.13;-0.55;-0.58;-0.58;0.13;-0.55	5.4	5.4	0.78164	.	1.211440	0.05680	N	0.590239	T	0.67988	0.2952	L	0.46157	1.445	0.29947	N	0.820543	B;B;B	0.26318	0.034;0.146;0.146	B;B;B	0.25140	0.015;0.034;0.058	T	0.58651	-0.7599	10	0.46703	T	0.11	-11.4643	11.4179	0.49962	0.0:0.073:0.0:0.927	.	202;202;202	Q5HYK7;Q5HYK7-2;Q5HYK7-3	SH319_HUMAN;.;.	G	202	ENSP00000387030:D202G;ENSP00000302913:D202G;ENSP00000416708:D202G;ENSP00000404542:D202G;ENSP00000415694:D202G;ENSP00000386848:D202G;ENSP00000423449:D202G	ENSP00000302913:D202G	D	-	2	0	SH3D19	152315361	1.000000	0.71417	0.986000	0.45419	0.030000	0.12068	3.918000	0.56432	2.046000	0.60703	0.368000	0.22195	GAC	.	.		0.537	SH3D19-002	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335132.3	NM_001009555		C	152095911	T	C	152095911	3	2	263	1	0	0	0	0	1	0	0	0	14264	1667	58	2	1827	2	SH3D19	4	152095911	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	9066646	152095911	39058365	101	38475										
FHDC1	85462	hgsc.bcm.edu	37	chr4	153864458	153864458	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ccaggcctacccccaactacTcacatgaacggctacagcca	6	18	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr4:153864458T>C	ENST00000511601.1	+	2	437	c.249T>C	c.(247-249)acT>acC	p.T83T	FHDC1_ENST00000260008.3_Silent_p.T83T			Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1	83									ARFIP1/FHDC1(2)	NS(2)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	43	all_hematologic(180;0.093)					CCCCAACTACTCACATGAACG	0.552																																					p.T83T		Atlas-SNP	.											.	FHDC1	102	.	0			c.T249C						.						59	66	63					4																	153864458		2202	4292	6494	SO:0001819	synonymous_variant	85462	exon1			AACTACTCACATG	AB051514	CCDS34081.1	4q31.3	2014-02-12	2007-11-29		ENSG00000137460	ENSG00000137460			29363	protein-coding gene	gene with protein product						15138637	Standard	NM_033393		Approved	KIAA1727	uc003inf.2	Q9C0D6	OTTHUMG00000161452	ENST00000511601.1:c.249T>C	chr4.hg19:g.153864458T>C		96.0	0.0		108.0	5.0	NM_033393		Silent	SNP	ENST00000511601.1	hg19	CCDS34081.1																																																																																			.	.		0.552	FHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364981.2	NM_033393		C	153864458	T	C	153864458	2	2	263	1	0	0	0	0	0	0	0	1	5884	1538	54	2		2	FHDC1	4	153864458	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	1768547	153864458	37289818	102	38476										
C4orf46	201725	hgsc.bcm.edu	37	chr4	159592902	159592902	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gtctgaagaggagggagaagAgggaggcggcgggggcggcg	25	5	1	4			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr4:159592902A>G	ENST00000379205.4	-	1	296	c.52T>C	c.(52-54)Tct>Cct	p.S18P	ETFDH_ENST00000307738.5_5'Flank|ETFDH_ENST00000511912.1_5'Flank|C4orf46_ENST00000508836.1_Intron|C4orf46_ENST00000508457.1_Missense_Mutation_p.S18P	NM_001008393.2	NP_001008394.1	Q504U0	CD046_HUMAN	chromosome 4 open reading frame 46	18										kidney(1)|lung(3)|skin(1)	5						GAGGGAGAAGAGGGAGGCGGC	0.672																																					p.S18P		Atlas-SNP	.											.	C4orf46	11	.	0			c.T52C						.						13	15	14					4																	159592902		2190	4270	6460	SO:0001583	missense	201725	exon1			GAGAAGAGGGAGG		CCDS34088.1	4q32.1	2014-07-30			ENSG00000205208	ENSG00000205208			27320	protein-coding gene	gene with protein product	"renal cancer differentiation gene 1"						Standard	NM_001008393		Approved	LOC201725, RCDG1	uc003iqa.3	Q504U0	OTTHUMG00000161919	ENST00000379205.4:c.52T>C	chr4.hg19:g.159592902A>G	ENSP00000368503:p.Ser18Pro	174.0	0.0		125.0	9.0	NM_001008393	B3KNH7	Missense_Mutation	SNP	ENST00000379205.4	hg19	CCDS34088.1	.	.	.	.	.	.	.	.	.	.	A	12.61	1.990088	0.35131	.	.	ENSG00000205208	ENST00000379205;ENST00000508457	.	.	.	4.11	2.9	0.33743	.	0.160078	0.29806	N	0.011151	T	0.16385	0.0394	N	0.24115	0.695	0.09310	N	1	P	0.41848	0.763	B	0.40285	0.325	T	0.11717	-1.0576	9	0.09590	T	0.72	.	6.4111	0.21692	0.8862:0.0:0.1138:0.0	.	18	Q504U0	CD046_HUMAN	P	18	.	ENSP00000368503:S18P	S	-	1	0	C4orf46	159812352	0.393000	0.25237	0.001000	0.08648	0.004000	0.04260	3.458000	0.53014	0.722000	0.32252	0.460000	0.39030	TCT	.	.		0.672	C4orf46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366378.1	NM_001008393		G	159592902	A	G	159592902	3	3	263	1	0	0	0	0	1	0	0	0	2276	304	11	2	297	2	C4orf46	4	159592902	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	5728444	159592902	31561374	103	38477										
KIAA1712	80817	hgsc.bcm.edu	37	chr4	175225512	175225512	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tcagtggcaggtttatgaccTcaggaaaggtatgcaaccac	11	9	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr4:175225512T>C	ENST00000503780.1	+	6	913	c.499T>C	c.(499-501)Tca>Cca	p.S167P	CEP44_ENST00000426172.1_Missense_Mutation_p.S167P|CEP44_ENST00000457424.2_Missense_Mutation_p.S167P|CEP44_ENST00000296519.4_Missense_Mutation_p.S167P	NM_001040157.2	NP_001035247.1	Q9C0F1	CEP44_HUMAN	centrosomal protein 44kDa	167						centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|spindle pole (GO:0000922)				endometrium(2)|large_intestine(4)|lung(5)|stomach(1)	12						GTTTATGACCTCAGGAAAGGT	0.368																																					p.S167P		Atlas-SNP	.											.	CEP44	35	.	0			c.T499C						.						61	64	63					4																	175225512		2203	4300	6503	SO:0001583	missense	80817	exon6			ATGACCTCAGGAA	AB051499	CCDS34106.1, CCDS47163.1	4q34	2014-02-20	2011-05-06	2011-05-06	ENSG00000164118	ENSG00000164118			29356	protein-coding gene	gene with protein product			"KIAA1712"	KIAA1712		21399614	Standard	NM_001040157		Approved		uc010iro.2	Q9C0F1	OTTHUMG00000160752	ENST00000503780.1:c.499T>C	chr4.hg19:g.175225512T>C	ENSP00000423153:p.Ser167Pro	146.0	0.0		166.0	12.0	NM_001040157	A8K8W9|A8MW11|B3KT53|D3DP42|Q8IXZ4	Missense_Mutation	SNP	ENST00000503780.1	hg19	CCDS34106.1	.	.	.	.	.	.	.	.	.	.	T	14.41	2.527136	0.44969	.	.	ENSG00000164118	ENST00000503780;ENST00000457424;ENST00000515299;ENST00000426172;ENST00000296519	T;T;T;T;T	0.54279	0.62;0.58;0.7;0.58;0.62	5.02	5.02	0.67125	.	0.299367	0.28420	N	0.015409	T	0.69424	0.3109	M	0.70595	2.14	0.33950	D	0.644319	D;D	0.76494	0.999;0.999	D;D	0.85130	0.996;0.997	T	0.79405	-0.1817	10	0.62326	D	0.03	.	11.418	0.49965	0.0:0.0:0.0:1.0	.	167;167	Q9C0F1-2;Q9C0F1	.;CEP44_HUMAN	P	167	ENSP00000423153:S167P;ENSP00000389427:S167P;ENSP00000421128:S167P;ENSP00000408221:S167P;ENSP00000296519:S167P	ENSP00000296519:S167P	S	+	1	0	CEP44	175462087	1.000000	0.71417	0.973000	0.42090	0.039000	0.13416	3.892000	0.56235	2.002000	0.58637	0.383000	0.25322	TCA	.	.		0.368	CEP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362109.2	NM_030633		C	175225512	T	C	175225512	3	2	263	1	0	0	0	0	1	0	0	0	8262	1551	54	2	513	2	KIAA1712	4	175225512	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	15632610	175225512	15928764	104	38478										
SNX25	83891	hgsc.bcm.edu	37	chr4	186185597	186185597	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	actctctttatttagacatgAagaacagccaagaccttttg	6	9	1	4			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr4:186185597A>G	ENST00000504273.1	+	4	539	c.245A>G	c.(244-246)gAa>gGa	p.E82G	SNX25_ENST00000264694.8_Missense_Mutation_p.E82G			Q9H3E2	SNX25_HUMAN	sorting nexin 25	82	PXA. {ECO:0000255|PROSITE- ProRule:PRU00147, ECO:0000255|PROSITE- ProRule:PRU00553}.				negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein transport (GO:0015031)|receptor catabolic process (GO:0032801)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	endosome (GO:0005768)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			NS(1)|breast(4)|endometrium(2)|kidney(4)|large_intestine(8)|lung(13)|ovary(2)|pancreas(2)|prostate(2)|urinary_tract(2)	40		all_lung(41;1.03e-13)|Lung NSC(41;2.5e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;2.13e-24)|Epithelial(43;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.6e-11)|BRCA - Breast invasive adenocarcinoma(30;0.00013)|Colorectal(24;0.000165)|GBM - Glioblastoma multiforme(59;0.000357)|COAD - Colon adenocarcinoma(29;0.000887)|STAD - Stomach adenocarcinoma(60;0.00118)|LUSC - Lung squamous cell carcinoma(40;0.0129)|READ - Rectum adenocarcinoma(43;0.228)		TTTAGACATGAAGAACAGCCA	0.343																																					p.E82G		Atlas-SNP	.											.	SNX25	100	.	0			c.A245G						.						126	120	122					4																	186185597		2203	4300	6503	SO:0001583	missense	83891	exon4			GACATGAAGAACA	AF113223	CCDS34116.1	4q35.1	2011-05-03			ENSG00000109762	ENSG00000109762		"Sorting nexins"	21883	protein-coding gene	gene with protein product						12461558	Standard	NM_031953		Approved	SBBI31	uc003ixh.3	Q9H3E2	OTTHUMG00000160475	ENST00000504273.1:c.245A>G	chr4.hg19:g.186185597A>G	ENSP00000426255:p.Glu82Gly	104.0	0.0		60.0	4.0	NM_031953	Q3ZT30|Q8N6K3	Missense_Mutation	SNP	ENST00000504273.1	hg19	CCDS34116.1	.	.	.	.	.	.	.	.	.	.	A	14.87	2.663181	0.47572	.	.	ENSG00000109762	ENST00000504273;ENST00000264694	T;T	0.11277	2.79;2.79	5.15	5.15	0.70609	Phox-associated domain (2);	0.000000	0.85682	D	0.000000	T	0.11024	0.0269	L	0.28740	0.885	0.53688	D	0.999975	B	0.31752	0.338	B	0.37015	0.239	T	0.26087	-1.0113	10	0.25106	T	0.35	-19.9126	15.1313	0.72527	1.0:0.0:0.0:0.0	.	82	Q9H3E2	SNX25_HUMAN	G	82	ENSP00000426255:E82G;ENSP00000264694:E82G	ENSP00000264694:E82G	E	+	2	0	SNX25	186422591	1.000000	0.71417	1.000000	0.80357	0.862000	0.49288	7.845000	0.86875	2.163000	0.67991	0.533000	0.62120	GAA	.	.		0.343	SNX25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360756.1	NM_031953		G	186185597	A	G	186185597	3	3	263	1	0	0	0	0	1	0	0	0	14911	246	9	2	255	2	SNX25	4	186185597	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	10960085	186185597	4968679	105	38479										
SLC9A3	6550	hgsc.bcm.edu	37	chr5	477525	477525	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ccacgttgtcggtgctggggGagcggatgaaggccagggac	19	9	0	1	rs371187218		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr5:477525G>T	ENST00000264938.3	-	11	1691	c.1682C>A	c.(1681-1683)tCc>tAc	p.S561Y	CTD-2228K2.7_ENST00000606319.1_RNA|SLC9A3_ENST00000514375.1_Missense_Mutation_p.S552Y|CTD-2228K2.7_ENST00000607005.1_RNA|CTD-2228K2.7_ENST00000606288.1_RNA|CTD-2228K2.7_ENST00000607286.1_RNA	NM_004174.2	NP_004165.2	P48764	SL9A3_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3	561					ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|sodium:proton antiporter activity (GO:0015385)			NS(2)|biliary_tract(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(2)|lung(16)|prostate(3)|skin(2)|urinary_tract(1)	37			Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			GGTGCTGGGGGAGCGGATGAA	0.642																																					p.S561Y		Atlas-SNP	.											.	SLC9A3	89	.	0			c.C1682A						.	G	TYR/SER	0,4406		0,0,2203	84	63	70		1682	4.9	1	5		70	1,8599	1.2+/-3.3	0,1,4299	no	missense	SLC9A3	NM_004174.2	144	0,1,6502	TT,TG,GG		0.0116,0.0,0.0077	probably-damaging	561/835	477525	1,13005	2203	4300	6503	SO:0001583	missense	6550	exon11			CTGGGGGAGCGGA		CCDS3855.1, CCDS64116.1	5p15.3	2013-05-22	2012-03-22		ENSG00000066230	ENSG00000066230		"Solute carriers"	11073	protein-coding gene	gene with protein product		182307	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 3", "solute carrier family 9 (sodium/hydrogen exchanger), member 3"	NHE3		8096830	Standard	NM_004174		Approved		uc003jbe.2	P48764	OTTHUMG00000090315	ENST00000264938.3:c.1682C>A	chr5.hg19:g.477525G>T	ENSP00000264938:p.Ser561Tyr	106.0	0.0		189.0	44.0	NM_004174	B7ZKR2|E9PF67|Q3MIW3	Missense_Mutation	SNP	ENST00000264938.3	hg19	CCDS3855.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.764383	0.89932	0.0	1.16E-4	ENSG00000066230	ENST00000264938;ENST00000514375	T;T	0.76839	-1.05;-1.05	4.88	4.88	0.63580	.	0.114937	0.64402	D	0.000011	D	0.88062	0.6336	M	0.77103	2.36	0.41372	D	0.987493	D;D	0.76494	0.997;0.999	D;D	0.83275	0.931;0.996	D	0.88561	0.3123	10	0.45353	T	0.12	.	17.6513	0.88164	0.0:0.0:1.0:0.0	.	552;561	E9PF67;P48764	.;SL9A3_HUMAN	Y	561;552	ENSP00000264938:S561Y;ENSP00000422983:S552Y	ENSP00000264938:S561Y	S	-	2	0	SLC9A3	530525	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.478000	0.73596	2.251000	0.74343	0.561000	0.74099	TCC	.	.		0.642	SLC9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206677.2	NM_004174		T	477525	G	T	477525	3	4	263	1	0	0	0	0	1	0	0	0	14728	1174	41	3	850	3	SLC9A3	5	477525	Missense_Mutation	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10		477525	180437735	106	38480										
ROPN1L	83853	hgsc.bcm.edu	37	chr5	10450066	10450066	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gctgtgttttccaaacagtgTcaccacaagcggtatgtgga	11	9	1	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr5:10450066T>C	ENST00000503804.1	+	4	779	c.258T>C	c.(256-258)tgT>tgC	p.C86C	ROPN1L_ENST00000274134.4_Silent_p.C86C|ROPN1L_ENST00000510520.1_3'UTR			Q96C74	ROP1L_HUMAN	rhophilin associated tail protein 1-like	86					epithelial cilium movement (GO:0003351)|regulation of protein phosphorylation (GO:0001932)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(1)	14						CCAAACAGTGTCACCACAAGC	0.418																																					p.C86C		Atlas-SNP	.											.	ROPN1L	33	.	0			c.T258C						.						86	79	81					5																	10450066		2203	4300	6503	SO:0001819	synonymous_variant	83853	exon3			ACAGTGTCACCAC	AF239723	CCDS3879.1	5p15	2011-01-20	2011-01-20		ENSG00000145491	ENSG00000145491			24060	protein-coding gene	gene with protein product	"radial spoke head 11 homolog (Chlamydomonas)"	611756	"ropporin 1-like"			11278869	Standard	NM_031916		Approved	ASP, FLJ25776, RSPH11	uc021xwo.1	Q96C74	OTTHUMG00000090507	ENST00000503804.1:c.258T>C	chr5.hg19:g.10450066T>C		71.0	0.0		96.0	4.0	NM_031916	D3DTC9|Q9BZX0	Silent	SNP	ENST00000503804.1	hg19	CCDS3879.1																																																																																			.	.		0.418	ROPN1L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367033.1	NM_031916		C	10450066	T	C	10450066	2	2	263	1	0	0	0	0	0	0	0	1	13540	1673	58	2		2	ROPN1L	5	10450066	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	9972541	10450066	170465194	107	38481										
MYO10	4651	hgsc.bcm.edu	37	chr5	16783454	16783454	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	caataaatacctgctttcaaGaatagctcgttcaacacagg	6	10	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr5:16783454G>T	ENST00000513610.1	-	5	1046	c.592C>A	c.(592-594)Ctt>Att	p.L198I		NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	198	Myosin motor.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						CTGCTTTCAAGAATAGCTCGT	0.358																																					p.L198I		Atlas-SNP	.											.	MYO10	198	.	0			c.C592A						.						81	74	76					5																	16783454		1848	4103	5951	SO:0001583	missense	4651	exon5			TTTCAAGAATAGC	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"Myosins / Myosin superfamily : Class X", "Pleckstrin homology (PH) domain containing"	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.592C>A	chr5.hg19:g.16783454G>T	ENSP00000421280:p.Leu198Ile	54.0	0.0		105.0	20.0	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Missense_Mutation	SNP	ENST00000513610.1	hg19	CCDS54834.1	.	.	.	.	.	.	.	.	.	.	G	14.64	2.596256	0.46318	.	.	ENSG00000145555	ENST00000513610;ENST00000513882;ENST00000502436	D;D;D	0.89270	-2.49;-2.49;-2.49	5.52	5.52	0.82312	Myosin head, motor domain (2);	.	.	.	.	D	0.91023	0.7176	M	0.73430	2.235	0.80722	D	1	P;D	0.55605	0.868;0.972	P;P	0.52672	0.706;0.528	D	0.91402	0.5144	9	0.72032	D	0.01	.	9.9945	0.41891	0.1488:0.0:0.8512:0.0	.	165;198	E9PCN3;Q9HD67	.;MYO10_HUMAN	I	198;209;165	ENSP00000421280:L198I;ENSP00000421309:L209I;ENSP00000426783:L165I	ENSP00000426783:L165I	L	-	1	0	MYO10	16836454	1.000000	0.71417	0.904000	0.35570	0.346000	0.29079	2.650000	0.46665	2.595000	0.87683	0.655000	0.94253	CTT	.	.		0.358	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		T	16783454	G	T	16783454	3	4	263	1	0	0	0	0	1	0	0	0	10071	942	33	3	5732	3	MYO10	5	16783454	Missense_Mutation	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	6333388	16783454	164131806	108	38482										
NIPBL	25836	hgsc.bcm.edu	37	chr5	37063996	37063996	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gcaattacctcactgcttggAggaggcagccctaaaaataa	9	10	1	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr5:37063996A>G	ENST00000282516.8	+	46	8464	c.7965A>G	c.(7963-7965)ggA>ggG	p.G2655G	NIPBL_ENST00000448238.2_Silent_p.G2655G	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	2655					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			CACTGCTTGGAGGAGGCAGCC	0.493																																					p.G2655G		Atlas-SNP	.											.	NIPBL	513	.	0			c.A7965G						.						104	102	103					5																	37063996		2203	4300	6503	SO:0001819	synonymous_variant	25836	exon46			GCTTGGAGGAGGC	AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"sister chromatid cohesion 2 homolog (yeast)"	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.7965A>G	chr5.hg19:g.37063996A>G		64.0	0.0		99.0	4.0	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Silent	SNP	ENST00000282516.8	hg19	CCDS3920.1	.	.	.	.	.	.	.	.	.	.	A	13.03	2.114178	0.37339	.	.	ENSG00000164190	ENST00000513819;ENST00000507919	T	0.80738	-1.41	5.5	4.31	0.51392	.	.	.	.	.	D	0.83427	0.5252	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.81040	-0.1113	5	.	.	.	-13.6719	12.4483	0.55664	0.8597:0.1402:0.0:0.0	.	.	.	.	G	123;161	ENSP00000421504:E123G	.	E	+	2	0	NIPBL	37099753	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.834000	0.69361	0.871000	0.35750	0.482000	0.46254	GAG	.	.		0.493	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		G	37063996	A	G	37063996	2	3	263	1	0	0	0	0	0	0	0	1	10437	291	11	2		2	NIPBL	5	37063996	Silent	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	20280542	37063996	143851264	109	38483										
ITGA2	3673	hgsc.bcm.edu	37	chr5	52356813	52356813	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gcaaattataccggccagatAgtgctatatagtgtgaatga	10	6	0	3			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr5:52356813A>T	ENST00000296585.5	+	12	1538	c.1395A>T	c.(1393-1395)atA>atT	p.I465I		NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	465					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular response to hormone stimulus (GO:0032870)|collagen-activated signaling pathway (GO:0038065)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|hepatocyte differentiation (GO:0070365)|hypotonic response (GO:0006971)|integrin-mediated signaling pathway (GO:0007229)|mammary gland development (GO:0030879)|mesodermal cell differentiation (GO:0048333)|organ morphogenesis (GO:0009887)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell projection organization (GO:0031346)|positive regulation of collagen binding (GO:0033343)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA binding (GO:0043388)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|response to amine (GO:0014075)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to muscle activity (GO:0014850)|response to organic cyclic compound (GO:0014070)|skin morphogenesis (GO:0043589)|substrate-dependent cell migration (GO:0006929)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	axon terminus (GO:0043679)|basal part of cell (GO:0045178)|cell outer membrane (GO:0009279)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin alpha2-beta1 complex (GO:0034666)|integrin complex (GO:0008305)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)			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)				CCGGCCAGATAGTGCTATATA	0.438																																					p.I465I		Atlas-SNP	.											.	ITGA2	211	.	0			c.A1395T						.						111	104	106					5																	52356813		2203	4300	6503	SO:0001819	synonymous_variant	3673	exon12			CCAGATAGTGCTA		CCDS3957.1	5q11.2	2010-03-23			ENSG00000164171	ENSG00000164171		"CD molecules", "Integrins"	6137	protein-coding gene	gene with protein product		192974		CD49B			Standard	NM_002203		Approved	CD49b	uc003joy.3	P17301	OTTHUMG00000131165	ENST00000296585.5:c.1395A>T	chr5.hg19:g.52356813A>T		189.0	0.0		194.0	73.0	NM_002203	Q14595	Silent	SNP	ENST00000296585.5	hg19	CCDS3957.1																																																																																			.	.		0.438	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203		T	52356813	A	T	52356813	2	4	263	1	0	0	0	0	0	0	0	1	7884	410	15	4		4	ITGA2	5	52356813	Silent	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	15292817	52356813	128558447	110	38484										
SKIV2L2	23517	hgsc.bcm.edu	37	chr5	54635841	54635841	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tgttttcacatttgtaggtaTgccattgcattggccttaag	9	7	1	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr5:54635841T>C	ENST00000230640.5	+	6	773	c.519T>C	c.(517-519)taT>taC	p.Y173Y	SKIV2L2_ENST00000545714.1_Silent_p.Y72Y	NM_015360.4	NP_056175.3	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2 (S. cerevisiae)	173	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				maturation of 5.8S rRNA (GO:0000460)|mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			NS(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|lung(12)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)				TTTGTAGGTATGCCATTGCAT	0.308																																					p.Y173Y	Melanoma(2;92 134 23744 29976 33782)	Atlas-SNP	.											.	SKIV2L2	104	.	0			c.T519C						.						92	88	89					5																	54635841		2203	4300	6503	SO:0001819	synonymous_variant	23517	exon6			TAGGTATGCCATT	D29641	CCDS3967.1	5q11.2	2008-11-25	2005-02-18	2005-02-18	ENSG00000039123	ENSG00000039123			18734	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 118"		"KIAA0052"	KIAA0052			Standard	NM_015360		Approved	Mtr4, Dob1, fSAP118	uc003jpy.4	P42285	OTTHUMG00000097019	ENST00000230640.5:c.519T>C	chr5.hg19:g.54635841T>C		73.0	0.0		93.0	5.0	NM_015360	Q2M386|Q6MZZ8|Q6P170|Q8N5R0|Q8TAG2	Silent	SNP	ENST00000230640.5	hg19	CCDS3967.1																																																																																			.	.		0.308	SKIV2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214108.1			C	54635841	T	C	54635841	2	2	263	1	0	0	0	0	0	0	0	1	14375	1471	51	2		2	SKIV2L2	5	54635841	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	2279028	54635841	126279419	111	38485										
IL31RA	133396	hgsc.bcm.edu	37	chr5	55206415	55206415	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ctggagtccctgaaacgaaaGacctcttacattgttcaggt	9	10	2	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr5:55206415G>T	ENST00000447346.2	+	12	1622	c.1557G>T	c.(1555-1557)aaG>aaT	p.K519N	IL31RA_ENST00000490985.1_Missense_Mutation_p.K377N|IL31RA_ENST00000354961.4_Missense_Mutation_p.K500N|IL31RA_ENST00000359040.5_Missense_Mutation_p.K519N|IL31RA_ENST00000396834.1_Missense_Mutation_p.K500N	NM_001242636.1|NM_139017.5	NP_001229565.1|NP_620586.3	Q8NI17	IL31R_HUMAN	interleukin 31 receptor A	487					cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|homeostatic process (GO:0042592)|JAK-STAT cascade (GO:0007259)|macrophage differentiation (GO:0030225)|MAPK cascade (GO:0000165)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of macrophage activation (GO:0043031)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cytokine binding (GO:0019955)|cytokine receptor activity (GO:0004896)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)	21		Lung NSC(810;6.93e-05)|Prostate(74;0.00741)|Breast(144;0.0544)|Ovarian(174;0.223)				TGAAACGAAAGACCTCTTACA	0.468																																					p.K519N		Atlas-SNP	.											.	IL31RA	84	.	0			c.G1557T						.						156	135	142					5																	55206415		2203	4300	6503	SO:0001583	missense	133396	exon12			ACGAAAGACCTCT	AY499339	CCDS3970.2, CCDS56365.1, CCDS56366.1, CCDS56367.1, CCDS75244.1, CCDS75245.1	5q11.2	2013-02-11			ENSG00000164509	ENSG00000164509		"Interleukins and interleukin receptors", "Fibronectin type III domain containing"	18969	protein-coding gene	gene with protein product		609510				15184896, 11877449	Standard	NM_139017		Approved	CRL3, GLM-R, CRL, Glmr, IL-31RA	uc003jql.3	Q8NI17	OTTHUMG00000097045	ENST00000447346.2:c.1557G>T	chr5.hg19:g.55206415G>T	ENSP00000415900:p.Lys519Asn	233.0	0.0		267.0	105.0	NM_001242637	A6NIF8|Q2TBA1|Q6EBC3|Q6EBC4|Q6EBC5|Q6EBC6|Q6UWL8|Q8WYJ0	Missense_Mutation	SNP	ENST00000447346.2	hg19	CCDS3970.2	.	.	.	.	.	.	.	.	.	.	G	7.502	0.652814	0.14580	.	.	ENSG00000164509	ENST00000396834;ENST00000447346;ENST00000359040;ENST00000490985;ENST00000354961	T;T;T;T;T	0.56275	0.47;0.47;0.47;0.47;0.47	5.01	2.27	0.28462	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.713450	0.14220	N	0.333513	T	0.29389	0.0732	N	0.17082	0.46	0.80722	D	1	B;B;B;B	0.06786	0.001;0.001;0.001;0.001	B;B;B;B	0.08055	0.003;0.003;0.002;0.003	T	0.07252	-1.0782	10	0.22109	T	0.4	-3.1832	3.2914	0.06950	0.1018:0.3087:0.4529:0.1366	.	487;519;500;519	Q8NI17;Q8NI17-5;Q8NI17-3;Q8NI17-2	IL31R_HUMAN;.;.;.	N	500;519;519;377;500	ENSP00000380046:K500N;ENSP00000415900:K519N;ENSP00000351935:K519N;ENSP00000427533:K377N;ENSP00000347047:K500N	ENSP00000347047:K500N	K	+	3	2	IL31RA	55242172	0.932000	0.31603	0.868000	0.34077	0.953000	0.61014	0.524000	0.22940	0.380000	0.24823	0.557000	0.71058	AAG	.	.		0.468	IL31RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214148.1	NM_139017		T	55206415	G	T	55206415	3	4	263	1	0	0	0	0	1	0	0	0	7700	933	33	3	1603	3	IL31RA	5	55206415	Missense_Mutation	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	570574	55206415	125708845	112	38486										
C5orf35	133383	hgsc.bcm.edu	37	chr5	56205565	56205565	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gcactgaacctaagccacaaCccgaggtgagagggcgggac	14	12	0	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr5:56205565C>T	ENST00000285947.2	+	1	479	c.93C>T	c.(91-93)aaC>aaT	p.N31N	AC008937.3_ENST00000453721.1_RNA|SETD9_ENST00000475908.1_Intron|SETD9_ENST00000541720.1_Silent_p.N31N	NM_153706.3	NP_714917.2	Q8NE22	SETD9_HUMAN	SET domain containing 9	31							methyltransferase activity (GO:0008168)										TAAGCCACAACCCGAGGTGAG	0.677																																					p.N31N		Atlas-SNP	.											.	.	.	.	0			c.C93T						.						47	31	37					5																	56205565		2203	4300	6503	SO:0001819	synonymous_variant	133383	exon1			CCACAACCCGAGG	BC036528	CCDS3972.1	5q11.2	2012-02-23	2012-02-23	2012-02-23	ENSG00000155542	ENSG00000155542			28508	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 35"	C5orf35		20930037	Standard	NM_153706		Approved	MGC33648	uc003jqx.3	Q8NE22	OTTHUMG00000059485	ENST00000285947.2:c.93C>T	chr5.hg19:g.56205565C>T		131.0	0.0		132.0	52.0	NM_153706	F5H713	Silent	SNP	ENST00000285947.2	hg19	CCDS3972.1																																																																																			.	.		0.677	SETD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132304.2	NM_153706		T	56205565	C	T	56205565	2	4	263	1	0	0	0	0	0	0	0	1	2296	506	18	3		3	C5orf35	5	56205565	Silent	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	999150	56205565	124709695	113	38487										
KIF2A	3796	hgsc.bcm.edu	37	chr5	61659121	61659121	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tgtgttgaagatgtactgaaActcattgacataggcaacag	10	6	1	4			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr5:61659121A>G	ENST00000401507.3	+	13	1547	c.1236A>G	c.(1234-1236)aaA>aaG	p.K412K	KIF2A_ENST00000381103.2_Silent_p.K392K|KIF2A_ENST00000407818.3_Silent_p.K412K|KIF2A_ENST00000509663.2_Intron|KIF2A_ENST00000506857.1_Silent_p.K366K	NM_001243953.1|NM_004520.4	NP_001230882.1|NP_004511.2	O00139	KIF2A_HUMAN	kinesin heavy chain member 2A	412	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|nervous system development (GO:0007399)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(3)|ovary(1)|skin(1)	15		Lung NSC(810;8.94e-06)|Prostate(74;0.0132)|Ovarian(174;0.051)|Breast(144;0.077)		Lung(70;0.14)		ATGTACTGAAACTCATTGACA	0.368																																					p.K412K		Atlas-SNP	.											.	KIF2A	69	.	0			c.A1236G						.						84	80	82					5																	61659121		2203	4300	6503	SO:0001819	synonymous_variant	3796	exon13			ACTGAAACTCATT	BC031828	CCDS3980.2, CCDS47216.1, CCDS58949.1	5q12-q13	2008-02-05	2006-09-26	2006-09-26	ENSG00000068796	ENSG00000068796		"Kinesins"	6318	protein-coding gene	gene with protein product		602591	"kinesin heavy chain member 2"	KIF2		9177777	Standard	NM_001098511		Approved	HK2	uc003jsz.4	O00139	OTTHUMG00000097755	ENST00000401507.3:c.1236A>G	chr5.hg19:g.61659121A>G		45.0	0.0		92.0	6.0	NM_001098511	A5YM42|A5YM54|B4DY54|D3DW97|E9PB70|Q7Z5I3|Q8N5Q7	Silent	SNP	ENST00000401507.3	hg19	CCDS3980.2	.	.	.	.	.	.	.	.	.	.	A	10.40	1.339866	0.24339	.	.	ENSG00000068796	ENST00000512006	.	.	.	5.56	1.99	0.26369	.	.	.	.	.	T	0.54191	0.1843	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44298	-0.9337	4	.	.	.	.	6.5643	0.22503	0.3959:0.0:0.6041:0.0	.	.	.	.	S	48	.	.	N	+	2	0	KIF2A	61694878	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.439000	0.44846	0.437000	0.26423	0.533000	0.62120	AAC	.	.		0.368	KIF2A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317989.1	NM_004520		G	61659121	A	G	61659121	2	3	263	1	0	0	0	0	0	0	0	1	8306	40	2	2		2	KIF2A	5	61659121	Silent	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	5453556	61659121	119256139	114	38488										
TNPO1	3842	hgsc.bcm.edu	37	chr5	72168546	72168546	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gcacattgattcttttattgAggtaagacttgttcttgtct	8	6	3	3			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr5:72168546A>G	ENST00000337273.5	+	7	1103	c.677A>G	c.(676-678)gAg>gGg	p.E226G	TNPO1_ENST00000447967.2_3'UTR|TNPO1_ENST00000454282.1_Splice_Site_p.E176G|TNPO1_ENST00000523768.1_Splice_Site_p.E176G|TNPO1_ENST00000506351.2_Splice_Site_p.E218G	NM_002270.3	NP_002261.3	Q92973	TNPO1_HUMAN	transportin 1	226					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|protein import into nucleus, translocation (GO:0000060)|RNA metabolic process (GO:0016070)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(6)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	36		Lung NSC(167;0.0053)|Ovarian(174;0.0175)		OV - Ovarian serous cystadenocarcinoma(47;6.14e-54)		TCTTTTATTGAGGTAAGACTT	0.373																																					p.E226G		Atlas-SNP	.											.	TNPO1	90	.	0			c.A677G						.						142	123	130					5																	72168546		2203	4300	6503	SO:0001630	splice_region_variant	3842	exon7			TTATTGAGGTAAG	U70322	CCDS4016.1, CCDS43329.1	5q13.1	2009-01-12	2004-01-29	2004-01-30	ENSG00000083312	ENSG00000083312		"Importins"	6401	protein-coding gene	gene with protein product	"importin 2"	602901	"karyopherin (importin) beta 2"	KPNB2		8808633, 9144189	Standard	NM_153188		Approved	MIP, TRN, IPO2, MIP1	uc003kci.4	Q92973	OTTHUMG00000100967	ENST00000337273.5:c.678+1A>G	chr5.hg19:g.72168546A>G		117.0	0.0		133.0	6.0	NM_002270	B4DVC6|Q92957|Q92975	Missense_Mutation	SNP	ENST00000337273.5	hg19	CCDS43329.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.076948	0.76415	.	.	ENSG00000083312	ENST00000337273;ENST00000454282;ENST00000523768;ENST00000506351	T;T;T;T	0.68331	-0.32;-0.32;-0.32;-0.32	5.78	5.78	0.91487	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.67581	0.2908	M	0.67397	2.05	0.80722	D	1	B;B	0.19073	0.033;0.01	B;B	0.21151	0.033;0.015	T	0.65919	-0.6051	10	0.66056	D	0.02	-15.7147	16.4053	0.83662	1.0:0.0:0.0:0.0	.	176;226	Q92973-3;Q92973	.;TNPO1_HUMAN	G	226;176;176;218	ENSP00000336712:E226G;ENSP00000398524:E176G;ENSP00000428899:E176G;ENSP00000425118:E218G	ENSP00000336712:E226G	E	+	2	0	TNPO1	72204302	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.822000	0.92013	2.333000	0.79357	0.482000	0.46254	GAG	.	.		0.373	TNPO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000218577.3	NM_002270	Missense_Mutation	G	72168546	A	G	72168546	5	3	263	1	0	0	0	0	0	0	1	0	16350	318	11	2	703	2	TNPO1	5	72168546	Splice_Site	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	10509425	72168546	108746714	115	38489										
VCAN	1462	hgsc.bcm.edu	37	chr5	82835029	82835029	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	acagcagaagtggaaggtacGaaagctccagtagagaagga	14	6	0	2	rs563628544		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr5:82835029G>A	ENST00000265077.3	+	8	6772	c.6207G>A	c.(6205-6207)acG>acA	p.T2069T	VCAN_ENST00000342785.4_Intron|VCAN_ENST00000502527.2_Intron|VCAN-AS1_ENST00000513899.1_RNA|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000343200.5_Silent_p.T1082T|VCAN_ENST00000512590.2_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	2069	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	TGGAAGGTACGAAAGCTCCAG	0.443																																					p.T2069T		Atlas-SNP	.											.	VCAN	498	.	0			c.G6207A						.						68	65	66					5																	82835029		2203	4300	6503	SO:0001819	synonymous_variant	1462	exon8			AGGTACGAAAGCT	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.6207G>A	chr5.hg19:g.82835029G>A		66.0	0.0		91.0	36.0	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Silent	SNP	ENST00000265077.3	hg19	CCDS4060.1																																																																																			.	.		0.443	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		A	82835029	G	A	82835029	2	1	263	1	0	0	0	0	0	0	0	1	17153	1045	37	1		1	VCAN	5	82835029	Silent	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	10666483	82835029	98080231	116	38490										
GPR98	84059	hgsc.bcm.edu	37	chr5	89954088	89954088	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tggtttcacaggagcttgtaTaccagaggtaagtagtgagc	13	6	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr5:89954088T>C	ENST00000405460.2	+	21	4841	c.4745T>C	c.(4744-4746)aTa>aCa	p.I1582T		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	1582	Calx-beta 11. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		GGAGCTTGTATACCAGAGGTA	0.368																																					p.I1582T		Atlas-SNP	.											GPR98,NS,NS,0,1	GPR98	605	.	0			c.T4745C						.						66	63	64					5																	89954088		1814	4080	5894	SO:0001583	missense	84059	exon21			CTTGTATACCAGA	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.4745T>C	chr5.hg19:g.89954088T>C	ENSP00000384582:p.Ile1582Thr	165.0	0.0		189.0	73.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.559747	0.86335	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000399043	T	0.30182	1.54	5.75	5.75	0.90469	Na-Ca exchanger/integrin-beta4 (1);	0.000000	0.85682	D	0.000000	T	0.46171	0.1379	L	0.38838	1.175	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.27971	-1.0058	10	0.35671	T	0.21	.	16.0573	0.80814	0.0:0.0:0.0:1.0	.	1582	Q8WXG9	GPR98_HUMAN	T	1582	ENSP00000384582:I1582T	ENSP00000296619:I1582T	I	+	2	0	GPR98	89989844	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.777000	0.85628	2.191000	0.70037	0.528000	0.53228	ATA	.	.		0.368	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		C	89954088	T	C	89954088	3	2	263	1	0	0	0	0	1	0	0	0	6730	1406	49	2	4827	2	GPR98	5	89954088	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	7119059	89954088	90961172	117	38491										
ERAP2	64167	hgsc.bcm.edu	37	chr5	96215717	96215717	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	atgctacccagtttatcatcTtgcacagcaaagatcttgaa	6	10	3	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr5:96215717T>C	ENST00000437043.3	+	2	1039	c.328T>C	c.(328-330)Ttg>Ctg	p.L110L	ERAP2_ENST00000379904.4_Silent_p.L110L|CTD-2260A17.2_ENST00000501338.1_Intron|ERAP2_ENST00000510309.1_Silent_p.L110L	NM_001130140.1|NM_022350.3	NP_001123612.1|NP_071745.1	Q6P179	ERAP2_HUMAN	endoplasmic reticulum aminopeptidase 2	110					antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|regulation of blood pressure (GO:0008217)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24		all_cancers(142;0.000311)|all_epithelial(76;1.54e-06)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0596)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0703)		GTTTATCATCTTGCACAGCAA	0.433																																					p.L110L		Atlas-SNP	.											.	ERAP2	77	.	0			c.T328C						.						77	68	71					5																	96215717		2203	4300	6503	SO:0001819	synonymous_variant	64167	exon2			ATCATCTTGCACA	AF191545	CCDS4086.1	5q15	2007-11-21			ENSG00000164308	ENSG00000164308			29499	protein-coding gene	gene with protein product	"leukocyte-derived arginine aminopeptidase"	609497				12799365, 15908954	Standard	NM_022350		Approved	L-RAP, LRAP	uc003kmt.3	Q6P179	OTTHUMG00000128718	ENST00000437043.3:c.328T>C	chr5.hg19:g.96215717T>C		125.0	0.0		100.0	4.0	NM_001130140	Q7Z5K1|Q8TD32|Q8WVJ4|Q9HBX2	Silent	SNP	ENST00000437043.3	hg19	CCDS4086.1																																																																																			.	.		0.433	ERAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250623.2	NM_022350		C	96215717	T	C	96215717	2	2	263	1	0	0	0	0	0	0	0	1	5206	1606	56	2		2	ERAP2	5	96215717	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	6261629	96215717	84699543	118	38492										
AP3S1	1176	hgsc.bcm.edu	37	chr5	115249174	115249174	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tataaaagtgccaaacctgcCctcttttaaataaaaatgta	4	8	1	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr5:115249174C>A	ENST00000316788.7	+	6	1126	c.569C>A	c.(568-570)cCc>cAc	p.P190H	AP3S1_ENST00000505423.1_3'UTR	NM_001284.2	NP_001275.1	Q92572	AP3S1_HUMAN	adaptor-related protein complex 3, sigma 1 subunit	190					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|insulin receptor signaling pathway (GO:0008286)|intracellular protein transport (GO:0006886)	AP-3 adaptor complex (GO:0030123)|AP-type membrane coat adaptor complex (GO:0030119)|Golgi apparatus (GO:0005794)|transport vesicle (GO:0030133)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|pancreas(1)|prostate(1)	12		all_cancers(142;0.00377)|all_epithelial(76;0.000129)|Prostate(80;0.0132)|Ovarian(225;0.0776)|Lung NSC(810;0.245)		OV - Ovarian serous cystadenocarcinoma(64;1.08e-07)|Epithelial(69;1.11e-06)|all cancers(49;5.2e-05)		CCAAACCTGCCCTCTTTTAAA	0.403																																					p.P190H		Atlas-SNP	.											.	AP3S1	25	.	0			c.C569A						.						69	73	72					5																	115249174		2202	4300	6502	SO:0001583	missense	1176	exon6			ACCTGCCCTCTTT	D63643	CCDS4123.1	5q22	2010-06-29			ENSG00000177879	ENSG00000177879			2013	protein-coding gene	gene with protein product		601507		CLAPS3		8697810, 9118953	Standard	NM_001284		Approved		uc003krl.3	Q92572	OTTHUMG00000128887	ENST00000316788.7:c.569C>A	chr5.hg19:g.115249174C>A	ENSP00000325369:p.Pro190His	225.0	0.0		231.0	40.0	NM_001284	O00647|O00676|O00721|O00727|Q53XL4|Q6ICQ2	Missense_Mutation	SNP	ENST00000316788.7	hg19	CCDS4123.1	.	.	.	.	.	.	.	.	.	.	C	19.54	3.847210	0.71603	.	.	ENSG00000177879	ENST00000316788	T	0.44881	0.91	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.37571	0.1008	N	0.22421	0.69	0.80722	D	1	P;P	0.43885	0.72;0.82	B;B	0.42112	0.376;0.376	T	0.29671	-1.0004	10	0.87932	D	0	6.6671	19.8996	0.96980	0.0:1.0:0.0:0.0	.	190;190	B2R4I8;Q92572	.;AP3S1_HUMAN	H	190	ENSP00000325369:P190H	ENSP00000325369:P190H	P	+	2	0	AP3S1	115277073	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.686000	0.84128	2.878000	0.98634	0.650000	0.86243	CCC	.	.		0.403	AP3S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250847.2			A	115249174	C	A	115249174	3	1	263	1	0	0	0	0	1	0	0	0	749	623	22	3	591	3	AP3S1	5	115249174	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	19033457	115249174	65666086	119	38493										
SLC12A2	6558	hgsc.bcm.edu	37	chr5	127484452	127484452	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ttttctttcattaggctctaTgtaaggacaacatctaccca	5	10	4	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr5:127484452T>C	ENST00000262461.2	+	12	2077	c.1888T>C	c.(1888-1890)Tgt>Cgt	p.C630R	SLC12A2_ENST00000343225.4_Missense_Mutation_p.C630R	NM_001046.2	NP_001037.1	P55011	S12A2_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 2	630					ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|branching involved in mammary gland duct morphogenesis (GO:0060444)|chloride transmembrane transport (GO:1902476)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|gamma-aminobutyric acid signaling pathway (GO:0007214)|hyperosmotic response (GO:0006972)|ion transport (GO:0006811)|mammary duct terminal end bud growth (GO:0060763)|multicellular organism growth (GO:0035264)|positive regulation of cell volume (GO:0045795)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transepithelial ammonium transport (GO:0070634)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ammonium transmembrane transporter activity (GO:0008519)|sodium:potassium:chloride symporter activity (GO:0008511)			breast(3)|endometrium(5)|kidney(5)|large_intestine(12)|lung(16)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		all_cancers(142;0.0972)|Prostate(80;0.151)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Bumetanide(DB00887)|Potassium Chloride(DB00761)|Quinethazone(DB01325)	TTAGGCTCTATGTAAGGACAA	0.328																																					p.C630R		Atlas-SNP	.											.	SLC12A2	119	.	0			c.T1888C						.						136	137	137					5																	127484452		2203	4298	6501	SO:0001583	missense	6558	exon12			GCTCTATGTAAGG		CCDS4144.1, CCDS58965.1	5q23.3	2014-06-13	2013-07-18		ENSG00000064651	ENSG00000064651		"Solute carriers"	10911	protein-coding gene	gene with protein product	"bumetanide-sensitive sodium-(potassium)-chloride cotransporter 1", "basolateral Na-K-Cl symporter", "protein phosphatase 1, regulatory subunit 141"	600840				7629105	Standard	NM_001256461		Approved	NKCC1, BSC, BSC2, PPP1R141	uc003kus.3	P55011	OTTHUMG00000128983	ENST00000262461.2:c.1888T>C	chr5.hg19:g.127484452T>C	ENSP00000262461:p.Cys630Arg	66.0	0.0		97.0	4.0	NM_001046	Q8N713|Q8WWH7	Missense_Mutation	SNP	ENST00000262461.2	hg19	CCDS4144.1	.	.	.	.	.	.	.	.	.	.	T	19.72	3.879696	0.72294	.	.	ENSG00000064651	ENST00000262461;ENST00000343225	D;D	0.98901	-5.22;-5.22	4.95	4.95	0.65309	Amino acid permease domain (1);	0.107305	0.64402	D	0.000002	D	0.99227	0.9731	M	0.90483	3.12	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.99177	1.0866	10	0.87932	D	0	.	15.0598	0.71944	0.0:0.0:0.0:1.0	.	630;630	P55011-3;P55011	.;S12A2_HUMAN	R	630	ENSP00000262461:C630R;ENSP00000340878:C630R	ENSP00000262461:C630R	C	+	1	0	SLC12A2	127512351	1.000000	0.71417	0.989000	0.46669	0.834000	0.47266	7.798000	0.85924	2.202000	0.70862	0.477000	0.44152	TGT	.	.		0.328	SLC12A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250972.1	NM_001046		C	127484452	T	C	127484452	3	2	263	1	0	0	0	0	1	0	0	0	14398	1464	51	2	1934	2	SLC12A2	5	127484452	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	12235278	127484452	53430808	120	38494										
IRF1	3659	hgsc.bcm.edu	37	chr5	131825125	131825125	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cgggatttggttggaattaaTctgcatctctagccagggtc	12	8	2	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr5:131825125T>G	ENST00000245414.4	-	2	304	c.46A>C	c.(46-48)Att>Ctt	p.I16L	IRF1_ENST00000405885.2_Missense_Mutation_p.I16L|IRF1_ENST00000463784.1_Intron	NM_002198.2	NP_002189.1	P10914	IRF1_HUMAN	interferon regulatory factor 1	16					apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cell cycle arrest (GO:0007050)|cellular response to interferon-beta (GO:0035458)|cellular response to mechanical stimulus (GO:0071260)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of cell proliferation (GO:0008285)|negative regulation of regulatory T cell differentiation (GO:0045590)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|regulation of adaptive immune response (GO:0002819)|regulation of CD8-positive, alpha-beta T cell proliferation (GO:2000564)|regulation of cell cycle (GO:0051726)|regulation of innate immune response (GO:0045088)|regulation of MyD88-dependent toll-like receptor signaling pathway (GO:0034124)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(2)|prostate(2)|skin(1)|urinary_tract(1)	11		all_cancers(142;0.026)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	LUAD - Lung adenocarcinoma(142;0.247)		TTGGAATTAATCTGCATCTCT	0.473																																					p.I16L		Atlas-SNP	.											.	IRF1	26	.	0			c.A46C						.						110	109	110					5																	131825125		2203	4300	6503	SO:0001583	missense	3659	exon2			AATTAATCTGCAT		CCDS4155.1	5q23-q31	2008-07-18			ENSG00000125347	ENSG00000125347			6116	protein-coding gene	gene with protein product	"interferon regulatory factor-1"	147575				2726461, 1680796	Standard	NM_002198		Approved	MAR	uc003kxa.2	P10914	OTTHUMG00000059497	ENST00000245414.4:c.46A>C	chr5.hg19:g.131825125T>G	ENSP00000245414:p.Ile16Leu	114.0	0.0		128.0	41.0	NM_002198	Q96GG7	Missense_Mutation	SNP	ENST00000245414.4	hg19	CCDS4155.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.544270	0.86022	.	.	ENSG00000125347	ENST00000245414;ENST00000405885;ENST00000437654;ENST00000458069	D;D;D;D	0.98192	-4.78;-4.78;-4.78;-4.78	5.59	5.59	0.84812	Winged helix-turn-helix transcription repressor DNA-binding (1);Interferon regulatory factor DNA-binding domain (4);	0.000000	0.85682	D	0.000000	D	0.98560	0.9519	L	0.60845	1.875	0.80722	D	1	P;D	0.55385	0.924;0.971	D;D	0.76575	0.972;0.988	D	0.99891	1.1134	10	0.87932	D	0	-14.9777	16.0664	0.80878	0.0:0.0:0.0:1.0	.	16;16	Q5FBX3;P10914	.;IRF1_HUMAN	L	16	ENSP00000245414:I16L;ENSP00000384406:I16L;ENSP00000405655:I16L;ENSP00000396318:I16L	ENSP00000245414:I16L	I	-	1	0	IRF1	131853024	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.905000	0.87416	2.254000	0.74563	0.459000	0.35465	ATT	.	.		0.473	IRF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132340.1	NM_002198		G	131825125	T	G	131825125	3	3	263	1	0	0	0	0	1	0	0	0	7836	1435	50	5	967	5	IRF1	5	131825125	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	4340673	131825125	49090135	121	38495										
ZCCHC10	54819	hgsc.bcm.edu	37	chr5	132334321	132334321	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gttcatcgtcagagctgctaTctgtgctggtgctactgcta	11	10	3	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr5:132334321T>C	ENST00000509437.1	-	5	540	c.533A>G	c.(532-534)gAt>gGt	p.D178G	ZCCHC10_ENST00000513541.1_3'UTR|ZCCHC10_ENST00000508080.1_5'UTR|ZCCHC10_ENST00000355372.2_Missense_Mutation_p.D172G|ZCCHC10_ENST00000509008.1_3'UTR|ZCCHC10_ENST00000513848.1_Missense_Mutation_p.D142G|ZCCHC10_ENST00000324170.3_Missense_Mutation_p.D156G			Q8TBK6	ZCH10_HUMAN	zinc finger, CCHC domain containing 10	178	Ser-rich.						nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AGAGCTGCTATCTGTGCTGGT	0.453																																					p.D156G		Atlas-SNP	.											.	ZCCHC10	7	.	0			c.A467G						.						74	77	76					5																	132334321		2203	4300	6503	SO:0001583	missense	54819	exon4			CTGCTATCTGTGC	BC005211	CCDS4165.1, CCDS75300.1, CCDS75301.1, CCDS75302.1	5q31.1	2008-05-02			ENSG00000155329	ENSG00000155329		"Zinc fingers, CCHC domain containing"	25954	protein-coding gene	gene with protein product						12477932	Standard	XM_005272024		Approved	FLJ20094	uc003kyg.3	Q8TBK6	OTTHUMG00000129013	ENST00000509437.1:c.533A>G	chr5.hg19:g.132334321T>C	ENSP00000423276:p.Asp178Gly	82.0	0.0		100.0	36.0	NM_017665	Q9NXR4	Missense_Mutation	SNP	ENST00000509437.1	hg19		.	.	.	.	.	.	.	.	.	.	T	12.00	1.806386	0.31961	.	.	ENSG00000155329	ENST00000324170;ENST00000355372;ENST00000509437;ENST00000513848	.	.	.	4.82	2.4	0.29515	.	0.427167	0.24242	N	0.040252	T	0.46678	0.1405	.	.	.	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.38993	-0.9635	8	0.72032	D	0.01	.	8.8543	0.35219	0.0:0.1573:0.0:0.8427	.	142;178;156	G3XAM1;Q8TBK6;Q8TBK6-2	.;ZCH10_HUMAN;.	G	156;172;178;142	.	ENSP00000324274:D156G	D	-	2	0	ZCCHC10	132362220	0.350000	0.24878	0.029000	0.17559	0.718000	0.41266	1.131000	0.31406	0.298000	0.22638	0.460000	0.39030	GAT	.	.		0.453	ZCCHC10-004	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000370163.1	NM_017665		C	132334321	T	C	132334321	3	2	263	1	0	0	0	0	1	0	0	0	17594	1435	50	2	49	2	ZCCHC10	5	132334321	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	509196	132334321	48580939	122	38496										
PCDHA3	56145	hgsc.bcm.edu	37	chr5	140181074	140181074	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	accgcgaggaactgtgcgggCggagcgcggagtgcagcatc	18	11	0	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr5:140181074C>T	ENST00000522353.2	+	1	292	c.292C>T	c.(292-294)Cgg>Tgg	p.R98W	PCDHA3_ENST00000532566.2_Missense_Mutation_p.R98W|PCDHA2_ENST00000526136.1_Intron|PCDHA2_ENST00000520672.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA1_ENST00000504120.2_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	98	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.R98W(2)		NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACTGTGCGGGCGGAGCGCGGA	0.567																																					p.R98W		Atlas-SNP	.											PCDHA3_ENST00000522353,rectum,carcinoma,0,2	PCDHA3	396	.	2	Substitution - Missense(2)	large_intestine(2)	c.C292T						.						127	142	137					5																	140181074		2203	4300	6503	SO:0001583	missense	56145	exon1			TGCGGGCGGAGCG	AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"Cadherins / Protocadherins : Clustered"	8669	other	complex locus constituent	"KIAA0345-like 11"	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.292C>T	chr5.hg19:g.140181074C>T	ENSP00000429808:p.Arg98Trp	59.0	0.0		71.0	3.0	NM_031497	O75286	Missense_Mutation	SNP	ENST00000522353.2	hg19	CCDS54915.1	.	.	.	.	.	.	.	.	.	.	N	3.113	-0.182174	0.06340	.	.	ENSG00000255408	ENST00000522353;ENST00000532566	T;T	0.28666	1.6;1.6	4.51	1.59	0.23543	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	0.000000	0.38005	U	0.001845	T	0.27594	0.0678	M	0.66378	2.025	0.09310	N	1	P;B	0.35226	0.491;0.091	B;B	0.35039	0.194;0.106	T	0.18335	-1.0340	10	0.59425	D	0.04	.	5.4105	0.16346	0.3787:0.4499:0.0978:0.0737	.	98;98	Q9Y5H8-2;Q9Y5H8	.;PCDA3_HUMAN	W	98	ENSP00000429808:R98W;ENSP00000434086:R98W	ENSP00000429808:R98W	R	+	1	2	PCDHA3	140161258	0.000000	0.05858	0.664000	0.29753	0.048000	0.14542	-1.633000	0.02022	-0.140000	0.11394	-1.595000	0.00837	CGG	.	.		0.567	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906		T	140181074	C	T	140181074	3	4	263	1	0	0	0	0	1	0	0	0	11534	759	27	1	294	1	PCDHA3	5	140181074	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	7846753	140181074	40734186	123	38497										
ARAP3	64411	hgsc.bcm.edu	37	chr5	141038204	141038204	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tataaacttccatgatgaggTctccagcctgagacagctga	9	10	1	4			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr5:141038204T>C	ENST00000239440.4	-	24	3418	c.3353A>G	c.(3352-3354)gAc>gGc	p.D1118G	ARAP3_ENST00000513878.1_Missense_Mutation_p.D780G|ARAP3_ENST00000508305.1_Missense_Mutation_p.D949G|ARAP3_ENST00000512390.1_5'UTR	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	1118	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						CATGATGAGGTCTCCAGCCTG	0.498																																					p.D1118G		Atlas-SNP	.											.	ARAP3	139	.	0			c.A3353G						.						44	43	43					5																	141038204		2203	4300	6503	SO:0001583	missense	64411	exon24			ATGAGGTCTCCAG	AJ310567	CCDS4266.1	5q31.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000120318	ENSG00000120318		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	24097	protein-coding gene	gene with protein product		606647	"centaurin, delta 3"	CENTD3		11804589, 12015138	Standard	XM_005268497		Approved	FLJ21065, DRAG1	uc003llm.3	Q8WWN8	OTTHUMG00000129610	ENST00000239440.4:c.3353A>G	chr5.hg19:g.141038204T>C	ENSP00000239440:p.Asp1118Gly	81.0	0.0		87.0	6.0	NM_022481	B4DIT1|D3DQE3	Missense_Mutation	SNP	ENST00000239440.4	hg19	CCDS4266.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.823844	0.90873	.	.	ENSG00000120318	ENST00000508305;ENST00000239440;ENST00000513878	T;T;T	0.20738	2.05;2.75;2.63	5.99	5.99	0.97316	Ras-association (1);	0.047372	0.85682	D	0.000000	T	0.45955	0.1368	M	0.75777	2.31	0.80722	D	1	D;D;P	0.67145	0.992;0.996;0.885	D;P;P	0.63113	0.911;0.825;0.492	T	0.46034	-0.9220	10	0.87932	D	0	.	16.126	0.81395	0.0:0.0:0.0:1.0	.	780;949;1118	B4DIT1;G5E9Y3;Q8WWN8	.;.;ARAP3_HUMAN	G	949;1118;780	ENSP00000421826:D949G;ENSP00000239440:D1118G;ENSP00000421468:D780G	ENSP00000239440:D1118G	D	-	2	0	ARAP3	141018388	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.544000	0.82117	2.292000	0.77174	0.533000	0.62120	GAC	.	.		0.498	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481		C	141038204	T	C	141038204	3	2	263	1	0	0	0	0	1	0	0	0	840	1667	58	2	1321	2	ARAP3	5	141038204	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	857130	141038204	39877056	124	38498										
FBXO38	81545	hgsc.bcm.edu	37	chr5	147807217	147807217	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gccccaggaatcccaaaggaGaactagcaggtgttctgatg	12	10	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr5:147807217G>A	ENST00000340253.5	+	15	2528	c.2360G>A	c.(2359-2361)aGa>aAa	p.R787K	FBXO38_ENST00000513826.1_Intron|FBXO38_ENST00000394370.3_Missense_Mutation_p.R787K|CTD-2283N19.1_ENST00000520980.2_RNA|FBXO38_ENST00000296701.6_Intron			Q6PIJ6	FBX38_HUMAN	F-box protein 38	787					cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)			ATG4C/FBXO38(2)	NS(1)|breast(2)|endometrium(7)|kidney(5)|large_intestine(9)|lung(15)|ovary(5)|prostate(2)|skin(2)|stomach(2)|urinary_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCCAAAGGAGAACTAGCAGG	0.572																																					p.R787K		Atlas-SNP	.											.	FBXO38	115	.	0			c.G2360A						.						56	51	53					5																	147807217		2203	4300	6503	SO:0001583	missense	81545	exon15			AAAGGAGAACTAG	BC005873	CCDS43384.1, CCDS64285.1	5q33.1	2008-02-05			ENSG00000145868	ENSG00000145868		"F-boxes /  "other""	28844	protein-coding gene	gene with protein product		608533				12477932	Standard	NM_030793		Approved	MOKA, SP329, FLJ13962, Fbx38	uc003lpg.2	Q6PIJ6	OTTHUMG00000129929	ENST00000340253.5:c.2360G>A	chr5.hg19:g.147807217G>A	ENSP00000342023:p.Arg787Lys	82.0	0.0		100.0	33.0	NM_030793	Q6PK72|Q7Z2U0|Q86VN3|Q9BXY6|Q9H837|Q9HC40	Missense_Mutation	SNP	ENST00000340253.5	hg19		.	.	.	.	.	.	.	.	.	.	G	13.21	2.169095	0.38315	.	.	ENSG00000145868	ENST00000340253;ENST00000394370	T;T	0.32988	1.51;1.43	6.04	6.04	0.98038	.	0.233362	0.46145	D	0.000307	T	0.23171	0.0560	N	0.24115	0.695	0.80722	D	1	B;P	0.36837	0.206;0.571	B;B	0.33392	0.124;0.163	T	0.02411	-1.1163	10	0.24483	T	0.36	-16.3308	19.1586	0.93522	0.0:0.0:1.0:0.0	.	787;787	Q6PIJ6-2;Q6PIJ6	.;FBX38_HUMAN	K	787	ENSP00000342023:R787K;ENSP00000377895:R787K	ENSP00000342023:R787K	R	+	2	0	FBXO38	147787410	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.698000	0.68302	2.873000	0.98535	0.563000	0.77884	AGA	.	.		0.572	FBXO38-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000252185.2	NM_030793		A	147807217	G	A	147807217	3	1	263	1	0	0	0	0	1	0	0	0	5754	942	33	3	2414	3	FBXO38	5	147807217	Missense_Mutation	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	6769013	147807217	33108043	125	38499										
ZNF300	91975	hgsc.bcm.edu	37	chr5	150275250	150275250	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gtacatatataaggtttttcTcctgtgtgaattctctgatg	8	6	2	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr5:150275250T>C	ENST00000274599.5	-	6	1971	c.1551A>G	c.(1549-1551)ggA>ggG	p.G517G	ZNF300_ENST00000418587.2_Silent_p.G481G|ZNF300_ENST00000446148.2_Silent_p.G533G|ZNF300_ENST00000427179.1_3'UTR|ZNF300_ENST00000394226.2_Silent_p.G517G	NM_052860.2	NP_443092.1	Q96RE9	ZN300_HUMAN	zinc finger protein 300	517					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)	27		Medulloblastoma(196;0.109)|all_hematologic(541;0.131)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AAGGTTTTTCTCCTGTGTGAA	0.423																																					p.G533G		Atlas-SNP	.											.	ZNF300	69	.	0			c.A1599G						.						48	50	49					5																	150275250		2203	4298	6501	SO:0001819	synonymous_variant	91975	exon7			TTTTTCTCCTGTG	AF395541	CCDS4311.2, CCDS54939.1, CCDS54940.1	5q33.1	2013-01-08			ENSG00000145908	ENSG00000145908		"Zinc fingers, C2H2-type", "-"	13091	protein-coding gene	gene with protein product		612429				14746915	Standard	NM_052860		Approved		uc021yfx.1	Q96RE9	OTTHUMG00000130076	ENST00000274599.5:c.1551A>G	chr5.hg19:g.150275250T>C		62.0	0.0		73.0	4.0	NM_001172831	A8MY91|B3KU35|B4DU78|F5GWS1|Q06DQ3|Q17RP3|Q5H9N5	Silent	SNP	ENST00000274599.5	hg19	CCDS4311.2																																																																																			.	.		0.423	ZNF300-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_052860		C	150275250	T	C	150275250	2	2	263	1	0	0	0	0	0	0	0	1	17846	1538	54	2		2	ZNF300	5	150275250	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	2468033	150275250	30640010	126	38500										
FAT2	2196	hgsc.bcm.edu	37	chr5	150908876	150908876	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gtcactgagggaagaggagcTcttccggctgcactcaatgg	14	10	3	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr5:150908876T>C	ENST00000261800.5	-	14	9901	c.9889A>G	c.(9889-9891)Agc>Ggc	p.S3297G		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3297	Cadherin 29. {ECO:0000255|PROSITE- ProRule:PRU00043}.|Poly-Ser.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GAAGAGGAGCTCTTCCGGCTG	0.522																																					p.S3297G		Atlas-SNP	.											.	FAT2	465	.	0			c.A9889G						.						148	137	141					5																	150908876		2203	4300	6503	SO:0001583	missense	2196	exon14			AGGAGCTCTTCCG	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.9889A>G	chr5.hg19:g.150908876T>C	ENSP00000261800:p.Ser3297Gly	106.0	0.0		122.0	44.0	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	hg19	CCDS4317.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	3.941|3.941	-0.014242|-0.014242	0.07681|0.07681	.|.	.|.	ENSG00000086570|ENSG00000086570	ENST00000520200|ENST00000261800	.|T	.|0.29917	.|1.55	5.58|5.58	1.56|1.56	0.23342|0.23342	.|Cadherin (4);Cadherin-like (1);	.|0.268112	.|0.32416	.|N	.|0.006121	T|T	0.05547|0.05547	0.0146|0.0146	N|N	0.00204|0.00204	-1.855|-1.855	0.26777|0.26777	N|N	0.96967|0.96967	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.42447|0.42447	-0.9451|-0.9451	5|10	.|0.02654	.|T	.|1	.|.	9.0585|9.0585	0.36421|0.36421	0.0:0.5909:0.0:0.4091|0.0:0.5909:0.0:0.4091	.|.	.|3297	.|Q9NYQ8	.|FAT2_HUMAN	G|G	155|3297	.|ENSP00000261800:S3297G	.|ENSP00000261800:S3297G	E|S	-|-	2|1	0|0	FAT2|FAT2	150889069|150889069	0.036000|0.036000	0.19791|0.19791	0.999000|0.999000	0.59377|0.59377	0.968000|0.968000	0.65278|0.65278	0.598000|0.598000	0.24074|0.24074	0.246000|0.246000	0.21394|0.21394	0.519000|0.519000	0.50382|0.50382	GAG|AGC	.	.		0.522	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		C	150908876	T	C	150908876	3	2	263	1	0	0	0	0	1	0	0	0	5698	1551	54	2	3200	2	FAT2	5	150908876	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	633626	150908876	30006384	127	38501										
UBLCP1	134510	hgsc.bcm.edu	37	chr5	158705274	158705274	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tcttggtgttatatggggaaAgttttcggagttttacagca	12	4	1	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr5:158705274A>G	ENST00000296786.6	+	9	1039	c.713A>G	c.(712-714)aAg>aGg	p.K238R		NM_145049.3	NP_659486.2	Q8WVY7	UBCP1_HUMAN	ubiquitin-like domain containing CTD phosphatase 1	238	FCP1 homology. {ECO:0000255|PROSITE- ProRule:PRU00336}.|Phosphatase.					nucleolus (GO:0005730)|nucleus (GO:0005634)	phosphoprotein phosphatase activity (GO:0004721)			endometrium(1)|kidney(3)|large_intestine(4)|ovary(1)	9	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ATATGGGGAAAGTTTTCGGAG	0.328																																					p.K238R		Atlas-SNP	.											.	UBLCP1	27	.	0			c.A713G						.						97	97	97					5																	158705274		2203	4300	6503	SO:0001583	missense	134510	exon9			GGGGAAAGTTTTC	AK057996	CCDS4345.1	5q33.3	2010-06-21			ENSG00000164332	ENSG00000164332	3.1.3.16	"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	28110	protein-coding gene	gene with protein product	"CTD phosphatase-like with ubiquitin domain 1"	609867				15883030	Standard	NM_145049		Approved	MGC10067, CPUB1	uc003lxq.2	Q8WVY7	OTTHUMG00000130305	ENST00000296786.6:c.713A>G	chr5.hg19:g.158705274A>G	ENSP00000296786:p.Lys238Arg	46.0	0.0		74.0	4.0	NM_145049	D3DQJ7|Q96DK5	Missense_Mutation	SNP	ENST00000296786.6	hg19	CCDS4345.1	.	.	.	.	.	.	.	.	.	.	A	18.87	3.715111	0.68844	.	.	ENSG00000164332	ENST00000296786	.	.	.	5.44	4.27	0.50696	HAD-superfamily hydrolase, subfamily IIID (1);NLI interacting factor (3);HAD-like domain (2);	0.000000	0.85682	D	0.000000	T	0.77150	0.4088	M	0.82716	2.605	0.51767	D	0.999936	D	0.89917	1.0	D	0.74023	0.982	T	0.75833	-0.3178	9	0.33141	T	0.24	-10.282	10.2956	0.43623	0.9245:0.0:0.0755:0.0	.	238	Q8WVY7	UBCP1_HUMAN	R	238	.	ENSP00000296786:K238R	K	+	2	0	UBLCP1	158637852	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.905000	0.92613	0.987000	0.38709	-0.290000	0.09829	AAG	.	.		0.328	UBLCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252650.2	NM_145049		G	158705274	A	G	158705274	3	3	263	1	0	0	0	0	1	0	0	0	16906	72	3	2	743	2	UBLCP1	5	158705274	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	7796398	158705274	22209986	128	38502										
CCDC99	54908	hgsc.bcm.edu	37	chr5	169031187	169031187	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gtgtcttctaaatctactccAgagacccagtgccctcaaca	6	14	4	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr5:169031187A>G	ENST00000265295.4	+	12	2073	c.1794A>G	c.(1792-1794)ccA>ccG	p.P598P		NM_017785.4	NP_060255.3			spindle apparatus coiled-coil protein 1																		AATCTACTCCAGAGACCCAGT	0.363																																					p.P598P		Atlas-SNP	.											.	.	.	.	0			c.A1794G						.						77	83	81					5																	169031187		2203	4300	6503	SO:0001819	synonymous_variant	54908	exon12			TACTCCAGAGACC	BC012568	CCDS4370.1	5q35.1	2012-09-27	2012-09-27	2012-09-27	ENSG00000040275	ENSG00000040275			26010	protein-coding gene	gene with protein product	"spindly homolog (Drosophila)"		"coiled-coil domain containing 99"	CCDC99		20427577	Standard	NM_017785		Approved	FLJ20364, hSpindly	uc003mae.4	Q96EA4	OTTHUMG00000130438	ENST00000265295.4:c.1794A>G	chr5.hg19:g.169031187A>G		69.0	0.0		97.0	4.0	NM_017785		Silent	SNP	ENST00000265295.4	hg19	CCDS4370.1																																																																																			.	.		0.363	SPDL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252829.2	NM_017785		G	169031187	A	G	169031187	2	3	263	1	0	0	0	0	0	0	0	1	2878	175	7	2		2	CCDC99	5	169031187	Silent	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	10325913	169031187	11884073	129	38503										
RNF44	22838	hgsc.bcm.edu	37	chr5	175958000	175958000	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gatagggcacaggcagctgcTgcatggtgcacgcctggata	15	10	0	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr5:175958000T>C	ENST00000274811.4	-	5	1012	c.488A>G	c.(487-489)cAg>cGg	p.Q163R	RNF44_ENST00000509404.1_5'Flank|RNF44_ENST00000537487.1_Missense_Mutation_p.Q82R	NM_014901.4	NP_055716.1	Q7L0R7	RNF44_HUMAN	ring finger protein 44	163	Pro-rich.						zinc ion binding (GO:0008270)			endometrium(2)|lung(3)|prostate(1)|skin(1)|stomach(1)	8	all_cancers(89;0.0029)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGGCAGCTGCTGCATGGTGCA	0.657																																					p.Q163R		Atlas-SNP	.											.	RNF44	33	.	0			c.A488G						.						15	18	17					5																	175958000		2197	4277	6474	SO:0001583	missense	22838	exon5			AGCTGCTGCATGG	AB029023	CCDS4404.1	5q35.3	2013-01-09			ENSG00000146083	ENSG00000146083		"RING-type (C3HC4) zinc fingers"	19180	protein-coding gene	gene with protein product						10470851	Standard	NM_014901		Approved	KIAA1100	uc003mek.1	Q7L0R7	OTTHUMG00000130664	ENST00000274811.4:c.488A>G	chr5.hg19:g.175958000T>C	ENSP00000274811:p.Gln163Arg	57.0	0.0		91.0	4.0	NM_014901	B4DYE0|Q8ND05|Q9UPQ2	Missense_Mutation	SNP	ENST00000274811.4	hg19	CCDS4404.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.696638	0.88830	.	.	ENSG00000146083	ENST00000274811;ENST00000537487	T;T	0.43294	0.95;0.95	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.59918	0.2229	M	0.65498	2.005	0.43550	D	0.995856	D	0.69078	0.997	D	0.81914	0.995	T	0.56360	-0.7992	10	0.14656	T	0.56	-20.6712	15.378	0.74630	0.0:0.0:0.0:1.0	.	163	Q7L0R7	RNF44_HUMAN	R	163;82	ENSP00000274811:Q163R;ENSP00000440352:Q82R	ENSP00000274811:Q163R	Q	-	2	0	RNF44	175890606	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	5.866000	0.69590	2.051000	0.60960	0.459000	0.35465	CAG	.	.		0.657	RNF44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253156.2			C	175958000	T	C	175958000	3	2	263	1	0	0	0	0	1	0	0	0	13511	1580	55	2	838	2	RNF44	5	175958000	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	6926813	175958000	4957260	130	38504										
FLT4	2324	hgsc.bcm.edu	37	chr5	180036905	180036905	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ccacccttcatgtgaagtacCacagagcctttgtaggtcgt	9	12	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr5:180036905C>A	ENST00000261937.6	-	28	3885	c.3807G>T	c.(3805-3807)gtG>gtT	p.V1269V	FLT4_ENST00000502649.1_Splice_Site_p.V1269V|FLT4_ENST00000393347.3_Splice_Site_p.V1269V	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	1269					blood vessel morphogenesis (GO:0048514)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|lymph vessel development (GO:0001945)|lymphangiogenesis (GO:0001946)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein autophosphorylation (GO:0046777)|regulation of blood vessel remodeling (GO:0060312)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(6)|large_intestine(5)|liver(2)|lung(37)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TGTGAAGTACCACAGAGCCTT	0.607																																					p.V1269V	Colon(97;1075 1466 27033 27547 35871)	Atlas-SNP	.											.	FLT4	356	.	0			c.G3807T						.						135	127	129					5																	180036905		2203	4300	6503	SO:0001630	splice_region_variant	2324	exon28			AAGTACCACAGAG	X68203	CCDS4457.1, CCDS43412.1	5q34-q35	2013-01-29			ENSG00000037280	ENSG00000037280	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3767	protein-coding gene	gene with protein product		136352				1319394	Standard	NM_002020		Approved	VEGFR3, PCL	uc003mlz.4	P35916	OTTHUMG00000130931	ENST00000261937.6:c.3807+1G>T	chr5.hg19:g.180036905C>A		109.0	0.0		124.0	49.0	NM_182925	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Silent	SNP	ENST00000261937.6	hg19	CCDS4457.1																																																																																			.	.		0.607	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4		Silent	A	180036905	C	A	180036905	5	1	263	1	0	0	0	0	0	0	1	0	5952	608	21	3	304	3	FLT4	5	180036905	Splice_Site	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	4078905	180036905	878355	131	38505										
MAS1L	116511	hgsc.bcm.edu	37	chr6	29454972	29454972	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ctcgacacacacatcacaagTgaaaggatagcatggaagag	10	9	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr6:29454972T>C	ENST00000377127.3	-	1	766	c.708A>G	c.(706-708)tcA>tcG	p.S236S		NM_052967.1	NP_443199.1	P35410	MAS1L_HUMAN	MAS1 proto-oncogene like, G protein-coupled receptor	236					G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(7)|pancreas(1)|prostate(2)|skin(2)	28						ACATCACAAGTGAAAGGATAG	0.453																																					p.S236S	NSCLC(153;755 1987 3859 11251 32945)	Atlas-SNP	.											.	MAS1L	66	.	0			c.A708G						.						45	47	46					6																	29454972		2203	4300	6503	SO:0001819	synonymous_variant	116511	exon1			CACAAGTGAAAGG	S78653	CCDS4661.1	6p22.1	2014-06-26	2014-06-26		ENSG00000204687	ENSG00000204687		"GPCR / Class A : Orphans"	13961	protein-coding gene	gene with protein product		607235	"MAS1 oncogene-like"				Standard	NM_052967		Approved	MAS-L, MRG, dJ994E9.2	uc011dlq.2	P35410	OTTHUMG00000031089	ENST00000377127.3:c.708A>G	chr6.hg19:g.29454972T>C		53.0	0.0		83.0	4.0	NM_052967	Q5SUN5	Silent	SNP	ENST00000377127.3	hg19	CCDS4661.1																																																																																			.	.		0.453	MAS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076126.2	NM_052967		C	29454972	T	C	29454972	2	2	263	1	0	0	0	0	0	0	0	1	9330	1683	59	2		2	MAS1L	6	29454972	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10		29454972	141660095	132	38506										
HLA-E	3133	hgsc.bcm.edu	37	chr6	30458995	30458995	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ctgggccctgggcttctaccCtgcggagatcacactgacct	11	15	2	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr6:30458995C>G	ENST00000376630.4	+	4	757	c.692C>G	c.(691-693)cCt>cGt	p.P231R		NM_005516.5	NP_005507.3	P13747	HLAE_HUMAN	major histocompatibility complex, class I, E	231	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of endogenous peptide antigen via MHC class Ib (GO:0002476)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of natural killer cell mediated immunity (GO:0002717)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protection from natural killer cell mediated cytotoxicity (GO:0042270)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	MHC class I protein binding (GO:0042288)|peptide antigen binding (GO:0042605)			breast(2)|central_nervous_system(4)|endometrium(1)|kidney(3)|large_intestine(2)|lung(1)|ovary(3)|skin(1)|urinary_tract(1)	18						GGCTTCTACCCTGCGGAGATC	0.622																																					p.P231R		Atlas-SNP	.											.	HLA-E	35	.	0			c.C692G						.						112	124	120					6																	30458995		1511	2708	4219	SO:0001583	missense	3133	exon4			TCTACCCTGCGGA	M20022	CCDS34379.1	6p21.3	2013-01-11			ENSG00000204592	ENSG00000204592		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4962	protein-coding gene	gene with protein product		143010				3131426	Standard	NM_005516		Approved		uc003nqg.3	P13747	OTTHUMG00000031155	ENST00000376630.4:c.692C>G	chr6.hg19:g.30458995C>G	ENSP00000365817:p.Pro231Arg	130.0	0.0		166.0	58.0	NM_005516	Q30169|Q9BT83|Q9GIY7|Q9GIY8	Missense_Mutation	SNP	ENST00000376630.4	hg19	CCDS34379.1	.	.	.	.	.	.	.	.	.	.	.	15.63	2.890421	0.52014	.	.	ENSG00000204592	ENST00000376630	T	0.57907	0.37	1.67	1.67	0.24075	.	0.000000	0.41712	U	0.000826	T	0.75781	0.3896	H	0.99682	4.7	0.27796	N	0.942642	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.66056	-0.6018	10	0.87932	D	0	.	6.7735	0.23607	0.0:1.0:0.0:0.0	.	272;231	E7ENN9;Q6DU44	.;.	R	231	ENSP00000365817:P231R	ENSP00000365817:P231R	P	+	2	0	HLA-E	30566974	0.989000	0.36119	1.000000	0.80357	0.989000	0.77384	3.777000	0.55364	1.235000	0.43724	0.462000	0.41574	CCT	.	.		0.622	HLA-E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076282.2	NM_005516		G	30458995	C	G	30458995	3	3	263	1	0	0	0	0	1	0	0	0	7219	681	24	4	706	4	HLA-E	6	30458995	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	1004023	30458995	140656072	133	38507										
MDC1	9656	hgsc.bcm.edu	37	chr6	30679231	30679231	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ggaagggccaagctcttgggGtggagtcaacatgaaggcct	16	8	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr6:30679231G>A	ENST00000376406.3	-	7	2826	c.2179C>T	c.(2179-2181)Ccc>Tcc	p.P727S	MDC1-AS1_ENST00000442150.1_RNA|MDC1_ENST00000494654.1_5'Flank|MDC1_ENST00000376405.2_Missense_Mutation_p.P727S	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	727				Missing (in Ref. 2; CAH18685). {ECO:0000305}.	DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intra-S DNA damage checkpoint (GO:0031573)	chromosome (GO:0005694)|focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	FHA domain binding (GO:0070975)|protein C-terminus binding (GO:0008022)			breast(2)|kidney(1)|ovary(1)	4						AGCTCTTGGGGTGGAGTCAAC	0.493								Other conserved DNA damage response genes																													p.P727S		Atlas-SNP	.											.	MDC1	218	.	0			c.C2179T						.						168	124	140					6																	30679231		1511	2709	4220	SO:0001583	missense	9656	exon7			CTTGGGGTGGAGT	D79992	CCDS34384.1	6p21.3	2010-02-17	2009-06-12		ENSG00000137337	ENSG00000137337			21163	protein-coding gene	gene with protein product		607593				10975465, 12607005	Standard	NM_014641		Approved	NFBD1, KIAA0170, Em:AB023051.5	uc003nrg.4	Q14676	OTTHUMG00000031075	ENST00000376406.3:c.2179C>T	chr6.hg19:g.30679231G>A	ENSP00000365588:p.Pro727Ser	184.0	0.0		228.0	83.0	NM_014641	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Missense_Mutation	SNP	ENST00000376406.3	hg19	CCDS34384.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.15|13.15	2.151893|2.151893	0.38021|0.38021	.|.	.|.	ENSG00000137337|ENSG00000137337	ENST00000376406;ENST00000376405;ENST00000429610;ENST00000422104|ENST00000417033	T;T|.	0.09538|.	3.12;2.97|.	5.1|5.1	4.23|4.23	0.50019|0.50019	.|.	0.000000|.	0.37906|.	N|.	0.001891|.	T|T	0.31071|0.31071	0.0785|0.0785	M|M	0.62723|0.62723	1.935|1.935	0.09310|0.09310	N|N	1|1	P;B;P|.	0.50943|.	0.94;0.259;0.886|.	P;B;B|.	0.47015|.	0.534;0.103;0.381|.	T|T	0.17745|0.17745	-1.0359|-1.0359	10|5	0.72032|.	D|.	0.01|.	0.1256|0.1256	9.6749|9.6749	0.40034|0.40034	0.097:0.0:0.903:0.0|0.097:0.0:0.903:0.0	.|.	727;727;727|.	Q14676-2;Q14676;Q14676-4|.	.;MDC1_HUMAN;.|.	S|I	727;727;727;598|51	ENSP00000365588:P727S;ENSP00000365587:P727S|.	ENSP00000365587:P727S|.	P|T	-|-	1|2	0|0	MDC1|MDC1	30787210|30787210	0.139000|0.139000	0.22563|0.22563	0.026000|0.026000	0.17262|0.17262	0.178000|0.178000	0.23041|0.23041	1.202000|1.202000	0.32271|0.32271	1.280000|1.280000	0.44463|0.44463	0.549000|0.549000	0.68633|0.68633	CCC|ACC	.	.		0.493	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641		A	30679231	G	A	30679231	3	1	263	1	0	0	0	0	1	0	0	0	9412	1261	44	3	4126	3	MDC1	6	30679231	Missense_Mutation	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	220236	30679231	140435836	134	38508										
BAT2	7916	hgsc.bcm.edu	37	chr6	31594920	31594920	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tcctgccccaaagcctccccTacccccacctcaccggggcc	6	24	1	0	rs563072458	byFrequency	TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr6:31594920T>A	ENST00000376033.2	+	11	1469	c.1235T>A	c.(1234-1236)cTa>cAa	p.L412Q	PRRC2A_ENST00000376007.4_Missense_Mutation_p.L412Q	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	412	2 X type B repeats.|4 X 57 AA type A repeats.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						AAGCCTCCCCTACCCCCACCT	0.652													T|||	2	0.000399361	0	0	5008	,	,		12301	0		0	False		,,,				2504	0.002				p.L412Q		Atlas-SNP	.											.	PRRC2A	152	.	0			c.T1235A						.						17	19	18					6																	31594920		2202	4296	6498	SO:0001583	missense	7916	exon11			CTCCCCTACCCCC	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"HLA-B associated transcript 2"	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.1235T>A	chr6.hg19:g.31594920T>A	ENSP00000365201:p.Leu412Gln	78.0	0.0		86.0	4.0	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	hg19	CCDS4708.1	.	.	.	.	.	.	.	.	.	.	T	10.86	1.468575	0.26335	.	.	ENSG00000204469	ENST00000424184;ENST00000435052;ENST00000376007;ENST00000376033	T;T	0.03889	3.77;3.77	4.7	3.79	0.43588	.	0.135480	0.34245	N	0.004132	T	0.01222	0.0040	N	0.08118	0	0.43279	D	0.995246	B	0.22604	0.072	B	0.21708	0.036	T	0.45862	-0.9232	10	0.87932	D	0	-1.9103	10.3471	0.43911	0.0:0.9054:0.0:0.0946	.	412	P48634	PRC2A_HUMAN	Q	412	ENSP00000365175:L412Q;ENSP00000365201:L412Q	ENSP00000365175:L412Q	L	+	2	0	PRRC2A	31702899	1.000000	0.71417	0.999000	0.59377	0.889000	0.51656	2.958000	0.49145	1.329000	0.45376	-0.177000	0.13119	CTA	.	.		0.652	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686		A	31594920	T	A	31594920	3	1	263	1	0	0	0	0	1	0	0	0	1319	1522	53	4	1273	4	BAT2	6	31594920	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	915689	31594920	139520147	135	38509										
BAT5	7920	hgsc.bcm.edu	37	chr6	31669898	31669898	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ctccagggcacggggctgatAgtacgtatcctgccaaaaca	11	12	0	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr6:31669898A>G	ENST00000395952.3	-	2	304	c.142T>C	c.(142-144)Tat>Cat	p.Y48H	ABHD16A_ENST00000538874.1_5'UTR|ABHD16A_ENST00000375842.4_5'UTR|XXbac-BPG32J3.20_ENST00000461287.1_3'UTR|MIR4646_ENST00000580775.1_RNA|ABHD16A_ENST00000440843.2_Intron	NM_021160.2	NP_066983.1	O95870	ABHGA_HUMAN	abhydrolase domain containing 16A	48						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)			endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	10						CGGGGCTGATAGTACGTATCC	0.562																																					p.Y48H		Atlas-SNP	.											.	ABHD16A	34	.	0			c.T142C						.						140	94	110					6																	31669898		1511	2709	4220	SO:0001583	missense	7920	exon2			GCTGATAGTACGT	AF129756	CCDS4713.1, CCDS54988.1	6p21.3	2013-01-17	2010-12-09	2010-12-09	ENSG00000204427	ENSG00000204427		"Abhydrolase domain containing"	13921	protein-coding gene	gene with protein product		142620	"HLA-B associated transcript 5"	BAT5		2911734, 2813433	Standard	NM_021160		Approved	NG26, D6S82E	uc003nvy.2	O95870	OTTHUMG00000031177	ENST00000395952.3:c.142T>C	chr6.hg19:g.31669898A>G	ENSP00000379282:p.Tyr48His	77.0	0.0		93.0	4.0	NM_021160	A2BEY3|B7Z4R6|Q5SRR1|Q5SRR2|Q8WYH0|Q9NW33	Missense_Mutation	SNP	ENST00000395952.3	hg19	CCDS4713.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.410599	0.83340	.	.	ENSG00000204427	ENST00000395952	.	.	.	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.61048	0.2316	M	0.78456	2.415	0.80722	D	1	D	0.61697	0.99	P	0.53313	0.723	T	0.69525	-0.5122	9	0.87932	D	0	-1.4182	12.2692	0.54695	1.0:0.0:0.0:0.0	.	48	O95870	ABHGA_HUMAN	H	48	.	ENSP00000379282:Y48H	Y	-	1	0	ABHD16A	31777877	1.000000	0.71417	0.999000	0.59377	0.966000	0.64601	4.574000	0.60900	2.155000	0.67459	0.459000	0.35465	TAT	.	.		0.562	ABHD16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076342.4			G	31669898	A	G	31669898	3	3	263	1	0	0	0	0	1	0	0	0	1324	420	15	2	1610	2	BAT5	6	31669898	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	74978	31669898	139445169	136	38510										
COL11A2	1302	hgsc.bcm.edu	37	chr6	33137627	33137627	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ccttgacacctggctcgcccTggatccctggagatcctgac	10	16	0	3			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr6:33137627T>C	ENST00000374708.4	-	48	3671	c.3413A>G	c.(3412-3414)cAg>cGg	p.Q1138R	COL11A2_ENST00000395197.1_Missense_Mutation_p.Q1164R|COL11A2_ENST00000374714.1_Missense_Mutation_p.Q1198R|COL11A2_ENST00000374713.1_Missense_Mutation_p.Q1177R|COL11A2_ENST00000357486.1_Missense_Mutation_p.Q1203R|COL11A2_ENST00000361917.1_Missense_Mutation_p.Q1117R|COL11A2_ENST00000374712.1_Missense_Mutation_p.Q1143R|COL11A2_ENST00000341947.2_Missense_Mutation_p.Q1224R|COL11A2_ENST00000477772.1_Intron	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	1224	Collagen-like 6.|Triple-helical region.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						TGGCTCGCCCTGGATCCCTGG	0.557																																					p.Q1224R	Melanoma(1;90 116 3946 5341 17093)	Atlas-SNP	.											COL11A2,NS,carcinoma,0,1	COL11A2	124	.	0			c.A3671G						.						119	103	108					6																	33137627		2203	4300	6503	SO:0001583	missense	1302	exon50			TCGCCCTGGATCC	U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"Collagens"	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000374708.4:c.3413A>G	chr6.hg19:g.33137627T>C	ENSP00000363840:p.Gln1138Arg	67.0	1.0		86.0	8.0	NM_080680	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Missense_Mutation	SNP	ENST00000374708.4	hg19	CCDS43452.1	.	.	.	.	.	.	.	.	.	.	T	13.54	2.268174	0.40095	.	.	ENSG00000204248	ENST00000374708;ENST00000341947;ENST00000357486;ENST00000374714;ENST00000374713;ENST00000395197;ENST00000374712;ENST00000361917	D;D;D;D;D;D;D;D	0.93488	-3.23;-3.23;-3.23;-3.23;-3.23;-3.23;-3.23;-3.23	4.52	3.35	0.38373	.	0.525252	0.17997	N	0.155038	T	0.71542	0.3352	N	0.03304	-0.355	0.26544	N	0.974033	B;B;B	0.19331	0.034;0.034;0.035	B;B;B	0.17098	0.017;0.017;0.011	T	0.64896	-0.6299	10	0.39692	T	0.17	.	9.4239	0.38567	0.0:0.0:0.1908:0.8092	.	1117;1138;1224	P13942-8;P13942-6;P13942	.;.;COBA2_HUMAN	R	1138;1224;1203;1198;1177;1164;1143;1117	ENSP00000363840:Q1138R;ENSP00000339915:Q1224R;ENSP00000350079:Q1203R;ENSP00000363846:Q1198R;ENSP00000363845:Q1177R;ENSP00000378623:Q1164R;ENSP00000363844:Q1143R;ENSP00000355123:Q1117R	ENSP00000339915:Q1224R	Q	-	2	0	COL11A2	33245605	0.996000	0.38824	1.000000	0.80357	0.995000	0.86356	0.685000	0.25378	1.908000	0.55244	0.448000	0.29417	CAG	.	.		0.557	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2			C	33137627	T	C	33137627	3	2	263	1	0	0	0	0	1	0	0	0	3670	1580	55	2	1607	2	COL11A2	6	33137627	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	1467729	33137627	137977440	137	38511										
SYNGAP1	8831	hgsc.bcm.edu	37	chr6	33405455	33405455	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	accatgccaggacaacagccGccgggtagacaatgtgctaa	11	12	0	1	rs538281267		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr6:33405455G>A	ENST00000418600.2	+	8	874	c.773G>A	c.(772-774)cGc>cAc	p.R258H	SYNGAP1_ENST00000428982.2_Missense_Mutation_p.R199H|SYNGAP1_ENST00000293748.5_Missense_Mutation_p.R258H|MIR5004_ENST00000579078.1_RNA|SYNGAP1_ENST00000496374.1_3'UTR	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	258	C2.				dendrite development (GO:0016358)|negative regulation of axonogenesis (GO:0050771)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|pattern specification process (GO:0007389)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|receptor clustering (GO:0043113)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of MAPK cascade (GO:0043408)|regulation of synapse structure and activity (GO:0050803)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Rab GTPase activator activity (GO:0005097)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(15)|ovary(7)|pancreas(1)|stomach(1)|urinary_tract(1)	43						GACAACAGCCGCCGGGTAGAC	0.542													G|||	1	0.000199681	0	0.0014	5008	,	,		13786	0		0	False		,,,				2504	0				p.R258H		Atlas-SNP	.											.	SYNGAP1	202	.	0			c.G773A						.						160	180	173					6																	33405455		2203	4300	6503	SO:0001583	missense	8831	exon8			ACAGCCGCCGGGT	AB067525	CCDS34434.2	6p21.3	2010-06-25	2010-06-25		ENSG00000197283	ENSG00000197283			11497	protein-coding gene	gene with protein product		603384	"synaptic Ras GTPase activating protein 1 homolog (rat)"			9581761, 18323856	Standard	NM_006772		Approved	SYNGAP, RASA5, KIAA1938	uc011dri.2	Q96PV0	OTTHUMG00000031096	ENST00000418600.2:c.773G>A	chr6.hg19:g.33405455G>A	ENSP00000403636:p.Arg258His	59.0	0.0		64.0	24.0	NM_006772	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Missense_Mutation	SNP	ENST00000418600.2	hg19	CCDS34434.2	.	.	.	.	.	.	.	.	.	.	G	20.7	4.041630	0.75732	.	.	ENSG00000197283	ENST00000293748;ENST00000418600;ENST00000449372;ENST00000428982	D;D;D	0.93488	-3.23;-3.23;-3.23	4.51	4.51	0.55191	SynGAP C2 domain, N-terminal (1);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.64402	D	0.000001	D	0.96097	0.8728	M	0.80028	2.48	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.997	D;D;P	0.83275	0.991;0.996;0.842	D	0.96595	0.9440	10	0.87932	D	0	.	14.7891	0.69827	0.0:0.0:1.0:0.0	.	258;258;258	Q96PV0;Q96PV0-4;B7ZCA0	SYGP1_HUMAN;.;.	H	258;258;258;199	ENSP00000293748:R258H;ENSP00000403636:R258H;ENSP00000412475:R199H	ENSP00000293748:R258H	R	+	2	0	SYNGAP1	33513433	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.860000	0.86993	2.341000	0.79615	0.655000	0.94253	CGC	.	.		0.542	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407		A	33405455	G	A	33405455	3	1	263	1	0	0	0	0	1	0	0	0	15462	1087	38	1	803	1	SYNGAP1	6	33405455	Missense_Mutation	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	267828	33405455	137709612	138	38512										
IP6K3	117283	hgsc.bcm.edu	37	chr6	33696059	33696059	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ggcctgtgctgtctttccagAggtgcactgtgacggtacct	13	11	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr6:33696059A>G	ENST00000293756.4	-	3	544	c.218T>C	c.(217-219)cTc>cCc	p.L73P	IP6K3_ENST00000451316.1_Missense_Mutation_p.L73P	NM_054111.4	NP_473452.2	Q96PC2	IP6K3_HUMAN	inositol hexakisphosphate kinase 3	73					inositol phosphate biosynthetic process (GO:0032958)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol metabolic process (GO:0046488)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol hexakisphosphate 6-kinase activity (GO:0000831)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			skin(1)	1						GTCTTTCCAGAGGTGCACTGT	0.597																																					p.L73P		Atlas-SNP	.											.	IP6K3	52	.	0			c.T218C						.						69	63	65					6																	33696059		2203	4300	6503	SO:0001583	missense	117283	exon4			TTCCAGAGGTGCA	AF393812	CCDS34435.1	6p21.31	2009-01-05	2009-01-05	2008-12-22	ENSG00000161896	ENSG00000161896			17269	protein-coding gene	gene with protein product		606993	"inositol hexaphosphate kinase 3"	IHPK3		11502751	Standard	NM_054111		Approved	INSP6K3	uc003ofb.2	Q96PC2	OTTHUMG00000014531	ENST00000293756.4:c.218T>C	chr6.hg19:g.33696059A>G	ENSP00000293756:p.Leu73Pro	89.0	0.0		113.0	6.0	NM_001142883	Q96MQ9	Missense_Mutation	SNP	ENST00000293756.4	hg19	CCDS34435.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.198304	0.79015	.	.	ENSG00000161896	ENST00000451316;ENST00000293756	T;T	0.13778	2.56;2.56	5.69	5.69	0.88448	.	0.000000	0.56097	D	0.000039	T	0.28896	0.0717	M	0.75447	2.3	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.04467	-1.0949	10	0.72032	D	0.01	-37.138	14.1824	0.65583	1.0:0.0:0.0:0.0	.	73	Q96PC2	IP6K3_HUMAN	P	73	ENSP00000398861:L73P;ENSP00000293756:L73P	ENSP00000293756:L73P	L	-	2	0	IP6K3	33804037	1.000000	0.71417	0.990000	0.47175	0.960000	0.62799	6.743000	0.74848	2.168000	0.68352	0.533000	0.62120	CTC	.	.		0.597	IP6K3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040203.1	NM_054111		G	33696059	A	G	33696059	3	3	263	1	0	0	0	0	1	0	0	0	7799	304	11	2	1030	2	IP6K3	6	33696059	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	290604	33696059	137419008	139	38513										
TEAD3	7005	hgsc.bcm.edu	37	chr6	35443341	35443341	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gccacccagagcccccactcAcctccaccttctctaccacc	3	24	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr6:35443341A>G	ENST00000402886.3	-	9	1015		c.e9+1		TEAD3_ENST00000338863.7_Splice_Site			Q99594	TEAD3_HUMAN	TEA domain family member 3						female pregnancy (GO:0007565)|gene expression (GO:0010467)|hippo signaling (GO:0035329)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	10						GCCCCCACTCACCTCCACCTT	0.582																																					.		Atlas-SNP	.											.	TEAD3	52	.	0			c.1041+2T>C						.						56	70	65					6																	35443341		2186	4289	6475	SO:0001630	splice_region_variant	7005	exon12			CCACTCACCTCCA	X94439	CCDS47414.1	6p21.2	2008-07-28			ENSG00000007866	ENSG00000007866			11716	protein-coding gene	gene with protein product		603170		TEAD5		9889009, 9148898	Standard	NM_003214		Approved	TEF-5, ETFR-1	uc003oku.4	Q99594	OTTHUMG00000014571	ENST00000402886.3:c.861+1T>C	chr6.hg19:g.35443341A>G		95.0	0.0		131.0	6.0	NM_003214	O95910|Q5BJG7|Q8N6Y4	Splice_Site	SNP	ENST00000402886.3	hg19		.	.	.	.	.	.	.	.	.	.	A	19.64	3.866026	0.71949	.	.	ENSG00000007866	ENST00000338863;ENST00000402886;ENST00000373905	.	.	.	4.82	4.82	0.62117	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.7159	0.62695	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TEAD3	35551319	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	8.992000	0.93519	2.023000	0.59567	0.374000	0.22700	.	.	.		0.582	TEAD3-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316961.2		Intron	G	35443341	A	G	35443341	5	3	263	1	0	0	0	0	0	0	1	0	15755	173	6	2	276	2	TEAD3	6	35443341	Splice_Site	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	1747282	35443341	135671726	140	38514										
GPR111	222611	hgsc.bcm.edu	37	chr6	47649351	47649351	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	actattggggctattttggaAgccagtcttttggaaaatgt	11	5	1	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr6:47649351A>G	ENST00000296862.1	+	6	1056	c.1056A>G	c.(1054-1056)gaA>gaG	p.E352E	GPR111_ENST00000507065.1_Silent_p.E284E|GPR111_ENST00000398742.2_Silent_p.E284E			Q8IZF7	GP111_HUMAN	G protein-coupled receptor 111	352					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(2)|lung(15)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29						CTATTTTGGAAGCCAGTCTTT	0.433																																					p.E284E		Atlas-SNP	.											.	GPR111	123	.	0			c.A852G						.						128	123	124					6																	47649351		1866	4103	5969	SO:0001819	synonymous_variant	222611	exon7			TTTGGAAGCCAGT	AB065684		6p12.3	2014-08-08			ENSG00000164393	ENSG00000164393		"-", "GPCR / Class B : Orphans"	18991	protein-coding gene	gene with protein product						12435584	Standard	NM_153839		Approved	hGPCR35, PGR20	uc003oyy.3	Q8IZF7	OTTHUMG00000046168	ENST00000296862.1:c.1056A>G	chr6.hg19:g.47649351A>G		71.0	0.0		96.0	4.0	NM_153839	Q2PNZ1|Q86SL6|Q8NGU5|Q8TDT5	Silent	SNP	ENST00000296862.1	hg19																																																																																				.	.		0.433	GPR111-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000106423.2	NM_153839		G	47649351	A	G	47649351	2	3	263	1	0	0	0	0	0	0	0	1	6636	69	3	2		2	GPR111	6	47649351	Silent	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	12206010	47649351	123465716	141	38515										
DST	667	hgsc.bcm.edu	37	chr6	56443682	56443682	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tctaaaagcacttcagccgtTttcttcagtttctctacagc	5	12	5	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr6:56443682T>C	ENST00000361203.3	-	46	12331	c.12324A>G	c.(12322-12324)aaA>aaG	p.K4108K	DST_ENST00000244364.6_Silent_p.K1696K|DST_ENST00000370788.2_Silent_p.K2022K|DST_ENST00000421834.2_Silent_p.K2022K|DST_ENST00000446842.2_Silent_p.K3784K|DST_ENST00000370754.5_Silent_p.K4288K|DST_ENST00000312431.6_Silent_p.K4108K|DST_ENST00000370769.4_Silent_p.K4110K			Q03001	DYST_HUMAN	dystonin	4108					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			CTTCAGCCGTTTTCTTCAGTT	0.403																																					p.K1696K		Atlas-SNP	.											.	DST	1427	.	0			c.A5088G						.						76	77	77					6																	56443682		1839	4086	5925	SO:0001819	synonymous_variant	667	exon31			AGCCGTTTTCTTC	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.12324A>G	chr6.hg19:g.56443682T>C		85.0	0.0		118.0	5.0	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000361203.3	hg19																																																																																				.	.		0.403	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		C	56443682	T	C	56443682	2	2	263	1	0	0	0	0	0	0	0	1	4785	1838	64	2		2	DST	6	56443682	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	8794331	56443682	114671385	142	38516										
COL12A1	1303	hgsc.bcm.edu	37	chr6	75806978	75806978	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ttagttcttaccggcggcccTggtgggcccctgggtcccat	13	14	1	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr6:75806978T>C	ENST00000322507.8	-	59	8877	c.8568A>G	c.(8566-8568)ccA>ccG	p.P2856P	COL12A1_ENST00000511023.1_5'UTR|COL12A1_ENST00000483888.2_Silent_p.P2856P|COL12A1_ENST00000416123.2_Silent_p.P2780P|COL12A1_ENST00000345356.6_Silent_p.P1692P	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	2856	Collagen-like 3.|Triple-helical region (COL2) with 1 imperfection.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						CCGGCGGCCCTGGTGGGCCCC	0.468																																					p.P2856P		Atlas-SNP	.											.	COL12A1	385	.	0			c.A8568G						.						106	109	108					6																	75806978		1826	4084	5910	SO:0001819	synonymous_variant	1303	exon59			CGGCCCTGGTGGG	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.8568A>G	chr6.hg19:g.75806978T>C		110.0	0.0		72.0	4.0	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Silent	SNP	ENST00000322507.8	hg19	CCDS43482.1																																																																																			.	.		0.468	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		C	75806978	T	C	75806978	2	2	263	1	0	0	0	0	0	0	0	1	3671	1567	55	2		2	COL12A1	6	75806978	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	19363296	75806978	95308089	143	38517										
COL12A1	1303	hgsc.bcm.edu	37	chr6	75864133	75864133	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	atgtaactcaatttcttaccAgaagataaaattggcataac	5	7	2	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr6:75864133A>G	ENST00000322507.8	-	17	3873	c.3564T>C	c.(3562-3564)tcT>tcC	p.S1188S	COL12A1_ENST00000483888.2_Splice_Site_p.S1188S|COL12A1_ENST00000416123.2_Splice_Site_p.S1188S|COL12A1_ENST00000345356.6_Intron	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	1188					cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						ATTTCTTACCAGAAGATAAAA	0.343																																					p.S1188S		Atlas-SNP	.											.	COL12A1	385	.	0			c.T3564C						.						107	104	105					6																	75864133		1834	4087	5921	SO:0001630	splice_region_variant	1303	exon17			CTTACCAGAAGAT	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.3565+1T>C	chr6.hg19:g.75864133A>G		87.0	0.0		95.0	4.0	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Silent	SNP	ENST00000322507.8	hg19	CCDS43482.1																																																																																			.	.		0.343	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370	Silent	G	75864133	A	G	75864133	5	3	263	1	0	0	0	0	0	0	1	0	3671	202	7	2	5827	2	COL12A1	6	75864133	Splice_Site	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	57155	75864133	95250934	144	38518										
SENP6	26054	hgsc.bcm.edu	37	chr6	76405605	76405605	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tctataaacgccttaatcagAgagagaggagaaatcatgaa	9	6	3	4			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr6:76405605A>G	ENST00000447266.2	+	17	2639	c.2161A>G	c.(2161-2163)Aga>Gga	p.R721G	SENP6_ENST00000370014.3_Missense_Mutation_p.R721G|SENP6_ENST00000370010.2_Missense_Mutation_p.R714G|SENP6_ENST00000541192.1_Missense_Mutation_p.R317G	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	721	Protease.				protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				CCTTAATCAGAGAGAGAGGAG	0.323																																					p.R721G		Atlas-SNP	.											.	SENP6	189	.	0			c.A2161G						.						73	73	73					6																	76405605		1824	4080	5904	SO:0001583	missense	26054	exon17			AATCAGAGAGAGA		CCDS43483.1, CCDS47454.1	6q13-q14.3	2008-02-05	2005-08-17		ENSG00000112701	ENSG00000112701			20944	protein-coding gene	gene with protein product		605003	"SUMO1/sentrin specific protease 6"				Standard	NM_015571		Approved	SUSP1, KIAA0797	uc003pid.4	Q9GZR1	OTTHUMG00000015060	ENST00000447266.2:c.2161A>G	chr6.hg19:g.76405605A>G	ENSP00000402527:p.Arg721Gly	154.0	0.0		97.0	4.0	NM_015571	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Missense_Mutation	SNP	ENST00000447266.2	hg19	CCDS47454.1	.	.	.	.	.	.	.	.	.	.	A	16.22	3.060324	0.55432	.	.	ENSG00000112701	ENST00000370010;ENST00000370014;ENST00000447266;ENST00000541192	T;T;T;T	0.28666	1.6;1.6;1.6;1.6	5.94	4.75	0.60458	.	0.040834	0.85682	D	0.000000	T	0.29458	0.0734	L	0.35414	1.06	0.52099	D	0.99994	B;D	0.60575	0.167;0.988	B;D	0.66979	0.196;0.948	T	0.05566	-1.0877	10	0.41790	T	0.15	-22.3027	13.1509	0.59488	0.8664:0.1335:0.0:0.0	.	714;721	Q9GZR1-2;Q9GZR1	.;SENP6_HUMAN	G	714;721;721;317	ENSP00000359027:R714G;ENSP00000359031:R721G;ENSP00000402527:R721G;ENSP00000441715:R317G	ENSP00000359027:R714G	R	+	1	2	SENP6	76462325	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.746000	0.62133	1.034000	0.39945	0.455000	0.32223	AGA	.	.		0.323	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	NM_015571		G	76405605	A	G	76405605	3	3	263	1	0	0	0	0	1	0	0	0	14065	296	11	2	2227	2	SENP6	6	76405605	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	541472	76405605	94709462	145	38519										
CGA	1081	hgsc.bcm.edu	37	chr6	87795550	87795550	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tgaaaccccccattactgtgAcctaaaggggaaggaaaaaa	9	9	0	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr6:87795550A>G	ENST00000369582.2	-	4	375	c.275T>C	c.(274-276)gTc>gCc	p.V92A	RN7SKP209_ENST00000516888.1_RNA	NM_000735.3	NP_000726.1	P01215	GLHA_HUMAN	glycoprotein hormones, alpha polypeptide	92					cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|cellular response to hormone stimulus (GO:0032870)|developmental growth (GO:0048589)|follicle-stimulating hormone secretion (GO:0046884)|gonad development (GO:0008406)|luteinizing hormone secretion (GO:0032275)|negative regulation of organ growth (GO:0046621)|peptide hormone processing (GO:0016486)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(1)	15		all_cancers(76;5.98e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;5.29e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.000102)		BRCA - Breast invasive adenocarcinoma(108;0.0484)		CATTACTGTGACCTAAAGGGG	0.348																																					p.V123A		Atlas-SNP	.											CGA,colon,carcinoma,0,1	CGA	22	.	0			c.T368C						.						52	51	51					6																	87795550		2203	4300	6503	SO:0001630	splice_region_variant	1081	exon5			ACTGTGACCTAAA	V00518	CCDS5007.1, CCDS75492.1	6q14-q21	2013-02-26			ENSG00000135346	ENSG00000135346		"Endogenous ligands"	1885	protein-coding gene	gene with protein product	"follicle-stimulating hormone alpha subunit", "chorionic gonadotropin, alpha polypeptide", "luteinizing hormone alpha chain", "lutropin alpha chain", "thyroid-stimulating hormone alpha chain", "glycoprotein hormones alpha chain"	118850				6286817	Standard	NM_000735		Approved	HCG, GPHa, GPHA1, FSHA, LHA, TSHA	uc021zci.1	P01215	OTTHUMG00000015161	ENST00000369582.2:c.274-1T>C	chr6.hg19:g.87795550A>G		89.0	2.0		64.0	3.0	NM_001252383		Missense_Mutation	SNP	ENST00000369582.2	hg19	CCDS5007.1	.	.	.	.	.	.	.	.	.	.	A	3.929	-0.016529	0.07681	.	.	ENSG00000135346	ENST00000369582	.	.	.	5.73	1.89	0.25635	.	0.510013	0.19481	N	0.113210	T	0.16514	0.0397	L	0.31371	0.925	0.32973	D	0.522561	B	0.13594	0.008	B	0.16289	0.015	T	0.07404	-1.0774	9	0.22706	T	0.39	-26.6509	7.1256	0.25469	0.5016:0.0:0.4984:0.0	.	92	P01215	GLHA_HUMAN	A	92	.	ENSP00000358595:V92A	V	-	2	0	CGA	87852269	0.993000	0.37304	0.958000	0.39756	0.069000	0.16628	1.617000	0.36943	0.356000	0.24157	-0.182000	0.12963	GTC	.	.		0.348	CGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041425.1	NM_000735	Missense_Mutation	G	87795550	A	G	87795550	5	3	263	1	0	0	0	0	0	0	1	0	3297	289	10	2	79	2	CGA	6	87795550	Splice_Site	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	11389945	87795550	83319517	146	38520										
ANKRD6	22881	hgsc.bcm.edu	37	chr6	90340295	90340295	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cgtcttctgactgtacaggcTcccgactgagaaacgtcaag	10	12	3	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr6:90340295T>C	ENST00000522441.1	+	16	2397	c.1756T>C	c.(1756-1758)Tcc>Ccc	p.S586P	ANKRD6_ENST00000339746.4_Missense_Mutation_p.S586P|LYRM2_ENST00000520441.1_Intron|ANKRD6_ENST00000369408.5_Missense_Mutation_p.S551P|ANKRD6_ENST00000520793.1_Missense_Mutation_p.S522P|ANKRD6_ENST00000447838.2_Missense_Mutation_p.S581P	NM_001242811.1	NP_001229740.1	Q9Y2G4	ANKR6_HUMAN	ankyrin repeat domain 6	586					negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of JNK cascade (GO:0046330)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(3)|large_intestine(7)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|stomach(2)	21		all_cancers(76;1.22e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;1.83e-05)|Lung NSC(302;0.239)		BRCA - Breast invasive adenocarcinoma(108;0.0209)		CTGTACAGGCTCCCGACTGAG	0.582																																					p.S586P		Atlas-SNP	.											.	ANKRD6	51	.	0			c.T1756C						.						30	31	31					6																	90340295		1975	4151	6126	SO:0001583	missense	22881	exon16			ACAGGCTCCCGAC	AB023174	CCDS47460.1, CCDS56441.1, CCDS56442.1, CCDS56443.1	6q14.2-q16.1	2013-03-20			ENSG00000135299	ENSG00000135299		"Ankyrin repeat domain containing"	17280	protein-coding gene	gene with protein product		610583					Standard	NM_001242809		Approved	KIAA0957	uc003pni.4	Q9Y2G4	OTTHUMG00000015202	ENST00000522441.1:c.1756T>C	chr6.hg19:g.90340295T>C	ENSP00000430985:p.Ser586Pro	130.0	0.0		99.0	5.0	NM_001242809	B3KUC3|Q5JUJ4|Q5JUJ5|Q8IUQ8|Q9NU24|Q9UFQ9	Missense_Mutation	SNP	ENST00000522441.1	hg19	CCDS56441.1	.	.	.	.	.	.	.	.	.	.	T	13.08	2.130650	0.37630	.	.	ENSG00000135299	ENST00000369408;ENST00000339746;ENST00000447838;ENST00000522441;ENST00000520793	T;T;T;T;T	0.72615	0.56;0.58;0.82;0.58;-0.67	4.9	3.71	0.42584	.	0.000000	0.56097	D	0.000022	T	0.66356	0.2781	L	0.57536	1.79	0.80722	D	1	B;P;P;P	0.49862	0.31;0.811;0.929;0.811	B;B;P;B	0.52424	0.177;0.403;0.698;0.35	T	0.70680	-0.4805	10	0.66056	D	0.02	-3.9454	12.2295	0.54480	0.0:0.0:0.1421:0.8579	.	522;586;551;581	B3KUC3;Q9Y2G4;Q9Y2G4-1;C9JJE8	.;ANKR6_HUMAN;.;.	P	551;586;581;586;522	ENSP00000358416:S551P;ENSP00000345767:S586P;ENSP00000396771:S581P;ENSP00000430985:S586P;ENSP00000429782:S522P	ENSP00000345767:S586P	S	+	1	0	ANKRD6	90397016	0.999000	0.42202	0.711000	0.30485	0.221000	0.24807	3.487000	0.53222	0.963000	0.38082	0.460000	0.39030	TCC	.	.		0.582	ANKRD6-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376594.1			C	90340295	T	C	90340295	3	2	263	1	0	0	0	0	1	0	0	0	685	1551	54	2	1799	2	ANKRD6	6	90340295	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	2544745	90340295	80774772	147	38521										
MDN1	23195	hgsc.bcm.edu	37	chr6	90411385	90411385	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tgttctgagacagtctgaacTtctttgtaatatctttaaag	7	6	4	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr6:90411385T>C	ENST00000369393.3	-	55	8434	c.8319A>G	c.(8317-8319)gaA>gaG	p.E2773E	MDN1_ENST00000428876.1_Silent_p.E2773E			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	2773					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		CAGTCTGAACTTCTTTGTAAT	0.423																																					p.E2773E		Atlas-SNP	.											.	MDN1	478	.	0			c.A8319G						.						41	42	41					6																	90411385		2203	4300	6503	SO:0001819	synonymous_variant	23195	exon55			CTGAACTTCTTTG	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.8319A>G	chr6.hg19:g.90411385T>C		59.0	0.0		46.0	4.0	NM_014611	O15019|Q5T794	Silent	SNP	ENST00000369393.3	hg19	CCDS5024.1																																																																																			.	.		0.423	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			C	90411385	T	C	90411385	2	2	263	1	0	0	0	0	0	0	0	1	9424	1606	56	2		2	MDN1	6	90411385	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	71090	90411385	80703682	148	38522										
BACH2	60468	hgsc.bcm.edu	37	chr6	90661367	90661367	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cagagttctcgcagtcctcgTgtgggcgctggcacgcagca	14	13	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr6:90661367T>C	ENST00000257749.4	-	7	1165	c.458A>G	c.(457-459)cAc>cGc	p.H153R	RP3-512E2.2_ENST00000445838.1_RNA|BACH2_ENST00000537989.1_Missense_Mutation_p.H153R|RP3-512E2.2_ENST00000413986.1_RNA|BACH2_ENST00000343122.3_Missense_Mutation_p.H153R	NM_021813.2	NP_068585.1	Q9BYV9	BACH2_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 2	153						cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	45		all_cancers(76;7.37e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.0063)		BRCA - Breast invasive adenocarcinoma(108;0.0799)		GCAGTCCTCGTGTGGGCGCTG	0.592																																					p.H153R		Atlas-SNP	.											.	BACH2	224	.	0			c.A458G						.						89	85	86					6																	90661367		2203	4300	6503	SO:0001583	missense	60468	exon5			TCCTCGTGTGGGC	AL121787	CCDS5026.1	6q15	2013-01-10			ENSG00000112182	ENSG00000112182		"BTB/POZ domain containing", "basic leucine zipper proteins"	14078	protein-coding gene	gene with protein product		605394				10949928, 12829606	Standard	NM_001170794		Approved	BTBD25	uc003pnw.3	Q9BYV9	OTTHUMG00000015216	ENST00000257749.4:c.458A>G	chr6.hg19:g.90661367T>C	ENSP00000257749:p.His153Arg	79.0	0.0		46.0	4.0	NM_001170794	E1P518|Q59H70|Q5T793|Q9NTS5	Missense_Mutation	SNP	ENST00000257749.4	hg19	CCDS5026.1	.	.	.	.	.	.	.	.	.	.	T	7.081	0.570218	0.13560	.	.	ENSG00000112182	ENST00000257749;ENST00000537989;ENST00000343122	T;T;T	0.37584	1.19;1.19;1.19	5.68	3.23	0.37069	.	0.270736	0.35262	N	0.003322	T	0.07188	0.0182	N	0.24115	0.695	0.27078	N	0.963169	B	0.20052	0.041	B	0.24155	0.051	T	0.40289	-0.9571	10	0.09590	T	0.72	-11.3991	8.2679	0.31827	0.0:0.0693:0.1342:0.7965	.	153	Q9BYV9	BACH2_HUMAN	R	153	ENSP00000257749:H153R;ENSP00000437473:H153R;ENSP00000345642:H153R	ENSP00000257749:H153R	H	-	2	0	BACH2	90718088	0.366000	0.25014	0.367000	0.25926	0.466000	0.32739	0.643000	0.24750	0.404000	0.25506	0.460000	0.39030	CAC	.	.		0.592	BACH2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041522.2	NM_021813		C	90661367	T	C	90661367	3	2	263	1	0	0	0	0	1	0	0	0	1284	1696	59	2	2079	2	BACH2	6	90661367	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	249982	90661367	80453700	149	38523										
SFRS18	25957	hgsc.bcm.edu	37	chr6	99862518	99862518	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ggccactgctgccaaggctgTcctccttgatcccacatccc	8	18	0	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr6:99862518T>C	ENST00000369239.5	-	3	222	c.18A>G	c.(16-18)ggA>ggG	p.G6G	PNISR_ENST00000438806.1_Silent_p.G6G|PNISR_ENST00000466057.1_5'UTR	NM_032870.2	NP_116259.2	Q8TF01	PNISR_HUMAN	PNN-interacting serine/arginine-rich protein	6	Gln-rich.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24						GCCAAGGCTGTCCTCCTTGAT	0.363																																					p.G6G		Atlas-SNP	.											.	PNISR	74	.	0			c.A18G						.						136	125	129					6																	99862518		2203	4300	6503	SO:0001819	synonymous_variant	25957	exon2			AGGCTGTCCTCCT	AK027759	CCDS5043.1	6q16.3	2011-06-06	2011-06-06	2011-06-06	ENSG00000132424	ENSG00000132424			21222	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 111", "splicing factor, arginine/serine-rich 18"	C6orf111, SFRS18		14578391	Standard	NM_032870		Approved	FLJ14752, bA98I9.2, DKFZp564B0769, SRrp130	uc021zdd.1	Q8TF01	OTTHUMG00000015262	ENST00000369239.5:c.18A>G	chr6.hg19:g.99862518T>C		106.0	0.0		76.0	4.0	NM_015491	A8K540|E1P5D2|Q5T064|Q5T065|Q6P2B4|Q6P2N4|Q6PJ93|Q6PK36|Q7Z640|Q8N2L1|Q8TF00|Q96K10|Q96SI3|Q96SM5|Q9P076|Q9P0C0|Q9Y4N3	Silent	SNP	ENST00000369239.5	hg19	CCDS5043.1																																																																																			.	.		0.363	PNISR-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041598.1	NM_032870		C	99862518	T	C	99862518	2	2	263	1	0	0	0	0	0	0	0	1	14189	1654	58	2		2	SFRS18	6	99862518	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	9201151	99862518	71252549	150	38524										
AIM1	202	hgsc.bcm.edu	37	chr6	106967048	106967048	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gaactaaatcttaaaaccccTaagaatcttgacagtttggg	7	8	2	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr6:106967048T>C	ENST00000369066.3	+	2	1228	c.741T>C	c.(739-741)ccT>ccC	p.P247P		NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)		p.P247P(1)		breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		TTAAAACCCCTAAGAATCTTG	0.403																																					p.P247P		Atlas-SNP	.											AIM1,NS,carcinoma,0,1	AIM1	161	.	1	Substitution - coding silent(1)	breast(1)	c.T741C						.						53	54	54					6																	106967048		2203	4300	6503	SO:0001819	synonymous_variant	202	exon2			AACCCCTAAGAAT	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"suppression of tumorigenicity 4", "beta-gamma crystallin domain containing 1"	601797	"suppression of tumorigenicity 4 (malignant melanoma)"	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.741T>C	chr6.hg19:g.106967048T>C		51.0	0.0		36.0	3.0	NM_001624	Q6P2P0|Q9BTM3	Silent	SNP	ENST00000369066.3	hg19	CCDS34506.1																																																																																			.	.		0.403	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1			C	106967048	T	C	106967048	2	2	263	1	0	0	0	0	0	0	0	1	430	1509	53	2		2	AIM1	6	106967048	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	7104530	106967048	64148019	151	38525										
HEY2	23493	hgsc.bcm.edu	37	chr6	126080600	126080600	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tcagaagtgcctcctgcccaCggctctgctctcctcacggc	9	18	4	1	rs376521140		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr6:126080600C>T	ENST00000368364.3	+	5	863	c.666C>T	c.(664-666)caC>caT	p.H222H	HEY2_ENST00000368365.1_Silent_p.H176H	NM_012259.2	NP_036391.1	Q9UBP5	HEY2_HUMAN	hes-related family bHLH transcription factor with YRPW motif 2	222					anterior/posterior axis specification (GO:0009948)|arterial endothelial cell differentiation (GO:0060842)|ascending aorta morphogenesis (GO:0035910)|atrial septum morphogenesis (GO:0060413)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate commitment (GO:0045165)|cochlea development (GO:0090102)|coronary vasculature morphogenesis (GO:0060977)|dorsal aorta morphogenesis (GO:0035912)|endocardial cushion to mesenchymal transition involved in heart valve formation (GO:0003199)|heart trabecula formation (GO:0060347)|labyrinthine layer blood vessel development (GO:0060716)|mesenchymal cell development (GO:0014031)|muscular septum morphogenesis (GO:0003150)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cardiac vascular smooth muscle cell differentiation (GO:2000723)|negative regulation of gene expression (GO:0010629)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription by transcription factor localization (GO:0010621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000820)|negative regulation of transcription initiation from RNA polymerase II promoter (GO:0060633)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of heart rate (GO:0010460)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein-DNA complex assembly (GO:0065004)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of auditory receptor cell differentiation (GO:0045607)|regulation of vasculogenesis (GO:2001212)|smooth muscle cell differentiation (GO:0051145)|tricuspid valve formation (GO:0003195)|tricuspid valve morphogenesis (GO:0003186)|umbilical cord morphogenesis (GO:0036304)|vascular smooth muscle cell development (GO:0097084)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell development (GO:0055015)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	histone deacetylase binding (GO:0042826)|microsatellite binding (GO:0035939)|protein binding transcription factor activity (GO:0000988)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.H222H(1)		breast(1)|large_intestine(7)|lung(5)|prostate(1)	14				UCEC - Uterine corpus endometrioid carcinoma (4;0.0608)|GBM - Glioblastoma multiforme(226;0.0361)|all cancers(137;0.193)		CTCCTGCCCACGGCTCTGCTC	0.657																																					p.H222H		Atlas-SNP	.											HEY2,NS,carcinoma,0,1	HEY2	44	.	1	Substitution - coding silent(1)	prostate(1)	c.C666T						.	C		1,4405		0,1,2202	160	152	155		666	-2.8	1	6		155	0,8600		0,0,4300	no	coding-synonymous	HEY2	NM_012259.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		222/338	126080600	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	23493	exon5			TGCCCACGGCTCT	AJ249545	CCDS5131.1	6q	2013-10-17	2013-10-17		ENSG00000135547	ENSG00000135547		"Basic helix-loop-helix proteins"	4881	protein-coding gene	gene with protein product		604674	"hairy/enhancer-of-split related with YRPW motif 2"			10415358	Standard	NM_012259		Approved	bHLHb32, HERP1, HESR2	uc003qad.3	Q9UBP5	OTTHUMG00000015512	ENST00000368364.3:c.666C>T	chr6.hg19:g.126080600C>T		80.0	0.0		48.0	32.0	NM_012259		Silent	SNP	ENST00000368364.3	hg19	CCDS5131.1																																																																																			.	.		0.657	HEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042077.1			T	126080600	C	T	126080600	2	4	263	1	0	0	0	0	0	0	0	1	7088	535	19	1		1	HEY2	6	126080600	Silent	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	19113552	126080600	45034467	152	38526										
PPIL4	85313	hgsc.bcm.edu	37	chr6	149867088	149867088	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tcaccacgcggccgttcttcGgtgtacaagtcgatgacgac	11	13	2	1	rs200555722		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr6:149867088G>A	ENST00000253329.2	-	1	86	c.54C>T	c.(52-54)acC>acT	p.T18T		NM_139126.3	NP_624311.1	Q8WUA2	PPIL4_HUMAN	peptidylprolyl isomerase (cyclophilin)-like 4	18	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				protein folding (GO:0006457)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(4)|large_intestine(1)|lung(4)|prostate(1)|urinary_tract(1)	13		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.11e-11)|GBM - Glioblastoma multiforme(68;0.0885)		GCCGTTCTTCGGTGTACAAGT	0.647																																					p.T18T		Atlas-SNP	.											.	PPIL4	36	.	0			c.C54T						.						34	28	30					6																	149867088		2199	4290	6489	SO:0001819	synonymous_variant	85313	exon1			TTCTTCGGTGTAC		CCDS34550.1	6q25.1	2013-02-12			ENSG00000131013	ENSG00000131013		"RNA binding motif (RRM) containing"	15702	protein-coding gene	gene with protein product		607609					Standard	NM_139126		Approved		uc003qmo.2	Q8WUA2	OTTHUMG00000015788	ENST00000253329.2:c.54C>T	chr6.hg19:g.149867088G>A		86.0	0.0		49.0	4.0	NM_139126	B2RD34|Q7Z3Q5	Silent	SNP	ENST00000253329.2	hg19	CCDS34550.1																																																																																			.	G|0.997;C|0.003		0.647	PPIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042642.1			A	149867088	G	A	149867088	2	1	263	1	0	0	0	0	0	0	0	1	12341	1103	39	1		1	PPIL4	6	149867088	Silent	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	23786488	149867088	21247979	153	38527										
PLEKHG1	57480	hgsc.bcm.edu	37	chr6	151121959	151121959	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gctgcctctggggtcctatcTcttgaaaccagttcagcgga	11	12	3	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr6:151121959T>C	ENST00000358517.2	+	6	945	c.734T>C	c.(733-735)cTc>cCc	p.L245P	PLEKHG1_ENST00000367328.1_Missense_Mutation_p.L245P			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	245	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(19)|ovary(5)|prostate(4)|stomach(1)|urinary_tract(3)	53			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		GGGTCCTATCTCTTGAAACCA	0.483																																					p.L245P		Atlas-SNP	.											.	PLEKHG1	97	.	0			c.T734C						.						120	117	118					6																	151121959		2203	4300	6503	SO:0001583	missense	57480	exon7			CCTATCTCTTGAA	AB033035	CCDS34552.1	6q25.1	2013-01-11			ENSG00000120278	ENSG00000120278		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	20884	protein-coding gene	gene with protein product						10574462	Standard	XM_005267064		Approved	KIAA1209, ARHGEF41	uc003qny.1	Q9ULL1	OTTHUMG00000015824	ENST00000358517.2:c.734T>C	chr6.hg19:g.151121959T>C	ENSP00000351318:p.Leu245Pro	105.0	0.0		93.0	4.0	NM_001029884	Q5T1F2	Missense_Mutation	SNP	ENST00000358517.2	hg19	CCDS34552.1	.	.	.	.	.	.	.	.	.	.	T	28.2	4.900260	0.92035	.	.	ENSG00000120278	ENST00000367328;ENST00000535018;ENST00000358517	D;D	0.84298	-1.83;-1.83	6.16	6.16	0.99307	Dbl homology (DH) domain (5);	0.000000	0.85682	D	0.000000	D	0.95799	0.8633	H	0.99090	4.425	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.97705	1.0187	10	0.87932	D	0	.	16.8061	0.85666	0.0:0.0:0.0:1.0	.	52;245;245	Q5EBL9;Q5JYA6;Q9ULL1	.;.;PKHG1_HUMAN	P	245	ENSP00000356297:L245P;ENSP00000351318:L245P	ENSP00000351318:L245P	L	+	2	0	PLEKHG1	151163652	1.000000	0.71417	0.996000	0.52242	0.991000	0.79684	8.040000	0.89188	2.367000	0.80283	0.528000	0.53228	CTC	.	.		0.483	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042691.1			C	151121959	T	C	151121959	3	2	263	1	0	0	0	0	1	0	0	0	12077	1551	54	2	752	2	PLEKHG1	6	151121959	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	1254871	151121959	19993108	154	38528										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152623096	152623096	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cccctcgacctcggtcaccgTcagcagcatggtggcgtgct	12	16	2	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr6:152623096T>C	ENST00000367255.5	-	92	18050	c.17449A>G	c.(17449-17451)Acg>Gcg	p.T5817A	SYNE1_ENST00000341594.5_Missense_Mutation_p.T5429A|SYNE1_ENST00000356820.4_Missense_Mutation_p.T341A|SYNE1_ENST00000448038.1_Missense_Mutation_p.T5746A|SYNE1_ENST00000423061.1_Missense_Mutation_p.T5746A|SYNE1_ENST00000265368.4_Missense_Mutation_p.T5817A	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	5817					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TCGGTCACCGTCAGCAGCATG	0.592										HNSCC(10;0.0054)																											p.T5817A		Atlas-SNP	.											.	SYNE1	3227	.	0			c.A17449G						.						78	74	75					6																	152623096		2203	4300	6503	SO:0001583	missense	23345	exon92			TCACCGTCAGCAG	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.17449A>G	chr6.hg19:g.152623096T>C	ENSP00000356224:p.Thr5817Ala	105.0	0.0		88.0	4.0	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	T	28.0	4.878561	0.91740	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820;ENST00000540663;ENST00000537033	T;T;T;T;T;T;T	0.55588	0.68;0.68;0.68;0.68;0.68;0.68;0.51	5.61	5.61	0.85477	.	0.000000	0.64402	D	0.000008	T	0.52370	0.1730	L	0.29908	0.895	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	T	0.52786	-0.8529	10	0.35671	T	0.21	.	16.101	0.81172	0.0:0.0:0.0:1.0	.	232;5817;5817;5746	B7ZBD0;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	A	5817;5746;5817;5746;5429;341;39;39	ENSP00000356224:T5817A;ENSP00000396024:T5746A;ENSP00000265368:T5817A;ENSP00000390975:T5746A;ENSP00000341887:T5429A;ENSP00000349276:T341A;ENSP00000437411:T39A	ENSP00000265368:T5817A	T	-	1	0	SYNE1	152664789	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.628000	0.83189	2.263000	0.75096	0.528000	0.53228	ACG	.	.		0.592	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		C	152623096	T	C	152623096	3	2	263	1	0	0	0	0	1	0	0	0	15460	1667	58	2	9237	2	SYNE1	6	152623096	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	1501137	152623096	18491971	155	38529										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152647436	152647436	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	aacatcctgaaatacctctgCaagagatccacttgggcacc	7	13	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr6:152647436C>T	ENST00000367255.5	-	79	15889	c.15288G>A	c.(15286-15288)ttG>ttA	p.L5096L	SYNE1_ENST00000341594.5_Intron|SYNE1_ENST00000448038.1_Silent_p.L5025L|SYNE1_ENST00000423061.1_Silent_p.L5025L|SYNE1_ENST00000265368.4_Silent_p.L5096L	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	5096					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.L5096F(2)|p.L5025F(1)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		AATACCTCTGCAAGAGATCCA	0.428										HNSCC(10;0.0054)																											p.L5096L		Atlas-SNP	.											SYNE1_ENST00000423061,NS,carcinoma,0,3	SYNE1	3227	.	3	Substitution - Missense(3)	lung(3)	c.G15288A						.						72	76	75					6																	152647436		2203	4300	6503	SO:0001819	synonymous_variant	23345	exon79			CCTCTGCAAGAGA	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.15288G>A	chr6.hg19:g.152647436C>T		63.0	0.0		45.0	2.0	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	hg19	CCDS5236.2																																																																																			.	.		0.428	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152647436	C	T	152647436	2	4	263	1	0	0	0	0	0	0	0	1	15460	709	25	3		3	SYNE1	6	152647436	Silent	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	24340	152647436	18467631	156	38530										
TMEM181	57583	hgsc.bcm.edu	37	chr6	159005001	159005001	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ttcagctaaagccaattcaaAtactttcaaatccactgtct	3	11	4	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr6:159005001A>G	ENST00000367090.3	+	4	606	c.595A>G	c.(595-597)Ata>Gta	p.I199V		NM_020823.1	NP_065874.1	Q9P2C4	TM181_HUMAN	transmembrane protein 181	199					pathogenesis (GO:0009405)	integral component of membrane (GO:0016021)	toxic substance binding (GO:0015643)			central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(1)	22		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;8.15e-18)|BRCA - Breast invasive adenocarcinoma(81;1.38e-05)		GCCAATTCAAATACTTTCAAA	0.348																																					p.I199V		Atlas-SNP	.											.	TMEM181	47	.	0			c.A595G						.						118	104	109					6																	159005001		1861	4099	5960	SO:0001583	missense	57583	exon4			ATTCAAATACTTT	AB037844	CCDS43520.1	6q25.3	2012-08-10	2006-10-19	2006-10-19	ENSG00000146433	ENSG00000146433			20958	protein-coding gene	gene with protein product		613209	"G protein-coupled receptor 178", "KIAA1423"	KIAA1423, GPR178		16452613	Standard	NM_020823		Approved		uc003qrm.4	Q9P2C4	OTTHUMG00000015913	ENST00000367090.3:c.595A>G	chr6.hg19:g.159005001A>G	ENSP00000356057:p.Ile199Val	65.0	0.0		48.0	4.0	NM_020823	Q5VTU1	Missense_Mutation	SNP	ENST00000367090.3	hg19	CCDS43520.1	.	.	.	.	.	.	.	.	.	.	A	7.991	0.753328	0.15778	.	.	ENSG00000146433	ENST00000314630;ENST00000367090	.	.	.	5.62	0.334	0.15948	.	0.235735	0.43747	D	0.000534	T	0.05686	0.0149	N	0.14661	0.345	0.09310	N	1	B;B	0.17268	0.007;0.021	B;B	0.13407	0.009;0.006	T	0.37150	-0.9718	9	0.23891	T	0.37	.	5.1626	0.15070	0.3299:0.2924:0.0:0.3777	.	199;110	Q9P2C4;Q8N4V6	TM181_HUMAN;.	V	106;199	.	ENSP00000323755:I106V	I	+	1	0	TMEM181	158924989	0.159000	0.22864	0.617000	0.29091	0.995000	0.86356	0.689000	0.25437	0.363000	0.24346	0.528000	0.53228	ATA	.	.		0.348	TMEM181-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042873.1	NM_020823		G	159005001	A	G	159005001	3	3	263	1	0	0	0	0	1	0	0	0	16115	101	4	2	609	2	TMEM181	6	159005001	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	6357565	159005001	12110066	157	38531										
PMS2	5395	hgsc.bcm.edu	37	chr7	6026652	6026652	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	agaactggaaagaatttcttCttttttaaaacgctttgtgt	7	5	2	2	rs63750739		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr7:6026652C>G	ENST00000265849.7	-	11	1849	c.1744G>C	c.(1744-1746)Gaa>Caa	p.E582Q	PMS2_ENST00000406569.3_Intron|PMS2_ENST00000441476.2_Missense_Mutation_p.E476Q|PMS2_ENST00000382321.4_Intron|PMS2_ENST00000469652.1_Intron	NM_000535.5	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	582					ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|single base insertion or deletion binding (GO:0032138)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(11)|lung(13)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)		AGAATTTCTTCTTTTTTAAAA	0.383			"Mis, N, F"			"colorectal, endometrial, ovarian, medulloblastoma, glioma"		Direct reversal of damage;Mismatch excision repair (MMR)	Turcot syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.E582Q		Atlas-SNP	.	yes	Rec		"Hereditary non-polyposis colorectal cancer, Turcot syndrome"	7	7p22	5395	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)		E	.	PMS2	88	.	0			c.G1744C						.						102	111	108					7																	6026652		2203	4300	6503	SO:0001583	missense	5395	exon11	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	TTTCTTCTTTTTT		CCDS5343.1	7p22.1	2014-09-17	2001-11-28		ENSG00000122512	ENSG00000122512			9122	protein-coding gene	gene with protein product		600259	"postmeiotic segregation increased (S. cerevisiae) 2"	PMSL2		8072530	Standard	NM_000535		Approved	H_DJ0042M02.9, HNPCC4	uc003spl.3	P54278	OTTHUMG00000023135	ENST00000265849.7:c.1744G>C	chr7.hg19:g.6026652C>G	ENSP00000265849:p.Glu582Gln	77.0	0.0		86.0	41.0	NM_000535	B2R610|Q52LH6|Q5FBW9|Q5FBX1|Q5FBX2|Q75MR2	Missense_Mutation	SNP	ENST00000265849.7	hg19	CCDS5343.1	.	.	.	.	.	.	.	.	.	.	c	13.74	2.328625	0.41197	.	.	ENSG00000122512	ENST00000265849;ENST00000382322;ENST00000441476	T;T	0.46063	0.88;0.88	5.49	3.68	0.42216	.	0.158719	0.53938	D	0.000045	T	0.50463	0.1617	M	0.68952	2.095	0.09310	N	1	D;D	0.62365	0.977;0.991	P;P	0.58331	0.611;0.837	T	0.37056	-0.9722	10	0.33940	T	0.23	-7.4577	5.998	0.19505	0.0:0.6986:0.0:0.3014	.	582;476	P54278;C9J167	PMS2_HUMAN;.	Q	582;535;476	ENSP00000265849:E582Q;ENSP00000392843:E476Q	ENSP00000265849:E582Q	E	-	1	0	PMS2	5993178	0.929000	0.31497	0.018000	0.16275	0.083000	0.17756	3.430000	0.52807	1.337000	0.45525	-0.384000	0.06662	GAA	.	.		0.383	PMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207353.3	NM_000535		G	6026652	C	G	6026652	3	3	263	1	0	0	0	0	1	0	0	0	12152	922	32	4	864	4	PMS2	7	6026652	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10		6026652	153112011	158	38532										
ITGB8	3696	hgsc.bcm.edu	37	chr7	20438493	20438493	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gtctctgcagaagctcatttCagaagtgaaagttcaggtgg	12	7	4	3			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr7:20438493C>A	ENST00000222573.4	+	9	1841	c.1157C>A	c.(1156-1158)tCa>tAa	p.S386*	ITGB8_ENST00000537992.1_Nonsense_Mutation_p.S251*	NM_002214.2	NP_002205.1	P26012	ITB8_HUMAN	integrin, beta 8	386					cartilage development (GO:0051216)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|ganglioside metabolic process (GO:0001573)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of gene expression (GO:0010629)|placenta blood vessel development (GO:0060674)|positive regulation of gene expression (GO:0010628)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	extracellular matrix protein binding (GO:1990430)|receptor activity (GO:0004872)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(4)|stomach(2)|urinary_tract(1)	37						AAGCTCATTTCAGAAGTGAAA	0.388																																					p.S386X		Atlas-SNP	.											.	ITGB8	159	.	0			c.C1157A						.						83	84	83					7																	20438493		2203	4300	6503	SO:0001587	stop_gained	3696	exon9			TCATTTCAGAAGT		CCDS5370.1	7p15.3	2010-03-23			ENSG00000105855	ENSG00000105855		"Integrins"	6163	protein-coding gene	gene with protein product		604160					Standard	XM_005249751		Approved		uc003suu.3	P26012	OTTHUMG00000023594	ENST00000222573.4:c.1157C>A	chr7.hg19:g.20438493C>A	ENSP00000222573:p.Ser386*	127.0	0.0		159.0	60.0	NM_002214	A4D133|B4DHD4	Nonsense_Mutation	SNP	ENST00000222573.4	hg19	CCDS5370.1	.	.	.	.	.	.	.	.	.	.	C	43	10.295639	0.99378	.	.	ENSG00000105855	ENST00000537992;ENST00000222573	.	.	.	5.5	5.5	0.81552	.	0.000000	0.64402	D	0.000018	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.4084	0.94658	0.0:1.0:0.0:0.0	.	.	.	.	X	251;386	.	ENSP00000222573:S386X	S	+	2	0	ITGB8	20405018	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.010000	0.70753	2.593000	0.87608	0.655000	0.94253	TCA	.	.		0.388	ITGB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059915.3	NM_002214		A	20438493	C	A	20438493	4	1	263	1	0	0	0	0	0	1	0	0	7910	838	29	3	1191	3	ITGB8	7	20438493	Nonsense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	14411841	20438493	138700170	159	38533										
HOXA11	3207	hgsc.bcm.edu	37	chr7	27224736	27224736	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tggcaaatacatgttagaggAgcagggaccacgctcatcaa	11	9	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr7:27224736A>G	ENST00000006015.3	-	1	99	c.28T>C	c.(28-30)Tcc>Ccc	p.S10P	HOXA11-AS_ENST00000479766.1_RNA|RP1-170O19.14_ENST00000523331.1_lincRNA|HOXA11-AS_ENST00000520395.1_RNA|HOXA11-AS_ENST00000522674.1_RNA|HOXA11-AS_ENST00000522863.1_RNA|HOXA11-AS_ENST00000520360.1_RNA	NM_005523.5	NP_005514.1	P31270	HXA11_HUMAN	homeobox A11	10					anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|developmental growth (GO:0048589)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal joint morphogenesis (GO:0060272)|male gonad development (GO:0008584)|mesodermal cell fate specification (GO:0007501)|metanephros development (GO:0001656)|multicellular organismal development (GO:0007275)|organ induction (GO:0001759)|positive regulation of cell development (GO:0010720)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)|uterus development (GO:0060065)	nucleus (GO:0005634)|protein complex (GO:0043234)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(8)|ovary(1)|skin(2)	16						ATGTTAGAGGAGCAGGGACCA	0.522			T	NUP98	CML						OREG0003747	type=REGULATORY REGION|Gene=BC025338|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.S10P		Atlas-SNP	.		Dom	yes		7	7p15-p14.2	3207	homeo box A11		L	.	HOXA11	29	.	0			c.T28C						.						67	70	69					7																	27224736		2202	4300	6502	SO:0001583	missense	3207	exon1			TAGAGGAGCAGGG		CCDS5411.1	7p15.2	2014-09-17	2005-12-22		ENSG00000005073	ENSG00000005073		"Homeoboxes / ANTP class : HOXL subclass"	5101	protein-coding gene	gene with protein product		142958	"homeo box A11"	HOX1I, HOX1		1973146, 1358459	Standard	NM_005523		Approved		uc003syx.3	P31270	OTTHUMG00000023437	ENST00000006015.3:c.28T>C	chr7.hg19:g.27224736A>G	ENSP00000006015:p.Ser10Pro	45.0	0.0	792	95.0	4.0	NM_005523	A4D190	Missense_Mutation	SNP	ENST00000006015.3	hg19	CCDS5411.1	.	.	.	.	.	.	.	.	.	.	A	13.16	2.154163	0.38021	.	.	ENSG00000005073	ENST00000006015	D	0.91521	-2.86	5.61	4.45	0.53987	.	0.127561	0.53938	D	0.000048	D	0.85405	0.5689	L	0.29908	0.895	0.46437	D	0.999042	P	0.50943	0.94	P	0.44860	0.462	T	0.82512	-0.0420	9	.	.	.	.	11.3758	0.49726	0.9292:0.0:0.0708:0.0	.	10	P31270	HXA11_HUMAN	P	10	ENSP00000006015:S10P	.	S	-	1	0	HOXA11	27191261	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.441000	0.66569	0.951000	0.37770	0.533000	0.62120	TCC	.	.		0.522	HOXA11-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358754.1			G	27224736	A	G	27224736	3	3	263	1	0	0	0	0	1	0	0	0	7299	304	11	2	921	2	HOXA11	7	27224736	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	6786243	27224736	131913927	160	38534										
EVX1	2128	hgsc.bcm.edu	37	chr7	27285511	27285511	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gctcctctccccaggtgtggTtccagaaccggcgcatgaag	12	14	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr7:27285511T>C	ENST00000496902.4	+	3	1177	c.691T>C	c.(691-693)Ttc>Ctc	p.F231L	EVX1-AS_ENST00000519050.1_RNA|EVX1-AS_ENST00000517726.1_RNA|EVX1_ENST00000222761.3_3'UTR|EVX1_ENST00000535619.1_Missense_Mutation_p.F49L|EVX1-AS_ENST00000519218.1_RNA			P49640	EVX1_HUMAN	even-skipped homeobox 1	231					embryo development ending in birth or egg hatching (GO:0009792)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter involved in ventral spinal cord interneuron specification (GO:0021913)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|liver(1)|lung(10)|prostate(1)|skin(1)	14						CCAGGTGTGGTTCCAGAACCG	0.652																																					p.F231L		Atlas-SNP	.											.	EVX1	23	.	0			c.T691C						.						25	24	24					7																	27285511		2199	4274	6473	SO:0001583	missense	2128	exon3			GTGTGGTTCCAGA		CCDS5413.1	7p15.2	2012-03-09	2007-02-15		ENSG00000106038	ENSG00000106038		"Homeoboxes / ANTP class : HOXL subclass"	3506	protein-coding gene	gene with protein product		142996	"eve, even-skipped homeobox homolog 1 (Drosophila)"			1684419	Standard	XM_005249640		Approved		uc003szd.1	P49640	OTTHUMG00000023093	ENST00000496902.4:c.691T>C	chr7.hg19:g.27285511T>C	ENSP00000419266:p.Phe231Leu	113.0	0.0		100.0	4.0	NM_001989	A4D199|B4DQJ0	Missense_Mutation	SNP	ENST00000496902.4	hg19	CCDS5413.1	.	.	.	.	.	.	.	.	.	.	T	27.7	4.854868	0.91355	.	.	ENSG00000106038	ENST00000496902;ENST00000535619	D;D	0.99741	-6.6;-6.6	5.22	5.22	0.72569	Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.99771	0.9906	H	0.96239	3.79	0.80722	D	1	D	0.60575	0.988	D	0.67382	0.951	D	0.97274	0.9913	10	0.66056	D	0.02	-16.1599	12.2557	0.54623	0.0:0.0:0.1415:0.8585	.	231	P49640	EVX1_HUMAN	L	231;49	ENSP00000419266:F231L;ENSP00000446458:F49L	ENSP00000419266:F231L	F	+	1	0	EVX1	27252036	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.583000	0.82559	1.968000	0.57251	0.459000	0.35465	TTC	.	.		0.652	EVX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358750.3			C	27285511	T	C	27285511	3	2	263	1	0	0	0	0	1	0	0	0	5296	1725	60	2	701	2	EVX1	7	27285511	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	60775	27285511	131853152	161	38535										
NPC1L1	29881	hgsc.bcm.edu	37	chr7	44555505	44555505	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	aagatctgaatgagctgggcCttggcgaggcccaggacaag	15	9	1	3			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr7:44555505C>T	ENST00000289547.4	-	19	3829	c.3774G>A	c.(3772-3774)aaG>aaA	p.K1258K	NPC1L1_ENST00000381160.3_Silent_p.K1231K|NPC1L1_ENST00000546276.1_Silent_p.K1185K	NM_013389.2	NP_037521.2	Q9UHC9	NPCL1_HUMAN	NPC1-like 1	1258					cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intestinal cholesterol absorption (GO:0030299)|lipoprotein metabolic process (GO:0042157)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)	brush border membrane (GO:0031526)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|hedgehog receptor activity (GO:0008158)|myosin V binding (GO:0031489)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(7)|lung(27)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	57					Ezetimibe(DB00973)	TGAGCTGGGCCTTGGCGAGGC	0.612																																					p.K1258K		Atlas-SNP	.											.	NPC1L1	141	.	0			c.G3774A						.						61	63	62					7																	44555505		2203	4300	6503	SO:0001819	synonymous_variant	29881	exon19			CTGGGCCTTGGCG		CCDS5491.1, CCDS43575.1, CCDS75587.1	7p13	2012-11-15	2012-11-15		ENSG00000015520	ENSG00000015520			7898	protein-coding gene	gene with protein product		608010	"NPC1 (Niemann-Pick disease, type C1, gene)-like 1"			10783261	Standard	NM_013389		Approved		uc003tlb.3	Q9UHC9	OTTHUMG00000023691	ENST00000289547.4:c.3774G>A	chr7.hg19:g.44555505C>T		68.0	0.0		93.0	38.0	NM_013389	A4D2J7|B7ZLE6|D3DVK9|Q17RV5|Q6R3Q4|Q9UHC8	Silent	SNP	ENST00000289547.4	hg19	CCDS5491.1																																																																																			.	.		0.612	NPC1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251256.1	NM_013389		T	44555505	C	T	44555505	2	4	263	1	0	0	0	0	0	0	0	1	10580	680	24	3		3	NPC1L1	7	44555505	Silent	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	17269994	44555505	114583158	162	38536										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48312769	48312769	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tcaattatttaagtttgacaTgaatgttttcacatctcttc	4	7	3	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr7:48312769T>C	ENST00000435803.1	+	17	3530	c.3506T>C	c.(3505-3507)aTg>aCg	p.M1169T		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1169					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						AAGTTTGACATGAATGTTTTC	0.383																																					p.M1169T		Atlas-SNP	.											.	ABCA13	1192	.	0			c.T3506C						.						94	90	92					7																	48312769		1841	4090	5931	SO:0001583	missense	154664	exon17			TTGACATGAATGT	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.3506T>C	chr7.hg19:g.48312769T>C	ENSP00000411096:p.Met1169Thr	70.0	0.0		97.0	4.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	T	0	-2.737869	0.00088	.	.	ENSG00000179869	ENST00000435803	D	0.84730	-1.89	5.64	-9.06	0.00727	.	1.722330	0.03242	N	0.180484	T	0.67832	0.2935	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.53344	-0.8452	9	.	.	.	.	2.7457	0.05267	0.1976:0.4092:0.1999:0.1933	.	1169	Q86UQ4	ABCAD_HUMAN	T	1169	ENSP00000411096:M1169T	.	M	+	2	0	ABCA13	48283315	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.817000	0.04472	-1.192000	0.02691	-0.460000	0.05396	ATG	.	.		0.383	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		C	48312769	T	C	48312769	3	2	263	1	0	0	0	0	1	0	0	0	31	1464	51	2	3401	2	ABCA13	7	48312769	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	3757264	48312769	110825894	163	38537										
MLXIPL	51085	hgsc.bcm.edu	37	chr7	73010987	73010987	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	accgctgggcgctgggggtgAgagccgctccgctttgggga	19	11	0	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr7:73010987A>G	ENST00000313375.3	-	11	1851	c.1804T>C	c.(1804-1806)Tca>Cca	p.S602P	MLXIPL_ENST00000354613.1_Missense_Mutation_p.S602P|MLXIPL_ENST00000429400.2_Missense_Mutation_p.S602P|MLXIPL_ENST00000414749.2_Missense_Mutation_p.S602P|MLXIPL_ENST00000395189.1_Missense_Mutation_p.S509P|MLXIPL_ENST00000434326.1_Missense_Mutation_p.S508P	NM_032951.2|NM_032953.2	NP_116569.1|NP_116571.1	Q9NP71	MLXPL_HUMAN	MLX interacting protein-like	602					anatomical structure morphogenesis (GO:0009653)|energy reserve metabolic process (GO:0006112)|fatty acid homeostasis (GO:0055089)|glucose homeostasis (GO:0042593)|glucose mediated signaling pathway (GO:0010255)|intracellular signal transduction (GO:0035556)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of oxidative phosphorylation (GO:0090324)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular metabolic process (GO:0031325)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of glycolytic process (GO:0045821)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of energy homeostasis (GO:2000505)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride homeostasis (GO:0070328)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	carbohydrate response element binding (GO:0035538)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			cervix(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	13		Lung NSC(55;0.0659)|all_lung(88;0.152)				GCTGGGGGTGAGAGCCGCTCC	0.687																																					p.S602P		Atlas-SNP	.											.	MLXIPL	54	.	0			c.T1804C						.						6	7	7					7																	73010987		2118	4155	6273	SO:0001583	missense	51085	exon11			GGGGTGAGAGCCG	AK055029	CCDS5553.1, CCDS5554.1, CCDS47605.1, CCDS47606.1	7q11.23	2013-05-21	2005-10-31	2005-10-31	ENSG00000009950	ENSG00000009950			12744	protein-coding gene	gene with protein product	"carbohydrate response element binding protein"	605678	"Williams Beuren syndrome chromosome region 14"	WBSCR14		9860302	Standard	XM_005250399		Approved	WS-bHLH, MIO, CHREBP, MONDOB, bHLHd14	uc003tyn.1	Q9NP71	OTTHUMG00000129995	ENST00000313375.3:c.1804T>C	chr7.hg19:g.73010987A>G	ENSP00000320886:p.Ser602Pro	85.0	0.0		129.0	6.0	NM_032954	C5HU02|C5HU03|C5HU04|Q96E48|Q9BY03|Q9BY04|Q9BY05|Q9BY06|Q9Y2P3	Missense_Mutation	SNP	ENST00000313375.3	hg19	CCDS5553.1	.	.	.	.	.	.	.	.	.	.	a	15.85	2.954943	0.53293	.	.	ENSG00000009950	ENST00000414749;ENST00000429400;ENST00000313375;ENST00000354613;ENST00000395189;ENST00000434326	T;T;T;T;T;T	0.28666	2.16;2.25;2.25;2.18;1.63;1.6	3.95	3.95	0.45737	.	0.000000	0.50627	U	0.000109	T	0.45776	0.1359	L	0.53249	1.67	0.35335	D	0.785927	D;D;D;D;D	0.89917	1.0;0.967;0.981;0.998;0.999	D;D;D;D;D	0.87578	0.998;0.939;0.972;0.992;0.993	T	0.54153	-0.8336	10	0.35671	T	0.21	-10.1367	9.4089	0.38480	1.0:0.0:0.0:0.0	.	509;602;602;602;602	Q9NP71-6;Q9NP71;Q9NP71-2;Q9NP71-3;Q9NP71-4	.;MLXPL_HUMAN;.;.;.	P	602;602;602;602;509;508	ENSP00000412330:S602P;ENSP00000406296:S602P;ENSP00000320886:S602P;ENSP00000346629:S602P;ENSP00000378616:S509P;ENSP00000392636:S508P	ENSP00000320886:S602P	S	-	1	0	MLXIPL	72648923	0.982000	0.34865	0.959000	0.39883	0.796000	0.44982	5.910000	0.69931	1.792000	0.52537	0.434000	0.28630	TCA	.	.		0.687	MLXIPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252262.1	NM_032951		G	73010987	A	G	73010987	3	3	263	1	0	0	0	0	1	0	0	0	9646	304	11	2	782	2	MLXIPL	7	73010987	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	24698218	73010987	86127676	164	38538										
SEMA3A	10371	hgsc.bcm.edu	37	chr7	83590840	83590840	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cttttccaaacttgttcacaGaactcatccattgtgttgag	6	10	2	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr7:83590840G>T	ENST00000265362.4	-	17	2477	c.2163C>A	c.(2161-2163)ttC>ttA	p.F721L	SEMA3A_ENST00000436949.1_Missense_Mutation_p.F721L	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	721					apoptotic process (GO:0006915)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|dendrite morphogenesis (GO:0048813)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of epithelial cell migration (GO:0010633)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neural crest cell migration involved in sympathetic nervous system development (GO:1903045)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of male gonad development (GO:2000020)|positive regulation of neuron migration (GO:2001224)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of heart rate (GO:0002027)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sensory system development (GO:0048880)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular region (GO:0005576)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|neuropilin binding (GO:0038191)|receptor activity (GO:0004872)	p.F721F(1)		breast(3)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						CTTGTTCACAGAACTCATCCA	0.453																																					p.F721L		Atlas-SNP	.											SEMA3A,pharynx,carcinoma,0,1	SEMA3A	121	.	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.C2163A						.						195	170	178					7																	83590840		2203	4300	6503	SO:0001583	missense	10371	exon17			TTCACAGAACTCA	L26081	CCDS5599.1	7p12.1	2013-01-11			ENSG00000075213	ENSG00000075213		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10723	protein-coding gene	gene with protein product	"sema III"	603961		SEMAD		8269517, 7748561	Standard	NM_006080		Approved	SEMA1, SemD, coll-1, Hsema-I	uc003uhz.3	Q14563	OTTHUMG00000023443	ENST00000265362.4:c.2163C>A	chr7.hg19:g.83590840G>T	ENSP00000265362:p.Phe721Leu	238.0	0.0		549.0	109.0	NM_006080		Missense_Mutation	SNP	ENST00000265362.4	hg19	CCDS5599.1	.	.	.	.	.	.	.	.	.	.	G	14.22	2.469099	0.43839	.	.	ENSG00000075213	ENST00000265362;ENST00000436949	T;T	0.25749	1.78;1.78	5.78	3.03	0.35002	.	0.043033	0.85682	D	0.000000	T	0.17023	0.0409	N	0.22421	0.69	0.58432	D	0.999997	B	0.09022	0.002	B	0.09377	0.004	T	0.04103	-1.0977	10	0.42905	T	0.14	.	11.115	0.48256	0.1987:0.0:0.8013:0.0	.	721	Q14563	SEM3A_HUMAN	L	721	ENSP00000265362:F721L;ENSP00000415260:F721L	ENSP00000265362:F721L	F	-	3	2	SEMA3A	83428776	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.253000	0.51469	0.473000	0.27368	-0.140000	0.14226	TTC	.	.		0.453	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080		T	83590840	G	T	83590840	3	4	263	1	0	0	0	0	1	0	0	0	14039	933	33	3	156	3	SEMA3A	7	83590840	Missense_Mutation	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	10579853	83590840	75547823	165	38539										
LMTK2	22853	hgsc.bcm.edu	37	chr7	97821985	97821985	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	aacttactaaaaggctcattGtccagcaaagaacacataaa	5	9	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr7:97821985G>A	ENST00000297293.5	+	11	2501	c.2208G>A	c.(2206-2208)ttG>ttA	p.L736L		NM_014916.3	NP_055731.2	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2	736					early endosome to late endosome transport (GO:0045022)|endocytic recycling (GO:0032456)|negative regulation of catalytic activity (GO:0043086)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor recycling (GO:0001881)|transferrin transport (GO:0033572)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|myosin VI binding (GO:0070853)|protein phosphatase inhibitor activity (GO:0004864)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|pancreas(2)|skin(2)|stomach(3)	59	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)					AAGGCTCATTGTCCAGCAAAG	0.313																																					p.L736L		Atlas-SNP	.											LMTK2_ENST00000297293,NS,carcinoma,0,2	LMTK2	228	.	0			c.G2208A						.						45	49	47					7																	97821985		2202	4300	6502	SO:0001819	synonymous_variant	22853	exon11			CTCATTGTCCAGC	AB029002	CCDS5654.1	7q22.1	2014-06-12			ENSG00000164715	ENSG00000164715			17880	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 100"	610989				15005709	Standard	NM_014916		Approved	KIAA1079, KPI2, KPI-2, cprk, LMR2, BREK, AATYK2, PPP1R100	uc003upd.2	Q8IWU2	OTTHUMG00000154256	ENST00000297293.5:c.2208G>A	chr7.hg19:g.97821985G>A		30.0	0.0		40.0	3.0	NM_014916	A4D272|Q75MG7|Q9UPS3	Silent	SNP	ENST00000297293.5	hg19	CCDS5654.1																																																																																			.	.		0.313	LMTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334560.1	NM_014916		A	97821985	G	A	97821985	2	1	263	1	0	0	0	0	0	0	0	1	8868	1368	48	3		3	LMTK2	7	97821985	Silent	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	14231145	97821985	61316678	166	38540										
PILRB	29990	hgsc.bcm.edu	37	chr7	99957138	99957139	+	Silent	DNP	CC	CC	GT													0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ggactgctgtgcctcctcctCctgtggtggaggagaaggaa					rs369458364		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr7:99957138_99957139CC>GT	ENST00000452089.1	+	8	1692_1693	c.633_634CC>GT	c.(631-636)ctCCtg>ctGTtg	p.211_212LL>LL	STAG3L5P-PVRIG2P-PILRB_ENST00000310771.4_RNA|PILRB_ENST00000610247.1_Silent_p.211_212LL>LL|PILRB_ENST00000448382.1_Missense_Mutation_p.P264V|PILRB_ENST00000444073.1_Silent_p.211_212LL>LL|PILRB_ENST00000609309.1_Silent_p.211_212LL>LL			Q9UKJ0	PILRB_HUMAN	paired immunoglobin-like type 2 receptor beta	211				Missing (in Ref. 2; CAC19193). {ECO:0000305}.	activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)				endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	13	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GCCTCCTCCTCCTGTGGTGGAG	0.55																																					p.L211L|p.L212L		Atlas-SNP	.											.	PILRB	26	.	0			c.C633G|c.C634T						.																																			SO:0001819	synonymous_variant	29990	exon3			CCTCCTCCTGTGG|CTCCTCCTGTGGT	AF161081, AJ400845	CCDS43622.1	7q22.1	2014-05-16			ENSG00000121716	ENSG00000121716		"Immunoglobulin superfamily / V-set domain containing"	18297	protein-coding gene	gene with protein product		605342				10660620	Standard	NM_178238		Approved	FDFACT1, FDFACT2	uc022ail.1	Q9UKJ0	OTTHUMG00000155363	Exception_encountered	chr7.hg19:g.99957138_99957139delinsGT		84.0	0.0		126.0|120.0	16.0|9.0	NM_178238	Q69YF9|Q9HBS0	Silent	SNP	ENST00000452089.1	hg19	CCDS43622.1																																																																																			.	.		0.55	PILRB-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339923.2	NM_178238		GT	99957139	CC	GT	99957138	2	3	263	1	0	0	0	0	0	0	0	1	11935	855	30	4		4	PILRB	7	99957138	Silent	DNP	CC	TCGA-FV-A2QR-01A-11D-A20W-10	2135153	99957138	59181525	167	38541										
IFRD1	3475	hgsc.bcm.edu	37	chr7	112095823	112095823	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tcttttacctaataggtggcCagcatcgaaatgttcagcct	8	10	2	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr7:112095823C>T	ENST00000403825.3	+	2	361	c.100C>T	c.(100-102)Cag>Tag	p.Q34*	IFRD1_ENST00000005558.4_Nonsense_Mutation_p.Q34*|IFRD1_ENST00000429071.1_Nonsense_Mutation_p.Q34*|IFRD1_ENST00000535603.1_5'UTR	NM_001550.3	NP_001541.2	O00458	IFRD1_HUMAN	interferon-related developmental regulator 1	34					adult somatic muscle development (GO:0007527)|multicellular organismal development (GO:0007275)|myoblast fate determination (GO:0007518)	nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(5)|urinary_tract(1)	15						AATAGGTGGCCAGCATCGAAA	0.343																																					p.Q34X		Atlas-SNP	.											IFRD1,NS,carcinoma,0,1	IFRD1	46	.	0			c.C100T						.						121	116	118					7																	112095823		2203	4300	6503	SO:0001587	stop_gained	3475	exon3			GGTGGCCAGCATC	Y10313	CCDS34736.1, CCDS56504.1	7q31.1	2005-10-17			ENSG00000006652	ENSG00000006652			5456	protein-coding gene	gene with protein product		603502				9722946	Standard	NM_001550		Approved	PC4, TIS7	uc003vgh.3	O00458	OTTHUMG00000155124	ENST00000403825.3:c.100C>T	chr7.hg19:g.112095823C>T	ENSP00000384477:p.Gln34*	37.0	0.0		39.0	2.0	NM_001007245	B7Z5G1|O75234|Q5U013|Q9BVE4	Nonsense_Mutation	SNP	ENST00000403825.3	hg19	CCDS34736.1	.	.	.	.	.	.	.	.	.	.	C	37	6.138153	0.97315	.	.	ENSG00000006652	ENST00000005558;ENST00000445335;ENST00000403825;ENST00000429071	.	.	.	5.06	5.06	0.68205	.	0.220196	0.47455	D	0.000237	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06236	T	0.91	-10.1224	18.7821	0.91937	0.0:1.0:0.0:0.0	.	.	.	.	X	34	.	ENSP00000005558:Q34X	Q	+	1	0	IFRD1	111883059	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.207000	0.77899	2.506000	0.84524	0.460000	0.39030	CAG	.	.		0.343	IFRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338700.1	NM_001550		T	112095823	C	T	112095823	4	4	263	1	0	0	0	0	0	1	0	0	7562	595	21	3	106	3	IFRD1	7	112095823	Nonsense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	12138685	112095823	47042840	168	38542										
GRM8	2918	hgsc.bcm.edu	37	chr7	126079220	126079220	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	atatgttgtcttggtagaggAagctgttaagataaatgagg	13	2	1	3			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr7:126079220A>G	ENST00000339582.2	-	11	3488	c.2680T>C	c.(2680-2682)Tcc>Ccc	p.S894P	GRM8_ENST00000358373.3_3'UTR|GRM8_ENST00000444921.2_Missense_Mutation_p.S894P			O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8	894					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of cAMP biosynthetic process (GO:0030818)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(16)|lung(62)|ovary(5)|pancreas(1)|prostate(1)|skin(14)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(4)	125		Prostate(267;0.186)				TTGGTAGAGGAAGCTGTTAAG	0.284										HNSCC(24;0.065)																											p.S894P		Atlas-SNP	.											.	GRM8	377	.	0			c.T2680C						.						177	178	177					7																	126079220		2203	4300	6503	SO:0001583	missense	2918	exon10			TAGAGGAAGCTGT		CCDS5794.1, CCDS47696.1	7q31.3-q32.1	2012-08-29			ENSG00000179603	ENSG00000179603		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4600	protein-coding gene	gene with protein product		601116				8824806	Standard	NM_000845		Approved	GLUR8, GPRC1H, mGlu8, MGLUR8	uc003vlr.2	O00222	OTTHUMG00000022888	ENST00000339582.2:c.2680T>C	chr7.hg19:g.126079220A>G	ENSP00000344173:p.Ser894Pro	50.0	0.0		63.0	4.0	NM_000845	A4D0Y3|B0FZ74|B0M0L0|O15493|O95945|O95946|Q3MIV9|Q52M02|Q6J165	Missense_Mutation	SNP	ENST00000339582.2	hg19	CCDS5794.1	.	.	.	.	.	.	.	.	.	.	A	10.98	1.504844	0.26949	.	.	ENSG00000179603	ENST00000339582;ENST00000444921	D;D	0.88277	-2.36;-2.36	4.75	4.75	0.60458	.	1.030880	0.07662	N	0.933914	T	0.74374	0.3708	N	0.02539	-0.55	0.80722	D	1	P	0.47350	0.894	B	0.35413	0.202	T	0.69266	-0.5190	10	0.37606	T	0.19	.	13.4167	0.60972	1.0:0.0:0.0:0.0	.	894	O00222	GRM8_HUMAN	P	894	ENSP00000344173:S894P;ENSP00000409790:S894P	ENSP00000344173:S894P	S	-	1	0	GRM8	125866456	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	4.675000	0.61619	1.760000	0.52011	0.402000	0.26972	TCC	.	.		0.284	GRM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059209.4			G	126079220	A	G	126079220	3	3	263	1	0	0	0	0	1	0	0	0	6812	246	9	2	50	2	GRM8	7	126079220	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	13983397	126079220	33059443	169	38543										
PAX4	5078	hgsc.bcm.edu	37	chr7	127252032	127252032	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	attcctggggcaacccttggTacagtcagcccctgggaagc	12	13	1	0	rs370406503		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr7:127252032T>C	ENST00000341640.2	-	7	919	c.714A>G	c.(712-714)gtA>gtG	p.V238V	PAX4_ENST00000338516.3_Intron|PAX4_ENST00000378740.2_Silent_p.V238V|PAX4_ENST00000463946.1_Silent_p.V236V	NM_006193.2	NP_006184.2	O43316	PAX4_HUMAN	paired box 4	246					cell differentiation (GO:0030154)|circadian rhythm (GO:0007623)|endocrine pancreas development (GO:0031018)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|positive regulation of cell differentiation (GO:0045597)|response to cAMP (GO:0051591)|response to drug (GO:0042493)|retina development in camera-type eye (GO:0060041)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)			cervix(1)|kidney(2)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35						CAACCCTTGGTACAGTCAGCC	0.557																																					p.V238V	Ovarian(113;737 1605 7858 27720 34092)	Atlas-SNP	.											.	PAX4	66	.	0			c.A714G						.	T		1,4405	2.1+/-5.4	0,1,2202	65	59	61		714	-2.5	0	7		61	0,8600		0,0,4300	no	coding-synonymous	PAX4	NM_006193.2		0,1,6502	CC,CT,TT		0.0,0.0227,0.0077		238/344	127252032	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	5078	exon7			CCTTGGTACAGTC		CCDS5797.1	7q32.1	2011-06-20	2007-07-12		ENSG00000106331	ENSG00000106331		"Paired boxes", "Homeoboxes / PRD class"	8618	protein-coding gene	gene with protein product		167413	"paired box gene 4"				Standard	NM_006193		Approved	MODY9	uc010lld.1	O43316	OTTHUMG00000157562	ENST00000341640.2:c.714A>G	chr7.hg19:g.127252032T>C		59.0	0.0		75.0	4.0	NM_006193	O95161|Q6B0H0	Silent	SNP	ENST00000341640.2	hg19	CCDS5797.1																																																																																			.	.		0.557	PAX4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349165.1			C	127252032	T	C	127252032	2	2	263	1	0	0	0	0	0	0	0	1	11490	1625	57	2		2	PAX4	7	127252032	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	1172812	127252032	31886631	170	38544										
WEE2	494551	hgsc.bcm.edu	37	chr7	141420771	141420771	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gaagtttatgctcacgcagtGcttgggcatcacccccatgt	10	12	2	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr7:141420771G>A	ENST00000397541.2	+	5	1201	c.795G>A	c.(793-795)gtG>gtA	p.V265V	WEE2-AS1_ENST00000486906.1_RNA|WEE2-AS1_ENST00000471512.1_RNA|WEE2-AS1_ENST00000484172.1_RNA|WEE2-AS1_ENST00000462383.1_RNA|WEE2-AS1_ENST00000465110.1_RNA|WEE2-AS1_ENST00000478332.1_RNA|WEE2-AS1_ENST00000488785.1_RNA|WEE2-AS1_ENST00000495800.1_RNA|WEE2-AS1_ENST00000459753.1_RNA	NM_001105558.1	NP_001099028.1	P0C1S8	WEE2_HUMAN	WEE1 homolog 2 (S. pombe)	265	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				female meiotic division (GO:0007143)|female pronucleus assembly (GO:0035038)|mitotic nuclear division (GO:0007067)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of oocyte maturation (GO:1900194)|regulation of meiosis I (GO:0060631)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(2)|stomach(1)	31	Melanoma(164;0.0171)					CTCACGCAGTGCTTGGGCATC	0.393																																					p.V265V		Atlas-SNP	.											.	WEE2	59	.	0			c.G795A						.						151	142	145					7																	141420771		1900	4114	6014	SO:0001819	synonymous_variant	494551	exon5			CGCAGTGCTTGGG	AK131218	CCDS43660.1	7q32	2008-07-02			ENSG00000214102	ENSG00000214102			19684	protein-coding gene	gene with protein product		614084					Standard	NM_001105558		Approved	FLJ16107	uc003vwn.2	P0C1S8	OTTHUMG00000157536	ENST00000397541.2:c.795G>A	chr7.hg19:g.141420771G>A		75.0	0.0		96.0	4.0	NM_001105558		Silent	SNP	ENST00000397541.2	hg19	CCDS43660.1																																																																																			.	.		0.393	WEE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349091.1	NM_001105558		A	141420771	G	A	141420771	2	1	263	1	0	0	0	0	0	0	0	1	17360	1306	46	3		3	WEE2	7	141420771	Silent	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	14168739	141420771	17717892	171	38545										
SSBP1	6742	hgsc.bcm.edu	37	chr7	141441987	141441987	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	aggtacttcgtcagtttgtaAgacatgagtccgaaacaact	9	8	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr7:141441987A>G	ENST00000481508.1	+	3	478	c.43A>G	c.(43-45)Aga>Gga	p.R15G	SSBP1_ENST00000265304.6_Missense_Mutation_p.R15G|SSBP1_ENST00000484178.1_Missense_Mutation_p.R15G|SSBP1_ENST00000465582.1_Missense_Mutation_p.R15G|SSBP1_ENST00000498107.1_Missense_Mutation_p.R15G|SSBP1_ENST00000469123.1_3'UTR	NM_001256510.1	NP_001243439.1	Q04837	SSBP_HUMAN	single-stranded DNA binding protein 1, mitochondrial	15					DNA replication (GO:0006260)|mitochondrion morphogenesis (GO:0070584)|positive regulation of helicase activity (GO:0051096)	extracellular vesicular exosome (GO:0070062)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|single-stranded DNA binding (GO:0003697)			large_intestine(3)|lung(1)|ovary(1)|pancreas(1)|skin(1)	7	Melanoma(164;0.0171)					TCAGTTTGTAAGACATGAGTC	0.313																																					p.R15G		Atlas-SNP	.											.	SSBP1	17	.	0			c.A43G						.						123	111	115					7																	141441987		2202	4300	6502	SO:0001583	missense	6742	exon3			TTTGTAAGACATG	M94556	CCDS5866.1	7q34	2012-05-25	2012-05-25		ENSG00000106028	ENSG00000106028			11317	protein-coding gene	gene with protein product		600439	"single-stranded DNA-binding protein", "single-stranded DNA binding protein 1"			7789991	Standard	NM_001256510		Approved	SSBP, mtSSB	uc031szi.1	Q04837	OTTHUMG00000157572	ENST00000481508.1:c.43A>G	chr7.hg19:g.141441987A>G	ENSP00000419665:p.Arg15Gly	41.0	0.0		61.0	4.0	NM_001256513		Missense_Mutation	SNP	ENST00000481508.1	hg19	CCDS5866.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.500008	0.85176	.	.	ENSG00000106028	ENST00000265304;ENST00000498107;ENST00000467681;ENST00000465582;ENST00000463093;ENST00000484178;ENST00000473783;ENST00000481508	.	.	.	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.77246	0.4102	M	0.64997	1.995	0.58432	D	0.999999	D;D	0.76494	0.999;0.999	D;D	0.83275	0.994;0.996	T	0.78440	-0.2203	9	0.56958	D	0.05	-24.6187	16.188	0.81967	1.0:0.0:0.0:0.0	.	15;15	B7Z268;Q04837	.;SSBP_HUMAN	G	15	.	ENSP00000265304:R15G	R	+	1	2	SSBP1	141088456	1.000000	0.71417	0.996000	0.52242	0.984000	0.73092	3.683000	0.54663	2.216000	0.71823	0.528000	0.53228	AGA	.	.		0.313	SSBP1-006	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000349187.1	NM_003143		G	141441987	A	G	141441987	3	3	263	1	0	0	0	0	1	0	0	0	15194	64	3	2	49	2	SSBP1	7	141441987	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	21216	141441987	17696676	172	38546										
GIMAP8	155038	hgsc.bcm.edu	37	chr7	150171348	150171348	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cggacatctcatctttaaagAacattgactcagaagttaga	7	8	3	4			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr7:150171348A>G	ENST00000307271.3	+	4	1505	c.931A>G	c.(931-933)Aac>Gac	p.N311D		NM_175571.2	NP_783161.1	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	311	AIG1-type G 2.					cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(26)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)		ATCTTTAAAGAACATTGACTC	0.453																																					p.N311D		Atlas-SNP	.											.	GIMAP8	136	.	0			c.A931G						.						73	79	77					7																	150171348		2203	4300	6503	SO:0001583	missense	155038	exon4			TTAAAGAACATTG	AL834361	CCDS34777.1	7q36.1	2014-04-04			ENSG00000171115	ENSG00000171115		"GTPases, IMAP"	21792	protein-coding gene	gene with protein product	"immune-associated nucleotide-binding protein 9"					15474311	Standard	XM_005249951		Approved	DKFZp667I133, hIAN6, IAN9	uc003whj.3	Q8ND71	OTTHUMG00000158327	ENST00000307271.3:c.931A>G	chr7.hg19:g.150171348A>G	ENSP00000305107:p.Asn311Asp	63.0	0.0		126.0	31.0	NM_175571		Missense_Mutation	SNP	ENST00000307271.3	hg19	CCDS34777.1	.	.	.	.	.	.	.	.	.	.	A	0.331	-0.956063	0.02267	.	.	ENSG00000171115	ENST00000307271	T	0.60797	0.16	4.47	-4.85	0.03142	AIG1 (1);	1.311810	0.05394	N	0.539498	T	0.18087	0.0434	N	0.00991	-1.07	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.19745	-1.0296	10	0.05833	T	0.94	.	2.3223	0.04214	0.479:0.1544:0.2523:0.1143	.	311	Q8ND71	GIMA8_HUMAN	D	311	ENSP00000305107:N311D	ENSP00000305107:N311D	N	+	1	0	GIMAP8	149802281	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-2.558000	0.00923	-0.941000	0.03700	-0.297000	0.09499	AAC	.	.		0.453	GIMAP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350701.1	NM_175571		G	150171348	A	G	150171348	3	3	263	1	0	0	0	0	1	0	0	0	6393	246	9	2	941	2	GIMAP8	7	150171348	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	8729361	150171348	8967315	173	38547										
PAXIP1	22976	hgsc.bcm.edu	37	chr7	154759592	154759592	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	taatccgcaattgcaaacacAcatcccaataagaagccttc	4	13	0	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr7:154759592A>G	ENST00000404141.1	-	8	1981	c.1827T>C	c.(1825-1827)tgT>tgC	p.C609C	PAXIP1_ENST00000397192.1_Silent_p.C609C|PAXIP1_ENST00000473219.1_5'UTR			Q6ZW49	PAXI1_HUMAN	PAX interacting (with transcription-activation domain) protein 1	609	BRCT 3. {ECO:0000255|PROSITE- ProRule:PRU00033}.|Gln-rich.|Interaction with TP53BP1.				adipose tissue development (GO:0060612)|chorion development (GO:0060717)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|endothelial cell migration (GO:0043542)|histone H3-K4 methylation (GO:0051568)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K36 methylation (GO:0000416)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of isotype switching (GO:0045830)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	33	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0296)	UCEC - Uterine corpus endometrioid carcinoma (81;0.178)		TTGCAAACACACATCCCAATA	0.403																																					p.C609C		Atlas-SNP	.											PAXIP1_ENST00000397192,colon,carcinoma,0,2	PAXIP1	150	.	0			c.T1827C						.						79	74	75					7																	154759592		1900	4119	6019	SO:0001819	synonymous_variant	22976	exon8			AAACACACATCCC	U80735	CCDS47753.1	7q36	2007-07-06	2005-04-05	2005-04-05	ENSG00000157212	ENSG00000157212			8624	protein-coding gene	gene with protein product		608254	"PAX transcription activation domain interacting protein 1 like"	PAXIP1L		9225980	Standard	XM_005249539		Approved	CAGF29, CAGF28, TNRC2, PTIP	uc022aqf.1	Q6ZW49	OTTHUMG00000151322	ENST00000404141.1:c.1827T>C	chr7.hg19:g.154759592A>G		71.0	1.0		75.0	4.0	NM_007349	O15404|Q6N099|Q6ZWH9|Q7Z315|Q86UN0|Q8N4P9|Q96HP2	Silent	SNP	ENST00000404141.1	hg19	CCDS47753.1																																																																																			.	.		0.403	PAXIP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322223.1	NM_007349		G	154759592	A	G	154759592	2	3	263	1	0	0	0	0	0	0	0	1	11496	157	6	2		2	PAXIP1	7	154759592	Silent	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	4588244	154759592	4379071	174	38548										
INSIG1	3638	hgsc.bcm.edu	37	chr7	155090257	155090257	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	atcatcgcctgttgcagaggAgcctcgtgctcttctcggtt	11	12	3	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr7:155090257A>G	ENST00000340368.4	+	2	473	c.262A>G	c.(262-264)Agc>Ggc	p.S88G	INSIG1_ENST00000344756.4_Intron|AC144652.1_ENST00000609974.1_lincRNA|INSIG1_ENST00000342407.5_Missense_Mutation_p.S88G	NM_005542.4	NP_005533.2	O15503	INSI1_HUMAN	insulin induced gene 1	88					cell proliferation (GO:0008283)|cholesterol biosynthetic process (GO:0006695)|cranial suture morphogenesis (GO:0060363)|inner ear morphogenesis (GO:0042472)|metabolic process (GO:0008152)|middle ear morphogenesis (GO:0042474)|negative regulation of cargo loading into COPII-coated vesicle (GO:1901303)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of steroid biosynthetic process (GO:0010894)|palate development (GO:0060021)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)|triglyceride metabolic process (GO:0006641)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|SREBP-SCAP-Insig complex (GO:0032937)				endometrium(2)|kidney(2)|large_intestine(1)|lung(11)|prostate(1)|upper_aerodigestive_tract(2)	19	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GTTGCAGAGGAGCCTCGTGCT	0.667																																					p.S88G		Atlas-SNP	.											.	INSIG1	20	.	0			c.A262G						.						51	47	48					7																	155090257		2202	4299	6501	SO:0001583	missense	3638	exon2			CAGAGGAGCCTCG		CCDS5938.1, CCDS5939.1	7q36	2008-07-18			ENSG00000186480	ENSG00000186480			6083	protein-coding gene	gene with protein product	"INSIG-1 membrane protein"	602055				9268630	Standard	NM_005542		Approved	CL-6, MGC1405	uc003wly.3	O15503	OTTHUMG00000151330	ENST00000340368.4:c.262A>G	chr7.hg19:g.155090257A>G	ENSP00000344741:p.Ser88Gly	59.0	0.0		77.0	4.0	NM_198337	A4D2N1|A8K6L0|Q53XW8|Q9BUV5	Missense_Mutation	SNP	ENST00000340368.4	hg19	CCDS5938.1	.	.	.	.	.	.	.	.	.	.	A	11.38	1.621302	0.28889	.	.	ENSG00000186480	ENST00000340368;ENST00000425172;ENST00000342407	T;T;T	0.43294	0.95;0.99;1.05	4.85	1.18	0.20946	.	0.092218	0.85682	N	0.000000	T	0.15132	0.0365	N	0.00771	-1.2	0.80722	D	1	P;B	0.37370	0.592;0.004	B;B	0.42738	0.396;0.01	T	0.07635	-1.0762	10	0.14656	T	0.56	.	8.3313	0.32189	0.7662:0.0:0.2338:0.0	.	88;88	A4D2N1;O15503	.;INSI1_HUMAN	G	88	ENSP00000344741:S88G;ENSP00000414691:S88G;ENSP00000344035:S88G	ENSP00000344741:S88G	S	+	1	0	INSIG1	154721190	1.000000	0.71417	0.896000	0.35187	0.993000	0.82548	4.629000	0.61290	-0.029000	0.13827	0.529000	0.55759	AGC	.	.		0.667	INSIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322244.3	NM_198336		G	155090257	A	G	155090257	3	3	263	1	0	0	0	0	1	0	0	0	7774	304	11	2	264	2	INSIG1	7	155090257	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	330665	155090257	4048406	175	38549										
MTMR9	66036	hgsc.bcm.edu	37	chr8	11174246	11174246	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	taacaccaagcagaagtgggAggctcctgtatttcttctct	9	10	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr8:11174246A>G	ENST00000221086.3	+	8	1651	c.1178A>G	c.(1177-1179)gAg>gGg	p.E393G	AF131216.6_ENST00000498997.2_RNA|MTMR9_ENST00000526292.1_Missense_Mutation_p.E308G	NM_015458.3	NP_056273.2	Q96QG7	MTMR9_HUMAN	myotubularin related protein 9	393	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.					cytoplasm (GO:0005737)	enzyme regulator activity (GO:0030234)|phosphatase activity (GO:0016791)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|urinary_tract(2)	16			STAD - Stomach adenocarcinoma(15;0.215)	COAD - Colon adenocarcinoma(149;0.0678)		CAGAAGTGGGAGGCTCCTGTA	0.498																																					p.E393G		Atlas-SNP	.											.	MTMR9	58	.	0			c.A1178G						.						96	79	85					8																	11174246		2203	4300	6503	SO:0001583	missense	66036	exon8			AGTGGGAGGCTCC	AJ297823	CCDS5979.1	8p23-p22	2011-06-09	2002-09-05	2002-09-06	ENSG00000104643	ENSG00000104643		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	14596	protein-coding gene	gene with protein product		606260	"myotubularin related protein 8"	C8orf9, MTMR8		11472061, 11896452, 12890864	Standard	NM_015458		Approved	DKFZp434K171, LIP-STYX	uc003wtm.3	Q96QG7	OTTHUMG00000090647	ENST00000221086.3:c.1178A>G	chr8.hg19:g.11174246A>G	ENSP00000221086:p.Glu393Gly	191.0	0.0		139.0	6.0	NM_015458	B7Z291|Q52LU3|Q8WW11|Q96QG6|Q9NX50	Missense_Mutation	SNP	ENST00000221086.3	hg19	CCDS5979.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.510468	0.85389	.	.	ENSG00000104643	ENST00000221086;ENST00000526292	D;D	0.90444	-2.67;-2.67	4.87	4.87	0.63330	Myotubularin phosphatase domain (1);	.	.	.	.	D	0.89455	0.6720	M	0.85630	2.765	0.80722	D	1	P	0.41498	0.752	B	0.33042	0.157	D	0.89023	0.3436	9	0.31617	T	0.26	.	13.7877	0.63119	1.0:0.0:0.0:0.0	.	393	Q96QG7	MTMR9_HUMAN	G	393;308	ENSP00000221086:E393G;ENSP00000433239:E308G	ENSP00000221086:E393G	E	+	2	0	MTMR9	11211656	1.000000	0.71417	0.998000	0.56505	0.965000	0.64279	8.924000	0.92827	2.054000	0.61138	0.482000	0.46254	GAG	.	.		0.498	MTMR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207307.2	NM_015458		G	11174246	A	G	11174246	3	3	263	1	0	0	0	0	1	0	0	0	9959	304	11	2	1208	2	MTMR9	8	11174246	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10		11174246	135189776	176	38550										
VPS37A	137492	hgsc.bcm.edu	37	chr8	17132309	17132309	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ttccatttcttcctccatatCctccacaagaagcaaacagg	4	14	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr8:17132309C>A	ENST00000324849.4	+	5	1158	c.484C>A	c.(484-486)Cct>Act	p.P162T	VPS37A_ENST00000324815.3_Missense_Mutation_p.S171Y|VPS37A_ENST00000521829.1_Missense_Mutation_p.P137T	NM_001145152.1|NM_152415.2	NP_001138624.1|NP_689628.2	Q8NEZ2	VP37A_HUMAN	vacuolar protein sorting 37 homolog A (S. cerevisiae)	162					cell death (GO:0008219)|endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|membrane organization (GO:0061024)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)				autonomic_ganglia(1)|breast(1)|kidney(2)|large_intestine(1)|lung(4)|skin(1)	10				Colorectal(111;0.0553)|COAD - Colon adenocarcinoma(73;0.212)		TCCTCCATATCCTCCACAAGA	0.418																																					p.P162T		Atlas-SNP	.											.	VPS37A	22	.	0			c.C484A						.						105	89	95					8																	17132309		2203	4300	6503	SO:0001583	missense	137492	exon5			CCATATCCTCCAC		CCDS6001.1, CCDS47811.1	8p22	2012-06-29	2006-04-04		ENSG00000155975	ENSG00000155975			24928	protein-coding gene	gene with protein product	"hepatocellular carcinoma related protein 1"	609927	"vacuolar protein sorting 37A (yeast)", "polyglutamine binding protein 2"	PQBP2		15240819, 15218037, 22717650	Standard	NM_152415		Approved	FLJ32642, HCRP1, SPG53	uc003wxj.3	Q8NEZ2	OTTHUMG00000130785	ENST00000324849.4:c.484C>A	chr8.hg19:g.17132309C>A	ENSP00000318629:p.Pro162Thr	174.0	0.0		117.0	65.0	NM_152415	Q336D5|Q6NW27|Q8N3D7|Q8TBL7|Q96DL9	Missense_Mutation	SNP	ENST00000324849.4	hg19	CCDS6001.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.66|11.66	1.705839|1.705839	0.30232|0.30232	.|.	.|.	ENSG00000155975|ENSG00000155975	ENST00000324849;ENST00000521829|ENST00000324815	T;T|.	0.57595|.	0.39;0.45|.	4.25|4.25	3.38|3.38	0.38709|0.38709	.|.	0.436137|.	0.25823|.	N|.	0.028073|.	T|T	0.51295|0.51295	0.1666|0.1666	L|L	0.47716|0.47716	1.5|1.5	0.23473|0.23473	N|N	0.997602|0.997602	B;B|.	0.33583|.	0.418;0.047|.	B;B|.	0.30855|.	0.121;0.014|.	T|T	0.48410|0.48410	-0.9038|-0.9038	10|6	0.62326|0.72032	D|D	0.03|0.01	-13.1633|-13.1633	13.3433|13.3433	0.60557|0.60557	0.0:0.9219:0.0:0.0781|0.0:0.9219:0.0:0.0781	.|.	137;162|.	Q8NEZ2-2;Q8NEZ2|.	.;VP37A_HUMAN|.	T|Y	162;137|171	ENSP00000318629:P162T;ENSP00000429680:P137T|.	ENSP00000318629:P162T|ENSP00000318173:S171Y	P|S	+|+	1|2	0|0	VPS37A|VPS37A	17176680|17176680	0.785000|0.785000	0.28726|0.28726	0.708000|0.708000	0.30435|0.30435	0.272000|0.272000	0.26649|0.26649	2.024000|2.024000	0.41049|0.41049	1.398000|1.398000	0.46701|0.46701	-0.232000|-0.232000	0.12228|0.12228	CCT|TCC	.	.		0.418	VPS37A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253301.2	NM_152415		A	17132309	C	A	17132309	3	1	263	1	0	0	0	0	1	0	0	0	17220	855	30	3	502	3	VPS37A	8	17132309	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	5958063	17132309	129231713	177	38551										
ATP6V1B2	526	hgsc.bcm.edu	37	chr8	20074766	20074766	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	aatgtgctgccctcactatcAcggttaatgaagtctgctat	8	10	3	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr8:20074766A>G	ENST00000276390.2	+	12	1237	c.1197A>G	c.(1195-1197)tcA>tcG	p.S399S		NM_001693.3	NP_001684.2	P21281	VATB2_HUMAN	ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B2	399					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|proton-transporting V-type ATPase, V1 domain (GO:0033180)|ruffle (GO:0001726)	ATP binding (GO:0005524)|hydrogen ion transmembrane transporter activity (GO:0015078)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			endometrium(1)|kidney(2)|lung(5)|prostate(1)	9				Colorectal(74;0.0535)|COAD - Colon adenocarcinoma(73;0.211)	Gallium nitrate(DB05260)	CCTCACTATCACGGTTAATGA	0.378																																					p.S399S	Pancreas(119;1230 1726 3901 4036 31644)	Atlas-SNP	.											.	ATP6V1B2	34	.	0			c.A1197G						.						201	174	184					8																	20074766		2203	4300	6503	SO:0001819	synonymous_variant	526	exon12			ACTATCACGGTTA	L35249	CCDS6014.1	8p21.3	2010-04-21	2006-01-13	2002-05-10	ENSG00000147416	ENSG00000147416	3.6.3.14	"ATPases / V-type"	854	protein-coding gene	gene with protein product		606939	"ATPase, H+ transporting, lysosomal (vacuolar proton pump), beta polypeptide, 56/58kD, isoform 2", "ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B, isoform 2"	VPP3, ATP6B2		2145275, 14580332	Standard	NM_001693		Approved	VATB, Vma2, HO57	uc003wzp.3	P21281	OTTHUMG00000131073	ENST00000276390.2:c.1197A>G	chr8.hg19:g.20074766A>G		80.0	0.0		95.0	4.0	NM_001693	B2R5Z3|D3DSQ5|Q14544|Q15859|Q96IR0	Silent	SNP	ENST00000276390.2	hg19	CCDS6014.1																																																																																			.	.		0.378	ATP6V1B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253732.1	NM_001693		G	20074766	A	G	20074766	2	3	263	1	0	0	0	0	0	0	0	1	1179	146	6	2		2	ATP6V1B2	8	20074766	Silent	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	2942457	20074766	126289256	178	38552										
POLR3D	661	hgsc.bcm.edu	37	chr8	22106822	22106822	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	atcaagcaggagaaagaccgAgtacgctcagacagaggcct	12	10	2	4			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr8:22106822A>G	ENST00000397802.4	+	6	1136	c.921A>G	c.(919-921)cgA>cgG	p.R307R	POLR3D_ENST00000306433.4_Splice_Site_p.R307R			P05423	RPC4_HUMAN	polymerase (RNA) III (DNA directed) polypeptide D, 44kDa	307					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)	13				Colorectal(74;0.0146)|COAD - Colon adenocarcinoma(73;0.061)		AGAAAGACCGAGTACGCTCAG	0.607																																					p.R307R		Atlas-SNP	.											.	POLR3D	26	.	0			c.A921G						.						59	51	54					8																	22106822		2203	4300	6503	SO:0001630	splice_region_variant	661	exon7			AGACCGAGTACGC	M17754	CCDS34858.1	8q21	2013-01-21	2003-04-01	2003-04-04	ENSG00000168495	ENSG00000168495		"RNA polymerase subunits"	1080	protein-coding gene	gene with protein product		187280	"BN51 (BHK21) temperature sensitivity complementing"	BN51T		12391170, 11279001	Standard	NM_001722		Approved	TSBN51, RPC4	uc003xbl.3	P05423	OTTHUMG00000163778	ENST00000397802.4:c.921+1A>G	chr8.hg19:g.22106822A>G		90.0	0.0		84.0	5.0	NM_001722	Q6FI28|Q9BPV7|Q9BPZ1|Q9BXB3	Silent	SNP	ENST00000397802.4	hg19	CCDS34858.1																																																																																			.	.		0.607	POLR3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375434.2	NM_001722	Silent	G	22106822	A	G	22106822	5	3	263	1	0	0	0	0	0	0	1	0	12240	318	11	2	943	2	POLR3D	8	22106822	Splice_Site	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	2032056	22106822	124257200	179	38553										
EXTL3	2137	hgsc.bcm.edu	37	chr8	28575571	28575571	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ccccgagagcagttcacggtGgtgatgttgacttatgagcg	14	9	1	4			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr8:28575571G>T	ENST00000220562.4	+	3	2897	c.1995G>T	c.(1993-1995)gtG>gtT	p.V665V	EXTL3_ENST00000519886.1_Intron|EXTL3_ENST00000523149.1_Silent_p.V281V	NM_001440.2	NP_001431.1	O43909	EXTL3_HUMAN	exostosin-like glycosyltransferase 3	665					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|positive regulation of cell growth (GO:0030307)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0001888)|metal ion binding (GO:0046872)			biliary_tract(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(8)|ovary(1)|prostate(2)|skin(2)|soft_tissue(1)|urinary_tract(1)	36		Ovarian(32;0.069)		KIRC - Kidney renal clear cell carcinoma(542;0.107)|Kidney(114;0.129)|Colorectal(74;0.228)		AGTTCACGGTGGTGATGTTGA	0.542																																					p.V665V		Atlas-SNP	.											.	EXTL3	83	.	0			c.G1995T						.						132	125	127					8																	28575571		2203	4300	6503	SO:0001819	synonymous_variant	2137	exon3			CACGGTGGTGATG	U76188	CCDS6070.1	8p22-p12	2013-03-01	2013-03-01		ENSG00000012232	ENSG00000012232	2.4.1.223	"Exostosin glycosyltransferase family"	3518	protein-coding gene	gene with protein product	"REG receptor", "glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase"	605744	"exostoses (multiple)-like 3"			9479495, 9450183, 11257457	Standard	NM_001440		Approved	botv, REGR	uc003xgz.2	O43909	OTTHUMG00000102146	ENST00000220562.4:c.1995G>T	chr8.hg19:g.28575571G>T		222.0	1.0		165.0	94.0	NM_001440	D3DST8|O00225|Q53XT3	Silent	SNP	ENST00000220562.4	hg19	CCDS6070.1																																																																																			.	.		0.542	EXTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219987.3	NM_001440		T	28575571	G	T	28575571	2	4	263	1	0	0	0	0	0	0	0	1	5329	1335	47	3		3	EXTL3	8	28575571	Silent	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	6468749	28575571	117788451	180	38554										
FGFR1	2260	hgsc.bcm.edu	37	chr8	38285912	38285912	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ttctttctcctctgaagaggAgtcatcatcatcatcatcat	5	11	9	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr8:38285912A>G	ENST00000447712.2	-	4	1341	c.400T>C	c.(400-402)Tcc>Ccc	p.S134P	FGFR1_ENST00000425967.3_Missense_Mutation_p.S167P|RP11-350N15.4_ENST00000528407.1_RNA|FGFR1_ENST00000341462.5_Missense_Mutation_p.S137P|FGFR1_ENST00000326324.6_Missense_Mutation_p.S45P|FGFR1_ENST00000335922.5_Missense_Mutation_p.S126P|FGFR1_ENST00000397091.5_Missense_Mutation_p.S134P|FGFR1_ENST00000397113.2_Missense_Mutation_p.S134P|FGFR1_ENST00000397103.1_Missense_Mutation_p.S45P|FGFR1_ENST00000532791.1_Missense_Mutation_p.S134P|FGFR1_ENST00000356207.5_Missense_Mutation_p.S45P|FGFR1_ENST00000397108.4_Missense_Mutation_p.S134P	NM_001174063.1|NM_015850.3|NM_023110.2	NP_001167534.1|NP_056934.2|NP_075598.2	P11362	FGFR1_HUMAN	fibroblast growth factor receptor 1	134					angiogenesis (GO:0001525)|auditory receptor cell development (GO:0060117)|axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell maturation (GO:0048469)|cell migration (GO:0016477)|chondrocyte differentiation (GO:0002062)|chordate embryonic development (GO:0043009)|embryonic limb morphogenesis (GO:0030326)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lung-associated mesenchyme development (GO:0060484)|MAPK cascade (GO:0000165)|mesenchymal cell differentiation (GO:0048762)|midbrain development (GO:0030901)|middle ear morphogenesis (GO:0042474)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|outer ear morphogenesis (GO:0042473)|paraxial mesoderm development (GO:0048339)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)|regulation of cell differentiation (GO:0045595)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of lateral mesodermal cell fate specification (GO:0048378)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ventricular zone neuroblast division (GO:0021847)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)		FGFR1/ZNF703(2)	breast(2)|central_nervous_system(7)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(18)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	50	all_cancers(2;9.05e-47)|all_epithelial(2;2.64e-50)|all_lung(3;1.71e-23)|Lung NSC(2;3.61e-23)|Colorectal(12;0.000442)	Breast(189;1.48e-05)|all_lung(54;0.00354)|Lung NSC(58;0.0138)|Hepatocellular(245;0.065)	Epithelial(3;3.96e-34)|all cancers(3;3.06e-30)|BRCA - Breast invasive adenocarcinoma(5;2.28e-21)|COAD - Colon adenocarcinoma(9;0.24)		Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	TCTGAAGAGGAGtcatcatca	0.493		1	T	"BCR, FOP, ZNF198, CEP1"	"MPD, NHL"		"Pfeiffer syndrome, Kallman syndrome"																														p.S167P	Melanoma(146;1153 1840 21453 21841 43625)	Atlas-SNP	.		Dom	yes		8	8p11.2-p11.1	2260	fibroblast growth factor receptor 1	yes	L	.	FGFR1	284	.	0			c.T499C						.						169	174	172					8																	38285912		1978	4159	6137	SO:0001583	missense	2260	exon5			AAGAGGAGTCATC	M34185	CCDS6107.2, CCDS43730.1, CCDS43731.1, CCDS43732.1, CCDS55221.1, CCDS55222.1, CCDS55223.1	8p11.23-p11.22	2014-04-03	2008-08-01		ENSG00000077782	ENSG00000077782	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3688	protein-coding gene	gene with protein product	"Pfeiffer syndrome"	136350	"fms-related tyrosine kinase 2"	FLT2, KAL2		2162671	Standard	NM_015850		Approved	H2, H3, H4, H5, CEK, FLG, BFGFR, N-SAM, CD331	uc011lbu.2	P11362	OTTHUMG00000147366	ENST00000447712.2:c.400T>C	chr8.hg19:g.38285912A>G	ENSP00000400162:p.Ser134Pro	123.0	0.0		84.0	4.0	NM_001174067	A8K6T9|A8K8V5|C1KBH8|P17049|Q02063|Q02065|Q14306|Q14307|Q53H63|Q59H40|Q5BJG2|Q8N685|Q9UD50|Q9UDF0|Q9UDF1|Q9UDF2	Missense_Mutation	SNP	ENST00000447712.2	hg19	CCDS6107.2	.	.	.	.	.	.	.	.	.	.	A	20.3	3.962112	0.74016	.	.	ENSG00000077782	ENST00000397091;ENST00000425967;ENST00000447712;ENST00000341462;ENST00000310729;ENST00000532791;ENST00000397113;ENST00000356207;ENST00000335922;ENST00000326324;ENST00000397103;ENST00000397108;ENST00000326296;ENST00000525001;ENST00000526742;ENST00000529552;ENST00000530568;ENST00000434187	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.79845	-1.23;-1.23;-1.27;-1.25;-1.28;-1.23;-1.21;-1.31;-1.17;-1.18;-1.23;-1.1;-1.05;-1.01;-0.97;-1.12	5.69	5.69	0.88448	.	0.113142	0.64402	D	0.000006	D	0.82591	0.5070	N	0.19112	0.55	0.80722	D	1	D;P;P;P;P;P;P;D;D;D;D;D	0.71674	0.998;0.945;0.951;0.951;0.909;0.945;0.882;0.96;0.993;0.99;0.995;0.977	D;P;P;P;P;D;B;P;P;D;D;P	0.79784	0.993;0.82;0.886;0.886;0.665;0.959;0.444;0.809;0.88;0.915;0.991;0.907	D	0.84807	0.0788	10	0.56958	D	0.05	.	15.1202	0.72438	1.0:0.0:0.0:0.0	.	45;45;134;167;45;45;45;134;126;45;45;134	B5A959;P11362-3;P11362-7;P11362-21;B5A958;P11362-14;P11362-4;P11362;P11362-20;P11362-16;P11362-18;P11362-2	.;.;.;.;.;.;.;FGFR1_HUMAN;.;.;.;.	P	134;167;134;137;134;134;134;45;126;45;45;134;137;134;45;45;45;45	ENSP00000380280:S134P;ENSP00000393312:S167P;ENSP00000400162:S134P;ENSP00000340636:S137P;ENSP00000432972:S134P;ENSP00000380302:S134P;ENSP00000348537:S45P;ENSP00000337247:S126P;ENSP00000327229:S45P;ENSP00000380292:S45P;ENSP00000380297:S134P;ENSP00000434712:S134P;ENSP00000433569:S45P;ENSP00000435283:S45P;ENSP00000434473:S45P;ENSP00000392645:S45P	ENSP00000311337:S134P	S	-	1	0	FGFR1	38405069	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.949000	0.56668	2.174000	0.68829	0.460000	0.39030	TCC	.	.		0.493	FGFR1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				G	38285912	A	G	38285912	3	3	263	1	0	0	0	0	1	0	0	0	5871	304	11	2	2368	2	FGFR1	8	38285912	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	9710341	38285912	108078110	181	38555										
IDO2	169355	hgsc.bcm.edu	37	chr8	39840206	39840206	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cttgcccttccatttgtcgaAgtctccaggaacttggggct	10	12	1	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr8:39840206A>G	ENST00000389060.4	+	4	351	c.351A>G	c.(349-351)gaA>gaG	p.E117E	IDO2_ENST00000343295.4_3'UTR|RP11-44K6.3_ENST00000517623.1_RNA|IDO2_ENST00000502986.2_Silent_p.E130E			Q6ZQW0	I23O2_HUMAN	indoleamine 2,3-dioxygenase 2	117					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)|tryptophan catabolic process to kynurenine (GO:0019441)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	heme binding (GO:0020037)|indoleamine 2,3-dioxygenase activity (GO:0033754)|metal ion binding (GO:0046872)|tryptophan 2,3-dioxygenase activity (GO:0004833)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)	18						CATTTGTCGAAGTCTCCAGGA	0.468																																					p.E130E		Atlas-SNP	.											.	IDO2	78	.	0			c.A390G						.						75	74	75					8																	39840206		1882	4107	5989	SO:0001819	synonymous_variant	169355	exon5			TGTCGAAGTCTCC	AK128691		8p11.21	2012-04-19	2009-01-07	2009-01-07	ENSG00000188676	ENSG00000188676			27269	protein-coding gene	gene with protein product		612129	"indoleamine-pyrrole 2,3 dioxygenase-like 1"	INDOL1			Standard	NM_194294		Approved		uc010lwy.1	Q6ZQW0	OTTHUMG00000141271	ENST00000389060.4:c.351A>G	chr8.hg19:g.39840206A>G		85.0	0.0		70.0	5.0	NM_194294	A4UD41	Silent	SNP	ENST00000389060.4	hg19																																																																																				.	.		0.468	IDO2-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372742.1	NM_194294		G	39840206	A	G	39840206	2	3	263	1	0	0	0	0	0	0	0	1	7511	69	3	2		2	IDO2	8	39840206	Silent	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	1554294	39840206	106523816	182	38556										
AP3M2	10947	hgsc.bcm.edu	37	chr8	42022975	42022975	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tgttggatgatgtcagcttcCatccttgtgttcgtttcaaa	9	8	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr8:42022975C>T	ENST00000518421.1	+	7	991	c.700C>T	c.(700-702)Cat>Tat	p.H234Y	AP3M2_ENST00000174653.3_Missense_Mutation_p.H234Y|AP3M2_ENST00000517922.1_Missense_Mutation_p.H234Y|AP3M2_ENST00000520685.1_Intron|AP3M2_ENST00000396926.3_Missense_Mutation_p.H234Y	NM_001134296.1	NP_001127768.1	P53677	AP3M2_HUMAN	adaptor-related protein complex 3, mu 2 subunit	234	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|intracellular protein transport (GO:0006886)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)				endometrium(3)|kidney(1)|large_intestine(1)|lung(10)|prostate(1)|stomach(1)	17	all_cancers(6;8.14e-25)|all_epithelial(6;2.41e-27)|all_lung(13;5.09e-13)|Lung NSC(13;8.38e-12)|Ovarian(28;0.00438)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983)	BRCA - Breast invasive adenocarcinoma(8;5.23e-10)|Colorectal(10;0.00165)|OV - Ovarian serous cystadenocarcinoma(14;0.00346)|Lung(22;0.00467)|COAD - Colon adenocarcinoma(11;0.0171)|LUSC - Lung squamous cell carcinoma(45;0.024)			TGTCAGCTTCCATCCTTGTGT	0.493																																					p.H234Y		Atlas-SNP	.											.	AP3M2	41	.	0			c.C700T						.						291	236	255					8																	42022975		2203	4300	6503	SO:0001583	missense	10947	exon7			AGCTTCCATCCTT	D38293	CCDS6125.1	8p11.2	2008-07-07			ENSG00000070718	ENSG00000070718			570	protein-coding gene	gene with protein product		610469				7601449	Standard	NM_006803		Approved	CLA20, AP47B	uc003xoo.3	P53677	OTTHUMG00000164060	ENST00000518421.1:c.700C>T	chr8.hg19:g.42022975C>T	ENSP00000428787:p.His234Tyr	245.0	0.0		329.0	140.0	NM_001134296	B2RCR0|D3DSY2|Q7Z472	Missense_Mutation	SNP	ENST00000518421.1	hg19	CCDS6125.1	.	.	.	.	.	.	.	.	.	.	C	34	5.319393	0.95682	.	.	ENSG00000070718	ENST00000518421;ENST00000174653;ENST00000396926;ENST00000521280;ENST00000517922;ENST00000517499	T;T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.68;0.68	5.83	5.83	0.93111	Clathrin adaptor, mu subunit, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.81555	0.4847	H	0.97732	4.065	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.87460	0.2407	10	0.87932	D	0	-22.8363	20.126	0.97982	0.0:1.0:0.0:0.0	.	234;234	E7ER80;P53677	.;AP3M2_HUMAN	Y	234;234;234;119;234;97	ENSP00000428787:H234Y;ENSP00000174653:H234Y;ENSP00000380132:H234Y;ENSP00000430616:H119Y;ENSP00000429435:H234Y;ENSP00000429037:H97Y	ENSP00000174653:H234Y	H	+	1	0	AP3M2	42142132	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.487000	0.81328	2.749000	0.94314	0.655000	0.94253	CAT	.	.		0.493	AP3M2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376996.1			T	42022975	C	T	42022975	3	4	263	1	0	0	0	0	1	0	0	0	748	594	21	3	718	3	AP3M2	8	42022975	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	2182769	42022975	104341047	183	38557										
FNTA	2339	hgsc.bcm.edu	37	chr8	42939883	42939883	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gatcgtggtctttccaaataTcctaatctgttaaatcaatt	5	8	3	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr8:42939883T>C	ENST00000302279.3	+	8	1070	c.876T>C	c.(874-876)taT>taC	p.Y292Y	FNTA_ENST00000342116.4_Silent_p.Y225Y|FNTA_ENST00000529687.1_Silent_p.Y141Y	NM_002027.2	NP_002018.1	P49354	FNTA_HUMAN	farnesyltransferase, CAAX box, alpha	292					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|phototransduction, visible light (GO:0007603)|positive regulation of deacetylase activity (GO:0090045)|positive regulation of tubulin deacetylation (GO:0090044)|protein farnesylation (GO:0018343)|protein geranylgeranylation (GO:0018344)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|transforming growth factor beta receptor signaling pathway (GO:0007179)	CAAX-protein geranylgeranyltransferase complex (GO:0005953)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule associated complex (GO:0005875)|protein farnesyltransferase complex (GO:0005965)	alpha-tubulin binding (GO:0043014)|CAAX-protein geranylgeranyltransferase activity (GO:0004662)|microtubule binding (GO:0008017)|protein farnesyltransferase activity (GO:0004660)|protein geranylgeranyltransferase activity (GO:0004661)			cervix(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(8)|ovary(1)|prostate(1)|urinary_tract(1)	16	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)			TTTCCAAATATCCTAATCTGT	0.343																																					p.Y292Y		Atlas-SNP	.											.	FNTA	34	.	0			c.T876C						.						70	67	68					8																	42939883		2203	4300	6503	SO:0001819	synonymous_variant	2339	exon8			CAAATATCCTAAT	L10413	CCDS6140.1	8p11.21	2011-06-27			ENSG00000168522	ENSG00000168522		"Prenyltransferase alpha subunit repeat containing"	3782	protein-coding gene	gene with protein product	"protein prenyltransferase alpha subunit repeat containing 2"	134635				8276393	Standard	NR_033698		Approved	FPTA, PGGT1A, PTAR2	uc003xps.3	P49354	OTTHUMG00000165279	ENST00000302279.3:c.876T>C	chr8.hg19:g.42939883T>C		89.0	0.0		104.0	6.0	NM_002027	A6NJW0|Q53XJ9|Q9UDC1	Silent	SNP	ENST00000302279.3	hg19	CCDS6140.1																																																																																			.	.		0.343	FNTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383178.1	NM_002027		C	42939883	T	C	42939883	2	2	263	1	0	0	0	0	0	0	0	1	5985	1442	50	2		2	FNTA	8	42939883	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	916908	42939883	103424139	184	38558										
PCMTD1	115294	hgsc.bcm.edu	37	chr8	52746162	52746162	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tggtctttctgcactccagcTccacaataaattcgatcata	5	12	3	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr8:52746162T>C	ENST00000360540.5	-	5	904	c.498A>G	c.(496-498)ggA>ggG	p.G166G	PCMTD1_ENST00000544451.1_Silent_p.G90G|PCMTD1_ENST00000522514.1_Silent_p.G166G|PCMTD1_ENST00000519559.1_5'UTR	NM_052937.2	NP_443169.2	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	166						cytoplasm (GO:0005737)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)			NS(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(17)|prostate(2)|skin(8)|soft_tissue(1)	37		Lung NSC(129;0.0795)|all_lung(136;0.144)				GCACTCCAGCTCCACAATAAA	0.388																																					p.G166G		Atlas-SNP	.											.	PCMTD1	73	.	0			c.A498G						.						147	131	136					8																	52746162		2203	4300	6503	SO:0001819	synonymous_variant	115294	exon4			TCCAGCTCCACAA		CCDS6148.1, CCDS69480.1	8q11.23	2010-08-05			ENSG00000168300	ENSG00000168300			30483	protein-coding gene	gene with protein product							Standard	XM_005251146		Approved	FLJ10883	uc003xqx.4	Q96MG8	OTTHUMG00000164246	ENST00000360540.5:c.498A>G	chr8.hg19:g.52746162T>C		84.0	0.0		74.0	4.0	NM_052937	Q96FK9	Silent	SNP	ENST00000360540.5	hg19	CCDS6148.1	.	.	.	.	.	.	.	.	.	.	T	10.67	1.414317	0.25465	.	.	ENSG00000168300	ENST00000519554	.	.	.	5.48	-7.11	0.01542	.	.	.	.	.	T	0.35189	0.0923	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37865	-0.9687	4	.	.	.	-29.4437	1.9579	0.03380	0.4189:0.1175:0.1001:0.3635	.	.	.	.	G	58	.	.	E	-	2	0	PCMTD1	52908715	0.984000	0.35163	0.871000	0.34182	0.972000	0.66771	0.110000	0.15437	-1.607000	0.01589	-0.468000	0.05107	GAG	.	.		0.388	PCMTD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377909.2	NM_052937		C	52746162	T	C	52746162	2	2	263	1	0	0	0	0	0	0	0	1	11595	1538	54	2		2	PCMTD1	8	52746162	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	9806279	52746162	93617860	185	38559										
RP1	6101	hgsc.bcm.edu	37	chr8	55537397	55537397	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tatatccttctgaagatgatAttgagaaatcaattattttt	5	4	2	4			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr8:55537397A>G	ENST00000220676.1	+	4	1103	c.955A>G	c.(955-957)Att>Gtt	p.I319V		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	319					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			TGAAGATGATATTGAGAAATC	0.313																																					p.I319V	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.A955G						.						61	64	63					8																	55537397		2203	4298	6501	SO:0001583	missense	6101	exon4			GATGATATTGAGA	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.955A>G	chr8.hg19:g.55537397A>G	ENSP00000220676:p.Ile319Val	79.0	0.0		94.0	4.0	NM_006269		Missense_Mutation	SNP	ENST00000220676.1	hg19	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	A	7.976	0.750055	0.15778	.	.	ENSG00000104237	ENST00000220676	T	0.28454	1.61	5.08	-1.72	0.08107	.	0.574928	0.16670	N	0.204416	T	0.14657	0.0354	N	0.16166	0.38	0.28204	N	0.927216	B	0.21606	0.058	B	0.22386	0.039	T	0.30357	-0.9981	10	0.17369	T	0.5	.	9.8635	0.41129	0.627:0.0:0.373:0.0	.	319	P56715	RP1_HUMAN	V	319	ENSP00000220676:I319V	ENSP00000220676:I319V	I	+	1	0	RP1	55699950	1.000000	0.71417	0.981000	0.43875	0.996000	0.88848	2.456000	0.44997	-0.591000	0.05859	0.533000	0.62120	ATT	.	.		0.313	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		G	55537397	A	G	55537397	3	3	263	1	0	0	0	0	1	0	0	0	13547	449	16	2	965	2	RP1	8	55537397	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	2791235	55537397	90826625	186	38560										
CHD7	55636	hgsc.bcm.edu	37	chr8	61707642	61707642	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cagacttagacaaaacacccCcaccatctcctcctcctgaa	3	18	1	3	rs200277422		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr8:61707642C>T	ENST00000423902.2	+	4	2673	c.2194C>T	c.(2194-2196)Cca>Tca	p.P732S	CHD7_ENST00000525508.1_Missense_Mutation_p.P732S|CHD7_ENST00000524602.1_Intron	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	732					adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.556_871dup(1)		NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			CAAAACACCCCCACCATCTCC	0.418																																					p.P732S		Atlas-SNP	.											.	CHD7	534	.	1	Insertion - In frame(1)	lung(1)	c.C2194T	GRCh37	CM060907	CHD7	M		.						100	101	101					8																	61707642		1835	4076	5911	SO:0001583	missense	55636	exon4			ACACCCCCACCAT	AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"CHARGE association"	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.2194C>T	chr8.hg19:g.61707642C>T	ENSP00000392028:p.Pro732Ser	57.0	0.0		79.0	4.0	NM_017780	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Missense_Mutation	SNP	ENST00000423902.2	hg19	CCDS47865.1	.	.	.	.	.	.	.	.	.	.	C	14.78	2.637130	0.47049	.	.	ENSG00000171316	ENST00000307121;ENST00000423902;ENST00000525508	T;T	0.81415	-1.49;-1.11	5.46	5.46	0.80206	.	0.000000	0.40818	N	0.001004	T	0.74535	0.3729	L	0.36672	1.1	0.58432	D	0.999997	B	0.26081	0.141	B	0.31016	0.123	T	0.68663	-0.5349	10	0.09843	T	0.71	-10.8861	19.6793	0.95956	0.0:1.0:0.0:0.0	.	732	Q9P2D1	CHD7_HUMAN	S	732	ENSP00000392028:P732S;ENSP00000436027:P732S	ENSP00000307304:P732S	P	+	1	0	CHD7	61870196	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.292000	0.72725	2.713000	0.92767	0.655000	0.94253	CCA	.	C|0.998;G|0.002		0.418	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762		T	61707642	C	T	61707642	3	4	263	1	0	0	0	0	1	0	0	0	3332	623	22	3	2204	3	CHD7	8	61707642	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	6170245	61707642	84656380	187	38561										
SULF1	23213	hgsc.bcm.edu	37	chr8	70541861	70541861	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	agagtgcagcctgcctggccTcacttgcttcacgcatgaca	10	14	2	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr8:70541861T>C	ENST00000260128.4	+	19	2948	c.2231T>C	c.(2230-2232)cTc>cCc	p.L744P	SULF1_ENST00000402687.4_Missense_Mutation_p.L744P|SULF1_ENST00000419716.3_Missense_Mutation_p.L744P|SULF1_ENST00000521946.1_3'UTR|SULF1_ENST00000458141.2_Missense_Mutation_p.L744P	NM_015170.2	NP_055985.2	Q8IWU6	SULF1_HUMAN	sulfatase 1	744					apoptotic process (GO:0006915)|bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of prostatic bud formation (GO:0060686)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|central_nervous_system(3)|endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)			CTGCCTGGCCTCACTTGCTTC	0.542																																					p.L744P		Atlas-SNP	.											.	SULF1	153	.	0			c.T2231C						.						133	117	123					8																	70541861		2203	4300	6503	SO:0001583	missense	23213	exon19			CTGGCCTCACTTG	AB029000	CCDS6204.1	8q13.2	2014-09-11			ENSG00000137573	ENSG00000137573			20391	protein-coding gene	gene with protein product		610012				12368295	Standard	NM_015170		Approved	KIAA1077, SULF-1	uc003xyd.2	Q8IWU6	OTTHUMG00000164466	ENST00000260128.4:c.2231T>C	chr8.hg19:g.70541861T>C	ENSP00000260128:p.Leu744Pro	109.0	0.0		120.0	6.0	NM_001128205	Q86YV8|Q8NCA2|Q9UPS5	Missense_Mutation	SNP	ENST00000260128.4	hg19	CCDS6204.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.382067	0.82792	.	.	ENSG00000137573	ENST00000458141;ENST00000260128;ENST00000402687;ENST00000419716	T;T;T;T	0.26660	1.72;1.72;1.72;1.72	4.75	4.75	0.60458	Alkaline-phosphatase-like, core domain (1);	0.063902	0.64402	D	0.000004	T	0.48484	0.1502	M	0.81942	2.565	0.80722	D	1	D	0.67145	0.996	P	0.60609	0.877	T	0.50767	-0.8789	10	0.38643	T	0.18	.	14.4268	0.67220	0.0:0.0:0.0:1.0	.	744	Q8IWU6	SULF1_HUMAN	P	744	ENSP00000403040:L744P;ENSP00000260128:L744P;ENSP00000385704:L744P;ENSP00000390315:L744P	ENSP00000260128:L744P	L	+	2	0	SULF1	70704415	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	7.838000	0.86804	1.977000	0.57605	0.533000	0.62120	CTC	.	.		0.542	SULF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378885.2	NM_015170		C	70541861	T	C	70541861	3	2	263	1	0	0	0	0	1	0	0	0	15385	1551	54	2	2289	2	SULF1	8	70541861	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	8834219	70541861	75822161	188	38562										
SLCO5A1	81796	hgsc.bcm.edu	37	chr8	70744610	70744610	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ccgagaaggttttgctgaggTccaccctgtggttacagtcc	12	11	0	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr8:70744610T>C	ENST00000260126.4	-	2	1005	c.299A>G	c.(298-300)gAc>gGc	p.D100G	SLCO5A1_ENST00000524945.1_Missense_Mutation_p.D100G|RP11-159H10.3_ENST00000528800.2_RNA|RP11-159H10.3_ENST00000501104.2_RNA|SLCO5A1_ENST00000528658.1_5'UTR|SLCO5A1_ENST00000530307.1_Missense_Mutation_p.D100G|RP11-159H10.3_ENST00000533300.1_RNA	NM_030958.2	NP_112220.2	Q9H2Y9	SO5A1_HUMAN	solute carrier organic anion transporter family, member 5A1	100						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	53	Breast(64;0.0654)		Epithelial(68;0.0141)|OV - Ovarian serous cystadenocarcinoma(28;0.0315)|all cancers(69;0.0594)			TTTGCTGAGGTCCACCCTGTG	0.642											OREG0018815	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D100G		Atlas-SNP	.											.	SLCO5A1	142	.	0			c.A299G						.						100	95	97					8																	70744610		2203	4300	6503	SO:0001583	missense	81796	exon2			CTGAGGTCCACCC	AF205075	CCDS6205.1, CCDS55242.1, CCDS55243.1	8q13.1	2013-05-22	2003-11-25	2003-11-26	ENSG00000137571	ENSG00000137571		"Solute carriers"	19046	protein-coding gene	gene with protein product		613543	"solute carrier family 21 (organic anion transporter), member 15"	SLC21A15		12507753	Standard	NM_030958		Approved	OATPRP4, OATP-J, OATP5A1	uc003xyl.3	Q9H2Y9	OTTHUMG00000165121	ENST00000260126.4:c.299A>G	chr8.hg19:g.70744610T>C	ENSP00000260126:p.Asp100Gly	117.0	0.0	1124	138.0	18.0	NM_030958	A4QPC2|B2RPF7|B3KMU7|E9PKK5|G3V1C0	Missense_Mutation	SNP	ENST00000260126.4	hg19	CCDS6205.1	.	.	.	.	.	.	.	.	.	.	T	5.441	0.266496	0.10294	.	.	ENSG00000137571	ENST00000260126;ENST00000524945;ENST00000530307	T;T;T	0.41758	1.09;1.46;0.99	5.52	4.31	0.51392	.	0.238346	0.27504	N	0.019071	T	0.24275	0.0588	N	0.19112	0.55	0.22796	N	0.998724	B;B;B;B	0.06786	0.0;0.0;0.0;0.001	B;B;B;B	0.08055	0.0;0.0;0.001;0.003	T	0.06197	-1.0840	10	0.41790	T	0.15	.	5.3437	0.15998	0.0:0.1244:0.19:0.6856	.	100;100;100;100	B4DR09;E9PKK5;Q9H2Y9;G3V1C0	.;.;SO5A1_HUMAN;.	G	100	ENSP00000260126:D100G;ENSP00000434422:D100G;ENSP00000431611:D100G	ENSP00000260126:D100G	D	-	2	0	SLCO5A1	70907164	0.065000	0.20965	0.904000	0.35570	0.498000	0.33706	0.787000	0.26858	2.100000	0.63781	0.454000	0.30748	GAC	.	.		0.642	SLCO5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381990.3	NM_030958		C	70744610	T	C	70744610	3	2	263	1	0	0	0	0	1	0	0	0	14746	1667	58	2	2283	2	SLCO5A1	8	70744610	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	202749	70744610	75619412	189	38563										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77616371	77616371	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tcaaggcaggaaaatgggcaGagcacatcaaagctatgtgg	13	7	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr8:77616371G>A	ENST00000521891.2	+	2	496	c.48G>A	c.(46-48)caG>caA	p.Q16Q	ZFHX4_ENST00000455469.2_Silent_p.Q16Q|ZFHX4_ENST00000518282.1_Silent_p.Q16Q|ZFHX4_ENST00000517683.1_Intron|ZFHX4_ENST00000050961.6_Silent_p.Q16Q	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	16					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			AAAATGGGCAGAGCACATCAA	0.498										HNSCC(33;0.089)																											p.Q16Q		Atlas-SNP	.											ZFHX4,NS,carcinoma,0,1	ZFHX4	878	.	0			c.G48A						.						54	53	53					8																	77616371		1985	4193	6178	SO:0001819	synonymous_variant	79776	exon2			TGGGCAGAGCACA		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.48G>A	chr8.hg19:g.77616371G>A		126.0	0.0		144.0	63.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Silent	SNP	ENST00000521891.2	hg19	CCDS47878.2																																																																																			.	.		0.498	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		A	77616371	G	A	77616371	2	1	263	1	0	0	0	0	0	0	0	1	17650	933	33	3		3	ZFHX4	8	77616371	Silent	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	6871761	77616371	68747651	190	38564										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77768488	77768488	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ttcctccagtccttctccccGgaatgaacggtccatcctcc	6	18	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr8:77768488G>A	ENST00000521891.2	+	10	9779	c.9331G>A	c.(9331-9333)Gga>Aga	p.G3111R	ZFHX4_ENST00000455469.2_Missense_Mutation_p.G3066R|ZFHX4_ENST00000518282.1_Missense_Mutation_p.G3085R|ZFHX4_ENST00000050961.6_Missense_Mutation_p.G3066R	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	3066	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			CCTTCTCCCCGGAATGAACGG	0.522										HNSCC(33;0.089)																											p.G3111R		Atlas-SNP	.											.	ZFHX4	878	.	0			c.G9331A						.						42	43	42					8																	77768488		1939	4142	6081	SO:0001583	missense	79776	exon10			CTCCCCGGAATGA		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.9331G>A	chr8.hg19:g.77768488G>A	ENSP00000430497:p.Gly3111Arg	66.0	0.0		69.0	5.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	hg19	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	G	18.00	3.525555	0.64860	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.60040	0.26;0.25;0.25;0.22	5.45	5.45	0.79879	.	0.000000	0.43579	U	0.000559	T	0.77491	0.4138	M	0.74881	2.28	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;1.0;0.999	T	0.78912	-0.2017	10	0.87932	D	0	.	19.4735	0.94973	0.0:0.0:1.0:0.0	.	3066;3066;3111	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	R	3111;3095;3066;3066;3085	ENSP00000430497:G3111R;ENSP00000399605:G3066R;ENSP00000050961:G3066R;ENSP00000430848:G3085R	ENSP00000050961:G3066R	G	+	1	0	ZFHX4	77931043	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.657000	0.98554	2.836000	0.97738	0.655000	0.94253	GGA	.	.		0.522	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		A	77768488	G	A	77768488	3	1	263	1	0	0	0	0	1	0	0	0	17650	1117	39	1	9365	1	ZFHX4	8	77768488	Missense_Mutation	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	152117	77768488	68595534	191	38565										
TMEM67	91147	hgsc.bcm.edu	37	chr8	94822029	94822029	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ttaggttcataaggaaatggAttactttataaaagataagt	8	2	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr8:94822029A>G	ENST00000453321.3	+	26	2736	c.2678A>G	c.(2677-2679)gAt>gGt	p.D893G	TMEM67_ENST00000409623.3_Missense_Mutation_p.D812G	NM_153704.5	NP_714915.3	Q5HYA8	MKS3_HUMAN	transmembrane protein 67	893					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of centrosome duplication (GO:0010826)	centrosome (GO:0005813)|ciliary membrane (GO:0060170)|cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)	filamin binding (GO:0031005)|unfolded protein binding (GO:0051082)			breast(3)|endometrium(8)|kidney(5)|large_intestine(4)|liver(2)|lung(15)|ovary(2)|skin(1)|urinary_tract(1)	41	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.00896)			AAGGAAATGGATTACTTTATA	0.299																																					p.D893G		Atlas-SNP	.											.	TMEM67	187	.	0			c.A2678G						.						39	44	42					8																	94822029		2203	4286	6489	SO:0001583	missense	91147	exon26			AAATGGATTACTT	BX648768	CCDS6258.2, CCDS47893.1	8q22.1	2014-09-17			ENSG00000164953	ENSG00000164953			28396	protein-coding gene	gene with protein product	"Meckelin"	609884	"Meckel syndrome, type 3"	MKS3		12384791, 16415887, 19508969	Standard	NM_153704		Approved	MGC26979, JBTS6, NPHP11	uc011lgk.2	Q5HYA8	OTTHUMG00000153119	ENST00000453321.3:c.2678A>G	chr8.hg19:g.94822029A>G	ENSP00000389998:p.Asp893Gly	90.0	0.0		92.0	4.0	NM_153704	B3KRU5|B3KT47|G5E9H2|Q3ZCX3|Q7Z5T8|Q8IZ06	Missense_Mutation	SNP	ENST00000453321.3	hg19	CCDS6258.2	.	.	.	.	.	.	.	.	.	.	A	23.9	4.476383	0.84640	.	.	ENSG00000164953	ENST00000453321;ENST00000409623	D;D	0.97256	-4.31;-4.31	5.75	5.75	0.90469	.	0.051018	0.85682	D	0.000000	D	0.98235	0.9416	M	0.73598	2.24	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.995	D	0.99316	1.0905	10	0.72032	D	0.01	-18.6676	16.0656	0.80867	1.0:0.0:0.0:0.0	.	893;812;812	Q5HYA8;B3KRU5;G5E9H2	MKS3_HUMAN;.;.	G	893;812	ENSP00000389998:D893G;ENSP00000386966:D812G	ENSP00000314488:D883G	D	+	2	0	TMEM67	94891205	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.874000	0.92363	2.203000	0.70933	0.377000	0.23210	GAT	.	.		0.299	TMEM67-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329641.2	NM_153704		G	94822029	A	G	94822029	3	3	263	1	0	0	0	0	1	0	0	0	16211	333	12	2	2918	2	TMEM67	8	94822029	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	17053541	94822029	51541993	192	38566										
NCALD	83988	hgsc.bcm.edu	37	chr8	102731720	102731720	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ccatatattttcttaaactcTtccattgacaaatgtccact	2	11	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr8:102731720T>C	ENST00000311028.3	-	5	516	c.138A>G	c.(136-138)gaA>gaG	p.E46E	NCALD_ENST00000521599.1_Silent_p.E46E|NCALD_ENST00000519508.2_Silent_p.E46E|NCALD_ENST00000220931.6_Silent_p.E46E|NCALD_ENST00000395923.1_Silent_p.E46E|NCALD_ENST00000522951.1_Silent_p.E46E	NM_001040624.1|NM_001040626.1	NP_001035714.1|NP_001035716.1	P61601	NCALD_HUMAN	neurocalcin delta	46	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				calcium-mediated signaling (GO:0019722)|regulation of systemic arterial blood pressure (GO:0003073)|synaptic transmission (GO:0007268)|vesicle-mediated transport (GO:0016192)	clathrin coat of trans-Golgi network vesicle (GO:0030130)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|clathrin binding (GO:0030276)|tubulin binding (GO:0015631)			endometrium(1)|large_intestine(2)|lung(4)|prostate(1)	8	all_cancers(14;8.94e-08)|all_epithelial(15;7.03e-10)|Lung NSC(17;1.36e-05)|all_lung(17;2.7e-05)		all cancers(13;1.09e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000699)			TCTTAAACTCTTCCATTGACA	0.443																																					p.E46E		Atlas-SNP	.											.	NCALD	16	.	0			c.A138G						.						108	119	115					8																	102731720		2203	4300	6503	SO:0001819	synonymous_variant	83988	exon4			AAACTCTTCCATT	AF052142	CCDS6292.1	8q22.3	2014-08-12			ENSG00000104490	ENSG00000104490		"EF-hand domain containing"	7655	protein-coding gene	gene with protein product		606722				11267673	Standard	XM_006716672		Approved		uc003ykk.3	P61601	OTTHUMG00000164876	ENST00000311028.3:c.138A>G	chr8.hg19:g.102731720T>C		120.0	0.0		121.0	5.0	NM_001040627	P29554|Q8IYC3|Q9H0W2	Silent	SNP	ENST00000311028.3	hg19	CCDS6292.1																																																																																			.	.		0.443	NCALD-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380732.2			C	102731720	T	C	102731720	2	2	263	1	0	0	0	0	0	0	0	1	10210	1606	56	2		2	NCALD	8	102731720	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	7909691	102731720	43632302	193	38567										
RIMS2	9699	hgsc.bcm.edu	37	chr8	104898200	104898200	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tgactcactacggaaacagcAccacttagatcctagctctg	7	13	2	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr8:104898200A>G	ENST00000436393.2	+	2	948	c.707A>G	c.(706-708)cAc>cGc	p.H236R	RIMS2_ENST00000406091.3_Missense_Mutation_p.H458R|RIMS2_ENST00000507740.1_Missense_Mutation_p.H266R|RIMS2_ENST00000262231.10_Missense_Mutation_p.H266R			Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	489					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			CGGAAACAGCACCACTTAGAT	0.463										HNSCC(12;0.0054)																											p.H458R		Atlas-SNP	.											.	RIMS2	1357	.	0			c.A1373G						.						98	91	93					8																	104898200		1950	4147	6097	SO:0001583	missense	9699	exon4			AACAGCACCACTT	AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"RAB3 interacting protein 3"	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000436393.2:c.707A>G	chr8.hg19:g.104898200A>G	ENSP00000390665:p.His236Arg	79.0	0.0		109.0	5.0	NM_001100117	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Missense_Mutation	SNP	ENST00000436393.2	hg19		.	.	.	.	.	.	.	.	.	.	A	15.31	2.795966	0.50208	.	.	ENSG00000176406	ENST00000504942;ENST00000329869;ENST00000406091;ENST00000402998;ENST00000515551;ENST00000262231;ENST00000507740;ENST00000408894;ENST00000436393	T;T;T;T;T;T;T	0.17691	2.26;2.74;2.32;2.48;2.39;2.31;2.71	5.65	5.65	0.86999	.	.	.	.	.	T	0.30978	0.0782	L	0.43152	1.355	0.80722	D	1	P;D;P;P;D	0.58620	0.885;0.983;0.876;0.905;0.967	B;P;P;P;P	0.60012	0.443;0.867;0.734;0.578;0.692	T	0.00967	-1.1497	9	0.39692	T	0.17	.	15.8726	0.79132	1.0:0.0:0.0:0.0	.	489;236;266;266;458	Q9UQ26;D6RA03;Q9UQ26-1;Q9UQ26-3;F8WD47	RIMS2_HUMAN;.;.;.;.	R	458;489;458;489;266;266;266;266;236	ENSP00000427018:H458R;ENSP00000384892:H458R;ENSP00000425205:H266R;ENSP00000262231:H266R;ENSP00000423559:H266R;ENSP00000386228:H266R;ENSP00000390665:H236R	ENSP00000262231:H266R	H	+	2	0	RIMS2	104967376	1.000000	0.71417	0.994000	0.49952	0.899000	0.52679	7.347000	0.79356	2.143000	0.66587	0.460000	0.39030	CAC	.	.		0.463	RIMS2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000367217.1	NM_001100117		G	104898200	A	G	104898200	3	3	263	1	0	0	0	0	1	0	0	0	13383	159	6	2	1513	2	RIMS2	8	104898200	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	2166480	104898200	41465822	194	38568										
RIMS2	9699	hgsc.bcm.edu	37	chr8	105257145	105257145	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tttgtttctatctctgcagaAgcaggaggtaaaaaactaag	9	6	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr8:105257145A>G	ENST00000436393.2	+	24	3631	c.3390A>G	c.(3388-3390)gaA>gaG	p.E1130E	RIMS2_ENST00000339750.2_Splice_Site_p.E48E|RIMS2_ENST00000406091.3_Splice_Site_p.K1112K|RIMS2_ENST00000507740.1_Splice_Site_p.K926K|RIMS2_ENST00000262231.10_Splice_Site_p.K951K			Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	1174					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			TCTCTGCAGAAGCAGGAGGTA	0.443										HNSCC(12;0.0054)																											p.K1112K		Atlas-SNP	.											RIMS2_ENST00000507740,NS,carcinoma,0,4	RIMS2	1357	.	0			c.A3336G						.						106	107	107					8																	105257145		1861	4107	5968	SO:0001630	splice_region_variant	9699	exon20			TGCAGAAGCAGGA	AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"RAB3 interacting protein 3"	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000436393.2:c.3389-1A>G	chr8.hg19:g.105257145A>G		69.0	1.0		66.0	3.0	NM_001100117	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Silent	SNP	ENST00000436393.2	hg19																																																																																				.	.		0.443	RIMS2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000367217.1	NM_001100117	Silent	G	105257145	A	G	105257145	5	3	263	1	0	0	0	0	0	0	1	0	13383	86	3	2	3610	2	RIMS2	8	105257145	Splice_Site	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	358945	105257145	41106877	195	38569										
SAMD12	401474	hgsc.bcm.edu	37	chr8	119452108	119452108	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ttgaatgactcactgtagatCtgatactgattcggacaatg	9	7	2	5			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr8:119452108C>G	ENST00000314727.4	-	3	421	c.285G>C	c.(283-285)caG>caC	p.Q95H	SAMD12_ENST00000409003.4_Missense_Mutation_p.Q95H	NM_207506.2	NP_997389.2	Q8N8I0	SAM12_HUMAN	sterile alpha motif domain containing 12	95	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.									endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(2)	9	all_cancers(13;3.91e-25)|Lung NSC(37;1.13e-07)|Ovarian(258;0.0249)		STAD - Stomach adenocarcinoma(47;0.00391)			CACTGTAGATCTGATACTGAT	0.428																																					p.Q95H		Atlas-SNP	.											.	SAMD12	24	.	0			c.G285C						.						242	204	217					8																	119452108		2203	4300	6503	SO:0001583	missense	401474	exon3			GTAGATCTGATAC	AK096777	CCDS6325.1, CCDS47913.1	8q24.12	2013-01-10			ENSG00000177570	ENSG00000177570		"Sterile alpha motif (SAM) domain containing"	31750	protein-coding gene	gene with protein product							Standard	NM_207506		Approved	FLJ39458	uc003yom.2	Q8N8I0	OTTHUMG00000059817	ENST00000314727.4:c.285G>C	chr8.hg19:g.119452108C>G	ENSP00000314173:p.Gln95His	172.0	0.0		176.0	70.0	NM_207506	Q0P502	Missense_Mutation	SNP	ENST00000314727.4	hg19	CCDS6325.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	11.83|11.83|11.83	1.754250|1.754250|1.754250	0.31046|0.31046|0.31046	.|.|.	.|.|.	ENSG00000177570|ENSG00000177570|ENSG00000177570	ENST00000453675|ENST00000409003;ENST00000524796;ENST00000314727;ENST00000526328|ENST00000526765	.|T;T;T;T|.	.|0.30981|.	.|1.51;1.51;1.51;1.51|.	5.68|5.68|5.68	3.49|3.49|3.49	0.39957|0.39957|0.39957	.|Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 2 (1);|.	.|0.059657|.	.|0.64402|.	.|N|.	.|0.000002|.	T|T|T	0.42877|0.42877|0.42877	0.1222|0.1222|0.1222	L|L|L	0.34521|0.34521|0.34521	1.04|1.04|1.04	0.36478|0.36478|0.36478	D|D|D	0.867694|0.867694|0.867694	.|B;B|.	.|0.20368|.	.|0.0;0.044|.	.|B;B|.	.|0.24848|.	.|0.001;0.056|.	T|T|T	0.40850|0.40850|0.40850	-0.9541|-0.9541|-0.9541	5|9|5	.|.|.	.|.|.	.|.|.	-6.6264|-6.6264|-6.6264	5.9633|5.9633|5.9633	0.19310|0.19310|0.19310	0.0:0.607:0.1501:0.243|0.0:0.607:0.1501:0.243|0.0:0.607:0.1501:0.243	.|.|.	.|95;95|.	.|B8ZZB7;Q8N8I0|.	.|.;SAM12_HUMAN|.	H|H|T	92|95;87;95;95|110	.|ENSP00000387133:Q95H;ENSP00000435927:Q87H;ENSP00000314173:Q95H;ENSP00000431360:Q95H|.	.|.|.	D|Q|R	-|-|-	1|3|2	0|2|0	SAMD12|SAMD12|SAMD12	119521289|119521289|119521289	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.998000|0.998000|0.998000	0.95712|0.95712|0.95712	2.308000|2.308000|2.308000	0.43690|0.43690|0.43690	0.630000|0.630000|0.630000	0.30394|0.30394|0.30394	0.561000|0.561000|0.561000	0.74099|0.74099|0.74099	GAT|CAG|AGA	.	.		0.428	SAMD12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132989.3	NM_207506		G	119452108	C	G	119452108	3	3	263	1	0	0	0	0	1	0	0	0	13832	912	32	4	355	4	SAMD12	8	119452108	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	14194963	119452108	26911914	196	38570										
ZHX2	22882	hgsc.bcm.edu	37	chr8	123964092	123964092	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cccctctacgtgtgtgcagaAtgtaacttcacaaccaaaaa	6	12	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr8:123964092A>T	ENST00000314393.4	+	3	1177	c.342A>T	c.(340-342)gaA>gaT	p.E114D		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	114					mRNA catabolic process (GO:0006402)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	45	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			TGTGTGCAGAATGTAACTTCA	0.488																																					p.E114D	Esophageal Squamous(94;1056 1388 11767 13799 49639)	Atlas-SNP	.											.	ZHX2	106	.	0			c.A342T						.						104	94	97					8																	123964092		2203	4300	6503	SO:0001583	missense	22882	exon3			TGCAGAATGTAAC	AB020661	CCDS6336.1	8q24.13	2012-03-09	2004-01-23		ENSG00000178764	ENSG00000178764		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	18513	protein-coding gene	gene with protein product		609185	"zinc-fingers and homeoboxes 2"			10048485, 12741956	Standard	XM_005250837		Approved	KIAA0854	uc003ypk.1	Q9Y6X8	OTTHUMG00000165077	ENST00000314393.4:c.342A>T	chr8.hg19:g.123964092A>T	ENSP00000314709:p.Glu114Asp	43.0	0.0		75.0	21.0	NM_014943		Missense_Mutation	SNP	ENST00000314393.4	hg19	CCDS6336.1	.	.	.	.	.	.	.	.	.	.	A	17.07	3.295241	0.60086	.	.	ENSG00000178764	ENST00000314393	T	0.53640	0.61	5.56	-0.804	0.10882	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	0.058448	0.64402	D	0.000003	T	0.52837	0.1759	L	0.46157	1.445	0.34967	D	0.752741	D	0.69078	0.997	D	0.64410	0.925	T	0.59936	-0.7360	10	0.49607	T	0.09	-19.01	9.7281	0.40344	0.6344:0.0:0.3656:0.0	.	114	Q9Y6X8	ZHX2_HUMAN	D	114	ENSP00000314709:E114D	ENSP00000314709:E114D	E	+	3	2	ZHX2	124033273	1.000000	0.71417	0.994000	0.49952	0.991000	0.79684	1.042000	0.30303	-0.124000	0.11724	0.374000	0.22700	GAA	.	.		0.488	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943		T	123964092	A	T	123964092	3	4	263	1	0	0	0	0	1	0	0	0	17691	98	4	4	344	4	ZHX2	8	123964092	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	4511984	123964092	22399930	197	38571										
ZFAT	57623	hgsc.bcm.edu	37	chr8	135545117	135545124	+	Frame_Shift_Del	DEL	CACGTTGG	CACGTTGG	-													0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gctgccagctccccggtgccCacgttggcatactcctcatt					rs554415466|rs374006917		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	CACGTTGG	CACGTTGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr8:135545117_135545124delCACGTTGG	ENST00000377838.3	-	12	3242_3249	c.3068_3075delCCAACGTG	c.(3067-3075)gccaacgtgfs	p.ANV1023fs	ZFAT_ENST00000520214.1_Frame_Shift_Del_p.ANV1011fs|ZFAT_ENST00000517307.1_5'UTR|ZFAT_ENST00000520727.1_Frame_Shift_Del_p.ANV1011fs|ZFAT_ENST00000429442.2_Frame_Shift_Del_p.ANV1011fs|ZFAT_ENST00000520356.1_Frame_Shift_Del_p.ANV1011fs|ZFAT_ENST00000523399.1_Frame_Shift_Del_p.ANV961fs	NM_001174157.1|NM_020863.3	NP_001167628.1|NP_065914.2	Q9P243	ZFAT_HUMAN	zinc finger and AT hook domain containing	1023					hematopoietic progenitor cell differentiation (GO:0002244)|spongiotrophoblast layer development (GO:0060712)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(9)|large_intestine(8)|lung(16)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)			CCCCGGTGCCCACGTTGGCATACTCCTC	0.615																																					p.1023_1026del		Atlas-Indel,Pindel	.											.	ZFAT	265	.	0			c.3069_3076del						.																																			SO:0001589	frameshift_variant	57623	exon12			.	BC025423	CCDS43768.1, CCDS47924.1, CCDS43768.2, CCDS55275.1, CCDS55276.1	8q24.23	2008-06-05	2008-01-25	2008-01-25	ENSG00000066827	ENSG00000066827		"Zinc fingers, C2H2-type"	19899	protein-coding gene	gene with protein product		610931	"zinc finger protein 406"	ZNF406, ZFAT1		10819331, 18329245	Standard	NM_020863		Approved	KIAA1485	uc003yup.3	Q9P243	OTTHUMG00000164321	ENST00000377838.3:c.3068_3075delCCAACGTG	chr8.hg19:g.135545117_135545124delCACGTTGG	ENSP00000367069:p.Ala1023fs	66.0	0.0		63.0	10.0	NM_020863	B7ZL15|E9PER3|Q3MIM5|Q6PJ01|Q75PJ6|Q75PJ7|Q75PJ9|Q86X64	Frame_Shift_Del	DEL	ENST00000377838.3	hg19	CCDS47924.1																																																																																			.	.		0.615	ZFAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378272.1	NM_001029939		-	135545124	CACGTTGG	-	135545117	7	5	263	1	0	1	0	1	0	0	0	0	17647	581	21	0	676	0	ZFAT	8	135545117	Frame_Shift_Del	DEL	CACGTTGG	TCGA-FV-A2QR-01A-11D-A20W-10	11581025	135545117	10818905	198	38572										
NFKBIL2	4796	hgsc.bcm.edu	37	chr8	145659589	145659589	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gtaagctgggcctggtccagGgccagggagcaggcgctgaa	18	10	0	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr8:145659589G>A	ENST00000409379.3	-	21	3188	c.3159C>T	c.(3157-3159)gcC>gcT	p.A1053A	AC084125.4_ENST00000544423.1_RNA	NM_013432.4	NP_038460.4	Q96HA7	TONSL_HUMAN	tonsoku-like, DNA repair protein	1053					cytoplasmic sequestering of transcription factor (GO:0042994)|double-strand break repair via homologous recombination (GO:0000724)|regulation of RNA biosynthetic process (GO:2001141)|replication fork processing (GO:0031297)	cytoplasm (GO:0005737)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	histone binding (GO:0042393)|transcription corepressor activity (GO:0003714)			biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|lung(14)|ovary(3)|prostate(1)|skin(1)	26						CCTGGTCCAGGGCCAGGGAGC	0.687																																					p.A1053A		Atlas-SNP	.											.	TONSL	128	.	0			c.C3159T						.						17	19	18					8																	145659589		2197	4287	6484	SO:0001819	synonymous_variant	4796	exon21			GTCCAGGGCCAGG		CCDS34968.2	8q24.3	2013-01-10	2010-12-02	2010-11-30	ENSG00000160949	ENSG00000160949		"Ankyrin repeat domain containing"	7801	protein-coding gene	gene with protein product		604546	"nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 2"	NFKBIL2		7738005, 11246458	Standard	NM_013432		Approved	IKBR	uc011llg.2	Q96HA7	OTTHUMG00000153122	ENST00000409379.3:c.3159C>T	chr8.hg19:g.145659589G>A		123.0	0.0		100.0	9.0	NM_013432	B5MDP0|C9JKB1|C9JNV8|Q13006|Q9UGJ2	Silent	SNP	ENST00000409379.3	hg19	CCDS34968.2																																																																																			.	.		0.687	TONSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329668.2	NM_013432		A	145659589	G	A	145659589	2	1	263	1	0	0	0	0	0	0	0	1	10391	1219	43	3		3	NFKBIL2	8	145659589	Silent	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	10114472	145659589	704433	199	38573										
GLDC	2731	hgsc.bcm.edu	37	chr9	6554742	6554742	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cttgtgaagatttaggtgcgAgacatcagacccgaagtctc	11	9	2	4			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr9:6554742A>G	ENST00000321612.6	-	19	2392	c.2242T>C	c.(2242-2244)Tcg>Ccg	p.S748P		NM_000170.2	NP_000161.2	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)	748					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|glycine dehydrogenase (decarboxylating) activity (GO:0004375)|lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)			cervix(1)|endometrium(2)|large_intestine(5)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)	TTTAGGTGCGAGACATCAGAC	0.552																																					p.S748P		Atlas-SNP	.											.	GLDC	118	.	0			c.T2242C						.						64	54	57					9																	6554742		2203	4300	6503	SO:0001583	missense	2731	exon19			GGTGCGAGACATC	D90239	CCDS34987.1	9p22	2014-09-17	2006-05-22		ENSG00000178445	ENSG00000178445	1.4.4.2		4313	protein-coding gene	gene with protein product	"glycine cleavage system protein P", "glycine decarboxylase"	238300	"glycine dehydrogenase (decarboxylating; glycine decarboxylase, glycine cleavage system protein P)"			1993704, 1996985	Standard	NM_000170		Approved	GCSP, NKH	uc003zkc.3	P23378	OTTHUMG00000019524	ENST00000321612.6:c.2242T>C	chr9.hg19:g.6554742A>G	ENSP00000370737:p.Ser748Pro	52.0	0.0		74.0	5.0	NM_000170	Q2M2F8	Missense_Mutation	SNP	ENST00000321612.6	hg19	CCDS34987.1	.	.	.	.	.	.	.	.	.	.	A	18.54	3.645367	0.67358	.	.	ENSG00000178445	ENST00000321612	D	0.98060	-4.69	5.37	5.37	0.77165	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.99099	0.9690	H	0.96365	3.81	0.80722	D	1	D	0.76494	0.999	D	0.68621	0.959	D	0.99271	1.0893	10	0.72032	D	0.01	-11.6913	15.6542	0.77121	1.0:0.0:0.0:0.0	.	748	P23378	GCSP_HUMAN	P	748	ENSP00000370737:S748P	ENSP00000370737:S748P	S	-	1	0	GLDC	6544742	1.000000	0.71417	0.997000	0.53966	0.288000	0.27193	8.927000	0.92846	2.162000	0.67917	0.379000	0.24179	TCG	.	.		0.552	GLDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051674.2	NM_000170		G	6554742	A	G	6554742	3	3	263	1	0	0	0	0	1	0	0	0	6441	304	11	2	848	2	GLDC	9	6554742	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10		6554742	134658689	200	38574										
C9orf93	203238	hgsc.bcm.edu	37	chr9	15695299	15695299	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tgaaagaattggaatcgatcTtggacagctttactgtgtcg	11	6	1	2	rs545117191		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr9:15695299T>C	ENST00000380701.3	+	11	1610	c.1282T>C	c.(1282-1284)Ttg>Ctg	p.L428L	CCDC171_ENST00000297641.3_Silent_p.L428L	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	428																	GGAATCGATCTTGGACAGCTT	0.388																																					p.L428L		Atlas-SNP	.											.	.	.	.	0			c.T1282C						.						168	157	161					9																	15695299		2203	4300	6503	SO:0001819	synonymous_variant	203238	exon11			TCGATCTTGGACA	AY422473	CCDS6481.1	9p22.2	2012-03-26	2012-03-26	2012-03-26	ENSG00000164989	ENSG00000164989			29828	protein-coding gene	gene with protein product	"myosin tail domain containing protein"		"chromosome 9 open reading frame 93"	C9orf93		14702039	Standard	NM_173550		Approved	FLJ39267, FLJ46740, Em:AL513423.1, bA778P13.1, bA536D16.1	uc003zmd.3	Q6TFL3	OTTHUMG00000019584	ENST00000380701.3:c.1282T>C	chr9.hg19:g.15695299T>C		96.0	0.0		95.0	4.0	NM_173550	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	Silent	SNP	ENST00000380701.3	hg19	CCDS6481.1																																																																																			.	.		0.388	CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051768.4	NM_173550		C	15695299	T	C	15695299	2	2	263	1	0	0	0	0	0	0	0	1	2508	1606	56	2		2	C9orf93	9	15695299	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	9140557	15695299	125518132	201	38575										
PLIN2	123	hgsc.bcm.edu	37	chr9	19116605	19116605	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gcacgtggtctggagctgctGagtcaggttgcgggcaattg	17	8	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr9:19116605G>C	ENST00000276914.2	-	8	1134	c.955C>G	c.(955-957)Cag>Gag	p.Q319E	PLIN2_ENST00000411567.1_Missense_Mutation_p.Q238E	NM_001122.3	NP_001113.2	Q99541	PLIN2_HUMAN	perilipin 2	319					cellular lipid metabolic process (GO:0044255)|lipid storage (GO:0019915)|long-chain fatty acid transport (GO:0015909)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|lipid particle (GO:0005811)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	19						TGGAGCTGCTGAGTCAGGTTG	0.473																																					p.Q319E		Atlas-SNP	.											.	PLIN2	41	.	0			c.C955G						.						146	120	129					9																	19116605		2203	4300	6503	SO:0001583	missense	123	exon8			GCTGCTGAGTCAG	X97324	CCDS6490.1	9p22.1	2009-08-12	2009-08-12	2009-08-12	ENSG00000147872	ENSG00000147872		"Perilipins"	248	protein-coding gene	gene with protein product	"adipophilin"	103195	"adipose differentiation-related protein"	ADFP		9003395, 19638644	Standard	NM_001122		Approved	ADRP	uc003zno.3	Q99541	OTTHUMG00000019624	ENST00000276914.2:c.955C>G	chr9.hg19:g.19116605G>C	ENSP00000276914:p.Gln319Glu	200.0	0.0		217.0	97.0	NM_001122	Q9BSC3	Missense_Mutation	SNP	ENST00000276914.2	hg19	CCDS6490.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.755120	0.89843	.	.	ENSG00000147872	ENST00000411567;ENST00000276914	T;T	0.06068	3.35;3.35	6.0	6.0	0.97389	.	0.000000	0.85682	D	0.000000	T	0.29850	0.0746	M	0.82132	2.575	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.00184	-1.1944	10	0.40728	T	0.16	.	20.4945	0.99205	0.0:0.0:1.0:0.0	.	319	Q99541	PLIN2_HUMAN	E	238;319	ENSP00000415270:Q238E;ENSP00000276914:Q319E	ENSP00000276914:Q319E	Q	-	1	0	PLIN2	19106605	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	9.835000	0.99442	2.846000	0.97976	0.650000	0.86243	CAG	.	.		0.473	PLIN2-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051835.1	NM_001122		C	19116605	G	C	19116605	3	2	263	1	0	0	0	0	1	0	0	0	12099	1299	45	4	362	4	PLIN2	9	19116605	Missense_Mutation	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	3421306	19116605	122096826	202	38576										
MLLT3	4300	hgsc.bcm.edu	37	chr9	20414041	20414041	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cactggtgatggtgagtaagTtactatctggttttggctct	12	6	2	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr9:20414041T>C	ENST00000380338.4	-	5	1089	c.803A>G	c.(802-804)aAc>aGc	p.N268S	MIR4473_ENST00000583731.1_RNA|MLLT3_ENST00000429426.2_Missense_Mutation_p.N265S|MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000475957.1_5'UTR	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3	268					anterior/posterior pattern specification (GO:0009952)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of transcription, DNA-templated (GO:0006355)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		GGTGAGTAAGTTACTATCTGG	0.398			T	MLL	ALL																																p.N268S		Atlas-SNP	.		Dom	yes		9	9p22	4300	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 (AF9)"		L	.	MLLT3	125	.	0			c.A803G						.						278	280	279					9																	20414041		2203	4300	6503	SO:0001583	missense	4300	exon5			AGTAAGTTACTAT	L13744	CCDS6494.1	9p22	2008-02-05	2001-11-28		ENSG00000171843	ENSG00000171843			7136	protein-coding gene	gene with protein product		159558	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 3"			8506309, 8414510	Standard	NM_001286691		Approved	AF-9, AF9, YEATS3	uc003zoe.2	P42568	OTTHUMG00000019650	ENST00000380338.4:c.803A>G	chr9.hg19:g.20414041T>C	ENSP00000369695:p.Asn268Ser	439.0	1.0		451.0	179.0	NM_004529	B1AMQ2|B2R7B3|B7Z755|D3DRJ8|Q8IVB0	Missense_Mutation	SNP	ENST00000380338.4	hg19	CCDS6494.1	.	.	.	.	.	.	.	.	.	.	T	0.009	-1.835467	0.00579	.	.	ENSG00000171843	ENST00000380338;ENST00000429426;ENST00000540751	.	.	.	5.88	1.92	0.25849	.	0.417336	0.26492	N	0.024065	T	0.35856	0.0946	L	0.29908	0.895	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.11717	-1.0576	9	0.06891	T	0.86	-17.8633	7.2808	0.26310	0.0:0.219:0.1242:0.6568	.	265;268	B7Z755;P42568	.;AF9_HUMAN	S	268;265;307	.	ENSP00000369695:N268S	N	-	2	0	MLLT3	20404041	1.000000	0.71417	0.998000	0.56505	0.318000	0.28184	1.235000	0.32671	0.499000	0.27970	-0.250000	0.11733	AAC	.	.		0.398	MLLT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051872.1	NM_004529		C	20414041	T	C	20414041	3	2	263	1	0	0	0	0	1	0	0	0	9637	1725	60	2	931	2	MLLT3	9	20414041	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	1297436	20414041	120799390	203	38577										
IFNA6	3443	hgsc.bcm.edu	37	chr9	21350645	21350645	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	aggtctgctgaatcacctcaTggaggacagagatggcttca	12	9	4	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr9:21350645T>G	ENST00000380210.1	-	1	732	c.242A>C	c.(241-243)cAt>cCt	p.H81P		NM_021002.2	NP_066282.1	P05013	IFNA6_HUMAN	interferon, alpha 6	81					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			large_intestine(3)|lung(7)|skin(1)	11				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.116)		AATCACCTCATGGAGGACAGA	0.473																																					p.H81P		Atlas-SNP	.											.	IFNA6	27	.	0			c.A242C						.						107	104	105					9																	21350645		2203	4300	6503	SO:0001583	missense	3443	exon1			ACCTCATGGAGGA		CCDS6504.1	9p22	2010-12-10			ENSG00000120235	ENSG00000120235		"Interferons"	5427	protein-coding gene	gene with protein product		147566				1385305	Standard	NM_021002		Approved	IFN-alphaK	uc011lni.2	P05013	OTTHUMG00000019676	ENST00000380210.1:c.242A>C	chr9.hg19:g.21350645T>G	ENSP00000369558:p.His81Pro	193.0	0.0		239.0	110.0	NM_021002	Q5VYQ1	Missense_Mutation	SNP	ENST00000380210.1	hg19	CCDS6504.1	.	.	.	.	.	.	.	.	.	.	T	19.15	3.772671	0.69992	.	.	ENSG00000120235	ENST00000380210	T	0.03745	3.82	3.78	2.55	0.30701	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.749872	0.12726	N	0.444311	T	0.19087	0.0458	M	0.89353	3.025	0.09310	N	1	D	0.67145	0.996	D	0.83275	0.996	T	0.04781	-1.0927	10	0.87932	D	0	.	7.2998	0.26413	0.0:0.1115:0.0:0.8885	.	81	P05013	IFNA6_HUMAN	P	81	ENSP00000369558:H81P	ENSP00000369558:H81P	H	-	2	0	IFNA6	21340645	0.776000	0.28616	0.009000	0.14445	0.827000	0.46813	1.890000	0.39728	0.379000	0.24794	0.482000	0.46254	CAT	.	.		0.473	IFNA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051905.1	NM_021002		G	21350645	T	G	21350645	3	3	263	1	0	0	0	0	1	0	0	0	7550	1464	51	5	329	5	IFNA6	9	21350645	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	936604	21350645	119862786	204	38578										
PRUNE2	158471	hgsc.bcm.edu	37	chr9	79324155	79324155	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	atgactgttgcagtgactgaGgaggaatgtcagtctcctct	12	8	3	3			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr9:79324155G>T	ENST00000376718.3	-	8	3158	c.3035C>A	c.(3034-3036)cCt>cAt	p.P1012H	PRUNE2_ENST00000428286.1_Missense_Mutation_p.P653H	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	1012					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						CAGTGACTGAGGAGGAATGTC	0.448																																					p.P1012H		Atlas-SNP	.											.	PRUNE2	331	.	0			c.C3035A						.						122	95	103					9																	79324155		1568	3582	5150	SO:0001583	missense	158471	exon8			GACTGAGGAGGAA	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.3035C>A	chr9.hg19:g.79324155G>T	ENSP00000365908:p.Pro1012His	151.0	0.0		176.0	9.0	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	hg19	CCDS47982.1	.	.	.	.	.	.	.	.	.	.	G	16.65	3.183169	0.57800	.	.	ENSG00000106772	ENST00000376718;ENST00000428286;ENST00000422033	T;T	0.46063	0.88;0.88	5.94	4.13	0.48395	.	0.894418	0.09666	N	0.771839	T	0.36991	0.0987	N	0.24115	0.695	0.09310	N	0.999998	D	0.63880	0.993	P	0.49999	0.628	T	0.17410	-1.0370	10	0.87932	D	0	-1.3206	6.0112	0.19578	0.156:0.0:0.6561:0.1879	.	1012	Q8WUY3	PRUN2_HUMAN	H	1012;653;1011	ENSP00000365908:P1012H;ENSP00000397425:P653H	ENSP00000365908:P1012H	P	-	2	0	PRUNE2	78513975	.	.	0.002000	0.10522	0.222000	0.24845	.	.	0.873000	0.35799	0.561000	0.74099	CCT	.	.		0.448	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		T	79324155	G	T	79324155	3	4	263	1	0	0	0	0	1	0	0	0	12653	1000	35	3	6279	3	PRUNE2	9	79324155	Missense_Mutation	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	57973510	79324155	61889276	205	38579										
TXN	7295	hgsc.bcm.edu	37	chr9	113018699	113018699	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cggtagcgcgtaccttgctcTcgatctgcttcaccatcttg	9	14	4	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr9:113018699T>C	ENST00000374517.5	-	1	221	c.17A>G	c.(16-18)gAg>gGg	p.E6G	TXN_ENST00000374515.5_Missense_Mutation_p.E6G	NM_003329.3	NP_003320.2	P10599	THIO_HUMAN	thioredoxin	6	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell proliferation (GO:0008283)|cell redox homeostasis (GO:0045454)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|glycerol ether metabolic process (GO:0006662)|innate immune response (GO:0045087)|negative regulation of protein export from nucleus (GO:0046826)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|oxidation-reduction process (GO:0055114)|positive regulation of DNA binding (GO:0043388)|regulation of protein import into nucleus, translocation (GO:0033158)|response to radiation (GO:0009314)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	peptide disulfide oxidoreductase activity (GO:0015037)|poly(A) RNA binding (GO:0044822)|protein disulfide oxidoreductase activity (GO:0015035)			kidney(1)|skin(1)	2				OV - Ovarian serous cystadenocarcinoma(323;7.36e-07)		TACCTTGCTCTCGATCTGCTT	0.642																																					p.E6G		Atlas-SNP	.											.	TXN	6	.	0			c.A17G						.						43	35	38					9																	113018699		2203	4298	6501	SO:0001583	missense	7295	exon1			TTGCTCTCGATCT	X77584	CCDS35103.1, CCDS59139.1	9q31	2008-02-05			ENSG00000136810	ENSG00000136810			12435	protein-coding gene	gene with protein product		187700					Standard	NM_003329		Approved	TRX	uc004bep.2	P10599	OTTHUMG00000020480	ENST00000374517.5:c.17A>G	chr9.hg19:g.113018699T>C	ENSP00000363641:p.Glu6Gly	52.0	0.0		65.0	6.0	NM_001244938	B1ALW1|O60744|Q53X69|Q96KI3|Q9UDG5	Missense_Mutation	SNP	ENST00000374517.5	hg19	CCDS35103.1	.	.	.	.	.	.	.	.	.	.	T	14.08	2.427853	0.43122	.	.	ENSG00000136810	ENST00000374517;ENST00000374515	T;T	0.03301	3.98;3.98	4.34	4.34	0.51931	Thioredoxin domain (1);Thioredoxin-like fold (3);	0.176785	0.34268	N	0.004104	T	0.05044	0.0135	L	0.53617	1.68	0.35802	D	0.823206	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.15122	-1.0448	10	0.38643	T	0.18	-3.3249	10.467	0.44614	0.0:0.0:0.0:1.0	.	6;6	B1ALW1;P10599	.;THIO_HUMAN	G	6	ENSP00000363641:E6G;ENSP00000363639:E6G	ENSP00000363639:E6G	E	-	2	0	TXN	112058520	0.905000	0.30787	0.796000	0.32109	0.868000	0.49771	1.251000	0.32862	1.896000	0.54893	0.459000	0.35465	GAG	.	.		0.642	TXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053614.1			C	113018699	T	C	113018699	3	2	263	1	0	0	0	0	1	0	0	0	16805	1551	54	2	320	2	TXN	9	113018699	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	33694544	113018699	28194732	206	38580										
HSDL2	84263	hgsc.bcm.edu	37	chr9	115232768	115232768	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	aattgaagattaaaggtaacAtggccctagcaatcaaattg	8	6	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr9:115232768A>G	ENST00000398805.3	+	11	1428	c.1201A>G	c.(1201-1203)Atg>Gtg	p.M401V	HSDL2_ENST00000262542.7_Missense_Mutation_p.M281V|HSDL2_ENST00000398803.1_Missense_Mutation_p.M328V|HSDL2_ENST00000539114.1_Missense_Mutation_p.M196V	NM_032303.4	NP_115679.2	Q6YN16	HSDL2_HUMAN	hydroxysteroid dehydrogenase like 2	401	SCP2.					membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)	oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|cervix(2)|endometrium(1)|large_intestine(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(2)	13						TAAAGGTAACATGGCCCTAGC	0.368																																					p.M401V		Atlas-SNP	.											.	HSDL2	24	.	0			c.A1201G						.						87	80	82					9																	115232768		1844	4093	5937	SO:0001583	missense	84263	exon11			GGTAACATGGCCC	AY093428	CCDS43864.1, CCDS56582.1	9q32	2011-09-14			ENSG00000119471	ENSG00000119471		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	18572	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 13C, member 1"		"chromosome 9 open reading frame 99"	C9orf99		12834046, 19027726	Standard	NM_032303		Approved	SDR13C1	uc004bga.2	Q6YN16	OTTHUMG00000020504	ENST00000398805.3:c.1201A>G	chr9.hg19:g.115232768A>G	ENSP00000381785:p.Met401Val	54.0	0.0		42.0	4.0	NM_032303	A8K1L4|A8K8X1|A8MSV3|Q658M8|Q9BT58	Missense_Mutation	SNP	ENST00000398805.3	hg19	CCDS43864.1	.	.	.	.	.	.	.	.	.	.	A	15.09	2.729957	0.48833	.	.	ENSG00000119471	ENST00000398805;ENST00000398803;ENST00000262542;ENST00000539114	T;T;T;T	0.23552	1.9;1.9;1.9;1.9	5.89	4.74	0.60224	SCP2 sterol-binding domain (2);	0.076479	0.85682	D	0.000000	T	0.42449	0.1203	M	0.64997	1.995	0.49915	D	0.999839	B;B;D	0.55172	0.029;0.134;0.97	B;B;P	0.58520	0.011;0.167;0.84	T	0.33420	-0.9869	10	0.87932	D	0	.	11.7592	0.51892	0.8528:0.1472:0.0:0.0	.	328;328;401	Q6YN16-2;B2R923;Q6YN16	.;.;HSDL2_HUMAN	V	401;328;281;196	ENSP00000381785:M401V;ENSP00000381783:M328V;ENSP00000262542:M281V;ENSP00000442278:M196V	ENSP00000262542:M281V	M	+	1	0	HSDL2	114272589	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.859000	0.69539	1.029000	0.39812	0.455000	0.32223	ATG	.	.		0.368	HSDL2-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053681.1	NM_032303		G	115232768	A	G	115232768	3	3	263	1	0	0	0	0	1	0	0	0	7403	217	8	2	1243	2	HSDL2	9	115232768	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	2214069	115232768	25980663	207	38581										
COL27A1	85301	hgsc.bcm.edu	37	chr9	117015214	117015214	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tggagagcctggaccccaggTaagcaaagccctcgtgatcc	12	13	0	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr9:117015214T>A	ENST00000356083.3	+	27	3532		c.e27+2			NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1						extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						GGACCCCAGGTAAGCAAAGCC	0.552																																					.		Atlas-SNP	.											.	COL27A1	200	.	0			c.3141+2T>A						.						113	102	106					9																	117015214		2203	4300	6503	SO:0001630	splice_region_variant	85301	exon27			CCCAGGTAAGCAA	AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"Collagens"	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.3141+2T>A	chr9.hg19:g.117015214T>A		128.0	0.0		166.0	58.0	NM_032888	Q66K43|Q96JF7	Splice_Site	SNP	ENST00000356083.3	hg19	CCDS6802.1	.	.	.	.	.	.	.	.	.	.	T	15.39	2.818321	0.50633	.	.	ENSG00000196739	ENST00000356083;ENST00000357257	.	.	.	4.69	4.69	0.59074	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.7228	0.46050	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	COL27A1	116055035	1.000000	0.71417	1.000000	0.80357	0.559000	0.35586	2.612000	0.46343	2.091000	0.63221	0.459000	0.35465	.	.	.		0.552	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	Intron	A	117015214	T	A	117015214	5	1	263	1	0	0	0	0	0	0	1	0	3687	1652	57	4	3249	4	COL27A1	9	117015214	Splice_Site	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	1782446	117015214	24198217	208	38582										
OR5C1	392391	hgsc.bcm.edu	37	chr9	125551531	125551531	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ctgtgccctccagatgtttgTctttgcaggtctggctgata	11	10	2	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr9:125551531T>C	ENST00000373680.2	+	1	382	c.320T>C	c.(319-321)gTc>gCc	p.V107A		NM_001001923.1	NP_001001923.1	Q8NGR4	OR5C1_HUMAN	olfactory receptor, family 5, subfamily C, member 1	107						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|large_intestine(5)|lung(6)|pancreas(1)|prostate(5)|skin(1)	20						CAGATGTTTGTCTTTGCAGGT	0.562																																					p.V107A		Atlas-SNP	.											.	OR5C1	45	.	0			c.T320C						.						136	122	127					9																	125551531		2203	4300	6503	SO:0001583	missense	392391	exon1			TGTTTGTCTTTGC	AF399514	CCDS35131.1	9q34.2	2012-08-09			ENSG00000148215	ENSG00000148215		"GPCR / Class A : Olfactory receptors"	8331	protein-coding gene	gene with protein product				OR5C2P			Standard	NM_001001923		Approved	OR9-F, hRPK-465_F_21	uc011lzd.2	Q8NGR4	OTTHUMG00000020622	ENST00000373680.2:c.320T>C	chr9.hg19:g.125551531T>C	ENSP00000362784:p.Val107Ala	86.0	0.0		101.0	5.0	NM_001001923	B2RN54|B9EGT0|Q96RC4	Missense_Mutation	SNP	ENST00000373680.2	hg19	CCDS35131.1	.	.	.	.	.	.	.	.	.	.	T	15.47	2.842709	0.51057	.	.	ENSG00000148215	ENST00000373680	T	0.00397	7.57	5.11	5.11	0.69529	GPCR, rhodopsin-like superfamily (1);	0.255751	0.20247	U	0.096172	T	0.00300	0.0009	L	0.33137	0.985	0.25192	N	0.990127	B	0.23937	0.094	B	0.22386	0.039	T	0.51639	-0.8680	10	0.72032	D	0.01	.	14.0288	0.64601	0.0:0.0:0.0:1.0	.	107	Q8NGR4	OR5C1_HUMAN	A	107	ENSP00000362784:V107A	ENSP00000362784:V107A	V	+	2	0	OR5C1	124591352	0.000000	0.05858	0.965000	0.40720	0.994000	0.84299	0.438000	0.21559	2.151000	0.67156	0.528000	0.53228	GTC	.	.		0.562	OR5C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053953.1			C	125551531	T	C	125551531	3	2	263	1	0	0	0	0	1	0	0	0	11162	1667	58	2	322	2	OR5C1	9	125551531	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	8536317	125551531	15661900	209	38583										
CRB2	286204	hgsc.bcm.edu	37	chr9	126139301	126139301	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tggggcccggctggagatggAcagtgtcctcaaggtgccac	16	11	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr9:126139301A>G	ENST00000373631.3	+	13	3819	c.3818A>G	c.(3817-3819)gAc>gGc	p.D1273G	CRB2_ENST00000373629.2_Missense_Mutation_p.D941G|DENND1A_ENST00000473039.1_5'Flank	NM_173689.5	NP_775960.4	Q5IJ48	CRUM2_HUMAN	crumbs family member 2	1273					cardiovascular system development (GO:0072358)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|mesoderm formation (GO:0001707)|negative regulation of endopeptidase activity (GO:0010951)|notochord formation (GO:0014028)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|somitogenesis (GO:0001756)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)			NS(2)|breast(1)|cervix(1)|endometrium(2)|lung(11)|ovary(1)|prostate(2)|skin(3)	23						CTGGAGATGGACAGTGTCCTC	0.647																																					p.D1273G		Atlas-SNP	.											.	CRB2	86	.	0			c.A3818G						.						19	22	21					9																	126139301		2199	4295	6494	SO:0001583	missense	286204	exon13			AGATGGACAGTGT	AK095783	CCDS6852.2	9q33.2	2014-02-06	2014-02-06		ENSG00000148204	ENSG00000148204			18688	protein-coding gene	gene with protein product		609720	"crumbs homolog 2 (Drosophila)"			14767562	Standard	XM_005251934		Approved	FLJ38464, FLJ16786	uc004bnx.1	Q5IJ48	OTTHUMG00000020638	ENST00000373631.3:c.3818A>G	chr9.hg19:g.126139301A>G	ENSP00000362734:p.Asp1273Gly	142.0	0.0		137.0	6.0	NM_173689	A2A3N4|Q0QD46|Q5JS41|Q5JS43|Q6ZTA9|Q6ZWI6	Missense_Mutation	SNP	ENST00000373631.3	hg19	CCDS6852.2	.	.	.	.	.	.	.	.	.	.	.	18.97	3.735006	0.69189	.	.	ENSG00000148204	ENST00000373631;ENST00000373629	D;D	0.90069	-2.03;-2.61	5.27	5.27	0.74061	.	0.000000	0.45361	D	0.000364	T	0.80287	0.4595	N	0.16166	0.38	0.80722	D	1	P	0.51537	0.946	B	0.41723	0.365	T	0.80398	-0.1399	10	0.27082	T	0.32	.	15.1857	0.72999	1.0:0.0:0.0:0.0	.	1273	Q5IJ48	CRUM2_HUMAN	G	1273;941	ENSP00000362734:D1273G;ENSP00000362732:D941G	ENSP00000362732:D941G	D	+	2	0	CRB2	125179122	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.897000	0.48664	1.992000	0.58205	0.402000	0.26972	GAC	.	.		0.647	CRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053990.3	NM_173689		G	126139301	A	G	126139301	3	3	263	1	0	0	0	0	1	0	0	0	3851	275	10	2	3868	2	CRB2	9	126139301	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	587770	126139301	15074130	210	38584										
FPGS	2356	hgsc.bcm.edu	37	chr9	130573285	130573285	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	agaggtgtcatccacaggcaAcgcaggtgagaggtgacagg	16	8	1	3			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr9:130573285A>G	ENST00000373247.2	+	14	1399	c.1349A>G	c.(1348-1350)aAc>aGc	p.N450S	FPGS_ENST00000373225.3_Missense_Mutation_p.N400S|FPGS_ENST00000373245.1_3'UTR|FPGS_ENST00000460181.1_3'UTR|FPGS_ENST00000393706.2_Missense_Mutation_p.N424S	NM_004957.4	NP_004948.4	Q05932	FOLC_HUMAN	folylpolyglutamate synthase	450					brain development (GO:0007420)|folic acid metabolic process (GO:0046655)|liver development (GO:0001889)|nucleobase-containing compound metabolic process (GO:0006139)|one-carbon metabolic process (GO:0006730)|organ regeneration (GO:0031100)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|tetrahydrofolylpolyglutamate synthase activity (GO:0004326)			endometrium(2)|kidney(1)|lung(3)|ovary(1)	7					Methotrexate(DB00563)|Pralatrexate(DB06813)|Raltitrexed(DB00293)	TCCACAGGCAACGCAGGTGAG	0.572																																					p.N450S		Atlas-SNP	.											.	FPGS	30	.	0			c.A1349G						.						52	38	43					9																	130573285		2202	4299	6501	SO:0001583	missense	2356	exon14			CAGGCAACGCAGG		CCDS35148.1, CCDS35149.1, CCDS75905.1	9q34.11	2013-09-19			ENSG00000136877	ENSG00000136877	6.3.2.17		3824	protein-coding gene	gene with protein product		136510					Standard	NM_004957		Approved		uc004bsg.1	Q05932	OTTHUMG00000020716	ENST00000373247.2:c.1349A>G	chr9.hg19:g.130573285A>G	ENSP00000362344:p.Asn450Ser	46.0	0.0		62.0	4.0	NM_004957	B3KPW4|B7Z2Z3|F5H0K6|Q5JU19|Q5JU22|Q6P2P6	Missense_Mutation	SNP	ENST00000373247.2	hg19	CCDS35148.1	.	.	.	.	.	.	.	.	.	.	A	2.321	-0.355672	0.05138	.	.	ENSG00000136877	ENST00000373247;ENST00000393706;ENST00000373225	T;T;T	0.13420	2.99;3.0;2.59	5.27	2.86	0.33363	.	0.479409	0.24664	N	0.036616	T	0.06188	0.0160	N	0.20685	0.6	0.28886	N	0.894126	B;B	0.09022	0.002;0.0	B;B	0.15484	0.013;0.002	T	0.40757	-0.9546	10	0.06494	T	0.89	-17.5316	4.2368	0.10630	0.6931:0.0:0.1602:0.1467	.	424;450	Q05932-4;Q05932	.;FOLC_HUMAN	S	450;424;400	ENSP00000362344:N450S;ENSP00000377309:N424S;ENSP00000362322:N400S	ENSP00000362322:N400S	N	+	2	0	FPGS	129613106	0.477000	0.25909	0.053000	0.19242	0.865000	0.49528	1.960000	0.40422	0.314000	0.23086	-0.375000	0.07067	AAC	.	.		0.572	FPGS-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054251.1			G	130573285	A	G	130573285	3	3	263	1	0	0	0	0	1	0	0	0	6044	43	2	2	1403	2	FPGS	9	130573285	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	4433984	130573285	10640146	211	38585										
SETX	23064	hgsc.bcm.edu	37	chr9	135202230	135202230	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	aaaggtttagatgcaggaggAggcaagccaggtttacgaaa	14	5	0	1	rs151237267	byFrequency	TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr9:135202230A>G	ENST00000224140.5	-	10	4937	c.4755T>C	c.(4753-4755)ccT>ccC	p.P1585P	SETX_ENST00000393220.1_Silent_p.P1585P|SETX_ENST00000372169.2_Silent_p.P1585P	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	1585					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		ATGCAGGAGGAGGCAAGCCAG	0.403																																					p.P1585P		Atlas-SNP	.											.	SETX	234	.	0			c.T4755C						.						105	93	97					9																	135202230		2203	4300	6503	SO:0001819	synonymous_variant	23064	exon10			AGGAGGAGGCAAG	AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"amyotrophic lateral sclerosis 4", "spinocerebellar ataxia, recessive, non-Friedreich type 1"	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.4755T>C	chr9.hg19:g.135202230A>G		127.0	0.0		127.0	6.0	NM_015046	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Silent	SNP	ENST00000224140.5	hg19	CCDS6947.1																																																																																			.	A|0.995;C|0.005		0.403	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046		G	135202230	A	G	135202230	2	3	263	1	0	0	0	0	0	0	0	1	14156	291	11	2		2	SETX	9	135202230	Silent	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	4628945	135202230	6011201	212	38586										
TSC1	7248	hgsc.bcm.edu	37	chr9	135798881	135798881	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	caacgacgtcagtgtccatcTgcaggagaaaaggtcaaaca	10	10	3	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr9:135798881T>C	ENST00000298552.3	-	6	585		c.e6-2		TSC1_ENST00000545250.1_Splice_Site|TSC1_ENST00000440111.2_Splice_Site|TSC1_ENST00000403810.1_Splice_Site|TSC1_ENST00000475903.1_Splice_Site	NM_000368.4|NM_001162426.1|NM_001162427.1	NP_000359.1|NP_001155898.1|NP_001155899.1	Q92574	TSC1_HUMAN	tuberous sclerosis 1						activation of Rho GTPase activity (GO:0032862)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|insulin receptor signaling pathway (GO:0008286)|kidney development (GO:0001822)|myelination (GO:0042552)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of TOR signaling (GO:0032007)|negative regulation of translation (GO:0017148)|neural tube closure (GO:0001843)|positive regulation of focal adhesion assembly (GO:0051894)|potassium ion transport (GO:0006813)|protein heterooligomerization (GO:0051291)|protein stabilization (GO:0050821)|regulation of cell cycle (GO:0051726)|regulation of cell-matrix adhesion (GO:0001952)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of protein kinase activity (GO:0045859)|regulation of stress fiber assembly (GO:0051492)|regulation of translation (GO:0006417)|response to insulin (GO:0032868)|rRNA export from nucleus (GO:0006407)|synapse organization (GO:0050808)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|lamellipodium (GO:0030027)|membrane (GO:0016020)|protein complex (GO:0043234)|TSC1-TSC2 complex (GO:0033596)	chaperone binding (GO:0051087)|GTPase regulator activity (GO:0030695)|protein N-terminus binding (GO:0047485)			NS(1)|bone(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(9)|lung(20)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	65				OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06)		AGTGTCCATCTGCAGGAGAAA	0.473			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												.		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 1	9	9q34	7248	tuberous sclerosis 1 gene		"E, O"	.	TSC1	167	.	0			c.211-2A>G						.						105	89	94					9																	135798881		2203	4300	6503	SO:0001630	splice_region_variant	7248	exon6	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	TCCATCTGCAGGA	AF013168	CCDS6956.1, CCDS55350.1	9q34	2014-09-17			ENSG00000165699	ENSG00000165699			12362	protein-coding gene	gene with protein product		605284		TSC		9242607, 10806479	Standard	NM_000368		Approved	KIAA0243, LAM, hamartin	uc004cca.2	Q92574	OTTHUMG00000020844	ENST00000298552.3:c.364-2A>G	chr9.hg19:g.135798881T>C		119.0	0.0		127.0	7.0	NM_001162427	B7Z897|Q5VVN5	Splice_Site	SNP	ENST00000298552.3	hg19	CCDS6956.1	.	.	.	.	.	.	.	.	.	.	T	16.25	3.070589	0.55539	.	.	ENSG00000165699	ENST00000298552;ENST00000440111;ENST00000545250;ENST00000403810	.	.	.	5.25	5.25	0.73442	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3559	0.66738	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	TSC1	134788702	1.000000	0.71417	0.419000	0.26584	0.649000	0.38597	7.482000	0.81143	1.994000	0.58287	0.533000	0.62120	.	.	.		0.473	TSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054799.1		Intron	C	135798881	T	C	135798881	5	2	263	1	0	0	0	0	0	0	1	0	16620	1594	55	2	3204	2	TSC1	9	135798881	Splice_Site	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	596651	135798881	5414550	213	38587										
C9orf173	25920	hgsc.bcm.edu	37	chr9	140147365	140147365	+	5'Flank	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cgcctgcagagcccccgctcGccggccttctcgatgagccg	12	19	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr9:140147365G>A	ENST00000343053.4	+	0	0				C9orf173_ENST00000388931.3_Silent_p.S248S|C9orf173_ENST00000412566.1_Silent_p.S248S	NM_015456.3	NP_056271.2	Q8WX92	NELFB_HUMAN	negative elongation factor complex member B						gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|NELF complex (GO:0032021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											GCCCCCGCTCGCCGGCCTTCT	0.647																																					p.S248S		Atlas-SNP	.											.	C9orf173	19	.	0			c.G744A						.						9	11	11					9																	140147365		1876	4087	5963	SO:0001631	upstream_gene_variant	441476	exon5			CCGCTCGCCGGCC	AF464935	CCDS7040.1	9q34	2013-01-31	2013-01-31	2013-01-31	ENSG00000188986	ENSG00000188986			24324	protein-coding gene	gene with protein product		611180	"cofactor of BRCA1"	COBRA1		11230166, 10574461, 17910036, 17659869	Standard	NM_015456		Approved	KIAA1182, NELF-B	uc004cmm.4	Q8WX92	OTTHUMG00000131778		chr9.hg19:g.140147365G>A	Exception_encountered	63.0	0.0		70.0	36.0	NM_001004353	A2BFA3|Q96EW5|Q9H9R4|Q9ULN8|Q9Y3W0	Silent	SNP	ENST00000343053.4	hg19	CCDS7040.1																																																																																			.	.		0.647	NELFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254710.1	NM_015456		A	140147365	G	A	140147365	1	1	263	0	1	0	0	0	0	0	0	0	2474	1074	38	1		1	C9orf173	9	140147365	5'Flank	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	4348484	140147365	1066066	214	38588										
C10orf113	387638	hgsc.bcm.edu	37	chr10	21435343	21435344	+	Missense_Mutation	DNP	CT	CT	AA													0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tgattagtaaagcacaaacaCtctctctcatataagctaga					rs45546236|rs72102767	byFrequency	TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C|T	C|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr10:21435343_21435344CT>AA	ENST00000534331.1	-	1	144_145	c.94_95AG>TT	c.(94-96)AGt>TTt	p.S32F	C10orf113_ENST00000377118.4_Missense_Mutation_p.S22F|NEBL_ENST00000417816.2_Intron|C10orf113_ENST00000529198.1_Missense_Mutation_p.S32F	NM_001010896.2	NP_001010896.2	Q5VZT2	CJ113_HUMAN	chromosome 10 open reading frame 113	32										endometrium(1)|large_intestine(1)|lung(1)|ovary(3)|pancreas(1)	7						AGCACAAACACTCTCTCTCATA	0.396																																					p.S32I|p.S32C		Atlas-SNP	.											.	C10orf113	32	.	0			c.G95T|c.A94T						.																																			SO:0001583	missense	387638	exon1			CAAACACTCTCTC|AAACACTCTCTCT		CCDS31162.1, CCDS31162.2, CCDS53496.1	10p12.31	2012-06-12			ENSG00000204683	ENSG00000204683			31447	protein-coding gene	gene with protein product							Standard	NM_001010896		Approved	bA165O3.1	uc001iqm.3	Q5VZT2	OTTHUMG00000017786	ENST00000534331.1:c.94_95delinsAA	chr10.hg19:g.21435343_21435344delinsAA	ENSP00000433646:p.Ser32Phe	64.0|65.0	0.0		101.0|103.0	5.0|6.0	NM_001177483	B9EIM9|E9PRX7	Missense_Mutation	SNP	ENST00000534331.1	hg19	CCDS31162.2																																																																																			.	.		0.396	C10orf113-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047108.3	NM_001010896		AA	21435344	CT	AA	21435343	3	1	263	1	0	0	0	0	1	0	0	0	1586	565	20	3	415	3	C10orf113	10	21435343	Missense_Mutation	DNP	CT	TCGA-FV-A2QR-01A-11D-A20W-10		21435343	114099404	215	38589										
MYO3A	53904	hgsc.bcm.edu	37	chr10	26443748	26443748	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	acaaacggttgcatcatattTtagagtaagatattaaacta	6	5	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr10:26443748T>C	ENST00000265944.5	+	25	2955	c.2789T>C	c.(2788-2790)tTt>tCt	p.F930S	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	930	Myosin motor.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						GCATCATATTTTAGAGTAAGA	0.403																																					p.F930S		Atlas-SNP	.											.	MYO3A	371	.	0			c.T2789C						.						102	105	104					10																	26443748		2203	4300	6503	SO:0001583	missense	53904	exon25			CATATTTTAGAGT	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.2789T>C	chr10.hg19:g.26443748T>C	ENSP00000265944:p.Phe930Ser	68.0	0.0		90.0	4.0	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	hg19	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	T	28.7	4.943328	0.92593	.	.	ENSG00000095777	ENST00000265944	T	0.75050	-0.9	5.56	5.56	0.83823	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.92034	0.7476	H	0.99011	4.4	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95176	0.8295	10	0.87932	D	0	.	16.0048	0.80354	0.0:0.0:0.0:1.0	.	930	Q8NEV4	MYO3A_HUMAN	S	930	ENSP00000265944:F930S	ENSP00000265944:F930S	F	+	2	0	MYO3A	26483754	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.997000	0.88414	2.237000	0.73441	0.528000	0.53228	TTT	.	.		0.403	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		C	26443748	T	C	26443748	3	2	263	1	0	0	0	0	1	0	0	0	10085	1841	64	2	2879	2	MYO3A	10	26443748	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	5008405	26443748	109090999	216	38590										
DDX50	79009	hgsc.bcm.edu	37	chr10	70694063	70694063	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tggcaaccaatgtggctgccCgtggtttggacattcctgaa	12	10	0	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr10:70694063C>T	ENST00000373585.3	+	9	1455	c.1348C>T	c.(1348-1350)Cgt>Tgt	p.R450C	DDX50_ENST00000466265.1_Intron	NM_024045.1	NP_076950.1	Q9BQ39	DDX50_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 50	450	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.					membrane (GO:0016020)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	29						TGTGGCTGCCCGTGGTTTGGA	0.403																																					p.R450C		Atlas-SNP	.											.	DDX50	65	.	0			c.C1348T						.						83	85	84					10																	70694063		2203	4300	6503	SO:0001583	missense	79009	exon9			GCTGCCCGTGGTT	AF334103	CCDS7283.1	10q22.2	2010-09-30			ENSG00000107625	ENSG00000107625		"DEAD-boxes"	17906	protein-coding gene	gene with protein product		610373				11891046	Standard	NM_024045		Approved	GU2, MGC3199, GUB, RH-II/GuB	uc001jou.3	Q9BQ39	OTTHUMG00000018362	ENST00000373585.3:c.1348C>T	chr10.hg19:g.70694063C>T	ENSP00000362687:p.Arg450Cys	52.0	0.0		66.0	24.0	NM_024045	Q5VX37|Q8WV76|Q9BWI8	Missense_Mutation	SNP	ENST00000373585.3	hg19	CCDS7283.1	.	.	.	.	.	.	.	.	.	.	C	31	5.079049	0.94050	.	.	ENSG00000107625	ENST00000373585;ENST00000541832	T	0.79247	-1.25	5.48	5.48	0.80851	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.93151	0.7819	H	0.97852	4.09	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95239	0.8349	10	0.87932	D	0	-7.8583	19.7088	0.96084	0.0:1.0:0.0:0.0	.	450	Q9BQ39	DDX50_HUMAN	C	450	ENSP00000362687:R450C	ENSP00000362687:R450C	R	+	1	0	DDX50	70364069	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.165000	0.77544	2.722000	0.93159	0.561000	0.74099	CGT	.	.		0.403	DDX50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048363.1	NM_024045		T	70694063	C	T	70694063	3	4	263	1	0	0	0	0	1	0	0	0	4370	652	23	1	1382	1	DDX50	10	70694063	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	44250315	70694063	64840684	217	38591										
MYST4	23522	hgsc.bcm.edu	37	chr10	76741556	76741556	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ctttaacagattaccaaagcTttacctgtgtgaattctgtc	6	9	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr10:76741556T>C	ENST00000287239.4	+	11	2732	c.2243T>C	c.(2242-2244)cTt>cCt	p.L748P	KAT6B_ENST00000372714.1_Missense_Mutation_p.L456P|KAT6B_ENST00000372725.1_Missense_Mutation_p.L456P|KAT6B_ENST00000372724.1_Missense_Mutation_p.L456P|KAT6B_ENST00000372711.1_Missense_Mutation_p.L565P|KAT6B_ENST00000490365.1_3'UTR	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	748	Catalytic.|MYST-type HAT.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										TTACCAAAGCTTTACCTGTGT	0.299																																					p.L748P		Atlas-SNP	.											.	.	.	.	0			c.T2243C						.						46	56	53					10																	76741556		2202	4299	6501	SO:0001583	missense	23522	exon11			CAAAGCTTTACCT	AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	17582	protein-coding gene	gene with protein product	"MOZ-related factor"	605880	"MYST histone acetyltransferase (monocytic leukemia) 4"	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.2243T>C	chr10.hg19:g.76741556T>C	ENSP00000287239:p.Leu748Pro	52.0	0.0		76.0	4.0	NM_012330	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Missense_Mutation	SNP	ENST00000287239.4	hg19	CCDS7345.1	.	.	.	.	.	.	.	.	.	.	T	15.52	2.857335	0.51376	.	.	ENSG00000156650	ENST00000372725;ENST00000372724;ENST00000287239;ENST00000372714;ENST00000372711	D;D;D;D;D	0.85955	-1.99;-1.99;-2.05;-1.99;-2.03	5.73	5.73	0.89815	.	0.000000	0.41294	D	0.000915	D	0.92795	0.7709	M	0.83953	2.67	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.996	D	0.93761	0.7067	10	0.87932	D	0	-8.7284	16.0173	0.80450	0.0:0.0:0.0:1.0	.	565;456;748	Q8WYB5-2;Q8WYB5-3;Q8WYB5	.;.;KAT6B_HUMAN	P	456;456;748;456;565	ENSP00000361810:L456P;ENSP00000361809:L456P;ENSP00000287239:L748P;ENSP00000361799:L456P;ENSP00000361796:L565P	ENSP00000287239:L748P	L	+	2	0	KAT6B	76411562	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.191000	0.70037	0.528000	0.53228	CTT	.	.		0.299	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330		C	76741556	T	C	76741556	3	2	263	1	0	0	0	0	1	0	0	0	10114	1609	56	2	2277	2	MYST4	10	76741556	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	6047493	76741556	58793191	218	38592										
DUPD1	338599	hgsc.bcm.edu	37	chr10	76818256	76818256	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cattcttgaggcttgtcttcActtctccagatgtcatttta	6	10	5	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr10:76818256A>T	ENST00000338487.5	-	1	16	c.17T>A	c.(16-18)gTg>gAg	p.V6E		NM_001003892.1	NP_001003892.1	Q68J44	DUPD1_HUMAN	dual specificity phosphatase and pro isomerase domain containing 1	6					protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|endometrium(2)|lung(5)|ovary(2)|urinary_tract(1)	11	all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348)					GCTTGTCTTCACTTCTCCAGA	0.532																																					p.V6E		Atlas-SNP	.											.	DUPD1	30	.	0			c.T17A						.						68	65	66					10																	76818256		2203	4300	6503	SO:0001583	missense	338599	exon1			GTCTTCACTTCTC		CCDS31223.1	10q22.3	2011-06-09			ENSG00000188716	ENSG00000188716		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	23481	protein-coding gene	gene with protein product							Standard	NM_001003892		Approved	DUSP27	uc001jwq.1	Q68J44	OTTHUMG00000018512	ENST00000338487.5:c.17T>A	chr10.hg19:g.76818256A>T	ENSP00000340609:p.Val6Glu	53.0	0.0		79.0	23.0	NM_001003892	B2RP93	Missense_Mutation	SNP	ENST00000338487.5	hg19	CCDS31223.1	.	.	.	.	.	.	.	.	.	.	A	0.014	-1.578326	0.00879	.	.	ENSG00000188716	ENST00000338487	T	0.04706	3.57	5.13	1.99	0.26369	.	3.565550	0.00861	N	0.001920	T	0.04452	0.0122	L	0.27053	0.805	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.42799	-0.9430	10	0.11794	T	0.64	0.0675	6.265	0.20922	0.1029:0.363:0.5341:0.0	.	6	Q68J44	DUPD1_HUMAN	E	6	ENSP00000340609:V6E	ENSP00000340609:V6E	V	-	2	0	DUPD1	76488262	0.002000	0.14202	0.020000	0.16555	0.727000	0.41649	1.316000	0.33620	0.530000	0.28619	-0.468000	0.05107	GTG	.	.		0.532	DUPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048777.2	XM_291741		T	76818256	A	T	76818256	3	4	263	1	0	0	0	0	1	0	0	0	4806	159	6	4	657	4	DUPD1	10	76818256	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	76700	76818256	58716491	219	38593										
DUSP13	142891	hgsc.bcm.edu	37	chr10	76868819	76868819	+	5'Flank	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gtccacacggctgcaagaagActtccctgcccgcaggagct	11	15	0	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr10:76868819A>G	ENST00000542569.1	+	0	0				SAMD8_ENST00000372690.3_5'Flank|DUSP13_ENST00000607131.1_5'UTR|DUSP13_ENST00000607009.1_5'UTR|DUSP13_ENST00000491677.2_5'UTR|DUSP13_ENST00000372700.3_Missense_Mutation_p.S33P|SAMD8_ENST00000372687.4_5'Flank|DUSP13_ENST00000372702.3_Missense_Mutation_p.S33P	NM_001174156.1|NM_144660.2	NP_001167627.1|NP_653261.1	Q96LT4	SAMD8_HUMAN	sterile alpha motif domain containing 8						ceramide biosynthetic process (GO:0046513)|regulation of ceramide biosynthetic process (GO:2000303)|sphingomyelin biosynthetic process (GO:0006686)	integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)	transferase activity (GO:0016740)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)	12	all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348)					CTGCAAGAAGACTTCCCTGCC	0.632																																					p.S33P		Atlas-SNP	.											.	DUSP13	82	.	0			c.T97C						.						101	79	86					10																	76868819		2203	4300	6503	SO:0001631	upstream_gene_variant	51207	exon1			AAGAAGACTTCCC	AK057811	CCDS7347.1, CCDS53543.1	10q22.3	2013-01-10			ENSG00000156671	ENSG00000156671		"Sterile alpha motif (SAM) domain containing"	26320	protein-coding gene	gene with protein product		611575					Standard	NM_144660		Approved	FLJ25082	uc001jwx.2	Q96LT4	OTTHUMG00000018515		chr10.hg19:g.76868819A>G	Exception_encountered	64.0	0.0		84.0	4.0	NM_001007272	Q5JSC5|Q5JSC8|Q66K52	Missense_Mutation	SNP	ENST00000542569.1	hg19	CCDS53543.1	.	.	.	.	.	.	.	.	.	.	A	0.377	-0.931020	0.02359	.	.	ENSG00000079393	ENST00000372702;ENST00000372700	T;T	0.61274	0.12;3.34	5.52	-0.013	0.13986	.	.	.	.	.	T	0.28599	0.0708	N	0.08118	0	0.09310	N	0.999996	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.13045	-1.0524	9	0.29301	T	0.29	.	0.9259	0.01324	0.3726:0.2841:0.1141:0.2292	.	33;33	Q9UII6-4;Q6B8I1	.;MDSP_HUMAN	P	33	ENSP00000361787:S33P;ENSP00000361785:S33P	ENSP00000361785:S33P	S	-	1	0	DUSP13	76538825	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	-1.077000	0.03416	-0.286000	0.09076	-0.219000	0.12488	TCT	.	.		0.632	SAMD8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_144660		G	76868819	A	G	76868819	1	3	263	0	1	0	0	0	0	0	0	0	4815	275	10	2		2	DUSP13	10	76868819	5'Flank	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	50563	76868819	58665928	220	38594										
FAS	355	hgsc.bcm.edu	37	chr10	90762898	90762898	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tactacagttgagactcagaActtggaaggcctgcatcatg	10	9	2	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr10:90762898A>G	ENST00000355279.2	+	2	143	c.143A>G	c.(142-144)aAc>aGc	p.N48S	FAS_ENST00000357339.2_Missense_Mutation_p.N48S|FAS_ENST00000355740.2_Missense_Mutation_p.N48S|FAS_ENST00000313771.5_3'UTR|FAS_ENST00000352159.4_Missense_Mutation_p.N48S			P49327	FAS_HUMAN	Fas cell surface death receptor	0	Beta-ketoacyl synthase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.0161)		Colorectal(12;0.000136)|COAD - Colon adenocarcinoma(12;0.000193)	Cerulenin(DB01034)|Orlistat(DB01083)	GAGACTCAGAACTTGGAAGGC	0.438																																					p.N48S		Atlas-SNP	.											.	FAS	47	.	0			c.A143G						.						131	118	122					10																	90762898		2203	4300	6503	SO:0001583	missense	355	exon2			CTCAGAACTTGGA	M67454	CCDS7393.1, CCDS7394.1, CCDS7395.1	10q24.1	2014-09-17	2013-05-22	2005-01-07	ENSG00000026103	ENSG00000026103		"Tumor necrosis factor receptor superfamily", "CD molecules"	11920	protein-coding gene	gene with protein product	"TNF receptor superfamily member 6"	134637	"tumor necrosis factor receptor superfamily, member 6", "Fas (TNF receptor superfamily, member 6)"	FAS1, APT1, TNFRSF6		1385299, 1385309	Standard	NM_000043		Approved	CD95, APO-1	uc001kfr.3	P25445	OTTHUMG00000018701	ENST00000355279.2:c.143A>G	chr10.hg19:g.90762898A>G	ENSP00000347426:p.Asn48Ser	109.0	0.0		72.0	4.0	NM_152872	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000355279.2	hg19	CCDS7395.1	.	.	.	.	.	.	.	.	.	.	A	8.300	0.819796	0.16678	.	.	ENSG00000026103	ENST00000540197;ENST00000355740;ENST00000352159;ENST00000357339;ENST00000355279;ENST00000371875	T;T;T;T	0.76186	-1.0;-1.0;-1.0;-1.0	3.65	1.54	0.23209	.	.	.	.	.	T	0.65491	0.2696	L	0.44542	1.39	0.09310	N	1	P;P;P;P	0.46220	0.874;0.814;0.867;0.717	P;B;B;B	0.47402	0.546;0.225;0.316;0.113	T	0.52328	-0.8590	9	0.18710	T	0.47	-2.2449	3.6119	0.08063	0.1628:0.2595:0.5777:0.0	.	48;48;48;48	P25445-4;P25445-6;Q5T9P3;P25445	.;.;.;TNR6_HUMAN	S	75;48;48;48;48;48	ENSP00000347979:N48S;ENSP00000345601:N48S;ENSP00000349896:N48S;ENSP00000347426:N48S	ENSP00000345601:N48S	N	+	2	0	FAS	90752878	0.009000	0.17119	0.002000	0.10522	0.054000	0.15201	1.069000	0.30641	0.401000	0.25424	0.459000	0.35465	AAC	.	.		0.438	FAS-011	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000049280.2			G	90762898	A	G	90762898	3	3	263	1	0	0	0	0	1	0	0	0	5689	43	2	2	149	2	FAS	10	90762898	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	13894079	90762898	44771849	221	38595										
TBC1D12	23232	hgsc.bcm.edu	37	chr10	96260080	96260080	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ggaaatgaactaaatatcacTcctggtttgtattctacgtt	7	7	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr10:96260080T>C	ENST00000225235.4	+	6	1625	c.1515T>C	c.(1513-1515)acT>acC	p.T505T		NM_015188.1	NP_056003.1	O60347	TBC12_HUMAN	TBC1 domain family, member 12	505	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						Rab GTPase activator activity (GO:0005097)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(2)	20		Colorectal(252;0.0429)				TAAATATCACTCCTGGTTTGT	0.413																																					p.T505T		Atlas-SNP	.											.	TBC1D12	51	.	0			c.T1515C						.						140	128	132					10																	96260080		1872	4104	5976	SO:0001819	synonymous_variant	23232	exon6			TATCACTCCTGGT	AB011180	CCDS41553.1	10q23.33	2013-09-20			ENSG00000108239	ENSG00000108239			29082	protein-coding gene	gene with protein product						9628581	Standard	NM_015188		Approved	KIAA0608	uc001kjr.2	O60347	OTTHUMG00000018794	ENST00000225235.4:c.1515T>C	chr10.hg19:g.96260080T>C		120.0	0.0		70.0	4.0	NM_015188	Q5VYA6|Q8WX26|Q8WX59|Q9UG83	Silent	SNP	ENST00000225235.4	hg19	CCDS41553.1																																																																																			.	.		0.413	TBC1D12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049482.2			C	96260080	T	C	96260080	2	2	263	1	0	0	0	0	0	0	0	1	15616	1538	54	2		2	TBC1D12	10	96260080	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	5497182	96260080	39274667	222	38596										
HPSE2	60495	hgsc.bcm.edu	37	chr10	100904083	100904083	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gccttctccctttggagctcCagcataacatcagggtgctg	10	13	2	0	rs200038077		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr10:100904083C>T	ENST00000370552.3	-	3	581	c.522G>A	c.(520-522)ctG>ctA	p.L174L	HPSE2_ENST00000370546.1_Silent_p.L174L|HPSE2_ENST00000370549.1_Silent_p.L174L|HPSE2_ENST00000404542.1_Intron	NM_021828.4	NP_068600.4	Q8WWQ2	HPSE2_HUMAN	heparanase 2 (inactive)	174					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	intracellular (GO:0005622)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	heparan sulfate proteoglycan binding (GO:0043395)|heparanase activity (GO:0030305)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	40				Epithelial(162;1.8e-09)|all cancers(201;4.72e-07)		TTTGGAGCTCCAGCATAACAT	0.428																																					p.L174L		Atlas-SNP	.											.	HPSE2	203	.	0			c.G522A						.						113	111	112					10																	100904083		2203	4300	6503	SO:0001819	synonymous_variant	60495	exon3			GAGCTCCAGCATA	AF282885	CCDS7477.1, CCDS53567.1, CCDS53568.1	10q23-q24	2014-05-09	2014-05-09		ENSG00000172987	ENSG00000172987			18374	protein-coding gene	gene with protein product		613469	"urofacial syndrome", "heparanase 2"	UFS		11027606, 20605132, 9199567, 20576607	Standard	NM_021828		Approved	HPA2, HPR2	uc001kpn.2	Q8WWQ2	OTTHUMG00000018880	ENST00000370552.3:c.522G>A	chr10.hg19:g.100904083C>T		69.0	0.0		62.0	4.0	NM_001166246	Q5VUH4|Q5VUH5|Q5VUH6|Q8WWQ1|Q9HB37|Q9HB38|Q9HB39	Silent	SNP	ENST00000370552.3	hg19	CCDS7477.1																																																																																			.	C|0.999;T|0.001		0.428	HPSE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049789.1	NM_021828		T	100904083	C	T	100904083	2	4	263	1	0	0	0	0	0	0	0	1	7354	581	21	3		3	HPSE2	10	100904083	Silent	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	4644003	100904083	34630664	223	38597										
CHUK	1147	hgsc.bcm.edu	37	chr10	101978562	101978562	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	caaatatacactttggatccTtcttcttaatcttctcatgc	3	11	4	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr10:101978562T>C	ENST00000370397.7	-	8	796	c.710A>G	c.(709-711)aAg>aGg	p.K237R		NM_001278.3	NP_001269.3	O15111	IKKA_HUMAN	conserved helix-loop-helix ubiquitous kinase	237	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				anatomical structure morphogenesis (GO:0009653)|cellular response to tumor necrosis factor (GO:0071356)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|morphogenesis of an epithelial sheet (GO:0002011)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hydroperoxide (GO:0033194)|response to lipopolysaccharide (GO:0032496)|response to toxic substance (GO:0009636)|response to virus (GO:0009615)|Rho protein signal transduction (GO:0007266)|skeletal muscle contraction (GO:0003009)|striated muscle cell differentiation (GO:0051146)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|scaffold protein binding (GO:0097110)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(9)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	27		Colorectal(252;0.117)		Epithelial(162;2.05e-10)|all cancers(201;1.91e-08)	Acetylcysteine(DB06151)|Aminosalicylic Acid(DB00233)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	CTTTGGATCCTTCTTCTTAAT	0.323																																					p.K237R	Ovarian(159;52 1904 10536 35305 37148)	Atlas-SNP	.											CHUK,caecum,carcinoma,0,5	CHUK	71	.	0			c.A710G						.						118	111	113					10																	101978562		2203	4300	6503	SO:0001583	missense	1147	exon8			GGATCCTTCTTCT	AF009225	CCDS7488.1	10q24-q25	2008-08-01			ENSG00000213341	ENSG00000213341			1974	protein-coding gene	gene with protein product		600664		TCF16		7558004, 16902410	Standard	XR_246062		Approved	IKK1, IKK-alpha, IkBKA, NFKBIKA, IKKA	uc001kqp.3	O15111	OTTHUMG00000018899	ENST00000370397.7:c.710A>G	chr10.hg19:g.101978562T>C	ENSP00000359424:p.Lys237Arg	118.0	0.0		79.0	4.0	NM_001278	O14666|Q13132|Q5W0I4|Q92467	Missense_Mutation	SNP	ENST00000370397.7	hg19	CCDS7488.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.582282	0.86748	.	.	ENSG00000213341	ENST00000370397	T	0.65549	-0.16	5.92	5.92	0.95590	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.77350	0.4117	M	0.69248	2.105	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.79470	-0.1790	10	0.72032	D	0.01	-16.8521	14.3262	0.66523	0.0:0.0:0.0:1.0	.	237	O15111	IKKA_HUMAN	R	237	ENSP00000359424:K237R	ENSP00000359424:K237R	K	-	2	0	CHUK	101968552	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.661000	0.83786	2.263000	0.75096	0.533000	0.62120	AAG	.	.		0.323	CHUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049836.1	NM_001278		C	101978562	T	C	101978562	3	2	263	1	0	0	0	0	1	0	0	0	3418	1609	56	2	1583	2	CHUK	10	101978562	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	1074479	101978562	33556185	224	38598										
BTRC	8945	hgsc.bcm.edu	37	chr10	103190119	103190119	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cagtgctctatgcccaggtcTctgtggctgggctgctccag	13	13	2	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr10:103190119T>C	ENST00000370187.3	+	2	184	c.66T>C	c.(64-66)tcT>tcC	p.S22S	BTRC_ENST00000393441.4_Silent_p.S7S|BTRC_ENST00000408038.2_Intron	NM_033637.3	NP_378663.1	Q9Y297	FBW1A_HUMAN	beta-transducin repeat containing E3 ubiquitin protein ligase	22					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cellular response to organic cyclic compound (GO:0071407)|G2/M transition of mitotic cell cycle (GO:0000086)|mammary gland epithelial cell proliferation (GO:0033598)|mitotic cell cycle (GO:0000278)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of proteolysis (GO:0045862)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein dephosphorylation (GO:0006470)|protein destabilization (GO:0031648)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|rhythmic process (GO:0048511)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(4)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|stomach(1)|urinary_tract(1)	27		Colorectal(252;0.234)		Epithelial(162;1.05e-08)|all cancers(201;6.59e-07)		TGCCCAGGTCTCTGTGGCTGG	0.542																																					p.S22S		Atlas-SNP	.											.	BTRC	64	.	0			c.T66C						.						77	74	75					10																	103190119		2203	4300	6503	SO:0001819	synonymous_variant	8945	exon2			CAGGTCTCTGTGG	Y14153	CCDS7511.1, CCDS7512.1, CCDS73183.1	10q24.32	2013-01-10	2012-02-23		ENSG00000166167	ENSG00000166167		"F-boxes / WD-40 domains", "WD repeat domain containing"	1144	protein-coding gene	gene with protein product		603482	"beta-transducin repeat containing"			9660940, 10331953, 18354483	Standard	NM_033637		Approved	bTrCP, betaTrCP, FBXW1A, Fwd1, beta-TrCP1, bTrCP1	uc001kta.4	Q9Y297	OTTHUMG00000018932	ENST00000370187.3:c.66T>C	chr10.hg19:g.103190119T>C		146.0	0.0		82.0	4.0	NM_001256856	B5MD49|Q5W141|Q5W142|Q9Y213	Silent	SNP	ENST00000370187.3	hg19	CCDS7512.1																																																																																			.	.		0.542	BTRC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049936.1	NM_033637		C	103190119	T	C	103190119	2	2	263	1	0	0	0	0	0	0	0	1	1571	1538	54	2		2	BTRC	10	103190119	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	1211557	103190119	32344628	225	38599										
PPRC1	23082	hgsc.bcm.edu	37	chr10	103908392	103908392	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cctcttttgtcaggtacagcTcttatcgttcacatgaccat	6	12	4	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr10:103908392T>C	ENST00000278070.2	+	11	4597	c.4558T>C	c.(4558-4560)Tct>Cct	p.S1520P	PPRC1_ENST00000489648.1_3'UTR|PPRC1_ENST00000413464.2_Missense_Mutation_p.S1256P|PPRC1_ENST00000370012.1_Missense_Mutation_p.S487P	NM_015062.3	NP_055877.3	Q5VV67	PPRC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator-related 1	1520	Arg-rich.|Ser-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(10)|lung(19)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Colorectal(252;0.122)		Epithelial(162;4.97e-08)|all cancers(201;8.99e-07)		CAGGTACAGCTCTTATCGTTC	0.502																																					p.S1520P		Atlas-SNP	.											.	PPRC1	151	.	0			c.T4558C						.						184	172	176					10																	103908392		2203	4300	6503	SO:0001583	missense	23082	exon11			TACAGCTCTTATC	AF325193	CCDS7529.1, CCDS73186.1	10q24.32	2013-02-12	2006-10-17		ENSG00000148840	ENSG00000148840		"RNA binding motif (RRM) containing"	30025	protein-coding gene	gene with protein product			"peroxisome proliferative activated receptor, gamma, coactivator-related 1"			9628581, 11340167	Standard	XM_005269656		Approved	PRC, KIAA0595, MGC74642	uc001kum.3	Q5VV67	OTTHUMG00000018948	ENST00000278070.2:c.4558T>C	chr10.hg19:g.103908392T>C	ENSP00000278070:p.Ser1520Pro	130.0	0.0		97.0	4.0	NM_015062	Q5VV66|Q6P3U5|Q6P3W1|Q76N31|Q9BUJ3|Q9BZE5|Q9Y4E0	Missense_Mutation	SNP	ENST00000278070.2	hg19	CCDS7529.1	.	.	.	.	.	.	.	.	.	.	t	11.12	1.545661	0.27652	.	.	ENSG00000148840	ENST00000278070;ENST00000413464;ENST00000370012	T;T;T	0.38401	1.14;1.14;1.14	5.43	4.27	0.50696	Nucleotide-binding, alpha-beta plait (1);	0.578506	0.20168	N	0.097792	T	0.23649	0.0572	N	0.19112	0.55	0.20074	N	0.999934	B;B;B	0.28419	0.134;0.211;0.03	B;B;B	0.22601	0.018;0.04;0.013	T	0.10823	-1.0613	10	0.36615	T	0.2	.	12.6748	0.56887	0.0:0.0:0.138:0.862	.	1256;1398;1520	E7EVG6;Q5VV67-2;Q5VV67	.;.;PPRC1_HUMAN	P	1520;1256;487	ENSP00000278070:S1520P;ENSP00000399743:S1256P;ENSP00000359029:S487P	ENSP00000278070:S1520P	S	+	1	0	PPRC1	103898382	1.000000	0.71417	0.998000	0.56505	0.964000	0.63967	2.524000	0.45589	0.965000	0.38133	0.448000	0.29417	TCT	.	.		0.502	PPRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050021.1	NM_015062		C	103908392	T	C	103908392	3	2	263	1	0	0	0	0	1	0	0	0	12422	1551	54	2	4600	2	PPRC1	10	103908392	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	718273	103908392	31626355	226	38600										
TAF5	6877	hgsc.bcm.edu	37	chr10	105139430	105139430	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gatgacgaggatgaagagggAgaaaatgaagaaggaaaacc	15	3	0	6			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr10:105139430A>G	ENST00000369839.3	+	4	1202	c.1179A>G	c.(1177-1179)ggA>ggG	p.G393G	TAF5_ENST00000351396.4_Silent_p.G393G	NM_006951.3	NP_008882.2	Q15542	TAF5_HUMAN	TAF5 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 100kDa	393					chromatin modification (GO:0016568)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	protein dimerization activity (GO:0046983)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)	15		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;1.83e-09)|all cancers(201;1.4e-08)|BRCA - Breast invasive adenocarcinoma(275;0.198)		ATGAAGAGGGAGAAAATGAAG	0.343																																					p.G393G		Atlas-SNP	.											.	TAF5	47	.	0			c.A1179G						.						69	66	67					10																	105139430		2203	4300	6503	SO:0001819	synonymous_variant	6877	exon4			AGAGGGAGAAAAT	X95525	CCDS7547.1	10q24-q25.2	2013-01-10	2002-08-29	2001-12-07	ENSG00000148835	ENSG00000148835		"WD repeat domain containing"	11539	protein-coding gene	gene with protein product		601787	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, D, 100kD"	TAF2D		8884287, 8942982	Standard	NM_006951		Approved	TAFII100	uc001kwv.3	Q15542	OTTHUMG00000018985	ENST00000369839.3:c.1179A>G	chr10.hg19:g.105139430A>G		134.0	0.0		89.0	4.0	NM_006951	A8K5B4|B2RMR0|B7ZKJ6|Q53EM4|Q5SYD5|Q86UZ7|Q9Y4K5	Silent	SNP	ENST00000369839.3	hg19	CCDS7547.1																																																																																			.	.		0.343	TAF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050144.1			G	105139430	A	G	105139430	2	3	263	1	0	0	0	0	0	0	0	1	15543	291	11	2		2	TAF5	10	105139430	Silent	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	1231038	105139430	30395317	227	38601										
COL17A1	1308	hgsc.bcm.edu	37	chr10	105830329	105830329	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	acatcatccaattctgtcccTgtgaaagaatccacagacgt	6	12	2	3			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr10:105830329T>C	ENST00000353479.5	-	9	754		c.e9-2		COL17A1_ENST00000393211.3_Splice_Site|COL17A1_ENST00000369733.3_Splice_Site	NM_000494.3	NP_000485.3	Q9UMD9	COHA1_HUMAN	collagen, type XVII, alpha 1						cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|hemidesmosome (GO:0030056)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				NS(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|liver(1)|lung(22)|ovary(5)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	62		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		ATTCTGTCCCTGTGAAAGAAT	0.512																																					.		Atlas-SNP	.											.	COL17A1	149	.	0			c.464-2A>G	GRCh37	CS063258	COL17A1	S		.						119	113	115					10																	105830329		2203	4300	6503	SO:0001630	splice_region_variant	1308	exon10			TGTCCCTGTGAAA	M91669	CCDS7554.1	10q24.3	2013-01-16			ENSG00000065618	ENSG00000065618		"Collagens"	2194	protein-coding gene	gene with protein product		113811		BPAG2		7916703	Standard	NM_000494		Approved	BP180	uc001kxr.3	Q9UMD9	OTTHUMG00000018998	ENST00000353479.5:c.464-2A>G	chr10.hg19:g.105830329T>C		58.0	0.0		43.0	4.0	NM_000494	Q02802|Q5JV36|Q99018|Q9NQK9|Q9UC14	Splice_Site	SNP	ENST00000353479.5	hg19	CCDS7554.1	.	.	.	.	.	.	.	.	.	.	T	17.36	3.370316	0.61624	.	.	ENSG00000065618	ENST00000353479;ENST00000369733;ENST00000541872;ENST00000393211	.	.	.	5.92	5.92	0.95590	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0249	0.80536	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	COL17A1	105820319	1.000000	0.71417	0.998000	0.56505	0.526000	0.34562	7.000000	0.76290	2.270000	0.75569	0.459000	0.35465	.	.	.		0.512	COL17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050181.1	NM_130778, NM_000494	Intron	C	105830329	T	C	105830329	5	2	263	1	0	0	0	0	0	0	1	0	3676	1594	55	2	4223	2	COL17A1	10	105830329	Splice_Site	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	690899	105830329	29704418	228	38602										
SMC3	9126	hgsc.bcm.edu	37	chr10	112356255	112356255	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tgttagaaaagcagaagaagAactaggtgaacttgaagcaa	11	4	0	6			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr10:112356255A>G	ENST00000361804.4	+	19	2189	c.2063A>G	c.(2062-2064)gAa>gGa	p.E688G		NM_005445.3	NP_005436.1	Q9UQE7	SMC3_HUMAN	structural maintenance of chromosomes 3	688					DNA repair (GO:0006281)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid cohesion (GO:0007064)|mitotic spindle organization (GO:0007052)|negative regulation of DNA endoreduplication (GO:0032876)|regulation of DNA replication (GO:0006275)|signal transduction (GO:0007165)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	basement membrane (GO:0005604)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cohesin core heterodimer (GO:0008280)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear matrix (GO:0016363)|nuclear meiotic cohesin complex (GO:0034991)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|dynein binding (GO:0045502)|microtubule motor activity (GO:0003777)|protein heterodimerization activity (GO:0046982)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(5)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.00206)|all cancers(201;0.0227)|BRCA - Breast invasive adenocarcinoma(275;0.127)		GCAGAAGAAGAACTAGGTGAA	0.403																																					p.E688G		Atlas-SNP	.											.	SMC3	103	.	0			c.A2063G						.						107	108	108					10																	112356255		2203	4300	6503	SO:0001583	missense	9126	exon19			AAGAAGAACTAGG	AF020043	CCDS31285.1	10q25	2014-09-17	2006-07-06	2006-07-06	ENSG00000108055	ENSG00000108055		"Structural maintenance of chromosomes proteins", "Proteoglycans / Extracellular Matrix : Other"	2468	protein-coding gene	gene with protein product	"bamacan proteoglycan"	606062	"chondroitin sulfate proteoglycan 6 (bamacan)"	CSPG6		9506951, 10358101	Standard	NM_005445		Approved	HCAP, BAM, SMC3L1, bamacan	uc001kze.3	Q9UQE7	OTTHUMG00000019042	ENST00000361804.4:c.2063A>G	chr10.hg19:g.112356255A>G	ENSP00000354720:p.Glu688Gly	61.0	0.0		61.0	4.0	NM_005445	A8K156|O60464|Q5T482	Missense_Mutation	SNP	ENST00000361804.4	hg19	CCDS31285.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.959914	0.74016	.	.	ENSG00000108055	ENST00000361804	D	0.89050	-2.46	5.13	5.13	0.70059	SMCs flexible hinge (1);RecF/RecN/SMC (1);	0.000000	0.85682	D	0.000000	D	0.90219	0.6942	M	0.66939	2.045	0.80722	D	1	P	0.49961	0.93	P	0.48524	0.58	D	0.90969	0.4818	10	0.56958	D	0.05	.	14.9491	0.71057	1.0:0.0:0.0:0.0	.	688	Q9UQE7	SMC3_HUMAN	G	688	ENSP00000354720:E688G	ENSP00000354720:E688G	E	+	2	0	SMC3	112346245	1.000000	0.71417	1.000000	0.80357	0.561000	0.35649	8.962000	0.93254	1.930000	0.55929	0.260000	0.18958	GAA	.	.		0.403	SMC3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050337.1	NM_005445		G	112356255	A	G	112356255	3	3	263	1	0	0	0	0	1	0	0	0	14799	246	9	2	2137	2	SMC3	10	112356255	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	6525926	112356255	23178492	229	38603										
VWA2	340706	hgsc.bcm.edu	37	chr10	116044664	116044664	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ccagaatggaggcacatgtgTtccagaaggactggacggct	14	9	0	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr10:116044664T>C	ENST00000392982.3	+	10	1182	c.932T>C	c.(931-933)gTt>gCt	p.V311A	VWA2_ENST00000603594.1_Missense_Mutation_p.V311A			Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	311	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				calcium-independent cell-matrix adhesion (GO:0007161)|protein homooligomerization (GO:0051260)|regulation of insulin receptor signaling pathway (GO:0046626)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Epithelial(162;0.036)|all cancers(201;0.0793)		GGCACATGTGTTCCAGAAGGA	0.602																																					p.V311A		Atlas-SNP	.											.	VWA2	64	.	0			c.T932C						.						84	66	72					10																	116044664		2203	4300	6503	SO:0001583	missense	340706	exon10			CATGTGTTCCAGA	AK127756	CCDS7589.1, CCDS7589.2	10q25.3	2009-11-06			ENSG00000165816	ENSG00000165816			24709	protein-coding gene	gene with protein product						15580307, 14506275	Standard	NM_001272046		Approved	FLJ45857, FLJ16213, CCSP-2, AMACO, NET42	uc001lbl.2	Q5GFL6	OTTHUMG00000019082	ENST00000392982.3:c.932T>C	chr10.hg19:g.116044664T>C	ENSP00000376708:p.Val311Ala	75.0	0.0		65.0	4.0	NM_001272046	A1A5D4|B5MDJ8|Q6ZS39|Q6ZWJ7|Q708C5|Q70UZ8	Missense_Mutation	SNP	ENST00000392982.3	hg19		.	.	.	.	.	.	.	.	.	.	T	18.93	3.727647	0.69074	.	.	ENSG00000165816	ENST00000392982;ENST00000298715	D	0.93488	-3.23	5.49	5.49	0.81192	EGF (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.291582	0.32593	N	0.005886	D	0.91825	0.7413	L	0.39467	1.215	0.28003	N	0.935209	P;P	0.48640	0.913;0.894	P;P	0.48334	0.574;0.525	D	0.87768	0.2603	10	0.49607	T	0.09	.	13.8431	0.63451	0.0:0.0:0.0:1.0	.	311;311	Q5GFL6;Q5GFL6-2	VWA2_HUMAN;.	A	311	ENSP00000376708:V311A	ENSP00000298715:V311A	V	+	2	0	VWA2	116034654	1.000000	0.71417	0.395000	0.26283	0.403000	0.30841	7.370000	0.79589	2.076000	0.62316	0.533000	0.62120	GTT	.	.		0.602	VWA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050456.3	NM_198496		C	116044664	T	C	116044664	3	2	263	1	0	0	0	0	1	0	0	0	17254	1725	60	2	966	2	VWA2	10	116044664	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	3688409	116044664	19490083	230	38604										
SEC23IP	11196	hgsc.bcm.edu	37	chr10	121677482	121677482	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	aaaagtaggaatggagataaAccatctgcatgcactcttta	8	7	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr10:121677482A>G	ENST00000369075.3	+	9	1751	c.1679A>G	c.(1678-1680)aAc>aGc	p.N560S	SEC23IP_ENST00000543134.1_Missense_Mutation_p.N349S	NM_007190.3	NP_009121.1	Q9Y6Y8	S23IP_HUMAN	SEC23 interacting protein	560					acrosome assembly (GO:0001675)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|single fertilization (GO:0007338)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear endoplasmic reticulum (GO:0097038)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	36		Lung NSC(174;0.109)|all_lung(145;0.142)|all_neural(114;0.234)		all cancers(201;0.00515)		ATGGAGATAAACCATCTGCAT	0.383																																					p.N560S		Atlas-SNP	.											.	SEC23IP	100	.	0			c.A1679G						.						101	99	100					10																	121677482		2203	4300	6503	SO:0001583	missense	11196	exon9			AGATAAACCATCT	AB019435	CCDS7618.1	10q26.11-q26.12	2013-01-10			ENSG00000107651	ENSG00000107651		"Sterile alpha motif (SAM) domain containing"	17018	protein-coding gene	gene with protein product						10400679	Standard	NM_007190		Approved	p125	uc001leu.2	Q9Y6Y8	OTTHUMG00000019161	ENST00000369075.3:c.1679A>G	chr10.hg19:g.121677482A>G	ENSP00000358071:p.Asn560Ser	101.0	0.0		93.0	5.0	NM_007190	D3DRD2|Q8IXH5|Q9BUK5	Missense_Mutation	SNP	ENST00000369075.3	hg19	CCDS7618.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.305968	0.81247	.	.	ENSG00000107651	ENST00000369075;ENST00000543134	T;T	0.50548	0.74;0.74	5.51	4.35	0.52113	.	0.040106	0.85682	D	0.000000	T	0.76040	0.3932	H	0.96048	3.76	0.80722	D	1	D;D	0.71674	0.998;0.995	D;D	0.66196	0.942;0.936	T	0.83041	-0.0157	10	0.87932	D	0	-24.6233	12.8103	0.57635	0.8631:0.1369:0.0:0.0	.	349;560	F5H0L8;Q9Y6Y8	.;S23IP_HUMAN	S	560;349	ENSP00000358071:N560S;ENSP00000438773:N349S	ENSP00000358071:N560S	N	+	2	0	SEC23IP	121667472	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.071000	0.93980	0.998000	0.38996	0.533000	0.62120	AAC	.	.		0.383	SEC23IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050688.1			G	121677482	A	G	121677482	3	3	263	1	0	0	0	0	1	0	0	0	14008	43	2	2	1713	2	SEC23IP	10	121677482	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	5632818	121677482	13857265	231	38605										
LRDD	55367	hgsc.bcm.edu	37	chr11	802841	802841	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ggccaagtcagctggcacagAggccaggaggttgctgtgca	16	10	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr11:802841A>G	ENST00000347755.5	-	4	901	c.760T>C	c.(760-762)Tct>Cct	p.S254P	PIDD_ENST00000411829.2_Missense_Mutation_p.S254P|PIDD_ENST00000534649.1_5'Flank	NM_145886.3|NM_145887.3	NP_665893.2|NP_665894.2																					GCTGGCACAGAGGCCAGGAGG	0.677																																					p.S254P		Atlas-SNP	.											.	PIDD	76	.	0			c.T760C						.						18	22	21					11																	802841		2183	4282	6465	SO:0001583	missense	55367	exon4			GCACAGAGGCCAG																												ENST00000347755.5:c.760T>C	chr11.hg19:g.802841A>G	ENSP00000337797:p.Ser254Pro	127.0	0.0		147.0	6.0	NM_145887		Missense_Mutation	SNP	ENST00000347755.5	hg19	CCDS7716.1	.	.	.	.	.	.	.	.	.	.	A	12.88	2.070568	0.36566	.	.	ENSG00000177595	ENST00000411829;ENST00000347755	T;T	0.20463	2.07;2.07	4.44	3.28	0.37604	.	0.718142	0.12984	N	0.423012	T	0.26593	0.0650	L	0.28608	0.87	0.09310	N	1	D;D;D	0.71674	0.996;0.998;0.998	P;P;P	0.62649	0.806;0.876;0.905	T	0.08006	-1.0743	10	0.48119	T	0.1	.	4.876	0.13656	0.5276:0.1404:0.0:0.332	.	254;108;254	Q9HB75;Q9HB75-3;Q9HB75-2	PIDD_HUMAN;.;.	P	254	ENSP00000416801:S254P;ENSP00000337797:S254P	ENSP00000337797:S254P	S	-	1	0	PIDD	792841	0.987000	0.35691	0.030000	0.17652	0.066000	0.16364	2.542000	0.45744	0.719000	0.32188	0.454000	0.30748	TCT	.	.		0.677	PIDD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257103.1			G	802841	A	G	802841	3	3	263	1	0	0	0	0	1	0	0	0	8945	304	11	2	2024	2	LRDD	11	802841	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10		802841	134203675	232	38606										
OR51G1	79324	hgsc.bcm.edu	37	chr11	4944635	4944635	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	aaaaacacctaagtgactttAtaaactgaaacttcttaatg	4	7	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr11:4944635A>G	ENST00000321961.2	-	1	1002	c.935T>C	c.(934-936)aTa>aCa	p.I312T	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001005237.1	NP_001005237.1	Q8NGK1	O51G1_HUMAN	olfactory receptor, family 51, subfamily G, member 1	312						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			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)		AAGTGACTTTATAAACTGAAA	0.413																																					p.I312T		Atlas-SNP	.											.	OR51G1	74	.	0			c.T935C						.						93	92	92					11																	4944635		2201	4298	6499	SO:0001583	missense	79324	exon1			GACTTTATAAACT	AB065793	CCDS31366.1	11p15.4	2012-08-09			ENSG00000176879	ENSG00000176879		"GPCR / Class A : Olfactory receptors"	14738	protein-coding gene	gene with protein product				OR51G3P			Standard	NM_001005237		Approved		uc010qyr.2	Q8NGK1	OTTHUMG00000066532	ENST00000321961.2:c.935T>C	chr11.hg19:g.4944635A>G	ENSP00000322546:p.Ile312Thr	113.0	0.0		117.0	16.0	NM_001005237	B9EGW8|Q6IFH6	Missense_Mutation	SNP	ENST00000321961.2	hg19	CCDS31366.1	.	.	.	.	.	.	.	.	.	.	A	8.544	0.873893	0.17395	.	.	ENSG00000176879	ENST00000321961	T	0.36878	1.23	4.17	2.96	0.34315	.	1.754140	0.03997	U	0.295786	T	0.19167	0.0460	N	0.03608	-0.345	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.09509	-1.0671	10	0.31617	T	0.26	.	7.6017	0.28079	0.7844:0.2156:0.0:0.0	.	312	Q8NGK1	O51G1_HUMAN	T	312	ENSP00000322546:I312T	ENSP00000322546:I312T	I	-	2	0	OR51G1	4901211	0.002000	0.14202	0.097000	0.21041	0.664000	0.39144	1.714000	0.37961	1.746000	0.51805	0.455000	0.32223	ATA	.	.		0.413	OR51G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142345.1	NM_001005237		G	4944635	A	G	4944635	3	3	263	1	0	0	0	0	1	0	0	0	11107	449	16	2	32	2	OR51G1	11	4944635	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	4141794	4944635	130061881	233	38607										
AMPD3	272	hgsc.bcm.edu	37	chr11	10500172	10500172	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gcagccagtccggccatgtcTcccacaacccctgtggtcac	9	18	2	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr11:10500172T>C	ENST00000396554.3	+	3	689	c.348T>C	c.(346-348)tcT>tcC	p.S116S	AMPD3_ENST00000444303.2_Intron	NM_000480.2	NP_000471.1	Q01432	AMPD3_HUMAN	adenosine monophosphate deaminase 3	107					ADP metabolic process (GO:0046031)|AMP catabolic process (GO:0006196)|ATP metabolic process (GO:0046034)|energy homeostasis (GO:0097009)|IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(3)|skin(1)	25				all cancers(16;1.14e-08)|Epithelial(150;2.83e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0291)		CGGCCATGTCTCCCACAACCC	0.592																																					p.S116S		Atlas-SNP	.											.	AMPD3	68	.	0			c.T348C						.						103	111	108					11																	10500172		2201	4294	6495	SO:0001819	synonymous_variant	272	exon3			CATGTCTCCCACA	M84722	CCDS7802.1, CCDS41617.1, CCDS44537.1, CCDS53601.1	11p15	2010-02-10	2010-02-10			ENSG00000133805	3.5.4.6		470	protein-coding gene	gene with protein product	"erythrocyte-specific AMP deaminase"	102772	"adenosine monophosphate deaminase (isoform E)"			1400401	Standard	NM_001172430		Approved		uc001min.1	Q01432		ENST00000396554.3:c.348T>C	chr11.hg19:g.10500172T>C		89.0	0.0		114.0	5.0	NM_000480	A0AUX0|B7Z2S2|B7Z763|B7Z877	Silent	SNP	ENST00000396554.3	hg19	CCDS7802.1																																																																																			.	.		0.592	AMPD3-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385783.2	NM_000480		C	10500172	T	C	10500172	2	2	263	1	0	0	0	0	0	0	0	1	587	1538	54	2		2	AMPD3	11	10500172	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	5555537	10500172	124506344	234	38608										
EIF4G2	1982	hgsc.bcm.edu	37	chr11	10824623	10824623	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tgatcgtctttggtccattgTcaagaaaagccttgcgagga	11	8	2	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr11:10824623T>C	ENST00000526148.1	-	11	1460	c.950A>G	c.(949-951)gAc>gGc	p.D317G	EIF4G2_ENST00000339995.5_Missense_Mutation_p.D317G|RP11-685M7.5_ENST00000532365.1_RNA|EIF4G2_ENST00000396525.2_Missense_Mutation_p.D317G|EIF4G2_ENST00000525681.1_Missense_Mutation_p.D317G|SNORD97_ENST00000459187.1_RNA|EIF4G2_ENST00000525995.1_5'Flank	NM_001172705.1	NP_001166176			eukaryotic translation initiation factor 4 gamma, 2											NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	43				all cancers(16;2.8e-07)|Epithelial(150;4.18e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		TGGTCCATTGTCAAGAAAAGC	0.348																																					p.D317G		Atlas-SNP	.											.	EIF4G2	89	.	0			c.A950G						.						86	82	83					11																	10824623		2201	4294	6495	SO:0001583	missense	1982	exon11			CCATTGTCAAGAA	U73824	CCDS31428.1, CCDS41618.1	11p15	2005-09-29			ENSG00000110321	ENSG00000110321			3297	protein-coding gene	gene with protein product		602325				9030685, 9032289	Standard	NM_001042559		Approved	DAP5, NAT1, p97	uc001mjc.3	P78344	OTTHUMG00000165823	ENST00000526148.1:c.950A>G	chr11.hg19:g.10824623T>C	ENSP00000433664:p.Asp317Gly	99.0	0.0		125.0	5.0	NM_001172705		Missense_Mutation	SNP	ENST00000526148.1	hg19	CCDS31428.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.322942	0.81580	.	.	ENSG00000110321	ENST00000526148;ENST00000525681;ENST00000339995;ENST00000396525;ENST00000429377;ENST00000531416	T;T;T;T;T	0.26660	2.04;2.04;2.04;2.05;1.72	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.43765	0.1262	L	0.59436	1.845	0.50171	D	0.999854	D;D;D	0.62365	0.991;0.985;0.985	P;P;P	0.56751	0.805;0.714;0.643	T	0.48091	-0.9065	9	0.66056	D	0.02	-7.3949	16.6407	0.85098	0.0:0.0:0.0:1.0	.	317;317;390	P78344-2;P78344;B4DZF2	.;IF4G2_HUMAN;.	G	317;317;317;317;390;317	ENSP00000433664:D317G;ENSP00000433371:D317G;ENSP00000340281:D317G;ENSP00000379778:D317G;ENSP00000431583:D317G	ENSP00000340281:D317G	D	-	2	0	EIF4G2	10781199	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.910000	0.87451	2.326000	0.78906	0.533000	0.62120	GAC	.	.		0.348	EIF4G2-006	KNOWN	alternative_5_UTR|non_ATG_start|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386603.1	NM_001418		C	10824623	T	C	10824623	3	2	263	1	0	0	0	0	1	0	0	0	5039	1667	58	2	1821	2	EIF4G2	11	10824623	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	324451	10824623	124181893	235	38609										
SERGEF	26297	hgsc.bcm.edu	37	chr11	18026056	18026056	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	taactggccaaaggagttggAtccacatgatagaacttgac	10	8	0	3			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr11:18026056A>G	ENST00000265965.5	-	4	530	c.379T>C	c.(379-381)Tcc>Ccc	p.S127P	SERGEF_ENST00000532265.1_Missense_Mutation_p.S13P|RP1-59M18.2_ENST00000525523.1_RNA|SERGEF_ENST00000532212.1_5'UTR|SERGEF_ENST00000528200.1_Missense_Mutation_p.S127P	NM_012139.2	NP_036271.1	Q9UGK8	SRGEF_HUMAN	secretion regulating guanine nucleotide exchange factor	127					negative regulation of protein secretion (GO:0050709)|positive regulation of Ran GTPase activity (GO:0032853)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)	Ran guanyl-nucleotide exchange factor activity (GO:0005087)			autonomic_ganglia(1)|central_nervous_system(1)|large_intestine(5)|lung(5)	12						AAGGAGTTGGATCCACATGAT	0.428																																					p.S127P		Atlas-SNP	.											.	SERGEF	38	.	0			c.T379C						.						97	77	84					11																	18026056		2200	4293	6493	SO:0001583	missense	26297	exon4			AGTTGGATCCACA	AJ243950	CCDS7828.1	11p14.3	2006-03-09			ENSG00000129158	ENSG00000129158			17499	protein-coding gene	gene with protein product		606051				10571079, 12459492	Standard	NM_012139		Approved	DelGEF, Gnefr	uc001mnm.3	Q9UGK8	OTTHUMG00000166420	ENST00000265965.5:c.379T>C	chr11.hg19:g.18026056A>G	ENSP00000265965:p.Ser127Pro	48.0	0.0		62.0	4.0	NM_012139	Q9UGK9	Missense_Mutation	SNP	ENST00000265965.5	hg19	CCDS7828.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.283639	0.80803	.	.	ENSG00000129158	ENST00000265965;ENST00000528200;ENST00000532265;ENST00000529728;ENST00000530613;ENST00000532389	D;D;D;D;D;D	0.85258	-1.5;-1.5;-1.96;-1.96;-1.96;-1.96	5.42	5.42	0.78866	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.85682	D	0.000000	D	0.94278	0.8162	H	0.96301	3.8	0.48452	D	0.999659	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.91635	0.966;0.999;0.994;0.996	D	0.94401	0.7623	10	0.34782	T	0.22	-6.2116	13.1018	0.59224	1.0:0.0:0.0:0.0	.	13;13;127;127	B4DFC0;E9PMV6;Q9UGK8-2;Q9UGK8	.;.;.;SRGEF_HUMAN	P	127;127;13;13;13;13	ENSP00000265965:S127P;ENSP00000434188:S127P;ENSP00000431314:S13P;ENSP00000437297:S13P;ENSP00000436080:S13P;ENSP00000435898:S13P	ENSP00000265965:S127P	S	-	1	0	SERGEF	17982632	0.998000	0.40836	1.000000	0.80357	0.999000	0.98932	3.999000	0.57031	2.282000	0.76494	0.533000	0.62120	TCC	.	.		0.428	SERGEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389538.1	NM_012139		G	18026056	A	G	18026056	3	3	263	1	0	0	0	0	1	0	0	0	14092	333	12	2	1029	2	SERGEF	11	18026056	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	7201433	18026056	116980460	236	38610										
FBXO3	26273	hgsc.bcm.edu	37	chr11	33770421	33770421	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	aggccttctcaggaagtgcaTcttttgacatttcaatccta	7	10	3	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr11:33770421T>C	ENST00000265651.3	-	9	968	c.950A>G	c.(949-951)gAt>gGt	p.D317G	FBXO3_ENST00000532057.1_Missense_Mutation_p.D4G|FBXO3_ENST00000526785.1_Missense_Mutation_p.D204G|FBXO3_ENST00000530401.1_Missense_Mutation_p.D312G|FBXO3_ENST00000534136.1_Missense_Mutation_p.D317G|FBXO3_ENST00000448981.2_Missense_Mutation_p.D317G|FBXO3_ENST00000531080.1_Missense_Mutation_p.D4G	NM_012175.3	NP_036307.2	Q9UK99	FBX3_HUMAN	F-box protein 3	317	ApaG. {ECO:0000255|PROSITE- ProRule:PRU00412}.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|pancreas(1)|stomach(1)	13		Lung NSC(402;0.0804)		BRCA - Breast invasive adenocarcinoma(625;0.00315)|Lung(977;0.00488)|LUSC - Lung squamous cell carcinoma(625;0.008)		AGGAAGTGCATCTTTTGACAT	0.423																																					p.D317G		Atlas-SNP	.											.	FBXO3	37	.	0			c.A950G						.						95	89	91					11																	33770421		2202	4298	6500	SO:0001583	missense	26273	exon9			AGTGCATCTTTTG	AK001943	CCDS7887.1, CCDS44566.1	11p13	2006-07-07	2004-06-15		ENSG00000110429	ENSG00000110429		"F-boxes /  "other""	13582	protein-coding gene	gene with protein product		609089	"F-box only protein 3"			10531037	Standard	NM_033406		Approved	FBX3, FBA	uc001muz.3	Q9UK99	OTTHUMG00000166244	ENST00000265651.3:c.950A>G	chr11.hg19:g.33770421T>C	ENSP00000265651:p.Asp317Gly	72.0	0.0		88.0	4.0	NM_012175	B3KY16|D3DR05|Q86X90|Q9H0V2|Q9NUX2	Missense_Mutation	SNP	ENST00000265651.3	hg19	CCDS7887.1	.	.	.	.	.	.	.	.	.	.	T	15.66	2.898632	0.52227	.	.	ENSG00000110429	ENST00000526785;ENST00000265651;ENST00000530401;ENST00000531080;ENST00000532057;ENST00000534136;ENST00000448981	T;T;T;T;T	0.51817	0.69;0.69;0.71;0.7;0.71	5.46	5.46	0.80206	ApaG domain (4);	0.349704	0.34603	N	0.003827	T	0.44329	0.1288	L	0.41356	1.27	0.44956	D	0.997975	P;P;P	0.42296	0.775;0.775;0.704	B;B;B	0.41412	0.356;0.356;0.294	T	0.47799	-0.9089	10	0.66056	D	0.02	-21.3837	15.5183	0.75842	0.0:0.0:0.0:1.0	.	312;317;317	Q9UK99-3;Q9UK99-2;Q9UK99	.;.;FBX3_HUMAN	G	204;317;312;4;4;317;317	ENSP00000435680:D204G;ENSP00000265651:D317G;ENSP00000433781:D312G;ENSP00000431745:D317G;ENSP00000408836:D317G	ENSP00000265651:D317G	D	-	2	0	FBXO3	33726997	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.681000	0.46926	2.090000	0.63153	0.402000	0.26972	GAT	.	.		0.423	FBXO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388665.1	NM_012175		C	33770421	T	C	33770421	3	2	263	1	0	0	0	0	1	0	0	0	5747	1435	50	2	486	2	FBXO3	11	33770421	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	15744365	33770421	101236095	237	38611										
AMBRA1	55626	hgsc.bcm.edu	37	chr11	46431903	46431903	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tggtcccagtagtactcaacAccagagtttaaggccctaaa	8	11	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr11:46431903A>G	ENST00000458649.2	-	16	3550	c.3132T>C	c.(3130-3132)ggT>ggC	p.G1044G	AMBRA1_ENST00000314845.3_Silent_p.G954G|AMBRA1_ENST00000534300.1_Silent_p.G984G|AMBRA1_ENST00000426438.1_Silent_p.G1015G|AMBRA1_ENST00000528950.1_Silent_p.G1015G|AMBRA1_ENST00000298834.3_Silent_p.G984G|AMBRA1_ENST00000533727.1_Silent_p.G925G			Q9C0C7	AMRA1_HUMAN	autophagy/beclin-1 regulator 1	1044					autophagy (GO:0006914)|cell differentiation (GO:0030154)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neural tube development (GO:0021915)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|phagocytic vesicle (GO:0045335)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	39				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)		AGTACTCAACACCAGAGTTTA	0.507																																					p.G1047G		Atlas-SNP	.											.	AMBRA1	201	.	0			c.T3141C						.						104	92	96					11																	46431903		2201	4299	6500	SO:0001819	synonymous_variant	55626	exon18			CTCAACACCAGAG	AB051523	CCDS31475.1, CCDS58132.1, CCDS73281.1	11p11.2	2013-01-09			ENSG00000110497	ENSG00000110497		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	25990	protein-coding gene	gene with protein product	"WD repeat domain 94", "DDB1 and CUL4 associated factor 3"	611359				17622796, 17603510, 17589504	Standard	NM_001267782		Approved	FLJ20294, KIAA1736, WDR94, DCAF3	uc001ncv.3	Q9C0C7	OTTHUMG00000166500	ENST00000458649.2:c.3132T>C	chr11.hg19:g.46431903A>G		79.0	0.0		96.0	4.0	NM_001267782	A6XN33|D3DQP8|G3V193|Q86XD6|Q9H8Z0|Q9NXE7	Silent	SNP	ENST00000458649.2	hg19																																																																																				.	.		0.507	AMBRA1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000390103.1	NM_017749		G	46431903	A	G	46431903	2	3	263	1	0	0	0	0	0	0	0	1	565	146	6	2		2	AMBRA1	11	46431903	Silent	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	12661482	46431903	88574613	238	38612										
SPI1	6688	hgsc.bcm.edu	37	chr11	47380554	47380554	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gcacatccggggcaggtaggAgacctggacggtgggggaag	20	8	0	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr11:47380554A>G	ENST00000378538.3	-	4	556	c.334T>C	c.(334-336)Tcc>Ccc	p.S112P	SPI1_ENST00000533030.1_Intron|SPI1_ENST00000227163.4_Missense_Mutation_p.S113P|SPI1_ENST00000533968.1_Missense_Mutation_p.S112P	NM_001080547.1|NM_003120.2	NP_001074016.1|NP_003111.2	P17947	SPI1_HUMAN	Spi-1 proto-oncogene	112					anatomical structure regression (GO:0060033)|apoptotic process involved in patterning of blood vessels (GO:1902262)|erythrocyte differentiation (GO:0030218)|granulocyte differentiation (GO:0030851)|histone H3 acetylation (GO:0043966)|hypermethylation of CpG island (GO:0044027)|lymphocyte differentiation (GO:0030098)|lymphoid progenitor cell differentiation (GO:0002320)|macrophage differentiation (GO:0030225)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of histone H4 acetylation (GO:0090241)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of erythrocyte differentiation (GO:0045646)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|somatic stem cell maintenance (GO:0035019)	nuclear chromatin (GO:0000790)	core promoter binding (GO:0001047)|NFAT protein binding (GO:0051525)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(2)|lung(4)|ovary(1)	8				Lung(87;0.0967)		GGCAGGTAGGAGACCTGGACG	0.662																																					p.S113P		Atlas-SNP	.											.	SPI1	21	.	0			c.T337C						.						20	22	21					11																	47380554		2197	4288	6485	SO:0001583	missense	6688	exon4			GGTAGGAGACCTG	X52056	CCDS7933.2, CCDS44591.1	11p12-p11.22	2014-06-25	2014-06-25		ENSG00000066336	ENSG00000066336			11241	protein-coding gene	gene with protein product	"hematopoietic transcription factor PU.1", "31 kDa transforming protein"	165170	"spleen focus forming virus (SFFV) proviral integration oncogene"			1693183	Standard	NM_003120		Approved	PU.1, SPI-A, OF, SFPI1, SPI-1	uc001nfb.1	P17947	OTTHUMG00000150150	ENST00000378538.3:c.334T>C	chr11.hg19:g.47380554A>G	ENSP00000367799:p.Ser112Pro	225.0	0.0		306.0	13.0	NM_001080547		Missense_Mutation	SNP	ENST00000378538.3	hg19	CCDS7933.2	.	.	.	.	.	.	.	.	.	.	A	5.171	0.217116	0.09810	.	.	ENSG00000066336	ENST00000378538;ENST00000227163;ENST00000533968	T;T;T	0.32023	1.47;1.47;1.47	4.64	-1.75	0.08031	.	0.299208	0.37809	N	0.001934	T	0.12603	0.0306	N	0.16066	0.365	0.44627	D	0.997603	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.15867	-1.0422	10	0.19147	T	0.46	-10.7714	5.854	0.18710	0.5077:0.0:0.3691:0.1232	.	112;112;113	F5H3K6;P17947;P17947-2	.;SPI1_HUMAN;.	P	112;113;112	ENSP00000367799:S112P;ENSP00000227163:S113P;ENSP00000438846:S112P	ENSP00000227163:S113P	S	-	1	0	SPI1	47337130	0.088000	0.21588	0.993000	0.49108	0.528000	0.34623	-0.341000	0.07811	-0.386000	0.07821	-0.411000	0.06167	TCC	.	.		0.662	SPI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316571.1	NM_003120		G	47380554	A	G	47380554	3	3	263	1	0	0	0	0	1	0	0	0	15064	304	11	2	486	2	SPI1	11	47380554	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	948651	47380554	87625962	239	38613										
OR4S2	219431	hgsc.bcm.edu	37	chr11	55418935	55418935	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ttcaccctgtgttgaaacttGcctgcacagaaacatacatt	6	11	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr11:55418935G>T	ENST00000312422.2	+	1	556	c.556G>T	c.(556-558)Gcc>Tcc	p.A186S		NM_001004059.2	NP_001004059.2	Q8NH73	OR4S2_HUMAN	olfactory receptor, family 4, subfamily S, member 2	186						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(4)|lung(28)|ovary(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_epithelial(135;0.0748)				GTTGAAACTTGCCTGCACAGA	0.438																																					p.A186S		Atlas-SNP	.											.	OR4S2	89	.	0			c.G556T						.						265	199	222					11																	55418935		2182	4053	6235	SO:0001583	missense	219431	exon1			AAACTTGCCTGCA	BK004390	CCDS31505.1	11q11	2012-08-09	2002-11-13	2002-11-15	ENSG00000174982	ENSG00000174982		"GPCR / Class A : Olfactory receptors"	15183	protein-coding gene	gene with protein product			"olfactory receptor, family 4, subfamily S, member 2 pseudogene"	OR4S2P			Standard	NM_001004059		Approved	OST725	uc001nhs.1	Q8NH73	OTTHUMG00000166799	ENST00000312422.2:c.556G>T	chr11.hg19:g.55418935G>T	ENSP00000310337:p.Ala186Ser	235.0	0.0		301.0	114.0	NM_001004059	Q6IF72	Missense_Mutation	SNP	ENST00000312422.2	hg19	CCDS31505.1	.	.	.	.	.	.	.	.	.	.	G	18.09	3.546866	0.65198	.	.	ENSG00000174982	ENST00000312422	T	0.00021	9.02	5.35	4.43	0.53597	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000063	T	0.00210	0.0006	L	0.39326	1.205	0.31411	N	0.675523	D	0.58620	0.983	P	0.54544	0.755	T	0.63906	-0.6531	10	0.62326	D	0.03	.	12.213	0.54389	0.0:0.0:0.692:0.308	.	186	Q8NH73	OR4S2_HUMAN	S	186	ENSP00000310337:A186S	ENSP00000310337:A186S	A	+	1	0	OR4S2	55175511	0.000000	0.05858	1.000000	0.80357	0.954000	0.61252	-0.531000	0.06171	1.231000	0.43661	0.542000	0.68232	GCC	.	.		0.438	OR4S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391503.1	NM_001004059		T	55418935	G	T	55418935	3	4	263	1	0	0	0	0	1	0	0	0	11092	1319	46	3	558	3	OR4S2	11	55418935	Missense_Mutation	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	8038381	55418935	79587581	240	38614										
OR5M10	390167	hgsc.bcm.edu	37	chr11	56344846	56344847	+	Missense_Mutation	DNP	TT	TT	AG													0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tacatagcgatccaatgccaTtgaagcaaggaagtaaaact					rs148438199	byFrequency	TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr11:56344846_56344847TT>AG	ENST00000526812.2	-	1	416_417	c.351_352AA>CT	c.(349-354)tcAAtg>tcCTtg	p.M118L		NM_001004741.1	NP_001004741.1	Q6IEU7	OR5MA_HUMAN	olfactory receptor, family 5, subfamily M, member 10	118						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(15)|upper_aerodigestive_tract(2)|urinary_tract(2)	25						TCCAATGCCATTGAAGCAAGGA	0.45																																					p.M118L|p.S117S		Atlas-SNP	.											.,1|.	OR5M10	56	.	0			c.A352T|c.A351C						.																																			SO:0001583	missense	390167	exon1			ATGCCATTGAAGC|TGCCATTGAAGCA	BK004515	CCDS53630.1	11q11	2012-08-09				ENSG00000254834		"GPCR / Class A : Olfactory receptors"	15290	protein-coding gene	gene with protein product							Standard	NM_001004741		Approved		uc001niz.1	Q6IEU7		ENST00000526812.2:c.351_352delinsAG	chr11.hg19:g.56344846_56344847delinsAG	ENSP00000436004:p.Met118Leu	80.0	0.0		115.0|114.0	13.0|12.0	NM_001004741	B9EIL9	Missense_Mutation|Silent	SNP	ENST00000526812.2	hg19	CCDS53630.1																																																																																			.	.		0.45	OR5M10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391609.1	NM_001004741		AG	56344847	TT	AG	56344846	3	1	263	1	0	0	0	0	1	0	0	0	11182	1493	52	4	599	4	OR5M10	11	56344846	Missense_Mutation	DNP	TT	TCGA-FV-A2QR-01A-11D-A20W-10	925911	56344846	78661670	241	38615	189	2								
OR5M10	390167	hgsc.bcm.edu	37	chr11	56344851	56344851	+	Missense_Mutation	SNP	G	G	C													0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	agcgatccaatgccattgaaGcaaggaagtaaaactcagtg					rs148438199	byFrequency	TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr11:56344851G>C	ENST00000526812.2	-	1	412	c.347C>G	c.(346-348)gCt>gGt	p.A116G		NM_001004741.1	NP_001004741.1	Q6IEU7	OR5MA_HUMAN	olfactory receptor, family 5, subfamily M, member 10	116						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(15)|upper_aerodigestive_tract(2)|urinary_tract(2)	25						TGCCATTGAAGCAAGGAAGTA	0.458																																					p.A116G		Atlas-SNP	.											.	OR5M10	56	.	0			c.C347G						.						170	146	154					11																	56344851		1999	4171	6170	SO:0001583	missense	390167	exon1			ATTGAAGCAAGGA	BK004515	CCDS53630.1	11q11	2012-08-09				ENSG00000254834		"GPCR / Class A : Olfactory receptors"	15290	protein-coding gene	gene with protein product							Standard	NM_001004741		Approved		uc001niz.1	Q6IEU7		ENST00000526812.2:c.347C>G	chr11.hg19:g.56344851G>C	ENSP00000436004:p.Ala116Gly	81.0	0.0		120.0	5.0	NM_001004741	B9EIL9	Missense_Mutation	SNP	ENST00000526812.2	hg19	CCDS53630.1	.	.	.	.	.	.	.	.	.	.	G	6.112	0.388856	0.11581	.	.	ENSG00000254834	ENST00000526812	T	0.02032	4.49	4.04	2.12	0.27331	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.03783	0.0107	M	0.62266	1.93	0.09310	N	1	B	0.12630	0.006	B	0.17433	0.018	T	0.28713	-1.0035	9	0.62326	D	0.03	.	9.6505	0.39895	0.1688:0.0:0.8312:0.0	.	116	Q6IEU7	OR5MA_HUMAN	G	116	ENSP00000436004:A116G	ENSP00000436004:A116G	A	-	2	0	OR5M10	56101427	0.001000	0.12720	0.001000	0.08648	0.008000	0.06430	1.138000	0.31491	0.455000	0.26910	0.632000	0.83419	GCT	.	.		0.458	OR5M10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391609.1	NM_001004741		C	56344851	G	C	56344851	3	2	263	1	0	0	0	0	1	0	0	0	11182	971	34	4	604	4	OR5M10	11	56344851	Missense_Mutation	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	5	56344851	78661665	242	38616	189	2								
TNKS1BP1	85456	hgsc.bcm.edu	37	chr11	57076580	57076580	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	aacagccggtcaggttcatgTctctcaagctcaggccacct	9	14	5	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr11:57076580T>C	ENST00000532437.1	-	5	3916	c.3605A>G	c.(3604-3606)gAc>gGc	p.D1202G	TNKS1BP1_ENST00000530920.1_5'Flank|TNKS1BP1_ENST00000358252.3_Missense_Mutation_p.D1202G			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	1202	Acidic.|Gly-rich.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)			breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				CAGGTTCATGTCTCTCAAGCT	0.582																																					p.D1202G		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.A3605G						.						113	124	120					11																	57076580		2201	4296	6497	SO:0001583	missense	85456	exon6			TTCATGTCTCTCA	AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.3605A>G	chr11.hg19:g.57076580T>C	ENSP00000437271:p.Asp1202Gly	116.0	0.0		125.0	5.0	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Missense_Mutation	SNP	ENST00000532437.1	hg19	CCDS7951.1	.	.	.	.	.	.	.	.	.	.	T	5.180	0.218776	0.09810	.	.	ENSG00000149115	ENST00000358252;ENST00000532437	T;T	0.32988	1.43;1.43	5.05	2.68	0.31781	.	0.360712	0.23602	N	0.046431	T	0.21427	0.0516	L	0.34521	1.04	0.09310	N	1	B	0.32101	0.356	B	0.33454	0.164	T	0.12604	-1.0541	10	0.44086	T	0.13	-16.7742	7.7382	0.28827	0.0:0.1715:0.0:0.8285	.	1202	Q9C0C2	TB182_HUMAN	G	1202	ENSP00000350990:D1202G;ENSP00000437271:D1202G	ENSP00000350990:D1202G	D	-	2	0	TNKS1BP1	56833156	0.001000	0.12720	0.001000	0.08648	0.010000	0.07245	0.986000	0.29590	0.736000	0.32559	0.379000	0.24179	GAC	.	.		0.582	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396		C	57076580	T	C	57076580	3	2	263	1	0	0	0	0	1	0	0	0	16335	1667	58	2	1608	2	TNKS1BP1	11	57076580	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	731729	57076580	77929936	243	38617										
MPEG1	219972	hgsc.bcm.edu	37	chr11	58979671	58979671	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ggctgtcttggaggaaggagGccctgaggtggtcctcctga	17	9	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr11:58979671G>A	ENST00000361050.3	-	1	753	c.668C>T	c.(667-669)gCc>gTc	p.A223V	RN7SL42P_ENST00000579786.1_RNA	NM_001039396.1	NP_001034485.1	Q2M385	MPEG1_HUMAN	macrophage expressed 1	223	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.					integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(21)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		all_epithelial(135;0.125)				GAGGAAGGAGGCCCTGAGGTG	0.557																																					p.A223V		Atlas-SNP	.											.	MPEG1	72	.	0			c.C668T						.						55	55	55					11																	58979671		1959	4125	6084	SO:0001583	missense	219972	exon1			AAGGAGGCCCTGA	AK097211	CCDS41650.1	11q12.1	2013-07-31				ENSG00000197629			29619	protein-coding gene	gene with protein product	"macrophage expressed gene 1"	610390				7888681, 23257510	Standard	NM_001039396		Approved	MPG1	uc001nnu.4	Q2M385		ENST00000361050.3:c.668C>T	chr11.hg19:g.58979671G>A	ENSP00000354335:p.Ala223Val	44.0	0.0		49.0	21.0	NM_001039396	Q2M1T6|Q8TEF8	Missense_Mutation	SNP	ENST00000361050.3	hg19	CCDS41650.1	.	.	.	.	.	.	.	.	.	.	G	8.324	0.824912	0.16678	.	.	ENSG00000197629	ENST00000361050	D	0.84370	-1.84	5.21	4.27	0.50696	Membrane attack complex component/perforin (MACPF) domain (3);	1.165770	0.06199	N	0.682903	T	0.78136	0.4236	N	0.14661	0.345	0.09310	N	1	B	0.27910	0.193	B	0.30716	0.119	T	0.65804	-0.6079	10	0.42905	T	0.14	-1.5054	12.5026	0.55964	0.0:0.215:0.785:0.0	.	223	Q2M385	MPEG1_HUMAN	V	223	ENSP00000354335:A223V	ENSP00000354335:A223V	A	-	2	0	MPEG1	58736247	0.837000	0.29446	0.052000	0.19188	0.161000	0.22273	4.656000	0.61483	1.107000	0.41642	0.650000	0.86243	GCC	.	.		0.557	MPEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370027.1	NM_001039396		A	58979671	G	A	58979671	3	1	263	1	0	0	0	0	1	0	0	0	9732	1203	42	3	1486	3	MPEG1	11	58979671	Missense_Mutation	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	1903091	58979671	76026845	244	38618										
FADS3	3995	hgsc.bcm.edu	37	chr11	61641336	61641336	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gtcaccagacttcttcagggAcctgggaggtgggggtggca	17	9	3	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr11:61641336A>G	ENST00000278829.2	-	12	1440	c.1288T>C	c.(1288-1290)Tcc>Ccc	p.S430P	FADS3_ENST00000525588.1_Splice_Site_p.S402P|FADS3_ENST00000527697.1_Splice_Site_p.S315P|FADS3_ENST00000540820.1_3'UTR	NM_021727.3	NP_068373.1	Q9Y5Q0	FADS3_HUMAN	fatty acid desaturase 3	430					unsaturated fatty acid biosynthetic process (GO:0006636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water (GO:0016717)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						TTCTTCAGGGACCTGGGAGGT	0.607																																					p.S430P		Atlas-SNP	.											.	FADS3	29	.	0			c.T1288C						.						27	25	26					11																	61641336		2202	4298	6500	SO:0001630	splice_region_variant	3995	exon12			TCAGGGACCTGGG		CCDS8013.1	11q12-q13.1	2013-01-25			ENSG00000221968	ENSG00000221968	1.14.19.3	"Fatty acid desaturases"	3576	protein-coding gene	gene with protein product	"delta-9-desaturase"	606150		LLCDL3			Standard	NM_021727		Approved	CYB5RP	uc001nsm.3	Q9Y5Q0	OTTHUMG00000167500	ENST00000278829.2:c.1287-1T>C	chr11.hg19:g.61641336A>G		132.0	0.0		242.0	10.0	NM_021727	O60426	Missense_Mutation	SNP	ENST00000278829.2	hg19	CCDS8013.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	19.38|19.38	3.817282|3.817282	0.70912|0.70912	.|.	.|.	ENSG00000221968|ENSG00000221968	ENST00000527697;ENST00000278829;ENST00000525588|ENST00000525094	T;T;T|.	0.59083|.	1.88;0.29;0.3|.	4.78|4.78	3.64|3.64	0.41730|0.41730	.|.	.|.	.|.	.|.	.|.	T|T	0.77718|0.77718	0.4172|0.4172	M|M	0.90759|0.90759	3.145|3.145	0.80722|0.80722	D|D	1|1	D;D|.	0.62365|.	0.991;0.975|.	D;P|.	0.65874|.	0.939;0.905|.	T|T	0.78713|0.78713	-0.2097|-0.2097	9|5	0.48119|.	T|.	0.1|.	-10.1189|-10.1189	9.7867|9.7867	0.40681|0.40681	0.8455:0.0:0.0:0.1545|0.8455:0.0:0.0:0.1545	.|.	315;430|.	E9PKP8;Q9Y5Q0|.	.;FADS3_HUMAN|.	P|A	315;430;402|100	ENSP00000431533:S315P;ENSP00000278829:S430P;ENSP00000432206:S402P|.	ENSP00000278829:S430P|.	S|V	-|-	1|2	0|0	FADS3|FADS3	61397912|61397912	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.924000|0.924000	0.55760|0.55760	5.326000|5.326000	0.65875|0.65875	0.669000|0.669000	0.31146|0.31146	0.454000|0.454000	0.30748|0.30748	TCC|GTC	.	.		0.607	FADS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394836.1		Missense_Mutation	G	61641336	A	G	61641336	5	3	263	1	0	0	0	0	0	0	1	0	5372	289	10	2	53	2	FADS3	11	61641336	Splice_Site	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	2661665	61641336	73365180	245	38619										
SLC22A11	55867	hgsc.bcm.edu	37	chr11	64326710	64326710	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ctggggcctcctctcctaccGgtgagtgcctccgctcctcc	10	19	1	1	rs571324325		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr11:64326710G>A	ENST00000301891.4	+	2	871	c.497G>A	c.(496-498)cGg>cAg	p.R166Q	SLC22A11_ENST00000377581.3_Splice_Site_p.R166Q|SLC22A11_ENST00000377585.3_Splice_Site_p.R166Q|SLC22A11_ENST00000490834.1_Intron	NM_018484.2	NP_060954.1	Q9NSA0	S22AB_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 11	166					organic anion transport (GO:0015711)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|organic anion transmembrane transporter activity (GO:0008514)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	23					Aminohippurate(DB00345)|Aspartame(DB00168)|Benzylpenicillin(DB01053)|Bumetanide(DB00887)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefazolin(DB01327)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Ceftriaxone(DB01212)|Cimetidine(DB00501)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Doxycycline(DB00254)|Estradiol(DB00783)|Furosemide(DB00695)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Methotrexate(DB00563)|Minocycline(DB01017)|Novobiocin(DB01051)|Oxytetracycline(DB00595)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pravastatin(DB00175)|Probenecid(DB01032)|Salicylic acid(DB00936)|Tetracycline(DB00759)|Zidovudine(DB00495)	CTCTCCTACCGGTGAGTGCCT	0.587													G|||	1	0.000199681	8e-04	0	5008	,	,		15989	0		0	False		,,,				2504	0				p.R166Q		Atlas-SNP	.											.	SLC22A11	54	.	0			c.G497A						.						95	84	87					11																	64326710		2201	4297	6498	SO:0001630	splice_region_variant	55867	exon2			CCTACCGGTGAGT	AB026116	CCDS8074.1	11q13.3	2013-05-22	2008-01-11		ENSG00000168065	ENSG00000168065		"Solute carriers"	18120	protein-coding gene	gene with protein product		607097				10660625, 15576633, 17229912	Standard	NM_018484		Approved	OAT4	uc001oai.3	Q9NSA0	OTTHUMG00000045142	ENST00000301891.4:c.497+1G>A	chr11.hg19:g.64326710G>A		67.0	0.0		98.0	39.0	NM_018484	A8K426|Q53GR2|Q6ZP72|Q8NBU4	Missense_Mutation	SNP	ENST00000301891.4	hg19	CCDS8074.1	.	.	.	.	.	.	.	.	.	.	.	20.6	4.013927	0.75161	.	.	ENSG00000168065	ENST00000301891;ENST00000377585;ENST00000377581	T;T;T	0.68181	-0.31;-0.31;-0.31	3.37	2.43	0.29744	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	U	0.000000	T	0.81103	0.4753	M	0.91090	3.175	0.31483	N	0.666961	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.78974	-0.1992	10	0.87932	D	0	.	4.328	0.11050	0.1216:0.0:0.6521:0.2262	.	166;166;166	Q9NSA0-2;A6NCG2;Q9NSA0	.;.;S22AB_HUMAN	Q	166	ENSP00000301891:R166Q;ENSP00000366809:R166Q;ENSP00000366804:R166Q	ENSP00000301891:R166Q	R	+	2	0	SLC22A11	64083286	0.993000	0.37304	0.914000	0.36105	0.153000	0.21895	1.303000	0.33470	0.746000	0.32786	0.485000	0.47835	CGG	.	.		0.587	SLC22A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104886.4	NM_018484	Missense_Mutation	A	64326710	G	A	64326710	5	1	263	1	0	0	0	0	0	0	1	0	14457	1130	39	1	503	1	SLC22A11	11	64326710	Splice_Site	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	2685374	64326710	70679806	246	38620										
LTBP3	4054	hgsc.bcm.edu	37	chr11	65315205	65315205	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ccacgtgcaggcggtagccgCggttgcagtggcaattgtag	16	10	0	0	rs150534522		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr11:65315205C>G	ENST00000301873.5	-	13	2202	c.1934G>C	c.(1933-1935)cGc>cCc	p.R645P	LTBP3_ENST00000532932.1_Missense_Mutation_p.R75P|LTBP3_ENST00000536982.1_Missense_Mutation_p.R271P|LTBP3_ENST00000322147.4_Missense_Mutation_p.R645P|LTBP3_ENST00000529189.1_5'Flank	NM_001130144.2	NP_001123616.1	Q9NS15	LTBP3_HUMAN	latent transforming growth factor beta binding protein 3	645	Cys-rich.|EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|extracellular matrix organization (GO:0030198)|lung saccule development (GO:0060430)|negative regulation of bone mineralization (GO:0030502)|negative regulation of chondrocyte differentiation (GO:0032331)|positive regulation of bone resorption (GO:0045780)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of mesenchymal stem cell proliferation (GO:1902462)|transforming growth factor beta activation (GO:0036363)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|prostate(2)|upper_aerodigestive_tract(3)	23						GCGGTAGCCGCGGTTGCAGTG	0.711																																					p.R645P		Atlas-SNP	.											LTBP3,colon,carcinoma,0,1	LTBP3	55	.	0			c.G1934C						.						9	11	10					11																	65315205		2165	4255	6420	SO:0001583	missense	4054	exon13			TAGCCGCGGTTGC	AF135960	CCDS8103.1, CCDS44647.1	11q12	2011-10-20			ENSG00000168056	ENSG00000168056		"Latent transforming growth factor, beta binding proteins"	6716	protein-coding gene	gene with protein product		602090		LTBP2		7719025	Standard	NM_001164266		Approved		uc001oej.3	Q9NS15	OTTHUMG00000166575	ENST00000301873.5:c.1934G>C	chr11.hg19:g.65315205C>G	ENSP00000301873:p.Arg645Pro	34.0	0.0		40.0	5.0	NM_001130144	O15107|Q96HB9|Q9H7K2|Q9UFN4	Missense_Mutation	SNP	ENST00000301873.5	hg19	CCDS44647.1	.	.	.	.	.	.	.	.	.	.	C	11.99	1.804536	0.31869	.	.	ENSG00000168056	ENST00000322147;ENST00000301873;ENST00000532932;ENST00000536982;ENST00000530866	D;D;D;D;D	0.91945	-2.94;-2.94;-2.94;-2.94;-2.94	4.39	4.39	0.52855	EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.344897	0.30999	N	0.008453	D	0.84051	0.5387	N	0.01076	-1.035	0.30505	N	0.77	D;B;B;P;B;B	0.67145	0.996;0.013;0.005;0.8;0.004;0.114	P;B;B;B;B;B	0.62491	0.903;0.011;0.003;0.301;0.007;0.135	T	0.79176	-0.1911	10	0.18710	T	0.47	.	9.6673	0.39992	0.2078:0.7922:0.0:0.0	.	556;271;528;645;645;75	E9PKW1;F5GWC4;B9EG76;Q9NS15;Q9NS15-2;E9PJR2	.;.;.;LTBP3_HUMAN;.;.	P	645;645;75;271;556	ENSP00000326647:R645P;ENSP00000301873:R645P;ENSP00000435530:R75P;ENSP00000441912:R271P;ENSP00000435276:R556P	ENSP00000301873:R645P	R	-	2	0	LTBP3	65071781	0.006000	0.16342	1.000000	0.80357	0.802000	0.45316	-0.053000	0.11846	2.272000	0.75746	0.313000	0.20887	CGC	.	.		0.711	LTBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390538.1	NM_021070		G	65315205	C	G	65315205	3	3	263	1	0	0	0	0	1	0	0	0	9084	768	27	4	2041	4	LTBP3	11	65315205	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	988495	65315205	69691311	247	38621										
DKFZp761E198	91056	hgsc.bcm.edu	37	chr11	65547419	65547419	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gcaacaggctgagtggctggAcagggccttcctgccccagc	14	14	0	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr11:65547419A>G	ENST00000532090.2	-	2	755	c.545T>C	c.(544-546)gTc>gCc	p.V182A		NM_138368.4	NP_612377.4	Q2VPB7	AP5B1_HUMAN	adaptor-related protein complex 5, beta 1 subunit	182	Leu-rich.				endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-type membrane coat adaptor complex (GO:0030119)|lysosomal membrane (GO:0005765)				lung(1)	1						GAGTGGCTGGACAGGGCCTTC	0.692																																					p.V182A		Atlas-SNP	.											.	AP5B1	40	.	0			c.T545C						.						9	12	11					11																	65547419		1888	4108	5996	SO:0001583	missense	91056	exon2			GGCTGGACAGGGC	JQ313135	CCDS58146.1	11q13.1	2012-02-29			ENSG00000254470	ENSG00000254470			25104	protein-coding gene	gene with protein product		614367				22022230	Standard	NM_138368		Approved	PP1030, AP-5, DKFZp761E198	uc031qbm.1	Q2VPB7	OTTHUMG00000166593	ENST00000532090.2:c.545T>C	chr11.hg19:g.65547419A>G	ENSP00000454303:p.Val182Ala	115.0	0.0		100.0	6.0	NM_138368	A1L0S6|H6WUK2|Q0D2Q2|Q8N3J7|Q8WYH6	Missense_Mutation	SNP	ENST00000532090.2	hg19	CCDS58146.1																																																																																			.	.		0.692	AP5B1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390636.2	NM_138368		G	65547419	A	G	65547419	3	3	263	1	0	0	0	0	1	0	0	0	4545	275	10	2	2095	2	DKFZp761E198	11	65547419	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	232214	65547419	69459097	248	38622										
ANKRD13D	338692	hgsc.bcm.edu	37	chr11	67067337	67067337	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gtccttcctggggatggcgcAgcagcattcctcccacaccg	11	16	0	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr11:67067337A>G	ENST00000447274.2	+	9	1834	c.659A>G	c.(658-660)cAg>cGg	p.Q220R	ANKRD13D_ENST00000511455.2_Missense_Mutation_p.Q307R|ANKRD13D_ENST00000514166.1_Missense_Mutation_p.Q220R|ANKRD13D_ENST00000308440.6_Missense_Mutation_p.Q220R|ANKRD13D_ENST00000515828.1_5'Flank			Q6ZTN6	AN13D_HUMAN	ankyrin repeat domain 13 family, member D	220						endosome (GO:0005768)|plasma membrane (GO:0005886)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|ovary(1)	9			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)			GGGATGGCGCAGCAGCATTCC	0.687																																					p.Q307R		Atlas-SNP	.											.	ANKRD13D	71	.	0			c.A920G						.						55	50	51					11																	67067337		2200	4295	6495	SO:0001583	missense	338692	exon9			TGGCGCAGCAGCA	AK027313	CCDS31616.1, CCDS31616.2	11q13.2	2013-01-11		2005-08-09	ENSG00000172932	ENSG00000172932		"Ankyrin repeat domain containing"	27880	protein-coding gene	gene with protein product		615126					Standard	NM_207354		Approved		uc001okd.2	Q6ZTN6	OTTHUMG00000162929	ENST00000447274.2:c.659A>G	chr11.hg19:g.67067337A>G	ENSP00000402616:p.Gln220Arg	108.0	0.0		100.0	4.0	NM_207354	D6RCN6|Q0VAK0|Q0VGC3|Q6ZVD0|Q86SU1	Missense_Mutation	SNP	ENST00000447274.2	hg19		.	.	.	.	.	.	.	.	.	.	A	20.3	3.966936	0.74131	.	.	ENSG00000172932	ENST00000447274;ENST00000511455;ENST00000308440;ENST00000514166	T;T;T;T	0.45668	0.89;0.89;0.89;0.89	4.53	4.53	0.55603	.	0.085250	0.47455	D	0.000240	T	0.33411	0.0862	L	0.27053	0.805	0.45676	D	0.998597	P;P	0.47191	0.591;0.891	B;B	0.43082	0.399;0.407	T	0.13255	-1.0516	10	0.44086	T	0.13	-23.3046	13.6837	0.62502	1.0:0.0:0.0:0.0	.	307;220	Q6ZTN6-3;Q6ZTN6	.;AN13D_HUMAN	R	220;307;220;220	ENSP00000402616:Q220R;ENSP00000427130:Q307R;ENSP00000310874:Q220R;ENSP00000444404:Q220R	ENSP00000310874:Q220R	Q	+	2	0	ANKRD13D	66823913	1.000000	0.71417	1.000000	0.80357	0.681000	0.39784	8.780000	0.91799	1.905000	0.55150	0.260000	0.18958	CAG	.	.		0.687	ANKRD13D-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000371067.2	NM_207354		G	67067337	A	G	67067337	3	3	263	1	0	0	0	0	1	0	0	0	644	188	7	2	954	2	ANKRD13D	11	67067337	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	1519918	67067337	67939179	249	38623										
ARHGEF17	9828	hgsc.bcm.edu	37	chr11	73076917	73076917	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	agggacacaccggccacgtcCgcttcttggctgcagtccag	12	15	1	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr11:73076917C>A	ENST00000263674.3	+	20	6270	c.5920C>A	c.(5920-5922)Cgc>Agc	p.R1974S		NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	1974					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(2)	32						CGGCCACGTCCGCTTCTTGGC	0.647																																					p.R1974S		Atlas-SNP	.											.	ARHGEF17	117	.	0			c.C5920A						.						53	53	53					11																	73076917		2200	4293	6493	SO:0001583	missense	9828	exon20			CACGTCCGCTTCT	AF378754	CCDS8221.1	11q13.3	2011-11-16			ENSG00000110237	ENSG00000110237		"Rho guanine nucleotide exchange factors"	21726	protein-coding gene	gene with protein product	"Rho-specific guanine-nucleotide exchange factor 164 kDa", "tumor endothelial marker 4"					11559528, 12071859	Standard	NM_014786		Approved	TEM4, KIAA0337, p164-RhoGEF	uc001otu.3	Q96PE2	OTTHUMG00000167971	ENST00000263674.3:c.5920C>A	chr11.hg19:g.73076917C>A	ENSP00000263674:p.Arg1974Ser	72.0	0.0		90.0	28.0	NM_014786	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Missense_Mutation	SNP	ENST00000263674.3	hg19	CCDS8221.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.580432	0.86645	.	.	ENSG00000110237	ENST00000263674	T	0.34667	1.35	5.28	5.28	0.74379	WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.61677	0.2366	M	0.78049	2.395	0.80722	D	1	D	0.89917	1.0	D	0.67725	0.953	T	0.64356	-0.6427	10	0.62326	D	0.03	-21.8845	18.0725	0.89415	0.0:1.0:0.0:0.0	.	1974	Q96PE2	ARHGH_HUMAN	S	1974	ENSP00000263674:R1974S	ENSP00000263674:R1974S	R	+	1	0	ARHGEF17	72754565	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.172000	0.65003	2.755000	0.94549	0.655000	0.94253	CGC	.	.		0.647	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786		A	73076917	C	A	73076917	3	1	263	1	0	0	0	0	1	0	0	0	900	652	23	1	5998	1	ARHGEF17	11	73076917	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	6009580	73076917	61929599	250	38624										
FAM168A	23201	hgsc.bcm.edu	37	chr11	73179515	73179515	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gcacggggctgtaaacagggTtcattgtggaagactgagga	16	6	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr11:73179515T>C	ENST00000064778.4	-	2	289	c.5A>G	c.(4-6)aAc>aGc	p.N2S	FAM168A_ENST00000356467.4_Missense_Mutation_p.N2S|FAM168A_ENST00000450446.2_Missense_Mutation_p.N2S			Q92567	F168A_HUMAN	family with sequence similarity 168, member A	2										endometrium(3)|kidney(1)|lung(1)	5						GTAAACAGGGTTCATTGTGGA	0.458																																					p.N2S		Atlas-SNP	.											.	FAM168A	18	.	0			c.A5G						.						96	92	94					11																	73179515		1877	4096	5973	SO:0001583	missense	23201	exon2			ACAGGGTTCATTG	BC014932	CCDS41689.1, CCDS66165.1, CCDS73346.1	11q13.4	2008-06-11	2008-06-11	2008-06-11		ENSG00000054965			28999	protein-coding gene	gene with protein product	"tongue cancer chemotherapy resistance-associated protein 1"		"KIAA0280"	KIAA0280			Standard	XM_005273852		Approved	TCRP1	uc001oty.1	Q92567		ENST00000064778.4:c.5A>G	chr11.hg19:g.73179515T>C	ENSP00000064778:p.Asn2Ser	69.0	0.0		74.0	4.0	NM_015159	A2ICY2|A2ID81|Q86UG2	Missense_Mutation	SNP	ENST00000064778.4	hg19		.	.	.	.	.	.	.	.	.	.	T	21.9	4.210023	0.79240	.	.	ENSG00000054965	ENST00000064778;ENST00000450446;ENST00000356467	.	.	.	5.4	5.4	0.78164	.	0.090529	0.64402	D	0.000001	T	0.73814	0.3635	M	0.62723	1.935	0.46279	D	0.998968	D;P;P	0.56035	0.974;0.927;0.927	D;D;D	0.70487	0.969;0.953;0.953	T	0.69457	-0.5140	9	0.15066	T	0.55	.	14.9051	0.70711	0.0:0.0:0.0:1.0	.	2;2;2	Q92567-3;Q92567;Q92567-2	.;F168A_HUMAN;.	S	2	.	ENSP00000064778:N2S	N	-	2	0	FAM168A	72857163	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.405000	0.73272	2.165000	0.68154	0.460000	0.39030	AAC	.	.		0.458	FAM168A-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000397424.1	NM_015159		C	73179515	T	C	73179515	3	2	263	1	0	0	0	0	1	0	0	0	5490	1725	60	2	726	2	FAM168A	11	73179515	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	102598	73179515	61827001	251	38625										
MYO7A	4647	hgsc.bcm.edu	37	chr11	76858854	76858854	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ctccccgcaggaacactggaTctctccgcagaacgcaacgc	9	17	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr11:76858854T>C	ENST00000409709.3	+	4	415	c.143T>C	c.(142-144)aTc>aCc	p.I48T	MYO7A_ENST00000458637.2_Missense_Mutation_p.I48T|MYO7A_ENST00000409893.1_Missense_Mutation_p.I48T|MYO7A_ENST00000409619.2_Missense_Mutation_p.I37T	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	48					actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						GAACACTGGATCTCTCCGCAG	0.687																																					p.I48T		Atlas-SNP	.											.	MYO7A	164	.	0			c.T143C						.						34	38	37					11																	76858854		2145	4238	6383	SO:0001583	missense	4647	exon4			ACTGGATCTCTCC	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"A-kinase anchor proteins", "Myosins / Myosin superfamily : Class VII"	7606	protein-coding gene	gene with protein product		276903	"myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.143T>C	chr11.hg19:g.76858854T>C	ENSP00000386331:p.Ile48Thr	95.0	0.0		147.0	7.0	NM_001127179	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Missense_Mutation	SNP	ENST00000409709.3	hg19	CCDS53683.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.611471	0.87258	.	.	ENSG00000137474	ENST00000409709;ENST00000409893;ENST00000458637;ENST00000409619;ENST00000358342;ENST00000343356;ENST00000341717;ENST00000343419	T;T;T;T	0.71461	-0.57;-0.57;-0.57;-0.57	4.86	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.81536	0.4843	M	0.66378	2.025	0.80722	D	1	P;D;P	0.65815	0.945;0.995;0.893	P;D;P	0.66979	0.65;0.948;0.504	D	0.83844	0.0259	10	0.72032	D	0.01	.	14.6277	0.68635	0.0:0.0:0.0:1.0	.	48;48;48	B9A012;F8VUN5;Q13402	.;.;MYO7A_HUMAN	T	48;48;48;37;47;47;47;47	ENSP00000386331:I48T;ENSP00000386689:I48T;ENSP00000392185:I48T;ENSP00000386635:I37T	ENSP00000345075:I47T	I	+	2	0	MYO7A	76536502	1.000000	0.71417	1.000000	0.80357	0.806000	0.45545	7.522000	0.81844	2.041000	0.60428	0.374000	0.22700	ATC	.	.		0.687	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260		C	76858854	T	C	76858854	3	2	263	1	0	0	0	0	1	0	0	0	10091	1435	50	2	153	2	MYO7A	11	76858854	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	3679339	76858854	58147662	252	38626										
KDM4D	55693	hgsc.bcm.edu	37	chr11	94732090	94732104	+	In_Frame_Del	DEL	CTGGGCCCCTGTGCC	CTGGGCCCCTGTGCC	-													0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gtcaaggcttctgggtgcagCtgggcccctgtgccctaagt					rs373516844		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	CTGGGCCCCTGTGCC	CTGGGCCCCTGTGCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr11:94732090_94732104delCTGGGCCCCTGTGCC	ENST00000335080.5	+	3	2386_2400	c.1554_1568delCTGGGCCCCTGTGCC	c.(1552-1569)agctgggcccctgtgccc>agc	p.WAPVP519del	KDM4D_ENST00000536741.1_In_Frame_Del_p.WAPVP519del	NM_018039.2	NP_060509.2	Q6B0I6	KDM4D_HUMAN	lysine (K)-specific demethylase 4D	519					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	blood microparticle (GO:0072562)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			endometrium(4)|kidney(2)|large_intestine(2)|liver(2)|lung(16)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						CTGGGTGCAGCTGGGCCCCTGTGCCCTAAGTCCAC	0.549																																					p.518_523del		Atlas-Indel,Pindel	.											.	KDM4D	58	.	0			c.1553_1567del						.																																			SO:0001651	inframe_deletion	55693	exon3			.	AK001113	CCDS8302.1	11q21	2012-03-28	2009-04-06	2009-04-06	ENSG00000186280	ENSG00000186280		"Chromatin-modifying enzymes / K-demethylases"	25498	protein-coding gene	gene with protein product		609766	"jumonji domain containing 2D"	JMJD2D		15138608	Standard	NM_018039		Approved	FLJ10251	uc001pfe.3	Q6B0I6	OTTHUMG00000167838	ENST00000335080.5:c.1554_1568delCTGGGCCCCTGTGCC	chr11.hg19:g.94732090_94732104delCTGGGCCCCTGTGCC	ENSP00000334181:p.Trp519_Pro523del	125.0	0.0		135.0	20.0	NM_018039	B3KPC4|Q0VF39|Q9NT41|Q9NW76	In_Frame_Del	DEL	ENST00000335080.5	hg19	CCDS8302.1																																																																																			.	.		0.549	KDM4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396558.2	NM_018039		-	94732104	CTGGGCCCCTGTGCC	-	94732090	7	5	263	1	0	1	0	1	0	0	0	0	8140	796	28	0	1556	0	KDM4D	11	94732090	In_Frame_Del	DEL	CTGGGCCCCTGTGCC	TCGA-FV-A2QR-01A-11D-A20W-10	17873236	94732090	40274426	253	38627										
CADM1	23705	hgsc.bcm.edu	37	chr11	115049371	115049371	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	aagctttgcttacctttatgTctggcaaaatagcgccccag	8	11	1	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr11:115049371T>C	ENST00000452722.3	-	9	1223	c.1203A>G	c.(1201-1203)agA>agG	p.R401R	CADM1_ENST00000537140.1_5'UTR|CADM1_ENST00000536727.1_Silent_p.R402R|CADM1_ENST00000542447.2_Silent_p.R373R|CADM1_ENST00000331581.6_Silent_p.R430R|CADM1_ENST00000537058.1_Silent_p.R412R	NM_014333.3	NP_055148.3			cell adhesion molecule 1											cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(9)|ovary(2)|skin(1)	32	all_hematologic(175;0.0628)	all_cancers(61;2.98e-14)|all_epithelial(67;2.64e-08)|all_hematologic(158;0.000154)|Melanoma(852;0.000952)|Acute lymphoblastic leukemia(157;0.00101)|Breast(348;0.0102)|Medulloblastoma(222;0.0429)|Prostate(24;0.145)|all_neural(223;0.237)		BRCA - Breast invasive adenocarcinoma(274;5.01e-06)|Epithelial(105;0.000305)|all cancers(92;0.00303)		TACCTTTATGTCTGGCAAAAT	0.527																																					p.R401R		Atlas-SNP	.											.	CADM1	74	.	0			c.A1203G						.						174	165	168					11																	115049371		2201	4296	6497	SO:0001819	synonymous_variant	23705	exon9			TTTATGTCTGGCA	AB017563	CCDS8373.1, CCDS53711.1, CCDS73397.1, CCDS73398.1, CCDS73399.1	11q23.2	2013-01-29	2007-02-07	2007-02-07	ENSG00000182985	ENSG00000182985		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5951	protein-coding gene	gene with protein product	"nectin-like 2"	605686	"tumor suppressor in lung cancer 1", "immunoglobulin superfamily, member 4"	TSLC1, IGSF4		10610705	Standard	NM_014333		Approved	NECL2, ST17, BL2, SYNCAM, IGSF4A, Necl-2, SYNCAM1, RA175	uc001ppi.4	Q9BY67	OTTHUMG00000168202	ENST00000452722.3:c.1203A>G	chr11.hg19:g.115049371T>C		45.0	0.0		54.0	4.0	NM_014333		Silent	SNP	ENST00000452722.3	hg19	CCDS8373.1	.	.	.	.	.	.	.	.	.	.	T	5.760	0.324542	0.10900	.	.	ENSG00000182985	ENST00000545380	.	.	.	5.0	3.87	0.44632	.	.	.	.	.	T	0.61160	0.2325	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57888	-0.7733	4	.	.	.	.	10.4248	0.44371	0.0:0.0763:0.0:0.9237	.	.	.	.	A	372	.	.	T	-	1	0	CADM1	114554581	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.823000	0.55715	0.950000	0.37743	0.533000	0.62120	ACA	.	.		0.527	CADM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398753.2	NM_014333		C	115049371	T	C	115049371	2	2	263	1	0	0	0	0	0	0	0	1	2568	1664	58	2		2	CADM1	11	115049371	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	20317281	115049371	19957145	254	38628										
CEP164	22897	hgsc.bcm.edu	37	chr11	117222640	117222640	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gtcaacttctggggccattaAgaagaagaaaaaaaaaaagg	10	5	2	3			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr11:117222640A>C	ENST00000278935.3	+	5	476	c.329A>C	c.(328-330)aAg>aCg	p.K110T		NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	110	Interaction with ATRIP.|Lys-rich.			K -> N (in Ref. 5; AAH54015). {ECO:0000305}.	cilium assembly (GO:0042384)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(7)|large_intestine(12)|lung(18)|ovary(3)|prostate(3)	47	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		GGGGCCATTaagaagaagaaa	0.512																																					p.K110T		Atlas-SNP	.											.	CEP164	121	.	0			c.A329C						.						47	47	47					11																	117222640		2201	4296	6497	SO:0001583	missense	22897	exon4			CCATTAAGAAGAA	AB028975	CCDS31683.1	11q23.3	2014-02-20			ENSG00000110274	ENSG00000110274			29182	protein-coding gene	gene with protein product		614848				10470851, 14654843	Standard	NM_014956		Approved	KIAA1052, NPHP15	uc001prc.3	Q9UPV0	OTTHUMG00000167070	ENST00000278935.3:c.329A>C	chr11.hg19:g.117222640A>C	ENSP00000278935:p.Lys110Thr	57.0	0.0		87.0	6.0	NM_001271933	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	Missense_Mutation	SNP	ENST00000278935.3	hg19	CCDS31683.1	.	.	.	.	.	.	.	.	.	.	A	13.02	2.111278	0.37242	.	.	ENSG00000110274	ENST00000525734;ENST00000533153;ENST00000278935;ENST00000525416;ENST00000545330;ENST00000527609;ENST00000533570;ENST00000529538	T;T;T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19;-0.19;-0.19	5.95	5.95	0.96441	.	0.625053	0.15094	N	0.280936	T	0.73426	0.3585	L	0.60455	1.87	0.30319	N	0.787799	D;B;P;D	0.69078	0.997;0.264;0.873;0.996	D;B;P;D	0.66847	0.921;0.049;0.544;0.947	T	0.72093	-0.4394	10	0.52906	T	0.07	-16.947	10.3413	0.43879	0.9238:0.0:0.0762:0.0	.	110;64;110;110	E9PI34;B7Z884;Q9UPV0;Q9UPV0-2	.;.;CE164_HUMAN;.	T	110;64;110;64;64;110;110;110	ENSP00000436609:K110T;ENSP00000436034:K64T;ENSP00000278935:K110T;ENSP00000435759:K64T;ENSP00000436351:K110T;ENSP00000431302:K110T	ENSP00000278935:K110T	K	+	2	0	CEP164	116727850	1.000000	0.71417	0.997000	0.53966	0.353000	0.29299	5.568000	0.67385	2.279000	0.76181	0.533000	0.62120	AAG	.	.		0.512	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1	NM_014956		C	117222640	A	C	117222640	3	2	263	1	0	0	0	0	1	0	0	0	3251	72	3	5	339	5	CEP164	11	117222640	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	2173269	117222640	17783876	255	38629										
MLL	4297	hgsc.bcm.edu	37	chr11	118368716	118368716	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gtaaattgtgctttgtggtcAgcggaagtgtttgaagatga	14	3	1	3			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr11:118368716A>G	ENST00000389506.5	+	21	5721	c.5721A>G	c.(5719-5721)tcA>tcG	p.S1907S	KMT2A_ENST00000354520.4_Silent_p.S1869S|KMT2A_ENST00000534358.1_Silent_p.S1910S			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	1907					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										CTTTGTGGTCAGCGGAAGTGT	0.378																																					p.S1910S		Atlas-SNP	.											.	MLL	548	.	0			c.A5730G						.						162	151	155					11																	118368716		2200	4296	6496	SO:0001819	synonymous_variant	4297	exon21			GTGGTCAGCGGAA	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.5721A>G	chr11.hg19:g.118368716A>G		93.0	0.0		95.0	4.0	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Silent	SNP	ENST00000389506.5	hg19	CCDS31686.1																																																																																			.	.		0.378	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		G	118368716	A	G	118368716	2	3	263	1	0	0	0	0	0	0	0	1	9629	175	7	2		2	MLL	11	118368716	Silent	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	1146076	118368716	16637800	256	38630										
CXCR5	643	hgsc.bcm.edu	37	chr11	118764607	118764607	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tctgtgggctgggtcctgggGaccttcctctgcaaaactgt	13	11	2	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr11:118764607G>A	ENST00000292174.4	+	2	530	c.354G>A	c.(352-354)ggG>ggA	p.G118G	BCL9L_ENST00000334801.3_3'UTR	NM_001716.4|NM_032966.2	NP_001707.1|NP_116743.1	P32302	CXCR5_HUMAN	chemokine (C-X-C motif) receptor 5	118					B cell activation (GO:0042113)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of cytokinesis (GO:0032467)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-X-C chemokine receptor activity (GO:0016494)|G-protein coupled receptor activity (GO:0004930)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(5)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.62e-05)		GGGTCCTGGGGACCTTCCTCT	0.622																																					p.G118G		Atlas-SNP	.											.	CXCR5	34	.	0			c.G354A						.						81	72	75					11																	118764607		2200	4295	6495	SO:0001819	synonymous_variant	643	exon2			CCTGGGGACCTTC	X68829	CCDS8402.1	11q23.3	2012-08-08	2008-01-22	2008-01-22	ENSG00000160683	ENSG00000160683		"CD molecules", "GPCR / Class A : Chemokine receptors : C-X-C motif"	1060	protein-coding gene	gene with protein product		601613	"Burkitt lymphoma receptor 1, GTP-binding protein", "Burkitt lymphoma receptor 1, GTP binding protein (chemokine (C-X-C motif) receptor 5)"	BLR1		1425907	Standard	NM_001716		Approved	MDR15, CD185	uc001pue.4	P32302	OTTHUMG00000166345	ENST00000292174.4:c.354G>A	chr11.hg19:g.118764607G>A		173.0	0.0		177.0	42.0	NM_001716	Q14811	Silent	SNP	ENST00000292174.4	hg19	CCDS8402.1																																																																																			.	.		0.622	CXCR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389309.1	NM_001716		A	118764607	G	A	118764607	2	1	263	1	0	0	0	0	0	0	0	1	4096	1161	41	3		3	CXCR5	11	118764607	Silent	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	395891	118764607	16241909	257	38631										
BCL9L	283149	hgsc.bcm.edu	37	chr11	118769314	118769314	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cgccccccacgccccgctgcTtcatcagcatgaaattctgc	7	19	3	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr11:118769314T>C	ENST00000334801.3	-	8	5274	c.4310A>G	c.(4309-4311)aAg>aGg	p.K1437R	BCL9L_ENST00000526143.1_5'UTR	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	1437					canonical Wnt signaling pathway (GO:0060070)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell morphogenesis (GO:0022604)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|transcription coactivator activity (GO:0003713)			NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		GCCCCGCTGCTTCATCAGCAT	0.682																																					p.K1437R		Atlas-SNP	.											.	BCL9L	254	.	0			c.A4310G						.						20	20	20					11																	118769314		2191	4280	6471	SO:0001583	missense	283149	exon8			CGCTGCTTCATCA	AB094091	CCDS8403.1	11q23.3	2012-06-06				ENSG00000186174			23688	protein-coding gene	gene with protein product		609004				12964048	Standard	NM_182557		Approved	DLNB11	uc001pug.3	Q86UU0		ENST00000334801.3:c.4310A>G	chr11.hg19:g.118769314T>C	ENSP00000335320:p.Lys1437Arg	159.0	0.0		113.0	5.0	NM_182557	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Missense_Mutation	SNP	ENST00000334801.3	hg19	CCDS8403.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.124169	0.77436	.	.	ENSG00000186174	ENST00000334801;ENST00000526143;ENST00000525300;ENST00000431085	T	0.70282	-0.47	4.23	4.23	0.50019	.	0.163061	0.28635	N	0.014659	T	0.79246	0.4413	L	0.52573	1.65	0.58432	D	0.999995	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.986	T	0.80379	-0.1407	10	0.54805	T	0.06	-22.3707	13.6054	0.62044	0.0:0.0:0.0:1.0	.	1432;1437	Q86UU0-2;Q86UU0	.;BCL9L_HUMAN	R	1437;1400;683;1392	ENSP00000335320:K1437R	ENSP00000335320:K1437R	K	-	2	0	BCL9L	118274524	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	7.213000	0.77950	1.671000	0.50874	0.254000	0.18369	AAG	.	.		0.682	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557		C	118769314	T	C	118769314	3	2	263	1	0	0	0	0	1	0	0	0	1382	1609	56	2	193	2	BCL9L	11	118769314	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	4707	118769314	16237202	258	38632										
ABCG4	64137	hgsc.bcm.edu	37	chr11	119030961	119030961	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tgtgtccggtggtctactgcAgcattgtgtactggatgacg	14	8	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr11:119030961A>G	ENST00000449422.2	+	13	1650	c.1462A>G	c.(1462-1464)Agc>Ggc	p.S488G	ABCG4_ENST00000531739.1_Missense_Mutation_p.S488G|ABCG4_ENST00000307417.3_Missense_Mutation_p.S488G	NM_001142505.1	NP_001135977.1	Q9H172	ABCG4_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 4	488	ABC transmembrane type-2.				cholesterol efflux (GO:0033344)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cholesterol transporter activity (GO:0017127)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(28)|ovary(2)|prostate(1)|skin(1)	44	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		GGTCTACTGCAGCATTGTGTA	0.647																																					p.S488G		Atlas-SNP	.											.	ABCG4	77	.	0			c.A1462G						.						91	81	84					11																	119030961		2200	4295	6495	SO:0001583	missense	64137	exon13			TACTGCAGCATTG	AJ300465	CCDS8415.1	11q23	2012-03-14			ENSG00000172350	ENSG00000172350		"ATP binding cassette transporters / subfamily G"	13884	protein-coding gene	gene with protein product	"putative ABC transporter", "ATP-binding cassette, subfamily G, member 4"	607784				11435397	Standard	NM_022169		Approved	WHITE2	uc001pvs.3	Q9H172	OTTHUMG00000166169	ENST00000449422.2:c.1462A>G	chr11.hg19:g.119030961A>G	ENSP00000406874:p.Ser488Gly	108.0	0.0		141.0	6.0	NM_022169	A8K1B5|Q8WWH0|Q8WWH1|Q8WWH2	Missense_Mutation	SNP	ENST00000449422.2	hg19	CCDS8415.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.383268	0.82792	.	.	ENSG00000172350	ENST00000307417;ENST00000449422;ENST00000531739	T;T;T	0.72051	-0.62;-0.62;-0.62	5.2	5.2	0.72013	ABC-2 type transporter (1);	0.110385	0.85682	D	0.000000	T	0.73606	0.3608	M	0.67700	2.07	0.58432	D	0.999999	P	0.42010	0.768	P	0.45167	0.472	T	0.75442	-0.3316	10	0.45353	T	0.12	-27.4158	15.2835	0.73810	1.0:0.0:0.0:0.0	.	488	Q9H172	ABCG4_HUMAN	G	488	ENSP00000304111:S488G;ENSP00000406874:S488G;ENSP00000434318:S488G	ENSP00000304111:S488G	S	+	1	0	ABCG4	118536171	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.358000	0.79466	2.196000	0.70406	0.456000	0.33151	AGC	.	.		0.647	ABCG4-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388215.1	NM_022169		G	119030961	A	G	119030961	3	3	263	1	0	0	0	0	1	0	0	0	70	188	7	2	1508	2	ABCG4	11	119030961	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	261647	119030961	15975555	259	38633										
SORL1	6653	hgsc.bcm.edu	37	chr11	121420770	121420770	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ccctcctgtgccttgccctgTgggttctacttacaggagaa	10	13	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr11:121420770T>C	ENST00000260197.7	+	15	2282	c.2153T>C	c.(2152-2154)gTg>gCg	p.V718A		NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	718					cell death (GO:0008219)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902960)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of neurofibrillary tangle assembly (GO:1902997)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of tau-protein kinase activity (GO:1902948)|positive regulation of choline O-acetyltransferase activity (GO:1902771)|positive regulation of early endosome to recycling endosome transport (GO:1902955)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|positive regulation of protein localization to early endosome (GO:1902966)|post-Golgi vesicle-mediated transport (GO:0006892)|protein maturation (GO:0051604)|protein retention in Golgi apparatus (GO:0045053)|protein targeting (GO:0006605)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|receptor-mediated endocytosis (GO:0006898)|regulation of smooth muscle cell migration (GO:0014910)|signal transduction (GO:0007165)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|nuclear envelope lumen (GO:0005641)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)|beta-amyloid binding (GO:0001540)|low-density lipoprotein particle binding (GO:0030169)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(2)|lung(34)|ovary(5)|pancreas(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(2)	91		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		CCTTGCCCTGTGGGTTCTACT	0.502																																					p.V718A		Atlas-SNP	.											.	SORL1	218	.	0			c.T2153C						.						114	106	109					11																	121420770		2203	4299	6502	SO:0001583	missense	6653	exon15			GCCCTGTGGGTTC	Y08110	CCDS8436.1	11q23.2-q24.4	2014-06-05	2011-01-25		ENSG00000137642	ENSG00000137642		"Fibronectin type III domain containing"	11185	protein-coding gene	gene with protein product	"LDLR relative with 11 ligand-binding repeats"	602005	"chromosome 11 open reading frame 32", "sortilin-related receptor, L(DLR class) A repeats-containing"	C11orf32		9157966, 8940146	Standard	NM_003105		Approved	gp250, LR11, LRP9, SorLA, SorLA-1	uc001pxx.3	Q92673	OTTHUMG00000166057	ENST00000260197.7:c.2153T>C	chr11.hg19:g.121420770T>C	ENSP00000260197:p.Val718Ala	54.0	0.0		92.0	5.0	NM_003105	B2RNX7|Q92856	Missense_Mutation	SNP	ENST00000260197.7	hg19	CCDS8436.1	.	.	.	.	.	.	.	.	.	.	T	9.968	1.224614	0.22457	.	.	ENSG00000137642	ENST00000260197	D	0.90844	-2.74	5.38	3.03	0.35002	VPS10 (1);	0.262628	0.36740	N	0.002423	T	0.79441	0.4446	N	0.21097	0.63	0.80722	D	1	B	0.14805	0.011	B	0.12837	0.008	T	0.64943	-0.6288	10	0.07175	T	0.84	.	7.3355	0.26607	0.1289:0.0705:0.0:0.8006	.	718	Q92673	SORL_HUMAN	A	718	ENSP00000260197:V718A	ENSP00000260197:V718A	V	+	2	0	SORL1	120925980	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.837000	0.55820	0.338000	0.23692	0.533000	0.62120	GTG	.	.		0.502	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2	NM_003105		C	121420770	T	C	121420770	3	2	263	1	0	0	0	0	1	0	0	0	14949	1696	59	2	2211	2	SORL1	11	121420770	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	2389809	121420770	13585746	260	38634										
ARHGAP32	9743	hgsc.bcm.edu	37	chr11	128932247	128932247	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tcaataacagaaacaatgtcTcccacctaggagaatcaaaa	5	10	3	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr11:128932247T>C	ENST00000310343.9	-	9	848	c.849A>G	c.(847-849)ggA>ggG	p.G283G	ARHGAP32_ENST00000524655.1_Silent_p.G209G	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	283	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)|phosphatidylinositol binding (GO:0035091)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(28)|ovary(3)|prostate(6)|urinary_tract(3)	60						AAACAATGTCTCCCACCTAGG	0.383																																					p.G283G		Atlas-SNP	.											.	ARHGAP32	307	.	0			c.A849G						.						99	89	92					11																	128932247		1566	3579	5145	SO:0001819	synonymous_variant	9743	exon9			AATGTCTCCCACC	AB018255	CCDS31718.1, CCDS44769.1	11q24.3	2011-06-29			ENSG00000134909	ENSG00000134909		"Rho GTPase activating proteins"	17399	protein-coding gene	gene with protein product		608541				12446789, 12819203, 17663722	Standard	NM_014715		Approved	GRIT, KIAA0712, MGC1892, RICS, GC-GAP	uc009zcp.3	A7KAX9	OTTHUMG00000165774	ENST00000310343.9:c.849A>G	chr11.hg19:g.128932247T>C		43.0	0.0		47.0	4.0	NM_001142685	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Silent	SNP	ENST00000310343.9	hg19	CCDS44769.1																																																																																			.	.		0.383	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715		C	128932247	T	C	128932247	2	2	263	1	0	0	0	0	0	0	0	1	881	1538	54	2		2	ARHGAP32	11	128932247	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	7511477	128932247	6074269	261	38635										
SLC6A13	6540	hgsc.bcm.edu	37	chr12	333670	333670	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gcgggtaagcgatgaaagccAggccagggcctacgacaagg	16	10	0	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:333670A>G	ENST00000343164.4	-	10	1122	c.1070T>C	c.(1069-1071)cTg>cCg	p.L357P	SLC6A13_ENST00000539668.1_5'Flank|SLC6A13_ENST00000445055.2_Missense_Mutation_p.L265P	NM_016615.4	NP_057699.2	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 13	357					neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(1)	28	all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239)			GATGAAAGCCAGGCCAGGGCC	0.627																																					p.L357P		Atlas-SNP	.											.	SLC6A13	62	.	0			c.T1070C						.						88	77	81					12																	333670		2203	4298	6501	SO:0001583	missense	6540	exon10			AAAGCCAGGCCAG	U76343	CCDS8502.1, CCDS53729.1, CCDS58198.1	12p13.33	2013-07-19	2013-07-19		ENSG00000010379	ENSG00000010379		"Solute carriers"	11046	protein-coding gene	gene with protein product	"GABA transporter 2"	615097	"solute carrier family 6 (neurotransmitter transporter, GABA), member 13"				Standard	NM_001243392		Approved	GAT2	uc001qic.2	Q9NSD5	OTTHUMG00000168053	ENST00000343164.4:c.1070T>C	chr12.hg19:g.333670A>G	ENSP00000339260:p.Leu357Pro	152.0	0.0		176.0	63.0	NM_016615	B4DJL1|Q8TCC2|Q8WW56	Missense_Mutation	SNP	ENST00000343164.4	hg19	CCDS8502.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.118608	0.77323	.	.	ENSG00000010379	ENST00000445055;ENST00000313154;ENST00000343164	D;D	0.84873	-1.91;-1.91	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	D	0.96364	0.8814	H	0.99806	4.795	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.98476	1.0603	10	0.87932	D	0	.	15.8025	0.78463	1.0:0.0:0.0:0.0	.	265;336;357	B4DJL1;B4DJS3;Q9NSD5	.;.;S6A13_HUMAN	P	265;336;357	ENSP00000407104:L265P;ENSP00000339260:L357P	ENSP00000318097:L336P	L	-	2	0	SLC6A13	203931	1.000000	0.71417	1.000000	0.80357	0.621000	0.37620	9.339000	0.96797	2.138000	0.66242	0.368000	0.22195	CTG	.	.		0.627	SLC6A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397801.1	NM_016615		G	333670	A	G	333670	3	3	263	1	0	0	0	0	1	0	0	0	14691	188	7	2	762	2	SLC6A13	12	333670	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10		333670	133518225	262	38636										
CD163L1	283316	hgsc.bcm.edu	37	chr12	7510070	7510070	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tagcatcttcacaaccatggTtgggggtgtcatctgaaaga	11	8	4	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:7510070T>A	ENST00000313599.3	-	19	4349	c.4292A>T	c.(4291-4293)aAc>aTc	p.N1431I	CD163L1_ENST00000416109.2_Missense_Mutation_p.N1441I|CD163L1_ENST00000396630.1_Missense_Mutation_p.N1399I			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	1431						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						ACAACCATGGTTGGGGGTGTC	0.458																																					p.N1431I		Atlas-SNP	.											.	CD163L1	238	.	0			c.A4292T						.						79	79	79					12																	7510070		2203	4300	6503	SO:0001583	missense	283316	exon19			CCATGGTTGGGGG	AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"CD163 antigen-like 1"			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.4292A>T	chr12.hg19:g.7510070T>A	ENSP00000315945:p.Asn1431Ile	52.0	0.0		74.0	24.0	NM_174941	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Missense_Mutation	SNP	ENST00000313599.3	hg19	CCDS8577.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0|0	-2.765064|-2.765064	0.00082|0.00082	.|.	.|.	ENSG00000177675|ENSG00000177675	ENST00000313599;ENST00000416109;ENST00000396630|ENST00000539726	T;T;T|.	0.01963|.	5.0;5.0;4.53|.	1.07|1.07	-2.14|-2.14	0.07123|0.07123	.|.	.|.	.|.	.|.	.|.	T|T	0.13030|0.13030	0.0316|0.0316	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B;B|.	0.25169|.	0.119;0.036|.	B;B|.	0.23018|.	0.029;0.043|.	T|T	0.07009|0.07009	-1.0795|-1.0795	9|5	0.36615|.	T|.	0.2|.	.|.	0.8518|0.8518	0.01174|0.01174	0.2098:0.163:0.1491:0.4781|0.2098:0.163:0.1491:0.4781	.|.	1441;1431|.	E7EVK4;Q9NR16|.	.;C163B_HUMAN|.	I|H	1431;1441;1399|86	ENSP00000315945:N1431I;ENSP00000393474:N1441I;ENSP00000379871:N1399I|.	ENSP00000315945:N1431I|.	N|Q	-|-	2|3	0|2	CD163L1|CD163L1	7401337|7401337	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-2.776000|-2.776000	0.00776|0.00776	-3.939000|-3.939000	0.00089|0.00089	-3.420000|-3.420000	0.00038|0.00038	AAC|CAA	.	.		0.458	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941		A	7510070	T	A	7510070	3	1	263	1	0	0	0	0	1	0	0	0	2970	1725	60	4	73	4	CD163L1	12	7510070	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	7176400	7510070	126341825	263	38637										
PLCZ1	89869	hgsc.bcm.edu	37	chr12	18841123	18841123	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cctttgttagatgatgaatgAgtaagaggcaactggatacc	11	6	0	5			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:18841123A>G	ENST00000538330.1	-	9	1218	c.837T>C	c.(835-837)acT>acC	p.T279T	PLCZ1_ENST00000266505.7_Silent_p.T497T|PLCZ1_ENST00000435379.1_Silent_p.T302T|PLCZ1_ENST00000447925.2_Silent_p.T495T|PLCZ1_ENST00000534932.1_5'UTR|PLCZ1_ENST00000539875.1_Silent_p.T304T|PLCZ1_ENST00000541695.1_Silent_p.T360T					phospholipase C, zeta 1											NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	31	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241)					ATGATGAATGAGTAAGAGGCA	0.294																																					p.T497T		Atlas-SNP	.											PLCZ1,lower_third,carcinoma,0,1	PLCZ1	107	.	0			c.T1491C						.						93	102	99					12																	18841123		2203	4298	6501	SO:0001819	synonymous_variant	89869	exon13			TGAATGAGTAAGA	AY035866	CCDS8680.1	12p13.31	2013-01-10			ENSG00000139151	ENSG00000139151	3.1.4.11	"EF-hand domain containing"	19218	protein-coding gene	gene with protein product		608075				12117804	Standard	NM_033123		Approved	NYD-SP27, PLCzeta	uc021qvx.2	Q86YW0	OTTHUMG00000168937	ENST00000538330.1:c.837T>C	chr12.hg19:g.18841123A>G		29.0	0.0		44.0	2.0	NM_033123		Silent	SNP	ENST00000538330.1	hg19		.	.	.	.	.	.	.	.	.	.	A	0.757	-0.770799	0.02974	.	.	ENSG00000139151	ENST00000536023	.	.	.	4.43	-0.12	0.13539	.	.	.	.	.	T	0.34019	0.0883	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.30534	-0.9975	4	.	.	.	.	9.098	0.36651	0.429:0.0:0.571:0.0	.	.	.	.	P	67	.	.	S	-	1	0	PLCZ1	18732390	0.000000	0.05858	0.000000	0.03702	0.378000	0.30076	0.358000	0.20216	-0.099000	0.12263	0.260000	0.18958	TCA	.	.		0.294	PLCZ1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000401666.3	NM_033123		G	18841123	A	G	18841123	2	3	263	1	0	0	0	0	0	0	0	1	12053	291	11	2		2	PLCZ1	12	18841123	Silent	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	11331053	18841123	115010772	264	38638										
PLEKHA5	54477	hgsc.bcm.edu	37	chr12	19436349	19436349	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	agtatctgcagtgtaaccccTtccactcatgacaagacatt	6	12	2	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:19436349T>C	ENST00000299275.6	+	11	1437	c.1431T>C	c.(1429-1431)ccT>ccC	p.P477P	PLEKHA5_ENST00000359180.3_Silent_p.P477P|PLEKHA5_ENST00000424268.1_Silent_p.P369P|PLEKHA5_ENST00000543806.1_Silent_p.P369P|PLEKHA5_ENST00000309364.4_Silent_p.P477P|PLEKHA5_ENST00000538714.1_Silent_p.P477P|PLEKHA5_ENST00000429027.2_Silent_p.P483P|PLEKHA5_ENST00000317589.4_Silent_p.P477P|PLEKHA5_ENST00000355397.3_Silent_p.P477P|PLEKHA5_ENST00000510738.2_3'UTR|PLEKHA5_ENST00000539256.1_Silent_p.P235P	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5	477					reproductive system development (GO:0061458)	cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					GTGTAACCCCTTCCACTCATG	0.517																																					p.P483P	Pancreas(196;329 2193 11246 14234 19524)	Atlas-SNP	.											.	PLEKHA5	198	.	0			c.T1449C						.						85	79	81					12																	19436349		2203	4300	6503	SO:0001819	synonymous_variant	54477	exon12			AACCCCTTCCACT	AF302150	CCDS8682.1, CCDS44840.1, CCDS44840.2, CCDS55809.1, CCDS58213.1, CCDS58214.1	12p12	2013-01-10			ENSG00000052126	ENSG00000052126		"Pleckstrin homology (PH) domain containing"	30036	protein-coding gene	gene with protein product		607770				11214970, 11001876	Standard	NM_001143821		Approved	PEPP2, KIAA1686, FLJ10667	uc031qgo.1	Q9HAU0	OTTHUMG00000167921	ENST00000299275.6:c.1431T>C	chr12.hg19:g.19436349T>C		85.0	0.0		92.0	5.0	NM_001256470	A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	Silent	SNP	ENST00000299275.6	hg19	CCDS8682.1																																																																																			.	.		0.517	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	NM_019012		C	19436349	T	C	19436349	2	2	263	1	0	0	0	0	0	0	0	1	12068	1596	56	2		2	PLEKHA5	12	19436349	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	595226	19436349	114415546	265	38639										
ARNTL2	56938	hgsc.bcm.edu	37	chr12	27573461	27573461	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cagtgacatccagtggacccTctagcctttgatttttaact	7	11	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:27573461T>C	ENST00000266503.5	+	17	1925	c.1907T>C	c.(1906-1908)cTc>cCc	p.L636P	ARNTL2_ENST00000395901.2_Missense_Mutation_p.L599P|ARNTL2_ENST00000544915.1_Missense_Mutation_p.L602P|ARNTL2_ENST00000546179.1_3'UTR|RP11-165P7.1_ENST00000500498.2_RNA|ARNTL2_ENST00000261178.5_Missense_Mutation_p.L588P|ARNTL2_ENST00000311001.5_Missense_Mutation_p.L622P|ARNTL2_ENST00000542388.1_Missense_Mutation_p.L551P			Q8WYA1	BMAL2_HUMAN	aryl hydrocarbon receptor nuclear translocator-like 2	636					circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	E-box binding (GO:0070888)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(1)|skin(2)|urinary_tract(1)	21	Colorectal(261;0.0847)|Lung SC(9;0.184)					CAGTGGACCCTCTAGCCTTTG	0.398																																					p.L636P		Atlas-SNP	.											.	ARNTL2	54	.	0			c.T1907C						.						67	72	70					12																	27573461		2203	4300	6503	SO:0001583	missense	56938	exon17			GGACCCTCTAGCC	AF246961	CCDS8712.1, CCDS58219.1, CCDS58220.1, CCDS58221.1, CCDS58222.1	12p12.2-p11.2	2013-05-21			ENSG00000029153	ENSG00000029153		"Basic helix-loop-helix proteins"	18984	protein-coding gene	gene with protein product		614517				10864977, 10964693	Standard	NM_020183		Approved	BMAL2, MOP9, CLIF, PASD9, bHLHe6	uc001rht.2	Q8WYA1	OTTHUMG00000169257	ENST00000266503.5:c.1907T>C	chr12.hg19:g.27573461T>C	ENSP00000266503:p.Leu636Pro	74.0	0.0		67.0	5.0	NM_020183	B7Z429|F5H402|Q8WYA2|Q8WYA3|Q8WYA4|Q96J63|Q9H2M4|Q9NS70|Q9NYQ4|Q9NYQ5	Missense_Mutation	SNP	ENST00000266503.5	hg19	CCDS8712.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	16.51|16.51	3.144285|3.144285	0.57044|0.57044	.|.	.|.	ENSG00000029153|ENSG00000029153	ENST00000544915;ENST00000395901;ENST00000311001;ENST00000261178;ENST00000266503;ENST00000542388|ENST00000457040	T;T;T;T;T;T|.	0.20332|.	2.22;2.21;2.08;2.24;2.08;2.3|.	3.63|3.63	3.63|3.63	0.41609|0.41609	.|.	0.092201|.	0.41823|.	D|.	0.000819|.	T|T	0.72495|0.72495	0.3467|0.3467	M|M	0.79258|0.79258	2.445|2.445	0.80722|0.80722	D|D	1|1	D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D|.	0.97110|.	1.0;1.0;1.0;0.996;1.0|.	T|T	0.73898|0.73898	-0.3837|-0.3837	10|5	0.87932|.	D|.	0|.	.|.	11.2885|11.2885	0.49237|0.49237	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	602;599;588;622;636|.	Q8WYA1-5;Q8WYA1-3;Q8WYA1-4;Q8WYA1-2;Q8WYA1|.	.;.;.;.;BMAL2_HUMAN|.	P|P	602;599;622;588;636;551|588	ENSP00000442438:L602P;ENSP00000379238:L599P;ENSP00000312247:L622P;ENSP00000261178:L588P;ENSP00000266503:L636P;ENSP00000445836:L551P|.	ENSP00000261178:L588P|.	L|S	+|+	2|1	0|0	ARNTL2|ARNTL2	27464728|27464728	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.882000|0.882000	0.50991|0.50991	2.907000|2.907000	0.48743|0.48743	1.648000|1.648000	0.50643|0.50643	0.460000|0.460000	0.39030|0.39030	CTC|TCT	.	.		0.398	ARNTL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403162.1	NM_020183		C	27573461	T	C	27573461	3	2	263	1	0	0	0	0	1	0	0	0	968	1551	54	2	1973	2	ARNTL2	12	27573461	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	8137112	27573461	106278434	266	38640										
C12orf35	55196	hgsc.bcm.edu	37	chr12	32136525	32136525	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tcagcaaatctcacaggagtCaaggaatagtactgttgtga	10	7	3	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:32136525C>T	ENST00000312561.4	+	4	3050	c.2636C>T	c.(2635-2637)tCa>tTa	p.S879L	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	879																	TCACAGGAGTCAAGGAATAGT	0.368																																					p.S879L		Atlas-SNP	.											.	.	.	.	0			c.C2636T						.						113	104	107					12																	32136525		2203	4300	6503	SO:0001583	missense	55196	exon4			AGGAGTCAAGGAA	AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 35"	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.2636C>T	chr12.hg19:g.32136525C>T	ENSP00000310338:p.Ser879Leu	137.0	0.0		170.0	47.0	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Missense_Mutation	SNP	ENST00000312561.4	hg19	CCDS8725.2	.	.	.	.	.	.	.	.	.	.	C	15.50	2.853414	0.51270	.	.	ENSG00000174718	ENST00000312561	T	0.13420	2.59	5.26	3.11	0.35812	.	1.228570	0.05849	N	0.620894	T	0.13756	0.0333	L	0.48362	1.52	0.09310	N	1	B	0.28713	0.22	B	0.25614	0.062	T	0.29212	-1.0019	9	.	.	.	.	7.5112	0.27575	0.0:0.7065:0.1722:0.1213	.	879	Q9HCM1	CL035_HUMAN	L	879	ENSP00000310338:S879L	.	S	+	2	0	C12orf35	32027792	0.001000	0.12720	0.001000	0.08648	0.004000	0.04260	1.297000	0.33400	1.175000	0.42826	0.655000	0.94253	TCA	.	.		0.368	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169		T	32136525	C	T	32136525	3	4	263	1	0	0	0	0	1	0	0	0	1684	838	29	3	2638	3	C12orf35	12	32136525	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	4563064	32136525	101715370	267	38641										
SLC38A1	81539	hgsc.bcm.edu	37	chr12	46598344	46598344	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gaaaaaaaccatacagctcaAggaaaatccactagtatagc	6	9	1	0	rs148843987		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:46598344A>G	ENST00000398637.5	-	10	1370	c.676T>C	c.(676-678)Ttg>Ctg	p.L226L	SLC38A1_ENST00000549633.1_5'UTR|SLC38A1_ENST00000546893.1_Silent_p.L226L|SLC38A1_ENST00000439706.1_Silent_p.L226L|SLC38A1_ENST00000549049.1_Silent_p.L226L|SLC38A1_ENST00000552197.1_Silent_p.L226L	NM_001077484.1|NM_001278387.1|NM_001278388.1|NM_001278389.1|NM_030674.3	NP_001070952.1|NP_001265316.1|NP_001265317.1|NP_001265318.1|NP_109599.3	Q9H2H9	S38A1_HUMAN	solute carrier family 38, member 1	226					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|ion transport (GO:0006811)|neurotransmitter uptake (GO:0001504)|neutral amino acid transport (GO:0015804)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neutral amino acid transmembrane transporter activity (GO:0015175)|sodium:amino acid symporter activity (GO:0005283)	p.L226L(1)		NS(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(2)	23	Lung SC(27;0.137)|Renal(347;0.236)		all cancers(1;0.00805)|OV - Ovarian serous cystadenocarcinoma(5;0.0106)|Epithelial(2;0.0344)			ATACAGCTCAAGGAAAATCCA	0.299																																					p.L226L		Atlas-SNP	.											SLC38A1,hand,malignant_melanoma,0,1	SLC38A1	58	.	1	Substitution - coding silent(1)	skin(1)	c.T676C						.						163	154	157					12																	46598344		1819	4073	5892	SO:0001819	synonymous_variant	81539	exon10			AGCTCAAGGAAAA	AF271070	CCDS41774.1, CCDS61106.1	12q13.11	2013-05-22				ENSG00000111371		"Solute carriers"	13447	protein-coding gene	gene with protein product		608490				10891391	Standard	NM_030674		Approved	ATA1, NAT2, SAT1	uc001rpc.3	Q9H2H9		ENST00000398637.5:c.676T>C	chr12.hg19:g.46598344A>G		53.0	0.0		58.0	3.0	NM_030674	Q8NC61|Q8NCF8|Q96JX2|Q9H2Q2	Silent	SNP	ENST00000398637.5	hg19	CCDS41774.1																																																																																			.	.		0.299	SLC38A1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404218.2			G	46598344	A	G	46598344	2	3	263	1	0	0	0	0	0	0	0	1	14616	69	3	2		2	SLC38A1	12	46598344	Silent	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	14461819	46598344	87253551	268	38642										
DDN	23109	hgsc.bcm.edu	37	chr12	49391026	49391026	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gagccccaagatgcggaaagTgcgctcctccagtgtggagt	14	11	0	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:49391026T>C	ENST00000421952.2	-	2	1654	c.1633A>G	c.(1633-1635)Act>Gct	p.T545A	RP11-386G11.3_ENST00000549516.1_RNA|RP11-386G11.5_ENST00000552933.1_RNA|RP11-386G11.5_ENST00000547395.1_RNA|RP11-386G11.5_ENST00000552284.1_RNA|RP11-386G11.5_ENST00000547866.1_RNA	NM_015086.1	NP_055901.2	O94850	DEND_HUMAN	dendrin	545	Interaction with CD2AP and NPHS1. {ECO:0000250}.					cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)	8						ATGCGGAAAGTGCGCTCCTCC	0.697																																					p.T545A		Atlas-SNP	.											.	DDN	54	.	0			c.A1633G						.						15	18	17					12																	49391026		2179	4252	6431	SO:0001583	missense	23109	exon2			GGAAAGTGCGCTC	AB018292	CCDS31791.2	12q13	2008-02-05			ENSG00000181418	ENSG00000181418			24458	protein-coding gene	gene with protein product		610588					Standard	NM_015086		Approved	KIAA0749	uc001rsv.1	O94850	OTTHUMG00000156183	ENST00000421952.2:c.1633A>G	chr12.hg19:g.49391026T>C	ENSP00000390590:p.Thr545Ala	68.0	0.0		49.0	4.0	NM_015086		Missense_Mutation	SNP	ENST00000421952.2	hg19	CCDS31791.2	.	.	.	.	.	.	.	.	.	.	T	0.009	-1.820079	0.00595	.	.	ENSG00000181418	ENST00000421952	T	0.35789	1.29	3.77	0.45	0.16624	.	0.358287	0.20559	N	0.089941	T	0.09730	0.0239	N	0.02916	-0.46	0.23693	N	0.997094	B	0.02656	0.0	B	0.01281	0.0	T	0.28996	-1.0026	10	0.02654	T	1	-0.2369	2.6788	0.05087	0.2864:0.3595:0.0:0.354	.	545	O94850	DEND_HUMAN	A	545	ENSP00000390590:T545A	ENSP00000390590:T545A	T	-	1	0	DDN	47677293	0.652000	0.27349	0.998000	0.56505	0.082000	0.17680	-0.220000	0.09215	0.071000	0.16664	-0.366000	0.07423	ACT	.	.		0.697	DDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343335.1			C	49391026	T	C	49391026	3	2	263	1	0	0	0	0	1	0	0	0	4335	1696	59	2	506	2	DDN	12	49391026	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	2792682	49391026	84460869	269	38643										
NCKAP5L	57701	hgsc.bcm.edu	37	chr12	50189186	50189186	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	accttggttggtgacttggaAgggagcttggtggggctgct	18	6	0	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:50189186A>G	ENST00000335999.6	-	8	2658	c.2457T>C	c.(2455-2457)ccT>ccC	p.P819P		NM_001037806.3	NP_001032895.2	Q9HCH0	NCK5L_HUMAN	NCK-associated protein 5-like	815	Pro-rich.									central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(8)|prostate(2)	18						GTGACTTGGAAGGGAGCTTGG	0.637																																					p.P819P		Atlas-SNP	.											.	NCKAP5L	142	.	0			c.T2457C						.						71	75	74					12																	50189186		1956	4129	6085	SO:0001819	synonymous_variant	57701	exon8			CTTGGAAGGGAGC	AB046822	CCDS41781.2	12q13.12	2009-08-14	2009-08-14	2009-08-14	ENSG00000167566	ENSG00000167566			29321	protein-coding gene	gene with protein product		615104	"KIAA1602"	KIAA1602			Standard	NM_001037806		Approved		uc009zlk.2	Q9HCH0	OTTHUMG00000156969	ENST00000335999.6:c.2457T>C	chr12.hg19:g.50189186A>G		43.0	0.0		65.0	5.0	NM_001037806	Q2TB26|Q71RH1|Q8N4W1|Q96HX2	Silent	SNP	ENST00000335999.6	hg19	CCDS41781.2	.	.	.	.	.	.	.	.	.	.	A	7.397	0.632023	0.14322	.	.	ENSG00000167566	ENST00000433948	.	.	.	5.0	-5.43	0.02632	.	.	.	.	.	T	0.34571	0.0902	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40040	-0.9584	4	.	.	.	-8.5755	0.3128	0.00290	0.3303:0.2175:0.2375:0.2146	.	.	.	.	L	534	.	.	F	-	1	0	NCKAP5L	48475453	0.966000	0.33281	0.864000	0.33941	0.979000	0.70002	0.063000	0.14410	-0.871000	0.04042	0.459000	0.35465	TTC	.	.		0.637	NCKAP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346884.2	XM_035497		G	50189186	A	G	50189186	2	3	263	1	0	0	0	0	0	0	0	1	10233	59	3	2		2	NCKAP5L	12	50189186	Silent	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	798160	50189186	83662709	270	38644										
CSRNP2	81566	hgsc.bcm.edu	37	chr12	51457625	51457625	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ccacagccctcttcattgtcCgtgcggaaggggaggcttga	13	12	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:51457625C>A	ENST00000228515.1	-	5	1833	c.1536G>T	c.(1534-1536)acG>acT	p.T512T		NM_030809.2	NP_110436.1	Q9H175	CSRN2_HUMAN	cysteine-serine-rich nuclear protein 2	512					apoptotic process (GO:0006915)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|urinary_tract(1)	14						CTTCATTGTCCGTGCGGAAGG	0.557																																					p.T512T		Atlas-SNP	.											.	CSRNP2	47	.	0			c.G1536T						.						65	67	67					12																	51457625		2203	4300	6503	SO:0001819	synonymous_variant	81566	exon5			ATTGTCCGTGCGG	AJ298133	CCDS8807.1	12q13.11-q13.12	2012-04-17	2009-01-07	2009-01-07				"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	16006	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 72"		"chromosome 12 open reading frame 22", "family with sequence similarity 130, member A1"	C12orf22, FAM130A1		17726538	Standard	NM_030809		Approved	C12ORF2, TAIP-12, PPP1R72	uc001rxu.2	Q9H175		ENST00000228515.1:c.1536G>T	chr12.hg19:g.51457625C>A		154.0	0.0		152.0	71.0	NM_030809		Silent	SNP	ENST00000228515.1	hg19	CCDS8807.1																																																																																			.	.		0.557	CSRNP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404893.1			A	51457625	C	A	51457625	2	1	263	1	0	0	0	0	0	0	0	1	3966	639	23	1		1	CSRNP2	12	51457625	Silent	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	1268439	51457625	82394270	271	38645										
CSRNP2	81566	hgsc.bcm.edu	37	chr12	51457641	51457641	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tgtccgtgcggaaggggaggCttgagggggaccaggaaggg	22	6	0	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:51457641C>A	ENST00000228515.1	-	5	1817	c.1520G>T	c.(1519-1521)aGc>aTc	p.S507I		NM_030809.2	NP_110436.1	Q9H175	CSRN2_HUMAN	cysteine-serine-rich nuclear protein 2	507					apoptotic process (GO:0006915)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|urinary_tract(1)	14						GAAGGGGAGGCTTGAGGGGGA	0.552																																					p.S507I		Atlas-SNP	.											.	CSRNP2	47	.	0			c.G1520T						.						76	80	79					12																	51457641		2203	4300	6503	SO:0001583	missense	81566	exon5			GGGAGGCTTGAGG	AJ298133	CCDS8807.1	12q13.11-q13.12	2012-04-17	2009-01-07	2009-01-07				"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	16006	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 72"		"chromosome 12 open reading frame 22", "family with sequence similarity 130, member A1"	C12orf22, FAM130A1		17726538	Standard	NM_030809		Approved	C12ORF2, TAIP-12, PPP1R72	uc001rxu.2	Q9H175		ENST00000228515.1:c.1520G>T	chr12.hg19:g.51457641C>A	ENSP00000228515:p.Ser507Ile	166.0	0.0		169.0	76.0	NM_030809		Missense_Mutation	SNP	ENST00000228515.1	hg19	CCDS8807.1	.	.	.	.	.	.	.	.	.	.	C	2.280	-0.365020	0.05103	.	.	ENSG00000110925	ENST00000228515	T	0.44881	0.91	4.7	-5.93	0.02254	.	0.731516	0.13256	N	0.401675	T	0.25568	0.0622	N	0.19112	0.55	0.09310	N	0.999992	B	0.24963	0.115	B	0.32624	0.149	T	0.31998	-0.9923	10	0.59425	D	0.04	-0.9344	9.8188	0.40869	0.0:0.1756:0.117:0.7074	.	507	Q9H175	CSRN2_HUMAN	I	507	ENSP00000228515:S507I	ENSP00000228515:S507I	S	-	2	0	CSRNP2	49743908	0.028000	0.19301	0.029000	0.17559	0.059000	0.15707	-2.027000	0.01433	-1.102000	0.03023	-0.474000	0.04947	AGC	.	.		0.552	CSRNP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404893.1			A	51457641	C	A	51457641	3	1	263	1	0	0	0	0	1	0	0	0	3966	797	28	3	115	3	CSRNP2	12	51457641	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	16	51457641	82394254	272	38646										
CELA1	1990	hgsc.bcm.edu	37	chr12	51723604	51723604	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tcaccaagcaatggagggggCccccagagtcaccctgcagg	13	14	2	1	rs201129231		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:51723604C>G	ENST00000293636.1	-	7	663	c.623G>C	c.(622-624)gGc>gCc	p.G208A		NM_001971.5	NP_001962.3	Q9UNI1	CELA1_HUMAN	chymotrypsin-like elastase family, member 1	208	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				exocrine pancreas development (GO:0031017)|inflammatory response (GO:0006954)|multicellular organism growth (GO:0035264)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas morphogenesis (GO:0061113)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15						ATGGAGGGGGCCCCCAGAGTC	0.552																																					p.G208A		Atlas-SNP	.											.	CELA1	39	.	0			c.G623C						.						59	61	60					12																	51723604		2203	4300	6503	SO:0001583	missense	1990	exon7			AGGGGGCCCCCAG		CCDS8812.1	12q13	2012-10-02	2009-05-05	2009-05-05	ENSG00000139610	ENSG00000139610			3308	protein-coding gene	gene with protein product		130120	"elastase 1, pancreatic"	ELA1			Standard	NM_001971		Approved		uc001ryi.1	Q9UNI1	OTTHUMG00000167523	ENST00000293636.1:c.623G>C	chr12.hg19:g.51723604C>G	ENSP00000293636:p.Gly208Ala	46.0	0.0		35.0	4.0	NM_001971	Q5MLF0|Q6DJT0|Q6ISM6	Missense_Mutation	SNP	ENST00000293636.1	hg19	CCDS8812.1	.	.	.	.	.	.	.	.	.	.	C	14.99	2.699931	0.48307	.	.	ENSG00000139610	ENST00000293636	D	0.96300	-3.97	5.37	4.46	0.54185	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.85682	D	0.000000	D	0.97949	0.9325	M	0.83483	2.645	0.80722	D	1	D	0.76494	0.999	D	0.74023	0.982	D	0.98693	1.0697	10	0.87932	D	0	-20.8256	14.5125	0.67797	0.1481:0.8519:0.0:0.0	rs60311818	208	Q9UNI1	CELA1_HUMAN	A	208	ENSP00000293636:G208A	ENSP00000293636:G208A	G	-	2	0	CELA1	50009871	1.000000	0.71417	0.033000	0.17914	0.084000	0.17831	7.543000	0.82106	1.357000	0.45904	0.484000	0.47621	GGC	.	C|0.999;G|0.001		0.552	CELA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394901.1	NM_001971		G	51723604	C	G	51723604	3	3	263	1	0	0	0	0	1	0	0	0	3212	739	26	4	161	4	CELA1	12	51723604	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	265963	51723604	82128291	273	38647										
BAZ2A	11176	hgsc.bcm.edu	37	chr12	56995380	56995380	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gggagtgggttggtcctcagAaactgcagggggcggtgtgg	21	6	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:56995380A>G	ENST00000551812.1	-	20	4220	c.4027T>C	c.(4027-4029)Tct>Cct	p.S1343P	BAZ2A_ENST00000553222.1_5'Flank|BAZ2A_ENST00000179765.5_Missense_Mutation_p.S1311P|BAZ2A_ENST00000549884.1_Missense_Mutation_p.S1341P|BAZ2A_ENST00000379441.3_Missense_Mutation_p.S1313P	NM_013449.3	NP_038477.2	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	1343	Pro-rich.				chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA methylation (GO:0006306)|heterochromatin assembly involved in chromatin silencing (GO:0070869)|histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|histone H4 deacetylation (GO:0070933)|histone H4-K20 methylation (GO:0034770)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|nucleolus (GO:0005730)|rDNA heterochromatin (GO:0033553)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|lysine-acetylated histone binding (GO:0070577)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(15)|urinary_tract(1)	31						TGGTCCTCAGAAACTGCAGGG	0.557																																					p.S1343P		Atlas-SNP	.											.	BAZ2A	263	.	0			c.T4027C						.						39	46	44					12																	56995380		2022	4169	6191	SO:0001583	missense	11176	exon20			CCTCAGAAACTGC	AB032254	CCDS44924.1, CCDS73483.1	12q13.3	2013-01-28				ENSG00000076108		"Zinc fingers, PHD-type"	962	protein-coding gene	gene with protein product	"TTF-I interacting peptide 5"	605682				10662543, 11532953	Standard	XM_005268596		Approved	KIAA0314, TIP5, WALp3	uc001slq.1	Q9UIF9	OTTHUMG00000170332	ENST00000551812.1:c.4027T>C	chr12.hg19:g.56995380A>G	ENSP00000446880:p.Ser1343Pro	67.0	0.0		88.0	5.0	NM_013449	B3KN66|O00536|O15030|Q68DI8|Q96H26	Missense_Mutation	SNP	ENST00000551812.1	hg19	CCDS44924.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.86|15.86	2.957999|2.957999	0.53400|0.53400	.|.	.|.	ENSG00000076108|ENSG00000076108	ENST00000547453|ENST00000379441;ENST00000179765;ENST00000551812;ENST00000549787;ENST00000549884	.|T;T;T;T;T	.|0.71698	.|-0.3;-0.29;-0.3;-0.59;-0.3	5.33|5.33	5.33|5.33	0.75918|0.75918	.|.	.|0.265653	.|0.32081	.|N	.|0.006602	T|T	0.75474|0.75474	0.3854|0.3854	L|L	0.43152|0.43152	1.355|1.355	0.35549|0.35549	D|D	0.803695|0.803695	.|B;D;B;B	.|0.57899	.|0.089;0.981;0.158;0.022	.|B;P;B;B	.|0.61592	.|0.035;0.891;0.045;0.02	T|T	0.81230|0.81230	-0.1027|-0.1027	5|10	.|0.48119	.|T	.|0.1	.|.	11.9893|11.9893	0.53166|0.53166	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|1341;1343;1343;1316	.|F8VU39;Q9UIF9-3;Q9UIF9;Q9UIF9-2	.|.;.;BAZ2A_HUMAN;.	S|P	11|1313;1311;1343;279;1341	.|ENSP00000368754:S1313P;ENSP00000179765:S1311P;ENSP00000446880:S1343P;ENSP00000448760:S279P;ENSP00000447941:S1341P	.|ENSP00000179765:S1311P	F|S	-|-	2|1	0|0	BAZ2A|BAZ2A	55281647|55281647	0.916000|0.916000	0.31088|0.31088	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	1.877000|1.877000	0.39598|0.39598	2.155000|2.155000	0.67459|0.67459	0.533000|0.533000	0.62120|0.62120	TTC|TCT	.	.		0.557	BAZ2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408561.1	NM_013449		G	56995380	A	G	56995380	3	3	263	1	0	0	0	0	1	0	0	0	1331	246	9	2	1730	2	BAZ2A	12	56995380	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	5271776	56995380	76856515	274	38648										
LRP1	4035	hgsc.bcm.edu	37	chr12	57569808	57569808	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gcaacaccatcgccctggacTtccacctcagccagagcgcc	8	19	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:57569808T>C	ENST00000243077.3	+	24	4376	c.3910T>C	c.(3910-3912)Ttc>Ctc	p.F1304L		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	1304					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	CGCCCTGGACTTCCACCTCAG	0.602											OREG0021937	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F1304L		Atlas-SNP	.											.	LRP1	428	.	0			c.T3910C						.						146	113	124					12																	57569808		2203	4300	6503	SO:0001583	missense	4035	exon24			CTGGACTTCCACC	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"CD molecules", "Low density lipoprotein receptors"	6692	protein-coding gene	gene with protein product		107770	"alpha-2-macroglobulin receptor"	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.3910T>C	chr12.hg19:g.57569808T>C	ENSP00000243077:p.Phe1304Leu	106.0	0.0	1024	117.0	7.0	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	hg19	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.418626	0.83559	.	.	ENSG00000123384	ENST00000243077	D	0.91996	-2.95	4.9	4.9	0.64082	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	D	0.000001	D	0.95762	0.8621	M	0.84511	2.7	0.80722	D	1	P	0.52842	0.956	D	0.65010	0.931	D	0.95846	0.8870	10	0.52906	T	0.07	.	13.6488	0.62299	0.0:0.0:0.0:1.0	.	1304	Q07954	LRP1_HUMAN	L	1304	ENSP00000243077:F1304L	ENSP00000243077:F1304L	F	+	1	0	LRP1	55856075	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.868000	0.87116	2.063000	0.61619	0.533000	0.62120	TTC	.	.		0.602	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		C	57569808	T	C	57569808	3	2	263	1	0	0	0	0	1	0	0	0	8960	1609	56	2	4004	2	LRP1	12	57569808	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	574428	57569808	76282087	275	38649										
KIF5A	3798	hgsc.bcm.edu	37	chr12	57966045	57966045	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tggtggatgagctgtctcagAaggtggtaagtggtgtgcca	17	5	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:57966045A>G	ENST00000455537.2	+	14	1838	c.1564A>G	c.(1564-1566)Aag>Gag	p.K522E	KIF5A_ENST00000286452.5_Missense_Mutation_p.K433E	NM_004984.2	NP_004975.2	Q12840	KIF5A_HUMAN	kinesin family member 5A	522					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein localization (GO:0008104)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(32)|ovary(2)|prostate(2)|skin(2)	62						GCTGTCTCAGAAGGTGGTAAG	0.577																																					p.K522E		Atlas-SNP	.											.	KIF5A	143	.	0			c.A1564G						.						80	77	78					12																	57966045		2201	4298	6499	SO:0001583	missense	3798	exon14			TCTCAGAAGGTGG	U06698	CCDS8945.1	12q13.13	2011-07-15	2004-02-13			ENSG00000155980		"Kinesins"	6323	protein-coding gene	gene with protein product		602821	"spastic paraplegia 10 (autosomal dominant)"	SPG10		9858832, 10441583, 16489470	Standard	NM_004984		Approved	D12S1889, NKHC, MY050	uc001sor.1	Q12840	OTTHUMG00000170143	ENST00000455537.2:c.1564A>G	chr12.hg19:g.57966045A>G	ENSP00000408979:p.Lys522Glu	93.0	0.0		93.0	4.0	NM_004984	A6H8M5|Q4LE26	Missense_Mutation	SNP	ENST00000455537.2	hg19	CCDS8945.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.056761	0.76074	.	.	ENSG00000155980	ENST00000455537;ENST00000286452	D;D	0.81996	-1.56;-1.56	4.65	4.65	0.58169	.	0.000000	0.85682	D	0.000000	D	0.89949	0.6863	M	0.79805	2.47	0.58432	D	0.999994	D;D	0.63880	0.982;0.993	P;D	0.64687	0.889;0.928	D	0.90751	0.4657	10	0.54805	T	0.06	.	13.4909	0.61395	1.0:0.0:0.0:0.0	.	433;522	B7Z2M7;Q12840	.;KIF5A_HUMAN	E	522;433	ENSP00000408979:K522E;ENSP00000286452:K433E	ENSP00000286452:K433E	K	+	1	0	KIF5A	56252312	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.139000	0.94554	2.102000	0.63906	0.459000	0.35465	AAG	.	.		0.577	KIF5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407634.1	NM_004984		G	57966045	A	G	57966045	3	3	263	1	0	0	0	0	1	0	0	0	8314	247	9	2	1618	2	KIF5A	12	57966045	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	396237	57966045	75885850	276	38650										
TBK1	29110	hgsc.bcm.edu	37	chr12	64889483	64889483	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tttcttccttaaatagtgtaGaaaaactacaagtcctgtta	5	7	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:64889483G>C	ENST00000331710.5	+	15	1987	c.1648G>C	c.(1648-1650)Gaa>Caa	p.E550Q		NM_013254.3	NP_037386.1	Q9UHD2	TBK1_HUMAN	TANK-binding kinase 1	550					defense response to Gram-positive bacterium (GO:0050830)|defense response to virus (GO:0051607)|dendritic cell proliferation (GO:0044565)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of gene expression (GO:0010629)|negative regulation of type I interferon production (GO:0032480)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|response to virus (GO:0009615)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|type I interferon production (GO:0032606)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)	ATP binding (GO:0005524)|nucleic acid binding (GO:0003676)|phosphoprotein binding (GO:0051219)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)	20				GBM - Glioblastoma multiforme(28;0.0386)		AAATAGTGTAGAAAAACTACA	0.289																																					p.E550Q		Atlas-SNP	.											.	TBK1	149	.	0			c.G1648C						.						42	43	43					12																	64889483		2202	4300	6502	SO:0001583	missense	29110	exon15			AGTGTAGAAAAAC	AF191838	CCDS8968.1	12q14.2	2006-06-10			ENSG00000183735	ENSG00000183735			11584	protein-coding gene	gene with protein product		604834				10581243, 10783893	Standard	NM_013254		Approved	NAK	uc001ssc.2	Q9UHD2	OTTHUMG00000168796	ENST00000331710.5:c.1648G>C	chr12.hg19:g.64889483G>C	ENSP00000329967:p.Glu550Gln	58.0	0.0		109.0	50.0	NM_013254	A8K4S4|Q8IYV3|Q9NUJ5	Missense_Mutation	SNP	ENST00000331710.5	hg19	CCDS8968.1	.	.	.	.	.	.	.	.	.	.	G	6.703	0.498447	0.12762	.	.	ENSG00000183735	ENST00000331710	T	0.08807	3.05	4.77	4.77	0.60923	.	0.178480	0.50627	D	0.000115	T	0.19685	0.0473	L	0.32530	0.975	0.58432	D	0.999998	D	0.63880	0.993	D	0.72982	0.979	T	0.02015	-1.1229	9	.	.	.	-15.0624	18.6721	0.91516	0.0:0.0:1.0:0.0	.	550	Q9UHD2	TBK1_HUMAN	Q	550	ENSP00000329967:E550Q	.	E	+	1	0	TBK1	63175750	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	8.249000	0.89833	2.582000	0.87167	0.655000	0.94253	GAA	.	.		0.289	TBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401130.1	NM_013254		C	64889483	G	C	64889483	3	2	263	1	0	0	0	0	1	0	0	0	15652	943	33	4	1702	4	TBK1	12	64889483	Missense_Mutation	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	6923438	64889483	68962412	277	38651										
CAND1	55832	hgsc.bcm.edu	37	chr12	67701207	67701207	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tgcccgaagctcagtggttaCggctgtgaaatttacaattt	10	8	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:67701207C>T	ENST00000545606.1	+	11	3397	c.2960C>T	c.(2959-2961)aCg>aTg	p.T987M		NM_018448.3	NP_060918.2	Q86VP6	CAND1_HUMAN	cullin-associated and neddylation-dissociated 1	987					cell differentiation (GO:0030154)|negative regulation of catalytic activity (GO:0043086)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|protein ubiquitination (GO:0016567)|SCF complex assembly (GO:0010265)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				NS(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)	35			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)		TCAGTGGTTACGGCTGTGAAA	0.363																																					p.T987M		Atlas-SNP	.											.	CAND1	100	.	0			c.C2960T						.						72	67	69					12																	67701207		2203	4298	6501	SO:0001583	missense	55832	exon11			TGGTTACGGCTGT		CCDS8977.1	12q14	2008-02-05			ENSG00000111530	ENSG00000111530			30688	protein-coding gene	gene with protein product	"TBP interacting protein"	607727				10048485, 8954946	Standard	NM_018448		Approved	TIP120A, DKFZp434M1414, KIAA0829, TIP120	uc001stn.2	Q86VP6	OTTHUMG00000169060	ENST00000545606.1:c.2960C>T	chr12.hg19:g.67701207C>T	ENSP00000442318:p.Thr987Met	57.0	0.0		82.0	34.0	NM_018448	B2RAU3|O94918|Q6PIY4|Q8NDJ4|Q96JZ9|Q96T19|Q9BTC4|Q9H0G2|Q9P0H7|Q9UF85	Missense_Mutation	SNP	ENST00000545606.1	hg19	CCDS8977.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.2|28.2	4.897587|4.897587	0.91962|0.91962	.|.	.|.	ENSG00000111530|ENSG00000111530	ENST00000540047|ENST00000545606;ENST00000299218;ENST00000544619	.|T;T	.|0.20200	.|2.09;2.09	5.26|5.26	5.26|5.26	0.73747|0.73747	.|Armadillo-like helical (1);Armadillo-type fold (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.55162|0.55162	0.1903|0.1903	M|M	0.88842|0.88842	2.985|2.985	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.80764	.|0.994;0.935	T|T	0.62124|0.62124	-0.6920|-0.6920	5|9	.|.	.|.	.|.	-13.9614|-13.9614	19.2139|19.2139	0.93768|0.93768	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|819;987	.|Q86VP6-2;Q86VP6	.|.;CAND1_HUMAN	W|M	401|987;987;527	.|ENSP00000442318:T987M;ENSP00000444089:T527M	.|.	R|T	+|+	1|2	2|0	CAND1|CAND1	65987474|65987474	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.970000|0.970000	0.65996|0.65996	7.719000|7.719000	0.84751|0.84751	2.628000|2.628000	0.89032|0.89032	0.585000|0.585000	0.79938|0.79938	CGG|ACG	.	.		0.363	CAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402105.1	NM_018448		T	67701207	C	T	67701207	3	4	263	1	0	0	0	0	1	0	0	0	2617	536	19	1	3002	1	CAND1	12	67701207	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	2811724	67701207	66150688	278	38652										
NAV3	89795	hgsc.bcm.edu	37	chr12	78513703	78513703	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	caggatccaagtatccagatAttgcctcacccacatttcga	6	13	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:78513703A>G	ENST00000397909.2	+	15	3900	c.3727A>G	c.(3727-3729)Att>Gtt	p.I1243V	NAV3_ENST00000228327.6_Missense_Mutation_p.I1243V|NAV3_ENST00000266692.7_Missense_Mutation_p.I1243V|NAV3_ENST00000536525.2_Missense_Mutation_p.I1243V			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1243	Ser-rich.					membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						GTATCCAGATATTGCCTCACC	0.428										HNSCC(70;0.22)																											p.I1243V		Atlas-SNP	.											.	NAV3	506	.	0			c.A3727G						.						53	52	52					12																	78513703		1872	4117	5989	SO:0001583	missense	89795	exon15			CCAGATATTGCCT	AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.3727A>G	chr12.hg19:g.78513703A>G	ENSP00000381007:p.Ile1243Val	155.0	0.0		200.0	75.0	NM_014903	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.33|10.33	1.319165|1.319165	0.23994|0.23994	.|.	.|.	ENSG00000067798|ENSG00000067798	ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692|ENST00000552895	T;T;T;T|.	0.26223|.	1.9;1.9;1.88;1.75|.	5.31|5.31	5.31|5.31	0.75309|0.75309	.|.	0.000000|.	0.40554|.	U|.	0.001076|.	T|T	0.49355|0.49355	0.1552|0.1552	N|N	0.16567|0.16567	0.415|0.415	0.80722|0.80722	D|D	1|1	B;D;D;D|.	0.63880|.	0.089;0.993;0.988;0.991|.	B;D;D;D|.	0.74674|.	0.052;0.984;0.968;0.978|.	T|T	0.46386|0.46386	-0.9195|-0.9195	10|5	0.06494|.	T|.	0.89|.	-17.4833|-17.4833	15.2698|15.2698	0.73693|0.73693	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	1243;1243;1243;1243|.	E7EUC6;Q8IVL0-3;Q8IVL0;Q8IVL0-2|.	.;.;NAV3_HUMAN;.|.	V|C	1243|314	ENSP00000446132:I1243V;ENSP00000381007:I1243V;ENSP00000228327:I1243V;ENSP00000266692:I1243V|.	ENSP00000228327:I1243V|.	I|Y	+|+	1|2	0|0	NAV3|NAV3	77037834|77037834	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.936000|0.936000	0.57629|0.57629	9.017000|9.017000	0.93651|0.93651	2.010000|2.010000	0.58986|0.58986	0.533000|0.533000	0.62120|0.62120	ATT|TAT	.	.		0.428	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		G	78513703	A	G	78513703	3	3	263	1	0	0	0	0	1	0	0	0	10194	449	16	2	3785	2	NAV3	12	78513703	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	10812496	78513703	55338192	279	38653										
CEP290	80184	hgsc.bcm.edu	37	chr12	88444170	88444170	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	agatctgacattttgagctgTgtctctagatcttttatttt	7	6	3	4			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:88444170T>C	ENST00000552810.1	-	53	7513	c.7170A>G	c.(7168-7170)acA>acG	p.T2390T	RNA5SP364_ENST00000516938.1_RNA|CEP290_ENST00000309041.7_Silent_p.T2392T|CEP290_ENST00000397838.3_Silent_p.T1450T|CEP290_ENST00000547691.2_Silent_p.T1450T	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	2390					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						TTTTGAGCTGTGTCTCTAGAT	0.308																																					p.T2390T		Atlas-SNP	.											.	CEP290	195	.	0			c.A7170G						.						105	90	94					12																	88444170		1809	4074	5883	SO:0001819	synonymous_variant	80184	exon53			GAGCTGTGTCTCT	AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"Joubert syndrome 5", "nephrocystin-6", "cancer/testis antigen 87", "POC3 centriolar protein homolog (Chlamydomonas)", "Meckel syndrome, type 4"	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.7170A>G	chr12.hg19:g.88444170T>C		41.0	0.0		65.0	4.0	NM_025114	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Silent	SNP	ENST00000552810.1	hg19	CCDS55858.1																																																																																			.	.		0.308	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		C	88444170	T	C	88444170	2	2	263	1	0	0	0	0	0	0	0	1	3255	1683	59	2		2	CEP290	12	88444170	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	9930467	88444170	45407725	280	38654										
CEP290	80184	hgsc.bcm.edu	37	chr12	88486591	88486591	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ctgttccaccttctgtgcatCcaaattgattttggtaagct	7	10	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:88486591C>A	ENST00000552810.1	-	29	3671	c.3328G>T	c.(3328-3330)Gat>Tat	p.D1110Y	CEP290_ENST00000309041.7_Missense_Mutation_p.D1112Y|CEP290_ENST00000397838.3_Missense_Mutation_p.D170Y|CEP290_ENST00000547691.2_Missense_Mutation_p.D170Y	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	1110					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						TTCTGTGCATCCAAATTGATT	0.348																																					p.D1110Y		Atlas-SNP	.											.	CEP290	195	.	0			c.G3328T						.						203	192	195					12																	88486591		1900	4119	6019	SO:0001583	missense	80184	exon29			GTGCATCCAAATT	AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"Joubert syndrome 5", "nephrocystin-6", "cancer/testis antigen 87", "POC3 centriolar protein homolog (Chlamydomonas)", "Meckel syndrome, type 4"	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.3328G>T	chr12.hg19:g.88486591C>A	ENSP00000448012:p.Asp1110Tyr	176.0	0.0		177.0	64.0	NM_025114	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Missense_Mutation	SNP	ENST00000552810.1	hg19	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.466119	0.84425	.	.	ENSG00000198707	ENST00000547691;ENST00000552810;ENST00000309041;ENST00000397838	T;T;T;T	0.64438	0.48;-0.1;-0.1;0.48	5.83	5.83	0.93111	.	0.183068	0.56097	D	0.000025	T	0.64091	0.2567	L	0.34521	1.04	0.48901	D	0.999726	P	0.48503	0.911	P	0.49226	0.603	T	0.66428	-0.5926	10	0.72032	D	0.01	.	20.1133	0.97917	0.0:1.0:0.0:0.0	.	1110	O15078	CE290_HUMAN	Y	170;1110;1112;170	ENSP00000446905:D170Y;ENSP00000448012:D1110Y;ENSP00000308021:D1112Y;ENSP00000380938:D170Y	ENSP00000308021:D1112Y	D	-	1	0	CEP290	87010722	1.000000	0.71417	0.998000	0.56505	0.980000	0.70556	5.464000	0.66719	2.762000	0.94881	0.591000	0.81541	GAT	.	.		0.348	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		A	88486591	C	A	88486591	3	1	263	1	0	0	0	0	1	0	0	0	3255	855	30	3	4215	3	CEP290	12	88486591	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	42421	88486591	45365304	281	38655										
WSCD2	9671	hgsc.bcm.edu	37	chr12	108642083	108642083	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tgcagccctcaaagggcggaAcctaacgggtgtccccgatg	13	13	1	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:108642083A>G	ENST00000332082.4	+	10	2479	c.1661A>G	c.(1660-1662)aAc>aGc	p.N554S	WSCD2_ENST00000261400.3_Missense_Mutation_p.N574S|WSCD2_ENST00000549903.1_Missense_Mutation_p.N574S|WSCD2_ENST00000547525.1_Missense_Mutation_p.N554S			Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	554						integral component of membrane (GO:0016021)				breast(4)|endometrium(3)|kidney(1)|large_intestine(16)|liver(2)|lung(23)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	57						AAAGGGCGGAACCTAACGGGT	0.582																																					p.N554S		Atlas-SNP	.											.	WSCD2	125	.	0			c.A1661G						.						53	56	55					12																	108642083		2012	4191	6203	SO:0001583	missense	9671	exon9			GGCGGAACCTAAC		CCDS41828.1	12q23.3	2008-02-05				ENSG00000075035			29117	protein-coding gene	gene with protein product							Standard	NM_014653		Approved	KIAA0789	uc001tms.3	Q2TBF2		ENST00000332082.4:c.1661A>G	chr12.hg19:g.108642083A>G	ENSP00000331933:p.Asn554Ser	70.0	0.0		95.0	4.0	NM_014653	B2RN48|B4DES1|Q8IY35|Q9Y4B7	Missense_Mutation	SNP	ENST00000332082.4	hg19	CCDS41828.1	.	.	.	.	.	.	.	.	.	.	A	15.70	2.911584	0.52439	.	.	ENSG00000075035	ENST00000547525;ENST00000261400;ENST00000332082;ENST00000549903	T;T;T;T	0.36520	1.25;1.28;1.25;1.28	4.63	4.63	0.57726	.	0.047841	0.85682	D	0.000000	T	0.46698	0.1406	M	0.74881	2.28	0.47862	D	0.999532	P;P	0.51351	0.944;0.793	P;B	0.48270	0.572;0.138	T	0.52786	-0.8529	10	0.54805	T	0.06	-58.837	13.2043	0.59787	1.0:0.0:0.0:0.0	.	574;554	Q2TBF2-2;Q2TBF2	.;WSCD2_HUMAN	S	554;574;554;574	ENSP00000448047:N554S;ENSP00000261400:N574S;ENSP00000331933:N554S;ENSP00000447272:N574S	ENSP00000261400:N574S	N	+	2	0	WSCD2	107166213	1.000000	0.71417	0.996000	0.52242	0.573000	0.36030	5.832000	0.69337	1.726000	0.51525	0.533000	0.62120	AAC	.	.		0.582	WSCD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405554.1	NM_014653		G	108642083	A	G	108642083	3	3	263	1	0	0	0	0	1	0	0	0	17422	43	2	2	1691	2	WSCD2	12	108642083	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	20155492	108642083	25209812	282	38656										
DAO	1610	hgsc.bcm.edu	37	chr12	109288106	109288106	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ggctggggcgctacaacgagAccccctgctgcagccaggcc	14	16	0	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:109288106A>G	ENST00000228476.3	+	7	779	c.575A>G	c.(574-576)gAc>gGc	p.D192G	DAO_ENST00000551281.1_Missense_Mutation_p.D126G	NM_001917.4	NP_001908.3	P14920	OXDA_HUMAN	D-amino-acid oxidase	192					cellular nitrogen compound metabolic process (GO:0034641)|D-alanine catabolic process (GO:0055130)|D-serine catabolic process (GO:0036088)|D-serine metabolic process (GO:0070178)|dopamine biosynthetic process (GO:0042416)|glyoxylate metabolic process (GO:0046487)|leucine metabolic process (GO:0006551)|proline catabolic process (GO:0006562)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	cofactor binding (GO:0048037)|D-amino-acid oxidase activity (GO:0003884)|FAD binding (GO:0071949)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|prostate(2)|skin(1)	26					Flavin adenine dinucleotide(DB03147)	CTACAACGAGACCCCCTGCTG	0.552																																					p.D192G		Atlas-SNP	.											.	DAO	58	.	0			c.A575G						.						63	50	54					12																	109288106		2203	4300	6503	SO:0001583	missense	1610	exon7			AACGAGACCCCCT	D11370	CCDS9122.1	12q24.11	2013-09-20			ENSG00000110887	ENSG00000110887	1.4.3.3		2671	protein-coding gene	gene with protein product		124050				1356107, 8182053	Standard	NM_001917		Approved	DAMOX	uc001tnr.4	P14920	OTTHUMG00000169360	ENST00000228476.3:c.575A>G	chr12.hg19:g.109288106A>G	ENSP00000228476:p.Asp192Gly	98.0	0.0		92.0	4.0	NM_001917	B2R7I5|Q16758|Q8N6R2	Missense_Mutation	SNP	ENST00000228476.3	hg19	CCDS9122.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.198837	0.79015	.	.	ENSG00000110887	ENST00000551281;ENST00000228476;ENST00000547768;ENST00000547166	D;D;D;T	0.81659	-1.52;-1.52;-1.52;-0.26	5.51	5.51	0.81932	FAD dependent oxidoreductase (1);	0.000000	0.85682	D	0.000000	D	0.93028	0.7781	H	0.97131	3.945	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95116	0.8242	10	0.87932	D	0	-11.3905	14.4973	0.67698	1.0:0.0:0.0:0.0	.	192;175	P14920;Q7Z312	OXDA_HUMAN;.	G	126;192;69;192	ENSP00000446853:D126G;ENSP00000228476:D192G;ENSP00000449967:D69G;ENSP00000447104:D192G	ENSP00000228476:D192G	D	+	2	0	DAO	107812235	1.000000	0.71417	0.996000	0.52242	0.715000	0.41141	8.942000	0.92970	2.108000	0.64289	0.409000	0.27619	GAC	.	.		0.552	DAO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403682.1			G	109288106	A	G	109288106	3	3	263	1	0	0	0	0	1	0	0	0	4233	275	10	2	597	2	DAO	12	109288106	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	646023	109288106	24563789	283	38657										
ACACB	32	hgsc.bcm.edu	37	chr12	109613960	109613960	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tttgtcctttgcacccaggcAgcagaaagaattggttttcc	9	10	0	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:109613960A>G	ENST00000338432.7	+	9	1448	c.1329A>G	c.(1327-1329)gcA>gcG	p.A443A	ACACB_ENST00000377854.5_Silent_p.A443A|ACACB_ENST00000377848.3_Silent_p.A443A|ACACB_ENST00000543080.1_3'UTR			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	443	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.|Biotin carboxylation.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	GCACCCAGGCAGCAGAAAGAA	0.542																																					p.A443A		Atlas-SNP	.											.	ACACB	330	.	0			c.A1329G						.						240	253	248					12																	109613960		2203	4300	6503	SO:0001819	synonymous_variant	32	exon8			CCAGGCAGCAGAA	U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 2"	601557	"acetyl-Coenzyme A carboxylase beta"			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.1329A>G	chr12.hg19:g.109613960A>G		74.0	0.0		94.0	4.0	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Silent	SNP	ENST00000338432.7	hg19	CCDS31898.1																																																																																			.	.		0.542	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093		G	109613960	A	G	109613960	2	3	263	1	0	0	0	0	0	0	0	1	107	175	7	2		2	ACACB	12	109613960	Silent	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	325854	109613960	24237935	284	38658										
ANAPC7	51434	hgsc.bcm.edu	37	chr12	110812082	110812082	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gagtggcatccgtgggactcTcctccttctccatcttctgc	9	15	4	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:110812082T>C	ENST00000455511.3	-	11	1667	c.1667A>G	c.(1666-1668)gAg>gGg	p.E556G	ANAPC7_ENST00000481473.1_5'UTR	NM_016238.2	NP_057322.2	Q9UJX3	APC7_HUMAN	anaphase promoting complex subunit 7	556					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)			breast(3)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)	19						CGTGGGACTCTCCTCCTTCTC	0.577																																					p.E556G		Atlas-SNP	.											.	ANAPC7	68	.	0			c.A1667G						.						133	103	113					12																	110812082		2203	4300	6503	SO:0001583	missense	51434	exon11			GGACTCTCCTCCT	AF191340	CCDS9145.2, CCDS44971.1	12q13.12	2013-01-10			ENSG00000196510	ENSG00000196510		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	17380	protein-coding gene	gene with protein product		606949					Standard	NM_016238		Approved	APC7	uc001tqo.2	Q9UJX3	OTTHUMG00000157009	ENST00000455511.3:c.1667A>G	chr12.hg19:g.110812082T>C	ENSP00000394394:p.Glu556Gly	57.0	0.0		83.0	5.0	NM_016238	Q96AC4|Q96GF4|Q9BU24|Q9NT16	Missense_Mutation	SNP	ENST00000455511.3	hg19	CCDS9145.2	.	.	.	.	.	.	.	.	.	.	T	12.53	1.965737	0.34659	.	.	ENSG00000196510	ENST00000455511;ENST00000481473;ENST00000486321	T	0.65732	-0.17	5.88	4.71	0.59529	.	0.089296	0.85682	N	0.000000	T	0.37433	0.1003	N	0.03608	-0.345	0.80722	D	1	B	0.11235	0.004	B	0.06405	0.002	T	0.11641	-1.0579	10	0.25751	T	0.34	-29.7449	12.1758	0.54184	0.0:0.0673:0.0:0.9327	.	556	Q9UJX3	APC7_HUMAN	G	556;130;154	ENSP00000394394:E556G	ENSP00000394394:E556G	E	-	2	0	ANAPC7	109296465	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.973000	0.70456	1.016000	0.39470	0.459000	0.35465	GAG	.	.		0.577	ANAPC7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347075.3	NM_016238		C	110812082	T	C	110812082	3	2	263	1	0	0	0	0	1	0	0	0	606	1551	54	2	136	2	ANAPC7	12	110812082	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	1198122	110812082	23039813	285	38659										
ARPC3	10094	hgsc.bcm.edu	37	chr12	110874444	110874444	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ggaatgggaaaattagtgatTcccagcgtatacatttcttt	9	6	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:110874444T>C	ENST00000228825.7	-	5	443	c.297A>G	c.(295-297)ggA>ggG	p.G99G	RP11-478C19.2_ENST00000550231.1_RNA	NM_001278556.1|NM_005719.2	NP_001265485.1|NP_005710.1	O15145	ARPC3_HUMAN	actin related protein 2/3 complex, subunit 3, 21kDa	99					Arp2/3 complex-mediated actin nucleation (GO:0034314)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|membrane (GO:0016020)	structural constituent of cytoskeleton (GO:0005200)			lung(1)|ovary(1)	2						AATTAGTGATTCCCAGCGTAT	0.383																																					p.G99G		Atlas-SNP	.											.	ARPC3	7	.	0			c.A297G						.						130	122	125					12																	110874444		2203	4300	6503	SO:0001819	synonymous_variant	10094	exon5			AGTGATTCCCAGC	AF006086	CCDS9146.1	12q24	2011-07-06	2002-08-29		ENSG00000111229	ENSG00000111229		"Actin related protein 2/3 complex subunits"	706	protein-coding gene	gene with protein product		604225	"actin related protein 2/3 complex, subunit 3 (21 kD)"			9230079, 9359840	Standard	NM_001278556		Approved	p21-Arc, ARC21	uc001tqq.3	O15145	OTTHUMG00000134333	ENST00000228825.7:c.297A>G	chr12.hg19:g.110874444T>C		102.0	0.0		94.0	4.0	NM_005719	O00554	Silent	SNP	ENST00000228825.7	hg19	CCDS9146.1																																																																																			.	.		0.383	ARPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259487.2			C	110874444	T	C	110874444	2	2	263	1	0	0	0	0	0	0	0	1	972	1770	62	2		2	ARPC3	12	110874444	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	62362	110874444	22977451	286	38660										
ACAD10	80724	hgsc.bcm.edu	37	chr12	112186252	112186252	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	taaaaatcatccggcctctgAcggtgtatggactggaagat	11	8	2	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:112186252A>G	ENST00000313698.4	+	17	2772	c.2617A>G	c.(2617-2619)Acg>Gcg	p.T873A	ACAD10_ENST00000455480.2_Missense_Mutation_p.T904A|ACAD10_ENST00000413681.3_3'UTR|ACAD10_ENST00000392636.2_Missense_Mutation_p.T475A	NM_025247.5	NP_079523.3	Q6JQN1	ACD10_HUMAN	acyl-CoA dehydrogenase family, member 10	873						mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|hydrolase activity (GO:0016787)|transferase activity, transferring phosphorus-containing groups (GO:0016772)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(17)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(5)	47						CCGGCCTCTGACGGTGTATGG	0.587																																					p.T904A		Atlas-SNP	.											.	ACAD10	93	.	0			c.A2710G						.						66	69	68					12																	112186252		2203	4300	6503	SO:0001583	missense	80724	exon18			CCTCTGACGGTGT	AY323912	CCDS31903.1, CCDS44973.1	12q24.12	2012-10-02	2010-04-30		ENSG00000111271	ENSG00000111271			21597	protein-coding gene	gene with protein product		611181	"acyl-Coenzyme A dehydrogenase family, member 10"			15560374	Standard	NM_025247		Approved	MGC5601	uc009zvx.3	Q6JQN1	OTTHUMG00000169602	ENST00000313698.4:c.2617A>G	chr12.hg19:g.112186252A>G	ENSP00000325137:p.Thr873Ala	63.0	0.0		97.0	4.0	NM_001136538	G3XAJ0|Q8N828|Q8NAP2|Q96BX5	Missense_Mutation	SNP	ENST00000313698.4	hg19	CCDS31903.1	.	.	.	.	.	.	.	.	.	.	A	13.24	2.178374	0.38511	.	.	ENSG00000111271	ENST00000392636;ENST00000413681;ENST00000455480;ENST00000313698	D;D;D	0.98835	-5.17;-5.17;-5.17	5.87	3.41	0.39046	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA oxidase/dehydrogenase, central domain (1);	0.374922	0.25951	N	0.027258	D	0.96250	0.8777	L	0.39147	1.195	0.26255	N	0.978663	B;B;B	0.29988	0.116;0.008;0.264	B;B;B	0.33454	0.081;0.011;0.164	D	0.90202	0.4258	10	0.26408	T	0.33	.	10.3102	0.43704	0.7443:0.0:0.0:0.2557	.	904;873;873	G3XAJ0;Q6JQN1;Q6JQN1-2	.;ACD10_HUMAN;.	A	475;873;904;873	ENSP00000376411:T475A;ENSP00000389813:T904A;ENSP00000325137:T873A	ENSP00000325137:T873A	T	+	1	0	ACAD10	110670635	0.945000	0.32115	0.786000	0.31890	0.439000	0.31926	1.603000	0.36794	0.417000	0.25871	0.533000	0.62120	ACG	.	.		0.587	ACAD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368307.1	NM_025247		G	112186252	A	G	112186252	3	3	263	1	0	0	0	0	1	0	0	0	108	275	10	2	2776	2	ACAD10	12	112186252	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	1311808	112186252	21665643	287	38661										
RPH3A	22895	hgsc.bcm.edu	37	chr12	113319635	113319635	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ctacgttaagctgcacctccTgccgggagccagcaaggtac	11	14	0	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:113319635T>C	ENST00000389385.4	+	15	1807	c.1310T>C	c.(1309-1311)cTg>cCg	p.L437P	RPH3A_ENST00000543106.2_Missense_Mutation_p.L437P|RPH3A_ENST00000551052.1_Missense_Mutation_p.L433P|RPH3A_ENST00000415485.3_Missense_Mutation_p.L437P|RPH3A_ENST00000548866.1_Missense_Mutation_p.L388P|RPH3A_ENST00000447659.2_Missense_Mutation_p.L388P|RPH3A_ENST00000420983.2_Missense_Mutation_p.L437P|RPH3A_ENST00000549913.2_3'UTR	NM_001143854.1|NM_014954.3	NP_001137326.1|NP_055769.2	Q9Y2J0	RP3A_HUMAN	rabphilin 3A	437	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				intracellular protein transport (GO:0006886)	cell junction (GO:0030054)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylinositol phosphate binding (GO:1901981)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)|ovary(3)|prostate(4)|skin(6)|urinary_tract(1)	47				BRCA - Breast invasive adenocarcinoma(302;0.00453)		CTGCACCTCCTGCCGGGAGCC	0.592																																					p.L437P		Atlas-SNP	.											.	RPH3A	98	.	0			c.T1310C						.						93	87	89					12																	113319635		2203	4300	6503	SO:0001583	missense	22895	exon15			ACCTCCTGCCGGG	AB023202	CCDS31904.1, CCDS44979.1	12q24.13	2014-07-02	2014-07-02		ENSG00000089169	ENSG00000089169		"Synaptotagmins"	17056	protein-coding gene	gene with protein product		612159	"rabphilin 3A homolog (mouse)"			10231032, 7822236	Standard	NM_014954		Approved	KIAA0985, rabphilin, exophilin-1	uc001ttz.3	Q9Y2J0	OTTHUMG00000169713	ENST00000389385.4:c.1310T>C	chr12.hg19:g.113319635T>C	ENSP00000374036:p.Leu437Pro	99.0	0.0		111.0	5.0	NM_001143854	B7Z3C3|Q96AE0	Missense_Mutation	SNP	ENST00000389385.4	hg19	CCDS44979.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.249630	0.80024	.	.	ENSG00000089169	ENST00000543106;ENST00000389385;ENST00000447659;ENST00000551052;ENST00000415485;ENST00000548866;ENST00000420983;ENST00000549913;ENST00000552755	T;T;T;T;T;T;T	0.24350	1.86;1.86;1.86;1.86;1.86;1.86;1.86	5.34	5.34	0.76211	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.47455	D	0.000224	T	0.56529	0.1991	M	0.87456	2.885	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;1.0;0.999	T	0.64960	-0.6284	10	0.87932	D	0	.	14.329	0.66541	0.0:0.0:0.0:1.0	.	388;437;437;433	F8VP47;B7Z9Z7;Q9Y2J0;Q9Y2J0-2	.;.;RP3A_HUMAN;.	P	437;437;388;433;437;388;437;89;89	ENSP00000440384:L437P;ENSP00000374036:L437P;ENSP00000413254:L388P;ENSP00000448297:L433P;ENSP00000405357:L437P;ENSP00000450347:L388P;ENSP00000408889:L437P	ENSP00000374036:L437P	L	+	2	0	RPH3A	111804018	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.673000	0.83973	2.029000	0.59856	0.459000	0.35465	CTG	.	.		0.592	RPH3A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405561.1	NM_014954		C	113319635	T	C	113319635	3	2	263	1	0	0	0	0	1	0	0	0	13566	1580	55	2	1360	2	RPH3A	12	113319635	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	1133383	113319635	20532260	288	38662										
OAS3	4940	hgsc.bcm.edu	37	chr12	113384738	113384738	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gactgtcaactatggcttcgAggaccctgcagttgggcagt	13	10	1	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:113384738A>G	ENST00000228928.7	+	4	1006	c.827A>G	c.(826-828)gAg>gGg	p.E276G	OAS3_ENST00000546638.1_3'UTR|RP1-71H24.1_ENST00000552784.1_RNA	NM_006187.2	NP_006178.2	Q9Y6K5	OAS3_HUMAN	2'-5'-oligoadenylate synthetase 3, 100kDa	276	OAS domain 1.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|nucleobase-containing compound metabolic process (GO:0006139)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|skin(2)	27						TATGGCTTCGAGGACCCTGCA	0.572																																					p.E276G		Atlas-SNP	.											.	OAS3	63	.	0			c.A827G						.						81	84	83					12																	113384738		1991	4169	6160	SO:0001583	missense	4940	exon4			GCTTCGAGGACCC	AF063613	CCDS44981.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111331			8088	protein-coding gene	gene with protein product		603351	"2'-5'-oligoadenylate synthetase 3 (100 kD)"			9790745	Standard	NM_006187		Approved		uc001tug.3	Q9Y6K5	OTTHUMG00000169795	ENST00000228928.7:c.827A>G	chr12.hg19:g.113384738A>G	ENSP00000228928:p.Glu276Gly	141.0	0.0		150.0	6.0	NM_006187	Q2HJ14|Q9H3P5	Missense_Mutation	SNP	ENST00000228928.7	hg19	CCDS44981.1	.	.	.	.	.	.	.	.	.	.	A	15.55	2.867603	0.51588	.	.	ENSG00000111331	ENST00000228928;ENST00000323881	T	0.48522	0.81	4.23	3.08	0.35506	-oligoadenylate synthetase 1, domain 2/C-terminal (2);-5&apos (2);2&apos (2);	.	.	.	.	T	0.46964	0.1420	M	0.75150	2.29	0.18873	N	0.999987	B	0.21071	0.051	B	0.24394	0.053	T	0.49204	-0.8964	9	0.87932	D	0	.	6.4409	0.21849	0.8871:0.0:0.1129:0.0	.	276	Q9Y6K5	OAS3_HUMAN	G	276	ENSP00000228928:E276G	ENSP00000228928:E276G	E	+	2	0	OAS3	111869121	0.051000	0.20477	0.144000	0.22314	0.809000	0.45718	2.017000	0.40981	0.765000	0.33221	-0.250000	0.11733	GAG	.	.		0.572	OAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405920.1			G	113384738	A	G	113384738	3	3	263	1	0	0	0	0	1	0	0	0	10810	304	11	2	841	2	OAS3	12	113384738	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	65103	113384738	20467157	289	38663										
TPCN1	53373	hgsc.bcm.edu	37	chr12	113730811	113730811	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cgtcctggagctctaccgggAggcacggggggcctcctcgg	17	14	1	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:113730811A>G	ENST00000335509.6	+	26	2500	c.2186A>G	c.(2185-2187)gAg>gGg	p.E729G	TPCN1_ENST00000392569.4_Missense_Mutation_p.E661G|TPCN1_ENST00000550785.1_Missense_Mutation_p.E801G|TPCN1_ENST00000541517.1_Missense_Mutation_p.E801G	NM_017901.4	NP_060371.2	Q9ULQ1	TPC1_HUMAN	two pore segment channel 1	729					calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|voltage-gated calcium channel activity (GO:0005245)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(2)|prostate(3)|skin(3)|urinary_tract(1)	40						CTCTACCGGGAGGCACGGGGG	0.612																																					p.E801G		Atlas-SNP	.											.	TPCN1	109	.	0			c.A2402G						.						45	46	46					12																	113730811		2203	4300	6503	SO:0001583	missense	53373	exon27			ACCGGGAGGCACG	AB032995	CCDS31908.1, CCDS44985.1	12q24.21	2011-07-05			ENSG00000186815	ENSG00000186815		"Voltage-gated ion channels / Two-pore channels"	18182	protein-coding gene	gene with protein product		609666				10574461, 10753632, 16382101	Standard	XM_005253905		Approved	KIAA1169, FLJ20612, TPC1	uc001tux.3	Q9ULQ1	OTTHUMG00000169625	ENST00000335509.6:c.2186A>G	chr12.hg19:g.113730811A>G	ENSP00000335300:p.Glu729Gly	71.0	0.0		87.0	5.0	NM_001143819	A7E258|Q86XS9|Q8NC20	Missense_Mutation	SNP	ENST00000335509.6	hg19	CCDS31908.1	.	.	.	.	.	.	.	.	.	.	A	10.90	1.481676	0.26598	.	.	ENSG00000186815	ENST00000335509;ENST00000550785;ENST00000541517;ENST00000392569	T;T;T;T	0.46451	0.87;0.87;0.87;0.87	5.24	1.39	0.22231	.	0.394007	0.29034	N	0.013344	T	0.27063	0.0663	L	0.44542	1.39	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.0	T	0.11665	-1.0578	10	0.26408	T	0.33	-11.939	3.1944	0.06628	0.4881:0.0:0.3309:0.181	.	801;729	Q9ULQ1-3;Q9ULQ1	.;TPC1_HUMAN	G	729;801;801;661	ENSP00000335300:E729G;ENSP00000448083:E801G;ENSP00000438125:E801G;ENSP00000376350:E661G	ENSP00000335300:E729G	E	+	2	0	TPCN1	112215194	0.393000	0.25237	0.658000	0.29665	0.726000	0.41606	0.433000	0.21477	0.320000	0.23234	0.459000	0.35465	GAG	.	.		0.612	TPCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405156.3	NM_017901		G	113730811	A	G	113730811	3	3	263	1	0	0	0	0	1	0	0	0	16410	304	11	2	2504	2	TPCN1	12	113730811	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	346073	113730811	20121084	290	38664										
CIT	11113	hgsc.bcm.edu	37	chr12	120172998	120172998	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gtaagctgcatctctcgttcCgtgatctcccggcggagatg	12	12	2	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:120172998C>T	ENST00000261833.7	-	24	3049	c.2997G>A	c.(2995-2997)acG>acA	p.T999T	CIT_ENST00000392521.2_Silent_p.T1041T|CIT_ENST00000537607.1_5'UTR	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	999					cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		TCTCTCGTTCCGTGATCTCCC	0.498																																					p.T1041T		Atlas-SNP	.											.	CIT	535	.	0			c.G3123A						.						170	146	154					12																	120172998		2203	4300	6503	SO:0001819	synonymous_variant	11113	exon25			TCGTTCCGTGATC	AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966			1985	protein-coding gene	gene with protein product	"serine/threonine kinase 21"	605629	"citron (rho-interacting, serine/threonine kinase 21)"			9792683	Standard	NM_001206999		Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000261833.7:c.2997G>A	chr12.hg19:g.120172998C>T		371.0	0.0		450.0	155.0	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Silent	SNP	ENST00000261833.7	hg19	CCDS9192.1	.	.	.	.	.	.	.	.	.	.	C	12.82	2.053691	0.36277	.	.	ENSG00000122966	ENST00000392520;ENST00000546026	.	.	.	5.23	-10.5	0.00291	.	.	.	.	.	T	0.39489	0.1080	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53222	-0.8469	4	.	.	.	.	3.3542	0.07163	0.1814:0.2758:0.3843:0.1584	.	.	.	.	Q	627;25	.	.	R	-	2	0	CIT	118657381	0.000000	0.05858	0.083000	0.20561	0.966000	0.64601	-6.437000	0.00066	-4.113000	0.00072	-0.294000	0.09567	CGG	.	.		0.498	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174		T	120172998	C	T	120172998	2	4	263	1	0	0	0	0	0	0	0	1	3440	639	23	1		1	CIT	12	120172998	Silent	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	6442187	120172998	13678897	291	38665										
OASL	8638	hgsc.bcm.edu	37	chr12	121469367	121469367	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tccaggaccaccgcaggcctTgatcaggctcacatagacct	9	15	2	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:121469367T>C	ENST00000257570.5	-	3	805	c.535A>G	c.(535-537)Aag>Gag	p.K179E	OASL_ENST00000339275.5_Missense_Mutation_p.K179E	NM_003733.3	NP_003724.1	Q15646	OASL_HUMAN	2'-5'-oligoadenylate synthetase-like	179					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|thyroid hormone receptor binding (GO:0046966)|transferase activity (GO:0016740)			NS(1)|endometrium(3)|large_intestine(4)|lung(4)|skin(2)	14	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CCGCAGGCCTTGATCAGGCTC	0.552																																					p.K179E	Colon(192;517 2041 31392 31913 39966)	Atlas-SNP	.											.	OASL	49	.	0			c.A535G						.						78	76	76					12																	121469367		2203	4300	6503	SO:0001583	missense	8638	exon3			AGGCCTTGATCAG	AF063611	CCDS9211.1, CCDS9212.1, CCDS73536.1	12q24.2	2008-08-05			ENSG00000135114	ENSG00000135114			8090	protein-coding gene	gene with protein product		603281				10087211	Standard	NM_003733		Approved	TRIP14, p59OASL	uc001tzj.2	Q15646	OTTHUMG00000154981	ENST00000257570.5:c.535A>G	chr12.hg19:g.121469367T>C	ENSP00000257570:p.Lys179Glu	59.0	0.0		64.0	4.0	NM_198213	B2RAZ2|I1YDD2|O75686|Q17R95|Q9Y6K6|Q9Y6K7	Missense_Mutation	SNP	ENST00000257570.5	hg19	CCDS9211.1	.	.	.	.	.	.	.	.	.	.	C	7.540	0.660485	0.14645	.	.	ENSG00000135114	ENST00000257570;ENST00000339275	T;T	0.08896	3.04;3.04	5.52	-9.7	0.00521	-oligoadenylate synthetase 1, domain 2/C-terminal (2);-5&apos (2);2&apos (2);	2.095300	0.02164	N	0.059085	T	0.03871	0.0109	N	0.11131	0.1	0.09310	N	1	B;B	0.12013	0.005;0.004	B;B	0.15870	0.009;0.014	T	0.32587	-0.9901	10	0.06891	T	0.86	0.0239	12.1162	0.53866	0.0:0.5402:0.0995:0.3604	.	179;179	Q15646-2;Q15646	.;OASL_HUMAN	E	179	ENSP00000257570:K179E;ENSP00000341125:K179E	ENSP00000257570:K179E	K	-	1	0	OASL	119953750	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-1.390000	0.02528	-2.539000	0.00486	-2.397000	0.00225	AAG	.	.		0.552	OASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337875.2	NM_003733		C	121469367	T	C	121469367	3	2	263	1	0	0	0	0	1	0	0	0	10811	1821	63	2	1025	2	OASL	12	121469367	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	1296369	121469367	12382528	292	38666										
CLIP1	6249	hgsc.bcm.edu	37	chr12	122864937	122864937	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gccgtaggtgtcttcagagcTgtgcttccaggcttcaggat	13	10	3	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:122864937T>C	ENST00000540338.1	-	1	104	c.63A>G	c.(61-63)acA>acG	p.T21T	CLIP1_ENST00000361654.4_Silent_p.T21T|CLIP1_ENST00000302528.7_Silent_p.T21T|CLIP1_ENST00000358808.2_Silent_p.T21T|CLIP1_ENST00000537178.1_Silent_p.T21T			P30622	CLIP1_HUMAN	CAP-GLY domain containing linker protein 1	21					microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|positive regulation of microtubule polymerization (GO:0031116)|transport (GO:0006810)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|intermediate filament (GO:0005882)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	metal ion binding (GO:0046872)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|nucleic acid binding (GO:0003676)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|endometrium(4)|kidney(5)|large_intestine(16)|liver(1)|lung(21)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)		TCTTCAGAGCTGTGCTTCCAG	0.398																																					p.T21T		Atlas-SNP	.											.	CLIP1	126	.	0			c.A63G						.						115	111	113					12																	122864937		2203	4300	6503	SO:0001819	synonymous_variant	6249	exon2			CAGAGCTGTGCTT		CCDS9232.1, CCDS9233.1, CCDS58285.1	12q24.3	2013-01-17	2007-01-05	2007-01-05	ENSG00000130779	ENSG00000130779			10461	protein-coding gene	gene with protein product	"restin"	179838	"restin (Reed-Steinberg cell-expressed intermediate filament-associated protein)"	RSN		8222754	Standard	NM_001247997		Approved	CYLN1, CLIP170, CLIP, CLIP-170	uc001ucg.2	P30622	OTTHUMG00000168922	ENST00000540338.1:c.63A>G	chr12.hg19:g.122864937T>C		51.0	0.0		74.0	4.0	NM_002956	A0AVD3|Q17RS4|Q29RG0	Silent	SNP	ENST00000540338.1	hg19	CCDS58285.1																																																																																			.	.		0.398	CLIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401625.1	NM_002956		C	122864937	T	C	122864937	2	2	263	1	0	0	0	0	0	0	0	1	3534	1567	55	2		2	CLIP1	12	122864937	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	1395570	122864937	10986958	293	38667										
EP400	57634	hgsc.bcm.edu	37	chr12	132527997	132527997	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	attagaggagctagctgactTcatggagcaggtttgggcat	14	6	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:132527997T>C	ENST00000333577.4	+	34	6573	c.6464T>C	c.(6463-6465)tTc>tCc	p.F2155S	EP400_ENST00000332482.4_Missense_Mutation_p.F2082S|EP400_ENST00000389562.2_Missense_Mutation_p.F2118S|EP400_ENST00000330386.6_Missense_Mutation_p.F2038S|EP400_ENST00000389561.2_Missense_Mutation_p.F2119S			Q96L91	EP400_HUMAN	E1A binding protein p400	2155					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		CTAGCTGACTTCATGGAGCAG	0.408																																					p.F2119S		Atlas-SNP	.											.	EP400	370	.	0			c.T6356C						.						115	104	108					12																	132527997		2203	4300	6503	SO:0001583	missense	57634	exon33			CTGACTTCATGGA	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"trinucleotide repeat containing 12"	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.6464T>C	chr12.hg19:g.132527997T>C	ENSP00000333602:p.Phe2155Ser	82.0	0.0		82.0	4.0	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Missense_Mutation	SNP	ENST00000333577.4	hg19		.	.	.	.	.	.	.	.	.	.	T	11.83	1.756523	0.31137	.	.	ENSG00000183495	ENST00000333577;ENST00000389561;ENST00000389562;ENST00000332482;ENST00000330386;ENST00000541296	D;D;D;D;D	0.89875	-2.58;-2.57;-2.57;-2.57;-2.57	5.74	5.74	0.90152	.	0.169215	0.50627	D	0.000107	D	0.88153	0.6360	L	0.51422	1.61	0.40413	D	0.979764	P;P;P	0.45827	0.867;0.867;0.867	B;B;B	0.44044	0.439;0.439;0.439	D	0.89987	0.4105	10	0.87932	D	0	.	16.0315	0.80582	0.0:0.0:0.0:1.0	.	2119;2038;2118	Q96L91-2;Q96L91-4;Q96L91-5	.;.;.	S	2155;2119;2118;2082;2038;2119	ENSP00000333602:F2155S;ENSP00000374212:F2119S;ENSP00000374213:F2118S;ENSP00000331737:F2082S;ENSP00000330620:F2038S	ENSP00000330620:F2038S	F	+	2	0	EP400	131093950	1.000000	0.71417	0.997000	0.53966	0.355000	0.29361	7.305000	0.78891	2.186000	0.69663	0.455000	0.32223	TTC	.	.		0.408	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		C	132527997	T	C	132527997	3	2	263	1	0	0	0	0	1	0	0	0	5151	1783	62	2	6479	2	EP400	12	132527997	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	9663060	132527997	1323898	294	38668										
P2RX2	22953	hgsc.bcm.edu	37	chr12	133196677	133196677	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ccggtggaagatggggcctcTgtcaggtgcacctgcgcccc	15	14	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr12:133196677T>C	ENST00000389110.3	+	5	586	c.549T>C	c.(547-549)tcT>tcC	p.S183S	P2RX2_ENST00000350048.5_Silent_p.S159S|P2RX2_ENST00000348800.5_Silent_p.S183S|P2RX2_ENST00000352418.4_Silent_p.S111S|P2RX2_ENST00000351222.4_Silent_p.S91S|P2RX2_ENST00000449132.2_Missense_Mutation_p.C148R|P2RX2_ENST00000343948.4_Silent_p.S183S	NM_170682.2|NM_170683.2|NM_174873.1	NP_733782.1|NP_733783.1|NP_777362.1	Q9UBL9	P2RX2_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 2	183					behavioral response to pain (GO:0048266)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of hypoxic conditions in blood by carotid body chemoreceptor signaling (GO:0003029)|ion transmembrane transport (GO:0034220)|neuromuscular junction development (GO:0007528)|neuromuscular synaptic transmission (GO:0007274)|neuronal action potential (GO:0019228)|peristalsis (GO:0030432)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|response to ATP (GO:0033198)|response to carbohydrate (GO:0009743)|response to hypoxia (GO:0001666)|sensory perception of sound (GO:0007605)|sensory perception of taste (GO:0050909)|skeletal muscle fiber development (GO:0048741)|urinary bladder smooth muscle contraction (GO:0014832)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|dendritic spine (GO:0043197)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|cadmium ion binding (GO:0046870)|cobalt ion binding (GO:0050897)|copper ion binding (GO:0005507)|drug binding (GO:0008144)|extracellular ATP-gated cation channel activity (GO:0004931)|identical protein binding (GO:0042802)|ligand-gated ion channel activity (GO:0015276)|mercury ion binding (GO:0045340)|nickel cation binding (GO:0016151)|phosphatidylinositol binding (GO:0035091)|purinergic nucleotide receptor activity (GO:0001614)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|kidney(2)|large_intestine(2)|liver(2)|lung(8)|ovary(1)|prostate(3)	20	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0767)		OV - Ovarian serous cystadenocarcinoma(86;2.32e-08)|Epithelial(86;8.62e-08)|all cancers(50;4.5e-06)		ATGGGGCCTCTGTCAGGTGCA	0.677																																					p.S183S		Atlas-SNP	.											.	P2RX2	49	.	0			c.T549C						.						11	10	11					12																	133196677		2193	4290	6483	SO:0001819	synonymous_variant	22953	exon5			GGCCTCTGTCAGG	AF109387	CCDS31930.1, CCDS31931.1, CCDS31932.1, CCDS31933.1, CCDS31934.1, CCDS31935.1, CCDS61286.1, CCDS73548.1	12q24.33	2013-03-22			ENSG00000187848	ENSG00000187848		"Purinergic receptors", "Ligand-gated ion channels / Purinergic receptors, ionotropic"	15459	protein-coding gene	gene with protein product		600844	"deafness, autosomal dominant 41"	DFNA41		10570044, 7523952, 23345450	Standard	XM_005266154		Approved	P2X2	uc001ukk.1	Q9UBL9	OTTHUMG00000168018	ENST00000389110.3:c.549T>C	chr12.hg19:g.133196677T>C		94.0	0.0		96.0	4.0	NM_170683	A6NGB4|A6NH93|A6NHC2|A6NHU3|A6NIG9|Q6V9R6|Q9NR37|Q9NR38|Q9UHD5|Q9UHD6|Q9UHD7|Q9Y637|Q9Y638	Silent	SNP	ENST00000389110.3	hg19	CCDS31931.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	7.770|7.770	0.707287|0.707287	0.15239|0.15239	.|.	.|.	ENSG00000187848|ENSG00000187848	ENST00000449132|ENST00000542301;ENST00000536121;ENST00000535910	T|.	0.17370|.	2.28|.	4.78|4.78	-9.55|-9.55	0.00569|0.00569	.|.	.|.	.|.	.|.	.|.	T|T	0.14874|0.14874	0.0359|0.0359	.|.	.|.	.|.	0.26071|0.26071	N|N	0.981224|0.981224	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	T|T	0.06826|0.06826	-1.0805|-1.0805	8|4	0.87932|.	D|.	0|.	-10.4783|-10.4783	1.2559|1.2559	0.01991|0.01991	0.2128:0.2955:0.258:0.2337|0.2128:0.2955:0.258:0.2337	.|.	148|.	Q9UBL9-7|.	.|.	R|P	148|194;169;139	ENSP00000405531:C148R|.	ENSP00000405531:C148R|.	C|L	+|+	1|2	0|0	P2RX2|P2RX2	131706750|131706750	0.053000|0.053000	0.20554|0.20554	0.000000|0.000000	0.03702|0.03702	0.256000|0.256000	0.26092|0.26092	-0.742000|-0.742000	0.04850|0.04850	-4.223000|-4.223000	0.00063|0.00063	-2.060000|-2.060000	0.00399|0.00399	TGT|CTG	.	.		0.677	P2RX2-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397542.1			C	133196677	T	C	133196677	2	2	263	1	0	0	0	0	0	0	0	1	11349	1567	55	2		2	P2RX2	12	133196677	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	668680	133196677	655218	295	38669										
ZMYM2	7750	hgsc.bcm.edu	37	chr13	20567643	20567643	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ttttattgaacgaagacctcCtgagactaaaaacagaacca	6	9	0	4			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr13:20567643C>T	ENST00000382874.2	+	4	621	c.431C>T	c.(430-432)cCt>cTt	p.P144L	ZMYM2_ENST00000382881.3_Missense_Mutation_p.P144L|ZMYM2_ENST00000382869.3_Missense_Mutation_p.P144L|ZMYM2_ENST00000382871.2_Missense_Mutation_p.P144L	NM_001190964.1	NP_001177893.1	Q9UBW7	ZMYM2_HUMAN	zinc finger, MYM-type 2	144					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|PML body (GO:0016605)	ubiquitin conjugating enzyme binding (GO:0031624)|zinc ion binding (GO:0008270)			large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	10		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)		CGAAGACCTCCTGAGACTAAA	0.383																																					p.P144L		Atlas-SNP	.											.	ZMYM2	191	.	0			c.C431T						.						101	106	105					13																	20567643		2108	4249	6357	SO:0001583	missense	7750	exon4			GACCTCCTGAGAC	AF012126	CCDS45016.1	13q11-q12	2013-01-08	2006-07-13	2006-07-13	ENSG00000121741	ENSG00000121741		"Zinc fingers, MYM type"	12989	protein-coding gene	gene with protein product		602221	"zinc finger protein 198"	ZNF198		9499416, 9425908	Standard	XM_005266517		Approved	RAMP, FIM, MYM	uc001ums.3	Q9UBW7	OTTHUMG00000016507	ENST00000382874.2:c.431C>T	chr13.hg19:g.20567643C>T	ENSP00000372327:p.Pro144Leu	91.0	0.0		113.0	43.0	NM_001190964	A6NDG0|A6NI02|O43212|O43434|O60898|Q5W0Q4|Q5W0T3|Q63HP0|Q8NE39|Q9H0V5|Q9H538|Q9UEU2	Missense_Mutation	SNP	ENST00000382874.2	hg19	CCDS45016.1	.	.	.	.	.	.	.	.	.	.	C	12.54	1.968388	0.34754	.	.	ENSG00000121741	ENST00000382869;ENST00000456228;ENST00000382881;ENST00000382874;ENST00000382871	T;T;T;T	0.32023	1.47;1.47;1.47;1.47	5.39	4.45	0.53987	.	0.742403	0.12412	N	0.471194	T	0.29126	0.0724	L	0.52573	1.65	0.80722	D	1	B;B;B	0.20261	0.002;0.002;0.043	B;B;B	0.18871	0.008;0.008;0.023	T	0.03296	-1.1051	10	0.34782	T	0.22	-0.1595	10.415	0.44316	0.0:0.8386:0.0:0.1614	.	144;144;144	A8K126;Q9UBW7;Q9UBW7-2	.;ZMYM2_HUMAN;.	L	144	ENSP00000372322:P144L;ENSP00000372334:P144L;ENSP00000372327:P144L;ENSP00000372324:P144L	ENSP00000372322:P144L	P	+	2	0	ZMYM2	19465643	0.338000	0.24775	0.837000	0.33122	0.982000	0.71751	1.128000	0.31369	1.232000	0.43678	0.650000	0.86243	CCT	.	.		0.383	ZMYM2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044051.2	NM_003453		T	20567643	C	T	20567643	3	4	263	1	0	0	0	0	1	0	0	0	17715	681	24	3	433	3	ZMYM2	13	20567643	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10		20567643	94602235	296	38670										
LATS2	26524	hgsc.bcm.edu	37	chr13	21555755	21555755	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cacatcatcccagaggtcgcTgggctccatgctgtcctgtc	10	15	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr13:21555755T>C	ENST00000382592.4	-	6	2920	c.2515A>G	c.(2515-2517)Agc>Ggc	p.S839G	LATS2_ENST00000542899.1_Missense_Mutation_p.S839G	NM_014572.2	NP_055387.2			large tumor suppressor kinase 2											breast(4)|central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(2)	45		all_cancers(29;4.74e-22)|all_epithelial(30;1.45e-18)|all_lung(29;4.69e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000781)|Epithelial(112;0.00144)|OV - Ovarian serous cystadenocarcinoma(117;0.0183)|Lung(94;0.0375)|LUSC - Lung squamous cell carcinoma(192;0.104)		CAGAGGTCGCTGGGCTCCATG	0.512																																					p.S839G		Atlas-SNP	.											.	LATS2	176	.	0			c.A2515G						.						53	49	51					13																	21555755		2203	4300	6503	SO:0001583	missense	26524	exon6			GGTCGCTGGGCTC	AB028019	CCDS9294.1	13q11-q12	2013-04-25	2013-04-25		ENSG00000150457	ENSG00000150457			6515	protein-coding gene	gene with protein product		604861	"LATS (large tumor suppressor, Drosophila) homolog 2", "LATS, large tumor suppressor, homolog 2 (Drosophila)"			10673337	Standard	NM_014572		Approved		uc001unr.4	Q9NRM7	OTTHUMG00000016531	ENST00000382592.4:c.2515A>G	chr13.hg19:g.21555755T>C	ENSP00000372035:p.Ser839Gly	98.0	0.0		89.0	4.0	NM_014572		Missense_Mutation	SNP	ENST00000382592.4	hg19	CCDS9294.1	.	.	.	.	.	.	.	.	.	.	T	13.23	2.175109	0.38413	.	.	ENSG00000150457	ENST00000382592;ENST00000542899	T;T	0.61510	0.1;0.1	5.69	-1.69	0.08186	Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.201497	0.43919	N	0.000502	T	0.39860	0.1094	L	0.28458	0.855	0.42515	D	0.992982	B	0.06786	0.001	B	0.08055	0.003	T	0.11108	-1.0601	10	0.44086	T	0.13	.	10.5325	0.44986	0.0:0.4384:0.0:0.5616	.	839	Q9NRM7	LATS2_HUMAN	G	839	ENSP00000372035:S839G;ENSP00000441817:S839G	ENSP00000372035:S839G	S	-	1	0	LATS2	20453755	0.996000	0.38824	0.103000	0.21229	0.731000	0.41821	1.413000	0.34725	-0.240000	0.09696	-0.262000	0.10625	AGC	.	.		0.512	LATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044102.1			C	21555755	T	C	21555755	3	2	263	1	0	0	0	0	1	0	0	0	8656	1580	55	2	763	2	LATS2	13	21555755	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	988112	21555755	93614123	297	38671										
SPATA13	221178	hgsc.bcm.edu	37	chr13	24797158	24797158	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ggccaggccccgcagcccccTgtgcaggctcggacctgaaa	13	17	0	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr13:24797158T>C	ENST00000382095.4	+	2	185				SPATA13_ENST00000382108.3_Missense_Mutation_p.C31R|SPATA13_ENST00000424834.2_Missense_Mutation_p.C31R|RP11-307N16.6_ENST00000382141.4_Missense_Mutation_p.C31R	NM_153023.2	NP_694568.1	Q96N96	SPT13_HUMAN	spermatogenesis associated 13						cell migration (GO:0016477)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell migration (GO:0030334)	cytoplasm (GO:0005737)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			breast(4)|endometrium(2)|large_intestine(9)|lung(4)|ovary(1)|prostate(1)|skin(2)	23		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)		CGCAGCCCCCTGTGCAGGCTC	0.682																																					p.C31R		Atlas-SNP	.											.	SPATA13	92	.	0			c.T91C						.						65	74	71					13																	24797158		692	1591	2283	SO:0001627	intron_variant	221178	exon2			GCCCCCTGTGCAG	AK055770	CCDS9305.1, CCDS53857.1, CCDS66517.1, CCDS66518.1, CCDS73553.1	13q12.13	2013-01-10			ENSG00000182957	ENSG00000182957		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	23222	protein-coding gene	gene with protein product		613324					Standard	NM_001286795		Approved	FLJ31208, ARHGEF29	uc021rhg.1	Q96N96	OTTHUMG00000016578	ENST00000382095.4:c.-222-26457T>C	chr13.hg19:g.24797158T>C		80.0	0.0		94.0	4.0	NM_001166271	A2VEA9|A6NF85|B4DQB1|B4DSZ0|B4DVM8|J3KPJ7|J3KQH2|Q5VX68|Q6ZML1|Q8N873|Q8TEK6	Missense_Mutation	SNP	ENST00000382095.4	hg19	CCDS9305.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.07|12.07	1.827986|1.827986	0.32329|0.32329	.|.	.|.	ENSG00000182957|ENSG00000182957	ENST00000382108|ENST00000424834	T|.	0.75589|.	-0.95|.	5.26|5.26	1.25|1.25	0.21368|0.21368	.|.	0.421206|.	0.16753|.	U|.	0.200941|.	T|T	0.38665|0.38665	0.1049|0.1049	L|L	0.39898|0.39898	1.24|1.24	0.09310|0.09310	N|N	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.27971|0.27971	-1.0058|-1.0058	8|5	0.72032|.	D|.	0.01|.	.|.	11.7859|11.7859	0.52043|0.52043	0.0:0.0:0.4601:0.5399|0.0:0.0:0.4601:0.5399	.|.	.|.	.|.	.|.	R|P	31|68	ENSP00000371542:C31R|.	ENSP00000371542:C31R|.	C|L	+|+	1|2	0|0	SPATA13|SPATA13	23695158|23695158	0.429000|0.429000	0.25530|0.25530	0.000000|0.000000	0.03702|0.03702	0.015000|0.015000	0.08874|0.08874	2.005000|2.005000	0.40864|0.40864	0.054000|0.054000	0.16065|0.16065	0.397000|0.397000	0.26171|0.26171	TGT|CTG	.	.		0.682	SPATA13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044180.2	NM_153023		C	24797158	T	C	24797158	1	2	263	0	1	0	0	0	0	0	0	0	15015	1580	55	2		2	SPATA13	13	24797158	Intron	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	3241403	24797158	90372720	298	38672										
ATP12A	479	hgsc.bcm.edu	37	chr13	25266639	25266639	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	agaacctggaggctgtggagAccctcggctccacctccatc	11	15	0	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr13:25266639A>G	ENST00000381946.3	+	9	1308	c.1141A>G	c.(1141-1143)Acc>Gcc	p.T381A	ATP12A_ENST00000218548.6_Missense_Mutation_p.T387A			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	381					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		GGCTGTGGAGACCCTCGGCTC	0.562																																					p.T387A	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-SNP	.											.	ATP12A	172	.	0			c.A1159G						.						91	82	85					13																	25266639		2203	4300	6503	SO:0001583	missense	479	exon9			GTGGAGACCCTCG	L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"ATPases / P-type"	13816	protein-coding gene	gene with protein product	"ATPase, Na+K+ transporting, alpha-1 polypeptide-like", "potassium-transporting ATPase alpha chain 2", "proton pump", "non-gastric H(+)/K(+) ATPase alpha subunit", "sodium/potassium ATPase, alpha polypeptide-like"	182360	"ATPase, Na+/K+ transporting, alpha polypeptide-like 1"	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.1141A>G	chr13.hg19:g.25266639A>G	ENSP00000371372:p.Thr381Ala	66.0	0.0		87.0	4.0	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Missense_Mutation	SNP	ENST00000381946.3	hg19	CCDS31948.1	.	.	.	.	.	.	.	.	.	.	A	28.3	4.907853	0.92107	.	.	ENSG00000075673	ENST00000218548;ENST00000381946	D;D	0.91521	-2.86;-2.86	5.63	5.63	0.86233	ATPase, P-type, cytoplasmic domain N (1);ATPase, P-type, ATPase-associated domain (1);	0.000000	0.85682	D	0.000000	D	0.95799	0.8633	M	0.88031	2.925	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.995	D	0.96432	0.9320	10	0.87932	D	0	.	13.789	0.63128	1.0:0.0:0.0:0.0	.	387;381	P54707-2;P54707	.;AT12A_HUMAN	A	387;381	ENSP00000218548:T387A;ENSP00000371372:T381A	ENSP00000218548:T387A	T	+	1	0	ATP12A	24164639	1.000000	0.71417	0.987000	0.45799	0.989000	0.77384	9.079000	0.94032	2.145000	0.66743	0.533000	0.62120	ACC	.	.		0.562	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676		G	25266639	A	G	25266639	3	3	263	1	0	0	0	0	1	0	0	0	1122	275	10	2	1193	2	ATP12A	13	25266639	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	469481	25266639	89903239	299	38673										
ATP12A	479	hgsc.bcm.edu	37	chr13	25266681	25266681	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tctgctcggacaagactgggAcactgacccagaacaggatg	12	11	1	3			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr13:25266681A>G	ENST00000381946.3	+	9	1350	c.1183A>G	c.(1183-1185)Aca>Gca	p.T395A	ATP12A_ENST00000218548.6_Missense_Mutation_p.T401A			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	395					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		CAAGACTGGGACACTGACCCA	0.532																																					p.T401A	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-SNP	.											.	ATP12A	172	.	0			c.A1201G						.						97	85	89					13																	25266681		2203	4300	6503	SO:0001583	missense	479	exon9			ACTGGGACACTGA	L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"ATPases / P-type"	13816	protein-coding gene	gene with protein product	"ATPase, Na+K+ transporting, alpha-1 polypeptide-like", "potassium-transporting ATPase alpha chain 2", "proton pump", "non-gastric H(+)/K(+) ATPase alpha subunit", "sodium/potassium ATPase, alpha polypeptide-like"	182360	"ATPase, Na+/K+ transporting, alpha polypeptide-like 1"	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.1183A>G	chr13.hg19:g.25266681A>G	ENSP00000371372:p.Thr395Ala	101.0	0.0		125.0	7.0	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Missense_Mutation	SNP	ENST00000381946.3	hg19	CCDS31948.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.456532	0.84317	.	.	ENSG00000075673	ENST00000218548;ENST00000381946	D;D	0.99143	-5.48;-5.48	5.63	5.63	0.86233	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.85682	D	0.000000	D	0.99588	0.9851	H	0.98577	4.27	0.80722	D	1	D;D	0.76494	0.999;0.996	D;D	0.85130	0.997;0.99	D	0.97737	1.0206	10	0.87932	D	0	.	13.789	0.63128	1.0:0.0:0.0:0.0	.	401;395	P54707-2;P54707	.;AT12A_HUMAN	A	401;395	ENSP00000218548:T401A;ENSP00000371372:T395A	ENSP00000218548:T401A	T	+	1	0	ATP12A	24164681	1.000000	0.71417	0.983000	0.44433	0.716000	0.41182	7.246000	0.78247	2.145000	0.66743	0.533000	0.62120	ACA	.	.		0.532	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676		G	25266681	A	G	25266681	3	3	263	1	0	0	0	0	1	0	0	0	1122	275	10	2	1235	2	ATP12A	13	25266681	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	42	25266681	89903197	300	38674										
BRCA2	675	hgsc.bcm.edu	37	chr13	32937516	32937516	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tgaacttacagatgggtggtAtgctgttaaggcccagttag	13	6	0	2	rs80359064		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr13:32937516A>G	ENST00000380152.3	+	18	8410	c.8177A>G	c.(8176-8178)tAt>tGt	p.Y2726C	BRCA2_ENST00000544455.1_Missense_Mutation_p.Y2726C			P51587	BRCA2_HUMAN	breast cancer 2, early onset	2726					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		GATGGGTGGTATGCTGTTAAG	0.403			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											p.Y2726C	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	.	BRCA2	812	.	0			c.A8177G						.	A	CYS/TYR	0,4406		0,0,2203	148	143	145	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	8177	5.5	1	13	dbSNP_132	145	1,8599	1.2+/-3.3	0,1,4299	no	missense	BRCA2	NM_000059.3	194	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	probably-damaging	2726/3419	32937516	1,13005	2203	4300	6503	SO:0001583	missense	675	exon18	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	GGTGGTATGCTGT	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.8177A>G	chr13.hg19:g.32937516A>G	ENSP00000369497:p.Tyr2726Cys	139.0	0.0		168.0	66.0	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	hg19	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	A	17.10	3.302460	0.60195	0.0	1.16E-4	ENSG00000139618	ENST00000380152;ENST00000544455	D;D	0.95482	-3.72;-3.72	5.49	5.49	0.81192	Nucleic acid-binding, OB-fold-like (1);BRCA2, oligonucleotide/oligosaccharide-binding 1 (1);	0.000000	0.85682	D	0.000000	D	0.98283	0.9431	M	0.93197	3.39	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.99560	1.0968	10	0.87932	D	0	.	15.5697	0.76323	1.0:0.0:0.0:0.0	.	2726	P51587	BRCA2_HUMAN	C	2726	ENSP00000369497:Y2726C;ENSP00000439902:Y2726C	ENSP00000369497:Y2726C	Y	+	2	0	BRCA2	31835516	1.000000	0.71417	0.992000	0.48379	0.414000	0.31173	8.962000	0.93254	2.084000	0.62774	0.260000	0.18958	TAT	.	.		0.403	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		G	32937516	A	G	32937516	3	3	263	1	0	0	0	0	1	0	0	0	1501	449	16	2	8243	2	BRCA2	13	32937516	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	7670835	32937516	82232362	301	38675										
BRCA2	675	hgsc.bcm.edu	37	chr13	32953916	32953924	+	In_Frame_Del	DEL	GATTTATAT	GATTTATAT	-													0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gtatttggcgtccatcatcaGatttatattctctgttaaca					rs397508026|rs397508027|rs80359736|rs80359737|rs397508028		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	GATTTATAT	GATTTATAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr13:32953916_32953924delGATTTATAT	ENST00000380152.3	+	23	9216_9224	c.8983_8991delGATTTATAT	c.(8983-8991)gatttatatdel	p.DLY2995del	BRCA2_ENST00000544455.1_In_Frame_Del_p.DLY2995del			P51587	BRCA2_HUMAN	breast cancer 2, early onset	2995					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)	p.Y2997*(2)		NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TCCATCATCAGATTTATATTCTCTGTTAA	0.311			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											p.2994_2997del	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	Atlas-Indel,Pindel	.	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	.	BRCA2	812	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.8982_8990del	GRCh37	CM070045	BRCA2	M		.																																			SO:0001651	inframe_deletion	675	exon23	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	.	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.8983_8991delGATTTATAT	chr13.hg19:g.32953916_32953924delGATTTATAT	ENSP00000369497:p.Asp2995_Tyr2997del	175.0	0.0		162.0	17.0	NM_000059	O00183|O15008|Q13879|Q5TBJ7	In_Frame_Del	DEL	ENST00000380152.3	hg19	CCDS9344.1																																																																																			.	.		0.311	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		-	32953924	GATTTATAT	-	32953916	7	5	263	1	0	1	0	1	0	0	0	0	1501	942	33	0	9069	0	BRCA2	13	32953916	In_Frame_Del	DEL	GATTTATAT	TCGA-FV-A2QR-01A-11D-A20W-10	16400	32953916	82215962	302	38676										
NBEA	26960	hgsc.bcm.edu	37	chr13	36046643	36046643	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tacttcgaggtagatgaggaTgattctgccttcaagaagat	11	6	2	5			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr13:36046643T>C	ENST00000400445.3	+	41	7089	c.6555T>C	c.(6553-6555)gaT>gaC	p.D2185D	NBEA_ENST00000379939.2_Silent_p.D2182D|NBEA_ENST00000540320.1_Silent_p.D2185D|NBEA_ENST00000310336.4_Silent_p.D2185D	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	2185					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		TAGATGAGGATGATTCTGCCT	0.498																																					p.D2185D		Atlas-SNP	.											.	NBEA	340	.	0			c.T6555C						.						90	90	90					13																	36046643		1997	4175	6172	SO:0001819	synonymous_variant	26960	exon41			TGAGGATGATTCT	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.6555T>C	chr13.hg19:g.36046643T>C		88.0	0.0		94.0	4.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Silent	SNP	ENST00000400445.3	hg19	CCDS45026.1																																																																																			.	.		0.498	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		C	36046643	T	C	36046643	2	2	263	1	0	0	0	0	0	0	0	1	10196	1461	51	2		2	NBEA	13	36046643	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	3092727	36046643	79123235	303	38677										
WBP4	11193	hgsc.bcm.edu	37	chr13	41642739	41642739	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	accagtaaccagcactatccCacctacctcgacatcaaatc	3	17	1	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr13:41642739C>T	ENST00000379487.3	+	5	705	c.305C>T	c.(304-306)cCa>cTa	p.P102L	WBP4_ENST00000542082.1_Missense_Mutation_p.P81L	NM_007187.3	NP_009118.1	O75554	WBP4_HUMAN	WW domain binding protein 4	102					mRNA cis splicing, via spliceosome (GO:0045292)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spliceosomal complex (GO:0005681)	nucleic acid binding (GO:0003676)|proline-rich region binding (GO:0070064)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|prostate(1)|skin(1)	12		Lung NSC(96;3.55e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;3.11e-09)|Epithelial(112;3.37e-06)|OV - Ovarian serous cystadenocarcinoma(117;8.3e-05)|GBM - Glioblastoma multiforme(144;0.00102)|BRCA - Breast invasive adenocarcinoma(63;0.07)		AGCACTATCCCACCTACCTCG	0.383																																					p.P102L		Atlas-SNP	.											.	WBP4	40	.	0			c.C305T						.						73	76	75					13																	41642739		2203	4300	6503	SO:0001583	missense	11193	exon5			CTATCCCACCTAC	AF071185	CCDS9375.1	13q13.3	2012-10-17	2012-10-17		ENSG00000120688	ENSG00000120688			12739	protein-coding gene	gene with protein product	"formin binding protein 21"	604981				9724750	Standard	NM_007187		Approved	FBP21, MGC117310	uc001uxt.3	O75554	OTTHUMG00000016784	ENST00000379487.3:c.305C>T	chr13.hg19:g.41642739C>T	ENSP00000368801:p.Pro102Leu	50.0	0.0		64.0	4.0	NM_007187	B7Z4M2|Q32P29	Missense_Mutation	SNP	ENST00000379487.3	hg19	CCDS9375.1	.	.	.	.	.	.	.	.	.	.	C	8.289	0.817387	0.16607	.	.	ENSG00000120688	ENST00000379487;ENST00000542082	.	.	.	5.55	4.68	0.58851	.	0.243771	0.32533	N	0.005966	T	0.32346	0.0826	N	0.14661	0.345	0.35028	D	0.758557	B;B	0.25312	0.123;0.085	B;B	0.22386	0.02;0.039	T	0.37731	-0.9693	9	0.49607	T	0.09	-0.9466	6.8715	0.24123	0.1827:0.7291:0.0:0.0882	.	81;102	B7Z4M2;O75554	.;WBP4_HUMAN	L	102;81	.	ENSP00000368801:P102L	P	+	2	0	WBP4	40540739	0.293000	0.24371	0.958000	0.39756	0.155000	0.21991	2.705000	0.47127	1.270000	0.44297	0.655000	0.94253	CCA	.	.		0.383	WBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044655.2	NM_007187		T	41642739	C	T	41642739	3	4	263	1	0	0	0	0	1	0	0	0	17276	594	21	3	323	3	WBP4	13	41642739	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	5596096	41642739	73527139	304	38678										
NAA16	79612	hgsc.bcm.edu	37	chr13	41941630	41941630	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ccatacatactgcatgagaaAgatgacccttcgtgcctatg	8	11	0	3			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr13:41941630A>G	ENST00000379406.3	+	14	1919	c.1595A>G	c.(1594-1596)aAg>aGg	p.K532R	NAA16_ENST00000497143.1_3'UTR	NM_024561.4	NP_078837.3	Q6N069	NAA16_HUMAN	N(alpha)-acetyltransferase 16, NatA auxiliary subunit	532					N-terminal protein amino acid acetylation (GO:0006474)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NatA complex (GO:0031415)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ribosome binding (GO:0043022)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|urinary_tract(2)	31						TGCATGAGAAAGATGACCCTT	0.333																																					p.K532R		Atlas-SNP	.											.	NAA16	74	.	0			c.A1595G						.						101	96	97					13																	41941630		2203	4300	6503	SO:0001583	missense	79612	exon14			TGAGAAAGATGAC	AL833341	CCDS9379.1, CCDS45044.1	13q14.11	2013-01-10	2010-01-14	2010-01-14	ENSG00000172766	ENSG00000172766		"N(alpha)-acetyltransferase subunits", "Tetratricopeptide (TTC) repeat domain containing"	26164	protein-coding gene	gene with protein product			"NMDA receptor regulated 1-like"	NARG1L		11483580, 19660095	Standard	NM_024561		Approved	FLJ22054, MGC40612, PRO2435	uc001uyf.2	Q6N069	OTTHUMG00000016791	ENST00000379406.3:c.1595A>G	chr13.hg19:g.41941630A>G	ENSP00000368716:p.Lys532Arg	74.0	0.0		91.0	4.0	NM_024561	B0QZ59|Q5VSP9|Q6P2D5|Q8N5J3|Q8N870	Missense_Mutation	SNP	ENST00000379406.3	hg19	CCDS9379.1	.	.	.	.	.	.	.	.	.	.	A	18.27	3.587641	0.66105	.	.	ENSG00000172766	ENST00000379406	T	0.57752	0.38	5.27	4.09	0.47781	.	0.076964	0.52532	N	0.000061	T	0.55878	0.1948	M	0.64567	1.98	0.80722	D	1	B	0.26635	0.155	B	0.39935	0.314	T	0.52373	-0.8584	10	0.36615	T	0.2	-7.9668	10.9292	0.47207	0.9259:0.0:0.0741:0.0	.	532	Q6N069	NAA16_HUMAN	R	532	ENSP00000368716:K532R	ENSP00000368716:K532R	K	+	2	0	NAA16	40839630	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.784000	0.68990	0.846000	0.35142	0.477000	0.44152	AAG	.	.		0.333	NAA16-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044672.2	NM_018527		G	41941630	A	G	41941630	3	3	263	1	0	0	0	0	1	0	0	0	10128	72	3	2	1682	2	NAA16	13	41941630	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	298891	41941630	73228248	305	38679										
C13orf31	144811	hgsc.bcm.edu	37	chr13	44455558	44455558	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gggagggctttttaaacagtCcattgaaataaacgtaatca	9	6	1	1	rs150202700		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr13:44455558C>A	ENST00000441843.1	+	2	922	c.437C>A	c.(436-438)tCc>tAc	p.S146Y	LACC1_ENST00000325686.6_Missense_Mutation_p.S146Y|CCDC122_ENST00000476570.2_5'Flank|CCDC122_ENST00000444614.3_5'Flank	NM_001128303.1	NP_001121775.1	Q8IV20	LACC1_HUMAN	laccase (multicopper oxidoreductase) domain containing 1	146																	TTTAAACAGTCCATTGAAATA	0.328																																					p.S146Y		Atlas-SNP	.											.	.	.	.	0			c.C437A						.	C	TYR/SER,TYR/SER	0,4406		0,0,2203	77	83	81		437,437	3.9	0.7	13	dbSNP_134	81	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	LACC1	NM_001128303.1,NM_153218.2	144,144	0,2,6501	AA,AC,CC		0.0233,0.0,0.0154	possibly-damaging,possibly-damaging	146/431,146/431	44455558	2,13004	2203	4300	6503	SO:0001583	missense	144811	exon2			AACAGTCCATTGA	AK096044	CCDS9391.1	13q14.11	2012-05-11	2011-08-09	2011-08-09	ENSG00000179630	ENSG00000179630			26789	protein-coding gene	gene with protein product		613409	"chromosome 13 open reading frame 31"	C13orf31		16740638, 22504414	Standard	NM_153218		Approved	FLJ38725	uc010acg.3	Q8IV20	OTTHUMG00000016826	ENST00000441843.1:c.437C>A	chr13.hg19:g.44455558C>A	ENSP00000391747:p.Ser146Tyr	76.0	0.0		76.0	25.0	NM_001128303	A2A3Z6|Q8N8X5	Missense_Mutation	SNP	ENST00000441843.1	hg19	CCDS9391.1	.	.	.	.	.	.	.	.	.	.	C	11.82	1.752758	0.31046	0.0	2.33E-4	ENSG00000179630	ENST00000441843;ENST00000425906;ENST00000325686	T;T	0.49432	0.78;0.78	5.66	3.87	0.44632	.	0.582429	0.19783	N	0.106171	T	0.51176	0.1659	M	0.70595	2.14	0.20307	N	0.999917	P	0.52842	0.956	P	0.44732	0.459	T	0.50048	-0.8873	10	0.66056	D	0.02	0.0021	13.1243	0.59344	0.4207:0.5793:0.0:0.0	.	146	Q8IV20	LACC1_HUMAN	Y	146	ENSP00000391747:S146Y;ENSP00000317619:S146Y	ENSP00000317619:S146Y	S	+	2	0	LACC1	43353558	0.002000	0.14202	0.658000	0.29665	0.241000	0.25554	1.504000	0.35726	0.793000	0.33875	0.655000	0.94253	TCC	.	C|1.000;A|0.000		0.328	LACC1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044726.3	NM_153218		A	44455558	C	A	44455558	3	1	263	1	0	0	0	0	1	0	0	0	1728	855	30	3	439	3	C13orf31	13	44455558	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	2513928	44455558	70714320	306	38680										
TDRD3	81550	hgsc.bcm.edu	37	chr13	61084796	61084796	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gcagggggcgaataagatctGaagatgaagaggacctggga	17	5	1	5			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr13:61084796G>A	ENST00000196169.3	+	10	1557	c.769G>A	c.(769-771)Gaa>Aaa	p.E257K	TDRD3_ENST00000535286.1_Missense_Mutation_p.E350K|TDRD3_ENST00000377881.2_Missense_Mutation_p.E257K|TDRD3_ENST00000377894.2_Missense_Mutation_p.E257K	NM_001146071.1|NM_030794.2	NP_001139543.1|NP_110421.1	Q9H7E2	TDRD3_HUMAN	tudor domain containing 3	257					chromatin modification (GO:0016568)|regulation of RNA biosynthetic process (GO:2001141)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|methylated histone binding (GO:0035064)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)	p.E257Q(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	40		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)		AATAAGATCTGAAGATGAAGA	0.368																																					p.E350K	Colon(36;164 906 35820 50723)	Atlas-SNP	.											TDRD3_ENST00000535286,NS,carcinoma,0,2	TDRD3	123	.	1	Substitution - Missense(1)	lung(1)	c.G1048A						.						102	104	104					13																	61084796		2203	4300	6503	SO:0001583	missense	81550	exon10			AGATCTGAAGATG	AK023578	CCDS9441.1, CCDS53872.1	13q14.3	2013-01-23			ENSG00000083544	ENSG00000083544		"Tudor domain containing"	20612	protein-coding gene	gene with protein product		614392					Standard	NM_030794		Approved	FLJ21007	uc010aeg.3	Q9H7E2	OTTHUMG00000017007	ENST00000196169.3:c.769G>A	chr13.hg19:g.61084796G>A	ENSP00000196169:p.Glu257Lys	35.0	0.0		43.0	3.0	NM_001146070	B2MWP9|Q53XA6|Q6P992	Missense_Mutation	SNP	ENST00000196169.3	hg19	CCDS9441.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.984215	0.93044	.	.	ENSG00000083544	ENST00000196169;ENST00000377881;ENST00000377894;ENST00000535286	D;D;D;D	0.93906	-3.31;-3.31;-3.31;-3.3	5.73	5.73	0.89815	.	0.047482	0.85682	D	0.000000	D	0.95825	0.8641	M	0.64997	1.995	0.80722	D	1	D;D;D	0.71674	0.992;0.998;0.991	P;D;P	0.80764	0.901;0.994;0.718	D	0.93270	0.6651	10	0.16420	T	0.52	-25.2901	19.8994	0.96980	0.0:0.0:1.0:0.0	.	350;256;257	Q9H7E2-3;Q9H7E2-2;Q9H7E2	.;.;TDRD3_HUMAN	K	257;257;257;350	ENSP00000196169:E257K;ENSP00000367113:E257K;ENSP00000367126:E257K;ENSP00000440190:E350K	ENSP00000196169:E257K	E	+	1	0	TDRD3	59982797	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	9.042000	0.93793	2.703000	0.92315	0.650000	0.86243	GAA	.	.		0.368	TDRD3-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045175.2	NM_030794		A	61084796	G	A	61084796	3	1	263	1	0	0	0	0	1	0	0	0	15747	1291	45	3	1086	3	TDRD3	13	61084796	Missense_Mutation	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	16629238	61084796	54085082	307	38681										
SCEL	8796	hgsc.bcm.edu	37	chr13	78143580	78143580	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tgctactactcctgtaaagaAgaagaggtaggatgaactca	10	7	1	4			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr13:78143580A>G	ENST00000349847.3	+	8	557	c.473A>G	c.(472-474)aAg>aGg	p.K158R	SCEL_ENST00000377246.3_Missense_Mutation_p.K158R|SCEL_ENST00000535157.1_Missense_Mutation_p.K158R	NM_144777.2	NP_659001.2	O95171	SCEL_HUMAN	sciellin	158					embryo development (GO:0009790)|epidermis development (GO:0008544)|keratinocyte differentiation (GO:0030216)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(18)|ovary(5)|prostate(1)|stomach(1)|urinary_tract(1)	40		Acute lymphoblastic leukemia(28;0.0282)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0233)		CCTGTAAAGAAGAAGAGGTAG	0.433																																					p.K158R		Atlas-SNP	.											.	SCEL	85	.	0			c.A473G						.						126	113	117					13																	78143580		2203	4300	6503	SO:0001583	missense	8796	exon8			TAAAGAAGAAGAG	AF045941	CCDS9458.1, CCDS9459.1, CCDS53877.1	13q22	2008-07-18			ENSG00000136155	ENSG00000136155			10573	protein-coding gene	gene with protein product		604112				9813070	Standard	NM_003843		Approved	FLJ21667, MGC22531	uc001vki.3	O95171	OTTHUMG00000017107	ENST00000349847.3:c.473A>G	chr13.hg19:g.78143580A>G	ENSP00000302579:p.Lys158Arg	56.0	0.0		65.0	4.0	NM_003843	B7Z797|F5H651|Q53H61|Q5W0S8|Q5W0S9|Q86X00	Missense_Mutation	SNP	ENST00000349847.3	hg19	CCDS9459.1	.	.	.	.	.	.	.	.	.	.	A	15.07	2.725093	0.48833	.	.	ENSG00000136155	ENST00000348770;ENST00000535157;ENST00000377246;ENST00000349847	T;T;T	0.26518	1.73;1.73;1.73	5.1	5.1	0.69264	.	0.000000	0.64402	D	0.000007	T	0.47948	0.1473	M	0.69823	2.125	0.35269	D	0.780255	D;D;D	0.76494	0.998;0.999;0.999	D;D;D	0.81914	0.994;0.99;0.995	T	0.61456	-0.7059	10	0.59425	D	0.04	-29.7879	11.4487	0.50138	1.0:0.0:0.0:0.0	.	158;158;158	F5H651;O95171-2;O95171	.;.;SCEL_HUMAN	R	135;158;158;158	ENSP00000437895:K158R;ENSP00000366454:K158R;ENSP00000302579:K158R	ENSP00000315127:K135R	K	+	2	0	SCEL	77041581	1.000000	0.71417	1.000000	0.80357	0.053000	0.15095	2.531000	0.45650	2.261000	0.74972	0.528000	0.53228	AAG	.	.		0.433	SCEL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045339.2	NM_144777		G	78143580	A	G	78143580	3	3	263	1	0	0	0	0	1	0	0	0	13903	72	3	2	499	2	SCEL	13	78143580	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	17058784	78143580	37026298	308	38682										
SLC10A2	6555	hgsc.bcm.edu	37	chr13	103701761	103701761	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tggtggaacatagctgcgtgTtctgcatccccgtttcaaaa	10	10	2	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr13:103701761T>C	ENST00000245312.3	-	5	1393	c.797A>G	c.(796-798)aAc>aGc	p.N266S		NM_000452.2	NP_000443	Q12908	NTCP2_HUMAN	solute carrier family 10 (sodium/bile acid cotransporter), member 2	266					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteasome complex (GO:0000502)	bile acid:sodium symporter activity (GO:0008508)			breast(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_neural(89;0.0662)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)				Aciclovir(DB00787)|Cyclosporine(DB00091)|Ursodeoxycholic acid(DB01586)|Valaciclovir(DB00577)	TAGCTGCGTGTTCTGCATCCC	0.458																																					p.N266S		Atlas-SNP	.											.	SLC10A2	67	.	0			c.A797G						.						148	111	124					13																	103701761		2203	4300	6503	SO:0001583	missense	6555	exon5			TGCGTGTTCTGCA	U10417	CCDS9506.1	13q33	2013-07-18	2013-07-18		ENSG00000125255	ENSG00000125255		"Solute carriers"	10906	protein-coding gene	gene with protein product		601295		ASBT, ISBT		8661017	Standard	NM_000452		Approved		uc001vpy.4	Q12908	OTTHUMG00000017313	ENST00000245312.3:c.797A>G	chr13.hg19:g.103701761T>C	ENSP00000245312:p.Asn266Ser	143.0	0.0		187.0	70.0	NM_000452	A1L4F4|Q13839	Missense_Mutation	SNP	ENST00000245312.3	hg19	CCDS9506.1	.	.	.	.	.	.	.	.	.	.	T	19.08	3.758437	0.69763	.	.	ENSG00000125255	ENST00000245312	T	0.75938	-0.98	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.88062	0.6336	M	0.87971	2.92	0.58432	D	0.999993	D	0.89917	1.0	D	0.87578	0.998	D	0.90071	0.4163	10	0.87932	D	0	-20.8516	16.2484	0.82467	0.0:0.0:0.0:1.0	.	266	Q12908	NTCP2_HUMAN	S	266	ENSP00000245312:N266S	ENSP00000245312:N266S	N	-	2	0	SLC10A2	102499762	1.000000	0.71417	0.951000	0.38953	0.146000	0.21551	7.989000	0.88205	2.291000	0.77112	0.533000	0.62120	AAC	.	.		0.458	SLC10A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045716.1			C	103701761	T	C	103701761	3	2	263	1	0	0	0	0	1	0	0	0	14389	1725	60	2	257	2	SLC10A2	13	103701761	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	25558181	103701761	11468117	309	38683										
DHRS4L1	728635	hgsc.bcm.edu	37	chr14	24517998	24517998	+	RNA	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ctgcctagcacctggacttaTcaagactagcttcagcagga	9	12	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr14:24517998T>C	ENST00000558293.1	+	0	646					NR_102693.1																						CCTGGACTTATCAAGACTAGC	0.522																																					p.I218T		Atlas-SNP	.											.	.	.	.	0			c.T653C						.						141	137	139					14																	24517998		2203	4298	6501			728635	exon8			GACTTATCAAGAC																													chr14.hg19:g.24517998T>C		674.0	0.0		875.0	333.0	NM_001082488		Missense_Mutation	SNP	ENST00000558293.1	hg19		.	.	.	.	.	.	.	.	.	.	T	10.56	1.384474	0.25031	.	.	ENSG00000225766	ENST00000397065	.	.	.	4.67	4.67	0.58626	NAD(P)-binding domain (1);	.	.	.	.	T	0.70360	0.3215	L	0.60455	1.87	0.50813	D	0.999890	D	0.89917	1.0	D	0.97110	1.0	T	0.76694	-0.2865	7	0.46703	T	0.11	.	12.0988	0.53772	0.0:0.0:0.0:1.0	.	218	P0CG22	DR4L1_HUMAN	T	218	.	ENSP00000380255:I218T	I	+	2	0	AL136295.1	23587838	1.000000	0.71417	1.000000	0.80357	0.068000	0.16541	6.335000	0.72949	1.958000	0.56883	0.329000	0.21502	ATC	.	.		0.522	RP11-468E2.9-005	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417272.1			C	24517998	T	C	24517998	1	2	263	0	1	0	0	0	0	0	0	0	4495	1435	50	2		2	DHRS4L1	14	24517998	RNA	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10		24517998	82831542	310	38684										
LRRC16B	90668	hgsc.bcm.edu	37	chr14	24523470	24523470	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ggtggagagctccttcaatgTcctggagatccgtgccttca	12	11	2	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr14:24523470T>C	ENST00000342740.5	+	4	360	c.206T>C	c.(205-207)gTc>gCc	p.V69A	LRRC16B_ENST00000334420.7_5'UTR	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	69						cytoplasm (GO:0005737)				breast(3)|central_nervous_system(2)|cervix(3)|endometrium(7)|kidney(1)|large_intestine(9)|liver(1)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	52				GBM - Glioblastoma multiforme(265;0.019)		TCCTTCAATGTCCTGGAGATC	0.597																																					p.V69A		Atlas-SNP	.											.	LRRC16B	120	.	0			c.T206C						.						81	72	75					14																	24523470		2203	4300	6503	SO:0001583	missense	90668	exon4			TCAATGTCCTGGA	AI017934	CCDS32054.1	14q11.2-q12	2010-09-10	2008-02-12	2008-02-12					20272	protein-coding gene	gene with protein product		614716	"chromosome 14 open reading frame 121"	C14orf121		19846667	Standard	NM_138360		Approved	BC008134, crml-1, CARMIL3	uc001wlj.2	Q8ND23		ENST00000342740.5:c.206T>C	chr14.hg19:g.24523470T>C	ENSP00000340467:p.Val69Ala	61.0	0.0		94.0	4.0	NM_138360	Q8TEF7|Q96HS9	Missense_Mutation	SNP	ENST00000342740.5	hg19	CCDS32054.1	.	.	.	.	.	.	.	.	.	.	T	16.61	3.170924	0.57584	.	.	ENSG00000186648	ENST00000342740	T	0.15603	2.41	4.8	4.8	0.61643	.	0.519033	0.18193	N	0.148762	T	0.12732	0.0309	N	0.22421	0.69	0.80722	D	1	P	0.48764	0.915	B	0.41088	0.347	T	0.03335	-1.1047	10	0.66056	D	0.02	-21.357	11.0069	0.47639	0.0:0.0:0.0:1.0	.	69	Q8ND23	LR16B_HUMAN	A	69	ENSP00000340467:V69A	ENSP00000340467:V69A	V	+	2	0	LRRC16B	23593310	1.000000	0.71417	1.000000	0.80357	0.835000	0.47333	3.764000	0.55264	1.914000	0.55421	0.379000	0.24179	GTC	.	.		0.597	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360		C	24523470	T	C	24523470	3	2	263	1	0	0	0	0	1	0	0	0	8981	1667	58	2	220	2	LRRC16B	14	24523470	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	5472	24523470	82826070	311	38685										
NYNRIN	57523	hgsc.bcm.edu	37	chr14	24879219	24879219	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cagcagtaagcaccagtttcAgatggaggggctcctggggg	16	9	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr14:24879219A>C	ENST00000382554.3	+	4	2537	c.2219A>C	c.(2218-2220)cAg>cCg	p.Q740P		NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	740					DNA integration (GO:0015074)	integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(8)|lung(21)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	56						CACCAGTTTCAGATGGAGGGG	0.637																																					p.Q740P		Atlas-SNP	.											.	NYNRIN	120	.	0			c.A2219C						.						21	24	23					14																	24879219		1938	4122	6060	SO:0001583	missense	57523	exon4			AGTTTCAGATGGA	AB037726	CCDS45090.1	14q11.2	2009-10-14	2009-10-14	2009-10-14		ENSG00000205978			20165	protein-coding gene	gene with protein product	"Cousin of GIN1"		"KIAA1305"	KIAA1305		19561090, 17114934	Standard	NM_025081		Approved	FLJ11811, CGIN1	uc001wpf.4	Q9P2P1		ENST00000382554.3:c.2219A>C	chr14.hg19:g.24879219A>C	ENSP00000371994:p.Gln740Pro	98.0	0.0		138.0	8.0	NM_025081	Q6P153|Q86TR3|Q9HAC4	Missense_Mutation	SNP	ENST00000382554.3	hg19	CCDS45090.1	.	.	.	.	.	.	.	.	.	.	A	10.33	1.320603	0.23994	.	.	ENSG00000205978	ENST00000382554	T	0.10860	2.83	4.85	0.987	0.19790	.	.	.	.	.	T	0.06096	0.0158	N	0.24115	0.695	0.09310	N	1	P	0.46277	0.875	B	0.38378	0.272	T	0.31138	-0.9954	9	0.66056	D	0.02	.	3.7416	0.08532	0.5625:0.0:0.0946:0.3429	.	740	Q9P2P1	NYNRI_HUMAN	P	740	ENSP00000371994:Q740P	ENSP00000371994:Q740P	Q	+	2	0	NYNRIN	23949059	0.036000	0.19791	0.001000	0.08648	0.004000	0.04260	0.934000	0.28910	0.070000	0.16634	-0.256000	0.11100	CAG	.	.		0.637	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412939.1			C	24879219	A	C	24879219	3	2	263	1	0	0	0	0	1	0	0	0	10805	188	7	5	2229	5	NYNRIN	14	24879219	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	355749	24879219	82470321	312	38686										
AKAP6	9472	hgsc.bcm.edu	37	chr14	33291695	33291695	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	catgcagaatgccaaacagcTctcccttttatctcatagtt	5	12	2	1	rs386776215		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr14:33291695T>C	ENST00000280979.4	+	13	4846	c.4676T>C	c.(4675-4677)cTc>cCc	p.L1559P	AKAP6_ENST00000557272.1_Intron	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	1559					action potential (GO:0001508)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cAMP biosynthetic process (GO:0030818)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell growth (GO:0030307)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of delayed rectifier potassium channel activity (GO:1902261)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of potassium ion transmembrane transport (GO:1901381)|positive regulation of protein phosphatase type 2B activity (GO:0032514)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|protein targeting (GO:0006605)|regulation of membrane repolarization (GO:0060306)|regulation of protein kinase A signaling (GO:0010738)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	calcium channel complex (GO:0034704)|caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|junctional sarcoplasmic reticulum membrane (GO:0014701)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	adenylate cyclase binding (GO:0008179)|ion channel binding (GO:0044325)|protein anchor (GO:0043495)|protein complex scaffold (GO:0032947)|protein kinase A binding (GO:0051018)|protein kinase A regulatory subunit binding (GO:0034237)			NS(2)|breast(10)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(25)|lung(42)|ovary(5)|pancreas(2)|prostate(3)|skin(9)|urinary_tract(2)	122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		GCCAAACAGCTCTCCCTTTTA	0.413																																					p.L1559P	Melanoma(49;821 1200 7288 13647 42351)	Atlas-SNP	.											.	AKAP6	308	.	0			c.T4676C						.						114	121	118					14																	33291695		2203	4300	6503	SO:0001583	missense	9472	exon13			AACAGCTCTCCCT	AB002309	CCDS9644.1	14q12	2008-08-11			ENSG00000151320	ENSG00000151320		"A-kinase anchor proteins"	376	protein-coding gene	gene with protein product	"protein kinase A anchoring protein 6"	604691				7721854, 9205841	Standard	NM_004274		Approved	KIAA0311, mAKAP, AKAP100, PRKA6, ADAP6	uc001wrq.3	Q13023	OTTHUMG00000140207	ENST00000280979.4:c.4676T>C	chr14.hg19:g.33291695T>C	ENSP00000280979:p.Leu1559Pro	90.0	0.0		93.0	4.0	NM_004274	A7E242|A7E2D4|O15028	Missense_Mutation	SNP	ENST00000280979.4	hg19	CCDS9644.1	.	.	.	.	.	.	.	.	.	.	T	8.626	0.892436	0.17613	.	.	ENSG00000151320	ENST00000280979	T	0.05996	3.36	5.79	4.65	0.58169	.	0.374376	0.27567	N	0.018797	T	0.06234	0.0161	L	0.38838	1.175	0.80722	D	1	B	0.13145	0.007	B	0.08055	0.003	T	0.20538	-1.0272	10	0.49607	T	0.09	-3.9077	9.9309	0.41521	0.0:0.0763:0.0:0.9237	.	1559	Q13023	AKAP6_HUMAN	P	1559	ENSP00000280979:L1559P	ENSP00000280979:L1559P	L	+	2	0	AKAP6	32361446	0.999000	0.42202	1.000000	0.80357	0.937000	0.57800	2.066000	0.41452	2.209000	0.71365	0.528000	0.53228	CTC	.	.		0.413	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274		C	33291695	T	C	33291695	3	2	263	1	0	0	0	0	1	0	0	0	455	1551	54	2	4722	2	AKAP6	14	33291695	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	8412476	33291695	74057845	313	38687										
BAZ1A	11177	hgsc.bcm.edu	37	chr14	35227928	35227928	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	acctggattttagaaacaagTttcaaaaaaggccagctgtc	8	8	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr14:35227928T>C	ENST00000382422.2	-	24	4695	c.4368A>G	c.(4366-4368)aaA>aaG	p.K1456K	BAZ1A_ENST00000358716.4_Silent_p.K1424K|BAZ1A_ENST00000360310.1_Silent_p.K1456K			Q9NRL2	BAZ1A_HUMAN	bromodomain adjacent to zinc finger domain, 1A	1456	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.				chromatin remodeling (GO:0006338)|DNA-dependent DNA replication (GO:0006261)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	ACF complex (GO:0016590)|CHRAC (GO:0008623)|nuclear chromosome (GO:0000228)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(2)|large_intestine(7)|lung(19)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	Breast(36;0.0388)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;7.23e-05)|Lung(238;0.00019)|Epithelial(34;0.0793)|all cancers(34;0.175)	GBM - Glioblastoma multiforme(112;0.0659)		TAGAAACAAGTTTCAAAAAAG	0.373																																					p.K1456K		Atlas-SNP	.											.	BAZ1A	128	.	0			c.A4368G						.						78	74	75					14																	35227928		2203	4300	6503	SO:0001819	synonymous_variant	11177	exon25			AACAAGTTTCAAA	AB032252	CCDS9651.1, CCDS41943.1	14q13.2	2013-01-28			ENSG00000198604	ENSG00000198604		"Zinc fingers, PHD-type"	960	protein-coding gene	gene with protein product		605680				10662543	Standard	NM_013448		Approved	hACF1, ACF1, WALp1, WCRF180	uc001wsk.3	Q9NRL2	OTTHUMG00000140216	ENST00000382422.2:c.4368A>G	chr14.hg19:g.35227928T>C		58.0	0.0		65.0	4.0	NM_013448	Q9NZ15|Q9P065|Q9UIG1|Q9Y3V3	Silent	SNP	ENST00000382422.2	hg19	CCDS9651.1																																																																																			.	.		0.373	BAZ1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276646.1			C	35227928	T	C	35227928	2	2	263	1	0	0	0	0	0	0	0	1	1329	1722	60	2		2	BAZ1A	14	35227928	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	1936233	35227928	72121612	314	38688										
LRFN5	145581	hgsc.bcm.edu	37	chr14	42357029	42357029	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cttcagatatctcaacttctAccaagtcaggttctaataca	4	11	5	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr14:42357029A>G	ENST00000298119.4	+	3	2390	c.1201A>G	c.(1201-1203)Acc>Gcc	p.T401A	LRFN5_ENST00000554171.1_Missense_Mutation_p.T401A|LRFN5_ENST00000554120.1_Missense_Mutation_p.T401A	NM_152447.3	NP_689660.2	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III domain containing 5	401						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(67)|ovary(5)|pancreas(3)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(2)	120			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		CTCAACTTCTACCAAGTCAGG	0.368										HNSCC(30;0.082)																											p.T401A		Atlas-SNP	.											.	LRFN5	269	.	0			c.A1201G						.						83	84	83					14																	42357029		2203	4300	6503	SO:0001583	missense	145581	exon3			ACTTCTACCAAGT	AK055365	CCDS9678.1	14q21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000165379	ENSG00000165379		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	20360	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 8"	612811	"chromosome 14 open reading frame 146"	C14orf146		16828986	Standard	NM_152447		Approved	FIGLER8, SALM5	uc001wvm.3	Q96NI6	OTTHUMG00000140261	ENST00000298119.4:c.1201A>G	chr14.hg19:g.42357029A>G	ENSP00000298119:p.Thr401Ala	62.0	0.0		92.0	4.0	NM_152447	B3KU78|Q86XL2	Missense_Mutation	SNP	ENST00000298119.4	hg19	CCDS9678.1	.	.	.	.	.	.	.	.	.	.	A	5.968	0.362503	0.11296	.	.	ENSG00000165379	ENST00000298119;ENST00000554120;ENST00000554171	T;T;T	0.52057	0.78;0.69;0.68	5.4	5.4	0.78164	.	0.000000	0.64402	D	0.000018	T	0.27798	0.0684	N	0.12831	0.26	0.58432	D	0.999999	B;B	0.14438	0.0;0.01	B;B	0.12156	0.003;0.007	T	0.12016	-1.0564	10	0.07990	T	0.79	.	13.6708	0.62424	1.0:0.0:0.0:0.0	.	401;401	G3V364;Q96NI6	.;LRFN5_HUMAN	A	401	ENSP00000298119:T401A;ENSP00000451897:T401A;ENSP00000451067:T401A	ENSP00000298119:T401A	T	+	1	0	LRFN5	41426779	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	5.920000	0.70017	2.165000	0.68154	0.460000	0.39030	ACC	.	.		0.368	LRFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276786.1	NM_152447		G	42357029	A	G	42357029	3	3	263	1	0	0	0	0	1	0	0	0	8950	391	14	2	1203	2	LRFN5	14	42357029	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	7129101	42357029	64992511	315	38689										
C14orf101	54916	hgsc.bcm.edu	37	chr14	57083976	57083976	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tcattgttctttgcttggagAgcaaatttagatatttcaaa	7	5	3	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr14:57083976A>G	ENST00000261556.6	+	9	1139	c.1017A>G	c.(1015-1017)agA>agG	p.R339R	TMEM260_ENST00000538838.1_Silent_p.R339R|TMEM260_ENST00000553335.1_3'UTR|TMEM260_ENST00000536419.1_5'UTR	NM_017799.3	NP_060269.3	Q9NX78	TM260_HUMAN	transmembrane protein 260	339						integral component of membrane (GO:0016021)											TTGCTTGGAGAGCAAATTTAG	0.313																																					p.R339R		Atlas-SNP	.											.	.	.	.	0			c.A1017G						.						128	122	124					14																	57083976		2202	4299	6501	SO:0001819	synonymous_variant	0	exon9			TTGGAGAGCAAAT	AK000399	CCDS9727.2	14q22.2	2013-03-08	2013-03-08	2013-03-08	ENSG00000070269	ENSG00000070269			20185	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 101"	C14orf101			Standard	XR_245695		Approved	FLJ20392	uc001xcm.3	Q9NX78	OTTHUMG00000152337	ENST00000261556.6:c.1017A>G	chr14.hg19:g.57083976A>G		109.0	0.0		108.0	5.0	NM_017799	A8KAN4|B3KPF5|Q86XE1	Silent	SNP	ENST00000261556.6	hg19	CCDS9727.2																																																																																			.	.		0.313	TMEM260-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276924.1	NM_017799		G	57083976	A	G	57083976	2	3	263	1	0	0	0	0	0	0	0	1	1736	301	11	2		2	C14orf101	14	57083976	Silent	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	14726947	57083976	50265564	316	38690										
C14orf135	64430	hgsc.bcm.edu	37	chr14	60585412	60585412	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	atggcagctggaagtttaggTaagtaaatgggttgtgctca	14	4	1	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr14:60585412T>C	ENST00000406854.1	+	7	2496		c.e7+2		PCNXL4_ENST00000406949.1_Splice_Site|PCNXL4_ENST00000535349.1_Splice_Site|PCNXL4_ENST00000404681.2_Splice_Site|PCNXL4_ENST00000317623.4_Splice_Site			Q63HM2	PCX4_HUMAN	pecanex-like 4 (Drosophila)							integral component of membrane (GO:0016021)											GAAGTTTAGGTAAGTAAATGG	0.398																																					.		Atlas-SNP	.											.	.	.	.	0			c.1240+2T>C						.						66	49	55					14																	60585412		2203	4300	6503	SO:0001630	splice_region_variant	64430	exon6			TTTAGGTAAGTAA	AK022861		14q23.1	2012-07-18	2012-07-18	2012-07-18	ENSG00000126773	ENSG00000126773			20349	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 135"	C14orf135			Standard	NM_022495		Approved		uc001xer.4	Q63HM2	OTTHUMG00000150361	ENST00000406854.1:c.1942+2T>C	chr14.hg19:g.60585412T>C		80.0	0.0		100.0	4.0	NM_022495	A8MXM2|Q9BQG8|Q9H9F2	Splice_Site	SNP	ENST00000406854.1	hg19		.	.	.	.	.	.	.	.	.	.	T	22.6	4.308018	0.81247	.	.	ENSG00000126773	ENST00000317623;ENST00000406854;ENST00000406949;ENST00000404681;ENST00000554534	.	.	.	6.16	6.16	0.99307	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.8061	0.85666	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	C14orf135	59655165	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.033000	0.76504	2.367000	0.80283	0.528000	0.53228	.	.	.		0.398	PCNXL4-005	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000317847.1	NM_022495	Intron	C	60585412	T	C	60585412	5	2	263	1	0	0	0	0	0	0	1	0	1747	1652	57	2	1260	2	C14orf135	14	60585412	Splice_Site	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	3501436	60585412	46764128	317	38691										
ZFYVE26	23503	hgsc.bcm.edu	37	chr14	68220472	68220472	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ccatcttctacatttttcccTcccagcatgacctgaaaagg	5	14	2	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr14:68220472T>C	ENST00000347230.4	-	39	7278	c.7140A>G	c.(7138-7140)ggA>ggG	p.G2380G	RN7SL213P_ENST00000463482.2_RNA|ZFYVE26_ENST00000557306.1_Silent_p.G226G	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	2380					cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		CATTTTTCCCTCCCAGCATGA	0.393																																					p.G2380G		Atlas-SNP	.											.	ZFYVE26	223	.	0			c.A7140G						.						73	63	66					14																	68220472		2203	4300	6503	SO:0001819	synonymous_variant	23503	exon39			TTTCCCTCCCAGC	AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"Zinc fingers, FYVE domain containing"	20761	protein-coding gene	gene with protein product	"spastizin", "FYVE-CENT"	612012	"spastic paraplegia 15 (complicated, autosomal recessive)"	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.7140A>G	chr14.hg19:g.68220472T>C		61.0	0.0		77.0	4.0	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Silent	SNP	ENST00000347230.4	hg19	CCDS9788.1																																																																																			.	.		0.393	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346		C	68220472	T	C	68220472	2	2	263	1	0	0	0	0	0	0	0	1	17683	1538	54	2		2	ZFYVE26	14	68220472	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	7635060	68220472	39129068	318	38692										
C14orf1	11161	hgsc.bcm.edu	37	chr14	76117958	76117958	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	agataccggagcccgaccagCatacccaggatggagaaacc	11	13	0	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr14:76117958C>T	ENST00000256319.6	-	5	808	c.363G>A	c.(361-363)atG>atA	p.M121I	FLVCR2_ENST00000556241.1_Intron|FLVCR2_ENST00000553587.1_Intron	NM_007176.3	NP_009107.1	Q9UKR5	ERG28_HUMAN	chromosome 14 open reading frame 1	121					sterol biosynthetic process (GO:0016126)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	6		all_epithelial(191;0.125)|all_neural(303;0.13)|Myeloproliferative disorder(585;0.163)		BRCA - Breast invasive adenocarcinoma(234;0.00147)		GCCCGACCAGCATACCCAGGA	0.473																																					p.M121I		Atlas-SNP	.											.	C14orf1	13	.	0			c.G363A						.						162	161	161					14																	76117958		2203	4300	6503	SO:0001583	missense	11161	exon5			GACCAGCATACCC	AF134159	CCDS9845.1	14q24.3	2012-08-16			ENSG00000133935	ENSG00000133935			1187	protein-coding gene	gene with protein product		604576				10449901, 12958361, 11160377	Standard	NM_007176		Approved	NET51, ERG28	uc001xrt.3	Q9UKR5	OTTHUMG00000171488	ENST00000256319.6:c.363G>A	chr14.hg19:g.76117958C>T	ENSP00000256319:p.Met121Ile	76.0	0.0		104.0	37.0	NM_007176	Q9P093|Q9UPI2	Missense_Mutation	SNP	ENST00000256319.6	hg19	CCDS9845.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.949887	0.92660	.	.	ENSG00000133935	ENST00000256319	.	.	.	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.85831	0.5788	M	0.91818	3.245	0.80722	D	1	D	0.57899	0.981	D	0.67900	0.954	D	0.88229	0.2902	9	0.72032	D	0.01	-35.6857	19.4226	0.94727	0.0:1.0:0.0:0.0	.	121	Q9UKR5	ERG28_HUMAN	I	121	.	ENSP00000256319:M121I	M	-	3	0	C14orf1	75187711	1.000000	0.71417	0.990000	0.47175	0.871000	0.50021	7.226000	0.78060	2.684000	0.91462	0.650000	0.86243	ATG	.	.		0.473	C14orf1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413683.1	NM_007176		T	76117958	C	T	76117958	3	4	263	1	0	0	0	0	1	0	0	0	1735	710	25	3	63	3	C14orf1	14	76117958	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	7897486	76117958	31231582	319	38693										
C14orf102	55051	hgsc.bcm.edu	37	chr14	90755002	90755002	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	agagcatgaagcatttagccAggctaattaggcggctacag	12	8	0	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr14:90755002A>G	ENST00000354366.3	-	11	2949	c.2717T>C	c.(2716-2718)cTg>cCg	p.L906P	NRDE2_ENST00000357904.3_Missense_Mutation_p.L675P	NM_017970.3	NP_060440.2	Q9H7Z3	NRDE2_HUMAN	NRDE-2, necessary for RNA interference, domain containing	906																	GCATTTAGCCAGGCTAATTAG	0.483																																					p.L906P		Atlas-SNP	.											.	.	.	.	0			c.T2717C						.						63	60	61					14																	90755002		2203	4300	6503	SO:0001583	missense	55051	exon11			TTAGCCAGGCTAA	AK000870	CCDS9890.1	14q32.11	2012-12-14	2012-09-25	2012-09-25	ENSG00000119720	ENSG00000119720			20186	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 102"	C14orf102			Standard	NM_017970		Approved	FLJ14051	uc001xyi.2	Q9H7Z3	OTTHUMG00000171020	ENST00000354366.3:c.2717T>C	chr14.hg19:g.90755002A>G	ENSP00000346335:p.Leu906Pro	45.0	0.0		72.0	4.0	NM_017970	B4DH71|Q4G0A7|Q9NWH6	Missense_Mutation	SNP	ENST00000354366.3	hg19	CCDS9890.1	.	.	.	.	.	.	.	.	.	.	A	14.54	2.566942	0.45694	.	.	ENSG00000119720	ENST00000354366;ENST00000357904	T;T	0.34859	1.56;1.34	4.84	4.84	0.62591	.	0.086877	0.47852	D	0.000207	T	0.55593	0.1930	M	0.76002	2.32	0.80722	D	1	D;D	0.58620	0.971;0.983	P;P	0.59761	0.732;0.863	T	0.58896	-0.7555	10	0.48119	T	0.1	-8.3797	14.5799	0.68282	1.0:0.0:0.0:0.0	.	675;906	E9PBK4;Q9H7Z3	.;CN102_HUMAN	P	906;675	ENSP00000346335:L906P;ENSP00000350579:L675P	ENSP00000346335:L906P	L	-	2	0	C14orf102	89824755	0.509000	0.26163	0.044000	0.18714	0.075000	0.17131	5.159000	0.64923	2.038000	0.60285	0.528000	0.53228	CTG	.	.		0.483	NRDE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411264.1	NM_017970		G	90755002	A	G	90755002	3	3	263	1	0	0	0	0	1	0	0	0	1737	188	7	2	793	2	C14orf102	14	90755002	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	14637044	90755002	16594538	320	38694										
CCDC88C	440193	hgsc.bcm.edu	37	chr14	91806281	91806281	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ccgcaggtggagcaccatgcTcctcgacagggcctccagct	12	16	0	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr14:91806281T>C	ENST00000389857.6	-	7	657	c.571A>G	c.(571-573)Agc>Ggc	p.S191G		NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	191					protein destabilization (GO:0031648)|protein homooligomerization (GO:0051260)|regulation of protein phosphorylation (GO:0001932)|Wnt signaling pathway (GO:0016055)		PDZ domain binding (GO:0030165)|protein self-association (GO:0043621)			central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(6)|pancreas(1)|urinary_tract(1)	24		all_cancers(154;0.0468)				AGCACCATGCTCCTCGACAGG	0.667																																					p.S191G		Atlas-SNP	.											.	CCDC88C	192	.	0			c.A571G						.						14	18	16					14																	91806281		2043	4182	6225	SO:0001583	missense	440193	exon7			CCATGCTCCTCGA		CCDS45151.1	14q32.12	2014-07-30	2007-05-31	2007-05-31		ENSG00000015133			19967	protein-coding gene	gene with protein product	"Dvl-associating protein with a high frequency of leucine residues", "spinocerebellar ataxia 40"	611204	"KIAA1509"	KIAA1509		17185515, 25062847	Standard	NM_001080414		Approved	DAPLE, HkRP2, SCA40	uc010aty.3	Q9P219		ENST00000389857.6:c.571A>G	chr14.hg19:g.91806281T>C	ENSP00000374507:p.Ser191Gly	147.0	0.0		181.0	12.0	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Missense_Mutation	SNP	ENST00000389857.6	hg19	CCDS45151.1	.	.	.	.	.	.	.	.	.	.	T	19.17	3.775385	0.70107	.	.	ENSG00000015133	ENST00000389857;ENST00000541408	T	0.17370	2.28	5.18	5.18	0.71444	.	0.246855	0.27526	U	0.018968	T	0.14570	0.0352	N	0.16656	0.425	0.80722	D	1	B	0.26547	0.152	B	0.32928	0.155	T	0.08994	-1.0695	10	0.72032	D	0.01	-16.8104	15.0422	0.71799	0.0:0.0:0.0:1.0	.	191	Q9P219	DAPLE_HUMAN	G	191;155	ENSP00000374507:S191G	ENSP00000374507:S191G	S	-	1	0	CCDC88C	90876034	1.000000	0.71417	0.838000	0.33150	0.968000	0.65278	6.276000	0.72601	1.942000	0.56320	0.459000	0.35465	AGC	.	.		0.667	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353		C	91806281	T	C	91806281	3	2	263	1	0	0	0	0	1	0	0	0	2867	1551	54	2	5611	2	CCDC88C	14	91806281	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	1051279	91806281	15543259	321	38695										
SLC24A4	123041	hgsc.bcm.edu	37	chr14	92953018	92953024	+	Frame_Shift_Del	DEL	TATCGGA	TATCGGA	-													0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cacattctgcaggtgactatTatcggatacacacttgggat							TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	TATCGGA	TATCGGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr14:92953018_92953024delTATCGGA	ENST00000532405.1	+	14	1657_1663	c.1431_1437delTATCGGA	c.(1429-1437)attatcggafs	p.IIG477fs	SLC24A4_ENST00000393265.2_Frame_Shift_Del_p.IIG413fs|SLC24A4_ENST00000298877.1_Frame_Shift_Del_p.IIG460fs|SLC24A4_ENST00000351924.5_Frame_Shift_Del_p.IIG441fs|SLC24A4_ENST00000531433.1_Frame_Shift_Del_p.IIG458fs			Q8NFF2	NCKX4_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 4	477					amelogenesis (GO:0097186)|cellular calcium ion homeostasis (GO:0006874)|ion transport (GO:0006811)|response to stimulus (GO:0050896)|sensory perception of smell (GO:0007608)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)	p.I461I(1)|p.G462R(1)		breast(3)|endometrium(2)|kidney(2)|large_intestine(6)|lung(20)|ovary(2)|skin(1)	36		all_cancers(154;0.0347)|all_epithelial(191;0.163)		Colorectal(1;0.00242)|COAD - Colon adenocarcinoma(157;0.047)|Epithelial(152;0.0781)|READ - Rectum adenocarcinoma(1;0.176)|all cancers(159;0.182)		AGGTGACTATTATCGGATACACACTTG	0.478																																					p.477_479del	NSCLC(10;315 435 10383 28450 38798)	Atlas-Indel,Pindel	.											.	SLC24A4	112	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	ovary(1)|large_intestine(1)	c.1430_1436del						.																																			SO:0001589	frameshift_variant	123041	exon14			.	AF520704	CCDS9903.1, CCDS45155.1, CCDS45156.1, CCDS9903.2, CCDS45155.2	14q32.12	2013-05-22			ENSG00000140090	ENSG00000140090		"Solute carriers"	10978	protein-coding gene	gene with protein product		609840					Standard	NM_153646		Approved	NCKX4	uc001yak.3	Q8NFF2	OTTHUMG00000167589	ENST00000532405.1:c.1431_1437delTATCGGA	chr14.hg19:g.92953018_92953024delTATCGGA	ENSP00000431840:p.Ile477fs	224.0	0.0		240.0	38.0	NM_153646	B4DHE7|B9ZVY2|Q8N8U6|Q8NCX1|Q8NFF0|Q8NFF1	Frame_Shift_Del	DEL	ENST00000532405.1	hg19	CCDS9903.2																																																																																			.	.		0.478	SLC24A4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395240.1	NM_153646		-	92953024	TATCGGA	-	92953018	7	5	263	1	0	1	0	1	0	0	0	0	14483	1742	61	0	1434	0	SLC24A4	14	92953018	Frame_Shift_Del	DEL	TATCGGA	TCGA-FV-A2QR-01A-11D-A20W-10	1146737	92953018	14396522	322	38696										
YY1	7528	hgsc.bcm.edu	37	chr14	100742844	100742844	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	aagggctgcacaaagatgttCagggataactcggccatgag	13	8	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr14:100742844C>G	ENST00000262238.4	+	4	1181	c.921C>G	c.(919-921)ttC>ttG	p.F307L		NM_003403.3	NP_003394.1	P25490	TYY1_HUMAN	YY1 transcription factor	307	Binding to DNA.|Involved in nuclear matrix association.				anterior/posterior pattern specification (GO:0009952)|camera-type eye morphogenesis (GO:0048593)|cell differentiation (GO:0030154)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|chromosome organization (GO:0051276)|double-strand break repair via homologous recombination (GO:0000724)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to prostaglandin F (GO:0034696)|response to UV-C (GO:0010225)|RNA localization (GO:0006403)|spermatogenesis (GO:0007283)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|four-way junction DNA binding (GO:0000400)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|large_intestine(1)|liver(2)|lung(1)|prostate(4)|skin(1)	11		Melanoma(154;0.152)				CAAAGATGTTCAGGGATAACT	0.428																																					p.F307L		Atlas-SNP	.											.	YY1	20	.	0			c.C921G						.						76	73	74					14																	100742844		2203	4300	6503	SO:0001583	missense	7528	exon4			GATGTTCAGGGAT	BC020324	CCDS9957.1	14q	2013-01-08			ENSG00000100811	ENSG00000100811		"INO80 complex subunits", "Zinc fingers, C2H2-type"	12856	protein-coding gene	gene with protein product	"INO80 complex subunit S", "Yin and Yang 1 protein"	600013				1655281, 7912122	Standard	NM_003403		Approved	NF-E1, DELTA, UCRBP, YIN-YANG-1, INO80S	uc001ygy.2	P25490	OTTHUMG00000150479	ENST00000262238.4:c.921C>G	chr14.hg19:g.100742844C>G	ENSP00000262238:p.Phe307Leu	85.0	0.0		105.0	27.0	NM_003403	Q14935	Missense_Mutation	SNP	ENST00000262238.4	hg19	CCDS9957.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.566514	0.86439	.	.	ENSG00000100811	ENST00000262238;ENST00000553625	T	0.18502	2.21	5.63	5.63	0.86233	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	U	0.000000	T	0.40423	0.1116	L	0.55743	1.74	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	T	0.02844	-1.1103	10	0.52906	T	0.07	.	20.0344	0.97551	0.0:1.0:0.0:0.0	.	307	P25490	TYY1_HUMAN	L	307;117	ENSP00000262238:F307L	ENSP00000262238:F307L	F	+	3	2	YY1	99812597	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.943000	0.70211	2.803000	0.96430	0.650000	0.86243	TTC	.	.		0.428	YY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318277.1	NM_003403		G	100742844	C	G	100742844	3	3	263	1	0	0	0	0	1	0	0	0	17522	825	29	4	935	4	YY1	14	100742844	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	7789826	100742844	6606696	323	38697										
GABRB3	2562	hgsc.bcm.edu	37	chr15	26828551	26828551	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gtccatcatgcatgctgctgTcgtggtgattctgaaataca	10	9	2	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr15:26828551T>C	ENST00000311550.5	-	5	583	c.472A>G	c.(472-474)Aca>Gca	p.T158A	GABRB3_ENST00000541819.2_Missense_Mutation_p.T214A|GABRB3_ENST00000400188.3_Missense_Mutation_p.T87A|GABRB3_ENST00000545868.1_Missense_Mutation_p.T73A|GABRB3_ENST00000299267.4_Missense_Mutation_p.T158A	NM_000814.5|NM_001278631.1	NP_000805.1|NP_001265560.1	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 3	158					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|GABA-gated chloride ion channel activity (GO:0022851)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(41)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	68		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ivermectin(DB00602)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Piperazine(DB00592)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CATGCTGCTGTCGTGGTGATT	0.468																																					p.T158A		Atlas-SNP	.											.	GABRB3	338	.	0			c.A472G						.						148	131	137					15																	26828551		2203	4300	6503	SO:0001583	missense	2562	exon5			CTGCTGTCGTGGT		CCDS10018.1, CCDS10019.1, CCDS53920.1, CCDS53921.1	15q12	2012-06-22			ENSG00000166206	ENSG00000166206		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4083	protein-coding gene	gene with protein product	"GABA(A) receptor, beta 3"	137192					Standard	NM_000814		Approved		uc001zaz.3	P28472	OTTHUMG00000129231	ENST00000311550.5:c.472A>G	chr15.hg19:g.26828551T>C	ENSP00000308725:p.Thr158Ala	93.0	0.0		78.0	4.0	NM_021912	B7Z2W1|B7Z825|F5H3D2|H7BYV8|Q14352|Q96FM5	Missense_Mutation	SNP	ENST00000311550.5	hg19	CCDS10019.1	.	.	.	.	.	.	.	.	.	.	T	11.78	1.741182	0.30865	.	.	ENSG00000166206	ENST00000311550;ENST00000541819;ENST00000299267;ENST00000400188;ENST00000545868;ENST00000555094	T;T;T;T;T;T	0.80033	-1.33;-1.33;-1.33;-1.33;-1.33;-1.33	4.76	4.76	0.60689	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	D	0.91112	0.7202	M	0.91768	3.24	0.80722	D	1	D;D;D	0.76494	0.994;0.999;0.995	D;D;D	0.76071	0.918;0.987;0.945	D	0.92932	0.6364	10	0.72032	D	0.01	.	13.74	0.62842	0.0:0.0:0.0:1.0	.	214;158;158	F5H7N0;P28472-2;P28472	.;.;GBRB3_HUMAN	A	158;214;158;87;73;73	ENSP00000308725:T158A;ENSP00000442408:T214A;ENSP00000299267:T158A;ENSP00000383049:T87A;ENSP00000439169:T73A;ENSP00000452272:T73A	ENSP00000299267:T158A	T	-	1	0	GABRB3	24379644	1.000000	0.71417	0.466000	0.27168	0.730000	0.41778	7.854000	0.86942	1.900000	0.55004	0.528000	0.53228	ACA	.	.		0.468	GABRB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251352.2			C	26828551	T	C	26828551	3	2	263	1	0	0	0	0	1	0	0	0	6176	1667	58	2	969	2	GABRB3	15	26828551	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10		26828551	75702841	324	38698										
C15orf52	388115	hgsc.bcm.edu	37	chr15	40628995	40628995	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	agcaatggtgggggctgtagTttctggtggctcctgggacc	17	8	1	0	rs143912259		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr15:40628995T>C	ENST00000559313.1	-	8	909	c.894A>G	c.(892-894)aaA>aaG	p.K298K	C15orf52_ENST00000557973.1_5'Flank|C15orf52_ENST00000397536.2_Silent_p.K88K	NM_207380.2	NP_997263.2	Q6ZUT6	CO052_HUMAN	chromosome 15 open reading frame 52	298							poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|urinary_tract(1)	19		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.06e-06)|Colorectal(105;0.0107)|BRCA - Breast invasive adenocarcinoma(123;0.0505)|READ - Rectum adenocarcinoma(2;0.0649)|Lung(196;0.0781)|LUAD - Lung adenocarcinoma(183;0.0841)		GGGGCTGTAGTTTCTGGTGGC	0.577																																					p.K298K		Atlas-SNP	.											.	C15orf52	47	.	0			c.A894G						.	T		0,4406		0,0,2203	57	63	61		894	2.6	0.1	15	dbSNP_134	61	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	C15orf52	NM_207380.2		0,1,6502	CC,CT,TT		0.0116,0.0,0.0077		298/535	40628995	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	388115	exon8			CTGTAGTTTCTGG	AK124643	CCDS10055.2	15q15.1	2007-06-14			ENSG00000188549	ENSG00000188549			33488	protein-coding gene	gene with protein product							Standard	NM_207380		Approved	FLJ43339	uc001zlh.4	Q6ZUT6	OTTHUMG00000129981	ENST00000559313.1:c.894A>G	chr15.hg19:g.40628995T>C		64.0	0.0		74.0	39.0	NM_207380	B9EIQ8|Q68DG9|Q6ZTM3|Q6ZU22	Silent	SNP	ENST00000559313.1	hg19	CCDS10055.2																																																																																			.	T|1.000;C|0.000		0.577	C15orf52-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319567.2	NM_207380		C	40628995	T	C	40628995	2	2	263	1	0	0	0	0	0	0	0	1	1802	1722	60	2		2	C15orf52	15	40628995	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	13800444	40628995	61902397	325	38699										
SPTBN5	51332	hgsc.bcm.edu	37	chr15	42163597	42163597	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gatcctgctgcctctgacggAccatggggccagcactgtgc	13	14	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr15:42163597A>G	ENST00000320955.6	-	29	5650	c.5423T>C	c.(5422-5424)gTc>gCc	p.V1808A		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	1808					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		CCTCTGACGGACCATGGGGCC	0.667																																					p.V1773A		Atlas-SNP	.											.	SPTBN5	171	.	0			c.T5318C						.						12	14	13					15																	42163597		1990	4115	6105	SO:0001583	missense	51332	exon29			TGACGGACCATGG	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"beta V spectrin"	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.5423T>C	chr15.hg19:g.42163597A>G	ENSP00000317790:p.Val1808Ala	212.0	0.0		153.0	7.0	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	hg19		.	.	.	.	.	.	.	.	.	.	.	5.207	0.223659	0.09863	.	.	ENSG00000137877	ENST00000320955	T	0.54866	0.55	4.7	-0.9	0.10544	.	0.740862	0.12022	N	0.506785	T	0.21022	0.0506	N	0.01771	-0.73	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.24977	-1.0145	10	0.18276	T	0.48	.	7.8825	0.29631	0.7049:0.0:0.2951:0.0	.	1808	Q9NRC6	SPTN5_HUMAN	A	1808	ENSP00000317790:V1808A	ENSP00000317790:V1808A	V	-	2	0	SPTBN5	39950889	0.006000	0.16342	0.000000	0.03702	0.022000	0.10575	0.645000	0.24782	-0.130000	0.11599	-0.337000	0.08149	GTC	.	.		0.667	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642		G	42163597	A	G	42163597	3	3	263	1	0	0	0	0	1	0	0	0	15137	275	10	2	5761	2	SPTBN5	15	42163597	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	1534602	42163597	60367795	326	38700										
CEP152	22995	hgsc.bcm.edu	37	chr15	49033896	49033896	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cagcattcataatctttttcTcagccctgtggggaattcca	7	11	3	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr15:49033896T>C	ENST00000380950.2	-	26	4182	c.3995A>G	c.(3994-3996)gAg>gGg	p.E1332G	CEP152_ENST00000399334.3_Missense_Mutation_p.E1276G|CEP152_ENST00000325747.5_Missense_Mutation_p.E1239G	NM_001194998.1|NM_014985.3	NP_001181927.1|NP_055800.2	O94986	CE152_HUMAN	centrosomal protein 152kDa	1332					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)			breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		AATCTTTTTCTCAGCCCTGTG	0.383																																					p.E1332G		Atlas-SNP	.											.	CEP152	145	.	0			c.A3995G						.						149	137	141					15																	49033896		1807	4077	5884	SO:0001583	missense	22995	exon26			TTTTTCTCAGCCC	AB020719	CCDS42033.1, CCDS58361.1	15q21.1	2014-02-20							29298	protein-coding gene	gene with protein product	"asterless"	613529	"microcephaly, primary autosomal recessive 4"	MCPH4		14654843, 21131973	Standard	NM_014985		Approved	KIAA0912, SCKL5	uc001zwz.3	O94986		ENST00000380950.2:c.3995A>G	chr15.hg19:g.49033896T>C	ENSP00000370337:p.Glu1332Gly	70.0	0.0		89.0	4.0	NM_001194998	E7ER66|Q17RV1|Q6NTA0	Missense_Mutation	SNP	ENST00000380950.2	hg19	CCDS58361.1	.	.	.	.	.	.	.	.	.	.	T	18.12	3.553265	0.65425	.	.	ENSG00000103995	ENST00000380950;ENST00000325747;ENST00000399334	T;T;T	0.66280	0.06;-0.01;-0.2	5.87	5.87	0.94306	.	0.065981	0.64402	D	0.000015	T	0.74129	0.3676	M	0.68593	2.085	0.58432	D	0.999999	D;D;D	0.63046	0.985;0.992;0.992	P;P;P	0.57101	0.676;0.813;0.813	T	0.77395	-0.2604	10	0.87932	D	0	-15.8868	16.2774	0.82651	0.0:0.0:0.0:1.0	.	1239;1332;1276	O94986-1;E7ER66;O94986	.;.;CE152_HUMAN	G	1332;1239;1276	ENSP00000370337:E1332G;ENSP00000321000:E1239G;ENSP00000382271:E1276G	ENSP00000321000:E1239G	E	-	2	0	CEP152	46821188	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.451000	0.80668	2.247000	0.74100	0.482000	0.46254	GAG	.	.		0.383	CEP152-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417365.1	NM_014985		C	49033896	T	C	49033896	3	2	263	1	0	0	0	0	1	0	0	0	3250	1551	54	2	1145	2	CEP152	15	49033896	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	6870299	49033896	53497496	327	38701										
RORA	6095	hgsc.bcm.edu	37	chr15	60806947	60806947	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	attgctttgctgacttctccTgaaaaagccctgtgatatgg	9	9	1	3			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr15:60806947T>C	ENST00000335670.6	-	4	392	c.292A>G	c.(292-294)Agg>Ggg	p.R98G	RP11-219B17.1_ENST00000559824.1_RNA|RP11-219B17.1_ENST00000559902.1_RNA|RORA_ENST00000261523.5_Missense_Mutation_p.R131G|RORA_ENST00000309157.4_Missense_Mutation_p.R123G|RP11-219B17.1_ENST00000501579.2_RNA|RP11-219B17.1_ENST00000558235.1_RNA|RORA_ENST00000449337.2_Missense_Mutation_p.R43G|RP11-219B17.1_ENST00000558140.1_RNA|RORA_ENST00000560004.1_5'UTR	NM_134261.2	NP_599023.1	P35398	RORA_HUMAN	RAR-related orphan receptor A	98					angiogenesis (GO:0001525)|cellular response to hypoxia (GO:0071456)|cellular response to sterol (GO:0036315)|cerebellar granule cell precursor proliferation (GO:0021930)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|circadian regulation of gene expression (GO:0032922)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|muscle cell differentiation (GO:0042692)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|nitric oxide biosynthetic process (GO:0006809)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of cholesterol homeostasis (GO:2000188)|regulation of glucose metabolic process (GO:0010906)|regulation of macrophage activation (GO:0043030)|regulation of smoothened signaling pathway (GO:0008589)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription involved in cell fate commitment (GO:0060850)|regulation of transcription, DNA-templated (GO:0006355)|T-helper 17 cell differentiation (GO:0072539)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)|xenobiotic metabolic process (GO:0006805)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	direct ligand regulated sequence-specific DNA binding transcription factor activity (GO:0098531)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|oxysterol binding (GO:0008142)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator binding (GO:0001223)|transcription corepressor binding (GO:0001222)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	21						TGACTTCTCCTGAAAAAGCCC	0.423																																					p.R131G		Atlas-SNP	.											.	RORA	114	.	0			c.A391G						.						119	111	114					15																	60806947		2203	4300	6503	SO:0001583	missense	6095	exon5			TTCTCCTGAAAAA	U04897	CCDS10177.1, CCDS10178.1, CCDS10179.1, CCDS45271.1	15q21-q22	2013-01-16			ENSG00000069667	ENSG00000069667		"Nuclear hormone receptors"	10258	protein-coding gene	gene with protein product		600825				7926749	Standard	NM_134261		Approved	RZRA, ROR1, ROR2, ROR3, NR1F1	uc002agv.3	P35398	OTTHUMG00000132769	ENST00000335670.6:c.292A>G	chr15.hg19:g.60806947T>C	ENSP00000335087:p.Arg98Gly	107.0	0.0		99.0	4.0	NM_134260	P35397|P35399|P45445|Q495X4|Q96H83	Missense_Mutation	SNP	ENST00000335670.6	hg19	CCDS10177.1	.	.	.	.	.	.	.	.	.	.	T	19.56	3.850811	0.71719	.	.	ENSG00000069667	ENST00000335670;ENST00000449337;ENST00000309157;ENST00000261523	D;D;D;D	0.97870	-4.58;-4.58;-4.58;-4.58	6.17	3.74	0.42951	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (5);	0.038962	0.85682	D	0.000000	D	0.99052	0.9675	H	0.96080	3.765	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.992;0.999;0.998	D	0.99250	1.0887	10	0.87932	D	0	.	13.0657	0.59032	0.0:0.0:0.3841:0.6159	.	98;123;131;43	P35398-2;P35398-3;P35398;P35398-4	.;.;RORA_HUMAN;.	G	98;43;123;131	ENSP00000335087:R98G;ENSP00000402971:R43G;ENSP00000309753:R123G;ENSP00000261523:R131G	ENSP00000261523:R131G	R	-	1	2	RORA	58594239	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.038000	0.57318	1.119000	0.41883	0.533000	0.62120	AGG	.	.		0.423	RORA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256142.2			C	60806947	T	C	60806947	3	2	263	1	0	0	0	0	1	0	0	0	13543	1579	55	2	1311	2	RORA	15	60806947	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	11773051	60806947	41724445	328	38702										
CLN6	54982	hgsc.bcm.edu	37	chr15	68504129	68504129	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	acccaccaggtggatgctggCacccatgatgaagatgatga	12	10	0	5			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr15:68504129C>T	ENST00000249806.5	-	4	527	c.370G>A	c.(370-372)Gcc>Acc	p.A124T	CLN6_ENST00000538696.1_Missense_Mutation_p.A156T|CLN6_ENST00000564752.1_Missense_Mutation_p.A124T|CLN6_ENST00000418702.2_Intron|RP11-315D16.2_ENST00000562767.1_Intron|CLN6_ENST00000566347.1_Intron|CLN6_ENST00000565471.1_Intron	NM_017882.2	NP_060352.1	Q9NWW5	CLN6_HUMAN	ceroid-lipofuscinosis, neuronal 6, late infantile, variant	124					cell death (GO:0008219)|cellular macromolecule catabolic process (GO:0044265)|cholesterol metabolic process (GO:0008203)|ganglioside metabolic process (GO:0001573)|glycosaminoglycan metabolic process (GO:0030203)|locomotion involved in locomotory behavior (GO:0031987)|lysosomal lumen acidification (GO:0007042)|positive regulation of proteolysis (GO:0045862)|protein catabolic process (GO:0030163)|visual perception (GO:0007601)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)			large_intestine(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	7						TGGATGCTGGCACCCATGATG	0.587																																					p.A124T		Atlas-SNP	.											.	CLN6	16	.	0			c.G370A						.						126	117	120					15																	68504129		2200	4298	6498	SO:0001583	missense	54982	exon4			TGCTGGCACCCAT	AK000568	CCDS10227.1	15q23	2014-09-17			ENSG00000128973	ENSG00000128973			2077	protein-coding gene	gene with protein product		606725				9097964, 11727201	Standard	NM_017882		Approved	FLJ20561, HsT18960, nclf	uc002arf.3	Q9NWW5	OTTHUMG00000133286	ENST00000249806.5:c.370G>A	chr15.hg19:g.68504129C>T	ENSP00000249806:p.Ala124Thr	95.0	0.0		95.0	4.0	NM_017882	A8K560|B4DDH6|Q6IAB1|Q96SR0	Missense_Mutation	SNP	ENST00000249806.5	hg19	CCDS10227.1	.	.	.	.	.	.	.	.	.	.	C	18.22	3.575549	0.65878	.	.	ENSG00000128973	ENST00000249806;ENST00000538696	D;D	0.95342	-3.68;-3.68	5.14	4.13	0.48395	.	0.057879	0.64402	D	0.000002	D	0.92185	0.7522	L	0.40543	1.245	0.80722	D	1	P;P	0.45531	0.86;0.767	P;B	0.44561	0.453;0.359	D	0.91988	0.5600	10	0.39692	T	0.17	-38.2012	16.3115	0.82873	0.1413:0.8587:0.0:0.0	.	156;124	B4DDH6;Q9NWW5	.;CLN6_HUMAN	T	124;156	ENSP00000249806:A124T;ENSP00000445770:A156T	ENSP00000249806:A124T	A	-	1	0	CLN6	66291183	0.990000	0.36364	1.000000	0.80357	0.992000	0.81027	2.868000	0.48436	2.388000	0.81334	0.511000	0.50034	GCC	.	.		0.587	CLN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257066.1	NM_017882		T	68504129	C	T	68504129	3	4	263	1	0	0	0	0	1	0	0	0	3547	710	25	3	581	3	CLN6	15	68504129	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	7697182	68504129	34027263	329	38703										
ITGA11	22801	hgsc.bcm.edu	37	chr15	68620599	68620599	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gatctgaaccactgggcgggAcctggaggagaagggccagt	17	9	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr15:68620599A>G	ENST00000315757.7	-	16	1989	c.1903T>C	c.(1903-1905)Tcc>Ccc	p.S635P	ITGA11_ENST00000423218.2_Splice_Site_p.S635P	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	635					cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|collagen-activated signaling pathway (GO:0038065)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|osteoblast differentiation (GO:0001649)|substrate-dependent cell migration (GO:0006929)	focal adhesion (GO:0005925)|integrin alpha11-beta1 complex (GO:0034681)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(6)|lung(22)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	52						ACTGGGCGGGACCTGGAGGAG	0.602																																					p.S635P		Atlas-SNP	.											.	ITGA11	110	.	0			c.T1903C						.						73	78	76					15																	68620599		1993	4170	6163	SO:0001630	splice_region_variant	22801	exon16			GGCGGGACCTGGA	AF109681	CCDS45291.1	15q22.3-q23	2010-03-23				ENSG00000137809		"Integrins"	6136	protein-coding gene	gene with protein product		604789				10486209	Standard	NM_001004439		Approved	HsT18964	uc002ari.3	Q9UKX5		ENST00000315757.7:c.1902-1T>C	chr15.hg19:g.68620599A>G		92.0	0.0		130.0	8.0	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Missense_Mutation	SNP	ENST00000315757.7	hg19	CCDS45291.1	.	.	.	.	.	.	.	.	.	.	A	15.52	2.858117	0.51376	.	.	ENSG00000137809	ENST00000315757;ENST00000423218;ENST00000535491	T;T	0.61742	0.08;0.08	5.7	1.85	0.25348	Integrin alpha-2 (1);	0.224650	0.48286	D	0.000193	T	0.67988	0.2952	M	0.71036	2.16	0.45567	D	0.998519	D;D	0.58620	0.983;0.982	D;P	0.66979	0.948;0.895	T	0.66400	-0.5933	10	0.87932	D	0	.	6.2284	0.20722	0.4256:0.3435:0.0:0.2309	.	635;635	A8K8T0;Q9UKX5	.;ITA11_HUMAN	P	635;635;270	ENSP00000327290:S635P;ENSP00000403392:S635P	ENSP00000327290:S635P	S	-	1	0	ITGA11	66407653	1.000000	0.71417	1.000000	0.80357	0.379000	0.30106	2.434000	0.44802	0.419000	0.25927	0.459000	0.35465	TCC	.	.		0.602	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211	Missense_Mutation	G	68620599	A	G	68620599	5	3	263	1	0	0	0	0	0	0	1	0	7883	289	10	2	1723	2	ITGA11	15	68620599	Splice_Site	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	116470	68620599	33910793	330	38704										
MYO9A	4649	hgsc.bcm.edu	37	chr15	72170493	72170493	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cacccagtgaatcacgctgcTcaagcctcatcgtcttttcc	6	16	4	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr15:72170493T>C	ENST00000356056.5	-	31	6291	c.5819A>G	c.(5818-5820)gAg>gGg	p.E1940G	MYO9A_ENST00000424560.1_Missense_Mutation_p.E2011G|MYO9A_ENST00000444904.1_Missense_Mutation_p.E1921G|MYO9A_ENST00000564571.1_Missense_Mutation_p.E1940G	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	1940	Tail.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)			NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						ATCACGCTGCTCAAGCCTCAT	0.373																																					p.E1940G		Atlas-SNP	.											.	MYO9A	203	.	0			c.A5819G						.						86	85	85					15																	72170493		2199	4297	6496	SO:0001583	missense	4649	exon31			CGCTGCTCAAGCC	AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"Myosins / Myosin superfamily : Class IX"	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.5819A>G	chr15.hg19:g.72170493T>C	ENSP00000348349:p.Glu1940Gly	120.0	0.0		184.0	9.0	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	hg19	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	T	16.81	3.224819	0.58668	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904	T;T;T	0.14640	2.49;2.49;2.49	5.21	5.21	0.72293	.	.	.	.	.	T	0.38321	0.1036	M	0.76574	2.34	0.51012	D	0.999909	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.982	T	0.25813	-1.0121	9	0.87932	D	0	.	15.373	0.74581	0.0:0.0:0.0:1.0	.	2011;1940	B2RTY4-4;B2RTY4	.;MYO9A_HUMAN	G	1940;2011;1921	ENSP00000348349:E1940G;ENSP00000399162:E2011G;ENSP00000398250:E1921G	ENSP00000348349:E1940G	E	-	2	0	MYO9A	69957547	1.000000	0.71417	1.000000	0.80357	0.100000	0.18952	7.628000	0.83189	2.075000	0.62263	0.482000	0.46254	GAG	.	.		0.373	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901		C	72170493	T	C	72170493	3	2	263	1	0	0	0	0	1	0	0	0	10093	1551	54	2	1875	2	MYO9A	15	72170493	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	3549894	72170493	30360899	331	38705										
SCAMP5	192683	hgsc.bcm.edu	37	chr15	75310253	75310253	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	atggcattcttctttaccttCatggctcagttggtcatcag	8	10	6	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr15:75310253C>T	ENST00000361900.6	+	6	543	c.336C>T	c.(334-336)ttC>ttT	p.F112F	SCAMP5_ENST00000562212.1_Silent_p.F112F|SCAMP5_ENST00000425597.3_Silent_p.F112F|SCAMP5_ENST00000568081.1_Silent_p.F45F|SCAMP5_ENST00000545456.1_Silent_p.F41F|SCAMP5_ENST00000565923.1_3'UTR	NM_001178111.1	NP_001171582.1	Q8TAC9	SCAM5_HUMAN	secretory carrier membrane protein 5	112					exocytosis (GO:0006887)|negative regulation of endocytosis (GO:0045806)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|positive regulation of cytokine secretion (GO:0050715)|protein transport (GO:0015031)|response to endoplasmic reticulum stress (GO:0034976)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)|synapse (GO:0045202)|trans-Golgi network membrane (GO:0032588)				large_intestine(1)|lung(1)|ovary(1)|urinary_tract(2)	5						TCTTTACCTTCATGGCTCAGT	0.632																																					p.F112F		Atlas-SNP	.											.	SCAMP5	34	.	0			c.C336T						.						127	126	126					15																	75310253		2078	4202	6280	SO:0001819	synonymous_variant	192683	exon6			TACCTTCATGGCT	AL833230	CCDS45306.1	15q24.2	2014-05-20			ENSG00000198794	ENSG00000198794		"Secretory carrier membrane proteins"	30386	protein-coding gene	gene with protein product		613766				12477932	Standard	NM_001178111		Approved	MGC24969	uc002azk.2	Q8TAC9	OTTHUMG00000172704	ENST00000361900.6:c.336C>T	chr15.hg19:g.75310253C>T		121.0	0.0		135.0	50.0	NM_001178111	B3KPJ7|B7Z762|D3DW71|Q8N3M4	Silent	SNP	ENST00000361900.6	hg19	CCDS45306.1																																																																																			.	.		0.632	SCAMP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420015.2	NM_138967		T	75310253	C	T	75310253	2	4	263	1	0	0	0	0	0	0	0	1	13889	825	29	3		3	SCAMP5	15	75310253	Silent	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	3139760	75310253	27221139	332	38706										
IQGAP1	8826	hgsc.bcm.edu	37	chr15	91043300	91043300	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	agctaaagtaaatgtcaaccTcctgatcttccttctcaaca	4	12	3	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr15:91043300T>C	ENST00000268182.5	+	38	5058	c.4934T>C	c.(4933-4935)cTc>cCc	p.L1645P	IQGAP1_ENST00000560738.1_Missense_Mutation_p.L1073P	NM_003870.3	NP_003861.1	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	1645	C2.				cellular response to calcium ion (GO:0071277)|cellular response to epidermal growth factor stimulus (GO:0071364)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerular visceral epithelial cell development (GO:0072015)|negative regulation of catalytic activity (GO:0043086)|negative regulation of dephosphorylation (GO:0035305)|neuron projection extension (GO:1990138)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|regulation of cytokine production (GO:0001817)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	actin filament (GO:0005884)|axon (GO:0030424)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|midbody (GO:0030496)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activator activity (GO:0043539)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			AATGTCAACCTCCTGATCTTC	0.398																																					p.L1645P		Atlas-SNP	.											.	IQGAP1	140	.	0			c.T4934C						.						99	91	93					15																	91043300		2198	4298	6496	SO:0001583	missense	8826	exon38			TCAACCTCCTGAT	D29640	CCDS10362.1	15q26.1	2008-07-18			ENSG00000140575	ENSG00000140575			6110	protein-coding gene	gene with protein product	"RasGAP-like with IQ motifs"	603379				8051149, 8670801	Standard	XM_005254984		Approved	p195, KIAA0051, SAR1, HUMORFA01	uc002bpl.1	P46940	OTTHUMG00000149832	ENST00000268182.5:c.4934T>C	chr15.hg19:g.91043300T>C	ENSP00000268182:p.Leu1645Pro	94.0	0.0		96.0	5.0	NM_003870	A7MBM3	Missense_Mutation	SNP	ENST00000268182.5	hg19	CCDS10362.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.583534	0.86748	.	.	ENSG00000140575	ENST00000268182	T	0.03242	4.0	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.21387	0.0515	M	0.85859	2.78	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.994;0.998	T	0.00595	-1.1653	10	0.66056	D	0.02	-14.7305	15.1546	0.72730	0.0:0.0:0.0:1.0	.	266;1645	B4DNP4;P46940	.;IQGA1_HUMAN	P	1645	ENSP00000268182:L1645P	ENSP00000268182:L1645P	L	+	2	0	IQGAP1	88844304	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.901000	0.87382	2.180000	0.69256	0.454000	0.30748	CTC	.	.		0.398	IQGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313493.1	NM_003870		C	91043300	T	C	91043300	3	2	263	1	0	0	0	0	1	0	0	0	7823	1551	54	2	5084	2	IQGAP1	15	91043300	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	15733047	91043300	11488092	333	38707										
LRRC28	123355	hgsc.bcm.edu	37	chr15	99892588	99892588	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	atccagatttaggtcgatctCgagaactacagtatgtatac	8	8	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr15:99892588C>T	ENST00000301981.3	+	7	847	c.607C>T	c.(607-609)Cga>Tga	p.R203*	LRRC28_ENST00000422500.2_Nonsense_Mutation_p.R134*|LRRC28_ENST00000331450.5_Intron|LRRC28_ENST00000447360.2_Nonsense_Mutation_p.R203*|LRRC28_ENST00000442993.2_3'UTR|LRRC28_ENST00000558879.1_Intron	NM_144598.2	NP_653199.2	Q86X40	LRC28_HUMAN	leucine rich repeat containing 28	203										endometrium(2)|large_intestine(3)|lung(6)|prostate(1)	12	Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00106)			AGGTCGATCTCGAGAACTACA	0.353																																					p.R203X		Atlas-SNP	.											LRRC28,NS,malignant_melanoma,0,1	LRRC28	38	.	0			c.C607T						.						166	156	160					15																	99892588		2197	4297	6494	SO:0001587	stop_gained	123355	exon7			CGATCTCGAGAAC	AK091588	CCDS10380.1, CCDS66873.1	15q26.3	2004-06-29			ENSG00000168904	ENSG00000168904			28355	protein-coding gene	gene with protein product						12975309	Standard	XM_005254861		Approved	MGC24976, FLJ34269, FLJ45242	uc002bva.1	Q86X40	OTTHUMG00000149854	ENST00000301981.3:c.607C>T	chr15.hg19:g.99892588C>T	ENSP00000304923:p.Arg203*	33.0	0.0		25.0	2.0	NM_144598	A8KA22|Q6UY49|Q6ZSS6	Nonsense_Mutation	SNP	ENST00000301981.3	hg19	CCDS10380.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.692475	0.88735	.	.	ENSG00000168904	ENST00000301981;ENST00000447360;ENST00000422500	.	.	.	5.52	4.6	0.57074	.	0.131334	0.49916	D	0.000129	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	.	13.6262	0.62165	0.0:0.9257:0.0:0.0743	.	.	.	.	X	203;203;134	.	ENSP00000304923:R203X	R	+	1	2	LRRC28	97710111	1.000000	0.71417	0.992000	0.48379	0.991000	0.79684	4.317000	0.59184	1.334000	0.45468	0.655000	0.94253	CGA	.	.		0.353	LRRC28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313546.1	NM_144598		T	99892588	C	T	99892588	4	4	263	1	0	0	0	0	0	1	0	0	8991	876	31	1	629	1	LRRC28	15	99892588	Nonsense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	8849288	99892588	2638804	334	38708										
SNRPA1	6627	hgsc.bcm.edu	37	chr15	101827183	101827183	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	aaatcacatacaatctgtaaTgcttcttattggttaccgga	6	8	3	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr15:101827183T>C	ENST00000254193.6	-	5	461	c.389A>G	c.(388-390)cAt>cGt	p.H130R	SNRPA1_ENST00000560856.1_5'UTR	NM_003090.2	NP_003081.2	P09661	RU2A_HUMAN	small nuclear ribonucleoprotein polypeptide A'	130	LRRCT.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U2 snRNP (GO:0005686)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)	6	Lung NSC(78;0.00156)|all_lung(78;0.00195)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.00113)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			CAATCTGTAATGCTTCTTATT	0.373																																					p.H130R		Atlas-SNP	.											.	SNRPA1	11	.	0			c.A389G						.						114	117	116					15																	101827183		2203	4299	6502	SO:0001583	missense	6627	exon5			CTGTAATGCTTCT	AJ130971	CCDS10391.1	15q26.3	2011-10-11			ENSG00000131876	ENSG00000131876			11152	protein-coding gene	gene with protein product		603521				2928112	Standard	NM_003090		Approved	Lea1	uc002bww.3	P09661	OTTHUMG00000149871	ENST00000254193.6:c.389A>G	chr15.hg19:g.101827183T>C	ENSP00000254193:p.His130Arg	64.0	0.0		87.0	4.0	NM_003090	B2R5I6|Q8TBD2	Missense_Mutation	SNP	ENST00000254193.6	hg19	CCDS10391.1	.	.	.	.	.	.	.	.	.	.	T	26.2	4.715126	0.89112	.	.	ENSG00000131876	ENST00000254193	T	0.60548	0.18	5.62	5.62	0.85841	U2A&apos (1);/phosphoprotein 32 family A, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.57140	0.2033	L	0.58969	1.84	0.80722	D	1	B	0.25105	0.118	B	0.28991	0.097	T	0.56396	-0.7986	10	0.48119	T	0.1	-22.7339	14.9907	0.71387	0.0:0.0:0.0:1.0	.	130	P09661	RU2A_HUMAN	R	130	ENSP00000254193:H130R	ENSP00000254193:H130R	H	-	2	0	SNRPA1	99644706	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.564000	0.82326	2.127000	0.65507	0.533000	0.62120	CAT	.	.		0.373	SNRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313621.2	NM_003090		C	101827183	T	C	101827183	3	2	263	1	0	0	0	0	1	0	0	0	14875	1464	51	2	398	2	SNRPA1	15	101827183	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	1934595	101827183	704209	335	38709										
TELO2	9894	hgsc.bcm.edu	37	chr16	1551668	1551668	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ccttgtttccttaaagcacgTccctcgttccagccacggca	7	16	0	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr16:1551668T>C	ENST00000262319.6	+	11	1645	c.1366T>C	c.(1366-1368)Tcc>Ccc	p.S456P		NM_016111.3	NP_057195.2	Q9Y4R8	TELO2_HUMAN	telomere maintenance 2	456					regulation of TOR signaling (GO:0032006)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	protein complex binding (GO:0032403)			NS(1)|endometrium(1)|kidney(5)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	19		Hepatocellular(780;0.219)				TTAAAGCACGTCCCTCGTTCC	0.607																																					p.S456P		Atlas-SNP	.											.	TELO2	44	.	0			c.T1366C						.						56	69	64					16																	1551668		2195	4300	6495	SO:0001583	missense	9894	exon11			AGCACGTCCCTCG	AL080126	CCDS32363.1	16p13.3	2013-08-06	2013-08-06		ENSG00000100726	ENSG00000100726			29099	protein-coding gene	gene with protein product		611140	"TEL2, telomere maintenance 2, homolog (S. cerevisiae)"			9734811, 11230166, 12670948	Standard	NM_016111		Approved	KIAA0683, hCLK2, TEL2	uc002cly.3	Q9Y4R8	OTTHUMG00000044471	ENST00000262319.6:c.1366T>C	chr16.hg19:g.1551668T>C	ENSP00000262319:p.Ser456Pro	121.0	0.0		138.0	6.0	NM_016111	D3DU73|O75168|Q7LDV4|Q9BR21	Missense_Mutation	SNP	ENST00000262319.6	hg19	CCDS32363.1	.	.	.	.	.	.	.	.	.	.	T	10.03	1.237542	0.22711	.	.	ENSG00000100726	ENST00000437914;ENST00000262319	D	0.84223	-1.82	5.18	-7.91	0.01165	.	1.609610	0.02739	N	0.116080	T	0.60547	0.2277	N	0.01742	-0.745	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.55560	-0.8122	10	0.27785	T	0.31	-1.6602	6.2357	0.20762	0.1148:0.5761:0.1259:0.1832	.	456	Q9Y4R8	TELO2_HUMAN	P	70;456	ENSP00000262319:S456P	ENSP00000262319:S456P	S	+	1	0	TELO2	1491669	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.063000	0.00622	-1.421000	0.02007	0.533000	0.62120	TCC	.	.		0.607	TELO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103602.2	NM_016111		C	1551668	T	C	1551668	3	2	263	1	0	0	0	0	1	0	0	0	15772	1667	58	2	1404	2	TELO2	16	1551668	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10		1551668	88803085	336	38710										
PKD1	5310	hgsc.bcm.edu	37	chr16	2153323	2153323	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cggccgcagggttgctgctgTccagggtgaccacagcaccg	15	14	0	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr16:2153323T>C	ENST00000262304.4	-	23	8943	c.8735A>G	c.(8734-8736)gAc>gGc	p.D2912G	PKD1_ENST00000423118.1_Missense_Mutation_p.D2912G|PKD1_ENST00000561991.1_5'Flank	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	2912					anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						GTTGCTGCTGTCCAGGGTGAC	0.697																																					p.D2912G		Atlas-SNP	.											.	PKD1	184	.	0			c.A8735G						.						22	25	24					16																	2153323		2144	4222	6366	SO:0001583	missense	5310	exon23			CTGCTGTCCAGGG	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"Voltage-gated ion channels / Transient receptor potential cation channels"	9008	protein-coding gene	gene with protein product	"polycystin 1", "transient receptor potential cation channel, subfamily P, member 1"	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.8735A>G	chr16.hg19:g.2153323T>C	ENSP00000262304:p.Asp2912Gly	110.0	0.0		86.0	4.0	NM_000296	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	hg19	CCDS32369.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	5.630|5.630	0.300866|0.300866	0.10678|0.10678	.|.	.|.	ENSG00000008710|ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101|ENST00000382481	T;T|.	0.70164|.	-0.46;-0.46|.	4.89|4.89	3.8|3.8	0.43715|0.43715	.|.	0.427016|.	0.27836|.	N|.	0.017643|.	T|T	0.34019|0.34019	0.0883|0.0883	N|N	0.19112|0.19112	0.55|0.55	0.22975|0.22975	N|N	0.998482|0.998482	P;B|.	0.34615|.	0.459;0.002|.	B;B|.	0.30401|.	0.115;0.003|.	T|T	0.26538|0.26538	-1.0100|-1.0100	10|6	0.23302|0.87932	T|D	0.38|0	.|.	10.4202|10.4202	0.44346|0.44346	0.0:0.077:0.0:0.923|0.0:0.077:0.0:0.923	.|.	2912;2912|.	P98161-3;P98161|.	.;PKD1_HUMAN|.	G|A	2912;2912;2247|1150	ENSP00000262304:D2912G;ENSP00000399501:D2912G|.	ENSP00000262304:D2912G|ENSP00000371921:T1150A	D|T	-|-	2|1	0|0	PKD1|PKD1	2093324|2093324	0.986000|0.986000	0.35501|0.35501	0.184000|0.184000	0.23157|0.23157	0.533000|0.533000	0.34776|0.34776	3.312000|3.312000	0.51927|0.51927	0.888000|0.888000	0.36160|0.36160	0.454000|0.454000	0.30748|0.30748	GAC|ACA	.	.		0.697	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			C	2153323	T	C	2153323	3	2	263	1	0	0	0	0	1	0	0	0	11972	1667	58	2	4272	2	PKD1	16	2153323	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	601655	2153323	88201430	337	38711										
TIGD7	91151	hgsc.bcm.edu	37	chr16	3348989	3348989	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tgattagaaccagaagttgaAggcccactgaaggagtcctt	11	8	0	5			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr16:3348989A>G	ENST00000396862.1	-	2	3454	c.1626T>C	c.(1624-1626)ccT>ccC	p.P542P	TIGD7_ENST00000574598.1_5'Flank|TIGD7_ENST00000268674.2_Silent_p.P542P	NM_033208.3	NP_149985.2	Q6NT04	TIGD7_HUMAN	tigger transposable element derived 7	542						nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	12						CAGAAGTTGAAGGCCCACTGA	0.353																																					p.P542P		Atlas-SNP	.											.	TIGD7	41	.	0			c.T1626C						.						50	51	50					16																	3348989		2197	4300	6497	SO:0001819	synonymous_variant	91151	exon2			AGTTGAAGGCCCA	AF251050	CCDS10500.1	16p13.11	2008-02-05			ENSG00000140993	ENSG00000140993			18331	protein-coding gene	gene with protein product		612969					Standard	NM_033208		Approved	Sancho	uc002cus.3	Q6NT04	OTTHUMG00000129325	ENST00000396862.1:c.1626T>C	chr16.hg19:g.3348989A>G		92.0	0.0		80.0	4.0	NM_033208	Q9BXZ0	Silent	SNP	ENST00000396862.1	hg19	CCDS10500.1																																																																																			.	.		0.353	TIGD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251465.1	NM_033208		G	3348989	A	G	3348989	2	3	263	1	0	0	0	0	0	0	0	1	15916	59	3	2		2	TIGD7	16	3348989	Silent	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	1195666	3348989	87005764	338	38712										
NLRC3	197358	hgsc.bcm.edu	37	chr16	3602250	3602250	+	RNA	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gcatctgccatccgctgggcTcccatgggcccgatgctgtt	12	15	1	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr16:3602250T>C	ENST00000301749.7	-	0	2703				NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000603507.1_RNA|NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000419350.2_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						TCCGCTGGGCTCCCATGGGCC	0.557																																					p.G766G		Atlas-SNP	.											.	NLRC3	103	.	0			c.A2298G						.						82	78	79					16																	3602250		1925	4142	6067			197358	exon10			CTGGGCTCCCATG	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"Nucleotide-binding domain and leucine rich repeat containing"	29889	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3", "NOD-like receptor C3"	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		chr16.hg19:g.3602250T>C		92.0	0.0		117.0	5.0	NM_178844	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Silent	SNP	ENST00000301749.7	hg19																																																																																				.	.		0.557	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844		C	3602250	T	C	3602250	1	2	263	0	1	0	0	0	0	0	0	0	10477	1538	54	2		2	NLRC3	16	3602250	RNA	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	253261	3602250	86752503	339	38713										
ATF7IP2	80063	hgsc.bcm.edu	37	chr16	10527419	10527419	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	aggatgttttcagaaaacgaGgaaaatgttaaacgcatgaa	10	4	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr16:10527419G>A	ENST00000396560.2	+	4	1100	c.873G>A	c.(871-873)gaG>gaA	p.E291E	ATF7IP2_ENST00000543967.1_Intron|ATF7IP2_ENST00000396559.1_Silent_p.E291E|ATF7IP2_ENST00000324570.5_Silent_p.E291E|ATF7IP2_ENST00000356427.2_Silent_p.E291E	NM_024997.3	NP_079273.2	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting protein 2	291					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				large_intestine(3)	3						CAGAAAACGAGGAAAATGTTA	0.328																																					p.E291E		Atlas-SNP	.											.	ATF7IP2	40	.	0			c.G873A						.						58	60	60					16																	10527419		2196	4299	6495	SO:0001819	synonymous_variant	80063	exon4			AAACGAGGAAAAT	AK022730	CCDS10540.1, CCDS58422.1	16p13.2	2008-02-05			ENSG00000166669	ENSG00000166669			20397	protein-coding gene	gene with protein product		613645					Standard	NM_001256160		Approved	FLJ12668	uc002czu.3	Q5U623	OTTHUMG00000129749	ENST00000396560.2:c.873G>A	chr16.hg19:g.10527419G>A		168.0	0.0		190.0	47.0	NM_024997	B2RNR2|Q53EZ7|Q658U2|Q6IS97|Q8N9X8|Q9H9L6	Silent	SNP	ENST00000396560.2	hg19	CCDS10540.1																																																																																			.	.		0.328	ATF7IP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251961.1	NM_024997		A	10527419	G	A	10527419	2	1	263	1	0	0	0	0	0	0	0	1	1088	991	35	3		3	ATF7IP2	16	10527419	Silent	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	6925169	10527419	79827334	340	38714										
CIITA	4261	hgsc.bcm.edu	37	chr16	10989540	10989540	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tcccagaacccgacacagacAccatcaactgcgaccagttc	6	17	1	2	rs143732812		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr16:10989540A>G	ENST00000324288.8	+	3	347	c.214A>G	c.(214-216)Acc>Gcc	p.T72A	CIITA_ENST00000381835.5_Missense_Mutation_p.T72A|CIITA_ENST00000537380.1_3'UTR	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	72	Asp/Glu-rich (acidic).				aging (GO:0007568)|cellular response to electrical stimulus (GO:0071257)|cellular response to exogenous dsRNA (GO:0071360)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to antibiotic (GO:0046677)|response to interferon-gamma (GO:0034341)|transcription, DNA-templated (GO:0006351)	cell surface (GO:0009986)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|GTP binding (GO:0005525)|kinase activity (GO:0016301)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transferase activity, transferring acyl groups (GO:0016746)			central_nervous_system(1)|large_intestine(7)|ovary(1)|skin(1)|stomach(2)	12						CGACACAGACACCATCAACTG	0.562			T	"FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"	"PMBL, Hodgkin Lymphona, "																																p.T72A		Atlas-SNP	.		Dom	yes		16	16p13	4261	"class II, major histocompatibility complex, transactivator"		L	.	CIITA	92	.	0			c.A214G						.	A	ALA/THR	0,4394		0,0,2197	93	88	90		214	4.8	1	16	dbSNP_134	90	2,8598	2.2+/-6.3	0,2,4298	yes	missense	CIITA	NM_000246.3	58	0,2,6495	GG,GA,AA		0.0233,0.0,0.0154	probably-damaging	72/1131	10989540	2,12992	2197	4300	6497	SO:0001583	missense	4261	exon3			ACAGACACCATCA	U18259	CCDS10544.1, CCDS66943.1, CCDS73826.1	16p13	2014-09-17	2005-08-12	2005-08-12	ENSG00000179583	ENSG00000179583		"Nucleotide-binding domain and leucine rich repeat containing"	7067	protein-coding gene	gene with protein product	"NLR family, acid domain containing", "nucleotide-binding oligomerization domain, leucine rich repeat and acid domain containing"	600005	"MHC class II transactivator"	MHC2TA		8402893	Standard	NM_000246		Approved	C2TA, NLRA	uc002dai.4	P33076	OTTHUMG00000129753	ENST00000324288.8:c.214A>G	chr16.hg19:g.10989540A>G	ENSP00000316328:p.Thr72Ala	102.0	0.0		136.0	6.0	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Missense_Mutation	SNP	ENST00000324288.8	hg19	CCDS10544.1	.	.	.	.	.	.	.	.	.	.	A	19.16	3.774165	0.69992	0.0	2.33E-4	ENSG00000179583	ENST00000324288;ENST00000381835;ENST00000388910;ENST00000537380	D;T	0.85702	-2.02;0.52	4.78	4.78	0.61160	.	0.000000	0.48286	D	0.000195	D	0.89497	0.6732	L	0.57536	1.79	0.25508	N	0.987483	D;D;D;D;D;D	0.76494	0.999;0.993;0.997;0.997;0.998;0.998	D;D;D;D;D;P	0.85130	0.997;0.978;0.917;0.917;0.948;0.839	T	0.82016	-0.0666	10	0.46703	T	0.11	.	10.7295	0.46087	1.0:0.0:0.0:0.0	.	72;72;72;72;72;72	F5H2J4;E9PFE0;A0N0N9;P33076;F2Z2G8;Q96KL4	.;.;.;C2TA_HUMAN;.;.	A	72	ENSP00000316328:T72A;ENSP00000371257:T72A	ENSP00000316328:T72A	T	+	1	0	CIITA	10897041	1.000000	0.71417	0.987000	0.45799	0.963000	0.63663	4.088000	0.57678	1.801000	0.52704	0.533000	0.62120	ACC	.	A|1.000;G|0.000		0.562	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246		G	10989540	A	G	10989540	3	3	263	1	0	0	0	0	1	0	0	0	3430	159	6	2	224	2	CIITA	16	10989540	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	462121	10989540	79365213	341	38715										
ACSM2A	123876	hgsc.bcm.edu	37	chr16	20497902	20497902	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ttgtttttcaacagatagagTttgtcttgaacctgcccaag	8	8	2	3			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr16:20497902T>C	ENST00000573854.1	+	14	1750	c.1636T>C	c.(1636-1638)Ttt>Ctt	p.F546L	ACSM2A_ENST00000536134.1_Missense_Mutation_p.F318L|ACSM2A_ENST00000219054.6_Missense_Mutation_p.F546L|ACSM2A_ENST00000575690.1_Missense_Mutation_p.F546L|ACSM2A_ENST00000396104.2_Missense_Mutation_p.F546L|ACSM2A_ENST00000417235.2_Missense_Mutation_p.F467L|AC137056.1_ENST00000593357.1_5'Flank	NM_001010845.2	NP_001010845	Q08AH3	ACS2A_HUMAN	acyl-CoA synthetase medium-chain family member 2A	546					fatty acid metabolic process (GO:0006631)|glucose homeostasis (GO:0042593)|medium-chain fatty-acyl-CoA metabolic process (GO:0036112)|triglyceride homeostasis (GO:0070328)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(34)|ovary(1)|skin(6)|stomach(1)	51						ACAGATAGAGTTTGTCTTGAA	0.493																																					p.F546L		Atlas-SNP	.											.	ACSM2A	120	.	0			c.T1636C						.						140	138	139					16																	20497902		2203	4298	6501	SO:0001583	missense	123876	exon15			ATAGAGTTTGTCT	AK091878, AK096039	CCDS32401.1	16p12.3	2014-08-08	2007-06-20	2007-06-20	ENSG00000183747	ENSG00000183747		"Acyl-CoA synthetase family"	32017	protein-coding gene	gene with protein product		614358	"acyl-CoA synthetase medium-chain family member 2"	ACSM2			Standard	NM_001010845		Approved	A-923A4.1, MGC150530	uc010bwe.3	Q08AH3	OTTHUMG00000177401	ENST00000573854.1:c.1636T>C	chr16.hg19:g.20497902T>C	ENSP00000459451:p.Phe546Leu	149.0	0.0		163.0	8.0	NM_001010845	B3KTT9|O75202	Missense_Mutation	SNP	ENST00000573854.1	hg19	CCDS32401.1	.	.	.	.	.	.	.	.	.	.	T	17.10	3.301749	0.60195	.	.	ENSG00000183747	ENST00000417235;ENST00000219054;ENST00000536134;ENST00000396104	T;T;T;T	0.59906	0.23;0.23;0.23;0.23	3.74	3.74	0.42951	.	0.000000	0.45126	D	0.000390	T	0.69378	0.3104	L	0.56769	1.78	0.80722	D	1	D	0.65815	0.995	D	0.72982	0.979	T	0.72181	-0.4368	10	0.87932	D	0	-13.4765	10.867	0.46862	0.0:0.0:0.0:1.0	.	546	Q08AH3	ACS2A_HUMAN	L	467;546;318;546	ENSP00000392169:F467L;ENSP00000219054:F546L;ENSP00000445082:F318L;ENSP00000379411:F546L	ENSP00000219054:F546L	F	+	1	0	ACSM2A	20405403	1.000000	0.71417	0.990000	0.47175	0.321000	0.28281	5.650000	0.67944	1.565000	0.49641	0.254000	0.18369	TTT	.	.		0.493	ACSM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436764.1	NM_001010845		C	20497902	T	C	20497902	3	2	263	1	0	0	0	0	1	0	0	0	183	1725	60	2	1686	2	ACSM2A	16	20497902	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	9508362	20497902	69856851	342	38716										
DNAH3	55567	hgsc.bcm.edu	37	chr16	21139101	21139101	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gcaattttcccgctagtattTctgctgttcgaacaaacctg	7	11	1	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr16:21139101T>C	ENST00000261383.3	-	8	1114	c.1115A>G	c.(1114-1116)gAa>gGa	p.E372G	DNAH3_ENST00000415178.1_Missense_Mutation_p.E372G|CTC-508F8.1_ENST00000575612.1_RNA	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	372	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			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)		CGCTAGTATTTCTGCTGTTCG	0.458																																					p.E372G		Atlas-SNP	.											.	DNAH3	1142	.	0			c.A1115G						.						130	129	129					16																	21139101		2201	4300	6501	SO:0001583	missense	55567	exon8			AGTATTTCTGCTG	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"Axonemal dyneins"	2949	protein-coding gene	gene with protein product		603334	"dynein, axonemal, heavy polypeptide 3"			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.1115A>G	chr16.hg19:g.21139101T>C	ENSP00000261383:p.Glu372Gly	58.0	0.0		89.0	4.0	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	hg19	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	T	15.79	2.938486	0.52972	.	.	ENSG00000158486	ENST00000261383;ENST00000415178;ENST00000396036	T;T	0.26223	1.75;1.9	5.42	5.42	0.78866	.	0.067691	0.56097	D	0.000021	T	0.38983	0.1061	M	0.65975	2.015	0.34727	D	0.729321	B;P	0.52061	0.229;0.95	B;P	0.52554	0.053;0.702	T	0.53961	-0.8364	10	0.36615	T	0.2	.	12.9781	0.58547	0.0:0.0:0.0:1.0	.	372;343	Q8TD57;Q8TD57-2	DYH3_HUMAN;.	G	372;372;343	ENSP00000261383:E372G;ENSP00000394245:E372G	ENSP00000261383:E372G	E	-	2	0	DNAH3	21046602	1.000000	0.71417	0.958000	0.39756	0.936000	0.57629	3.781000	0.55394	2.055000	0.61198	0.460000	0.39030	GAA	.	.		0.458	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		C	21139101	T	C	21139101	3	2	263	1	0	0	0	0	1	0	0	0	4605	1783	62	2	11454	2	DNAH3	16	21139101	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	641199	21139101	69215652	343	38717										
HS3ST2	9956	hgsc.bcm.edu	37	chr16	22926369	22926369	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	catcttcaacatgtcccgagAcaccaagctgatcgtggttg	9	12	2	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr16:22926369A>G	ENST00000261374.3	+	2	1024	c.590A>G	c.(589-591)gAc>gGc	p.D197G		NM_006043.1	NP_006034.1	Q9Y278	HS3S2_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 2	197					carbohydrate metabolic process (GO:0005975)|circadian rhythm (GO:0007623)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 2 activity (GO:0033871)|sulfotransferase activity (GO:0008146)			breast(2)|kidney(1)|large_intestine(5)|liver(2)|lung(5)|ovary(1)|pancreas(2)|skin(1)	19				GBM - Glioblastoma multiforme(48;0.0299)		ATGTCCCGAGACACCAAGCTG	0.577																																					p.D197G		Atlas-SNP	.											.	HS3ST2	59	.	0			c.A590G						.						124	111	115					16																	22926369		2197	4300	6497	SO:0001583	missense	9956	exon2			CCCGAGACACCAA	AF105374	CCDS10606.1	16p12	2008-02-05			ENSG00000122254	ENSG00000122254	2.8.2.23	"Sulfotransferases, membrane-bound"	5195	protein-coding gene	gene with protein product		604056				9988767	Standard	NM_006043		Approved	3OST2	uc002dli.3	Q9Y278	OTTHUMG00000094785	ENST00000261374.3:c.590A>G	chr16.hg19:g.22926369A>G	ENSP00000261374:p.Asp197Gly	89.0	0.0		81.0	4.0	NM_006043	Q52LZ1	Missense_Mutation	SNP	ENST00000261374.3	hg19	CCDS10606.1	.	.	.	.	.	.	.	.	.	.	A	15.19	2.761313	0.49468	.	.	ENSG00000122254	ENST00000261374;ENST00000540146	T	0.44083	0.93	5.25	5.25	0.73442	Sulfotransferase domain (1);	0.331796	0.35739	N	0.003019	T	0.37679	0.1012	L	0.45051	1.395	0.49915	D	0.999839	B	0.09022	0.002	B	0.18871	0.023	T	0.14364	-1.0475	10	0.40728	T	0.16	.	14.3773	0.66886	1.0:0.0:0.0:0.0	.	197	Q9Y278	HS3S2_HUMAN	G	197;205	ENSP00000261374:D197G	ENSP00000261374:D197G	D	+	2	0	HS3ST2	22833870	1.000000	0.71417	0.981000	0.43875	0.974000	0.67602	7.576000	0.82467	1.999000	0.58509	0.459000	0.35465	GAC	.	.		0.577	HS3ST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211598.1	NM_006043		G	22926369	A	G	22926369	3	3	263	1	0	0	0	0	1	0	0	0	7373	275	10	2	596	2	HS3ST2	16	22926369	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	1787268	22926369	67428384	344	38718										
TNRC6A	27327	hgsc.bcm.edu	37	chr16	24801289	24801289	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	aaggtttcattcagtggtcaAcctcaaaatattaccactga	6	9	4	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr16:24801289A>G	ENST00000395799.3	+	6	1455	c.1326A>G	c.(1324-1326)caA>caG	p.Q442Q	TNRC6A_ENST00000315183.7_Silent_p.Q442Q	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	442	Interaction with argonaute family proteins.|Sufficient for interaction with AGO1, AGO3 and AGO4.|Sufficient for interaction with AGO2.				cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		TCAGTGGTCAACCTCAAAATA	0.423																																					p.Q442Q		Atlas-SNP	.											.	TNRC6A	171	.	0			c.A1326G						.						64	61	62					16																	24801289		2197	4300	6497	SO:0001819	synonymous_variant	27327	exon6			TGGTCAACCTCAA	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"Trinucleotide (CAG) repeat containing"	11969	protein-coding gene	gene with protein product		610739	"trinucleotide repeat containing 6"	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.1326A>G	chr16.hg19:g.24801289A>G		72.0	0.0		83.0	4.0	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Silent	SNP	ENST00000395799.3	hg19	CCDS10624.2																																																																																			.	.		0.423	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		G	24801289	A	G	24801289	2	3	263	1	0	0	0	0	0	0	0	1	16355	40	2	2		2	TNRC6A	16	24801289	Silent	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	1874920	24801289	65553464	345	38719										
TNRC6A	27327	hgsc.bcm.edu	37	chr16	24801444	24801444	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	aatgaatcatcctcagatgcAggctccatcaggtatgaatg	9	9	3	3			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr16:24801444A>G	ENST00000395799.3	+	6	1610	c.1481A>G	c.(1480-1482)cAg>cGg	p.Q494R	TNRC6A_ENST00000315183.7_Missense_Mutation_p.Q494R	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	494	Interaction with argonaute family proteins.|Sufficient for interaction with AGO1, AGO3 and AGO4.|Sufficient for interaction with AGO2.				cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		CCTCAGATGCAGGCTCCATCA	0.483																																					p.Q494R		Atlas-SNP	.											.	TNRC6A	171	.	0			c.A1481G						.						90	83	85					16																	24801444		2197	4300	6497	SO:0001583	missense	27327	exon6			AGATGCAGGCTCC	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"Trinucleotide (CAG) repeat containing"	11969	protein-coding gene	gene with protein product		610739	"trinucleotide repeat containing 6"	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.1481A>G	chr16.hg19:g.24801444A>G	ENSP00000379144:p.Gln494Arg	90.0	0.0		86.0	4.0	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	hg19	CCDS10624.2	.	.	.	.	.	.	.	.	.	.	A	9.243	1.038871	0.19669	.	.	ENSG00000090905	ENST00000315183;ENST00000395799	T;T	0.12879	2.64;2.66	5.69	4.59	0.56863	.	0.153542	0.45606	D	0.000346	T	0.13372	0.0324	L	0.58101	1.795	0.80722	D	1	B;B;P	0.35011	0.358;0.358;0.48	B;B;B	0.30855	0.116;0.117;0.121	T	0.04708	-1.0932	10	0.13853	T	0.58	-0.8115	12.9948	0.58640	0.865:0.135:0.0:0.0	.	241;494;494	Q8NDV7-2;Q8NDV7-6;Q8NDV7	.;.;TNR6A_HUMAN	R	494	ENSP00000326900:Q494R;ENSP00000379144:Q494R	ENSP00000326900:Q494R	Q	+	2	0	TNRC6A	24708945	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.681000	0.61663	0.962000	0.38057	0.460000	0.39030	CAG	.	.		0.483	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		G	24801444	A	G	24801444	3	3	263	1	0	0	0	0	1	0	0	0	16355	188	7	2	1503	2	TNRC6A	16	24801444	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	155	24801444	65553309	346	38720										
NFATC2IP	84901	hgsc.bcm.edu	37	chr16	28967623	28967623	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tcttcccactcaaaatccgtTgccgggctgacctggtcaga	9	14	3	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr16:28967623T>C	ENST00000320805.4	+	5	886	c.811T>C	c.(811-813)Tgc>Cgc	p.C271R	NFATC2IP_ENST00000562977.1_Intron|NFATC2IP_ENST00000564978.1_Intron|RP11-264B17.2_ENST00000568057.1_RNA|MIR4517_ENST00000578855.1_RNA|NFATC2IP_ENST00000568148.1_5'Flank|RP11-264B17.2_ENST00000569974.1_RNA	NM_032815.3	NP_116204.3	Q8NCF5	NF2IP_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2 interacting protein	271					cytokine production (GO:0001816)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(1)|lung(5)|ovary(2)	11						CAAAATCCGTTGCCGGGCTGA	0.607																																					p.C271R		Atlas-SNP	.											.	NFATC2IP	24	.	0			c.T811C						.						43	42	42					16																	28967623		2197	4300	6497	SO:0001583	missense	84901	exon5			ATCCGTTGCCGGG	AK074761	CCDS10645.1	16p11.2	2010-09-13			ENSG00000176953	ENSG00000176953			25906	protein-coding gene	gene with protein product		614525				15698469	Standard	NM_032815		Approved	FLJ14639, NIP45, RAD60, ESC2	uc002dru.3	Q8NCF5	OTTHUMG00000097763	ENST00000320805.4:c.811T>C	chr16.hg19:g.28967623T>C	ENSP00000324792:p.Cys271Arg	68.0	0.0		90.0	4.0	NM_032815	B7Z4G5|Q66K34|Q6NVK1|Q8NFR2|Q96ST9	Missense_Mutation	SNP	ENST00000320805.4	hg19	CCDS10645.1	.	.	.	.	.	.	.	.	.	.	T	14.89	2.669835	0.47677	.	.	ENSG00000176953	ENST00000320805	T	0.21543	2.0	5.49	5.49	0.81192	Ubiquitin (1);	0.123818	0.53938	D	0.000049	T	0.22166	0.0534	L	0.45581	1.43	0.80722	D	1	P	0.48503	0.911	B	0.43809	0.432	T	0.01452	-1.1351	10	0.37606	T	0.19	-12.6719	12.0051	0.53255	0.0:0.0:0.0:1.0	.	271	Q8NCF5	NF2IP_HUMAN	R	271	ENSP00000324792:C271R	ENSP00000324792:C271R	C	+	1	0	NFATC2IP	28875124	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	3.615000	0.54167	2.076000	0.62316	0.533000	0.62120	TGC	.	.		0.607	NFATC2IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214999.2	NM_032815		C	28967623	T	C	28967623	3	2	263	1	0	0	0	0	1	0	0	0	10372	1812	63	2	829	2	NFATC2IP	16	28967623	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	4166179	28967623	61387130	347	38721										
SRCAP	10847	hgsc.bcm.edu	37	chr16	30732698	30732698	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ctgctgctgccaccaccactTctaccaccacggcaactgct	6	19	1	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr16:30732698T>C	ENST00000262518.4	+	21	3827	c.3442T>C	c.(3442-3444)Tct>Cct	p.S1148P	SRCAP_ENST00000344771.4_Intron|SRCAP_ENST00000395059.2_Missense_Mutation_p.S1148P	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	1148	Pro-rich.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			CACCACCACTTCTACCACCAC	0.632																																					p.S1148P		Atlas-SNP	.											.	SRCAP	298	.	0			c.T3442C						.						96	84	88					16																	30732698		2197	4300	6497	SO:0001583	missense	10847	exon21			ACCACTTCTACCA	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.3442T>C	chr16.hg19:g.30732698T>C	ENSP00000262518:p.Ser1148Pro	69.0	0.0		100.0	5.0	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	hg19	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	T	9.295	1.051668	0.19827	.	.	ENSG00000080603	ENST00000262518;ENST00000395059	D;D	0.91180	-2.8;-2.79	4.4	3.3	0.37823	.	.	.	.	.	T	0.80014	0.4546	N	0.14661	0.345	0.80722	D	1	B;B	0.10296	0.003;0.003	B;B	0.14578	0.011;0.005	T	0.73145	-0.4075	9	0.54805	T	0.06	-6.1346	5.0633	0.14568	0.1614:0.0897:0.0:0.7489	.	1148;1148	Q6ZRS2-2;Q6ZRS2	.;SRCAP_HUMAN	P	1148	ENSP00000262518:S1148P;ENSP00000378499:S1148P	ENSP00000262518:S1148P	S	+	1	0	SRCAP	30640199	0.002000	0.14202	0.455000	0.27031	0.780000	0.44128	0.621000	0.24418	1.011000	0.39340	0.455000	0.32223	TCT	.	.		0.632	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		C	30732698	T	C	30732698	3	2	263	1	0	0	0	0	1	0	0	0	15150	1783	62	2	3516	2	SRCAP	16	30732698	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	1765075	30732698	59622055	348	38722										
ZNF629	23361	hgsc.bcm.edu	37	chr16	30793663	30793663	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tctccgcagtgggagcagatGtaggtcttggaggacagcag	16	8	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr16:30793663G>A	ENST00000262525.4	-	3	2193	c.1986C>T	c.(1984-1986)taC>taT	p.Y662Y	RP11-2C24.6_ENST00000575562.1_RNA	NM_001080417.1	NP_001073886.1	Q9UEG4	ZN629_HUMAN	zinc finger protein 629	662					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(3)|urinary_tract(1)	22			Colorectal(24;0.198)			GGGAGCAGATGTAGGTCTTGG	0.627																																					p.Y662Y		Atlas-SNP	.											.	ZNF629	44	.	0			c.C1986T						.						16	17	17					16																	30793663		2033	4188	6221	SO:0001819	synonymous_variant	23361	exon3			GCAGATGTAGGTC	AB002324	CCDS45463.1	16p11.2	2013-01-08				ENSG00000102870		"Zinc fingers, C2H2-type"	29008	protein-coding gene	gene with protein product			"zinc finger protein 65"	ZNF65		9205841	Standard	NM_001080417		Approved	KIAA0326	uc002dzs.1	Q9UEG4		ENST00000262525.4:c.1986C>T	chr16.hg19:g.30793663G>A		58.0	0.0		56.0	18.0	NM_001080417	Q15938	Silent	SNP	ENST00000262525.4	hg19	CCDS45463.1																																																																																			.	.		0.627	ZNF629-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434291.1	NM_015309		A	30793663	G	A	30793663	2	1	263	1	0	0	0	0	0	0	0	1	18068	1372	48	3		3	ZNF629	16	30793663	Silent	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	60965	30793663	59561090	349	38723										
C16orf78	123970	hgsc.bcm.edu	37	chr16	49412388	49412388	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tgctccctccaaggccttagGaaagagattcaggaaggacg	12	10	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr16:49412388G>A	ENST00000299191.3	+	3	395	c.278G>A	c.(277-279)gGa>gAa	p.G93E		NM_144602.2	NP_653203.1	Q8WTQ4	CP078_HUMAN	chromosome 16 open reading frame 78	93						nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|upper_aerodigestive_tract(1)	22						AAGGCCTTAGGAAAGAGATTC	0.557																																					p.G93E		Atlas-SNP	.											C16orf78,NS,malignant_melanoma,0,1	C16orf78	57	.	0			c.G278A						.						37	33	34					16																	49412388		2198	4299	6497	SO:0001583	missense	123970	exon3			CCTTAGGAAAGAG	BC021181	CCDS10738.1	16q12.1	2008-02-05			ENSG00000166152	ENSG00000166152			28479	protein-coding gene	gene with protein product						12477932	Standard	NM_144602		Approved	MGC33367	uc002efr.3	Q8WTQ4	OTTHUMG00000133149	ENST00000299191.3:c.278G>A	chr16.hg19:g.49412388G>A	ENSP00000299191:p.Gly93Glu	42.0	0.0		43.0	14.0	NM_144602		Missense_Mutation	SNP	ENST00000299191.3	hg19	CCDS10738.1	.	.	.	.	.	.	.	.	.	.	G	0.051	-1.249016	0.01469	.	.	ENSG00000166152	ENST00000299191	T	0.41065	1.01	3.04	-3.04	0.05412	.	6.024030	0.00424	N	0.000066	T	0.23766	0.0575	N	0.24115	0.695	0.09310	N	0.999999	B	0.21606	0.058	B	0.14023	0.01	T	0.03463	-1.1034	9	.	.	.	0.8377	0.4665	0.00525	0.3689:0.1722:0.2698:0.1891	.	93	Q8WTQ4	CP078_HUMAN	E	93	ENSP00000299191:G93E	.	G	+	2	0	C16orf78	47969889	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.057000	0.03486	-0.666000	0.05310	0.462000	0.41574	GGA	.	.		0.557	C16orf78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256846.1	NM_144602		A	49412388	G	A	49412388	3	1	263	1	0	0	0	0	1	0	0	0	1837	1174	41	3	288	3	C16orf78	16	49412388	Missense_Mutation	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	18618725	49412388	40942365	350	38724										
CCDC135	84229	hgsc.bcm.edu	37	chr16	57758667	57758667	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	aaggacgcccagacttcctcTcctaccgccatgccagcttc	7	18	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr16:57758667T>C	ENST00000360716.3	+	13	1899	c.1678T>C	c.(1678-1680)Tcc>Ccc	p.S560P	CCDC135_ENST00000394337.4_Missense_Mutation_p.S560P|CCDC135_ENST00000336825.8_Missense_Mutation_p.S495P			Q8IY82	CC135_HUMAN		560					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30						AGACTTCCTCTCCTACCGCCA	0.577																																					p.S560P		Atlas-SNP	.											.	CCDC135	97	.	0			c.T1678C						.						84	72	76					16																	57758667		2198	4300	6498	SO:0001583	missense	84229	exon12			TTCCTCTCCTACC																												ENST00000360716.3:c.1678T>C	chr16.hg19:g.57758667T>C	ENSP00000353942:p.Ser560Pro	84.0	0.0		123.0	7.0	NM_032269	A8K943|Q8NAA0|Q9H080	Missense_Mutation	SNP	ENST00000360716.3	hg19	CCDS10787.1	.	.	.	.	.	.	.	.	.	.	.	10.56	1.384217	0.25031	.	.	ENSG00000159625	ENST00000394337;ENST00000336825;ENST00000360716	T;T;T	0.09817	3.1;2.94;3.1	5.29	1.24	0.21308	.	0.588107	0.18613	N	0.136106	T	0.14700	0.0355	M	0.63428	1.95	0.09310	N	0.999999	D;P	0.54601	0.967;0.813	P;B	0.45071	0.468;0.252	T	0.12400	-1.0549	10	0.39692	T	0.17	-22.956	13.273	0.60172	0.0:0.0:0.3834:0.6166	.	495;560	Q8IY82-2;Q8IY82	.;CC135_HUMAN	P	560;495;560	ENSP00000377869:S560P;ENSP00000338938:S495P;ENSP00000353942:S560P	ENSP00000338938:S495P	S	+	1	0	CCDC135	56316168	0.963000	0.33076	0.990000	0.47175	0.326000	0.28443	0.606000	0.24194	0.283000	0.22279	0.533000	0.62120	TCC	.	.		0.577	CCDC135-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433323.2			C	57758667	T	C	57758667	3	2	263	1	0	0	0	0	1	0	0	0	2771	1551	54	2	1720	2	CCDC135	16	57758667	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	8346279	57758667	32596086	351	38725										
ZNF319	57567	hgsc.bcm.edu	37	chr16	58031121	58031121	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cgtactgctgcttgaagcccAtggggcacaggtcgcacttg	13	12	0	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr16:58031121A>G	ENST00000299237.2	-	2	1671	c.1049T>C	c.(1048-1050)aTg>aCg	p.M350T	USB1_ENST00000561743.1_5'Flank	NM_020807.1	NP_065858.1	Q9P2F9	ZN319_HUMAN	zinc finger protein 319	350					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(2)|lung(4)|ovary(1)|urinary_tract(1)	8						CTTGAAGCCCATGGGGCACAG	0.652																																					p.M350T		Atlas-SNP	.											.	ZNF319	42	.	0			c.T1049C						.						65	58	60					16																	58031121		2198	4300	6498	SO:0001583	missense	57567	exon2			AAGCCCATGGGGC	AB037809	CCDS32462.1	16q21	2013-01-08				ENSG00000166188		"Zinc fingers, C2H2-type"	13644	protein-coding gene	gene with protein product						10718198, 11161788	Standard	XM_005256069		Approved	KIAA1388, Zfp319	uc002emx.1	Q9P2F9		ENST00000299237.2:c.1049T>C	chr16.hg19:g.58031121A>G	ENSP00000299237:p.Met350Thr	88.0	0.0		75.0	5.0	NM_020807	Q52LH8	Missense_Mutation	SNP	ENST00000299237.2	hg19	CCDS32462.1	.	.	.	.	.	.	.	.	.	.	A	8.695	0.908443	0.17833	.	.	ENSG00000166188	ENST00000299237	T	0.17370	2.28	4.97	3.86	0.44501	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	U	0.000000	T	0.20861	0.0502	N	0.14661	0.345	0.52501	D	0.999958	D	0.65815	0.995	D	0.63381	0.914	T	0.03212	-1.1060	10	0.87932	D	0	-22.5478	10.2792	0.43530	0.852:0.0:0.0:0.148	.	350	Q9P2F9	ZN319_HUMAN	T	350	ENSP00000299237:M350T	ENSP00000299237:M350T	M	-	2	0	ZNF319	56588622	1.000000	0.71417	1.000000	0.80357	0.013000	0.08279	6.098000	0.71458	0.725000	0.32318	-0.333000	0.08304	ATG	.	.		0.652	ZNF319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430317.1			G	58031121	A	G	58031121	3	3	263	1	0	0	0	0	1	0	0	0	17852	217	8	2	703	2	ZNF319	16	58031121	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	272454	58031121	32323632	352	38726										
AARS	16	hgsc.bcm.edu	37	chr16	70303590	70303590	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tggtccgagcgtggtcagccAgcacccggtaggccatgtca	14	13	2	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr16:70303590A>G	ENST00000261772.8	-	7	1036	c.893T>C	c.(892-894)cTg>cCg	p.L298P		NM_001605.2	NP_001596.2			alanyl-tRNA synthetase											breast(3)|cervix(2)|endometrium(5)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)	27		Ovarian(137;0.0365)		BRCA - Breast invasive adenocarcinoma(221;0.161)		GTGGTCAGCCAGCACCCGGTA	0.587																																					p.L298P		Atlas-SNP	.											.	AARS	62	.	0			c.T893C						.						210	178	189					16																	70303590		2198	4300	6498	SO:0001583	missense	16	exon7			TCAGCCAGCACCC	D32050	CCDS32474.1	16q22.1	2014-09-17			ENSG00000090861	ENSG00000090861	6.1.1.7	"Aminoacyl tRNA synthetases / Class II"	20	protein-coding gene	gene with protein product	"alanine tRNA ligase 1, cytoplasmic"	601065				8595897	Standard	NM_001605		Approved		uc002eyn.1	P49588	OTTHUMG00000177042	ENST00000261772.8:c.893T>C	chr16.hg19:g.70303590A>G	ENSP00000261772:p.Leu298Pro	89.0	0.0		107.0	5.0	NM_001605		Missense_Mutation	SNP	ENST00000261772.8	hg19	CCDS32474.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.717015	0.89205	.	.	ENSG00000090861	ENST00000261772	T	0.74947	-0.89	5.67	5.67	0.87782	Alanyl-tRNA synthetase, class IIc, anti-codon-binding domain (1);Alanyl-tRNA synthetase, class IIc, core domain (1);Alanyl-tRNA synthetase, class IIc, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.89842	0.6832	H	0.95260	3.645	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.992	D	0.92562	0.6059	10	0.87932	D	0	-13.6413	13.8675	0.63598	1.0:0.0:0.0:0.0	.	306;298	E7ETK8;P49588	.;SYAC_HUMAN	P	298	ENSP00000261772:L298P	ENSP00000261772:L298P	L	-	2	0	AARS	68861091	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.339000	0.96797	2.178000	0.69098	0.533000	0.62120	CTG	.	.		0.587	AARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435021.2	NM_001605		G	70303590	A	G	70303590	3	3	263	1	0	0	0	0	1	0	0	0	19	188	7	2	2073	2	AARS	16	70303590	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	12272469	70303590	20051163	353	38727										
COG4	25839	hgsc.bcm.edu	37	chr16	70553593	70553593	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	atcttactttcaatggtgttTtgctgttccaaaagagcatc	7	8	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr16:70553593T>C	ENST00000323786.5	-	2	234	c.213A>G	c.(211-213)caA>caG	p.Q71Q	COG4_ENST00000393612.4_Silent_p.Q67Q|COG4_ENST00000564653.1_Silent_p.Q71Q	NM_001195139.1|NM_015386.2	NP_001182068.1|NP_056201.2	Q9H9E3	COG4_HUMAN	component of oligomeric golgi complex 4	67	Interacts with SCFD1.				Golgi organization (GO:0007030)|Golgi vesicle prefusion complex stabilization (GO:0048213)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|pancreas(1)|prostate(2)	33		Ovarian(137;0.0694)				CAATGGTGTTTTGCTGTTCCA	0.443																																					p.Q71Q		Atlas-SNP	.											.	COG4	64	.	0			c.A213G						.						143	120	128					16																	70553593		2198	4300	6498	SO:0001819	synonymous_variant	25839	exon2			GGTGTTTTGCTGT	AL050101	CCDS10892.2, CCDS73909.1	16q22.1	2013-09-20			ENSG00000103051	ENSG00000103051		"Components of oligomeric golgi complex"	18620	protein-coding gene	gene with protein product		606976				11980916	Standard	NM_015386		Approved	COD1, DKFZP586E1519	uc002ezc.3	Q9H9E3	OTTHUMG00000128515	ENST00000323786.5:c.213A>G	chr16.hg19:g.70553593T>C		88.0	0.0		115.0	5.0	NM_015386	B4DMN8|C9JS23|Q96D40|Q9BRF0|Q9BVZ2|Q9H5Y4|Q9Y3W3	Silent	SNP	ENST00000323786.5	hg19	CCDS10892.2																																																																																			.	.		0.443	COG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250326.3			C	70553593	T	C	70553593	2	2	263	1	0	0	0	0	0	0	0	1	3662	1838	64	2		2	COG4	16	70553593	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	250003	70553593	19801160	354	38728										
HYDIN	54768	hgsc.bcm.edu	37	chr16	70884467	70884467	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ctcggccttgacatttaatgTcacagggtggactttctttt	9	9	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr16:70884467T>C	ENST00000393567.2	-	74	12685	c.12535A>G	c.(12535-12537)Aca>Gca	p.T4179A	RNU6ATAC25P_ENST00000408798.1_RNA	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	4179					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				ACATTTAATGTCACAGGGTGG	0.448																																					p.T4179A		Atlas-SNP	.											.	HYDIN	788	.	0			c.A12535G						.						31	30	30					16																	70884467		1822	4079	5901	SO:0001583	missense	54768	exon74			TTAATGTCACAGG	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.12535A>G	chr16.hg19:g.70884467T>C	ENSP00000377197:p.Thr4179Ala	149.0	0.0		212.0	39.0	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	hg19	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	T	11.89	1.774801	0.31411	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.01015	5.44	5.56	4.42	0.53409	.	0.269330	0.19193	U	0.120392	T	0.01627	0.0052	M	0.74881	2.28	0.51767	D	0.999937	B	0.14805	0.011	B	0.19391	0.025	T	0.50825	-0.8782	10	0.17832	T	0.49	.	9.8956	0.41316	0.3173:0.0:0.0:0.6827	.	4178	F8WD23	.	A	4179;4178	ENSP00000377197:T4179A	ENSP00000313052:T4178A	T	-	1	0	HYDIN	69441968	0.918000	0.31147	0.958000	0.39756	0.503000	0.33858	1.845000	0.39279	2.113000	0.64589	0.418000	0.28097	ACA	.	.		0.448	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			C	70884467	T	C	70884467	3	2	263	1	0	0	0	0	1	0	0	0	7476	1667	58	2	2882	2	HYDIN	16	70884467	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	330874	70884467	19470286	355	38729										
ADAMTS18	170692	hgsc.bcm.edu	37	chr16	77326981	77326981	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tctaatccatacctcgctccAcgaagaagcgacccactgta	6	15	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr16:77326981A>G	ENST00000282849.5	-	20	3599	c.3181T>C	c.(3181-3183)Tgg>Cgg	p.W1061R	RP11-538I12.3_ENST00000561672.1_RNA	NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	1061	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.				eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			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						ACCTCGCTCCACGAAGAAGCG	0.522																																					p.W1061R		Atlas-SNP	.											.	ADAMTS18	270	.	0			c.T3181C						.						72	67	69					16																	77326981		2198	4300	6498	SO:0001583	missense	170692	exon20			CGCTCCACGAAGA	AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"ADAM metallopeptidases with thrombospondin type 1 motif"	17110	protein-coding gene	gene with protein product		607512	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.3181T>C	chr16.hg19:g.77326981A>G	ENSP00000282849:p.Trp1061Arg	44.0	0.0		63.0	4.0	NM_199355	Q6P4R5|Q6ZWJ9	Missense_Mutation	SNP	ENST00000282849.5	hg19	CCDS10926.1	.	.	.	.	.	.	.	.	.	.	A	14.51	2.556594	0.45487	.	.	ENSG00000140873	ENST00000282849	T	0.77489	-1.1	5.79	4.7	0.59300	.	0.000000	0.85682	D	0.000000	D	0.92919	0.7747	H	0.99425	4.56	0.58432	D	0.999992	D;D	0.89917	0.991;1.0	P;D	0.91635	0.905;0.999	D	0.94072	0.7336	10	0.87932	D	0	.	11.6097	0.51052	0.8667:0.0:0.0:0.1333	.	1061;1061	Q8TE60-2;Q8TE60	.;ATS18_HUMAN	R	1061	ENSP00000282849:W1061R	ENSP00000282849:W1061R	W	-	1	0	ADAMTS18	75884482	1.000000	0.71417	0.791000	0.31998	0.009000	0.06853	8.596000	0.90844	1.013000	0.39391	0.455000	0.32223	TGG	.	.		0.522	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1			G	77326981	A	G	77326981	3	3	263	1	0	0	0	0	1	0	0	0	263	159	6	2	500	2	ADAMTS18	16	77326981	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	6442514	77326981	13027772	356	38730										
C16orf46	123775	hgsc.bcm.edu	37	chr16	81095083	81095083	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gcgctgctccggatcggtcaGcagggatatctgggccgctg	16	12	2	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr16:81095083G>A	ENST00000299578.5	-	4	1106	c.871C>T	c.(871-873)Ctg>Ttg	p.L291L	RP11-303E16.8_ENST00000564536.1_RNA|C16orf46_ENST00000378611.4_Silent_p.L291L|C16orf46_ENST00000444657.3_5'Flank	NM_152337.2	NP_689550.2	Q6P387	CP046_HUMAN	chromosome 16 open reading frame 46	291						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(2)|large_intestine(3)|lung(9)|prostate(1)|stomach(1)|urinary_tract(1)	18						GGATCGGTCAGCAGGGATATC	0.592																																					p.L291L		Atlas-SNP	.											.	C16orf46	57	.	0			c.C871T						.						105	101	102					16																	81095083		2202	4300	6502	SO:0001819	synonymous_variant	123775	exon3			CGGTCAGCAGGGA	BC064143	CCDS10932.1, CCDS42201.1	16q23.2	2012-10-09			ENSG00000166455	ENSG00000166455			26525	protein-coding gene	gene with protein product							Standard	NM_152337		Approved	FLJ32702	uc002fgc.4	Q6P387	OTTHUMG00000137629	ENST00000299578.5:c.871C>T	chr16.hg19:g.81095083G>A		184.0	0.0		208.0	67.0	NM_001100873	Q96MA7	Silent	SNP	ENST00000299578.5	hg19	CCDS10932.1																																																																																			.	.		0.592	C16orf46-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269054.2	NM_152337		A	81095083	G	A	81095083	2	1	263	1	0	0	0	0	0	0	0	1	1817	962	34	3		3	C16orf46	16	81095083	Silent	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	3768102	81095083	9259670	357	38731										
TAF1C	9013	hgsc.bcm.edu	37	chr16	84212770	84212770	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	atgcatccggagtcaactccTgggagggcggggtcgtgggg	19	9	1	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr16:84212770T>C	ENST00000567759.1	-	14	2569	c.2387A>G	c.(2386-2388)cAg>cGg	p.Q796R	TAF1C_ENST00000341690.6_Missense_Mutation_p.Q702R|TAF1C_ENST00000378541.4_Missense_Mutation_p.Q796R|TAF1C_ENST00000541676.1_Missense_Mutation_p.Q703R|TAF1C_ENST00000566732.1_Missense_Mutation_p.Q770R|TAF1C_ENST00000570117.1_Missense_Mutation_p.Q464R	NM_005679.3	NP_005670	Q15572	TAF1C_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kDa	796					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	26						AGTCAACTCCTGGGAGGGCGG	0.657																																					p.Q796R		Atlas-SNP	.											.	TAF1C	60	.	0			c.A2387G						.						23	20	21					16																	84212770		2199	4298	6497	SO:0001583	missense	9013	exon14			AACTCCTGGGAGG	L39059	CCDS32496.1, CCDS45535.1, CCDS58488.1, CCDS58489.1	16q24	2008-02-05	2002-08-29			ENSG00000103168			11534	protein-coding gene	gene with protein product		604905	"TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kD"			7801123	Standard	NM_005679		Approved	TAFI110, TAFI95, SL1, MGC:39976	uc010vnx.2	Q15572		ENST00000567759.1:c.2387A>G	chr16.hg19:g.84212770T>C	ENSP00000455265:p.Gln796Arg	71.0	0.0		68.0	4.0	NM_005679	B7Z5K5|B7Z5S4|B7Z908|B7Z9L7|Q59F67|Q8N6V3	Missense_Mutation	SNP	ENST00000567759.1	hg19	CCDS32496.1	.	.	.	.	.	.	.	.	.	.	T	14.52	2.559364	0.45590	.	.	ENSG00000103168	ENST00000378541;ENST00000541676;ENST00000341690;ENST00000544090	T;T;T	0.02606	4.23;4.23;4.23	5.3	4.15	0.48705	.	0.345909	0.23926	N	0.043192	T	0.11110	0.0271	M	0.68317	2.08	0.29661	N	0.843181	P;P;D;D	0.67145	0.582;0.713;0.996;0.981	B;B;D;D	0.75484	0.248;0.424;0.986;0.969	T	0.00783	-1.1568	10	0.87932	D	0	-23.2519	8.5069	0.33193	0.1715:0.0:0.0:0.8285	.	770;319;796;702	Q15572-6;F5H0H4;Q15572;Q15572-2	.;.;TAF1C_HUMAN;.	R	796;703;702;319	ENSP00000367802:Q796R;ENSP00000437900:Q703R;ENSP00000345305:Q702R	ENSP00000345305:Q702R	Q	-	2	0	TAF1C	82770271	0.997000	0.39634	0.996000	0.52242	0.085000	0.17905	1.148000	0.31614	2.005000	0.58758	0.533000	0.62120	CAG	.	.		0.657	TAF1C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000433045.2	NM_139353		C	84212770	T	C	84212770	3	2	263	1	0	0	0	0	1	0	0	0	15536	1580	55	2	226	2	TAF1C	16	84212770	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	3117687	84212770	6141983	358	38732										
ADAD2	161931	hgsc.bcm.edu	37	chr16	84229269	84229269	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tcttcctgcacctctacatcAgcaacacccccaagggcgcg	7	18	3	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr16:84229269A>G	ENST00000315906.5	+	6	1070	c.1018A>G	c.(1018-1020)Agc>Ggc	p.S340G	RP11-486L19.2_ENST00000565643.1_RNA|RP11-486L19.2_ENST00000536986.1_RNA|ADAD2_ENST00000268624.3_Missense_Mutation_p.S422G|RP11-486L19.2_ENST00000561900.1_RNA|RP11-486L19.2_ENST00000569834.1_RNA	NM_001145400.1	NP_001138872.1	Q8NCV1	ADAD2_HUMAN	adenosine deaminase domain containing 2	340	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				RNA processing (GO:0006396)		adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(1)	13						CCTCTACATCAGCAACACCCC	0.721																																					p.S422G		Atlas-SNP	.											.	ADAD2	46	.	0			c.A1264G						.						23	29	27					16																	84229269		2198	4298	6496	SO:0001583	missense	161931	exon7			TACATCAGCAACA	AF447586	CCDS10944.1, CCDS45536.1	16q24.1	2007-05-31			ENSG00000140955	ENSG00000140955			30714	protein-coding gene	gene with protein product							Standard	NM_139174		Approved	TENRL, FLJ00337	uc002fhr.2	Q8NCV1	OTTHUMG00000137637	ENST00000315906.5:c.1018A>G	chr16.hg19:g.84229269A>G	ENSP00000325153:p.Ser340Gly	118.0	0.0		70.0	4.0	NM_139174	B2RCL6|Q8NA94	Missense_Mutation	SNP	ENST00000315906.5	hg19	CCDS45536.1	.	.	.	.	.	.	.	.	.	.	A	16.89	3.246694	0.59103	.	.	ENSG00000140955	ENST00000315906;ENST00000268624	D;D	0.96265	-3.96;-3.96	5.22	5.22	0.72569	Adenosine deaminase/editase (2);	0.052582	0.85682	D	0.000000	D	0.98254	0.9422	M	0.92555	3.32	0.39297	D	0.964835	D;D	0.71674	0.998;0.998	D;D	0.69307	0.963;0.941	D	0.99910	1.1196	10	0.72032	D	0.01	-36.8217	11.7794	0.52003	1.0:0.0:0.0:0.0	.	340;422	Q8NCV1;Q8NCV1-2	ADAD2_HUMAN;.	G	340;422	ENSP00000325153:S340G;ENSP00000268624:S422G	ENSP00000268624:S422G	S	+	1	0	ADAD2	82786770	1.000000	0.71417	0.996000	0.52242	0.236000	0.25371	5.674000	0.68117	2.088000	0.63022	0.528000	0.53228	AGC	.	.		0.721	ADAD2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433385.1	NM_139174		G	84229269	A	G	84229269	3	3	263	1	0	0	0	0	1	0	0	0	232	188	7	2	1290	2	ADAD2	16	84229269	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	16499	84229269	6125484	359	38733										
ATP2C2	9914	hgsc.bcm.edu	37	chr16	84438813	84438813	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ctggaatgagtttgttgctgAcaacagcgaacctgtgtgga	13	7	0	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr16:84438813A>G	ENST00000262429.4	+	3	379	c.290A>G	c.(289-291)gAc>gGc	p.D97G	ATP2C2_ENST00000416219.2_Missense_Mutation_p.D97G	NM_014861.2	NP_055676.2	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2	97					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(3)|skin(5)|urinary_tract(1)	33						TTTGTTGCTGACAACAGCGAA	0.557																																					p.D97G		Atlas-SNP	.											.	ATP2C2	75	.	0			c.A290G						.						62	68	66					16																	84438813		2081	4219	6300	SO:0001583	missense	9914	exon3			TTGCTGACAACAG	AK091051	CCDS42207.1, CCDS67088.1	16q24.1	2010-04-20			ENSG00000064270	ENSG00000064270	3.6.3.8	"ATPases / P-type"	29103	protein-coding gene	gene with protein product	"secretory pathway calcium ATPase 2"	613082				9734811	Standard	XM_006721355		Approved	KIAA0703, SPCA2	uc002fhx.3	O75185		ENST00000262429.4:c.290A>G	chr16.hg19:g.84438813A>G	ENSP00000262429:p.Asp97Gly	128.0	0.0		144.0	6.0	NM_014861	B4DU76|E7ES94|Q5HYC3|Q5S053|Q68CQ2	Missense_Mutation	SNP	ENST00000262429.4	hg19	CCDS42207.1	.	.	.	.	.	.	.	.	.	.	A	3.574	-0.087034	0.07097	.	.	ENSG00000064270	ENST00000416219;ENST00000262429	T;T	0.78246	-1.16;-1.16	5.1	3.99	0.46301	ATPase, P-type cation-transporter, N-terminal (2);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.422774	0.23446	N	0.048095	T	0.60353	0.2262	N	0.20328	0.56	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.09377	0.004;0.002;0.002	T	0.42849	-0.9427	10	0.21540	T	0.41	.	9.4888	0.38946	0.9099:0.0:0.0901:0.0	.	97;114;97	E7ES94;O75185-2;O75185	.;.;AT2C2_HUMAN	G	97	ENSP00000397925:D97G;ENSP00000262429:D97G	ENSP00000262429:D97G	D	+	2	0	ATP2C2	82996314	0.969000	0.33509	0.006000	0.13384	0.013000	0.08279	3.270000	0.51600	2.041000	0.60428	0.482000	0.46254	GAC	.	.		0.557	ATP2C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433404.1	NM_014861		G	84438813	A	G	84438813	3	3	263	1	0	0	0	0	1	0	0	0	1144	275	10	2	300	2	ATP2C2	16	84438813	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	209544	84438813	5915940	360	38734										
KIAA0182	23199	hgsc.bcm.edu	37	chr16	85687882	85687996	+	Splice_Site	DEL	ATCTAGCGCCTTCCCGTGAGTCAGGAGACCTGGCTGTGTCCTGTGGTCAGTGGCCTATACCAGGCTCCTGCCCTGACTGGACGCTCTCCTCCCGCAGGATGCCGGCTCCAGGAGC	ATCTAGCGCCTTCCCGTGAGTCAGGAGACCTGGCTGTGTCCTGTGGTCAGTGGCCTATACCAGGCTCCTGCCCTGACTGGACGCTCTCCTCCCGCAGGATGCCGGCTCCAGGAGC	-													0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	actggacgctctcctcccgcAggatgccggctccaggagca					rs199907438|rs139026945|rs533754397|rs200326373|rs548173812|rs141495598|rs371288703|rs201414196|rs374027374|rs200380779|rs372447672|rs368790892|rs375693569|rs146142460|rs567937313|rs370331390|rs368266182|rs373938537|rs370775268	byFrequency	TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	ATCTAGCGCCTTCCCGTGAGTCAGGAGACCTGGCTGTGTCCTGTGGTCAGTGGCCTATACCAGGCTCCTGCCCTGACTGGACGCTCTCCTCCCGCAGGATGCCGGCTCCAGGAGC	ATCTAGCGCCTTCCCGTGAGTCAGGAGACCTGGCTGTGTCCTGTGGTCAGTGGCCTATACCAGGCTCCTGCCCTGACTGGACGCTCTCCTCCCGCAGGATGCCGGCTCCAGGAGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr16:85687882_85687996delATCTAGCGCCTTCCCGTGAGTCAGGAGACCTGGCTGTGTCCTGTGGTCAGTGGCCTATACCAGGCTCCTGCCCTGACTGGACGCTCTCCTCCCGCAGGATGCCGGCTCCAGGAGC	ENST00000253458.7	+	4	602_715	c.426_539delATCTAGCGCCTTCCCGTGAGTCAGGAGACCTGGCTGTGTCCTGTGGTCAGTGGCCTATACCAGGCTCCTGCCCTGACTGGACGCTCTCCTCCCGCAGGATGCCGGCTCCAGGAGC	c.(424-540)caatctagcgccttcccgtgagtcaggagacctggctgtgtcctgtggtcagtggcctataccaggctcctgccctgactggacgctctcctcccgcaggatgccggctccaggagc>cac	p.QSSAFP*VRRPGCVLWSVAYTRLLP*LDALLPQDAGSRS142fs	GSE1_ENST00000405402.2_Splice_Site_p.QSSAFP*VRRPGCVLWSVAYTRLLP*LDALLPQDAGSRS38fs|GSE1_ENST00000393243.1_Splice_Site_p.QSSAFP*VRRPGCVLWSVAYTRLLP*LDALLPQDAGSRS69fs	NM_014615.2	NP_055430.1	Q14687	GSE1_HUMAN	Gse1 coiled-coil protein	142																	CTCCTCCCGCAGGATGCCGGCTCCAGGAGCAGCAGTGGAGGTCGGGAACGCCTCATTGTGGAGCCCCCGCTCCCTCAGGAGAAGGCAGGGGGACCAGCCATCCCCTCGCACCTGCTCAGCACCCCCTACCCCTTC	0.648																																					p.143_148del		Pindel	.											.	.	.	.	0			c.427_443del						.																																			SO:0001630	splice_region_variant	23199	exon4			.	D80004	CCDS10952.1, CCDS45539.1, CCDS62007.1	16q24.1	2012-12-07	2012-12-07	2012-10-02	ENSG00000131149	ENSG00000131149			28979	protein-coding gene	gene with protein product	"genetic suppressor element 1"		"KIAA0182", "Gse1 coiled-coil protein homolog (mouse)"	KIAA0182		8724849, 8786132	Standard	NM_014615		Approved		uc002fix.4	Q14687	OTTHUMG00000137650	ENST00000253458.7:c.427-1ATCTAGCGCCTTCCCGTGAGTCAGGAGACCTGGCTGTGTCCTGTGGTCAGTGGCCTATACCAGGCTCCTGCCCTGACTGGACGCTCTCCTCCCGCAGGATGCCGGCTCCAGGAGC>-	chr16.hg19:g.85687882_85687996delATCTAGCGCCTTCCCGTGAGTCAGGAGACCTGGCTGTGTCCTGTGGTCAGTGGCCTATACCAGGCTCCTGCCCTGACTGGACGCTCTCCTCCCGCAGGATGCCGGCTCCAGGAGC		0.0	0.0		75.0	19.0	NM_014615	D3DUM4|Q8IY61|Q96GA4|Q9BW09	Frame_Shift_Del	DEL	ENST00000253458.7	hg19	CCDS10952.1																																																																																			.	.		0.648	GSE1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325527.1	NM_014615	Frame_Shift_Del	-	85687996	ATCTAGCGCCTTCCCGTGAGTCAGGAGACCTGGCTGTGTCCTGTGGTCAGTGGCCTATACCAGGCTCCTGCCCTGACTGGACGCTCTCCTCCCGCAGGATGCCGGCTCCAGGAGC	-	85687882	8	5	263	1	0	1	0	1	0	0	1	0	8168	202	7	0	439	0	KIAA0182	16	85687882	Splice_Site	DEL	ATCTAGCGCCTTCCCGTGAGTCAGGAGACCTGGCTGTGTCCTGTGGTCAGTGGCCTATACCAGGCTCCTGCCCTGACTGGACGCTCTCCTCCCGCAGGATGCCGGCTCCAGGAGC	TCGA-FV-A2QR-01A-11D-A20W-10	1249069	85687882	4666871	361	38735										
ACSF3	197322	hgsc.bcm.edu	37	chr16	89180759	89180759	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ccgcgtaggctgatggtctcAggctcagctgccctgcccct	12	16	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr16:89180759A>G	ENST00000317447.4	+	6	1367	c.990A>G	c.(988-990)tcA>tcG	p.S330S	ACSF3_ENST00000378345.4_Silent_p.S65S|CTD-2555A7.3_ENST00000562782.1_RNA|ACSF3_ENST00000406948.3_Silent_p.S330S	NM_001127214.2|NM_001243279.1|NM_001284316.1|NM_174917.3	NP_001120686.1|NP_001230208.1|NP_001271245.1|NP_777577.2	Q4G176	ACSF3_HUMAN	acyl-CoA synthetase family member 3	330					fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|malonate catabolic process (GO:0090410)	mitochondrion (GO:0005739)	acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)|malonyl-CoA synthetase activity (GO:0090409)			central_nervous_system(1)|endometrium(1)|kidney(2)|lung(9)|prostate(1)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(80;0.0281)		TGATGGTCTCAGGCTCAGCTG	0.632																																					p.S330S		Atlas-SNP	.											.	ACSF3	40	.	0			c.A990G						.						126	96	106					16																	89180759		2198	4300	6498	SO:0001819	synonymous_variant	197322	exon6			GGTCTCAGGCTCA	AK075499	CCDS10974.1, CCDS73926.1	16q24.3	2013-01-15			ENSG00000176715	ENSG00000176715		"Acyl-CoA synthetase family"	27288	protein-coding gene	gene with protein product	"malonyl-CoA synthetase"	614245				17762044, 21846720	Standard	XM_005256293		Approved		uc010cig.2	Q4G176	OTTHUMG00000138044	ENST00000317447.4:c.990A>G	chr16.hg19:g.89180759A>G		121.0	0.0		139.0	9.0	NM_174917	A8K4J8|C9JQL6|Q6INA0|Q8N2F7	Silent	SNP	ENST00000317447.4	hg19	CCDS10974.1	.	.	.	.	.	.	.	.	.	.	A	0.629	-0.817805	0.02776	.	.	ENSG00000176715	ENST00000543676	.	.	.	5.02	-10.0	0.00425	.	.	.	.	.	T	0.34395	0.0896	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40997	-0.9533	4	.	.	.	-7.3756	3.4117	0.07361	0.5049:0.0757:0.1169:0.3025	.	.	.	.	G	78	.	.	R	+	1	2	ACSF3	87708260	0.000000	0.05858	0.037000	0.18230	0.010000	0.07245	-3.958000	0.00325	-2.202000	0.00745	-1.584000	0.00852	AGG	.	.		0.632	ACSF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269919.1	NM_174917		G	89180759	A	G	89180759	2	3	263	1	0	0	0	0	0	0	0	1	176	175	7	2		2	ACSF3	16	89180759	Silent	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	3492877	89180759	1173994	362	38736										
PELP1	27043	hgsc.bcm.edu	37	chr17	4585844	4585844	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ataggtcatacaagccttcaTtccttccaatgctgactgct	6	12	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr17:4585844T>C	ENST00000574876.1	-	5	612	c.595A>G	c.(595-597)Atg>Gtg	p.M199V	PELP1_ENST00000572293.1_Missense_Mutation_p.M249V|PELP1_ENST00000570823.1_5'Flank|PELP1_ENST00000436683.2_Missense_Mutation_p.M52V|PELP1_ENST00000301396.4_Missense_Mutation_p.M199V|AC091153.4_ENST00000441700.2_RNA|PELP1_ENST00000269230.7_Missense_Mutation_p.M199V			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	199					cellular response to estrogen stimulus (GO:0071391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	15						CAAGCCTTCATTCCTTCCAAT	0.493																																					p.M199V		Atlas-SNP	.											.	PELP1	102	.	0			c.A595G						.						109	103	105					17																	4585844		2029	4188	6217	SO:0001583	missense	27043	exon5			CCTTCATTCCTTC		CCDS58503.1, CCDS58503.2, CCDS62038.1	17p13.2	2012-05-02	2008-02-21			ENSG00000141456			30134	protein-coding gene	gene with protein product		609455	"proline, glutamic acid and leucine rich protein 1"			11481323, 12682072	Standard	NM_014389		Approved	MNAR	uc002fyi.4	Q8IZL8		ENST00000574876.1:c.595A>G	chr17.hg19:g.4585844T>C	ENSP00000461625:p.Met199Val	75.0	0.0		61.0	4.0	NM_014389	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	Missense_Mutation	SNP	ENST00000574876.1	hg19	CCDS58503.1	.	.	.	.	.	.	.	.	.	.	t	15.50	2.851703	0.51270	.	.	ENSG00000141456	ENST00000301396;ENST00000269230;ENST00000436683	T;T;T	0.66460	-0.21;-0.11;-0.13	4.59	4.59	0.56863	.	0.051642	0.64402	D	0.000001	T	0.67702	0.2921	N	0.19112	0.55	0.30407	N	0.779429	D;D	0.53885	0.963;0.963	D;D	0.69824	0.966;0.966	T	0.67715	-0.5599	10	0.66056	D	0.02	-21.1964	10.2857	0.43566	0.0:0.0:0.0:1.0	.	52;199	E7EV54;Q8IZL8	.;PELP1_HUMAN	V	199;199;52	ENSP00000301396:M199V;ENSP00000269230:M199V;ENSP00000416231:M52V	ENSP00000269230:M199V	M	-	1	0	AC091153.1	4532593	1.000000	0.71417	0.997000	0.53966	0.820000	0.46376	6.190000	0.72057	1.934000	0.56057	0.375000	0.23000	ATG	.	.		0.493	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389		C	4585844	T	C	4585844	3	2	263	1	0	0	0	0	1	0	0	0	11734	1493	52	2	2849	2	PELP1	17	4585844	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10		4585844	76609366	363	38737										
DNAH2	146754	hgsc.bcm.edu	37	chr17	7721766	7721766	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	accaccatcgtcaactttgcTgttaaagaacaggtgggtac	9	10	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr17:7721766T>C	ENST00000572933.1	+	69	11984	c.10524T>C	c.(10522-10524)gcT>gcC	p.A3508A	DNAH2_ENST00000389173.2_Silent_p.A3508A			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	3508	AAA 5. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				TCAACTTTGCTGTTAAAGAAC	0.488																																					p.A3508A		Atlas-SNP	.											.	DNAH2	498	.	0			c.T10524C						.						171	168	169					17																	7721766		2203	4300	6503	SO:0001819	synonymous_variant	146754	exon68			CTTTGCTGTTAAA	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.10524T>C	chr17.hg19:g.7721766T>C		80.0	0.0		57.0	33.0	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Silent	SNP	ENST00000572933.1	hg19	CCDS32551.1																																																																																			.	.		0.488	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		C	7721766	T	C	7721766	2	2	263	1	0	0	0	0	0	0	0	1	4604	1567	55	2		2	DNAH2	17	7721766	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	3135922	7721766	73473444	364	38738										
CNTROB	116840	hgsc.bcm.edu	37	chr17	7842848	7842848	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	taggaggaggaaaggcaagcTctgactctgaggttggaggc	17	6	2	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr17:7842848T>C	ENST00000563694.1	+	8	1870	c.945T>C	c.(943-945)gcT>gcC	p.A315A	CNTROB_ENST00000565740.1_Silent_p.A315A|CNTROB_ENST00000380255.3_Silent_p.A315A|CNTROB_ENST00000380262.3_Silent_p.A315A	NM_053051.3	NP_444279.2	Q8N137	CNTRB_HUMAN	centrobin, centrosomal BRCA2 interacting protein	315					centriole replication (GO:0007099)|centrosome separation (GO:0051299)|cytokinesis (GO:0000910)	centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(9)	25		Prostate(122;0.173)				AAAGGCAAGCTCTGACTCTGA	0.577																																					p.A315A		Atlas-SNP	.											.	CNTROB	61	.	0			c.T945C						.						101	97	98					17																	7842848		2203	4300	6503	SO:0001819	synonymous_variant	116840	exon8			GCAAGCTCTGACT	AF331638	CCDS32557.1, CCDS11126.1	17p13.1	2006-03-15				ENSG00000170037			29616	protein-coding gene	gene with protein product	"centrobin"	611425				11984006, 16275750	Standard	NM_001037144		Approved	LIP8, PP1221	uc002gjp.3	Q8N137		ENST00000563694.1:c.945T>C	chr17.hg19:g.7842848T>C		135.0	0.0		85.0	6.0	NM_001037144	A6NHQ1|Q331K3|Q69YV7|Q8NCB8|Q8WXV3|Q96CQ7|Q9C060	Silent	SNP	ENST00000563694.1	hg19	CCDS11126.1																																																																																			.	.		0.577	CNTROB-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000421372.1	NM_053051		C	7842848	T	C	7842848	2	2	263	1	0	0	0	0	0	0	0	1	3653	1538	54	2		2	CNTROB	17	7842848	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	121082	7842848	73352362	365	38739										
EPN2	22905	hgsc.bcm.edu	37	chr17	19186829	19186873	+	In_Frame_Del	DEL	CTCCTCAAGGACGAGGAACGGTTGAAGGCTGAGAGGGCCCAGGCT	CTCCTCAAGGACGAGGAACGGTTGAAGGCTGAGAGGGCCCAGGCT	-													0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	agtcaaagcaactggtggctCtcctcaaggacgaggaacgg					rs377337201		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	CTCCTCAAGGACGAGGAACGGTTGAAGGCTGAGAGGGCCCAGGCT	CTCCTCAAGGACGAGGAACGGTTGAAGGCTGAGAGGGCCCAGGCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr17:19186829_19186873delCTCCTCAAGGACGAGGAACGGTTGAAGGCTGAGAGGGCCCAGGCT	ENST00000314728.5	+	3	881_925	c.397_441delCTCCTCAAGGACGAGGAACGGTTGAAGGCTGAGAGGGCCCAGGCT	c.(397-441)ctcctcaaggacgaggaacggttgaaggctgagagggcccaggctdel	p.LLKDEERLKAERAQA133del	EPN2_ENST00000395618.3_Intron|EPN2_ENST00000571254.1_In_Frame_Del_p.LLKDEERLKAERAQA133del|EPN2_ENST00000575595.1_Intron|EPN2_ENST00000347697.2_In_Frame_Del_p.LLKDEERLKAERAQA133del|EPN2_ENST00000395626.1_In_Frame_Del_p.LLKDEERLKAERAQA133del|EPN2_ENST00000395620.2_In_Frame_Del_p.LLKDEERLKAERAQA133del	NM_014964.4	NP_055779.2	O95208	EPN2_HUMAN	epsin 2	133	ENTH. {ECO:0000255|PROSITE- ProRule:PRU00243}.				embryonic organ development (GO:0048568)|endocytosis (GO:0006897)|in utero embryonic development (GO:0001701)|Notch signaling pathway (GO:0007219)	clathrin coat of endocytic vesicle (GO:0030128)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	lipid binding (GO:0008289)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	19	all_cancers(12;3.11e-05)|all_epithelial(12;0.00121)|Hepatocellular(7;0.00345)|Breast(13;0.143)					ACTGGTGGCTCTCCTCAAGGACGAGGAACGGTTGAAGGCTGAGAGGGCCCAGGCTCTCAAAACCA	0.584																																					p.132_147del		Pindel	.											.	EPN2	52	.	0			c.396_440del						.																																			SO:0001651	inframe_deletion	22905	exon3			.	AB028988	CCDS11203.1, CCDS11204.1, CCDS42277.1	17p11.2	2012-11-19			ENSG00000072134	ENSG00000072134			18639	protein-coding gene	gene with protein product	"Eps15 binding protein"	607263				10567358	Standard	NM_014964		Approved	KIAA1065, EHB21	uc002gvd.4	O95208	OTTHUMG00000178447	ENST00000314728.5:c.397_441delCTCCTCAAGGACGAGGAACGGTTGAAGGCTGAGAGGGCCCAGGCT	chr17.hg19:g.19186829_19186873delCTCCTCAAGGACGAGGAACGGTTGAAGGCTGAGAGGGCCCAGGCT	ENSP00000320543:p.Leu133_Ala147del	0.0	0.0		50.0	15.0	NM_148921	A8MTV8|B3KRX8|E9PBC2|O95207|Q52LD0|Q9H7Z2|Q9UPT7	In_Frame_Del	DEL	ENST00000314728.5	hg19	CCDS11203.1																																																																																			.	.		0.584	EPN2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132283.3	NM_014964		-	19186873	CTCCTCAAGGACGAGGAACGGTTGAAGGCTGAGAGGGCCCAGGCT	-	19186829	7	5	263	1	0	1	0	1	0	0	0	0	5188	913	32	0	399	0	EPN2	17	19186829	In_Frame_Del	DEL	CTCCTCAAGGACGAGGAACGGTTGAAGGCTGAGAGGGCCCAGGCT	TCGA-FV-A2QR-01A-11D-A20W-10	11343981	19186829	62008381	366	38740										
ULK2	9706	hgsc.bcm.edu	37	chr17	19700945	19700945	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ggtgggggcgctctgcagtcTagcacccgataagagagact	15	10	2	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr17:19700945T>C	ENST00000395544.4	-	18	2072	c.1573A>G	c.(1573-1575)Aga>Gga	p.R525G	ULK2_ENST00000580130.1_5'UTR|ULK2_ENST00000361658.2_Missense_Mutation_p.R525G	NM_014683.3	NP_055498.3	Q8IYT8	ULK2_HUMAN	unc-51 like autophagy activating kinase 2	525					autophagic vacuole assembly (GO:0000045)|axon extension (GO:0048675)|negative regulation of collateral sprouting (GO:0048671)|protein autophosphorylation (GO:0046777)|regulation of autophagy (GO:0010506)|response to starvation (GO:0042594)|signal transduction (GO:0007165)	ATG1/UKL1 signaling complex (GO:0034273)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|pre-autophagosomal structure membrane (GO:0034045)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			large_intestine(1)|skin(4)|stomach(1)	6	all_cancers(12;4.97e-05)|all_epithelial(12;0.00362)|Breast(13;0.186)					CTCTGCAGTCTAGCACCCGAT	0.517																																					p.R525G		Atlas-SNP	.											.	ULK2	142	.	0			c.A1573G						.						53	46	48					17																	19700945		2203	4300	6503	SO:0001583	missense	9706	exon18			GCAGTCTAGCACC	AB014523	CCDS11213.1	17p11.2	2014-02-12	2013-07-02		ENSG00000083290	ENSG00000083290	2.7.11.1		13480	protein-coding gene	gene with protein product		608650	"unc-51 (C. elegans)-like kinase 2", "unc-51-like kinase 2 (C. elegans)"			10557072	Standard	NM_014683		Approved	KIAA0623, Unc51.2, ATG1B	uc002gwn.3	Q8IYT8	OTTHUMG00000059511	ENST00000395544.4:c.1573A>G	chr17.hg19:g.19700945T>C	ENSP00000378914:p.Arg525Gly	42.0	0.0		33.0	4.0	NM_001142610	A8MY69|O75119	Missense_Mutation	SNP	ENST00000395544.4	hg19	CCDS11213.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.198751	0.79015	.	.	ENSG00000083290	ENST00000361658;ENST00000395544	T;T	0.36340	1.26;1.26	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.56046	0.1959	M	0.77820	2.39	0.44424	D	0.997341	D	0.65815	0.995	P	0.55455	0.776	T	0.61544	-0.7041	10	0.72032	D	0.01	-21.2887	15.642	0.77012	0.0:0.0:0.0:1.0	.	525	Q8IYT8	ULK2_HUMAN	G	525	ENSP00000354877:R525G;ENSP00000378914:R525G	ENSP00000354877:R525G	R	-	1	2	ULK2	19641537	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	2.643000	0.46604	2.288000	0.76882	0.533000	0.62120	AGA	.	.		0.517	ULK2-001	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132375.2	NM_014683		C	19700945	T	C	19700945	3	2	263	1	0	0	0	0	1	0	0	0	16991	1530	53	2	1577	2	ULK2	17	19700945	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	514116	19700945	61494265	367	38741										
KSR1	8844	hgsc.bcm.edu	37	chr17	25932752	25932752	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gaagctcttcaagaaagaggTgatgaactaccggcagacgc	12	9	2	5			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr17:25932752T>C	ENST00000319524.6	+	15	1973	c.1973T>C	c.(1972-1974)gTg>gCg	p.V658A	KSR1_ENST00000268763.6_Missense_Mutation_p.V521A|KSR1_ENST00000509603.2_Missense_Mutation_p.V636A|KSR1_ENST00000398988.3_Missense_Mutation_p.V521A			Q8IVT5	KSR1_HUMAN	kinase suppressor of ras 1	658	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				Ras protein signal transduction (GO:0007265)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(12)|prostate(2)|urinary_tract(1)	28	Lung NSC(42;0.00836)		BRCA - Breast invasive adenocarcinoma(3;0.00122)	UCEC - Uterine corpus endometrioid carcinoma (53;0.168)		AAGAAAGAGGTGATGAACTAC	0.627																																					p.V521A	Esophageal Squamous(88;1120 1336 6324 10502 16832)	Atlas-SNP	.											.	KSR1	151	.	0			c.T1562C						.						20	23	22					17																	25932752		2054	4184	6238	SO:0001583	missense	8844	exon15			AAGAGGTGATGAA	U43586	CCDS58532.1	17q11.2	2012-05-23	2005-12-14	2005-12-14	ENSG00000141068	ENSG00000141068			6465	protein-coding gene	gene with protein product		601132	"kinase suppressor of ras"	KSR		8521512	Standard	XM_006722151		Approved	RSU2	uc031qzj.1	Q8IVT5	OTTHUMG00000132051	ENST00000319524.6:c.1973T>C	chr17.hg19:g.25932752T>C	ENSP00000323178:p.Val658Ala	110.0	0.0		147.0	8.0	NM_014238	F8WEA9|H7BYU0|Q13476	Missense_Mutation	SNP	ENST00000319524.6	hg19		.	.	.	.	.	.	.	.	.	.	T	32	5.109239	0.94292	.	.	ENSG00000141068	ENST00000319524;ENST00000509603;ENST00000268763;ENST00000398982	T;T;T	0.44482	0.92;0.92;0.92	5.67	5.67	0.87782	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.64114	0.2569	M	0.71920	2.185	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.998	T	0.66736	-0.5848	10	0.59425	D	0.04	.	15.0899	0.72185	0.0:0.0:0.0:1.0	.	656;636	Q8IVT5;F5H0K8	KSR1_HUMAN;.	A	658;636;521;521	ENSP00000323178:V658A;ENSP00000438795:V636A;ENSP00000268763:V521A	ENSP00000268763:V521A	V	+	2	0	KSR1	22956879	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.925000	0.87563	2.165000	0.68154	0.533000	0.62120	GTG	.	.		0.627	KSR1-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_014238		C	25932752	T	C	25932752	3	2	263	1	0	0	0	0	1	0	0	0	8590	1696	59	2	1608	2	KSR1	17	25932752	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	6231807	25932752	55262458	368	38742										
TP53I13	90313	hgsc.bcm.edu	37	chr17	27899619	27899619	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ccttcctgctggtgctgctcAccctggccacgctctgcaca	9	18	2	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr17:27899619A>G	ENST00000301057.7	+	6	1088	c.973A>G	c.(973-975)Acc>Gcc	p.T325A	RP11-68I3.4_ENST00000579050.1_RNA|RP11-68I3.2_ENST00000581474.1_RNA	NM_138349.2	NP_612358.3	Q8NBR0	P5I13_HUMAN	tumor protein p53 inducible protein 13	325						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|kidney(1)|lung(1)|urinary_tract(1)	4				READ - Rectum adenocarcinoma(3;0.236)		GGTGCTGCTCACCCTGGCCAC	0.697																																					p.T325A		Atlas-SNP	.											.	TP53I13	17	.	0			c.A973G						.						8	9	9					17																	27899619		2110	4221	6331	SO:0001583	missense	90313	exon6			CTGCTCACCCTGG	AK075341	CCDS42289.1	17q11.2	2006-01-16				ENSG00000167543			25102	protein-coding gene	gene with protein product						14767535	Standard	NM_138349		Approved	DSCP1	uc002hee.3	Q8NBR0		ENST00000301057.7:c.973A>G	chr17.hg19:g.27899619A>G	ENSP00000301057:p.Thr325Ala	90.0	0.0		116.0	5.0	NM_138349	Q7L5U3	Missense_Mutation	SNP	ENST00000301057.7	hg19	CCDS42289.1	.	.	.	.	.	.	.	.	.	.	A	12.41	1.930467	0.34096	.	.	ENSG00000167543	ENST00000301057;ENST00000378818	.	.	.	4.52	4.52	0.55395	.	0.128822	0.51477	D	0.000095	T	0.43100	0.1232	L	0.38838	1.175	0.45554	D	0.998505	P	0.41393	0.748	B	0.43225	0.412	T	0.20273	-1.0280	9	0.13108	T	0.6	-23.8016	11.7479	0.51830	1.0:0.0:0.0:0.0	.	325	Q8NBR0	P5I13_HUMAN	A	325;92	.	ENSP00000301057:T325A	T	+	1	0	TP53I13	24923745	0.967000	0.33354	0.993000	0.49108	0.984000	0.73092	1.492000	0.35594	2.039000	0.60335	0.379000	0.24179	ACC	.	.		0.697	TP53I13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447804.2	NM_138349		G	27899619	A	G	27899619	3	3	263	1	0	0	0	0	1	0	0	0	16401	159	6	2	995	2	TP53I13	17	27899619	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	1966867	27899619	53295591	369	38743										
CPD	1362	hgsc.bcm.edu	37	chr17	28770949	28770949	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ctggagattactggcgtctcTtggttccaggaacttataaa	10	8	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr17:28770949T>C	ENST00000225719.4	+	11	2579	c.2503T>C	c.(2503-2505)Ttg>Ctg	p.L835L	CPD_ENST00000543464.2_Silent_p.L588L	NM_001304.4	NP_001295.2	O75976	CBPD_HUMAN	carboxypeptidase D	835	Carboxypeptidase-like 2.					extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metallocarboxypeptidase activity (GO:0004181)|serine-type carboxypeptidase activity (GO:0004185)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(13)|skin(5)|stomach(1)|urinary_tract(1)	36						CTGGCGTCTCTTGGTTCCAGG	0.448																																					p.L835L		Atlas-SNP	.											.	CPD	89	.	0			c.T2503C						.						166	166	166					17																	28770949		2203	4300	6503	SO:0001819	synonymous_variant	1362	exon11			CGTCTCTTGGTTC	U65090	CCDS11257.1, CCDS56025.1	17q11.2	2012-02-10			ENSG00000108582	ENSG00000108582	3.4.17.22		2301	protein-coding gene	gene with protein product	"metallocarboxypeptidase D"	603102				9628828, 9355738	Standard	NM_001304		Approved	GP180	uc002hfb.2	O75976	OTTHUMG00000132797	ENST00000225719.4:c.2503T>C	chr17.hg19:g.28770949T>C		61.0	0.0		90.0	5.0	NM_001304	B7Z7T9|B7ZAU4|F5GZH6|O15377|Q86SH9|Q86XE6	Silent	SNP	ENST00000225719.4	hg19	CCDS11257.1																																																																																			.	.		0.448	CPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256214.3	NM_001304		C	28770949	T	C	28770949	2	2	263	1	0	0	0	0	0	0	0	1	3800	1606	56	2		2	CPD	17	28770949	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	871330	28770949	52424261	370	38744										
NF1	4763	hgsc.bcm.edu	37	chr17	29576138	29576138	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tgtgccactgtttataccagGtatgcttacagttagagatt	9	7	0	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr17:29576138G>C	ENST00000358273.4	+	30	4493		c.e30+1		NF1_ENST00000356175.3_Splice_Site	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1						actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(5)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TTTATACCAGGTATGCTTACA	0.393			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																											.		Atlas-SNP	.	yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	NF1_ENST00000358273,NS,carcinoma,0,3	NF1	1586	.	13	Whole gene deletion(8)|Unknown(5)	soft_tissue(8)|autonomic_ganglia(2)|central_nervous_system(2)|lung(1)	c.4110+1G>C	GRCh37	CS000898|CS971829	NF1	S		.						150	136	141					17																	29576138		2203	4300	6503	SO:0001630	splice_region_variant	4763	exon30	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	TACCAGGTATGCT		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.4110+1G>C	chr17.hg19:g.29576138G>C		87.0	0.0		94.0	28.0	NM_000267	O00662|Q14284|Q14930|Q14931|Q9UMK3	Splice_Site	SNP	ENST00000358273.4	hg19	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.849295	0.91277	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735	.	.	.	5.74	5.74	0.90152	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.2982	0.98569	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NF1	26600264	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.378000	0.97191	2.873000	0.98535	0.563000	0.77884	.	.	.		0.393	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267	Intron	C	29576138	G	C	29576138	5	2	263	1	0	0	0	0	0	0	1	0	10365	1275	44	4	4290	4	NF1	17	29576138	Splice_Site	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	805189	29576138	51619072	371	38745										
ZNF830	91603	hgsc.bcm.edu	37	chr17	33289487	33289487	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	agaggatgaggagggacggtTggaccgccagattggggaga	20	5	0	4			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr17:33289487T>C	ENST00000361952.3	+	1	939	c.902T>C	c.(901-903)tTg>tCg	p.L301S	CCT6B_ENST00000421975.3_5'Flank|CCT6B_ENST00000314144.5_5'Flank|CCT6B_ENST00000436961.3_5'Flank	NM_052857.3	NP_443089.3	Q96NB3	ZN830_HUMAN	zinc finger protein 830	301					blastocyst growth (GO:0001832)|mitotic nuclear division (GO:0007067)|nuclear cell cycle DNA replication (GO:0033260)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|large_intestine(1)|liver(2)|lung(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		Ovarian(249;0.17)				GAGGGACGGTTGGACCGCCAG	0.473																																					p.L301S		Atlas-SNP	.											.	ZNF830	26	.	0			c.T902C						.						98	85	90					17																	33289487		2203	4300	6503	SO:0001583	missense	91603	exon1			GACGGTTGGACCG	AK055707	CCDS32618.1	17q12	2013-10-23	2008-03-25	2008-03-25	ENSG00000198783	ENSG00000198783			28291	protein-coding gene	gene with protein product	"orphan maintenance of genome 1"		"coiled-coil domain containing 16"	CCDC16		23066043	Standard	NM_052857		Approved	MGC20398, OMCG1	uc002hih.4	Q96NB3	OTTHUMG00000179771	ENST00000361952.3:c.902T>C	chr17.hg19:g.33289487T>C	ENSP00000354518:p.Leu301Ser	73.0	0.0		93.0	4.0	NM_052857	Q96F60|Q96GZ5|Q9BU38	Missense_Mutation	SNP	ENST00000361952.3	hg19	CCDS32618.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.336680	0.81801	.	.	ENSG00000198783	ENST00000361952	T	0.15952	2.38	6.08	6.08	0.98989	.	0.202340	0.37136	N	0.002231	T	0.35393	0.0930	L	0.52364	1.645	0.58432	D	0.99999	D	0.89917	1.0	D	0.77557	0.99	T	0.02958	-1.1089	10	0.52906	T	0.07	-24.5993	13.0356	0.58870	0.0:0.0:0.0:1.0	.	301	Q96NB3	ZN830_HUMAN	S	301	ENSP00000354518:L301S	ENSP00000354518:L301S	L	+	2	0	ZNF830	30313600	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.766000	0.74970	2.333000	0.79357	0.533000	0.62120	TTG	.	.		0.473	ZNF830-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448018.1	NM_052857		C	33289487	T	C	33289487	3	2	263	1	0	0	0	0	1	0	0	0	18199	1821	63	2	904	2	ZNF830	17	33289487	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	3713349	33289487	47905723	372	38746										
GAS2L2	246176	hgsc.bcm.edu	37	chr17	34073039	34073039	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gccttggacaggggttggagAacggacagactctggctccc	15	11	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr17:34073039A>G	ENST00000254466.6	-	6	1504	c.1477T>C	c.(1477-1479)Tct>Cct	p.S493P	GAS2L2_ENST00000587565.1_Missense_Mutation_p.S477P	NM_139285.3	NP_644814.1	Q8NHY3	GA2L2_HUMAN	growth arrest-specific 2 like 2	493					cell cycle arrest (GO:0007050)|microtubule bundle formation (GO:0001578)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	actin filament binding (GO:0051015)|cytoskeletal adaptor activity (GO:0008093)|microtubule binding (GO:0008017)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		GGGGTTGGAGAACGGACAGAC	0.627																																					p.S493P		Atlas-SNP	.											.	GAS2L2	94	.	0			c.T1477C						.						95	97	96					17																	34073039		2203	4300	6503	SO:0001583	missense	246176	exon6			TTGGAGAACGGAC	AF508784	CCDS11298.1	17q21	2014-05-06			ENSG00000132139	ENSG00000270765			24846	protein-coding gene	gene with protein product		611398				12584248	Standard	NM_139285		Approved	GAR17	uc002hjv.2	Q8NHY3	OTTHUMG00000188386	ENST00000254466.6:c.1477T>C	chr17.hg19:g.34073039A>G	ENSP00000254466:p.Ser493Pro	53.0	0.0		77.0	4.0	NM_139285	Q8NHY4	Missense_Mutation	SNP	ENST00000254466.6	hg19	CCDS11298.1	.	.	.	.	.	.	.	.	.	.	A	5.721	0.317597	0.10845	.	.	ENSG00000132139	ENST00000254466	T	0.25579	1.79	4.99	2.71	0.32032	.	0.511250	0.19144	N	0.121624	T	0.14141	0.0342	N	0.20986	0.625	0.09310	N	0.999999	B	0.24533	0.105	B	0.22880	0.042	T	0.19353	-1.0308	10	0.49607	T	0.09	-5.9467	3.2615	0.06850	0.6464:0.0:0.1822:0.1714	.	493	Q8NHY3	GA2L2_HUMAN	P	493	ENSP00000254466:S493P	ENSP00000254466:S493P	S	-	1	0	GAS2L2	31097152	0.005000	0.15991	0.000000	0.03702	0.004000	0.04260	0.273000	0.18662	0.362000	0.24319	-0.290000	0.09829	TCT	.	.		0.627	GAS2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256497.1	NM_139285		G	34073039	A	G	34073039	3	3	263	1	0	0	0	0	1	0	0	0	6255	246	9	2	1169	2	GAS2L2	17	34073039	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	783552	34073039	47122171	373	38747										
TOP2A	7153	hgsc.bcm.edu	37	chr17	38552571	38552571	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tttttcttttctgcctctgcTttcatttctatggttattcg	5	9	5	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr17:38552571T>C	ENST00000423485.1	-	28	3842	c.3684A>G	c.(3682-3684)aaA>aaG	p.K1228K		NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	1228					apoptotic chromosome condensation (GO:0030263)|ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA ligation (GO:0006266)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|embryonic cleavage (GO:0040016)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|positive regulation of apoptotic process (GO:0043065)|positive regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral genome replication (GO:0045070)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|DNA-dependent ATPase activity (GO:0008094)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(9)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	39		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	CTGCCTCTGCTTTCATTTCTA	0.448																																					p.K1228K		Atlas-SNP	.											.	TOP2A	124	.	0			c.A3684G						.						45	41	42					17																	38552571		1844	4079	5923	SO:0001819	synonymous_variant	7153	exon28			CTCTGCTTTCATT		CCDS45672.1	17q21-q22	2008-08-06	2002-08-29		ENSG00000131747	ENSG00000131747	5.99.1.2		11989	protein-coding gene	gene with protein product		126430	"topoisomerase (DNA) II alpha (170kD)"	TOP2			Standard	NM_001067		Approved		uc002huq.3	P11388	OTTHUMG00000155008	ENST00000423485.1:c.3684A>G	chr17.hg19:g.38552571T>C		69.0	0.0		46.0	4.0	NM_001067	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Silent	SNP	ENST00000423485.1	hg19	CCDS45672.1																																																																																			.	.		0.448	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1			C	38552571	T	C	38552571	2	2	263	1	0	0	0	0	0	0	0	1	16380	1606	56	2		2	TOP2A	17	38552571	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	4479532	38552571	42642639	374	38748										
KRTAP9-2	83899	hgsc.bcm.edu	37	chr17	39383332	39383332	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tgtggctccaactgctgccaGccctgctgccgcccagcctg	11	18	0	0	rs542786200	byFrequency	TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr17:39383332G>C	ENST00000377721.3	+	1	433	c.426G>C	c.(424-426)caG>caC	p.Q142H	KRTAP9-2_ENST00000455970.2_Missense_Mutation_p.Q126H	NM_031961.2	NP_114167.2	Q9BYQ4	KRA92_HUMAN	keratin associated protein 9-2	142	17 X 5 AA repeats of C-C-[RQVSGE]-[SPTQ]- [TASP].					keratin filament (GO:0045095)				large_intestine(1)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			ACTGCTGCCAGCCCTGCTGCC	0.612																																					p.Q142H		Atlas-SNP	.											.	KRTAP9-2	24	.	0			c.G426C						.						36	40	39					17																	39383332		2030	3937	5967	SO:0001583	missense	83899	exon1			CTGCCAGCCCTGC	AJ406946	CCDS32651.1	17q21.2	2013-06-25			ENSG00000239886	ENSG00000239886		"Keratin associated proteins"	16926	protein-coding gene	gene with protein product						11279113	Standard	NM_031961		Approved	KAP9.2	uc002hwf.3	Q9BYQ4	OTTHUMG00000133609	ENST00000377721.3:c.426G>C	chr17.hg19:g.39383332G>C	ENSP00000366950:p.Gln142His	181.0	0.0		239.0	17.0	NM_031961	Q17RK8|Q2TB15|Q6ISF6	Missense_Mutation	SNP	ENST00000377721.3	hg19	CCDS32651.1	.	.	.	.	.	.	.	.	.	.	.	18.41	3.618122	0.66787	.	.	ENSG00000239886	ENST00000377721;ENST00000455970	T;T	0.01705	5.37;4.68	3.29	2.28	0.28536	.	.	.	.	.	T	0.07369	0.0186	M	0.77103	2.36	0.22050	N	0.999392	D	0.65815	0.995	D	0.63488	0.915	T	0.16129	-1.0413	9	0.62326	D	0.03	.	6.2648	0.20919	0.2531:0.0:0.7468:0.0	.	142	Q9BYQ4	KRA92_HUMAN	H	142;126	ENSP00000366950:Q142H;ENSP00000398325:Q126H	ENSP00000366950:Q142H	Q	+	3	2	KRTAP9-2	36636858	0.019000	0.18553	0.997000	0.53966	0.702000	0.40608	-0.380000	0.07427	0.671000	0.31185	0.298000	0.19748	CAG	.	.		0.612	KRTAP9-2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257717.1			C	39383332	G	C	39383332	3	2	263	1	0	0	0	0	1	0	0	0	8582	962	34	4	428	4	KRTAP9-2	17	39383332	Missense_Mutation	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	830761	39383332	41811878	375	38749										
KRT17	3872	hgsc.bcm.edu	37	chr17	39778675	39778675	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	aatctgcatctccaggtcggCtctggccagggtcagctcat	11	13	5	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr17:39778675C>A	ENST00000311208.8	-	3	671	c.604G>T	c.(604-606)Gcc>Tcc	p.A202S	JUP_ENST00000540235.1_Missense_Mutation_p.A361S	NM_000422.2	NP_000413.1	Q04695	K1C17_HUMAN	keratin 17	202	Coil 1B.|Rod.				epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinization (GO:0031424)|morphogenesis of an epithelium (GO:0002009)|positive regulation of cell growth (GO:0030307)|positive regulation of hair follicle development (GO:0051798)|positive regulation of translation (GO:0045727)|signal transduction (GO:0007165)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	MHC class II protein binding (GO:0042289)|MHC class II receptor activity (GO:0032395)|structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	12		Breast(137;0.000307)				TCCAGGTCGGCTCTGGCCAGG	0.607																																					p.A202S	Pancreas(92;1242 2086 39193 50508)	Atlas-SNP	.											.	KRT17	57	.	0			c.G604T						.						75	77	77					17																	39778675		2203	4300	6503	SO:0001583	missense	3872	exon3			GGTCGGCTCTGGC	X62571	CCDS11402.1	17q21.2	2014-06-12			ENSG00000128422	ENSG00000128422		"-", "Intermediate filaments type I, keratins (acidic)"	6427	protein-coding gene	gene with protein product		148069		PCHC1		7539673, 1281771, 16831889	Standard	NM_000422		Approved		uc002hxh.2	Q04695	OTTHUMG00000133505	ENST00000311208.8:c.604G>T	chr17.hg19:g.39778675C>A	ENSP00000308452:p.Ala202Ser	438.0	0.0		608.0	224.0	NM_000422	A5Z1M9|A5Z1N0|A5Z1N1|A5Z1N2|A6NDV6|A6NKQ2|Q6IP98|Q8N1P6	Missense_Mutation	SNP	ENST00000311208.8	hg19	CCDS11402.1	.	.	.	.	.	.	.	.	.	.	C	13.51	2.258354	0.39896	.	.	ENSG00000128422;ENSG00000173801	ENST00000311208;ENST00000540235	T;T	0.76578	-1.03;-1.03	3.87	3.87	0.44632	Prefoldin (1);Filament (1);	0.000000	0.44097	D	0.000489	T	0.63165	0.2488	N	0.16790	0.44	0.24686	N	0.993332	B	0.23185	0.081	B	0.33799	0.17	T	0.50676	-0.8800	10	0.18710	T	0.47	.	10.1206	0.42618	0.0:0.9072:0.0:0.0928	.	202	Q04695	K1C17_HUMAN	S	202;361	ENSP00000308452:A202S;ENSP00000441751:A361S	ENSP00000441751:A361S	A	-	1	0	JUP;KRT17	37032201	0.388000	0.25197	0.983000	0.44433	0.957000	0.61999	1.001000	0.29783	2.164000	0.68074	0.655000	0.94253	GCC	.	.		0.607	KRT17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257460.1	NM_000422		A	39778675	C	A	39778675	3	1	263	1	0	0	0	0	1	0	0	0	8463	797	28	3	718	3	KRT17	17	39778675	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	395343	39778675	41416535	376	38750										
MPP3	4356	hgsc.bcm.edu	37	chr17	41907094	41907094	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	aaatcctcatcgatattgtcAggcagaggcgggagaacggg	14	8	2	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr17:41907094A>G	ENST00000398389.4	-	7	534	c.369T>C	c.(367-369)ccT>ccC	p.P123P	MPP3_ENST00000398393.1_Silent_p.P148P	NM_001932.4	NP_001923.2	Q13368	MPP3_HUMAN	membrane protein, palmitoylated 3 (MAGUK p55 subfamily member 3)	123					nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	guanylate kinase activity (GO:0004385)			endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	26		Breast(137;0.00394)		BRCA - Breast invasive adenocarcinoma(366;0.119)		CGATATTGTCAGGCAGAGGCG	0.547																																					p.P123P		Atlas-SNP	.											.	MPP3	42	.	0			c.T369C						.						67	74	72					17																	41907094		1952	4137	6089	SO:0001819	synonymous_variant	4356	exon7			ATTGTCAGGCAGA		CCDS42344.1	17q12-q21	2008-07-18			ENSG00000161647	ENSG00000161647			7221	protein-coding gene	gene with protein product	"MAGUK p55 subfamily member 3", "discs, large (Drosophila) homolog 3", "membrane protein palmitoylated 3"	601114		DLG3		8824795	Standard	NR_003562		Approved		uc002iei.4	Q13368	OTTHUMG00000133838	ENST00000398389.4:c.369T>C	chr17.hg19:g.41907094A>G		84.0	0.0		96.0	4.0	NM_001932	B2R7N0|D3DX47|Q4GX05|Q6PGR3|Q86SV1	Silent	SNP	ENST00000398389.4	hg19	CCDS42344.1																																																																																			.	.		0.547	MPP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258371.1	NM_001932		G	41907094	A	G	41907094	2	3	263	1	0	0	0	0	0	0	0	1	9744	175	7	2		2	MPP3	17	41907094	Silent	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	2128419	41907094	39288116	377	38751										
SPOP	8405	hgsc.bcm.edu	37	chr17	47684733	47684733	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	catcattgatttcaactcgaTtctatgccagaaaaactgaa	5	9	3	3			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr17:47684733T>C	ENST00000393328.2	-	9	1081	c.716A>G	c.(715-717)aAt>aGt	p.N239S	SPOP_ENST00000504102.1_Splice_Site_p.N239S|SPOP_ENST00000503676.1_Splice_Site_p.N239S|SPOP_ENST00000393331.3_Splice_Site_p.N239S|SPOP_ENST00000347630.2_Splice_Site_p.N239S	NM_003563.3	NP_003554.1	O43791	SPOP_HUMAN	speckle-type POZ protein	239	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.			N -> S (in Ref. 3; BAD96309). {ECO:0000305}.	glucose homeostasis (GO:0042593)|positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902237)|positive regulation of type B pancreatic cell apoptotic process (GO:2000676)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	Cul3-RING ubiquitin ligase complex (GO:0031463)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	ubiquitin protein ligase binding (GO:0031625)			endometrium(18)|kidney(1)|large_intestine(3)|liver(1)|lung(4)|ovary(3)|prostate(33)	63						TTCAACTCGATTCTATGCCAG	0.368										Prostate(2;0.17)																											p.N239S		Atlas-SNP	.											.	SPOP	91	.	0			c.A716G						.						74	70	72					17																	47684733		2203	4300	6503	SO:0001630	splice_region_variant	8405	exon8			ACTCGATTCTATG	AJ000644	CCDS11551.1	17q21.33	2013-01-09			ENSG00000121067	ENSG00000121067		"BTB/POZ domain containing"	11254	protein-coding gene	gene with protein product		602650				9414087	Standard	NM_001007227		Approved	TEF2, BTBD32	uc002ipg.3	O43791	OTTHUMG00000161496	ENST00000393328.2:c.715-1A>G	chr17.hg19:g.47684733T>C		81.0	0.0		67.0	4.0	NM_001007228	B2R6S3|D3DTW7|Q53HJ1	Missense_Mutation	SNP	ENST00000393328.2	hg19	CCDS11551.1	.	.	.	.	.	.	.	.	.	.	T	17.64	3.438941	0.63067	.	.	ENSG00000121067	ENST00000393328;ENST00000393331;ENST00000347630;ENST00000504102;ENST00000503536;ENST00000503676;ENST00000513872;ENST00000509079	T;T;T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16;-0.16;-0.16	5.43	5.43	0.79202	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	T	0.53465	0.1798	L	0.35723	1.085	0.80722	D	1	B	0.18968	0.032	B	0.18263	0.021	T	0.48948	-0.8989	10	0.35671	T	0.21	-14.0961	15.3001	0.73940	0.0:0.0:0.0:1.0	.	239	O43791	SPOP_HUMAN	S	239;239;239;239;123;239;192;239	ENSP00000377001:N239S;ENSP00000377004:N239S;ENSP00000240327:N239S;ENSP00000425905:N239S;ENSP00000420908:N239S;ENSP00000426986:N239S	ENSP00000240327:N239S	N	-	2	0	SPOP	45039732	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.868000	0.87116	2.279000	0.76181	0.533000	0.62120	AAT	.	.		0.368	SPOP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365154.2	NM_003563	Missense_Mutation	C	47684733	T	C	47684733	5	2	263	1	0	0	0	0	0	0	1	0	15099	1507	52	2	420	2	SPOP	17	47684733	Splice_Site	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	5777639	47684733	33510477	378	38752										
CACNA1G	8913	hgsc.bcm.edu	37	chr17	48703642	48703642	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tagagttggacacggagctgAgctggatttcaggagacctc	14	8	1	3			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr17:48703642A>G	ENST00000359106.5	+	38	6664	c.6664A>G	c.(6664-6666)Agc>Ggc	p.S2222G	CACNA1G_ENST00000358244.5_Intron|CACNA1G_ENST00000510115.1_Missense_Mutation_p.S2143G|CACNA1G_ENST00000507510.2_Missense_Mutation_p.S2177G|CACNA1G_ENST00000507336.1_Missense_Mutation_p.S2211G|CACNA1G_ENST00000512389.1_Missense_Mutation_p.S2118G|CACNA1G_ENST00000507896.1_Intron|CACNA1G_ENST00000515765.1_Missense_Mutation_p.S2166G|CACNA1G_ENST00000429973.2_Missense_Mutation_p.S2111G|CACNA1G_ENST00000503485.1_Missense_Mutation_p.S2095G|CACNA1G_ENST00000352832.5_Missense_Mutation_p.S2095G|CACNA1G_ENST00000502264.1_Missense_Mutation_p.S2151G|CACNA1G_ENST00000510366.1_Missense_Mutation_p.S2077G|CACNA1G_ENST00000514079.1_Missense_Mutation_p.S2136G|CACNA1G_ENST00000360761.4_Missense_Mutation_p.S2106G|CACNA1G_ENST00000505165.1_Intron|CACNA1G_ENST00000354983.4_Missense_Mutation_p.S2188G|CACNA1G_ENST00000442258.2_Missense_Mutation_p.S2088G|CACNA1G_ENST00000513689.2_Missense_Mutation_p.S2132G|CACNA1G_ENST00000507609.1_Missense_Mutation_p.S2122G|CACNA1G_ENST00000515411.1_Missense_Mutation_p.S2159G|CTB-22K21.2_ENST00000502435.1_RNA|CACNA1G_ENST00000514717.1_Missense_Mutation_p.S2072G|CACNA1G_ENST00000514181.1_Missense_Mutation_p.S2104G|CACNA1G_ENST00000513964.1_Missense_Mutation_p.S2084G|CACNA1G_ENST00000515165.1_Missense_Mutation_p.S2129G	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	2222					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	CACGGAGCTGAGCTGGATTTC	0.652											OREG0024569	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S2222G		Atlas-SNP	.											.	CACNA1G	659	.	0			c.A6664G						.						38	47	44					17																	48703642		1998	4164	6162	SO:0001583	missense	8913	exon38			GAGCTGAGCTGGA	AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.6664A>G	chr17.hg19:g.48703642A>G	ENSP00000352011:p.Ser2222Gly	96.0	0.0	956	123.0	5.0	NM_018896	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Missense_Mutation	SNP	ENST00000359106.5	hg19	CCDS45730.1	.	.	.	.	.	.	.	.	.	.	A	16.14	3.039723	0.55003	.	.	ENSG00000006283	ENST00000360761;ENST00000352832;ENST00000354983;ENST00000442258;ENST00000502264;ENST00000512389;ENST00000513964;ENST00000514717;ENST00000510366;ENST00000503485;ENST00000507510;ENST00000507336;ENST00000513689;ENST00000507609;ENST00000510115;ENST00000515165;ENST00000514181;ENST00000515765;ENST00000514079;ENST00000359106;ENST00000429973;ENST00000515411	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97232	-4.19;-4.18;-4.11;-4.19;-4.22;-4.21;-4.3;-4.26;-4.3;-4.29;-4.18;-4.13;-4.25;-4.18;-4.15;-4.22;-4.18;-4.18;-4.22;-4.13;-4.21;-4.17	5.32	4.17	0.49024	.	0.439112	0.25439	N	0.030675	D	0.96962	0.9008	L	0.42245	1.32	0.28302	N	0.923081	D;B;B;D;B;P;D;B;D;B;B;B;D;B;P;B;B;B;D;B;B;B	0.61080	0.989;0.004;0.002;0.964;0.002;0.885;0.964;0.001;0.964;0.202;0.354;0.212;0.964;0.215;0.89;0.035;0.021;0.146;0.989;0.227;0.003;0.001	D;B;B;D;B;P;D;B;D;B;B;B;D;B;P;B;B;B;D;B;B;B	0.70227	0.958;0.005;0.009;0.968;0.003;0.633;0.968;0.003;0.968;0.281;0.138;0.114;0.968;0.146;0.695;0.012;0.012;0.065;0.958;0.179;0.003;0.001	D	0.92695	0.6170	10	0.52906	T	0.07	.	10.6744	0.45776	0.84:0.16:0.0:0.0	.	2072;2084;2077;2159;2132;2104;2136;2095;2122;2151;2118;2211;2111;2166;2129;2199;2177;2095;2088;2143;2106;2222	Q19QZ5;Q19QZ1;Q19QZ4;Q19R07;Q19QY8;Q19R10;Q19QZ6;Q19QZ3;Q19R06;O43497-10;Q19QZ9;Q19QZ7;Q19R08;Q19QZ8;Q19R03;O43497-4;Q19R02;Q19R12;Q19R17;Q19R11;Q2TAC4;O43497	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;CAC1G_HUMAN	G	2106;2095;2188;2088;2151;2118;2084;2072;2077;2095;2177;2211;2132;2122;2143;2129;2104;2166;2136;2222;2111;2159	ENSP00000353990:S2106G;ENSP00000339302:S2095G;ENSP00000347078:S2188G;ENSP00000409759:S2088G;ENSP00000425522:S2151G;ENSP00000426261:S2118G;ENSP00000425451:S2084G;ENSP00000422407:S2072G;ENSP00000426814:S2077G;ENSP00000427238:S2095G;ENSP00000423112:S2177G;ENSP00000420918:S2211G;ENSP00000426172:S2132G;ENSP00000423045:S2122G;ENSP00000427173:S2143G;ENSP00000426098:S2129G;ENSP00000425698:S2104G;ENSP00000426232:S2166G;ENSP00000423317:S2136G;ENSP00000352011:S2222G;ENSP00000414388:S2111G;ENSP00000423155:S2159G	ENSP00000339302:S2095G	S	+	1	0	CACNA1G	46058641	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	1.298000	0.33412	2.010000	0.58986	0.379000	0.24179	AGC	.	.		0.652	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896		G	48703642	A	G	48703642	3	3	263	1	0	0	0	0	1	0	0	0	2546	304	11	2	7081	2	CACNA1G	17	48703642	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	1018909	48703642	32491568	379	38753										
CCDC45	90799	hgsc.bcm.edu	37	chr17	62528114	62528114	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gcagagtctaagaggtggccTcccaaagccaaataaagcag	11	10	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr17:62528114T>C	ENST00000556440.2	+	14	2156	c.1646T>C	c.(1645-1647)cTc>cCc	p.L549P	AC009994.2_ENST00000579926.1_RNA|CEP95_ENST00000553412.1_Missense_Mutation_p.L385P	NM_138363.1	NP_612372.1	Q96GE4	CEP95_HUMAN	centrosomal protein 95kDa	549						centrosome (GO:0005813)|cytoplasm (GO:0005737)|spindle pole (GO:0000922)				endometrium(1)|kidney(3)|large_intestine(5)|lung(3)|ovary(1)	13						AGAGGTGGCCTCCCAAAGCCA	0.428																																					p.L549P		Atlas-SNP	.											.	CEP95	103	.	0			c.T1646C						.						79	75	76					17																	62528114		1871	4096	5967	SO:0001583	missense	90799	exon14			GTGGCCTCCCAAA	AL832822	CCDS45763.1	17q24.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000258890	ENSG00000258890			25141	protein-coding gene	gene with protein product			"coiled-coil domain containing 45"	CCDC45		21399614	Standard	NM_138363		Approved	DKFZp667E1824	uc002jem.3	Q96GE4	OTTHUMG00000179174	ENST00000556440.2:c.1646T>C	chr17.hg19:g.62528114T>C	ENSP00000450461:p.Leu549Pro	57.0	0.0		80.0	4.0	NM_138363	B4DMD2|Q96M81	Missense_Mutation	SNP	ENST00000556440.2	hg19	CCDS45763.1	.	.	.	.	.	.	.	.	.	.	T	13.86	2.363258	0.41902	.	.	ENSG00000258890	ENST00000553956;ENST00000556440;ENST00000553412	T;T	0.34472	1.36;1.36	5.97	4.89	0.63831	.	0.942091	0.09055	N	0.855130	T	0.43809	0.1264	L	0.54323	1.7	0.28087	N	0.93197	D	0.56035	0.974	P	0.51135	0.66	T	0.20638	-1.0269	10	0.35671	T	0.21	0.0229	8.2179	0.31524	0.0:0.0693:0.1338:0.7969	.	549	Q96GE4	CEP95_HUMAN	P	484;549;385	ENSP00000450461:L549P;ENSP00000450906:L385P	ENSP00000438458:L484P	L	+	2	0	CEP95	59958576	0.101000	0.21875	0.994000	0.49952	0.384000	0.30261	0.957000	0.29215	1.048000	0.40298	0.533000	0.62120	CTC	.	.		0.428	CEP95-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445100.2	NM_138363		C	62528114	T	C	62528114	3	2	263	1	0	0	0	0	1	0	0	0	2818	1551	54	2	1700	2	CCDC45	17	62528114	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	13824472	62528114	18667096	380	38754										
HELZ	9931	hgsc.bcm.edu	37	chr17	65105654	65105654	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ggggatgaaagtggcgattaGggattgcatactgtgcgtgg	18	4	0	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr17:65105654G>A	ENST00000358691.5	-	29	4233	c.4067C>T	c.(4066-4068)cCt>cTt	p.P1356L	HELZ_ENST00000580168.1_Missense_Mutation_p.P1357L	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	1356						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					GTGGCGATTAGGGATTGCATA	0.463																																					p.P1356L		Atlas-SNP	.											.	HELZ	160	.	0			c.C4067T						.						197	199	198					17																	65105654		2018	4180	6198	SO:0001583	missense	9931	exon29			CGATTAGGGATTG	D29677	CCDS42374.1	17q24.2	2013-01-18			ENSG00000198265	ENSG00000198265		"Zinc fingers, CCCH-type domain containing"	16878	protein-coding gene	gene with protein product	"down-regulated in human cancers"	606699				10471385, 12691822	Standard	NM_014877		Approved	KIAA0054, HUMORF5, DHRC	uc002jfx.4	P42694	OTTHUMG00000179555	ENST00000358691.5:c.4067C>T	chr17.hg19:g.65105654G>A	ENSP00000351524:p.Pro1356Leu	305.0	0.0		501.0	131.0	NM_014877	I6L9H4	Missense_Mutation	SNP	ENST00000358691.5	hg19	CCDS42374.1	.	.	.	.	.	.	.	.	.	.	G	11.56	1.674680	0.29693	.	.	ENSG00000198265	ENST00000358691	D	0.83506	-1.73	5.82	5.82	0.92795	.	0.152258	0.64402	D	0.000011	T	0.81278	0.4789	L	0.34521	1.04	0.80722	D	1	D;D	0.54207	0.965;0.965	P;P	0.45913	0.497;0.497	D	0.83499	0.0074	10	0.87932	D	0	-15.2697	20.0939	0.97831	0.0:0.0:1.0:0.0	.	1357;1356	B7ZLW2;P42694	.;HELZ_HUMAN	L	1356	ENSP00000351524:P1356L	ENSP00000351524:P1356L	P	-	2	0	HELZ	62536116	1.000000	0.71417	0.904000	0.35570	0.364000	0.29643	6.629000	0.74267	2.756000	0.94617	0.643000	0.83706	CCT	.	.		0.463	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		A	65105654	G	A	65105654	3	1	263	1	0	0	0	0	1	0	0	0	7058	1000	35	3	1781	3	HELZ	17	65105654	Missense_Mutation	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	2577540	65105654	16089556	381	38755										
SDK2	54549	hgsc.bcm.edu	37	chr17	71386431	71386431	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cccgtgggcagtcacctctcTtctcggtggtcaccaccaag	10	16	4	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr17:71386431T>C	ENST00000392650.3	-	29	4187	c.4187A>G	c.(4186-4188)aAg>aGg	p.K1396R	SDK2_ENST00000388726.3_Missense_Mutation_p.K1396R	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	1396	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(15)|lung(31)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	86						GTCACCTCTCTTCTCGGTGGT	0.652																																					p.K1396R		Atlas-SNP	.											.	SDK2	219	.	0			c.A4187G						.						23	20	21					17																	71386431		2203	4297	6500	SO:0001583	missense	54549	exon29			CCTCTCTTCTCGG	AB040947	CCDS45769.1	17q21.31	2013-02-11	2011-12-09		ENSG00000069188	ENSG00000069188		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19308	protein-coding gene	gene with protein product		607217	"sidekick homolog 2 (chicken)"			12230981, 15213259	Standard	NM_001144952		Approved	FLJ10832, KIAA1514	uc010dfm.3	Q58EX2	OTTHUMG00000152726	ENST00000392650.3:c.4187A>G	chr17.hg19:g.71386431T>C	ENSP00000376421:p.Lys1396Arg	59.0	0.0		84.0	4.0	NM_001144952	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Missense_Mutation	SNP	ENST00000392650.3	hg19	CCDS45769.1	.	.	.	.	.	.	.	.	.	.	T	15.07	2.725484	0.48833	.	.	ENSG00000069188	ENST00000409227;ENST00000392650;ENST00000388726;ENST00000424778;ENST00000316893	T;T;T	0.60299	0.2;0.22;1.52	5.4	4.32	0.51571	Fibronectin, type III (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.55049	0.1896	M	0.71581	2.175	0.49582	D	0.999807	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.09377	0.004;0.002;0.004	T	0.51317	-0.8721	10	0.38643	T	0.18	.	11.1332	0.48360	0.0:0.0738:0.0:0.9262	.	1396;1396;1396	Q58EX2-2;Q58EX2;Q58EX2-3	.;SDK2_HUMAN;.	R	1020;1396;1396;572;1396	ENSP00000376421:K1396R;ENSP00000373378:K1396R;ENSP00000407098:K572R	ENSP00000324967:K1396R	K	-	2	0	SDK2	68898026	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	5.833000	0.69349	0.878000	0.35920	0.459000	0.35465	AAG	.	.		0.652	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064		C	71386431	T	C	71386431	3	2	263	1	0	0	0	0	1	0	0	0	13984	1609	56	2	2399	2	SDK2	17	71386431	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	6280777	71386431	9808779	382	38756										
SLC9A3R1	9368	hgsc.bcm.edu	37	chr17	72759578	72759578	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tcagggctggcggggacgagAccaagctgctggtggtggac	19	9	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr17:72759578A>G	ENST00000262613.5	+	3	871	c.676A>G	c.(676-678)Acc>Gcc	p.T226A	SLC9A3R1_ENST00000413388.2_Missense_Mutation_p.T70A	NM_004252.4	NP_004243.1	O14745	NHRF1_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3 regulator 1	226	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				actin cytoskeleton organization (GO:0030036)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|bile acid secretion (GO:0032782)|cellular phosphate ion homeostasis (GO:0030643)|cellular protein localization (GO:0034613)|glutathione transport (GO:0034635)|microvillus assembly (GO:0030033)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sodium ion transport (GO:0010766)|negative regulation of sodium:proton antiporter activity (GO:0032416)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|protein complex assembly (GO:0006461)|regulation of excretion (GO:0044062)|regulation of protein kinase activity (GO:0045859)|regulation of sodium:proton antiporter activity (GO:0032415)|renal absorption (GO:0070293)|renal phosphate ion absorption (GO:0097291)|renal sodium ion transport (GO:0003096)|Wnt signaling pathway (GO:0016055)	actin cytoskeleton (GO:0015629)|apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell periphery (GO:0071944)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|membrane raft (GO:0045121)|microvillus (GO:0005902)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)|vesicle (GO:0031982)	beta-2 adrenergic receptor binding (GO:0031698)|beta-catenin binding (GO:0008013)|chloride channel regulator activity (GO:0017081)|growth factor receptor binding (GO:0070851)|PDZ domain binding (GO:0030165)|phosphatase binding (GO:0019902)|protein self-association (GO:0043621)|receptor binding (GO:0005102)			large_intestine(4)	4						CGGGGACGAGACCAAGCTGCT	0.617																																					p.T226A		Atlas-SNP	.											.	SLC9A3R1	12	.	0			c.A676G						.						64	60	61					17																	72759578		2203	4300	6503	SO:0001583	missense	9368	exon3			GACGAGACCAAGC	AF015926	CCDS11705.1	17q25.1	2014-09-04	2012-03-22		ENSG00000109062	ENSG00000109062			11075	protein-coding gene	gene with protein product		604990	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 3 regulatory factor 1", "solute carrier family 9 (sodium/hydrogen exchanger), isoform 3 regulator 1", "solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 1"			9314537, 9430655	Standard	NM_004252		Approved	NHERF, EBP50	uc002jlo.4	O14745	OTTHUMG00000178863	ENST00000262613.5:c.676A>G	chr17.hg19:g.72759578A>G	ENSP00000262613:p.Thr226Ala	152.0	0.0		242.0	12.0	NM_004252	B3KY21|O43552|Q86WQ5	Missense_Mutation	SNP	ENST00000262613.5	hg19	CCDS11705.1	.	.	.	.	.	.	.	.	.	.	A	9.998	1.232662	0.22626	.	.	ENSG00000109062	ENST00000262613	T	0.26660	1.72	5.45	-0.171	0.13331	PDZ/DHR/GLGF (4);	0.286306	0.37095	N	0.002252	T	0.13628	0.0330	N	0.20530	0.585	0.31742	N	0.635708	B	0.02656	0.0	B	0.20767	0.031	T	0.25984	-1.0116	9	.	.	.	-22.0401	9.2428	0.37506	0.613:0.0:0.387:0.0	.	226	O14745	NHRF1_HUMAN	A	226	ENSP00000262613:T226A	.	T	+	1	0	SLC9A3R1	70271173	1.000000	0.71417	0.984000	0.44739	0.591000	0.36615	1.191000	0.32138	-0.292000	0.08999	-0.456000	0.05471	ACC	.	.		0.617	SLC9A3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443671.1			G	72759578	A	G	72759578	3	3	263	1	0	0	0	0	1	0	0	0	14729	275	10	2	686	2	SLC9A3R1	17	72759578	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	1373147	72759578	8435632	383	38757										
ITGB4	3691	hgsc.bcm.edu	37	chr17	73729645	73729645	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cctgcgggagggcgaggacaAgccgtgctccggccgtgggg	20	12	0	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr17:73729645A>G	ENST00000200181.3	+	13	1716	c.1529A>G	c.(1528-1530)aAg>aGg	p.K510R	ITGB4_ENST00000450894.3_Missense_Mutation_p.K510R|ITGB4_ENST00000584558.1_3'UTR|ITGB4_ENST00000579662.1_Missense_Mutation_p.K510R|ITGB4_ENST00000449880.2_Missense_Mutation_p.K510R|ITGB4_ENST00000339591.3_Missense_Mutation_p.K510R	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	510	Cysteine-rich tandem repeats.				amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			GGCGAGGACAAGCCGTGCTCC	0.632																																					p.K510R		Atlas-SNP	.											.	ITGB4	165	.	0			c.A1529G						.						60	51	54					17																	73729645		2203	4300	6503	SO:0001583	missense	3691	exon13			AGGACAAGCCGTG		CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"CD molecules", "Integrins", "Fibronectin type III domain containing"	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.1529A>G	chr17.hg19:g.73729645A>G	ENSP00000200181:p.Lys510Arg	52.0	0.0		96.0	4.0	NM_001005731	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Missense_Mutation	SNP	ENST00000200181.3	hg19	CCDS11727.1	.	.	.	.	.	.	.	.	.	.	A	8.535	0.872026	0.17322	.	.	ENSG00000132470	ENST00000450894;ENST00000200181;ENST00000339591;ENST00000449880	D;D;D	0.90133	-2.62;-2.62;-2.62	4.78	0.983	0.19767	.	0.210963	0.41194	D	0.000928	D	0.85864	0.5796	L	0.45744	1.44	0.22050	N	0.999391	P;P;P;P;P	0.42908	0.57;0.793;0.692;0.565;0.565	B;P;B;B;B	0.44518	0.25;0.452;0.366;0.07;0.156	T	0.77389	-0.2606	10	0.51188	T	0.08	.	5.0596	0.14550	0.6407:0.0:0.0796:0.2796	.	470;510;510;510;510	B4E3N0;P16144-5;P16144-3;A0AVL6;P16144	.;.;.;.;ITB4_HUMAN	R	426;510;510;510	ENSP00000200181:K510R;ENSP00000344079:K510R;ENSP00000400217:K510R	ENSP00000200181:K510R	K	+	2	0	ITGB4	71241240	0.997000	0.39634	0.208000	0.23602	0.289000	0.27227	2.950000	0.49081	0.184000	0.20083	0.454000	0.30748	AAG	.	.		0.632	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1			G	73729645	A	G	73729645	3	3	263	1	0	0	0	0	1	0	0	0	7906	72	3	2	1575	2	ITGB4	17	73729645	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	970067	73729645	7465565	384	38758										
CYGB	114757	hgsc.bcm.edu	37	chr17	74527573	74527573	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ccggttccaccttgtgcttgAgggcgtgggctttccccaca	12	14	0	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr17:74527573A>G	ENST00000293230.5	-	2	706	c.344T>C	c.(343-345)cTc>cCc	p.L115P	CYGB_ENST00000586160.1_5'Flank|PRCD_ENST00000592432.1_Intron|CYGB_ENST00000589342.1_Missense_Mutation_p.L115P|CYGB_ENST00000589145.1_Missense_Mutation_p.L50P|CYGB_ENST00000590175.1_Missense_Mutation_p.L50P	NM_134268.4	NP_599030.1	Q8WWM9	CYGB_HUMAN	cytoglobin	115	Globin.				oxidation-reduction process (GO:0055114)|oxygen transport (GO:0015671)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|oxygen transporter activity (GO:0005344)|peroxidase activity (GO:0004601)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)	7						CTTGTGCTTGAGGGCGTGGGC	0.642																																					p.L115P		Atlas-SNP	.											.	CYGB	9	.	0			c.T344C						.						107	91	97					17																	74527573		2203	4300	6503	SO:0001583	missense	114757	exon2			TGCTTGAGGGCGT	AJ315162	CCDS11746.1	17q25	2008-07-18				ENSG00000161544			16505	protein-coding gene	gene with protein product	"stellate cell activation-associated protein", "histoglobin"	608759				11919282	Standard	NM_134268		Approved	HGB, STAP	uc002jru.2	Q8WWM9		ENST00000293230.5:c.344T>C	chr17.hg19:g.74527573A>G	ENSP00000293230:p.Leu115Pro	57.0	0.0		119.0	5.0	NM_134268	Q541Y7|Q8N2X5	Missense_Mutation	SNP	ENST00000293230.5	hg19	CCDS11746.1	.	.	.	.	.	.	.	.	.	.	A	18.05	3.536854	0.65085	.	.	ENSG00000161544	ENST00000293230	D	0.92858	-3.12	5.52	5.52	0.82312	Globin-like (1);Globin, structural domain (1);	0.301352	0.35903	N	0.002907	D	0.91855	0.7422	M	0.75447	2.3	0.80722	D	1	B	0.15473	0.013	B	0.23275	0.045	D	0.89250	0.3590	10	0.51188	T	0.08	-10.1027	15.6427	0.77020	1.0:0.0:0.0:0.0	.	115	Q8WWM9	CYGB_HUMAN	P	115	ENSP00000293230:L115P	ENSP00000293230:L115P	L	-	2	0	CYGB	72039168	1.000000	0.71417	1.000000	0.80357	0.572000	0.35998	7.076000	0.76806	2.100000	0.63781	0.379000	0.24179	CTC	.	.		0.642	CYGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450590.1	NM_134268		G	74527573	A	G	74527573	3	3	263	1	0	0	0	0	1	0	0	0	4141	304	11	2	240	2	CYGB	17	74527573	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	797928	74527573	6667637	385	38759										
DNAH17	8632	hgsc.bcm.edu	37	chr17	76464900	76464900	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tcctcggccacctgggagtcTgtcatcaggaacaccgaggg	13	13	3	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr17:76464900T>C	ENST00000585328.1	-	55	8686	c.8562A>G	c.(8560-8562)acA>acG	p.T2854T	DNAH17_ENST00000586052.1_5'UTR|DNAH17_ENST00000389840.5_Silent_p.T2845T	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	2845	AAA 4. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			CCTGGGAGTCTGTCATCAGGA	0.567																																					p.T2859T		Atlas-SNP	.											.	DNAH17	347	.	0			c.A8577G						.						83	88	87					17																	76464900		2088	4202	6290	SO:0001819	synonymous_variant	8632	exon55			GGAGTCTGTCATC	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"Axonemal dyneins"	2946	protein-coding gene	gene with protein product		610063	"dynein, axonemal, heavy polypeptide 17", "dynein, axonemal, heavy chain like 1", "dynein, axonemal, heavy like 1"	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.8562A>G	chr17.hg19:g.76464900T>C		62.0	0.0		111.0	5.0	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	hg19																																																																																				.	.		0.567	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		C	76464900	T	C	76464900	2	2	263	1	0	0	0	0	0	0	0	1	4603	1567	55	2		2	DNAH17	17	76464900	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	1937327	76464900	4730310	386	38760										
CHMP6	79643	hgsc.bcm.edu	37	chr17	78972946	78972946	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gcaggcggagctggtggcagCttcgtaacgtggcctcgtct	16	11	1	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr17:78972946C>G	ENST00000325167.5	+	8	677	c.599C>G	c.(598-600)gCt>gGt	p.A200G	CTD-2561B21.7_ENST00000577061.2_RNA|CTD-2561B21.7_ENST00000576215.1_RNA	NM_024591.4	NP_078867.2	Q96FZ7	CHMP6_HUMAN	charged multivesicular body protein 6	200					endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	protein N-terminus binding (GO:0047485)			lung(2)|ovary(1)	3	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0175)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			CTGGTGGCAGCTTCGTAACGT	0.617																																					p.A200G		Atlas-SNP	.											.	CHMP6	16	.	0			c.C599G						.						119	98	105					17																	78972946		2203	4300	6503	SO:0001583	missense	79643	exon8			TGGCAGCTTCGTA	BC010108	CCDS11774.1	17q25.3	2014-08-13	2011-09-21		ENSG00000176108	ENSG00000176108		"Charged multivesicular body proteins"	25675	protein-coding gene	gene with protein product		610901	"chromatin modifying protein 6"			11559748, 15511219	Standard	NM_024591		Approved	FLJ11749, VPS20	uc002jyw.4	Q96FZ7	OTTHUMG00000177645	ENST00000325167.5:c.599C>G	chr17.hg19:g.78972946C>G	ENSP00000317468:p.Ala200Gly	95.0	0.0		128.0	37.0	NM_024591	A8K7U0|Q53FU4|Q9HAE8	Missense_Mutation	SNP	ENST00000325167.5	hg19	CCDS11774.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.484349	0.84854	.	.	ENSG00000176108	ENST00000325167	T	0.61040	0.14	4.77	4.77	0.60923	.	0.132704	0.49305	D	0.000158	T	0.72277	0.3440	L	0.60455	1.87	0.58432	D	0.999993	D	0.76494	0.999	D	0.78314	0.991	T	0.75602	-0.3261	10	0.72032	D	0.01	-16.2775	15.5945	0.76569	0.0:1.0:0.0:0.0	.	200	Q96FZ7	CHMP6_HUMAN	G	200	ENSP00000317468:A200G	ENSP00000317468:A200G	A	+	2	0	CHMP6	76587541	0.974000	0.33945	0.920000	0.36463	0.904000	0.53231	2.383000	0.44354	2.180000	0.69256	0.645000	0.84053	GCT	.	.		0.617	CHMP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438215.1	NM_024591		G	78972946	C	G	78972946	3	3	263	1	0	0	0	0	1	0	0	0	3362	797	28	4	629	4	CHMP6	17	78972946	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	2508046	78972946	2222264	387	38761										
VAPA	9218	hgsc.bcm.edu	37	chr18	9931911	9931911	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cacctcgccggtactgtgtgAggcccaacagtggaattatt	11	11	0	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr18:9931911A>G	ENST00000400000.2	+	2	439	c.184A>G	c.(184-186)Agg>Ggg	p.R62G	VAPA_ENST00000340541.4_Missense_Mutation_p.R62G|VAPA_ENST00000584796.1_3'UTR	NM_003574.5|NM_194434.2	NP_003565.4|NP_919415.2	Q9P0L0	VAPA_HUMAN	VAMP (vesicle-associated membrane protein)-associated protein A, 33kDa	62	MSP. {ECO:0000255|PROSITE- ProRule:PRU00132}.				cell death (GO:0008219)|membrane fusion (GO:0061025)|neuron projection development (GO:0031175)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein localization to endoplasmic reticulum (GO:0070972)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	protein heterodimerization activity (GO:0046982)|signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)			breast(1)|lung(2)|prostate(1)	4						GTACTGTGTGAGGCCCAACAG	0.398																																					p.R62G		Atlas-SNP	.											.	VAPA	28	.	0			c.A184G						.						81	86	84					18																	9931911		2138	4272	6410	SO:0001583	missense	9218	exon2			TGTGTGAGGCCCA		CCDS11847.2, CCDS11848.2	18p11.2	2008-07-28	2002-08-29		ENSG00000101558	ENSG00000101558			12648	protein-coding gene	gene with protein product		605703	"VAMP (vesicle-associated membrane protein)-associated protein A (33kD)"			9920726, 9657962	Standard	NM_003574		Approved	hVAP-33, VAP-A	uc002koj.3	Q9P0L0	OTTHUMG00000131603	ENST00000400000.2:c.184A>G	chr18.hg19:g.9931911A>G	ENSP00000382880:p.Arg62Gly	73.0	0.0		97.0	4.0	NM_003574	A6NDZ0|D3DUI3|O75453|Q5U0E7|Q9UBZ2	Missense_Mutation	SNP	ENST00000400000.2	hg19	CCDS11848.2	.	.	.	.	.	.	.	.	.	.	A	22.0	4.235121	0.79800	.	.	ENSG00000101558	ENST00000340541;ENST00000400000	T;T	0.74947	-0.89;-0.89	5.57	-1.77	0.07982	PapD-like (2);	0.000000	0.85682	D	0.000000	D	0.90796	0.7110	H	0.98351	4.21	0.80722	D	1	D;D	0.76494	0.991;0.999	D;D	0.85130	0.995;0.997	D	0.93121	0.6525	9	.	.	.	-17.51	18.0014	0.89198	0.322:0.678:0.0:0.0	.	62;62	Q9P0L0;Q9P0L0-2	VAPA_HUMAN;.	G	62	ENSP00000345656:R62G;ENSP00000382880:R62G	.	R	+	1	2	VAPA	9921911	1.000000	0.71417	0.990000	0.47175	0.982000	0.71751	1.157000	0.31724	-0.425000	0.07371	0.533000	0.62120	AGG	.	.		0.398	VAPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254490.1			G	9931911	A	G	9931911	3	3	263	1	0	0	0	0	1	0	0	0	17136	295	11	2	190	2	VAPA	18	9931911	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10		9931911	68145337	388	38762										
DSG4	147409	hgsc.bcm.edu	37	chr18	28971041	28971041	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tctttttcatcttgattaagCaacacagtatgtacaacctg	5	9	3	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr18:28971041C>T	ENST00000308128.4	+	7	820	c.685C>T	c.(685-687)Caa>Taa	p.Q229*	RP11-534N16.1_ENST00000581856.1_RNA|RP11-534N16.1_ENST00000578477.1_RNA|DSG4_ENST00000359747.4_Splice_Site_p.Q229*|RP11-534N16.1_ENST00000581452.1_RNA	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4	229	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.		Missing (in HYPT6). {ECO:0000269|PubMed:12705872, ECO:0000269|PubMed:15191570}.		anagen (GO:0042640)|BMP signaling pathway (GO:0030509)|homophilic cell adhesion (GO:0007156)|keratinocyte differentiation (GO:0030216)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(6)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(11)|liver(2)|lung(35)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			CTTGATTAAGCAACACAGTAT	0.388																																					p.Q229X		Atlas-SNP	.											.	DSG4	343	.	0			c.C685T						.						123	104	110					18																	28971041		2203	4300	6503	SO:0001630	splice_region_variant	147409	exon7			ATTAAGCAACACA	AY177664, AY168788	CCDS11897.1, CCDS45845.1	18q12.1	2010-01-26			ENSG00000175065	ENSG00000175065		"Cadherins / Major cadherins"	21307	protein-coding gene	gene with protein product		607892				12648213	Standard	NM_001134453		Approved	CDHF13, LAH	uc002kwq.2	Q86SJ6	OTTHUMG00000131979	ENST00000308128.4:c.685-1C>T	chr18.hg19:g.28971041C>T		84.0	0.0		83.0	4.0	NM_001134453	A2RUI1|Q6Y9L9|Q8IXV4	Nonsense_Mutation	SNP	ENST00000308128.4	hg19	CCDS11897.1	.	.	.	.	.	.	.	.	.	.	C	36	5.647942	0.96714	.	.	ENSG00000175065	ENST00000308128;ENST00000359747	.	.	.	5.99	2.97	0.34412	.	0.251262	0.21026	N	0.081431	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.427	0.94746	0.0:0.5373:0.4627:0.0	.	.	.	.	X	229	.	.	Q	+	1	0	DSG4	27225039	0.972000	0.33761	1.000000	0.80357	0.711000	0.40976	-0.014000	0.12656	0.817000	0.34445	0.655000	0.94253	CAA	.	.		0.388	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254941.1	NM_177986	Nonsense_Mutation	T	28971041	C	T	28971041	5	4	263	1	0	0	0	0	0	0	1	0	4781	724	25	3	711	3	DSG4	18	28971041	Splice_Site	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	19039130	28971041	49106207	389	38763										
ASXL3	80816	hgsc.bcm.edu	37	chr18	31326119	31326119	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tgggcatgaaacaagtttccTatgaccagaatgaaatgaaa	9	6	0	5			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr18:31326119T>C	ENST00000269197.5	+	12	6307	c.6307T>C	c.(6307-6309)Tat>Cat	p.Y2103H		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	2103					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						ACAAGTTTCCTATGACCAGAA	0.413																																					p.Y2103H		Atlas-SNP	.											.	ASXL3	405	.	0			c.T6307C						.						90	90	90					18																	31326119		1853	4098	5951	SO:0001583	missense	80816	exon12			GTTTCCTATGACC	AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"KIAA1713", "additional sex combs like 3 (Drosophila)"	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.6307T>C	chr18.hg19:g.31326119T>C	ENSP00000269197:p.Tyr2103His	48.0	0.0		80.0	4.0	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	hg19	CCDS45847.1	.	.	.	.	.	.	.	.	.	.	T	16.83	3.230122	0.58777	.	.	ENSG00000141431	ENST00000269197	T	0.17370	2.28	5.86	5.86	0.93980	.	.	.	.	.	T	0.27832	0.0685	N	0.24115	0.695	0.41471	D	0.988105	D	0.89917	1.0	D	0.80764	0.994	T	0.05869	-1.0859	9	0.24483	T	0.36	.	16.2605	0.82541	0.0:0.0:0.0:1.0	.	2103	Q9C0F0	ASXL3_HUMAN	H	2103	ENSP00000269197:Y2103H	ENSP00000269197:Y2103H	Y	+	1	0	ASXL3	29580117	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.153000	0.71819	2.237000	0.73441	0.460000	0.39030	TAT	.	.		0.413	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			C	31326119	T	C	31326119	3	2	263	1	0	0	0	0	1	0	0	0	1068	1522	53	2	6353	2	ASXL3	18	31326119	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	2355078	31326119	46751129	390	38764										
ALPK2	115701	hgsc.bcm.edu	37	chr18	56247584	56247584	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cttataaggatgttccttctCatcaatctgatttgcccttt	5	10	3	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr18:56247584C>A	ENST00000361673.3	-	4	637	c.424G>T	c.(424-426)Gag>Tag	p.E142*	ALPK2_ENST00000587399.1_5'Flank	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	142						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						TGTTCCTTCTCATCAATCTGA	0.493																																					p.E142X		Atlas-SNP	.											.	ALPK2	487	.	0			c.G424T						.						279	268	272					18																	56247584		2139	4236	6375	SO:0001587	stop_gained	115701	exon4			CCTTCTCATCAAT	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"Immunoglobulin superfamily / I-set domain containing"	20565	protein-coding gene	gene with protein product	"heart alpha-kinase"					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.424G>T	chr18.hg19:g.56247584C>A	ENSP00000354991:p.Glu142*	270.0	1.0		306.0	125.0	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Nonsense_Mutation	SNP	ENST00000361673.3	hg19	CCDS11966.2	.	.	.	.	.	.	.	.	.	.	C	34	5.320269	0.95682	.	.	ENSG00000198796	ENST00000361673	.	.	.	5.78	2.78	0.32641	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-0.0203	3.2863	0.06932	0.1426:0.5675:0.1381:0.1518	.	.	.	.	X	142	.	ENSP00000354991:E142X	E	-	1	0	ALPK2	54398564	0.001000	0.12720	0.002000	0.10522	0.096000	0.18686	0.715000	0.25822	0.732000	0.32470	0.467000	0.42956	GAG	.	.		0.493	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947		A	56247584	C	A	56247584	4	1	263	1	0	0	0	0	0	1	0	0	545	835	29	3	6128	3	ALPK2	18	56247584	Nonsense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	24921465	56247584	21829664	391	38765										
PIGN	23556	hgsc.bcm.edu	37	chr18	59713126	59713126	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tgggtttgccacatagtctgAgtttcttcgttgtgagcagc	12	8	2	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr18:59713126A>G	ENST00000357637.5	-	31	3174	c.2759T>C	c.(2758-2760)cTc>cCc	p.L920P	PIGN_ENST00000400334.3_Missense_Mutation_p.L920P	NM_176787.4	NP_789744.1	O95427	PIGN_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class N	920					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22		Colorectal(73;0.187)				ACATAGTCTGAGTTTCTTCGT	0.448																																					p.L920P		Atlas-SNP	.											.	PIGN	62	.	0			c.T2759C						.						102	100	101					18																	59713126		2006	4195	6201	SO:0001583	missense	23556	exon31			AGTCTGAGTTTCT	AF109219	CCDS45879.1	18q21.33	2013-02-26	2006-06-28		ENSG00000197563	ENSG00000197563		"Phosphatidylinositol glycan anchor biosynthesis"	8967	protein-coding gene	gene with protein product		606097	"phosphatidylinositol glycan, class N"			10069808, 10574991	Standard	NM_012327		Approved	MDC4, PIG-N	uc021ulb.1	O95427	OTTHUMG00000180098	ENST00000357637.5:c.2759T>C	chr18.hg19:g.59713126A>G	ENSP00000350263:p.Leu920Pro	77.0	0.0		94.0	5.0	NM_176787	Q7L8F8|Q8TC01|Q9NT05	Missense_Mutation	SNP	ENST00000357637.5	hg19	CCDS45879.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.089235	0.76756	.	.	ENSG00000197563	ENST00000357637;ENST00000400334	T;T	0.32272	1.46;1.46	5.23	5.23	0.72850	.	0.165198	0.41001	D	0.000968	T	0.52289	0.1725	M	0.75777	2.31	0.80722	D	1	D;D	0.89917	0.993;1.0	P;D	0.65987	0.868;0.94	T	0.53732	-0.8397	10	0.45353	T	0.12	-11.2283	12.6467	0.56738	1.0:0.0:0.0:0.0	.	920;920	B2RCI8;O95427	.;PIGN_HUMAN	P	920	ENSP00000350263:L920P;ENSP00000383188:L920P	ENSP00000350263:L920P	L	-	2	0	PIGN	57864106	1.000000	0.71417	0.923000	0.36655	0.920000	0.55202	6.969000	0.76092	1.963000	0.57068	0.460000	0.39030	CTC	.	.		0.448	PIGN-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449757.2	NM_176787		G	59713126	A	G	59713126	3	3	263	1	0	0	0	0	1	0	0	0	11902	304	11	2	40	2	PIGN	18	59713126	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	3465542	59713126	18364122	392	38766										
SERPINB10	5273	hgsc.bcm.edu	37	chr18	61587033	61587033	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gtctttcagaaatatttagaAgacatgaaaacatattttgg	7	4	2	4	rs149788289		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr18:61587033A>G	ENST00000238508.3	+	5	443	c.384A>G	c.(382-384)gaA>gaG	p.E128E		NM_005024.1	NP_005015.1	P48595	SPB10_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 10	128					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)|skin(3)|stomach(2)	24		Esophageal squamous(42;0.131)				AATATTTAGAAGACATGAAAA	0.328																																					p.E128E		Atlas-SNP	.											.	SERPINB10	53	.	0			c.A384G						.	A		1,4405	2.1+/-5.4	0,1,2202	66	81	76		384	0.3	1	18	dbSNP_134	76	0,8598		0,0,4299	no	coding-synonymous	SERPINB10	NM_005024.1		0,1,6501	GG,GA,AA		0.0,0.0227,0.0077		128/398	61587033	1,13003	2203	4299	6502	SO:0001819	synonymous_variant	5273	exon4			TTTAGAAGACATG	U35459	CCDS11990.1	18q21.3	2014-02-18	2005-08-18		ENSG00000242550	ENSG00000242550		"Serine (or cysteine) peptidase inhibitors"	8942	protein-coding gene	gene with protein product	"protease inhibitor 10 (ovalbumin type, bomapin)"	602058	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10"	PI10		9268635, 10871600, 24172014	Standard	NM_005024		Approved	bomapin		P48595	OTTHUMG00000060594	ENST00000238508.3:c.384A>G	chr18.hg19:g.61587033A>G		66.0	0.0		75.0	4.0	NM_005024	Q4VAX4|Q4VAX7	Silent	SNP	ENST00000238508.3	hg19	CCDS11990.1																																																																																			.	A|1.000;G|0.000		0.328	SERPINB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134012.3	NM_005024		G	61587033	A	G	61587033	2	3	263	1	0	0	0	0	0	0	0	1	14112	69	3	2		2	SERPINB10	18	61587033	Silent	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	1873907	61587033	16490215	393	38767										
MUM1	84939	hgsc.bcm.edu	37	chr19	1362334	1362334	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gaagacgaggagccaccaagAgtccttttataccacggtaa	10	10	0	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr19:1362334A>G	ENST00000415183.3	+	5	1226	c.1200A>G	c.(1198-1200)agA>agG	p.R400R	MUM1_ENST00000311401.5_Silent_p.R331R|MUM1_ENST00000344663.3_Silent_p.R400R|MUM1_ENST00000591806.1_Silent_p.R400R			Q2TAK8	MUM1_HUMAN	melanoma associated antigen (mutated) 1	399					chromatin organization (GO:0006325)|DNA repair (GO:0006281)	nucleus (GO:0005634)	nucleosome binding (GO:0031491)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AGCCACCAAGAGTCCTTTTAT	0.582																																					p.R400R		Atlas-SNP	.											.	MUM1	54	.	0			c.A1200G						.						58	55	56					19																	1362334		2203	4300	6503	SO:0001819	synonymous_variant	84939	exon6			ACCAAGAGTCCTT	AK075241	CCDS12062.1	19p13.3	2008-02-05				ENSG00000160953			29641	protein-coding gene	gene with protein product						11042152, 7644523	Standard	NM_032853		Approved	MUM-1	uc002lrz.2	Q2TAK8		ENST00000415183.3:c.1200A>G	chr19.hg19:g.1362334A>G		80.0	0.0		95.0	5.0	NM_032853	A1L489|B5ME02|B7ZLY8|J3KQD6|Q13109|Q5XKB9|Q8N2I4|Q96A67	Silent	SNP	ENST00000415183.3	hg19																																																																																				.	.		0.582	MUM1-016	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000449510.1	NM_032853		G	1362334	A	G	1362334	2	3	263	1	0	0	0	0	0	0	0	1	9994	301	11	2		2	MUM1	19	1362334	Silent	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10		1362334	57766649	394	38768										
REXO1	57455	hgsc.bcm.edu	37	chr19	1816497	1816497	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tgtcagcgctgaacatgctcAgcagaacggcctggacgtca	12	12	3	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr19:1816497A>G	ENST00000170168.4	-	14	3483	c.3389T>C	c.(3388-3390)cTg>cCg	p.L1130P	MIR1909_ENST00000411312.1_RNA|CTB-31O20.3_ENST00000586259.1_RNA	NM_020695.3	NP_065746.3	Q8N1G1	REXO1_HUMAN	REX1, RNA exonuclease 1 homolog (S. cerevisiae)	1130	Exonuclease.					nucleus (GO:0005634)	exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	16		Ovarian(11;1.78e-06)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GAACATGCTCAGCAGAACGGC	0.672																																					p.L1130P		Atlas-SNP	.											.	REXO1	55	.	0			c.T3389C						.						56	45	49					19																	1816497		2201	4300	6501	SO:0001583	missense	57455	exon14			ATGCTCAGCAGAA	AB032964	CCDS32866.1	19p13.3	2014-05-28	2005-08-22	2005-08-22	ENSG00000079313	ENSG00000079313			24616	protein-coding gene	gene with protein product	"elongin A binding protein 1"	609614	"transcription elongation factor B polypeptide 3 binding protein 1"	TCEB3BP1		10574461	Standard	NM_020695		Approved	EloA-BP1, KIAA1138	uc002lua.4	Q8N1G1	OTTHUMG00000179991	ENST00000170168.4:c.3389T>C	chr19.hg19:g.1816497A>G	ENSP00000170168:p.Leu1130Pro	71.0	0.0		77.0	4.0	NM_020695	Q9ULT2	Missense_Mutation	SNP	ENST00000170168.4	hg19	CCDS32866.1	.	.	.	.	.	.	.	.	.	.	a	15.00	2.702213	0.48307	.	.	ENSG00000079313	ENST00000170168;ENST00000543452	T	0.22134	1.97	4.01	4.01	0.46588	Exonuclease (1);Exonuclease, RNase T/DNA polymerase III (1);Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.54886	0.1886	M	0.93978	3.48	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.97110	0.995;1.0;1.0	T	0.67205	-0.5729	10	0.72032	D	0.01	-19.0048	12.5244	0.56077	1.0:0.0:0.0:0.0	.	116;439;1130	B4DVD3;B4DWY3;Q8N1G1	.;.;REXO1_HUMAN	P	1130;402	ENSP00000170168:L1130P	ENSP00000170168:L1130P	L	-	2	0	REXO1	1767497	1.000000	0.71417	0.998000	0.56505	0.216000	0.24613	6.600000	0.74132	1.792000	0.52537	0.454000	0.30748	CTG	.	.		0.672	REXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449200.1	NM_020695		G	1816497	A	G	1816497	3	3	263	1	0	0	0	0	1	0	0	0	13256	188	7	2	288	2	REXO1	19	1816497	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	454163	1816497	57312486	395	38769										
FZR1	51343	hgsc.bcm.edu	37	chr19	3530851	3530851	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gacctccgtgggctggtctgAgcgggtgagtgcagagggct	19	9	1	3			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr19:3530851A>G	ENST00000395095.3	+	7	716	c.716A>G	c.(715-717)gAg>gGg	p.E239G	FZR1_ENST00000313639.8_Missense_Mutation_p.E150G|FZR1_ENST00000441788.2_Missense_Mutation_p.E239G	NM_001136198.1	NP_001129670.1	Q9UM11	FZR_HUMAN	fizzy/cell division cycle 20 related 1 (Drosophila)	239					activation of anaphase-promoting complex activity (GO:0051488)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|DNA repair (GO:0006281)|G2 DNA damage checkpoint (GO:0031572)|lens fiber cell differentiation (GO:0070306)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of cell aging (GO:0090344)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of meiosis (GO:0040020)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(1)|kidney(4)|liver(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(2)	13				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00253)|STAD - Stomach adenocarcinoma(1328;0.18)		GGCTGGTCTGAGCGGGTGAGT	0.632																																					p.E239G		Atlas-SNP	.											.	FZR1	42	.	0			c.A716G						.						74	58	63					19																	3530851		2201	4300	6501	SO:0001583	missense	51343	exon7			GGTCTGAGCGGGT	AF083810	CCDS12109.1, CCDS45916.1, CCDS45917.1	19p13.3	2013-01-10				ENSG00000105325		"WD repeat domain containing"	24824	protein-coding gene	gene with protein product		603619				9734353, 11003657	Standard	NM_016263		Approved	HCDH1, CDH1, HCDH, FZR, FZR2, KIAA1242, CDC20C	uc010dtk.2	Q9UM11		ENST00000395095.3:c.716A>G	chr19.hg19:g.3530851A>G	ENSP00000378529:p.Glu239Gly	67.0	0.0		87.0	4.0	NM_001136198	O75869|Q86U66|Q96NW8|Q9UI96|Q9ULH8|Q9UM10|Q9UNQ1|Q9Y2T8	Missense_Mutation	SNP	ENST00000395095.3	hg19	CCDS45916.1	.	.	.	.	.	.	.	.	.	.	A	19.29	3.799849	0.70567	.	.	ENSG00000105325	ENST00000441788;ENST00000395095;ENST00000313639	T;T;T	0.29397	1.57;1.57;5.01	4.75	4.75	0.60458	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.39545	0.1082	L	0.28054	0.825	0.80722	D	1	B;P;D	0.89917	0.004;0.887;1.0	B;P;D	0.91635	0.012;0.528;0.999	T	0.11251	-1.0595	10	0.22706	T	0.39	-42.9006	13.0749	0.59081	1.0:0.0:0.0:0.0	.	239;150;239	Q9UM11;Q9UM11-3;Q9UM11-2	FZR_HUMAN;.;.	G	239;239;150	ENSP00000410369:E239G;ENSP00000378529:E239G;ENSP00000321800:E150G	ENSP00000321800:E150G	E	+	2	0	FZR1	3481851	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	9.015000	0.93640	1.782000	0.52362	0.533000	0.62120	GAG	.	.		0.632	FZR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452869.2	NM_016263		G	3530851	A	G	3530851	3	3	263	1	0	0	0	0	1	0	0	0	6146	304	11	2	742	2	FZR1	19	3530851	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	1714354	3530851	55598132	396	38770										
ANKRD24	170961	hgsc.bcm.edu	37	chr19	4200121	4200121	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gggtgcggccagctgtctggAggtgatgatagctcatggca	17	8	2	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr19:4200121A>G	ENST00000600132.1	+	5	572	c.296A>G	c.(295-297)gAg>gGg	p.E99G	ANKRD24_ENST00000318934.4_Missense_Mutation_p.E99G|ANKRD24_ENST00000262970.5_Missense_Mutation_p.E189G	NM_133475.1	NP_597732.1	Q8TF21	ANR24_HUMAN	ankyrin repeat domain 24	99										endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)	21				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0233)|STAD - Stomach adenocarcinoma(1328;0.181)		AGCTGTCTGGAGGTGATGATA	0.652																																					p.E99G		Atlas-SNP	.											.	ANKRD24	180	.	0			c.A296G						.						26	28	27					19																	4200121		1982	4152	6134	SO:0001583	missense	170961	exon5			GTCTGGAGGTGAT	AB075861	CCDS45925.1	19p13.3	2013-01-10				ENSG00000089847		"Ankyrin repeat domain containing"	29424	protein-coding gene	gene with protein product						11853319	Standard	NM_133475		Approved	KIAA1981	uc010dtt.1	Q8TF21		ENST00000600132.1:c.296A>G	chr19.hg19:g.4200121A>G	ENSP00000471252:p.Glu99Gly	100.0	0.0		114.0	5.0	NM_133475	O75268|O95781	Missense_Mutation	SNP	ENST00000600132.1	hg19	CCDS45925.1	.	.	.	.	.	.	.	.	.	.	A	19.83	3.900249	0.72754	.	.	ENSG00000089847	ENST00000318934;ENST00000262970	T;T	0.68025	-0.3;-0.3	4.17	4.17	0.49024	Ankyrin repeat-containing domain (4);	.	.	.	.	T	0.73450	0.3588	L	0.43757	1.38	0.46185	D	0.998912	D;D	0.89917	1.0;0.971	D;P	0.91635	0.999;0.908	T	0.73994	-0.3807	9	0.52906	T	0.07	-18.7771	10.5727	0.45209	1.0:0.0:0.0:0.0	.	99;189	Q8TF21;Q8TF21-2	ANR24_HUMAN;.	G	99;189	ENSP00000321731:E99G;ENSP00000262970:E189G	ENSP00000262970:E189G	E	+	2	0	ANKRD24	4151121	1.000000	0.71417	1.000000	0.80357	0.806000	0.45545	7.568000	0.82369	1.510000	0.48803	0.260000	0.18958	GAG	.	.		0.652	ANKRD24-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458188.1	XM_114000		G	4200121	A	G	4200121	3	3	263	1	0	0	0	0	1	0	0	0	653	304	11	2	310	2	ANKRD24	19	4200121	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	669270	4200121	54928862	397	38771										
DCAF15	90379	hgsc.bcm.edu	37	chr19	14071164	14071164	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cacagggatcttcgagacagTcagtgtaggcgacctgactg	13	10	2	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr19:14071164T>C	ENST00000254337.6	+	11	1613	c.1592T>C	c.(1591-1593)gTc>gCc	p.V531A		NM_138353.2	NP_612362.2	Q66K64	DCA15_HUMAN	DDB1 and CUL4 associated factor 15	531					protein ubiquitination (GO:0016567)					breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)	11						TTCGAGACAGTCAGTGTAGGC	0.612											OREG0025301	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V531A		Atlas-SNP	.											.	DCAF15	30	.	0			c.T1592C						.						136	118	124					19																	14071164		2203	4300	6503	SO:0001583	missense	90379	exon11			AGACAGTCAGTGT	BC002926	CCDS32926.1	19p13.12	2009-07-17	2009-07-17	2009-07-17	ENSG00000132017	ENSG00000132017		"DDB1 and CUL4 associated factors"	25095	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 72"	C19orf72			Standard	NM_138353		Approved	MGC99481	uc002mxt.3	Q66K64		ENST00000254337.6:c.1592T>C	chr19.hg19:g.14071164T>C	ENSP00000254337:p.Val531Ala	115.0	0.0	692	85.0	4.0	NM_138353	B3KS86|Q96DW0|Q9BU31	Missense_Mutation	SNP	ENST00000254337.6	hg19	CCDS32926.1	.	.	.	.	.	.	.	.	.	.	t	25.6	4.658600	0.88154	.	.	ENSG00000132017	ENST00000254337	.	.	.	4.35	4.35	0.52113	.	0.000000	0.64402	D	0.000006	T	0.46600	0.1401	L	0.32530	0.975	0.53005	D	0.999965	D	0.61697	0.99	P	0.46339	0.513	T	0.53049	-0.8493	9	0.87932	D	0	-26.9513	12.8094	0.57631	0.0:0.0:0.0:1.0	.	531	Q66K64	DCA15_HUMAN	A	531	.	ENSP00000254337:V531A	V	+	2	0	DCAF15	13932164	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.958000	0.76025	1.748000	0.51833	0.459000	0.35465	GTC	.	.		0.612	DCAF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458099.1	NM_138353		C	14071164	T	C	14071164	3	2	263	1	0	0	0	0	1	0	0	0	4269	1667	58	2	1634	2	DCAF15	19	14071164	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	9871043	14071164	45057819	398	38772										
FKBP8	23770	hgsc.bcm.edu	37	chr19	18649200	18649200	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gtccacagccgtcttcagggTcacctccaggcacagggccg	12	16	3	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr19:18649200T>C	ENST00000596558.2	-	5	704	c.595A>G	c.(595-597)Acc>Gcc	p.T199A	FKBP8_ENST00000453489.2_Missense_Mutation_p.T228A|FKBP8_ENST00000222308.4_Missense_Mutation_p.T199A|AC005387.2_ENST00000596596.1_RNA|FKBP8_ENST00000610101.1_Intron|FKBP8_ENST00000608443.1_Missense_Mutation_p.T200A|FKBP8_ENST00000597960.3_Missense_Mutation_p.T200A			Q14318	FKBP8_HUMAN	FK506 binding protein 8, 38kDa	199	PPIase FKBP-type. {ECO:0000255|PROSITE- ProRule:PRU00277}.				apoptotic process (GO:0006915)|camera-type eye development (GO:0043010)|cell fate specification (GO:0001708)|chaperone-mediated protein folding (GO:0061077)|dorsal/ventral neural tube patterning (GO:0021904)|intracellular signal transduction (GO:0035556)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|positive regulation of BMP signaling pathway (GO:0030513)|protein peptidyl-prolyl isomerization (GO:0000413)|regulation of gene expression (GO:0010468)|smoothened signaling pathway (GO:0007224)|viral process (GO:0016032)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)	FK506 binding (GO:0005528)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)	15						GTCTTCAGGGTCACCTCCAGG	0.682																																					p.T200A		Atlas-SNP	.											.	FKBP8	69	.	0			c.A598G						.						22	24	23					19																	18649200		2203	4298	6501	SO:0001583	missense	23770	exon5			TCAGGGTCACCTC	L37033	CCDS32961.1	19p12	2013-01-10	2002-08-29		ENSG00000105701	ENSG00000105701		"Tetratricopeptide (TTC) repeat domain containing"	3724	protein-coding gene	gene with protein product	"FK506-binding protein 8 (38kD)"	604840	"FK506-binding protein 8 (38kD)"			7543869	Standard	NM_012181		Approved	FKBP38, FKBPr38	uc002njj.1	Q14318		ENST00000596558.2:c.595A>G	chr19.hg19:g.18649200T>C	ENSP00000472302:p.Thr199Ala	118.0	0.0		113.0	5.0	NM_012181	C8C9T5|Q53GU3|Q7Z349|Q86YK6	Missense_Mutation	SNP	ENST00000596558.2	hg19		.	.	.	.	.	.	.	.	.	.	T	9.304	1.053800	0.19907	.	.	ENSG00000105701	ENST00000222308;ENST00000453489	T;T	0.55930	0.49;0.49	3.79	1.48	0.22813	Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain (2);	0.376195	0.26631	N	0.023302	T	0.31231	0.0790	N	0.26042	0.785	0.80722	D	1	B;B;B;B	0.31026	0.001;0.008;0.304;0.014	B;B;B;B	0.29785	0.001;0.007;0.107;0.002	T	0.12734	-1.0536	10	0.56958	D	0.05	-42.0738	1.4621	0.02398	0.3049:0.2869:0.0:0.4082	.	228;143;199;200	B7Z6M0;B2R8G6;Q14318;Q14318-2	.;.;FKBP8_HUMAN;.	A	200;228	ENSP00000222308:T200A;ENSP00000388891:T228A	ENSP00000222308:T200A	T	-	1	0	FKBP8	18510200	1.000000	0.71417	0.992000	0.48379	0.598000	0.36846	0.618000	0.24373	0.507000	0.28148	-0.496000	0.04628	ACC	.	.		0.682	FKBP8-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000466374.3	NM_012181		C	18649200	T	C	18649200	3	2	263	1	0	0	0	0	1	0	0	0	5922	1667	58	2	663	2	FKBP8	19	18649200	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	4578036	18649200	40479783	399	38773										
ZNF681	148213	hgsc.bcm.edu	37	chr19	23938330	23938330	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tccagagagaattctatggcCacatccctaaatttcaatgg	7	10	2	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr19:23938330C>A	ENST00000402377.3	-	2	168	c.27G>T	c.(25-27)gtG>gtT	p.V9V	ZNF681_ENST00000395385.3_Intron	NM_138286.2	NP_612143.2	Q96N22	ZN681_HUMAN	zinc finger protein 681	9	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(3)	21		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				ATTCTATGGCCACATCCCTAA	0.418																																					p.V9V		Atlas-SNP	.											.	ZNF681	76	.	0			c.G27T						.						64	70	68					19																	23938330		2203	4300	6503	SO:0001819	synonymous_variant	148213	exon2			TATGGCCACATCC	AK056088	CCDS12414.2	19p12	2013-01-08			ENSG00000196172	ENSG00000196172		"Zinc fingers, C2H2-type", "-"	26457	protein-coding gene	gene with protein product	"hypothetical protein FLJ31526"						Standard	NM_138286		Approved	FLJ31526	uc002nrk.4	Q96N22	OTTHUMG00000150831	ENST00000402377.3:c.27G>T	chr19.hg19:g.23938330C>A		36.0	0.0		36.0	10.0	NM_138286	B3KVF7	Silent	SNP	ENST00000402377.3	hg19	CCDS12414.2																																																																																			.	.		0.418	ZNF681-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320248.2	NM_138286		A	23938330	C	A	23938330	2	1	263	1	0	0	0	0	0	0	0	1	18103	581	21	3		3	ZNF681	19	23938330	Silent	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	5289130	23938330	35190653	400	38774										
MLL4	9757	hgsc.bcm.edu	37	chr19	36229022	36229022	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	catcgacgcgggggagatggTcatcgagtactctggcattg	15	9	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr19:36229022T>C	ENST00000222270.7	+	36	7802	c.7802T>C	c.(7801-7803)gTc>gCc	p.V2601A	IGFLR1_ENST00000587101.1_5'Flank|KMT2B_ENST00000420124.1_Missense_Mutation_p.V2601A|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	2601	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										GGGGAGATGGTCATCGAGTAC	0.597																																					p.V2601A		Atlas-SNP	.											.	MLL4	229	.	0			c.T7802C						.						86	93	90					19																	36229022		2114	4215	6329	SO:0001583	missense	8085	exon36			AGATGGTCATCGA	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"Chromatin-modifying enzymes / K-methyltransferases"	15840	protein-coding gene	gene with protein product	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.7802T>C	chr19.hg19:g.36229022T>C	ENSP00000222270:p.Val2601Ala	68.0	0.0		100.0	6.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Missense_Mutation	SNP	ENST00000222270.7	hg19	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	T	12.32	1.903623	0.33628	.	.	ENSG00000105663	ENST00000222270;ENST00000420124	D;D	0.88201	-2.35;-2.35	4.83	4.83	0.62350	SET domain (3);	0.000000	0.40469	N	0.001091	D	0.96355	0.8811	H	0.97440	4.005	0.58432	D	0.999996	D	0.89917	1.0	D	0.91635	0.999	D	0.97524	1.0075	10	0.87932	D	0	.	13.504	0.61474	0.0:0.0:0.0:1.0	.	2601	Q9UMN6	MLL4_HUMAN	A	2601	ENSP00000222270:V2601A;ENSP00000398837:V2601A	ENSP00000222270:V2601A	V	+	2	0	AD000671.1	40920862	1.000000	0.71417	1.000000	0.80357	0.151000	0.21798	6.112000	0.71547	2.034000	0.60081	0.379000	0.24179	GTC	.	.		0.597	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727		C	36229022	T	C	36229022	3	2	263	1	0	0	0	0	1	0	0	0	9632	1667	58	2	7944	2	MLL4	19	36229022	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	12290692	36229022	22899961	401	38775										
NPHS1	4868	hgsc.bcm.edu	37	chr19	36342181	36342181	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tacccaggatggagaggatcActctgggagacacgagctcg	14	10	2	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr19:36342181A>T	ENST00000378910.5	-	3	379	c.380T>A	c.(379-381)gTg>gAg	p.V127E	NPHS1_ENST00000591817.1_5'Flank|NPHS1_ENST00000353632.6_Missense_Mutation_p.V127E	NM_004646.3	NP_004637.1	O60500	NPHN_HUMAN	nephrosis 1, congenital, Finnish type (nephrin)	127	Ig-like C2-type 1.				cell adhesion (GO:0007155)|excretion (GO:0007588)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell development (GO:0072015)|JNK cascade (GO:0007254)|myoblast fusion (GO:0007520)|positive regulation of actin filament polymerization (GO:0030838)|regulation of excretion (GO:0044062)|skeletal muscle tissue development (GO:0007519)	cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)	myosin binding (GO:0017022)			NS(2)|breast(1)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(1)|lung(26)|ovary(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GGAGAGGATCACTCTGGGAGA	0.637																																					p.V127E		Atlas-SNP	.											.	NPHS1	165	.	0			c.T380A						.						37	40	39					19																	36342181		2203	4300	6503	SO:0001583	missense	4868	exon3			AGGATCACTCTGG		CCDS32996.1	19q12-q13.1	2014-09-17				ENSG00000161270		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7908	protein-coding gene	gene with protein product		602716				9915943, 9660941	Standard	NM_004646		Approved	CNF, NPHN	uc002oby.3	O60500		ENST00000378910.5:c.380T>A	chr19.hg19:g.36342181A>T	ENSP00000368190:p.Val127Glu	82.0	0.0		110.0	26.0	NM_004646	A6NDH2|C3RX61	Missense_Mutation	SNP	ENST00000378910.5	hg19	CCDS32996.1	.	.	.	.	.	.	.	.	.	.	A	15.11	2.734747	0.48939	.	.	ENSG00000161270	ENST00000378910;ENST00000353632	T;T	0.51325	0.71;0.71	5.92	4.9	0.64082	Immunoglobulin subtype (1);Immunoglobulin-like (1);	0.328619	0.27518	N	0.019013	T	0.51873	0.1700	L	0.36672	1.1	0.36219	D	0.851889	D	0.67145	0.996	D	0.63957	0.92	T	0.61618	-0.7026	10	0.72032	D	0.01	-14.0379	6.1768	0.20449	0.7554:0.1642:0.0804:0.0	.	127	O60500	NPHN_HUMAN	E	127	ENSP00000368190:V127E;ENSP00000343634:V127E	ENSP00000343634:V127E	V	-	2	0	NPHS1	41034021	0.997000	0.39634	1.000000	0.80357	0.190000	0.23558	2.197000	0.42696	1.050000	0.40346	0.529000	0.55759	GTG	.	.		0.637	NPHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452553.1			T	36342181	A	T	36342181	3	4	263	1	0	0	0	0	1	0	0	0	10591	159	6	4	3453	4	NPHS1	19	36342181	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	113159	36342181	22786802	402	38776										
C19orf33	64073	hgsc.bcm.edu	37	chr19	38795554	38795554	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	agaagcccaaagtgaagaagAaggagaagggcaagaaggag	16	4	0	6	rs79297344|rs369605535|rs201239475	byFrequency	TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr19:38795554A>G	ENST00000301246.5	+	4	372	c.271A>G	c.(271-273)Aag>Gag	p.K91E	C19orf33_ENST00000588605.1_3'UTR	NM_033520.1	NP_277055.1	Q9GZP8	IMUP_HUMAN	chromosome 19 open reading frame 33	91						nucleus (GO:0005634)						all_cancers(60;1.07e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			AGTgaagaagaaggagaaggg	0.597																																					p.K91E		Atlas-SNP	.											.	C19orf33	9	.	0			c.A271G						.						89	91	90					19																	38795554		2203	4300	6503	SO:0001583	missense	64073	exon4			AAGAAGAAGGAGA	AF213678	CCDS12511.1	19q13.2	2012-10-26			ENSG00000167644	ENSG00000167644			16668	protein-coding gene	gene with protein product	"immortalization-upregulated protein", "HAI-2 related small protein", "hepatocyte growth factor activator inhibitor type 2-related small protein"					11080599	Standard	NM_033520		Approved	IMUP-1, IMUP-2, H2RSP, IMUP	uc002ohu.1	Q9GZP8	OTTHUMG00000181894	ENST00000301246.5:c.271A>G	chr19.hg19:g.38795554A>G	ENSP00000301246:p.Lys91Glu	226.0	0.0		310.0	14.0	NM_033520	Q0P6G2|Q96H58|Q9HCR4	Missense_Mutation	SNP	ENST00000301246.5	hg19	CCDS12511.1	.	.	.	.	.	.	.	.	.	.	A	13.22	2.172420	0.38315	.	.	ENSG00000167644	ENST00000301246	.	.	.	4.25	-6.0	0.02206	.	.	.	.	.	T	0.14013	0.0339	N	0.03608	-0.345	0.09310	N	0.999997	B	0.14012	0.009	B	0.09377	0.004	T	0.30650	-0.9971	8	0.87932	D	0	-21.5778	7.463	0.27306	0.3041:0.1311:0.5648:0.0	.	91	Q9GZP8	IMUP_HUMAN	E	91	.	ENSP00000301246:K91E	K	+	1	0	C19orf33	43487394	0.991000	0.36638	0.001000	0.08648	0.349000	0.29174	2.688000	0.46984	-1.165000	0.02786	0.454000	0.30748	AAG	.	.		0.597	C19orf33-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458168.1	NM_033520		G	38795554	A	G	38795554	3	3	263	1	0	0	0	0	1	0	0	0	1921	247	9	2	285	2	C19orf33	19	38795554	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	2453373	38795554	20333429	403	38777										
KCNK6	9424	hgsc.bcm.edu	37	chr19	38817935	38817935	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ccccctccgtgccctgccagTttcaatgcggatgaggacga	11	15	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr19:38817935T>C	ENST00000263372.3	+	3	941	c.834T>C	c.(832-834)agT>agC	p.S278S		NM_004823.1	NP_004814.1	Q9Y257	KCNK6_HUMAN	potassium channel, subfamily K, member 6	278					negative regulation of systemic arterial blood pressure (GO:0003085)|potassium ion transport (GO:0006813)|regulation of resting membrane potential (GO:0060075)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(3)	17	all_cancers(60;5.83e-07)		Lung(45;0.00047)|LUSC - Lung squamous cell carcinoma(53;0.000613)		Ibutilide(DB00308)|Quinidine(DB00908)	GCCCTGCCAGTTTCAATGCGG	0.662																																					p.S278S		Atlas-SNP	.											.	KCNK6	37	.	0			c.T834C						.						67	62	64					19																	38817935		2203	4300	6503	SO:0001819	synonymous_variant	9424	exon3			TGCCAGTTTCAAT	AF117708	CCDS12513.1	19q13.1	2012-03-07				ENSG00000099337		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6281	protein-coding gene	gene with protein product		603939				10075682, 10393428, 16382106	Standard	NM_004823		Approved	K2p6.1, TWIK-2	uc002oic.3	Q9Y257		ENST00000263372.3:c.834T>C	chr19.hg19:g.38817935T>C		94.0	0.0		114.0	6.0	NM_004823	Q9HB47	Silent	SNP	ENST00000263372.3	hg19	CCDS12513.1																																																																																			.	.		0.662	KCNK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460524.1	NM_004823		C	38817935	T	C	38817935	2	2	263	1	0	0	0	0	0	0	0	1	8079	1722	60	2		2	KCNK6	19	38817935	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	22381	38817935	20311048	404	38778										
RYR1	6261	hgsc.bcm.edu	37	chr19	38939069	38939069	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	taccgggcagtacctagcgcTcaccgaggaccagggcctgg	14	14	1	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr19:38939069T>C	ENST00000359596.3	+	10	875	c.875T>C	c.(874-876)cTc>cCc	p.L292P	RYR1_ENST00000355481.4_Missense_Mutation_p.L292P|RYR1_ENST00000360985.3_Missense_Mutation_p.L292P			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	292	MIR 4. {ECO:0000255|PROSITE- ProRule:PRU00131}.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	TACCTAGCGCTCACCGAGGAC	0.647																																					p.L292P		Atlas-SNP	.											.	RYR1	708	.	0			c.T875C						.						114	109	111					19																	38939069		2203	4300	6503	SO:0001583	missense	6261	exon10			TAGCGCTCACCGA	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.875T>C	chr19.hg19:g.38939069T>C	ENSP00000352608:p.Leu292Pro	68.0	0.0		82.0	4.0	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	T	6.625	0.483843	0.12581	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.87334	-2.24;-2.24;-2.24	4.43	4.43	0.53597	MIR motif (2);MIR (2);	0.112548	0.36665	U	0.002462	D	0.91774	0.7398	M	0.73962	2.25	0.58432	D	0.999993	D;D	0.89917	0.999;1.0	D;D	0.81914	0.952;0.995	D	0.92029	0.5632	10	0.87932	D	0	.	9.1714	0.37083	0.0:0.0:0.1836:0.8164	.	292;292	P21817-2;P21817	.;RYR1_HUMAN	P	292	ENSP00000352608:L292P;ENSP00000347667:L292P;ENSP00000354254:L292P	ENSP00000347667:L292P	L	+	2	0	RYR1	43630909	1.000000	0.71417	0.978000	0.43139	0.268000	0.26511	5.596000	0.67570	1.867000	0.54127	0.402000	0.26972	CTC	.	.		0.647	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			C	38939069	T	C	38939069	3	2	263	1	0	0	0	0	1	0	0	0	13783	1551	54	2	913	2	RYR1	19	38939069	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	121134	38939069	20189914	405	38779										
SPTBN4	57731	hgsc.bcm.edu	37	chr19	41029483	41029483	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cgtgcaggctgcagagggccTgctgaggcagggcaacatct	16	11	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr19:41029483T>C	ENST00000352632.3	+	17	3880	c.3794T>C	c.(3793-3795)cTg>cCg	p.L1265P	SPTBN4_ENST00000595535.1_Missense_Mutation_p.L1265P|SPTBN4_ENST00000392025.1_5'Flank|SPTBN4_ENST00000598249.1_Missense_Mutation_p.L1265P|SPTBN4_ENST00000338932.3_Missense_Mutation_p.L1265P|SPTBN4_ENST00000344104.3_Missense_Mutation_p.L1265P			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	1265					actin filament capping (GO:0051693)|adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cardiac conduction (GO:0061337)|central nervous system projection neuron axonogenesis (GO:0021952)|clustering of voltage-gated sodium channels (GO:0045162)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization to plasma membrane (GO:0090002)|fertilization (GO:0009566)|negative regulation of heart rate (GO:0010459)|positive regulation of multicellular organism growth (GO:0040018)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of sodium ion transport (GO:0002028)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|axon hillock (GO:0043203)|axon initial segment (GO:0043194)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|nuclear matrix (GO:0016363)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|PML body (GO:0016605)|spectrin (GO:0008091)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phosphatase binding (GO:0019902)|phospholipid binding (GO:0005543)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			breast(4)|central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	73			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GCAGAGGGCCTGCTGAGGCAG	0.632																																					p.L1265P		Atlas-SNP	.											.	SPTBN4	213	.	0			c.T3794C						.						59	50	53					19																	41029483		2203	4300	6503	SO:0001583	missense	57731	exon17			AGGGCCTGCTGAG	AF082075	CCDS12559.1, CCDS42569.1	19q13.13	2013-01-10				ENSG00000160460		"Pleckstrin homology (PH) domain containing"	14896	protein-coding gene	gene with protein product		606214				11086001	Standard	NM_020971		Approved	SPTBN3, KIAA1642	uc002onz.3	Q9H254		ENST00000352632.3:c.3794T>C	chr19.hg19:g.41029483T>C	ENSP00000263373:p.Leu1265Pro	62.0	0.0		86.0	5.0	NM_020971	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Missense_Mutation	SNP	ENST00000352632.3	hg19	CCDS12559.1	.	.	.	.	.	.	.	.	.	.	t	17.41	3.382082	0.61845	.	.	ENSG00000160460	ENST00000428507;ENST00000352632;ENST00000338932;ENST00000344104	T;T;T	0.55413	0.53;0.52;0.52	4.31	4.31	0.51392	.	0.000000	0.48286	U	0.000182	T	0.65984	0.2744	M	0.65677	2.01	0.80722	D	1	D;D	0.61080	0.989;0.957	P;P	0.61003	0.726;0.882	T	0.70317	-0.4905	10	0.72032	D	0.01	.	12.6154	0.56573	0.0:0.0:0.0:1.0	.	1265;1265	Q9H254;Q71S06	SPTN4_HUMAN;.	P	1265	ENSP00000263373:L1265P;ENSP00000340345:L1265P;ENSP00000340741:L1265P	ENSP00000340345:L1265P	L	+	2	0	SPTBN4	45721323	1.000000	0.71417	1.000000	0.80357	0.411000	0.31082	7.684000	0.84104	1.819000	0.53055	0.139000	0.15985	CTG	.	.		0.632	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2			C	41029483	T	C	41029483	3	2	263	1	0	0	0	0	1	0	0	0	15136	1580	55	2	3856	2	SPTBN4	19	41029483	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	2090414	41029483	18099500	406	38780										
SPTBN4	57731	hgsc.bcm.edu	37	chr19	41066144	41066144	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cgaggccatcgctagccgggAgcaggaggtgctgcagggtt	18	10	0	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr19:41066144A>G	ENST00000352632.3	+	27	5836	c.5750A>G	c.(5749-5751)gAg>gGg	p.E1917G	SPTBN4_ENST00000595535.1_Missense_Mutation_p.E1917G|SPTBN4_ENST00000392025.1_Missense_Mutation_p.E660G|SPTBN4_ENST00000598249.1_Missense_Mutation_p.E1917G|SPTBN4_ENST00000338932.3_Missense_Mutation_p.E1917G|SPTBN4_ENST00000392023.1_Missense_Mutation_p.E593G			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	1917					actin filament capping (GO:0051693)|adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cardiac conduction (GO:0061337)|central nervous system projection neuron axonogenesis (GO:0021952)|clustering of voltage-gated sodium channels (GO:0045162)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization to plasma membrane (GO:0090002)|fertilization (GO:0009566)|negative regulation of heart rate (GO:0010459)|positive regulation of multicellular organism growth (GO:0040018)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of sodium ion transport (GO:0002028)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|axon hillock (GO:0043203)|axon initial segment (GO:0043194)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|nuclear matrix (GO:0016363)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|PML body (GO:0016605)|spectrin (GO:0008091)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phosphatase binding (GO:0019902)|phospholipid binding (GO:0005543)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			breast(4)|central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	73			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GCTAGCCGGGAGCAGGAGGTG	0.667																																					p.E1917G		Atlas-SNP	.											.	SPTBN4	213	.	0			c.A5750G						.						75	63	67					19																	41066144		2203	4300	6503	SO:0001583	missense	57731	exon27			GCCGGGAGCAGGA	AF082075	CCDS12559.1, CCDS42569.1	19q13.13	2013-01-10				ENSG00000160460		"Pleckstrin homology (PH) domain containing"	14896	protein-coding gene	gene with protein product		606214				11086001	Standard	NM_020971		Approved	SPTBN3, KIAA1642	uc002onz.3	Q9H254		ENST00000352632.3:c.5750A>G	chr19.hg19:g.41066144A>G	ENSP00000263373:p.Glu1917Gly	145.0	0.0		156.0	7.0	NM_020971	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Missense_Mutation	SNP	ENST00000352632.3	hg19	CCDS12559.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.694104	0.88735	.	.	ENSG00000160460	ENST00000428507;ENST00000352632;ENST00000338932;ENST00000392025;ENST00000392023	T;T;T;T	0.50277	0.75;0.75;0.75;0.75	4.66	4.66	0.58398	.	0.000000	0.64402	U	0.000008	T	0.69504	0.3118	M	0.83223	2.63	0.48236	D	0.999613	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.997;0.998;0.993	T	0.73531	-0.3953	10	0.52906	T	0.07	.	13.2011	0.59769	1.0:0.0:0.0:0.0	.	660;593;1917;1917	C9JY79;E9PGQ5;Q9H254;Q71S06	.;.;SPTN4_HUMAN;.	G	1917;1917;1917;660;593	ENSP00000263373:E1917G;ENSP00000340345:E1917G;ENSP00000375879:E660G;ENSP00000375877:E593G	ENSP00000340345:E1917G	E	+	2	0	SPTBN4	45757984	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	8.981000	0.93465	1.962000	0.57031	0.482000	0.46254	GAG	.	.		0.667	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2			G	41066144	A	G	41066144	3	3	263	1	0	0	0	0	1	0	0	0	15136	304	11	2	5852	2	SPTBN4	19	41066144	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	36661	41066144	18062839	407	38781										
HNRNPUL1	11100	hgsc.bcm.edu	37	chr19	41800283	41800283	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gcctgctgctggcaagaccaCatgggccatcaaacatgcag	11	13	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr19:41800283C>A	ENST00000392006.3	+	9	1480	c.1307C>A	c.(1306-1308)aCa>aAa	p.T436K	HNRNPUL1_ENST00000602130.1_Missense_Mutation_p.T436K|HNRNPUL1_ENST00000263367.3_Missense_Mutation_p.T347K|HNRNPUL1_ENST00000595018.1_Missense_Mutation_p.T336K|HNRNPUL1_ENST00000378215.4_Missense_Mutation_p.T322K|HNRNPUL1_ENST00000352456.3_Missense_Mutation_p.T336K|HNRNPUL1_ENST00000593587.1_Missense_Mutation_p.T336K	NM_007040.3	NP_008971.2	Q9BUJ2	HNRL1_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 1	436	Necessary for interaction with TP53.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	29						GGCAAGACCACATGGGCCATC	0.542																																					p.T436K		Atlas-SNP	.											.	HNRNPUL1	73	.	0			c.C1307A						.						176	128	144					19																	41800283		2203	4300	6503	SO:0001583	missense	11100	exon9			AGACCACATGGGC	AJ007509	CCDS12576.1, CCDS12577.1	19q13.2	2013-06-12		2008-04-18	ENSG00000105323	ENSG00000105323			17011	protein-coding gene	gene with protein product	"E1B 55kDa associated protein 5"	605800		HNRPUL1		9733834, 12489984	Standard	XM_005258459		Approved	E1B-AP5, E1BAP5, FLJ12944	uc002oqb.4	Q9BUJ2	OTTHUMG00000182740	ENST00000392006.3:c.1307C>A	chr19.hg19:g.41800283C>A	ENSP00000375863:p.Thr436Lys	190.0	0.0		235.0	82.0	NM_007040	B3KMW7|O76022|Q6ZSZ0|Q7L8P4|Q8N6Z4|Q96G37|Q9HAL3|Q9UG75	Missense_Mutation	SNP	ENST00000392006.3	hg19	CCDS12576.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.505392	0.85282	.	.	ENSG00000105323	ENST00000352456;ENST00000392006;ENST00000378215;ENST00000263367	T;T;T;T	0.58797	0.31;0.31;0.31;0.31	5.46	3.35	0.38373	.	0.050683	0.85682	D	0.000000	T	0.75384	0.3842	M	0.85462	2.755	0.48975	D	0.999737	D;D;D;P;D;D	0.63046	0.985;0.969;0.968;0.934;0.992;0.981	D;D;P;P;D;P	0.70935	0.944;0.944;0.66;0.517;0.971;0.835	T	0.77736	-0.2476	10	0.62326	D	0.03	-11.1853	11.2933	0.49263	0.0:0.8505:0.0:0.1495	.	347;336;436;322;436;336	B7Z4B8;A8K3W4;Q9BUJ2-2;Q9BUJ2-3;Q9BUJ2;Q9BUJ2-4	.;.;.;.;HNRL1_HUMAN;.	K	336;436;322;347	ENSP00000340857:T336K;ENSP00000375863:T436K;ENSP00000367460:T322K;ENSP00000263367:T347K	ENSP00000263367:T347K	T	+	2	0	HNRNPUL1	46492123	1.000000	0.71417	0.727000	0.30756	0.994000	0.84299	5.833000	0.69349	0.872000	0.35775	0.655000	0.94253	ACA	.	.		0.542	HNRNPUL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463406.1	NM_144732, NM_007040		A	41800283	C	A	41800283	3	1	263	1	0	0	0	0	1	0	0	0	7283	478	17	3	1341	3	HNRNPUL1	19	41800283	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	734139	41800283	17328700	408	38782										
CIC	23152	hgsc.bcm.edu	37	chr19	42798458	42798458	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ttcacctttgaccgtacaggTgccgtggtgggcagaacttt	12	10	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr19:42798458T>C	ENST00000575354.2	+	18	4367		c.e18+2		CIC_ENST00000572681.2_Splice_Site|CIC_ENST00000160740.3_Splice_Site	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				ACCGTACAGGTGCCGTGGTGG	0.612			"Mis, F, S"		oligodendroglioma																																.		Atlas-SNP	.		Rec	yes		19	19q13.2	23152	capicua homolog		O	.	CIC	249	.	0			c.4327+2T>C						.						57	60	59					19																	42798458		2203	4300	6503	SO:0001630	splice_region_variant	23152	exon18			TACAGGTGCCGTG	AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"capicua (Drosophila) homolog", "capicua homolog (Drosophila)"			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.4327+2T>C	chr19.hg19:g.42798458T>C		71.0	0.0		69.0	4.0	NM_015125	Q7LGI1|Q9UEG5|Q9Y6T1	Splice_Site	SNP	ENST00000575354.2	hg19	CCDS12601.1	.	.	.	.	.	.	.	.	.	.	T	9.724	1.160352	0.21454	.	.	ENSG00000079432	ENST00000160740	.	.	.	4.19	3.18	0.36537	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.0498	0.30570	0.0:0.099:0.0:0.901	.	.	.	.	.	-1	.	.	.	+	.	.	CIC	47490298	1.000000	0.71417	0.123000	0.21794	0.692000	0.40212	6.651000	0.74372	0.968000	0.38212	0.482000	0.46254	.	.	.		0.612	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2		Intron	C	42798458	T	C	42798458	5	2	263	1	0	0	0	0	0	0	1	0	3426	1710	59	2	4399	2	CIC	19	42798458	Splice_Site	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	998175	42798458	16330525	409	38783										
MEGF8	1954	hgsc.bcm.edu	37	chr19	42855634	42855634	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tagccagtgcgcctggtgccAgtccacccacacctgcttcc	9	18	0	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr19:42855634A>G	ENST00000251268.6	+	17	2909	c.2909A>G	c.(2908-2910)cAg>cGg	p.Q970R	MEGF8_ENST00000334370.4_Missense_Mutation_p.Q903R	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	970					BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)			breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				GCCTGGTGCCAGTCCACCCAC	0.662																																					p.Q970R		Atlas-SNP	.											.	MEGF8	358	.	0			c.A2909G						.						53	40	44					19																	42855634		2203	4299	6502	SO:0001583	missense	1954	exon17			GGTGCCAGTCCAC	AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"HBV pre s2 binding protein 1"	604267	"EGF-like-domain, multiple 4", "chromosome 19 open reading frame 49"	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.2909A>G	chr19.hg19:g.42855634A>G	ENSP00000251268:p.Gln970Arg	76.0	0.0		81.0	4.0	NM_001271938	A8KAY0|O75097	Missense_Mutation	SNP	ENST00000251268.6	hg19		.	.	.	.	.	.	.	.	.	.	A	17.93	3.508461	0.64410	.	.	ENSG00000105429	ENST00000334370;ENST00000251268	T;T	0.21734	1.99;1.99	5.26	5.26	0.73747	.	0.075489	0.53938	D	0.000047	T	0.25680	0.0625	L	0.55990	1.75	0.80722	D	1	B;P	0.46512	0.329;0.879	B;P	0.45167	0.065;0.472	T	0.01706	-1.1291	10	0.35671	T	0.21	-18.4302	13.15	0.59484	1.0:0.0:0.0:0.0	.	970;903	Q7Z7M0;Q7Z7M0-2	MEGF8_HUMAN;.	R	903;970	ENSP00000334219:Q903R;ENSP00000251268:Q970R	ENSP00000251268:Q970R	Q	+	2	0	MEGF8	47547474	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.187000	0.72039	1.996000	0.58369	0.533000	0.62120	CAG	.	.		0.662	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410		G	42855634	A	G	42855634	3	3	263	1	0	0	0	0	1	0	0	0	9472	188	7	2	2770	2	MEGF8	19	42855634	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	57176	42855634	16273349	410	38784										
CADM4	199731	hgsc.bcm.edu	37	chr19	44127546	44127546	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tgaggaaggcttctcttgctTctccctgttcatccaagcca	8	13	3	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr19:44127546T>C	ENST00000222374.2	-	9	1151	c.1103A>G	c.(1102-1104)gAa>gGa	p.E368G	CADM4_ENST00000593506.1_5'Flank	NM_145296.1	NP_660339.1	Q8NFZ8	CADM4_HUMAN	cell adhesion molecule 4	368					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(3)|lung(4)|prostate(1)|skin(2)	12		Prostate(69;0.0199)				TTCTCTTGCTTCTCCCTGTTC	0.587																																					p.E368G		Atlas-SNP	.											.	CADM4	26	.	0			c.A1103G						.						150	148	149					19																	44127546		2203	4300	6503	SO:0001583	missense	199731	exon9			CTTGCTTCTCCCT	AF363368	CCDS12627.1	19q13.32	2013-01-29	2007-02-07	2007-02-07		ENSG00000105767		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	30825	protein-coding gene	gene with protein product	"nectin-like 4"	609744	"immunoglobulin superfamily, member 4C"	IGSF4C		11536053	Standard	NM_145296		Approved	TSLL2, Necl-4, SynCAM4	uc002oxc.1	Q8NFZ8		ENST00000222374.2:c.1103A>G	chr19.hg19:g.44127546T>C	ENSP00000222374:p.Glu368Gly	91.0	0.0		126.0	9.0	NM_145296	B2R7L5|Q9Y4A4	Missense_Mutation	SNP	ENST00000222374.2	hg19	CCDS12627.1	.	.	.	.	.	.	.	.	.	.	T	19.56	3.851232	0.71719	.	.	ENSG00000105767	ENST00000222374	T	0.62498	0.02	4.56	4.56	0.56223	.	0.000000	0.85682	D	0.000000	T	0.68842	0.3045	L	0.36672	1.1	0.46901	D	0.999245	D	0.71674	0.998	D	0.70227	0.968	T	0.71948	-0.4438	10	0.72032	D	0.01	.	12.2052	0.54348	0.0:0.0:0.0:1.0	.	368	Q8NFZ8	CADM4_HUMAN	G	368	ENSP00000222374:E368G	ENSP00000222374:E368G	E	-	2	0	CADM4	48819386	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.513000	0.73742	1.842000	0.53543	0.378000	0.23410	GAA	.	.		0.587	CADM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463352.1	NM_145296		C	44127546	T	C	44127546	3	2	263	1	0	0	0	0	1	0	0	0	2571	1783	62	2	67	2	CADM4	19	44127546	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	1271912	44127546	15001437	411	38785										
CEACAM20	125931	hgsc.bcm.edu	37	chr19	45026890	45026890	+	RNA	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cctccatcacctcaaccaccTccccactggcaacaccagac	3	22	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr19:45026890T>C	ENST00000454753.1	-	0	802							Q6UY09	CEA20_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 20							integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)	15		Prostate(69;0.0352)				CTCAACCACCTCCCCACTGGC	0.498																																					p.E175G		Atlas-SNP	.											.	CEACAM20	31	.	0			c.A524G						.						77	84	81					19																	45026890		2113	4235	6348			125931	exon4			ACCACCTCCCCAC	AY358129	CCDS74390.1, CCDS74391.1, CCDS74392.1, CCDS74393.1	19q13.31	2013-01-30			ENSG00000176395	ENSG00000273777		"Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Immunoglobulin superfamily / I-set domain containing"	24879	protein-coding gene	gene with protein product						12975309	Standard	NM_001102600		Approved	UNQ9366	uc010ejo.1	Q6UY09	OTTHUMG00000151532		chr19.hg19:g.45026890T>C		90.0	0.0		121.0	6.0	NM_001102600		Missense_Mutation	SNP	ENST00000454753.1	hg19																																																																																				.	.		0.498	CEACAM20-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000323032.1	NM_198444		C	45026890	T	C	45026890	1	2	263	0	1	0	0	0	0	0	0	0	3193	1551	54	2		2	CEACAM20	19	45026890	RNA	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	899344	45026890	14102093	412	38786										
SLC1A5	6510	hgsc.bcm.edu	37	chr19	47280496	47280496	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gatgatctttacgaagtccaAggactgctggctgagctgtg	13	8	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr19:47280496A>G	ENST00000542575.2	-	6	1853	c.1225T>C	c.(1225-1227)Ttg>Ctg	p.L409L	SLC1A5_ENST00000412532.2_Silent_p.L181L|SLC1A5_ENST00000594991.1_Silent_p.L233L|SLC1A5_ENST00000434726.2_Silent_p.L207L	NM_005628.2	NP_005619.1	Q15758	AAAT_HUMAN	solute carrier family 1 (neutral amino acid transporter), member 5	409					amino acid transport (GO:0006865)|extracellular amino acid transport (GO:0006860)|glutamine transport (GO:0006868)|ion transport (GO:0006811)|neutral amino acid transport (GO:0015804)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-glutamine transmembrane transporter activity (GO:0015186)|L-serine transmembrane transporter activity (GO:0015194)|neutral amino acid transmembrane transporter activity (GO:0015175)|receptor activity (GO:0004872)|sodium:dicarboxylate symporter activity (GO:0017153)|virus receptor activity (GO:0001618)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(2)|stomach(1)	13		all_epithelial(76;0.00314)|Ovarian(192;0.0798)|all_neural(266;0.107)		OV - Ovarian serous cystadenocarcinoma(262;0.000338)|all cancers(93;0.000882)|Epithelial(262;0.0211)|GBM - Glioblastoma multiforme(486;0.0341)	L-Asparagine(DB00174)|L-Glutamine(DB00130)	ACGAAGTCCAAGGACTGCTGG	0.612																																					p.L409L		Atlas-SNP	.											.	SLC1A5	31	.	0			c.T1225C						.						66	60	62					19																	47280496		2203	4300	6503	SO:0001819	synonymous_variant	6510	exon6			AGTCCAAGGACTG	U53347	CCDS12692.1, CCDS46125.1, CCDS46126.1	19q13.32	2013-07-15			ENSG00000105281	ENSG00000105281		"Solute carriers"	10943	protein-coding gene	gene with protein product		109190		RDRC, M7V1		8702519, 10051606	Standard	NM_005628		Approved	AAAT, ASCT2	uc002pfs.3	Q15758	OTTHUMG00000183434	ENST00000542575.2:c.1225T>C	chr19.hg19:g.47280496A>G		49.0	0.0		82.0	5.0	NM_005628	A8K9H5|B4DR77|B4DWS4|B7ZB81|D0EYG6|E9PC01|O95720|Q96RL9|Q9BWQ3|Q9UNP2	Silent	SNP	ENST00000542575.2	hg19	CCDS12692.1																																																																																			.	.		0.612	SLC1A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466630.1			G	47280496	A	G	47280496	2	3	263	1	0	0	0	0	0	0	0	1	14450	69	3	2		2	SLC1A5	19	47280496	Silent	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	2253606	47280496	11848487	413	38787										
PLA2G4C	8605	hgsc.bcm.edu	37	chr19	48565265	48565265	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tctcgattacctcgaaaggaTctccggcactgaagtcgaag	10	11	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr19:48565265T>C	ENST00000599921.1	-	14	1604	c.1247A>G	c.(1246-1248)gAt>gGt	p.D416G	CTD-2265M8.2_ENST00000601548.1_RNA|PLA2G4C_ENST00000596510.1_5'UTR|PLA2G4C_ENST00000354276.3_Missense_Mutation_p.D416G|PLA2G4C_ENST00000599111.1_Missense_Mutation_p.D426G|CTD-2265M8.2_ENST00000596552.1_RNA|CTD-2265M8.2_ENST00000601950.1_RNA|PLA2G4C_ENST00000413144.2_Missense_Mutation_p.D416G			Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC (cytosolic, calcium-independent)	416	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid metabolic process (GO:0019369)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|parturition (GO:0007567)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(12)|lung(13)|ovary(2)|prostate(1)|skin(3)	38		all_cancers(25;2.84e-05)|all_lung(116;4.62e-05)|Lung NSC(112;7.61e-05)|all_epithelial(76;0.000192)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;8.09e-05)|all cancers(93;0.000517)|Epithelial(262;0.0135)|GBM - Glioblastoma multiforme(486;0.0717)		CTCGAAAGGATCTCCGGCACT	0.627																																					p.D426G		Atlas-SNP	.											.	PLA2G4C	76	.	0			c.A1277G						.						90	88	89					19																	48565265		2203	4300	6503	SO:0001583	missense	8605	exon14			AAAGGATCTCCGG	AF065214	CCDS12710.1, CCDS54286.1, CCDS59403.1	19q13.3	2008-09-19					3.1.1.4		9037	protein-coding gene	gene with protein product		603602				9705332	Standard	NM_003706		Approved	cPLA2-gamma	uc002phx.3	Q9UP65		ENST00000599921.1:c.1247A>G	chr19.hg19:g.48565265T>C	ENSP00000469473:p.Asp416Gly	45.0	0.0		59.0	26.0	NM_001159322	B2RB71|B4DI40|O75457|Q6IBI8|Q9UG68	Missense_Mutation	SNP	ENST00000599921.1	hg19	CCDS12710.1	.	.	.	.	.	.	.	.	.	.	T	13.56	2.274278	0.40194	.	.	ENSG00000105499	ENST00000354276;ENST00000413144	T;T	0.11063	2.81;2.81	2.79	2.79	0.32731	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (2);	0.174869	0.36482	U	0.002575	T	0.08358	0.0208	L	0.31664	0.95	0.27953	N	0.93709	P;P	0.45428	0.858;0.835	B;B	0.43867	0.434;0.363	T	0.16394	-1.0404	10	0.27082	T	0.32	-5.1386	7.4822	0.27411	0.0:0.0:0.0:1.0	.	426;416	B4DI40;Q9UP65	.;PA24C_HUMAN	G	416	ENSP00000346228:D416G;ENSP00000400036:D416G	ENSP00000346228:D416G	D	-	2	0	PLA2G4C	53257077	1.000000	0.71417	0.386000	0.26170	0.550000	0.35303	3.354000	0.52254	1.045000	0.40225	0.333000	0.21579	GAT	.	.		0.627	PLA2G4C-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465551.1			C	48565265	T	C	48565265	3	2	263	1	0	0	0	0	1	0	0	0	12012	1435	50	2	398	2	PLA2G4C	19	48565265	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	1284769	48565265	10563718	414	38788										
HRC	3270	hgsc.bcm.edu	37	chr19	49657886	49657886	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ccatactcagtggaggcctcCtcttcctcctcctcctcctc	5	20	2	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr19:49657886C>T	ENST00000252825.4	-	1	795	c.609G>A	c.(607-609)gaG>gaA	p.E203E	HRC_ENST00000595625.1_Silent_p.E203E	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	203	4 X tandem repeats, acidic.|6 X approximate tandem repeats.|Glu-rich (acidic).				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		TGGAGGcctcctcttcctcct	0.572																																					p.E203E	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											.	HRC	85	.	0			c.G609A						.						123	91	102					19																	49657886		2203	4300	6503	SO:0001819	synonymous_variant	3270	exon1			GGCCTCCTCTTCC		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"histidine-rich calcium-binding protein"			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.609G>A	chr19.hg19:g.49657886C>T		137.0	0.0		158.0	10.0	NM_002152	Q504Y6	Silent	SNP	ENST00000252825.4	hg19	CCDS12759.1																																																																																			.	.		0.572	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152		T	49657886	C	T	49657886	2	4	263	1	0	0	0	0	0	0	0	1	7361	680	24	3		3	HRC	19	49657886	Silent	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	1092621	49657886	9471097	415	38789										
HRC	3270	hgsc.bcm.edu	37	chr19	49657916	49657916	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tcctcctcctcctcctcctcTtctccttcatcatcttcccc	0	23	5	0	rs7409255		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr19:49657916T>C	ENST00000252825.4	-	1	765	c.579A>G	c.(577-579)gaA>gaG	p.E193E	HRC_ENST00000595625.1_Silent_p.E193E	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	193	4 X tandem repeats, acidic.|6 X approximate tandem repeats.|Glu-rich (acidic).				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		cctcctcctcttcTCCTTCAT	0.557																																					p.E193E	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											.	HRC	85	.	0			c.A579G						.						119	95	103					19																	49657916		2203	4300	6503	SO:0001819	synonymous_variant	3270	exon1			CTCCTCTTCTCCT		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"histidine-rich calcium-binding protein"			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.579A>G	chr19.hg19:g.49657916T>C		129.0	0.0		173.0	16.0	NM_002152	Q504Y6	Silent	SNP	ENST00000252825.4	hg19	CCDS12759.1																																																																																			.	.		0.557	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152		C	49657916	T	C	49657916	2	2	263	1	0	0	0	0	0	0	0	1	7361	1606	56	2		2	HRC	19	49657916	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	30	49657916	9471067	416	38790										
BRSK1	84446	hgsc.bcm.edu	37	chr19	55815939	55815939	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	agtccggtcttttccttttcAccggagccgggggctggaga	14	11	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr19:55815939A>G	ENST00000309383.1	+	14	1645	c.1368A>G	c.(1366-1368)tcA>tcG	p.S456S	BRSK1_ENST00000590333.1_Silent_p.S472S|BRSK1_ENST00000326848.7_Silent_p.S151S|BRSK1_ENST00000588584.1_3'UTR	NM_032430.1	NP_115806.1	Q8TDC3	BRSK1_HUMAN	BR serine/threonine kinase 1	456					axonogenesis (GO:0007409)|cellular response to DNA damage stimulus (GO:0006974)|centrosome duplication (GO:0051298)|establishment of cell polarity (GO:0030010)|G2 DNA damage checkpoint (GO:0031572)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|protein phosphorylation (GO:0006468)|response to UV (GO:0009411)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|gamma-tubulin binding (GO:0043015)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(15)|ovary(2)|prostate(2)|skin(6)|stomach(1)	48		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0474)		TTTCCTTTTCACCGGAGCCGG	0.652																																					p.S456S		Atlas-SNP	.											.	BRSK1	192	.	0			c.A1368G						.						7	8	8					19																	55815939		2151	4218	6369	SO:0001819	synonymous_variant	84446	exon14			CTTTTCACCGGAG	AB058714	CCDS12921.1	19q13.4	2008-02-05				ENSG00000160469			18994	protein-coding gene	gene with protein product		609235				14976552	Standard	NM_032430		Approved	KIAA1811	uc002qkg.3	Q8TDC3		ENST00000309383.1:c.1368A>G	chr19.hg19:g.55815939A>G		46.0	0.0		73.0	5.0	NM_032430	F1DG44|Q5J5B5|Q8NDD0|Q8NDR4|Q8TDC2|Q96AV4|Q96JL4	Silent	SNP	ENST00000309383.1	hg19	CCDS12921.1																																																																																			.	.		0.652	BRSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452787.1	NM_032430		G	55815939	A	G	55815939	2	3	263	1	0	0	0	0	0	0	0	1	1525	146	6	2		2	BRSK1	19	55815939	Silent	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	6158023	55815939	3313044	417	38791										
ZNF835	90485	hgsc.bcm.edu	37	chr19	57175640	57175640	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ctgaagagcgcgccgcagtcCtggcacgtgtagggcttctc	14	13	1	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr19:57175640C>A	ENST00000537055.2	-	2	1158	c.927G>T	c.(925-927)caG>caT	p.Q309H		NM_001005850.2	NP_001005850.2	Q9Y2P0	ZN835_HUMAN	zinc finger protein 835	309					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(22)|pancreas(3)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	47						CGCCGCAGTCCTGGCACGTGT	0.711																																					p.Q309H		Atlas-SNP	.											.	ZNF835	106	.	0			c.G927T						.						17	17	17					19																	57175640		2196	4298	6494	SO:0001583	missense	90485	exon2			GCAGTCCTGGCAC	AK023017	CCDS56105.1	19q13.43	2013-01-08			ENSG00000127903	ENSG00000127903		"Zinc fingers, C2H2-type"	34332	protein-coding gene	gene with protein product							Standard	NM_001005850		Approved	BC37295_3	uc010ygn.2	Q9Y2P0		ENST00000537055.2:c.927G>T	chr19.hg19:g.57175640C>A	ENSP00000444747:p.Gln309His	16.0	0.0		21.0	12.0	NM_001005850	B7Z5Y0|G3V1S0	Missense_Mutation	SNP	ENST00000537055.2	hg19	CCDS56105.1	.	.	.	.	.	.	.	.	.	.	C	10.02	1.236947	0.22711	.	.	ENSG00000127903	ENST00000342088;ENST00000537055	T	0.07800	3.16	2.12	-3.63	0.04529	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04724	0.0128	N	0.21097	0.63	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.39820	-0.9595	9	0.54805	T	0.06	.	3.6697	0.08269	0.1257:0.5286:0.1992:0.1465	.	331	Q9Y2P0	ZN835_HUMAN	H	331;309	ENSP00000444747:Q309H	ENSP00000341756:Q331H	Q	-	3	2	ZNF835	61867452	0.000000	0.05858	0.001000	0.08648	0.271000	0.26615	-5.498000	0.00118	-0.746000	0.04766	-0.258000	0.10820	CAG	.	.		0.711	ZNF835-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459800.1	NM_001005850		A	57175640	C	A	57175640	3	1	263	1	0	0	0	0	1	0	0	0	18201	680	24	3	688	3	ZNF835	19	57175640	Missense_Mutation	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	1359701	57175640	1953343	418	38792										
ZNF264	9422	hgsc.bcm.edu	37	chr19	57723920	57723920	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ggagagaagccctatgagtgCgtggagtgtggaaaggcctt	17	6	0	2	rs145421065		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr19:57723920C>T	ENST00000263095.6	+	4	1869	c.1455C>T	c.(1453-1455)tgC>tgT	p.C485C	ZNF264_ENST00000536056.1_Silent_p.C485C	NM_003417.4	NP_003408.1	O43296	ZN264_HUMAN	zinc finger protein 264	485					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.C485C(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(8)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	27		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0135)		CCTATGAGTGCGTGGAGTGTG	0.522																																					p.C485C		Atlas-SNP	.											ZNF264,colon,carcinoma,0,1	ZNF264	65	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1455T						.	T		0,4406		0,0,2203	64	64	64		1455	0.1	0.3	19	dbSNP_134	64	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ZNF264	NM_003417.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		485/628	57723920	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9422	exon4			TGAGTGCGTGGAG	AB007872	CCDS33127.1	19q13.4	2013-01-08				ENSG00000083844		"Zinc fingers, C2H2-type", "-"	13057	protein-coding gene	gene with protein product		604668				9455477	Standard	NM_003417		Approved	KIAA0412	uc002qob.3	O43296		ENST00000263095.6:c.1455C>T	chr19.hg19:g.57723920C>T		50.0	0.0		72.0	3.0	NM_003417	A8K8Y9|Q9P1V0	Silent	SNP	ENST00000263095.6	hg19	CCDS33127.1																																																																																			.	C|1.000;T|0.000		0.522	ZNF264-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465080.1			T	57723920	C	T	57723920	2	4	263	1	0	0	0	0	0	0	0	1	17819	776	27	1		1	ZNF264	19	57723920	Silent	SNP	C	TCGA-FV-A2QR-01A-11D-A20W-10	548280	57723920	1405063	419	38793										
PSMF1	9491	hgsc.bcm.edu	37	chr20	1145055	1145055	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ggcctcccgaaccgacttccTccaggcgctgtgcccccagg	11	19	0	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr20:1145055T>C	ENST00000335877.6	+	6	875	c.699T>C	c.(697-699)ccT>ccC	p.P233P	PSMF1_ENST00000381898.4_Silent_p.P145P|PSMF1_ENST00000484891.1_3'UTR|PSMF1_ENST00000333082.3_Silent_p.P233P|PSMF1_ENST00000246015.4_Silent_p.P233P|PSMF1_ENST00000438768.2_Silent_p.P171P	NM_006814.3	NP_006805.2	Q92530	PSMF1_HUMAN	proteasome (prosome, macropain) inhibitor subunit 1 (PI31)	233	Pro-rich.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteasomal protein catabolic process (GO:1901799)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome core complex (GO:0005839)	endopeptidase inhibitor activity (GO:0004866)|proteasome binding (GO:0070628)			endometrium(1)|kidney(1)|large_intestine(3)|lung(8)	13						ACCGACTTCCTCCAGGCGCTG	0.602																																					p.P233P		Atlas-SNP	.											.	PSMF1	27	.	0			c.T699C						.						146	157	153					20																	1145055		2203	4300	6503	SO:0001819	synonymous_variant	9491	exon6			ACTTCCTCCAGGC	D88378	CCDS13010.1	20p13	2008-07-02			ENSG00000125818	ENSG00000125818		"Proteasome (prosome, macropain) subunits"	9571	protein-coding gene	gene with protein product	"proteasome inhibitor hP131 subunit"					10363639	Standard	NM_006814		Approved	PI31	uc002wen.4	Q92530	OTTHUMG00000031656	ENST00000335877.6:c.699T>C	chr20.hg19:g.1145055T>C		111.0	0.0		118.0	6.0	NM_006814	A0AVQ9|D3DVW3|Q9H4I1	Silent	SNP	ENST00000335877.6	hg19	CCDS13010.1	.	.	.	.	.	.	.	.	.	.	T	11.21	1.571433	0.28003	.	.	ENSG00000125818	ENST00000435720	.	.	.	6.07	-0.646	0.11472	.	.	.	.	.	T	0.40297	0.1111	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.25467	-1.0131	4	.	.	.	-11.7571	1.6783	0.02827	0.1123:0.1958:0.2565:0.4353	.	.	.	.	P	75	.	.	S	+	1	0	PSMF1	1093055	0.888000	0.30383	1.000000	0.80357	0.937000	0.57800	-0.156000	0.10100	0.161000	0.19458	-0.333000	0.08304	TCC	.	.		0.602	PSMF1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077504.2	NM_178578		C	1145055	T	C	1145055	2	2	263	1	0	0	0	0	0	0	0	1	12722	1538	54	2		2	PSMF1	20	1145055	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10		1145055	61880465	420	38794										
CST5	1473	hgsc.bcm.edu	37	chr20	23860229	23860229	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	atggatgccacctgccaaggTcctagattgggccgaggcac	13	12	0	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr20:23860229T>C	ENST00000304710.4	-	1	158	c.85A>G	c.(85-87)Acc>Gcc	p.T29A		NM_001900.4	NP_001891.2	P28325	CYTD_HUMAN	cystatin D	29					negative regulation of endopeptidase activity (GO:0010951)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|kidney(1)|large_intestine(1)|lung(6)|skin(1)|stomach(1)	11						CCTGCCAAGGTCCTAGATTGG	0.562																																					p.T29A		Atlas-SNP	.											.	CST5	24	.	0			c.A85G						.						109	100	103					20																	23860229		2203	4300	6503	SO:0001583	missense	1473	exon1			CCAAGGTCCTAGA		CCDS13162.1	20p11.21	2008-04-15			ENSG00000170367	ENSG00000170367			2477	protein-coding gene	gene with protein product		123858				1939105	Standard	NM_001900		Approved		uc002wtr.1	P28325	OTTHUMG00000032089	ENST00000304710.4:c.85A>G	chr20.hg19:g.23860229T>C	ENSP00000307132:p.Thr29Ala	63.0	0.0		99.0	4.0	NM_001900	Q5JRF5|Q9UCA0	Missense_Mutation	SNP	ENST00000304710.4	hg19	CCDS13162.1	.	.	.	.	.	.	.	.	.	.	t	0.005	-2.131770	0.00338	.	.	ENSG00000170367	ENST00000304710	T	0.09723	2.95	1.25	-2.49	0.06403	Proteinase inhibitor I25, cystatin (1);	1.234540	0.06060	N	0.658135	T	0.03871	0.0109	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.37911	-0.9685	10	0.06494	T	0.89	.	2.8229	0.05477	0.0:0.3238:0.2528:0.4234	.	29	P28325	CYTD_HUMAN	A	29	ENSP00000307132:T29A	ENSP00000307132:T29A	T	-	1	0	CST5	23808229	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.492000	0.06467	-1.140000	0.02877	-0.497000	0.04613	ACC	.	.		0.562	CST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078355.2	NM_001900		C	23860229	T	C	23860229	3	2	263	1	0	0	0	0	1	0	0	0	3977	1667	58	2	355	2	CST5	20	23860229	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	22715174	23860229	39165291	421	38795										
NINL	22981	hgsc.bcm.edu	37	chr20	25478915	25478915	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cggcactgtccactgtcatgAgctcgttgtcaagggcccag	12	13	2	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr20:25478915A>G	ENST00000278886.6	-	9	1173	c.1100T>C	c.(1099-1101)cTc>cCc	p.L367P	NINL_ENST00000422516.1_Missense_Mutation_p.L367P	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	367					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|microtubule (GO:0005874)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(13)|lung(25)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	57						CACTGTCATGAGCTCGTTGTC	0.617																																					p.L367P		Atlas-SNP	.											.	NINL	148	.	0			c.T1100C						.						104	77	86					20																	25478915		2203	4300	6503	SO:0001583	missense	22981	exon9			GTCATGAGCTCGT		CCDS33452.1	20p11.22-p11.1	2013-01-10			ENSG00000101004	ENSG00000101004		"EF-hand domain containing"	29163	protein-coding gene	gene with protein product	"ninein-like protein"	609580				10231032	Standard	XM_005260678		Approved	KIAA0980, NLP	uc002wux.1	Q9Y2I6	OTTHUMG00000032127	ENST00000278886.6:c.1100T>C	chr20.hg19:g.25478915A>G	ENSP00000278886:p.Leu367Pro	86.0	0.0		108.0	6.0	NM_025176	A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	Missense_Mutation	SNP	ENST00000278886.6	hg19	CCDS33452.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.150665	0.78001	.	.	ENSG00000101004	ENST00000278886;ENST00000422516	T;T	0.48201	1.09;0.82	5.32	5.32	0.75619	.	0.000000	0.64402	D	0.000017	T	0.69151	0.3079	M	0.78637	2.42	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.73668	-0.3910	10	0.87932	D	0	-17.8188	14.3876	0.66956	1.0:0.0:0.0:0.0	.	367;367	Q9Y2I6-2;Q9Y2I6	.;NINL_HUMAN	P	367	ENSP00000278886:L367P;ENSP00000410431:L367P	ENSP00000278886:L367P	L	-	2	0	NINL	25426915	1.000000	0.71417	0.941000	0.38009	0.915000	0.54546	7.128000	0.77217	2.234000	0.73211	0.460000	0.39030	CTC	.	.		0.617	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078445.3	NM_025176		G	25478915	A	G	25478915	3	3	263	1	0	0	0	0	1	0	0	0	10429	304	11	2	3112	2	NINL	20	25478915	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	1618686	25478915	37546605	422	38796										
ID1	3397	hgsc.bcm.edu	37	chr20	30193564	30193564	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cgggggccgagggctgccggTccgggctccgctcagcaccc	17	17	1	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr20:30193564T>C	ENST00000376112.3	+	1	479	c.374T>C	c.(373-375)gTc>gCc	p.V125A	ID1_ENST00000376105.3_Missense_Mutation_p.V125A|MIR3193_ENST00000578262.1_RNA	NM_002165.3	NP_002156.2	P41134	ID1_HUMAN	inhibitor of DNA binding 1, dominant negative helix-loop-helix protein	125					angiogenesis (GO:0001525)|blood vessel endothelial cell migration (GO:0043534)|blood vessel morphogenesis (GO:0048514)|BMP signaling pathway (GO:0030509)|collagen metabolic process (GO:0032963)|endothelial cell morphogenesis (GO:0001886)|heart development (GO:0007507)|lung morphogenesis (GO:0060425)|lung vasculature development (GO:0060426)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA binding (GO:0043392)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription by transcription factor localization (GO:0010621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein destabilization (GO:0031648)|regulation of angiogenesis (GO:0045765)|regulation of MAPK cascade (GO:0043408)|response to antibiotic (GO:0046677)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|ovary(1)|pancreas(1)	4	all_cancers(5;7.12e-06)|Lung NSC(7;3.95e-06)|all_epithelial(3;4.36e-06)|all_lung(7;6.68e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Epithelial(4;1.99e-05)|all cancers(5;0.000169)|Colorectal(19;0.00202)|COAD - Colon adenocarcinoma(19;0.0264)			GGGCTGCCGGTCCGGGCTCCG	0.612																																					p.V125A	NSCLC(123;1618 1779 21803 28680 33854)	Atlas-SNP	.											.	ID1	12	.	0			c.T374C						.						12	16	15					20																	30193564		2201	4299	6500	SO:0001583	missense	3397	exon1			TGCCGGTCCGGGC		CCDS13185.1, CCDS13186.1	20q11	2013-05-21			ENSG00000125968	ENSG00000125968		"Basic helix-loop-helix proteins"	5360	protein-coding gene	gene with protein product	"DNA-binding protein inhibitor ID-1"	600349				8294468	Standard	NM_002165		Approved	dJ857M17.1.2, bHLHb24	uc002wwg.2	P41134	OTTHUMG00000032181	ENST00000376112.3:c.374T>C	chr20.hg19:g.30193564T>C	ENSP00000365280:p.Val125Ala	121.0	0.0		108.0	5.0	NM_002165	A8K537|E1P5L4|O00651|O00652|Q16371|Q16377|Q5TE66|Q5TE67|Q969Z7|Q9H0Z5|Q9H109	Missense_Mutation	SNP	ENST00000376112.3	hg19	CCDS13185.1	.	.	.	.	.	.	.	.	.	.	T	0.014	-1.597810	0.00857	.	.	ENSG00000125968	ENST00000376112;ENST00000376105	T;T	0.40225	1.08;1.04	4.97	0.418	0.16429	Helix-loop-helix DNA-binding (1);	1.230310	0.05808	N	0.613462	T	0.19886	0.0478	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.20840	-1.0263	10	0.10636	T	0.68	-7.1757	5.2237	0.15383	0.0:0.4539:0.1556:0.3905	.	125;125	P41134-2;P41134	.;ID1_HUMAN	A	125	ENSP00000365280:V125A;ENSP00000365273:V125A	ENSP00000365273:V125A	V	+	2	0	ID1	29657225	0.188000	0.23250	0.017000	0.16124	0.002000	0.02628	2.757000	0.47557	-0.013000	0.14199	-0.250000	0.11733	GTC	.	.		0.612	ID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078550.1	NM_002165		C	30193564	T	C	30193564	3	2	263	1	0	0	0	0	1	0	0	0	7498	1667	58	2	376	2	ID1	20	30193564	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	4714649	30193564	32831956	423	38797										
SNX21	90203	hgsc.bcm.edu	37	chr20	44469288	44469288	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ctccctgcagctctacacccTcgccgtgatcggcccaggac	9	19	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr20:44469288T>C	ENST00000491381.1	+	4	526	c.458T>C	c.(457-459)cTc>cCc	p.L153P	SNX21_ENST00000462307.1_Missense_Mutation_p.S157P|SNX21_ENST00000344780.4_3'UTR|SNX21_ENST00000372541.1_Missense_Mutation_p.S148P|SNX21_ENST00000372542.1_Missense_Mutation_p.L144P|SNX21_ENST00000342644.5_Missense_Mutation_p.L153P			Q969T3	SNX21_HUMAN	sorting nexin family member 21	153	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|pancreas(1)	7		Myeloproliferative disorder(115;0.0122)				CTCTACACCCTCGCCGTGATC	0.637																																					p.S157P		Atlas-SNP	.											.	SNX21	23	.	0			c.T469C						.						83	87	85					20																	44469288		2203	4300	6503	SO:0001583	missense	90203	exon5			ACACCCTCGCCGT	AK095851	CCDS13376.1, CCDS13377.1, CCDS42883.1	20q13.12	2013-01-10	2006-07-24	2006-07-24	ENSG00000124104	ENSG00000124104		"Sorting nexins", "Tetratricopeptide (TTC) repeat domain containing"	16154	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 161"	C20orf161		12461558, 12459172	Standard	NM_152897		Approved	dJ337O18.4, SNX-L	uc002xpv.1	Q969T3	OTTHUMG00000032624	ENST00000491381.1:c.458T>C	chr20.hg19:g.44469288T>C	ENSP00000418593:p.Leu153Pro	76.0	0.0		86.0	4.0	NM_001042633	Q5JZH5|Q5JZH6|Q5JZH7|Q8WUR6|Q9BR16	Missense_Mutation	SNP	ENST00000491381.1	hg19	CCDS13377.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.8|20.8	4.053847|4.053847	0.75960|0.75960	.|.	.|.	ENSG00000124104|ENSG00000124104	ENST00000491381;ENST00000342644;ENST00000372542|ENST00000462307;ENST00000372541;ENST00000372545	T;T;T|.	0.33438|.	1.41;1.41;1.41|.	4.34|4.34	4.34|4.34	0.51931|0.51931	Phox homologous domain (4);|.	0.057080|.	0.64402|.	D|.	0.000003|.	T|T	0.59797|0.59797	0.2220|0.2220	L|L	0.43152|0.43152	1.355|1.355	0.29353|0.29353	N|N	0.865224|0.865224	D;D;D|D;D	0.61080|0.76494	0.963;0.963;0.989|0.999;0.999	P;P;P|D;D	0.61070|0.85130	0.576;0.691;0.883|0.997;0.997	T|T	0.54649|0.54649	-0.8262|-0.8262	10|7	0.87932|.	D|.	0|.	-14.7447|-14.7447	12.8601|12.8601	0.57908|0.57908	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	144;153;153|148;157	Q5JZH3;Q969T3;Q5JZH5|Q5JZH4;Q5JZH7	.;SNX21_HUMAN;.|.;.	P|P	153;153;144|157;148;149	ENSP00000418593:L153P;ENSP00000344586:L153P;ENSP00000361620:L144P|.	ENSP00000344586:L153P|.	L|S	+|+	2|1	0|0	SNX21|SNX21	43902695|43902695	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.943000|0.943000	0.58893|0.58893	6.505000|6.505000	0.73708|0.73708	1.828000|1.828000	0.53243|0.53243	0.379000|0.379000	0.24179|0.24179	CTC|TCG	.	.		0.637	SNX21-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079534.1	NM_033421		C	44469288	T	C	44469288	3	2	263	1	0	0	0	0	1	0	0	0	14908	1551	54	2	487	2	SNX21	20	44469288	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	14275724	44469288	18556232	424	38798										
LRRC3	81543	hgsc.bcm.edu	37	chr21	45877204	45877204	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cgcctacgtcgtgtactatgTgcgccacaaccaggaggatg	12	12	0	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr21:45877204T>C	ENST00000291592.4	+	2	994	c.677T>C	c.(676-678)gTg>gCg	p.V226A	LRRC3-AS1_ENST00000426578.1_RNA|LRRC3DN_ENST00000596691.1_5'Flank	NM_030891.3	NP_112153.1	Q9BY71	LRRC3_HUMAN	leucine rich repeat containing 3	226						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|lung(1)|urinary_tract(1)	5		Breast(209;0.00908)		COAD - Colon adenocarcinoma(84;0.148)|Lung(125;0.195)		GTGTACTATGTGCGCCACAAC	0.667																																					p.V226A		Atlas-SNP	.											.	LRRC3	22	.	0			c.T677C						.						69	71	70					21																	45877204		2203	4300	6503	SO:0001583	missense	81543	exon2			ACTATGTGCGCCA	AB058646	CCDS13711.1	21q22.3	2011-12-07	2002-06-20		ENSG00000160233	ENSG00000160233			14965	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 102"	C21orf102		12036297	Standard	NM_030891		Approved		uc002zfa.3	Q9BY71	OTTHUMG00000040847	ENST00000291592.4:c.677T>C	chr21.hg19:g.45877204T>C	ENSP00000291592:p.Val226Ala	84.0	0.0		77.0	5.0	NM_030891	Q0VDJ2	Missense_Mutation	SNP	ENST00000291592.4	hg19	CCDS13711.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.789267	0.90367	.	.	ENSG00000160233	ENST00000291592	T	0.59906	0.23	4.87	4.87	0.63330	.	0.078166	0.50627	D	0.000106	T	0.74718	0.3753	M	0.74881	2.28	0.58432	D	0.999999	D	0.89917	1.0	D	0.74348	0.983	T	0.78730	-0.2090	10	0.87932	D	0	-36.4029	14.48	0.67576	0.0:0.0:0.0:1.0	.	226	Q9BY71	LRRC3_HUMAN	A	226	ENSP00000291592:V226A	ENSP00000291592:V226A	V	+	2	0	LRRC3	44701632	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	4.935000	0.63498	1.969000	0.57287	0.402000	0.26972	GTG	.	.		0.667	LRRC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098095.3			C	45877204	T	C	45877204	3	2	263	1	0	0	0	0	1	0	0	0	8993	1696	59	2	679	2	LRRC3	21	45877204	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10		45877204	2252691	425	38799										
PCBP3	54039	hgsc.bcm.edu	37	chr21	47360058	47360058	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ggtcctcagagcgtcagatcAccatcacggggaccccggcc	12	16	4	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr21:47360058A>G	ENST00000400314.1	+	15	1362	c.1024A>G	c.(1024-1026)Acc>Gcc	p.T342A	PCBP3_ENST00000400304.1_Missense_Mutation_p.T332A|PCBP3_ENST00000400310.1_Missense_Mutation_p.T322A|PCBP3_ENST00000449640.1_Missense_Mutation_p.T342A|PCBP3_ENST00000400308.1_Missense_Mutation_p.T316A|PCBP3_ENST00000400309.1_Missense_Mutation_p.T341A			P57721	PCBP3_HUMAN	poly(rC) binding protein 3	342	KH 3. {ECO:0000255|PROSITE- ProRule:PRU00117}.				mRNA metabolic process (GO:0016071)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			biliary_tract(1)|endometrium(3)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17	all_hematologic(128;0.24)			Colorectal(79;0.0411)|READ - Rectum adenocarcinoma(84;0.0649)		GCGTCAGATCACCATCACGGG	0.557																																					p.T342A		Atlas-SNP	.											.	PCBP3	82	.	0			c.A1024G						.						64	73	70					21																	47360058		2141	4254	6395	SO:0001583	missense	54039	exon13			CAGATCACCATCA	AF176329	CCDS42974.2, CCDS46652.1	21q22.3	2013-07-16	2001-11-28		ENSG00000183570	ENSG00000183570			8651	protein-coding gene	gene with protein product		608502	"poly(rC)-binding protein 3"			10936052	Standard	NM_020528		Approved		uc002zhq.2	P57721	OTTHUMG00000090399	ENST00000400314.1:c.1024A>G	chr21.hg19:g.47360058A>G	ENSP00000383168:p.Thr342Ala	73.0	0.0		90.0	4.0	NM_020528	A8MPS2|A8MQ26|B7WNN9|B7WPC1|Q8N9K6|Q96EP6	Missense_Mutation	SNP	ENST00000400314.1	hg19	CCDS42974.2	.	.	.	.	.	.	.	.	.	.	A	26.4	4.730733	0.89390	.	.	ENSG00000183570	ENST00000400314;ENST00000400310;ENST00000400309;ENST00000400308;ENST00000449640;ENST00000346743;ENST00000400305;ENST00000400304	T;T;T;T;T;T;T	0.34472	1.36;1.36;1.36;1.36;1.36;1.36;1.36	4.08	4.08	0.47627	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.000000	0.85682	D	0.000000	T	0.65502	0.2697	M	0.89968	3.075	0.80722	D	1	D;D;D;D;D	0.89917	0.999;0.999;1.0;0.999;1.0	D;D;D;D;D	0.87578	0.998;0.994;0.985;0.998;0.985	T	0.74188	-0.3746	10	0.87932	D	0	-2.4496	13.2327	0.59953	1.0:0.0:0.0:0.0	.	332;316;341;342;322	E9PFP8;P57721-2;P57721-4;P57721;P57721-5	.;.;.;PCBP3_HUMAN;.	A	342;322;341;316;342;322;293;332	ENSP00000383168:T342A;ENSP00000383165:T322A;ENSP00000383164:T341A;ENSP00000383163:T316A;ENSP00000401198:T342A;ENSP00000383160:T293A;ENSP00000383159:T332A	ENSP00000330225:T322A	T	+	1	0	PCBP3	46184486	1.000000	0.71417	0.988000	0.46212	0.985000	0.73830	8.532000	0.90613	1.705000	0.51264	0.448000	0.29417	ACC	.	.		0.557	PCBP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206808.2			G	47360058	A	G	47360058	3	3	263	1	0	0	0	0	1	0	0	0	11511	159	6	2	1074	2	PCBP3	21	47360058	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	1482854	47360058	769837	426	38800										
SUSD2	56241	hgsc.bcm.edu	37	chr22	24582054	24582054	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	acattcaatgggcgcggagaGtacgtgctgctggaggcagc	16	9	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr22:24582054G>A	ENST00000358321.3	+	9	1671	c.1410G>A	c.(1408-1410)gaG>gaA	p.E470E		NM_019601.3	NP_062547.1	Q9UGT4	SUSD2_HUMAN	sushi domain containing 2	470	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	26						GGCGCGGAGAGTACGTGCTGC	0.662																																					p.E470E		Atlas-SNP	.											.	SUSD2	68	.	0			c.G1410A						.						31	32	32					22																	24582054		2203	4300	6503	SO:0001819	synonymous_variant	56241	exon9			CGGAGAGTACGTG	AK026431	CCDS13824.1	22q11-q12	2005-08-16			ENSG00000099994	ENSG00000099994			30667	protein-coding gene	gene with protein product		615825				12477932	Standard	NM_019601		Approved	BK65A6.2, FLJ22778	uc002zzn.1	Q9UGT4	OTTHUMG00000150792	ENST00000358321.3:c.1410G>A	chr22.hg19:g.24582054G>A		136.0	0.0		220.0	52.0	NM_019601	Q9H5Y6	Silent	SNP	ENST00000358321.3	hg19	CCDS13824.1																																																																																			.	.		0.662	SUSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320088.1	NM_019601		A	24582054	G	A	24582054	2	1	263	1	0	0	0	0	0	0	0	1	15423	1020	36	3		3	SUSD2	22	24582054	Silent	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10		24582054	26722512	427	38801										
MORC2	22880	hgsc.bcm.edu	37	chr22	31333805	31333805	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cagcccagccccattaccgaTggcaatatccttccaatact	5	16	0	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr22:31333805T>C	ENST00000397641.3	-	14	1774	c.1366A>G	c.(1366-1368)Atc>Gtc	p.I456V	MORC2_ENST00000215862.4_Missense_Mutation_p.I394V|MORC2_ENST00000469915.1_Intron			Q9Y6X9	MORC2_HUMAN	MORC family CW-type zinc finger 2	456						cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	21						CCATTACCGATGGCAATATCC	0.547																																					p.I394V		Atlas-SNP	.											.	MORC2	78	.	0			c.A1180G						.						92	88	89					22																	31333805		2203	4300	6503	SO:0001583	missense	22880	exon15			TACCGATGGCAAT	AB020659	CCDS33636.1	22q12.2	2005-06-15	2005-06-15	2005-06-15	ENSG00000133422	ENSG00000133422			23573	protein-coding gene	gene with protein product			"zinc finger, CW-type with coiled-coil domain 1", "zinc finger, CW type with coiled-coil domain 1"	ZCWCC1		14607086	Standard	XM_005261391		Approved	ZCW3, KIAA0852, AC004542.C22.1	uc003aje.1	Q9Y6X9	OTTHUMG00000151193	ENST00000397641.3:c.1366A>G	chr22.hg19:g.31333805T>C	ENSP00000380763:p.Ile456Val	140.0	0.0		228.0	110.0	NM_014941	B2RNB1|Q9UF28|Q9Y6V2	Missense_Mutation	SNP	ENST00000397641.3	hg19		.	.	.	.	.	.	.	.	.	.	T	13.73	2.323669	0.41096	.	.	ENSG00000133422	ENST00000397641;ENST00000215862	T;T	0.13420	2.59;2.59	5.33	3.16	0.36331	.	0.000000	0.85682	D	0.000000	T	0.10337	0.0253	L	0.40543	1.245	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.18241	-1.0343	10	0.21014	T	0.42	.	8.2169	0.31516	0.0:0.1606:0.0:0.8394	.	456	Q9Y6X9	MORC2_HUMAN	V	456;394	ENSP00000380763:I456V;ENSP00000215862:I394V	ENSP00000215862:I394V	I	-	1	0	MORC2	29663805	1.000000	0.71417	0.997000	0.53966	0.712000	0.41017	5.909000	0.69923	0.398000	0.25338	0.413000	0.27773	ATC	.	.		0.547	MORC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000321710.2	NM_014941		C	31333805	T	C	31333805	3	2	263	1	0	0	0	0	1	0	0	0	9711	1464	51	2	1784	2	MORC2	22	31333805	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	6751751	31333805	19970761	428	38802										
TNRC6B	23112	hgsc.bcm.edu	37	chr22	40660706	40660706	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ccccagactcaacccttggaGgtgctgctgcttcaaattat	8	13	2	1	rs367663125		TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr22:40660706G>A	ENST00000454349.2	+	5	683	c.472G>A	c.(472-474)Ggt>Agt	p.G158S	TNRC6B_ENST00000301923.9_Intron|TNRC6B_ENST00000402203.1_Intron|TNRC6B_ENST00000335727.9_Missense_Mutation_p.G158S	NM_001162501.1	NP_001155973.1	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B	158	Interaction with argonaute proteins.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)	1						AACCCTTGGAGGTGCTGCTGC	0.493																																					p.G158S		Atlas-SNP	.											.	TNRC6B	195	.	0			c.G472A						.						41	39	40					22																	40660706		1889	4121	6010	SO:0001583	missense	23112	exon5			CTTGGAGGTGCTG	AB029016	CCDS46712.1, CCDS46713.1, CCDS54533.1	22q13	2006-08-22			ENSG00000100354	ENSG00000100354		"Trinucleotide (CAG) repeat containing"	29190	protein-coding gene	gene with protein product		610740					Standard	NM_015088		Approved	KIAA1093	uc011aor.2	Q9UPQ9	OTTHUMG00000151114	ENST00000454349.2:c.472G>A	chr22.hg19:g.40660706G>A	ENSP00000401946:p.Gly158Ser	94.0	0.0		138.0	36.0	NM_001162501	B0QY73|B0QY78|B4DGC0|Q5TH52|Q8TBX2	Missense_Mutation	SNP	ENST00000454349.2	hg19	CCDS54533.1	.	.	.	.	.	.	.	.	.	.	G	11.84	1.758997	0.31137	.	.	ENSG00000100354	ENST00000454349;ENST00000400140;ENST00000335727	T;T	0.11495	2.78;2.77	5.44	5.44	0.79542	.	0.327663	0.32736	N	0.005701	T	0.08537	0.0212	N	0.14661	0.345	0.45837	D	0.998709	P;P	0.46784	0.884;0.705	B;B	0.41466	0.358;0.271	T	0.41251	-0.9519	10	0.22706	T	0.39	-4.8462	18.2777	0.90088	0.0:0.0:1.0:0.0	.	158;158	Q9UPQ9;Q9UPQ9-1	TNR6B_HUMAN;.	S	158	ENSP00000401946:G158S;ENSP00000338371:G158S	ENSP00000338371:G158S	G	+	1	0	TNRC6B	38990652	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.979000	0.63806	2.559000	0.86315	0.650000	0.86243	GGT	.	.		0.493	TNRC6B-202	KNOWN	basic|CCDS	protein_coding	protein_coding				A	40660706	G	A	40660706	3	1	263	1	0	0	0	0	1	0	0	0	16356	1000	35	3	611	3	TNRC6B	22	40660706	Missense_Mutation	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	9326901	40660706	10643860	429	38803										
XRCC6	2547	hgsc.bcm.edu	37	chr22	42057392	42057407	+	Frame_Shift_Del	DEL	AGCTTGTTTACCCACC	AGCTTGTTTACCCACC	-													0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cttggtggatgagtttaaggAgcttgtttacccaccagatt							TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	AGCTTGTTTACCCACC	AGCTTGTTTACCCACC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr22:42057392_42057407delAGCTTGTTTACCCACC	ENST00000359308.4	+	11	2235_2250	c.1580_1595delAGCTTGTTTACCCACC	c.(1579-1596)gagcttgtttacccaccafs	p.ELVYPP527fs	XRCC6_ENST00000405506.1_Frame_Shift_Del_p.ELVYPP477fs|XRCC6_ENST00000405878.1_Frame_Shift_Del_p.ELVYPP527fs|XRCC6_ENST00000428575.2_Frame_Shift_Del_p.ELVYPP394fs|XRCC6_ENST00000360079.3_Frame_Shift_Del_p.ELVYPP527fs|XRCC6_ENST00000402580.3_Frame_Shift_Del_p.ELVYPP486fs			P12956	XRCC6_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 6	527					brain development (GO:0007420)|cellular hyperosmotic salinity response (GO:0071475)|cellular response to X-ray (GO:0071481)|DNA duplex unwinding (GO:0032508)|DNA ligation (GO:0006266)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|telomere maintenance (GO:0000723)|transcription, DNA-templated (GO:0006351)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	cytosol (GO:0005829)|Ku70:Ku80 complex (GO:0043564)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nuclear telomere cap complex (GO:0000783)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	5'-deoxyribose-5-phosphate lyase activity (GO:0051575)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|telomeric DNA binding (GO:0042162)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|liver(2)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	31						GAGTTTAAGGAGCTTGTTTACCCACCAGATTACAAT	0.417								Non-homologous end-joining																													p.527_532del		Pindel	.											.	XRCC6	64	.	0			c.1579_1594del						.																																			SO:0001589	frameshift_variant	2547	exon12			.	J04607	CCDS14021.1, CCDS74870.1, CCDS74871.1	22q13.2	2011-09-12	2008-07-31	2005-05-06	ENSG00000196419	ENSG00000196419			4055	protein-coding gene	gene with protein product	"Ku autoantigen, 70kDa"	152690	"thyroid autoantigen 70kD (Ku antigen)", "thyroid autoantigen 70kDa (Ku antigen)"	G22P1		9200330, 9223317	Standard	NM_001469		Approved	D22S731, D22S671, KU70, ML8	uc003bao.1	P12956	OTTHUMG00000151190	ENST00000359308.4:c.1580_1595delAGCTTGTTTACCCACC	chr22.hg19:g.42057392_42057407delAGCTTGTTTACCCACC	ENSP00000352257:p.Glu527fs	0.0	0.0		101.0	14.0	NM_001469	B1AHC8|Q6FG89|Q9UCQ2|Q9UCQ3	Frame_Shift_Del	DEL	ENST00000359308.4	hg19	CCDS14021.1																																																																																			.	.		0.417	XRCC6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321688.1	NM_001469		-	42057407	AGCTTGTTTACCCACC	-	42057392	7	5	263	1	0	1	0	1	0	0	0	0	17472	304	11	0	1622	0	XRCC6	22	42057392	Frame_Shift_Del	DEL	AGCTTGTTTACCCACC	TCGA-FV-A2QR-01A-11D-A20W-10	1396686	42057392	9247174	430	38804										
ZBED4	9889	hgsc.bcm.edu	37	chr22	50280096	50280096	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cagctgcgaccagtgggaggTcatgcagtccgtgtgccgtg	16	11	1	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr22:50280096T>C	ENST00000216268.5	+	2	3263	c.2786T>C	c.(2785-2787)gTc>gCc	p.V929A		NM_014838.2	NP_055653.2	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	929						cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	44		all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)|BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		CAGTGGGAGGTCATGCAGTCC	0.587																																					p.V929A		Atlas-SNP	.											.	ZBED4	102	.	0			c.T2786C						.						110	85	94					22																	50280096		2203	4300	6503	SO:0001583	missense	9889	exon2			GGGAGGTCATGCA	AB014537	CCDS33677.1	22q13.33	2013-05-03			ENSG00000100426	ENSG00000100426		"Zinc fingers, BED-type"	20721	protein-coding gene	gene with protein product		612552				23533661	Standard	NM_014838		Approved	KIAA0637	uc003bix.2	O75132	OTTHUMG00000150291	ENST00000216268.5:c.2786T>C	chr22.hg19:g.50280096T>C	ENSP00000216268:p.Val929Ala	165.0	0.0		111.0	5.0	NM_014838	B2RZH1|Q1ECU0|Q9UGG8	Missense_Mutation	SNP	ENST00000216268.5	hg19	CCDS33677.1	.	.	.	.	.	.	.	.	.	.	T	18.85	3.711297	0.68730	.	.	ENSG00000100426	ENST00000216268	T	0.22336	1.96	5.95	5.95	0.96441	Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.27241	0.0668	M	0.73598	2.24	0.80722	D	1	P	0.36282	0.546	B	0.32211	0.142	T	0.03863	-1.0997	10	0.42905	T	0.14	-28.266	16.4046	0.83654	0.0:0.0:0.0:1.0	.	929	O75132	ZBED4_HUMAN	A	929	ENSP00000216268:V929A	ENSP00000216268:V929A	V	+	2	0	ZBED4	48666100	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.509000	0.81698	2.277000	0.76020	0.533000	0.62120	GTC	.	.		0.587	ZBED4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317408.2	NM_014838		C	50280096	T	C	50280096	3	2	263	1	0	0	0	0	1	0	0	0	17535	1667	58	2	2788	2	ZBED4	22	50280096	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	8222704	50280096	1024470	431	38805										
PIM3	415116	hgsc.bcm.edu	37	chr22	50355358	50355358	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ggtcgtgcaccgcgacattaAggacgaaaatctgcttgtgg	13	9	1	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chr22:50355358A>G	ENST00000360612.4	+	4	950	c.515A>G	c.(514-516)aAg>aGg	p.K172R		NM_001001852.3	NP_001001852.2	Q86V86	PIM3_HUMAN	Pim-3 proto-oncogene, serine/threonine kinase	172	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|histone phosphorylation (GO:0016572)|negative regulation of apoptotic process (GO:0043066)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle (GO:0007346)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)						all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.196)|LUAD - Lung adenocarcinoma(64;0.247)		CGCGACATTAAGGACGAAAAT	0.667																																					p.K172R		Atlas-SNP	.											PIM3_ENST00000360612,NS,carcinoma,0,1	PIM3	15	.	0			c.A515G						.						27	24	25					22																	50355358		2202	4297	6499	SO:0001583	missense	415116	exon4			ACATTAAGGACGA	BC052239	CCDS33678.1	22q13	2014-06-25	2014-06-25		ENSG00000198355	ENSG00000198355			19310	protein-coding gene	gene with protein product		610580	"pim-3 oncogene"			12477932	Standard	NM_001001852		Approved		uc003bjb.3	Q86V86	OTTHUMG00000150290	ENST00000360612.4:c.515A>G	chr22.hg19:g.50355358A>G	ENSP00000353824:p.Lys172Arg	109.0	0.0		74.0	4.0	NM_001001852	A5D8X8|A8K7J0|B1B0P0|Q68BM2	Missense_Mutation	SNP	ENST00000360612.4	hg19	CCDS33678.1	.	.	.	.	.	.	.	.	.	.	a	17.56	3.419246	0.62622	.	.	ENSG00000198355	ENST00000360612	D	0.90900	-2.75	3.59	2.54	0.30619	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.187158	0.44483	U	0.000456	D	0.95900	0.8665	H	0.95850	3.73	0.50039	D	0.999843	D	0.76494	0.999	D	0.77557	0.99	D	0.94870	0.8029	10	0.87932	D	0	.	7.3647	0.26766	0.8887:0.0:0.1113:0.0	.	172	Q86V86	PIM3_HUMAN	R	172	ENSP00000353824:K172R	ENSP00000353824:K172R	K	+	2	0	PIM3	48741362	1.000000	0.71417	1.000000	0.80357	0.011000	0.07611	5.519000	0.67074	1.258000	0.44101	0.378000	0.23410	AAG	.	.		0.667	PIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317406.1	NM_001001852		G	50355358	A	G	50355358	3	3	263	1	0	0	0	0	1	0	0	0	11938	72	3	2	529	2	PIM3	22	50355358	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	75262	50355358	949208	432	38806										
STS	412	hgsc.bcm.edu	37	chrX	7177425	7177425	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ggatgagctgtcacagcaagActgacttctgtcaccaccct	9	13	3	3			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chrX:7177425A>G	ENST00000217961.4	+	5	653	c.433A>G	c.(433-435)Act>Gct	p.T145A		NM_000351.4	NP_000342.2	P08842	STS_HUMAN	steroid sulfatase (microsomal), isozyme S	145					cellular protein metabolic process (GO:0044267)|epidermis development (GO:0008544)|female pregnancy (GO:0007565)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|steroid catabolic process (GO:0006706)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|steryl-sulfatase activity (GO:0004773)|sulfuric ester hydrolase activity (GO:0008484)			NS(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|prostate(2)|skin(1)	27		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)			Norelgestromin(DB06713)	TCACAGCAAGACTGACTTCTG	0.483									Ichthyosis																												p.T145A		Atlas-SNP	.											.	STS	64	.	0			c.A433G						.						152	125	134					X																	7177425		2203	4299	6502	SO:0001583	missense	412	exon5	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	AGCAAGACTGACT	M16505	CCDS14127.1	Xp22.32	2013-06-10	2007-07-19		ENSG00000101846	ENSG00000101846	3.1.6.2	"Arylsulfatase family"	11425	protein-coding gene	gene with protein product	"arylsulfatase C"	300747	"steroid sulfatase (microsomal), arylsulfatase C, isozyme S"	ARSC1			Standard	NM_000351		Approved	ARSC	uc004cry.4	P08842	OTTHUMG00000021102	ENST00000217961.4:c.433A>G	chrX.hg19:g.7177425A>G	ENSP00000217961:p.Thr145Ala	60.0	0.0		98.0	4.0	NM_000351	B2RA47	Missense_Mutation	SNP	ENST00000217961.4	hg19	CCDS14127.1	.	.	.	.	.	.	.	.	.	.	A	1.900	-0.453277	0.04540	.	.	ENSG00000101846	ENST00000217961	D	0.98684	-5.07	3.83	-0.286	0.12862	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	1.562600	0.03793	N	0.263203	D	0.95023	0.8389	N	0.24115	0.695	0.09310	N	1	B	0.06786	0.001	B	0.12837	0.008	D	0.90215	0.4267	10	0.19147	T	0.46	.	3.4685	0.07558	0.3877:0.0:0.4126:0.1997	.	145	P08842	STS_HUMAN	A	145	ENSP00000217961:T145A	ENSP00000217961:T145A	T	+	1	0	STS	7187425	0.000000	0.05858	0.000000	0.03702	0.404000	0.30871	0.286000	0.18902	-0.102000	0.12197	0.486000	0.48141	ACT	.	.		0.483	STS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055686.1	NM_000351		G	7177425	A	G	7177425	3	3	263	1	0	0	0	0	1	0	0	0	15347	275	10	2	451	2	STS	23	7177425	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10		7177425	148093135	433	38807										
DMD	1756	hgsc.bcm.edu	37	chrX	31497178	31497178	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tcgtacagtctcaagagtacTcatgattacaggttctttag	8	8	3	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chrX:31497178T>C	ENST00000357033.4	-	58	8796	c.8590A>G	c.(8590-8592)Agt>Ggt	p.S2864G	DMD_ENST00000541735.1_Missense_Mutation_p.S404G|DMD_ENST00000378677.2_Missense_Mutation_p.S2860G|DMD_ENST00000343523.2_Missense_Mutation_p.S404G|DMD_ENST00000378707.3_Missense_Mutation_p.S404G|DMD_ENST00000445312.1_5'UTR|DMD_ENST00000359836.1_Missense_Mutation_p.S404G|DMD_ENST00000474231.1_Missense_Mutation_p.S404G	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	2864					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				TCAAGAGTACTCATGATTACA	0.393																																					p.S2864G		Atlas-SNP	.											.	DMD	2127	.	0			c.A8590G						.						96	85	89					X																	31497178		2202	4300	6502	SO:0001583	missense	1756	exon58			GAGTACTCATGAT	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.8590A>G	chrX.hg19:g.31497178T>C	ENSP00000354923:p.Ser2864Gly	72.0	0.0		93.0	4.0	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	hg19	CCDS14233.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.00|11.00	1.511477|1.511477	0.27036|0.27036	.|.	.|.	ENSG00000198947|ENSG00000198947	ENST00000465285|ENST00000534884;ENST00000378682;ENST00000378684;ENST00000358062;ENST00000378677;ENST00000357033;ENST00000359836;ENST00000343523;ENST00000542849;ENST00000535280;ENST00000378707;ENST00000541735;ENST00000474231	.|T;T;T;T;T;T;T;T	.|0.36157	.|1.27;1.27;1.27;1.27;1.27;1.27;1.27;1.27	5.14|5.14	5.14|5.14	0.70334|0.70334	.|.	.|0.159222	.|0.28533	.|U	.|0.015006	T|T	0.42854|0.42854	0.1221|0.1221	L|L	0.37850|0.37850	1.14|1.14	0.31735|0.31735	N|N	0.636534|0.636534	.|P;B;B;B;B;B;B;B;B;B;B	.|0.42337	.|0.776;0.001;0.001;0.001;0.001;0.002;0.001;0.001;0.0;0.001;0.007	.|P;B;B;B;B;B;B;B;B;B;B	.|0.51615	.|0.675;0.001;0.003;0.001;0.001;0.02;0.003;0.002;0.001;0.001;0.011	T|T	0.52873|0.52873	-0.8517|-0.8517	5|10	.|0.52906	.|T	.|0.07	.|.	14.2317|14.2317	0.65898|0.65898	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|2856;2864;2860;1523;1520;404;404;404;404;404;2741	.|P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6;F8VX32;E7ESB2;E7EQS5;E7EQR9;F5GZY3;F5GZT3	.|.;DMD_HUMAN;.;.;.;.;.;.;.;.;.	G|G	592|2856;1523;1520;560;2860;2864;404;404;2864;2741;404;404;404	.|ENSP00000350765:S560G;ENSP00000367948:S2860G;ENSP00000354923:S2864G;ENSP00000352894:S404G;ENSP00000340057:S404G;ENSP00000367979:S404G;ENSP00000444119:S404G;ENSP00000417123:S404G	.|ENSP00000340057:S404G	E|S	-|-	2|1	0|0	DMD|DMD	31407099|31407099	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	4.244000|4.244000	0.58728|0.58728	1.807000|1.807000	0.52817|0.52817	0.486000|0.486000	0.48141|0.48141	GAG|AGT	.	.		0.393	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		C	31497178	T	C	31497178	3	2	263	1	0	0	0	0	1	0	0	0	4582	1551	54	2	2669	2	DMD	23	31497178	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	24319753	31497178	123773382	434	38808										
CXorf59	286464	hgsc.bcm.edu	37	chrX	36156122	36156122	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	taaattttgacaaagaccttTcagatggtcttgtttttgca	7	6	2	3			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chrX:36156122T>C	ENST00000313548.4	+	9	1279	c.1093T>C	c.(1093-1095)Tca>Cca	p.S365P		NM_173695.2	NP_775966.1	Q8N9S7	CHDC2_HUMAN	calponin homology domain containing 2	365	CH.					integral component of membrane (GO:0016021)											CAAAGACCTTTCAGATGGTCT	0.313																																					p.S365P		Atlas-SNP	.											.	.	.	.	0			c.T1093C						.						88	78	82					X																	36156122		2202	4298	6500	SO:0001583	missense	286464	exon9			GACCTTTCAGATG	AK093920	CCDS14238.1	Xp21.1	2014-08-07	2012-11-28	2012-11-28	ENSG00000176034	ENSG00000176034			26708	protein-coding gene	gene with protein product			"chromosome X open reading frame 59"	CXorf59			Standard	NM_173695		Approved	FLJ36601, RP13-11B7.1	uc004ddk.1	Q8N9S7	OTTHUMG00000021351	ENST00000313548.4:c.1093T>C	chrX.hg19:g.36156122T>C	ENSP00000324767:p.Ser365Pro	98.0	0.0		91.0	4.0	NM_173695		Missense_Mutation	SNP	ENST00000313548.4	hg19	CCDS14238.1	.	.	.	.	.	.	.	.	.	.	T	6.114	0.389327	0.11581	.	.	ENSG00000176034	ENST00000378660;ENST00000313548	D;D	0.95821	-3.82;-3.82	5.22	-2.22	0.06952	Calponin homology domain (3);	2.060390	0.02581	N	0.098904	D	0.89047	0.6604	N	0.14661	0.345	0.09310	N	1	D	0.62365	0.991	P	0.44447	0.45	T	0.82108	-0.0620	10	0.62326	D	0.03	2.1806	0.3007	0.00273	0.2519:0.1604:0.254:0.3337	.	365	Q8N9S7	CX059_HUMAN	P	365	ENSP00000367929:S365P;ENSP00000324767:S365P	ENSP00000324767:S365P	S	+	1	0	CXorf59	36066043	0.023000	0.18921	0.005000	0.12908	0.013000	0.08279	0.026000	0.13599	-0.859000	0.04105	-0.549000	0.04216	TCA	.	.		0.313	CHDC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_173695		C	36156122	T	C	36156122	3	2	263	1	0	0	0	0	1	0	0	0	4117	1783	62	2	1123	2	CXorf59	23	36156122	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	4658944	36156122	119114438	435	38809										
KDM5C	8242	hgsc.bcm.edu	37	chrX	53226132	53226132	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cccccagctgccgccccctcTccaacagggactgcagtagc	9	20	1	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chrX:53226132T>C	ENST00000375401.3	-	19	3249	c.2717A>G	c.(2716-2718)gAg>gGg	p.E906G	KDM5C_ENST00000375379.3_Missense_Mutation_p.E906G|KDM5C_ENST00000375383.3_Missense_Mutation_p.E865G|KDM5C_ENST00000404049.3_Missense_Mutation_p.E905G|KDM5C_ENST00000452825.3_Missense_Mutation_p.E839G	NM_001282622.1|NM_004187.3	NP_001269551.1|NP_004178.2	P41229	KDM5C_HUMAN	lysine (K)-specific demethylase 5C	906					histone H3-K4 demethylation (GO:0034720)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-K4 specific) (GO:0032453)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(30)|large_intestine(9)|lung(17)|oesophagus(1)|ovary(6)|prostate(1)|salivary_gland(1)|skin(1)|upper_aerodigestive_tract(2)	82						CCGCCCCCTCTCCAACAGGGA	0.667			"N, F, S"		clear cell renal carcinoma																																p.E906G		Atlas-SNP	.		Rec	yes		X	Xp11.22-p11.21	8242	lysine (K)-specific demethylase 5C (JARID1C)		E	.	KDM5C	385	.	0			c.A2717G						.						20	18	19					X																	53226132		2197	4291	6488	SO:0001583	missense	8242	exon19			CCCCTCTCCAACA	Z29650	CCDS14351.1, CCDS55417.1, CCDS65269.1	Xp11.22-p11.21	2014-01-31	2009-04-06	2009-04-06	ENSG00000126012	ENSG00000126012		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	11114	protein-coding gene	gene with protein product		314690	"Jumonji, AT rich interactive domain 1C (RBP2-like)", "Smcy homolog, X-linked (mouse)", "jumonji, AT rich interactive domain 1C", "mental retardation, X-linked 13"	SMCX, JARID1C, MRX13		7951230, 8162017, 19826449	Standard	NM_004187		Approved	DXS1272E, XE169	uc004drz.3	P41229	OTTHUMG00000021606	ENST00000375401.3:c.2717A>G	chrX.hg19:g.53226132T>C	ENSP00000364550:p.Glu906Gly	68.0	0.0		76.0	6.0	NM_004187	B0QZ44|B4E3I2|F5H3T1|Q5JUX3|Q5JUX4|Q5JUX5|Q7Z5S5	Missense_Mutation	SNP	ENST00000375401.3	hg19	CCDS14351.1	.	.	.	.	.	.	.	.	.	.	T	19.96	3.923702	0.73213	.	.	ENSG00000126012	ENST00000452825;ENST00000375401;ENST00000404049;ENST00000375379;ENST00000375383	T;T;T;T;T	0.53206	0.63;0.63;0.63;0.63;0.63	4.44	4.44	0.53790	Lysine-specific demethylase-like domain (1);	0.244325	0.38959	N	0.001501	T	0.60766	0.2294	M	0.80847	2.515	0.46654	D	0.99914	P;P;P	0.46142	0.846;0.873;0.873	P;P;P	0.51945	0.557;0.685;0.685	T	0.66085	-0.6011	10	0.72032	D	0.01	-11.5249	10.9016	0.47056	0.0:0.0:0.0:1.0	.	839;905;906	F5H3T1;B0QZ44;P41229	.;.;KDM5C_HUMAN	G	839;906;905;906;865	ENSP00000445176:E839G;ENSP00000364550:E906G;ENSP00000385394:E905G;ENSP00000364528:E906G;ENSP00000364532:E865G	ENSP00000364528:E906G	E	-	2	0	KDM5C	53242857	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	3.765000	0.55272	1.466000	0.48025	0.481000	0.45027	GAG	.	.		0.667	KDM5C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056737.2	NM_004187		C	53226132	T	C	53226132	3	2	263	1	0	0	0	0	1	0	0	0	8144	1551	54	2	2095	2	KDM5C	23	53226132	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	17070010	53226132	102044428	436	38810										
FOXR2	139628	hgsc.bcm.edu	37	chrX	55650773	55650773	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	agcattaagaaacaacccccActgtggcctcagtgtgcagg	10	12	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chrX:55650773A>G	ENST00000339140.3	+	1	941	c.629A>G	c.(628-630)cAc>cGc	p.H210R		NM_198451.3	NP_940853.1	Q6PJQ5	FOXR2_HUMAN	forkhead box R2	210					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|liver(1)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	19						AACAACCCCCACTGTGGCCTC	0.493																																					p.H210R		Atlas-SNP	.											.	FOXR2	42	.	0			c.A629G						.						86	82	83					X																	55650773		2203	4300	6503	SO:0001583	missense	139628	exon1			ACCCCCACTGTGG	BC012934	CCDS35308.1	Xp11	2006-12-15			ENSG00000189299	ENSG00000189299		"Forkhead boxes"	30469	protein-coding gene	gene with protein product						15202009, 15202027	Standard	NM_198451		Approved	MGC21658, FOXN6	uc004duo.3	Q6PJQ5	OTTHUMG00000021661	ENST00000339140.3:c.629A>G	chrX.hg19:g.55650773A>G	ENSP00000427329:p.His210Arg	59.0	0.0		86.0	4.0	NM_198451		Missense_Mutation	SNP	ENST00000339140.3	hg19	CCDS35308.1	.	.	.	.	.	.	.	.	.	.	A	3.516	-0.098815	0.07010	.	.	ENSG00000189299	ENST00000339140	D	0.95205	-3.64	3.26	0.147	0.14838	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.399896	0.24957	N	0.034244	D	0.82870	0.5131	N	0.04090	-0.28	0.09310	N	1	P	0.45283	0.855	B	0.41510	0.359	T	0.78534	-0.2167	10	0.34782	T	0.22	.	4.8913	0.13728	0.6006:0.2772:0.0:0.1221	.	210	Q6PJQ5	FOXR2_HUMAN	R	210	ENSP00000427329:H210R	ENSP00000427329:H210R	H	+	2	0	FOXR2	55667498	0.001000	0.12720	0.001000	0.08648	0.092000	0.18411	1.135000	0.31454	-0.075000	0.12798	-0.371000	0.07208	CAC	.	.		0.493	FOXR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056877.2	NM_198451		G	55650773	A	G	55650773	3	3	263	1	0	0	0	0	1	0	0	0	6040	159	6	2	631	2	FOXR2	23	55650773	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	2424641	55650773	99619787	437	38811										
PJA1	64219	hgsc.bcm.edu	37	chrX	68382107	68382107	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	tggtcactcctcgcttcccgTttgtcttcagggtactttgg	10	12	3	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chrX:68382107T>C	ENST00000361478.1	-	2	1352	c.975A>G	c.(973-975)aaA>aaG	p.K325K	PJA1_ENST00000374584.3_Silent_p.K137K|PJA1_ENST00000374583.1_Silent_p.K325K|PJA1_ENST00000477231.1_5'Flank|PJA1_ENST00000374571.4_Silent_p.K270K	NM_001032396.2|NM_022368.4|NM_145119.3	NP_001027568.1|NP_071763.2|NP_660095.1	Q8NG27	PJA1_HUMAN	praja ring finger 1, E3 ubiquitin protein ligase	325					protein catabolic process (GO:0030163)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(5)|lung(12)|ovary(1)	21						TCGCTTCCCGTTTGTCTTCAG	0.552																																					p.K325K		Atlas-SNP	.											.	PJA1	106	.	0			c.A975G						.						110	64	79					X																	68382107		2203	4300	6503	SO:0001819	synonymous_variant	64219	exon2			TTCCCGTTTGTCT	AK021892	CCDS14392.1, CCDS14393.1, CCDS35316.1	Xq13.1	2013-01-09	2012-02-23		ENSG00000181191	ENSG00000181191		"RING-type (C3HC4) zinc fingers"	16648	protein-coding gene	gene with protein product		300420	"praja 1", "praja ring finger 1"			12036302	Standard	NM_001032396		Approved	FLJ11830, RNF70	uc004dxh.3	Q8NG27	OTTHUMG00000021753	ENST00000361478.1:c.975A>G	chrX.hg19:g.68382107T>C		68.0	0.0		88.0	5.0	NM_145119	A2A322|Q5JUT8|Q5JUT9|Q8NG28|Q9HAC1	Silent	SNP	ENST00000361478.1	hg19	CCDS14393.1																																																																																			.	.		0.552	PJA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057031.2	NM_145119		C	68382107	T	C	68382107	2	2	263	1	0	0	0	0	0	0	0	1	11970	1722	60	2		2	PJA1	23	68382107	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	12731334	68382107	86888453	438	38812										
ERCC6L	54821	hgsc.bcm.edu	37	chrX	71426725	71426725	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ttacagagttctgaagatccTcgattgtaaagagctctctt	8	8	2	4			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chrX:71426725T>C	ENST00000334463.3	-	2	2027	c.1892A>G	c.(1891-1893)gAg>gGg	p.E631G	ERCC6L_ENST00000373657.1_Missense_Mutation_p.E508G|PIN4_ENST00000423432.2_Intron	NM_017669.2	NP_060139.2	Q2NKX8	ERC6L_HUMAN	excision repair cross-complementation group 6-like	631					mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			breast(2)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(9)|lung(9)|ovary(3)|skin(1)	38	Renal(35;0.156)					CTGAAGATCCTCGATTGTAAA	0.383																																					p.E631G		Atlas-SNP	.											.	ERCC6L	98	.	0			c.A1892G						.						67	63	64					X																	71426725		2203	4300	6503	SO:0001583	missense	54821	exon2			AGATCCTCGATTG	AK000112	CCDS35329.1	Xq13.1	2014-03-07	2014-03-07		ENSG00000186871	ENSG00000186871			20794	protein-coding gene	gene with protein product	"PLK1-interacting checkpoint helicase"	300687	"excision repair cross-complementing rodent repair deficiency, complementation group 6-like"			17218258	Standard	NM_017669		Approved	FLJ20105, PICH, RAD26L	uc004eaq.1	Q2NKX8	OTTHUMG00000021810	ENST00000334463.3:c.1892A>G	chrX.hg19:g.71426725T>C	ENSP00000334675:p.Glu631Gly	82.0	0.0		83.0	6.0	NM_017669	Q8NCI1|Q96H93|Q9NXQ8	Missense_Mutation	SNP	ENST00000334463.3	hg19	CCDS35329.1	.	.	.	.	.	.	.	.	.	.	T	8.600	0.886525	0.17540	.	.	ENSG00000186871	ENST00000373657;ENST00000334463	T;T	0.24908	1.83;1.83	5.46	-0.0729	0.13737	.	.	.	.	.	T	0.11922	0.0290	N	0.11364	0.135	0.35020	D	0.757755	B	0.12013	0.005	B	0.12156	0.007	T	0.26224	-1.0109	9	0.23302	T	0.38	-1.9592	9.0927	0.36621	0.0:0.4003:0.0:0.5997	.	631	Q2NKX8	ERC6L_HUMAN	G	508;631	ENSP00000362761:E508G;ENSP00000334675:E631G	ENSP00000334675:E631G	E	-	2	0	ERCC6L	71343450	1.000000	0.71417	0.753000	0.31225	0.978000	0.69477	2.744000	0.47450	-0.028000	0.13850	0.481000	0.45027	GAG	.	.		0.383	ERCC6L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057174.2	NM_017669		C	71426725	T	C	71426725	3	2	263	1	0	0	0	0	1	0	0	0	5220	1551	54	2	1864	2	ERCC6L	23	71426725	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	3044618	71426725	83843835	439	38813										
IL1RAPL2	26280	hgsc.bcm.edu	37	chrX	104728324	104728324	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	gctttactcacagacaagccTcccaagccattgttccccat	5	16	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chrX:104728324T>C	ENST00000372582.1	+	6	1473	c.717T>C	c.(715-717)ccT>ccC	p.P239P	IL1RAPL2_ENST00000344799.4_Silent_p.P239P	NM_017416.1	NP_059112.1	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2	239	Ig-like C2-type 3.				central nervous system development (GO:0007417)|cytokine-mediated signaling pathway (GO:0019221)	integral component of membrane (GO:0016021)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)			breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(23)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						CAGACAAGCCTCCCAAGCCAT	0.393																																					p.P239P		Atlas-SNP	.											.	IL1RAPL2	105	.	0			c.T717C						.						103	92	96					X																	104728324		2203	4300	6503	SO:0001819	synonymous_variant	26280	exon6			CAAGCCTCCCAAG	AF181285	CCDS14517.1	Xq22	2013-01-11			ENSG00000189108	ENSG00000189108		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5997	protein-coding gene	gene with protein product		300277				10757639	Standard	NM_017416		Approved	IL-1R9, TIGIRR-1, IL1RAPL-2, IL1R9	uc004elz.1	Q9NP60	OTTHUMG00000022141	ENST00000372582.1:c.717T>C	chrX.hg19:g.104728324T>C		180.0	0.0		431.0	23.0	NM_017416	Q2M3U3|Q9NZN0	Silent	SNP	ENST00000372582.1	hg19	CCDS14517.1																																																																																			.	.		0.393	IL1RAPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057785.1	NM_017416		C	104728324	T	C	104728324	2	2	263	1	0	0	0	0	0	0	0	1	7671	1538	54	2		2	IL1RAPL2	23	104728324	Silent	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	33301599	104728324	50542236	440	38814										
KIAA1210	57481	hgsc.bcm.edu	37	chrX	118221124	118221124	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	cttctcaccgctgctctgctTtacaggtacattcactgggc	8	14	3	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chrX:118221124T>C	ENST00000402510.2	-	11	4068	c.4069A>G	c.(4069-4071)Aag>Gag	p.K1357E		NM_020721.1	NP_065772.1	Q9ULL0	K1210_HUMAN	KIAA1210	1357										breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(31)|ovary(4)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	64						CTGCTCTGCTTTACAGGTACA	0.473																																					p.K1357E		Atlas-SNP	.											.	KIAA1210	171	.	0			c.A4069G						.						201	192	195					X																	118221124		1967	4139	6106	SO:0001583	missense	57481	exon11			TCTGCTTTACAGG	AB033036	CCDS48156.1	Xq24	2012-10-04			ENSG00000250423	ENSG00000250423			29218	protein-coding gene	gene with protein product						10574462	Standard	NM_020721		Approved		uc004era.4	Q9ULL0	OTTHUMG00000162980	ENST00000402510.2:c.4069A>G	chrX.hg19:g.118221124T>C	ENSP00000384670:p.Lys1357Glu	43.0	0.0		92.0	4.0	NM_020721	B7ZCI8|Q5JPN4	Missense_Mutation	SNP	ENST00000402510.2	hg19	CCDS48156.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.488|0.488	-0.876829|-0.876829	0.02550|0.02550	.|.	.|.	ENSG00000250423|ENSG00000248857	ENST00000402510|ENST00000440399	T|.	0.08370|.	3.1|.	4.34|4.34	-2.17|-2.17	0.07059|0.07059	.|.	.|.	.|.	.|.	.|.	T|T	0.13798|0.13798	0.0334|0.0334	N|N	0.05124|0.05124	-0.11|-0.11	0.09310|0.09310	N|N	1|1	B|.	0.12630|.	0.006|.	B|.	0.14023|.	0.01|.	T|T	0.27331|0.27331	-1.0077|-1.0077	9|5	0.07030|.	T|.	0.85|.	.|.	5.429|5.429	0.16442|0.16442	0.0:0.2972:0.155:0.5478|0.0:0.2972:0.155:0.5478	.|.	1357|.	Q9ULL0|.	K1210_HUMAN|.	E|R	1357|763	ENSP00000384670:K1357E|.	ENSP00000384670:K1357E|.	K|K	-|-	1|2	0|0	RP13-347D8.6|KIAA1210	118105152|118105152	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.003000|0.003000	0.03518|0.03518	-0.726000|-0.726000	0.04936|0.04936	-0.654000|-0.654000	0.05394|0.05394	-0.700000|-0.700000	0.03674|0.03674	AAG|AAA	.	.		0.473	KIAA1210-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371251.2	NM_020721		C	118221124	T	C	118221124	3	2	263	1	0	0	0	0	1	0	0	0	8223	1850	64	2	1076	2	KIAA1210	23	118221124	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	13492800	118221124	37049436	441	38815										
HCFC1	3054	hgsc.bcm.edu	37	chrX	153230097	153230097	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	accaaacaccaggaggcgagTcccgtcacacacgaagccat	9	15	1	0			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chrX:153230097T>C	ENST00000310441.7	-	2	1240	c.274A>G	c.(274-276)Act>Gct	p.T92A	HCFC1_ENST00000354233.3_Missense_Mutation_p.T92A|HCFC1_ENST00000461098.1_5'Flank|HCFC1_ENST00000369984.4_Missense_Mutation_p.T92A	NM_005334.2	NP_005325.2	P51610	HCFC1_HUMAN	host cell factor C1	92					cell cycle (GO:0007049)|chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein stabilization (GO:0050821)|regulation of protein complex assembly (GO:0043254)|regulation of transcription, DNA-templated (GO:0006355)|release from viral latency (GO:0019046)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|membrane (GO:0016020)|mitochondrion (GO:0005739)|MLL1 complex (GO:0071339)|MLL5-L complex (GO:0070688)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(3)|large_intestine(3)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					AGGAGGCGAGTCCCGTCACAC	0.582																																					p.T92A		Atlas-SNP	.											.	HCFC1	284	.	0			c.A274G						.						116	127	123					X																	153230097		2162	4245	6407	SO:0001583	missense	3054	exon2			GGCGAGTCCCGTC		CCDS44020.1	Xq28	2014-06-12	2014-06-09		ENSG00000172534	ENSG00000172534			4839	protein-coding gene	gene with protein product	"VP16-accessory protein", "protein phosphatase 1, regulatory subunit 89"	300019	"mental retardation, X-linked 3", "host cell factor C1 (VP16-accessory protein)"	HFC1, MRX3		8392914, 23000143	Standard	XM_005274664		Approved	HCF-1, HCF1, CFF, VCAF, MGC70925, PPP1R89	uc004fjp.3	P51610	OTTHUMG00000024222	ENST00000310441.7:c.274A>G	chrX.hg19:g.153230097T>C	ENSP00000309555:p.Thr92Ala	97.0	0.0		250.0	11.0	NM_005334	Q6P4G5	Missense_Mutation	SNP	ENST00000310441.7	hg19	CCDS44020.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.582380	0.86748	.	.	ENSG00000172534	ENST00000310441;ENST00000369984;ENST00000354233	T;T;T	0.66460	-0.21;-0.21;1.0	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	D	0.82986	0.5156	M	0.87328	2.875	0.58432	D	0.999997	D	0.61697	0.99	D	0.71870	0.975	D	0.85997	0.1492	10	0.72032	D	0.01	.	13.4587	0.61214	0.0:0.0:0.0:1.0	.	92	P51610	HCFC1_HUMAN	A	92	ENSP00000309555:T92A;ENSP00000359001:T92A;ENSP00000346174:T92A	ENSP00000309555:T92A	T	-	1	0	HCFC1	152883291	1.000000	0.71417	0.597000	0.28824	0.948000	0.59901	7.607000	0.82883	1.821000	0.53095	0.381000	0.24937	ACT	.	.		0.582	HCFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061099.4	NM_005334		C	153230097	T	C	153230097	3	2	263	1	0	0	0	0	1	0	0	0	7000	1667	58	2	5933	2	HCFC1	23	153230097	Missense_Mutation	SNP	T	TCGA-FV-A2QR-01A-11D-A20W-10	35008973	153230097	2040463	442	38816										
G6PD	2539	hgsc.bcm.edu	37	chrX	153774307	153774307	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ctgatggaaggcatcgccctGgaaaagctcttcccgcagga	12	12	1	1			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chrX:153774307G>A	ENST00000393564.2	-	2	176	c.64C>T	c.(64-66)Cag>Tag	p.Q22*	IKBKG_ENST00000369609.5_Intron|G6PD_ENST00000393562.2_Nonsense_Mutation_p.Q52*|IKBKG_ENST00000263518.6_5'Flank|IKBKG_ENST00000369601.3_5'Flank|IKBKG_ENST00000470142.1_5'Flank|IKBKG_ENST00000393549.2_5'Flank|G6PD_ENST00000497281.1_5'UTR|IKBKG_ENST00000455588.2_5'Flank|IKBKG_ENST00000369602.3_5'Flank|IKBKG_ENST00000369606.4_5'Flank|IKBKG_ENST00000369607.1_Intron|G6PD_ENST00000369620.2_Nonsense_Mutation_p.Q22*	NM_001042351.1	NP_001035810.1	P11413	G6PD_HUMAN	glucose-6-phosphate dehydrogenase	22					carbohydrate metabolic process (GO:0005975)|cellular response to oxidative stress (GO:0034599)|cholesterol biosynthetic process (GO:0006695)|cytokine production (GO:0001816)|erythrocyte maturation (GO:0043249)|glucose 6-phosphate metabolic process (GO:0051156)|glutathione metabolic process (GO:0006749)|lipid metabolic process (GO:0006629)|NADP metabolic process (GO:0006739)|NADPH regeneration (GO:0006740)|negative regulation of protein glutathionylation (GO:0010734)|oxidation-reduction process (GO:0055114)|pentose biosynthetic process (GO:0019322)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, oxidative branch (GO:0009051)|regulation of neuron apoptotic process (GO:0043523)|response to ethanol (GO:0045471)|response to food (GO:0032094)|response to organic cyclic compound (GO:0014070)|ribose phosphate biosynthetic process (GO:0046390)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	glucose binding (GO:0005536)|glucose-6-phosphate dehydrogenase activity (GO:0004345)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(3)|ovary(4)	18	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GCATCGCCCTGGAAAAGCTCT	0.562																																					p.Q52X		Atlas-SNP	.											.	G6PD	73	.	0			c.C154T						.						161	143	149					X																	153774307		2203	4300	6503	SO:0001587	stop_gained	2539	exon2			CGCCCTGGAAAAG	X03674	CCDS14756.2, CCDS44023.1	Xq28	2014-09-17			ENSG00000160211	ENSG00000160211	1.1.1.49		4057	protein-coding gene	gene with protein product		305900				3012556, 2428611	Standard	NM_000402		Approved	G6PD1	uc004flx.1	P11413	OTTHUMG00000024237	ENST00000393564.2:c.64C>T	chrX.hg19:g.153774307G>A	ENSP00000377194:p.Gln22*	33.0	0.0		60.0	4.0	NM_000402	D3DWX9|Q16000|Q16765|Q8IU70|Q8IU88|Q8IUA6|Q96PQ2	Nonsense_Mutation	SNP	ENST00000393564.2	hg19	CCDS44023.1	.	.	.	.	.	.	.	.	.	.	G	32	5.178082	0.94846	.	.	ENSG00000160211	ENST00000393562;ENST00000291567;ENST00000393564;ENST00000369620;ENST00000439227;ENST00000440967;ENST00000433845	.	.	.	5.78	5.78	0.91487	.	0.318081	0.34223	N	0.004148	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.36615	T	0.2	.	14.2085	0.65750	0.0:0.0:1.0:0.0	.	.	.	.	X	52;22;22;22;22;22;22	.	ENSP00000291567:Q22X	Q	-	1	0	G6PD	153427501	1.000000	0.71417	1.000000	0.80357	0.109000	0.19521	5.134000	0.64770	2.429000	0.82318	0.600000	0.82982	CAG	.	.		0.562	G6PD-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061170.3	NM_000402		A	153774307	G	A	153774307	4	1	263	1	0	0	0	0	0	1	0	0	6154	1357	47	3	1531	3	G6PD	23	153774307	Nonsense_Mutation	SNP	G	TCGA-FV-A2QR-01A-11D-A20W-10	544210	153774307	1496253	443	38817										
USP9Y	8287	hgsc.bcm.edu	37	chrY	14928278	14928278	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ggatgagaagcaggacagtgAggtaaattttaatactgttt	12	3	0	2			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chrY:14928278A>G	ENST00000338981.3	+	32	5774	c.4829A>G	c.(4828-4830)gAg>gGg	p.E1610G	USP9Y_ENST00000426564.2_3'UTR	NM_004654.3	NP_004645.2	O00507	USP9Y_HUMAN	ubiquitin specific peptidase 9, Y-linked	1610	USP.				BMP signaling pathway (GO:0030509)|protein deubiquitination (GO:0016579)|spermatogenesis (GO:0007283)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)	co-SMAD binding (GO:0070410)|cysteine-type peptidase activity (GO:0008234)|ubiquitin-specific protease activity (GO:0004843)			kidney(1)|large_intestine(8)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						CAGGACAGTGAGGTAAATTTT	0.388																																					p.E1610G		Atlas-SNP	.											.	USP9Y	49	.	0			c.A4829G						.						38	37	37					Y																	14928278		583	1911	2494	SO:0001630	splice_region_variant	8287	exon32			ACAGTGAGGTAAA	Y13618	CCDS14781.1	Yq11.2	2010-04-09	2009-03-17		ENSG00000114374	ENSG00000114374		"Ubiquitin-specific peptidases"	12633	protein-coding gene	gene with protein product	"fat facets-like homolog (Drosophila)"	400005	"ubiquitin specific peptidase 9, Y-linked (fat facets-like, Drosophila)"			8922996, 9384609, 19246359	Standard	NM_004654		Approved	DFFRY	uc004fst.1	O00507	OTTHUMG00000036469	ENST00000338981.3:c.4830+1A>G	chrY.hg19:g.14928278A>G		54.0	0.0		87.0	4.0	NM_004654	O14601	Missense_Mutation	SNP	ENST00000338981.3	hg19	CCDS14781.1																																																																																			.	.		0.388	USP9Y-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088703.2	NM_004654	Missense_Mutation	G	14928278	A	G	14928278	5	3	263	1	0	0	0	0	0	0	1	0	17106	318	11	2	4947	2	USP9Y	24	14928278	Splice_Site	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10		14928278	44445288	444	38818										
USP9Y	8287	hgsc.bcm.edu	37	chrY	14951989	14951989	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0338600451467269	15	1	1.27603502507864	3.06248406018873	0.765621015047182	1	1	0	ggataatgtaaactcagaaaAtgagttgattgaacagaaag	10	3	1	5			TCGA-FV-A2QR-01A-11D-A20W-10	TCGA-FV-A2QR-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34b26fff-981d-4f15-b59f-68a9208af0f5	39ada55b-dcea-4e2e-81da-374a3020c56e	g.chrY:14951989A>G	ENST00000338981.3	+	36	6482	c.5537A>G	c.(5536-5538)aAt>aGt	p.N1846S	USP9Y_ENST00000426564.2_3'UTR	NM_004654.3	NP_004645.2	O00507	USP9Y_HUMAN	ubiquitin specific peptidase 9, Y-linked	1846	USP.				BMP signaling pathway (GO:0030509)|protein deubiquitination (GO:0016579)|spermatogenesis (GO:0007283)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)	co-SMAD binding (GO:0070410)|cysteine-type peptidase activity (GO:0008234)|ubiquitin-specific protease activity (GO:0004843)			kidney(1)|large_intestine(8)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						AACTCAGAAAATGAGTTGATT	0.418																																					p.N1846S		Atlas-SNP	.											.	USP9Y	49	.	0			c.A5537G						.						77	68	70					Y																	14951989		593	1952	2545	SO:0001583	missense	8287	exon36			CAGAAAATGAGTT	Y13618	CCDS14781.1	Yq11.2	2010-04-09	2009-03-17		ENSG00000114374	ENSG00000114374		"Ubiquitin-specific peptidases"	12633	protein-coding gene	gene with protein product	"fat facets-like homolog (Drosophila)"	400005	"ubiquitin specific peptidase 9, Y-linked (fat facets-like, Drosophila)"			8922996, 9384609, 19246359	Standard	NM_004654		Approved	DFFRY	uc004fst.1	O00507	OTTHUMG00000036469	ENST00000338981.3:c.5537A>G	chrY.hg19:g.14951989A>G	ENSP00000342812:p.Asn1846Ser	48.0	0.0		68.0	4.0	NM_004654	O14601	Missense_Mutation	SNP	ENST00000338981.3	hg19	CCDS14781.1																																																																																			.	.		0.418	USP9Y-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088703.2	NM_004654		G	14951989	A	G	14951989	3	3	263	1	0	0	0	0	1	0	0	0	17106	101	4	2	5671	2	USP9Y	24	14951989	Missense_Mutation	SNP	A	TCGA-FV-A2QR-01A-11D-A20W-10	23711	14951989	44421577	445	38819										
SH3GLB1	51100	hgsc.bcm.edu	37	chr1	87170595	87170595	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	cgcctaggatgaatatcatgGacttcaacgtgaagaagctg	11	8	2	3			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr1:87170595G>A	ENST00000370558.4	+	1	337	c.13G>A	c.(13-15)Gac>Aac	p.D5N	SH3GLB1_ENST00000482504.1_Missense_Mutation_p.D5N|SH3GLB1_ENST00000535010.1_5'UTR|RP4-612B15.3_ENST00000565575.1_RNA	NM_001206651.1|NM_001206653.1|NM_016009.4	NP_001193580.1|NP_001193582.1|NP_057093.1	Q9Y371	SHLB1_HUMAN	SH3-domain GRB2-like endophilin B1	5	Membrane-binding amphipathic helix.				'de novo' posttranslational protein folding (GO:0051084)|apoptotic process (GO:0006915)|phosphatidic acid biosynthetic process (GO:0006654)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrial outer membrane (GO:0005741)|protein complex (GO:0043234)	fatty acid binding (GO:0005504)|identical protein binding (GO:0042802)|lysophosphatidic acid acyltransferase activity (GO:0042171)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|stomach(1)	11		Lung NSC(277;0.209)		all cancers(265;0.0136)|Epithelial(280;0.0414)		GAATATCATGGACTTCAACGT	0.726																																					p.D5N		Atlas-SNP	.											.	SH3GLB1	57	.	0			c.G13A						.						13	15	14					1																	87170595		2199	4291	6490	SO:0001583	missense	51100	exon1			ATCATGGACTTCA	AF263293	CCDS710.1, CCDS55612.1, CCDS55613.1, CCDS72819.1	1p22.3	2012-04-17	2001-12-04		ENSG00000097033	ENSG00000097033		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	10833	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 70"	609287	"SH3-domain, GRB2-like, endophilin B1"			11161816, 11259440	Standard	NM_016009		Approved	CGI-61, KIAA0491, Bif-1, PPP1R70	uc001dly.3	Q9Y371	OTTHUMG00000010257	ENST00000370558.4:c.13G>A	chr1.hg19:g.87170595G>A	ENSP00000473267:p.Asp5Asn	4.0	0.0		13.0	8.0	NM_001206652	B4E182|Q5H8U5|Q9H3Z0|Q9NR47|Q9NYA9	Missense_Mutation	SNP	ENST00000370558.4	hg19	CCDS710.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.658029	0.88154	.	.	ENSG00000097033	ENST00000212369;ENST00000482504	T	0.39229	1.09	4.75	4.75	0.60458	.	0.000000	0.85682	D	0.000000	T	0.43787	0.1263	L	0.57536	1.79	0.80722	D	1	D;P	0.55385	0.971;0.546	P;B	0.55749	0.783;0.21	T	0.28554	-1.0040	10	0.34782	T	0.22	-3.5255	15.9302	0.79654	0.0:0.0:1.0:0.0	.	5;5	Q9Y371-2;Q9Y371	.;SHLB1_HUMAN	N	5	ENSP00000418744:D5N	ENSP00000212369:D5N	D	+	1	0	SH3GLB1	86943183	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	5.699000	0.68310	2.161000	0.67846	0.561000	0.74099	GAC	.	.		0.726	SH3GLB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028287.2	NM_016009		A	87170595	G	A	87170595	3	1	264	1	0	0	0	0	1	0	0	0	14268	1174	41	3	15	3	SH3GLB1	1	87170595	Missense_Mutation	SNP	G	TCGA-FV-A3I0-01A-11D-A22F-10		87170595	162080026	1	38820										
FLG2	388698	hgsc.bcm.edu	37	chr1	152327575	152327575	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	cagtcccatgttgtccaaagCcactggactgacctgagcct	9	14	0	2			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr1:152327575C>T	ENST00000388718.5	-	3	2759	c.2687G>A	c.(2686-2688)gGc>gAc	p.G896D	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000445097.1_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	896	Ser-rich.				establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TTGTCCAAAGCCACTGGACTG	0.493																																					p.G896D		Atlas-SNP	.											.,1	FLG2	431	.	0			c.G2687A						.						308	266	281					1																	152327575		2198	4262	6460	SO:0001583	missense	388698	exon3			CCAAAGCCACTGG	AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"EF-hand domain containing"	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.2687G>A	chr1.hg19:g.152327575C>T	ENSP00000373370:p.Gly896Asp	152.0	0.0		162.0	30.0	NM_001014342	Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	hg19	CCDS30861.1	.	.	.	.	.	.	.	.	.	.	C	4.843	0.156628	0.09236	.	.	ENSG00000143520	ENST00000388718	T	0.03831	3.79	4.05	3.11	0.35812	.	.	.	.	.	T	0.01800	0.0057	L	0.56769	1.78	0.09310	N	1	P	0.41978	0.767	B	0.33846	0.171	T	0.43310	-0.9399	9	0.19147	T	0.46	-2.7266	9.8431	0.41010	0.0:0.8945:0.0:0.1055	.	896	Q5D862	FILA2_HUMAN	D	896	ENSP00000373370:G896D	ENSP00000373370:G896D	G	-	2	0	FLG2	150594199	0.000000	0.05858	0.003000	0.11579	0.005000	0.04900	-0.023000	0.12456	2.111000	0.64477	0.650000	0.86243	GGC	.	.		0.493	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		T	152327575	C	T	152327575	3	4	264	1	0	0	0	0	1	0	0	0	5931	739	26	3	4492	3	FLG2	1	152327575	Missense_Mutation	SNP	C	TCGA-FV-A3I0-01A-11D-A22F-10	65156980	152327575	96923046	2	38821										
S100A7	6278	hgsc.bcm.edu	37	chr1	153430321	153430321	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	cagggcgctgctccatggctCtgcttgtggtagtctgtggc	15	11	2	0			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr1:153430321C>A	ENST00000368723.3	-	3	377	c.267G>T	c.(265-267)caG>caT	p.Q89H	S100A7_ENST00000368722.1_Missense_Mutation_p.Q89H	NM_002963.3	NP_002954.2	P31151	S10A7_HUMAN	S100 calcium binding protein A7	89					angiogenesis (GO:0001525)|defense response to Gram-negative bacterium (GO:0050829)|epidermis development (GO:0008544)|innate immune response (GO:0045087)|keratinocyte differentiation (GO:0030216)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of granulocyte chemotaxis (GO:0071624)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of T cell chemotaxis (GO:0010820)|response to lipopolysaccharide (GO:0032496)|response to reactive oxygen species (GO:0000302)|sequestering of metal ion (GO:0051238)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|RAGE receptor binding (GO:0050786)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(2)|lung(5)|skin(2)	10	all_lung(78;2.4e-33)|Lung NSC(65;8.13e-32)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			CTCCATGGCTCTGCTTGTGGT	0.522																																					p.Q89H		Atlas-SNP	.											.	S100A7	23	.	0			c.G267T						.						89	81	83					1																	153430321		2203	4300	6503	SO:0001583	missense	6278	exon3			ATGGCTCTGCTTG	BC034687	CCDS1039.1	1q21	2013-01-10	2006-09-11		ENSG00000143556	ENSG00000143556		"S100 calcium binding proteins", "EF-hand domain containing"	10497	protein-coding gene	gene with protein product		600353	"S100 calcium-binding protein A7 (psoriasin 1)", "S100 calcium binding protein A7 (psoriasin 1)"	PSOR1		1940442	Standard	NM_002963		Approved	S100A7c	uc001fbv.1	P31151	OTTHUMG00000013123	ENST00000368723.3:c.267G>T	chr1.hg19:g.153430321C>A	ENSP00000357712:p.Gln89His	199.0	0.0		199.0	35.0	NM_002963	Q5SY67|Q6FGE3|Q9H1E2	Missense_Mutation	SNP	ENST00000368723.3	hg19	CCDS1039.1	.	.	.	.	.	.	.	.	.	.	.	1.191	-0.635439	0.03584	.	.	ENSG00000143556	ENST00000368723;ENST00000368722	T;T	0.06528	3.29;3.29	2.15	-1.25	0.09405	EF-hand-like domain (1);	.	.	.	.	T	0.01061	0.0035	N	0.24115	0.695	0.09310	N	1	B	0.13594	0.008	B	0.08055	0.003	T	0.47446	-0.9117	9	0.25106	T	0.35	.	4.8606	0.13581	0.0:0.4455:0.4112:0.1433	.	89	P31151	S10A7_HUMAN	H	89	ENSP00000357712:Q89H;ENSP00000357711:Q89H	ENSP00000357711:Q89H	Q	-	3	2	S100A7	151696945	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-0.992000	0.03724	-0.385000	0.07833	-1.050000	0.02344	CAG	.	.		0.522	S100A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036789.1	NM_002963		A	153430321	C	A	153430321	3	1	264	1	0	0	0	0	1	0	0	0	13798	912	32	3	42	3	S100A7	1	153430321	Missense_Mutation	SNP	C	TCGA-FV-A3I0-01A-11D-A22F-10	1102746	153430321	95820300	3	38822										
DUSP27	92235	hgsc.bcm.edu	37	chr1	167096333	167096333	+	Silent	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	gacagctccacggccagcggGagcattcccctgtctgcgtt	12	15	1	0			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr1:167096333G>C	ENST00000361200.2	+	6	2131	c.1965G>C	c.(1963-1965)ggG>ggC	p.G655G	DUSP27_ENST00000485151.1_Intron|DUSP27_ENST00000271385.5_Silent_p.G655G|DUSP27_ENST00000443333.1_Silent_p.G655G			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	655					protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						CGGCCAGCGGGAGCATTCCCC	0.642																																					p.G655G		Atlas-SNP	.											.	DUSP27	235	.	0			c.G1965C						.						46	41	43					1																	167096333		2203	4300	6503	SO:0001819	synonymous_variant	92235	exon5			CAGCGGGAGCATT	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.1965G>C	chr1.hg19:g.167096333G>C		69.0	0.0		92.0	17.0	NM_001080426	A0AUM4|Q9C074	Silent	SNP	ENST00000361200.2	hg19	CCDS30932.1																																																																																			.	.		0.642	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426		C	167096333	G	C	167096333	2	2	264	1	0	0	0	0	0	0	0	1	4826	1161	41	4		4	DUSP27	1	167096333	Silent	SNP	G	TCGA-FV-A3I0-01A-11D-A22F-10	13666012	167096333	82154288	4	38823										
FAIM3	9214	hgsc.bcm.edu	37	chr1	207083133	207083133	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	gatgttgttttgggagcgcgGtcgcggcgacccgcggggcc	19	11	0	0			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr1:207083133G>T	ENST00000367091.3	-	6	1065	c.922C>A	c.(922-924)Ccg>Acg	p.P308T	FAIM3_ENST00000420007.2_Missense_Mutation_p.T264N|FAIM3_ENST00000442471.2_Missense_Mutation_p.P196T|FAIM3_ENST00000528654.1_Intron	NM_005449.4	NP_005440.1	O60667	FAIM3_HUMAN	Fas apoptotic inhibitory molecule 3	308	Arg-rich.				cellular defense response (GO:0006968)|immune system process (GO:0002376)|negative regulation of apoptotic process (GO:0043066)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	15	Breast(84;0.201)					TGGGAGCGCGGTCGCGGCGAC	0.741																																					p.P308T		Atlas-SNP	.											.	FAIM3	36	.	0			c.C922A						.																																			SO:0001583	missense	9214	exon6			AGCGCGGTCGCGG	AF057557	CCDS1473.1, CCDS44304.1	1q32.1	2013-01-11			ENSG00000162894	ENSG00000162894		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14315	protein-coding gene	gene with protein product		606015				9586636, 1563211	Standard	NM_005449		Approved	TOSO	uc001hey.3	O60667	OTTHUMG00000036457	ENST00000367091.3:c.922C>A	chr1.hg19:g.207083133G>T	ENSP00000356058:p.Pro308Thr	0.0	0.0		8.0	7.0	NM_005449	A8K7J2|B7Z6Z0|D9MWM3	Missense_Mutation	SNP	ENST00000367091.3	hg19	CCDS1473.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.135|7.135	0.580590|0.580590	0.13686|0.13686	.|.	.|.	ENSG00000162894|ENSG00000162894	ENST00000367091;ENST00000442471|ENST00000420007	T|T	0.30182|0.25250	1.54|1.81	4.03|4.03	2.0|2.0	0.26442|0.26442	.|.	0.680688|.	0.12822|.	N|.	0.436345|.	T|T	0.28732|0.28732	0.0712|0.0712	L|L	0.48642|0.48642	1.525|1.525	0.09310|0.09310	N|N	1|1	P;P;P|.	0.47762|.	0.9;0.9;0.839|.	P;P;B|.	0.44477|.	0.451;0.451;0.264|.	T|T	0.16335|0.16335	-1.0406|-1.0406	10|7	0.72032|0.51188	D|T	0.01|0.08	-4.1866|-4.1866	8.9996|8.9996	0.36074|0.36074	0.0:0.0:0.6046:0.3954|0.0:0.0:0.6046:0.3954	.|.	217;196;308|.	B7Z497;B7Z6Z0;O60667|.	.;.;FAIM3_HUMAN|.	T|N	308;196|264	ENSP00000356058:P308T|ENSP00000403356:T264N	ENSP00000356058:P308T|ENSP00000403356:T264N	P|T	-|-	1|2	0|0	FAIM3|FAIM3	205149756|205149756	0.030000|0.030000	0.19436|0.19436	0.818000|0.818000	0.32626|0.32626	0.056000|0.056000	0.15407|0.15407	0.927000|0.927000	0.28818|0.28818	0.885000|0.885000	0.36088|0.36088	-0.268000|-0.268000	0.10319|0.10319	CCG|ACC	.	.		0.741	FAIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088677.1	NM_005449		T	207083133	G	T	207083133	3	4	264	1	0	0	0	0	1	0	0	0	5382	1261	44	3	262	3	FAIM3	1	207083133	Missense_Mutation	SNP	G	TCGA-FV-A3I0-01A-11D-A22F-10	39986800	207083133	42167488	5	38824										
USH2A	7399	hgsc.bcm.edu	37	chr1	215932017	215932017	+	Nonsense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	gatagatttcttctggtgttGacataggtgtttgaacaatg	11	4	2	3			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr1:215932017G>C	ENST00000307340.3	-	58	11695	c.11309C>G	c.(11308-11310)tCa>tGa	p.S3770*	USH2A_ENST00000366943.2_Nonsense_Mutation_p.S3770*	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3770	Fibronectin type-III 22. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			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)		TTCTGGTGTTGACATAGGTGT	0.333										HNSCC(13;0.011)																											p.S3770X		Atlas-SNP	.											.	USH2A	1168	.	0			c.C11309G						.						176	174	175					1																	215932017		2203	4300	6503	SO:0001587	stop_gained	7399	exon58			GGTGTTGACATAG	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.11309C>G	chr1.hg19:g.215932017G>C	ENSP00000305941:p.Ser3770*	94.0	0.0		82.0	12.0	NM_206933	Q5VVM9|Q6S362|Q9NS27	Nonsense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	G	52	19.742314	0.99923	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	.	.	.	5.68	-7.82	0.01205	.	1.983460	0.03128	N	0.164734	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07813	T	0.8	.	15.1906	0.73041	0.1031:0.4361:0.4607:0.0	.	.	.	.	X	3770	.	ENSP00000305941:S3770X	S	-	2	0	USH2A	213998640	0.000000	0.05858	0.000000	0.03702	0.286000	0.27126	-0.264000	0.08658	-1.017000	0.03367	-0.353000	0.07706	TCA	.	.		0.333	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		C	215932017	G	C	215932017	4	2	264	1	0	0	0	0	0	1	0	0	17051	1294	45	4	4359	4	USH2A	1	215932017	Nonsense_Mutation	SNP	G	TCGA-FV-A3I0-01A-11D-A22F-10	8848884	215932017	33318604	6	38825										
USH2A	7399	hgsc.bcm.edu	37	chr1	216495239	216495239	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	actcacatgaagtccttcagTgaagctctcctgggagcaga	10	11	3	3			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr1:216495239T>C	ENST00000307340.3	-	9	2016	c.1630A>G	c.(1630-1632)Act>Gct	p.T544A	USH2A_ENST00000366942.3_Missense_Mutation_p.T544A|USH2A_ENST00000366943.2_Missense_Mutation_p.T544A	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	544	Laminin EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00460}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			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)		AGTCCTTCAGTGAAGCTCTCC	0.413										HNSCC(13;0.011)																											p.T544A		Atlas-SNP	.											.	USH2A	1168	.	0			c.A1630G						.						153	141	145					1																	216495239		2203	4300	6503	SO:0001583	missense	7399	exon9			CTTCAGTGAAGCT	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.1630A>G	chr1.hg19:g.216495239T>C	ENSP00000305941:p.Thr544Ala	172.0	0.0		121.0	92.0	NM_007123	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	T	19.37	3.815269	0.70912	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	T;T;T	0.63580	-0.05;-0.05;-0.05	5.65	4.49	0.54785	EGF-like, laminin (3);	0.000000	0.43579	U	0.000554	D	0.83229	0.5209	M	0.93594	3.435	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.996;0.998	D	0.86437	0.1764	10	0.87932	D	0	.	12.6812	0.56922	0.0:0.0:0.1379:0.8621	.	544;544	O75445-2;O75445	.;USH2A_HUMAN	A	544	ENSP00000305941:T544A;ENSP00000355910:T544A;ENSP00000355909:T544A	ENSP00000305941:T544A	T	-	1	0	USH2A	214561862	1.000000	0.71417	0.960000	0.40013	0.643000	0.38383	4.814000	0.62627	0.911000	0.36747	0.455000	0.32223	ACT	.	.		0.413	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		C	216495239	T	C	216495239	3	2	264	1	0	0	0	0	1	0	0	0	17051	1696	59	2	14248	2	USH2A	1	216495239	Missense_Mutation	SNP	T	TCGA-FV-A3I0-01A-11D-A22F-10	563222	216495239	32755382	7	38826										
SMC6	79677	hgsc.bcm.edu	37	chr2	17877588	17877588	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	ctctttcatatccagttctcGtttctttttatttaaggtat	4	8	4	0			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr2:17877588G>A	ENST00000448223.2	-	22	2769	c.2500C>T	c.(2500-2502)Cga>Tga	p.R834*	SMC6_ENST00000351948.4_Nonsense_Mutation_p.R834*|SMC6_ENST00000381272.4_Nonsense_Mutation_p.R860*|SMC6_ENST00000402989.1_Nonsense_Mutation_p.R834*	NM_001142286.1	NP_001135758.1	Q96SB8	SMC6_HUMAN	structural maintenance of chromosomes 6	834					cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|intracellular (GO:0005622)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			NS(1)|biliary_tract(1)|breast(6)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TCCAGTTCTCGTTTCTTTTTA	0.318																																					p.R834X		Atlas-SNP	.											.	SMC6	102	.	0			c.C2500T						.						145	140	142					2																	17877588		2202	4300	6502	SO:0001587	stop_gained	79677	exon22			GTTCTCGTTTCTT	AJ310551	CCDS1690.1	2p24.3	2008-02-05	2006-07-06	2006-07-06	ENSG00000163029	ENSG00000163029		"Structural maintenance of chromosomes proteins"	20466	protein-coding gene	gene with protein product		609387	"SMC6 structural maintenance of chromosomes 6-like 1 (yeast)"	SMC6L1		11230166	Standard	NM_024624		Approved	FLJ22116	uc002rcn.3	Q96SB8	OTTHUMG00000090675	ENST00000448223.2:c.2500C>T	chr2.hg19:g.17877588G>A	ENSP00000404092:p.Arg834*	139.0	0.0		111.0	18.0	NM_001142286	A8K8Q6|D6W518|Q05BV4|Q9H0X3|Q9H6M0	Nonsense_Mutation	SNP	ENST00000448223.2	hg19	CCDS1690.1	.	.	.	.	.	.	.	.	.	.	G	41	9.072005	0.99055	.	.	ENSG00000163029	ENST00000448223;ENST00000351948;ENST00000381272;ENST00000402989	.	.	.	5.27	2.02	0.26589	.	0.424462	0.24703	N	0.036291	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08837	T	0.75	.	7.1425	0.25564	0.0:0.2992:0.3276:0.3732	.	.	.	.	X	834;834;860;834	.	ENSP00000323439:R834X	R	-	1	2	SMC6	17741069	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	0.408000	0.21065	0.652000	0.30806	0.591000	0.81541	CGA	.	.		0.318	SMC6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207359.1	NM_024624		A	17877588	G	A	17877588	4	1	264	1	0	0	0	0	0	1	0	0	14802	1153	40	1	803	1	SMC6	2	17877588	Nonsense_Mutation	SNP	G	TCGA-FV-A3I0-01A-11D-A22F-10		17877588	225321785	8	38827										
DPYSL5	56896	hgsc.bcm.edu	37	chr2	27156166	27156166	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	ggtcaacgtgtccagtatctCggctggtgacgttatcgcag	13	10	2	1	rs372829541		TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr2:27156166C>T	ENST00000288699.6	+	7	913	c.755C>T	c.(754-756)tCg>tTg	p.S252L	DPYSL5_ENST00000401478.1_Missense_Mutation_p.S252L	NM_001253724.1|NM_020134.3	NP_001240653.1|NP_064519.2	Q9BPU6	DPYL5_HUMAN	dihydropyrimidinase-like 5	252					axon guidance (GO:0007411)|nervous system development (GO:0007399)|pyrimidine nucleobase catabolic process (GO:0006208)|signal transduction (GO:0007165)	cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)	p.S252L(1)		breast(1)|endometrium(5)|large_intestine(2)|lung(13)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	27	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCCAGTATCTCGGCTGGTGAC	0.517																																					p.S252L		Atlas-SNP	.											DPYSL5,NS,carcinoma,0,1	DPYSL5	69	.	1	Substitution - Missense(1)	lung(1)	c.C755T						.	C	LEU/SER	0,4406		0,0,2203	246	178	201		755	6	1	2		201	1,8599	1.2+/-3.3	0,1,4299	no	missense	DPYSL5	NM_020134.3	145	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	252/565	27156166	1,13005	2203	4300	6503	SO:0001583	missense	56896	exon7			GTATCTCGGCTGG	AF264015	CCDS1730.1	2p23.3	2008-02-05			ENSG00000157851	ENSG00000157851			20637	protein-coding gene	gene with protein product		608383				10851247, 11034345	Standard	NM_020134		Approved	CRMP5, Ulip6, CRMP-5, CRAM	uc002rhu.4	Q9BPU6	OTTHUMG00000097071	ENST00000288699.6:c.755C>T	chr2.hg19:g.27156166C>T	ENSP00000288699:p.Ser252Leu	119.0	0.0		118.0	55.0	NM_001253724	Q8TCL6|Q9NQC4|Q9NRY9	Missense_Mutation	SNP	ENST00000288699.6	hg19	CCDS1730.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.303258	0.81136	0.0	1.16E-4	ENSG00000157851	ENST00000288699;ENST00000401478	D;D	0.90385	-2.66;-2.66	6.04	6.04	0.98038	Amidohydrolase 1 (1);	0.110781	0.64402	D	0.000007	D	0.87212	0.6121	L	0.48174	1.505	0.46478	D	0.999068	P	0.40360	0.714	B	0.31390	0.129	D	0.87568	0.2476	10	0.54805	T	0.06	-9.1882	19.3507	0.94384	0.0:1.0:0.0:0.0	.	252	Q9BPU6	DPYL5_HUMAN	L	252	ENSP00000288699:S252L;ENSP00000385549:S252L	ENSP00000288699:S252L	S	+	2	0	DPYSL5	27009670	0.999000	0.42202	0.998000	0.56505	0.991000	0.79684	4.261000	0.58841	2.873000	0.98535	0.561000	0.74099	TCG	.	.		0.517	DPYSL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214187.2	NM_020134		T	27156166	C	T	27156166	3	4	264	1	0	0	0	0	1	0	0	0	4752	893	31	1	777	1	DPYSL5	2	27156166	Missense_Mutation	SNP	C	TCGA-FV-A3I0-01A-11D-A22F-10	9278578	27156166	216043207	9	38828										
PLB1	151056	hgsc.bcm.edu	37	chr2	28825786	28825786	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	aagtgcccagtgcagcaggcCaggtaggcaggtcctggctg	16	11	0	0			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr2:28825786C>T	ENST00000327757.5	+	39	2816	c.2772C>T	c.(2770-2772)gcC>gcT	p.A924A	PLB1_ENST00000422425.2_Silent_p.A913A|PLB1_ENST00000541605.1_5'UTR	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	924	4 X 308-326 AA approximate repeats.				glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(31)|ovary(6)|prostate(1)|skin(7)|stomach(2)	69	Acute lymphoblastic leukemia(172;0.155)					TGCAGCAGGCCAGGTAGGCAG	0.602																																					p.A924A		Atlas-SNP	.											.	PLB1	255	.	0			c.C2772T						.						95	88	90					2																	28825786		2203	4300	6503	SO:0001819	synonymous_variant	151056	exon39			GCAGGCCAGGTAG		CCDS33168.1, CCDS54340.1	2p23.3	2014-03-14			ENSG00000163803	ENSG00000163803	3.1.1.4, 3.1.1.5		30041	protein-coding gene	gene with protein product		610179				12150957	Standard	NM_153021		Approved	PLB, FLJ30866	uc002rmb.2	Q6P1J6	OTTHUMG00000152014	ENST00000327757.5:c.2772C>T	chr2.hg19:g.28825786C>T		30.0	0.0		29.0	11.0	NM_153021	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Silent	SNP	ENST00000327757.5	hg19	CCDS33168.1	.	.	.	.	.	.	.	.	.	.	C	13.22	2.172781	0.38413	.	.	ENSG00000163803	ENST00000404858	.	.	.	5.97	5.02	0.67125	.	.	.	.	.	T	0.56746	0.2006	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54036	-0.8353	4	.	.	.	-10.3566	6.5975	0.22683	0.2544:0.6554:0.0:0.0902	.	.	.	.	L	912	.	.	P	+	2	0	PLB1	28679290	1.000000	0.71417	1.000000	0.80357	0.766000	0.43426	1.273000	0.33121	2.828000	0.97474	0.655000	0.94253	CCA	.	.		0.602	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2			T	28825786	C	T	28825786	2	4	264	1	0	0	0	0	0	0	0	1	12033	581	21	3		3	PLB1	2	28825786	Silent	SNP	C	TCGA-FV-A3I0-01A-11D-A22F-10	1669620	28825786	214373587	10	38829										
THADA	63892	hgsc.bcm.edu	37	chr2	43458154	43458154	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	cataagagtcccaaacactgAgaactagggtgtcttcccct	8	12	1	2			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr2:43458154A>C	ENST00000405006.4	-	38	6146	c.5795T>G	c.(5794-5796)cTc>cGc	p.L1932R	THADA_ENST00000415080.2_Missense_Mutation_p.L1613R|THADA_ENST00000330266.7_Intron|THADA_ENST00000405975.2_Missense_Mutation_p.L1932R|AC010883.5_ENST00000423354.1_RNA	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	1932										breast(1)|endometrium(9)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	66		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				CCAAACACTGAGAACTAGGGT	0.488																																					p.L1932R		Atlas-SNP	.											.	THADA	131	.	0			c.T5795G						.						68	66	67					2																	43458154		1922	4135	6057	SO:0001583	missense	63892	exon38			ACACTGAGAACTA	AY149629	CCDS46268.1, CCDS62901.1, CCDS62902.1	2p21	2008-02-05			ENSG00000115970	ENSG00000115970			19217	protein-coding gene	gene with protein product		611800				12063398, 11214970	Standard	NM_022065		Approved	FLJ21877, KIAA1767, GITA	uc002rsx.4	Q6YHU6	OTTHUMG00000152398	ENST00000405006.4:c.5795T>G	chr2.hg19:g.43458154A>C	ENSP00000385995:p.Leu1932Arg	104.0	0.0		132.0	65.0	NM_001083953	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Missense_Mutation	SNP	ENST00000405006.4	hg19	CCDS46268.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.787|9.787	1.176942|1.176942	0.21787|0.21787	.|.	.|.	ENSG00000115970|ENSG00000115970	ENST00000405975;ENST00000356975;ENST00000415080;ENST00000405006|ENST00000407351	T;T;T|.	0.15718|.	2.62;2.4;2.62|.	4.37|4.37	0.111|0.111	0.14619|0.14619	.|.	0.265855|.	0.22804|.	N|.	0.055439|.	T|T	0.38665|0.38665	0.1049|0.1049	M|M	0.62723|0.62723	1.935|1.935	0.09310|0.09310	N|N	1|1	B;B|.	0.09022|.	0.002;0.002|.	B;B|.	0.10450|.	0.005;0.005|.	T|T	0.36744|0.36744	-0.9735|-0.9735	10|5	0.87932|.	D|.	0|.	.|.	1.6077|1.6077	0.02687|0.02687	0.5019:0.143:0.0861:0.269|0.5019:0.143:0.0861:0.269	.|.	1859;1932|.	B6ZDQ0;Q6YHU6|.	.;THADA_HUMAN|.	R|A	1932;1859;1613;1932|1172	ENSP00000386088:L1932R;ENSP00000416048:L1613R;ENSP00000385995:L1932R|.	ENSP00000349464:L1859R|.	L|S	-|-	2|1	0|0	THADA|THADA	43311658|43311658	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.007000|0.007000	0.05969|0.05969	-0.050000|-0.050000	0.11904|0.11904	0.181000|0.181000	0.19994|0.19994	0.533000|0.533000	0.62120|0.62120	CTC|TCA	.	.		0.488	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326070.3	NM_022065		C	43458154	A	C	43458154	3	2	264	1	0	0	0	0	1	0	0	0	15855	304	11	5	70	5	THADA	2	43458154	Missense_Mutation	SNP	A	TCGA-FV-A3I0-01A-11D-A22F-10	14632368	43458154	199741219	11	38830										
CLEC4F	165530	hgsc.bcm.edu	37	chr2	71043685	71043685	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	gcattggctccttccaaactAtttcttaaaacctggttctg	6	11	2	0			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr2:71043685A>G	ENST00000272367.2	-	4	904	c.828T>C	c.(826-828)aaT>aaC	p.N276N	CLEC4F_ENST00000426626.1_Silent_p.N276N	NM_001258027.1|NM_173535.2	NP_001244956.1|NP_775806.2	Q8N1N0	CLC4F_HUMAN	C-type lectin domain family 4, member F	276					endocytosis (GO:0006897)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			endometrium(1)|large_intestine(5)|lung(18)|ovary(5)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	37						CTTCCAAACTATTTCTTAAAA	0.408																																					p.N276N	Colon(107;10 2157 6841 26035)	Atlas-SNP	.											.	CLEC4F	95	.	0			c.T828C						.						75	79	78					2																	71043685		2202	4298	6500	SO:0001819	synonymous_variant	165530	exon4			CAAACTATTTCTT	AK096429	CCDS1910.1	2p13.3	2008-02-05	2005-02-09	2005-02-11	ENSG00000152672	ENSG00000152672		"C-type lectin domain containing"	25357	protein-coding gene	gene with protein product			"C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 13"	CLECSF13		8889548, 1846367	Standard	NM_001258027		Approved	FLJ39110, KCLR	uc002shf.3	Q8N1N0	OTTHUMG00000129713	ENST00000272367.2:c.828T>C	chr2.hg19:g.71043685A>G		250.0	0.0		208.0	110.0	NM_173535	A4QPA5	Silent	SNP	ENST00000272367.2	hg19	CCDS1910.1																																																																																			.	.		0.408	CLEC4F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251922.1	NM_173535		G	71043685	A	G	71043685	2	3	264	1	0	0	0	0	0	0	0	1	3518	446	16	2		2	CLEC4F	2	71043685	Silent	SNP	A	TCGA-FV-A3I0-01A-11D-A22F-10	27585531	71043685	172155688	12	38831										
DYSF	8291	hgsc.bcm.edu	37	chr2	71892431	71892431	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	aagaatattccattgaagagAtaggtgagctgccacatgac	10	7	0	5			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr2:71892431A>G	ENST00000258104.3	+	46	5474	c.5197A>G	c.(5197-5199)Ata>Gta	p.I1733V	DYSF_ENST00000410041.1_Missense_Mutation_p.I1751V|DYSF_ENST00000409366.1_Missense_Mutation_p.I1755V|DYSF_ENST00000413539.2_Missense_Mutation_p.I1764V|DYSF_ENST00000479049.2_3'UTR|DYSF_ENST00000409651.1_Missense_Mutation_p.I1765V|DYSF_ENST00000410020.3_Missense_Mutation_p.I1772V|DYSF_ENST00000409762.1_Missense_Mutation_p.I1750V|DYSF_ENST00000429174.2_Missense_Mutation_p.I1754V|DYSF_ENST00000409744.1_Missense_Mutation_p.I1741V|DYSF_ENST00000394120.2_Missense_Mutation_p.I1734V|DYSF_ENST00000409582.3_Missense_Mutation_p.I1771V	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	1733					plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						CATTGAAGAGATAGGTGAGCT	0.517																																					p.I1772V		Atlas-SNP	.											.	DYSF	536	.	0			c.A5314G						.						69	67	68					2																	71892431		2203	4300	6503	SO:0001583	missense	8291	exon47			GAAGAGATAGGTG	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"fer-1-like family member 1"	603009	"limb girdle muscular dystrophy 2B (autosomal recessive)"	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.5197A>G	chr2.hg19:g.71892431A>G	ENSP00000258104:p.Ile1733Val	48.0	0.0		59.0	33.0	NM_001130987	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Missense_Mutation	SNP	ENST00000258104.3	hg19	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	A	11.11	1.542111	0.27563	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	D;D;D;D;D;D;D;D;D;D;D	0.82619	-1.63;-1.63;-1.62;-1.62;-1.63;-1.63;-1.63;-1.62;-1.62;-1.62;-1.63	5.41	2.9	0.33743	.	0.181095	0.48767	N	0.000161	T	0.63873	0.2548	N	0.11427	0.14	0.41804	D	0.989933	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.32425	0.001;0.371;0.203;0.171;0.082;0.171;0.004;0.009;0.004;0.371;0.005;0.032;0.036;0.082;0.021	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.34991	0.002;0.193;0.096;0.193;0.096;0.193;0.022;0.022;0.01;0.193;0.064;0.061;0.027;0.096;0.012	T	0.55244	-0.8171	10	0.24483	T	0.36	-3.3791	5.4205	0.16398	0.6056:0.3027:0.0917:0.0	.	497;1765;1772;1755;1720;1751;1741;1750;1740;1764;1771;1754;1719;1734;1733	B7Z8G4;O75923-8;O75923-13;O75923-10;O75923-9;O75923-11;O75923-12;O75923-5;O75923-6;O75923-2;O75923-7;O75923-4;O75923-3;O75923-14;O75923	.;.;.;.;.;.;.;.;.;.;.;.;.;.;DYSF_HUMAN	V	1764;1750;1771;1754;1733;1765;1734;1741;1755;1772;1751	ENSP00000407046:I1764V;ENSP00000387137:I1750V;ENSP00000386547:I1771V;ENSP00000398305:I1754V;ENSP00000258104:I1733V;ENSP00000386683:I1765V;ENSP00000377678:I1734V;ENSP00000386285:I1741V;ENSP00000386512:I1755V;ENSP00000386881:I1772V;ENSP00000386617:I1751V	ENSP00000258104:I1733V	I	+	1	0	DYSF	71745939	0.986000	0.35501	0.399000	0.26333	0.586000	0.36452	1.720000	0.38022	0.896000	0.36366	0.533000	0.62120	ATA	.	.		0.517	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494		G	71892431	A	G	71892431	3	3	264	1	0	0	0	0	1	0	0	0	4861	333	12	2	5638	2	DYSF	2	71892431	Missense_Mutation	SNP	A	TCGA-FV-A3I0-01A-11D-A22F-10	848746	71892431	171306942	13	38832										
HK2	3099	hgsc.bcm.edu	37	chr2	75113781	75113781	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	tggctgtggatgagctttcaCtcaaccccggcaagcagagg	13	11	2	2			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr2:75113781C>T	ENST00000290573.2	+	15	2800	c.2200C>T	c.(2200-2202)Ctc>Ttc	p.L734F	HK2_ENST00000409174.1_Missense_Mutation_p.L706F	NM_000189.4	NP_000180.2	P52789	HXK2_HUMAN	hexokinase 2	734	Catalytic.|Hexokinase type-2 2.				apoptotic mitochondrial changes (GO:0008637)|carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose transport (GO:0008645)|lactation (GO:0007595)|regulation of glucose import (GO:0046324)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|glucose binding (GO:0005536)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	43						TGAGCTTTCACTCAACCCCGG	0.547																																					p.L734F		Atlas-SNP	.											.	HK2	85	.	0			c.C2200T						.						74	77	76					2																	75113781		2203	4300	6503	SO:0001583	missense	3099	exon15			CTTTCACTCAACC		CCDS1956.1	2p13	2010-03-19			ENSG00000159399	ENSG00000159399	2.7.1.1		4923	protein-coding gene	gene with protein product		601125					Standard	NM_000189		Approved		uc002snd.3	P52789	OTTHUMG00000129972	ENST00000290573.2:c.2200C>T	chr2.hg19:g.75113781C>T	ENSP00000290573:p.Leu734Phe	49.0	0.0		51.0	27.0	NM_000189	D6W5J2|Q8WU87|Q9UN82	Missense_Mutation	SNP	ENST00000290573.2	hg19	CCDS1956.1	.	.	.	.	.	.	.	.	.	.	C	15.79	2.937196	0.52972	.	.	ENSG00000159399	ENST00000290573;ENST00000535740;ENST00000409174	D;D	0.96774	-4.12;-4.12	5.49	4.62	0.57501	Hexokinase, C-terminal (1);	0.170671	0.52532	D	0.000073	D	0.97723	0.9253	M	0.89353	3.025	0.46609	D	0.99912	D	0.67145	0.996	P	0.59221	0.854	D	0.98080	1.0403	10	0.72032	D	0.01	-25.3378	11.8844	0.52594	0.0:0.9169:0.0:0.0831	.	734	P52789	HXK2_HUMAN	F	734;734;706	ENSP00000290573:L734F;ENSP00000387140:L706F	ENSP00000290573:L734F	L	+	1	0	HK2	74967289	0.867000	0.29959	0.992000	0.48379	0.993000	0.82548	1.812000	0.38952	1.566000	0.49654	0.655000	0.94253	CTC	.	.		0.547	HK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252238.2	NM_000189		T	75113781	C	T	75113781	3	4	264	1	0	0	0	0	1	0	0	0	7200	565	20	3	2258	3	HK2	2	75113781	Missense_Mutation	SNP	C	TCGA-FV-A3I0-01A-11D-A22F-10	3221350	75113781	168085592	14	38833										
TGFBRAP1	9392	hgsc.bcm.edu	37	chr2	105885897	105885897	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	acctgggctgcatcaaattcGgtggcgtggcggttcagcag	15	10	2	0			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr2:105885897G>A	ENST00000393359.2	-	11	2664	c.2238C>T	c.(2236-2238)acC>acT	p.T746T	TGFBRAP1_ENST00000258449.1_Silent_p.T746T			Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor associated protein 1	746					intracellular protein transport (GO:0006886)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|membrane (GO:0016020)	SMAD binding (GO:0046332)|small GTPase regulator activity (GO:0005083)|transforming growth factor beta receptor binding (GO:0005160)			central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	31						CATCAAATTCGGTGGCGTGGC	0.627																																					p.T746T	Esophageal Squamous(183;794 2019 9730 21801 48859)	Atlas-SNP	.											.	TGFBRAP1	70	.	0			c.C2238T						.						28	30	29					2																	105885897		2203	4300	6503	SO:0001819	synonymous_variant	9392	exon11			AAATTCGGTGGCG	AF022795	CCDS2067.1	2q12.1	2008-02-05			ENSG00000135966	ENSG00000135966			16836	protein-coding gene	gene with protein product		606237				9545258, 11278302	Standard	NM_001142621		Approved	TRAP-1, TRAP1	uc002tcr.4	Q8WUH2	OTTHUMG00000130809	ENST00000393359.2:c.2238C>T	chr2.hg19:g.105885897G>A		90.0	0.0		110.0	40.0	NM_004257	A8K5R7|D3DVJ8|O60466	Silent	SNP	ENST00000393359.2	hg19	CCDS2067.1																																																																																			.	.		0.627	TGFBRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253354.2	NM_004257		A	105885897	G	A	105885897	2	1	264	1	0	0	0	0	0	0	0	1	15839	1103	39	1		1	TGFBRAP1	2	105885897	Silent	SNP	G	TCGA-FV-A3I0-01A-11D-A22F-10	30772116	105885897	137313476	15	38834										
CDCA7	83879	hgsc.bcm.edu	37	chr2	174231134	174231134	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	ttcgaaaccgttatggtgaaGaggtcagggatgctctgctg	14	7	2	2			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr2:174231134G>A	ENST00000347703.3	+	7	1066	c.922G>A	c.(922-924)Gag>Aag	p.E308K	CDCA7_ENST00000410101.3_Missense_Mutation_p.E343K|CDCA7_ENST00000306721.3_Missense_Mutation_p.E387K|CDCA7_ENST00000392567.2_Intron|CDCA7_ENST00000410019.3_Missense_Mutation_p.E266K	NM_145810.2	NP_665809.1	Q9BWT1	CDCA7_HUMAN	cell division cycle associated 7	308	Mediates transcriptional activity.				apoptotic process (GO:0006915)|regulation of cell proliferation (GO:0042127)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)	18			OV - Ovarian serous cystadenocarcinoma(117;0.116)			TTATGGTGAAGAGGTCAGGGA	0.547																																					p.E387K		Atlas-SNP	.											.	CDCA7	48	.	0			c.G1159A						.						129	120	123					2																	174231134		2203	4300	6503	SO:0001583	missense	83879	exon8			GGTGAAGAGGTCA	BG354580	CCDS2252.1, CCDS2253.1	2q31.1	2008-02-05			ENSG00000144354	ENSG00000144354			14628	protein-coding gene	gene with protein product		609937				11598121, 12188893	Standard	NM_145810		Approved	FLJ14736, JPO1	uc002uic.1	Q9BWT1	OTTHUMG00000132296	ENST00000347703.3:c.922G>A	chr2.hg19:g.174231134G>A	ENSP00000272789:p.Glu308Lys	88.0	0.0		94.0	28.0	NM_031942	B4DLP8|B4DV66|Q53EW5|Q580W9|Q658K4|Q658N4|Q8NBY9|Q96BV8|Q96SP5	Missense_Mutation	SNP	ENST00000347703.3	hg19	CCDS2253.1	.	.	.	.	.	.	.	.	.	.	G	36	5.797466	0.96952	.	.	ENSG00000144354	ENST00000347703;ENST00000306721;ENST00000410101;ENST00000410019	T;T;T;T	0.47177	0.85;0.86;0.85;0.86	5.67	5.67	0.87782	Zinc-finger domain of monoamine-oxidase A repressor R1 (1);	0.049200	0.85682	D	0.000000	T	0.57548	0.2061	L	0.31476	0.935	0.80722	D	1	P;P;D;P	0.56521	0.908;0.955;0.976;0.887	P;D;P;P	0.63113	0.881;0.911;0.867;0.7	T	0.55515	-0.8129	10	0.45353	T	0.12	-25.6724	19.773	0.96379	0.0:0.0:1.0:0.0	.	266;343;308;387	B4DLP8;B4DV66;Q9BWT1;Q9BWT1-2	.;.;CDCA7_HUMAN;.	K	308;387;343;266	ENSP00000272789:E308K;ENSP00000306968:E387K;ENSP00000386656:E343K;ENSP00000386833:E266K	ENSP00000306968:E387K	E	+	1	0	CDCA7	173939380	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.831000	0.99420	2.677000	0.91161	0.655000	0.94253	GAG	.	.		0.547	CDCA7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255400.1	NM_031942		A	174231134	G	A	174231134	3	1	264	1	0	0	0	0	1	0	0	0	3092	943	33	3	1189	3	CDCA7	2	174231134	Missense_Mutation	SNP	G	TCGA-FV-A3I0-01A-11D-A22F-10	68345237	174231134	68968239	16	38835										
BAP1	51533	hgsc.bcm.edu	37	chr3	52442000	52442062	+	5'Flank	DEL	CCTTCATGCGACTCAGGGTGGGTCCCAGGTCCACGCTGCTGCAGTTCAGGAGCACGCTCAGCA	CCTTCATGCGACTCAGGGTGGGTCCCAGGTCCACGCTGCTGCAGTTCAGGAGCACGCTCAGCA	-													0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	gctgaaacccttggtgaagtCcttcatgcgactcagggtgg					rs576176888|rs117382883|rs375700254|rs527433244|rs140641333	byFrequency	TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	CCTTCATGCGACTCAGGGTGGGTCCCAGGTCCACGCTGCTGCAGTTCAGGAGCACGCTCAGCA	CCTTCATGCGACTCAGGGTGGGTCCCAGGTCCACGCTGCTGCAGTTCAGGAGCACGCTCAGCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr3:52442000_52442062delCCTTCATGCGACTCAGGGTGGGTCCCAGGTCCACGCTGCTGCAGTTCAGGAGCACGCTCAGCA	ENST00000327906.3	+	0	0				BAP1_ENST00000460680.1_In_Frame_Del_p.96_117LLSVLLNCSSVDLGPTLSRMKD>Y|BAP1_ENST00000296288.5_In_Frame_Del_p.96_117LLSVLLNCSSVDLGPTLSRMKD>Y	NM_016483.4	NP_057567.3	Q9BWX1	PHF7_HUMAN	PHD finger protein 7							Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)	p.L112P(1)|p.V106M(1)|p.L100fs*20(1)|p.L108fs*17(1)		breast(2)|large_intestine(4)|lung(3)	9				BRCA - Breast invasive adenocarcinoma(193;1.71e-05)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)|OV - Ovarian serous cystadenocarcinoma(275;0.0275)		TTGGTGAAGTCCTTCATGCGACTCAGGGTGGGTCCCAGGTCCACGCTGCTGCAGTTCAGGAGCACGCTCAGCAAGGCATGAGT	0.559																																					p.96_117del		Pindel	.											.	BAP1	371	.	4	Substitution - Missense(2)|Deletion - Frameshift(2)	kidney(2)|ovary(1)|pleura(1)	c.288_350del						.																																			SO:0001631	upstream_gene_variant	8314	exon5			.	AY014283	CCDS2854.1, CCDS2855.1	3p21.31	2013-01-28			ENSG00000010318	ENSG00000010318		"Zinc fingers, PHD-type"	18458	protein-coding gene	gene with protein product						11042152, 11829468	Standard	NM_016483		Approved	NYD-SP6, HSPC226	uc003ddy.3	Q9BWX1	OTTHUMG00000158495		chr3.hg19:g.52442000_52442062delCCTTCATGCGACTCAGGGTGGGTCCCAGGTCCACGCTGCTGCAGTTCAGGAGCACGCTCAGCA	Exception_encountered	122.0	0.0		40.0	21.0	NM_004656	K4DI82	In_Frame_Del	DEL	ENST00000327906.3	hg19	CCDS2854.1																																																																																			.	.		0.559	PHF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351155.1	NM_016483		-	52442062	CCTTCATGCGACTCAGGGTGGGTCCCAGGTCCACGCTGCTGCAGTTCAGGAGCACGCTCAGCA	-	52442000	6	5	264	0	1	1	0	1	0	0	0	0	1311	855	30	0		0	BAP1	3	52442000	5'Flank	DEL	CCTTCATGCGACTCAGGGTGGGTCCCAGGTCCACGCTGCTGCAGTTCAGGAGCACGCTCAGCA	TCGA-FV-A3I0-01A-11D-A22F-10		52442000	145580430	17	38836										
PBRM1	55193	hgsc.bcm.edu	37	chr3	52584506	52584506	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	tccttcaatgtatttcaggtAggcctctgagtgaagaagcc	10	9	3	3			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr3:52584506A>G	ENST00000296302.7	-	29	4829	c.4828T>C	c.(4828-4830)Tac>Cac	p.Y1610H	PBRM1_ENST00000394830.3_Missense_Mutation_p.Y1503H|SMIM4_ENST00000476842.1_Intron|PBRM1_ENST00000356770.4_Missense_Mutation_p.Y1523H|PBRM1_ENST00000337303.4_Missense_Mutation_p.Y1503H|PBRM1_ENST00000409114.3_Missense_Mutation_p.Y1573H|PBRM1_ENST00000409767.1_Missense_Mutation_p.Y1518H|PBRM1_ENST00000409057.1_Missense_Mutation_p.Y1555H|PBRM1_ENST00000410007.1_Missense_Mutation_p.Y1530H|RNU6-856P_ENST00000516959.1_RNA			Q86U86	PB1_HUMAN	polybromo 1	1610					chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TATTTCAGGTAGGCCTCTGAG	0.517			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																p.Y1503H		Atlas-SNP	.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1	1252	.	0			c.T4507C						.						75	75	75					3																	52584506		2203	4300	6503	SO:0001583	missense	55193	exon29			TCAGGTAGGCCTC	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.4828T>C	chr3.hg19:g.52584506A>G	ENSP00000296302:p.Tyr1610His	49.0	0.0		35.0	28.0	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Missense_Mutation	SNP	ENST00000296302.7	hg19		.	.	.	.	.	.	.	.	.	.	A	19.37	3.813720	0.70912	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767	T;T;T;T;T;T;T;T	0.72167	-0.6;-0.56;-0.53;-0.35;-0.63;-0.59;0.23;-0.36	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	D	0.84406	0.5465	M	0.79475	2.455	0.48040	D	0.999579	D;D;D;D;D;D;D;D	0.89917	0.999;0.999;0.999;0.999;1.0;0.998;0.999;0.999	D;D;D;D;D;D;D;D	0.85130	0.996;0.996;0.996;0.996;0.997;0.991;0.996;0.996	D	0.86482	0.1792	10	0.87932	D	0	-7.1164	15.9958	0.80243	1.0:0.0:0.0:0.0	.	1530;1503;1555;1573;1518;1610;1523;1503	Q86U86-9;Q86U86-4;Q86U86-2;Q86U86-8;Q86U86-7;Q86U86;Q86U86-3;Q86U86-5	.;.;.;.;.;PB1_HUMAN;.;.	H	1523;1503;1610;1503;1555;1530;1573;1518	ENSP00000349213:Y1523H;ENSP00000378307:Y1503H;ENSP00000296302:Y1610H;ENSP00000338302:Y1503H;ENSP00000386593:Y1555H;ENSP00000386529:Y1530H;ENSP00000386643:Y1573H;ENSP00000386601:Y1518H	ENSP00000296302:Y1610H	Y	-	1	0	PBRM1	52559546	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.188000	0.69820	0.533000	0.62120	TAC	.	.		0.517	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165		G	52584506	A	G	52584506	3	3	264	1	0	0	0	0	1	0	0	0	11500	420	15	2	249	2	PBRM1	3	52584506	Missense_Mutation	SNP	A	TCGA-FV-A3I0-01A-11D-A22F-10	142506	52584506	145437924	18	38837										
FILIP1L	11259	hgsc.bcm.edu	37	chr3	99643072	99643072	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	tgtttgcccaaagcagccttAcctttcacattcctgttcta	5	13	2	0			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr3:99643072A>G	ENST00000354552.3	-	4	1076		c.e4+1		CMSS1_ENST00000496116.1_Intron|FILIP1L_ENST00000331335.5_Splice_Site|FILIP1L_ENST00000398326.2_Splice_Site|CMSS1_ENST00000421999.2_Intron	NM_182909.2	NP_878913.2	Q4L180	FIL1L_HUMAN	filamin A interacting protein 1-like							cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	35						AAGCAGCCTTACCTTTCACAT	0.408																																					.		Atlas-SNP	.											.	FILIP1L	154	.	0			c.605+2T>C						.						262	243	249					3																	99643072		1933	4141	6074	SO:0001630	splice_region_variant	11259	exon5			AGCCTTACCTTTC		CCDS43117.1, CCDS43118.1, CCDS43119.1, CCDS63700.1, CCDS74969.1	3q12.1	2011-10-21			ENSG00000168386	ENSG00000168386			24589	protein-coding gene	gene with protein product	"downregulated in ovarian cancer 1", "GPBP-interacting protein of 130 kDa"	612993				8314147, 15935955, 21832087	Standard	NM_001282793		Approved	DOC-1, GIP130	uc003dtm.3	Q4L180	OTTHUMG00000159055	ENST00000354552.3:c.605+1T>C	chr3.hg19:g.99643072A>G		189.0	0.0		192.0	37.0	NM_182909	B2CNV7|B2CNV8|Q13597|Q2YDY5|Q6KFX5|Q6KFX6|Q6KFX7|Q8IUM3|Q8N6Z0	Splice_Site	SNP	ENST00000354552.3	hg19	CCDS43117.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.620208	0.87460	.	.	ENSG00000168386	ENST00000354552;ENST00000331335;ENST00000398326	.	.	.	5.5	5.5	0.81552	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.5956	0.76578	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	FILIP1L	101125762	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	8.589000	0.90817	2.100000	0.63781	0.477000	0.44152	.	.	.		0.408	FILIP1L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353069.1	NM_014890	Intron	G	99643072	A	G	99643072	5	3	264	1	0	0	0	0	0	0	1	0	5903	405	14	2	2833	2	FILIP1L	3	99643072	Splice_Site	SNP	A	TCGA-FV-A3I0-01A-11D-A22F-10	47058566	99643072	98379358	19	38838										
SLCO2A1	6578	hgsc.bcm.edu	37	chr3	133654650	133654650	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	gcatcgttgtcatagtaggcGcaggcccctcgcctccccaa	10	16	1	0			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr3:133654650G>A	ENST00000310926.4	-	13	2055	c.1782C>T	c.(1780-1782)tgC>tgT	p.C594C	SLCO2A1_ENST00000493729.1_Silent_p.C518C	NM_005630.2	NP_005621.2	Q92959	SO2A1_HUMAN	solute carrier organic anion transporter family, member 2A1	594					lipid transport (GO:0006869)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lipid transporter activity (GO:0005319)|prostaglandin transmembrane transporter activity (GO:0015132)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(2)|stomach(2)	30					Alprostadil(DB00770)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Furosemide(DB00695)|Iloprost(DB01088)|Phenobarbital(DB01174)|Pyruvic acid(DB00119)	CATAGTAGGCGCAGGCCCCTC	0.597																																					p.C594C		Atlas-SNP	.											.	SLCO2A1	72	.	0			c.C1782T						.						76	65	69					3																	133654650		2203	4300	6503	SO:0001819	synonymous_variant	6578	exon13			GTAGGCGCAGGCC		CCDS3084.1	3q21	2013-05-22	2003-11-25	2003-11-26	ENSG00000174640	ENSG00000174640		"Solute carriers"	10955	protein-coding gene	gene with protein product		601460	"solute carrier family 21 (prostaglandin transporter), member 2", "matrin F/G 1"	SLC21A2, MATR1		8787677, 9618293	Standard	NM_005630		Approved	PGT, OATP2A1	uc003eqa.4	Q92959	OTTHUMG00000159745	ENST00000310926.4:c.1782C>T	chr3.hg19:g.133654650G>A		115.0	0.0		118.0	33.0	NM_005630	Q86V98|Q8IUN2	Silent	SNP	ENST00000310926.4	hg19	CCDS3084.1																																																																																			.	.		0.597	SLCO2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357131.1	NM_005630		A	133654650	G	A	133654650	2	1	264	1	0	0	0	0	0	0	0	1	14741	1079	38	1		1	SLCO2A1	3	133654650	Silent	SNP	G	TCGA-FV-A3I0-01A-11D-A22F-10	34011578	133654650	64367780	20	38839										
MRFAP1	93621	hgsc.bcm.edu	37	chr4	6642727	6642727	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	gcgtcgctgacgcgcgagcaCgggcgggcgtacctgcggaa	18	13	0	1			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr4:6642727C>T	ENST00000320912.4	+	2	791	c.138C>T	c.(136-138)caC>caT	p.H46H	MRFAP1_ENST00000507420.1_Silent_p.H46H|MRFAP1_ENST00000382581.4_Silent_p.H46H	NM_001272053.1	NP_001258982.1			Morf4 family associated protein 1											lung(1)	1						CGCGCGAGCACGGGCGGGCGT	0.622																																					p.H46H		Atlas-SNP	.											.	MRFAP1	10	.	0			c.C138T						.						75	72	73					4																	6642727		2203	4300	6503	SO:0001819	synonymous_variant	93621	exon2			CGAGCACGGGCGG	AF116272	CCDS3389.1	4p16.1	2011-01-27	2011-01-27		ENSG00000179010	ENSG00000179010			24549	protein-coding gene	gene with protein product						15367658	Standard	NM_033296		Approved	PAM14, PGR1	uc003gjh.2	Q9Y605	OTTHUMG00000125504	ENST00000320912.4:c.138C>T	chr4.hg19:g.6642727C>T		98.0	0.0		118.0	89.0	NM_001272053		Silent	SNP	ENST00000320912.4	hg19	CCDS3389.1																																																																																			.	.		0.622	MRFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246831.1	NM_033296		T	6642727	C	T	6642727	2	4	264	1	0	0	0	0	0	0	0	1	9770	535	19	1		1	MRFAP1	4	6642727	Silent	SNP	C	TCGA-FV-A3I0-01A-11D-A22F-10		6642727	184511549	21	38840										
LAP3	51056	hgsc.bcm.edu	37	chr4	17579110	17579110	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	tgttcttgctgcctcttccgGctgcggggcgagtagtcgtc	14	12	2	0			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr4:17579110G>A	ENST00000226299.4	+	1	296	c.22G>A	c.(22-24)Gct>Act	p.A8T	LAP3_ENST00000606142.1_5'Flank	NM_015907.2	NP_056991.2	P28838	AMPL_HUMAN	leucine aminopeptidase 3	8					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)			endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|urinary_tract(1)	20						GCCTCTTCCGGCTGCGGGGCG	0.697																																					p.A8T		Atlas-SNP	.											.	LAP3	50	.	0			c.G22A						.						23	22	22					4																	17579110		2201	4294	6495	SO:0001583	missense	51056	exon1			CTTCCGGCTGCGG	AF061738	CCDS3422.1	4p15.33	2012-07-25	2003-09-12		ENSG00000002549	ENSG00000002549	3.4.11.1		18449	protein-coding gene	gene with protein product		170250	"peptidase S"	PEPS		6350155, 689684	Standard	NM_015907		Approved	LAPEP, LAP	uc003gph.1	P28838	OTTHUMG00000048214	ENST00000226299.4:c.22G>A	chr4.hg19:g.17579110G>A	ENSP00000226299:p.Ala8Thr	17.0	0.0		76.0	13.0	NM_015907	B3KMQ3|Q6IAM6|Q6P0L6|Q9UQE3	Missense_Mutation	SNP	ENST00000226299.4	hg19	CCDS3422.1	.	.	.	.	.	.	.	.	.	.	G	35	5.435778	0.96168	.	.	ENSG00000002549	ENST00000226299	T	0.44881	0.91	5.39	5.39	0.77823	.	0.156705	0.56097	D	0.000024	T	0.42966	0.1226	N	0.08118	0	0.35161	D	0.770648	D	0.63880	0.993	D	0.74674	0.984	T	0.52931	-0.8509	10	0.29301	T	0.29	-19.3561	14.9931	0.71406	0.0:0.0:1.0:0.0	.	8	P28838	AMPL_HUMAN	T	8	ENSP00000226299:A8T	ENSP00000226299:A8T	A	+	1	0	LAP3	17188208	1.000000	0.71417	0.999000	0.59377	0.971000	0.66376	2.853000	0.48317	2.684000	0.91462	0.585000	0.79938	GCT	.	.		0.697	LAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250365.1			A	17579110	G	A	17579110	3	1	264	1	0	0	0	0	1	0	0	0	8632	1203	42	3	24	3	LAP3	4	17579110	Missense_Mutation	SNP	G	TCGA-FV-A3I0-01A-11D-A22F-10	10936383	17579110	173575166	22	38841										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79366872	79366872	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	aatatcaccattgaggtaaaGactttggaagttggaaaggt	11	4	1	2			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr4:79366872G>C	ENST00000325942.6	+	42	6302	c.5862G>C	c.(5860-5862)aaG>aaC	p.K1954N	FRAS1_ENST00000264895.6_Intron	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	1954					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						TTGAGGTAAAGACTTTGGAAG	0.378																																					p.K1954N		Atlas-SNP	.											.	FRAS1	779	.	0			c.G5862C						.						178	178	178					4																	79366872		1861	4101	5962	SO:0001583	missense	80144	exon42			GGTAAAGACTTTG	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.5862G>C	chr4.hg19:g.79366872G>C	ENSP00000326330:p.Lys1954Asn	148.0	0.0		148.0	21.0	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000325942.6	hg19	CCDS54772.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.571|7.571	0.666717|0.666717	0.14710|0.14710	.|.	.|.	ENSG00000138759|ENSG00000138759	ENST00000510944|ENST00000325942	.|T	.|0.19105	.|2.17	5.45|5.45	0.83|0.83	0.18854|0.18854	.|.	.|.	.|.	.|.	.|.	T|T	0.22126|0.22126	0.0533|0.0533	L|L	0.50333|0.50333	1.59|1.59	0.09310|0.09310	N|N	1|1	.|D	.|0.53619	.|0.961	.|P	.|0.49637	.|0.617	T|T	0.14117|0.14117	-1.0484|-1.0484	5|9	.|0.25751	.|T	.|0.34	.|.	5.2101|5.2101	0.15312|0.15312	0.2942:0.0:0.5726:0.1332|0.2942:0.0:0.5726:0.1332	.|.	.|1954	.|A2RRR8	.|.	H|N	404|1954	.|ENSP00000326330:K1954N	.|ENSP00000326330:K1954N	D|K	+|+	1|3	0|2	FRAS1|FRAS1	79585896|79585896	0.470000|0.470000	0.25854|0.25854	0.001000|0.001000	0.08648|0.08648	0.009000|0.009000	0.06853|0.06853	1.119000|1.119000	0.31258|0.31258	-0.061000|-0.061000	0.13110|0.13110	-1.353000|-1.353000	0.01230|0.01230	GAC|AAG	.	.		0.378	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2			C	79366872	G	C	79366872	3	2	264	1	0	0	0	0	1	0	0	0	6050	933	33	4	6028	4	FRAS1	4	79366872	Missense_Mutation	SNP	G	TCGA-FV-A3I0-01A-11D-A22F-10	61787762	79366872	111787404	23	38842										
FHDC1	85462	hgsc.bcm.edu	37	chr4	153896719	153896719	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	agctttgggatctgtgggtaGcagcgaccctgagaacaaag	14	8	1	1			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr4:153896719G>A	ENST00000511601.1	+	12	2464	c.2276G>A	c.(2275-2277)aGc>aAc	p.S759N	FHDC1_ENST00000260008.3_Missense_Mutation_p.S759N			Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1	759									ARFIP1/FHDC1(2)	NS(2)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	43	all_hematologic(180;0.093)					TCTGTGGGTAGCAGCGACCCT	0.607																																					p.S759N		Atlas-SNP	.											.	FHDC1	102	.	0			c.G2276A						.						53	53	53					4																	153896719		2203	4300	6503	SO:0001583	missense	85462	exon11			TGGGTAGCAGCGA	AB051514	CCDS34081.1	4q31.3	2014-02-12	2007-11-29		ENSG00000137460	ENSG00000137460			29363	protein-coding gene	gene with protein product						15138637	Standard	NM_033393		Approved	KIAA1727	uc003inf.2	Q9C0D6	OTTHUMG00000161452	ENST00000511601.1:c.2276G>A	chr4.hg19:g.153896719G>A	ENSP00000427567:p.Ser759Asn	67.0	0.0		78.0	17.0	NM_033393		Missense_Mutation	SNP	ENST00000511601.1	hg19	CCDS34081.1	.	.	.	.	.	.	.	.	.	.	G	9.834	1.189087	0.21954	.	.	ENSG00000137460	ENST00000511601;ENST00000260008	T;T	0.32515	1.45;1.45	5.47	1.95	0.26073	.	0.583830	0.14959	N	0.288451	T	0.13798	0.0334	N	0.24115	0.695	0.09310	N	1	P	0.38335	0.627	B	0.32677	0.15	T	0.08911	-1.0699	10	0.18710	T	0.47	.	3.7374	0.08515	0.0963:0.3498:0.4236:0.1303	.	759	Q9C0D6	FHDC1_HUMAN	N	759	ENSP00000427567:S759N;ENSP00000260008:S759N	ENSP00000260008:S759N	S	+	2	0	FHDC1	154116169	0.998000	0.40836	0.033000	0.17914	0.178000	0.23041	2.753000	0.47524	1.240000	0.43803	0.563000	0.77884	AGC	.	.		0.607	FHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364981.2	NM_033393		A	153896719	G	A	153896719	3	1	264	1	0	0	0	0	1	0	0	0	5884	971	34	3	2318	3	FHDC1	4	153896719	Missense_Mutation	SNP	G	TCGA-FV-A3I0-01A-11D-A22F-10	74529847	153896719	37257557	24	38843										
ACCN5	51802	hgsc.bcm.edu	37	chr4	156784657	156784657	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	tcttttccacatattgaaccTcaatggacgttgtggttggc	9	9	2	1			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr4:156784657T>A	ENST00000537611.2	-	2	336	c.290A>T	c.(289-291)gAg>gTg	p.E97V	TDO2_ENST00000506181.1_Intron	NM_017419.2	NP_059115.1	Q9NY37	ASIC5_HUMAN	acid-sensing (proton-gated) ion channel family member 5	97					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrogen ion channel activity (GO:0015252)|ligand-gated sodium channel activity (GO:0015280)										ATATTGAACCTCAATGGACGT	0.393																																					p.E97V		Atlas-SNP	.											.	.	.	.	0			c.A290T						.						85	73	77					4																	156784657		2203	4300	6503	SO:0001583	missense	51802	exon2			TGAACCTCAATGG	AJ252011	CCDS3793.1	4q32.1	2012-10-03	2012-03-02	2012-03-02	ENSG00000256394	ENSG00000256394			17537	protein-coding gene	gene with protein product			"amiloride-sensitive cation channel 5, intestinal"	ACCN5		10767424	Standard	NM_017419		Approved	INAC, HINAC	uc003ipe.1	Q9NY37	OTTHUMG00000161941	ENST00000537611.2:c.290A>T	chr4.hg19:g.156784657T>A	ENSP00000442477:p.Glu97Val	99.0	0.0		104.0	19.0	NM_017419		Missense_Mutation	SNP	ENST00000537611.2	hg19	CCDS3793.1	.	.	.	.	.	.	.	.	.	.	T	8.227	0.803802	0.16467	.	.	ENSG00000256394	ENST00000537611	T	0.65732	-0.17	4.34	3.12	0.35913	.	1.299300	0.05484	N	0.555311	T	0.56529	0.1991	L	0.52126	1.63	0.09310	N	0.999997	B	0.14438	0.01	B	0.18263	0.021	T	0.41233	-0.9520	10	0.34782	T	0.22	-25.0944	6.5124	0.22228	0.1898:0.0:0.1295:0.6807	.	97	Q9NY37	ACCN5_HUMAN	V	97	ENSP00000442477:E97V	ENSP00000264432:E97V	E	-	2	0	ACCN5	157004107	0.426000	0.25506	0.101000	0.21167	0.855000	0.48748	1.320000	0.33666	0.761000	0.33130	0.528000	0.53228	GAG	.	.		0.393	ASIC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366464.1			A	156784657	T	A	156784657	3	1	264	1	0	0	0	0	1	0	0	0	132	1551	54	4	1263	4	ACCN5	4	156784657	Missense_Mutation	SNP	T	TCGA-FV-A3I0-01A-11D-A22F-10	2887938	156784657	34369619	25	38844										
PRKAA1	5562	hgsc.bcm.edu	37	chr5	40777637	40777637	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	caaggctccgaatcttctgtCgattgagtatcttcacagct	8	11	4	1			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr5:40777637C>T	ENST00000397128.2	-	2	187	c.179G>A	c.(178-180)cGa>cAa	p.R60Q	PRKAA1_ENST00000296800.4_Missense_Mutation_p.R51Q|PRKAA1_ENST00000354209.3_Missense_Mutation_p.R60Q	NM_006251.5|NM_206907.3	NP_006242.5|NP_996790.3	Q13131	AAPK1_HUMAN	protein kinase, AMP-activated, alpha 1 catalytic subunit	60	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|cell cycle arrest (GO:0007050)|cellular response to ethanol (GO:0071361)|cellular response to glucose starvation (GO:0042149)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|cholesterol biosynthetic process (GO:0006695)|cold acclimation (GO:0009631)|fatty acid biosynthetic process (GO:0006633)|fatty acid homeostasis (GO:0055089)|fatty acid oxidation (GO:0019395)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glucose import in response to insulin stimulus (GO:2001274)|negative regulation of glucosylceramide biosynthetic process (GO:0046318)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of gene expression (GO:0010628)|positive regulation of glycolytic process (GO:0045821)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|regulation of energy homeostasis (GO:2000505)|regulation of transcription, DNA-templated (GO:0006355)|regulation of vesicle-mediated transport (GO:0060627)|response to activity (GO:0014823)|response to caffeine (GO:0031000)|response to camptothecin (GO:1901563)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	AMP-activated protein kinase complex (GO:0031588)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)	[acetyl-CoA carboxylase] kinase activity (GO:0050405)|[hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity (GO:0047322)|AMP-activated protein kinase activity (GO:0004679)|ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)|chromatin binding (GO:0003682)|histone serine kinase activity (GO:0035174)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|tau-protein kinase activity (GO:0050321)			breast(1)	1					Acetylsalicylic acid(DB00945)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Phenformin(DB00914)	AATCTTCTGTCGATTGAGTAT	0.348																																					p.R60Q		Atlas-SNP	.											.	PRKAA1	27	.	0			c.G179A						.						85	81	82					5																	40777637		1818	4086	5904	SO:0001583	missense	5562	exon2			TTCTGTCGATTGA		CCDS3932.2, CCDS3933.2	5p13.1	2012-10-03			ENSG00000132356	ENSG00000132356			9376	protein-coding gene	gene with protein product	"AMPK, alpha, 1"	602739				8557660	Standard	XM_006714481		Approved	AMPKa1	uc003jmb.3	Q13131	OTTHUMG00000162269	ENST00000397128.2:c.179G>A	chr5.hg19:g.40777637C>T	ENSP00000380317:p.Arg60Gln	198.0	0.0		271.0	28.0	NM_006251	A8MTQ6|B2R7E1|O00286|Q5D0E1|Q86VS1|Q9UNQ4	Missense_Mutation	SNP	ENST00000397128.2	hg19	CCDS3932.2	.	.	.	.	.	.	.	.	.	.	C	29.3	4.998296	0.93227	.	.	ENSG00000132356	ENST00000397128;ENST00000354209;ENST00000296800	T;T;T	0.65364	-0.15;-0.15;-0.15	5.81	5.81	0.92471	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.70859	0.3272	N	0.21324	0.655	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	T	0.74097	-0.3775	10	0.87932	D	0	-7.7554	20.066	0.97704	0.0:1.0:0.0:0.0	.	60;60	Q13131;Q13131-2	AAPK1_HUMAN;.	Q	60;60;51	ENSP00000380317:R60Q;ENSP00000346148:R60Q;ENSP00000296800:R51Q	ENSP00000296800:R51Q	R	-	2	0	AC008810.1	40813394	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	7.484000	0.81180	2.730000	0.93505	0.650000	0.86243	CGA	.	.		0.348	PRKAA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253833.2	NM_006251		T	40777637	C	T	40777637	3	4	264	1	0	0	0	0	1	0	0	0	12505	884	31	1	1581	1	PRKAA1	5	40777637	Missense_Mutation	SNP	C	TCGA-FV-A3I0-01A-11D-A22F-10		40777637	140137623	26	38845										
ABCC10	89845	hgsc.bcm.edu	37	chr6	43406411	43406411	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	tgtccaagggctttggcctgGccacccaggaaccctggatc	12	14	0	0			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr6:43406411G>A	ENST00000372530.4	+	8	2220	c.2005G>A	c.(2005-2007)Gcc>Acc	p.A669T	ABCC10_ENST00000244533.3_Missense_Mutation_p.A641T	NM_001198934.1	NP_001185863.1	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	669	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(8)|lung(21)|ovary(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)		Cyclosporine(DB00091)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Estradiol(DB00783)|Etoposide(DB00773)|Gemcitabine(DB00441)|Methotrexate(DB00563)|Paclitaxel(DB01229)|Sildenafil(DB00203)|Tenofovir(DB00300)|Verapamil(DB00661)|Vincristine(DB00541)	CTTTGGCCTGGCCACCCAGGA	0.592																																					p.A669T		Atlas-SNP	.											.	ABCC10	118	.	0			c.G2005A						.						101	96	98					6																	43406411		2203	4300	6503	SO:0001583	missense	89845	exon8			GGCCTGGCCACCC	U66684	CCDS4896.1, CCDS56430.1	6p12.3	2012-03-14			ENSG00000124574	ENSG00000124574		"ATP binding cassette transporters / subfamily C"	52	protein-coding gene	gene with protein product		612509				8894702	Standard	NM_033450		Approved	EST182763, MRP7, SIMRP7	uc003ouy.1	Q5T3U5	OTTHUMG00000014733	ENST00000372530.4:c.2005G>A	chr6.hg19:g.43406411G>A	ENSP00000361608:p.Ala669Thr	41.0	0.0		103.0	19.0	NM_001198934	Q8NHX7|Q9H7N2|Q9NXY3|Q9UF48	Missense_Mutation	SNP	ENST00000372530.4	hg19	CCDS56430.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.810282	0.90707	.	.	ENSG00000124574	ENST00000372515;ENST00000372530;ENST00000244533	D;D;D	0.90676	-2.71;-2.71;-2.71	5.61	5.61	0.85477	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.132335	0.49916	D	0.000128	D	0.90000	0.6878	L	0.58510	1.815	0.51482	D	0.999926	P;P	0.40794	0.729;0.659	B;P	0.45971	0.439;0.499	D	0.90438	0.4429	10	0.56958	D	0.05	-44.5866	19.6435	0.95767	0.0:0.0:1.0:0.0	.	641;669	Q5T3U5-2;Q5T3U5	.;MRP7_HUMAN	T	225;669;641	ENSP00000361593:A225T;ENSP00000361608:A669T;ENSP00000244533:A641T	ENSP00000244533:A641T	A	+	1	0	ABCC10	43514389	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.799000	0.85936	2.640000	0.89533	0.655000	0.94253	GCC	.	.		0.592	ABCC10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040603.2	NM_033450		A	43406411	G	A	43406411	3	1	264	1	0	0	0	0	1	0	0	0	50	1203	42	3	1943	3	ABCC10	6	43406411	Missense_Mutation	SNP	G	TCGA-FV-A3I0-01A-11D-A22F-10		43406411	127708656	27	38846										
SESN1	27244	hgsc.bcm.edu	37	chr6	109315748	109315748	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	gacttgcctcttcttcatctCgacattcctgtaactgcctc	5	15	4	0			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr6:109315748C>A	ENST00000356644.7	-	6	954	c.860G>T	c.(859-861)cGa>cTa	p.R287L	SESN1_ENST00000436639.2_Missense_Mutation_p.R346L|SESN1_ENST00000302071.2_Missense_Mutation_p.R221L	NM_001199933.1	NP_001186862.1	Q9Y6P5	SESN1_HUMAN	sestrin 1	287					cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|negative regulation of cell proliferation (GO:0008285)|regulation of protein kinase B signaling (GO:0051896)|regulation of response to reactive oxygen species (GO:1901031)	nucleus (GO:0005634)				cervix(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	10		all_cancers(87;6.45e-05)|Acute lymphoblastic leukemia(125;3.55e-10)|all_hematologic(75;1.68e-07)|all_epithelial(87;0.0106)|Colorectal(196;0.0637)		Epithelial(106;0.0014)|BRCA - Breast invasive adenocarcinoma(108;0.00146)|all cancers(137;0.0031)|OV - Ovarian serous cystadenocarcinoma(136;0.0117)		TTCTTCATCTCGACATTCCTG	0.378																																					p.R346L		Atlas-SNP	.											.	SESN1	29	.	0			c.G1037T						.						145	119	128					6																	109315748		2203	4300	6503	SO:0001583	missense	27244	exon6			TCATCTCGACATT	AF033120	CCDS5070.1, CCDS56444.1, CCDS56445.1	6q21	2008-10-23			ENSG00000080546	ENSG00000080546			21595	protein-coding gene	gene with protein product		606103				9926927, 7938006	Standard	NM_014454		Approved	SEST1, PA26	uc003psu.3	Q9Y6P5	OTTHUMG00000015338	ENST00000356644.7:c.860G>T	chr6.hg19:g.109315748C>A	ENSP00000349061:p.Arg287Leu	85.0	0.0		54.0	17.0	NM_014454	Q2M2B7|Q5T316|Q9NV00|Q9UPD5|Q9Y6P6	Missense_Mutation	SNP	ENST00000356644.7	hg19	CCDS56445.1	.	.	.	.	.	.	.	.	.	.	C	34	5.356975	0.95854	.	.	ENSG00000080546	ENST00000436639;ENST00000302071;ENST00000356644	T;T;T	0.23348	1.91;1.91;1.91	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.39332	0.1074	L	0.60957	1.885	0.80722	D	1	D;D	0.69078	0.996;0.997	D;D	0.81914	0.992;0.995	T	0.01858	-1.1259	10	0.24483	T	0.36	-8.1299	19.8401	0.96679	0.0:1.0:0.0:0.0	.	346;287	Q9Y6P5-2;Q9Y6P5	.;SESN1_HUMAN	L	346;221;287	ENSP00000393762:R346L;ENSP00000306734:R221L;ENSP00000349061:R287L	ENSP00000306734:R221L	R	-	2	0	SESN1	109422441	0.991000	0.36638	0.999000	0.59377	0.991000	0.79684	2.939000	0.48995	2.675000	0.91044	0.591000	0.81541	CGA	.	.		0.378	SESN1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041738.4	NM_014454		A	109315748	C	A	109315748	3	1	264	1	0	0	0	0	1	0	0	0	14139	884	31	1	638	1	SESN1	6	109315748	Missense_Mutation	SNP	C	TCGA-FV-A3I0-01A-11D-A22F-10	65909337	109315748	61799319	28	38847										
SNX8	29886	hgsc.bcm.edu	37	chr7	2302995	2302995	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	gggtcgtgtcagaccctattGcactgagggagcaagcacac	13	11	1	2			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr7:2302995G>T	ENST00000222990.3	-	7	827	c.785C>A	c.(784-786)gCa>gAa	p.A262E		NM_013321.2	NP_037453.1	Q9Y5X2	SNX8_HUMAN	sorting nexin 8	262					early endosome to Golgi transport (GO:0034498)|intracellular protein transport (GO:0006886)	early endosome membrane (GO:0031901)	identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)			breast(2)|endometrium(5)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(2)|skin(3)	26		Ovarian(82;0.11)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0853)|OV - Ovarian serous cystadenocarcinoma(56;3.79e-14)		AGACCCTATTGCACTGAGGGA	0.617																																					p.A262E		Atlas-SNP	.											.	SNX8	46	.	0			c.C785A						.						32	31	31					7																	2302995		2202	4298	6500	SO:0001583	missense	29886	exon7			CCTATTGCACTGA	AF121858	CCDS5331.1	7p22.3	2010-08-05			ENSG00000106266	ENSG00000106266		"Sorting nexins"	14972	protein-coding gene	gene with protein product		614905					Standard	NM_013321		Approved	Mvp1	uc003slw.3	Q9Y5X2	OTTHUMG00000151512	ENST00000222990.3:c.785C>A	chr7.hg19:g.2302995G>T	ENSP00000222990:p.Ala262Glu	41.0	0.0		36.0	16.0	NM_013321	A4D207|Q96I67	Missense_Mutation	SNP	ENST00000222990.3	hg19	CCDS5331.1	.	.	.	.	.	.	.	.	.	.	G	3.713	-0.059067	0.07317	.	.	ENSG00000106266	ENST00000222990	T	0.21734	1.99	5.47	5.47	0.80525	.	0.257277	0.36703	N	0.002452	T	0.10508	0.0257	N	0.04959	-0.14	0.38254	D	0.941698	B	0.02656	0.0	B	0.08055	0.003	T	0.09975	-1.0650	10	0.05525	T	0.97	.	17.5154	0.87771	0.0:0.0:1.0:0.0	.	262	Q9Y5X2	SNX8_HUMAN	E	262	ENSP00000222990:A262E	ENSP00000222990:A262E	A	-	2	0	SNX8	2269521	1.000000	0.71417	0.440000	0.26846	0.050000	0.14768	5.773000	0.68898	2.570000	0.86706	0.655000	0.94253	GCA	.	.		0.617	SNX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322949.2			T	2302995	G	T	2302995	3	4	264	1	0	0	0	0	1	0	0	0	14923	1319	46	3	632	3	SNX8	7	2302995	Missense_Mutation	SNP	G	TCGA-FV-A3I0-01A-11D-A22F-10		2302995	156835668	29	38848										
SP4	6671	hgsc.bcm.edu	37	chr7	21470288	21470288	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	catcaccccagtgtcttcaaGtggtggcacaactcttgctc	8	14	4	0			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr7:21470288G>C	ENST00000222584.3	+	3	1723	c.1505G>C	c.(1504-1506)aGt>aCt	p.S502T		NM_003112.3	NP_003103.2	Q02446	SP4_HUMAN	Sp4 transcription factor	502					regulation of heart contraction (GO:0008016)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(11)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	35						GTGTCTTCAAGTGGTGGCACA	0.458																																					p.S502T		Atlas-SNP	.											.	SP4	91	.	0			c.G1505C						.						122	125	124					7																	21470288		2203	4300	6503	SO:0001583	missense	6671	exon3			CTTCAAGTGGTGG		CCDS5373.1	7p15	2013-01-08			ENSG00000105866	ENSG00000105866		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	11209	protein-coding gene	gene with protein product		600540				1454515	Standard	XM_005249828		Approved	SPR-1, HF1B, MGC130008, MGC130009	uc003sva.3	Q02446	OTTHUMG00000094801	ENST00000222584.3:c.1505G>C	chr7.hg19:g.21470288G>C	ENSP00000222584:p.Ser502Thr	143.0	0.0		172.0	94.0	NM_003112	O60402|Q32M52	Missense_Mutation	SNP	ENST00000222584.3	hg19	CCDS5373.1	.	.	.	.	.	.	.	.	.	.	G	16.86	3.240152	0.58995	.	.	ENSG00000105866	ENST00000222584	T	0.10005	2.92	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.12817	0.0311	L	0.36672	1.1	0.48975	D	0.999737	P	0.48764	0.915	B	0.44108	0.441	T	0.06991	-1.0796	10	0.27082	T	0.32	.	18.8556	0.92251	0.0:0.0:1.0:0.0	.	502	Q02446	SP4_HUMAN	T	502	ENSP00000222584:S502T	ENSP00000222584:S502T	S	+	2	0	SP4	21436813	1.000000	0.71417	0.998000	0.56505	0.975000	0.68041	6.201000	0.72124	2.758000	0.94735	0.655000	0.94253	AGT	.	.		0.458	SP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211617.2	NM_003112		C	21470288	G	C	21470288	3	2	264	1	0	0	0	0	1	0	0	0	14981	1029	36	4	1515	4	SP4	7	21470288	Missense_Mutation	SNP	G	TCGA-FV-A3I0-01A-11D-A22F-10	19167293	21470288	137668375	30	38849										
ZNF777	27153	hgsc.bcm.edu	37	chr7	149152627	149152627	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	agagatctggaaaggggtgtCcttttgggaaaccgggctct	15	7	2	1			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr7:149152627C>G	ENST00000247930.4	-	2	810	c.487G>C	c.(487-489)Gac>Cac	p.D163H		NM_015694.2	NP_056509.2	Q9ULD5	ZN777_HUMAN	zinc finger protein 777	163					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(5)|lung(17)|ovary(1)|skin(2)|urinary_tract(1)	26	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			AAAGGGGTGTCCTTTTGGGAA	0.602																																					p.D163H		Atlas-SNP	.											.	ZNF777	63	.	0			c.G487C						.						85	95	92					7																	149152627		1975	4159	6134	SO:0001583	missense	27153	exon2			GGGTGTCCTTTTG	AB033111	CCDS43675.1	7q36.1	2013-01-08			ENSG00000196453	ENSG00000196453		"Zinc fingers, C2H2-type", "-"	22213	protein-coding gene	gene with protein product							Standard	NM_015694		Approved	KIAA1285	uc003wfv.3	Q9ULD5	OTTHUMG00000158967	ENST00000247930.4:c.487G>C	chr7.hg19:g.149152627C>G	ENSP00000247930:p.Asp163His	60.0	0.0		72.0	31.0	NM_015694	Q8N2R2|Q8N659	Missense_Mutation	SNP	ENST00000247930.4	hg19	CCDS43675.1	.	.	.	.	.	.	.	.	.	.	C	16.39	3.109725	0.56398	.	.	ENSG00000196453	ENST00000247930	T	0.05717	3.4	4.27	4.27	0.50696	.	0.288428	0.24808	N	0.035429	T	0.08714	0.0216	N	0.24115	0.695	0.36565	D	0.872672	P	0.48503	0.911	P	0.51016	0.656	T	0.23368	-1.0190	10	0.59425	D	0.04	-30.4442	12.0974	0.53763	0.0:1.0:0.0:0.0	.	163	Q9ULD5-2	.	H	163	ENSP00000247930:D163H	ENSP00000247930:D163H	D	-	1	0	ZNF777	148783560	0.006000	0.16342	1.000000	0.80357	0.923000	0.55619	0.355000	0.20163	2.217000	0.71921	0.563000	0.77884	GAC	.	.		0.602	ZNF777-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352708.1	NM_015694		G	149152627	C	G	149152627	3	3	264	1	0	0	0	0	1	0	0	0	18165	855	30	4	2028	4	ZNF777	7	149152627	Missense_Mutation	SNP	C	TCGA-FV-A3I0-01A-11D-A22F-10	127682339	149152627	9986036	31	38850										
CPA6	57094	hgsc.bcm.edu	37	chr8	68658311	68658311	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	agaatcttcaaaaagagccaGcaaagaggcaggaaagcagc	11	8	2	3	rs376152262		TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr8:68658311G>T	ENST00000297770.4	-	1	269	c.54C>A	c.(52-54)tgC>tgA	p.C18*	CPA6_ENST00000297769.4_De_novo_Start_OutOfFrame|CPA6_ENST00000518549.1_Nonsense_Mutation_p.C18*	NM_020361.4	NP_065094.3	Q8N4T0	CBPA6_HUMAN	carboxypeptidase A6	18						proteinaceous extracellular matrix (GO:0005578)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(5)	26			Epithelial(68;0.04)|OV - Ovarian serous cystadenocarcinoma(28;0.0593)|all cancers(69;0.136)			AAAAGAGCCAGCAAAGAGGCA	0.512																																					p.C18X		Atlas-SNP	.											.	CPA6	69	.	0			c.C54A						.						48	48	48					8																	68658311		2203	4300	6503	SO:0001587	stop_gained	57094	exon1			GAGCCAGCAAAGA	AF221594	CCDS6200.1	8q12.3	2012-02-10			ENSG00000165078	ENSG00000165078			17245	protein-coding gene	gene with protein product		609562				11836249	Standard	NM_020361		Approved	CPAH	uc003xxq.4	Q8N4T0	OTTHUMG00000164575	ENST00000297770.4:c.54C>A	chr8.hg19:g.68658311G>T	ENSP00000297770:p.Cys18*	88.0	0.0		75.0	28.0	NM_020361	Q8NEX8|Q8TDE8|Q9NRI9	Nonsense_Mutation	SNP	ENST00000297770.4	hg19	CCDS6200.1	.	.	.	.	.	.	.	.	.	.	G	39	7.869385	0.98534	.	.	ENSG00000165078	ENST00000297770;ENST00000518549	.	.	.	5.62	4.64	0.57946	.	0.390953	0.25078	N	0.033309	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.4399	0.21845	0.1512:0.0:0.8488:0.0	.	.	.	.	X	18	.	ENSP00000297770:C18X	C	-	3	2	CPA6	68820865	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.341000	0.52151	2.640000	0.89533	0.655000	0.94253	TGC	.	.		0.512	CPA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379296.2	NM_020361		T	68658311	G	T	68658311	4	4	264	1	0	0	0	0	0	1	0	0	3796	963	34	3	1303	3	CPA6	8	68658311	Nonsense_Mutation	SNP	G	TCGA-FV-A3I0-01A-11D-A22F-10		68658311	77705711	32	38851										
TM7SF4	81501	hgsc.bcm.edu	37	chr8	105361092	105361092	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	ttgattgcagctggcacaggGatcgtcatcttgggacacgt	13	9	2	1			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr8:105361092G>T	ENST00000297581.2	+	2	361	c.312G>T	c.(310-312)ggG>ggT	p.G104G	DCSTAMP_ENST00000517991.1_Silent_p.G104G|DPYS_ENST00000521601.1_Intron	NM_030788.3	NP_110415.1	Q9H295	DCSTP_HUMAN	dendrocyte expressed seven transmembrane protein	104					cellular response to interleukin-4 (GO:0071353)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to tumor necrosis factor (GO:0071356)|membrane fusion (GO:0061025)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of cell growth (GO:0030308)|osteoclast differentiation (GO:0030316)|osteoclast fusion (GO:0072675)|positive regulation of bone resorption (GO:0045780)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of monocyte differentiation (GO:0045657)	cell surface (GO:0009986)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)											CTGGCACAGGGATCGTCATCT	0.438																																					p.G104G		Atlas-SNP	.											.	.	.	.	0			c.G312T						.						65	64	65					8																	105361092		2203	4300	6503	SO:0001819	synonymous_variant	81501	exon2			CACAGGGATCGTC	AF305068	CCDS6301.1, CCDS59111.1	8q22.3	2012-08-10	2012-03-27	2012-03-27	ENSG00000164935	ENSG00000164935			18549	protein-coding gene	gene with protein product	"Dendritic cells (DC)-specific transmembrane protein", "IL-Four INDuced"	605933	"transmembrane 7 superfamily member 4"	TM7SF4		11169400, 11345591	Standard	NM_030788		Approved	DC-STAMP, FIND	uc003ylx.2	Q9H295	OTTHUMG00000164890	ENST00000297581.2:c.312G>T	chr8.hg19:g.105361092G>T		121.0	0.0		155.0	25.0	NM_001257317	B7ZVW2|E7ESG0|Q2M2D5	Silent	SNP	ENST00000297581.2	hg19	CCDS6301.1																																																																																			.	.		0.438	DCSTAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380810.1	NM_030788		T	105361092	G	T	105361092	2	4	264	1	0	0	0	0	0	0	0	1	15991	1161	41	3		3	TM7SF4	8	105361092	Silent	SNP	G	TCGA-FV-A3I0-01A-11D-A22F-10	36702781	105361092	41002930	33	38852										
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110495324	110495324	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	cctgtctctgatggatgctgTggattggcaggtagacaaaa	13	7	1	2			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr8:110495324T>A	ENST00000378402.5	+	57	9670	c.9566T>A	c.(9565-9567)gTg>gAg	p.V3189E		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	3189					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			ATGGATGCTGTGGATTGGCAG	0.378										HNSCC(38;0.096)																											p.V3189E		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.T9566A						.						84	80	81					8																	110495324		1870	4094	5964	SO:0001583	missense	93035	exon57			ATGCTGTGGATTG	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.9566T>A	chr8.hg19:g.110495324T>A	ENSP00000367655:p.Val3189Glu	102.0	0.0		134.0	35.0	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	hg19	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.453744	0.84209	.	.	ENSG00000205038	ENST00000378402;ENST00000526472	D;D	0.85773	-2.03;-2.03	5.63	5.63	0.86233	.	0.000000	0.64402	D	0.000001	D	0.94142	0.8121	H	0.94222	3.51	0.44092	D	0.996859	D	0.76494	0.999	D	0.75484	0.986	D	0.95130	0.8254	10	0.56958	D	0.05	.	13.7881	0.63121	0.0:0.0:0.0:1.0	.	3189	Q86WI1	PKHL1_HUMAN	E	3189;117	ENSP00000367655:V3189E;ENSP00000437376:V117E	ENSP00000367655:V3189E	V	+	2	0	PKHD1L1	110564500	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	6.173000	0.71937	2.144000	0.66660	0.477000	0.44152	GTG	.	.		0.378	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		A	110495324	T	A	110495324	3	1	264	1	0	0	0	0	1	0	0	0	11981	1696	59	4	9792	4	PKHD1L1	8	110495324	Missense_Mutation	SNP	T	TCGA-FV-A3I0-01A-11D-A22F-10	5134232	110495324	35868698	34	38853										
ATAD2	29028	hgsc.bcm.edu	37	chr8	124361670	124361670	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	catccataagagctagcaggGtggaaacaatagaactaaat	9	7	0	2			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr8:124361670G>A	ENST00000287394.5	-	14	1768	c.1661C>T	c.(1660-1662)aCc>aTc	p.T554I	MIR548AA1_ENST00000384971.2_RNA|ATAD2_ENST00000521903.1_Intron	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	554					ATP catabolic process (GO:0006200)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	48	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			AGCTAGCAGGGTGGAAACAAT	0.358																																					p.T554I		Atlas-SNP	.											.	ATAD2	160	.	0			c.C1661T						.						97	92	93					8																	124361670		2203	4300	6503	SO:0001583	missense	29028	exon14			AGCAGGGTGGAAA	BC019909	CCDS6343.1	8q24.13	2014-01-21		2007-02-08	ENSG00000156802	ENSG00000156802		"ATPases / AAA-type"	30123	protein-coding gene	gene with protein product		611941				12477932	Standard	NM_014109		Approved	PRO2000, DKFZp667N1320, MGC5254, MGC29843, CT137	uc003yqh.4	Q6PL18	OTTHUMG00000165090	ENST00000287394.5:c.1661C>T	chr8.hg19:g.124361670G>A	ENSP00000287394:p.Thr554Ile	51.0	0.0		59.0	31.0	NM_014109	Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	Missense_Mutation	SNP	ENST00000287394.5	hg19	CCDS6343.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.979088	0.92982	.	.	ENSG00000156802	ENST00000287394	D	0.93247	-3.19	5.7	5.7	0.88788	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.045489	0.85682	D	0.000000	D	0.95043	0.8395	L	0.31926	0.97	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95521	0.8594	10	0.87932	D	0	-12.3641	19.8338	0.96646	0.0:0.0:1.0:0.0	.	554	Q6PL18	ATAD2_HUMAN	I	554	ENSP00000287394:T554I	ENSP00000287394:T554I	T	-	2	0	ATAD2	124430851	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.869000	0.99810	2.692000	0.91855	0.591000	0.81541	ACC	.	.		0.358	ATAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381766.2	NM_014109		A	124361670	G	A	124361670	3	1	264	1	0	0	0	0	1	0	0	0	1071	1261	44	3	2571	3	ATAD2	8	124361670	Missense_Mutation	SNP	G	TCGA-FV-A3I0-01A-11D-A22F-10	13866346	124361670	22002352	35	38854										
DGAT1	8694	hgsc.bcm.edu	37	chr8	145540267	145540267	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	gagcacgtagtagtcgtggaCgtacatgaggacggctattg	15	7	0	1			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr8:145540267C>T	ENST00000332324.4	-	17	1690	c.1417G>A	c.(1417-1419)Gtc>Atc	p.V473I	GS1-393G12.12_ENST00000525023.1_RNA|DGAT1_ENST00000527438.1_5'UTR	NM_012079.4	NP_036211.2	O75907	DGAT1_HUMAN	diacylglycerol O-acyltransferase 1	473					acylglycerol acyl-chain remodeling (GO:0036155)|cellular lipid metabolic process (GO:0044255)|diacylglycerol metabolic process (GO:0046339)|glycerophospholipid biosynthetic process (GO:0046474)|lipid storage (GO:0019915)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride metabolic process (GO:0006641)|very-low-density lipoprotein particle assembly (GO:0034379)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	diacylglycerol O-acyltransferase activity (GO:0004144)|retinol O-fatty-acyltransferase activity (GO:0050252)|transferase activity, transferring acyl groups (GO:0016746)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	9	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.94e-40)|Epithelial(56;7.67e-40)|all cancers(56;7.88e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0441)|Colorectal(110;0.055)			TAGTCGTGGACGTACATGAGG	0.612																																					p.V473I		Atlas-SNP	.											.	DGAT1	26	.	0			c.G1417A						.						63	49	53					8																	145540267		2197	4295	6492	SO:0001583	missense	8694	exon17			CGTGGACGTACAT	AF059202	CCDS6420.1	8q24.3	2014-05-06	2010-06-24	2001-11-09	ENSG00000185000	ENSG00000185000	2.3.1.20		2843	protein-coding gene	gene with protein product		604900	"diacylglycerol O-acyltransferase homolog 1 (mouse)"			9756920	Standard	NM_012079		Approved	ARGP1, DGAT	uc003zbv.3	O75907	OTTHUMG00000174606	ENST00000332324.4:c.1417G>A	chr8.hg19:g.145540267C>T	ENSP00000332258:p.Val473Ile	37.0	0.0		69.0	40.0	NM_012079	B2RWQ2|D3DWL6|Q96BB8	Missense_Mutation	SNP	ENST00000332324.4	hg19	CCDS6420.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.3|25.3	4.618925|4.618925	0.87460|0.87460	.|.	.|.	ENSG00000185000|ENSG00000185000	ENST00000526479|ENST00000332324	.|T	.|0.72394	.|-0.65	4.55|4.55	4.55|4.55	0.56014|0.56014	.|.	.|0.074813	.|0.52532	.|D	.|0.000065	T|T	0.78375|0.78375	0.4273|0.4273	M|M	0.68952|0.68952	2.095|2.095	0.80722|0.80722	D|D	1|1	D|D	0.69078|0.62365	0.997|0.991	P|P	0.58130|0.56163	0.833|0.793	T|T	0.80301|0.80301	-0.1440|-0.1440	8|10	0.87932|0.52906	D|T	0|0.07	-11.1254|-11.1254	14.8307|14.8307	0.70146|0.70146	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	307|473	E9PS80|O75907	.|DGAT1_HUMAN	H|I	307|473	.|ENSP00000332258:V473I	ENSP00000435883:R307H|ENSP00000332258:V473I	R|V	-|-	2|1	0|0	DGAT1|DGAT1	145511075|145511075	1.000000|1.000000	0.71417|0.71417	0.992000|0.992000	0.48379|0.48379	0.807000|0.807000	0.45602|0.45602	4.972000|4.972000	0.63756|0.63756	2.368000|2.368000	0.80403|0.80403	0.561000|0.561000	0.74099|0.74099	CGT|GTC	.	.		0.612	DGAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382059.3	NM_012079		T	145540267	C	T	145540267	3	4	264	1	0	0	0	0	1	0	0	0	4459	536	19	1	53	1	DGAT1	8	145540267	Missense_Mutation	SNP	C	TCGA-FV-A3I0-01A-11D-A22F-10	21178597	145540267	823755	36	38855										
MPDZ	8777	hgsc.bcm.edu	37	chr9	13109010	13109010	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	cctccaactatactgaagccTaagccatctggtcctcgctc	6	16	1	1			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr9:13109010T>A	ENST00000319217.7	-	46	6238	c.5991A>T	c.(5989-5991)ttA>ttT	p.L1997F	MPDZ_ENST00000381015.4_Missense_Mutation_p.L1997F|MPDZ_ENST00000546205.1_Missense_Mutation_p.L2011F|MPDZ_ENST00000538841.1_Missense_Mutation_p.L856F|MPDZ_ENST00000447879.1_Missense_Mutation_p.L1964F|MPDZ_ENST00000541093.1_Missense_Mutation_p.L231F|MPDZ_ENST00000541718.1_Missense_Mutation_p.L1968F|MPDZ_ENST00000536827.1_Missense_Mutation_p.L1935F|MPDZ_ENST00000381022.2_Missense_Mutation_p.L1968F	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	1997	PDZ 13. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		TACTGAAGCCTAAGCCATCTG	0.383																																					p.L1968F		Atlas-SNP	.											.	MPDZ	324	.	0			c.A5904T						.						39	39	39					9																	13109010		1866	4100	5966	SO:0001583	missense	8777	exon45			GAAGCCTAAGCCA	AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.5991A>T	chr9.hg19:g.13109010T>A	ENSP00000320006:p.Leu1997Phe	51.0	0.0		59.0	31.0	NM_003829	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Missense_Mutation	SNP	ENST00000319217.7	hg19		.	.	.	.	.	.	.	.	.	.	T	19.95	3.921071	0.73213	.	.	ENSG00000107186	ENST00000319217;ENST00000541718;ENST00000381022;ENST00000438511;ENST00000541093;ENST00000545857;ENST00000538841;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000399902;ENST00000546205	T;T;T;T;T;T;T;T;T;T;T	0.53640	0.61;0.61;0.61;0.61;0.61;0.61;0.61;0.61;0.61;0.61;0.61	5.44	-4.4	0.03600	PDZ/DHR/GLGF (4);	0.000000	0.35320	N	0.003289	T	0.53562	0.1804	L	0.56280	1.765	0.46356	D	0.999002	D;D;D;D;D;D;D;D	0.89917	1.0;0.999;0.999;1.0;1.0;1.0;1.0;0.998	D;D;D;D;D;D;D;D	0.97110	0.999;0.978;0.967;0.999;0.999;0.999;1.0;0.951	T	0.56980	-0.7889	10	0.72032	D	0.01	.	7.8076	0.29211	0.2071:0.4643:0.0:0.3286	.	1935;856;702;1964;1877;1968;1997;690	B7ZMI4;B7ZB24;B4DGX5;O75970-3;E7EPZ1;O75970-2;O75970;B3KRN5	.;.;.;.;.;.;MPDZ_HUMAN;.	F	1997;1968;1968;538;231;933;856;1935;1964;1997;1877;2011	ENSP00000320006:L1997F;ENSP00000439807:L1968F;ENSP00000370410:L1968F;ENSP00000415964:L538F;ENSP00000445259:L231F;ENSP00000444230:L933F;ENSP00000444717:L856F;ENSP00000444151:L1935F;ENSP00000415208:L1964F;ENSP00000370403:L1997F;ENSP00000446358:L2011F	ENSP00000320006:L1997F	L	-	3	2	MPDZ	13099010	0.026000	0.19158	0.990000	0.47175	0.997000	0.91878	-0.794000	0.04584	-0.363000	0.08101	0.533000	0.62120	TTA	.	.		0.383	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829		A	13109010	T	A	13109010	3	1	264	1	0	0	0	0	1	0	0	0	9731	1519	53	4	229	4	MPDZ	9	13109010	Missense_Mutation	SNP	T	TCGA-FV-A3I0-01A-11D-A22F-10		13109010	128104421	37	38856										
ABCA1	19	hgsc.bcm.edu	37	chr9	107547843	107547843	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	cacttccaggaaatgcaagtCcaaagaaatcctggacaggc	9	11	0	1			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr9:107547843C>G	ENST00000374736.3	-	49	6873	c.6479G>C	c.(6478-6480)gGa>gCa	p.G2160A		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	2160					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	AAATGCAAGTCCAAAGAAATC	0.438																																					p.G2160A		Atlas-SNP	.											.	ABCA1	244	.	0			c.G6479C						.						100	102	102					9																	107547843		2203	4300	6503	SO:0001583	missense	19	exon49			GCAAGTCCAAAGA	AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"ATP binding cassette transporters / subfamily A"	29	protein-coding gene	gene with protein product	"Tangier disease"	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.6479G>C	chr9.hg19:g.107547843C>G	ENSP00000363868:p.Gly2160Ala	84.0	0.0		60.0	7.0	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Missense_Mutation	SNP	ENST00000374736.3	hg19	CCDS6762.1	.	.	.	.	.	.	.	.	.	.	C	9.251	1.040816	0.19669	.	.	ENSG00000165029	ENST00000374736	D	0.82526	-1.62	6.0	4.08	0.47627	.	0.215214	0.49916	D	0.000138	T	0.60196	0.2250	N	0.02802	-0.49	0.80722	D	1	B	0.06786	0.001	B	0.08055	0.003	T	0.50600	-0.8809	10	0.12430	T	0.62	.	10.5915	0.45312	0.0:0.7862:0.0:0.2138	.	2160	O95477	ABCA1_HUMAN	A	2160	ENSP00000363868:G2160A	ENSP00000363868:G2160A	G	-	2	0	ABCA1	106587664	0.998000	0.40836	1.000000	0.80357	0.985000	0.73830	1.613000	0.36900	0.794000	0.33899	0.650000	0.86243	GGA	.	.		0.438	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502		G	107547843	C	G	107547843	3	3	264	1	0	0	0	0	1	0	0	0	28	855	30	4	314	4	ABCA1	9	107547843	Missense_Mutation	SNP	C	TCGA-FV-A3I0-01A-11D-A22F-10	94438833	107547843	33665588	38	38857										
SEC16A	9919	hgsc.bcm.edu	37	chr9	139370175	139370175	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	gtctcccttacttcaccaacCacgttggcgcgatctgcctc	7	17	3	0			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr9:139370175C>A	ENST00000371706.3	-	1	1392	c.1359G>T	c.(1357-1359)gtG>gtT	p.V453V	SEC16A_ENST00000313050.7_Silent_p.V631V|SEC16A_ENST00000290037.6_Silent_p.V453V|SEC16A_ENST00000431893.2_Silent_p.V453V			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	453					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|protein transport (GO:0015031)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)				breast(1)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(15)|lung(14)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)		CTTCACCAACCACGTTGGCGC	0.527																																					p.V631V		Atlas-SNP	.											.	SEC16A	249	.	0			c.G1893T						.						36	41	39					9																	139370175		2129	4230	6359	SO:0001819	synonymous_variant	9919	exon3			ACCAACCACGTTG	AK074565	CCDS55351.1, CCDS75936.1	9q34.3	2007-06-20	2007-06-20	2007-06-20	ENSG00000148396	ENSG00000148396			29006	protein-coding gene	gene with protein product		612854	"KIAA0310"	KIAA0310		9205841	Standard	NM_014866		Approved	p250	uc004chx.3	O15027	OTTHUMG00000020932	ENST00000371706.3:c.1359G>T	chr9.hg19:g.139370175C>A		66.0	0.0		45.0	33.0	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Silent	SNP	ENST00000371706.3	hg19																																																																																				.	.		0.527	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459		A	139370175	C	A	139370175	2	1	264	1	0	0	0	0	0	0	0	1	14001	581	21	3		3	SEC16A	9	139370175	Silent	SNP	C	TCGA-FV-A3I0-01A-11D-A22F-10	31822332	139370175	1843256	39	38858										
ANKRD30A	91074	hgsc.bcm.edu	37	chr10	37506693	37506693	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	atgaaaaaattagggaagaaTtaggaagaatcgaagagcag	12	2	0	4			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr10:37506693T>C	ENST00000602533.1	+	33	3085	c.2986T>C	c.(2986-2988)Tta>Cta	p.L996L	ANKRD30A_ENST00000374660.1_Silent_p.L1115L|ANKRD30A_ENST00000361713.1_Silent_p.L996L			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	1052					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						TAGGGAAGAATTAGGAAGAAT	0.323																																					p.L996L		Atlas-SNP	.											.	ANKRD30A	448	.	0			c.T2986C						.						61	61	61					10																	37506693		1804	4062	5866	SO:0001819	synonymous_variant	91074	exon33			GAAGAATTAGGAA	AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"Ankyrin repeat domain containing"	17234	protein-coding gene	gene with protein product	"breast cancer antigen NY-BR-1"	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.2986T>C	chr10.hg19:g.37506693T>C		279.0	0.0		217.0	46.0	NM_052997	Q5W025	Silent	SNP	ENST00000602533.1	hg19																																																																																				.	.		0.323	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997		C	37506693	T	C	37506693	2	2	264	1	0	0	0	0	0	0	0	1	658	1490	52	2		2	ANKRD30A	10	37506693	Silent	SNP	T	TCGA-FV-A3I0-01A-11D-A22F-10		37506693	98028054	40	38859										
HERC4	26091	hgsc.bcm.edu	37	chr10	69797855	69797855	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	aaaactaatgcttacctttaGaaagtgcaagtgaatgatag	8	5	0	3			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr10:69797855G>C	ENST00000395198.3	-	5	705	c.458C>G	c.(457-459)tCt>tGt	p.S153C	HERC4_ENST00000277817.6_Missense_Mutation_p.S43C|HERC4_ENST00000412272.2_Missense_Mutation_p.S153C|HERC4_ENST00000373700.4_Missense_Mutation_p.S153C|HERC4_ENST00000395187.2_Missense_Mutation_p.L100V	NM_022079.2	NP_071362.1	Q5GLZ8	HERC4_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 4	153					cell differentiation (GO:0030154)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	27						CTTACCTTTAGAAAGTGCAAG	0.318																																					p.S153C		Atlas-SNP	.											.	HERC4	78	.	0			c.C458G						.						80	78	79					10																	69797855		2203	4299	6502	SO:0001583	missense	26091	exon5			CCTTTAGAAAGTG	AY221963	CCDS7274.1, CCDS41533.1, CCDS60541.1, CCDS60542.1	10q21.3	2013-09-20	2012-02-23		ENSG00000148634	ENSG00000148634			24521	protein-coding gene	gene with protein product		609248	"hect domain and RLD 4"			10997877	Standard	NM_022079		Approved	DKFZP564G092, KIAA1593	uc001jng.4	Q5GLZ8	OTTHUMG00000018343	ENST00000395198.3:c.458C>G	chr10.hg19:g.69797855G>C	ENSP00000378624:p.Ser153Cys	158.0	0.0		125.0	27.0	NM_022079	Q5GC98|Q5GC99|Q5GCA0|Q8IXP9|Q9HCH9	Missense_Mutation	SNP	ENST00000395198.3	hg19	CCDS41533.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.6|24.6	4.546086|4.546086	0.86022|0.86022	.|.	.|.	ENSG00000148634|ENSG00000148634	ENST00000395187|ENST00000277817;ENST00000412272;ENST00000395198;ENST00000373700;ENST00000513996	T|T;T;T;T;D	0.14893|0.81821	2.47|-1.48;-1.48;-1.48;-1.48;-1.54	5.25|5.25	5.25|5.25	0.73442|0.73442	.|Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	.|0.125660	.|0.56097	.|D	.|0.000023	D|D	0.87047|0.87047	0.6080|0.6080	L|L	0.53249|0.53249	1.67|1.67	0.80722|0.80722	D|D	1|1	.|D;P;D;D	.|0.76494	.|0.999;0.864;0.984;0.975	.|D;B;P;P	.|0.63192	.|0.912;0.318;0.881;0.764	D|D	0.88278|0.88278	0.2934|0.2934	7|10	0.14252|0.87932	T|D	0.57|0	.|.	18.8473|18.8473	0.92212|0.92212	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|153;153;153;153	.|Q5GLZ8-3;A8K9U4;Q5GLZ8-2;Q5GLZ8	.|.;.;.;HERC4_HUMAN	V|C	100|43;153;153;153;177	ENSP00000378614:L100V|ENSP00000277817:S43C;ENSP00000416504:S153C;ENSP00000378624:S153C;ENSP00000362804:S153C;ENSP00000427191:S177C	ENSP00000378614:L100V|ENSP00000277817:S43C	L|S	-|-	1|2	2|0	HERC4|HERC4	69467861|69467861	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	9.809000|9.809000	0.99208|0.99208	2.452000|2.452000	0.82932|0.82932	0.563000|0.563000	0.77884|0.77884	CTA|TCT	.	.		0.318	HERC4-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359262.1	NM_015601		C	69797855	G	C	69797855	3	2	264	1	0	0	0	0	1	0	0	0	7069	942	33	4	2803	4	HERC4	10	69797855	Missense_Mutation	SNP	G	TCGA-FV-A3I0-01A-11D-A22F-10	32291162	69797855	65736892	41	38860										
FGFR2	2263	hgsc.bcm.edu	37	chr10	123325033	123325033	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	atagaggccggagtctctagGcgtggcgccctttatctgca	13	11	2	1			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr10:123325033G>A	ENST00000358487.5	-	3	567	c.295C>T	c.(295-297)Cct>Tct	p.P99S	FGFR2_ENST00000359354.2_Missense_Mutation_p.P99S|FGFR2_ENST00000351936.6_Missense_Mutation_p.P99S|FGFR2_ENST00000369056.1_Missense_Mutation_p.P99S|FGFR2_ENST00000457416.2_Missense_Mutation_p.P99S|FGFR2_ENST00000357555.5_Intron|FGFR2_ENST00000490349.1_5'UTR|FGFR2_ENST00000360144.3_Intron|FGFR2_ENST00000346997.2_Missense_Mutation_p.P99S|FGFR2_ENST00000369060.4_Missense_Mutation_p.P99S|FGFR2_ENST00000356226.4_Intron|FGFR2_ENST00000369061.4_Missense_Mutation_p.P99S|FGFR2_ENST00000369059.1_Intron	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2	99	Ig-like C2-type 1.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)			breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	GAGTCTCTAGGCGTGGCGCCC	0.537		5	Mis		"gastric. NSCLC, endometrial"		"Crouzon, Pfeiffer, and Apert syndromes"		Saethre-Chotzen syndrome;Apert syndrome																												p.P99S		Atlas-SNP	.		Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	.	FGFR2	758	.	0			c.C295T						.						174	149	157					10																	123325033		2203	4300	6503	SO:0001583	missense	2263	exon3	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	CTCTAGGCGTGGC	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3689	protein-coding gene	gene with protein product	"Crouzon syndrome", "Pfeiffer syndrome"	176943	"bacteria-expressed kinase", "keratinocyte growth factor receptor", "craniofacial dysostosis 1", "Jackson-Weiss syndrome"	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.295C>T	chr10.hg19:g.123325033G>A	ENSP00000351276:p.Pro99Ser	75.0	0.0		78.0	44.0	NM_022970	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	Missense_Mutation	SNP	ENST00000358487.5	hg19	CCDS31298.1	.	.	.	.	.	.	.	.	.	.	G	10.52	1.373326	0.24857	.	.	ENSG00000066468	ENST00000369062;ENST00000369061;ENST00000358487;ENST00000369060;ENST00000346997;ENST00000457416;ENST00000351936;ENST00000369056;ENST00000369058;ENST00000359354	T;T;T;T;T;T;T;T;T	0.12879	2.64;2.64;2.64;2.64;2.64;2.64;2.64;2.64;2.64	5.24	1.16	0.20824	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.273628	0.42172	N	0.000759	T	0.11110	0.0271	L	0.41079	1.255	0.50039	D	0.999849	B;B;B;B;B;B;B;B	0.22541	0.003;0.071;0.011;0.009;0.016;0.02;0.011;0.029	B;B;B;B;B;B;B;B	0.34346	0.021;0.18;0.023;0.014;0.025;0.023;0.057;0.013	T	0.16100	-1.0414	10	0.23891	T	0.37	.	5.3591	0.16077	0.3175:0.1354:0.5472:0.0	.	118;118;99;118;99;99;118;99	D3DRD9;D3DRD4;B5A960;D3DRD5;P21802-18;P21802;D3DRE0;P21802-17	.;.;.;.;.;FGFR2_HUMAN;.;.	S	99	ENSP00000358057:P99S;ENSP00000351276:P99S;ENSP00000358056:P99S;ENSP00000263451:P99S;ENSP00000410294:P99S;ENSP00000309878:P99S;ENSP00000358052:P99S;ENSP00000358054:P99S;ENSP00000352309:P99S	ENSP00000263451:P99S	P	-	1	0	FGFR2	123315023	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	1.958000	0.40402	0.262000	0.21774	0.643000	0.83706	CCT	.	.		0.537	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141		A	123325033	G	A	123325033	3	1	264	1	0	0	0	0	1	0	0	0	5874	1203	42	3	2490	3	FGFR2	10	123325033	Missense_Mutation	SNP	G	TCGA-FV-A3I0-01A-11D-A22F-10	53527178	123325033	12209714	42	38861										
TACC2	10579	hgsc.bcm.edu	37	chr10	123843951	123843951	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	ggggtgctgggcacacggacGggccccactctcagacagca	15	14	1	1			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr10:123843951G>T	ENST00000369005.1	+	4	2276	c.1936G>T	c.(1936-1938)Ggg>Tgg	p.G646W	TACC2_ENST00000515603.1_Missense_Mutation_p.G646W|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000453444.2_Missense_Mutation_p.G646W|TACC2_ENST00000334433.3_Missense_Mutation_p.G646W|TACC2_ENST00000515273.1_Missense_Mutation_p.G646W	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	646					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				GCACACGGACGGGCCCCACTC	0.612																																					p.G646W		Atlas-SNP	.											.	TACC2	271	.	0			c.G1936T						.						36	34	34					10																	123843951		2203	4300	6503	SO:0001583	missense	10579	exon4			ACGGACGGGCCCC	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.1936G>T	chr10.hg19:g.123843951G>T	ENSP00000358001:p.Gly646Trp	32.0	0.0		30.0	16.0	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	hg19	CCDS7626.1	.	.	.	.	.	.	.	.	.	.	G	15.54	2.863732	0.51482	.	.	ENSG00000138162	ENST00000369005;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000453444;ENST00000340076	T;T;T;T;T	0.04317	3.69;3.65;3.65;3.69;3.65	5.21	-8.51	0.00923	.	1.128570	0.06872	N	0.800925	T	0.05960	0.0155	N	0.14661	0.345	0.09310	N	1	D;D;D	0.63880	0.993;0.993;0.993	P;P;P	0.60609	0.877;0.877;0.877	T	0.32824	-0.9892	10	0.72032	D	0.01	4.0547	8.3674	0.32395	0.2891:0.22:0.4909:0.0	.	646;646;646	E9PBC6;E7EMZ9;O95359	.;.;TACC2_HUMAN	W	646;646;646;646;646;636	ENSP00000358001:G646W;ENSP00000424467:G646W;ENSP00000427618:G646W;ENSP00000334280:G646W;ENSP00000395048:G646W	ENSP00000334280:G646W	G	+	1	0	TACC2	123833941	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.239000	0.02916	-1.296000	0.02353	-0.258000	0.10820	GGG	.	.		0.612	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1			T	123843951	G	T	123843951	3	4	264	1	0	0	0	0	1	0	0	0	15517	1116	39	1	1946	1	TACC2	10	123843951	Missense_Mutation	SNP	G	TCGA-FV-A3I0-01A-11D-A22F-10	518918	123843951	11690796	43	38862										
MUC5B	727897	hgsc.bcm.edu	37	chr11	1277989	1277989	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	acgcacacatgggcatctgcGtgcaggcctgccgtaagctc	12	14	1	0			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr11:1277989G>A	ENST00000529681.1	+	39	16283	c.16225G>A	c.(16225-16227)Gtg>Atg	p.V5409M	MUC5B_ENST00000447027.1_Missense_Mutation_p.V5412M	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	5409					cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		GGGCATCTGCGTGCAGGCCTG	0.652																																					p.V5409M		Atlas-SNP	.											.	MUC5B	473	.	0			c.G16225A						.						15	20	18					11																	1277989		1999	4114	6113	SO:0001583	missense	727897	exon39			ATCTGCGTGCAGG	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.16225G>A	chr11.hg19:g.1277989G>A	ENSP00000436812:p.Val5409Met	23.0	0.0		39.0	10.0	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	hg19	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	G	8.473	0.858093	0.17178	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000546052;ENST00000406844	T;T	0.64803	-0.12;-0.12	4.21	4.21	0.49690	.	.	.	.	.	T	0.81522	0.4840	M	0.88450	2.955	0.23636	N	0.997236	D;D	0.89917	1.0;1.0	D;D	0.71656	0.944;0.974	T	0.73707	-0.3898	9	0.87932	D	0	.	14.4235	0.67200	0.0:0.0:1.0:0.0	.	5746;5412	A7Y9J9;E9PBJ0	.;.	M	5409;5412;5353;308;5121	ENSP00000436812:V5409M;ENSP00000415793:V5412M	ENSP00000343037:V5353M	V	+	1	0	MUC5B	1234565	0.330000	0.24705	0.754000	0.31244	0.032000	0.12392	2.765000	0.47621	2.063000	0.61619	0.416000	0.27883	GTG	.	.		0.652	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		A	1277989	G	A	1277989	3	1	264	1	0	0	0	0	1	0	0	0	9988	1145	40	1	16388	1	MUC5B	11	1277989	Missense_Mutation	SNP	G	TCGA-FV-A3I0-01A-11D-A22F-10		1277989	133728527	44	38863										
STIM1	6786	hgsc.bcm.edu	37	chr11	4076832	4076832	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	cctcagtatgaggagaccttCcggaagctgcagctcagtgg	13	11	2	2			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr11:4076832C>A	ENST00000300737.4	+	4	1031	c.462C>A	c.(460-462)ttC>ttA	p.F154L	STIM1_ENST00000527484.1_3'UTR|STIM1_ENST00000527651.1_Missense_Mutation_p.F154L	NM_003156.3	NP_003147.2	Q13586	STIM1_HUMAN	stromal interaction molecule 1	154	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				activation of store-operated calcium channel activity (GO:0032237)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|regulation of calcium ion transport (GO:0051924)|regulation of store-operated calcium entry (GO:2001256)|store-operated calcium entry (GO:0002115)	cortical endoplasmic reticulum (GO:0032541)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|growth cone (GO:0030426)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of plasma membrane (GO:0005887)|microtubule (GO:0005874)	calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|microtubule plus-end binding (GO:0051010)|store-operated calcium channel activity (GO:0015279)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|liver(1)|lung(14)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30		Breast(177;0.00159)|Medulloblastoma(188;0.00258)|all_neural(188;0.0233)		BRCA - Breast invasive adenocarcinoma(625;0.114)|LUSC - Lung squamous cell carcinoma(625;0.141)		AGGAGACCTTCCGGAAGCTGC	0.547																																					p.F154L		Atlas-SNP	.											.	STIM1	55	.	0			c.C462A						.						85	74	78					11																	4076832		2201	4298	6499	SO:0001583	missense	6786	exon4			GACCTTCCGGAAG	BC021300, U52426	CCDS7749.1, CCDS60706.1, CCDS73247.1	11p15.5	2014-09-17			ENSG00000167323	ENSG00000167323		"Sterile alpha motif (SAM) domain containing"	11386	protein-coding gene	gene with protein product		605921				8921403, 11463338, 11983428	Standard	NM_003156		Approved	GOK, D11S4896E	uc021qco.1	Q13586	OTTHUMG00000133360	ENST00000300737.4:c.462C>A	chr11.hg19:g.4076832C>A	ENSP00000300737:p.Phe154Leu	112.0	0.0		123.0	17.0	NM_003156	E9PQJ4|Q8N382	Missense_Mutation	SNP	ENST00000300737.4	hg19	CCDS7749.1	.	.	.	.	.	.	.	.	.	.	C	17.63	3.436533	0.62955	.	.	ENSG00000167323	ENST00000525403;ENST00000300737;ENST00000527651;ENST00000532610;ENST00000532919;ENST00000530554;ENST00000525055;ENST00000528656	D;D;D;D;D;T;T;D	0.89552	-2.53;-2.53;-2.53;-2.53;-2.53;0.35;0.35;-2.53	5.78	4.88	0.63580	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 2 (1);	0.053094	0.85682	D	0.000000	D	0.88262	0.6389	M	0.76574	2.34	0.80722	D	1	B;B	0.31485	0.325;0.158	B;B	0.31686	0.134;0.095	D	0.87626	0.2513	10	0.72032	D	0.01	-32.2044	12.6938	0.56992	0.0:0.9203:0.0:0.0797	.	154;154	E9PQJ4;Q13586	.;STIM1_HUMAN	L	80;154;154;80;80;80;80;80	ENSP00000432210:F80L;ENSP00000300737:F154L;ENSP00000436208:F154L;ENSP00000434848:F80L;ENSP00000433949:F80L;ENSP00000431878:F80L;ENSP00000431191:F80L;ENSP00000432378:F80L	ENSP00000300737:F154L	F	+	3	2	STIM1	4033408	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.830000	0.48136	1.462000	0.47948	0.591000	0.81541	TTC	.	.		0.547	STIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257196.1	NM_003156		A	4076832	C	A	4076832	3	1	264	1	0	0	0	0	1	0	0	0	15298	854	30	3	476	3	STIM1	11	4076832	Missense_Mutation	SNP	C	TCGA-FV-A3I0-01A-11D-A22F-10	2798843	4076832	130929684	45	38864										
APBB1	322	hgsc.bcm.edu	37	chr11	6422643	6422643	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	ttaccaagcagcgggcattaCgccgttcggccatgatctga	11	12	1	2	rs142613637		TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr11:6422643C>G	ENST00000609360.1	-	11	1619	c.1520G>C	c.(1519-1521)cGt>cCt	p.R507P	APBB1_ENST00000608704.1_Missense_Mutation_p.R248P|APBB1_ENST00000529519.1_Missense_Mutation_p.R32P|APBB1_ENST00000609331.1_Missense_Mutation_p.R272P|APBB1_ENST00000299402.6_Missense_Mutation_p.R505P|APBB1_ENST00000608645.1_Missense_Mutation_p.R248P|APBB1_ENST00000530885.1_Missense_Mutation_p.R285P|APBB1_ENST00000608394.1_Missense_Mutation_p.R248P|APBB1_ENST00000311051.3_Missense_Mutation_p.R505P|APBB1_ENST00000389906.2_Missense_Mutation_p.R507P|APBB1_ENST00000608655.1_Missense_Mutation_p.R287P	NM_001164.3	NP_001155.1	O00213	APBB1_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 1 (Fe65)	507	PID 1. {ECO:0000255|PROSITE- ProRule:PRU00148}.				apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|histone H4 acetylation (GO:0043967)|negative regulation of cell growth (GO:0030308)|negative regulation of thymidylate synthase biosynthetic process (GO:0050760)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|proline-rich region binding (GO:0070064)|transcription factor binding (GO:0008134)			breast(4)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|prostate(2)|skin(1)|urinary_tract(1)	24		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;6.49e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)		GCGGGCATTACGCCGTTCGGC	0.567																																					p.R507P	GBM(147;1810 2556 5672 39622)	Atlas-SNP	.											.	APBB1	73	.	0			c.G1520C						.	C	PRO/ARG,PRO/ARG	0,4402		0,0,2201	65	60	62		1520,1514	4.9	1	11	dbSNP_134	62	1,8591	1.2+/-3.3	0,1,4295	no	missense,missense	APBB1	NM_001164.2,NM_145689.1	103,103	0,1,6496	GG,GC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	507/711,505/709	6422643	1,12993	2201	4296	6497	SO:0001583	missense	322	exon10			GCATTACGCCGTT	L77864	CCDS31410.1, CCDS58114.1, CCDS66015.1, CCDS66016.1, CCDS66017.1, CCDS66018.1	11p15	2008-02-01				ENSG00000166313			581	protein-coding gene	gene with protein product		602709		RIR		8955346, 8894693	Standard	NM_001164		Approved	Fe65	uc001mcy.1	O00213		ENST00000609360.1:c.1520G>C	chr11.hg19:g.6422643C>G	ENSP00000477213:p.Arg507Pro	48.0	0.0		38.0	16.0	NM_001164	A1E379|A6NH82|A6NL69|B7Z1J5|B7Z1J6|B7Z2Y0|D3DQT2|Q7Z324|Q96A93|V9GYK0|V9GYT4	Missense_Mutation	SNP	ENST00000609360.1	hg19		.	.	.	.	.	.	.	.	.	.	C	16.58	3.162721	0.57368	0.0	1.16E-4	ENSG00000166313	ENST00000299402;ENST00000311051;ENST00000389906;ENST00000539758;ENST00000536523;ENST00000544288;ENST00000530885	T;T;T;T	0.19938	2.11;2.11;2.11;2.11	4.94	4.94	0.65067	Phosphotyrosine interaction domain (3);	0.164923	0.41097	D	0.000957	T	0.38401	0.1039	L	0.43923	1.385	0.45762	D	0.998657	D;D;D;D	0.89917	1.0;0.998;0.994;0.999	D;D;D;D	0.72338	0.977;0.931;0.912;0.971	T	0.09997	-1.0649	10	0.52906	T	0.07	-6.0845	15.6382	0.76973	0.0:1.0:0.0:0.0	.	110;507;285;505	B7Z4M4;O00213;B7Z2Y0;O00213-2	.;APBB1_HUMAN;.;.	P	505;505;507;356;248;272;285	ENSP00000299402:R505P;ENSP00000311912:R505P;ENSP00000374556:R507P;ENSP00000433338:R285P	ENSP00000299402:R505P	R	-	2	0	APBB1	6379219	0.739000	0.28196	1.000000	0.80357	0.997000	0.91878	1.084000	0.30828	2.269000	0.75478	0.655000	0.94253	CGT	.	C|1.000;G|0.000		0.567	APBB1-023	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471831.1	NM_001164		G	6422643	C	G	6422643	3	3	264	1	0	0	0	0	1	0	0	0	759	536	19	4	632	4	APBB1	11	6422643	Missense_Mutation	SNP	C	TCGA-FV-A3I0-01A-11D-A22F-10	2345811	6422643	128583873	46	38865										
OR2D3	120775	hgsc.bcm.edu	37	chr11	6942827	6942827	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	actacttttgtgaacctcctGccctcctgaagctggcttcc	7	15	0	2			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr11:6942827G>T	ENST00000317834.3	+	1	623	c.595G>T	c.(595-597)Gcc>Tcc	p.A199S		NM_001004684.1	NP_001004684.1	Q8NGH3	OR2D3_HUMAN	olfactory receptor, family 2, subfamily D, member 3	199						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|large_intestine(7)|lung(12)|prostate(3)|skin(1)|stomach(1)	27		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		TGAACCTCCTGCCCTCCTGAA	0.488																																					p.A199S		Atlas-SNP	.											.	OR2D3	51	.	0			c.G595T						.						113	96	102					11																	6942827		2201	4296	6497	SO:0001583	missense	120775	exon1			CCTCCTGCCCTCC	BK004294	CCDS31417.1	11p15.4	2012-08-09			ENSG00000178358	ENSG00000178358		"GPCR / Class A : Olfactory receptors"	15146	protein-coding gene	gene with protein product							Standard	NM_001004684		Approved		uc010rav.2	Q8NGH3	OTTHUMG00000165742	ENST00000317834.3:c.595G>T	chr11.hg19:g.6942827G>T	ENSP00000320560:p.Ala199Ser	249.0	0.0		264.0	135.0	NM_001004684	B2RP06|Q6IFG8|Q96R51	Missense_Mutation	SNP	ENST00000317834.3	hg19	CCDS31417.1	.	.	.	.	.	.	.	.	.	.	G	17.54	3.416187	0.62511	.	.	ENSG00000178358	ENST00000317834	T	0.00107	8.72	5.17	5.17	0.71159	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44483	D	0.000448	T	0.00241	0.0007	L	0.35723	1.085	0.35845	D	0.826304	B	0.31790	0.34	B	0.43783	0.431	D	0.86135	0.1577	10	0.52906	T	0.07	-47.4386	16.5766	0.84681	0.0:0.0:1.0:0.0	.	199	Q8NGH3	OR2D3_HUMAN	S	199	ENSP00000320560:A199S	ENSP00000320560:A199S	A	+	1	0	OR2D3	6899403	0.044000	0.20184	1.000000	0.80357	0.973000	0.67179	0.386000	0.20702	2.865000	0.98341	0.655000	0.94253	GCC	.	.		0.488	OR2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385987.1	NM_001004684		T	6942827	G	T	6942827	3	4	264	1	0	0	0	0	1	0	0	0	11004	1319	46	3	597	3	OR2D3	11	6942827	Missense_Mutation	SNP	G	TCGA-FV-A3I0-01A-11D-A22F-10	520184	6942827	128063689	47	38866										
HPS5	11234	hgsc.bcm.edu	37	chr11	18333521	18333521	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	tgaatgagatggagtcctccTcctgaactgcccaaagccaa	9	12	0	3			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr11:18333521T>C	ENST00000349215.3	-	3	436	c.159A>G	c.(157-159)ggA>ggG	p.G53G	HPS5_ENST00000531848.1_5'UTR|HPS5_ENST00000396253.3_5'UTR|HPS5_ENST00000438420.2_5'UTR	NM_181507.1	NP_852608.1	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5	53					blood coagulation (GO:0007596)|organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						GGAGTCCTCCTCCTGAACTGC	0.453									Hermansky-Pudlak syndrome																												p.G53G		Atlas-SNP	.											.	HPS5	70	.	0			c.A159G						.						119	125	123					11																	18333521		2199	4293	6492	SO:0001819	synonymous_variant	11234	exon3	Familial Cancer Database	HPS, HPS1-8	TCCTCCTCCTGAA	AB023234	CCDS7836.1, CCDS7837.1	11p14	2014-06-18			ENSG00000110756	ENSG00000110756			17022	protein-coding gene	gene with protein product		607521				10231032, 10094488	Standard	NM_181507		Approved		uc001mod.1	Q9UPZ3	OTTHUMG00000166612	ENST00000349215.3:c.159A>G	chr11.hg19:g.18333521T>C		57.0	0.0		59.0	12.0	NM_181507	A8K6J8|A8K8S1|D3DQX9|D3DQY0|O95942|Q8N4U0	Silent	SNP	ENST00000349215.3	hg19	CCDS7836.1																																																																																			.	.		0.453	HPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390808.1	NM_181507		C	18333521	T	C	18333521	2	2	264	1	0	0	0	0	0	0	0	1	7351	1538	54	2		2	HPS5	11	18333521	Silent	SNP	T	TCGA-FV-A3I0-01A-11D-A22F-10	11390694	18333521	116672995	48	38867										
SLC35C1	55343	hgsc.bcm.edu	37	chr11	45832329	45832329	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	ctcctctccccactgcagggGgcttctggcttggtgtggac	13	14	2	0			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr11:45832329G>A	ENST00000314134.3	+	2	1934	c.538G>A	c.(538-540)Ggc>Agc	p.G180S	SLC35C1_ENST00000442528.2_Missense_Mutation_p.G167S|SLC35C1_ENST00000456334.1_Missense_Mutation_p.G167S|CTD-2210P24.6_ENST00000534128.1_lincRNA	NM_018389.4	NP_060859.4	Q96A29	FUCT1_HUMAN	solute carrier family 35 (GDP-fucose transporter), member C1	180					carbohydrate transport (GO:0008643)|lipid glycosylation (GO:0030259)|negative regulation of Notch signaling pathway (GO:0045746)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)				endometrium(3)|kidney(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	10				GBM - Glioblastoma multiforme(35;0.227)		CACTGCAGGGGGCTTCTGGCT	0.612																																					p.G180S		Atlas-SNP	.											.	SLC35C1	23	.	0			c.G538A						.						33	36	35					11																	45832329		2203	4299	6502	SO:0001583	missense	55343	exon2			GCAGGGGGCTTCT		CCDS7914.1, CCDS44575.1	11p11.2	2014-09-17	2013-07-17			ENSG00000181830		"Solute carriers"	20197	protein-coding gene	gene with protein product		605881	"solute carrier family 35, member C1"			11326279, 11326280	Standard	NM_018389		Approved	FUCT1, FLJ11320	uc010rgm.2	Q96A29		ENST00000314134.3:c.538G>A	chr11.hg19:g.45832329G>A	ENSP00000313318:p.Gly180Ser	30.0	0.0		54.0	17.0	NM_018389	B2RDB2|Q9BV76|Q9NUJ8	Missense_Mutation	SNP	ENST00000314134.3	hg19	CCDS7914.1	.	.	.	.	.	.	.	.	.	.	G	36	5.620545	0.96660	.	.	ENSG00000181830	ENST00000442528;ENST00000456334;ENST00000530670;ENST00000314134;ENST00000540685	D;D;D	0.85339	-1.97;-1.97;-1.97	6.08	6.08	0.98989	Drug/metabolite transporter (1);	0.092273	0.85682	D	0.000000	D	0.94188	0.8135	M	0.90650	3.135	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93188	0.6580	10	0.45353	T	0.12	-31.4081	20.6634	0.99662	0.0:0.0:1.0:0.0	.	180	Q96A29	FUCT1_HUMAN	S	167;167;101;180;180	ENSP00000412408:G167S;ENSP00000399779:G167S;ENSP00000313318:G180S	ENSP00000313318:G180S	G	+	1	0	SLC35C1	45788905	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.538000	0.98072	2.894000	0.99253	0.655000	0.94253	GGC	.	.		0.612	SLC35C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390139.1	NM_018389		A	45832329	G	A	45832329	3	1	264	1	0	0	0	0	1	0	0	0	14594	1232	43	3	544	3	SLC35C1	11	45832329	Missense_Mutation	SNP	G	TCGA-FV-A3I0-01A-11D-A22F-10	27498808	45832329	89174187	49	38868										
SUV420H1	51111	hgsc.bcm.edu	37	chr11	67925241	67925241	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	ttttccaactattaacctcaAgcgcttagctggaggaagag	9	9	1	1			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr11:67925241A>C	ENST00000304363.4	-	11	2925	c.2572T>G	c.(2572-2574)Ttg>Gtg	p.L858V		NM_017635.3	NP_060105	Q4FZB7	SV421_HUMAN	suppressor of variegation 4-20 homolog 1 (Drosophila)	858					histone H4-K20 trimethylation (GO:0034773)|muscle organ development (GO:0007517)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome, centromeric region (GO:0000780)	histone methyltransferase activity (H4-K20 specific) (GO:0042799)|histone-lysine N-methyltransferase activity (GO:0018024)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(15)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46						ATTAACCTCAAGCGCTTAGCT	0.398																																					p.L858V		Atlas-SNP	.											.	SUV420H1	125	.	0			c.T2572G						.						64	65	65					11																	67925241		2200	4294	6494	SO:0001583	missense	51111	exon11			ACCTCAAGCGCTT	AL512763	CCDS31623.1, CCDS44660.1	11q13.2	2011-07-01			ENSG00000110066	ENSG00000110066		"Chromatin-modifying enzymes / K-methyltransferases"	24283	protein-coding gene	gene with protein product		610881				10810093, 11401438	Standard	NM_016028		Approved	CGI-85, KMT5B	uc001onm.1	Q4FZB7	OTTHUMG00000150484	ENST00000304363.4:c.2572T>G	chr11.hg19:g.67925241A>C	ENSP00000305899:p.Leu858Val	135.0	0.0		178.0	101.0	NM_017635	B7WNX7|Q3SX56|Q4V775|Q6P150|Q96E44|Q9BUL0|Q9H022|Q9H2K3|Q9NXV3|Q9Y393	Missense_Mutation	SNP	ENST00000304363.4	hg19	CCDS31623.1	.	.	.	.	.	.	.	.	.	.	A	15.22	2.769480	0.49680	.	.	ENSG00000110066	ENST00000304363	T	0.63096	-0.02	5.71	-5.41	0.02648	.	0.000000	0.85682	D	0.000000	T	0.66137	0.2759	L	0.32530	0.975	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.68221	-0.5466	10	0.87932	D	0	-13.6599	17.731	0.88377	0.7574:0.0:0.2426:0.0	.	858	Q4FZB7	SV421_HUMAN	V	858	ENSP00000305899:L858V	ENSP00000305899:L858V	L	-	1	2	SUV420H1	67681817	0.025000	0.19082	0.001000	0.08648	0.981000	0.71138	0.170000	0.16663	-1.557000	0.01692	0.402000	0.26972	TTG	.	.		0.398	SUV420H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318319.1	NM_017635		C	67925241	A	C	67925241	3	2	264	1	0	0	0	0	1	0	0	0	15429	69	3	5	89	5	SUV420H1	11	67925241	Missense_Mutation	SNP	A	TCGA-FV-A3I0-01A-11D-A22F-10	22092912	67925241	67081275	50	38869										
CMAS	55907	hgsc.bcm.edu	37	chr12	22199469	22199479	+	Frame_Shift_Del	DEL	GCGGCCCTGGA	GCGGCCCTGGA	-													0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	tcattggctgggtcctgcgtGcggccctggattcaggggcc							TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	GCGGCCCTGGA	GCGGCCCTGGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr12:22199469_22199479delGCGGCCCTGGA	ENST00000229329.2	+	1	362_372	c.232_242delGCGGCCCTGGA	c.(232-243)gcggccctggatfs	p.AALD78fs		NM_018686.4	NP_061156.1	Q8NFW8	NEUA_HUMAN	cytidine monophosphate N-acetylneuraminic acid synthetase	78					lipopolysaccharide biosynthetic process (GO:0009103)|N-acetylneuraminate metabolic process (GO:0006054)	membrane (GO:0016020)|nucleus (GO:0005634)	N-acylneuraminate cytidylyltransferase activity (GO:0008781)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	24						GGTCCTGCGTGCGGCCCTGGATTCAGGGGCC	0.701																																					p.77_81del		Atlas-Indel,Pindel	.											.	CMAS	45	.	0			c.231_241del						.																																			SO:0001589	frameshift_variant	55907	exon1			.	AF271388	CCDS8696.1	12p12.1	2008-08-04			ENSG00000111726	ENSG00000111726			18290	protein-coding gene	gene with protein product	"CMP-Neu5Ac synthetase"	603316				8889549, 7566098	Standard	NM_018686		Approved		uc001rfm.4	Q8NFW8	OTTHUMG00000169097	ENST00000229329.2:c.232_242delGCGGCCCTGGA	chr12.hg19:g.22199469_22199479delGCGGCCCTGGA	ENSP00000229329:p.Ala78fs	24.0	0.0		79.0	39.0	NM_018686	Q96AX5|Q9NQZ0	Frame_Shift_Del	DEL	ENST00000229329.2	hg19	CCDS8696.1																																																																																			.	.		0.701	CMAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402235.1	NM_018686		-	22199479	GCGGCCCTGGA	-	22199469	7	5	264	1	0	1	0	1	0	0	0	0	3577	1319	46	0	234	0	CMAS	12	22199469	Frame_Shift_Del	DEL	GCGGCCCTGGA	TCGA-FV-A3I0-01A-11D-A22F-10		22199469	111652426	51	38870										
RARG	5916	hgsc.bcm.edu	37	chr12	53607025	53607025	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	gggctcctccaggtccatgcGgtctatggggacaagtatac	13	11	1	0			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr12:53607025G>A	ENST00000425354.2	-	9	1508	c.1021C>T	c.(1021-1023)Cgc>Tgc	p.R341C	RARG_ENST00000543726.1_Missense_Mutation_p.R319C|RARG_ENST00000327550.3_Missense_Mutation_p.R269C|RARG_ENST00000338561.5_Missense_Mutation_p.R330C|RARG_ENST00000394426.1_Missense_Mutation_p.R341C|RARG_ENST00000543762.1_5'UTR	NM_000966.5	NP_000957.1	P13631	RARG_HUMAN	retinoic acid receptor, gamma	341	Ligand-binding.				anterior/posterior pattern specification (GO:0009952)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|embryonic camera-type eye development (GO:0031076)|embryonic eye morphogenesis (GO:0048048)|embryonic hindlimb morphogenesis (GO:0035116)|face development (GO:0060324)|gene expression (GO:0010467)|glandular epithelial cell development (GO:0002068)|growth plate cartilage chondrocyte growth (GO:0003430)|Harderian gland development (GO:0070384)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of programmed cell death (GO:0043068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of cell size (GO:0008361)|regulation of myelination (GO:0031641)|response to retinoic acid (GO:0032526)|retinal pigment epithelium development (GO:0003406)|retinoic acid receptor signaling pathway (GO:0048384)|trachea cartilage development (GO:0060534)|transcription initiation from RNA polymerase II promoter (GO:0006367)	integral component of membrane (GO:0016021)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|retinoic acid receptor activity (GO:0003708)|retinoid X receptor binding (GO:0046965)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.R341C(1)		breast(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Tazarotene(DB00799)|Tretinoin(DB00755)	AGGTCCATGCGGTCTATGGGG	0.607											OREG0021862	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R341C		Atlas-SNP	.											RARG,NS,carcinoma,0,1	RARG	53	.	1	Substitution - Missense(1)	breast(1)	c.C1021T						.						34	37	36					12																	53607025		2203	4300	6503	SO:0001583	missense	5916	exon9			CCATGCGGTCTAT	M57707	CCDS8850.1, CCDS41790.1, CCDS58236.1, CCDS58237.1	12q13	2013-01-16			ENSG00000172819	ENSG00000172819		"Nuclear hormone receptors"	9866	protein-coding gene	gene with protein product		180190				1849262	Standard	NM_001042728		Approved	RARC, NR1B3	uc001scf.3	P13631	OTTHUMG00000048077	ENST00000425354.2:c.1021C>T	chr12.hg19:g.53607025G>A	ENSP00000388510:p.Arg341Cys	36.0	0.0	993	67.0	35.0	NM_000966	B7Z492|B7Z4F1|B7ZAE4|J3KNP6|P22932|Q15281|Q52LZ8|Q9BYX8|Q9H1I3|Q9UJ38	Missense_Mutation	SNP	ENST00000425354.2	hg19	CCDS8850.1	.	.	.	.	.	.	.	.	.	.	G	33	5.266300	0.95399	.	.	ENSG00000172819	ENST00000425354;ENST00000394426;ENST00000327550;ENST00000338561;ENST00000543726	T;T;T;T;T	0.40476	1.03;1.03;1.03;1.03;1.03	5.42	5.42	0.78866	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.053635	0.85682	D	0.000000	T	0.71350	0.3329	M	0.89095	3.005	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.999	T	0.76091	-0.3086	10	0.62326	D	0.03	.	18.3727	0.90412	0.0:0.0:1.0:0.0	.	319;341;330	B7Z4F1;P13631;F1D8P1	.;RARG_HUMAN;.	C	341;341;269;330;319	ENSP00000388510:R341C;ENSP00000377947:R341C;ENSP00000332695:R269C;ENSP00000343698:R330C;ENSP00000444335:R319C	ENSP00000332695:R269C	R	-	1	0	RARG	51893292	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	9.837000	0.99465	2.712000	0.92718	0.563000	0.77884	CGC	.	.		0.607	RARG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109404.2	NM_000966		A	53607025	G	A	53607025	3	1	264	1	0	0	0	0	1	0	0	0	13069	1116	39	1	351	1	RARG	12	53607025	Missense_Mutation	SNP	G	TCGA-FV-A3I0-01A-11D-A22F-10	31407556	53607025	80244870	52	38871										
UTP20	27340	hgsc.bcm.edu	37	chr12	101736252	101736253	+	Frame_Shift_Ins	INS	-	-	AC													0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	gttgatattctggtgacagtINSacaaaacttgttaaagcatt							TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr12:101736252_101736253insAC	ENST00000261637.4	+	33	4304_4305	c.4130_4131insAC	c.(4129-4134)gtacaafs	p.Q1378fs		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	1378					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						CTGGTGACAGTACAAAACTTGT	0.312																																					p.V1377fs		Atlas-Indel,Pindel	.											.	UTP20	222	.	0			c.4130_4131insAC						.																																			SO:0001589	frameshift_variant	27340	exon33			.	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"down regulated in metastasis"	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.4131_4132dupAC	chr12.hg19:g.101736253_101736254dupAC	ENSP00000261637:p.Gln1378fs	81.0	0.0		111.0	52.0	NM_014503	Q9H3H4	Frame_Shift_Ins	INS	ENST00000261637.4	hg19	CCDS9081.1																																																																																			.	.		0.312	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		AC	101736253	-	AC	101736252	7	5	264	1	0	1	1	0	0	0	0	0	17114	1638	57	0	4260	0	UTP20	12	101736252	Frame_Shift_Ins	INS	-	TCGA-FV-A3I0-01A-11D-A22F-10	48129227	101736252	32115643	53	38872										
PIWIL1	9271	hgsc.bcm.edu	37	chr12	130827612	130827612	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	ttatttggccgtggacggcaGagaggaacagcaggaggaac	16	7	0	1			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr12:130827612G>C	ENST00000245255.3	+	3	428	c.156G>C	c.(154-156)caG>caC	p.Q52H		NM_001190971.1|NM_004764.4	NP_001177900.1|NP_004755.2	Q96J94	PIWL1_HUMAN	piwi-like RNA-mediated gene silencing 1	52					gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|mRNA cap binding complex (GO:0005845)|P granule (GO:0043186)|polysome (GO:0005844)	mRNA binding (GO:0003729)|piRNA binding (GO:0034584)|single-stranded RNA binding (GO:0003727)			breast(6)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(26)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	57	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.02e-06)|Epithelial(86;3.85e-05)|all cancers(50;4.65e-05)		GTGGACGGCAGAGAGGAACAG	0.443																																					p.Q52H		Atlas-SNP	.											.	PIWIL1	157	.	0			c.G156C						.						67	58	61					12																	130827612		2203	4300	6503	SO:0001583	missense	9271	exon3			ACGGCAGAGAGGA	AF104260	CCDS9268.1	12q24.33	2014-01-21	2013-02-15		ENSG00000125207	ENSG00000125207		"Argonaute/PIWI family"	9007	protein-coding gene	gene with protein product		605571	"piwi (Drosophila)-like 1", "piwi-like 1 (Drosophila)"			9851978, 12906857	Standard	NM_004764		Approved	PIWI, HIWI, CT80.1	uc001uik.3	Q96J94	OTTHUMG00000168382	ENST00000245255.3:c.156G>C	chr12.hg19:g.130827612G>C	ENSP00000245255:p.Gln52His	167.0	0.0		218.0	35.0	NM_004764	A4F266|O95404|Q8NA60|Q8TBY5|Q96JD5	Missense_Mutation	SNP	ENST00000245255.3	hg19	CCDS9268.1	.	.	.	.	.	.	.	.	.	.	G	15.33	2.802030	0.50315	.	.	ENSG00000125207	ENST00000245255;ENST00000546060;ENST00000539400;ENST00000539995;ENST00000535956;ENST00000542723	T;T;T;T;T;T	0.09630	2.96;2.96;2.96;2.96;2.96;2.96	5.13	4.22	0.49857	.	0.310182	0.35585	N	0.003101	T	0.28333	0.0700	M	0.67953	2.075	0.50632	D	0.999889	D;D	0.67145	0.996;0.994	D;D	0.79108	0.992;0.986	T	0.00411	-1.1756	10	0.45353	T	0.12	-11.8924	12.125	0.53913	0.0847:0.0:0.9153:0.0	.	52;52	Q96J94;Q96J94-2	PIWL1_HUMAN;.	H	52	ENSP00000245255:Q52H;ENSP00000442086:Q52H;ENSP00000440677:Q52H;ENSP00000439096:Q52H;ENSP00000444353:Q52H;ENSP00000438582:Q52H	ENSP00000245255:Q52H	Q	+	3	2	PIWIL1	129393565	1.000000	0.71417	0.997000	0.53966	0.438000	0.31896	3.187000	0.50950	2.544000	0.85801	0.467000	0.42956	CAG	.	.		0.443	PIWIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399510.1			C	130827612	G	C	130827612	3	2	264	1	0	0	0	0	1	0	0	0	11966	933	33	4	162	4	PIWIL1	12	130827612	Missense_Mutation	SNP	G	TCGA-FV-A3I0-01A-11D-A22F-10	29091360	130827612	3024283	54	38873										
KTN1	3895	hgsc.bcm.edu	37	chr14	56079097	56079097	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	tcgttgaaacttcaagtagtGttagggaaagaaaaaagaag	11	3	1	3			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr14:56079097G>T	ENST00000395314.3	+	2	399	c.331G>T	c.(331-333)Gtt>Ttt	p.V111F	KTN1_ENST00000438792.2_Missense_Mutation_p.V111F|KTN1_ENST00000395309.3_Missense_Mutation_p.V111F|KTN1_ENST00000413890.2_Missense_Mutation_p.V111F|KTN1_ENST00000395308.1_Missense_Mutation_p.V111F|KTN1_ENST00000416613.1_Missense_Mutation_p.V111F|KTN1_ENST00000395311.1_Missense_Mutation_p.V111F	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	111					microtubule-based movement (GO:0007018)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|large_intestine(8)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	19						TTCAAGTAGTGTTAGGGAAAG	0.388			T	RET	papillary thryoid																																p.V111F		Atlas-SNP	.		Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	.	KTN1	147	.	0			c.G331T						.						82	86	85					14																	56079097		2203	4300	6503	SO:0001583	missense	3895	exon2			AGTAGTGTTAGGG		CCDS41957.1, CCDS41958.1, CCDS41959.1	14q22.1	2008-05-02			ENSG00000126777	ENSG00000126777			6467	protein-coding gene	gene with protein product		600381				9605849	Standard	NM_001079521		Approved	KIAA0004, CG1	uc001xcc.3	Q86UP2	OTTHUMG00000140312	ENST00000395314.3:c.331G>T	chr14.hg19:g.56079097G>T	ENSP00000378725:p.Val111Phe	119.0	0.0		157.0	49.0	NM_004986	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Missense_Mutation	SNP	ENST00000395314.3	hg19	CCDS41957.1	.	.	.	.	.	.	.	.	.	.	G	15.21	2.764921	0.49574	.	.	ENSG00000126777	ENST00000413890;ENST00000395309;ENST00000438792;ENST00000395314;ENST00000395308;ENST00000395311;ENST00000416613	D;D;D;D;D;D;D	0.99167	-5.51;-5.51;-5.51;-5.51;-5.51;-5.51;-5.51	5.9	3.98	0.46160	.	0.305062	0.23883	N	0.043633	D	0.97291	0.9114	L	0.36672	1.1	0.33721	D	0.616973	P;D;P;P	0.55800	0.842;0.973;0.842;0.677	B;P;B;B	0.49999	0.394;0.628;0.394;0.394	D	0.98036	1.0379	10	0.62326	D	0.03	-9.83	5.5939	0.17317	0.2328:0.2687:0.4985:0.0	.	111;111;111;111	B4DZ88;Q86UP2-2;Q17RZ5;Q86UP2	.;.;.;KTN1_HUMAN	F	111	ENSP00000394992:V111F;ENSP00000378720:V111F;ENSP00000391964:V111F;ENSP00000378725:V111F;ENSP00000378719:V111F;ENSP00000378722:V111F;ENSP00000388807:V111F	ENSP00000378719:V111F	V	+	1	0	KTN1	55148850	0.813000	0.29090	1.000000	0.80357	0.965000	0.64279	-0.075000	0.11431	1.504000	0.48704	0.591000	0.81541	GTT	.	.		0.388	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2			T	56079097	G	T	56079097	3	4	264	1	0	0	0	0	1	0	0	0	8594	1377	48	3	333	3	KTN1	14	56079097	Missense_Mutation	SNP	G	TCGA-FV-A3I0-01A-11D-A22F-10		56079097	51270443	55	38874										
RIN3	79890	hgsc.bcm.edu	37	chr14	93118817	93118817	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	gacaactggcctcgaccctcCcagctcccttagagaacgct	8	17	0	1			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr14:93118817C>T	ENST00000216487.7	+	6	1582	c.1423C>T	c.(1423-1425)Cca>Tca	p.P475S	RIN3_ENST00000418924.2_3'UTR	NM_024832.3	NP_079108.3	Q8TB24	RIN3_HUMAN	Ras and Rab interactor 3	475	Pro-rich.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)	GTPase activator activity (GO:0005096)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(4)|kidney(2)|large_intestine(7)|lung(19)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36		all_cancers(154;0.0701)				CTCGACCCTCCCAGCTCCCTT	0.632																																					p.P475S		Atlas-SNP	.											.	RIN3	81	.	0			c.C1423T						.						83	104	97					14																	93118817		2203	4300	6503	SO:0001583	missense	79890	exon6			ACCCTCCCAGCTC	BC025248	CCDS32144.1	14q32.13	2008-08-29				ENSG00000100599			18751	protein-coding gene	gene with protein product		610223				11733506	Standard	NM_024832		Approved	FLJ22439	uc001yap.3	Q8TB24		ENST00000216487.7:c.1423C>T	chr14.hg19:g.93118817C>T	ENSP00000216487:p.Pro475Ser	57.0	0.0		28.0	23.0	NM_024832	Q76LB3|Q8NF30|Q8TEE8|Q8WYP4|Q9H6A5|Q9HAG1	Missense_Mutation	SNP	ENST00000216487.7	hg19	CCDS32144.1	.	.	.	.	.	.	.	.	.	.	C	10.69	1.421498	0.25639	.	.	ENSG00000100599	ENST00000216487;ENST00000428147	T	0.05580	3.42	4.49	2.65	0.31530	.	11.404600	0.00166	N	0.000005	T	0.06234	0.0161	L	0.38531	1.155	0.18873	N	0.999981	P;B;B;P	0.45715	0.865;0.024;0.013;0.787	B;B;B;B	0.39503	0.301;0.008;0.003;0.158	T	0.38415	-0.9662	10	0.12103	T	0.63	0.0344	5.4136	0.16361	0.0:0.6096:0.1637:0.2267	.	475;521;400;475	Q8TB24-4;Q86U22;Q6ZRC2;Q8TB24	.;.;.;RIN3_HUMAN	S	475;399	ENSP00000216487:P475S	ENSP00000216487:P475S	P	+	1	0	RIN3	92188570	0.000000	0.05858	0.000000	0.03702	0.441000	0.31987	0.524000	0.22940	0.356000	0.24157	0.491000	0.48974	CCA	.	.		0.632	RIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412269.1			T	93118817	C	T	93118817	3	4	264	1	0	0	0	0	1	0	0	0	13388	623	22	3	1445	3	RIN3	14	93118817	Missense_Mutation	SNP	C	TCGA-FV-A3I0-01A-11D-A22F-10	37039720	93118817	14230723	56	38875										
OR4N4	283694	hgsc.bcm.edu	37	chr15	22382912	22382912	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	ctgctatgcaatgatgttggCtctgtggcttgggggttttg	15	6	1	1			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr15:22382912C>T	ENST00000328795.4	+	1	531	c.440C>T	c.(439-441)gCt>gTt	p.A147V	RP11-69H14.6_ENST00000558896.1_RNA	NM_001005241.2	NP_001005241.2	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N, member 4	147						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A147D(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(19)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	40		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		ATGATGTTGGCTCTGTGGCTT	0.527																																					p.A147V		Atlas-SNP	.											OR4N4,NS,carcinoma,0,1	OR4N4	108	.	1	Substitution - Missense(1)	lung(1)	c.C440T						.						141	123	129					15																	22382912		2189	4262	6451	SO:0001583	missense	283694	exon1			TGTTGGCTCTGTG	AI018459	CCDS32173.1	15q11.2	2012-08-09				ENSG00000183706		"GPCR / Class A : Olfactory receptors"	15375	protein-coding gene	gene with protein product							Standard	NM_001005241		Approved		uc010tzv.2	Q8N0Y3		ENST00000328795.4:c.440C>T	chr15.hg19:g.22382912C>T	ENSP00000332500:p.Ala147Val	352.0	1.0		393.0	26.0	NM_001005241	Q6IEY3|Q6IF56	Missense_Mutation	SNP	ENST00000328795.4	hg19	CCDS32173.1	.	.	.	.	.	.	.	.	.	.	.	2.349	-0.349272	0.05173	.	.	ENSG00000183706	ENST00000328795	T	0.36878	1.23	3.37	0.203	0.15195	GPCR, rhodopsin-like superfamily (1);	0.978321	0.08345	N	0.960256	T	0.26846	0.0657	L	0.46741	1.465	0.09310	N	1	B	0.15473	0.013	B	0.22880	0.042	T	0.36768	-0.9734	10	0.07644	T	0.81	-1.223	6.6776	0.23103	0.0:0.5516:0.3429:0.1055	.	147	Q8N0Y3	OR4N4_HUMAN	V	147	ENSP00000332500:A147V	ENSP00000332500:A147V	A	+	2	0	OR4N4	19884276	0.000000	0.05858	0.074000	0.20217	0.128000	0.20619	-0.513000	0.06305	-0.056000	0.13221	-0.714000	0.03626	GCT	.	.		0.527	OR4N4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414922.1			T	22382912	C	T	22382912	3	4	264	1	0	0	0	0	1	0	0	0	11087	797	28	3	442	3	OR4N4	15	22382912	Missense_Mutation	SNP	C	TCGA-FV-A3I0-01A-11D-A22F-10		22382912	80148480	57	38876										
TRIP4	9325	hgsc.bcm.edu	37	chr15	64698610	64698610	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	gcgaattaagtctggtctggAgaaggctatcaagcataaag	12	6	3	1			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr15:64698610A>G	ENST00000261884.3	+	6	839	c.779A>G	c.(778-780)gAg>gGg	p.E260G	TRIP4_ENST00000559565.1_Intron	NM_016213.4	NP_057297.2	Q15650	TRIP4_HUMAN	thyroid hormone receptor interactor 4	260					positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21						TCTGGTCTGGAGAAGGCTATC	0.383																																					p.E260G		Atlas-SNP	.											.	TRIP4	43	.	0			c.A779G						.						95	92	93					15																	64698610		2203	4300	6503	SO:0001583	missense	9325	exon6			GTCTGGAGAAGGC	L40371	CCDS10194.1	15q22.1	2014-02-17			ENSG00000103671	ENSG00000103671		"-"	12310	protein-coding gene	gene with protein product	"zinc finger, C2HC5-type"	604501				7776974	Standard	NM_016213		Approved	HsT17391, ZC2HC5	uc002anm.3	Q15650	OTTHUMG00000133033	ENST00000261884.3:c.779A>G	chr15.hg19:g.64698610A>G	ENSP00000261884:p.Glu260Gly	98.0	0.0		113.0	24.0	NM_016213	B2RAS0|Q96ED7|Q9UKH0	Missense_Mutation	SNP	ENST00000261884.3	hg19	CCDS10194.1	.	.	.	.	.	.	.	.	.	.	A	28.8	4.955375	0.92726	.	.	ENSG00000103671	ENST00000261884	.	.	.	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.66218	0.2767	M	0.79123	2.44	0.80722	D	1	P	0.41420	0.749	B	0.40477	0.33	T	0.68716	-0.5335	9	0.39692	T	0.17	0.0375	16.3265	0.82983	1.0:0.0:0.0:0.0	.	260	Q15650	TRIP4_HUMAN	G	260	.	ENSP00000261884:E260G	E	+	2	0	TRIP4	62485663	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.553000	0.90686	2.313000	0.78055	0.455000	0.32223	GAG	.	.		0.383	TRIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256635.2	NM_016213		G	64698610	A	G	64698610	3	3	264	1	0	0	0	0	1	0	0	0	16573	304	11	2	801	2	TRIP4	15	64698610	Missense_Mutation	SNP	A	TCGA-FV-A3I0-01A-11D-A22F-10	42315698	64698610	37832782	58	38877										
NLRC3	197358	hgsc.bcm.edu	37	chr16	3613089	3613089	+	RNA	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	gctcagggacaggttggcctCctgggcacaggcgtcggaca	16	12	1	0			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr16:3613089C>T	ENST00000301749.7	-	0	2254				NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000603507.1_RNA|NLRC3_ENST00000324659.8_RNA|NLRC3_ENST00000448023.2_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						AGGTTGGCCTCCTGGGCACAG	0.706																																					p.E617K		Atlas-SNP	.											.	NLRC3	103	.	0			c.G1849A						.						7	10	9					16																	3613089		1992	4146	6138			197358	exon5			TGGCCTCCTGGGC	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"Nucleotide-binding domain and leucine rich repeat containing"	29889	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3", "NOD-like receptor C3"	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		chr16.hg19:g.3613089C>T		21.0	0.0		58.0	40.0	NM_178844	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Missense_Mutation	SNP	ENST00000301749.7	hg19		.	.	.	.	.	.	.	.	.	.	C	13.91	2.378785	0.42207	.	.	ENSG00000167984	ENST00000419350;ENST00000301749;ENST00000359128;ENST00000448023;ENST00000324659	T;T;T;T	0.79141	-0.76;-0.79;-0.77;-1.24	5.15	4.2	0.49525	.	0.067509	0.64402	D	0.000012	T	0.67655	0.2916	.	.	.	0.23050	N	0.998376	B	0.25441	0.126	B	0.24394	0.053	T	0.59862	-0.7374	9	0.46703	T	0.11	.	11.0252	0.47741	0.0:0.9091:0.0:0.0909	.	664	C9JLH9	.	K	617;617;617;664;599	ENSP00000301749:E617K;ENSP00000352039:E617K;ENSP00000414415:E664K;ENSP00000323897:E599K	ENSP00000301749:E617K	E	-	1	0	NLRC3	3553090	0.995000	0.38212	0.013000	0.15412	0.778000	0.44026	3.188000	0.50958	1.166000	0.42689	0.655000	0.94253	GAG	.	.		0.706	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844		T	3613089	C	T	3613089	1	4	264	0	1	0	0	0	0	0	0	0	10477	864	30	3		3	NLRC3	16	3613089	RNA	SNP	C	TCGA-FV-A3I0-01A-11D-A22F-10		3613089	86741664	59	38878										
N4BP1	9683	hgsc.bcm.edu	37	chr16	48595690	48595690	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	gtatgcctttcttcagaatcAgaaaatctccttttctgaca	5	10	5	3			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr16:48595690A>T	ENST00000262384.3	-	2	1100	c.864T>A	c.(862-864)tcT>tcA	p.S288S	RP11-44I10.3_ENST00000563994.1_RNA	NM_153029.3	NP_694574.3	O75113	N4BP1_HUMAN	NEDD4 binding protein 1	288					cellular response to UV (GO:0034644)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein ubiquitination (GO:0031397)	nucleolus (GO:0005730)|PML body (GO:0016605)				breast(3)|kidney(2)|lung(11)|urinary_tract(1)	17		all_cancers(37;0.179)|all_lung(18;0.11)				CTTCAGAATCAGAAAATCTCC	0.393																																					p.S288S		Atlas-SNP	.											.	N4BP1	121	.	0			c.T864A						.						80	77	78					16																	48595690		1832	4081	5913	SO:0001819	synonymous_variant	9683	exon2			AGAATCAGAAAAT	AK026937	CCDS45479.1	16q12.1	2008-01-18				ENSG00000102921			29850	protein-coding gene	gene with protein product						9734811, 11717310	Standard	NM_153029		Approved		uc002efp.3	O75113		ENST00000262384.3:c.864T>A	chr16.hg19:g.48595690A>T		98.0	0.0		67.0	44.0	NM_153029	A7MD49|Q2YDX1	Silent	SNP	ENST00000262384.3	hg19	CCDS45479.1																																																																																			.	.		0.393	N4BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429920.1	NM_014664		T	48595690	A	T	48595690	2	4	264	1	0	0	0	0	0	0	0	1	10118	175	7	4		4	N4BP1	16	48595690	Silent	SNP	A	TCGA-FV-A3I0-01A-11D-A22F-10	44982601	48595690	41759063	60	38879										
MT1F	4494	hgsc.bcm.edu	37	chr16	56692645	56692645	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	gagtgcaaatgcacctcctgCaagaagagtgagtgtgaggc	14	8	0	4			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr16:56692645C>T	ENST00000334350.6	+	2	452	c.87C>T	c.(85-87)tgC>tgT	p.C29C	MT1F_ENST00000394501.2_Silent_p.C30C|MT1F_ENST00000568475.1_Silent_p.C29C			P04733	MT1F_HUMAN	metallothionein 1F	29	Beta.				cellular response to cadmium ion (GO:0071276)|cellular response to zinc ion (GO:0071294)|negative regulation of growth (GO:0045926)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)										GCACCTCCTGCAAGAAGAGTG	0.567																																					p.C29C	Colon(159;794 1866 3818 8748 33331)	Atlas-SNP	.											.	MT1F	3	.	0			c.C87T						.						57	55	56					16																	56692645		2198	4300	6498	SO:0001819	synonymous_variant	4494	exon2			CTCCTGCAAGAAG	BC029453	CCDS32456.1	16q13	2008-02-05	2007-03-02			ENSG00000198417		"Metallothioneins"	7398	protein-coding gene	gene with protein product		156352		MT1		6089206, 2581970	Standard	NM_005949		Approved		uc002ejt.3	P04733		ENST00000334350.6:c.87C>T	chr16.hg19:g.56692645C>T		54.0	0.0		42.0	25.0	NM_005949	Q9UI97	Silent	SNP	ENST00000334350.6	hg19	CCDS32456.1																																																																																			.	.		0.567	MT1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433995.2	NM_005949		T	56692645	C	T	56692645	2	4	264	1	0	0	0	0	0	0	0	1	9909	718	25	3		3	MT1F	16	56692645	Silent	SNP	C	TCGA-FV-A3I0-01A-11D-A22F-10	8096955	56692645	33662108	61	38880										
KDM6B	23135	hgsc.bcm.edu	37	chr17	7755291	7755291	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	caccaggagaataacaacttCtgctccgtcaacatcaacat	5	13	3	1			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr17:7755291C>T	ENST00000448097.2	+	18	4519	c.4188C>T	c.(4186-4188)ttC>ttT	p.F1396F	KDM6B_ENST00000254846.5_Silent_p.F1396F			O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	1396	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				cardiac muscle cell differentiation (GO:0055007)|cellular response to hydrogen peroxide (GO:0070301)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|mesodermal cell differentiation (GO:0048333)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|skin(5)	37						ATAACAACTTCTGCTCCGTCA	0.612											OREG0024145	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F1396F		Atlas-SNP	.											.	KDM6B	95	.	0			c.C4188T						.						75	66	69					17																	7755291		2203	4299	6502	SO:0001819	synonymous_variant	23135	exon18			CAACTTCTGCTCC	AB002344	CCDS32552.1	17p13.1	2011-07-01	2009-04-17	2009-04-17		ENSG00000132510		"Chromatin-modifying enzymes / K-demethylases"	29012	protein-coding gene	gene with protein product		611577	"jumonji domain containing 3", "jumonji domain containing 3, histone lysine demethylase"	JMJD3		10662545, 9205841	Standard	NM_001080424		Approved	KIAA0346	uc002giw.1	O15054		ENST00000448097.2:c.4188C>T	chr17.hg19:g.7755291C>T		79.0	0.0	644	89.0	14.0	NM_001080424	C9IZ40|Q96G33	Silent	SNP	ENST00000448097.2	hg19																																																																																				.	.		0.612	KDM6B-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440248.1	XM_043272		T	7755291	C	T	7755291	2	4	264	1	0	0	0	0	0	0	0	1	8147	912	32	3		3	KDM6B	17	7755291	Silent	SNP	C	TCGA-FV-A3I0-01A-11D-A22F-10		7755291	73439919	62	38881										
C17orf56	146705	hgsc.bcm.edu	37	chr17	79203158	79203158	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	agacctggctcccagggagaGgcacagcgtcggtcagcagg	16	12	1	2			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr17:79203158G>C	ENST00000300714.3	-	12	1205	c.1148C>G	c.(1147-1149)cCt>cGt	p.P383R	ENTHD2_ENST00000374769.2_Missense_Mutation_p.P299R|AC027601.1_ENST00000575922.1_RNA|AC027601.1_ENST00000569559.1_RNA	NM_144679.2	NP_653280.1	Q96N21	AP4AT_HUMAN	ENTH domain containing 2	383	Pro-rich.					cytoplasmic vesicle (GO:0031410)											CCCAGGGAGAGGCACAGCGTC	0.701																																					p.P383R		Atlas-SNP	.											.	.	.	.	0			c.C1148G						.						11	9	10					17																	79203158		2164	4270	6434	SO:0001583	missense	146705	exon12			GGGAGAGGCACAG	AK056090	CCDS11779.1	17q25.3	2012-07-18	2012-07-18	2012-07-18	ENSG00000167302	ENSG00000167302			26458	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 56"	C17orf56			Standard	NM_144679		Approved	FLJ31528	uc002jzu.2	Q96N21	OTTHUMG00000177866	ENST00000300714.3:c.1148C>G	chr17.hg19:g.79203158G>C	ENSP00000300714:p.Pro383Arg	138.0	0.0		101.0	40.0	NM_144679	Q6ZQU0|Q6ZSQ9	Missense_Mutation	SNP	ENST00000300714.3	hg19	CCDS11779.1	.	.	.	.	.	.	.	.	.	.	G	17.96	3.517162	0.64634	.	.	ENSG00000167302	ENST00000300714;ENST00000374769	T;T	0.64085	-0.08;-0.08	4.48	4.48	0.54585	.	0.000000	0.64402	D	0.000005	T	0.76870	0.4048	M	0.67953	2.075	0.29709	N	0.839528	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.74957	-0.3487	10	0.87932	D	0	-15.6768	15.0886	0.72174	0.0:0.0:1.0:0.0	.	383;299	Q96N21;Q96N21-2	CQ056_HUMAN;.	R	383;299	ENSP00000300714:P383R;ENSP00000363901:P299R	ENSP00000300714:P383R	P	-	2	0	C17orf56	76817753	0.998000	0.40836	0.206000	0.23566	0.255000	0.26057	2.330000	0.43885	2.310000	0.77875	0.591000	0.81541	CCT	.	.		0.701	ENTHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439315.1	NM_144679		C	79203158	G	C	79203158	3	2	264	1	0	0	0	0	1	0	0	0	1866	1000	35	4	433	4	C17orf56	17	79203158	Missense_Mutation	SNP	G	TCGA-FV-A3I0-01A-11D-A22F-10	71447867	79203158	1992052	63	38882										
KCNN1	3780	hgsc.bcm.edu	37	chr19	18092829	18092829	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	aacaagatcaccttcaacacGcgcttcgtcatgaagacact	6	13	3	3	rs374014650		TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr19:18092829G>A	ENST00000222249.9	+	5	1129	c.810G>A	c.(808-810)acG>acA	p.T270T		NM_002248.3	NP_002239.2	Q92952	KCNN1_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 1	270					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			endometrium(1)|kidney(1)|lung(5)|urinary_tract(1)	8					Miconazole(DB01110)|Procaine(DB00721)	CCTTCAACACGCGCTTCGTCA	0.607																																					p.T270T		Atlas-SNP	.											.	KCNN1	74	.	0			c.G810A						.	G		1,4403	2.1+/-5.4	0,1,2201	55	40	45		810	-6.9	1	19		45	0,8600		0,0,4300	no	coding-synonymous	KCNN1	NM_002248.3		0,1,6501	AA,AG,GG		0.0,0.0227,0.0077		270/544	18092829	1,13003	2202	4300	6502	SO:0001819	synonymous_variant	3780	exon5			CAACACGCGCTTC	U69883	CCDS67611.1	19p13.1	2012-07-05				ENSG00000105642		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6290	protein-coding gene	gene with protein product		602982				8781233, 10516439, 16382103	Standard	NM_002248		Approved	KCa2.1, hSK1	uc002nht.3	Q92952		ENST00000222249.9:c.810G>A	chr19.hg19:g.18092829G>A		35.0	0.0		100.0	17.0	NM_002248	Q5KR10|Q6DJU4	Silent	SNP	ENST00000222249.9	hg19																																																																																				.	.		0.607	KCNN1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471896.2	NM_002248		A	18092829	G	A	18092829	2	1	264	1	0	0	0	0	0	0	0	1	8087	1074	38	1		1	KCNN1	19	18092829	Silent	SNP	G	TCGA-FV-A3I0-01A-11D-A22F-10		18092829	41036154	64	38883										
MED25	81857	hgsc.bcm.edu	37	chr19	50331706	50331706	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	tgaccgctctgcccctgcagGttcatgggcgggggtggtga	17	11	2	2			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr19:50331706G>T	ENST00000312865.6	+	4	359	c.306G>T	c.(304-306)aaG>aaT	p.K102N	MED25_ENST00000538643.1_Intron	NM_030973.3	NP_112235.2	Q71SY5	MED25_HUMAN	mediator complex subunit 25	102	Interaction with the Mediator complex.				cell death (GO:0008219)|gene expression (GO:0010467)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of chromatin binding (GO:0035563)|positive regulation of mediator complex assembly (GO:2001178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|transcription factor binding (GO:0008134)	p.K102N(2)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)|stomach(1)|urinary_tract(1)	17		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00822)|GBM - Glioblastoma multiforme(134;0.0122)		GCCCCTGCAGGTTCATGGGCG	0.607																																					p.K102N	GBM(51;894 1657 37868)	Atlas-SNP	.											MED25_ENST00000312881,NS,carcinoma,0,2	MED25	98	.	2	Substitution - Missense(2)	lung(2)	c.G306T						.						84	90	88					19																	50331706		2203	4300	6503	SO:0001630	splice_region_variant	81857	exon4			CTGCAGGTTCATG	AL136746	CCDS33075.1	19q13.3	2014-09-17	2007-07-30			ENSG00000104973			28845	protein-coding gene	gene with protein product		610197	"mediator of RNA polymerase II transcription, subunit 25 homolog (S. cerevisiae)"			9110174, 11230166	Standard	NM_030973		Approved	ARC92, ACID1, TCBAP0758, DKFZp434K0512	uc002ppw.2	Q71SY5		ENST00000312865.6:c.306-1G>T	chr19.hg19:g.50331706G>T		63.0	0.0		86.0	46.0	NM_030973	A8K095|B9TX30|O95783|Q6P143|Q6QMH5|Q707U4|Q8TB55|Q9H0L5|Q9HB34	Missense_Mutation	SNP	ENST00000312865.6	hg19	CCDS33075.1	.	.	.	.	.	.	.	.	.	.	G	11.63	1.697289	0.30142	.	.	ENSG00000104973	ENST00000355584;ENST00000377077;ENST00000312881;ENST00000312865;ENST00000456294;ENST00000542221;ENST00000544580	T	0.15603	2.41	4.89	4.89	0.63831	.	0.329600	0.32372	N	0.006197	T	0.13243	0.0321	L	0.29908	0.895	0.80722	D	1	B	0.26708	0.157	B	0.31191	0.125	T	0.10451	-1.0629	9	.	.	.	.	11.4311	0.50041	0.0868:0.0:0.9131:0.0	.	102	Q71SY5	MED25_HUMAN	N	102	ENSP00000326767:K102N	.	K	+	3	2	MED25	55023518	1.000000	0.71417	1.000000	0.80357	0.080000	0.17528	6.350000	0.73017	2.709000	0.92574	0.655000	0.94253	AAG	.	.		0.607	MED25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465316.1	NM_030973	Missense_Mutation	T	50331706	G	T	50331706	5	4	264	1	0	0	0	0	0	0	1	0	9452	1275	44	3	320	3	MED25	19	50331706	Splice_Site	SNP	G	TCGA-FV-A3I0-01A-11D-A22F-10	32238877	50331706	8797277	65	38884										
ZNF578	147660	hgsc.bcm.edu	37	chr19	53014990	53014990	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	catagacttcatactggagaGaaatcttacaaatgtgaaga	8	6	2	4			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr19:53014990G>T	ENST00000421239.2	+	6	1600	c.1356G>T	c.(1354-1356)gaG>gaT	p.E452D	CTD-3099C6.5_ENST00000599143.1_RNA	NM_001099694.1	NP_001093164.1	Q96N58	ZN578_HUMAN	zinc finger protein 578	452					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)								GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)		ATACTGGAGAGAAATCTTACA	0.378																																					p.E452D		Atlas-SNP	.											ENSG00000221895,caecum,carcinoma,0,1	.	.	.	0			c.G1356T						.						57	62	61					19																	53014990		2198	4299	6497	SO:0001583	missense	147660	exon6			TGGAGAGAAATCT	AK095562	CCDS54310.1	19q13.41	2013-09-20			ENSG00000258405	ENSG00000258405		"Zinc fingers, C2H2-type", "-"	26449	protein-coding gene	gene with protein product							Standard	NM_001099694		Approved	FLJ31384	uc002pzp.4	Q96N58	OTTHUMG00000156468	ENST00000421239.2:c.1356G>T	chr19.hg19:g.53014990G>T	ENSP00000459216:p.Glu452Asp	89.0	0.0		128.0	41.0	NM_001099694	B4DR51|I3L1Y6	Missense_Mutation	SNP	ENST00000421239.2	hg19	CCDS54310.1	.	.	.	.	.	.	.	.	.	.	-	9.737	1.163935	0.21538	.	.	ENSG00000258405	ENST00000553364	.	.	.	1.48	1.48	0.22813	.	.	.	.	.	T	0.32734	0.0839	M	0.64080	1.96	0.20196	N	0.999921	P	0.35272	0.493	B	0.27796	0.083	T	0.16808	-1.0390	7	.	.	.	.	5.7898	0.18353	0.1891:0.0:0.8109:0.0	.	452	G3V4F6	.	D	452	.	.	E	+	3	2	ZNF578	57706802	0.966000	0.33281	0.306000	0.25113	0.059000	0.15707	0.768000	0.26590	0.835000	0.34877	0.297000	0.19635	GAG	.	.		0.378	ZNF578-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344298.3	NM_152472		T	53014990	G	T	53014990	3	4	264	1	0	0	0	0	1	0	0	0	18025	933	33	3	1366	3	ZNF578	19	53014990	Missense_Mutation	SNP	G	TCGA-FV-A3I0-01A-11D-A22F-10	2683284	53014990	6113993	66	38885										
ZIM3	114026	hgsc.bcm.edu	37	chr19	57646911	57646911	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	ttttctcatgattaatgcagGatgatttccaggaaaaggct	9	6	1	2			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr19:57646911G>C	ENST00000269834.1	-	5	1179	c.794C>G	c.(793-795)tCc>tGc	p.S265C	U3_ENST00000516874.1_RNA	NM_052882.1	NP_443114.1	Q96PE6	ZIM3_HUMAN	zinc finger, imprinted 3	265					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(27)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	52		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.243)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		ATTAATGCAGGATGATTTCCA	0.358																																					p.S265C		Atlas-SNP	.											ZIM3,NS,carcinoma,0,1	ZIM3	107	.	0			c.C794G						.						120	117	118					19																	57646911		2203	4300	6503	SO:0001583	missense	114026	exon5			ATGCAGGATGATT	AF365931	CCDS33125.1	19q13.4	2013-01-08				ENSG00000141946		"Zinc fingers, C2H2-type", "-"	16366	protein-coding gene	gene with protein product							Standard	NM_052882		Approved	ZNF657	uc002qnz.1	Q96PE6		ENST00000269834.1:c.794C>G	chr19.hg19:g.57646911G>C	ENSP00000269834:p.Ser265Cys	181.0	1.0		224.0	31.0	NM_052882	Q14CA6	Missense_Mutation	SNP	ENST00000269834.1	hg19	CCDS33125.1	.	.	.	.	.	.	.	.	.	.	G	10.58	1.390922	0.25118	.	.	ENSG00000141946	ENST00000269834	T	0.16073	2.37	2.53	-1.12	0.09808	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13415	0.0325	L	0.45744	1.44	0.09310	N	1	B	0.09022	0.002	B	0.12837	0.008	T	0.31194	-0.9952	9	0.49607	T	0.09	.	5.1386	0.14947	0.1453:0.3671:0.4876:0.0	.	265	Q96PE6	ZIM3_HUMAN	C	265	ENSP00000269834:S265C	ENSP00000269834:S265C	S	-	2	0	ZIM3	62338723	0.000000	0.05858	0.122000	0.21767	0.619000	0.37552	-3.324000	0.00512	0.017000	0.15025	0.313000	0.20887	TCC	.	.		0.358	ZIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465078.1			C	57646911	G	C	57646911	3	2	264	1	0	0	0	0	1	0	0	0	17700	1174	41	4	628	4	ZIM3	19	57646911	Missense_Mutation	SNP	G	TCGA-FV-A3I0-01A-11D-A22F-10	4631921	57646911	1482072	67	38886										
ZSCAN4	201516	hgsc.bcm.edu	37	chr19	58187569	58187569	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	accatccgagaataatcttgGatcagaaaattcagcgtttc	7	9	3	2			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr19:58187569G>A	ENST00000318203.5	+	3	753	c.56G>A	c.(55-57)gGa>gAa	p.G19E		NM_152677.2	NP_689890.1	Q8NAM6	ZSCA4_HUMAN	zinc finger and SCAN domain containing 4	19					telomere maintenance via telomere lengthening (GO:0010833)|transcription, DNA-templated (GO:0006351)	nuclear chromosome, telomeric region (GO:0000784)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|large_intestine(5)|liver(2)|lung(17)|ovary(1)|skin(1)|stomach(1)	30		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		AATAATCTTGGATCAGAAAAT	0.383																																					p.G19E		Atlas-SNP	.											.	ZSCAN4	72	.	0			c.G56A						.						68	66	67					19																	58187569		2203	4300	6503	SO:0001583	missense	201516	exon3			ATCTTGGATCAGA	AK092424	CCDS12958.1	19q13.43	2013-01-08	2004-11-01	2004-11-02		ENSG00000180532		"-", "Zinc fingers, C2H2-type"	23709	protein-coding gene	gene with protein product		613419	"zinc finger protein 494"	ZNF494			Standard	NM_152677		Approved	FLJ35105	uc002qpu.3	Q8NAM6		ENST00000318203.5:c.56G>A	chr19.hg19:g.58187569G>A	ENSP00000321963:p.Gly19Glu	109.0	0.0		158.0	88.0	NM_152677	Q3MIQ2	Missense_Mutation	SNP	ENST00000318203.5	hg19	CCDS12958.1	.	.	.	.	.	.	.	.	.	.	G	6.895	0.534679	0.13188	.	.	ENSG00000180532	ENST00000318203	T	0.06371	3.31	4.15	-5.94	0.02247	.	1.438360	0.04789	N	0.431291	T	0.03390	0.0098	N	0.20986	0.625	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.43458	-0.9390	10	0.17832	T	0.49	0.1698	2.6352	0.04956	0.5529:0.1327:0.1803:0.1341	.	19	Q8NAM6	ZSCA4_HUMAN	E	19	ENSP00000321963:G19E	ENSP00000321963:G19E	G	+	2	0	ZSCAN4	62879381	0.000000	0.05858	0.000000	0.03702	0.406000	0.30931	0.020000	0.13466	-1.125000	0.02932	0.655000	0.94253	GGA	.	.		0.383	ZSCAN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466812.1	NM_152677		A	58187569	G	A	58187569	3	1	264	1	0	0	0	0	1	0	0	0	18252	1174	41	3	58	3	ZSCAN4	19	58187569	Missense_Mutation	SNP	G	TCGA-FV-A3I0-01A-11D-A22F-10	540658	58187569	941414	68	38887										
ZNF551	90233	hgsc.bcm.edu	37	chr19	58199625	58199625	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	caaatctaacctcattcgacAtcggagagttcacactgaag	7	11	3	2			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr19:58199625A>G	ENST00000282296.5	+	3	2167	c.1982A>G	c.(1981-1983)cAt>cGt	p.H661R	AC003006.7_ENST00000599221.1_Intron|ZNF551_ENST00000356715.4_Missense_Mutation_p.H645R|AC003006.7_ENST00000594684.1_Intron|ZNF551_ENST00000596085.1_Intron			Q7Z340	ZN551_HUMAN	zinc finger protein 551	661					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)	15		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		CTCATTCGACATCGGAGAGTT	0.428																																					p.H661R		Atlas-SNP	.											.	ZNF551	65	.	0			c.A1982G						.						87	85	86					19																	58199625		2203	4300	6503	SO:0001583	missense	90233	exon3			TTCGACATCGGAG	BX538151	CCDS12959.1, CCDS12959.2	19q13.43	2013-09-20			ENSG00000204519	ENSG00000204519		"Zinc fingers, C2H2-type", "-"	25108	protein-coding gene	gene with protein product							Standard	NM_138347		Approved	DKFZp686H1038	uc002qpw.5	Q7Z340	OTTHUMG00000183470	ENST00000282296.5:c.1982A>G	chr19.hg19:g.58199625A>G	ENSP00000282296:p.His661Arg	50.0	0.0		71.0	14.0	NM_138347	B4DU22|P17034|Q8N246|Q9BRY1	Missense_Mutation	SNP	ENST00000282296.5	hg19	CCDS12959.2	.	.	.	.	.	.	.	.	.	.	A	15.22	2.768991	0.49680	.	.	ENSG00000204519	ENST00000356715;ENST00000282296	.	.	.	2.42	2.42	0.29668	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.77458	0.4133	M	0.94142	3.5	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.65294	-0.6203	8	0.87932	D	0	.	9.4987	0.39004	1.0:0.0:0.0:0.0	.	661	Q7Z340	ZN551_HUMAN	R	661;645	.	ENSP00000282296:H645R	H	+	2	0	ZNF551	62891437	0.033000	0.19621	0.001000	0.08648	0.008000	0.06430	1.870000	0.39529	1.118000	0.41863	0.379000	0.24179	CAT	.	.		0.428	ZNF551-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466803.2	NM_138347		G	58199625	A	G	58199625	3	3	264	1	0	0	0	0	1	0	0	0	17998	217	8	2	1944	2	ZNF551	19	58199625	Missense_Mutation	SNP	A	TCGA-FV-A3I0-01A-11D-A22F-10	12056	58199625	929358	69	38888										
SAMSN1	64092	hgsc.bcm.edu	37	chr21	15858388	15858388	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	tgacttatttaaggagatgtCtgagctcaaggataggggct	13	5	2	3			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr21:15858388C>A	ENST00000400566.1	-	8	1048	c.967G>T	c.(967-969)Gac>Tac	p.D323Y	SAMSN1_ENST00000400564.1_Missense_Mutation_p.D155Y|SAMSN1_ENST00000285670.2_Missense_Mutation_p.D391Y	NM_022136.4	NP_071419.3	Q9NSI8	SAMN1_HUMAN	SAM domain, SH3 domain and nuclear localization signals 1	323					negative regulation of adaptive immune response (GO:0002820)|negative regulation of B cell activation (GO:0050869)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)	cell projection (GO:0042995)|cytosol (GO:0005829)|nucleus (GO:0005634)	phosphotyrosine binding (GO:0001784)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	24				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.00118)|Colorectal(24;0.00961)|Lung(58;0.164)		AAGGAGATGTCTGAGCTCAAG	0.403																																					p.D391Y		Atlas-SNP	.											.	SAMSN1	112	.	0			c.G1171T						.						77	68	71					21																	15858388		1844	4092	5936	SO:0001583	missense	64092	exon9			AGATGTCTGAGCT	AF222927	CCDS42906.1, CCDS58786.1, CCDS74774.1	21q11	2013-01-10	2006-12-13		ENSG00000155307	ENSG00000155307		"SAM and SH3 domain containing", "Sterile alpha motif (SAM) domain containing"	10528	protein-coding gene	gene with protein product	"nuclear localization signals, SAM and SH3 domain containing 1", "SAM and SH3 domain containing 2", "hematopoietic adapter-containing SH3 and sterile &#945;-motif (SAM) domains 1", "Src homology domain 3 (SH3)-containing adapter protein SH3 lymphocyte protein 2"	607978				11536050, 11594764	Standard	NM_022136		Approved	NASH1, SASH2, SH3D6B, HACS1, SLy2	uc002yjv.1	Q9NSI8	OTTHUMG00000074317	ENST00000400566.1:c.967G>T	chr21.hg19:g.15858388C>A	ENSP00000383411:p.Asp323Tyr	137.0	0.0		149.0	37.0	NM_001256370	B3KWJ3|F8WAA1|Q8NFF7|Q9C041	Missense_Mutation	SNP	ENST00000400566.1	hg19	CCDS42906.1	.	.	.	.	.	.	.	.	.	.	C	10.93	1.490225	0.26686	.	.	ENSG00000155307	ENST00000285670;ENST00000400566;ENST00000400564	T;T	0.47528	0.84;0.87	5.96	4.99	0.66335	.	0.951458	0.08934	N	0.872550	T	0.53786	0.1818	L	0.60455	1.87	0.38207	D	0.940354	P;P;P	0.45474	0.834;0.859;0.666	B;P;B	0.46389	0.311;0.515;0.126	T	0.52268	-0.8598	10	0.72032	D	0.01	-8.7687	11.2823	0.49201	0.0:0.7921:0.1323:0.0756	.	155;391;323	Q9NSI8-2;F8WAA1;Q9NSI8	.;.;SAMN1_HUMAN	Y	391;323;155	ENSP00000285670:D391Y;ENSP00000383411:D323Y	ENSP00000285670:D391Y	D	-	1	0	SAMSN1	14780259	1.000000	0.71417	0.997000	0.53966	0.249000	0.25844	2.171000	0.42453	1.371000	0.46172	0.591000	0.81541	GAC	.	.		0.403	SAMSN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157914.1			A	15858388	C	A	15858388	3	1	264	1	0	0	0	0	1	0	0	0	13845	913	32	3	158	3	SAMSN1	21	15858388	Missense_Mutation	SNP	C	TCGA-FV-A3I0-01A-11D-A22F-10		15858388	32271507	70	38889										
IGSF5	150084	hgsc.bcm.edu	37	chr21	41137531	41137531	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	cctgaagggctcccaggctcGcttcaactgcaccgtctccc	9	18	2	1	rs372378189		TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chr21:41137531G>T	ENST00000380588.4	+	3	273	c.170G>T	c.(169-171)cGc>cTc	p.R57L	IGSF5_ENST00000479378.1_3'UTR	NM_001080444.1	NP_001073913.1	Q9NSI5	IGSF5_HUMAN	immunoglobulin superfamily, member 5	57	Ig-like V-type 1.				single organismal cell-cell adhesion (GO:0016337)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)		p.R57H(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(7)|skin(2)|stomach(1)	23		Prostate(19;5.35e-06)				TCCCAGGCTCGCTTCAACTGC	0.527																																					p.R57L		Atlas-SNP	.											IGSF5,rectum,carcinoma,0,1	IGSF5	62	.	1	Substitution - Missense(1)	large_intestine(1)	c.G170T						.						71	63	66					21																	41137531		2203	4300	6503	SO:0001583	missense	150084	exon3			AGGCTCGCTTCAA		CCDS33562.1	21q22.2	2013-01-29			ENSG00000183067	ENSG00000183067		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5952	protein-coding gene	gene with protein product	"junctional adhesion molecule 4"	610638					Standard	NM_001080444		Approved	JAM4	uc002yyo.3	Q9NSI5	OTTHUMG00000086724	ENST00000380588.4:c.170G>T	chr21.hg19:g.41137531G>T	ENSP00000369962:p.Arg57Leu	49.0	0.0		62.0	23.0	NM_001080444		Missense_Mutation	SNP	ENST00000380588.4	hg19	CCDS33562.1	.	.	.	.	.	.	.	.	.	.	G	15.56	2.868593	0.51588	.	.	ENSG00000183067	ENST00000380588	T	0.26810	1.71	4.05	2.18	0.27775	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.290921	0.33631	N	0.004711	T	0.40398	0.1115	M	0.64997	1.995	0.34166	D	0.669226	D	0.69078	0.997	D	0.66979	0.948	T	0.49818	-0.8899	10	0.30078	T	0.28	-12.2058	9.2585	0.37597	0.1767:0.0:0.8233:0.0	.	57	Q9NSI5	IGSF5_HUMAN	L	57	ENSP00000369962:R57L	ENSP00000369962:R57L	R	+	2	0	IGSF5	40059401	0.998000	0.40836	0.999000	0.59377	0.533000	0.34776	1.174000	0.31932	0.430000	0.26230	-0.142000	0.14014	CGC	.	.		0.527	IGSF5-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195005.1			T	41137531	G	T	41137531	3	4	264	1	0	0	0	0	1	0	0	0	7611	1087	38	1	180	1	IGSF5	21	41137531	Missense_Mutation	SNP	G	TCGA-FV-A3I0-01A-11D-A22F-10	25279143	41137531	6992364	71	38890										
DCAF8L2	347442	hgsc.bcm.edu	37	chrX	27765469	27765469	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0833333333333333	6	1	1.09921962095875	2.59815546772069	0.510351966873706	0.619909502262444	1	0	aagaacagcctcgggcgggtCcacaaggcagtggcggcaac	15	12	0	1			TCGA-FV-A3I0-01A-11D-A22F-10	TCGA-FV-A3I0-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5df489bc-6178-49e4-8a42-506f70300dff	741183d6-2363-4cbf-b5f9-4548e1cab32b	g.chrX:27765469C>T	ENST00000451261.2	+	5	856	c.457C>T	c.(457-459)Cca>Tca	p.P153S		NM_001136533.1	NP_001130005.1	P0C7V8	DC8L2_HUMAN	DDB1 and CUL4 associated factor 8-like 2	153	Glu-rich.									central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						TCGGGCGGGTCCACAAGGCAG	0.617																																					p.P153S		Atlas-SNP	.											.	DCAF8L2	79	.	0			c.C457T						.						20	20	20					X																	27765469		691	1591	2282	SO:0001583	missense	347442	exon1			GCGGGTCCACAAG		CCDS59162.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17		ENSG00000189186		"WD repeat domain containing"	31811	protein-coding gene	gene with protein product			"WD repeat domain 42C"	WDR42C			Standard	NM_001136533		Approved		uc011mjy.2	P0C7V8		ENST00000451261.2:c.457C>T	chrX.hg19:g.27765469C>T	ENSP00000462745:p.Pro153Ser	86.0	0.0		68.0	60.0	NM_001136533	B2RXH9|J3KT06	Missense_Mutation	SNP	ENST00000451261.2	hg19	CCDS59162.1																																																																																			.	.		0.617	DCAF8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056143.4	XM_293354		T	27765469	C	T	27765469	3	4	264	1	0	0	0	0	1	0	0	0	4280	855	30	3	459	3	DCAF8L2	23	27765469	Missense_Mutation	SNP	C	TCGA-FV-A3I0-01A-11D-A22F-10		27765469	127505091	72	38891										
GPR157	80045	hgsc.bcm.edu	37	chr1	9188904	9188904	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	actccgtagaagtaggaggcGgccgagagcaggtcggccag	17	10	0	2			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr1:9188904G>A	ENST00000377411.4	-	1	325	c.183C>T	c.(181-183)gcC>gcT	p.A61A	GPR157_ENST00000414642.2_Silent_p.A61A	NM_024980.4	NP_079256.4	Q5UAW9	GP157_HUMAN	G protein-coupled receptor 157	61						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			lung(4)|prostate(1)	5	all_lung(157;0.185)	all_epithelial(116;5.02e-20)|all_lung(118;3.6e-06)|Lung NSC(185;7.93e-06)|Renal(390;0.000147)|Breast(348;0.000688)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.16e-07)|COAD - Colon adenocarcinoma(227;7.73e-05)|Kidney(185;0.000252)|KIRC - Kidney renal clear cell carcinoma(229;0.000917)|STAD - Stomach adenocarcinoma(132;0.00178)|BRCA - Breast invasive adenocarcinoma(304;0.00186)|READ - Rectum adenocarcinoma(331;0.0642)		AGTAGGAGGCGGCCGAGAGCA	0.706																																					p.A61A		Atlas-SNP	.											.	GPR157	14	.	0			c.C183T						.						12	12	12					1																	9188904		2191	4289	6480	SO:0001819	synonymous_variant	80045	exon1			GGAGGCGGCCGAG	AK022194	CCDS100.2	1p36.22	2012-08-21			ENSG00000180758	ENSG00000180758		"GPCR / Class B : Orphans"	23687	protein-coding gene	gene with protein product						10574461	Standard	XM_005263496		Approved	FLJ12132	uc001apq.1	Q5UAW9	OTTHUMG00000001758	ENST00000377411.4:c.183C>T	chr1.hg19:g.9188904G>A		28.0	0.0		43.0	17.0	NM_024980	A2A334|Q8WWB8|Q9HA73	Silent	SNP	ENST00000377411.4	hg19	CCDS100.2																																																																																			.	.		0.706	GPR157-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127658.2	NM_024980		A	9188904	G	A	9188904	2	1	265	1	0	0	0	0	0	0	0	1	6670	1103	39	1		1	GPR157	1	9188904	Silent	SNP	G	TCGA-FV-A3I1-01A-11D-A22F-10		9188904	240061717	1	38892										
MRPS15	64960	hgsc.bcm.edu	37	chr1	36923570	36923570	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	cataactgcggatcttgacaGacaaggcaataactgaaacc	8	10	1	3	rs376585999		TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr1:36923570G>C	ENST00000373116.5	-	6	559	c.398C>G	c.(397-399)tCt>tGt	p.S133C	MRPS15_ENST00000488606.1_5'UTR	NM_031280.3	NP_112570.2	P82914	RT15_HUMAN	mitochondrial ribosomal protein S15	133					translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)	14		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GATCTTGACAGACAAGGCAAT	0.473																																					p.S133C		Atlas-SNP	.											.	MRPS15	21	.	0			c.C398G						.	G	CYS/SER	0,4406		0,0,2203	147	133	138		398	5.5	1	1		138	1,8599	1.2+/-3.3	0,1,4299	no	missense	MRPS15	NM_031280.3	112	0,1,6502	CC,CG,GG		0.0116,0.0,0.0077	possibly-damaging	133/258	36923570	1,13005	2203	4300	6503	SO:0001583	missense	64960	exon6			TTGACAGACAAGG	AB049946	CCDS411.1	1p34.3	2012-09-13			ENSG00000116898	ENSG00000116898		"Mitochondrial ribosomal proteins / small subunits"	14504	protein-coding gene	gene with protein product		611979					Standard	NM_031280		Approved	FLJ11564	uc001cas.2	P82914	OTTHUMG00000008042	ENST00000373116.5:c.398C>G	chr1.hg19:g.36923570G>C	ENSP00000362208:p.Ser133Cys	104.0	0.0		121.0	35.0	NM_031280	B2RD82|Q9H2K1	Missense_Mutation	SNP	ENST00000373116.5	hg19	CCDS411.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.474612	0.84640	0.0	1.16E-4	ENSG00000116898	ENST00000373116	.	.	.	5.49	5.49	0.81192	S15/NS1, RNA-binding (2);	0.144121	0.64402	D	0.000008	T	0.67979	0.2951	L	0.61036	1.89	0.36412	D	0.863802	P	0.52577	0.954	P	0.52109	0.69	T	0.76493	-0.2939	9	0.87932	D	0	-1.174	18.3538	0.90348	0.0:0.0:1.0:0.0	.	133	P82914	RT15_HUMAN	C	133	.	ENSP00000362208:S133C	S	-	2	0	MRPS15	36696157	1.000000	0.71417	0.956000	0.39512	0.934000	0.57294	6.430000	0.73391	2.559000	0.86315	0.563000	0.77884	TCT	.	.		0.473	MRPS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022052.2	NM_031280		C	36923570	G	C	36923570	3	2	265	1	0	0	0	0	1	0	0	0	9834	942	33	4	387	4	MRPS15	1	36923570	Missense_Mutation	SNP	G	TCGA-FV-A3I1-01A-11D-A22F-10	27734666	36923570	212327051	2	38893										
CYP4A22	284541	hgsc.bcm.edu	37	chr1	47609480	47609481	+	Frame_Shift_Ins	INS	-	-	T													0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	tagtgacctgaacagcctggINSttttttgctgtatgaggaat							TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr1:47609480_47609481insT	ENST00000371891.3	+	6	713_714	c.682_683insT	c.(682-684)gttfs	p.V228fs	CYP4A22-AS1_ENST00000444042.2_lincRNA|CYP4A22_ENST00000371890.3_Intron|CYP4A22_ENST00000485117.1_3'UTR|CYP4A22_ENST00000294337.3_Frame_Shift_Ins_p.V228fs	NM_001010969.2	NP_001010969.2	Q5TCH4	CP4AM_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 22	228						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						GAACAGCCTGGTTTTTTGCTGT	0.55																																					p.V228fs	Pancreas(88;1240 1470 2099 14214 37557)	Atlas-INDEL	.											CYP4A22,NS,malignant_melanoma,0,1	CYP4A22	60	.	0			c.682_683insT						.																																			SO:0001589	frameshift_variant	284541	exon6			.		CCDS30707.1	1p33	2007-12-14			ENSG00000162365	ENSG00000162365		"Cytochrome P450s"	20575	protein-coding gene	gene with protein product		615341					Standard	XM_005270768		Approved		uc001cqv.1	Q5TCH4	OTTHUMG00000007845	ENST00000371891.3:c.688dupT	chr1.hg19:g.47609486_47609486dupT	ENSP00000360958:p.Val228fs	189.0	0.0		157.0	48.0	NM_001010969	Q5TCH3|Q6JXK7|Q6JXK8|Q9NRM4	Frame_Shift_Ins	INS	ENST00000371891.3	hg19	CCDS30707.1																																																																																			.	.		0.55	CYP4A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021635.1	XM_208213		T	47609481	-	T	47609480	7	5	265	1	0	1	1	0	0	0	0	0	4186	1261	44	0	704	0	CYP4A22	1	47609480	Frame_Shift_Ins	INS	-	TCGA-FV-A3I1-01A-11D-A22F-10	10685910	47609480	201641141	3	38894										
ITGB3BP	23421	hgsc.bcm.edu	37	chr1	63974243	63974243	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	cttcagtgatcttttaacacTacaaacaaaaaatttaaaga	3	7	2	2			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr1:63974243T>C	ENST00000271002.10	-	2	87		c.e2-2		ITGB3BP_ENST00000371092.3_Splice_Site|ITGB3BP_ENST00000283568.8_Splice_Site	NM_014288.4	NP_055103.3	Q13352	CENPR_HUMAN	integrin beta 3 binding protein (beta3-endonexin)						apoptotic signaling pathway (GO:0097190)|cell adhesion (GO:0007155)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleosome assembly (GO:0006334)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|signal transducer activity (GO:0004871)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|upper_aerodigestive_tract(1)	9						CTTTTAACACTACAAACAAAA	0.269																																					.		Atlas-SNP	.											.	ITGB3BP	20	.	0			c.6-2A>G						.						25	25	25					1																	63974243		2150	4205	6355	SO:0001630	splice_region_variant	23421	exon3			TAACACTACAAAC	U37139	CCDS30736.1, CCDS55603.1	1p31.3	2013-11-05			ENSG00000142856	ENSG00000142856			6157	protein-coding gene	gene with protein product	"centromere protein R"	605494				7593198, 10490654	Standard	NM_014288		Approved	NRIF3, HSU37139, TAP20, CENPR	uc001dbb.2	Q13352	OTTHUMG00000013364	ENST00000271002.10:c.6-2A>G	chr1.hg19:g.63974243T>C		256.0	0.0		311.0	99.0	NM_014288	B2R7D8|Q13353|Q5RJ42|Q5RJ44|Q5RJ45|Q7KYX2|Q96CD5|Q9UKB6	Splice_Site	SNP	ENST00000271002.10	hg19	CCDS30736.1	.	.	.	.	.	.	.	.	.	.	T	12.22	1.872969	0.33069	.	.	ENSG00000142856	ENST00000271002;ENST00000371092;ENST00000283568	.	.	.	5.33	5.33	0.75918	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3195	0.74109	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	ITGB3BP	63746831	1.000000	0.71417	0.998000	0.56505	0.510000	0.34073	3.690000	0.54713	2.011000	0.59026	0.528000	0.53228	.	.	.		0.269	ITGB3BP-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000037242.2	NM_014288	Intron	C	63974243	T	C	63974243	5	2	265	1	0	0	0	0	0	0	1	0	7905	1536	53	2	557	2	ITGB3BP	1	63974243	Splice_Site	SNP	T	TCGA-FV-A3I1-01A-11D-A22F-10	16364763	63974243	185276378	4	38895										
DEPDC1	55635	hgsc.bcm.edu	37	chr1	68944871	68944874	+	Frame_Shift_Del	DEL	GTAA	GTAA	-													0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	atgtttttccactgcagtctGtaagtaagagggtacttgaa					rs534583672		TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	GTAA	GTAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr1:68944871_68944874delGTAA	ENST00000456315.2	-	10	2179_2182	c.2065_2068delTTAC	c.(2065-2070)ttacagfs	p.LQ689fs	DEPDC1_ENST00000370966.5_Frame_Shift_Del_p.LQ405fs|RP4-694A7.2_ENST00000425820.1_RNA	NM_001114120.1	NP_001107592.1	Q5TB30	DEP1A_HUMAN	DEP domain containing 1	689					intracellular signal transduction (GO:0035556)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	GTPase activator activity (GO:0005096)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13				OV - Ovarian serous cystadenocarcinoma(397;7.21e-36)		ACTGCAGTCTGTAAGTAAGAGGGT	0.377																																					p.689_690del		Atlas-Indel,Pindel	.											.	DEPDC1	102	.	0			c.2066_2069del						.																																			SO:0001589	frameshift_variant	55635	exon10			.	AK000361	CCDS644.1, CCDS44159.1	1p31.2	2008-08-19			ENSG00000024526	ENSG00000024526			22949	protein-coding gene	gene with protein product		612002					Standard	NM_001114120		Approved	DEP.8, FLJ20354, SDP35, DEPDC1A	uc001dem.4	Q5TB30	OTTHUMG00000009212	ENST00000456315.2:c.2065_2068delTTAC	chr1.hg19:g.68944875_68944878delGTAA	ENSP00000412292:p.Leu689fs	208.0	0.0		172.0	51.0	NM_001114120	A8QXE0|A8QXE1|Q05DU3|Q5TB28|Q9H9I3|Q9NX21|Q9NXZ0	Frame_Shift_Del	DEL	ENST00000456315.2	hg19	CCDS44159.1																																																																																			.	.		0.377	DEPDC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025514.2	NM_017779		-	68944874	GTAA	-	68944871	7	5	265	1	0	1	0	1	0	0	0	0	4441	1386	48	0	379	0	DEPDC1	1	68944871	Frame_Shift_Del	DEL	GTAA	TCGA-FV-A3I1-01A-11D-A22F-10	4970628	68944871	180305750	5	38896										
DPYD	1806	hgsc.bcm.edu	37	chr1	98164998	98164998	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	agcacaacttatacttgcagGcccagcaccaaaaagagcaa	7	12	0	1			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr1:98164998G>A	ENST00000370192.3	-	6	689	c.589C>T	c.(589-591)Cct>Tct	p.P197S	DPYD_ENST00000423006.2_3'UTR|DPYD_ENST00000474241.1_5'UTR	NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	197					beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase catabolic process (GO:0006145)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymidine catabolic process (GO:0006214)|thymine catabolic process (GO:0006210)|UMP biosynthetic process (GO:0006222)|uracil catabolic process (GO:0006212)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|dihydroorotate dehydrogenase activity (GO:0004152)|dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(18)|lung(30)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	ATACTTGCAGGCCCAGCACCA	0.423																																					p.P197S		Atlas-SNP	.											.	DPYD	219	.	0			c.C589T						.						161	159	160					1																	98164998		2203	4300	6503	SO:0001583	missense	1806	exon6			TTGCAGGCCCAGC	U20938	CCDS30777.1, CCDS53346.1	1p22	2014-09-17			ENSG00000188641	ENSG00000188641	1.3.1.2		3012	protein-coding gene	gene with protein product		612779				7713523	Standard	NM_000110		Approved	DPD	uc001drv.3	Q12882	OTTHUMG00000039683	ENST00000370192.3:c.589C>T	chr1.hg19:g.98164998G>A	ENSP00000359211:p.Pro197Ser	145.0	0.0		162.0	51.0	NM_000110	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Missense_Mutation	SNP	ENST00000370192.3	hg19	CCDS30777.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.776208	0.90195	.	.	ENSG00000188641	ENST00000370192	D	0.96774	-4.12	5.5	5.5	0.81552	Alpha-helical ferredoxin (1);	0.000000	0.85682	D	0.000000	D	0.98356	0.9454	M	0.86502	2.82	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99177	1.0866	10	0.87932	D	0	-15.1612	19.3869	0.94560	0.0:0.0:1.0:0.0	.	197	Q12882	DPYD_HUMAN	S	197	ENSP00000359211:P197S	ENSP00000359211:P197S	P	-	1	0	DPYD	97937586	1.000000	0.71417	0.997000	0.53966	0.999000	0.98932	9.431000	0.97494	2.591000	0.87537	0.585000	0.79938	CCT	.	.		0.423	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110		A	98164998	G	A	98164998	3	1	265	1	0	0	0	0	1	0	0	0	4747	1203	42	3	2560	3	DPYD	1	98164998	Missense_Mutation	SNP	G	TCGA-FV-A3I1-01A-11D-A22F-10	29220127	98164998	151085623	6	38897										
LPPR4	9890	hgsc.bcm.edu	37	chr1	99771771	99771771	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	gaccaccatggtcctggcaaTcagtacctcaaaatccagcc	7	15	2	0			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr1:99771771T>C	ENST00000370185.3	+	7	1994	c.1497T>C	c.(1495-1497)aaT>aaC	p.N499N	LPPR4_ENST00000457765.1_Silent_p.N441N|LPPR4_ENST00000370184.1_Silent_p.N341N	NM_014839.4	NP_055654.2	Q7Z2D5	LPPR4_HUMAN		499					axonogenesis (GO:0007409)|inner ear development (GO:0048839)|phospholipid dephosphorylation (GO:0046839)	integral component of plasma membrane (GO:0005887)	lipid phosphatase activity (GO:0042577)|phosphatidate phosphatase activity (GO:0008195)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(39)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	72		all_epithelial(167;3.54e-06)|all_lung(203;0.00139)|Lung NSC(277;0.00202)		Epithelial(280;0.0736)|all cancers(265;0.0975)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)|Colorectal(170;0.22)		GTCCTGGCAATCAGTACCTCA	0.572																																					p.N499N		Atlas-SNP	.											.	LPPR4	143	.	0			c.T1497C						.						159	161	160					1																	99771771		2203	4300	6503	SO:0001819	synonymous_variant	0	exon7			TGGCAATCAGTAC																												ENST00000370185.3:c.1497T>C	chr1.hg19:g.99771771T>C		93.0	0.0		96.0	38.0	NM_014839	E7EPS1|O75043|Q5T9R9|Q86XQ5|Q8N3F1|Q96MP0	Silent	SNP	ENST00000370185.3	hg19	CCDS757.1																																																																																			.	.		0.572	LPPR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029670.2			C	99771771	T	C	99771771	2	2	265	1	0	0	0	0	0	0	0	1	8936	1432	50	2		2	LPPR4	1	99771771	Silent	SNP	T	TCGA-FV-A3I1-01A-11D-A22F-10	1606773	99771771	149478850	7	38898										
CEP350	9857	hgsc.bcm.edu	37	chr1	180062616	180062617	+	Frame_Shift_Ins	INS	-	-	T													0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	gacaggctgttggaactcaaINSgtcccctactgagctgatga							TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr1:180062616_180062617insT	ENST00000367607.3	+	34	7794_7795	c.7376_7377insT	c.(7375-7380)aagtccfs	p.KS2459fs	CEP350_ENST00000490141.1_3'UTR	NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	2459					microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						TTGGAACTCAAGTCCCCTACTG	0.465																																					p.K2459fs		Atlas-INDEL	.											.	CEP350	418	.	0			c.7376_7377insT						.																																			SO:0001589	frameshift_variant	9857	exon34			.	AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"centrosome associated protein 350"					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	Exception_encountered	chr1.hg19:g.180062616_180062617insT	ENSP00000356579:p.Lys2459fs	252.0	0.0		325.0	156.0	NM_014810	O75068|Q8TDK3|Q8WY20	Frame_Shift_Ins	INS	ENST00000367607.3	hg19	CCDS1336.1																																																																																			.	.		0.465	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810		T	180062617	-	T	180062616	7	5	265	1	0	1	1	0	0	0	0	0	3256	72	3	0	7506	0	CEP350	1	180062616	Frame_Shift_Ins	INS	-	TCGA-FV-A3I1-01A-11D-A22F-10	80290845	180062616	69188005	8	38899										
LAD1	3898	hgsc.bcm.edu	37	chr1	201351823	201351823	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	tcctgggtcctgctgatccaCaggttgagccttgatgtcac	11	12	1	3			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr1:201351823C>T	ENST00000391967.2	-	8	1732	c.1431G>A	c.(1429-1431)ctG>ctA	p.L477L	LAD1_ENST00000367313.3_Silent_p.L491L|LAD1_ENST00000488842.1_5'UTR	NM_005558.3	NP_005549.2	O00515	LAD1_HUMAN	ladinin 1	477						basement membrane (GO:0005604)	structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(6)|prostate(2)|skin(2)	19						TGCTGATCCACAGGTTGAGCC	0.547																																					p.L477L		Atlas-SNP	.											.	LAD1	42	.	0			c.G1431A						.						91	64	73					1																	201351823		2203	4300	6503	SO:0001819	synonymous_variant	3898	exon8			GATCCACAGGTTG	U42408	CCDS1410.1	1q25.1-q32.3	2008-02-05			ENSG00000159166	ENSG00000159166			6472	protein-coding gene	gene with protein product		602314				8618013, 9119369	Standard	NM_005558		Approved		uc001gwm.3	O00515	OTTHUMG00000035737	ENST00000391967.2:c.1431G>A	chr1.hg19:g.201351823C>T		55.0	0.0		53.0	16.0	NM_005558	O95614|Q96GD8	Silent	SNP	ENST00000391967.2	hg19	CCDS1410.1																																																																																			.	.		0.547	LAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086946.1	NM_005558		T	201351823	C	T	201351823	2	4	265	1	0	0	0	0	0	0	0	1	8608	465	17	3		3	LAD1	1	201351823	Silent	SNP	C	TCGA-FV-A3I1-01A-11D-A22F-10	21289207	201351823	47898798	9	38900										
ODC1	4953	hgsc.bcm.edu	37	chr2	10581663	10581663	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	ccctgacatcacatagtagaTcgtcggcctctggaagccat	9	13	2	2			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr2:10581663T>C	ENST00000234111.4	-	11	1723	c.1213A>G	c.(1213-1215)Atc>Gtc	p.I405V	ODC1_ENST00000405333.1_Missense_Mutation_p.I405V|ODC1_ENST00000446285.1_5'Flank	NM_002539.1	NP_002530.1	P11926	DCOR_HUMAN	ornithine decarboxylase 1	405					cellular nitrogen compound metabolic process (GO:0034641)|kidney development (GO:0001822)|polyamine metabolic process (GO:0006595)|positive regulation of cell proliferation (GO:0008284)|putrescine biosynthetic process from ornithine (GO:0033387)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|response to virus (GO:0009615)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ornithine decarboxylase activity (GO:0004586)|protein homodimerization activity (GO:0042803)			NS(1)|central_nervous_system(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|skin(3)	19	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.161)	Spermine(DB00127)	ACATAGTAGATCGTCGGCCTC	0.502																																					p.I405V		Atlas-SNP	.											.	ODC1	40	.	0			c.A1213G						.						59	53	55					2																	10581663		2203	4300	6503	SO:0001583	missense	4953	exon11			AGTAGATCGTCGG		CCDS1672.1	2p25	2012-10-02			ENSG00000115758	ENSG00000115758	4.1.1.17		8109	protein-coding gene	gene with protein product		165640					Standard	NM_002539		Approved	ODC	uc002rao.1	P11926	OTTHUMG00000090450	ENST00000234111.4:c.1213A>G	chr2.hg19:g.10581663T>C	ENSP00000234111:p.Ile405Val	118.0	0.0		140.0	98.0	NM_002539	Q53TU3|Q6LDS9	Missense_Mutation	SNP	ENST00000234111.4	hg19	CCDS1672.1	.	.	.	.	.	.	.	.	.	.	T	7.060	0.566151	0.13560	.	.	ENSG00000115758	ENST00000234111;ENST00000405333;ENST00000537630	T;T	0.37411	1.2;1.2	5.66	5.66	0.87406	Orn/DAP/Arg decarboxylase 2, C-terminal (1);Alanine racemase/group IV decarboxylase, C-terminal (2);	0.172204	0.56097	D	0.000037	T	0.20251	0.0487	N	0.16307	0.4	0.47341	D	0.999399	B	0.02656	0.0	B	0.09377	0.004	T	0.07966	-1.0745	10	0.06757	T	0.87	.	11.8398	0.52346	0.0:0.0:0.146:0.854	.	405	P11926	DCOR_HUMAN	V	405;405;276	ENSP00000234111:I405V;ENSP00000385333:I405V	ENSP00000234111:I405V	I	-	1	0	ODC1	10499114	1.000000	0.71417	0.907000	0.35723	0.830000	0.47004	3.927000	0.56499	2.157000	0.67596	0.482000	0.46254	ATC	.	.		0.502	ODC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206896.2			C	10581663	T	C	10581663	3	2	265	1	0	0	0	0	1	0	0	0	10834	1435	50	2	180	2	ODC1	2	10581663	Missense_Mutation	SNP	T	TCGA-FV-A3I1-01A-11D-A22F-10		10581663	232617710	10	38901										
NFE2L2	4780	hgsc.bcm.edu	37	chr2	178098960	178098974	+	In_Frame_Del	DEL	CTATATCTTGCCTCC	CTATATCTTGCCTCC	-													0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	ttctcgacttactccaagatCtatatcttgcctccaaagta							TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	CTATATCTTGCCTCC	CTATATCTTGCCTCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr2:178098960_178098974delCTATATCTTGCCTCC	ENST00000397062.3	-	2	625_639	c.71_85delGGAGGCAAGATATAG	c.(70-87)tggaggcaagatatagat>tat	p.24_29WRQDID>Y	NFE2L2_ENST00000423513.1_In_Frame_Del_p.8_13WRQDID>Y|NFE2L2_ENST00000446151.2_In_Frame_Del_p.8_13WRQDID>Y|NFE2L2_ENST00000464747.1_In_Frame_Del_p.8_13WRQDID>Y|NFE2L2_ENST00000397063.4_In_Frame_Del_p.8_13WRQDID>Y	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	24					cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D29H(11)|p.W24C(5)|p.D29N(2)|p.D29Y(2)|p.Q26K(1)|p.D27H(1)|p.Q26L(1)|p.Q26E(1)|p.D27Y(1)|p.I28T(1)|p.Q26P(1)		central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			ACTCCAAGATCTATATCTTGCCTCCAAAGTATGTC	0.349			Mis		"NSCLC, HNSCC"					HNSCC(56;0.16)																											p.24_29del		Atlas-Indel,Pindel	.		Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	NFE2L2,bladder,carcinoma,-1,8	NFE2L2	225	.	27	Substitution - Missense(27)	lung(16)|oesophagus(4)|upper_aerodigestive_tract(3)|cervix(1)|endometrium(1)|liver(1)|kidney(1)	c.72_86del						.																																			SO:0001651	inframe_deletion	4780	exon2			.		CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"basic leucine zipper proteins"	7782	protein-coding gene	gene with protein product	"NF-E2-related factor 2"	600492	"nuclear factor (erythroid-derived 2)-like 2"			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.71_85delGGAGGCAAGATATAG	chr2.hg19:g.178098960_178098974delCTATATCTTGCCTCC	ENSP00000380252:p.Trp24_Asp29delinsTyr	127.0	0.0		159.0	125.0	NM_006164	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	In_Frame_Del	DEL	ENST00000397062.3	hg19	CCDS42782.1																																																																																			.	.		0.349	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4	NM_006164		-	178098974	CTATATCTTGCCTCC	-	178098960	7	5	265	1	0	1	0	1	0	0	0	0	10377	913	32	0	1748	0	NFE2L2	2	178098960	In_Frame_Del	DEL	CTATATCTTGCCTCC	TCGA-FV-A3I1-01A-11D-A22F-10	167517297	178098960	65100413	11	38902										
SETD2	29072	hgsc.bcm.edu	37	chr3	47098921	47098921	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	acaacttccggcgttcctctGtagaaagtttattgcggtct	9	10	2	1			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr3:47098921G>A	ENST00000409792.3	-	15	6395	c.6353C>T	c.(6352-6354)aCa>aTa	p.T2118I		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	2118					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		GCGTTCCTCTGTAGAAAGTTT	0.428			"N, F, S, Mis"		clear cell renal carcinoma																																p.T2118I		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.C6353T						.						70	72	71					3																	47098921		2203	4300	6503	SO:0001583	missense	29072	exon15			TCCTCTGTAGAAA	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.6353C>T	chr3.hg19:g.47098921G>A	ENSP00000386759:p.Thr2118Ile	98.0	0.0		96.0	24.0	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	hg19	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	G	23.6	4.437857	0.83885	.	.	ENSG00000181555	ENST00000451092;ENST00000409792	T	0.25414	1.8	4.98	4.98	0.66077	.	0.000000	0.64402	D	0.000010	T	0.47801	0.1465	L	0.50333	1.59	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.44483	-0.9325	10	0.87932	D	0	.	18.7956	0.91993	0.0:0.0:1.0:0.0	.	2118;2118	F2Z317;Q9BYW2	.;SETD2_HUMAN	I	2118	ENSP00000386759:T2118I	ENSP00000386759:T2118I	T	-	2	0	SETD2	47073925	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.171000	0.94802	2.755000	0.94549	0.655000	0.94253	ACA	.	.		0.428	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		A	47098921	G	A	47098921	3	1	265	1	0	0	0	0	1	0	0	0	14146	1377	48	3	1369	3	SETD2	3	47098921	Missense_Mutation	SNP	G	TCGA-FV-A3I1-01A-11D-A22F-10		47098921	150923509	12	38903										
ROBO1	6091	hgsc.bcm.edu	37	chr3	78685014	78685014	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	ggtttccagtgcttctcgccAgagtccccgctgccattgtt	10	14	1	1			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr3:78685014A>G	ENST00000464233.1	-	23	3395	c.3282T>C	c.(3280-3282)tcT>tcC	p.S1094S	ROBO1_ENST00000467549.1_Silent_p.S994S|ROBO1_ENST00000436010.2_Silent_p.S1055S|ROBO1_ENST00000495273.1_Silent_p.S1049S	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	1094					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		GCTTCTCGCCAGAGTCCCCGC	0.517																																					p.S1094S		Atlas-SNP	.											.	ROBO1	833	.	0			c.T3282C						.						172	173	173					3																	78685014		2149	4260	6409	SO:0001819	synonymous_variant	6091	exon23			CTCGCCAGAGTCC	AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.3282T>C	chr3.hg19:g.78685014A>G		178.0	0.0		178.0	60.0	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Silent	SNP	ENST00000464233.1	hg19	CCDS54611.1																																																																																			.	.		0.517	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		G	78685014	A	G	78685014	2	3	265	1	0	0	0	0	0	0	0	1	13528	175	7	2		2	ROBO1	3	78685014	Silent	SNP	A	TCGA-FV-A3I1-01A-11D-A22F-10	31586093	78685014	119337416	13	38904										
OR5H14	403273	hgsc.bcm.edu	37	chr3	97868346	97868346	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	gtaatatatctcatcaccatCatggggaatcttggtctgat	8	8	5	1			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr3:97868346C>A	ENST00000437310.1	+	1	177	c.117C>A	c.(115-117)atC>atA	p.I39I	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005514.1	NP_001005514.1	A6NHG9	O5H14_HUMAN	olfactory receptor, family 5, subfamily H, member 14	39						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	31						TCATCACCATCATGGGGAATC	0.408																																					p.I39I		Atlas-SNP	.											.	OR5H14	56	.	0			c.C117A						.						207	210	209					3																	97868346		2203	4297	6500	SO:0001819	synonymous_variant	403273	exon1			CACCATCATGGGG		CCDS33798.1	3q11.2	2013-09-23			ENSG00000236032	ENSG00000236032		"GPCR / Class A : Olfactory receptors"	31286	protein-coding gene	gene with protein product							Standard	NM_001005514		Approved		uc003dsg.1	A6NHG9	OTTHUMG00000160079	ENST00000437310.1:c.117C>A	chr3.hg19:g.97868346C>A		556.0	0.0		565.0	189.0	NM_001005514	B9EH15	Silent	SNP	ENST00000437310.1	hg19	CCDS33798.1																																																																																			.	.		0.408	OR5H14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359112.1			A	97868346	C	A	97868346	2	1	265	1	0	0	0	0	0	0	0	1	11169	816	29	3		3	OR5H14	3	97868346	Silent	SNP	C	TCGA-FV-A3I1-01A-11D-A22F-10	19183332	97868346	100154084	14	38905										
BBX	56987	hgsc.bcm.edu	37	chr3	107510138	107510138	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	cttcttggatgccattcaccCtacagaaggtaagacaagca	8	11	2	2	rs138504832		TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr3:107510138C>T	ENST00000325805.8	+	15	2632	c.2345C>T	c.(2344-2346)cCt>cTt	p.P782L	BBX_ENST00000415149.2_Missense_Mutation_p.P752L|BBX_ENST00000416476.2_Silent_p.L446L|BBX_ENST00000473542.1_3'UTR|BBX_ENST00000402543.1_Intron|BBX_ENST00000406780.1_Missense_Mutation_p.P752L			Q8WY36	BBX_HUMAN	bobby sox homolog (Drosophila)	782					bone development (GO:0060348)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(18)|ovary(4)|pancreas(1)|skin(2)	49			OV - Ovarian serous cystadenocarcinoma(3;0.112)			GCCATTCACCCTACAGAAGGT	0.338																																					p.P782L		Atlas-SNP	.											.	BBX	156	.	0			c.C2345T						.						97	93	94					3																	107510138		2203	4300	6503	SO:0001583	missense	56987	exon15			TTCACCCTACAGA	AF168718	CCDS2950.1, CCDS46881.1, CCDS63712.1	3q13.1	2008-07-18			ENSG00000114439	ENSG00000114439			14422	protein-coding gene	gene with protein product	"x 001 protein"					11680820	Standard	NM_001142568		Approved	MDS001, HSPC339, HBP2	uc010hpr.4	Q8WY36	OTTHUMG00000150360	ENST00000325805.8:c.2345C>T	chr3.hg19:g.107510138C>T	ENSP00000319974:p.Pro782Leu	215.0	0.0		230.0	53.0	NM_001142568	A2RRM7|Q2TAJ1|Q7L3J8|Q7LBY8|Q8NDB0|Q8WY35|Q9H0J6	Missense_Mutation	SNP	ENST00000325805.8	hg19	CCDS46881.1	.	.	.	.	.	.	.	.	.	.	C	15.57	2.872662	0.51695	.	.	ENSG00000114439	ENST00000415149;ENST00000325805;ENST00000406780	T;T;T	0.30448	1.53;1.81;1.53	5.11	4.16	0.48862	.	0.577026	0.19862	N	0.104420	T	0.16171	0.0389	N	0.19112	0.55	0.36056	D	0.841114	P;B	0.36222	0.544;0.4	B;B	0.27170	0.072;0.077	T	0.14783	-1.0460	10	0.87932	D	0	-8.2148	7.6738	0.28473	0.0:0.8847:0.0:0.1153	.	782;752	Q8WY36;Q8WY36-2	BBX_HUMAN;.	L	752;782;752	ENSP00000408358:P752L;ENSP00000319974:P782L;ENSP00000385530:P752L	ENSP00000319974:P782L	P	+	2	0	BBX	108992828	0.999000	0.42202	1.000000	0.80357	0.982000	0.71751	1.992000	0.40737	2.656000	0.90262	0.557000	0.71058	CCT	.	C|1.000;A|0.000		0.338	BBX-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317820.1	NM_020235		T	107510138	C	T	107510138	3	4	265	1	0	0	0	0	1	0	0	0	1343	681	24	3	2391	3	BBX	3	107510138	Missense_Mutation	SNP	C	TCGA-FV-A3I1-01A-11D-A22F-10	9641792	107510138	90512292	15	38906										
COPG	22820	hgsc.bcm.edu	37	chr3	128973580	128973580	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	gtgcgagccctctgccagatCactgatgtgagtcgtgccgg	14	12	2	3			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr3:128973580C>A	ENST00000314797.6	+	6	497	c.393C>A	c.(391-393)atC>atA	p.I131I		NM_016128.3	NP_057212.1	Q9Y678	COPG1_HUMAN	coatomer protein complex, subunit gamma 1	131					COPI coating of Golgi vesicle (GO:0048205)|establishment of Golgi localization (GO:0051683)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|organelle transport along microtubule (GO:0072384)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)	structural molecule activity (GO:0005198)										TCTGCCAGATCACTGATGTGA	0.562																																					p.I131I		Atlas-SNP	.											.	.	.	.	0			c.C393A						.						54	57	56					3																	128973580		2203	4300	6503	SO:0001819	synonymous_variant	22820	exon6			CCAGATCACTGAT	AB047846	CCDS33851.1	3q21.3	2012-02-23	2012-02-23	2012-02-23	ENSG00000181789	ENSG00000181789			2236	protein-coding gene	gene with protein product	"coat protein gamma-cop"	615525	"coatomer protein complex, subunit gamma"	COPG		11056392	Standard	NM_016128		Approved		uc003els.3	Q9Y678	OTTHUMG00000159451	ENST00000314797.6:c.393C>A	chr3.hg19:g.128973580C>A		41.0	0.0		45.0	11.0	NM_016128	A8K6M8|B3KMF6|Q54AC4	Silent	SNP	ENST00000314797.6	hg19	CCDS33851.1																																																																																			.	.		0.562	COPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355456.1	NM_016128		A	128973580	C	A	128973580	2	1	265	1	0	0	0	0	0	0	0	1	3733	816	29	3		3	COPG	3	128973580	Silent	SNP	C	TCGA-FV-A3I1-01A-11D-A22F-10	21463442	128973580	69048850	16	38907										
GPR87	53836	hgsc.bcm.edu	37	chr3	151017871	151017871	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	ttacttggtaattttgcaagCgtcaagttgaaccccattct	7	9	2	1			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr3:151017871C>A	ENST00000260843.4	-	2	482	c.18G>T	c.(16-18)acG>acT	p.T6T	MED12L_ENST00000273432.4_Intron|MED12L_ENST00000474524.1_Intron|MED12L_ENST00000491549.1_Intron	NM_023915.3	NP_076404.3	Q9BY21	GPR87_HUMAN	G protein-coupled receptor 87	6					negative regulation of adenylate cyclase activity (GO:0007194)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			endometrium(6)|large_intestine(6)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	19			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			ATTTTGCAAGCGTCAAGTTGA	0.408																																					p.T6T		Atlas-SNP	.											.	GPR87	52	.	0			c.G18T						.						105	96	99					3																	151017871		2203	4300	6503	SO:0001819	synonymous_variant	53836	exon2			TGCAAGCGTCAAG	AF237763	CCDS3157.1	3q24	2012-08-21			ENSG00000138271	ENSG00000138271		"GPCR / Class A : Orphans"	4538	protein-coding gene	gene with protein product		606379		GPR95		11273702	Standard	NM_023915		Approved		uc003eyt.2	Q9BY21	OTTHUMG00000159858	ENST00000260843.4:c.18G>T	chr3.hg19:g.151017871C>A		84.0	0.0		84.0	4.0	NM_023915	Q5KU35|Q96JZ8|Q9BXC2	Silent	SNP	ENST00000260843.4	hg19	CCDS3157.1																																																																																			.	.		0.408	GPR87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357788.1			A	151017871	C	A	151017871	2	1	265	1	0	0	0	0	0	0	0	1	6724	755	27	1		1	GPR87	3	151017871	Silent	SNP	C	TCGA-FV-A3I1-01A-11D-A22F-10	22044291	151017871	47004559	17	38908										
NLGN1	22871	hgsc.bcm.edu	37	chr3	173998534	173998534	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	aactgacatcactttcagacCtacgagaaaaaattctgtac	5	10	3	3			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr3:173998534C>A	ENST00000457714.1	+	7	2342	c.1913C>A	c.(1912-1914)cCt>cAt	p.P638H	NLGN1_ENST00000361589.4_Missense_Mutation_p.P638H|NLGN1_ENST00000545397.1_Missense_Mutation_p.P638H|NLGN1_ENST00000401917.3_Missense_Mutation_p.P678H	NM_014932.2	NP_055747.1	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	655					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|calcium-dependent cell-cell adhesion (GO:0016339)|cytoskeletal matrix organization at active zone (GO:0048789)|establishment of protein localization (GO:0045184)|heterophilic cell-cell adhesion (GO:0007157)|N-methyl-D-aspartate receptor clustering (GO:0097114)|nervous system development (GO:0007399)|neurexin clustering (GO:0097115)|neuron cell-cell adhesion (GO:0007158)|neuronal signal transduction (GO:0023041)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|positive regulation of synaptic vesicle exocytosis (GO:2000302)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|protein homooligomerization (GO:0051260)|protein localization to synapse (GO:0035418)|protein targeting (GO:0006605)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuron differentiation (GO:0045664)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|synapse assembly (GO:0007416)|synaptic vesicle clustering (GO:0097091)|synaptic vesicle targeting (GO:0016080)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|filopodium tip (GO:0032433)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|PDZ domain binding (GO:0030165)|protein dimerization activity (GO:0046983)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(2)|lung(54)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	83	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			ACTTTCAGACCTACGAGAAAA	0.438																																					p.P638H		Atlas-SNP	.											.	NLGN1	209	.	0			c.C1913A						.						122	121	121					3																	173998534		2203	4300	6503	SO:0001583	missense	22871	exon7			TCAGACCTACGAG	AB028993	CCDS3222.1	3q26.32	2008-07-18			ENSG00000169760	ENSG00000169760			14291	protein-coding gene	gene with protein product		600568				10767552, 10819331	Standard	NM_014932		Approved	KIAA1070	uc003fio.1	Q8N2Q7	OTTHUMG00000157005	ENST00000457714.1:c.1913C>A	chr3.hg19:g.173998534C>A	ENSP00000392500:p.Pro638His	166.0	0.0		148.0	40.0	NM_014932	Q9UPT2	Missense_Mutation	SNP	ENST00000457714.1	hg19	CCDS3222.1	.	.	.	.	.	.	.	.	.	.	C	15.40	2.821953	0.50633	.	.	ENSG00000169760	ENST00000457714;ENST00000361589;ENST00000545397;ENST00000401917	T;T;T;T	0.68765	-0.35;-0.35;-0.35;-0.35	5.59	5.59	0.84812	.	0.055473	0.64402	D	0.000001	T	0.55130	0.1901	N	0.12961	0.28	0.58432	D	0.999999	B	0.16166	0.016	B	0.17722	0.019	T	0.52503	-0.8567	10	0.72032	D	0.01	.	19.9651	0.97262	0.0:1.0:0.0:0.0	.	638	Q8N2Q7-2	.	H	638;638;638;678	ENSP00000392500:P638H;ENSP00000354541:P638H;ENSP00000441108:P638H;ENSP00000385750:P678H	ENSP00000354541:P638H	P	+	2	0	NLGN1	175481228	0.993000	0.37304	0.999000	0.59377	0.968000	0.65278	2.911000	0.48774	2.793000	0.96121	0.655000	0.94253	CCT	.	.		0.438	NLGN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347054.3	NM_014932		A	173998534	C	A	173998534	3	1	265	1	0	0	0	0	1	0	0	0	10470	681	24	3	1931	3	NLGN1	3	173998534	Missense_Mutation	SNP	C	TCGA-FV-A3I1-01A-11D-A22F-10	22980663	173998534	24023896	18	38909										
PPEF2	5470	hgsc.bcm.edu	37	chr4	76794280	76794280	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	gctgcagagggagcacccacCttgcggttgtgacagaattc	13	11	0	3			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr4:76794280C>A	ENST00000286719.7	-	12	1862	c.1506G>T	c.(1504-1506)aaG>aaT	p.K502N		NM_006239.2	NP_006230.2	O14830	PPE2_HUMAN	protein phosphatase, EF-hand calcium binding domain 2	502	Catalytic.				detection of stimulus involved in sensory perception (GO:0050906)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|protein dephosphorylation (GO:0006470)|regulation of JUN kinase activity (GO:0043506)|regulation of MAP kinase activity (GO:0043405)|visual perception (GO:0007601)	cilium (GO:0005929)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|Hsp70 protein binding (GO:0030544)|Hsp90 protein binding (GO:0051879)|iron ion binding (GO:0005506)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	50			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			GAGCACCCACCTTGCGGTTGT	0.478																																					p.K502N	NSCLC(105;1359 1603 15961 44567 47947)	Atlas-SNP	.											.	PPEF2	108	.	0			c.G1506T						.						130	119	123					4																	76794280		2203	4300	6503	SO:0001630	splice_region_variant	5470	exon12			ACCCACCTTGCGG	AF023456	CCDS34013.1	4q21.1	2013-01-10			ENSG00000156194	ENSG00000156194		"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits", "EF-hand domain containing"	9244	protein-coding gene	gene with protein product	"protein phosphatase 7, catalytic subunit, beta isozyme"	602256				9326663, 12051765	Standard	NM_006239		Approved	PPP7CB	uc003hix.3	O14830	OTTHUMG00000160915	ENST00000286719.7:c.1506+1G>T	chr4.hg19:g.76794280C>A		76.0	0.0		92.0	21.0	NM_006239	O14831	Missense_Mutation	SNP	ENST00000286719.7	hg19	CCDS34013.1	.	.	.	.	.	.	.	.	.	.	C	14.94	2.684002	0.47991	.	.	ENSG00000156194	ENST00000286719;ENST00000337500	T	0.05925	3.37	4.85	4.01	0.46588	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (2);	0.048452	0.85682	D	0.000000	T	0.16385	0.0394	L	0.46614	1.455	0.48830	D	0.999719	P;D	0.89917	0.929;1.0	P;D	0.85130	0.734;0.997	T	0.01093	-1.1454	9	.	.	.	-3.0911	10.8508	0.46769	0.0:0.9083:0.0:0.0917	.	502;502	O14830-2;O14830	.;PPE2_HUMAN	N	502	ENSP00000286719:K502N	.	K	-	3	2	PPEF2	77013304	1.000000	0.71417	1.000000	0.80357	0.026000	0.11368	5.382000	0.66213	1.274000	0.44362	0.563000	0.77884	AAG	.	.		0.478	PPEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362929.1	NM_006239	Missense_Mutation	A	76794280	C	A	76794280	5	1	265	1	0	0	0	0	0	0	1	0	12317	695	24	3	779	3	PPEF2	4	76794280	Splice_Site	SNP	C	TCGA-FV-A3I1-01A-11D-A22F-10		76794280	114359996	19	38910										
ODZ3	55714	hgsc.bcm.edu	37	chr4	183659598	183659598	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	cgtgtttggacctgactctgTgggaaaagaggactgccatt	13	8	1	2			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr4:183659598T>C	ENST00000511685.1	+	18	3403	c.3280T>C	c.(3280-3282)Tgg>Cgg	p.W1094R	TENM3_ENST00000502950.1_3'UTR|TENM3_ENST00000406950.2_Missense_Mutation_p.W1094R			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1094					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										CCTGACTCTGTGGGAAAAGAG	0.468																																					p.W1094R		Atlas-SNP	.											.	.	.	.	0			c.T3280C						.						260	252	254					4																	183659598		1946	4161	6107	SO:0001583	missense	55714	exon17			ACTCTGTGGGAAA	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.3280T>C	chr4.hg19:g.183659598T>C	ENSP00000424226:p.Trp1094Arg	136.0	0.0		155.0	48.0	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	hg19	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.410027	0.83340	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	D;D	0.92595	-3.07;-3.07	5.25	5.25	0.73442	.	.	.	.	.	D	0.96491	0.8855	M	0.88310	2.945	0.80722	D	1	D	0.71674	0.998	D	0.77557	0.99	D	0.97256	0.9901	9	0.87932	D	0	.	15.3185	0.74102	0.0:0.0:0.0:1.0	.	1094	Q9P273	TEN3_HUMAN	R	1094	ENSP00000424226:W1094R;ENSP00000385276:W1094R	ENSP00000385276:W1094R	W	+	1	0	ODZ3	183896592	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.868000	0.87116	2.206000	0.71126	0.533000	0.62120	TGG	.	.		0.468	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			C	183659598	T	C	183659598	3	2	265	1	0	0	0	0	1	0	0	0	10845	1696	59	2	3346	2	ODZ3	4	183659598	Missense_Mutation	SNP	T	TCGA-FV-A3I1-01A-11D-A22F-10	106865318	183659598	7494678	20	38911										
OCLN	100506658	hgsc.bcm.edu	37	chr5	68805338	68805338	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	caagagcagcaaagggcttcAtgttggccatggctgccttt	12	10	1	1			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr5:68805338A>T	ENST00000355237.2	+	3	857	c.421A>T	c.(421-423)Atg>Ttg	p.M141L	OCLN_ENST00000380766.2_Missense_Mutation_p.M141L|OCLN_ENST00000538151.1_Intron|OCLN_ENST00000396442.2_Missense_Mutation_p.M141L|OCLN_ENST00000542132.1_Intron	NM_002538.3	NP_002529.1	Q16625	OCLN_HUMAN	occludin	141	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				apoptotic process (GO:0006915)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|protein complex assembly (GO:0006461)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethionine metabolic process (GO:0046500)|tight junction assembly (GO:0070830)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	protein domain specific binding (GO:0019904)|structural molecule activity (GO:0005198)|thiopurine S-methyltransferase activity (GO:0008119)			endometrium(2)|large_intestine(1)|liver(1)|prostate(1)|skin(1)	6		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)		AAAGGGCTTCATGTTGGCCAT	0.463																																					p.M141L		Atlas-SNP	.											.	OCLN	22	.	0			c.A421T						.						159	112	128					5																	68805338		2203	4300	6503	SO:0001583	missense	100506658	exon3			GGCTTCATGTTGG	U49184	CCDS4006.1, CCDS54864.1	5q13.1	2014-06-13			ENSG00000197822	ENSG00000197822			8104	protein-coding gene	gene with protein product	"tight junction protein occludin TM4 minus", "phosphatase 1, regulatory subunit 115"	602876				8601611	Standard	NM_002538		Approved	PPP1R115	uc003jwu.3	Q16625	OTTHUMG00000099356	ENST00000355237.2:c.421A>T	chr5.hg19:g.68805338A>T	ENSP00000347379:p.Met141Leu	289.0	0.0		318.0	111.0	NM_001205254	B5BU70|D2DU64|D2DU65|D2IGC0|D2IGC1|E2CYV9|Q5U1V4|Q8N6K1	Missense_Mutation	SNP	ENST00000355237.2	hg19	CCDS4006.1	.	.	.	.	.	.	.	.	.	.	A	5.070	0.198593	0.09652	.	.	ENSG00000197822	ENST00000355237;ENST00000396442;ENST00000380766	T;T;T	0.24350	1.86;1.86;1.86	5.82	1.38	0.22167	Marvel (1);MARVEL-like domain (1);	0.486738	0.23288	N	0.049833	T	0.07458	0.0188	N	0.02142	-0.665	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.19712	-1.0297	10	0.18276	T	0.48	-20.5348	4.9156	0.13844	0.5703:0.2415:0.0:0.1882	.	141	Q16625	OCLN_HUMAN	L	141	ENSP00000347379:M141L;ENSP00000379719:M141L;ENSP00000370143:M141L	ENSP00000347379:M141L	M	+	1	0	OCLN	68841094	1.000000	0.71417	0.980000	0.43619	0.626000	0.37791	1.178000	0.31981	0.353000	0.24079	-0.887000	0.02937	ATG	.	.		0.463	OCLN-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216794.1	NM_002538		T	68805338	A	T	68805338	3	4	265	1	0	0	0	0	1	0	0	0	10829	217	8	4	427	4	OCLN	5	68805338	Missense_Mutation	SNP	A	TCGA-FV-A3I1-01A-11D-A22F-10		68805338	112109922	21	38912										
EDIL3	10085	hgsc.bcm.edu	37	chr5	83680126	83680126	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	tccgggtcccgacgccttacCtttgccgaactgggggacac	12	15	0	0			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr5:83680126C>T	ENST00000296591.5	-	1	485	c.67G>A	c.(67-69)Ggt>Agt	p.G23S	CTD-2269F5.1_ENST00000515688.1_RNA|CTD-2269F5.1_ENST00000509406.1_RNA|CTD-2269F5.1_ENST00000502253.1_RNA|EDIL3_ENST00000380138.3_Splice_Site_p.G23S|CTD-2269F5.1_ENST00000507060.1_RNA|CTD-2269F5.1_ENST00000514696.1_RNA	NM_005711.3	NP_005702.3	O43854	EDIL3_HUMAN	EGF-like repeats and discoidin I-like domains 3	23					cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|prostate(5)|skin(3)	31		Lung NSC(167;0.000121)|all_lung(232;0.000154)|Ovarian(174;0.0425)		OV - Ovarian serous cystadenocarcinoma(54;4.3e-40)|Epithelial(54;4.79e-32)|all cancers(79;1.54e-26)		GACGCCTTACCTTTGCCGAAC	0.697																																					p.G23S		Atlas-SNP	.											.	EDIL3	94	.	0			c.G67A						.						64	69	68					5																	83680126		2203	4300	6503	SO:0001630	splice_region_variant	10085	exon1			CCTTACCTTTGCC	U70312	CCDS4062.1, CCDS64195.1	5q14	2008-02-05			ENSG00000164176	ENSG00000164176			3173	protein-coding gene	gene with protein product		606018				9420328	Standard	NM_005711		Approved	DEL1	uc003kio.1	O43854	OTTHUMG00000119047	ENST00000296591.5:c.67+1G>A	chr5.hg19:g.83680126C>T		36.0	0.0		46.0	15.0	NM_005711	B2R763|O43855|Q5D094|Q8N610	Missense_Mutation	SNP	ENST00000296591.5	hg19	CCDS4062.1	.	.	.	.	.	.	.	.	.	.	C	15.49	2.849616	0.51270	.	.	ENSG00000164176	ENST00000296591;ENST00000380138	D;D	0.92752	-3.09;-3.1	4.26	4.26	0.50523	Epidermal growth factor-like, type 3 (1);	0.317991	0.22874	N	0.054593	D	0.85557	0.5724	N	0.21508	0.67	0.42244	D	0.991945	B;B	0.30021	0.004;0.265	B;B	0.33454	0.001;0.164	T	0.82086	-0.0631	9	.	.	.	-7.018	12.3834	0.55320	0.0:1.0:0.0:0.0	.	23;23	O43854-2;O43854	.;EDIL3_HUMAN	S	23	ENSP00000296591:G23S;ENSP00000369483:G23S	.	G	-	1	0	EDIL3	83715882	1.000000	0.71417	1.000000	0.80357	0.304000	0.27724	4.017000	0.57167	2.389000	0.81357	0.491000	0.48974	GGT	.	.		0.697	EDIL3-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239258.1	NM_005711	Missense_Mutation	T	83680126	C	T	83680126	5	4	265	1	0	0	0	0	0	0	1	0	4917	695	24	3	1419	3	EDIL3	5	83680126	Splice_Site	SNP	C	TCGA-FV-A3I1-01A-11D-A22F-10	14874788	83680126	97235134	22	38913										
WDR36	134430	hgsc.bcm.edu	37	chr5	110456277	110456277	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	aatagtcatgcttcctggtaCttgtcaaacccaaggtaatt	7	9	2	0			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr5:110456277C>A	ENST00000513710.2	+	18	2160	c.2156C>A	c.(2155-2157)aCt>aAt	p.T719N	WDR36_ENST00000506538.2_Missense_Mutation_p.T719N			Q8NI36	WDR36_HUMAN	WD repeat domain 36	719					regulation of axon extension (GO:0030516)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|rRNA processing (GO:0006364)|visual perception (GO:0007601)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(9)|kidney(4)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(142;2.72e-05)|all_epithelial(76;4.4e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0418)|Ovarian(225;0.0443)|Colorectal(57;0.0465)|all_lung(232;0.0508)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.39e-08)|Epithelial(69;1.82e-07)|all cancers(49;2.04e-05)|COAD - Colon adenocarcinoma(37;0.111)		CTTCCTGGTACTTGTCAAACC	0.348																																					p.T719N		Atlas-SNP	.											.	WDR36	111	.	0			c.C2156A						.						135	132	133					5																	110456277		2202	4300	6502	SO:0001583	missense	134430	exon18			CTGGTACTTGTCA	AF385437	CCDS4102.1	5q22.2	2013-01-09			ENSG00000134987	ENSG00000134987		"WD repeat domain containing"	30696	protein-coding gene	gene with protein product		609669	"glaucoma 1, open angle, G"	GLC1G		15590835, 15677485	Standard	NM_139281		Approved	TA-WDRP, UTP21	uc003kpd.3	Q8NI36	OTTHUMG00000128790	ENST00000513710.2:c.2156C>A	chr5.hg19:g.110456277C>A	ENSP00000424628:p.Thr719Asn	91.0	0.0		104.0	26.0	NM_139281	A2RUS4|Q68E02|Q8N1Q2	Missense_Mutation	SNP	ENST00000513710.2	hg19	CCDS4102.1	.	.	.	.	.	.	.	.	.	.	C	11.82	1.751290	0.31046	.	.	ENSG00000134987	ENST00000506538;ENST00000513710	T;T	0.66995	-0.24;-0.24	5.72	3.92	0.45320	.	0.403741	0.32769	N	0.005679	T	0.61464	0.2349	L	0.54323	1.7	0.80722	D	1	B	0.12013	0.005	B	0.14578	0.011	T	0.60198	-0.7310	10	0.87932	D	0	-15.5734	12.0033	0.53243	0.0:0.8124:0.1218:0.0658	.	719	Q8NI36	WDR36_HUMAN	N	719	ENSP00000423067:T719N;ENSP00000424628:T719N	ENSP00000423067:T719N	T	+	2	0	WDR36	110484176	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.627000	0.54252	0.858000	0.35431	0.650000	0.86243	ACT	.	.		0.348	WDR36-008	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000373504.3	NM_139281		A	110456277	C	A	110456277	3	1	265	1	0	0	0	0	1	0	0	0	17305	565	20	3	2226	3	WDR36	5	110456277	Missense_Mutation	SNP	C	TCGA-FV-A3I1-01A-11D-A22F-10	26776151	110456277	70458983	23	38914										
MYOT	9499	hgsc.bcm.edu	37	chr5	137219116	137219116	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	tgtgtcatggtatctaaatgGaagaacagttcaatcagatg	10	5	4	2			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr5:137219116G>T	ENST00000239926.4	+	7	1234	c.860G>T	c.(859-861)gGa>gTa	p.G287V	MYOT_ENST00000421631.2_Missense_Mutation_p.G103V|RP11-381K20.2_ENST00000508281.2_RNA|MYOT_ENST00000515645.1_Missense_Mutation_p.G172V|RP11-381K20.2_ENST00000514616.1_RNA|MYOT_ENST00000509812.1_Intron	NM_006790.2	NP_006781	Q9UBF9	MYOTI_HUMAN	myotilin	287	Ig-like C2-type 1.|Necessary for interaction with ACTA1.|Necessary for interaction with FLNC.				muscle contraction (GO:0006936)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	structural constituent of muscle (GO:0008307)			cervix(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	23			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TATCTAAATGGAAGAACAGTT	0.413																																					p.G287V		Atlas-SNP	.											MYOT,colon,carcinoma,0,1	MYOT	50	.	0			c.G860T						.						134	126	129					5																	137219116		2203	4300	6503	SO:0001583	missense	9499	exon7			TAAATGGAAGAAC	AF133820	CCDS4194.1, CCDS47268.1, CCDS75309.1	5q31.2	2014-09-17	2005-09-07	2005-09-07	ENSG00000120729	ENSG00000120729		"Immunoglobulin superfamily / I-set domain containing"	12399	protein-coding gene	gene with protein product		604103	"titin immunoglobulin domain protein (myotilin)", "limb-girdle muscular dystrophy 1A (autosomal dominant)"	TTID, LGMD1A, LGMD1		10486214, 10369880	Standard	NM_006790		Approved		uc003lbv.3	Q9UBF9	OTTHUMG00000129154	ENST00000239926.4:c.860G>T	chr5.hg19:g.137219116G>T	ENSP00000239926:p.Gly287Val	169.0	0.0		185.0	55.0	NM_006790	A0A4R6|B4DT79	Missense_Mutation	SNP	ENST00000239926.4	hg19	CCDS4194.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.938922	0.92526	.	.	ENSG00000120729	ENST00000239926;ENST00000421631;ENST00000515645	T;T;T	0.80033	-1.33;-1.33;-1.33	5.08	5.08	0.68730	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000009	D	0.94407	0.8201	H	0.98754	4.32	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96772	0.9569	10	0.87932	D	0	.	18.8467	0.92210	0.0:0.0:1.0:0.0	.	287	Q9UBF9	MYOTI_HUMAN	V	287;103;172	ENSP00000239926:G287V;ENSP00000391185:G103V;ENSP00000426281:G172V	ENSP00000239926:G287V	G	+	2	0	MYOT	137247015	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.813000	0.99286	2.497000	0.84241	0.655000	0.94253	GGA	.	.		0.413	MYOT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251219.2	NM_006790		T	137219116	G	T	137219116	3	4	265	1	0	0	0	0	1	0	0	0	10103	1174	41	3	882	3	MYOT	5	137219116	Missense_Mutation	SNP	G	TCGA-FV-A3I1-01A-11D-A22F-10	26762839	137219116	43696144	24	38915										
ANKHD1	54882	hgsc.bcm.edu	37	chr5	139889380	139889380	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	aaaggtcactacaaattttgTgaactcctgattcataggtg	8	7	2	2			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr5:139889380T>C	ENST00000360839.2	+	21	4078	c.3924T>C	c.(3922-3924)tgT>tgC	p.C1308C	ANKHD1-EIF4EBP3_ENST00000532219.1_Silent_p.C1308C|ANKHD1_ENST00000297183.6_Silent_p.C1308C	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	1308						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACAAATTTTGTGAACTCCTGA	0.353																																					p.C1308C		Atlas-SNP	.											.	ANKHD1	233	.	0			c.T3924C						.						71	68	69					5																	139889380		2203	4300	6503	SO:0001819	synonymous_variant	54882	exon21			ATTTTGTGAACTC	AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503		"Ankyrin repeat domain containing"	24714	protein-coding gene	gene with protein product		610500				10470851, 11230166, 16098192	Standard	NM_017747		Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.3924T>C	chr5.hg19:g.139889380T>C		104.0	0.0		165.0	56.0	NM_017747	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Silent	SNP	ENST00000360839.2	hg19	CCDS4225.1	.	.	.	.	.	.	.	.	.	.	T	8.191	0.795937	0.16327	.	.	ENSG00000131503	ENST00000246149	.	.	.	5.49	4.31	0.51392	.	.	.	.	.	T	0.61362	0.2341	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59532	-0.7437	4	.	.	.	.	11.0534	0.47903	0.0:0.1264:0.0:0.8736	.	.	.	.	A	534	.	.	V	+	2	0	ANKHD1	139869564	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.373000	0.52394	2.213000	0.71641	0.477000	0.44152	GTG	.	.		0.353	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747		C	139889380	T	C	139889380	2	2	265	1	0	0	0	0	0	0	0	1	628	1702	59	2		2	ANKHD1	5	139889380	Silent	SNP	T	TCGA-FV-A3I1-01A-11D-A22F-10	2670264	139889380	41025880	25	38916										
PCDHA10	56139	hgsc.bcm.edu	37	chr5	140235699	140235699	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	tcgcttcttctcctcgcagcCtgggaggtggggagcggcca	15	13	2	0			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr5:140235699C>T	ENST00000307360.5	+	1	66	c.66C>T	c.(64-66)gcC>gcT	p.A22A	PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA10_ENST00000506939.2_Silent_p.A22A|PCDHA7_ENST00000525929.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	22					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(11)|cervix(1)|endometrium(11)|kidney(5)|large_intestine(13)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	79			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCTCGCAGCCTGGGAGGTGG	0.597																																					p.A22A		Atlas-SNP	.											.	PCDHA10	358	.	0			c.C66T						.						58	68	64					5																	140235699		2196	4273	6469	SO:0001819	synonymous_variant	56139	exon1			CGCAGCCTGGGAG	AF152475	CCDS34255.1, CCDS54921.1, CCDS75325.1	5q31	2010-11-26			ENSG00000250120	ENSG00000250120		"Cadherins / Protocadherins : Clustered"	8664	other	complex locus constituent	"KIAA0345-like 4", "ortholog to mouse CNR8"	606316		CNRS8		10380929	Standard	NM_018901		Approved	CNR8, CRNR8, CNRN8, PCDH-ALPHA10		Q9Y5I2	OTTHUMG00000163372	ENST00000307360.5:c.66C>T	chr5.hg19:g.140235699C>T		64.0	0.0		76.0	52.0	NM_031859	A1L493|O75280|Q9NRU2	Silent	SNP	ENST00000307360.5	hg19	CCDS54921.1																																																																																			.	.		0.597	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901		T	140235699	C	T	140235699	2	4	265	1	0	0	0	0	0	0	0	1	11529	668	24	3		3	PCDHA10	5	140235699	Silent	SNP	C	TCGA-FV-A3I1-01A-11D-A22F-10	346319	140235699	40679561	26	38917										
ZNF354B	117608	hgsc.bcm.edu	37	chr5	178310382	178310382	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	tggtaaatccttcagtcgaaGgtctgggctttttatacatc	9	8	2	0			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr5:178310382G>C	ENST00000322434.3	+	5	1155	c.929G>C	c.(928-930)aGg>aCg	p.R310T	RNU1-39P_ENST00000383897.1_RNA	NM_058230.2	NP_478137.1	Q96LW1	Z354B_HUMAN	zinc finger protein 354B	310					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|kidney(2)|large_intestine(7)|liver(2)|lung(2)|ovary(2)|stomach(3)|urinary_tract(1)	21	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TTCAGTCGAAGGTCTGGGCTT	0.413																																					p.R310T		Atlas-SNP	.											.	ZNF354B	67	.	0			c.G929C						.						65	65	65					5																	178310382		2203	4300	6503	SO:0001583	missense	117608	exon5			GTCGAAGGTCTGG	AK057737	CCDS4439.1	5q35.3	2013-01-08			ENSG00000178338	ENSG00000178338		"Zinc fingers, C2H2-type", "-"	17197	protein-coding gene	gene with protein product							Standard	NM_058230		Approved	KID2, FLJ25008	uc003mjl.3	Q96LW1	OTTHUMG00000130896	ENST00000322434.3:c.929G>C	chr5.hg19:g.178310382G>C	ENSP00000327143:p.Arg310Thr	201.0	0.0		203.0	63.0	NM_058230	A8K0V2|Q5U5Z4	Missense_Mutation	SNP	ENST00000322434.3	hg19	CCDS4439.1	.	.	.	.	.	.	.	.	.	.	G	7.390	0.630654	0.14322	.	.	ENSG00000178338	ENST00000322434	T	0.35605	1.3	3.62	2.72	0.32119	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.23806	0.0576	L	0.39245	1.2	0.09310	N	1	B	0.30870	0.298	B	0.25614	0.062	T	0.09228	-1.0684	9	0.22109	T	0.4	-9.7869	5.9037	0.18980	0.2414:0.0:0.7586:0.0	.	310	Q96LW1	Z354B_HUMAN	T	310	ENSP00000327143:R310T	ENSP00000327143:R310T	R	+	2	0	ZNF354B	178242988	0.000000	0.05858	0.869000	0.34112	0.127000	0.20565	0.091000	0.15046	1.855000	0.53841	0.561000	0.74099	AGG	.	.		0.413	ZNF354B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253482.1	NM_058230		C	178310382	G	C	178310382	3	2	265	1	0	0	0	0	1	0	0	0	17880	1000	35	4	943	4	ZNF354B	5	178310382	Missense_Mutation	SNP	G	TCGA-FV-A3I1-01A-11D-A22F-10	38074683	178310382	2604878	27	38918										
TFAP2A	7020	hgsc.bcm.edu	37	chr6	10398750	10398750	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	ttttgtccatggccttgaggGcctcggtgagatagttctgc	13	9	1	2			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr6:10398750G>T	ENST00000482890.1	-	8	1566	c.1214C>A	c.(1213-1215)gCc>gAc	p.A405D	TFAP2A_ENST00000379608.3_Missense_Mutation_p.A399D|TFAP2A_ENST00000497266.1_5'Flank|TFAP2A_ENST00000319516.4_Missense_Mutation_p.A401D|TFAP2A_ENST00000379604.2_Missense_Mutation_p.A405D|TFAP2A_ENST00000379613.3_Missense_Mutation_p.A407D			P05549	AP2A_HUMAN	transcription factor AP-2 alpha (activating enhancer binding protein 2 alpha)	405	H-S-H (helix-span-helix), dimerization.				anterior neuropore closure (GO:0021506)|basement membrane organization (GO:0071711)|bone morphogenesis (GO:0060349)|cellular response to iron ion (GO:0071281)|cornea development in camera-type eye (GO:0061303)|embryonic body morphogenesis (GO:0010172)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|embryonic pattern specification (GO:0009880)|epidermis morphogenesis (GO:0048730)|eyelid development in camera-type eye (GO:0061029)|face morphogenesis (GO:0060325)|forebrain neuron development (GO:0021884)|inner ear morphogenesis (GO:0042472)|keratinocyte development (GO:0003334)|kidney development (GO:0001822)|lens induction in camera-type eye (GO:0060235)|metanephric nephron development (GO:0072210)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell development (GO:0014032)|oculomotor nerve formation (GO:0021623)|optic cup structural organization (GO:0003409)|optic vesicle morphogenesis (GO:0003404)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cell migration (GO:0030335)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of tooth mineralization (GO:0070172)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell differentiation (GO:0045595)|regulation of neuron differentiation (GO:0045664)|retina layer formation (GO:0010842)|sensory perception of sound (GO:0007605)|sympathetic nervous system development (GO:0048485)|transcription from RNA polymerase II promoter (GO:0006366)|trigeminal nerve development (GO:0021559)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1)	13	Breast(50;0.0427)|Ovarian(93;0.0991)	all_hematologic(90;0.107)				GGCCTTGAGGGCCTCGGTGAG	0.572																																					p.A405D		Atlas-SNP	.											.	TFAP2A	129	.	0			c.C1214A						.						272	279	277					6																	10398750		2203	4300	6503	SO:0001583	missense	7020	exon7			TTGAGGGCCTCGG	X52611	CCDS4510.1, CCDS34337.1, CCDS43422.1	6p24.3	2013-09-19	2001-11-28		ENSG00000137203	ENSG00000137203			11742	protein-coding gene	gene with protein product		107580	"transcription factor AP-2 alpha (activating enhancer-binding protein 2 alpha)"	TFAP2, AP2TF		1916817, 3063603	Standard	NM_001032280		Approved	AP-2	uc003myr.3	P05549	OTTHUMG00000014235	ENST00000482890.1:c.1214C>A	chr6.hg19:g.10398750G>T	ENSP00000418541:p.Ala405Asp	150.0	0.0		151.0	60.0	NM_003220	Q13777|Q5TAV5|Q8N1C6	Missense_Mutation	SNP	ENST00000482890.1	hg19	CCDS4510.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.075335	0.76415	.	.	ENSG00000137203	ENST00000379613;ENST00000379604;ENST00000319516;ENST00000379608;ENST00000482890	D;D;D;D;D	0.97575	-4.44;-4.44;-4.44;-4.44;-4.44	5.23	5.23	0.72850	Transcription factor AP-2, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98311	0.9440	M	0.78223	2.4	0.80722	D	1	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.97110	0.998;0.971;1.0	D	0.99372	1.0920	10	0.72032	D	0.01	-10.3232	18.824	0.92109	0.0:0.0:1.0:0.0	.	401;405;399	Q5TAV5;P05549;Q8N1C6	.;AP2A_HUMAN;.	D	407;405;401;399;405	ENSP00000368933:A407D;ENSP00000368924:A405D;ENSP00000316516:A401D;ENSP00000368928:A399D;ENSP00000418541:A405D	ENSP00000316516:A401D	A	-	2	0	TFAP2A	10506736	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.863000	0.99569	2.438000	0.82558	0.655000	0.94253	GCC	.	.		0.572	TFAP2A-007	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353619.2	NM_003220		T	10398750	G	T	10398750	3	4	265	1	0	0	0	0	1	0	0	0	15802	1203	42	3	103	3	TFAP2A	6	10398750	Missense_Mutation	SNP	G	TCGA-FV-A3I1-01A-11D-A22F-10		10398750	160716317	28	38919										
ZBTB9	221504	hgsc.bcm.edu	37	chr6	33424110	33424110	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	accttcagccttcggcctttTggctgtggcatctgcaacaa	9	13	2	0			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr6:33424110T>A	ENST00000395064.2	+	2	1501	c.1233T>A	c.(1231-1233)ttT>ttA	p.F411L		NM_152735.3	NP_689948.1	Q96C00	ZBTB9_HUMAN	zinc finger and BTB domain containing 9	411					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|skin(1)|upper_aerodigestive_tract(2)	11						TTCGGCCTTTTGGCTGTGGCA	0.567																																					p.F411L		Atlas-SNP	.											.	ZBTB9	23	.	0			c.T1233A						.						79	63	68					6																	33424110		2203	4300	6503	SO:0001583	missense	221504	exon2			GCCTTTTGGCTGT	AK122644	CCDS4780.1	6p21.31	2013-01-09			ENSG00000213588	ENSG00000213588		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	28323	protein-coding gene	gene with protein product						12477932	Standard	NM_152735		Approved	MGC23166, ZNF919	uc003oeq.3	Q96C00	OTTHUMG00000140180	ENST00000395064.2:c.1233T>A	chr6.hg19:g.33424110T>A	ENSP00000378503:p.Phe411Leu	44.0	0.0		44.0	8.0	NM_152735	A2AB19	Missense_Mutation	SNP	ENST00000395064.2	hg19	CCDS4780.1	.	.	.	.	.	.	.	.	.	.	T	19.41	3.822422	0.71028	.	.	ENSG00000213588	ENST00000395064	T	0.50548	0.74	5.1	2.42	0.29668	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.251437	0.26143	U	0.026084	T	0.47838	0.1467	M	0.67517	2.055	0.36311	D	0.857653	D	0.76494	0.999	D	0.65874	0.939	T	0.52388	-0.8582	10	0.72032	D	0.01	.	7.2285	0.26028	0.0:0.2261:0.0:0.7739	.	411	Q96C00	ZBTB9_HUMAN	L	411	ENSP00000378503:F411L	ENSP00000378503:F411L	F	+	3	2	ZBTB9	33532088	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	0.488000	0.22371	0.293000	0.22520	0.533000	0.62120	TTT	.	.		0.567	ZBTB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276533.1	NM_152735		A	33424110	T	A	33424110	3	1	265	1	0	0	0	0	1	0	0	0	17573	1809	63	4	1235	4	ZBTB9	6	33424110	Missense_Mutation	SNP	T	TCGA-FV-A3I1-01A-11D-A22F-10	23025360	33424110	137690957	29	38920										
EYS	346007	hgsc.bcm.edu	37	chr6	66044982	66044982	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	agcccatctgagaaaacataGataccgatattcctgactgt	7	10	1	3			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr6:66044982G>T	ENST00000370621.3	-	11	2183	c.1657C>A	c.(1657-1659)Cta>Ata	p.L553I	EYS_ENST00000370616.2_Missense_Mutation_p.L553I|EYS_ENST00000370618.3_Missense_Mutation_p.L553I|EYS_ENST00000342421.5_Missense_Mutation_p.L553I|EYS_ENST00000503581.1_Missense_Mutation_p.L553I|EYS_ENST00000393380.2_Missense_Mutation_p.L553I			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	553					detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						AGAAAACATAGATACCGATAT	0.353																																					p.L553I		Atlas-SNP	.											.	EYS	527	.	0			c.C1657A						.						178	162	167					6																	66044982		2203	4300	6503	SO:0001583	missense	346007	exon11			AACATAGATACCG		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.1657C>A	chr6.hg19:g.66044982G>T	ENSP00000359655:p.Leu553Ile	140.0	0.0		143.0	53.0	NM_001142801	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	hg19		.	.	.	.	.	.	.	.	.	.	g	8.908	0.957920	0.18507	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616;ENST00000393380;ENST00000342421;ENST00000370618	D;D;D;D;D;D	0.81821	-1.54;-1.54;-1.54;-1.54;-1.54;-1.54	3.8	0.572	0.17357	.	.	.	.	.	T	0.42017	0.1184	N	0.24115	0.695	0.09310	N	1	B;B;B	0.27997	0.015;0.129;0.197	B;B;B	0.20767	0.031;0.031;0.014	T	0.17806	-1.0357	9	0.33940	T	0.23	.	3.6042	0.08037	0.1284:0.0:0.4253:0.4463	.	553;553;553	Q5T1H1-1;Q5T1H1-2;Q5SZM4	.;.;.	I	553	ENSP00000424243:L553I;ENSP00000359655:L553I;ENSP00000359650:L553I;ENSP00000377042:L553I;ENSP00000341818:L553I;ENSP00000359652:L553I	ENSP00000341818:L553I	L	-	1	2	EYS	66101703	0.000000	0.05858	0.001000	0.08648	0.013000	0.08279	0.527000	0.22987	0.671000	0.31185	0.491000	0.48974	CTA	.	.		0.353	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		T	66044982	G	T	66044982	3	4	265	1	0	0	0	0	1	0	0	0	5334	933	33	3	7871	3	EYS	6	66044982	Missense_Mutation	SNP	G	TCGA-FV-A3I1-01A-11D-A22F-10	32620872	66044982	105070085	30	38921										
FAM184A	79632	hgsc.bcm.edu	37	chr6	119345814	119345814	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	aatgatgattctaaaacttgAatctttcttctaaggtctag	6	6	5	3			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr6:119345814A>C	ENST00000338891.7	-	2	767	c.324T>G	c.(322-324)atT>atG	p.I108M	FAM184A_ENST00000522284.1_De_novo_Start_InFrame|FAM184A_ENST00000521531.1_Missense_Mutation_p.I108M|FAM184A_ENST00000352896.5_De_novo_Start_InFrame|FAM184A_ENST00000368475.4_De_novo_Start_InFrame|RP11-351A11.1_ENST00000518570.1_RNA	NM_024581.4	NP_078857.5	Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A	108						extracellular space (GO:0005615)				breast(2)|central_nervous_system(2)|endometrium(2)|kidney(5)|large_intestine(19)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(5)	52						CTAAAACTTGAATCTTTCTTC	0.333																																					p.I108M		Atlas-SNP	.											.	FAM184A	109	.	0			c.T324G						.						98	88	91					6																	119345814		1836	4090	5926	SO:0001583	missense	79632	exon2			AACTTGAATCTTT	BC009055	CCDS43499.1, CCDS43500.1, CCDS75508.1	6q22.31	2008-08-14	2008-08-14	2008-08-14	ENSG00000111879	ENSG00000111879			20991	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 60"	C6orf60		11230166	Standard	NM_024581		Approved	FLJ13942	uc003pyj.3	Q8NB25	OTTHUMG00000015471	ENST00000338891.7:c.324T>G	chr6.hg19:g.119345814A>C	ENSP00000342604:p.Ile108Met	206.0	0.0		231.0	73.0	NM_024581	B9DI75|F8W8D6|Q5TBS9|Q7Z323|Q96GY8|Q9H0J8|Q9H851	Missense_Mutation	SNP	ENST00000338891.7	hg19	CCDS43499.1	.	.	.	.	.	.	.	.	.	.	A	13.01	2.110681	0.37242	.	.	ENSG00000111879	ENST00000338891;ENST00000521531	T;T	0.31769	1.48;1.48	5.82	-1.67	0.08238	.	0.060841	0.64402	D	0.000004	T	0.34774	0.0909	M	0.68317	2.08	0.80722	D	1	D	0.69078	0.997	D	0.63703	0.917	T	0.45308	-0.9270	10	0.62326	D	0.03	-12.4391	12.8401	0.57797	0.514:0.0:0.486:0.0	.	108	Q8NB25	F184A_HUMAN	M	108	ENSP00000342604:I108M;ENSP00000430442:I108M	ENSP00000342604:I108M	I	-	3	3	FAM184A	119387513	0.998000	0.40836	0.998000	0.56505	0.371000	0.29859	0.745000	0.26259	-0.061000	0.13110	-0.250000	0.11733	ATT	.	.		0.333	FAM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042009.3	NM_024581		C	119345814	A	C	119345814	3	2	265	1	0	0	0	0	1	0	0	0	5516	242	9	5	3166	5	FAM184A	6	119345814	Missense_Mutation	SNP	A	TCGA-FV-A3I1-01A-11D-A22F-10	53300832	119345814	51769253	31	38922										
SMPDL3A	10924	hgsc.bcm.edu	37	chr6	123110566	123110566	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	tccggcctcgggctgcccgtGgcgcccgcaggcggcaggaa	17	16	0	0			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr6:123110566G>T	ENST00000368440.4	+	1	252	c.75G>T	c.(73-75)gtG>gtT	p.V25V	SMPDL3A_ENST00000539041.1_5'UTR|SMPDL3A_ENST00000487215.1_3'UTR	NM_006714.3	NP_006705.1	Q92484	ASM3A_HUMAN	sphingomyelin phosphodiesterase, acid-like 3A	25					sphingomyelin catabolic process (GO:0006685)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			breast(1)|cervix(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	10				GBM - Glioblastoma multiforme(226;0.236)		GGCTGCCCGTGGCGCCCGCAG	0.736											OREG0017641	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V25V		Atlas-SNP	.											.	SMPDL3A	31	.	0			c.G75T						.						4	4	4					6																	123110566		1594	2978	4572	SO:0001819	synonymous_variant	10924	exon1			GCCCGTGGCGCCC	AK000184	CCDS5128.1, CCDS69190.1	6q22.32	2006-04-12			ENSG00000172594	ENSG00000172594			17389	protein-coding gene	gene with protein product	"acid sphingomyelinase-like phosphodiesterase 3a"	610728				12442002	Standard	XM_005266798		Approved	FLJ20177, ASM3A, ASML3a, yR36GH4.1	uc003pzg.3	Q92484	OTTHUMG00000015490	ENST00000368440.4:c.75G>T	chr6.hg19:g.123110566G>T		3.0	0.0	1524	20.0	6.0	NM_006714	B7Z729|Q8WV13	Silent	SNP	ENST00000368440.4	hg19	CCDS5128.1																																																																																			.	.		0.736	SMPDL3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042039.1	NM_006714		T	123110566	G	T	123110566	2	4	265	1	0	0	0	0	0	0	0	1	14823	1335	47	3		3	SMPDL3A	6	123110566	Silent	SNP	G	TCGA-FV-A3I1-01A-11D-A22F-10	3764752	123110566	48004501	32	38923										
MAP3K4	4216	hgsc.bcm.edu	37	chr6	161470524	161470524	+	Nonsense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	aaaagacttaaatcagaaatTaaggattatgggcactgttt	8	4	1	2			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr6:161470524T>G	ENST00000392142.4	+	3	1368	c.1220T>G	c.(1219-1221)tTa>tGa	p.L407*	MAP3K4_ENST00000366920.2_Nonsense_Mutation_p.L407*|MAP3K4_ENST00000348824.7_Nonsense_Mutation_p.L407*|MAP3K4_ENST00000366919.2_Nonsense_Mutation_p.L407*	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	407					activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		AATCAGAAATTAAGGATTATG	0.428																																					p.L407X		Atlas-SNP	.											.	MAP3K4	364	.	0			c.T1220G						.						78	81	80					6																	161470524		2203	4300	6503	SO:0001587	stop_gained	4216	exon3			AGAAATTAAGGAT	AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.1220T>G	chr6.hg19:g.161470524T>G	ENSP00000375986:p.Leu407*	164.0	0.0		171.0	64.0	NM_006724	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Nonsense_Mutation	SNP	ENST00000392142.4	hg19	CCDS34565.1	.	.	.	.	.	.	.	.	.	.	T	38	7.227635	0.98150	.	.	ENSG00000085511	ENST00000366919;ENST00000392142;ENST00000540111;ENST00000366920;ENST00000348824	.	.	.	5.96	5.96	0.96718	.	0.000000	0.64402	D	0.000012	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.5699	16.4447	0.83919	0.0:0.0:0.0:1.0	.	.	.	.	X	407	.	ENSP00000297332:L407X	L	+	2	0	MAP3K4	161390514	1.000000	0.71417	0.031000	0.17742	0.938000	0.57974	7.671000	0.83941	2.284000	0.76573	0.528000	0.53228	TTA	.	.		0.428	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3			G	161470524	T	G	161470524	4	3	265	1	0	0	0	0	0	1	0	0	9261	1764	61	5	1230	5	MAP3K4	6	161470524	Nonsense_Mutation	SNP	T	TCGA-FV-A3I1-01A-11D-A22F-10	38359958	161470524	9644543	33	38924										
DFNA5	1687	hgsc.bcm.edu	37	chr7	24758722	24758722	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	acacttctcctcgacctgcaTgtgctcagagatcacacact	6	15	3	1			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr7:24758722T>C	ENST00000342947.3	-	4	945	c.520A>G	c.(520-522)Atg>Gtg	p.M174V	DFNA5_ENST00000409970.1_Missense_Mutation_p.M10V|DFNA5_ENST00000419307.1_Missense_Mutation_p.M10V|DFNA5_ENST00000545231.1_Missense_Mutation_p.M10V|DFNA5_ENST00000559637.1_5'UTR|DFNA5_ENST00000409775.3_Missense_Mutation_p.M174V	NM_004403.2	NP_004394.1	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5	174			M -> T (in dbSNP:rs876306).		apoptotic process (GO:0006915)|inner ear receptor cell differentiation (GO:0060113)|negative regulation of cell proliferation (GO:0008285)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(3)|stomach(1)	19						TCGACCTGCATGTGCTCAGAG	0.572																																					p.M174V	GBM(78;184 1250 20134 20900 23600)	Atlas-SNP	.											.	DFNA5	51	.	0			c.A520G						.						244	191	209					7																	24758722		2203	4300	6503	SO:0001583	missense	1687	exon4			CCTGCATGTGCTC	AF007790	CCDS5389.1, CCDS47563.1	7p15	2011-07-01			ENSG00000105928	ENSG00000105928			2810	protein-coding gene	gene with protein product		608798				8589696, 9450185	Standard	NM_004403		Approved	ICERE-1	uc010kus.1	O60443	OTTHUMG00000023237	ENST00000342947.3:c.520A>G	chr7.hg19:g.24758722T>C	ENSP00000339587:p.Met174Val	51.0	0.0		27.0	15.0	NM_001127453	A4D156|B2RAX9|B3KT05|O14590|Q08AQ8|Q9UBV3	Missense_Mutation	SNP	ENST00000342947.3	hg19	CCDS5389.1	.	.	.	.	.	.	.	.	.	.	T	0.003	-2.425193	0.00186	.	.	ENSG00000105928	ENST00000342947;ENST00000419307;ENST00000545231;ENST00000409970;ENST00000409775;ENST00000414428	T;T;T;T;T;T	0.38077	2.07;2.07;2.07;2.07;2.07;1.16	5.17	-2.25	0.06888	.	0.789923	0.11854	N	0.523022	T	0.07999	0.0200	N	0.00170	-1.935	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41142	-0.9525	10	0.23302	T	0.38	-3.339	11.0721	0.48010	0.0:0.3196:0.0:0.6804	.	174;174	A4FTY0;O60443	.;DFNA5_HUMAN	V	174;10;10;10;174;10	ENSP00000339587:M174V;ENSP00000401332:M10V;ENSP00000442661:M10V;ENSP00000387119:M10V;ENSP00000386670:M174V;ENSP00000413963:M10V	ENSP00000339587:M174V	M	-	1	0	DFNA5	24725247	0.000000	0.05858	0.002000	0.10522	0.016000	0.09150	-1.261000	0.02855	-0.268000	0.09312	-0.242000	0.12053	ATG	.	.		0.572	DFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214060.2	NM_004403		C	24758722	T	C	24758722	3	2	265	1	0	0	0	0	1	0	0	0	4456	1464	51	2	998	2	DFNA5	7	24758722	Missense_Mutation	SNP	T	TCGA-FV-A3I1-01A-11D-A22F-10		24758722	134379941	34	38925										
ZC3HAV1	56829	hgsc.bcm.edu	37	chr7	138764382	138764382	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	gtagaagttatatctgtggcCactccatcagcattattatt	7	8	2	1			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr7:138764382C>A	ENST00000242351.5	-	4	1621	c.1305G>T	c.(1303-1305)gtG>gtT	p.V435V	ZC3HAV1_ENST00000464606.1_Silent_p.V435V|ZC3HAV1_ENST00000471652.1_Silent_p.V435V	NM_020119.3	NP_064504.2	Q7Z2W4	ZCCHV_HUMAN	zinc finger CCCH-type, antiviral 1	435					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of mRNA catabolic process (GO:0061014)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(4)|skin(1)	37						TATCTGTGGCCACTCCATCAG	0.448																																					p.V435V		Atlas-SNP	.											.	ZC3HAV1	75	.	0			c.G1305T						.						103	104	104					7																	138764382		2203	4300	6503	SO:0001819	synonymous_variant	56829	exon4			TGTGGCCACTCCA	BX571742	CCDS5851.1, CCDS55171.1	7q34	2012-07-05			ENSG00000105939	ENSG00000105939		"Zinc fingers, CCCH-type domain containing", "Poly (ADP-ribose) polymerases"	23721	protein-coding gene	gene with protein product	"zinc finger antiviral protein", " CCCH-type zinc finger antiviral protein"	607312				12215647, 12851707	Standard	NM_024625		Approved	ZAP, FLB6421, FLJ13288, MGC48898, ZC3HDC2, ZC3H2, PARP13	uc003vun.3	Q7Z2W4	OTTHUMG00000157471	ENST00000242351.5:c.1305G>T	chr7.hg19:g.138764382C>A		188.0	0.0		240.0	112.0	NM_024625	A4D1R2|A4D1S4|Q8IW57|Q8TAJ3|Q96N79|Q9H8R9|Q9P0Y7	Silent	SNP	ENST00000242351.5	hg19	CCDS5851.1																																																																																			.	.		0.448	ZC3HAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348915.1	NM_020119		A	138764382	C	A	138764382	2	1	265	1	0	0	0	0	0	0	0	1	17590	581	21	3		3	ZC3HAV1	7	138764382	Silent	SNP	C	TCGA-FV-A3I1-01A-11D-A22F-10	114005660	138764382	20374281	35	38926										
EPHA1	2041	hgsc.bcm.edu	37	chr7	143095957	143095957	+	Missense_Mutation	SNP	G	G	T													0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	tgacatcctggcgtccccccGtatctgctgggggttcccaa					rs370810516		TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr7:143095957G>T	ENST00000275815.3	-	6	1159	c.1073C>A	c.(1072-1074)aCg>aAg	p.T358K		NM_005232.4	NP_005223.4	P21709	EPHA1_HUMAN	EPH receptor A1	358	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				activation of Rho GTPase activity (GO:0032862)|angiogenesis (GO:0001525)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of cell migration (GO:0030336)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of stress fiber assembly (GO:0051496)|protein autophosphorylation (GO:0046777)|regulation of Rac GTPase activity (GO:0032314)|substrate adhesion-dependent cell spreading (GO:0034446)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(21)|ovary(4)|skin(1)|stomach(1)|urinary_tract(3)	51	Melanoma(164;0.205)	Myeloproliferative disorder(862;0.0255)				GCGTCCCCCCGTATCTGCTGG	0.667																																					p.T358K		Atlas-SNP	.											.	EPHA1	193	.	0			c.C1073A						.						32	29	30					7																	143095957		2203	4300	6503	SO:0001583	missense	2041	exon6			CCCCCCGTATCTG	M18391	CCDS5884.1	7q32-q36	2013-02-11	2004-10-28		ENSG00000146904	ENSG00000146904	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3385	protein-coding gene	gene with protein product		179610	"EphA1"	EPHT, EPHT1		9267020	Standard	NM_005232		Approved	EPH	uc003wcz.3	P21709	OTTHUMG00000155894	ENST00000275815.3:c.1073C>A	chr7.hg19:g.143095957G>T	ENSP00000275815:p.Thr358Lys	32.0	0.0		47.0	23.0	NM_005232	A1L3V3|B5A966|B5A967|Q15405	Missense_Mutation	SNP	ENST00000275815.3	hg19	CCDS5884.1	.	.	.	.	.	.	.	.	.	.	G	10.87	1.473010	0.26423	.	.	ENSG00000146904	ENST00000275815	T	0.57752	0.38	5.09	-6.72	0.01755	Fibronectin, type III (4);Immunoglobulin-like fold (1);	1.799430	0.02200	N	0.062196	T	0.53318	0.1789	L	0.52905	1.665	0.09310	N	1	B	0.22480	0.07	B	0.32211	0.142	T	0.55829	-0.8079	10	0.62326	D	0.03	.	15.5735	0.76356	0.1555:0.0:0.7204:0.1241	.	358	P21709	EPHA1_HUMAN	K	358	ENSP00000275815:T358K	ENSP00000275815:T358K	T	-	2	0	EPHA1	142806079	0.000000	0.05858	0.000000	0.03702	0.518000	0.34316	-0.376000	0.07465	-1.224000	0.02581	-1.021000	0.02439	ACG	.	.		0.667	EPHA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342154.1			T	143095957	G	T	143095957	3	4	265	1	0	0	0	0	1	0	0	0	5167	1145	40	1	1909	1	EPHA1	7	143095957	Missense_Mutation	SNP	G	TCGA-FV-A3I1-01A-11D-A22F-10	4331575	143095957	16042706	36	38927	190	2								
EPHA1	2041	hgsc.bcm.edu	37	chr7	143095959	143095959	+	Missense_Mutation	SNP	A	A	T													0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	acatcctggcgtccccccgtAtctgctgggggttcccaacg							TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr7:143095959A>T	ENST00000275815.3	-	6	1157	c.1071T>A	c.(1069-1071)gaT>gaA	p.D357E		NM_005232.4	NP_005223.4	P21709	EPHA1_HUMAN	EPH receptor A1	357	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				activation of Rho GTPase activity (GO:0032862)|angiogenesis (GO:0001525)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of cell migration (GO:0030336)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of stress fiber assembly (GO:0051496)|protein autophosphorylation (GO:0046777)|regulation of Rac GTPase activity (GO:0032314)|substrate adhesion-dependent cell spreading (GO:0034446)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(21)|ovary(4)|skin(1)|stomach(1)|urinary_tract(3)	51	Melanoma(164;0.205)	Myeloproliferative disorder(862;0.0255)				GTCCCCCCGTATCTGCTGGGG	0.662																																					p.D357E		Atlas-SNP	.											.	EPHA1	193	.	0			c.T1071A						.						31	28	29					7																	143095959		2203	4300	6503	SO:0001583	missense	2041	exon6			CCCCGTATCTGCT	M18391	CCDS5884.1	7q32-q36	2013-02-11	2004-10-28		ENSG00000146904	ENSG00000146904	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3385	protein-coding gene	gene with protein product		179610	"EphA1"	EPHT, EPHT1		9267020	Standard	NM_005232		Approved	EPH	uc003wcz.3	P21709	OTTHUMG00000155894	ENST00000275815.3:c.1071T>A	chr7.hg19:g.143095959A>T	ENSP00000275815:p.Asp357Glu	32.0	0.0		46.0	22.0	NM_005232	A1L3V3|B5A966|B5A967|Q15405	Missense_Mutation	SNP	ENST00000275815.3	hg19	CCDS5884.1	.	.	.	.	.	.	.	.	.	.	A	14.08	2.429602	0.43122	.	.	ENSG00000146904	ENST00000275815	T	0.56103	0.48	5.09	-3.69	0.04450	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000006	T	0.43255	0.1239	L	0.58428	1.81	0.21064	N	0.999799	B	0.25390	0.125	B	0.18263	0.021	T	0.31024	-0.9958	10	0.42905	T	0.14	.	13.8412	0.63439	0.466:0.0:0.534:0.0	.	357	P21709	EPHA1_HUMAN	E	357	ENSP00000275815:D357E	ENSP00000275815:D357E	D	-	3	2	EPHA1	142806081	0.001000	0.12720	0.001000	0.08648	0.505000	0.33919	-0.171000	0.09883	-0.851000	0.04147	-0.263000	0.10527	GAT	.	.		0.662	EPHA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342154.1			T	143095959	A	T	143095959	3	4	265	1	0	0	0	0	1	0	0	0	5167	446	16	4	1911	4	EPHA1	7	143095959	Missense_Mutation	SNP	A	TCGA-FV-A3I1-01A-11D-A22F-10	2	143095959	16042704	37	38928	190	2								
RP1	6101	hgsc.bcm.edu	37	chr8	55539906	55539906	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	tgatgctcacaaggctaccaAcaaatcttcagaaacacttg	6	11	3	2			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr8:55539906A>G	ENST00000220676.1	+	4	3612	c.3464A>G	c.(3463-3465)aAc>aGc	p.N1155S		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	1155					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			AAGGCTACCAACAAATCTTCA	0.413																																					p.N1155S	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.A3464G						.						96	93	94					8																	55539906		2203	4300	6503	SO:0001583	missense	6101	exon4			CTACCAACAAATC	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.3464A>G	chr8.hg19:g.55539906A>G	ENSP00000220676:p.Asn1155Ser	196.0	0.0		244.0	58.0	NM_006269		Missense_Mutation	SNP	ENST00000220676.1	hg19	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	A	0.167	-1.075663	0.01903	.	.	ENSG00000104237	ENST00000220676	T	0.19532	2.14	5.7	-7.47	0.01365	.	1.011940	0.07920	N	0.975778	T	0.07369	0.0186	N	0.03324	-0.35	0.09310	N	1	B	0.14438	0.01	B	0.10450	0.005	T	0.47799	-0.9089	10	0.09843	T	0.71	-0.6741	13.0879	0.59151	0.2607:0.1047:0.6345:0.0	.	1155	P56715	RP1_HUMAN	S	1155	ENSP00000220676:N1155S	ENSP00000220676:N1155S	N	+	2	0	RP1	55702459	0.005000	0.15991	0.000000	0.03702	0.035000	0.12851	-0.013000	0.12678	-0.880000	0.03997	0.460000	0.39030	AAC	.	.		0.413	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		G	55539906	A	G	55539906	3	3	265	1	0	0	0	0	1	0	0	0	13547	43	2	2	3474	2	RP1	8	55539906	Missense_Mutation	SNP	A	TCGA-FV-A3I1-01A-11D-A22F-10		55539906	90824116	38	38929										
MATN2	4147	hgsc.bcm.edu	37	chr8	99045370	99045370	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	gaagacaatcttttacggtcTacacaaaagctttcccattc	5	11	2	1			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr8:99045370T>C	ENST00000520016.1	+	16	2806	c.2682T>C	c.(2680-2682)tcT>tcC	p.S894S	MATN2_ENST00000522025.2_Silent_p.S610S|MATN2_ENST00000521689.1_Silent_p.S875S|MATN2_ENST00000254898.5_Silent_p.S894S|RPL30_ENST00000518164.1_Intron|MATN2_ENST00000524308.1_Silent_p.S853S			O00339	MATN2_HUMAN	matrilin 2	894						proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			TTTTACGGTCTACACAAAAGC	0.368																																					p.S894S		Atlas-SNP	.											.	MATN2	165	.	0			c.T2682C						.						75	65	68					8																	99045370		1812	4081	5893	SO:0001819	synonymous_variant	4147	exon17			ACGGTCTACACAA	U69263	CCDS55264.1, CCDS55265.1	8q22.1-q22.2	2008-05-15							6908	protein-coding gene	gene with protein product		602108				9083061, 11852232	Standard	XM_005250920		Approved		uc003yic.3	O00339		ENST00000520016.1:c.2682T>C	chr8.hg19:g.99045370T>C		141.0	0.0		190.0	52.0	NM_002380	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Silent	SNP	ENST00000520016.1	hg19	CCDS55264.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.829|9.829	1.187959|1.187959	0.21954|0.21954	.|.	.|.	ENSG00000132561|ENSG00000132561	ENST00000519582;ENST00000522135|ENST00000518154	.|.	.|.	.|.	5.76|5.76	-1.82|-1.82	0.07857|0.07857	.|.	.|.	.|.	.|.	.|.	T|T	0.39172|0.39172	0.1068|0.1068	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.33599|0.33599	-0.9862|-0.9862	4|4	.|.	.|.	.|.	-7.9502|-7.9502	1.1258|1.1258	0.01735|0.01735	0.3777:0.0909:0.2656:0.2659|0.3777:0.0909:0.2656:0.2659	.|.	.|.	.|.	.|.	P|H	131;57|658	.|.	.|.	L|Y	+|+	2|1	0|0	MATN2|MATN2	99114546|99114546	0.965000|0.965000	0.33210|0.33210	0.930000|0.930000	0.37139|0.37139	0.985000|0.985000	0.73830|0.73830	-0.112000|-0.112000	0.10791|0.10791	0.091000|0.091000	0.17302|0.17302	0.533000|0.533000	0.62120|0.62120	CTA|TAC	.	.		0.368	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1			C	99045370	T	C	99045370	2	2	265	1	0	0	0	0	0	0	0	1	9343	1509	53	2		2	MATN2	8	99045370	Silent	SNP	T	TCGA-FV-A3I1-01A-11D-A22F-10	43505464	99045370	47318652	39	38930										
C9orf64	84267	hgsc.bcm.edu	37	chr9	86571114	86571114	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	tgttgacggcggcgcacaggGaccagtacccactgtatgtt	13	11	0	1			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr9:86571114G>A	ENST00000376344.3	-	1	518	c.302C>T	c.(301-303)tCc>tTc	p.S101F	C9orf64_ENST00000376340.2_5'UTR|C9orf64_ENST00000314700.1_5'UTR	NM_032307.3	NP_115683.3	Q5T6V5	CI064_HUMAN	chromosome 9 open reading frame 64	101										central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	15						GGCGCACAGGGACCAGTACCC	0.547																																					p.S101F		Atlas-SNP	.											.	C9orf64	28	.	0			c.C302T						.						133	132	133					9																	86571114		2074	4207	6281	SO:0001583	missense	84267	exon1			CACAGGGACCAGT	AK090882	CCDS6666.2	9q22.1	2014-06-11			ENSG00000165118	ENSG00000165118			28144	protein-coding gene	gene with protein product		611342				24911101	Standard	NM_032307		Approved	MGC10999	uc004anb.3	Q5T6V5	OTTHUMG00000020111	ENST00000376344.3:c.302C>T	chr9.hg19:g.86571114G>A	ENSP00000365522:p.Ser101Phe	27.0	0.0		25.0	10.0	NM_032307	B2RPI6|Q8N2B1|Q9BT18	Missense_Mutation	SNP	ENST00000376344.3	hg19	CCDS6666.2	.	.	.	.	.	.	.	.	.	.	G	35	5.542036	0.96474	.	.	ENSG00000165118	ENST00000376344	.	.	.	5.3	5.3	0.74995	.	0.353084	0.29389	N	0.012286	T	0.81654	0.4868	M	0.86805	2.84	0.80722	D	1	P	0.47484	0.896	P	0.54210	0.745	D	0.84544	0.0640	9	0.66056	D	0.02	-5.9596	19.3129	0.94198	0.0:0.0:1.0:0.0	.	101	Q5T6V5	CI064_HUMAN	F	101	.	ENSP00000365522:S101F	S	-	2	0	C9orf64	85760934	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.447000	0.97595	2.645000	0.89757	0.563000	0.77884	TCC	.	.		0.547	C9orf64-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052865.1	NM_032307		A	86571114	G	A	86571114	3	1	265	1	0	0	0	0	1	0	0	0	2491	1174	41	3	739	3	C9orf64	9	86571114	Missense_Mutation	SNP	G	TCGA-FV-A3I1-01A-11D-A22F-10		86571114	54642317	40	38931										
MYO3A	53904	hgsc.bcm.edu	37	chr10	26414368	26414368	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	gggcagatgagctacaagaaGctctcacctcccactgtgtg	11	12	1	3			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr10:26414368G>T	ENST00000265944.5	+	19	2111	c.1945G>T	c.(1945-1947)Gct>Tct	p.A649S	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	649	Myosin motor.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.A649S(1)		NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						GCTACAAGAAGCTCTCACCTC	0.433																																					p.A649S		Atlas-SNP	.											MYO3A,NS,carcinoma,0,1	MYO3A	371	.	1	Substitution - Missense(1)	endometrium(1)	c.G1945T						.						97	89	91					10																	26414368		2203	4300	6503	SO:0001583	missense	53904	exon19			CAAGAAGCTCTCA	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.1945G>T	chr10.hg19:g.26414368G>T	ENSP00000265944:p.Ala649Ser	165.0	0.0		127.0	34.0	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	hg19	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	G	34	5.388171	0.95988	.	.	ENSG00000095777	ENST00000265944	D	0.87887	-2.31	5.91	5.91	0.95273	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.92756	0.7697	M	0.69185	2.1	0.80722	D	1	D	0.71674	0.998	D	0.67382	0.951	D	0.91608	0.5300	10	0.46703	T	0.11	.	20.2872	0.98536	0.0:0.0:1.0:0.0	.	649	Q8NEV4	MYO3A_HUMAN	S	649	ENSP00000265944:A649S	ENSP00000265944:A649S	A	+	1	0	MYO3A	26454374	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.869000	0.99810	2.799000	0.96334	0.585000	0.79938	GCT	.	.		0.433	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		T	26414368	G	T	26414368	3	4	265	1	0	0	0	0	1	0	0	0	10085	971	34	3	2011	3	MYO3A	10	26414368	Missense_Mutation	SNP	G	TCGA-FV-A3I1-01A-11D-A22F-10		26414368	109120379	41	38932										
CDHR1	92211	hgsc.bcm.edu	37	chr10	85971460	85971460	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	aaatattccacctatgggacTggggcagacctgtaagtaga	11	8	0	2			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr10:85971460T>A	ENST00000372117.3	+	14	1645	c.1542T>A	c.(1540-1542)acT>acA	p.T514T	CDHR1_ENST00000332904.3_Silent_p.T514T|CDHR1_ENST00000440770.2_Silent_p.T218T	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1	514	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cellular process (GO:0009987)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						CCTATGGGACTGGGGCAGACC	0.587																																					p.T514T		Atlas-SNP	.											.	CDHR1	122	.	0			c.T1542A						.						112	111	112					10																	85971460		2203	4300	6503	SO:0001819	synonymous_variant	92211	exon14			TGGGACTGGGGCA	AB053448	CCDS7372.1, CCDS53548.1	10q23.1	2014-01-28	2010-01-25	2010-01-25	ENSG00000148600	ENSG00000148600		"Cadherins / Cadherin-related"	14550	protein-coding gene	gene with protein product		609502	"protocadherin 21"	PCDH21		11597768	Standard	NM_001171971		Approved	KIAA1775, CORD15, RP65	uc001kcv.3	Q96JP9	OTTHUMG00000018634	ENST00000372117.3:c.1542T>A	chr10.hg19:g.85971460T>A		83.0	0.0		88.0	24.0	NM_001171971	Q69YZ8|Q8IXY5	Silent	SNP	ENST00000372117.3	hg19	CCDS7372.1																																																																																			.	.		0.587	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100		A	85971460	T	A	85971460	2	1	265	1	0	0	0	0	0	0	0	1	3120	1567	55	4		4	CDHR1	10	85971460	Silent	SNP	T	TCGA-FV-A3I1-01A-11D-A22F-10	59557092	85971460	49563287	42	38933										
KIF20B	9585	hgsc.bcm.edu	37	chr10	91522476	91522476	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	ttccaaaacctgagttagagAttcaatttacacctttacag	5	9	1	2			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr10:91522476A>G	ENST00000371728.3	+	29	4938	c.4873A>G	c.(4873-4875)Att>Gtt	p.I1625V	KIF20B_ENST00000478929.1_3'UTR|KIF20B_ENST00000260753.4_Missense_Mutation_p.I1585V|KIF20B_ENST00000394289.2_Missense_Mutation_p.I1625V|KIF20B_ENST00000416354.1_Missense_Mutation_p.I1655V	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	1625	Interaction with PIN1.				ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|neural tube closure (GO:0001843)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization (GO:0070201)|regulation of mitosis (GO:0007088)|regulation of neuron migration (GO:2001222)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|WW domain binding (GO:0050699)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	58						TGAGTTAGAGATTCAATTTAC	0.418																																					p.I1585V		Atlas-SNP	.											.	KIF20B	191	.	0			c.A4753G						.						88	82	84					10																	91522476		2203	4300	6503	SO:0001583	missense	9585	exon29			TTAGAGATTCAAT	L16782	CCDS7407.1, CCDS60590.1	10q23.31	2009-08-06	2008-07-31	2008-07-31	ENSG00000138182	ENSG00000138182			7212	protein-coding gene	gene with protein product	"cancer/testis antigen 90"	605498	"M-phase phosphoprotein 1"	MPHOSPH1		8885239, 8290587, 11470801	Standard	NM_016195		Approved	MPP1, KRMP1, CT90	uc001kgr.1	Q96Q89	OTTHUMG00000018725	ENST00000371728.3:c.4873A>G	chr10.hg19:g.91522476A>G	ENSP00000360793:p.Ile1625Val	73.0	0.0		64.0	15.0	NM_016195	A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Missense_Mutation	SNP	ENST00000371728.3	hg19		.	.	.	.	.	.	.	.	.	.	A	28.2	4.902998	0.92035	.	.	ENSG00000138182	ENST00000260753;ENST00000416354;ENST00000394289;ENST00000371728	T;T;T;T	0.55760	0.5;0.5;0.5;0.5	6.06	6.06	0.98353	.	0.000000	0.51477	D	0.000097	T	0.71126	0.3303	M	0.68952	2.095	0.58432	D	0.999994	D;D	0.76494	0.999;0.999	D;D	0.80764	0.987;0.994	T	0.73911	-0.3833	10	0.87932	D	0	-17.8459	15.5919	0.76537	1.0:0.0:0.0:0.0	.	1625;1585	Q96Q89;Q96Q89-3	KI20B_HUMAN;.	V	1585;1655;1625;1625	ENSP00000260753:I1585V;ENSP00000411545:I1655V;ENSP00000377830:I1625V;ENSP00000360793:I1625V	ENSP00000260753:I1585V	I	+	1	0	KIF20B	91512456	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.147000	0.89628	2.324000	0.78689	0.533000	0.62120	ATT	.	.		0.418	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195		G	91522476	A	G	91522476	3	3	265	1	0	0	0	0	1	0	0	0	8296	333	12	2	4863	2	KIF20B	10	91522476	Missense_Mutation	SNP	A	TCGA-FV-A3I1-01A-11D-A22F-10	5551016	91522476	44012271	43	38934										
LDB1	8861	hgsc.bcm.edu	37	chr10	103870721	103870721	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	atgcatcccaccagagattgTcacactcctagggagcatgg	10	12	1	1			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr10:103870721T>C	ENST00000425280.1	-	5	599	c.257A>G	c.(256-258)gAc>gGc	p.D86G	LDB1_ENST00000361198.5_Missense_Mutation_p.D50G|LDB1_ENST00000490751.1_5'UTR	NM_001113407.1	NP_001106878.1	Q86U70	LDB1_HUMAN	LIM domain binding 1	86					anterior/posterior axis specification (GO:0009948)|cellular component assembly (GO:0022607)|cerebellar Purkinje cell differentiation (GO:0021702)|epithelial structure maintenance (GO:0010669)|gastrulation with mouth forming second (GO:0001702)|hair follicle development (GO:0001942)|head development (GO:0060322)|histone H3-K4 acetylation (GO:0043973)|multicellular organismal development (GO:0007275)|negative regulation of erythrocyte differentiation (GO:0045647)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron differentiation (GO:0030182)|positive regulation of cell adhesion (GO:0045785)|positive regulation of hemoglobin biosynthetic process (GO:0046985)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription, DNA-templated (GO:0006355)|somatic stem cell maintenance (GO:0035019)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery (GO:0000972)|Wnt signaling pathway (GO:0016055)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|enzyme binding (GO:0019899)|LIM domain binding (GO:0030274)|protein homodimerization activity (GO:0042803)|RNA polymerase II activating transcription factor binding (GO:0001102)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(1)|skin(1)	21		Colorectal(252;0.122)		Epithelial(162;1.11e-07)|all cancers(201;1.82e-06)		CCAGAGATTGTCACACTCCTA	0.512																																					p.D86G		Atlas-SNP	.											.	LDB1	61	.	0			c.A257G						.						141	138	139					10																	103870721		2203	4300	6503	SO:0001583	missense	8861	exon5			AGATTGTCACACT	AF068652	CCDS7528.1, CCDS44472.1	10q24-q25	2008-08-01			ENSG00000198728	ENSG00000198728			6532	protein-coding gene	gene with protein product	"carboxy terminal LIM domain protein 2"	603451				9503020, 9799849	Standard	NM_003893		Approved	NLI, CLIM2	uc009xwz.3	Q86U70	OTTHUMG00000018950	ENST00000425280.1:c.257A>G	chr10.hg19:g.103870721T>C	ENSP00000392466:p.Asp86Gly	95.0	0.0		91.0	39.0	NM_001113407	B4DUC4|O75479|O96010|Q1EQX1|Q9UGM4	Missense_Mutation	SNP	ENST00000425280.1	hg19	CCDS44472.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.588789	0.86851	.	.	ENSG00000198728	ENST00000361198;ENST00000425280	.	.	.	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.81422	0.4819	M	0.84948	2.725	0.80722	D	1	D;D	0.89917	0.997;1.0	D;D	0.91635	0.992;0.999	D	0.84672	0.0712	9	0.87932	D	0	-1.6521	15.6438	0.77033	0.0:0.0:0.0:1.0	.	86;50	Q86U70;Q86U70-3	LDB1_HUMAN;.	G	50;86	.	ENSP00000354616:D50G	D	-	2	0	LDB1	103860711	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.040000	0.89188	2.172000	0.68678	0.459000	0.35465	GAC	.	.		0.512	LDB1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001113407		C	103870721	T	C	103870721	3	2	265	1	0	0	0	0	1	0	0	0	8704	1667	58	2	1006	2	LDB1	10	103870721	Missense_Mutation	SNP	T	TCGA-FV-A3I1-01A-11D-A22F-10	12348245	103870721	31664026	44	38935										
MRGPRE	116534	hgsc.bcm.edu	37	chr11	3249346	3249346	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	atgccgaagggcaggccgcaGaagaggaagaggaggacggt	19	7	0	3	rs531538794		TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr11:3249346G>T	ENST00000389832.5	-	2	990	c.684C>A	c.(682-684)ttC>ttA	p.F228L	MRGPRE_ENST00000436689.2_Missense_Mutation_p.F227L|AC109309.4_ENST00000418995.2_RNA			Q86SM8	MRGRE_HUMAN	MAS-related GPR, member E	228						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(6)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	19		Medulloblastoma(188;0.00106)|all_epithelial(84;0.00111)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00529)|LUSC - Lung squamous cell carcinoma(625;0.19)		GCAGGCCGCAGAAGAGGAAGA	0.657																																					p.F228L		Atlas-SNP	.											.	MRGPRE	35	.	0			c.C684A						.						16	22	20					11																	3249346		2058	4183	6241	SO:0001583	missense	116534	exon2			GCCGCAGAAGAGG	AY255572	CCDS41603.1, CCDS41603.2	11p15.5	2012-08-21	2004-03-25		ENSG00000184350	ENSG00000184350		"GPCR / Class A : Orphans"	30694	protein-coding gene	gene with protein product		607232	"G protein-coupled receptor 167"	GPR167		11551509	Standard	NM_001039165		Approved	mrgE	uc001lxq.5	Q86SM8	OTTHUMG00000011708	ENST00000389832.5:c.684C>A	chr11.hg19:g.3249346G>T	ENSP00000374482:p.Phe228Leu	38.0	0.0		32.0	13.0	NM_001039165	Q2M1V7	Missense_Mutation	SNP	ENST00000389832.5	hg19		.	.	.	.	.	.	.	.	.	.	g	0.404	-0.916686	0.02415	.	.	ENSG00000184350	ENST00000436689;ENST00000389832	.	.	.	3.9	1.87	0.25490	GPCR, rhodopsin-like superfamily (1);	0.576644	0.14260	U	0.330849	T	0.12944	0.0314	N	0.11106	0.095	0.09310	N	1	B	0.19817	0.039	B	0.12156	0.007	T	0.31724	-0.9933	9	0.02654	T	1	-15.8633	2.6616	0.05028	0.1085:0.1805:0.526:0.185	.	227	Q86SM8	MRGRE_HUMAN	L	228;227	.	ENSP00000374482:F227L	F	-	3	2	MRGPRE	3205922	0.002000	0.14202	0.002000	0.10522	0.009000	0.06853	0.359000	0.20233	0.833000	0.34828	-0.379000	0.06801	TTC	.	.		0.657	MRGPRE-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000032346.5	XM_171536		T	3249346	G	T	3249346	3	4	265	1	0	0	0	0	1	0	0	0	9773	933	33	3	258	3	MRGPRE	11	3249346	Missense_Mutation	SNP	G	TCGA-FV-A3I1-01A-11D-A22F-10		3249346	131757170	45	38936										
CAPRIN1	4076	hgsc.bcm.edu	37	chr11	34112151	34112151	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	cgtctcagcctcaagtatttCaggctgggacaagcaaacct	9	12	3	0			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr11:34112151C>T	ENST00000341394.4	+	14	1669	c.1480C>T	c.(1480-1482)Cag>Tag	p.Q494*	CAPRIN1_ENST00000529307.1_Nonsense_Mutation_p.Q413*|CAPRIN1_ENST00000389645.3_Nonsense_Mutation_p.Q494*|CAPRIN1_ENST00000532820.1_Nonsense_Mutation_p.Q494*|CAPRIN1_ENST00000530820.1_Nonsense_Mutation_p.Q494*|CAPRIN1_ENST00000533657.1_3'UTR	NM_005898.4	NP_005889.3	Q14444	CAPR1_HUMAN	cell cycle associated protein 1	494					negative regulation of translation (GO:0017148)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)	18		Acute lymphoblastic leukemia(5;0.00045)|all_hematologic(20;0.0016)				TCAAGTATTTCAGGCTGGGAC	0.408																																					p.Q494X		Atlas-SNP	.											.	CAPRIN1	110	.	0			c.C1480T						.						117	98	105					11																	34112151		2202	4298	6500	SO:0001587	stop_gained	4076	exon14			GTATTTCAGGCTG	BC001731	CCDS31453.1, CCDS31454.1	11p13	2010-08-03	2007-03-27	2007-03-27	ENSG00000135387	ENSG00000135387			6743	protein-coding gene	gene with protein product	"cytoplasmic activation/proliferation-associated protein-1"	601178	"membrane component, chromosome 11, surface marker 1", "GPI-anchored membrane protein 1"	M11S1, GPIAP1		7657653, 16177067, 17210633, 14764709, 15471883	Standard	NM_005898		Approved	caprin-1, RNG105	uc001mvh.1	Q14444	OTTHUMG00000166248	ENST00000341394.4:c.1480C>T	chr11.hg19:g.34112151C>T	ENSP00000340329:p.Gln494*	136.0	0.0		134.0	6.0	NM_203364	A6NMY7|D3DR06|Q15074|Q6IMN4|Q6IMN7|Q9BV09	Nonsense_Mutation	SNP	ENST00000341394.4	hg19	CCDS31453.1	.	.	.	.	.	.	.	.	.	.	C	39	7.570292	0.98365	.	.	ENSG00000135387	ENST00000341394;ENST00000389645;ENST00000532820;ENST00000530820;ENST00000529307	.	.	.	5.72	5.72	0.89469	.	0.543163	0.21376	N	0.075556	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.19590	T	0.45	.	19.8734	0.96858	0.0:1.0:0.0:0.0	.	.	.	.	X	494;494;494;494;413	.	ENSP00000340329:Q494X	Q	+	1	0	CAPRIN1	34068727	1.000000	0.71417	1.000000	0.80357	0.555000	0.35460	7.277000	0.78572	2.689000	0.91719	0.650000	0.86243	CAG	.	.		0.408	CAPRIN1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000388680.2	NM_005898		T	34112151	C	T	34112151	4	4	265	1	0	0	0	0	0	1	0	0	2637	827	29	3	1530	3	CAPRIN1	11	34112151	Nonsense_Mutation	SNP	C	TCGA-FV-A3I1-01A-11D-A22F-10	30862805	34112151	100894365	46	38937										
SLC22A10	387775	hgsc.bcm.edu	37	chr11	63059095	63059095	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	atgctggtgggaggcatcatAggtggccatgtctcagacag	15	8	2	1			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr11:63059095A>T	ENST00000332793.6	+	2	488	c.486A>T	c.(484-486)atA>atT	p.I162I	SLC22A10_ENST00000526800.1_Silent_p.I110I|SLC22A10_ENST00000525620.1_Intron|SLC22A10_ENST00000544661.1_Silent_p.I7I|SLC22A10_ENST00000535888.1_Intron	NM_001039752.3	NP_001034841.3	Q63ZE4	S22AA_HUMAN	solute carrier family 22, member 10	162						integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28					Conjugated Estrogens(DB00286)|Probenecid(DB01032)|Salicylic acid(DB00936)	GAGGCATCATAGGTGGCCATG	0.433																																					p.I162I		Atlas-SNP	.											.	SLC22A10	79	.	0			c.A486T						.						147	145	145					11																	63059095		2074	4239	6313	SO:0001819	synonymous_variant	387775	exon2			CATCATAGGTGGC	AP003420	CCDS41661.1	11q12.3	2013-05-22	2008-01-11		ENSG00000184999	ENSG00000184999		"Solute carriers"	18057	protein-coding gene	gene with protein product		607580	"solute carrier family 22 (organic anion/cation transporter), member 10"			11327718	Standard	NM_001039752		Approved	OAT5, hOAT5	uc009yor.3	Q63ZE4	OTTHUMG00000165197	ENST00000332793.6:c.486A>T	chr11.hg19:g.63059095A>T		110.0	0.0		115.0	33.0	NM_001039752	Q68CJ0	Silent	SNP	ENST00000332793.6	hg19	CCDS41661.1																																																																																			.	.		0.433	SLC22A10-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382622.3	NM_001039752		T	63059095	A	T	63059095	2	4	265	1	0	0	0	0	0	0	0	1	14456	410	15	4		4	SLC22A10	11	63059095	Silent	SNP	A	TCGA-FV-A3I1-01A-11D-A22F-10	28946944	63059095	71947421	47	38938										
KAT5	10524	hgsc.bcm.edu	37	chr11	65482196	65482196	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	aagtacggccgtagtctcaaGtgtcttcagcgtcatttggt	11	9	4	0			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr11:65482196G>T	ENST00000377046.3	+	8	1094	c.822G>T	c.(820-822)aaG>aaT	p.K274N	KAT5_ENST00000530446.1_Missense_Mutation_p.K255N|KAT5_ENST00000341318.4_Missense_Mutation_p.K307N|KAT5_ENST00000352980.4_Missense_Mutation_p.K222N|KAT5_ENST00000534650.1_Missense_Mutation_p.K63N	NM_006388.3	NP_006379.2	Q92993	KAT5_HUMAN	K(lysine) acetyltransferase 5	274	MYST-type HAT.				androgen receptor signaling pathway (GO:0030521)|cellular response to estradiol stimulus (GO:0071392)|chromatin organization (GO:0006325)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|double-strand break repair (GO:0006302)|histone acetylation (GO:0016573)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of growth (GO:0040008)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)|Swr1 complex (GO:0000812)|transcription factor complex (GO:0005667)	androgen receptor binding (GO:0050681)|histone acetyltransferase activity (GO:0004402)|metal ion binding (GO:0046872)|repressing transcription factor binding (GO:0070491)|transcription coactivator activity (GO:0003713)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)	21						GTAGTCTCAAGTGTCTTCAGC	0.577																																					p.K307N		Atlas-SNP	.											.	KAT5	36	.	0			c.G921T						.						264	234	244					11																	65482196		2201	4297	6498	SO:0001583	missense	10524	exon7			TCTCAAGTGTCTT	U74667	CCDS8109.1, CCDS8110.1, CCDS31610.1, CCDS55771.1	11q13	2013-01-10	2008-07-04	2008-07-04	ENSG00000172977	ENSG00000172977		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing"	5275	protein-coding gene	gene with protein product	"Tat interacting protein, 60kDa", "K-acetyltransferase 5"	601409	"HIV-1 Tat interactive protein, 60kDa"	HTATIP		8607265	Standard	NM_006388		Approved	TIP60, PLIP, cPLA2, HTATIP1, ESA1, ZC2HC5	uc001ofk.3	Q92993	OTTHUMG00000166617	ENST00000377046.3:c.822G>T	chr11.hg19:g.65482196G>T	ENSP00000366245:p.Lys274Asn	162.0	0.0		162.0	53.0	NM_182710	B4E3C7|C9JL99|O95624|Q13430|Q17RW5|Q561W3|Q6GSE8|Q9BWK7	Missense_Mutation	SNP	ENST00000377046.3	hg19	CCDS31610.1	.	.	.	.	.	.	.	.	.	.	G	18.79	3.698762	0.68501	.	.	ENSG00000172977	ENST00000377046;ENST00000352980;ENST00000341318;ENST00000530446;ENST00000531880;ENST00000534650	T;T;T;T;T	0.52754	0.89;0.88;0.88;0.88;0.65	4.97	4.97	0.65823	Acyl-CoA N-acyltransferase (1);	0.000000	0.85682	D	0.000000	T	0.43875	0.1267	M	0.67625	2.065	0.58432	D	0.999997	P;P;B;B	0.42039	0.507;0.769;0.383;0.403	B;B;B;B	0.32724	0.12;0.131;0.151;0.072	T	0.50550	-0.8815	10	0.41790	T	0.15	-21.4041	15.7539	0.78009	0.0:0.0:1.0:0.0	.	255;307;222;274	B4E3C7;Q92993-3;Q92993-2;Q92993	.;.;.;KAT5_HUMAN	N	274;222;307;255;268;63	ENSP00000366245:K274N;ENSP00000344955:K222N;ENSP00000340330:K307N;ENSP00000434765:K255N;ENSP00000436012:K268N	ENSP00000340330:K307N	K	+	3	2	KAT5	65238772	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.448000	0.52943	2.567000	0.86603	0.561000	0.74099	AAG	.	.		0.577	KAT5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390866.2	NM_006388		T	65482196	G	T	65482196	3	4	265	1	0	0	0	0	1	0	0	0	7992	1020	36	3	947	3	KAT5	11	65482196	Missense_Mutation	SNP	G	TCGA-FV-A3I1-01A-11D-A22F-10	2423101	65482196	69524320	48	38939										
RAB6A	5870	hgsc.bcm.edu	37	chr11	73431941	73431941	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	taaaaagtcaatgccaattgTtgcctgtaaaacaaaacaaa	5	7	1	0			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr11:73431941T>C	ENST00000336083.3	-	3	588	c.133A>G	c.(133-135)Aca>Gca	p.T45A	RP11-456I15.2_ENST00000538624.1_RNA|RAB6A_ENST00000541588.1_Missense_Mutation_p.T45A|RAB6A_ENST00000536566.1_Missense_Mutation_p.T12A|RAB6A_ENST00000310653.6_Missense_Mutation_p.T45A	NM_198896.1	NP_942599.1	P20340	RAB6A_HUMAN	RAB6A, member RAS oncogene family	45					antigen processing and presentation (GO:0019882)|early endosome to Golgi transport (GO:0034498)|GTP catabolic process (GO:0006184)|minus-end-directed organelle transport along microtubule (GO:0072385)|peptidyl-cysteine methylation (GO:0018125)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)|protein domain specific binding (GO:0019904)			large_intestine(2)|lung(2)	4						ATGCCAATTGTTGCCTGTAAA	0.328																																					p.T45A		Atlas-SNP	.											.	RAB6A	17	.	0			c.A133G						.						106	105	105					11																	73431941		2199	4293	6492	SO:0001583	missense	5870	exon3			CAATTGTTGCCTG	AF130986	CCDS8223.1, CCDS8224.1, CCDS58155.1, CCDS58156.1	11q13.3	2008-08-08			ENSG00000175582	ENSG00000175582		"RAB, member RAS oncogene"	9786	protein-coding gene	gene with protein product		179513		RAB6			Standard	NM_001243718		Approved		uc001ouf.3	P20340	OTTHUMG00000134308	ENST00000336083.3:c.133A>G	chr11.hg19:g.73431941T>C	ENSP00000336850:p.Thr45Ala	113.0	0.0		118.0	31.0	NM_002869	A8K133|B7Z772|F5H668|Q1W5D8|Q5U0A8|Q9UBE4	Missense_Mutation	SNP	ENST00000336083.3	hg19	CCDS8224.1	.	.	.	.	.	.	.	.	.	.	T	29.0	4.965060	0.92855	.	.	ENSG00000175582	ENST00000310653;ENST00000336083;ENST00000393571;ENST00000536566;ENST00000541588;ENST00000539750;ENST00000535748;ENST00000542366	D;D;D;D	0.87491	-2.26;-2.26;-2.26;-2.26	5.55	5.55	0.83447	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.95752	0.8618	H	0.96720	3.87	0.54753	D	0.999986	D;P;P	0.89917	1.0;0.947;0.459	D;D;P	0.83275	0.996;0.915;0.645	D	0.97089	0.9789	10	0.87932	D	0	-0.0428	15.0229	0.71643	0.0:0.0:0.0:1.0	.	45;45;45	Q1W5D8;P20340;P20340-2	.;RAB6A_HUMAN;.	A	45;45;45;12;45;45;45;45	ENSP00000311449:T45A;ENSP00000336850:T45A;ENSP00000437863:T12A;ENSP00000445350:T45A	ENSP00000311449:T45A	T	-	1	0	RAB6A	73109589	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.312000	0.78968	2.330000	0.79161	0.477000	0.44152	ACA	.	.		0.328	RAB6A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259241.2			C	73431941	T	C	73431941	3	2	265	1	0	0	0	0	1	0	0	0	12966	1725	60	2	627	2	RAB6A	11	73431941	Missense_Mutation	SNP	T	TCGA-FV-A3I1-01A-11D-A22F-10	7949745	73431941	61574575	49	38940										
NCAM1	4684	hgsc.bcm.edu	37	chr11	112832332	112832363	+	5'UTR	DEL	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	-													0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	ccctcccagccagcagattaCaatgctgccaaactaaggat					rs6589347|rs11284059|rs559828324|rs201772924|rs563686839|rs7105734|rs112306738		TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr11:112832332_112832363delCATCCCTCCCAGCCAGCAGATTACAATGCTGC	ENST00000533760.1	+	0	243_274				NCAM1_ENST00000397957.4_3'UTR|RP11-629G13.1_ENST00000532002.1_RNA|RP11-629G13.1_ENST00000500537.2_RNA	NM_001242608.1	NP_001229537.1	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		CAGCAGATTACAATGCTGCCAAACTAAGGATTTCATTTGGACTTTGTTTTTC	0.491																																					.		Pindel	.											.	NCAM1	372	.	0			.						.																																			SO:0001623	5_prime_UTR_variant	4684	wholegene			.		CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000533760.1:c.-326CATCCCTCCCAGCCAGCAGATTACAATGCTGC>-	chr11.hg19:g.112832332_112832363delCATCCCTCCCAGCCAGCAGATTACAATGCTGC		167.0	0.0		160.0	26.0	NM_001242608	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Frame_Shift_Del	DEL	ENST00000533760.1	hg19																																																																																				.	.		0.491	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394068.2	NM_000615		-	112832363	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	-	112832332	6	5	265	0	1	1	0	1	0	0	0	0	10211	493	17	0		0	NCAM1	11	112832332	5'UTR	DEL	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	TCGA-FV-A3I1-01A-11D-A22F-10	39400391	112832332	22174184	50	38941										
TNFRSF1A	7132	hgsc.bcm.edu	37	chr12	6443355	6443355	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	tctccctgtcccctaggtgaGggaccagtccaataacccct	8	16	1	1			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr12:6443355G>T	ENST00000162749.2	-	2	394	c.95C>A	c.(94-96)cCt>cAt	p.P32H	TNFRSF1A_ENST00000540022.1_Missense_Mutation_p.P32H|TNFRSF1A_ENST00000366159.4_Missense_Mutation_p.P32H|TNFRSF1A_ENST00000437813.3_5'UTR	NM_001065.3	NP_001056.1	P19438	TNR1A_HUMAN	tumor necrosis factor receptor superfamily, member 1A	32					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-6 production (GO:0032715)|positive regulation of angiogenesis (GO:0045766)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|prostaglandin metabolic process (GO:0006693)|protein heterooligomerization (GO:0051291)|response to alkaloid (GO:0043279)|response to amino acid (GO:0043200)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to wounding (GO:0009611)|tetrapyrrole metabolic process (GO:0033013)|viral process (GO:0016032)	axon (GO:0030424)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	tumor necrosis factor-activated receptor activity (GO:0005031)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	19						CCCTAGGTGAGGGACCAGTCC	0.502																																					p.P32H		Atlas-SNP	.											.	TNFRSF1A	39	.	0			c.C95A						.						109	110	110					12																	6443355		2203	4300	6503	SO:0001583	missense	7132	exon2			AGGTGAGGGACCA	M75866	CCDS8542.1	12p13.2	2014-09-17			ENSG00000067182	ENSG00000067182		"Tumor necrosis factor receptor superfamily", "CD molecules"	11916	protein-coding gene	gene with protein product		191190		TNFR1		1655358, 2158863	Standard	NM_001065		Approved	TNF-R, TNFAR, TNFR60, TNF-R-I, CD120a, TNF-R55	uc001qnu.3	P19438	OTTHUMG00000168267	ENST00000162749.2:c.95C>A	chr12.hg19:g.6443355G>T	ENSP00000162749:p.Pro32His	117.0	0.0		116.0	43.0	NM_001065	A8K4X3|B2RDE4|B3KPQ1|B4DQB7|B4E309|B5M0B5|D3DUR1|Q9UCA4	Missense_Mutation	SNP	ENST00000162749.2	hg19	CCDS8542.1	.	.	.	.	.	.	.	.	.	.	G	16.79	3.220583	0.58560	.	.	ENSG00000067182	ENST00000162749;ENST00000540022;ENST00000539372;ENST00000366159;ENST00000440083;ENST00000536194	D;D;D;D;D;D	0.98849	-3.03;-3.17;-3.77;-4.19;-5.18;-5.05	3.89	3.89	0.44902	.	0.615734	0.16129	N	0.228289	D	0.98454	0.9485	L	0.58101	1.795	0.09310	N	0.999992	D;D;D	0.76494	0.997;0.999;0.997	P;D;P	0.66351	0.781;0.943;0.817	D	0.94886	0.8043	10	0.42905	T	0.14	-2.6243	11.2473	0.49004	0.0:0.0:1.0:0.0	.	32;32;32	B5M0B5;F5H061;P19438	.;.;TNR1A_HUMAN	H	32	ENSP00000162749:P32H;ENSP00000438343:P32H;ENSP00000442059:P32H;ENSP00000380389:P32H;ENSP00000413224:P32H;ENSP00000442919:P32H	ENSP00000162749:P32H	P	-	2	0	TNFRSF1A	6313616	0.656000	0.27385	0.939000	0.37840	0.786000	0.44442	2.233000	0.43027	2.022000	0.59522	0.563000	0.77884	CCT	.	.		0.502	TNFRSF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399038.1	NM_001065		T	6443355	G	T	6443355	3	4	265	1	0	0	0	0	1	0	0	0	16308	1000	35	3	1308	3	TNFRSF1A	12	6443355	Missense_Mutation	SNP	G	TCGA-FV-A3I1-01A-11D-A22F-10		6443355	127408540	51	38942										
MLL2	8085	hgsc.bcm.edu	37	chr12	49427419	49427420	+	Missense_Mutation	DNP	CC	CC	AT													0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	ctgaagggccagccagggatCcagccccaccagaatgttgc							TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr12:49427419_49427420CC>AT	ENST00000301067.7	-	39	11067_11068	c.11068_11069GG>AT	c.(11068-11070)GGa>ATa	p.G3690I	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3690	Gln-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										AGCCAGGGATCCAGCCCCACCA	0.594																																					p.G3690V|p.G3690R		Atlas-SNP	.											.	MLL2	1173	.	0			c.G11069T|c.G11068A						.																																			SO:0001583	missense	8085	exon39			AGGGATCCAGCCC|GGGATCCAGCCCC	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.11068_11069delinsAT	chr12.hg19:g.49427419_49427420delinsAT	ENSP00000301067:p.Gly3690Ile	58.0|59.0	0.0		52.0	14.0	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	hg19	CCDS44873.1																																																																																			.	.		0.594	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			AT	49427420	CC	AT	49427419	3	1	265	1	0	0	0	0	1	0	0	0	9630	855	30	3	5608	3	MLL2	12	49427419	Missense_Mutation	DNP	CC	TCGA-FV-A3I1-01A-11D-A22F-10	42984064	49427419	84424476	52	38943										
NOS1	4842	hgsc.bcm.edu	37	chr12	117723945	117723945	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	tggatcctgcccacacagcgCgaggcattccgccaggcgtg	13	15	0	0			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr12:117723945C>T	ENST00000338101.4	-	5	1258	c.1254G>A	c.(1252-1254)tcG>tcA	p.S418S	NOS1_ENST00000344089.3_3'UTR|NOS1_ENST00000317775.6_Silent_p.S418S			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		CCACACAGCGCGAGGCATTCC	0.562																																					p.S418S	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											NOS1,caecum,carcinoma,0,1	NOS1	240	.	0			c.G1254A						.						130	131	130					12																	117723945		2168	4298	6466	SO:0001819	synonymous_variant	4842	exon6			ACAGCGCGAGGCA		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.1254G>A	chr12.hg19:g.117723945C>T		157.0	0.0		122.0	32.0	NM_000620		Silent	SNP	ENST00000338101.4	hg19	CCDS55890.1																																																																																			.	.		0.562	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1			T	117723945	C	T	117723945	2	4	265	1	0	0	0	0	0	0	0	1	10550	755	27	1		1	NOS1	12	117723945	Silent	SNP	C	TCGA-FV-A3I1-01A-11D-A22F-10	68296526	117723945	16127950	53	38944										
HS6ST3	266722	hgsc.bcm.edu	37	chr13	97484795	97484795	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	ccagtgtcacgttacctgagCgagtggaaacatgtccagag	12	10	1	2	rs368146960		TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr13:97484795C>T	ENST00000376705.2	+	2	783	c.759C>T	c.(757-759)agC>agT	p.S253S		NM_153456.3	NP_703157.2	Q8IZP7	H6ST3_HUMAN	heparan sulfate 6-O-sulfotransferase 3	253	3'-phosphate binding. {ECO:0000255}.				heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)	integral component of membrane (GO:0016021)	heparan sulfate 6-O-sulfotransferase activity (GO:0017095)			NS(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|skin(1)	20	all_neural(89;0.0878)|Medulloblastoma(90;0.163)					GTTACCTGAGCGAGTGGAAAC	0.473																																					p.S253S		Atlas-SNP	.											.	HS6ST3	54	.	0			c.C759T						.	C		1,4405	2.1+/-5.4	0,1,2202	67	68	68		759	-3.3	1	13		68	0,8600		0,0,4300	no	coding-synonymous	HS6ST3	NM_153456.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		253/472	97484795	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	266722	exon2			CCTGAGCGAGTGG	AF539426	CCDS9481.1	13q32.2	2007-12-04			ENSG00000185352	ENSG00000185352		"Sulfotransferases, membrane-bound"	19134	protein-coding gene	gene with protein product		609401					Standard	NM_153456		Approved		uc001vmw.4	Q8IZP7	OTTHUMG00000017232	ENST00000376705.2:c.759C>T	chr13.hg19:g.97484795C>T		87.0	0.0		89.0	27.0	NM_153456	Q5W0L0|Q68CW6	Silent	SNP	ENST00000376705.2	hg19	CCDS9481.1																																																																																			.	.		0.473	HS6ST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045517.2	NM_153456		T	97484795	C	T	97484795	2	4	265	1	0	0	0	0	0	0	0	1	7381	767	27	1		1	HS6ST3	13	97484795	Silent	SNP	C	TCGA-FV-A3I1-01A-11D-A22F-10		97484795	17685083	54	38945										
APBA2	321	hgsc.bcm.edu	37	chr15	29398965	29398965	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	atcggggaccagatcatgtcCatcaatggcaccagcctggt	11	12	2	1			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr15:29398965C>T	ENST00000558402.1	+	13	2459	c.1860C>T	c.(1858-1860)tcC>tcT	p.S620S	APBA2_ENST00000558259.1_Silent_p.S620S|APBA2_ENST00000561069.1_Silent_p.S620S|APBA2_ENST00000411764.1_Silent_p.S608S|APBA2_ENST00000558330.1_Silent_p.S608S			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	620	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				in utero embryonic development (GO:0001701)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|liver(2)|lung(33)|stomach(1)|urinary_tract(1)	59		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		AGATCATGTCCATCAATGGCA	0.657																																					p.S620S		Atlas-SNP	.											.	APBA2	132	.	0			c.C1860T						.						64	60	61					15																	29398965		2203	4300	6503	SO:0001819	synonymous_variant	321	exon11			CATGTCCATCAAT	AB014719	CCDS10022.1, CCDS45197.1	15q11-q12	2008-07-18	2008-07-18		ENSG00000034053	ENSG00000034053			579	protein-coding gene	gene with protein product		602712	"X11-like", "amyloid beta (A4) precursor protein-binding, family A, member 2 (X11-like)"	X11L, MINT2		8955346	Standard	NM_005503		Approved	D15S1518E, LIN-10, MGC:14091, HsT16821	uc001zck.3	Q99767	OTTHUMG00000129255	ENST00000558402.1:c.1860C>T	chr15.hg19:g.29398965C>T		101.0	0.0		121.0	40.0	NM_005503	E9PGI4|O60571|Q5XKC0	Silent	SNP	ENST00000558402.1	hg19	CCDS10022.1																																																																																			.	.		0.657	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503		T	29398965	C	T	29398965	2	4	265	1	0	0	0	0	0	0	0	1	757	581	21	3		3	APBA2	15	29398965	Silent	SNP	C	TCGA-FV-A3I1-01A-11D-A22F-10		29398965	73132427	55	38946										
SPTBN5	51332	hgsc.bcm.edu	37	chr15	42158099	42158099	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	tcaccaacattcatcttcacCtcctgtgaaggccgagggtg	9	13	4	1			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr15:42158099C>T	ENST00000320955.6	-	39	7052	c.6825G>A	c.(6823-6825)gaG>gaA	p.E2275E	MIR4310_ENST00000582950.1_RNA	NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	2275					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		TCATCTTCACCTCCTGTGAAG	0.667																																					p.E2240E		Atlas-SNP	.											.	SPTBN5	171	.	0			c.G6720A						.						13	17	16					15																	42158099		2046	4170	6216	SO:0001819	synonymous_variant	51332	exon39			CTTCACCTCCTGT	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"beta V spectrin"	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.6825G>A	chr15.hg19:g.42158099C>T		61.0	0.0		70.0	20.0	NM_016642		Silent	SNP	ENST00000320955.6	hg19																																																																																				.	.		0.667	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642		T	42158099	C	T	42158099	2	4	265	1	0	0	0	0	0	0	0	1	15137	680	24	3		3	SPTBN5	15	42158099	Silent	SNP	C	TCGA-FV-A3I1-01A-11D-A22F-10	12759134	42158099	60373293	56	38947										
HDC	3067	hgsc.bcm.edu	37	chr15	50534990	50534990	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	ggagatgaggttcccaacccGagggctgggttgggaagtac	17	8	0	2			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr15:50534990G>A	ENST00000267845.3	-	12	1858	c.1456C>T	c.(1456-1458)Cgg>Tgg	p.R486W	RN7SL494P_ENST00000461517.2_RNA|HDC_ENST00000543581.1_Missense_Mutation_p.R453W	NM_002112.3	NP_002103.2	Q9UBI9	HDC_HUMAN	histidine decarboxylase	0					respiratory tube development (GO:0030323)	membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		all_lung(180;0.0138)		all cancers(107;1.12e-06)|GBM - Glioblastoma multiforme(94;9.95e-05)		TTCCCAACCCGAGGGCTGGGT	0.567																																					p.R486W	GBM(95;1627 1936 6910 9570)	Atlas-SNP	.											.	HDC	86	.	0			c.C1456T						.						42	47	45					15																	50534990		2196	4295	6491	SO:0001583	missense	3067	exon12			CAACCCGAGGGCT		CCDS10134.1	15q21.2	2013-09-20			ENSG00000140287	ENSG00000140287	4.1.1.22		4855	protein-coding gene	gene with protein product		142704				1487235	Standard	NM_002112		Approved		uc001zxz.3	P19113	OTTHUMG00000131644	ENST00000267845.3:c.1456C>T	chr15.hg19:g.50534990G>A	ENSP00000267845:p.Arg486Trp	69.0	0.0		60.0	17.0	NM_002112		Missense_Mutation	SNP	ENST00000267845.3	hg19	CCDS10134.1	.	.	.	.	.	.	.	.	.	.	G	9.894	1.204922	0.22205	.	.	ENSG00000140287	ENST00000267845;ENST00000543581	T;T	0.09723	3.05;2.95	5.95	2.89	0.33648	.	0.851923	0.10338	N	0.686708	T	0.08626	0.0214	L	0.34521	1.04	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.31138	-0.9954	10	0.66056	D	0.02	-0.653	4.7158	0.12894	0.0822:0.2438:0.549:0.125	.	453;486	B7ZM01;P19113	.;DCHS_HUMAN	W	486;453	ENSP00000267845:R486W;ENSP00000440252:R453W	ENSP00000267845:R486W	R	-	1	2	HDC	48322282	0.446000	0.25665	0.029000	0.17559	0.246000	0.25737	1.871000	0.39539	0.844000	0.35094	0.563000	0.77884	CGG	.	.		0.567	HDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254540.1			A	50534990	G	A	50534990	3	1	265	1	0	0	0	0	1	0	0	0	7024	1057	37	1	536	1	HDC	15	50534990	Missense_Mutation	SNP	G	TCGA-FV-A3I1-01A-11D-A22F-10	8376891	50534990	51996402	57	38948										
TP53	7157	hgsc.bcm.edu	37	chr17	7578271	7578271	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	ttccttccactcggataagaTgctgaggaggggccagacct	12	11	0	3			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr17:7578271T>C	ENST00000269305.4	-	6	767	c.578A>G	c.(577-579)cAt>cGt	p.H193R	TP53_ENST00000445888.2_Missense_Mutation_p.H193R|TP53_ENST00000574684.1_Intron|TP53_ENST00000359597.4_Missense_Mutation_p.H193R|TP53_ENST00000413465.2_Missense_Mutation_p.H193R|TP53_ENST00000420246.2_Missense_Mutation_p.H193R|TP53_ENST00000455263.2_Missense_Mutation_p.H193R	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	193	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		H -> D (in sporadic cancers; somatic mutation).|H -> L (in sporadic cancers; somatic mutation).|H -> N (in sporadic cancers; somatic mutation).|H -> P (in sporadic cancers; somatic mutation).|H -> Q (in sporadic cancers; somatic mutation).|H -> R (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7887414}.|H -> Y (in sporadic cancers; somatic mutation).|QH -> HN (in a sporadic cancer; somatic mutation).|QH -> HY (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.H193R(80)|p.H193L(42)|p.H193P(18)|p.0?(8)|p.?(6)|p.H61R(4)|p.H100R(4)|p.H100L(4)|p.H61L(4)|p.A189_V197delAPPQHLIRV(4)|p.P191_E198>Q(3)|p.H193fs*16(3)|p.P191fs*53(2)|p.H61P(2)|p.H100P(2)|p.A189fs*53(1)|p.P191fs*6(1)|p.H193_I195delHLI(1)|p.P59_E66>Q(1)|p.P191fs*15(1)|p.P98_E105>Q(1)|p.H193_I195>AP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TCGGATAAGATGCTGAGGAGG	0.562		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.H193R	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,carcinoma,0,1	TP53	33396	.	193	Substitution - Missense(160)|Whole gene deletion(8)|Complex - deletion inframe(6)|Unknown(6)|Deletion - In frame(5)|Deletion - Frameshift(4)|Insertion - Frameshift(3)|Complex - frameshift(1)	lung(36)|upper_aerodigestive_tract(26)|ovary(20)|breast(18)|oesophagus(14)|haematopoietic_and_lymphoid_tissue(12)|endometrium(12)|biliary_tract(10)|liver(9)|stomach(7)|central_nervous_system(6)|large_intestine(6)|urinary_tract(5)|skin(5)|bone(4)|pancreas(2)|prostate(1)	c.A578G	GRCh37	CM083194|CM951225	TP53	M		.						97	87	90					17																	7578271		2203	4300	6503	SO:0001583	missense	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	ATAAGATGCTGAG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.578A>G	chr17.hg19:g.7578271T>C	ENSP00000269305:p.His193Arg	121.0	1.0		66.0	32.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	14.03	2.413611	0.42817	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99850	-7.16;-7.16;-7.16;-7.16;-7.16;-7.16;-7.16;-7.16	5.41	4.33	0.51752	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99825	0.9922	M	0.92738	3.34	0.58432	D	0.999992	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D	0.97536	1.0083	10	0.72032	D	0.01	-29.0766	9.707	0.40222	0.0:0.0827:0.0:0.9173	.	154;193;193;100;193;193;193	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	R	193;193;193;193;193;193;182;100;61;100;61	ENSP00000410739:H193R;ENSP00000352610:H193R;ENSP00000269305:H193R;ENSP00000398846:H193R;ENSP00000391127:H193R;ENSP00000391478:H193R;ENSP00000425104:H61R;ENSP00000423862:H100R	ENSP00000269305:H193R	H	-	2	0	TP53	7518996	1.000000	0.71417	0.814000	0.32528	0.023000	0.10783	7.996000	0.88334	1.001000	0.39076	-0.256000	0.11100	CAT	.	.		0.562	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7578271	T	C	7578271	3	2	265	1	0	0	0	0	1	0	0	0	16396	1464	51	2	716	2	TP53	17	7578271	Missense_Mutation	SNP	T	TCGA-FV-A3I1-01A-11D-A22F-10		7578271	73616939	58	38949										
ZNF559	84527	hgsc.bcm.edu	37	chr19	9453375	9453375	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	gactgtcaacagtgtgggaaAgccttcattcgatcctcatt	9	10	3	0			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr19:9453375A>C	ENST00000393883.2	+	6	1896	c.1248A>C	c.(1246-1248)aaA>aaC	p.K416N	ZNF559_ENST00000538743.1_Missense_Mutation_p.K336N|ZNF177_ENST00000446085.4_Intron|ZNF177_ENST00000602738.1_Intron|ZNF559_ENST00000603380.1_Missense_Mutation_p.K416N|ZNF177_ENST00000602856.1_Intron|CTC-325H20.2_ENST00000592371.1_lincRNA|ZNF177_ENST00000541595.2_Intron|ZNF559_ENST00000586255.1_Intron|ZNF559_ENST00000317221.7_3'UTR|ZNF177_ENST00000605471.1_Intron|ZNF559_ENST00000587557.1_Missense_Mutation_p.K480N	NM_001202412.1	NP_001189341.1	Q9BR84	ZN559_HUMAN	zinc finger protein 559	416					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|large_intestine(7)|lung(15)|ovary(1)|urinary_tract(1)	26						AGTGTGGGAAAGCCTTCATTC	0.408																																					p.K480N		Atlas-SNP	.											.	ZNF559	77	.	0			c.A1440C						.						86	69	74					19																	9453375		2203	4300	6503	SO:0001583	missense	84527	exon6			TGGGAAAGCCTTC	AL389937	CCDS12211.1, CCDS59349.1, CCDS62531.1, CCDS62532.1	19p13.2	2013-09-20			ENSG00000188321	ENSG00000188321		"Zinc fingers, C2H2-type", "-"	28197	protein-coding gene	gene with protein product						12477932	Standard	NM_001202406		Approved	MGC13105	uc002mle.4	Q9BR84	OTTHUMG00000179942	ENST00000393883.2:c.1248A>C	chr19.hg19:g.9453375A>C	ENSP00000377461:p.Lys416Asn	144.0	0.0		87.0	47.0	NM_001202406	K7EMG6	Missense_Mutation	SNP	ENST00000393883.2	hg19	CCDS12211.1	.	.	.	.	.	.	.	.	.	.	A	15.88	2.962572	0.53400	.	.	ENSG00000188321	ENST00000317221;ENST00000538743;ENST00000393883	T;T	0.27890	1.64;1.64	2.22	2.22	0.28083	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.55449	0.1921	M	0.86805	2.84	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.995;0.999;0.995	T	0.59731	-0.7399	9	0.72032	D	0.01	.	8.3425	0.32252	1.0:0.0:0.0:0.0	.	416;416;336	B3KPL8;Q9BR84;B4DP29	.;ZN559_HUMAN;.	N	416;336;416	ENSP00000442832:K336N;ENSP00000377461:K416N	ENSP00000325393:K416N	K	+	3	2	ZNF559	9314375	0.012000	0.17670	0.956000	0.39512	0.177000	0.22998	0.111000	0.15458	1.272000	0.44329	0.260000	0.18958	AAA	.	.		0.408	ZNF559-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449021.1	NM_032497		C	9453375	A	C	9453375	3	2	265	1	0	0	0	0	1	0	0	0	18005	69	3	5	1262	5	ZNF559	19	9453375	Missense_Mutation	SNP	A	TCGA-FV-A3I1-01A-11D-A22F-10		9453375	49675608	59	38950										
LHB	3972	hgsc.bcm.edu	37	chr19	49519808	49519808	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	gccccaggcagctcaccatgGtggggcagtagccggcacag	15	14	1	0			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr19:49519808G>T	ENST00000221421.2	-	2	178	c.179C>A	c.(178-180)aCc>aAc	p.T60N	CTB-60B18.10_ENST00000600007.1_lincRNA	NM_000894.2	NP_000885.1	P01229	LSHB_HUMAN	luteinizing hormone beta polypeptide	60					cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|male gonad development (GO:0008584)|peptide hormone processing (GO:0016486)|progesterone biosynthetic process (GO:0006701)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)			cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	8		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)		GCTCACCATGGTGGGGCAGTA	0.662																																					p.T60N		Atlas-SNP	.											.	LHB	20	.	0			c.C179A						.						48	40	43					19																	49519808		2193	4263	6456	SO:0001583	missense	3972	exon2			ACCATGGTGGGGC		CCDS12748.1	19q13.3	2013-02-26				ENSG00000104826		"Endogenous ligands"	6584	protein-coding gene	gene with protein product	"lutropin, beta chain", "interstitial cell stimulating hormone, beta chain", "luteinizing hormone beta subunit"	152780				1191677	Standard	NM_000894		Approved	LSH-B, CGB4, hLHB	uc002plt.3	P01229		ENST00000221421.2:c.179C>A	chr19.hg19:g.49519808G>T	ENSP00000221421:p.Thr60Asn	83.0	0.0		86.0	43.0	NM_000894	Q9UDI0	Missense_Mutation	SNP	ENST00000221421.2	hg19	CCDS12748.1	.	.	.	.	.	.	.	.	.	.	G	14.56	2.573017	0.45798	.	.	ENSG00000104826	ENST00000221421;ENST00000391870	D	0.92752	-3.1	4.03	2.97	0.34412	Cystine knot (1);Gonadotropin, beta subunit, conserved site (1);	0.103789	0.64402	D	0.000006	D	0.94430	0.8208	M	0.67397	2.05	0.36147	D	0.847169	D	0.71674	0.998	D	0.91635	0.999	D	0.95358	0.8453	10	0.87932	D	0	-18.2195	9.8631	0.41127	0.0:0.7858:0.2142:0.0	.	60	P01229	LSHB_HUMAN	N	60;76	ENSP00000221421:T60N	ENSP00000221421:T60N	T	-	2	0	LHB	54211620	1.000000	0.71417	1.000000	0.80357	0.617000	0.37484	1.932000	0.40143	1.035000	0.39972	-0.539000	0.04255	ACC	.	.		0.662	LHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466246.1	NM_000894		T	49519808	G	T	49519808	3	4	265	1	0	0	0	0	1	0	0	0	8770	1261	44	3	254	3	LHB	19	49519808	Missense_Mutation	SNP	G	TCGA-FV-A3I1-01A-11D-A22F-10	40066433	49519808	9609175	60	38951										
CACNG7	59284	hgsc.bcm.edu	37	chr19	54417766	54417766	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	ccccccaggtcgggagaaagGtcgctgtgtggcctcagaat	14	12	1	2			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr19:54417766G>T	ENST00000391767.1	+	3	421	c.209G>T	c.(208-210)gGt>gTt	p.G70V	CACNG7_ENST00000391766.1_Missense_Mutation_p.G70V|CACNG7_ENST00000222212.2_Missense_Mutation_p.G70V|CACNG7_ENST00000468076.1_Intron			P62955	CCG7_HUMAN	calcium channel, voltage-dependent, gamma subunit 7	70					calcium ion transport (GO:0006816)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0711)		CGGGAGAAAGGTCGCTGTGTG	0.557																																					p.G70V		Atlas-SNP	.											CACNG7,caecum,carcinoma,0,2	CACNG7	58	.	0			c.G209T						.						68	60	63					19																	54417766		2203	4300	6503	SO:0001583	missense	59284	exon2			AGAAAGGTCGCTG	AF288387	CCDS12868.1	19q13.4	2008-05-02			ENSG00000105605	ENSG00000105605		"Calcium channel subunits"	13626	protein-coding gene	gene with protein product		606899				11170751	Standard	NM_031896		Approved		uc002qcr.2	P62955	OTTHUMG00000064852	ENST00000391767.1:c.209G>T	chr19.hg19:g.54417766G>T	ENSP00000375647:p.Gly70Val	140.0	0.0		127.0	31.0	NM_031896	Q52LL8|Q8VBX3|Q8WXS6|Q9BXT1	Missense_Mutation	SNP	ENST00000391767.1	hg19	CCDS12868.1	.	.	.	.	.	.	.	.	.	.	G	18.74	3.688098	0.68271	.	.	ENSG00000105605	ENST00000391767;ENST00000222212;ENST00000391766	D;D;D	0.88431	-2.38;-2.38;-2.38	3.14	3.14	0.36123	.	0.000000	0.85682	D	0.000000	D	0.93158	0.7821	M	0.82193	2.58	0.80722	D	1	D	0.61697	0.99	D	0.63033	0.91	D	0.92969	0.6396	10	0.46703	T	0.11	-8.4437	12.5577	0.56263	0.0:0.0:1.0:0.0	.	70	P62955	CCG7_HUMAN	V	70	ENSP00000375647:G70V;ENSP00000222212:G70V;ENSP00000375646:G70V	ENSP00000222212:G70V	G	+	2	0	CACNG7	59109578	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.208000	0.89748	2.084000	0.62774	0.561000	0.74099	GGT	.	.		0.557	CACNG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139240.2			T	54417766	G	T	54417766	3	4	265	1	0	0	0	0	1	0	0	0	2564	1261	44	3	215	3	CACNG7	19	54417766	Missense_Mutation	SNP	G	TCGA-FV-A3I1-01A-11D-A22F-10	4897958	54417766	4711217	61	38952										
NOP56	10528	hgsc.bcm.edu	37	chr20	2635458	2635458	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	tctgtcagcttgtaaagcacAgctggggctgggacacagct	13	10	2	0			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chr20:2635458A>G	ENST00000329276.5	+	5	950	c.434A>G	c.(433-435)cAg>cGg	p.Q145R	SNORD110_ENST00000408189.1_RNA|MIR1292_ENST00000408135.1_RNA|SNORD56_ENST00000413522.1_RNA|SNORD57_ENST00000448188.1_RNA|SNORD86_ENST00000391196.1_RNA|SNORA51_ENST00000606420.1_RNA	NM_006392.3	NP_006383.2	O00567	NOP56_HUMAN	NOP56 ribonucleoprotein	145					cell death (GO:0008219)|rRNA processing (GO:0006364)	box C/D snoRNP complex (GO:0031428)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|snoRNA binding (GO:0030515)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25						TGTAAAGCACAGCTGGGGCTG	0.522																																					p.Q145R		Atlas-SNP	.											.	NOP56	73	.	0			c.A434G						.						167	164	165					20																	2635458		2203	4300	6503	SO:0001583	missense	10528	exon5			AAGCACAGCTGGG	Y12065	CCDS13030.1	20p13	2012-12-10	2012-12-10	2009-01-13	ENSG00000101361	ENSG00000101361			15911	protein-coding gene	gene with protein product	"spinocerebellar ataxia 36"	614154	"nucleolar protein 5A (56kD with KKE/D repeat)", "nucleolar protein 5A (56kDa with KKE/D repeat)", "NOP56 ribonucleoprotein homolog (yeast)"	NOL5A		9372940, 21683323	Standard	NR_027700		Approved	SCA36	uc002wgh.3	O00567	OTTHUMG00000031703	ENST00000329276.5:c.434A>G	chr20.hg19:g.2635458A>G	ENSP00000370589:p.Gln145Arg	60.0	0.0		50.0	19.0	NM_006392	Q2M3T6|Q9NQ05	Missense_Mutation	SNP	ENST00000329276.5	hg19	CCDS13030.1	.	.	.	.	.	.	.	.	.	.	A	17.31	3.356329	0.61293	.	.	ENSG00000101361	ENST00000329276;ENST00000445139	T;T	0.59638	0.25;0.86	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	T	0.68668	0.3026	M	0.84433	2.695	0.80722	D	1	D	0.56035	0.974	P	0.48089	0.566	T	0.75243	-0.3386	10	0.62326	D	0.03	-26.6734	14.2555	0.66048	1.0:0.0:0.0:0.0	.	145	O00567	NOP56_HUMAN	R	145	ENSP00000370589:Q145R;ENSP00000388497:Q145R	ENSP00000370589:Q145R	Q	+	2	0	NOP56	2583458	1.000000	0.71417	0.929000	0.37066	0.001000	0.01503	9.090000	0.94144	2.245000	0.73994	0.454000	0.30748	CAG	.	.		0.522	NOP56-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077631.2	NM_006392		G	2635458	A	G	2635458	3	3	265	1	0	0	0	0	1	0	0	0	10548	188	7	2	452	2	NOP56	20	2635458	Missense_Mutation	SNP	A	TCGA-FV-A3I1-01A-11D-A22F-10		2635458	60390062	62	38953										
ZFX	7543	hgsc.bcm.edu	37	chrX	24229378	24229378	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	ctttaaacggcacgttatttCcattcacacgaaagactatc	5	11	1	1			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chrX:24229378C>A	ENST00000379177.1	+	11	2730	c.2303C>A	c.(2302-2304)tCc>tAc	p.S768Y	ZFX_ENST00000304543.5_Missense_Mutation_p.S768Y|ZFX_ENST00000540034.1_Missense_Mutation_p.S807Y|ZFX_ENST00000539115.1_Missense_Mutation_p.S539Y|ZFX_ENST00000338565.3_Missense_Mutation_p.S718Y|ZFX_ENST00000379188.3_Missense_Mutation_p.S768Y	NM_001178085.1|NM_003410.3	NP_001171556.1|NP_003401.2	P17010	ZFX_HUMAN	zinc finger protein, X-linked	768					death (GO:0016265)|fertilization (GO:0009566)|homeostasis of number of cells (GO:0048872)|multicellular organism growth (GO:0035264)|oocyte development (GO:0048599)|ovarian follicle development (GO:0001541)|parental behavior (GO:0060746)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription coactivator activity (GO:0003713)			cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(2)|lung(4)|ovary(2)|prostate(1)	24						CACGTTATTTCCATTCACACG	0.433																																					p.S768Y	Esophageal Squamous(20;306 562 7346 32868 37983)	Atlas-SNP	.											.	ZFX	61	.	0			c.C2303A						.						159	132	141					X																	24229378		2203	4300	6503	SO:0001583	missense	7543	exon10			TTATTTCCATTCA		CCDS14211.1, CCDS55390.1	Xp22.1-p21.3	2013-01-08			ENSG00000005889	ENSG00000005889		"Zinc fingers, C2H2-type"	12869	protein-coding gene	gene with protein product		314980					Standard	NM_003410		Approved	ZNF926	uc022bua.1	P17010	OTTHUMG00000021264	ENST00000379177.1:c.2303C>A	chrX.hg19:g.24229378C>A	ENSP00000368475:p.Ser768Tyr	352.0	0.0		310.0	111.0	NM_003410	B9EG97|O43668|Q8WYJ8	Missense_Mutation	SNP	ENST00000379177.1	hg19	CCDS14211.1	.	.	.	.	.	.	.	.	.	.	C	17.95	3.513648	0.64522	.	.	ENSG00000005889	ENST00000539115;ENST00000379188;ENST00000535562;ENST00000379177;ENST00000304543;ENST00000540034;ENST00000338565	T;T;T;T;T;T	0.15372	2.43;2.43;2.43;2.43;2.43;2.43	5.19	5.19	0.71726	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	D	0.000003	T	0.45756	0.1358	M	0.77406	2.37	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.97110	0.999;1.0;0.998	T	0.49184	-0.8966	10	0.72032	D	0.01	-6.9146	18.0792	0.89437	0.0:1.0:0.0:0.0	.	807;490;768	B9EG97;F5GYV7;P17010	.;.;ZFX_HUMAN	Y	539;768;490;768;768;807;718	ENSP00000438233:S539Y;ENSP00000368486:S768Y;ENSP00000368475:S768Y;ENSP00000304985:S768Y;ENSP00000441382:S807Y;ENSP00000343384:S718Y	ENSP00000304985:S768Y	S	+	2	0	ZFX	24139299	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.776000	0.85560	2.291000	0.77112	0.594000	0.82650	TCC	.	.		0.433	ZFX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056084.1	NM_003410		A	24229378	C	A	24229378	3	1	265	1	0	0	0	0	1	0	0	0	17676	855	30	3	2388	3	ZFX	23	24229378	Missense_Mutation	SNP	C	TCGA-FV-A3I1-01A-11D-A22F-10		24229378	131041182	63	38954										
FAM47A	158724	hgsc.bcm.edu	37	chrX	34149524	34149524	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	aagggtatttaccaggctctGtgggttcgtcagttgtcttc	12	8	3	0			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chrX:34149524G>C	ENST00000346193.3	-	1	923	c.872C>G	c.(871-873)aCa>aGa	p.T291R		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	291										NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	97						ACCAGGCTCTGTGGGTTCGTC	0.572																																					p.T291R		Atlas-SNP	.											.	FAM47A	249	.	0			c.C872G						.						24	26	25					X																	34149524		2202	4300	6502	SO:0001583	missense	158724	exon1			GGCTCTGTGGGTT	BC026171	CCDS43926.1	Xp21.1	2004-08-09			ENSG00000185448	ENSG00000185448			29962	protein-coding gene	gene with protein product	"similar to hypothetical protein FLJ35782"					12477932	Standard	NM_203408		Approved	MGC27003	uc004ddg.3	Q5JRC9	OTTHUMG00000021339	ENST00000346193.3:c.872C>G	chrX.hg19:g.34149524G>C	ENSP00000345029:p.Thr291Arg	156.0	0.0		136.0	43.0	NM_203408	A8K8I9|Q8TAA0	Missense_Mutation	SNP	ENST00000346193.3	hg19	CCDS43926.1	.	.	.	.	.	.	.	.	.	.	g	1.507	-0.550591	0.03996	.	.	ENSG00000185448	ENST00000346193	T	0.19105	2.17	0.13	0.13	0.14746	.	.	.	.	.	T	0.21186	0.0510	L	0.38175	1.15	0.09310	N	0.999999	P	0.47106	0.89	P	0.52554	0.702	T	0.21381	-1.0247	8	0.18276	T	0.48	.	.	.	.	.	291	Q5JRC9	FA47A_HUMAN	R	291	ENSP00000345029:T291R	ENSP00000345029:T291R	T	-	2	0	FAM47A	34059445	0.848000	0.29623	0.032000	0.17829	0.032000	0.12392	0.110000	0.15437	0.171000	0.19730	0.173000	0.16961	ACA	.	.		0.572	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408		C	34149524	G	C	34149524	3	2	265	1	0	0	0	0	1	0	0	0	5577	1377	48	4	1507	4	FAM47A	23	34149524	Missense_Mutation	SNP	G	TCGA-FV-A3I1-01A-11D-A22F-10	9920146	34149524	121121036	64	38955										
MAOB	4129	hgsc.bcm.edu	37	chrX	43655030	43655030	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	ctccacaaggacattttctcTtgtctggtcaatgtagatca	7	10	4	1			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chrX:43655030T>A	ENST00000378069.4	-	7	871	c.724A>T	c.(724-726)Aga>Tga	p.R242*	MAOB_ENST00000487544.1_5'Flank|MAOB_ENST00000536181.1_Nonsense_Mutation_p.R226*|MAOB_ENST00000538942.1_Nonsense_Mutation_p.R226*	NM_000898.4	NP_000889.3	P27338	AOFB_HUMAN	monoamine oxidase B	242					negative regulation of serotonin secretion (GO:0014063)|positive regulation of dopamine metabolic process (GO:0045964)|response to aluminum ion (GO:0010044)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|primary amine oxidase activity (GO:0008131)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(2)|skin(5)	21					Amantadine(DB00915)|Amphetamine(DB00182)|Dopamine(DB00988)|Ephedra(DB01363)|Flavin adenine dinucleotide(DB03147)|Furazolidone(DB00614)|Isocarboxazid(DB01247)|Linezolid(DB00601)|Methamphetamine(DB01577)|Moclobemide(DB01171)|Nandrolone decanoate(DB08804)|Nicotine(DB00184)|Pargyline(DB01626)|Phenelzine(DB00780)|Phentermine(DB00191)|Procaine(DB00721)|Rasagiline(DB01367)|Selegiline(DB01037)|Sertraline(DB01104)|Tranylcypromine(DB00752)|Zonisamide(DB00909)	ACATTTTCTCTTGTCTGGTCA	0.448																																					p.R242X		Atlas-SNP	.											.	MAOB	52	.	0			c.A724T						.						169	141	151					X																	43655030		2203	4300	6503	SO:0001587	stop_gained	4129	exon7			TTTCTCTTGTCTG		CCDS14261.1	Xp11.4-p11.3	2008-02-05			ENSG00000069535	ENSG00000069535	1.4.3.4		6834	protein-coding gene	gene with protein product		309860					Standard	NM_000898		Approved		uc004dfz.4	P27338	OTTHUMG00000021388	ENST00000378069.4:c.724A>T	chrX.hg19:g.43655030T>A	ENSP00000367309:p.Arg242*	121.0	0.0		116.0	44.0	NM_000898	B2R6R3|B7Z5H3|D3DWC3|Q7Z6S2	Nonsense_Mutation	SNP	ENST00000378069.4	hg19	CCDS14261.1	.	.	.	.	.	.	.	.	.	.	T	37	6.394621	0.97533	.	.	ENSG00000069535	ENST00000378069;ENST00000536181;ENST00000538942	.	.	.	5.29	4.39	0.52855	.	0.049371	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	-9.4189	9.8539	0.41073	0.0:0.8363:0.0:0.1637	.	.	.	.	X	242;226;226	.	ENSP00000367309:R242X	R	-	1	2	MAOB	43539974	0.880000	0.30214	0.997000	0.53966	0.771000	0.43674	1.737000	0.38197	1.113000	0.41760	-0.383000	0.06682	AGA	.	.		0.448	MAOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056303.1	NM_000898		A	43655030	T	A	43655030	4	1	265	1	0	0	0	0	0	1	0	0	9235	1617	56	4	874	4	MAOB	23	43655030	Nonsense_Mutation	SNP	T	TCGA-FV-A3I1-01A-11D-A22F-10	9505506	43655030	111615530	65	38956										
MTMR8	55613	hgsc.bcm.edu	37	chrX	63548663	63548663	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	agaacttactgaatgttgtaGggcacagtactaggattgag	12	5	0	3			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chrX:63548663G>T	ENST00000374852.3	-	12	1537	c.1470C>A	c.(1468-1470)ccC>ccA	p.P490P	MTMR8_ENST00000453546.1_Intron|MTMR8_ENST00000478487.1_5'Flank	NM_017677.3	NP_060147.2	Q96EF0	MTMR8_HUMAN	myotubularin related protein 8	490	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.					nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)	p.0?(1)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|skin(3)	37						GAATGTTGTAGGGCACAGTAC	0.458																																					p.P490P		Atlas-SNP	.											.	MTMR8	178	.	1	Whole gene deletion(1)	ovary(1)	c.C1470A						.						143	123	130					X																	63548663		2203	4300	6503	SO:0001819	synonymous_variant	55613	exon12			GTTGTAGGGCACA	AK000133	CCDS14379.1	Xq11.2-q12	2013-01-11			ENSG00000102043	ENSG00000102043		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	16825	protein-coding gene	gene with protein product						11275328	Standard	NM_017677		Approved	FLJ20126	uc004dvs.3	Q96EF0	OTTHUMG00000021707	ENST00000374852.3:c.1470C>A	chrX.hg19:g.63548663G>T		26.0	0.0		35.0	12.0	NM_017677	Q5JT99|Q9NXP6	Silent	SNP	ENST00000374852.3	hg19	CCDS14379.1	.	.	.	.	.	.	.	.	.	.	G	7.410	0.634610	0.14322	.	.	ENSG00000102043	ENST00000442913	.	.	.	2.93	0.856	0.19019	.	.	.	.	.	T	0.43144	0.1234	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.25847	-1.0120	4	.	.	.	.	2.3034	0.04168	0.4169:0.0:0.3475:0.2357	.	.	.	.	I	294	.	.	L	-	1	2	MTMR8	63465388	1.000000	0.71417	0.987000	0.45799	0.982000	0.71751	0.850000	0.27737	0.427000	0.26145	0.506000	0.49869	CTA	.	.		0.458	MTMR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056949.2	NM_017677		T	63548663	G	T	63548663	2	4	265	1	0	0	0	0	0	0	0	1	9958	987	35	3		3	MTMR8	23	63548663	Silent	SNP	G	TCGA-FV-A3I1-01A-11D-A22F-10	19893633	63548663	91721897	66	38957										
FAM127C	441518	hgsc.bcm.edu	37	chrX	134156305	134156305	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0303030303030303	2	1	0.750465549348231	2.25139664804469	0.450279329608939	1	1	0	tgaggaacgtcaccttcaggGcgtcgttggagaacgtgttc	14	9	2	2			TCGA-FV-A3I1-01A-11D-A22F-10	TCGA-FV-A3I1-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	992d9566-b1da-421a-bf36-d23382b115fa	5cce4752-30c6-4bc7-8c28-90617e8dcd3b	g.chrX:134156305G>A	ENST00000391440.1	-	1	254	c.185C>T	c.(184-186)gCc>gTc	p.A62V		NM_001078173.1	NP_001071641.1	Q17RB0	F127C_HUMAN	family with sequence similarity 127, member C	62										breast(1)|endometrium(2)|large_intestine(1)|lung(2)	6	Acute lymphoblastic leukemia(192;0.000127)					CACCTTCAGGGCGTCGTTGGA	0.602																																					p.A62V		Atlas-SNP	.											.	FAM127C	27	.	0			c.C185T						.						63	68	67					X																	134156305		2097	4207	6304	SO:0001583	missense	441518	exon1			TTCAGGGCGTCGT	BC048268	CCDS43996.1	Xq26.3	2014-05-16			ENSG00000212747	ENSG00000212747			33156	protein-coding gene	gene with protein product						9403077, 15716091	Standard	NM_001078173		Approved	MAR8B, CXX1c	uc004eyc.1	Q17RB0	OTTHUMG00000022464	ENST00000391440.1:c.185C>T	chrX.hg19:g.134156305G>A	ENSP00000375268:p.Ala62Val	137.0	0.0		160.0	54.0	NM_001078173		Missense_Mutation	SNP	ENST00000391440.1	hg19	CCDS43996.1	.	.	.	.	.	.	.	.	.	.	g	14.44	2.535163	0.45176	.	.	ENSG00000212747	ENST00000391440	T	0.30448	1.53	2.35	1.38	0.22167	.	1.095140	0.07417	U	0.893459	T	0.30792	0.0776	M	0.66939	2.045	0.21627	N	0.999616	B	0.31949	0.348	B	0.32980	0.156	T	0.30475	-0.9977	10	0.34782	T	0.22	.	5.3275	0.15915	0.0:0.0:0.6638:0.3362	.	62	Q17RB0	F127C_HUMAN	V	62	ENSP00000375268:A62V	ENSP00000375268:A62V	A	-	2	0	FAM127C	133983971	0.747000	0.28283	0.967000	0.41034	0.955000	0.61496	0.112000	0.15479	0.360000	0.24265	0.436000	0.28706	GCC	.	.		0.602	FAM127C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058389.2	NM_001078173		A	134156305	G	A	134156305	3	1	265	1	0	0	0	0	1	0	0	0	5438	1203	42	3	160	3	FAM127C	23	134156305	Missense_Mutation	SNP	G	TCGA-FV-A3I1-01A-11D-A22F-10	70607642	134156305	21114255	67	38958										
PHTF1	10745	hgsc.bcm.edu	37	chr1	114255975	114255975	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	tctaatctctggtcgacattGtctcctcttaatgataggat	7	9	4	1	rs61730007	byFrequency	TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr1:114255975G>A	ENST00000369604.1	-	8	1192	c.709C>T	c.(709-711)Caa>Taa	p.Q237*	PHTF1_ENST00000393357.2_Nonsense_Mutation_p.Q237*|PHTF1_ENST00000447664.2_Intron|PHTF1_ENST00000369596.2_Nonsense_Mutation_p.Q184*|PHTF1_ENST00000369600.1_Nonsense_Mutation_p.Q184*|PHTF1_ENST00000369598.1_Nonsense_Mutation_p.Q192*|PHTF1_ENST00000474926.1_5'UTR|PHTF1_ENST00000357783.2_Nonsense_Mutation_p.Q237*			Q9UMS5	PHTF1_HUMAN	putative homeodomain transcription factor 1	237					transcription, DNA-templated (GO:0006351)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GGTCGACATTGTCTCCTCTTA	0.343																																					p.Q237X		Atlas-SNP	.											.	PHTF1	69	.	0			c.C709T						.						146	143	144					1																	114255975		2203	4300	6503	SO:0001587	stop_gained	10745	exon7			GACATTGTCTCCT	AJ011863	CCDS861.1	1p13-p11	2008-07-18			ENSG00000116793	ENSG00000116793			8939	protein-coding gene	gene with protein product		604950		PHTF		10395808	Standard	NM_006608		Approved		uc009wgp.1	Q9UMS5	OTTHUMG00000011800	ENST00000369604.1:c.709C>T	chr1.hg19:g.114255975G>A	ENSP00000358617:p.Gln237*	175.0	0.0		216.0	72.0	NM_006608	Q5VWP7|Q5VWP8|Q9BUP2|Q9H1X8	Nonsense_Mutation	SNP	ENST00000369604.1	hg19	CCDS861.1	.	.	.	.	.	.	.	.	.	.	G	41	8.969095	0.99019	.	.	ENSG00000116793	ENST00000369597;ENST00000393357;ENST00000369596;ENST00000369598;ENST00000369600;ENST00000369604;ENST00000357783	.	.	.	5.55	4.62	0.57501	.	0.524935	0.20981	N	0.082206	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	0.10377	T	0.69	-4.9277	10.4484	0.44507	0.0:0.1453:0.7037:0.1509	.	.	.	.	X	192;237;184;192;184;237;237	.	ENSP00000350428:Q237X	Q	-	1	0	PHTF1	114057498	1.000000	0.71417	0.885000	0.34714	0.601000	0.36947	3.570000	0.53834	1.314000	0.45095	0.467000	0.42956	CAA	.	G|0.991;T|0.009		0.343	PHTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032666.1	NM_006608		A	114255975	G	A	114255975	4	1	266	1	0	0	0	0	0	1	0	0	11871	1386	48	3	1627	3	PHTF1	1	114255975	Nonsense_Mutation	SNP	G	TCGA-FV-A3R2-01A-11D-A22F-10		114255975	134994646	1	38959										
KIF14	9928	hgsc.bcm.edu	37	chr1	200587131	200587131	+	Frame_Shift_Del	DEL	G	G	-													0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	tttgatatccaacttgctctGagtaggtttcgttgtcaagt							TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr1:200587131delG	ENST00000367350.4	-	2	1159	c.721delC	c.(721-723)cagfs	p.Q241fs		NM_014875.2	NP_055690.1	Q15058	KIF14_HUMAN	kinesin family member 14	241	Required for PRC1-binding.				ATP catabolic process (GO:0006200)|cytoskeleton-dependent intracellular transport (GO:0030705)|establishment of protein localization (GO:0045184)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of integrin activation (GO:0033624)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of Rap protein signal transduction (GO:0032487)|substrate adhesion-dependent cell spreading (GO:0034446)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|PDZ domain binding (GO:0030165)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(8)|kidney(8)|large_intestine(15)|lung(13)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	61						AACTTGCTCTGAGTAGGTTTC	0.383																																					p.Q241fs		Atlas-Indel,Pindel	.											.	KIF14	156	.	0			c.722delA						.						168	172	171					1																	200587131		2203	4300	6503	SO:0001589	frameshift_variant	9928	exon2			.	D26361	CCDS30963.1	1q32.1	2008-03-03			ENSG00000118193	ENSG00000118193		"Kinesins"	19181	protein-coding gene	gene with protein product		611279				7584044	Standard	NM_014875		Approved	KIAA0042	uc010ppk.1	Q15058	OTTHUMG00000035723	ENST00000367350.4:c.721delC	chr1.hg19:g.200587131delG	ENSP00000356319:p.Gln241fs	156.0	0.0		135.0	56.0	NM_014875	Q14CI8|Q4G0A5|Q5T1W3	Frame_Shift_Del	DEL	ENST00000367350.4	hg19	CCDS30963.1																																																																																			.	.		0.383	KIF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086878.1	NM_014875		-	200587131	G	-	200587131	7	5	266	1	0	1	0	1	0	0	0	0	8285	1299	45	0	4341	0	KIF14	1	200587131	Frame_Shift_Del	DEL	G	TCGA-FV-A3R2-01A-11D-A22F-10	86331156	200587131	48663490	2	38960										
LGR6	59352	hgsc.bcm.edu	37	chr1	202249945	202249945	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	cgcatccagcatctggggacCcacagcttcgaggggctgca	13	14	1	0			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr1:202249945C>A	ENST00000367278.3	+	6	770	c.681C>A	c.(679-681)acC>acA	p.T227T	LGR6_ENST00000439764.2_Intron|LGR6_ENST00000255432.7_Silent_p.T175T|LGR6_ENST00000308543.3_3'UTR	NM_001017403.1	NP_001017403.1	Q9HBX8	LGR6_HUMAN	leucine-rich repeat containing G protein-coupled receptor 6	227					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of Wnt signaling pathway (GO:0030177)|Wnt signaling pathway (GO:0016055)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	36						ATCTGGGGACCCACAGCTTCG	0.562																																					p.T227T		Atlas-SNP	.											.	LGR6	102	.	0			c.C681A						.						125	111	116					1																	202249945		2203	4300	6503	SO:0001819	synonymous_variant	59352	exon6			GGGGACCCACAGC	AF190501	CCDS1424.1, CCDS30971.1, CCDS30972.1	1q32.1	2012-08-21	2011-01-25		ENSG00000133067	ENSG00000133067		"GPCR / Class A : Orphans"	19719	protein-coding gene	gene with protein product		606653	"leucine-rich repeat-containing G protein-coupled receptor 6"			10935549	Standard	XM_005245404		Approved	FLJ14471	uc001gxu.3	Q9HBX8	OTTHUMG00000041383	ENST00000367278.3:c.681C>A	chr1.hg19:g.202249945C>A		44.0	0.0		73.0	26.0	NM_001017403	Q5T509|Q5T512|Q6UY15|Q86VU0|Q96K69|Q9BYD7	Silent	SNP	ENST00000367278.3	hg19	CCDS30971.1																																																																																			.	.		0.562	LGR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099143.1	NM_021636		A	202249945	C	A	202249945	2	1	266	1	0	0	0	0	0	0	0	1	8767	610	22	3		3	LGR6	1	202249945	Silent	SNP	C	TCGA-FV-A3R2-01A-11D-A22F-10	1662814	202249945	47000676	3	38961										
OR2T11	127077	hgsc.bcm.edu	37	chr1	248790035	248790035	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	gacacttcttgcggttcatcAggactgggtatctcagaggg	13	9	4	1			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr1:248790035A>G	ENST00000330803.2	-	1	456	c.395T>C	c.(394-396)cTg>cCg	p.L132P		NM_001001964.1	NP_001001964.1	Q8NH01	O2T11_HUMAN	olfactory receptor, family 2, subfamily T, member 11 (gene/pseudogene)	132						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|large_intestine(5)|lung(20)|skin(2)	28	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GCGGTTCATCAGGACTGGGTA	0.537																																					p.L132P		Atlas-SNP	.											.	OR2T11	64	.	0			c.T395C						.						50	57	55					1																	248790035		2050	4232	6282	SO:0001583	missense	127077	exon1			TTCATCAGGACTG	BK004476	CCDS31122.1	1q44	2013-10-10	2013-10-10		ENSG00000183130	ENSG00000183130		"GPCR / Class A : Olfactory receptors"	19574	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily T, member 11"				Standard	NM_001001964		Approved	OR2T11Q	uc001ier.1	Q8NH01	OTTHUMG00000040384	ENST00000330803.2:c.395T>C	chr1.hg19:g.248790035A>G	ENSP00000328934:p.Leu132Pro	86.0	0.0		88.0	40.0	NM_001001964	Q6IEY6	Missense_Mutation	SNP	ENST00000330803.2	hg19	CCDS31122.1	.	.	.	.	.	.	.	.	.	.	.	15.10	2.733512	0.48939	.	.	ENSG00000183130	ENST00000330803	T	0.33654	1.4	4.38	4.38	0.52667	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35739	N	0.003008	T	0.66587	0.2804	M	0.92880	3.355	0.53005	D	0.999962	D	0.89917	1.0	D	0.72338	0.977	T	0.75701	-0.3226	10	0.87932	D	0	.	12.724	0.57159	1.0:0.0:0.0:0.0	.	132	Q8NH01	O2T11_HUMAN	P	132	ENSP00000328934:L132P	ENSP00000328934:L132P	L	-	2	0	OR2T11	246856658	0.001000	0.12720	0.445000	0.26908	0.376000	0.30014	1.352000	0.34033	1.820000	0.53075	0.533000	0.62120	CTG	.	.		0.537	OR2T11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097134.1	NM_001001964		G	248790035	A	G	248790035	3	3	266	1	0	0	0	0	1	0	0	0	11027	188	7	2	559	2	OR2T11	1	248790035	Missense_Mutation	SNP	A	TCGA-FV-A3R2-01A-11D-A22F-10	46540090	248790035	460586	4	38962										
SPTBN1	6711	hgsc.bcm.edu	37	chr2	54853192	54853192	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	tagccgtggccagggagctcGaggccgagaattaccacgac	14	12	0	1			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr2:54853192G>A	ENST00000356805.4	+	12	1746	c.1465G>A	c.(1465-1467)Gag>Aag	p.E489K	SPTBN1_ENST00000333896.5_Missense_Mutation_p.E476K	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	489					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			CAGGGAGCTCGAGGCCGAGAA	0.582																																					p.E489K		Atlas-SNP	.											.	SPTBN1	378	.	0			c.G1465A						.						104	101	102					2																	54853192		2203	4300	6503	SO:0001583	missense	6711	exon12			GAGCTCGAGGCCG		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"Pleckstrin homology (PH) domain containing"	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.1465G>A	chr2.hg19:g.54853192G>A	ENSP00000349259:p.Glu489Lys	134.0	0.0		108.0	42.0	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Missense_Mutation	SNP	ENST00000356805.4	hg19	CCDS33198.1	.	.	.	.	.	.	.	.	.	.	G	36	5.600953	0.96614	.	.	ENSG00000115306	ENST00000356805;ENST00000389980;ENST00000333896	T;T;T	0.50548	0.74;0.74;0.74	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.58694	0.2140	L	0.49699	1.58	0.80722	D	1	P;D	0.60575	0.88;0.988	B;P	0.54238	0.212;0.746	T	0.57980	-0.7717	10	0.51188	T	0.08	.	19.5969	0.95544	0.0:0.0:1.0:0.0	.	476;489	Q01082-3;Q01082	.;SPTB2_HUMAN	K	489;489;476	ENSP00000349259:E489K;ENSP00000374630:E489K;ENSP00000334156:E476K	ENSP00000334156:E476K	E	+	1	0	SPTBN1	54706696	1.000000	0.71417	0.952000	0.39060	0.885000	0.51271	9.802000	0.99131	2.634000	0.89283	0.650000	0.86243	GAG	.	.		0.582	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			A	54853192	G	A	54853192	3	1	266	1	0	0	0	0	1	0	0	0	15134	1059	37	1	1620	1	SPTBN1	2	54853192	Missense_Mutation	SNP	G	TCGA-FV-A3R2-01A-11D-A22F-10		54853192	188346181	5	38963										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141660519	141660519	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	acaactttcaccgtctacatCcagcttccaaccttcataac	2	16	3	0			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr2:141660519C>A	ENST00000389484.3	-	23	4707	c.3736G>T	c.(3736-3738)Gat>Tat	p.D1246Y		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1246	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CCGTCTACATCCAGCTTCCAA	0.378										TSP Lung(27;0.18)																											p.D1246Y	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											LRP1B,NS,malignant_melanoma,0,1	LRP1B	1315	.	0			c.G3736T						.						152	140	144					2																	141660519		2203	4300	6503	SO:0001583	missense	53353	exon23			CTACATCCAGCTT	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.3736G>T	chr2.hg19:g.141660519C>A	ENSP00000374135:p.Asp1246Tyr	120.0	1.0		116.0	46.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	18.12	3.553433	0.65425	.	.	ENSG00000168702	ENST00000389484;ENST00000544579;ENST00000434794	D;D	0.88431	-2.38;-2.38	5.44	3.62	0.41486	Epidermal growth factor-like (1);EGF-like region, conserved site (1);	0.390918	0.25189	N	0.032471	D	0.90981	0.7164	M	0.77406	2.37	0.36641	D	0.876823	P;P	0.51933	0.949;0.681	P;B	0.55871	0.786;0.235	D	0.91653	0.5336	10	0.62326	D	0.03	.	5.4998	0.16823	0.0:0.6243:0.0:0.3757	.	429;1246	Q96NT6;Q9NZR2	.;LRP1B_HUMAN	Y	1246;1184;391	ENSP00000374135:D1246Y;ENSP00000413239:D391Y	ENSP00000374135:D1246Y	D	-	1	0	LRP1B	141376989	0.601000	0.26907	0.966000	0.40874	0.845000	0.48019	1.583000	0.36579	1.428000	0.47296	0.585000	0.79938	GAT	.	.		0.378	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		A	141660519	C	A	141660519	3	1	266	1	0	0	0	0	1	0	0	0	8964	855	30	3	10339	3	LRP1B	2	141660519	Missense_Mutation	SNP	C	TCGA-FV-A3R2-01A-11D-A22F-10	86807327	141660519	101538854	6	38964										
CACNB4	785	hgsc.bcm.edu	37	chr2	152695776	152695776	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	atgctgagaactggaagacaAgcggttcctactcttccgag	11	10	1	2			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr2:152695776A>T	ENST00000539935.1	-	14	1487	c.1420T>A	c.(1420-1422)Ttg>Atg	p.L474M	CACNB4_ENST00000360283.6_Missense_Mutation_p.L441M|CACNB4_ENST00000427385.1_Missense_Mutation_p.L456M|CACNB4_ENST00000201943.5_Missense_Mutation_p.L412M|CACNB4_ENST00000534999.1_Missense_Mutation_p.L440M|CACNB4_ENST00000397327.2_Missense_Mutation_p.L427M	NM_000726.3|NM_001145798.1	NP_000717.2|NP_001139270.1	O00305	CACB4_HUMAN	calcium channel, voltage-dependent, beta 4 subunit	474					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|cAMP metabolic process (GO:0046058)|cellular calcium ion homeostasis (GO:0006874)|detection of light stimulus involved in visual perception (GO:0050908)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|membrane depolarization (GO:0051899)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|neuronal action potential propagation (GO:0019227)|Peyer's patch development (GO:0048541)|regulation of voltage-gated calcium channel activity (GO:1901385)|spleen development (GO:0048536)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)|transport (GO:0006810)	cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)	11				BRCA - Breast invasive adenocarcinoma(221;0.156)	Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	CTGGAAGACAAGCGGTTCCTA	0.463																																					p.L474M		Atlas-SNP	.											.	CACNB4	108	.	0			c.T1420A						.						113	113	113					2																	152695776		1985	4183	6168	SO:0001583	missense	785	exon14			AAGACAAGCGGTT	AF038852	CCDS46426.1, CCDS46427.1, CCDS46428.1, CCDS54409.1	2q22-q23	2009-09-04			ENSG00000182389	ENSG00000182389		"Calcium channel subunits"	1404	protein-coding gene	gene with protein product		601949				9628818	Standard	NM_000726		Approved	EJM4	uc002tya.3	O00305	OTTHUMG00000155091	ENST00000539935.1:c.1420T>A	chr2.hg19:g.152695776A>T	ENSP00000438949:p.Leu474Met	173.0	0.0		180.0	77.0	NM_000726	A7BJ74|A8K1Y4|B4DG40|O60515|Q6B000|Q96L40	Missense_Mutation	SNP	ENST00000539935.1	hg19	CCDS46426.1	.	.	.	.	.	.	.	.	.	.	A	10.18	1.278017	0.23307	.	.	ENSG00000182389	ENST00000539935;ENST00000360283;ENST00000543269;ENST00000439467;ENST00000534999;ENST00000397327;ENST00000427385;ENST00000201943;ENST00000339254	T;T;T;T;T;T;T	0.73897	-0.7;-0.7;-0.7;-0.7;-0.69;-0.7;-0.79	5.26	4.12	0.48240	.	0.136662	0.51477	D	0.000092	T	0.53753	0.1816	N	0.11560	0.145	0.51012	D	0.999903	B;B;B;B	0.18610	0.006;0.017;0.017;0.029	B;B;B;B	0.17979	0.009;0.015;0.015;0.02	T	0.51560	-0.8690	10	0.33141	T	0.24	-8.5623	10.4536	0.44537	0.9235:0.0:0.0765:0.0	.	412;474;456;440	A7BJ74;O00305;B4DG40;O00305-2	.;CACB4_HUMAN;.;.	M	474;441;369;469;440;427;456;412;475	ENSP00000438949:L474M;ENSP00000353425:L441M;ENSP00000390161:L469M;ENSP00000443893:L440M;ENSP00000380490:L427M;ENSP00000410978:L456M;ENSP00000201943:L412M	ENSP00000201943:L412M	L	-	1	2	CACNB4	152404022	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.249000	0.51437	1.988000	0.58038	0.377000	0.23210	TTG	.	.		0.463	CACNB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000338385.4	NM_000726.3		T	152695776	A	T	152695776	3	4	266	1	0	0	0	0	1	0	0	0	2557	69	3	4	146	4	CACNB4	2	152695776	Missense_Mutation	SNP	A	TCGA-FV-A3R2-01A-11D-A22F-10	11035257	152695776	90503597	7	38965										
RFTN2	130132	hgsc.bcm.edu	37	chr2	198436936	198436936	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	gcaggttgtgacgaggttgtGtctaatccgatgcttctact	12	8	2	1			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr2:198436936G>T	ENST00000295049.4	-	9	1838	c.1302C>A	c.(1300-1302)gaC>gaA	p.D434E		NM_144629.2	NP_653230.2	Q52LD8	RFTN2_HUMAN	raftlin family member 2	434					dsRNA transport (GO:0033227)|response to exogenous dsRNA (GO:0043330)	plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(13)|urinary_tract(3)	30						ACGAGGTTGTGTCTAATCCGA	0.527																																					p.D434E		Atlas-SNP	.											.	RFTN2	68	.	0			c.C1302A						.						284	228	247					2																	198436936		2203	4300	6503	SO:0001583	missense	130132	exon9			GGTTGTGTCTAAT	AK055136	CCDS2323.1	2q33.1	2008-02-05	2006-09-28	2006-09-28	ENSG00000162944	ENSG00000162944			26402	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 11"	C2orf11			Standard	NM_144629		Approved	FLJ30574, Raftlin-2	uc002uuo.4	Q52LD8	OTTHUMG00000132746	ENST00000295049.4:c.1302C>A	chr2.hg19:g.198436936G>T	ENSP00000295049:p.Asp434Glu	162.0	0.0		170.0	62.0	NM_144629	Q14DH4|Q2TA69|Q53QE0|Q53SE1|Q96NM3	Missense_Mutation	SNP	ENST00000295049.4	hg19	CCDS2323.1	.	.	.	.	.	.	.	.	.	.	G	12.13	1.844456	0.32606	.	.	ENSG00000162944	ENST00000295049;ENST00000454447	T;T	0.30182	1.54;1.54	4.84	0.951	0.19579	.	0.929500	0.09076	N	0.852065	T	0.24314	0.0589	L	0.29908	0.895	0.23227	N	0.998087	D	0.56035	0.974	P	0.46275	0.51	T	0.14309	-1.0477	10	0.40728	T	0.16	-11.1573	5.7903	0.18357	0.2988:0.129:0.5722:0.0	.	434	Q52LD8	RFTN2_HUMAN	E	434;126	ENSP00000295049:D434E;ENSP00000387459:D126E	ENSP00000295049:D434E	D	-	3	2	RFTN2	198145181	1.000000	0.71417	0.007000	0.13788	0.042000	0.13812	2.750000	0.47500	-0.000000	0.14550	0.561000	0.74099	GAC	.	.		0.527	RFTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256106.2	NM_144629		T	198436936	G	T	198436936	3	4	266	1	0	0	0	0	1	0	0	0	13274	1368	48	3	207	3	RFTN2	2	198436936	Missense_Mutation	SNP	G	TCGA-FV-A3R2-01A-11D-A22F-10	45741160	198436936	44762437	8	38966										
ANKMY1	51281	hgsc.bcm.edu	37	chr2	241463777	241463777	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	tgatgatgaaaggattggaaCaactgggaattttggaggtt	14	2	0	3			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr2:241463777C>T	ENST00000272972.3	-	7	1304	c.1090G>A	c.(1090-1092)Gtt>Att	p.V364I	ANKMY1_ENST00000536462.1_Missense_Mutation_p.V176I|ANKMY1_ENST00000462004.1_5'Flank|ANKMY1_ENST00000403283.1_Missense_Mutation_p.V302I|ANKMY1_ENST00000405523.3_Missense_Mutation_p.V223I|ANKMY1_ENST00000391987.1_Missense_Mutation_p.V364I|ANKMY1_ENST00000373320.4_Missense_Mutation_p.V134I|ANKMY1_ENST00000361678.4_Missense_Mutation_p.V223I|ANKMY1_ENST00000401804.1_Missense_Mutation_p.V453I|ANKMY1_ENST00000373318.2_Missense_Mutation_p.V223I|ANKMY1_ENST00000406958.1_Missense_Mutation_p.V223I|ANKMY1_ENST00000405002.1_Missense_Mutation_p.V134I	NM_016552.2	NP_057636.2	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1	364							metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	30		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.03e-30)|all cancers(36;4.78e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.45e-14)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.8e-06)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.01)|Colorectal(34;0.0101)|COAD - Colon adenocarcinoma(134;0.0476)		AGGATTGGAACAACTGGGAAT	0.448																																					p.V364I		Atlas-SNP	.											.	ANKMY1	112	.	0			c.G1090A						.						40	44	43					2																	241463777		2201	4295	6496	SO:0001583	missense	51281	exon7			TTGGAACAACTGG	AB034636	CCDS2535.1, CCDS2536.1, CCDS63184.1, CCDS63185.1, CCDS74681.1	2q37.3	2013-01-10			ENSG00000144504	ENSG00000144504		"Zinc fingers, MYND-type", "Ankyrin repeat domain containing"	20987	protein-coding gene	gene with protein product							Standard	XM_005247020		Approved	FLJ20499, ZMYND13	uc002vyz.1	Q9P2S6	OTTHUMG00000133355	ENST00000272972.3:c.1090G>A	chr2.hg19:g.241463777C>T	ENSP00000272972:p.Val364Ile	65.0	0.0		56.0	17.0	NM_016552	B2RB78|Q4ZFV3|Q8IYX5|Q8NDK5|Q9H0V8|Q9NX10	Missense_Mutation	SNP	ENST00000272972.3	hg19	CCDS2536.1	.	.	.	.	.	.	.	.	.	.	C	4.064	0.009642	0.07912	.	.	ENSG00000144504	ENST00000373318;ENST00000406958;ENST00000272972;ENST00000361678;ENST00000391987;ENST00000373320;ENST00000403283;ENST00000401804;ENST00000536462;ENST00000405523;ENST00000405002	T;T;T;T;T;T;T;T;T;T;T	0.56103	2.88;3.59;0.5;2.21;0.5;4.36;2.44;0.48;2.16;2.18;2.44	3.16	-4.41	0.03590	Ankyrin repeat-containing domain (1);	1.581880	0.04098	N	0.312380	T	0.30823	0.0777	N	0.14661	0.345	0.09310	N	1	B;B;B;B;B;B;B	0.33171	0.003;0.003;0.013;0.002;0.002;0.4;0.003	B;B;B;B;B;B;B	0.30646	0.002;0.002;0.008;0.001;0.001;0.118;0.002	T	0.20840	-1.0263	10	0.51188	T	0.08	-32.2219	5.1322	0.14917	0.0:0.3825:0.37:0.2475	.	364;176;134;223;223;223;364	Q4ZFV3;F5H558;Q9P2S6-4;Q6GPI0;B5MBY4;Q9P2S6-2;Q9P2S6	.;.;.;.;.;.;ANKY1_HUMAN	I	223;223;364;223;364;134;302;453;176;223;134	ENSP00000362415:V223I;ENSP00000384555:V223I;ENSP00000272972:V364I;ENSP00000355097:V223I;ENSP00000375847:V364I;ENSP00000362417:V134I;ENSP00000383968:V302I;ENSP00000385887:V453I;ENSP00000444707:V176I;ENSP00000385635:V223I;ENSP00000385145:V134I	ENSP00000272972:V364I	V	-	1	0	ANKMY1	241112450	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.170000	0.09897	-0.920000	0.03799	-0.339000	0.08088	GTT	.	.		0.448	ANKMY1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257187.2	NM_017844		T	241463777	C	T	241463777	3	4	266	1	0	0	0	0	1	0	0	0	634	478	17	3	1779	3	ANKMY1	2	241463777	Missense_Mutation	SNP	C	TCGA-FV-A3R2-01A-11D-A22F-10	43026841	241463777	1735596	9	38967										
SATB1	6304	hgsc.bcm.edu	37	chr3	18462375	18462375	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	ctgctccaggcgggcaatctTggctggtggacccttcggat	14	12	1	0			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr3:18462375T>G	ENST00000338745.6	-	2	1819	c.85A>C	c.(85-87)Aag>Cag	p.K29Q	SATB1_ENST00000493952.2_Missense_Mutation_p.K29Q|SATB1_ENST00000417717.2_Missense_Mutation_p.K29Q|TBC1D5_ENST00000414318.2_Intron|SATB1_ENST00000454909.2_Missense_Mutation_p.K29Q	NM_002971.4	NP_002962.1	Q01826	SATB1_HUMAN	SATB homeobox 1	29					activated T cell proliferation (GO:0050798)|apoptotic process (GO:0006915)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|epidermis development (GO:0008544)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|reflex (GO:0060004)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(2)|endometrium(6)|large_intestine(4)|lung(10)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	32						CGGGCAATCTTGGCTGGTGGA	0.512																																					p.K29Q		Atlas-SNP	.											.	SATB1	96	.	0			c.A85C						.						134	137	136					3																	18462375		2203	4300	6503	SO:0001583	missense	6304	exon2			CAATCTTGGCTGG		CCDS2631.1, CCDS56242.1	3p24.3	2011-07-19	2007-02-15		ENSG00000182568	ENSG00000182568		"Homeoboxes / CUT class"	10541	protein-coding gene	gene with protein product		602075	"special AT-rich sequence binding protein 1 (binds to nuclear matrix/scaffold-associating DNA)"			1505028	Standard	NM_002971		Approved		uc003cbj.3	Q01826	OTTHUMG00000129890	ENST00000338745.6:c.85A>C	chr3.hg19:g.18462375T>G	ENSP00000341024:p.Lys29Gln	134.0	0.0		164.0	95.0	NM_002971	B3KXF1|C9JTR6|Q59EQ0	Missense_Mutation	SNP	ENST00000338745.6	hg19	CCDS2631.1	.	.	.	.	.	.	.	.	.	.	T	28.8	4.949754	0.92660	.	.	ENSG00000182568	ENST00000338745;ENST00000454909;ENST00000417717;ENST00000440737;ENST00000452260;ENST00000415069;ENST00000457005;ENST00000414509;ENST00000444341	T;T;T;T;T;T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21	5.83	5.83	0.93111	.	0.093160	0.64402	D	0.000001	T	0.79100	0.4389	L	0.53249	1.67	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.80921	-0.1166	10	0.87932	D	0	-26.1861	16.2147	0.82198	0.0:0.0:0.0:1.0	.	29;29	Q01826-2;Q01826	.;SATB1_HUMAN	Q	29	ENSP00000341024:K29Q;ENSP00000399708:K29Q;ENSP00000399518:K29Q;ENSP00000402982:K29Q;ENSP00000406727:K29Q;ENSP00000390529:K29Q;ENSP00000398072:K29Q;ENSP00000408871:K29Q;ENSP00000391344:K29Q	ENSP00000341024:K29Q	K	-	1	0	SATB1	18437379	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.665000	0.83852	2.231000	0.72958	0.460000	0.39030	AAG	.	.		0.512	SATB1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252138.4	NM_001131010		G	18462375	T	G	18462375	3	3	266	1	0	0	0	0	1	0	0	0	13868	1821	63	5	2246	5	SATB1	3	18462375	Missense_Mutation	SNP	T	TCGA-FV-A3R2-01A-11D-A22F-10		18462375	179560055	10	38968										
C3orf59	151963	hgsc.bcm.edu	37	chr3	192516790	192516790	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	ctcctggcaaaggacagccgCcattcattgtccttcttacc	7	15	2	0			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr3:192516790C>T	ENST00000392452.2	-	2	1181	c.861G>A	c.(859-861)tgG>tgA	p.W287*		NM_178496.3	NP_848591.2	Q8IYB1	M21D2_HUMAN	Mab-21 domain containing 2	287							protein complex binding (GO:0032403)			endometrium(3)|kidney(1)|large_intestine(4)|lung(17)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	31						AGGACAGCCGCCATTCATTGT	0.507																																					p.W287X		Atlas-SNP	.											.	MB21D2	75	.	0			c.G861A						.						43	37	39					3																	192516790		2203	4300	6503	SO:0001587	stop_gained	151963	exon2			CAGCCGCCATTCA	AK056276	CCDS3302.2	3q28-q29	2011-02-23	2011-02-23	2011-02-23	ENSG00000180611	ENSG00000180611			30438	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 59"	C3orf59		12477932	Standard	NM_178496		Approved		uc011bsp.2	Q8IYB1	OTTHUMG00000155768	ENST00000392452.2:c.861G>A	chr3.hg19:g.192516790C>T	ENSP00000376246:p.Trp287*	56.0	0.0		79.0	47.0	NM_178496	Q86VD8	Nonsense_Mutation	SNP	ENST00000392452.2	hg19	CCDS3302.2	.	.	.	.	.	.	.	.	.	.	C	38	6.718924	0.97788	.	.	ENSG00000180611	ENST00000392452	.	.	.	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.3039	18.4392	0.90658	0.0:1.0:0.0:0.0	.	.	.	.	X	287	.	ENSP00000376246:W287X	W	-	3	0	MB21D2	193999484	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.783000	0.85696	2.593000	0.87608	0.655000	0.94253	TGG	.	.		0.507	MB21D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341543.1	NM_178496		T	192516790	C	T	192516790	4	4	266	1	0	0	0	0	0	1	0	0	2239	740	26	3	618	3	C3orf59	3	192516790	Nonsense_Mutation	SNP	C	TCGA-FV-A3R2-01A-11D-A22F-10	174054415	192516790	5505640	11	38969										
LNX1	84708	hgsc.bcm.edu	37	chr4	54373548	54373548	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	gcatggttggcaactgcactCccgctctttgtccttcgaag	10	13	1	0			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr4:54373548C>G	ENST00000263925.7	-	4	1025	c.711G>C	c.(709-711)ggG>ggC	p.G237G	LNX1-AS1_ENST00000511989.1_RNA|LNX1_ENST00000306888.2_Silent_p.G141G|LNX1-AS1_ENST00000514364.1_RNA|LNX1-AS1_ENST00000510785.1_RNA|FIP1L1_ENST00000507166.1_Intron	NM_001126328.2	NP_001119800.1	Q8TBB1	LNX1_HUMAN	ligand of numb-protein X 1, E3 ubiquitin protein ligase	237	Interaction with MAGEB18.				protein homooligomerization (GO:0051260)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.G141G(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|endometrium(3)|large_intestine(11)|lung(6)|ovary(3)|urinary_tract(4)	32	all_neural(26;0.153)		GBM - Glioblastoma multiforme(3;8.2e-46)|LUSC - Lung squamous cell carcinoma(32;0.0134)			CAACTGCACTCCCGCTCTTTG	0.478																																					p.G237G		Atlas-SNP	.											LNX1,NS,carcinoma,0,1	LNX1	139	.	1	Substitution - coding silent(1)	lung(1)	c.G711C						.						130	121	124					4																	54373548		2203	4300	6503	SO:0001819	synonymous_variant	84708	exon4			TGCACTCCCGCTC	AF237782	CCDS3492.1, CCDS47057.1	4q12	2013-01-09	2012-02-23	2005-11-04	ENSG00000072201	ENSG00000072201		"RING-type (C3HC4) zinc fingers"	6657	protein-coding gene	gene with protein product		609732	"ligand of numb-protein X", "ligand of numb-protein X 1"	LNX		11521506, 11782429	Standard	NM_032622		Approved	MPDZ, PDZRN2	uc003hag.5	Q8TBB1	OTTHUMG00000102099	ENST00000263925.7:c.711G>C	chr4.hg19:g.54373548C>G		115.0	0.0		110.0	37.0	NM_001126328	Q4W5K7|Q8N4C2|Q96MJ7|Q9BY20	Silent	SNP	ENST00000263925.7	hg19	CCDS47057.1																																																																																			.	.		0.478	LNX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219934.2			G	54373548	C	G	54373548	2	3	266	1	0	0	0	0	0	0	0	1	8874	842	30	4		4	LNX1	4	54373548	Silent	SNP	C	TCGA-FV-A3R2-01A-11D-A22F-10		54373548	136780728	12	38970										
SHROOM3	57619	hgsc.bcm.edu	37	chr4	77661969	77661969	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	ggccgtggcccccagaggccGgacgctcggctcctccgtag	15	17	0	1			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr4:77661969G>A	ENST00000296043.6	+	5	3596	c.2643G>A	c.(2641-2643)ccG>ccA	p.P881P		NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	881					actin cytoskeleton organization (GO:0030036)|apical protein localization (GO:0045176)|cell morphogenesis (GO:0000902)|cellular pigment accumulation (GO:0043482)|columnar/cuboidal epithelial cell development (GO:0002066)|neural tube closure (GO:0001843)|pattern specification process (GO:0007389)|regulation of cell shape (GO:0008360)	adherens junction (GO:0005912)|apical junction complex (GO:0043296)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)				NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(29)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	60			Lung(101;0.0903)			CCCAGAGGCCGGACGCTCGGC	0.701																																					p.P881P		Atlas-SNP	.											.	SHROOM3	134	.	0			c.G2643A						.						10	13	12					4																	77661969		2112	4128	6240	SO:0001819	synonymous_variant	57619	exon5			GAGGCCGGACGCT	AB055660	CCDS3579.2	4q21.1	2009-11-25			ENSG00000138771	ENSG00000138771			30422	protein-coding gene	gene with protein product		604570				10589677, 16615870	Standard	NM_020859		Approved	ShrmL, SHRM, KIAA1481, APXL3	uc011cbx.2	Q8TF72	OTTHUMG00000157075	ENST00000296043.6:c.2643G>A	chr4.hg19:g.77661969G>A		5.0	0.0		9.0	6.0	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Silent	SNP	ENST00000296043.6	hg19	CCDS3579.2																																																																																			.	.		0.701	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859		A	77661969	G	A	77661969	2	1	266	1	0	0	0	0	0	0	0	1	14310	1103	39	1		1	SHROOM3	4	77661969	Silent	SNP	G	TCGA-FV-A3R2-01A-11D-A22F-10	23288421	77661969	113492307	13	38971										
MRPL1	65008	hgsc.bcm.edu	37	chr4	78806454	78806454	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	gttcttagtttgccatacccAtttgcttccgaaatcaataa	5	10	2	0			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr4:78806454A>G	ENST00000315567.8	+	4	776	c.447A>G	c.(445-447)ccA>ccG	p.P149P	MRPL1_ENST00000506674.1_3'UTR	NM_020236.3	NP_064621.3	Q9BYD6	RM01_HUMAN	mitochondrial ribosomal protein L1	149					translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)	17						TGCCATACCCATTTGCTTCCG	0.328																																					p.P149P		Atlas-SNP	.											.	MRPL1	37	.	0			c.A447G						.						129	129	129					4																	78806454		2202	4300	6502	SO:0001819	synonymous_variant	65008	exon4			ATACCCATTTGCT	AB049474	CCDS3583.2	4q21.1	2012-09-13			ENSG00000169288	ENSG00000169288		"Mitochondrial ribosomal proteins / large subunits"	14275	protein-coding gene	gene with protein product		611821					Standard	NM_020236		Approved	BM022	uc003hku.2	Q9BYD6	OTTHUMG00000130200	ENST00000315567.8:c.447A>G	chr4.hg19:g.78806454A>G		131.0	0.0		127.0	55.0	NM_020236	A6NG03|Q4W5B8|Q6IAG4|Q96BW3|Q9H793|Q9NRL5	Silent	SNP	ENST00000315567.8	hg19	CCDS3583.2	.	.	.	.	.	.	.	.	.	.	A	1.625	-0.520506	0.04171	.	.	ENSG00000169288	ENST00000502384	.	.	.	5.71	-3.31	0.04988	.	.	.	.	.	T	0.37865	0.1019	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33317	-0.9873	4	.	.	.	-2.3981	0.9725	0.01419	0.2409:0.3202:0.133:0.3059	.	.	.	.	V	103	.	.	I	+	1	0	MRPL1	79025478	0.812000	0.29077	0.677000	0.29947	0.045000	0.14185	-0.258000	0.08733	-0.665000	0.05317	0.524000	0.50904	ATT	.	.		0.328	MRPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252518.3	NM_020236		G	78806454	A	G	78806454	2	3	266	1	0	0	0	0	0	0	0	1	9783	204	8	2		2	MRPL1	4	78806454	Silent	SNP	A	TCGA-FV-A3R2-01A-11D-A22F-10	1144485	78806454	112347822	14	38972										
CDH9	1007	hgsc.bcm.edu	37	chr5	26889956	26889956	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	tttatttacctgcccaggttTtgcattttcacaaacaaatg	5	9	1	0			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr5:26889956T>C	ENST00000231021.4	-	9	1673	c.1501A>G	c.(1501-1503)Aaa>Gaa	p.K501E		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	501	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						TGCCCAGGTTTTGCATTTTCA	0.308																																					p.K501E	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											.	CDH9	305	.	0			c.A1501G						.						81	83	82					5																	26889956		2203	4300	6503	SO:0001583	missense	1007	exon9			CAGGTTTTGCATT	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"Cadherins / Major cadherins"	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.1501A>G	chr5.hg19:g.26889956T>C	ENSP00000231021:p.Lys501Glu	95.0	0.0		139.0	48.0	NM_016279	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	hg19	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.084226	0.76642	.	.	ENSG00000113100	ENST00000231021	T	0.51574	0.7	5.31	5.31	0.75309	Cadherin (3);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.53367	0.1792	M	0.71581	2.175	0.52501	D	0.999951	B;B	0.28636	0.107;0.218	B;B	0.38327	0.256;0.271	T	0.51896	-0.8647	9	.	.	.	.	14.0813	0.64925	0.0:0.0:0.0:1.0	.	94;501	B4DFP0;Q9ULB4	.;CADH9_HUMAN	E	501	ENSP00000231021:K501E	.	K	-	1	0	CDH9	26925713	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.664000	0.83830	2.010000	0.58986	0.450000	0.29827	AAA	.	.		0.308	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		C	26889956	T	C	26889956	3	2	266	1	0	0	0	0	1	0	0	0	3119	1850	64	2	884	2	CDH9	5	26889956	Missense_Mutation	SNP	T	TCGA-FV-A3R2-01A-11D-A22F-10		26889956	154025304	15	38973										
VCAN	1462	hgsc.bcm.edu	37	chr5	82836955	82836955	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	gagattgaaggaataaaagcTgaagcaaaagccctggatga	12	5	0	4			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr5:82836955T>A	ENST00000265077.3	+	8	8698	c.8133T>A	c.(8131-8133)gcT>gcA	p.A2711A	VCAN-AS1_ENST00000513899.1_RNA|VCAN_ENST00000512590.2_Intron|VCAN_ENST00000343200.5_Silent_p.A1724A|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000342785.4_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	2711	GAG-beta.			IKAEA -> EFREV (in Ref. 7; AAA36437). {ECO:0000305}.	carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	GAATAAAAGCTGAAGCAAAAG	0.423																																					p.A2711A		Atlas-SNP	.											.	VCAN	498	.	0			c.T8133A						.						61	58	59					5																	82836955		2203	4300	6503	SO:0001819	synonymous_variant	1462	exon8			AAAAGCTGAAGCA	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.8133T>A	chr5.hg19:g.82836955T>A		88.0	0.0		94.0	27.0	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Silent	SNP	ENST00000265077.3	hg19	CCDS4060.1																																																																																			.	.		0.423	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		A	82836955	T	A	82836955	2	1	266	1	0	0	0	0	0	0	0	1	17153	1567	55	4		4	VCAN	5	82836955	Silent	SNP	T	TCGA-FV-A3R2-01A-11D-A22F-10	55946999	82836955	98078305	16	38974										
SKP1	6500	hgsc.bcm.edu	37	chr5	133494206	133494206	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	aaggtcttgcgaatctcctcAggagttttccccttgatcat	8	11	4	1			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr5:133494206A>C	ENST00000353411.6	-	5	579	c.396T>G	c.(394-396)ccT>ccG	p.P132P	SKP1_ENST00000522552.1_Silent_p.P132P|SKP1_ENST00000517625.1_Silent_p.P132P|SKP1_ENST00000522855.1_Silent_p.P132P|SKP1_ENST00000521216.1_Silent_p.P132P	NM_170679.2	NP_733779.1	P63208	SKP1_HUMAN	S-phase kinase-associated protein 1	132	Interaction with the F-box domain of F- box proteins. {ECO:0000250}.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|histone H2A monoubiquitination (GO:0035518)|mitotic cell cycle (GO:0000278)|Notch signaling pathway (GO:0007219)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|viral process (GO:0016032)	Cul7-RING ubiquitin ligase complex (GO:0031467)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|SCF ubiquitin ligase complex (GO:0019005)	ubiquitin-protein transferase activity (GO:0004842)			large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GAATCTCCTCAGGAGTTTTCC	0.408																																					p.P132P		Atlas-SNP	.											.	SKP1	10	.	0			c.T396G						.						143	138	139					5																	133494206		2203	4300	6503	SO:0001819	synonymous_variant	6500	exon5			CTCCTCAGGAGTT	U33760	CCDS4171.1, CCDS4172.1	5q31	2011-11-18	2007-11-13	2007-11-13	ENSG00000113558	ENSG00000113558			10899	protein-coding gene	gene with protein product		601434	"S-phase kinase-associated protein 1A (p19A)"	SKP1A		7553852, 8646875	Standard	NM_006930		Approved	EMC19, OCP2, TCEB1L, MGC34403, OCP-II, p19A	uc003kzc.4	P63208	OTTHUMG00000129117	ENST00000353411.6:c.396T>G	chr5.hg19:g.133494206A>C		106.0	0.0		126.0	44.0	NM_170679	D3DQ97|D3DQ98|P34991|Q8TAY2	Silent	SNP	ENST00000353411.6	hg19	CCDS4171.1																																																																																			.	.		0.408	SKP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251162.2	NM_170679		C	133494206	A	C	133494206	2	2	266	1	0	0	0	0	0	0	0	1	14376	175	7	5		5	SKP1	5	133494206	Silent	SNP	A	TCGA-FV-A3R2-01A-11D-A22F-10	50657251	133494206	47421054	17	38975										
TMEM173	340061	hgsc.bcm.edu	37	chr5	138856001	138856001	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	ctgccgcaggtgccggagaaCctcctgggacagcgagaagc	15	13	0	2			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr5:138856001C>A	ENST00000330794.4	-	8	1318	c.985G>T	c.(985-987)Gtt>Ttt	p.V329F	TMEM173_ENST00000511850.1_5'Flank	NM_198282.2	NP_938023.1	Q86WV6	STING_HUMAN	transmembrane protein 173	329	c-di-GMP-binding domain (CBD).				activation of innate immune response (GO:0002218)|apoptotic process (GO:0006915)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-beta production (GO:0032608)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	cyclic-di-GMP binding (GO:0035438)|cyclic-GMP-AMP binding (GO:0061507)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|transcription factor binding (GO:0008134)			endometrium(1)|kidney(1)|lung(6)|upper_aerodigestive_tract(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			TGCCGGAGAACCTCCTGGGAC	0.557																																					p.V329F		Atlas-SNP	.											.	TMEM173	19	.	0			c.G985T						.						56	54	55					5																	138856001		2203	4300	6503	SO:0001583	missense	340061	exon8			GGAGAACCTCCTG		CCDS4215.1	5q31.2	2009-11-06			ENSG00000184584	ENSG00000184584			27962	protein-coding gene	gene with protein product		612374				12477932	Standard	XM_005268445		Approved	FLJ38577, NET23	uc003lep.3	Q86WV6	OTTHUMG00000129239	ENST00000330794.4:c.985G>T	chr5.hg19:g.138856001C>A	ENSP00000331288:p.Val329Phe	33.0	0.0		67.0	13.0	NM_198282	A8K3P6|B6EB35|D6RBX0|D6RE01|D6RID9	Missense_Mutation	SNP	ENST00000330794.4	hg19	CCDS4215.1	.	.	.	.	.	.	.	.	.	.	C	12.50	1.956615	0.34565	.	.	ENSG00000184584	ENST00000330794	T	0.27720	1.65	5.19	3.04	0.35103	.	0.129349	0.49305	D	0.000144	T	0.23210	0.0561	L	0.36672	1.1	0.38398	D	0.94559	P	0.49090	0.919	B	0.43274	0.414	T	0.06058	-1.0848	10	0.72032	D	0.01	-6.136	5.9319	0.19144	0.0:0.1885:0.0:0.8115	.	329	Q86WV6	TM173_HUMAN	F	329	ENSP00000331288:V329F	ENSP00000331288:V329F	V	-	1	0	TMEM173	138836185	0.825000	0.29262	0.989000	0.46669	0.235000	0.25334	1.011000	0.29911	0.421000	0.25980	-0.379000	0.06801	GTT	.	.		0.557	TMEM173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251338.1	NM_198282		A	138856001	C	A	138856001	3	1	266	1	0	0	0	0	1	0	0	0	16104	507	18	3	158	3	TMEM173	5	138856001	Missense_Mutation	SNP	C	TCGA-FV-A3R2-01A-11D-A22F-10	5361795	138856001	42059259	18	38976										
ATP10B	23120	hgsc.bcm.edu	37	chr5	160033981	160033981	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	ccacagcttctgaggtgatgGatggtgtcttggaaggtaag	15	6	2	2			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr5:160033981G>T	ENST00000327245.5	-	19	3797	c.2951C>A	c.(2950-2952)tCc>tAc	p.S984Y		NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	984					phospholipid translocation (GO:0045332)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1)	75	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TGAGGTGATGGATGGTGTCTT	0.468																																					p.S984Y		Atlas-SNP	.											.	ATP10B	201	.	0			c.C2951A						.						127	120	122					5																	160033981		1949	4140	6089	SO:0001583	missense	23120	exon19			GTGATGGATGGTG	AB018258	CCDS43394.1	5q34	2010-04-20	2007-09-19		ENSG00000118322	ENSG00000118322		"ATPases / P-type"	13543	protein-coding gene	gene with protein product			"ATPase, Class V, type 10B"			9872452, 11015572	Standard	NM_025153		Approved	ATPVB, KIAA0715, FLJ21477	uc003lym.1	O94823	OTTHUMG00000163551	ENST00000327245.5:c.2951C>A	chr5.hg19:g.160033981G>T	ENSP00000313600:p.Ser984Tyr	187.0	1.0		300.0	166.0	NM_025153	Q9H725	Missense_Mutation	SNP	ENST00000327245.5	hg19	CCDS43394.1	.	.	.	.	.	.	.	.	.	.	G	11.41	1.631877	0.29068	.	.	ENSG00000118322	ENST00000327245	T	0.06218	3.33	5.05	5.05	0.67936	HAD-like domain (1);	0.544252	0.18094	N	0.151903	T	0.13372	0.0324	M	0.68593	2.085	0.19575	N	0.999966	P	0.49253	0.921	P	0.48952	0.596	T	0.08576	-1.0715	9	.	.	.	.	10.9146	0.47129	0.0959:0.0:0.9041:0.0	.	984	O94823	AT10B_HUMAN	Y	984	ENSP00000313600:S984Y	.	S	-	2	0	ATP10B	159966559	0.024000	0.19004	0.078000	0.20375	0.061000	0.15899	2.123000	0.41996	2.344000	0.79699	0.563000	0.77884	TCC	.	.		0.468	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374127.1	NM_025153		T	160033981	G	T	160033981	3	4	266	1	0	0	0	0	1	0	0	0	1117	1174	41	3	1466	3	ATP10B	5	160033981	Missense_Mutation	SNP	G	TCGA-FV-A3R2-01A-11D-A22F-10	21177980	160033981	20881279	19	38977										
GMNN	51053	hgsc.bcm.edu	37	chr6	24785914	24785914	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	ttgaatcactggataatcagGaatttgattctgaagaagaa	9	4	3	5			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr6:24785914G>C	ENST00000230056.3	+	7	849	c.517G>C	c.(517-519)Gaa>Caa	p.E173Q	GMNN_ENST00000356509.3_Missense_Mutation_p.E173Q	NM_015895.4	NP_056979.1	O75496	GEMI_HUMAN	geminin, DNA replication inhibitor	173	Homeodomain binding.				mitotic cell cycle (GO:0000278)|negative regulation of cell cycle (GO:0045786)|negative regulation of DNA replication (GO:0008156)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)			endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(1)	10						GGATAATCAGGAATTTGATTC	0.353																																					p.E173Q		Atlas-SNP	.											.	GMNN	19	.	0			c.G517C						.						86	89	88					6																	24785914		2203	4300	6503	SO:0001583	missense	51053	exon7			AATCAGGAATTTG	AF067855	CCDS4560.1	6p21.32	2008-10-31			ENSG00000112312	ENSG00000112312			17493	protein-coding gene	gene with protein product		602842				9635433	Standard	NM_001251989		Approved	Gem	uc003nem.3	O75496	OTTHUMG00000014363	ENST00000230056.3:c.517G>C	chr6.hg19:g.24785914G>C	ENSP00000230056:p.Glu173Gln	71.0	0.0		143.0	40.0	NM_001251991	B3KMM8|Q9H1Z1	Missense_Mutation	SNP	ENST00000230056.3	hg19	CCDS4560.1	.	.	.	.	.	.	.	.	.	.	G	17.12	3.309312	0.60414	.	.	ENSG00000112312	ENST00000356509;ENST00000230056;ENST00000378054	T;T;T	0.15487	2.42;2.42;2.42	5.95	5.95	0.96441	.	0.453554	0.25810	N	0.028155	T	0.17534	0.0421	M	0.68317	2.08	0.31892	N	0.617107	D	0.54397	0.966	P	0.52109	0.69	T	0.06499	-1.0823	10	0.30854	T	0.27	-9.3621	12.2941	0.54836	0.0772:0.0:0.9228:0.0	.	173	O75496	GEMI_HUMAN	Q	173	ENSP00000348902:E173Q;ENSP00000230056:E173Q;ENSP00000367293:E173Q	ENSP00000230056:E173Q	E	+	1	0	GMNN	24893893	1.000000	0.71417	1.000000	0.80357	0.652000	0.38707	4.852000	0.62904	2.824000	0.97209	0.655000	0.94253	GAA	.	.		0.353	GMNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040021.2	NM_015895		C	24785914	G	C	24785914	3	2	266	1	0	0	0	0	1	0	0	0	6501	1175	41	4	539	4	GMNN	6	24785914	Missense_Mutation	SNP	G	TCGA-FV-A3R2-01A-11D-A22F-10		24785914	146329153	20	38978										
OR12D2	26529	hgsc.bcm.edu	37	chr6	29364910	29364910	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	ctgtacccagatggccatcaCaatctgggtcattggttttt	9	10	3	1			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr6:29364910C>A	ENST00000383555.2	+	1	495	c.434C>A	c.(433-435)aCa>aAa	p.T145K	OR5V1_ENST00000377154.1_Intron	NM_013936.3	NP_039224.2	P58182	O12D2_HUMAN	olfactory receptor, family 12, subfamily D, member 2 (gene/pseudogene)	145						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(20)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	31						ATGGCCATCACAATCTGGGTC	0.488																																					p.T145K		Atlas-SNP	.											.	OR12D2	42	.	0			c.C434A						.						142	137	139					6																	29364910		1511	2709	4220	SO:0001583	missense	26529	exon1			CCATCACAATCTG		CCDS4659.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000168787	ENSG00000168787		"GPCR / Class A : Olfactory receptors"	8178	protein-coding gene	gene with protein product			"olfactory receptor, family 12, subfamily D, member 2"				Standard	NM_013936		Approved	hs6M1-20	uc003nmf.4	P58182	OTTHUMG00000031049	ENST00000383555.2:c.434C>A	chr6.hg19:g.29364910C>A	ENSP00000373047:p.Thr145Lys	160.0	0.0		227.0	63.0	NM_013936	B0S862|Q5SUN9|Q6IET9	Missense_Mutation	SNP	ENST00000383555.2	hg19	CCDS4659.1	.	.	.	.	.	.	.	.	.	.	C	3.847	-0.032719	0.07543	.	.	ENSG00000168787	ENST00000383555	T	0.37752	1.18	3.94	0.994	0.19832	GPCR, rhodopsin-like superfamily (1);	0.428574	0.21811	N	0.068773	T	0.21186	0.0510	M	0.75085	2.285	0.09310	N	1	P	0.34699	0.464	B	0.39971	0.315	T	0.13872	-1.0493	10	0.48119	T	0.1	.	6.8125	0.23812	0.0:0.685:0.1437:0.1713	.	145	P58182	O12D2_HUMAN	K	145	ENSP00000373047:T145K	ENSP00000373047:T145K	T	+	2	0	OR12D2	29472889	0.000000	0.05858	0.001000	0.08648	0.052000	0.14988	0.451000	0.21779	0.308000	0.22923	0.205000	0.17691	ACA	.	.		0.488	OR12D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076054.2			A	29364910	C	A	29364910	3	1	266	1	0	0	0	0	1	0	0	0	10940	478	17	3	436	3	OR12D2	6	29364910	Missense_Mutation	SNP	C	TCGA-FV-A3R2-01A-11D-A22F-10	4578996	29364910	141750157	21	38979										
HSPA1L	3305	hgsc.bcm.edu	37	chr6	31778524	31778524	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	tcagggcagtcatcacgcccCcagccgtctccagccccagg	10	19	4	0			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr6:31778524C>T	ENST00000375654.4	-	2	1415	c.1226G>A	c.(1225-1227)gGg>gAg	p.G409E	HSPA1L_ENST00000417199.3_Missense_Mutation_p.G409E	NM_005527.3	NP_005518.3	P34931	HS71L_HUMAN	heat shock 70kDa protein 1-like	409					binding of sperm to zona pellucida (GO:0007339)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)	blood microparticle (GO:0072562)|cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(10)|ovary(3)|pleura(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34						CATCACGCCCCCAGCCGTCTC	0.602																																					p.G409E		Atlas-SNP	.											.	HSPA1L	185	.	0			c.G1226A						.						78	74	75					6																	31778524		2203	4300	6503	SO:0001583	missense	3305	exon2			ACGCCCCCAGCCG	D85730	CCDS34413.1	6p21.3	2014-01-21	2002-08-29		ENSG00000204390	ENSG00000204390		"Heat shock proteins / HSP70"	5234	protein-coding gene	gene with protein product		140559	"heat shock 70kD protein-like 1"			9685725, 9349405	Standard	NM_005527		Approved	HSP70-HOM, hum70t	uc003nxh.3	P34931	OTTHUMG00000031208	ENST00000375654.4:c.1226G>A	chr6.hg19:g.31778524C>T	ENSP00000364805:p.Gly409Glu	104.0	0.0		149.0	38.0	NM_005527	A6NNB0|B0UXW8|O75634|Q2HXR3|Q8NE72|Q96QC9|Q9UQM1	Missense_Mutation	SNP	ENST00000375654.4	hg19	CCDS34413.1	.	.	.	.	.	.	.	.	.	.	C	13.71	2.319751	0.41096	.	.	ENSG00000204390	ENST00000375654;ENST00000417199;ENST00000375653	T;T	0.05996	3.36;3.36	5.2	5.2	0.72013	.	0.000000	0.35407	N	0.003222	T	0.39410	0.1077	H	0.99454	4.575	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.65311	-0.6199	10	0.87932	D	0	-17.4554	16.2725	0.82628	0.0:1.0:0.0:0.0	.	409	P34931	HS71L_HUMAN	E	409;409;354	ENSP00000364805:G409E;ENSP00000387691:G409E	ENSP00000364804:G354E	G	-	2	0	HSPA1L	31886503	1.000000	0.71417	0.390000	0.26220	0.006000	0.05464	5.930000	0.70104	2.704000	0.92352	0.585000	0.79938	GGG	.	.		0.602	HSPA1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076416.2			T	31778524	C	T	31778524	3	4	266	1	0	0	0	0	1	0	0	0	7419	623	22	3	703	3	HSPA1L	6	31778524	Missense_Mutation	SNP	C	TCGA-FV-A3R2-01A-11D-A22F-10	2413614	31778524	139336543	22	38980										
IP6K3	117283	hgsc.bcm.edu	37	chr6	33690707	33690707	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	gcctcgtgaggatgcgggctGcctggggctctttctggtgg	18	10	2	1			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr6:33690707G>A	ENST00000293756.4	-	6	1349	c.1023C>T	c.(1021-1023)ggC>ggT	p.G341G	IP6K3_ENST00000451316.1_Silent_p.G341G	NM_054111.4	NP_473452.2	Q96PC2	IP6K3_HUMAN	inositol hexakisphosphate kinase 3	341					inositol phosphate biosynthetic process (GO:0032958)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol metabolic process (GO:0046488)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol hexakisphosphate 6-kinase activity (GO:0000831)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			skin(1)	1						GATGCGGGCTGCCTGGGGCTC	0.562																																					p.G341G		Atlas-SNP	.											.	IP6K3	52	.	0			c.C1023T						.						70	71	71					6																	33690707		2203	4300	6503	SO:0001819	synonymous_variant	117283	exon7			CGGGCTGCCTGGG	AF393812	CCDS34435.1	6p21.31	2009-01-05	2009-01-05	2008-12-22	ENSG00000161896	ENSG00000161896			17269	protein-coding gene	gene with protein product		606993	"inositol hexaphosphate kinase 3"	IHPK3		11502751	Standard	NM_054111		Approved	INSP6K3	uc003ofb.2	Q96PC2	OTTHUMG00000014531	ENST00000293756.4:c.1023C>T	chr6.hg19:g.33690707G>A		107.0	0.0		166.0	41.0	NM_001142883	Q96MQ9	Silent	SNP	ENST00000293756.4	hg19	CCDS34435.1																																																																																			.	.		0.562	IP6K3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040203.1	NM_054111		A	33690707	G	A	33690707	2	1	266	1	0	0	0	0	0	0	0	1	7799	1306	46	3		3	IP6K3	6	33690707	Silent	SNP	G	TCGA-FV-A3R2-01A-11D-A22F-10	1912183	33690707	137424360	23	38981										
FIG4	9896	hgsc.bcm.edu	37	chr6	110059526	110059526	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	gatacagacttttatttttcAggggtatttgggatctgtag	11	4	2	1			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr6:110059526A>G	ENST00000230124.3	+	7	770		c.e7-1		FIG4_ENST00000368941.1_Intron|FIG4_ENST00000441478.2_Intron	NM_014845.5	NP_055660.1	Q92562	FIG4_HUMAN	FIG4 phosphoinositide 5-phosphatase						cell death (GO:0008219)|locomotory behavior (GO:0007626)|myelin assembly (GO:0032288)|negative regulation of myelination (GO:0031642)|neuron development (GO:0048666)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of neuron projection development (GO:0010976)|small molecule metabolic process (GO:0044281)|vacuole organization (GO:0007033)	early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)	phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphatidylinositol-4-phosphate phosphatase activity (GO:0043812)			central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)	32		all_cancers(87;8.63e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000124)|all_lung(197;0.0187)|Colorectal(196;0.0492)|Lung SC(18;0.0548)		OV - Ovarian serous cystadenocarcinoma(136;0.0355)|Epithelial(106;0.038)|all cancers(137;0.0425)|BRCA - Breast invasive adenocarcinoma(108;0.079)		TTTATTTTTCAGGGGTATTTG	0.323																																					.		Atlas-SNP	.											.	FIG4	77	.	0			c.647-2A>G						.						107	112	110					6																	110059526		2203	4298	6501	SO:0001630	splice_region_variant	9896	exon7			TTTTTCAGGGGTA	D87464	CCDS5078.1	6q21	2014-09-17	2014-08-04	2007-07-30	ENSG00000112367	ENSG00000112367			16873	protein-coding gene	gene with protein product		609390	"KIAA0274", "FIG4 homolog (S. cerevisiae)", "FIG4 homolog, SAC1 lipid phosphatase domain containing (S. cerevisiae)"	KIAA0274		9039502, 11274189, 17572665	Standard	NM_014845		Approved	SAC3, hSac3, dJ249I4.1, ALS11, CMT4J	uc003ptt.2	Q92562	OTTHUMG00000015352	ENST00000230124.3:c.647-1A>G	chr6.hg19:g.110059526A>G		121.0	0.0		90.0	54.0	NM_014845	Q53H49|Q5TCS6	Splice_Site	SNP	ENST00000230124.3	hg19	CCDS5078.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.162390	0.78226	.	.	ENSG00000112367	ENST00000230124;ENST00000454215	.	.	.	5.77	5.77	0.91146	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0957	0.81123	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FIG4	110166219	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	8.617000	0.90927	2.199000	0.70637	0.533000	0.62120	.	.	.		0.323	FIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041768.1	NM_014845	Intron	G	110059526	A	G	110059526	5	3	266	1	0	0	0	0	0	0	1	0	5896	202	7	2	671	2	FIG4	6	110059526	Splice_Site	SNP	A	TCGA-FV-A3R2-01A-11D-A22F-10	76368819	110059526	61055541	24	38982										
BMPER	168667	hgsc.bcm.edu	37	chr7	34118587	34118587	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	gactgctcctcccctgcctcGcccttccaggtgctggtgaa	10	17	0	1			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr7:34118587G>T	ENST00000297161.2	+	13	1571	c.1197G>T	c.(1195-1197)tcG>tcT	p.S399S	BMPER_ENST00000426693.1_Silent_p.S399S	NM_133468.4	NP_597725.1	Q8N8U9	BMPER_HUMAN	BMP binding endothelial regulator	399	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|endothelial cell activation (GO:0042118)|inner ear development (GO:0048839)|negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of endothelial cell migration (GO:0010594)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|ureteric bud development (GO:0001657)	extracellular space (GO:0005615)		p.S399S(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(24)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						CCCCTGCCTCGCCCTTCCAGG	0.582																																					p.S399S		Atlas-SNP	.											BMPER,NS,carcinoma,0,1	BMPER	131	.	1	Substitution - coding silent(1)	lung(1)	c.G1197T						.						99	105	103					7																	34118587		2203	4300	6503	SO:0001819	synonymous_variant	168667	exon13			TGCCTCGCCCTTC		CCDS5442.1	7p14.3	2009-02-18			ENSG00000164619	ENSG00000164619			24154	protein-coding gene	gene with protein product	"crossveinless-2"	608699				12897139, 14766204	Standard	NM_133468		Approved	Cv2, CRIM3	uc011kap.2	Q8N8U9	OTTHUMG00000128675	ENST00000297161.2:c.1197G>T	chr7.hg19:g.34118587G>T		58.0	0.0		70.0	21.0	NM_133468	A8K1P8|Q8TF36	Silent	SNP	ENST00000297161.2	hg19	CCDS5442.1																																																																																			.	.		0.582	BMPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250570.2	NM_133468		T	34118587	G	T	34118587	2	4	266	1	0	0	0	0	0	0	0	1	1468	1074	38	1		1	BMPER	7	34118587	Silent	SNP	G	TCGA-FV-A3R2-01A-11D-A22F-10		34118587	125020076	25	38983										
TYW1	55253	hgsc.bcm.edu	37	chr7	66463919	66463919	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	tggagtgaagattttttatgGttctcagactggaacagcga	12	5	1	3	rs542889524		TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr7:66463919G>T	ENST00000359626.5	+	3	415	c.251G>T	c.(250-252)gGt>gTt	p.G84V		NM_018264.2	NP_060734.2	Q9NV66	TYW1_HUMAN	tRNA-yW synthesizing protein 1 homolog (S. cerevisiae)	84	Flavodoxin-like. {ECO:0000255|PROSITE- ProRule:PRU00088}.				tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity (GO:0016491)			breast(1)|endometrium(8)|kidney(10)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(3)|stomach(2)|urinary_tract(2)	46		Lung NSC(55;0.0846)|all_lung(88;0.183)				ATTTTTTATGGTTCTCAGACT	0.368																																					p.G84V		Atlas-SNP	.											.	TYW1	71	.	0			c.G251T						.						115	111	112					7																	66463919		2203	4300	6503	SO:0001583	missense	55253	exon3			TTTATGGTTCTCA	AK001762	CCDS5538.1	7q11.21	2007-11-29	2007-11-29	2007-11-29	ENSG00000198874	ENSG00000198874			25598	protein-coding gene	gene with protein product	"tRNA-yW synthesizing protein 1 homolog A (S. cerevisiae)"	611243	"radical S-adenosyl methionine and flavodoxin domains 1"	RSAFD1		16162496, 17150819	Standard	NM_018264		Approved	FLJ10900, MGC23001, MGC60291, YPL207W, TYW1A	uc003tvn.4	Q9NV66	OTTHUMG00000129723	ENST00000359626.5:c.251G>T	chr7.hg19:g.66463919G>T	ENSP00000352645:p.Gly84Val	89.0	0.0		131.0	35.0	NM_018264	Q6PJG8|Q75MG8|Q75MN3|Q86V12|Q8IVS7|Q9H9C4	Missense_Mutation	SNP	ENST00000359626.5	hg19	CCDS5538.1	.	.	.	.	.	.	.	.	.	.	G	17.29	3.351430	0.61183	.	.	ENSG00000198874	ENST00000359626;ENST00000442959	T;D	0.87571	-0.15;-2.27	4.45	3.52	0.40303	Flavodoxin/nitric oxide synthase (2);	0.066589	0.64402	U	0.000013	D	0.94689	0.8287	H	0.96398	3.815	0.80722	D	1	D	0.76494	0.999	D	0.74348	0.983	D	0.94988	0.8132	9	.	.	.	.	10.4509	0.44522	0.0:0.1967:0.8033:0.0	.	84	Q9NV66	TYW1_HUMAN	V	84	ENSP00000352645:G84V;ENSP00000398897:G84V	.	G	+	2	0	TYW1	66101354	1.000000	0.71417	1.000000	0.80357	0.871000	0.50021	4.002000	0.57053	2.328000	0.79073	0.563000	0.77884	GGT	.	.		0.368	TYW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251932.2	NM_018264		T	66463919	G	T	66463919	3	4	266	1	0	0	0	0	1	0	0	0	16833	1261	44	3	261	3	TYW1	7	66463919	Missense_Mutation	SNP	G	TCGA-FV-A3R2-01A-11D-A22F-10	32345332	66463919	92674744	26	38984										
PPP1R3A	5506	hgsc.bcm.edu	37	chr7	113519285	113519285	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	tcctcaaaacatttccagttCttgatgaacaaacttgacca	4	11	2	3			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr7:113519285C>T	ENST00000284601.3	-	4	1930	c.1862G>A	c.(1861-1863)aGa>aAa	p.R621K		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	621					glycogen metabolic process (GO:0005977)	integral component of membrane (GO:0016021)				NS(2)|breast(8)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|liver(1)|lung(43)|ovary(10)|pancreas(7)|prostate(3)|skin(15)|stomach(1)|upper_aerodigestive_tract(2)	121						ATTTCCAGTTCTTGATGAACA	0.383																																					p.R621K		Atlas-SNP	.											.	PPP1R3A	317	.	0			c.G1862A						.						94	92	92					7																	113519285		2203	4300	6503	SO:0001583	missense	5506	exon4			CCAGTTCTTGATG	AF024578	CCDS5759.1	7q31.1	2012-04-17	2011-10-04	2001-07-02	ENSG00000154415	ENSG00000154415	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9291	protein-coding gene	gene with protein product	"glycogen-associated regulatory subunit of protein phosphatase-1", "protein phosphatase 1 regulatory subunit GM"	600917	"protein phosphatase 1, regulatory (inhibitor) subunit 3A (glycogen and sarcoplasmic reticulum binding subunit, skeletal muscle)", "protein phosphatase 1, regulatory (inhibitor) subunit 3A"	PPP1R3		7926294	Standard	NM_002711		Approved	GM	uc010ljy.1	Q16821	OTTHUMG00000156944	ENST00000284601.3:c.1862G>A	chr7.hg19:g.113519285C>T	ENSP00000284601:p.Arg621Lys	273.0	0.0		309.0	163.0	NM_002711	A0AVQ2|A4D0T6|O43476|Q75LN8|Q7KYM8|Q86UI6	Missense_Mutation	SNP	ENST00000284601.3	hg19	CCDS5759.1	.	.	.	.	.	.	.	.	.	.	C	1.268	-0.613821	0.03690	.	.	ENSG00000154415	ENST00000284601	T	0.17528	2.27	6.02	-1.78	0.07957	.	0.538685	0.18505	N	0.139238	T	0.12390	0.0301	M	0.67953	2.075	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.30060	-0.9991	10	0.17369	T	0.5	-0.4639	2.544	0.04732	0.1062:0.2339:0.1966:0.4633	.	621	Q16821	PPR3A_HUMAN	K	621	ENSP00000284601:R621K	ENSP00000284601:R621K	R	-	2	0	PPP1R3A	113306521	0.158000	0.22850	0.683000	0.30040	0.044000	0.14063	0.130000	0.15850	-0.035000	0.13691	-0.727000	0.03589	AGA	.	.		0.383	PPP1R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346724.1	NM_002711		T	113519285	C	T	113519285	3	4	266	1	0	0	0	0	1	0	0	0	12383	913	32	3	1510	3	PPP1R3A	7	113519285	Missense_Mutation	SNP	C	TCGA-FV-A3R2-01A-11D-A22F-10	47055366	113519285	45619378	27	38985										
WNT2	7472	hgsc.bcm.edu	37	chr7	116955172	116955172	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	attcatcagggctctggcatCctttcctttcctttcctttg	6	13	3	0			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr7:116955172C>T	ENST00000265441.3	-	3	840	c.541G>A	c.(541-543)Gat>Aat	p.D181N	AC002465.2_ENST00000436097.1_RNA	NM_003391.2	NP_003382.1	P09544	WNT2_HUMAN	wingless-type MMTV integration site family member 2	181					atrial cardiac muscle tissue morphogenesis (GO:0055009)|canonical Wnt signaling pathway (GO:0060070)|cardiac epithelial to mesenchymal transition (GO:0060317)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|iris morphogenesis (GO:0061072)|labyrinthine layer blood vessel development (GO:0060716)|lens development in camera-type eye (GO:0002088)|lung development (GO:0030324)|lung induction (GO:0060492)|mammary gland epithelium development (GO:0061180)|neuron differentiation (GO:0030182)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)			breast(2)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|ovary(3)|prostate(1)|skin(2)	31	all_epithelial(6;2.24e-06)|Lung NSC(10;0.000936)|all_lung(10;0.00109)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		GCTCTGGCAtcctttcctttc	0.463																																					p.D181N		Atlas-SNP	.											.	WNT2	56	.	0			c.G541A						.						132	121	125					7																	116955172		2203	4300	6503	SO:0001583	missense	7472	exon3			TGGCATCCTTTCC	X07876	CCDS5771.1	7q31	2013-02-28			ENSG00000105989	ENSG00000105989		"Wingless-type MMTV integration sites", "Endogenous ligands"	12780	protein-coding gene	gene with protein product	"secreted growth factor"	147870		INT1L1		2971536	Standard	NM_003391		Approved	IRP	uc003viz.3	P09544	OTTHUMG00000023428	ENST00000265441.3:c.541G>A	chr7.hg19:g.116955172C>T	ENSP00000265441:p.Asp181Asn	195.0	0.0		354.0	94.0	NM_003391	A4D0V1|Q75N05|Q9UDP9	Missense_Mutation	SNP	ENST00000265441.3	hg19	CCDS5771.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.353979	0.82243	.	.	ENSG00000105989	ENST00000265441	T	0.76839	-1.05	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.88028	0.6327	M	0.73319	2.225	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.86549	0.1833	10	0.45353	T	0.12	.	20.0965	0.97849	0.0:1.0:0.0:0.0	.	181;181	A4D0V1;P09544	.;WNT2_HUMAN	N	181	ENSP00000265441:D181N	ENSP00000265441:D181N	D	-	1	0	WNT2	116742408	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.050000	0.71063	2.824000	0.97209	0.655000	0.94253	GAT	.	.		0.463	WNT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059749.3	NM_003391		T	116955172	C	T	116955172	3	4	266	1	0	0	0	0	1	0	0	0	17401	855	30	3	553	3	WNT2	7	116955172	Missense_Mutation	SNP	C	TCGA-FV-A3R2-01A-11D-A22F-10	3435887	116955172	42183491	28	38986										
KCNH2	3757	hgsc.bcm.edu	37	chr7	150644109	150644109	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	ctctgtagcagctgcaggacAgtggccatgtctgcactcag	12	12	3	0			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr7:150644109A>T	ENST00000262186.5	-	14	3587	c.3186T>A	c.(3184-3186)acT>acA	p.T1062T	KCNH2_ENST00000330883.4_Silent_p.T722T|KCNH2_ENST00000392968.2_Silent_p.T966T	NM_000238.3	NP_000229.1	Q12809	KCNH2_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 2	1062					cardiac muscle contraction (GO:0060048)|cellular response to drug (GO:0035690)|membrane depolarization during action potential (GO:0086010)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of potassium ion export (GO:1902303)|negative regulation of potassium ion transmembrane transport (GO:1901380)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|identical protein binding (GO:0042802)|inward rectifier potassium channel activity (GO:0005242)|phosphorelay sensor kinase activity (GO:0000155)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			NS(1)|cervix(1)|endometrium(10)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	42	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Alfuzosin(DB00346)|Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Cisapride(DB00604)|Dofetilide(DB00204)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Halofantrine(DB01218)|Ibutilide(DB00308)|Imipramine(DB00458)|Miconazole(DB01110)|Pimozide(DB01100)|Prazosin(DB00457)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terazosin(DB01162)|Thioridazine(DB00679)|Verapamil(DB00661)	GCTGCAGGACAGTGGCCATGT	0.667																																					p.T1062T	GBM(137;110 1844 13671 20123 45161)	Atlas-SNP	.											.	KCNH2	157	.	0			c.T3186A						.						40	43	42					7																	150644109		2203	4300	6503	SO:0001819	synonymous_variant	3757	exon14			CAGGACAGTGGCC	U04270	CCDS5910.1, CCDS5911.1	7q36.1	2014-09-17			ENSG00000055118	ENSG00000055118		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6251	protein-coding gene	gene with protein product		152427		LQT2		18616963, 7842012, 8159766, 16382104	Standard	NM_000238		Approved	Kv11.1, HERG, erg1	uc003wic.3	Q12809	OTTHUMG00000158341	ENST00000262186.5:c.3186T>A	chr7.hg19:g.150644109A>T		98.0	0.0		166.0	46.0	NM_000238	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Silent	SNP	ENST00000262186.5	hg19	CCDS5910.1																																																																																			.	.		0.667	KCNH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350741.2	NM_000238		T	150644109	A	T	150644109	2	4	266	1	0	0	0	0	0	0	0	1	8041	175	7	4		4	KCNH2	7	150644109	Silent	SNP	A	TCGA-FV-A3R2-01A-11D-A22F-10	33688937	150644109	8494554	29	38987										
PI15	51050	hgsc.bcm.edu	37	chr8	75761417	75761417	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	gttcatcttgtcctccaagtTatgggggatcttgtactgac	10	9	3	1			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr8:75761417T>A	ENST00000260113.2	+	6	885	c.706T>A	c.(706-708)Tat>Aat	p.Y236N	PI15_ENST00000523773.1_Missense_Mutation_p.Y236N|RP11-758M4.4_ENST00000518128.1_RNA|RP11-758M4.4_ENST00000523860.1_RNA|RP11-758M4.4_ENST00000522914.1_RNA	NM_015886.3	NP_056970.1	O43692	PI15_HUMAN	peptidase inhibitor 15	236						extracellular vesicular exosome (GO:0070062)	peptidase inhibitor activity (GO:0030414)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|pancreas(1)|skin(1)	30	Breast(64;0.137)		BRCA - Breast invasive adenocarcinoma(89;0.104)|Epithelial(68;0.118)			TCCTCCAAGTTATGGGGGATC	0.393																																					p.Y236N		Atlas-SNP	.											.	PI15	73	.	0			c.T706A						.						199	177	184					8																	75761417		2203	4300	6503	SO:0001583	missense	51050	exon6			CCAAGTTATGGGG	D45027	CCDS6218.1	8q13.3	2005-08-17	2005-08-17		ENSG00000137558	ENSG00000137558			8946	protein-coding gene	gene with protein product		607076	"protease inhibitor 15"			8882727, 9473672	Standard	XM_005251255		Approved	P25TI	uc003yal.3	O43692	OTTHUMG00000164528	ENST00000260113.2:c.706T>A	chr8.hg19:g.75761417T>A	ENSP00000260113:p.Tyr236Asn	191.0	0.0		259.0	65.0	NM_015886	Q68CY1	Missense_Mutation	SNP	ENST00000260113.2	hg19	CCDS6218.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.465498	0.84425	.	.	ENSG00000137558	ENST00000260113;ENST00000523773	T;T	0.10099	2.91;2.91	5.15	5.15	0.70609	.	0.059145	0.64402	D	0.000001	T	0.36331	0.0963	M	0.82630	2.6	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.14531	-1.0469	10	0.46703	T	0.11	.	15.4212	0.75011	0.0:0.0:0.0:1.0	.	236	O43692	PI15_HUMAN	N	236	ENSP00000260113:Y236N;ENSP00000428567:Y236N	ENSP00000260113:Y236N	Y	+	1	0	PI15	75923972	1.000000	0.71417	0.992000	0.48379	0.949000	0.60115	7.482000	0.81143	2.285000	0.76669	0.477000	0.44152	TAT	.	.		0.393	PI15-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379115.1	NM_015886		A	75761417	T	A	75761417	3	1	266	1	0	0	0	0	1	0	0	0	11877	1754	61	4	724	4	PI15	8	75761417	Missense_Mutation	SNP	T	TCGA-FV-A3R2-01A-11D-A22F-10		75761417	70602605	30	38988										
ANGPT1	284	hgsc.bcm.edu	37	chr8	108334350	108334350	+	5'UTR	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	atttctaagattttatgttcTaataaactacaaggaagtga	6	4	2	2			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr8:108334350T>A	ENST00000520734.1	-	0	267				ANGPT1_ENST00000520052.1_5'UTR|ANGPT1_ENST00000518386.1_5'Flank			Q15389	ANGP1_HUMAN	angiopoietin 1						activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell-substrate adhesion (GO:0031589)|glomerulus vasculature development (GO:0072012)|hemopoiesis (GO:0030097)|heparin biosynthetic process (GO:0030210)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of vascular permeability (GO:0043116)|positive chemotaxis (GO:0050918)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of receptor internalization (GO:0002092)|protein localization to cell surface (GO:0034394)|regulation of satellite cell proliferation (GO:0014842)|sprouting angiogenesis (GO:0002040)|Tie signaling pathway (GO:0048014)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(13)|ovary(4)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	43	Breast(1;5.06e-08)		OV - Ovarian serous cystadenocarcinoma(57;5.53e-09)			TTTTATGTTCTAATAAACTAC	0.303																																					p.L194F		Atlas-SNP	.											.	ANGPT1	111	.	0			c.A582T						.						82	78	80					8																	108334350		2203	4300	6503	SO:0001623	5_prime_UTR_variant	284	exon4			ATGTTCTAATAAA	D13628	CCDS6306.1, CCDS56551.1	8q23.1	2013-02-06			ENSG00000154188	ENSG00000154188		"Fibrinogen C domain containing"	484	protein-coding gene	gene with protein product		601667				9545648	Standard	NM_001146		Approved	KIAA0003, Ang1	uc003ymn.3	Q15389	OTTHUMG00000164812	ENST00000520734.1:c.-19A>T	chr8.hg19:g.108334350T>A		129.0	0.0		210.0	45.0	NM_001199859	Q5HYA0	Missense_Mutation	SNP	ENST00000520734.1	hg19		.	.	.	.	.	.	.	.	.	.	T	17.54	3.414374	0.62511	.	.	ENSG00000154188	ENST00000517746;ENST00000297450;ENST00000395820	T;T	0.44881	0.91;0.91	5.77	4.61	0.57282	.	0.000000	0.56097	D	0.000027	T	0.59473	0.2196	M	0.76838	2.35	0.80722	D	1	D;D	0.64830	0.994;0.994	D;D	0.65140	0.932;0.932	T	0.61869	-0.6974	10	0.87932	D	0	.	7.4641	0.27312	0.1346:0.0711:0.0:0.7943	.	194;194	Q5HYA0;Q15389	.;ANGP1_HUMAN	F	194;194;6	ENSP00000428340:L194F;ENSP00000297450:L194F	ENSP00000297450:L194F	L	-	3	2	ANGPT1	108403526	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	2.466000	0.45084	1.017000	0.39495	0.533000	0.62120	TTA	.	.		0.303	ANGPT1-002	PUTATIVE	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000380428.2	NM_001146, NM_139290		A	108334350	T	A	108334350	1	1	266	0	1	0	0	0	0	0	0	0	610	1519	53	4		4	ANGPT1	8	108334350	5'UTR	SNP	T	TCGA-FV-A3R2-01A-11D-A22F-10	32572933	108334350	38029672	31	38989										
FER1L6	654463	hgsc.bcm.edu	37	chr8	125072474	125072474	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	gttgagccaccagacatcacCcagatctacccggttcctgc	8	16	2	3			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr8:125072474C>G	ENST00000522917.1	+	23	3134	c.2928C>G	c.(2926-2928)acC>acG	p.T976T	FER1L6-AS2_ENST00000520031.1_RNA|FER1L6-AS2_ENST00000601180.1_RNA|FER1L6_ENST00000399018.1_Silent_p.T976T	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	976						integral component of membrane (GO:0016021)				NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			CAGACATCACCCAGATCTACC	0.572																																					p.T976T		Atlas-SNP	.											.	FER1L6	268	.	0			c.C2928G						.						104	116	112					8																	125072474		2198	4297	6495	SO:0001819	synonymous_variant	654463	exon23			CATCACCCAGATC	AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"fer-1-like 6 (C. elegans)"				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.2928C>G	chr8.hg19:g.125072474C>G		52.0	0.0		71.0	13.0	NM_001039112		Silent	SNP	ENST00000522917.1	hg19	CCDS43767.1																																																																																			.	.		0.572	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112		G	125072474	C	G	125072474	2	3	266	1	0	0	0	0	0	0	0	1	5823	610	22	4		4	FER1L6	8	125072474	Silent	SNP	C	TCGA-FV-A3R2-01A-11D-A22F-10	16738124	125072474	21291548	32	38990										
ZNF618	114991	hgsc.bcm.edu	37	chr9	116731402	116731402	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	gggtttcttttgcaggctgaCggagccagtgcagccggaag	16	9	1	1			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr9:116731402C>T	ENST00000374126.5	+	2	138	c.39C>T	c.(37-39)gaC>gaT	p.D13D	ZNF618_ENST00000288466.7_Silent_p.D13D			Q5T7W0	ZN618_HUMAN	zinc finger protein 618	13					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|lung(10)|urinary_tract(1)	16						TGCAGGCTGACGGAGCCAGTG	0.557																																					p.D13D		Atlas-SNP	.											.	ZNF618	184	.	0			c.C39T						.						134	149	144					9																	116731402		2016	4205	6221	SO:0001819	synonymous_variant	114991	exon2			GGCTGACGGAGCC	BC012922	CCDS48008.1	9q33.1	2010-04-21			ENSG00000157657	ENSG00000157657		"Zinc fingers, C2H2-type"	29416	protein-coding gene	gene with protein product	"neural precursor cell expressed, developmentally down-regulated 10"					11853319	Standard	NM_133374		Approved	KIAA1952, NEDD10	uc004bic.3	Q5T7W0	OTTHUMG00000020532	ENST00000374126.5:c.39C>T	chr9.hg19:g.116731402C>T		30.0	0.0		20.0	16.0	NM_133374	B9EG82|Q4G0X6|Q5T7W1|Q6ZT53|Q7Z6B9|Q8TF49|Q96E49	Silent	SNP	ENST00000374126.5	hg19																																																																																				.	.		0.557	ZNF618-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000053749.1	XM_054983		T	116731402	C	T	116731402	2	4	266	1	0	0	0	0	0	0	0	1	18057	535	19	1		1	ZNF618	9	116731402	Silent	SNP	C	TCGA-FV-A3R2-01A-11D-A22F-10		116731402	24482029	33	38991										
TSC1	7248	hgsc.bcm.edu	37	chr9	135786464	135786464	+	Frame_Shift_Del	DEL	T	T	-													0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	aggagaagttggaggagtggTcataccacaaaccatagatg							TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr9:135786464delT	ENST00000298552.3	-	11	1287	c.1066delA	c.(1066-1068)accfs	p.T357fs	TSC1_ENST00000545250.1_Frame_Shift_Del_p.T306fs|TSC1_ENST00000440111.2_Frame_Shift_Del_p.T357fs	NM_000368.4|NM_001162426.1|NM_001162427.1	NP_000359.1|NP_001155898.1|NP_001155899.1	Q92574	TSC1_HUMAN	tuberous sclerosis 1	357					activation of Rho GTPase activity (GO:0032862)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|insulin receptor signaling pathway (GO:0008286)|kidney development (GO:0001822)|myelination (GO:0042552)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of TOR signaling (GO:0032007)|negative regulation of translation (GO:0017148)|neural tube closure (GO:0001843)|positive regulation of focal adhesion assembly (GO:0051894)|potassium ion transport (GO:0006813)|protein heterooligomerization (GO:0051291)|protein stabilization (GO:0050821)|regulation of cell cycle (GO:0051726)|regulation of cell-matrix adhesion (GO:0001952)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of protein kinase activity (GO:0045859)|regulation of stress fiber assembly (GO:0051492)|regulation of translation (GO:0006417)|response to insulin (GO:0032868)|rRNA export from nucleus (GO:0006407)|synapse organization (GO:0050808)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|lamellipodium (GO:0030027)|membrane (GO:0016020)|protein complex (GO:0043234)|TSC1-TSC2 complex (GO:0033596)	chaperone binding (GO:0051087)|GTPase regulator activity (GO:0030695)|protein N-terminus binding (GO:0047485)	p.?(1)		NS(1)|bone(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(9)|lung(20)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	65				OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06)		GGAGGAGTGGTCATACCACAA	0.438			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.T356fs		Atlas-Indel,Pindel	.	yes	Rec		Tuberous sclerosis 1	9	9q34	7248	tuberous sclerosis 1 gene		"E, O"	TSC1,NS,neuroblastoma,0,1	TSC1	167	.	1	Unknown(1)	bone(1)	c.1067delC						.						618	584	596					9																	135786464		2203	4300	6503	SO:0001589	frameshift_variant	7248	exon11	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	.	AF013168	CCDS6956.1, CCDS55350.1	9q34	2014-09-17			ENSG00000165699	ENSG00000165699			12362	protein-coding gene	gene with protein product		605284		TSC		9242607, 10806479	Standard	NM_000368		Approved	KIAA0243, LAM, hamartin	uc004cca.2	Q92574	OTTHUMG00000020844	ENST00000298552.3:c.1066delA	chr9.hg19:g.135786464delT	ENSP00000298552:p.Thr357fs	86.0	0.0		49.0	28.0	NM_001162426	B7Z897|Q5VVN5	Frame_Shift_Del	DEL	ENST00000298552.3	hg19	CCDS6956.1																																																																																			.	.		0.438	TSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054799.1			-	135786464	T	-	135786464	7	5	266	1	0	1	0	1	0	0	0	0	16620	1667	58	0	2480	0	TSC1	9	135786464	Frame_Shift_Del	DEL	T	TCGA-FV-A3R2-01A-11D-A22F-10	19055062	135786464	5426967	34	38992										
FANK1	92565	hgsc.bcm.edu	37	chr10	127697046	127697046	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	tgcggtgtcgggaaatcagaGggtggcctctcttctaattg	14	8	3	1			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr10:127697046G>T	ENST00000368693.1	+	8	880	c.776G>T	c.(775-777)aGg>aTg	p.R259M	FANK1_ENST00000477963.1_3'UTR|FANK1_ENST00000368695.1_Missense_Mutation_p.R253M			Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains 1	259						cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(10)|ovary(1)|urinary_tract(1)	21		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)				GGAAATCAGAGGGTGGCCTCT	0.532																																					p.R259M		Atlas-SNP	.											.	FANK1	46	.	0			c.G776T						.						111	107	109					10																	127697046		2203	4300	6503	SO:0001583	missense	92565	exon8			ATCAGAGGGTGGC	BC024189	CCDS31309.1	10q26.2	2013-02-11	2005-03-01		ENSG00000203780	ENSG00000203780		"Ankyrin repeat domain containing", "Fibronectin type III domain containing"	23527	protein-coding gene	gene with protein product		611640	"fibronectin type 3 and ankyrin repeat domains 1"			12477932	Standard	NM_145235		Approved		uc001ljh.4	Q8TC84	OTTHUMG00000019241	ENST00000368693.1:c.776G>T	chr10.hg19:g.127697046G>T	ENSP00000357682:p.Arg259Met	89.0	0.0		109.0	41.0	NM_145235	Q6UXY9|Q6X7T6	Missense_Mutation	SNP	ENST00000368693.1	hg19	CCDS31309.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.49|11.49	1.653705|1.653705	0.29425|0.29425	.|.	.|.	ENSG00000203780|ENSG00000203780	ENST00000456942|ENST00000368695;ENST00000368693;ENST00000368691;ENST00000368692	.|T;T;T	.|0.65732	.|-0.14;-0.14;-0.17	5.62|5.62	0.54|0.54	0.17163|0.17163	.|Ankyrin repeat-containing domain (4);	.|1.429690	.|0.04021	.|N	.|0.299830	T|T	0.59649|0.59649	0.2209|0.2209	L|L	0.37507|0.37507	1.11|1.11	0.58432|0.58432	D|D	0.999997|0.999997	.|P;P;P	.|0.48016	.|0.904;0.786;0.73	.|B;B;P	.|0.44623	.|0.443;0.326;0.455	T|T	0.50898|0.50898	-0.8773|-0.8773	5|10	.|0.72032	.|D	.|0.01	-2.3728|-2.3728	11.8524|11.8524	0.52419|0.52419	0.881:0.0:0.119:0.0|0.881:0.0:0.119:0.0	.|.	.|285;259;259	.|Q8TC84-3;Q8TC84-2;Q8TC84	.|.;.;FANK1_HUMAN	W|M	154|253;259;237;285	.|ENSP00000357684:R253M;ENSP00000357682:R259M;ENSP00000357680:R237M	.|ENSP00000357680:R237M	G|R	+|+	1|2	0|0	FANK1|FANK1	127687036|127687036	0.324000|0.324000	0.24652|0.24652	0.287000|0.287000	0.24848|0.24848	0.048000|0.048000	0.14542|0.14542	0.655000|0.655000	0.24933|0.24933	-0.135000|-0.135000	0.11495|0.11495	0.655000|0.655000	0.94253|0.94253	GGG|AGG	.	.		0.532	FANK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_145235		T	127697046	G	T	127697046	3	4	266	1	0	0	0	0	1	0	0	0	5680	1000	35	3	806	3	FANK1	10	127697046	Missense_Mutation	SNP	G	TCGA-FV-A3R2-01A-11D-A22F-10		127697046	7837701	35	38993										
IFITM5	387733	hgsc.bcm.edu	37	chr11	299408	299408	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	ctcgaggcggggggtgcgggGcccccagtgtgagggctgtg	22	10	0	1			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr11:299408G>A	ENST00000382614.2	-	1	118	c.83C>T	c.(82-84)gCc>gTc	p.A28V		NM_001025295.2	NP_001020466.1	A6NNB3	IFM5_HUMAN	interferon induced transmembrane protein 5	28					bone mineralization (GO:0030282)|regulation of bone mineralization (GO:0030500)|response to biotic stimulus (GO:0009607)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;5.73e-28)|Epithelial(43;3.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.14e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0328)|LUSC - Lung squamous cell carcinoma(625;0.122)		GGGGTGCGGGGCCCCCAGTGT	0.682																																					p.A28V		Atlas-SNP	.											.	IFITM5	12	.	0			c.C83T						.						22	22	22					11																	299408		2184	4278	6462	SO:0001583	missense	387733	exon1			TGCGGGGCCCCCA	AA463818, CR747200, DY654432	CCDS31323.1	11p15.5	2010-05-12			ENSG00000206013	ENSG00000206013			16644	protein-coding gene	gene with protein product		614757				11106657, 12659663, 18442316	Standard	NM_001025295		Approved	fragilis4, Hrmp1, BRIL	uc001low.2	A6NNB3	OTTHUMG00000165355	ENST00000382614.2:c.83C>T	chr11.hg19:g.299408G>A	ENSP00000372059:p.Ala28Val	35.0	0.0		61.0	29.0	NM_001025295		Missense_Mutation	SNP	ENST00000382614.2	hg19	CCDS31323.1	.	.	.	.	.	.	.	.	.	.	G	10.12	1.262466	0.23051	.	.	ENSG00000206013	ENST00000382614	D	0.86164	-2.08	4.23	3.3	0.37823	.	0.733349	0.12020	N	0.507048	T	0.81688	0.4875	L	0.38175	1.15	0.09310	N	1	B	0.23442	0.085	B	0.25759	0.063	T	0.68135	-0.5489	10	0.33940	T	0.23	-5.7791	11.9061	0.52713	0.0:0.0:0.8239:0.1761	.	28	A6NNB3	IFM5_HUMAN	V	28	ENSP00000372059:A28V	ENSP00000372059:A28V	A	-	2	0	IFITM5	289408	0.091000	0.21658	0.001000	0.08648	0.018000	0.09664	1.957000	0.40392	0.722000	0.32252	0.561000	0.74099	GCC	.	.		0.682	IFITM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383588.1	NM_001025295		A	299408	G	A	299408	3	1	266	1	0	0	0	0	1	0	0	0	7538	1203	42	3	323	3	IFITM5	11	299408	Missense_Mutation	SNP	G	TCGA-FV-A3R2-01A-11D-A22F-10		299408	134707108	36	38994										
LGR4	55366	hgsc.bcm.edu	37	chr11	27389536	27389536	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	gtctgagacaaaggaatcttCttcatctgcataatcagagt	8	8	6	2			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr11:27389536C>A	ENST00000379214.4	-	18	3177	c.2734G>T	c.(2734-2736)Gaa>Taa	p.E912*	LGR4_ENST00000389858.4_Nonsense_Mutation_p.E888*	NM_018490.2	NP_060960.2	Q9BXB1	LGR4_HUMAN	leucine-rich repeat containing G protein-coupled receptor 4	912					bone mineralization (GO:0030282)|bone remodeling (GO:0046849)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cell differentiation involved in metanephros development (GO:0072202)|epithelial cell proliferation (GO:0050673)|innate immune response (GO:0045087)|male genitalia development (GO:0030539)|metanephric glomerulus development (GO:0072224)|metanephric nephron tubule morphogenesis (GO:0072282)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast differentiation (GO:0001649)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(10)|ovary(1)	32						AAGGAATCTTCTTCATCTGCA	0.532																																					p.E912X		Atlas-SNP	.											.	LGR4	87	.	0			c.G2734T						.						74	75	75					11																	27389536		2202	4299	6501	SO:0001587	stop_gained	55366	exon18			AATCTTCTTCATC	AF257182	CCDS31449.1	11p14-p13	2012-08-21	2011-01-25	2004-11-12	ENSG00000205213	ENSG00000205213		"GPCR / Class A : Orphans"	13299	protein-coding gene	gene with protein product		606666	"G protein-coupled receptor 48", "leucine-rich repeat-containing G protein-coupled receptor 4"	GPR48		10894923	Standard	NM_018490		Approved		uc001mrj.4	Q9BXB1	OTTHUMG00000133508	ENST00000379214.4:c.2734G>T	chr11.hg19:g.27389536C>A	ENSP00000368516:p.Glu912*	83.0	0.0		58.0	17.0	NM_018490	A6NCH3|G5E9B3|Q8N537|Q9NYD1	Nonsense_Mutation	SNP	ENST00000379214.4	hg19	CCDS31449.1	.	.	.	.	.	.	.	.	.	.	C	43	10.343996	0.99388	.	.	ENSG00000205213	ENST00000379214;ENST00000389858	.	.	.	5.78	5.78	0.91487	.	0.261784	0.44097	D	0.000482	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	20.005	0.97433	0.0:1.0:0.0:0.0	.	.	.	.	X	912;888	.	ENSP00000368516:E912X	E	-	1	0	LGR4	27346112	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.625000	0.83145	2.745000	0.94114	0.555000	0.69702	GAA	.	.		0.532	LGR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257467.1	NM_018490		A	27389536	C	A	27389536	4	1	266	1	0	0	0	0	0	1	0	0	8765	922	32	3	125	3	LGR4	11	27389536	Nonsense_Mutation	SNP	C	TCGA-FV-A3R2-01A-11D-A22F-10	27090128	27389536	107616980	37	38995										
DAGLA	747	hgsc.bcm.edu	37	chr11	61502408	61502408	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	ggctgtaatgccattgccatCcggcgccacttcctggacga	11	14	0	0			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr11:61502408C>A	ENST00000257215.5	+	10	1178	c.1062C>A	c.(1060-1062)atC>atA	p.I354I		NM_006133.2	NP_006124.1	Q9Y4D2	DGLA_HUMAN	diacylglycerol lipase, alpha	354					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|cell death (GO:0008219)|diacylglycerol catabolic process (GO:0046340)|endocannabinoid signaling pathway (GO:0071926)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|liver(2)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	43				READ - Rectum adenocarcinoma(4;0.219)		CCATTGCCATCCGGCGCCACT	0.632																																					p.I354I		Atlas-SNP	.											.	DAGLA	109	.	0			c.C1062A						.						218	198	205					11																	61502408		2202	4299	6501	SO:0001819	synonymous_variant	747	exon10			TGCCATCCGGCGC	AB014559	CCDS31578.1	11q12.3	2008-03-18	2007-02-28	2007-02-28		ENSG00000134780	3.1.1.-		1165	protein-coding gene	gene with protein product	"neural stem cell-derived dendrite regulator"	614015	"chromosome 11 open reading frame 11"	C11orf11		9734811	Standard	NM_006133		Approved	KIAA0659, NSDDR, DAGLALPHA	uc001nsa.3	Q9Y4D2		ENST00000257215.5:c.1062C>A	chr11.hg19:g.61502408C>A		56.0	0.0		37.0	11.0	NM_006133	A7E233|Q6WQJ0	Silent	SNP	ENST00000257215.5	hg19	CCDS31578.1																																																																																			.	.		0.632	DAGLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398516.1	NM_006133		A	61502408	C	A	61502408	2	1	266	1	0	0	0	0	0	0	0	1	4228	845	30	3		3	DAGLA	11	61502408	Silent	SNP	C	TCGA-FV-A3R2-01A-11D-A22F-10	34112872	61502408	73504108	38	38996										
OR10G8	219869	hgsc.bcm.edu	37	chr11	123900948	123900948	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	tgactgttggaatagtggccTcgggctgctttgtcctgata	13	8	0	2			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr11:123900948T>C	ENST00000431524.1	+	1	652	c.619T>C	c.(619-621)Tcg>Ccg	p.S207P		NM_001004464.1	NP_001004464.1	Q8NGN5	O10G8_HUMAN	olfactory receptor, family 10, subfamily G, member 8	207						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(7)|large_intestine(2)|lung(21)|ovary(1)|prostate(5)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	44		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		AATAGTGGCCTCGGGCTGCTT	0.537																																					p.S207P		Atlas-SNP	.											.	OR10G8	132	.	0			c.T619C						.						193	169	177					11																	123900948		2201	4299	6500	SO:0001583	missense	219869	exon1			GTGGCCTCGGGCT	AB065755	CCDS31704.1	11q24.1	2012-08-09			ENSG00000234560	ENSG00000234560		"GPCR / Class A : Olfactory receptors"	14845	protein-coding gene	gene with protein product							Standard	NM_001004464		Approved		uc001pzp.1	Q8NGN5	OTTHUMG00000165968	ENST00000431524.1:c.619T>C	chr11.hg19:g.123900948T>C	ENSP00000389072:p.Ser207Pro	246.0	0.0		215.0	95.0	NM_001004464	B2RNJ3|Q6IEV2	Missense_Mutation	SNP	ENST00000431524.1	hg19	CCDS31704.1	.	.	.	.	.	.	.	.	.	.	T	10.03	1.239663	0.22711	.	.	ENSG00000234560	ENST00000431524	T	0.37584	1.19	2.91	2.91	0.33838	GPCR, rhodopsin-like superfamily (1);	0.953949	0.08599	N	0.921764	T	0.41971	0.1182	N	0.12961	0.28	0.09310	N	1	D	0.53151	0.958	D	0.65573	0.936	T	0.42783	-0.9431	10	0.72032	D	0.01	.	11.0743	0.48021	0.0:0.0:0.0:1.0	.	207	Q8NGN5	O10G8_HUMAN	P	207	ENSP00000389072:S207P	ENSP00000389072:S207P	S	+	1	0	OR10G8	123406158	0.000000	0.05858	0.780000	0.31762	0.263000	0.26337	0.369000	0.20416	1.319000	0.45190	0.455000	0.32223	TCG	.	.		0.537	OR10G8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387270.1	NM_001004464		C	123900948	T	C	123900948	3	2	266	1	0	0	0	0	1	0	0	0	10912	1551	54	2	621	2	OR10G8	11	123900948	Missense_Mutation	SNP	T	TCGA-FV-A3R2-01A-11D-A22F-10	62398540	123900948	11105568	39	38997										
FOXRED1	55572	hgsc.bcm.edu	37	chr11	126145999	126145999	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	accagcctgtggaatgcgccAttgtgatcaacgcagccgga	12	12	1	1			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr11:126145999A>G	ENST00000263578.5	+	8	930	c.856A>G	c.(856-858)Att>Gtt	p.I286V	FOXRED1_ENST00000442061.2_Missense_Mutation_p.I116V|FOXRED1_ENST00000534011.1_3'UTR|FOXRED1_ENST00000532125.1_Missense_Mutation_p.I272V	NM_017547.3	NP_060017.1	Q96CU9	FXRD1_HUMAN	FAD-dependent oxidoreductase domain containing 1	286						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)			breast(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(1)	15	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0729)		GGAATGCGCCATTGTGATCAA	0.642																																					p.I286V		Atlas-SNP	.											.	FOXRED1	38	.	0			c.A856G						.						32	30	31					11																	126145999		2201	4295	6496	SO:0001583	missense	55572	exon8			TGCGCCATTGTGA		CCDS8471.1	11q24.2	2006-02-03			ENSG00000110074	ENSG00000110074			26927	protein-coding gene	gene with protein product		613622				10497265	Standard	NM_017547		Approved	H17	uc001qdi.3	Q96CU9	OTTHUMG00000165827	ENST00000263578.5:c.856A>G	chr11.hg19:g.126145999A>G	ENSP00000263578:p.Ile286Val	94.0	0.0		81.0	25.0	NM_017547	B3KN84|B4DHU2|Q71MG0|Q9BU39|Q9UKY9	Missense_Mutation	SNP	ENST00000263578.5	hg19	CCDS8471.1	.	.	.	.	.	.	.	.	.	.	A	7.716	0.696190	0.15106	.	.	ENSG00000110074	ENST00000263578;ENST00000442061;ENST00000532125	T;T;T	0.80653	-1.4;-1.4;-1.4	5.61	-4.83	0.03161	FAD dependent oxidoreductase (1);	0.654096	0.16038	N	0.232524	T	0.49355	0.1552	N	0.05230	-0.09	0.22096	N	0.999364	B;B;B	0.13145	0.001;0.007;0.001	B;B;B	0.22753	0.002;0.041;0.002	T	0.51442	-0.8705	10	0.06757	T	0.87	-1.6918	4.9131	0.13833	0.2152:0.4994:0.1921:0.0933	.	272;153;286	Q96CU9-3;B4DI59;Q96CU9	.;.;FXRD1_HUMAN	V	286;116;272	ENSP00000263578:I286V;ENSP00000404371:I116V;ENSP00000434178:I272V	ENSP00000263578:I286V	I	+	1	0	FOXRED1	125651209	0.004000	0.15560	0.071000	0.20095	0.665000	0.39181	-1.127000	0.03251	-0.798000	0.04444	-1.834000	0.00590	ATT	.	.		0.642	FOXRED1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386434.1	NM_017547		G	126145999	A	G	126145999	3	3	266	1	0	0	0	0	1	0	0	0	6041	217	8	2	886	2	FOXRED1	11	126145999	Missense_Mutation	SNP	A	TCGA-FV-A3R2-01A-11D-A22F-10	2245051	126145999	8860517	40	38998										
ADCY6	112	hgsc.bcm.edu	37	chr12	49176704	49176704	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	aggctgagggcgggcgggtgCggcgtggaaagccagcagca	21	9	0	1			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr12:49176704C>A	ENST00000307885.4	-	1	1208	c.514G>T	c.(514-516)Gca>Tca	p.A172S	ADCY6_ENST00000550422.1_Missense_Mutation_p.A172S|ADCY6_ENST00000357869.3_Missense_Mutation_p.A172S	NM_015270.3	NP_056085.1	O43306	ADCY6_HUMAN	adenylate cyclase 6	172					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|dopamine receptor signaling pathway (GO:0007212)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|negative regulation of neuron projection development (GO:0010977)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(16)|prostate(1)|skin(1)|urinary_tract(1)	29						CGGGCGGGTGCGGCGTGGAAA	0.647																																					p.A172S		Atlas-SNP	.											ADCY6,bladder,carcinoma,0,1	ADCY6	81	.	0			c.G514T						.						33	34	34					12																	49176704		2203	4300	6503	SO:0001583	missense	112	exon2			CGGGTGCGGCGTG		CCDS8767.1, CCDS8768.1	12q12-q13	2013-02-04				ENSG00000174233	4.6.1.1	"Adenylate cyclases"	237	protein-coding gene	gene with protein product		600294					Standard	NM_015270		Approved	AC6	uc001rsh.4	O43306		ENST00000307885.4:c.514G>T	chr12.hg19:g.49176704C>A	ENSP00000311405:p.Ala172Ser	43.0	0.0		52.0	23.0	NM_020983	Q9NR75|Q9UDB0	Missense_Mutation	SNP	ENST00000307885.4	hg19	CCDS8767.1	.	.	.	.	.	.	.	.	.	.	C	4.574	0.106554	0.08780	.	.	ENSG00000174233	ENST00000357869;ENST00000550422;ENST00000307885	T;T;T	0.23754	1.89;1.89;1.89	5.36	5.36	0.76844	.	0.587296	0.16428	N	0.214838	T	0.14960	0.0361	N	0.11201	0.11	0.09310	N	1	B;B	0.18863	0.031;0.002	B;B	0.20184	0.028;0.003	T	0.13469	-1.0508	10	0.33940	T	0.23	.	11.3629	0.49655	0.0:0.9154:0.0:0.0846	.	172;172	O43306-2;O43306	.;ADCY6_HUMAN	S	172	ENSP00000350536:A172S;ENSP00000446730:A172S;ENSP00000311405:A172S	ENSP00000311405:A172S	A	-	1	0	ADCY6	47462971	0.003000	0.15002	0.130000	0.21974	0.136000	0.21042	1.090000	0.30902	2.515000	0.84797	0.462000	0.41574	GCA	.	.		0.647	ADCY6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408863.1	NM_020983		A	49176704	C	A	49176704	3	1	266	1	0	0	0	0	1	0	0	0	298	768	27	1	3076	1	ADCY6	12	49176704	Missense_Mutation	SNP	C	TCGA-FV-A3R2-01A-11D-A22F-10		49176704	84675191	41	38999										
HNRNPA1	3178	hgsc.bcm.edu	37	chr12	54676893	54676893	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	aggaggcggccctggttactCtggaggaagcagaggctatg	17	8	1	1			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr12:54676893C>G	ENST00000340913.6	+	8	835	c.782C>G	c.(781-783)tCt>tGt	p.S261C	HNRNPA1_ENST00000547276.1_Intron|HNRNPA1_ENST00000546500.1_Intron|HNRNPA1_ENST00000330752.8_Intron|RP11-968A15.8_ENST00000553061.1_RNA	NM_002136.2|NM_031157.2	NP_002127.1|NP_112420.1	P09651	ROA1_HUMAN	heterogeneous nuclear ribonucleoprotein A1	261	Gly-rich.				cell death (GO:0008219)|gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|mRNA transport (GO:0051028)|nuclear export (GO:0051168)|nuclear import (GO:0051170)|RNA export from nucleus (GO:0006405)|RNA splicing (GO:0008380)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)|single-stranded RNA binding (GO:0003727)			endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	20						CCTGGTTACTCTGGAGGAAGC	0.488																																					p.S261C	Colon(83;502 1289 8436 16406 24870)	Atlas-SNP	.											.	HNRNPA1	72	.	0			c.C782G						.						55	57	56					12																	54676893		2005	4171	6176	SO:0001583	missense	3178	exon8			GTTACTCTGGAGG	BC009600	CCDS41793.1, CCDS44909.1	12q13.1	2013-10-11		2007-08-16	ENSG00000135486	ENSG00000135486		"RNA binding motif (RRM) containing"	5031	protein-coding gene	gene with protein product		164017		HNRPA1		1733858	Standard	XR_245923		Approved	hnRNPA1, hnRNP-A1	uc001sfl.3	P09651		ENST00000340913.6:c.782C>G	chr12.hg19:g.54676893C>G	ENSP00000341826:p.Ser261Cys	71.0	0.0		81.0	34.0	NM_031157	A8K4Z8|Q3MIB7|Q6PJZ7	Missense_Mutation	SNP	ENST00000340913.6	hg19	CCDS44909.1	.	.	.	.	.	.	.	.	.	.	C	11.31	1.600276	0.28534	.	.	ENSG00000135486	ENST00000340913	D	0.88818	-2.43	3.87	2.98	0.34508	.	.	.	.	.	D	0.85869	0.5797	L	0.55213	1.73	0.80722	D	1	P	0.46064	0.872	P	0.45071	0.468	T	0.83188	-0.0085	9	0.41790	T	0.15	.	7.6131	0.28142	0.0:0.8837:0.0:0.1163	.	261	P09651	ROA1_HUMAN	C	261	ENSP00000341826:S261C	ENSP00000341826:S261C	S	+	2	0	HNRNPA1	52963160	0.992000	0.36948	1.000000	0.80357	0.981000	0.71138	1.421000	0.34815	1.222000	0.43521	0.305000	0.20034	TCT	.	.		0.488	HNRNPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000405480.1	NM_031157		G	54676893	C	G	54676893	3	3	266	1	0	0	0	0	1	0	0	0	7266	913	32	4	812	4	HNRNPA1	12	54676893	Missense_Mutation	SNP	C	TCGA-FV-A3R2-01A-11D-A22F-10	5500189	54676893	79175002	42	39000										
ANO4	121601	hgsc.bcm.edu	37	chr12	101520844	101520844	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	agcacaccacaacgagtggcCgtgaccatgtaggtgagagg	14	10	0	2			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr12:101520844C>A	ENST00000392977.3	+	27	3074	c.2864C>A	c.(2863-2865)cCg>cAg	p.P955Q	ANO4_ENST00000550015.1_Missense_Mutation_p.P475Q|ANO4_ENST00000299222.9_Missense_Mutation_p.P475Q|ANO4_ENST00000392979.3_Missense_Mutation_p.P920Q			Q32M45	ANO4_HUMAN	anoctamin 4	955					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)	p.P920L(1)		NS(1)|biliary_tract(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(4)|prostate(5)|skin(7)|stomach(2)|urinary_tract(1)	78						AACGAGTGGCCGTGACCATGT	0.483										HNSCC(74;0.22)																											p.P920Q		Atlas-SNP	.											ANO4,rectum,carcinoma,0,1	ANO4	183	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2759A						.						97	66	76					12																	101520844		2203	4300	6503	SO:0001583	missense	121601	exon26			AGTGGCCGTGACC	AK091540	CCDS31884.1, CCDS66445.1	12q23.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000151572	ENSG00000151572		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	23837	protein-coding gene	gene with protein product		610111	"transmembrane protein 16D"	TMEM16D		12739008, 15067359, 24692353	Standard	NM_178826		Approved	FLJ34221, FLJ34272, FLJ35277	uc001thw.2	Q32M45		ENST00000392977.3:c.2864C>A	chr12.hg19:g.101520844C>A	ENSP00000376703:p.Pro955Gln	87.0	0.0		73.0	26.0	NM_178826	Q8NAJ0|Q8NB39|Q8NB53	Missense_Mutation	SNP	ENST00000392977.3	hg19		.	.	.	.	.	.	.	.	.	.	C	25.2	4.614633	0.87359	.	.	ENSG00000151572	ENST00000392979;ENST00000299222;ENST00000392977;ENST00000550015	T;T;T;T	0.72282	-0.59;-0.33;-0.64;-0.33	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.78039	0.4221	L	0.27053	0.805	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.80165	-0.1496	10	0.87932	D	0	.	19.9299	0.97115	0.0:1.0:0.0:0.0	.	475;955;920	Q32M45-3;Q32M45;Q32M45-2	.;ANO4_HUMAN;.	Q	920;475;955;475	ENSP00000376705:P920Q;ENSP00000299222:P475Q;ENSP00000376703:P955Q;ENSP00000450192:P475Q	ENSP00000299222:P475Q	P	+	2	0	ANO4	100044975	1.000000	0.71417	0.972000	0.41901	0.680000	0.39746	7.772000	0.85439	2.769000	0.95229	0.655000	0.94253	CCG	.	.		0.483	ANO4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409295.1	NM_178826		A	101520844	C	A	101520844	3	1	266	1	0	0	0	0	1	0	0	0	699	652	23	1	2857	1	ANO4	12	101520844	Missense_Mutation	SNP	C	TCGA-FV-A3R2-01A-11D-A22F-10	46843951	101520844	32331051	43	39001										
KSR2	283455	hgsc.bcm.edu	37	chr12	118298110	118298110	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	ggtcacctccaggacctcctTgcgcacatcgacgattcgga	10	15	1	0			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr12:118298110T>A	ENST00000339824.5	-	2	1034	c.307A>T	c.(307-309)Aag>Tag	p.K103*	KSR2_ENST00000425217.1_Nonsense_Mutation_p.K74*			Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2	103					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(25)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					AGGACCTCCTTGCGCACATCG	0.632																																					p.K74X		Atlas-SNP	.											.	KSR2	208	.	0			c.A220T						.						57	61	60					12																	118298110		1568	3582	5150	SO:0001587	stop_gained	283455	exon2			CCTCCTTGCGCAC	AY345972	CCDS61250.1	12q24.22-q24.23	2014-08-12			ENSG00000171435	ENSG00000171435			18610	protein-coding gene	gene with protein product		610737				12471243	Standard	NM_173598		Approved	FLJ25965	uc001two.2	Q6VAB6	OTTHUMG00000169020	ENST00000339824.5:c.307A>T	chr12.hg19:g.118298110T>A	ENSP00000339952:p.Lys103*	24.0	0.0		23.0	8.0	NM_173598	A0PJT2|Q3B828|Q8N775	Nonsense_Mutation	SNP	ENST00000339824.5	hg19		.	.	.	.	.	.	.	.	.	.	T	35	5.493094	0.96339	.	.	ENSG00000171435	ENST00000425217;ENST00000339824	.	.	.	4.54	2.09	0.27110	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.5154	0.22244	0.0:0.0849:0.1567:0.7585	.	.	.	.	X	74;103	.	ENSP00000339952:K103X	K	-	1	0	KSR2	116782493	1.000000	0.71417	0.999000	0.59377	0.712000	0.41017	3.307000	0.51888	0.332000	0.23536	0.260000	0.18958	AAG	.	.		0.632	KSR2-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401987.2	NM_173598		A	118298110	T	A	118298110	4	1	266	1	0	0	0	0	0	1	0	0	8591	1821	63	4	2621	4	KSR2	12	118298110	Nonsense_Mutation	SNP	T	TCGA-FV-A3R2-01A-11D-A22F-10	16777266	118298110	15553785	44	39002										
ZNF410	57862	hgsc.bcm.edu	37	chr14	74363143	74363143	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	cagactgtacagaaatccccGgagtttttgtccacttcaga	8	11	1	3	rs150263864		TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr14:74363143G>A	ENST00000555044.1	+	4	488	c.294G>A	c.(292-294)ccG>ccA	p.P98P	ZNF410_ENST00000412490.3_3'UTR|RP5-1021I20.5_ENST00000554009.1_RNA|ZNF410_ENST00000324593.6_Silent_p.P98P|RP5-1021I20.4_ENST00000556551.2_3'UTR|ZNF410_ENST00000442160.3_Silent_p.P115P|ZNF410_ENST00000334521.4_Silent_p.P45P|ZNF410_ENST00000540593.1_Intron|ZNF410_ENST00000556797.1_Silent_p.P45P	NM_001242928.1|NM_021188.2	NP_001229857.1|NP_067011.1	Q86VK4	ZN410_HUMAN	zinc finger protein 410	98					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|large_intestine(3)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	13				BRCA - Breast invasive adenocarcinoma(234;0.00369)		AGAAATCCCCGGAGTTTTTGT	0.478																																					p.P115P		Atlas-SNP	.											.	ZNF410	25	.	0			c.G345A						.	G	,,,,	1,4405	2.1+/-5.4	0,1,2202	137	132	133		345,294,,,294	-10.4	0.4	14	dbSNP_134	133	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,intron,utr-5,coding-synonymous	ZNF410	NM_001242924.1,NM_001242926.1,NM_001242927.1,NM_001242928.1,NM_021188.2	,,,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,,,	115/517,98/432,,,98/479	74363143	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	57862	exon5			ATCCCCGGAGTTT	U90919	CCDS9821.1, CCDS55929.1, CCDS55930.1, CCDS55931.1	14q24.3	2013-01-08				ENSG00000119725		"Zinc fingers, C2H2-type"	20144	protein-coding gene	gene with protein product						12370286	Standard	NM_001242924		Approved	APA1, APA-1	uc010arz.2	Q86VK4		ENST00000555044.1:c.294G>A	chr14.hg19:g.74363143G>A		100.0	0.0		122.0	33.0	NM_001242924	B4DDV5|B4DR78|O00153|Q9BQ19	Silent	SNP	ENST00000555044.1	hg19	CCDS9821.1	.	.	.	.	.	.	.	.	.	.	G	6.079	0.382894	0.11524	2.27E-4	0.0	ENSG00000119725	ENST00000458102	.	.	.	5.3	-10.4	0.00318	.	.	.	.	.	.	.	.	.	.	.	0.58432	D	0.999997	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.2662	0.31815	0.6921:0.0737:0.1204:0.1138	.	.	.	.	.	-1	.	.	.	+	.	.	ZNF410	73432896	0.026000	0.19158	0.400000	0.26346	0.160000	0.22226	-1.039000	0.03550	-2.003000	0.00962	-0.948000	0.02665	.	.	G|1.000;A|0.000		0.478	ZNF410-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412597.1	NM_021188		A	74363143	G	A	74363143	2	1	266	1	0	0	0	0	0	0	0	1	17905	1103	39	1		1	ZNF410	14	74363143	Silent	SNP	G	TCGA-FV-A3R2-01A-11D-A22F-10		74363143	32986397	45	39003										
GSTZ1	2954	hgsc.bcm.edu	37	chr14	77796672	77796672	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	ggtgaccatggctgatctgtGcttggtgcctcaggtggcaa	15	9	2	2			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr14:77796672G>T	ENST00000556627.1	+	7	544	c.413G>T	c.(412-414)tGc>tTc	p.C138F	GSTZ1_ENST00000393734.1_Missense_Mutation_p.C110F|GSTZ1_ENST00000554279.1_Missense_Mutation_p.C151F|GSTZ1_ENST00000216465.5_Missense_Mutation_p.C165F|GSTZ1_ENST00000557053.1_Missense_Mutation_p.C68F|GSTZ1_ENST00000557639.1_Missense_Mutation_p.C110F|GSTZ1_ENST00000553586.1_Missense_Mutation_p.C166F|GSTZ1_ENST00000361389.4_Missense_Mutation_p.C110F|GSTZ1_ENST00000349555.3_Missense_Mutation_p.C123F			O43708	MAAI_HUMAN	glutathione S-transferase zeta 1	165	GST C-terminal.				cellular nitrogen compound metabolic process (GO:0034641)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|L-phenylalanine catabolic process (GO:0006559)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	glutathione peroxidase activity (GO:0004602)|glutathione transferase activity (GO:0004364)|maleylacetoacetate isomerase activity (GO:0016034)|protein homodimerization activity (GO:0042803)			lung(2)|prostate(1)	3			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)	Glutathione(DB00143)	GCTGATCTGTGCTTGGTGCCT	0.612																																					p.C165F		Atlas-SNP	.											.	GSTZ1	35	.	0			c.G494T						.						196	173	180					14																	77796672		2203	4300	6503	SO:0001583	missense	2954	exon8			ATCTGTGCTTGGT	U86529	CCDS9858.1, CCDS9859.1, CCDS9860.1	14q24.3	2012-06-22	2012-06-22		ENSG00000100577	ENSG00000100577	5.2.1.2, 2.5.1.18	"Glutathione S-transferases / Soluble"	4643	protein-coding gene	gene with protein product	"maleylacetoacetate isomerase"	603758	"glutathione transferase zeta 1"			9396740, 9417084	Standard	NM_001513		Approved	GSTZ1-1, MAAI, MAI	uc001xtj.3	O43708	OTTHUMG00000171551	ENST00000556627.1:c.413G>T	chr14.hg19:g.77796672G>T	ENSP00000450487:p.Cys138Phe	79.0	0.0		72.0	27.0	NM_145870	A6NED0|A6NNB8|A8MWD7|B2RCK3|O15308|O75430|Q6IB17|Q7Z610|Q9BV63	Missense_Mutation	SNP	ENST00000556627.1	hg19		.	.	.	.	.	.	.	.	.	.	G	18.00	3.524815	0.64747	.	.	ENSG00000100577	ENST00000216465;ENST00000361389;ENST00000554279;ENST00000557639;ENST00000349555;ENST00000556627;ENST00000557053;ENST00000393734;ENST00000553586	T;T;T;T;T;T;T;T;T	0.01998	4.51;4.51;4.51;4.51;4.51;4.51;4.51;4.51;4.51	5.62	5.62	0.85841	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);Glutathione S-transferase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.05686	0.0149	L	0.55017	1.72	0.80722	D	1	P;D	0.56035	0.763;0.974	P;P	0.48627	0.582;0.584	T	0.35992	-0.9766	10	0.45353	T	0.12	-0.1006	16.5453	0.84444	0.0:0.0:1.0:0.0	.	123;165	A6NED0;O43708	.;MAAI_HUMAN	F	165;110;151;110;123;138;68;110;166	ENSP00000216465:C165F;ENSP00000354959:C110F;ENSP00000452498:C151F;ENSP00000451927:C110F;ENSP00000314404:C123F;ENSP00000450487:C138F;ENSP00000451150:C68F;ENSP00000377335:C110F;ENSP00000451976:C166F	ENSP00000216465:C165F	C	+	2	0	GSTZ1	76866425	1.000000	0.71417	1.000000	0.80357	0.828000	0.46876	6.841000	0.75374	2.648000	0.89879	0.462000	0.41574	TGC	.	.		0.612	GSTZ1-012	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000414090.1	NM_145870		T	77796672	G	T	77796672	3	4	266	1	0	0	0	0	1	0	0	0	6857	1319	46	3	524	3	GSTZ1	14	77796672	Missense_Mutation	SNP	G	TCGA-FV-A3R2-01A-11D-A22F-10	3433529	77796672	29552868	46	39004										
BTBD7	55727	hgsc.bcm.edu	37	chr14	93720038	93720038	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	aagagtcgaggacgaacataGatgccagcatttttttgccg	11	8	0	2			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr14:93720038G>T	ENST00000334746.5	-	7	2014	c.1707C>A	c.(1705-1707)atC>atA	p.I569I	BTBD7_ENST00000554565.1_Silent_p.I218I|BTBD7_ENST00000393170.2_Silent_p.I143I	NM_001002860.2	NP_001002860.2	Q9P203	BTBD7_HUMAN	BTB (POZ) domain containing 7	569					multicellular organismal development (GO:0007275)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)	nucleus (GO:0005634)				breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|skin(8)|upper_aerodigestive_tract(1)	35		all_cancers(154;0.08)		Epithelial(152;0.196)|COAD - Colon adenocarcinoma(157;0.212)|all cancers(159;0.223)		GACGAACATAGATGCCAGCAT	0.403																																					p.I569I		Atlas-SNP	.											.	BTBD7	112	.	0			c.C1707A						.						172	155	161					14																	93720038		2203	4300	6503	SO:0001819	synonymous_variant	55727	exon7			AACATAGATGCCA	AB040958	CCDS32146.1, CCDS32147.1, CCDS73684.1	14q32.13	2013-01-08			ENSG00000011114	ENSG00000011114		"BTB/POZ domain containing"	18269	protein-coding gene	gene with protein product		610386				10819331, 11527404	Standard	NM_001289133		Approved	FLJ10648, FUP1	uc001ybo.3	Q9P203	OTTHUMG00000171269	ENST00000334746.5:c.1707C>A	chr14.hg19:g.93720038G>T		72.0	0.0		90.0	33.0	NM_001002860	A8K5V7|Q69Z05|Q7Z308|Q86TS0|Q9HAA4|Q9NVM0	Silent	SNP	ENST00000334746.5	hg19	CCDS32146.1																																																																																			.	.		0.403	BTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412701.1	NM_001002860		T	93720038	G	T	93720038	2	4	266	1	0	0	0	0	0	0	0	1	1548	932	33	3		3	BTBD7	14	93720038	Silent	SNP	G	TCGA-FV-A3R2-01A-11D-A22F-10	15923366	93720038	13629502	47	39005										
NARG2	79664	hgsc.bcm.edu	37	chr15	60740303	60740303	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	ttcctgaggagctaggtattCcgatgtatcttcaacatagt	9	8	2	1			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr15:60740303C>T	ENST00000261520.4	-	11	2395	c.2161G>A	c.(2161-2163)Gaa>Aaa	p.E721K	NARG2_ENST00000439632.1_Missense_Mutation_p.E584K	NM_024611.4	NP_078887.2														breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	32						GCTAGGTATTCCGATGTATCT	0.368																																					p.E721K		Atlas-SNP	.											.	NARG2	82	.	0			c.G2161A						.						75	71	73					15																	60740303		2203	4300	6503	SO:0001583	missense	79664	exon11			GGTATTCCGATGT																												ENST00000261520.4:c.2161G>A	chr15.hg19:g.60740303C>T	ENSP00000261520:p.Glu721Lys	62.0	0.0		77.0	31.0	NM_024611		Missense_Mutation	SNP	ENST00000261520.4	hg19	CCDS10176.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.819076	0.90873	.	.	ENSG00000128915	ENST00000261520;ENST00000439632	.	.	.	5.99	5.02	0.67125	NMDA receptor-regulated gene protein 2 (1);	0.096319	0.64402	D	0.000001	T	0.66416	0.2787	L	0.44542	1.39	0.39315	D	0.96514	D	0.63046	0.992	D	0.63192	0.912	T	0.69179	-0.5213	9	0.72032	D	0.01	-28.0583	14.1784	0.65557	0.0:0.8508:0.1492:0.0	.	721	Q659A1	NARG2_HUMAN	K	721;584	.	ENSP00000261520:E721K	E	-	1	0	NARG2	58527595	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	1.964000	0.40462	2.831000	0.97527	0.650000	0.86243	GAA	.	.		0.368	NARG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256136.1			T	60740303	C	T	60740303	3	4	266	1	0	0	0	0	1	0	0	0	10178	864	30	3	811	3	NARG2	15	60740303	Missense_Mutation	SNP	C	TCGA-FV-A3R2-01A-11D-A22F-10		60740303	41791089	48	39006										
AXIN1	8312	hgsc.bcm.edu	37	chr16	360070	360070	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	tgtatggggggatcccatccCtgtccaggagaaagaggcag	15	9	0	2			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr16:360070C>A	ENST00000262320.3	-	4	1391		c.e4-1		AXIN1_ENST00000354866.3_Splice_Site|AXIN1_ENST00000481769.1_Splice_Site	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1						activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				GATCCCATCCCTGTCCAGGAG	0.627																																					.		Atlas-SNP	.											.	AXIN1	290	.	0			c.1020-1G>T						.						50	34	39					16																	360070		2201	4300	6501	SO:0001630	splice_region_variant	8312	exon5			CCATCCCTGTCCA	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.1020-1G>T	chr16.hg19:g.360070C>A		35.0	0.0		24.0	12.0	NM_181050	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Splice_Site	SNP	ENST00000262320.3	hg19	CCDS10405.1	.	.	.	.	.	.	.	.	.	.	C	13.15	2.150069	0.37923	.	.	ENSG00000103126	ENST00000262320;ENST00000354866	.	.	.	4.84	4.84	0.62591	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.9963	0.89185	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	AXIN1	300071	1.000000	0.71417	0.995000	0.50966	0.058000	0.15608	7.310000	0.78947	2.257000	0.74773	0.456000	0.33151	.	.	.		0.627	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3		Intron	A	360070	C	A	360070	5	1	266	1	0	0	0	0	0	0	1	0	1236	695	24	3	1601	3	AXIN1	16	360070	Splice_Site	SNP	C	TCGA-FV-A3R2-01A-11D-A22F-10		360070	89994683	49	39007										
PRPF8	10594	hgsc.bcm.edu	37	chr17	1580416	1580416	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	cagctcaaggtcaaaatgtgActccactcgctgctttgtta	8	11	2	1			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr17:1580416A>T	ENST00000572621.1	-	14	2300	c.2035T>A	c.(2035-2037)Tca>Aca	p.S679T	PRPF8_ENST00000304992.6_Missense_Mutation_p.S679T			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	679					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		TCAAAATGTGACTCCACTCGC	0.512																																					p.S679T		Atlas-SNP	.											.	PRPF8	169	.	0			c.T2035A						.						167	141	150					17																	1580416		2203	4300	6503	SO:0001583	missense	10594	exon15			AATGTGACTCCAC	AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231			17340	protein-coding gene	gene with protein product		607300	"PRP8 pre-mRNA processing factor 8 homolog (yeast)", "PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)"	RP13		11468273, 10411133	Standard	NM_006445		Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.2035T>A	chr17.hg19:g.1580416A>T	ENSP00000460348:p.Ser679Thr	53.0	0.0		59.0	21.0	NM_006445	O14547|O75965	Missense_Mutation	SNP	ENST00000572621.1	hg19	CCDS11010.1	.	.	.	.	.	.	.	.	.	.	A	15.59	2.879960	0.51801	.	.	ENSG00000174231	ENST00000304992	D	0.83335	-1.71	5.94	5.94	0.96194	PROCN (1);	0.000000	0.85682	D	0.000000	D	0.89677	0.6784	M	0.76838	2.35	0.80722	D	1	D	0.55800	0.973	P	0.60068	0.868	D	0.88651	0.3182	10	0.33940	T	0.23	.	16.3951	0.83601	1.0:0.0:0.0:0.0	.	679	Q6P2Q9	PRP8_HUMAN	T	679	ENSP00000304350:S679T	ENSP00000304350:S679T	S	-	1	0	PRPF8	1527166	1.000000	0.71417	0.982000	0.44146	0.566000	0.35808	9.297000	0.96120	2.272000	0.75746	0.460000	0.39030	TCA	.	.		0.512	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2			T	1580416	A	T	1580416	3	4	266	1	0	0	0	0	1	0	0	0	12587	275	10	4	5088	4	PRPF8	17	1580416	Missense_Mutation	SNP	A	TCGA-FV-A3R2-01A-11D-A22F-10		1580416	79614794	50	39008										
TP53	7157	hgsc.bcm.edu	37	chr17	7577022	7577022	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	ttgtcctgcttgcttacctcGcttagtgctccctgggggca	11	13	0	0	rs121913344		TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr17:7577022G>A	ENST00000269305.4	-	8	1105	c.916C>T	c.(916-918)Cga>Tga	p.R306*	TP53_ENST00000445888.2_Nonsense_Mutation_p.R306*|TP53_ENST00000455263.2_Nonsense_Mutation_p.R306*|TP53_ENST00000359597.4_Nonsense_Mutation_p.R306*|TP53_ENST00000420246.2_Nonsense_Mutation_p.R306*|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Intron	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	306	Interaction with CARM1.|Interaction with HIPK1. {ECO:0000250}.		R -> P (in LFS; germline mutation and in a sporadic cancer; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R306*(133)|p.0?(8)|p.?(3)|p.R306fs*39(2)|p.K305fs*1(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TGCTTACCTCGCTTAGTGCTC	0.562	R306*(HCC1937_BREAST)|R306*(JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R306*(MFE296_ENDOMETRIUM)|R306*(MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R306*(RCM1_LARGE_INTESTINE)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.R306X	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,NS,adenocarcinoma,0,166	TP53	33396	.	147	Substitution - Nonsense(133)|Whole gene deletion(8)|Unknown(3)|Deletion - Frameshift(2)|Insertion - Frameshift(1)	large_intestine(39)|breast(21)|upper_aerodigestive_tract(15)|ovary(11)|central_nervous_system(10)|oesophagus(10)|stomach(8)|lung(8)|endometrium(6)|bone(4)|pancreas(3)|haematopoietic_and_lymphoid_tissue(3)|biliary_tract(3)|kidney(2)|NS(2)|urinary_tract(1)|liver(1)	c.C916T	GRCh37	CM971506	TP53	M	rs121913344	.						120	106	110					17																	7577022		2203	4300	6503	SO:0001587	stop_gained	7157	exon8	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	TACCTCGCTTAGT	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.916C>T	chr17.hg19:g.7577022G>A	ENSP00000269305:p.Arg306*	64.0	1.0		39.0	21.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.782988	0.90282	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	.	.	.	5.26	3.21	0.36854	.	1.348720	0.05032	N	0.474808	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.4785	0.44678	0.0:0.0:0.6334:0.3666	.	.	.	.	X	306;306;306;306;306;295;174	.	ENSP00000269305:R306X	R	-	1	2	TP53	7517747	1.000000	0.71417	0.970000	0.41538	0.345000	0.29048	2.280000	0.43443	0.735000	0.32537	0.561000	0.74099	CGA	.	.		0.562	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577022	G	A	7577022	4	1	266	1	0	0	0	0	0	1	0	0	16396	1095	38	1	370	1	TP53	17	7577022	Nonsense_Mutation	SNP	G	TCGA-FV-A3R2-01A-11D-A22F-10	5996606	7577022	73618188	51	39009										
TMEM88	92162	hgsc.bcm.edu	37	chr17	7758491	7758491	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	tgcgctgttcttgtaacagcCcagaatctgctggtggctgc	12	11	2	1			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr17:7758491C>T	ENST00000301599.6	+	1	109	c.99C>T	c.(97-99)gcC>gcT	p.A33A	CYB5D1_ENST00000570446.1_5'Flank|CYB5D1_ENST00000571846.1_5'Flank|CYB5D1_ENST00000332439.4_5'Flank|LSMD1_ENST00000570555.1_5'Flank|TMEM88_ENST00000574668.1_Silent_p.A33A	NM_203411.1	NP_981956.1	Q6PEY1	TMM88_HUMAN	transmembrane protein 88	33					multicellular organismal development (GO:0007275)|Wnt signaling pathway (GO:0016055)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				lung(1)	1		all_cancers(10;0.00528)|Prostate(122;0.202)				TTGTAACAGCCCAGAATCTGC	0.637																																					p.A33A		Atlas-SNP	.											.	TMEM88	6	.	0			c.C99T						.						75	68	71					17																	7758491		2203	4300	6503	SO:0001819	synonymous_variant	92162	exon1			AACAGCCCAGAAT	BC057812	CCDS11121.1	17p13.1	2005-12-13				ENSG00000167874			32371	protein-coding gene	gene with protein product							Standard	NM_203411		Approved	MGC71744, FLJ20025	uc002giy.3	Q6PEY1		ENST00000301599.6:c.99C>T	chr17.hg19:g.7758491C>T		46.0	0.0		25.0	18.0	NM_203411		Silent	SNP	ENST00000301599.6	hg19	CCDS11121.1																																																																																			.	.		0.637	TMEM88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440252.1	NM_203411		T	7758491	C	T	7758491	2	4	266	1	0	0	0	0	0	0	0	1	16227	610	22	3		3	TMEM88	17	7758491	Silent	SNP	C	TCGA-FV-A3R2-01A-11D-A22F-10	181469	7758491	73436719	52	39010										
CHD3	1107	hgsc.bcm.edu	37	chr17	7811224	7811224	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	cctagcagaagatgtaaaagGtgaccgggagcttcgaccag	13	9	0	3			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr17:7811224G>T	ENST00000330494.7	+	34	5189	c.5039G>T	c.(5038-5040)gGt>gTt	p.G1680V	CHD3_ENST00000380358.4_Missense_Mutation_p.G1739V|SCARNA21_ENST00000517026.1_RNA|CHD3_ENST00000358181.4_Missense_Mutation_p.G1646V	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	1680	Required for interaction with PCNT.				centrosome organization (GO:0051297)|chromatin assembly or disassembly (GO:0006333)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|spindle organization (GO:0007051)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(11)|kidney(6)|large_intestine(13)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	65		Prostate(122;0.202)				GATGTAAAAGGTGACCGGGAG	0.547																																					p.G1739V		Atlas-SNP	.											.	CHD3	169	.	0			c.G5216T						.						81	73	76					17																	7811224		2203	4300	6503	SO:0001583	missense	1107	exon34			TAAAAGGTGACCG	U08379	CCDS32553.2, CCDS32554.1, CCDS32555.1	17p13	2013-01-28			ENSG00000170004	ENSG00000170004		"Zinc fingers, PHD-type"	1918	protein-coding gene	gene with protein product		602120				9326634, 7560064	Standard	NM_001005271		Approved	Mi-2a, ZFH, Mi2-ALPHA	uc002gjd.2	Q12873	OTTHUMG00000150427	ENST00000330494.7:c.5039G>T	chr17.hg19:g.7811224G>T	ENSP00000332628:p.Gly1680Val	74.0	0.0		24.0	15.0	NM_001005271	D3DTQ9|E9PG89|Q9Y4I0	Missense_Mutation	SNP	ENST00000330494.7	hg19	CCDS32554.1	.	.	.	.	.	.	.	.	.	.	G	11.35	1.611752	0.28712	.	.	ENSG00000170004	ENST00000380358;ENST00000358181;ENST00000330494;ENST00000439235	D;D;D	0.90069	-2.61;-2.53;-2.54	4.65	-0.0728	0.13738	.	0.156126	0.29900	N	0.010920	T	0.67249	0.2873	N	0.08118	0	0.46586	D	0.999116	B;P;B;B	0.37864	0.01;0.61;0.019;0.013	B;B;B;B	0.32864	0.003;0.154;0.006;0.003	T	0.56450	-0.7977	10	0.30078	T	0.28	-11.2383	0.5219	0.00613	0.2433:0.1397:0.218:0.399	.	257;1646;1680;1739	B3KWV4;Q12873-2;Q12873;E9PG89	.;.;CHD3_HUMAN;.	V	1739;1646;1680;8	ENSP00000369716:G1739V;ENSP00000350907:G1646V;ENSP00000332628:G1680V	ENSP00000332628:G1680V	G	+	2	0	CHD3	7751949	0.078000	0.21339	0.949000	0.38748	0.883000	0.51084	0.246000	0.18160	0.170000	0.19704	-0.314000	0.08810	GGT	.	.		0.547	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1	NM_001005273		T	7811224	G	T	7811224	3	4	266	1	0	0	0	0	1	0	0	0	3328	1261	44	3	5454	3	CHD3	17	7811224	Missense_Mutation	SNP	G	TCGA-FV-A3R2-01A-11D-A22F-10	52733	7811224	73383986	53	39011										
ODF4	146852	hgsc.bcm.edu	37	chr17	8243610	8243610	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	acagcttccgctggatggccCaggtgttggcctctgagctc	13	13	1	1			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr17:8243610C>T	ENST00000328248.2	+	1	429	c.241C>T	c.(241-243)Cag>Tag	p.Q81*	ODF4_ENST00000584943.1_Intron|RP11-849F2.4_ENST00000585275.1_lincRNA	NM_153007.4	NP_694552.2	Q2M2E3	ODFP4_HUMAN	outer dense fiber of sperm tails 4	81					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|outer dense fiber (GO:0001520)				endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|stomach(1)	8						CTGGATGGCCCAGGTGTTGGC	0.562																																					p.Q81X		Atlas-SNP	.											.	ODF4	23	.	0			c.C241T						.						65	57	60					17																	8243610		2203	4300	6503	SO:0001587	stop_gained	146852	exon1			ATGGCCCAGGTGT	AB081120	CCDS11140.1	17p13	2010-09-27			ENSG00000184650	ENSG00000184650			19056	protein-coding gene	gene with protein product	"cancer/testis antigen 136"	610097					Standard	NM_153007		Approved	OPPO1, CT136	uc002gle.1	Q2M2E3	OTTHUMG00000108190	ENST00000328248.2:c.241C>T	chr17.hg19:g.8243610C>T	ENSP00000331086:p.Gln81*	67.0	0.0		41.0	28.0	NM_153007	Q8J021	Nonsense_Mutation	SNP	ENST00000328248.2	hg19	CCDS11140.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.202207	0.79127	.	.	ENSG00000184650	ENST00000328248	.	.	.	4.89	3.86	0.44501	.	0.164598	0.29314	N	0.012508	.	.	.	.	.	.	0.21386	N	0.999706	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-18.6581	9.4822	0.38908	0.2263:0.7737:0.0:0.0	.	.	.	.	X	81	.	ENSP00000331086:Q81X	Q	+	1	0	ODF4	8184335	0.713000	0.27926	0.208000	0.23602	0.013000	0.08279	1.788000	0.38714	2.526000	0.85167	0.655000	0.94253	CAG	.	.		0.562	ODF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226996.1			T	8243610	C	T	8243610	4	4	266	1	0	0	0	0	0	1	0	0	10842	595	21	3	243	3	ODF4	17	8243610	Nonsense_Mutation	SNP	C	TCGA-FV-A3R2-01A-11D-A22F-10	432386	8243610	72951600	54	39012										
GOSR2	9570	hgsc.bcm.edu	37	chr17	45015970	45015970	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	tctcttctgccccaggggacTcagaagaagatccttgacat	9	12	3	4			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr17:45015970T>G	ENST00000393456.2	+	6	540	c.483T>G	c.(481-483)acT>acG	p.T161T	GOSR2_ENST00000576910.2_Silent_p.T114T|GOSR2_ENST00000439730.2_Silent_p.T161T|RP11-156P1.2_ENST00000571841.1_Silent_p.T161T|GOSR2_ENST00000225567.4_Silent_p.T161T	NM_004287.3	NP_004278.2	O14653	GOSR2_HUMAN	golgi SNAP receptor complex member 2	161					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane fusion (GO:0061025)|protein transport (GO:0015031)	Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transporter activity (GO:0005215)			kidney(1)|large_intestine(2)|liver(1)|lung(1)|ovary(1)|skin(1)	7			BRCA - Breast invasive adenocarcinoma(9;0.102)			CCCAGGGGACTCAGAAGAAGA	0.478																																					p.T161T		Atlas-SNP	.											.	GOSR2	38	.	0			c.T483G						.						265	266	266					17																	45015970		2203	4300	6503	SO:0001819	synonymous_variant	9570	exon6			GGGGACTCAGAAG	AF007548	CCDS11507.1, CCDS42355.1, CCDS45719.1	17q21	2006-02-10				ENSG00000108433			4431	protein-coding gene	gene with protein product		604027				9349823, 10198168	Standard	XM_005257843		Approved	GS27, Bos1	uc002ikz.3	O14653		ENST00000393456.2:c.483T>G	chr17.hg19:g.45015970T>G		69.0	0.0		68.0	22.0	NM_004287	D3DXJ5|D3DXJ6|Q8N4B8|Q96DA5|Q9BZZ4	Silent	SNP	ENST00000393456.2	hg19	CCDS42355.1																																																																																			.	.		0.478	GOSR2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440438.1			G	45015970	T	G	45015970	2	3	266	1	0	0	0	0	0	0	0	1	6586	1538	54	5		5	GOSR2	17	45015970	Silent	SNP	T	TCGA-FV-A3R2-01A-11D-A22F-10	36772360	45015970	36179240	55	39013										
UNC13D	201294	hgsc.bcm.edu	37	chr17	73840324	73840324	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	ccggggccatttggggcgggGgatcctgtagatctctgact	16	10	1	2			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr17:73840324G>A	ENST00000207549.4	-	1	474	c.95C>T	c.(94-96)cCc>cTc	p.P32L	UNC13D_ENST00000412096.2_Missense_Mutation_p.P32L|UNC13D_ENST00000587504.1_5'Flank	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	unc-13 homolog D (C. elegans)	32					defense response to virus (GO:0051607)|germinal center formation (GO:0002467)|granuloma formation (GO:0002432)|natural killer cell degranulation (GO:0043320)|phagocytosis (GO:0006909)|positive regulation of exocytosis (GO:0045921)|regulation of mast cell degranulation (GO:0043304)	endosome (GO:0005768)|exocytic vesicle (GO:0070382)|lysosome (GO:0005764)|membrane (GO:0016020)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)			TTGGGGCGGGGGATCCTGTAG	0.652									Familial Hemophagocytic Lymphohistiocytosis																												p.P32L		Atlas-SNP	.											.	UNC13D	68	.	0			c.C95T						.						43	49	47					17																	73840324		2202	4300	6502	SO:0001583	missense	201294	exon1	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	GGCGGGGGATCCT	AK024474	CCDS11730.1	17q25.3	2014-09-17				ENSG00000092929			23147	protein-coding gene	gene with protein product		608897					Standard	NM_199242		Approved	Munc13-4	uc002jpp.3	Q70J99		ENST00000207549.4:c.95C>T	chr17.hg19:g.73840324G>A	ENSP00000207549:p.Pro32Leu	27.0	0.0		21.0	10.0	NM_199242	B4DWG9|Q9H7K5	Missense_Mutation	SNP	ENST00000207549.4	hg19	CCDS11730.1	.	.	.	.	.	.	.	.	.	.	G	11.46	1.644735	0.29246	.	.	ENSG00000092929	ENST00000207549;ENST00000412096;ENST00000448606	T;T	0.70164	-0.43;-0.46	4.04	2.0	0.26442	.	0.495999	0.17124	N	0.186104	T	0.54447	0.1859	L	0.48642	1.525	0.09310	N	1	B	0.27823	0.19	B	0.24155	0.051	T	0.50684	-0.8799	10	0.72032	D	0.01	-0.5365	6.5283	0.22312	0.2264:0.0:0.7736:0.0	.	32	Q70J99	UN13D_HUMAN	L	32	ENSP00000207549:P32L;ENSP00000388093:P32L	ENSP00000207549:P32L	P	-	2	0	UNC13D	71351919	0.397000	0.25270	0.000000	0.03702	0.497000	0.33675	1.716000	0.37981	0.369000	0.24510	0.561000	0.74099	CCC	.	.		0.652	UNC13D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448847.2	XM_113950		A	73840324	G	A	73840324	3	1	266	1	0	0	0	0	1	0	0	0	17002	1232	43	3	3305	3	UNC13D	17	73840324	Missense_Mutation	SNP	G	TCGA-FV-A3R2-01A-11D-A22F-10	28824354	73840324	7354886	56	39014										
POTEC	388468	hgsc.bcm.edu	37	chr18	14542851	14542851	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	gcagtgacagcaccacttgcCcatcttgctcctgagcgtct	9	15	2	2			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr18:14542851C>A	ENST00000358970.5	-	1	294	c.295G>T	c.(295-297)Ggc>Tgc	p.G99C	POTEC_ENST00000389891.4_5'UTR	NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	99										NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						CACCACTTGCCCATCTTGCTC	0.622																																					p.G99C		Atlas-SNP	.											POTEC,NS,carcinoma,0,1	POTEC	129	.	0			c.G295T						.						39	45	43					18																	14542851		692	1591	2283	SO:0001583	missense	388468	exon1			ACTTGCCCATCTT	BX649118	CCDS45835.1	18p11.21	2013-01-10	2008-11-26	2008-11-26	ENSG00000183206	ENSG00000183206		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	33894	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 6"		"ANKRD26-like family B, member 2"	A26B2			Standard	NM_001137671		Approved	POTE18, POTE-18, DKFZp686J0529, CT104.6	uc010dln.3	B2RU33	OTTHUMG00000162963	ENST00000358970.5:c.295G>T	chr18.hg19:g.14542851C>A	ENSP00000351856:p.Gly99Cys	247.0	0.0		268.0	91.0	NM_001137671		Missense_Mutation	SNP	ENST00000358970.5	hg19	CCDS45835.1	.	.	.	.	.	.	.	.	.	.	C	5.295	0.239815	0.10023	.	.	ENSG00000183206	ENST00000358970;ENST00000389891	T	0.37915	1.17	0.399	0.399	0.16325	.	.	.	.	.	T	0.35913	0.0948	L	0.39898	1.24	0.09310	N	1	D	0.55172	0.97	P	0.51487	0.671	T	0.19451	-1.0305	8	0.66056	D	0.02	.	.	.	.	.	99	B2RU33	POTEC_HUMAN	C	99	ENSP00000351856:G99C	ENSP00000351856:G99C	G	-	1	0	POTEC	14532851	0.000000	0.05858	0.010000	0.14722	0.029000	0.11900	-0.174000	0.09839	0.448000	0.26722	0.175000	0.17021	GGC	.	.		0.622	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269		A	14542851	C	A	14542851	3	1	266	1	0	0	0	0	1	0	0	0	12271	623	22	3	1377	3	POTEC	18	14542851	Missense_Mutation	SNP	C	TCGA-FV-A3R2-01A-11D-A22F-10		14542851	63534397	57	39015										
TCF4	6925	hgsc.bcm.edu	37	chr18	52901914	52901914	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	atcttcacgatgggtccccaCctgaaagggcgagaggaacc	12	12	2	2			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr18:52901914C>T	ENST00000356073.4	-	16	1962	c.1351G>A	c.(1351-1353)Gtg>Atg	p.V451M	TCF4_ENST00000564228.1_Splice_Site_p.V380M|TCF4_ENST00000566286.1_Splice_Site_p.V448M|TCF4_ENST00000544241.2_Splice_Site_p.V380M|TCF4_ENST00000567880.1_Splice_Site_p.V391M|TCF4_ENST00000537856.3_Splice_Site_p.V321M|TCF4_ENST00000543082.1_Splice_Site_p.V409M|TCF4_ENST00000570177.2_Splice_Site_p.V321M|TCF4_ENST00000561992.1_Splice_Site_p.V321M|TCF4_ENST00000398339.1_Splice_Site_p.V553M|TCF4_ENST00000564403.2_Splice_Site_p.V457M|TCF4_ENST00000537578.1_Splice_Site_p.V427M|TCF4_ENST00000354452.3_Splice_Site_p.V451M|TCF4_ENST00000568673.1_Splice_Site_p.V427M|TCF4_ENST00000566279.1_Splice_Site_p.V391M|TCF4_ENST00000565018.2_Splice_Site_p.V451M|TCF4_ENST00000457482.3_Splice_Site_p.V291M|TCF4_ENST00000570287.2_Splice_Site_p.V291M|TCF4_ENST00000540999.1_Splice_Site_p.V427M|TCF4_ENST00000561831.3_Splice_Site_p.V291M|TCF4_ENST00000568740.1_Splice_Site_p.V426M|TCF4_ENST00000564999.1_Splice_Site_p.V451M	NM_003199.2	NP_003190.1	P15884	ITF2_HUMAN	transcription factor 4	451					DNA-templated transcription, initiation (GO:0006352)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein-DNA complex assembly (GO:0065004)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase recruiting transcription factor activity (GO:0001011)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TFIIB-class binding transcription factor activity (GO:0001087)|TFIIB-class transcription factor binding (GO:0001093)			breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	41				Colorectal(16;0.00108)|READ - Rectum adenocarcinoma(59;0.0649)|COAD - Colon adenocarcinoma(17;0.0718)		TGGGTCCCCACCTGAAAGGGC	0.567											OREG0024990	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V553M		Atlas-SNP	.											.	TCF4	178	.	0			c.G1657A						.						77	81	80					18																	52901914		2203	4300	6503	SO:0001630	splice_region_variant	6925	exon17			TCCCCACCTGAAA	M74719	CCDS11960.1, CCDS42438.1, CCDS58623.1, CCDS58624.1, CCDS58625.1, CCDS58626.1, CCDS58627.1, CCDS58628.1, CCDS58629.1, CCDS58630.1, CCDS58631.1, CCDS59321.1	18q21.1	2013-05-21			ENSG00000196628	ENSG00000196628		"Basic helix-loop-helix proteins"	11634	protein-coding gene	gene with protein product		602272				9302263, 2308860	Standard	NM_001083962		Approved	SEF2-1B, ITF2, bHLHb19, E2-2	uc002lga.3	P15884	OTTHUMG00000132713	ENST00000356073.4:c.1351-1G>A	chr18.hg19:g.52901914C>T		45.0	0.0	988	27.0	16.0	NM_001243226	B3KT62|B3KUC0|B4DT37|B4DUG3|B7Z5M6|B7Z6Y1|G0LNT9|G0LNU0|G0LNU1|G0LNU2|G0LNU4|G0LNU5|G0LNU8|G0LNU9|G0LNV0|G0LNV1|G0LNV2|H3BPQ1|Q08AP2|Q08AP3|Q15439|Q15440|Q15441	Missense_Mutation	SNP	ENST00000356073.4	hg19	CCDS11960.1	.	.	.	.	.	.	.	.	.	.	C	18.05	3.537000	0.65085	.	.	ENSG00000196628	ENST00000354452;ENST00000457482;ENST00000356073;ENST00000543082;ENST00000540999;ENST00000537578;ENST00000544241;ENST00000537856;ENST00000398339	T;T;T;T;T;T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27;-0.27;-0.27;-0.27;-0.27;-0.27	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.79621	0.4477	L	0.56396	1.775	0.80722	D	1	P;D;D;D;D;P;P;P;D	0.89917	0.928;0.995;1.0;0.993;0.968;0.935;0.935;0.815;0.994	P;D;D;D;P;P;P;B;D	0.80764	0.737;0.965;0.994;0.943;0.652;0.737;0.737;0.387;0.986	T	0.78239	-0.2281	10	0.45353	T	0.12	-2.8082	18.3978	0.90504	0.0:1.0:0.0:0.0	.	427;451;291;553;451;409;380;291;448	B7Z5M6;G0LNT9;G0LNV1;E9PH57;P15884;B3KUC0;B3KT62;G0LNU9;G0LNU5	.;.;.;.;ITF2_HUMAN;.;.;.;.	M	451;291;451;409;427;427;380;321;553	ENSP00000346440:V451M;ENSP00000409447:V291M;ENSP00000348374:V451M;ENSP00000439656:V409M;ENSP00000445202:V427M;ENSP00000440731:V427M;ENSP00000441562:V380M;ENSP00000439827:V321M;ENSP00000381382:V553M	ENSP00000346440:V451M	V	-	1	0	TCF4	51052912	1.000000	0.71417	0.998000	0.56505	0.941000	0.58515	6.414000	0.73318	2.723000	0.93209	0.563000	0.77884	GTG	.	.		0.567	TCF4-002	KNOWN	upstream_uORF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256014.1	NM_003199	Missense_Mutation	T	52901914	C	T	52901914	5	4	266	1	0	0	0	0	0	0	1	0	15710	521	18	3	680	3	TCF4	18	52901914	Splice_Site	SNP	C	TCGA-FV-A3R2-01A-11D-A22F-10	38359063	52901914	25175334	58	39016										
NETO1	81832	hgsc.bcm.edu	37	chr18	70417752	70417752	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	cgaggctgtttgatctgtacGatgacagagatgataatgag	13	5	1	5	rs145217972		TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr18:70417752G>A	ENST00000327305.6	-	9	1743	c.1086C>T	c.(1084-1086)atC>atT	p.I362I	NETO1_ENST00000583169.1_Silent_p.I362I|NETO1_ENST00000299430.2_Silent_p.I361I|RNA5SP460_ENST00000516789.1_RNA	NM_138966.3	NP_620416	Q8TDF5	NETO1_HUMAN	neuropilin (NRP) and tolloid (TLL)-like 1	362					memory (GO:0007613)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|receptor localization to synapse (GO:0097120)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|visual learning (GO:0008542)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|kainate selective glutamate receptor complex (GO:0032983)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				NS(3)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(36)|ovary(2)|prostate(3)|skin(3)|stomach(1)	63		Esophageal squamous(42;0.129)		READ - Rectum adenocarcinoma(1;0.0487)		TGATCTGTACGATGACAGAGA	0.453																																					p.I362I		Atlas-SNP	.											.	NETO1	178	.	0			c.C1086T						.	G	,	1,4405	2.1+/-5.4	0,1,2202	94	79	84		1086,1086	-5.1	1	18	dbSNP_134	84	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	NETO1	NM_001201465.1,NM_138966.3	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	362/534,362/534	70417752	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	81832	exon9			CTGTACGATGACA	AF448838	CCDS12000.1, CCDS42444.1	18q22.2	2008-08-01			ENSG00000166342	ENSG00000166342			13823	protein-coding gene	gene with protein product		607973				11943477, 12810072	Standard	NM_138999		Approved	BTCL1, BCTL1	uc002lkw.3	Q8TDF5	OTTHUMG00000132834	ENST00000327305.6:c.1086C>T	chr18.hg19:g.70417752G>A		58.0	0.0		71.0	21.0	NM_001201465	Q86W85|Q8ND78|Q8TDF4	Silent	SNP	ENST00000327305.6	hg19	CCDS12000.1																																																																																			.	G|1.000;A|0.000		0.453	NETO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256301.2	NM_138999		A	70417752	G	A	70417752	2	1	266	1	0	0	0	0	0	0	0	1	10348	1048	37	1		1	NETO1	18	70417752	Silent	SNP	G	TCGA-FV-A3R2-01A-11D-A22F-10	17515838	70417752	7659496	59	39017										
MUC16	94025	hgsc.bcm.edu	37	chr19	9057255	9057255	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	tggttccaggttctgtgcttGtgtctgtagtcttcaccatg	11	9	4	0			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr19:9057255G>T	ENST00000397910.4	-	3	30394	c.30191C>A	c.(30190-30192)aCa>aAa	p.T10064K		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10066	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TTCTGTGCTTGTGTCTGTAGT	0.468																																					p.T10064K		Atlas-SNP	.											.	MUC16	4315	.	0			c.C30191A						.						93	85	87					19																	9057255		1963	4172	6135	SO:0001583	missense	94025	exon3			GTGCTTGTGTCTG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.30191C>A	chr19.hg19:g.9057255G>T	ENSP00000381008:p.Thr10064Lys	110.0	0.0		90.0	45.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	2.945	-0.218029	0.06101	.	.	ENSG00000181143	ENST00000397910	T	0.23348	1.91	2.35	-2.18	0.07037	.	.	.	.	.	T	0.14570	0.0352	N	0.19112	0.55	.	.	.	B	0.20550	0.046	B	0.26416	0.069	T	0.26430	-1.0103	8	0.87932	D	0	.	4.6718	0.12692	0.305:0.2249:0.4701:0.0	.	10064	B5ME49	.	K	10064	ENSP00000381008:T10064K	ENSP00000381008:T10064K	T	-	2	0	MUC16	8918255	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.161000	0.10026	-0.743000	0.04784	-1.595000	0.00837	ACA	.	.		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9057255	G	T	9057255	3	4	266	1	0	0	0	0	1	0	0	0	9982	1377	48	3	13660	3	MUC16	19	9057255	Missense_Mutation	SNP	G	TCGA-FV-A3R2-01A-11D-A22F-10		9057255	50071728	60	39018										
CACNA1A	773	hgsc.bcm.edu	37	chr19	13387893	13387893	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	ctgcactcaccttgatcaccAtctcaaaggtaaagacgcct	6	14	3	2			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr19:13387893A>G	ENST00000360228.5	-	23	3871	c.3872T>C	c.(3871-3873)aTg>aCg	p.M1291T	CACNA1A_ENST00000573710.2_Missense_Mutation_p.M1292T	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	1292					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	CTTGATCACCATCTCAAAGGT	0.453											OREG0025295	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.M1292T		Atlas-SNP	.											.	CACNA1A	715	.	0			c.T3875C						.						105	94	98					19																	13387893		1909	4123	6032	SO:0001583	missense	773	exon23			ATCACCATCTCAA	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.3872T>C	chr19.hg19:g.13387893A>G	ENSP00000353362:p.Met1291Thr	48.0	0.0	687	55.0	17.0	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	hg19	CCDS45998.1	.	.	.	.	.	.	.	.	.	.	A	13.47	2.247403	0.39697	.	.	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084	D	0.97575	-4.44	4.54	4.54	0.55810	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.97663	0.9234	M	0.63843	1.955	0.58432	D	0.999999	D;D;D	0.76494	0.996;0.999;0.961	D;D;P	0.69142	0.952;0.962;0.584	D	0.98239	1.0487	10	0.87932	D	0	.	12.8714	0.57966	1.0:0.0:0.0:0.0	.	1292;1295;1291	O00555;E9PD31;Q9NS88	CAC1A_HUMAN;.;.	T	1291;1295;1292;1292	ENSP00000353362:M1291T	ENSP00000317661:M1292T	M	-	2	0	CACNA1A	13248893	1.000000	0.71417	1.000000	0.80357	0.819000	0.46315	8.712000	0.91403	1.690000	0.51089	0.482000	0.46254	ATG	.	.		0.453	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		G	13387893	A	G	13387893	3	3	266	1	0	0	0	0	1	0	0	0	2540	217	8	2	3850	2	CACNA1A	19	13387893	Missense_Mutation	SNP	A	TCGA-FV-A3R2-01A-11D-A22F-10	4330638	13387893	45741090	61	39019										
KIAA0355	9710	hgsc.bcm.edu	37	chr19	34810943	34810943	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	ccagaaaaaaagaacagcggCagtggcggcggcttatctgg	14	9	1	2			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr19:34810943C>T	ENST00000299505.6	+	3	1500	c.627C>T	c.(625-627)ggC>ggT	p.G209G		NM_014686.3	NP_055501.2	O15063	K0355_HUMAN	KIAA0355	209										breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	41	Esophageal squamous(110;0.162)					AGAACAGCGGCAGTGGCGGCG	0.562																																					p.G209G		Atlas-SNP	.											.	KIAA0355	105	.	0			c.C627T						.						85	82	83					19																	34810943		2203	4300	6503	SO:0001819	synonymous_variant	9710	exon3			CAGCGGCAGTGGC		CCDS12436.1	19q13.12	2012-11-29			ENSG00000166398	ENSG00000166398			29016	protein-coding gene	gene with protein product						9205841	Standard	NM_014686		Approved		uc002nvd.4	O15063	OTTHUMG00000180505	ENST00000299505.6:c.627C>T	chr19.hg19:g.34810943C>T		107.0	0.0		95.0	41.0	NM_014686	Q2M3W4	Silent	SNP	ENST00000299505.6	hg19	CCDS12436.1																																																																																			.	.		0.562	KIAA0355-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451678.4	NM_014686		T	34810943	C	T	34810943	2	4	266	1	0	0	0	0	0	0	0	1	8179	697	25	3		3	KIAA0355	19	34810943	Silent	SNP	C	TCGA-FV-A3R2-01A-11D-A22F-10	21423050	34810943	24318040	62	39020										
NUP62	23636	hgsc.bcm.edu	37	chr19	50411919	50411919	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	agcctcttctggtccagcttCaccttctccacctcgcggtg	8	17	4	0			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr19:50411919C>A	ENST00000596217.1	-	2	3033	c.1146G>T	c.(1144-1146)gtG>gtT	p.V382V	NUP62_ENST00000597029.1_Silent_p.V382V|NUP62_ENST00000413454.1_Silent_p.V382V|NUP62_ENST00000597723.1_Silent_p.V306V|IL4I1_ENST00000595948.1_Intron|NUP62_ENST00000422090.2_Silent_p.V382V|IL4I1_ENST00000341114.3_Intron|NUP62_ENST00000352066.3_Silent_p.V382V|NUP62_ENST00000600583.1_5'Flank			P37198	NUP62_HUMAN	nucleoporin 62kDa	382					carbohydrate metabolic process (GO:0005975)|cell aging (GO:0007569)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|hormone-mediated signaling pathway (GO:0009755)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of programmed cell death (GO:0043069)|negative regulation of Ras protein signal transduction (GO:0046580)|nucleocytoplasmic transport (GO:0006913)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|regulation of Ras protein signal transduction (GO:0046578)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleocytoplasmic shuttling complex (GO:0031074)|pore complex (GO:0046930)|ribonucleoprotein complex (GO:0030529)	chromatin binding (GO:0003682)|receptor signaling complex scaffold activity (GO:0030159)|SH2 domain binding (GO:0042169)|structural constituent of nuclear pore (GO:0017056)|thyroid hormone receptor binding (GO:0046966)|ubiquitin binding (GO:0043130)			breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|stomach(1)|urinary_tract(2)	19		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00242)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		GGTCCAGCTTCACCTTCTCCA	0.607																																					p.V382V		Atlas-SNP	.											.	NUP62	50	.	0			c.G1146T						.						112	106	108					19																	50411919		2203	4300	6503	SO:0001819	synonymous_variant	23636	exon3			CAGCTTCACCTTC	X58521	CCDS12788.1	19q13.33	2013-09-20	2002-08-29		ENSG00000213024	ENSG00000213024			8066	protein-coding gene	gene with protein product	"nuclear pore glycoprotein p62"	605815	"nucleoporin 62kD"			1915414	Standard	NM_016553		Approved	p62, DKFZp547L134, IBSN, SNDI, MGC841, FLJ20822, FLJ43869	uc002pqx.3	P37198	OTTHUMG00000183077	ENST00000596217.1:c.1146G>T	chr19.hg19:g.50411919C>A		54.0	0.0		58.0	22.0	NM_153719	B3KWU5|Q503A4|Q6GTM2|Q96C43|Q9NSL1	Silent	SNP	ENST00000596217.1	hg19	CCDS12788.1																																																																																			.	.		0.607	NUP62-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464991.1	NM_153719		A	50411919	C	A	50411919	2	1	266	1	0	0	0	0	0	0	0	1	10777	813	29	3		3	NUP62	19	50411919	Silent	SNP	C	TCGA-FV-A3R2-01A-11D-A22F-10	15600976	50411919	8717064	63	39021										
SHANK1	50944	hgsc.bcm.edu	37	chr19	51169520	51169526	+	Frame_Shift_Del	DEL	CCCACTG	CCCACTG	-													0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	tggtggctgtctccgcctccCccactgcctcctcgggccca							TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	CCCACTG	CCCACTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr19:51169520_51169526delCCCACTG	ENST00000293441.1	-	22	5709_5715	c.5691_5697delCAGTGGG	c.(5689-5697)ggcagtgggfs	p.GSG1897fs	SHANK1_ENST00000359082.3_Frame_Shift_Del_p.GSG1888fs|SYT3_ENST00000544769.1_Intron|SHANK1_ENST00000391814.1_Frame_Shift_Del_p.GSG1905fs|SHANK1_ENST00000391813.1_Frame_Shift_Del_p.GSG1284fs	NM_016148.2	NP_057232.2	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	1897	Poly-Gly.				adult behavior (GO:0030534)|associative learning (GO:0008306)|cytoskeletal anchoring at plasma membrane (GO:0007016)|dendritic spine morphogenesis (GO:0060997)|determination of affect (GO:0050894)|habituation (GO:0046959)|long-term memory (GO:0007616)|negative regulation of actin filament bundle assembly (GO:0032232)|neuromuscular process controlling balance (GO:0050885)|olfactory behavior (GO:0042048)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|protein complex assembly (GO:0006461)|protein localization to synapse (GO:0035418)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|righting reflex (GO:0060013)|social behavior (GO:0035176)|synapse maturation (GO:0060074)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|excitatory synapse (GO:0060076)|intracellular (GO:0005622)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ankyrin repeat binding (GO:0071532)|GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|somatostatin receptor binding (GO:0031877)			breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	64		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)		CTCCGCCTCCCCCACTGCCTCCTCGGG	0.662																																					p.1898_1900del		Atlas-Indel,Pindel	.											.	SHANK1	210	.	0			c.5692_5698del						.																																			SO:0001589	frameshift_variant	50944	exon22			.	AF163302	CCDS12799.1	19q13.3	2013-01-10			ENSG00000161681	ENSG00000161681		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	15474	protein-coding gene	gene with protein product	"somatostatin receptor-interacting protein"	604999				10551867	Standard	NM_016148		Approved	SSTRIP, SPANK-1, synamon	uc002psx.1	Q9Y566	OTTHUMG00000137380	ENST00000293441.1:c.5691_5697delCAGTGGG	chr19.hg19:g.51169520_51169526delCCCACTG	ENSP00000293441:p.Gly1897fs	33.0	0.0		42.0	19.0	NM_016148	A8MXP5|B7WNY6|Q9NYW9	Frame_Shift_Del	DEL	ENST00000293441.1	hg19	CCDS12799.1																																																																																			.	.		0.662	SHANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268071.1	NM_016148		-	51169526	CCCACTG	-	51169520	7	5	266	1	0	1	0	1	0	0	0	0	14279	610	22	0	796	0	SHANK1	19	51169520	Frame_Shift_Del	DEL	CCCACTG	TCGA-FV-A3R2-01A-11D-A22F-10	757601	51169520	7959463	64	39022										
P2RX6	9127	hgsc.bcm.edu	37	chr22	21380718	21380718	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	ctcatctgcaggccaaggccCcgaaagcaaccgccaactct	8	17	3	0			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr22:21380718C>T	ENST00000413302.2	+	12	1286	c.1138C>T	c.(1138-1140)Ccg>Tcg	p.P380S	P2RX6_ENST00000336296.2_Missense_Mutation_p.P370S|P2RX6_ENST00000402329.3_3'UTR|P2RX6_ENST00000443995.3_Missense_Mutation_p.P327S|P2RX6_ENST00000401443.1_Missense_Mutation_p.P354S			O15547	P2RX6_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 6	380					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|muscle contraction (GO:0006936)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|channel activity (GO:0015267)|extracellular ATP-gated cation channel activity (GO:0004931)|identical protein binding (GO:0042802)|purinergic nucleotide receptor activity (GO:0001614)|transmembrane signaling receptor activity (GO:0004888)										GGCCAAGGCCCCGAAAGCAAC	0.632																																					p.P380S		Atlas-SNP	.											.	.	.	.	0			c.C1138T						.						42	38	39					22																	21380718		2202	4296	6498	SO:0001583	missense	9127	exon12			AAGGCCCCGAAAG		CCDS13788.2, CCDS54504.1	22q11.21	2012-01-17	2008-03-28	2008-03-28	ENSG00000099957	ENSG00000099957		"Purinergic receptors", "Ligand-gated ion channels / Purinergic receptors, ionotropic"	8538	protein-coding gene	gene with protein product		608077	"purinergic receptor P2X-like 1, orphan receptor"	P2RXL1		9242461, 10591208, 8786426	Standard	NM_005446		Approved	P2XM, MGC129625, P2X6	uc010gsu.1	O15547	OTTHUMG00000150689	ENST00000413302.2:c.1138C>T	chr22.hg19:g.21380718C>T	ENSP00000416193:p.Pro380Ser	65.0	0.0		57.0	19.0	NM_005446	F6V3D7|Q32MB6|Q58F04|Q6IC33|Q9UL50	Missense_Mutation	SNP	ENST00000413302.2	hg19	CCDS13788.2	.	.	.	.	.	.	.	.	.	.	C	21.1	4.091536	0.76756	.	.	ENSG00000099957	ENST00000413302;ENST00000336296;ENST00000401443;ENST00000443995	T;T;T;T	0.03920	3.76;3.76;3.76;3.76	4.54	3.53	0.40419	.	0.000000	0.53938	D	0.000043	T	0.13200	0.0320	L	0.59436	1.845	0.23758	N	0.996924	D;P	0.76494	0.999;0.551	D;B	0.70935	0.971;0.209	T	0.06570	-1.0819	10	0.27082	T	0.32	-9.0567	8.801	0.34909	0.0:0.8993:0.0:0.1007	.	380;354	O15547;F6V3D7	P2RX6_HUMAN;.	S	380;370;354;327	ENSP00000416193:P380S;ENSP00000338797:P370S;ENSP00000385309:P354S;ENSP00000408088:P327S	ENSP00000338797:P370S	P	+	1	0	P2RX6	19710718	0.136000	0.22515	0.512000	0.27736	0.659000	0.38960	3.664000	0.54525	1.506000	0.48736	0.655000	0.94253	CCG	.	.		0.632	P2RX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319625.2	NM_005446		T	21380718	C	T	21380718	3	4	266	1	0	0	0	0	1	0	0	0	11353	623	22	3	1184	3	P2RX6	22	21380718	Missense_Mutation	SNP	C	TCGA-FV-A3R2-01A-11D-A22F-10		21380718	29923848	65	39023										
MAPK1	5594	hgsc.bcm.edu	37	chr22	22160192	22160192	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	ggaaggcttgaggtcacggtGcagaacgttagctgaatgga	16	6	1	3			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr22:22160192G>A	ENST00000215832.6	-	3	627	c.439C>T	c.(439-441)Cac>Tac	p.H147Y	MAPK1_ENST00000398822.3_Missense_Mutation_p.H147Y|MAPK1_ENST00000544786.1_Missense_Mutation_p.H147Y	NM_002745.4	NP_002736.3	P28482	MK01_HUMAN	mitogen-activated protein kinase 1	147	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|caveolin-mediated endocytosis (GO:0072584)|cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|chemotaxis (GO:0006935)|cytosine metabolic process (GO:0019858)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|labyrinthine layer blood vessel development (GO:0060716)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|mammary gland epithelial cell proliferation (GO:0033598)|MAPK cascade (GO:0000165)|MAPK import into nucleus (GO:0000189)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell differentiation (GO:0045596)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|Ras protein signal transduction (GO:0007265)|regulation of cytoskeleton organization (GO:0051493)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of protein stability (GO:0031647)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of stress-activated MAPK cascade (GO:0032872)|response to epidermal growth factor (GO:0070849)|response to estrogen (GO:0043627)|response to exogenous dsRNA (GO:0043330)|response to stress (GO:0006950)|response to toxic substance (GO:0009636)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perikaryon (GO:0043204)|protein complex (GO:0043234)|pseudopodium (GO:0031143)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MAP kinase activity (GO:0004707)|phosphatase binding (GO:0019902)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Colorectal(54;0.105)	all_lung(157;3.89e-05)		READ - Rectum adenocarcinoma(21;0.0689)	Arsenic trioxide(DB01169)|Isoprenaline(DB01064)	AGGTCACGGTGCAGAACGTTA	0.428																																					p.H147Y		Atlas-SNP	.											.	MAPK1	38	.	0			c.C439T						.						200	179	186					22																	22160192		2203	4300	6503	SO:0001583	missense	5594	exon3			CACGGTGCAGAAC	M84489	CCDS13795.1	22q11.2	2014-09-17			ENSG00000100030	ENSG00000100030	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinases"	6871	protein-coding gene	gene with protein product		176948		PRKM2, PRKM1			Standard	NM_138957		Approved	ERK, ERK2, p41mapk, MAPK2	uc002zvn.3	P28482	OTTHUMG00000030508	ENST00000215832.6:c.439C>T	chr22.hg19:g.22160192G>A	ENSP00000215832:p.His147Tyr	156.0	0.0		135.0	46.0	NM_002745	A8CZ64	Missense_Mutation	SNP	ENST00000215832.6	hg19	CCDS13795.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.444037	0.83993	.	.	ENSG00000100030	ENST00000215832;ENST00000415911;ENST00000398822;ENST00000544786	T;T;T	0.72051	-0.62;-0.62;-0.62	4.77	3.76	0.43208	Serine/threonine-protein kinase-like domain (1);MAP kinase, conserved site (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.046654	0.85682	N	0.000000	D	0.87120	0.6098	M	0.93678	3.445	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.90244	0.4288	10	0.87932	D	0	-7.6907	13.3578	0.60638	0.0765:0.0:0.9235:0.0	.	147;147	A8CZ64;P28482	.;MK01_HUMAN	Y	147;135;147;147	ENSP00000215832:H147Y;ENSP00000381803:H147Y;ENSP00000440842:H147Y	ENSP00000215832:H147Y	H	-	1	0	MAPK1	20490192	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	9.640000	0.98453	1.374000	0.46228	0.650000	0.86243	CAC	.	.		0.428	MAPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000075396.2			A	22160192	G	A	22160192	3	1	266	1	0	0	0	0	1	0	0	0	9280	1319	46	3	667	3	MAPK1	22	22160192	Missense_Mutation	SNP	G	TCGA-FV-A3R2-01A-11D-A22F-10	779474	22160192	29144374	66	39024										
BRD1	23774	hgsc.bcm.edu	37	chr22	50169766	50169766	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	cagaggctccagcaccgaggCggcggcatcagtggagatcc	15	13	1	2	rs540212211		TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chr22:50169766C>T	ENST00000216267.8	-	10	3256	c.2770G>A	c.(2770-2772)Gcc>Acc	p.A924T	BRD1_ENST00000542442.1_Missense_Mutation_p.A612T|BRD1_ENST00000404760.1_Missense_Mutation_p.A1055T|BRD1_ENST00000457780.2_3'UTR|BRD1_ENST00000342989.5_Missense_Mutation_p.A650T|BRD1_ENST00000404034.1_Missense_Mutation_p.A924T	NM_014577.1	NP_055392.1	O95696	BRD1_HUMAN	bromodomain containing 1	924					histone H3 acetylation (GO:0043966)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleus (GO:0005634)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(3)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	37		all_cancers(38;6.11e-10)|all_epithelial(38;8.06e-09)|all_lung(38;6.64e-05)|Lung NSC(38;0.0011)|Breast(42;0.00235)|Ovarian(80;0.0139)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0369)|BRCA - Breast invasive adenocarcinoma(115;0.21)		AGCACCGAGGCGGCGGCATCA	0.692													C|||	1	0.000199681	0	0	5008	,	,		11138	0		0	False		,,,				2504	0.001				p.A924T		Atlas-SNP	.											.	BRD1	144	.	0			c.G2770A						.						52	48	49					22																	50169766		2203	4300	6503	SO:0001583	missense	23774	exon10			CCGAGGCGGCGGC	AF005067	CCDS14080.1	22q13.33	2008-07-01	2002-01-14		ENSG00000100425	ENSG00000100425			1102	protein-coding gene	gene with protein product	"BR140-like"	604589	"bromodomain-containing 1"			10591208, 10602503	Standard	NM_014577		Approved	BRL, BRPF2	uc003biv.3	O95696	OTTHUMG00000150288	ENST00000216267.8:c.2770G>A	chr22.hg19:g.50169766C>T	ENSP00000216267:p.Ala924Thr	7.0	0.0		12.0	7.0	NM_014577	A6ZJA4	Missense_Mutation	SNP	ENST00000216267.8	hg19	CCDS14080.1	.	.	.	.	.	.	.	.	.	.	C	6.565	0.472478	0.12461	.	.	ENSG00000100425	ENST00000216267;ENST00000404034;ENST00000404760;ENST00000542442;ENST00000342989;ENST00000419212	T;T;T;T;T	0.26223	2.68;2.68;2.67;1.75;2.13	4.45	4.45	0.53987	.	0.208414	0.50627	D	0.000106	T	0.10165	0.0249	N	0.04043	-0.29	0.80722	D	1	B;B;B;B	0.14012	0.001;0.009;0.001;0.001	B;B;B;B	0.04013	0.001;0.001;0.0;0.001	T	0.19451	-1.0305	10	0.12766	T	0.61	.	8.5562	0.33483	0.0:0.8571:0.0:0.1429	.	1055;650;924;1055	Q86X06;B7Z926;O95696;O95696-2	.;.;BRD1_HUMAN;.	T	924;924;1055;612;650;515	ENSP00000216267:A924T;ENSP00000384076:A924T;ENSP00000385858:A1055T;ENSP00000437514:A612T;ENSP00000345886:A650T	ENSP00000216267:A924T	A	-	1	0	BRD1	48555770	0.963000	0.33076	0.942000	0.38095	0.012000	0.07955	1.992000	0.40737	2.304000	0.77564	0.585000	0.79938	GCC	.	.		0.692	BRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317402.1	NM_014577		T	50169766	C	T	50169766	3	4	266	1	0	0	0	0	1	0	0	0	1503	768	27	1	418	1	BRD1	22	50169766	Missense_Mutation	SNP	C	TCGA-FV-A3R2-01A-11D-A22F-10	28009574	50169766	1134800	67	39025										
RGAG1	57529	hgsc.bcm.edu	37	chrX	109695878	109695878	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	gagagacacagcttctggagCaatgtccacatcacaaatga	9	10	2	2			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chrX:109695878C>T	ENST00000465301.2	+	3	2279	c.2033C>T	c.(2032-2034)gCa>gTa	p.A678V	RGAG1_ENST00000540313.1_Missense_Mutation_p.A678V	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	678										NS(1)|autonomic_ganglia(1)|breast(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	73						GCTTCTGGAGCAATGTCCACA	0.507																																					p.A678V		Atlas-SNP	.											.	RGAG1	168	.	0			c.C2033T						.						109	90	97					X																	109695878		2203	4300	6503	SO:0001583	missense	57529	exon3			CTGGAGCAATGTC	AY121804	CCDS14552.1	Xq23	2008-02-05			ENSG00000243978	ENSG00000243978			29245	protein-coding gene	gene with protein product						10718198, 15716091, 16093683	Standard	NM_020769		Approved	KIAA1318, Mart9, Mar9	uc004eor.2	Q8NET4	OTTHUMG00000022196	ENST00000465301.2:c.2033C>T	chrX.hg19:g.109695878C>T	ENSP00000419786:p.Ala678Val	79.0	0.0		48.0	38.0	NM_020769	Q9P2M8	Missense_Mutation	SNP	ENST00000465301.2	hg19	CCDS14552.1	.	.	.	.	.	.	.	.	.	.	C	4.134	0.023173	0.08006	.	.	ENSG00000243978	ENST00000465301;ENST00000540313	T;T	0.50001	0.76;0.76	4.08	-1.83	0.07833	.	1.573820	0.04513	N	0.383154	T	0.33030	0.0849	L	0.34521	1.04	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.11060	-1.0603	9	.	.	.	2.2927	4.7846	0.13219	0.1646:0.3668:0.0:0.4686	.	678	Q8NET4	RGAG1_HUMAN	V	678	ENSP00000419786:A678V;ENSP00000441452:A678V	.	A	+	2	0	RGAG1	109582534	0.001000	0.12720	0.000000	0.03702	0.348000	0.29142	-0.810000	0.04505	-0.564000	0.06070	0.600000	0.82982	GCA	.	.		0.507	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	NM_020769		T	109695878	C	T	109695878	3	4	266	1	0	0	0	0	1	0	0	0	13289	710	25	3	2035	3	RGAG1	23	109695878	Missense_Mutation	SNP	C	TCGA-FV-A3R2-01A-11D-A22F-10		109695878	45574682	68	39026										
ARHGAP36	158763	hgsc.bcm.edu	37	chrX	130219933	130219933	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	taacttggccttggtgtttgGatctgctctcctgaaaaaag	10	8	2	1			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chrX:130219933G>T	ENST00000276211.5	+	9	1496	c.1151G>T	c.(1150-1152)gGa>gTa	p.G384V	ARHGAP36_ENST00000370921.1_Missense_Mutation_p.G248V|ARHGAP36_ENST00000370922.1_Missense_Mutation_p.G372V	NM_144967.3	NP_659404.2	Q6ZRI8	RHG36_HUMAN	Rho GTPase activating protein 36	384	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(16)|lung(31)|ovary(4)|prostate(4)|skin(3)|urinary_tract(2)	71						TTGGTGTTTGGATCTGCTCTC	0.478																																					p.G384V		Atlas-SNP	.											.	ARHGAP36	171	.	0			c.G1151T						.						245	232	236					X																	130219933		2203	4300	6503	SO:0001583	missense	158763	exon9			TGTTTGGATCTGC		CCDS14628.1, CCDS65320.1	Xq26.1	2011-06-29			ENSG00000147256	ENSG00000147256		"Rho GTPase activating proteins"	26388	protein-coding gene	gene with protein product							Standard	NM_144967		Approved	FLJ30058	uc004evz.3	Q6ZRI8	OTTHUMG00000022402	ENST00000276211.5:c.1151G>T	chrX.hg19:g.130219933G>T	ENSP00000276211:p.Gly384Val	80.0	0.0		80.0	61.0	NM_144967	B7Z234|B7Z439|Q5JRL9|Q5JRM0|Q5JRM1|Q96NU6	Missense_Mutation	SNP	ENST00000276211.5	hg19	CCDS14628.1	.	.	.	.	.	.	.	.	.	.	G	14.42	2.530778	0.45073	.	.	ENSG00000147256	ENST00000276211;ENST00000370922;ENST00000412432;ENST00000370921	T;T;T;T	0.49720	0.77;0.77;0.77;0.77	4.71	4.71	0.59529	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.43416	D	0.000578	T	0.74581	0.3735	M	0.93507	3.425	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	T	0.81086	-0.1092	10	0.87932	D	0	.	11.8103	0.52179	0.0:0.0:1.0:0.0	.	353;372;384	Q6ZRI8-2;Q6ZRI8-4;Q6ZRI8	.;.;RHG36_HUMAN	V	384;372;353;248	ENSP00000276211:G384V;ENSP00000359960:G372V;ENSP00000408515:G353V;ENSP00000359959:G248V	ENSP00000276211:G384V	G	+	2	0	ARHGAP36	130047614	1.000000	0.71417	1.000000	0.80357	0.415000	0.31203	6.835000	0.75344	2.170000	0.68504	0.529000	0.55759	GGA	.	.		0.478	ARHGAP36-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355073.1	NM_144967		T	130219933	G	T	130219933	3	4	266	1	0	0	0	0	1	0	0	0	883	1174	41	3	1181	3	ARHGAP36	23	130219933	Missense_Mutation	SNP	G	TCGA-FV-A3R2-01A-11D-A22F-10	20524055	130219933	25050627	69	39027										
USP9Y	8287	hgsc.bcm.edu	37	chrY	14968377	14968377	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0285714285714286	2	1	0.499656593406593	1.74879807692308	0.291466346153846	1	1	0	atcagtgcataaaatgtatgGtagctctatttagcagttgt	9	5	2	0			TCGA-FV-A3R2-01A-11D-A22F-10	TCGA-FV-A3R2-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b9098b7c-eab0-4ef5-b968-8d3024bf32f7	3600db40-c4e6-463b-89f9-a95454c88e2b	g.chrY:14968377G>T	ENST00000338981.3	+	43	8122	c.7177G>T	c.(7177-7179)Gta>Tta	p.V2393L	USP9Y_ENST00000426564.2_3'UTR	NM_004654.3	NP_004645.2	O00507	USP9Y_HUMAN	ubiquitin specific peptidase 9, Y-linked	2393					BMP signaling pathway (GO:0030509)|protein deubiquitination (GO:0016579)|spermatogenesis (GO:0007283)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)	co-SMAD binding (GO:0070410)|cysteine-type peptidase activity (GO:0008234)|ubiquitin-specific protease activity (GO:0004843)			kidney(1)|large_intestine(8)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						AAAATGTATGGTAGCTCTATT	0.383																																					p.V2393L		Atlas-SNP	.											.	USP9Y	49	.	0			c.G7177T						.						79	85	84					Y																	14968377		604	1939	2543	SO:0001583	missense	8287	exon43			TGTATGGTAGCTC	Y13618	CCDS14781.1	Yq11.2	2010-04-09	2009-03-17		ENSG00000114374	ENSG00000114374		"Ubiquitin-specific peptidases"	12633	protein-coding gene	gene with protein product	"fat facets-like homolog (Drosophila)"	400005	"ubiquitin specific peptidase 9, Y-linked (fat facets-like, Drosophila)"			8922996, 9384609, 19246359	Standard	NM_004654		Approved	DFFRY	uc004fst.1	O00507	OTTHUMG00000036469	ENST00000338981.3:c.7177G>T	chrY.hg19:g.14968377G>T	ENSP00000342812:p.Val2393Leu	118.0	0.0		92.0	75.0	NM_004654	O14601	Missense_Mutation	SNP	ENST00000338981.3	hg19	CCDS14781.1	.	.	.	.	.	.	.	.	.	.	-	13.72	2.321304	0.41096	.	.	ENSG00000114374	ENST00000453031	.	.	.	2.34	2.34	0.29019	.	.	.	.	.	T	0.56761	0.2007	M	0.76328	2.33	.	.	.	.	.	.	.	.	.	T	0.60031	-0.7342	3	.	.	.	.	.	.	.	.	.	.	.	C	74	.	.	W	+	3	0	USP9Y	13477771	1.000000	0.71417	1.000000	0.80357	0.117000	0.20001	8.981000	0.93465	1.336000	0.45506	0.271000	0.19318	TGG	.	.		0.383	USP9Y-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088703.2	NM_004654		T	14968377	G	T	14968377	3	4	266	1	0	0	0	0	1	0	0	0	17106	1261	44	3	7339	3	USP9Y	24	14968377	Missense_Mutation	SNP	G	TCGA-FV-A3R2-01A-11D-A22F-10		14968377	44405189	70	39028										
NEK2	4751	hgsc.bcm.edu	37	chr1	211848801	211848801	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	atggtgtacaacacttcataGtcctcagcccgggaaggcat	10	11	2	0			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr1:211848801G>T	ENST00000366999.4	-	1	159	c.21C>A	c.(19-21)gaC>gaA	p.D7E	NEK2_ENST00000540251.1_Intron|NEK2_ENST00000366998.3_Missense_Mutation_p.D7E|RP11-122M14.1_ENST00000415202.1_RNA	NM_002497.3	NP_002488.1	P51955	NEK2_HUMAN	NIMA-related kinase 2	7					blastocyst development (GO:0001824)|centrosome separation (GO:0051299)|chromosome segregation (GO:0007059)|G2/M transition of mitotic cell cycle (GO:0000086)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of centriole-centriole cohesion (GO:1903126)|negative regulation of DNA binding (GO:0043392)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of mitosis (GO:0007088)|regulation of mitotic centrosome separation (GO:0046602)|spindle assembly (GO:0051225)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|microtubule (GO:0005874)|midbody (GO:0030496)|nucleus (GO:0005634)|protein complex (GO:0043234)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|stomach(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.00203)|all cancers(67;0.0339)|Epithelial(68;0.0546)		ACACTTCATAGTCCTCAGCCC	0.647																																					p.D7E		Atlas-SNP	.											.	NEK2	49	.	0			c.C21A						.						62	62	62					1																	211848801		2203	4300	6503	SO:0001583	missense	4751	exon1			TTCATAGTCCTCA	U11050	CCDS1500.1, CCDS55682.1, CCDS73024.1	1q32.3	2014-06-12	2012-11-15		ENSG00000117650	ENSG00000117650			7745	protein-coding gene	gene with protein product	"HsPK 21", "protein phosphatase 1, regulatory subunit 111"	604043	"NIMA (never in mitosis gene a)-related kinase 2"			8274451, 24043777	Standard	NM_002497		Approved	NLK1, NEK2A, RP67, PPP1R111	uc001hir.2	P51955	OTTHUMG00000037121	ENST00000366999.4:c.21C>A	chr1.hg19:g.211848801G>T	ENSP00000355966:p.Asp7Glu	80.0	0.0		67.0	10.0	NM_002497	Q53FD6|Q5I1Z9|Q5VXZ1|Q6NZX8|Q7Z634|Q86XH2|Q96QN9	Missense_Mutation	SNP	ENST00000366999.4	hg19	CCDS1500.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.035155	0.75617	.	.	ENSG00000117650	ENST00000366999;ENST00000366998	T;T	0.25749	1.78;1.78	5.35	5.35	0.76521	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.29652	0.0740	M	0.68317	2.08	0.80722	D	1	P;P;P	0.40083	0.525;0.578;0.702	B;B;B	0.40636	0.205;0.18;0.335	T	0.01409	-1.1362	10	0.25106	T	0.35	.	12.8788	0.58006	0.074:0.0:0.926:0.0	.	7;7;7	P51955-2;P51955;P51955-4	.;NEK2_HUMAN;.	E	7	ENSP00000355966:D7E;ENSP00000355965:D7E	ENSP00000355965:D7E	D	-	3	2	NEK2	209915424	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.547000	0.45786	2.941000	0.99782	0.655000	0.94253	GAC	.	.		0.647	NEK2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090154.1	NM_002497		T	211848801	G	T	211848801	3	4	267	1	0	0	0	0	1	0	0	0	10333	1020	36	3	1348	3	NEK2	1	211848801	Missense_Mutation	SNP	G	TCGA-FV-A3R3-01A-11D-A22F-10		211848801	37401820	1	39029										
FMN2	56776	hgsc.bcm.edu	37	chr1	240371393	240371393	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	acctccccctctacccggagCgggcataccccctccgcccc	7	24	1	0	rs201701711		TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr1:240371393C>A	ENST00000319653.9	+	5	3511	c.3281C>A	c.(3280-3282)gCg>gAg	p.A1094E		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1094	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CTACCCGGAGCGGGCATACCC	0.731																																					p.A1094E		Atlas-SNP	.											.	FMN2	451	.	0			c.C3281A						.						5	7	6					1																	240371393		1888	3892	5780	SO:0001583	missense	56776	exon5			CCGGAGCGGGCAT	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.3281C>A	chr1.hg19:g.240371393C>A	ENSP00000318884:p.Ala1094Glu	76.0	0.0		58.0	13.0	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	hg19	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	c	7.269	0.606854	0.14002	.	.	ENSG00000155816	ENST00000319653	T	0.59083	0.29	3.16	-1.05	0.10036	Actin-binding FH2/DRF autoregulatory (1);Formin Homology 1 (2);	2.671950	0.01759	N	0.030419	T	0.42988	0.1227	L	0.33189	0.99	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.05869	-1.0859	9	.	.	.	.	3.0177	0.06065	0.364:0.3658:0.0:0.2702	.	1094	Q9NZ56	FMN2_HUMAN	E	1094	ENSP00000318884:A1094E	.	A	+	2	0	FMN2	238438016	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.328000	0.01112	-0.352000	0.08237	-0.350000	0.07774	GCG	.	C|0.999;T|0.001		0.731	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		A	240371393	C	A	240371393	3	1	267	1	0	0	0	0	1	0	0	0	5958	768	27	1	3299	1	FMN2	1	240371393	Missense_Mutation	SNP	C	TCGA-FV-A3R3-01A-11D-A22F-10	28522592	240371393	8879228	2	39030										
GLI2	2736	hgsc.bcm.edu	37	chr2	121747077	121747077	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	aggcctacaggctagccctgGgggcctggacagcacgcagc	15	14	0	0			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr2:121747077G>A	ENST00000452319.1	+	14	3647	c.3587G>A	c.(3586-3588)gGg>gAg	p.G1196E	GLI2_ENST00000314490.11_Intron|GLI2_ENST00000361492.4_Missense_Mutation_p.G1196E					GLI family zinc finger 2											NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				GCTAGCCCTGGGGGCCTGGAC	0.672																																					p.G1196E		Atlas-SNP	.											.	GLI2	187	.	0			c.G3587A						.						13	17	15					2																	121747077		2182	4252	6434	SO:0001583	missense	2736	exon13			GCCCTGGGGGCCT		CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"Zinc fingers, C2H2-type"	4318	protein-coding gene	gene with protein product	"tax-responsive element-2 holding protein", "tax helper protein 1", "tax helper protein 2"	165230	"GLI-Kruppel family member GLI2", "glioma-associated oncogene family zinc finger 2"			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.3587G>A	chr2.hg19:g.121747077G>A	ENSP00000390436:p.Gly1196Glu	63.0	0.0		78.0	19.0	NM_005270		Missense_Mutation	SNP	ENST00000452319.1	hg19	CCDS33283.1	.	.	.	.	.	.	.	.	.	.	G	4.102	0.016996	0.07959	.	.	ENSG00000074047	ENST00000452319;ENST00000361492	T;T	0.13196	2.61;2.61	4.72	2.81	0.32909	.	0.692268	0.14606	N	0.309348	T	0.09024	0.0223	L	0.41236	1.265	0.09310	N	1	B;P	0.36535	0.421;0.557	B;B	0.31101	0.058;0.124	T	0.22138	-1.0225	9	.	.	.	.	5.287	0.15706	0.1455:0.0:0.5539:0.3006	.	1196;851	P10070;P10070-2	GLI2_HUMAN;.	E	1196	ENSP00000390436:G1196E;ENSP00000354586:G1196E	.	G	+	2	0	GLI2	121463547	0.005000	0.15991	0.002000	0.10522	0.088000	0.18126	0.755000	0.26405	1.176000	0.42840	0.449000	0.29647	GGG	.	.		0.672	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270		A	121747077	G	A	121747077	3	1	267	1	0	0	0	0	1	0	0	0	6446	1232	43	3	3637	3	GLI2	2	121747077	Missense_Mutation	SNP	G	TCGA-FV-A3R3-01A-11D-A22F-10		121747077	121452296	3	39031										
PTPN23	25930	hgsc.bcm.edu	37	chr3	47452056	47452056	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	gccactgcccacgccttacaCctaccctgcaggggctaagc	9	18	0	0			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr3:47452056C>T	ENST00000265562.4	+	20	2845	c.2768C>T	c.(2767-2769)aCc>aTc	p.T923I	PTPN23_ENST00000431726.1_Missense_Mutation_p.T797I	NM_015466.2	NP_056281.1	Q9H3S7	PTN23_HUMAN	protein tyrosine phosphatase, non-receptor type 23	923	His.|Pro-rich.				cilium morphogenesis (GO:0060271)|negative regulation of epithelial cell migration (GO:0010633)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of adherens junction organization (GO:1903393)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of homophilic cell adhesion (GO:1903387)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|central_nervous_system(1)|large_intestine(5)|lung(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.000271)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		ACGCCTTACACCTACCCTGCA	0.682																																					p.T923I		Atlas-SNP	.											.	PTPN23	85	.	0			c.C2768T						.						32	32	32					3																	47452056		2203	4300	6503	SO:0001583	missense	25930	exon20			CTTACACCTACCC	AB025194	CCDS2754.1	3p21.3	2011-06-09			ENSG00000076201	ENSG00000076201		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	14406	protein-coding gene	gene with protein product		606584				11095967	Standard	NM_015466		Approved	DKFZP564F0923, KIAA1471, HD-PTP	uc003crf.1	Q9H3S7	OTTHUMG00000133520	ENST00000265562.4:c.2768C>T	chr3.hg19:g.47452056C>T	ENSP00000265562:p.Thr923Ile	135.0	0.0		62.0	18.0	NM_015466	A8K0D7|Q7KZF8|Q8N6Z5|Q9BSR5|Q9P257|Q9UG03|Q9UMZ4	Missense_Mutation	SNP	ENST00000265562.4	hg19	CCDS2754.1	.	.	.	.	.	.	.	.	.	.	C	4.877	0.162968	0.09287	.	.	ENSG00000076201	ENST00000265562	T	0.02552	4.25	4.88	3.99	0.46301	.	0.875688	0.09919	N	0.738743	T	0.02380	0.0073	N	0.14661	0.345	0.21355	N	0.999711	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.48007	-0.9072	10	0.21540	T	0.41	-5.1617	11.0456	0.47857	0.0:0.8117:0.1883:0.0	.	797;923	B4DST5;Q9H3S7	.;PTN23_HUMAN	I	923	ENSP00000265562:T923I	ENSP00000265562:T923I	T	+	2	0	PTPN23	47427060	0.003000	0.15002	0.086000	0.20670	0.099000	0.18886	1.465000	0.35299	1.013000	0.39391	0.557000	0.71058	ACC	.	.		0.682	PTPN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257492.2	NM_015466		T	47452056	C	T	47452056	3	4	267	1	0	0	0	0	1	0	0	0	12803	507	18	3	2846	3	PTPN23	3	47452056	Missense_Mutation	SNP	C	TCGA-FV-A3R3-01A-11D-A22F-10		47452056	150570374	4	39032										
SMC4	10051	hgsc.bcm.edu	37	chr3	160141354	160141354	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	ataccttagtagctgacaacTtggatcaagccacaagagta	8	9	1	2			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr3:160141354T>G	ENST00000357388.3	+	14	2612	c.2161T>G	c.(2161-2163)Ttg>Gtg	p.L721V	RP11-432B6.3_ENST00000483754.1_Intron|SMC4_ENST00000360111.2_Missense_Mutation_p.L721V|SMC4_ENST00000462787.1_Missense_Mutation_p.L721V|SMC4_ENST00000469762.1_Missense_Mutation_p.L696V|SMC4_ENST00000344722.5_Missense_Mutation_p.L721V	NM_001002800.1	NP_001002800.1	Q9NTJ3	SMC4_HUMAN	structural maintenance of chromosomes 4	721	Flexible hinge.				kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)|mitotic sister chromatid segregation (GO:0000070)	condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(15)|lung(20)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			AGCTGACAACTTGGATCAAGC	0.338																																					p.L721V		Atlas-SNP	.											.	SMC4	135	.	0			c.T2161G						.						161	173	169					3																	160141354		2203	4300	6503	SO:0001583	missense	10051	exon13			GACAACTTGGATC	AF092564	CCDS3189.1, CCDS75046.1	3q26.1	2006-07-06	2006-07-06	2006-07-06	ENSG00000113810	ENSG00000113810		"Structural maintenance of chromosomes proteins"	14013	protein-coding gene	gene with protein product		605575	"SMC4 (structural maintenance of chromosomes 4, yeast)-like 1", "SMC4 structural maintenance of chromosomes 4-like 1 (yeast)"	SMC4L1		9789013, 10319587	Standard	NM_005496		Approved	hCAP-C, CAP-C	uc003fdh.3	Q9NTJ3	OTTHUMG00000159006	ENST00000357388.3:c.2161T>G	chr3.hg19:g.160141354T>G	ENSP00000349961:p.Leu721Val	85.0	0.0		103.0	24.0	NM_005496	A6NLT9|D3DNL8|O95752|Q8NDL4|Q9UNT9	Missense_Mutation	SNP	ENST00000357388.3	hg19	CCDS3189.1	.	.	.	.	.	.	.	.	.	.	T	18.67	3.674261	0.67928	.	.	ENSG00000113810	ENST00000357388;ENST00000360111;ENST00000469762;ENST00000462787;ENST00000344722;ENST00000545277	D;D;D;D;D	0.88741	-2.42;-2.42;-2.42;-2.42;-2.42	5.87	4.7	0.59300	SMCs flexible hinge (3);RecF/RecN/SMC (1);	0.058771	0.64402	D	0.000001	D	0.93697	0.7986	M	0.88031	2.925	0.53005	D	0.999965	D;D;B;D	0.61697	0.978;0.964;0.005;0.99	P;D;B;D	0.64237	0.833;0.919;0.034;0.923	D	0.93114	0.6519	10	0.87932	D	0	-8.8311	7.3892	0.26901	0.0:0.1099:0.1315:0.7586	.	721;696;696;721	Q9NTJ3-2;B3KXX5;E9PD53;Q9NTJ3	.;.;.;SMC4_HUMAN	V	721;721;696;721;721;315	ENSP00000349961:L721V;ENSP00000353225:L721V;ENSP00000417964:L696V;ENSP00000420734:L721V;ENSP00000341382:L721V	ENSP00000341382:L721V	L	+	1	2	SMC4	161624048	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	2.064000	0.41432	1.024000	0.39682	0.528000	0.53228	TTG	.	.		0.338	SMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352862.1			G	160141354	T	G	160141354	3	3	267	1	0	0	0	0	1	0	0	0	14800	1606	56	5	2211	5	SMC4	3	160141354	Missense_Mutation	SNP	T	TCGA-FV-A3R3-01A-11D-A22F-10	112689298	160141354	37881076	5	39033										
ARHGAP24	83478	hgsc.bcm.edu	37	chr4	86643102	86643102	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	caatgaagagaacccagggaAgttcctttttgaagtagttc	10	7	0	3			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr4:86643102A>T	ENST00000395184.1	+	3	711	c.245A>T	c.(244-246)aAg>aTg	p.K82M	ARHGAP24_ENST00000506421.1_3'UTR|MIR4451_ENST00000580577.1_RNA|ARHGAP24_ENST00000503995.1_Missense_Mutation_p.K82M	NM_001025616.2	NP_001020787.2	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24	82	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of ruffle assembly (GO:1900028)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|wound healing, spreading of epidermal cells (GO:0035313)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)	Rac GTPase activator activity (GO:0030675)	p.K82T(1)		breast(3)|cervix(1)|endometrium(3)|large_intestine(4)|lung(10)|skin(1)|stomach(1)|urinary_tract(1)	24		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		AACCCAGGGAAGTTCCTTTTT	0.383																																					p.K82M		Atlas-SNP	.											ARHGAP24_ENST00000395184,NS,carcinoma,0,1	ARHGAP24	116	.	1	Substitution - Missense(1)	prostate(1)	c.A245T						.						129	128	128					4																	86643102		2203	4300	6503	SO:0001583	missense	83478	exon3			CAGGGAAGTTCCT	AK091196	CCDS3611.1, CCDS34025.1, CCDS43246.1	4q22.1	2013-01-10			ENSG00000138639	ENSG00000138639		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	25361	protein-coding gene	gene with protein product		610586				11230166, 15254788	Standard	NM_001042669		Approved	DKFZP564B1162, FLJ33877, FilGAP	uc003hpk.3	Q8N264	OTTHUMG00000130427	ENST00000395184.1:c.245A>T	chr4.hg19:g.86643102A>T	ENSP00000378611:p.Lys82Met	207.0	0.0		172.0	22.0	NM_001025616	Q4KMG1|Q6ZNV3|Q86TI5|Q86WE4|Q9H0T6	Missense_Mutation	SNP	ENST00000395184.1	hg19	CCDS34025.1	.	.	.	.	.	.	.	.	.	.	A	16.28	3.079527	0.55753	.	.	ENSG00000138639	ENST00000395184;ENST00000503995	T;T	0.14516	2.5;2.5	4.97	4.97	0.65823	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.40979	0.1139	M	0.88181	2.935	0.80722	D	1	P;B;D	0.69078	0.955;0.018;0.997	P;B;D	0.63192	0.768;0.074;0.912	T	0.50709	-0.8796	10	0.87932	D	0	.	13.9319	0.64001	1.0:0.0:0.0:0.0	.	82;82;227	Q8N264;Q8N264-4;Q8N264-5	RHG24_HUMAN;.;.	M	82	ENSP00000378611:K82M;ENSP00000423206:K82M	ENSP00000378611:K82M	K	+	2	0	ARHGAP24	86862126	1.000000	0.71417	0.985000	0.45067	0.939000	0.58152	6.030000	0.70903	1.998000	0.58463	0.528000	0.53228	AAG	.	.		0.383	ARHGAP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252815.2	NM_031305		T	86643102	A	T	86643102	3	4	267	1	0	0	0	0	1	0	0	0	873	72	3	4	251	4	ARHGAP24	4	86643102	Missense_Mutation	SNP	A	TCGA-FV-A3R3-01A-11D-A22F-10		86643102	104511174	6	39034										
GRIA2	2891	hgsc.bcm.edu	37	chr4	158254023	158254023	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	agtgatgactgaagccttccGcaacctaaggaagcaaagaa	10	9	0	4			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr4:158254023G>A	ENST00000264426.9	+	7	1214	c.935G>A	c.(934-936)cGc>cAc	p.R312H	GRIA2_ENST00000393815.2_Missense_Mutation_p.R265H|GRIA2_ENST00000296526.7_Missense_Mutation_p.R312H|GRIA2_ENST00000449365.1_Missense_Mutation_p.R265H|GRIA2_ENST00000507898.1_Missense_Mutation_p.R265H	NM_001083619.1	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2	312					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(2)|lung(32)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	79	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	GAAGCCTTCCGCAACCTAAGG	0.463																																					p.R312H		Atlas-SNP	.											.	GRIA2	358	.	0			c.G935A						.						99	105	103					4																	158254023		2203	4300	6503	SO:0001583	missense	2891	exon7			CCTTCCGCAACCT		CCDS3797.1, CCDS43274.1, CCDS43275.1	4q32.1	2012-08-29			ENSG00000120251	ENSG00000120251		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4572	protein-coding gene	gene with protein product		138247		GLUR2		1311100	Standard	NM_001083619		Approved	GluA2, GLURB	uc003ipl.4	P42262	OTTHUMG00000133836	ENST00000264426.9:c.935G>A	chr4.hg19:g.158254023G>A	ENSP00000264426:p.Arg312His	121.0	0.0		118.0	15.0	NM_000826	A8MT92|I6L997|Q96FP6	Missense_Mutation	SNP	ENST00000264426.9	hg19	CCDS43274.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.213521	0.79352	.	.	ENSG00000120251	ENST00000507898;ENST00000393815;ENST00000296526;ENST00000264426;ENST00000449365	D;D;D;D;D	0.81499	-1.5;-1.5;-1.5;-1.5;-1.5	5.09	5.09	0.68999	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.85771	0.5774	L	0.42245	1.32	0.80722	D	1	D;B;D	0.89917	1.0;0.04;0.999	D;B;D	0.74674	0.95;0.002;0.984	D	0.83595	0.0125	10	0.28530	T	0.3	.	18.4737	0.90783	0.0:0.0:1.0:0.0	.	312;312;265	P42262;P42262-2;A8MT92	GRIA2_HUMAN;.;.	H	265;265;312;312;265	ENSP00000426845:R265H;ENSP00000377403:R265H;ENSP00000296526:R312H;ENSP00000264426:R312H;ENSP00000389837:R265H	ENSP00000264426:R312H	R	+	2	0	GRIA2	158473473	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	9.869000	0.99810	2.341000	0.79615	0.557000	0.71058	CGC	.	.		0.463	GRIA2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000258367.2			A	158254023	G	A	158254023	3	1	267	1	0	0	0	0	1	0	0	0	6777	1087	38	1	961	1	GRIA2	4	158254023	Missense_Mutation	SNP	G	TCGA-FV-A3R3-01A-11D-A22F-10	71610921	158254023	32900253	7	39035										
LIFR	3977	hgsc.bcm.edu	37	chr5	38482266	38482266	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	tgatcgagtttccagaacctCaacattatttggggtacaag	9	8	1	2			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr5:38482266C>A	ENST00000263409.4	-	20	2887	c.2725G>T	c.(2725-2727)Gag>Tag	p.E909*	LIFR_ENST00000453190.2_Nonsense_Mutation_p.E909*	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	909					cell surface receptor signaling pathway (GO:0007166)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|leukemia inhibitory factor signaling pathway (GO:0048861)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|leukemia inhibitory factor receptor activity (GO:0004923)			NS(2)|breast(4)|endometrium(6)|kidney(2)|large_intestine(30)|liver(2)|lung(21)|ovary(3)|skin(5)|stomach(1)|urinary_tract(2)	78	all_lung(31;0.00021)					TCCAGAACCTCAACATTATTT	0.383			T	PLAG1	salivary adenoma																																p.E909X	Melanoma(13;4 730 6426 9861 34751)	Atlas-SNP	.		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	.	LIFR	348	.	0			c.G2725T						.						61	63	62					5																	38482266		2203	4300	6503	SO:0001587	stop_gained	3977	exon20			GAACCTCAACATT	X61615	CCDS3927.1	5p13-p12	2013-02-11	2006-05-17		ENSG00000113594	ENSG00000113594		"CD molecules", "Fibronectin type III domain containing"	6597	protein-coding gene	gene with protein product		151443	"leukemia inhibitory factor receptor"			1915266	Standard	NM_001127671		Approved	CD118	uc003jli.2	P42702	OTTHUMG00000131138	ENST00000263409.4:c.2725G>T	chr5.hg19:g.38482266C>A	ENSP00000263409:p.Glu909*	90.0	0.0		86.0	14.0	NM_002310	Q6LCD9	Nonsense_Mutation	SNP	ENST00000263409.4	hg19	CCDS3927.1	.	.	.	.	.	.	.	.	.	.	C	40	8.492486	0.98834	.	.	ENSG00000113594	ENST00000263409;ENST00000453190	.	.	.	6.06	6.06	0.98353	.	0.466719	0.26307	N	0.025129	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.45353	T	0.12	-30.0859	20.6397	0.99537	0.0:1.0:0.0:0.0	.	.	.	.	X	909	.	ENSP00000263409:E909X	E	-	1	0	LIFR	38518023	0.999000	0.42202	0.996000	0.52242	0.979000	0.70002	5.114000	0.64648	2.880000	0.98712	0.650000	0.86243	GAG	.	.		0.383	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310		A	38482266	C	A	38482266	4	1	267	1	0	0	0	0	0	1	0	0	8789	835	29	3	572	3	LIFR	5	38482266	Nonsense_Mutation	SNP	C	TCGA-FV-A3R3-01A-11D-A22F-10		38482266	142432994	8	39036										
PDE4D	5144	hgsc.bcm.edu	37	chr5	58511685	58511685	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	ggatcgatacaggaaggactCccgtcgttgactgtggacaa	13	9	0	1			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr5:58511685C>A	ENST00000340635.6	-	2	740	c.565G>T	c.(565-567)Gag>Tag	p.E189*	PDE4D_ENST00000502484.2_Nonsense_Mutation_p.E128*|PDE4D_ENST00000405755.2_Nonsense_Mutation_p.E67*|PDE4D_ENST00000360047.5_Nonsense_Mutation_p.E53*|PDE4D_ENST00000546160.1_Nonsense_Mutation_p.E128*|PDE4D_ENST00000502575.1_Nonsense_Mutation_p.E125*|PDE4D_ENST00000507116.1_Nonsense_Mutation_p.E125*|PDE4D_ENST00000503258.1_Nonsense_Mutation_p.E59*|PDE4D_ENST00000503947.1_5'UTR	NM_001104631.1	NP_001098101.1	Q08499	PDE4D_HUMAN	phosphodiesterase 4D, cAMP-specific	189					adrenergic receptor signaling pathway (GO:0071875)|adrenergic receptor signaling pathway involved in positive regulation of heart rate (GO:0086024)|aging (GO:0007568)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to lipopolysaccharide (GO:0071222)|establishment of endothelial barrier (GO:0061028)|multicellular organism growth (GO:0035264)|negative regulation of heart contraction (GO:0045822)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of relaxation of cardiac muscle (GO:1901898)|neutrophil chemotaxis (GO:0030593)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-5 production (GO:0032754)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of receptor activity (GO:0010469)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|smooth muscle contraction (GO:0006939)|T cell receptor signaling pathway (GO:0050852)	calcium channel complex (GO:0034704)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|ATPase binding (GO:0051117)|beta-2 adrenergic receptor binding (GO:0031698)|cAMP binding (GO:0030552)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|pancreas(1)	15		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Caffeine(DB00201)|Dyphylline(DB00651)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Roflumilast(DB01656)	AGGAAGGACTCCCGTCGTTGA	0.532																																					p.E189X		Atlas-SNP	.											.	PDE4D	345	.	0			c.G565T						.						108	106	107					5																	58511685		1906	4121	6027	SO:0001587	stop_gained	5144	exon2			AGGACTCCCGTCG		CCDS47213.1, CCDS54858.1, CCDS54859.1, CCDS56369.1, CCDS56370.1, CCDS56371.1, CCDS56372.1, CCDS56373.1	5q12	2010-06-24	2010-06-24				3.1.4.17	"Phosphodiesterases"	8783	protein-coding gene	gene with protein product	"phosphodiesterase E3 dunce homolog (Drosophila)"	600129	"phosphodiesterase 4D, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E3)"	DPDE3			Standard	NM_006203		Approved		uc003jsa.2	Q08499		ENST00000340635.6:c.565G>T	chr5.hg19:g.58511685C>A	ENSP00000345502:p.Glu189*	97.0	0.0		76.0	25.0	NM_001104631	O43433|Q13549|Q13550|Q13551|Q7Z2L8|Q8IV84|Q8IVA9|Q8IVD2|Q8IVD3|Q96HL4|Q9HCX7	Nonsense_Mutation	SNP	ENST00000340635.6	hg19	CCDS47213.1	.	.	.	.	.	.	.	.	.	.	C	45	11.328100	0.99547	.	.	ENSG00000113448	ENST00000340635;ENST00000356665;ENST00000360047;ENST00000507116;ENST00000503258;ENST00000405755;ENST00000502484;ENST00000546160;ENST00000502575	.	.	.	4.66	4.66	0.58398	.	0.282883	0.32918	N	0.005489	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	17.9427	0.89030	0.0:1.0:0.0:0.0	.	.	.	.	X	189;58;53;125;59;67;128;128;125	.	ENSP00000308485:E125X	E	-	1	0	PDE4D	58547442	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.776000	0.85560	2.296000	0.77279	0.591000	0.81541	GAG	.	.		0.532	PDE4D-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367940.3			A	58511685	C	A	58511685	4	1	267	1	0	0	0	0	0	1	0	0	11651	864	30	3	1920	3	PDE4D	5	58511685	Nonsense_Mutation	SNP	C	TCGA-FV-A3R3-01A-11D-A22F-10	20029419	58511685	122403575	9	39037										
PCDHGA4	56111	hgsc.bcm.edu	37	chr5	140736620	140736620	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	cagcgagccgggactatttgCagtggggctgcacacaggcg	16	11	0	0			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr5:140736620C>T	ENST00000571252.1	+	1	1853	c.1853C>T	c.(1852-1854)gCa>gTa	p.A618V	PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018917.2	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4	618	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGACTATTTGCAGTGGGGCTG	0.622																																					p.A618V		Atlas-SNP	.											.	PCDHGA4	150	.	0			c.C1853T						.						37	45	42					5																	140736620		2197	4297	6494	SO:0001583	missense	56111	exon1			TATTTGCAGTGGG	AF152511	CCDS58979.1, CCDS58979.2, CCDS75331.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8702	other	protocadherin		606291				10380929	Standard	NM_018917		Approved	PCDH-GAMMA-A4		Q9Y5G9		ENST00000571252.1:c.1853C>T	chr5.hg19:g.140736620C>T	ENSP00000458570:p.Ala618Val	177.0	0.0		143.0	15.0	NM_018917	Q9Y5D3	Missense_Mutation	SNP	ENST00000571252.1	hg19	CCDS58979.1																																																																																			.	.		0.622	PCDHGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437959.1	NM_018917		T	140736620	C	T	140736620	3	4	267	1	0	0	0	0	1	0	0	0	11565	710	25	3	1855	3	PCDHGA4	5	140736620	Missense_Mutation	SNP	C	TCGA-FV-A3R3-01A-11D-A22F-10	82224935	140736620	40178640	10	39038										
BMP5	653	hgsc.bcm.edu	37	chr6	55620459	55620459	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	acaacaaggctttggtacgtGgtcaggaaacatcagatgaa	11	7	2	2			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr6:55620459G>C	ENST00000370830.3	-	7	1935	c.1237C>G	c.(1237-1239)Cac>Gac	p.H413D	BMP5_ENST00000446683.2_Missense_Mutation_p.H376D	NM_021073.2	NP_066551.1	P22003	BMP5_HUMAN	bone morphogenetic protein 5	413					cartilage development (GO:0051216)|growth (GO:0040007)|male genitalia development (GO:0030539)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of steroid biosynthetic process (GO:0010894)|ossification (GO:0001503)|pattern specification process (GO:0007389)|positive regulation of dendrite development (GO:1900006)|positive regulation of DNA-dependent DNA replication (GO:2000105)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system development (GO:0001501)|type B pancreatic cell development (GO:0003323)	extracellular space (GO:0005615)|membrane-bounded vesicle (GO:0031988)	BMP receptor binding (GO:0070700)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	45	Lung NSC(77;0.0462)		LUSC - Lung squamous cell carcinoma(124;0.181)			TTTGGTACGTGGTCAGGAAAC	0.308																																					p.H413D		Atlas-SNP	.											.	BMP5	94	.	0			c.C1237G						.						105	104	104					6																	55620459		2203	4299	6502	SO:0001583	missense	653	exon7			GTACGTGGTCAGG		CCDS4958.1	6p12.1	2014-01-30			ENSG00000112175	ENSG00000112175		"Bone morphogenetic proteins", "Endogenous ligands"	1072	protein-coding gene	gene with protein product		112265				1427904, 11580864	Standard	NM_021073		Approved		uc003pcq.3	P22003	OTTHUMG00000014903	ENST00000370830.3:c.1237C>G	chr6.hg19:g.55620459G>C	ENSP00000359866:p.His413Asp	242.0	0.0		266.0	20.0	NM_021073	B4E0Y4|Q9H547|Q9NTM5	Missense_Mutation	SNP	ENST00000370830.3	hg19	CCDS4958.1	.	.	.	.	.	.	.	.	.	.	G	9.080	0.998956	0.19121	.	.	ENSG00000112175	ENST00000370830;ENST00000446683	D;D	0.83335	-1.71;-1.71	5.73	5.73	0.89815	Transforming growth factor-beta, C-terminal (3);	0.045134	0.85682	D	0.000000	T	0.66376	0.2783	N	0.12182	0.205	0.48762	D	0.999708	B;B	0.29805	0.131;0.257	B;B	0.36030	0.145;0.216	T	0.65405	-0.6176	10	0.28530	T	0.3	.	20.2699	0.98469	0.0:0.0:1.0:0.0	.	376;413	B4E0Y4;P22003	.;BMP5_HUMAN	D	413;376	ENSP00000359866:H413D;ENSP00000391818:H376D	ENSP00000359866:H413D	H	-	1	0	BMP5	55728418	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	4.582000	0.60957	2.854000	0.98071	0.655000	0.94253	CAC	.	.		0.308	BMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041000.1			C	55620459	G	C	55620459	3	2	267	1	0	0	0	0	1	0	0	0	1463	1348	47	4	131	4	BMP5	6	55620459	Missense_Mutation	SNP	G	TCGA-FV-A3R3-01A-11D-A22F-10		55620459	115494608	11	39039										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152644792	152644792	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	tattcaagaagagttaagagCtctgctttcgatgctttctc	8	8	3	3			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr6:152644792C>T	ENST00000367255.5	-	82	16339	c.15738G>A	c.(15736-15738)gaG>gaA	p.E5246E	SYNE1_ENST00000448038.1_Silent_p.E5175E|SYNE1_ENST00000341594.5_Silent_p.E4939E|SYNE1_ENST00000423061.1_Silent_p.E5175E|SYNE1_ENST00000265368.4_Silent_p.E5246E	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	5246					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.E5246D(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GAGTTAAGAGCTCTGCTTTCG	0.488										HNSCC(10;0.0054)																											p.E5246E		Atlas-SNP	.											SYNE1_ENST00000265368,NS,carcinoma,0,2	SYNE1	3227	.	2	Substitution - Missense(2)	ovary(2)	c.G15738A						.						102	95	97					6																	152644792		2203	4300	6503	SO:0001819	synonymous_variant	23345	exon82			TAAGAGCTCTGCT	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.15738G>A	chr6.hg19:g.152644792C>T		86.0	0.0		69.0	4.0	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	hg19	CCDS5236.2																																																																																			.	.		0.488	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152644792	C	T	152644792	2	4	267	1	0	0	0	0	0	0	0	1	15460	796	28	3		3	SYNE1	6	152644792	Silent	SNP	C	TCGA-FV-A3R3-01A-11D-A22F-10	97024333	152644792	18470275	12	39040										
ZBTB10	65986	hgsc.bcm.edu	37	chr8	81412242	81412243	+	Frame_Shift_Ins	INS	-	-	A													0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	tctgtcttcatcacgggatcINSaaaaaattgccagtttttgg					rs199777283		TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr8:81412242_81412243insA	ENST00000430430.1	+	3	2265_2266	c.1486_1487insA	c.(1486-1488)caafs	p.Q496fs	ZBTB10_ENST00000455036.3_Frame_Shift_Ins_p.Q496fs|ZBTB10_ENST00000379091.4_Frame_Shift_Ins_p.Q204fs|ZBTB10_ENST00000426744.2_Frame_Shift_Ins_p.Q496fs	NM_001277145.1	NP_001264074.1	Q96DT7	ZBT10_HUMAN	zinc finger and BTB domain containing 10	496					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(4)	20	all_cancers(3;1.68e-09)|all_epithelial(4;5.13e-11)|Lung NSC(7;1.75e-07)|all_lung(9;7.38e-07)|Breast(3;2.96e-06)		BRCA - Breast invasive adenocarcinoma(6;0.000434)|Epithelial(68;0.00486)|all cancers(69;0.0296)			ATCACGGGATCAAAAAATTGCC	0.361																																					p.Q496fs		Atlas-INDEL	.											.	ZBTB10	51	.	0			c.1486_1487insA						.																																			SO:0001589	frameshift_variant	65986	exon2			.	AK022814	CCDS47880.1, CCDS64920.1	8q13-q21.1	2013-01-09			ENSG00000205189	ENSG00000205189		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	30953	protein-coding gene	gene with protein product						12477932	Standard	NM_001105539		Approved	RINZF, FLJ12752	uc003ybx.5	Q96DT7	OTTHUMG00000155016	ENST00000430430.1:c.1492dupA	chr8.hg19:g.81412248_81412248dupA	ENSP00000387462:p.Gln496fs	72.0	0.0		91.0	26.0	NM_023929	A4FVD0|Q86W96|Q8IXI9|Q96MH9	Frame_Shift_Ins	INS	ENST00000430430.1	hg19	CCDS47880.1																																																																																			.	.		0.361	ZBTB10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338055.2	NM_023929		A	81412243	-	A	81412242	7	5	267	1	0	1	1	0	0	0	0	0	17538	827	29	0	1492	0	ZBTB10	8	81412242	Frame_Shift_Ins	INS	-	TCGA-FV-A3R3-01A-11D-A22F-10		81412242	64951780	13	39041										
AKNA	80709	hgsc.bcm.edu	37	chr9	117122236	117122236	+	Frame_Shift_Del	DEL	A	A	-													0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	ccttgtgcctgagtcgggccAgggggtcctgtggcctgtcc							TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr9:117122236delA	ENST00000307564.4	-	10	2392	c.2231delT	c.(2230-2232)ctgfs	p.L744fs	AKNA_ENST00000374088.3_Frame_Shift_Del_p.L744fs|AKNA_ENST00000223791.3_Frame_Shift_Del_p.L204fs|AKNA_ENST00000312033.3_Frame_Shift_Del_p.L744fs|AKNA_ENST00000374075.5_Frame_Shift_Del_p.L663fs	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	744					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						GAGTCGGGCCAGGGGGTCCTG	0.632																																					p.L744fs		Atlas-INDEL	.											.	AKNA	119	.	0			c.2232delG						.						92	73	80					9																	117122236		2203	4300	6503	SO:0001589	frameshift_variant	80709	exon10			.	AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.2231delT	chr9.hg19:g.117122236delA	ENSP00000303769:p.Leu744fs	76.0	0.0		49.0	11.0	NM_030767	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Frame_Shift_Del	DEL	ENST00000307564.4	hg19	CCDS6805.1																																																																																			.	.		0.632	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767		-	117122236	A	-	117122236	7	5	267	1	0	1	0	1	0	0	0	0	463	188	7	0	2140	0	AKNA	9	117122236	Frame_Shift_Del	DEL	A	TCGA-FV-A3R3-01A-11D-A22F-10		117122236	24091195	14	39042										
KRT83	3889	hgsc.bcm.edu	37	chr12	52712959	52712959	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	cttcttcttgtagccctccaGcacctcctgcacgtggttga	8	15	2	1			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr12:52712959G>T	ENST00000293670.3	-	2	636	c.574C>A	c.(574-576)Ctg>Atg	p.L192M		NM_002282.3	NP_002273.3	P78385	KRT83_HUMAN	keratin 83	192	Coil 1B.|Rod.				aging (GO:0007568)|epidermis development (GO:0008544)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(9)|prostate(1)|skin(4)|stomach(7)|upper_aerodigestive_tract(1)	32	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		TAGCCCTCCAGCACCTCCTGC	0.622																																					p.L192M	GBM(41;747 834 12702 24089 39393)|Esophageal Squamous(97;805 1414 12559 28198 31861)	Atlas-SNP	.											.	KRT83	64	.	0			c.C574A						.						138	147	144					12																	52712959		2203	4300	6503	SO:0001583	missense	3889	exon2			CCTCCAGCACCTC	X99141	CCDS8823.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000170523	ENSG00000170523		"-", "Intermediate filaments type II, keratins (basic)"	6460	protein-coding gene	gene with protein product	"hard keratin type II"	602765	"keratin, hair, basic, 3"	KRTHB3		9084137, 16831889	Standard	NM_002282		Approved	Hb-3	uc001saf.2	P78385	OTTHUMG00000169632	ENST00000293670.3:c.574C>A	chr12.hg19:g.52712959G>T	ENSP00000293670:p.Leu192Met	142.0	0.0		121.0	31.0	NM_002282	A1A4S9|B2RC21|Q6NT21|Q9NSB3	Missense_Mutation	SNP	ENST00000293670.3	hg19	CCDS8823.1	.	.	.	.	.	.	.	.	.	.	G	15.52	2.857935	0.51376	.	.	ENSG00000170523	ENST00000293670	D	0.88431	-2.38	4.81	2.89	0.33648	Filament (1);	0.000000	0.33712	U	0.004633	D	0.88047	0.6332	L	0.58428	1.81	0.27882	N	0.939653	B	0.32324	0.364	P	0.46320	0.512	T	0.80400	-0.1398	10	0.45353	T	0.12	.	3.2963	0.06968	0.0818:0.262:0.3858:0.2704	.	192	P78385	KRT83_HUMAN	M	192	ENSP00000293670:L192M	ENSP00000293670:L192M	L	-	1	2	KRT83	50999226	0.977000	0.34250	1.000000	0.80357	0.998000	0.95712	1.893000	0.39758	0.490000	0.27771	0.563000	0.77884	CTG	.	.		0.622	KRT83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405182.1	NM_002282		T	52712959	G	T	52712959	3	4	267	1	0	0	0	0	1	0	0	0	8506	962	34	3	939	3	KRT83	12	52712959	Missense_Mutation	SNP	G	TCGA-FV-A3R3-01A-11D-A22F-10		52712959	81138936	15	39043										
TM9SF2	9375	hgsc.bcm.edu	37	chr13	100206607	100206607	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	gattccacgtcagattcctgAacagtcgttctacacgaagc	8	12	2	2			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr13:100206607A>G	ENST00000376387.4	+	14	1728	c.1538A>G	c.(1537-1539)gAa>gGa	p.E513G		NM_004800.1	NP_004791.1	Q99805	TM9S2_HUMAN	transmembrane 9 superfamily member 2	513					transport (GO:0006810)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)	17	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.218)					CAGATTCCTGAACAGTCGTTC	0.398																																					p.E513G		Atlas-SNP	.											.	TM9SF2	52	.	0			c.A1538G						.						169	159	162					13																	100206607		2203	4300	6503	SO:0001583	missense	9375	exon14			TTCCTGAACAGTC	U81006	CCDS9493.1	13q32.2	2011-03-28			ENSG00000125304	ENSG00000125304			11865	protein-coding gene	gene with protein product		604678				9729438	Standard	NM_004800		Approved	P76	uc001voj.2	Q99805	OTTHUMG00000017272	ENST00000376387.4:c.1538A>G	chr13.hg19:g.100206607A>G	ENSP00000365567:p.Glu513Gly	167.0	0.0		145.0	24.0	NM_004800	A8K399|Q2TAY5	Missense_Mutation	SNP	ENST00000376387.4	hg19	CCDS9493.1	.	.	.	.	.	.	.	.	.	.	A	17.73	3.462123	0.63513	.	.	ENSG00000125304	ENST00000376387	T	0.48201	0.82	5.93	5.93	0.95920	.	0.046005	0.85682	D	0.000000	T	0.57858	0.2082	M	0.87900	2.915	0.80722	D	1	B;B	0.19706	0.038;0.014	B;B	0.24394	0.053;0.053	T	0.58864	-0.7561	10	0.52906	T	0.07	-16.5071	16.3943	0.83563	1.0:0.0:0.0:0.0	.	479;513	E9PHW5;Q99805	.;TM9S2_HUMAN	G	513	ENSP00000365567:E513G	ENSP00000365567:E513G	E	+	2	0	TM9SF2	99004608	1.000000	0.71417	0.931000	0.37212	0.994000	0.84299	7.076000	0.76806	2.281000	0.76405	0.533000	0.62120	GAA	.	.		0.398	TM9SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045602.3			G	100206607	A	G	100206607	3	3	267	1	0	0	0	0	1	0	0	0	15993	246	9	2	1592	2	TM9SF2	13	100206607	Missense_Mutation	SNP	A	TCGA-FV-A3R3-01A-11D-A22F-10		100206607	14963271	16	39044										
COQ6	51004	hgsc.bcm.edu	37	chr14	74422552	74422552	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	ctgataatgtttgataaggaTaatttagatgacatgggcta	10	3	0	4			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr14:74422552T>G	ENST00000334571.2	+	4	442	c.402T>G	c.(400-402)gaT>gaG	p.D134E	COQ6_ENST00000394026.4_Missense_Mutation_p.D109E|COQ6_ENST00000554920.1_Missense_Mutation_p.D134E|COQ6_ENST00000238709.4_Missense_Mutation_p.D59E|COQ6_ENST00000555552.1_3'UTR	NM_182476.2	NP_872282.1	Q9Y2Z9	COQ6_HUMAN	coenzyme Q6 monooxygenase	134					small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	cell projection (GO:0042995)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)			breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	16				BRCA - Breast invasive adenocarcinoma(234;0.00337)		TTGATAAGGATAATTTAGATG	0.468																																					p.D134E		Atlas-SNP	.											.	COQ6	27	.	0			c.T402G						.						185	174	178					14																	74422552		2203	4300	6503	SO:0001583	missense	51004	exon4			TAAGGATAATTTA	AF132944	CCDS9823.1, CCDS9824.1, CCDS9824.2	14q24.1	2013-05-01	2013-05-01		ENSG00000119723	ENSG00000119723			20233	protein-coding gene	gene with protein product		614647	"coenzyme Q6 homolog (yeast)", "coenzyme Q6 homolog, monooxygenase (yeast)", "coenzyme Q6 homolog, monooxygenase (S. cerevisiae)"			21540551	Standard	NM_182476		Approved	CGI-10	uc001xph.3	Q9Y2Z9	OTTHUMG00000171260	ENST00000334571.2:c.402T>G	chr14.hg19:g.74422552T>G	ENSP00000333946:p.Asp134Glu	122.0	0.0		91.0	17.0	NM_182476	B7Z3K8|Q53GG6|Q86U30|Q96CA1|Q96CK2	Missense_Mutation	SNP	ENST00000334571.2	hg19	CCDS9823.1	.	.	.	.	.	.	.	.	.	.	T	15.15	2.747178	0.49257	.	.	ENSG00000119723	ENST00000394026;ENST00000555376;ENST00000238709;ENST00000553462;ENST00000334571;ENST00000556300;ENST00000554153;ENST00000557584;ENST00000554920;ENST00000557205;ENST00000554320;ENST00000555392	T;T;T;T	0.41400	1.0;1.0;1.0;1.0	5.51	-1.29	0.09288	.	0.283457	0.44285	N	0.000467	T	0.17916	0.0430	N	0.12663	0.25	0.45962	D	0.998787	B;B;B;B;B;B;B;B	0.29988	0.264;0.036;0.234;0.012;0.0;0.036;0.019;0.001	B;B;B;B;B;B;B;B	0.28465	0.057;0.086;0.09;0.004;0.002;0.023;0.015;0.002	T	0.06215	-1.0839	10	0.20519	T	0.43	-1.5003	6.1558	0.20335	0.0:0.2834:0.1231:0.5935	.	79;134;79;109;134;59;59;59	B7Z8E9;B7Z357;B7Z262;B7Z3K8;Q9Y2Z9;G3V3A1;G3XA86;Q86U30	.;.;.;.;COQ6_HUMAN;.;.;.	E	109;59;59;59;134;134;79;79;134;79;59;59	ENSP00000377594:D109E;ENSP00000238709:D59E;ENSP00000333946:D134E;ENSP00000451123:D59E	ENSP00000238709:D59E	D	+	3	2	COQ6	73492305	0.360000	0.24964	0.743000	0.31040	0.968000	0.65278	-0.499000	0.06413	-0.346000	0.08312	0.459000	0.35465	GAT	.	.		0.468	COQ6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412616.1			G	74422552	T	G	74422552	3	3	267	1	0	0	0	0	1	0	0	0	3751	1403	49	5	416	5	COQ6	14	74422552	Missense_Mutation	SNP	T	TCGA-FV-A3R3-01A-11D-A22F-10		74422552	32926988	17	39045										
VPS13C	54832	hgsc.bcm.edu	37	chr15	62182512	62182512	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	aaccaaggcaacatcatcggTgaaaagcaaaactctctggc	8	11	2	1			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr15:62182512T>C	ENST00000261517.5	-	67	9266	c.9193A>G	c.(9193-9195)Acc>Gcc	p.T3065A	VPS13C_ENST00000249837.3_Missense_Mutation_p.T3022A|VPS13C_ENST00000395896.4_Missense_Mutation_p.T3065A|VPS13C_ENST00000395898.3_Missense_Mutation_p.T3022A	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						ACATCATCGGTGAAAAGCAAA	0.453																																					p.T3065A		Atlas-SNP	.											.	VPS13C	506	.	0			c.A9193G						.						89	78	82					15																	62182512		2203	4300	6503	SO:0001583	missense	54832	exon67			CATCGGTGAAAAG	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"vacuolar protein sorting 13C (yeast)"				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.9193A>G	chr15.hg19:g.62182512T>C	ENSP00000261517:p.Thr3065Ala	112.0	0.0		70.0	16.0	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	hg19	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	T	26.9	4.783518	0.90282	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.52295	0.67;0.67;0.67	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.75332	0.3835	M	0.90870	3.155	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.999;1.0;0.997	T	0.81906	-0.0718	10	0.87932	D	0	.	15.6116	0.76727	0.0:0.0:0.0:1.0	.	3022;3065;3022;3065	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	A	3022;3065;3065;3065	ENSP00000249837:T3022A;ENSP00000261517:T3065A;ENSP00000379233:T3065A	ENSP00000249837:T3022A	T	-	1	0	VPS13C	59969804	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.503000	0.81632	2.079000	0.62486	0.533000	0.62120	ACC	.	.		0.453	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		C	62182512	T	C	62182512	3	2	267	1	0	0	0	0	1	0	0	0	17206	1696	59	2	2172	2	VPS13C	15	62182512	Missense_Mutation	SNP	T	TCGA-FV-A3R3-01A-11D-A22F-10		62182512	40348880	18	39046										
FSD2	123722	hgsc.bcm.edu	37	chr15	83451591	83451591	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	gtgacacatctcctctattgTttccatcagttctttgcaag	6	11	4	1			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr15:83451591T>C	ENST00000334574.8	-	4	1103	c.922A>G	c.(922-924)Aca>Gca	p.T308A	FSD2_ENST00000541889.1_Missense_Mutation_p.T308A			A1L4K1	FSD2_HUMAN	fibronectin type III and SPRY domain containing 2	308										breast(2)|central_nervous_system(1)|large_intestine(5)|lung(10)	18						TCCTCTATTGTTTCCATCAGT	0.378																																					p.T308A		Atlas-SNP	.											.	FSD2	45	.	0			c.A922G						.						305	288	293					15																	83451591		1894	4118	6012	SO:0001583	missense	123722	exon4			CTATTGTTTCCAT	AK122875	CCDS45332.1, CCDS61738.1	15q25.2	2013-02-11	2006-01-11	2006-01-11		ENSG00000186628		"Fibronectin type III domain containing"	18024	protein-coding gene	gene with protein product			"SPRY domain containing 1"	SPRYD1			Standard	NM_001007122		Approved	RP11-127F21	uc002bjd.2	A1L4K1		ENST00000334574.8:c.922A>G	chr15.hg19:g.83451591T>C	ENSP00000335651:p.Thr308Ala	286.0	0.0		220.0	24.0	NM_001007122	B3KVG1|B7ZM02	Missense_Mutation	SNP	ENST00000334574.8	hg19	CCDS45332.1	.	.	.	.	.	.	.	.	.	.	T	17.50	3.404838	0.62288	.	.	ENSG00000186628	ENST00000334574;ENST00000541889	T;T	0.63417	0.44;-0.04	6.04	3.69	0.42338	.	0.108638	0.64402	D	0.000012	T	0.58119	0.2100	M	0.66939	2.045	0.31242	N	0.695044	B;P	0.47762	0.354;0.9	B;B	0.43990	0.217;0.438	T	0.62201	-0.6904	10	0.41790	T	0.15	-13.9101	6.0078	0.19557	0.1232:0.1369:0.0:0.74	.	308;308	B7ZM02;A1L4K1	.;FSD2_HUMAN	A	308	ENSP00000335651:T308A;ENSP00000444078:T308A	ENSP00000335651:T308A	T	-	1	0	FSD2	81248645	1.000000	0.71417	0.793000	0.32043	0.950000	0.60333	2.497000	0.45354	0.497000	0.27926	0.459000	0.35465	ACA	.	.		0.378	FSD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418385.1	NM_001007122		C	83451591	T	C	83451591	3	2	267	1	0	0	0	0	1	0	0	0	6079	1725	60	2	1367	2	FSD2	15	83451591	Missense_Mutation	SNP	T	TCGA-FV-A3R3-01A-11D-A22F-10	21269079	83451591	19079801	19	39047										
AKAP13	11214	hgsc.bcm.edu	37	chr15	86265519	86265519	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	tccagagtgcatattgcttgTaactcagcggattaccaagt	9	9	1	1			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr15:86265519T>G	ENST00000394518.2	+	25	6532	c.6437T>G	c.(6436-6438)gTa>gGa	p.V2146G	AKAP13_ENST00000361243.2_Missense_Mutation_p.V2150G|AKAP13_ENST00000394510.2_Missense_Mutation_p.V391G|AKAP13_ENST00000560579.1_3'UTR	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	2146	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.|Interaction with ESR1.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						ATATTGCTTGTAACTCAGCGG	0.413																																					p.V2150G	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.T6449G						.						237	226	230					15																	86265519		2202	4299	6501	SO:0001583	missense	11214	exon25			TGCTTGTAACTCA	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"A-kinase anchor proteins", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	371	protein-coding gene	gene with protein product		604686	"lymphoid blast crisis oncogene"	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.6437T>G	chr15.hg19:g.86265519T>G	ENSP00000378026:p.Val2146Gly	136.0	0.0		138.0	14.0	NM_006738	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	hg19	CCDS32319.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.824186	0.90955	.	.	ENSG00000170776	ENST00000426424;ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540;ENST00000394510	T;T;T	0.68765	-0.35;-0.35;-0.35	5.69	5.69	0.88448	Dbl homology (DH) domain (5);	.	.	.	.	T	0.79747	0.4499	L	0.61218	1.895	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.81276	-0.1006	9	0.62326	D	0.03	.	15.117	0.72410	0.0:0.0:0.0:1.0	.	2126;2146;2150	Q12802-4;Q12802;Q12802-2	.;AKP13_HUMAN;.	G	226;2150;2146;2149;2125;391	ENSP00000354718:V2150G;ENSP00000378026:V2146G;ENSP00000378018:V391G	ENSP00000354718:V2150G	V	+	2	0	AKAP13	84066523	1.000000	0.71417	0.994000	0.49952	0.986000	0.74619	7.698000	0.84413	2.150000	0.67090	0.533000	0.62120	GTA	.	.		0.413	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200		G	86265519	T	G	86265519	3	3	267	1	0	0	0	0	1	0	0	0	449	1638	57	5	6601	5	AKAP13	15	86265519	Missense_Mutation	SNP	T	TCGA-FV-A3R3-01A-11D-A22F-10	2813928	86265519	16265873	20	39048										
SLC5A11	115584	hgsc.bcm.edu	37	chr16	24902218	24902218	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	gcggttggtgggatggaaggActgaaggagaagtacttctt	17	4	1	2			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr16:24902218A>G	ENST00000347898.3	+	9	1315	c.693A>G	c.(691-693)ggA>ggG	p.G231G	SLC5A11_ENST00000424767.2_Silent_p.G196G|SLC5A11_ENST00000545376.1_Silent_p.G161G|SLC5A11_ENST00000567758.1_Silent_p.G196G|SLC5A11_ENST00000449109.2_Intron|SLC5A11_ENST00000569071.1_Intron|SLC5A11_ENST00000565769.1_Silent_p.G167G|SLC5A11_ENST00000539472.1_Silent_p.G167G|SLC5A11_ENST00000568579.1_Silent_p.G161G	NM_052944.3	NP_443176.2			solute carrier family 5 (sodium/inositol cotransporter), member 11											endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(30)|ovary(2)|prostate(2)|urinary_tract(1)	49				GBM - Glioblastoma multiforme(48;0.0365)		GGATGGAAGGACTGAAGGAGA	0.547																																					p.G231G		Atlas-SNP	.											.	SLC5A11	97	.	0			c.A693G						.						136	138	138					16																	24902218		2197	4300	6497	SO:0001819	synonymous_variant	115584	exon9			GGAAGGACTGAAG	AF292385	CCDS10625.1, CCDS58437.1, CCDS58438.1, CCDS58439.1, CCDS58440.1	16p12.1	2013-07-19	2013-07-19		ENSG00000158865	ENSG00000158865		"Solute carriers"	23091	protein-coding gene	gene with protein product		610238	"solute carrier family 5 (sodium/glucose cotransporter), member 11"			12039040, 12133831	Standard	NM_001258414		Approved	KST1, SMIT2, SGLT6	uc002dmu.4	Q8WWX8	OTTHUMG00000097003	ENST00000347898.3:c.693A>G	chr16.hg19:g.24902218A>G		84.0	0.0		61.0	12.0	NM_052944		Silent	SNP	ENST00000347898.3	hg19	CCDS10625.1																																																																																			.	.		0.547	SLC5A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214091.3	NM_052944		G	24902218	A	G	24902218	2	3	267	1	0	0	0	0	0	0	0	1	14678	262	10	2		2	SLC5A11	16	24902218	Silent	SNP	A	TCGA-FV-A3R3-01A-11D-A22F-10		24902218	65452535	21	39049										
POLR2A	5430	hgsc.bcm.edu	37	chr17	7400976	7400976	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	tttttcctcacaggccatgcAgaagtctgggcgtcccctca	9	14	3	1			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr17:7400976A>T	ENST00000322644.6	+	7	1388	c.989A>T	c.(988-990)cAg>cTg	p.Q330L	POLR2A_ENST00000572844.1_Missense_Mutation_p.Q330L	NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	330					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA-directed RNA polymerase activity (GO:0003968)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(17)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	50		Prostate(122;0.173)				CAGGCCATGCAGAAGTCTGGG	0.602																																					p.Q330L		Atlas-SNP	.											.	POLR2A	157	.	0			c.A989T						.						48	49	49					17																	7400976		2203	4300	6503	SO:0001583	missense	5430	exon7			CCATGCAGAAGTC			17p13.1	2013-01-21	2002-08-29		ENSG00000181222	ENSG00000181222	2.7.7.6	"RNA polymerase subunits"	9187	protein-coding gene	gene with protein product	"DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit", "RNA polymerase II subunit B1"	180660	"polymerase (RNA) II (DNA directed) polypeptide A (220kD)"	POLR2			Standard	NM_000937		Approved	POLRA, RPB1	uc002ghf.4	P24928	OTTHUMG00000177594	ENST00000322644.6:c.989A>T	chr17.hg19:g.7400976A>T	ENSP00000314949:p.Gln330Leu	89.0	0.0		73.0	20.0	NM_000937	A6NN93|B9EH88|Q6NX41	Missense_Mutation	SNP	ENST00000322644.6	hg19	CCDS32548.1	.	.	.	.	.	.	.	.	.	.	A	16.49	3.138761	0.56936	.	.	ENSG00000181222	ENST00000535204;ENST00000322644	T	0.25250	1.81	5.74	5.74	0.90152	RNA polymerase, N-terminal (1);RNA polymerase Rpb1, domain 1 (1);	0.000000	0.85682	D	0.000000	T	0.46386	0.1390	M	0.74258	2.255	0.80722	D	1	P;B	0.44195	0.828;0.249	P;B	0.53912	0.737;0.143	T	0.47032	-0.9148	10	0.87932	D	0	-10.9531	15.0177	0.71600	1.0:0.0:0.0:0.0	.	330;330	P24928;Q6NX41	RPB1_HUMAN;.	L	286;330	ENSP00000314949:Q330L	ENSP00000314949:Q330L	Q	+	2	0	SLC35G6	7341700	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.444000	0.90323	2.189000	0.69895	0.460000	0.39030	CAG	.	.		0.602	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	NM_000937		T	7400976	A	T	7400976	3	4	267	1	0	0	0	0	1	0	0	0	12223	188	7	4	1015	4	POLR2A	17	7400976	Missense_Mutation	SNP	A	TCGA-FV-A3R3-01A-11D-A22F-10		7400976	73794234	22	39050										
MUC16	94025	hgsc.bcm.edu	37	chr19	9060181	9060181	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	ggtaagggtaccccttgatgTagccccaggagaacctgttt	12	10	0	2			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr19:9060181T>G	ENST00000397910.4	-	3	27468	c.27265A>C	c.(27265-27267)Aca>Cca	p.T9089P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9091	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CCCCTTGATGTAGCCCCAGGA	0.478																																					p.T9089P		Atlas-SNP	.											.	MUC16	4315	.	0			c.A27265C						.						179	166	170					19																	9060181		1922	4131	6053	SO:0001583	missense	94025	exon3			TTGATGTAGCCCC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.27265A>C	chr19.hg19:g.9060181T>G	ENSP00000381008:p.Thr9089Pro	111.0	0.0		108.0	14.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	3.272	-0.148960	0.06585	.	.	ENSG00000181143	ENST00000397910	T	0.02579	4.24	2.5	-4.99	0.03010	.	.	.	.	.	T	0.01730	0.0055	N	0.24115	0.695	.	.	.	B	0.28713	0.22	B	0.27076	0.076	T	0.44360	-0.9333	8	0.87932	D	0	.	0.1031	0.00050	0.3214:0.2327:0.1631:0.2828	.	9089	B5ME49	.	P	9089	ENSP00000381008:T9089P	ENSP00000381008:T9089P	T	-	1	0	MUC16	8921181	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.710000	0.05024	-1.618000	0.01568	-0.658000	0.03865	ACA	.	.		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	9060181	T	G	9060181	3	3	267	1	0	0	0	0	1	0	0	0	9982	1638	57	5	16586	5	MUC16	19	9060181	Missense_Mutation	SNP	T	TCGA-FV-A3R3-01A-11D-A22F-10		9060181	50068802	23	39051										
ZNF793	390927	hgsc.bcm.edu	37	chr19	38028241	38028241	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	ccacctacagaaaaaccccaCgtctgtagtgagtgtgggaa	10	11	1	2	rs371897623		TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr19:38028241C>T	ENST00000587143.1	+	6	916	c.681C>T	c.(679-681)caC>caT	p.H227H	ZNF793_ENST00000589319.1_Intron|ZNF793_ENST00000445217.1_Silent_p.H227H|ZNF793_ENST00000588578.1_3'UTR|ZNF793_ENST00000542455.1_Silent_p.H227H			Q6ZN11	ZN793_HUMAN	zinc finger protein 793	227					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(2)|lung(1)	3			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AAAAACCCCACGTCTGTAGTG	0.473																																					p.H227H	Melanoma(44;400 1431 1499 19093)	Atlas-SNP	.											ZNF793_ENST00000445217,NS,carcinoma,0,1	ZNF793	50	.	0			c.C681T						.	C		1,4047		0,1,2023	31	33	32		681	-6.8	0.1	19		32	0,8414		0,0,4207	no	coding-synonymous	ZNF793	NM_001013659.2		0,1,6230	TT,TC,CC		0.0,0.0247,0.0080		227/407	38028241	1,12461	2024	4207	6231	SO:0001819	synonymous_variant	390927	exon8			ACCCCACGTCTGT	AK131417	CCDS46062.1	19q13.12	2013-01-08				ENSG00000188227		"Zinc fingers, C2H2-type", "-"	33115	protein-coding gene	gene with protein product							Standard	NM_001013659		Approved		uc010efm.3	Q6ZN11		ENST00000587143.1:c.681C>T	chr19.hg19:g.38028241C>T		59.0	0.0		72.0	15.0	NM_001013659	E9PGN4|Q7Z3Q9	Silent	SNP	ENST00000587143.1	hg19	CCDS46062.1																																																																																			.	.		0.473	ZNF793-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458621.1	NM_001013659		T	38028241	C	T	38028241	2	4	267	1	0	0	0	0	0	0	0	1	18180	535	19	1		1	ZNF793	19	38028241	Silent	SNP	C	TCGA-FV-A3R3-01A-11D-A22F-10	28968060	38028241	21100742	24	39052										
ZNF607	84775	hgsc.bcm.edu	37	chr19	38189048	38189048	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	agtatgaactctatgatgtaTactaagttcatggctactat	7	6	2	2	rs371361210		TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr19:38189048T>A	ENST00000355202.4	-	5	2579	c.1984A>T	c.(1984-1986)Ata>Tta	p.I662L	ZNF607_ENST00000395835.3_Missense_Mutation_p.I661L|CTD-2528L19.4_ENST00000586606.2_Intron	NM_032689.4	NP_116078.4	Q96SK3	ZN607_HUMAN	zinc finger protein 607	662					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|lung(8)|urinary_tract(1)	27			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)			CTATGATGTATACTAAGTTCA	0.378																																					p.I662L		Atlas-SNP	.											.	ZNF607	82	.	0			c.A1984T						.	T	LEU/ILE,LEU/ILE	0,4406		0,0,2203	110	108	109		1981,1984	-3.9	0.3	19		109	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ZNF607	NM_001172677.1,NM_032689.4	5,5	0,1,6502	AA,AT,TT		0.0116,0.0,0.0077	benign,benign	661/696,662/697	38189048	1,13005	2203	4300	6503	SO:0001583	missense	84775	exon5			GATGTATACTAAG	AK127464	CCDS33006.1, CCDS54259.1	19q13.1	2013-01-08				ENSG00000198182		"Zinc fingers, C2H2-type", "-"	28192	protein-coding gene	gene with protein product						14702039	Standard	NM_032689		Approved	MGC13071, FLJ14802	uc002ohc.2	Q96SK3		ENST00000355202.4:c.1984A>T	chr19.hg19:g.38189048T>A	ENSP00000347338:p.Ile662Leu	123.0	0.0		120.0	22.0	NM_032689	F5H141|Q6ZMN2|Q6ZMN4|Q96C40	Missense_Mutation	SNP	ENST00000355202.4	hg19	CCDS33006.1	.	.	.	.	.	.	.	.	.	.	T	11.15	1.553069	0.27739	0.0	1.16E-4	ENSG00000198182	ENST00000355202;ENST00000395835	T;T	0.17854	2.25;2.25	1.96	-3.91	0.04168	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10380	0.0254	L	0.31926	0.97	0.09310	N	1	B;B	0.13145	0.004;0.007	B;B	0.17433	0.001;0.018	T	0.37454	-0.9705	9	0.29301	T	0.29	.	5.837	0.18613	0.0:0.137:0.4228:0.4402	.	662;661	Q96SK3;F5H141	ZN607_HUMAN;.	L	662;661	ENSP00000347338:I662L;ENSP00000438015:I661L	ENSP00000347338:I662L	I	-	1	0	ZNF607	42880888	0.000000	0.05858	0.340000	0.25575	0.870000	0.49936	-4.480000	0.00227	-0.467000	0.06932	0.379000	0.24179	ATA	.	.		0.378	ZNF607-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459502.2	NM_032689		A	38189048	T	A	38189048	3	1	267	1	0	0	0	0	1	0	0	0	18048	1406	49	4	110	4	ZNF607	19	38189048	Missense_Mutation	SNP	T	TCGA-FV-A3R3-01A-11D-A22F-10	160807	38189048	20939935	25	39053										
EPB41L1	2036	hgsc.bcm.edu	37	chr20	34761813	34761813	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	gtgacccctgcaggccacggCcacccagaggccaactccaa	10	18	0	2			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr20:34761813C>A	ENST00000338074.2	+	2	275	c.114C>A	c.(112-114)ggC>ggA	p.G38G	EPB41L1_ENST00000373950.2_Intron|EPB41L1_ENST00000373946.3_Intron|EPB41L1_ENST00000373941.1_Silent_p.G38G|EPB41L1_ENST00000202028.5_Intron|EPB41L1_ENST00000441639.1_Intron	NM_001258329.1|NM_012156.2	NP_001245258.1|NP_036288.2	Q9H4G0	E41L1_HUMAN	erythrocyte membrane protein band 4.1-like 1	38					cortical actin cytoskeleton organization (GO:0030866)|synaptic transmission (GO:0007268)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(10)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	37	Breast(12;0.0239)					CAGGCCACGGCCACCCAGAGG	0.662																																					p.G38G		Atlas-SNP	.											.	EPB41L1	111	.	0			c.C114A						.						37	34	35					20																	34761813		2203	4300	6503	SO:0001819	synonymous_variant	2036	exon3			CCACGGCCACCCA	AB002336	CCDS13271.1, CCDS13272.1, CCDS58771.1	20q11.2-q12	2003-03-17			ENSG00000088367	ENSG00000088367			3378	protein-coding gene	gene with protein product		602879				9570967, 9828140	Standard	NM_012156		Approved	KIAA0338	uc002xfb.3	Q9H4G0	OTTHUMG00000032378	ENST00000338074.2:c.114C>A	chr20.hg19:g.34761813C>A		81.0	0.0		71.0	17.0	NM_001258329	O15046|Q4VXM6|Q4VXM7|Q4VXM8|Q4VXN4|Q6ZT61|Q8IUU7|Q96CV5|Q96L65	Silent	SNP	ENST00000338074.2	hg19	CCDS13271.1																																																																																			.	.		0.662	EPB41L1-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078978.3	NM_012156		A	34761813	C	A	34761813	2	1	267	1	0	0	0	0	0	0	0	1	5154	726	26	3		3	EPB41L1	20	34761813	Silent	SNP	C	TCGA-FV-A3R3-01A-11D-A22F-10		34761813	28263707	26	39054										
DHX35	60625	hgsc.bcm.edu	37	chr20	37621023	37621023	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	atcatgctggatgaagcccaCgagaggaccttgtacactga	11	10	1	3	rs549854740		TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr20:37621023C>T	ENST00000252011.3	+	7	570	c.537C>T	c.(535-537)caC>caT	p.H179H	DHX35_ENST00000373325.2_Silent_p.H179H|DHX35_ENST00000373323.4_Silent_p.H148H	NM_021931.3	NP_068750.2	Q9H5Z1	DHX35_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 35	179	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(13)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	40		Myeloproliferative disorder(115;0.00878)				ATGAAGCCCACGAGAGGACCT	0.413													C|||	1	0.000199681	0	0	5008	,	,		19396	0		0	False		,,,				2504	0.001				p.H179H		Atlas-SNP	.											.	DHX35	82	.	0			c.C537T						.						223	199	207					20																	37621023		2203	4300	6503	SO:0001819	synonymous_variant	60625	exon7			AGCCCACGAGAGG	AK026412	CCDS13310.1, CCDS54463.1	20q11.22-q12	2003-06-13	2003-06-13	2003-06-13	ENSG00000101452	ENSG00000101452		"DEAH-boxes"	15861	protein-coding gene	gene with protein product			"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 35"	C20orf15, DDX35			Standard	NM_001190809		Approved	FLJ22759, KAIA0875	uc002xjh.3	Q9H5Z1	OTTHUMG00000032463	ENST00000252011.3:c.537C>T	chr20.hg19:g.37621023C>T		138.0	0.0		130.0	11.0	NM_021931	A2RTX3|B4E0J0|F5GXM6|Q5THR0|Q9H4H7|Q9H6T6	Silent	SNP	ENST00000252011.3	hg19	CCDS13310.1																																																																																			.	.		0.413	DHX35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079212.2	NM_021931		T	37621023	C	T	37621023	2	4	267	1	0	0	0	0	0	0	0	1	4510	535	19	1		1	DHX35	20	37621023	Silent	SNP	C	TCGA-FV-A3R3-01A-11D-A22F-10	2859210	37621023	25404497	27	39055										
PCK1	5105	hgsc.bcm.edu	37	chr20	56139383	56139383	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	gcgtttactgggaaggcattGatgagccgctagcttcaggt	14	8	1	2			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr20:56139383G>A	ENST00000319441.4	+	7	1284	c.1120G>A	c.(1120-1122)Gat>Aat	p.D374N	PCK1_ENST00000535860.1_Missense_Mutation_p.D242N|PCK1_ENST00000543666.1_Missense_Mutation_p.D57N	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	374					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			GGAAGGCATTGATGAGCCGCT	0.557																																					p.D374N		Atlas-SNP	.											PCK1,right_upper_lobe,carcinoma,0,1	PCK1	95	.	0			c.G1120A						.						104	91	96					20																	56139383		2203	4300	6503	SO:0001583	missense	5105	exon7			GGCATTGATGAGC		CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.1120G>A	chr20.hg19:g.56139383G>A	ENSP00000319814:p.Asp374Asn	131.0	0.0		94.0	16.0	NM_002591	A8K437|B4DT64|Q8TCA3|Q9UJD2	Missense_Mutation	SNP	ENST00000319441.4	hg19	CCDS13460.1	.	.	.	.	.	.	.	.	.	.	G	13.35	2.210471	0.39102	.	.	ENSG00000124253	ENST00000540165;ENST00000319441;ENST00000543666;ENST00000535860	T;T;T	0.09911	2.93;2.93;2.93	5.31	5.31	0.75309	.	0.086985	0.85682	D	0.000000	T	0.16128	0.0388	M	0.76574	2.34	0.80722	D	1	B;B	0.15930	0.002;0.015	B;B	0.22753	0.013;0.041	T	0.01635	-1.1307	10	0.35671	T	0.21	-44.3202	12.6654	0.56840	0.0757:0.0:0.9243:0.0	.	57;374	B4DT64;P35558	.;PCKGC_HUMAN	N	56;374;57;242	ENSP00000319814:D374N;ENSP00000445767:D57N;ENSP00000444342:D242N	ENSP00000319814:D374N	D	+	1	0	PCK1	55572789	1.000000	0.71417	0.228000	0.23943	0.120000	0.20174	7.505000	0.81655	2.636000	0.89361	0.655000	0.94253	GAT	.	.		0.557	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2			A	56139383	G	A	56139383	3	1	267	1	0	0	0	0	1	0	0	0	11590	1290	45	3	1142	3	PCK1	20	56139383	Missense_Mutation	SNP	G	TCGA-FV-A3R3-01A-11D-A22F-10	18518360	56139383	6886137	28	39056										
GNAS	2778	hgsc.bcm.edu	37	chr20	57484420	57484420	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	ttcaggacctgcttcgctgcCgtgtcctgacttctggaatc	10	13	2	1	rs11554273		TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr20:57484420C>T	ENST00000371085.3	+	8	1025	c.601C>T	c.(601-603)Cgt>Tgt	p.R201C	GNAS_ENST00000306090.10_Missense_Mutation_p.R187C|GNAS_ENST00000464624.2_3'UTR|GNAS_ENST00000354359.7_Missense_Mutation_p.R202C|GNAS_ENST00000371100.4_Missense_Mutation_p.R844C|GNAS_ENST00000371095.3_Missense_Mutation_p.R187C|GNAS_ENST00000313949.7_3'UTR|GNAS_ENST00000265620.7_Missense_Mutation_p.R186C|GNAS_ENST00000371102.4_Missense_Mutation_p.R830C|GNAS_ENST00000371075.3_3'UTR	NM_000516.4	NP_000507.1	P63092	GNAS2_HUMAN	GNAS complex locus	201			R -> C (in MAS and somatotrophinoma; dbSNP:rs11554273). {ECO:0000269|PubMed:1944469, ECO:0000269|PubMed:2549426}.|R -> G (in MAS). {ECO:0000269|PubMed:10571700}.|R -> H (in MAS, somatotrophinoma and AIMAH1). {ECO:0000269|PubMed:12727968, ECO:0000269|PubMed:1594625, ECO:0000269|PubMed:1944469, ECO:0000269|PubMed:2549426}.|R -> L (in non-MAS endocrine tumors). {ECO:0000269|PubMed:7751320}.|R -> S (in AIMAH1, pituitary tumor and polyostotic fibrous dysplasia). {ECO:0000269|PubMed:12727968, ECO:0000269|PubMed:8766942, ECO:0000269|PubMed:9267696}.		activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|bone development (GO:0060348)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|cognition (GO:0050890)|developmental growth (GO:0048589)|energy reserve metabolic process (GO:0006112)|hair follicle placode formation (GO:0060789)|intracellular transport (GO:0046907)|platelet aggregation (GO:0070527)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of insulin secretion (GO:0050796)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intrinsic component of membrane (GO:0031224)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	adenylate cyclase activity (GO:0004016)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)	p.R201C(228)|p.R844C(9)|p.R201S(5)		adrenal_gland(12)|autonomic_ganglia(1)|biliary_tract(5)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(37)|liver(9)|lung(9)|ovary(16)|pancreas(56)|parathyroid(5)|pituitary(228)|prostate(2)|small_intestine(1)|stomach(1)|testis(2)|thyroid(35)|upper_aerodigestive_tract(3)|urinary_tract(1)	441	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			GCTTCGCTGCCGTGTCCTGAC	0.428			Mis		pituitary adenoma		"McCune-Albright syndrome; pseudohypoparathyroidism, type IA"			TSP Lung(22;0.16)																											p.R844C	Colon(117;935 1597 6045 8307 46442)	Atlas-SNP	.		Dom	yes		20	20q13.2	2778	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	yes	E	GNAS_ENST00000371100,NS,adenocarcinoma,0,338	GNAS	867	.	242	Substitution - Missense(242)	pituitary(141)|pancreas(35)|large_intestine(14)|ovary(12)|thyroid(10)|adrenal_gland(7)|biliary_tract(6)|parathyroid(5)|liver(3)|kidney(3)|testis(2)|upper_aerodigestive_tract(2)|autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)	c.C2530T						.						80	78	79					20																	57484420		2203	4300	6503	SO:0001583	missense	2778	exon8			CGCTGCCGTGTCC	M21142	CCDS13471.1, CCDS13472.1, CCDS42892.1, CCDS46622.1, CCDS46623.1, CCDS46624.1	20q13.2-q13.3	2010-03-01	2001-12-19	2001-12-20	ENSG00000087460	ENSG00000087460			4392	protein-coding gene	gene with protein product	"secretogranin VI"	139320	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	GNAS1			Standard	NM_000516		Approved	NESP55, NESP, GNASXL, GPSA, SCG6	uc002xzw.3	O95467	OTTHUMG00000033069	ENST00000371085.3:c.601C>T	chr20.hg19:g.57484420C>T	ENSP00000360126:p.Arg201Cys	97.0	0.0		95.0	28.0	NM_080425	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Missense_Mutation	SNP	ENST00000371085.3	hg19	CCDS13472.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.215896	0.79352	.	.	ENSG00000087460	ENST00000371100;ENST00000371102;ENST00000371095;ENST00000371085;ENST00000354359;ENST00000265620;ENST00000306090	D;D;D;D;D;D;D	0.99466	-5.95;-5.95;-5.95;-5.95;-5.95;-2.99;-5.95	5.53	4.53	0.55603	G protein alpha subunit, helical insertion (2);	0.000000	0.85682	D	0.000000	D	0.99775	0.9907	H	0.99732	4.735	0.80722	D	1	D;D;D;D	0.89917	0.999;0.983;0.979;1.0	D;P;P;D	0.97110	0.939;0.845;0.643;1.0	D	0.96814	0.9599	10	0.87932	D	0	.	13.0593	0.58997	0.2437:0.7563:0.0:0.0	rs11554273	201;202;186;844	P63092;A6NI00;P63092-3;Q5JWF2	GNAS2_HUMAN;.;.;GNAS1_HUMAN	C	844;830;187;201;202;186;187	ENSP00000360141:R844C;ENSP00000360143:R830C;ENSP00000360136:R187C;ENSP00000360126:R201C;ENSP00000346328:R202C;ENSP00000265620:R186C;ENSP00000304472:R187C	ENSP00000265620:R186C	R	+	1	0	GNAS	56917815	1.000000	0.71417	0.998000	0.56505	0.941000	0.58515	4.055000	0.57441	2.596000	0.87737	0.563000	0.77884	CGT	.	C|1.000		0.428	GNAS-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080431.2	NM_000516		T	57484420	C	T	57484420	3	4	267	1	0	0	0	0	1	0	0	0	6518	652	23	1	3448	1	GNAS	20	57484420	Missense_Mutation	SNP	C	TCGA-FV-A3R3-01A-11D-A22F-10	1345037	57484420	5541100	29	39057										
DIDO1	11083	hgsc.bcm.edu	37	chr20	61511712	61511712	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	cccttcaaactgggcgggggCgcccgtcacctcgttatacg	12	15	2	0			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chr20:61511712C>T	ENST00000266070.4	-	16	5921	c.5596G>A	c.(5596-5598)Gcc>Acc	p.A1866T	DIDO1_ENST00000395343.1_Missense_Mutation_p.A1866T	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	1866	Pro-rich.				apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					TGGGCGGGGGCGCCCGTCACC	0.612																																					p.A1866T	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											.	DIDO1	321	.	0			c.G5596A						.						43	47	46					20																	61511712		2202	4295	6497	SO:0001583	missense	11083	exon16			CGGGGGCGCCCGT	AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"Zinc fingers, PHD-type"	2680	protein-coding gene	gene with protein product		604140	"chromosome 20 open reading frame 158", "death associated transcription factor 1"	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.5596G>A	chr20.hg19:g.61511712C>T	ENSP00000266070:p.Ala1866Thr	50.0	0.0		53.0	9.0	NM_001193369	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Missense_Mutation	SNP	ENST00000266070.4	hg19	CCDS33506.1	.	.	.	.	.	.	.	.	.	.	C	3.128	-0.179083	0.06380	.	.	ENSG00000101191	ENST00000266070;ENST00000395343	T;T	0.08282	3.11;3.11	4.97	-1.09	0.09904	.	0.536184	0.15455	N	0.261401	T	0.06325	0.0163	N	0.22421	0.69	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.28073	-1.0055	10	0.45353	T	0.12	-1.363	13.92	0.63926	0.0:0.5771:0.3057:0.1173	.	1866	Q9BTC0	DIDO1_HUMAN	T	1866	ENSP00000266070:A1866T;ENSP00000378752:A1866T	ENSP00000266070:A1866T	A	-	1	0	DIDO1	60982157	0.085000	0.21516	0.000000	0.03702	0.006000	0.05464	0.270000	0.18607	-0.453000	0.07076	-1.332000	0.01269	GCC	.	.		0.612	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796		T	61511712	C	T	61511712	3	4	267	1	0	0	0	0	1	0	0	0	4524	768	27	1	1130	1	DIDO1	20	61511712	Missense_Mutation	SNP	C	TCGA-FV-A3R3-01A-11D-A22F-10	4027292	61511712	1513808	30	39058										
ITIH5L	347365	hgsc.bcm.edu	37	chrX	54785172	54785172	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	atgcgccgggctattccccgGttttccagggacaggcggcg	15	13	0	0			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chrX:54785172G>A	ENST00000218436.6	-	8	1364	c.1335C>T	c.(1333-1335)aaC>aaT	p.N445N		NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	445	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)										CTATTCCCCGGTTTTCCAGGG	0.582																																					p.N445N		Atlas-SNP	.											.	.	.	.	0			c.C1335T						.						53	47	49					X																	54785172		2203	4300	6503	SO:0001819	synonymous_variant	347365	exon8			TCCCCGGTTTTCC	AY358170	CCDS14361.1	Xp11.22-p11.21	2011-10-26	2011-10-26	2011-10-26	ENSG00000102313	ENSG00000102313			28907	protein-coding gene	gene with protein product			"inter-alpha (globulin) inhibitor H5-like"	ITIH5L		12975309	Standard	NM_198510		Approved	UNQ6369	uc004dtj.2	Q6UXX5	OTTHUMG00000021634	ENST00000218436.6:c.1335C>T	chrX.hg19:g.54785172G>A		120.0	0.0		80.0	24.0	NM_198510	A6NN03	Silent	SNP	ENST00000218436.6	hg19	CCDS14361.1																																																																																			.	.		0.582	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056814.2	NM_198510		A	54785172	G	A	54785172	2	1	267	1	0	0	0	0	0	0	0	1	7917	1252	44	3		3	ITIH5L	23	54785172	Silent	SNP	G	TCGA-FV-A3R3-01A-11D-A22F-10		54785172	100485388	31	39059										
ZXDA	7789	hgsc.bcm.edu	37	chrX	57936066	57936066	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	gggcacaggtacagcaccacGcctggaccagagcccagcag	13	15	0	1			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chrX:57936066G>A	ENST00000358697.4	-	1	1001	c.789C>T	c.(787-789)ggC>ggT	p.G263G		NM_007156.4	NP_009087.1	P98168	ZXDA_HUMAN	zinc finger, X-linked, duplicated A	263					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(9)|kidney(1)|large_intestine(7)|lung(13)|ovary(2)|prostate(2)|skin(1)	37						ACAGCACCACGCCTGGACCAG	0.731																																					p.G263G		Atlas-SNP	.											.	ZXDA	70	.	0			c.C789T						.						9	10	10					X																	57936066		2182	4274	6456	SO:0001819	synonymous_variant	7789	exon1			CACCACGCCTGGA	L14787	CCDS14376.1	Xp11.21	2013-01-08			ENSG00000198205	ENSG00000198205		"Zinc fingers, C2H2-type"	13198	protein-coding gene	gene with protein product	"zinc finger protein 896"	300235				8268913	Standard	NM_007156		Approved	ZNF896	uc004dve.3	P98168	OTTHUMG00000021688	ENST00000358697.4:c.789C>T	chrX.hg19:g.57936066G>A		36.0	0.0		36.0	11.0	NM_007156	Q9UJP7	Silent	SNP	ENST00000358697.4	hg19	CCDS14376.1																																																																																			.	.		0.731	ZXDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056925.1	NM_007156		A	57936066	G	A	57936066	2	1	267	1	0	0	0	0	0	0	0	1	18265	1074	38	1		1	ZXDA	23	57936066	Silent	SNP	G	TCGA-FV-A3R3-01A-11D-A22F-10	3150894	57936066	97334494	32	39060										
MID2	11043	hgsc.bcm.edu	37	chrX	107084301	107084301	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	ccactgccatgtctagcgagCgaattgcttgccaattctgt	9	12	2	0			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chrX:107084301C>T	ENST00000262843.6	+	2	954	c.406C>T	c.(406-408)Cga>Tga	p.R136*	MID2_ENST00000443968.2_Nonsense_Mutation_p.R136*	NM_012216.3|NM_052817.2	NP_036348.2|NP_438112.2	Q9UJV3	TRIM1_HUMAN	midline 2	136					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein localization to microtubule (GO:0035372)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	ligase activity (GO:0016874)|microtubule binding (GO:0008017)|phosphoprotein binding (GO:0051219)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)|ovary(1)|prostate(2)	19						GTCTAGCGAGCGAATTGCTTG	0.562																																					p.R136X		Atlas-SNP	.											.	MID2	122	.	0			c.C406T						.						42	38	39					X																	107084301		2203	4300	6503	SO:0001587	stop_gained	11043	exon2			AGCGAGCGAATTG		CCDS14532.2, CCDS14533.2	Xq22.1-q22.2	2013-02-11			ENSG00000080561	ENSG00000080561		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Fibronectin type III domain containing"	7096	protein-coding gene	gene with protein product		300204				10400986	Standard	NM_012216		Approved	FXY2, TRIM1, RNF60	uc004enl.3	Q9UJV3	OTTHUMG00000022171	ENST00000262843.6:c.406C>T	chrX.hg19:g.107084301C>T	ENSP00000262843:p.Arg136*	90.0	0.0		75.0	12.0	NM_012216	A6NEL8|A6PVI5|Q5JYF5|Q8WWK1|Q9UJR9	Nonsense_Mutation	SNP	ENST00000262843.6	hg19	CCDS14532.2	.	.	.	.	.	.	.	.	.	.	C	18.02	3.530285	0.64860	.	.	ENSG00000080561	ENST00000451923;ENST00000262843;ENST00000443968	.	.	.	5.94	-0.583	0.11706	.	0.168083	0.38778	N	0.001561	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07325	T	0.83	.	17.1355	0.86738	0.7736:0.2264:0.0:0.0	.	.	.	.	X	116;136;136	.	ENSP00000262843:R136X	R	+	1	2	MID2	106970957	0.011000	0.17503	0.748000	0.31131	0.960000	0.62799	0.541000	0.23207	-0.644000	0.05465	0.600000	0.82982	CGA	.	.		0.562	MID2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057852.2	NM_012216		T	107084301	C	T	107084301	4	4	267	1	0	0	0	0	0	1	0	0	9587	760	27	1	412	1	MID2	23	107084301	Nonsense_Mutation	SNP	C	TCGA-FV-A3R3-01A-11D-A22F-10	49148235	107084301	48186259	33	39061										
AMMECR1	9949	hgsc.bcm.edu	37	chrX	109444278	109444278	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0294117647058824	1	1	0.533333333333333	0	0.571428571428571	1	1	0	tggtctgtatatggtcccatCctgtagagagatgaccagat	11	8	1	4			TCGA-FV-A3R3-01A-11D-A22F-10	TCGA-FV-A3R3-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c285c2fa-24b4-47a1-874d-86e74b002b05	64edddfd-f366-4d51-a8b4-a357b2c68e6c	g.chrX:109444278C>T	ENST00000262844.5	-	5	958	c.791G>A	c.(790-792)gGa>gAa	p.G264E	AMMECR1_ENST00000372057.1_Splice_Site_p.G141E|AMMECR1_ENST00000372059.2_Splice_Site_p.G227E	NM_015365.2	NP_056180.1	Q9Y4X0	AMMR1_HUMAN	Alport syndrome, mental retardation, midface hypoplasia and elliptocytosis chromosomal region gene 1	264	AMMECR1. {ECO:0000255|PROSITE- ProRule:PRU00467}.									large_intestine(1)|lung(4)|ovary(1)|stomach(1)	7						ATGGTCCCATCCTGTAGAGAG	0.383																																					p.G264E		Atlas-SNP	.											.	AMMECR1	16	.	0			c.G791A						.						171	148	156					X																	109444278		2203	4300	6503	SO:0001630	splice_region_variant	9949	exon5			TCCCATCCTGTAG	AJ007014	CCDS14551.1, CCDS35368.1, CCDS55476.1	Xq22.3	2014-06-17	2008-09-12		ENSG00000101935	ENSG00000101935			467	protein-coding gene	gene with protein product		300195				10049589, 9480748	Standard	NM_001171689		Approved		uc004eoo.3	Q9Y4X0	OTTHUMG00000022197	ENST00000262844.5:c.791-1G>A	chrX.hg19:g.109444278C>T		97.0	0.0		72.0	10.0	NM_015365	Q5JYV9|Q6P9D8|Q8WX22|Q9UIQ8	Missense_Mutation	SNP	ENST00000262844.5	hg19	CCDS14551.1	.	.	.	.	.	.	.	.	.	.	C	18.32	3.597226	0.66332	.	.	ENSG00000101935	ENST00000262844;ENST00000372059;ENST00000372057	.	.	.	5.8	4.94	0.65067	AMMECR1 domain (2);	0.000000	0.85682	D	0.000000	T	0.73353	0.3576	M	0.75884	2.315	0.80722	D	1	P;P	0.49696	0.911;0.927	P;P	0.54706	0.55;0.759	T	0.75470	-0.3306	9	0.52906	T	0.07	.	13.9424	0.64064	0.0:0.9255:0.0:0.0745	.	227;264	Q9Y4X0-3;Q9Y4X0	.;AMER1_HUMAN	E	264;227;141	.	ENSP00000262844:G264E	G	-	2	0	AMMECR1	109330934	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.487000	0.81328	1.206000	0.43276	0.600000	0.82982	GGA	.	.		0.383	AMMECR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057907.1		Missense_Mutation	T	109444278	C	T	109444278	5	4	267	1	0	0	0	0	0	0	1	0	578	869	30	3	218	3	AMMECR1	23	109444278	Splice_Site	SNP	C	TCGA-FV-A3R3-01A-11D-A22F-10	2359977	109444278	45826282	34	39062										
CAPZB	832	hgsc.bcm.edu	37	chr1	19746233	19746233	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	aggtccaaggcacagtccagCtgctgatcactctgtggagg	13	11	2	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr1:19746233C>G	ENST00000375142.1	-	2	61	c.15G>C	c.(13-15)caG>caC	p.Q5H	CAPZB_ENST00000433834.1_Missense_Mutation_p.Q34H|CAPZB_ENST00000264202.6_Missense_Mutation_p.Q5H|CAPZB_ENST00000401084.2_Missense_Mutation_p.Q5H|CAPZB_ENST00000264203.3_Missense_Mutation_p.Q31H|CAPZB_ENST00000375144.1_5'UTR|CAPZB_ENST00000482808.1_5'UTR	NM_001206540.1	NP_001193469.1	P47756	CAPZB_HUMAN	capping protein (actin filament) muscle Z-line, beta	5					actin cytoskeleton organization (GO:0030036)|barbed-end actin filament capping (GO:0051016)|blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|muscle fiber development (GO:0048747)|negative regulation of microtubule polymerization (GO:0031115)|neuron projection development (GO:0031175)|regulation of cell morphogenesis (GO:0022604)|regulation of protein kinase C signaling (GO:0090036)	acrosomal vesicle (GO:0001669)|actin cytoskeleton (GO:0015629)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|F-actin capping protein complex (GO:0008290)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|membrane (GO:0016020)|WASH complex (GO:0071203)|Z disc (GO:0030018)	actin binding (GO:0003779)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|urinary_tract(1)	7		Colorectal(325;3.93e-05)|Renal(390;0.000147)|all_lung(284;0.000169)|Lung NSC(340;0.000202)|Breast(348;0.000496)|Ovarian(437;0.00428)|Myeloproliferative disorder(586;0.0262)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Kidney(64;8.63e-06)|BRCA - Breast invasive adenocarcinoma(304;4.06e-05)|KIRC - Kidney renal clear cell carcinoma(64;0.000175)|GBM - Glioblastoma multiforme(114;0.000525)|STAD - Stomach adenocarcinoma(196;0.00779)|READ - Rectum adenocarcinoma(331;0.103)|Lung(427;0.173)		CACAGTCCAGCTGCTGATCAC	0.493																																					p.Q5H		.	.											.	CAPZB	.	.	0			c.G15C						.						62	62	62					1																	19746233		2044	4211	6255	SO:0001583	missense	832	exon2			GTCCAGCTGCTGA	U03271	CCDS41277.1, CCDS55579.1, CCDS72717.1, CCDS72718.1	1p36.1	2014-05-09			ENSG00000077549	ENSG00000077549			1491	protein-coding gene	gene with protein product		601572					Standard	NM_004930		Approved		uc021ohr.1	P47756	OTTHUMG00000002556	ENST00000375142.1:c.15G>C	1.37:g.19746233C>G	ENSP00000364284:p.Gln5His	90.0	0.0		95.0	5.0	NM_004930	Q32Q68|Q5U0L4|Q8TB49|Q9NUC4	Missense_Mutation	SNP	ENST00000375142.1	37	CCDS55579.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.318273	0.81469	.	.	ENSG00000077549	ENST00000401084;ENST00000264203;ENST00000375142;ENST00000433834;ENST00000375145;ENST00000264202	.	.	.	5.96	5.05	0.67936	.	0.000000	0.85682	D	0.000000	D	0.84474	0.5480	M	0.91872	3.25	0.80722	D	1	D;D;D	0.89917	1.0;0.989;1.0	D;D;D	0.97110	1.0;0.992;0.979	D	0.87323	0.2319	9	0.62326	D	0.03	-11.5398	12.8466	0.57833	0.0:0.9215:0.0:0.0785	.	34;31;5	B1AK88;B1AK85;P47756-2	.;.;.	H	5;31;5;34;67;5	.	ENSP00000264202:Q5H	Q	-	3	2	CAPZB	19618820	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.306000	0.59117	1.522000	0.49001	0.655000	0.94253	CAG	.	.		0.493	CAPZB-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007260.1			G	19746233	C	G	19746233	3	3	268	1	0	0	0	0	1	0	0	0	2645	796	28	4	835	4	CAPZB	1	19746233	Missense_Mutation	SNP	C	TCGA-FV-A495-01A-11D-A25V-10		19746233	229504388	1	39063										
USP1	7398	hgsc.bcm.edu	37	chr1	62913095	62913095	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	cgcgttgcttggaatgtgaaAgtttaacagaaagaagagaa	12	4	0	4			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr1:62913095A>G	ENST00000339950.4	+	7	2148	c.1333A>G	c.(1333-1335)Agt>Ggt	p.S445G	USP1_ENST00000371146.1_Missense_Mutation_p.S445G	NM_003368.4	NP_003359.3	O94782	UBP1_HUMAN	ubiquitin specific peptidase 1	445	USP.				DNA repair (GO:0006281)|monoubiquitinated protein deubiquitination (GO:0035520)|protein deubiquitination (GO:0016579)|regulation of DNA repair (GO:0006282)|response to UV (GO:0009411)|skeletal system development (GO:0001501)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|prostate(2)|stomach(1)	19		all_neural(321;0.0281)		BRCA - Breast invasive adenocarcinoma(111;8.01e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00245)|OV - Ovarian serous cystadenocarcinoma(397;0.0535)		GGAATGTGAAAGTTTAACAGA	0.368																																					p.S445G	Ovarian(122;1846 2315 3982 19504)	.	.											.	USP1	.	.	0			c.A1333G						.						128	128	128					1																	62913095		2203	4300	6503	SO:0001583	missense	7398	exon7			TGTGAAAGTTTAA		CCDS621.1	1p31.3	2008-05-14	2005-08-08		ENSG00000162607	ENSG00000162607		"Ubiquitin-specific peptidases"	12607	protein-coding gene	gene with protein product		603478	"ubiquitin specific protease 1"			12838346	Standard	NM_003368		Approved		uc001dak.2	O94782	OTTHUMG00000008972	ENST00000339950.4:c.1333A>G	1.37:g.62913095A>G	ENSP00000343526:p.Ser445Gly	94.0	0.0		103.0	9.0	NM_001017415	A0PJ95|D3DQ57|Q05BX7|Q59H66|Q9UFR0|Q9UNJ3	Missense_Mutation	SNP	ENST00000339950.4	37	CCDS621.1	.	.	.	.	.	.	.	.	.	.	A	18.79	3.699753	0.68501	.	.	ENSG00000162607	ENST00000371146;ENST00000339950	T;T	0.30981	1.51;1.51	5.79	4.6	0.57074	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.137895	0.64402	D	0.000003	T	0.31040	0.0784	N	0.25890	0.77	0.35654	D	0.812016	D	0.54964	0.969	P	0.56163	0.793	T	0.24977	-1.0145	10	0.27082	T	0.32	-13.7836	9.0434	0.36331	0.6765:0.0:0.0:0.3235	.	445	O94782	UBP1_HUMAN	G	445	ENSP00000360188:S445G;ENSP00000343526:S445G	ENSP00000343526:S445G	S	+	1	0	USP1	62685683	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.157000	0.58144	2.215000	0.71742	0.528000	0.53228	AGT	.	.		0.368	USP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024881.1	NM_001017415		G	62913095	A	G	62913095	3	3	268	1	0	0	0	0	1	0	0	0	17055	72	3	2	1355	2	USP1	1	62913095	Missense_Mutation	SNP	A	TCGA-FV-A495-01A-11D-A25V-10	43166862	62913095	186337526	2	39064										
LEPR	3953	hgsc.bcm.edu	37	chr1	66102511	66102511	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	gtcaagggtatcgtgcccatTcccagccccctgtttattca	8	14	2	0			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr1:66102511T>A	ENST00000349533.6	+	20	3496	c.3311T>A	c.(3310-3312)tTc>tAc	p.F1104Y	LEPR_ENST00000406510.3_Missense_Mutation_p.F171Y	NM_002303.5	NP_002294.2	O15243	OBRG_HUMAN	leptin receptor	0					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(22)|skin(2)	36				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		TCGTGCCCATTCCCAGCCCCC	0.398																																					p.F1104Y		.	.											.	LEPR	.	.	0			c.T3311A						.						71	69	70					1																	66102511		2203	4300	6503	SO:0001583	missense	3953	exon20			GCCCATTCCCAGC	U43168	CCDS631.1, CCDS30740.1, CCDS30741.1, CCDS55604.1	1p31	2014-09-17			ENSG00000116678	ENSG00000116678		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6554	protein-coding gene	gene with protein product		601007				8548812, 8812446	Standard	NM_001003680		Approved	OBR, CD295	uc001dci.3	P48357	OTTHUMG00000009115	ENST00000349533.6:c.3311T>A	1.37:g.66102511T>A	ENSP00000330393:p.Phe1104Tyr	157.0	0.0		135.0	7.0	NM_002303	Q6FHL5	Missense_Mutation	SNP	ENST00000349533.6	37	CCDS631.1	.	.	.	.	.	.	.	.	.	.	T	14.26	2.480913	0.44044	.	.	ENSG00000116678	ENST00000349533;ENST00000406510	T	0.59224	0.28	5.64	3.14	0.36123	.	0.557233	0.20745	N	0.086474	T	0.58075	0.2097	M	0.69823	2.125	0.30912	N	0.728979	D	0.76494	0.999	D	0.64687	0.928	T	0.55952	-0.8059	10	0.52906	T	0.07	-10.0424	8.5838	0.33646	0.1289:0.0:0.135:0.7361	.	1104	P48357	LEPR_HUMAN	Y	1104;171	ENSP00000330393:F1104Y	ENSP00000330393:F1104Y	F	+	2	0	LEPR	65875099	0.841000	0.29509	0.805000	0.32314	0.025000	0.11179	3.803000	0.55560	0.936000	0.37367	0.477000	0.44152	TTC	.	.		0.398	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303		A	66102511	T	A	66102511	3	1	268	1	0	0	0	0	1	0	0	0	8737	1783	62	4	3611	4	LEPR	1	66102511	Missense_Mutation	SNP	T	TCGA-FV-A495-01A-11D-A25V-10	3189416	66102511	183148110	3	39065										
TET3	200424	hgsc.bcm.edu	37	chr2	74275063	74275063	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	tttgcacctagtccctccagGgacagcctgctgccccctac	8	18	0	0			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr2:74275063G>C	ENST00000409262.3	+	1	1614	c.1614G>C	c.(1612-1614)agG>agC	p.R538S		NM_144993.1	NP_659430.1	O43151	TET3_HUMAN	tet methylcytosine dioxygenase 3	538					DNA demethylation (GO:0080111)|DNA demethylation of male pronucleus (GO:0044727)|histone H3-K4 trimethylation (GO:0080182)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methylcytosine dioxygenase activity (GO:0070579)			NS(1)|breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GTCCCTCCAGGGACAGCCTGC	0.647																																					p.R538S		.	.											.	.	.	.	0			c.G1614C						.						24	26	25					2																	74275063		1969	4152	6121	SO:0001583	missense	200424	exon1			CTCCAGGGACAGC		CCDS46339.1, CCDS46339.2	2p13.1	2011-09-30	2011-09-30		ENSG00000187605	ENSG00000187605			28313	protein-coding gene	gene with protein product		613555	"tet oncogene family member 3"			9455477	Standard	XM_005264187		Approved	MGC22014, hCG_40738	uc031roi.1	O43151	OTTHUMG00000152823	ENST00000409262.3:c.1614G>C	2.37:g.74275063G>C	ENSP00000386869:p.Arg538Ser	101.0	0.0		135.0	7.0	NM_144993	A6NEI3|Q86Z24|Q8TBM9	Missense_Mutation	SNP	ENST00000409262.3	37	CCDS46339.1	.	.	.	.	.	.	.	.	.	.	G	7.786	0.710455	0.15239	.	.	ENSG00000187605	ENST00000305799;ENST00000409262;ENST00000233310	T;T	0.21361	2.01;2.81	5.29	5.29	0.74685	.	.	.	.	.	T	0.11665	0.0284	N	0.08118	0	0.26247	N	0.978788	B	0.06786	0.001	B	0.06405	0.002	T	0.10382	-1.0632	9	0.09338	T	0.73	.	15.9628	0.79945	0.0:0.0:1.0:0.0	.	538	O43151	TET3_HUMAN	S	580;538;538	ENSP00000307803:R580S;ENSP00000386869:R538S	ENSP00000233310:R538S	R	+	3	2	TET3	74128571	0.862000	0.29867	1.000000	0.80357	0.993000	0.82548	2.284000	0.43478	2.746000	0.94184	0.591000	0.81541	AGG	.	.		0.647	TET3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328141.4			C	74275063	G	C	74275063	3	2	268	1	0	0	0	0	1	0	0	0	15786	1223	43	4	1616	4	TET3	2	74275063	Missense_Mutation	SNP	G	TCGA-FV-A495-01A-11D-A25V-10		74275063	168924310	4	39066										
CLASP1	23332	hgsc.bcm.edu	37	chr2	122216520	122216520	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	aatggcttcagctccatggtCaaacttattccccagaactg	7	12	2	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr2:122216520C>T	ENST00000263710.4	-	13	1599	c.1210G>A	c.(1210-1212)Gac>Aac	p.D404N	CLASP1_ENST00000541859.1_Missense_Mutation_p.D173N|CLASP1_ENST00000409078.3_Missense_Mutation_p.D404N|CLASP1_ENST00000455322.2_Missense_Mutation_p.D404N|CLASP1_ENST00000397587.3_Missense_Mutation_p.D404N|CLASP1_ENST00000545861.1_Missense_Mutation_p.D172N|CLASP1_ENST00000541377.1_Missense_Mutation_p.D404N|CLASP1_ENST00000430234.1_5'UTR	NM_015282.2	NP_056097.1	Q7Z460	CLAP1_HUMAN	cytoplasmic linker associated protein 1	404					axon guidance (GO:0007411)|cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|establishment or maintenance of cell polarity (GO:0007163)|exit from mitosis (GO:0010458)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)	cell cortex (GO:0005938)|centrosomal corona (GO:0031592)|centrosome (GO:0005813)|cortical microtubule cytoskeleton (GO:0030981)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|spindle microtubule (GO:0005876)	kinetochore binding (GO:0043515)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)	47	Renal(3;0.0496)					GCTCCATGGTCAAACTTATTC	0.358																																					p.D404N		.	.											.	CLASP1	.	.	0			c.G1210A						.						145	140	141					2																	122216520		1846	4096	5942	SO:0001583	missense	23332	exon13			CATGGTCAAACTT	AB014522		2q14.2-q14.3	2013-01-18			ENSG00000074054	ENSG00000074054			17088	protein-coding gene	gene with protein product	"multiple asters 1"	605852				9734811, 10899121, 16914514	Standard	NM_015282		Approved	KIAA0622, MAST1	uc002tnc.3	Q7Z460	OTTHUMG00000153331	ENST00000263710.4:c.1210G>A	2.37:g.122216520C>T	ENSP00000263710:p.Asp404Asn	61.0	0.0		103.0	22.0	NM_001207051	B7ZLX3|O75118|Q2KHQ9|Q5H9P0|Q8N5B8|Q9BQT5	Missense_Mutation	SNP	ENST00000263710.4	37		.	.	.	.	.	.	.	.	.	.	C	35	5.554197	0.96501	.	.	ENSG00000074054	ENST00000263710;ENST00000455322;ENST00000397587;ENST00000541377;ENST00000541859;ENST00000409078;ENST00000545861	T;T;T;T;T;T;T	0.52754	0.65;0.65;0.65;0.65;0.65;0.65;0.65	5.45	5.45	0.79879	Armadillo-type fold (1);CLASP N-terminal domain (1);	0.086182	0.85682	D	0.000000	T	0.59500	0.2198	L	0.46670	1.46	0.80722	D	1	D;D;D;B	0.57571	0.975;0.969;0.98;0.306	P;P;P;P	0.57244	0.762;0.649;0.816;0.521	T	0.56214	-0.8016	10	0.44086	T	0.13	.	19.6233	0.95669	0.0:1.0:0.0:0.0	.	404;404;404;404	E7EUA5;F5GWS0;B7ZLX3;Q7Z460	.;.;.;CLAP1_HUMAN	N	404;404;404;404;173;404;172	ENSP00000263710:D404N;ENSP00000389372:D404N;ENSP00000380717:D404N;ENSP00000441625:D404N;ENSP00000441770:D173N;ENSP00000386442:D404N;ENSP00000438620:D172N	ENSP00000263710:D404N	D	-	1	0	CLASP1	121932990	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.782000	0.85680	2.714000	0.92807	0.655000	0.94253	GAC	.	.		0.358	CLASP1-201	KNOWN	basic	protein_coding	protein_coding		NM_015282		T	122216520	C	T	122216520	3	4	268	1	0	0	0	0	1	0	0	0	3456	826	29	3	3570	3	CLASP1	2	122216520	Missense_Mutation	SNP	C	TCGA-FV-A495-01A-11D-A25V-10	47941457	122216520	120982853	5	39067										
ARL5A	26225	hgsc.bcm.edu	37	chr2	152670806	152670806	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	ttacttcctattgtaggagaTgtatgtacaacttcattcat	6	7	2	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr2:152670806T>C	ENST00000295087.8	-	3	443	c.132A>G	c.(130-132)acA>acG	p.T44T	ARL5A_ENST00000428992.2_Silent_p.T7T	NM_001037174.1|NM_012097.3	NP_001032251.1|NP_036229.1	Q9Y689	ARL5A_HUMAN	ADP-ribosylation factor-like 5A	44					small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)			breast(1)|large_intestine(2)|liver(1)|lung(2)	6				BRCA - Breast invasive adenocarcinoma(221;0.153)		TTGTAGGAGATGTATGTACAA	0.338																																					p.T44T		.	.											.	ARL5A	.	.	0			c.A132G						.						97	101	100					2																	152670806		2203	4294	6497	SO:0001819	synonymous_variant	26225	exon3			AGGAGATGTATGT	AF100740	CCDS2195.1, CCDS46425.1	2q23.3	2014-05-09	2005-11-03	2005-11-03	ENSG00000162980	ENSG00000162980		"ADP-ribosylation factors-like", "ADP-ribosylation factors"	696	protein-coding gene	gene with protein product		608960	"ADP-ribosylation factor-like 5"	ARL5			Standard	NM_012097		Approved		uc002txx.1	Q9Y689	OTTHUMG00000131887	ENST00000295087.8:c.132A>G	2.37:g.152670806T>C		195.0	0.0		196.0	48.0	NM_012097	Q580I5	Silent	SNP	ENST00000295087.8	37	CCDS2195.1																																																																																			.	.		0.338	ARL5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254837.1			C	152670806	T	C	152670806	2	2	268	1	0	0	0	0	0	0	0	1	939	1451	51	2		2	ARL5A	2	152670806	Silent	SNP	T	TCGA-FV-A495-01A-11D-A25V-10	30454286	152670806	90528567	6	39068										
SGOL2	151246	hgsc.bcm.edu	37	chr2	201399836	201399838	+	In_Frame_Del	DEL	AAG	AAG	-													0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	tgaaaagatgctattgcaaaAagaagtagagaaactgaatt							TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr2:201399836_201399838delAAG	ENST00000357799.4	+	3	349_351	c.251_253delAAG	c.(250-255)aaagaa>aaa	p.E85del	SGOL2_ENST00000409203.3_In_Frame_Del_p.E85del	NM_001160033.1|NM_001160046.1|NM_152524.5	NP_001153505.1|NP_001153518.1|NP_689737.4	Q562F6	SGOL2_HUMAN	shugoshin-like 2 (S. pombe)	85					meiotic sister chromatid cohesion, centromeric (GO:0051754)|mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)		p.E85Q(1)		NS(2)|breast(2)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	46						CTATTGCAAAAAGAAGTAGAGAA	0.3																																					p.84_84del		.	.											.	SGOL2	.	.	1	Substitution - Missense(1)	lung(1)	c.250_252del						.																																			SO:0001651	inframe_deletion	151246	exon3			.	AY094614	CCDS42796.1	2q33.2	2008-02-05			ENSG00000163535	ENSG00000163535			30812	protein-coding gene	gene with protein product		612425					Standard	NM_001160046		Approved	TRIPIN, FLJ25211	uc002uvw.2	Q562F6	OTTHUMG00000154535	ENST00000357799.4:c.251_253delAAG	2.37:g.201399839_201399841delAAG	ENSP00000350447:p.Glu85del	40.0	0.0		80.0	16.0	NM_152524	Q53RR9|Q53T20|Q86XY4|Q8IWK2|Q8IZK1|Q8N1Q5|Q96LQ3	In_Frame_Del	DEL	ENST00000357799.4	37	CCDS42796.1																																																																																			.	.		0.3	SGOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335834.1	NM_152524		-	201399838	AAG	-	201399836	7	5	268	1	0	1	0	1	0	0	0	0	14232	14	1	0	257	0	SGOL2	2	201399836	In_Frame_Del	DEL	AAG	TCGA-FV-A495-01A-11D-A25V-10	48729030	201399836	41799537	7	39069										
SPHKAP	80309	hgsc.bcm.edu	37	chr2	228882436	228882436	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	actccgttaggttcatgatcTtggctgccacttcattggca	9	11	3	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr2:228882436T>G	ENST00000392056.3	-	7	3180	c.3134A>C	c.(3133-3135)aAg>aCg	p.K1045T	SPHKAP_ENST00000344657.5_Missense_Mutation_p.K1045T	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	1045						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)			NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		GTTCATGATCTTGGCTGCCAC	0.517																																					p.K1045T		.	.											.	SPHKAP	.	.	0			c.A3134C						.						84	79	81					2																	228882436		2203	4300	6503	SO:0001583	missense	80309	exon7			ATGATCTTGGCTG		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"A-kinase anchor proteins"	30619	protein-coding gene	gene with protein product	"sphingosine kinase type 1-interacting protein"	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.3134A>C	2.37:g.228882436T>G	ENSP00000375909:p.Lys1045Thr	84.0	0.0		98.0	24.0	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	37	CCDS46537.1	.	.	.	.	.	.	.	.	.	.	T	18.17	3.565446	0.65651	.	.	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.18960	2.18;2.19	6.08	4.93	0.64822	.	0.086238	0.85682	D	0.000000	T	0.33000	0.0848	L	0.29908	0.895	0.49582	D	0.999805	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.83275	0.962;0.928;0.996	T	0.06954	-1.0798	10	0.72032	D	0.01	.	11.239	0.48958	0.0:0.0706:0.0:0.9294	.	76;1045;1045	B3KR30;Q2M3C7;Q2M3C7-2	.;SPKAP_HUMAN;.	T	1045	ENSP00000375909:K1045T;ENSP00000339886:K1045T	ENSP00000339886:K1045T	K	-	2	0	SPHKAP	228590680	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.291000	0.59025	1.134000	0.42165	0.533000	0.62120	AAG	.	.		0.517	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623		G	228882436	T	G	228882436	3	3	268	1	0	0	0	0	1	0	0	0	15063	1609	56	5	1992	5	SPHKAP	2	228882436	Missense_Mutation	SNP	T	TCGA-FV-A495-01A-11D-A25V-10	27482600	228882436	14316937	8	39070										
COL6A3	1293	hgsc.bcm.edu	37	chr2	238245049	238245049	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	acagatggctgatttataatAgtcacaggctttgttgtggt	11	5	1	2	rs537384335		TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr2:238245049A>G	ENST00000295550.4	-	40	9146	c.8694T>C	c.(8692-8694)acT>acC	p.T2898T	COL6A3_ENST00000472056.1_Silent_p.T2291T|COL6A3_ENST00000353578.4_Silent_p.T2692T|COL6A3_ENST00000346358.4_Silent_p.T2698T|COL6A3_ENST00000347401.3_Silent_p.T2697T|COL6A3_ENST00000409809.1_Silent_p.T2692T	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2898	Nonhelical region.|Thr-rich.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		GATTTATAATAGTCACAGGCT	0.552													A|||	1	0.000199681	0	0	5008	,	,		16037	0.001		0	False		,,,				2504	0				p.T2898T		.	.											.	COL6A3	.	.	0			c.T8694C						.						146	150	149					2																	238245049		2203	4300	6503	SO:0001819	synonymous_variant	1293	exon40			TATAATAGTCACA	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.8694T>C	2.37:g.238245049A>G		86.0	0.0		123.0	23.0	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			.	.		0.552	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		G	238245049	A	G	238245049	2	3	268	1	0	0	0	0	0	0	0	1	3703	407	15	2		2	COL6A3	2	238245049	Silent	SNP	A	TCGA-FV-A495-01A-11D-A25V-10	9362613	238245049	4954324	9	39071										
ITPR1	3708	hgsc.bcm.edu	37	chr3	4693825	4693829	+	Frame_Shift_Del	DEL	TGTCG	TGTCG	-													0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	aggtggtccagcatgacccaTgtcggggcggagcagggtat					rs377049416		TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	TGTCG	TGTCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr3:4693825_4693829delTGTCG	ENST00000443694.2	+	9	874_878	c.874_878delTGTCG	c.(874-879)tgtcggfs	p.CR292fs	ITPR1_ENST00000302640.8_Frame_Shift_Del_p.CR292fs|ITPR1_ENST00000354582.6_Frame_Shift_Del_p.CR292fs|ITPR1_ENST00000544951.1_Frame_Shift_Del_p.CR292fs|ITPR1_ENST00000423119.2_Frame_Shift_Del_p.CR292fs|ITPR1_ENST00000456211.2_Frame_Shift_Del_p.CR292fs|ITPR1_ENST00000357086.4_Frame_Shift_Del_p.CR292fs			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	292					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	GCATGACCCATGTCGGGGCGGAGCA	0.493																																					p.291_293del		.	.											.	ITPR1	.	.	0			c.873_877del						.																																			SO:0001589	frameshift_variant	3708	exon11			.	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"Ion channels / Inositol triphosphate receptors"	6180	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 94"	147265	"spinocerebellar ataxia 15", "spinocerebellar ataxia 16", "spinocerebellar ataxia 29"	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.874_878delTGTCG	3.37:g.4693825_4693829delTGTCG	ENSP00000401671:p.Cys292fs	116.0	0.0		156.0	35.0	NM_001099952	E7EPX7|E9PDE9|Q14660|Q99897	Frame_Shift_Del	DEL	ENST00000443694.2	37	CCDS54551.1																																																																																			.	.		0.493	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		-	4693829	TGTCG	-	4693825	7	5	268	1	0	1	0	1	0	0	0	0	7929	1464	51	0	908	0	ITPR1	3	4693825	Frame_Shift_Del	DEL	TGTCG	TCGA-FV-A495-01A-11D-A25V-10		4693825	193328605	10	39072										
RARB	5915	hgsc.bcm.edu	37	chr3	25622157	25622157	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	aacgtctgcctggtttcactGgcttgaccatcgcagaccaa	9	13	2	2			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr3:25622157G>T	ENST00000404969.1	+	5	751	c.751G>T	c.(751-753)Ggc>Tgc	p.G251C	RARB_ENST00000437042.2_Missense_Mutation_p.G132C|RARB_ENST00000462272.1_3'UTR|RARB_ENST00000458646.1_Missense_Mutation_p.G132C|RARB_ENST00000330688.4_Missense_Mutation_p.G244C			P10826	RARB_HUMAN	retinoic acid receptor, beta	251	Ligand-binding.				embryonic digestive tract development (GO:0048566)|embryonic eye morphogenesis (GO:0048048)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|glandular epithelial cell development (GO:0002068)|growth plate cartilage development (GO:0003417)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of myelination (GO:0031641)|retinal pigment epithelium development (GO:0003406)|signal transduction (GO:0007165)|striatum development (GO:0021756)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ureteric bud development (GO:0001657)|ventricular cardiac muscle cell differentiation (GO:0055012)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|drug binding (GO:0008144)|retinoic acid receptor activity (GO:0003708)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(3)|kidney(1)|large_intestine(10)|lung(11)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	28					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Tamibarotene(DB04942)|Tazarotene(DB00799)	TGGTTTCACTGGCTTGACCAT	0.532																																					p.G244C		.	.											.	RARB	.	.	0			c.G730T						.						140	123	129					3																	25622157		2203	4300	6503	SO:0001583	missense	5915	exon5			TTCACTGGCTTGA	Y00291	CCDS2642.1, CCDS46775.1	3p24	2013-01-16			ENSG00000077092	ENSG00000077092		"Nuclear hormone receptors"	9865	protein-coding gene	gene with protein product		180220					Standard	NM_016152		Approved	HAP, NR1B2, RRB2	uc003cdh.3	P10826	OTTHUMG00000130480	ENST00000404969.1:c.751G>T	3.37:g.25622157G>T	ENSP00000385865:p.Gly251Cys	92.0	0.0		100.0	4.0	NM_000965	P12891|Q00989|Q15298|Q9UN48	Missense_Mutation	SNP	ENST00000404969.1	37		.	.	.	.	.	.	.	.	.	.	G	14.09	2.430876	0.43122	.	.	ENSG00000077092	ENST00000383772;ENST00000404969;ENST00000538226;ENST00000437042;ENST00000330688;ENST00000458646	T;T;T;T;T	0.36878	1.23;1.23;1.23;1.23;1.23	5.2	0.492	0.16872	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.279370	0.40469	N	0.001084	T	0.30916	0.0780	N	0.22421	0.69	0.24569	N	0.993934	P;P	0.48089	0.905;0.758	P;P	0.51701	0.581;0.677	T	0.15378	-1.0439	10	0.66056	D	0.02	.	8.563	0.33523	0.5988:0.0:0.4012:0.0	.	251;244	P10826;F1D8S6	RARB_HUMAN;.	C	251;251;251;132;244;132	ENSP00000373282:G251C;ENSP00000385865:G251C;ENSP00000398840:G132C;ENSP00000332296:G244C;ENSP00000391391:G132C	ENSP00000332296:G244C	G	+	1	0	RARB	25597161	0.048000	0.20356	0.772000	0.31596	0.655000	0.38815	0.467000	0.22035	0.146000	0.19002	-0.424000	0.05967	GGC	.	.		0.532	RARB-201	KNOWN	basic	protein_coding	protein_coding		NM_000965, NM_016152		T	25622157	G	T	25622157	3	4	268	1	0	0	0	0	1	0	0	0	13068	1348	47	3	748	3	RARB	3	25622157	Missense_Mutation	SNP	G	TCGA-FV-A495-01A-11D-A25V-10	20928332	25622157	172400273	11	39073										
SCN5A	6331	hgsc.bcm.edu	37	chr3	38645342	38645342	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	ttttgccatggagggcgtggCcaggagccgaggttccggga	18	9	0	0			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr3:38645342C>T	ENST00000333535.4	-	12	1900	c.1751G>A	c.(1750-1752)gGc>gAc	p.G584D	SCN5A_ENST00000425664.1_Missense_Mutation_p.G584D|SCN5A_ENST00000443581.1_Missense_Mutation_p.G584D|SCN5A_ENST00000414099.2_Missense_Mutation_p.G584D|SCN5A_ENST00000449557.2_Missense_Mutation_p.G584D|SCN5A_ENST00000450102.2_Missense_Mutation_p.G584D|SCN5A_ENST00000413689.1_Missense_Mutation_p.G584D|SCN5A_ENST00000423572.2_Missense_Mutation_p.G584D|SCN5A_ENST00000455624.2_Missense_Mutation_p.G584D|SCN5A_ENST00000451551.2_Missense_Mutation_p.G584D			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit	584					AV node cell to bundle of His cell communication (GO:0086067)|brainstem development (GO:0003360)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|cardiac ventricle development (GO:0003231)|cellular response to calcium ion (GO:0071277)|cerebellum development (GO:0021549)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane depolarization during SA node cell action potential (GO:0086046)|neuronal action potential (GO:0019228)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of action potential (GO:0045760)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of sodium ion transport (GO:0010765)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|telencephalon development (GO:0021537)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	ankyrin binding (GO:0030506)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)			NS(3)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|lung(27)|ovary(6)|pancreas(3)|prostate(10)|skin(9)|upper_aerodigestive_tract(4)	107	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Ajmaline(DB01426)|Aprindine(DB01429)|Benzonatate(DB00868)|Carbamazepine(DB00564)|Cinchocaine(DB00527)|Cocaine(DB00907)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lidocaine(DB00281)|Mexiletine(DB00379)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)|Ranolazine(DB00243)|Riluzole(DB00740)|Tocainide(DB01056)|Valproic Acid(DB00313)|Verapamil(DB00661)|Zonisamide(DB00909)	GAGGGCGTGGCCAGGAGCCGA	0.667																																					p.G584D		.	.											.	SCN5A	.	.	0			c.G1751A						.						75	82	80					3																	38645342		2007	4170	6177	SO:0001583	missense	6331	exon12			GCGTGGCCAGGAG	AJ310893	CCDS46796.1, CCDS46797.1, CCDS46798.1, CCDS46799.1, CCDS54569.1, CCDS54570.1	3p21	2014-09-17	2007-01-23		ENSG00000183873	ENSG00000183873		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10593	protein-coding gene	gene with protein product	"long QT syndrome 3"	600163	"sodium channel, voltage-gated, type V, alpha (long QT syndrome 3)"	CMD1E		7842012, 15466643, 16382098	Standard	NM_198056		Approved	Nav1.5, LQT3, HB1, HBBD, PFHB1, IVF, HB2, HH1, SSS1, CDCD2, CMPD2, ICCD	uc021wvl.1	Q14524	OTTHUMG00000156166	ENST00000333535.4:c.1751G>A	3.37:g.38645342C>T	ENSP00000328968:p.Gly584Asp	48.0	0.0		64.0	13.0	NM_001160160	A5H1P8|A6N922|A6N923|B2RTU0|E7ET19|E9PEF3|E9PEK2|E9PFW7|Q59H93|Q75RX9|Q75RY0|Q86UR3|Q8IZC9|Q96J69	Missense_Mutation	SNP	ENST00000333535.4	37	CCDS46796.1	.	.	.	.	.	.	.	.	.	.	C	7.277	0.608360	0.14002	.	.	ENSG00000183873	ENST00000414099;ENST00000423572;ENST00000413689;ENST00000451551;ENST00000443581;ENST00000425664;ENST00000333535;ENST00000455624;ENST00000450102;ENST00000449557	D;D;D;D;D;D;D;D;D;D	0.90844	-2.74;-2.74;-2.74;-2.74;-2.74;-2.74;-2.74;-2.74;-2.74;-2.74	4.02	3.11	0.35812	Domain of unknown function DUF3451 (1);	0.678658	0.12881	N	0.431419	D	0.87116	0.6097	L	0.50333	1.59	0.29187	N	0.876133	B;B;B;B;B;B;B	0.25351	0.095;0.124;0.032;0.011;0.052;0.029;0.042	B;B;B;B;B;B;B	0.33121	0.099;0.158;0.022;0.038;0.112;0.049;0.084	T	0.78792	-0.2065	10	0.28530	T	0.3	.	7.8391	0.29387	0.0:0.7761:0.0:0.2239	.	584;584;584;584;584;584;584	E9PEF3;E9PHB6;Q14524-6;E9PG18;Q14524;Q14524-2;E9PEK2	.;.;.;.;SCN5A_HUMAN;.;.	D	584	ENSP00000398962:G584D;ENSP00000398266:G584D;ENSP00000410257:G584D;ENSP00000388797:G584D;ENSP00000397915:G584D;ENSP00000416634:G584D;ENSP00000328968:G584D;ENSP00000399524:G584D;ENSP00000403355:G584D;ENSP00000413996:G584D	ENSP00000328968:G584D	G	-	2	0	SCN5A	38620346	0.128000	0.22383	0.541000	0.28102	0.890000	0.51754	0.777000	0.26718	2.067000	0.61834	0.561000	0.74099	GGC	.	.		0.667	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	NM_198056		T	38645342	C	T	38645342	3	4	268	1	0	0	0	0	1	0	0	0	13937	739	26	3	4367	3	SCN5A	3	38645342	Missense_Mutation	SNP	C	TCGA-FV-A495-01A-11D-A25V-10	13023185	38645342	159377088	12	39074										
ITIH4	3700	hgsc.bcm.edu	37	chr3	52863215	52863215	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	acagtattggccctattgacCactcggctggtgacgaccgt	11	12	0	2			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr3:52863215C>T	ENST00000266041.4	-	2	267	c.171G>A	c.(169-171)gtG>gtA	p.V57V	RP5-966M1.6_ENST00000468472.1_3'UTR|ITIH4_ENST00000406595.1_Silent_p.V57V|ITIH4_ENST00000485816.1_Silent_p.V57V|ITIH4_ENST00000346281.5_Silent_p.V57V|ITIH4_ENST00000434759.3_Intron|RP5-966M1.6_ENST00000513520.1_5'Flank	NM_002218.4	NP_002209.2	Q14624	ITIH4_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 4	57	VIT. {ECO:0000255|PROSITE- ProRule:PRU00801}.				acute-phase response (GO:0006953)|hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)|response to cytokine (GO:0034097)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)		CCCTATTGACCACTCGGCTGG	0.562																																					p.V57V		.	.											.	ITIH4	.	.	0			c.G171A						.						163	135	145					3																	52863215		2203	4300	6503	SO:0001819	synonymous_variant	3700	exon2			ATTGACCACTCGG	D38535	CCDS2865.1, CCDS54596.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055955	ENSG00000055955			6169	protein-coding gene	gene with protein product	"plasma Kallikrein-sensitive glycoprotein"	600564	"inter-alpha (globulin) inhibitor H4 (plasma Kallikrein-sensitive glycoprotein)"	ITIHL1		9480842, 7805892	Standard	NM_002218		Approved	IHRP, H4P	uc003dfz.3	Q14624	OTTHUMG00000159023	ENST00000266041.4:c.171G>A	3.37:g.52863215C>T		105.0	0.0		127.0	37.0	NM_001166449	B7Z545|E9PGN5|Q15135|Q9P190|Q9UQ54	Silent	SNP	ENST00000266041.4	37	CCDS2865.1																																																																																			.	.		0.562	ITIH4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317715.1	NM_002218		T	52863215	C	T	52863215	2	4	268	1	0	0	0	0	0	0	0	1	7915	581	21	3		3	ITIH4	3	52863215	Silent	SNP	C	TCGA-FV-A495-01A-11D-A25V-10	14217873	52863215	145159215	13	39075										
MYH15	22989	hgsc.bcm.edu	37	chr3	108147461	108147461	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	ttctacctggccctcgagctCagccaggctgtctgcatgtc	10	15	3	0			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr3:108147461C>G	ENST00000273353.3	-	28	3696	c.3640G>C	c.(3640-3642)Gag>Cag	p.E1214Q		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	1214						cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.E1214Q(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						CCCTCGAGCTCAGCCAGGCTG	0.493																																					p.E1214Q		.	.											.	MYH15	.	.	1	Substitution - Missense(1)	lung(1)	c.G3640C						.						141	132	135					3																	108147461		1933	4148	6081	SO:0001583	missense	22989	exon28			CGAGCTCAGCCAG	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"Myosins / Myosin superfamily : Class II"	31073	protein-coding gene	gene with protein product		609929	"myosin, heavy polypeptide 15"			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.3640G>C	3.37:g.108147461C>G	ENSP00000273353:p.Glu1214Gln	228.0	0.0		297.0	12.0	NM_014981		Missense_Mutation	SNP	ENST00000273353.3	37	CCDS43127.1	.	.	.	.	.	.	.	.	.	.	C	12.99	2.103060	0.37145	.	.	ENSG00000144821	ENST00000273353	D	0.83419	-1.72	5.37	2.64	0.31445	Myosin tail (1);	.	.	.	.	D	0.90442	0.7007	M	0.86343	2.81	0.42253	D	0.99198	D	0.63880	0.993	D	0.69654	0.965	D	0.89990	0.4107	9	0.87932	D	0	.	10.5166	0.44894	0.0:0.791:0.0:0.209	.	1214	Q9Y2K3	MYH15_HUMAN	Q	1214	ENSP00000273353:E1214Q	ENSP00000273353:E1214Q	E	-	1	0	MYH15	109630151	0.953000	0.32496	0.000000	0.03702	0.018000	0.09664	2.188000	0.42612	0.358000	0.24211	-0.142000	0.14014	GAG	.	.		0.493	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988		G	108147461	C	G	108147461	3	3	268	1	0	0	0	0	1	0	0	0	10043	835	29	4	2260	4	MYH15	3	108147461	Missense_Mutation	SNP	C	TCGA-FV-A495-01A-11D-A25V-10	55284246	108147461	89874969	14	39076										
ZIC1	7545	hgsc.bcm.edu	37	chr3	147128637	147128637	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	aagtcgtgcaacaaaactttCagcaccatgcacgagctagt	8	11	1	0			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr3:147128637C>T	ENST00000282928.4	+	1	1467	c.738C>T	c.(736-738)ttC>ttT	p.F246F		NM_003412.3	NP_003403.2	Q15915	ZIC1_HUMAN	Zic family member 1	246					adult walking behavior (GO:0007628)|brain development (GO:0007420)|cell differentiation (GO:0030154)|inner ear morphogenesis (GO:0042472)|pattern specification process (GO:0007389)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord development (GO:0021510)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(4)|cervix(1)|endometrium(2)|large_intestine(8)|lung(38)|ovary(1)|prostate(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	63						ACAAAACTTTCAGCACCATGC	0.572																																					p.F246F		.	.											.	ZIC1	.	.	0			c.C738T						.						93	86	89					3																	147128637		2203	4300	6503	SO:0001819	synonymous_variant	7545	exon1			AACTTTCAGCACC	D76435	CCDS3136.1	3q24	2013-01-08	2011-05-19		ENSG00000152977	ENSG00000152977		"Zinc fingers, C2H2-type"	12872	protein-coding gene	gene with protein product		600470	"Zic family member 1 (odd-paired Drosophila homolog)", "Zic family member 1 (odd-paired homolog, Drosophila)"			8542595	Standard	NM_003412		Approved	ZIC, ZNF201	uc003ewe.3	Q15915	OTTHUMG00000159456	ENST00000282928.4:c.738C>T	3.37:g.147128637C>T		153.0	0.0		184.0	46.0	NM_003412	Q2M3N1	Silent	SNP	ENST00000282928.4	37	CCDS3136.1																																																																																			.	.		0.572	ZIC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355497.1	NM_003412		T	147128637	C	T	147128637	2	4	268	1	0	0	0	0	0	0	0	1	17693	825	29	3		3	ZIC1	3	147128637	Silent	SNP	C	TCGA-FV-A495-01A-11D-A25V-10	38981176	147128637	50893793	15	39077										
SSR3	6747	hgsc.bcm.edu	37	chr3	156266720	156266720	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	tctttctccttccgagacatCtttctattatcagcttcaga	4	12	6	2			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr3:156266720C>A	ENST00000265044.2	-	3	427	c.333G>T	c.(331-333)aaG>aaT	p.K111N	SSR3_ENST00000467789.1_Missense_Mutation_p.K111N|SSR3_ENST00000463503.1_Missense_Mutation_p.K59N|SSR3_ENST00000496050.1_Missense_Mutation_p.K59N|SSR3_ENST00000478842.1_5'UTR|SSR3_ENST00000476217.1_Missense_Mutation_p.K111N	NM_007107.3	NP_009038.1	Q9UNL2	SSRG_HUMAN	signal sequence receptor, gamma (translocon-associated protein gamma)	111					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	integral component of endoplasmic reticulum membrane (GO:0030176)|Sec61 translocon complex (GO:0005784)				endometrium(1)|prostate(2)	3			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			TCCGAGACATCTTTCTATTAT	0.358																																					p.K111N		.	.											.	SSR3	.	.	0			c.G333T						.						91	90	90					3																	156266720		2203	4300	6503	SO:0001583	missense	6747	exon3			AGACATCTTTCTA	BC017203	CCDS3176.1	3q25.31	2004-02-27			ENSG00000114850	ENSG00000114850			11325	protein-coding gene	gene with protein product		606213					Standard	NM_007107		Approved	TRAPG	uc003fau.3	Q9UNL2	OTTHUMG00000158632	ENST00000265044.2:c.333G>T	3.37:g.156266720C>A	ENSP00000265044:p.Lys111Asn	60.0	0.0		71.0	19.0	NM_007107	B2R7D0|B4E2P2|D3DNK5|Q549M4	Missense_Mutation	SNP	ENST00000265044.2	37	CCDS3176.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.712930	0.89112	.	.	ENSG00000114850	ENST00000265044;ENST00000467789;ENST00000476217;ENST00000463503;ENST00000496050	.	.	.	5.41	5.41	0.78517	.	0.046835	0.85682	D	0.000000	D	0.85923	0.5810	M	0.89904	3.07	0.80722	D	1	D;D	0.89917	0.992;1.0	D;D	0.91635	0.954;0.999	D	0.88349	0.2980	9	0.87932	D	0	-20.4262	19.5475	0.95305	0.0:1.0:0.0:0.0	.	111;111	B4E2P2;Q9UNL2	.;SSRG_HUMAN	N	111;111;111;59;59	.	ENSP00000265044:K111N	K	-	3	2	SSR3	157749414	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.174000	0.50847	2.680000	0.91292	0.650000	0.86243	AAG	.	.		0.358	SSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351521.1	NM_007107		A	156266720	C	A	156266720	3	1	268	1	0	0	0	0	1	0	0	0	15207	912	32	3	236	3	SSR3	3	156266720	Missense_Mutation	SNP	C	TCGA-FV-A495-01A-11D-A25V-10	9138083	156266720	41755710	16	39078										
ZNF141	7700	hgsc.bcm.edu	37	chr4	366775	366775	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	ggcaaatcatttcagaagttTtcacacctaactcaacataa	4	10	4	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr4:366775T>A	ENST00000240499.7	+	4	698	c.549T>A	c.(547-549)ttT>ttA	p.F183L	ZNF141_ENST00000505939.1_Intron|ZNF141_ENST00000512994.1_Missense_Mutation_p.F183L	NM_003441.2	NP_003432.1	Q15928	ZN141_HUMAN	zinc finger protein 141	183					anatomical structure morphogenesis (GO:0009653)|limb morphogenesis (GO:0035108)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|kidney(3)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(1)	18						TTCAGAAGTTTTCACACCTAA	0.333																																					p.F183L		.	.											.	ZNF141	.	.	0			c.T549A						.						70	74	73					4																	366775		2203	4300	6503	SO:0001583	missense	7700	exon4			GAAGTTTTCACAC	L15309	CCDS33931.1	4p16.3	2013-01-08	2006-06-13			ENSG00000131127		"Zinc fingers, C2H2-type", "-"	12926	protein-coding gene	gene with protein product		194648	"zinc finger protein 141 (clone pHZ-44)"	D4S90		8268908	Standard	NM_003441		Approved	pHZ-44	uc003gaa.2	Q15928		ENST00000240499.7:c.549T>A	4.37:g.366775T>A	ENSP00000240499:p.Phe183Leu	64.0	0.0		85.0	20.0	NM_003441	Q6DK07	Missense_Mutation	SNP	ENST00000240499.7	37	CCDS33931.1	.	.	.	.	.	.	.	.	.	.	T	0.635	-0.815479	0.02776	.	.	ENSG00000131127	ENST00000512994;ENST00000240499	T;T	0.26660	7.3;1.72	1.23	-2.46	0.06461	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08935	0.0221	N	0.10760	0.04	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.33701	-0.9858	9	0.10902	T	0.67	.	3.277	0.06902	0.2426:0.5471:0.0:0.2104	.	183;183	D6RIY0;Q15928	.;ZN141_HUMAN	L	183	ENSP00000425799:F183L;ENSP00000240499:F183L	ENSP00000240499:F183L	F	+	3	2	ZNF141	356775	.	.	0.001000	0.08648	0.014000	0.08584	.	.	-1.419000	0.02012	-0.756000	0.03474	TTT	.	.		0.333	ZNF141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357710.1	NM_003441		A	366775	T	A	366775	3	1	268	1	0	0	0	0	1	0	0	0	17745	1838	64	4	563	4	ZNF141	4	366775	Missense_Mutation	SNP	T	TCGA-FV-A495-01A-11D-A25V-10		366775	190787501	17	39079										
EVC2	132884	hgsc.bcm.edu	37	chr4	5633629	5633629	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	agatactgtgcagttcatttCtctggaaaacagccagctgt	9	9	2	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr4:5633629C>T	ENST00000344408.5	-	11	1654	c.1601G>A	c.(1600-1602)aGa>aAa	p.R534K	EVC2_ENST00000344938.1_Missense_Mutation_p.R534K|EVC2_ENST00000310917.2_Missense_Mutation_p.R454K	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	534					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						CAGTTCATTTCTCTGGAAAAC	0.433																																					p.R534K		.	.											.	EVC2	.	.	0			c.G1601A						.						107	110	109					4																	5633629		2203	4300	6503	SO:0001583	missense	132884	exon11			TCATTTCTCTGGA	AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.1601G>A	4.37:g.5633629C>T	ENSP00000342144:p.Arg534Lys	71.0	0.0		73.0	12.0	NM_147127	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	37	CCDS3382.2	.	.	.	.	.	.	.	.	.	.	C	16.10	3.028483	0.54790	.	.	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	D;D;D	0.86865	-2.18;-2.18;-2.18	4.79	4.79	0.61399	.	0.125045	0.52532	D	0.000064	D	0.92704	0.7681	M	0.70275	2.135	0.37810	D	0.928021	D	0.89917	1.0	D	0.87578	0.998	D	0.93501	0.6844	10	0.44086	T	0.13	-20.5355	17.2176	0.86948	0.0:1.0:0.0:0.0	.	534	Q86UK5	LBN_HUMAN	K	534;454;534	ENSP00000339954:R534K;ENSP00000311683:R454K;ENSP00000342144:R534K	ENSP00000311683:R454K	R	-	2	0	EVC2	5684530	0.996000	0.38824	0.847000	0.33407	0.040000	0.13550	4.481000	0.60250	2.353000	0.79882	0.505000	0.49811	AGA	.	.		0.433	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127		T	5633629	C	T	5633629	3	4	268	1	0	0	0	0	1	0	0	0	5288	913	32	3	2373	3	EVC2	4	5633629	Missense_Mutation	SNP	C	TCGA-FV-A495-01A-11D-A25V-10	5266854	5633629	185520647	18	39080										
STIM2	57620	hgsc.bcm.edu	37	chr4	27024472	27024472	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	aacctcgccacacatcatgtTcctcagctggcaacgacagt	7	15	2	0			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr4:27024472T>G	ENST00000467087.1	+	12	2623	c.2095T>G	c.(2095-2097)Tcc>Gcc	p.S699A	STIM2_ENST00000382009.3_Missense_Mutation_p.S794A|STIM2_ENST00000237364.5_Missense_Mutation_p.S786A|STIM2_ENST00000412829.2_3'UTR|STIM2_ENST00000467011.1_3'UTR|STIM2_ENST00000465503.1_Missense_Mutation_p.S707A			Q9P246	STIM2_HUMAN	stromal interaction molecule 2	699					activation of store-operated calcium channel activity (GO:0032237)|calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|positive regulation of calcium ion transport (GO:0051928)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|store-operated calcium channel activity (GO:0015279)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	25		Breast(46;0.0503)				CACATCATGTTCCTCAGCTGG	0.483																																					p.S707A		.	.											.	STIM2	.	.	0			c.T2119G						.						99	91	94					4																	27024472		2203	4300	6503	SO:0001583	missense	57620	exon13			TCATGTTCCTCAG	AB040915	CCDS3440.1, CCDS3440.2, CCDS54751.1, CCDS54752.1	4p15.2	2013-01-10			ENSG00000109689	ENSG00000109689		"Sterile alpha motif (SAM) domain containing"	19205	protein-coding gene	gene with protein product		610841				11463338	Standard	NM_020860		Approved		uc003gsh.4	Q9P246	OTTHUMG00000097805	ENST00000467087.1:c.2095T>G	4.37:g.27024472T>G	ENSP00000419073:p.Ser699Ala	103.0	0.0		118.0	23.0	NM_001169118	A6H8L7|B7ZVY0|Q96BF1|Q9BQH2|Q9H8R1	Missense_Mutation	SNP	ENST00000467087.1	37	CCDS3440.2	.	.	.	.	.	.	.	.	.	.	T	13.25	2.180558	0.38511	.	.	ENSG00000109689	ENST00000467087;ENST00000382009;ENST00000237364;ENST00000465503	T;T;T;T	0.78126	-1.12;-1.15;-1.15;-1.13	5.87	5.87	0.94306	.	0.113494	0.64402	D	0.000009	T	0.71978	0.3404	L	0.27053	0.805	0.80722	D	1	P;P	0.46859	0.817;0.885	B;P	0.48304	0.369;0.573	T	0.75202	-0.3401	10	0.66056	D	0.02	.	10.8542	0.46789	0.0:0.0701:0.0:0.9299	.	794;786	E9PGD0;F5GXJ4	.;.	A	699;794;786;707	ENSP00000419073:S699A;ENSP00000371439:S794A;ENSP00000237364:S786A;ENSP00000417569:S707A	ENSP00000237364:S786A	S	+	1	0	STIM2	26633570	0.997000	0.39634	0.940000	0.37924	0.939000	0.58152	3.157000	0.50716	2.371000	0.80710	0.533000	0.62120	TCC	.	.		0.483	STIM2-001	KNOWN	non_ATG_start|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215063.2	NM_020860		G	27024472	T	G	27024472	3	3	268	1	0	0	0	0	1	0	0	0	15299	1783	62	5	2210	5	STIM2	4	27024472	Missense_Mutation	SNP	T	TCGA-FV-A495-01A-11D-A25V-10	21390843	27024472	164129804	19	39081										
ATP8A1	10396	hgsc.bcm.edu	37	chr4	42553255	42553255	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	cgggtgttcttccagtgaaaAcaaaattcaattgcttggct	9	8	2	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr4:42553255A>G	ENST00000381668.5	-	18	1793	c.1562T>C	c.(1561-1563)gTt>gCt	p.V521A	ATP8A1_ENST00000264449.10_Missense_Mutation_p.V506A	NM_006095.2	NP_006086.1	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	521					cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	51					Phosphatidylserine(DB00144)	TCCAGTGAAAACAAAATTCAA	0.338																																					p.V521A		.	.											.	ATP8A1	.	.	0			c.T1562C						.						123	126	125					4																	42553255		2203	4300	6503	SO:0001583	missense	10396	exon18			GTGAAAACAAAAT	AF067820	CCDS3466.1, CCDS47049.1	4p13	2010-04-20	2007-09-19		ENSG00000124406	ENSG00000124406		"ATPases / P-type"	13531	protein-coding gene	gene with protein product		609542	"ATPase, aminophospholipid transporter (APLT), Class I, type 8A, member 1"			10198212, 9548971	Standard	NM_006095		Approved	ATPIA	uc003gwr.2	Q9Y2Q0	OTTHUMG00000099403	ENST00000381668.5:c.1562T>C	4.37:g.42553255A>G	ENSP00000371084:p.Val521Ala	147.0	0.0		152.0	41.0	NM_006095	Q32M35|Q32M36|Q4W5J7|Q4W5P2	Missense_Mutation	SNP	ENST00000381668.5	37	CCDS3466.1	.	.	.	.	.	.	.	.	.	.	A	18.32	3.598513	0.66332	.	.	ENSG00000124406	ENST00000381668;ENST00000264449	T;T	0.65732	-0.17;-0.17	5.49	5.49	0.81192	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.067148	0.64402	D	0.000014	T	0.76140	0.3946	M	0.70108	2.13	0.80722	D	1	D;P;D	0.55605	0.963;0.813;0.972	D;P;P	0.68621	0.959;0.714;0.826	T	0.73288	-0.4030	10	0.22109	T	0.4	.	15.5992	0.76611	1.0:0.0:0.0:0.0	.	506;506;521	B4DII6;Q32M35;Q9Y2Q0	.;.;AT8A1_HUMAN	A	521;506	ENSP00000371084:V521A;ENSP00000264449:V506A	ENSP00000264449:V506A	V	-	2	0	ATP8A1	42248012	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	6.521000	0.73778	2.080000	0.62538	0.477000	0.44152	GTT	.	.		0.338	ATP8A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216861.2	NM_006095		G	42553255	A	G	42553255	3	3	268	1	0	0	0	0	1	0	0	0	1192	43	2	2	2012	2	ATP8A1	4	42553255	Missense_Mutation	SNP	A	TCGA-FV-A495-01A-11D-A25V-10	15528783	42553255	148601021	20	39082										
UGT2B4	7363	hgsc.bcm.edu	37	chr4	70360887	70360889	+	In_Frame_Del	DEL	CTT	CTT	-													0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	tcactgtagaactgatcccaCttcttcatgtcaaatatttg							TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr4:70360887_70360889delCTT	ENST00000305107.6	-	1	737_739	c.691_693delAAG	c.(691-693)aagdel	p.K231del	UGT2B4_ENST00000381096.3_In_Frame_Del_p.K95del|UGT2B4_ENST00000506580.1_Intron|UGT2B4_ENST00000512583.1_In_Frame_Del_p.K231del	NM_021139.2	NP_066962.2	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B4	231					cellular glucuronidation (GO:0052695)|estrogen catabolic process (GO:0006711)|metabolic process (GO:0008152)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(29)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	47					Canagliflozin(DB08907)|Codeine(DB00318)|Dapagliflozin(DB06292)|Flurbiprofen(DB00712)|Ibuprofen(DB01050)|Morphine(DB00295)	ACTGATCCCACTTCTTCATGTCA	0.32																																					p.231_232del		.	.											.	UGT2B4	.	.	0			c.692_694del						.																																			SO:0001651	inframe_deletion	7363	exon1			.	BC026264	CCDS43234.1, CCDS75137.1	4q13	2008-02-05	2005-07-20			ENSG00000156096		"UDP glucuronosyltransferases"	12553	protein-coding gene	gene with protein product		600067	"UDP glycosyltransferase 2 family, polypeptide B4"			3109396, 7835904	Standard	NM_021139		Approved	UGT2B11	uc003hek.4	P06133		ENST00000305107.6:c.691_693delAAG	4.37:g.70360890_70360892delCTT	ENSP00000305221:p.Lys231del	102.0	0.0		99.0	15.0	NM_021139	A6NCP7|B4DT75|G5E9X8|O60731|O60867|O75614|P36538|Q1HBF9|Q6QQX7	In_Frame_Del	DEL	ENST00000305107.6	37	CCDS43234.1																																																																																			.	.		0.32	UGT2B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365526.1	NM_021139		-	70360889	CTT	-	70360887	7	5	268	1	0	1	0	1	0	0	0	0	16976	564	20	0	917	0	UGT2B4	4	70360887	In_Frame_Del	DEL	CTT	TCGA-FV-A495-01A-11D-A25V-10	27807632	70360887	120793389	21	39083										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13820597	13820597	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	ggaggatggttgattaaaccAgcttcttcaacctgaaaaca	9	8	2	2			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr5:13820597A>G	ENST00000265104.4	-	41	6803	c.6699T>C	c.(6697-6699)gcT>gcC	p.A2233A		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2233	AAA 2. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TGATTAAACCAGCTTCTTCAA	0.502									Kartagener syndrome																												p.A2233A		.	.											.	DNAH5	.	.	0			c.T6699C						.						86	80	82					5																	13820597		2203	4300	6503	SO:0001819	synonymous_variant	1767	exon41	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	TAAACCAGCTTCT	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.6699T>C	5.37:g.13820597A>G		76.0	0.0		116.0	26.0	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			.	.		0.502	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		G	13820597	A	G	13820597	2	3	268	1	0	0	0	0	0	0	0	1	4606	175	7	2		2	DNAH5	5	13820597	Silent	SNP	A	TCGA-FV-A495-01A-11D-A25V-10		13820597	167094663	22	39084										
BRIX1	55299	hgsc.bcm.edu	37	chr5	34925045	34925045	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	gaagttttggaggaccaactTtatatgaaaatcctcactac	7	8	1	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr5:34925045T>G	ENST00000336767.5	+	9	1120	c.757T>G	c.(757-759)Tta>Gta	p.L253V	BRIX1_ENST00000506023.1_3'UTR	NM_018321.3	NP_060791.3	Q8TDN6	BRX1_HUMAN	BRX1, biogenesis of ribosomes, homolog (S. cerevisiae)	253					ribosome biogenesis (GO:0042254)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|large_intestine(2)|lung(1)	4						AGGACCAACTTTATATGAAAA	0.383																																					p.L253V		.	.											.	BRIX1	.	.	0			c.T757G						.						63	62	62					5																	34925045		2203	4300	6503	SO:0001583	missense	55299	exon9			CCAACTTTATATG		CCDS34143.1	5p13.2	2009-09-25	2009-09-25	2009-09-25	ENSG00000113460	ENSG00000113460			24170	protein-coding gene	gene with protein product			"brix domain containing 2"	BXDC2		12477932	Standard	NM_018321		Approved	BRIX, FLJ11100	uc003jja.3	Q8TDN6	OTTHUMG00000162021	ENST00000336767.5:c.757T>G	5.37:g.34925045T>G	ENSP00000338862:p.Leu253Val	24.0	0.0		33.0	7.0	NM_018321	A8K0P5|Q3ZTT4|Q8N453|Q96DH1	Missense_Mutation	SNP	ENST00000336767.5	37	CCDS34143.1	.	.	.	.	.	.	.	.	.	.	T	20.5	3.995448	0.74703	.	.	ENSG00000113460	ENST00000336767	T	0.57107	0.42	5.82	3.47	0.39725	.	0.000000	0.85682	D	0.000000	T	0.61211	0.2329	L	0.56396	1.775	0.50813	D	0.999896	D	0.65815	0.995	P	0.61722	0.893	T	0.60031	-0.7342	10	0.46703	T	0.11	-10.5824	8.4913	0.33102	0.0:0.2767:0.0:0.7233	.	253	Q8TDN6	BRX1_HUMAN	V	253	ENSP00000338862:L253V	ENSP00000338862:L253V	L	+	1	2	BRIX1	34960802	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.744000	0.47450	1.035000	0.39972	0.533000	0.62120	TTA	.	.		0.383	BRIX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366826.2	NM_018321		G	34925045	T	G	34925045	3	3	268	1	0	0	0	0	1	0	0	0	1517	1838	64	5	791	5	BRIX1	5	34925045	Missense_Mutation	SNP	T	TCGA-FV-A495-01A-11D-A25V-10	21104448	34925045	145990215	23	39085										
GIN1	54826	hgsc.bcm.edu	37	chr5	102433403	102433403	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	ctttgattgtgttaggtgtaCtttccgttgggttaacagtt	11	5	0	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr5:102433403C>T	ENST00000399004.2	-	5	816	c.722G>A	c.(721-723)aGt>aAt	p.S241N	GIN1_ENST00000508629.1_Intron	NM_017676.2	NP_060146.2	Q9NXP7	GIN1_HUMAN	gypsy retrotransposon integrase 1	241	Integrase catalytic. {ECO:0000255|PROSITE-ProRule:PRU00457}.				DNA integration (GO:0015074)		nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(142;3.23e-07)|all_epithelial(76;3.64e-10)|Prostate(80;0.00914)|Ovarian(225;0.0139)|Lung NSC(167;0.0212)|Colorectal(57;0.0249)|all_lung(232;0.0283)		Epithelial(69;3.57e-14)|COAD - Colon adenocarcinoma(37;0.00794)		GTTAGGTGTACTTTCCGTTGG	0.368																																					p.S241N		.	.											.	GIN1	.	.	0			c.G722A						.						228	206	213					5																	102433403		1896	4125	6021	SO:0001583	missense	54826	exon5			GGTGTACTTTCCG	BC015325	CCDS43349.1	5q21.1	2008-02-11	2007-06-13	2007-06-13		ENSG00000145723			25959	protein-coding gene	gene with protein product	"gypsy integrase 1", "Ty3/Gypsy integrase 1"		"zinc finger, H2C2 domain containing"	ZH2C2		11470852	Standard	NM_017676		Approved	FLJ20125, GIN-1, TGIN1	uc003koa.1	Q9NXP7		ENST00000399004.2:c.722G>A	5.37:g.102433403C>T	ENSP00000381970:p.Ser241Asn	91.0	0.0		127.0	7.0	NM_017676	B2RXF7|B4DIV4|Q6AI03|Q96BR2	Missense_Mutation	SNP	ENST00000399004.2	37	CCDS43349.1	.	.	.	.	.	.	.	.	.	.	C	4.471	0.087301	0.08583	.	.	ENSG00000145723	ENST00000399004	T	0.45276	0.9	5.66	3.87	0.44632	Integrase, catalytic core (1);Ribonuclease H-like (1);	0.293446	0.29002	N	0.013459	T	0.25419	0.0618	N	0.12182	0.205	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.02450	-1.1157	10	0.33141	T	0.24	-1.3883	12.3179	0.54969	0.0:0.8084:0.1218:0.0698	.	241	Q9NXP7	GIN1_HUMAN	N	241	ENSP00000381970:S241N	ENSP00000381970:S241N	S	-	2	0	GIN1	102461302	0.996000	0.38824	0.431000	0.26735	0.005000	0.04900	0.690000	0.25451	0.320000	0.23234	-0.810000	0.03169	AGT	.	.		0.368	GIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370478.3	NM_017676		T	102433403	C	T	102433403	3	4	268	1	0	0	0	0	1	0	0	0	6394	565	20	3	862	3	GIN1	5	102433403	Missense_Mutation	SNP	C	TCGA-FV-A495-01A-11D-A25V-10	67508358	102433403	78481857	24	39086										
FBN2	2201	hgsc.bcm.edu	37	chr5	127686699	127686699	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	caggtccccttcaggctgtcTgaaaaggaacaggaaaggtt	12	9	2	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr5:127686699T>C	ENST00000508053.1	-	27	3649		c.e27-2		FBN2_ENST00000508989.1_Splice_Site|FBN2_ENST00000262464.4_Splice_Site			P35556	FBN2_HUMAN	fibrillin 2						anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		TCAGGCTGTCTGAAAAGGAAC	0.453																																					.		.	.											.	FBN2	.	.	0			c.2675-2A>G						.						62	65	64					5																	127686699		2203	4300	6503	SO:0001630	splice_region_variant	2201	exon22			GCTGTCTGAAAAG	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.2675-2A>G	5.37:g.127686699T>C		51.0	0.0		94.0	6.0	NM_001999	B4DU01|Q59ES6	Splice_Site	SNP	ENST00000508053.1	37	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.002478	0.74932	.	.	ENSG00000138829	ENST00000262464;ENST00000508053;ENST00000508989	.	.	.	3.95	3.95	0.45737	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.8805	0.63680	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	FBN2	127714598	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	7.779000	0.85648	2.014000	0.59158	0.460000	0.39030	.	.	.		0.453	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999	Intron	C	127686699	T	C	127686699	5	2	268	1	0	0	0	0	0	0	1	0	5711	1594	55	2	6245	2	FBN2	5	127686699	Splice_Site	SNP	T	TCGA-FV-A495-01A-11D-A25V-10	25253296	127686699	53228561	25	39087										
PCDHA5	56143	hgsc.bcm.edu	37	chr5	140203594	140203594	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	gttgtgctccagcgcggtggGgagctggtcgtactcgcagc	17	11	0	0			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr5:140203594G>T	ENST00000529859.1	+	1	2234	c.2234G>T	c.(2233-2235)gGg>gTg	p.G745V	PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000378126.3_Missense_Mutation_p.G745V|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Missense_Mutation_p.G745V	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	745					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(3)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCGCGGTGGGGAGCTGGTCG	0.652																																					p.G745V		.	.											.	PCDHA5	.	.	0			c.G2234T						.						66	61	63					5																	140203594		2203	4300	6503	SO:0001583	missense	56143	exon1			CGGTGGGGAGCTG	AF152483	CCDS54917.1	5q31	2010-11-26				ENSG00000204965		"Cadherins / Protocadherins : Clustered"	8671	other	complex locus constituent	"ortholog of mouse CNR6", "KIAA0345-like 9"	606311		CNRS6		10380929, 10662547	Standard	NM_018908		Approved	CNR6, CRNR6, CNRN6, PCDH-ALPHA5		Q9Y5H7		ENST00000529859.1:c.2234G>T	5.37:g.140203594G>T	ENSP00000436557:p.Gly745Val	88.0	0.0		129.0	16.0	NM_018908	O75284|Q8N4R3	Missense_Mutation	SNP	ENST00000529859.1	37	CCDS54917.1	.	.	.	.	.	.	.	.	.	.	G	16.75	3.208401	0.58343	.	.	ENSG00000204965	ENST00000529619;ENST00000529859;ENST00000378126	T;T;T	0.26518	1.73;1.73;1.73	3.92	3.05	0.35203	.	.	.	.	.	T	0.58308	0.2113	M	0.93375	3.41	0.47094	D	0.999312	D;D;D	0.76494	0.999;0.997;0.999	D;D;D	0.78314	0.98;0.991;0.982	T	0.67650	-0.5616	9	0.87932	D	0	.	11.7041	0.51587	0.0887:0.0:0.9113:0.0	.	745;745;745	Q9Y5H7;Q9Y5H7-3;Q9Y5H7-2	PCDA5_HUMAN;.;.	V	745	ENSP00000433416:G745V;ENSP00000436557:G745V;ENSP00000367366:G745V	ENSP00000367366:G745V	G	+	2	0	PCDHA5	140183778	0.999000	0.42202	1.000000	0.80357	0.744000	0.42396	2.866000	0.48420	0.761000	0.33130	0.491000	0.48974	GGG	.	.		0.652	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908		T	140203594	G	T	140203594	3	4	268	1	0	0	0	0	1	0	0	0	11536	1232	43	3	2236	3	PCDHA5	5	140203594	Missense_Mutation	SNP	G	TCGA-FV-A495-01A-11D-A25V-10	12516895	140203594	40711666	26	39088										
PCDHAC1	56135	hgsc.bcm.edu	37	chr5	140307840	140307840	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	cccagcaggaacttttcgttGctgaaaacaatggccctggg	11	11	0	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr5:140307840G>C	ENST00000253807.2	+	1	1363	c.1363G>C	c.(1363-1365)Gct>Cct	p.A455P	PCDHA1_ENST00000504120.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHAC1_ENST00000409700.3_Missense_Mutation_p.A455P|PCDHA4_ENST00000530339.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA10_ENST00000506939.2_Intron	NM_018898.3	NP_061721.2	Q9H158	PCDC1_HUMAN	protocadherin alpha subfamily C, 1	455	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|liver(2)|lung(13)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	65			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACTTTTCGTTGCTGAAAACAA	0.517																																					p.A455P		.	.											.	PCDHAC1	.	.	0			c.G1363C						.						64	69	67					5																	140307840		2203	4300	6503	SO:0001583	missense	56135	exon1			TTCGTTGCTGAAA	AF152473	CCDS4241.1	5q31	2010-11-26			ENSG00000248383	ENSG00000248383		"Cadherins / Protocadherins : Clustered"	8676	other	complex locus constituent	"PCDH-ALPHA-C1"	606320				10380929	Standard	NM_018898		Approved			Q9H158	OTTHUMG00000129603	ENST00000253807.2:c.1363G>C	5.37:g.140307840G>C	ENSP00000253807:p.Ala455Pro	34.0	0.0		57.0	6.0	NM_031882	Q9Y5F5|Q9Y5I5	Missense_Mutation	SNP	ENST00000253807.2	37	CCDS4241.1	.	.	.	.	.	.	.	.	.	.	G	9.142	1.014065	0.19277	.	.	ENSG00000248383	ENST00000409700;ENST00000253807	T;T	0.03330	3.97;3.97	5.54	5.54	0.83059	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.01940	0.0061	N	0.01438	-0.865	0.23464	N	0.997621	B;B	0.06786	0.001;0.0	B;B	0.12156	0.007;0.004	T	0.49513	-0.8932	9	0.22109	T	0.4	.	13.7462	0.62876	0.0735:0.0:0.9265:0.0	.	455;455	Q9H158;Q9H158-2	PCDC1_HUMAN;.	P	455	ENSP00000386356:A455P;ENSP00000253807:A455P	ENSP00000253807:A455P	A	+	1	0	PCDHAC1	140288024	0.003000	0.15002	1.000000	0.80357	0.934000	0.57294	0.556000	0.23438	2.599000	0.87857	0.462000	0.41574	GCT	.	.		0.517	PCDHAC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251798.1	NM_018898		C	140307840	G	C	140307840	3	2	268	1	0	0	0	0	1	0	0	0	11541	1319	46	4	1365	4	PCDHAC1	5	140307840	Missense_Mutation	SNP	G	TCGA-FV-A495-01A-11D-A25V-10	104246	140307840	40607420	27	39089										
ADRB2	154	hgsc.bcm.edu	37	chr5	148207094	148207094	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	aaaggcagctccagaagattGacaaatctgagggccgcttc	11	10	1	4			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr5:148207094G>C	ENST00000305988.4	+	1	939	c.700G>C	c.(700-702)Gac>Cac	p.D234H		NM_000024.5	NP_000015	P07550	ADRB2_HUMAN	adrenoceptor beta 2, surface	234					activation of adenylate cyclase activity (GO:0007190)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|bone resorption (GO:0045453)|brown fat cell differentiation (GO:0050873)|cell surface receptor signaling pathway (GO:0007166)|desensitization of G-protein coupled receptor protein signaling pathway by arrestin (GO:0002032)|diet induced thermogenesis (GO:0002024)|endosome to lysosome transport (GO:0008333)|heat generation (GO:0031649)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of smooth muscle contraction (GO:0045986)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor-mediated endocytosis (GO:0006898)|regulation of sodium ion transport (GO:0002028)|regulation of vasodilation (GO:0042312)|response to cold (GO:0009409)|vasodilation by norepinephrine-epinephrine involved in regulation of systemic arterial blood pressure (GO:0002025)	apical plasma membrane (GO:0016324)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	beta2-adrenergic receptor activity (GO:0004941)|norepinephrine binding (GO:0051380)|potassium channel regulator activity (GO:0015459)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(1)|lung(8)|ovary(1)|prostate(3)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Acebutolol(DB01193)|Alprenolol(DB00866)|Amitriptyline(DB00321)|Amphetamine(DB00182)|Arbutamine(DB01102)|Arformoterol(DB01274)|Asenapine(DB06216)|Atenolol(DB00335)|Bambuterol(DB01408)|Betaxolol(DB00195)|Bethanidine(DB00217)|Bevantolol(DB01295)|Bisoprolol(DB00612)|Bopindolol(DB08807)|Bupranolol(DB08808)|Cabergoline(DB00248)|Carteolol(DB00521)|Carvedilol(DB01136)|Clenbuterol(DB01407)|Desipramine(DB01151)|Dipivefrin(DB00449)|Dobutamine(DB00841)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Fenoterol(DB01288)|Formoterol(DB00983)|Indacaterol(DB05039)|Isoetarine(DB00221)|Isoprenaline(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Mephentermine(DB01365)|Metipranolol(DB01214)|Metoprolol(DB00264)|Mirtazapine(DB00370)|Nadolol(DB01203)|Nebivolol(DB04861)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Orciprenaline(DB00816)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Phenoxybenzamine(DB00925)|Phenylpropanolamine(DB00397)|Pindolol(DB00960)|Pirbuterol(DB01291)|Procaterol(DB01366)|Propranolol(DB00571)|Pseudoephedrine(DB00852)|Ritodrine(DB00867)|Salbutamol(DB01001)|Salmeterol(DB00938)|Sotalol(DB00489)|Terbutaline(DB00871)|Timolol(DB00373)|Trimipramine(DB00726)	CCAGAAGATTGACAAATCTGA	0.547																																					p.D234H		.	.											.	ADRB2	.	.	0			c.G700C						.						107	101	103					5																	148207094		2203	4300	6503	SO:0001583	missense	154	exon1			AAGATTGACAAAT	AF022953	CCDS4292.1	5q31-q32	2012-08-08	2012-05-09		ENSG00000169252	ENSG00000169252		"GPCR / Class A : Adrenoceptors : beta"	286	protein-coding gene	gene with protein product		109690	"adrenergic, beta-2-, receptor, surface"	ADRB2R			Standard	NM_000024		Approved	ADRBR, BAR, B2AR	uc003lpr.2	P07550	OTTHUMG00000129933	ENST00000305988.4:c.700G>C	5.37:g.148207094G>C	ENSP00000305372:p.Asp234His	80.0	0.0		106.0	40.0	NM_000024	B0LPE4|B2R7X2|O14823|O14824|O14825|O14826|Q4JG18|Q53GA6|Q6GMT4|Q6P4D8|Q8NEQ9|Q96EC3|Q9UCZ0|Q9UCZ1|Q9UCZ2|Q9UCZ3|Q9UH95|Q9UHA1|Q9UMZ5	Missense_Mutation	SNP	ENST00000305988.4	37	CCDS4292.1	.	.	.	.	.	.	.	.	.	.	G	17.67	3.446533	0.63178	.	.	ENSG00000169252	ENST00000305988	T	0.36520	1.25	5.44	5.44	0.79542	GPCR, rhodopsin-like superfamily (1);	0.097714	0.64402	D	0.000002	T	0.52240	0.1722	L	0.39898	1.24	0.54753	D	0.999989	D	0.67145	0.996	D	0.65010	0.931	T	0.51694	-0.8673	10	0.87932	D	0	.	19.4568	0.94895	0.0:0.0:1.0:0.0	.	234	P07550	ADRB2_HUMAN	H	234	ENSP00000305372:D234H	ENSP00000305372:D234H	D	+	1	0	ADRB2	148187287	1.000000	0.71417	0.997000	0.53966	0.722000	0.41435	6.600000	0.74132	2.832000	0.97577	0.655000	0.94253	GAC	.	.		0.547	ADRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252189.1	NM_000024		C	148207094	G	C	148207094	3	2	268	1	0	0	0	0	1	0	0	0	341	1290	45	4	702	4	ADRB2	5	148207094	Missense_Mutation	SNP	G	TCGA-FV-A495-01A-11D-A25V-10	7899254	148207094	32708166	28	39090										
GRIA1	2890	hgsc.bcm.edu	37	chr5	153085452	153085460	+	In_Frame_Del	DEL	GTGAGTGTT	GTGAGTGTT	-													0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	ttgtttttgcctacattggaGtgagtgttgtcctcttcctg							TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	GTGAGTGTT	GTGAGTGTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr5:153085452_153085460delGTGAGTGTT	ENST00000285900.5	+	11	1991_1999	c.1648_1656delGTGAGTGTT	c.(1648-1656)gtgagtgttdel	p.VSV550del	GRIA1_ENST00000518142.1_In_Frame_Del_p.VSV470del|GRIA1_ENST00000518783.1_In_Frame_Del_p.VSV560del|GRIA1_ENST00000521843.2_In_Frame_Del_p.VSV481del|GRIA1_ENST00000340592.5_In_Frame_Del_p.VSV550del|GRIA1_ENST00000448073.4_In_Frame_Del_p.VSV560del	NM_000827.3|NM_001258019.1	NP_000818.2|NP_001244948.1	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1	550					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|axonal spine (GO:0044308)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|neuron spine (GO:0044309)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|PDZ domain binding (GO:0030165)			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)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Perampanel(DB08883)|Sevoflurane(DB01236)	CTACATTGGAGTGAGTGTTGTCCTCTTCC	0.469																																					p.559_562del		.	.											.	GRIA1	.	.	0			c.1677_1685del						.																																			SO:0001651	inframe_deletion	2890	exon11			.		CCDS4322.1, CCDS47318.1, CCDS58986.1, CCDS58987.1, CCDS58988.1, CCDS58989.1	5q33	2012-08-29			ENSG00000155511	ENSG00000155511		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4571	protein-coding gene	gene with protein product		138248		GLUR1		1652753, 1319477	Standard	NM_000827		Approved	GluA1, GLURA	uc011dcy.2	P42261	OTTHUMG00000130148	ENST00000285900.5:c.1648_1656delGTGAGTGTT	5.37:g.153085452_153085460delGTGAGTGTT	ENSP00000285900:p.Val550_Val552del	271.0	0.0		378.0	34.0	NM_001258021	B7Z2S0|B7Z2W8|B7Z3F6|B7Z9G9|D3DQI4|E7ESV8|Q2NKM6	In_Frame_Del	DEL	ENST00000285900.5	37	CCDS4322.1																																																																																			.	.		0.469	GRIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252456.3			-	153085460	GTGAGTGTT	-	153085452	7	5	268	1	0	1	0	1	0	0	0	0	6776	1029	36	0	1690	0	GRIA1	5	153085452	In_Frame_Del	DEL	GTGAGTGTT	TCGA-FV-A495-01A-11D-A25V-10	4878358	153085452	27829808	29	39091										
DOK3	79930	hgsc.bcm.edu	37	chr5	176931755	176931755	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	gcacctcaccttgtcggagcCgaacttgcgcaggaagtggt	13	12	1	0			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr5:176931755C>T	ENST00000357198.4	-	5	806	c.802G>A	c.(802-804)Ggc>Agc	p.G268S	DOK3_ENST00000312943.6_Missense_Mutation_p.G212S|RP11-1334A24.6_ENST00000506025.1_RNA|DOK3_ENST00000501403.2_Missense_Mutation_p.G212S|DOK3_ENST00000377112.4_Missense_Mutation_p.G110S	NM_024872.2	NP_079148.2	Q7L591	DOK3_HUMAN	docking protein 3	268	IRS-type PTB. {ECO:0000255|PROSITE- ProRule:PRU00389}.				Ras protein signal transduction (GO:0007265)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|lung(7)	13	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.191)			TTGTCGGAGCCGAACTTGCGC	0.682																																					p.G268S		.	.											.	DOK3	.	.	0			c.G802A						.						50	56	54					5																	176931755		2202	4299	6501	SO:0001583	missense	79930	exon5			CGGAGCCGAACTT	AK026223	CCDS4426.1, CCDS47349.1, CCDS47350.1	5q35	2008-02-05			ENSG00000146094	ENSG00000146094			24583	protein-coding gene	gene with protein product		611435				10733577, 12595900	Standard	NM_024872		Approved	FLJ22570	uc003mhk.3	Q7L591	OTTHUMG00000130850	ENST00000357198.4:c.802G>A	5.37:g.176931755C>T	ENSP00000349727:p.Gly268Ser	101.0	0.0		135.0	28.0	NM_024872	E9PAT0|H7BXS0|Q8N864|Q9BQB3|Q9H666	Missense_Mutation	SNP	ENST00000357198.4	37	CCDS4426.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.644690	0.87859	.	.	ENSG00000146094	ENST00000312943;ENST00000377112;ENST00000357198;ENST00000501403;ENST00000510380	D;D;D;D;D	0.93763	-3.28;-3.28;-3.28;-3.28;-3.28	4.83	4.83	0.62350	Pleckstrin homology-type (1);Insulin receptor substrate-1, PTB (3);	0.000000	0.64402	D	0.000014	D	0.97170	0.9075	M	0.90542	3.125	0.52099	D	0.999947	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;0.999;1.0	D	0.98104	1.0416	10	0.87932	D	0	-8.5005	15.681	0.77367	0.0:1.0:0.0:0.0	.	268;110;212;98	Q7L591;E9PAT0;Q7L591-3;Q7L591-2	DOK3_HUMAN;.;.;.	S	212;110;268;212;212	ENSP00000325174:G212S;ENSP00000366316:G110S;ENSP00000349727:G268S;ENSP00000421688:G212S;ENSP00000422395:G212S	ENSP00000325174:G212S	G	-	1	0	DOK3	176864361	1.000000	0.71417	1.000000	0.80357	0.634000	0.38068	6.198000	0.72106	2.216000	0.71823	0.491000	0.48974	GGC	.	.		0.682	DOK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253420.4	NM_024872		T	176931755	C	T	176931755	3	4	268	1	0	0	0	0	1	0	0	0	4700	652	23	1	1048	1	DOK3	5	176931755	Missense_Mutation	SNP	C	TCGA-FV-A495-01A-11D-A25V-10	23846303	176931755	3983505	30	39092										
PRSS16	10279	hgsc.bcm.edu	37	chr6	27220730	27220730	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	tgtaccgagttcggcttctgTaagtgactggcctaacccta	10	11	1	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr6:27220730T>C	ENST00000230582.3	+	9	1165		c.e9+2		PRSS16_ENST00000421826.2_Splice_Site|PRSS16_ENST00000377456.2_Intron	NM_005865.3	NP_005856.1	Q9NQE7	TSSP_HUMAN	protease, serine, 16 (thymus)						protein catabolic process (GO:0030163)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|lysosome (GO:0005764)	serine-type peptidase activity (GO:0008236)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	26						TCGGCTTCTGTAAGTGACTGG	0.512																																					.	NSCLC(178;1118 2105 17078 23587 44429)	.	.											.	PRSS16	.	.	0			c.1150+2T>C						.						199	170	180					6																	27220730		2203	4300	6503	SO:0001630	splice_region_variant	10279	exon9			CTTCTGTAAGTGA	AF052514	CCDS4623.1	6p21	2010-05-07			ENSG00000112812	ENSG00000112812		"Serine peptidases / Serine peptidases"	9480	protein-coding gene	gene with protein product		607169				10527559	Standard	NM_005865		Approved	TSSP	uc003nja.3	Q9NQE7	OTTHUMG00000016167	ENST00000230582.3:c.1150+2T>C	6.37:g.27220730T>C		133.0	0.0		166.0	12.0	NM_005865	O75416	Splice_Site	SNP	ENST00000230582.3	37	CCDS4623.1	.	.	.	.	.	.	.	.	.	.	T	16.52	3.146248	0.57044	.	.	ENSG00000112812	ENST00000421826;ENST00000230582;ENST00000343467;ENST00000485993;ENST00000475106	.	.	.	4.26	4.26	0.50523	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.6381	0.51215	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	PRSS16	27328709	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	3.912000	0.56386	1.927000	0.55829	0.460000	0.39030	.	.	.		0.512	PRSS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043418.2		Intron	C	27220730	T	C	27220730	5	2	268	1	0	0	0	0	0	0	1	0	12628	1652	57	2	1186	2	PRSS16	6	27220730	Splice_Site	SNP	T	TCGA-FV-A495-01A-11D-A25V-10		27220730	143894337	31	39093										
MICA	100507436	hgsc.bcm.edu	37	chr6	31378413	31378413	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	ggtacatctggatggtcagcCcttcctgcgctatgacaggc	12	12	2	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr6:31378413C>T	ENST00000449934.2	+	2	218	c.164C>T	c.(163-165)cCc>cTc	p.P55L	HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				GATGGTCAGCCCTTCCTGCGC	0.557																																					p.P55L		.	.											.	.	.	.	0			c.C164T						.						33	36	35					6																	31378413		692	1591	2283	SO:0001583	missense	100507436	exon2			GTCAGCCCTTCCT	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"Immunoglobulin superfamily / C1-set domain containing"	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	ENST00000449934.2:c.164C>T	6.37:g.31378413C>T	ENSP00000413079:p.Pro55Leu	217.0	0.0		235.0	56.0	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	.	.	.	.	.	.	.	.	.	.	N	1.771	-0.484375	0.04383	.	.	ENSG00000204520	ENST00000364810;ENST00000399172;ENST00000449934;ENST00000421350	T;T	0.00675	5.88;5.88	2.89	-3.87	0.04218	.	2.158990	0.02591	N	0.099933	T	0.00178	0.0005	N	0.05230	-0.09	0.09310	N	1	B	0.24533	0.105	B	0.21708	0.036	T	0.44772	-0.9306	10	0.66056	D	0.02	.	3.6447	0.08180	0.1773:0.4171:0.0:0.4056	.	55	Q96QC4	.	L	55;55;55;42	ENSP00000413079:P55L;ENSP00000402410:P42L	ENSP00000365394:P55L	P	+	2	0	MICA	31486392	0.000000	0.05858	0.000000	0.03702	0.074000	0.17049	-2.758000	0.00787	-0.905000	0.03871	-0.818000	0.03119	CCC	.	.		0.557	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519		T	31378413	C	T	31378413	3	4	268	1	0	0	0	0	1	0	0	0	9577	623	22	3	170	3	MICA	6	31378413	Missense_Mutation	SNP	C	TCGA-FV-A495-01A-11D-A25V-10	4157683	31378413	139736654	32	39094										
KCNK16	83795	hgsc.bcm.edu	37	chr6	39285579	39285579	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	tacctgggagcgcctgggacGgtcctcccatctttcaatgg	12	13	2	0			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr6:39285579G>T	ENST00000373229.5	-	3	491	c.478C>A	c.(478-480)Cgt>Agt	p.R160S	KCNK16_ENST00000437525.2_Missense_Mutation_p.R160S|KCNK16_ENST00000425054.2_Missense_Mutation_p.R160S|KCNK16_ENST00000373227.4_Missense_Mutation_p.R160S|KCNK16_ENST00000507712.1_Missense_Mutation_p.R95S	NM_032115.3	NP_115491.1	Q96T55	KCNKG_HUMAN	potassium channel, subfamily K, member 16	160					potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)	13						CGCCTGGGACGGTCCTCCCAT	0.592																																					p.R160S		.	.											.	KCNK16	.	.	0			c.C478A						.						34	33	33					6																	39285579		2203	4299	6502	SO:0001583	missense	83795	exon3			TGGGACGGTCCTC	AF358909	CCDS4843.1, CCDS47420.1, CCDS47421.1, CCDS47422.1	6p21.2-p21.1	2012-03-07			ENSG00000095981	ENSG00000095981		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	14464	protein-coding gene	gene with protein product		607369				11263999, 16382106	Standard	NM_032115		Approved	K2p16.1, TALK-1, TALK1	uc003ooq.3	Q96T55	OTTHUMG00000014645	ENST00000373229.5:c.478C>A	6.37:g.39285579G>T	ENSP00000362326:p.Arg160Ser	66.0	0.0		103.0	30.0	NM_001135106	B5TJL9|Q2M2N9|Q5TCF3|Q6X6Z3|Q6X6Z4|Q6X6Z5|Q9H591	Missense_Mutation	SNP	ENST00000373229.5	37	CCDS4843.1	.	.	.	.	.	.	.	.	.	.	G	11.08	1.533589	0.27387	.	.	ENSG00000095981	ENST00000373229;ENST00000425054;ENST00000507712;ENST00000373227;ENST00000437525	T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96	5.35	3.54	0.40534	.	0.993224	0.08190	N	0.983964	T	0.09555	0.0235	N	0.10733	0.035	0.09310	N	1	B;B;B;B	0.18610	0.002;0.029;0.001;0.001	B;B;B;B	0.15484	0.001;0.013;0.003;0.001	T	0.35126	-0.9801	10	0.46703	T	0.11	.	8.1516	0.31143	0.0763:0.0:0.5902:0.3334	.	160;160;160;160	B5TJL9;Q96T55-5;Q96T55-4;Q96T55	.;.;.;KCNKG_HUMAN	S	160;160;95;160;160	ENSP00000362326:R160S;ENSP00000391498:R160S;ENSP00000423842:R95S;ENSP00000362324:R160S;ENSP00000415375:R160S	ENSP00000362324:R160S	R	-	1	0	KCNK16	39393557	0.935000	0.31712	0.997000	0.53966	0.856000	0.48823	1.792000	0.38754	0.617000	0.30160	0.561000	0.74099	CGT	.	.		0.592	KCNK16-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040452.2	NM_032115		T	39285579	G	T	39285579	3	4	268	1	0	0	0	0	1	0	0	0	8072	1116	39	1	852	1	KCNK16	6	39285579	Missense_Mutation	SNP	G	TCGA-FV-A495-01A-11D-A25V-10	7907166	39285579	131829488	33	39095										
CUL9	23113	hgsc.bcm.edu	37	chr6	43181019	43181022	+	Frame_Shift_Del	DEL	TCAA	TCAA	-													0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	gatgtggctgctgctgaaatTcaatcagacagaggtgcttc							TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	TCAA	TCAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr6:43181019_43181022delTCAA	ENST00000252050.4	+	27	5429_5432	c.5345_5348delTCAA	c.(5344-5349)ttcaatfs	p.FN1782fs	CUL9_ENST00000502937.1_3'UTR|CUL9_ENST00000354495.3_Frame_Shift_Del_p.FN1672fs|CUL9_ENST00000372647.2_Frame_Shift_Del_p.FN1782fs|RP3-330M21.5_ENST00000500590.1_RNA	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	1782					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						CTGCTGAAATTCAATCAGACAGAG	0.549																																					p.1782_1783del		.	.											.	CUL9-529	.	.	0			c.5344_5347del						.																																			SO:0001589	frameshift_variant	23113	exon27			.	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"parkin-like cytoplasmic p53 binding protein", "p53-associated parkin-like cytoplasmic protein"	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.5345_5348delTCAA	6.37:g.43181019_43181022delTCAA	ENSP00000252050:p.Phe1782fs	120.0	0.0		116.0	20.0	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Frame_Shift_Del	DEL	ENST00000252050.4	37	CCDS4890.1																																																																																			.	.		0.549	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		-	43181022	TCAA	-	43181019	7	5	268	1	0	1	0	1	0	0	0	0	4063	1783	62	0	5447	0	CUL9	6	43181019	Frame_Shift_Del	DEL	TCAA	TCGA-FV-A495-01A-11D-A25V-10	3895440	43181019	127934048	34	39096										
YIPF3	25844	hgsc.bcm.edu	37	chr6	43480544	43480544	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	accaacagccagaagaggtaGaagagggcgtggaggtggat	17	6	0	4			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr6:43480544G>C	ENST00000372422.2	-	7	917	c.735C>G	c.(733-735)ttC>ttG	p.F245L	YIPF3_ENST00000506469.1_Missense_Mutation_p.F251L|LRRC73_ENST00000372441.1_5'Flank	NM_015388.3	NP_056203.2	Q9GZM5	YIPF3_HUMAN	Yip1 domain family, member 3	245					cell differentiation (GO:0030154)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)				large_intestine(2)|lung(4)|pancreas(1)|prostate(1)|skin(1)	9	all_cancers(18;3.79e-05)|Lung NSC(15;0.00217)|all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00736)|OV - Ovarian serous cystadenocarcinoma(102;0.0711)			AGAAGAGGTAGAAGAGGGCGT	0.557																																					p.F245L		.	.											.	YIPF3	.	.	0			c.C735G						.						101	86	91					6																	43480544		2203	4300	6503	SO:0001583	missense	25844	exon7			GAGGTAGAAGAGG	AK000946	CCDS4899.1	6p21.1	2009-10-06	2005-07-04	2005-07-04	ENSG00000137207	ENSG00000137207		"Yip1 domain family"	21023	protein-coding gene	gene with protein product		609775	"chromosome 6 open reading frame 109"	C6orf109			Standard	NM_015388		Approved	DKFZp566C243, KLIP1, dJ337H4.3, FinGER3	uc003ovl.2	Q9GZM5	OTTHUMG00000014738	ENST00000372422.2:c.735C>G	6.37:g.43480544G>C	ENSP00000361499:p.Phe245Leu	155.0	0.0		190.0	37.0	NM_015388	Q5JTD2|Q6FI85|Q8NI57|Q9NWE3|Q9Y3U9	Missense_Mutation	SNP	ENST00000372422.2	37	CCDS4899.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.027438	0.75390	.	.	ENSG00000137207	ENST00000372422;ENST00000506469;ENST00000503972	T;T;T	0.48836	0.81;0.8;1.02	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.59649	0.2209	M	0.73962	2.25	0.80722	D	1	D;D;D	0.56035	0.974;0.974;0.974	D;D;D	0.70487	0.969;0.953;0.969	T	0.64702	-0.6345	10	0.87932	D	0	-16.1626	11.9234	0.52806	0.1263:0.0:0.8737:0.0	.	251;210;245	E7EQR8;Q5JTD5;Q9GZM5	.;.;YIPF3_HUMAN	L	245;251;211	ENSP00000361499:F245L;ENSP00000425494:F251L;ENSP00000421461:F211L	ENSP00000361499:F245L	F	-	3	2	YIPF3	43588522	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	4.644000	0.61397	2.467000	0.83353	0.563000	0.77884	TTC	.	.		0.557	YIPF3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040639.2	NM_015388		C	43480544	G	C	43480544	3	2	268	1	0	0	0	0	1	0	0	0	17494	933	33	4	329	4	YIPF3	6	43480544	Missense_Mutation	SNP	G	TCGA-FV-A495-01A-11D-A25V-10	299525	43480544	127634523	35	39097										
C6orf170	221322	hgsc.bcm.edu	37	chr6	121625734	121625734	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	gctgaaagagtaggaatatgAttttccctagaaagaaagta	10	4	0	5			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr6:121625734A>G	ENST00000398212.2	-	7	856	c.807T>C	c.(805-807)aaT>aaC	p.N269N	TBC1D32_ENST00000275159.6_Silent_p.N269N	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	269					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)										TAGGAATATGATTTTCCCTAG	0.284																																					p.N269N		.	.											.	C6orf170	.	.	0			c.T807C						.						62	60	61					6																	121625734		1812	4067	5879	SO:0001819	synonymous_variant	221322	exon7			AATATGATTTTCC	AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"broad-minded homolog"	615867	"chromosome 6 open reading frame 171", "chromosome 6 open reading frame 170"	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.807T>C	6.37:g.121625734A>G		76.0	0.0		60.0	10.0	NM_152730	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Silent	SNP	ENST00000398212.2	37	CCDS43501.1																																																																																			.	.		0.284	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730		G	121625734	A	G	121625734	2	3	268	1	0	0	0	0	0	0	0	1	2346	330	12	2		2	C6orf170	6	121625734	Silent	SNP	A	TCGA-FV-A495-01A-11D-A25V-10	78145190	121625734	49489333	36	39098										
KIAA1244	57221	hgsc.bcm.edu	37	chr6	138640960	138640960	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	ctctgccaatttcaagcacgCtattggtctgtcctgtgagc	9	12	3	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr6:138640960C>T	ENST00000251691.4	+	28	4761	c.4595C>T	c.(4594-4596)gCt>gTt	p.A1532V		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		TTCAAGCACGCTATTGGTCTG	0.502																																					p.A1532V		.	.											.	KIAA1244	.	.	0			c.C4595T						.						146	138	140					6																	138640960		2203	4300	6503	SO:0001583	missense	57221	exon28			AGCACGCTATTGG	AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	21213	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 33"		"chromosome 6 open reading frame 92"	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.4595C>T	6.37:g.138640960C>T	ENSP00000251691:p.Ala1532Val	168.0	0.0		182.0	61.0	NM_020340		Missense_Mutation	SNP	ENST00000251691.4	37	CCDS5189.2	.	.	.	.	.	.	.	.	.	.	C	28.3	4.907619	0.92107	.	.	ENSG00000112379	ENST00000251691	T	0.21031	2.03	5.4	5.4	0.78164	.	0.053335	0.85682	D	0.000000	T	0.36524	0.0970	L	0.53249	1.67	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.05989	-1.0852	10	0.59425	D	0.04	-30.519	19.5504	0.95315	0.0:1.0:0.0:0.0	.	1532	Q5TH69	BIG3_HUMAN	V	1532	ENSP00000251691:A1532V	ENSP00000251691:A1532V	A	+	2	0	KIAA1244	138682653	1.000000	0.71417	1.000000	0.80357	0.816000	0.46133	7.600000	0.82769	2.688000	0.91661	0.655000	0.94253	GCT	.	.		0.502	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340		T	138640960	C	T	138640960	3	4	268	1	0	0	0	0	1	0	0	0	8226	797	28	3	4705	3	KIAA1244	6	138640960	Missense_Mutation	SNP	C	TCGA-FV-A495-01A-11D-A25V-10	17015226	138640960	32474107	37	39099										
TARP	6966	hgsc.bcm.edu	37	chr7	38305036	38305036	+	RNA	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	tacatctgtgttctttgtccAgtgacttttctggcaccgtt	8	10	3	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr7:38305036A>G	ENST00000443402.2	-	0	243					NM_001003799.1|NM_001003806.1	NP_001003799.1|NP_001003806.1	P0CF51	TRGC1_HUMAN	T cell receptor gamma constant 1							integral component of membrane (GO:0016021)											TTCTTTGTCCAGTGACTTTTC	0.408																																					p.L20P		.	.											.	.	.	.	0			c.T59C						.						192	180	184					7																	38305036		1844	4101	5945			0	exon2			TTGTCCAGTGACT	M14996		7p14	2012-02-07			ENSG00000211689	ENSG00000211689		"T cell receptors / TRG locus"	12275	other	T cell receptor gene	"T-cell receptor, gamma, constant region C1"	186970		TCRGC1		2879283	Standard	NG_001336		Approved	C1		P0CF51	OTTHUMG00000155219		7.37:g.38305036A>G		181.0	0.0		240.0	65.0	NM_001003806		Missense_Mutation	SNP	ENST00000443402.2	37																																																																																				.	.		0.408	TRGC1-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	TR_C_gene	TR_C_gene	OTTHUMT00000338825.3	NG_001336		G	38305036	A	G	38305036	1	3	268	0	1	0	0	0	0	0	0	0	15573	188	7	2		2	TARP	7	38305036	RNA	SNP	A	TCGA-FV-A495-01A-11D-A25V-10		38305036	120833627	38	39100										
GLI3	2737	hgsc.bcm.edu	37	chr7	42262748	42262748	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	ccattagaagtggtgctggaGgcaacggctttctcgctcac	12	11	2	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr7:42262748G>A	ENST00000395925.3	-	2	189	c.105C>T	c.(103-105)gcC>gcT	p.A35A	GLI3_ENST00000437480.1_Silent_p.A35A	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	35					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						TGGTGCTGGAGGCAACGGCTT	0.507									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																												p.A35A		.	.											.	GLI3	.	.	0			c.C105T						.						215	200	205					7																	42262748		2203	4300	6503	SO:0001819	synonymous_variant	2737	exon2	Familial Cancer Database	;	GCTGGAGGCAACG		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"Zinc fingers, C2H2-type"	4319	protein-coding gene	gene with protein product	"zinc finger protein GLI3", "oncogene GLI3", "DNA-binding protein"	165240	"Greig cephalopolysyndactyly syndrome", "GLI-Kruppel family member GLI3", "glioma-associated oncogene family zinc finger 3"	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.105C>T	7.37:g.42262748G>A		96.0	0.0		81.0	23.0	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Silent	SNP	ENST00000395925.3	37	CCDS5465.1																																																																																			.	.		0.507	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168		A	42262748	G	A	42262748	2	1	268	1	0	0	0	0	0	0	0	1	6447	987	35	3		3	GLI3	7	42262748	Silent	SNP	G	TCGA-FV-A495-01A-11D-A25V-10	3957712	42262748	116875915	39	39101										
PAX4	5078	hgsc.bcm.edu	37	chr7	127255087	127255087	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	ttgcttcccccaatgcccttTggctccaagacacctgtgcg	8	16	0	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr7:127255087T>C	ENST00000341640.2	-	2	388	c.183A>G	c.(181-183)ccA>ccG	p.P61P	PAX4_ENST00000378740.2_Silent_p.P61P|PAX4_ENST00000463946.1_Silent_p.P59P|PAX4_ENST00000338516.3_Silent_p.P69P	NM_006193.2	NP_006184.2	O43316	PAX4_HUMAN	paired box 4	69	Paired. {ECO:0000255|PROSITE- ProRule:PRU00381}.				cell differentiation (GO:0030154)|circadian rhythm (GO:0007623)|endocrine pancreas development (GO:0031018)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|positive regulation of cell differentiation (GO:0045597)|response to cAMP (GO:0051591)|response to drug (GO:0042493)|retina development in camera-type eye (GO:0060041)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)			cervix(1)|kidney(2)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35						CAATGCCCTTTGGCTCCAAGA	0.572																																					p.P61P	Ovarian(113;737 1605 7858 27720 34092)	.	.											.	PAX4	.	.	0			c.A183G						.						100	93	95					7																	127255087		2203	4300	6503	SO:0001819	synonymous_variant	5078	exon2			GCCCTTTGGCTCC		CCDS5797.1	7q32.1	2011-06-20	2007-07-12		ENSG00000106331	ENSG00000106331		"Paired boxes", "Homeoboxes / PRD class"	8618	protein-coding gene	gene with protein product		167413	"paired box gene 4"				Standard	NM_006193		Approved	MODY9	uc010lld.1	O43316	OTTHUMG00000157562	ENST00000341640.2:c.183A>G	7.37:g.127255087T>C		70.0	0.0		86.0	6.0	NM_006193	O95161|Q6B0H0	Silent	SNP	ENST00000341640.2	37	CCDS5797.1																																																																																			.	.		0.572	PAX4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349165.1			C	127255087	T	C	127255087	2	2	268	1	0	0	0	0	0	0	0	1	11490	1799	63	2		2	PAX4	7	127255087	Silent	SNP	T	TCGA-FV-A495-01A-11D-A25V-10	84992339	127255087	31883576	40	39102										
BMP1	649	hgsc.bcm.edu	37	chr8	22052004	22052004	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	gactatggccacattcaatcGcccaactacccagacgatta	6	14	1	1	rs199778498		TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr8:22052004G>A	ENST00000306385.5	+	11	2014	c.1344G>A	c.(1342-1344)tcG>tcA	p.S448S	BMP1_ENST00000306349.8_Silent_p.S448S|BMP1_ENST00000397814.3_Silent_p.S448S|BMP1_ENST00000397816.3_Silent_p.S448S|BMP1_ENST00000354870.5_3'UTR	NM_006129.4	NP_006120.1	P13497	BMP1_HUMAN	bone morphogenetic protein 1	448	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lipoprotein metabolic process (GO:0042157)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of cartilage development (GO:0061036)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(3)	30				Colorectal(74;0.00229)|COAD - Colon adenocarcinoma(73;0.0661)|READ - Rectum adenocarcinoma(644;0.11)		ACATTCAATCGCCCAACTACC	0.582													G|||	1	0.000199681	8e-04	0	5008	,	,		18059	0		0	False		,,,				2504	0				p.S448S		.	.											.	BMP1	.	.	0			c.G1344A						.						123	112	116					8																	22052004		2203	4300	6503	SO:0001819	synonymous_variant	649	exon11			TCAATCGCCCAAC		CCDS6026.1, CCDS34856.1	8p21	2013-02-06	2004-08-09		ENSG00000168487	ENSG00000168487	3.4.24.19	"Bone morphogenetic proteins"	1067	protein-coding gene	gene with protein product	"procollagen C-endopeptidase"	112264	"procollagen C-endopeptidase"	PCOLC		2004778	Standard	NM_006129		Approved		uc003xbg.3	P13497	OTTHUMG00000097761	ENST00000306385.5:c.1344G>A	8.37:g.22052004G>A		131.0	0.0		120.0	51.0	NM_001199	A8K6F5|B2RN46|D3DSR0|Q13292|Q13872|Q14874|Q99421|Q99422|Q99423|Q9UL38	Silent	SNP	ENST00000306385.5	37	CCDS6026.1																																																																																			G|0.999;A|0.000	.		0.582	BMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214995.2	NM_006132		A	22052004	G	A	22052004	2	1	268	1	0	0	0	0	0	0	0	1	1456	1074	38	1		1	BMP1	8	22052004	Silent	SNP	G	TCGA-FV-A495-01A-11D-A25V-10		22052004	124312018	41	39103										
SLC7A13	157724	hgsc.bcm.edu	37	chr8	87235302	87235302	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	acgcagtaaatatgcatttgGgaattgttgttctgggcttc	11	6	1	0			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr8:87235302G>A	ENST00000297524.3	-	2	819	c.716C>T	c.(715-717)cCc>cTc	p.P239L	SLC7A13_ENST00000419776.2_Missense_Mutation_p.P230L|SLC7A13_ENST00000520624.1_5'UTR	NM_138817.2	NP_620172.2	Q8TCU3	S7A13_HUMAN	solute carrier family 7 (anionic amino acid transporter), member 13	239						integral component of membrane (GO:0016021)	amino acid transmembrane transporter activity (GO:0015171)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	45						TATGCATTTGGGAATTGTTGT	0.353																																					p.P239L		.	.											.	SLC7A13	.	.	0			c.C716T						.						144	149	147					8																	87235302		2203	4300	6503	SO:0001583	missense	157724	exon2			CATTTGGGAATTG	AJ417661	CCDS34917.1	8q21.3	2013-07-15	2011-07-12		ENSG00000164893	ENSG00000164893		"Solute carriers"	23092	protein-coding gene	gene with protein product						11907033, 11943479	Standard	XM_005250804		Approved	AGT-1, XAT2	uc003ydq.1	Q8TCU3	OTTHUMG00000163663	ENST00000297524.3:c.716C>T	8.37:g.87235302G>A	ENSP00000297524:p.Pro239Leu	63.0	0.0		87.0	22.0	NM_138817	Q05C37|Q08AH9|Q96N84	Missense_Mutation	SNP	ENST00000297524.3	37	CCDS34917.1	.	.	.	.	.	.	.	.	.	.	G	16.39	3.109520	0.56398	.	.	ENSG00000164893	ENST00000297524;ENST00000419776	D;D	0.91740	-2.9;-2.9	4.23	0.0393	0.14204	Amino acid permease domain (1);	0.337202	0.25596	N	0.029592	D	0.94706	0.8292	M	0.86178	2.8	0.22728	N	0.998808	P;D	0.67145	0.808;0.996	P;D	0.67382	0.517;0.951	D	0.88177	0.2868	10	0.66056	D	0.02	.	8.1044	0.30877	0.3936:0.0:0.6064:0.0	.	230;239	Q8TCU3-2;Q8TCU3	.;S7A13_HUMAN	L	239;230	ENSP00000297524:P239L;ENSP00000410982:P230L	ENSP00000297524:P239L	P	-	2	0	SLC7A13	87304418	0.868000	0.29978	0.003000	0.11579	0.501000	0.33797	1.038000	0.30254	0.053000	0.16036	0.557000	0.71058	CCC	.	.		0.353	SLC7A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374704.1	NM_138817		A	87235302	G	A	87235302	3	1	268	1	0	0	0	0	1	0	0	0	14710	1232	43	3	708	3	SLC7A13	8	87235302	Missense_Mutation	SNP	G	TCGA-FV-A495-01A-11D-A25V-10	65183298	87235302	59128720	42	39104										
FAM82B	51115	hgsc.bcm.edu	37	chr8	87492510	87492511	+	Frame_Shift_Ins	INS	-	-	A													0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	aagaaattttcttaccaaatINSacccataaggtgaattgaag							TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr8:87492510_87492511insA	ENST00000406452.3	-	6	795_796	c.636_637insT	c.(634-639)ggtattfs	p.I213fs	RMDN1_ENST00000519966.1_Frame_Shift_Ins_p.I183fs|RMDN1_ENST00000430676.2_Frame_Shift_Ins_p.I183fs|RMDN1_ENST00000523911.1_Frame_Shift_Ins_p.I169fs	NM_016033.2	NP_057117.2	Q96DB5	RMD1_HUMAN	regulator of microtubule dynamics 1	213						microtubule (GO:0005874)|mitochondrion (GO:0005739)											TCTTACCAAATACCCATAAGGT	0.238																																					p.I213fs		.	.											.	.	.	.	0			c.637_638insT						.																																			SO:0001589	frameshift_variant	51115	exon6			.	AK000672	CCDS34918.1, CCDS69509.1, CCDS69510.1	8q21.3	2013-01-11	2013-01-11	2013-01-11	ENSG00000176623	ENSG00000176623			24285	protein-coding gene	gene with protein product		611871	"family with sequence similarity 82, member B"	FAM82B		10810093	Standard	NM_016033		Approved	CGI-90, FLJ20665, RMD1	uc003ydu.3	Q96DB5	OTTHUMG00000163692	ENST00000406452.3:c.637dupT	8.37:g.87492511_87492511dupA	ENSP00000385927:p.Ile213fs	112.0	0.0		111.0	34.0	NM_016033	A9UMZ8|B4DNF5|B4DZW6|B5MC61|C9JSC6|E7EVI2|Q9Y398	Frame_Shift_Ins	INS	ENST00000406452.3	37	CCDS34918.1																																																																																			.	.		0.238	RMDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374770.2	NM_016033		A	87492511	-	A	87492510	7	5	268	1	0	1	1	0	0	0	0	0	5640	1406	49	0	327	0	FAM82B	8	87492510	Frame_Shift_Ins	INS	-	TCGA-FV-A495-01A-11D-A25V-10	257208	87492510	58871512	43	39105										
DECR1	1666	hgsc.bcm.edu	37	chr8	91031397	91031397	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	atcaaagttgcaggacatccTaatgtaagtgtagcaatgat	9	6	1	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr8:91031397T>C	ENST00000220764.2	+	4	502	c.414T>C	c.(412-414)ccT>ccC	p.P138P	DECR1_ENST00000522161.1_Silent_p.P129P|DECR1_ENST00000519007.1_3'UTR	NM_001359.1	NP_001350.1	Q16698	DECR_HUMAN	2,4-dienoyl CoA reductase 1, mitochondrial	138					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	2,4-dienoyl-CoA reductase (NADPH) activity (GO:0008670)|NADPH binding (GO:0070402)|oxidoreductase activity, acting on NAD(P)H (GO:0016651)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	15			BRCA - Breast invasive adenocarcinoma(11;0.00953)			CAGGACATCCTAATGTAAGTG	0.373																																					p.P138P		.	.											.	DECR1	.	.	0			c.T414C						.						126	106	113					8																	91031397		2203	4300	6503	SO:0001819	synonymous_variant	1666	exon4			ACATCCTAATGTA	L26050	CCDS6250.1	8q21.3	2011-09-14			ENSG00000104325	ENSG00000104325		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	2753	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 18C, member 1"	222745		DECR		7818482, 19027726	Standard	NM_001359		Approved	SDR18C1	uc003yek.1	Q16698	OTTHUMG00000163829	ENST00000220764.2:c.414T>C	8.37:g.91031397T>C		78.0	0.0		106.0	37.0	NM_001359	B7Z6B8|Q2M304|Q93085	Silent	SNP	ENST00000220764.2	37	CCDS6250.1																																																																																			.	.		0.373	DECR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375822.1			C	91031397	T	C	91031397	2	2	268	1	0	0	0	0	0	0	0	1	4384	1509	53	2		2	DECR1	8	91031397	Silent	SNP	T	TCGA-FV-A495-01A-11D-A25V-10	3538887	91031397	55332625	44	39106										
RGS22	26166	hgsc.bcm.edu	37	chr8	100994297	100994297	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	aagcagttgataatagttgtAatcttcttctggatgacaga	9	5	3	3			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr8:100994297A>G	ENST00000360863.6	-	22	3422	c.3228T>C	c.(3226-3228)atT>atC	p.I1076I	RGS22_ENST00000523437.1_Silent_p.I1064I|RGS22_ENST00000523287.1_Silent_p.I895I	NM_015668.3	NP_056483.3	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22	1076	RGS 2. {ECO:0000255|PROSITE- ProRule:PRU00171}.				positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)		RGS22/SYCP1(2)	breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(33)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	68			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			TAATAGTTGTAATCTTCTTCT	0.373																																					p.I1076I		.	.											.	RGS22	.	.	0			c.T3228C						.						120	114	116					8																	100994297		1863	4100	5963	SO:0001819	synonymous_variant	26166	exon22			AGTTGTAATCTTC	AY009106	CCDS43758.1, CCDS69521.1, CCDS75775.1	8q22.2	2014-01-21	2007-08-14		ENSG00000132554	ENSG00000132554		"Regulators of G-protein signaling"	24499	protein-coding gene	gene with protein product		615650	"regulator of G-protein signalling 22"				Standard	XM_005250856		Approved	DKFZP434I092, PRTD-NY2, CT145	uc003yjb.1	Q8NE09	OTTHUMG00000164802	ENST00000360863.6:c.3228T>C	8.37:g.100994297A>G		83.0	0.0		95.0	31.0	NM_015668	A8K944|Q569L2|Q86Y71|Q9BYZ4|Q9UFN6	Silent	SNP	ENST00000360863.6	37	CCDS43758.1																																																																																			.	.		0.373	RGS22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380365.1	NM_015668		G	100994297	A	G	100994297	2	3	268	1	0	0	0	0	0	0	0	1	13320	358	13	2		2	RGS22	8	100994297	Silent	SNP	A	TCGA-FV-A495-01A-11D-A25V-10	9962900	100994297	45369725	45	39107										
RIMS2	9699	hgsc.bcm.edu	37	chr8	104930679	104930679	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	atcatttcagagatataccgCgaatacctgatagcacacat	6	10	2	2			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr8:104930679C>A	ENST00000436393.2	+	7	1622	c.1381C>A	c.(1381-1383)Cga>Aga	p.R461R	RIMS2_ENST00000262231.10_Silent_p.R538R|RIMS2_ENST00000406091.3_Silent_p.R683R|RIMS2_ENST00000507740.1_Silent_p.R491R			Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	761					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			AGATATACCGCGAATACCTGA	0.299										HNSCC(12;0.0054)																											p.R683R		.	.											.	RIMS2	.	.	0			c.C2047A						.						96	94	95					8																	104930679		1808	4085	5893	SO:0001819	synonymous_variant	9699	exon9			ATACCGCGAATAC	AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"RAB3 interacting protein 3"	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000436393.2:c.1381C>A	8.37:g.104930679C>A		121.0	0.0		121.0	25.0	NM_001100117	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Silent	SNP	ENST00000436393.2	37																																																																																				.	.		0.299	RIMS2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000367217.1	NM_001100117		A	104930679	C	A	104930679	2	1	268	1	0	0	0	0	0	0	0	1	13383	760	27	1		1	RIMS2	8	104930679	Silent	SNP	C	TCGA-FV-A495-01A-11D-A25V-10	3936382	104930679	41433343	46	39108										
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110417294	110417294	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	gaagatcaaggtaaccagccCatgtgtggaagctaattcat	10	8	2	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr8:110417294C>T	ENST00000378402.5	+	16	1708	c.1604C>T	c.(1603-1605)cCa>cTa	p.P535L		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	535					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			GTAACCAGCCCATGTGTGGAA	0.299										HNSCC(38;0.096)																											p.P535L		.	.											.	PKHD1L1	.	.	0			c.C1604T						.						31	30	30					8																	110417294		1810	4066	5876	SO:0001583	missense	93035	exon16			CCAGCCCATGTGT	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.1604C>T	8.37:g.110417294C>T	ENSP00000367655:p.Pro535Leu	97.0	0.0		99.0	24.0	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	C	14.66	2.600458	0.46423	.	.	ENSG00000205038	ENST00000378402	D	0.84800	-1.9	5.8	5.8	0.92144	.	0.278061	0.36519	N	0.002559	D	0.83027	0.5165	M	0.70595	2.14	0.35090	D	0.764237	B	0.22480	0.07	B	0.15484	0.013	D	0.83584	0.0119	10	0.49607	T	0.09	.	10.9095	0.47099	0.0:0.9151:0.0:0.0849	.	535	Q86WI1	PKHL1_HUMAN	L	535	ENSP00000367655:P535L	ENSP00000367655:P535L	P	+	2	0	PKHD1L1	110486470	0.878000	0.30173	0.972000	0.41901	0.974000	0.67602	3.024000	0.49674	2.752000	0.94435	0.650000	0.86243	CCA	.	.		0.299	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		T	110417294	C	T	110417294	3	4	268	1	0	0	0	0	1	0	0	0	11981	594	21	3	1666	3	PKHD1L1	8	110417294	Missense_Mutation	SNP	C	TCGA-FV-A495-01A-11D-A25V-10	5486615	110417294	35946728	47	39109										
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110539189	110539189	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	tagtaattagctgtctggttGgaagaatgtggctcttggaa	13	4	2	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr8:110539189G>T	ENST00000378402.5	+	77	12765	c.12661G>T	c.(12661-12663)Gga>Tga	p.G4221*		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	4221					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			CTGTCTGGTTGGAAGAATGTG	0.403										HNSCC(38;0.096)																											p.G4221X		.	.											.	PKHD1L1	.	.	0			c.G12661T						.						89	94	92					8																	110539189		1987	4190	6177	SO:0001587	stop_gained	93035	exon77			CTGGTTGGAAGAA	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.12661G>T	8.37:g.110539189G>T	ENSP00000367655:p.Gly4221*	123.0	0.0		127.0	28.0	NM_177531	Q567P2|Q9UF27	Nonsense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	G	32	5.153435	0.94645	.	.	ENSG00000205038	ENST00000378402;ENST00000526472	.	.	.	5.64	4.75	0.60458	.	0.510568	0.17727	N	0.164015	.	.	.	.	.	.	0.58432	A	0.999992	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	12.5101	0.56002	0.0:0.1676:0.8324:0.0	.	.	.	.	X	4221;1149	.	ENSP00000367655:G4221X	G	+	1	0	PKHD1L1	110608365	0.998000	0.40836	0.333000	0.25482	0.227000	0.25037	3.285000	0.51716	1.338000	0.45544	0.650000	0.86243	GGA	.	.		0.403	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		T	110539189	G	T	110539189	4	4	268	1	0	0	0	0	0	1	0	0	11981	1349	47	3	12967	3	PKHD1L1	8	110539189	Nonsense_Mutation	SNP	G	TCGA-FV-A495-01A-11D-A25V-10	121895	110539189	35824833	48	39110										
PLEC	5339	hgsc.bcm.edu	37	chr8	144995161	144995161	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	tccggcccgtgcggaactgcCgcagcaggtcccgccgctgc	14	18	0	0			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr8:144995161C>T	ENST00000322810.4	-	32	9408	c.9239G>A	c.(9238-9240)cGg>cAg	p.R3080Q	PLEC_ENST00000527096.1_Missense_Mutation_p.R2966Q|PLEC_ENST00000357649.2_Missense_Mutation_p.R2947Q|PLEC_ENST00000345136.3_Missense_Mutation_p.R2943Q|PLEC_ENST00000356346.3_Missense_Mutation_p.R2929Q|PLEC_ENST00000354589.3_Missense_Mutation_p.R2943Q|PLEC_ENST00000354958.2_Missense_Mutation_p.R2921Q|PLEC_ENST00000398774.2_Missense_Mutation_p.R2911Q|PLEC_ENST00000436759.2_Missense_Mutation_p.R2970Q	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	3080	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						GCGGAACTGCCGCAGCAGGTC	0.597																																					p.R3080Q		.	.											.	PLEC	.	.	0			c.G9239A						.						39	46	43					8																	144995161		2152	4248	6400	SO:0001583	missense	5339	exon32			AACTGCCGCAGCA	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"plectin 1, intermediate filament binding protein, 500kD", "epidermolysis bullosa simplex 1 (Ogna)", "plectin 1, intermediate filament binding protein 500kDa"	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.9239G>A	8.37:g.144995161C>T	ENSP00000323856:p.Arg3080Gln	49.0	0.0		39.0	4.0	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	37	CCDS43772.1	.	.	.	.	.	.	.	.	.	.	C	13.58	2.279686	0.40294	.	.	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	T;T;T;T;T;T;T;T;T	0.75821	-0.93;-0.93;-0.97;-0.97;-0.95;-0.93;-0.93;-0.94;-0.93	4.82	2.99	0.34606	.	0.092502	0.43416	N	0.000564	T	0.67097	0.2857	M	0.65320	2	0.40794	D	0.983284	B;B;B;B;B;B;B;B	0.11235	0.004;0.004;0.004;0.002;0.004;0.004;0.004;0.004	B;B;B;B;B;B;B;B	0.09377	0.004;0.004;0.004;0.002;0.004;0.004;0.004;0.004	T	0.58825	-0.7568	10	0.16896	T	0.51	.	10.7299	0.46089	0.0:0.836:0.0:0.164	.	2970;2929;2921;3080;2911;2943;2947;2943	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	Q	2943;2947;2943;2911;3080;2921;2929;2970;2966	ENSP00000344848:R2943Q;ENSP00000350277:R2947Q;ENSP00000346602:R2943Q;ENSP00000381756:R2911Q;ENSP00000323856:R3080Q;ENSP00000347044:R2921Q;ENSP00000348702:R2929Q;ENSP00000388180:R2970Q;ENSP00000434583:R2966Q	ENSP00000323856:R3080Q	R	-	2	0	PLEC	145067149	0.970000	0.33590	1.000000	0.80357	0.975000	0.68041	2.446000	0.44908	0.546000	0.28920	0.448000	0.29417	CGG	.	.		0.597	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		T	144995161	C	T	144995161	3	4	268	1	0	0	0	0	1	0	0	0	12061	652	23	1	4819	1	PLEC	8	144995161	Missense_Mutation	SNP	C	TCGA-FV-A495-01A-11D-A25V-10	34455972	144995161	1368861	49	39111										
TLE1	7088	hgsc.bcm.edu	37	chr9	84208092	84208092	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	gtggttgagggtgttgatctGgcgagcatgccgggggattc	19	6	1	2			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr9:84208092G>A	ENST00000376499.3	-	15	2493	c.1429C>T	c.(1429-1431)Cag>Tag	p.Q477*		NM_005077.3	NP_005068.2	Q04724	TLE1_HUMAN	transducin-like enhancer of split 1 (E(sp1) homolog, Drosophila)	477					multicellular organismal development (GO:0007275)|negative regulation of anoikis (GO:2000811)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation of gene expression (GO:0010628)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription factor binding (GO:0008134)			NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	29						GTGTTGATCTGGCGAGCATGC	0.617																																					p.Q477X	NSCLC(155;1437 1995 30668 39354 45875)|Melanoma(16;266 781 14000 47728 51870)	.	.											.	TLE1	.	.	0			c.C1429T						.						121	114	116					9																	84208092		2203	4300	6503	SO:0001587	stop_gained	7088	exon15			TGATCTGGCGAGC		CCDS6661.1	9q21.32	2013-01-10	2001-11-28		ENSG00000196781	ENSG00000196781		"WD repeat domain containing"	11837	protein-coding gene	gene with protein product	"enhancer of split groucho 1"	600189	"transducin-like enhancer of split 1, homolog of Drosophila E(sp1)"			8365415, 8808280	Standard	NM_005077		Approved	ESG1, GRG1, ESG	uc004aly.3	Q04724	OTTHUMG00000021008	ENST00000376499.3:c.1429C>T	9.37:g.84208092G>A	ENSP00000365682:p.Gln477*	129.0	0.0		154.0	56.0	NM_005077	A8K495|Q5T3G4|Q969V9	Nonsense_Mutation	SNP	ENST00000376499.3	37	CCDS6661.1	.	.	.	.	.	.	.	.	.	.	g	49	14.973096	0.99817	.	.	ENSG00000196781	ENST00000376499	.	.	.	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-16.5744	20.422	0.99049	0.0:0.0:1.0:0.0	.	.	.	.	X	477	.	ENSP00000365682:Q477X	Q	-	1	0	TLE1	83397912	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.869000	0.99810	2.832000	0.97577	0.655000	0.94253	CAG	.	.		0.617	TLE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055407.1	NM_005077		A	84208092	G	A	84208092	4	1	268	1	0	0	0	0	0	1	0	0	15953	1357	47	3	907	3	TLE1	9	84208092	Nonsense_Mutation	SNP	G	TCGA-FV-A495-01A-11D-A25V-10		84208092	57005339	50	39112										
CDK5RAP2	55755	hgsc.bcm.edu	37	chr9	123298712	123298712	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	tcgtgcatcttcttcatctcTgaaagcttgctttccaaacg	6	12	4	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr9:123298712T>C	ENST00000349780.4	-	7	779	c.600A>G	c.(598-600)tcA>tcG	p.S200S	CDK5RAP2_ENST00000360190.4_Silent_p.S200S|CDK5RAP2_ENST00000359309.3_Silent_p.S200S|CDK5RAP2_ENST00000360822.3_Silent_p.S200S	NM_018249.4	NP_060719.4	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	200					brain development (GO:0007420)|centrosome organization (GO:0051297)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of centriole replication (GO:0046600)|negative regulation of neuron differentiation (GO:0045665)|neurogenesis (GO:0022008)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of spindle checkpoint (GO:0090231)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)			breast(6)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	58						TCTTCATCTCTGAAAGCTTGC	0.537																																					p.S200S		.	.											.	CDK5RAP2	.	.	0			c.A600G						.						140	119	126					9																	123298712		2203	4300	6503	SO:0001819	synonymous_variant	55755	exon7			CATCTCTGAAAGC	BK005504	CCDS6823.1, CCDS43871.1, CCDS75888.1	9q33.3	2014-02-21			ENSG00000136861	ENSG00000136861			18672	protein-coding gene	gene with protein product	"centrosomin"	608201	"microcephaly, primary autosomal recessive 3"	MCPH3		10721722, 17764569, 24466316	Standard	NM_018249		Approved	C48, FLJ10867, CEP215	uc004bkf.4	Q96SN8	OTTHUMG00000021043	ENST00000349780.4:c.600A>G	9.37:g.123298712T>C		72.0	0.0		82.0	29.0	NM_018249	Q5JV18|Q7Z3L4|Q7Z3U1|Q7Z7I6|Q9BSW0|Q9H6J6|Q9HCD9|Q9NV90|Q9UIW9	Silent	SNP	ENST00000349780.4	37	CCDS6823.1																																																																																			.	.		0.537	CDK5RAP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055535.1	NM_018249		C	123298712	T	C	123298712	2	2	268	1	0	0	0	0	0	0	0	1	3148	1567	55	2		2	CDK5RAP2	9	123298712	Silent	SNP	T	TCGA-FV-A495-01A-11D-A25V-10	39090620	123298712	17914719	51	39113										
PCDH15	65217	hgsc.bcm.edu	37	chr10	56129002	56129002	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	ttttttgttgatgcactggaCctgcaccacaatggagtgta	10	8	0	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr10:56129002C>G	ENST00000320301.6	-	5	746	c.352G>C	c.(352-354)Gtc>Ctc	p.V118L	PCDH15_ENST00000395430.1_Missense_Mutation_p.V118L|PCDH15_ENST00000395433.1_Missense_Mutation_p.V96L|PCDH15_ENST00000395440.1_Missense_Mutation_p.V118L|PCDH15_ENST00000437009.1_Missense_Mutation_p.V118L|PCDH15_ENST00000373957.3_Missense_Mutation_p.V96L|PCDH15_ENST00000395432.2_Missense_Mutation_p.V118L|PCDH15_ENST00000414778.1_Missense_Mutation_p.V123L|PCDH15_ENST00000395445.1_Missense_Mutation_p.V118L|PCDH15_ENST00000395442.1_Missense_Mutation_p.V118L|PCDH15_ENST00000409834.1_Intron|PCDH15_ENST00000373955.1_Missense_Mutation_p.V118L|PCDH15_ENST00000395438.1_Missense_Mutation_p.V118L|PCDH15_ENST00000395446.1_Missense_Mutation_p.V118L|PCDH15_ENST00000373965.2_Missense_Mutation_p.V118L|PCDH15_ENST00000361849.3_Missense_Mutation_p.V118L	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	118	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				ATGCACTGGACCTGCACCACA	0.403										HNSCC(58;0.16)																											p.V123L		.	.											.	PCDH15	.	.	0			c.G367C						.						129	103	112					10																	56129002		2203	4300	6503	SO:0001583	missense	65217	exon6			ACTGGACCTGCAC	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.352G>C	10.37:g.56129002C>G	ENSP00000322604:p.Val118Leu	89.0	0.0		76.0	22.0	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	37	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	C	16.19	3.052838	0.55218	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000395445;ENST00000395446;ENST00000395442;ENST00000395440;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000373957;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009;ENST00000373955	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.58060	0.54;0.64;0.58;0.51;0.43;0.66;0.56;0.41;0.42;0.49;0.36;0.42;0.42;0.53;0.63	5.52	5.52	0.82312	Cadherin (1);	.	.	.	.	T	0.63307	0.2500	L	0.29908	0.895	0.42086	D	0.991277	D;P;P;P;P;P;D;P;P;B;P;P;D;P;P	0.63046	0.992;0.876;0.719;0.719;0.947;0.876;0.992;0.908;0.719;0.376;0.908;0.949;0.97;0.949;0.719	D;P;B;B;P;P;D;P;B;B;B;P;P;P;B	0.77004	0.989;0.464;0.349;0.349;0.78;0.464;0.989;0.53;0.349;0.264;0.411;0.53;0.779;0.53;0.349	T	0.61936	-0.6960	9	0.39692	T	0.17	.	19.0325	0.92963	0.0:1.0:0.0:0.0	.	96;118;118;123;118;118;118;118;118;118;118;123;118;96;118	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;A2A3D8;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	L	118;123;118;118;118;118;118;118;118;118;96;96;118;118;123;118;118	ENSP00000363076:V118L;ENSP00000410304:V123L;ENSP00000378826:V118L;ENSP00000378832:V118L;ENSP00000378833:V118L;ENSP00000378829:V118L;ENSP00000378827:V118L;ENSP00000378820:V118L;ENSP00000354950:V118L;ENSP00000378821:V96L;ENSP00000363068:V96L;ENSP00000322604:V118L;ENSP00000378818:V118L;ENSP00000412628:V118L;ENSP00000363066:V118L	ENSP00000322604:V118L	V	-	1	0	PCDH15	55799008	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	4.918000	0.63376	2.590000	0.87494	0.585000	0.79938	GTC	.	.		0.403	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		G	56129002	C	G	56129002	3	3	268	1	0	0	0	0	1	0	0	0	11520	507	18	4	7275	4	PCDH15	10	56129002	Missense_Mutation	SNP	C	TCGA-FV-A495-01A-11D-A25V-10		56129002	79405745	52	39114										
MYOF	26509	hgsc.bcm.edu	37	chr10	95161196	95161196	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	ctgggggatgtcctcagctcGgtagattttcagcaagaagg	14	8	2	2	rs199504349		TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr10:95161196G>A	ENST00000359263.4	-	12	1095	c.1096C>T	c.(1096-1098)Cga>Tga	p.R366*	MYOF_ENST00000371501.4_Nonsense_Mutation_p.R366*|MYOF_ENST00000371489.1_Nonsense_Mutation_p.R366*|MYOF_ENST00000358334.5_Nonsense_Mutation_p.R366*|MYOF_ENST00000371502.4_Nonsense_Mutation_p.R366*	NM_013451.3	NP_038479.1	Q9NZM1	MYOF_HUMAN	myoferlin	366	C2 3. {ECO:0000255|PROSITE- ProRule:PRU00041}.				blood circulation (GO:0008015)|cellular response to heat (GO:0034605)|muscle contraction (GO:0006936)|plasma membrane repair (GO:0001778)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)	caveola (GO:0005901)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)			NS(2)|autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(7)|large_intestine(15)|lung(14)|ovary(4)|prostate(4)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						TCCTCAGCTCGGTAGATTTTC	0.423																																					p.R366X		.	.											.	MYOF	.	.	0			c.C1096T						.						115	111	113					10																	95161196		1918	4134	6052	SO:0001587	stop_gained	26509	exon12			CAGCTCGGTAGAT	AB033033	CCDS41550.1, CCDS41551.1	10q24	2014-06-27	2008-11-26	2008-11-26	ENSG00000138119	ENSG00000138119			3656	protein-coding gene	gene with protein product	"fer-1-like family member 3"	604603	"fer-1 (C.elegans)-like 3 (myoferlin)", "fer-1-like 3, myoferlin (C. elegans)"	FER1L3		10607832, 10995573, 17702744	Standard	NM_013451		Approved	KIAA1207	uc001kin.3	Q9NZM1	OTTHUMG00000018772	ENST00000359263.4:c.1096C>T	10.37:g.95161196G>A	ENSP00000352208:p.Arg366*	56.0	0.0		98.0	28.0	NM_133337	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	Nonsense_Mutation	SNP	ENST00000359263.4	37	CCDS41551.1	.	.	.	.	.	.	.	.	.	.	G	38	6.761573	0.97821	.	.	ENSG00000138119	ENST00000358334;ENST00000359263;ENST00000371501;ENST00000371502;ENST00000371489	.	.	.	5.64	3.63	0.41609	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.56	12.5443	0.56190	0.0:0.0:0.4562:0.5438	.	.	.	.	X	366	.	ENSP00000351094:R366X	R	-	1	2	MYOF	95151186	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	0.585000	0.23879	1.571000	0.49722	0.650000	0.86243	CGA	.	.		0.423	MYOF-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049423.2	NM_013451		A	95161196	G	A	95161196	4	1	268	1	0	0	0	0	0	1	0	0	10098	1124	39	1	5261	1	MYOF	10	95161196	Nonsense_Mutation	SNP	G	TCGA-FV-A495-01A-11D-A25V-10	39032194	95161196	40373551	53	39115										
PLCE1	51196	hgsc.bcm.edu	37	chr10	96084287	96084287	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	ccaaagcaagtggaaaggtgCaggaaaattcatccttaagc	10	8	1	0			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr10:96084287C>A	ENST00000371380.3	+	30	6918	c.6683C>A	c.(6682-6684)gCa>gAa	p.A2228E	PLCE1_ENST00000260766.3_Missense_Mutation_p.A2228E|PLCE1_ENST00000371385.3_Missense_Mutation_p.A1920E|NOC3L_ENST00000543788.1_Intron|PLCE1_ENST00000371375.1_Missense_Mutation_p.A1920E			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1	2228	Ras-associating 2. {ECO:0000255|PROSITE- ProRule:PRU00166}.				activation of MAPK activity (GO:0000187)|calcium-mediated signaling (GO:0019722)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|diacylglycerol biosynthetic process (GO:0006651)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerulus development (GO:0032835)|heart development (GO:0007507)|inositol phosphate metabolic process (GO:0043647)|inositol phosphate-mediated signaling (GO:0048016)|lipid catabolic process (GO:0016042)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|phospholipid metabolic process (GO:0006644)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of GTPase activity (GO:0043547)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|Ras protein signal transduction (GO:0007265)|regulation of cell growth (GO:0001558)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of protein kinase activity (GO:0045859)|regulation of Ras protein signal transduction (GO:0046578)|regulation of smooth muscle contraction (GO:0006940)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)|guanyl-nucleotide exchange factor activity (GO:0005085)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|Ras GTPase binding (GO:0017016)|receptor signaling protein activity (GO:0005057)			liver(1)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	8		Colorectal(252;0.0458)				TGGAAAGGTGCAGGAAAATTC	0.423																																					p.A2228E		.	.											.	PLCE1	.	.	0			c.C6683A						.						138	137	137					10																	96084287		1879	4109	5988	SO:0001583	missense	51196	exon31			AAGGTGCAGGAAA		CCDS41552.1, CCDS53555.1	10q23	2010-02-22			ENSG00000138193	ENSG00000138193	3.1.4.11		17175	protein-coding gene	gene with protein product	"nephrosis type 3"	608414				11022047, 11022048	Standard	NM_016341		Approved	KIAA1516, PLCE, NPHS3	uc001kjk.3	Q9P212	OTTHUMG00000018789	ENST00000371380.3:c.6683C>A	10.37:g.96084287C>A	ENSP00000360431:p.Ala2228Glu	59.0	0.0		56.0	24.0	NM_016341	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Missense_Mutation	SNP	ENST00000371380.3	37	CCDS41552.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.685569	0.88639	.	.	ENSG00000138193	ENST00000260766;ENST00000371380;ENST00000371385;ENST00000371375	T;T;T;T	0.17213	2.29;2.29;2.29;2.29	5.59	5.59	0.84812	Ras-association (3);	0.126776	0.52532	D	0.000068	T	0.35508	0.0934	L	0.39633	1.23	0.80722	D	1	D;D;D	0.71674	0.998;0.995;0.998	D;D;D	0.74348	0.983;0.922;0.983	T	0.01961	-1.1239	10	0.54805	T	0.06	.	19.2024	0.93715	0.0:1.0:0.0:0.0	.	2212;1920;2228	B7ZM61;Q9P212-2;Q9P212	.;.;PLCE1_HUMAN	E	2228;2228;1920;1920	ENSP00000260766:A2228E;ENSP00000360431:A2228E;ENSP00000360438:A1920E;ENSP00000360426:A1920E	ENSP00000260766:A2228E	A	+	2	0	PLCE1	96074277	1.000000	0.71417	1.000000	0.80357	0.670000	0.39368	5.731000	0.68554	2.628000	0.89032	0.655000	0.94253	GCA	.	.		0.423	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049469.3	NM_016341		A	96084287	C	A	96084287	3	1	268	1	0	0	0	0	1	0	0	0	12043	710	25	3	7087	3	PLCE1	10	96084287	Missense_Mutation	SNP	C	TCGA-FV-A495-01A-11D-A25V-10	923091	96084287	39450460	54	39116										
PSMD13	5719	hgsc.bcm.edu	37	chr11	251919	251919	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	tgacctgggtgcagccccgaGtgttggatttgcaacaggtg	15	9	0	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr11:251919G>C	ENST00000532097.1	+	12	1522	c.1018G>C	c.(1018-1020)Gtg>Ctg	p.V340L	PSMD13_ENST00000352303.5_Missense_Mutation_p.V313L|PSMD13_ENST00000532025.1_3'UTR|PSMD13_ENST00000431206.2_Missense_Mutation_p.V342L	NM_002817.3	NP_002808.3	Q9UNM6	PSD13_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 13	340					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|meiosis I (GO:0007127)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				NS(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	10		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.79e-27)|Epithelial(43;4e-26)|OV - Ovarian serous cystadenocarcinoma(40;6.02e-21)|BRCA - Breast invasive adenocarcinoma(625;3.93e-05)|Lung(200;0.112)|LUSC - Lung squamous cell carcinoma(625;0.129)		GCAGCCCCGAGTGTTGGATTT	0.502																																					p.V342L		.	.											.	PSMD13	.	.	0			c.G1024C						.						161	162	162					11																	251919		2203	4300	6503	SO:0001583	missense	5719	exon10			CCCCGAGTGTTGG	AB009398	CCDS7692.1, CCDS44504.1	11p15.5	2008-05-22			ENSG00000185627	ENSG00000185627		"Proteasome (prosome, macropain) subunits"	9558	protein-coding gene	gene with protein product		603481				9714768, 8811196	Standard	NM_002817		Approved	p40.5, Rpn9	uc001loo.2	Q9UNM6	OTTHUMG00000119072	ENST00000532097.1:c.1018G>C	11.37:g.251919G>C	ENSP00000436186:p.Val340Leu	124.0	0.0		196.0	10.0	NM_175932	B3KT15|O75831|Q53XU2|Q9UNV3	Missense_Mutation	SNP	ENST00000532097.1	37	CCDS7692.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.997097	0.74818	.	.	ENSG00000185627	ENST00000532097;ENST00000538343;ENST00000431206;ENST00000352303	T;T;T	0.26373	1.87;1.82;1.74	5.07	5.07	0.68467	Proteasome component (PCI) domain (1);	0.000000	0.85682	D	0.000000	T	0.60663	0.2286	M	0.91038	3.17	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;0.999	D;D;D;D	0.87578	0.998;0.993;0.949;0.949	T	0.69289	-0.5184	10	0.62326	D	0.03	.	17.2159	0.86944	0.0:0.0:1.0:0.0	.	342;275;340;340	Q9UNM6-2;B4DJ66;B2RBM7;Q9UNM6	.;.;.;PSD13_HUMAN	L	340;275;342;313	ENSP00000436186:V340L;ENSP00000396937:V342L;ENSP00000333811:V313L	ENSP00000333811:V313L	V	+	1	0	PSMD13	241919	1.000000	0.71417	0.991000	0.47740	0.314000	0.28054	9.086000	0.94088	2.643000	0.89663	0.563000	0.77884	GTG	.	.		0.502	PSMD13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239286.2	NM_002817		C	251919	G	C	251919	3	2	268	1	0	0	0	0	1	0	0	0	12708	1029	36	4	1145	4	PSMD13	11	251919	Missense_Mutation	SNP	G	TCGA-FV-A495-01A-11D-A25V-10		251919	134754597	55	39117										
FADD	8772	hgsc.bcm.edu	37	chr11	70049591	70049591	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	cccgttcctggtgctgctgcActcggtgtcgtccagcctgt	12	15	0	0			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr11:70049591A>G	ENST00000301838.4	+	1	323	c.26A>G	c.(25-27)cAc>cGc	p.H9R	RP11-805J14.5_ENST00000526174.1_RNA	NM_003824.3	NP_003815.1	Q13158	FADD_HUMAN	Fas (TNFRSF6)-associated via death domain	9	DED. {ECO:0000255|PROSITE- ProRule:PRU00065}.				activation of cysteine-type endopeptidase activity (GO:0097202)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|innate immune response (GO:0045087)|lymph node development (GO:0048535)|motor neuron apoptotic process (GO:0097049)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic signaling pathway (GO:0097527)|negative regulation of activation-induced cell death of T cells (GO:0070236)|negative regulation of necroptotic process (GO:0060546)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of apoptotic process (GO:0043065)|positive regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation (GO:2000454)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of proteolysis (GO:0045862)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|protein heterooligomerization (GO:0051291)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRAIL-activated apoptotic signaling pathway (GO:0036462)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	CD95 death-inducing signaling complex (GO:0031265)|cell body (GO:0044297)|cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|ripoptosome (GO:0097342)	death effector domain binding (GO:0035877)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|tumor necrosis factor receptor superfamily binding (GO:0032813)			endometrium(1)|lung(4)|ovary(1)|pancreas(1)|urinary_tract(2)	9	Esophageal squamous(2;1.19e-45)		LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)			GTGCTGCTGCACTCGGTGTCG	0.721																																					p.H9R		.	.											.	FADD	.	.	0			c.A26G						.						10	8	9					11																	70049591		2162	4215	6377	SO:0001583	missense	8772	exon1			TGCTGCACTCGGT	U24231	CCDS8196.1	11q13.3	2014-09-17			ENSG00000168040	ENSG00000168040			3573	protein-coding gene	gene with protein product	"Fas-associating protein with death domain", "Fas-associating death domain-containing protein", "mediator of receptor-induced toxicity", "growth-inhibiting gene 3 protein"	602457				7536190, 7538907	Standard	NM_003824		Approved	MORT1, GIG3	uc001opm.2	Q13158	OTTHUMG00000167264	ENST00000301838.4:c.26A>G	11.37:g.70049591A>G	ENSP00000301838:p.His9Arg	53.0	0.0		56.0	10.0	NM_003824	Q14866|Q6IBR4	Missense_Mutation	SNP	ENST00000301838.4	37	CCDS8196.1	.	.	.	.	.	.	.	.	.	.	A	9.187	1.025171	0.19433	.	.	ENSG00000168040	ENST00000301838	D	0.82255	-1.59	4.39	4.39	0.52855	DEATH-like (2);Death effector (3);	0.135643	0.49305	D	0.000156	D	0.85318	0.5669	M	0.68317	2.08	0.34444	D	0.699976	D	0.76494	0.999	D	0.63488	0.915	D	0.84295	0.0502	10	0.09590	T	0.72	-39.3521	7.5388	0.27727	0.8087:0.0:0.0:0.1913	.	9	Q13158	FADD_HUMAN	R	9	ENSP00000301838:H9R	ENSP00000301838:H9R	H	+	2	0	FADD	69727239	0.836000	0.29430	0.996000	0.52242	0.931000	0.56810	1.406000	0.34646	1.752000	0.51891	0.402000	0.26972	CAC	.	.		0.721	FADD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393902.1	NM_003824		G	70049591	A	G	70049591	3	3	268	1	0	0	0	0	1	0	0	0	5369	159	6	2	28	2	FADD	11	70049591	Missense_Mutation	SNP	A	TCGA-FV-A495-01A-11D-A25V-10	69797672	70049591	64956925	56	39118										
KRTAP5-7	440050	hgsc.bcm.edu	37	chr11	71238736	71238762	+	In_Frame_Del	DEL	CTGCTGTTCCTCAGGCTGTGGGTCATC	CTGCTGTTCCTCAGGCTGTGGGTCATC	-													0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	tccagctgctgtaagccctgCtgctgttcctcaggctgtgg					rs533945918|rs79842834	byFrequency	TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	CTGCTGTTCCTCAGGCTGTGGGTCATC	CTGCTGTTCCTCAGGCTGTGGGTCATC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr11:71238736_71238762delCTGCTGTTCCTCAGGCTGTGGGTCATC	ENST00000398536.4	+	1	424_450	c.390_416delCTGCTGTTCCTCAGGCTGTGGGTCATC	c.(388-417)tgctgctgttcctcaggctgtgggtcatcc>tgc	p.CCSSGCGSS131del		NM_001012503.1	NP_001012521.1	Q6L8G8	KRA57_HUMAN	keratin associated protein 5-7	131	7 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)		p.G137W(1)		breast(1)|endometrium(1)|kidney(3)|lung(6)|ovary(1)	12						gtaagccctgctgctgttcctcaggctgtgggtcatcctgctgccag	0.604																																					p.130_139del		.	.											.	KRTAP5-7	.	.	1	Substitution - Missense(1)	lung(1)	c.389_415del						.																																			SO:0001651	inframe_deletion	440050	exon1			.	AB126076	CCDS41682.1	11q13.4	2008-02-05			ENSG00000244411	ENSG00000244411		"Keratin associated proteins"	23602	protein-coding gene	gene with protein product						15144888	Standard	NM_001012503		Approved	KRTAP5.7, KRTAP5-3	uc001oqq.1	Q6L8G8	OTTHUMG00000057570	ENST00000398536.4:c.390_416delCTGCTGTTCCTCAGGCTGTGGGTCATC	11.37:g.71238736_71238762delCTGCTGTTCCTCAGGCTGTGGGTCATC	ENSP00000417330:p.Cys131_Ser139del	156.0	0.0		180.0	23.0	NM_001012503	B2RNM3|Q701N5	In_Frame_Del	DEL	ENST00000398536.4	37	CCDS41682.1																																																																																			.	.		0.604	KRTAP5-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127953.1			-	71238762	CTGCTGTTCCTCAGGCTGTGGGTCATC	-	71238736	7	5	268	1	0	1	0	1	0	0	0	0	8575	805	28	0	392	0	KRTAP5-7	11	71238736	In_Frame_Del	DEL	CTGCTGTTCCTCAGGCTGTGGGTCATC	TCGA-FV-A495-01A-11D-A25V-10	1189145	71238736	63767780	57	39119										
KRT79	338785	hgsc.bcm.edu	37	chr12	53225247	53225247	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	tgagctctgagtccagcctcCcccgctcgctctgaagtctg	10	16	3	3			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr12:53225247C>T	ENST00000330553.5	-	2	675	c.641G>A	c.(640-642)gGg>gAg	p.G214E		NM_175834.2	NP_787028.1	Q5XKE5	K2C79_HUMAN	keratin 79	214	Coil 1B.|Rod.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	enzyme binding (GO:0019899)|structural molecule activity (GO:0005198)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GTCCAGCCTCCCCCGCTCGCT	0.617																																					p.G214E		.	.											.	KRT79	.	.	0			c.G641A						.						114	114	114					12																	53225247		2203	4300	6503	SO:0001583	missense	338785	exon2			AGCCTCCCCCGCT	AJ564105	CCDS8839.1	12q13.13	2014-02-12	2007-07-03		ENSG00000185640	ENSG00000185640		"-", "Intermediate filaments type II, keratins (basic)"	28930	protein-coding gene	gene with protein product	"keratin 6-like"	611160				11683385	Standard	NM_175834		Approved	K6L, KRT6L	uc001sbb.3	Q5XKE5	OTTHUMG00000169878	ENST00000330553.5:c.641G>A	12.37:g.53225247C>T	ENSP00000328358:p.Gly214Glu	96.0	0.0		105.0	7.0	NM_175834	Q6P465|Q7Z793	Missense_Mutation	SNP	ENST00000330553.5	37	CCDS8839.1	.	.	.	.	.	.	.	.	.	.	C	7.898	0.733846	0.15574	.	.	ENSG00000185640	ENST00000330553	T	0.73789	-0.78	4.29	3.4	0.38934	Filament (1);	0.000000	0.50627	D	0.000117	T	0.67581	0.2908	M	0.64404	1.975	0.23010	N	0.99843	B	0.25007	0.116	B	0.30572	0.117	T	0.56171	-0.8023	10	0.31617	T	0.26	.	5.7978	0.18397	0.2856:0.6186:0.0:0.0958	.	214	Q5XKE5	K2C79_HUMAN	E	214	ENSP00000328358:G214E	ENSP00000328358:G214E	G	-	2	0	KRT79	51511514	0.000000	0.05858	0.953000	0.39169	0.650000	0.38633	-0.892000	0.04131	1.410000	0.46936	0.561000	0.74099	GGG	.	.		0.617	KRT79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406376.1	NM_175834		T	53225247	C	T	53225247	3	4	268	1	0	0	0	0	1	0	0	0	8501	623	22	3	998	3	KRT79	12	53225247	Missense_Mutation	SNP	C	TCGA-FV-A495-01A-11D-A25V-10		53225247	80626648	58	39120										
NACA	4666	hgsc.bcm.edu	37	chr12	57115063	57115063	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	gggctgttccagaggatgacTggggaaaaggaacttctaaa	14	6	1	2			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr12:57115063T>A	ENST00000454682.1	-	3	532	c.251A>T	c.(250-252)cAg>cTg	p.Q84L	NACA_ENST00000548563.1_Intron|NACA_ENST00000356769.3_Intron|NACA_ENST00000551793.1_Intron|NACA_ENST00000393891.4_Intron|NACA_ENST00000550952.1_Missense_Mutation_p.Q84L|NACA_ENST00000552540.1_Intron|NACA_ENST00000546392.1_Intron	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	84	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						AGAGGATGACTGGGGAAAAGG	0.567			T	BCL6	NHL																																p.Q84L		.	.		Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	.	NACA	.	.	0			c.A251T						.						62	59	60					12																	57115063		1568	3582	5150	SO:0001583	missense	4666	exon3			GATGACTGGGGAA	X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"nascent-polypeptide-associated complex alpha polypeptide"			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.251A>T	12.37:g.57115063T>A	ENSP00000403817:p.Gln84Leu	48.0	0.0		61.0	8.0	NM_001113203		Missense_Mutation	SNP	ENST00000454682.1	37		.	.	.	.	.	.	.	.	.	.	T	10.18	1.280477	0.23392	.	.	ENSG00000196531	ENST00000454682;ENST00000550952	T;T	0.62639	0.01;0.62	3.22	1.98	0.26296	.	.	.	.	.	T	0.36799	0.0980	N	0.08118	0	0.21105	N	0.999788	B;B	0.29862	0.259;0.011	B;B	0.24394	0.053;0.01	T	0.26121	-1.0112	9	0.87932	D	0	.	5.4196	0.16394	0.2506:0.0:0.0:0.7494	.	84;84	E9PAV3;F8VU71	.;.	L	84	ENSP00000403817:Q84L;ENSP00000448035:Q84L	ENSP00000403817:Q84L	Q	-	2	0	NACA	55401330	0.983000	0.35010	0.954000	0.39281	0.318000	0.28184	0.836000	0.27545	0.402000	0.25451	0.254000	0.18369	CAG	.	.		0.567	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594		A	57115063	T	A	57115063	3	1	268	1	0	0	0	0	1	0	0	0	10142	1580	55	4	6013	4	NACA	12	57115063	Missense_Mutation	SNP	T	TCGA-FV-A495-01A-11D-A25V-10	3889816	57115063	76736832	59	39121										
XPOT	11260	hgsc.bcm.edu	37	chr12	64833062	64833062	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	tatcttcaacaagaatacctGccctccttgcaagtagctcc	5	14	2	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr12:64833062G>T	ENST00000332707.5	+	23	3301	c.2772G>T	c.(2770-2772)ctG>ctT	p.L924L		NM_007235.4	NP_009166.2	O43592	XPOT_HUMAN	exportin, tRNA	924	Necessary for tRNA-binding, cytoplasmic localization and nuclear export.				intracellular protein transport (GO:0006886)|tRNA export from nucleus (GO:0006409)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(7)|lung(12)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				GBM - Glioblastoma multiforme(28;0.0404)		AAGAATACCTGCCCTCCTTGC	0.378																																					p.L924L		.	.											.	XPOT	.	.	0			c.G2772T						.						104	91	96					12																	64833062		2203	4300	6503	SO:0001819	synonymous_variant	11260	exon23			ATACCTGCCCTCC	AF039022	CCDS31852.1	12q14.1	2012-10-17	2012-10-17		ENSG00000184575	ENSG00000184575		"Exportins"	12826	protein-coding gene	gene with protein product		603180	"exportin, tRNA (nuclear export receptor for tRNAs)"			9660920, 9512417	Standard	NM_007235		Approved	XPO3	uc001ssb.3	O43592	OTTHUMG00000168794	ENST00000332707.5:c.2772G>T	12.37:g.64833062G>T		71.0	0.0		95.0	4.0	NM_007235	A6NLH1|O43784|Q8WUG2|Q9BVS7	Silent	SNP	ENST00000332707.5	37	CCDS31852.1																																																																																			.	.		0.378	XPOT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401122.1	NM_007235		T	64833062	G	T	64833062	2	4	268	1	0	0	0	0	0	0	0	1	17465	1306	46	3		3	XPOT	12	64833062	Silent	SNP	G	TCGA-FV-A495-01A-11D-A25V-10	7717999	64833062	69018833	60	39122										
SRRM4	84530	hgsc.bcm.edu	37	chr12	119563215	119563215	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	ccggccccgaaagtctcaccGccaccgccatcaccgctgcc	8	22	2	0	rs550204730		TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr12:119563215G>A	ENST00000267260.4	+	7	933	c.545G>A	c.(544-546)cGc>cAc	p.R182H	SRRM4_ENST00000537597.1_3'UTR	NM_194286.3	NP_919262.2	A7MD48	SRRM4_HUMAN	serine/arginine repetitive matrix 4	182	Ser-rich.				cell differentiation (GO:0030154)|mRNA processing (GO:0006397)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	mRNA binding (GO:0003729)	p.R182H(1)		breast(2)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	24						AAGTCTCACCGCCACCGCCAT	0.602													G|||	1	0.000199681	0	0	5008	,	,		15184	0		0	False		,,,				2504	0.001				p.R182H		.	.											.	SRRM4	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G545A						.						38	49	45					12																	119563215		2004	4161	6165	SO:0001583	missense	84530	exon7			CTCACCGCCACCG	AB058756	CCDS44994.1	12q24.23	2009-09-22	2009-09-21	2009-09-21	ENSG00000139767	ENSG00000139767			29389	protein-coding gene	gene with protein product	"neural-specific SR-related protein of 100 kDa"	613103	"KIAA1853"	KIAA1853		19737518	Standard	NM_194286		Approved	nSR100	uc001txa.2	A7MD48	OTTHUMG00000168928	ENST00000267260.4:c.545G>A	12.37:g.119563215G>A	ENSP00000267260:p.Arg182His	70.0	0.0		72.0	23.0	NM_194286	A8K5P6|B2RZH7|Q7Z5F0|Q96JH4	Missense_Mutation	SNP	ENST00000267260.4	37	CCDS44994.1	.	.	.	.	.	.	.	.	.	.	G	18.70	3.679542	0.68042	.	.	ENSG00000139767	ENST00000267260	T	0.32515	1.45	5.66	5.66	0.87406	.	0.068529	0.64402	D	0.000014	T	0.50326	0.1609	L	0.53249	1.67	0.42620	D	0.993344	D	0.89917	1.0	D	0.85130	0.997	T	0.36578	-0.9742	10	0.36615	T	0.2	-20.2207	15.2504	0.73539	0.0:0.0:1.0:0.0	.	182	A7MD48	SRRM4_HUMAN	H	182	ENSP00000267260:R182H	ENSP00000267260:R182H	R	+	2	0	SRRM4	118047598	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.257000	0.51500	2.648000	0.89879	0.655000	0.94253	CGC	.	.		0.602	SRRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401640.2	NM_194286		A	119563215	G	A	119563215	3	1	268	1	0	0	0	0	1	0	0	0	15186	1087	38	1	571	1	SRRM4	12	119563215	Missense_Mutation	SNP	G	TCGA-FV-A495-01A-11D-A25V-10	54730153	119563215	14288680	61	39123										
SBNO1	55206	hgsc.bcm.edu	37	chr12	123782650	123782650	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	gcactgaaccacataatacaTaatatgtacggcaacgaaga	7	9	0	2			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr12:123782650T>A	ENST00000602398.1	-	31	4041	c.3914A>T	c.(3913-3915)tAt>tTt	p.Y1305F	SBNO1_ENST00000602750.1_Missense_Mutation_p.Y1304F|SBNO1_ENST00000420886.2_Missense_Mutation_p.Y1305F|SBNO1_ENST00000267176.4_Missense_Mutation_p.Y1304F			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	1305					regulation of transcription, DNA-templated (GO:0006355)					NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		ACATAATACATAATATGTACG	0.433																																					p.Y1305F		.	.											.	SBNO1	.	.	0			c.A3914T						.						143	126	132					12																	123782650		2203	4300	6503	SO:0001583	missense	55206	exon30			AATACATAATATG	AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"sno, strawberry notch homolog 1 (Drosophila)"				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.3914A>T	12.37:g.123782650T>A	ENSP00000473665:p.Tyr1305Phe	100.0	0.0		138.0	42.0	NM_001167856	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Missense_Mutation	SNP	ENST00000602398.1	37	CCDS53844.1	.	.	.	.	.	.	.	.	.	.	T	13.25	2.181519	0.38511	.	.	ENSG00000139697	ENST00000420886;ENST00000267176	D;D	0.82711	-1.64;-1.64	6.03	6.03	0.97812	.	0.239229	0.35525	N	0.003153	T	0.71863	0.3390	N	0.16201	0.385	0.33421	D	0.579876	B;B	0.09022	0.001;0.002	B;B	0.09377	0.002;0.004	T	0.71813	-0.4479	10	0.27785	T	0.31	-4.6331	16.6126	0.84892	0.0:0.0:0.0:1.0	.	1305;1304	A3KN83;A3KN83-2	SBNO1_HUMAN;.	F	1305;1304	ENSP00000387361:Y1305F;ENSP00000267176:Y1304F	ENSP00000267176:Y1304F	Y	-	2	0	SBNO1	122348603	1.000000	0.71417	0.881000	0.34555	0.991000	0.79684	2.571000	0.45990	2.322000	0.78497	0.529000	0.55759	TAT	.	.		0.433	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183		A	123782650	T	A	123782650	3	1	268	1	0	0	0	0	1	0	0	0	13877	1406	49	4	275	4	SBNO1	12	123782650	Missense_Mutation	SNP	T	TCGA-FV-A495-01A-11D-A25V-10	4219435	123782650	10069245	62	39124										
OR4K17	390436	hgsc.bcm.edu	37	chr14	20586348	20586348	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	accattaagaaccactctccTactgggcaatctaaagcccg	6	14	2	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr14:20586348T>C	ENST00000315543.4	+	1	783	c.783T>C	c.(781-783)ccT>ccC	p.P261P		NM_001004715.1	NP_001004715.1	Q8NGC6	OR4KH_HUMAN	olfactory receptor, family 4, subfamily K, member 17	233						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(4)|lung(12)|pancreas(1)|skin(3)	21	all_cancers(95;0.00108)		Epithelial(56;7.58e-07)|all cancers(55;3.77e-06)	GBM - Glioblastoma multiforme(265;0.0144)		ACCACTCTCCTACTGGGCAAT	0.443																																					p.P261P		.	.											OR4K17,arm,malignant_melanoma,+2	OR4K17	.	.	0			c.T783C						.						144	137	140					14																	20586348		2203	4300	6503	SO:0001819	synonymous_variant	390436	exon1			CTCTCCTACTGGG		CCDS32030.1	14q11.2	2013-09-23			ENSG00000176230	ENSG00000176230		"GPCR / Class A : Olfactory receptors"	15355	protein-coding gene	gene with protein product							Standard	NM_001004715		Approved		uc001vwo.1	Q8NGC6	OTTHUMG00000170783	ENST00000315543.4:c.783T>C	14.37:g.20586348T>C		145.0	0.0		150.0	6.0	NM_001004715	Q6IF12	Silent	SNP	ENST00000315543.4	37	CCDS32030.1																																																																																			.	.		0.443	OR4K17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410346.1			C	20586348	T	C	20586348	2	2	268	1	0	0	0	0	0	0	0	1	11080	1509	53	2		2	OR4K17	14	20586348	Silent	SNP	T	TCGA-FV-A495-01A-11D-A25V-10		20586348	86763192	63	39125										
HECTD1	25831	hgsc.bcm.edu	37	chr14	31570253	31570253	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	catgtattgactgatggataGcttgcatcagtagcatcaac	9	8	2	2	rs11549801		TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr14:31570253G>T	ENST00000399332.1	-	43	8204	c.7716C>A	c.(7714-7716)agC>agA	p.S2572R	HECTD1_ENST00000553700.1_Missense_Mutation_p.S2572R	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	2572	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		CTGATGGATAGCTTGCATCAG	0.383																																					p.S2572R		.	.											.	HECTD1	.	.	0			c.C7716A						.						109	100	103					14																	31570253		1940	4153	6093	SO:0001583	missense	25831	exon43			TGGATAGCTTGCA	AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"Ankyrin repeat domain containing"	20157	protein-coding gene	gene with protein product			"HECT domain containing 1"			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.7716C>A	14.37:g.31570253G>T	ENSP00000382269:p.Ser2572Arg	92.0	0.0		87.0	4.0	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Missense_Mutation	SNP	ENST00000399332.1	37	CCDS41939.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.89|14.89	2.669368|2.669368	0.47677|0.47677	.|.	.|.	ENSG00000092148|ENSG00000092148	ENST00000554882|ENST00000553700;ENST00000261312;ENST00000399332;ENST00000399323	.|T;T	.|0.54479	.|0.57;0.57	5.81|5.81	4.74|4.74	0.60224|0.60224	.|HECT (4);	.|0.000000	.|0.85682	.|U	.|0.000000	T|T	0.49966|0.49966	0.1588|0.1588	N|N	0.05608|0.05608	-0.0099999999999999|-0.0099999999999999	0.58432|0.58432	D|D	0.999998|0.999998	.|D	.|0.67145	.|0.996	.|D	.|0.75020	.|0.985	T|T	0.47947|0.47947	-0.9077|-0.9077	5|10	.|0.26408	.|T	.|0.33	-7.7378|-7.7378	13.504|13.504	0.61474|0.61474	0.117:0.0:0.883:0.0|0.117:0.0:0.883:0.0	.|.	.|2572	.|Q9ULT8	.|HECD1_HUMAN	D|R	938|2572;2574;2572;133	.|ENSP00000450697:S2572R;ENSP00000382269:S2572R	.|ENSP00000261312:S2574R	A|S	-|-	2|3	0|2	HECTD1|HECTD1	30640004|30640004	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	3.728000|3.728000	0.54991|0.54991	2.743000|2.743000	0.94032|0.94032	0.650000|0.650000	0.86243|0.86243	GCT|AGC	.	.		0.383	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			T	31570253	G	T	31570253	3	4	268	1	0	0	0	0	1	0	0	0	7048	962	34	3	120	3	HECTD1	14	31570253	Missense_Mutation	SNP	G	TCGA-FV-A495-01A-11D-A25V-10	10983905	31570253	75779287	64	39126										
MAGEL2	54551	hgsc.bcm.edu	37	chr15	23889752	23889752	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	tctcggaggatgactttcacCatctccgagcgctggacagg	12	12	3	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr15:23889752C>A	ENST00000532292.1	-	1	1423	c.1329G>T	c.(1327-1329)atG>atT	p.M443I		NM_019066.4	NP_061939.3	Q9UJ55	MAGL2_HUMAN	MAGE-like 2	326	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				Arp2/3 complex-mediated actin nucleation (GO:0034314)|protein K63-linked ubiquitination (GO:0070534)|retrograde transport, endosome to Golgi (GO:0042147)	endosome (GO:0005768)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;1.84e-06)|Epithelial(43;1.2e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)		TGACTTTCACCATCTCCGAGC	0.488																																					p.M1046I		.	.											.	.	.	.	0			c.G3138T						.						60	59	59					15																	23889752		1998	4184	6182	SO:0001583	missense	54551	exon1			TTTCACCATCTCC	AJ243531	CCDS73700.1	15q11-q12	2008-07-18				ENSG00000254585			6814	protein-coding gene	gene with protein product		605283		NDNL1		10556298	Standard	NM_019066		Approved	nM15	uc001ywj.4	Q9UJ55		ENST00000532292.1:c.1329G>T	15.37:g.23889752C>A	ENSP00000433433:p.Met443Ile	190.0	0.0		188.0	39.0	NM_019066		Missense_Mutation	SNP	ENST00000532292.1	37		.	.	.	.	.	.	.	.	.	.	C	13.89	2.370795	0.42003	.	.	ENSG00000254585	ENST00000532292	.	.	.	4.78	3.79	0.43588	.	.	.	.	.	T	0.39332	0.1074	L	0.39566	1.225	0.25990	N	0.982256	.	.	.	.	.	.	T	0.16158	-1.0412	5	.	.	.	.	9.7898	0.40699	0.205:0.795:0.0:0.0	.	.	.	.	L	475	.	.	W	-	2	0	MAGEL2	21440845	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	1.889000	0.39718	2.644000	0.89710	0.591000	0.81541	TGG	.	.		0.488	MAGEL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395182.2	NM_019066		A	23889752	C	A	23889752	3	1	268	1	0	0	0	0	1	0	0	0	9198	594	21	3	615	3	MAGEL2	15	23889752	Missense_Mutation	SNP	C	TCGA-FV-A495-01A-11D-A25V-10		23889752	78641640	65	39127										
SCG3	29106	hgsc.bcm.edu	37	chr15	51975586	51975586	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	ccaagaatcgaaaactgatcGatgattatgactctactaag	7	8	1	4			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr15:51975586G>A	ENST00000220478.3	+	4	755	c.352G>A	c.(352-354)Gat>Aat	p.D118N	SCG3_ENST00000542355.2_De_novo_Start_OutOfFrame	NM_013243.3	NP_037375.2	Q8WXD2	SCG3_HUMAN	secretogranin III	118					blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|membrane (GO:0016020)|secretory granule lumen (GO:0034774)	poly(A) RNA binding (GO:0044822)	p.D118N(1)		breast(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21				all cancers(107;0.00488)		AAAACTGATCGATGATTATGA	0.323																																					p.D118N		.	.											.	SCG3	.	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.G352A						.						108	114	112					15																	51975586		2195	4293	6488	SO:0001583	missense	29106	exon4			CTGATCGATGATT	AF078851	CCDS10142.1, CCDS53947.1	15q21.2	2013-09-23			ENSG00000104112	ENSG00000104112			13707	protein-coding gene	gene with protein product		611796				2053134, 8825061	Standard	NM_013243		Approved	SGIII, FLJ90833	uc002abh.3	Q8WXD2	OTTHUMG00000131748	ENST00000220478.3:c.352G>A	15.37:g.51975586G>A	ENSP00000220478:p.Asp118Asn	25.0	0.0		34.0	4.0	NM_013243	A8K2B0|B3KQP6|B4DK99|F5H3R8|Q96C83|Q96GE8|Q9Y6G7	Missense_Mutation	SNP	ENST00000220478.3	37	CCDS10142.1	.	.	.	.	.	.	.	.	.	.	G	18.52	3.642686	0.67244	.	.	ENSG00000104112	ENST00000220478	T	0.27256	1.68	6.07	5.17	0.71159	.	0.351936	0.35739	N	0.003004	T	0.23727	0.0574	L	0.27053	0.805	0.80722	D	1	P	0.49253	0.921	B	0.44108	0.441	T	0.02917	-1.1094	10	0.87932	D	0	-37.4805	15.3604	0.74469	0.0664:0.0:0.9336:0.0	.	118	Q8WXD2	SCG3_HUMAN	N	118	ENSP00000220478:D118N	ENSP00000220478:D118N	D	+	1	0	SCG3	49762878	1.000000	0.71417	0.936000	0.37596	0.668000	0.39293	8.797000	0.91882	1.586000	0.49944	0.655000	0.94253	GAT	.	.		0.323	SCG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254670.2	NM_013243		A	51975586	G	A	51975586	3	1	268	1	0	0	0	0	1	0	0	0	13907	1058	37	1	366	1	SCG3	15	51975586	Missense_Mutation	SNP	G	TCGA-FV-A495-01A-11D-A25V-10	28085834	51975586	50555806	66	39128										
GRAMD2	196996	hgsc.bcm.edu	37	chr15	72455767	72455767	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	aggaccccagcctggcatggGccatgcccacctcccaccat	9	19	0	0			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr15:72455767G>A	ENST00000309731.7	-	10	809	c.796C>T	c.(796-798)Ccc>Tcc	p.P266S	GRAMD2_ENST00000564184.1_5'UTR	NM_001012642.2	NP_001012660.1	Q8IUY3	GRAM2_HUMAN	GRAM domain containing 2	266						integral component of membrane (GO:0016021)				cervix(2)|endometrium(1)|large_intestine(4)|lung(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	13						CCTGGCATGGGCCATGCCCAC	0.532																																					p.P266S		.	.											.	GRAMD2	.	.	0			c.C796T						.						100	105	103					15																	72455767		2199	4297	6496	SO:0001583	missense	196996	exon10			GCATGGGCCATGC	AK002016	CCDS32283.1	15q23	2006-11-29	2005-11-03	2005-11-03					27287	protein-coding gene	gene with protein product						12477932	Standard	NM_001012642		Approved		uc002atq.3	Q8IUY3		ENST00000309731.7:c.796C>T	15.37:g.72455767G>A	ENSP00000311657:p.Pro266Ser	71.0	0.0		110.0	36.0	NM_001012642	B3KT68	Missense_Mutation	SNP	ENST00000309731.7	37	CCDS32283.1	.	.	.	.	.	.	.	.	.	.	G	0.027	-1.363682	0.01235	.	.	ENSG00000175318	ENST00000309731	T	0.28069	1.63	3.07	2.1	0.27182	.	7.794120	0.00166	N	0.000001	T	0.20210	0.0486	N	0.22421	0.69	0.09310	N	1	B	0.22276	0.067	B	0.18561	0.022	T	0.20306	-1.0279	10	0.06891	T	0.86	.	7.2428	0.26106	0.1437:0.0:0.8563:0.0	.	266	Q8IUY3	GRAM2_HUMAN	S	266	ENSP00000311657:P266S	ENSP00000311657:P266S	P	-	1	0	GRAMD2	70242821	0.000000	0.05858	0.030000	0.17652	0.067000	0.16453	0.213000	0.17521	0.817000	0.34445	0.655000	0.94253	CCC	.	.		0.532	GRAMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420040.1	NM_001012642		A	72455767	G	A	72455767	3	1	268	1	0	0	0	0	1	0	0	0	6759	1203	42	3	280	3	GRAMD2	15	72455767	Missense_Mutation	SNP	G	TCGA-FV-A495-01A-11D-A25V-10	20480181	72455767	30075625	67	39129										
CHD2	1106	hgsc.bcm.edu	37	chr15	93499777	93499777	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	ctctttattgtataaaactcTgattgatttcaagtccaacc	4	9	3	2			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr15:93499777T>C	ENST00000394196.4	+	16	2966	c.1898T>C	c.(1897-1899)cTg>cCg	p.L633P	CHD2_ENST00000557381.1_Missense_Mutation_p.L633P	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	633	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			TATAAAACTCTGATTGATTTC	0.448																																					p.L633P		.	.											.	CHD2	.	.	0			c.T1898C						.						113	113	113					15																	93499777		2197	4297	6494	SO:0001583	missense	1106	exon16			AAACTCTGATTGA	AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.1898T>C	15.37:g.93499777T>C	ENSP00000377747:p.Leu633Pro	51.0	0.0		46.0	12.0	NM_001271	C6G482|Q96IP5	Missense_Mutation	SNP	ENST00000394196.4	37	CCDS10374.2	.	.	.	.	.	.	.	.	.	.	T	26.5	4.747868	0.89663	.	.	ENSG00000173575	ENST00000394196;ENST00000557381	D;D	0.94650	-3.48;-3.48	5.51	5.51	0.81932	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.27710	U	0.018167	D	0.98507	0.9502	H	0.98738	4.315	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.81914	0.995;0.995	D	0.99802	1.1036	10	0.87932	D	0	-10.3973	15.6322	0.76920	0.0:0.0:0.0:1.0	.	633;633	O14647;O14647-2	CHD2_HUMAN;.	P	633	ENSP00000377747:L633P;ENSP00000451366:L633P	ENSP00000377747:L633P	L	+	2	0	CHD2	91300781	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.036000	0.88901	2.097000	0.63578	0.455000	0.32223	CTG	.	.		0.448	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271		C	93499777	T	C	93499777	3	2	268	1	0	0	0	0	1	0	0	0	3327	1580	55	2	1960	2	CHD2	15	93499777	Missense_Mutation	SNP	T	TCGA-FV-A495-01A-11D-A25V-10	21044010	93499777	9031615	68	39130										
HAGHL	84264	hgsc.bcm.edu	37	chr16	777559	777559	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	ggacaactacatgtacctggTcatcgaggagctcacgcgcg	12	12	2	0			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr16:777559T>G	ENST00000341413.4	+	2	331	c.50T>G	c.(49-51)gTc>gGc	p.V17G	HAGHL_ENST00000561546.1_Missense_Mutation_p.V17G|CCDC78_ENST00000293889.6_5'Flank|HAGHL_ENST00000549114.1_Missense_Mutation_p.V17G|HAGHL_ENST00000564545.1_Missense_Mutation_p.V17G|HAGHL_ENST00000389703.3_Missense_Mutation_p.V17G|NARFL_ENST00000562862.1_5'Flank|HAGHL_ENST00000564537.1_Missense_Mutation_p.V17G			Q6PII5	HAGHL_HUMAN	hydroxyacylglutathione hydrolase-like	17							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			lung(3)	3		Hepatocellular(780;0.00335)				ATGTACCTGGTCATCGAGGAG	0.692																																					p.V17G	Pancreas(46;538 1326 12403 32360)	.	.											.	HAGHL	.	.	0			c.T50G						.						68	51	57					16																	777559		2189	4295	6484	SO:0001583	missense	84264	exon1			ACCTGGTCATCGA	AK054841	CCDS32354.1	16p13.3	2008-02-05	2003-11-04						14177	protein-coding gene	gene with protein product			"hydroxyacyl glutathione hydrolase-like"			12477932	Standard	XM_005255629		Approved	MGC2605	uc002cjo.1	Q6PII5		ENST00000341413.4:c.50T>G	16.37:g.777559T>G	ENSP00000341952:p.Val17Gly	95.0	0.0		130.0	27.0	NM_032304	A6NCC4|D3DU64|Q59FX8|Q96BZ3|Q96NR5|Q96S11|Q9BT45	Missense_Mutation	SNP	ENST00000341413.4	37		.	.	.	.	.	.	.	.	.	.	T	23.8	4.460644	0.84317	.	.	ENSG00000103253	ENST00000549114;ENST00000341413;ENST00000389701;ENST00000389703	D;D;D	0.85339	-1.97;-1.97;-1.97	3.43	3.43	0.39272	Beta-lactamase-like (2);	0.185073	0.33834	N	0.004506	D	0.92625	0.7657	M	0.90650	3.135	0.58432	D	0.999998	D;D;D;D	0.89917	0.996;0.998;0.999;1.0	D;D;D;D	0.91635	0.995;0.995;0.996;0.999	D	0.93250	0.6634	10	0.87932	D	0	-14.7484	10.8824	0.46946	0.0:0.0:0.0:1.0	.	17;17;17;17	B4DED4;Q6PII5-2;Q6PII5-3;Q6PII5	.;.;.;HAGHL_HUMAN	G	17	ENSP00000447170:V17G;ENSP00000341952:V17G;ENSP00000374353:V17G	ENSP00000341952:V17G	V	+	2	0	HAGHL	717560	1.000000	0.71417	0.565000	0.28409	0.790000	0.44656	4.243000	0.58721	1.431000	0.47355	0.459000	0.35465	GTC	.	.		0.692	HAGHL-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409607.1	NM_032304		G	777559	T	G	777559	3	3	268	1	0	0	0	0	1	0	0	0	6955	1667	58	5	52	5	HAGHL	16	777559	Missense_Mutation	SNP	T	TCGA-FV-A495-01A-11D-A25V-10		777559	89577194	69	39131										
NETO2	81831	hgsc.bcm.edu	37	chr16	47117548	47117548	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	atcaaacacttcttggaaccCggttttattaaaagcggttt	7	8	2	0			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr16:47117548C>G	ENST00000562435.1	-	9	1546	c.1162G>C	c.(1162-1164)Ggg>Cgg	p.G388R	NETO2_ENST00000303155.5_Missense_Mutation_p.G381R	NM_018092.4	NP_060562.3	Q8NC67	NETO2_HUMAN	neuropilin (NRP) and tolloid (TLL)-like 2	388					regulation of kainate selective glutamate receptor activity (GO:2000312)	kainate selective glutamate receptor complex (GO:0032983)|postsynaptic density (GO:0014069)				breast(1)|cervix(1)|endometrium(1)|large_intestine(8)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	29		all_cancers(37;0.00114)|all_lung(18;0.00432)|Lung NSC(13;0.0384)|Breast(268;0.174)				TCTTGGAACCCGGTTTTATTA	0.403										HNSCC(25;0.065)																											p.G388R		.	.											.	NETO2	.	.	0			c.G1162C						.						82	87	86					16																	47117548		2203	4300	6503	SO:0001583	missense	81831	exon9			GGAACCCGGTTTT	AK001292	CCDS10727.1, CCDS58460.1	16q11.2	2008-08-04			ENSG00000171208	ENSG00000171208			14644	protein-coding gene	gene with protein product		607974				11943477	Standard	NM_018092		Approved	FLJ10430, NEOT2	uc002eer.2	Q8NC67	OTTHUMG00000133101	ENST00000562435.1:c.1162G>C	16.37:g.47117548C>G	ENSP00000455169:p.Gly388Arg	83.0	0.0		57.0	23.0	NM_018092	J3KNF1|Q7Z381|Q8ND51|Q96SP4|Q9NVY8	Missense_Mutation	SNP	ENST00000562435.1	37	CCDS10727.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.294527	0.81025	.	.	ENSG00000171208	ENST00000303155	.	.	.	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.74030	0.3663	L	0.47716	1.5	0.80722	D	1	P;D;D	0.71674	0.864;0.986;0.998	P;P;D	0.69142	0.62;0.842;0.962	T	0.68606	-0.5364	9	0.30854	T	0.27	.	20.0124	0.97464	0.0:1.0:0.0:0.0	.	245;388;64	B7Z4I7;Q8NC67;Q8NC67-2	.;NETO2_HUMAN;.	R	388	.	ENSP00000306726:G388R	G	-	1	0	NETO2	45675049	1.000000	0.71417	0.998000	0.56505	0.978000	0.69477	4.804000	0.62554	2.749000	0.94314	0.655000	0.94253	GGG	.	.		0.403	NETO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256766.2	NM_018092		G	47117548	C	G	47117548	3	3	268	1	0	0	0	0	1	0	0	0	10349	652	23	4	419	4	NETO2	16	47117548	Missense_Mutation	SNP	C	TCGA-FV-A495-01A-11D-A25V-10	46339989	47117548	43237205	70	39132										
RANBP10	57610	hgsc.bcm.edu	37	chr16	67839340	67839340	+	Frame_Shift_Del	DEL	C	C	-													0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	gaagggcttacccatctcttCctttgctgacaatcttcact							TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr16:67839340delC	ENST00000317506.3	-	2	453	c.338delG	c.(337-339)ggafs	p.G113fs	RANBP10_ENST00000602677.1_Frame_Shift_Del_p.G113fs|RANBP10_ENST00000411657.2_Intron|TSNAXIP1_ENST00000415766.3_5'Flank|TSNAXIP1_ENST00000388833.3_5'Flank|RANBP10_ENST00000602887.1_5'UTR|RANBP10_ENST00000536251.1_5'UTR|RANBP10_ENST00000448631.2_Frame_Shift_Del_p.G113fs|RANBP10_ENST00000425512.2_5'UTR|TSNAXIP1_ENST00000561639.1_5'Flank	NM_020850.1	NP_065901.1	Q6VN20	RBP10_HUMAN	RAN binding protein 10	113	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				microtubule cytoskeleton organization (GO:0000226)	cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)	Ran guanyl-nucleotide exchange factor activity (GO:0005087)			endometrium(5)|kidney(2)|large_intestine(3)|lung(10)|ovary(2)|skin(1)	23		Acute lymphoblastic leukemia(13;4.34e-06)|all_hematologic(13;0.000643)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00522)|Epithelial(162;0.025)|all cancers(182;0.157)		CCCATCTCTTCCTTTGCTGAC	0.507																																					p.G113fs		.	.											.	RANBP10	.	.	0			c.339delA						.						74	69	71					16																	67839340		2198	4300	6498	SO:0001589	frameshift_variant	57610	exon2			.	AB040897	CCDS32469.1	16q22	2008-02-05				ENSG00000141084			29285	protein-coding gene	gene with protein product		614031				14684163	Standard	NM_020850		Approved	KIAA1464	uc002eud.3	Q6VN20		ENST00000317506.3:c.338delG	16.37:g.67839340delC	ENSP00000316589:p.Gly113fs	65.0	0.0		91.0	33.0	NM_020850	A4FTY2|B4DID0|B4DQH9|E7EW27|Q9P264	Frame_Shift_Del	DEL	ENST00000317506.3	37	CCDS32469.1																																																																																			.	.		0.507	RANBP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467896.1	NM_020850		-	67839340	C	-	67839340	7	5	268	1	0	1	0	1	0	0	0	0	13041	855	30	0	1576	0	RANBP10	16	67839340	Frame_Shift_Del	DEL	C	TCGA-FV-A495-01A-11D-A25V-10	20721792	67839340	22515413	71	39133										
FUK	197258	hgsc.bcm.edu	37	chr16	70508239	70508239	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	ggagagggacaagtggctaaGcaggtgtgtactaatggagg	18	4	0	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr16:70508239G>T	ENST00000288078.6	+	16	2217	c.1985G>T	c.(1984-1986)aGc>aTc	p.S662I	FUK_ENST00000378912.2_Missense_Mutation_p.S694I|FUK_ENST00000571514.1_Missense_Mutation_p.S153I	NM_145059.2	NP_659496.2	Q8N0W3	FUK_HUMAN	fucokinase	662						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|fucokinase activity (GO:0050201)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(11)|ovary(2)|prostate(2)	23		Ovarian(137;0.0694)				AAGTGGCTAAGCAGGTGTGTA	0.602																																					p.S662I		.	.											.	FUK	.	.	0			c.G1985T						.						20	25	23					16																	70508239		2044	4186	6230	SO:0001583	missense	197258	exon16			GGCTAAGCAGGTG		CCDS10891.2	16q22.1	2008-02-05			ENSG00000157353	ENSG00000157353	2.7.1.52		29500	protein-coding gene	gene with protein product	"L-fucose kinase"	608675				12056818	Standard	XM_006721161		Approved	FLJ39408	uc002eyy.3	Q8N0W3	OTTHUMG00000074085	ENST00000288078.6:c.1985G>T	16.37:g.70508239G>T	ENSP00000288078:p.Ser662Ile	85.0	0.0		94.0	4.0	NM_145059	Q5PSM3|Q5XKL6|Q6ZRA0|Q96MT9	Missense_Mutation	SNP	ENST00000288078.6	37	CCDS10891.2	.	.	.	.	.	.	.	.	.	.	G	16.15	3.041285	0.55003	.	.	ENSG00000157353	ENST00000288078;ENST00000378912	T;T	0.08546	3.12;3.08	5.74	3.74	0.42951	.	0.198587	0.51477	D	0.000087	T	0.09024	0.0223	L	0.55481	1.735	0.80722	D	1	P;P;P	0.46706	0.883;0.664;0.498	B;B;B	0.40038	0.317;0.246;0.312	T	0.07252	-1.0782	10	0.56958	D	0.05	-25.636	8.2473	0.31695	0.1354:0.1404:0.7242:0.0	.	694;568;662	Q8N0W3-2;B2RDL5;Q8N0W3	.;.;FUK_HUMAN	I	662;694	ENSP00000288078:S662I;ENSP00000368192:S694I	ENSP00000288078:S662I	S	+	2	0	FUK	69065740	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	2.924000	0.48876	1.399000	0.46721	0.655000	0.94253	AGC	.	.		0.602	FUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157291.2	NM_145059		T	70508239	G	T	70508239	3	4	268	1	0	0	0	0	1	0	0	0	6104	971	34	3	2043	3	FUK	16	70508239	Missense_Mutation	SNP	G	TCGA-FV-A495-01A-11D-A25V-10	2668899	70508239	19846514	72	39134										
CYTSB	92521	hgsc.bcm.edu	37	chr17	20109082	20109082	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	aggccagtgctgtggagcagAcggcagagagctgcgaagtt	17	8	0	2			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr17:20109082A>G	ENST00000261503.5	+	4	1771	c.1720A>G	c.(1720-1722)Acg>Gcg	p.T574A	SPECC1_ENST00000584527.1_5'Flank|SPECC1_ENST00000395527.4_Missense_Mutation_p.T574A|SPECC1_ENST00000536879.1_Intron|SPECC1_ENST00000472876.1_Intron|SPECC1_ENST00000395530.2_Missense_Mutation_p.T493A|SPECC1_ENST00000395525.3_Missense_Mutation_p.T493A|SPECC1_ENST00000395529.3_Missense_Mutation_p.T574A|AC004702.2_ENST00000580225.1_lincRNA|SPECC1_ENST00000395522.2_Missense_Mutation_p.T493A	NM_001033553.2	NP_001028725.1	Q5M775	CYTSB_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1	574					cell adhesion (GO:0007155)	nucleus (GO:0005634)				breast(1)|large_intestine(3)|ovary(4)	8				KIRC - Kidney renal clear cell carcinoma(2;0.166)|Kidney(2;0.196)		TGTGGAGCAGACGGCAGAGAG	0.458																																					p.T574A		.	.											.	SPECC1	.	.	0			c.A1720G						.						68	71	70					17																	20109082		2203	4300	6503	SO:0001583	missense	92521	exon4			GAGCAGACGGCAG	AY816329, AB041533	CCDS32590.1, CCDS42280.1, CCDS42281.1, CCDS45628.1, CCDS58531.1	17p11.2	2012-11-19	2010-09-17	2010-09-17	ENSG00000128487	ENSG00000128487			30615	protein-coding gene	gene with protein product	"sperm antigen HCMOGT 1", "cytokinesis and spindle organization B", "cytospin B"	608793				15602574, 18763323, 15087372	Standard	NM_001033553		Approved	HCMOGT-1, FLJ36955, NSP, CYTSB	uc002gwq.3	Q5M775	OTTHUMG00000179808	ENST00000261503.5:c.1720A>G	17.37:g.20109082A>G	ENSP00000261503:p.Thr574Ala	63.0	0.0		66.0	21.0	NM_001033553	B4DHH0|B7WNS8|Q5IBP1|Q5IBP2|Q5IBP3|Q5IBP4|Q5M772|Q5M773|Q5M774|Q86XT8|Q8N4U4|Q8WU84|Q9HCQ3	Missense_Mutation	SNP	ENST00000261503.5	37	CCDS32590.1	.	.	.	.	.	.	.	.	.	.	A	0.007	-1.970897	0.00457	.	.	ENSG00000128487	ENST00000395530;ENST00000261503;ENST00000395529;ENST00000395522;ENST00000395527;ENST00000395525	T;T;T;T	0.61040	0.14;3.11;3.12;3.12	5.59	0.284	0.15701	.	0.776014	0.13105	N	0.413497	T	0.29458	0.0734	N	0.17474	0.49	0.09310	N	0.999998	B;B;B;B;B	0.09022	0.0;0.002;0.001;0.0;0.0	B;B;B;B;B	0.04013	0.0;0.001;0.001;0.001;0.0	T	0.25467	-1.0131	10	0.02654	T	1	-0.2262	4.116	0.10081	0.42:0.0:0.4083:0.1718	.	574;493;493;574;574	A8MV89;Q5M775-4;Q5M775-3;Q5M775-2;Q5M775	.;.;.;.;CYTSB_HUMAN	A	574;574;574;493;493;493	ENSP00000261503:T574A;ENSP00000378900:T574A;ENSP00000378893:T493A;ENSP00000378896:T493A	ENSP00000261503:T574A	T	+	1	0	SPECC1	20049674	0.039000	0.19947	0.000000	0.03702	0.001000	0.01503	2.753000	0.47524	0.394000	0.25230	0.533000	0.62120	ACG	.	.		0.458	SPECC1-018	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441206.1	NM_152904		G	20109082	A	G	20109082	3	3	268	1	0	0	0	0	1	0	0	0	4212	275	10	2	1774	2	CYTSB	17	20109082	Missense_Mutation	SNP	A	TCGA-FV-A495-01A-11D-A25V-10		20109082	61086128	73	39135										
KIAA1012	22878	hgsc.bcm.edu	37	chr18	29419280	29419280	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	aaataaagctcaaaccttttTtgatgaaatggatgattaaa	6	4	1	3			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr18:29419280T>C	ENST00000283351.4	-	27	4313	c.3978A>G	c.(3976-3978)caA>caG	p.Q1326Q	TRAPPC8_ENST00000582539.1_Silent_p.Q1272Q	NM_014939.3	NP_055754	Q9Y2L5	TPPC8_HUMAN	trafficking protein particle complex 8	1326					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(7)|liver(2)|lung(13)|ovary(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						CAAACCTTTTTTGATGAAATG	0.338																																					p.Q1326Q		.	.											.	TRAPPC8	.	.	0			c.A3978G						.						92	96	95					18																	29419280		2203	4300	6503	SO:0001819	synonymous_variant	22878	exon27			CCTTTTTTGATGA	AB023229	CCDS11901.1	18q12.1	2011-10-10	2010-06-29	2010-06-29	ENSG00000153339	ENSG00000153339		"Trafficking protein particle complex"	29169	protein-coding gene	gene with protein product	"general sporulation gene 1 homolog (S. cerevisiae)"	614136	"KIAA1012"	KIAA1012		10231032, 11230166	Standard	NM_014939		Approved	HsT2706, TRS85, GSG1	uc002kxc.4	Q9Y2L5	OTTHUMG00000132267	ENST00000283351.4:c.3978A>G	18.37:g.29419280T>C		41.0	0.0		50.0	19.0	NM_014939	A0JP15|B3KME5|Q9H0L2	Silent	SNP	ENST00000283351.4	37	CCDS11901.1																																																																																			.	.		0.338	TRAPPC8-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255355.1	NM_014939		C	29419280	T	C	29419280	2	2	268	1	0	0	0	0	0	0	0	1	8213	1838	64	2		2	KIAA1012	18	29419280	Silent	SNP	T	TCGA-FV-A495-01A-11D-A25V-10		29419280	48657968	74	39136										
ZNF441	126068	hgsc.bcm.edu	37	chr19	11892231	11892231	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	tcacactggggagagaccctAtaagtgtaaactatgtggga	12	7	1	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr19:11892231A>G	ENST00000357901.4	+	4	1694	c.1592A>G	c.(1591-1593)tAt>tGt	p.Y531C	ZNF441_ENST00000454339.2_Missense_Mutation_p.Y464C	NM_152355.2	NP_689568.2	Q8N8Z8	ZN441_HUMAN	zinc finger protein 441	531					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GAGAGACCCTATAAGTGTAAA	0.418																																					p.Y531C		.	.											.	ZNF441	.	.	0			c.A1592G						.						50	52	51					19																	11892231		2203	4299	6502	SO:0001583	missense	126068	exon4			GACCCTATAAGTG	AK095956	CCDS12266.2	19p13.13	2013-01-08			ENSG00000197044	ENSG00000197044		"Zinc fingers, C2H2-type", "-"	20875	protein-coding gene	gene with protein product							Standard	NM_152355		Approved	FLJ38637	uc010dyj.3	Q8N8Z8	OTTHUMG00000154449	ENST00000357901.4:c.1592A>G	19.37:g.11892231A>G	ENSP00000350576:p.Tyr531Cys	38.0	0.0		42.0	10.0	NM_152355		Missense_Mutation	SNP	ENST00000357901.4	37	CCDS12266.2	.	.	.	.	.	.	.	.	.	.	-	14.46	2.540618	0.45280	.	.	ENSG00000197044	ENST00000409902;ENST00000357901;ENST00000454339	T;T	0.25414	1.8;1.8	1.22	0.153	0.14897	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.26340	0.0643	M	0.75085	2.285	0.09310	N	1	P	0.46220	0.874	B	0.42738	0.396	T	0.23368	-1.0190	9	0.87932	D	0	.	2.1633	0.03830	0.3523:0.0:0.3807:0.2669	.	531	Q8N8Z8	ZN441_HUMAN	C	487;531;464	ENSP00000350576:Y531C;ENSP00000403738:Y464C	ENSP00000350576:Y531C	Y	+	2	0	ZNF441	11753231	0.001000	0.12720	0.015000	0.15790	0.883000	0.51084	0.225000	0.17757	-0.012000	0.14223	0.254000	0.18369	TAT	.	.		0.418	ZNF441-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335273.3	NM_152355		G	11892231	A	G	11892231	3	3	268	1	0	0	0	0	1	0	0	0	17929	449	16	2	1606	2	ZNF441	19	11892231	Missense_Mutation	SNP	A	TCGA-FV-A495-01A-11D-A25V-10		11892231	47236752	75	39137										
ZNF430	80264	hgsc.bcm.edu	37	chr19	21240807	21240807	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	aacaaagtaattcatactggAgagaaaccctacaaatgtga	7	7	1	2			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr19:21240807A>G	ENST00000261560.5	+	5	1874	c.1693A>G	c.(1693-1695)Aga>Gga	p.R565G	AC012627.1_ENST00000578233.1_RNA	NM_001172671.1|NM_025189.3	NP_001166142.1|NP_079465.3	Q9H8G1	ZN430_HUMAN	zinc finger protein 430	565					regulation of transcription, DNA-templated (GO:0006355)|substantia nigra development (GO:0021762)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	23						TTCATACTGGAGAGAAACCCT	0.388																																					p.R565G		.	.											.	ZNF430	.	.	0			c.A1693G						.						29	32	31					19																	21240807		2157	4271	6428	SO:0001583	missense	80264	exon5			TACTGGAGAGAAA	AK023721	CCDS32978.1	19p12	2013-01-08				ENSG00000118620		"Zinc fingers, C2H2-type", "-"	20808	protein-coding gene	gene with protein product							Standard	NM_025189		Approved	FLJ13659	uc002npj.3	Q9H8G1		ENST00000261560.5:c.1693A>G	19.37:g.21240807A>G	ENSP00000261560:p.Arg565Gly	25.0	0.0		19.0	11.0	NM_025189	Q86V70	Missense_Mutation	SNP	ENST00000261560.5	37	CCDS32978.1	.	.	.	.	.	.	.	.	.	.	.	8.708	0.911376	0.17833	.	.	ENSG00000118620	ENST00000261560	T	0.05580	3.42	0.381	0.381	0.16228	.	.	.	.	.	T	0.01320	0.0043	N	0.00500	-1.43	0.27793	N	0.942753	B;B	0.17038	0.02;0.0	B;B	0.04013	0.001;0.0	T	0.46665	-0.9175	9	0.02654	T	1	.	4.4892	0.11805	0.6706:0.3294:0.0:0.0	.	564;565	Q2NKJ9;Q9H8G1	.;ZN430_HUMAN	G	565	ENSP00000261560:R565G	ENSP00000261560:R565G	R	+	1	2	ZNF430	21032647	0.109000	0.22037	0.594000	0.28785	0.566000	0.35808	-1.489000	0.02306	0.378000	0.24764	0.369000	0.22263	AGA	.	.		0.388	ZNF430-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463539.1	NM_025189		G	21240807	A	G	21240807	3	3	268	1	0	0	0	0	1	0	0	0	17919	296	11	2	1711	2	ZNF430	19	21240807	Missense_Mutation	SNP	A	TCGA-FV-A495-01A-11D-A25V-10	9348576	21240807	37888176	76	39138										
ZNF536	9745	hgsc.bcm.edu	37	chr19	31038889	31038889	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	tccgcactgtgactatgccgGcacgcagtcagcatccttaa	9	14	1	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr19:31038889G>A	ENST00000355537.3	+	4	2510	c.2363G>A	c.(2362-2364)gGc>gAc	p.G788D		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	788					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					GACTATGCCGGCACGCAGTCA	0.507																																					p.G788D		.	.											.	ZNF536	.	.	0			c.G2363A						.						65	69	68					19																	31038889		2203	4300	6503	SO:0001583	missense	9745	exon4			ATGCCGGCACGCA		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"Zinc fingers, C2H2-type"	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.2363G>A	19.37:g.31038889G>A	ENSP00000347730:p.Gly788Asp	85.0	0.0		79.0	14.0	NM_014717	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	37	CCDS32984.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.072364	0.76415	.	.	ENSG00000198597	ENST00000355537	T	0.18338	2.22	6.08	6.08	0.98989	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.35158	0.0922	L	0.34521	1.04	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.00998	-1.1486	10	0.51188	T	0.08	-33.1648	20.6721	0.99693	0.0:0.0:1.0:0.0	.	788;788	A7E228;O15090	.;ZN536_HUMAN	D	788	ENSP00000347730:G788D	ENSP00000347730:G788D	G	+	2	0	ZNF536	35730729	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.467000	0.97671	2.894000	0.99253	0.591000	0.81541	GGC	.	.		0.507	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		A	31038889	G	A	31038889	3	1	268	1	0	0	0	0	1	0	0	0	17989	1203	42	3	2373	3	ZNF536	19	31038889	Missense_Mutation	SNP	G	TCGA-FV-A495-01A-11D-A25V-10	9798082	31038889	28090094	77	39139										
PPP5C	5536	hgsc.bcm.edu	37	chr19	46850460	46850460	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	ggagctcaagactcaggccaAtgactacttcaaaggtgcgc	11	11	3	2			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr19:46850460A>G	ENST00000012443.4	+	1	210	c.107A>G	c.(106-108)aAt>aGt	p.N36S	PPP5C_ENST00000391919.1_5'UTR	NM_006247.3	NP_006238.1	P53041	PPP5_HUMAN	protein phosphatase 5, catalytic subunit	36					cell death (GO:0008219)|DNA repair (GO:0006281)|mitotic nuclear division (GO:0007067)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein dephosphorylation (GO:0006470)|protein heterooligomerization (GO:0051291)|response to morphine (GO:0043278)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|RNA binding (GO:0003723)|signal transducer activity (GO:0004871)			endometrium(4)|kidney(1)|large_intestine(5)|liver(2)|lung(4)|ovary(1)|pancreas(1)	18		Ovarian(192;0.0731)|all_neural(266;0.196)		OV - Ovarian serous cystadenocarcinoma(262;0.000196)|all cancers(93;0.00192)|GBM - Glioblastoma multiforme(486;0.0499)|Epithelial(262;0.0504)		ACTCAGGCCAATGACTACTTC	0.677											OREG0025570	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N36S		.	.											.	PPP5C	.	.	0			c.A107G						.						25	22	23					19																	46850460		2197	4297	6494	SO:0001583	missense	5536	exon1			AGGCCAATGACTA		CCDS12684.1	19q13.3	2013-01-10			ENSG00000011485	ENSG00000011485	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits", "Tetratricopeptide (TTC) repeat domain containing"	9322	protein-coding gene	gene with protein product		600658		PPP5		8666404	Standard	NM_006247		Approved	PP5	uc002pem.3	P53041	OTTHUMG00000134287	ENST00000012443.4:c.107A>G	19.37:g.46850460A>G	ENSP00000012443:p.Asn36Ser	37.0	0.0	942	53.0	9.0	NM_006247	Q16722|Q53XV2	Missense_Mutation	SNP	ENST00000012443.4	37	CCDS12684.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.044402	0.75732	.	.	ENSG00000011485	ENST00000012443;ENST00000451918	T	0.65178	-0.14	3.43	3.43	0.39272	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.64402	U	0.000002	D	0.82921	0.5142	H	0.95151	3.63	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.994	D	0.86187	0.1610	10	0.87932	D	0	-21.7574	10.1632	0.42864	1.0:0.0:0.0:0.0	.	36;36	B2R6R6;P53041	.;PPP5_HUMAN	S	36	ENSP00000012443:N36S	ENSP00000012443:N36S	N	+	2	0	PPP5C	51542300	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	5.523000	0.67099	1.552000	0.49463	0.379000	0.24179	AAT	.	.		0.677	PPP5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258969.2	NM_006247		G	46850460	A	G	46850460	3	3	268	1	0	0	0	0	1	0	0	0	12418	101	4	2	109	2	PPP5C	19	46850460	Missense_Mutation	SNP	A	TCGA-FV-A495-01A-11D-A25V-10	15811571	46850460	12278523	78	39140										
ZNF175	7728	hgsc.bcm.edu	37	chr19	52090484	52090484	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	ctctttgcccaacagagaatTcatagtgtaggaaacctcca	7	11	2	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr19:52090484T>A	ENST00000262259.2	+	5	1258	c.900T>A	c.(898-900)atT>atA	p.I300I	ZNF175_ENST00000436511.2_Intron	NM_007147.2	NP_009078.1	Q9Y473	ZN175_HUMAN	zinc finger protein 175	300					defense response to virus (GO:0051607)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24		all_neural(266;0.0299)		GBM - Glioblastoma multiforme(134;0.000426)|OV - Ovarian serous cystadenocarcinoma(262;0.0257)		AACAGAGAATTCATAGTGTAG	0.423																																					p.I300I		.	.											.	ZNF175	.	.	0			c.T900A						.						97	100	99					19																	52090484		2203	4299	6502	SO:0001819	synonymous_variant	7728	exon5			GAGAATTCATAGT	D50419	CCDS12837.1	19q13.4	2013-01-08			ENSG00000105497	ENSG00000105497		"Zinc fingers, C2H2-type", "-"	12964	protein-coding gene	gene with protein product		601139				8838321	Standard	NM_007147		Approved	OTK18	uc002pxb.3	Q9Y473	OTTHUMG00000167771	ENST00000262259.2:c.900T>A	19.37:g.52090484T>A		102.0	0.0		131.0	33.0	NM_007147	A8K9H2	Silent	SNP	ENST00000262259.2	37	CCDS12837.1																																																																																			.	.		0.423	ZNF175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396205.1	NM_007147		A	52090484	T	A	52090484	2	1	268	1	0	0	0	0	0	0	0	1	17760	1771	62	4		4	ZNF175	19	52090484	Silent	SNP	T	TCGA-FV-A495-01A-11D-A25V-10	5240024	52090484	7038499	79	39141										
LILRB1	10859	hgsc.bcm.edu	37	chr19	55143640	55143640	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	atgcttatgactcgaactctCcctatgagtggtctctaccc	7	13	2	2			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr19:55143640C>T	ENST00000396331.1	+	6	970	c.613C>T	c.(613-615)Ccc>Tcc	p.P205S	LILRB1_ENST00000448689.1_Missense_Mutation_p.P205S|LILRB1_ENST00000396317.1_Missense_Mutation_p.P205S|LILRB1_ENST00000396327.3_Missense_Mutation_p.P205S|AC009892.1_ENST00000578908.1_RNA|LILRB1_ENST00000427581.2_Missense_Mutation_p.P241S|LILRB1_ENST00000418536.2_Missense_Mutation_p.P205S|LILRB1_ENST00000396332.4_Missense_Mutation_p.P205S|LILRB1_ENST00000434867.2_Missense_Mutation_p.P205S|LILRB1_ENST00000324602.7_Missense_Mutation_p.P205S|LILRB1_ENST00000396321.2_Missense_Mutation_p.P205S|LILRB1_ENST00000396315.1_Missense_Mutation_p.P205S	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	205	Ig-like C2-type 2.				cellular response to lipopolysaccharide (GO:0071222)|defense response to virus (GO:0051607)|dendritic cell differentiation (GO:0097028)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma production (GO:0032609)|interferon-gamma secretion (GO:0072643)|negative regulation of alpha-beta T cell activation (GO:0046636)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of CD8-positive, alpha-beta T cell activation (GO:2001186)|negative regulation of cell cycle (GO:0045786)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of endocytosis (GO:0045806)|negative regulation of interferon-beta secretion (GO:0035548)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-12 secretion (GO:2001183)|negative regulation of mononuclear cell proliferation (GO:0032945)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of osteoclast development (GO:2001205)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transforming growth factor-beta secretion (GO:2001202)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of gamma-delta T cell activation involved in immune response (GO:2001193)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor internalization (GO:0031623)|regulation of immune response (GO:0050776)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation involved in immune response (GO:0002309)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	HLA-A specific inhibitory MHC class I receptor activity (GO:0030107)|HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)|MHC class I protein binding (GO:0042288)|MHC class I receptor activity (GO:0032393)|protein homodimerization activity (GO:0042803)|protein phosphatase 1 binding (GO:0008157)|SH2 domain binding (GO:0042169)	p.P205T(2)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	74				GBM - Glioblastoma multiforme(193;0.0188)		CTCGAACTCTCCCTATGAGTG	0.607										HNSCC(37;0.09)																											p.P205S		.	.											.	LILRB1	.	.	2	Substitution - Missense(2)	lung(2)	c.C613T						.						157	155	156					19																	55143640		2203	4300	6503	SO:0001583	missense	10859	exon5			AACTCTCCCTATG	AF009220	CCDS42614.1, CCDS42615.1, CCDS42616.1, CCDS42617.1, CCDS62803.1	19q13.4	2013-01-11						"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6605	protein-coding gene	gene with protein product		604811				9285411, 9382880	Standard	XM_006726246		Approved	LIR-1, ILT2, MIR-7, CD85, LIR1, CD85j	uc002qgm.3	Q8NHL6		ENST00000396331.1:c.613C>T	19.37:g.55143640C>T	ENSP00000379622:p.Pro205Ser	280.0	0.0		290.0	69.0	NM_001081637	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Missense_Mutation	SNP	ENST00000396331.1	37	CCDS42617.1	.	.	.	.	.	.	.	.	.	.	C	5.476	0.272920	0.10349	.	.	ENSG00000104972	ENST00000396321;ENST00000418536;ENST00000448689;ENST00000396331;ENST00000396327;ENST00000324602;ENST00000434867;ENST00000396332;ENST00000427581;ENST00000396317;ENST00000396315	T;T;T;T;T;T;T;T;T;T;T	0.22743	1.94;1.94;1.94;1.94;1.94;1.94;1.94;1.94;1.94;1.94;1.94	1.49	0.396	0.16309	Immunoglobulin-like fold (1);	0.431079	0.19689	N	0.108302	T	0.21881	0.0527	M	0.64630	1.985	0.09310	N	1	D;P;P;P;B	0.55172	0.97;0.662;0.92;0.637;0.327	P;B;B;B;B	0.47470	0.548;0.096;0.186;0.082;0.044	T	0.10847	-1.0612	10	0.56958	D	0.05	.	3.6471	0.08189	0.0:0.7403:0.0:0.2597	.	205;205;205;205;205	A8MVE2;Q8NHL6-3;A2IXV4;Q8NHL6-2;Q8NHL6	.;.;.;.;LIRB1_HUMAN	S	205;205;205;205;205;205;205;205;241;205;205	ENSP00000379614:P205S;ENSP00000391514:P205S;ENSP00000409968:P205S;ENSP00000379622:P205S;ENSP00000379618:P205S;ENSP00000315997:P205S;ENSP00000405243:P205S;ENSP00000379623:P205S;ENSP00000395004:P241S;ENSP00000379610:P205S;ENSP00000379608:P205S	ENSP00000315997:P205S	P	+	1	0	LILRB1	59835452	0.000000	0.05858	0.002000	0.10522	0.012000	0.07955	-0.125000	0.10579	0.181000	0.19994	0.184000	0.17185	CCC	.	.		0.607	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4			T	55143640	C	T	55143640	3	4	268	1	0	0	0	0	1	0	0	0	8799	855	30	3	627	3	LILRB1	19	55143640	Missense_Mutation	SNP	C	TCGA-FV-A495-01A-11D-A25V-10	3053156	55143640	3985343	80	39142										
FIZ1	84922	hgsc.bcm.edu	37	chr19	56104976	56104976	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	ggagaagcggagctcgcagaCcaggcagcagtagggtttct	16	9	1	2			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr19:56104976C>T	ENST00000221665.3	-	3	420	c.331G>A	c.(331-333)Gtc>Atc	p.V111I	FIZ1_ENST00000592585.1_Intron	NM_032836.2	NP_116225.2	Q96SL8	FIZ1_HUMAN	FLT3-interacting zinc finger 1	111					positive regulation of protein phosphorylation (GO:0001934)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|receptor tyrosine kinase binding (GO:0030971)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)	11			BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)		AGCTCGCAGACCAGGCAGCAG	0.667																																					p.V111I		.	.											.	FIZ1	.	.	0			c.G331A						.						12	17	15					19																	56104976		1893	3702	5595	SO:0001583	missense	84922	exon3			CGCAGACCAGGCA	AK027674	CCDS12928.1	19q13.42	2013-01-08				ENSG00000179943		"Zinc fingers, C2H2-type"	25917	protein-coding gene	gene with protein product		609133				12566383	Standard	NM_032836		Approved	FLJ14768, ZNF798	uc002qli.4	Q96SL8		ENST00000221665.3:c.331G>A	19.37:g.56104976C>T	ENSP00000221665:p.Val111Ile	108.0	0.0		127.0	27.0	NM_032836	A2RU72|Q6ZMJ7	Missense_Mutation	SNP	ENST00000221665.3	37	CCDS12928.1	.	.	.	.	.	.	.	.	.	.	C	12.10	1.837455	0.32513	.	.	ENSG00000179943	ENST00000221665	T	0.18016	2.24	3.63	2.59	0.31030	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12732	0.0309	N	0.20304	0.555	0.80722	D	1	B	0.24618	0.107	B	0.33690	0.168	T	0.12477	-1.0546	9	0.72032	D	0.01	-17.0241	8.6145	0.33822	0.0:0.8818:0.0:0.1182	.	111	Q96SL8	FIZ1_HUMAN	I	111	ENSP00000221665:V111I	ENSP00000221665:V111I	V	-	1	0	FIZ1	60796788	0.000000	0.05858	1.000000	0.80357	0.987000	0.75469	1.225000	0.32551	2.028000	0.59812	0.561000	0.74099	GTC	.	.		0.667	FIZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453350.1	NM_032836		T	56104976	C	T	56104976	3	4	268	1	0	0	0	0	1	0	0	0	5908	507	18	3	1163	3	FIZ1	19	56104976	Missense_Mutation	SNP	C	TCGA-FV-A495-01A-11D-A25V-10	961336	56104976	3024007	81	39143										
PEG3	5178	hgsc.bcm.edu	37	chr19	57327699	57327699	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	tctttcgagaatgaattttcTgatgctcactgagctctgag	9	8	4	5			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr19:57327699T>A	ENST00000326441.9	-	10	2474	c.2111A>T	c.(2110-2112)cAg>cTg	p.Q704L	ZIM2_ENST00000593711.1_Intron|PEG3_ENST00000423103.2_Missense_Mutation_p.Q704L|ZIM2_ENST00000391708.3_Intron|ZIM2_ENST00000601070.1_Intron|PEG3_ENST00000598410.1_Missense_Mutation_p.Q580L|ZIM2_ENST00000221722.5_Intron|PEG3_ENST00000593695.1_Missense_Mutation_p.Q578L|ZIM2_ENST00000599935.1_Intron	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	704					apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		ATGAATTTTCTGATGCTCACT	0.428																																					p.Q704L		.	.											.	PEG3	.	.	0			c.A2111T						.						70	68	69					19																	57327699		2203	4300	6503	SO:0001583	missense	5178	exon9			ATTTTCTGATGCT	AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"Zinc fingers, C2H2-type", "-", "-", "-"	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.2111A>T	19.37:g.57327699T>A	ENSP00000326581:p.Gln704Leu	100.0	0.0		101.0	20.0	NM_001146184	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Missense_Mutation	SNP	ENST00000326441.9	37	CCDS12948.1	.	.	.	.	.	.	.	.	.	.	T	12.95	2.092830	0.36952	.	.	ENSG00000198300	ENST00000326441;ENST00000423103	T;T	0.15256	2.44;2.44	4.05	-1.05	0.10036	.	0.925177	0.08914	N	0.875485	T	0.21227	0.0511	M	0.85462	2.755	.	.	.	B;B;B	0.26672	0.006;0.072;0.156	B;B;B	0.21360	0.003;0.021;0.034	T	0.29488	-1.0010	9	0.72032	D	0.01	-8.765	4.9444	0.13982	0.3408:0.0:0.2755:0.3837	.	580;704;639	A7E2B8;Q9GZU2;Q96Q96	.;PEG3_HUMAN;.	L	704	ENSP00000326581:Q704L;ENSP00000403051:Q704L	ENSP00000326581:Q704L	Q	-	2	0	ZIM2	62019511	0.000000	0.05858	0.179000	0.23059	0.984000	0.73092	-0.672000	0.05244	-0.324000	0.08589	0.477000	0.44152	CAG	.	.		0.428	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2			A	57327699	T	A	57327699	3	1	268	1	0	0	0	0	1	0	0	0	11729	1580	55	4	2659	4	PEG3	19	57327699	Missense_Mutation	SNP	T	TCGA-FV-A495-01A-11D-A25V-10	1222723	57327699	1801284	82	39144										
C20orf103	24141	hgsc.bcm.edu	37	chr20	9510307	9510307	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	agagcataaatgcccagtggAtgagcgggagcaactggaag	15	7	0	2			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr20:9510307A>G	ENST00000246070.2	+	6	1175	c.683A>G	c.(682-684)gAt>gGt	p.D228G	LAMP5_ENST00000427562.2_Missense_Mutation_p.D184G	NM_012261.3	NP_036393.1	Q9UJQ1	LAMP5_HUMAN	lysosomal-associated membrane protein family, member 5	228						cytoplasmic vesicle membrane (GO:0030659)|dendrite membrane (GO:0032590)|early endosome membrane (GO:0031901)|endoplasmic reticulum-Golgi intermediate compartment membrane (GO:0033116)|endosome membrane (GO:0010008)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)											TGCCCAGTGGATGAGCGGGAG	0.468																																					p.D228G		.	.											.	.	.	.	0			c.A683G						.						94	78	83					20																	9510307		2203	4300	6503	SO:0001583	missense	24141	exon6			CAGTGGATGAGCG	AL121740	CCDS13106.1, CCDS56177.1	20p12	2013-03-14	2011-11-25	2011-11-25	ENSG00000125869	ENSG00000125869			16097	protein-coding gene	gene with protein product	"brain and dendritic cell associated LAMP"	614641	"chromosome 20 open reading frame 103"	C20orf103		11780052, 21642595	Standard	NM_012261		Approved	dJ1119D9.3, BAD-LAMP, UNC-43	uc002wni.2	Q9UJQ1	OTTHUMG00000031851	ENST00000246070.2:c.683A>G	20.37:g.9510307A>G	ENSP00000246070:p.Asp228Gly	105.0	0.0		153.0	25.0	NM_012261	B4DHZ7|B7Z9Z9	Missense_Mutation	SNP	ENST00000246070.2	37	CCDS13106.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.043371	0.75732	.	.	ENSG00000125869	ENST00000246070;ENST00000427562	T;T	0.43294	0.95;0.95	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.51346	0.1669	N	0.24115	0.695	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.47484	-0.9114	9	.	.	.	-18.7431	16.8061	0.85666	1.0:0.0:0.0:0.0	.	184;228	Q9UJQ1-2;Q9UJQ1	.;CT103_HUMAN	G	228;184	ENSP00000246070:D228G;ENSP00000406360:D184G	.	D	+	2	0	C20orf103	9458307	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	8.451000	0.90343	2.367000	0.80283	0.528000	0.53228	GAT	.	.		0.468	LAMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077946.2	NM_012261		G	9510307	A	G	9510307	3	3	268	1	0	0	0	0	1	0	0	0	2077	333	12	2	705	2	C20orf103	20	9510307	Missense_Mutation	SNP	A	TCGA-FV-A495-01A-11D-A25V-10		9510307	53515213	83	39145										
OVOL2	58495	hgsc.bcm.edu	37	chr20	18005322	18005322	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	ctcaggctggtattctcctgGtgtgcggatgtcagcttgcc	13	11	3	0			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr20:18005322G>C	ENST00000278780.6	-	4	1028	c.786C>G	c.(784-786)caC>caG	p.H262Q	OVOL2_ENST00000483661.1_5'UTR	NM_021220.2	NP_067043.2	Q9BRP0	OVOL2_HUMAN	ovo-like zinc finger 2	262					angiogenesis (GO:0001525)|dorsal/ventral pattern formation (GO:0009953)|embryonic digestive tract morphogenesis (GO:0048557)|endocardium formation (GO:0060214)|heart looping (GO:0001947)|heart trabecula formation (GO:0060347)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell migration (GO:0001755)|neural fold formation (GO:0001842)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle (GO:0051726)|regulation of keratinocyte proliferation (GO:0010837)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(3)	6						TATTCTCCTGGTGTGCGGATG	0.532																																					p.H262Q		.	.											.	OVOL2	.	.	0			c.C786G						.						99	81	87					20																	18005322		2203	4300	6503	SO:0001583	missense	58495	exon4			CTCCTGGTGTGCG	AK022284	CCDS13132.1	20p11.23	2013-10-17	2013-10-17	2005-05-31	ENSG00000125850	ENSG00000125850		"Zinc fingers, C2H2-type"	15804	protein-coding gene	gene with protein product			"zinc finger protein 339", "ovo-like 2 (Drosophila)"	ZNF339			Standard	NM_021220		Approved	bA504H3.3, HOVO2	uc002wqi.1	Q9BRP0	OTTHUMG00000031960	ENST00000278780.6:c.786C>G	20.37:g.18005322G>C	ENSP00000278780:p.His262Gln	237.0	0.0		293.0	22.0	NM_021220	Q5T8B4|Q9BX22|Q9HA54|Q9Y4M0	Missense_Mutation	SNP	ENST00000278780.6	37	CCDS13132.1	.	.	.	.	.	.	.	.	.	.	G	7.012	0.556918	0.13436	.	.	ENSG00000125850	ENST00000278780	T	0.07327	3.2	5.0	1.56	0.23342	.	0.670225	0.14280	N	0.329599	T	0.04137	0.0115	N	0.08118	0	0.21064	N	0.999797	B	0.21381	0.055	B	0.14023	0.01	T	0.44360	-0.9333	10	0.14656	T	0.56	-10.0163	11.7714	0.51960	0.086:0.6517:0.2622:0.0	.	262	Q9BRP0	OVOL2_HUMAN	Q	262	ENSP00000278780:H262Q	ENSP00000278780:H262Q	H	-	3	2	OVOL2	17953322	0.708000	0.27876	0.229000	0.23960	0.108000	0.19459	0.180000	0.16860	0.463000	0.27118	0.467000	0.42956	CAC	.	.		0.532	OVOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078148.5	NM_021220		C	18005322	G	C	18005322	3	2	268	1	0	0	0	0	1	0	0	0	11336	1252	44	4	45	4	OVOL2	20	18005322	Missense_Mutation	SNP	G	TCGA-FV-A495-01A-11D-A25V-10	8495015	18005322	45020198	84	39146										
LBP	3929	hgsc.bcm.edu	37	chr20	36983752	36983752	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	gcttctctccccaggtggctGttgaacctcttccacaacca	7	16	2	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr20:36983752G>A	ENST00000217407.2	+	5	692	c.531G>A	c.(529-531)ctG>ctA	p.L177L		NM_004139.3	NP_004130.2	P18428	LBP_HUMAN	lipopolysaccharide binding protein	177					acute-phase response (GO:0006953)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of molecule of bacterial origin (GO:0032490)|innate immune response (GO:0045087)|leukocyte chemotaxis involved in inflammatory response (GO:0002232)|lipopolysaccharide transport (GO:0015920)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation involved in immune response (GO:0002281)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of tumor necrosis factor production (GO:0032720)|opsonization (GO:0008228)|positive regulation of chemokine production (GO:0032722)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of macrophage activation (GO:0043032)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of respiratory burst involved in inflammatory response (GO:0060265)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|response to lipopolysaccharide (GO:0032496)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)|lipoteichoic acid binding (GO:0070891)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(1)|urinary_tract(1)	28		Myeloproliferative disorder(115;0.00878)				CCAGGTGGCTGTTGAACCTCT	0.597																																					p.L177L		.	.											.	LBP	.	.	0			c.G531A						.						105	84	91					20																	36983752		2203	4299	6502	SO:0001819	synonymous_variant	3929	exon5			GTGGCTGTTGAAC		CCDS13304.1	20q11.23	2011-08-16	2001-11-28		ENSG00000129988	ENSG00000129988		"BPI fold containing"	6517	protein-coding gene	gene with protein product	"BPI fold containing family D, member 2"	151990	"lipopolysaccharide-binding protein"			8432532	Standard	NM_004139		Approved	BPIFD2	uc002xic.2	P18428	OTTHUMG00000032447	ENST00000217407.2:c.531G>A	20.37:g.36983752G>A		92.0	0.0		102.0	39.0	NM_004139	B2R938|O43438|Q92672|Q9H403|Q9UD66	Silent	SNP	ENST00000217407.2	37	CCDS13304.1																																																																																			.	.		0.597	LBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079174.2	NM_004139		A	36983752	G	A	36983752	2	1	268	1	0	0	0	0	0	0	0	1	8660	1364	48	3		3	LBP	20	36983752	Silent	SNP	G	TCGA-FV-A495-01A-11D-A25V-10	18978430	36983752	26041768	85	39147										
CTCFL	140690	hgsc.bcm.edu	37	chr20	56073609	56073609	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	cgcaacccgaatccctctcaCttatccatcgtgttgaggag	8	14	1	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr20:56073609C>T	ENST00000608263.1	-	10	2650	c.1989G>A	c.(1987-1989)aaG>aaA	p.K663K	CTCFL_ENST00000609232.1_Silent_p.K663K|CTCFL_ENST00000371196.2_Silent_p.K663K|CTCFL_ENST00000243914.3_Silent_p.K663K|CTCFL_ENST00000429804.3_Silent_p.K613K|CTCFL_ENST00000423479.3_Splice_Site	NM_001269041.1	NP_001255970.1	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor (zinc finger protein)-like	663					cell cycle (GO:0007049)|DNA methylation involved in gamete generation (GO:0043046)|histone methylation (GO:0016571)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of histone H3-K4 methylation (GO:0051569)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(28)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			ATCCCTCTCACTTATCCATCG	0.473																																					p.K663K		.	.											.	CTCFL	.	.	0			c.G1989A						.						178	148	158					20																	56073609		2203	4300	6503	SO:0001819	synonymous_variant	140690	exon10			CTCTCACTTATCC		CCDS13459.1, CCDS58776.1, CCDS58777.1, CCDS58778.1, CCDS58779.1, CCDS58780.1, CCDS58781.1, CCDS58782.1, CCDS68161.1, CCDS68162.1, CCDS68163.1, CCDS68164.1	20q13.31	2013-01-08			ENSG00000124092	ENSG00000124092		"Zinc fingers, C2H2-type"	16234	protein-coding gene	gene with protein product	"cancer/testis antigen 27"	607022					Standard	NM_001269040		Approved	dJ579F20.2, BORIS, CT27	uc010giw.1	Q8NI51	OTTHUMG00000032829	ENST00000608263.1:c.1989G>A	20.37:g.56073609C>T		111.0	0.0		159.0	41.0	NM_001269041	A0S6W1|A1L4C6|A6XGL8|A6XGM2|A6XGM3|A6XGM8|A6XGN0|A6XGN1|A6XGN2|A6XGN3|A6XGN4|E7EQ27|E7EUE3|E9PBA9|Q5JUG4|Q9BZ30|Q9NQJ3	Silent	SNP	ENST00000608263.1	37	CCDS13459.1	.	.	.	.	.	.	.	.	.	.	C	7.543	0.661041	0.14645	.	.	ENSG00000124092	ENST00000423479	.	.	.	3.85	2.9	0.33743	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.3667	0.38228	0.0:0.7825:0.2175:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CTCFL	55507015	0.141000	0.22595	0.097000	0.21041	0.181000	0.23173	0.604000	0.24164	0.822000	0.34565	0.491000	0.48974	.	.	.		0.473	CTCFL-019	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472040.1	NM_080618		T	56073609	C	T	56073609	2	4	268	1	0	0	0	0	0	0	0	1	4003	564	20	3		3	CTCFL	20	56073609	Silent	SNP	C	TCGA-FV-A495-01A-11D-A25V-10	19089857	56073609	6951911	86	39148										
CACNG2	10369	hgsc.bcm.edu	37	chr22	36960731	36960731	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	gcctggaggtagtccgtggcGcgggccgtggcccgcagctg	19	13	0	0			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chr22:36960731G>A	ENST00000300105.6	-	4	1620	c.639C>T	c.(637-639)cgC>cgT	p.R213R	RP5-1119A7.17_ENST00000562756.1_RNA	NM_006078.3	NP_006069.1	Q9Y698	CCG2_HUMAN	calcium channel, voltage-dependent, gamma subunit 2	213					membrane depolarization (GO:0051899)|membrane hyperpolarization (GO:0060081)|neuromuscular junction development (GO:0007528)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)	p.R213R(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	18						AGTCCGTGGCGCGGGCCGTGG	0.677																																					p.R213R		.	.											.	CACNG2	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C639T						.						78	93	88					22																	36960731		2203	4298	6501	SO:0001819	synonymous_variant	10369	exon4			CGTGGCGCGGGCC	AF096322	CCDS13931.1	22q13.1	2006-08-01			ENSG00000166862	ENSG00000166862		"Calcium channel subunits"	1406	protein-coding gene	gene with protein product		602911					Standard	NM_006078		Approved	stargazin, MGC138502, MGC138504	uc003aps.2	Q9Y698	OTTHUMG00000030612	ENST00000300105.6:c.639C>T	22.37:g.36960731G>A		20.0	0.0		22.0	10.0	NM_006078	Q2M1M1|Q5TGT3|Q9UGZ7	Silent	SNP	ENST00000300105.6	37	CCDS13931.1																																																																																			.	.		0.677	CACNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075500.2			A	36960731	G	A	36960731	2	1	268	1	0	0	0	0	0	0	0	1	2559	1074	38	1		1	CACNG2	22	36960731	Silent	SNP	G	TCGA-FV-A495-01A-11D-A25V-10		36960731	14343835	87	39149										
CXorf58	254158	hgsc.bcm.edu	37	chrX	23953337	23953337	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	gcagttttttcgatgaggccCctgcattttctggcggcaga	12	10	1	2			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chrX:23953337C>A	ENST00000379211.3	+	7	1129	c.580C>A	c.(580-582)Cct>Act	p.P194T		NM_001169574.1|NM_152761.2	NP_001163045.1|NP_689974.2	Q96LI9	CX058_HUMAN	chromosome X open reading frame 58	194										breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|prostate(1)	14						CGATGAGGCCCCTGCATTTTC	0.428																																					p.P194T		.	.											.	CXorf58	.	.	0			c.C580A						.						106	111	109					X																	23953337		2203	4300	6503	SO:0001583	missense	254158	exon7			GAGGCCCCTGCAT	AK058173	CCDS14209.1	Xp22.11	2012-11-28			ENSG00000165182	ENSG00000165182			26356	protein-coding gene	gene with protein product							Standard	NM_152761		Approved	FLJ25444	uc004daz.1	Q96LI9	OTTHUMG00000021258	ENST00000379211.3:c.580C>A	X.37:g.23953337C>A	ENSP00000368511:p.Pro194Thr	37.0	0.0		26.0	8.0	NM_152761		Missense_Mutation	SNP	ENST00000379211.3	37	CCDS14209.1	.	.	.	.	.	.	.	.	.	.	c	14.66	2.603234	0.46423	.	.	ENSG00000165182	ENST00000379211	T	0.28255	1.62	5.91	5.05	0.67936	.	0.083612	0.50627	D	0.000117	T	0.53786	0.1818	M	0.72894	2.215	0.40526	D	0.980881	D;D	0.89917	1.0;1.0	D;D	0.75484	0.986;0.986	T	0.58651	-0.7599	10	0.66056	D	0.02	-19.7543	13.0656	0.59032	0.0:0.9199:0.0:0.0801	.	194;194	B7ZLS7;Q96LI9	.;CX058_HUMAN	T	194	ENSP00000368511:P194T	ENSP00000368511:P194T	P	+	1	0	CXorf58	23863258	0.996000	0.38824	0.835000	0.33067	0.025000	0.11179	4.603000	0.61105	1.254000	0.44035	0.417000	0.27973	CCT	.	.		0.428	CXorf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056071.1	NM_152761		A	23953337	C	A	23953337	3	1	268	1	0	0	0	0	1	0	0	0	4116	623	22	3	602	3	CXorf58	23	23953337	Missense_Mutation	SNP	C	TCGA-FV-A495-01A-11D-A25V-10		23953337	131317223	88	39150										
DMD	1756	hgsc.bcm.edu	37	chrX	31165436	31165436	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	gtgtaactgtgactccagctGtttattgtggtcttccagga	11	8	1	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chrX:31165436G>A	ENST00000357033.4	-	75	10959	c.10753C>T	c.(10753-10755)Cag>Tag	p.Q3585*	DMD_ENST00000378723.3_Nonsense_Mutation_p.Q517*|DMD_ENST00000343523.2_Nonsense_Mutation_p.Q1015*|DMD_ENST00000378702.4_Nonsense_Mutation_p.Q517*|DMD_ENST00000378677.2_Nonsense_Mutation_p.Q3581*|DMD_ENST00000378680.2_Nonsense_Mutation_p.Q407*|DMD_ENST00000541735.1_Nonsense_Mutation_p.Q1015*|DMD_ENST00000474231.1_Nonsense_Mutation_p.Q1125*|DMD_ENST00000378707.3_Nonsense_Mutation_p.Q1125*|DMD_ENST00000361471.4_Nonsense_Mutation_p.Q504*|DMD_ENST00000359836.1_Nonsense_Mutation_p.Q1112*	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	3585					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				GACTCCAGCTGTTTATTGTGG	0.493																																					p.Q3585X		.	.											.	DMD	.	.	0			c.C10753T						.						90	81	84					X																	31165436		2202	4300	6502	SO:0001587	stop_gained	1756	exon75			CCAGCTGTTTATT	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.10753C>T	X.37:g.31165436G>A	ENSP00000354923:p.Gln3585*	154.0	0.0		165.0	10.0	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Nonsense_Mutation	SNP	ENST00000357033.4	37	CCDS14233.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	53|53	21.192109|21.192109	0.99938|0.99938	.|.	.|.	ENSG00000198947|ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000378723;ENST00000358062;ENST00000378677;ENST00000357033;ENST00000359836;ENST00000343523;ENST00000542849;ENST00000535280;ENST00000378707;ENST00000541735;ENST00000378702;ENST00000474231;ENST00000361471;ENST00000378680|ENST00000465285	.|.	.|.	.|.	4.62|4.62	4.62|4.62	0.57501|0.57501	.|.	0.000000|.	0.33515|.	U|.	0.004830|.	.|T	.|0.71668	.|0.3367	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.74856	.|-0.3522	.|3	0.22706|.	T|.	0.39|.	.|.	16.7086|16.7086	0.85379|0.85379	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|I	3577;2244;2241;517;1268;3581;3585;1112;1015;3585;3462;1125;1015;517;1125;504;407|1313	.|.	ENSP00000340057:Q1015X|.	Q|T	-|-	1|2	0|0	DMD|DMD	31075357|31075357	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	9.657000|9.657000	0.98554|0.98554	2.118000|2.118000	0.64928|0.64928	0.513000|0.513000	0.50165|0.50165	CAG|ACA	.	.		0.493	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		A	31165436	G	A	31165436	4	1	268	1	0	0	0	0	0	1	0	0	4582	1386	48	3	410	3	DMD	23	31165436	Nonsense_Mutation	SNP	G	TCGA-FV-A495-01A-11D-A25V-10	7212099	31165436	124105124	89	39151										
GPR173	54328	hgsc.bcm.edu	37	chrX	53106558	53106558	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	gatcgccggctttggccgtgGgcccatgccaccaaccctgc	12	17	0	0			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chrX:53106558G>A	ENST00000332582.4	+	2	1246	c.755G>A	c.(754-756)gGg>gAg	p.G252E		NM_018969.5	NP_061842.1	Q9NS66	GP173_HUMAN	G protein-coupled receptor 173	252					negative regulation of neuron migration (GO:2001223)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|gonadotropin-releasing hormone receptor activity (GO:0004968)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)	16						TTTGGCCGTGGGCCCATGCCA	0.657																																					p.G252E		.	.											.	GPR173	.	.	0			c.G755A						.						30	25	27					X																	53106558		2193	4292	6485	SO:0001583	missense	54328	exon2			GCCGTGGGCCCAT	AB040801	CCDS14349.1	Xp11	2012-08-21	2006-02-15		ENSG00000184194	ENSG00000184194		"GPCR / Class A : Orphans"	18186	protein-coding gene	gene with protein product		300253	"G-protein coupled receptor 173", "G protein coupled receptor 173"			10833454	Standard	NM_018969		Approved	SREB3	uc004dru.3	Q9NS66	OTTHUMG00000021596	ENST00000332582.4:c.755G>A	X.37:g.53106558G>A	ENSP00000331600:p.Gly252Glu	40.0	0.0		49.0	10.0	NM_018969	B1B0A5	Missense_Mutation	SNP	ENST00000332582.4	37	CCDS14349.1	.	.	.	.	.	.	.	.	.	.	G	19.14	3.769867	0.69992	.	.	ENSG00000184194	ENST00000332582	T	0.47177	0.85	5.03	5.03	0.67393	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.66626	0.2808	M	0.75447	2.3	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.64601	-0.6369	10	0.23891	T	0.37	-6.4962	14.8667	0.70422	0.0:0.0:1.0:0.0	.	252	Q9NS66	GP173_HUMAN	E	252	ENSP00000331600:G252E	ENSP00000331600:G252E	G	+	2	0	GPR173	53123283	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.869000	0.99810	2.094000	0.63399	0.529000	0.55759	GGG	.	.		0.657	GPR173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056717.2	NM_018969		A	53106558	G	A	53106558	3	1	268	1	0	0	0	0	1	0	0	0	6679	1232	43	3	757	3	GPR173	23	53106558	Missense_Mutation	SNP	G	TCGA-FV-A495-01A-11D-A25V-10	21941122	53106558	102164002	90	39152										
PFKFB1	5207	hgsc.bcm.edu	37	chrX	54989780	54989780	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	tggtaaacccaccatgatcaCcattgtgggggaattggtaa	11	8	1	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chrX:54989780C>T	ENST00000375006.3	-	2	203	c.133G>A	c.(133-135)Gtg>Atg	p.V45M	PFKFB1_ENST00000545676.1_Intron|PFKFB1_ENST00000374992.2_Missense_Mutation_p.V45M	NM_002625.2	NP_002616.2	P16118	F261_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1	45	6-phosphofructo-2-kinase.				carbohydrate metabolic process (GO:0005975)|dephosphorylation (GO:0016311)|energy reserve metabolic process (GO:0006112)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|intracellular signal transduction (GO:0035556)|organ regeneration (GO:0031100)|positive regulation of glucokinase activity (GO:0033133)|response to cAMP (GO:0051591)|response to glucagon (GO:0033762)|response to glucocorticoid (GO:0051384)|response to insulin (GO:0032868)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase complex (GO:0043540)|cytosol (GO:0005829)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)|fructose-6-phosphate binding (GO:0070095)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(11)|ovary(1)	24						ACCATGATCACCATTGTGGGG	0.443																																					p.V45M		.	.											.	PFKFB1	.	.	0			c.G133A						.						151	126	134					X																	54989780		2203	4300	6503	SO:0001583	missense	5207	exon2			TGATCACCATTGT		CCDS14364.1, CCDS65273.1	Xp11.21	2012-07-13			ENSG00000158571	ENSG00000158571	2.7.1.105, 3.1.3.46		8872	protein-coding gene	gene with protein product		311790		PFRX		9119406	Standard	NM_002625		Approved		uc004dty.2	P16118	OTTHUMG00000021643	ENST00000375006.3:c.133G>A	X.37:g.54989780C>T	ENSP00000364145:p.Val45Met	172.0	0.0		159.0	50.0	NM_001271804	B2RA88|B4DUN5|Q5JXS5|Q99951	Missense_Mutation	SNP	ENST00000375006.3	37	CCDS14364.1	.	.	.	.	.	.	.	.	.	.	C	16.19	3.052740	0.55218	.	.	ENSG00000158571	ENST00000375006;ENST00000374992	T	0.51817	0.69	5.51	5.51	0.81932	6-phosphofructo-2-kinase (1);	0.054916	0.64402	D	0.000001	T	0.70527	0.3234	M	0.88377	2.95	0.29349	N	0.865493	P;D	0.65815	0.922;0.995	P;D	0.69479	0.776;0.964	T	0.72054	-0.4406	10	0.72032	D	0.01	-15.1306	10.9929	0.47559	0.0:0.9104:0.0:0.0896	.	45;45	Q4VBA9;P16118	.;F261_HUMAN	M	45	ENSP00000364131:V45M	ENSP00000364131:V45M	V	-	1	0	PFKFB1	55006505	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	1.753000	0.38359	2.454000	0.82982	0.600000	0.82982	GTG	.	.		0.443	PFKFB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056847.1			T	54989780	C	T	54989780	3	4	268	1	0	0	0	0	1	0	0	0	11769	507	18	3	1334	3	PFKFB1	23	54989780	Missense_Mutation	SNP	C	TCGA-FV-A495-01A-11D-A25V-10	1883222	54989780	100280780	91	39153										
ARR3	407	hgsc.bcm.edu	37	chrX	69501565	69501565	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	gaggagtttacgcggaaaggCgaggaggagagccagaaggc	19	6	0	2			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chrX:69501565C>T	ENST00000307959.8	+	17	1167	c.1116C>T	c.(1114-1116)ggC>ggT	p.G372G	RAB41_ENST00000276066.4_5'Flank|RAB41_ENST00000374473.2_5'Flank	NM_004312.2	NP_004303.2	P36575	ARRC_HUMAN	arrestin 3, retinal (X-arrestin)	372					endocytosis (GO:0006897)|regulation of protein phosphorylation (GO:0001932)|signal transduction (GO:0007165)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|synapse (GO:0045202)				endometrium(3)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|skin(1)	16						CGCGGAAAGGCGAGGAGGAGA	0.582																																					p.G372G		.	.											.	ARR3	.	.	0			c.C1116T						.						77	52	60					X																	69501565		2195	4292	6487	SO:0001819	synonymous_variant	407	exon17			GAAAGGCGAGGAG		CCDS14399.1	Xq13.1	2013-10-11			ENSG00000120500	ENSG00000120500			710	protein-coding gene	gene with protein product	"arrestin 4"	301770				8224247	Standard	NM_004312		Approved	ARRX	uc004dyb.2	P36575	OTTHUMG00000021768	ENST00000307959.8:c.1116C>T	X.37:g.69501565C>T		89.0	0.0		100.0	25.0	NM_004312	B5B0B9|Q5JT23|Q5JT24|Q6IBF5|Q96EN2	Silent	SNP	ENST00000307959.8	37	CCDS14399.1																																																																																			.	.		0.582	ARR3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057055.2	NM_004312		T	69501565	C	T	69501565	2	4	268	1	0	0	0	0	0	0	0	1	979	755	27	1		1	ARR3	23	69501565	Silent	SNP	C	TCGA-FV-A495-01A-11D-A25V-10	14511785	69501565	85768995	92	39154										
CHIC1	53344	hgsc.bcm.edu	37	chrX	72783227	72783227	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	gtcgtcgccgtcgtcgtcgtCgtcggtatctgggcccgacg	15	14	1	0			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chrX:72783227C>A	ENST00000373502.5	+	1	184	c.107C>A	c.(106-108)tCg>tAg	p.S36*	CHIC1_ENST00000373504.6_Nonsense_Mutation_p.S36*|MAP2K4P1_ENST00000602584.1_RNA	NM_001039840.2	NP_001034929.2	Q5VXU3	CHIC1_HUMAN	cysteine-rich hydrophobic domain 1	36	Ser-rich.					cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(1)|lung(2)	4	Renal(35;0.156)					tcgtcgtcgtcgtcgGTATCT	0.607																																					p.S36X		.	.											.	CHIC1	.	.	0			c.C107A						.						21	12	15					X																	72783227		2115	4120	6235	SO:0001587	stop_gained	53344	exon1			CGTCGTCGTCGGT	Y11897	CCDS35335.2, CCDS75993.1	Xq13.2	2008-05-14			ENSG00000204116	ENSG00000204116			1934	protein-coding gene	gene with protein product		300922				9321471, 11257495	Standard	NM_001039840		Approved	BRX	uc004ebk.4	Q5VXU3	OTTHUMG00000021835	ENST00000373502.5:c.107C>A	X.37:g.72783227C>A	ENSP00000362601:p.Ser36*	107.0	0.0		136.0	9.0	NM_001039840	A0PJZ2|B0QZ87|B9EGS5|Q5CZ84	Nonsense_Mutation	SNP	ENST00000373502.5	37	CCDS35335.2	.	.	.	.	.	.	.	.	.	.	C	37	6.154708	0.97329	.	.	ENSG00000204116	ENST00000373502;ENST00000373504	.	.	.	3.76	3.76	0.43208	.	0.000000	0.33980	N	0.004379	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.6976	10.2822	0.43545	0.0:1.0:0.0:0.0	.	.	.	.	X	36	.	ENSP00000362601:S36X	S	+	2	0	CHIC1	72699952	1.000000	0.71417	0.978000	0.43139	0.845000	0.48019	3.058000	0.49939	1.886000	0.54624	0.422000	0.28245	TCG	.	.		0.607	CHIC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057233.3			A	72783227	C	A	72783227	4	1	268	1	0	0	0	0	0	1	0	0	3345	893	31	1	109	1	CHIC1	23	72783227	Nonsense_Mutation	SNP	C	TCGA-FV-A495-01A-11D-A25V-10	3281662	72783227	82487333	93	39155										
GPR174	84636	hgsc.bcm.edu	37	chrX	78426850	78426850	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	tggtctgcatcagtgtgcgaCgattttggtttctcatgtac	11	8	3	0			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chrX:78426850C>G	ENST00000276077.1	+	1	382	c.346C>G	c.(346-348)Cga>Gga	p.R116G		NM_032553.1	NP_115942.1	Q9BXC1	GP174_HUMAN	G protein-coupled receptor 174	116						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(19)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	38						CAGTGTGCGACGATTTTGGTT	0.473										HNSCC(63;0.18)																											p.R116G		.	.											.	GPR174	.	.	0			c.C346G						.						215	189	198					X																	78426850		2203	4300	6503	SO:0001583	missense	84636	exon1			GTGCGACGATTTT	AF345567	CCDS14443.1	Xq13.3	2012-08-21			ENSG00000147138	ENSG00000147138		"GPCR / Class A : Orphans"	30245	protein-coding gene	gene with protein product		300903					Standard	NM_032553		Approved	FKSG79	uc004edg.1	Q9BXC1	OTTHUMG00000021898	ENST00000276077.1:c.346C>G	X.37:g.78426850C>G	ENSP00000276077:p.Arg116Gly	445.0	0.0		491.0	124.0	NM_032553	Q2M3F7	Missense_Mutation	SNP	ENST00000276077.1	37	CCDS14443.1	.	.	.	.	.	.	.	.	.	.	c	14.69	2.610026	0.46527	.	.	ENSG00000147138	ENST00000276077	D	0.97161	-4.27	5.13	2.19	0.27852	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.98658	0.9550	M	0.93854	3.465	0.45704	D	0.998618	D	0.89917	1.0	D	0.97110	1.0	D	0.98771	1.0728	10	0.87932	D	0	.	13.4568	0.61204	0.7035:0.2965:0.0:0.0	.	116	Q9BXC1	GP174_HUMAN	G	116	ENSP00000276077:R116G	ENSP00000276077:R116G	R	+	1	2	GPR174	78313506	0.071000	0.21146	0.962000	0.40283	0.977000	0.68977	0.530000	0.23036	0.010000	0.14839	0.534000	0.68092	CGA	.	.		0.473	GPR174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057327.1	NM_032553		G	78426850	C	G	78426850	3	3	268	1	0	0	0	0	1	0	0	0	6680	528	19	4	348	4	GPR174	23	78426850	Missense_Mutation	SNP	C	TCGA-FV-A495-01A-11D-A25V-10	5643623	78426850	76843710	94	39156										
BHLHB9	80823	hgsc.bcm.edu	37	chrX	102004068	102004068	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	ccaaagcaaaagccaagacaGggtctaagacagatgcagta	10	9	1	3			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chrX:102004068G>A	ENST00000372735.1	+	4	730	c.145G>A	c.(145-147)Ggg>Agg	p.G49R	BHLHB9_ENST00000457056.1_Missense_Mutation_p.G49R|BHLHB9_ENST00000361229.4_Missense_Mutation_p.G49R|BHLHB9_ENST00000447531.1_Missense_Mutation_p.G49R|BHLHB9_ENST00000448867.1_Missense_Mutation_p.G49R			Q6PI77	BHLH9_HUMAN	basic helix-loop-helix domain containing, class B, 9	49					learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of neurogenesis (GO:0050769)|positive regulation of synapse assembly (GO:0051965)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(8)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						AGCCAAGACAGGGTCTAAGAC	0.502																																					p.G49R		.	.											.	BHLHB9	.	.	0			c.G145A						.						124	104	111					X																	102004068		2203	4300	6503	SO:0001583	missense	80823	exon2			AAGACAGGGTCTA	AB051488	CCDS14502.1	Xq23	2014-03-21			ENSG00000198908	ENSG00000198908		"Basic helix-loop-helix proteins", "Armadillo repeat containing"	29353	protein-coding gene	gene with protein product		300921				11214970, 15034937, 16221301	Standard	NM_030639		Approved	p60TRP, KIAA1701, GASP3	uc011mrv.2	Q6PI77	OTTHUMG00000022060	ENST00000372735.1:c.145G>A	X.37:g.102004068G>A	ENSP00000361820:p.Gly49Arg	368.0	0.0		376.0	108.0	NM_001142530	Q9C0G2	Missense_Mutation	SNP	ENST00000372735.1	37	CCDS14502.1	.	.	.	.	.	.	.	.	.	.	G	1.823	-0.471646	0.04445	.	.	ENSG00000198908	ENST00000457056;ENST00000361229;ENST00000447531;ENST00000448867;ENST00000372735	T;T;T;T;T	0.11930	2.73;2.73;2.73;2.73;2.73	4.28	-3.31	0.04988	.	1.568470	0.04744	N	0.423386	T	0.06371	0.0164	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.32877	-0.9890	9	.	.	.	-6.4705	1.6255	0.02722	0.428:0.2486:0.1954:0.1279	.	49	Q6PI77	BHLH9_HUMAN	R	49	ENSP00000403226:G49R;ENSP00000354675:G49R;ENSP00000405893:G49R;ENSP00000391722:G49R;ENSP00000361820:G49R	.	G	+	1	0	BHLHB9	101890724	0.012000	0.17670	0.000000	0.03702	0.145000	0.21501	0.668000	0.25127	-1.017000	0.03367	-0.494000	0.04653	GGG	.	.		0.502	BHLHB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057630.1	NM_030639		A	102004068	G	A	102004068	3	1	268	1	0	0	0	0	1	0	0	0	1420	1000	35	3	147	3	BHLHB9	23	102004068	Missense_Mutation	SNP	G	TCGA-FV-A495-01A-11D-A25V-10	23577218	102004068	53266492	95	39157										
AMOT	154796	hgsc.bcm.edu	37	chrX	112022293	112022293	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	gtccaggaccggtagctggaCttgcaggaacctcagcctga	13	12	1	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chrX:112022293C>G	ENST00000524145.1	-	11	3163	c.3089G>C	c.(3088-3090)aGt>aCt	p.S1030T	MIR4329_ENST00000582643.1_RNA|AMOT_ENST00000371962.1_Missense_Mutation_p.S798T|AMOT_ENST00000371959.3_Missense_Mutation_p.S1030T|AMOT_ENST00000304758.1_Missense_Mutation_p.S621T			Q4VCS5	AMOT_HUMAN	angiomotin	1030					actin cytoskeleton organization (GO:0030036)|blood vessel endothelial cell migration (GO:0043534)|cell migration involved in gastrulation (GO:0042074)|cell-cell junction assembly (GO:0007043)|cellular protein localization (GO:0034613)|chemotaxis (GO:0006935)|establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|gastrulation with mouth forming second (GO:0001702)|hippo signaling (GO:0035329)|in utero embryonic development (GO:0001701)|negative regulation of angiogenesis (GO:0016525)|negative regulation of GTPase activity (GO:0034260)|negative regulation of vascular permeability (GO:0043116)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell size (GO:0045793)|positive regulation of embryonic development (GO:0040019)|positive regulation of stress fiber assembly (GO:0051496)|regulation of cell migration (GO:0030334)|regulation of small GTPase mediated signal transduction (GO:0051056)|vasculogenesis (GO:0001570)	actin filament (GO:0005884)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|ruffle (GO:0001726)|stress fiber (GO:0001725)|tight junction (GO:0005923)	angiostatin binding (GO:0043532)|receptor activity (GO:0004872)	p.S621N(1)|p.S1030N(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	43						GGTAGCTGGACTTGCAGGAAC	0.527																																					p.S1030T		.	.											.	AMOT	.	.	2	Substitution - Missense(2)	skin(2)	c.G3089C						.						115	107	109					X																	112022293		2203	4300	6503	SO:0001583	missense	154796	exon10			GCTGGACTTGCAG	AB028994	CCDS14563.1, CCDS48154.1	Xq23	2006-02-08			ENSG00000126016	ENSG00000126016			17810	protein-coding gene	gene with protein product		300410				11257124, 16043488, 12406577	Standard	NM_001113490		Approved	KIAA1071	uc004epr.3	Q4VCS5	OTTHUMG00000022216	ENST00000524145.1:c.3089G>C	X.37:g.112022293C>G	ENSP00000429013:p.Ser1030Thr	259.0	0.0		252.0	43.0	NM_001113490	Q504X5|Q9HD27|Q9UPT1	Missense_Mutation	SNP	ENST00000524145.1	37	CCDS48154.1	.	.	.	.	.	.	.	.	.	.	C	12.08	1.831304	0.32329	.	.	ENSG00000126016	ENST00000304758;ENST00000371959;ENST00000371962;ENST00000524145	T;T;T;T	0.46063	0.88;2.28;2.54;2.28	4.28	0.247	0.15521	.	0.705051	0.13947	N	0.351777	T	0.19644	0.0472	N	0.19112	0.55	0.20196	N	0.999923	B	0.02656	0.0	B	0.04013	0.001	T	0.30937	-0.9961	10	0.02654	T	1	0.0862	6.2461	0.20818	0.0:0.3096:0.4931:0.1973	.	1030	Q4VCS5	AMOT_HUMAN	T	621;1030;798;1030	ENSP00000305557:S621T;ENSP00000361027:S1030T;ENSP00000361030:S798T;ENSP00000429013:S1030T	ENSP00000305557:S621T	S	-	2	0	AMOT	111908949	0.818000	0.29161	0.980000	0.43619	0.980000	0.70556	-0.107000	0.10873	-0.083000	0.12618	0.529000	0.55759	AGT	.	.		0.527	AMOT-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378570.1	NM_133265		G	112022293	C	G	112022293	3	3	268	1	0	0	0	0	1	0	0	0	582	565	20	4	173	4	AMOT	23	112022293	Missense_Mutation	SNP	C	TCGA-FV-A495-01A-11D-A25V-10	10018225	112022293	43248267	96	39158										
SLC9A6	10479	hgsc.bcm.edu	37	chrX	135067806	135067806	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	cttcggacggcggcggcggaGaggctagagccatggacgag	19	10	0	2			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chrX:135067806G>A	ENST00000370698.3	+	1	180	c.145G>A	c.(145-147)Gag>Aag	p.E49K	SLC9A6_ENST00000370695.4_Missense_Mutation_p.E49K|SLC9A6_ENST00000370701.1_5'UTR	NM_006359.2	NP_006350.1	Q92581	SL9A6_HUMAN	solute carrier family 9, subfamily A (NHE6, cation proton antiporter 6), member 6	49					axon extension (GO:0048675)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|dendrite extension (GO:0097484)|dendritic spine development (GO:0060996)|ion transport (GO:0006811)|neuron projection morphogenesis (GO:0048812)|regulation of neurotrophin TRK receptor signaling pathway (GO:0051386)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon terminus (GO:0043679)|axonal spine (GO:0044308)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome membrane (GO:0031901)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)|synapse (GO:0045202)	sodium:proton antiporter activity (GO:0015385)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(18)|ovary(2)|upper_aerodigestive_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					CGGCGGCGGAGAGGCTAGAGC	0.667																																					p.E49K		.	.											.	SLC9A6	.	.	0			c.G145A						.						56	56	56					X																	135067806		2203	4299	6502	SO:0001583	missense	10479	exon1			GGCGGAGAGGCTA	AF030409	CCDS14654.1, CCDS44003.1, CCDS55504.1	Xq26.3	2013-05-22	2012-03-22		ENSG00000198689	ENSG00000198689		"Solute carriers"	11079	protein-coding gene	gene with protein product		300231	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 6", "solute carrier family 9 (sodium/hydrogen exchanger), member 6"			9507001	Standard	NM_001042537		Approved	NHE6, KIAA0267	uc004ezk.3	Q92581	OTTHUMG00000022498	ENST00000370698.3:c.145G>A	X.37:g.135067806G>A	ENSP00000359732:p.Glu49Lys	69.0	0.0		60.0	15.0	NM_006359	A6NIQ9|A8K160|B4DU30|B7ZAE0|Q3ZCW7|Q5JPP8|Q5JPP9|Q86VS0	Missense_Mutation	SNP	ENST00000370698.3	37	CCDS14654.1	.	.	.	.	.	.	.	.	.	.	g	11.88	1.771441	0.31320	.	.	ENSG00000198689	ENST00000370698;ENST00000370695	T;T	0.55413	0.52;0.53	4.71	3.57	0.40892	.	0.686932	0.14603	N	0.309493	T	0.33411	0.0862	L	0.29908	0.895	0.09310	N	1	B;B	0.09022	0.002;0.0	B;B	0.04013	0.001;0.001	T	0.28235	-1.0050	10	0.07644	T	0.81	.	6.4153	0.21714	0.1867:0.0:0.8133:0.0	.	49;49	Q92581-2;Q92581	.;SL9A6_HUMAN	K	49	ENSP00000359732:E49K;ENSP00000359729:E49K	ENSP00000359729:E49K	E	+	1	0	SLC9A6	134895472	0.800000	0.28916	0.002000	0.10522	0.807000	0.45602	4.606000	0.61126	0.514000	0.28300	0.373000	0.22412	GAG	.	.		0.667	SLC9A6-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058450.1	NM_006359		A	135067806	G	A	135067806	3	1	268	1	0	0	0	0	1	0	0	0	14733	943	33	3	147	3	SLC9A6	23	135067806	Missense_Mutation	SNP	G	TCGA-FV-A495-01A-11D-A25V-10	23045513	135067806	20202754	97	39159										
SLITRK2	84631	hgsc.bcm.edu	37	chrX	144903985	144903985	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	ctcagtgtgttaaccgtggcCgggatcttacagacagagag	13	9	2	2			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chrX:144903985C>A	ENST00000370490.1	+	1	4297	c.42C>A	c.(40-42)gcC>gcA	p.A14A	SLITRK2_ENST00000434188.2_Silent_p.A14A|SLITRK2_ENST00000447897.2_Silent_p.A14A|SLITRK2_ENST00000428560.2_Silent_p.A14A|SLITRK2_ENST00000413937.2_Silent_p.A14A			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	14					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					TAACCGTGGCCGGGATCTTAC	0.502																																					p.A14A		.	.											.	SLITRK2	.	.	0			c.C42A						.						62	58	60					X																	144903985		2203	4300	6503	SO:0001819	synonymous_variant	84631	exon5			CGTGGCCGGGATC	Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"slit-like 1 (Drosophila)"	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.42C>A	X.37:g.144903985C>A		167.0	0.0		199.0	37.0	NM_001144005	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Silent	SNP	ENST00000370490.1	37	CCDS14680.1																																																																																			.	.		0.502	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539		A	144903985	C	A	144903985	2	1	268	1	0	0	0	0	0	0	0	1	14758	639	23	1		1	SLITRK2	23	144903985	Silent	SNP	C	TCGA-FV-A495-01A-11D-A25V-10	9836179	144903985	10366575	98	39160										
FLNA	2316	hgsc.bcm.edu	37	chrX	153586830	153586830	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0707070707070707	7	1	1.19949494949495	1.88492063492063	0.942460317460317	1	1	0	tacctccggggtacctcttcAtctccatacagtactgagat	7	13	3	1			TCGA-FV-A495-01A-11D-A25V-10	TCGA-FV-A495-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	84fe77b4-f6cc-49bf-a6b9-1621ec9394f8	88a0f90d-e075-45da-b4bf-8dfc9fd6b6a8	g.chrX:153586830A>T	ENST00000369850.3	-	27	4817	c.4581T>A	c.(4579-4581)gaT>gaA	p.D1527E	FLNA_ENST00000369856.3_5'Flank|FLNA_ENST00000422373.1_Missense_Mutation_p.D1527E|FLNA_ENST00000360319.4_Missense_Mutation_p.D1527E|FLNA_ENST00000344736.4_Missense_Mutation_p.D1527E	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha	1527	Interaction with furin. {ECO:0000250}.				actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|cilium assembly (GO:0042384)|cytoplasmic sequestering of protein (GO:0051220)|early endosome to late endosome transport (GO:0045022)|epithelial to mesenchymal transition (GO:0001837)|establishment of protein localization (GO:0045184)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription factor import into nucleus (GO:0042993)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|receptor clustering (GO:0043113)|spindle assembly involved in mitosis (GO:0090307)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical dendrite (GO:0097440)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|Myb complex (GO:0031523)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|Fc-gamma receptor I complex binding (GO:0034988)|glycoprotein binding (GO:0001948)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)|Rho GTPase binding (GO:0017048)|signal transducer activity (GO:0004871)|small GTPase binding (GO:0031267)|transcription factor binding (GO:0008134)			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GTACCTCTTCATCTCCATACA	0.587																																					p.D1527E		.	.											.	FLNA	.	.	0			c.T4581A						.						76	76	76					X																	153586830		2127	4231	6358	SO:0001583	missense	2316	exon27			CTCTTCATCTCCA	X70082	CCDS44021.1, CCDS48194.1	Xq28	2009-07-23	2009-07-23		ENSG00000196924	ENSG00000196924			3754	protein-coding gene	gene with protein product	"actin binding protein 280"	300017	"filamin A, alpha (actin binding protein 280)"	FLN1, FLN, OPD2, OPD1		8406501, 12612583	Standard	NM_001456		Approved	ABP-280	uc004fkk.2	P21333	OTTHUMG00000022712	ENST00000369850.3:c.4581T>A	X.37:g.153586830A>T	ENSP00000358866:p.Asp1527Glu	154.0	0.0		164.0	29.0	NM_001456	E9KL45|Q5HY53|Q5HY55|Q8NF52	Missense_Mutation	SNP	ENST00000369850.3	37	CCDS48194.1	.	.	.	.	.	.	.	.	.	.	A	11.54	1.670550	0.29693	.	.	ENSG00000196924	ENST00000360319;ENST00000369852;ENST00000422373;ENST00000369850;ENST00000344736	D;D;D;D	0.91792	-2.91;-2.91;-2.91;-2.91	5.47	-10.9	0.00192	Immunoglobulin E-set (2);Immunoglobulin-like fold (1);	0.267031	0.32918	N	0.005497	T	0.80813	0.4695	L	0.39514	1.22	0.54753	D	0.999982	B;B	0.19073	0.033;0.019	B;B	0.25291	0.059;0.029	T	0.61783	-0.6992	10	0.25106	T	0.35	.	4.4855	0.11788	0.5713:0.1392:0.2026:0.0869	.	1527;1527	P21333-2;P21333	.;FLNA_HUMAN	E	1527;1500;1527;1527;1527	ENSP00000353467:D1527E;ENSP00000416926:D1527E;ENSP00000358866:D1527E;ENSP00000358863:D1527E	ENSP00000358863:D1527E	D	-	3	2	FLNA	153240024	0.000000	0.05858	0.145000	0.22337	0.767000	0.43475	-4.369000	0.00245	-2.879000	0.00320	-0.577000	0.04142	GAT	.	.		0.587	FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058942.3			T	153586830	A	T	153586830	3	4	268	1	0	0	0	0	1	0	0	0	5941	214	8	4	3450	4	FLNA	23	153586830	Missense_Mutation	SNP	A	TCGA-FV-A495-01A-11D-A25V-10	8682845	153586830	1683730	99	39161										
AJAP1	55966	hgsc.bcm.edu	37	chr1	4772487	4772487	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	gttcatcgcctgggggcccaCgggggacgaggaggccctgg	19	12	1	0			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr1:4772487C>T	ENST00000378191.4	+	2	938	c.557C>T	c.(556-558)aCg>aTg	p.T186M	AJAP1_ENST00000378190.3_Missense_Mutation_p.T186M	NM_018836.3	NP_061324.1	Q9UKB5	AJAP1_HUMAN	adherens junctions associated protein 1	186	Thr-rich.				cell adhesion (GO:0007155)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|urinary_tract(1)	24	all_cancers(77;0.071)|Ovarian(185;0.0721)	all_cancers(23;1.77e-36)|all_epithelial(116;1.26e-21)|all_lung(118;3.51e-08)|Lung NSC(185;3.47e-06)|all_neural(13;8.84e-06)|all_hematologic(16;7.61e-05)|Breast(487;0.000507)|Renal(390;0.0007)|Colorectal(325;0.00117)|Hepatocellular(190;0.0071)|Glioma(11;0.0155)|Myeloproliferative disorder(586;0.0258)|Ovarian(437;0.0409)|Lung SC(97;0.133)|Medulloblastoma(700;0.215)		Epithelial(90;3.89e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.97e-19)|GBM - Glioblastoma multiforme(42;3.71e-19)|Colorectal(212;4.57e-06)|COAD - Colon adenocarcinoma(227;0.00019)|Kidney(185;0.000969)|BRCA - Breast invasive adenocarcinoma(365;0.00122)|STAD - Stomach adenocarcinoma(132;0.00578)|KIRC - Kidney renal clear cell carcinoma(229;0.0126)|READ - Rectum adenocarcinoma(331;0.0689)		TGGGGGCCCACGGGGGACGAG	0.652																																					p.T186M		Atlas-SNP	.											.	AJAP1	68	.	0			c.C557T						.						19	19	19					1																	4772487		2199	4299	6498	SO:0001583	missense	55966	exon2			GGCCCACGGGGGA	AF175409	CCDS54.1	1p36.32	2008-02-05	2008-01-08		ENSG00000196581	ENSG00000196581			30801	protein-coding gene	gene with protein product	"transmembrane protein SHREW1"	610972				14595118	Standard	NM_001042478		Approved	SHREW1, SHREW-1, MOT8	uc001aln.3	Q9UKB5	OTTHUMG00000000645	ENST00000378191.4:c.557C>T	chr1.hg19:g.4772487C>T	ENSP00000367433:p.Thr186Met	52.0	0.0		40.0	13.0	NM_018836	Q9Y229	Missense_Mutation	SNP	ENST00000378191.4	hg19	CCDS54.1	.	.	.	.	.	.	.	.	.	.	C	16.09	3.023501	0.54683	.	.	ENSG00000196581	ENST00000378190;ENST00000378191	T;T	0.64085	-0.08;-0.08	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	T	0.69922	0.3165	L	0.32530	0.975	0.53688	D	0.999979	D	0.89917	1.0	D	0.91635	0.999	T	0.73196	-0.4059	10	0.87932	D	0	-13.4007	14.0163	0.64525	0.0:1.0:0.0:0.0	.	186	Q9UKB5	AJAP1_HUMAN	M	186	ENSP00000367432:T186M;ENSP00000367433:T186M	ENSP00000367432:T186M	T	+	2	0	AJAP1	4672347	1.000000	0.71417	1.000000	0.80357	0.784000	0.44337	5.784000	0.68990	2.362000	0.80069	0.313000	0.20887	ACG	.	.		0.652	AJAP1-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001542.3	NM_018836		T	4772487	C	T	4772487	3	4	269	1	0	0	0	0	1	0	0	0	438	536	19	1	563	1	AJAP1	1	4772487	Missense_Mutation	SNP	C	TCGA-FV-A496-01A-11D-A25V-10		4772487	244478134	1	39162										
CAMTA1	23261	hgsc.bcm.edu	37	chr1	7724692	7724692	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	gaggtcaccatggagacctcGcaggcggcggaagggagcga	18	10	1	1	rs567138522	byFrequency	TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr1:7724692G>T	ENST00000303635.7	+	9	2292	c.2085G>T	c.(2083-2085)tcG>tcT	p.S695S	CAMTA1_ENST00000439411.2_Silent_p.S695S	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	695					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		TGGAGACCTCGCAGGCGGCGG	0.627			T	WWTR1	epitheliod hemangioendothelioma																																p.S695S		Atlas-SNP	.		Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	.	CAMTA1	226	.	0			c.G2085T						.						56	54	55					1																	7724692		2203	4300	6503	SO:0001819	synonymous_variant	23261	exon9			GACCTCGCAGGCG	AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735			18806	protein-coding gene	gene with protein product		611501				11925432	Standard	NM_001195563		Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.2085G>T	chr1.hg19:g.7724692G>T		114.0	0.0		113.0	79.0	NM_015215	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Silent	SNP	ENST00000303635.7	hg19	CCDS30576.1																																																																																			.	.		0.627	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3	NM_015215		T	7724692	G	T	7724692	2	4	269	1	0	0	0	0	0	0	0	1	2615	1074	38	1		1	CAMTA1	1	7724692	Silent	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	2952205	7724692	241525929	2	39163										
PPCS	79717	hgsc.bcm.edu	37	chr1	42922564	42922564	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	ccgctctgcggccttcgggcCcagccctttcgggcttgctg	13	17	1	0	rs372401432		TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr1:42922564C>T	ENST00000372561.3	+	1	335	c.328C>T	c.(328-330)Cca>Tca	p.P110S	ZMYND12_ENST00000433602.2_5'Flank|PPCS_ENST00000372556.3_Intron|PPCS_ENST00000472013.1_3'UTR|PPCS_ENST00000372560.3_Missense_Mutation_p.P110S|PPCS_ENST00000455780.1_Intron|PPCS_ENST00000372562.1_Intron|ZMYND12_ENST00000372565.3_5'Flank	NM_024664.2	NP_078940.2	Q9HAB8	PPCS_HUMAN	phosphopantothenoylcysteine synthetase	110					coenzyme A biosynthetic process (GO:0015937)|coenzyme biosynthetic process (GO:0009108)|pantothenate metabolic process (GO:0015939)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	phosphopantothenate--cysteine ligase activity (GO:0004632)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|skin(3)	12	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GCCTTCGGGCCCAGCCCTTTC	0.657																																					p.P110S		Atlas-SNP	.											.	PPCS	30	.	0			c.C328T						.	C	,SER/PRO	0,3754		0,0,1877	58	62	61		,328	1.5	0	1		61	1,8179		0,1,4089	no	intron,missense	PPCS	NM_001077447.1,NM_024664.2	,74	0,1,5966	TT,TC,CC		0.0122,0.0,0.0084	,benign	,110/312	42922564	1,11933	1877	4090	5967	SO:0001583	missense	79717	exon1			TCGGGCCCAGCCC	AK021900	CCDS41311.1, CCDS41312.1	1p34.2	2008-02-05			ENSG00000127125	ENSG00000127125	6.3.2.5		25686	protein-coding gene	gene with protein product		609853				11923312	Standard	NM_024664		Approved	FLJ11838	uc001chl.3	Q9HAB8	OTTHUMG00000007332	ENST00000372561.3:c.328C>T	chr1.hg19:g.42922564C>T	ENSP00000361642:p.Pro110Ser	72.0	0.0		46.0	4.0	NM_024664	Q3KQT2|Q5VVM0	Missense_Mutation	SNP	ENST00000372561.3	hg19	CCDS41311.1	.	.	.	.	.	.	.	.	.	.	C	2.603	-0.292498	0.05568	0.0	1.22E-4	ENSG00000127125	ENST00000372560;ENST00000372561	.	.	.	5.96	1.52	0.23074	DNA/pantothenate metabolism flavoprotein, C-terminal (3);	0.881385	0.10426	N	0.676059	T	0.21801	0.0525	N	0.14661	0.345	0.18873	N	0.999985	B	0.02656	0.0	B	0.04013	0.001	T	0.28396	-1.0045	9	0.10636	T	0.68	-0.0012	7.3416	0.26640	0.0:0.472:0.3703:0.1577	.	110	Q9HAB8	PPCS_HUMAN	S	110	.	ENSP00000361641:P110S	P	+	1	0	PPCS	42695151	0.000000	0.05858	0.001000	0.08648	0.359000	0.29487	-0.130000	0.10498	0.325000	0.23359	0.650000	0.86243	CCA	.	.		0.657	PPCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019166.1	NM_024664		T	42922564	C	T	42922564	3	4	269	1	0	0	0	0	1	0	0	0	12314	623	22	3	330	3	PPCS	1	42922564	Missense_Mutation	SNP	C	TCGA-FV-A496-01A-11D-A25V-10	35197872	42922564	206328057	3	39164										
SLC6A9	6536	hgsc.bcm.edu	37	chr1	44468280	44468280	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	ccgcggacaaacagaatggtCagcaccacgtaggggaacgt	13	11	1	1			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr1:44468280C>T	ENST00000360584.2	-	7	1172	c.981G>A	c.(979-981)ctG>ctA	p.L327L	SLC6A9_ENST00000372306.3_Silent_p.L254L|SLC6A9_ENST00000372307.3_Silent_p.L189L|SLC6A9_ENST00000357730.2_Silent_p.L273L|SLC6A9_ENST00000537678.1_Silent_p.L189L|SLC6A9_ENST00000475075.2_Silent_p.L143L|SLC6A9_ENST00000372310.3_Silent_p.L254L	NM_201649.3	NP_964012.2	P48067	SC6A9_HUMAN	solute carrier family 6 (neurotransmitter transporter, glycine), member 9	327					transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycine:sodium symporter activity (GO:0015375)|neurotransmitter:sodium symporter activity (GO:0005328)			endometrium(3)|large_intestine(8)|lung(7)|ovary(1)|skin(1)|urinary_tract(2)	22	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)			Glycine(DB00145)	ACAGAATGGTCAGCACCACGT	0.612																																					p.L327L		Atlas-SNP	.											.	SLC6A9	109	.	0			c.G981A						.						111	111	111					1																	44468280		2203	4300	6503	SO:0001819	synonymous_variant	6536	exon7			AATGGTCAGCACC	S70609	CCDS30695.1, CCDS41316.1, CCDS41317.1	1p33	2013-05-22			ENSG00000196517	ENSG00000196517		"Solute carriers"	11056	protein-coding gene	gene with protein product		601019				8183239, 7587377	Standard	NM_006934		Approved	GLYT1	uc001cll.4	P48067	OTTHUMG00000008294	ENST00000360584.2:c.981G>A	chr1.hg19:g.44468280C>T		143.0	0.0		113.0	5.0	NM_201649	A6NDH1|A6NII2|A6NNZ8|Q5TAB8|Q5TAB9|Q5TAC0	Silent	SNP	ENST00000360584.2	hg19	CCDS41317.1																																																																																			.	.		0.612	SLC6A9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000022825.2	NM_201649		T	44468280	C	T	44468280	2	4	269	1	0	0	0	0	0	0	0	1	14706	813	29	3		3	SLC6A9	1	44468280	Silent	SNP	C	TCGA-FV-A496-01A-11D-A25V-10	1545716	44468280	204782341	4	39165										
ZFYVE9	9372	hgsc.bcm.edu	37	chr1	52761566	52761566	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	gatcatttctcatttccataGtttatccatgcccactattc	3	12	2	0			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr1:52761566G>T	ENST00000371591.1	+	11	3381		c.e11-1		ZFYVE9_ENST00000357206.2_Splice_Site|ZFYVE9_ENST00000287727.3_Splice_Site	NM_004799.2|NM_007324.2	NP_004790.2|NP_015563.2	O95405	ZFYV9_HUMAN	zinc finger, FYVE domain containing 9						endocytosis (GO:0006897)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|SMAD protein complex assembly (GO:0007183)|SMAD protein import into nucleus (GO:0007184)|transforming growth factor beta receptor signaling pathway (GO:0007179)	early endosome (GO:0005769)|early endosome membrane (GO:0031901)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|serine-type peptidase activity (GO:0008236)			breast(1)|central_nervous_system(4)|endometrium(3)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	53						CATTTCCATAGTTTATCCATG	0.333																																					.		Atlas-SNP	.											.	ZFYVE9	131	.	0			c.3074-1G>T						.						145	134	138					1																	52761566		2203	4300	6503	SO:0001630	splice_region_variant	9372	exon11			TCCATAGTTTATC	AF104304	CCDS563.1, CCDS564.1	1p32.3	2014-06-13	2004-05-21	2004-05-26	ENSG00000157077	ENSG00000157077		"Zinc fingers, FYVE domain containing"	6775	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 173"	603755	"MAD, mothers against decapentaplegic homolog (Drosophila) interacting protein, receptor activation anchor"	MADHIP		9865696	Standard	NM_007324		Approved	SMADIP, SARA, PPP1R173	uc001cto.4	O95405	OTTHUMG00000008061	ENST00000371591.1:c.3251-1G>T	chr1.hg19:g.52761566G>T		131.0	0.0		94.0	5.0	NM_007324	Q5T0F6|Q5T0F7|Q9UNE1|Q9Y5R7	Splice_Site	SNP	ENST00000371591.1	hg19	CCDS563.1	.	.	.	.	.	.	.	.	.	.	G	19.41	3.821726	0.71028	.	.	ENSG00000157077	ENST00000357206;ENST00000287727;ENST00000371591	.	.	.	4.69	4.69	0.59074	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.2263	0.89918	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ZFYVE9	52534154	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	9.520000	0.98027	2.607000	0.88179	0.585000	0.79938	.	.	.		0.333	ZFYVE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022083.1	NM_007324	Intron	T	52761566	G	T	52761566	5	4	269	1	0	0	0	0	0	0	1	0	17686	1043	36	3	3299	3	ZFYVE9	1	52761566	Splice_Site	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	8293286	52761566	196489055	5	39166										
HORMAD1	84072	hgsc.bcm.edu	37	chr1	150680868	150680868	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	gtagacaacatgctagattcGttgctttggtttttactaga	9	6	0	3	rs368484414		TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr1:150680868G>A	ENST00000361824.2	-	9	516	c.411C>T	c.(409-411)aaC>aaT	p.N137N	HORMAD1_ENST00000322343.7_Silent_p.N130N|HORMAD1_ENST00000368993.2_Silent_p.N137N|HORMAD1_ENST00000368995.4_Silent_p.N57N	NM_032132.4	NP_115508.2	Q86X24	HORM1_HUMAN	HORMA domain containing 1	137	HORMA. {ECO:0000255|PROSITE- ProRule:PRU00109}.				blastocyst development (GO:0001824)|meiotic DNA double-strand break formation (GO:0042138)|meiotic nuclear division (GO:0007126)|meiotic recombination checkpoint (GO:0051598)|meiotic sister chromatid cohesion (GO:0051177)|oogenesis (GO:0048477)|regulation of homologous chromosome segregation (GO:0060629)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(3)	16	all_cancers(9;3.23e-52)|all_epithelial(9;4.68e-43)|all_lung(15;5.74e-35)|Lung NSC(24;2.09e-31)|Breast(34;0.0009)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;2.32e-23)|all cancers(9;5.21e-23)|OV - Ovarian serous cystadenocarcinoma(6;6.72e-15)|BRCA - Breast invasive adenocarcinoma(12;0.000479)|LUSC - Lung squamous cell carcinoma(543;0.171)			TGCTAGATTCGTTGCTTTGGT	0.323																																					p.N137N		Atlas-SNP	.											.	HORMAD1	59	.	0			c.C411T						.	G	,	0,4406		0,0,2203	99	92	94		390,411	-2.7	0	1		94	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	HORMAD1	NM_001199829.1,NM_032132.4	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	130/388,137/395	150680868	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	84072	exon9			AGATTCGTTGCTT	AL136755	CCDS967.1, CCDS55633.1	1q21.2	2009-03-09			ENSG00000143452	ENSG00000143452			25245	protein-coding gene	gene with protein product	"cancer/testis antigen 46"	609824				11230166, 15999985	Standard	NM_032132		Approved	DKFZP434A1315, CT46	uc001evk.2	Q86X24	OTTHUMG00000035005	ENST00000361824.2:c.411C>T	chr1.hg19:g.150680868G>A		147.0	0.0		170.0	21.0	NM_032132	A6NMK2|B3KUK1|Q4G114|Q5T5I3|Q5T5I4|Q5T5I5|Q6FIC1|Q9H0K8	Silent	SNP	ENST00000361824.2	hg19	CCDS967.1																																																																																			.	.		0.323	HORMAD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084722.1	NM_032132		A	150680868	G	A	150680868	2	1	269	1	0	0	0	0	0	0	0	1	7295	1136	40	1		1	HORMAD1	1	150680868	Silent	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	97919302	150680868	98569753	6	39167										
NUP210L	91181	hgsc.bcm.edu	37	chr1	154018769	154018769	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	gagccatcatactgaccttgGtagctgtgatgagccgagtt	12	9	1	3			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr1:154018769G>A	ENST00000368559.3	-	26	3631	c.3560C>T	c.(3559-3561)aCc>aTc	p.T1187I	NUP210L_ENST00000368553.1_Missense_Mutation_p.T120I|NUP210L_ENST00000271854.3_Missense_Mutation_p.T1187I	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	1187					Sertoli cell development (GO:0060009)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|lung(34)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|urinary_tract(2)	80	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			ACTGACCTTGGTAGCTGTGAT	0.453																																					p.T1187I		Atlas-SNP	.											.	NUP210L	181	.	0			c.C3560T						.						93	91	92					1																	154018769		1918	4139	6057	SO:0001583	missense	91181	exon26			ACCTTGGTAGCTG	AK125924	CCDS41399.1, CCDS53370.1	1q21.3	2008-02-05			ENSG00000143552	ENSG00000143552			29915	protein-coding gene	gene with protein product							Standard	NM_207308		Approved		uc001fdw.3	Q5VU65	OTTHUMG00000035852	ENST00000368559.3:c.3560C>T	chr1.hg19:g.154018769G>A	ENSP00000357547:p.Thr1187Ile	146.0	0.0		209.0	9.0	NM_001159484	E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	Missense_Mutation	SNP	ENST00000368559.3	hg19	CCDS41399.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.133262	0.77662	.	.	ENSG00000143552	ENST00000368559;ENST00000368553;ENST00000271854	T;T;T	0.25414	3.37;1.8;3.13	5.71	4.8	0.61643	.	0.164042	0.43579	D	0.000560	T	0.20981	0.0505	M	0.69358	2.11	0.31704	N	0.640329	P;P	0.52577	0.954;0.91	P;B	0.49799	0.622;0.343	T	0.07009	-1.0795	10	0.33141	T	0.24	-8.4839	11.5364	0.50639	0.0829:0.0:0.9171:0.0	.	1187;1187	E7EP56;Q5VU65	.;P210L_HUMAN	I	1187;120;1187	ENSP00000357547:T1187I;ENSP00000357541:T120I;ENSP00000271854:T1187I	ENSP00000271854:T1187I	T	-	2	0	NUP210L	152285393	0.993000	0.37304	0.725000	0.30721	0.986000	0.74619	6.245000	0.72398	1.425000	0.47237	0.650000	0.86243	ACC	.	.		0.453	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308		A	154018769	G	A	154018769	3	1	269	1	0	0	0	0	1	0	0	0	10770	1261	44	3	2166	3	NUP210L	1	154018769	Missense_Mutation	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	3337901	154018769	95231852	7	39168										
ATP1A4	480	hgsc.bcm.edu	37	chr1	160121863	160121863	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	gggaagaaagggacagtggcTccccatgaccagagtccaag	14	10	0	3			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr1:160121863T>G	ENST00000368081.4	+	1	504	c.33T>G	c.(31-33)gcT>gcG	p.A11A		NM_144699.3	NP_653300.2	Q13733	AT1A4_HUMAN	ATPase, Na+/K+ transporting, alpha 4 polypeptide	11					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|fertilization (GO:0009566)|ion transmembrane transport (GO:0034220)|potassium ion transport (GO:0006813)|regulation of cellular pH (GO:0030641)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(34)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	75	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GGACAGTGGCTCCCCATGACC	0.498																																					p.A11A		Atlas-SNP	.											.	ATP1A4	167	.	0			c.T33G						.						64	64	64					1																	160121863		2203	4300	6503	SO:0001819	synonymous_variant	480	exon1			AGTGGCTCCCCAT	BC028297	CCDS1197.1, CCDS44255.1	1q23.2	2012-10-22	2002-02-25		ENSG00000132681	ENSG00000132681		"ATPases / P-type"	14073	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-4", "sodium pump subunit alpha-4", "sodium-potassium ATPase catalytic subunit alpha-4"	607321	"ATPase, Na+/K+ transporting, alpha polypeptide-like 2"	ATP1AL2		1981991, 3035563	Standard	NM_144699		Approved		uc001fve.4	Q13733	OTTHUMG00000031609	ENST00000368081.4:c.33T>G	chr1.hg19:g.160121863T>G		38.0	0.0		31.0	14.0	NM_144699	Q504T2|Q7Z4I9|Q8TBN8|Q8WXA7|Q8WXH7|Q8WY13	Silent	SNP	ENST00000368081.4	hg19	CCDS1197.1																																																																																			.	.		0.498	ATP1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077415.1	NM_144699		G	160121863	T	G	160121863	2	3	269	1	0	0	0	0	0	0	0	1	1131	1538	54	5		5	ATP1A4	1	160121863	Silent	SNP	T	TCGA-FV-A496-01A-11D-A25V-10	6103094	160121863	89128758	8	39169										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181700351	181700351	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	accacatgtcgatgtgggagCcacgcagcagccacctgtat	11	13	0	0			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr1:181700351C>A	ENST00000367573.2	+	19	2281	c.2281C>A	c.(2281-2283)Cca>Aca	p.P761T	CACNA1E_ENST00000367570.1_Missense_Mutation_p.P761T|CACNA1E_ENST00000357570.5_Missense_Mutation_p.P712T|CACNA1E_ENST00000360108.3_Intron|CACNA1E_ENST00000358338.5_Intron|CACNA1E_ENST00000526775.1_Intron|CACNA1E_ENST00000367567.4_Missense_Mutation_p.P368T	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	761					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						GATGTGGGAGCCACGCAGCAG	0.517																																					p.P761T		Atlas-SNP	.											.	CACNA1E	778	.	0			c.C2281A						.						166	186	180					1																	181700351		2171	4248	6419	SO:0001583	missense	777	exon19			TGGGAGCCACGCA	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.2281C>A	chr1.hg19:g.181700351C>A	ENSP00000356545:p.Pro761Thr	282.0	0.0		404.0	75.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	C	14.83	2.653682	0.47362	.	.	ENSG00000198216	ENST00000367570;ENST00000357570;ENST00000367567;ENST00000367573	D;D;D;D	0.96041	-3.8;-3.82;-3.89;-3.8	5.23	5.23	0.72850	.	1.451740	0.03413	N	0.205023	D	0.91523	0.7323	N	0.08118	0	0.37560	D	0.919042	P	0.50819	0.939	P	0.47206	0.541	T	0.81942	-0.0702	10	0.12103	T	0.63	.	11.8669	0.52499	0.0:0.919:0.0:0.081	.	761	Q15878-3	.	T	761;712;368;761	ENSP00000356542:P761T;ENSP00000350183:P712T;ENSP00000356539:P368T;ENSP00000356545:P761T	ENSP00000350183:P712T	P	+	1	0	CACNA1E	179966974	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	5.094000	0.64523	2.417000	0.82017	0.650000	0.86243	CCA	.	.		0.517	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		A	181700351	C	A	181700351	3	1	269	1	0	0	0	0	1	0	0	0	2544	739	26	3	2355	3	CACNA1E	1	181700351	Missense_Mutation	SNP	C	TCGA-FV-A496-01A-11D-A25V-10	21578488	181700351	67550270	9	39170										
SLC30A10	55532	hgsc.bcm.edu	37	chr1	220089062	220089067	+	In_Frame_Del	DEL	AAGTCC	AAGTCC	-													0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	gtgagttgcagagcaacagtAagtccttctgctccaggggt					rs370815252		TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	AAGTCC	AAGTCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr1:220089062_220089067delAAGTCC	ENST00000366926.3	-	4	1343_1348	c.1182_1187delGGACTT	c.(1180-1188)aaggactta>aaa	p.DL395del	SLC30A10_ENST00000484079.1_5'UTR|SLC30A10_ENST00000536446.1_In_Frame_Del_p.DL150del	NM_018713.2	NP_061183.2	Q6XR72	ZNT10_HUMAN	solute carrier family 30, member 10	395					zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation transmembrane transporter activity (GO:0008324)			NS(1)|endometrium(1)|large_intestine(1)|lung(9)|skin(1)	13				GBM - Glioblastoma multiforme(131;0.051)|all cancers(67;0.209)		GAGCAACAGTAAGTCCTTCTGCTCCA	0.529																																					p.395_396del	Colon(76;360 1614 43677 51136)	Atlas-Indel,Pindel	.											SLC30A10,NS,carcinoma,0,1	SLC30A10	58	.	0			c.1183_1188del						.																																			SO:0001651	inframe_deletion	55532	exon4			.	AY212919	CCDS31026.1	1q41	2013-05-22			ENSG00000196660	ENSG00000196660		"Solute carriers"	25355	protein-coding gene	gene with protein product	"zinc transporter 8"	611146				15154973	Standard	NR_046437		Approved	DKFZp547M236, ZnT-10, ZRC1, ZNT8	uc001hlw.3	Q6XR72	OTTHUMG00000037434	ENST00000366926.3:c.1182_1187delGGACTT	chr1.hg19:g.220089062_220089067delAAGTCC	ENSP00000355893:p.Asp395_Leu396del	175.0	0.0		244.0	22.0	NM_018713	Q49AL9|Q9NPW0	In_Frame_Del	DEL	ENST00000366926.3	hg19	CCDS31026.1																																																																																			.	.		0.529	SLC30A10-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357709.1	NM_018713		-	220089067	AAGTCC	-	220089062	7	5	269	1	0	1	0	1	0	0	0	0	14569	372	13	0	274	0	SLC30A10	1	220089062	In_Frame_Del	DEL	AAGTCC	TCGA-FV-A496-01A-11D-A25V-10	38388711	220089062	29161559	10	39171										
TARBP1	6894	hgsc.bcm.edu	37	chr1	234536930	234536930	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	tgatattctctactcacctcTagacaataatccttgagtgg	6	10	3	3			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr1:234536930T>A	ENST00000040877.1	-	25	4067	c.4068A>T	c.(4066-4068)ctA>ctT	p.L1356L	TARBP1_ENST00000483404.1_5'UTR	NM_005646.3	NP_005637.3	Q13395	TARB1_HUMAN	TAR (HIV-1) RNA binding protein 1	1356					regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA processing (GO:0006396)	nucleus (GO:0005634)	RNA binding (GO:0003723)|RNA methyltransferase activity (GO:0008173)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(7)|large_intestine(6)|lung(22)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	55	Ovarian(103;0.0339)	all_cancers(173;0.00995)|Prostate(94;0.0115)|all_epithelial(177;0.172)	OV - Ovarian serous cystadenocarcinoma(106;0.000263)			TACTCACCTCTAGACAATAAT	0.348																																					p.L1356L		Atlas-SNP	.											.	TARBP1	111	.	0			c.A4068T						.						96	89	91					1																	234536930		2203	4300	6503	SO:0001819	synonymous_variant	6894	exon25			CACCTCTAGACAA		CCDS1601.1	1q42.2	2012-06-12	2007-06-26		ENSG00000059588	ENSG00000059588			11568	protein-coding gene	gene with protein product	"tRNA methyltransferase 3 homolog (S. cerevisiae)"	605052	"Tar (HIV-1) RNA binding protein 1"			1936997	Standard	NM_005646		Approved	TRP-185, TRM3	uc001hwd.3	Q13395	OTTHUMG00000037947	ENST00000040877.1:c.4068A>T	chr1.hg19:g.234536930T>A		64.0	0.0		78.0	46.0	NM_005646	Q9H581	Silent	SNP	ENST00000040877.1	hg19	CCDS1601.1																																																																																			.	.		0.348	TARBP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092616.1	NM_005646		A	234536930	T	A	234536930	2	1	269	1	0	0	0	0	0	0	0	1	15570	1509	53	4		4	TARBP1	1	234536930	Silent	SNP	T	TCGA-FV-A496-01A-11D-A25V-10	14447868	234536930	14713691	11	39172										
USP34	9736	hgsc.bcm.edu	37	chr2	61505325	61505325	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	cttcccttgaaaatttaaagGgtggtttgtgtttaacaaca	8	6	0	1			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr2:61505325G>T	ENST00000398571.2	-	41	5484	c.5408C>A	c.(5407-5409)cCc>cAc	p.P1803H		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	1803					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			AAATTTAAAGGGTGGTTTGTG	0.363																																					p.P1803H		Atlas-SNP	.											.	USP34	334	.	0			c.C5408A						.						92	80	84					2																	61505325		1864	4094	5958	SO:0001583	missense	9736	exon41			TTAAAGGGTGGTT	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"Ubiquitin-specific peptidases"	20066	protein-coding gene	gene with protein product		615295	"ubiquitin specific protease 34"			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.5408C>A	chr2.hg19:g.61505325G>T	ENSP00000381577:p.Pro1803His	55.0	0.0		85.0	4.0	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	hg19	CCDS42686.1	.	.	.	.	.	.	.	.	.	.	G	18.08	3.544449	0.65198	.	.	ENSG00000115464	ENST00000263989;ENST00000398569;ENST00000398571;ENST00000453734	T;T	0.04119	3.8;3.7	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.16854	0.0405	M	0.70595	2.14	0.58432	D	0.999997	D	0.69078	0.997	P	0.55545	0.778	T	0.00065	-1.2147	10	0.87932	D	0	.	17.5316	0.87816	0.0:0.0:1.0:0.0	.	1803	Q70CQ2	UBP34_HUMAN	H	1651;1651;1803;81	ENSP00000381577:P1803H;ENSP00000410559:P81H	ENSP00000263989:P1651H	P	-	2	0	USP34	61358829	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.544000	0.98092	2.582000	0.87167	0.563000	0.77884	CCC	.	.		0.363	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			T	61505325	G	T	61505325	3	4	269	1	0	0	0	0	1	0	0	0	17080	1232	43	3	5392	3	USP34	2	61505325	Missense_Mutation	SNP	G	TCGA-FV-A496-01A-11D-A25V-10		61505325	181694048	12	39173										
XPO1	7514	hgsc.bcm.edu	37	chr2	61726908	61726909	+	Missense_Mutation	DNP	TC	TC	AT													0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	cactagagaaatcaaatactTcttcactcaagagtttaaga							TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr2:61726908_61726909TC>AT	ENST00000401558.2	-	7	1256_1257	c.529_530GA>AT	c.(529-531)GAa>ATa	p.E177I	XPO1_ENST00000406957.1_Missense_Mutation_p.E177I|XPO1_ENST00000404992.2_Missense_Mutation_p.E177I	NM_003400.3	NP_003391.1	O14980	XPO1_HUMAN	exportin 1	177	Necessary for HTLV-1 Rex-mediated mRNA export.				gene expression (GO:0010467)|intracellular transport of virus (GO:0075733)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|mRNA transport (GO:0051028)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein export from nucleus (GO:0006611)|protein localization to nucleus (GO:0034504)|regulation of centrosome duplication (GO:0010824)|regulation of protein catabolic process (GO:0042176)|regulation of protein export from nucleus (GO:0046825)|response to drug (GO:0042493)|ribosomal large subunit export from nucleus (GO:0000055)|ribosomal small subunit export from nucleus (GO:0000056)|RNA metabolic process (GO:0016070)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)	annulate lamellae (GO:0005642)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleocytoplasmic transporter activity (GO:0005487)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	39			LUSC - Lung squamous cell carcinoma(7;5.71e-05)|Epithelial(17;0.0662)|all cancers(80;0.226)			ATCAAATACTTCTTCACTCAAG	0.327			Mis		CLL																																p.E177V|p.E177K		Atlas-SNP	.	-'	Dom	yes		2	2p15	7514	"exportin 1 (CRM1 homolog, yeast)"		L	.	XPO1	108	.	0			c.A530T|c.G529A						.																																			SO:0001583	missense	7514	exon7			AATACTTCTTCAC|ATACTTCTTCACT	Y08614	CCDS33205.1	2p15	2014-02-19	2014-02-19		ENSG00000082898	ENSG00000082898		"Exportins"	12825	protein-coding gene	gene with protein product	"chromosome region maintenance 1 homolog (yeast)"	602559	"exportin 1 (CRM1, yeast, homolog)", "exportin 1 (CRM1 homolog, yeast)"			9205132, 9368044	Standard	XM_005264544		Approved	CRM1, emb	uc002sbj.3	O14980	OTTHUMG00000152316	ENST00000401558.2:c.529_530delinsAT	chr2.hg19:g.61726908_61726909delinsAT	ENSP00000384863:p.Glu177Ile	113.0|115.0	0.0		127.0|126.0	7.0|6.0	NM_003400	A6NL14|A8K1K5|D6W5E2|Q63HP8|Q68CP3|Q99433	Missense_Mutation	SNP	ENST00000401558.2	hg19	CCDS33205.1																																																																																			.	.		0.327	XPO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325872.3	NM_003400		AT	61726909	TC	AT	61726908	3	1	269	1	0	0	0	0	1	0	0	0	17460	1783	62	4	2761	4	XPO1	2	61726908	Missense_Mutation	DNP	TC	TCGA-FV-A496-01A-11D-A25V-10	221583	61726908	181472465	13	39174										
RGPD4	285190	hgsc.bcm.edu	37	chr2	108499260	108499260	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	gtagtgaaagagagagacttCttcctgttataaatacgatg	10	5	1	3	rs570292087		TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr2:108499260C>A	ENST00000408999.3	+	22	5274	c.5197C>A	c.(5197-5199)Ctt>Att	p.L1733I	RGPD4_ENST00000354986.4_Missense_Mutation_p.L1733I	NM_182588.2	NP_872394.2	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4	1733	GRIP. {ECO:0000255|PROSITE- ProRule:PRU00250}.				protein targeting to Golgi (GO:0000042)					breast(1)|endometrium(7)|kidney(4)|lung(23)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(3)	43						AGAGAGACTTCTTCCTGTTAT	0.453																																					p.L1733I		Atlas-SNP	.											RGPD4,NS,carcinoma,0,1	RGPD4	112	.	0			c.C5197A						.						92	87	88					2																	108499260		692	1578	2270	SO:0001583	missense	285190	exon22			AGACTTCTTCCTG	BX537861	CCDS46381.1	2q12.3	2013-01-10			ENSG00000196862	ENSG00000196862		"Tetratricopeptide (TTC) repeat domain containing"	32417	protein-coding gene	gene with protein product		612707				15710750, 15815621	Standard	NM_182588		Approved	RGP4, DKFZp686P0288	uc010ywk.2	Q7Z3J3	OTTHUMG00000153208	ENST00000408999.3:c.5197C>A	chr2.hg19:g.108499260C>A	ENSP00000386810:p.Leu1733Ile	937.0	0.0		1025.0	200.0	NM_182588	B9A029	Missense_Mutation	SNP	ENST00000408999.3	hg19	CCDS46381.1	.	.	.	.	.	.	.	.	.	.	-	14.11	2.436512	0.43224	.	.	ENSG00000196862	ENST00000354986;ENST00000408999;ENST00000439322	T;T	0.40756	1.02;1.02	0.854	0.854	0.19007	GRIP (3);	.	.	.	.	T	0.28532	0.0706	L	0.39085	1.19	0.21499	N	0.999668	P	0.43352	0.804	B	0.37508	0.252	T	0.17961	-1.0352	9	0.87932	D	0	-0.7016	6.0524	0.19792	0.2992:0.7008:0.0:0.0	.	1733	Q7Z3J3	RGPD4_HUMAN	I	1733;1733;1100	ENSP00000347081:L1733I;ENSP00000386810:L1733I	ENSP00000347081:L1733I	L	+	1	0	RGPD4	107865692	1.000000	0.71417	0.918000	0.36340	0.887000	0.51463	1.684000	0.37649	0.767000	0.33267	0.398000	0.26397	CTT	.	.		0.453	RGPD4-001	NOVEL	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330096.2	XM_496581		A	108499260	C	A	108499260	3	1	269	1	0	0	0	0	1	0	0	0	13303	913	32	3	5283	3	RGPD4	2	108499260	Missense_Mutation	SNP	C	TCGA-FV-A496-01A-11D-A25V-10	46772352	108499260	134700113	14	39175										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141128766	141128766	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	acctcatctgaaccatcagcAcaatcatattctccattaca	2	14	5	1			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr2:141128766A>C	ENST00000389484.3	-	70	11828	c.10857T>G	c.(10855-10857)tgT>tgG	p.C3619W		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	3619	LDL-receptor class A 28. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		AACCATCAGCACAATCATATT	0.303										TSP Lung(27;0.18)																											p.C3619W	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.T10857G						.						35	34	35					2																	141128766		2201	4289	6490	SO:0001583	missense	53353	exon70			ATCAGCACAATCA	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.10857T>G	chr2.hg19:g.141128766A>C	ENSP00000374135:p.Cys3619Trp	211.0	0.0		271.0	36.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	A	16.33	3.094241	0.56075	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.99919	-8.0	5.2	4.05	0.47172	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.99941	0.9974	H	0.99619	4.66	0.80722	D	1	D	0.67145	0.996	P	0.62649	0.905	D	0.96673	0.9498	10	0.87932	D	0	.	8.409	0.32632	0.8479:0.0:0.1521:0.0	.	3619	Q9NZR2	LRP1B_HUMAN	W	3619;3557	ENSP00000374135:C3619W	ENSP00000374135:C3619W	C	-	3	2	LRP1B	140845236	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.679000	0.54634	0.926000	0.37118	0.482000	0.46254	TGT	.	.		0.303	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		C	141128766	A	C	141128766	3	2	269	1	0	0	0	0	1	0	0	0	8964	157	6	5	3030	5	LRP1B	2	141128766	Missense_Mutation	SNP	A	TCGA-FV-A496-01A-11D-A25V-10	32629506	141128766	102070607	15	39176										
NEB	4703	hgsc.bcm.edu	37	chr2	152466364	152466364	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	cttttttgcttggataatgtCgttttgatccggcatgcatg	10	7	0	1			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr2:152466364C>G	ENST00000172853.10	-	77	11707	c.11560G>C	c.(11560-11562)Gac>Cac	p.D3854H	NEB_ENST00000604864.1_Missense_Mutation_p.D4097H|NEB_ENST00000603639.1_Missense_Mutation_p.D4097H|NEB_ENST00000409198.1_Missense_Mutation_p.D3854H|NEB_ENST00000427231.2_Missense_Mutation_p.D4097H|NEB_ENST00000397345.3_Missense_Mutation_p.D4097H			P20929	NEBU_HUMAN	nebulin	3854					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TGGATAATGTCGTTTTGATCC	0.433																																					p.D4097H		Atlas-SNP	.											NEB_ENST00000427231,NS,carcinoma,0,3	NEB	1697	.	0			c.G12289C						.						223	208	213					2																	152466364		1960	4149	6109	SO:0001583	missense	4703	exon81			TAATGTCGTTTTG	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.11560G>C	chr2.hg19:g.152466364C>G	ENSP00000172853:p.Asp3854His	170.0	1.0		210.0	48.0	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	hg19		.	.	.	.	.	.	.	.	.	.	C	24.0	4.481740	0.84747	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.51817	0.69;0.69;0.69;0.69	5.55	5.55	0.83447	.	0.043254	0.85682	D	0.000000	T	0.75932	0.3917	M	0.89601	3.045	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.79329	-0.1848	10	0.56958	D	0.05	.	19.8667	0.96806	0.0:1.0:0.0:0.0	.	3854	P20929	NEBU_HUMAN	H	3854;4097;4097;3854	ENSP00000386259:D3854H;ENSP00000380505:D4097H;ENSP00000416578:D4097H;ENSP00000172853:D3854H	ENSP00000172853:D3854H	D	-	1	0	NEB	152174610	1.000000	0.71417	0.992000	0.48379	0.994000	0.84299	4.802000	0.62539	2.773000	0.95371	0.655000	0.94253	GAC	.	.		0.433	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		G	152466364	C	G	152466364	3	3	269	1	0	0	0	0	1	0	0	0	10311	884	31	4	13805	4	NEB	2	152466364	Missense_Mutation	SNP	C	TCGA-FV-A496-01A-11D-A25V-10	11337598	152466364	90733009	16	39177										
SCN9A	6335	hgsc.bcm.edu	37	chr2	167056365	167056366	+	Frame_Shift_Del	DEL	AG	AG	-													0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	acgtttcaatcaaatcagctAgaaacatacctgtatgtgga							TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr2:167056365_167056366delAG	ENST00000409435.1	-	26	4782_4783	c.4783_4784delCT	c.(4783-4785)ctafs	p.L1595fs	SCN9A_ENST00000409672.1_Frame_Shift_Del_p.L1584fs|SCN9A_ENST00000303354.6_Frame_Shift_Del_p.L1596fs|SCN9A_ENST00000375387.4_Frame_Shift_Del_p.L1596fs|AC010127.3_ENST00000447809.2_RNA			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	1595					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CAAATCAGCTAGAAACATACCT	0.381																																					p.1584_1584del		Atlas-Indel,Pindel	.											.	SCN9A	296	.	0			c.4751_4752del						.																																			SO:0001589	frameshift_variant	6335	exon27			.	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10597	protein-coding gene	gene with protein product		603415	"sodium channel, voltage-gated, type IX, alpha polypeptide"			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.4783_4784delCT	chr2.hg19:g.167056365_167056366delAG	ENSP00000386330:p.Leu1595fs	96.0	0.0		122.0	51.0	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Frame_Shift_Del	DEL	ENST00000409435.1	hg19	CCDS46441.1																																																																																			.	.		0.381	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977		-	167056366	AG	-	167056365	7	5	269	1	0	1	0	1	0	0	0	0	13940	420	15	0	1186	0	SCN9A	2	167056365	Frame_Shift_Del	DEL	AG	TCGA-FV-A496-01A-11D-A25V-10	14590001	167056365	76143008	17	39178										
NBEAL1	65065	hgsc.bcm.edu	37	chr2	204067444	204067444	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	ttagctacagattactgtggAatacatttgatttctggttc	8	6	1	2			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr2:204067444A>T	ENST00000449802.1	+	50	7692	c.7359A>T	c.(7357-7359)ggA>ggT	p.G2453G		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	2453										NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						ATTACTGTGGAATACATTTGA	0.323																																					p.G2453G		Atlas-SNP	.											.	NBEAL1	266	.	0			c.A7359T						.						130	124	126					2																	204067444		1858	4093	5951	SO:0001819	synonymous_variant	65065	exon50			CTGTGGAATACAT	AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"WD repeat domain containing"	20681	protein-coding gene	gene with protein product		609816	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17", "amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.7359A>T	chr2.hg19:g.204067444A>T		121.0	0.0		130.0	7.0	NM_001114132	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Silent	SNP	ENST00000449802.1	hg19	CCDS46495.1																																																																																			.	.		0.323	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4			T	204067444	A	T	204067444	2	4	269	1	0	0	0	0	0	0	0	1	10197	233	9	4		4	NBEAL1	2	204067444	Silent	SNP	A	TCGA-FV-A496-01A-11D-A25V-10	37011079	204067444	39131929	18	39179										
CCDC108	255101	hgsc.bcm.edu	37	chr2	219874178	219874178	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	cccctatcatgggactcacaGacacctgttgatttggggaa	10	11	2	2			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr2:219874178G>A	ENST00000341552.5	-	28	4540	c.4457C>T	c.(4456-4458)tCt>tTt	p.S1486F	CCDC108_ENST00000453220.1_Missense_Mutation_p.S1486F|CCDC108_ENST00000441968.1_Missense_Mutation_p.S1486F|AC097468.4_ENST00000441450.1_RNA	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108	1486						integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(1)|lung(34)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GGGACTCACAGACACCTGTTG	0.527																																					p.S1486F		Atlas-SNP	.											.	CCDC108	208	.	0			c.C4457T						.						51	47	49					2																	219874178		2201	4296	6497	SO:0001583	missense	255101	exon28			CTCACAGACACCT	NM_194302, AL833882, AK127189	CCDS2430.2, CCDS2431.2, CCDS63125.1, CCDS63126.1	2q35	2008-02-05			ENSG00000181378	ENSG00000181378			25325	protein-coding gene	gene with protein product		614270				12477932	Standard	NM_194302		Approved	DKFZp434O0527, MGC35338	uc002vjl.2	Q6ZU64	OTTHUMG00000133013	ENST00000341552.5:c.4457C>T	chr2.hg19:g.219874178G>A	ENSP00000340776:p.Ser1486Phe	120.0	0.0		91.0	36.0	NM_194302	A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Missense_Mutation	SNP	ENST00000341552.5	hg19	CCDS2430.2	.	.	.	.	.	.	.	.	.	.	G	17.47	3.398867	0.62177	.	.	ENSG00000181378	ENST00000341552;ENST00000441968;ENST00000453220	T;T;T	0.05925	3.37;3.37;3.37	5.43	3.51	0.40186	.	0.536026	0.15834	N	0.242372	T	0.10895	0.0266	L	0.54323	1.7	0.80722	D	1	D	0.62365	0.991	P	0.50970	0.655	T	0.04593	-1.0940	10	0.66056	D	0.02	-7.6728	6.1582	0.20350	0.0941:0.0:0.722:0.1838	.	1486	Q6ZU64	CC108_HUMAN	F	1486	ENSP00000340776:S1486F;ENSP00000413377:S1486F;ENSP00000409117:S1486F	ENSP00000340776:S1486F	S	-	2	0	CCDC108	219582422	0.327000	0.24678	0.995000	0.50966	0.895000	0.52256	1.555000	0.36277	1.306000	0.44926	0.555000	0.69702	TCT	.	.		0.527	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4	NM_194302		A	219874178	G	A	219874178	3	1	269	1	0	0	0	0	1	0	0	0	2745	942	33	3	1352	3	CCDC108	2	219874178	Missense_Mutation	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	15806734	219874178	23325195	19	39180										
UGT1A4	54657	hgsc.bcm.edu	37	chr2	234628158	234628158	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	ccatactttttctgccccttAtgcaagtcttgcctctgagc	6	14	3	1			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr2:234628158A>G	ENST00000373409.3	+	1	735	c.692A>G	c.(691-693)tAt>tGt	p.Y231C	UGT1A6_ENST00000305139.6_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A5_ENST00000373414.3_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A1_ENST00000608381.1_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A6_ENST00000480628.1_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A7_ENST00000373426.3_Intron	NM_007120.2	NP_009051.1	P22310	UD14_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A4	231					cellular glucuronidation (GO:0052695)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|skin(2)|urinary_tract(1)	26		Breast(86;0.000765)|all_lung(227;0.00266)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0456)|Lung SC(224;0.128)		Epithelial(121;3.49e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000504)|Lung(119;0.0026)|LUSC - Lung squamous cell carcinoma(224;0.00624)	Asenapine(DB06216)|Clozapine(DB00363)|Ezogabine(DB04953)|Lamotrigine(DB00555)|Midazolam(DB00683)|Paricalcitol(DB00910)|Tamoxifen(DB00675)|Trifluoperazine(DB00831)|Valproic Acid(DB00313)	TCTGCCCCTTATGCAAGTCTT	0.498																																					p.Y231C	Melanoma(99;1011 1962 13201 26492)	Atlas-SNP	.											.	UGT1A4	63	.	0			c.A692G						.						238	225	230					2																	234628158		2203	4300	6503	SO:0001583	missense	54657	exon1			CCCCTTATGCAAG	M84128	CCDS33405.1	2q37.1	2014-01-10	2005-07-20		ENSG00000244474	ENSG00000244474		"UDP glucuronosyltransferases"	12536	other	complex locus constituent		606429	"UDP glycosyltransferase 1 family, polypeptide A4"			9295054, 1339448	Standard	NM_007120		Approved	HUG-BR2, UGT1D	uc002vux.3	P22310	OTTHUMG00000059119	ENST00000373409.3:c.692A>G	chr2.hg19:g.234628158A>G	ENSP00000362508:p.Tyr231Cys	289.0	0.0		299.0	85.0	NM_007120	B2R937|B8K288|Q5DT00	Missense_Mutation	SNP	ENST00000373409.3	hg19	CCDS33405.1	.	.	.	.	.	.	.	.	.	.	A	12.85	2.062683	0.36373	.	.	ENSG00000244474	ENST00000373409	T	0.62639	0.01	4.49	0.06	0.14334	.	.	.	.	.	T	0.81735	0.4885	M	0.93978	3.48	0.09310	N	1	D;D	0.89917	1.0;0.998	D;D	0.79108	0.992;0.976	T	0.70945	-0.4734	9	0.87932	D	0	.	10.6371	0.45571	0.5786:0.0:0.0:0.4214	.	231;231	B8K288;P22310	.;UD14_HUMAN	C	231	ENSP00000362508:Y231C	ENSP00000362508:Y231C	Y	+	2	0	UGT1A4	234292897	0.000000	0.05858	0.002000	0.10522	0.008000	0.06430	-2.217000	0.01220	0.081000	0.16988	0.402000	0.26972	TAT	.	.		0.498	UGT1A4-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130984.1	NM_007120		G	234628158	A	G	234628158	3	3	269	1	0	0	0	0	1	0	0	0	16962	449	16	2	694	2	UGT1A4	2	234628158	Missense_Mutation	SNP	A	TCGA-FV-A496-01A-11D-A25V-10	14753980	234628158	8571215	20	39181										
CACNA1D	776	hgsc.bcm.edu	37	chr3	53845180	53845180	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	gggacgctatgcaagggaccCaaaatttgtgtcagcaacaa	11	9	1	0			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr3:53845180C>T	ENST00000350061.5	+	48	6744	c.6233C>T	c.(6232-6234)cCa>cTa	p.P2078L	CACNA1D_ENST00000288139.4_Missense_Mutation_p.P2098L|CACNA1D_ENST00000544977.1_3'UTR|CACNA1D_ENST00000422281.2_Missense_Mutation_p.P2054L	NM_001128840.1	NP_001122312.1	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type, alpha 1D subunit	2078					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|energy reserve metabolic process (GO:0006112)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during SA node cell action potential (GO:0086052)|positive regulation of calcium ion transport (GO:0051928)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|ankyrin binding (GO:0030506)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)|voltage-gated calcium channel activity involved in cardiac muscle cell action potential (GO:0086007)|voltage-gated calcium channel activity involved SA node cell action potential (GO:0086059)			breast(3)|central_nervous_system(9)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(13)|liver(1)|lung(29)|ovary(6)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	90				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	GCAAGGGACCCAAAATTTGTG	0.532																																					p.P2098L		Atlas-SNP	.											.	CACNA1D	324	.	0			c.C6293T						.						109	102	105					3																	53845180		2203	4300	6503	SO:0001583	missense	776	exon49			GGGACCCAAAATT	AB209171	CCDS2872.1, CCDS46848.1, CCDS46849.1	3p14.3	2012-03-07			ENSG00000157388	ENSG00000157388		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1391	protein-coding gene	gene with protein product		114206		CCHL1A2, CACNL1A2		1664412	Standard	NM_000720		Approved	Cav1.3, CACH3, CACN4	uc003dgu.5	Q01668	OTTHUMG00000158278	ENST00000350061.5:c.6233C>T	chr3.hg19:g.53845180C>T	ENSP00000288133:p.Pro2078Leu	196.0	0.0		203.0	13.0	NM_000720	B0FYA3|Q13916|Q13931|Q71UT1|Q9UDC3	Missense_Mutation	SNP	ENST00000350061.5	hg19	CCDS46848.1	.	.	.	.	.	.	.	.	.	.	C	33	5.219502	0.95139	.	.	ENSG00000157388	ENST00000350061;ENST00000288139;ENST00000422281;ENST00000481478	T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2	5.39	5.39	0.77823	.	0.340044	0.26334	N	0.024973	T	0.80929	0.4718	M	0.79475	2.455	0.80722	D	1	D;D;D;D	0.89917	1.0;0.998;1.0;1.0	D;D;D;D	0.91635	0.999;0.974;0.997;0.999	T	0.82596	-0.0379	10	0.87932	D	0	.	19.5276	0.95213	0.0:1.0:0.0:0.0	.	2054;1771;2078;2098	B0FYA3;Q59GD8;Q01668;Q01668-2	.;.;CAC1D_HUMAN;.	L	2078;2098;2054;1771	ENSP00000288133:P2078L;ENSP00000288139:P2098L;ENSP00000409174:P2054L;ENSP00000418014:P1771L	ENSP00000288139:P2098L	P	+	2	0	CACNA1D	53820220	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	7.757000	0.85209	2.710000	0.92621	0.655000	0.94253	CCA	.	.		0.532	CACNA1D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350557.1	NM_000720		T	53845180	C	T	53845180	3	4	269	1	0	0	0	0	1	0	0	0	2543	594	21	3	6595	3	CACNA1D	3	53845180	Missense_Mutation	SNP	C	TCGA-FV-A496-01A-11D-A25V-10		53845180	144177250	21	39182										
ROBO2	6092	hgsc.bcm.edu	37	chr3	77656991	77656991	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	gaaaaataaaaactcttctaAaccacagaaaaacaatggat	4	7	2	1			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr3:77656991A>C	ENST00000461745.1	+	21	4079	c.3179A>C	c.(3178-3180)aAa>aCa	p.K1060T	ROBO2_ENST00000469233.1_3'UTR|ROBO2_ENST00000332191.8_Missense_Mutation_p.K1060T|ROBO2_ENST00000487694.3_Missense_Mutation_p.K1076T	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	1060					apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)			NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		AACTCTTCTAAACCACAGAAA	0.433																																					p.K1060T		Atlas-SNP	.											.	ROBO2	527	.	0			c.A3179C						.						71	74	73					3																	77656991		1833	4089	5922	SO:0001583	missense	6092	exon21			CTTCTAAACCACA	AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10250	protein-coding gene	gene with protein product		602431	"roundabout (axon guidance receptor, Drosophila) homolog 2"			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.3179A>C	chr3.hg19:g.77656991A>C	ENSP00000417164:p.Lys1060Thr	76.0	0.0		79.0	15.0	NM_002942	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	hg19	CCDS43109.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	A|A|A	17.66|17.66|17.66	3.444552|3.444552|3.444552	0.63178|0.63178|0.63178	.|.|.	.|.|.	ENSG00000185008|ENSG00000185008|ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000461745;ENST00000332191|ENST00000490991|ENST00000471893	T;T;T|.|.	0.75154|.|.	-0.91;-0.87;-0.59|.|.	5.95|5.95|5.95	5.95|5.95|5.95	0.96441|0.96441|0.96441	.|.|.	0.000000|.|.	0.48286|.|.	D|.|.	0.000182|.|.	T|T|.	0.72486|0.72486|.	0.3466|0.3466|.	M|M|M	0.64997|0.64997|0.64997	1.995|1.995|1.995	.|.|.	.|.|.	.|.|.	P;D;D|.|.	0.61080|.|.	0.664;0.989;0.985|.|.	B;P;P|.|.	0.61592|.|.	0.115;0.891;0.777|.|.	T|T|.	0.72707|0.72707|.	-0.4212|-0.4212|.	9|4|.	0.59425|.|.	D|.|.	0.04|.|.	.|.|.	16.4237|16.4237|16.4237	0.83790|0.83790|0.83790	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.|.	1076;1060;1060|.|.	Q19AB5;F8W703;Q9HCK4|.|.	.;.;ROBO2_HUMAN|.|.	T|H|Y	1076;1076;1060;1060|217|176	ENSP00000417335:K1076T;ENSP00000417164:K1060T;ENSP00000327536:K1060T|.|.	ENSP00000327536:K1060T|.|.	K|N|X	+|+|+	2|1|3	0|0|2	ROBO2|ROBO2|ROBO2	77739681|77739681|77739681	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.995000|0.995000|0.995000	0.50966|0.50966|0.50966	0.984000|0.984000|0.984000	0.73092|0.73092|0.73092	8.962000|8.962000|8.962000	0.93254|0.93254|0.93254	2.279000|2.279000|2.279000	0.76181|0.76181|0.76181	0.533000|0.533000|0.533000	0.62120|0.62120|0.62120	AAA|AAC|TAA	.	.		0.433	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		C	77656991	A	C	77656991	3	2	269	1	0	0	0	0	1	0	0	0	13529	14	1	5	3263	5	ROBO2	3	77656991	Missense_Mutation	SNP	A	TCGA-FV-A496-01A-11D-A25V-10	23811811	77656991	120365439	22	39183										
NFKBIZ	64332	hgsc.bcm.edu	37	chr3	101571988	101571988	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	atggaagatgttcatctcaaTgaacccaaacaggagagcag	10	8	2	3			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr3:101571988T>G	ENST00000326172.5	+	5	733	c.618T>G	c.(616-618)aaT>aaG	p.N206K	NFKBIZ_ENST00000394054.2_Missense_Mutation_p.N106K|NFKBIZ_ENST00000326151.5_Missense_Mutation_p.N206K	NM_031419.3	NP_113607.1	Q9BYH8	IKBZ_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, zeta	206					inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24						TTCATCTCAATGAACCCAAAC	0.458																																					p.N206K		Atlas-SNP	.											.	NFKBIZ	55	.	0			c.T618G						.						96	104	101					3																	101571988		2203	4300	6503	SO:0001583	missense	64332	exon5			TCTCAATGAACCC	AF548362	CCDS2946.1, CCDS43123.1	3p12-q12	2013-01-10			ENSG00000144802	ENSG00000144802		"Ankyrin repeat domain containing"	29805	protein-coding gene	gene with protein product	"IL-1 inducible nuclear ankyrin-repeat protein"	608004				12565889, 16513645	Standard	NM_031419		Approved	MAIL, FLJ34463, INAP	uc003dvp.3	Q9BYH8	OTTHUMG00000159194	ENST00000326172.5:c.618T>G	chr3.hg19:g.101571988T>G	ENSP00000325663:p.Asn206Lys	88.0	0.0		88.0	36.0	NM_031419	B3KNR2|D3DN54|Q8IUL4|Q8NAZ8	Missense_Mutation	SNP	ENST00000326172.5	hg19	CCDS2946.1	.	.	.	.	.	.	.	.	.	.	T	10.42	1.345338	0.24426	.	.	ENSG00000144802	ENST00000483180;ENST00000394054;ENST00000326151;ENST00000326172;ENST00000491281	T;T;T;T	0.56103	0.52;0.48;0.48;0.55	5.26	2.81	0.32909	.	0.797452	0.11878	N	0.520791	T	0.41419	0.1158	L	0.46157	1.445	0.31838	N	0.623881	B;B	0.30021	0.078;0.265	B;B	0.28139	0.025;0.086	T	0.41963	-0.9479	10	0.12430	T	0.62	0.7596	9.3716	0.38256	0.0:0.1482:0.0:0.8518	.	206;206	Q9BYH8-3;Q9BYH8	.;IKBZ_HUMAN	K	106;106;206;206;106	ENSP00000419800:N106K;ENSP00000377618:N106K;ENSP00000325593:N206K;ENSP00000325663:N206K	ENSP00000325593:N206K	N	+	3	2	NFKBIZ	103054678	0.023000	0.18921	0.724000	0.30704	0.304000	0.27724	0.038000	0.13862	0.789000	0.33779	0.460000	0.39030	AAT	.	.		0.458	NFKBIZ-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353793.1	NM_031419		G	101571988	T	G	101571988	3	3	269	1	0	0	0	0	1	0	0	0	10392	1461	51	5	636	5	NFKBIZ	3	101571988	Missense_Mutation	SNP	T	TCGA-FV-A496-01A-11D-A25V-10	23914997	101571988	96450442	23	39184										
ECE2	9718	hgsc.bcm.edu	37	chr3	184008634	184008634	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	gggccatgagttgacgcatgCctttgatgaccaaggtaggg	15	8	0	4			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr3:184008634C>A	ENST00000402825.3	+	16	2174	c.2174C>A	c.(2173-2175)gCc>gAc	p.A725D	EIF2B5_ENST00000444495.1_Intron|ECE2_ENST00000357474.5_Missense_Mutation_p.A653D|ECE2_ENST00000359140.4_Missense_Mutation_p.A578D|ECE2_ENST00000404464.3_Missense_Mutation_p.A607D	NM_014693.3	NP_055508.3	O60344	ECE2_HUMAN	endothelin converting enzyme 2	725	Endothelin-converting enzyme 2 region.				brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|cell-cell signaling (GO:0007267)|heart development (GO:0007507)|peptide hormone processing (GO:0016486)	cytoplasmic vesicle membrane (GO:0030659)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|methyltransferase activity (GO:0008168)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(13)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(4)	49	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TTGACGCATGCCTTTGATGAC	0.587																																					p.A725D		Atlas-SNP	.											.	ECE2	303	.	0			c.C2174A						.						108	102	104					3																	184008634		2203	4300	6503	SO:0001583	missense	9718	exon16			CGCATGCCTTTGA	AF428263	CCDS3255.1, CCDS33899.1, CCDS3256.2, CCDS43179.1, CCDS46969.1	3q27.1	2007-07-26			ENSG00000145194	ENSG00000145194			13275	protein-coding gene	gene with protein product		610145				11718899	Standard	NM_032331		Approved	KIAA0604, MGC2408	uc003fni.4	O60344	OTTHUMG00000150551	ENST00000402825.3:c.2174C>A	chr3.hg19:g.184008634C>A	ENSP00000384223:p.Ala725Asp	180.0	0.0		146.0	7.0	NM_014693	A5PLK8|Q6NTG7|Q6UW36|Q8NFD7|Q96NX3|Q96NX4|Q9BRZ8	Missense_Mutation	SNP	ENST00000402825.3	hg19	CCDS3256.2	.	.	.	.	.	.	.	.	.	.	C	24.5	4.534659	0.85812	.	.	ENSG00000145194	ENST00000402825;ENST00000359140;ENST00000404464;ENST00000357474;ENST00000430587	D;D;D;D;D	0.86097	-2.07;-2.07;-2.07;-2.07;-2.07	5.38	5.38	0.77491	Peptidase M13, neprilysin, C-terminal (2);Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.95427	0.8515	H	0.97214	3.96	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;0.966;1.0;1.0;1.0	D	0.97041	0.9757	10	0.87932	D	0	-20.1971	17.6892	0.88265	0.0:1.0:0.0:0.0	.	327;578;596;607;653;578;725	B4DHU4;B4DKF3;B4DF19;O60344-2;O60344-5;O60344-3;O60344	.;.;.;.;.;.;ECE2_HUMAN	D	725;578;607;653;599	ENSP00000384223:A725D;ENSP00000352052:A578D;ENSP00000385846:A607D;ENSP00000350066:A653D;ENSP00000398444:A599D	ENSP00000350066:A653D	A	+	2	0	ECE2	185491328	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	7.484000	0.81180	2.494000	0.84150	0.561000	0.74099	GCC	.	.		0.587	ECE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318874.3	NM_014693		A	184008634	C	A	184008634	3	1	269	1	0	0	0	0	1	0	0	0	4892	739	26	3	2800	3	ECE2	3	184008634	Missense_Mutation	SNP	C	TCGA-FV-A496-01A-11D-A25V-10	82436646	184008634	14013796	24	39185										
VPS8	23355	hgsc.bcm.edu	37	chr3	184711798	184711798	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	tttatggaaaaggaaaacttGgagaaatccagggacttatc	10	5	0	1			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr3:184711798G>C	ENST00000437079.3	+	43	3784	c.3613G>C	c.(3613-3615)Gga>Cga	p.G1205R	VPS8_ENST00000287546.4_Missense_Mutation_p.G1205R|VPS8_ENST00000446204.2_Missense_Mutation_p.G1113R|VPS8_ENST00000436792.2_Missense_Mutation_p.G1203R	NM_001009921.2	NP_001009921.1	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog (S. cerevisiae)	1205							zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)			AGGAAAACTTGGAGAAATCCA	0.299																																					p.G1205R		Atlas-SNP	.											.	VPS8	109	.	0			c.G3613C						.						60	55	57					3																	184711798		1793	4060	5853	SO:0001583	missense	23355	exon42			AAACTTGGAGAAA	AK056661	CCDS46972.1	3q27.2	2006-07-07	2006-07-07	2006-07-07	ENSG00000156931	ENSG00000156931			29122	protein-coding gene	gene with protein product			"KIAA0804"	KIAA0804		9872452	Standard	NM_001009921		Approved	FLJ32099	uc003fpb.1	Q8N3P4	OTTHUMG00000156707	ENST00000437079.3:c.3613G>C	chr3.hg19:g.184711798G>C	ENSP00000397879:p.Gly1205Arg	160.0	0.0		113.0	5.0	NM_001009921	A8K8Q8|B9EIQ1|C9JB61|O94896|Q63HP2|Q9BVP9|Q9H9B0	Missense_Mutation	SNP	ENST00000437079.3	hg19	CCDS46971.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.616400	0.87359	.	.	ENSG00000156931	ENST00000287546;ENST00000437079;ENST00000436792;ENST00000446204	T;T;T;T	0.21191	2.02;2.02;2.02;2.03	5.83	5.83	0.93111	.	0.220796	0.46442	D	0.000286	T	0.42698	0.1214	L	0.49126	1.545	0.46437	D	0.999046	D;D;D	0.89917	1.0;0.972;0.997	D;P;D	0.71184	0.963;0.861;0.972	T	0.02173	-1.1201	10	0.35671	T	0.21	-28.8427	20.1099	0.97909	0.0:0.0:1.0:0.0	.	1205;1113;1203	Q8N3P4;Q8N3P4-2;Q8N3P4-3	VPS8_HUMAN;.;.	R	1205;1205;1203;1113	ENSP00000287546:G1205R;ENSP00000397879:G1205R;ENSP00000404704:G1203R;ENSP00000405483:G1113R	ENSP00000287546:G1205R	G	+	1	0	VPS8	186194492	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.985000	0.76193	2.753000	0.94483	0.585000	0.79938	GGA	.	.		0.299	VPS8-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015303		C	184711798	G	C	184711798	3	2	269	1	0	0	0	0	1	0	0	0	17233	1349	47	4	3775	4	VPS8	3	184711798	Missense_Mutation	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	703164	184711798	13310632	25	39186										
ZNF721	170960	hgsc.bcm.edu	37	chr4	438107	438107	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	tcatacttttacagcctttcCttaattgtaaattatcatgc	3	9	2	0			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr4:438107C>A	ENST00000338977.5	-	2	161	c.113G>T	c.(112-114)aGg>aTg	p.R38M	ZNF721_ENST00000506646.1_Intron|ABCA11P_ENST00000451020.2_RNA|ZNF721_ENST00000511833.2_Missense_Mutation_p.R50M|ZNF721_ENST00000507078.1_Intron			Q8TF20	ZN721_HUMAN	zinc finger protein 721	38					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(2)|large_intestine(15)|lung(6)|ovary(1)|skin(1)|stomach(5)|urinary_tract(1)	33						ACAGCCTTTCCTTAATTGTAA	0.343																																					p.W50L		Atlas-SNP	.											.	ZNF721	205	.	0			c.G149T						.						61	68	66					4																	438107		2115	4273	6388	SO:0001583	missense	170960	exon3			CCTTTCCTTAATT	AK092362	CCDS46991.1	4p16.3	2013-01-08			ENSG00000182903	ENSG00000182903		"Zinc fingers, C2H2-type", "-"	29425	protein-coding gene	gene with protein product						11853319	Standard	NM_133474		Approved	KIAA1982	uc003gag.4	Q8TF20		ENST00000338977.5:c.113G>T	chr4.hg19:g.438107C>A	ENSP00000340524:p.Arg38Met	127.0	0.0		135.0	23.0	NM_133474	Q69YG7	Missense_Mutation	SNP	ENST00000338977.5	hg19		.	.	.	.	.	.	.	.	.	.	C	9.822	1.186023	0.21870	.	.	ENSG00000182903	ENST00000338977;ENST00000511833;ENST00000505900	T;T;T	0.06768	3.26;3.29;5.94	1.03	1.03	0.20045	.	.	.	.	.	T	0.09113	0.0225	M	0.67397	2.05	0.09310	N	1	B;B;B	0.27594	0.114;0.114;0.182	B;B;B	0.21708	0.016;0.016;0.036	T	0.28170	-1.0052	9	0.54805	T	0.06	.	4.203	0.10476	0.3959:0.6041:0.0:0.0	.	38;50;50	Q8TF20;D9N162;Q8TF20-2	ZN721_HUMAN;.;.	M	38;50;82	ENSP00000340524:R38M;ENSP00000428878:R50M;ENSP00000421325:R82M	ENSP00000340524:R38M	R	-	2	0	ZNF721	428107	0.000000	0.05858	0.003000	0.11579	0.114000	0.19823	-0.455000	0.06762	0.486000	0.27676	0.195000	0.17529	AGG	.	.		0.343	ZNF721-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000357939.1	NM_133474		A	438107	C	A	438107	3	1	269	1	0	0	0	0	1	0	0	0	18137	681	24	3	2626	3	ZNF721	4	438107	Missense_Mutation	SNP	C	TCGA-FV-A496-01A-11D-A25V-10		438107	190716169	26	39187										
BEND4	389206	hgsc.bcm.edu	37	chr4	42145862	42145862	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	tttcccaatgtgacagtgctCctgtctttcgttgtaacttg	8	10	1	1			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr4:42145862C>T	ENST00000502486.1	-	3	1216	c.637G>A	c.(637-639)Gag>Aag	p.E213K	BEND4_ENST00000504360.1_Missense_Mutation_p.E209K	NM_207406.3	NP_997289.2	Q6ZU67	BEND4_HUMAN	BEN domain containing 4	213										NS(2)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(15)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	26						TGACAGTGCTCCTGTCTTTCG	0.438																																					p.E213K		Atlas-SNP	.											.	BEND4	67	.	0			c.G637A						.						99	99	99					4																	42145862		1927	4152	6079	SO:0001583	missense	389206	exon3			AGTGCTCCTGTCT	AK092951	CCDS47048.1	4p13	2012-11-22	2008-10-03	2008-10-03	ENSG00000188848	ENSG00000188848		"BEN domain containing"	23815	protein-coding gene	gene with protein product			"coiled-coil domain containing 4"	CCDC4			Standard	NM_207406		Approved	FLJ35632, FLJ43965	uc003gwn.3	Q6ZU67	OTTHUMG00000160531	ENST00000502486.1:c.637G>A	chr4.hg19:g.42145862C>T	ENSP00000421169:p.Glu213Lys	266.0	0.0		284.0	77.0	NM_001159547	A1A5D6|A1A5D7|C9JQZ5|Q58A26|Q58A27	Missense_Mutation	SNP	ENST00000502486.1	hg19	CCDS47048.1	.	.	.	.	.	.	.	.	.	.	C	16.22	3.061525	0.55432	.	.	ENSG00000188848	ENST00000411720;ENST00000502486;ENST00000504360	.	.	.	5.72	5.72	0.89469	.	0.247257	0.40144	N	0.001169	T	0.35128	0.0921	N	0.08118	0	0.47547	D	0.999458	P;B;B	0.35272	0.493;0.181;0.277	B;B;B	0.27380	0.079;0.036;0.079	T	0.39583	-0.9607	9	0.72032	D	0.01	-5.0808	19.8965	0.96963	0.0:1.0:0.0:0.0	.	135;213;213	Q6ZU67-3;Q6ZU67;Q6ZU67-2	.;BEND4_HUMAN;.	K	84;213;209	.	ENSP00000412495:E84K	E	-	1	0	BEND4	41840619	1.000000	0.71417	0.998000	0.56505	0.281000	0.26958	5.434000	0.66526	2.717000	0.92951	0.655000	0.94253	GAG	.	.		0.438	BEND4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360975.2	NM_207406		T	42145862	C	T	42145862	3	4	269	1	0	0	0	0	1	0	0	0	1400	864	30	3	983	3	BEND4	4	42145862	Missense_Mutation	SNP	C	TCGA-FV-A496-01A-11D-A25V-10	41707755	42145862	149008414	27	39188										
ALB	213	hgsc.bcm.edu	37	chr4	74276072	74276073	+	Frame_Shift_Del	DEL	AG	AG	-													0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	gaaggcttcgtctgccaaacAgagactcaagtgtgccagtc					rs3210163		TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr4:74276072_74276073delAG	ENST00000503124.1	+	4	416_417	c.209_210delAG	c.(208-210)cagfs	p.Q70fs	ALB_ENST00000295897.4_Frame_Shift_Del_p.Q220fs|ALB_ENST00000509063.1_Frame_Shift_Del_p.Q220fs|ALB_ENST00000505649.1_3'UTR|ALB_ENST00000401494.3_Frame_Shift_Del_p.Q105fs|ALB_ENST00000415165.2_Intron			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TCTGCCAAACAGAGACTCAAGT	0.366																																					p.220_220del		Pindel	.											.	ALB	132	.	0			c.658_659del						.																																			SO:0001589	frameshift_variant	213	exon6			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.209_210delAG	chr4.hg19:g.74276074_74276075delAG	ENSP00000421027:p.Gln70fs	140.0	0.0		137.0	28.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Frame_Shift_Del	DEL	ENST00000503124.1	hg19																																																																																				.	.		0.366	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		-	74276073	AG	-	74276072	7	5	269	1	0	1	0	1	0	0	0	0	486	188	7	0	681	0	ALB	4	74276072	Frame_Shift_Del	DEL	AG	TCGA-FV-A496-01A-11D-A25V-10	32130210	74276072	116878204	28	39189										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79398969	79398969	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	tgttggttcctttgtgacagGtccagtttgatgagcgagag	14	6	0	4			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr4:79398969G>A	ENST00000264895.6	+	55	8292	c.7852G>A	c.(7852-7854)Gtc>Atc	p.V2618I		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	2614	Calx-beta 1.				cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						TTTGTGACAGGTCCAGTTTGA	0.498																																					p.V2618I		Atlas-SNP	.											.	FRAS1	779	.	0			c.G7852A						.						67	62	63					4																	79398969		2062	4206	6268	SO:0001630	splice_region_variant	80144	exon55			TGACAGGTCCAGT	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.7852-1G>A	chr4.hg19:g.79398969G>A		199.0	0.0		207.0	110.0	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000264895.6	hg19	CCDS54771.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.2|20.2	3.957404|3.957404	0.73902|0.73902	.|.	.|.	ENSG00000138759|ENSG00000138759	ENST00000512123|ENST00000264895	.|T	.|0.31769	.|1.48	5.69|5.69	5.69|5.69	0.88448|0.88448	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.49270|0.49270	0.1547|0.1547	L|L	0.39633|0.39633	1.23|1.23	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.91635	.|0.999	T|T	0.18650|0.18650	-1.0330|-1.0330	5|9	.|.	.|.	.|.	.|.	20.181|20.181	0.98201|0.98201	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|2618	.|E9PHH6	.|.	D|I	846|2618	.|ENSP00000264895:V2618I	.|.	G|V	+|+	2|1	0|0	FRAS1|FRAS1	79617993|79617993	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.479000|0.479000	0.33129|0.33129	9.278000|9.278000	0.95766|0.95766	2.840000|2.840000	0.97914|0.97914	0.655000|0.655000	0.94253|0.94253	GGT|GTC	.	.		0.498	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			Missense_Mutation	A	79398969	G	A	79398969	5	1	269	1	0	0	0	0	0	0	1	0	6050	1275	44	3	8145	3	FRAS1	4	79398969	Splice_Site	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	5122897	79398969	111755307	29	39190										
GPRIN3	285513	hgsc.bcm.edu	37	chr4	90170573	90170573	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	gtttacaggacctcatttcaGagtcacagatggctccctgc	9	12	3	2			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr4:90170573G>T	ENST00000609438.1	-	2	1207	c.689C>A	c.(688-690)tCt>tAt	p.S230Y	GPRIN3_ENST00000333209.4_Missense_Mutation_p.S230Y	NM_198281.2	NP_938022.2	Q6ZVF9	GRIN3_HUMAN	GPRIN family member 3	230										breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|prostate(2)|skin(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;5.67e-05)		CCTCATTTCAGAGTCACAGAT	0.547																																					p.S230Y		Atlas-SNP	.											.	GPRIN3	90	.	0			c.C689A						.						49	53	52					4																	90170573		2203	4300	6503	SO:0001583	missense	285513	exon2			ATTTCAGAGTCAC	AK124616	CCDS34030.1	4q22.1	2006-08-24				ENSG00000185477			27733	protein-coding gene	gene with protein product		611241				15488195	Standard	NM_198281		Approved	GRIN3, FLJ42625	uc003hsm.1	Q6ZVF9		ENST00000609438.1:c.689C>A	chr4.hg19:g.90170573G>T	ENSP00000476603:p.Ser230Tyr	60.0	0.0		62.0	20.0	NM_198281	Q8IVE4	Missense_Mutation	SNP	ENST00000609438.1	hg19	CCDS34030.1	.	.	.	.	.	.	.	.	.	.	G	12.69	2.014707	0.35511	.	.	ENSG00000185477	ENST00000333209	T	0.11604	2.76	5.15	2.39	0.29439	.	0.838313	0.09746	N	0.761294	T	0.12135	0.0295	N	0.19112	0.55	0.09310	N	1	P	0.40875	0.731	P	0.49752	0.621	T	0.34925	-0.9809	10	0.45353	T	0.12	-3.2931	8.0316	0.30467	0.1495:0.1335:0.717:0.0	.	230	Q6ZVF9	GRIN3_HUMAN	Y	230	ENSP00000328672:S230Y	ENSP00000328672:S230Y	S	-	2	0	GPRIN3	90389596	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	0.794000	0.26958	0.802000	0.34089	0.650000	0.86243	TCT	.	.		0.547	GPRIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363540.2	NM_198281		T	90170573	G	T	90170573	3	4	269	1	0	0	0	0	1	0	0	0	6740	942	33	3	1645	3	GPRIN3	4	90170573	Missense_Mutation	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	10771604	90170573	100983703	30	39191										
ANK2	287	hgsc.bcm.edu	37	chr4	114274746	114274746	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	ccaaagagcagctgcagacaGttcaagataaggcagggaag	13	8	1	3			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr4:114274746G>C	ENST00000357077.4	+	38	5025	c.4972G>C	c.(4972-4974)Gtt>Ctt	p.V1658L	ANK2_ENST00000264366.6_Missense_Mutation_p.V1625L|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000394537.3_Intron|ANK2_ENST00000510275.2_Intron|ANK2_ENST00000506722.1_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	1658					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		GCTGCAGACAGTTCAAGATAA	0.473																																					p.V1658L		Atlas-SNP	.											.	ANK2	576	.	0			c.G4972C						.						81	80	80					4																	114274746		2203	4300	6503	SO:0001583	missense	287	exon38			CAGACAGTTCAAG	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.4972G>C	chr4.hg19:g.114274746G>C	ENSP00000349588:p.Val1658Leu	76.0	0.0		52.0	25.0	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	hg19	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	G	0.004	-2.287877	0.00248	.	.	ENSG00000145362	ENST00000503423;ENST00000504454;ENST00000357077;ENST00000264366	T;T;T;T	0.66099	0.07;-0.05;-0.17;-0.19	5.29	4.43	0.53597	.	1.852170	0.03076	N	0.157916	T	0.41328	0.1154	N	0.12182	0.205	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.001;0.003	T	0.41787	-0.9489	10	0.10902	T	0.67	.	2.5139	0.04663	0.1517:0.1464:0.5281:0.1739	.	1625;1658	Q01484;Q01484-4	ANK2_HUMAN;.	L	1571;1673;1658;1625	ENSP00000421011:V1571L;ENSP00000424722:V1673L;ENSP00000349588:V1658L;ENSP00000264366:V1625L	ENSP00000264366:V1625L	V	+	1	0	ANK2	114494195	0.000000	0.05858	0.001000	0.08648	0.149000	0.21700	0.507000	0.22675	1.184000	0.42957	0.655000	0.94253	GTT	.	.		0.473	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		C	114274746	G	C	114274746	3	2	269	1	0	0	0	0	1	0	0	0	621	1029	36	4	5187	4	ANK2	4	114274746	Missense_Mutation	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	24104173	114274746	76879530	31	39192										
SDHA	6389	hgsc.bcm.edu	37	chr5	223682	223682	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	atctgctaaagtttcagattCcgtaagttcatgctttttgt	7	7	3	1	rs369321221		TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr5:223682C>T	ENST00000264932.6	+	2	264	c.149C>T	c.(148-150)tCc>tTc	p.S50F	SDHA_ENST00000510361.1_Splice_Site_p.S50F|SDHA_ENST00000504309.1_Splice_Site_p.S50F	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	50					cellular metabolic process (GO:0044237)|nervous system development (GO:0007399)|oxidation-reduction process (GO:0055114)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|tricarboxylic acid cycle (GO:0006099)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex II (GO:0005749)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|succinate dehydrogenase (ubiquinone) activity (GO:0008177)			NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|liver(2)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	40			Epithelial(17;0.0159)|all cancers(22;0.0236)|OV - Ovarian serous cystadenocarcinoma(19;0.0674)|Lung(60;0.113)		Succinic acid(DB00139)	GTTTCAGATTCCGTAAGTTCA	0.408									Familial Paragangliomas																												p.S50F		Atlas-SNP	.											.	SDHA	80	.	0			c.C149T						.						81	78	79					5																	223682		2203	4300	6503	SO:0001630	splice_region_variant	6389	exon2	Familial Cancer Database	Hereditary Glomus Tumors, Familial Paragangliomas, Hereditary Paragangliomas, type 1-3: PGL1, PGL2, PGL3, incl. Familial Carotid Body Paraganglioma and Sensorineural Hearing Loss	CAGATTCCGTAAG	BC001380	CCDS3853.1	5p15	2014-09-17			ENSG00000073578	ENSG00000073578		"Mitochondrial respiratory chain complex / Complex II"	10680	protein-coding gene	gene with protein product		600857		SDH2		7798181	Standard	XM_005248329		Approved	FP, SDHF	uc003jao.4	P31040	OTTHUMG00000090275	ENST00000264932.6:c.150+1C>T	chr5.hg19:g.223682C>T		355.0	0.0		331.0	75.0	NM_004168	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Missense_Mutation	SNP	ENST00000264932.6	hg19	CCDS3853.1	.	.	.	.	.	.	.	.	.	.	c	7.855	0.724921	0.15439	.	.	ENSG00000073578	ENST00000264932;ENST00000327872;ENST00000504309;ENST00000510361	T;T;T	0.72725	-0.68;0.17;-0.62	5.81	4.93	0.64822	.	0.516501	0.18259	U	0.146684	T	0.62011	0.2393	L	0.45581	1.43	0.27511	N	0.951698	P;P;P;B;P	0.44478	0.529;0.836;0.748;0.356;0.529	B;B;B;B;B	0.40329	0.163;0.326;0.243;0.322;0.322	T	0.55186	-0.8180	10	0.08381	T	0.77	.	14.5541	0.68089	0.0:0.8526:0.1474:0.0	.	50;50;50;50;56	E9PBJ5;B4DYN5;D6RFM5;P31040;Q59GW8	.;.;.;DHSA_HUMAN;.	F	50	ENSP00000264932:S50F;ENSP00000426514:S50F;ENSP00000427703:S50F	ENSP00000264932:S50F	S	+	2	0	SDHA	276682	0.993000	0.37304	0.034000	0.17996	0.243000	0.25628	3.607000	0.54102	1.423000	0.47198	0.557000	0.71058	TCC	.	.		0.408	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168	Missense_Mutation	T	223682	C	T	223682	5	4	269	1	0	0	0	0	0	0	1	0	13978	869	30	3	155	3	SDHA	5	223682	Splice_Site	SNP	C	TCGA-FV-A496-01A-11D-A25V-10		223682	180691578	32	39193										
FBN2	2201	hgsc.bcm.edu	37	chr5	127705012	127705012	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	tgattcctccatagcaggtaCtgcgcatgtgagtatctaaa	9	9	1	2			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr5:127705012C>A	ENST00000508053.1	-	22	3085	c.2111G>T	c.(2110-2112)aGt>aTt	p.S704I	FBN2_ENST00000262464.4_Missense_Mutation_p.S704I|Y_RNA_ENST00000384560.1_RNA|FBN2_ENST00000508989.1_Missense_Mutation_p.S671I|FBN2_ENST00000511489.1_5'UTR			P35556	FBN2_HUMAN	fibrillin 2	704	TB 3.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		ATAGCAGGTACTGCGCATGTG	0.453																																					p.S704I		Atlas-SNP	.											.	FBN2	858	.	0			c.G2111T						.						138	106	117					5																	127705012		2203	4300	6503	SO:0001583	missense	2201	exon16			CAGGTACTGCGCA	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.2111G>T	chr5.hg19:g.127705012C>A	ENSP00000424571:p.Ser704Ile	66.0	0.0		48.0	17.0	NM_001999	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	hg19	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	C	19.95	3.921631	0.73213	.	.	ENSG00000138829	ENST00000262464;ENST00000508053;ENST00000508989	D;D;D	0.92299	-3.01;-3.01;-2.87	4.35	4.35	0.52113	Matrix fibril-associated (2);TGF-beta binding (1);	0.063358	0.64402	D	0.000014	D	0.94785	0.8316	M	0.76328	2.33	0.53005	D	0.999962	D;P	0.62365	0.991;0.845	P;B	0.57152	0.814;0.273	D	0.95075	0.8208	10	0.62326	D	0.03	.	18.1762	0.89762	0.0:1.0:0.0:0.0	.	671;704	D6RJI3;P35556	.;FBN2_HUMAN	I	704;704;671	ENSP00000262464:S704I;ENSP00000424571:S704I;ENSP00000425596:S671I	ENSP00000262464:S704I	S	-	2	0	FBN2	127732911	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.555000	0.45854	2.707000	0.92482	0.655000	0.94253	AGT	.	.		0.453	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		A	127705012	C	A	127705012	3	1	269	1	0	0	0	0	1	0	0	0	5711	565	20	3	6827	3	FBN2	5	127705012	Missense_Mutation	SNP	C	TCGA-FV-A496-01A-11D-A25V-10	127481330	127705012	53210248	33	39194										
EBF1	1879	hgsc.bcm.edu	37	chr5	158139190	158139190	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	ggggagttggcagctgagccGttgaggaaggtgggggagcc	22	6	0	2			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr5:158139190G>A	ENST00000313708.6	-	14	1803	c.1521C>T	c.(1519-1521)aaC>aaT	p.N507N	EBF1_ENST00000380654.4_Silent_p.N476N|EBF1_ENST00000517373.1_Intron|EBF1_ENST00000518836.1_5'UTR	NM_024007.3	NP_076870.1	Q9UH73	COE1_HUMAN	early B-cell factor 1	507	Pro/Ser/Thr-rich.				multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)		HMGA2/EBF1(2)	breast(3)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(18)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42	Renal(175;0.00196)	Acute lymphoblastic leukemia(3;2.99e-06)|all_hematologic(3;0.000772)|Medulloblastoma(196;0.037)|all_neural(177;0.143)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CAGCTGAGCCGTTGAGGAAGG	0.562			T	HMGA2	lipoma																																p.N507N		Atlas-SNP	.		Dom	yes		5	5q34	1879	early B-cell factor 1		M	.	EBF1	110	.	0			c.C1521T						.						73	56	62					5																	158139190		2203	4300	6503	SO:0001819	synonymous_variant	1879	exon14			TGAGCCGTTGAGG	AF208502	CCDS4343.1	5q34	2008-02-05	2006-09-26	2006-09-26	ENSG00000164330	ENSG00000164330			3126	protein-coding gene	gene with protein product		164343	"early B-cell factor"	EBF		8012110	Standard	NM_024007		Approved	OLF1	uc010jip.3	Q9UH73	OTTHUMG00000130304	ENST00000313708.6:c.1521C>T	chr5.hg19:g.158139190G>A		117.0	0.0		84.0	25.0	NM_024007	Q8IW11	Silent	SNP	ENST00000313708.6	hg19	CCDS4343.1																																																																																			.	.		0.562	EBF1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000252649.1	NM_024007		A	158139190	G	A	158139190	2	1	269	1	0	0	0	0	0	0	0	1	4882	1136	40	1		1	EBF1	5	158139190	Silent	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	30434178	158139190	22776070	34	39195										
ADAMTS2	9509	hgsc.bcm.edu	37	chr5	178552067	178552067	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	gcgtcattgcagtgcttggcGtgcacggagcgggtggtgtt	18	8	1	0			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr5:178552067G>A	ENST00000251582.7	-	19	2966	c.2865C>T	c.(2863-2865)caC>caT	p.H955H		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	955	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|protein processing (GO:0016485)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(31)|ovary(1)|pancreas(3)|prostate(2)|skin(7)	72	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		AGTGCTTGGCGTGCACGGAGC	0.692																																					p.H955H		Atlas-SNP	.											ADAMTS2,caecum,carcinoma,0,1	ADAMTS2	190	.	0			c.C2865T						.						100	102	101					5																	178552067		2203	4300	6503	SO:0001819	synonymous_variant	9509	exon19			CTTGGCGTGCACG	AJ003125	CCDS4444.1, CCDS34311.1	5q23-q24	2008-07-18	2005-08-19		ENSG00000087116	ENSG00000087116		"ADAM metallopeptidases with thrombospondin type 1 motif"	218	protein-coding gene	gene with protein product	"procollagen I N-proteinase", "procollagen N-endopeptidase"	604539	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2"			10094461, 15373769	Standard	NM_014244		Approved	ADAMTS-3, hPCPNI, PCINP, ADAM-TS2, NPI	uc003mjw.3	O95450	OTTHUMG00000130915	ENST00000251582.7:c.2865C>T	chr5.hg19:g.178552067G>A		60.0	0.0		27.0	4.0	NM_014244		Silent	SNP	ENST00000251582.7	hg19	CCDS4444.1																																																																																			.	.		0.692	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244		A	178552067	G	A	178552067	2	1	269	1	0	0	0	0	0	0	0	1	265	1136	40	1		1	ADAMTS2	5	178552067	Silent	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	20412877	178552067	2363193	35	39196										
C6orf27	80737	hgsc.bcm.edu	37	chr6	31742377	31742377	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	cctggggcagctcaactcctCgcaatcggagcaggtaggat	13	12	1	0			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr6:31742377C>T	ENST00000375688.4	-	5	837	c.637G>A	c.(637-639)Gag>Aag	p.E213K	VWA7_ENST00000467576.1_5'UTR|VWA7_ENST00000375686.3_Missense_Mutation_p.E213K|VWA7_ENST00000447450.1_Missense_Mutation_p.E213K			Q9Y334	VWA7_HUMAN	von Willebrand factor A domain containing 7	213						extracellular region (GO:0005576)											CTCAACTCCTCGCAATCGGAG	0.572																																					p.E213K		Atlas-SNP	.											.	.	.	.	0			c.G637A						.						66	57	60					6																	31742377		1511	2707	4218	SO:0001583	missense	80737	exon5			ACTCCTCGCAATC		CCDS4721.2	6p21	2011-12-13	2011-12-13	2011-12-13	ENSG00000204396	ENSG00000204396			13939	protein-coding gene	gene with protein product		609693	"chromosome 6 open reading frame 27"	C6orf27			Standard	NM_025258		Approved	G7c, NG37	uc011dog.2	Q9Y334	OTTHUMG00000031132	ENST00000375688.4:c.637G>A	chr6.hg19:g.31742377C>T	ENSP00000364840:p.Glu213Lys	42.0	0.0		56.0	18.0	NM_025258	A2BEX8|A6NHR6|B0V041|Q5SSR5|Q96QC8|Q9UMP9	Missense_Mutation	SNP	ENST00000375688.4	hg19	CCDS4721.2	.	.	.	.	.	.	.	.	.	.	C	2.625	-0.287659	0.05605	.	.	ENSG00000204396	ENST00000375688;ENST00000375686;ENST00000447450	T;T;T	0.29917	2.76;2.54;1.55	5.51	3.71	0.42584	.	0.582575	0.18142	N	0.150398	T	0.06234	0.0161	L	0.29908	0.895	0.09310	N	1	P	0.50710	0.938	B	0.39840	0.311	T	0.13764	-1.0497	10	0.09843	T	0.71	-8.3979	7.4193	0.27063	0.1646:0.7501:0.0:0.0853	.	213	Q9Y334	G7C_HUMAN	K	213	ENSP00000364840:E213K;ENSP00000364838:E213K;ENSP00000390554:E213K	ENSP00000364838:E213K	E	-	1	0	C6orf27	31850356	0.001000	0.12720	0.030000	0.17652	0.030000	0.12068	0.417000	0.21214	0.774000	0.33427	-0.126000	0.14955	GAG	.	.		0.572	VWA7-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076233.2	NM_025258		T	31742377	C	T	31742377	3	4	269	1	0	0	0	0	1	0	0	0	2364	893	31	1	2089	1	C6orf27	6	31742377	Missense_Mutation	SNP	C	TCGA-FV-A496-01A-11D-A25V-10		31742377	139372690	36	39197										
PEX6	5190	hgsc.bcm.edu	37	chr6	42932089	42932089	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	gctcctagcaggcagcaaacTtgcgctggatgcgcttgtac	12	12	0	0			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr6:42932089T>G	ENST00000304611.8	-	17	2996	c.2927A>C	c.(2926-2928)aAg>aCg	p.K976T	PEX6_ENST00000244546.4_3'UTR	NM_000287.3	NP_000278.3	Q13608	PEX6_HUMAN	peroxisomal biogenesis factor 6	976					ATP catabolic process (GO:0006200)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix, translocation (GO:0016561)|protein stabilization (GO:0050821)|protein targeting to peroxisome (GO:0006625)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)			NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(3)	15			all cancers(41;0.00235)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0562)			GGCAGCAAACTTGCGCTGGAT	0.632																																					p.K976T		Atlas-SNP	.											.	PEX6	44	.	0			c.A2927C						.						38	40	39					6																	42932089		2203	4299	6502	SO:0001583	missense	5190	exon17			GCAAACTTGCGCT	U56602	CCDS4877.1	6p22-p11	2010-04-21			ENSG00000124587	ENSG00000124587		"ATPases / AAA-type"	8859	protein-coding gene	gene with protein product		601498				8670792	Standard	NM_000287		Approved	PXAAA1, PAF-2	uc003otf.3	Q13608	OTTHUMG00000014713	ENST00000304611.8:c.2927A>C	chr6.hg19:g.42932089T>G	ENSP00000303511:p.Lys976Thr	122.0	0.0		104.0	42.0	NM_000287	Q5T8W1|Q8WYQ0|Q8WYQ1|Q8WYQ2|Q99476	Missense_Mutation	SNP	ENST00000304611.8	hg19	CCDS4877.1	.	.	.	.	.	.	.	.	.	.	T	16.62	3.173788	0.57692	.	.	ENSG00000124587	ENST00000304611	D	0.94613	-3.47	5.97	5.97	0.96955	.	0.126822	0.64402	D	0.000001	D	0.84488	0.5483	N	0.25201	0.72	0.80722	D	1	P	0.38250	0.624	B	0.35550	0.205	D	0.85440	0.1154	10	0.19147	T	0.46	-28.3012	16.1238	0.81380	0.0:0.0:0.0:1.0	.	976	Q13608	PEX6_HUMAN	T	976	ENSP00000303511:K976T	ENSP00000303511:K976T	K	-	2	0	PEX6	43040067	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	5.289000	0.65656	2.288000	0.76882	0.533000	0.62120	AAG	.	.		0.632	PEX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040569.1	NM_000287		G	42932089	T	G	42932089	3	3	269	1	0	0	0	0	1	0	0	0	11759	1609	56	5	19	5	PEX6	6	42932089	Missense_Mutation	SNP	T	TCGA-FV-A496-01A-11D-A25V-10	11189712	42932089	128182978	37	39198										
KLHDC3	116138	hgsc.bcm.edu	37	chr6	42986679	42986679	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	ccagtgctgctgtattgttgGtgacaagattgtcctctttg	11	8	1	2			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr6:42986679G>T	ENST00000326974.4	+	8	1094	c.899G>T	c.(898-900)gGt>gTt	p.G300V	KLHDC3_ENST00000244670.8_Missense_Mutation_p.G166V|RRP36_ENST00000244496.5_5'Flank|KLHDC3_ENST00000332245.8_Missense_Mutation_p.G241V	NM_057161.3	NP_476502.1	Q9BQ90	KLDC3_HUMAN	kelch domain containing 3	300					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|reciprocal meiotic recombination (GO:0007131)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)	chromatin binding (GO:0003682)			cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9			Colorectal(64;0.00237)|all cancers(41;0.0034)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0539)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			TGTATTGTTGGTGACAAGATT	0.512																																					p.G300V		Atlas-SNP	.											.	KLHDC3	23	.	0			c.G899T						.						63	72	69					6																	42986679		2202	4300	6502	SO:0001583	missense	116138	exon8			TTGTTGGTGACAA	AB055925	CCDS4880.1	6p21.1	2003-06-12			ENSG00000124702	ENSG00000124702			20704	protein-coding gene	gene with protein product		611248				12444059, 12606021	Standard	NM_057161		Approved	PEAS, hPeas, dJ20C7.3	uc003otl.3	Q9BQ90	OTTHUMG00000014714	ENST00000326974.4:c.899G>T	chr6.hg19:g.42986679G>T	ENSP00000313995:p.Gly300Val	91.0	0.0		73.0	13.0	NM_057161	A8K2W9	Missense_Mutation	SNP	ENST00000326974.4	hg19	CCDS4880.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.073867	0.76415	.	.	ENSG00000124702	ENST00000326974;ENST00000432243;ENST00000244670;ENST00000394096;ENST00000426116;ENST00000332245	T;T;T	0.72051	-0.62;-0.62;-0.62	5.41	5.41	0.78517	.	0.158508	0.56097	D	0.000030	T	0.74336	0.3703	M	0.78456	2.415	0.80722	D	1	P;P;P;P	0.48834	0.851;0.849;0.881;0.916	B;B;B;P	0.48334	0.431;0.276;0.433;0.574	T	0.79052	-0.1961	10	0.87932	D	0	-4.2416	19.5682	0.95404	0.0:0.0:1.0:0.0	.	300;241;166;300	E7ENU0;E7ERR0;F8W6A4;Q9BQ90	.;.;.;KLDC3_HUMAN	V	300;300;166;300;273;241	ENSP00000313995:G300V;ENSP00000244670:G166V;ENSP00000331562:G241V	ENSP00000244670:G166V	G	+	2	0	KLHDC3	43094657	1.000000	0.71417	1.000000	0.80357	0.810000	0.45777	9.095000	0.94175	2.706000	0.92434	0.205000	0.17691	GGT	.	.		0.512	KLHDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040570.1	NM_057161		T	42986679	G	T	42986679	3	4	269	1	0	0	0	0	1	0	0	0	8366	1261	44	3	925	3	KLHDC3	6	42986679	Missense_Mutation	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	54590	42986679	128128388	38	39199										
DEFB110	245913	hgsc.bcm.edu	37	chr6	49989618	49989618	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	taaaattgtgacccaaaagtGcagaataaagaaaaaaagtt	7	4	0	3			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr6:49989618G>T	ENST00000371148.2	-	1	76	c.31C>A	c.(31-33)Cac>Aac	p.H11N	DEFB110_ENST00000393660.2_Missense_Mutation_p.H11N	NM_001037497.1	NP_001032586.1	Q30KQ9	DB110_HUMAN	defensin, beta 110 locus	11					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				endometrium(1)|lung(1)|ovary(1)	3	Lung NSC(77;0.042)					ACCCAAAAGTGCAGAATAAAG	0.308																																					p.H11N		Atlas-SNP	.											.	DEFB110	5	.	0			c.C31A						.						33	37	36					6																	49989618		2201	4296	6497	SO:0001583	missense	245913	exon1			AAAAGTGCAGAAT	DQ012014, BC148541	CCDS43473.1, CCDS34475.1	6p12.3	2010-11-26	2010-11-26		ENSG00000203970	ENSG00000203970		"Defensins, beta"	18091	protein-coding gene	gene with protein product			"defensin, beta 110"			11854508, 16033865	Standard	NM_001037728		Approved	DEFB-10, DEFB-11, DEFB111	uc003pac.3	Q30KQ9	OTTHUMG00000160208	ENST00000371148.2:c.31C>A	chr6.hg19:g.49989618G>T	ENSP00000360190:p.His11Asn	45.0	0.0		51.0	11.0	NM_001037728	Q30KR0	Missense_Mutation	SNP	ENST00000371148.2	hg19	CCDS34475.1	.	.	.	.	.	.	.	.	.	.	G	7.164	0.586354	0.13749	.	.	ENSG00000203970	ENST00000393660;ENST00000371148	T	0.17854	2.25	4.64	2.77	0.32553	.	0.190119	0.26173	N	0.025911	T	0.02727	0.0082	.	.	.	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.01281	0.0;0.0	T	0.44907	-0.9297	8	.	.	.	-2.6558	6.6037	0.22714	0.0991:0.1808:0.7201:0.0	.	11;11	Q30KQ9-2;Q30KQ9	.;DB110_HUMAN	N	11	ENSP00000377270:H11N	.	H	-	1	0	DEFB110	50097577	1.000000	0.71417	0.958000	0.39756	0.109000	0.19521	2.418000	0.44662	0.631000	0.30412	0.467000	0.42956	CAC	.	.		0.308	DEFB110-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359664.1	NM_001037728		T	49989618	G	T	49989618	3	4	269	1	0	0	0	0	1	0	0	0	4402	1319	46	3	316	3	DEFB110	6	49989618	Missense_Mutation	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	7002939	49989618	121125449	39	39200										
DST	667	hgsc.bcm.edu	37	chr6	56489962	56489962	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	atacttttattacctcttgaAtaatgagatctgctgaactc	5	8	2	3			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr6:56489962A>G	ENST00000361203.3	-	31	4197	c.4190T>C	c.(4189-4191)aTt>aCt	p.I1397T	DST_ENST00000370788.2_Missense_Mutation_p.I1397T|DST_ENST00000312431.6_Missense_Mutation_p.I1397T|DST_ENST00000370754.5_Missense_Mutation_p.I1575T|DST_ENST00000421834.2_Missense_Mutation_p.I1397T|DST_ENST00000244364.6_Missense_Mutation_p.I1071T|DST_ENST00000370769.4_Missense_Mutation_p.I1397T|DST_ENST00000518935.1_Missense_Mutation_p.I1071T|DST_ENST00000446842.2_Missense_Mutation_p.I1071T|DST_ENST00000370765.6_Missense_Mutation_p.I1071T			Q03001	DYST_HUMAN	dystonin	1397					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TACCTCTTGAATAATGAGATC	0.348																																					p.I1071T		Atlas-SNP	.											.	DST	1427	.	0			c.T3212C						.						124	127	126					6																	56489962		2203	4300	6503	SO:0001583	missense	667	exon21			TCTTGAATAATGA	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.4190T>C	chr6.hg19:g.56489962A>G	ENSP00000354508:p.Ile1397Thr	68.0	0.0		87.0	4.0	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.50|12.50	1.955908|1.955908	0.34471|0.34471	.|.	.|.	ENSG00000151914|ENSG00000151914	ENST00000522360|ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000312431;ENST00000370788;ENST00000361203;ENST00000439203;ENST00000520645;ENST00000370765;ENST00000518935	.|T;T;T;T;T;T;T;T;T;T;T;T	.|0.33438	.|1.41;1.41;1.41;1.41;1.41;1.41;1.41;1.41;1.41;1.41;1.41;1.41	4.99|4.99	4.99|4.99	0.66335|0.66335	.|.	.|0.000000	.|0.49305	.|D	.|0.000150	T|T	0.17746|0.17746	0.0426|0.0426	N|N	0.26130|0.26130	0.795|0.795	.|.	.|.	.|.	.|B;D;D;B;B;P;B;B	.|0.60575	.|0.002;0.988;0.985;0.004;0.041;0.542;0.002;0.034	.|B;P;B;B;B;P;B;B	.|0.52957	.|0.003;0.714;0.444;0.004;0.078;0.525;0.003;0.028	T|T	0.02813|0.02813	-1.1107|-1.1107	4|9	.|0.12430	.|T	.|0.62	.|.	14.9983|14.9983	0.71451|0.71451	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|1397;1397;1575;1071;1071;1071;1397;1071	.|Q5TBT1;E7ERU2;E9PEB9;Q6P0N6;Q03001-3;Q03001-9;Q03001;Q03001-8	.|.;.;.;.;.;.;DYST_HUMAN;.	L|T	69|1071;1575;1397;1397;1071;1397;1397;1397;1071;1437;1071;1071	.|ENSP00000244364:I1071T;ENSP00000359790:I1575T;ENSP00000359805:I1397T;ENSP00000400883:I1397T;ENSP00000393645:I1071T;ENSP00000307959:I1397T;ENSP00000359824:I1397T;ENSP00000354508:I1397T;ENSP00000404924:I1071T;ENSP00000431030:I1437T;ENSP00000359801:I1071T;ENSP00000431003:I1071T	.|ENSP00000244364:I1071T	F|I	-|-	1|2	0|0	DST|DST	56597921|56597921	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	4.554000|4.554000	0.60760|0.60760	2.008000|2.008000	0.58898|0.58898	0.460000|0.460000	0.39030|0.39030	TTC|ATT	.	.		0.348	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		G	56489962	A	G	56489962	3	3	269	1	0	0	0	0	1	0	0	0	4785	101	4	2	17199	2	DST	6	56489962	Missense_Mutation	SNP	A	TCGA-FV-A496-01A-11D-A25V-10	6500344	56489962	114625105	40	39201										
C6orf165	154313	hgsc.bcm.edu	37	chr6	88128105	88128105	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	aagcgctatataatatacgaCaatatgaggtcttccttcag	7	8	2	1	rs140570931		TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr6:88128105C>A	ENST00000507897.1	+	7	894	c.811C>A	c.(811-813)Caa>Aaa	p.Q271K	C6ORF165_ENST00000369562.4_Missense_Mutation_p.Q271K			Q8IYR0	CF165_HUMAN	chromosome 6 open reading frame 165	271										NS(1)|central_nervous_system(1)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0419)		TAATATACGACAATATGAGGT	0.403																																					p.Q271K		Atlas-SNP	.											.	C6orf165	116	.	0			c.C811A						.						98	105	103					6																	88128105		2203	4300	6503	SO:0001583	missense	154313	exon7			ATACGACAATATG	BC035083	CCDS34498.1	6q15	2012-02-07			ENSG00000213204	ENSG00000213204			21405	protein-coding gene	gene with protein product							Standard	NM_001031743		Approved	FLJ25974, dJ382I10.1	uc003plv.3	Q8IYR0	OTTHUMG00000015173	ENST00000507897.1:c.811C>A	chr6.hg19:g.88128105C>A	ENSP00000426769:p.Gln271Lys	88.0	0.0		101.0	23.0	NM_001031743	A8K969|E1P507|Q8N9U4	Missense_Mutation	SNP	ENST00000507897.1	hg19	CCDS34498.1	.	.	.	.	.	.	.	.	.	.	C	19.81	3.897363	0.72639	.	.	ENSG00000213204	ENST00000369562	T	0.50277	0.75	5.16	5.16	0.70880	.	0.109289	0.64402	D	0.000005	T	0.64638	0.2616	M	0.80847	2.515	0.80722	D	1	D;D	0.67145	0.996;0.993	D;D	0.65573	0.936;0.936	T	0.66964	-0.5790	10	0.51188	T	0.08	.	18.607	0.91270	0.0:1.0:0.0:0.0	.	271;271	Q8IYR0;E1P509	CF165_HUMAN;.	K	271	ENSP00000358575:Q271K	ENSP00000358575:Q271K	Q	+	1	0	C6orf165	88184824	1.000000	0.71417	0.855000	0.33649	0.352000	0.29268	6.706000	0.74649	2.575000	0.86900	0.591000	0.81541	CAA	.	C|1.000;T|0.000		0.403	C6orf165-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000470406.1	NM_178823		A	88128105	C	A	88128105	3	1	269	1	0	0	0	0	1	0	0	0	2343	479	17	3	833	3	C6orf165	6	88128105	Missense_Mutation	SNP	C	TCGA-FV-A496-01A-11D-A25V-10	31638143	88128105	82986962	41	39202										
KIAA0776	23376	hgsc.bcm.edu	37	chr6	96997391	96997391	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	gcacaatcaaggacttgcaaGaagaagtttcaaacctgtac	8	9	2	2			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr6:96997391G>A	ENST00000369278.4	+	14	1690	c.1624G>A	c.(1624-1626)Gaa>Aaa	p.E542K		NM_015323.4	NP_056138.1	O94874	UFL1_HUMAN	UFM1-specific ligase 1	542					negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein ubiquitination (GO:0031397)|osteoblast differentiation (GO:0001649)|protein ufmylation (GO:0071569)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	UFM1 conjugating enzyme activity (GO:0071568)										GGACTTGCAAGAAGAAGTTTC	0.348																																					p.E542K		Atlas-SNP	.											.	.	.	.	0			c.G1624A						.						67	64	65					6																	96997391		2203	4298	6501	SO:0001583	missense	23376	exon14			TTGCAAGAAGAAG	BC036379	CCDS5034.1	6q16.3	2011-08-18	2011-08-18	2011-08-18	ENSG00000014123	ENSG00000014123			23039	protein-coding gene	gene with protein product	"novel LZAP-binding protein", "Regulator of CDK5RAP3 and DDRGK1"	613372	"KIAA0776"	KIAA0776		20018847, 20164180, 20228063, 20531390	Standard	NM_015323		Approved	NLBP, Maxer, RCAD	uc003por.3	O94874	OTTHUMG00000015238	ENST00000369278.4:c.1624G>A	chr6.hg19:g.96997391G>A	ENSP00000358283:p.Glu542Lys	115.0	0.0		120.0	6.0	NM_015323	A0PJ53|B4DJ57|C0H5X5|Q8N765|Q9NTQ0	Missense_Mutation	SNP	ENST00000369278.4	hg19	CCDS5034.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.944818	0.92593	.	.	ENSG00000014123	ENST00000369278	T	0.42513	0.97	5.64	5.64	0.86602	.	0.044345	0.85682	D	0.000000	T	0.41419	0.1158	M	0.71296	2.17	0.80722	D	1	P	0.52577	0.954	P	0.47673	0.554	T	0.21143	-1.0254	10	0.28530	T	0.3	-26.5139	18.6746	0.91524	0.0:0.0:1.0:0.0	.	542	O94874	UFL1_HUMAN	K	542	ENSP00000358283:E542K	ENSP00000358283:E542K	E	+	1	0	KIAA0776	97104112	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.755000	0.91646	2.646000	0.89796	0.650000	0.86243	GAA	.	.		0.348	UFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041557.1	NM_015323		A	96997391	G	A	96997391	3	1	269	1	0	0	0	0	1	0	0	0	8202	943	33	3	1678	3	KIAA0776	6	96997391	Missense_Mutation	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	8869286	96997391	74117676	42	39203										
TIAM2	26230	hgsc.bcm.edu	37	chr6	155504406	155504406	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	atgagatcatgaccttaaatGgggaagctgtgtctgatctt	11	6	3	3	rs76467763		TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr6:155504406G>T	ENST00000461783.3	+	16	4109	c.2836G>T	c.(2836-2838)Ggg>Tgg	p.G946W	TIAM2_ENST00000318981.5_Missense_Mutation_p.G946W|TIAM2_ENST00000528391.2_Missense_Mutation_p.G282W|TIAM2_ENST00000456144.1_Missense_Mutation_p.G946W|TIAM2_ENST00000367174.2_Missense_Mutation_p.G322W|TIAM2_ENST00000456877.2_Missense_Mutation_p.G258W|TIAM2_ENST00000360366.4_Missense_Mutation_p.G970W|TIAM2_ENST00000529824.2_Missense_Mutation_p.G946W			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	946	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				apoptotic signaling pathway (GO:0097190)|cellular lipid metabolic process (GO:0044255)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(20)|lung(21)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	65		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		GACCTTAAATGGGGAAGCTGT	0.468																																					p.G946W		Atlas-SNP	.											.	TIAM2	161	.	0			c.G2836T						.						91	94	93					6																	155504406		2203	4300	6503	SO:0001583	missense	26230	exon13			TTAAATGGGGAAG		CCDS34558.1, CCDS34559.1	6q25	2013-01-10			ENSG00000146426	ENSG00000146426		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11806	protein-coding gene	gene with protein product		604709				10512681	Standard	NM_012454		Approved	STEF	uc003qqe.3	Q8IVF5	OTTHUMG00000015880	ENST00000461783.3:c.2836G>T	chr6.hg19:g.155504406G>T	ENSP00000437188:p.Gly946Trp	106.0	0.0		113.0	28.0	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Missense_Mutation	SNP	ENST00000461783.3	hg19	CCDS34558.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.200618	0.79015	.	.	ENSG00000146426	ENST00000461783;ENST00000528928;ENST00000528535;ENST00000456144;ENST00000318981;ENST00000367174;ENST00000360366;ENST00000529824;ENST00000456877;ENST00000528391	T;T;T;T;T;T;T;T;T	0.45276	0.9;0.9;0.9;0.9;0.9;0.9;0.9;0.9;0.9	5.67	5.67	0.87782	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.65015	0.2651	M	0.84683	2.71	0.53688	D	0.999975	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	T	0.70063	-0.4975	10	0.87932	D	0	.	17.9536	0.89061	0.0:0.0:1.0:0.0	.	282;946;970;946	E9PKT1;Q8IVF5-2;Q8IVF5-5;Q8IVF5	.;.;.;TIAM2_HUMAN	W	946;1192;946;946;946;322;970;946;258;282	ENSP00000437188:G946W;ENSP00000434901:G946W;ENSP00000407746:G946W;ENSP00000327315:G946W;ENSP00000356142:G322W;ENSP00000353528:G970W;ENSP00000433348:G946W;ENSP00000407183:G258W;ENSP00000435335:G282W	ENSP00000327315:G946W	G	+	1	0	TIAM2	155546098	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.749000	0.62155	2.677000	0.91161	0.655000	0.94253	GGG	.	.		0.468	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454		T	155504406	G	T	155504406	3	4	269	1	0	0	0	0	1	0	0	0	15906	1348	47	3	2878	3	TIAM2	6	155504406	Missense_Mutation	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	58507015	155504406	15610661	43	39204										
TMEM181	57583	hgsc.bcm.edu	37	chr6	159029441	159029441	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	gacctctttcagtccatgttCctgtgcgccctgctgctctt	8	15	3	0			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr6:159029441C>T	ENST00000367090.3	+	9	1172	c.1161C>T	c.(1159-1161)ttC>ttT	p.F387F		NM_020823.1	NP_065874.1	Q9P2C4	TM181_HUMAN	transmembrane protein 181	387					pathogenesis (GO:0009405)	integral component of membrane (GO:0016021)	toxic substance binding (GO:0015643)			central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(1)	22		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;8.15e-18)|BRCA - Breast invasive adenocarcinoma(81;1.38e-05)		AGTCCATGTTCCTGTGCGCCC	0.602																																					p.F387F		Atlas-SNP	.											.	TMEM181	47	.	0			c.C1161T						.						143	140	141					6																	159029441		2135	4267	6402	SO:0001819	synonymous_variant	57583	exon9			CATGTTCCTGTGC	AB037844	CCDS43520.1	6q25.3	2012-08-10	2006-10-19	2006-10-19	ENSG00000146433	ENSG00000146433			20958	protein-coding gene	gene with protein product		613209	"G protein-coupled receptor 178", "KIAA1423"	KIAA1423, GPR178		16452613	Standard	NM_020823		Approved		uc003qrm.4	Q9P2C4	OTTHUMG00000015913	ENST00000367090.3:c.1161C>T	chr6.hg19:g.159029441C>T		366.0	0.0		315.0	141.0	NM_020823	Q5VTU1	Silent	SNP	ENST00000367090.3	hg19	CCDS43520.1																																																																																			.	.		0.602	TMEM181-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042873.1	NM_020823		T	159029441	C	T	159029441	2	4	269	1	0	0	0	0	0	0	0	1	16115	854	30	3		3	TMEM181	6	159029441	Silent	SNP	C	TCGA-FV-A496-01A-11D-A25V-10	3525035	159029441	12085626	44	39205										
SDK1	221935	hgsc.bcm.edu	37	chr7	4008918	4008918	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	ttctggccagtggctctgtcCggattcctaggttcatgctt	11	11	3	0			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr7:4008918C>T	ENST00000404826.2	+	11	1715	c.1576C>T	c.(1576-1578)Cgg>Tgg	p.R526W	SDK1_ENST00000389531.3_Missense_Mutation_p.R526W	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	526	Ig-like C2-type 5.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.R526R(1)		NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		TGGCTCTGTCCGGATTCCTAG	0.502																																					p.R526W		Atlas-SNP	.											SDK1,colon,carcinoma,-1,1	SDK1	361	.	1	Substitution - coding silent(1)	lung(1)	c.C1576T						.						282	305	297					7																	4008918		2203	4300	6503	SO:0001583	missense	221935	exon11			TCTGTCCGGATTC	AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19307	protein-coding gene	gene with protein product		607216	"sidekick homolog 1 (chicken)", "sidekick homolog 1, cell adhesion molecule (chicken)"			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.1576C>T	chr7.hg19:g.4008918C>T	ENSP00000385899:p.Arg526Trp	145.0	1.0		185.0	68.0	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	hg19	CCDS34590.1	.	.	.	.	.	.	.	.	.	.	C	32	5.107054	0.94292	.	.	ENSG00000146555	ENST00000404826;ENST00000389531	T;T	0.68903	-0.36;-0.36	5.63	4.75	0.60458	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.349472	0.25648	N	0.029229	T	0.75729	0.3889	L	0.50333	1.59	0.39917	D	0.974102	D	0.76494	0.999	D	0.63192	0.912	T	0.77624	-0.2518	10	0.45353	T	0.12	.	16.2941	0.82762	0.1335:0.8665:0.0:0.0	.	526	Q7Z5N4	SDK1_HUMAN	W	526	ENSP00000385899:R526W;ENSP00000374182:R526W	ENSP00000374182:R526W	R	+	1	2	SDK1	3975444	1.000000	0.71417	0.956000	0.39512	0.995000	0.86356	5.694000	0.68272	1.515000	0.48885	0.655000	0.94253	CGG	.	.		0.502	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744		T	4008918	C	T	4008918	3	4	269	1	0	0	0	0	1	0	0	0	13983	643	23	1	1618	1	SDK1	7	4008918	Missense_Mutation	SNP	C	TCGA-FV-A496-01A-11D-A25V-10		4008918	155129745	45	39206										
PAPOLB	56903	hgsc.bcm.edu	37	chr7	4900131	4900131	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	agccctaacccaatcacccaCattgtacgaaattcttccat	3	15	2	0			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr7:4900131C>T	ENST00000404991.1	-	1	1494	c.1308G>A	c.(1306-1308)atG>atA	p.M436I	RADIL_ENST00000536091.1_Intron|RADIL_ENST00000399583.3_Intron	NM_020144.4	NP_064529.4	Q9NRJ5	PAPOB_HUMAN	poly(A) polymerase beta (testis specific)	436					mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)			kidney(1)|large_intestine(6)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	14		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.089)|OV - Ovarian serous cystadenocarcinoma(56;2.06e-14)		CAATCACCCACATTGTACGAA	0.393																																					p.M437I		Atlas-SNP	.											.	PAPOLB	93	.	0			c.G1311A						.						140	151	147					7																	4900131		2190	4297	6487	SO:0001583	missense	56903	exon1			CACCCACATTGTA	AF218840		7p22.1	2008-02-08			ENSG00000218823	ENSG00000218823	2.7.7.19		15970	protein-coding gene	gene with protein product		607436				11150526	Standard	NM_020144		Approved	PAPT	uc003snk.3	Q9NRJ5	OTTHUMG00000151759	ENST00000404991.1:c.1308G>A	chr7.hg19:g.4900131C>T	ENSP00000384700:p.Met436Ile	184.0	0.0		273.0	55.0	NM_020144	Q75LH1|Q8NE14	Missense_Mutation	SNP	ENST00000404991.1	hg19		.	.	.	.	.	.	.	.	.	.	C	16.13	3.036662	0.54896	.	.	ENSG00000218823	ENST00000404991	.	.	.	5.06	5.06	0.68205	.	.	.	.	.	T	0.72914	0.3520	M	0.62723	1.935	0.58432	D	0.999994	P	0.43973	0.823	P	0.55112	0.769	T	0.72541	-0.4262	8	0.49607	T	0.09	.	16.3421	0.83085	0.0:1.0:0.0:0.0	.	437	A4D1Z6	.	I	436	.	ENSP00000384700:M436I	M	-	3	0	PAPOLB	4866657	1.000000	0.71417	0.999000	0.59377	0.977000	0.68977	7.320000	0.79064	2.809000	0.96659	0.467000	0.42956	ATG	.	.		0.393	PAPOLB-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000323797.1	NM_020144		T	4900131	C	T	4900131	3	4	269	1	0	0	0	0	1	0	0	0	11439	478	17	3	606	3	PAPOLB	7	4900131	Missense_Mutation	SNP	C	TCGA-FV-A496-01A-11D-A25V-10	891213	4900131	154238532	46	39207										
HDAC9	9734	hgsc.bcm.edu	37	chr7	18767353	18767353	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	tacctcacccagcaatggacCgccccctccagcctggctct	7	20	2	0			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr7:18767353C>A	ENST00000432645.2	+	12	1873	c.1873C>A	c.(1873-1875)Cgc>Agc	p.R625S	HDAC9_ENST00000441542.2_Missense_Mutation_p.R628S|HDAC9_ENST00000406451.4_Missense_Mutation_p.R625S|HDAC9_ENST00000401921.1_Missense_Mutation_p.R584S	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	625					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|regulation of skeletal muscle fiber development (GO:0048742)|regulation of striated muscle cell differentiation (GO:0051153)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|liver(2)|lung(37)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	82	all_lung(11;0.187)				Valproic Acid(DB00313)	AGCAATGGACCGCCCCCTCCA	0.527																																					p.R628S		Atlas-SNP	.											HDAC9_ENST00000262069,left_lower_lobe,carcinoma,0,4	HDAC9	560	.	0			c.C1882A						.						41	46	44					7																	18767353		1988	4143	6131	SO:0001583	missense	9734	exon12			ATGGACCGCCCCC	AF124924	CCDS47553.1, CCDS47554.1, CCDS47555.1, CCDS47557.1, CCDS56465.1, CCDS56466.1, CCDS56467.1, CCDS56468.1, CCDS75565.1	7p21.1	2008-05-15			ENSG00000048052	ENSG00000048052			14065	protein-coding gene	gene with protein product		606543				10523670, 10487760	Standard	NM_178425		Approved	KIAA0744, HDAC, MITR, HD7, HDAC7B	uc003sui.3	Q9UKV0	OTTHUMG00000152487	ENST00000432645.2:c.1873C>A	chr7.hg19:g.18767353C>A	ENSP00000410337:p.Arg625Ser	205.0	0.0		284.0	18.0	NM_178425	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Missense_Mutation	SNP	ENST00000432645.2	hg19	CCDS47555.1	.	.	.	.	.	.	.	.	.	.	C	5.499	0.276989	0.10403	.	.	ENSG00000048052	ENST00000406451;ENST00000401921;ENST00000432645;ENST00000441542;ENST00000341009	T;T;T;T	0.57107	0.43;0.42;0.42;0.43	4.87	1.44	0.22558	.	0.387462	0.22358	N	0.061105	T	0.35537	0.0935	L	0.36672	1.1	0.80722	D	1	B;B;B;B;B;B;B	0.19817	0.001;0.01;0.034;0.01;0.02;0.01;0.039	B;B;B;B;B;B;B	0.17979	0.003;0.01;0.018;0.018;0.008;0.018;0.02	T	0.10337	-1.0634	10	0.09338	T	0.73	-24.6513	9.38	0.38306	0.0:0.7311:0.0:0.2689	.	625;537;584;628;625;625;603	Q9UKV0-4;Q9UKV0-2;Q9UKV0-6;Q9UKV0-7;Q9UKV0;Q9UKV0-5;Q8N879	.;.;.;.;HDAC9_HUMAN;.;.	S	625;584;625;628;537	ENSP00000384657:R625S;ENSP00000383912:R584S;ENSP00000410337:R625S;ENSP00000408617:R628S	ENSP00000339165:R537S	R	+	1	0	HDAC9	18733878	1.000000	0.71417	0.829000	0.32907	0.991000	0.79684	1.096000	0.30976	0.150000	0.19136	0.557000	0.71058	CGC	.	.		0.527	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1			A	18767353	C	A	18767353	3	1	269	1	0	0	0	0	1	0	0	0	7023	652	23	1	1979	1	HDAC9	7	18767353	Missense_Mutation	SNP	C	TCGA-FV-A496-01A-11D-A25V-10	13867222	18767353	140371310	47	39208										
TNS3	64759	hgsc.bcm.edu	37	chr7	47384383	47384383	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	tttgtgctgactggctgggcTgctcagcgggggctcaggtg	18	9	2	1			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr7:47384383T>A	ENST00000398879.1	-	20	2986	c.2620A>T	c.(2620-2622)Agc>Tgc	p.S874C	TNS3_ENST00000355730.3_Missense_Mutation_p.S634C|TNS3_ENST00000311160.9_Missense_Mutation_p.S874C			Q68CZ2	TENS3_HUMAN	tensin 3	874					cell migration (GO:0016477)|lung alveolus development (GO:0048286)|positive regulation of cell proliferation (GO:0008284)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(17)|endometrium(5)|kidney(4)|large_intestine(7)|liver(1)|lung(16)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	64						CTGGCTGGGCTGCTCAGCGGG	0.617																																					p.S874C		Atlas-SNP	.											.	TNS3	140	.	0			c.A2620T						.						40	48	46					7																	47384383		1954	4147	6101	SO:0001583	missense	64759	exon20			CTGGGCTGCTCAG	AF378756	CCDS5506.2	7p12.3	2013-02-14	2005-05-13	2005-05-13	ENSG00000136205	ENSG00000136205		"SH2 domain containing"	21616	protein-coding gene	gene with protein product	"tumor endothelial marker 6"	606825	"tensin-like SH2 domain-containing 1"	TENS1		11559528	Standard	NM_022748		Approved	TEM6, H_NH0549I23.2, FLJ13732	uc003tnw.3	Q68CZ2	OTTHUMG00000074075	ENST00000398879.1:c.2620A>T	chr7.hg19:g.47384383T>A	ENSP00000381854:p.Ser874Cys	49.0	0.0		68.0	32.0	NM_022748	B2RNV1|Q6IPQ2|Q8IZW7|Q8NAD0|Q96PE0|Q96S48	Missense_Mutation	SNP	ENST00000398879.1	hg19	CCDS5506.2	.	.	.	.	.	.	.	.	.	.	T	10.55	1.380436	0.24944	.	.	ENSG00000136205	ENST00000311160;ENST00000538633;ENST00000398879;ENST00000355730;ENST00000545849;ENST00000457718	D;D;D;D	0.94280	-2.96;-2.96;-3.39;-3.07	5.43	-1.98	0.07480	.	1.316600	0.04948	N	0.459690	D	0.85600	0.5734	N	0.17082	0.46	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.73642	-0.3918	10	0.62326	D	0.03	-3.4579	4.9134	0.13833	0.0:0.2763:0.2842:0.4395	.	874	Q68CZ2	TENS3_HUMAN	C	874;984;874;634;330;977	ENSP00000312143:S874C;ENSP00000381854:S874C;ENSP00000347968:S634C;ENSP00000414358:S977C	ENSP00000312143:S874C	S	-	1	0	TNS3	47350908	0.010000	0.17322	0.001000	0.08648	0.363000	0.29612	0.195000	0.17155	-0.205000	0.10219	0.379000	0.24179	AGC	.	.		0.617	TNS3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157253.1	NM_022748		A	47384383	T	A	47384383	3	1	269	1	0	0	0	0	1	0	0	0	16359	1580	55	4	1765	4	TNS3	7	47384383	Missense_Mutation	SNP	T	TCGA-FV-A496-01A-11D-A25V-10	28617030	47384383	111754280	48	39209										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48559880	48559880	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	tgctacactgggaccttctgCgatggccaaggtgggttctg	14	10	2	0			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr7:48559880C>T	ENST00000435803.1	+	53	14065	c.14041C>T	c.(14041-14043)Cga>Tga	p.R4681*	ABCA13_ENST00000544596.1_Nonsense_Mutation_p.R411*	NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	4681					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						GGACCTTCTGCGATGGCCAAG	0.493																																					p.R4681X		Atlas-SNP	.											.	ABCA13	1192	.	0			c.C14041T						.						43	40	41					7																	48559880		1923	4151	6074	SO:0001587	stop_gained	154664	exon53			CTTCTGCGATGGC	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.14041C>T	chr7.hg19:g.48559880C>T	ENSP00000411096:p.Arg4681*	165.0	0.0		191.0	8.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Nonsense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	C	55	24.171996	0.99959	.	.	ENSG00000179869	ENST00000435803;ENST00000411975;ENST00000544596	.	.	.	5.32	2.39	0.29439	.	0.977254	0.08337	N	0.961457	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.16420	T	0.52	.	2.8352	0.05512	0.1517:0.5483:0.1381:0.1618	.	.	.	.	X	4681;454;411	.	ENSP00000391042:R454X	R	+	1	2	ABCA13	48530426	0.001000	0.12720	0.003000	0.11579	0.882000	0.50991	0.918000	0.28678	0.188000	0.20168	0.655000	0.94253	CGA	.	.		0.493	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		T	48559880	C	T	48559880	4	4	269	1	0	0	0	0	0	1	0	0	31	760	27	1	14080	1	ABCA13	7	48559880	Nonsense_Mutation	SNP	C	TCGA-FV-A496-01A-11D-A25V-10	1175497	48559880	110578783	49	39210										
SEMA3C	10512	hgsc.bcm.edu	37	chr7	80435065	80435065	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	ctatatacattccagagaaaAgctcctcatctatgaaaaag	5	9	2	2			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr7:80435065A>T	ENST00000265361.3	-	7	1109	c.548T>A	c.(547-549)cTt>cAt	p.L183H	SEMA3C_ENST00000544525.1_Missense_Mutation_p.L201H|SEMA3C_ENST00000536800.1_Missense_Mutation_p.L35H|SEMA3C_ENST00000419255.2_Missense_Mutation_p.L183H	NM_006379.3	NP_006370.1	Q99985	SEM3C_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	183	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|blood vessel remodeling (GO:0001974)|cardiac right ventricle morphogenesis (GO:0003215)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|immune response (GO:0006955)|limb bud formation (GO:0060174)|neural crest cell migration (GO:0001755)|neural tube development (GO:0021915)|outflow tract morphogenesis (GO:0003151)|post-embryonic development (GO:0009791)|pulmonary myocardium development (GO:0003350)|response to drug (GO:0042493)|somitogenesis (GO:0001756)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						TCCAGAGAAAAGCTCCTCATC	0.323																																					p.L183H		Atlas-SNP	.											.	SEMA3C	106	.	0			c.T548A						.						59	56	57					7																	80435065		2203	4298	6501	SO:0001583	missense	10512	exon7			GAGAAAAGCTCCT	AB000220	CCDS5596.1	7q21-q31	2013-01-11			ENSG00000075223	ENSG00000075223		"Semaphorins", "Immunoglobulin superfamily / I-set domain containing"	10725	protein-coding gene	gene with protein product		602645		SEMAE		7748561, 9168980	Standard	NM_006379		Approved	SemE	uc003uhj.3	Q99985	OTTHUMG00000023447	ENST00000265361.3:c.548T>A	chr7.hg19:g.80435065A>T	ENSP00000265361:p.Leu183His	31.0	0.0		51.0	8.0	NM_006379	B4DRL8	Missense_Mutation	SNP	ENST00000265361.3	hg19	CCDS5596.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.480304	0.84747	.	.	ENSG00000075223	ENST00000265361;ENST00000419255;ENST00000544525;ENST00000536800	T;T;T;T	0.23348	1.91;1.91;1.91;1.91	5.17	5.17	0.71159	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.65450	0.2692	H	0.96889	3.9	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	T	0.78730	-0.2090	10	0.87932	D	0	.	15.0131	0.71565	1.0:0.0:0.0:0.0	.	35;201;183	B4DRL8;F5H1Z7;Q99985	.;.;SEM3C_HUMAN	H	183;183;201;35	ENSP00000265361:L183H;ENSP00000411193:L183H;ENSP00000445649:L201H;ENSP00000438258:L35H	ENSP00000265361:L183H	L	-	2	0	SEMA3C	80273001	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.308000	0.96247	1.946000	0.56461	0.482000	0.46254	CTT	.	.		0.323	SEMA3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253279.1	NM_006379		T	80435065	A	T	80435065	3	4	269	1	0	0	0	0	1	0	0	0	14041	72	3	4	1755	4	SEMA3C	7	80435065	Missense_Mutation	SNP	A	TCGA-FV-A496-01A-11D-A25V-10	31875185	80435065	78703598	50	39211										
TRPV5	56302	hgsc.bcm.edu	37	chr7	142625797	142625797	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	gtctcttaccacagtgttacCctccactccagccagcttga	6	16	1	1	rs377425606		TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr7:142625797C>T	ENST00000265310.1	-	6	1099	c.751G>A	c.(751-753)Ggt>Agt	p.G251S	TRPV5_ENST00000442623.1_Missense_Mutation_p.G251S	NM_019841.4	NP_062815.2	Q9NQA5	TRPV5_HUMAN	transient receptor potential cation channel, subfamily V, member 5	251					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|ion transmembrane transport (GO:0034220)|protein tetramerization (GO:0051262)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(14)|lung(32)|ovary(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	67	Melanoma(164;0.059)					ACAGTGTTACCCTCCACTCCA	0.587																																					p.G251S		Atlas-SNP	.											.	TRPV5	164	.	0			c.G751A						.	C	SER/GLY	1,4405	2.1+/-5.4	0,1,2202	87	80	82		751	4.1	1	7		82	0,8600		0,0,4300	no	missense	TRPV5	NM_019841.4	56	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	251/730	142625797	1,13005	2203	4300	6503	SO:0001583	missense	56302	exon6			TGTTACCCTCCAC	AJ271207	CCDS5875.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000127412	ENSG00000127412		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	3145	protein-coding gene	gene with protein product		606679	"epithelial calcium channel 1"	ECAC1		10944439, 10945469, 16382100	Standard	NM_019841		Approved	CaT2	uc003wby.1	Q9NQA5	OTTHUMG00000157157	ENST00000265310.1:c.751G>A	chr7.hg19:g.142625797C>T	ENSP00000265310:p.Gly251Ser	153.0	0.0		95.0	12.0	NM_019841	A4D2H7|E9PBZ6|Q8N4C1|Q8NDW5|Q8NDX7|Q8NDX8|Q96PM6	Missense_Mutation	SNP	ENST00000265310.1	hg19	CCDS5875.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.378337	0.82682	2.27E-4	0.0	ENSG00000127412	ENST00000265310;ENST00000439304;ENST00000442623	D;T;D	0.90955	-2.76;0.35;-2.76	4.09	4.09	0.47781	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	D	0.96337	0.8805	M	0.93763	3.455	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.80764	0.936;0.994	D	0.97376	0.9979	10	0.72032	D	0.01	-14.0059	15.8322	0.78764	0.0:1.0:0.0:0.0	.	251;251	E9PBZ6;Q9NQA5	.;TRPV5_HUMAN	S	251;245;251	ENSP00000265310:G251S;ENSP00000406361:G245S;ENSP00000406572:G251S	ENSP00000265310:G251S	G	-	1	0	TRPV5	142335919	1.000000	0.71417	1.000000	0.80357	0.696000	0.40369	7.434000	0.80377	2.278000	0.76064	0.462000	0.41574	GGT	.	.		0.587	TRPV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347660.1	NM_019841		T	142625797	C	T	142625797	3	4	269	1	0	0	0	0	1	0	0	0	16614	623	22	3	1478	3	TRPV5	7	142625797	Missense_Mutation	SNP	C	TCGA-FV-A496-01A-11D-A25V-10	62190732	142625797	16512866	51	39212										
PIWIL2	55124	hgsc.bcm.edu	37	chr8	22136992	22136992	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	ccaggctgttggccacaagcTtctaaacctttggacccagc	9	14	1	0			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr8:22136992T>G	ENST00000454009.2	+	2	602	c.93T>G	c.(91-93)gcT>gcG	p.A31A	PIWIL2_ENST00000356766.6_Silent_p.A31A|PIWIL2_ENST00000521356.1_Silent_p.A31A	NM_001135721.1	NP_001129193.1	Q8TC59	PIWL2_HUMAN	piwi-like RNA-mediated gene silencing 2	31					DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|germ-line stem cell maintenance (GO:0030718)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|piRNA metabolic process (GO:0034587)|positive regulation of meiosis I (GO:0060903)|positive regulation of translation (GO:0045727)|RNA 5'-end processing (GO:0000966)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|P granule (GO:0043186)|pi-body (GO:0071546)|polysome (GO:0005844)	mRNA binding (GO:0003729)|piRNA binding (GO:0034584)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(14)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	46				Colorectal(74;0.018)|COAD - Colon adenocarcinoma(73;0.0707)		GGCCACAAGCTTCTAAACCTT	0.602																																					p.A31A		Atlas-SNP	.											.	PIWIL2	100	.	0			c.T93G						.						111	102	105					8																	22136992		2203	4300	6503	SO:0001819	synonymous_variant	55124	exon2			ACAAGCTTCTAAA	AK001213	CCDS6029.1	8p24	2013-02-15	2013-02-15		ENSG00000197181	ENSG00000197181		"Argonaute/PIWI family"	17644	protein-coding gene	gene with protein product	"Hiwi-like", "cancer/testis antigen 80"	610312	"piwi-like 2 (Drosophila)"			11279525, 12906857	Standard	NM_018068		Approved	HILI, FLJ10351, Mili, CT80	uc003xbn.2	Q8TC59	OTTHUMG00000097767	ENST00000454009.2:c.93T>G	chr8.hg19:g.22136992T>G		113.0	0.0		117.0	52.0	NM_001135721	A8K4S3|A8K8S5|B0AZN9|B0AZP2|B4DR22|E7ECA4|Q96SW6|Q9NW28	Silent	SNP	ENST00000454009.2	hg19	CCDS6029.1																																																																																			.	.		0.602	PIWIL2-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000375438.1			G	22136992	T	G	22136992	2	3	269	1	0	0	0	0	0	0	0	1	11967	1596	56	5		5	PIWIL2	8	22136992	Silent	SNP	T	TCGA-FV-A496-01A-11D-A25V-10		22136992	124227030	52	39213										
TRPA1	8989	hgsc.bcm.edu	37	chr8	72967815	72967815	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	tgtcttgtaggagcctctgaCaggtattgatacgcccataa	10	9	2	2			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr8:72967815C>A	ENST00000262209.4	-	12	1592	c.1385G>T	c.(1384-1386)tGt>tTt	p.C462F	RP11-383H13.1_ENST00000457356.4_3'UTR	NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	462					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	GAGCCTCTGACAGGTATTGAT	0.398																																					p.C462F		Atlas-SNP	.											.	TRPA1	256	.	0			c.G1385T						.						52	54	53					8																	72967815		2203	4296	6499	SO:0001583	missense	8989	exon12			CTCTGACAGGTAT	Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	497	protein-coding gene	gene with protein product		604775	"ankyrin-like with transmembrane domains 1"	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.1385G>T	chr8.hg19:g.72967815C>A	ENSP00000262209:p.Cys462Phe	320.0	0.0		345.0	74.0	NM_007332	A6NIN6	Missense_Mutation	SNP	ENST00000262209.4	hg19	CCDS34908.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.141239	0.77775	.	.	ENSG00000104321	ENST00000523582;ENST00000262209	T;T	0.63744	-0.06;-0.06	5.27	5.27	0.74061	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.80076	0.4557	M	0.76574	2.34	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.82206	-0.0572	10	0.72032	D	0.01	-16.8115	18.8668	0.92294	0.0:1.0:0.0:0.0	.	462	O75762	TRPA1_HUMAN	F	314;462	ENSP00000428151:C314F;ENSP00000262209:C462F	ENSP00000262209:C462F	C	-	2	0	TRPA1	73130369	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.187000	0.77730	2.452000	0.82932	0.557000	0.71058	TGT	.	.		0.398	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332		A	72967815	C	A	72967815	3	1	269	1	0	0	0	0	1	0	0	0	16592	478	17	3	2038	3	TRPA1	8	72967815	Missense_Mutation	SNP	C	TCGA-FV-A496-01A-11D-A25V-10	50830823	72967815	73396207	53	39214										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113519031	113519031	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	gtgaaagaataaagcctgaaGatcctgttaaattgcctcca	8	8	0	4			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr8:113519031G>T	ENST00000297405.5	-	29	5028	c.4784C>A	c.(4783-4785)tCt>tAt	p.S1595Y	CSMD3_ENST00000455883.2_Missense_Mutation_p.S1491Y|CSMD3_ENST00000352409.3_Missense_Mutation_p.S1595Y|CSMD3_ENST00000343508.3_Missense_Mutation_p.S1555Y	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1595	CUB 9. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						AAAGCCTGAAGATCCTGTTAA	0.343										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.S1595Y		Atlas-SNP	.											.	CSMD3	2325	.	0			c.C4784A						.						102	96	98					8																	113519031		2203	4300	6503	SO:0001583	missense	114788	exon29			CCTGAAGATCCTG	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.4784C>A	chr8.hg19:g.113519031G>T	ENSP00000297405:p.Ser1595Tyr	80.0	0.0		85.0	31.0	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.954010	0.73902	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.19938	2.11;2.11;2.11;2.11;2.11	4.99	4.99	0.66335	CUB (5);	0.000000	0.64402	D	0.000001	T	0.42154	0.1190	L	0.52266	1.64	0.42082	D	0.991254	D;D;D	0.69078	0.997;0.997;0.985	D;D;P	0.71656	0.926;0.974;0.905	T	0.25882	-1.0119	10	0.62326	D	0.03	.	18.4644	0.90750	0.0:0.0:1.0:0.0	.	1491;1595;1555	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	Y	1555;1595;935;1491;1595	ENSP00000345799:S1555Y;ENSP00000297405:S1595Y;ENSP00000341558:S935Y;ENSP00000412263:S1491Y;ENSP00000343124:S1595Y	ENSP00000297405:S1595Y	S	-	2	0	CSMD3	113588207	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.657000	0.98554	2.587000	0.87381	0.557000	0.71058	TCT	.	.		0.343	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	113519031	G	T	113519031	3	4	269	1	0	0	0	0	1	0	0	0	3948	942	33	3	6511	3	CSMD3	8	113519031	Missense_Mutation	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	40551216	113519031	32844991	54	39215										
ASAP1	50807	hgsc.bcm.edu	37	chr8	131104271	131104271	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	tgaggtagtgggctgggaggGtcggatagggttctcttgtg	20	4	1	1			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr8:131104271G>T	ENST00000518721.1	-	25	2747	c.2520C>A	c.(2518-2520)gaC>gaA	p.D840E	ASAP1_ENST00000357668.1_Missense_Mutation_p.D840E	NM_001247996.1|NM_018482.3	NP_001234925.1|NP_060952.2	Q9ULH1	ASAP1_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 1	840	Pro-rich.				cilium morphogenesis (GO:0060271)|regulation of ARF GTPase activity (GO:0032312)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|zinc ion binding (GO:0008270)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(22)|ovary(6)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	68						GGCTGGGAGGGTCGGATAGGG	0.597																																					p.D840E		Atlas-SNP	.											.	ASAP1	133	.	0			c.C2520A						.						109	116	114					8																	131104271		2203	4300	6503	SO:0001583	missense	50807	exon25			GGGAGGGTCGGAT	AB033075	CCDS6362.1, CCDS75788.1	8q24.1-q24.2	2013-01-11	2008-09-22	2008-09-22	ENSG00000153317	ENSG00000153317		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	2720	protein-coding gene	gene with protein product	"centaurin, beta 4"	605953	"development and differentiation enhancing factor 1"	DDEF1		9819391	Standard	NM_018482		Approved	PAP, KIAA1249, ZG14P, CENTB4	uc003yta.2	Q9ULH1	OTTHUMG00000164772	ENST00000518721.1:c.2520C>A	chr8.hg19:g.131104271G>T	ENSP00000429900:p.Asp840Glu	77.0	0.0		86.0	40.0	NM_018482	B2RNV3	Missense_Mutation	SNP	ENST00000518721.1	hg19	CCDS6362.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.11|15.11	2.735669|2.735669	0.49045|0.49045	.|.	.|.	ENSG00000153317|ENSG00000153317	ENST00000343135;ENST00000357668;ENST00000518721|ENST00000524124	T;T|.	0.05786|.	3.39;3.39|.	5.3|5.3	3.48|3.48	0.39840|0.39840	.|.	0.612156|.	0.16915|.	N|.	0.194339|.	T|T	0.61261|0.61261	0.2333|0.2333	L|L	0.54323|0.54323	1.7|1.7	0.58432|0.58432	D|D	0.999991|0.999991	D;D;D|.	0.61697|.	0.984;0.984;0.99|.	D;D;D|.	0.75484|.	0.967;0.967;0.986|.	T|T	0.59440|0.59440	-0.7454|-0.7454	10|5	0.07813|.	T|.	0.8|.	.|.	12.0001|12.0001	0.53226|0.53226	0.1497:0.0:0.8503:0.0|0.1497:0.0:0.8503:0.0	.|.	840;840;843|.	B2RNV3;Q9ULH1;Q9ULH1-2|.	.;ASAP1_HUMAN;.|.	E|T	843;840;840|661	ENSP00000350297:D840E;ENSP00000429900:D840E|.	ENSP00000344591:D843E|.	D|P	-|-	3|1	2|0	ASAP1|ASAP1	131173453|131173453	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.971000|0.971000	0.66376|0.66376	4.780000|4.780000	0.62382|0.62382	1.373000|1.373000	0.46208|0.46208	-0.463000|-0.463000	0.05309|0.05309	GAC|CCC	.	.		0.597	ASAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380170.1	NM_018482		T	131104271	G	T	131104271	3	4	269	1	0	0	0	0	1	0	0	0	1010	1252	44	3	893	3	ASAP1	8	131104271	Missense_Mutation	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	17585240	131104271	15259751	55	39216										
SLC1A1	6505	hgsc.bcm.edu	37	chr9	4583116	4583116	+	Frame_Shift_Del	DEL	T	T	-													0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	accatggtgattgtgctgagTgccgtgggcctgcccgccga							TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr9:4583116delT	ENST00000262352.3	+	11	1508	c.1272delT	c.(1270-1272)agtfs	p.S424fs		NM_004170.5	NP_004161.4	P43005	EAA3_HUMAN	solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1	424					D-aspartate import (GO:0070779)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glutamate binding (GO:0016595)|glutamate:sodium symporter activity (GO:0015501)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|pancreas(1)|skin(1)	15		Acute lymphoblastic leukemia(2;0.0359)|Breast(48;0.0457)		GBM - Glioblastoma multiforme(50;0.0124)|Lung(218;0.183)	L-Aspartic Acid(DB00128)|Pregabalin(DB00230)	TTGTGCTGAGTGCCGTGGGCC	0.597																																					p.S424fs		Atlas-INDEL	.											.	SLC1A1	43	.	0			c.1271delG						.						137	115	122					9																	4583116		2203	4300	6503	SO:0001589	frameshift_variant	6505	exon11			.		CCDS6452.1	9p24	2013-05-22			ENSG00000106688	ENSG00000106688		"Solute carriers"	10939	protein-coding gene	gene with protein product		133550				8020993	Standard	NM_004170		Approved	EAAC1, EAAT3	uc003zij.2	P43005	OTTHUMG00000019468	ENST00000262352.3:c.1272delT	chr9.hg19:g.4583116delT	ENSP00000262352:p.Ser424fs	195.0	0.0		168.0	13.0	NM_004170	O75587|Q5VZ24|Q8N199|Q9UEW2	Frame_Shift_Del	DEL	ENST00000262352.3	hg19	CCDS6452.1																																																																																			.	.		0.597	SLC1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051571.1			-	4583116	T	-	4583116	7	5	269	1	0	1	0	1	0	0	0	0	14446	1693	59	0	1314	0	SLC1A1	9	4583116	Frame_Shift_Del	DEL	T	TCGA-FV-A496-01A-11D-A25V-10		4583116	136630315	56	39217	191	2								
SLC1A1	6505	hgsc.bcm.edu	37	chr9	4583118	4583133	+	Frame_Shift_Del	DEL	CCGTGGGCCTGCCCGC	CCGTGGGCCTGCCCGC	-													0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	catggtgattgtgctgagtgCcgtgggcctgcccgccgagg					rs139707526|rs199857691		TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	CCGTGGGCCTGCCCGC	CCGTGGGCCTGCCCGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr9:4583118_4583133delCCGTGGGCCTGCCCGC	ENST00000262352.3	+	11	1510_1525	c.1274_1289delCCGTGGGCCTGCCCGC	c.(1273-1290)gccgtgggcctgcccgccfs	p.AVGLPA425fs		NM_004170.5	NP_004161.4	P43005	EAA3_HUMAN	solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1	425					D-aspartate import (GO:0070779)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glutamate binding (GO:0016595)|glutamate:sodium symporter activity (GO:0015501)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)	p.V426V(1)|p.A430T(1)		endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|pancreas(1)|skin(1)	15		Acute lymphoblastic leukemia(2;0.0359)|Breast(48;0.0457)		GBM - Glioblastoma multiforme(50;0.0124)|Lung(218;0.183)	L-Aspartic Acid(DB00128)|Pregabalin(DB00230)	GTGCTGAGTGCCGTGGGCCTGCCCGCCGAGGATGTC	0.606																																					p.425_430del		Atlas-INDEL	.											.	SLC1A1	43	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	c.1273_1288del						.																																			SO:0001589	frameshift_variant	6505	exon11			.		CCDS6452.1	9p24	2013-05-22			ENSG00000106688	ENSG00000106688		"Solute carriers"	10939	protein-coding gene	gene with protein product		133550				8020993	Standard	NM_004170		Approved	EAAC1, EAAT3	uc003zij.2	P43005	OTTHUMG00000019468	ENST00000262352.3:c.1274_1289delCCGTGGGCCTGCCCGC	chr9.hg19:g.4583118_4583133delCCGTGGGCCTGCCCGC	ENSP00000262352:p.Ala425fs	196.0	0.0		165.0	13.0	NM_004170	O75587|Q5VZ24|Q8N199|Q9UEW2	Frame_Shift_Del	DEL	ENST00000262352.3	hg19	CCDS6452.1																																																																																			.	.		0.606	SLC1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051571.1			-	4583133	CCGTGGGCCTGCCCGC	-	4583118	7	5	269	1	0	1	0	1	0	0	0	0	14446	739	26	0	1316	0	SLC1A1	9	4583118	Frame_Shift_Del	DEL	CCGTGGGCCTGCCCGC	TCGA-FV-A496-01A-11D-A25V-10	2	4583118	136630313	57	39218	191	2								
C9orf23	138716	hgsc.bcm.edu	37	chr9	34610870	34610870	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	ggagctgggcatggaacccaGgccagggggtgctcctgggg	20	10	0	0			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr9:34610870G>C	ENST00000297613.4	-	2	704	c.424C>G	c.(424-426)Ctg>Gtg	p.L142V	RPP25L_ENST00000378959.4_Missense_Mutation_p.L142V|DCTN3_ENST00000479399.1_5'Flank	NM_148179.2	NP_680545.1	Q8N5L8	RP25L_HUMAN	ribonuclease P/MRP 25kDa subunit-like	142						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)										ATGGAACCCAGGCCAGGGGGT	0.662																																					p.L142V		Atlas-SNP	.											.	.	.	.	0			c.C424G						.						41	47	45					9																	34610870		2203	4299	6502	SO:0001583	missense	138716	exon2			AACCCAGGCCAGG	BC032136	CCDS6559.1	9p11.2	2012-03-06	2012-03-06	2012-03-06	ENSG00000164967	ENSG00000164967			19909	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 23"	C9orf23		16998185	Standard	NM_148178		Approved	bA296L22.5, MGC29635	uc003zuv.3	Q8N5L8	OTTHUMG00000000443	ENST00000297613.4:c.424C>G	chr9.hg19:g.34610870G>C	ENSP00000297613:p.Leu142Val	49.0	0.0		30.0	12.0	NM_148179	D3DRM5	Missense_Mutation	SNP	ENST00000297613.4	hg19	CCDS6559.1	.	.	.	.	.	.	.	.	.	.	G	15.27	2.783663	0.49891	.	.	ENSG00000164967	ENST00000378959;ENST00000297613	.	.	.	4.72	1.82	0.25136	.	0.238192	0.34750	N	0.003719	T	0.28200	0.0696	N	0.12746	0.255	0.32825	D	0.503318	P	0.46578	0.88	P	0.50270	0.636	T	0.28776	-1.0033	9	0.14656	T	0.56	-34.9387	8.3213	0.32130	0.2625:0.0:0.7375:0.0	.	142	Q8N5L8	CI023_HUMAN	V	142	.	ENSP00000297613:L142V	L	-	1	2	C9orf23	34600870	0.560000	0.26570	1.000000	0.80357	0.978000	0.69477	0.259000	0.18405	0.604000	0.29930	0.643000	0.83706	CTG	.	.		0.662	RPP25L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001130.1	NM_148179		C	34610870	G	C	34610870	3	2	269	1	0	0	0	0	1	0	0	0	2476	991	35	4	71	4	C9orf23	9	34610870	Missense_Mutation	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	30027752	34610870	106602561	58	39219										
ASPN	54829	hgsc.bcm.edu	37	chr9	95228783	95228783	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	tgtgggacagatacagccttCgcaacttctttgtggttaga	11	8	1	2	rs371768627		TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr9:95228783C>T	ENST00000375544.3	-	4	701	c.458G>A	c.(457-459)cGa>cAa	p.R153Q	CENPP_ENST00000375587.3_Intron|ASPN_ENST00000375543.1_Missense_Mutation_p.R153Q|ASPN_ENST00000395538.3_Missense_Mutation_p.R153Q	NM_017680.4	NP_060150	Q9BXN1	ASPN_HUMAN	asporin	153					bone mineralization (GO:0030282)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|skin(1)	9						ATACAGCCTTCGCAACTTCTT	0.358																																					p.R153Q		Atlas-SNP	.											.	ASPN	52	.	0			c.G458A						.	C	,GLN/ARG,GLN/ARG	0,4406		0,0,2203	231	219	223		,458,458	5.6	1	9		223	1,8599	1.2+/-3.3	0,1,4299	no	intron,missense,missense	ASPN,CENPP	NM_001012267.1,NM_001193335.1,NM_017680.4	,43,43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,possibly-damaging,possibly-damaging	,153/244,153/381	95228783	1,13005	2203	4300	6503	SO:0001583	missense	54829	exon4			AGCCTTCGCAACT	AF316824		9q22.31	2008-05-14	2007-02-15		ENSG00000106819	ENSG00000106819		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	14872	protein-coding gene	gene with protein product	"asporin proteoglycan"	608135	"asporin (LRR class 1)"				Standard	NM_017680		Approved	FLJ20129, SLRR1C, PLAP1	uc004ase.2	Q9BXN1	OTTHUMG00000020227	ENST00000375544.3:c.458G>A	chr9.hg19:g.95228783C>T	ENSP00000364694:p.Arg153Gln	202.0	0.0		210.0	17.0	NM_001193335	Q5TBF3|Q96K79|Q96LD0|Q9NXP3	Missense_Mutation	SNP	ENST00000375544.3	hg19		.	.	.	.	.	.	.	.	.	.	C	12.04	1.817561	0.32145	0.0	1.16E-4	ENSG00000106819	ENST00000375544;ENST00000375543;ENST00000395538	T;T;T	0.58060	0.36;0.36;0.36	5.55	5.55	0.83447	.	0.180534	0.46442	D	0.000297	T	0.45696	0.1355	L	0.48174	1.505	0.32410	N	0.55075	B;B	0.22746	0.015;0.074	B;B	0.15484	0.013;0.012	T	0.49062	-0.8978	10	0.06757	T	0.87	.	19.8869	0.96915	0.0:1.0:0.0:0.0	.	153;153	Q5TBF2;Q9BXN1	.;ASPN_HUMAN	Q	153	ENSP00000364694:R153Q;ENSP00000364693:R153Q;ENSP00000378909:R153Q	ENSP00000364693:R153Q	R	-	2	0	ASPN	94268604	0.993000	0.37304	0.995000	0.50966	0.947000	0.59692	2.669000	0.46825	2.780000	0.95670	0.655000	0.94253	CGA	.	.		0.358	ASPN-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000053094.1	NM_017680		T	95228783	C	T	95228783	3	4	269	1	0	0	0	0	1	0	0	0	1057	884	31	1	704	1	ASPN	9	95228783	Missense_Mutation	SNP	C	TCGA-FV-A496-01A-11D-A25V-10	60617913	95228783	45984648	59	39220										
LRRTM3	347731	hgsc.bcm.edu	37	chr10	68687250	68687251	+	Missense_Mutation	DNP	GA	GA	TT													0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	ttggacctgggatataaccgGatccgaagtttagccaggaa							TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr10:68687250_68687251GA>TT	ENST00000361320.4	+	2	1154_1155	c.576_577GA>TT	c.(574-579)cgGAtc>cgTTtc	p.I193F	CTNNA3_ENST00000373744.4_Intron|CTNNA3_ENST00000433211.2_Intron	NM_178011.3	NP_821079.3	Q86VH5	LRRT3_HUMAN	leucine rich repeat transmembrane neuronal 3	193					positive regulation of beta-amyloid formation (GO:1902004)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	41						GATATAACCGGATCCGAAGTTT	0.47																																					p.R192R|p.I193F		Atlas-SNP	.											.	LRRTM3	241	.	0			c.G576T|c.A577T						.																																			SO:0001583	missense	347731	exon2			TAACCGGATCCGA|AACCGGATCCGAA	BX640611	CCDS7270.1	10q22.1	2007-01-22				ENSG00000198739			19410	protein-coding gene	gene with protein product		610869				12676565	Standard	XR_247527		Approved		uc001jmz.1	Q86VH5		Exception_encountered	chr10.hg19:g.68687250_68687251delinsTT	ENSP00000355187:p.Ile193Phe	78.0|81.0	0.0		54.0|53.0	4.0|5.0	NM_178011	A8K2A3|Q2NKX7|Q6N0A3	Silent|Missense_Mutation	SNP	ENST00000361320.4	hg19	CCDS7270.1																																																																																			.	.		0.47	LRRTM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048277.2	NM_178011		TT	68687251	GA	TT	68687250	3	4	269	1	0	0	0	0	1	0	0	0	9050	1161	41	3	582	3	LRRTM3	10	68687250	Missense_Mutation	DNP	GA	TCGA-FV-A496-01A-11D-A25V-10		68687250	66847497	60	39221										
NUP160	23279	hgsc.bcm.edu	37	chr11	47801951	47801951	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	agcttggagaagctgatcaaTagaggagtatggaagccaca	13	6	1	3	rs62000434		TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr11:47801951T>C	ENST00000378460.2	-	35	4211	c.4165A>G	c.(4165-4167)Att>Gtt	p.I1389V	NUP160_ENST00000530326.1_Intron	NM_015231.1	NP_056046.1	Q12769	NU160_HUMAN	nucleoporin 160kDa	1389					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)			NS(1)|biliary_tract(2)|breast(7)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(15)|ovary(6)|prostate(2)|skin(2)|urinary_tract(2)	53						AGCTGATCAATAGAGGAGTAT	0.463																																					p.I1389V		Atlas-SNP	.											.	NUP160	116	.	0			c.A4165G						.						101	95	97					11																	47801951		2201	4298	6499	SO:0001583	missense	23279	exon35			GATCAATAGAGGA	D83781	CCDS31484.1	11p11.12	2008-07-21	2002-08-29		ENSG00000030066	ENSG00000030066			18017	protein-coding gene	gene with protein product		607614	"nucleoporin 160kD"			11684705	Standard	NM_015231		Approved	KIAA0197, FLJ22583	uc001ngm.3	Q12769	OTTHUMG00000166534	ENST00000378460.2:c.4165A>G	chr11.hg19:g.47801951T>C	ENSP00000367721:p.Ile1389Val	97.0	0.0		114.0	30.0	NM_015231	B4DYE8|B4E2J9|Q08AD3|Q7Z5X6|Q96GB3|Q9H660	Missense_Mutation	SNP	ENST00000378460.2	hg19	CCDS31484.1	.	.	.	.	.	.	.	.	.	.	T	26.4	4.737736	0.89573	.	.	ENSG00000030066	ENST00000378460	T	0.48201	0.82	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.57961	0.2089	L	0.55481	1.735	0.80722	D	1	D	0.61697	0.99	P	0.54544	0.755	T	0.59123	-0.7513	10	0.51188	T	0.08	.	15.8267	0.78711	0.0:0.0:0.0:1.0	.	1389	Q12769	NU160_HUMAN	V	1389	ENSP00000367721:I1389V	ENSP00000367721:I1389V	I	-	1	0	NUP160	47758527	1.000000	0.71417	0.857000	0.33713	0.975000	0.68041	5.404000	0.66344	2.214000	0.71695	0.477000	0.44152	ATT	.	T|0.987;C|0.013		0.463	NUP160-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390239.2	NM_015231		C	47801951	T	C	47801951	3	2	269	1	0	0	0	0	1	0	0	0	10766	1406	49	2	153	2	NUP160	11	47801951	Missense_Mutation	SNP	T	TCGA-FV-A496-01A-11D-A25V-10		47801951	87204565	61	39222										
PTPRJ	5795	hgsc.bcm.edu	37	chr11	48185171	48185171	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	ccgattctggtgcattgcagGtacgcagatggcacgtcacg	13	11	2	1			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr11:48185171G>T	ENST00000418331.2	+	23	4071		c.e23+1			NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J						contact inhibition (GO:0060242)|heart development (GO:0007507)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of vascular permeability (GO:0043116)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of cell adhesion (GO:0045785)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion (GO:0030155)|vasculogenesis (GO:0001570)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|mitogen-activated protein kinase binding (GO:0051019)|phosphatase activity (GO:0016791)|platelet-derived growth factor receptor binding (GO:0005161)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|endometrium(7)|kidney(7)|large_intestine(5)|lung(15)|ovary(1)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						TGCATTGCAGGTACGCAGATG	0.463																																					.		Atlas-SNP	.											.	PTPRJ	225	.	0			c.3719+1G>T						.						93	64	73					11																	48185171		2201	4298	6499	SO:0001630	splice_region_variant	5795	exon23			TTGCAGGTACGCA	U10886	CCDS7945.1, CCDS44596.1	11p11.2	2013-02-11			ENSG00000149177	ENSG00000149177		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9673	protein-coding gene	gene with protein product		600925				7937872, 7994032	Standard	NM_001098503		Approved	DEP1, HPTPeta, CD148	uc001ngp.4	Q12913	OTTHUMG00000166573	ENST00000418331.2:c.3719+1G>T	chr11.hg19:g.48185171G>T		102.0	0.0		106.0	57.0	NM_002843	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Splice_Site	SNP	ENST00000418331.2	hg19	CCDS7945.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.221721	0.79464	.	.	ENSG00000149177	ENST00000418331	.	.	.	5.44	5.44	0.79542	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.7469	0.85475	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PTPRJ	48141747	1.000000	0.71417	1.000000	0.80357	0.643000	0.38383	9.823000	0.99369	2.545000	0.85829	0.650000	0.86243	.	.	.		0.463	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1		Intron	T	48185171	G	T	48185171	5	4	269	1	0	0	0	0	0	0	1	0	12819	1275	44	3	3819	3	PTPRJ	11	48185171	Splice_Site	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	383220	48185171	86821345	62	39223										
OR5T1	390155	hgsc.bcm.edu	37	chr11	56044023	56044051	+	Frame_Shift_Del	DEL	TTTGCGGAACAAAGATGTAAAGGAGGCAA	TTTGCGGAACAAAGATGTAAAGGAGGCAA	-													0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	ctgaatcccatcatctacagTttgcggaacaaagatgtaaa					rs148135770|rs374592813|rs549381739|rs143790336	byFrequency	TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	TTTGCGGAACAAAGATGTAAAGGAGGCAA	TTTGCGGAACAAAGATGTAAAGGAGGCAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr11:56044023_56044051delTTTGCGGAACAAAGATGTAAAGGAGGCAA	ENST00000313033.2	+	1	995_1023	c.909_937delTTTGCGGAACAAAGATGTAAAGGAGGCAA	c.(907-939)agtttgcggaacaaagatgtaaaggaggcaatcfs	p.LRNKDVKEAI304fs		NM_001004745.1	NP_001004745.1	Q8NG75	OR5T1_HUMAN	olfactory receptor, family 5, subfamily T, member 1	304						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R305W(1)|p.R305P(1)		NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(27)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	43	Esophageal squamous(21;0.00448)					TCATCTACAGTTTGCGGAACAAAGATGTAAAGGAGGCAATCAAAAGATT	0.358																																					p.303_312del		Pindel	.											.	OR5T1	95	.	2	Substitution - Missense(2)	lung(1)|kidney(1)	c.908_936del						.																																			SO:0001589	frameshift_variant	390155	exon1			.	AB065962	CCDS31525.1	11q11	2012-08-09		2004-03-10	ENSG00000181698	ENSG00000181698		"GPCR / Class A : Olfactory receptors"	14821	protein-coding gene	gene with protein product				OR5T1P			Standard	NM_001004745		Approved		uc001nio.1	Q8NG75	OTTHUMG00000166853	ENST00000313033.2:c.909_937delTTTGCGGAACAAAGATGTAAAGGAGGCAA	chr11.hg19:g.56044023_56044051delTTTGCGGAACAAAGATGTAAAGGAGGCAA	ENSP00000323612:p.Leu304fs	138.0	0.0		80.0	12.0	NM_001004745	B2RNM9	Frame_Shift_Del	DEL	ENST00000313033.2	hg19	CCDS31525.1																																																																																			.	.		0.358	OR5T1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391600.1	NM_001004745		-	56044051	TTTGCGGAACAAAGATGTAAAGGAGGCAA	-	56044023	7	5	269	1	0	1	0	1	0	0	0	0	11190	1722	60	0	911	0	OR5T1	11	56044023	Frame_Shift_Del	DEL	TTTGCGGAACAAAGATGTAAAGGAGGCAA	TCGA-FV-A496-01A-11D-A25V-10	7858852	56044023	78962493	63	39224										
CTNND1	1500	hgsc.bcm.edu	37	chr11	57577636	57577637	+	Missense_Mutation	DNP	GG	GG	TT													0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	ttgtattacagacaatctggGgatataaggaactgcggaag							TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr11:57577636_57577637GG>TT	ENST00000399050.4	+	16	3027_3028	c.2491_2492GG>TT	c.(2491-2493)GGa>TTa	p.G831L	CTNND1_ENST00000525902.1_Missense_Mutation_p.G508L|CTNND1_ENST00000361796.4_Missense_Mutation_p.G825L|CTNND1_ENST00000528621.1_Missense_Mutation_p.G771L|CTNND1_ENST00000526938.1_Missense_Mutation_p.G831L|CTNND1_ENST00000399039.4_Missense_Mutation_p.G831L|CTNND1_ENST00000533667.1_Missense_Mutation_p.G502L|CTNND1_ENST00000524630.1_Missense_Mutation_p.G825L|CTNND1_ENST00000426142.2_Missense_Mutation_p.G724L|CTNND1_ENST00000532787.1_Missense_Mutation_p.G724L|CTNND1_ENST00000529873.1_Missense_Mutation_p.G771L|CTNND1_ENST00000530748.1_Missense_Mutation_p.G777L|CTNND1_ENST00000361391.6_Missense_Mutation_p.G825L|CTNND1_ENST00000526772.1_Missense_Mutation_p.G502L|CTNND1_ENST00000428599.2_Missense_Mutation_p.G825L|CTNND1_ENST00000530094.1_Missense_Mutation_p.G724L|CTNND1_ENST00000532245.1_Missense_Mutation_p.G724L|CTNND1_ENST00000534579.1_Missense_Mutation_p.G771L|CTNND1_ENST00000528232.1_Missense_Mutation_p.G730L|CTNND1_ENST00000527467.1_Missense_Mutation_p.G508L|CTNND1_ENST00000532844.1_Missense_Mutation_p.G777L|CTNND1_ENST00000529526.1_Missense_Mutation_p.G771L|CTNND1_ENST00000526357.1_Missense_Mutation_p.G771L|CTNND1_ENST00000529986.1_Missense_Mutation_p.G724L|CTNND1_ENST00000531014.1_Missense_Mutation_p.G502L|CTNND1_ENST00000360682.6_Missense_Mutation_p.G831L|CTNND1_ENST00000415361.2_Missense_Mutation_p.G730L|CTNND1_ENST00000532463.1_Missense_Mutation_p.G724L|CTNND1_ENST00000361332.4_Missense_Mutation_p.G825L|CTNND1_ENST00000358694.6_Missense_Mutation_p.G825L|CTNND1_ENST00000529919.1_Missense_Mutation_p.G831L|CTNND1_ENST00000532649.1_Missense_Mutation_p.G771L	NM_001085458.1	NP_001078927.1	O60716	CTND1_HUMAN	catenin (cadherin-associated protein), delta 1	831					adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|regulation of transcription, DNA-templated (GO:0006355)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)|zonula adherens (GO:0005915)	cadherin binding (GO:0045296)|receptor binding (GO:0005102)			breast(5)|endometrium(8)|kidney(4)|large_intestine(7)|liver(2)|lung(16)|ovary(1)|upper_aerodigestive_tract(2)	45		all_epithelial(135;0.155)				GACAATCTGGGGATATAAGGAA	0.386																																					p.G831X|p.G831V		Atlas-SNP	.											CTNND1_ENST00000399050,NS,carcinoma,0,2|.	CTNND1	203	.	0			c.G2491T|c.G2492T						.																																			SO:0001583	missense	1500	exon16			ATCTGGGGATATA|TCTGGGGATATAA	AB002382	CCDS44604.1, CCDS44605.1, CCDS44606.1, CCDS44607.1, CCDS44608.1, CCDS44609.1, CCDS53632.1, CCDS53633.1, CCDS53634.1, CCDS55763.1, CCDS55764.1, CCDS55765.1, CCDS55766.1, CCDS55767.1, CCDS73290.1	11q12.1	2013-02-14				ENSG00000198561		"Armadillo repeat containing"	2515	protein-coding gene	gene with protein product		601045		CTNND		8808291	Standard	NM_001085460		Approved	KIAA0384, p120, p120cas, p120ctn	uc001nmc.4	O60716		Exception_encountered	chr11.hg19:g.57577636_57577637delinsTT	ENSP00000382004:p.Gly831Leu	37.0	0.0		48.0	12.0	NM_001085458	A8K939|O15088|O60713|O60714|O60715|O60935|Q6DHZ7|Q6RBX8|Q9UP71|Q9UP72|Q9UP73	Nonsense_Mutation|Missense_Mutation	SNP	ENST00000399050.4	hg19	CCDS44604.1																																																																																			.	.		0.386	CTNND1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393944.1	NM_001331		TT	57577637	GG	TT	57577636	3	4	269	1	0	0	0	0	1	0	0	0	4021	1233	43	3	2545	3	CTNND1	11	57577636	Missense_Mutation	DNP	GG	TCGA-FV-A496-01A-11D-A25V-10	1533613	57577636	77428880	64	39225										
INCENP	3619	hgsc.bcm.edu	37	chr11	61912532	61912532	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	gcaggcagaaggtggaggagGacaagcggcggcggctggag	22	7	0	1			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr11:61912532G>A	ENST00000394818.3	+	12	1886	c.1684G>A	c.(1684-1686)Gac>Aac	p.D562N	INCENP_ENST00000278849.4_Missense_Mutation_p.D558N	NM_001040694.1	NP_001035784.1	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	562					chromosome segregation (GO:0007059)|cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	central element (GO:0000801)|chromocenter (GO:0010369)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lateral element (GO:0000800)|microtubule (GO:0005874)|midbody (GO:0030496)|pericentric heterochromatin (GO:0005721)|protein complex (GO:0043234)|spindle (GO:0005819)				breast(1)|endometrium(1)|kidney(6)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						GGTGGAGGAGGACAAGCGGCG	0.672																																					p.D562N		Atlas-SNP	.											.	INCENP	122	.	0			c.G1684A						.						45	44	44					11																	61912532		2202	4299	6501	SO:0001583	missense	3619	exon12			GAGGAGGACAAGC	AF282265	CCDS31582.1, CCDS44624.1	11q12.3	2013-01-17	2002-08-29		ENSG00000149503	ENSG00000149503			6058	protein-coding gene	gene with protein product		604411	"inner centromere protein antigens (135kD, 155kD)"			1860899, 11453556	Standard	NM_001040694		Approved	FLJ31633	uc001nsw.1	Q9NQS7	OTTHUMG00000167470	ENST00000394818.3:c.1684G>A	chr11.hg19:g.61912532G>A	ENSP00000378295:p.Asp562Asn	102.0	0.0		91.0	49.0	NM_001040694	A8MQD2|Q5Y192	Missense_Mutation	SNP	ENST00000394818.3	hg19	CCDS44624.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.473169	0.84640	.	.	ENSG00000149503	ENST00000394818;ENST00000278849	T;T	0.43294	0.95;0.95	5.93	5.93	0.95920	.	0.204219	0.34555	N	0.003880	T	0.58538	0.2129	L	0.60455	1.87	0.39734	D	0.971641	D;D;D	0.65815	0.995;0.992;0.986	P;P;P	0.59357	0.722;0.856;0.722	T	0.57124	-0.7865	10	0.48119	T	0.1	.	17.8376	0.88704	0.0:0.0:1.0:0.0	.	558;558;562	B3KPD3;Q9NQS7-2;Q9NQS7	.;.;INCE_HUMAN	N	562;558	ENSP00000378295:D562N;ENSP00000278849:D558N	ENSP00000278849:D558N	D	+	1	0	INCENP	61669108	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.557000	0.67313	2.815000	0.96918	0.561000	0.74099	GAC	.	.		0.672	INCENP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394723.2	NM_020238		A	61912532	G	A	61912532	3	1	269	1	0	0	0	0	1	0	0	0	7742	1174	41	3	1726	3	INCENP	11	61912532	Missense_Mutation	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	4334896	61912532	73093984	65	39226										
LGALS12	85329	hgsc.bcm.edu	37	chr11	63277947	63277947	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	ctgaacagccatttgtggagGgcagcagagagtacccagct	13	10	0	2			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr11:63277947G>A	ENST00000394618.3	+	5	862	c.571G>A	c.(571-573)Ggc>Agc	p.G191S	LGALS12_ENST00000255684.5_Missense_Mutation_p.G191S|LGALS12_ENST00000340246.5_Missense_Mutation_p.G192S|LGALS12_ENST00000415491.2_Missense_Mutation_p.G130S|LGALS12_ENST00000425950.2_Missense_Mutation_p.G130S	NM_001142535.1|NM_033101.3	NP_001136007.1|NP_149092.2	Q96DT0	LEG12_HUMAN	lectin, galactoside-binding, soluble, 12	191					intrinsic apoptotic signaling pathway (GO:0097193)	nucleus (GO:0005634)	lactose binding (GO:0030395)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	16						ATTTGTGGAGGGCAGCAGAGA	0.557																																					p.G192S		Atlas-SNP	.											.	LGALS12	35	.	0			c.G574A						.						116	93	101					11																	63277947		2201	4298	6499	SO:0001583	missense	85329	exon5			GTGGAGGGCAGCA	AF222695	CCDS8045.1, CCDS44633.1, CCDS44634.1, CCDS44635.1, CCDS53648.1	11q13	2011-08-04	2008-07-25		ENSG00000133317	ENSG00000133317		"Lectins, galactoside-binding"	15788	protein-coding gene	gene with protein product	"galectin 12"	606096				11283015, 11435439	Standard	NM_033101		Approved	GRIP1	uc001nxc.2	Q96DT0	OTTHUMG00000167807	ENST00000394618.3:c.571G>A	chr11.hg19:g.63277947G>A	ENSP00000378116:p.Gly191Ser	164.0	0.0		237.0	46.0	NM_001142535	B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Missense_Mutation	SNP	ENST00000394618.3	hg19	CCDS8045.1	.	.	.	.	.	.	.	.	.	.	G	8.955	0.969137	0.18659	.	.	ENSG00000133317	ENST00000255684;ENST00000394618;ENST00000340246;ENST00000415491;ENST00000425950	T;T;T;T;T	0.09163	3.36;3.53;3.47;3.28;3.01	5.64	4.72	0.59763	.	0.096801	0.45867	D	0.000327	T	0.08133	0.0203	L	0.51422	1.61	0.36773	D	0.883912	P;P;B;P	0.43287	0.802;0.525;0.383;0.802	B;B;B;B	0.34489	0.184;0.164;0.095;0.184	T	0.18871	-1.0323	10	0.12430	T	0.62	-30.4601	9.5019	0.39022	0.0936:0.0:0.9064:0.0	.	151;192;191;191	Q9NZ03;G5E970;Q96DT0-3;Q96DT0	.;.;.;LEG12_HUMAN	S	191;191;192;130;130	ENSP00000255684:G191S;ENSP00000378116:G191S;ENSP00000339374:G192S;ENSP00000394659:G130S;ENSP00000399093:G130S	ENSP00000255684:G191S	G	+	1	0	LGALS12	63034523	1.000000	0.71417	0.767000	0.31495	0.519000	0.34347	2.694000	0.47035	2.654000	0.90174	0.609000	0.83330	GGC	.	.		0.557	LGALS12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396378.1	NM_033101		A	63277947	G	A	63277947	3	1	269	1	0	0	0	0	1	0	0	0	8748	1232	43	3	592	3	LGALS12	11	63277947	Missense_Mutation	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	1365415	63277947	71728569	66	39227										
SF1	7536	hgsc.bcm.edu	37	chr11	64537468	64537468	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	agcagccccacaaagttgatTtctgggtactcatcttgtgg	10	10	3	1			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr11:64537468T>G	ENST00000377390.3	-	5	784	c.447A>C	c.(445-447)gaA>gaC	p.E149D	SF1_ENST00000433274.2_Missense_Mutation_p.E123D|SF1_ENST00000422298.2_Missense_Mutation_p.E34D|SF1_ENST00000227503.9_Missense_Mutation_p.E149D|SF1_ENST00000489544.1_5'Flank|SF1_ENST00000377394.3_Missense_Mutation_p.E149D|SF1_ENST00000334944.5_Missense_Mutation_p.E149D|SF1_ENST00000377387.1_Missense_Mutation_p.E274D	NM_004630.3	NP_004621.2	Q15637	SF01_HUMAN	splicing factor 1	149	KH. {ECO:0000255|PROSITE- ProRule:PRU00117}.				Leydig cell differentiation (GO:0033327)|male sex determination (GO:0030238)|mRNA 3'-splice site recognition (GO:0000389)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of smooth muscle cell proliferation (GO:0048662)|regulation of steroid biosynthetic process (GO:0050810)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal complex assembly (GO:0000245)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|ribosome (GO:0005840)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(12)|ovary(2)|skin(2)	31						CAAAGTTGATTTCTGGGTACT	0.468																																					p.E274D		Atlas-SNP	.											.	SF1	124	.	0			c.A822C						.						92	80	84					11																	64537468		2201	4297	6498	SO:0001583	missense	7536	exon5			GTTGATTTCTGGG	D26120	CCDS8080.1, CCDS8081.1, CCDS31599.1, CCDS44642.1, CCDS44642.2, CCDS53660.1, CCDS53661.1	11q13	2014-09-17	2001-12-19	2002-01-11	ENSG00000168066	ENSG00000168066		"Zinc fingers, CCHC domain containing"	12950	protein-coding gene	gene with protein product		601516	"zinc finger protein 162"	ZNF162		7912130, 9573336	Standard	NM_201997		Approved	ZFM1, ZCCHC25	uc001oaz.2	Q15637	OTTHUMG00000066833	ENST00000377390.3:c.447A>C	chr11.hg19:g.64537468T>G	ENSP00000366607:p.Glu149Asp	84.0	0.0		109.0	50.0	NM_001178030	B7Z1Q1|C9JJE2|Q14818|Q14819|Q15913|Q8IY00|Q92744|Q92745|Q969H7|Q9BW01|Q9UEI0	Missense_Mutation	SNP	ENST00000377390.3	hg19	CCDS31599.1	.	.	.	.	.	.	.	.	.	.	T	10.78	1.445870	0.25987	.	.	ENSG00000168066	ENST00000377387;ENST00000377390;ENST00000227503;ENST00000377394;ENST00000334944;ENST00000422298;ENST00000433274	T;T;T;T;T;T;T	0.39406	1.08;1.08;1.08;1.08;1.08;1.08;1.08	6.04	-1.36	0.09085	K Homology (1);	0.000000	0.85682	D	0.000000	T	0.18215	0.0437	N	0.05230	-0.09	0.45183	D	0.998196	B;B;B;B;B;B	0.27229	0.013;0.135;0.01;0.082;0.067;0.172	B;B;B;B;B;B	0.24394	0.053;0.024;0.017;0.053;0.031;0.046	T	0.05852	-1.0860	10	0.23891	T	0.37	.	11.574	0.50850	0.0:0.5902:0.0:0.4098	.	34;149;149;149;149;274	B4DX42;Q15637-6;Q15637-4;Q15637;Q15637-2;Q15637-5	.;.;.;SF01_HUMAN;.;.	D	274;149;149;149;149;34;123	ENSP00000366604:E274D;ENSP00000366607:E149D;ENSP00000227503:E149D;ENSP00000366611:E149D;ENSP00000334414:E149D;ENSP00000413084:E34D;ENSP00000396793:E123D	ENSP00000227503:E149D	E	-	3	2	SF1	64294044	0.745000	0.28261	0.998000	0.56505	0.145000	0.21501	-0.185000	0.09684	-0.038000	0.13624	0.460000	0.39030	GAA	.	.		0.468	SF1-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000143242.1	NM_004630		G	64537468	T	G	64537468	3	3	269	1	0	0	0	0	1	0	0	0	14160	1838	64	5	1646	5	SF1	11	64537468	Missense_Mutation	SNP	T	TCGA-FV-A496-01A-11D-A25V-10	1259521	64537468	70469048	67	39228										
ODZ4	26011	hgsc.bcm.edu	37	chr11	78380618	78380618	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	ccgctgcctcaggaagccatCctcatccatcttgtattgca	7	15	3	0			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr11:78380618C>T	ENST00000278550.7	-	32	7234	c.6772G>A	c.(6772-6774)Gat>Aat	p.D2258N		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	2258					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										AGGAAGCCATCCTCATCCATC	0.577																																					p.D2258N		Atlas-SNP	.											.	.	.	.	0			c.G6772A						.						167	172	170					11																	78380618		2173	4266	6439	SO:0001583	missense	26011	exon32			AGCCATCCTCATC	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"odz, odd Oz/ten-m homolog 4 (Drosophila)"	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.6772G>A	chr11.hg19:g.78380618C>T	ENSP00000278550:p.Asp2258Asn	177.0	0.0		244.0	15.0	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Missense_Mutation	SNP	ENST00000278550.7	hg19	CCDS44688.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.567626	0.86439	.	.	ENSG00000149256	ENST00000278550;ENST00000530738	D;T	0.89681	-2.55;0.99	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	D	0.93703	0.7988	M	0.67953	2.075	0.80722	D	1	D	0.69078	0.997	D	0.77004	0.989	D	0.92953	0.6382	9	.	.	.	.	18.8078	0.92045	0.0:1.0:0.0:0.0	.	2258	Q6N022	TEN4_HUMAN	N	2258;722	ENSP00000278550:D2258N;ENSP00000431711:D722N	.	D	-	1	0	ODZ4	78058266	1.000000	0.71417	0.999000	0.59377	0.933000	0.57130	7.651000	0.83577	2.677000	0.91161	0.655000	0.94253	GAT	.	.		0.577	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			T	78380618	C	T	78380618	3	4	269	1	0	0	0	0	1	0	0	0	10846	855	30	3	1549	3	ODZ4	11	78380618	Missense_Mutation	SNP	C	TCGA-FV-A496-01A-11D-A25V-10	13843150	78380618	56625898	68	39229										
JAM3	83700	hgsc.bcm.edu	37	chr11	134014143	134014143	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	gtcttttctgtaggagacttGgcgggtcgtgcagaaatact	13	7	2	2			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr11:134014143G>C	ENST00000299106.4	+	4	423	c.264G>C	c.(262-264)ttG>ttC	p.L88F	JAM3_ENST00000529443.2_Missense_Mutation_p.L133F|JAM3_ENST00000524969.1_3'UTR|JAM3_ENST00000441717.3_Intron			Q9BX67	JAM3_HUMAN	junctional adhesion molecule 3	88	Ig-like V-type.				adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|establishment of cell polarity (GO:0030010)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|myelination (GO:0042552)|myeloid progenitor cell differentiation (GO:0002318)|neutrophil homeostasis (GO:0001780)|regulation of actin cytoskeleton organization by cell-cell adhesion (GO:0090138)|regulation of neutrophil chemotaxis (GO:0090022)|spermatid development (GO:0007286)|transmission of nerve impulse (GO:0019226)	cell-cell contact zone (GO:0044291)|desmosome (GO:0030057)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|paranodal junction (GO:0033010)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	integrin binding (GO:0005178)			breast(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)	10	all_hematologic(175;0.127)	all_cancers(12;1.06e-21)|all_epithelial(12;3.37e-16)|all_lung(97;7.03e-06)|Lung NSC(97;1.67e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0506)|Esophageal squamous(93;0.0566)		Epithelial(10;1.55e-09)|BRCA - Breast invasive adenocarcinoma(10;1.35e-08)|all cancers(11;2.81e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00402)|Lung(977;0.245)		TAGGAGACTTGGCGGGTCGTG	0.483																																					p.L88F		Atlas-SNP	.											.	JAM3	41	.	0			c.G264C						.						95	89	91					11																	134014143		2201	4297	6498	SO:0001583	missense	83700	exon4			AGACTTGGCGGGT	AF356518	CCDS8494.1, CCDS55799.1, CCDS8494.2	11q25	2013-01-29			ENSG00000166086	ENSG00000166086		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15532	protein-coding gene	gene with protein product		606871					Standard	NM_032801		Approved	JAM-C, JAMC	uc001qhb.3	Q9BX67	OTTHUMG00000167130	ENST00000299106.4:c.264G>C	chr11.hg19:g.134014143G>C	ENSP00000299106:p.Leu88Phe	64.0	0.0		94.0	21.0	NM_032801	B3KWG9|Q8WWL8|Q96FL1	Missense_Mutation	SNP	ENST00000299106.4	hg19	CCDS8494.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	3.957|3.957	-0.011062|-0.011062	0.07727|0.07727	.|.	.|.	ENSG00000166086|ENSG00000166086	ENST00000534549|ENST00000299106	.|T	.|0.58652	.|0.32	5.47|5.47	2.58|2.58	0.30949|0.30949	.|Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.|0.161867	.|0.42682	.|D	.|0.000679	T|T	0.39572|0.39572	0.1083|0.1083	L|L	0.37507|0.37507	1.11|1.11	0.40407|0.40407	D|D	0.979719|0.979719	.|B	.|0.17465	.|0.022	.|B	.|0.25987	.|0.065	T|T	0.09618|0.09618	-1.0666|-1.0666	5|10	.|0.11794	.|T	.|0.64	.|.	3.7926|3.7926	0.08727|0.08727	0.1372:0.1226:0.5986:0.1417|0.1372:0.1226:0.5986:0.1417	.|.	.|88	.|Q9BX67	.|JAM3_HUMAN	R|F	33|133	.|ENSP00000299106:L133F	.|ENSP00000299106:L133F	G|L	+|+	1|3	0|2	JAM3|JAM3	133519353|133519353	1.000000|1.000000	0.71417|0.71417	0.863000|0.863000	0.33907|0.33907	0.626000|0.626000	0.37791|0.37791	1.020000|1.020000	0.30027|0.30027	0.288000|0.288000	0.22398|0.22398	0.561000|0.561000	0.74099|0.74099	GGC|TTG	.	.		0.483	JAM3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000393303.4	NM_032801		C	134014143	G	C	134014143	3	2	269	1	0	0	0	0	1	0	0	0	7953	1339	47	4	413	4	JAM3	11	134014143	Missense_Mutation	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	55633525	134014143	992373	69	39230										
INHBE	83729	hgsc.bcm.edu	37	chr12	57849890	57849890	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	cgggcagactccacttcagcCtacagctccctgctcacttt	7	17	2	1			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr12:57849890C>T	ENST00000266646.2	+	2	528	c.312C>T	c.(310-312)gcC>gcT	p.A104A	INHBE_ENST00000551553.1_3'UTR	NM_031479.3	NP_113667.1	P58166	INHBE_HUMAN	inhibin, beta E	104					growth (GO:0040007)	extracellular region (GO:0005576)				breast(2)|central_nervous_system(1)|large_intestine(2)|lung(7)|prostate(1)|skin(2)	15						CCACTTCAGCCTACAGCTCCC	0.582											OREG0021944	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A104A	GBM(191;1808 2166 15720 36624 50371)	Atlas-SNP	.											.	INHBE	38	.	0			c.C312T						.						207	209	208					12																	57849890		2203	4300	6503	SO:0001819	synonymous_variant	83729	exon2			TTCAGCCTACAGC		CCDS8939.1	12q13.2	2008-02-05				ENSG00000139269			24029	protein-coding gene	gene with protein product		612031				12242034	Standard	NM_031479		Approved	activin, MGC4638	uc001snw.3	P58166		ENST00000266646.2:c.312C>T	chr12.hg19:g.57849890C>T		69.0	0.0	1026	98.0	6.0	NM_031479		Silent	SNP	ENST00000266646.2	hg19	CCDS8939.1																																																																																			.	.		0.582	INHBE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406773.1	NM_031479		T	57849890	C	T	57849890	2	4	269	1	0	0	0	0	0	0	0	1	7753	668	24	3		3	INHBE	12	57849890	Silent	SNP	C	TCGA-FV-A496-01A-11D-A25V-10		57849890	76002005	70	39231										
PIP4K2C	79837	hgsc.bcm.edu	37	chr12	57985226	57985226	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	acccgctggtgggtgtgttcCtgtggggcgtagcccactcg	16	12	0	0			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr12:57985226C>T	ENST00000354947.5	+	1	170	c.154C>T	c.(154-156)Ctg>Ttg	p.L52L	PIP4K2C_ENST00000422156.3_Silent_p.L52L|PIP4K2C_ENST00000540759.2_Silent_p.L52L|PIP4K2C_ENST00000550465.1_Silent_p.L52L			Q8TBX8	PI42C_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, gamma	52	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	1-phosphatidylinositol-5-phosphate 4-kinase activity (GO:0016309)|ATP binding (GO:0005524)|identical protein binding (GO:0042802)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(13)|pancreas(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	33	Melanoma(17;0.122)					GGGTGTGTTCCTGTGGGGCGT	0.652																																					p.L52L		Atlas-SNP	.											.	PIP4K2C	50	.	0			c.C154T						.						88	94	92					12																	57985226		2203	4300	6503	SO:0001819	synonymous_variant	79837	exon1			GTGTTCCTGTGGG	AK125526	CCDS8946.1, CCDS53808.1, CCDS55839.1	12q13.3	2014-09-04	2007-08-14	2007-08-14	ENSG00000166908	ENSG00000166908			23786	protein-coding gene	gene with protein product			"phosphatidylinositol-4-phosphate 5-kinase, type II, gamma"	PIP5K2C		9367159	Standard	NM_024779		Approved	FLJ22055	uc001sot.3	Q8TBX8	OTTHUMG00000170144	ENST00000354947.5:c.154C>T	chr12.hg19:g.57985226C>T		222.0	0.0		201.0	90.0	NM_001146258	B2RDL3|B4DM11|B4DY44|Q9H6N2	Silent	SNP	ENST00000354947.5	hg19	CCDS8946.1																																																																																			.	.		0.652	PIP4K2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407644.1	NM_024779		T	57985226	C	T	57985226	2	4	269	1	0	0	0	0	0	0	0	1	11947	680	24	3		3	PIP4K2C	12	57985226	Silent	SNP	C	TCGA-FV-A496-01A-11D-A25V-10	135336	57985226	75866669	71	39232										
GCN1L1	10985	hgsc.bcm.edu	37	chr12	120602471	120602471	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	gaactttgttgccagtgagtCtatgcgggtggtcaaggaaa	14	6	2	1			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr12:120602471C>A	ENST00000300648.6	-	17	1679	c.1667G>T	c.(1666-1668)aGa>aTa	p.R556I		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	556					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GCCAGTGAGTCTATGCGGGTG	0.473																																					p.R556I		Atlas-SNP	.											.	GCN1L1	207	.	0			c.G1667T						.						140	141	141					12																	120602471		1986	4147	6133	SO:0001583	missense	10985	exon17			GTGAGTCTATGCG	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.1667G>T	chr12.hg19:g.120602471C>A	ENSP00000300648:p.Arg556Ile	193.0	0.0		175.0	13.0	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Missense_Mutation	SNP	ENST00000300648.6	hg19	CCDS41847.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.998322	0.93227	.	.	ENSG00000089154	ENST00000300648	T	0.04603	3.59	5.83	5.83	0.93111	Domain of unknown function DUF3554 (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.19644	0.0472	L	0.59436	1.845	0.80722	D	1	D	0.71674	0.998	D	0.68353	0.957	T	0.00013	-1.2414	10	0.51188	T	0.08	.	20.1184	0.97949	0.0:1.0:0.0:0.0	.	556	Q92616	GCN1L_HUMAN	I	556	ENSP00000300648:R556I	ENSP00000300648:R556I	R	-	2	0	GCN1L1	119086854	1.000000	0.71417	0.968000	0.41197	0.968000	0.65278	6.304000	0.72800	2.769000	0.95229	0.655000	0.94253	AGA	.	.		0.473	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1			A	120602471	C	A	120602471	3	1	269	1	0	0	0	0	1	0	0	0	6307	913	32	3	6516	3	GCN1L1	12	120602471	Missense_Mutation	SNP	C	TCGA-FV-A496-01A-11D-A25V-10	62617245	120602471	13249424	72	39233										
TMEM132D	121256	hgsc.bcm.edu	37	chr12	129559354	129559354	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	taactttgatgtttgccgttCcaacagctaacacactcttc	5	12	1	1			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr12:129559354C>T	ENST00000422113.2	-	9	2692	c.2366G>A	c.(2365-2367)gGa>gAa	p.G789E	TMEM132D_ENST00000389441.4_Missense_Mutation_p.G327E	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	789					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		GTTTGCCGTTCCAACAGCTAA	0.478																																					p.G789E		Atlas-SNP	.											.	TMEM132D	299	.	0			c.G2366A						.						190	155	167					12																	129559354		2203	4300	6503	SO:0001583	missense	121256	exon9			GCCGTTCCAACAG	AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 153"	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.2366G>A	chr12.hg19:g.129559354C>T	ENSP00000408581:p.Gly789Glu	371.0	0.0		323.0	25.0	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	hg19	CCDS9266.1	.	.	.	.	.	.	.	.	.	.	C	13.54	2.268332	0.40095	.	.	ENSG00000151952	ENST00000389441;ENST00000422113	T;T	0.13657	2.57;2.57	4.2	4.2	0.49525	.	0.000000	0.85682	D	0.000000	T	0.44371	0.1290	M	0.88450	2.955	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.81914	0.989;0.995	T	0.56444	-0.7978	9	.	.	.	-25.8194	16.8845	0.86072	0.0:1.0:0.0:0.0	.	789;327	Q14C87;Q14C87-2	T132D_HUMAN;.	E	327;789	ENSP00000374092:G327E;ENSP00000408581:G789E	.	G	-	2	0	TMEM132D	128125307	1.000000	0.71417	0.045000	0.18777	0.030000	0.12068	5.735000	0.68587	2.033000	0.60031	0.462000	0.41574	GGA	.	.		0.478	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448		T	129559354	C	T	129559354	3	4	269	1	0	0	0	0	1	0	0	0	16062	855	30	3	937	3	TMEM132D	12	129559354	Missense_Mutation	SNP	C	TCGA-FV-A496-01A-11D-A25V-10	8956883	129559354	4292541	73	39234										
NUDT15	55270	hgsc.bcm.edu	37	chr13	48611931	48611931	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	ggcggccaggagtcggagtcGgagtcgtggtgaccagctgc	19	10	0	1			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr13:48611931G>T	ENST00000258662.2	+	1	229	c.49G>T	c.(49-51)Gga>Tga	p.G17*	SUCLA2_ENST00000543413.1_5'UTR	NM_018283.1	NP_060753.1	Q9NV35	NUD15_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 15	17	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				dGTP catabolic process (GO:0006203)|GTP catabolic process (GO:0006184)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity (GO:0035539)|8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity (GO:0008413)|metal ion binding (GO:0046872)			endometrium(1)|kidney(3)|large_intestine(2)|lung(1)	7		all_cancers(8;3.75e-25)|all_epithelial(8;1.78e-13)|all_lung(13;2.85e-06)|Breast(56;0.000141)|all_hematologic(8;0.000219)|Lung NSC(96;0.000226)|Prostate(109;0.00132)|Acute lymphoblastic leukemia(8;0.0167)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;4.83e-07)		AGTCGGAGTCGGAGTCGTGGT	0.677											OREG0022405	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G17X		Atlas-SNP	.											.	NUDT15	12	.	0			c.G49T						.						26	26	26					13																	48611931		2194	4293	6487	SO:0001587	stop_gained	55270	exon1			GGAGTCGGAGTCG		CCDS9407.1	13q14.12	2006-04-12			ENSG00000136159	ENSG00000136159		"Nudix motif containing"	23063	protein-coding gene	gene with protein product		615792				12767940	Standard	NM_018283		Approved	MTH2, FLJ10956	uc001vbw.1	Q9NV35	OTTHUMG00000016890	ENST00000258662.2:c.49G>T	chr13.hg19:g.48611931G>T	ENSP00000258662:p.Gly17*	47.0	0.0	955	46.0	5.0	NM_018283	A2RUR6|Q32Q27|Q6P2C9	Nonsense_Mutation	SNP	ENST00000258662.2	hg19	CCDS9407.1	.	.	.	.	.	.	.	.	.	.	G	38	6.976415	0.97975	.	.	ENSG00000136159	ENST00000258662	.	.	.	5.57	5.57	0.84162	.	0.049745	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-8.5895	18.1197	0.89567	0.0:0.0:1.0:0.0	.	.	.	.	X	17	.	ENSP00000258662:G17X	G	+	1	0	NUDT15	47509932	1.000000	0.71417	0.127000	0.21898	0.024000	0.10985	8.098000	0.89540	2.634000	0.89283	0.655000	0.94253	GGA	.	.		0.677	NUDT15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044862.3	NM_018283		T	48611931	G	T	48611931	4	4	269	1	0	0	0	0	0	1	0	0	10740	1117	39	1	51	1	NUDT15	13	48611931	Nonsense_Mutation	SNP	G	TCGA-FV-A496-01A-11D-A25V-10		48611931	66557947	74	39235										
SLITRK1	114798	hgsc.bcm.edu	37	chr13	84454076	84454076	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	gtttccgtggaggtctatctGgatgatggaggttaactggt	15	5	2	1			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr13:84454076G>T	ENST00000377084.2	-	1	2452	c.1567C>A	c.(1567-1569)Cag>Aag	p.Q523K		NM_001281503.1|NM_052910.1	NP_001268432.1|NP_443142.1	Q96PX8	SLIK1_HUMAN	SLIT and NTRK-like family, member 1	523					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|homeostatic process (GO:0042592)|multicellular organism growth (GO:0035264)	integral component of membrane (GO:0016021)				NS(2)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(36)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	80	Medulloblastoma(90;0.18)	Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.07)		AGGTCTATCTGGATGATGGAG	0.557																																					p.Q523K		Atlas-SNP	.											.	SLITRK1	196	.	0			c.C1567A						.						53	54	54					13																	84454076		2203	4300	6503	SO:0001583	missense	114798	exon1			CTATCTGGATGAT	AB067497	CCDS9464.1	13q31.1	2004-01-08	2004-01-08		ENSG00000178235	ENSG00000178235			20297	protein-coding gene	gene with protein product		609678	"leucine rich repeat containing 12"	LRRC12		14557068, 12975309	Standard	NM_001281503		Approved	KIAA1910	uc001vlk.3	Q96PX8	OTTHUMG00000017149	ENST00000377084.2:c.1567C>A	chr13.hg19:g.84454076G>T	ENSP00000366288:p.Gln523Lys	96.0	0.0		142.0	29.0	NM_052910	Q5U5I6|Q96SF9	Missense_Mutation	SNP	ENST00000377084.2	hg19	CCDS9464.1	.	.	.	.	.	.	.	.	.	.	G	19.31	3.803158	0.70682	.	.	ENSG00000178235	ENST00000377084	T	0.50813	0.73	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.54498	0.1862	L	0.41356	1.27	0.80722	D	1	P	0.51653	0.947	P	0.54100	0.742	T	0.55490	-0.8133	10	0.56958	D	0.05	-11.0837	17.693	0.88273	0.0:0.0:1.0:0.0	.	523	Q96PX8	SLIK1_HUMAN	K	523	ENSP00000366288:Q523K	ENSP00000366288:Q523K	Q	-	1	0	SLITRK1	83352077	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.841000	0.86834	2.603000	0.88011	0.655000	0.94253	CAG	.	.		0.557	SLITRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045396.1	NM_052910		T	84454076	G	T	84454076	3	4	269	1	0	0	0	0	1	0	0	0	14757	1357	47	3	527	3	SLITRK1	13	84454076	Missense_Mutation	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	35842145	84454076	30715802	75	39236										
TFDP1	7027	hgsc.bcm.edu	37	chr13	114277525	114277525	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	cctcgtggccgttcacccctCcaccgtcaacccgctcggga	9	20	2	0			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr13:114277525C>T	ENST00000375370.5	+	4	322	c.110C>T	c.(109-111)tCc>tTc	p.S37F	TFDP1_ENST00000544902.1_5'UTR|TFDP1_ENST00000538138.1_5'UTR|TFDP1_ENST00000465174.1_3'UTR	NM_007111.4	NP_009042.1	Q14186	TFDP1_HUMAN	transcription factor Dp-1	37					anoikis (GO:0043276)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|epidermis development (GO:0008544)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic cell cycle (GO:0000278)|Notch signaling pathway (GO:0007219)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA biosynthetic process (GO:2000278)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(10)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	26	Lung NSC(43;0.0113)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.132)|all_epithelial(44;0.0731)|all_lung(25;0.149)|Breast(118;0.153)	all cancers(43;0.0576)			GTTCACCCCTCCACCGTCAAC	0.562										TSP Lung(29;0.18)																											p.S37F		Atlas-SNP	.											.	TFDP1	70	.	0			c.C110T						.						98	74	82					13																	114277525		2202	4300	6502	SO:0001583	missense	7027	exon4			ACCCCTCCACCGT	BC011685	CCDS9538.1	13q34	2008-07-18			ENSG00000198176	ENSG00000198176			11749	protein-coding gene	gene with protein product		189902				8413592, 9027491	Standard	NM_007111		Approved	Dp-1, DRTF1, DP1	uc001vtw.3	Q14186	OTTHUMG00000017388	ENST00000375370.5:c.110C>T	chr13.hg19:g.114277525C>T	ENSP00000364519:p.Ser37Phe	119.0	0.0		196.0	53.0	NM_007111	B4DLQ9|Q5JSB4|Q8IZL5	Missense_Mutation	SNP	ENST00000375370.5	hg19	CCDS9538.1	.	.	.	.	.	.	.	.	.	.	C	10.08	1.253504	0.22965	.	.	ENSG00000198176	ENST00000375370;ENST00000408980;ENST00000453989	T;T;T	0.34472	1.77;1.38;1.36	4.65	3.81	0.43845	.	0.247570	0.42294	D	0.000735	T	0.33059	0.0850	L	0.58101	1.795	0.80722	D	1	B;P;P	0.43431	0.075;0.807;0.807	B;B;B	0.36504	0.028;0.226;0.226	T	0.19844	-1.0293	10	0.56958	D	0.05	.	12.6444	0.56725	0.0:0.9193:0.0:0.0807	.	37;37;37	Q5JSB5;Q5JSB6;Q14186	.;.;TFDP1_HUMAN	F	37	ENSP00000364519:S37F;ENSP00000386145:S37F;ENSP00000401389:S37F	ENSP00000364519:S37F	S	+	2	0	TFDP1	113325526	0.999000	0.42202	0.071000	0.20095	0.096000	0.18686	4.600000	0.61083	0.950000	0.37743	0.491000	0.48974	TCC	.	.		0.562	TFDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045918.3	NM_007111		T	114277525	C	T	114277525	3	4	269	1	0	0	0	0	1	0	0	0	15812	855	30	3	120	3	TFDP1	13	114277525	Missense_Mutation	SNP	C	TCGA-FV-A496-01A-11D-A25V-10	29823449	114277525	892353	76	39237										
SUPT16H	11198	hgsc.bcm.edu	37	chr14	21821900	21821902	+	In_Frame_Del	DEL	TCC	TCC	-													0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	atgaataatcttcatcactgTcctcctcttcctcttcatag							TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr14:21821900_21821902delTCC	ENST00000216297.2	-	24	3218_3220	c.2880_2882delGGA	c.(2878-2883)gaggac>gac	p.E960del		NM_007192.3	NP_009123.1	Q9Y5B9	SP16H_HUMAN	suppressor of Ty 16 homolog (S. cerevisiae)	960	Glu-rich (acidic).				DNA repair (GO:0006281)|DNA replication (GO:0006260)|gene expression (GO:0010467)|nucleosome disassembly (GO:0006337)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_cancers(95;0.00115)		Epithelial(56;1.62e-06)|all cancers(55;1.49e-05)	GBM - Glioblastoma multiforme(265;0.0159)		TTCATCACTGTCCTCCTCTTCCT	0.409																																					p.961_961del		Atlas-Indel,Pindel	.											.	SUPT16H	84	.	0			c.2881_2883del						.																																			SO:0001651	inframe_deletion	11198	exon24			.	AF152961	CCDS9569.1	14q11.1	2008-08-13	2001-11-28		ENSG00000092201	ENSG00000092201			11465	protein-coding gene	gene with protein product	"facilitates chromatin remodeling 140 kDa subunit"	605012	"suppressor of Ty (S.cerevisiae) 16 homolog"			9489704, 11239457	Standard	NM_007192		Approved	FACT, FACTP140, SPT16/CDC68, FLJ14010, FLJ10857, CDC68	uc001wao.2	Q9Y5B9	OTTHUMG00000029685	ENST00000216297.2:c.2880_2882delGGA	chr14.hg19:g.21821903_21821905delTCC	ENSP00000216297:p.Glu960del	211.0	0.0		247.0	39.0	NM_007192	Q6GMT8|Q6P2F1|Q6PJM1|Q9NRX0	In_Frame_Del	DEL	ENST00000216297.2	hg19	CCDS9569.1																																																																																			.	.		0.409	SUPT16H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074025.2			-	21821902	TCC	-	21821900	7	5	269	1	0	1	0	1	0	0	0	0	15411	1667	58	0	273	0	SUPT16H	14	21821900	In_Frame_Del	DEL	TCC	TCGA-FV-A496-01A-11D-A25V-10		21821900	85527640	77	39238										
CFL2	1073	hgsc.bcm.edu	37	chr14	35182517	35182517	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	ttgtttcgtatgtggcatcgTacaaagcatatcggcaatca	9	8	1	0			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr14:35182517T>C	ENST00000341223.3	-	2	405	c.254A>G	c.(253-255)tAc>tGc	p.Y85C	CFL2_ENST00000556161.1_Missense_Mutation_p.Y68C|CFL2_ENST00000298159.6_Missense_Mutation_p.Y85C|CFL2_ENST00000555765.1_Missense_Mutation_p.Y68C	NM_001243645.1|NM_021914.7	NP_001230574.1|NP_068733.1	Q9Y281	COF2_HUMAN	cofilin 2 (muscle)	85	ADF-H. {ECO:0000255|PROSITE- ProRule:PRU00599}.				actin filament depolymerization (GO:0030042)|muscle cell cellular homeostasis (GO:0046716)|positive regulation of actin filament depolymerization (GO:0030836)|regulation of dendritic spine morphogenesis (GO:0061001)|sarcomere organization (GO:0045214)	actin cytoskeleton (GO:0015629)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|nucleus (GO:0005634)				breast(3)|endometrium(2)|lung(3)	8	Breast(36;0.0361)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;6.07e-06)|Lung(238;2.23e-05)|Epithelial(34;0.0387)|all cancers(34;0.0814)	GBM - Glioblastoma multiforme(112;0.0424)		TGTGGCATCGTACAAAGCATA	0.378																																					p.Y85C		Atlas-SNP	.											.	CFL2	22	.	0			c.A254G						.						106	102	104					14																	35182517		2203	4300	6503	SO:0001583	missense	1073	exon2			GCATCGTACAAAG	AF087867	CCDS9649.1, CCDS9650.1, CCDS58311.1	14q13.2	2014-09-17			ENSG00000165410	ENSG00000165410			1875	protein-coding gene	gene with protein product	"nemaline myopathy type 7"	601443				8800436	Standard	NM_138638		Approved	NEM7	uc001wsh.3	Q9Y281	OTTHUMG00000029536	ENST00000341223.3:c.254A>G	chr14.hg19:g.35182517T>C	ENSP00000340635:p.Tyr85Cys	94.0	0.0		118.0	62.0	NM_021914	G3V5P4	Missense_Mutation	SNP	ENST00000341223.3	hg19	CCDS9650.1	.	.	.	.	.	.	.	.	.	.	T	17.69	3.451023	0.63290	.	.	ENSG00000165410	ENST00000341223;ENST00000298159;ENST00000555765;ENST00000556161	D;D;D;D	0.85773	-2.03;-2.03;-2.03;-2.03	6.02	6.02	0.97574	Actin-binding, cofilin/tropomyosin type (3);	0.000000	0.85682	D	0.000000	D	0.95050	0.8397	H	0.96460	3.825	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96435	0.9322	10	0.87932	D	0	-4.9599	16.5446	0.84426	0.0:0.0:0.0:1.0	.	85	Q9Y281	COF2_HUMAN	C	85;85;68;68	ENSP00000340635:Y85C;ENSP00000298159:Y85C;ENSP00000452451:Y68C;ENSP00000452188:Y68C	ENSP00000298159:Y85C	Y	-	2	0	CFL2	34252268	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.967000	0.87967	2.311000	0.77944	0.533000	0.62120	TAC	.	.		0.378	CFL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276639.1	NM_138638		C	35182517	T	C	35182517	3	2	269	1	0	0	0	0	1	0	0	0	3293	1638	57	2	258	2	CFL2	14	35182517	Missense_Mutation	SNP	T	TCGA-FV-A496-01A-11D-A25V-10	13360617	35182517	72167023	78	39239										
FSCB	84075	hgsc.bcm.edu	37	chr14	44975318	44975318	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	tcagttgatggctgtacttgGacatgggtctcttcagcagg	13	8	3	1			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr14:44975318G>T	ENST00000340446.4	-	1	1164	c.873C>A	c.(871-873)gtC>gtA	p.V291V	RP11-163M18.1_ENST00000556228.1_RNA|RP11-163M18.1_ENST00000557465.1_RNA|RP11-163M18.1_ENST00000555433.1_RNA	NM_032135.3	NP_115511.3	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	291						sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(47)|ovary(2)|pancreas(1)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	89				GBM - Glioblastoma multiforme(112;0.128)		GCTGTACTTGGACATGGGTCT	0.512																																					p.V291V		Atlas-SNP	.											.	FSCB	173	.	0			c.C873A						.						54	54	54					14																	44975318		2203	4300	6503	SO:0001819	synonymous_variant	84075	exon1			TACTTGGACATGG	AK124110	CCDS9679.1	14q21.3	2007-11-22	2007-11-22	2007-11-22	ENSG00000189139	ENSG00000189139			20494	protein-coding gene	gene with protein product		611779	"chromosome 14 open reading frame 155"	C14orf155		17855365	Standard	NM_032135		Approved	DKFZP434F1017	uc001wvn.3	Q5H9T9	OTTHUMG00000140262	ENST00000340446.4:c.873C>A	chr14.hg19:g.44975318G>T		45.0	0.0		41.0	5.0	NM_032135	Q5H9U7|Q86YI2|Q9H0J3	Silent	SNP	ENST00000340446.4	hg19	CCDS9679.1																																																																																			.	.		0.512	FSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276788.1	NM_032135		T	44975318	G	T	44975318	2	4	269	1	0	0	0	0	0	0	0	1	6074	1161	41	3		3	FSCB	14	44975318	Silent	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	9792801	44975318	62374222	79	39240										
SIX4	51804	hgsc.bcm.edu	37	chr14	61186834	61186834	+	Nonsense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	taccattgctcacaatgtttGatgacatttttggtgggttc	9	7	1	2			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr14:61186834G>C	ENST00000216513.4	-	2	1252	c.1193C>G	c.(1192-1194)tCa>tGa	p.S398*		NM_017420.4	NP_059116.3	Q9UIU6	SIX4_HUMAN	SIX homeobox 4	398					anatomical structure morphogenesis (GO:0009653)|embryonic cranial skeleton morphogenesis (GO:0048701)|generation of neurons (GO:0048699)|inner ear morphogenesis (GO:0042472)|metanephric mesenchyme development (GO:0072075)|myoblast migration (GO:0051451)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of ureteric bud formation (GO:0072107)|regulation of branch elongation involved in ureteric bud branching (GO:0072095)|regulation of protein localization (GO:0032880)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|skeletal muscle tissue development (GO:0007519)|thymus development (GO:0048538)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(1)|large_intestine(11)|liver(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28				OV - Ovarian serous cystadenocarcinoma(108;0.0275)		CACAATGTTTGATGACATTTT	0.423																																					p.S398X		Atlas-SNP	.											.	SIX4	69	.	0			c.C1193G						.						124	98	107					14																	61186834		2203	4300	6503	SO:0001587	stop_gained	51804	exon2			ATGTTTGATGACA	AB024687	CCDS9749.2	14q23.1	2012-10-02	2007-07-13		ENSG00000100625	ENSG00000100625		"Homeoboxes / SINE class"	10890	protein-coding gene	gene with protein product		606342	"sine oculis homeobox (Drosophila) homolog 4", "sine oculis homeobox homolog 4 (Drosophila)"			10512683, 10640827	Standard	NM_017420		Approved	AREC3	uc001xfc.3	Q9UIU6	OTTHUMG00000028996	ENST00000216513.4:c.1193C>G	chr14.hg19:g.61186834G>C	ENSP00000216513:p.Ser398*	143.0	0.0		160.0	31.0	NM_017420	Q4QQH5|Q4V764	Nonsense_Mutation	SNP	ENST00000216513.4	hg19	CCDS9749.2	.	.	.	.	.	.	.	.	.	.	G	34	5.400052	0.96030	.	.	ENSG00000100625	ENST00000216513;ENST00000554079;ENST00000556952	.	.	.	5.72	5.72	0.89469	.	0.304520	0.32314	N	0.006276	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	19.8965	0.96963	0.0:0.0:1.0:0.0	.	.	.	.	X	398;71;390	.	ENSP00000216513:S398X	S	-	2	0	SIX4	60256587	0.984000	0.35163	1.000000	0.80357	0.996000	0.88848	5.897000	0.69831	2.717000	0.92951	0.655000	0.94253	TCA	.	.		0.423	SIX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072397.2			C	61186834	G	C	61186834	4	2	269	1	0	0	0	0	0	1	0	0	14364	1294	45	4	1160	4	SIX4	14	61186834	Nonsense_Mutation	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	16211516	61186834	46162706	80	39241										
EIF2B2	8892	hgsc.bcm.edu	37	chr14	75471535	75471535	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	tctcccgaacagtagaggccTtcctcaaagaggctgcccga	10	14	2	2			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr14:75471535T>G	ENST00000266126.5	+	4	609	c.529T>G	c.(529-531)Ttc>Gtc	p.F177V	RP11-950C14.3_ENST00000554430.1_RNA	NM_014239.3	NP_055054.1	P49770	EI2BB_HUMAN	eukaryotic translation initiation factor 2B, subunit 2 beta, 39kDa	177					cellular protein metabolic process (GO:0044267)|cellular response to stimulus (GO:0051716)|central nervous system development (GO:0007417)|gene expression (GO:0010467)|myelination (GO:0042552)|oligodendrocyte development (GO:0014003)|ovarian follicle development (GO:0001541)|positive regulation of GTPase activity (GO:0043547)|regulation of translational initiation (GO:0006446)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to peptide hormone (GO:0043434)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation initiation factor 2B complex (GO:0005851)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|translation initiation factor activity (GO:0003743)			endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)	11				BRCA - Breast invasive adenocarcinoma(234;0.00661)		AGTAGAGGCCTTCCTCAAAGA	0.498																																					p.F177V		Atlas-SNP	.											.	EIF2B2	22	.	0			c.T529G	GRCh37	CD067166	EIF2B2	D		.						87	86	86					14																	75471535		2203	4300	6503	SO:0001583	missense	8892	exon4			GAGGCCTTCCTCA		CCDS9836.1	14q24.3	2008-08-11	2002-08-29			ENSG00000119718			3258	protein-coding gene	gene with protein product		606454	"eukaryotic translation initiation factor 2B, subunit 2 (beta, 39kD)"			8887689	Standard	NM_014239		Approved	EIF2B, EIF-2Bbeta	uc001xrc.2	P49770		ENST00000266126.5:c.529T>G	chr14.hg19:g.75471535T>G	ENSP00000266126:p.Phe177Val	48.0	0.0		89.0	21.0	NM_014239	O43201	Missense_Mutation	SNP	ENST00000266126.5	hg19	CCDS9836.1	.	.	.	.	.	.	.	.	.	.	T	32	5.165451	0.94768	.	.	ENSG00000119718	ENST00000266126	D	0.90504	-2.68	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	D	0.95771	0.8624	M	0.86343	2.81	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	D	0.96412	0.9305	10	0.87932	D	0	-29.0445	15.827	0.78718	0.0:0.0:0.0:1.0	.	177	P49770	EI2BB_HUMAN	V	177	ENSP00000266126:F177V	ENSP00000266126:F177V	F	+	1	0	EIF2B2	74541288	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.805000	0.86005	2.324000	0.78689	0.533000	0.62120	TTC	.	.		0.498	EIF2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414993.1	NM_014239		G	75471535	T	G	75471535	3	3	269	1	0	0	0	0	1	0	0	0	5003	1609	56	5	543	5	EIF2B2	14	75471535	Missense_Mutation	SNP	T	TCGA-FV-A496-01A-11D-A25V-10	14284701	75471535	31878005	81	39242										
RTL1	388015	hgsc.bcm.edu	37	chr14	101349498	101349498	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	tcatgccgtgcctctctaggGcaatgcatggcgggggcggg	17	11	2	0			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr14:101349498G>A	ENST00000534062.1	-	1	1686	c.1628C>T	c.(1627-1629)gCc>gTc	p.A543V	MIR433_ENST00000384837.1_RNA|MIR136_ENST00000385207.1_RNA|MIR127_ENST00000384876.1_RNA|MIR431_ENST00000385266.1_RNA|MIR432_ENST00000606207.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	543					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)				breast(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(5)|pancreas(1)|prostate(2)|skin(2)	21						CCTCTCTAGGGCAATGCATGG	0.612																																					p.A543V		Atlas-SNP	.											.	RTL1	120	.	0			c.C1628T						.						34	36	35					14																	101349498		692	1591	2283	SO:0001583	missense	388015	exon1			TCTAGGGCAATGC		CCDS53910.1	14q32.2	2012-04-18			ENSG00000254656	ENSG00000254656			14665	protein-coding gene	gene with protein product		611896				16155747, 15854907, 12796779	Standard	NM_001134888		Approved	PEG11, MART1, Mar1	uc010txj.1	A6NKG5	OTTHUMG00000167573	ENST00000534062.1:c.1628C>T	chr14.hg19:g.101349498G>A	ENSP00000435342:p.Ala543Val	161.0	0.0		189.0	36.0	NM_001134888	E9PKS8	Missense_Mutation	SNP	ENST00000534062.1	hg19	CCDS53910.1	.	.	.	.	.	.	.	.	.	.	G	13.04	2.118516	0.37436	.	.	ENSG00000254656	ENST00000534062	T	0.23950	1.88	3.8	2.9	0.33743	.	0.256197	0.20606	N	0.089068	T	0.24236	0.0587	M	0.62723	1.935	0.19300	N	0.999977	P	0.48162	0.906	B	0.41571	0.36	T	0.14952	-1.0454	10	0.52906	T	0.07	.	6.8456	0.23987	0.0:0.196:0.6016:0.2024	.	543	E9PKS8	.	V	543	ENSP00000435342:A543V	ENSP00000435342:A543V	A	-	2	0	RTL1	100419251	0.089000	0.21612	0.485000	0.27403	0.387000	0.30353	1.592000	0.36676	1.173000	0.42796	-0.165000	0.13383	GCC	.	.		0.612	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888		A	101349498	G	A	101349498	3	1	269	1	0	0	0	0	1	0	0	0	13739	1203	42	3	2452	3	RTL1	14	101349498	Missense_Mutation	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	25877963	101349498	6000042	82	39243										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105414938	105414938	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	ggccttgacgtccacctccaCgctgggcagagacacctcca	10	17	0	2	rs112406618	byFrequency	TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr14:105414938C>T	ENST00000333244.5	-	7	6969	c.6850G>A	c.(6850-6852)Gtg>Atg	p.V2284M	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2284						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)		p.V2284M(1)		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)			TCCACCTCCACGCTGGGCAGA	0.617													.|||	2	0.000399361	8e-04	0.0014	5008	,	,		19314	0		0	False		,,,				2504	0				p.V2284M		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,0,2	AHNAK2	719	.	1	Substitution - Missense(1)	endometrium(1)	c.G6850A						.	T	MET/VAL	9,3983		0,9,1987	140	157	152		6850	-1.2	0	14	dbSNP_132	152	0,8338		0,0,4169	no	missense	AHNAK2	NM_138420.2	21	0,9,6156	TT,TC,CC		0.0,0.2255,0.073	probably-damaging	2284/5796	105414938	9,12321	1996	4169	6165	SO:0001583	missense	113146	exon7			CCTCCACGCTGGG	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.6850G>A	chr14.hg19:g.105414938C>T	ENSP00000353114:p.Val2284Met	227.0	0.0		446.0	57.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	hg19	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	N	15.86	2.958906	0.53400	0.002255	0.0	ENSG00000185567	ENST00000333244	T	0.00682	5.86	4.28	-1.2	0.09554	.	.	.	.	.	T	0.01156	0.0038	L	0.41492	1.28	0.09310	N	1	D	0.59767	0.986	P	0.55112	0.769	T	0.47661	-0.9100	9	0.44086	T	0.13	.	0.8829	0.01238	0.2396:0.3287:0.2347:0.197	.	2284	Q8IVF2	AHNK2_HUMAN	M	2284	ENSP00000353114:V2284M	ENSP00000353114:V2284M	V	-	1	0	AHNAK2	104485983	0.000000	0.05858	0.028000	0.17463	0.194000	0.23727	-2.346000	0.01096	-0.605000	0.05753	0.485000	0.47835	GTG	.	C|0.500;T|0.500		0.617	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		T	105414938	C	T	105414938	3	4	269	1	0	0	0	0	1	0	0	0	415	536	19	1	10541	1	AHNAK2	14	105414938	Missense_Mutation	SNP	C	TCGA-FV-A496-01A-11D-A25V-10	4065440	105414938	1934602	83	39244										
ADAL	161823	hgsc.bcm.edu	37	chr15	43643144	43643144	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	ccccttttcatctagaactcTgtttgacctcaaacgtcaaa	4	13	5	2			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr15:43643144T>C	ENST00000562188.1	+	9	794	c.778T>C	c.(778-780)Tgt>Cgt	p.C260R	ADAL_ENST00000422466.2_Missense_Mutation_p.C260R|ADAL_ENST00000428046.3_Missense_Mutation_p.C233R			Q6DHV7	ADAL_HUMAN	adenosine deaminase-like	260					adenosine catabolic process (GO:0006154)|drug metabolic process (GO:0017144)|inosine biosynthetic process (GO:0046103)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	adenosine deaminase activity (GO:0004000)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|lung(2)|prostate(1)|skin(1)	7		all_cancers(109;7.96e-11)|all_epithelial(112;2.96e-09)|Lung NSC(122;8.91e-07)|all_lung(180;8.8e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;9.31e-07)		TCTAGAACTCTGTTTGACCTC	0.383																																					p.C233R		Atlas-SNP	.											.	ADAL	48	.	0			c.T697C						.						298	234	254					15																	43643144		690	1590	2280	SO:0001583	missense	161823	exon11			GAACTCTGTTTGA		CCDS32214.1, CCDS53936.1	15q15.3	2014-08-08			ENSG00000168803	ENSG00000168803			31853	protein-coding gene	gene with protein product							Standard	NM_001012969		Approved		uc010udo.2	Q6DHV7	OTTHUMG00000176646	ENST00000562188.1:c.778T>C	chr15.hg19:g.43643144T>C	ENSP00000456242:p.Cys260Arg	212.0	0.0		116.0	38.0	NM_001159280	A6NHZ3|B4DQM8	Missense_Mutation	SNP	ENST00000562188.1	hg19		.	.	.	.	.	.	.	.	.	.	T	23.1	4.379751	0.82682	.	.	ENSG00000168803	ENST00000422466;ENST00000428046	D;D	0.88975	-2.45;-2.45	5.69	5.69	0.88448	Adenosine/AMP deaminase (1);	.	.	.	.	D	0.95900	0.8665	H	0.94345	3.525	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96873	0.9641	9	0.87932	D	0	1.2022	13.9004	0.63799	0.0:0.0:0.0:1.0	.	233;260	B4DQM8;Q6DHV7	.;ADAL_HUMAN	R	260;233	ENSP00000398744:C260R;ENSP00000413074:C233R	ENSP00000398744:C260R	C	+	1	0	ADAL	41430436	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.312000	0.78968	2.170000	0.68504	0.528000	0.53228	TGT	.	.		0.383	ADAL-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432960.1	XM_091156		C	43643144	T	C	43643144	3	2	269	1	0	0	0	0	1	0	0	0	233	1580	55	2	844	2	ADAL	15	43643144	Missense_Mutation	SNP	T	TCGA-FV-A496-01A-11D-A25V-10		43643144	58888248	84	39245										
MSLN	10232	hgsc.bcm.edu	37	chr16	815541	815541	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	gcacagccccccgtcgacatGgtctgtctccacgatggacg	11	16	2	0			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr16:815541G>T	ENST00000382862.3	+	9	814	c.719G>T	c.(718-720)tGg>tTg	p.W240L	MSLN_ENST00000563941.1_Missense_Mutation_p.W240L|MSLN_ENST00000566549.1_Missense_Mutation_p.W240L|MSLN_ENST00000545450.2_Missense_Mutation_p.W240L	NM_013404.4	NP_037536.2	Q13421	MSLN_HUMAN	mesothelin	240					cell adhesion (GO:0007155)|pancreas development (GO:0031016)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|kidney(2)|lung(11)|pancreas(1)|prostate(1)|skin(3)	20		Hepatocellular(780;0.00335)				CCGTCGACATGGTCTGTCTCC	0.692																																					p.W240L		Atlas-SNP	.											.	MSLN	109	.	0			c.G719T						.						34	35	34					16																	815541		2181	4284	6465	SO:0001583	missense	10232	exon10			CGACATGGTCTGT	U40434	CCDS32356.1, CCDS45370.1	16p13.3	2008-04-16			ENSG00000102854	ENSG00000102854			7371	protein-coding gene	gene with protein product		601051				7665620, 8552591	Standard	NM_005823		Approved	CAK1, MPF	uc002cjw.2	Q13421	OTTHUMG00000047992	ENST00000382862.3:c.719G>T	chr16.hg19:g.815541G>T	ENSP00000372313:p.Trp240Leu	78.0	0.0		40.0	4.0	NM_005823	D3DU65|Q14859|Q4VQD5|Q96GR6|Q96KJ5|Q9BR17|Q9BTR2|Q9UCB2|Q9UK57	Missense_Mutation	SNP	ENST00000382862.3	hg19	CCDS32356.1	.	.	.	.	.	.	.	.	.	.	G	16.19	3.051760	0.55218	.	.	ENSG00000102854	ENST00000446427;ENST00000445361;ENST00000545450;ENST00000382862	T;T	0.19394	2.15;2.15	2.98	2.98	0.34508	.	0.194918	0.36591	U	0.002514	T	0.39279	0.1072	M	0.61703	1.905	0.43114	D	0.994829	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.999;0.996;0.998	T	0.27331	-1.0077	10	0.87932	D	0	-0.4912	9.2171	0.37353	0.0:0.0:1.0:0.0	.	239;240;240;240	Q13421-4;Q13421;Q13421-2;Q13421-3	.;MSLN_HUMAN;.;.	L	240	ENSP00000442965:W240L;ENSP00000372313:W240L	ENSP00000372313:W240L	W	+	2	0	MSLN	755542	0.305000	0.24481	0.110000	0.21437	0.011000	0.07611	0.687000	0.25407	1.483000	0.48342	0.551000	0.68910	TGG	.	.		0.692	MSLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109253.2			T	815541	G	T	815541	3	4	269	1	0	0	0	0	1	0	0	0	9890	1357	47	3	749	3	MSLN	16	815541	Missense_Mutation	SNP	G	TCGA-FV-A496-01A-11D-A25V-10		815541	89539212	85	39246										
USP7	7874	hgsc.bcm.edu	37	chr16	9000399	9000399	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	gtccttaggatctgttttttGcaaaaattcatcaagtggta	8	6	3	0			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr16:9000399G>A	ENST00000344836.4	-	13	1510	c.1312C>T	c.(1312-1314)Caa>Taa	p.Q438*	USP7_ENST00000381886.4_Nonsense_Mutation_p.Q422*|USP7_ENST00000535863.1_Nonsense_Mutation_p.Q339*	NM_003470.2	NP_003461.2	Q93009	UBP7_HUMAN	ubiquitin specific peptidase 7 (herpes virus-associated)	438	USP.				maintenance of DNA methylation (GO:0010216)|multicellular organismal development (GO:0007275)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|protein deubiquitination (GO:0016579)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|transcription-coupled nucleotide-excision repair (GO:0006283)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|p53 binding (GO:0002039)|protein C-terminus binding (GO:0008022)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(13)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	48						TCTGTTTTTTGCAAAAATTCA	0.323																																					p.Q438X		Atlas-SNP	.											.	USP7	116	.	0			c.C1312T						.						76	77	77					16																	9000399		2197	4300	6497	SO:0001587	stop_gained	7874	exon13			TTTTTTGCAAAAA	Z72499	CCDS32385.1, CCDS66941.1	16p13.3	2008-04-11	2005-08-08			ENSG00000187555		"Ubiquitin-specific peptidases"	12630	protein-coding gene	gene with protein product		602519	"ubiquitin specific protease 7 (herpes virus-associated)"	HAUSP		12838346, 9925944	Standard	NM_003470		Approved		uc002czl.2	Q93009		ENST00000344836.4:c.1312C>T	chr16.hg19:g.9000399G>A	ENSP00000343535:p.Gln438*	39.0	0.0		40.0	22.0	NM_003470	A6NMY8|B7Z815|H0Y3G8	Nonsense_Mutation	SNP	ENST00000344836.4	hg19	CCDS32385.1	.	.	.	.	.	.	.	.	.	.	G	39	7.318442	0.98207	.	.	ENSG00000187555	ENST00000344836;ENST00000381886;ENST00000535863;ENST00000544549;ENST00000542333	.	.	.	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	.	19.0925	0.93233	0.0:0.0:1.0:0.0	.	.	.	.	X	438;446;339;339;380	.	ENSP00000343535:Q438X	Q	-	1	0	USP7	8907900	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.751000	0.98889	2.509000	0.84616	0.561000	0.74099	CAA	.	.		0.323	USP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434268.2			A	9000399	G	A	9000399	4	1	269	1	0	0	0	0	0	1	0	0	17103	1328	46	3	2072	3	USP7	16	9000399	Nonsense_Mutation	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	8184858	9000399	81354354	86	39247										
ITGAD	3681	hgsc.bcm.edu	37	chr16	31419146	31419146	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	ctgaataccatcagctcagcGcctccgcaggaccacgtgtt	9	15	2	1	rs141660381		TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr16:31419146G>A	ENST00000389202.2	+	9	967	c.918G>A	c.(916-918)gcG>gcA	p.A306A		NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	306	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				activated T cell proliferation (GO:0050798)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)	cell surface (GO:0009986)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(43)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						TCAGCTCAGCGCCTCCGCAGG	0.582																																					p.A306A		Atlas-SNP	.											.	ITGAD	154	.	0			c.G918A						.	G		0,4394		0,0,2197	58	54	56		918	-3.6	0	16	dbSNP_134	56	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	ITGAD	NM_005353.2		0,5,6492	AA,AG,GG		0.0581,0.0,0.0385		306/1162	31419146	5,12989	2197	4300	6497	SO:0001819	synonymous_variant	3681	exon9			CTCAGCGCCTCCG	U40274	CCDS32438.1	16p13.1-p11	2010-03-23				ENSG00000156886		"CD molecules", "Integrins"	6146	protein-coding gene	gene with protein product		602453				8666289, 9598326	Standard	NM_005353		Approved	CD11d, ADB2	uc002ebv.1	Q13349		ENST00000389202.2:c.918G>A	chr16.hg19:g.31419146G>A		124.0	0.0		167.0	33.0	NM_005353	Q15575|Q15576	Silent	SNP	ENST00000389202.2	hg19	CCDS32438.1	.	.	.	.	.	.	.	.	.	.	g	7.901	0.734461	0.15574	0.0	5.81E-4	ENSG00000156886	ENST00000316569	.	.	.	5.01	-3.62	0.04543	.	.	.	.	.	T	0.19366	0.0465	.	.	.	0.19300	N	0.999975	B	0.21147	0.052	B	0.11329	0.006	T	0.33599	-0.9862	7	0.87932	D	0	.	0.5817	0.00713	0.2558:0.1337:0.1902:0.4203	.	339	B7Z6V7	.	T	203	.	ENSP00000323325:A203T	A	+	1	0	ITGAD	31326647	0.000000	0.05858	0.000000	0.03702	0.850000	0.48378	-0.461000	0.06712	-0.184000	0.10567	0.586000	0.80456	GCC	.	G|1.000;A|0.000		0.582	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353		A	31419146	G	A	31419146	2	1	269	1	0	0	0	0	0	0	0	1	7893	1074	38	1		1	ITGAD	16	31419146	Silent	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	22418747	31419146	58935607	87	39248										
CDH8	1006	hgsc.bcm.edu	37	chr16	61687728	61687728	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	tcattatctgcctcatgcagCcttacatttataaattcatc	3	11	4	0			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr16:61687728C>G	ENST00000577390.1	-	12	3138	c.2184G>C	c.(2182-2184)agG>agC	p.R728S	CDH8_ENST00000577730.1_Intron|CDH8_ENST00000299345.6_Intron	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	728					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|response to cold (GO:0009409)|synaptic transmission, glutamatergic (GO:0035249)	axon terminus (GO:0043679)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4)	112		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		CCTCATGCAGCCTTACATTTA	0.483																																					p.R728S		Atlas-SNP	.											.	CDH8	273	.	0			c.G2184C						.						88	92	91					16																	61687728		2203	4300	6503	SO:0001583	missense	1006	exon12			ATGCAGCCTTACA	L34060	CCDS10802.1	16q22.1	2010-01-26			ENSG00000150394	ENSG00000150394		"Cadherins / Major cadherins"	1767	protein-coding gene	gene with protein product		603008				9615235, 2059658	Standard	NM_001796		Approved		uc002eog.2	P55286	OTTHUMG00000137493	ENST00000577390.1:c.2184G>C	chr16.hg19:g.61687728C>G	ENSP00000462701:p.Arg728Ser	63.0	0.0		58.0	8.0	NM_001796	B3KWC1|Q14DC6|Q9ULB2	Missense_Mutation	SNP	ENST00000577390.1	hg19	CCDS10802.1	.	.	.	.	.	.	.	.	.	.	C	15.98	2.992335	0.54041	.	.	ENSG00000150394	ENST00000299345	.	.	.	5.7	4.75	0.60458	Cadherin, cytoplasmic domain (1);	0.000000	0.85682	D	0.000000	T	0.77545	0.4146	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.79720	-0.1685	9	0.87932	D	0	.	13.1998	0.59761	0.0:0.9241:0.0:0.0759	.	728	P55286	CADH8_HUMAN	S	728	.	ENSP00000299345:R728S	R	-	3	2	CDH8	60245229	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.604000	0.46274	2.679000	0.91253	0.655000	0.94253	AGG	.	.		0.483	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796		G	61687728	C	G	61687728	3	3	269	1	0	0	0	0	1	0	0	0	3118	738	26	4	219	4	CDH8	16	61687728	Missense_Mutation	SNP	C	TCGA-FV-A496-01A-11D-A25V-10	30268582	61687728	28667025	88	39249										
OSGIN1	29948	hgsc.bcm.edu	37	chr16	83999421	83999421	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	caggggctgactttgcagtgGatcctgaccagccgctgagc	14	12	0	3			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr16:83999421G>A	ENST00000343939.2	+	7	1875	c.1492G>A	c.(1492-1494)Gat>Aat	p.D498N	OSGIN1_ENST00000361711.3_Missense_Mutation_p.D415N|OSGIN1_ENST00000393306.1_Missense_Mutation_p.D415N|NECAB2_ENST00000305202.4_5'Flank			Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1	498					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|negative regulation of cell growth (GO:0030308)|positive regulation of apoptotic process (GO:0043065)		growth factor activity (GO:0008083)			autonomic_ganglia(1)|large_intestine(1)|lung(7)|prostate(2)|upper_aerodigestive_tract(1)	12						CTTTGCAGTGGATCCTGACCA	0.657																																					p.D415N		Atlas-SNP	.											.	OSGIN1	33	.	0			c.G1243A						.						55	54	55					16																	83999421		2198	4298	6496	SO:0001583	missense	29948	exon6			GCAGTGGATCCTG	AY258066	CCDS10939.1	16q23.3	2010-11-23			ENSG00000140961	ENSG00000140961			30093	protein-coding gene	gene with protein product	"bone marrow stromal cell-derived growth inhibitor", "pregnancy induced growth inhibitor"	607975				11459809, 14570898	Standard	NM_182981		Approved	BDGI, OKL38	uc002fhc.3	Q9UJX0	OTTHUMG00000137640	ENST00000343939.2:c.1492G>A	chr16.hg19:g.83999421G>A	ENSP00000343376:p.Asp498Asn	252.0	0.0		223.0	49.0	NM_182981	Q52M33|Q86UQ1|Q96S88|Q9BZ70	Missense_Mutation	SNP	ENST00000343939.2	hg19		.	.	.	.	.	.	.	.	.	.	G	15.18	2.757584	0.49468	.	.	ENSG00000140961	ENST00000343939;ENST00000361711;ENST00000393306	T;T;T	0.39229	1.09;1.09;1.09	4.56	4.56	0.56223	.	0.197713	0.52532	D	0.000067	T	0.53367	0.1792	L	0.56124	1.755	0.80722	D	1	D	0.71674	0.998	P	0.57425	0.82	T	0.50642	-0.8804	10	0.30854	T	0.27	-35.4649	16.3197	0.82945	0.0:0.0:1.0:0.0	.	498	Q9UJX0	OSGI1_HUMAN	N	498;415;415	ENSP00000343376:D498N;ENSP00000355374:D415N;ENSP00000376983:D415N	ENSP00000343376:D498N	D	+	1	0	OSGIN1	82556922	1.000000	0.71417	0.417000	0.26559	0.655000	0.38815	5.608000	0.67654	2.082000	0.62665	0.313000	0.20887	GAT	.	.		0.657	OSGIN1-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000269081.1	NM_013370		A	83999421	G	A	83999421	3	1	269	1	0	0	0	0	1	0	0	0	11298	1174	41	3	1518	3	OSGIN1	16	83999421	Missense_Mutation	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	22311693	83999421	6355332	89	39250										
NXN	64359	hgsc.bcm.edu	37	chr17	704279	704279	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	atctcctccacgtccatcacGtacttggcccgggctgacat	8	16	2	1	rs532098882		TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr17:704279G>T	ENST00000336868.3	-	8	1309	c.1218C>A	c.(1216-1218)taC>taA	p.Y406*	NXN_ENST00000537628.2_Nonsense_Mutation_p.Y157*|NXN_ENST00000538650.1_Nonsense_Mutation_p.Y97*|NXN_ENST00000575801.1_Nonsense_Mutation_p.Y298*	NM_022463.4	NP_071908.2	Q6DKJ4	NXN_HUMAN	nucleoredoxin	406					cardiovascular system development (GO:0072358)|cell differentiation (GO:0030154)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein-disulfide reductase activity (GO:0047134)|thioredoxin-disulfide reductase activity (GO:0004791)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|ovary(2)|pancreas(1)|prostate(1)	13				UCEC - Uterine corpus endometrioid carcinoma (25;0.0237)		CGTCCATCACGTACTTGGCCC	0.587																																					p.Y406X		Atlas-SNP	.											.	NXN	32	.	0			c.C1218A						.						76	66	70					17																	704279		2203	4300	6503	SO:0001587	stop_gained	64359	exon8			CATCACGTACTTG		CCDS10998.1, CCDS56013.1	17p13	2007-08-10			ENSG00000167693	ENSG00000167693			18008	protein-coding gene	gene with protein product		612895					Standard	NM_022463		Approved	FLJ12614, NRX	uc002fsa.3	Q6DKJ4	OTTHUMG00000090307	ENST00000336868.3:c.1218C>A	chr17.hg19:g.704279G>T	ENSP00000337443:p.Tyr406*	84.0	0.0		57.0	4.0	NM_022463	B4DXQ0|D3DTH2|Q3SWW6|Q6P3U6|Q7L4C6|Q9H9Q1	Nonsense_Mutation	SNP	ENST00000336868.3	hg19	CCDS10998.1	.	.	.	.	.	.	.	.	.	.	G	31	5.061164	0.93846	.	.	ENSG00000167693	ENST00000336868;ENST00000538650;ENST00000537628	.	.	.	5.99	-0.522	0.11928	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.5946	10.7899	0.46426	0.5289:0.0:0.4711:0.0	.	.	.	.	X	406;97;298	.	ENSP00000337443:Y406X	Y	-	3	2	NXN	651029	1.000000	0.71417	0.989000	0.46669	0.983000	0.72400	2.541000	0.45735	-0.257000	0.09459	-1.105000	0.02106	TAC	.	.		0.587	NXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206669.1			T	704279	G	T	704279	4	4	269	1	0	0	0	0	0	1	0	0	10796	1140	40	1	93	1	NXN	17	704279	Nonsense_Mutation	SNP	G	TCGA-FV-A496-01A-11D-A25V-10		704279	80490931	90	39251										
POLR2A	5430	hgsc.bcm.edu	37	chr17	7417050	7417070	+	In_Frame_Del	DEL	CCCAGCTACAGCCCCAGCTCG	CCCAGCTACAGCCCCAGCTCG	-													0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	caacctataccccaagctcaCccagctacagccccagctcg					rs199873553|rs370656689|rs1058386		TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	CCCAGCTACAGCCCCAGCTCG	CCCAGCTACAGCCCCAGCTCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr17:7417050_7417070delCCCAGCTACAGCCCCAGCTCG	ENST00000322644.6	+	29	5866_5886	c.5467_5487delCCCAGCTACAGCCCCAGCTCG	c.(5467-5487)cccagctacagccccagctcgdel	p.PSYSPSS1823del		NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	1823	C-terminal domain (CTD); 52 X 7 AA approximate tandem repeats of Y-[ST]-P- [STQ]-[ST]-P-[SRTEVKGN].				7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA-directed RNA polymerase activity (GO:0003968)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(17)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	50		Prostate(122;0.173)				CCCAAGCTCAcccagctacagccccagctcgcccagctaca	0.57																																					p.1822_1829del		Atlas-Indel,Pindel	.											.	POLR2A	157	.	0			c.5466_5486del						.																																			SO:0001651	inframe_deletion	5430	exon29			.			17p13.1	2013-01-21	2002-08-29		ENSG00000181222	ENSG00000181222	2.7.7.6	"RNA polymerase subunits"	9187	protein-coding gene	gene with protein product	"DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit", "RNA polymerase II subunit B1"	180660	"polymerase (RNA) II (DNA directed) polypeptide A (220kD)"	POLR2			Standard	NM_000937		Approved	POLRA, RPB1	uc002ghf.4	P24928	OTTHUMG00000177594	ENST00000322644.6:c.5467_5487delCCCAGCTACAGCCCCAGCTCG	chr17.hg19:g.7417050_7417070delCCCAGCTACAGCCCCAGCTCG	ENSP00000314949:p.Pro1823_Ser1829del	207.0	0.0		127.0	37.0	NM_000937	A6NN93|B9EH88|Q6NX41	In_Frame_Del	DEL	ENST00000322644.6	hg19	CCDS32548.1																																																																																			.	.		0.57	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	NM_000937		-	7417070	CCCAGCTACAGCCCCAGCTCG	-	7417050	7	5	269	1	0	1	0	1	0	0	0	0	12223	507	18	0	5581	0	POLR2A	17	7417050	In_Frame_Del	DEL	CCCAGCTACAGCCCCAGCTCG	TCGA-FV-A496-01A-11D-A25V-10	6712771	7417050	73778160	91	39252										
TP53	7157	hgsc.bcm.edu	37	chr17	7579380	7579380	+	Frame_Shift_Del	DEL	A	A	-													0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	gaaaccgtagctgccctggtAggttttctgggaagggacag							TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr17:7579380delA	ENST00000269305.4	-	4	496	c.307delT	c.(307-309)tacfs	p.Y103fs	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Frame_Shift_Del_p.Y103fs|TP53_ENST00000455263.2_Frame_Shift_Del_p.Y103fs|TP53_ENST00000359597.4_Frame_Shift_Del_p.Y103fs|TP53_ENST00000445888.2_Frame_Shift_Del_p.Y103fs|TP53_ENST00000420246.2_Frame_Shift_Del_p.Y103fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	103	Interaction with HIPK1. {ECO:0000250}.|Interaction with WWOX.|Required for interaction with ZNF385A.				apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.Y103fs*19(3)|p.K101_Y103>N(3)|p.Q100fs*37(3)|p.G59fs*23(3)|p.V73fs*9(1)|p.W91fs*13(1)|p.P13fs*18(1)|p.S33fs*23(1)|p.Y103fs*15(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CTGCCCTGGTAGGTTTTCTGG	0.637		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.Y103fs	Pancreas(47;798 1329 9957 10801)	Pindel	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	.	TP53	33396	.	25	Deletion - Frameshift(14)|Whole gene deletion(8)|Complex - deletion inframe(3)	central_nervous_system(5)|bone(4)|upper_aerodigestive_tract(3)|ovary(3)|prostate(3)|lung(2)|breast(2)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)|liver(1)	c.308delA						.						53	53	53					17																	7579380		2203	4300	6503	SO:0001589	frameshift_variant	7157	exon4	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	.	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.307delT	chr17.hg19:g.7579380delA	ENSP00000269305:p.Tyr103fs	153.0	0.0		87.0	40.0	NM_001126112	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Del	DEL	ENST00000269305.4	hg19	CCDS11118.1																																																																																			.	.		0.637	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		-	7579380	A	-	7579380	7	5	269	1	0	1	0	1	0	0	0	0	16396	420	15	0	995	0	TP53	17	7579380	Frame_Shift_Del	DEL	A	TCGA-FV-A496-01A-11D-A25V-10	162330	7579380	73615830	92	39253										
MYOCD	93649	hgsc.bcm.edu	37	chr17	12655884	12655884	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	ctgtcacttttcctgtcacaCccaacacgctgcccaattac	4	17	2	0			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr17:12655884C>A	ENST00000343344.4	+	10	1279	c.1279C>A	c.(1279-1281)Ccc>Acc	p.P427T	AC005358.1_ENST00000609971.1_Missense_Mutation_p.P331T|MYOCD_ENST00000425538.1_Missense_Mutation_p.P427T|MYOCD_ENST00000395988.1_3'UTR			Q8IZQ8	MYCD_HUMAN	myocardin	427					cardiac muscle cell differentiation (GO:0055007)|cardiac ventricle development (GO:0003231)|cardiocyte differentiation (GO:0035051)|cell growth involved in cardiac muscle cell development (GO:0061049)|cellular component maintenance (GO:0043954)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hypoxia (GO:0071456)|digestive tract development (GO:0048565)|ductus arteriosus closure (GO:0097070)|hepatic stellate cell activation (GO:0035733)|lung alveolus development (GO:0048286)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of skeletal muscle cell differentiation (GO:2001015)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cardiac vascular smooth muscle cell differentiation (GO:2000724)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cell growth by extracellular stimulus (GO:0001560)|regulation of histone acetylation (GO:0035065)|regulation of myoblast differentiation (GO:0045661)|regulation of smooth muscle cell differentiation (GO:0051150)|response to hypoxia (GO:0001666)|smooth muscle cell differentiation (GO:0051145)|urinary bladder development (GO:0060157)|uterus development (GO:0060065)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(2)|lung(33)|ovary(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	70				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)		TCCTGTCACACCCAACACGCT	0.572																																					p.P427T		Atlas-SNP	.											.	MYOCD	291	.	0			c.C1279A						.						147	131	136					17																	12655884		2203	4300	6503	SO:0001583	missense	93649	exon10			GTCACACCCAACA	AF532596	CCDS11163.1, CCDS54091.1	17p11.2	2004-03-01			ENSG00000141052	ENSG00000141052			16067	protein-coding gene	gene with protein product		606127				11439182, 12397177	Standard	XM_005256863		Approved	MYCD	uc002gno.2	Q8IZQ8	OTTHUMG00000058767	ENST00000343344.4:c.1279C>A	chr17.hg19:g.12655884C>A	ENSP00000341835:p.Pro427Thr	108.0	0.0		125.0	32.0	NM_001146312	Q5UBU5|Q8N7Q1	Missense_Mutation	SNP	ENST00000343344.4	hg19	CCDS11163.1	.	.	.	.	.	.	.	.	.	.	C	11.37	1.619684	0.28801	.	.	ENSG00000141052	ENST00000395982;ENST00000425538;ENST00000343344;ENST00000395988;ENST00000443061	T;T	0.44881	0.93;0.91	5.66	4.67	0.58626	.	0.050975	0.85682	D	0.000000	T	0.55386	0.1917	L	0.55834	1.745	0.53005	D	0.999969	D;D;D;D	0.89917	0.983;1.0;1.0;1.0	P;D;D;D	0.97110	0.904;1.0;0.998;0.995	T	0.52689	-0.8542	10	0.07644	T	0.81	-16.7553	15.309	0.74016	0.0:0.859:0.141:0.0	.	146;331;427;427	E9PEP9;Q8IZQ8-2;Q8IZQ8-3;Q8IZQ8	.;.;.;MYCD_HUMAN	T	146;427;427;331;132	ENSP00000341835:P427T;ENSP00000400148:P132T	ENSP00000341835:P427T	P	+	1	0	MYOCD	12596609	1.000000	0.71417	0.042000	0.18584	0.762000	0.43233	7.519000	0.81809	1.355000	0.45865	0.591000	0.81541	CCC	.	.		0.572	MYOCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129950.1	NM_153604		A	12655884	C	A	12655884	3	1	269	1	0	0	0	0	1	0	0	0	10096	507	18	3	1317	3	MYOCD	17	12655884	Missense_Mutation	SNP	C	TCGA-FV-A496-01A-11D-A25V-10	5076504	12655884	68539326	93	39254										
FLII	2314	hgsc.bcm.edu	37	chr17	18154288	18154288	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	tggcctccccgccaatccagTagtagatctcccagttgagg	10	14	1	2			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr17:18154288T>C	ENST00000327031.4	-	14	1865	c.1640A>G	c.(1639-1641)tAc>tGc	p.Y547C	FLII_ENST00000545457.2_Missense_Mutation_p.Y492C|FLII_ENST00000584444.1_5'Flank|FLII_ENST00000578558.1_Missense_Mutation_p.Y546C|FLII_ENST00000579294.1_Missense_Mutation_p.Y536C|FLII_ENST00000379450.4_Missense_Mutation_p.Y461C	NM_002018.3	NP_002009.1	Q13045	FLII_HUMAN	flightless I homolog (Drosophila)	547	Interaction with ACTL6A.				multicellular organismal development (GO:0007275)|muscle contraction (GO:0006936)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	actin binding (GO:0003779)			central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32	all_neural(463;0.228)					GCCAATCCAGTAGTAGATCTC	0.602																																					p.Y547C		Atlas-SNP	.											.	FLII	79	.	0			c.A1640G						.						67	69	68					17																	18154288		2203	4300	6503	SO:0001583	missense	2314	exon14			ATCCAGTAGTAGA	U01184	CCDS11192.1, CCDS58521.1, CCDS58522.1	17p11.2	2008-07-18	2001-11-28		ENSG00000177731	ENSG00000177731			3750	protein-coding gene	gene with protein product		600362	"flightless I (Drosophila) homolog"			7825574	Standard	NM_002018		Approved	FLI, FLIL, Fli1, MGC39265	uc002gsr.2	Q13045	OTTHUMG00000059389	ENST00000327031.4:c.1640A>G	chr17.hg19:g.18154288T>C	ENSP00000324573:p.Tyr547Cys	223.0	0.0		211.0	26.0	NM_002018	B4DIL0|F5H407|J3QLG3	Missense_Mutation	SNP	ENST00000327031.4	hg19	CCDS11192.1	.	.	.	.	.	.	.	.	.	.	T	26.5	4.739550	0.89573	.	.	ENSG00000177731	ENST00000327031;ENST00000545457;ENST00000379450	T;T	0.56103	0.48;0.48	5.91	5.91	0.95273	Gelsolin domain (1);	0.000000	0.85682	D	0.000000	T	0.75451	0.3851	M	0.83384	2.64	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.979;0.979;0.994;0.992;0.999	T	0.79408	-0.1816	10	0.87932	D	0	-34.5379	16.3436	0.83110	0.0:0.0:0.0:1.0	.	461;461;547;547;516	E7EPM0;B4DIL0;F5H407;Q13045;B4DIX0	.;.;.;FLII_HUMAN;.	C	547;547;461	ENSP00000324573:Y547C;ENSP00000368763:Y461C	ENSP00000324573:Y547C	Y	-	2	0	FLII	18095013	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.706000	0.84615	2.269000	0.75478	0.533000	0.62120	TAC	.	.		0.602	FLII-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132032.2	NM_002018		C	18154288	T	C	18154288	3	2	269	1	0	0	0	0	1	0	0	0	5933	1638	57	2	2237	2	FLII	17	18154288	Missense_Mutation	SNP	T	TCGA-FV-A496-01A-11D-A25V-10	5498404	18154288	63040922	94	39255										
IKZF3	22806	hgsc.bcm.edu	37	chr17	37922298	37922298	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	ggcgggggcttgaggagttcGtaagagcggggaacctcctt	18	8	0	2			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr17:37922298G>A	ENST00000346872.3	-	8	1336	c.1275C>T	c.(1273-1275)taC>taT	p.Y425Y	IKZF3_ENST00000377958.2_Silent_p.Y338Y|IKZF3_ENST00000377945.3_Silent_p.Y291Y|RP11-94L15.2_ENST00000488188.2_lincRNA|IKZF3_ENST00000439167.2_Silent_p.Y352Y|IKZF3_ENST00000394189.2_Silent_p.Y243Y|IKZF3_ENST00000377952.2_Silent_p.Y204Y|IKZF3_ENST00000350532.3_Silent_p.Y386Y|IKZF3_ENST00000346243.3_Silent_p.Y347Y|IKZF3_ENST00000535189.1_Silent_p.Y391Y|IKZF3_ENST00000439016.2_Silent_p.Y330Y|IKZF3_ENST00000467757.1_Silent_p.Y369Y|IKZF3_ENST00000351680.3_Silent_p.Y386Y|IKZF3_ENST00000583368.1_Silent_p.Y178Y|IKZF3_ENST00000377944.3_Silent_p.Y282Y	NM_012481.4	NP_036613.2	Q9UKT9	IKZF3_HUMAN	IKAROS family zinc finger 3 (Aiolos)	425					B cell activation (GO:0042113)|mesoderm development (GO:0007498)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of B cell proliferation (GO:0030888)|regulation of lymphocyte differentiation (GO:0045619)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(6)|large_intestine(4)|liver(1)|lung(13)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	42	Breast(7;4.5e-103)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			TGAGGAGTTCGTAAGAGCGGG	0.552																																					p.Y425Y		Atlas-SNP	.											IKZF3,colon,carcinoma,0,2	IKZF3	79	.	0			c.C1275T						.						146	142	143					17																	37922298		2203	4300	6503	SO:0001819	synonymous_variant	22806	exon8			GAGTTCGTAAGAG	AF129512	CCDS11346.1, CCDS11347.1, CCDS11348.1, CCDS11349.1, CCDS11350.1, CCDS11351.1, CCDS58539.1, CCDS58540.1, CCDS58541.1, CCDS58542.1, CCDS58543.1, CCDS58544.1, CCDS58545.1, CCDS74055.1	17q11.2	2013-01-08	2006-08-25	2006-08-25	ENSG00000161405	ENSG00000161405		"Zinc fingers, C2H2-type", "IKAROS zinc fingers"	13178	protein-coding gene	gene with protein product		606221	"zinc finger protein, subfamily 1A, 3 (Aiolos)"	ZNFN1A3		9155026, 10552935	Standard	NM_012481		Approved	Aiolos	uc002hsu.4	Q9UKT9	OTTHUMG00000133250	ENST00000346872.3:c.1275C>T	chr17.hg19:g.37922298G>A		130.0	0.0		132.0	27.0	NM_012481	B4DVV5|Q69BL6|Q69BL7|Q69BL8|Q69BL9|Q69BM0|Q69BM1|Q69BM2|Q69BM3|Q69BM5|Q8N574|Q8WWQ9|Q8WWR0|Q8WWR1|Q8WWR2|Q8WWR3	Silent	SNP	ENST00000346872.3	hg19	CCDS11346.1	.	.	.	.	.	.	.	.	.	.	G	5.978	0.364475	0.11296	.	.	ENSG00000161405	ENST00000439167;ENST00000439016	.	.	.	5.72	-2.11	0.07187	.	.	.	.	.	T	0.63165	0.2488	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60525	-0.7246	4	.	.	.	-11.5725	12.7773	0.57455	0.5173:0.0:0.4827:0.0	.	.	.	.	M	340;379	.	.	T	-	2	0	IKZF3	35175824	0.288000	0.24324	0.970000	0.41538	0.920000	0.55202	-0.286000	0.08399	-0.393000	0.07739	-1.105000	0.02106	ACG	.	.		0.552	IKZF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257004.2	NM_012481		A	37922298	G	A	37922298	2	1	269	1	0	0	0	0	0	0	0	1	7625	1140	40	1		1	IKZF3	17	37922298	Silent	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	19768010	37922298	43272912	95	39256										
ACLY	47	hgsc.bcm.edu	37	chr17	40028400	40028400	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	gatcagctgtcaccatcagaCacatctcaatgaactggcaa	7	12	4	2			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr17:40028400C>T	ENST00000352035.2	-	24	2808	c.2678G>A	c.(2677-2679)tGt>tAt	p.C893Y	ACLY_ENST00000590151.1_Missense_Mutation_p.C893Y|ACLY_ENST00000393896.2_Missense_Mutation_p.C883Y|ACLY_ENST00000537919.1_Missense_Mutation_p.C622Y|ACLY_ENST00000588779.1_5'Flank|ACLY_ENST00000353196.1_Missense_Mutation_p.C883Y	NM_001096.2	NP_001087.2	P53396	ACLY_HUMAN	ATP citrate lyase	893					ATP catabolic process (GO:0006200)|cellular carbohydrate metabolic process (GO:0044262)|cellular lipid metabolic process (GO:0044255)|citrate metabolic process (GO:0006101)|coenzyme A metabolic process (GO:0015936)|energy reserve metabolic process (GO:0006112)|lipid biosynthetic process (GO:0008610)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	citrate lyase complex (GO:0009346)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP citrate synthase activity (GO:0003878)|cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)		NTN1/ACLY(2)	breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(4)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	28		Breast(137;0.000143)				CACCATCAGACACATCTCAAT	0.567																																					p.C893Y	Colon(64;807 1396 15971 30971)	Atlas-SNP	.											.	ACLY	85	.	0			c.G2678A						.						74	62	66					17																	40028400		2203	4300	6503	SO:0001583	missense	47	exon24			ATCAGACACATCT	X64330	CCDS11412.1, CCDS11413.1	17q21.2	2010-04-27			ENSG00000131473	ENSG00000131473	2.3.3.8		115	protein-coding gene	gene with protein product	"ATP citrate synthase"	108728				1371749, 8088842	Standard	NM_001096		Approved	ATPCL, CLATP, ACL	uc002hyg.3	P53396	OTTHUMG00000133507	ENST00000352035.2:c.2678G>A	chr17.hg19:g.40028400C>T	ENSP00000253792:p.Cys893Tyr	113.0	0.0		112.0	21.0	NM_001096	B4DIM0|B4E3P0|Q13037|Q9BRL0	Missense_Mutation	SNP	ENST00000352035.2	hg19	CCDS11412.1	.	.	.	.	.	.	.	.	.	.	C	16.55	3.153538	0.57259	.	.	ENSG00000131473	ENST00000352035;ENST00000401700;ENST00000353196;ENST00000537919;ENST00000393896	T;T;D;T	0.88509	-1.39;-1.4;-2.39;-1.4	6.17	5.21	0.72293	Citrate synthase-like, large alpha subdomain (1);Citrate synthase-like, core (1);	0.000000	0.85682	D	0.000000	D	0.94036	0.8089	M	0.74389	2.26	0.80722	D	1	D;D;D;P;D	0.76494	0.999;0.999;0.963;0.912;0.999	D;D;P;P;D	0.87578	0.998;0.994;0.71;0.813;0.998	D	0.94705	0.7887	10	0.87932	D	0	.	15.565	0.76284	0.0:0.9345:0.0:0.0655	.	622;937;947;883;893	B4E3P0;B4DIM0;E7ENH9;G3XAI4;P53396	.;.;.;.;ACLY_HUMAN	Y	893;947;883;622;883	ENSP00000253792:C893Y;ENSP00000345398:C883Y;ENSP00000445349:C622Y;ENSP00000377474:C883Y	ENSP00000253792:C893Y	C	-	2	0	ACLY	37281926	1.000000	0.71417	1.000000	0.80357	0.025000	0.11179	7.770000	0.85390	1.636000	0.50526	-0.136000	0.14681	TGT	.	.		0.567	ACLY-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257465.1	NM_001096		T	40028400	C	T	40028400	3	4	269	1	0	0	0	0	1	0	0	0	143	478	17	3	651	3	ACLY	17	40028400	Missense_Mutation	SNP	C	TCGA-FV-A496-01A-11D-A25V-10	2106102	40028400	41166810	96	39257										
MYCBPAP	84073	hgsc.bcm.edu	37	chr17	48601116	48601116	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	cggtctccctgacccaggacGtttttgaggatgagaggaaa	13	9	1	3			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr17:48601116G>A	ENST00000323776.5	+	12	1897	c.1735G>A	c.(1735-1737)Gtt>Att	p.V579I	MYCBPAP_ENST00000436259.2_Missense_Mutation_p.V542I	NM_032133.4	NP_115509.4			MYCBP associated protein											breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(8)|ovary(4)|pancreas(1)|skin(2)|urinary_tract(2)	31	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;1.23e-09)			GACCCAGGACGTTTTTGAGGA	0.532																																					p.V579I		Atlas-SNP	.											.	MYCBPAP	135	.	0			c.G1735A						.						56	55	56					17																	48601116		2203	4300	6503	SO:0001583	missense	84073	exon12			CAGGACGTTTTTG	BC028393	CCDS32680.2	17q21.33	2004-02-19			ENSG00000136449	ENSG00000136449			19677	protein-coding gene	gene with protein product		609835				12151104	Standard	NM_032133		Approved	AMAP-1, DKFZp434N1415	uc010wmr.2	Q8TBZ2	OTTHUMG00000157184	ENST00000323776.5:c.1735G>A	chr17.hg19:g.48601116G>A	ENSP00000323184:p.Val579Ile	111.0	0.0		99.0	54.0	NM_032133		Missense_Mutation	SNP	ENST00000323776.5	hg19	CCDS32680.2	.	.	.	.	.	.	.	.	.	.	G	0.008	-1.899122	0.00517	.	.	ENSG00000136449	ENST00000323776;ENST00000436259	T;T	0.43294	0.95;0.95	5.74	-4.73	0.03259	.	0.746389	0.12709	N	0.445652	T	0.09686	0.0238	N	0.00823	-1.155	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.39663	-0.9603	10	0.07644	T	0.81	0.2452	6.9197	0.24380	0.3277:0.3947:0.2775:0.0	.	542	Q8TBZ2	MYBPP_HUMAN	I	579;542	ENSP00000323184:V579I;ENSP00000397209:V542I	ENSP00000323184:V579I	V	+	1	0	MYCBPAP	45956115	0.000000	0.05858	0.004000	0.12327	0.007000	0.05969	-0.215000	0.09279	-0.450000	0.07107	-1.058000	0.02302	GTT	.	.		0.532	MYCBPAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347814.1	NM_032133		A	48601116	G	A	48601116	3	1	269	1	0	0	0	0	1	0	0	0	10028	1145	40	1	1781	1	MYCBPAP	17	48601116	Missense_Mutation	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	8572716	48601116	32594094	97	39258										
LUC7L3	51747	hgsc.bcm.edu	37	chr17	48823123	48823123	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	aagaacctgatcgtgatgagCgtctaaaaaaggagaagcaa	11	6	1	5			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr17:48823123C>T	ENST00000505658.1	+	8	925	c.736C>T	c.(736-738)Cgt>Tgt	p.R246C	LUC7L3_ENST00000240304.1_Missense_Mutation_p.R246C|LUC7L3_ENST00000393227.2_Missense_Mutation_p.R246C|LUC7L3_ENST00000544170.1_Missense_Mutation_p.R170C			O95232	LC7L3_HUMAN	LUC7-like 3 (S. cerevisiae)	246	Arg/Ser-rich.|Glu-rich.				mRNA splice site selection (GO:0006376)|RNA splicing (GO:0008380)	focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|U1 snRNP (GO:0005685)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)	12						TCGTGATGAGCGTCTAAAAAA	0.363																																					p.R246C		Atlas-SNP	.											.	LUC7L3	32	.	0			c.C736T						.						33	34	34					17																	48823123		2171	4281	6452	SO:0001583	missense	51747	exon8			GATGAGCGTCTAA		CCDS11573.1	17q21.33	2010-02-17			ENSG00000108848	ENSG00000108848			24309	protein-coding gene	gene with protein product	"cisplatin resistance associated overexpressed protein", "CRE-associated protein"	609434				10631324, 12565863	Standard	NM_016424		Approved	LUC7A, CROP, OA48-18, CREAP-1, FLJ11063, CRA, hLuc7A	uc002iss.3	O95232	OTTHUMG00000162257	ENST00000505658.1:c.736C>T	chr17.hg19:g.48823123C>T	ENSP00000425092:p.Arg246Cys	58.0	0.0		73.0	13.0	NM_006107	B3KN54|D3DTY1|Q6PHR9|Q9NUY0|Q9P2S7	Missense_Mutation	SNP	ENST00000505658.1	hg19	CCDS11573.1	.	.	.	.	.	.	.	.	.	.	C	17.58	3.425715	0.62733	.	.	ENSG00000108848	ENST00000505658;ENST00000393227;ENST00000240304;ENST00000544170	T;T;T;T	0.32023	1.48;1.47;1.48;1.47	5.95	5.95	0.96441	.	0.309371	0.34484	N	0.003928	T	0.53658	0.1810	M	0.61703	1.905	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.83275	0.993;0.993;0.996	T	0.49495	-0.8934	10	0.54805	T	0.06	-8.3748	15.8482	0.78907	0.1363:0.8637:0.0:0.0	.	170;246;246	B4DJ96;O95232;A8K3C5	.;LC7L3_HUMAN;.	C	246;246;246;170	ENSP00000425092:R246C;ENSP00000376919:R246C;ENSP00000240304:R246C;ENSP00000444253:R170C	ENSP00000240304:R246C	R	+	1	0	LUC7L3	46178122	0.998000	0.40836	1.000000	0.80357	0.947000	0.59692	2.870000	0.48451	2.824000	0.97209	0.655000	0.94253	CGT	.	.		0.363	LUC7L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368205.2	NM_016424		T	48823123	C	T	48823123	3	4	269	1	0	0	0	0	1	0	0	0	9093	768	27	1	766	1	LUC7L3	17	48823123	Missense_Mutation	SNP	C	TCGA-FV-A496-01A-11D-A25V-10	222007	48823123	32372087	98	39259										
EFCAB3	146779	hgsc.bcm.edu	37	chr17	60493468	60493468	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	ggggatttgattgggatggaCtctagaaatgagtcctttta	13	4	1	3			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr17:60493468C>T	ENST00000305286.3	+	10	1173	c.1095C>T	c.(1093-1095)gaC>gaT	p.D365D	EFCAB3_ENST00000450662.2_Silent_p.D417D	NM_173503.3	NP_775774.1	Q8N7B9	EFCB3_HUMAN	EF-hand calcium binding domain 3	365							calcium ion binding (GO:0005509)			cervix(1)|endometrium(2)|large_intestine(5)|lung(6)|skin(3)	17			BRCA - Breast invasive adenocarcinoma(2;2.27e-11)			TTGGGATGGACTCTAGAAATG	0.398																																					p.D417D		Atlas-SNP	.											.	EFCAB3	71	.	0			c.C1251T						.						116	117	117					17																	60493468		2203	4300	6503	SO:0001819	synonymous_variant	146779	exon12			GATGGACTCTAGA	AK098684	CCDS11632.1, CCDS45751.1	17q23.3	2013-01-10			ENSG00000172421	ENSG00000172421		"EF-hand domain containing"	26379	protein-coding gene	gene with protein product						12477932	Standard	NM_173503		Approved	FLJ25818	uc010wpc.2	Q8N7B9	OTTHUMG00000179175	ENST00000305286.3:c.1095C>T	chr17.hg19:g.60493468C>T		107.0	0.0		190.0	44.0	NM_001144933	J3KQM8	Silent	SNP	ENST00000305286.3	hg19	CCDS11632.1																																																																																			.	.		0.398	EFCAB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379114.1	NM_173503		T	60493468	C	T	60493468	2	4	269	1	0	0	0	0	0	0	0	1	4937	564	20	3		3	EFCAB3	17	60493468	Silent	SNP	C	TCGA-FV-A496-01A-11D-A25V-10	11670345	60493468	20701742	99	39260										
ABCA5	23461	hgsc.bcm.edu	37	chr17	67300830	67300830	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	agatgataatccataaaggaAaaaaagcagaaatatcacaa	6	5	1	3			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr17:67300830A>T	ENST00000392676.3	-	7	974	c.910T>A	c.(910-912)Ttc>Atc	p.F304I	ABCA5_ENST00000392677.2_Missense_Mutation_p.F304I|ABCA5_ENST00000588877.1_Missense_Mutation_p.F304I			Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 5	304					cholesterol efflux (GO:0033344)|high-density lipoprotein particle remodeling (GO:0034375)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|reverse cholesterol transport (GO:0043691)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(18)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	54	Breast(10;3.72e-11)				Tacrolimus(DB00864)	CCATAAAGGAAAAAAAGCAGA	0.308																																					p.F304I		Atlas-SNP	.											.	ABCA5	162	.	0			c.T910A						.						43	43	43					17																	67300830		2203	4295	6498	SO:0001583	missense	23461	exon6			AAAGGAAAAAAAG	U66672	CCDS11685.1	17q24.3	2012-03-14			ENSG00000154265	ENSG00000154265		"ATP binding cassette transporters / subfamily A"	35	protein-coding gene	gene with protein product		612503				8894702	Standard	NM_172232		Approved	EST90625	uc002jig.2	Q8WWZ7		ENST00000392676.3:c.910T>A	chr17.hg19:g.67300830A>T	ENSP00000376443:p.Phe304Ile	57.0	0.0		113.0	41.0	NM_018672	Q8IVJ2|Q96LJ1|Q96MS4|Q96PZ9|Q9NY14	Missense_Mutation	SNP	ENST00000392676.3	hg19	CCDS11685.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.517016	0.85495	.	.	ENSG00000154265	ENST00000392677;ENST00000392676	T;T	0.79554	-1.28;-1.28	5.54	5.54	0.83059	.	0.000000	0.64402	D	0.000003	D	0.87489	0.6190	M	0.71036	2.16	0.48341	D	0.999638	D;D	0.89917	0.989;1.0	P;D	0.71870	0.857;0.975	D	0.87546	0.2462	9	.	.	.	.	11.6476	0.51269	0.8518:0.1482:0.0:0.0	.	304;304	Q8WWZ7-2;Q8WWZ7	.;ABCA5_HUMAN	I	304	ENSP00000376444:F304I;ENSP00000376443:F304I	.	F	-	1	0	ABCA5	64812425	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.128000	0.64733	2.086000	0.62901	0.460000	0.39030	TTC	.	.		0.308	ABCA5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450654.1	NM_018672		T	67300830	A	T	67300830	3	4	269	1	0	0	0	0	1	0	0	0	35	14	1	4	4150	4	ABCA5	17	67300830	Missense_Mutation	SNP	A	TCGA-FV-A496-01A-11D-A25V-10	6807362	67300830	13894380	100	39261										
ST6GALNAC1	55808	hgsc.bcm.edu	37	chr17	74625422	74625422	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	tcagcttcctggtctggcccCcatttccttgggtcgtcttt	9	14	3	0			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr17:74625422C>A	ENST00000156626.7	-	2	702	c.503G>T	c.(502-504)gGg>gTg	p.G168V	ST6GALNAC1_ENST00000590878.1_5'UTR	NM_018414.3	NP_060884.1	Q9NSC7	SIA7A_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 1	168					oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity (GO:0001665)|sialyltransferase activity (GO:0008373)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(11)|prostate(1)|upper_aerodigestive_tract(1)	22						GGTCTGGCCCCCATTTCCTTG	0.582																																					p.G168V		Atlas-SNP	.											.	ST6GALNAC1	42	.	0			c.G503T						.						176	154	162					17																	74625422		2203	4300	6503	SO:0001583	missense	55808	exon2			TGGCCCCCATTTC	Y11339	CCDS11748.1	17q25.3	2013-03-01	2005-02-07	2005-02-07	ENSG00000070526	ENSG00000070526		"Sialyltransferases"	23614	protein-coding gene	gene with protein product		610138	"sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) A"	SIAT7A			Standard	NM_001289107		Approved	ST6GalNAcI	uc002jsh.3	Q9NSC7	OTTHUMG00000180369	ENST00000156626.7:c.503G>T	chr17.hg19:g.74625422C>A	ENSP00000156626:p.Gly168Val	269.0	0.0		439.0	32.0	NM_018414	Q6UW90|Q9NSC6	Missense_Mutation	SNP	ENST00000156626.7	hg19	CCDS11748.1	.	.	.	.	.	.	.	.	.	.	C	13.39	2.221649	0.39300	.	.	ENSG00000070526	ENST00000156626;ENST00000359088	T;T	0.34667	1.47;1.35	3.77	-3.86	0.04230	.	1.585260	0.03407	N	0.204202	T	0.40570	0.1122	L	0.38175	1.15	0.09310	N	1	D	0.57899	0.981	P	0.55161	0.77	T	0.48139	-0.9061	10	0.38643	T	0.18	-1.3588	9.5701	0.39422	0.0:0.3291:0.0:0.6709	.	168	Q9NSC7	SIA7A_HUMAN	V	168	ENSP00000156626:G168V;ENSP00000351991:G168V	ENSP00000156626:G168V	G	-	2	0	ST6GALNAC1	72137017	0.000000	0.05858	0.000000	0.03702	0.045000	0.14185	-1.400000	0.02504	-0.747000	0.04759	-0.339000	0.08088	GGG	.	.		0.582	ST6GALNAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450974.1	NM_018414		A	74625422	C	A	74625422	3	1	269	1	0	0	0	0	1	0	0	0	15238	623	22	3	1331	3	ST6GALNAC1	17	74625422	Missense_Mutation	SNP	C	TCGA-FV-A496-01A-11D-A25V-10	7324592	74625422	6569788	101	39262										
PHLPP1	23239	hgsc.bcm.edu	37	chr18	60612502	60612502	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	ttatgcagctcccagagatcAaggtatgtggtttcatttca	9	8	3	1			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr18:60612502A>G	ENST00000262719.5	+	12	3556	c.3322A>G	c.(3322-3324)Aag>Gag	p.K1108E	PHLPP1_ENST00000400316.4_Missense_Mutation_p.K596E			O60346	PHLP1_HUMAN	PH domain and leucine rich repeat protein phosphatase 1	1108					apoptotic process (GO:0006915)|entrainment of circadian clock (GO:0009649)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			endometrium(2)|kidney(2)|lung(13)	17						CCCAGAGATCAAGGTATGTGG	0.453																																					p.K1108E		Atlas-SNP	.											.	PHLPP1	164	.	0			c.A3322G						.						91	86	87					18																	60612502		1920	4129	6049	SO:0001583	missense	23239	exon12			GAGATCAAGGTAT	AB011178	CCDS45881.1, CCDS45881.2	18q21.32	2013-01-11	2009-05-26	2009-05-26	ENSG00000081913	ENSG00000081913		"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent", "Pleckstrin homology (PH) domain containing"	20610	protein-coding gene	gene with protein product		609396	"pleckstrin homology domain containing, family E (with leucine rich repeats) member 1", "PH domain and leucine rich repeat protein phosphatase"	PLEKHE1, PHLPP		10570941, 15808505	Standard	NM_194449		Approved	KIAA0606, SCOP	uc021ule.1	O60346	OTTHUMG00000150629	ENST00000262719.5:c.3322A>G	chr18.hg19:g.60612502A>G	ENSP00000262719:p.Lys1108Glu	160.0	0.0		89.0	4.0	NM_194449	A1A4F5|Q641Q7|Q6P4C4|Q6PJI6|Q86TN6|Q96FK2|Q9NUY1	Missense_Mutation	SNP	ENST00000262719.5	hg19	CCDS45881.2	.	.	.	.	.	.	.	.	.	.	A	27.4	4.827543	0.90955	.	.	ENSG00000081913	ENST00000400316;ENST00000262719	T;T	0.16897	2.31;2.31	4.92	4.92	0.64577	.	.	.	.	.	T	0.19525	0.0469	L	0.40543	1.245	0.80722	D	1	D	0.58620	0.983	P	0.47744	0.556	T	0.02358	-1.1171	9	0.22109	T	0.4	-25.4687	15.0124	0.71560	1.0:0.0:0.0:0.0	.	1108	O60346	PHLP1_HUMAN	E	596;1108	ENSP00000383170:K596E;ENSP00000262719:K1108E	ENSP00000262719:K1108E	K	+	1	0	PHLPP1	58763482	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	8.794000	0.91867	2.192000	0.70111	0.533000	0.62120	AAG	.	.		0.453	PHLPP1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319249.2	NM_194449		G	60612502	A	G	60612502	3	3	269	1	0	0	0	0	1	0	0	0	11863	131	5	2	3368	2	PHLPP1	18	60612502	Missense_Mutation	SNP	A	TCGA-FV-A496-01A-11D-A25V-10		60612502	17464746	102	39263										
DNAJB1	3337	hgsc.bcm.edu	37	chr19	14629102	14629102	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	tggcggcggtaggcccgcttGatctcctcgtccgacgcgcc	14	16	1	1			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr19:14629102G>A	ENST00000254322.2	-	1	130	c.60C>T	c.(58-60)atC>atT	p.I20I	DNAJB1_ENST00000396969.4_Intron	NM_006145.1	NP_006136.1	P25685	DNJB1_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 1	20	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				chaperone cofactor-dependent protein refolding (GO:0070389)|chaperone mediated protein folding requiring cofactor (GO:0051085)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of ATPase activity (GO:0032781)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|unfolded protein binding (GO:0051082)			NS(1)|breast(1)|cervix(3)|endometrium(1)|kidney(1)|lung(7)|prostate(1)|urinary_tract(1)	16				GBM - Glioblastoma multiforme(1328;0.0476)		AGGCCCGCTTGATCTCCTCGT	0.692																																					p.I20I		Atlas-SNP	.											.	DNAJB1	38	.	0			c.C60T						.						38	31	33					19																	14629102		2202	4298	6500	SO:0001819	synonymous_variant	3337	exon1			CCGCTTGATCTCC	D49547	CCDS12312.1, CCDS74295.1	19p13.12	2014-08-12			ENSG00000132002	ENSG00000132002		"Heat shock proteins / DNAJ (HSP40)"	5270	protein-coding gene	gene with protein product	"radial spoke 16 homolog B (Chlamydomonas)"	604572		HSPF1		8975727, 8250930	Standard	XM_006722733		Approved	Hsp40, Sis1, RSPH16B	uc002myz.1	P25685	OTTHUMG00000183289	ENST00000254322.2:c.60C>T	chr19.hg19:g.14629102G>A		26.0	0.0		28.0	20.0	NM_006145	B4DX52	Silent	SNP	ENST00000254322.2	hg19	CCDS12312.1																																																																																			.	.		0.692	DNAJB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465987.1	NM_006145		A	14629102	G	A	14629102	2	1	269	1	0	0	0	0	0	0	0	1	4617	1280	45	3		3	DNAJB1	19	14629102	Silent	SNP	G	TCGA-FV-A496-01A-11D-A25V-10		14629102	44499881	103	39264										
LSM14A	26065	hgsc.bcm.edu	37	chr19	34687544	34687544	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	atgattttccttcagtcctcActaggctcatcgacttcttc	5	13	4	1			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr19:34687544A>G	ENST00000433627.5	+	3	366	c.291A>G	c.(289-291)tcA>tcG	p.S97S	LSM14A_ENST00000540746.2_Silent_p.S97S|LSM14A_ENST00000544216.3_Silent_p.S97S	NM_001114093.1	NP_001107565.1	Q8ND56	LS14A_HUMAN	LSM14A, SCD6 homolog A (S. cerevisiae)	97					cytoplasmic mRNA processing body assembly (GO:0033962)|multicellular organismal development (GO:0007275)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of translation (GO:0006417)|RIG-I signaling pathway (GO:0039529)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|intracellular membrane-bounded organelle (GO:0043231)	double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(7)|skin(1)	22	Esophageal squamous(110;0.162)					TTCAGTCCTCACTAGGCTCAT	0.393																																					p.S97S		Atlas-SNP	.											LSM14A,NS,carcinoma,0,1	LSM14A	44	.	0			c.A291G						.						171	152	159					19																	34687544		2203	4300	6503	SO:0001819	synonymous_variant	26065	exon3			GTCCTCACTAGGC	AL834398	CCDS12435.1, CCDS46040.1	19q13.12	2010-01-27	2006-12-21	2006-01-24		ENSG00000257103			24489	protein-coding gene	gene with protein product		610677	"chromosome 19 open reading frame 13", "family with sequence similarity 61, member A", "LSM14 homolog A (SCD6, S. cerevisiae)"	C19orf13, FAM61A		12477932	Standard	NM_015578		Approved	DKFZP434D1335, RAP55A, RAP55	uc002nva.4	Q8ND56		ENST00000433627.5:c.291A>G	chr19.hg19:g.34687544A>G		166.0	0.0		137.0	63.0	NM_001114093	B4DTG6|Q76LX7|Q96AR3|Q96K73|Q96SN5|Q9UFR3	Silent	SNP	ENST00000433627.5	hg19	CCDS46040.1																																																																																			.	.		0.393	LSM14A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451576.3	NM_015578		G	34687544	A	G	34687544	2	3	269	1	0	0	0	0	0	0	0	1	9063	146	6	2		2	LSM14A	19	34687544	Silent	SNP	A	TCGA-FV-A496-01A-11D-A25V-10	20058442	34687544	24441439	104	39265										
RASGRP4	115727	hgsc.bcm.edu	37	chr19	38912788	38912788	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	ttccggtgcattcctggtggGacttcctgtgggcacagccc	13	13	0	0			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr19:38912788G>A	ENST00000587738.1	-	2	99	c.29C>T	c.(28-30)tCc>tTc	p.S10F	RASGRP4_ENST00000293062.9_Missense_Mutation_p.S10F|RASGRP4_ENST00000433821.2_Missense_Mutation_p.S10F|RASGRP4_ENST00000587753.1_Missense_Mutation_p.S10F|RASGRP4_ENST00000454404.2_Missense_Mutation_p.S10F|RASGRP4_ENST00000426920.2_Missense_Mutation_p.S10F|RASGRP4_ENST00000586305.1_Missense_Mutation_p.S10F			Q8TDF6	GRP4_HUMAN	RAS guanyl releasing protein 4	10					activation of phospholipase C activity (GO:0007202)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|myeloid cell differentiation (GO:0030099)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|response to extracellular stimulus (GO:0009991)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|GTP-dependent protein binding (GO:0030742)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			cervix(1)|kidney(1)|large_intestine(4)|lung(12)|pancreas(1)|prostate(3)|skin(1)	23	all_cancers(60;4.21e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			TTCCTGGTGGGACTTCCTGTG	0.602																																					p.S10F		Atlas-SNP	.											.	RASGRP4	54	.	0			c.C29T						.						33	38	36					19																	38912788		1921	4128	6049	SO:0001583	missense	115727	exon2			TGGTGGGACTTCC	AY048119	CCDS46068.1, CCDS54262.1, CCDS54263.1, CCDS54264.1	19q13.1	2013-01-10						"EF-hand domain containing"	18958	protein-coding gene	gene with protein product		607320				11956218	Standard	NM_170604		Approved		uc021uub.1	Q8TDF6		ENST00000587738.1:c.29C>T	chr19.hg19:g.38912788G>A	ENSP00000465772:p.Ser10Phe	93.0	0.0		112.0	6.0	NM_001146206	A6H8M4|C0LTP2|C0LTP3|C0LTP4|C0LTP5|C0LTP7|C9J416|C9JHZ1|Q8N858|Q96QN5|Q96QN6|Q96QN7	Missense_Mutation	SNP	ENST00000587738.1	hg19	CCDS46068.1	.	.	.	.	.	.	.	.	.	.	G	15.99	2.995087	0.54041	.	.	ENSG00000171777	ENST00000433821;ENST00000293062;ENST00000426920;ENST00000405332;ENST00000454404	T;T;T;T	0.33654	1.4;1.4;1.4;1.4	4.07	2.93	0.34026	.	0.827806	0.10518	N	0.665357	T	0.49915	0.1585	L	0.56769	1.78	0.39437	D	0.967186	D;D;D;D;D;D;D	0.61697	0.984;0.984;0.99;0.976;0.99;0.986;0.976	P;P;P;P;P;P;P	0.57371	0.819;0.75;0.527;0.556;0.804;0.748;0.459	T	0.54748	-0.8247	10	0.72032	D	0.01	-23.1122	11.5958	0.50972	0.0:0.1823:0.8177:0.0	.	10;10;10;10;10;10;10	C0LTP5;C0LTP7;C0LTP2;C0LTP4;C0LTP3;Q8TDF6-2;Q8TDF6	.;.;.;.;.;.;GRP4_HUMAN	F	10	ENSP00000411878:S10F;ENSP00000293062:S10F;ENSP00000445966:S10F;ENSP00000416463:S10F	ENSP00000293062:S10F	S	-	2	0	RASGRP4	43604628	1.000000	0.71417	1.000000	0.80357	0.625000	0.37756	3.129000	0.50500	2.284000	0.76573	0.462000	0.41574	TCC	.	.		0.602	RASGRP4-013	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460540.1	NM_170604		A	38912788	G	A	38912788	3	1	269	1	0	0	0	0	1	0	0	0	13092	1174	41	3	2056	3	RASGRP4	19	38912788	Missense_Mutation	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	4225244	38912788	20216195	105	39266										
CYP2A7	1549	hgsc.bcm.edu	37	chr19	41387953	41387953	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	caccttcatgatggagtcacAtatgtgctctgtgttcagct	9	10	4	1			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr19:41387953A>T	ENST00000301146.4	-	1	704	c.163T>A	c.(163-165)Tgt>Agt	p.C55S	CTC-490E21.12_ENST00000601627.1_Intron|CYP2A7_ENST00000291764.3_Missense_Mutation_p.C55S	NM_000764.2	NP_000755.2	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 7	55						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			ATGGAGTCACATATGTGCTCT	0.592																																					p.C55S		Atlas-SNP	.											.	CYP2A7	71	.	0			c.T163A						.						90	68	76					19																	41387953		2203	4300	6503	SO:0001583	missense	1549	exon1			AGTCACATATGTG	NM_000764	CCDS12569.1, CCDS42570.1	19q13.2	2013-07-25	2003-01-14		ENSG00000198077	ENSG00000198077		"Cytochrome P450s"	2611	protein-coding gene	gene with protein product		608054	"cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 7"			7668294, 15128046	Standard	NM_030589		Approved	CYP2A	uc002opm.3	P20853	OTTHUMG00000182715	ENST00000301146.4:c.163T>A	chr19.hg19:g.41387953A>T	ENSP00000301146:p.Cys55Ser	264.0	0.0		290.0	131.0	NM_000764	Q13121	Missense_Mutation	SNP	ENST00000301146.4	hg19	CCDS12569.1	.	.	.	.	.	.	.	.	.	.	A	5.616	0.298363	0.10622	.	.	ENSG00000198077	ENST00000301146;ENST00000291764	T;T	0.11604	5.13;2.76	2.33	2.33	0.28932	.	0.372378	0.27358	U	0.019728	T	0.04679	0.0127	N	0.04746	-0.17	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.09377	0.002;0.004	T	0.41875	-0.9484	10	0.21014	T	0.42	.	9.3499	0.38131	1.0:0.0:0.0:0.0	.	55;55	F8W816;P20853	.;CP2A7_HUMAN	S	55	ENSP00000301146:C55S;ENSP00000291764:C55S	ENSP00000291764:C55S	C	-	1	0	CYP2A7	46079793	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	0.930000	0.28858	1.072000	0.40860	0.155000	0.16302	TGT	.	.		0.592	CYP2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463269.2	NM_030589		T	41387953	A	T	41387953	3	4	269	1	0	0	0	0	1	0	0	0	4165	217	8	4	1367	4	CYP2A7	19	41387953	Missense_Mutation	SNP	A	TCGA-FV-A496-01A-11D-A25V-10	2475165	41387953	17741030	106	39267										
CABP5	56344	hgsc.bcm.edu	37	chr19	48543934	48543934	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	gtaacccatcgtcctcatgaGattccccagatccttacaag	6	14	1	2			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr19:48543934G>C	ENST00000293255.2	-	3	296	c.166C>G	c.(166-168)Ctc>Gtc	p.L56V		NM_019855.4	NP_062829.1	Q9NP86	CABP5_HUMAN	calcium binding protein 5	56	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				signal transduction (GO:0007165)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(3)|lung(3)|prostate(2)|skin(2)	11		all_cancers(25;1.86e-08)|all_lung(116;1.14e-06)|all_epithelial(76;1.16e-06)|Lung NSC(112;2.54e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;4.09e-05)|all cancers(93;0.000322)|Epithelial(262;0.01)|GBM - Glioblastoma multiforme(486;0.058)		GTCCTCATGAGATTCCCCAGA	0.517																																					p.L56V		Atlas-SNP	.											.	CABP5	28	.	0			c.C166G						.						125	106	112					19																	48543934		2203	4300	6503	SO:0001583	missense	56344	exon3			TCATGAGATTCCC	AF169159	CCDS12709.1	19q13.33	2014-08-12			ENSG00000105507	ENSG00000105507		"EF-hand domain containing"	13714	protein-coding gene	gene with protein product		607315	"calcium binding protein 3"	CABP3		10625670	Standard	NM_019855		Approved	CaBP3	uc002phu.2	Q9NP86	OTTHUMG00000183139	ENST00000293255.2:c.166C>G	chr19.hg19:g.48543934G>C	ENSP00000293255:p.Leu56Val	148.0	0.0		240.0	30.0	NM_019855	A0AUY4	Missense_Mutation	SNP	ENST00000293255.2	hg19	CCDS12709.1	.	.	.	.	.	.	.	.	.	.	G	8.758	0.922908	0.18056	.	.	ENSG00000105507	ENST00000293255	T	0.64618	-0.11	4.4	4.4	0.53042	EF-hand-like domain (1);	0.000000	0.64402	D	0.000001	T	0.34077	0.0885	N	0.04508	-0.205	0.40675	D	0.982254	B	0.21071	0.051	B	0.29077	0.098	T	0.32613	-0.9900	10	0.02654	T	1	-17.8162	8.9843	0.35983	0.1046:0.0:0.8954:0.0	.	56	Q9NP86	CABP5_HUMAN	V	56	ENSP00000293255:L56V	ENSP00000293255:L56V	L	-	1	0	CABP5	53235746	0.947000	0.32204	1.000000	0.80357	0.994000	0.84299	0.921000	0.28718	2.403000	0.81681	0.549000	0.68633	CTC	.	.		0.517	CABP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465212.1	NM_019855		C	48543934	G	C	48543934	3	2	269	1	0	0	0	0	1	0	0	0	2536	942	33	4	371	4	CABP5	19	48543934	Missense_Mutation	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	7155981	48543934	10585049	107	39268										
ZNF776	284309	hgsc.bcm.edu	37	chr19	58264871	58264871	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	catatgaaaaaaaattggatGacgatgcaaaccatcatcaa	6	7	2	2			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr19:58264871G>A	ENST00000317178.5	+	3	636	c.373G>A	c.(373-375)Gac>Aac	p.D125N	AC003006.7_ENST00000594684.1_Missense_Mutation_p.D125N	NM_173632.3	NP_775903.3	Q68DI1	ZN776_HUMAN	zinc finger protein 776	125					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(2)|kidney(13)|large_intestine(3)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	31		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0256)		AAAATTGGATGACGATGCAAA	0.428																																					p.D125N		Atlas-SNP	.											.	ZNF776	115	.	0			c.G373A						.						90	84	86					19																	58264871		2203	4300	6503	SO:0001583	missense	284309	exon3			TTGGATGACGATG	AK095607	CCDS12962.2	19q13.43	2013-01-08			ENSG00000152443	ENSG00000152443		"Zinc fingers, C2H2-type", "-"	26765	protein-coding gene	gene with protein product							Standard	NM_173632		Approved	FLJ38288		Q68DI1	OTTHUMG00000156943	ENST00000317178.5:c.373G>A	chr19.hg19:g.58264871G>A	ENSP00000321812:p.Asp125Asn	84.0	0.0		106.0	20.0	NM_173632	Q6ZS36|Q8N968	Missense_Mutation	SNP	ENST00000317178.5	hg19	CCDS12962.2	.	.	.	.	.	.	.	.	.	.	G	5.507	0.278589	0.10403	.	.	ENSG00000152443	ENST00000317178	T	0.06768	3.26	1.5	-2.99	0.05497	.	.	.	.	.	T	0.05364	0.0142	L	0.52573	1.65	0.09310	N	1	P;B	0.46020	0.871;0.43	B;B	0.34180	0.177;0.065	T	0.34527	-0.9825	9	0.23302	T	0.38	.	5.0607	0.14555	0.0:0.1443:0.3998:0.4559	.	125;125	Q68DI1;B4DSC6	ZN776_HUMAN;.	N	125	ENSP00000321812:D125N	ENSP00000321812:D125N	D	+	1	0	ZNF776	62956683	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-3.658000	0.00401	-0.759000	0.04684	0.313000	0.20887	GAC	.	.		0.428	ZNF776-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346722.2	NM_173632		A	58264871	G	A	58264871	3	1	269	1	0	0	0	0	1	0	0	0	18164	1290	45	3	383	3	ZNF776	19	58264871	Missense_Mutation	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	9720937	58264871	864112	108	39269										
ZNF776	284309	hgsc.bcm.edu	37	chr19	58265306	58265306	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	cttatcagtgtggacaatgtGatgaatcattttggtataag	10	4	2	2			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr19:58265306G>A	ENST00000317178.5	+	3	1071	c.808G>A	c.(808-810)Gat>Aat	p.D270N		NM_173632.3	NP_775903.3	Q68DI1	ZN776_HUMAN	zinc finger protein 776	270					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(2)|kidney(13)|large_intestine(3)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	31		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0256)		TGGACAATGTGATGAATCATT	0.388																																					p.D270N		Atlas-SNP	.											.	ZNF776	115	.	0			c.G808A						.						91	83	85					19																	58265306		2203	4300	6503	SO:0001583	missense	284309	exon3			CAATGTGATGAAT	AK095607	CCDS12962.2	19q13.43	2013-01-08			ENSG00000152443	ENSG00000152443		"Zinc fingers, C2H2-type", "-"	26765	protein-coding gene	gene with protein product							Standard	NM_173632		Approved	FLJ38288		Q68DI1	OTTHUMG00000156943	ENST00000317178.5:c.808G>A	chr19.hg19:g.58265306G>A	ENSP00000321812:p.Asp270Asn	68.0	0.0		82.0	10.0	NM_173632	Q6ZS36|Q8N968	Missense_Mutation	SNP	ENST00000317178.5	hg19	CCDS12962.2	.	.	.	.	.	.	.	.	.	.	G	28.6	4.935238	0.92458	.	.	ENSG00000152443	ENST00000317178	T	0.04083	3.71	1.79	1.79	0.24919	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06462	0.0166	L	0.41027	1.25	0.80722	D	1	P;P	0.44429	0.835;0.811	P;B	0.44732	0.459;0.313	T	0.38757	-0.9646	9	0.72032	D	0.01	.	10.5453	0.45056	0.0:0.0:1.0:0.0	.	270;270	Q68DI1;B4DSC6	ZN776_HUMAN;.	N	270	ENSP00000321812:D270N	ENSP00000321812:D270N	D	+	1	0	ZNF776	62957118	1.000000	0.71417	0.020000	0.16555	0.900000	0.52787	4.772000	0.62324	0.992000	0.38840	0.305000	0.20034	GAT	.	.		0.388	ZNF776-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346722.2	NM_173632		A	58265306	G	A	58265306	3	1	269	1	0	0	0	0	1	0	0	0	18164	1290	45	3	818	3	ZNF776	19	58265306	Missense_Mutation	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	435	58265306	863677	109	39270										
HSPA12B	116835	hgsc.bcm.edu	37	chr20	3728929	3728929	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	ctggagcccgaggccgcctcGgtatactgccgcaagctgcg	14	15	0	0			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr20:3728929G>A	ENST00000254963.2	+	8	886	c.741G>A	c.(739-741)tcG>tcA	p.S247S	HSPA12B_ENST00000542646.1_Silent_p.S81S	NM_001197327.1|NM_052970.4	NP_001184256.1|NP_443202.3	Q96MM6	HS12B_HUMAN	heat shock 70kD protein 12B	247							ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	14						AGGCCGCCTCGGTATACTGCC	0.682																																					p.S247S		Atlas-SNP	.											.	HSPA12B	43	.	0			c.G741A						.						57	53	55					20																	3728929		2203	4300	6503	SO:0001819	synonymous_variant	116835	exon8			CGCCTCGGTATAC	AK056712	CCDS13061.1	20p13	2011-09-02	2003-04-10	2003-04-10	ENSG00000132622	ENSG00000132622		"Heat shock proteins / HSP70"	16193	protein-coding gene	gene with protein product		610702	"chromosome 20 open reading frame 60"	C20orf60		12552099	Standard	NM_052970		Approved	dJ1009E24.2	uc002wjd.3	Q96MM6	OTTHUMG00000031755	ENST00000254963.2:c.741G>A	chr20.hg19:g.3728929G>A		78.0	0.0		83.0	17.0	NM_052970	D3DVX7|Q2TAK3|Q9BR52	Silent	SNP	ENST00000254963.2	hg19	CCDS13061.1																																																																																			.	.		0.682	HSPA12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077756.2	NM_052970		A	3728929	G	A	3728929	2	1	269	1	0	0	0	0	0	0	0	1	7414	1103	39	1		1	HSPA12B	20	3728929	Silent	SNP	G	TCGA-FV-A496-01A-11D-A25V-10		3728929	59296591	110	39271										
RBM12	10137	hgsc.bcm.edu	37	chr20	34241969	34241969	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	aacacaaaaaccagcctcatGtggtgatcttgaccttgatc	7	11	2	3			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr20:34241969G>T	ENST00000374114.3	-	3	1539	c.1276C>A	c.(1276-1278)Cat>Aat	p.H426N	CPNE1_ENST00000317677.5_5'Flank|CPNE1_ENST00000397442.1_Intron|CPNE1_ENST00000317619.3_Intron|RBM12_ENST00000374104.3_Missense_Mutation_p.H426N|CPNE1_ENST00000397446.1_Intron|CPNE1_ENST00000397445.1_Intron|RP1-309K20.6_ENST00000541176.2_Intron|CPNE1_ENST00000397443.1_Intron|RBM12_ENST00000359646.1_Missense_Mutation_p.H426N|CPNE1_ENST00000352393.4_Intron	NM_001198838.1|NM_001198840.1|NM_006047.5	NP_001185767.1|NP_001185769.1|NP_006038.2	Q9NTZ6	RBM12_HUMAN	RNA binding motif protein 12	426						nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(7)|kidney(1)|large_intestine(3)|lung(14)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			CCAGCCTCATGTGGTGATCTT	0.423											OREG0004044	type=REGULATORY REGION|Gene=CPNE1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.H426N		Atlas-SNP	.											.	RBM12	93	.	0			c.C1276A						.						82	88	86					20																	34241969		2203	4300	6503	SO:0001583	missense	10137	exon2			CCTCATGTGGTGA	AJ289772	CCDS13261.1	20q11.21	2013-02-12			ENSG00000244462	ENSG00000244462		"RNA binding motif (RRM) containing"	9898	protein-coding gene	gene with protein product		607179				11435693	Standard	NM_006047		Approved	HRIHFB2091, KIAA0765, SWAN	uc021wcq.1	Q9NTZ6	OTTHUMG00000032350	ENST00000374114.3:c.1276C>A	chr20.hg19:g.34241969G>T	ENSP00000363228:p.His426Asn	75.0	0.0	846	77.0	4.0	NM_001198840	B3KRU2|E1P5R6|O94865|Q8N3B1|Q9H196	Missense_Mutation	SNP	ENST00000374114.3	hg19	CCDS13261.1	.	.	.	.	.	.	.	.	.	.	G	15.02	2.708023	0.48412	.	.	ENSG00000244462	ENST00000374114;ENST00000359646;ENST00000374104;ENST00000349942	T;T;T	0.14516	2.5;2.5;2.5	4.77	3.83	0.44106	.	0.066271	0.64402	D	0.000012	T	0.15609	0.0376	L	0.55481	1.735	0.80722	D	1	B	0.12013	0.005	B	0.19666	0.026	T	0.03157	-1.1066	10	0.40728	T	0.16	-0.7006	13.2267	0.59919	0.0764:0.0:0.9236:0.0	.	426	Q9NTZ6	RBM12_HUMAN	N	426;426;426;225	ENSP00000363228:H426N;ENSP00000352668:H426N;ENSP00000363217:H426N	ENSP00000339879:H225N	H	-	1	0	RBM12	33705383	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	7.390000	0.79816	1.251000	0.43983	0.549000	0.68633	CAT	.	.		0.423	RBM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078894.1	NM_006047		T	34241969	G	T	34241969	3	4	269	1	0	0	0	0	1	0	0	0	13128	1377	48	3	1526	3	RBM12	20	34241969	Missense_Mutation	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	30513040	34241969	28783551	111	39272										
TGIF2	60436	hgsc.bcm.edu	37	chr20	35219383	35219383	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	tcggaaggatggcaaagaccCtaatcagtttaccatttccc	8	11	1	1			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr20:35219383C>T	ENST00000373874.2	+	3	462	c.263C>T	c.(262-264)cCt>cTt	p.P88L	RP5-977B1.11_ENST00000561134.1_RNA|TGIF2_ENST00000373872.4_Missense_Mutation_p.P88L|TGIF2-C20orf24_ENST00000558530.1_Intron	NM_001199514.1|NM_001199515.1	NP_001186443.1|NP_001186444.1	Q9GZN2	TGIF2_HUMAN	TGFB-induced factor homeobox 2	88					gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nodal signaling pathway (GO:0038092)|positive regulation of neuron differentiation (GO:0045666)|regulation of gastrulation (GO:0010470)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(3)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	14	Breast(12;0.114)	Myeloproliferative disorder(115;0.00878)				GGCAAAGACCCTAATCAGTTT	0.567																																					p.P88L		Atlas-SNP	.											.	TGIF2	26	.	0			c.C263T						.						117	132	127					20																	35219383		2203	4300	6503	SO:0001583	missense	60436	exon3			AAGACCCTAATCA	AB042646	CCDS13278.1	20q11.23	2012-12-12	2007-02-07		ENSG00000118707	ENSG00000118707		"Homeoboxes / TALE class"	15764	protein-coding gene	gene with protein product		607294	"TGFB-induced factor 2 (TALE family homeobox)"			11006116	Standard	NM_021809		Approved		uc021wcv.1	Q9GZN2	OTTHUMG00000172332	ENST00000373874.2:c.263C>T	chr20.hg19:g.35219383C>T	ENSP00000362981:p.Pro88Leu	86.0	0.0		97.0	47.0	NM_021809	B2R9U3|E1P5T9|H0YNI0	Missense_Mutation	SNP	ENST00000373874.2	hg19	CCDS13278.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.458391	0.84317	.	.	ENSG00000118707	ENST00000373874;ENST00000373872	D;D	0.83250	-1.7;-1.7	5.71	4.74	0.60224	Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.89125	0.6626	L	0.58583	1.82	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.89794	0.3970	10	0.62326	D	0.03	-17.9974	14.9153	0.70792	0.144:0.856:0.0:0.0	.	88	Q9GZN2	TGIF2_HUMAN	L	88	ENSP00000362981:P88L;ENSP00000362979:P88L	ENSP00000362979:P88L	P	+	2	0	TGIF2	34652797	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.440000	0.80464	1.348000	0.45733	0.561000	0.74099	CCT	.	.		0.567	TGIF2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079004.2	NM_021809		T	35219383	C	T	35219383	3	4	269	1	0	0	0	0	1	0	0	0	15841	681	24	3	269	3	TGIF2	20	35219383	Missense_Mutation	SNP	C	TCGA-FV-A496-01A-11D-A25V-10	977414	35219383	27806137	112	39273										
DNAJC28	54943	hgsc.bcm.edu	37	chr21	34861366	34861366	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	cttcacctttactctgactgGcatttgtttgttctatcaca	5	11	4	1			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr21:34861366G>T	ENST00000314399.3	-	2	773	c.335C>A	c.(334-336)gCc>gAc	p.A112D	DNAJC28_ENST00000402202.1_Missense_Mutation_p.A112D|DNAJC28_ENST00000381947.3_Missense_Mutation_p.A112D	NM_017833.3	NP_060303.2	Q9NX36	DJC28_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 28	112	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.									endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(5)|skin(1)|urinary_tract(1)	18						ACTCTGACTGGCATTTGTTTG	0.363																																					p.A112D		Atlas-SNP	.											.	DNAJC28	47	.	0			c.C335A						.						120	107	111					21																	34861366		2203	4300	6503	SO:0001583	missense	54943	exon2			TGACTGGCATTTG	AK000468	CCDS13626.1	21q22.11	2011-09-02	2008-06-17	2008-06-17	ENSG00000177692	ENSG00000177692		"Heat shock proteins / DNAJ (HSP40)"	1297	protein-coding gene	gene with protein product	"Orf28"		"chromosome 21 open reading frame 55"	C21orf55			Standard	NM_017833		Approved	C21orf78	uc002yrw.3	Q9NX36	OTTHUMG00000065531	ENST00000314399.3:c.335C>A	chr21.hg19:g.34861366G>T	ENSP00000320303:p.Ala112Asp	96.0	0.0		81.0	4.0	NM_001040192	D3DSF2	Missense_Mutation	SNP	ENST00000314399.3	hg19	CCDS13626.1	.	.	.	.	.	.	.	.	.	.	G	4.123	0.020985	0.08006	.	.	ENSG00000177692	ENST00000381947;ENST00000314399;ENST00000402202	.	.	.	5.38	-0.142	0.13448	.	0.610436	0.17181	N	0.183892	T	0.14313	0.0346	N	0.14661	0.345	0.09310	N	1	B	0.30763	0.294	B	0.27887	0.084	T	0.19811	-1.0294	9	0.13108	T	0.6	-0.1273	3.7087	0.08411	0.0778:0.2096:0.3908:0.3218	.	112	Q9NX36	DJC28_HUMAN	D	112	.	ENSP00000320303:A112D	A	-	2	0	DNAJC28	33783236	0.000000	0.05858	0.010000	0.14722	0.220000	0.24768	0.577000	0.23758	0.236000	0.21180	-0.136000	0.14681	GCC	.	.		0.363	DNAJC28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140454.3			T	34861366	G	T	34861366	3	4	269	1	0	0	0	0	1	0	0	0	4648	1203	42	3	835	3	DNAJC28	21	34861366	Missense_Mutation	SNP	G	TCGA-FV-A496-01A-11D-A25V-10		34861366	13268529	113	39274										
UFD1L	7353	hgsc.bcm.edu	37	chr22	19463069	19463069	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	gagaagcagcggtactgtgtGgagaagcggttttggaagac	17	5	0	3			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr22:19463069G>C	ENST00000263202.10	-	2	189	c.60C>G	c.(58-60)tcC>tcG	p.S20S	UFD1L_ENST00000399523.1_Silent_p.S20S|UFD1L_ENST00000484101.1_5'UTR|UFD1L_ENST00000360834.4_Silent_p.S20S	NM_001035247.2|NM_005659.6	NP_001030324.2|NP_005650.2	Q92890	UFD1_HUMAN	ubiquitin fusion degradation 1 like (yeast)	20					proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|skeletal system development (GO:0001501)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			large_intestine(3)|upper_aerodigestive_tract(1)	4	Colorectal(54;0.0993)					GGTACTGTGTGGAGAAGCGGT	0.438																																					p.S20S		Atlas-SNP	.											.	UFD1L	25	.	0			c.C60G						.						137	124	129					22																	19463069		2203	4300	6503	SO:0001819	synonymous_variant	7353	exon2			CTGTGTGGAGAAG	AJ239058	CCDS13761.1, CCDS33600.1, CCDS33600.2	22q11.2	2014-05-02	2005-10-10		ENSG00000070010	ENSG00000070010			12520	protein-coding gene	gene with protein product		601754	"ubiquitin fusion degradation 1-like"			9063746	Standard	NM_005659		Approved	UFD1	uc002zpm.2	Q92890	OTTHUMG00000150130	ENST00000263202.10:c.60C>G	chr22.hg19:g.19463069G>C		117.0	0.0		137.0	22.0	NM_005659	A8MW31|Q9Y5N0	Silent	SNP	ENST00000263202.10	hg19	CCDS13761.1																																																																																			.	.		0.438	UFD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316460.6			C	19463069	G	C	19463069	2	2	269	1	0	0	0	0	0	0	0	1	16950	1335	47	4		4	UFD1L	22	19463069	Silent	SNP	G	TCGA-FV-A496-01A-11D-A25V-10		19463069	31841497	114	39275										
RFPL3	10738	hgsc.bcm.edu	37	chr22	32756294	32756294	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	ttcctcctcatttctgacgaCctcaggagcgtccgaagtgg	10	13	3	1			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr22:32756294C>A	ENST00000249007.4	+	2	634	c.429C>A	c.(427-429)gaC>gaA	p.D143E	RFPL3_ENST00000397468.1_Missense_Mutation_p.D114E|RFPL3_ENST00000382088.3_Missense_Mutation_p.D114E|RFPL3S_ENST00000382084.4_3'UTR|RFPL3S_ENST00000461833.1_5'Flank|RFPL3S_ENST00000400234.1_3'UTR	NM_001098535.1	NP_001092005.1	O75679	RFPL3_HUMAN	ret finger protein-like 3	143	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.						zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|stomach(1)	15						TTTCTGACGACCTCAGGAGCG	0.522																																					p.D143E		Atlas-SNP	.											.	RFPL3	91	.	0			c.C429A						.						131	118	123					22																	32756294		2203	4300	6503	SO:0001583	missense	10738	exon2			TGACGACCTCAGG	AJ010232	CCDS13904.1, CCDS43011.1	22q12	2006-04-25			ENSG00000128276	ENSG00000128276			9980	protein-coding gene	gene with protein product		605970				10508838	Standard	NM_006604		Approved		uc010gwn.3	O75679	OTTHUMG00000030290	ENST00000249007.4:c.429C>A	chr22.hg19:g.32756294C>A	ENSP00000249007:p.Asp143Glu	288.0	0.0		348.0	81.0	NM_001098535	A2A279|Q6IC03|Q6IC04|Q6NSX3|Q8N5R4	Missense_Mutation	SNP	ENST00000249007.4	hg19	CCDS43011.1	.	.	.	.	.	.	.	.	.	.	C	12.72	2.023273	0.35701	.	.	ENSG00000128276	ENST00000397468;ENST00000249007;ENST00000382088	T;T;T	0.18016	2.24;2.24;2.24	0.664	0.664	0.17890	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	.	.	.	.	T	0.35335	0.0928	M	0.79475	2.455	0.51233	D	0.999911	D	0.71674	0.998	D	0.69479	0.964	T	0.18808	-1.0325	9	0.87932	D	0	.	7.1611	0.25664	0.0:0.9999:0.0:1.0E-4	.	143	O75679	RFPL3_HUMAN	E	114;143;114	ENSP00000380609:D114E;ENSP00000249007:D143E;ENSP00000371520:D114E	ENSP00000249007:D143E	D	+	3	2	RFPL3	31086294	0.003000	0.15002	0.119000	0.21687	0.033000	0.12548	-0.268000	0.08607	0.624000	0.30286	0.194000	0.17425	GAC	.	.		0.522	RFPL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075172.3	NM_006604		A	32756294	C	A	32756294	3	1	269	1	0	0	0	0	1	0	0	0	13270	506	18	3	435	3	RFPL3	22	32756294	Missense_Mutation	SNP	C	TCGA-FV-A496-01A-11D-A25V-10	13293225	32756294	18548272	115	39276										
FBLN1	2192	hgsc.bcm.edu	37	chr22	45939311	45939311	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	gtgccagcgctaccccgggcGcctgtgtggccacaagtgcg	15	15	0	0			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chr22:45939311G>A	ENST00000327858.6	+	11	1321	c.1226G>A	c.(1225-1227)cGc>cAc	p.R409H	FBLN1_ENST00000402984.3_Missense_Mutation_p.R447H|FBLN1_ENST00000442170.2_Missense_Mutation_p.R409H|FBLN1_ENST00000348697.2_Missense_Mutation_p.R409H|FBLN1_ENST00000476366.1_3'UTR|FBLN1_ENST00000340923.5_Missense_Mutation_p.R409H|FBLN1_ENST00000262722.7_Missense_Mutation_p.R409H	NM_006486.2	NP_006477	P23142	FBLN1_HUMAN	fibulin 1	409	EGF-like 6; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.|Self-association and FN1-binding; calcium is necessary for homotypic binding, but not for heterotypic binding.				embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|viral process (GO:0016032)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)|peptidase activator activity (GO:0016504)			biliary_tract(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)	30		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		TACCCCGGGCGCCTGTGTGGC	0.607																																					p.R409H		Atlas-SNP	.											.	FBLN1	143	.	0			c.G1226A						.						59	51	54					22																	45939311		2203	4300	6503	SO:0001583	missense	2192	exon11			CCGGGCGCCTGTG		CCDS14067.1, CCDS14068.1, CCDS14069.1, CCDS43028.1	22q13.31	2010-06-15			ENSG00000077942	ENSG00000077942		"Fibulins"	3600	protein-coding gene	gene with protein product		135820				2269669, 1400330	Standard	NM_006485		Approved	FBLN	uc003bgj.1	P23142	OTTHUMG00000151340	ENST00000327858.6:c.1226G>A	chr22.hg19:g.45939311G>A	ENSP00000331544:p.Arg409His	35.0	0.0		50.0	24.0	NM_006487	B0QY42|B1AHL4|P23143|P23144|P37888|Q5TIC4|Q8TBH8|Q9HBQ5|Q9UC21|Q9UGR4|Q9UH41	Missense_Mutation	SNP	ENST00000327858.6	hg19	CCDS14067.1	.	.	.	.	.	.	.	.	.	.	G	18.11	3.551577	0.65311	.	.	ENSG00000077942	ENST00000348697;ENST00000402984;ENST00000262722;ENST00000327858;ENST00000442170;ENST00000340923	D;D;D;D;D;D	0.86030	-1.63;-2.06;-1.93;-1.75;-1.7;-1.61	5.13	5.13	0.70059	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	T	0.70228	0.3200	N	0.03917	-0.325	0.80722	D	1	P;B;B;P	0.41214	0.742;0.269;0.362;0.727	B;B;B;B	0.35353	0.139;0.042;0.091;0.201	T	0.77422	-0.2594	10	0.54805	T	0.06	.	18.5383	0.91018	0.0:0.0:1.0:0.0	.	447;409;409;409	B1AHL2;P23142;B1AHL4;P23142-4	.;FBLN1_HUMAN;.;.	H	409;447;409;409;409;409	ENSP00000262723:R409H;ENSP00000385521:R447H;ENSP00000262722:R409H;ENSP00000331544:R409H;ENSP00000393812:R409H;ENSP00000342212:R409H	ENSP00000262722:R409H	R	+	2	0	FBLN1	44317975	1.000000	0.71417	1.000000	0.80357	0.587000	0.36485	6.455000	0.73497	2.539000	0.85634	0.563000	0.77884	CGC	.	.		0.607	FBLN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322287.1	NM_006486		A	45939311	G	A	45939311	3	1	269	1	0	0	0	0	1	0	0	0	5706	1087	38	1	1268	1	FBLN1	22	45939311	Missense_Mutation	SNP	G	TCGA-FV-A496-01A-11D-A25V-10	13183017	45939311	5365255	116	39277										
CYLC1	1538	hgsc.bcm.edu	37	chrX	83128349	83128349	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	aattccaagaagacaaacacTgaattcctacatacaaagaa	4	9	0	4			TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chrX:83128349T>A	ENST00000329312.4	+	4	670	c.633T>A	c.(631-633)acT>acA	p.T211T		NM_021118.1	NP_066941.1	P35663	CYLC1_HUMAN	cylicin, basic protein of sperm head cytoskeleton 1	211					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	acrosomal matrix (GO:0043159)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	58						AGACAAACACTGAATTCCTAC	0.313																																					p.T211T		Atlas-SNP	.											.	CYLC1	272	.	0			c.T633A						.						25	24	24					X																	83128349		2191	4278	6469	SO:0001819	synonymous_variant	1538	exon4			AAACACTGAATTC	Z22780	CCDS35341.1, CCDS75998.1	Xq21.1	2008-07-31			ENSG00000183035	ENSG00000183035			2582	protein-coding gene	gene with protein product	"cylicin 1"	300768				7737358, 8354692	Standard	NM_021118		Approved		uc004eei.2	P35663	OTTHUMG00000021922	ENST00000329312.4:c.633T>A	chrX.hg19:g.83128349T>A		84.0	0.0		64.0	28.0	NM_021118	A0AVQ8|Q5JQQ9	Silent	SNP	ENST00000329312.4	hg19	CCDS35341.1																																																																																			.	.		0.313	CYLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057371.1	NM_021118		A	83128349	T	A	83128349	2	1	269	1	0	0	0	0	0	0	0	1	4143	1567	55	4		4	CYLC1	23	83128349	Silent	SNP	T	TCGA-FV-A496-01A-11D-A25V-10		83128349	72142211	117	39278										
CAPN6	827	hgsc.bcm.edu	37	chrX	110497516	110497516	+	Frame_Shift_Del	DEL	T	T	-													0.0683760683760684	8	1	1.06297476108797	1.56493506493506	0.96030106257379	0.193027325346615	0.751940625889747	0	atacctttgtccaatgagacTcctgaacagccaaacaggaa							TCGA-FV-A496-01A-11D-A25V-10	TCGA-FV-A496-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6ad1a2-f1eb-44d1-9852-f5752afcf5eb	b736880f-ab1f-41fa-8776-38421620f821	g.chrX:110497516delT	ENST00000324068.1	-	3	448	c.281delA	c.(280-282)gagfs	p.E94fs	CAPN6_ENST00000541758.1_5'UTR	NM_014289.3	NP_055104.2	Q9Y6Q1	CAN6_HUMAN	calpain 6	94	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				microtubule bundle formation (GO:0001578)|proteolysis (GO:0006508)|regulation of cytoskeleton organization (GO:0051493)	perinuclear region of cytoplasm (GO:0048471)|spindle microtubule (GO:0005876)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|microtubule binding (GO:0008017)			cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(25)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	47						CCAATGAGACTCCTGAACAGC	0.453																																					p.E94fs		Atlas-Indel,Pindel	.											.	CAPN6	120	.	0			c.282delG						.						147	124	132					X																	110497516		2203	4300	6503	SO:0001589	frameshift_variant	827	exon3			.	AF029232	CCDS14555.1	Xq23	2008-07-29			ENSG00000077274	ENSG00000077274			1483	protein-coding gene	gene with protein product		300146				9503024, 9339374	Standard	NM_014289		Approved	CAPNX, CalpM, CANPX	uc004epc.2	Q9Y6Q1	OTTHUMG00000022203	ENST00000324068.1:c.281delA	chrX.hg19:g.110497516delT	ENSP00000317214:p.Glu94fs	123.0	0.0		88.0	74.0	NM_014289	D3DUY7|Q9UEQ1|Q9UJA8	Frame_Shift_Del	DEL	ENST00000324068.1	hg19	CCDS14555.1																																																																																			.	.		0.453	CAPN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057922.1			-	110497516	T	-	110497516	7	5	269	1	0	1	0	1	0	0	0	0	2632	1551	54	0	1688	0	CAPN6	23	110497516	Frame_Shift_Del	DEL	T	TCGA-FV-A496-01A-11D-A25V-10	27369167	110497516	44773044	118	39279										
HBXIP	10542	hgsc.bcm.edu	37	chr1	110950487	110950487	+	5'Flank	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	ggtgacctgcacctggctccAtggcggaaccggccggcacg	15	15	0	1			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr1:110950487A>G	ENST00000602318.1	-	0	0				LAMTOR5-AS1_ENST00000608499.1_RNA|LAMTOR5_ENST00000602858.1_5'Flank|LAMTOR5-AS1_ENST00000598454.1_RNA|LAMTOR5-AS1_ENST00000608602.1_RNA|LAMTOR5-AS1_ENST00000609244.1_RNA|LAMTOR5_ENST00000256644.4_Start_Codon_SNP_p.M1T|LAMTOR5_ENST00000474861.2_5'Flank|LAMTOR5-AS1_ENST00000590826.1_RNA|LAMTOR5-AS1_ENST00000457535.1_RNA|LAMTOR5_ENST00000483260.1_5'Flank|LAMTOR5-AS1_ENST00000587691.1_RNA|LAMTOR5-AS1_ENST00000590413.1_RNA|LAMTOR5-AS1_ENST00000610148.1_RNA|LAMTOR5-AS1_ENST00000608486.1_RNA|LAMTOR5-AS1_ENST00000608253.1_RNA|LAMTOR5-AS1_ENST00000609709.1_RNA|LAMTOR5-AS1_ENST00000609512.1_RNA|LAMTOR5-AS1_ENST00000608067.1_RNA			O43504	LTOR5_HUMAN	late endosomal/lysosomal adaptor, MAPK and MTOR activator 5						cellular response to amino acid stimulus (GO:0071230)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of GTPase activity (GO:0043547)|positive regulation of TOR signaling (GO:0032008)|protein localization to lysosome (GO:0061462)|regulation of cell size (GO:0008361)|response to virus (GO:0009615)|viral genome replication (GO:0019079)	cytosol (GO:0005829)|lysosome (GO:0005764)|Ragulator complex (GO:0071986)											ACCTGGCTCCATGGCGGAACC	0.607																																					p.M1T		Atlas-SNP	.											.	.	.	.	0			c.T2C						.						23	24	24					1																	110950487		2202	4300	6502	SO:0001631	upstream_gene_variant	10542	exon1			GGCTCCATGGCGG	AF029890	CCDS824.1	1p12	2012-09-24	2012-09-24	2012-09-24	ENSG00000134248	ENSG00000134248			17955	protein-coding gene	gene with protein product	"HBx-interacting protein", "hepatitis B virus x-interacting protein (9.6kD)"	608521	"hepatitis B virus x interacting protein"	HBXIP		9499022, 22980980	Standard	NM_006402		Approved	XIP, MGC71071	uc001dzr.3	O43504	OTTHUMG00000011568		chr1.hg19:g.110950487A>G	Exception_encountered	137.0	0.0		132.0	28.0	NM_006402	Q6IBD8	Missense_Mutation	SNP	ENST00000602318.1	hg19		.	.	.	.	.	.	.	.	.	.	A	8.799	0.932524	0.18131	.	.	ENSG00000134248	ENST00000256644	.	.	.	2.79	-1.36	0.09085	.	.	.	.	.	T	0.25158	0.0611	.	.	.	0.40597	D	0.981544	.	.	.	.	.	.	T	0.23511	-1.0186	4	.	.	.	12.3757	2.9096	0.05732	0.2253:0.4913:0.0:0.2833	.	.	.	.	T	1	.	.	M	-	2	0	HBXIP	110752010	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.177000	0.03096	-0.282000	0.09128	-0.656000	0.03901	ATG	.	.		0.607	LAMTOR5-007	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467909.1	NM_006402		G	110950487	A	G	110950487	1	3	270	0	1	0	0	0	0	0	0	0	6997	217	8	2		2	HBXIP	1	110950487	5'Flank	SNP	A	TCGA-FV-A4ZP-01A-12D-A25V-10		110950487	138300134	1	39280										
SPAG17	200162	hgsc.bcm.edu	37	chr1	118629516	118629516	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	ttttctccctctctgagagaCagagtgagggcagaagggac	13	9	2	5			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr1:118629516C>A	ENST00000336338.5	-	11	1540	c.1475G>T	c.(1474-1476)tGt>tTt	p.C492F		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	492						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		CTCTGAGAGACAGAGTGAGGG	0.488																																					p.C492F		Atlas-SNP	.											SPAG17,colon,carcinoma,0,1	SPAG17	263	.	0			c.G1475T						.						130	124	126					1																	118629516		2203	4300	6503	SO:0001583	missense	200162	exon11			GAGAGACAGAGTG		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.1475G>T	chr1.hg19:g.118629516C>A	ENSP00000337804:p.Cys492Phe	177.0	0.0		125.0	25.0	NM_206996	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	hg19	CCDS899.1	.	.	.	.	.	.	.	.	.	.	C	17.91	3.503450	0.64298	.	.	ENSG00000155761	ENST00000336338	T	0.18960	2.18	5.32	5.32	0.75619	.	0.540233	0.21061	N	0.080831	T	0.33235	0.0856	M	0.73962	2.25	0.31059	N	0.714391	D	0.69078	0.997	D	0.66497	0.944	T	0.12268	-1.0554	10	0.54805	T	0.06	.	13.077	0.59093	0.0:0.7916:0.2084:0.0	.	492	Q6Q759	SPG17_HUMAN	F	492	ENSP00000337804:C492F	ENSP00000337804:C492F	C	-	2	0	SPAG17	118431039	0.998000	0.40836	0.998000	0.56505	0.976000	0.68499	1.903000	0.39858	2.655000	0.90218	0.655000	0.94253	TGT	.	.		0.488	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		A	118629516	C	A	118629516	3	1	270	1	0	0	0	0	1	0	0	0	14994	478	17	3	5348	3	SPAG17	1	118629516	Missense_Mutation	SNP	C	TCGA-FV-A4ZP-01A-12D-A25V-10	7679029	118629516	130621105	2	39281										
TARS2	80222	hgsc.bcm.edu	37	chr1	150461451	150461451	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	ctgctgaagttcaacactggCagatactgcagtggctgctc	11	11	1	2			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr1:150461451C>G	ENST00000369064.3	+	3	309	c.275C>G	c.(274-276)gCa>gGa	p.A92G	TARS2_ENST00000369054.2_Missense_Mutation_p.A92G|TARS2_ENST00000606933.1_Missense_Mutation_p.A92G|TARS2_ENST00000438568.2_Missense_Mutation_p.A92G	NM_025150.3	NP_079426.2	Q9BW92	SYTM_HUMAN	threonyl-tRNA synthetase 2, mitochondrial (putative)	92					gene expression (GO:0010467)|mitochondrial threonyl-tRNA aminoacylation (GO:0070159)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|threonine-tRNA ligase activity (GO:0004829)			cervix(1)|endometrium(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	35	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.51e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)		L-Threonine(DB00156)	TCAACACTGGCAGATACTGCA	0.453																																					p.A92G		Atlas-SNP	.											.	TARS2	91	.	0			c.C275G						.						134	146	142					1																	150461451		2203	4300	6503	SO:0001583	missense	80222	exon3			CACTGGCAGATAC	BC007824	CCDS952.1, CCDS60251.1, CCDS60252.1	1q21.2	2012-10-26	2007-02-23	2007-02-23	ENSG00000143374	ENSG00000143374	6.1.1.3	"Aminoacyl tRNA synthetases / Class II"	30740	protein-coding gene	gene with protein product	"threonine tRNA ligase 2, mitochondrial"	612805	"threonyl-tRNA synthetase-like 1"	TARSL1			Standard	NM_001271895		Approved	FLJ12528	uc001euq.4	Q9BW92	OTTHUMG00000012809	ENST00000369064.3:c.275C>G	chr1.hg19:g.150461451C>G	ENSP00000358060:p.Ala92Gly	72.0	0.0		101.0	17.0	NM_001271896	Q53GW7|Q96I50|Q9H9V2	Missense_Mutation	SNP	ENST00000369064.3	hg19	CCDS952.1	.	.	.	.	.	.	.	.	.	.	C	19.05	3.752192	0.69533	.	.	ENSG00000143374	ENST00000438568;ENST00000369054;ENST00000369064;ENST00000369053	.	.	.	5.05	5.05	0.67936	TGS-like (1);TGS (1);Beta-grasp fold, ferredoxin-type (1);	0.066074	0.64402	D	0.000011	T	0.73345	0.3575	M	0.78344	2.41	0.45634	D	0.998568	D;D	0.69078	0.995;0.997	D;D	0.65773	0.932;0.938	T	0.74396	-0.3679	8	.	.	.	0.9546	15.9261	0.79618	0.0:1.0:0.0:0.0	.	92;92	Q9H9V2;Q9BW92	.;SYTM_HUMAN	G	92	.	.	A	+	2	0	TARS2	148728075	0.998000	0.40836	1.000000	0.80357	0.908000	0.53690	4.021000	0.57196	2.614000	0.88457	0.555000	0.69702	GCA	.	.		0.453	TARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035847.1	NM_025150		G	150461451	C	G	150461451	3	3	270	1	0	0	0	0	1	0	0	0	15575	710	25	4	285	4	TARS2	1	150461451	Missense_Mutation	SNP	C	TCGA-FV-A4ZP-01A-12D-A25V-10	31831935	150461451	98789170	3	39282										
CRNN	49860	hgsc.bcm.edu	37	chr1	152382192	152382192	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	ggtatgcaagttgccctggtCcagcctgaggatcactgtct	12	11	2	1			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr1:152382192C>G	ENST00000271835.3	-	3	1428	c.1366G>C	c.(1366-1368)Gac>Cac	p.D456H	RP1-91G5.3_ENST00000411804.1_RNA	NM_016190.2	NP_057274.1	Q9UBG3	CRNN_HUMAN	cornulin	456					response to heat (GO:0009408)|single organismal cell-cell adhesion (GO:0016337)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(16)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			TTGCCCTGGTCCAGCCTGAGG	0.557																																					p.D456H		Atlas-SNP	.											.	CRNN	78	.	0			c.G1366C						.						190	146	161					1																	152382192		2203	4300	6503	SO:0001583	missense	49860	exon3			CCTGGTCCAGCCT	AF077831	CCDS1010.1	1q21	2014-01-28	2005-06-13	2005-06-13	ENSG00000143536	ENSG00000143536		"EF-hand domain containing"	1230	protein-coding gene	gene with protein product		611312	"chromosome 1 open reading frame 10"	C1orf10		11056050, 15854041	Standard	NM_016190		Approved	SEP53	uc001ezx.2	Q9UBG3	OTTHUMG00000012383	ENST00000271835.3:c.1366G>C	chr1.hg19:g.152382192C>G	ENSP00000271835:p.Asp456His	225.0	0.0		321.0	33.0	NM_016190	B2RE60|Q8N613	Missense_Mutation	SNP	ENST00000271835.3	hg19	CCDS1010.1	.	.	.	.	.	.	.	.	.	.	C	15.18	2.756006	0.49362	.	.	ENSG00000143536	ENST00000271835	T	0.18338	2.22	4.92	4.01	0.46588	.	0.365222	0.23528	N	0.047203	T	0.19927	0.0479	M	0.64170	1.965	0.23845	N	0.996686	D	0.71674	0.998	D	0.62955	0.909	T	0.03524	-1.1028	10	0.87932	D	0	.	9.3273	0.38001	0.0:0.9023:0.0:0.0977	.	456	Q9UBG3	CRNN_HUMAN	H	456	ENSP00000271835:D456H	ENSP00000271835:D456H	D	-	1	0	CRNN	150648816	0.006000	0.16342	0.068000	0.19968	0.005000	0.04900	0.880000	0.28159	1.282000	0.44496	0.650000	0.86243	GAC	.	.		0.557	CRNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034503.1	NM_016190		G	152382192	C	G	152382192	3	3	270	1	0	0	0	0	1	0	0	0	3894	855	30	4	125	4	CRNN	1	152382192	Missense_Mutation	SNP	C	TCGA-FV-A4ZP-01A-12D-A25V-10	1920741	152382192	96868429	4	39283										
ARHGEF2	9181	hgsc.bcm.edu	37	chr1	155935533	155935533	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	aggggtagatggccgagcttGgccgctcccggatggttgct	17	10	0	1			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr1:155935533G>C	ENST00000361247.4	-	5	458	c.359C>G	c.(358-360)cCa>cGa	p.P120R	ARHGEF2_ENST00000368315.4_Missense_Mutation_p.P121R|ARHGEF2_ENST00000462460.2_Missense_Mutation_p.P165R|ARHGEF2_ENST00000477754.2_Intron|ARHGEF2_ENST00000313695.7_Missense_Mutation_p.P93R|ARHGEF2_ENST00000368316.1_Missense_Mutation_p.P93R|ARHGEF2_ENST00000313667.4_Missense_Mutation_p.P120R	NM_001162383.1|NM_001162384.1	NP_001155855.1|NP_001155856.1	Q92974	ARHG2_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 2	120					actin filament organization (GO:0007015)|apoptotic signaling pathway (GO:0097190)|cell morphogenesis (GO:0000902)|cellular hyperosmotic response (GO:0071474)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to tumor necrosis factor (GO:0071356)|establishment of mitotic spindle orientation (GO:0000132)|innate immune response (GO:0045087)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress (GO:1902219)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of necroptotic process (GO:0060546)|negative regulation of neurogenesis (GO:0050768)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cell proliferation (GO:0042127)|regulation of Rho protein signal transduction (GO:0035023)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)|vesicle (GO:0031982)	microtubule binding (GO:0008017)|Rac GTPase binding (GO:0048365)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho GTPase binding (GO:0017048)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(4)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|skin(2)	40	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					GGCCGAGCTTGGCCGCTCCCG	0.622																																					p.P120R	Melanoma(178;35 2768 6610 28839)	Atlas-SNP	.											.	ARHGEF2	81	.	0			c.C359G						.						38	45	43					1																	155935533		2203	4300	6503	SO:0001583	missense	9181	exon5			GAGCTTGGCCGCT	AB014551	CCDS1125.1, CCDS53375.1, CCDS53376.1	1q21-q22	2013-01-10	2009-06-12		ENSG00000116584	ENSG00000116584		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	682	protein-coding gene	gene with protein product		607560	"rho/rac guanine nucleotide exchange factor (GEF) 2"			9857026, 9734811	Standard	NM_004723		Approved	LFP40, GEF-H1, KIAA0651, P40	uc001fmt.2	Q92974	OTTHUMG00000017464	ENST00000361247.4:c.359C>G	chr1.hg19:g.155935533G>C	ENSP00000354837:p.Pro120Arg	23.0	0.0		75.0	5.0	NM_001162383	D3DVA6|O75142|Q15079|Q5VY92|Q8TDA3|Q8WUG4|Q9H023	Missense_Mutation	SNP	ENST00000361247.4	hg19	CCDS53376.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.436471	0.83885	.	.	ENSG00000116584	ENST00000313695;ENST00000361247;ENST00000368315;ENST00000368316;ENST00000435736;ENST00000543433;ENST00000313667	T;T;T;T;T	0.68765	-0.35;-0.22;-0.24;-0.35;-0.35	4.97	4.97	0.65823	.	0.000000	0.47852	D	0.000213	T	0.78110	0.4232	M	0.74647	2.275	0.58432	D	0.999994	D;D;D;D	0.89917	0.998;0.969;1.0;0.993	D;P;D;D	0.91635	0.985;0.766;0.999;0.949	T	0.80353	-0.1418	10	0.72032	D	0.01	-29.5863	15.7654	0.78123	0.0:0.0:1.0:0.0	.	165;165;120;120	B7Z977;D3DVA5;Q92974;Q92974-2	.;.;ARHG2_HUMAN;.	R	93;120;121;93;165;93;120	ENSP00000315325:P93R;ENSP00000354837:P120R;ENSP00000357298:P121R;ENSP00000357299:P93R;ENSP00000314787:P120R	ENSP00000314787:P120R	P	-	2	0	ARHGEF2	154202157	1.000000	0.71417	0.972000	0.41901	0.912000	0.54170	9.382000	0.97209	2.596000	0.87737	0.561000	0.74099	CCA	.	.		0.622	ARHGEF2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046204.2	NM_004723		C	155935533	G	C	155935533	3	2	270	1	0	0	0	0	1	0	0	0	903	1348	47	4	2673	4	ARHGEF2	1	155935533	Missense_Mutation	SNP	G	TCGA-FV-A4ZP-01A-12D-A25V-10	3553341	155935533	93315088	5	39284										
C1orf110	339512	hgsc.bcm.edu	37	chr1	162824806	162824806	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	aatttgttttccagtgttccCatctggctttagagcaacat	7	9	1	1			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr1:162824806C>A	ENST00000367910.1	-	4	778	c.658G>T	c.(658-660)Ggg>Tgg	p.G220W	C1orf110_ENST00000524691.1_Intron|C1orf110_ENST00000367912.2_Intron|C1orf110_ENST00000367911.2_Intron	NM_178550.4	NP_848645.3	Q86UF4	CA110_HUMAN	chromosome 1 open reading frame 110	220										endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	12						CCAGTGTTCCCATCTGGCTTT	0.463																																					p.G220W		Atlas-SNP	.											.	C1orf110	22	.	0			c.G658T						.						165	153	157					1																	162824806		1951	4166	6117	SO:0001583	missense	339512	exon4			TGTTCCCATCTGG	BC040018	CCDS44269.1	1q23.3	2012-06-26			ENSG00000185860	ENSG00000185860			28736	protein-coding gene	gene with protein product						12477932	Standard	NM_178550		Approved	MGC48998	uc001gck.2	Q86UF4	OTTHUMG00000034421	ENST00000367910.1:c.658G>T	chr1.hg19:g.162824806C>A	ENSP00000356886:p.Gly220Trp	247.0	0.0		258.0	28.0	NM_178550	Q5JSG1|Q6ZW57	Missense_Mutation	SNP	ENST00000367910.1	hg19	CCDS44269.1	.	.	.	.	.	.	.	.	.	.	C	11.34	1.609365	0.28623	.	.	ENSG00000185860	ENST00000367910	.	.	.	4.09	-4.94	0.03057	.	1.631300	0.03254	N	0.182241	T	0.06962	0.0177	L	0.27053	0.805	0.32358	N	0.557544	B	0.09022	0.002	B	0.10450	0.005	T	0.16364	-1.0405	8	0.37606	T	0.19	2.7745	0.7306	0.00956	0.2174:0.182:0.1615:0.4392	.	220	Q86UF4	CA110_HUMAN	W	220	.	ENSP00000356886:G220W	G	-	1	0	C1orf110	161091430	0.001000	0.12720	0.000000	0.03702	0.009000	0.06853	0.775000	0.26689	-0.804000	0.04410	-0.181000	0.13052	GGG	.	.		0.463	C1orf110-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083211.2	NM_178550		A	162824806	C	A	162824806	3	1	270	1	0	0	0	0	1	0	0	0	1985	594	21	3	254	3	C1orf110	1	162824806	Missense_Mutation	SNP	C	TCGA-FV-A4ZP-01A-12D-A25V-10	6889273	162824806	86425815	6	39285										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181725193	181725193	+	Frame_Shift_Del	DEL	C	C	-													0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	cattatctgggccctgctgaCcctcttcaccgtctccacag							TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr1:181725193delC	ENST00000367573.2	+	29	4091	c.4091delC	c.(4090-4092)accfs	p.T1364fs	CACNA1E_ENST00000358338.5_Frame_Shift_Del_p.T1296fs|CACNA1E_ENST00000357570.5_Frame_Shift_Del_p.T1315fs|CACNA1E_ENST00000360108.3_Frame_Shift_Del_p.T1345fs|CACNA1E_ENST00000367570.1_Frame_Shift_Del_p.T1364fs|CACNA1E_ENST00000367567.4_Frame_Shift_Del_p.T971fs|CACNA1E_ENST00000526775.1_Frame_Shift_Del_p.T1345fs	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1364					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						GCCCTGCTGACCCTCTTCACC	0.522																																					p.T1364fs		Atlas-Indel,Pindel	.											.	CACNA1E	778	.	0			c.4090delA						.						68	70	69					1																	181725193		2053	4216	6269	SO:0001589	frameshift_variant	777	exon29			.	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.4091delC	chr1.hg19:g.181725193delC	ENSP00000356545:p.Thr1364fs	149.0	0.0		162.0	62.0	NM_000721	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Frame_Shift_Del	DEL	ENST00000367573.2	hg19	CCDS55664.1																																																																																			.	.		0.522	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		-	181725193	C	-	181725193	7	5	270	1	0	1	0	1	0	0	0	0	2544	507	18	0	4205	0	CACNA1E	1	181725193	Frame_Shift_Del	DEL	C	TCGA-FV-A4ZP-01A-12D-A25V-10	18900387	181725193	67525428	7	39286										
PKP1	5317	hgsc.bcm.edu	37	chr1	201291111	201291111	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	ctccttggtccccagtctgtGgaaaactgcatgtgtgttct	10	11	2	0	rs376484047		TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr1:201291111G>A	ENST00000352845.3	+	9	1416	c.1416G>A	c.(1414-1416)gtG>gtA	p.V472V	PKP1_ENST00000263946.3_Silent_p.V472V|PKP1_ENST00000367324.3_Silent_p.V451V			Q13835	PKP1_HUMAN	plakophilin 1	472					apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|intermediate filament bundle assembly (GO:0045110)|multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|lamin binding (GO:0005521)|signal transducer activity (GO:0004871)|structural constituent of epidermis (GO:0030280)			NS(2)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(5)|prostate(1)	22						CCCAGTCTGTGGAAAACTGCA	0.622																																					p.V472V		Atlas-SNP	.											.	PKP1	127	.	0			c.G1416A						.	G	,	1,4405	2.1+/-5.4	0,1,2202	118	94	102		1416,1353	5.4	1	1		102	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PKP1	NM_000299.3,NM_001005337.2	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	472/748,451/727	201291111	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	5317	exon9			GTCTGTGGAAAAC	X79293	CCDS30966.1, CCDS30967.1	1q32	2014-06-18	2014-06-18		ENSG00000081277	ENSG00000081277		"Armadillo repeat containing"	9023	protein-coding gene	gene with protein product	"ectodermal dysplasia/skin fragility syndrome"	601975	"plakophilin 1 (ectodermal dysplasia/skin fragility syndrome)"			9272178	Standard	NM_001005337		Approved	B6P	uc001gwd.3	Q13835	OTTHUMG00000035729	ENST00000352845.3:c.1416G>A	chr1.hg19:g.201291111G>A		119.0	0.0		113.0	18.0	NM_000299	O00645|Q14CA0|Q15152	Silent	SNP	ENST00000352845.3	hg19	CCDS30966.1																																																																																			.	.		0.622	PKP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000086897.1	NM_000299		A	201291111	G	A	201291111	2	1	270	1	0	0	0	0	0	0	0	1	11993	1335	47	3		3	PKP1	1	201291111	Silent	SNP	G	TCGA-FV-A4ZP-01A-12D-A25V-10	19565918	201291111	47959510	8	39287										
DISC1	27185	hgsc.bcm.edu	37	chr1	231858293	231858293	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	tcttcttggcagctggaaccAattgctttggatccaccatg	9	11	2	0			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr1:231858293A>G	ENST00000317586.4	+	3	1109	c.1056A>G	c.(1054-1056)ccA>ccG	p.P352P	TSNAX-DISC1_ENST00000602962.1_Intron|DISC1_ENST00000602281.1_Intron|DISC1_ENST00000366636.4_Intron|DISC1_ENST00000537876.1_Intron|DISC1_ENST00000602873.1_Intron|DISC1_ENST00000366637.3_Intron|DISC1_ENST00000539444.1_Intron|DISC1_ENST00000535983.1_Intron|DISC1_ENST00000366633.3_Intron|DISC1_ENST00000439617.2_Intron	NM_001012958.1	NP_001012976.1	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1	352	Interaction with TRAF3IP1.				canonical Wnt signaling pathway (GO:0060070)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cerebral cortex radially oriented cell migration (GO:0021799)|microtubule cytoskeleton organization (GO:0000226)|mitochondrial calcium ion homeostasis (GO:0051560)|neuron migration (GO:0001764)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neuron projection development (GO:0010975)|regulation of synapse maturation (GO:0090128)|TOR signaling (GO:0031929)	cell junction (GO:0030054)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|postsynaptic membrane (GO:0045211)				breast(1)|cervix(1)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	15		all_cancers(173;0.0208)|Prostate(94;0.0975)				AGCTGGAACCAATTGCTTTGG	0.398																																					p.N418D		Atlas-SNP	.											.	DISC1	207	.	0			c.A1252G						.						114	105	108					1																	231858293		2203	4300	6503	SO:0001819	synonymous_variant	27185	exon5			GGAACCAATTGCT	AF222980	CCDS31055.1, CCDS31056.1, CCDS53482.1, CCDS53483.1, CCDS53484.1, CCDS59205.1, CCDS59206.1, CCDS59207.1	1q42.1	2008-02-05			ENSG00000162946	ENSG00000162946			2888	protein-coding gene	gene with protein product		605210				10814723	Standard	NM_001164550		Approved		uc010pxh.2	Q9NRI5	OTTHUMG00000037835	ENST00000317586.4:c.1056A>G	chr1.hg19:g.231858293A>G		121.0	0.0		125.0	12.0	NM_001164550	A6NLH2|C4P091|C4P095|C4P0A1|C4P0A3|C4P0B3|C4P0B6|C4P0C1|C9J6D0|O75045|Q5VT44|Q5VT45|Q8IXJ0|Q8IXJ1|Q9BX19|Q9NRI3|Q9NRI4	Missense_Mutation	SNP	ENST00000317586.4	hg19	CCDS31056.1	.	.	.	.	.	.	.	.	.	.	A	8.375	0.836251	0.16891	.	.	ENSG00000162946	ENST00000366632	.	.	.	4.39	4.39	0.52855	.	.	.	.	.	T	0.64929	0.2643	.	.	.	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.64321	0.924;0.924	T	0.60707	-0.7210	7	0.17832	T	0.49	.	11.08	0.48053	1.0:0.0:0.0:0.0	.	418;376	C4P0D2;C4P0D0	.;.	D	227	.	ENSP00000355592:N227D	N	+	1	0	DISC1	229924916	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	0.627000	0.24506	1.820000	0.53075	0.528000	0.53228	AAT	.	.		0.398	DISC1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000092355.2	NM_018662		G	231858293	A	G	231858293	2	3	270	1	0	0	0	0	0	0	0	1	4540	130	5	2		2	DISC1	1	231858293	Silent	SNP	A	TCGA-FV-A4ZP-01A-12D-A25V-10	30567182	231858293	17392328	9	39288										
LHCGR	3973	hgsc.bcm.edu	37	chr2	48925801	48925801	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	cagcagtggctggggtaagtCaacgtggcctccaggagatt	15	9	1	1			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr2:48925801C>T	ENST00000294954.7	-	9	840	c.819G>A	c.(817-819)ttG>ttA	p.L273L	LHCGR_ENST00000401907.1_Silent_p.L273L|STON1-GTF2A1L_ENST00000402114.2_Intron|LHCGR_ENST00000403273.1_Silent_p.L273L|LHCGR_ENST00000344775.3_Intron|LHCGR_ENST00000405626.1_Silent_p.L273L	NM_000233.3	NP_000224.2	P22888	LSHR_HUMAN	luteinizing hormone/choriogonadotropin receptor	273					activation of adenylate cyclase activity (GO:0007190)|cellular response to gonadotropin stimulus (GO:0071371)|cognition (GO:0050890)|development of secondary male sexual characteristics (GO:0046544)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|ovarian follicle development (GO:0001541)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|regulation of steroid hormone biosynthetic process (GO:0090030)|seminiferous tubule development (GO:0072520)|spermatogenesis (GO:0007283)|uterus development (GO:0060065)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	choriogonadotropin hormone binding (GO:0038106)|choriogonadotropin hormone receptor activity (GO:0035472)|luteinizing hormone receptor activity (GO:0004964)			NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(3)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	56		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Buserelin(DB06719)|Cetrorelix(DB00050)|Choriogonadotropin alfa(DB00097)|Goserelin(DB00014)|Lutropin alfa(DB00044)|Menotropins(DB00032)	TGGGGTAAGTCAACGTGGCCT	0.433																																					p.L273L		Atlas-SNP	.											.	LHCGR	154	.	0			c.G819A						.						107	107	107					2																	48925801		2203	4300	6503	SO:0001819	synonymous_variant	3973	exon9			GTAAGTCAACGTG		CCDS1842.1	2p21	2012-08-10			ENSG00000138039	ENSG00000138039		"GPCR / Class A : Gonadotropin and TSH receptors"	6585	protein-coding gene	gene with protein product		152790	"hypergonadotropic hypogonadism"	HHG			Standard	NM_000233		Approved	LHR, LCGR, LGR2, ULG5	uc002rwu.4	P22888	OTTHUMG00000129257	ENST00000294954.7:c.819G>A	chr2.hg19:g.48925801C>T		74.0	0.0		64.0	5.0	NM_000233	Q14751|Q15996|Q9UEW9	Silent	SNP	ENST00000294954.7	hg19	CCDS1842.1																																																																																			.	.		0.433	LHCGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251364.4	NM_000233.3		T	48925801	C	T	48925801	2	4	270	1	0	0	0	0	0	0	0	1	8771	825	29	3		3	LHCGR	2	48925801	Silent	SNP	C	TCGA-FV-A4ZP-01A-12D-A25V-10		48925801	194273572	10	39289										
FN1	2335	hgsc.bcm.edu	37	chr2	216249663	216249663	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	tcagtaggctggtgggggtcGcagcaacaacttccaggtcc	14	11	1	0	rs202245868		TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr2:216249663G>T	ENST00000359671.1	-	28	4641	c.4376C>A	c.(4375-4377)gCg>gAg	p.A1459E	FN1_ENST00000357867.4_Missense_Mutation_p.A1459E|FN1_ENST00000356005.4_Missense_Mutation_p.A1459E|FN1_ENST00000354785.4_Missense_Mutation_p.A1550E|FN1_ENST00000446046.1_Missense_Mutation_p.A1459E|FN1_ENST00000421182.1_Missense_Mutation_p.A1459E|FN1_ENST00000346544.3_Missense_Mutation_p.A1459E|FN1_ENST00000357009.2_Missense_Mutation_p.A1459E|FN1_ENST00000443816.1_Missense_Mutation_p.A1459E|FN1_ENST00000345488.5_Missense_Mutation_p.A1459E|FN1_ENST00000323926.6_Missense_Mutation_p.A1550E|FN1_ENST00000336916.4_Missense_Mutation_p.A1459E|FN1_ENST00000432072.2_Missense_Mutation_p.A1550E|FN1_ENST00000490833.1_5'Flank			P02751	FINC_HUMAN	fibronectin 1	1459	Cell-attachment.|Fibronectin type-III 10. {ECO:0000255|PROSITE-ProRule:PRU00316}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	GGTGGGGGTCGCAGCAACAAC	0.433																																					p.A1550E		Atlas-SNP	.											.	FN1	521	.	0			c.C4649A						.						58	59	59					2																	216249663		2203	4300	6503	SO:0001583	missense	2335	exon29			GGGGTCGCAGCAA		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"Fibronectin type III domain containing", "Endogenous ligands"	3778	protein-coding gene	gene with protein product	"migration-stimulating factor", "cold-insoluble globulin"	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.4376C>A	chr2.hg19:g.216249663G>T	ENSP00000352696:p.Ala1459Glu	377.0	0.0		348.0	42.0	NM_212482	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Missense_Mutation	SNP	ENST00000359671.1	hg19		.	.	.	.	.	.	.	.	.	.	G	16.09	3.024409	0.54683	.	.	ENSG00000115414	ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000265313;ENST00000359671;ENST00000346544;ENST00000345488;ENST00000357009;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005;ENST00000456923	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.56941	0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43	6.02	6.02	0.97574	.	0.690178	0.14110	N	0.340748	T	0.46814	0.1412	N	0.17278	0.47	0.22581	N	0.998968	B;B;B;B;B;B;B;B;B;B	0.34241	0.264;0.033;0.237;0.066;0.444;0.003;0.31;0.171;0.096;0.033	B;B;B;B;B;B;B;B;B;B	0.37508	0.106;0.045;0.131;0.066;0.252;0.007;0.17;0.106;0.066;0.066	T	0.51529	-0.8694	10	0.66056	D	0.02	.	20.5407	0.99260	0.0:0.0:1.0:0.0	.	1550;1550;1459;1459;1459;1459;1460;1459;1459;1550	P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;E7ERA1;P02751-9;P02751-14;P02751-15	.;.;.;.;.;.;.;.;.;.	E	1459;1550;1459;1459;1550;1460;1459;1459;1459;1459;1459;1459;1550;1459;266	ENSP00000394423:A1459E;ENSP00000323534:A1550E;ENSP00000338200:A1459E;ENSP00000350534:A1459E;ENSP00000346839:A1550E;ENSP00000352696:A1459E;ENSP00000265312:A1459E;ENSP00000273049:A1459E;ENSP00000349509:A1459E;ENSP00000410422:A1459E;ENSP00000415018:A1459E;ENSP00000399538:A1550E;ENSP00000348285:A1459E;ENSP00000416139:A266E	ENSP00000265313:A1460E	A	-	2	0	FN1	215957908	0.997000	0.39634	0.009000	0.14445	0.298000	0.27526	7.628000	0.83189	2.865000	0.98341	0.655000	0.94253	GCG	.	G|1.000;A|0.000		0.433	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		T	216249663	G	T	216249663	3	4	270	1	0	0	0	0	1	0	0	0	5970	1087	38	1	2856	1	FN1	2	216249663	Missense_Mutation	SNP	G	TCGA-FV-A4ZP-01A-12D-A25V-10	167323862	216249663	26949710	11	39290										
CAND2	23066	hgsc.bcm.edu	37	chr3	12859283	12859283	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	ctgcgagggtgctgaggaggGcacccggggggtggtggccg	23	9	0	1			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr3:12859283G>T	ENST00000456430.2	+	10	2893	c.2852G>T	c.(2851-2853)gGc>gTc	p.G951V	CAND2_ENST00000295989.5_Missense_Mutation_p.G858V	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	951					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						GCTGAGGAGGGCACCCGGGGG	0.672																																					p.G951V	GBM(43;676 868 1633 6395 37496)	Atlas-SNP	.											.	CAND2	138	.	0			c.G2852T						.						63	75	71					3																	12859283		2038	4177	6215	SO:0001583	missense	23066	exon10			AGGAGGGCACCCG		CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"TBP interacting protein"	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.2852G>T	chr3.hg19:g.12859283G>T	ENSP00000387641:p.Gly951Val	90.0	0.0		68.0	10.0	NM_001162499	B9EGM9|E9KL24	Missense_Mutation	SNP	ENST00000456430.2	hg19	CCDS54554.1	.	.	.	.	.	.	.	.	.	.	G	19.64	3.864563	0.71949	.	.	ENSG00000144712	ENST00000295989;ENST00000456430	T;T	0.56611	0.45;0.45	4.64	4.64	0.57946	Armadillo-like helical (1);Armadillo-type fold (1);	0.067453	0.64402	D	0.000018	T	0.78259	0.4255	M	0.92268	3.29	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.996;0.999	T	0.83210	-0.0074	10	0.52906	T	0.07	-39.1272	15.364	0.74507	0.0:0.0:1.0:0.0	.	951;858	O75155;O75155-2	CAND2_HUMAN;.	V	858;951	ENSP00000295989:G858V;ENSP00000387641:G951V	ENSP00000295989:G858V	G	+	2	0	CAND2	12834283	1.000000	0.71417	1.000000	0.80357	0.893000	0.52053	9.618000	0.98365	2.289000	0.77006	0.561000	0.74099	GGC	.	.		0.672	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617		T	12859283	G	T	12859283	3	4	270	1	0	0	0	0	1	0	0	0	2618	1203	42	3	2890	3	CAND2	3	12859283	Missense_Mutation	SNP	G	TCGA-FV-A4ZP-01A-12D-A25V-10		12859283	185163147	12	39291										
SACM1L	22908	hgsc.bcm.edu	37	chr3	45754687	45754687	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	agaactttctgcacagccagAggtaatgtacacgaaataaa	8	8	1	2			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr3:45754687A>T	ENST00000389061.5	+	6	746	c.542A>T	c.(541-543)gAg>gTg	p.E181V	SACM1L_ENST00000541314.1_Splice_Site_p.E120V|SACM1L_ENST00000418611.1_Splice_Site_p.E78V	NM_014016.3	NP_054735.3	Q9NTJ5	SAC1_HUMAN	SAC1 suppressor of actin mutations 1-like (yeast)	181	SAC. {ECO:0000255|PROSITE- ProRule:PRU00183}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of endoplasmic reticulum membrane (GO:0030176)	phosphatase activity (GO:0016791)|phosphatidylinositol bisphosphate phosphatase activity (GO:0034593)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphatidylinositol-4-phosphate phosphatase activity (GO:0043812)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.0102)|KIRC - Kidney renal clear cell carcinoma(197;0.0234)|Kidney(197;0.0277)		GCACAGCCAGAGGTAATGTAC	0.358																																					p.E181V		Atlas-SNP	.											.	SACM1L	38	.	0			c.A542T						.						73	74	73					3																	45754687		2203	4300	6503	SO:0001630	splice_region_variant	22908	exon6			AGCCAGAGGTAAT	AB020658	CCDS33745.1	3p21.3	2010-03-11			ENSG00000211456	ENSG00000211456			17059	protein-coding gene	gene with protein product		606569				10048485, 11352561	Standard	NM_014016		Approved	SAC1, KIAA0851	uc003cos.2	Q9NTJ5	OTTHUMG00000156653	ENST00000389061.5:c.543+1A>T	chr3.hg19:g.45754687A>T		21.0	0.0		18.0	7.0	NM_014016	A8K527|B4DK71|O94935|Q7LA14|Q7LA22|Q96AX7|Q9NQ46|Q9NQ57	Missense_Mutation	SNP	ENST00000389061.5	hg19	CCDS33745.1	.	.	.	.	.	.	.	.	.	.	A	30	5.055486	0.93793	.	.	ENSG00000211456	ENST00000418611;ENST00000389061;ENST00000541314	T;T;T	0.58358	0.34;0.34;0.34	5.79	5.79	0.91817	Synaptojanin, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.66147	0.2760	L	0.56340	1.77	0.80722	D	1	D;P	0.59767	0.986;0.885	D;P	0.64144	0.922;0.566	T	0.63817	-0.6551	10	0.35671	T	0.21	-20.9518	16.1323	0.81449	1.0:0.0:0.0:0.0	.	120;181	B4DK71;Q9NTJ5	.;SAC1_HUMAN	V	78;181;120	ENSP00000396387:E78V;ENSP00000373713:E181V;ENSP00000443373:E120V	ENSP00000373713:E181V	E	+	2	0	SACM1L	45729691	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.833000	0.92089	2.223000	0.72356	0.454000	0.30748	GAG	.	.		0.358	SACM1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345065.2	NM_014016	Missense_Mutation	T	45754687	A	T	45754687	5	4	270	1	0	0	0	0	0	0	1	0	13818	318	11	4	564	4	SACM1L	3	45754687	Splice_Site	SNP	A	TCGA-FV-A4ZP-01A-12D-A25V-10	32895404	45754687	152267743	13	39292										
MYH15	22989	hgsc.bcm.edu	37	chr3	108127246	108127246	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	ctggtttgtcagattagaaaTctcttctggagacagaggta	11	6	3	4			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr3:108127246T>G	ENST00000273353.3	-	33	4617	c.4561A>C	c.(4561-4563)Att>Ctt	p.I1521L		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	1521						cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						AGATTAGAAATCTCTTCTGGA	0.413																																					p.I1521L		Atlas-SNP	.											.	MYH15	223	.	0			c.A4561C						.						120	108	112					3																	108127246		1850	4096	5946	SO:0001583	missense	22989	exon33			TAGAAATCTCTTC	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"Myosins / Myosin superfamily : Class II"	31073	protein-coding gene	gene with protein product		609929	"myosin, heavy polypeptide 15"			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.4561A>C	chr3.hg19:g.108127246T>G	ENSP00000273353:p.Ile1521Leu	88.0	0.0		108.0	25.0	NM_014981		Missense_Mutation	SNP	ENST00000273353.3	hg19	CCDS43127.1	.	.	.	.	.	.	.	.	.	.	T	18.45	3.627648	0.66901	.	.	ENSG00000144821	ENST00000273353	T	0.79141	-1.24	5.56	1.82	0.25136	Myosin tail (1);	.	.	.	.	T	0.73837	0.3638	L	0.49571	1.57	0.34368	D	0.691686	B	0.29481	0.245	B	0.37550	0.253	T	0.74417	-0.3672	9	0.62326	D	0.03	.	9.4452	0.38693	0.0:0.1906:0.0:0.8094	.	1521	Q9Y2K3	MYH15_HUMAN	L	1521	ENSP00000273353:I1521L	ENSP00000273353:I1521L	I	-	1	0	MYH15	109609936	1.000000	0.71417	0.995000	0.50966	0.994000	0.84299	2.129000	0.42055	0.073000	0.16731	0.533000	0.62120	ATT	.	.		0.413	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988		G	108127246	T	G	108127246	3	3	270	1	0	0	0	0	1	0	0	0	10043	1435	50	5	1319	5	MYH15	3	108127246	Missense_Mutation	SNP	T	TCGA-FV-A4ZP-01A-12D-A25V-10	62372559	108127246	89895184	14	39293										
KIAA1211	57482	hgsc.bcm.edu	37	chr4	57181429	57181429	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	gtccagcacgccctaccgtcGtccctgagcgttccccacac	8	20	0	1			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr4:57181429G>A	ENST00000504228.1	+	6	1866	c.1761G>A	c.(1759-1761)tcG>tcA	p.S587S	KIAA1211_ENST00000541073.1_Silent_p.S580S|KIAA1211_ENST00000264229.6_Silent_p.S587S			Q6ZU35	K1211_HUMAN	KIAA1211	587										endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					CCCTACCGTCGTCCCTGAGCG	0.677																																					p.S587S		Atlas-SNP	.											.	KIAA1211	178	.	0			c.G1761A						.						17	24	22					4																	57181429		2047	4179	6226	SO:0001819	synonymous_variant	57482	exon8			ACCGTCGTCCCTG	AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.1761G>A	chr4.hg19:g.57181429G>A		24.0	0.0		32.0	14.0	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Silent	SNP	ENST00000504228.1	hg19	CCDS43230.1																																																																																			.	.		0.677	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722		A	57181429	G	A	57181429	2	1	270	1	0	0	0	0	0	0	0	1	8224	1132	40	1		1	KIAA1211	4	57181429	Silent	SNP	G	TCGA-FV-A4ZP-01A-12D-A25V-10		57181429	133972847	15	39294										
LPHN3	23284	hgsc.bcm.edu	37	chr4	62599267	62599267	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	ttttggacctctggatagtaGatcaggtaagttcaaccttt	9	7	3	1			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr4:62599267G>T	ENST00000514591.1	+	7	1519	c.1190G>T	c.(1189-1191)aGa>aTa	p.R397I	LPHN3_ENST00000508693.1_Missense_Mutation_p.R465I|LPHN3_ENST00000511324.1_Missense_Mutation_p.R465I|LPHN3_ENST00000512091.2_Missense_Mutation_p.R397I|LPHN3_ENST00000545650.1_Missense_Mutation_p.R397I|LPHN3_ENST00000507164.1_Missense_Mutation_p.R465I|LPHN3_ENST00000507625.1_Missense_Mutation_p.R465I|LPHN3_ENST00000506746.1_Missense_Mutation_p.R465I|LPHN3_ENST00000506700.1_Missense_Mutation_p.R397I|LPHN3_ENST00000514157.1_Missense_Mutation_p.R397I|LPHN3_ENST00000509896.1_Missense_Mutation_p.R465I|LPHN3_ENST00000514996.1_Missense_Mutation_p.R397I|LPHN3_ENST00000506720.1_Missense_Mutation_p.R465I|LPHN3_ENST00000504896.1_Missense_Mutation_p.R397I|LPHN3_ENST00000508946.1_Missense_Mutation_p.R397I			Q9HAR2	LPHN3_HUMAN	latrophilin 3	397					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						CTGGATAGTAGATCAGGTAAG	0.353																																					p.R397I		Atlas-SNP	.											.	LPHN3	800	.	0			c.G1190T						.						34	32	33					4																	62599267		1832	4090	5922	SO:0001583	missense	23284	exon5			ATAGTAGATCAGG	AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"-", "GPCR / Class B : Orphans"	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.1190G>T	chr4.hg19:g.62599267G>T	ENSP00000422533:p.Arg397Ile	142.0	0.0		113.0	13.0	NM_015236	E9PE04|O94867|Q9NWK5	Missense_Mutation	SNP	ENST00000514591.1	hg19	CCDS54768.1	.	.	.	.	.	.	.	.	.	.	G	12.74	2.028304	0.35797	.	.	ENSG00000150471	ENST00000512091;ENST00000514591;ENST00000509896;ENST00000511324;ENST00000506700;ENST00000534975;ENST00000545650;ENST00000295349;ENST00000280009;ENST00000507164;ENST00000508693;ENST00000507625;ENST00000514157;ENST00000504896;ENST00000508946;ENST00000506720;ENST00000506746;ENST00000514996	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.70749	-0.48;-0.47;-0.5;-0.5;-0.48;-0.47;-0.5;-0.49;-0.49;-0.47;-0.47;-0.48;-0.5;-0.51;-0.48	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.51856	0.1699	N	0.19112	0.55	0.80722	D	1	B;P;P	0.38020	0.244;0.543;0.615	B;B;B	0.29785	0.107;0.096;0.107	T	0.58956	-0.7544	10	0.56958	D	0.05	.	11.4352	0.50064	0.0827:0.0:0.9173:0.0	.	397;465;397	E9PE04;E7EN28;Q9HAR2-2	.;.;.	I	397;397;465;465;397;397;397;397;397;465;465;465;397;397;397;465;465;397	ENSP00000423388:R397I;ENSP00000422533:R397I;ENSP00000423787:R465I;ENSP00000425033:R465I;ENSP00000424120:R397I;ENSP00000439831:R397I;ENSP00000421476:R465I;ENSP00000424030:R465I;ENSP00000421372:R465I;ENSP00000425201:R397I;ENSP00000423434:R397I;ENSP00000421627:R397I;ENSP00000420931:R465I;ENSP00000425884:R465I;ENSP00000424258:R397I	ENSP00000280009:R397I	R	+	2	0	LPHN3	62281862	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	6.469000	0.73555	2.471000	0.83476	0.557000	0.71058	AGA	.	.		0.353	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1			T	62599267	G	T	62599267	3	4	270	1	0	0	0	0	1	0	0	0	8926	942	33	3	1208	3	LPHN3	4	62599267	Missense_Mutation	SNP	G	TCGA-FV-A4ZP-01A-12D-A25V-10	5417838	62599267	128555009	16	39295										
HPSE	10855	hgsc.bcm.edu	37	chr4	84222134	84222134	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	tggaaagtaatccatgaggtCccaaaggtcttagaaggtat	11	6	1	2			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr4:84222134C>T	ENST00000405413.2	-	12	1587	c.1451G>A	c.(1450-1452)gGa>gAa	p.G484E	HPSE_ENST00000311412.5_Missense_Mutation_p.G484E|HPSE_ENST00000512196.1_Missense_Mutation_p.G410E|HPSE_ENST00000513463.1_Missense_Mutation_p.G426E	NM_006665.5	NP_006656.2	Q9Y251	HPSE_HUMAN	heparanase	484					carbohydrate metabolic process (GO:0005975)|cell-matrix adhesion (GO:0007160)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan catabolic process (GO:0030200)|positive regulation of blood coagulation (GO:0030194)|positive regulation of hair follicle development (GO:0051798)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation vascular endothelial growth factor production (GO:0010575)|proteoglycan metabolic process (GO:0006029)|regulation of hair follicle development (GO:0051797)|small molecule metabolic process (GO:0044281)|vascular wound healing (GO:0061042)	extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|membrane raft (GO:0045121)|nucleus (GO:0005634)	beta-glucuronidase activity (GO:0004566)|heparanase activity (GO:0030305)|protein dimerization activity (GO:0046983)|syndecan binding (GO:0045545)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	20		Hepatocellular(203;0.114)		COAD - Colon adenocarcinoma(81;0.141)	Dalteparin(DB06779)|Heparin(DB01109)	TCCATGAGGTCCCAAAGGTCT	0.368																																					p.G484E		Atlas-SNP	.											.	HPSE	55	.	0			c.G1451A						.						102	104	103					4																	84222134		2203	4299	6502	SO:0001583	missense	10855	exon11			TGAGGTCCCAAAG	AF144325	CCDS3602.1, CCDS54774.1, CCDS56337.1	4q21.3	2008-02-05			ENSG00000173083	ENSG00000173083			5164	protein-coding gene	gene with protein product		604724				10395325, 10395326	Standard	NM_006665		Approved	HPA, HSE1, HPSE1	uc003hoj.4	Q9Y251	OTTHUMG00000130425	ENST00000405413.2:c.1451G>A	chr4.hg19:g.84222134C>T	ENSP00000384262:p.Gly484Glu	88.0	0.0		70.0	15.0	NM_001098540	A9JIG7|C7F7I3|C7F7I4|E9PCA9|E9PGR1|Q53GE5|Q9UL39	Missense_Mutation	SNP	ENST00000405413.2	hg19	CCDS3602.1	.	.	.	.	.	.	.	.	.	.	C	12.33	1.906633	0.33628	.	.	ENSG00000173083	ENST00000311412;ENST00000405413;ENST00000512196;ENST00000513463	T;T;T;T	0.46451	0.87;0.87;0.93;0.92	4.55	3.69	0.42338	.	0.159887	0.56097	D	0.000033	T	0.58409	0.2120	M	0.69463	2.115	0.24690	N	0.993311	D;D;D;P	0.89917	1.0;0.969;0.982;0.928	D;P;P;P	0.85130	0.997;0.52;0.713;0.52	T	0.46289	-0.9202	10	0.54805	T	0.06	-14.6443	10.1559	0.42823	0.0:0.9007:0.0:0.0993	.	410;426;426;484	E9PCA9;A9JIG7;E9PGR1;Q9Y251	.;.;.;HPSE_HUMAN	E	484;484;410;426	ENSP00000308107:G484E;ENSP00000384262:G484E;ENSP00000423265:G410E;ENSP00000421365:G426E	ENSP00000308107:G484E	G	-	2	0	HPSE	84441158	0.848000	0.29623	0.377000	0.26055	0.306000	0.27790	3.052000	0.49893	2.513000	0.84729	0.650000	0.86243	GGA	.	.		0.368	HPSE-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252812.2	NM_006665		T	84222134	C	T	84222134	3	4	270	1	0	0	0	0	1	0	0	0	7353	855	30	3	188	3	HPSE	4	84222134	Missense_Mutation	SNP	C	TCGA-FV-A4ZP-01A-12D-A25V-10	21622867	84222134	106932142	17	39296										
TACR3	6870	hgsc.bcm.edu	37	chr4	104511152	104511152	+	Splice_Site	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	tcttgaagccagctcgaaatCtgaggaaaagcaggccacag	11	10	2	2			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr4:104511152C>G	ENST00000304883.2	-	5	1226		c.e5-1		RP11-297P16.3_ENST00000512401.1_RNA|RP11-297P16.3_ENST00000502936.1_RNA	NM_001059.2	NP_001050.1	P29371	NK3R_HUMAN	tachykinin receptor 3						aging (GO:0007568)|hyperosmotic salinity response (GO:0042538)|positive regulation of blood pressure (GO:0045777)|positive regulation of heart rate (GO:0010460)|positive regulation of uterine smooth muscle contraction (GO:0070474)|regulation of dopamine metabolic process (GO:0042053)|regulation of feeding behavior (GO:0060259)|response to cocaine (GO:0042220)|response to estradiol (GO:0032355)|response to morphine (GO:0043278)|tachykinin receptor signaling pathway (GO:0007217)	cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	tachykinin receptor activity (GO:0004995)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	51		Hepatocellular(203;0.217)		UCEC - Uterine corpus endometrioid carcinoma (10;0.22)|OV - Ovarian serous cystadenocarcinoma(123;3.4e-08)		AGCTCGAAATCTGAGGAAAAG	0.418																																					.		Atlas-SNP	.											.	TACR3	102	.	0			c.1086-1G>C						.						47	47	47					4																	104511152		2203	4300	6503	SO:0001630	splice_region_variant	6870	exon6			CGAAATCTGAGGA	M89473	CCDS3664.1	4q25	2012-08-08			ENSG00000169836	ENSG00000169836		"GPCR / Class A : Tachykinin receptors"	11528	protein-coding gene	gene with protein product	"neurokinin beta receptor"	162332				1374246	Standard	NM_001059		Approved	NK3R	uc003hxe.1	P29371	OTTHUMG00000131124	ENST00000304883.2:c.1086-1G>C	chr4.hg19:g.104511152C>G		105.0	0.0		77.0	14.0	NM_001059	Q0P510	Splice_Site	SNP	ENST00000304883.2	hg19	CCDS3664.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.342453	0.81911	.	.	ENSG00000169836	ENST00000304883	.	.	.	5.81	5.81	0.92471	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.0794	0.93175	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TACR3	104730601	1.000000	0.71417	0.996000	0.52242	0.888000	0.51559	7.356000	0.79445	2.746000	0.94184	0.591000	0.81541	.	.	.		0.418	TACR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253804.1	NM_001059	Intron	G	104511152	C	G	104511152	5	3	270	1	0	0	0	0	0	0	1	0	15522	927	32	4	316	4	TACR3	4	104511152	Splice_Site	SNP	C	TCGA-FV-A4ZP-01A-12D-A25V-10	20289018	104511152	86643124	18	39297										
TRAM1L1	133022	hgsc.bcm.edu	37	chr4	118005773	118005789	+	Frame_Shift_Del	DEL	CAAGATAAACACAATGG	CAAGATAAACACAATGG	-													0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	attaaagtcacaagtctaccCaagataaacacaatggccca							TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	CAAGATAAACACAATGG	CAAGATAAACACAATGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr4:118005773_118005789delCAAGATAAACACAATGG	ENST00000310754.4	-	1	947_963	c.761_777delCCATTGTGTTTATCTTG	c.(760-777)gccattgtgtttatcttgfs	p.AIVFIL254fs		NM_152402.2	NP_689615.2	Q8N609	TR1L1_HUMAN	translocation associated membrane protein 1-like 1	254	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22						CAAGTCTACCCAAGATAAACACAATGGCCCACAGAGA	0.415																																					p.254_260del		Atlas-Indel,Pindel	.											.	TRAM1L1	55	.	0			c.762_778del						.																																			SO:0001589	frameshift_variant	133022	exon1			.	AK074617	CCDS3707.1	4q26	2008-02-05			ENSG00000174599	ENSG00000174599			28371	protein-coding gene	gene with protein product						12477932	Standard	NM_152402		Approved	MGC26568	uc003ibv.4	Q8N609	OTTHUMG00000132956	ENST00000310754.4:c.761_777delCCATTGTGTTTATCTTG	chr4.hg19:g.118005773_118005789delCAAGATAAACACAATGG	ENSP00000309402:p.Ala254fs	115.0	0.0		59.0	14.0	NM_152402	Q8N2L7	Frame_Shift_Del	DEL	ENST00000310754.4	hg19	CCDS3707.1																																																																																			.	.		0.415	TRAM1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256513.1	NM_152402		-	118005789	CAAGATAAACACAATGG	-	118005773	7	5	270	1	0	1	0	1	0	0	0	0	16467	593	21	0	336	0	TRAM1L1	4	118005773	Frame_Shift_Del	DEL	CAAGATAAACACAATGG	TCGA-FV-A4ZP-01A-12D-A25V-10	13494621	118005773	73148503	19	39298										
C5orf42	65250	hgsc.bcm.edu	37	chr5	37176032	37176032	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	tagaaatttctgaactcgtaTctacttgcattgattgagga	8	6	2	4			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr5:37176032T>C	ENST00000508244.1	-	30	6050	c.5957A>G	c.(5956-5958)gAt>gGt	p.D1986G	C5orf42_ENST00000425232.2_Missense_Mutation_p.D1986G|C5orf42_ENST00000274258.7_Missense_Mutation_p.D866G			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	1986						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			TGAACTCGTATCTACTTGCAT	0.348																																					p.D1986G		Atlas-SNP	.											.	C5orf42	422	.	0			c.A5957G						.						195	207	203					5																	37176032		2203	4300	6503	SO:0001583	missense	65250	exon31			CTCGTATCTACTT		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.5957A>G	chr5.hg19:g.37176032T>C	ENSP00000421690:p.Asp1986Gly	82.0	0.0		141.0	21.0	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	hg19	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	T	17.83	3.486665	0.63962	.	.	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	T;T;T;T	0.28666	1.62;1.62;1.6;1.6	5.77	5.77	0.91146	.	0.077668	0.45126	D	0.000397	T	0.46288	0.1385	L	0.48642	1.525	0.30868	N	0.7328	D;D	0.76494	0.999;0.996	D;D	0.67382	0.951;0.929	T	0.50154	-0.8861	10	0.40728	T	0.16	.	13.4698	0.61276	0.0:0.0:0.0:1.0	.	1986;866	E9PH94;Q9H799	.;CE042_HUMAN	G	1986;1986;866;1034;866	ENSP00000421690:D1986G;ENSP00000389014:D1986G;ENSP00000274258:D866G;ENSP00000424223:D1034G	ENSP00000274258:D866G	D	-	2	0	C5orf42	37211789	0.998000	0.40836	0.920000	0.36463	0.099000	0.18886	4.272000	0.58908	2.203000	0.70933	0.533000	0.62120	GAT	.	.		0.348	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		C	37176032	T	C	37176032	3	2	270	1	0	0	0	0	1	0	0	0	2303	1435	50	2	3724	2	C5orf42	5	37176032	Missense_Mutation	SNP	T	TCGA-FV-A4ZP-01A-12D-A25V-10		37176032	143739228	20	39299										
TNPO1	3842	hgsc.bcm.edu	37	chr5	72144312	72144312	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	cccagacaccaccatccagaGaaccgtgcaacaagtatcct	6	16	0	2			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr5:72144312G>T	ENST00000337273.5	+	2	542	c.116G>T	c.(115-117)aGa>aTa	p.R39I	TNPO1_ENST00000506351.2_Missense_Mutation_p.R31I|TNPO1_ENST00000454282.1_Missense_Mutation_p.R39I|TNPO1_ENST00000447967.2_Missense_Mutation_p.R31I|TNPO1_ENST00000513944.1_3'UTR|TNPO1_ENST00000523768.1_Missense_Mutation_p.R39I	NM_002270.3	NP_002261.3	Q92973	TNPO1_HUMAN	transportin 1	39					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|protein import into nucleus, translocation (GO:0000060)|RNA metabolic process (GO:0016070)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(6)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	36		Lung NSC(167;0.0053)|Ovarian(174;0.0175)		OV - Ovarian serous cystadenocarcinoma(47;6.14e-54)		ACCATCCAGAGAACCGTGCAA	0.652																																					p.R39I		Atlas-SNP	.											.	TNPO1	90	.	0			c.G116T						.						82	71	75					5																	72144312		2203	4300	6503	SO:0001583	missense	3842	exon2			TCCAGAGAACCGT	U70322	CCDS4016.1, CCDS43329.1	5q13.1	2009-01-12	2004-01-29	2004-01-30	ENSG00000083312	ENSG00000083312		"Importins"	6401	protein-coding gene	gene with protein product	"importin 2"	602901	"karyopherin (importin) beta 2"	KPNB2		8808633, 9144189	Standard	NM_153188		Approved	MIP, TRN, IPO2, MIP1	uc003kci.4	Q92973	OTTHUMG00000100967	ENST00000337273.5:c.116G>T	chr5.hg19:g.72144312G>T	ENSP00000336712:p.Arg39Ile	49.0	0.0		60.0	4.0	NM_002270	B4DVC6|Q92957|Q92975	Missense_Mutation	SNP	ENST00000337273.5	hg19	CCDS43329.1	.	.	.	.	.	.	.	.	.	.	G	16.47	3.131614	0.56828	.	.	ENSG00000083312	ENST00000337273;ENST00000454282;ENST00000447967;ENST00000523768;ENST00000506351	T;T;T;T;T	0.68181	-0.31;-0.31;-0.31;-0.31;-0.31	3.06	2.14	0.27477	Armadillo-like helical (1);Armadillo-type fold (1);	0.110918	0.64402	D	0.000015	T	0.70684	0.3252	M	0.85859	2.78	0.80722	D	1	P;B	0.47762	0.9;0.134	P;B	0.44359	0.447;0.126	T	0.75491	-0.3299	10	0.66056	D	0.02	-1.2586	12.0099	0.53280	0.0:0.1769:0.8231:0.0	.	39;39	Q92973-3;Q92973	.;TNPO1_HUMAN	I	39;39;31;39;31	ENSP00000336712:R39I;ENSP00000398524:R39I;ENSP00000415164:R31I;ENSP00000428899:R39I;ENSP00000425118:R31I	ENSP00000336712:R39I	R	+	2	0	TNPO1	72180068	1.000000	0.71417	0.998000	0.56505	0.959000	0.62525	6.708000	0.74660	0.580000	0.29522	0.305000	0.20034	AGA	.	.		0.652	TNPO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000218577.3	NM_002270		T	72144312	G	T	72144312	3	4	270	1	0	0	0	0	1	0	0	0	16350	942	33	3	122	3	TNPO1	5	72144312	Missense_Mutation	SNP	G	TCGA-FV-A4ZP-01A-12D-A25V-10	34968280	72144312	108770948	21	39300										
PCDHGA5	56110	hgsc.bcm.edu	37	chr5	140745937	140745937	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	gacctaggcagtatcaagacCcccattgaccctgaggatct	9	13	2	3			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr5:140745937C>A	ENST00000518069.1	+	1	2040	c.2040C>A	c.(2038-2040)acC>acA	p.T680T	PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018918.2|NM_032054.1	NP_061741.1|NP_114443.1	Q9Y5G8	PCDG5_HUMAN	protocadherin gamma subfamily A, 5	680	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(5)|upper_aerodigestive_tract(3)	18			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTATCAAGACCCCCATTGACC	0.602																																					p.T680T		Atlas-SNP	.											.	PCDHGA5	215	.	0			c.C2040A						.						293	309	303					5																	140745937		2201	4299	6500	SO:0001819	synonymous_variant	56110	exon1			CAAGACCCCCATT	AF152512	CCDS54925.1, CCDS75333.1	5q31	2010-01-26				ENSG00000253485		"Cadherins / Protocadherins : Clustered"	8703	other	protocadherin	"cadherin ME3"	606292				10380929	Standard	NM_018918		Approved	CDH-GAMMA-A5, ME3, PCDH-GAMMA-A5		Q9Y5G8		ENST00000518069.1:c.2040C>A	chr5.hg19:g.140745937C>A		174.0	0.0		191.0	40.0	NM_032054	Q2M3F5|Q9Y5D2	Silent	SNP	ENST00000518069.1	hg19	CCDS54925.1																																																																																			.	.		0.602	PCDHGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374742.1	NM_018918		A	140745937	C	A	140745937	2	1	270	1	0	0	0	0	0	0	0	1	11566	610	22	3		3	PCDHGA5	5	140745937	Silent	SNP	C	TCGA-FV-A4ZP-01A-12D-A25V-10	68601625	140745937	40169323	22	39301										
GPRC6A	222545	hgsc.bcm.edu	37	chr6	117113958	117113958	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	aacctggatgcccgtgcaagTgaagataataaggatcggtc	12	8	0	2			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr6:117113958T>C	ENST00000310357.3	-	6	2149	c.2128A>G	c.(2128-2130)Act>Gct	p.T710A	GPRC6A_ENST00000368549.3_Missense_Mutation_p.T639A|GPRC6A_ENST00000530250.1_Missense_Mutation_p.T535A	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	710					calcium-mediated signaling (GO:0019722)|response to amino acid (GO:0043200)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|liver(1)|lung(24)|ovary(5)|pancreas(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)	65		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		CCCGTGCAAGTGAAGATAATA	0.438																																					p.T710A		Atlas-SNP	.											.	GPRC6A	152	.	0			c.A2128G						.						81	76	77					6																	117113958		2203	4300	6503	SO:0001583	missense	222545	exon6			TGCAAGTGAAGAT	AF502962	CCDS5112.1, CCDS69184.1, CCDS69185.1	6q22.31	2014-01-30	2014-01-30		ENSG00000173612	ENSG00000173612		"GPCR / Class C : Calcium-sensing receptors"	18510	protein-coding gene	gene with protein product			"G protein-coupled receptor, family C, group 6, member A"				Standard	NM_001286354		Approved	bA86F4.3	uc003pxj.1	Q5T6X5	OTTHUMG00000015447	ENST00000310357.3:c.2128A>G	chr6.hg19:g.117113958T>C	ENSP00000309493:p.Thr710Ala	110.0	0.0		103.0	15.0	NM_148963	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Missense_Mutation	SNP	ENST00000310357.3	hg19	CCDS5112.1	.	.	.	.	.	.	.	.	.	.	T	2.357	-0.347610	0.05208	.	.	ENSG00000173612	ENST00000310357;ENST00000368549;ENST00000530250	D;D;D	0.87029	-2.2;-2.2;-2.2	4.61	2.14	0.27477	GPCR, family 3, C-terminal (2);	0.224010	0.31312	N	0.007873	T	0.53658	0.1810	N	0.12831	0.26	0.09310	N	1	B;P;B	0.44090	0.151;0.826;0.259	B;B;B	0.40101	0.052;0.319;0.186	T	0.55755	-0.8091	10	0.27082	T	0.32	.	5.1681	0.15096	0.2764:0.0776:0.0:0.646	.	639;535;710	Q5T6X5-3;Q5T6X5-2;Q5T6X5	.;.;GPC6A_HUMAN	A	710;639;535	ENSP00000309493:T710A;ENSP00000357537:T639A;ENSP00000433465:T535A	ENSP00000309493:T710A	T	-	1	0	GPRC6A	117220651	0.017000	0.18338	0.015000	0.15790	0.005000	0.04900	0.397000	0.20883	0.265000	0.21872	-0.353000	0.07706	ACT	.	.		0.438	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2			C	117113958	T	C	117113958	3	2	270	1	0	0	0	0	1	0	0	0	6737	1696	59	2	656	2	GPRC6A	6	117113958	Missense_Mutation	SNP	T	TCGA-FV-A4ZP-01A-12D-A25V-10		117113958	54001109	23	39302										
THEMIS	387357	hgsc.bcm.edu	37	chr6	128135050	128135051	+	Missense_Mutation	DNP	GG	GG	TT													0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	gacttcgacatctagactggGgaggatgcggattatatctt							TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr6:128135050_128135051GG>TT	ENST00000368248.2	-	4	883_884	c.735_736CC>AA	c.(733-738)ctCCcc>ctAAcc	p.P246T	THEMIS_ENST00000543064.1_Missense_Mutation_p.P246T|THEMIS_ENST00000537166.1_Missense_Mutation_p.P211T|THEMIS_ENST00000368250.1_Missense_Mutation_p.P167T	NM_001010923.2	NP_001010923.1	Q8N1K5	THMS1_HUMAN	thymocyte selection associated	246	CABIT 1.				negative T cell selection (GO:0043383)|positive T cell selection (GO:0043368)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(3)	60						TCTAGACTGGGGAGGATGCGGA	0.351																																					p.P246T|p.L245L		Atlas-SNP	.											THEMIS,NS,carcinoma,0,1|.	THEMIS	168	.	0			c.C736A|c.C735A						.																																			SO:0001583	missense	387357	exon4			GACTGGGGAGGAT|ACTGGGGAGGATG	AK094863	CCDS34534.1, CCDS55055.1	6q22.33	2012-02-08	2009-06-25	2009-06-25	ENSG00000172673	ENSG00000172673			21569	protein-coding gene	gene with protein product	"thymocyte expressed molecule involved in selection"	613607	"chromosome 6 open reading frame 207", "chromosome 6 open reading frame 190", "thymocyte selection pathway associated"	C6orf207, C6orf190, TSEPA		19597499, 19597498, 19597497	Standard	NM_001010923		Approved	bA325O24.4, FLJ40584, bA325O24.3	uc011ebt.2	Q8N1K5	OTTHUMG00000015534	ENST00000368248.2:c.735_736delinsTT	chr6.hg19:g.128135050_128135051delinsTT	ENSP00000357231:p.Pro246Thr	80.0|79.0	0.0		63.0	16.0	NM_001010923	A1L4F0|A8K7N1|B3KT31|B3KW32|B3KY07|F5H1J9|Q5T3C4|Q5T3C5|Q6MZT7	Missense_Mutation|Silent	SNP	ENST00000368248.2	hg19	CCDS34534.1																																																																																			.	.		0.351	THEMIS-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_001010923		TT	128135051	GG	TT	128135050	3	4	270	1	0	0	0	0	1	0	0	0	15875	1232	43	3	1322	3	THEMIS	6	128135050	Missense_Mutation	DNP	GG	TCGA-FV-A4ZP-01A-12D-A25V-10	11021092	128135050	42980017	24	39303										
MRPL32	64983	hgsc.bcm.edu	37	chr7	42976921	42976921	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	ttttgtttattgttttaaagAacaacatagacgtttgtcct	6	5	0	2			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr7:42976921A>G	ENST00000223324.2	+	3	500	c.313A>G	c.(313-315)Aac>Gac	p.N105D	MRPL32_ENST00000496564.1_Intron	NM_031903.2	NP_114109.1	Q9BYC8	RM32_HUMAN	mitochondrial ribosomal protein L32	105					translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrial ribosome (GO:0005761)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(1)|large_intestine(2)|lung(6)	10						TGTTTTAAAGAACAACATAGA	0.368																																					p.N105D		Atlas-SNP	.											.	MRPL32	25	.	0			c.A313G						.						125	117	119					7																	42976921		2203	4300	6503	SO:0001630	splice_region_variant	64983	exon3			TTAAAGAACAACA	AB051343	CCDS5468.1	7p14	2012-09-13			ENSG00000106591	ENSG00000106591		"Mitochondrial ribosomal proteins / large subunits"	14035	protein-coding gene	gene with protein product		611839				11543634	Standard	NM_031903		Approved	HSPC283, L32mt, MRP-L32, bMRP-59b	uc003tia.3	Q9BYC8	OTTHUMG00000155180	ENST00000223324.2:c.313-1A>G	chr7.hg19:g.42976921A>G		167.0	0.0		251.0	67.0	NM_031903	Q96Q68|Q9P098	Missense_Mutation	SNP	ENST00000223324.2	hg19	CCDS5468.1	.	.	.	.	.	.	.	.	.	.	A	10.20	1.285418	0.23478	.	.	ENSG00000106591	ENST00000223324	.	.	.	5.9	0.948	0.19561	.	0.698413	0.15874	N	0.240395	T	0.27629	0.0679	L	0.27053	0.805	0.33983	D	0.648258	B	0.17852	0.024	B	0.18871	0.023	T	0.18840	-1.0324	8	.	.	.	-6.3114	4.1015	0.10015	0.5604:0.2598:0.0651:0.1147	.	105	Q9BYC8	RM32_HUMAN	D	105	.	.	N	+	1	0	MRPL32	42943446	0.961000	0.32948	0.958000	0.39756	0.561000	0.35649	1.973000	0.40550	0.135000	0.18707	0.528000	0.53228	AAC	.	.		0.368	MRPL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338669.1	NM_031903	Missense_Mutation	G	42976921	A	G	42976921	5	3	270	1	0	0	0	0	0	0	1	0	9804	260	9	2	323	2	MRPL32	7	42976921	Splice_Site	SNP	A	TCGA-FV-A4ZP-01A-12D-A25V-10		42976921	116161742	25	39304										
TOX	9760	hgsc.bcm.edu	37	chr8	59750851	59750851	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	tccccatatcagaggcaggcCgcttctctccaccattgatc	7	16	2	2			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr8:59750851C>T	ENST00000361421.1	-	5	933	c.713G>A	c.(712-714)cGg>cAg	p.R238Q		NM_014729.2	NP_055544.1	O94900	TOX_HUMAN	thymocyte selection-associated high mobility group box	238						nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(13)|prostate(1)|skin(2)|stomach(1)	33		all_cancers(86;0.165)|Myeloproliferative disorder(644;0.00452)|all_lung(136;0.036)|Lung NSC(129;0.0464)|all_epithelial(80;0.0607)				AGAGGCAGGCCGCTTCTCTCC	0.433																																					p.R238Q	Pancreas(161;610 1969 17913 21374 22725)	Atlas-SNP	.											.	TOX	83	.	0			c.G713A						.						54	63	60					8																	59750851		2199	4298	6497	SO:0001583	missense	9760	exon5			GCAGGCCGCTTCT		CCDS34897.1	8q12.2-q12.3	2009-04-17			ENSG00000198846	ENSG00000198846			18988	protein-coding gene	gene with protein product		606863				9872452, 11850626	Standard	NM_014729		Approved	KIAA0808, TOX1	uc003xtw.1	O94900	OTTHUMG00000164331	ENST00000361421.1:c.713G>A	chr8.hg19:g.59750851C>T	ENSP00000354842:p.Arg238Gln	22.0	0.0		37.0	5.0	NM_014729	Q96AV5	Missense_Mutation	SNP	ENST00000361421.1	hg19	CCDS34897.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.454202	0.84209	.	.	ENSG00000198846	ENST00000361421	T	0.16324	2.35	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.25975	0.0633	L	0.52206	1.635	0.58432	D	0.999994	D	0.57899	0.981	P	0.47603	0.551	T	0.00289	-1.1844	9	.	.	.	.	20.0368	0.97565	0.0:1.0:0.0:0.0	.	238	O94900	TOX_HUMAN	Q	238	ENSP00000354842:R238Q	.	R	-	2	0	TOX	59913405	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.818000	0.86416	2.727000	0.93392	0.591000	0.81541	CGG	.	.		0.433	TOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378307.1	NM_014729		T	59750851	C	T	59750851	3	4	270	1	0	0	0	0	1	0	0	0	16392	652	23	1	887	1	TOX	8	59750851	Missense_Mutation	SNP	C	TCGA-FV-A4ZP-01A-12D-A25V-10		59750851	86613171	26	39305										
RALYL	138046	hgsc.bcm.edu	37	chr8	85799965	85799965	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	tgccgatggagaagagatgaCagatgggatagaggaggact	17	4	0	5			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr8:85799965C>T	ENST00000521268.1	+	8	1917	c.812C>T	c.(811-813)aCa>aTa	p.T271I	RALYL_ENST00000518566.1_Missense_Mutation_p.T260I|RALYL_ENST00000523850.1_Missense_Mutation_p.T198I|RALYL_ENST00000521695.1_Missense_Mutation_p.T271I|RALYL_ENST00000517638.1_Missense_Mutation_p.T284I|RALYL_ENST00000521376.1_Intron|RALYL_ENST00000522455.1_Missense_Mutation_p.T271I	NM_173848.5	NP_776247.3	Q86SE5	RALYL_HUMAN	RALY RNA binding protein-like	271							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)	24						GAAGAGATGACAGATGGGATA	0.483																																					p.T284I		Atlas-SNP	.											.	RALYL	123	.	0			c.C851T						.						155	159	157					8																	85799965		2011	4174	6185	SO:0001583	missense	138046	exon8			AGATGACAGATGG		CCDS55252.1, CCDS55253.1, CCDS75760.1, CCDS75761.1	8q21.2	2013-07-16			ENSG00000184672	ENSG00000184672		"RNA binding motif (RRM) containing"	27036	protein-coding gene	gene with protein product		614648				12688537	Standard	NM_001100391		Approved	HNRPCL3	uc003yct.4	Q86SE5	OTTHUMG00000164628	ENST00000521268.1:c.812C>T	chr8.hg19:g.85799965C>T	ENSP00000430367:p.Thr271Ile	135.0	0.0		278.0	18.0	NM_001100391	B3KTH2|G3V129|Q6ZW87|Q8N1C2	Missense_Mutation	SNP	ENST00000521268.1	hg19	CCDS55253.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.554996	0.86231	.	.	ENSG00000184672	ENST00000522455;ENST00000521695;ENST00000521268;ENST00000518566;ENST00000517638;ENST00000523850	T;T;T;T;T;T	0.15718	2.81;2.81;2.81;2.8;2.8;2.4	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.41119	0.1145	M	0.63428	1.95	0.80722	D	1	D;D;D;D	0.76494	0.995;0.999;0.999;0.995	D;D;D;D	0.80764	0.979;0.994;0.994;0.979	T	0.10222	-1.0639	10	0.44086	T	0.13	-7.1315	18.7753	0.91908	0.0:1.0:0.0:0.0	.	260;198;284;271	B3KT61;Q86SE5-2;G3V129;Q86SE5	.;.;.;RALYL_HUMAN	I	271;271;271;260;284;198	ENSP00000430394:T271I;ENSP00000428667:T271I;ENSP00000430367:T271I;ENSP00000430065:T260I;ENSP00000430128:T284I;ENSP00000428807:T198I	ENSP00000430128:T284I	T	+	2	0	RALYL	85962520	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.474000	0.73578	2.445000	0.82738	0.561000	0.74099	ACA	.	.		0.483	RALYL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379448.1			T	85799965	C	T	85799965	3	4	270	1	0	0	0	0	1	0	0	0	13035	478	17	3	881	3	RALYL	8	85799965	Missense_Mutation	SNP	C	TCGA-FV-A4ZP-01A-12D-A25V-10	26049114	85799965	60564057	27	39306										
TMEM2	23670	hgsc.bcm.edu	37	chr9	74355033	74355033	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	cttctggccatccacagtatAaaattctctttgggcaagag	8	10	2	1			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr9:74355033A>G	ENST00000377044.4	-	5	1689	c.1150T>C	c.(1150-1152)Tat>Cat	p.Y384H	TMEM2_ENST00000377066.5_Missense_Mutation_p.Y384H	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	384					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		TCCACAGTATAAAATTCTCTT	0.408																																					p.Y384H		Atlas-SNP	.											.	TMEM2	112	.	0			c.T1150C						.						111	107	108					9																	74355033		2203	4300	6503	SO:0001583	missense	23670	exon5			CAGTATAAAATTC		CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.1150T>C	chr9.hg19:g.74355033A>G	ENSP00000366243:p.Tyr384His	88.0	0.0		85.0	21.0	NM_001135820	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Missense_Mutation	SNP	ENST00000377044.4	hg19	CCDS6638.1	.	.	.	.	.	.	.	.	.	.	A	7.603	0.673129	0.14776	.	.	ENSG00000135048	ENST00000377044;ENST00000377066	T;T	0.72942	-0.7;-0.59	5.65	3.26	0.37387	.	0.522566	0.22405	N	0.060494	T	0.43166	0.1235	N	0.11427	0.14	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.09574	-1.0668	10	0.15066	T	0.55	.	3.445	0.07477	0.5441:0.2613:0.0689:0.1257	.	384;384	Q9UHN6;Q9UHN6-2	TMEM2_HUMAN;.	H	384	ENSP00000366243:Y384H;ENSP00000366266:Y384H	ENSP00000366243:Y384H	Y	-	1	0	TMEM2	73544853	0.999000	0.42202	0.996000	0.52242	0.957000	0.61999	0.876000	0.28092	0.402000	0.25451	0.402000	0.26972	TAT	.	.		0.408	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390		G	74355033	A	G	74355033	3	3	270	1	0	0	0	0	1	0	0	0	16136	362	13	2	3081	2	TMEM2	9	74355033	Missense_Mutation	SNP	A	TCGA-FV-A4ZP-01A-12D-A25V-10		74355033	66858398	28	39307										
CEP78	84131	hgsc.bcm.edu	37	chr9	80861605	80861605	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	ctcttgacctgcaacagtgcGgcctcaccaatgaaggagca	10	13	2	2			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr9:80861605G>T	ENST00000424347.2	+	6	1088	c.799G>T	c.(799-801)Ggc>Tgc	p.G267C	CEP78_ENST00000277082.5_Missense_Mutation_p.G267C|CEP78_ENST00000376597.4_Missense_Mutation_p.G267C|CEP78_ENST00000415759.2_Missense_Mutation_p.G267C|CEP78_ENST00000376598.2_Missense_Mutation_p.G267C			Q5JTW2	CEP78_HUMAN	centrosomal protein 78kDa	267					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)				breast(1)|cervix(1)|endometrium(5)|large_intestine(7)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	21						GCAACAGTGCGGCCTCACCAA	0.413																																					p.G267C		Atlas-SNP	.											.	CEP78	79	.	0			c.G799T						.						76	74	75					9																	80861605		1837	4102	5939	SO:0001583	missense	84131	exon6			CAGTGCGGCCTCA	BC058931	CCDS47984.1, CCDS47985.1	9q21.2	2014-02-20	2005-12-01	2005-12-01	ENSG00000148019	ENSG00000148019			25740	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 81"	C9orf81		14654843	Standard	NM_001098802		Approved	FLJ12643	uc004aky.4	Q5JTW2	OTTHUMG00000020062	ENST00000424347.2:c.799G>T	chr9.hg19:g.80861605G>T	ENSP00000411284:p.Gly267Cys	64.0	0.0		76.0	4.0	NM_001098802	A1A4S8|E9PHX5|Q5BJE3|Q5JTW0|Q5JTW1|Q9H9N3	Missense_Mutation	SNP	ENST00000424347.2	hg19		.	.	.	.	.	.	.	.	.	.	G	21.4	4.138721	0.77775	.	.	ENSG00000148019	ENST00000424347;ENST00000415085;ENST00000415759;ENST00000376597;ENST00000277082;ENST00000376598	T;T;T;T;T	0.54675	0.56;0.56;0.56;0.56;0.56	5.61	5.61	0.85477	.	0.141721	0.44097	D	0.000498	T	0.71771	0.3379	M	0.73753	2.245	0.54753	D	0.999985	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;0.999;1.0	T	0.74654	-0.3593	10	0.87932	D	0	-13.3175	13.9467	0.64089	0.0751:0.0:0.9249:0.0	.	180;267;267;267	B7Z8H9;E9PHX5;Q5JTW2-2;Q5JTW2	.;.;.;CEP78_HUMAN	C	267	ENSP00000411284:G267C;ENSP00000399286:G267C;ENSP00000365782:G267C;ENSP00000277082:G267C;ENSP00000365783:G267C	ENSP00000277082:G267C	G	+	1	0	CEP78	80051425	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	8.880000	0.92407	2.627000	0.88993	0.561000	0.74099	GGC	.	.		0.413	CEP78-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000052766.2	XM_095991		T	80861605	G	T	80861605	3	4	270	1	0	0	0	0	1	0	0	0	3264	1116	39	1	821	1	CEP78	9	80861605	Missense_Mutation	SNP	G	TCGA-FV-A4ZP-01A-12D-A25V-10	6506572	80861605	60351826	29	39308										
GALNT12	79695	hgsc.bcm.edu	37	chr9	101608380	101608380	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	ctgcgaagaaactgccccagAgaatcagaagttcatcttgc	9	11	3	3			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr9:101608380A>G	ENST00000375011.3	+	9	1580	c.1580A>G	c.(1579-1581)gAg>gGg	p.E527G	RP11-92C4.3_ENST00000433997.1_RNA|RP11-92C4.3_ENST00000589257.1_RNA	NM_024642.4	NP_078918.3	Q8IXK2	GLT12_HUMAN	polypeptide N-acetylgalactosaminyltransferase 12	527	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(1)|endometrium(2)|large_intestine(3)|lung(8)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	17		Acute lymphoblastic leukemia(62;0.0559)				ACTGCCCCAGAGAATCAGAAG	0.502																																					p.E527G		Atlas-SNP	.											.	GALNT12	37	.	0			c.A1580G						.						140	128	132					9																	101608380		2203	4300	6503	SO:0001583	missense	79695	exon9			CCCCAGAGAATCA	AB078146	CCDS6737.1	9q22.33	2014-03-13	2014-03-13		ENSG00000119514	ENSG00000119514	2.4.1.41	"Glycosyltransferase family 2 domain containing"	19877	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 12"	610290	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 12 (GalNAc-T12)"			12135769	Standard	NM_024642		Approved	GalNAc-T12	uc004ayz.3	Q8IXK2	OTTHUMG00000020348	ENST00000375011.3:c.1580A>G	chr9.hg19:g.101608380A>G	ENSP00000364150:p.Glu527Gly	257.0	0.0		252.0	44.0	NM_024642	Q5TCF7|Q8NG54|Q96CT9|Q9H771	Missense_Mutation	SNP	ENST00000375011.3	hg19	CCDS6737.1	.	.	.	.	.	.	.	.	.	.	A	10.24	1.296467	0.23650	.	.	ENSG00000119514	ENST00000375011	T	0.28069	1.63	5.93	5.93	0.95920	Ricin B-related lectin (1);Ricin B lectin (3);	0.348674	0.34178	N	0.004194	T	0.35364	0.0929	L	0.39692	1.235	0.46954	D	0.999265	P	0.49559	0.925	P	0.49922	0.626	T	0.03212	-1.1060	10	0.33141	T	0.24	.	14.3318	0.66561	1.0:0.0:0.0:0.0	.	527	Q8IXK2	GLT12_HUMAN	G	527	ENSP00000364150:E527G	ENSP00000364150:E527G	E	+	2	0	GALNT12	100648201	1.000000	0.71417	0.349000	0.25694	0.161000	0.22273	2.696000	0.47052	2.271000	0.75665	0.533000	0.62120	GAG	.	.		0.502	GALNT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053382.1	NM_024642		G	101608380	A	G	101608380	3	3	270	1	0	0	0	0	1	0	0	0	6218	304	11	2	1614	2	GALNT12	9	101608380	Missense_Mutation	SNP	A	TCGA-FV-A4ZP-01A-12D-A25V-10	20746775	101608380	39605051	30	39309										
TLR4	7099	hgsc.bcm.edu	37	chr9	120475751	120475751	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	tattcctatcactcagaaacCtcatttaccttgacatttct	2	12	4	2			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr9:120475751C>T	ENST00000355622.6	+	3	1446	c.1345C>T	c.(1345-1347)Ctc>Ttc	p.L449F	TLR4_ENST00000472304.1_3'UTR|TLR4_ENST00000394487.4_Missense_Mutation_p.L409F	NM_138554.4|NM_138557.2	NP_612564.1|NP_612567.1	O00206	TLR4_HUMAN	toll-like receptor 4	449					activation of MAPK activity (GO:0000187)|B cell proliferation involved in immune response (GO:0002322)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|detection of fungus (GO:0016046)|detection of lipopolysaccharide (GO:0032497)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|innate immune response (GO:0045087)|interferon-gamma production (GO:0032609)|intestinal epithelial structure maintenance (GO:0060729)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-23 production (GO:0032707)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of tumor necrosis factor production (GO:0032720)|nitric oxide production involved in inflammatory response (GO:0002537)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine production (GO:0032722)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 production (GO:0032732)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070430)|positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070434)|positive regulation of platelet activation (GO:0010572)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cytokine secretion (GO:0050707)|response to lipopolysaccharide (GO:0032496)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|lipopolysaccharide receptor complex (GO:0046696)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(66)|ovary(4)|pancreas(1)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	103					Naloxone(DB01183)	ACTCAGAAACCTCATTTACCT	0.393																																					p.L449F		Atlas-SNP	.											.	TLR4	220	.	0			c.C1345T						.						97	96	97					9																	120475751		2203	4300	6503	SO:0001583	missense	7099	exon3			AGAAACCTCATTT	U88880	CCDS6818.1	9q33.1	2013-01-23			ENSG00000136869	ENSG00000136869		"CD molecules"	11850	protein-coding gene	gene with protein product		603030				9435236, 9237759	Standard	NM_138554		Approved	hToll, CD284, TLR-4, ARMD10	uc004bjz.4	O00206	OTTHUMG00000021046	ENST00000355622.6:c.1345C>T	chr9.hg19:g.120475751C>T	ENSP00000363089:p.Leu449Phe	123.0	0.0		83.0	11.0	NM_138554	A8K1Y8|A9XLP9|A9XLQ0|A9XLQ1|B4E194|D1CS52|D1CS53|Q5VZI8|Q5VZI9|Q9UK78|Q9UM57	Missense_Mutation	SNP	ENST00000355622.6	hg19	CCDS6818.1	.	.	.	.	.	.	.	.	.	.	C	18.00	3.524352	0.64747	.	.	ENSG00000136869	ENST00000394487;ENST00000355622	T;T	0.06294	3.32;3.32	5.92	5.92	0.95590	.	0.000000	0.64402	D	0.000010	T	0.38585	0.1046	M	0.93763	3.455	0.44221	D	0.997058	D	0.89917	1.0	D	0.97110	1.0	T	0.48151	-0.9060	10	0.87932	D	0	.	20.3213	0.98679	0.0:1.0:0.0:0.0	.	449	O00206	TLR4_HUMAN	F	409;449	ENSP00000377997:L409F;ENSP00000363089:L449F	ENSP00000363089:L449F	L	+	1	0	TLR4	119515572	0.981000	0.34729	0.099000	0.21106	0.834000	0.47266	2.744000	0.47450	2.810000	0.96702	0.650000	0.86243	CTC	.	.		0.393	TLR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055549.3	NM_138554		T	120475751	C	T	120475751	3	4	270	1	0	0	0	0	1	0	0	0	15968	681	24	3	1355	3	TLR4	9	120475751	Missense_Mutation	SNP	C	TCGA-FV-A4ZP-01A-12D-A25V-10	18867371	120475751	20737680	31	39310										
BAT2L1	84726	hgsc.bcm.edu	37	chr9	134363453	134363453	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	caggctgctggcctgggtgcCtcccagatgttggactccca	13	14	0	1			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr9:134363453C>T	ENST00000357304.4	+	27	6250	c.6195C>T	c.(6193-6195)gcC>gcT	p.A2065A	PRRC2B_ENST00000405995.1_Silent_p.A1371A|SNORD62B_ENST00000426867.1_RNA|PRRC2B_ENST00000372249.1_Silent_p.A162A|PRRC2B_ENST00000458550.1_Silent_p.A1371A|SNORD62A_ENST00000428514.1_RNA	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	2065							poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						GCCTGGGTGCCTCCCAGATGT	0.587																																					p.A2065A		Atlas-SNP	.											.	PRRC2B	266	.	0			c.C6195T						.						24	26	26					9																	134363453		1970	4140	6110	SO:0001819	synonymous_variant	84726	exon27			GGGTGCCTCCCAG	AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"KIAA0515", "HLA-B associated transcript 2-like", "HLA-B associated transcript 2-like 1"	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.6195C>T	chr9.hg19:g.134363453C>T		108.0	0.0		113.0	14.0	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Silent	SNP	ENST00000357304.4	hg19	CCDS48044.1	.	.	.	.	.	.	.	.	.	.	C	10.21	1.287123	0.23478	.	.	ENSG00000130723	ENST00000320547	.	.	.	4.82	3.91	0.45181	.	.	.	.	.	T	0.62048	0.2396	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59867	-0.7373	4	.	.	.	-23.7936	11.898	0.52667	0.0:0.9144:0.0:0.0856	.	.	.	.	F	72	.	.	L	+	1	0	PRRC2B	133353274	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	1.153000	0.31676	2.382000	0.81193	0.561000	0.74099	CTC	.	.		0.587	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	134363453	C	T	134363453	2	4	270	1	0	0	0	0	0	0	0	1	1320	668	24	3		3	BAT2L1	9	134363453	Silent	SNP	C	TCGA-FV-A4ZP-01A-12D-A25V-10	13887702	134363453	6849978	32	39311										
ANKRD30A	91074	hgsc.bcm.edu	37	chr10	37442511	37442511	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	ttttaacagagtctctgtgaGactgtttcacagaaggatgt	10	6	2	3			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr10:37442511G>A	ENST00000602533.1	+	13	1650	c.1551G>A	c.(1549-1551)gaG>gaA	p.E517E	ANKRD30A_ENST00000361713.1_Silent_p.E517E|ANKRD30A_ENST00000374660.1_Silent_p.E517E			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	573					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						GTCTCTGTGAGACTGTTTCAC	0.269																																					p.E517E		Atlas-SNP	.											.	ANKRD30A	448	.	0			c.G1551A						.						104	106	106					10																	37442511		1794	4063	5857	SO:0001819	synonymous_variant	91074	exon13			CTGTGAGACTGTT	AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"Ankyrin repeat domain containing"	17234	protein-coding gene	gene with protein product	"breast cancer antigen NY-BR-1"	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.1551G>A	chr10.hg19:g.37442511G>A		886.0	0.0		900.0	66.0	NM_052997	Q5W025	Silent	SNP	ENST00000602533.1	hg19																																																																																				.	.		0.269	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997		A	37442511	G	A	37442511	2	1	270	1	0	0	0	0	0	0	0	1	658	933	33	3		3	ANKRD30A	10	37442511	Silent	SNP	G	TCGA-FV-A4ZP-01A-12D-A25V-10		37442511	98092236	33	39312										
ARID5B	84159	hgsc.bcm.edu	37	chr10	63851583	63851583	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	tcagatccccaccgctgcagCttctccaagcatcaccttaa	5	17	3	1			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr10:63851583C>A	ENST00000279873.7	+	10	2771	c.2361C>A	c.(2359-2361)agC>agA	p.S787R	ARID5B_ENST00000309334.5_Missense_Mutation_p.S544R	NM_032199.2	NP_115575.1	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)	787					adipose tissue development (GO:0060612)|adrenal gland development (GO:0030325)|cell development (GO:0048468)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|fat pad development (GO:0060613)|female gonad development (GO:0008585)|fibroblast migration (GO:0010761)|kidney development (GO:0001822)|liver development (GO:0001889)|male gonad development (GO:0008584)|multicellular organism growth (GO:0035264)|muscle organ morphogenesis (GO:0048644)|negative regulation of transcription, DNA-templated (GO:0045892)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|post-embryonic development (GO:0009791)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(13)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	Prostate(12;0.016)|all_hematologic(501;0.215)					ACCGCTGCAGCTTCTCCAAGC	0.502																																					p.S787R		Atlas-SNP	.											.	ARID5B	125	.	0			c.C2361A						.						93	95	94					10																	63851583		2203	4300	6503	SO:0001583	missense	84159	exon10			CTGCAGCTTCTCC	M73837	CCDS31208.1, CCDS58082.1	10q11.22	2013-02-07			ENSG00000150347	ENSG00000150347		"-"	17362	protein-coding gene	gene with protein product		608538				11483573, 11478881	Standard	NM_032199		Approved	FLJ21150, MRF2	uc001jlt.2	Q14865	OTTHUMG00000018298	ENST00000279873.7:c.2361C>A	chr10.hg19:g.63851583C>A	ENSP00000279873:p.Ser787Arg	98.0	0.0		96.0	16.0	NM_032199	B4DLB3|Q05DG6|Q32Q59|Q5VST4|Q6NZ42|Q7Z3M4|Q8N421|Q9H786	Missense_Mutation	SNP	ENST00000279873.7	hg19	CCDS31208.1	.	.	.	.	.	.	.	.	.	.	C	10.59	1.392859	0.25118	.	.	ENSG00000150347	ENST00000279873;ENST00000309334	T;T	0.43688	0.95;0.94	5.87	2.68	0.31781	.	0.509120	0.25783	N	0.028325	T	0.27798	0.0684	L	0.34521	1.04	0.18873	N	0.999986	B	0.33448	0.412	B	0.31614	0.133	T	0.13818	-1.0495	10	0.46703	T	0.11	-4.3184	7.1541	0.25626	0.0:0.566:0.0:0.434	.	787	Q14865	ARI5B_HUMAN	R	787;544	ENSP00000279873:S787R;ENSP00000308862:S544R	ENSP00000279873:S787R	S	+	3	2	ARID5B	63521589	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	0.770000	0.26618	0.827000	0.34685	0.655000	0.94253	AGC	.	.		0.502	ARID5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048233.1	XM_084482		A	63851583	C	A	63851583	3	1	270	1	0	0	0	0	1	0	0	0	922	796	28	3	2399	3	ARID5B	10	63851583	Missense_Mutation	SNP	C	TCGA-FV-A4ZP-01A-12D-A25V-10	26409072	63851583	71683164	34	39313										
LRIT1	26103	hgsc.bcm.edu	37	chr10	86001094	86001094	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	ctggccttgctgccatcaccCatgatatggaggctgcagct	11	13	1	1			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr10:86001094C>A	ENST00000372105.3	-	1	123	c.102G>T	c.(100-102)atG>atT	p.M34I		NM_015613.2	NP_056428.1	Q9P2V4	LRIT1_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 1	34	LRRNT.					integral component of endoplasmic reticulum membrane (GO:0030176)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|skin(1)	23						TGCCATCACCCATGATATGGA	0.642																																					p.M34I		Atlas-SNP	.											.	LRIT1	73	.	0			c.G102T						.						35	35	35					10																	86001094		2203	4298	6501	SO:0001583	missense	26103	exon1			ATCACCCATGATA	AB031547	CCDS7373.1	10q23	2013-02-11	2007-06-19	2007-06-19	ENSG00000148602	ENSG00000148602		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	23404	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 9"		"leucine rich repeat containing 21"	LRRC21		10777785	Standard	NM_015613		Approved	PAL, DKFZP434K091, FIGLER9	uc001kcz.1	Q9P2V4	OTTHUMG00000018632	ENST00000372105.3:c.102G>T	chr10.hg19:g.86001094C>A	ENSP00000361177:p.Met34Ile	153.0	0.0		181.0	70.0	NM_015613	Q0QD41|Q9Y4N7	Missense_Mutation	SNP	ENST00000372105.3	hg19	CCDS7373.1	.	.	.	.	.	.	.	.	.	.	C	10.88	1.474448	0.26423	.	.	ENSG00000148602	ENST00000372105	T	0.34072	1.38	4.31	3.36	0.38483	Leucine-rich repeat-containing N-terminal (1);	0.172115	0.39834	N	0.001256	T	0.17152	0.0412	N	0.14661	0.345	0.22754	N	0.99877	B	0.02656	0.0	B	0.01281	0.0	T	0.12016	-1.0564	10	0.17832	T	0.49	.	6.0871	0.19973	0.0:0.5717:0.3174:0.1109	.	34	Q9P2V4	LRIT1_HUMAN	I	34	ENSP00000361177:M34I	ENSP00000361177:M34I	M	-	3	0	LRIT1	85991074	0.974000	0.33945	1.000000	0.80357	0.851000	0.48451	0.272000	0.18644	2.205000	0.71048	0.491000	0.48974	ATG	.	.		0.642	LRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049109.1	NM_015613		A	86001094	C	A	86001094	3	1	270	1	0	0	0	0	1	0	0	0	8956	594	21	3	1785	3	LRIT1	10	86001094	Missense_Mutation	SNP	C	TCGA-FV-A4ZP-01A-12D-A25V-10	22149511	86001094	49533653	35	39314										
CHUK	1147	hgsc.bcm.edu	37	chr10	101953098	101953098	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	tgacagagaatgatcatgttCtgctgaagtcgggggcagcc	14	8	2	4			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr10:101953098C>T	ENST00000370397.7	-	19	2151	c.2065G>A	c.(2065-2067)Gaa>Aaa	p.E689K	CHUK_ENST00000590930.1_5'UTR|RP11-316M21.7_ENST00000443919.1_RNA	NM_001278.3	NP_001269.3	O15111	IKKA_HUMAN	conserved helix-loop-helix ubiquitous kinase	689					anatomical structure morphogenesis (GO:0009653)|cellular response to tumor necrosis factor (GO:0071356)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|morphogenesis of an epithelial sheet (GO:0002011)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hydroperoxide (GO:0033194)|response to lipopolysaccharide (GO:0032496)|response to toxic substance (GO:0009636)|response to virus (GO:0009615)|Rho protein signal transduction (GO:0007266)|skeletal muscle contraction (GO:0003009)|striated muscle cell differentiation (GO:0051146)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|scaffold protein binding (GO:0097110)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(9)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	27		Colorectal(252;0.117)		Epithelial(162;2.05e-10)|all cancers(201;1.91e-08)	Acetylcysteine(DB06151)|Aminosalicylic Acid(DB00233)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	TGATCATGTTCTGCTGAAGTC	0.473																																					p.E689K	Ovarian(159;52 1904 10536 35305 37148)	Atlas-SNP	.											.	CHUK	71	.	0			c.G2065A						.						127	109	115					10																	101953098		2203	4300	6503	SO:0001583	missense	1147	exon19			CATGTTCTGCTGA	AF009225	CCDS7488.1	10q24-q25	2008-08-01			ENSG00000213341	ENSG00000213341			1974	protein-coding gene	gene with protein product		600664		TCF16		7558004, 16902410	Standard	XR_246062		Approved	IKK1, IKK-alpha, IkBKA, NFKBIKA, IKKA	uc001kqp.3	O15111	OTTHUMG00000018899	ENST00000370397.7:c.2065G>A	chr10.hg19:g.101953098C>T	ENSP00000359424:p.Glu689Lys	115.0	0.0		119.0	24.0	NM_001278	O14666|Q13132|Q5W0I4|Q92467	Missense_Mutation	SNP	ENST00000370397.7	hg19	CCDS7488.1	.	.	.	.	.	.	.	.	.	.	C	8.738	0.918202	0.17982	.	.	ENSG00000213341	ENST00000370397	T	0.71103	-0.54	5.73	4.82	0.62117	.	0.692508	0.15390	N	0.264899	T	0.57051	0.2027	L	0.36672	1.1	0.26122	N	0.980533	B	0.17667	0.023	B	0.14578	0.011	T	0.39702	-0.9601	10	0.06236	T	0.91	-8.2869	12.3854	0.55328	0.0:0.8127:0.1873:0.0	.	689	O15111	IKKA_HUMAN	K	689	ENSP00000359424:E689K	ENSP00000359424:E689K	E	-	1	0	CHUK	101943088	1.000000	0.71417	0.993000	0.49108	0.946000	0.59487	2.494000	0.45329	1.391000	0.46566	0.650000	0.86243	GAA	.	.		0.473	CHUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049836.1	NM_001278		T	101953098	C	T	101953098	3	4	270	1	0	0	0	0	1	0	0	0	3418	922	32	3	184	3	CHUK	10	101953098	Missense_Mutation	SNP	C	TCGA-FV-A4ZP-01A-12D-A25V-10	15952004	101953098	33581649	36	39315										
DCHS1	8642	hgsc.bcm.edu	37	chr11	6650989	6650989	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	ggacgctgtactcctgctgcTggaaagtaggcgcctcgtcg	14	12	0	0			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr11:6650989T>C	ENST00000299441.3	-	11	5360	c.4949A>G	c.(4948-4950)cAg>cGg	p.Q1650R	RP11-732A19.6_ENST00000526633.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	1650	Cadherin 16. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CTCCTGCTGCTGGAAAGTAGG	0.652																																					p.Q1650R		Atlas-SNP	.											.	DCHS1	277	.	0			c.A4949G						.						40	41	41					11																	6650989		2201	4296	6497	SO:0001583	missense	8642	exon11			TGCTGCTGGAAAG	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"Cadherins / Cadherin-related"	13681	protein-coding gene	gene with protein product	"cadherin-related family member 6"	603057	"protocadherin 16", "dachsous 1 (Drosophila)"	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.4949A>G	chr11.hg19:g.6650989T>C	ENSP00000299441:p.Gln1650Arg	58.0	0.0		66.0	9.0	NM_003737	O15098	Missense_Mutation	SNP	ENST00000299441.3	hg19	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	T	4.728	0.135420	0.09032	.	.	ENSG00000166341	ENST00000299441	T	0.01705	4.68	5.25	-0.211	0.13172	Cadherin (2);Cadherin-like (1);	0.544274	0.15628	N	0.252516	T	0.01870	0.0059	L	0.33339	1.005	0.23739	N	0.996971	B	0.18166	0.026	B	0.20184	0.028	T	0.44112	-0.9349	10	0.19147	T	0.46	.	14.6338	0.68676	0.0:0.0:0.488:0.512	.	1650	Q96JQ0	PCD16_HUMAN	R	1650	ENSP00000299441:Q1650R	ENSP00000299441:Q1650R	Q	-	2	0	DCHS1	6607565	0.758000	0.28405	0.997000	0.53966	0.048000	0.14542	0.832000	0.27490	0.083000	0.17047	-0.460000	0.05396	CAG	.	.		0.652	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		C	6650989	T	C	6650989	3	2	270	1	0	0	0	0	1	0	0	0	4289	1580	55	2	4991	2	DCHS1	11	6650989	Missense_Mutation	SNP	T	TCGA-FV-A4ZP-01A-12D-A25V-10		6650989	128355527	37	39316										
SBF2	81846	hgsc.bcm.edu	37	chr11	9829584	9829584	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	agaactgtaagaagactggaGcaaaaccactcccctgacag	9	11	0	4			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr11:9829584G>T	ENST00000256190.8	-	32	4543	c.4406C>A	c.(4405-4407)gCt>gAt	p.A1469D	SBF2-AS1_ENST00000525636.1_RNA|SBF2-AS1_ENST00000534671.1_RNA|SBF2-AS1_ENST00000498905.2_RNA	NM_030962.3	NP_112224.1	Q86WG5	MTMRD_HUMAN	SET binding factor 2	1469	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				cell death (GO:0008219)|myelination (GO:0042552)|positive regulation of Rab GTPase activity (GO:0032851)|protein tetramerization (GO:0051262)	membrane (GO:0016020)|vacuolar membrane (GO:0005774)	phosphatase activity (GO:0016791)|phosphatase regulator activity (GO:0019208)|phosphatidylinositol binding (GO:0035091)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(4)|endometrium(8)|kidney(2)|large_intestine(8)|lung(16)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)		GAAGACTGGAGCAAAACCACT	0.438																																					p.A1469D		Atlas-SNP	.											.	SBF2	146	.	0			c.C4406A						.						83	70	75					11																	9829584		2201	4294	6495	SO:0001583	missense	81846	exon32			ACTGGAGCAAAAC	AB051553	CCDS31427.1	11p15.3	2014-09-17	2004-11-12	2004-11-12	ENSG00000133812	ENSG00000133812		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins", "DENN/MADD domain containing", "Pleckstrin homology (PH) domain containing"	2135	protein-coding gene	gene with protein product	"myotubularin related 13"	607697	"Charcot-Marie-Tooth neuropathy 4B2 (autosomal recessive, with myelin outfolding)", "DENN/MADD domain containing 7B"	CMT4B2		10644431	Standard	NM_030962		Approved	KIAA1766, MTMR13, DENND7B	uc001mib.2	Q86WG5	OTTHUMG00000165890	ENST00000256190.8:c.4406C>A	chr11.hg19:g.9829584G>T	ENSP00000256190:p.Ala1469Asp	96.0	0.0		102.0	5.0	NM_030962	Q3MJF0|Q68DQ3|Q6P459|Q6PJD1|Q7Z325|Q7Z621|Q86VE2|Q96FE2|Q9C097	Missense_Mutation	SNP	ENST00000256190.8	hg19	CCDS31427.1	.	.	.	.	.	.	.	.	.	.	G	19.79	3.892446	0.72524	.	.	ENSG00000133812	ENST00000256190	D	0.93604	-3.25	5.91	5.91	0.95273	Myotubularin phosphatase domain (1);	0.414893	0.31051	N	0.008348	D	0.94414	0.8203	M	0.80508	2.5	0.48040	D	0.999579	P	0.36465	0.554	B	0.43575	0.424	D	0.94257	0.7499	10	0.87932	D	0	.	13.4829	0.61348	0.0708:0.0:0.9291:0.0	.	1469	Q86WG5	MTMRD_HUMAN	D	1469	ENSP00000256190:A1469D	ENSP00000256190:A1469D	A	-	2	0	SBF2	9786160	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.061000	0.89467	2.793000	0.96121	0.655000	0.94253	GCT	.	.		0.438	SBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386911.2	NM_030962		T	9829584	G	T	9829584	3	4	270	1	0	0	0	0	1	0	0	0	13874	971	34	3	1179	3	SBF2	11	9829584	Missense_Mutation	SNP	G	TCGA-FV-A4ZP-01A-12D-A25V-10	3178595	9829584	125176932	38	39317										
TEAD1	7003	hgsc.bcm.edu	37	chr11	12958680	12958680	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	taacaaacagggatacacaaGaaactctactctgcatggcc	7	11	2	1			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr11:12958680G>A	ENST00000526600.1	+	8	1127	c.904G>A	c.(904-906)Gaa>Aaa	p.E302K	TEAD1_ENST00000361985.2_Missense_Mutation_p.E398K|TEAD1_ENST00000527636.1_Missense_Mutation_p.E398K|TEAD1_ENST00000361905.4_Missense_Mutation_p.E383K|TEAD1_ENST00000334310.6_Missense_Mutation_p.E329K|TEAD1_ENST00000527575.1_Missense_Mutation_p.E340K			P28347	TEAD1_HUMAN	TEA domain family member 1 (SV40 transcriptional enhancer factor)	398	Transcriptional activation. {ECO:0000255}.				gene expression (GO:0010467)|hippo signaling (GO:0035329)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)	17				Epithelial(150;0.00223)|BRCA - Breast invasive adenocarcinoma(625;0.236)		GGATACACAAGAAACTCTACT	0.353																																					p.E398K		Atlas-SNP	.											.	TEAD1	40	.	0			c.G1192A						.						97	90	92					11																	12958680		2200	4294	6494	SO:0001583	missense	7003	exon13			ACACAAGAAACTC	X84839	CCDS7810.1, CCDS7810.2	11p15.4	2008-11-12				ENSG00000187079			11714	protein-coding gene	gene with protein product		189967	"atrophia areata, peripapillary chorioretinal degeneration"	TCF13, AA		1851669, 9889009, 15016762	Standard	NM_021961		Approved	TEF-1	uc021qdx.1	P28347		ENST00000526600.1:c.904G>A	chr11.hg19:g.12958680G>A	ENSP00000435393:p.Glu302Lys	160.0	0.0		152.0	23.0	NM_021961	A4FUP2|E7EV65	Missense_Mutation	SNP	ENST00000526600.1	hg19		.	.	.	.	.	.	.	.	.	.	G	26.4	4.736256	0.89482	.	.	ENSG00000187079	ENST00000361905;ENST00000527636;ENST00000527575;ENST00000334310;ENST00000361985;ENST00000526600	T;T;T;T;T;T	0.31769	1.48;1.48;1.48;1.48;1.48;1.48	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.68109	0.2965	M	0.93507	3.425	0.52501	D	0.999956	D;D;D	0.89917	0.978;0.999;1.0	D;D;D	0.91635	0.966;0.998;0.999	T	0.76838	-0.2811	10	0.87932	D	0	-5.4151	19.2947	0.94117	0.0:0.0:1.0:0.0	.	329;302;398	A4FUP2;E9PKB7;P28347	.;.;TEAD1_HUMAN	K	383;398;340;329;398;302	ENSP00000355332:E383K;ENSP00000435233:E398K;ENSP00000435977:E340K;ENSP00000334754:E329K;ENSP00000354588:E398K;ENSP00000435393:E302K	ENSP00000334754:E329K	E	+	1	0	TEAD1	12915256	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.803000	0.99136	2.652000	0.90054	0.650000	0.86243	GAA	.	.		0.353	TEAD1-007	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000387220.1	NM_021961		A	12958680	G	A	12958680	3	1	270	1	0	0	0	0	1	0	0	0	15753	943	33	3	1234	3	TEAD1	11	12958680	Missense_Mutation	SNP	G	TCGA-FV-A4ZP-01A-12D-A25V-10	3129096	12958680	122047836	39	39318										
GLYATL1	92292	hgsc.bcm.edu	37	chr11	58722261	58722261	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	aggagatgactgatgacatgGattcatacacaaacgtatat	9	6	1	4			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr11:58722261G>A	ENST00000317391.4	+	6	545	c.205G>A	c.(205-207)Gat>Aat	p.D69N	GLYATL1_ENST00000300079.5_Missense_Mutation_p.D100N|RP11-142C4.6_ENST00000533954.1_RNA	NM_001220494.1	NP_001207423.1	Q969I3	GLYL1_HUMAN	glycine-N-acyltransferase-like 1	69						mitochondrion (GO:0005739)	glutamine N-acyltransferase activity (GO:0047946)|glycine N-acyltransferase activity (GO:0047961)			NS(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(19)|ovary(1)|skin(4)|urinary_tract(1)	34					Glycine(DB00145)	TGATGACATGGATTCATACAC	0.363																																					p.D100N		Atlas-SNP	.											.	GLYATL1	89	.	0			c.G298A						.						94	88	90					11																	58722261		2201	4295	6496	SO:0001583	missense	92292	exon5			GACATGGATTCAT	AK091965	CCDS31556.1, CCDS55768.1	11q12.1	2014-08-12			ENSG00000166840	ENSG00000166840			30519	protein-coding gene	gene with protein product		614761				12477932	Standard	NM_080661		Approved	MGC15397, FLJ34646	uc001nnh.2	Q969I3	OTTHUMG00000167221	ENST00000317391.4:c.205G>A	chr11.hg19:g.58722261G>A	ENSP00000322223:p.Asp69Asn	225.0	0.0		150.0	35.0	NM_080661	A6NDT0|Q7Z510|Q8NAW8	Missense_Mutation	SNP	ENST00000317391.4	hg19	CCDS55768.1	.	.	.	.	.	.	.	.	.	.	.	12.76	2.036001	0.35893	.	.	ENSG00000166840	ENST00000526351;ENST00000317391;ENST00000532726;ENST00000300079	T;T;T;T	0.28255	1.62;1.62;1.62;1.62	2.37	0.244	0.15507	Acyl-CoA N-acyltransferase (1);Glycine N-acyltransferase, N-terminal (1);	0.680488	0.12904	U	0.429543	T	0.29976	0.0750	M	0.83223	2.63	0.09310	N	0.999999	B;B	0.30033	0.17;0.266	B;B	0.25506	0.015;0.061	T	0.27191	-1.0081	10	0.46703	T	0.11	.	3.6059	0.08042	0.1662:0.2604:0.5733:0.0	.	100;69	Q969I3-2;Q969I3	.;GLYL1_HUMAN	N	92;69;69;100	ENSP00000434652:D92N;ENSP00000322223:D69N;ENSP00000436116:D69N;ENSP00000300079:D100N	ENSP00000300079:D100N	D	+	1	0	GLYATL1	58478837	0.404000	0.25328	0.000000	0.03702	0.038000	0.13279	1.183000	0.32041	-0.073000	0.12842	0.195000	0.17529	GAT	.	.		0.363	GLYATL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393783.1	NM_080661		A	58722261	G	A	58722261	3	1	270	1	0	0	0	0	1	0	0	0	6488	1174	41	3	316	3	GLYATL1	11	58722261	Missense_Mutation	SNP	G	TCGA-FV-A4ZP-01A-12D-A25V-10	45763581	58722261	76284255	40	39319										
SLC35F2	54733	hgsc.bcm.edu	37	chr11	107663412	107663412	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	caggttgtcaatcccaatgcTggtgactggaggcacgctgc	13	11	1	1			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr11:107663412T>C	ENST00000525815.1	-	8	1474	c.1054A>G	c.(1054-1056)Agc>Ggc	p.S352G	SLC35F2_ENST00000265836.7_Missense_Mutation_p.S204G|SLC35F2_ENST00000525071.1_Silent_p.P349P|SLC35F2_ENST00000429869.1_Missense_Mutation_p.S352G|SLC35F2_ENST00000375682.4_Missense_Mutation_p.S305G	NM_017515.4	NP_059985.2	Q8IXU6	S35F2_HUMAN	solute carrier family 35, member F2	352					transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(61;9.46e-06)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;0.000111)|all_hematologic(158;0.000315)|all_epithelial(67;0.00197)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)|Epithelial(105;0.000105)|all cancers(92;0.00217)		ATCCCAATGCTGGTGACTGGA	0.592																																					p.S352G		Atlas-SNP	.											.	SLC35F2	29	.	0			c.A1054G						.						56	61	59					11																	107663412		1996	4181	6177	SO:0001583	missense	54733	exon8			CAATGCTGGTGAC		CCDS41709.1	11q22.3	2013-05-22			ENSG00000110660	ENSG00000110660		"Solute carriers"	23615	protein-coding gene	gene with protein product						9119394	Standard	NM_017515		Approved	FLJ13018	uc001pjq.3	Q8IXU6	OTTHUMG00000166366	ENST00000525815.1:c.1054A>G	chr11.hg19:g.107663412T>C	ENSP00000436785:p.Ser352Gly	120.0	0.0		79.0	20.0	NM_017515	Q14963|Q5JPA8|Q6ZRQ3|Q9H947	Missense_Mutation	SNP	ENST00000525815.1	hg19	CCDS41709.1	.	.	.	.	.	.	.	.	.	.	T	14.66	2.601920	0.46423	.	.	ENSG00000110660	ENST00000525815;ENST00000265836;ENST00000375682;ENST00000429869	.	.	.	5.13	-0.488	0.12056	.	0.648971	0.16728	N	0.201974	T	0.29556	0.0737	L	0.43152	1.355	0.26718	N	0.970839	B	0.22080	0.064	B	0.30943	0.122	T	0.22208	-1.0223	9	0.28530	T	0.3	.	3.3906	0.07287	0.2951:0.1757:0.0:0.5292	.	352	Q8IXU6	S35F2_HUMAN	G	352;204;305;352	.	ENSP00000265836:S204G	S	-	1	0	SLC35F2	107168622	0.965000	0.33210	0.980000	0.43619	0.782000	0.44232	-0.021000	0.12504	-0.235000	0.09767	-0.336000	0.08194	AGC	.	.		0.592	SLC35F2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389417.1	NM_017515		C	107663412	T	C	107663412	3	2	270	1	0	0	0	0	1	0	0	0	14604	1580	55	2	74	2	SLC35F2	11	107663412	Missense_Mutation	SNP	T	TCGA-FV-A4ZP-01A-12D-A25V-10	48941151	107663412	27343104	41	39320										
KLRK1	22914	hgsc.bcm.edu	37	chr12	10531200	10531200	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	aaggctggcattttgagacaTacaagaagcctggctctcat	10	9	1	2			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr12:10531200T>C	ENST00000240618.6	-	6	522	c.382A>G	c.(382-384)Atg>Gtg	p.M128V	KLRC4-KLRK1_ENST00000539300.1_3'UTR|RP11-277P12.20_ENST00000500682.1_RNA|KLRK1_ENST00000540818.1_Missense_Mutation_p.M128V	NM_001199805.1|NM_007360.3	NP_001186734.1|NP_031386.2	P26718	NKG2D_HUMAN	killer cell lectin-like receptor subfamily K, member 1	128	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cell differentiation (GO:0030154)|innate immune response (GO:0045087)|natural killer cell activation (GO:0030101)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|skin(1)	9						TTTTGAGACATACAAGAAGCC	0.368																																					p.M128V		Atlas-SNP	.											.	.	.	.	0			c.A382G						.						93	97	95					12																	10531200		2203	4300	6503	SO:0001583	missense	0	exon11			GAGACATACAAGA	AJ001687	CCDS8623.1	12p13.2-p12.3	2010-02-17	2003-02-19		ENSG00000213809	ENSG00000213809		"Killer cell lectin-like receptors", "CD molecules"	18788	protein-coding gene	gene with protein product		611817	"DNA segment on chromosome 12 (unique) 2489 expressed sequence"	D12S2489E		9683661, 2007850	Standard	NM_007360		Approved	NKG2D, KLR, NKG2-D, CD314	uc009zhj.3	P26718	OTTHUMG00000168574	ENST00000240618.6:c.382A>G	chr12.hg19:g.10531200T>C	ENSP00000240618:p.Met128Val	93.0	0.0		60.0	23.0	NM_001199805	A8K7K5|A8K7P4|Q9NR41	Missense_Mutation	SNP	ENST00000240618.6	hg19	CCDS8623.1	.	.	.	.	.	.	.	.	.	.	T	0.005	-2.219305	0.00286	.	.	ENSG00000213809	ENST00000240618;ENST00000540818	T;T	0.62498	0.02;0.02	5.96	-10.6	0.00265	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.711003	0.13304	N	0.398000	T	0.24774	0.0601	N	0.10664	0.02	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.12156	0.007;0.002	T	0.39563	-0.9608	10	0.02654	T	1	.	7.2069	0.25911	0.0964:0.5271:0.1015:0.275	.	109;128	Q1HEA1;P26718	.;NKG2D_HUMAN	V	128	ENSP00000240618:M128V;ENSP00000446003:M128V	ENSP00000240618:M128V	M	-	1	0	KLRK1	10422467	0.001000	0.12720	0.000000	0.03702	0.028000	0.11728	-0.835000	0.04386	-1.503000	0.01812	-1.127000	0.01993	ATG	.	.		0.368	KLRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400269.1	NM_007360		C	10531200	T	C	10531200	3	2	270	1	0	0	0	0	1	0	0	0	8432	1406	49	2	280	2	KLRK1	12	10531200	Missense_Mutation	SNP	T	TCGA-FV-A4ZP-01A-12D-A25V-10		10531200	123320695	42	39321										
MON2	23041	hgsc.bcm.edu	37	chr12	62926222	62926222	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	tttttcataatttcagcttaGaaatgttggacaaagttgag	8	4	2	2			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr12:62926222G>T	ENST00000393632.2	+	12	1796	c.1405G>T	c.(1405-1407)Gaa>Taa	p.E469*	MON2_ENST00000552738.1_Nonsense_Mutation_p.E469*|MON2_ENST00000552115.1_Nonsense_Mutation_p.E469*|MON2_ENST00000393630.3_Nonsense_Mutation_p.E469*|MON2_ENST00000280379.6_Nonsense_Mutation_p.E469*|MON2_ENST00000546600.1_Nonsense_Mutation_p.E469*|MON2_ENST00000393629.2_Nonsense_Mutation_p.E469*	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	469					actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		TTTCAGCTTAGAAATGTTGGA	0.328																																					p.E469X		Atlas-SNP	.											MON2,NS,carcinoma,0,1	MON2	160	.	0			c.G1405T						.						97	84	89					12																	62926222		2203	4300	6503	SO:0001587	stop_gained	23041	exon12			AGCTTAGAAATGT		CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987			29177	protein-coding gene	gene with protein product			"MON2 homolog (yeast)"			16301316, 24285343	Standard	NM_015026		Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000393632.2:c.1405G>T	chr12.hg19:g.62926222G>T	ENSP00000377252:p.Glu469*	122.0	0.0		124.0	19.0	NM_015026	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Nonsense_Mutation	SNP	ENST00000393632.2	hg19	CCDS31849.1	.	.	.	.	.	.	.	.	.	.	G	41	8.997676	0.99031	.	.	ENSG00000061987	ENST00000393632;ENST00000393630;ENST00000280379;ENST00000546600;ENST00000261188;ENST00000552738;ENST00000393629;ENST00000552115	.	.	.	5.4	4.51	0.55191	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-6.3575	14.2964	0.66316	0.072:0.0:0.928:0.0	.	.	.	.	X	469;469;469;469;397;469;469;469	.	.	E	+	1	0	MON2	61212489	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	9.869000	0.99810	1.259000	0.44117	0.563000	0.77884	GAA	.	.		0.328	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026		T	62926222	G	T	62926222	4	4	270	1	0	0	0	0	0	1	0	0	9709	943	33	3	1451	3	MON2	12	62926222	Nonsense_Mutation	SNP	G	TCGA-FV-A4ZP-01A-12D-A25V-10	52395022	62926222	70925673	43	39322										
BRCA2	675	hgsc.bcm.edu	37	chr13	32914479	32914479	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	agatgcttcattacaaaacgCaagacaagtgttttctgaaa	7	7	2	3	rs80358834		TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr13:32914479C>G	ENST00000380152.3	+	11	6220	c.5987C>G	c.(5986-5988)gCa>gGa	p.A1996G	BRCA2_ENST00000544455.1_Missense_Mutation_p.A1996G			P51587	BRCA2_HUMAN	breast cancer 2, early onset	1996					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TTACAAAACGCAAGACAAGTG	0.378			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											p.A1996G	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	.	BRCA2	812	.	0			c.C5987G						.						64	69	67					13																	32914479		2202	4298	6500	SO:0001583	missense	675	exon11	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	AAAACGCAAGACA	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.5987C>G	chr13.hg19:g.32914479C>G	ENSP00000369497:p.Ala1996Gly	66.0	0.0		56.0	22.0	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	hg19	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.598770	0.87055	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	D;D	0.82344	-1.6;-1.6	5.72	5.72	0.89469	.	0.086607	0.50627	D	0.000120	D	0.91236	0.7238	M	0.75264	2.295	0.50813	D	0.999898	D	0.89917	1.0	D	0.72338	0.977	D	0.91407	0.5148	10	0.72032	D	0.01	.	19.8965	0.96963	0.0:1.0:0.0:0.0	.	1996	P51587	BRCA2_HUMAN	G	1996	ENSP00000369497:A1996G;ENSP00000439902:A1996G	ENSP00000369497:A1996G	A	+	2	0	BRCA2	31812479	1.000000	0.71417	0.973000	0.42090	0.975000	0.68041	6.118000	0.71583	2.717000	0.92951	0.655000	0.94253	GCA	.	.		0.378	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		G	32914479	C	G	32914479	3	3	270	1	0	0	0	0	1	0	0	0	1501	710	25	4	6025	4	BRCA2	13	32914479	Missense_Mutation	SNP	C	TCGA-FV-A4ZP-01A-12D-A25V-10		32914479	82255399	44	39323										
PCDH17	27253	hgsc.bcm.edu	37	chr13	58206732	58206732	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	tatgggcccctgccctcactCtcaagaacctcaactactcc	5	18	3	1			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr13:58206732C>A	ENST00000377918.3	+	1	78	c.52C>A	c.(52-54)Ctc>Atc	p.L18I		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	18	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(30)|liver(2)|lung(54)|ovary(4)|pancreas(2)|prostate(5)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		TGCCCTCACTCTCAAGAACCT	0.612																																					p.L18I	Melanoma(72;952 1291 1619 12849 33676)	Atlas-SNP	.											.	PCDH17	304	.	0			c.C52A						.						48	44	46					13																	58206732		2203	4300	6503	SO:0001583	missense	27253	exon1			CTCACTCTCAAGA	AF029343	CCDS31986.1	13q21.1	2010-01-26			ENSG00000118946	ENSG00000118946		"Cadherins / Protocadherins : Non-clustered"	14267	protein-coding gene	gene with protein product		611760				10835267	Standard	NM_001040429		Approved	PCDH68, PCH68	uc001vhq.1	O14917	OTTHUMG00000016992	ENST00000377918.3:c.52C>A	chr13.hg19:g.58206732C>A	ENSP00000367151:p.Leu18Ile	103.0	0.0		98.0	23.0	NM_001040429	A8K1R5|Q5VVW9|Q5VVX0	Missense_Mutation	SNP	ENST00000377918.3	hg19	CCDS31986.1	.	.	.	.	.	.	.	.	.	.	C	12.88	2.070716	0.36566	.	.	ENSG00000118946	ENST00000377918	T	0.15487	2.42	5.55	4.7	0.59300	Cadherin (2);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.34861	0.0912	M	0.76328	2.33	0.42050	D	0.991119	D;D	0.57571	0.972;0.98	P;P	0.59643	0.861;0.729	T	0.11275	-1.0594	9	.	.	.	.	10.0683	0.42317	0.0:0.7905:0.1386:0.0709	.	18;18	O14917-2;O14917	.;PCD17_HUMAN	I	18	ENSP00000367151:L18I	.	L	+	1	0	PCDH17	57104733	0.804000	0.28969	0.984000	0.44739	0.843000	0.47879	1.364000	0.34171	1.570000	0.49709	0.655000	0.94253	CTC	.	.		0.612	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429		A	58206732	C	A	58206732	3	1	270	1	0	0	0	0	1	0	0	0	11521	913	32	3	54	3	PCDH17	13	58206732	Missense_Mutation	SNP	C	TCGA-FV-A4ZP-01A-12D-A25V-10	25292253	58206732	56963146	45	39324										
LMO7	4008	hgsc.bcm.edu	37	chr13	76381696	76381696	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	acataccaaaattgatcccaCttctggcccaaggctcataa	5	13	2	1			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr13:76381696C>A	ENST00000321797.8	+	8	1299	c.578C>A	c.(577-579)aCt>aAt	p.T193N	LMO7_ENST00000357063.3_Missense_Mutation_p.T478N|LMO7_ENST00000341547.4_Intron|LMO7_ENST00000377534.3_Missense_Mutation_p.T478N|LMO7_ENST00000526202.1_Intron|LMO7_ENST00000465261.2_Missense_Mutation_p.T193N|RP11-29G8.3_ENST00000563635.1_RNA			Q8WWI1	LMO7_HUMAN	LIM domain 7	478					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(20)|lung(15)|ovary(2)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		ATTGATCCCACTTCTGGCCCA	0.468																																					p.T193N		Atlas-SNP	.											.	LMO7	334	.	0			c.C578A						.						102	90	94					13																	76381696		1568	3582	5150	SO:0001583	missense	4008	exon7			ATCCCACTTCTGG	AF092557	CCDS9454.1, CCDS53876.1	13q22.2	2008-02-05	2004-06-15		ENSG00000136153	ENSG00000136153			6646	protein-coding gene	gene with protein product	"F-box only protein 20"	604362	"LIM domain only 7"	FBXO20		9826547, 10531035	Standard	NM_005358		Approved	FBX20, KIAA0858	uc021rkq.1	Q8WWI1	OTTHUMG00000017093	ENST00000321797.8:c.578C>A	chr13.hg19:g.76381696C>A	ENSP00000317802:p.Thr193Asn	86.0	0.0		84.0	39.0	NM_015842	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Missense_Mutation	SNP	ENST00000321797.8	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.3|24.3	4.514042|4.514042	0.85389|0.85389	.|.	.|.	ENSG00000136153|ENSG00000136153	ENST00000447038|ENST00000357063;ENST00000377534;ENST00000321797;ENST00000465261;ENST00000526528	.|T;T;T;T	.|0.56275	.|0.47;0.47;0.47;0.47	5.72|5.72	5.72|5.72	0.89469|0.89469	.|.	.|0.055457	.|0.64402	.|D	.|0.000001	T|T	0.72145|0.72145	0.3424|0.3424	M|M	0.66939|0.66939	2.045|2.045	0.54753|0.54753	D|D	0.999988|0.999988	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.69307	.|0.963;0.963	T|T	0.73382|0.73382	-0.4000|-0.4000	5|10	.|0.72032	.|D	.|0.01	-17.5198|-17.5198	19.8807|19.8807	0.96899|0.96899	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|478;193	.|Q8WWI1;E9PLH4	.|LMO7_HUMAN;.	Q|N	101|478;478;193;193;99	.|ENSP00000349571:T478N;ENSP00000366757:T478N;ENSP00000317802:T193N;ENSP00000433352:T193N	.|ENSP00000317802:T193N	H|T	+|+	3|2	2|0	LMO7|LMO7	75279697|75279697	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.921000|0.921000	0.55340|0.55340	7.206000|7.206000	0.77891|0.77891	2.698000|2.698000	0.92095|0.92095	0.655000|0.655000	0.94253|0.94253	CAC|ACT	.	.		0.468	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3	NM_005358		A	76381696	C	A	76381696	3	1	270	1	0	0	0	0	1	0	0	0	8864	565	20	3	1475	3	LMO7	13	76381696	Missense_Mutation	SNP	C	TCGA-FV-A4ZP-01A-12D-A25V-10	18174964	76381696	38788182	46	39325										
UBAC2	337867	hgsc.bcm.edu	37	chr13	100020041	100020041	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	gtgtgttgatctctttttagGgaggaatgatcaattggaat	12	3	2	2			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr13:100020041G>A	ENST00000403766.3	+	8	943	c.808G>A	c.(808-810)Gga>Aga	p.G270R	UBAC2_ENST00000460562.1_3'UTR|UBAC2_ENST00000376440.2_Splice_Site_p.G235R	NM_001144072.1	NP_001137544.1	Q8NBM4	UBAC2_HUMAN	UBA domain containing 2	270					protein localization to endoplasmic reticulum (GO:0070972)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)	10	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					CTCTTTTTAGGGAGGAATGAT	0.458																																					p.G270R		Atlas-SNP	.											.	UBAC2	23	.	0			c.G808A						.						140	123	129					13																	100020041		2203	4300	6503	SO:0001630	splice_region_variant	337867	exon8			TTTTAGGGAGGAA	AK055110	CCDS9490.1, CCDS45064.1	13q32.3	2012-02-01	2007-04-20	2007-04-20	ENSG00000134882	ENSG00000134882			20486	protein-coding gene	gene with protein product			"phosphoglycerate dehydrogenase like 1"	PHGDHL1			Standard	NM_177967		Approved	FLJ30548, RP11-178C10.1	uc001voa.4	Q8NBM4	OTTHUMG00000017267	ENST00000403766.3:c.808-1G>A	chr13.hg19:g.100020041G>A		153.0	0.0		142.0	45.0	NM_001144072	B3KNV7|Q0VAB5|Q5W0W6|Q5W0W9|Q6GQR2|Q6P4B0|Q8N2E8|Q96NW2	Missense_Mutation	SNP	ENST00000403766.3	hg19	CCDS45064.1	.	.	.	.	.	.	.	.	.	.	G	19.65	3.867522	0.72065	.	.	ENSG00000134882	ENST00000403766;ENST00000355700;ENST00000376440	.	.	.	5.56	3.83	0.44106	.	0.328328	0.34628	N	0.003816	T	0.68192	0.2974	M	0.65975	2.015	0.43517	D	0.995789	B;D;D;P	0.69078	0.214;0.997;0.979;0.828	B;D;P;B	0.64410	0.062;0.925;0.606;0.223	T	0.66156	-0.5994	8	.	.	.	-15.2089	8.4545	0.32890	0.179:0.0:0.821:0.0	.	200;235;270;270	B7Z6T7;Q8NBM4-2;A8K2S7;Q8NBM4	.;.;.;UBAC2_HUMAN	R	270;136;235	.	.	G	+	1	0	UBAC2	98818042	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.457000	0.66672	0.709000	0.31976	0.561000	0.74099	GGA	.	.		0.458	UBAC2-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045588.1	NM_177967	Missense_Mutation	A	100020041	G	A	100020041	5	1	270	1	0	0	0	0	0	0	1	0	16850	1246	43	3	998	3	UBAC2	13	100020041	Splice_Site	SNP	G	TCGA-FV-A4ZP-01A-12D-A25V-10	23638345	100020041	15149837	47	39326										
C13orf39	196541	hgsc.bcm.edu	37	chr13	103339396	103339396	+	Frame_Shift_Del	DEL	C	C	-													0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	tgttcctccaagtattgacaCaaagccatagcctaaaaaat							TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr13:103339396delC	ENST00000267273.6	-	3	299	c.294delG	c.(292-294)ttgfs	p.L98fs		NM_001010977.1	NP_001010977.1	Q5VZV1	MT21C_HUMAN	methyltransferase like 21C	98					peptidyl-lysine methylation (GO:0018022)|protein methylation (GO:0006479)	nucleus (GO:0005634)	protein-lysine N-methyltransferase activity (GO:0016279)			breast(1)|large_intestine(3)|lung(2)|skin(1)	7						AGTATTGACACAAAGCCATAG	0.393																																					p.C99fs		Atlas-INDEL	.											.	METTL21C	23	.	0			c.295delT						.						72	70	70					13																	103339396		2203	4300	6503	SO:0001589	frameshift_variant	196541	exon3			.		CCDS32003.1	13q33.1	2011-03-03	2011-03-03	2011-03-03	ENSG00000139780	ENSG00000139780			33717	protein-coding gene	gene with protein product		615259	"chromosome 13 open reading frame 39"	C13orf39			Standard	NM_001010977		Approved	LOC196541	uc001vpj.4	Q5VZV1	OTTHUMG00000017304	ENST00000267273.6:c.294delG	chr13.hg19:g.103339396delC	ENSP00000267273:p.Leu98fs	74.0	0.0		64.0	10.0	NM_001010977		Frame_Shift_Del	DEL	ENST00000267273.6	hg19	CCDS32003.1																																																																																			.	.		0.393	METTL21C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045682.2	NM_001010977		-	103339396	C	-	103339396	7	5	270	1	0	1	0	1	0	0	0	0	1734	477	17	0	508	0	C13orf39	13	103339396	Frame_Shift_Del	DEL	C	TCGA-FV-A4ZP-01A-12D-A25V-10	3319355	103339396	11830482	48	39327										
C14orf73	91828	hgsc.bcm.edu	37	chr14	103568956	103568956	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	ggtgcggcaggaggtgcagcCcgcgtatgcggcggccggct	20	12	0	0	rs371500721		TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr14:103568956C>T	ENST00000380069.3	+	2	972	c.896C>T	c.(895-897)cCc>cTc	p.P299L		NM_001077594.1	NP_001071062.1	Q17RC7	EX3L4_HUMAN	exocyst complex component 3-like 4	299					exocytosis (GO:0006887)	exocyst (GO:0000145)				cervix(2)|endometrium(2)|lung(4)|ovary(1)|skin(1)	10						GAGGTGCAGCCCGCGTATGCG	0.731													C|||	1	0.000199681	0	0	5008	,	,		11558	0		0.001	False		,,,				2504	0				p.P299L		Atlas-SNP	.											.	EXOC3L4	35	.	0			c.C896T						.	C	LEU/PRO	0,3814		0,0,1907	4	7	6		896	4.3	0.8	14		6	6,7644		0,6,3819	no	missense	EXOC3L4	NM_001077594.1	98	0,6,5726	TT,TC,CC		0.0784,0.0,0.0523	probably-damaging	299/723	103568956	6,11458	1907	3825	5732	SO:0001583	missense	91828	exon2			TGCAGCCCGCGTA	AK000671	CCDS32163.1	14q32.32	2011-01-31	2011-01-31	2011-01-31	ENSG00000205436	ENSG00000205436			20120	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 73"	C14orf73			Standard	NM_001077594		Approved		uc001ymk.3	Q17RC7		ENST00000380069.3:c.896C>T	chr14.hg19:g.103568956C>T	ENSP00000369409:p.Pro299Leu	2.0	0.0		5.0	4.0	NM_001077594	Q14CR2	Missense_Mutation	SNP	ENST00000380069.3	hg19	CCDS32163.1	.	.	.	.	.	.	.	.	.	.	C	12.99	2.104215	0.37145	0.0	7.84E-4	ENSG00000205436	ENST00000380069	T	0.09911	2.93	4.33	4.33	0.51752	.	0.390087	0.23470	N	0.047831	T	0.25531	0.0621	M	0.65975	2.015	0.50467	D	0.999877	D	0.69078	0.997	D	0.65874	0.939	T	0.00664	-1.1620	10	0.72032	D	0.01	-33.0873	8.042	0.30527	0.0:0.8914:0.0:0.1086	.	299	Q17RC7	EX3L4_HUMAN	L	299	ENSP00000369409:P299L	ENSP00000369409:P299L	P	+	2	0	EXOC3L4	102638709	0.041000	0.20044	0.834000	0.33040	0.184000	0.23303	1.627000	0.37050	2.242000	0.73789	0.491000	0.48974	CCC	.	.		0.731	EXOC3L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415663.1	XM_941093		T	103568956	C	T	103568956	3	4	270	1	0	0	0	0	1	0	0	0	1781	623	22	3	902	3	C14orf73	14	103568956	Missense_Mutation	SNP	C	TCGA-FV-A4ZP-01A-12D-A25V-10		103568956	3780584	49	39328										
SHCBP1	79801	hgsc.bcm.edu	37	chr16	46651615	46651615	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	gatggctcaaggaccttctcCaagaactcagctgtgaattc	9	11	3	2			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr16:46651615C>T	ENST00000303383.3	-	3	584	c.318G>A	c.(316-318)ttG>ttA	p.L106L	SHCBP1_ENST00000564272.1_5'Flank	NM_024745.4	NP_079021	Q8NEM2	SHCBP_HUMAN	SHC SH2-domain binding protein 1	106					fibroblast growth factor receptor signaling pathway (GO:0008543)|regulation of neural precursor cell proliferation (GO:2000177)					breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		all_cancers(37;0.00404)|all_epithelial(9;0.00527)|all_lung(18;0.0413)|Lung NSC(13;0.213)				GGACCTTCTCCAAGAACTCAG	0.448																																					p.L106L		Atlas-SNP	.											.	SHCBP1	54	.	0			c.G318A						.						111	102	105					16																	46651615		2203	4300	6503	SO:0001819	synonymous_variant	79801	exon3			CTTCTCCAAGAAC	AK055931	CCDS10720.1	16q11	2008-02-05			ENSG00000171241	ENSG00000171241			29547	protein-coding gene	gene with protein product		611027				10086341	Standard	NM_024745		Approved	FLJ22009	uc002eec.4	Q8NEM2	OTTHUMG00000132540	ENST00000303383.3:c.318G>A	chr16.hg19:g.46651615C>T		111.0	0.0		99.0	4.0	NM_024745	Q96N60|Q9BVS0|Q9H6P6	Silent	SNP	ENST00000303383.3	hg19	CCDS10720.1																																																																																			.	.		0.448	SHCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255740.1	NM_024745		T	46651615	C	T	46651615	2	4	270	1	0	0	0	0	0	0	0	1	14289	593	21	3		3	SHCBP1	16	46651615	Silent	SNP	C	TCGA-FV-A4ZP-01A-12D-A25V-10		46651615	43703138	50	39329										
TP53	7157	hgsc.bcm.edu	37	chr17	7577082	7577082	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	tttcttgcggagattctcttCctctgtgcgccggtctctcc	9	14	4	1			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr17:7577082C>T	ENST00000269305.4	-	8	1045	c.856G>A	c.(856-858)Gaa>Aaa	p.E286K	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.E286K|TP53_ENST00000420246.2_Missense_Mutation_p.E286K|TP53_ENST00000445888.2_Missense_Mutation_p.E286K|TP53_ENST00000413465.2_Intron|TP53_ENST00000359597.4_Missense_Mutation_p.E286K	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	286	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		E -> A (in LFS; germline mutation and in sporadic cancers; somatic mutation).|E -> D (in sporadic cancers; somatic mutation).|E -> G (in sporadic cancers; somatic mutation).|E -> K (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:11023613, ECO:0000269|PubMed:8316628}.|E -> L (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|E -> Q (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:8829627}.|E -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.E286K(58)|p.E286*(22)|p.0?(8)|p.E286Q(5)|p.?(2)|p.E286fs*59(2)|p.E286fs*17(2)|p.R283fs*16(2)|p.R282_E287delRRTEEE(1)|p.L265_K305del41(1)|p.T284fs*57(1)|p.T284_G293del10(1)|p.E285_L289delEEENL(1)|p.R283fs*56(1)|p.E285fs*13(1)|p.G279fs*59(1)|p.R283fs*59(1)|p.V272_K292del21(1)|p.E285_N288delEEEN(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	AGATTCTCTTCCTCTGTGCGC	0.557		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.E286K	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,NS,malignant_melanoma,0,1	TP53	33396	.	112	Substitution - Missense(63)|Substitution - Nonsense(22)|Deletion - Frameshift(11)|Whole gene deletion(8)|Deletion - In frame(6)|Unknown(2)	lung(18)|upper_aerodigestive_tract(13)|breast(10)|large_intestine(9)|urinary_tract(9)|skin(9)|oesophagus(9)|haematopoietic_and_lymphoid_tissue(8)|liver(7)|central_nervous_system(6)|bone(4)|ovary(3)|stomach(2)|vulva(1)|soft_tissue(1)|eye(1)|biliary_tract(1)|endometrium(1)	c.G856A	GRCh37	CM076567	TP53	M		.						95	81	86					17																	7577082		2203	4300	6503	SO:0001583	missense	7157	exon8	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	TCTCTTCCTCTGT	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.856G>A	chr17.hg19:g.7577082C>T	ENSP00000269305:p.Glu286Lys	91.0	1.0		107.0	66.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.310731	0.81358	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99856	-7.21;-7.21;-7.21;-7.21;-7.21;-7.21	4.99	4.99	0.66335	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99883	0.9944	M	0.92077	3.27	0.58432	D	0.999999	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.77557	0.983;0.985;0.982;0.99	D	0.96355	0.9261	10	0.87932	D	0	-23.2961	15.807	0.78520	0.0:1.0:0.0:0.0	.	286;286;286;286	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	K	286;286;286;286;286;275;154	ENSP00000352610:E286K;ENSP00000269305:E286K;ENSP00000398846:E286K;ENSP00000391127:E286K;ENSP00000391478:E286K;ENSP00000425104:E154K	ENSP00000269305:E286K	E	-	1	0	TP53	7517807	1.000000	0.71417	0.972000	0.41901	0.455000	0.32408	7.587000	0.82613	2.579000	0.87056	0.462000	0.41574	GAA	.	.		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7577082	C	T	7577082	3	4	270	1	0	0	0	0	1	0	0	0	16396	864	30	3	430	3	TP53	17	7577082	Missense_Mutation	SNP	C	TCGA-FV-A4ZP-01A-12D-A25V-10		7577082	73618128	51	39330										
VEZF1	7716	hgsc.bcm.edu	37	chr17	56056622	56056622	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	tgttgctgctgctgctgctgCtgctgctgctgctgctgctg	14	12	0	0			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr17:56056622C>T	ENST00000581208.1	-	5	1069	c.1029G>A	c.(1027-1029)caG>caA	p.Q343Q	VEZF1_ENST00000584396.1_Silent_p.Q334Q	NM_007146.2	NP_009077.2	Q14119	VEZF1_HUMAN	vascular endothelial zinc finger 1	343	Poly-Gln.				angiogenesis (GO:0001525)|cellular defense response (GO:0006968)|endothelial cell development (GO:0001885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(2)|lung(5)|ovary(1)	10						gctgctgctgctgctgctgct	0.453																																					p.Q343Q		Atlas-SNP	.											.	VEZF1	50	.	0			c.G1029A						.																																			SO:0001819	synonymous_variant	7716	exon5			CTGCTGCTGCTGC	D28118	CCDS32687.1	17q22	2012-10-05	2006-08-16	2006-08-16	ENSG00000136451	ENSG00000136451		"Zinc fingers, C2H2-type"	12949	protein-coding gene	gene with protein product		606747	"zinc finger protein 161"	ZNF161		8035792	Standard	XM_005257643		Approved	DB1	uc002ivf.1	Q14119	OTTHUMG00000178777	ENST00000581208.1:c.1029G>A	chr17.hg19:g.56056622C>T		130.0	0.0		224.0	34.0	NM_007146		Silent	SNP	ENST00000581208.1	hg19	CCDS32687.1																																																																																			.	.		0.453	VEZF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443321.1			T	56056622	C	T	56056622	2	4	270	1	0	0	0	0	0	0	0	1	17170	796	28	3		3	VEZF1	17	56056622	Silent	SNP	C	TCGA-FV-A4ZP-01A-12D-A25V-10	48479540	56056622	25138588	52	39331										
STRADA	92335	hgsc.bcm.edu	37	chr17	61791458	61791458	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	atgctattgactctgagctcGcatcattggtctaaaaaaga	8	8	3	3			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr17:61791458G>A	ENST00000336174.6	-	5	246	c.134C>T	c.(133-135)gCg>gTg	p.A45V	STRADA_ENST00000582137.1_Missense_Mutation_p.A16V|RP11-51F16.8_ENST00000580553.1_3'UTR|STRADA_ENST00000447001.3_Intron|STRADA_ENST00000580039.1_Intron|STRADA_ENST00000245865.5_5'UTR|STRADA_ENST00000579340.1_5'UTR|STRADA_ENST00000375840.4_5'UTR|STRADA_ENST00000392950.4_Missense_Mutation_p.A8V	NM_001003787.2	NP_001003787.1	Q7RTN6	STRAA_HUMAN	STE20-related kinase adaptor alpha	45					activation of protein kinase activity (GO:0032147)|cell cycle arrest (GO:0007050)|insulin receptor signaling pathway (GO:0008286)|protein export from nucleus (GO:0006611)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase binding (GO:0019900)|protein kinase activator activity (GO:0030295)|transferase activity, transferring phosphorus-containing groups (GO:0016772)	p.A45V(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|liver(1)|lung(2)|ovary(1)|prostate(2)	13						CTCTGAGCTCGCATCATTGGT	0.473																																					p.A45V		Atlas-SNP	.											STRADA,NS,carcinoma,0,1	STRADA	27	.	1	Substitution - Missense(1)	kidney(1)	c.C134T						.						117	98	104					17																	61791458		2203	4300	6503	SO:0001583	missense	92335	exon5			GAGCTCGCATCAT	AF308302	CCDS11642.1, CCDS32703.1, CCDS42367.1, CCDS54156.1, CCDS58585.1	17q23.3	2014-09-04			ENSG00000266173	ENSG00000266173			30172	protein-coding gene	gene with protein product	"STE20-like pseudokinase"	608626				12805220, 17921699	Standard	NM_153335		Approved	NY-BR-96, LYK5, Stlk, STRAD	uc002jbm.3	Q7RTN6	OTTHUMG00000178908	ENST00000336174.6:c.134C>T	chr17.hg19:g.61791458G>A	ENSP00000336655:p.Ala45Val	106.0	1.0		132.0	64.0	NM_001003787	B4DDE3|B4DW17|J3KTC9|Q5JPI2|Q7Z4K9|Q8NC31|Q8NCF1|Q9H272	Missense_Mutation	SNP	ENST00000336174.6	hg19	CCDS32703.1	.	.	.	.	.	.	.	.	.	.	G	15.87	2.961836	0.53400	.	.	ENSG00000125695	ENST00000336174;ENST00000392950;ENST00000245865	T;T	0.56103	0.54;0.48	5.66	5.66	0.87406	Protein kinase-like domain (1);	0.140365	0.48767	D	0.000164	T	0.43389	0.1245	N	0.24115	0.695	0.80722	D	1	P;P;P;P	0.49253	0.555;0.921;0.456;0.555	B;B;B;B	0.40256	0.08;0.324;0.118;0.08	T	0.48281	-0.9049	10	0.59425	D	0.04	.	19.7543	0.96284	0.0:0.0:1.0:0.0	.	16;8;8;45	B4DW17;Q7RTN6-2;Q7RTN6-3;Q7RTN6	.;.;.;STRAA_HUMAN	V	45;8;7	ENSP00000336655:A45V;ENSP00000376677:A8V	ENSP00000245865:A7V	A	-	2	0	STRADA	59145190	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.567000	0.73983	2.680000	0.91292	0.561000	0.74099	GCG	.	.		0.473	STRADA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443894.1			A	61791458	G	A	61791458	3	1	270	1	0	0	0	0	1	0	0	0	15339	1087	38	1	1255	1	STRADA	17	61791458	Missense_Mutation	SNP	G	TCGA-FV-A4ZP-01A-12D-A25V-10	5734836	61791458	19403752	53	39332										
MYOM1	8736	hgsc.bcm.edu	37	chr18	3083787	3083787	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	gtaagttctcatttacttacTtgtgggaccagttaactttc	7	8	1	0			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr18:3083787T>A	ENST00000356443.4	-	33	4817	c.4484A>T	c.(4483-4485)aAt>aTt	p.N1495I	MYOM1_ENST00000261606.7_Splice_Site_p.N1399I|MYOM1_ENST00000400569.3_Splice_Site_p.N1495I	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	1495					muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						ATTTACTTACTTGTGGGACCA	0.483																																					p.N1495I		Atlas-SNP	.											.	MYOM1	192	.	0			c.A4484T						.						59	56	57					18																	3083787		1872	4099	5971	SO:0001630	splice_region_variant	8736	exon33			ACTTACTTGTGGG	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7613	protein-coding gene	gene with protein product	"skelemin"	603508	"myomesin 1 (skelemin) (185kD)", "myomesin 1 (skelemin) 185kDa", "myomesin 1, 185kDa"			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.4484+1A>T	chr18.hg19:g.3083787T>A		41.0	0.0		63.0	9.0	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	hg19	CCDS45824.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.758566	0.89843	.	.	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.42131	0.98;0.98;0.98	5.84	5.84	0.93424	Immunoglobulin-like fold (1);	0.044427	0.85682	D	0.000000	T	0.57286	0.2043	L	0.51422	1.61	0.80722	D	1	P;P	0.51057	0.941;0.492	P;P	0.62649	0.905;0.467	T	0.53380	-0.8447	9	.	.	.	.	16.2302	0.82332	0.0:0.0:0.0:1.0	.	1399;1495	P52179-2;P52179	.;MYOM1_HUMAN	I	1495;1495;1399	ENSP00000348821:N1495I;ENSP00000383413:N1495I;ENSP00000261606:N1399I	.	N	-	2	0	MYOM1	3073787	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.040000	0.89188	2.228000	0.72767	0.533000	0.62120	AAT	.	.		0.483	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	Missense_Mutation	A	3083787	T	A	3083787	5	1	270	1	0	0	0	0	0	0	1	0	10100	1623	56	4	597	4	MYOM1	18	3083787	Splice_Site	SNP	T	TCGA-FV-A4ZP-01A-12D-A25V-10		3083787	74993461	54	39333										
TXNDC2	84203	hgsc.bcm.edu	37	chr18	9887134	9887134	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	cagcaaaacccatccagcccAagctgggcaatattgccaag	8	14	0	0			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr18:9887134A>T	ENST00000306084.6	+	2	857	c.658A>T	c.(658-660)Aag>Tag	p.K220*	TXNDC2_ENST00000536353.2_Intron|TXNDC2_ENST00000357775.5_Nonsense_Mutation_p.K153*	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN	thioredoxin domain containing 2 (spermatozoa)	220	22 X 15 AA approximate tandem repeat of Q-P-K-X-G-D-I-P-K-S-[PS]-E-[KE]-X-I.				cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|glycerol ether metabolic process (GO:0006662)|multicellular organismal development (GO:0007275)|oxidation-reduction process (GO:0055114)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)	nutrient reservoir activity (GO:0045735)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)|thioredoxin-disulfide reductase activity (GO:0004791)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|skin(7)|urinary_tract(1)	31						CATCCAGCCCAAGCTGGGCAA	0.557																																					p.K220X		Atlas-SNP	.											.	TXNDC2	168	.	0			c.A658T						.						132	135	134					18																	9887134		2203	4300	6503	SO:0001587	stop_gained	84203	exon2			CAGCCCAAGCTGG	AF080095	CCDS11846.1, CCDS42414.1	18p11.31-p11.2	2009-03-11	2009-03-11	2007-08-16	ENSG00000168454	ENSG00000168454			16470	protein-coding gene	gene with protein product	"sperm-specific thioredoxin 1"					11230166, 11399755	Standard	NM_001098529		Approved	SPTRX1	uc002koi.4	Q86VQ3	OTTHUMG00000131602	ENST00000306084.6:c.658A>T	chr18.hg19:g.9887134A>T	ENSP00000304908:p.Lys220*	142.0	0.0		143.0	7.0	NM_001098529	A5YM73|Q8N7U4|Q96RX3|Q9H0L8	Nonsense_Mutation	SNP	ENST00000306084.6	hg19	CCDS42414.1	.	.	.	.	.	.	.	.	.	.	a	32	5.105591	0.94292	.	.	ENSG00000168454	ENST00000357775;ENST00000306084;ENST00000426718	.	.	.	3.17	3.17	0.36434	.	1.422770	0.04949	N	0.459936	.	.	.	.	.	.	0.32652	N	0.51932	.	.	.	.	.	.	.	.	.	.	.	.	.	-7.3162	9.811	0.40824	1.0:0.0:0.0:0.0	.	.	.	.	X	153;220;220	.	.	K	+	1	0	TXNDC2	9877134	0.000000	0.05858	0.055000	0.19348	0.237000	0.25408	0.195000	0.17155	1.484000	0.48361	0.519000	0.50382	AAG	.	.		0.557	TXNDC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254487.1			T	9887134	A	T	9887134	4	4	270	1	0	0	0	0	0	1	0	0	16812	131	5	4	664	4	TXNDC2	18	9887134	Nonsense_Mutation	SNP	A	TCGA-FV-A4ZP-01A-12D-A25V-10	6803347	9887134	68190114	55	39334										
SLC14A1	6563	hgsc.bcm.edu	37	chr18	43310324	43310324	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	atggttagagtggacagcccCactatggttaggggtgaaaa	14	6	0	2			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr18:43310324C>A	ENST00000321925.4	+	3	271	c.39C>A	c.(37-39)ccC>ccA	p.P13P	RP11-116O18.3_ENST00000586213.1_RNA|SLC14A1_ENST00000535474.1_Intron|SLC14A1_ENST00000402943.2_Intron|SLC14A1_ENST00000436407.3_Silent_p.P69P|SLC14A1_ENST00000415427.3_Silent_p.P69P|SLC14A1_ENST00000591943.1_3'UTR|SLC14A1_ENST00000502059.2_Intron|RP11-116O18.3_ENST00000589510.1_RNA|SLC14A1_ENST00000586142.1_Silent_p.P13P|SLC14A1_ENST00000589700.1_Silent_p.P13P	NM_001128588.3|NM_001146036.2|NM_015865.6	NP_001122060.3|NP_001139508.2|NP_056949.4	Q13336	UT1_HUMAN	solute carrier family 14 (urea transporter), member 1 (Kidd blood group)	13					transmembrane transport (GO:0055085)|urea transmembrane transport (GO:0071918)|urea transport (GO:0015840)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	urea channel activity (GO:0015265)|urea transmembrane transporter activity (GO:0015204)|water transmembrane transporter activity (GO:0005372)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(11)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	21						TGGACAGCCCCACTATGGTTA	0.517																																					p.P69P		Atlas-SNP	.											.	SLC14A1	84	.	0			c.C207A						.						112	100	104					18																	43310324		2203	4300	6503	SO:0001819	synonymous_variant	6563	exon2			CAGCCCCACTATG	BC040128	CCDS11925.1, CCDS45860.1	18q11-q12	2014-07-19	2014-01-02		ENSG00000141469	ENSG00000141469		"Blood group antigens", "Solute carriers"	10918	protein-coding gene	gene with protein product		613868	"Kidd blood group", "solute carrier family 14 (urea transporter), member 1"	JK		7797558	Standard	NM_001146037		Approved	HsT1341, RACH1, RACH2	uc010dnk.3	Q13336	OTTHUMG00000132617	ENST00000321925.4:c.39C>A	chr18.hg19:g.43310324C>A		104.0	0.0		165.0	12.0	NM_001146037	A8K0P3|B3KR62|B3KVX3|C9EHF2|Q86VM5	Silent	SNP	ENST00000321925.4	hg19	CCDS11925.1																																																																																			.	.		0.517	SLC14A1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255860.2	NM_015865		A	43310324	C	A	43310324	2	1	270	1	0	0	0	0	0	0	0	1	14411	581	21	3		3	SLC14A1	18	43310324	Silent	SNP	C	TCGA-FV-A4ZP-01A-12D-A25V-10	33423190	43310324	34766924	56	39335										
ARID3A	1820	hgsc.bcm.edu	37	chr19	932472	932472	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	gacctcggggaggatgaggaGgaggaggaggaggattacga	21	4	0	1			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr19:932472G>C	ENST00000263620.3	+	3	750	c.423G>C	c.(421-423)gaG>gaC	p.E141D		NM_005224.2	NP_005215.1	Q99856	ARI3A_HUMAN	AT rich interactive domain 3A (BRIGHT-like)	141	Acidic.|Glu-rich.					cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	10		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		aggatgaggaggaggaggagg	0.662																																					p.E141D	Pancreas(29;54 1022 32760 50921)	Atlas-SNP	.											.	ARID3A	35	.	0			c.G423C						.						14	12	13					19																	932472		2189	4272	6461	SO:0001583	missense	1820	exon3			TGAGGAGGAGGAG	U88047	CCDS12050.1	19p13.3	2013-02-07	2006-11-08	2004-01-30		ENSG00000116017		"-"	3031	protein-coding gene	gene with protein product		603265	"dead ringer-like 1 (Drosophila)", "AT rich interactive domain 3A (BRIGHT- like)"	DRIL1		9722953	Standard	NM_005224		Approved	BRIGHT	uc002lql.3	Q99856		ENST00000263620.3:c.423G>C	chr19.hg19:g.932472G>C	ENSP00000263620:p.Glu141Asp	53.0	0.0		59.0	13.0	NM_005224	Q5I858|Q6P9C6|Q8IZA7|Q8N4Z3	Missense_Mutation	SNP	ENST00000263620.3	hg19	CCDS12050.1	.	.	.	.	.	.	.	.	.	.	G	11.69	1.713060	0.30413	.	.	ENSG00000116017	ENST00000263620	T	0.17528	2.27	3.66	1.25	0.21368	.	0.809613	0.10420	U	0.676796	T	0.09730	0.0239	L	0.29908	0.895	0.25290	N	0.989363	B	0.06786	0.001	B	0.04013	0.001	T	0.40117	-0.9580	10	0.13853	T	0.58	.	3.683	0.08317	0.2274:0.0:0.5806:0.1919	.	141	Q99856	ARI3A_HUMAN	D	141	ENSP00000263620:E141D	ENSP00000263620:E141D	E	+	3	2	ARID3A	883472	0.039000	0.19947	0.423000	0.26634	0.846000	0.48090	-1.707000	0.01893	0.701000	0.31803	0.457000	0.33378	GAG	.	.		0.662	ARID3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458219.1	NM_005224		C	932472	G	C	932472	3	2	270	1	0	0	0	0	1	0	0	0	916	991	35	4	429	4	ARID3A	19	932472	Missense_Mutation	SNP	G	TCGA-FV-A4ZP-01A-12D-A25V-10		932472	58196511	57	39336										
MUC16	94025	hgsc.bcm.edu	37	chr19	9060557	9060557	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	accactggagatgtcactttGgatggctctgggaggcctgg	15	9	2	1			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr19:9060557G>A	ENST00000397910.4	-	3	27092	c.26889C>T	c.(26887-26889)tcC>tcT	p.S8963S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	8965	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						ATGTCACTTTGGATGGCTCTG	0.453																																					p.S8963S		Atlas-SNP	.											.	MUC16	4315	.	0			c.C26889T						.						205	191	195					19																	9060557		1974	4164	6138	SO:0001819	synonymous_variant	94025	exon3			CACTTTGGATGGC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.26889C>T	chr19.hg19:g.9060557G>A		308.0	0.0		305.0	65.0	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.453	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9060557	G	A	9060557	2	1	270	1	0	0	0	0	0	0	0	1	9982	1335	47	3		3	MUC16	19	9060557	Silent	SNP	G	TCGA-FV-A4ZP-01A-12D-A25V-10	8128085	9060557	50068426	58	39337										
ZNF791	163049	hgsc.bcm.edu	37	chr19	12739344	12739344	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	ctataaatgtaaagaatgtgGgaaatctttcagtgcacgcc	9	7	2	1			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr19:12739344G>A	ENST00000343325.4	+	4	1163	c.1001G>A	c.(1000-1002)gGg>gAg	p.G334E	ZNF791_ENST00000540038.1_Missense_Mutation_p.G225E|ZNF791_ENST00000458122.3_Missense_Mutation_p.G302E|AC010422.1_ENST00000408416.1_RNA|ZNF791_ENST00000446165.1_3'UTR|ZNF490_ENST00000465656.1_Intron	NM_153358.2	NP_699189.2	Q3KP31	ZN791_HUMAN	zinc finger protein 791	334					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(5)|lung(6)|ovary(2)|prostate(3)	19						AAAGAATGTGGGAAATCTTTC	0.403																																					p.G334E		Atlas-SNP	.											.	ZNF791	53	.	0			c.G1001A						.						50	55	53					19																	12739344		2203	4300	6503	SO:0001583	missense	163049	exon4			AATGTGGGAAATC	AK074877	CCDS12273.1	19p13.2-p13.13	2013-01-08			ENSG00000173875	ENSG00000173875		"Zinc fingers, C2H2-type", "-"	26895	protein-coding gene	gene with protein product							Standard	NM_153358		Approved	FLJ90396	uc002mua.2	Q3KP31	OTTHUMG00000156426	ENST00000343325.4:c.1001G>A	chr19.hg19:g.12739344G>A	ENSP00000342974:p.Gly334Glu	38.0	0.0		52.0	20.0	NM_153358	B7Z586|Q8NC99	Missense_Mutation	SNP	ENST00000343325.4	hg19	CCDS12273.1	.	.	.	.	.	.	.	.	.	.	G	17.31	3.357771	0.61403	.	.	ENSG00000173875	ENST00000343325;ENST00000393303;ENST00000458122;ENST00000540038	T;T;T	0.58210	0.35;0.35;0.35	1.83	1.83	0.25207	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.63058	0.2479	M	0.61703	1.905	0.38136	D	0.938308	D	0.71674	0.998	D	0.65140	0.932	T	0.65602	-0.6128	9	0.49607	T	0.09	.	9.2247	0.37398	0.0:0.0:1.0:0.0	.	334	Q3KP31	ZN791_HUMAN	E	334;316;302;225	ENSP00000342974:G334E;ENSP00000441761:G302E;ENSP00000441038:G225E	ENSP00000342974:G334E	G	+	2	0	ZNF791	12600344	1.000000	0.71417	0.586000	0.28679	0.918000	0.54935	4.460000	0.60108	1.007000	0.39238	0.491000	0.48974	GGG	.	.		0.403	ZNF791-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344140.1	NM_153358		A	12739344	G	A	12739344	3	1	270	1	0	0	0	0	1	0	0	0	18178	1232	43	3	1015	3	ZNF791	19	12739344	Missense_Mutation	SNP	G	TCGA-FV-A4ZP-01A-12D-A25V-10	3678787	12739344	46389639	59	39338										
LPHN1	22859	hgsc.bcm.edu	37	chr19	14274081	14274081	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	ctcagtcagtgtgtccgtgcGgtaggggatccagggcatca	15	10	3	0	rs369670781		TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr19:14274081G>A	ENST00000340736.6	-	6	844	c.547C>T	c.(547-549)Cgc>Tgc	p.R183C	LPHN1_ENST00000361434.3_Missense_Mutation_p.R178C|CTB-55O6.12_ENST00000588387.1_RNA|LPHN1_ENST00000591528.1_5'UTR|CTB-55O6.12_ENST00000592086.1_RNA	NM_001008701.2	NP_001008701.1	O94910	LPHN1_HUMAN	latrophilin 1	183	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|heterophilic cell-cell adhesion (GO:0007157)|neuropeptide signaling pathway (GO:0007218)|positive regulation of synapse maturation (GO:0090129)	axon (GO:0030424)|cell junction (GO:0030054)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)			central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						GTGTCCGTGCGGTAGGGGATC	0.657																																					p.R183C		Atlas-SNP	.											.	LPHN1	107	.	0			c.C547T						.	G	CYS/ARG,CYS/ARG	0,4406		0,0,2203	86	65	72		547,532	4	1	19		72	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	LPHN1	NM_001008701.2,NM_014921.4	180,180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	183/1475,178/1470	14274081	1,13005	2203	4300	6503	SO:0001583	missense	22859	exon6			CCGTGCGGTAGGG	AB020628	CCDS12307.1, CCDS32928.1	19p13.2	2014-08-08				ENSG00000072071		"-", "GPCR / Class B : Orphans"	20973	protein-coding gene	gene with protein product						10994649	Standard	NM_014921		Approved	KIAA0821, CIRL1, LEC2	uc010xnn.2	O94910		ENST00000340736.6:c.547C>T	chr19.hg19:g.14274081G>A	ENSP00000340688:p.Arg183Cys	134.0	0.0		160.0	38.0	NM_001008701	Q96IE7|Q9BU07|Q9HAR3	Missense_Mutation	SNP	ENST00000340736.6	hg19	CCDS32928.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.427192	0.83667	0.0	1.16E-4	ENSG00000072071	ENST00000340736;ENST00000361434	D;D	0.89343	-2.5;-2.5	5.06	3.98	0.46160	Olfactomedin-like (3);	0.000000	0.85682	D	0.000000	D	0.94656	0.8277	M	0.88640	2.97	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.993;0.998	D	0.95163	0.8283	10	0.87932	D	0	.	12.7117	0.57094	0.0:0.0:0.8356:0.1644	.	178;183	O94910-2;O94910	.;LPHN1_HUMAN	C	183;178	ENSP00000340688:R183C;ENSP00000355328:R178C	ENSP00000340688:R183C	R	-	1	0	LPHN1	14135081	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.219000	0.72231	2.347000	0.79759	0.655000	0.94253	CGC	.	.		0.657	LPHN1-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459696.1	NM_014921		A	14274081	G	A	14274081	3	1	270	1	0	0	0	0	1	0	0	0	8924	1116	39	1	3953	1	LPHN1	19	14274081	Missense_Mutation	SNP	G	TCGA-FV-A4ZP-01A-12D-A25V-10	1534737	14274081	44854902	60	39339										
CLPTM1	1209	hgsc.bcm.edu	37	chr19	45488541	45488541	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	tgctgacaggagagacagaaGcggacccagaaatgatcaag	13	8	1	5			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr19:45488541G>A	ENST00000337392.5	+	6	802	c.652G>A	c.(652-654)Gcg>Acg	p.A218T	CLPTM1_ENST00000589158.1_3'UTR|CLPTM1_ENST00000541297.2_Missense_Mutation_p.A204T|CLPTM1_ENST00000546079.1_Missense_Mutation_p.A116T	NM_001282175.1|NM_001282176.1|NM_001294.2	NP_001269104.1|NP_001269105.1|NP_001285.1	O96005	CLPT1_HUMAN	cleft lip and palate associated transmembrane protein 1	218					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of T cell differentiation in thymus (GO:0033081)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00354)|Epithelial(262;0.187)		AGAGACAGAAGCGGACCCAGA	0.532																																					p.A218T		Atlas-SNP	.											.	CLPTM1	109	.	0			c.G652A						.						104	99	100					19																	45488541		2203	4300	6503	SO:0001583	missense	1209	exon6			ACAGAAGCGGACC	AF037339	CCDS12651.1, CCDS74394.1, CCDS74395.1	19q13.3	2008-02-05				ENSG00000104853			2087	protein-coding gene	gene with protein product		604783				9828125	Standard	NM_001294		Approved		uc002pai.3	O96005		ENST00000337392.5:c.652G>A	chr19.hg19:g.45488541G>A	ENSP00000336994:p.Ala218Thr	115.0	0.0		100.0	27.0	NM_001294	B3KQH2|B4DDS3|B4E2X9|B7Z9X9|F5H8J3|Q53ET6|Q9BSS5	Missense_Mutation	SNP	ENST00000337392.5	hg19	CCDS12651.1	.	.	.	.	.	.	.	.	.	.	G	18.27	3.587693	0.66105	.	.	ENSG00000104853	ENST00000546079;ENST00000541297;ENST00000337392;ENST00000347493	.	.	.	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.50667	0.1629	L	0.39633	1.23	0.80722	D	1	P;B;B	0.37276	0.589;0.444;0.444	B;B;B	0.39027	0.259;0.288;0.288	T	0.44174	-0.9345	9	0.19147	T	0.46	-14.6335	16.3245	0.82970	0.0:0.0:1.0:0.0	.	204;218;218	F5H8J3;B3KQH2;O96005	.;.;CLPT1_HUMAN	T	116;204;218;218	.	ENSP00000336994:A218T	A	+	1	0	CLPTM1	50180381	1.000000	0.71417	0.998000	0.56505	0.895000	0.52256	8.519000	0.90563	2.450000	0.82876	0.650000	0.86243	GCG	.	.		0.532	CLPTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453267.1	NM_001294		A	45488541	G	A	45488541	3	1	270	1	0	0	0	0	1	0	0	0	3556	971	34	3	674	3	CLPTM1	19	45488541	Missense_Mutation	SNP	G	TCGA-FV-A4ZP-01A-12D-A25V-10	31214460	45488541	13640442	61	39340										
C20orf196	149840	hgsc.bcm.edu	37	chr20	5843711	5843711	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	aacaaaataactcctggaccGctgagaacttctggcttgac	8	11	1	2			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr20:5843711G>A	ENST00000303142.6	+	3	307	c.220G>A	c.(220-222)Gct>Act	p.A74T		NM_152504.2	NP_689717.2	Q8IYI0	CT196_HUMAN	chromosome 20 open reading frame 196	74										endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|stomach(1)	9						CTCCTGGACCGCTGAGAACTT	0.413																																					p.A74T		Atlas-SNP	.											.	C20orf196	17	.	0			c.G220A						.						54	59	57					20																	5843711		2203	4300	6503	SO:0001583	missense	149840	exon3			TGGACCGCTGAGA	AK057796	CCDS13091.1	20p12.3	2006-07-07			ENSG00000171984	ENSG00000171984			26318	protein-coding gene	gene with protein product						12477932	Standard	NM_152504		Approved	FLJ25067	uc002wmf.3	Q8IYI0	OTTHUMG00000031813	ENST00000303142.6:c.220G>A	chr20.hg19:g.5843711G>A	ENSP00000305875:p.Ala74Thr	79.0	0.0		90.0	9.0	NM_152504	A8K9J3|Q5TGA9|Q96LU1	Missense_Mutation	SNP	ENST00000303142.6	hg19	CCDS13091.1	.	.	.	.	.	.	.	.	.	.	T	6.629	0.484505	0.12641	.	.	ENSG00000171984	ENST00000303142;ENST00000378971;ENST00000445603;ENST00000442185	T;T;T	0.44881	0.91;0.91;0.91	5.64	1.84	0.25277	.	0.896271	0.09593	N	0.781229	T	0.17323	0.0416	N	0.02011	-0.69	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.20806	-1.0264	10	0.66056	D	0.02	-10.2391	4.9941	0.14230	0.3636:0.0:0.2744:0.362	.	74	Q8IYI0	CT196_HUMAN	T	74;74;74;121	ENSP00000305875:A74T;ENSP00000399331:A74T;ENSP00000410534:A121T	ENSP00000305875:A74T	A	+	1	0	C20orf196	5791711	0.366000	0.25014	0.033000	0.17914	0.002000	0.02628	1.084000	0.30828	0.073000	0.16731	-1.207000	0.01640	GCT	.	.		0.413	C20orf196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077882.2	NM_152504		A	5843711	G	A	5843711	3	1	270	1	0	0	0	0	1	0	0	0	2103	1087	38	1	226	1	C20orf196	20	5843711	Missense_Mutation	SNP	G	TCGA-FV-A4ZP-01A-12D-A25V-10		5843711	57181809	62	39341										
PTPRT	11122	hgsc.bcm.edu	37	chr20	40980875	40980875	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	ttgaacactttccccctctgGctcgagaggtcagcacttgg	10	13	2	2			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr20:40980875G>C	ENST00000373187.1	-	10	1610	c.1611C>G	c.(1609-1611)agC>agG	p.S537R	PTPRT_ENST00000373184.1_Missense_Mutation_p.S537R|PTPRT_ENST00000356100.2_Missense_Mutation_p.S537R|PTPRT_ENST00000373198.4_Missense_Mutation_p.S537R|PTPRT_ENST00000373190.1_Missense_Mutation_p.S537R|PTPRT_ENST00000373201.1_Missense_Mutation_p.S537R|PTPRT_ENST00000373193.3_Missense_Mutation_p.S537R			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	537	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)			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)				TCCCCCTCTGGCTCGAGAGGT	0.527																																					p.S537R		Atlas-SNP	.											PTPRT,right_upper_lobe,carcinoma,0,1	PTPRT	372	.	0			c.C1611G						.						78	83	81					20																	40980875		1957	4137	6094	SO:0001583	missense	11122	exon10			CCTCTGGCTCGAG	AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.1611C>G	chr20.hg19:g.40980875G>C	ENSP00000362283:p.Ser537Arg	101.0	0.0		86.0	15.0	NM_007050	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Missense_Mutation	SNP	ENST00000373187.1	hg19	CCDS42874.1	.	.	.	.	.	.	.	.	.	.	G	15.73	2.919965	0.52653	.	.	ENSG00000196090	ENST00000373190;ENST00000373187;ENST00000373193;ENST00000356100;ENST00000373198;ENST00000373184;ENST00000373201	T;T;T;T;T;T;T	0.35236	1.32;1.32;1.32;1.32;1.32;1.32;1.32	5.88	4.93	0.64822	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.097628	0.64402	D	0.000001	T	0.17916	0.0430	N	0.02765	-0.5	0.41397	D	0.987659	B;B	0.32731	0.382;0.302	B;B	0.36766	0.149;0.232	T	0.08722	-1.0708	10	0.48119	T	0.1	.	9.3838	0.38329	0.0716:0.0:0.7841:0.1443	.	537;537	O14522-1;O14522	.;PTPRT_HUMAN	R	537	ENSP00000362286:S537R;ENSP00000362283:S537R;ENSP00000362289:S537R;ENSP00000348408:S537R;ENSP00000362294:S537R;ENSP00000362280:S537R;ENSP00000362297:S537R	ENSP00000348408:S537R	S	-	3	2	PTPRT	40414289	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.924000	0.40065	2.777000	0.95525	0.551000	0.68910	AGC	.	.		0.527	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			C	40980875	G	C	40980875	3	2	270	1	0	0	0	0	1	0	0	0	12827	1194	42	4	2863	4	PTPRT	20	40980875	Missense_Mutation	SNP	G	TCGA-FV-A4ZP-01A-12D-A25V-10	35137164	40980875	22044645	63	39342										
ZNF512B	57473	hgsc.bcm.edu	37	chr20	62597492	62597583	+	Splice_Site	DEL	GACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCT	GACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCT	-													0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	gacctgggacgagcccccatAccttttcttaccactgttcc					rs200518817|rs376642783|rs540039560|rs200940725|rs371234637|rs139142804|rs146666443	byFrequency	TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	GACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCT	GACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr20:62597492_62597583delGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCT	ENST00000450537.1	-	5	1005_1095	c.945_1035delAGGGAGGAACAGTGGTAAGAAAAGGTATGGGGGCTCGTCCCAGGTCGGGGAGGAACAGTGGTAAGAAAAGGTATGGGGGCTCGTCCCAGGTC	c.(943-1035)agagggaggaacagtggtaagaaaaggtatgggggctcgtcccaggtcggggaggaacagtggtaagaaaaggtatgggggctcgtcccaggt>ag	p.RGRNSGKKRYGGSSQVGEEQW*EKVWGLVPG315fs	ZNF512B_ENST00000217130.3_Splice_Site_p.RGRNSGKKRYGGSSQVGEEQW*EKVWGLVPG315fs|ZNF512B_ENST00000369888.1_Splice_Site_p.RGRNSGKKRYGGSSQVGEEQW*EKVWGLVPG315fs			Q96KM6	Z512B_HUMAN	zinc finger protein 512B	315					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(4)|skin(1)	33	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					GAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCTGTGGCACGAGGTGCTTTGTTCTCCGACCTGGTCAGCAGCACCATTTTGCAGGGCGGTGTGTGTCTGCTGATAGCAA	0.575																																					p.338_345del		Pindel	.											.	ZNF512B	72	.	0			c.1012_1034del						.																																			SO:0001630	splice_region_variant	57473	exon5			.	AB033022	CCDS13548.1	20q13.33	2011-02-09			ENSG00000196700	ENSG00000196700			29212	protein-coding gene	gene with protein product						10574462	Standard	NM_020713		Approved	GM632, MGC149845, MGC149846	uc002yhl.2	Q96KM6	OTTHUMG00000033008	ENST00000450537.1:c.1034+1AGGGAGGAACAGTGGTAAGAAAAGGTATGGGGGCTCGTCCCAGGTCGGGGAGGAACAGTGGTAAGAAAAGGTATGGGGGCTCGTCCCAGGTC>-	chr20.hg19:g.62597492_62597583delGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCT		279.0	0.0		330.0	24.0	NM_020713	Q08AK9|Q9ULM4	Frame_Shift_Del	DEL	ENST00000450537.1	hg19	CCDS13548.1																																																																																			.	.		0.575	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713	Frame_Shift_Del	-	62597583	GACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCT	-	62597492	8	5	270	1	0	1	0	1	0	0	1	0	17972	405	14	0	1694	0	ZNF512B	20	62597492	Splice_Site	DEL	GACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCT	TCGA-FV-A4ZP-01A-12D-A25V-10	21616617	62597492	428028	64	39343										
PI4KA	5297	hgsc.bcm.edu	37	chr22	21153477	21153477	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	tgctgtaggatctgcagaatGggctccatgaccttcggggt	14	9	1	2			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr22:21153477G>A	ENST00000572273.1	-	16	1964	c.1734C>T	c.(1732-1734)ccC>ccT	p.P578P	PI4KA_ENST00000255882.6_Silent_p.P636P			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	578					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi-associated vesicle membrane (GO:0030660)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			breast(3)|endometrium(8)|kidney(9)|large_intestine(19)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|salivary_gland(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	79	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			TCTGCAGAATGGGCTCCATGA	0.557																																					p.P636P	GBM(136;1332 1831 3115 23601 50806)	Atlas-SNP	.											.	PI4KA	313	.	0			c.C1908T						.						93	80	84					22																	21153477		2203	4300	6503	SO:0001819	synonymous_variant	5297	exon16			CAGAATGGGCTCC	L36151	CCDS33603.1, CCDS33603.2	22q11.21	2011-05-25	2007-08-14	2007-08-02	ENSG00000241973	ENSG00000241973			8983	protein-coding gene	gene with protein product		600286		PIK4CA		7961848, 8662589	Standard	NM_002650		Approved	PI4K-ALPHA, pi4K230	uc002zsz.5	P42356	OTTHUMG00000167440	ENST00000572273.1:c.1734C>T	chr22.hg19:g.21153477G>A		60.0	0.0		64.0	17.0	NM_058004	Q7Z625|Q9UPG2	Silent	SNP	ENST00000572273.1	hg19																																																																																				.	.		0.557	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004		A	21153477	G	A	21153477	2	1	270	1	0	0	0	0	0	0	0	1	11882	1335	47	3		3	PI4KA	22	21153477	Silent	SNP	G	TCGA-FV-A4ZP-01A-12D-A25V-10		21153477	30151089	65	39344										
ZNF280B	140883	hgsc.bcm.edu	37	chr22	22843682	22843682	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	ttggtttcttgtatgttcttCtgtggttcaggctctttctc	9	8	6	0			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chr22:22843682C>T	ENST00000406426.1	-	4	784	c.42G>A	c.(40-42)caG>caA	p.Q14Q	ZNF280B_ENST00000360412.2_Silent_p.Q14Q			Q86YH2	Z280B_HUMAN	zinc finger protein 280B	14					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(2)	22	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)		GTATGTTCTTCTGTGGTTCAG	0.388																																					p.Q14Q		Atlas-SNP	.											.	ZNF280B	67	.	0			c.G42A						.						141	124	129					22																	22843682		2203	4300	6503	SO:0001819	synonymous_variant	140883	exon4			GTTCTTCTGTGGT	AK097608	CCDS13799.1	22q11.2	2007-09-20	2007-09-20	2007-09-20	ENSG00000198477	ENSG00000275004			23022	protein-coding gene	gene with protein product			"zinc finger protein 279", "suppressor of hairy wing homolog 2 (Drosophila)"	ZNF279, SUHW2		9074928	Standard	NM_080764		Approved	5'OY11.1, ZNF632	uc002zwc.1	Q86YH2	OTTHUMG00000151066	ENST00000406426.1:c.42G>A	chr22.hg19:g.22843682C>T		316.0	0.0		293.0	45.0	NM_080764		Silent	SNP	ENST00000406426.1	hg19	CCDS13799.1																																																																																			.	.		0.388	ZNF280B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321170.2	NM_080764		T	22843682	C	T	22843682	2	4	270	1	0	0	0	0	0	0	0	1	17830	912	32	3		3	ZNF280B	22	22843682	Silent	SNP	C	TCGA-FV-A4ZP-01A-12D-A25V-10	1690205	22843682	28460884	66	39345										
OTUD5	55593	hgsc.bcm.edu	37	chrX	48814825	48814825	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	gcggcttctttttggggagtAtagtcatggctgcactgccg	14	9	2	0			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chrX:48814825A>G	ENST00000156084.4	-	1	68	c.8T>C	c.(7-9)aTa>aCa	p.I3T	OTUD5_ENST00000376488.3_Missense_Mutation_p.I3T|RNU6-722P_ENST00000411377.1_RNA|OTUD5_ENST00000396743.3_Missense_Mutation_p.I3T|OTUD5_ENST00000428668.2_Intron|OTUD5_ENST00000484499.1_5'Flank	NM_017602.3	NP_060072.1	Q96G74	OTUD5_HUMAN	OTU deubiquitinase 5	3					innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|response to lipopolysaccharide (GO:0032496)	cytosol (GO:0005829)	ubiquitin-specific protease activity (GO:0004843)			endometrium(2)|large_intestine(3)|lung(6)|pancreas(2)	13						TTTGGGGAGTATAGTCATGGC	0.731																																					p.I3T		Atlas-SNP	.											.	OTUD5	66	.	0			c.T8C						.						1	2	1					X																	48814825		652	1617	2269	SO:0001583	missense	55593	exon1			GGGAGTATAGTCA		CCDS14313.1, CCDS48104.1, CCDS48105.1	Xp11.23	2014-06-09	2014-02-24		ENSG00000068308	ENSG00000068308		"OTU domain containing"	25402	protein-coding gene	gene with protein product		300713	"OTU domain containing 5"			24143256	Standard	NM_001136157		Approved	DKFZp761A052, DUBA	uc004dlu.3	Q96G74	OTTHUMG00000024130	ENST00000156084.4:c.8T>C	chrX.hg19:g.48814825A>G	ENSP00000156084:p.Ile3Thr	47.0	0.0		55.0	43.0	NM_001136157	B4DGG7|G5E9D7|Q4KMN9|Q8N6T5|Q9H650|Q9H9U0|Q9NT65	Missense_Mutation	SNP	ENST00000156084.4	hg19	CCDS14313.1	.	.	.	.	.	.	.	.	.	.	A	15.52	2.857657	0.51376	.	.	ENSG00000068308	ENST00000396743;ENST00000453548;ENST00000156084;ENST00000376488	.	.	.	3.19	3.19	0.36642	.	0.000000	0.64402	D	0.000007	T	0.53594	0.1806	N	0.24115	0.695	0.45250	D	0.998251	P;D	0.54772	0.947;0.968	D;D	0.72625	0.95;0.978	T	0.56214	-0.8016	9	0.87932	D	0	8.2187	7.1699	0.25712	1.0:0.0:0.0:0.0	.	3;3	Q96G74;G5E9D7	OTUD5_HUMAN;.	T	3	.	ENSP00000156084:I3T	I	-	2	0	OTUD5	48699769	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	5.576000	0.67437	1.500000	0.48636	0.416000	0.27883	ATA	.	.		0.731	OTUD5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000060799.1	NM_017602		G	48814825	A	G	48814825	3	3	270	1	0	0	0	0	1	0	0	0	11324	449	16	2	1743	2	OTUD5	23	48814825	Missense_Mutation	SNP	A	TCGA-FV-A4ZP-01A-12D-A25V-10		48814825	106455735	67	39346										
ARHGEF6	9459	hgsc.bcm.edu	37	chrX	135863020	135863020	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	6	1	1.15742793791574	0.909407665505226	1.22420262664165	0.140866873065015	0.729941291585128	0	caaagatataagccatgtcaCgatttgttcttctggattca	7	8	4	1			TCGA-FV-A4ZP-01A-12D-A25V-10	TCGA-FV-A4ZP-11A-12D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	34a92167-000d-4968-bfc4-0a818857cbd4	d898cddf-8721-4cee-8a60-926c4c0dfc7c	g.chrX:135863020C>T	ENST00000250617.6	-	1	1227	c.22G>A	c.(22-24)Gtg>Atg	p.V8M		NM_004840.2	NP_004831.1	Q15052	ARHG6_HUMAN	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	8	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell junction assembly (GO:0034329)|JNK cascade (GO:0007254)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|intracellular (GO:0005622)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(1)|lung(14)|prostate(1)	38	Acute lymphoblastic leukemia(192;0.000127)					AGCCATGTCACGATTTGTTCT	0.463																																					p.V8M		Atlas-SNP	.											.	ARHGEF6	111	.	0			c.G22A						.						91	80	84					X																	135863020		2203	4300	6503	SO:0001583	missense	9459	exon1			ATGTCACGATTTG	D13631	CCDS14660.1	Xq26	2013-01-10	2002-05-23		ENSG00000129675	ENSG00000129675		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	685	protein-coding gene	gene with protein product	"Rac/Cdc42 guanine exchange factor (GEF) 6", "PAK-interacting exchange factor, alpha", "rho guanine nucleotide exchange factor 6"	300267	"mental retardation, X-linked 46"	MRX46		7584048, 9659915	Standard	NM_004840		Approved	alphaPIX, Cool-2, KIAA0006, alpha-PIX, Cool2	uc004fab.3	Q15052	OTTHUMG00000022518	ENST00000250617.6:c.22G>A	chrX.hg19:g.135863020C>T	ENSP00000250617:p.Val8Met	41.0	0.0		36.0	25.0	NM_004840	A6NMW9|A8K6S7|B1AL37|Q15396|Q5JQ66|Q7Z3W1|Q86XH0	Missense_Mutation	SNP	ENST00000250617.6	hg19	CCDS14660.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.334154	0.81801	.	.	ENSG00000129675	ENST00000250617	D	0.95171	-3.63	6.03	6.03	0.97812	Calponin homology domain (5);	0.000000	0.85682	D	0.000000	D	0.97545	0.9196	M	0.82517	2.595	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.97880	1.0291	10	0.87932	D	0	.	19.4624	0.94922	0.0:1.0:0.0:0.0	.	8	Q15052	ARHG6_HUMAN	M	8	ENSP00000250617:V8M	ENSP00000250617:V8M	V	-	1	0	ARHGEF6	135690686	1.000000	0.71417	0.998000	0.56505	0.902000	0.53008	7.487000	0.81328	2.550000	0.86006	0.506000	0.49869	GTG	.	.		0.463	ARHGEF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058511.2	NM_004840		T	135863020	C	T	135863020	3	4	270	1	0	0	0	0	1	0	0	0	910	536	19	1	2396	1	ARHGEF6	23	135863020	Missense_Mutation	SNP	C	TCGA-FV-A4ZP-01A-12D-A25V-10	87048195	135863020	19407540	68	39347										
TNFRSF18	8784	hgsc.bcm.edu	37	chr1	1139782	1139782	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	gcccacccaggactcactctGtccaaggtttgcagtggcct	10	15	2	0			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr1:1139782G>T	ENST00000379268.2	-	3	514	c.395C>A	c.(394-396)aCa>aAa	p.T132K	TNFRSF18_ENST00000328596.6_Missense_Mutation_p.T132K|TNFRSF18_ENST00000486728.1_Missense_Mutation_p.T60K|TNFRSF18_ENST00000379265.5_Missense_Mutation_p.T132K	NM_004195.2|NM_148902.1	NP_004186.1|NP_683700.1	Q9Y5U5	TNR18_HUMAN	tumor necrosis factor receptor superfamily, member 18	132					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|signal transduction (GO:0007165)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	tumor necrosis factor-activated receptor activity (GO:0005031)			lung(1)	1	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;3.73e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.01e-21)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		GACTCACTCTGTCCAAGGTTT	0.642																																					p.T132K	GBM(157;472 1934 13810 14591 35952)	Atlas-SNP	.											.	TNFRSF18	13	.	0			c.C395A						.						29	32	31					1																	1139782		2194	4296	6490	SO:0001583	missense	8784	exon3			CACTCTGTCCAAG	AF125304	CCDS9.1, CCDS10.1, CCDS30552.1	1p36.3	2011-08-11			ENSG00000186891	ENSG00000186891		"Tumor necrosis factor receptor superfamily", "CD molecules"	11914	protein-coding gene	gene with protein product		603905				9177197, 10037686	Standard	NM_004195		Approved	AITR, GITR, CD357	uc001add.3	Q9Y5U5	OTTHUMG00000001414	ENST00000379268.2:c.395C>A	chr1.hg19:g.1139782G>T	ENSP00000368570:p.Thr132Lys	118.0	0.0		84.0	21.0	NM_148902	B1AME1|O95851|Q5U0I4|Q9NYJ9	Missense_Mutation	SNP	ENST00000379268.2	hg19	CCDS10.1	.	.	.	.	.	.	.	.	.	.	G	12.54	1.967950	0.34754	.	.	ENSG00000186891	ENST00000328596;ENST00000379268;ENST00000379265	T;T;T	0.69435	1.53;-0.4;-0.4	3.55	2.61	0.31194	TNFR/CD27/30/40/95 cysteine-rich region (1);	0.921830	0.09071	N	0.852911	T	0.66665	0.2812	M	0.64997	1.995	0.18873	N	0.999988	P;P;P	0.46512	0.782;0.879;0.879	B;P;P	0.45167	0.242;0.472;0.472	T	0.57248	-0.7844	10	0.87932	D	0	.	8.2734	0.31857	0.0:0.0:0.7637:0.2363	.	132;132;132	Q9Y5U5-2;Q9Y5U5;B1AME3	.;TNR18_HUMAN;.	K	132	ENSP00000328207:T132K;ENSP00000368570:T132K;ENSP00000368567:T132K	ENSP00000328207:T132K	T	-	2	0	TNFRSF18	1129645	0.035000	0.19736	0.105000	0.21289	0.513000	0.34164	1.456000	0.35201	1.051000	0.40369	0.655000	0.94253	ACA	.	.		0.642	TNFRSF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004083.2	NM_004195		T	1139782	G	T	1139782	3	4	271	1	0	0	0	0	1	0	0	0	16306	1377	48	3	595	3	TNFRSF18	1	1139782	Missense_Mutation	SNP	G	TCGA-FV-A4ZQ-01A-11D-A25V-10		1139782	248110839	1	39348										
VWA1	64856	hgsc.bcm.edu	37	chr1	1372313	1372313	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	ctcctttcccccaggtccacCagcatcagccccccgagggg	9	20	1	0			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr1:1372313C>T	ENST00000476993.1	+	2	158	c.80C>T	c.(79-81)cCa>cTa	p.P27L	VWA1_ENST00000404702.3_Intron|VWA1_ENST00000338660.5_Intron|RP4-758J18.10_ENST00000417917.1_lincRNA	NM_022834.4	NP_073745.2	Q6PCB0	VWA1_HUMAN	von Willebrand factor A domain containing 1	27					behavioral response to pain (GO:0048266)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|interstitial matrix (GO:0005614)				NS(1)|breast(1)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	8	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		CCAGGTCCACCAGCATCAGCC	0.647																																					p.P27L		Atlas-SNP	.											.	VWA1	15	.	0			c.C80T						.						48	54	52					1																	1372313		2201	4295	6496	SO:0001583	missense	64856	exon2			GTCCACCAGCATC	BC059409	CCDS27.1, CCDS28.1, CCDS28.2	1p36.33	2013-02-11			ENSG00000179403	ENSG00000179403		"Fibronectin type III domain containing"	30910	protein-coding gene	gene with protein product		611901				14527666, 12062410	Standard	NM_022834		Approved	FLJ22215, VWA-1, WARP	uc001afs.3	Q6PCB0	OTTHUMG00000002975	ENST00000476993.1:c.80C>T	chr1.hg19:g.1372313C>T	ENSP00000417185:p.Pro27Leu	185.0	0.0		127.0	35.0	NM_022834	A8K692|B3KUA1|E9PB53|Q7L5D7|Q9H6J5	Missense_Mutation	SNP	ENST00000476993.1	hg19	CCDS27.1	.	.	.	.	.	.	.	.	.	.	.	12.44	1.939867	0.34189	.	.	ENSG00000179403	ENST00000476993	T	0.61980	0.06	4.23	3.32	0.38043	.	0.658638	0.14155	U	0.337790	T	0.41696	0.1170	N	0.24115	0.695	0.09310	N	0.999998	P	0.35077	0.483	B	0.33392	0.163	T	0.16512	-1.0400	10	0.23891	T	0.37	-3.0384	5.5511	0.17091	0.2101:0.6861:0.0:0.1037	.	27	Q6PCB0	VWA1_HUMAN	L	27	ENSP00000417185:P27L	ENSP00000417185:P27L	P	+	2	0	VWA1	1362176	0.000000	0.05858	0.001000	0.08648	0.060000	0.15804	-0.194000	0.09559	1.134000	0.42165	0.645000	0.84053	CCA	.	.		0.647	VWA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008291.1	NM_022834		T	1372313	C	T	1372313	3	4	271	1	0	0	0	0	1	0	0	0	17253	594	21	3	86	3	VWA1	1	1372313	Missense_Mutation	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10	232531	1372313	247878308	2	39349										
USP48	84196	hgsc.bcm.edu	37	chr1	22084166	22084166	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	gatggtttaccttttttctcCtctcacagttgggatcatcg	8	10	3	0			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr1:22084166C>A	ENST00000308271.9	-	2	893	c.245G>T	c.(244-246)aGg>aTg	p.R82M	USP48_ENST00000421625.2_Missense_Mutation_p.R82M|USP48_ENST00000400301.1_Missense_Mutation_p.R82M|USP48_ENST00000529637.1_Missense_Mutation_p.R82M	NM_032236.5	NP_115612.4	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 48	82					ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			NS(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(14)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)		CTTTTTTCTCCTCTCACAGTT	0.343																																					p.R82M		Atlas-SNP	.											.	USP48	91	.	0			c.G245T						.						113	104	107					1																	22084166		2202	4300	6502	SO:0001583	missense	84196	exon2			TTTCTCCTCTCAC	AF502942	CCDS30623.1, CCDS44084.1	1p36.12	2008-02-05	2005-08-08	2004-04-07	ENSG00000090686	ENSG00000090686		"Ubiquitin-specific peptidases"	18533	protein-coding gene	gene with protein product			"ubiquitin specific protease 31", "ubiquitin specific protease 48"	USP31		12838346	Standard	XM_005246009		Approved	FLJ23277, FLJ11328, FLJ20103, FLJ23054, MGC14879	uc001bfb.3	Q86UV5	OTTHUMG00000007798	ENST00000308271.9:c.245G>T	chr1.hg19:g.22084166C>A	ENSP00000309262:p.Arg82Met	86.0	0.0		79.0	24.0	NM_001032730	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Missense_Mutation	SNP	ENST00000308271.9	hg19	CCDS30623.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.559412	0.86335	.	.	ENSG00000090686	ENST00000400301;ENST00000308271;ENST00000529637;ENST00000421625	T;T;T;T	0.06528	3.31;3.29;3.29;3.48	5.71	5.71	0.89125	.	0.096119	0.64402	D	0.000001	T	0.24084	0.0583	M	0.62723	1.935	0.80722	D	1	D;P;D;D;D;D	0.76494	0.999;0.92;0.999;0.998;0.999;0.998	D;P;D;D;D;P	0.71656	0.974;0.474;0.974;0.951;0.974;0.898	T	0.00039	-1.2241	10	0.66056	D	0.02	.	18.8507	0.92227	0.0:1.0:0.0:0.0	.	82;82;82;82;82;82	B7ZKS7;B7ZKS3;Q86UV5-7;Q86UV5-3;Q86UV5-2;Q86UV5	.;.;.;.;.;UBP48_HUMAN	M	82	ENSP00000383157:R82M;ENSP00000309262:R82M;ENSP00000431949:R82M;ENSP00000406256:R82M	ENSP00000309262:R82M	R	-	2	0	USP48	21956753	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.343000	0.79319	2.689000	0.91719	0.655000	0.94253	AGG	.	.		0.343	USP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021372.1	NM_032236		A	22084166	C	A	22084166	3	1	271	1	0	0	0	0	1	0	0	0	17094	681	24	3	2974	3	USP48	1	22084166	Missense_Mutation	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10	20711853	22084166	227166455	3	39350										
TCTEX1D1	200132	hgsc.bcm.edu	37	chr1	67242056	67242056	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	gaagaatatgaaccagagctCtgtagacagatgactaaaac	9	7	1	6			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr1:67242056C>T	ENST00000282670.2	+	4	434	c.306C>T	c.(304-306)ctC>ctT	p.L102L		NM_152665.2	NP_689878.2	Q8N7M0	TC1D1_HUMAN	Tctex1 domain containing 1	102										large_intestine(2)|lung(10)|skin(1)	13						AACCAGAGCTCTGTAGACAGA	0.393																																					p.L102L		Atlas-SNP	.											.	TCTEX1D1	27	.	0			c.C306T						.						108	107	108					1																	67242056		2203	4300	6503	SO:0001819	synonymous_variant	200132	exon4			AGAGCTCTGTAGA	AK098192	CCDS633.1	1p31.2	2008-02-05			ENSG00000152760	ENSG00000152760			26882	protein-coding gene	gene with protein product							Standard	NM_152665		Approved	FLJ40873	uc001dcv.3	Q8N7M0	OTTHUMG00000009162	ENST00000282670.2:c.306C>T	chr1.hg19:g.67242056C>T		180.0	0.0		144.0	51.0	NM_152665	Q06YR9|Q5VYE1	Silent	SNP	ENST00000282670.2	hg19	CCDS633.1																																																																																			.	.		0.393	TCTEX1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025399.2	NM_152665		T	67242056	C	T	67242056	2	4	271	1	0	0	0	0	0	0	0	1	15734	900	32	3		3	TCTEX1D1	1	67242056	Silent	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10	45157890	67242056	182008565	4	39351										
SH2D2A	9047	hgsc.bcm.edu	37	chr1	156785887	156785887	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	gatgggggcttcgtgactccCtgtgagcacaaagagggctg	16	9	0	3			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr1:156785887C>T	ENST00000368199.3	-	2	188		c.e2-1		NTRK1_ENST00000392302.2_Intron|SH2D2A_ENST00000368198.3_Intron|SH2D2A_ENST00000495306.1_Splice_Site|SH2D2A_ENST00000392306.2_Splice_Site	NM_001161443.1|NM_001161444.1|NM_003975.3	NP_001154915.1|NP_001154916.1|NP_003966.2	Q9NP31	SH22A_HUMAN	SH2 domain containing 2A						angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	SH3/SH2 adaptor activity (GO:0005070)			endometrium(1)|large_intestine(2)|lung(15)	18	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					TCGTGACTCCCTGTGAGCACA	0.607																																					.		Atlas-SNP	.											.	SH2D2A	78	.	0			c.35-1G>A						.						63	64	64					1																	156785887		2203	4300	6503	SO:0001630	splice_region_variant	9047	exon3			GACTCCCTGTGAG	AJ000553	CCDS1159.1, CCDS53380.1, CCDS53381.1	1q21	2013-02-14	2010-04-21		ENSG00000027869	ENSG00000027869		"SH2 domain containing"	10821	protein-coding gene	gene with protein product	"T lymphocyte specific adaptor protein", "T cell specific adapter protein TSAd", "T cell specific adpater protein TSAd"	604514	"SH2 domain protein 2A"			9468509	Standard	NM_003975		Approved	TSAd, F2771	uc009wsh.2	Q9NP31	OTTHUMG00000041305	ENST00000368199.3:c.35-1G>A	chr1.hg19:g.156785887C>T		152.0	0.0		126.0	42.0	NM_003975	O43817|Q5UBZ1|Q5VZS4|Q5VZS5|Q9UPA7	Splice_Site	SNP	ENST00000368199.3	hg19	CCDS1159.1	.	.	.	.	.	.	.	.	.	.	C	13.45	2.241884	0.39598	.	.	ENSG00000027869	ENST00000368199;ENST00000392306	.	.	.	4.9	4.9	0.64082	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.7748	0.63046	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SH2D2A	155052511	0.985000	0.35326	0.958000	0.39756	0.382000	0.30200	3.233000	0.51311	2.706000	0.92434	0.655000	0.94253	.	.	.		0.607	SH2D2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098982.1	NM_003975	Intron	T	156785887	C	T	156785887	5	4	271	1	0	0	0	0	0	0	1	0	14247	695	24	3	1193	3	SH2D2A	1	156785887	Splice_Site	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10	89543831	156785887	92464734	5	39352										
ATP1A4	480	hgsc.bcm.edu	37	chr1	160136811	160136811	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	ttatgctggcccgaatcgctGgcctctgcaaccgggctgac	12	14	1	1			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr1:160136811G>T	ENST00000368081.4	+	9	1771	c.1300G>T	c.(1300-1302)Ggc>Tgc	p.G434C		NM_144699.3	NP_653300.2	Q13733	AT1A4_HUMAN	ATPase, Na+/K+ transporting, alpha 4 polypeptide	434					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|fertilization (GO:0009566)|ion transmembrane transport (GO:0034220)|potassium ion transport (GO:0006813)|regulation of cellular pH (GO:0030641)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(34)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	75	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			CCGAATCGCTGGCCTCTGCAA	0.493																																					p.G434C		Atlas-SNP	.											.	ATP1A4	167	.	0			c.G1300T						.						74	78	76					1																	160136811		2203	4300	6503	SO:0001583	missense	480	exon9			ATCGCTGGCCTCT	BC028297	CCDS1197.1, CCDS44255.1	1q23.2	2012-10-22	2002-02-25		ENSG00000132681	ENSG00000132681		"ATPases / P-type"	14073	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-4", "sodium pump subunit alpha-4", "sodium-potassium ATPase catalytic subunit alpha-4"	607321	"ATPase, Na+/K+ transporting, alpha polypeptide-like 2"	ATP1AL2		1981991, 3035563	Standard	NM_144699		Approved		uc001fve.4	Q13733	OTTHUMG00000031609	ENST00000368081.4:c.1300G>T	chr1.hg19:g.160136811G>T	ENSP00000357060:p.Gly434Cys	65.0	0.0		79.0	4.0	NM_144699	Q504T2|Q7Z4I9|Q8TBN8|Q8WXA7|Q8WXH7|Q8WY13	Missense_Mutation	SNP	ENST00000368081.4	hg19	CCDS1197.1	.	.	.	.	.	.	.	.	.	.	G	13.10	2.137748	0.37728	.	.	ENSG00000132681	ENST00000368081	D	0.96802	-4.13	4.42	3.51	0.40186	ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.169650	0.50627	D	0.000102	D	0.93268	0.7855	N	0.16862	0.45	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	D	0.93482	0.6828	10	0.87932	D	0	.	6.6593	0.23004	0.208:0.0:0.792:0.0	.	434	Q13733	AT1A4_HUMAN	C	434	ENSP00000357060:G434C	ENSP00000357060:G434C	G	+	1	0	ATP1A4	158403435	0.289000	0.24334	0.780000	0.31762	0.923000	0.55619	1.953000	0.40352	1.096000	0.41439	0.650000	0.86243	GGC	.	.		0.493	ATP1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077415.1	NM_144699		T	160136811	G	T	160136811	3	4	271	1	0	0	0	0	1	0	0	0	1131	1348	47	3	1334	3	ATP1A4	1	160136811	Missense_Mutation	SNP	G	TCGA-FV-A4ZQ-01A-11D-A25V-10	3350924	160136811	89113810	6	39353										
NFASC	23114	hgsc.bcm.edu	37	chr1	204937427	204937427	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	tcatgtatccccagggcaccGcgagcagccagatggtgctt	12	13	1	1	rs535350909		TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr1:204937427G>A	ENST00000401399.1	+	8	956	c.757G>A	c.(757-759)Gcg>Acg	p.A253T	NFASC_ENST00000338515.6_Missense_Mutation_p.A253T|NFASC_ENST00000367169.4_Missense_Mutation_p.A253T|NFASC_ENST00000338586.6_Missense_Mutation_p.A253T|NFASC_ENST00000404907.1_Missense_Mutation_p.A264T|NFASC_ENST00000404076.1_Missense_Mutation_p.A247T|NFASC_ENST00000339876.6_Missense_Mutation_p.A253T|NFASC_ENST00000539706.1_Missense_Mutation_p.A264T|NFASC_ENST00000367172.4_Missense_Mutation_p.A253T|NFASC_ENST00000367170.4_Missense_Mutation_p.A253T|NFASC_ENST00000367171.4_Missense_Mutation_p.A253T|NFASC_ENST00000403080.1_Missense_Mutation_p.A253T|NFASC_ENST00000360049.4_Missense_Mutation_p.A264T|NFASC_ENST00000513543.1_Missense_Mutation_p.A264T			O94856	NFASC_HUMAN	neurofascin	253	Ig-like C2-type 3.				axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			CCAGGGCACCGCGAGCAGCCA	0.582													G|||	1	0.000199681	0	0.0014	5008	,	,		20359	0		0	False		,,,				2504	0				p.A264T		Atlas-SNP	.											NFASC_ENST00000403080,caecum,carcinoma,0,3	NFASC	396	.	0			c.G790A						.						128	110	116					1																	204937427		2203	4300	6503	SO:0001583	missense	23114	exon9			GGCACCGCGAGCA	AK027553	CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1	1q32.1	2013-02-11	2010-06-24		ENSG00000163531	ENSG00000163531		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	29866	protein-coding gene	gene with protein product		609145	"neurofascin homolog (chicken)"			1377696, 8672144	Standard	NM_015090		Approved	NRCAML, KIAA0756, FLJ46866, NF	uc001hbj.3	O94856	OTTHUMG00000151697	ENST00000401399.1:c.757G>A	chr1.hg19:g.204937427G>A	ENSP00000385637:p.Ala253Thr	132.0	0.0		104.0	30.0	NM_015090	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Missense_Mutation	SNP	ENST00000401399.1	hg19	CCDS53460.1	.	.	.	.	.	.	.	.	.	.	G	9.661	1.144147	0.21205	.	.	ENSG00000163531	ENST00000367172;ENST00000367171;ENST00000367170;ENST00000338515;ENST00000339876;ENST00000338586;ENST00000295776;ENST00000539706;ENST00000360049;ENST00000367169;ENST00000446412;ENST00000403080;ENST00000404076;ENST00000401399;ENST00000404907;ENST00000513543;ENST00000430393	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.72167	-0.04;-0.1;-0.03;-0.04;-0.03;-0.05;-0.01;0.0;-0.03;-0.63;-0.51;-0.09;-0.03;-0.01;0.0;0.01	5.29	-1.47	0.08772	.	0.430805	0.19615	N	0.110051	T	0.37679	0.1012	N	0.04297	-0.235	0.09310	N	0.999999	B;B;B;B;P;B;B	0.36378	0.004;0.062;0.019;0.033;0.55;0.025;0.17	B;B;B;B;B;B;B	0.22880	0.002;0.003;0.011;0.008;0.014;0.008;0.042	T	0.34700	-0.9818	10	0.21014	T	0.42	.	11.9988	0.53219	0.0:0.084:0.1395:0.7765	.	264;264;349;253;253;264;253	O94856-11;O94856-8;B4DRH7;F8W791;O94856-9;O94856-3;O94856-2	.;.;.;.;.;.;.	T	253;253;253;253;253;253;264;264;264;253;253;253;247;253;264;264;240	ENSP00000356140:A253T;ENSP00000356139:A253T;ENSP00000356138:A253T;ENSP00000342128:A253T;ENSP00000344786:A253T;ENSP00000343509:A253T;ENSP00000438614:A264T;ENSP00000353154:A264T;ENSP00000356137:A253T;ENSP00000412161:A253T;ENSP00000384875:A253T;ENSP00000385676:A247T;ENSP00000385637:A253T;ENSP00000384061:A264T;ENSP00000425908:A264T;ENSP00000415031:A240T	ENSP00000295776:A264T	A	+	1	0	NFASC	203204050	0.000000	0.05858	0.058000	0.19502	0.898000	0.52572	0.122000	0.15687	-0.135000	0.11495	-0.188000	0.12872	GCG	.	.		0.582	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388		A	204937427	G	A	204937427	3	1	271	1	0	0	0	0	1	0	0	0	10368	1087	38	1	838	1	NFASC	1	204937427	Missense_Mutation	SNP	G	TCGA-FV-A4ZQ-01A-11D-A25V-10	44800616	204937427	44313194	7	39354										
USH2A	7399	hgsc.bcm.edu	37	chr1	216062335	216062335	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	gattttctaggatgctgccaGgtgaccaacatcattcttga	9	9	3	2	rs373383107		TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr1:216062335G>A	ENST00000307340.3	-	41	8042	c.7656C>T	c.(7654-7656)acC>acT	p.T2552T	RP5-1111A8.3_ENST00000414995.1_RNA|USH2A_ENST00000366943.2_Silent_p.T2552T	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	2552	Fibronectin type-III 12. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.T2552K(1)		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)		GATGCTGCCAGGTGACCAACA	0.408										HNSCC(13;0.011)																											p.T2552T		Atlas-SNP	.											.,1	USH2A	1168	.	1	Substitution - Missense(1)	lung(1)	c.C7656T						.	G		1,4405	2.1+/-5.4	0,1,2202	93	92	92		7656	1.5	1	1		92	0,8600		0,0,4300	no	coding-synonymous	USH2A	NM_206933.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		2552/5203	216062335	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	7399	exon41			CTGCCAGGTGACC	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.7656C>T	chr1.hg19:g.216062335G>A		45.0	0.0		41.0	14.0	NM_206933	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	hg19	CCDS31025.1																																																																																			.	.		0.408	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		A	216062335	G	A	216062335	2	1	271	1	0	0	0	0	0	0	0	1	17051	987	35	3		3	USH2A	1	216062335	Silent	SNP	G	TCGA-FV-A4ZQ-01A-11D-A25V-10	11124908	216062335	33188286	8	39355										
SLC30A10	55532	hgsc.bcm.edu	37	chr1	220088994	220088994	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	gacgtgagccagaggcagtgCcccggggggacaacacagct	16	12	0	2			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr1:220088994C>A	ENST00000366926.3	-	4	1416	c.1255G>T	c.(1255-1257)Gca>Tca	p.A419S	SLC30A10_ENST00000536446.1_Missense_Mutation_p.A174S|SLC30A10_ENST00000484079.1_5'UTR	NM_018713.2	NP_061183.2	Q6XR72	ZNT10_HUMAN	solute carrier family 30, member 10	419					zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation transmembrane transporter activity (GO:0008324)			NS(1)|endometrium(1)|large_intestine(1)|lung(9)|skin(1)	13				GBM - Glioblastoma multiforme(131;0.051)|all cancers(67;0.209)		AGAGGCAGTGCCCCGGGGGGA	0.567																																					p.A419S	Colon(76;360 1614 43677 51136)	Atlas-SNP	.											.	SLC30A10	58	.	0			c.G1255T						.						91	88	89					1																	220088994		2203	4300	6503	SO:0001583	missense	55532	exon4			GCAGTGCCCCGGG	AY212919	CCDS31026.1	1q41	2013-05-22			ENSG00000196660	ENSG00000196660		"Solute carriers"	25355	protein-coding gene	gene with protein product	"zinc transporter 8"	611146				15154973	Standard	NR_046437		Approved	DKFZp547M236, ZnT-10, ZRC1, ZNT8	uc001hlw.3	Q6XR72	OTTHUMG00000037434	ENST00000366926.3:c.1255G>T	chr1.hg19:g.220088994C>A	ENSP00000355893:p.Ala419Ser	224.0	0.0		201.0	56.0	NM_018713	Q49AL9|Q9NPW0	Missense_Mutation	SNP	ENST00000366926.3	hg19	CCDS31026.1	.	.	.	.	.	.	.	.	.	.	C	8.728	0.915947	0.17907	.	.	ENSG00000196660	ENST00000366926;ENST00000536446	T;T	0.63913	-0.07;0.52	6.02	0.139	0.14798	.	0.547984	0.19101	N	0.122715	T	0.38453	0.1041	N	0.19112	0.55	0.09310	N	1	B	0.31680	0.335	B	0.22386	0.039	T	0.15954	-1.0419	9	.	.	.	-5.679	10.0805	0.42386	0.0:0.4524:0.4138:0.1337	.	419	Q6XR72	ZNT10_HUMAN	S	419;174	ENSP00000355893:A419S;ENSP00000439489:A174S	.	A	-	1	0	SLC30A10	218155617	0.000000	0.05858	0.003000	0.11579	0.100000	0.18952	0.215000	0.17562	0.113000	0.18004	0.650000	0.86243	GCA	.	.		0.567	SLC30A10-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357709.1	NM_018713		A	220088994	C	A	220088994	3	1	271	1	0	0	0	0	1	0	0	0	14569	739	26	3	206	3	SLC30A10	1	220088994	Missense_Mutation	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10	4026659	220088994	29161627	9	39356										
RAD51AP2	729475	hgsc.bcm.edu	37	chr2	17696823	17696823	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	ttttactattgtcagagcttCtgttgataaatatttagcag	7	5	2	2			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr2:17696823C>A	ENST00000399080.2	-	1	2883	c.2860G>T	c.(2860-2862)Gaa>Taa	p.E954*		NM_001099218.2	NP_001092688.1	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2	954										endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(10)|liver(1)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					GTCAGAGCTTCTGTTGATAAA	0.313																																					p.E954X		Atlas-SNP	.											.	RAD51AP2	134	.	0			c.G2860T						.						34	34	34					2																	17696823		1799	4075	5874	SO:0001587	stop_gained	729475	exon1			GAGCTTCTGTTGA	AK310498	CCDS42656.1	2p24.2	2009-01-13			ENSG00000214842	ENSG00000214842			34417	protein-coding gene	gene with protein product						16990250	Standard	NM_001099218		Approved	FLJ17540	uc002rcl.1	Q09MP3	OTTHUMG00000151761	ENST00000399080.2:c.2860G>T	chr2.hg19:g.17696823C>A	ENSP00000382030:p.Glu954*	160.0	0.0		123.0	44.0	NM_001099218		Nonsense_Mutation	SNP	ENST00000399080.2	hg19	CCDS42656.1	.	.	.	.	.	.	.	.	.	.	C	39	7.903963	0.98554	.	.	ENSG00000214842	ENST00000399080	.	.	.	5.17	4.28	0.50868	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-0.7505	12.5509	0.56225	0.0:0.9194:0.0:0.0806	.	.	.	.	X	954	.	ENSP00000382030:E954X	E	-	1	0	RAD51AP2	17560304	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	0.751000	0.26348	2.583000	0.87209	0.655000	0.94253	GAA	.	.		0.313	RAD51AP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323801.3	NM_001099218		A	17696823	C	A	17696823	4	1	271	1	0	0	0	0	0	1	0	0	13002	922	32	3	631	3	RAD51AP2	2	17696823	Nonsense_Mutation	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10		17696823	225502550	10	39357										
PUM2	23369	hgsc.bcm.edu	37	chr2	20490545	20490545	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	acgctgacctgctccagcacGgagaacctacaaaggtaaaa	9	12	0	2	rs530419740		TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr2:20490545G>C	ENST00000361078.2	-	9	1181	c.1159C>G	c.(1159-1161)Cgt>Ggt	p.R387G	PUM2_ENST00000536417.1_Missense_Mutation_p.R331G|PUM2_ENST00000403432.1_Missense_Mutation_p.R387G|PUM2_ENST00000319801.5_Missense_Mutation_p.R387G|PUM2_ENST00000338086.5_Missense_Mutation_p.R387G			Q8TB72	PUM2_HUMAN	pumilio RNA-binding family member 2	387	Ala-rich.|Gln-rich.				regulation of translation (GO:0006417)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nuclear membrane (GO:0031965)|perinuclear region of cytoplasm (GO:0048471)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(7)|lung(13)|ovary(2)|prostate(4)|urinary_tract(3)	42	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCTCCAGCACGGAGAACCTAC	0.408																																					p.R387G		Atlas-SNP	.											.	PUM2	91	.	0			c.C1159G						.						52	48	49					2																	20490545		2202	4298	6500	SO:0001583	missense	23369	exon9			CAGCACGGAGAAC	AF315591	CCDS1698.1, CCDS74486.1, CCDS74487.1	2p22-p21	2013-09-02	2013-09-02		ENSG00000055917	ENSG00000055917			14958	protein-coding gene	gene with protein product		607205	"pumilio (Drosphila) homolog 2", "pumilio homolog 2 (Drosophila)"			9039502, 12459267, 12511597	Standard	XM_005262607		Approved	PUMH2, KIAA0235	uc002rds.1	Q8TB72	OTTHUMG00000122098	ENST00000361078.2:c.1159C>G	chr2.hg19:g.20490545G>C	ENSP00000354370:p.Arg387Gly	137.0	0.0		103.0	36.0	NM_015317	B3KSL0|B4E2B6|D6W527|O00234|Q53TV7|Q8WY43|Q9HAN2	Missense_Mutation	SNP	ENST00000361078.2	hg19		.	.	.	.	.	.	.	.	.	.	G	19.65	3.866975	0.72065	.	.	ENSG00000055917	ENST00000338086;ENST00000361078;ENST00000319801;ENST00000440577;ENST00000403432;ENST00000536417	T;T;T;T;T;T	0.27557	1.8;2.04;1.97;1.66;1.8;1.79	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.49115	0.1538	L	0.58101	1.795	0.58432	D	0.999993	D;P;D	0.89917	0.997;0.798;1.0	D;B;D	0.91635	0.996;0.238;0.999	T	0.25502	-1.0130	10	0.21540	T	0.41	-3.2766	14.1158	0.65151	0.0:0.0:0.8496:0.1504	.	331;387;387	B4E2B6;B7ZL34;Q8TB72-3	.;.;.	G	387;387;387;278;387;331	ENSP00000338173:R387G;ENSP00000354370:R387G;ENSP00000326746:R387G;ENSP00000409905:R278G;ENSP00000385992:R387G;ENSP00000440093:R331G	ENSP00000326746:R387G	R	-	1	0	PUM2	20354026	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.145000	0.64839	2.615000	0.88500	0.591000	0.81541	CGT	.	.		0.408	PUM2-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015317		C	20490545	G	C	20490545	3	2	271	1	0	0	0	0	1	0	0	0	12841	1116	39	4	2083	4	PUM2	2	20490545	Missense_Mutation	SNP	G	TCGA-FV-A4ZQ-01A-11D-A25V-10	2793722	20490545	222708828	11	39358										
QPCT	25797	hgsc.bcm.edu	37	chr2	37580079	37580079	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	gaagctatgctgctcgtcagGtgagaacatgggacacaaac	12	9	1	1			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr2:37580079G>T	ENST00000338415.3	+	2	425		c.e2+1		QPCT_ENST00000537448.1_Intron	NM_012413.3	NP_036545.1	Q16769	QPCT_HUMAN	glutaminyl-peptide cyclotransferase						cellular protein modification process (GO:0006464)|peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase (GO:0017186)	extracellular vesicular exosome (GO:0070062)	glutaminyl-peptide cyclotransferase activity (GO:0016603)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)|stomach(2)	17		Ovarian(717;0.051)|all_hematologic(82;0.21)				TGCTCGTCAGGTGAGAACATG	0.463																																					.		Atlas-SNP	.											.	QPCT	34	.	0			c.267+1G>T						.						68	63	65					2																	37580079		2203	4300	6503	SO:0001630	splice_region_variant	25797	exon2			CGTCAGGTGAGAA	X71125	CCDS1790.1	2p22	2008-07-31	2008-07-31		ENSG00000115828	ENSG00000115828	2.3.2.5		9753	protein-coding gene	gene with protein product	"glutaminyl cyclase"	607065				7999256	Standard	NM_012413		Approved	QC, GCT	uc002rqg.3	Q16769	OTTHUMG00000100963	ENST00000338415.3:c.267+1G>T	chr2.hg19:g.37580079G>T		34.0	0.0		42.0	20.0	NM_012413	Q16770|Q3KRG6|Q53TR4	Splice_Site	SNP	ENST00000338415.3	hg19	CCDS1790.1	.	.	.	.	.	.	.	.	.	.	G	15.81	2.941799	0.53079	.	.	ENSG00000115828	ENST00000338415	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.8968	0.96969	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	QPCT	37433583	1.000000	0.71417	1.000000	0.80357	0.294000	0.27393	8.881000	0.92415	2.691000	0.91804	0.655000	0.94253	.	.	.		0.463	QPCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218572.2		Intron	T	37580079	G	T	37580079	5	4	271	1	0	0	0	0	0	0	1	0	12889	1275	44	3	274	3	QPCT	2	37580079	Splice_Site	SNP	G	TCGA-FV-A4ZQ-01A-11D-A25V-10	17089534	37580079	205619294	12	39359										
SPTBN1	6711	hgsc.bcm.edu	37	chr2	54858501	54858501	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	gctgctcacgcagcacgagaAcatcaagaacgagatcgaca	10	12	2	3			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr2:54858501A>G	ENST00000356805.4	+	16	3598	c.3317A>G	c.(3316-3318)aAc>aGc	p.N1106S	SPTBN1_ENST00000333896.5_Missense_Mutation_p.N1093S	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	1106					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			CAGCACGAGAACATCAAGAAC	0.572																																					p.N1106S		Atlas-SNP	.											.	SPTBN1	378	.	0			c.A3317G						.						161	132	142					2																	54858501		2203	4300	6503	SO:0001583	missense	6711	exon16			ACGAGAACATCAA		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"Pleckstrin homology (PH) domain containing"	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.3317A>G	chr2.hg19:g.54858501A>G	ENSP00000349259:p.Asn1106Ser	201.0	0.0		201.0	61.0	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Missense_Mutation	SNP	ENST00000356805.4	hg19	CCDS33198.1	.	.	.	.	.	.	.	.	.	.	A	11.45	1.643657	0.29246	.	.	ENSG00000115306	ENST00000356805;ENST00000333896	T;T	0.48522	0.81;0.81	5.56	5.56	0.83823	.	0.205919	0.51477	D	0.000083	T	0.20577	0.0495	N	0.00801	-1.175	0.41923	D	0.990521	B;B	0.02656	0.0;0.0	B;B	0.10450	0.003;0.005	T	0.15178	-1.0446	10	0.21540	T	0.41	.	15.727	0.77770	1.0:0.0:0.0:0.0	.	1093;1106	Q01082-3;Q01082	.;SPTB2_HUMAN	S	1106;1093	ENSP00000349259:N1106S;ENSP00000334156:N1093S	ENSP00000334156:N1093S	N	+	2	0	SPTBN1	54712005	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	2.957000	0.49137	2.118000	0.64928	0.533000	0.62120	AAC	.	.		0.572	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			G	54858501	A	G	54858501	3	3	271	1	0	0	0	0	1	0	0	0	15134	43	2	2	3488	2	SPTBN1	2	54858501	Missense_Mutation	SNP	A	TCGA-FV-A4ZQ-01A-11D-A25V-10	17278422	54858501	188340872	13	39360										
KIAA1841	84542	hgsc.bcm.edu	37	chr2	61324923	61324923	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	aagttcattgaatactgttgGcactggaatttatccctgct	8	8	1	1			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr2:61324923G>T	ENST00000402291.1	+	12	1542	c.1301G>T	c.(1300-1302)gGc>gTc	p.G434V	KIAA1841_ENST00000356719.2_Missense_Mutation_p.G434V|KIAA1841_ENST00000295031.5_Missense_Mutation_p.G434V|KIAA1841_ENST00000453873.1_Missense_Mutation_p.G434V	NM_001129993.1	NP_001123465.1	Q6NSI8	K1841_HUMAN	KIAA1841	434										breast(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	25			Epithelial(17;0.193)			AATACTGTTGGCACTGGAATT	0.383																																					p.G434V		Atlas-SNP	.											.	KIAA1841	95	.	0			c.G1301T						.						149	142	144					2																	61324923		2203	4300	6503	SO:0001583	missense	84542	exon12			CTGTTGGCACTGG	BC070104	CCDS1867.1, CCDS46296.1	2p15	2010-06-22			ENSG00000162929	ENSG00000162929			29387	protein-coding gene	gene with protein product						11347906	Standard	NM_032506		Approved		uc002saw.4	Q6NSI8	OTTHUMG00000129421	ENST00000402291.1:c.1301G>T	chr2.hg19:g.61324923G>T	ENSP00000385579:p.Gly434Val	204.0	0.0		165.0	43.0	NM_032506	Q49AF0|Q6ZND0|Q96JI6	Missense_Mutation	SNP	ENST00000402291.1	hg19	CCDS46296.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.640613	0.87859	.	.	ENSG00000162929	ENST00000402291;ENST00000295031;ENST00000356719;ENST00000453873	.	.	.	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	T	0.73401	0.3582	M	0.69823	2.125	0.80722	D	1	P;P	0.49635	0.909;0.926	P;P	0.51895	0.555;0.683	T	0.71279	-0.4640	9	0.39692	T	0.17	-8.8888	20.32	0.98661	0.0:0.0:1.0:0.0	.	434;434	Q6NSI8-2;Q6NSI8	.;K1841_HUMAN	V	434	.	ENSP00000295031:G434V	G	+	2	0	KIAA1841	61178427	1.000000	0.71417	1.000000	0.80357	0.676000	0.39594	4.950000	0.63603	2.799000	0.96334	0.579000	0.79373	GGC	.	.		0.383	KIAA1841-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325477.1	NM_032506		T	61324923	G	T	61324923	3	4	271	1	0	0	0	0	1	0	0	0	8270	1203	42	3	1339	3	KIAA1841	2	61324923	Missense_Mutation	SNP	G	TCGA-FV-A4ZQ-01A-11D-A25V-10	6466422	61324923	181874450	14	39361										
NFU1	27247	hgsc.bcm.edu	37	chr2	69642381	69642381	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	gatgcaaagaagtccatgatTgttgcataaatatctggttt	9	5	1	2			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr2:69642381T>A	ENST00000410022.2	-	5	625	c.420A>T	c.(418-420)acA>acT	p.T140T	NFU1_ENST00000462320.1_5'UTR|NFU1_ENST00000471185.1_5'UTR|NFU1_ENST00000303698.3_Silent_p.T116T|NFU1_ENST00000394305.1_5'UTR	NM_001002755.2	NP_001002755.1	Q9UMS0	NFU1_HUMAN	NFU1 iron-sulfur cluster scaffold	140					iron-sulfur cluster assembly (GO:0016226)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|iron ion binding (GO:0005506)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|prostate(1)|skin(1)	7						AGTCCATGATTGTTGCATAAA	0.368																																					p.T140T		Atlas-SNP	.											.	NFU1	19	.	0			c.A420T						.						96	94	94					2																	69642381		2203	4300	6503	SO:0001819	synonymous_variant	27247	exon5			CATGATTGTTGCA	AJ132584	CCDS33217.1, CCDS42694.1, CCDS46315.1	2p15-p13	2014-07-03	2014-07-03	2006-10-24	ENSG00000169599	ENSG00000169599			16287	protein-coding gene	gene with protein product		608100	"HIRA interacting protein 5", "NFU1 iron-sulfur cluster scaffold homolog (S. cerevisiae)"	HIRIP5		11342215, 12886008	Standard	NR_045631		Approved	CGI-33, NifU, NIFUC	uc002sfk.3	Q9UMS0	OTTHUMG00000152668	ENST00000410022.2:c.420A>T	chr2.hg19:g.69642381T>A		245.0	0.0		217.0	53.0	NM_001002755	B4DUL9|Q53QE5|Q6VNZ8|Q7Z5B1|Q7Z5B2|Q9Y322	Silent	SNP	ENST00000410022.2	hg19	CCDS33217.1																																																																																			.	.		0.368	NFU1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327279.3	NM_015700		A	69642381	T	A	69642381	2	1	271	1	0	0	0	0	0	0	0	1	10395	1799	63	4		4	NFU1	2	69642381	Silent	SNP	T	TCGA-FV-A4ZQ-01A-11D-A25V-10	8317458	69642381	173556992	15	39362										
KDM3A	55818	hgsc.bcm.edu	37	chr2	86709144	86709144	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	tccagcacagtcctccatacGtttaacagcacaattttgac	5	13	0	1			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr2:86709144G>A	ENST00000409556.1	+	18	2969	c.2604G>A	c.(2602-2604)acG>acA	p.T868T	KDM3A_ENST00000409064.1_Silent_p.T868T|KDM3A_ENST00000542128.1_Silent_p.T816T|KDM3A_ENST00000312912.5_Silent_p.T868T			Q9Y4C1	KDM3A_HUMAN	lysine (K)-specific demethylase 3A	868					androgen receptor signaling pathway (GO:0030521)|formaldehyde biosynthetic process (GO:0046293)|histone H3-K9 demethylation (GO:0033169)|histone H3-K9 dimethylation (GO:0036123)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of histone H3-K9 methylation (GO:0051573)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatid nucleus elongation (GO:0007290)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|dioxygenase activity (GO:0051213)|iron ion binding (GO:0005506)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|liver(1)|lung(13)|ovary(1)|prostate(3)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	47						TCCTCCATACGTTTAACAGCA	0.388																																					p.T868T	NSCLC(96;1150 1523 6936 46253 49736)	Atlas-SNP	.											.	KDM3A	179	.	0			c.G2604A						.						153	145	148					2																	86709144		2203	4300	6503	SO:0001819	synonymous_variant	55818	exon17			CCATACGTTTAAC	AB018285	CCDS1990.1	2p11.2	2011-07-01	2009-04-06	2009-04-06	ENSG00000115548	ENSG00000115548		"Chromatin-modifying enzymes / K-demethylases"	20815	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 2A"	611512	"jumonji domain containing 1", "jumonji domain containing 1A"	JMJD1, JMJD1A		9872452	Standard	NM_018433		Approved	TSGA, KIAA0742, JHMD2A	uc010ytj.2	Q9Y4C1	OTTHUMG00000130204	ENST00000409556.1:c.2604G>A	chr2.hg19:g.86709144G>A		169.0	0.0		177.0	54.0	NM_001146688	D6W5M3|Q53S72|Q68D47|Q68UT9|Q6N050|Q8IY08	Silent	SNP	ENST00000409556.1	hg19	CCDS1990.1																																																																																			.	.		0.388	KDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252522.2	NM_018433		A	86709144	G	A	86709144	2	1	271	1	0	0	0	0	0	0	0	1	8135	1132	40	1		1	KDM3A	2	86709144	Silent	SNP	G	TCGA-FV-A4ZQ-01A-11D-A25V-10	17066763	86709144	156490229	16	39363										
GAD1	2571	hgsc.bcm.edu	37	chr2	171700595	171700595	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	cagtgtttgtcctcatggaaCaaataacacttaagaagatg	8	7	1	2			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr2:171700595C>A	ENST00000358196.3	+	7	1229	c.679C>A	c.(679-681)Caa>Aaa	p.Q227K	GAD1_ENST00000429023.1_3'UTR	NM_000817.2	NP_000808.2	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 (brain, 67kDa)	227					gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate catabolic process (GO:0006538)|glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|protein-pyridoxal-5-phosphate linkage (GO:0018352)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(15)|ovary(1)|urinary_tract(2)	35						CCTCATGGAACAAATAACACT	0.368																																					p.Q227K		Atlas-SNP	.											.	GAD1	79	.	0			c.C679A						.						210	217	215					2																	171700595		2203	4300	6503	SO:0001583	missense	2571	exon7			ATGGAACAAATAA		CCDS2239.1, CCDS2240.1	2q31	2008-02-05	2002-08-29		ENSG00000128683	ENSG00000128683	4.1.1.15		4092	protein-coding gene	gene with protein product		605363	"glutamate decarboxylase 1 (brain, 67kD)"	GAD		1549570	Standard	XM_005246443		Approved		uc002ugi.3	Q99259	OTTHUMG00000044175	ENST00000358196.3:c.679C>A	chr2.hg19:g.171700595C>A	ENSP00000350928:p.Gln227Lys	213.0	0.0		182.0	42.0	NM_000817	Q49AK1|Q53TQ7|Q9BU91|Q9UHH4	Missense_Mutation	SNP	ENST00000358196.3	hg19	CCDS2239.1	.	.	.	.	.	.	.	.	.	.	C	16.02	3.002856	0.54254	.	.	ENSG00000128683	ENST00000358196	T	0.37058	1.22	6.17	6.17	0.99709	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	T	0.25754	0.0627	N	0.10733	0.035	0.80722	D	1	B	0.20459	0.045	B	0.21546	0.035	T	0.06552	-1.0820	10	0.33940	T	0.23	-11.5566	20.8794	0.99867	0.0:1.0:0.0:0.0	.	227	Q99259	DCE1_HUMAN	K	227	ENSP00000350928:Q227K	ENSP00000350928:Q227K	Q	+	1	0	GAD1	171408841	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.424000	0.80242	2.941000	0.99782	0.655000	0.94253	CAA	.	.		0.368	GAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102664.2			A	171700595	C	A	171700595	3	1	271	1	0	0	0	0	1	0	0	0	6187	479	17	3	742	3	GAD1	2	171700595	Missense_Mutation	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10	84991451	171700595	71498778	17	39364										
IKZF2	22807	hgsc.bcm.edu	37	chr2	213914450	213914450	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	cacttaccagaatgggtcctGaggtgtcctgtgagggcgtc	14	10	0	3			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr2:213914450G>A	ENST00000434687.1	-	6	870	c.561C>T	c.(559-561)ctC>ctT	p.L187L	IKZF2_ENST00000374319.4_Silent_p.L161L|IKZF2_ENST00000342002.2_Silent_p.L193L|IKZF2_ENST00000451136.2_Silent_p.L161L|IKZF2_ENST00000457361.1_Silent_p.L187L|IKZF2_ENST00000374327.4_Intron|IKZF2_ENST00000421754.2_Silent_p.L161L|IKZF2_ENST00000413091.3_Silent_p.L187L			Q9UKS7	IKZF2_HUMAN	IKAROS family zinc finger 2 (Helios)	187					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(7)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		Esophageal squamous(248;0.0559)|Renal(323;0.218)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;2.97e-07)|all cancers(144;1.53e-05)|LUSC - Lung squamous cell carcinoma(224;0.00599)|Lung(261;0.00792)		AATGGGTCCTGAGGTGTCCTG	0.428																																					p.L187L		Atlas-SNP	.											.	IKZF2	71	.	0			c.C561T						.						100	90	94					2																	213914450		2203	4300	6503	SO:0001819	synonymous_variant	22807	exon5			GGTCCTGAGGTGT	AF130863	CCDS2395.1, CCDS46507.1	2q13.1	2013-01-08	2006-08-25	2006-08-25	ENSG00000030419	ENSG00000030419		"Zinc fingers, C2H2-type", "IKAROS zinc fingers"	13177	protein-coding gene	gene with protein product		606234	"zinc finger protein, subfamily 1A, 2 (Helios)"	ZNFN1A2		9512513, 9560339	Standard	NM_001079526		Approved	Helios	uc002vem.3	Q9UKS7	OTTHUMG00000133005	ENST00000434687.1:c.561C>T	chr2.hg19:g.213914450G>A		80.0	0.0		81.0	30.0	NM_016260	Q53YJ5|Q6PQC5|Q6PQC6|Q6PQC7|Q6PQC8|Q6PQD0|Q6PQD1|Q8N6S1	Silent	SNP	ENST00000434687.1	hg19	CCDS2395.1																																																																																			.	.		0.428	IKZF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256593.3	NM_016260		A	213914450	G	A	213914450	2	1	271	1	0	0	0	0	0	0	0	1	7624	1277	45	3		3	IKZF2	2	213914450	Silent	SNP	G	TCGA-FV-A4ZQ-01A-11D-A25V-10	42213855	213914450	29284923	18	39365										
SPAG16	79582	hgsc.bcm.edu	37	chr2	214354720	214354720	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	ccatagatatgcaaccaaatCcaaacctgaatgtttctaaa	4	10	1	2			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr2:214354720C>T	ENST00000331683.5	+	10	1071	c.976C>T	c.(976-978)Cca>Tca	p.P326S	SPAG16_ENST00000374309.3_Missense_Mutation_p.P232S	NM_024532.4	NP_078808.3	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16	326					cilium assembly (GO:0042384)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|microtubule cytoskeleton (GO:0015630)|motile cilium (GO:0031514)|nucleus (GO:0005634)				endometrium(4)|kidney(1)|large_intestine(15)|lung(27)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	56		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)		GCAACCAAATCCAAACCTGAA	0.353																																					p.P326S		Atlas-SNP	.											.	SPAG16	134	.	0			c.C976T						.						62	71	68					2																	214354720		2202	4299	6501	SO:0001583	missense	79582	exon10			CCAAATCCAAACC	AF310672	CCDS2396.1, CCDS46508.1	2q34	2013-05-21			ENSG00000144451	ENSG00000144451		"WD repeat domain containing"	23225	protein-coding gene	gene with protein product		612173				12391165, 11867345	Standard	NM_024532		Approved	PF20, FLJ22724, DKFZp666P1710, WDR29	uc002veq.4	Q8N0X2	OTTHUMG00000133015	ENST00000331683.5:c.976C>T	chr2.hg19:g.214354720C>T	ENSP00000332592:p.Pro326Ser	97.0	0.0		106.0	36.0	NM_024532	Q498B7|Q658W1|Q68DB3|Q6I9Z6|Q8N9C7|Q9H601	Missense_Mutation	SNP	ENST00000331683.5	hg19	CCDS2396.1	.	.	.	.	.	.	.	.	.	.	C	2.046	-0.418774	0.04766	.	.	ENSG00000144451	ENST00000331683;ENST00000374309;ENST00000451561	T;T;T	0.60797	0.23;0.16;0.54	5.93	3.16	0.36331	.	0.301950	0.29246	N	0.012709	T	0.41811	0.1175	N	0.17082	0.46	0.09310	N	1	B;P;D;B	0.56746	0.028;0.952;0.977;0.028	B;B;P;B	0.46975	0.015;0.341;0.533;0.015	T	0.32052	-0.9921	10	0.15499	T	0.54	.	10.5382	0.45018	0.0:0.6729:0.2537:0.0734	.	232;177;266;326	B4DYB5;Q8N0X2-2;Q4G1A2;Q8N0X2	.;.;.;SPG16_HUMAN	S	326;232;12	ENSP00000332592:P326S;ENSP00000363428:P232S;ENSP00000416600:P12S	ENSP00000332592:P326S	P	+	1	0	SPAG16	214062965	0.955000	0.32602	0.001000	0.08648	0.005000	0.04900	1.062000	0.30555	0.120000	0.18254	-1.358000	0.01219	CCA	.	.		0.353	SPAG16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256601.2	NM_024532		T	214354720	C	T	214354720	3	4	271	1	0	0	0	0	1	0	0	0	14993	855	30	3	1030	3	SPAG16	2	214354720	Missense_Mutation	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10	440270	214354720	28844653	19	39366										
SPEG	10290	hgsc.bcm.edu	37	chr2	220348819	220348819	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	cccccgcaccccagcctgccCaagacaaggctccagagccc	8	22	0	2			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr2:220348819C>T	ENST00000312358.7	+	30	6766	c.6634C>T	c.(6634-6636)Caa>Taa	p.Q2212*	AC053503.11_ENST00000429882.1_RNA|SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	2212	Pro-rich.				cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		CCAGCCTGCCCAAGACAAGGC	0.667																																					p.Q2212X		Atlas-SNP	.											.	SPEG	272	.	0			c.C6634T						.						30	41	38					2																	220348819		2019	4144	6163	SO:0001587	stop_gained	10290	exon30			CCTGCCCAAGACA	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"Immunoglobulin superfamily / I-set domain containing"	16901	protein-coding gene	gene with protein product		615950	"aortic preferentially expressed gene 1"	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.6634C>T	chr2.hg19:g.220348819C>T	ENSP00000311684:p.Gln2212*	158.0	0.0		64.0	24.0	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Nonsense_Mutation	SNP	ENST00000312358.7	hg19	CCDS42824.1	.	.	.	.	.	.	.	.	.	.	C	46	12.391795	0.99663	.	.	ENSG00000072195	ENST00000312358;ENST00000265327	.	.	.	3.86	3.86	0.44501	.	1.010830	0.07972	N	0.984227	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	.	12.3783	0.55293	0.0:0.7758:0.2242:0.0	.	.	.	.	X	2212	.	ENSP00000265327:Q2212X	Q	+	1	0	SPEG	220057063	0.001000	0.12720	0.744000	0.31058	0.886000	0.51366	0.644000	0.24766	2.155000	0.67459	0.455000	0.32223	CAA	.	.		0.667	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		T	220348819	C	T	220348819	4	4	271	1	0	0	0	0	0	1	0	0	15051	595	21	3	6764	3	SPEG	2	220348819	Nonsense_Mutation	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10	5994099	220348819	22850554	20	39367										
ARMC9	80210	hgsc.bcm.edu	37	chr2	232209780	232209780	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	aaaggcccgtcacccccggcGgccacagaaacgggtaccca	11	17	1	1			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr2:232209780G>A	ENST00000349938.4	+	21	2166	c.1972G>A	c.(1972-1974)Ggc>Agc	p.G658S	ARMC9_ENST00000483477.1_3'UTR	NM_001271466.1|NM_025139.4	NP_001258395.1|NP_079415	Q7Z3E5	ARMC9_HUMAN	armadillo repeat containing 9	658						extracellular vesicular exosome (GO:0070062)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22		Renal(207;0.0112)|all_lung(227;0.0744)|all_hematologic(139;0.0749)|Acute lymphoblastic leukemia(138;0.167)|Medulloblastoma(418;0.184)|Lung NSC(271;0.205)		Epithelial(121;1.43e-10)|LUSC - Lung squamous cell carcinoma(224;0.017)|Lung(119;0.0189)		CACCCCCGGCGGCCACAGAAA	0.527																																					p.G658S		Atlas-SNP	.											.	ARMC9	129	.	0			c.G1972A						.																																			SO:0001583	missense	80210	exon21			CCCGGCGGCCACA	BC004514	CCDS2484.1, CCDS74666.1	2q37.1	2013-02-14			ENSG00000135931	ENSG00000135931		"Armadillo repeat containing"	20730	protein-coding gene	gene with protein product						11347906	Standard	NM_025139		Approved	FLJ12584, KIAA1868, ARM, KU-MEL-1	uc031rrs.1	Q7Z3E5	OTTHUMG00000133229	ENST00000349938.4:c.1972G>A	chr2.hg19:g.232209780G>A	ENSP00000258417:p.Gly658Ser	77.0	0.0		92.0	6.0	NM_025139	Q53TI3|Q6P162|Q7L594|Q86WG2|Q96JF9|Q9H9R8	Missense_Mutation	SNP	ENST00000349938.4	hg19	CCDS2484.1	.	.	.	.	.	.	.	.	.	.	G	13.56	2.273407	0.40194	.	.	ENSG00000135931	ENST00000349938;ENST00000359743	T	0.15952	2.38	5.01	4.01	0.46588	.	0.279259	0.35772	N	0.002993	T	0.07548	0.0190	N	0.08118	0	0.27636	N	0.947867	B	0.25048	0.117	B	0.15870	0.014	T	0.23547	-1.0185	10	0.22706	T	0.39	-11.6607	9.4346	0.38630	0.0:0.0:0.7373:0.2627	.	658	Q7Z3E5	ARMC9_HUMAN	S	658	ENSP00000258417:G658S	ENSP00000258417:G658S	G	+	1	0	ARMC9	231918024	0.999000	0.42202	0.986000	0.45419	0.625000	0.37756	3.257000	0.51500	2.483000	0.83821	0.563000	0.77884	GGC	.	.		0.527	ARMC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256966.3	NM_025139		A	232209780	G	A	232209780	3	1	271	1	0	0	0	0	1	0	0	0	958	1116	39	1	2050	1	ARMC9	2	232209780	Missense_Mutation	SNP	G	TCGA-FV-A4ZQ-01A-11D-A25V-10	11860961	232209780	10989593	21	39368										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266101	41266101	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	gcaacagtcttacctggactCtggaatccattctggtgcca	9	12	3	0	rs121913416|rs121913400		TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr3:41266101C>G	ENST00000349496.5	+	3	378	c.98C>G	c.(97-99)tCt>tGt	p.S33C	CTNNB1_ENST00000453024.1_Missense_Mutation_p.S26C|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S33C|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S33C|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S33C	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	33			Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> F (in PTR, MDB and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10666372}.|S -> L (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> Y (in colorectal cancer and PTR; enhances transactivation of target genes). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:9065402}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S33C(168)|p.S33F(97)|p.S33Y(60)|p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.S33L(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S33N(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.D32fs*9(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.S29_H36del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.D32_H36>D(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TACCTGGACTCTGGAATCCAT	0.488	S33C(SKMEL1_SKIN)|S33F(SW1573_LUNG)|S33Y(SW48_LARGE_INTESTINE)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S33C	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,0,359	CTNNB1	4904	.	468	Substitution - Missense(331)|Deletion - In frame(111)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(165)|central_nervous_system(82)|large_intestine(40)|endometrium(37)|stomach(32)|skin(21)|ovary(20)|pituitary(19)|pancreas(12)|lung(7)|biliary_tract(6)|soft_tissue(4)|bone(4)|breast(3)|prostate(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|parathyroid(2)|small_intestine(2)|thyroid(1)|NS(1)|urinary_tract(1)|adrenal_gland(1)	c.C98G						.						92	77	82					3																	41266101		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	TGGACTCTGGAAT	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.98C>G	chr3.hg19:g.41266101C>G	ENSP00000344456:p.Ser33Cys	306.0	0.0		287.0	76.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.381716	0.82792	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.51071	0.72;0.72;0.72;0.72;0.72;0.72;0.72;0.72;0.72	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.72053	0.3413	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74188	-0.3746	10	0.87932	D	0	-10.7796	19.9596	0.97236	0.0:1.0:0.0:0.0	.	33	P35222	CTNB1_HUMAN	C	26;33;33;33;33;26;33;33;33	ENSP00000400508:S26C;ENSP00000385604:S33C;ENSP00000412219:S33C;ENSP00000379486:S33C;ENSP00000344456:S33C;ENSP00000411226:S26C;ENSP00000379488:S33C;ENSP00000409302:S33C;ENSP00000401599:S33C	ENSP00000344456:S33C	S	+	2	0	CTNNB1	41241105	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.726000	0.93360	0.655000	0.94253	TCT	.	.		0.488	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266101	C	G	41266101	3	3	271	1	0	0	0	0	1	0	0	0	4018	913	32	4	104	4	CTNNB1	3	41266101	Missense_Mutation	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10		41266101	156756329	22	39369										
MYH15	22989	hgsc.bcm.edu	37	chr3	108204062	108204062	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	tcatcaggaagaaagcccaaGatgtccatggcttgctgtaa	10	9	2	2			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr3:108204062G>T	ENST00000273353.3	-	12	1106	c.1050C>A	c.(1048-1050)atC>atA	p.I350I		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	350	Myosin motor.					cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						GAAAGCCCAAGATGTCCATGG	0.458																																					p.I350I		Atlas-SNP	.											.	MYH15	223	.	0			c.C1050A						.						147	136	140					3																	108204062		1924	4143	6067	SO:0001819	synonymous_variant	22989	exon12			GCCCAAGATGTCC	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"Myosins / Myosin superfamily : Class II"	31073	protein-coding gene	gene with protein product		609929	"myosin, heavy polypeptide 15"			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.1050C>A	chr3.hg19:g.108204062G>T		125.0	0.0		121.0	66.0	NM_014981		Silent	SNP	ENST00000273353.3	hg19	CCDS43127.1																																																																																			.	.		0.458	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988		T	108204062	G	T	108204062	2	4	271	1	0	0	0	0	0	0	0	1	10043	932	33	3		3	MYH15	3	108204062	Silent	SNP	G	TCGA-FV-A4ZQ-01A-11D-A25V-10	66937961	108204062	89818368	23	39370										
KLHL6	89857	hgsc.bcm.edu	37	chr3	183209982	183209982	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	aggcaccagctgtcttccagCgggctgtaggcgtacagcgc	14	13	1	0			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr3:183209982C>G	ENST00000341319.3	-	7	1634	c.1599G>C	c.(1597-1599)ccG>ccC	p.P533P		NM_130446.2	NP_569713.2	Q8WZ60	KLHL6_HUMAN	kelch-like family member 6	533					B cell receptor signaling pathway (GO:0050853)|germinal center formation (GO:0002467)					breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44	all_cancers(143;9.2e-12)|Ovarian(172;0.0172)		all cancers(12;1.29e-44)|Epithelial(37;1.24e-38)|LUSC - Lung squamous cell carcinoma(7;2.58e-24)|Lung(8;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.32e-22)			TGTCTTCCAGCGGGCTGTAGG	0.632																																					p.P533P		Atlas-SNP	.											.	KLHL6	100	.	0			c.G1599C						.						24	24	24					3																	183209982		2200	4299	6499	SO:0001819	synonymous_variant	89857	exon7			TTCCAGCGGGCTG	AF441792	CCDS3245.2	3q27.3	2013-01-30	2013-01-30		ENSG00000172578	ENSG00000172578		"Kelch-like", "BTB/POZ domain containing"	18653	protein-coding gene	gene with protein product	"kelch-like protein KLHL6"	614214	"kelch-like 6 (Drosophila)"			11214971, 12617994	Standard	NM_130446		Approved	FLJ00029	uc003flr.3	Q8WZ60	OTTHUMG00000148673	ENST00000341319.3:c.1599G>C	chr3.hg19:g.183209982C>G		106.0	0.0		46.0	38.0	NM_130446	B2RB31|D3DNS8|Q8N5I1|Q8N892	Silent	SNP	ENST00000341319.3	hg19	CCDS3245.2																																																																																			.	.		0.632	KLHL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309024.1	NM_130446		G	183209982	C	G	183209982	2	3	271	1	0	0	0	0	0	0	0	1	8402	755	27	4		4	KLHL6	3	183209982	Silent	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10	75005920	183209982	14812448	24	39371										
LRRC33	375387	hgsc.bcm.edu	37	chr3	196387716	196387719	+	Frame_Shift_Del	DEL	TGGG	TGGG	-													0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	tccggggctggccagctgccTgggcagcctgcgcttgttca							TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	TGGG	TGGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr3:196387716_196387719delTGGG	ENST00000328557.4	+	3	1405_1408	c.1202_1205delTGGG	c.(1201-1206)ctgggcfs	p.LG401fs		NM_198565.1	NP_940967.1	Q86YC3	NRROS_HUMAN	negative regulator of reactive oxygen species	401					immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|superoxide metabolic process (GO:0006801)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)											GCCAGCTGCCTGGGCAGCCTGCGC	0.652																																					p.401_402del		Atlas-INDEL	.											.	LRRC33	91	.	0			c.1201_1204del						.																																			SO:0001589	frameshift_variant	375387	exon3			.	AY358322	CCDS3319.1	3q29	2013-07-02	2013-07-02	2013-07-02	ENSG00000174004	ENSG00000174004			24613	protein-coding gene	gene with protein product		615322	"leucine rich repeat containing 33"	LRRC33		12975309	Standard	NM_198565		Approved	UNQ3030, ELLP3030, MGC50789, GARPL1	uc003fwv.3	Q86YC3	OTTHUMG00000155569	ENST00000328557.4:c.1202_1205delTGGG	chr3.hg19:g.196387716_196387719delTGGG	ENSP00000328625:p.Leu401fs	52.0	0.0		38.0	27.0	NM_198565		Frame_Shift_Del	DEL	ENST00000328557.4	hg19	CCDS3319.1																																																																																			.	.		0.652	NRROS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340676.1	NM_198565		-	196387719	TGGG	-	196387716	7	5	271	1	0	1	0	1	0	0	0	0	8997	1580	55	0	1208	0	LRRC33	3	196387716	Frame_Shift_Del	DEL	TGGG	TCGA-FV-A4ZQ-01A-11D-A25V-10	13177734	196387716	1634714	25	39372	192	2								
LRRC33	375387	hgsc.bcm.edu	37	chr3	196387720	196387721	+	Frame_Shift_Ins	INS	-	-	A													0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	ggctggccagctgcctgggcINSagcctgcgcttgttcaacct							TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr3:196387720_196387721insA	ENST00000328557.4	+	3	1409_1410	c.1206_1207insA	c.(1207-1209)agcfs	p.S403fs		NM_198565.1	NP_940967.1	Q86YC3	NRROS_HUMAN	negative regulator of reactive oxygen species	403					immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|superoxide metabolic process (GO:0006801)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)											GCTGCCTGGGCAGCCTGCGCTT	0.649																																					p.G402fs		Atlas-INDEL	.											.	LRRC33	91	.	0			c.1206_1207insA						.																																			SO:0001589	frameshift_variant	375387	exon3			.	AY358322	CCDS3319.1	3q29	2013-07-02	2013-07-02	2013-07-02	ENSG00000174004	ENSG00000174004			24613	protein-coding gene	gene with protein product		615322	"leucine rich repeat containing 33"	LRRC33		12975309	Standard	NM_198565		Approved	UNQ3030, ELLP3030, MGC50789, GARPL1	uc003fwv.3	Q86YC3	OTTHUMG00000155569	ENST00000328557.4:c.1207dupA	chr3.hg19:g.196387721_196387721dupA	ENSP00000328625:p.Ser403fs	57.0	0.0		39.0	28.0	NM_198565		Frame_Shift_Ins	INS	ENST00000328557.4	hg19	CCDS3319.1																																																																																			.	.		0.649	NRROS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340676.1	NM_198565		A	196387721	-	A	196387720	7	5	271	1	0	1	1	0	0	0	0	0	8997	697	25	0	1212	0	LRRC33	3	196387720	Frame_Shift_Ins	INS	-	TCGA-FV-A4ZQ-01A-11D-A25V-10	4	196387720	1634710	26	39373	192	2								
FRAS1	80144	hgsc.bcm.edu	37	chr4	79166410	79166410	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	gaagtgcttcaaatagctgcCaaccaatgctgtcctgagtg	10	10	1	1			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr4:79166410C>T	ENST00000325942.6	+	4	680	c.240C>T	c.(238-240)gcC>gcT	p.A80A	FRAS1_ENST00000264895.6_Silent_p.A80A|FRAS1_ENST00000264899.6_Silent_p.A80A	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	80	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.				cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						AAATAGCTGCCAACCAATGCT	0.438																																					p.A80A		Atlas-SNP	.											.	FRAS1	779	.	0			c.C240T						.						92	87	89					4																	79166410		1958	4170	6128	SO:0001819	synonymous_variant	80144	exon4			AGCTGCCAACCAA	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.240C>T	chr4.hg19:g.79166410C>T		145.0	0.0		140.0	47.0	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000325942.6	hg19	CCDS54772.1	.	.	.	.	.	.	.	.	.	.	C	3.466	-0.108881	0.06924	.	.	ENSG00000138759	ENST00000502446	.	.	.	5.47	4.63	0.57726	.	.	.	.	.	T	0.69637	0.3133	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68838	-0.5303	4	.	.	.	.	13.6055	0.62046	0.0:0.9236:0.0:0.0764	.	.	.	.	L	9	.	.	P	+	2	0	FRAS1	79385434	0.998000	0.40836	0.998000	0.56505	0.228000	0.25075	0.656000	0.24948	1.438000	0.47492	0.655000	0.94253	CCA	.	.		0.438	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2			T	79166410	C	T	79166410	2	4	271	1	0	0	0	0	0	0	0	1	6050	581	21	3		3	FRAS1	4	79166410	Silent	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10		79166410	111987866	27	39374										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153253841	153253841	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	tgcttgtagcaggtctttggGttccaggaatgaaagcacat	12	7	1	1	rs112892452		TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr4:153253841G>T	ENST00000281708.4	-	6	2121	c.892C>A	c.(892-894)Ccc>Acc	p.P298T	FBXW7_ENST00000393956.3_Missense_Mutation_p.P122T|FBXW7_ENST00000603548.1_Missense_Mutation_p.P298T|FBXW7_ENST00000296555.5_Missense_Mutation_p.P180T|FBXW7_ENST00000263981.5_Missense_Mutation_p.P218T|FBXW7_ENST00000603841.1_Missense_Mutation_p.P298T	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	298	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.P298S(2)|p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				AGGTCTTTGGGTTCCAGGAAT	0.348			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																p.P298T		Atlas-SNP	.		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	FBXW7_NM_018315_2,colon,carcinoma,+2,2	FBXW7	2157	.	3	Substitution - Missense(2)|Unknown(1)	large_intestine(2)|haematopoietic_and_lymphoid_tissue(1)	c.C892A						.						61	61	61					4																	153253841		2203	4300	6503	SO:0001583	missense	55294	exon6			CTTTGGGTTCCAG	AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.892C>A	chr4.hg19:g.153253841G>T	ENSP00000281708:p.Pro298Thr	109.0	0.0		124.0	36.0	NM_033632	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	hg19	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.373299	0.82573	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.58940	0.3;0.3;0.3;0.3	6.16	6.16	0.99307	F-box domain, cyclin-like (2);F-box domain, Skp2-like (1);	0.091827	0.85682	D	0.000000	T	0.76314	0.3970	M	0.67569	2.06	0.80722	D	1	D;D;D;D	0.71674	0.998;0.998;0.997;0.997	D;D;D;D	0.72625	0.97;0.978;0.95;0.963	T	0.73975	-0.3813	10	0.52906	T	0.07	-10.96	20.8598	0.99761	0.0:0.0:1.0:0.0	.	122;298;180;218	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	T	298;180;218;122	ENSP00000281708:P298T;ENSP00000296555:P180T;ENSP00000263981:P218T;ENSP00000377528:P122T	ENSP00000263981:P218T	P	-	1	0	FBXW7	153473291	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.793000	0.99091	2.937000	0.99478	0.650000	0.86243	CCC	.	G|0.500;A|0.500		0.348	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			T	153253841	G	T	153253841	3	4	271	1	0	0	0	0	1	0	0	0	5777	1261	44	3	1259	3	FBXW7	4	153253841	Missense_Mutation	SNP	G	TCGA-FV-A4ZQ-01A-11D-A25V-10	74087431	153253841	37900435	28	39375										
HAPLN1	1404	hgsc.bcm.edu	37	chr5	82937472	82937472	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	ccaaccagcccgcatcacagCggtcatatccgagaattttc	7	15	2	1			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr5:82937472C>A	ENST00000274341.4	-	5	1758	c.908G>T	c.(907-909)cGc>cTc	p.R303L		NM_001884.3	NP_001875.1	P10915	HPLN1_HUMAN	hyaluronan and proteoglycan link protein 1	303	Link 2. {ECO:0000255|PROSITE- ProRule:PRU00323}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)			breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|liver(1)|lung(15)|ovary(1)|prostate(1)|skin(1)	34		Lung NSC(167;0.0484)|all_lung(232;0.0522)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;7.82e-42)|Epithelial(54;5.88e-35)|all cancers(79;1.14e-29)	Hyaluronan(DB08818)	CGCATCACAGCGGTCATATCC	0.557																																					p.R303L		Atlas-SNP	.											.	HAPLN1	79	.	0			c.G908T						.						124	128	126					5																	82937472		2203	4300	6503	SO:0001583	missense	1404	exon5			TCACAGCGGTCAT		CCDS4061.1	5q14.3	2013-01-11	2004-03-16	2004-03-17	ENSG00000145681	ENSG00000145681		"Immunoglobulin superfamily / V-set domain containing"	2380	protein-coding gene	gene with protein product	"Cartilage link protein", "hyaluronan and proteoglycan link protein 1"	115435	"cartilage linking protein 1"	CRTL1		2286376, 2320422	Standard	NM_001884		Approved		uc003kin.3	P10915	OTTHUMG00000119045	ENST00000274341.4:c.908G>T	chr5.hg19:g.82937472C>A	ENSP00000274341:p.Arg303Leu	216.0	0.0		269.0	66.0	NM_001884	B2R9A9	Missense_Mutation	SNP	ENST00000274341.4	hg19	CCDS4061.1	.	.	.	.	.	.	.	.	.	.	C	17.25	3.343143	0.61073	.	.	ENSG00000145681	ENST00000274341	T	0.26660	1.72	5.22	4.35	0.52113	C-type lectin fold (1);Link (4);C-type lectin-like (1);	0.000000	0.85682	D	0.000000	T	0.42698	0.1214	L	0.45581	1.43	0.80722	D	1	D	0.69078	0.997	D	0.74348	0.983	T	0.24764	-1.0151	10	0.46703	T	0.11	.	14.0672	0.64837	0.0:0.9273:0.0:0.0727	.	303	P10915	HPLN1_HUMAN	L	303	ENSP00000274341:R303L	ENSP00000274341:R303L	R	-	2	0	HAPLN1	82973228	1.000000	0.71417	1.000000	0.80357	0.704000	0.40688	6.031000	0.70911	1.326000	0.45319	0.655000	0.94253	CGC	.	.		0.557	HAPLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239256.2	NM_001884		A	82937472	C	A	82937472	3	1	271	1	0	0	0	0	1	0	0	0	6963	768	27	1	160	1	HAPLN1	5	82937472	Missense_Mutation	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10		82937472	97977788	29	39376										
PCDHB1	29930	hgsc.bcm.edu	37	chr5	140433269	140433269	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	gatgactgtaatttctctaaCaacctggtacaaggacaagg	9	8	1	1			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr5:140433269C>A	ENST00000306549.3	+	1	2291	c.2214C>A	c.(2212-2214)aaC>aaA	p.N738K		NM_013340.2	NP_037472.2	Q9Y5F3	PCDB1_HUMAN	protocadherin beta 1	738					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|liver(1)|lung(13)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	53			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ATTTCTCTAACAACCTGGTAC	0.373																																					p.N738K		Atlas-SNP	.											.	PCDHB1	148	.	0			c.C2214A						.						108	106	106					5																	140433269		2203	4300	6503	SO:0001583	missense	29930	exon1			CTCTAACAACCTG	AF152488	CCDS4243.1	5q31	2010-01-26			ENSG00000171815	ENSG00000171815		"Cadherins / Protocadherins : Clustered"	8680	other	protocadherin		606327				10380929	Standard	NM_013340		Approved	PCDH-BETA1	uc003lik.1	Q9Y5F3	OTTHUMG00000129627	ENST00000306549.3:c.2214C>A	chr5.hg19:g.140433269C>A	ENSP00000307234:p.Asn738Lys	129.0	0.0		135.0	36.0	NM_013340	Q2M257	Missense_Mutation	SNP	ENST00000306549.3	hg19	CCDS4243.1	.	.	.	.	.	.	.	.	.	.	C	8.207	0.799440	0.16397	.	.	ENSG00000171815	ENST00000306549	T	0.46451	0.87	5.91	3.91	0.45181	.	0.121727	0.36703	N	0.002448	T	0.31513	0.0799	L	0.36672	1.1	0.26899	N	0.967144	B	0.24258	0.1	B	0.19148	0.024	T	0.30621	-0.9972	10	0.72032	D	0.01	.	9.6089	0.39650	0.0:0.7886:0.0:0.2114	.	738	Q9Y5F3	PCDB1_HUMAN	K	738	ENSP00000307234:N738K	ENSP00000307234:N738K	N	+	3	2	PCDHB1	140413453	0.000000	0.05858	1.000000	0.80357	0.649000	0.38597	-0.506000	0.06359	1.521000	0.48983	0.655000	0.94253	AAC	.	.		0.373	PCDHB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251822.2	NM_013340		A	140433269	C	A	140433269	3	1	271	1	0	0	0	0	1	0	0	0	11543	477	17	3	2216	3	PCDHB1	5	140433269	Missense_Mutation	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10	57495797	140433269	40481991	30	39377										
NUP153	9972	hgsc.bcm.edu	37	chr6	17637675	17637675	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	acaggtatcacaatcccaagTgcctatcactggtttaaatt	6	10	2	0			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr6:17637675T>C	ENST00000262077.2	-	16	2172	c.2173A>G	c.(2173-2175)Act>Gct	p.T725A	NUP153_ENST00000537253.1_Missense_Mutation_p.T756A	NM_005124.2	NP_005115.2	P49790	NU153_HUMAN	nucleoporin 153kDa	725					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of RNA export from nucleus (GO:0046832)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)|viral penetration into host nucleus (GO:0075732)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleocytoplasmic transporter activity (GO:0005487)|protein anchor (GO:0043495)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			NS(2)|breast(6)|endometrium(4)|kidney(3)|large_intestine(7)|lung(23)|ovary(3)|skin(3)|urinary_tract(2)	53	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.125)	all cancers(50;0.0981)|Epithelial(50;0.112)			CAATCCCAAGTGCCTATCACT	0.413																																					p.T725A		Atlas-SNP	.											.	NUP153	116	.	0			c.A2173G						.						189	178	182					6																	17637675		2203	4300	6503	SO:0001583	missense	9972	exon16			CCCAAGTGCCTAT	Z25535	CCDS4541.1, CCDS64359.1, CCDS75407.1	6p22.3	2008-07-29	2002-08-29		ENSG00000124789	ENSG00000124789			8062	protein-coding gene	gene with protein product		603948	"nucleoporin 153kD"			8110839	Standard	NM_001278209		Approved	HNUP153	uc003ncd.2	P49790	OTTHUMG00000014312	ENST00000262077.2:c.2173A>G	chr6.hg19:g.17637675T>C	ENSP00000262077:p.Thr725Ala	280.0	0.0		338.0	207.0	NM_005124	B4DIK2|E7EPX5|F6QR24|Q4LE47|Q5T9I7|Q7Z743	Missense_Mutation	SNP	ENST00000262077.2	hg19	CCDS4541.1	.	.	.	.	.	.	.	.	.	.	T	16.29	3.080908	0.55753	.	.	ENSG00000124789	ENST00000262077;ENST00000430136;ENST00000537253	T;T	0.54675	0.56;0.56	6.11	4.92	0.64577	Zinc finger, RanBP2-type (3);	0.114054	0.39210	N	0.001434	T	0.26955	0.0660	N	0.12961	0.28	0.51482	D	0.999922	B;B;B	0.32188	0.359;0.057;0.287	B;B;B	0.39935	0.234;0.158;0.314	T	0.28933	-1.0028	10	0.59425	D	0.04	-8.2154	12.6328	0.56667	0.1242:0.0:0.0:0.8758	.	756;705;725	F6QR24;Q4LE47;P49790	.;.;NU153_HUMAN	A	725;705;756	ENSP00000262077:T725A;ENSP00000444029:T756A	ENSP00000262077:T725A	T	-	1	0	NUP153	17745654	1.000000	0.71417	0.999000	0.59377	0.576000	0.36127	3.939000	0.56591	1.091000	0.41335	0.533000	0.62120	ACT	.	.		0.413	NUP153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039953.1			C	17637675	T	C	17637675	3	2	271	1	0	0	0	0	1	0	0	0	10764	1696	59	2	2282	2	NUP153	6	17637675	Missense_Mutation	SNP	T	TCGA-FV-A4ZQ-01A-11D-A25V-10		17637675	153477392	31	39378										
ZNF318	24149	hgsc.bcm.edu	37	chr6	43322734	43322734	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	ggcagggggaatggcaggtcCctggtagttcggaggtatcc	18	8	0	0			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr6:43322734C>A	ENST00000361428.2	-	4	2415	c.2338G>T	c.(2338-2340)Gga>Tga	p.G780*	ZNF318_ENST00000318149.3_Nonsense_Mutation_p.G780*	NM_014345.2	NP_055160.2	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	780					meiotic nuclear division (GO:0007126)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(21)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	61			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)			ATGGCAGGTCCCTGGTAGTTC	0.527																																					p.G780X		Atlas-SNP	.											.	ZNF318	175	.	0			c.G2338T						.						134	130	132					6																	43322734		2203	4300	6503	SO:0001587	stop_gained	24149	exon4			CAGGTCCCTGGTA	AF090114	CCDS4895.2	6p21.1	2013-09-19			ENSG00000171467	ENSG00000171467		"Zinc fingers, C2H2-type"	13578	protein-coding gene	gene with protein product						10873617	Standard	NM_014345		Approved	HRIHFB2436, ZFP318	uc003oux.3	Q5VUA4	OTTHUMG00000014732	ENST00000361428.2:c.2338G>T	chr6.hg19:g.43322734C>A	ENSP00000354964:p.Gly780*	335.0	0.0		529.0	113.0	NM_014345	O94796|Q4G0E4|Q8NEM6|Q9UNU8|Q9Y2W9	Nonsense_Mutation	SNP	ENST00000361428.2	hg19	CCDS4895.2	.	.	.	.	.	.	.	.	.	.	C	38	6.770913	0.97825	.	.	ENSG00000171467	ENST00000318149;ENST00000361428	.	.	.	6.07	5.04	0.67666	.	0.269330	0.32655	N	0.005807	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-16.2477	3.9294	0.09278	0.1335:0.4963:0.2508:0.1194	.	.	.	.	X	780	.	ENSP00000323032:G780X	G	-	1	0	ZNF318	43430712	0.987000	0.35691	1.000000	0.80357	0.996000	0.88848	0.814000	0.27239	2.885000	0.99019	0.655000	0.94253	GGA	.	.		0.527	ZNF318-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040601.2	NM_014345		A	43322734	C	A	43322734	4	1	271	1	0	0	0	0	0	1	0	0	17851	632	22	3	4529	3	ZNF318	6	43322734	Nonsense_Mutation	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10	25685059	43322734	127792333	32	39379										
SLC22A16	85413	hgsc.bcm.edu	37	chr6	110752455	110752455	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	aggcgacacaccatgctgccGcttcccacagccagcgatct	9	17	1	0	rs145203259	byFrequency	TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr6:110752455G>T	ENST00000368919.3	-	7	1506	c.1440C>A	c.(1438-1440)agC>agA	p.S480R	SLC22A16_ENST00000439654.1_Missense_Mutation_p.S480R|SLC22A16_ENST00000330550.4_Missense_Mutation_p.S446R	NM_033125.3	NP_149116.2	Q86VW1	S22AG_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 16	480					acid secretion (GO:0046717)|amine transport (GO:0015837)|carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|organic cation transport (GO:0015695)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amine transmembrane transporter activity (GO:0005275)|carnitine transmembrane transporter activity (GO:0015226)|organic cation transmembrane transporter activity (GO:0015101)			breast(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	34		all_cancers(87;0.00221)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0485)|Colorectal(196;0.101)		OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.0921)|all cancers(137;0.115)	Doxorubicin(DB00997)|L-Carnitine(DB00583)	CCATGCTGCCGCTTCCCACAG	0.567																																					p.S480R		Atlas-SNP	.											.	SLC22A16	81	.	0			c.C1440A						.						71	64	66					6																	110752455		2203	4300	6503	SO:0001583	missense	85413	exon7			GCTGCCGCTTCCC		CCDS5084.1	6q21	2013-05-22	2008-01-11		ENSG00000004809	ENSG00000004809		"Solute carriers"	20302	protein-coding gene	gene with protein product		608276	"solute carrier family 22 (organic cation transporter), member 16"			12372408, 12089149, 17473959	Standard	NM_033125		Approved	FLIPT2, CT2, OKB1, OAT6	uc003puf.3	Q86VW1	OTTHUMG00000016171	ENST00000368919.3:c.1440C>A	chr6.hg19:g.110752455G>T	ENSP00000357915:p.Ser480Arg	43.0	0.0		28.0	14.0	NM_033125	O14567|Q5JXM1|Q8IUG8|Q8IZD5|Q96M90|Q96RU0	Missense_Mutation	SNP	ENST00000368919.3	hg19	CCDS5084.1	.	.	.	.	.	.	.	.	.	.	G	15.78	2.935048	0.52866	.	.	ENSG00000004809	ENST00000368919;ENST00000451557;ENST00000330550;ENST00000439654	T;T;T;T	0.74315	-0.83;-0.83;-0.83;-0.83	5.16	-2.45	0.06481	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.042699	0.85682	D	0.000000	T	0.78272	0.4257	M	0.83953	2.67	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.77557	0.99;0.982	T	0.79286	-0.1866	10	0.72032	D	0.01	.	10.1319	0.42685	0.4955:0.0:0.5045:0.0	.	480;446	Q86VW1;Q86VW1-2	S22AG_HUMAN;.	R	480;397;446;480	ENSP00000357915:S480R;ENSP00000395642:S397R;ENSP00000328583:S446R;ENSP00000408799:S480R	ENSP00000328583:S446R	S	-	3	2	SLC22A16	110859148	1.000000	0.71417	0.127000	0.21898	0.874000	0.50279	1.046000	0.30354	-0.786000	0.04516	-0.469000	0.05056	AGC	.	G|0.998;C|0.002		0.567	SLC22A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043428.1	NM_033125		T	110752455	G	T	110752455	3	4	271	1	0	0	0	0	1	0	0	0	14462	1078	38	1	301	1	SLC22A16	6	110752455	Missense_Mutation	SNP	G	TCGA-FV-A4ZQ-01A-11D-A25V-10	67429721	110752455	60362612	33	39380										
WDR27	253769	hgsc.bcm.edu	37	chr6	170065609	170065609	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	tcagcacacccggtgaccagCtgcctgctttctgcatcaat	8	15	3	1			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr6:170065609C>A	ENST00000448612.1	-	7	865	c.756G>T	c.(754-756)caG>caT	p.Q252H	WDR27_ENST00000423258.1_Missense_Mutation_p.Q125H|WDR27_ENST00000546525.1_5'UTR|WDR27_ENST00000420344.2_Missense_Mutation_p.S167I|WDR27_ENST00000333572.6_Missense_Mutation_p.Q252H	NM_182552.4	NP_872358.4	A2RRH5	WDR27_HUMAN	WD repeat domain 27	222						nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|skin(1)	12		Breast(66;1.53e-05)|Ovarian(120;0.216)		OV - Ovarian serous cystadenocarcinoma(33;6.48e-20)|BRCA - Breast invasive adenocarcinoma(81;3.56e-07)|GBM - Glioblastoma multiforme(31;0.00168)		CGGTGACCAGCTGCCTGCTTT	0.478																																					p.Q252H		Atlas-SNP	.											.	WDR27	129	.	0			c.G756T						.						70	74	72					6																	170065609		1974	4152	6126	SO:0001583	missense	253769	exon7			GACCAGCTGCCTG	AK131435	CCDS47520.1, CCDS47520.2, CCDS56459.1	6q27	2013-01-09	2003-06-18		ENSG00000184465	ENSG00000184465		"WD repeat domain containing"	21248	protein-coding gene	gene with protein product							Standard	NM_182552		Approved	MGC43690	uc003qwx.3	A2RRH5	OTTHUMG00000016061	ENST00000448612.1:c.756G>T	chr6.hg19:g.170065609C>A	ENSP00000416289:p.Gln252His	93.0	0.0		150.0	30.0	NM_182552	A5PLM8|C9JGV0|Q5T066	Missense_Mutation	SNP	ENST00000448612.1	hg19	CCDS47520.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.44|12.44	1.938168|1.938168	0.34189|0.34189	.|.	.|.	ENSG00000184465|ENSG00000184465	ENST00000448612;ENST00000333572;ENST00000423258|ENST00000420344	T;T;D|T	0.95788|0.52057	1.07;1.1;-3.81|0.68	5.18|5.18	3.04|3.04	0.35103|0.35103	.|.	0.249318|.	0.33457|.	N|.	0.004898|.	T|T	0.43612|0.43612	0.1255|0.1255	M|M	0.71581|0.71581	2.175|2.175	0.23816|0.23816	N|N	0.996764|0.996764	D;P;D|.	0.89917|.	1.0;0.927;1.0|.	D;P;D|.	0.91635|.	0.986;0.763;0.999|.	T|T	0.34354|0.34354	-0.9832|-0.9832	10|7	0.38643|0.87932	T|D	0.18|0	-26.8464|-26.8464	11.8546|11.8546	0.52429|0.52429	0.0:0.8239:0.0:0.1761|0.0:0.8239:0.0:0.1761	.|.	252;125;252|.	F2Z2U5;A2RRH5-2;C9JGV0|.	.;.;.|.	H|I	252;252;125|167	ENSP00000416289:Q252H;ENSP00000330265:Q252H;ENSP00000397869:Q125H|ENSP00000406114:S167I	ENSP00000330265:Q252H|ENSP00000406114:S167I	Q|S	-|-	3|2	2|0	WDR27|WDR27	169807534|169807534	1.000000|1.000000	0.71417|0.71417	0.815000|0.815000	0.32552|0.32552	0.006000|0.006000	0.05464|0.05464	2.266000|2.266000	0.43320|0.43320	1.185000|1.185000	0.42971|0.42971	-0.300000|-0.300000	0.09419|0.09419	CAG|AGC	.	.		0.478	WDR27-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000407334.1	NM_182552		A	170065609	C	A	170065609	3	1	271	1	0	0	0	0	1	0	0	0	17299	796	28	3	1893	3	WDR27	6	170065609	Missense_Mutation	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10	59313154	170065609	1049458	34	39381										
C6orf70	55780	hgsc.bcm.edu	37	chr6	170159125	170159125	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	caacctgcgtaacgtcttatGgcatgggtttgcgtcacctg	11	11	2	0			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr6:170159125G>T	ENST00000366773.3	+	6	602	c.569G>T	c.(568-570)tGg>tTg	p.W190L	ERMARD_ENST00000366772.2_Missense_Mutation_p.W190L|ERMARD_ENST00000588451.1_Missense_Mutation_p.W64L|ERMARD_ENST00000418781.3_Missense_Mutation_p.W190L|ERMARD_ENST00000392095.4_Missense_Mutation_p.W64L	NM_001278532.1|NM_018341.1	NP_001265461.1|NP_060811.1	Q5T6L9	EMARD_HUMAN	ER membrane-associated RNA degradation	190					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											AACGTCTTATGGCATGGGTTT	0.373																																					p.W190L		Atlas-SNP	.											.	C6orf70	63	.	0			c.G569T						.						210	188	195					6																	170159125		2203	4300	6503	SO:0001583	missense	55780	exon6			TCTTATGGCATGG	AK002014	CCDS34576.1, CCDS64572.1, CCDS64573.1, CCDS64574.1	6q27	2013-08-28	2013-08-28	2013-08-28	ENSG00000130023	ENSG00000130023			21056	protein-coding gene	gene with protein product		615532	"chromosome 6 open reading frame 70"	C6orf70		23768067	Standard	NM_018341		Approved	FLJ11152, dJ266L20.3	uc003qxg.1	Q5T6L9	OTTHUMG00000016067	ENST00000366773.3:c.569G>T	chr6.hg19:g.170159125G>T	ENSP00000355735:p.Trp190Leu	261.0	0.0		287.0	77.0	NM_018341	B4DFH0|F8WAF1|Q3ZCS8|Q5T6L8|Q9NUT5|Q9NVU2	Missense_Mutation	SNP	ENST00000366773.3	hg19	CCDS34576.1	.	.	.	.	.	.	.	.	.	.	G	18.27	3.587054	0.66105	.	.	ENSG00000130023	ENST00000366773;ENST00000366772;ENST00000418781;ENST00000392095	T;T	0.60920	0.15;0.26	5.28	5.28	0.74379	.	0.000000	0.50627	D	0.000117	T	0.72382	0.3453	M	0.76002	2.32	0.43503	D	0.995756	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.76124	-0.3074	10	0.87932	D	0	.	17.7022	0.88298	0.0:0.0:1.0:0.0	.	190;190;190	Q5T6L9-3;Q5T6L9-2;Q5T6L9	.;.;CF070_HUMAN	L	190;190;190;64	ENSP00000355735:W190L;ENSP00000375945:W64L	ENSP00000355734:W190L	W	+	2	0	C6orf70	169901050	1.000000	0.71417	0.996000	0.52242	0.368000	0.29767	5.941000	0.70195	2.469000	0.83416	0.655000	0.94253	TGG	.	.		0.373	ERMARD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043238.2	NM_018341		T	170159125	G	T	170159125	3	4	271	1	0	0	0	0	1	0	0	0	2372	1357	47	3	591	3	C6orf70	6	170159125	Missense_Mutation	SNP	G	TCGA-FV-A4ZQ-01A-11D-A25V-10	93516	170159125	955942	35	39382										
ASNS	440	hgsc.bcm.edu	37	chr7	97482459	97482459	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	aaggcttcttttggtcgccaGagaatctctttgggtatcag	11	8	3	1			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr7:97482459G>T	ENST00000394309.3	-	12	1860	c.1389C>A	c.(1387-1389)ctC>ctA	p.L463L	ASNS_ENST00000437628.1_Silent_p.L380L|ASNS_ENST00000444334.1_Silent_p.L442L|ASNS_ENST00000455086.1_Silent_p.L380L|ASNS_ENST00000422745.1_Silent_p.L442L|ASNS_ENST00000394308.3_Silent_p.L463L|ASNS_ENST00000175506.4_Silent_p.L463L	NM_133436.3	NP_597680.2	P08243	ASNS_HUMAN	asparagine synthetase (glutamine-hydrolyzing)	463	Asparagine synthetase.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|asparagine biosynthetic process (GO:0006529)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|cellular protein metabolic process (GO:0044267)|cellular response to glucose starvation (GO:0042149)|cellular response to hormone stimulus (GO:0032870)|endoplasmic reticulum unfolded protein response (GO:0030968)|glutamine metabolic process (GO:0006541)|L-asparagine biosynthetic process (GO:0070981)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|positive regulation of mitotic cell cycle (GO:0045931)|response to amino acid (GO:0043200)|response to follicle-stimulating hormone (GO:0032354)|response to light stimulus (GO:0009416)|response to mechanical stimulus (GO:0009612)|response to methotrexate (GO:0031427)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	asparagine synthase (glutamine-hydrolyzing) activity (GO:0004066)|ATP binding (GO:0005524)|cofactor binding (GO:0048037)			ovary(1)	1	all_cancers(62;6.64e-09)|all_epithelial(64;1.58e-09)|Esophageal squamous(72;0.00448)|Lung NSC(181;0.0342)|all_lung(186;0.0369)				Adenosine triphosphate(DB00171)|L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)|L-Glutamine(DB00130)	TTGGTCGCCAGAGAATCTCTT	0.383																																					p.L463L	Melanoma(70;6 1280 3108 3799 51123)|GBM(6;275 291 425 9929 27738)	Atlas-SNP	.											.	ASNS	97	.	0			c.C1389A						.						47	44	45					7																	97482459		2203	4300	6503	SO:0001819	synonymous_variant	440	exon12			TCGCCAGAGAATC	M27396	CCDS5652.1, CCDS55131.1, CCDS55132.1	7q21.3	2012-10-02	2010-05-07		ENSG00000070669	ENSG00000070669	6.3.5.4		753	protein-coding gene	gene with protein product		108370	"asparagine synthetase"				Standard	NM_001673		Approved		uc003uov.4	P08243	OTTHUMG00000022892	ENST00000394309.3:c.1389C>A	chr7.hg19:g.97482459G>T		108.0	0.0		78.0	4.0	NM_133436	A4D1I8|B4DXZ1|B7ZAA9|D6W5R3|E9PCI3|E9PCX6|P08184|Q15666|Q549T9|Q96HD0	Silent	SNP	ENST00000394309.3	hg19	CCDS5652.1																																																																																			.	.		0.383	ASNS-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333645.1	NM_001673, NM_183356		T	97482459	G	T	97482459	2	4	271	1	0	0	0	0	0	0	0	1	1048	929	33	3		3	ASNS	7	97482459	Silent	SNP	G	TCGA-FV-A4ZQ-01A-11D-A25V-10		97482459	61656204	36	39383										
TERF1	7013	hgsc.bcm.edu	37	chr8	73921159	73921159	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	ctcagcggccccgagcccgcGgggctgtgcggatggtaggg	19	13	1	0			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr8:73921159G>C	ENST00000276603.5	+	1	61	c.38G>C	c.(37-39)cGg>cCg	p.R13P	TERF1_ENST00000276602.6_Missense_Mutation_p.R13P	NM_017489.2	NP_059523.2	P54274	TERF1_HUMAN	telomeric repeat binding factor (NIMA-interacting) 1	13	Asp/Glu-rich (acidic).				age-dependent telomere shortening (GO:0001309)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of DNA replication (GO:0008156)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via semi-conservative replication (GO:0032214)|negative regulation of telomere maintenance via telomerase (GO:0032211)|positive regulation of apoptotic process (GO:0043065)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of mitosis (GO:0045840)|positive regulation of mitotic cell cycle (GO:0045931)|protein homooligomerization (GO:0051260)|response to drug (GO:0042493)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)|telomere maintenance via telomere shortening (GO:0010834)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nuclear telomere cap complex (GO:0000783)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|double-stranded telomeric DNA binding (GO:0003691)|microtubule binding (GO:0008017)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|telomeric DNA binding (GO:0042162)			central_nervous_system(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	9	Breast(64;0.218)		Epithelial(68;0.0984)			CCGAGCCCGCGGGGCTGTGCG	0.607																																					p.R13P		Atlas-SNP	.											.	TERF1	48	.	0			c.G38C						.						17	19	18					8																	73921159		2202	4300	6502	SO:0001583	missense	7013	exon1			GCCCGCGGGGCTG	U74382	CCDS6210.1, CCDS6211.1	8q21.11	2011-05-24			ENSG00000147601	ENSG00000147601			11728	protein-coding gene	gene with protein product		600951		TRBF1		9391075	Standard	NM_003218		Approved	PIN2, TRF1, TRF	uc003xzd.2	P54274	OTTHUMG00000164522	ENST00000276603.5:c.38G>C	chr8.hg19:g.73921159G>C	ENSP00000276603:p.Arg13Pro	241.0	0.0		318.0	48.0	NM_017489	A7XP29|Q15553|Q8NHT6|Q93029	Missense_Mutation	SNP	ENST00000276603.5	hg19	CCDS6211.1	.	.	.	.	.	.	.	.	.	.	G	19.21	3.784004	0.70222	.	.	ENSG00000147601	ENST00000276603;ENST00000276602;ENST00000518874	.	.	.	4.42	1.51	0.23008	.	0.284208	0.25674	N	0.029047	T	0.47266	0.1436	N	0.19112	0.55	0.24790	N	0.992765	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.48647	-0.9017	9	0.87932	D	0	.	13.6785	0.62469	0.0:0.4465:0.5535:0.0	.	13;13	P54274-2;P54274	.;TERF1_HUMAN	P	13	.	ENSP00000276602:R13P	R	+	2	0	TERF1	74083713	0.997000	0.39634	0.206000	0.23566	0.124000	0.20399	1.543000	0.36147	0.327000	0.23409	0.563000	0.77884	CGG	.	.		0.607	TERF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379093.1	NM_017489		C	73921159	G	C	73921159	3	2	271	1	0	0	0	0	1	0	0	0	15776	1116	39	4	40	4	TERF1	8	73921159	Missense_Mutation	SNP	G	TCGA-FV-A4ZQ-01A-11D-A25V-10		73921159	72442863	37	39384										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113651094	113651094	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	ttctctgtgatcagtaagtaGtcatgatggtcttccaaatg	9	7	4	2	rs145905619		TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr8:113651094G>C	ENST00000297405.5	-	21	3601	c.3357C>G	c.(3355-3357)gaC>gaG	p.D1119E	CSMD3_ENST00000455883.2_Missense_Mutation_p.D1015E|CSMD3_ENST00000343508.3_Missense_Mutation_p.D1079E|CSMD3_ENST00000352409.3_Missense_Mutation_p.D1119E	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1119	CUB 6. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.D1119D(1)|p.D1079D(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TCAGTAAGTAGTCATGATGGT	0.403										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.D1119E		Atlas-SNP	.											CSMD3_ENST00000343508,NS,carcinoma,-2,2	CSMD3	2325	.	2	Substitution - coding silent(2)	lung(2)	c.C3357G						.						111	105	107					8																	113651094		2203	4300	6503	SO:0001583	missense	114788	exon21			TAAGTAGTCATGA	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.3357C>G	chr8.hg19:g.113651094G>C	ENSP00000297405:p.Asp1119Glu	108.0	1.0		159.0	98.0	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.516832	0.85495	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.29917	1.55;1.55;1.55;1.55;1.55	5.15	4.28	0.50868	CUB (5);	0.000000	0.85682	D	0.000000	T	0.66257	0.2771	H	0.97682	4.055	0.34819	D	0.738495	B;B;P	0.39847	0.145;0.175;0.691	B;B;P	0.58454	0.101;0.162;0.839	T	0.78311	-0.2253	10	0.27785	T	0.31	.	13.4786	0.61322	0.0759:0.0:0.9241:0.0	.	1015;1119;1079	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	E	1079;1119;459;1015;1119	ENSP00000345799:D1079E;ENSP00000297405:D1119E;ENSP00000341558:D459E;ENSP00000412263:D1015E;ENSP00000343124:D1119E	ENSP00000297405:D1119E	D	-	3	2	CSMD3	113720270	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	4.855000	0.62925	1.188000	0.43014	0.491000	0.48974	GAC	.	G|1.000;A|0.000		0.403	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		C	113651094	G	C	113651094	3	2	271	1	0	0	0	0	1	0	0	0	3948	1020	36	4	7970	4	CSMD3	8	113651094	Missense_Mutation	SNP	G	TCGA-FV-A4ZQ-01A-11D-A25V-10	39729935	113651094	32712928	38	39385										
TRPS1	7227	hgsc.bcm.edu	37	chr8	116427073	116427073	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	gaatggcttttagtcaatgaAccctgggcttcgtatttact	9	8	1	1			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr8:116427073A>G	ENST00000220888.5	-	6	3183	c.3024T>C	c.(3022-3024)ggT>ggC	p.G1008G	TRPS1_ENST00000395715.3_Silent_p.G1021G|TRPS1_ENST00000520276.1_Silent_p.G1012G|TRPS1_ENST00000519076.1_Silent_p.G762G			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	1008	Mediates interaction with RNF4. {ECO:0000250}.				chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			TAGTCAATGAACCCTGGGCTT	0.453									Langer-Giedion syndrome																												p.G1021G		Atlas-SNP	.											.	TRPS1	516	.	0			c.T3063C						.						133	127	128					8																	116427073		1891	4127	6018	SO:0001819	synonymous_variant	7227	exon7	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	CAATGAACCCTGG	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"GATA zinc finger domain containing", "Zinc fingers, C2H2-type"	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.3024T>C	chr8.hg19:g.116427073A>G		170.0	0.0		302.0	45.0	NM_014112	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Silent	SNP	ENST00000220888.5	hg19		.	.	.	.	.	.	.	.	.	.	A	3.979	-0.006858	0.07773	.	.	ENSG00000104447	ENST00000518018	.	.	.	5.82	3.23	0.37069	.	.	.	.	.	T	0.59376	0.2189	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54957	-0.8215	4	.	.	.	.	9.6643	0.39974	0.8489:0.0:0.1511:0.0	.	.	.	.	L	133	.	.	F	-	1	0	TRPS1	116496249	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.581000	0.46077	0.898000	0.36418	0.533000	0.62120	TTC	.	.		0.453	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112		G	116427073	A	G	116427073	2	3	271	1	0	0	0	0	0	0	0	1	16608	30	2	2		2	TRPS1	8	116427073	Silent	SNP	A	TCGA-FV-A4ZQ-01A-11D-A25V-10	2775979	116427073	29936949	39	39386										
JAK2	3717	hgsc.bcm.edu	37	chr9	5072525	5072525	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	gccaaggcacttttacaaagAtttttaaaggcgtacgaaga	9	7	0	2	rs35668020		TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr9:5072525A>C	ENST00000381652.3	+	13	2169	c.1675A>C	c.(1675-1677)Att>Ctt	p.I559L	JAK2_ENST00000544510.1_Missense_Mutation_p.I410L|JAK2_ENST00000539801.1_Missense_Mutation_p.I559L	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	559	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)		BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	TTTTACAAAGATTTTTAAAGG	0.358		1	"T, Mis, O"	"ETV6, PCM1, BCR"	"ALL, AML, MPD,  CML"				Polycythemia Vera, Familial																												p.I559L		Atlas-SNP	.		Dom	yes		9	9p24	3717	Janus kinase 2		L	.	JAK2	35466	.	0			c.A1675C						.						56	58	57					9																	5072525		2202	4300	6502	SO:0001583	missense	3717	exon13	Familial Cancer Database		ACAAAGATTTTTA		CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"SH2 domain containing"	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.1675A>C	chr9.hg19:g.5072525A>C	ENSP00000371067:p.Ile559Leu	91.0	0.0		78.0	22.0	NM_004972	O14636|O75297	Missense_Mutation	SNP	ENST00000381652.3	hg19	CCDS6457.1	.	.	.	.	.	.	.	.	.	.	A	31	5.090264	0.94149	.	.	ENSG00000096968	ENST00000539801;ENST00000381652;ENST00000544510	T;T;T	0.35048	1.33;1.33;1.33	5.73	5.73	0.89815	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.045126	0.85682	D	0.000000	T	0.51007	0.1649	L	0.50919	1.6	0.58432	D	0.999996	D	0.59767	0.986	P	0.59056	0.851	T	0.51116	-0.8746	10	0.59425	D	0.04	-18.6877	16.0085	0.80380	1.0:0.0:0.0:0.0	.	559	O60674	JAK2_HUMAN	L	559;559;410	ENSP00000440387:I559L;ENSP00000371067:I559L;ENSP00000443103:I410L	ENSP00000371067:I559L	I	+	1	0	JAK2	5062525	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.152000	0.77419	2.185000	0.69588	0.477000	0.44152	ATT	.	.		0.358	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1			C	5072525	A	C	5072525	3	2	271	1	0	0	0	0	1	0	0	0	7947	333	12	5	1717	5	JAK2	9	5072525	Missense_Mutation	SNP	A	TCGA-FV-A4ZQ-01A-11D-A25V-10		5072525	136140906	40	39387										
OGN	4969	hgsc.bcm.edu	37	chr9	95155381	95155381	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	aacttacgtatgtctgcaaaAtctttggcagtcagcttttt	7	8	3	0			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr9:95155381A>G	ENST00000262551.4	-	4	834	c.414T>C	c.(412-414)gaT>gaC	p.D138D	OGN_ENST00000468743.1_5'UTR|OGN_ENST00000375561.5_Silent_p.D138D|CENPP_ENST00000375587.3_Intron	NM_033014.2	NP_148935.1	P20774	MIME_HUMAN	osteoglycin	138					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|negative regulation of smooth muscle cell proliferation (GO:0048662)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|prostate(1)|urinary_tract(1)	13						TGTCTGCAAAATCTTTGGCAG	0.338																																					p.D138D		Atlas-SNP	.											.	OGN	26	.	0			c.T414C						.						82	74	77					9																	95155381		2203	4300	6503	SO:0001819	synonymous_variant	4969	exon4			TGCAAAATCTTTG	AI424992	CCDS6695.1	9q22	2008-02-05	2007-02-16		ENSG00000106809	ENSG00000106809		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	8126	protein-coding gene	gene with protein product	"mimecan proteoglycan"	602383	"osteoglycin (osteoinductive factor)"			2372374	Standard	NM_033014		Approved	mimecan, OIF, SLRR3A	uc004asa.3	P20774	OTTHUMG00000020224	ENST00000262551.4:c.414T>C	chr9.hg19:g.95155381A>G		174.0	0.0		189.0	71.0	NM_033014	Q6FIB0|Q9UF90|Q9UNK5	Silent	SNP	ENST00000262551.4	hg19	CCDS6695.1																																																																																			.	.		0.338	OGN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053087.1	NM_024416		G	95155381	A	G	95155381	2	3	271	1	0	0	0	0	0	0	0	1	10855	98	4	2		2	OGN	9	95155381	Silent	SNP	A	TCGA-FV-A4ZQ-01A-11D-A25V-10	90082856	95155381	46058050	41	39388										
EPB41L4B	54566	hgsc.bcm.edu	37	chr9	112004035	112004035	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	tggacataatcaaaatggctGtcatctccactggccgatgc	9	11	3	0			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr9:112004035G>A	ENST00000374566.3	-	15	1927				EPB41L4B_ENST00000374557.4_Silent_p.D488D	NM_019114.3	NP_061987.3	Q9H329	E41LB_HUMAN	erythrocyte membrane protein band 4.1 like 4B						actomyosin structure organization (GO:0031032)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)	structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CAAAATGGCTGTCATCTCCAC	0.453																																					p.D488D		Atlas-SNP	.											.	EPB41L4B	111	.	0			c.C1464T						.						233	225	228					9																	112004035		1992	4185	6177	SO:0001627	intron_variant	54566	exon16			ATGGCTGTCATCT	AB032179	CCDS43859.1, CCDS43860.1	9q22.1-q22.3	2008-02-05			ENSG00000095203	ENSG00000095203			19818	protein-coding gene	gene with protein product		610340				10783258	Standard	NM_018424		Approved	EHM2	uc004bdz.1	Q9H329	OTTHUMG00000020470	ENST00000374566.3:c.1409+1862C>T	chr9.hg19:g.112004035G>A		225.0	0.0		231.0	78.0	NM_018424	Q5T4G5|Q5T4G6|Q9H328|Q9P2V3	Silent	SNP	ENST00000374566.3	hg19	CCDS43859.1																																																																																			.	.		0.453	EPB41L4B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053592.1	NM_018424		A	112004035	G	A	112004035	1	1	271	0	1	0	0	0	0	0	0	0	5158	1368	48	3		3	EPB41L4B	9	112004035	Intron	SNP	G	TCGA-FV-A4ZQ-01A-11D-A25V-10	16848654	112004035	29209396	42	39389										
PALM2	114299	hgsc.bcm.edu	37	chr9	112694224	112694224	+	Intron	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	cagatgcagtaaattacattTcctcccagcttcccgacctg	6	14	0	1			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr9:112694224T>A	ENST00000374531.2	+	6	474				PALM2-AKAP2_ENST00000374530.3_Missense_Mutation_p.S138T|AKAP2_ENST00000555236.1_Missense_Mutation_p.S138T|PALM2_ENST00000448454.2_Missense_Mutation_p.S140T|PALM2_ENST00000314527.4_Missense_Mutation_p.S138T|PALM2-AKAP2_ENST00000302798.7_Missense_Mutation_p.S138T|AKAP2_ENST00000510514.5_Missense_Mutation_p.S138T|PALM2_ENST00000483909.1_Intron	NM_001037293.2	NP_001032370.1	Q8IXS6	PALM2_HUMAN	paralemmin 2						regulation of cell shape (GO:0008360)	plasma membrane (GO:0005886)				breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(2)|skin(3)|upper_aerodigestive_tract(1)	18						AAATTACATTTCCTCCCAGCT	0.552																																					p.S138T		Atlas-SNP	.											.	PALM2-AKAP2	117	.	0			c.T412A						.						164	159	161					9																	112694224		2203	4300	6503	SO:0001627	intron_variant	445815	exon6			TACATTTCCTCCC	AJ312216	CCDS35099.1, CCDS48002.1, CCDS48002.2	9q31.3	2009-10-16			ENSG00000243444	ENSG00000243444			15845	protein-coding gene	gene with protein product						11478809	Standard	NM_001037293		Approved			Q8IXS6	OTTHUMG00000020479	ENST00000374531.2:c.400+6862T>A	chr9.hg19:g.112694224T>A		102.0	0.0		84.0	33.0	NM_007203	A9Z1X9|Q8N9D5|Q96DU1	Missense_Mutation	SNP	ENST00000374531.2	hg19	CCDS35099.1	.	.	.	.	.	.	.	.	.	.	T	14.15	2.449661	0.43531	.	.	ENSG00000243444;ENSG00000243444;ENSG00000243444;ENSG00000157654;ENSG00000157654;ENSG00000157654;ENSG00000241978;ENSG00000241978	ENST00000448454;ENST00000314527;ENST00000497711;ENST00000374530;ENST00000413420;ENST00000302798;ENST00000555236;ENST00000510514	T;T;T;T;T;T;T;T	0.29142	2.3;2.3;1.58;2.26;2.3;2.26;2.26;2.26	6.17	5.04	0.67666	.	0.369759	0.21007	N	0.081742	T	0.21881	0.0527	N	0.19112	0.55	0.34555	D	0.711741	B;B;B	0.32467	0.372;0.372;0.08	B;B;B	0.32805	0.153;0.153;0.093	T	0.31998	-0.9923	10	0.87932	D	0	-8.0463	11.3853	0.49782	0.0:0.0696:0.0:0.9304	.	138;138;140	Q9Y2D5-6;Q9Y2D5-4;D3YTA4	.;.;.	T	140;138;124;138;138;138;138;138	ENSP00000400206:S140T;ENSP00000323805:S138T;ENSP00000419747:S124T;ENSP00000363654:S138T;ENSP00000397839:S138T;ENSP00000305861:S138T;ENSP00000451476:S138T;ENSP00000421522:S138T	ENSP00000305861:S138T	S	+	1	0	PALM2-AKAP2;PALM2;AKAP2	111734045	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.753000	0.62183	1.165000	0.42670	0.533000	0.62120	TCC	.	.		0.552	PALM2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053604.1	NM_001037293		A	112694224	T	A	112694224	1	1	271	0	1	0	0	0	0	0	0	0	11418	1783	62	4		4	PALM2	9	112694224	Intron	SNP	T	TCGA-FV-A4ZQ-01A-11D-A25V-10	690189	112694224	28519207	43	39390										
NET1	10276	hgsc.bcm.edu	37	chr10	5488742	5488742	+	Intron	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	gggaagcatggtggcacatgAtgagactggaggtctcctac	15	8	1	2			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr10:5488742A>T	ENST00000355029.4	+	4	397				NET1_ENST00000542715.1_Intron|NET1_ENST00000380359.3_Missense_Mutation_p.D5V	NM_001047160.2	NP_001040625.1	Q7Z628	ARHG8_HUMAN	neuroepithelial cell transforming 1						apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to ionizing radiation (GO:0071479)|myoblast migration (GO:0051451)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(4)|kidney(2)|large_intestine(9)|lung(5)|prostate(2)|skin(1)	23						GTGGCACATGATGAGACTGGA	0.478																																					p.D5V		Atlas-SNP	.											.	NET1	82	.	0			c.A14T						.						134	125	128					10																	5488742		2203	4300	6503	SO:0001627	intron_variant	10276	exon1			CACATGATGAGAC	AJ010046	CCDS7067.1, CCDS41483.1	10p15	2013-01-10	2008-09-12		ENSG00000173848	ENSG00000173848		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	14592	protein-coding gene	gene with protein product		606450				8649828	Standard	NR_073040		Approved	ARHGEF8, NET1A	uc001iia.4	Q7Z628	OTTHUMG00000017596	ENST00000355029.4:c.256-5051A>T	chr10.hg19:g.5488742A>T		71.0	0.0		77.0	10.0	NM_005863	Q12773|Q96D82|Q99903|Q9UEN6	Missense_Mutation	SNP	ENST00000355029.4	hg19	CCDS41483.1	.	.	.	.	.	.	.	.	.	.	A	27.6	4.842753	0.91197	.	.	ENSG00000173848	ENST00000449083;ENST00000380359;ENST00000380337	T;T	0.19938	2.11;2.37	5.8	5.8	0.92144	.	.	.	.	.	T	0.28632	0.0709	L	0.43152	1.355	0.80722	D	1	D	0.61697	0.99	P	0.50570	0.644	T	0.01198	-1.1421	9	0.52906	T	0.07	.	14.9738	0.71254	1.0:0.0:0.0:0.0	.	5	Q5SQI7	.	V	5	ENSP00000403101:D5V;ENSP00000369717:D5V	ENSP00000369694:D5V	D	+	2	0	NET1	5478742	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	6.568000	0.73987	2.218000	0.71995	0.377000	0.23210	GAT	.	.		0.478	NET1-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000046553.3	NM_005863		T	5488742	A	T	5488742	1	4	271	0	1	0	0	0	0	0	0	0	10347	333	12	4		4	NET1	10	5488742	Intron	SNP	A	TCGA-FV-A4ZQ-01A-11D-A25V-10		5488742	130046005	44	39391										
GPAM	57678	hgsc.bcm.edu	37	chr10	113935464	113935464	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	aaggcgtcttgcaagccatcCgcggtgtctgtgaaaatgat	12	9	2	2	rs368640883		TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr10:113935464C>A	ENST00000348367.4	-	6	504	c.307G>T	c.(307-309)Gga>Tga	p.G103*	GPAM_ENST00000423155.1_Nonsense_Mutation_p.G103*|GPAM_ENST00000369425.1_Nonsense_Mutation_p.G103*			Q9HCL2	GPAT1_HUMAN	glycerol-3-phosphate acyltransferase, mitochondrial	103					acyl-CoA metabolic process (GO:0006637)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|defense response to virus (GO:0051607)|fatty acid homeostasis (GO:0055089)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|interleukin-2 secretion (GO:0070970)|negative regulation of activation-induced cell death of T cells (GO:0070236)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of multicellular organism growth (GO:0040018)|regulation of cytokine secretion (GO:0050707)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)	p.G103*(1)		breast(2)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Epithelial(162;0.0306)|all cancers(201;0.123)		GCAAGCCATCCGCGGTGTCTG	0.408																																					p.G103X	Ovarian(161;1017 2606 18293 52943)	Atlas-SNP	.											.	GPAM	68	.	1	Substitution - Nonsense(1)	lung(1)	c.G307T						.						92	84	87					10																	113935464		2203	4300	6503	SO:0001587	stop_gained	57678	exon6			GCCATCCGCGGTG	AL832464	CCDS7570.1	10q25.3	2009-07-15			ENSG00000119927	ENSG00000119927			24865	protein-coding gene	gene with protein product	"glycerol-3-phosphate acyltransferase 1, mitochondrial"	602395				10997877, 8369314	Standard	NM_020918		Approved	KIAA1560, MGC26846, GPAT1	uc001kzp.3	Q9HCL2	OTTHUMG00000019055	ENST00000348367.4:c.307G>T	chr10.hg19:g.113935464C>A	ENSP00000265276:p.Gly103*	64.0	0.0		79.0	29.0	NM_001244949	Q5VW51|Q86TA3	Nonsense_Mutation	SNP	ENST00000348367.4	hg19	CCDS7570.1	.	.	.	.	.	.	.	.	.	.	C	39	7.508122	0.98325	.	.	ENSG00000119927	ENST00000348367;ENST00000423155;ENST00000369425	.	.	.	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-21.0003	17.4284	0.87532	0.0:1.0:0.0:0.0	.	.	.	.	X	103	.	ENSP00000265276:G103X	G	-	1	0	GPAM	113925454	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.935000	0.75886	2.554000	0.86153	0.650000	0.86243	GGA	.	.		0.408	GPAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050377.1	NM_020918		A	113935464	C	A	113935464	4	1	271	1	0	0	0	0	0	1	0	0	6596	661	23	1	2247	1	GPAM	10	113935464	Nonsense_Mutation	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10	108446722	113935464	21599283	45	39392										
EBF3	253738	hgsc.bcm.edu	37	chr10	131676057	131676057	+	Frame_Shift_Del	DEL	T	T	-													0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	atctccgcatatctcgagggTtgcctgcattcttcaaacag							TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr10:131676057delT	ENST00000355311.5	-	7	683	c.611delA	c.(610-612)aacfs	p.N204fs	EBF3_ENST00000368648.3_Frame_Shift_Del_p.N204fs			Q9H4W6	COE3_HUMAN	early B-cell factor 3	204	Interaction with DNA. {ECO:0000250}.				multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	44		all_cancers(35;1.8e-08)|all_epithelial(44;8.26e-08)|Lung NSC(174;0.0091)|all_lung(145;0.0123)|Breast(234;0.039)|all_neural(114;0.0722)|Colorectal(57;0.0764)		OV - Ovarian serous cystadenocarcinoma(35;0.00513)		ATCTCGAGGGTTGCCTGCATT	0.363																																					p.N204fs		Atlas-Indel,Pindel	.											.	EBF3	193	.	0			c.612delC						.						120	107	112					10																	131676057		2203	4300	6503	SO:0001589	frameshift_variant	253738	exon7			.		CCDS31314.1	10q26.3	2007-03-30			ENSG00000108001	ENSG00000108001			19087	protein-coding gene	gene with protein product		607407				12355068	Standard	NM_001005463		Approved	COE3, DKFZp667B0210	uc001lki.2	Q9H4W6	OTTHUMG00000019265	ENST00000355311.5:c.611delA	chr10.hg19:g.131676057delT	ENSP00000347463:p.Asn204fs	93.0	0.0		78.0	23.0	NM_001005463	A0AUY1|Q5T6H9|Q9H4W5	Frame_Shift_Del	DEL	ENST00000355311.5	hg19																																																																																				.	.		0.363	EBF3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051015.2	NM_001005463		-	131676057	T	-	131676057	7	5	271	1	0	1	0	1	0	0	0	0	4884	1725	60	0	1084	0	EBF3	10	131676057	Frame_Shift_Del	DEL	T	TCGA-FV-A4ZQ-01A-11D-A25V-10	17740593	131676057	3858690	46	39393										
DPYSL4	10570	hgsc.bcm.edu	37	chr10	134012417	134012417	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	caggcaaactgcccgctgtaCgtcaccaaggtgatgagcaa	11	12	1	2			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr10:134012417C>A	ENST00000338492.4	+	8	917	c.753C>A	c.(751-753)taC>taA	p.Y251*	DPYSL4_ENST00000368627.1_Nonsense_Mutation_p.Y151*|DPYSL4_ENST00000368629.1_Nonsense_Mutation_p.Y151*	NM_006426.2	NP_006417.2	O14531	DPYL4_HUMAN	dihydropyrimidinase-like 4	251					axon guidance (GO:0007411)|nervous system development (GO:0007399)|pyrimidine nucleobase catabolic process (GO:0006208)	cytosol (GO:0005829)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)	p.Y251Y(1)		NS(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		all_cancers(35;4.33e-08)|all_epithelial(44;6.75e-06)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)|Colorectal(31;0.19)		OV - Ovarian serous cystadenocarcinoma(35;7.21e-05)|Epithelial(32;8.01e-05)|all cancers(32;9.29e-05)|BRCA - Breast invasive adenocarcinoma(275;0.206)		GCCCGCTGTACGTCACCAAGG	0.667																																					p.Y251X		Atlas-SNP	.											DPYSL4,NS,carcinoma,0,1	DPYSL4	91	.	1	Substitution - coding silent(1)	lung(1)	c.C753A						.						87	72	77					10																	134012417		2203	4300	6503	SO:0001587	stop_gained	10570	exon8			GCTGTACGTCACC	AB006713	CCDS7665.1	10q25.2-q26	2008-05-14			ENSG00000151640	ENSG00000151640			3016	protein-coding gene	gene with protein product		608407				8973361, 9652388	Standard	NM_006426		Approved	ULIP4, DRP-4	uc009ybb.3	O14531	OTTHUMG00000019283	ENST00000338492.4:c.753C>A	chr10.hg19:g.134012417C>A	ENSP00000339850:p.Tyr251*	247.0	1.0		189.0	84.0	NM_006426	B2RMQ1|D3DRG5|O00240|Q5T0Q7	Nonsense_Mutation	SNP	ENST00000338492.4	hg19	CCDS7665.1	.	.	.	.	.	.	.	.	.	.	C	10.42	1.346524	0.24426	.	.	ENSG00000151640	ENST00000338492;ENST00000368629;ENST00000368627	.	.	.	3.94	-7.88	0.01178	.	0.071166	0.64402	D	0.000018	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-21.1874	17.5002	0.87728	0.0:0.2251:0.0:0.7749	.	.	.	.	X	251;151;151	.	ENSP00000339850:Y251X	Y	+	3	2	DPYSL4	133862407	0.000000	0.05858	0.020000	0.16555	0.113000	0.19764	-2.192000	0.01245	-1.992000	0.00975	-0.477000	0.04895	TAC	.	.		0.667	DPYSL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051050.2			A	134012417	C	A	134012417	4	1	271	1	0	0	0	0	0	1	0	0	4751	547	19	1	783	1	DPYSL4	10	134012417	Nonsense_Mutation	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10	2336360	134012417	1522330	47	39394										
MUC5B	727897	hgsc.bcm.edu	37	chr11	1278847	1278847	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	gcaagcccctgccctgtgacGcccagggtcagcccccgccg	12	20	1	1			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr11:1278847G>T	ENST00000529681.1	+	41	16415	c.16357G>T	c.(16357-16359)Gcc>Tcc	p.A5453S	MUC5B_ENST00000447027.1_Missense_Mutation_p.A5456S	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	5453	VWFC 2. {ECO:0000255|PROSITE- ProRule:PRU00220}.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		GCCCTGTGACGCCCAGGGTCA	0.682																																					p.A5453S		Atlas-SNP	.											MUC5B,caecum,carcinoma,0,2	MUC5B	473	.	0			c.G16357T						.						35	47	43					11																	1278847		2129	4217	6346	SO:0001583	missense	727897	exon41			TGTGACGCCCAGG	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.16357G>T	chr11.hg19:g.1278847G>T	ENSP00000436812:p.Ala5453Ser	88.0	0.0		36.0	2.0	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	hg19	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	G	10.64	1.408307	0.25378	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000546052;ENST00000406844	T;T	0.16457	2.34;2.52	4.95	-0.941	0.10402	.	.	.	.	.	T	0.10937	0.0267	N	0.19112	0.55	0.09310	N	1	P;P	0.39404	0.672;0.672	B;B	0.37144	0.158;0.242	T	0.18493	-1.0335	9	0.87932	D	0	.	10.4547	0.44544	0.0834:0.5703:0.3463:0.0	.	5790;5456	A7Y9J9;E9PBJ0	.;.	S	5453;5456;5397;352;5165	ENSP00000436812:A5453S;ENSP00000415793:A5456S	ENSP00000343037:A5397S	A	+	1	0	MUC5B	1235423	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.628000	0.05515	-0.491000	0.06697	-0.333000	0.08304	GCC	.	.		0.682	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		T	1278847	G	T	1278847	3	4	271	1	0	0	0	0	1	0	0	0	9988	1087	38	1	16528	1	MUC5B	11	1278847	Missense_Mutation	SNP	G	TCGA-FV-A4ZQ-01A-11D-A25V-10		1278847	133727669	48	39395										
STK33	65975	hgsc.bcm.edu	37	chr11	8474374	8474374	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	agtctactaacttacccataTagataggagtcccacatgtg	7	10	1	1			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr11:8474374T>C	ENST00000447869.1	-	7	1784	c.866A>G	c.(865-867)tAt>tGt	p.Y289C	STK33_ENST00000396673.1_Missense_Mutation_p.Y289C|STK33_ENST00000473980.1_5'UTR|STK33_ENST00000358872.3_Missense_Mutation_p.Y102C|STK33_ENST00000534493.1_Missense_Mutation_p.Y248C|STK33_ENST00000315204.1_Missense_Mutation_p.Y289C|STK33_ENST00000396672.1_Missense_Mutation_p.Y289C			Q9BYT3	STK33_HUMAN	serine/threonine kinase 33	289	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|skin(3)	23				Epithelial(150;2.13e-06)|BRCA - Breast invasive adenocarcinoma(625;0.239)		CTTACCCATATAGATAGGAGT	0.458																																					p.Y289C		Atlas-SNP	.											.	STK33	147	.	0			c.A866G						.						120	127	125					11																	8474374		2201	4296	6497	SO:0001583	missense	65975	exon9			CCCATATAGATAG	AJ303380	CCDS7789.1, CCDS73253.1, CCDS73254.1	11p15.3	2010-03-10			ENSG00000130413	ENSG00000130413			14568	protein-coding gene	gene with protein product		607670				11738831	Standard	NM_030906		Approved		uc001mgj.1	Q9BYT3	OTTHUMG00000140275	ENST00000447869.1:c.866A>G	chr11.hg19:g.8474374T>C	ENSP00000416750:p.Tyr289Cys	53.0	0.0		88.0	5.0	NM_030906	Q658S6|Q8NEF5	Missense_Mutation	SNP	ENST00000447869.1	hg19	CCDS7789.1	.	.	.	.	.	.	.	.	.	.	T	18.37	3.608165	0.66558	.	.	ENSG00000130413	ENST00000447869;ENST00000315204;ENST00000396672;ENST00000358872;ENST00000396673;ENST00000444064;ENST00000534493;ENST00000524760	T;T;T;T;T;T;T;T	0.59638	0.46;0.46;0.46;0.46;0.46;0.46;0.46;0.25	5.22	5.22	0.72569	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.80560	0.4646	M	0.92412	3.305	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.85130	0.0974	10	0.87932	D	0	.	12.6203	0.56600	0.0:0.0:0.0:1.0	.	248;289	B4DDH2;Q9BYT3	.;STK33_HUMAN	C	289;289;289;102;289;44;248;201	ENSP00000416750:Y289C;ENSP00000320754:Y289C;ENSP00000379905:Y289C;ENSP00000351743:Y102C;ENSP00000379906:Y289C;ENSP00000415688:Y44C;ENSP00000436418:Y248C;ENSP00000436905:Y201C	ENSP00000320754:Y289C	Y	-	2	0	STK33	8430950	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.914000	0.69964	1.978000	0.57642	0.402000	0.26972	TAT	.	.		0.458	STK33-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276819.2	NM_030906		C	8474374	T	C	8474374	3	2	271	1	0	0	0	0	1	0	0	0	15315	1406	49	2	702	2	STK33	11	8474374	Missense_Mutation	SNP	T	TCGA-FV-A4ZQ-01A-11D-A25V-10	7195527	8474374	126532142	49	39396										
OR4A47	403253	hgsc.bcm.edu	37	chr11	48510880	48510880	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	tgatcattttttctgtgacaTgtatcccttattgaaactgg	7	7	2	3			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr11:48510880T>A	ENST00000446524.1	+	1	612	c.536T>A	c.(535-537)aTg>aAg	p.M179K		NM_001005512.2	NP_001005512.2	Q6IF82	O4A47_HUMAN	olfactory receptor, family 4, subfamily A, member 47	179						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(18)|ovary(1)|skin(1)|urinary_tract(2)	29						TTCTGTGACATGTATCCCTTA	0.448																																					p.M179K		Atlas-SNP	.											.	OR4A47	72	.	0			c.T536A						.						168	159	162					11																	48510880		2201	4298	6499	SO:0001583	missense	403253	exon1			GTGACATGTATCC	BK004380	CCDS31490.1	11p11.2	2012-08-09			ENSG00000237388	ENSG00000237388		"GPCR / Class A : Olfactory receptors"	31266	protein-coding gene	gene with protein product							Standard	NM_001005512		Approved		uc010rhx.2	Q6IF82	OTTHUMG00000166581	ENST00000446524.1:c.536T>A	chr11.hg19:g.48510880T>A	ENSP00000412752:p.Met179Lys	268.0	0.0		331.0	77.0	NM_001005512		Missense_Mutation	SNP	ENST00000446524.1	hg19	CCDS31490.1	.	.	.	.	.	.	.	.	.	.	N	10.61	1.399385	0.25291	.	.	ENSG00000237388	ENST00000446524	T	0.37235	1.21	4.84	3.72	0.42706	GPCR, rhodopsin-like superfamily (1);	0.087086	0.49916	D	0.000123	T	0.44456	0.1294	M	0.76574	2.34	0.09310	N	1	P	0.48998	0.918	P	0.49301	0.606	T	0.42344	-0.9457	10	0.87932	D	0	.	7.9607	0.30070	0.0:0.0985:0.0:0.9015	.	179	Q6IF82	O4A47_HUMAN	K	179	ENSP00000412752:M179K	ENSP00000412752:M179K	M	+	2	0	OR4A47	48467456	0.000000	0.05858	0.980000	0.43619	0.018000	0.09664	0.517000	0.22832	1.799000	0.52666	0.418000	0.28097	ATG	.	.		0.448	OR4A47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390559.1	NM_001005512		A	48510880	T	A	48510880	3	1	271	1	0	0	0	0	1	0	0	0	11051	1464	51	4	538	4	OR4A47	11	48510880	Missense_Mutation	SNP	T	TCGA-FV-A4ZQ-01A-11D-A25V-10	40036506	48510880	86495636	50	39397										
PC	5091	hgsc.bcm.edu	37	chr11	66616778	66616778	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	gaagacctgcctctggccggCccggttcaggtcgctcacgg	14	15	3	1			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr11:66616778C>A	ENST00000393958.2	-	21	3304	c.3211G>T	c.(3211-3213)Gcc>Tcc	p.A1071S	PC_ENST00000393960.1_Missense_Mutation_p.A1071S|PC_ENST00000529047.1_Missense_Mutation_p.A191S|PC_ENST00000528224.1_5'UTR|PC_ENST00000393955.2_Missense_Mutation_p.A1071S	NM_000920.3	NP_000911.2	P11498	PYC_HUMAN	pyruvate carboxylase	1071					biotin metabolic process (GO:0006768)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|oxaloacetate metabolic process (GO:0006107)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|pyruvate carboxylase activity (GO:0004736)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Melanoma(852;0.0525)		Lung(977;0.153)|LUSC - Lung squamous cell carcinoma(976;0.227)	Biotin(DB00121)|Pyruvic acid(DB00119)	CTCTGGCCGGCCCGGTTCAGG	0.637																																					p.A1071S		Atlas-SNP	.											.	PC	116	.	0			c.G3211T						.						43	46	45					11																	66616778		2200	4295	6495	SO:0001583	missense	5091	exon21			GGCCGGCCCGGTT	U04641	CCDS8152.1	11q13.4-q13.5	2012-07-11			ENSG00000173599	ENSG00000173599	6.4.1.1		8636	protein-coding gene	gene with protein product		608786				6548474	Standard	NM_022172		Approved	PCB	uc001ojn.1	P11498	OTTHUMG00000167099	ENST00000393958.2:c.3211G>T	chr11.hg19:g.66616778C>A	ENSP00000377530:p.Ala1071Ser	155.0	0.0		136.0	94.0	NM_000920	B4DN00|Q16705	Missense_Mutation	SNP	ENST00000393958.2	hg19	CCDS8152.1	.	.	.	.	.	.	.	.	.	.	C	11.91	1.780165	0.31502	.	.	ENSG00000173599	ENST00000529047;ENST00000393955;ENST00000393958;ENST00000393960	D;D;D;D	0.95622	-1.6;-3.76;-3.76;-3.76	4.98	3.12	0.35913	.	0.111356	0.64402	D	0.000013	D	0.91047	0.7183	L	0.36672	1.1	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	D	0.86008	0.1499	10	0.52906	T	0.07	-10.3766	9.3447	0.38100	0.0:0.8245:0.0:0.1755	.	1071	P11498	PYC_HUMAN	S	191;1071;1071;1071	ENSP00000435905:A191S;ENSP00000377527:A1071S;ENSP00000377530:A1071S;ENSP00000377532:A1071S	ENSP00000377527:A1071S	A	-	1	0	PC	66373354	0.998000	0.40836	0.682000	0.30024	0.946000	0.59487	3.700000	0.54786	0.691000	0.31592	0.462000	0.41574	GCC	.	.		0.637	PC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393115.1	NM_001040716		A	66616778	C	A	66616778	3	1	271	1	0	0	0	0	1	0	0	0	11506	739	26	3	333	3	PC	11	66616778	Missense_Mutation	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10	18105898	66616778	68389738	51	39398										
ODZ4	26011	hgsc.bcm.edu	37	chr11	78380651	78380651	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	gtattgcacgtcacccagccGagtgatgcggtcgcggatgt	14	11	1	1			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr11:78380651G>A	ENST00000278550.7	-	32	7201	c.6739C>T	c.(6739-6741)Cgg>Tgg	p.R2247W		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	2247					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										TCACCCAGCCGAGTGATGCGG	0.572																																					p.R2247W		Atlas-SNP	.											.	.	.	.	0			c.C6739T						.						169	173	172					11																	78380651		2165	4260	6425	SO:0001583	missense	26011	exon32			CCAGCCGAGTGAT	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"odz, odd Oz/ten-m homolog 4 (Drosophila)"	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.6739C>T	chr11.hg19:g.78380651G>A	ENSP00000278550:p.Arg2247Trp	308.0	1.0		256.0	87.0	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Missense_Mutation	SNP	ENST00000278550.7	hg19	CCDS44688.1	.	.	.	.	.	.	.	.	.	.	G	16.14	3.037410	0.54896	.	.	ENSG00000149256	ENST00000278550;ENST00000530738	D;T	0.90844	-2.74;0.7	5.14	2.77	0.32553	.	0.000000	0.85682	D	0.000000	D	0.93776	0.8010	M	0.72118	2.19	0.58432	D	0.999991	D	0.89917	1.0	D	0.79784	0.993	D	0.92223	0.5786	9	.	.	.	.	11.8898	0.52622	0.0:0.0:0.291:0.709	.	2247	Q6N022	TEN4_HUMAN	W	2247;711	ENSP00000278550:R2247W;ENSP00000431711:R711W	.	R	-	1	2	ODZ4	78058299	0.983000	0.35010	0.782000	0.31804	0.995000	0.86356	1.861000	0.39438	0.410000	0.25675	-0.262000	0.10625	CGG	.	.		0.572	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			A	78380651	G	A	78380651	3	1	271	1	0	0	0	0	1	0	0	0	10846	1057	37	1	1582	1	ODZ4	11	78380651	Missense_Mutation	SNP	G	TCGA-FV-A4ZQ-01A-11D-A25V-10	11763873	78380651	56625865	52	39399										
GRM5	2915	hgsc.bcm.edu	37	chr11	88330465	88330465	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	tccattgtcccaacttccaaCgttgatataatcaaagtaat	4	10	1	1			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr11:88330465C>T	ENST00000305447.4	-	5	1599	c.1450G>A	c.(1450-1452)Gtt>Att	p.V484I	GRM5_ENST00000418177.2_Missense_Mutation_p.V484I|GRM5_ENST00000305432.5_Missense_Mutation_p.V484I|GRM5_ENST00000455756.2_Missense_Mutation_p.V484I|GRM5_ENST00000393297.1_Missense_Mutation_p.V484I	NM_001143831.2	NP_001137303.1	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5	484					activation of MAPKKK activity (GO:0000185)|cognition (GO:0050890)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|learning (GO:0007612)|locomotory behavior (GO:0007626)|negative regulation of locomotion (GO:0040013)|phospholipase C-activating G-protein coupled glutamate receptor signaling pathway (GO:0007206)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(1)|breast(5)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(18)|lung(40)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)|Rufinamide(DB06201)	CAACTTCCAACGTTGATATAA	0.323																																					p.V484I		Atlas-SNP	.											.	GRM5	414	.	0			c.G1450A						.						164	138	147					11																	88330465		2201	4299	6500	SO:0001583	missense	2915	exon6			TTCCAACGTTGAT	D28538	CCDS8283.1, CCDS44694.1	11q14.3	2014-06-12			ENSG00000168959	ENSG00000168959		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4597	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 86"	604102				7908515	Standard	NM_001143831		Approved	MGLUR5, GPRC1E, mGlu5, PPP1R86	uc001pcq.3	P41594	OTTHUMG00000134306	ENST00000305447.4:c.1450G>A	chr11.hg19:g.88330465C>T	ENSP00000306138:p.Val484Ile	145.0	0.0		148.0	50.0	NM_000842	Q6J164	Missense_Mutation	SNP	ENST00000305447.4	hg19	CCDS44694.1	.	.	.	.	.	.	.	.	.	.	C	16.45	3.126877	0.56721	.	.	ENSG00000168959	ENST00000418177;ENST00000455756;ENST00000305432;ENST00000305447;ENST00000393297	D;D;D;D;D	0.89270	-2.49;-2.49;-2.49;-2.49;-2.49	5.4	5.4	0.78164	.	0.055747	0.64402	D	0.000001	D	0.92512	0.7622	L	0.46157	1.445	0.52501	D	0.999951	D;B	0.61697	0.99;0.003	D;B	0.74023	0.982;0.009	D	0.91393	0.5137	9	.	.	.	.	19.1637	0.93544	0.0:1.0:0.0:0.0	.	484;484	P41594-2;P41594	.;GRM5_HUMAN	I	484	ENSP00000402912:V484I;ENSP00000405690:V484I;ENSP00000305905:V484I;ENSP00000306138:V484I;ENSP00000376975:V484I	.	V	-	1	0	GRM5	87970113	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.098000	0.50259	2.539000	0.85634	0.650000	0.86243	GTT	.	.		0.323	GRM5-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259226.1	NM_000842		T	88330465	C	T	88330465	3	4	271	1	0	0	0	0	1	0	0	0	6809	536	19	1	2208	1	GRM5	11	88330465	Missense_Mutation	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10	9949814	88330465	46676051	53	39400										
CADM1	23705	hgsc.bcm.edu	37	chr11	115085403	115085403	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	acagcggtatgtaccattatCtgttttgtttaggttattga	9	5	1	1			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr11:115085403C>A	ENST00000452722.3	-	7	939	c.919G>T	c.(919-921)Gat>Tat	p.D307Y	CADM1_ENST00000537140.1_5'UTR|CADM1_ENST00000537058.1_Missense_Mutation_p.D307Y|CADM1_ENST00000542447.2_Missense_Mutation_p.D307Y|CADM1_ENST00000536727.1_Missense_Mutation_p.D307Y|CADM1_ENST00000331581.6_Missense_Mutation_p.D307Y	NM_014333.3	NP_055148.3			cell adhesion molecule 1											cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(9)|ovary(2)|skin(1)	32	all_hematologic(175;0.0628)	all_cancers(61;2.98e-14)|all_epithelial(67;2.64e-08)|all_hematologic(158;0.000154)|Melanoma(852;0.000952)|Acute lymphoblastic leukemia(157;0.00101)|Breast(348;0.0102)|Medulloblastoma(222;0.0429)|Prostate(24;0.145)|all_neural(223;0.237)		BRCA - Breast invasive adenocarcinoma(274;5.01e-06)|Epithelial(105;0.000305)|all cancers(92;0.00303)		GTACCATTATCTGTTTTGTTT	0.443																																					p.D307Y		Atlas-SNP	.											.	CADM1	74	.	0			c.G919T						.						261	226	238					11																	115085403		2201	4296	6497	SO:0001583	missense	23705	exon7			CATTATCTGTTTT	AB017563	CCDS8373.1, CCDS53711.1, CCDS73397.1, CCDS73398.1, CCDS73399.1	11q23.2	2013-01-29	2007-02-07	2007-02-07	ENSG00000182985	ENSG00000182985		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5951	protein-coding gene	gene with protein product	"nectin-like 2"	605686	"tumor suppressor in lung cancer 1", "immunoglobulin superfamily, member 4"	TSLC1, IGSF4		10610705	Standard	NM_014333		Approved	NECL2, ST17, BL2, SYNCAM, IGSF4A, Necl-2, SYNCAM1, RA175	uc001ppi.4	Q9BY67	OTTHUMG00000168202	ENST00000452722.3:c.919G>T	chr11.hg19:g.115085403C>A	ENSP00000395359:p.Asp307Tyr	546.0	0.0		477.0	131.0	NM_014333		Missense_Mutation	SNP	ENST00000452722.3	hg19	CCDS8373.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.60|14.60	2.584062|2.584062	0.46110|0.46110	.|.	.|.	ENSG00000182985|ENSG00000182985	ENST00000542447;ENST00000452722;ENST00000537058;ENST00000536727;ENST00000404468;ENST00000331581|ENST00000545380	D;D;D;D;D|.	0.81821|.	-1.54;-1.54;-1.54;-1.54;-1.54|.	5.62|5.62	5.62|5.62	0.85841|0.85841	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	0.053540|.	0.85682|.	D|.	0.000000|.	D|D	0.86431|0.86431	0.5931|0.5931	M|M	0.92026|0.92026	3.265|3.265	0.58432|0.58432	D|D	0.999994|0.999994	B;B;B;B;B|.	0.21753|.	0.001;0.001;0.003;0.06;0.025|.	B;B;B;B;B|.	0.37346|.	0.003;0.004;0.007;0.247;0.01|.	D|D	0.88726|0.88726	0.3233|0.3233	10|5	0.42905|.	T|.	0.14|.	.|.	19.6764|19.6764	0.95936|0.95936	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	307;307;308;307;307|.	Q9BY67-2;F5H0J4;A4FVB5;Q9BY67;A0A4Z1|.	.;.;.;CADM1_HUMAN;.|.	Y|I	307;307;307;307;266;307|305	ENSP00000439176:D307Y;ENSP00000395359:D307Y;ENSP00000439817:D307Y;ENSP00000440322:D307Y;ENSP00000329797:D307Y|.	ENSP00000329797:D307Y|.	D|R	-|-	1|2	0|0	CADM1|CADM1	114590613|114590613	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.946000|5.946000	0.70234|0.70234	2.660000|2.660000	0.90430|0.90430	0.655000|0.655000	0.94253|0.94253	GAT|AGA	.	.		0.443	CADM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398753.2	NM_014333		A	115085403	C	A	115085403	3	1	271	1	0	0	0	0	1	0	0	0	2568	913	32	3	425	3	CADM1	11	115085403	Missense_Mutation	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10	26754938	115085403	19921113	54	39401										
LRRIQ1	84125	hgsc.bcm.edu	37	chr12	85441061	85441061	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	ttttggatactgtgaagtggAagaaaaatgtagacagtctt	11	3	1	3			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr12:85441061A>G	ENST00000393217.2	+	6	552	c.491A>G	c.(490-492)gAa>gGa	p.E164G		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	164	Glu-rich.									breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		TGTGAAGTGGAAGAAAAATGT	0.333																																					p.E164G		Atlas-SNP	.											.	LRRIQ1	512	.	0			c.A491G						.						73	80	78					12																	85441061		2203	4299	6502	SO:0001583	missense	84125	exon6			AAGTGGAAGAAAA	AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.491A>G	chr12.hg19:g.85441061A>G	ENSP00000376910:p.Glu164Gly	117.0	0.0		115.0	23.0	NM_001079910	Q567P4|Q9BS17|Q9HA36	Missense_Mutation	SNP	ENST00000393217.2	hg19	CCDS41816.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.6|21.6	4.175993|4.175993	0.78564|0.78564	.|.	.|.	ENSG00000133640|ENSG00000133640	ENST00000256007;ENST00000378580;ENST00000393212;ENST00000393217|ENST00000533414	T;T|.	0.77098|.	0.78;-1.07|.	5.08|5.08	5.08|5.08	0.68730|0.68730	.|.	0.171337|.	0.43919|.	D|.	0.000515|.	T|T	0.65565|0.65565	0.2703|0.2703	L|L	0.61218|0.61218	1.895|1.895	0.34664|0.34664	D|D	0.722984|0.722984	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.91635|.	0.999;0.996;0.998|.	T|T	0.74423|0.74423	-0.3670|-0.3670	10|5	0.87932|.	D|.	0|.	.|.	13.4199|13.4199	0.60992|0.60992	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	164;164;164|.	Q96JM4-2;Q96JM4;C9JI57|.	.;LRIQ1_HUMAN;.|.	G|E	164|62	ENSP00000376906:E164G;ENSP00000376910:E164G|.	ENSP00000256007:E164G|.	E|K	+|+	2|1	0|0	LRRIQ1|LRRIQ1	83965192|83965192	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.977000|0.977000	0.68977|0.68977	5.313000|5.313000	0.65798|0.65798	1.911000|1.911000	0.55334|0.55334	0.477000|0.477000	0.44152|0.44152	GAA|AAG	.	.		0.333	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165		G	85441061	A	G	85441061	3	3	271	1	0	0	0	0	1	0	0	0	9038	246	9	2	509	2	LRRIQ1	12	85441061	Missense_Mutation	SNP	A	TCGA-FV-A4ZQ-01A-11D-A25V-10		85441061	48410834	55	39402										
UNG	7374	hgsc.bcm.edu	37	chr12	109540650	109540650	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	tggcttgctttcagtttggaGaacatttataaagagttgtc	10	5	1	2			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr12:109540650G>T	ENST00000242576.2	+	5	646	c.540G>T	c.(538-540)gaG>gaT	p.E180D	UNG_ENST00000336865.2_Missense_Mutation_p.E171D	NM_080911.2	NP_550433.1			uracil-DNA glycosylase											central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(4)|ovary(1)	9						TCAGTTTGGAGAACATTTATA	0.388								Base excision repair (BER), DNA glycosylases	Immune Deficiency with Hyper-IgM																												p.E180D		Atlas-SNP	.											.	UNG	30	.	0			c.G540T						.						56	60	59					12																	109540650		2203	4300	6503	SO:0001583	missense	7374	exon5	Familial Cancer Database	Hypogammaglobulinemia with Hyper-IgM, HIGM type I-V, XLHIGM	TTTGGAGAACATT	A64377	CCDS9124.1, CCDS9125.1	12q23-q24.1	2014-09-17			ENSG00000076248	ENSG00000076248	3.2.2.27		12572	protein-coding gene	gene with protein product	"uracil-DNA glycosylase 1, uracil-DNA glycosylase 2"	191525		DGU		1923798, 17101234	Standard	NM_080911		Approved	UDG, UNG1, UNG2, HIGM4	uc001tnz.2	P13051	OTTHUMG00000169247	ENST00000242576.2:c.540G>T	chr12.hg19:g.109540650G>T	ENSP00000242576:p.Glu180Asp	41.0	0.0		40.0	4.0	NM_080911		Missense_Mutation	SNP	ENST00000242576.2	hg19	CCDS9124.1	.	.	.	.	.	.	.	.	.	.	G	37	6.127343	0.97305	.	.	ENSG00000076248	ENST00000242576;ENST00000336865;ENST00000537518	T;T	0.52526	0.66;0.66	5.26	4.04	0.47022	Uracil-DNA glycosylase-like (3);	0.101382	0.64402	D	0.000003	T	0.38878	0.1057	L	0.44542	1.39	0.38750	D	0.954089	B;B	0.23490	0.086;0.068	B;B	0.28709	0.093;0.07	T	0.30851	-0.9964	10	0.44086	T	0.13	-16.8707	7.8749	0.29589	0.7637:0.0:0.2363:0.0	.	171;180	E5KTA6;P13051	.;UNG_HUMAN	D	180;171;137	ENSP00000242576:E180D;ENSP00000337398:E171D	ENSP00000242576:E180D	E	+	3	2	UNG	108025033	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	1.808000	0.38912	0.941000	0.37499	-0.300000	0.09419	GAG	.	.		0.388	UNG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403067.1	NM_080911		T	109540650	G	T	109540650	3	4	271	1	0	0	0	0	1	0	0	0	17014	933	33	3	663	3	UNG	12	109540650	Missense_Mutation	SNP	G	TCGA-FV-A4ZQ-01A-11D-A25V-10	24099589	109540650	24311245	56	39403										
RFC5	5985	hgsc.bcm.edu	37	chr12	118456923	118456923	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	tgaatgatctcatttctcatCaggacattctgagtaccagt	7	9	4	3			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr12:118456923C>G	ENST00000454402.2	+	2	230	c.112C>G	c.(112-114)Cag>Gag	p.Q38E	RFC5_ENST00000229043.3_5'UTR|RFC5_ENST00000392542.2_Missense_Mutation_p.Q17E	NM_001206801.1|NM_007370.5	NP_001193730.1|NP_031396.1	P40937	RFC5_HUMAN	replication factor C (activator 1) 5, 36.5kDa	38					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor C complex (GO:0005663)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			NS(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(3)	9	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CATTTCTCATCAGGACATTCT	0.358																																					p.Q38E		Atlas-SNP	.											.	RFC5	35	.	0			c.C112G						.						112	103	106					12																	118456923		2203	4300	6503	SO:0001583	missense	5985	exon2			TCTCATCAGGACA		CCDS9185.1, CCDS41843.2	12q24.3	2010-04-21	2002-08-29		ENSG00000111445	ENSG00000111445		"ATPases / AAA-type"	9973	protein-coding gene	gene with protein product		600407	"replication factor C (activator 1) 5 (36.5kD)"			7774928	Standard	NM_007370		Approved	RFC36	uc001twq.3	P40937	OTTHUMG00000156438	ENST00000454402.2:c.112C>G	chr12.hg19:g.118456923C>G	ENSP00000408295:p.Gln38Glu	53.0	0.0		88.0	24.0	NM_007370	A8MZ62|B3KSX8	Missense_Mutation	SNP	ENST00000454402.2	hg19	CCDS9185.1	.	.	.	.	.	.	.	.	.	.	C	2.404	-0.336975	0.05278	.	.	ENSG00000111445	ENST00000484086;ENST00000420967;ENST00000454402;ENST00000392542;ENST00000535092	T;T;T;T;T	0.37235	2.01;2.01;1.21;2.17;2.01	4.78	4.78	0.61160	.	0.264871	0.37955	N	0.001875	T	0.16896	0.0406	N	0.04636	-0.2	0.80722	D	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.0;0.001;0.001	T	0.10567	-1.0624	10	0.02654	T	1	-4.9009	16.7575	0.85503	0.0:1.0:0.0:0.0	.	17;52;38	A8MZ62;Q59GW7;P40937	.;.;RFC5_HUMAN	E	70;17;38;17;17	ENSP00000445917:Q70E;ENSP00000390340:Q17E;ENSP00000408295:Q38E;ENSP00000376325:Q17E;ENSP00000438252:Q17E	ENSP00000376325:Q17E	Q	+	1	0	RFC5	116941306	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.115000	0.57865	2.480000	0.83734	0.563000	0.77884	CAG	.	.		0.358	RFC5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344196.2	NM_007370		G	118456923	C	G	118456923	3	3	271	1	0	0	0	0	1	0	0	0	13263	827	29	4	124	4	RFC5	12	118456923	Missense_Mutation	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10	8916273	118456923	15394972	57	39404										
ATP12A	479	hgsc.bcm.edu	37	chr13	25265114	25265114	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	gaataaagcatctacttcccCtgtaggcactgtcaccggca	8	13	2	0			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr13:25265114C>T	ENST00000381946.3	+	8	966				ATP12A_ENST00000218548.6_Missense_Mutation_p.P271L			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide						ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		TCTACTTCCCCTGTAGGCACT	0.572																																					p.P271L	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-SNP	.											.	ATP12A	172	.	0			c.C812T						.						132	125	128					13																	25265114		2203	4300	6503	SO:0001627	intron_variant	479	exon8			CTTCCCCTGTAGG	L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"ATPases / P-type"	13816	protein-coding gene	gene with protein product	"ATPase, Na+K+ transporting, alpha-1 polypeptide-like", "potassium-transporting ATPase alpha chain 2", "proton pump", "non-gastric H(+)/K(+) ATPase alpha subunit", "sodium/potassium ATPase, alpha polypeptide-like"	182360	"ATPase, Na+/K+ transporting, alpha polypeptide-like 1"	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.800-6C>T	chr13.hg19:g.25265114C>T		241.0	0.0		200.0	60.0	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Missense_Mutation	SNP	ENST00000381946.3	hg19	CCDS31948.1	.	.	.	.	.	.	.	.	.	.	C	4.251	0.045541	0.08196	.	.	ENSG00000075673	ENST00000218548	D	0.92911	-3.13	5.02	4.09	0.47781	.	0.466770	0.15887	U	0.239723	D	0.86146	0.5863	.	.	.	0.33231	D	0.555972	B	0.06786	0.001	B	0.08055	0.003	D	0.84299	0.0504	9	0.45353	T	0.12	.	7.5117	0.27577	0.0:0.8826:0.0:0.1174	.	271	P54707-2	.	L	271	ENSP00000218548:P271L	ENSP00000218548:P271L	P	+	2	0	ATP12A	24163114	0.002000	0.14202	0.066000	0.19879	0.004000	0.04260	0.619000	0.24388	2.600000	0.87896	0.462000	0.41574	CCT	.	.		0.572	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676		T	25265114	C	T	25265114	1	4	271	0	1	0	0	0	0	0	0	0	1122	681	24	3		3	ATP12A	13	25265114	Intron	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10		25265114	89904764	58	39405										
MAB21L1	4081	hgsc.bcm.edu	37	chr13	36049768	36049768	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	gcatttaaaggccggcgtgaTctgcaccacgtacctatctc	9	13	2	1			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr13:36049768T>A	ENST00000379919.4	-	1	1064	c.508A>T	c.(508-510)Atc>Ttc	p.I170F	NBEA_ENST00000379939.2_Intron|NBEA_ENST00000310336.4_Intron|NBEA_ENST00000540320.1_Intron|NBEA_ENST00000537702.1_5'Flank|NBEA_ENST00000400445.3_Intron	NM_005584.4	NP_005575.1	Q13394	MB211_HUMAN	mab-21-like 1 (C. elegans)	170					anatomical structure morphogenesis (GO:0009653)|camera-type eye development (GO:0043010)|positive regulation of cell proliferation (GO:0008284)	nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	20		Breast(139;0.014)|Lung SC(185;0.051)|Prostate(109;0.202)		all cancers(112;9.63e-08)|Epithelial(112;1.37e-06)|BRCA - Breast invasive adenocarcinoma(63;0.000659)|OV - Ovarian serous cystadenocarcinoma(117;0.00372)|GBM - Glioblastoma multiforme(144;0.115)		GCCGGCGTGATCTGCACCACG	0.597																																					p.I170F		Atlas-SNP	.											.	MAB21L1	52	.	0			c.A508T						.						73	76	75					13																	36049768		2203	4300	6503	SO:0001583	missense	4081	exon1			GCGTGATCTGCAC	BC028170	CCDS9353.1	13q13.3	2008-02-05	2001-11-28		ENSG00000180660	ENSG00000180660			6757	protein-coding gene	gene with protein product		601280	"mab-21 (C. elegans)-like 1"			8733127	Standard	NM_005584		Approved	CAGR1		Q13394	OTTHUMG00000016723	ENST00000379919.4:c.508A>T	chr13.hg19:g.36049768T>A	ENSP00000369251:p.Ile170Phe	231.0	0.0		174.0	42.0	NM_005584	Q6I9T5	Missense_Mutation	SNP	ENST00000379919.4	hg19	CCDS9353.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.001112	0.74818	.	.	ENSG00000180660	ENST00000379919	T	0.08193	3.12	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.28433	0.0703	M	0.75085	2.285	0.80722	D	1	D	0.57257	0.979	D	0.67900	0.954	T	0.00827	-1.1550	10	0.44086	T	0.13	-31.8933	15.8843	0.79232	0.0:0.0:0.0:1.0	.	170	Q13394	MB211_HUMAN	F	170	ENSP00000369251:I170F	ENSP00000369251:I170F	I	-	1	0	MAB21L1	34947768	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.040000	0.89188	2.164000	0.68074	0.533000	0.62120	ATC	.	.		0.597	MAB21L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044459.3	NM_005584		A	36049768	T	A	36049768	3	1	271	1	0	0	0	0	1	0	0	0	9150	1435	50	4	575	4	MAB21L1	13	36049768	Missense_Mutation	SNP	T	TCGA-FV-A4ZQ-01A-11D-A25V-10	10784654	36049768	79120110	59	39406										
ELF1	1997	hgsc.bcm.edu	37	chr13	41525513	41525513	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	aggggaatccatattgaggaGtgcctcagcagcctcaatag	12	9	2	1			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr13:41525513G>T	ENST00000239882.3	-	4	627	c.313C>A	c.(313-315)Ctc>Atc	p.L105I	ELF1_ENST00000498824.1_5'UTR|ELF1_ENST00000442101.1_Missense_Mutation_p.L105I	NM_172373.3	NP_758961.1	P32519	ELF1_HUMAN	E74-like factor 1 (ets domain transcription factor)	105					cell differentiation (GO:0030154)|negative regulation of T cell receptor signaling pathway (GO:0050860)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine production (GO:0001817)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37		Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367)		all cancers(112;1.87e-08)|Epithelial(112;8.45e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000202)|GBM - Glioblastoma multiforme(144;0.00266)|BRCA - Breast invasive adenocarcinoma(63;0.072)		ATATTGAGGAGTGCCTCAGCA	0.378																																					p.L105I		Atlas-SNP	.											.	ELF1	65	.	0			c.C313A						.						110	100	103					13																	41525513		2203	4300	6503	SO:0001583	missense	1997	exon3			TGAGGAGTGCCTC	M82882	CCDS9374.1	13q13	2008-07-18			ENSG00000120690	ENSG00000120690			3316	protein-coding gene	gene with protein product		189973				1545787	Standard	NM_001145353		Approved		uc001uxs.3	P32519	OTTHUMG00000016783	ENST00000239882.3:c.313C>A	chr13.hg19:g.41525513G>T	ENSP00000239882:p.Leu105Ile	85.0	0.0		66.0	4.0	NM_001145353	B4E2I5|E9PDQ9|Q8N6F6|Q9UDE1	Missense_Mutation	SNP	ENST00000239882.3	hg19	CCDS9374.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.115596	0.77323	.	.	ENSG00000120690	ENST00000442101;ENST00000239882	T;T	0.62498	0.02;0.02	5.66	5.66	0.87406	.	0.000000	0.64402	D	0.000001	T	0.66147	0.2760	M	0.62266	1.93	0.51767	D	0.999938	B;B	0.29162	0.235;0.235	B;B	0.33568	0.166;0.166	T	0.65792	-0.6082	10	0.62326	D	0.03	.	19.7468	0.96255	0.0:0.0:1.0:0.0	.	105;105	E9PDQ9;P32519	.;ELF1_HUMAN	I	105	ENSP00000405580:L105I;ENSP00000239882:L105I	ENSP00000239882:L105I	L	-	1	0	ELF1	40423513	1.000000	0.71417	0.997000	0.53966	0.994000	0.84299	8.977000	0.93446	2.678000	0.91216	0.563000	0.77884	CTC	.	.		0.378	ELF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044654.3	NM_172373		T	41525513	G	T	41525513	3	4	271	1	0	0	0	0	1	0	0	0	5055	1029	36	3	1570	3	ELF1	13	41525513	Missense_Mutation	SNP	G	TCGA-FV-A4ZQ-01A-11D-A25V-10	5475745	41525513	73644365	60	39407										
AKAP11	11215	hgsc.bcm.edu	37	chr13	42872928	42872928	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	agagacttcaaagccatacaAtgatggtttgtttttcatta	7	6	2	2			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr13:42872928A>G	ENST00000025301.2	+	7	786	c.611A>G	c.(610-612)aAt>aGt	p.N204S		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	204					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2)	56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		AAGCCATACAATGATGGTTTG	0.333																																					p.N204S		Atlas-SNP	.											.	AKAP11	146	.	0			c.A611G						.						79	73	75					13																	42872928		2203	4299	6502	SO:0001583	missense	11215	exon7			CATACAATGATGG	AB014529	CCDS9383.1	13q	2012-04-17			ENSG00000023516	ENSG00000023516		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	369	protein-coding gene	gene with protein product	"AKAP 220", "A-kinase anchoring protein, 220kDa", "protein kinase A anchoring protein 11", "protein phosphatase 1, regulatory subunit 44"	604696				9734811, 8621616	Standard	NM_016248		Approved	KIAA0629, AKAP220, PRKA11, FLJ11304, DKFZp781I12161, PPP1R44	uc001uys.2	Q9UKA4	OTTHUMG00000016805	ENST00000025301.2:c.611A>G	chr13.hg19:g.42872928A>G	ENSP00000025301:p.Asn204Ser	87.0	0.0		56.0	22.0	NM_016248	O75124|Q9NUK7	Missense_Mutation	SNP	ENST00000025301.2	hg19	CCDS9383.1	.	.	.	.	.	.	.	.	.	.	A	9.749	1.166961	0.21621	.	.	ENSG00000023516	ENST00000025301	T	0.13420	2.59	6.07	-2.64	0.06114	.	0.868046	0.10272	N	0.694688	T	0.11410	0.0278	L	0.54323	1.7	0.09310	N	1	B	0.14438	0.01	B	0.10450	0.005	T	0.35624	-0.9781	10	0.29301	T	0.29	.	6.4947	0.22136	0.4416:0.2254:0.333:0.0	.	204	Q9UKA4	AKA11_HUMAN	S	204	ENSP00000025301:N204S	ENSP00000025301:N204S	N	+	2	0	AKAP11	41770928	0.004000	0.15560	0.004000	0.12327	0.005000	0.04900	0.208000	0.17415	-0.324000	0.08589	-0.912000	0.02778	AAT	.	.		0.333	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248		G	42872928	A	G	42872928	3	3	271	1	0	0	0	0	1	0	0	0	447	101	4	2	629	2	AKAP11	13	42872928	Missense_Mutation	SNP	A	TCGA-FV-A4ZQ-01A-11D-A25V-10	1347415	42872928	72296950	61	39408										
SIPA1L1	26037	hgsc.bcm.edu	37	chr14	72190403	72190403	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	tctgccagcccagtggttttCaccagtgcccggagttcacc	10	15	3	0			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr14:72190403C>T	ENST00000555818.1	+	16	4659	c.4311C>T	c.(4309-4311)ttC>ttT	p.F1437F	SIPA1L1_ENST00000554874.1_3'UTR|SIPA1L1_ENST00000537413.1_Silent_p.F891F|SIPA1L1_ENST00000381232.3_Silent_p.F1416F|SIPA1L1_ENST00000358550.2_Silent_p.F1416F	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	1437	Ser-rich.				actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		CAGTGGTTTTCACCAGTGCCC	0.532																																					p.F1437F		Atlas-SNP	.											.	SIPA1L1	219	.	0			c.C4311T						.						130	108	115					14																	72190403		2203	4300	6503	SO:0001819	synonymous_variant	26037	exon16			GGTTTTCACCAGT	AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.4311C>T	chr14.hg19:g.72190403C>T		149.0	0.0		97.0	32.0	NM_015556	J3KP19|O95321|Q9UDU4|Q9UNU4	Silent	SNP	ENST00000555818.1	hg19	CCDS9807.1																																																																																			.	.		0.532	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556		T	72190403	C	T	72190403	2	4	271	1	0	0	0	0	0	0	0	1	14344	825	29	3		3	SIPA1L1	14	72190403	Silent	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10		72190403	35159137	62	39409										
SERPINA9	327657	hgsc.bcm.edu	37	chr14	94936087	94936087	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	ctttgtggaggaagggcgggGgtatgcactgggggcattgg	21	5	0	0			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr14:94936087G>T	ENST00000380365.3	-	2	169	c.91C>A	c.(91-93)Ccc>Acc	p.P31T	SERPINA9_ENST00000424550.2_Intron|SERPINA9_ENST00000546329.1_Intron|SERPINA9_ENST00000337425.5_Missense_Mutation_p.P49T|SERPINA9_ENST00000298845.7_Missense_Mutation_p.P49T|SERPINA9_ENST00000448305.2_Intron|SERPINA9_ENST00000539349.1_5'Flank			Q86WD7	SPA9_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9	31					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(17)	21		all_cancers(154;0.0691)|all_epithelial(191;0.233)		Epithelial(152;0.144)|COAD - Colon adenocarcinoma(157;0.224)|all cancers(159;0.24)		GAAGGGCGGGGGTATGCACTG	0.552																																					p.P49T		Atlas-SNP	.											.	SERPINA9	105	.	0			c.C145A						.						80	84	83					14																	94936087		2027	4173	6200	SO:0001583	missense	327657	exon2			GGCGGGGGTATGC	AY185497	CCDS41982.1, CCDS41983.1, CCDS61542.1	14q32.1	2014-02-18	2005-08-18		ENSG00000170054	ENSG00000170054		"Serine (or cysteine) peptidase inhibitors"	15995	protein-coding gene	gene with protein product		615677	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9"			24172014	Standard	NM_175739		Approved	CENTERIN, SERPINA11b, GCET1	uc001ydf.3	Q86WD7	OTTHUMG00000167710	ENST00000380365.3:c.91C>A	chr14.hg19:g.94936087G>T	ENSP00000369723:p.Pro31Thr	119.0	0.0		109.0	37.0	NM_175739	B4DVH4|B9ZVX3|Q2T9J2|Q6UWP9|Q86WD4|Q86WD5|Q86WD6|Q86YP6|Q86YP7	Missense_Mutation	SNP	ENST00000380365.3	hg19		.	.	.	.	.	.	.	.	.	.	G	6.979	0.550733	0.13374	.	.	ENSG00000170054	ENST00000298845;ENST00000337425;ENST00000380365	D;D;D	0.88046	-2.33;-2.33;-2.33	3.89	-6.68	0.01778	Serpin domain (1);	4.024950	0.00695	U	0.000756	T	0.69187	0.3083	N	0.08118	0	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.06405	0.002;0.001;0.001	T	0.56805	-0.7918	10	0.62326	D	0.03	.	0.2398	0.00191	0.3017:0.2235:0.2498:0.225	.	31;49;49	Q86WD7;Q86WD7-7;Q86WD7-2	SPA9_HUMAN;.;.	T	49;49;31	ENSP00000298845:P49T;ENSP00000337133:P49T;ENSP00000369723:P31T	ENSP00000298845:P49T	P	-	1	0	SERPINA9	94005840	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-0.737000	0.04877	-1.346000	0.02211	-0.823000	0.03104	CCC	.	.		0.552	SERPINA9-008	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395803.2	NM_175739		T	94936087	G	T	94936087	3	4	271	1	0	0	0	0	1	0	0	0	14110	1232	43	3	1178	3	SERPINA9	14	94936087	Missense_Mutation	SNP	G	TCGA-FV-A4ZQ-01A-11D-A25V-10	22745684	94936087	12413453	63	39410										
KLC1	3831	hgsc.bcm.edu	37	chr14	104153537	104153537	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	agttcacgagagagtgagccAaagaaccccgggtaactatc	11	10	1	3			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr14:104153537A>G	ENST00000348520.6	+	13	1969				KLC1_ENST00000557450.1_Intron|KLC1_ENST00000334553.6_Silent_p.P590P|KLC1_ENST00000555836.1_Silent_p.P581P|KLC1_ENST00000246489.7_Silent_p.P590P|KLC1_ENST00000452929.2_Silent_p.P590P|KLC1_ENST00000347839.6_Silent_p.P581P|KLC1_ENST00000554280.1_Silent_p.P581P|RP11-73M18.6_ENST00000602827.1_RNA	NM_182923.3	NP_891553.2	Q07866	KLC1_HUMAN	kinesin light chain 1						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|stress granule disassembly (GO:0035617)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|growth cone (GO:0030426)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)|motor activity (GO:0003774)		KLC1/ALK(2)	NS(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(2)|prostate(1)|urinary_tract(1)	12		Melanoma(154;0.155)|all_epithelial(191;0.19)				AGAGTGAGCCAAAGAACCCCG	0.572																																					p.P590P		Atlas-SNP	.											.	KLC1	54	.	0			c.A1770G						.						74	63	67					14																	104153537		692	1591	2283	SO:0001627	intron_variant	3831	exon14			TGAGCCAAAGAAC	AF267530	CCDS32165.1, CCDS41996.1, CCDS45168.1	14q32.3	2013-01-10	2007-03-09	2007-03-09	ENSG00000126214	ENSG00000126214		"Tetratricopeptide (TTC) repeat domain containing"	6387	protein-coding gene	gene with protein product		600025	"kinesin 2 60/70kDa", "kinesin 2"	KNS2		8274221, 11106729	Standard	NM_005552		Approved	KNS2A, KLC, hKLC1S, hKLC1N, hKLC1P, hKLC1G, hKLC1R, hKLC1J, hKLC1B	uc010tyf.2	Q07866	OTTHUMG00000169227	ENST00000348520.6:c.1650+7655A>G	chr14.hg19:g.104153537A>G		111.0	0.0		76.0	18.0	NM_001130107	A6NF62|F8VTM4|Q7RTM2|Q7RTM3|Q7RTM5|Q7RTP9|Q7RTQ3|Q7RTQ5|Q7RTQ6|Q86SF5|Q86TF5|Q86V74|Q86V75|Q86V76|Q86V77|Q86V78|Q86V79|Q96H62	Silent	SNP	ENST00000348520.6	hg19	CCDS41996.1	.	.	.	.	.	.	.	.	.	.	A	9.069	0.996517	0.19043	.	.	ENSG00000126214	ENST00000537046	.	.	.	5.44	-10.9	0.00192	.	.	.	.	.	T	0.57533	0.2060	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.72268	-0.4343	4	.	.	.	.	14.081	0.64922	0.1478:0.6079:0.2442:0.0	.	.	.	.	E	221	.	.	K	+	1	0	KLC1	103223290	0.295000	0.24389	0.030000	0.17652	0.982000	0.71751	-0.028000	0.12350	-3.054000	0.00259	-0.408000	0.06270	AAA	.	.		0.572	KLC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402947.2	NM_005552		G	104153537	A	G	104153537	1	3	271	0	1	0	0	0	0	0	0	0	8342	117	5	2		2	KLC1	14	104153537	Intron	SNP	A	TCGA-FV-A4ZQ-01A-11D-A25V-10	9217450	104153537	3196003	64	39411										
B2M	567	hgsc.bcm.edu	37	chr15	45007635	45007635	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	cctcaggtactccaaagattCaggtttactcacgtcatcca	6	13	4	1			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr15:45007635C>T	ENST00000558401.1	+	2	152	c.82C>T	c.(82-84)Cag>Tag	p.Q28*	B2M_ENST00000559220.1_Intron|B2M_ENST00000559916.1_Nonsense_Mutation_p.Q28*|B2M_ENST00000544417.1_Nonsense_Mutation_p.Q28*	NM_004048.2	NP_004039.1	P61769	B2MG_HUMAN	beta-2-microglobulin	28	Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein refolding (GO:0042026)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to molecule of bacterial origin (GO:0002237)|retina homeostasis (GO:0001895)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cytoplasm (GO:0005737)|early endosome lumen (GO:0031905)|early endosome membrane (GO:0031901)|endoplasmic reticulum lumen (GO:0005788)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(30)|kidney(8)|large_intestine(6)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	59		all_cancers(109;1.88e-13)|all_epithelial(112;2.13e-11)|Lung NSC(122;2.22e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;4.16e-21)|GBM - Glioblastoma multiforme(94;8.97e-07)|COAD - Colon adenocarcinoma(120;0.0357)|Colorectal(105;0.0377)|Lung(196;0.0903)|LUSC - Lung squamous cell carcinoma(244;0.192)		TCCAAAGATTCAGGTTTACTC	0.418																																					p.Q28X		Atlas-SNP	.											.	B2M	99	.	0			c.C82T						.						152	152	152					15																	45007635		2198	4298	6496	SO:0001587	stop_gained	567	exon2			AAGATTCAGGTTT	AB021288	CCDS10113.1	15q21-q22.2	2013-01-11			ENSG00000166710	ENSG00000166710		"Immunoglobulin superfamily / C1-set domain containing"	914	protein-coding gene	gene with protein product		109700					Standard	NM_004048		Approved		uc001zuc.3	P61769	OTTHUMG00000131247	ENST00000558401.1:c.82C>T	chr15.hg19:g.45007635C>T	ENSP00000452780:p.Gln28*	69.0	0.0		103.0	55.0	NM_004048	P01884|Q540F8|Q6IAT8|Q9UCK0|Q9UD48|Q9UDF4	Nonsense_Mutation	SNP	ENST00000558401.1	hg19	CCDS10113.1	.	.	.	.	.	.	.	.	.	.	C	18.68	3.676633	0.67928	.	.	ENSG00000166710	ENST00000349264;ENST00000544417;ENST00000396754	.	.	.	5.82	5.82	0.92795	.	0.732245	0.13730	N	0.366742	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	15.5992	0.76611	0.0:1.0:0.0:0.0	.	.	.	.	X	28	.	ENSP00000340858:Q28X	Q	+	1	0	B2M	42794927	0.995000	0.38212	0.616000	0.29078	0.072000	0.16883	3.989000	0.56958	2.752000	0.94435	0.655000	0.94253	CAG	.	.		0.418	B2M-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254007.2	NM_004048		T	45007635	C	T	45007635	4	4	271	1	0	0	0	0	0	1	0	0	1244	827	29	3	88	3	B2M	15	45007635	Nonsense_Mutation	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10		45007635	57523757	65	39412										
RAB27A	5873	hgsc.bcm.edu	37	chr15	55527010	55527010	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	tccctgaaatcaatgcccacTgttgtgataaatttggagtt	8	8	1	2			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr15:55527010T>A	ENST00000396307.2	-	2	374	c.123A>T	c.(121-123)acA>acT	p.T41T	RAB27A_ENST00000564609.1_Silent_p.T41T|RAB27A_ENST00000569493.1_Silent_p.T41T|RAB27A_ENST00000336787.1_Silent_p.T41T	NM_004580.4	NP_004571.2	P51159	RB27A_HUMAN	RAB27A, member RAS oncogene family	41					antigen processing and presentation (GO:0019882)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cytotoxic T cell degranulation (GO:0043316)|exocytosis (GO:0006887)|exosomal secretion (GO:1990182)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|multivesicular body organization (GO:0036257)|multivesicular body sorting pathway (GO:0071985)|natural killer cell degranulation (GO:0043320)|positive regulation of exocytosis (GO:0045921)|positive regulation of gene expression (GO:0010628)|protein targeting (GO:0006605)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle transport (GO:0048489)	apical plasma membrane (GO:0016324)|dendrite (GO:0030425)|exocytic vesicle (GO:0070382)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|melanosome (GO:0042470)|multivesicular body membrane (GO:0032585)|photoreceptor outer segment (GO:0001750)|secretory granule membrane (GO:0030667)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(2)|liver(1)|lung(3)|ovary(1)|skin(1)	9				all cancers(107;0.0273)|GBM - Glioblastoma multiforme(80;0.0993)		CAATGCCCACTGTTGTGATAA	0.353																																					p.T41T		Atlas-SNP	.											.	RAB27A	18	.	0			c.A123T						.						122	122	122					15																	55527010		2193	4292	6485	SO:0001819	synonymous_variant	5873	exon3			GCCCACTGTTGTG	U38654	CCDS10153.1	15q15-q21.1	2014-09-17			ENSG00000069974	ENSG00000069974		"RAB, member RAS oncogene"	9766	protein-coding gene	gene with protein product		603868				7592656	Standard	NM_183235		Approved	RAB27, RAM, GS2, HsT18676	uc002acq.3	P51159	OTTHUMG00000131959	ENST00000396307.2:c.123A>T	chr15.hg19:g.55527010T>A		92.0	0.0		109.0	16.0	NM_183235	O00195|Q6FI40|Q9UIR9|Q9Y5U3	Silent	SNP	ENST00000396307.2	hg19	CCDS10153.1																																																																																			.	.		0.353	RAB27A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254918.1	NM_004580, NM_183236		A	55527010	T	A	55527010	2	1	271	1	0	0	0	0	0	0	0	1	12929	1567	55	4		4	RAB27A	15	55527010	Silent	SNP	T	TCGA-FV-A4ZQ-01A-11D-A25V-10	10519375	55527010	47004382	66	39413										
AXIN1	8312	hgsc.bcm.edu	37	chr16	396951	396951	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	agttctccctcctcaccaggCactgggggtcggggagcatc	13	14	2	0			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr16:396951C>A	ENST00000262320.3	-	2	446	c.75G>T	c.(73-75)gtG>gtT	p.V25V	AXIN1_ENST00000481769.1_Intron|AXIN1_ENST00000354866.3_Silent_p.V25V	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	25					activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				CCTCACCAGGCACTGGGGGTC	0.562																																					p.V25V		Atlas-SNP	.											.	AXIN1	290	.	0			c.G75T						.						49	54	53					16																	396951		2203	4300	6503	SO:0001819	synonymous_variant	8312	exon2			ACCAGGCACTGGG	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.75G>T	chr16.hg19:g.396951C>A		84.0	0.0		91.0	33.0	NM_181050	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Silent	SNP	ENST00000262320.3	hg19	CCDS10405.1																																																																																			.	.		0.562	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3			A	396951	C	A	396951	2	1	271	1	0	0	0	0	0	0	0	1	1236	697	25	3		3	AXIN1	16	396951	Silent	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10		396951	89957802	67	39414										
BCAR1	9564	hgsc.bcm.edu	37	chr16	75263466	75263466	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	tgctgggtgctgtggcccagCtccttgaccctctccaccat	10	16	1	1			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr16:75263466C>A	ENST00000162330.5	-	7	2682	c.2556G>T	c.(2554-2556)gaG>gaT	p.E852D	BCAR1_ENST00000535626.2_Missense_Mutation_p.E704D|BCAR1_ENST00000420641.3_Missense_Mutation_p.E870D|BCAR1_ENST00000538440.2_Missense_Mutation_p.E852D|BCAR1_ENST00000546196.1_Missense_Mutation_p.E823D|BCAR1_ENST00000393422.2_Missense_Mutation_p.E870D|BCAR1_ENST00000393420.6_Missense_Mutation_p.E870D|BCAR1_ENST00000542031.2_Missense_Mutation_p.E850D|BCAR1_ENST00000566982.1_5'UTR|BCAR1_ENST00000418647.3_Missense_Mutation_p.E898D|RP11-331F4.4_ENST00000489723.1_RNA	NM_001170717.1|NM_014567.3	NP_001164188.1|NP_055382.2	P56945	BCAR1_HUMAN	breast cancer anti-estrogen resistance 1	852					actin filament organization (GO:0007015)|antigen receptor-mediated signaling pathway (GO:0050851)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell division (GO:0051301)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epidermal growth factor receptor signaling pathway (GO:0007173)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell migration (GO:0010595)|regulation of apoptotic process (GO:0042981)|regulation of cell growth (GO:0001558)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(5)|endometrium(1)|kidney(6)|large_intestine(1)|liver(1)|lung(13)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)	35				BRCA - Breast invasive adenocarcinoma(221;0.169)		TGTGGCCCAGCTCCTTGACCC	0.706																																					p.E898D		Atlas-SNP	.											.	BCAR1	184	.	0			c.G2694T						.						23	19	21					16																	75263466		2193	4297	6490	SO:0001583	missense	9564	exon8			GCCCAGCTCCTTG	AJ242987	CCDS10915.1, CCDS54037.1, CCDS54038.1, CCDS54039.1, CCDS54040.1, CCDS54041.1, CCDS54042.1, CCDS54043.1	16q22-q23	2011-04-13			ENSG00000050820	ENSG00000050820		"Cas scaffolding proteins"	971	protein-coding gene	gene with protein product	"Crk-associated substrate", "Cas scaffolding protein family member 1"	602941				8413311, 10639512	Standard	NM_001170714		Approved	P130Cas, Crkas, CAS, CASS1	uc010vnb.2	P56945	OTTHUMG00000137604	ENST00000162330.5:c.2556G>T	chr16.hg19:g.75263466C>A	ENSP00000162330:p.Glu852Asp	45.0	0.0		12.0	5.0	NM_001170714	B3KWD7|B4DEV4|B4DGB5|B4DIW5|B7Z7X7|E9PCL5|E9PCV2|F5GXA2|F5GXV6|F5H7Z0|F8WA69|Q6QEF7	Missense_Mutation	SNP	ENST00000162330.5	hg19	CCDS10915.1	.	.	.	.	.	.	.	.	.	.	C	10.20	1.284630	0.23392	.	.	ENSG00000050820	ENST00000162330;ENST00000393422;ENST00000420641;ENST00000538440;ENST00000418647;ENST00000535626;ENST00000393420;ENST00000542031;ENST00000546196	T;T;T;T;T;T;T;T;T	0.23147	1.92;1.92;1.92;1.92;1.92;1.92;1.92;1.92;1.92	4.88	2.91	0.33838	CAS family, DUF3513 (1);	0.060220	0.64402	D	0.000005	T	0.23094	0.0558	N	0.16478	0.41	0.44531	D	0.997486	P;B;P;P;P;P;B;P;B	0.49635	0.926;0.216;0.926;0.909;0.909;0.861;0.445;0.926;0.257	D;B;D;P;P;P;B;D;B	0.65773	0.938;0.095;0.938;0.897;0.897;0.725;0.135;0.938;0.09	T	0.27365	-1.0076	10	0.07990	T	0.79	-43.4182	5.086	0.14682	0.0:0.523:0.2886:0.1884	.	870;704;898;850;870;870;852;852;642	B4DIW5;F5GXV6;E9PCL5;F5GXA2;F8WA69;E9PCV2;F5H7Z0;P56945;B3KWE2	.;.;.;.;.;.;.;BCAR1_HUMAN;.	D	852;870;870;852;898;704;870;850;823	ENSP00000162330:E852D;ENSP00000377074:E870D;ENSP00000392708:E870D;ENSP00000443841:E852D;ENSP00000391669:E898D;ENSP00000440370:E704D;ENSP00000377072:E870D;ENSP00000440415:E850D;ENSP00000442161:E823D	ENSP00000162330:E852D	E	-	3	2	BCAR1	73820967	0.992000	0.36948	1.000000	0.80357	0.994000	0.84299	0.297000	0.19101	1.183000	0.42943	0.467000	0.42956	GAG	.	.		0.706	BCAR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269017.1	NM_014567		A	75263466	C	A	75263466	3	1	271	1	0	0	0	0	1	0	0	0	1348	796	28	3	60	3	BCAR1	16	75263466	Missense_Mutation	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10	74866515	75263466	15091287	68	39415										
KLHDC4	54758	hgsc.bcm.edu	37	chr16	87788861	87788861	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	ctttggtccaggtgtcctttCtggtattgtagacatagagc	11	8	1	2			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr16:87788861C>T	ENST00000270583.5	-	4	366	c.308G>A	c.(307-309)aGa>aAa	p.R103K	KLHDC4_ENST00000347925.5_Missense_Mutation_p.R103K|KLHDC4_ENST00000353170.5_Missense_Mutation_p.R46K	NM_017566.3	NP_060036.2	Q8TBB5	KLDC4_HUMAN	kelch domain containing 4	103										breast(2)|endometrium(3)|lung(10)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(2)	21				BRCA - Breast invasive adenocarcinoma(80;0.0283)		GGTGTCCTTTCTGGTATTGTA	0.493																																					p.R103K		Atlas-SNP	.											.	KLHDC4	45	.	0			c.G308A						.						193	178	183					16																	87788861		2198	4300	6498	SO:0001583	missense	54758	exon4			TCCTTTCTGGTAT	AK001742	CCDS10963.1, CCDS54050.1, CCDS54051.1	16q24	2008-02-05			ENSG00000104731	ENSG00000104731			25272	protein-coding gene	gene with protein product							Standard	NM_001184854		Approved	DKFZp434G0522	uc002fki.3	Q8TBB5	OTTHUMG00000137657	ENST00000270583.5:c.308G>A	chr16.hg19:g.87788861C>T	ENSP00000270583:p.Arg103Lys	238.0	0.0		237.0	67.0	NM_001184856	D3DUN3|D3DUN4|D3DUN5|Q96F29|Q9BVN3	Missense_Mutation	SNP	ENST00000270583.5	hg19	CCDS10963.1	.	.	.	.	.	.	.	.	.	.	C	5.638	0.302437	0.10678	.	.	ENSG00000104731	ENST00000270583;ENST00000347925;ENST00000353170	T;T;T	0.64991	1.1;1.1;-0.13	5.12	2.11	0.27256	Kelch-type beta propeller (1);	0.265537	0.42964	N	0.000624	T	0.32315	0.0825	N	0.10733	0.035	0.37504	D	0.916887	B;B;B	0.11235	0.001;0.004;0.001	B;B;B	0.14023	0.002;0.01;0.007	T	0.30995	-0.9959	10	0.02654	T	1	-12.9156	7.8256	0.29313	0.0:0.6769:0.0:0.3231	.	46;103;103	Q8TBB5-2;Q8TBB5-3;Q8TBB5	.;.;KLDC4_HUMAN	K	103;103;46	ENSP00000270583:R103K;ENSP00000325717:R103K;ENSP00000262530:R46K	ENSP00000270583:R103K	R	-	2	0	KLHDC4	86346362	0.981000	0.34729	0.073000	0.20177	0.067000	0.16453	1.371000	0.34250	0.193000	0.20303	0.561000	0.74099	AGA	.	.		0.493	KLHDC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269109.2	NM_017566		T	87788861	C	T	87788861	3	4	271	1	0	0	0	0	1	0	0	0	8367	913	32	3	1286	3	KLHDC4	16	87788861	Missense_Mutation	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10	12525395	87788861	2565892	69	39416										
MNT	4335	hgsc.bcm.edu	37	chr17	2290884	2290884	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	ctggggacgatggctcagctTaggtgggcccaggcccgccc	16	14	1	0			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr17:2290884T>C	ENST00000174618.4	-	6	1465	c.1060A>G	c.(1060-1062)Aag>Gag	p.K354E	RP1-59D14.1_ENST00000571775.1_RNA|MNT_ENST00000575374.1_5'UTR	NM_020310.2	NP_064706.1	Q99583	MNT_HUMAN	MAX network transcriptional repressor	354					cell aging (GO:0007569)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of cell cycle (GO:0051726)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			endometrium(4)|large_intestine(5)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	12				Colorectal(2;1.37e-05)|READ - Rectum adenocarcinoma(2;8.68e-05)		TGGCTCAGCTTAGGTGGGCCC	0.677																																					p.K354E		Atlas-SNP	.											.	MNT	35	.	0			c.A1060G						.						128	143	138					17																	2290884		2200	4295	6495	SO:0001583	missense	4335	exon6			TCAGCTTAGGTGG	Y13444	CCDS11018.1	17p13.3	2013-11-15	2013-11-15		ENSG00000070444	ENSG00000070444		"MAX dimerization proteins", "Basic helix-loop-helix proteins"	7188	protein-coding gene	gene with protein product	"myc antagonist", "Max-interacting protein"	603039	"MAX binding protein", "MNT, MAX dimerization protein"			9598315	Standard	NM_020310		Approved	ROX, MXD6, MAD6, bHLHd3	uc002fur.3	Q99583	OTTHUMG00000090603	ENST00000174618.4:c.1060A>G	chr17.hg19:g.2290884T>C	ENSP00000174618:p.Lys354Glu	107.0	0.0		71.0	4.0	NM_020310	A8K6D1|D3DTI7|Q1ED38	Missense_Mutation	SNP	ENST00000174618.4	hg19	CCDS11018.1	.	.	.	.	.	.	.	.	.	.	T	15.25	2.776979	0.49786	.	.	ENSG00000070444	ENST00000174618;ENST00000404961	D	0.81579	-1.51	4.69	4.69	0.59074	.	0.417624	0.22887	N	0.054435	T	0.81108	0.4754	L	0.51422	1.61	0.32914	D	0.514858	D	0.59357	0.985	P	0.55923	0.787	T	0.82402	-0.0475	10	0.30078	T	0.28	-16.5808	8.119	0.30961	0.0:0.0915:0.0:0.9085	.	354	Q99583	MNT_HUMAN	E	354	ENSP00000174618:K354E	ENSP00000174618:K354E	K	-	1	0	MNT	2237634	0.997000	0.39634	1.000000	0.80357	0.998000	0.95712	1.680000	0.37607	1.749000	0.51849	0.482000	0.46254	AAG	.	.		0.677	MNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207158.1	NM_020310		C	2290884	T	C	2290884	3	2	271	1	0	0	0	0	1	0	0	0	9687	1763	61	2	692	2	MNT	17	2290884	Missense_Mutation	SNP	T	TCGA-FV-A4ZQ-01A-11D-A25V-10		2290884	78904326	70	39417										
TP53	7157	hgsc.bcm.edu	37	chr17	7577141	7577141	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	gcacctcaaagctgttccgtCccagtagattaccactactc	6	15	1	1	rs193920774		TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr17:7577141C>A	ENST00000269305.4	-	8	986	c.797G>T	c.(796-798)gGa>gTa	p.G266V	TP53_ENST00000359597.4_Missense_Mutation_p.G266V|TP53_ENST00000445888.2_Missense_Mutation_p.G266V|TP53_ENST00000420246.2_Missense_Mutation_p.G266V|TP53_ENST00000413465.2_Intron|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.G266V	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	266	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		G -> A (in sporadic cancers; somatic mutation).|G -> E (in sporadic cancers; somatic mutation).|G -> R (in sporadic cancers; somatic mutation).|G -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.G266E(50)|p.G266V(42)|p.0?(8)|p.?(3)|p.G266fs*79(3)|p.G262_F270delGNLLGRNSF(2)|p.G266A(2)|p.G266_E271delGRNSFE(2)|p.G262_S269delGNLLGRNS(2)|p.G266fs*4(1)|p.G266T(1)|p.L265_K305del41(1)|p.E258fs*71(1)|p.L265_R267delLGR(1)|p.G266_N268delGRN(1)|p.G262fs*2(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCTGTTCCGTCCCAGTAGATT	0.517		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.G266V	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,NS,carcinoma,0,1	TP53	33396	.	121	Substitution - Missense(95)|Deletion - In frame(9)|Whole gene deletion(8)|Deletion - Frameshift(6)|Unknown(3)	lung(23)|oesophagus(10)|haematopoietic_and_lymphoid_tissue(10)|large_intestine(9)|breast(9)|upper_aerodigestive_tract(8)|ovary(8)|urinary_tract(7)|pancreas(6)|skin(5)|central_nervous_system(4)|stomach(4)|bone(4)|liver(4)|endometrium(3)|vulva(1)|kidney(1)|thyroid(1)|cervix(1)|eye(1)|genital_tract(1)|biliary_tract(1)	c.G797T						.						50	44	46					17																	7577141		2203	4300	6503	SO:0001583	missense	7157	exon8	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	TTCCGTCCCAGTA	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.797G>T	chr17.hg19:g.7577141C>A	ENSP00000269305:p.Gly266Val	66.0	0.0		76.0	39.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.388215	0.82902	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99900	-7.62;-7.62;-7.62;-7.62;-7.62;-7.62	5.13	5.13	0.70059	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99906	0.9955	M	0.92367	3.3	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;0.999;0.999	D	0.96190	0.9137	10	0.87932	D	0	-13.0798	16.1198	0.81342	0.0:1.0:0.0:0.0	.	266;266;266;266	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	V	266;266;266;266;266;255;134	ENSP00000352610:G266V;ENSP00000269305:G266V;ENSP00000398846:G266V;ENSP00000391127:G266V;ENSP00000391478:G266V;ENSP00000425104:G134V	ENSP00000269305:G266V	G	-	2	0	TP53	7517866	1.000000	0.71417	0.996000	0.52242	0.744000	0.42396	7.587000	0.82613	2.667000	0.90743	0.462000	0.41574	GGA	.	.		0.517	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577141	C	A	7577141	3	1	271	1	0	0	0	0	1	0	0	0	16396	855	30	3	489	3	TP53	17	7577141	Missense_Mutation	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10	5286257	7577141	73618069	71	39418										
SSH2	85464	hgsc.bcm.edu	37	chr17	28022497	28022497	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	cagcctgatgttgtcttctgGgcggagtaaaatgaacattg	12	7	2	2			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr17:28022497G>C	ENST00000269033.3	-	4	407	c.256C>G	c.(256-258)Cca>Gca	p.P86A	SSH2_ENST00000324677.7_5'UTR|RP11-68I3.2_ENST00000581474.1_RNA|SSH2_ENST00000540801.1_Missense_Mutation_p.P113A	NM_001282129.1|NM_033389.2	NP_001269058.1|NP_203747.2	Q76I76	SSH2_HUMAN	slingshot protein phosphatase 2	86					actin cytoskeleton organization (GO:0030036)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of lamellipodium assembly (GO:0010591)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)	actin binding (GO:0003779)|DNA binding (GO:0003677)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)		SSH2/SUZ12(2)	breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TTGTCTTCTGGGCGGAGTAAA	0.373																																					p.P86A		Atlas-SNP	.											.	SSH2	107	.	0			c.C256G						.						178	147	158					17																	28022497		2203	4300	6503	SO:0001583	missense	85464	exon4			CTTCTGGGCGGAG	AB072359	CCDS11253.1, CCDS74024.1	17q11.2	2013-03-05	2013-03-05		ENSG00000141298	ENSG00000141298		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"	30580	protein-coding gene	gene with protein product		606779	"slingshot homolog 2 (Drosophila)"			11832213, 11214970	Standard	XM_005258059		Approved	KIAA1725	uc002heo.1	Q76I76	OTTHUMG00000132752	ENST00000269033.3:c.256C>G	chr17.hg19:g.28022497G>C	ENSP00000269033:p.Pro86Ala	142.0	0.0		130.0	74.0	NM_033389	Q8TDB5|Q8WYL1|Q8WYL2|Q96F40|Q96H36|Q9C0D8	Missense_Mutation	SNP	ENST00000269033.3	hg19	CCDS11253.1	.	.	.	.	.	.	.	.	.	.	G	12.81	2.050766	0.36181	.	.	ENSG00000141298	ENST00000269033;ENST00000540801;ENST00000394848;ENST00000324677	T;T	0.36699	1.24;1.24	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.44871	0.1314	M	0.71581	2.175	0.58432	D	0.999998	P;B;B;P;P	0.41624	0.72;0.041;0.154;0.694;0.757	P;B;B;B;B	0.47251	0.542;0.033;0.048;0.379;0.436	T	0.40194	-0.9576	10	0.05525	T	0.97	-11.9289	18.171	0.89745	0.0:0.0:1.0:0.0	.	113;86;93;86;86	F5H527;Q76I76-3;G5E957;Q76I76-4;Q76I76	.;.;.;.;SSH2_HUMAN	A	86;113;86;93	ENSP00000269033:P86A;ENSP00000444743:P113A	ENSP00000269033:P86A	P	-	1	0	SSH2	25046623	1.000000	0.71417	1.000000	0.80357	0.789000	0.44602	6.811000	0.75221	2.576000	0.86940	0.650000	0.86243	CCA	.	.		0.373	SSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256116.1	NM_033389		C	28022497	G	C	28022497	3	2	271	1	0	0	0	0	1	0	0	0	15200	1232	43	4	4063	4	SSH2	17	28022497	Missense_Mutation	SNP	G	TCGA-FV-A4ZQ-01A-11D-A25V-10	20445356	28022497	53172713	72	39419										
CDC27	996	hgsc.bcm.edu	37	chr17	45234594	45234729	+	Splice_Site	DEL	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	-													0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	cactagaatataagacacttAcaattgtgtcctggggtgtt					rs149474782|rs113608268|rs370849730|rs78395997|rs76624491|rs370261409|rs75353677|rs368304141|rs376818791|rs372212798|rs375653477|rs374472811|rs76359747|rs147617501|rs374614181|rs78108688|rs142987740|rs143453365|rs75990396|rs144985864|rs367644695|rs202182614|rs139751753|rs11570485|rs372926889|rs140171160|rs368750026|rs201098929|rs199899451|rs75175938|rs200340309|rs537990668	byFrequency	TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr17:45234594_45234729delCTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	ENST00000066544.3	-	6	590_724	c.497_631delAGTTCTTACGGAAACACCCCAGGACACAATTGTAAGTGTCTTATATTCTAGTGTTCAAAATATTATGAAAACTACAAAGAATGATCTGAACTAAATAATATATTGTGAATGACTTGGTAGAAATTTTCTGTTTCAG	c.(496-633)cagttcttacggaaacaccccaggacacaattgtaagtgtcttatattctagtgttcaaaatattatgaaaactacaaagaatgatctgaactaaataatatattgtgaatgacttggtagaaattttctgtttcaga>cga	p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF166fs	CDC27_ENST00000528748.1_5'UTR|CDC27_ENST00000446365.2_Splice_Site_p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF105fs|CDC27_ENST00000531206.1_Splice_Site_p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF166fs|CDC27_ENST00000527547.1_Splice_Site_p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF166fs	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	166					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)	p.T167T(7)|p.T171T(3)|p.V201I(2)|p.E199E(2)|p.T200T(2)|p.L173S(1)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACTGTCTCAGGCTGTCTGTGAGATAAACTATGATTAGGTACTTGTGTTGTGCAAGAGTTGGGCAGACAGTTGCTAAAGTTCTGTAAAGATGTGAATTTAAATGTTTGGTCAGGATC	0.342																																					p.201_211del		Pindel	.											.	CDC27	337	.	17	Substitution - coding silent(14)|Substitution - Missense(3)	large_intestine(6)|prostate(6)|kidney(4)|NS(1)	c.601_631del						.																																			SO:0001630	splice_region_variant	996	exon6			.	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1728	protein-coding gene	gene with protein product	"anaphase promoting complex subunit 3"	116946	"cell division cycle 27", "cell division cycle 27 homolog (S. cerevisiae)"	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.631-104AGTTCTTACGGAAACACCCCAGGACACAATTGTAAGTGTCTTATATTCTAGTGTTCAAAATATTATGAAAACTACAAAGAATGATCTGAACTAAATAATATATTGTGAATGACTTGGTAGAAATTTTCTGTTTCAG>-	chr17.hg19:g.45234594_45234729delCTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT		107.0	0.0		100.0	12.0	NM_001114091	G3V1C4|Q16349|Q96F35	Frame_Shift_Del	DEL	ENST00000066544.3	hg19	CCDS11509.1																																																																																			.	.		0.342	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		Frame_Shift_Del	-	45234729	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	-	45234594	8	5	271	1	0	1	0	1	0	0	1	0	3068	405	14	0	1916	0	CDC27	17	45234594	Splice_Site	DEL	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	TCGA-FV-A4ZQ-01A-11D-A25V-10	17212097	45234594	35960616	73	39420										
APOH	350	hgsc.bcm.edu	37	chr17	64210647	64210647	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	tagctacacttcttttccttAtttttgcagaagaaagaaac	5	8	1	3			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr17:64210647A>G	ENST00000205948.6	-	7	943	c.906T>C	c.(904-906)aaT>aaC	p.N302N		NM_000042.2	NP_000033.2	P02749	APOH_HUMAN	apolipoprotein H (beta-2-glycoprotein I)	302	Sushi-like.				blood coagulation, intrinsic pathway (GO:0007597)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood coagulation (GO:0030195)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of myeloid cell apoptotic process (GO:0033033)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|plasminogen activation (GO:0031639)|positive regulation of blood coagulation (GO:0030194)|positive regulation of lipoprotein lipase activity (GO:0051006)|regulation of fibrinolysis (GO:0051917)|triglyceride metabolic process (GO:0006641)|triglyceride transport (GO:0034197)	cell surface (GO:0009986)|chylomicron (GO:0042627)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipid binding (GO:0005543)			central_nervous_system(1)|kidney(3)|large_intestine(5)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(6;9.74e-08)			TCTTTTCCTTATTTTTGCAGA	0.388																																					p.N302N	Melanoma(155;624 1882 16869 48804 51309)	Atlas-SNP	.											.	APOH	45	.	0			c.T906C						.						170	152	158					17																	64210647		2203	4300	6503	SO:0001819	synonymous_variant	350	exon7			TTCCTTATTTTTG		CCDS11663.1	17q24.2	2013-01-24				ENSG00000091583		"Apolipoproteins"	616	protein-coding gene	gene with protein product	"beta-2-glycoprotein I"	138700		B2G1		1582254	Standard	NM_000042		Approved	BG	uc002jfn.4	P02749		ENST00000205948.6:c.906T>C	chr17.hg19:g.64210647A>G		196.0	0.0		187.0	37.0	NM_000042	B2R9M3|Q9UCN7	Silent	SNP	ENST00000205948.6	hg19	CCDS11663.1																																																																																			.	.		0.388	APOH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446926.1	NM_000042		G	64210647	A	G	64210647	2	3	271	1	0	0	0	0	0	0	0	1	804	446	16	2		2	APOH	17	64210647	Silent	SNP	A	TCGA-FV-A4ZQ-01A-11D-A25V-10	18976053	64210647	16984563	74	39421										
KPNA2	3838	hgsc.bcm.edu	37	chr17	66038335	66038335	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	atctgcttgggcactcactaAcattgcttctgggacatcag	9	11	4	0			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr17:66038335A>G	ENST00000537025.2	+	5	1057	c.437A>G	c.(436-438)aAc>aGc	p.N146S	KPNA2_ENST00000330459.3_Missense_Mutation_p.N146S			P52292	IMA1_HUMAN	karyopherin alpha 2 (RAG cohort 1, importin alpha 1)	146	NLS binding site (major). {ECO:0000250}.				cytokine-mediated signaling pathway (GO:0019221)|DNA metabolic process (GO:0006259)|NLS-bearing protein import into nucleus (GO:0006607)|regulation of DNA recombination (GO:0000018)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone deacetylase binding (GO:0042826)|nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)			breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|kidney(2)|lung(9)|prostate(1)|urinary_tract(2)	22	all_cancers(12;1.18e-09)		BRCA - Breast invasive adenocarcinoma(8;1.03e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)			GCACTCACTAACATTGCTTCT	0.473																																					p.N146S		Atlas-SNP	.											.	KPNA2	55	.	0			c.A437G						.						199	192	194					17																	66038335		2203	4298	6501	SO:0001583	missense	3838	exon5			TCACTAACATTGC	U09559	CCDS32713.1	17q24.2	2013-02-14						"Importins", "Armadillo repeat containing"	6395	protein-coding gene	gene with protein product		600685		RCH1		8016130, 7754385	Standard	NM_002266		Approved	SRP1alpha, IPOA1, QIP2	uc002jgk.3	P52292		ENST00000537025.2:c.437A>G	chr17.hg19:g.66038335A>G	ENSP00000438483:p.Asn146Ser	169.0	1.0		137.0	95.0	NM_002266	B9EJD6|Q53YE3|Q9BRU5	Missense_Mutation	SNP	ENST00000537025.2	hg19	CCDS32713.1	.	.	.	.	.	.	.	.	.	.	A	19.63	3.864378	0.71949	.	.	ENSG00000182481	ENST00000330459;ENST00000537025	D;D	0.83506	-1.73;-1.73	5.71	5.71	0.89125	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	U	0.000000	D	0.90686	0.7078	H	0.94808	3.585	0.80722	D	1	P	0.36683	0.565	P	0.44673	0.457	D	0.92305	0.5853	10	0.87932	D	0	.	15.9965	0.80250	1.0:0.0:0.0:0.0	.	146	P52292	IMA2_HUMAN	S	146	ENSP00000332455:N146S;ENSP00000438483:N146S	ENSP00000332455:N146S	N	+	2	0	KPNA2	63468797	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	9.230000	0.95299	2.174000	0.68829	0.460000	0.39030	AAC	.	.		0.473	KPNA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448111.1	NM_002266		G	66038335	A	G	66038335	3	3	271	1	0	0	0	0	1	0	0	0	8439	43	2	2	451	2	KPNA2	17	66038335	Missense_Mutation	SNP	A	TCGA-FV-A4ZQ-01A-11D-A25V-10	1827688	66038335	15156875	75	39422										
EVPL	2125	hgsc.bcm.edu	37	chr17	74006234	74006234	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	cctctccacctgggtgacctCcttggtcagcagatgaggct	11	14	2	3			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr17:74006234C>G	ENST00000301607.3	-	22	3305	c.3052G>C	c.(3052-3054)Gag>Cag	p.E1018Q	EVPL_ENST00000586740.1_Missense_Mutation_p.E1040Q	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	1018	Central fibrous rod domain.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						TGGGTGACCTCCTTGGTCAGC	0.667																																					p.E1018Q		Atlas-SNP	.											.	EVPL	155	.	0			c.G3052C						.						64	69	67					17																	74006234		2203	4299	6502	SO:0001583	missense	2125	exon22			TGACCTCCTTGGT	U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.3052G>C	chr17.hg19:g.74006234C>G	ENSP00000301607:p.Glu1018Gln	182.0	0.0		120.0	73.0	NM_001988	A0AUV5	Missense_Mutation	SNP	ENST00000301607.3	hg19	CCDS11737.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.212595	0.79240	.	.	ENSG00000167880	ENST00000301607	T	0.68624	-0.34	5.04	5.04	0.67666	.	0.104139	0.64402	D	0.000005	D	0.82912	0.5140	M	0.83223	2.63	0.58432	D	0.999992	P;D	0.89917	0.924;1.0	P;D	0.67103	0.505;0.949	D	0.85308	0.1077	10	0.62326	D	0.03	-43.8629	18.7358	0.91753	0.0:1.0:0.0:0.0	.	1040;1018	B7ZLH8;Q92817	.;EVPL_HUMAN	Q	1018	ENSP00000301607:E1018Q	ENSP00000301607:E1018Q	E	-	1	0	EVPL	71517829	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	7.776000	0.85560	2.501000	0.84356	0.491000	0.48974	GAG	.	.		0.667	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988		G	74006234	C	G	74006234	3	3	271	1	0	0	0	0	1	0	0	0	5294	864	30	4	3053	4	EVPL	17	74006234	Missense_Mutation	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10	7967899	74006234	7188976	76	39423										
C19orf29	58509	hgsc.bcm.edu	37	chr19	3623771	3623771	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	ccatgtactcctcaccccagCccatcttctcccgcttcttg	4	20	4	0			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr19:3623771C>A	ENST00000429344.2	-	2	609	c.557G>T	c.(556-558)gGc>gTc	p.G186V	CACTIN_ENST00000221899.3_Missense_Mutation_p.G118V|CACTIN_ENST00000248420.5_Missense_Mutation_p.G186V	NM_001080543.1	NP_001074012.1	Q8WUQ7	CATIN_HUMAN	cactin, spliceosome C complex subunit	186					cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|multicellular organismal development (GO:0007275)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)										CTCACCCCAGCCCATCTTCTC	0.632																																					p.G186V		Atlas-SNP	.											.	.	.	.	0			c.G557T						.						47	56	53					19																	3623771		2125	4233	6358	SO:0001583	missense	58509	exon2			CCCCAGCCCATCT	BC019848	CCDS45920.1	19p13.3	2012-06-08	2012-06-08	2012-06-08	ENSG00000105298	ENSG00000105298			29938	protein-coding gene	gene with protein product	"NY REN 24 antigen", "functional spliceosome-associated protein c", "cactin homolog (Drosophila)"		"chromosome 19 open reading frame 29"	C19orf29		8619474, 9110174, 21429463, 20829348	Standard	NM_001080543		Approved	NY-REN-24, fSAPc, cactin	uc002lyh.3	Q8WUQ7		ENST00000429344.2:c.557G>T	chr19.hg19:g.3623771C>A	ENSP00000415078:p.Gly186Val	177.0	0.0		110.0	40.0	NM_021231	A6NNA9|A9UL12|O75229|Q7LE08|Q9BTA6|Q9Y5A4	Missense_Mutation	SNP	ENST00000429344.2	hg19	CCDS45920.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808013	0.90707	.	.	ENSG00000105298	ENST00000429344;ENST00000248420;ENST00000221899	.	.	.	4.77	4.77	0.60923	.	0.000000	0.85682	D	0.000000	T	0.80037	0.4550	M	0.81112	2.525	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.82028	-0.0660	9	0.49607	T	0.09	.	16.8032	0.85619	0.0:1.0:0.0:0.0	.	186	Q8WUQ7	CS029_HUMAN	V	186;186;118	.	ENSP00000221899:G118V	G	-	2	0	C19orf29	3574771	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.721000	0.84768	2.204000	0.70986	0.561000	0.74099	GGC	.	.		0.632	CACTIN-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457370.2			A	3623771	C	A	3623771	3	1	271	1	0	0	0	0	1	0	0	0	1920	739	26	3	1755	3	C19orf29	19	3623771	Missense_Mutation	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10		3623771	55505212	77	39424										
JAK3	3718	hgsc.bcm.edu	37	chr19	17947999	17947999	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	cggtacgacacttggctcatCaagctcgctgcttccaggaa	10	13	2	0			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr19:17947999C>T	ENST00000527670.1	-	12	1754	c.1725G>A	c.(1723-1725)ttG>ttA	p.L575L	JAK3_ENST00000534444.1_Silent_p.L575L|JAK3_ENST00000458235.1_Silent_p.L575L|JAK3_ENST00000526008.1_5'Flank			P52333	JAK3_HUMAN	Janus kinase 3	575	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell differentiation (GO:0030183)|enzyme linked receptor protein signaling pathway (GO:0007167)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of dendritic cell cytokine production (GO:0002731)|negative regulation of FasL biosynthetic process (GO:0045221)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of T cell activation (GO:0050868)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|negative regulation of thymocyte apoptotic process (GO:0070244)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of T cell apoptotic process (GO:0070232)|response to interleukin-15 (GO:0070672)|response to interleukin-2 (GO:0070669)|response to interleukin-4 (GO:0070670)|response to interleukin-9 (GO:0071104)|STAT protein import into nucleus (GO:0007262)|T cell homeostasis (GO:0043029)|tyrosine phosphorylation of STAT protein (GO:0007260)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(85)|kidney(4)|large_intestine(11)|lung(22)|ovary(3)|prostate(5)|skin(1)|stomach(2)|upper_aerodigestive_tract(5)	147					Tofacitinib(DB08895)	CTTGGCTCATCAAGCTCGCTG	0.587		2	Mis		"acute megakaryocytic leukemia, ETP ALL"																																p.L575L		Atlas-SNP	.		Dom	yes		19	19p13.1	3718	Janus kinase 3		L	.	JAK3	341	.	0			c.G1725A						.						45	34	37					19																	17947999		2200	4293	6493	SO:0001819	synonymous_variant	3718	exon13			GCTCATCAAGCTC	U31601	CCDS12366.1	19p13-p12	2014-09-17	2009-04-23		ENSG00000105639	ENSG00000105639	2.7.10.1		6193	protein-coding gene	gene with protein product	"tyrosine-protein kinase JAK3", "leukocyte Janus kinase"	600173				8921370, 9226382	Standard	NM_000215		Approved	L-JAK, JAKL, LJAK, JAK3_HUMAN, JAK-3	uc002nhn.4	P52333	OTTHUMG00000165648	ENST00000527670.1:c.1725G>A	chr19.hg19:g.17947999C>T		94.0	0.0		130.0	26.0	NM_000215	Q13259|Q13260|Q13611|Q8N1E8|Q99699|Q9Y6S2	Silent	SNP	ENST00000527670.1	hg19	CCDS12366.1																																																																																			.	.		0.587	JAK3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385549.1	NM_000215		T	17947999	C	T	17947999	2	4	271	1	0	0	0	0	0	0	0	1	7948	825	29	3		3	JAK3	19	17947999	Silent	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10	14324228	17947999	41180984	78	39425										
EPS8L1	54869	hgsc.bcm.edu	37	chr19	55598089	55598089	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	ttcccgcctgcagagaaattCtcccagatgctcatcgtcaa	7	14	3	2			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr19:55598089C>G	ENST00000201647.6	+	18	1841	c.1785C>G	c.(1783-1785)ttC>ttG	p.F595L	EPS8L1_ENST00000540810.1_Missense_Mutation_p.F531L|EPS8L1_ENST00000586329.1_Intron|EPS8L1_ENST00000245618.5_Missense_Mutation_p.F468L|EPS8L1_ENST00000588359.1_Missense_Mutation_p.F281L	NM_133180.2	NP_573441.2	Q8TE68	ES8L1_HUMAN	EPS8-like 1	595					positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|T cell receptor binding (GO:0042608)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|prostate(1)	12			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		CAGAGAAATTCTCCCAGATGC	0.746																																					p.F595L	Ovarian(149;255 1863 3636 27051 29647)	Atlas-SNP	.											.	EPS8L1	122	.	0			c.C1785G						.						11	12	12					19																	55598089		2154	4213	6367	SO:0001583	missense	54869	exon18			GAAATTCTCCCAG	AK057052	CCDS12914.1, CCDS12915.1	19q13.42	2008-02-05				ENSG00000131037			21295	protein-coding gene	gene with protein product		614987				12620401	Standard	NM_133180		Approved	FLJ20258, DRC3, MGC23164, MGC4642	uc002qis.4	Q8TE68		ENST00000201647.6:c.1785C>G	chr19.hg19:g.55598089C>G	ENSP00000201647:p.Phe595Leu	67.0	0.0		49.0	10.0	NM_133180	Q71RE2|Q8NC10|Q96BB7|Q9BSQ2|Q9GZQ2|Q9NXH0	Missense_Mutation	SNP	ENST00000201647.6	hg19	CCDS12914.1	.	.	.	.	.	.	.	.	.	.	C	8.366	0.834156	0.16820	.	.	ENSG00000131037	ENST00000201647;ENST00000540810;ENST00000245618;ENST00000539118	T;T;T	0.05258	3.71;3.49;3.47	4.13	0.543	0.17179	.	5.188460	0.00931	N	0.002708	T	0.07188	0.0182	L	0.43152	1.355	0.40159	D	0.97704	B;B;B	0.21606	0.058;0.01;0.017	B;B;B	0.22880	0.042;0.005;0.006	T	0.43114	-0.9411	10	0.11485	T	0.65	-15.6465	7.2393	0.26088	0.0:0.6868:0.0:0.3132	.	374;468;595	Q8TE68-4;Q8TE68-2;Q8TE68	.;.;ES8L1_HUMAN	L	595;531;468;281	ENSP00000201647:F595L;ENSP00000437541:F531L;ENSP00000245618:F468L	ENSP00000201647:F595L	F	+	3	2	EPS8L1	60289901	0.922000	0.31269	0.986000	0.45419	0.727000	0.41649	0.917000	0.28665	0.098000	0.17522	0.305000	0.20034	TTC	.	.		0.746	EPS8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451713.1	NM_017729		G	55598089	C	G	55598089	3	3	271	1	0	0	0	0	1	0	0	0	5197	912	32	4	1903	4	EPS8L1	19	55598089	Missense_Mutation	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10	37650090	55598089	3530894	79	39426										
PTPRT	11122	hgsc.bcm.edu	37	chr20	41101120	41101120	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	ctatggcagcgggtcaccgcGtagccgaagggctcccactg	14	14	1	0	rs376152261		TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr20:41101120G>A	ENST00000373187.1	-	8	1235	c.1236C>T	c.(1234-1236)taC>taT	p.Y412Y	PTPRT_ENST00000373190.1_Silent_p.Y412Y|PTPRT_ENST00000373193.3_Silent_p.Y412Y|PTPRT_ENST00000356100.2_Silent_p.Y412Y|PTPRT_ENST00000373201.1_Silent_p.Y412Y|PTPRT_ENST00000373184.1_Silent_p.Y412Y|PTPRT_ENST00000373198.4_Silent_p.Y412Y			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	412	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.		Y -> F (in a colorectal cancer). {ECO:0000269|PubMed:15155950}.		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)	p.Y412*(1)		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)				GGGTCACCGCGTAGCCGAAGG	0.592																																					p.Y412Y		Atlas-SNP	.											PTPRT,colon,carcinoma,0,2	PTPRT	372	.	1	Substitution - Nonsense(1)	lung(1)	c.C1236T						.	G	,	1,4161		0,1,2080	52	60	57		1236,1236	-4.6	0.5	20		57	1,8477		0,1,4238	no	coding-synonymous,coding-synonymous	PTPRT	NM_007050.5,NM_133170.3	,	0,2,6318	AA,AG,GG		0.0118,0.024,0.0158	,	412/1442,412/1461	41101120	2,12638	2081	4239	6320	SO:0001819	synonymous_variant	11122	exon8			CACCGCGTAGCCG	AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.1236C>T	chr20.hg19:g.41101120G>A		138.0	0.0		231.0	24.0	NM_007050	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Silent	SNP	ENST00000373187.1	hg19	CCDS42874.1																																																																																			.	.		0.592	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			A	41101120	G	A	41101120	2	1	271	1	0	0	0	0	0	0	0	1	12827	1140	40	1		1	PTPRT	20	41101120	Silent	SNP	G	TCGA-FV-A4ZQ-01A-11D-A25V-10		41101120	21924400	80	39427										
ZNF512B	57473	hgsc.bcm.edu	37	chr20	62591366	62591366	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	ggccacaggctcctctggggTccgctccttgggctttcggc	14	15	1	0			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr20:62591366T>C	ENST00000450537.1	-	17	2614	c.2554A>G	c.(2554-2556)Acc>Gcc	p.T852A	ZNF512B_ENST00000369888.1_Missense_Mutation_p.T852A|ZNF512B_ENST00000217130.3_Missense_Mutation_p.T852A			Q96KM6	Z512B_HUMAN	zinc finger protein 512B	852					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(4)|skin(1)	33	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					TCCTCTGGGGTCCGCTCCTTG	0.647																																					p.T852A		Atlas-SNP	.											.	ZNF512B	72	.	0			c.A2554G						.						63	71	68					20																	62591366		2203	4300	6503	SO:0001583	missense	57473	exon17			CTGGGGTCCGCTC	AB033022	CCDS13548.1	20q13.33	2011-02-09			ENSG00000196700	ENSG00000196700			29212	protein-coding gene	gene with protein product						10574462	Standard	NM_020713		Approved	GM632, MGC149845, MGC149846	uc002yhl.2	Q96KM6	OTTHUMG00000033008	ENST00000450537.1:c.2554A>G	chr20.hg19:g.62591366T>C	ENSP00000393795:p.Thr852Ala	52.0	0.0		56.0	10.0	NM_020713	Q08AK9|Q9ULM4	Missense_Mutation	SNP	ENST00000450537.1	hg19	CCDS13548.1	.	.	.	.	.	.	.	.	.	.	T	7.460	0.644450	0.14451	.	.	ENSG00000196700	ENST00000369888;ENST00000450537;ENST00000217130	T;T;T	0.21361	2.01;2.01;2.01	4.38	-1.14	0.09741	.	0.321381	0.28694	N	0.014442	T	0.08891	0.0220	N	0.14661	0.345	0.19775	N	0.999956	B	0.02656	0.0	B	0.01281	0.0	T	0.16394	-1.0404	10	0.36615	T	0.2	-4.0453	3.8994	0.09154	0.2209:0.0:0.3466:0.4325	.	852	Q96KM6	Z512B_HUMAN	A	852	ENSP00000358904:T852A;ENSP00000393795:T852A;ENSP00000217130:T852A	ENSP00000217130:T852A	T	-	1	0	ZNF512B	62061810	1.000000	0.71417	0.005000	0.12908	0.040000	0.13550	0.936000	0.28938	-0.596000	0.05821	-0.755000	0.03482	ACC	.	.		0.647	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713		C	62591366	T	C	62591366	3	2	271	1	0	0	0	0	1	0	0	0	17972	1667	58	2	128	2	ZNF512B	20	62591366	Missense_Mutation	SNP	T	TCGA-FV-A4ZQ-01A-11D-A25V-10	21490246	62591366	434154	81	39428										
C21orf33	8209	hgsc.bcm.edu	37	chr21	45553649	45553649	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	cattcacgtccctgtcccccGgcggtcggacgccttcccag	10	19	1	0			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr21:45553649G>A	ENST00000291577.6	+	1	163	c.70G>A	c.(70-72)Ggc>Agc	p.G24S	C21orf33_ENST00000348499.5_Missense_Mutation_p.G24S|C21orf33_ENST00000493883.1_3'UTR|C21orf33_ENST00000427803.2_Missense_Mutation_p.G24S	NM_004649.6	NP_004640	P30042	ES1_HUMAN	chromosome 21 open reading frame 33	24						mitochondrion (GO:0005739)				NS(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	8				STAD - Stomach adenocarcinoma(101;0.168)|Colorectal(79;0.191)		CCTGTCCCCCGGCGGTCGGAC	0.716																																					p.G24S		Atlas-SNP	.											.	C21orf33	23	.	0			c.G70A						.						29	25	26					21																	45553649		2193	4292	6485	SO:0001583	missense	8209	exon1			TCCCCCGGCGGTC	Y07572	CCDS33580.1, CCDS33581.1	21q22.3	2008-07-29			ENSG00000160221	ENSG00000160221			1273	protein-coding gene	gene with protein product		601659				9150728, 8975701	Standard	NM_004649		Approved	KNP-Ia, GT335, ES1, HES1, D21S2048E, KNPI, KNPH, KNP-I	uc002zec.4	P30042	OTTHUMG00000086916	ENST00000291577.6:c.70G>A	chr21.hg19:g.45553649G>A	ENSP00000291577:p.Gly24Ser	54.0	0.0		13.0	9.0	NM_198155	A6NFJ6|A6NJY7|O00650|O00660|O15011|O15012|P55346|P78474|Q92505|Q92507	Missense_Mutation	SNP	ENST00000291577.6	hg19	CCDS33580.1	.	.	.	.	.	.	.	.	.	.	G	11.11	1.541740	0.27563	.	.	ENSG00000160221	ENST00000291577;ENST00000427803;ENST00000348499	T;T;T	0.31769	1.98;1.48;1.96	2.84	-5.5	0.02576	.	1.369470	0.04982	N	0.465762	T	0.17959	0.0431	L	0.29908	0.895	0.09310	N	1	B;B	0.17465	0.022;0.007	B;B	0.08055	0.003;0.002	T	0.18209	-1.0344	10	0.40728	T	0.16	0.0316	3.4514	0.07499	0.4881:0.0:0.1913:0.3206	.	24;24	P30042-2;P30042	.;ES1_HUMAN	S	24	ENSP00000291577:G24S;ENSP00000396655:G24S;ENSP00000344901:G24S	ENSP00000291577:G24S	G	+	1	0	C21orf33	44378077	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-2.220000	0.01217	-1.349000	0.02202	-0.339000	0.08088	GGC	.	.		0.716	C21orf33-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195824.1	NM_004649		A	45553649	G	A	45553649	3	1	271	1	0	0	0	0	1	0	0	0	2127	1116	39	1	72	1	C21orf33	21	45553649	Missense_Mutation	SNP	G	TCGA-FV-A4ZQ-01A-11D-A25V-10		45553649	2576246	82	39429										
MN1	4330	hgsc.bcm.edu	37	chr22	28193384	28193384	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	ctcattggcgtagctcgtgcTcacctcgtccgaggcgaact	11	14	2	0			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr22:28193384T>A	ENST00000302326.4	-	1	4102	c.3148A>T	c.(3148-3150)Agc>Tgc	p.S1050C		NM_002430.2	NP_002421.3	Q10571	MN1_HUMAN	meningioma (disrupted in balanced translocation) 1	1050					intramembranous ossification (GO:0001957)					NS(1)|breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	45						TAGCTCGTGCTCACCTCGTCC	0.637			T	ETV6	"AML, meningioma"																																p.S1050C		Atlas-SNP	.		Dom	yes		22	22q13	4330	meningioma (disrupted in balanced translocation) 1		"L, O"	.	MN1	122	.	0			c.A3148T						.						57	64	61					22																	28193384		2135	4227	6362	SO:0001583	missense	4330	exon1			TCGTGCTCACCTC	X82209	CCDS42998.1	22q12.1	2010-09-29			ENSG00000169184	ENSG00000169184			7180	protein-coding gene	gene with protein product	"probable tumor suppressor protein MN1"	156100	"meningioma chromosome region"	MGCR		7731706, 12569362	Standard	NM_002430		Approved	MGCR1-PEN, MGCR1	uc003adj.3	Q10571	OTTHUMG00000150975	ENST00000302326.4:c.3148A>T	chr22.hg19:g.28193384T>A	ENSP00000304956:p.Ser1050Cys	93.0	0.0		51.0	16.0	NM_002430	A9Z1V9	Missense_Mutation	SNP	ENST00000302326.4	hg19	CCDS42998.1	.	.	.	.	.	.	.	.	.	.	T	16.97	3.269105	0.59540	.	.	ENSG00000169184	ENST00000302326	T	0.54866	0.55	4.2	3.13	0.36017	.	0.110152	0.64402	D	0.000015	T	0.49201	0.1543	N	0.19112	0.55	0.30925	N	0.727574	D	0.65815	0.995	P	0.60415	0.874	T	0.50841	-0.8780	10	0.45353	T	0.12	-21.8263	8.8101	0.34963	0.0:0.094:0.0:0.906	.	1050	Q10571	MN1_HUMAN	C	1050	ENSP00000304956:S1050C	ENSP00000304956:S1050C	S	-	1	0	MN1	26523384	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.196000	0.58407	1.750000	0.51863	0.379000	0.24179	AGC	.	.		0.637	MN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320737.1	NM_002430		A	28193384	T	A	28193384	3	1	271	1	0	0	0	0	1	0	0	0	9682	1551	54	4	822	4	MN1	22	28193384	Missense_Mutation	SNP	T	TCGA-FV-A4ZQ-01A-11D-A25V-10		28193384	23111182	83	39430										
RPL3	6122	hgsc.bcm.edu	37	chr22	39709288	39709288	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	aaggtcaatcttctccagagCccgccgcttcgtctgcacca	8	16	4	1			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr22:39709288C>A	ENST00000216146.4	-	9	1248	c.1075G>T	c.(1075-1077)Gct>Tct	p.A359S	SNORD83A_ENST00000386747.1_RNA|SNORD83B_ENST00000386745.1_RNA|RPL3_ENST00000465618.1_5'UTR|RPL3_ENST00000401609.1_Missense_Mutation_p.A307S	NM_000967.3|NM_001033853.1	NP_000958.1|NP_001029025.1	P39023	RL3_HUMAN	ribosomal protein L3	359					cellular protein metabolic process (GO:0044267)|cellular response to interleukin-4 (GO:0071353)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			breast(1)|kidney(4)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	Melanoma(58;0.04)				Homoharringtonine(DB04865)	TTCTCCAGAGCCCGCCGCTTC	0.552																																					p.A359S		Atlas-SNP	.											.	RPL3	29	.	0			c.G1075T						.						32	32	32					22																	39709288		2203	4300	6503	SO:0001583	missense	6122	exon9			CCAGAGCCCGCCG	AB007166	CCDS13988.1	22q13	2011-04-06			ENSG00000100316	ENSG00000100316		"L ribosomal proteins"	10332	protein-coding gene	gene with protein product		604163				2891103, 9582194	Standard	NM_000967		Approved	L3	uc003axi.3	P39023	OTTHUMG00000151079	ENST00000216146.4:c.1075G>T	chr22.hg19:g.39709288C>A	ENSP00000346001:p.Ala359Ser	141.0	0.0		141.0	34.0	NM_000967	B2RDV9|Q15548|Q5I0G0	Missense_Mutation	SNP	ENST00000216146.4	hg19	CCDS13988.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.159945	0.78226	.	.	ENSG00000100316	ENST00000401609;ENST00000216146	T;T	0.42900	0.96;0.96	5.22	5.22	0.72569	Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	0.000000	0.85682	D	0.000000	T	0.45975	0.1369	M	0.64260	1.97	0.80722	D	1	B;B;B	0.23490	0.006;0.041;0.086	B;B;B	0.24848	0.02;0.043;0.056	T	0.42103	-0.9471	10	0.49607	T	0.09	.	18.7561	0.91833	0.0:1.0:0.0:0.0	.	307;359;310	G5E9G0;P39023;B3KS36	.;RL3_HUMAN;.	S	307;359	ENSP00000386101:A307S;ENSP00000346001:A359S	ENSP00000346001:A359S	A	-	1	0	RPL3	38039234	1.000000	0.71417	0.996000	0.52242	0.993000	0.82548	4.858000	0.62947	2.450000	0.82876	0.462000	0.41574	GCT	.	.		0.552	RPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321196.1	NM_000967		A	39709288	C	A	39709288	3	1	271	1	0	0	0	0	1	0	0	0	13594	739	26	3	144	3	RPL3	22	39709288	Missense_Mutation	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10	11515904	39709288	11595278	84	39431										
CELSR1	9620	hgsc.bcm.edu	37	chr22	46792623	46792623	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	gttcaggtgacaggcatccaCacagtttattccaaggtacc	9	11	1	1			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chr22:46792623C>A	ENST00000262738.3	-	13	5721	c.5722G>T	c.(5722-5724)Gtg>Ttg	p.V1908L		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	1908	EGF-like 6; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		CAGGCATCCACACAGTTTATT	0.592																																					p.V1908L		Atlas-SNP	.											CELSR1,NS,carcinoma,0,1	CELSR1	242	.	0			c.G5722T						.						52	41	45					22																	46792623		2202	4300	6502	SO:0001583	missense	9620	exon13			CATCCACACAGTT	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	1850	protein-coding gene	gene with protein product	"flamingo homolog 2 (Drosophila)"	604523	"cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.5722G>T	chr22.hg19:g.46792623C>A	ENSP00000262738:p.Val1908Leu	113.0	0.0		63.0	27.0	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	hg19	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	C	10.83	1.460286	0.26248	.	.	ENSG00000075275	ENST00000262738	T	0.69175	-0.38	4.45	3.42	0.39159	Epidermal growth factor-like (1);EGF-like region, conserved site (1);Epidermal growth factor-like, type 3 (1);	0.205114	0.31134	U	0.008197	T	0.52980	0.1768	L	0.42529	1.33	0.80722	D	1	B;B	0.27765	0.188;0.012	B;B	0.25614	0.062;0.013	T	0.46345	-0.9198	10	0.30078	T	0.28	.	7.5245	0.27647	0.1637:0.7498:0.0:0.0865	.	229;1908	B7Z7U7;Q9NYQ6	.;CELR1_HUMAN	L	1908	ENSP00000262738:V1908L	ENSP00000262738:V1908L	V	-	1	0	CELSR1	45171287	0.871000	0.30034	0.764000	0.31436	0.405000	0.30901	1.640000	0.37186	1.014000	0.39417	0.561000	0.74099	GTG	.	.		0.592	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		A	46792623	C	A	46792623	3	1	271	1	0	0	0	0	1	0	0	0	3223	478	17	3	3414	3	CELSR1	22	46792623	Missense_Mutation	SNP	C	TCGA-FV-A4ZQ-01A-11D-A25V-10	7083335	46792623	4511943	85	39432										
DIAPH2	1730	hgsc.bcm.edu	37	chrX	96369847	96369847	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.105882352941176	9	1	2.23648068669528	2.48497854077253	2.12998160637646	0.426986506746627	1	0	actcttgcctgtgaagaactGaagaaaagtgaaagctttaa	9	6	1	5			TCGA-FV-A4ZQ-01A-11D-A25V-10	TCGA-FV-A4ZQ-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d02597f8-3ac7-4165-a65f-0e134e5d215b	813ef938-cbe3-456a-ba15-01bca99c2880	g.chrX:96369847G>T	ENST00000324765.8	+	21	2819	c.2472G>T	c.(2470-2472)ctG>ctT	p.L824L	DIAPH2_ENST00000373061.3_Silent_p.L824L|DIAPH2_ENST00000355827.4_Silent_p.L824L|DIAPH2_ENST00000373049.4_Silent_p.L824L|DIAPH2_ENST00000373054.4_Silent_p.L820L			O60879	DIAP2_HUMAN	diaphanous-related formin 2	824	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin filament polymerization (GO:0030041)|cytokinesis (GO:0000910)|female gamete generation (GO:0007292)|multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)	endosome (GO:0005768)	receptor binding (GO:0005102)	p.L824L(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	51						GTGAAGAACTGAAGAAAAGTG	0.388																																					p.L824L		Atlas-SNP	.											.	DIAPH2	148	.	1	Substitution - coding silent(1)	breast(1)	c.G2472T						.						106	91	96					X																	96369847		2203	4300	6503	SO:0001819	synonymous_variant	1730	exon21			AGAACTGAAGAAA	Y15909	CCDS14467.1, CCDS14468.1	Xq22	2013-05-24	2013-05-24		ENSG00000147202	ENSG00000147202			2877	protein-coding gene	gene with protein product		300108	"diaphanous (Drosophila, homolog) 2", "diaphanous homolog 2 (Drosophila)"			9360932	Standard	NM_006729		Approved	POF, DIA, POF2, DIA2	uc004efu.4	O60879	OTTHUMG00000022689	ENST00000324765.8:c.2472G>T	chrX.hg19:g.96369847G>T		100.0	0.0		83.0	4.0	NM_007309	A6NG19|O60878|Q8WX06|Q8WX48|Q9UJL2	Silent	SNP	ENST00000324765.8	hg19	CCDS14467.1																																																																																			.	.		0.388	DIAPH2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058871.2	NM_006729, NM_007309		T	96369847	G	T	96369847	2	4	271	1	0	0	0	0	0	0	0	1	4521	1277	45	3		3	DIAPH2	23	96369847	Silent	SNP	G	TCGA-FV-A4ZQ-01A-11D-A25V-10		96369847	58900713	86	39433										
CELF3	11189	hgsc.bcm.edu	37	chr1	151679702	151679702	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	ggtgggcaccgggctgtagcCgttgacgcccagggcagccg	18	13	0	1			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr1:151679702C>T	ENST00000290583.4	-	8	1634	c.841G>A	c.(841-843)Ggc>Agc	p.G281S	CELF3_ENST00000290585.4_Intron|CELF3_ENST00000470688.1_5'UTR|RP11-98D18.1_ENST00000457548.1_RNA|CELF3_ENST00000392706.3_Missense_Mutation_p.G98S	NM_001172648.1|NM_007185.4	NP_001166119.1|NP_009116.3	Q5SZQ8	CELF3_HUMAN	CUGBP, Elav-like family member 3	281					mRNA splicing, via spliceosome (GO:0000398)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	21						GGGCTGTAGCCGTTGACGCCC	0.672																																					p.G281S		Atlas-SNP	.											.	CELF3	49	.	0			c.G841A						.						24	24	24					1																	151679702		2183	4275	6458	SO:0001583	missense	11189	exon8			TGTAGCCGTTGAC	U80759	CCDS1002.1, CCDS53367.1	1q21	2013-02-12	2010-02-19	2010-02-19	ENSG00000159409	ENSG00000159409		"Trinucleotide (CAG) repeat containing", "RNA binding motif (RRM) containing"	11967	protein-coding gene	gene with protein product	"expanded repeat domain, CAG/CTG 4", "CAG repeat domain", "CUG-BP and ETR-3 like factor 3"	612678	"trinucleotide repeat containing 4"	TNRC4		9225980	Standard	XM_005244859		Approved	CAGH4, BRUNOL1, ERDA4, MGC57297	uc001eys.2	Q5SZQ8	OTTHUMG00000013064	ENST00000290583.4:c.841G>A	chr1.hg19:g.151679702C>T	ENSP00000290583:p.Gly281Ser	103.0	0.0		125.0	17.0	NM_007185	B7ZKK6|O15414|Q499Y6|Q5SZQ7|Q6NVK0|Q8IZ98|Q9BZC2|Q9HB30	Missense_Mutation	SNP	ENST00000290583.4	hg19	CCDS1002.1	.	.	.	.	.	.	.	.	.	.	.	15.75	2.924379	0.52653	.	.	ENSG00000159409	ENST00000290583;ENST00000392706	T;T	0.16196	2.36;3.38	3.86	3.86	0.44501	.	0.193448	0.47093	D	0.000260	T	0.13200	0.0320	N	0.24115	0.695	0.41455	D	0.988006	D;P;B;P	0.76494	0.999;0.468;0.444;0.761	P;B;B;B	0.58520	0.84;0.18;0.035;0.145	T	0.06972	-1.0797	10	0.33940	T	0.23	-6.5762	14.5324	0.67936	0.0:1.0:0.0:0.0	.	98;281;281;280	B4DQL3;Q5SZQ8-2;Q5SZQ8;Q5SZQ8-3	.;.;CELF3_HUMAN;.	S	281;98	ENSP00000290583:G281S;ENSP00000376470:G98S	ENSP00000290583:G281S	G	-	1	0	CELF3	149946326	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.643000	0.37217	2.008000	0.58898	0.555000	0.69702	GGC	.	.		0.672	CELF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036663.2	NM_007185		T	151679702	C	T	151679702	3	4	272	1	0	0	0	0	1	0	0	0	3219	652	23	1	576	1	CELF3	1	151679702	Missense_Mutation	SNP	C	TCGA-G3-A25S-01A-11D-A16V-10		151679702	97570919	1	39434										
PBX1	5087	hgsc.bcm.edu	37	chr1	164768969	164768969	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	tcaccacccacgtgatgaatCtcctgcgagagcaaagccgg	10	14	2	3			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr1:164768969C>T	ENST00000420696.2	+	4	732	c.544C>T	c.(544-546)Ctc>Ttc	p.L182F	PBX1_ENST00000560641.1_Missense_Mutation_p.L77F|PBX1_ENST00000540246.1_Missense_Mutation_p.L77F|PBX1_ENST00000540236.1_Missense_Mutation_p.L182F|PBX1_ENST00000559240.1_Missense_Mutation_p.L182F|PBX1_ENST00000401534.1_Missense_Mutation_p.L182F|PBX1_ENST00000367897.1_Missense_Mutation_p.L182F	NM_001204961.1|NM_001204963.1|NM_002585.3	NP_001191890.1|NP_001191892.1|NP_002576.1	P40424	PBX1_HUMAN	pre-B-cell leukemia homeobox 1	182					adrenal gland development (GO:0030325)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic hemopoiesis (GO:0035162)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system development (GO:0048706)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|proximal/distal pattern formation (GO:0009954)|regulation of ossification (GO:0030278)|sex differentiation (GO:0007548)|spleen development (GO:0048536)|steroid biosynthetic process (GO:0006694)|thymus development (GO:0048538)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)		EWSR1/PBX1(3)	large_intestine(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	4						CGTGATGAATCTCCTGCGAGA	0.552			T	"TCF3, EWSR1"	"pre B-ALL, myoepithelioma"																																p.L182F		Atlas-SNP	.		Dom	yes		1	1q23	5087	pre-B-cell leukemia transcription factor 1		"L, M"	.	PBX1	60	.	0			c.C544T						.						90	82	84					1																	164768969		2203	4300	6503	SO:0001583	missense	5087	exon4			ATGAATCTCCTGC	M86546	CCDS1246.1, CCDS55654.1	1q23.3	2011-06-20	2007-01-30		ENSG00000185630	ENSG00000185630		"Homeoboxes / TALE class"	8632	protein-coding gene	gene with protein product		176310	"pre-B-cell leukemia transcription factor 1"				Standard	NM_002585		Approved		uc001gct.3	P40424	OTTHUMG00000034307	ENST00000420696.2:c.544C>T	chr1.hg19:g.164768969C>T	ENSP00000405890:p.Leu182Phe	58.0	0.0		83.0	16.0	NM_001204963	B4DSC1|F5H4U9|Q5T488	Missense_Mutation	SNP	ENST00000420696.2	hg19	CCDS1246.1	.	.	.	.	.	.	.	.	.	.	C	34	5.333251	0.95758	.	.	ENSG00000185630	ENST00000420696;ENST00000367897;ENST00000540236;ENST00000401534;ENST00000540246	T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97	5.76	5.76	0.90799	PBX (1);	0.000000	0.85682	D	0.000000	T	0.66277	0.2773	M	0.87269	2.87	0.80722	D	1	D;D;D;D;D	0.71674	0.996;0.998;0.995;0.998;0.996	D;D;D;D;D	0.78314	0.985;0.991;0.974;0.991;0.985	T	0.69412	-0.5152	10	0.54805	T	0.06	-11.2331	19.571	0.95419	0.0:1.0:0.0:0.0	.	77;182;182;182;182	B7Z774;A8K5V0;F5H4U9;P40424;Q53YC7	.;.;.;PBX1_HUMAN;.	F	182;182;182;182;77	ENSP00000405890:L182F;ENSP00000356872:L182F;ENSP00000439943:L182F;ENSP00000384856:L182F;ENSP00000440869:L77F	ENSP00000356872:L182F	L	+	1	0	PBX1	163035593	1.000000	0.71417	0.996000	0.52242	0.977000	0.68977	7.380000	0.79704	2.713000	0.92767	0.655000	0.94253	CTC	.	.		0.552	PBX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082864.4	NM_002585		T	164768969	C	T	164768969	3	4	272	1	0	0	0	0	1	0	0	0	11501	913	32	3	558	3	PBX1	1	164768969	Missense_Mutation	SNP	C	TCGA-G3-A25S-01A-11D-A16V-10	13089267	164768969	84481652	2	39435										
DHX9	1660	hgsc.bcm.edu	37	chr1	182852382	182852382	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	caatgtatgctatcataaggAaaagaggaagattctcacca	8	7	2	2			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr1:182852382A>T	ENST00000367549.3	+	25	3133	c.3023A>T	c.(3022-3024)gAa>gTa	p.E1008V	DHX9_ENST00000485081.1_3'UTR	NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	1008					ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|circadian rhythm (GO:0007623)|CRD-mediated mRNA stabilization (GO:0070934)|DNA duplex unwinding (GO:0032508)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of type I interferon production (GO:0032481)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|RNA polymerase II transcription factor binding (GO:0001085)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	49						TATCATAAGGAAAAGAGGAAG	0.413																																					p.E1008V	Colon(69;210 1162 3697 13559 39565)	Atlas-SNP	.											.	DHX9	114	.	0			c.A3023T						.						155	132	139					1																	182852382		1900	4120	6020	SO:0001583	missense	1660	exon25			ATAAGGAAAAGAG	L13848	CCDS41444.1	1q25	2013-05-13	2013-05-13	2003-06-20	ENSG00000135829	ENSG00000135829		"DEAH-boxes"	2750	protein-coding gene	gene with protein product	"NDH II", "RNA helicase A"	603115	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9 (RNA helicase A, nuclear DNA helicase II; leukophysin)", "DEAH (Asp-Glu-Ala-His) box polypeptide 9"	LKP, DDX9		8344961, 9111062	Standard	NM_001357		Approved	RHA	uc001gpr.3	Q08211	OTTHUMG00000035337	ENST00000367549.3:c.3023A>T	chr1.hg19:g.182852382A>T	ENSP00000356520:p.Glu1008Val	129.0	0.0		156.0	83.0	NM_001357	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Missense_Mutation	SNP	ENST00000367549.3	hg19	CCDS41444.1	.	.	.	.	.	.	.	.	.	.	A	27.6	4.848970	0.91277	.	.	ENSG00000135829	ENST00000367549	T	0.04275	3.66	5.39	5.39	0.77823	Domain of unknown function DUF1605 (1);	0.000000	0.85682	D	0.000000	T	0.18964	0.0455	M	0.85197	2.74	0.80722	D	1	P;P	0.47604	0.898;0.885	P;P	0.53722	0.733;0.665	T	0.00728	-1.1591	10	0.48119	T	0.1	.	15.4176	0.74983	1.0:0.0:0.0:0.0	.	287;1008	B3KU66;Q08211	.;DHX9_HUMAN	V	1008	ENSP00000356520:E1008V	ENSP00000356520:E1008V	E	+	2	0	DHX9	181119005	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.699000	0.91316	2.027000	0.59764	0.533000	0.62120	GAA	.	.		0.413	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588		T	182852382	A	T	182852382	3	4	272	1	0	0	0	0	1	0	0	0	4518	246	9	4	3117	4	DHX9	1	182852382	Missense_Mutation	SNP	A	TCGA-G3-A25S-01A-11D-A16V-10	18083413	182852382	66398239	3	39436										
YOD1	55432	hgsc.bcm.edu	37	chr1	207224106	207224106	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	cactcgggagggtatccgacGaggattcgctgaccgccggg	16	12	0	1			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr1:207224106G>A	ENST00000315927.4	-	1	316	c.270C>T	c.(268-270)ctC>ctT	p.L90L	YOD1_ENST00000391927.1_Silent_p.L46L|PFKFB2_ENST00000367079.2_5'Flank|PFKFB2_ENST00000411990.2_Intron|YOD1_ENST00000367084.1_Silent_p.L46L|PFKFB2_ENST00000367080.3_5'Flank	NM_018566.3	NP_061036.3	Q5VVQ6	OTU1_HUMAN	YOD1 deubiquitinase	90	UBX-like.			L -> F (in Ref. 1; BAC87233). {ECO:0000305}.	cellular amino acid metabolic process (GO:0006520)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein K11-linked deubiquitination (GO:0035871)|protein K27-linked deubiquitination (GO:1990167)|protein K29-linked deubiquitination (GO:0035523)|protein K33-linked deubiquitination (GO:1990168)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)		Lys48-specific deubiquitinase activity (GO:1990380)|metal ion binding (GO:0046872)|ubiquitin-specific protease activity (GO:0004843)			cervix(1)|endometrium(3)|large_intestine(1)|lung(3)|ovary(3)	11	Prostate(682;0.19)					GGTATCCGACGAGGATTCGCT	0.627																																					p.L90L		Atlas-SNP	.											.	YOD1	24	.	0			c.C270T						.						48	55	52					1																	207224106		2203	4299	6502	SO:0001819	synonymous_variant	55432	exon1			TCCGACGAGGATT		CCDS31002.1, CCDS60402.1	1q32.2	2013-06-04	2013-06-04		ENSG00000180667	ENSG00000180667		"OTU domain containing"	25035	protein-coding gene	gene with protein product		612023	"YOD1 OTU deubiquinating enzyme 1 homolog ( yeast)", "YOD1 OTU deubiquinating enzyme 1 homolog (S. cerevisiae)"				Standard	NM_001276320		Approved	DKFZp451J1719, OTUD2, DUBA8	uc001hfe.1	Q5VVQ6	OTTHUMG00000036032	ENST00000315927.4:c.270C>T	chr1.hg19:g.207224106G>A		68.0	0.0		123.0	11.0	NM_018566	B2RNX3|Q5VVQ5|Q6ZRS6|Q86T63|Q9P1L8	Silent	SNP	ENST00000315927.4	hg19	CCDS31002.1																																																																																			.	.		0.627	YOD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087837.1	NM_018566		A	207224106	G	A	207224106	2	1	272	1	0	0	0	0	0	0	0	1	17503	1045	37	1		1	YOD1	1	207224106	Silent	SNP	G	TCGA-G3-A25S-01A-11D-A16V-10	24371724	207224106	42026515	4	39437										
CR2	1380	hgsc.bcm.edu	37	chr1	207641906	207641906	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	tgtccagcacttcctatgatCcacaatggacatcacacaag	6	13	1	1			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr1:207641906C>T	ENST00000367058.3	+	3	669	c.480C>T	c.(478-480)atC>atT	p.I160I	CR2_ENST00000458541.2_Silent_p.I160I|CR2_ENST00000367059.3_Silent_p.I160I|CR2_ENST00000367057.3_Silent_p.I160I|CR2_ENST00000485707.1_3'UTR	NM_001877.4	NP_001868.2	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus) receptor 2	160	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|complement activation, classical pathway (GO:0006958)|immune response (GO:0006955)|innate immune response (GO:0045087)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	complement binding (GO:0001848)|complement receptor activity (GO:0004875)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|breast(3)|endometrium(4)|kidney(3)|large_intestine(12)|lung(26)|ovary(1)|pancreas(1)|prostate(1)|skin(12)|upper_aerodigestive_tract(3)|urinary_tract(1)	69						TTCCTATGATCCACAATGGAC	0.433																																					p.I160I		Atlas-SNP	.											.	CR2	164	.	0			c.C480T						.						202	188	192					1																	207641906		2203	4300	6503	SO:0001819	synonymous_variant	1380	exon3			TATGATCCACAAT	M26004	CCDS1478.1, CCDS31007.1	1q32	2014-09-17			ENSG00000117322	ENSG00000117322		"CD molecules", "Complement system"	2336	protein-coding gene	gene with protein product		120650					Standard	NM_001006658		Approved	CD21	uc001hfv.3	P20023	OTTHUMG00000036307	ENST00000367058.3:c.480C>T	chr1.hg19:g.207641906C>T		239.0	0.0		293.0	160.0	NM_001006658	C9JHD2|Q13866|Q14212|Q53EL2|Q5BKT9|Q5SR46|Q5SR48	Silent	SNP	ENST00000367058.3	hg19	CCDS1478.1																																																																																			.	.		0.433	CR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000088274.1	NM_001877		T	207641906	C	T	207641906	2	4	272	1	0	0	0	0	0	0	0	1	3844	845	30	3		3	CR2	1	207641906	Silent	SNP	C	TCGA-G3-A25S-01A-11D-A16V-10	417800	207641906	41608715	5	39438										
PCNXL2	80003	hgsc.bcm.edu	37	chr1	233397906	233397906	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	tgccattgtgaatctgcctaTtattgctaacccaacatgag	7	10	1	2			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr1:233397906T>C	ENST00000258229.9	-	3	599	c.365A>G	c.(364-366)aAt>aGt	p.N122S	PCNXL2_ENST00000430153.1_5'UTR	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	122						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				AATCTGCCTATTATTGCTAAC	0.448																																					p.N122S		Atlas-SNP	.											.	PCNXL2	204	.	0			c.A365G						.						183	192	189					1																	233397906		1949	4139	6088	SO:0001583	missense	80003	exon3			TGCCTATTATTGC	AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749			8736	protein-coding gene	gene with protein product			"pecanex (Drosophila)-like 2"			12477932	Standard	NM_014801		Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.365A>G	chr1.hg19:g.233397906T>C	ENSP00000258229:p.Asn122Ser	108.0	0.0		144.0	19.0	NM_014801	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Missense_Mutation	SNP	ENST00000258229.9	hg19	CCDS44335.1	.	.	.	.	.	.	.	.	.	.	T	11.91	1.779032	0.31502	.	.	ENSG00000135749	ENST00000258229	T	0.62232	0.04	5.2	-0.286	0.12862	.	.	.	.	.	T	0.42585	0.1209	N	0.22421	0.69	0.18873	N	0.999985	B	0.29162	0.235	B	0.29077	0.098	T	0.23868	-1.0176	9	0.23891	T	0.37	.	7.4045	0.26983	0.0:0.0763:0.4036:0.5201	.	122	A6NKB5	PCX2_HUMAN	S	122	ENSP00000258229:N122S	ENSP00000258229:N122S	N	-	2	0	PCNXL2	231464529	0.593000	0.26840	0.000000	0.03702	0.543000	0.35085	0.748000	0.26305	-0.226000	0.09899	0.533000	0.62120	AAT	.	.		0.448	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092480.3	NM_014801		C	233397906	T	C	233397906	3	2	272	1	0	0	0	0	1	0	0	0	11601	1493	52	2	6176	2	PCNXL2	1	233397906	Missense_Mutation	SNP	T	TCGA-G3-A25S-01A-11D-A16V-10	25756000	233397906	15852715	6	39439										
PLD5	200150	hgsc.bcm.edu	37	chr1	242451667	242451667	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	cagaggatgtagcttacctgAcatgctgatggatgagtgtg	14	6	0	4			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr1:242451667A>T	ENST00000536534.2	-	3	733	c.492T>A	c.(490-492)tgT>tgA	p.C164*	PLD5_ENST00000427495.1_Nonsense_Mutation_p.C102*|PLD5_ENST00000442594.2_Nonsense_Mutation_p.C72*			Q8N7P1	PLD5_HUMAN	phospholipase D family, member 5	164						integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(22)|ovary(6)|skin(3)|urinary_tract(1)	55	Melanoma(84;0.242)		OV - Ovarian serous cystadenocarcinoma(106;0.0329)			AGCTTACCTGACATGCTGATG	0.423																																					p.C164X		Atlas-SNP	.											.	PLD5	216	.	0			c.T492A						.						176	151	160					1																	242451667		2203	4300	6503	SO:0001587	stop_gained	200150	exon4			TACCTGACATGCT	AK098092	CCDS1621.1, CCDS1621.2, CCDS55692.1	1q43	2008-02-05			ENSG00000180287	ENSG00000180287			26879	protein-coding gene	gene with protein product							Standard	NM_001195811		Approved	FLJ40773	uc001hzn.2	Q8N7P1	OTTHUMG00000039867	ENST00000536534.2:c.492T>A	chr1.hg19:g.242451667A>T	ENSP00000440896:p.Cys164*	424.0	0.0		559.0	59.0	NM_152666	A1KXV0|B7Z324|Q494U9|Q8NB22	Nonsense_Mutation	SNP	ENST00000536534.2	hg19	CCDS1621.2	.	.	.	.	.	.	.	.	.	.	A	38	6.957052	0.97964	.	.	ENSG00000180287	ENST00000427495;ENST00000442594;ENST00000536534;ENST00000459864	.	.	.	4.33	3.17	0.36434	.	0.173929	0.52532	D	0.000062	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	-18.0311	6.029	0.19669	0.8142:0.0:0.1858:0.0	.	.	.	.	X	102;72;164;102	.	ENSP00000401285:C102X	C	-	3	2	PLD5	240518290	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.486000	0.35530	1.733000	0.51620	0.482000	0.46254	TGT	.	.		0.423	PLD5-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397213.2	NM_152666		T	242451667	A	T	242451667	4	4	272	1	0	0	0	0	0	1	0	0	12058	273	10	4	1150	4	PLD5	1	242451667	Nonsense_Mutation	SNP	A	TCGA-G3-A25S-01A-11D-A16V-10	9053761	242451667	6798954	7	39440										
ADSS	159	hgsc.bcm.edu	37	chr1	244595870	244595870	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	tatgagctctgtcagatataAtaagccttttttcccagcct	6	10	2	2			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr1:244595870A>T	ENST00000366535.3	-	4	699	c.383T>A	c.(382-384)aTt>aAt	p.I128N		NM_001126.3	NP_001117.2			adenylosuccinate synthase											endometrium(2)|kidney(1)|large_intestine(3)|lung(1)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	12	all_cancers(71;2.17e-05)|all_epithelial(71;0.00015)|all_neural(11;0.0269)|Breast(184;0.0654)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0874)|Lung NSC(105;0.121)	all_cancers(173;0.0896)|all_epithelial(177;0.172)	all cancers(7;9.71e-08)|GBM - Glioblastoma multiforme(7;1.28e-05)|OV - Ovarian serous cystadenocarcinoma(106;0.0014)			GTCAGATATAATAAGCCTTTT	0.254																																					p.I128N		Atlas-SNP	.											.	ADSS	49	.	0			c.T383A						.						61	69	66					1																	244595870		2198	4276	6474	SO:0001583	missense	159	exon4			GATATAATAAGCC	BC012356	CCDS1624.1	1q44	2008-02-05			ENSG00000035687	ENSG00000035687	6.3.4.4		292	protein-coding gene	gene with protein product		103060				2004783, 1592113	Standard	NM_001126		Approved		uc001iaj.3	P30520	OTTHUMG00000040102	ENST00000366535.3:c.383T>A	chr1.hg19:g.244595870A>T	ENSP00000355493:p.Ile128Asn	572.0	0.0		783.0	32.0	NM_001126		Missense_Mutation	SNP	ENST00000366535.3	hg19	CCDS1624.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.041942	0.75732	.	.	ENSG00000035687	ENST00000366535;ENST00000449326;ENST00000430700	T	0.44881	0.91	5.58	5.58	0.84498	.	0.257041	0.43416	D	0.000577	T	0.59142	0.2172	M	0.75777	2.31	0.53688	D	0.999976	P	0.51240	0.943	P	0.56788	0.806	T	0.57347	-0.7827	10	0.30078	T	0.28	-4.3992	15.7221	0.77721	1.0:0.0:0.0:0.0	.	128	P30520	PURA2_HUMAN	N	128;107;68	ENSP00000355493:I128N	ENSP00000355493:I128N	I	-	2	0	ADSS	242662493	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.521000	0.73778	2.253000	0.74438	0.455000	0.32223	ATT	.	.		0.254	ADSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096697.1	NM_001126		T	244595870	A	T	244595870	3	4	272	1	0	0	0	0	1	0	0	0	347	101	4	4	1027	4	ADSS	1	244595870	Missense_Mutation	SNP	A	TCGA-G3-A25S-01A-11D-A16V-10	2144203	244595870	4654751	8	39441										
OR2T4	127074	hgsc.bcm.edu	37	chr1	248524908	248524908	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	caacatcacctggatggccaGccacactggatggtcggatt	11	12	1	0	rs140989725		TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr1:248524908G>A	ENST00000366475.1	+	1	26	c.26G>A	c.(25-27)aGc>aAc	p.S9N		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	9						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TGGATGGCCAGCCACACTGGA	0.483																																					p.S9N		Atlas-SNP	.											OR2T4,NS,carcinoma,0,1	OR2T4	126	.	0			c.G26A						.						78	74	76					1																	248524908		2203	4300	6503	SO:0001583	missense	127074	exon1			TGGCCAGCCACAC	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"GPCR / Class A : Olfactory receptors"	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.26G>A	chr1.hg19:g.248524908G>A	ENSP00000355431:p.Ser9Asn	321.0	1.0		388.0	16.0	NM_001004696	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	hg19	CCDS31113.1	.	.	.	.	.	.	.	.	.	.	G	0.006	-2.037779	0.00402	.	.	ENSG00000196944	ENST00000366475	T	0.01821	4.62	1.77	-1.13	0.09775	.	.	.	.	.	T	0.00815	0.0027	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.47156	-0.9139	9	0.05351	T	0.99	.	4.3443	0.11126	0.6047:0.0:0.3953:0.0	.	9	Q8NH00	OR2T4_HUMAN	N	9	ENSP00000355431:S9N	ENSP00000355431:S9N	S	+	2	0	OR2T4	246591531	0.000000	0.05858	0.009000	0.14445	0.059000	0.15707	-0.336000	0.07863	-0.221000	0.09973	-0.745000	0.03516	AGC	.	.		0.483	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696		A	248524908	G	A	248524908	3	1	272	1	0	0	0	0	1	0	0	0	11036	971	34	3	28	3	OR2T4	1	248524908	Missense_Mutation	SNP	G	TCGA-G3-A25S-01A-11D-A16V-10	3929038	248524908	725713	9	39442										
SEMA4F	10505	hgsc.bcm.edu	37	chr2	74901762	74901762	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	gtgcttcgacctgagcttggGgcagggactcccatctttta	12	11	1	1			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr2:74901762G>C	ENST00000357877.2	+	8	1109	c.960G>C	c.(958-960)ggG>ggC	p.G320G	SEMA4F_ENST00000339773.5_Silent_p.G165G	NM_004263.3	NP_004254.2	O95754	SEM4F_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4F	320	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell-cell signaling (GO:0007267)|negative regulation of axon extension (GO:0030517)|nervous system development (GO:0007399)|retinal ganglion cell axon guidance (GO:0031290)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor activity (GO:0004872)			biliary_tract(1)|breast(2)|endometrium(8)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	45						CTGAGCTTGGGGCAGGGACTC	0.567																																					p.G320G		Atlas-SNP	.											.	SEMA4F	89	.	0			c.G960C						.						162	156	158					2																	74901762		2203	4300	6503	SO:0001819	synonymous_variant	10505	exon8			GCTTGGGGCAGGG	AF038652	CCDS1955.1, CCDS62942.1, CCDS74529.1	2p13.1	2008-05-21			ENSG00000135622	ENSG00000135622		"Semaphorins"	10734	protein-coding gene	gene with protein product	"m-Sema M"	603706		SEMAM		10051670	Standard	NM_004263		Approved	SEMAW	uc002sna.2	O95754	OTTHUMG00000129952	ENST00000357877.2:c.960G>C	chr2.hg19:g.74901762G>C		140.0	0.0		93.0	27.0	NM_004263	Q542Y7|Q9NS35	Silent	SNP	ENST00000357877.2	hg19	CCDS1955.1																																																																																			.	.		0.567	SEMA4F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252214.2	NM_004263		C	74901762	G	C	74901762	2	2	272	1	0	0	0	0	0	0	0	1	14050	1219	43	4		4	SEMA4F	2	74901762	Silent	SNP	G	TCGA-G3-A25S-01A-11D-A16V-10		74901762	168297611	10	39443										
REG1B	5968	hgsc.bcm.edu	37	chr2	79314699	79314699	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	gctcagagacaggaacatcaGggaggagatcagcatgaaga	14	7	3	4			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr2:79314699G>T	ENST00000305089.3	-	2	120	c.40C>A	c.(40-42)Ctg>Atg	p.L14M		NM_006507.3	NP_006498.1	P48304	REG1B_HUMAN	regenerating islet-derived 1 beta	14					cell proliferation (GO:0008283)	extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(40)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	51						AGGAACATCAGGGAGGAGATC	0.483																																					p.L14M		Atlas-SNP	.											REG1B,right_lower_lobe,carcinoma,0,1	REG1B	83	.	0			c.C40A						.						143	118	126					2																	79314699		2203	4300	6503	SO:0001583	missense	5968	exon2			ACATCAGGGAGGA		CCDS1963.1	2p12	2008-06-04	2008-06-04		ENSG00000172023	ENSG00000172023			9952	protein-coding gene	gene with protein product	"lithostathine 1 beta", "secretory pancreatic stone protein 2"	167771	"regenerating islet-derived 1 beta (pancreatic stone protein, pancreatic thread protein)"			8110835	Standard	NM_006507		Approved	REGL, PSPS2, REGH, REGI-BETA	uc002sny.2	P48304	OTTHUMG00000130019	ENST00000305089.3:c.40C>A	chr2.hg19:g.79314699G>T	ENSP00000303206:p.Leu14Met	148.0	0.0		106.0	30.0	NM_006507		Missense_Mutation	SNP	ENST00000305089.3	hg19	CCDS1963.1	.	.	.	.	.	.	.	.	.	.	g	15.90	2.969208	0.53614	.	.	ENSG00000172023	ENST00000305089	T	0.05382	3.45	2.71	1.8	0.24995	.	0.000000	0.29126	N	0.013075	T	0.22859	0.0552	M	0.86740	2.835	0.21627	N	0.999616	D;D	0.76494	0.999;0.999	D;D	0.83275	0.996;0.996	T	0.02307	-1.1179	10	0.72032	D	0.01	.	5.8691	0.18793	0.1547:0.0:0.8453:0.0	.	14;14	Q6ICS1;P48304	.;REG1B_HUMAN	M	14	ENSP00000303206:L14M	ENSP00000303206:L14M	L	-	1	2	REG1B	79168207	0.990000	0.36364	0.646000	0.29493	0.459000	0.32528	0.857000	0.27831	0.678000	0.31325	0.555000	0.69702	CTG	.	.		0.483	REG1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252292.2	NM_006507		T	79314699	G	T	79314699	3	4	272	1	0	0	0	0	1	0	0	0	13226	991	35	3	480	3	REG1B	2	79314699	Missense_Mutation	SNP	G	TCGA-G3-A25S-01A-11D-A16V-10	4412937	79314699	163884674	11	39444										
DNAH6	1768	hgsc.bcm.edu	37	chr2	84852030	84852030	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	gcattgctttcttcaggatcGctgctatctttgcctcatgg	9	11	4	0	rs368034415		TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr2:84852030G>T	ENST00000237449.6	+	28	4366	c.4358G>T	c.(4357-4359)cGc>cTc	p.R1453L	DNAH6_ENST00000389394.3_Missense_Mutation_p.R1453L|DNAH6_ENST00000398278.2_Missense_Mutation_p.R1453L			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	1453	AAA 1. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						CTTCAGGATCGCTGCTATCTT	0.468																																					p.R1453L		Atlas-SNP	.											.	DNAH6	194	.	0			c.G4358T						.						43	39	40					2																	84852030		692	1591	2283	SO:0001583	missense	1768	exon29			AGGATCGCTGCTA	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.4358G>T	chr2.hg19:g.84852030G>T	ENSP00000237449:p.Arg1453Leu	129.0	0.0		86.0	34.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	hg19	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.888389	0.91814	.	.	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.14640	2.49;2.49;2.49	5.73	5.73	0.89815	.	.	.	.	.	T	0.49287	0.1548	M	0.92219	3.285	0.52501	D	0.999957	D	0.89917	1.0	D	0.74023	0.982	T	0.60347	-0.7281	9	0.87932	D	0	.	18.6778	0.91535	0.0:0.0:1.0:0.0	.	1453	Q9C0G6	DYH6_HUMAN	L	1453	ENSP00000374045:R1453L;ENSP00000381326:R1453L;ENSP00000237449:R1453L	ENSP00000237449:R1453L	R	+	2	0	DNAH6	84705541	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	7.483000	0.81158	2.693000	0.91896	0.655000	0.94253	CGC	.	.		0.468	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		T	84852030	G	T	84852030	3	4	272	1	0	0	0	0	1	0	0	0	4607	1087	38	1	4468	1	DNAH6	2	84852030	Missense_Mutation	SNP	G	TCGA-G3-A25S-01A-11D-A16V-10	5537331	84852030	158347343	12	39445										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168097234	168097234	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	catctcagtttcatcaatatGttcaagaaactggtaagagt	7	7	4	2			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr2:168097234G>T	ENST00000409728.1	+	8	1218	c.1129G>T	c.(1129-1131)Gtt>Ttt	p.V377F	XIRP2_ENST00000409273.1_Missense_Mutation_p.V122F|XIRP2_ENST00000409605.1_Missense_Mutation_p.V122F|XIRP2_ENST00000409043.1_Missense_Mutation_p.V344F|XIRP2_ENST00000409195.1_Missense_Mutation_p.V344F|XIRP2_ENST00000295237.9_Missense_Mutation_p.V344F|XIRP2_ENST00000409756.2_Missense_Mutation_p.V344F|XIRP2_ENST00000420519.1_Missense_Mutation_p.V377F	NM_001199143.1	NP_001186072.1	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	169					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TCATCAATATGTTCAAGAAAC	0.348																																					p.V377F		Atlas-SNP	.											.	XIRP2	914	.	0			c.G1129T						.						119	115	116					2																	168097234		1853	4082	5935	SO:0001583	missense	129446	exon8			CAATATGTTCAAG	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409728.1:c.1129G>T	chr2.hg19:g.168097234G>T	ENSP00000386619:p.Val377Phe	184.0	0.0		164.0	71.0	NM_001199143	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409728.1	hg19	CCDS56143.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.468899	0.84533	.	.	ENSG00000163092	ENST00000409043;ENST00000409728;ENST00000409195;ENST00000409756;ENST00000420519;ENST00000295237;ENST00000409273;ENST00000409605	T;T;T;T;T;T;T;T	0.78816	-1.21;-1.21;4.1;-1.21;-1.21;4.1;4.11;-1.21	5.81	5.81	0.92471	.	0.325101	0.29321	N	0.012484	D	0.85600	0.5734	M	0.62723	1.935	0.39531	D	0.968665	D;D;D;D;D	0.89917	0.998;1.0;1.0;1.0;0.998	D;D;D;D;D	0.87578	0.943;0.997;0.998;0.996;0.935	T	0.81300	-0.0995	10	0.15499	T	0.54	-17.2181	17.5701	0.87933	0.0:0.0:1.0:0.0	.	169;344;377;169;122	A4UGR9;A4UGR9-4;A4UGR9-6;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.;.;.	F	344;377;344;344;377;344;122;122	ENSP00000386454:V344F;ENSP00000386619:V377F;ENSP00000386840:V344F;ENSP00000386724:V344F;ENSP00000415541:V377F;ENSP00000295237:V344F;ENSP00000387255:V122F;ENSP00000386981:V122F	ENSP00000295237:V344F	V	+	1	0	XIRP2	167805480	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.927000	0.56499	2.756000	0.94617	0.655000	0.94253	GTT	.	.		0.348	XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333552.1	NM_152381		T	168097234	G	T	168097234	3	4	272	1	0	0	0	0	1	0	0	0	17445	1377	48	3	1052	3	XIRP2	2	168097234	Missense_Mutation	SNP	G	TCGA-G3-A25S-01A-11D-A16V-10	83245204	168097234	75102139	13	39446										
CHL1	10752	hgsc.bcm.edu	37	chr3	423911	423911	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	ttgtctgaaagacagaacagGagtgttcggctgacctggga	14	7	1	4			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr3:423911G>T	ENST00000256509.2	+	17	2568	c.1926G>T	c.(1924-1926)agG>agT	p.R642S	CHL1-AS1_ENST00000417612.1_RNA|CHL1_ENST00000397491.2_Missense_Mutation_p.R626S	NM_001253387.1|NM_001253388.1|NM_006614.3	NP_001240316.1|NP_001240317.1|NP_006605.2	Q96FC9	DDX11_HUMAN	cell adhesion molecule L1-like	0					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			NS(1)|central_nervous_system(5)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|lung(31)|ovary(1)|prostate(4)|skin(10)|stomach(1)	93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		GACAGAACAGGAGTGTTCGGC	0.408																																					p.R642S		Atlas-SNP	.											.	CHL1	242	.	0			c.G1926T						.						89	94	92					3																	423911		2203	4300	6503	SO:0001583	missense	10752	exon15			GAACAGGAGTGTT	AF002246	CCDS2556.1, CCDS58812.1, CCDS74887.1	3p26	2013-05-01	2013-05-01		ENSG00000134121	ENSG00000134121		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	1939	protein-coding gene	gene with protein product	"neural cell adhesion molecule", "close homolog of L1"	607416	"cell adhesion molecule with homology to L1CAM (close homologue of L1)", "cell adhesion molecule with homology to L1CAM (close homolog of L1)"			9799093	Standard	NM_006614		Approved	CALL, L1CAM2, FLJ44930, MGC132578	uc003bot.3	O00533	OTTHUMG00000090601	ENST00000256509.2:c.1926G>T	chr3.hg19:g.423911G>T	ENSP00000256509:p.Arg642Ser	95.0	0.0		78.0	27.0	NM_001253388	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000256509.2	hg19	CCDS2556.1	.	.	.	.	.	.	.	.	.	.	G	19.70	3.876548	0.72180	.	.	ENSG00000134121	ENST00000256509;ENST00000397491	T;T	0.54479	0.57;0.57	5.13	2.09	0.27110	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.166021	0.49916	D	0.000128	T	0.58538	0.2129	L	0.47716	1.5	0.45464	D	0.998435	P;P;D	0.76494	0.954;0.954;0.999	P;P;D	0.74023	0.87;0.87;0.982	T	0.54609	-0.8268	10	0.52906	T	0.07	.	5.5079	0.16864	0.2909:0.25:0.4591:0.0	.	626;626;642	B3KX75;O00533;O00533-2	.;CHL1_HUMAN;.	S	642;626	ENSP00000256509:R642S;ENSP00000380628:R626S	ENSP00000256509:R642S	R	+	3	2	CHL1	398911	0.999000	0.42202	1.000000	0.80357	0.996000	0.88848	0.575000	0.23729	0.187000	0.20147	0.591000	0.81541	AGG	.	.		0.408	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614		T	423911	G	T	423911	3	4	272	1	0	0	0	0	1	0	0	0	3351	1165	41	3	1984	3	CHL1	3	423911	Missense_Mutation	SNP	G	TCGA-G3-A25S-01A-11D-A16V-10		423911	197598519	14	39447										
TRNT1	51095	hgsc.bcm.edu	37	chr3	3186326	3186329	+	Frame_Shift_Del	DEL	AGTT	AGTT	-													0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	gaagatttaaaaaataagaaAgttagatttgttggacatgc							TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	AGTT	AGTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr3:3186326_3186329delAGTT	ENST00000251607.6	+	5	642_645	c.540_543delAGTT	c.(538-543)aaagttfs	p.KV180fs	TRNT1_ENST00000280591.6_Frame_Shift_Del_p.KV180fs	NM_182916.2	NP_886552	Q96Q11	TRNT1_HUMAN	tRNA nucleotidyl transferase, CCA-adding, 1	180					protein targeting to mitochondrion (GO:0006626)|tRNA 3'-end processing (GO:0042780)|tRNA 3'-terminal CCA addition (GO:0001680)	intracellular (GO:0005622)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP:3'-cytidine-cytidine-tRNA adenylyltransferase activity (GO:0052929)|CTP:3'-cytidine-tRNA cytidylyltransferase activity (GO:0052928)|CTP:tRNA cytidylyltransferase activity (GO:0052927)|tRNA adenylyltransferase activity (GO:0004810)|tRNA binding (GO:0000049)			breast(2)|endometrium(3)|large_intestine(4)|lung(2)|urinary_tract(1)	12				Epithelial(13;0.00226)|OV - Ovarian serous cystadenocarcinoma(96;0.00592)|all cancers(10;0.011)		AAAATAAGAAAGTTAGATTTGTTG	0.26																																					p.180_181del		Atlas-Indel,Pindel	.											.	TRNT1	34	.	0			c.539_542del						.			0,4250		0,0,2125						5.7	1			56	1,8237		0,1,4118	no	frameshift	TRNT1	NM_182916.2		0,1,6243	A1A1,A1R,RR		0.0121,0.0,0.0080				1,12487				SO:0001589	frameshift_variant	51095	exon5			.	AF151805	CCDS2561.2	3p25.1	2002-05-30			ENSG00000072756	ENSG00000072756	2.7.7.25		17341	protein-coding gene	gene with protein product		612907				10810093, 11504732	Standard	NM_182916		Approved	MtCCA, CGI-47, CCA1	uc003bpp.4	Q96Q11	OTTHUMG00000090259	ENST00000251607.6:c.540_543delAGTT	chr3.hg19:g.3186326_3186329delAGTT	ENSP00000251607:p.Lys180fs	204.0	0.0		151.0	23.0	NM_182916	A8K2Z6|B7WP13|C9JKA2|Q8ND57|Q9BS97|Q9Y362	Frame_Shift_Del	DEL	ENST00000251607.6	hg19	CCDS2561.2																																																																																			.	.		0.26	TRNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337616.1			-	3186329	AGTT	-	3186326	7	5	272	1	0	1	0	1	0	0	0	0	16588	69	3	0	554	0	TRNT1	3	3186326	Frame_Shift_Del	DEL	AGTT	TCGA-G3-A25S-01A-11D-A16V-10	2762415	3186326	194836104	15	39448										
TTLL3	26140	hgsc.bcm.edu	37	chr3	9870684	9870685	+	Frame_Shift_Del	DEL	GA	GA	-													0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	actccatccagaagcacctgGagaactcatgccatcggcat					rs201240908		TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr3:9870684_9870685delGA	ENST00000547186.1	+	10	1375_1376	c.1159_1160delGA	c.(1159-1161)gagfs	p.E387fs	TTLL3_ENST00000466245.1_3'UTR|TTLL3_ENST00000383827.1_Frame_Shift_Del_p.E175fs|TTLL3_ENST00000426895.4_Frame_Shift_Del_p.E530fs|TTLL3_ENST00000455274.1_Frame_Shift_Del_p.E175fs|ARPC4-TTLL3_ENST00000397256.1_Frame_Shift_Del_p.E448fs|TTLL3_ENST00000427853.3_Frame_Shift_Del_p.E175fs|TTLL3_ENST00000397241.1_Frame_Shift_Del_p.E175fs|TTLL3_ENST00000430793.1_Frame_Shift_Del_p.E175fs	NM_001025930.3	NP_001021100.3	Q9Y4R7	TTLL3_HUMAN	tubulin tyrosine ligase-like family, member 3	387	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				axoneme assembly (GO:0035082)|cilium assembly (GO:0042384)|protein polyglycylation (GO:0018094)	axoneme (GO:0005930)|cilium (GO:0005929)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	protein-glycine ligase activity (GO:0070735)|protein-glycine ligase activity, initiating (GO:0070736)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(2)|skin(1)	26	Medulloblastoma(99;0.227)					GAAGCACCTGGAGAACTCATGC	0.569																																					p.529_530del		Atlas-Indel,Pindel	.											.	TTLL3	51	.	0			c.1587_1588del						.																																			SO:0001589	frameshift_variant	26140	exon10			.		CCDS43048.1, CCDS43048.2	3p25.3	2013-02-14			ENSG00000214021	ENSG00000214021		"Tubulin tyrosine ligase-like family"	24483	protein-coding gene	gene with protein product						11054573	Standard	NR_037162		Approved	DKFZP434B103, HOTTL	uc003btg.4	Q9Y4R7	OTTHUMG00000128439	ENST00000547186.1:c.1159_1160delGA	chr3.hg19:g.9870686_9870687delGA	ENSP00000446659:p.Glu387fs	50.0	0.0		36.0	15.0	NM_001025930	Q4KMS8|Q6AWA3|Q6ZU95|Q8NDN8|Q96GG8|Q9H876|Q9UI99	Frame_Shift_Del	DEL	ENST00000547186.1	hg19																																																																																				.	.		0.569	TTLL3-203	KNOWN	basic	protein_coding	protein_coding		NM_001025930.2		-	9870685	GA	-	9870684	7	5	272	1	0	1	0	1	0	0	0	0	16743	1175	41	0	1193	0	TTLL3	3	9870684	Frame_Shift_Del	DEL	GA	TCGA-G3-A25S-01A-11D-A16V-10	6684358	9870684	188151746	16	39449										
BSN	8927	hgsc.bcm.edu	37	chr3	49694892	49694892	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	gccgcaggtctcgtcttcccCgccactcagactcaggctct	9	18	5	1			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr3:49694892C>T	ENST00000296452.4	+	5	8017	c.7903C>T	c.(7903-7905)Cgc>Tgc	p.R2635C		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	2635					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)	p.R2635S(1)		breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		TCGTCTTCCCCGCCACTCAGA	0.647																																					p.R2635C		Atlas-SNP	.											.	BSN	272	.	1	Substitution - Missense(1)	lung(1)	c.C7903T						.						38	45	43					3																	49694892		2203	4300	6503	SO:0001583	missense	8927	exon5			CTTCCCCGCCACT	AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"zinc finger protein 231", "neuronal double zinc finger protein"	604020	"bassoon (presynaptic cytomatrix protein)"	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.7903C>T	chr3.hg19:g.49694892C>T	ENSP00000296452:p.Arg2635Cys	54.0	0.0		34.0	7.0	NM_003458	O43161|Q7LGH3	Missense_Mutation	SNP	ENST00000296452.4	hg19	CCDS2800.1	.	.	.	.	.	.	.	.	.	.	C	11.23	1.576314	0.28092	.	.	ENSG00000164061	ENST00000296452	T	0.25085	1.82	6.04	6.04	0.98038	.	0.120057	0.56097	D	0.000038	T	0.50051	0.1593	L	0.55481	1.735	0.58432	D	0.999998	D	0.89917	1.0	D	0.79108	0.992	T	0.40001	-0.9586	10	0.87932	D	0	-16.6587	20.1896	0.98226	0.0:1.0:0.0:0.0	.	2635	Q9UPA5	BSN_HUMAN	C	2635	ENSP00000296452:R2635C	ENSP00000296452:R2635C	R	+	1	0	BSN	49669896	0.706000	0.27856	1.000000	0.80357	0.994000	0.84299	1.335000	0.33839	2.873000	0.98535	0.561000	0.74099	CGC	.	.		0.647	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458		T	49694892	C	T	49694892	3	4	272	1	0	0	0	0	1	0	0	0	1532	652	23	1	7921	1	BSN	3	49694892	Missense_Mutation	SNP	C	TCGA-G3-A25S-01A-11D-A16V-10	39824208	49694892	148327538	17	39450										
TMPRSS7	344805	hgsc.bcm.edu	37	chr3	111764780	111764780	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	gctgtggacatggactctgtGgtactaaatggtgattgttg	14	5	1	1			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr3:111764780G>A	ENST00000452346.2	+	5	684	c.681G>A	c.(679-681)gtG>gtA	p.V227V	TMPRSS7_ENST00000419127.1_Silent_p.V114V			Q7RTY8	TMPS7_HUMAN	transmembrane protease, serine 7	227	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.				proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(2)|endometrium(6)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						TGGACTCTGTGGTACTAAATG	0.463																																					p.V114V		Atlas-SNP	.											.	TMPRSS7	126	.	0			c.G342A						.						260	226	236					3																	111764780		692	1591	2283	SO:0001819	synonymous_variant	344805	exon4			CTCTGTGGTACTA	BN000125	CCDS43129.2	3q13.2	2010-04-13	2004-03-16		ENSG00000176040	ENSG00000176040		"Serine peptidases / Transmembrane"	30846	protein-coding gene	gene with protein product			"type II transmembrane serine protease 7"			12838346	Standard	NM_001042575		Approved		uc010hqb.2	Q7RTY8	OTTHUMG00000157148	ENST00000452346.2:c.681G>A	chr3.hg19:g.111764780G>A		372.0	0.0		322.0	117.0	NM_001042575	C9J8P7|E9PAS3|Q17RH4	Silent	SNP	ENST00000452346.2	hg19																																																																																				.	.		0.463	TMPRSS7-003	NOVEL	NAGNAG_splice_site|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000347592.2	XM_293599		A	111764780	G	A	111764780	2	1	272	1	0	0	0	0	0	0	0	1	16267	1335	47	3		3	TMPRSS7	3	111764780	Silent	SNP	G	TCGA-G3-A25S-01A-11D-A16V-10	62069888	111764780	86257650	18	39451										
CCDC14	64770	hgsc.bcm.edu	37	chr3	123665744	123665744	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	acattttttgccttctgtacAtccttcactgtttttgtatc	4	10	2	0			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr3:123665744A>T	ENST00000488653.2	-	8	1341	c.1251T>A	c.(1249-1251)gaT>gaA	p.D417E	CCDC14_ENST00000483247.1_Intron|CCDC14_ENST00000489746.1_Missense_Mutation_p.D217E|CCDC14_ENST00000310351.4_Missense_Mutation_p.D257E|CCDC14_ENST00000433542.2_Missense_Mutation_p.D376E|CCDC14_ENST00000485727.1_Missense_Mutation_p.D217E			Q49A88	CCD14_HUMAN	coiled-coil domain containing 14	417					substantia nigra development (GO:0021762)	centrosome (GO:0005813)				NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)	21		Lung NSC(201;0.0371)|Prostate(884;0.0405)|Myeloproliferative disorder(1037;0.205)		Lung(219;0.00942)|GBM - Glioblastoma multiforme(114;0.159)		CCTTCTGTACATCCTTCACTG	0.378																																					p.D376E		Atlas-SNP	.											.	CCDC14	97	.	0			c.T1128A						.						194	198	197					3																	123665744		2203	4300	6503	SO:0001583	missense	64770	exon7			CTGTACATCCTTC	AL122079	CCDS3025.2	3q21.1	2014-03-20			ENSG00000175455	ENSG00000175455			25766	protein-coding gene	gene with protein product						12477932	Standard	NM_022757		Approved	FLJ12892, DKFZp434L1050	uc010hrt.3	Q49A88	OTTHUMG00000153005	ENST00000488653.2:c.1251T>A	chr3.hg19:g.123665744A>T	ENSP00000420180:p.Asp417Glu	74.0	0.0		63.0	9.0	NM_022757	B7Z2T2|B8ZZ41|B8ZZ58|D3DN98|Q7Z3N3|Q86T30|Q8IWF8|Q8WUJ8|Q96K47|Q9H9A3|Q9UFH0	Missense_Mutation	SNP	ENST00000488653.2	hg19		.	.	.	.	.	.	.	.	.	.	A	12.74	2.029283	0.35797	.	.	ENSG00000175455	ENST00000488653;ENST00000310351;ENST00000485727;ENST00000489746;ENST00000433542;ENST00000409697;ENST00000426152	T;T;T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98;0.98;0.98	5.65	1.96	0.26148	.	0.499970	0.20011	N	0.101136	T	0.30324	0.0761	L	0.53249	1.67	0.09310	N	1	B;B;B	0.28850	0.225;0.225;0.091	B;B;B	0.26094	0.048;0.048;0.066	T	0.15037	-1.0451	10	0.15952	T	0.53	.	5.7785	0.18294	0.6498:0.1321:0.218:0.0	.	417;376;217	Q49A88;Q49A88-6;Q49A88-4	CCD14_HUMAN;.;.	E	417;257;217;217;376;398;143	ENSP00000420180:D417E;ENSP00000312031:D257E;ENSP00000418002:D217E;ENSP00000418403:D217E;ENSP00000395706:D376E;ENSP00000386866:D398E;ENSP00000414655:D143E	ENSP00000312031:D257E	D	-	3	2	CCDC14	125148434	0.794000	0.28838	0.704000	0.30370	0.960000	0.62799	0.720000	0.25896	0.567000	0.29293	0.533000	0.62120	GAT	.	.		0.378	CCDC14-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_022757		T	123665744	A	T	123665744	3	4	272	1	0	0	0	0	1	0	0	0	2775	214	8	4	1634	4	CCDC14	3	123665744	Missense_Mutation	SNP	A	TCGA-G3-A25S-01A-11D-A16V-10	11900964	123665744	74356686	19	39452										
MBD4	8930	hgsc.bcm.edu	37	chr3	129155490	129155490	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	ggctgaacaaaatttgtttaTgatgccagaagttttttgtt	9	4	0	3			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr3:129155490T>A	ENST00000249910.1	-	3	1172	c.997A>T	c.(997-999)Ata>Tta	p.I333L	MBD4_ENST00000429544.2_Missense_Mutation_p.I333L|MBD4_ENST00000509587.1_Intron|MBD4_ENST00000393278.2_Intron|MBD4_ENST00000503197.1_Missense_Mutation_p.I333L|MBD4_ENST00000507208.1_Missense_Mutation_p.I333L	NM_003925.1	NP_003916.1	O95243	MBD4_HUMAN	methyl-CpG binding domain protein 4	333					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depyrimidination (GO:0045008)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|response to radiation (GO:0009314)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endodeoxyribonuclease activity (GO:0004520)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|satellite DNA binding (GO:0003696)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)	22						AATTTGTTTATGATGCCAGAA	0.348								Base excision repair (BER), DNA glycosylases																													p.I333L		Atlas-SNP	.											.	MBD4	53	.	0			c.A997T						.						88	96	93					3																	129155490		2202	4300	6502	SO:0001583	missense	8930	exon3			TGTTTATGATGCC	AF072250	CCDS3058.1, CCDS63766.1, CCDS63767.1, CCDS63768.1, CCDS63769.1	3q21.3	2004-03-02			ENSG00000129071	ENSG00000129071			6919	protein-coding gene	gene with protein product		603574				9774669, 10097147	Standard	NM_003925		Approved	MED1	uc003emh.2	O95243	OTTHUMG00000159463	ENST00000249910.1:c.997A>T	chr3.hg19:g.129155490T>A	ENSP00000249910:p.Ile333Leu	179.0	0.0		143.0	23.0	NM_003925	B4DZN2|D3DNC3|D3DNC4|E9PEE4|Q2MD36|Q7Z4T3|Q96F09	Missense_Mutation	SNP	ENST00000249910.1	hg19	CCDS3058.1	.	.	.	.	.	.	.	.	.	.	T	6.389	0.439882	0.12104	.	.	ENSG00000129071	ENST00000429544;ENST00000249910;ENST00000503197;ENST00000507208	D;D;D;D	0.92647	-2.88;-2.88;-3.08;-3.08	5.27	-2.26	0.06867	.	1.310070	0.04720	N	0.419243	D	0.82536	0.5058	L	0.27053	0.805	0.20074	N	0.999931	B;B;B;B	0.24920	0.07;0.114;0.048;0.07	B;B;B;B	0.20955	0.024;0.032;0.022;0.014	T	0.67569	-0.5637	10	0.20519	T	0.43	-0.255	1.3947	0.02258	0.1389:0.2731:0.1424:0.4455	.	333;333;333;333	E9PEE4;O95243-2;O95243-3;O95243	.;.;.;MBD4_HUMAN	L	333	ENSP00000394080:I333L;ENSP00000249910:I333L;ENSP00000424873:I333L;ENSP00000422327:I333L	ENSP00000249910:I333L	I	-	1	0	MBD4	130638180	0.001000	0.12720	0.012000	0.15200	0.201000	0.24016	-0.239000	0.08965	-0.254000	0.09500	-0.256000	0.11100	ATA	.	.		0.348	MBD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355529.1	NM_003925		A	129155490	T	A	129155490	3	1	272	1	0	0	0	0	1	0	0	0	9355	1464	51	4	769	4	MBD4	3	129155490	Missense_Mutation	SNP	T	TCGA-G3-A25S-01A-11D-A16V-10	5489746	129155490	68866940	20	39453										
COL6A6	131873	hgsc.bcm.edu	37	chr3	130289820	130289820	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	ggtttggggctctgaagtatGctgatgacccagaggtgctg	16	7	1	4			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr3:130289820G>A	ENST00000358511.6	+	6	2591	c.2560G>A	c.(2560-2562)Gct>Act	p.A854T	COL6A6_ENST00000453409.2_Missense_Mutation_p.A854T	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	854	Nonhelical region.|VWFA 5. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						TCTGAAGTATGCTGATGACCC	0.433																																					p.A854T		Atlas-SNP	.											.	COL6A6	497	.	0			c.G2560A						.						75	76	76					3																	130289820		1880	4118	5998	SO:0001583	missense	131873	exon6			AAGTATGCTGATG	AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.2560G>A	chr3.hg19:g.130289820G>A	ENSP00000351310:p.Ala854Thr	93.0	0.0		88.0	16.0	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	hg19	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	G	17.92	3.507212	0.64410	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	T;T	0.79454	-1.27;-1.27	4.87	3.85	0.44370	von Willebrand factor, type A (3);	0.108239	0.41294	D	0.000905	T	0.64832	0.2634	N	0.25380	0.74	0.29826	N	0.830448	P	0.34462	0.454	B	0.38156	0.266	T	0.65401	-0.6177	10	0.87932	D	0	.	5.8236	0.18540	0.0996:0.0:0.5249:0.3754	.	854	A6NMZ7	CO6A6_HUMAN	T	854	ENSP00000351310:A854T;ENSP00000399236:A854T	ENSP00000351310:A854T	A	+	1	0	COL6A6	131772510	0.002000	0.14202	0.932000	0.37286	0.924000	0.55760	0.555000	0.23422	2.424000	0.82194	0.561000	0.74099	GCT	.	.		0.433	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		A	130289820	G	A	130289820	3	1	272	1	0	0	0	0	1	0	0	0	3705	1319	46	3	2582	3	COL6A6	3	130289820	Missense_Mutation	SNP	G	TCGA-G3-A25S-01A-11D-A16V-10	1134330	130289820	67732610	21	39454										
NLGN1	22871	hgsc.bcm.edu	37	chr3	173322666	173322666	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	agccccaccaacaggggaacGtcgttttcagcctccagaac	9	15	1	1			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr3:173322666G>T	ENST00000457714.1	+	3	707	c.278G>T	c.(277-279)cGt>cTt	p.R93L	NLGN1_ENST00000545397.1_Missense_Mutation_p.R93L|NLGN1_ENST00000361589.4_Missense_Mutation_p.R93L|NLGN1_ENST00000401917.3_Missense_Mutation_p.R93L	NM_014932.2	NP_055747.1	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	93					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|calcium-dependent cell-cell adhesion (GO:0016339)|cytoskeletal matrix organization at active zone (GO:0048789)|establishment of protein localization (GO:0045184)|heterophilic cell-cell adhesion (GO:0007157)|N-methyl-D-aspartate receptor clustering (GO:0097114)|nervous system development (GO:0007399)|neurexin clustering (GO:0097115)|neuron cell-cell adhesion (GO:0007158)|neuronal signal transduction (GO:0023041)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|positive regulation of synaptic vesicle exocytosis (GO:2000302)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|protein homooligomerization (GO:0051260)|protein localization to synapse (GO:0035418)|protein targeting (GO:0006605)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuron differentiation (GO:0045664)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|synapse assembly (GO:0007416)|synaptic vesicle clustering (GO:0097091)|synaptic vesicle targeting (GO:0016080)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|filopodium tip (GO:0032433)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|PDZ domain binding (GO:0030165)|protein dimerization activity (GO:0046983)|receptor activity (GO:0004872)	p.R93L(2)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(2)|lung(54)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	83	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			ACAGGGGAACGTCGTTTTCAG	0.453																																					p.R93L		Atlas-SNP	.											NLGN1,caecum,adenoma,0,3	NLGN1	209	.	2	Substitution - Missense(2)	lung(2)	c.G278T						.						130	129	129					3																	173322666		2203	4300	6503	SO:0001583	missense	22871	exon3			GGGAACGTCGTTT	AB028993	CCDS3222.1	3q26.32	2008-07-18			ENSG00000169760	ENSG00000169760			14291	protein-coding gene	gene with protein product		600568				10767552, 10819331	Standard	NM_014932		Approved	KIAA1070	uc003fio.1	Q8N2Q7	OTTHUMG00000157005	ENST00000457714.1:c.278G>T	chr3.hg19:g.173322666G>T	ENSP00000392500:p.Arg93Leu	102.0	0.0		94.0	39.0	NM_014932	Q9UPT2	Missense_Mutation	SNP	ENST00000457714.1	hg19	CCDS3222.1	.	.	.	.	.	.	.	.	.	.	G	6.574	0.474179	0.12521	.	.	ENSG00000169760	ENST00000457714;ENST00000361589;ENST00000415045;ENST00000545397;ENST00000401917	T;T;T;T;T	0.58940	0.3;0.3;0.3;0.3;0.3	5.62	3.23	0.37069	.	0.229124	0.34314	N	0.004077	T	0.22666	0.0547	N	0.01410	-0.885	0.32782	N	0.502396	B;B	0.26195	0.004;0.144	B;B	0.18561	0.022;0.016	T	0.16630	-1.0396	10	0.23891	T	0.37	.	6.2449	0.20811	0.6324:0.0:0.3676:0.0	.	93;93	D2X2H5;Q8N2Q7-2	.;.	L	93	ENSP00000392500:R93L;ENSP00000354541:R93L;ENSP00000410374:R93L;ENSP00000441108:R93L;ENSP00000385750:R93L	ENSP00000354541:R93L	R	+	2	0	NLGN1	174805360	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	2.321000	0.43805	1.069000	0.40788	-0.373000	0.07131	CGT	.	.		0.453	NLGN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347054.3	NM_014932		T	173322666	G	T	173322666	3	4	272	1	0	0	0	0	1	0	0	0	10470	1145	40	1	280	1	NLGN1	3	173322666	Missense_Mutation	SNP	G	TCGA-G3-A25S-01A-11D-A16V-10	43032846	173322666	24699764	22	39455										
NLGN1	22871	hgsc.bcm.edu	37	chr3	173525610	173525610	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	tcatcacagtcaactatcgaCttggagtactcggtaagaag	9	9	3	1			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr3:173525610C>A	ENST00000457714.1	+	4	1063	c.634C>A	c.(634-636)Ctt>Att	p.L212I	NLGN1_ENST00000545397.1_Missense_Mutation_p.L212I|NLGN1_ENST00000361589.4_Missense_Mutation_p.L212I|NLGN1_ENST00000401917.3_Missense_Mutation_p.L252I	NM_014932.2	NP_055747.1	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	229					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|calcium-dependent cell-cell adhesion (GO:0016339)|cytoskeletal matrix organization at active zone (GO:0048789)|establishment of protein localization (GO:0045184)|heterophilic cell-cell adhesion (GO:0007157)|N-methyl-D-aspartate receptor clustering (GO:0097114)|nervous system development (GO:0007399)|neurexin clustering (GO:0097115)|neuron cell-cell adhesion (GO:0007158)|neuronal signal transduction (GO:0023041)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|positive regulation of synaptic vesicle exocytosis (GO:2000302)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|protein homooligomerization (GO:0051260)|protein localization to synapse (GO:0035418)|protein targeting (GO:0006605)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuron differentiation (GO:0045664)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|synapse assembly (GO:0007416)|synaptic vesicle clustering (GO:0097091)|synaptic vesicle targeting (GO:0016080)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|filopodium tip (GO:0032433)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|PDZ domain binding (GO:0030165)|protein dimerization activity (GO:0046983)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(2)|lung(54)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	83	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			CAACTATCGACTTGGAGTACT	0.388																																					p.L212I		Atlas-SNP	.											.	NLGN1	209	.	0			c.C634A						.						140	132	135					3																	173525610		2203	4300	6503	SO:0001583	missense	22871	exon4			TATCGACTTGGAG	AB028993	CCDS3222.1	3q26.32	2008-07-18			ENSG00000169760	ENSG00000169760			14291	protein-coding gene	gene with protein product		600568				10767552, 10819331	Standard	NM_014932		Approved	KIAA1070	uc003fio.1	Q8N2Q7	OTTHUMG00000157005	ENST00000457714.1:c.634C>A	chr3.hg19:g.173525610C>A	ENSP00000392500:p.Leu212Ile	137.0	0.0		97.0	52.0	NM_014932	Q9UPT2	Missense_Mutation	SNP	ENST00000457714.1	hg19	CCDS3222.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.987790	0.93106	.	.	ENSG00000169760	ENST00000457714;ENST00000361589;ENST00000415045;ENST00000545397;ENST00000401917	T;T;T;T;T	0.74947	-0.6;-0.6;-0.89;-0.6;-0.6	5.64	5.64	0.86602	.	0.000000	0.64402	D	0.000001	D	0.85128	0.5626	M	0.88377	2.95	0.80722	D	1	P;P	0.50066	0.931;0.605	P;P	0.50934	0.654;0.619	D	0.87424	0.2384	10	0.62326	D	0.03	.	19.6981	0.96039	0.0:1.0:0.0:0.0	.	252;212	D2X2H5;Q8N2Q7-2	.;.	I	212;212;252;212;252	ENSP00000392500:L212I;ENSP00000354541:L212I;ENSP00000410374:L252I;ENSP00000441108:L212I;ENSP00000385750:L252I	ENSP00000354541:L212I	L	+	1	0	NLGN1	175008304	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	6.085000	0.71343	2.665000	0.90641	0.557000	0.71058	CTT	.	.		0.388	NLGN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347054.3	NM_014932		A	173525610	C	A	173525610	3	1	272	1	0	0	0	0	1	0	0	0	10470	565	20	3	640	3	NLGN1	3	173525610	Missense_Mutation	SNP	C	TCGA-G3-A25S-01A-11D-A16V-10	202944	173525610	24496820	23	39456										
CD38	952	hgsc.bcm.edu	37	chr4	15839760	15839760	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	tccatgtgatgctcaatggaTcccgcagtaaaatctttgac	8	10	2	2			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr4:15839760T>C	ENST00000226279.3	+	5	768	c.631T>C	c.(631-633)Tcc>Ccc	p.S211P		NM_001775.2	NP_001766.2	P28907	CD38_HUMAN	CD38 molecule	211					apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|female pregnancy (GO:0007565)|long term synaptic depression (GO:0060292)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone resorption (GO:0045779)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell growth (GO:0030307)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of insulin secretion (GO:0032024)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vasoconstriction (GO:0045907)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hydroperoxide (GO:0033194)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	NAD(P)+ nucleosidase activity (GO:0050135)|NAD+ nucleosidase activity (GO:0003953)|phosphorus-oxygen lyase activity (GO:0016849)|transferase activity (GO:0016740)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|stomach(1)	14						GCTCAATGGATCCCGCAGTAA	0.383																																					p.S211P		Atlas-SNP	.											.	CD38	36	.	0			c.T631C						.						143	133	136					4																	15839760		2203	4300	6503	SO:0001583	missense	952	exon5			AATGGATCCCGCA	D84276	CCDS3417.1	4p15.32	2010-05-04	2006-03-28		ENSG00000004468	ENSG00000004468	3.2.2.5	"CD molecules"	1667	protein-coding gene	gene with protein product	"ADP-ribosyl cyclase 1", "NAD(+) nucleosidase"	107270	"CD38 antigen (p45)"			9074508, 2319135	Standard	NM_001775		Approved		uc003gol.1	P28907	OTTHUMG00000048206	ENST00000226279.3:c.631T>C	chr4.hg19:g.15839760T>C	ENSP00000226279:p.Ser211Pro	59.0	0.0		53.0	33.0	NM_001775	O00121|O00122|Q96HY4	Missense_Mutation	SNP	ENST00000226279.3	hg19	CCDS3417.1	.	.	.	.	.	.	.	.	.	.	T	13.69	2.312152	0.40895	.	.	ENSG00000004468	ENST00000226279;ENST00000510674	T;T	0.53857	0.6;0.6	5.4	5.4	0.78164	NAD(P)-binding domain (1);	0.112478	0.64402	D	0.000007	T	0.74703	0.3751	M	0.87381	2.88	0.40730	D	0.982734	D	0.89917	1.0	D	0.91635	0.999	T	0.80169	-0.1494	10	0.87932	D	0	-28.9521	12.0932	0.53739	0.0:0.0:0.0:1.0	.	211	P28907	CD38_HUMAN	P	211;99	ENSP00000226279:S211P;ENSP00000423047:S99P	ENSP00000226279:S211P	S	+	1	0	CD38	15448858	0.010000	0.17322	0.355000	0.25773	0.161000	0.22273	0.907000	0.28531	2.178000	0.69098	0.533000	0.62120	TCC	.	.		0.383	CD38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250322.2	NM_001775		C	15839760	T	C	15839760	3	2	272	1	0	0	0	0	1	0	0	0	3011	1435	50	2	649	2	CD38	4	15839760	Missense_Mutation	SNP	T	TCGA-G3-A25S-01A-11D-A16V-10		15839760	175314516	24	39457										
ALB	213	hgsc.bcm.edu	37	chr4	74283297	74283298	+	Frame_Shift_Ins	INS	-	-	T													0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	ccaagtgtcaactccaactcINSttgtagaggtctcaagaaac							TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr4:74283297_74283298insT	ENST00000503124.1	+	9	1096_1097	c.889_890insT	c.(889-891)cttfs	p.L297fs	ALB_ENST00000505649.1_Intron|ALB_ENST00000415165.2_Frame_Shift_Ins_p.L255fs|ALB_ENST00000401494.3_Frame_Shift_Ins_p.L332fs|ALB_ENST00000509063.1_Frame_Shift_Ins_p.L447fs|ALB_ENST00000295897.4_Frame_Shift_Ins_p.L447fs			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			AACTCCAACTCTTGTAGAGGTC	0.401																																					p.L447fs		Atlas-INDEL	.											.	ALB	132	.	0			c.1339_1340insT						.																																			SO:0001589	frameshift_variant	213	exon11			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.891dupT	chr4.hg19:g.74283299_74283299dupT	ENSP00000421027:p.Leu297fs	112.0	0.0		51.0	42.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Frame_Shift_Ins	INS	ENST00000503124.1	hg19																																																																																				.	.		0.401	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		T	74283298	-	T	74283297	7	5	272	1	0	1	1	0	0	0	0	0	486	913	32	0	1381	0	ALB	4	74283297	Frame_Shift_Ins	INS	-	TCGA-G3-A25S-01A-11D-A16V-10	58443537	74283297	116870979	25	39458										
ALB	213	hgsc.bcm.edu	37	chr4	74283386	74283387	+	Splice_Site	DEL	TG	TG	-													0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	atgccctgtgcagaagactaTgtgagtctttaaaaaaatat					rs78527483		TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr4:74283386_74283387delTG	ENST00000503124.1	+	9	1185	c.978delTG	c.(976-978)tat>ta	p.Y326fs	ALB_ENST00000505649.1_Intron|ALB_ENST00000415165.2_Splice_Site_p.Y284fs|ALB_ENST00000401494.3_Splice_Site_p.Y361fs|ALB_ENST00000509063.1_Splice_Site_p.Y476fs|ALB_ENST00000295897.4_Splice_Site_p.Y476fs			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CAGAAGACTATGTGAGTCttta	0.332																																					p.476_476del		Atlas-Indel,Pindel	.											.	ALB	132	.	0			c.1427_1428del						.																																			SO:0001630	splice_region_variant	213	exon11			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.978+1TG>-	chr4.hg19:g.74283388_74283389delTG		59.0	0.0		23.0	20.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Frame_Shift_Del	DEL	ENST00000503124.1	hg19																																																																																				.	.		0.332	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477	Frame_Shift_Del	-	74283387	TG	-	74283386	8	5	272	1	0	1	0	1	0	0	1	0	486	1478	51	0	1470	0	ALB	4	74283386	Splice_Site	DEL	TG	TCGA-G3-A25S-01A-11D-A16V-10	89	74283386	116870890	26	39459										
ZNF827	152485	hgsc.bcm.edu	37	chr4	146859553	146859553	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	gggctgctcctgcttcctccTgggcattttcccccttttct	8	16	1	0			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr4:146859553T>A	ENST00000508784.1	-	1	234	c.7A>T	c.(7-9)Agg>Tgg	p.R3W	ZNF827_ENST00000513320.1_Missense_Mutation_p.R3W|ZNF827_ENST00000379448.4_Missense_Mutation_p.R3W			Q17R98	ZN827_HUMAN	zinc finger protein 827	3					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	all_hematologic(180;0.151)					TGCTTCCTCCTGGGCATTTTC	0.572																																					p.R3W		Atlas-SNP	.											.	ZNF827	102	.	0			c.A7T						.						277	212	234					4																	146859553		2203	4300	6503	SO:0001583	missense	152485	exon1			TCCTCCTGGGCAT	AK091130	CCDS34072.1	4q31.22	2013-01-08			ENSG00000151612	ENSG00000151612		"Zinc fingers, C2H2-type"	27193	protein-coding gene	gene with protein product						12477932	Standard	NM_178835		Approved		uc003ikm.3	Q17R98	OTTHUMG00000161362	ENST00000508784.1:c.7A>T	chr4.hg19:g.146859553T>A	ENSP00000421863:p.Arg3Trp	160.0	0.0		96.0	68.0	NM_178835	B7ZL52|Q7Z4S7|Q8N279	Missense_Mutation	SNP	ENST00000508784.1	hg19		.	.	.	.	.	.	.	.	.	.	t	12.81	2.049397	0.36181	.	.	ENSG00000151612	ENST00000508784;ENST00000513320;ENST00000379448;ENST00000440280	T;T;T	0.09723	2.95;3.14;2.98	4.53	3.29	0.37713	.	0.376195	0.24303	U	0.039706	T	0.16854	0.0405	N	0.19112	0.55	0.42996	D	0.9945	B;D;D	0.76494	0.098;0.999;0.999	B;D;D	0.79784	0.221;0.984;0.993	T	0.02345	-1.1173	10	0.72032	D	0.01	.	9.5955	0.39571	0.0:0.0:0.177:0.823	.	3;3;3	G5E9Z1;Q17R98;Q17R98-2	.;ZN827_HUMAN;.	W	3	ENSP00000421863:R3W;ENSP00000423130:R3W;ENSP00000368761:R3W	ENSP00000368761:R3W	R	-	1	2	ZNF827	147079003	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	5.285000	0.65633	0.673000	0.31224	0.228000	0.17796	AGG	.	.		0.572	ZNF827-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000364654.2	NM_178835		A	146859553	T	A	146859553	3	1	272	1	0	0	0	0	1	0	0	0	18195	1579	55	4	3278	4	ZNF827	4	146859553	Missense_Mutation	SNP	T	TCGA-G3-A25S-01A-11D-A16V-10	72576167	146859553	44294723	27	39460										
ZNF131	7690	hgsc.bcm.edu	37	chr5	43161948	43161948	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	gtcagtaagaagcaaagaacTgggaaaaaaattcatgtatg	10	4	2	2			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr5:43161948T>C	ENST00000399534.1	+	5	1013	c.969T>C	c.(967-969)acT>acC	p.T323T	ZNF131_ENST00000509634.1_Silent_p.T289T|ZNF131_ENST00000509931.1_Intron|ZNF131_ENST00000306938.4_Silent_p.T289T|ZNF131_ENST00000505606.2_Silent_p.T289T|ZNF131_ENST00000509156.1_Silent_p.T323T			P52739	ZN131_HUMAN	zinc finger protein 131	323					regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(2)|kidney(1)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	17						AGCAAAGAACTGGGAAAAAAA	0.368																																					p.T289T		Atlas-SNP	.											.	ZNF131	51	.	0			c.T867C						.						63	59	60					5																	43161948		1871	4106	5977	SO:0001819	synonymous_variant	7690	exon6			AAGAACTGGGAAA	U09410	CCDS43313.1	5p12	2013-01-09	2006-06-13		ENSG00000172262	ENSG00000172262		"Zinc fingers, C2H2-type", "-", "BTB/POZ domain containing"	12915	protein-coding gene	gene with protein product	"zinc finger and BTB domain containing 35"	604073	"zinc finger protein 131 (clone pHZ-10)"				Standard	XM_005248359		Approved	ZBTB35, pHZ-10	uc003jnk.3	P52739	OTTHUMG00000162223	ENST00000399534.1:c.969T>C	chr5.hg19:g.43161948T>C		169.0	0.0		145.0	78.0	NM_003432	B4DRL3|Q6PIF0	Silent	SNP	ENST00000399534.1	hg19																																																																																				.	.		0.368	ZNF131-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000367982.1	NM_003432		C	43161948	T	C	43161948	2	2	272	1	0	0	0	0	0	0	0	1	17736	1567	55	2		2	ZNF131	5	43161948	Silent	SNP	T	TCGA-G3-A25S-01A-11D-A16V-10		43161948	137753312	28	39461										
ELL2	22936	hgsc.bcm.edu	37	chr5	95226823	95226823	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	ttacctgatactcttttgagCctggagaaaggcgctttctt	9	9	2	3			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr5:95226823C>A	ENST00000237853.4	-	10	2094	c.1745G>T	c.(1744-1746)gGc>gTc	p.G582V	ELL2_ENST00000431061.2_Missense_Mutation_p.G332V	NM_012081.5	NP_036213.2	O00472	ELL2_HUMAN	elongation factor, RNA polymerase II, 2	582					regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|transcription elongation from RNA polymerase II promoter (GO:0006368)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)	24		all_cancers(142;2.04e-06)|all_epithelial(76;3.1e-09)|all_lung(232;0.00309)|Lung NSC(167;0.00454)|Ovarian(225;0.0165)|Colorectal(57;0.0343)|Breast(839;0.198)		all cancers(79;2.16e-15)		CTCTTTTGAGCCTGGAGAAAG	0.428																																					p.G582V		Atlas-SNP	.											.	ELL2	63	.	0			c.G1745T						.						198	195	196					5																	95226823		2203	4300	6503	SO:0001583	missense	22936	exon10			TTTGAGCCTGGAG	U88629	CCDS4080.1	5q15	2010-11-29			ENSG00000118985	ENSG00000118985			17064	protein-coding gene	gene with protein product		601874				9108030	Standard	NM_012081		Approved		uc003klr.4	O00472	OTTHUMG00000122085	ENST00000237853.4:c.1745G>T	chr5.hg19:g.95226823C>A	ENSP00000237853:p.Gly582Val	119.0	0.0		145.0	86.0	NM_012081	B4DNK7	Missense_Mutation	SNP	ENST00000237853.4	hg19	CCDS4080.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.1|28.1	4.888928|4.888928	0.91814|0.91814	.|.	.|.	ENSG00000118985|ENSG00000118985	ENST00000508757|ENST00000237853;ENST00000431061	.|T;T	.|0.26223	.|1.75;1.75	6.16|6.16	6.16|6.16	0.99307|0.99307	.|Occludin/RNA polymerase II elongation factor, ELL domain (1);	.|0.043393	.|0.85682	.|D	.|0.000000	T|T	0.62490|0.62490	0.2432|0.2432	M|M	0.90369|0.90369	3.11|3.11	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.91635	.|0.999	T|T	0.67225|0.67225	-0.5724|-0.5724	5|10	.|0.87932	.|D	.|0	-1.8572|-1.8572	20.4549|20.4549	0.99139|0.99139	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|582	.|O00472	.|ELL2_HUMAN	S|V	100|582;332	.|ENSP00000237853:G582V;ENSP00000399704:G332V	.|ENSP00000237853:G582V	A|G	-|-	1|2	0|0	ELL2|ELL2	95252579|95252579	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.989000|0.989000	0.77384|0.77384	6.066000|6.066000	0.71185|0.71185	2.937000|2.937000	0.99478|0.99478	0.650000|0.650000	0.86243|0.86243	GCT|GGC	.	.		0.428	ELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242846.1	NM_012081		A	95226823	C	A	95226823	3	1	272	1	0	0	0	0	1	0	0	0	5065	739	26	3	189	3	ELL2	5	95226823	Missense_Mutation	SNP	C	TCGA-G3-A25S-01A-11D-A16V-10	52064875	95226823	85688437	29	39462										
DMXL1	1657	hgsc.bcm.edu	37	chr5	118485268	118485268	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	accatcttctaaacaagaacCtgttataacagattcgtaca	4	10	2	2			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr5:118485268C>T	ENST00000311085.8	+	18	3826	c.3746C>T	c.(3745-3747)cCt>cTt	p.P1249L	DMXL1_ENST00000539542.1_Missense_Mutation_p.P1249L	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	1249										breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		AAACAAGAACCTGTTATAACA	0.423																																					p.P1249L		Atlas-SNP	.											.	DMXL1	268	.	0			c.C3746T						.						85	79	81					5																	118485268		2202	4300	6502	SO:0001583	missense	1657	exon18			AAGAACCTGTTAT	AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"WD repeat domain containing"	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.3746C>T	chr5.hg19:g.118485268C>T	ENSP00000309690:p.Pro1249Leu	56.0	0.0		56.0	35.0	NM_005509		Missense_Mutation	SNP	ENST00000311085.8	hg19	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	C	1.114	-0.657206	0.03480	.	.	ENSG00000172869	ENST00000311085;ENST00000539542	T;T	0.09350	2.99;2.99	5.39	3.61	0.41365	.	0.469142	0.25487	N	0.030325	T	0.07683	0.0193	N	0.25647	0.755	0.34149	D	0.667335	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.17592	-1.0364	10	0.27785	T	0.31	-4.4666	9.6826	0.40078	0.0:0.7593:0.0:0.2407	.	1249;1249	F5H269;Q9Y485	.;DMXL1_HUMAN	L	1249	ENSP00000309690:P1249L;ENSP00000439479:P1249L	ENSP00000309690:P1249L	P	+	2	0	DMXL1	118513167	0.001000	0.12720	0.922000	0.36590	0.995000	0.86356	1.124000	0.31320	0.773000	0.33404	0.655000	0.94253	CCT	.	.		0.423	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		T	118485268	C	T	118485268	3	4	272	1	0	0	0	0	1	0	0	0	4596	681	24	3	3816	3	DMXL1	5	118485268	Missense_Mutation	SNP	C	TCGA-G3-A25S-01A-11D-A16V-10	23258445	118485268	62429992	30	39463										
PRR16	51334	hgsc.bcm.edu	37	chr5	120022233	120022233	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	ggaaagattcctcaccaaggCcctcccctccctcctacacc	5	20	1	1			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr5:120022233C>T	ENST00000407149.2	+	2	953	c.744C>T	c.(742-744)ggC>ggT	p.G248G	PRR16_ENST00000446965.1_Silent_p.G178G|PRR16_ENST00000505123.1_Silent_p.G178G|PRR16_ENST00000379551.2_Silent_p.G225G			Q569H4	LARGN_HUMAN	proline rich 16	248	Pro-rich.				positive regulation of cell size (GO:0045793)|positive regulation of translation (GO:0045727)					endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0464)|Prostate(80;0.00446)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.000126)|Epithelial(69;0.000331)|all cancers(49;0.00169)		CTCACCAAGGCCCTCCCCTCC	0.522																																					p.G225G		Atlas-SNP	.											.	PRR16	71	.	0			c.C675T						.						91	85	87					5																	120022233		2203	4300	6503	SO:0001819	synonymous_variant	51334	exon3			CCAAGGCCCTCCC	AF242769	CCDS4127.1, CCDS75290.1	5q23.1	2006-08-22			ENSG00000184838	ENSG00000184838			29654	protein-coding gene	gene with protein product		615931				15971941	Standard	XM_005272010		Approved	DSC54	uc003ksp.3	Q569H4	OTTHUMG00000128903	ENST00000407149.2:c.744C>T	chr5.hg19:g.120022233C>T		100.0	0.0		118.0	28.0	NM_016644	D3DSZ0|Q8IXY1|Q9NYI5	Silent	SNP	ENST00000407149.2	hg19																																																																																				.	.		0.522	PRR16-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000371059.1	NM_016644		T	120022233	C	T	120022233	2	4	272	1	0	0	0	0	0	0	0	1	12601	726	26	3		3	PRR16	5	120022233	Silent	SNP	C	TCGA-G3-A25S-01A-11D-A16V-10	1536965	120022233	60893027	31	39464										
FSTL4	23105	hgsc.bcm.edu	37	chr5	132585166	132585166	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	gcttccagatgattggtggcCtcaggtctccatggacggcg	14	11	2	2			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr5:132585166C>T	ENST00000265342.7	-	7	1079	c.830G>A	c.(829-831)aGg>aAg	p.R277K	FSTL4_ENST00000507112.1_5'UTR|CTB-49A3.5_ENST00000515122.1_RNA|CTB-49A3.5_ENST00000504312.1_RNA	NM_015082.1	NP_055897.1	Q6MZW2	FSTL4_HUMAN	follistatin-like 4	277	Ig-like 1.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(8)|skin(2)|upper_aerodigestive_tract(1)	23		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GATTGGTGGCCTCAGGTCTCC	0.587																																					p.R277K		Atlas-SNP	.											.	FSTL4	74	.	0			c.G830A						.						115	89	97					5																	132585166		2203	4300	6503	SO:0001583	missense	23105	exon7			GGTGGCCTCAGGT	AB028984	CCDS34238.1	5q31.1	2013-01-29			ENSG00000053108	ENSG00000053108		"EF-hand domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	21389	protein-coding gene	gene with protein product						10470851, 15527507	Standard	NM_015082		Approved	KIAA1061	uc003kyn.1	Q6MZW2	OTTHUMG00000162729	ENST00000265342.7:c.830G>A	chr5.hg19:g.132585166C>T	ENSP00000265342:p.Arg277Lys	74.0	0.0		91.0	13.0	NM_015082	Q8TBU0|Q9UPU1	Missense_Mutation	SNP	ENST00000265342.7	hg19	CCDS34238.1	.	.	.	.	.	.	.	.	.	.	C	31	5.103453	0.94245	.	.	ENSG00000053108	ENST00000265342;ENST00000360575	T	0.11821	2.74	5.51	5.51	0.81932	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.27489	0.0675	L	0.35542	1.07	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.01532	-1.1331	10	0.22706	T	0.39	-35.463	18.4076	0.90541	0.0:1.0:0.0:0.0	.	277	Q6MZW2	FSTL4_HUMAN	K	277;108	ENSP00000265342:R277K	ENSP00000265342:R277K	R	-	2	0	FSTL4	132613065	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	5.729000	0.68538	2.590000	0.87494	0.467000	0.42956	AGG	.	.		0.587	FSTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370212.1	XM_048786		T	132585166	C	T	132585166	3	4	272	1	0	0	0	0	1	0	0	0	6087	681	24	3	1738	3	FSTL4	5	132585166	Missense_Mutation	SNP	C	TCGA-G3-A25S-01A-11D-A16V-10	12562933	132585166	48330094	32	39465										
DNAJC18	202052	hgsc.bcm.edu	37	chr5	138764241	138764241	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	tcagacctttgaaagcatctGttgctccaggagcacagttc	9	11	2	2			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr5:138764241G>T	ENST00000302060.5	-	3	439	c.359C>A	c.(358-360)aCa>aAa	p.T120K		NM_152686.3	NP_689899.1	Q9H819	DJC18_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 18	120	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.					integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			GAAAGCATCTGTTGCTCCAGG	0.443																																					p.T120K		Atlas-SNP	.											.	DNAJC18	30	.	0			c.C359A						.						260	262	261					5																	138764241		2203	4300	6503	SO:0001583	missense	202052	exon3			GCATCTGTTGCTC	AK024054	CCDS4214.1	5q31.2	2011-09-02		2005-08-09	ENSG00000170464	ENSG00000170464		"Heat shock proteins / DNAJ (HSP40)"	28429	protein-coding gene	gene with protein product							Standard	NM_152686		Approved	MGC29463	uc003len.3	Q9H819	OTTHUMG00000129225	ENST00000302060.5:c.359C>A	chr5.hg19:g.138764241G>T	ENSP00000302843:p.Thr120Lys	60.0	0.0		81.0	26.0	NM_152686		Missense_Mutation	SNP	ENST00000302060.5	hg19	CCDS4214.1	.	.	.	.	.	.	.	.	.	.	G	32	5.124859	0.94429	.	.	ENSG00000170464	ENST00000302060;ENST00000515581;ENST00000515277	T;T;T	0.72505	-0.66;-0.66;-0.66	6.04	6.04	0.98038	Heat shock protein DnaJ, N-terminal (5);	0.000000	0.85682	D	0.000000	T	0.76955	0.4060	L	0.31804	0.96	0.80722	D	1	D;D	0.67145	0.996;0.993	D;P	0.70487	0.969;0.883	T	0.73219	-0.4052	10	0.32370	T	0.25	-12.0825	19.1586	0.93522	0.0:0.0:1.0:0.0	.	120;120	D6RB03;Q9H819	.;DJC18_HUMAN	K	120	ENSP00000302843:T120K;ENSP00000424572:T120K;ENSP00000425523:T120K	ENSP00000302843:T120K	T	-	2	0	DNAJC18	138792140	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.777000	0.99008	2.873000	0.98535	0.563000	0.77884	ACA	.	.		0.443	DNAJC18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374191.1	NM_152686		T	138764241	G	T	138764241	3	4	272	1	0	0	0	0	1	0	0	0	4639	1377	48	3	741	3	DNAJC18	5	138764241	Missense_Mutation	SNP	G	TCGA-G3-A25S-01A-11D-A16V-10	6179075	138764241	42151019	33	39466										
MYLK4	340156	hgsc.bcm.edu	37	chr6	2685624	2685624	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	ctggttcatgacgctgatctCgttcttcacctcctcctgag	8	14	4	3			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr6:2685624C>T	ENST00000274643.7	-	6	793	c.451G>A	c.(451-453)Gag>Aag	p.E151K	MYLK4_ENST00000268446.5_Missense_Mutation_p.E151K	NM_001012418.3	NP_001012418.2	Q86YV6	MYLK4_HUMAN	myosin light chain kinase family, member 4	151	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(10)|ovary(2)|skin(1)	23	Ovarian(93;0.0412)	all_hematologic(90;0.0897)				ACGCTGATCTCGTTCTTCACC	0.552																																					p.E151K		Atlas-SNP	.											.	MYLK4	74	.	0			c.G451A						.						233	183	200					6																	2685624		2203	4300	6503	SO:0001583	missense	340156	exon6			TGATCTCGTTCTT		CCDS34330.1	6p25.2	2008-01-23			ENSG00000145949	ENSG00000145949			27972	protein-coding gene	gene with protein product	"caMLCK like"						Standard	NM_001012418		Approved	SgK085	uc003mty.4	Q86YV6	OTTHUMG00000014121	ENST00000274643.7:c.451G>A	chr6.hg19:g.2685624C>T	ENSP00000274643:p.Glu151Lys	75.0	0.0		92.0	25.0	NM_001012418	A2RUC0|Q5TAW2	Missense_Mutation	SNP	ENST00000274643.7	hg19	CCDS34330.1	.	.	.	.	.	.	.	.	.	.	C	36	5.741166	0.96873	.	.	ENSG00000145949	ENST00000268446;ENST00000274643	T;T	0.73469	-0.75;-0.75	5.63	5.63	0.86233	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.46442	D	0.000299	D	0.89795	0.6818	H	0.95114	3.625	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.92270	0.5824	10	0.87932	D	0	.	18.6673	0.91495	0.0:1.0:0.0:0.0	.	151	Q86YV6	MYLK4_HUMAN	K	151	ENSP00000268446:E151K;ENSP00000274643:E151K	ENSP00000268446:E151K	E	-	1	0	MYLK4	2630623	1.000000	0.71417	0.997000	0.53966	0.990000	0.78478	7.805000	0.86005	2.649000	0.89929	0.603000	0.83216	GAG	.	.		0.552	MYLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039632.2	NM_001012418		T	2685624	C	T	2685624	3	4	272	1	0	0	0	0	1	0	0	0	10068	893	31	1	743	1	MYLK4	6	2685624	Missense_Mutation	SNP	C	TCGA-G3-A25S-01A-11D-A16V-10		2685624	168429443	34	39467										
PRL	5617	hgsc.bcm.edu	37	chr6	22294684	22294684	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	ggttatggatgtagtgggacAggacgacggcgcggtcaaac	17	7	1	0			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr6:22294684A>T	ENST00000306482.1	-	2	676	c.158T>A	c.(157-159)cTg>cAg	p.L53Q	RP3-404K8.2_ENST00000561912.1_RNA	NM_000948.5|NM_001163558.2	NP_000939.1|NP_001157030.1	P01236	PRL_HUMAN	prolactin	53					cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|circadian rhythm (GO:0007623)|female pregnancy (GO:0007565)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|multicellular organismal response to stress (GO:0033555)|ovulation cycle (GO:0042698)|parturition (GO:0007567)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of JAK-STAT cascade (GO:0046427)|regulation of multicellular organism growth (GO:0040014)|regulation of ossification (GO:0030278)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to nutrient (GO:0007584)|STAT protein import into nucleus (GO:0007262)	extracellular region (GO:0005576)|secretory granule (GO:0030141)	prolactin receptor binding (GO:0005148)			NS(1)|endometrium(2)|large_intestine(6)|lung(6)|prostate(1)	16	Ovarian(93;0.163)					GTAGTGGGACAGGACGACGGC	0.587																																					p.L53Q		Atlas-SNP	.											.	PRL	41	.	0			c.T158A						.						103	93	96					6																	22294684		2203	4300	6503	SO:0001583	missense	5617	exon2			TGGGACAGGACGA	D00411	CCDS4548.1	6p22.3	2013-09-16			ENSG00000172179	ENSG00000172179			9445	protein-coding gene	gene with protein product		176760					Standard	NM_000948		Approved		uc003ndq.3	P01236	OTTHUMG00000016111	ENST00000306482.1:c.158T>A	chr6.hg19:g.22294684A>T	ENSP00000302150:p.Leu53Gln	142.0	0.0		270.0	56.0	NM_000948	Q15199|Q92996	Missense_Mutation	SNP	ENST00000306482.1	hg19	CCDS4548.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.1|22.1	4.242959|4.242959	0.79912|0.79912	.|.	.|.	ENSG00000172179|ENSG00000172179	ENST00000438606|ENST00000306482	.|D	.|0.89939	.|-2.59	6.04|6.04	4.86|4.86	0.63082|0.63082	.|Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	.|0.256840	.|0.40222	.|N	.|0.001143	.|D	.|0.92652	.|0.7665	M|M	0.82323|0.82323	2.585|2.585	0.54753|0.54753	D|D	0.999985|0.999985	.|B;D	.|0.89917	.|0.222;1.0	.|P;D	.|0.81914	.|0.814;0.995	.|D	.|0.92698	.|0.6172	.|10	.|0.49607	.|T	.|0.09	.|-0.0438	12.5677|12.5677	0.56318|0.56318	0.8753:0.0:0.0:0.1247|0.8753:0.0:0.0:0.1247	.|.	.|53;54	.|P01236;Q5I0G2	.|PRL_HUMAN;.	.|Q	-1|53	.|ENSP00000302150:L53Q	.|ENSP00000302150:L53Q	.|L	-|-	.|2	.|0	PRL|PRL	22402663|22402663	0.999000|0.999000	0.42202|0.42202	0.943000|0.943000	0.38184|0.38184	0.954000|0.954000	0.61252|0.61252	4.588000|4.588000	0.60999|0.60999	1.068000|1.068000	0.40764|0.40764	0.460000|0.460000	0.39030|0.39030	.|CTG	.	.		0.587	PRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043327.1	NM_000948		T	22294684	A	T	22294684	3	4	272	1	0	0	0	0	1	0	0	0	12540	188	7	4	541	4	PRL	6	22294684	Missense_Mutation	SNP	A	TCGA-G3-A25S-01A-11D-A16V-10	19609060	22294684	148820383	35	39468										
CRIP3	401262	hgsc.bcm.edu	37	chr6	43274043	43274043	+	Missense_Mutation	SNP	C	C	T													0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	atttctgcctaatgacatcaCcttctcagctggtggtggaa							TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr6:43274043C>T	ENST00000274990.4	-	6	413	c.409G>A	c.(409-411)Gtg>Atg	p.V137M	ZNF318_ENST00000607252.1_5'Flank|CRIP3_ENST00000372569.3_Missense_Mutation_p.V137M			Q6Q6R5	CRIP3_HUMAN	cysteine-rich protein 3	137	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				T cell proliferation (GO:0042098)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)			AATGACATCACCTTCTCAGCT	0.572																																					p.V137M		Atlas-SNP	.											.	CRIP3	30	.	0			c.G409A						.						99	92	95					6																	43274043		2203	4300	6503	SO:0001583	missense	401262	exon6			ACATCACCTTCTC	AY555741	CCDS4894.2	6p21	2008-02-05			ENSG00000146215	ENSG00000146215			17751	protein-coding gene	gene with protein product						15380775	Standard	NM_206922		Approved	TLP-A, bA480N24.2, TLP	uc003ouu.1	Q6Q6R5	OTTHUMG00000014727	ENST00000274990.4:c.409G>A	chr6.hg19:g.43274043C>T	ENSP00000274990:p.Val137Met	43.0	0.0		53.0	50.0	NM_206922	A2A436|Q5T043|Q6Q6R4|Q6Q6R6|Q6Q6R7	Missense_Mutation	SNP	ENST00000274990.4	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.9|22.9	4.343643|4.343643	0.82022|0.82022	.|.	.|.	ENSG00000146215|ENSG00000146215	ENST00000416431|ENST00000372569;ENST00000451294;ENST00000274990	.|D;D;D	.|0.89050	.|-2.46;-2.46;-2.46	4.94|4.94	4.94|4.94	0.65067|0.65067	.|Zinc finger, LIM-type (5);	.|0.000000	.|0.64402	.|D	.|0.000009	D|D	0.91942|0.91942	0.7448|0.7448	M|M	0.68952|0.68952	2.095|2.095	0.54753|0.54753	D|D	0.999985|0.999985	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|1.0;0.999	D|D	0.90761|0.90761	0.4665|0.4665	5|10	.|0.34782	.|T	.|0.22	-0.8605|-0.8605	15.6476|15.6476	0.77068|0.77068	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|137;137	.|Q6Q6R5;Q6Q6R5-3	.|CRIP3_HUMAN;.	D|M	60|137;9;137	.|ENSP00000361650:V137M;ENSP00000397775:V9M;ENSP00000274990:V137M	.|ENSP00000274990:V137M	G|V	-|-	2|1	0|0	CRIP3|CRIP3	43382021|43382021	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.973000|0.973000	0.67179|0.67179	6.947000|6.947000	0.75959|0.75959	2.283000|2.283000	0.76528|0.76528	0.561000|0.561000	0.74099|0.74099	GGT|GTG	.	.		0.572	CRIP3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000313968.1			T	43274043	C	T	43274043	3	4	272	1	0	0	0	0	1	0	0	0	3878	507	18	3	217	3	CRIP3	6	43274043	Missense_Mutation	SNP	C	TCGA-G3-A25S-01A-11D-A16V-10	20979359	43274043	127841024	36	39469	193	2								
CRIP3	401262	hgsc.bcm.edu	37	chr6	43274045	43274046	+	Missense_Mutation	DNP	TT	TT	AC													0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	ttctgcctaatgacatcaccTtctcagctggtggtggaaag							TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr6:43274045_43274046TT>AC	ENST00000274990.4	-	6	410_411	c.406_407AA>GT	c.(406-408)AAg>GTg	p.K136V	ZNF318_ENST00000607252.1_5'Flank|CRIP3_ENST00000372569.3_Missense_Mutation_p.K136V			Q6Q6R5	CRIP3_HUMAN	cysteine-rich protein 3	136	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				T cell proliferation (GO:0042098)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)			TGACATCACCTTCTCAGCTGGT	0.569																																					p.K136M|p.K136E		Atlas-SNP	.											.	CRIP3	30	.	0			c.A407T|c.A406G						.																																			SO:0001583	missense	401262	exon6			ATCACCTTCTCAG|TCACCTTCTCAGC	AY555741	CCDS4894.2	6p21	2008-02-05			ENSG00000146215	ENSG00000146215			17751	protein-coding gene	gene with protein product						15380775	Standard	NM_206922		Approved	TLP-A, bA480N24.2, TLP	uc003ouu.1	Q6Q6R5	OTTHUMG00000014727	ENST00000274990.4:c.406_407delinsAC	chr6.hg19:g.43274045_43274046delinsAC	ENSP00000274990:p.Lys136Val	43.0	0.0		50.0	47.0|48.0	NM_206922	A2A436|Q5T043|Q6Q6R4|Q6Q6R6|Q6Q6R7	Missense_Mutation	SNP	ENST00000274990.4	hg19																																																																																				.	.		0.569	CRIP3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000313968.1			AC	43274046	TT	AC	43274045	3	1	272	1	0	0	0	0	1	0	0	0	3878	1609	56	4	219	4	CRIP3	6	43274045	Missense_Mutation	DNP	TT	TCGA-G3-A25S-01A-11D-A16V-10	2	43274045	127841022	37	39470	193	2								
GPR115	221393	hgsc.bcm.edu	37	chr6	47681793	47681793	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	taccacagaagatatcttagGaatggtacagattcccaggc	9	9	1	3			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr6:47681793G>A	ENST00000283303.2	+	6	1070	c.812G>A	c.(811-813)gGa>gAa	p.G271E	GPR115_ENST00000371220.1_Missense_Mutation_p.G328E|GPR115_ENST00000327753.3_Missense_Mutation_p.G271E|RN7SKP116_ENST00000516902.1_RNA	NM_153838.3	NP_722580.3	Q8IZF3	GP115_HUMAN	G protein-coupled receptor 115	271					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	52						GATATCTTAGGAATGGTACAG	0.443																																					p.G271E	GBM(22;431 510 9010 26644 32828)	Atlas-SNP	.											.	GPR115	140	.	0			c.G812A						.						60	61	61					6																	47681793		2203	4300	6503	SO:0001583	missense	221393	exon6			TCTTAGGAATGGT	AK095395	CCDS4922.2	6p12.3	2014-08-08			ENSG00000153294	ENSG00000153294		"-", "GPCR / Class B : Orphans"	19011	protein-coding gene	gene with protein product		614268				12435584	Standard	NM_153838		Approved	FLJ38076, PGR18	uc003oza.1	Q8IZF3	OTTHUMG00000014800	ENST00000283303.2:c.812G>A	chr6.hg19:g.47681793G>A	ENSP00000283303:p.Gly271Glu	61.0	0.0		93.0	24.0	NM_153838	B3KTD0|Q2PNZ0|Q5T5B5|Q5T5B6|Q86SN9|Q8IXE6	Missense_Mutation	SNP	ENST00000283303.2	hg19	CCDS4922.2	.	.	.	.	.	.	.	.	.	.	G	11.10	1.540544	0.27563	.	.	ENSG00000153294	ENST00000371220;ENST00000327753;ENST00000283303	T;T;T	0.37752	1.41;1.18;1.18	5.19	4.3	0.51218	.	0.085998	0.50627	D	0.000110	T	0.47691	0.1459	M	0.81497	2.545	0.19775	N	0.999958	D	0.76494	0.999	D	0.71414	0.973	T	0.47849	-0.9085	10	0.72032	D	0.01	-6.2359	12.3905	0.55356	0.0:0.0:0.8257:0.1743	.	271	Q8IZF3	GP115_HUMAN	E	328;271;271	ENSP00000360264:G328E;ENSP00000328319:G271E;ENSP00000283303:G271E	ENSP00000283303:G271E	G	+	2	0	GPR115	47789752	0.996000	0.38824	0.205000	0.23548	0.010000	0.07245	3.133000	0.50531	1.250000	0.43966	0.655000	0.94253	GGA	.	.		0.443	GPR115-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040819.2	NM_153838		A	47681793	G	A	47681793	3	1	272	1	0	0	0	0	1	0	0	0	6640	1174	41	3	830	3	GPR115	6	47681793	Missense_Mutation	SNP	G	TCGA-G3-A25S-01A-11D-A16V-10	4407748	47681793	123433274	38	39471										
PKHD1	5314	hgsc.bcm.edu	37	chr6	51824795	51824795	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	cagctgtgagtcctggaccaTctccggcagaactgtaaaga	11	11	1	3			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr6:51824795T>A	ENST00000371117.3	-	36	6056	c.5781A>T	c.(5779-5781)agA>agT	p.R1927S	PKHD1_ENST00000340994.4_Missense_Mutation_p.R1927S	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	1927					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					TCCTGGACCATCTCCGGCAGA	0.517											OREG0017492	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R1927S		Atlas-SNP	.											.	PKHD1	927	.	0			c.A5781T						.						115	104	108					6																	51824795		2203	4300	6503	SO:0001583	missense	5314	exon36			GGACCATCTCCGG	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.5781A>T	chr6.hg19:g.51824795T>A	ENSP00000360158:p.Arg1927Ser	60.0	0.0	980	122.0	13.0	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	hg19	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	T	12.71	2.018562	0.35606	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.88896	-2.23;-2.44	5.54	-1.88	0.07713	.	0.169465	0.38663	N	0.001612	T	0.67961	0.2949	L	0.27053	0.805	0.27444	N	0.953639	P;D	0.53151	0.922;0.958	P;B	0.45610	0.487;0.386	T	0.69323	-0.5175	10	0.33940	T	0.23	.	7.4349	0.27150	0.0:0.4524:0.1792:0.3684	.	1927;1927	P08F94-2;P08F94	.;PKHD1_HUMAN	S	1927	ENSP00000360158:R1927S;ENSP00000341097:R1927S	ENSP00000341097:R1927S	R	-	3	2	PKHD1	51932754	0.004000	0.15560	0.992000	0.48379	0.959000	0.62525	-1.021000	0.03615	-0.351000	0.08249	0.533000	0.62120	AGA	.	.		0.517	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		A	51824795	T	A	51824795	3	1	272	1	0	0	0	0	1	0	0	0	11980	1432	50	4	6610	4	PKHD1	6	51824795	Missense_Mutation	SNP	T	TCGA-G3-A25S-01A-11D-A16V-10	4143002	51824795	119290272	39	39472										
HTR1B	3351	hgsc.bcm.edu	37	chr6	78172410	78172410	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	ggcgtctgtttcaaaatccgGgagcgggcttctacgtagat	13	9	3	1			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr6:78172410G>A	ENST00000369947.2	-	1	1080	c.711C>T	c.(709-711)tcC>tcT	p.S237S		NM_000863.1	NP_000854.1	P28222	5HT1B_HUMAN	5-hydroxytryptamine (serotonin) receptor 1B, G protein-coupled	237					adenylate cyclase-inhibiting serotonin receptor signaling pathway (GO:0007198)|bone remodeling (GO:0046849)|cellular response to alkaloid (GO:0071312)|cellular response to drug (GO:0035690)|cellular response to temperature stimulus (GO:0071502)|drinking behavior (GO:0042756)|G-protein coupled receptor internalization (GO:0002031)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of behavior (GO:0050795)|regulation of dopamine secretion (GO:0014059)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to mineralocorticoid (GO:0051385)|synaptic transmission (GO:0007268)|vasoconstriction (GO:0042310)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|prostate(2)|upper_aerodigestive_tract(2)	25		all_cancers(76;0.0867)|Acute lymphoblastic leukemia(125;0.00119)|all_hematologic(105;0.0332)		BRCA - Breast invasive adenocarcinoma(397;0.205)	Almotriptan(DB00918)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bopindolol(DB08807)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Clozapine(DB00363)|Dihydroergotamine(DB00320)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Frovatriptan(DB00998)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Methysergide(DB00247)|Naratriptan(DB00952)|Olanzapine(DB00334)|Ondansetron(DB00904)|Penbutolol(DB01359)|Pergolide(DB01186)|Pindolol(DB00960)|Pramipexole(DB00413)|Propranolol(DB00571)|Quetiapine(DB01224)|Rizatriptan(DB00953)|Ropinirole(DB00268)|Sumatriptan(DB00669)|Yohimbine(DB01392)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)	TCAAAATCCGGGAGCGGGCTT	0.597																																					p.S237S		Atlas-SNP	.											.	HTR1B	55	.	0			c.C711T						.						51	57	55					6																	78172410		2203	4300	6503	SO:0001819	synonymous_variant	3351	exon1			AATCCGGGAGCGG	BC069065	CCDS4986.1	6q13	2012-08-08	2012-02-03		ENSG00000135312	ENSG00000135312		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5287	protein-coding gene	gene with protein product		182131	"5-hydroxytryptamine (serotonin) receptor 1B"			1348246, 11247661	Standard	NM_000863		Approved	S12, 5-HT1B, HTR1D2, 5-HT1DB	uc003pil.1	P28222	OTTHUMG00000015066	ENST00000369947.2:c.711C>T	chr6.hg19:g.78172410G>A		37.0	0.0		23.0	19.0	NM_000863	Q4VAY7	Silent	SNP	ENST00000369947.2	hg19	CCDS4986.1																																																																																			.	.		0.597	HTR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041292.1	NM_000863		A	78172410	G	A	78172410	2	1	272	1	0	0	0	0	0	0	0	1	7446	1219	43	3		3	HTR1B	6	78172410	Silent	SNP	G	TCGA-G3-A25S-01A-11D-A16V-10	26347615	78172410	92942657	40	39473										
GPR63	81491	hgsc.bcm.edu	37	chr6	97246970	97246970	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	ggtcggggtttcctacggctAaaggaaaagctacacaaaag	12	8	0	0			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr6:97246970A>G	ENST00000229955.3	-	2	983	c.638T>C	c.(637-639)tTa>tCa	p.L213S	GPR63_ENST00000417980.1_Missense_Mutation_p.L213S	NM_001143957.2|NM_030784.3	NP_001137429.1|NP_110411.1	Q9BZJ6	GPR63_HUMAN	G protein-coupled receptor 63	213						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			kidney(1)|large_intestine(5)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(76;6.89e-05)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.0618)|Colorectal(196;0.0721)		BRCA - Breast invasive adenocarcinoma(108;0.0912)		TCCTACGGCTAAAGGAAAAGC	0.458																																					p.L213S		Atlas-SNP	.											.	GPR63	60	.	0			c.T638C						.						75	75	75					6																	97246970		2203	4300	6503	SO:0001583	missense	81491	exon2			ACGGCTAAAGGAA	AF317654	CCDS5036.1	6q16.1-q16.3	2012-08-21			ENSG00000112218	ENSG00000112218		"GPCR / Class A : Orphans"	13302	protein-coding gene	gene with protein product		606915					Standard	NM_030784		Approved	PSP24(beta), PSP24B	uc003pou.3	Q9BZJ6	OTTHUMG00000015245	ENST00000229955.3:c.638T>C	chr6.hg19:g.97246970A>G	ENSP00000229955:p.Leu213Ser	58.0	0.0		25.0	15.0	NM_030784	Q9UJH3	Missense_Mutation	SNP	ENST00000229955.3	hg19	CCDS5036.1	.	.	.	.	.	.	.	.	.	.	A	11.24	1.580195	0.28180	.	.	ENSG00000112218	ENST00000536583;ENST00000417980;ENST00000229955;ENST00000369268	T;T;T	0.38560	1.13;1.13;1.13	5.3	4.13	0.48395	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000010	T	0.10337	0.0253	N	0.12422	0.21	0.54753	D	0.999985	B	0.32526	0.374	B	0.28991	0.097	T	0.08889	-1.0700	10	0.22109	T	0.4	-0.8812	11.3705	0.49697	0.9282:0.0:0.0718:0.0	.	213	Q9BZJ6	GPR63_HUMAN	S	237;213;213;213	ENSP00000393170:L213S;ENSP00000229955:L213S;ENSP00000358273:L213S	ENSP00000229955:L213S	L	-	2	0	GPR63	97353691	1.000000	0.71417	0.840000	0.33206	0.724000	0.41520	8.910000	0.92685	0.957000	0.37930	0.528000	0.53228	TTA	.	.		0.458	GPR63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041566.2			G	97246970	A	G	97246970	3	3	272	1	0	0	0	0	1	0	0	0	6712	372	13	2	625	2	GPR63	6	97246970	Missense_Mutation	SNP	A	TCGA-G3-A25S-01A-11D-A16V-10	19074560	97246970	73868097	41	39474										
RADIL	55698	hgsc.bcm.edu	37	chr7	4874647	4874647	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	ccccgtggtgcagcaccacgGtcctgtgccccacctcggag	12	18	0	0			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr7:4874647G>A	ENST00000399583.3	-	4	1194	c.1007C>T	c.(1006-1008)aCc>aTc	p.T336I	RADIL_ENST00000538469.1_Missense_Mutation_p.T96I|RADIL_ENST00000536091.1_Missense_Mutation_p.T336I	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	336	FHA.				multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		CAGCACCACGGTCCTGTGCCC	0.716																																					p.T336I		Atlas-SNP	.											.	RADIL	110	.	0			c.C1007T						.						13	17	16					7																	4874647		1949	4134	6083	SO:0001583	missense	55698	exon4			ACCACGGTCCTGT	AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.1007C>T	chr7.hg19:g.4874647G>A	ENSP00000382492:p.Thr336Ile	41.0	0.0		35.0	20.0	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	hg19	CCDS43544.1	.	.	.	.	.	.	.	.	.	.	-	12.21	1.870496	0.33069	.	.	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000544486;ENST00000536091;ENST00000538469	T;T;T	0.06371	3.31;3.31;3.31	4.45	4.45	0.53987	Forkhead-associated (FHA) domain (1);SMAD/FHA domain (1);	0.452476	0.23889	N	0.043575	T	0.08358	0.0208	L	0.47716	1.5	0.09310	N	1	B	0.16396	0.017	B	0.15870	0.014	T	0.15321	-1.0441	10	0.66056	D	0.02	-2.6864	14.2662	0.66121	0.0:0.0:1.0:0.0	.	336	Q96JH8	RADIL_HUMAN	I	336;307;70;336;96	ENSP00000382492:T336I;ENSP00000442533:T336I;ENSP00000442966:T96I	ENSP00000320946:T307I	T	-	2	0	RADIL	4841173	0.988000	0.35896	0.003000	0.11579	0.811000	0.45836	5.874000	0.69652	2.046000	0.60703	0.651000	0.88453	ACC	.	.		0.716	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059		A	4874647	G	A	4874647	3	1	272	1	0	0	0	0	1	0	0	0	13012	1261	44	3	2268	3	RADIL	7	4874647	Missense_Mutation	SNP	G	TCGA-G3-A25S-01A-11D-A16V-10		4874647	154264016	42	39475										
FIGNL1	63979	hgsc.bcm.edu	37	chr7	50514900	50514900	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	cacggtatgcatctgccttcGgtccggtacatatgccagat	10	12	1	1			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr7:50514900G>A	ENST00000419119.1	-	2	1639	c.86C>T	c.(85-87)cCg>cTg	p.P29L	FIGNL1_ENST00000356889.4_Missense_Mutation_p.P29L|FIGNL1_ENST00000395556.2_Missense_Mutation_p.P29L|FIGNL1_ENST00000433017.1_Missense_Mutation_p.P29L|FIGNL1_ENST00000435566.1_Missense_Mutation_p.P29L			Q6PIW4	FIGL1_HUMAN	fidgetin-like 1	29					ATP metabolic process (GO:0046034)|cellular response to ionizing radiation (GO:0071479)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|osteoblast differentiation (GO:0001649)|osteoblast proliferation (GO:0033687)|regulation of cell cycle (GO:0051726)|regulation of double-strand break repair via homologous recombination (GO:0010569)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|hydrolase activity (GO:0016787)|magnesium ion binding (GO:0000287)			endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	29	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;3.73e-08)|all_hematologic(4;7.51e-06)				ATCTGCCTTCGGTCCGGTACA	0.438																																					p.P29L		Atlas-SNP	.											.	FIGNL1	73	.	0			c.C86T						.						66	56	59					7																	50514900		2203	4300	6503	SO:0001583	missense	63979	exon4			GCCTTCGGTCCGG	AK023142	CCDS5510.1	7p12.2	2010-04-21			ENSG00000132436	ENSG00000132436		"ATPases / AAA-type"	13286	protein-coding gene	gene with protein product		615383					Standard	XM_005271783		Approved		uc003tpc.3	Q6PIW4	OTTHUMG00000022866	ENST00000419119.1:c.86C>T	chr7.hg19:g.50514900G>A	ENSP00000410811:p.Pro29Leu	82.0	0.0		70.0	20.0	NM_001042762	D3DVM6|Q86V18|Q8ND59|Q9H8P1|Q9H917	Missense_Mutation	SNP	ENST00000419119.1	hg19	CCDS5510.1	.	.	.	.	.	.	.	.	.	.	C	15.20	2.764053	0.49574	.	.	ENSG00000132436	ENST00000356889;ENST00000395556;ENST00000433017;ENST00000419119;ENST00000435566;ENST00000436590;ENST00000422854;ENST00000440350;ENST00000420829;ENST00000448788	T;T;T;T;T;T;T	0.20881	2.04;2.04;2.04;2.04;2.04;2.04;2.04	5.21	1.32	0.21799	.	0.129212	0.53938	D	0.000056	T	0.09905	0.0243	N	0.08118	0	0.24380	N	0.994792	B	0.09022	0.002	B	0.01281	0.0	T	0.22977	-1.0201	10	0.72032	D	0.01	-0.8423	8.2317	0.31601	0.0:0.1318:0.1152:0.753	.	29	Q6PIW4	FIGL1_HUMAN	L	29	ENSP00000349356:P29L;ENSP00000378924:P29L;ENSP00000399997:P29L;ENSP00000410811:P29L;ENSP00000394070:P29L;ENSP00000403012:P29L;ENSP00000388471:P29L	ENSP00000349356:P29L	P	-	2	0	FIGNL1	50482394	1.000000	0.71417	0.417000	0.26559	0.236000	0.25371	3.222000	0.51223	0.070000	0.16634	-2.631000	0.00153	CCG	.	.		0.438	FIGNL1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342579.1	NM_001042762		A	50514900	G	A	50514900	3	1	272	1	0	0	0	0	1	0	0	0	5900	1116	39	1	1942	1	FIGNL1	7	50514900	Missense_Mutation	SNP	G	TCGA-G3-A25S-01A-11D-A16V-10	45640253	50514900	108623763	43	39476										
SEMA3A	10371	hgsc.bcm.edu	37	chr7	83590805	83590805	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	tatgtcctggcctttgccgaCgttgttttcggtcccttttc	9	12	0	0	rs318240753		TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr7:83590805C>A	ENST00000265362.4	-	17	2512	c.2198G>T	c.(2197-2199)cGt>cTt	p.R733L	SEMA3A_ENST00000436949.1_Missense_Mutation_p.R733L	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	733	Arg/Lys-rich (basic).		R -> H (in HH16; phenotype consistent with Kallmann syndrome; dbSNP:rs318240753). {ECO:0000269|PubMed:22927827}.		apoptotic process (GO:0006915)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|dendrite morphogenesis (GO:0048813)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of epithelial cell migration (GO:0010633)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neural crest cell migration involved in sympathetic nervous system development (GO:1903045)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of male gonad development (GO:2000020)|positive regulation of neuron migration (GO:2001224)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of heart rate (GO:0002027)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sensory system development (GO:0048880)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular region (GO:0005576)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|neuropilin binding (GO:0038191)|receptor activity (GO:0004872)			breast(3)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						CCTTTGCCGACGTTGTTTTCG	0.458																																					p.R733L		Atlas-SNP	.											.	SEMA3A	121	.	0			c.G2198T						.						222	197	206					7																	83590805		2203	4300	6503	SO:0001583	missense	10371	exon17			TGCCGACGTTGTT	L26081	CCDS5599.1	7p12.1	2013-01-11			ENSG00000075213	ENSG00000075213		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10723	protein-coding gene	gene with protein product	"sema III"	603961		SEMAD		8269517, 7748561	Standard	NM_006080		Approved	SEMA1, SemD, coll-1, Hsema-I	uc003uhz.3	Q14563	OTTHUMG00000023443	ENST00000265362.4:c.2198G>T	chr7.hg19:g.83590805C>A	ENSP00000265362:p.Arg733Leu	234.0	0.0		182.0	76.0	NM_006080		Missense_Mutation	SNP	ENST00000265362.4	hg19	CCDS5599.1	.	.	.	.	.	.	.	.	.	.	C	14.44	2.537539	0.45176	.	.	ENSG00000075213	ENST00000265362;ENST00000436949	T;T	0.28255	1.62;1.62	6.08	6.08	0.98989	.	0.048367	0.85682	D	0.000000	T	0.23649	0.0572	N	0.13235	0.315	0.58432	D	0.999996	B	0.30563	0.285	B	0.28385	0.089	T	0.03739	-1.1008	10	0.44086	T	0.13	.	20.6634	0.99662	0.0:1.0:0.0:0.0	.	733	Q14563	SEM3A_HUMAN	L	733	ENSP00000265362:R733L;ENSP00000415260:R733L	ENSP00000265362:R733L	R	-	2	0	SEMA3A	83428741	1.000000	0.71417	0.998000	0.56505	0.968000	0.65278	4.589000	0.61006	2.894000	0.99253	0.655000	0.94253	CGT	.	.		0.458	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080		A	83590805	C	A	83590805	3	1	272	1	0	0	0	0	1	0	0	0	14039	536	19	1	121	1	SEMA3A	7	83590805	Missense_Mutation	SNP	C	TCGA-G3-A25S-01A-11D-A16V-10	33075905	83590805	75547858	44	39477										
OR2AE1	81392	hgsc.bcm.edu	37	chr7	99474046	99474046	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	agatggggaggaggaggagaAtgctgctgatgtacactgtg	18	4	0	3			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr7:99474046A>G	ENST00000316368.2	-	1	634	c.611T>C	c.(610-612)aTt>aCt	p.I204T		NM_001005276.1	NP_001005276.1	Q8NHA4	O2AE1_HUMAN	olfactory receptor, family 2, subfamily AE, member 1	204						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(2)	11	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)					GAGGAGGAGAATGCTGCTGAT	0.473																																					p.I204T		Atlas-SNP	.											.	OR2AE1	32	.	0			c.T611C						.						142	117	126					7																	99474046		2203	4300	6503	SO:0001583	missense	81392	exon1			AGGAGAATGCTGC	AC011904	CCDS34696.1	7q22.1	2014-02-19	2002-02-28		ENSG00000244623	ENSG00000244623		"GPCR / Class A : Olfactory receptors"	15087	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily AE, member 2"	OR2AE2			Standard	NM_001005276		Approved		uc003usc.1	Q8NHA4	OTTHUMG00000156650	ENST00000316368.2:c.611T>C	chr7.hg19:g.99474046A>G	ENSP00000313936:p.Ile204Thr	59.0	0.0		51.0	16.0	NM_001005276	B2RPD2	Missense_Mutation	SNP	ENST00000316368.2	hg19	CCDS34696.1	.	.	.	.	.	.	.	.	.	.	A	1.190	-0.635584	0.03584	.	.	ENSG00000244623	ENST00000316368	T	0.00107	8.72	3.62	2.45	0.29901	GPCR, rhodopsin-like superfamily (1);	0.838313	0.09926	N	0.737781	T	0.00144	0.0004	L	0.42744	1.35	0.09310	N	1	B	0.06786	0.001	B	0.15052	0.012	T	0.38023	-0.9680	10	0.72032	D	0.01	.	4.0514	0.09796	0.6773:0.2099:0.1128:0.0	.	204	Q8NHA4	O2AE1_HUMAN	T	204	ENSP00000313936:I204T	ENSP00000313936:I204T	I	-	2	0	OR2AE1	99311982	0.002000	0.14202	0.001000	0.08648	0.012000	0.07955	2.012000	0.40932	0.739000	0.32628	0.405000	0.27470	ATT	.	.		0.473	OR2AE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345053.1			G	99474046	A	G	99474046	3	3	272	1	0	0	0	0	1	0	0	0	10992	101	4	2	364	2	OR2AE1	7	99474046	Missense_Mutation	SNP	A	TCGA-G3-A25S-01A-11D-A16V-10	15883241	99474046	59664617	45	39478										
INSIG1	3638	hgsc.bcm.edu	37	chr7	155094019	155094019	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	tttagcagccctatctttggGcctttggtggacatttgatc	10	9	1	1			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr7:155094019G>A	ENST00000340368.4	+	4	807	c.596G>A	c.(595-597)gGc>gAc	p.G199D	INSIG1_ENST00000344756.4_Missense_Mutation_p.G47D|INSIG1_ENST00000342407.5_Intron	NM_005542.4	NP_005533.2	O15503	INSI1_HUMAN	insulin induced gene 1	199					cell proliferation (GO:0008283)|cholesterol biosynthetic process (GO:0006695)|cranial suture morphogenesis (GO:0060363)|inner ear morphogenesis (GO:0042472)|metabolic process (GO:0008152)|middle ear morphogenesis (GO:0042474)|negative regulation of cargo loading into COPII-coated vesicle (GO:1901303)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of steroid biosynthetic process (GO:0010894)|palate development (GO:0060021)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)|triglyceride metabolic process (GO:0006641)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|SREBP-SCAP-Insig complex (GO:0032937)				endometrium(2)|kidney(2)|large_intestine(1)|lung(11)|prostate(1)|upper_aerodigestive_tract(2)	19	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CTATCTTTGGGCCTTTGGTGG	0.433																																					p.G199D		Atlas-SNP	.											.	INSIG1	20	.	0			c.G596A						.						109	103	105					7																	155094019		2203	4300	6503	SO:0001583	missense	3638	exon4			CTTTGGGCCTTTG		CCDS5938.1, CCDS5939.1	7q36	2008-07-18			ENSG00000186480	ENSG00000186480			6083	protein-coding gene	gene with protein product	"INSIG-1 membrane protein"	602055				9268630	Standard	NM_005542		Approved	CL-6, MGC1405	uc003wly.3	O15503	OTTHUMG00000151330	ENST00000340368.4:c.596G>A	chr7.hg19:g.155094019G>A	ENSP00000344741:p.Gly199Asp	246.0	0.0		209.0	41.0	NM_005542	A4D2N1|A8K6L0|Q53XW8|Q9BUV5	Missense_Mutation	SNP	ENST00000340368.4	hg19	CCDS5938.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.921890	0.92319	.	.	ENSG00000186480	ENST00000340368;ENST00000344756	T;T	0.50001	0.76;0.81	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.70202	0.3197	M	0.74881	2.28	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.982;1.0	T	0.66697	-0.5858	10	0.35671	T	0.21	.	19.8944	0.96949	0.0:0.0:1.0:0.0	.	47;199	F5H6P3;O15503	.;INSI1_HUMAN	D	199;47	ENSP00000344741:G199D;ENSP00000340010:G47D	ENSP00000344741:G199D	G	+	2	0	INSIG1	154724954	1.000000	0.71417	0.958000	0.39756	0.644000	0.38419	9.113000	0.94321	2.695000	0.91970	0.650000	0.86243	GGC	.	.		0.433	INSIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322244.3	NM_198336		A	155094019	G	A	155094019	3	1	272	1	0	0	0	0	1	0	0	0	7774	1203	42	3	606	3	INSIG1	7	155094019	Missense_Mutation	SNP	G	TCGA-G3-A25S-01A-11D-A16V-10	55619973	155094019	4044644	46	39479										
ZBTB6	10773	hgsc.bcm.edu	37	chr9	125674263	125674263	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	ttgatacatcacaaaataaaTtctgctgtctcaaaagattc	4	8	3	2			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr9:125674263T>C	ENST00000373659.3	-	2	177	c.89A>G	c.(88-90)aAt>aGt	p.N30S		NM_006626.5	NP_006617.1	Q15916	ZBTB6_HUMAN	zinc finger and BTB domain containing 6	30					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|kidney(1)|large_intestine(2)|lung(1)|skin(1)	11						ACAAAATAAATTCTGCTGTCT	0.388																																					p.N30S		Atlas-SNP	.											.	ZBTB6	32	.	0			c.A89G						.						104	113	110					9																	125674263		2203	4300	6503	SO:0001583	missense	10773	exon2			AATAAATTCTGCT	X82018	CCDS6846.1	9q33.1-q33.3	2013-01-08	2006-04-10	2006-04-10	ENSG00000186130	ENSG00000186130		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	16764	protein-coding gene	gene with protein product		605976	"zinc finger protein 482"	ZNF482		7958847	Standard	NM_006626		Approved	ZID	uc004bnh.4	Q15916	OTTHUMG00000020628	ENST00000373659.3:c.89A>G	chr9.hg19:g.125674263T>C	ENSP00000362763:p.Asn30Ser	112.0	0.0		65.0	56.0	NM_006626	A8K8N6	Missense_Mutation	SNP	ENST00000373659.3	hg19	CCDS6846.1	.	.	.	.	.	.	.	.	.	.	T	16.66	3.186360	0.57909	.	.	ENSG00000186130	ENST00000373659	T	0.70399	-0.48	6.17	6.17	0.99709	BTB/POZ (1);BTB/POZ fold (2);	0.141133	0.64402	D	0.000006	T	0.75554	0.3865	L	0.33710	1.025	0.36865	D	0.888606	D	0.53151	0.958	P	0.60012	0.867	T	0.80625	-0.1299	10	0.62326	D	0.03	.	16.0034	0.80327	0.0:0.0:0.0:1.0	.	30	Q15916	ZBTB6_HUMAN	S	30	ENSP00000362763:N30S	ENSP00000362763:N30S	N	-	2	0	ZBTB6	124714084	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.824000	0.55723	2.371000	0.80710	0.533000	0.62120	AAT	.	.		0.388	ZBTB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053962.1	NM_006626		C	125674263	T	C	125674263	3	2	272	1	0	0	0	0	1	0	0	0	17567	1493	52	2	1189	2	ZBTB6	9	125674263	Missense_Mutation	SNP	T	TCGA-G3-A25S-01A-11D-A16V-10		125674263	15539168	47	39480										
CDK9	1025	hgsc.bcm.edu	37	chr9	130550943	130550943	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	gcaccaactcgccctcatcaGtcagctctgcggctccatca	7	18	5	0			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr9:130550943G>T	ENST00000373264.4	+	6	825	c.725G>T	c.(724-726)aGt>aTt	p.S242I	MIR3960_ENST00000583311.1_RNA|CDK9_ENST00000373265.2_Missense_Mutation_p.S359I	NM_001261.3	NP_001252.1	P50750	CDK9_HUMAN	cyclin-dependent kinase 9	242	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|cellular response to cytokine stimulus (GO:0071345)|DNA repair (GO:0006281)|gene expression (GO:0010467)|negative regulation of cell cycle arrest (GO:0071157)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|regulation of DNA repair (GO:0006282)|regulation of histone modification (GO:0031056)|replication fork arrest (GO:0043111)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|positive transcription elongation factor complex b (GO:0008024)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|DNA binding (GO:0003677)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)|snRNA binding (GO:0017069)|transcription regulatory region DNA binding (GO:0044212)			lung(1)	1						GCCCTCATCAGTCAGCTCTGC	0.652																																					p.S242I		Atlas-SNP	.											.	CDK9	22	.	0			c.G725T						.						60	54	56					9																	130550943		2203	4300	6503	SO:0001583	missense	1025	exon6			TCATCAGTCAGCT	L25676	CCDS6879.1	9q34.1	2011-11-08	2007-11-21		ENSG00000136807	ENSG00000136807		"Cyclin-dependent kinases"	1780	protein-coding gene	gene with protein product		603251	"cyclin-dependent kinase 9 (CDC2-related kinase)"	CDC2L4		8170997, 9356449	Standard	NM_001261		Approved	PITALRE, C-2k, TAK	uc004bse.2	P50750	OTTHUMG00000020715	ENST00000373264.4:c.725G>T	chr9.hg19:g.130550943G>T	ENSP00000362361:p.Ser242Ile	144.0	1.0		59.0	44.0	NM_001261	Q5JU24|Q5JU25|Q5U006|Q96TF1	Missense_Mutation	SNP	ENST00000373264.4	hg19	CCDS6879.1	.	.	.	.	.	.	.	.	.	.	G	19.71	3.877895	0.72294	.	.	ENSG00000136807	ENST00000373265;ENST00000373264	T;T	0.40225	1.04;1.04	5.13	5.13	0.70059	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.40423	0.1116	N	0.04508	-0.205	0.80722	D	1	D	0.56521	0.976	D	0.65323	0.934	T	0.44711	-0.9310	10	0.22109	T	0.4	-13.7553	17.5564	0.87890	0.0:0.0:1.0:0.0	.	242	P50750	CDK9_HUMAN	I	359;242	ENSP00000362362:S359I;ENSP00000362361:S242I	ENSP00000362361:S242I	S	+	2	0	CDK9	129590764	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	9.571000	0.98176	2.385000	0.81259	0.491000	0.48974	AGT	.	.		0.652	CDK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054235.1			T	130550943	G	T	130550943	3	4	272	1	0	0	0	0	1	0	0	0	3153	1029	36	3	747	3	CDK9	9	130550943	Missense_Mutation	SNP	G	TCGA-G3-A25S-01A-11D-A16V-10	4876680	130550943	10662488	48	39481										
TACR2	6865	hgsc.bcm.edu	37	chr10	71175879	71175879	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	ttgacgatgaagtagttggtGactgtgcgcatcctccgatg	13	8	0	3			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr10:71175879G>A	ENST00000373306.4	-	1	744	c.201C>T	c.(199-201)gtC>gtT	p.V67V		NM_001057.2	NP_001048.2	P21452	NK2R_HUMAN	tachykinin receptor 2	67					excretion (GO:0007588)|intestine smooth muscle contraction (GO:0014827)|muscle contraction (GO:0006936)|negative regulation of luteinizing hormone secretion (GO:0033685)|operant conditioning (GO:0035106)|positive regulation of acetylcholine secretion, neurotransmission (GO:0014057)|positive regulation of uterine smooth muscle contraction (GO:0070474)|positive regulation of vascular permeability (GO:0043117)|prolactin secretion (GO:0070459)|tachykinin receptor signaling pathway (GO:0007217)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	substance K receptor activity (GO:0016497)|tachykinin receptor activity (GO:0004995)			endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	11						AGTAGTTGGTGACTGTGCGCA	0.577																																					p.V67V		Atlas-SNP	.											.	TACR2	37	.	0			c.C201T						.						140	103	115					10																	71175879		2203	4300	6503	SO:0001819	synonymous_variant	6865	exon1			GTTGGTGACTGTG		CCDS7293.1	10q22.1	2012-09-20			ENSG00000075073	ENSG00000075073		"GPCR / Class A : Tachykinin receptors"	11527	protein-coding gene	gene with protein product		162321		TAC2R, NKNAR			Standard	NM_001057		Approved	SKR, NK2R	uc001jpn.2	P21452	OTTHUMG00000018377	ENST00000373306.4:c.201C>T	chr10.hg19:g.71175879G>A		50.0	0.0		82.0	27.0	NM_001057	A8K7I1|Q4QRI5|Q8NGQ8|Q9UDE6|Q9UDE7	Silent	SNP	ENST00000373306.4	hg19	CCDS7293.1																																																																																			.	.		0.577	TACR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048411.1			A	71175879	G	A	71175879	2	1	272	1	0	0	0	0	0	0	0	1	15521	1277	45	3		3	TACR2	10	71175879	Silent	SNP	G	TCGA-G3-A25S-01A-11D-A16V-10		71175879	64358868	49	39482										
CPN1	1369	hgsc.bcm.edu	37	chr10	101802222	101802222	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	cagctgcctcatctccatttCtttctttctggcttggggct	8	13	5	0			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr10:101802222C>T	ENST00000370418.3	-	9	1590	c.1339G>A	c.(1339-1341)Gaa>Aaa	p.E447K		NM_001308.2	NP_001299.1	P15169	CBPN_HUMAN	carboxypeptidase N, polypeptide 1	447					response to glucocorticoid (GO:0051384)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	33		Colorectal(252;0.234)		Epithelial(162;4.77e-10)|all cancers(201;3.82e-08)		ATCTCCATTTCTTTCTTTCTG	0.552																																					p.E447K		Atlas-SNP	.											.	CPN1	62	.	0			c.G1339A						.						97	86	90					10																	101802222		2203	4300	6503	SO:0001583	missense	1369	exon9			CCATTTCTTTCTT	X14329	CCDS7486.1	10q24.2	2012-02-10	2007-02-23		ENSG00000120054	ENSG00000120054	3.4.17.3		2312	protein-coding gene	gene with protein product	"anaphylatoxin inactivator", "arginine carboxypeptidase", "carboxypeptidase K", "kininase I", "lysine carboxypeptidase"	603103	"carboxypeptidase N, polypeptide 1, 50kD"			9628828, 2912725	Standard	NM_001308		Approved		uc001kql.2	P15169	OTTHUMG00000018896	ENST00000370418.3:c.1339G>A	chr10.hg19:g.101802222C>T	ENSP00000359446:p.Glu447Lys	80.0	0.0		83.0	35.0	NM_001308	B1AP59	Missense_Mutation	SNP	ENST00000370418.3	hg19	CCDS7486.1	.	.	.	.	.	.	.	.	.	.	C	7.828	0.719197	0.15372	.	.	ENSG00000120054	ENST00000370418	T	0.16457	2.34	4.02	1.14	0.20703	.	.	.	.	.	T	0.06142	0.0159	N	0.08118	0	0.09310	N	1	B	0.16166	0.016	B	0.14578	0.011	T	0.42310	-0.9459	9	0.07990	T	0.79	-13.8138	3.3415	0.07120	0.2046:0.5783:0.0:0.2171	.	447	P15169	CBPN_HUMAN	K	447	ENSP00000359446:E447K	ENSP00000359446:E447K	E	-	1	0	CPN1	101792212	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.022000	0.12480	0.252000	0.21531	-0.145000	0.13849	GAA	.	.		0.552	CPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049828.1	NM_001308		T	101802222	C	T	101802222	3	4	272	1	0	0	0	0	1	0	0	0	3811	922	32	3	41	3	CPN1	10	101802222	Missense_Mutation	SNP	C	TCGA-G3-A25S-01A-11D-A16V-10	30626343	101802222	33732525	50	39483										
TUBGCP2	10844	hgsc.bcm.edu	37	chr10	135099037	135099037	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	aggccgctcagcgccagctcCgtggggtcggcgtgcgccat	16	15	1	0			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr10:135099037C>A	ENST00000252936.3	-	11	1857	c.1818G>T	c.(1816-1818)acG>acT	p.T606T	TUBGCP2_ENST00000368563.2_Silent_p.T606T|TUBGCP2_ENST00000543663.1_Silent_p.T634T|TUBGCP2_ENST00000368562.1_Silent_p.T199T|TUBGCP2_ENST00000417178.2_Silent_p.T476T			Q9BSJ2	GCP2_HUMAN	tubulin, gamma complex associated protein 2	606					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|protein complex assembly (GO:0006461)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(16)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	35		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.87e-06)|all cancers(32;8.98e-06)|Epithelial(32;1.15e-05)		GCGCCAGCTCCGTGGGGTCGG	0.632																																					p.T634T		Atlas-SNP	.											.	TUBGCP2	79	.	0			c.G1902T						.						39	41	40					10																	135099037		2203	4300	6503	SO:0001819	synonymous_variant	10844	exon13			CAGCTCCGTGGGG	AF042379	CCDS7676.1, CCDS58104.1, CCDS58105.1	10q26.3	2008-07-28			ENSG00000130640	ENSG00000130640			18599	protein-coding gene	gene with protein product						9566967	Standard	NM_001256617		Approved	GCP2, Spc97p, SPBC97	uc010qvc.2	Q9BSJ2	OTTHUMG00000019319	ENST00000252936.3:c.1818G>T	chr10.hg19:g.135099037C>A		49.0	0.0		39.0	16.0	NM_001256617	B4DM18|B7ZKL8|F5H4E0|F5H4L0|O43632|Q5VWX7	Silent	SNP	ENST00000252936.3	hg19	CCDS7676.1																																																																																			.	.		0.632	TUBGCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051148.1			A	135099037	C	A	135099037	2	1	272	1	0	0	0	0	0	0	0	1	16781	639	23	1		1	TUBGCP2	10	135099037	Silent	SNP	C	TCGA-G3-A25S-01A-11D-A16V-10	33296815	135099037	435710	51	39484										
MUC6	4588	hgsc.bcm.edu	37	chr11	1026952	1026952	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	cccccttacgcaggcaacacCggtggccagcatctggcatg	11	16	1	0			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr11:1026952C>T	ENST00000421673.2	-	19	2433	c.2383G>A	c.(2383-2385)Ggt>Agt	p.G795S		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	795					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CAGGCAACACCGGTGGCCAGC	0.657																																					p.G795S		Atlas-SNP	.											.	MUC6	408	.	0			c.G2383A						.						15	17	16					11																	1026952		1986	4142	6128	SO:0001583	missense	4588	exon19			CAACACCGGTGGC	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"Mucins"	7517	protein-coding gene	gene with protein product		158374	"mucin 6, gastric"			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.2383G>A	chr11.hg19:g.1026952C>T	ENSP00000406861:p.Gly795Ser	60.0	0.0		84.0	30.0	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	hg19	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	c	17.51	3.407709	0.62399	.	.	ENSG00000184956	ENST00000421673	D	0.90069	-2.61	4.66	4.66	0.58398	Protease inhibitor I8, cysteine-rich trypsin inhibitor-like (2);	.	.	.	.	D	0.92737	0.7691	L	0.49350	1.555	0.35727	D	0.817651	D	0.89917	1.0	D	0.97110	1.0	D	0.94712	0.7893	9	0.49607	T	0.09	.	17.9246	0.88979	0.0:1.0:0.0:0.0	.	795	Q6W4X9	MUC6_HUMAN	S	795	ENSP00000406861:G795S	ENSP00000406861:G795S	G	-	1	0	MUC6	1016952	0.979000	0.34478	0.235000	0.24058	0.030000	0.12068	2.897000	0.48664	2.302000	0.77476	0.556000	0.70494	GGT	.	.		0.657	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540		T	1026952	C	T	1026952	3	4	272	1	0	0	0	0	1	0	0	0	9989	652	23	1	4996	1	MUC6	11	1026952	Missense_Mutation	SNP	C	TCGA-G3-A25S-01A-11D-A16V-10		1026952	133979564	52	39485										
CHRM4	1132	hgsc.bcm.edu	37	chr11	46406927	46406927	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	ttcgtgtcactttgcgctccCgggccgccatctgccgcttc	10	17	2	0			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr11:46406927C>T	ENST00000433765.2	-	1	1180	c.1181G>A	c.(1180-1182)cGg>cAg	p.R394Q		NM_000741.2	NP_000732.2	P08173	ACM4_HUMAN	cholinergic receptor, muscarinic 4	394					adenylate cyclase-inhibiting G-protein coupled acetylcholine receptor signaling pathway (GO:0007197)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|regulation of locomotion (GO:0040012)|signal transduction (GO:0007165)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)			breast(1)|endometrium(7)|kidney(1)|large_intestine(1)|lung(6)|prostate(3)|skin(1)	20				GBM - Glioblastoma multiforme(35;0.0254)|Lung(87;0.14)	Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Darifenacin(DB00496)|Desipramine(DB01151)|Doxepin(DB01142)|Fesoterodine(DB06702)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Isopropamide(DB01625)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paroxetine(DB00715)|Pethidine(DB00454)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Tolterodine(DB01036)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	TTTGCGCTCCCGGGCCGCCAT	0.637																																					p.R394Q	Esophageal Squamous(171;1020 1936 4566 30205 42542)	Atlas-SNP	.											.	CHRM4	47	.	0			c.G1181A						.						73	78	76					11																	46406927		2187	4290	6477	SO:0001583	missense	1132	exon1			CGCTCCCGGGCCG	M16405	CCDS44581.1	11p12-p11.2	2012-08-08			ENSG00000180720	ENSG00000180720		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1953	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 4"	118495				1577490	Standard	NM_000741		Approved		uc001nct.1	P08173	OTTHUMG00000154371	ENST00000433765.2:c.1181G>A	chr11.hg19:g.46406927C>T	ENSP00000409378:p.Arg394Gln	73.0	0.0		89.0	23.0	NM_000741	B2RPP4|Q0VD60|Q4VBK7	Missense_Mutation	SNP	ENST00000433765.2	hg19	CCDS44581.1	.	.	.	.	.	.	.	.	.	.	c	24.6	4.552364	0.86127	.	.	ENSG00000180720	ENST00000433765	T	0.72505	-0.66	4.58	4.58	0.56647	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	D	0.83394	0.5245	M	0.77820	2.39	0.58432	D	0.999993	D	0.69078	0.997	D	0.64877	0.93	D	0.86282	0.1668	9	0.87932	D	0	-12.9181	17.5685	0.87927	0.0:1.0:0.0:0.0	.	394	P08173	ACM4_HUMAN	Q	394	ENSP00000409378:R394Q	ENSP00000409378:R394Q	R	-	2	0	CHRM4	46363503	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.640000	0.83355	2.395000	0.81488	0.457000	0.33378	CGG	.	.		0.637	CHRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334985.1	NM_000741		T	46406927	C	T	46406927	3	4	272	1	0	0	0	0	1	0	0	0	3381	652	23	1	262	1	CHRM4	11	46406927	Missense_Mutation	SNP	C	TCGA-G3-A25S-01A-11D-A16V-10	45379975	46406927	88599589	53	39486										
TNKS1BP1	85456	hgsc.bcm.edu	37	chr11	57080609	57080609	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	acactccttcttccctgctgGaaacggccaagttgccagcc	8	16	1	0			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr11:57080609G>A	ENST00000532437.1	-	4	1864	c.1553C>T	c.(1552-1554)tCc>tTc	p.S518F	TNKS1BP1_ENST00000358252.3_Missense_Mutation_p.S518F|TNKS1BP1_ENST00000530920.1_5'Flank			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	518	Acidic.|Pro-rich.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)			breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				TTCCCTGCTGGAAACGGCCAA	0.652																																					p.S518F		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.C1553T						.						34	31	32					11																	57080609		2174	4245	6419	SO:0001583	missense	85456	exon5			CTGCTGGAAACGG	AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.1553C>T	chr11.hg19:g.57080609G>A	ENSP00000437271:p.Ser518Phe	28.0	0.0		85.0	21.0	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Missense_Mutation	SNP	ENST00000532437.1	hg19	CCDS7951.1	.	.	.	.	.	.	.	.	.	.	G	14.63	2.591782	0.46214	.	.	ENSG00000149115	ENST00000358252;ENST00000532437	T;T	0.37058	1.22;1.22	2.93	2.93	0.34026	.	0.557718	0.13538	N	0.380456	T	0.39886	0.1095	L	0.27053	0.805	0.09310	N	1	D	0.61697	0.99	P	0.60345	0.873	T	0.10567	-1.0624	10	0.54805	T	0.06	.	9.558	0.39351	0.0:0.0:1.0:0.0	.	518	Q9C0C2	TB182_HUMAN	F	518	ENSP00000350990:S518F;ENSP00000437271:S518F	ENSP00000350990:S518F	S	-	2	0	TNKS1BP1	56837185	0.039000	0.19947	0.017000	0.16124	0.072000	0.16883	1.973000	0.40550	1.964000	0.57103	0.462000	0.41574	TCC	.	.		0.652	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396		A	57080609	G	A	57080609	3	1	272	1	0	0	0	0	1	0	0	0	16335	1174	41	3	3664	3	TNKS1BP1	11	57080609	Missense_Mutation	SNP	G	TCGA-G3-A25S-01A-11D-A16V-10	10673682	57080609	77925907	54	39487										
CNIH2	254263	hgsc.bcm.edu	37	chr11	66050758	66050758	+	Nonsense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	gatggctctgaggtcatgtaTgatgcggtctccatcatgaa	12	8	4	3			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr11:66050758T>G	ENST00000311445.6	+	5	609	c.351T>G	c.(349-351)taT>taG	p.Y117*	CNIH2_ENST00000528852.1_Nonsense_Mutation_p.Y117*|CNIH2_ENST00000530519.1_3'UTR|YIF1A_ENST00000526497.1_5'Flank	NM_182553.2	NP_872359.1	Q6PI25	CNIH2_HUMAN	cornichon family AMPA receptor auxiliary protein 2	117					intracellular signal transduction (GO:0035556)|localization within membrane (GO:0051668)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of membrane potential (GO:0042391)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				endometrium(1)|large_intestine(1)|lung(2)|prostate(1)	5						AGGTCATGTATGATGCGGTCT	0.547											OREG0021100	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y117X		Atlas-SNP	.											.	CNIH2	15	.	0			c.T351G						.						223	207	213					11																	66050758		2200	4295	6495	SO:0001587	stop_gained	254263	exon5			CATGTATGATGCG	BC047953	CCDS8131.1	11q13.2	2013-08-28	2013-08-28		ENSG00000174871	ENSG00000174871			28744	protein-coding gene	gene with protein product		611288	"cornichon homolog 2 (Drosophila)"			12477932	Standard	NM_182553		Approved	MGC50896, Cnil, CNIH-2	uc001ohi.2	Q6PI25	OTTHUMG00000166919	ENST00000311445.6:c.351T>G	chr11.hg19:g.66050758T>G	ENSP00000310003:p.Tyr117*	62.0	0.0	1088	33.0	19.0	NM_182553		Nonsense_Mutation	SNP	ENST00000311445.6	hg19	CCDS8131.1	.	.	.	.	.	.	.	.	.	.	T	35	5.492071	0.96339	.	.	ENSG00000174871	ENST00000528852;ENST00000311445	.	.	.	5.63	3.04	0.35103	.	0.307408	0.36482	N	0.002566	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.5909	6.963	0.24608	0.0:0.2879:0.0:0.7121	.	.	.	.	X	117	.	ENSP00000310003:Y117X	Y	+	3	2	CNIH2	65807334	0.978000	0.34361	1.000000	0.80357	0.990000	0.78478	0.151000	0.16283	1.075000	0.40932	-0.256000	0.11100	TAT	.	.		0.547	CNIH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000391892.1	NM_182553		G	66050758	T	G	66050758	4	3	272	1	0	0	0	0	0	1	0	0	3605	1471	51	5	369	5	CNIH2	11	66050758	Nonsense_Mutation	SNP	T	TCGA-G3-A25S-01A-11D-A16V-10	8970149	66050758	68955758	55	39488										
CASP4	837	hgsc.bcm.edu	37	chr11	104820474	104820474	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	ggacttgtgctctggtctggTagcaaatgccctcagcgctg	13	11	3	0	rs559503139		TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr11:104820474T>C	ENST00000444739.2	-	5	1487	c.577A>G	c.(577-579)Acc>Gcc	p.T193A	CASP4_ENST00000531333.1_5'UTR|CASP4_ENST00000393150.3_Missense_Mutation_p.T137A	NM_001225.3	NP_001216.1	P49662	CASP4_HUMAN	caspase 4, apoptosis-related cysteine peptidase	193					apoptotic process (GO:0006915)|execution phase of apoptosis (GO:0097194)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of inflammatory response (GO:0050727)	AIM2 inflammasome complex (GO:0097169)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|IPAF inflammasome complex (GO:0072557)|membrane (GO:0016020)|mitochondrion (GO:0005739)|NLRP3 inflammasome complex (GO:0072559)	cysteine-type endopeptidase activity (GO:0004197)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(1)|skin(1)|urinary_tract(2)	23		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000854)|Epithelial(105;0.00879)|all cancers(92;0.0357)		TCTGGTCTGGTAGCAAATGCC	0.463													.|||	1	0.000199681	8e-04	0	5008	,	,		20995	0		0	False		,,,				2504	0				p.T193A		Atlas-SNP	.											.	CASP4	57	.	0			c.A577G						.						139	123	128					11																	104820474		2202	4299	6501	SO:0001583	missense	837	exon5			GTCTGGTAGCAAA	U25804	CCDS8327.1, CCDS41704.1	11q22.2-q22.3	2006-02-17	2005-08-17		ENSG00000196954	ENSG00000196954		"Caspases"	1505	protein-coding gene	gene with protein product		602664	"caspase 4, apoptosis-related cysteine protease"			7797510, 9250871	Standard	NM_001225		Approved	ICE(rel)II, ICH-2, TX	uc001pid.1	P49662	OTTHUMG00000166078	ENST00000444739.2:c.577A>G	chr11.hg19:g.104820474T>C	ENSP00000388566:p.Thr193Ala	101.0	0.0		50.0	10.0	NM_001225	A2NHL8|A2NHM0	Missense_Mutation	SNP	ENST00000444739.2	hg19	CCDS8327.1	.	.	.	.	.	.	.	.	.	.	T	0.004	-2.352862	0.00217	.	.	ENSG00000196954	ENST00000444739;ENST00000393150;ENST00000355546	T;T	0.18810	2.19;2.19	4.57	1.56	0.23342	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase precursor p45, core (1);Peptidase C14, ICE, catalytic subunit p20 (1);	0.561699	0.19933	N	0.102811	T	0.01976	0.0062	N	0.00014	-2.895	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.0;0.002	T	0.45963	-0.9225	10	0.02654	T	1	.	4.8181	0.13376	0.1489:0.6143:0.1457:0.0911	.	193;193	B4E2D2;P49662	.;CASP4_HUMAN	A	193;137;146	ENSP00000388566:T193A;ENSP00000376857:T137A	ENSP00000347741:T146A	T	-	1	0	CASP4	104325684	0.006000	0.16342	0.524000	0.27887	0.002000	0.02628	0.797000	0.26999	1.135000	0.42183	-0.147000	0.13772	ACC	.	.		0.463	CASP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387751.1	NM_001225		C	104820474	T	C	104820474	3	2	272	1	0	0	0	0	1	0	0	0	2675	1638	57	2	572	2	CASP4	11	104820474	Missense_Mutation	SNP	T	TCGA-G3-A25S-01A-11D-A16V-10	38769716	104820474	30186042	56	39489										
KBTBD3	143879	hgsc.bcm.edu	37	chr11	105925003	105925003	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	aaaagtcactgcaagctttgGataggaaggaaacttgaaga	11	5	1	2			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr11:105925003G>C	ENST00000526793.1	-	3	572	c.413C>G	c.(412-414)tCc>tGc	p.S138C	KBTBD3_ENST00000534815.1_Missense_Mutation_p.S59C|KBTBD3_ENST00000531837.1_Missense_Mutation_p.S138C	NM_152433.3	NP_689646.2	Q8NAB2	KBTB3_HUMAN	kelch repeat and BTB (POZ) domain containing 3	134										NS(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|prostate(1)	25		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.43e-05)|Epithelial(105;0.00418)|all cancers(92;0.0299)		GCAAGCTTTGGATAGGAAGGA	0.318																																					p.S138C		Atlas-SNP	.											.	KBTBD3	59	.	0			c.C413G						.						66	70	68					11																	105925003		2200	4298	6498	SO:0001583	missense	143879	exon3			GCTTTGGATAGGA	AK055247	CCDS8334.1	11q22.3	2013-01-08	2003-12-12	2003-12-17		ENSG00000182359		"BTB/POZ domain containing"	22934	protein-coding gene	gene with protein product			"BTB and kelch domain containing 3"	BKLHD3			Standard	NM_198439		Approved		uc001pjb.3	Q8NAB2		ENST00000526793.1:c.413C>G	chr11.hg19:g.105925003G>C	ENSP00000436262:p.Ser138Cys	138.0	0.0		72.0	26.0	NM_152433	Q6N066|Q86X38|Q96NK5	Missense_Mutation	SNP	ENST00000526793.1	hg19	CCDS8334.1	.	.	.	.	.	.	.	.	.	.	G	15.28	2.785454	0.49997	.	.	ENSG00000182359	ENST00000534815;ENST00000526793;ENST00000531837	T;T;T	0.70869	-0.52;-0.52;-0.52	5.36	5.36	0.76844	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.163800	0.56097	D	0.000028	T	0.67869	0.2939	N	0.13098	0.295	0.38045	D	0.935583	B;P	0.42456	0.347;0.78	P;P	0.49999	0.505;0.628	T	0.75263	-0.3379	10	0.72032	D	0.01	.	19.0932	0.93238	0.0:0.0:1.0:0.0	.	138;134	A8K1K0;Q8NAB2	.;KBTB3_HUMAN	C	59;138;138	ENSP00000431910:S59C;ENSP00000436262:S138C;ENSP00000432163:S138C	ENSP00000436262:S138C	S	-	2	0	KBTBD3	105430213	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.923000	0.56469	2.511000	0.84671	0.650000	0.86243	TCC	.	.		0.318	KBTBD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388705.2	NM_152433		C	105925003	G	C	105925003	3	2	272	1	0	0	0	0	1	0	0	0	8003	1174	41	4	1429	4	KBTBD3	11	105925003	Missense_Mutation	SNP	G	TCGA-G3-A25S-01A-11D-A16V-10	1104529	105925003	29081513	57	39490										
OR8B8	26493	hgsc.bcm.edu	37	chr11	124310110	124310110	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	tgacgtccttattcctcaggCtataaattaatgggttgagc	9	8	1	2	rs147220624	byFrequency	TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr11:124310110C>T	ENST00000328064.2	-	1	944	c.872G>A	c.(871-873)aGc>aAc	p.S291N		NM_012378.1	NP_036510.1	Q15620	OR8B8_HUMAN	olfactory receptor, family 8, subfamily B, member 8	291					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		ATTCCTCAGGCTATAAATTAA	0.408																																					p.S291N		Atlas-SNP	.											.	OR8B8	76	.	0			c.G872A						.						107	98	101					11																	124310110		2201	4299	6500	SO:0001583	missense	26493	exon1			CTCAGGCTATAAA	AF238488	CCDS8446.1	11q24.2	2012-08-09			ENSG00000197125	ENSG00000197125		"GPCR / Class A : Olfactory receptors"	8477	protein-coding gene	gene with protein product						9119360	Standard	NM_012378		Approved	TPCR85	uc010sal.2	Q15620	OTTHUMG00000165917	ENST00000328064.2:c.872G>A	chr11.hg19:g.124310110C>T	ENSP00000330280:p.Ser291Asn	66.0	0.0		35.0	16.0	NM_012378	A1L446|Q96RC8	Missense_Mutation	SNP	ENST00000328064.2	hg19	CCDS8446.1	.	.	.	.	.	.	.	.	.	.	C	13.92	2.379611	0.42207	.	.	ENSG00000197125	ENST00000328064	T	0.39056	1.1	3.81	3.81	0.43845	.	0.000000	0.56097	D	0.000036	T	0.76870	0.4048	H	0.98559	4.265	0.25578	N	0.98683	D	0.71674	0.998	D	0.66847	0.947	T	0.75889	-0.3158	10	0.87932	D	0	.	16.615	0.84904	0.0:1.0:0.0:0.0	.	291	Q15620	OR8B8_HUMAN	N	291	ENSP00000330280:S291N	ENSP00000330280:S291N	S	-	2	0	OR8B8	123815320	0.017000	0.18338	0.749000	0.31150	0.468000	0.32798	1.191000	0.32138	2.412000	0.81896	0.655000	0.94253	AGC	.	C|0.999;A|0.001		0.408	OR8B8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387056.1	NM_012378		T	124310110	C	T	124310110	3	4	272	1	0	0	0	0	1	0	0	0	11239	797	28	3	66	3	OR8B8	11	124310110	Missense_Mutation	SNP	C	TCGA-G3-A25S-01A-11D-A16V-10	18385107	124310110	10696406	58	39491										
OR8B8	26493	hgsc.bcm.edu	37	chr11	124310343	124310343	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	agagcataggaaatgaagatGgtgactgtgggcacaccaat	13	6	0	4			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr11:124310343G>T	ENST00000328064.2	-	1	711	c.639C>A	c.(637-639)acC>acA	p.T213T		NM_012378.1	NP_036510.1	Q15620	OR8B8_HUMAN	olfactory receptor, family 8, subfamily B, member 8	213					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		AAATGAAGATGGTGACTGTGG	0.488																																					p.T213T		Atlas-SNP	.											.	OR8B8	76	.	0			c.C639A						.						187	159	169					11																	124310343		2201	4299	6500	SO:0001819	synonymous_variant	26493	exon1			GAAGATGGTGACT	AF238488	CCDS8446.1	11q24.2	2012-08-09			ENSG00000197125	ENSG00000197125		"GPCR / Class A : Olfactory receptors"	8477	protein-coding gene	gene with protein product						9119360	Standard	NM_012378		Approved	TPCR85	uc010sal.2	Q15620	OTTHUMG00000165917	ENST00000328064.2:c.639C>A	chr11.hg19:g.124310343G>T		86.0	0.0		40.0	18.0	NM_012378	A1L446|Q96RC8	Silent	SNP	ENST00000328064.2	hg19	CCDS8446.1																																																																																			.	.		0.488	OR8B8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387056.1	NM_012378		T	124310343	G	T	124310343	2	4	272	1	0	0	0	0	0	0	0	1	11239	1335	47	3		3	OR8B8	11	124310343	Silent	SNP	G	TCGA-G3-A25S-01A-11D-A16V-10	233	124310343	10696173	59	39492										
NRIP2	83714	hgsc.bcm.edu	37	chr12	2944113	2944113	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	gctctctttccaacaggaggGtctccacgggagggaaagag	14	10	2	1			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr12:2944113G>A	ENST00000337508.4	-	1	77	c.37C>T	c.(37-39)Ccc>Tcc	p.P13S		NM_031474.2	NP_113662.1	Q9BQI9	NRIP2_HUMAN	nuclear receptor interacting protein 2	13					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	aspartic-type endopeptidase activity (GO:0004190)			central_nervous_system(1)|endometrium(2)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(31;0.000818)			CAACAGGAGGGTCTCCACGGG	0.587																																					p.P13S		Atlas-SNP	.											.	NRIP2	21	.	0			c.C37T						.						48	44	45					12																	2944113		2203	4300	6503	SO:0001583	missense	83714	exon1			AGGAGGGTCTCCA	AK054740	CCDS8514.1	12p13.33	2008-02-05			ENSG00000053702	ENSG00000053702			23078	protein-coding gene	gene with protein product						11230166	Standard	NM_031474		Approved	DKFZP761G1913	uc001qlc.3	Q9BQI9	OTTHUMG00000130616	ENST00000337508.4:c.37C>T	chr12.hg19:g.2944113G>A	ENSP00000337501:p.Pro13Ser	88.0	0.0		64.0	14.0	NM_031474	A2RRE3|B4DV61	Missense_Mutation	SNP	ENST00000337508.4	hg19	CCDS8514.1	.	.	.	.	.	.	.	.	.	.	G	9.806	1.181895	0.21787	.	.	ENSG00000053702	ENST00000337508;ENST00000546074	.	.	.	4.34	4.34	0.51931	.	.	.	.	.	T	0.49695	0.1572	L	0.43152	1.355	0.26649	N	0.972146	D	0.64830	0.994	P	0.56127	0.792	T	0.40979	-0.9534	8	0.87932	D	0	-12.3098	12.2247	0.54453	0.0:0.0:1.0:0.0	.	13	Q9BQI9	NRIP2_HUMAN	S	13	.	ENSP00000337501:P13S	P	-	1	0	NRIP2	2814374	0.998000	0.40836	0.942000	0.38095	0.031000	0.12232	1.929000	0.40114	2.259000	0.74868	0.484000	0.47621	CCC	.	.		0.587	NRIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253090.4	NM_031474		A	2944113	G	A	2944113	3	1	272	1	0	0	0	0	1	0	0	0	10662	1261	44	3	832	3	NRIP2	12	2944113	Missense_Mutation	SNP	G	TCGA-G3-A25S-01A-11D-A16V-10		2944113	130907782	60	39493										
DNAH10	196385	hgsc.bcm.edu	37	chr12	124257438	124257438	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	acatgctctgtacccctcttCccgaggagttcctggaccaa	8	15	2	0			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr12:124257438C>T	ENST00000409039.3	+	4	296	c.271C>T	c.(271-273)Ccc>Tcc	p.P91S		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	91	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		TACCCCTCTTCCCGAGGAGTT	0.463																																					p.P91S		Atlas-SNP	.											.	DNAH10	888	.	0			c.C271T						.						174	169	170					12																	124257438		1943	4158	6101	SO:0001583	missense	196385	exon4			CCTCTTCCCGAGG	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.271C>T	chr12.hg19:g.124257438C>T	ENSP00000386770:p.Pro91Ser	53.0	0.0		59.0	32.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	hg19	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	C	12.33	1.905933	0.33628	.	.	ENSG00000197653	ENST00000409039	T	0.23552	1.9	5.93	4.09	0.47781	.	.	.	.	.	T	0.16727	0.0402	N	0.24115	0.695	0.09310	N	1	B	0.10296	0.003	B	0.12837	0.008	T	0.25082	-1.0142	9	0.26408	T	0.33	.	8.4702	0.32980	0.0:0.7595:0.0:0.2405	.	91	Q8IVF4	DYH10_HUMAN	S	91	ENSP00000386770:P91S	ENSP00000386770:P91S	P	+	1	0	DNAH10	122823391	0.198000	0.23374	0.042000	0.18584	0.003000	0.03518	1.018000	0.30002	0.820000	0.34516	0.655000	0.94253	CCC	.	.		0.463	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			T	124257438	C	T	124257438	3	4	272	1	0	0	0	0	1	0	0	0	4600	855	30	3	285	3	DNAH10	12	124257438	Missense_Mutation	SNP	C	TCGA-G3-A25S-01A-11D-A16V-10	121313325	124257438	9594457	61	39494			1	48		2	2	12	C		2.878169e-05
DNAH10	196385	hgsc.bcm.edu	37	chr12	124257449	124257449	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	acccctcttcccgaggagttCctggaccaaaacgtggtgtt	10	13	1	0			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr12:124257449C>T	ENST00000409039.3	+	4	307	c.282C>T	c.(280-282)ttC>ttT	p.F94F		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	94	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		CCGAGGAGTTCCTGGACCAAA	0.468																																					p.F94F		Atlas-SNP	.											.	DNAH10	888	.	0			c.C282T						.						165	162	163					12																	124257449		1950	4163	6113	SO:0001819	synonymous_variant	196385	exon4			GGAGTTCCTGGAC	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.282C>T	chr12.hg19:g.124257449C>T		58.0	0.0		58.0	33.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	hg19	CCDS9255.2																																																																																			.	.		0.468	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			T	124257449	C	T	124257449	2	4	272	1	0	0	0	0	0	0	0	1	4600	854	30	3		3	DNAH10	12	124257449	Silent	SNP	C	TCGA-G3-A25S-01A-11D-A16V-10	11	124257449	9594446	62	39495			1	48		2	2	12	C		2.878169e-05
NBEA	26960	hgsc.bcm.edu	37	chr13	36229035	36229036	+	Frame_Shift_Ins	INS	-	-	C													0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	ggcagatcacagacctcgttINSgaccagagtatacaaatcaa							TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr13:36229035_36229036insC	ENST00000400445.3	+	53	8550_8551	c.8016_8017insC	c.(8017-8019)gacfs	p.D2673fs	NBEA_ENST00000379922.3_Frame_Shift_Ins_p.D251fs|NBEA_ENST00000310336.4_Frame_Shift_Ins_p.D2673fs|NBEA_ENST00000379939.2_Frame_Shift_Ins_p.D2670fs|NBEA_ENST00000540320.1_Frame_Shift_Ins_p.D2673fs|NBEA_ENST00000537702.1_Frame_Shift_Ins_p.D466fs	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	2673					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		CAGACCTCGTTGACCAGAGTAT	0.366																																					p.V2672fs		Atlas-INDEL	.											.	NBEA	340	.	0			c.8016_8017insC						.																																			SO:0001589	frameshift_variant	26960	exon53			.	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	Exception_encountered	chr13.hg19:g.36229035_36229036insC	ENSP00000383295:p.Asp2673fs	73.0	0.0		45.0	30.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Frame_Shift_Ins	INS	ENST00000400445.3	hg19	CCDS45026.1																																																																																			.	.		0.366	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		C	36229036	-	C	36229035	7	5	272	1	0	1	1	0	0	0	0	0	10196	1799	63	0	8226	0	NBEA	13	36229035	Frame_Shift_Ins	INS	-	TCGA-G3-A25S-01A-11D-A16V-10		36229035	78940843	63	39496										
FREM2	341640	hgsc.bcm.edu	37	chr13	39265055	39265055	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	ccaccaatgatgaacagccaGagatgtttatgagagaattt	9	7	0	5			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr13:39265055G>T	ENST00000280481.7	+	1	3790	c.3574G>T	c.(3574-3576)Gag>Tag	p.E1192*		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1192					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		TGAACAGCCAGAGATGTTTAT	0.418																																					p.E1192X		Atlas-SNP	.											.	FREM2	385	.	0			c.G3574T						.						229	219	222					13																	39265055		2203	4300	6503	SO:0001587	stop_gained	341640	exon1			CAGCCAGAGATGT	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.3574G>T	chr13.hg19:g.39265055G>T	ENSP00000280481:p.Glu1192*	136.0	0.0		55.0	44.0	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Nonsense_Mutation	SNP	ENST00000280481.7	hg19	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	G	44	11.144798	0.99522	.	.	ENSG00000150893	ENST00000280481	.	.	.	6.07	6.07	0.98685	.	0.199491	0.52532	D	0.000079	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18276	T	0.48	.	20.6439	0.99570	0.0:0.0:1.0:0.0	.	.	.	.	X	1192	.	ENSP00000280481:E1192X	E	+	1	0	FREM2	38163055	1.000000	0.71417	0.997000	0.53966	0.788000	0.44548	9.864000	0.99589	2.890000	0.99128	0.650000	0.86243	GAG	.	.		0.418	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		T	39265055	G	T	39265055	4	4	272	1	0	0	0	0	0	1	0	0	6053	943	33	3	3576	3	FREM2	13	39265055	Nonsense_Mutation	SNP	G	TCGA-G3-A25S-01A-11D-A16V-10	3036020	39265055	75904823	64	39497										
COL4A2	1284	hgsc.bcm.edu	37	chr13	111082761	111082761	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	ccattagggtgaacctggagAgcctggattggtcggtttcc	14	9	0	2			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr13:111082761A>G	ENST00000360467.5	+	9	869	c.563A>G	c.(562-564)gAg>gGg	p.E188G	COL4A2_ENST00000462309.1_3'UTR	NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	188	Triple-helical region.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	extracellular matrix structural constituent (GO:0005201)			NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	80	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			GAACCTGGAGAGCCTGGATTG	0.358																																					p.E188G		Atlas-SNP	.											.	COL4A2	178	.	0			c.A563G						.						86	85	85					13																	111082761		1807	4070	5877	SO:0001583	missense	1284	exon9			CTGGAGAGCCTGG	AK025912	CCDS41907.1	13q34	2013-09-05			ENSG00000134871	ENSG00000134871		"Collagens"	2203	protein-coding gene	gene with protein product	"canstatin", "collagen type IV alpha 2"	120090				2439508, 3025878	Standard	NM_001846		Approved	FLJ22259, DKFZp686I14213	uc001vqx.3	P08572	OTTHUMG00000017344	ENST00000360467.5:c.563A>G	chr13.hg19:g.111082761A>G	ENSP00000353654:p.Glu188Gly	114.0	0.0		76.0	27.0	NM_001846	Q14052|Q548C3|Q5VZA9|Q66K23	Missense_Mutation	SNP	ENST00000360467.5	hg19	CCDS41907.1	.	.	.	.	.	.	.	.	.	.	A	9.789	1.177348	0.21787	.	.	ENSG00000134871	ENST00000360467;ENST00000257309	D	0.93906	-3.31	5.19	5.19	0.71726	.	0.504141	0.17796	N	0.161738	D	0.94039	0.8090	M	0.76838	2.35	0.38545	D	0.949315	P	0.41784	0.762	P	0.48063	0.565	D	0.92822	0.6273	10	0.16896	T	0.51	.	13.6015	0.62022	1.0:0.0:0.0:0.0	.	188	P08572	CO4A2_HUMAN	G	188	ENSP00000353654:E188G	ENSP00000257309:E188G	E	+	2	0	COL4A2	109880762	0.899000	0.30636	0.967000	0.41034	0.394000	0.30568	2.243000	0.43115	1.943000	0.56356	0.528000	0.53228	GAG	.	.		0.358	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846		G	111082761	A	G	111082761	3	3	272	1	0	0	0	0	1	0	0	0	3692	304	11	2	593	2	COL4A2	13	111082761	Missense_Mutation	SNP	A	TCGA-G3-A25S-01A-11D-A16V-10	71817706	111082761	4087117	65	39498										
NFATC4	4776	hgsc.bcm.edu	37	chr14	24844908	24844908	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	ggaggccacagtgaaccgacTgcagagcaacgaggtaccag	14	11	0	2			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr14:24844908T>A	ENST00000250373.4	+	7	2057	c.1916T>A	c.(1915-1917)cTg>cAg	p.L639Q	NFATC4_ENST00000557767.1_5'UTR|NFATC4_ENST00000555393.1_5'UTR|NFATC4_ENST00000555590.1_Missense_Mutation_p.L652Q|NFATC4_ENST00000555453.1_Missense_Mutation_p.L627Q|NFATC4_ENST00000554050.1_Missense_Mutation_p.L639Q|NFATC4_ENST00000554661.1_Missense_Mutation_p.L569Q|NFATC4_ENST00000553469.1_Missense_Mutation_p.L671Q|NFATC4_ENST00000422617.3_Missense_Mutation_p.L627Q|NFATC4_ENST00000555802.1_5'UTR|NFATC4_ENST00000554591.1_Missense_Mutation_p.L702Q|NFATC4_ENST00000557451.1_Missense_Mutation_p.L569Q|NFATC4_ENST00000553708.1_Missense_Mutation_p.L639Q|NFATC4_ENST00000556169.1_Missense_Mutation_p.L627Q|NFATC4_ENST00000554344.1_Missense_Mutation_p.L569Q|NFATC4_ENST00000554966.1_Missense_Mutation_p.L652Q|NFATC4_ENST00000554473.1_Missense_Mutation_p.L174Q|NFATC4_ENST00000553879.1_Missense_Mutation_p.L569Q|NFATC4_ENST00000556279.1_Missense_Mutation_p.L671Q|NFATC4_ENST00000556759.1_Missense_Mutation_p.L174Q|NFATC4_ENST00000539237.2_Missense_Mutation_p.L671Q|NFATC4_ENST00000555167.1_Missense_Mutation_p.L174Q|NFATC4_ENST00000424781.2_Missense_Mutation_p.L652Q|NFATC4_ENST00000413692.2_Missense_Mutation_p.L702Q	NM_004554.4	NP_004545.2	Q14934	NFAC4_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4	639	IPT/TIG.				cellular respiration (GO:0045333)|cellular response to lithium ion (GO:0071285)|cellular response to UV (GO:0034644)|heart development (GO:0007507)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of synaptic plasticity (GO:0048167)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription coactivator activity (GO:0003713)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(7)|liver(4)|lung(12)|ovary(1)|skin(2)	34				GBM - Glioblastoma multiforme(265;0.018)		GTGAACCGACTGCAGAGCAAC	0.627																																					p.L702Q		Atlas-SNP	.											.	NFATC4	115	.	0			c.T2105A						.						56	39	45					14																	24844908		2195	4288	6483	SO:0001583	missense	4776	exon8			ACCGACTGCAGAG	BC053855	CCDS9629.1, CCDS45089.1, CCDS55909.1, CCDS55910.1, CCDS55911.1, CCDS73625.1	14q11.2	2009-11-24			ENSG00000100968	ENSG00000100968		"Nuclear factor of activated T-cells"	7778	protein-coding gene	gene with protein product		602699				7749981	Standard	NM_004554		Approved	NFAT3	uc010tok.2	Q14934	OTTHUMG00000029351	ENST00000250373.4:c.1916T>A	chr14.hg19:g.24844908T>A	ENSP00000250373:p.Leu639Gln	96.0	0.0		53.0	17.0	NM_001198967	B4DDG5|B4DY55|B5B2U7|B5B2U8|B5B2U9|B5B2V0|B5B2V1|B5B2V2|B5B2V3|B5B2V4|B5B2V5|B5B2V7|B5B2V8|B5B2V9|B5B2W0|B5B2W1|B5B2W2|B5B2W3|B5B2W4|B5B2W5|B5B2W6|B5B2W7|B5B2W8|B5B2W9|B5B2X0|Q7Z598|Q96H68	Missense_Mutation	SNP	ENST00000250373.4	hg19	CCDS9629.1	.	.	.	.	.	.	.	.	.	.	T	19.31	3.803041	0.70682	.	.	ENSG00000100968	ENST00000413692;ENST00000554591;ENST00000555590;ENST00000554966;ENST00000424781;ENST00000539237;ENST00000556279;ENST00000553469;ENST00000554050;ENST00000250373;ENST00000553708;ENST00000553879;ENST00000554344;ENST00000554661;ENST00000556169;ENST00000557451;ENST00000422617;ENST00000555453;ENST00000554473;ENST00000556759;ENST00000555167	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.29655	3.29;3.31;3.31;3.32;3.3;3.3;3.31;3.32;3.33;3.31;3.31;2.99;2.99;3.0;3.0;2.98;2.98;2.98;1.6;1.56;1.56	5.41	5.41	0.78517	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.290828	0.28730	N	0.014323	T	0.33265	0.0857	N	0.14661	0.345	0.80722	D	1	P;D;P;D;P;P;D;D;D;D;P;P;P	0.63880	0.936;0.981;0.935;0.993;0.935;0.935;0.981;0.993;0.993;0.981;0.935;0.935;0.947	P;P;P;P;P;P;P;P;P;P;P;P;P	0.59889	0.556;0.813;0.775;0.865;0.713;0.837;0.813;0.865;0.865;0.813;0.837;0.775;0.856	T	0.11616	-1.0580	10	0.40728	T	0.16	-1.8492	13.4467	0.61144	0.0:0.0:0.0:1.0	.	627;627;671;671;652;652;652;702;702;627;671;702;639	Q14934-17;Q14934-9;Q14934-14;Q14934-4;Q14934-15;Q14934-6;Q14934-7;Q14934-2;Q14934-3;Q14934-10;Q14934-5;Q14934-11;Q14934	.;.;.;.;.;.;.;.;.;.;.;.;NFAC4_HUMAN	Q	702;702;652;652;652;671;671;671;639;639;639;569;569;569;627;569;627;627;174;174;174	ENSP00000388910:L702Q;ENSP00000452039:L702Q;ENSP00000451224:L652Q;ENSP00000450644:L652Q;ENSP00000388668:L652Q;ENSP00000439350:L671Q;ENSP00000452270:L671Q;ENSP00000451502:L671Q;ENSP00000451151:L639Q;ENSP00000250373:L639Q;ENSP00000450590:L639Q;ENSP00000452349:L569Q;ENSP00000450469:L569Q;ENSP00000450733:L569Q;ENSP00000451454:L627Q;ENSP00000451284:L569Q;ENSP00000396788:L627Q;ENSP00000450686:L627Q;ENSP00000450810:L174Q;ENSP00000451183:L174Q;ENSP00000451395:L174Q	ENSP00000250373:L639Q	L	+	2	0	NFATC4	23914748	1.000000	0.71417	0.968000	0.41197	0.989000	0.77384	4.773000	0.62331	2.272000	0.75746	0.460000	0.39030	CTG	.	.		0.627	NFATC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073206.6	NM_004554		A	24844908	T	A	24844908	3	1	272	1	0	0	0	0	1	0	0	0	10374	1580	55	4	2135	4	NFATC4	14	24844908	Missense_Mutation	SNP	T	TCGA-G3-A25S-01A-11D-A16V-10		24844908	82504632	66	39499										
RHCG	51458	hgsc.bcm.edu	37	chr15	90023512	90023512	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	caatcatggcaaagaggtccGactggtacacagaattctgt	10	9	2	2			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr15:90023512G>T	ENST00000268122.4	-	4	718	c.650C>A	c.(649-651)tCg>tAg	p.S217*	RHCG_ENST00000544600.1_Nonsense_Mutation_p.S217*	NM_016321.1	NP_057405.1	Q9UBD6	RHCG_HUMAN	Rh family, C glycoprotein	217					amine transport (GO:0015837)|ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|cellular ion homeostasis (GO:0006873)|epithelial cell differentiation (GO:0030855)|homeostatic process (GO:0042592)|regulation of pH (GO:0006885)|transepithelial ammonium transport (GO:0070634)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ammonium transmembrane transporter activity (GO:0008519)|ankyrin binding (GO:0030506)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Lung NSC(78;0.0237)|all_lung(78;0.0478)					AAAGAGGTCCGACTGGTACAC	0.547																																					p.S217X		Atlas-SNP	.											.	RHCG	49	.	0			c.C650A						.						205	179	188					15																	90023512		2200	4299	6499	SO:0001587	stop_gained	51458	exon4			AGGTCCGACTGGT	AF081497	CCDS10351.1	15q25	2013-05-22	2006-02-23		ENSG00000140519	ENSG00000140519		"Solute carriers"	18140	protein-coding gene	gene with protein product		605381	"chromosome 15 open reading frame 6", "Rhesus blood group, C glycoprotein"	C15orf6		10852913	Standard	NM_016321		Approved	RHGK, PDRC2, SLC42A3	uc002bnz.2	Q9UBD6	OTTHUMG00000149647	ENST00000268122.4:c.650C>A	chr15.hg19:g.90023512G>T	ENSP00000268122:p.Ser217*	44.0	0.0		44.0	19.0	NM_016321	A8K4D4|Q6X3Y4	Nonsense_Mutation	SNP	ENST00000268122.4	hg19	CCDS10351.1	.	.	.	.	.	.	.	.	.	.	G	38	6.998013	0.97990	.	.	ENSG00000140519	ENST00000544600;ENST00000268122;ENST00000536247	.	.	.	5.59	5.59	0.84812	.	0.107977	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-3.7037	19.6374	0.95740	0.0:0.0:1.0:0.0	.	.	.	.	X	217;217;208	.	.	S	-	2	0	RHCG	87824516	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	9.830000	0.99415	2.647000	0.89833	0.558000	0.71614	TCG	.	.		0.547	RHCG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000312855.2	NM_016321		T	90023512	G	T	90023512	4	4	272	1	0	0	0	0	0	1	0	0	13341	1059	37	1	817	1	RHCG	15	90023512	Nonsense_Mutation	SNP	G	TCGA-G3-A25S-01A-11D-A16V-10		90023512	12507880	67	39500										
IQGAP1	8826	hgsc.bcm.edu	37	chr15	91020941	91020941	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	gattgtgacaggaaatcctaCggttattaaaatggttgtaa	10	4	0	1			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr15:91020941C>T	ENST00000268182.5	+	26	3273	c.3149C>T	c.(3148-3150)aCg>aTg	p.T1050M	IQGAP1_ENST00000560738.1_Missense_Mutation_p.T478M	NM_003870.3	NP_003861.1	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	1050	C1.|Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				cellular response to calcium ion (GO:0071277)|cellular response to epidermal growth factor stimulus (GO:0071364)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerular visceral epithelial cell development (GO:0072015)|negative regulation of catalytic activity (GO:0043086)|negative regulation of dephosphorylation (GO:0035305)|neuron projection extension (GO:1990138)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|regulation of cytokine production (GO:0001817)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	actin filament (GO:0005884)|axon (GO:0030424)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|midbody (GO:0030496)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activator activity (GO:0043539)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			GGAAATCCTACGGTTATTAAA	0.398																																					p.T1050M		Atlas-SNP	.											.	IQGAP1	140	.	0			c.C3149T						.						93	97	96					15																	91020941		2198	4298	6496	SO:0001583	missense	8826	exon26			ATCCTACGGTTAT	D29640	CCDS10362.1	15q26.1	2008-07-18			ENSG00000140575	ENSG00000140575			6110	protein-coding gene	gene with protein product	"RasGAP-like with IQ motifs"	603379				8051149, 8670801	Standard	XM_005254984		Approved	p195, KIAA0051, SAR1, HUMORFA01	uc002bpl.1	P46940	OTTHUMG00000149832	ENST00000268182.5:c.3149C>T	chr15.hg19:g.91020941C>T	ENSP00000268182:p.Thr1050Met	63.0	0.0		66.0	15.0	NM_003870	A7MBM3	Missense_Mutation	SNP	ENST00000268182.5	hg19	CCDS10362.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.929800	0.92389	.	.	ENSG00000140575	ENST00000268182	T	0.79749	-1.3	5.86	5.86	0.93980	Rho GTPase activation protein (1);Ras GTPase-activating protein (4);	0.000000	0.85682	D	0.000000	D	0.89399	0.6704	M	0.72118	2.19	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.87909	0.2696	10	0.42905	T	0.14	-16.0744	19.1654	0.93555	0.0:1.0:0.0:0.0	.	1050	P46940	IQGA1_HUMAN	M	1050	ENSP00000268182:T1050M	ENSP00000268182:T1050M	T	+	2	0	IQGAP1	88821945	1.000000	0.71417	0.993000	0.49108	0.976000	0.68499	7.755000	0.85180	2.778000	0.95560	0.655000	0.94253	ACG	.	.		0.398	IQGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313493.1	NM_003870		T	91020941	C	T	91020941	3	4	272	1	0	0	0	0	1	0	0	0	7823	536	19	1	3251	1	IQGAP1	15	91020941	Missense_Mutation	SNP	C	TCGA-G3-A25S-01A-11D-A16V-10	997429	91020941	11510451	68	39501										
TMC7	79905	hgsc.bcm.edu	37	chr16	19049310	19049310	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	gtattgttctggctgttttaGgggcatgcttttatgcaata	11	5	1	0			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr16:19049310G>T	ENST00000304381.5	+	8	1250	c.1120G>T	c.(1120-1122)Ggg>Tgg	p.G374W	TMC7_ENST00000569532.1_Missense_Mutation_p.G374W|TMC7_ENST00000421369.3_Missense_Mutation_p.G264W|TMC7_ENST00000561963.1_3'UTR	NM_024847.3	NP_079123.3	Q7Z402	TMC7_HUMAN	transmembrane channel-like 7	374					ion transport (GO:0006811)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	28						GGCTGTTTTAGGGGCATGCTT	0.398																																					p.G374W		Atlas-SNP	.											.	TMC7	75	.	0			c.G1120T						.						214	185	195					16																	19049310		2197	4300	6497	SO:0001583	missense	79905	exon8			GTTTTAGGGGCAT	AY263165	CCDS10573.1, CCDS53992.1, CCDS73837.1	16p13.11	2008-02-05			ENSG00000170537	ENSG00000170537			23000	protein-coding gene	gene with protein product						12812529, 12906855	Standard	XM_005255597		Approved	FLJ21240	uc002dfq.3	Q7Z402	OTTHUMG00000131456	ENST00000304381.5:c.1120G>T	chr16.hg19:g.19049310G>T	ENSP00000304710:p.Gly374Trp	177.0	0.0		161.0	85.0	NM_024847	E7ERB6|Q5H9Q8|Q7Z5M4|Q86WX0|Q9H766	Missense_Mutation	SNP	ENST00000304381.5	hg19	CCDS10573.1	.	.	.	.	.	.	.	.	.	.	G	12.27	1.886793	0.33348	.	.	ENSG00000170537	ENST00000304381;ENST00000421369	T;T	0.53640	0.61;0.61	5.5	3.51	0.40186	.	0.422877	0.25319	N	0.031530	T	0.37293	0.0998	L	0.52126	1.63	0.22601	N	0.998941	B;B	0.33904	0.229;0.431	B;B	0.31290	0.08;0.127	T	0.36040	-0.9764	10	0.59425	D	0.04	.	6.4874	0.22097	0.085:0.0:0.5074:0.4076	.	374;374	Q7Z402;B3KSZ3	TMC7_HUMAN;.	W	374;264	ENSP00000304710:G374W;ENSP00000397081:G264W	ENSP00000304710:G374W	G	+	1	0	TMC7	18956811	0.998000	0.40836	0.051000	0.19133	0.548000	0.35241	4.618000	0.61211	1.284000	0.44531	0.650000	0.86243	GGG	.	.		0.398	TMC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254276.3	NM_024847		T	19049310	G	T	19049310	3	4	272	1	0	0	0	0	1	0	0	0	16005	1000	35	3	1150	3	TMC7	16	19049310	Missense_Mutation	SNP	G	TCGA-G3-A25S-01A-11D-A16V-10		19049310	71305443	69	39502										
WBP2	23558	hgsc.bcm.edu	37	chr17	73851333	73851333	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	ttttcacctctcggtgttatTgacgatcactccgccgccct	7	15	3	1			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr17:73851333T>C	ENST00000591399.1	-	2	470	c.46A>G	c.(46-48)Aat>Gat	p.N16D	WBP2_ENST00000344296.4_5'UTR|WBP2_ENST00000590450.1_5'UTR|WBP2_ENST00000590221.1_Missense_Mutation_p.N16D|WBP2_ENST00000254806.3_Missense_Mutation_p.N16D|WBP2_ENST00000585462.1_5'UTR|WBP2_ENST00000433525.2_Missense_Mutation_p.N16D			Q969T9	WBP2_HUMAN	WW domain binding protein 2	16	GRAM.				cellular response to estrogen stimulus (GO:0071391)|establishment of protein localization (GO:0045184)|positive regulation of gene expression, epigenetic (GO:0045815)|positive regulation of histone H3-K14 acetylation (GO:0071442)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nuclear chromatin (GO:0000790)	chromatin DNA binding (GO:0031490)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription coactivator activity (GO:0001105)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	7			all cancers(21;2.61e-06)|Epithelial(20;2.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00092)|LUSC - Lung squamous cell carcinoma(166;0.154)			TCGGTGTTATTGACGATCACT	0.577																																					p.N16D		Atlas-SNP	.											.	WBP2	17	.	0			c.A46G						.						170	171	170					17																	73851333		2203	4300	6503	SO:0001583	missense	23558	exon1			TGTTATTGACGAT	U79458	CCDS11731.1	17q25	2008-02-01				ENSG00000132471			12738	protein-coding gene	gene with protein product		606962				7644498	Standard	NM_012478		Approved	WBP-2	uc002jps.3	Q969T9		ENST00000591399.1:c.46A>G	chr17.hg19:g.73851333T>C	ENSP00000467579:p.Asn16Asp	85.0	0.0		105.0	98.0	NM_012478	O95638	Missense_Mutation	SNP	ENST00000591399.1	hg19	CCDS11731.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.847164	0.91277	.	.	ENSG00000132471	ENST00000254806;ENST00000433525;ENST00000431190;ENST00000416574	D;D	0.88354	-2.37;-2.37	4.21	4.21	0.49690	GRAM (1);	0.117941	0.64402	D	0.000001	D	0.92364	0.7577	L	0.61036	1.89	0.80722	D	1	D;D;D;D	0.76494	0.988;0.999;0.998;0.998	P;D;D;D	0.71414	0.825;0.973;0.963;0.963	D	0.91452	0.5182	10	0.35671	T	0.21	-19.4032	13.7292	0.62776	0.0:0.0:0.0:1.0	.	16;16;16;16	B4DV07;B4DFG2;Q7Z511;Q969T9	.;.;.;WBP2_HUMAN	D	16	ENSP00000254806:N16D;ENSP00000415251:N16D	ENSP00000254806:N16D	N	-	1	0	WBP2	71362928	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	3.631000	0.54280	1.891000	0.54761	0.460000	0.39030	AAT	.	.		0.577	WBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448862.1	NM_012478		C	73851333	T	C	73851333	3	2	272	1	0	0	0	0	1	0	0	0	17274	1812	63	2	771	2	WBP2	17	73851333	Missense_Mutation	SNP	T	TCGA-G3-A25S-01A-11D-A16V-10		73851333	7343877	70	39503										
YES1	7525	hgsc.bcm.edu	37	chr18	742994	742994	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	agtggaacaagtttatcatgTcttaattttttcattatctg	6	5	4	0			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr18:742994T>C	ENST00000584307.1	-	8	1154	c.984A>G	c.(982-984)agA>agG	p.R328R	YES1_ENST00000577961.1_Silent_p.R333R|YES1_ENST00000314574.4_Silent_p.R328R			P07947	YES_HUMAN	YES proto-oncogene 1, Src family tyrosine kinase	328	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood coagulation (GO:0007596)|cellular protein modification process (GO:0006464)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|glucose transport (GO:0015758)|innate immune response (GO:0045087)|leukocyte migration (GO:0050900)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|regulation of vascular permeability (GO:0043114)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(1)	17					Dasatinib(DB01254)	GTTTATCATGTCTTAATTTTT	0.343																																					p.R328R		Atlas-SNP	.											.	YES1	50	.	0			c.A984G						.						107	105	106					18																	742994		2202	4300	6502	SO:0001819	synonymous_variant	7525	exon8			ATCATGTCTTAAT	M15990	CCDS11824.1	18p11.31-p11.21	2014-06-26	2014-06-26		ENSG00000176105	ENSG00000176105		"SH2 domain containing"	12841	protein-coding gene	gene with protein product		164880	"v-yes-1 Yamaguchi sarcoma viral oncogene homolog 1"			2983418	Standard	NM_005433		Approved	Yes, c-yes, HsT441	uc002kky.3	P07947	OTTHUMG00000131472	ENST00000584307.1:c.984A>G	chr18.hg19:g.742994T>C		184.0	0.0		132.0	69.0	NM_005433	A6NLB3|D3DUH1	Silent	SNP	ENST00000584307.1	hg19	CCDS11824.1																																																																																			.	.		0.343	YES1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440827.2	NM_005433		C	742994	T	C	742994	2	2	272	1	0	0	0	0	0	0	0	1	17489	1664	58	2		2	YES1	18	742994	Silent	SNP	T	TCGA-G3-A25S-01A-11D-A16V-10		742994	77334254	71	39504										
LAMA1	284217	hgsc.bcm.edu	37	chr18	6975955	6975955	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	cagcggtgctgctaccgaggTagaagagaagattatcgggt	15	7	0	3			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr18:6975955T>A	ENST00000389658.3	-	45	6563	c.6470A>T	c.(6469-6471)tAc>tTc	p.Y2157F	RN7SL537P_ENST00000584392.1_RNA	NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2157	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				GCTACCGAGGTAGAAGAGAAG	0.413																																					p.Y2157F		Atlas-SNP	.											.	LAMA1	458	.	0			c.A6470T						.						157	157	157					18																	6975955		2203	4300	6503	SO:0001583	missense	284217	exon45			CCGAGGTAGAAGA	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.6470A>T	chr18.hg19:g.6975955T>A	ENSP00000374309:p.Tyr2157Phe	109.0	0.0		89.0	24.0	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	hg19	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	T	17.68	3.450028	0.63290	.	.	ENSG00000101680	ENST00000389658	T	0.81415	-1.49	5.64	5.64	0.86602	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 1 (1);	0.074260	0.56097	D	0.000032	T	0.82185	0.4982	L	0.53249	1.67	0.42293	D	0.992142	P	0.48162	0.906	P	0.48400	0.576	D	0.84025	0.0356	10	0.56958	D	0.05	.	16.1482	0.81586	0.0:0.0:0.0:1.0	.	2157	P25391	LAMA1_HUMAN	F	2157	ENSP00000374309:Y2157F	ENSP00000374309:Y2157F	Y	-	2	0	LAMA1	6965955	1.000000	0.71417	1.000000	0.80357	0.569000	0.35902	5.803000	0.69129	2.272000	0.75746	0.523000	0.50628	TAC	.	.		0.413	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		A	6975955	T	A	6975955	3	1	272	1	0	0	0	0	1	0	0	0	8614	1638	57	4	2833	4	LAMA1	18	6975955	Missense_Mutation	SNP	T	TCGA-G3-A25S-01A-11D-A16V-10	6232961	6975955	71101293	72	39505										
MALT1	10892	hgsc.bcm.edu	37	chr18	56415027	56415027	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	tgccagtagagacaactgatGaaataccatttagtttctct	7	8	1	3			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr18:56415027G>A	ENST00000348428.3	+	17	2686	c.2428G>A	c.(2428-2430)Gaa>Aaa	p.E810K	MALT1_ENST00000345724.3_Missense_Mutation_p.E799K|RP11-126O1.4_ENST00000588835.1_RNA	NM_006785.2|NM_173844.1	NP_006776.1|NP_776216.1	Q9UDY8	MALT1_HUMAN	mucosa associated lymphoid tissue lymphoma translocation gene 1	810					activation of NF-kappaB-inducing kinase activity (GO:0007250)|B-1 B cell differentiation (GO:0001923)|defense response (GO:0006952)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|nuclear export (GO:0051168)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|protein oligomerization (GO:0051259)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of T cell receptor signaling pathway (GO:0050856)|response to fungus (GO:0009620)|response to molecule of bacterial origin (GO:0002237)|T cell proliferation (GO:0042098)|T cell receptor signaling pathway (GO:0050852)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)|protein self-association (GO:0043621)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(1)|large_intestine(7)|lung(1)|ovary(2)|skin(1)	12						GACAACTGATGAAATACCATT	0.378			T	BIRC3	MALT																																p.E810K		Atlas-SNP	.		Dom	yes		18	18q21	10892	mucosa associated lymphoid tissue lymphoma translocation gene 1		L	.	MALT1	55	.	0			c.G2428A						.						109	114	112					18																	56415027		2203	4300	6503	SO:0001583	missense	10892	exon17			ACTGATGAAATAC		CCDS11967.1, CCDS11968.1	18q21	2013-01-11			ENSG00000172175	ENSG00000172175		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6819	protein-coding gene	gene with protein product	"paracaspase"	604860		MLT		10339464, 10406266, 10523859	Standard	NM_006785		Approved		uc002lhm.1	Q9UDY8	OTTHUMG00000132761	ENST00000348428.3:c.2428G>A	chr18.hg19:g.56415027G>A	ENSP00000319279:p.Glu810Lys	100.0	0.0		81.0	35.0	NM_006785	Q9NTB7|Q9ULX4	Missense_Mutation	SNP	ENST00000348428.3	hg19	CCDS11967.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.438445	0.83885	.	.	ENSG00000172175	ENST00000348428;ENST00000345724	T;T	0.13901	2.55;2.56	5.77	5.77	0.91146	.	0.052727	0.64402	D	0.000001	T	0.21307	0.0513	L	0.56769	1.78	0.48185	D	0.999602	P;P	0.42692	0.787;0.682	B;B	0.41510	0.359;0.197	T	0.00536	-1.1683	10	0.66056	D	0.02	.	19.5879	0.95497	0.0:0.0:1.0:0.0	.	799;810	Q9UDY8-2;Q9UDY8	.;MALT1_HUMAN	K	810;799	ENSP00000319279:E810K;ENSP00000304161:E799K	ENSP00000304161:E799K	E	+	1	0	MALT1	54566007	1.000000	0.71417	0.800000	0.32199	0.962000	0.63368	7.196000	0.77805	2.745000	0.94114	0.650000	0.86243	GAA	.	.		0.378	MALT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256132.2			A	56415027	G	A	56415027	3	1	272	1	0	0	0	0	1	0	0	0	9211	1291	45	3	2494	3	MALT1	18	56415027	Missense_Mutation	SNP	G	TCGA-G3-A25S-01A-11D-A16V-10	49439072	56415027	21662221	73	39506										
SIN3B	23309	hgsc.bcm.edu	37	chr19	16989085	16989085	+	Frame_Shift_Del	DEL	G	G	-													0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	cctggaagcggctggtgggcGtggagagcgcctgcgacgtg							TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr19:16989085delG	ENST00000248054.5	+	18	3067	c.3046delG	c.(3046-3048)gtgfs	p.V1016fs	SIN3B_ENST00000595541.1_Frame_Shift_Del_p.V606fs|SIN3B_ENST00000594235.1_3'UTR|SIN3B_ENST00000379803.1_Frame_Shift_Del_p.V1048fs					SIN3 transcription regulator family member B											endometrium(4)|kidney(2)|large_intestine(8)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26						GCTGGTGGGCGTGGAGAGCGC	0.667																																					p.G1047fs		Atlas-INDEL	.											.	SIN3B	90	.	0			c.3141delC						.						20	16	17					19																	16989085		2192	4289	6481	SO:0001589	frameshift_variant	23309	exon19			.	AB014600	CCDS32946.1, CCDS74308.1	19p13.12	2013-08-21	2013-08-21						19354	protein-coding gene	gene with protein product		607777	"SIN3 homolog B, transcription regulator (yeast)", "SIN3 transcription regulator homolog B (yeast)"			9734811	Standard	XM_005259832		Approved	KIAA0700	uc002ney.2	O75182		ENST00000248054.5:c.3046delG	chr19.hg19:g.16989085delG	ENSP00000248054:p.Val1016fs	20.0	0.0		16.0	16.0	NM_015260		Frame_Shift_Del	DEL	ENST00000248054.5	hg19																																																																																				.	.		0.667	SIN3B-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000462846.1	NM_015260		-	16989085	G	-	16989085	7	5	272	1	0	1	0	1	0	0	0	0	14341	1145	40	0	3216	0	SIN3B	19	16989085	Frame_Shift_Del	DEL	G	TCGA-G3-A25S-01A-11D-A16V-10		16989085	42139898	74	39507										
PLCB1	23236	hgsc.bcm.edu	37	chr20	8626827	8626827	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	gggatgcatttctggaaaaaGcgtaagtcactctaatttta	9	6	3	0			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr20:8626827G>A	ENST00000338037.6	+	5	490	c.463G>A	c.(463-465)Gcc>Acc	p.A155T	PLCB1_ENST00000378641.3_Splice_Site_p.A155T|PLCB1_ENST00000378637.2_Splice_Site_p.A155T	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	155					activation of meiosis involved in egg activation (GO:0060466)|cerebral cortex development (GO:0021987)|fat cell differentiation (GO:0045444)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G2/M transition of mitotic cell cycle (GO:0000086)|glutamate receptor signaling pathway (GO:0007215)|inositol phosphate metabolic process (GO:0043647)|insulin-like growth factor receptor signaling pathway (GO:0048009)|interleukin-1-mediated signaling pathway (GO:0070498)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-15-mediated signaling pathway (GO:0035723)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|memory (GO:0007613)|negative regulation of monocyte extravasation (GO:2000438)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of CD24 biosynthetic process (GO:2000560)|positive regulation of developmental growth (GO:0048639)|positive regulation of embryonic development (GO:0040019)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of GTPase activity (GO:0043547)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fertilization (GO:0080154)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						TCTGGAAAAAGCGTAAGTCAC	0.408																																					p.S155S		Atlas-SNP	.											.	PLCB1	394	.	0			c.A463A						.						116	113	114					20																	8626827		2203	4300	6503	SO:0001630	splice_region_variant	23236	exon5			GAAAAAGCGTAAG	AB011153	CCDS13102.1, CCDS13103.1	20p12	2008-03-18			ENSG00000182621	ENSG00000182621	3.1.4.11		15917	protein-coding gene	gene with protein product		607120				10760467, 11118617	Standard	NM_015192		Approved	KIAA0581, PLC-I, PLC154	uc002wnb.4	Q9NQ66	OTTHUMG00000031849	ENST00000338037.6:c.464+1G>A	chr20.hg19:g.8626827G>A		137.0	0.0		121.0	16.0	NM_015192	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Silent	SNP	ENST00000338037.6	hg19	CCDS13102.1	.	.	.	.	.	.	.	.	.	.	G	19.99	3.929190	0.73327	.	.	ENSG00000182621	ENST00000378641;ENST00000338037;ENST00000378637;ENST00000404098;ENST00000441163;ENST00000535719	T;T;T;T	0.44881	0.91;0.91;0.91;0.91	6.07	6.07	0.98685	.	0.044969	0.85682	D	0.000000	T	0.67401	0.2889	M	0.80746	2.51	0.80722	D	1	P;B;D;D	0.76494	0.632;0.19;0.986;0.999	B;B;P;D	0.81914	0.271;0.05;0.828;0.995	T	0.60372	-0.7276	10	0.22706	T	0.39	.	20.2389	0.98366	0.0:0.0:1.0:0.0	.	54;155;155;154	B4DRC6;Q9NQ66;Q9NQ66-2;B1AK73	.;PLCB1_HUMAN;.;.	T	155;155;155;154;75;75	ENSP00000367908:A155T;ENSP00000338185:A155T;ENSP00000367904:A155T;ENSP00000384001:A154T	ENSP00000338185:A155T	A	+	1	0	PLCB1	8574827	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.109000	0.89561	2.890000	0.99128	0.650000	0.86243	GCC	.	.		0.408	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3		Missense_Mutation	A	8626827	G	A	8626827	5	1	272	1	0	0	0	0	0	0	1	0	12036	985	34	3	481	3	PLCB1	20	8626827	Splice_Site	SNP	G	TCGA-G3-A25S-01A-11D-A16V-10		8626827	54398693	75	39508										
KIF3B	9371	hgsc.bcm.edu	37	chr20	30897746	30897746	+	Frame_Shift_Del	DEL	A	A	-													0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	cggcccatgaaatgcccaagAccttcacctttgatgccgtc							TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr20:30897746delA	ENST00000375712.3	+	2	333	c.166delA	c.(166-168)accfs	p.T56fs	KIF3B_ENST00000418717.2_5'Flank	NM_004798.3	NP_004789.1	O15066	KIF3B_HUMAN	kinesin family member 3B	56	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				anterograde axon cargo transport (GO:0008089)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cytoskeleton-dependent intracellular transport (GO:0030705)|determination of left/right symmetry (GO:0007368)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic centrosome separation (GO:0007100)|mitotic spindle organization (GO:0007052)|plus-end-directed vesicle transport along microtubule (GO:0072383)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intraciliary transport particle (GO:0030990)|kinesin II complex (GO:0016939)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|plus-end kinesin complex (GO:0005873)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)|Rho GTPase binding (GO:0017048)			NS(2)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(5)|lung(9)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			AATGCCCAAGACCTTCACCTT	0.502																																					p.K55fs		Atlas-Indel,Pindel	.											.	KIF3B	75	.	0			c.165delG						.						159	135	143					20																	30897746		2203	4300	6503	SO:0001589	frameshift_variant	9371	exon2			.	AB002357	CCDS13200.1	20q11.21	2012-08-01			ENSG00000101350	ENSG00000101350		"Kinesins"	6320	protein-coding gene	gene with protein product		603754				9205841	Standard	NM_004798		Approved	KIAA0359, FLA8, KLP-11	uc002wxq.3	O15066	OTTHUMG00000032214	ENST00000375712.3:c.166delA	chr20.hg19:g.30897746delA	ENSP00000364864:p.Thr56fs	95.0	0.0		68.0	19.0	NM_004798	B2RMP4|B4DSR5|E1P5M5	Frame_Shift_Del	DEL	ENST00000375712.3	hg19	CCDS13200.1																																																																																			.	.		0.502	KIF3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078619.1	NM_004798		-	30897746	A	-	30897746	7	5	272	1	0	1	0	1	0	0	0	0	8310	275	10	0	168	0	KIF3B	20	30897746	Frame_Shift_Del	DEL	A	TCGA-G3-A25S-01A-11D-A16V-10	22270919	30897746	32127774	76	39509										
GDF5	8200	hgsc.bcm.edu	37	chr20	34022378	34022378	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	gcctggcacggagcgcacatCcagcaaggaggccggctgcc	15	15	0	0			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr20:34022378C>T	ENST00000374372.1	-	4	1338	c.835G>A	c.(835-837)Gat>Aat	p.D279N	GDF5OS_ENST00000374375.1_Missense_Mutation_p.S141F|GDF5_ENST00000374369.3_Missense_Mutation_p.D279N			P43026	GDF5_HUMAN	growth differentiation factor 5	279					cell-cell signaling (GO:0007267)|chondrocyte differentiation (GO:0002062)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix organization (GO:0030198)|forelimb morphogenesis (GO:0035136)|growth (GO:0040007)|hindlimb morphogenesis (GO:0035137)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuron differentiation (GO:0045666)|regulation of multicellular organism growth (GO:0040014)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	growth factor activity (GO:0008083)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(9)|skin(3)	26	Lung NSC(9;0.00642)|all_lung(11;0.0094)		BRCA - Breast invasive adenocarcinoma(18;0.00663)			GAGCGCACATCCAGCAAGGAG	0.687																																					p.D279N		Atlas-SNP	.											.	GDF5	66	.	0			c.G835A						.						12	14	13					20																	34022378		2179	4278	6457	SO:0001583	missense	8200	exon2			GCACATCCAGCAA	X80915	CCDS13254.1	20q11.2	2008-05-22	2007-04-12		ENSG00000125965	ENSG00000125965			4220	protein-coding gene	gene with protein product	"cartilage-derived morphogenetic protein-1"	601146				9288091, 9288098	Standard	NM_000557		Approved	CDMP1, BMP14	uc002xck.1	P43026	OTTHUMG00000032341	ENST00000374372.1:c.835G>A	chr20.hg19:g.34022378C>T	ENSP00000363492:p.Asp279Asn	50.0	0.0		51.0	12.0	NM_000557	E1P5Q2|Q96SB1	Missense_Mutation	SNP	ENST00000374372.1	hg19	CCDS13254.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	26.4|26.4	4.736835|4.736835	0.89482|0.89482	.|.	.|.	ENSG00000125965|ENSG00000204183	ENST00000374369;ENST00000374372|ENST00000374375	T;T|.	0.68903|.	-0.36;-0.36|.	4.56|4.56	4.56|4.56	0.56223|0.56223	Transforming growth factor-beta, N-terminal (1);|.	0.126917|.	0.50627|.	D|.	0.000104|.	T|T	0.76786|0.76786	0.4036|0.4036	M|M	0.74647|0.74647	2.275|2.275	0.58432|0.58432	D|D	0.999998|0.999998	D;D|.	0.71674|.	0.976;0.998|.	D;D|.	0.70935|.	0.926;0.971|.	T|T	0.80799|0.80799	-0.1221|-0.1221	10|6	0.66056|0.87932	D|D	0.02|0	.|.	17.5149|17.5149	0.87770|0.87770	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	279;279|.	F1T0J1;P43026|.	.;GDF5_HUMAN|.	N|F	279|141	ENSP00000363489:D279N;ENSP00000363492:D279N|.	ENSP00000363489:D279N|ENSP00000363495:S141F	D|S	-|+	1|2	0|0	GDF5|GDF5OS	33485792|33485792	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	4.774000|4.774000	0.62339|0.62339	2.353000|2.353000	0.79882|0.79882	0.491000|0.491000	0.48974|0.48974	GAT|TCC	.	.		0.687	GDF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078875.2			T	34022378	C	T	34022378	3	4	272	1	0	0	0	0	1	0	0	0	6324	855	30	3	674	3	GDF5	20	34022378	Missense_Mutation	SNP	C	TCGA-G3-A25S-01A-11D-A16V-10	3124632	34022378	29003142	77	39510										
L3MBTL	26013	hgsc.bcm.edu	37	chr20	42143656	42143656	+	Frame_Shift_Del	DEL	C	C	-													0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	ttggcccccgcagaggaccaCccccagaatcctccagaaga							TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr20:42143656delC	ENST00000427442.2	+	5	603	c.444delC	c.(442-444)cacfs	p.H148fs	L3MBTL1_ENST00000444063.1_Frame_Shift_Del_p.H80fs|L3MBTL1_ENST00000373134.1_Frame_Shift_Del_p.H80fs|L3MBTL1_ENST00000457824.1_3'UTR|L3MBTL1_ENST00000418998.1_Frame_Shift_Del_p.H148fs|L3MBTL1_ENST00000373135.3_Frame_Shift_Del_p.H80fs			Q9Y468	LMBL1_HUMAN	l(3)mbt-like 1 (Drosophila)	80					chromatin modification (GO:0016568)|hemopoiesis (GO:0030097)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of megakaryocyte differentiation (GO:0045652)|regulation of mitosis (GO:0007088)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|identical protein binding (GO:0042802)|methylated histone binding (GO:0035064)|nucleosomal histone binding (GO:0031493)|nucleosome binding (GO:0031491)|SAM domain binding (GO:0032093)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(3)|ovary(1)|skin(2)	7						CAGAGGACCACCCCCAGAATC	0.682																																					p.H148fs		Atlas-Indel,Pindel	.											.	L3MBTL1	105	.	0			c.443delA						.						37	36	36					20																	42143656		2203	4300	6503	SO:0001589	frameshift_variant	26013	exon5			.	U89358	CCDS13319.1, CCDS46602.1, CCDS46602.2	20q13.12	2013-01-10	2010-09-03	2010-09-03	ENSG00000185513	ENSG00000185513		"Zinc fingers, C2HC-type containing", "Sterile alpha motif (SAM) domain containing"	15905	protein-coding gene	gene with protein product	"lethal (3) malignant brain tumor l(3)"	608802	"l(3)mbt (Drosophila)-like", "l(3)mbt-like (Drosophila)"	L3MBTL		10445843, 17540172	Standard	NM_032107		Approved	ZC2HC3, dJ138B7.3, DKFZp586P1522, KIAA0681	uc010zwh.2	Q9Y468	OTTHUMG00000032503	ENST00000427442.2:c.444delC	chr20.hg19:g.42143656delC	ENSP00000402107:p.His148fs	42.0	0.0		65.0	22.0	NM_032107	B4DRC9|E1P5W7|Q5H8Y8|Q5H8Y9|Q8IUV7|Q9H1E6|Q9H1G5|Q9UG06|Q9UJB9|Q9Y4C9	Frame_Shift_Del	DEL	ENST00000427442.2	hg19	CCDS46602.2																																																																																			.	.		0.682	L3MBTL1-007	KNOWN	upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079300.3	NM_032107		-	42143656	C	-	42143656	7	5	272	1	0	1	0	1	0	0	0	0	8600	506	18	0	246	0	L3MBTL	20	42143656	Frame_Shift_Del	DEL	C	TCGA-G3-A25S-01A-11D-A16V-10	8121278	42143656	20881864	78	39511										
ZNF831	128611	hgsc.bcm.edu	37	chr20	57767023	57767023	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	ggaagccgtgcgccctgcagCggcagcaggcgacggcagcg	18	14	0	0			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr20:57767023C>A	ENST00000371030.2	+	1	949	c.949C>A	c.(949-951)Cgg>Agg	p.R317R		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	317							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					CGCCCTGCAGCGGCAGCAGGC	0.711																																					p.R317R		Atlas-SNP	.											.	ZNF831	287	.	0			c.C949A						.						13	16	15					20																	57767023		1691	3870	5561	SO:0001819	synonymous_variant	128611	exon1			CTGCAGCGGCAGC	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 174"	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.949C>A	chr20.hg19:g.57767023C>A		19.0	0.0		16.0	10.0	NM_178457	Q5TDR4|Q8TCP0	Silent	SNP	ENST00000371030.2	hg19	CCDS42894.1																																																																																			.	.		0.711	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		A	57767023	C	A	57767023	2	1	272	1	0	0	0	0	0	0	0	1	18200	759	27	1		1	ZNF831	20	57767023	Silent	SNP	C	TCGA-G3-A25S-01A-11D-A16V-10	15623367	57767023	5258497	79	39512										
USP25	29761	hgsc.bcm.edu	37	chr21	17197365	17197365	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	agattacctcacggtattacAacaaaggctagaaaggtatt	8	7	1	2			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr21:17197365A>G	ENST00000285679.6	+	12	1658	c.1289A>G	c.(1288-1290)cAa>cGa	p.Q430R	USP25_ENST00000400183.2_Missense_Mutation_p.Q430R|USP25_ENST00000285681.2_Missense_Mutation_p.Q430R|USP25_ENST00000351097.5_Intron	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	430	USP.				cellular protein modification process (GO:0006464)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|proteolysis (GO:0006508)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|SUMO binding (GO:0032183)|ubiquitin-specific protease activity (GO:0004843)			breast(4)|endometrium(6)|kidney(2)|large_intestine(13)|liver(5)|lung(14)|ovary(4)|prostate(1)|skin(1)|urinary_tract(2)	52				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)		ACGGTATTACAACAAAGGCTA	0.303																																					p.Q430R		Atlas-SNP	.											.	USP25	156	.	0			c.A1289G						.						97	97	97					21																	17197365		2203	4300	6503	SO:0001583	missense	29761	exon12			TATTACAACAAAG	AF170562	CCDS33515.1, CCDS63336.1, CCDS63337.1	21q11.2	2011-02-24	2005-08-08		ENSG00000155313	ENSG00000155313		"Ubiquitin-specific peptidases"	12624	protein-coding gene	gene with protein product		604736	"ubiquitin specific protease 25"			12838346, 10612803	Standard	NM_013396		Approved	USP21	uc002yjy.1	Q9UHP3	OTTHUMG00000074343	ENST00000285679.6:c.1289A>G	chr21.hg19:g.17197365A>G	ENSP00000285679:p.Gln430Arg	275.0	0.0		156.0	36.0	NM_013396	C0LSZ0|Q6DHZ9|Q9H9W1	Missense_Mutation	SNP	ENST00000285679.6	hg19	CCDS33515.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	23.0|23.0	4.367884|4.367884	0.82463|0.82463	.|.	.|.	ENSG00000155313|ENSG00000155313	ENST00000453553|ENST00000285681;ENST00000285679;ENST00000400183	.|T;T;T	.|0.74002	.|-0.8;-0.8;-0.8	5.74|5.74	5.74|5.74	0.90152|0.90152	.|Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	.|0.106920	.|0.64402	.|D	.|0.000003	D|D	0.82664|0.82664	0.5086|0.5086	L|L	0.52905|0.52905	1.665|1.665	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.71674	.|0.984;0.998;0.982	.|D;D;P	.|0.70487	.|0.917;0.969;0.828	T|T	0.82494|0.82494	-0.0429|-0.0429	5|10	.|0.45353	.|T	.|0.12	.|.	15.3343|15.3343	0.74238|0.74238	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|430;430;430	.|Q9UHP3-3;Q9UHP3-1;Q9UHP3	.|.;.;UBP25_HUMAN	D|R	13|430	.|ENSP00000285681:Q430R;ENSP00000285679:Q430R;ENSP00000383044:Q430R	.|ENSP00000285679:Q430R	N|Q	+|+	1|2	0|0	USP25|USP25	16119236|16119236	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.962000|0.962000	0.63368|0.63368	8.621000|8.621000	0.90949|0.90949	2.330000|2.330000	0.79161|0.79161	0.528000|0.528000	0.53228|0.53228	AAC|CAA	.	.		0.303	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1			G	17197365	A	G	17197365	3	3	272	1	0	0	0	0	1	0	0	0	17071	130	5	2	1335	2	USP25	21	17197365	Missense_Mutation	SNP	A	TCGA-G3-A25S-01A-11D-A16V-10		17197365	30932530	80	39513										
TTC3	7267	hgsc.bcm.edu	37	chr21	38538901	38538901	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	aacaaacattccacacgtgcAgatggttgccatacaggtaa	8	10	0	1			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chr21:38538901A>G	ENST00000399017.2	+	33	7132	c.4385A>G	c.(4384-4386)cAg>cGg	p.Q1462R	TTC3_ENST00000355666.1_Missense_Mutation_p.Q1462R|TTC3_ENST00000354749.2_Missense_Mutation_p.Q1462R|TTC3_ENST00000479930.1_3'UTR	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1462					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				CCACACGTGCAGATGGTTGCC	0.348																																					p.Q1462R	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.A4385G						.						40	38	38					21																	38538901		2203	4300	6503	SO:0001583	missense	7267	exon33			ACGTGCAGATGGT	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"RING-type (C3HC4) zinc fingers", "Tetratricopeptide (TTC) repeat domain containing"	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.4385A>G	chr21.hg19:g.38538901A>G	ENSP00000381981:p.Gln1462Arg	108.0	0.0		67.0	21.0	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	hg19	CCDS13651.1	.	.	.	.	.	.	.	.	.	.	A	3.781	-0.045728	0.07452	.	.	ENSG00000182670	ENST00000355666;ENST00000399017;ENST00000354749	T;T;T	0.07800	3.16;3.16;3.16	4.96	2.15	0.27550	.	0.452951	0.20187	N	0.097386	T	0.04092	0.0114	L	0.31065	0.9	0.09310	N	0.999997	B;P	0.35433	0.201;0.501	B;B	0.25140	0.032;0.058	T	0.36915	-0.9728	9	.	.	.	-3.6352	2.6852	0.05105	0.5413:0.2717:0.187:0.0	.	520;1462	Q5GIT6;P53804	.;TTC3_HUMAN	R	1462	ENSP00000347889:Q1462R;ENSP00000381981:Q1462R;ENSP00000346791:Q1462R	.	Q	+	2	0	TTC3	37460771	0.002000	0.14202	0.010000	0.14722	0.142000	0.21351	1.121000	0.31283	0.796000	0.33947	0.460000	0.39030	CAG	.	.		0.348	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1			G	38538901	A	G	38538901	3	3	272	1	0	0	0	0	1	0	0	0	16712	188	7	2	4511	2	TTC3	21	38538901	Missense_Mutation	SNP	A	TCGA-G3-A25S-01A-11D-A16V-10	21341536	38538901	9590994	81	39514										
REPS2	9185	hgsc.bcm.edu	37	chrX	17095520	17095520	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	4	1	0.837313224409999	0	0.89133343243645	0.0476190476190476	0.422902494331066	0	ctgaataaagtcttccagccCagtgtgccaggtgaagtgcc	11	11	1	2			TCGA-G3-A25S-01A-11D-A16V-10	TCGA-G3-A25S-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c05adc19-2e01-4712-a35a-69eee4d40998	084d16c3-f0e8-4cc5-b2a9-cb055fd6ebe5	g.chrX:17095520C>T	ENST00000357277.3	+	13	1677	c.1506C>T	c.(1504-1506)ccC>ccT	p.P502P	REPS2_ENST00000469714.1_Intron|REPS2_ENST00000303843.7_Silent_p.P501P|REPS2_ENST00000380064.4_Intron	NM_001080975.1|NM_004726.2	NP_001074444.1|NP_004717.2	Q8NFH8	REPS2_HUMAN	RALBP1 associated Eps domain containing 2	502	Pro-rich.				epidermal growth factor receptor signaling pathway (GO:0007173)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|ovary(2)|skin(3)|urinary_tract(1)	17	Hepatocellular(33;0.183)					TCTTCCAGCCCAGTGTGCCAG	0.602																																					p.P502P		Atlas-SNP	.											.	REPS2	76	.	0			c.C1506T						.						61	55	57					X																	17095520		2203	4300	6503	SO:0001819	synonymous_variant	9185	exon13			CCAGCCCAGTGTG	AF010233	CCDS14180.2, CCDS43919.1	Xp22.2	2013-01-10			ENSG00000169891	ENSG00000169891		"EF-hand domain containing"	9963	protein-coding gene	gene with protein product		300317				9422736, 9928989	Standard	NM_001080975		Approved	POB1	uc004cxv.1	Q8NFH8	OTTHUMG00000021199	ENST00000357277.3:c.1506C>T	chrX.hg19:g.17095520C>T		26.0	0.0		33.0	15.0	NM_004726	A6PWZ6|O43428|Q5JNZ8|Q8NFI5	Silent	SNP	ENST00000357277.3	hg19	CCDS14180.2																																																																																			.	.		0.602	REPS2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000316778.1	NM_004726		T	17095520	C	T	17095520	2	4	272	1	0	0	0	0	0	0	0	1	13244	581	21	3		3	REPS2	23	17095520	Silent	SNP	C	TCGA-G3-A25S-01A-11D-A16V-10		17095520	138175040	82	39515										
PLA2R1	22925	hgsc.bcm.edu	37	chr2	160804063	160804063	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	0.447252747252747	0	0.581428571428571	1	1	0	aactctgggtgttcagattgTcttgtttctgtgaagaaaag	11	5	4	3			TCGA-G3-A25T-01A-11D-A16V-10	TCGA-G3-A25T-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41840dc1-5ea2-4f01-a0d4-8b65add641c8	ad831284-a522-4712-b7b4-134b92be8125	g.chr2:160804063T>C	ENST00000283243.7	-	26	3923	c.3717A>G	c.(3715-3717)agA>agG	p.R1239R	PLA2R1_ENST00000392771.1_Silent_p.R1239R|PLA2R1_ENST00000460710.1_5'Flank	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	1239					cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)		PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						GTTCAGATTGTCTTGTTTCTG	0.328																																					p.R1239R		Atlas-SNP	.											.	PLA2R1	153	.	0			c.A3717G						.						96	105	102					2																	160804063		2201	4299	6500	SO:0001819	synonymous_variant	22925	exon26			AGATTGTCTTGTT	U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"C-type lectin domain containing"	9042	protein-coding gene	gene with protein product		604939	"phospholipase A2 receptor 1, 180kD"			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.3717A>G	chr2.hg19:g.160804063T>C		77.0	0.0		118.0	21.0	NM_001195641	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Silent	SNP	ENST00000283243.7	hg19	CCDS33309.1																																																																																			.	.		0.328	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1			C	160804063	T	C	160804063	2	2	273	1	0	0	0	0	0	0	0	1	12019	1664	58	2		2	PLA2R1	2	160804063	Silent	SNP	T	TCGA-G3-A25T-01A-11D-A16V-10		160804063	82395310	1	39516										
TTN	7273	hgsc.bcm.edu	37	chr2	179430304	179430304	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	0.447252747252747	0	0.581428571428571	1	1	0	tctcattataagccttgacaCggaactgatattcttgtcca	6	10	2	2	rs202149931|rs397517716		TCGA-G3-A25T-01A-11D-A16V-10	TCGA-G3-A25T-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41840dc1-5ea2-4f01-a0d4-8b65add641c8	ad831284-a522-4712-b7b4-134b92be8125	g.chr2:179430304C>T	ENST00000591111.1	-	276	75856	c.75632G>A	c.(75631-75633)cGt>cAt	p.R25211H	TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R24284H|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R17912H|TTN_ENST00000460472.2_Missense_Mutation_p.R17787H|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R26852H|TTN_ENST00000342175.6_Missense_Mutation_p.R17979H|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	25211	Fibronectin type-III 83. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGCCTTGACACGGAACTGATA	0.418													C|||	1	0.000199681	8e-04	0	5008	,	,		22005	0		0	False		,,,				2504	0				p.R26852H		Atlas-SNP	.											.	TTN	18412	.	0			c.G80555A						.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	2,3760		0,2,1879	190	188	189		53936,53735,72851,53360	3.7	1	2		189	1,8237		0,1,4118	no	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	29,29,29,29	0,3,5997	TT,TC,CC		0.0121,0.0532,0.025	benign,benign,benign,benign	17979/27119,17912/27052,24284/33424,17787/26927	179430304	3,11997	1881	4119	6000	SO:0001583	missense	7273	exon326			TTGACACGGAACT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.75632G>A	chr2.hg19:g.179430304C>T	ENSP00000465570:p.Arg25211His	70.0	0.0		97.0	26.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	10.81	1.454795	0.26161	5.32E-4	1.21E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.60920	0.15;0.15;0.15;0.15	5.48	3.65	0.41850	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.67258	0.2874	H	0.96142	3.775	0.48696	D	0.999696	B;B;B;B	0.29909	0.261;0.261;0.261;0.261	B;B;B;B	0.20184	0.028;0.028;0.028;0.028	T	0.76334	-0.2997	9	0.87932	D	0	.	12.1629	0.54113	0.0:0.8355:0.0:0.1645	.	17787;17912;17979;25211	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	H	24284;17787;17979;17912;17785	ENSP00000343764:R24284H;ENSP00000434586:R17787H;ENSP00000340554:R17979H;ENSP00000352154:R17912H	ENSP00000340554:R17979H	R	-	2	0	TTN	179138550	0.893000	0.30496	1.000000	0.80357	0.631000	0.37964	1.834000	0.39171	2.589000	0.87451	0.484000	0.47621	CGT	.	C|0.999;T|0.001		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179430304	C	T	179430304	3	4	273	1	0	0	0	0	1	0	0	0	16750	536	19	1	27572	1	TTN	2	179430304	Missense_Mutation	SNP	C	TCGA-G3-A25T-01A-11D-A16V-10	18626241	179430304	63769069	2	39517										
TTN	7273	hgsc.bcm.edu	37	chr2	179610836	179610836	+	Intron	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0434782608695652	1	1	0.447252747252747	0	0.581428571428571	1	1	0	agtgtgacttcccttctcctCgctaatcacgtatttaatat	5	11	2	1	rs141483365		TCGA-G3-A25T-01A-11D-A16V-10	TCGA-G3-A25T-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41840dc1-5ea2-4f01-a0d4-8b65add641c8	ad831284-a522-4712-b7b4-134b92be8125	g.chr2:179610836C>T	ENST00000591111.1	-	46	10585				TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000589042.1_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000360870.5_Missense_Mutation_p.E5431K			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCCTTCTCCTCGCTAATCACG	0.393													C|||	1	0.000199681	0	0.0014	5008	,	,		19328	0		0	False		,,,				2504	0				p.E5431K		Atlas-SNP	.											.	TTN	18412	.	0			c.G16291A						.	C	,,LYS/GLU,,	0,4406		0,0,2203	120	124	123		,,16291,,	5	1	2	dbSNP_134	123	1,8599	1.2+/-3.3	0,1,4299	no	intron,intron,missense,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,56,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,,,	,,5431/5605,,	179610836	1,13005	2203	4300	6503	SO:0001627	intron_variant	7273	exon46			TCTCCTCGCTAAT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10361-4188G>A	chr2.hg19:g.179610836C>T		91.0	0.0		101.0	23.0	NM_133379	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	4.889	0.165308	0.09339	0.0	1.16E-4	ENSG00000155657	ENST00000360870;ENST00000306136	T	0.66815	-0.23	5.88	5.01	0.66863	.	.	.	.	.	T	0.48021	0.1477	L	0.40543	1.245	0.20926	N	0.999822	P	0.38280	0.625	B	0.31337	0.128	T	0.36335	-0.9752	9	0.07813	T	0.8	.	7.0279	0.24950	0.0:0.6947:0.153:0.1523	.	5431	Q8WZ42-6	.	K	5431;712	ENSP00000354117:E5431K	ENSP00000304714:E712K	E	-	1	0	TTN	179319081	0.994000	0.37717	0.998000	0.56505	0.745000	0.42441	2.399000	0.44495	1.506000	0.48736	-0.123000	0.14984	GAG	.	C|1.000;T|0.000		0.393	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179610836	C	T	179610836	1	4	273	0	1	0	0	0	0	0	0	0	16750	893	31	1		1	TTN	2	179610836	Intron	SNP	C	TCGA-G3-A25T-01A-11D-A16V-10	180532	179610836	63588537	3	39518										
PAX3	5077	hgsc.bcm.edu	37	chr2	223066132	223066132	+	3'UTR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	0.447252747252747	0	0.581428571428571	1	1	0	aagtggacagttcacttacgCgatatctggcttgagataat	10	7	2	1			TCGA-G3-A25T-01A-11D-A16V-10	TCGA-G3-A25T-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41840dc1-5ea2-4f01-a0d4-8b65add641c8	ad831284-a522-4712-b7b4-134b92be8125	g.chr2:223066132C>T	ENST00000350526.4	-	0	2087				PAX3_ENST00000464706.1_5'Flank|PAX3_ENST00000336840.6_Splice_Site_p.S401S|PAX3_ENST00000409551.3_Missense_Mutation_p.A483T|PAX3_ENST00000392069.2_Splice_Site_p.A484T|PAX3_ENST00000392070.2_Missense_Mutation_p.A484T|PAX3_ENST00000344493.4_Silent_p.S401S	NM_181457.3	NP_852122.1	P23760	PAX3_HUMAN	paired box 3						apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|developmental pigmentation (GO:0048066)|heart development (GO:0007507)|mammary gland specification (GO:0060594)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|neuron fate commitment (GO:0048663)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of somitogenesis (GO:0014807)|sensory perception of sound (GO:0007605)|spinal cord association neuron differentiation (GO:0021527)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A484T(1)	PAX3/NCOA2(4)|PAX3/NCOA1(8)|PAX3/FOXO1(749)	NS(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(13)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	38		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;1.85e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TTCACTTACGCGATATCTGGC	0.443			T	"FOXO1A, NCOA1"	alveolar rhabdomyosarcoma		Waardenburg syndrome; craniofacial-deafness-hand syndrome																														p.A484T		Atlas-SNP	.		Dom	yes		2	2q35	5077	paired box gene 3	yes	M	PAX3,NS,carcinoma,0,1	PAX3	106	.	1	Substitution - Missense(1)	endometrium(1)	c.G1450A						.						88	89	88					2																	223066132		2203	4300	6503	SO:0001624	3_prime_UTR_variant	5077	exon9			CTTACGCGATATC		CCDS2449.1, CCDS2450.1, CCDS2451.1, CCDS42825.1, CCDS2448.1, CCDS42826.1, CCDS46522.1, CCDS46523.1	2q36.1	2011-06-20	2007-07-12		ENSG00000135903	ENSG00000135903		"Paired boxes", "Homeoboxes / PRD class"	8617	protein-coding gene	gene with protein product		606597	"Waardenburg syndrome 1", "paired box gene 3 (Waardenburg syndrome 1)"	WS1		1347149	Standard	NM_181461		Approved	HUP2	uc002vmt.2	P23760	OTTHUMG00000133157	ENST00000350526.4:c.*511G>A	chr2.hg19:g.223066132C>T		58.0	0.0		61.0	22.0	NM_181459	G5E9C1|Q16448|Q494Z3|Q494Z4|Q53T90|Q6GSJ9|Q86UQ2|Q86UQ3	Missense_Mutation	SNP	ENST00000350526.4	hg19	CCDS42826.1	.	.	.	.	.	.	.	.	.	.	C	16.10	3.027007	0.54683	.	.	ENSG00000135903	ENST00000392069;ENST00000392070;ENST00000409551	D;D;D	0.94537	-3.4;-3.44;-3.45	5.77	5.77	0.91146	.	1.499710	0.04241	N	0.336907	D	0.90573	0.7045	N	0.14661	0.345	0.80722	D	1	B;P	0.39920	0.005;0.695	B;B	0.29077	0.002;0.098	T	0.78831	-0.2049	10	0.66056	D	0.02	.	20.3627	0.98863	0.0:1.0:0.0:0.0	.	483;484	Q494Z4;G5E9C1	.;.	T	484;484;483	ENSP00000375921:A484T;ENSP00000375922:A484T;ENSP00000386750:A483T	ENSP00000375921:A484T	A	-	1	0	PAX3	222774376	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.015000	0.57152	2.885000	0.99019	0.655000	0.94253	GCT;GCG;GCG	.	.		0.443	PAX3-006	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328670.1			T	223066132	C	T	223066132	1	4	273	0	1	0	0	0	0	0	0	0	11489	782	27	1		1	PAX3	2	223066132	3'UTR	SNP	C	TCGA-G3-A25T-01A-11D-A16V-10	43455296	223066132	20133241	4	39519										
BAP1	8314	hgsc.bcm.edu	37	chr3	52439874	52439874	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	0.447252747252747	0	0.581428571428571	1	1	0	cttggactcctcaggcagctGtgactcttgagacttgtggg	13	10	2	2			TCGA-G3-A25T-01A-11D-A16V-10	TCGA-G3-A25T-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41840dc1-5ea2-4f01-a0d4-8b65add641c8	ad831284-a522-4712-b7b4-134b92be8125	g.chr3:52439874G>A	ENST00000460680.1	-	10	1309	c.838C>T	c.(838-840)Cag>Tag	p.Q280*	BAP1_ENST00000296288.5_Nonsense_Mutation_p.Q262*	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	191					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.Q280*(1)		NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		TCAGGCAGCTGTGACTCTTGA	0.567			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.Q280X	GBM(101;493 1458 7992 21037 25532)	Atlas-SNP	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	BAP1,NS,carcinoma,0,1	BAP1	371	.	1	Substitution - Nonsense(1)	breast(1)	c.C838T						.						70	69	70					3																	52439874		2203	4300	6503	SO:0001587	stop_gained	8314	exon10			GCAGCTGTGACTC	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.838C>T	chr3.hg19:g.52439874G>A	ENSP00000417132:p.Gln280*	39.0	0.0		28.0	19.0	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Nonsense_Mutation	SNP	ENST00000460680.1	hg19	CCDS2853.1	.	.	.	.	.	.	.	.	.	.	G	32	5.123994	0.94429	.	.	ENSG00000163930	ENST00000460680;ENST00000296288	.	.	.	5.35	5.35	0.76521	.	0.252992	0.42172	D	0.000752	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05620	T	0.96	-5.5978	19.4309	0.94765	0.0:0.0:1.0:0.0	.	.	.	.	X	280;262	.	ENSP00000296288:Q262X	Q	-	1	0	BAP1	52414914	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.676000	0.74498	2.663000	0.90544	0.561000	0.74099	CAG	.	.		0.567	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			A	52439874	G	A	52439874	4	1	273	1	0	0	0	0	0	1	0	0	1311	1386	48	3	1383	3	BAP1	3	52439874	Nonsense_Mutation	SNP	G	TCGA-G3-A25T-01A-11D-A16V-10		52439874	145582556	5	39520										
CD96	10225	hgsc.bcm.edu	37	chr3	111319663	111319663	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	0.447252747252747	0	0.581428571428571	1	1	0	ggtacatagtaataaaccagCccaatcagacaacttgacca	6	11	1	2			TCGA-G3-A25T-01A-11D-A16V-10	TCGA-G3-A25T-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41840dc1-5ea2-4f01-a0d4-8b65add641c8	ad831284-a522-4712-b7b4-134b92be8125	g.chr3:111319663C>G	ENST00000283285.5	+	8	1168	c.1037C>G	c.(1036-1038)gCc>gGc	p.A346G	CD96_ENST00000438817.2_Missense_Mutation_p.A330G|CD96_ENST00000352690.4_Missense_Mutation_p.A330G	NM_198196.2	NP_937839.1	P40200	TACT_HUMAN	CD96 molecule	346	Ig-like C2-type.				cell adhesion (GO:0007155)|immune response (GO:0006955)|regulation of immune response (GO:0050776)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(4)|liver(2)|lung(14)|skin(5)	35						AATAAACCAGCCCAATCAGAC	0.383									Opitz Trigonocephaly syndrome																												p.A346G		Atlas-SNP	.											.	CD96	75	.	0			c.C1037G						.						115	115	115					3																	111319663		2203	4300	6503	SO:0001583	missense	10225	exon8	Familial Cancer Database	C syndrome, Trigonocephaly syndrome	AACCAGCCCAATC	M88282	CCDS2958.1, CCDS2959.1	3p13-q13.2	2013-01-11	2006-03-28		ENSG00000153283	ENSG00000153283		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	16892	protein-coding gene	gene with protein product		606037	"CD96 antigen"			1313846	Standard	XR_241462		Approved	TACTILE	uc003dxx.3	P40200	OTTHUMG00000159275	ENST00000283285.5:c.1037C>G	chr3.hg19:g.111319663C>G	ENSP00000283285:p.Ala346Gly	79.0	0.0		64.0	35.0	NM_198196	Q5JPB3	Missense_Mutation	SNP	ENST00000283285.5	hg19	CCDS2959.1	.	.	.	.	.	.	.	.	.	.	C	10.49	1.365945	0.24684	.	.	ENSG00000153283	ENST00000352690;ENST00000283285;ENST00000438817	T;T;T	0.65916	-0.15;-0.13;-0.18	5.04	2.12	0.27331	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.999489	0.08098	N	0.998280	T	0.45196	0.1330	N	0.24115	0.695	0.09310	N	1	B;B;B;B	0.17852	0.024;0.019;0.01;0.01	B;B;B;B	0.19391	0.025;0.015;0.015;0.015	T	0.31861	-0.9928	10	0.26408	T	0.33	-1.9133	5.5991	0.17343	0.0:0.6406:0.1674:0.192	.	330;330;346;330	E9PEJ1;P40200-2;P40200;Q8WUE2	.;.;TACT_HUMAN;.	G	330;346;330	ENSP00000342040:A330G;ENSP00000283285:A346G;ENSP00000389801:A330G	ENSP00000283285:A346G	A	+	2	0	CD96	112802353	0.003000	0.15002	0.924000	0.36721	0.820000	0.46376	0.110000	0.15437	0.591000	0.29711	0.650000	0.86243	GCC	.	.		0.383	CD96-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354312.2			G	111319663	C	G	111319663	3	3	273	1	0	0	0	0	1	0	0	0	3050	739	26	4	1067	4	CD96	3	111319663	Missense_Mutation	SNP	C	TCGA-G3-A25T-01A-11D-A16V-10	58879789	111319663	86702767	6	39521										
TMCC1	23023	hgsc.bcm.edu	37	chr3	129389772	129389772	+	Frame_Shift_Del	DEL	C	C	-													0.0434782608695652	1	1	0.447252747252747	0	0.581428571428571	1	1	0	tgctctacctctctgagcttCctgtggtagtgctcaagttt							TCGA-G3-A25T-01A-11D-A16V-10	TCGA-G3-A25T-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41840dc1-5ea2-4f01-a0d4-8b65add641c8	ad831284-a522-4712-b7b4-134b92be8125	g.chr3:129389772delC	ENST00000393238.3	-	4	1252	c.912delG	c.(910-912)aggfs	p.R304fs	TMCC1_ENST00000432054.2_5'UTR|TMCC1_ENST00000426664.2_Frame_Shift_Del_p.R190fs|TMCC1_ENST00000329333.5_Frame_Shift_Del_p.R125fs	NM_001017395.3	NP_001017395.2	O94876	TMCC1_HUMAN	transmembrane and coiled-coil domain family 1	304						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)			PLXND1/TMCC1(4)	breast(1)|endometrium(3)|large_intestine(8)|lung(12)|skin(1)	25						CTCTGAGCTTCCTGTGGTAGT	0.517																																					p.K305fs		Atlas-INDEL	.											.	TMCC1	105	.	0			c.913delA						.						136	126	129					3																	129389772		2203	4300	6503	SO:0001589	frameshift_variant	23023	exon4			.	AB018322	CCDS33855.1	3q21.3	2010-04-19	2005-07-13		ENSG00000172765	ENSG00000172765		"Transmembrane and coiled-coil domain containing"	29116	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 1"			9872452	Standard	NR_033361		Approved	KIAA0779	uc021xdy.1	O94876	OTTHUMG00000159579	ENST00000393238.3:c.912delG	chr3.hg19:g.129389772delC	ENSP00000376930:p.Arg304fs	154.0	0.0		139.0	11.0	NM_001017395	A8K5Y3|B4DE04|Q68E06|Q8IXM8	Frame_Shift_Del	DEL	ENST00000393238.3	hg19	CCDS33855.1																																																																																			.	.		0.517	TMCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356418.2	NM_015008		-	129389772	C	-	129389772	7	5	273	1	0	1	0	1	0	0	0	0	16007	854	30	0	1061	0	TMCC1	3	129389772	Frame_Shift_Del	DEL	C	TCGA-G3-A25T-01A-11D-A16V-10	18070109	129389772	68632658	7	39522	194	3								
TMCC1	23023	hgsc.bcm.edu	37	chr3	129389773	129389787	+	In_Frame_Del	DEL	CTGTGGTAGTGCTCA	CTGTGGTAGTGCTCA	-													0.0434782608695652	1	1	0.447252747252747	0	0.581428571428571	1	1	0	gctctacctctctgagcttcCtgtggtagtgctcaagtttc					rs147183682		TCGA-G3-A25T-01A-11D-A16V-10	TCGA-G3-A25T-10A-01D-A16V-10	CTGTGGTAGTGCTCA	CTGTGGTAGTGCTCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41840dc1-5ea2-4f01-a0d4-8b65add641c8	ad831284-a522-4712-b7b4-134b92be8125	g.chr3:129389773_129389787delCTGTGGTAGTGCTCA	ENST00000393238.3	-	4	1237_1251	c.897_911delTGAGCACTACCACAG	c.(895-912)cttgagcactaccacagg>ctg	p.EHYHR300del	TMCC1_ENST00000432054.2_5'UTR|TMCC1_ENST00000426664.2_In_Frame_Del_p.EHYHR186del|TMCC1_ENST00000329333.5_In_Frame_Del_p.EHYHR121del	NM_001017395.3	NP_001017395.2	O94876	TMCC1_HUMAN	transmembrane and coiled-coil domain family 1	300						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)		p.H301D(1)	PLXND1/TMCC1(4)	breast(1)|endometrium(3)|large_intestine(8)|lung(12)|skin(1)	25						TCTGAGCTTCCTGTGGTAGTGCTCAAGTTTCTTTT	0.516																																					p.300_304del		Pindel	.											.	TMCC1	105	.	1	Substitution - Missense(1)	skin(1)	c.898_912del						.																																			SO:0001651	inframe_deletion	23023	exon4			.	AB018322	CCDS33855.1	3q21.3	2010-04-19	2005-07-13		ENSG00000172765	ENSG00000172765		"Transmembrane and coiled-coil domain containing"	29116	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 1"			9872452	Standard	NR_033361		Approved	KIAA0779	uc021xdy.1	O94876	OTTHUMG00000159579	ENST00000393238.3:c.897_911delTGAGCACTACCACAG	chr3.hg19:g.129389773_129389787delCTGTGGTAGTGCTCA	ENSP00000376930:p.Glu300_Arg304del	161.0	0.0		144.0	15.0	NM_001017395	A8K5Y3|B4DE04|Q68E06|Q8IXM8	In_Frame_Del	DEL	ENST00000393238.3	hg19	CCDS33855.1																																																																																			.	.		0.516	TMCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356418.2	NM_015008		-	129389787	CTGTGGTAGTGCTCA	-	129389773	7	5	273	1	0	1	0	1	0	0	0	0	16007	681	24	0	1062	0	TMCC1	3	129389773	In_Frame_Del	DEL	CTGTGGTAGTGCTCA	TCGA-G3-A25T-01A-11D-A16V-10	1	129389773	68632657	8	39523	194	3								
TMCC1	23023	hgsc.bcm.edu	37	chr3	129389775	129389787	+	Frame_Shift_Del	DEL	GTGGTAGTGCTCA	GTGGTAGTGCTCA	-													0.0434782608695652	1	1	0.447252747252747	0	0.581428571428571	1	1	0	tctacctctctgagcttcctGtggtagtgctcaagtttctt					rs147183682		TCGA-G3-A25T-01A-11D-A16V-10	TCGA-G3-A25T-10A-01D-A16V-10	GTGGTAGTGCTCA	GTGGTAGTGCTCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41840dc1-5ea2-4f01-a0d4-8b65add641c8	ad831284-a522-4712-b7b4-134b92be8125	g.chr3:129389775_129389787delGTGGTAGTGCTCA	ENST00000393238.3	-	4	1237_1249	c.897_909delTGAGCACTACCAC	c.(895-909)cttgagcactaccacfs	p.LEHYH299fs	TMCC1_ENST00000432054.2_5'UTR|TMCC1_ENST00000426664.2_Frame_Shift_Del_p.LEHYH185fs|TMCC1_ENST00000329333.5_Frame_Shift_Del_p.LEHYH120fs	NM_001017395.3	NP_001017395.2	O94876	TMCC1_HUMAN	transmembrane and coiled-coil domain family 1	299						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)		p.H301D(1)	PLXND1/TMCC1(4)	breast(1)|endometrium(3)|large_intestine(8)|lung(12)|skin(1)	25						TGAGCTTCCTGTGGTAGTGCTCAAGTTTCTTTT	0.516																																					p.300_304del		Atlas-INDEL	.											.	TMCC1	105	.	1	Substitution - Missense(1)	skin(1)	c.898_910del						.																																			SO:0001589	frameshift_variant	23023	exon4			.	AB018322	CCDS33855.1	3q21.3	2010-04-19	2005-07-13		ENSG00000172765	ENSG00000172765		"Transmembrane and coiled-coil domain containing"	29116	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 1"			9872452	Standard	NR_033361		Approved	KIAA0779	uc021xdy.1	O94876	OTTHUMG00000159579	ENST00000393238.3:c.897_909delTGAGCACTACCAC	chr3.hg19:g.129389775_129389787delGTGGTAGTGCTCA	ENSP00000376930:p.Leu299fs	152.0	0.0		137.0	11.0	NM_001017395	A8K5Y3|B4DE04|Q68E06|Q8IXM8	Frame_Shift_Del	DEL	ENST00000393238.3	hg19	CCDS33855.1																																																																																			.	.		0.516	TMCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356418.2	NM_015008		-	129389787	GTGGTAGTGCTCA	-	129389775	7	5	273	1	0	1	0	1	0	0	0	0	16007	1368	48	0	1064	0	TMCC1	3	129389775	Frame_Shift_Del	DEL	GTGGTAGTGCTCA	TCGA-G3-A25T-01A-11D-A16V-10	2	129389775	68632655	9	39524	194	3								
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123238013	123238013	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0434782608695652	1	1	0.447252747252747	0	0.581428571428571	1	1	0	aggccaaagtaatagatgatCtgaagtatgtacaatgattt	9	4	1	4			TCGA-G3-A25T-01A-11D-A16V-10	TCGA-G3-A25T-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41840dc1-5ea2-4f01-a0d4-8b65add641c8	ad831284-a522-4712-b7b4-134b92be8125	g.chr4:123238013C>T	ENST00000264501.4	+	62	11039	c.10666C>T	c.(10666-10668)Ctg>Ttg	p.L3556L	KIAA1109_ENST00000455637.1_Silent_p.L3556L|KIAA1109_ENST00000388738.3_Silent_p.L3556L			Q2LD37	K1109_HUMAN	KIAA1109	3556					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						AATAGATGATCTGAAGTATGT	0.328																																					p.L3556L		Atlas-SNP	.											.	KIAA1109	424	.	0			c.C10666T						.						88	88	88					4																	123238013		1822	4084	5906	SO:0001819	synonymous_variant	84162	exon60			GATGATCTGAAGT	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.10666C>T	chr4.hg19:g.123238013C>T		129.0	0.0		77.0	16.0	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Silent	SNP	ENST00000264501.4	hg19	CCDS43267.1	.	.	.	.	.	.	.	.	.	.	C	7.460	0.644447	0.14451	.	.	ENSG00000138688	ENST00000419325	.	.	.	5.61	5.61	0.85477	.	.	.	.	.	T	0.71256	0.3318	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.69457	-0.5140	4	.	.	.	.	14.8521	0.70306	0.0:0.9294:0.0:0.0706	.	.	.	.	F	1513	.	.	S	+	2	0	KIAA1109	123457463	1.000000	0.71417	0.997000	0.53966	0.937000	0.57800	4.655000	0.61476	2.637000	0.89404	0.655000	0.94253	TCT	.	.		0.328	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		T	123238013	C	T	123238013	2	4	273	1	0	0	0	0	0	0	0	1	8217	912	32	3		3	KIAA1109	4	123238013	Silent	SNP	C	TCGA-G3-A25T-01A-11D-A16V-10		123238013	67916263	10	39525										
KIAA0146	23514	hgsc.bcm.edu	37	chr8	48614552	48614552	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	0.447252747252747	0	0.581428571428571	1	1	0	tacccgttgcagtttctatgCcacggtgatttaccaaaaac	7	11	1	1			TCGA-G3-A25T-01A-11D-A16V-10	TCGA-G3-A25T-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41840dc1-5ea2-4f01-a0d4-8b65add641c8	ad831284-a522-4712-b7b4-134b92be8125	g.chr8:48614552C>G	ENST00000297423.4	+	14	2336	c.1952C>G	c.(1951-1953)gCc>gGc	p.A651G	SPIDR_ENST00000518074.1_Missense_Mutation_p.A591G|SPIDR_ENST00000517693.1_Missense_Mutation_p.A126G|SPIDR_ENST00000521214.1_3'UTR|SPIDR_ENST00000541342.1_Missense_Mutation_p.A581G	NM_001080394.2|NM_001282916.1	NP_001073863.1|NP_001269845.1	Q14159	SPIDR_HUMAN	scaffolding protein involved in DNA repair	651					cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of double-strand break repair (GO:2000781)|positive regulation of protein complex assembly (GO:0031334)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of establishment of protein localization to chromosome (GO:0070202)	nuclear chromosome (GO:0000228)											AGTTTCTATGCCACGGTGATT	0.438																																					p.A651G		Atlas-SNP	.											.	KIAA0146	64	.	0			c.C1952G						.						115	107	110					8																	48614552		1900	4127	6027	SO:0001583	missense	23514	exon14			TCTATGCCACGGT	AK055680	CCDS43737.1, CCDS64890.1, CCDS64891.1	8q11.21	2013-07-02	2013-07-02	2013-07-02	ENSG00000164808	ENSG00000164808			28971	protein-coding gene	gene with protein product		615384	"KIAA0146"	KIAA0146		8590280, 23509288	Standard	XM_005251189		Approved		uc003xqd.3	Q14159	OTTHUMG00000164176	ENST00000297423.4:c.1952C>G	chr8.hg19:g.48614552C>G	ENSP00000297423:p.Ala651Gly	121.0	0.0		126.0	59.0	NM_001080394	B4DFV2|B4E0Y6|Q96BI5	Missense_Mutation	SNP	ENST00000297423.4	hg19	CCDS43737.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.59|16.59	3.164646|3.164646	0.57476|0.57476	.|.	.|.	ENSG00000164808|ENSG00000164808	ENST00000297423;ENST00000518074;ENST00000541342;ENST00000519141;ENST00000517693;ENST00000519362;ENST00000522321;ENST00000518692;ENST00000521056|ENST00000519401	.|.	.|.	.|.	5.61|5.61	4.74|4.74	0.60224|0.60224	.|.	0.116963|.	0.56097|.	D|.	0.000027|.	T|T	0.60340|0.60340	0.2261|0.2261	L|L	0.51422|0.51422	1.61|1.61	0.34809|0.34809	D|D	0.737514|0.737514	B;B;P;D;P;B;D|.	0.89917|.	0.38;0.38;0.884;1.0;0.884;0.38;1.0|.	B;B;P;D;P;B;D|.	0.77004|.	0.178;0.178;0.636;0.989;0.826;0.178;0.989|.	T|T	0.68603|0.68603	-0.5365|-0.5365	9|5	0.40728|.	T|.	0.16|.	.|.	12.2897|12.2897	0.54810|0.54810	0.0:0.9208:0.0:0.0792|0.0:0.9208:0.0:0.0792	.|.	141;156;591;581;651;126;651|.	B4DZY2;B4DWT8;B4E0Y6;B4DFV2;B4DEV5;B3KP42;Q14159|.	.;.;.;.;.;.;K0146_HUMAN|.	G|A	651;591;581;156;126;126;12;12;12|333	.|.	ENSP00000297423:A651G|.	A|P	+|+	2|1	0|0	KIAA0146|KIAA0146	48777105|48777105	0.981000|0.981000	0.34729|0.34729	0.984000|0.984000	0.44739|0.44739	0.433000|0.433000	0.31745|0.31745	2.015000|2.015000	0.40961|0.40961	1.388000|1.388000	0.46506|0.46506	0.650000|0.650000	0.86243|0.86243	GCC|CCA	.	.		0.438	SPIDR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377611.1	NM_001080394		G	48614552	C	G	48614552	3	3	273	1	0	0	0	0	1	0	0	0	8166	739	26	4	2006	4	KIAA0146	8	48614552	Missense_Mutation	SNP	C	TCGA-G3-A25T-01A-11D-A16V-10		48614552	97749470	11	39526										
SLC30A8	169026	hgsc.bcm.edu	37	chr8	118170071	118170071	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	0.447252747252747	0	0.581428571428571	1	1	0	cgtttccagctgcgcagtggCggccaacattgtgtaagtca	12	11	1	0	rs141202988		TCGA-G3-A25T-01A-11D-A16V-10	TCGA-G3-A25T-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41840dc1-5ea2-4f01-a0d4-8b65add641c8	ad831284-a522-4712-b7b4-134b92be8125	g.chr8:118170071C>T	ENST00000456015.2	+	4	560	c.560C>T	c.(559-561)gCg>gTg	p.A187V	SLC30A8_ENST00000519688.1_Missense_Mutation_p.A138V|SLC30A8_ENST00000427715.2_Missense_Mutation_p.A138V|SLC30A8_ENST00000521243.1_Missense_Mutation_p.A138V	NM_173851.2	NP_776250.2	Q8IWU4	ZNT8_HUMAN	solute carrier family 30 (zinc transporter), member 8	187					cellular zinc ion homeostasis (GO:0006882)|insulin secretion (GO:0030073)|positive regulation of insulin secretion (GO:0032024)|regulation of sequestering of zinc ion (GO:0061088)|regulation of vesicle-mediated transport (GO:0060627)|response to glucose (GO:0009749)|response to interferon-gamma (GO:0034341)|response to interleukin-1 (GO:0070555)|sequestering of zinc ion (GO:0032119)|transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|secretory granule membrane (GO:0030667)	protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)	p.A187V(1)		breast(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(18)|ovary(2)|pancreas(2)|skin(5)	41	all_cancers(13;2.11e-22)|Lung NSC(37;6.08e-05)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.203)			TGCGCAGTGGCGGCCAACATT	0.517																																					p.A187V	Ovarian(162;1202 1922 6011 16223 52092)	Atlas-SNP	.											SLC30A8,caecum,carcinoma,-1,4	SLC30A8	102	.	1	Substitution - Missense(1)	ovary(1)	c.C560T						.	C	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	0,4406		0,0,2203	179	149	159		413,413,413,413,560	2.1	1	8	dbSNP_134	159	3,8597	3.0+/-9.4	0,3,4297	no	missense,missense,missense,missense,missense	SLC30A8	NM_001172811.1,NM_001172813.1,NM_001172814.1,NM_001172815.1,NM_173851.2	64,64,64,64,64	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	benign,benign,benign,benign,benign	138/321,138/321,138/321,138/321,187/370	118170071	3,13003	2203	4300	6503	SO:0001583	missense	169026	exon4			CAGTGGCGGCCAA		CCDS6322.1, CCDS55272.1	8q24.11	2014-08-12			ENSG00000164756			"Solute carriers"	20303	protein-coding gene	gene with protein product		611145					Standard	NM_001172811		Approved		uc003yoh.3	Q8IWU4	OTTHUMG00000164962	ENST00000456015.2:c.560C>T	chr8.hg19:g.118170071C>T	ENSP00000415011:p.Ala187Val	88.0	0.0		101.0	65.0	NM_173851	A0AVP9|A5YM39|B4DPE0|Q8TCL3	Missense_Mutation	SNP	ENST00000456015.2	hg19	CCDS6322.1	.	.	.	.	.	.	.	.	.	.	C	0.744	-0.775314	0.02951	0.0	3.49E-4	ENSG00000164756	ENST00000521243;ENST00000427715;ENST00000519688;ENST00000456015	T;T;T;T	0.61158	0.13;0.13;0.13;0.13	5.76	2.11	0.27256	.	0.832250	0.11028	N	0.607612	T	0.34135	0.0887	N	0.21240	0.645	0.25532	N	0.987267	B	0.06786	0.001	B	0.09377	0.004	T	0.29212	-1.0019	10	0.05620	T	0.96	0.941	4.8273	0.13423	0.0:0.2227:0.135:0.6423	.	187	Q8IWU4	ZNT8_HUMAN	V	138;138;138;187	ENSP00000428545:A138V;ENSP00000407505:A138V;ENSP00000431069:A138V;ENSP00000415011:A187V	ENSP00000407505:A138V	A	+	2	0	SLC30A8	118239252	0.389000	0.25205	0.993000	0.49108	0.213000	0.24496	1.004000	0.29822	0.101000	0.17610	0.650000	0.86243	GCG	.	C|1.000;T|0.000		0.517	SLC30A8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381205.1	NM_173851		T	118170071	C	T	118170071	3	4	273	1	0	0	0	0	1	0	0	0	14576	768	27	1	574	1	SLC30A8	8	118170071	Missense_Mutation	SNP	C	TCGA-G3-A25T-01A-11D-A16V-10	69555519	118170071	28193951	12	39527										
CST6	1474	hgsc.bcm.edu	37	chr11	65780325	65780325	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	0.447252747252747	0	0.581428571428571	1	1	0	cggcatcaagtacttcctgaCgatggagatggggagcacag	14	9	1	2			TCGA-G3-A25T-01A-11D-A16V-10	TCGA-G3-A25T-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41840dc1-5ea2-4f01-a0d4-8b65add641c8	ad831284-a522-4712-b7b4-134b92be8125	g.chr11:65780325C>A	ENST00000312134.2	+	2	473	c.269C>A	c.(268-270)aCg>aAg	p.T90K		NM_001323.3	NP_001314.1	Q15828	CYTM_HUMAN	cystatin E/M	90					anatomical structure morphogenesis (GO:0009653)|epidermis development (GO:0008544)|negative regulation of endopeptidase activity (GO:0010951)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			large_intestine(1)|lung(1)|ovary(1)	3						TACTTCCTGACGATGGAGATG	0.602																																					p.T90K		Atlas-SNP	.											CST6,rectum,carcinoma,0,1	CST6	14	.	0			c.C269A						.						80	66	71					11																	65780325		2201	4296	6497	SO:0001583	missense	1474	exon2			TCCTGACGATGGA	U62800	CCDS8126.1	11q13	2005-09-29			ENSG00000175315	ENSG00000175315			2478	protein-coding gene	gene with protein product		601891				9154125, 9099741	Standard	NM_001323		Approved		uc001ogr.3	Q15828	OTTHUMG00000166750	ENST00000312134.2:c.269C>A	chr11.hg19:g.65780325C>A	ENSP00000311313:p.Thr90Lys	53.0	0.0		35.0	25.0	NM_001323	Q540N7	Missense_Mutation	SNP	ENST00000312134.2	hg19	CCDS8126.1	.	.	.	.	.	.	.	.	.	.	C	14.42	2.529899	0.45073	.	.	ENSG00000175315	ENST00000312134	T	0.24538	1.85	5.66	2.77	0.32553	Proteinase inhibitor I25, cystatin, conserved site (1);Proteinase inhibitor I25, cystatin (2);	0.124523	0.52532	D	0.000071	T	0.23572	0.0570	L	0.58669	1.825	0.24883	N	0.992218	P	0.41420	0.749	B	0.42188	0.379	T	0.09015	-1.0694	10	0.30854	T	0.27	-17.3569	5.4001	0.16291	0.1613:0.6795:0.0:0.1592	.	90	Q15828	CYTM_HUMAN	K	90	ENSP00000311313:T90K	ENSP00000311313:T90K	T	+	2	0	CST6	65536901	0.591000	0.26824	0.190000	0.23270	0.220000	0.24768	0.865000	0.27940	0.327000	0.23409	0.563000	0.77884	ACG	.	.		0.602	CST6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391348.1	NM_001323		A	65780325	C	A	65780325	3	1	273	1	0	0	0	0	1	0	0	0	3978	536	19	1	275	1	CST6	11	65780325	Missense_Mutation	SNP	C	TCGA-G3-A25T-01A-11D-A16V-10		65780325	69226191	13	39528										
TAS2R30	259293	hgsc.bcm.edu	37	chr12	11286203	11286203	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	0.447252747252747	0	0.581428571428571	1	1	0	tgctgggatcttgagatcctTtgccatggagctgcatcttc	11	10	2	1			TCGA-G3-A25T-01A-11D-A16V-10	TCGA-G3-A25T-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41840dc1-5ea2-4f01-a0d4-8b65add641c8	ad831284-a522-4712-b7b4-134b92be8125	g.chr12:11286203T>A	ENST00000539585.1	-	1	1040	c.641A>T	c.(640-642)aAa>aTa	p.K214I	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_001097643.1	NP_001091112.1	P59541	T2R30_HUMAN	taste receptor, type 2, member 30	214					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	13						TTGAGATCCTTTGCCATGGAG	0.423																																					p.K214I		Atlas-SNP	.											.	TAS2R30	28	.	0			c.A641T						.						215	230	225					12																	11286203		2203	4300	6503	SO:0001583	missense	259293	exon1			GATCCTTTGCCAT	AX097746, AF494233	CCDS53750.1	12p13.2	2012-08-22				ENSG00000256188		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	19112	protein-coding gene	gene with protein product		613963	"taste receptor, type 2, member 47"	TAS2R47			Standard	NM_001097643		Approved	T2R30	uc009zhs.1	P59541		ENST00000539585.1:c.641A>T	chr12.hg19:g.11286203T>A	ENSP00000444736:p.Lys214Ile	131.0	0.0		205.0	22.0	NM_001097643	Q645X7	Missense_Mutation	SNP	ENST00000539585.1	hg19	CCDS53750.1	.	.	.	.	.	.	.	.	.	.	-	12.77	2.038617	0.35989	.	.	ENSG00000256188	ENST00000539585	T	0.38560	1.13	2.6	1.35	0.21983	.	.	.	.	.	T	0.59445	0.2194	M	0.79693	2.465	0.09310	N	1	D	0.64830	0.994	D	0.73708	0.981	T	0.45600	-0.9250	9	0.62326	D	0.03	.	4.7585	0.13095	0.278:0.0:0.0:0.722	.	214	P59541	T2R30_HUMAN	I	214	ENSP00000444736:K214I	ENSP00000444736:K214I	K	-	2	0	TAS2R30	11177470	0.000000	0.05858	0.002000	0.10522	0.010000	0.07245	-0.060000	0.11712	0.205000	0.20568	0.260000	0.18958	AAA	.	.		0.423	TAS2R30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400238.1	NM_001097643		A	11286203	T	A	11286203	3	1	273	1	0	0	0	0	1	0	0	0	15588	1841	64	4	322	4	TAS2R30	12	11286203	Missense_Mutation	SNP	T	TCGA-G3-A25T-01A-11D-A16V-10		11286203	122565692	14	39529										
PCID2	55795	hgsc.bcm.edu	37	chr13	113835485	113835485	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	0.447252747252747	0	0.581428571428571	1	1	0	caaatagatcagaatcatccTtttgttcttctgactagaac	5	9	4	4			TCGA-G3-A25T-01A-11D-A16V-10	TCGA-G3-A25T-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41840dc1-5ea2-4f01-a0d4-8b65add641c8	ad831284-a522-4712-b7b4-134b92be8125	g.chr13:113835485T>C	ENST00000337344.4	-	10	821	c.745A>G	c.(745-747)Agg>Ggg	p.R249G	PCID2_ENST00000375459.1_Missense_Mutation_p.R247G|PCID2_ENST00000375457.2_Missense_Mutation_p.R247G|PCID2_ENST00000375479.2_Missense_Mutation_p.R249G|PCID2_ENST00000493650.1_5'UTR|PCID2_ENST00000375477.1_Missense_Mutation_p.R249G|PCID2_ENST00000246505.5_Missense_Mutation_p.R303G	NM_001127202.2	NP_001120674.1	Q5JVF3	PCID2_HUMAN	PCI domain containing 2	249					negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity (GO:2000117)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mRNA stability (GO:0043488)|spleen development (GO:0048536)					breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)	20	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_lung(25;0.216)|all_epithelial(44;0.234)	all cancers(43;0.104)			AGAATCATCCTTTTGTTCTTC	0.433																																					p.R303G		Atlas-SNP	.											.	PCID2	30	.	0			c.A907G						.						146	126	133					13																	113835485		2203	4300	6503	SO:0001583	missense	55795	exon10			TCATCCTTTTGTT	AK002167	CCDS9532.2, CCDS58301.1, CCDS58302.1	13q34	2006-03-31			ENSG00000126226	ENSG00000126226			25653	protein-coding gene	gene with protein product		613713				12477932	Standard	NM_001127203		Approved	FLJ11305	uc031qnm.1	Q5JVF3	OTTHUMG00000017385	ENST00000337344.4:c.745A>G	chr13.hg19:g.113835485T>C	ENSP00000337405:p.Arg249Gly	54.0	0.0		31.0	11.0	NM_001258212	A6NK09|Q3ZCX1|Q5TC57|Q5TC58|Q9H7K1|Q9HBZ7|Q9NUK6|Q9NVY1|Q9NW44|Q9NWH3	Missense_Mutation	SNP	ENST00000337344.4	hg19	CCDS9532.2	.	.	.	.	.	.	.	.	.	.	T	17.51	3.406644	0.62399	.	.	ENSG00000126226	ENST00000337344;ENST00000375479;ENST00000375477;ENST00000246505;ENST00000375459;ENST00000375457;ENST00000375462;ENST00000246506;ENST00000351317	.	.	.	5.25	2.7	0.31948	PCI/PINT associated module (1);	0.000000	0.85682	D	0.000000	T	0.79275	0.4418	M	0.87038	2.855	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.71184	0.972;0.951	T	0.79799	-0.1651	9	0.52906	T	0.07	-30.4952	12.5786	0.56378	0.0:0.0:0.4358:0.5641	.	303;249	Q5JVF3-4;Q5JVF3	.;PCID2_HUMAN	G	249;249;249;303;247;247;226;249;226	.	ENSP00000246505:R303G	R	-	1	2	PCID2	112883486	0.990000	0.36364	0.994000	0.49952	0.878000	0.50629	1.076000	0.30729	0.269000	0.21961	0.460000	0.39030	AGG	.	.		0.433	PCID2-002	KNOWN	alternative_3_UTR|non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045897.1	NM_018386		C	113835485	T	C	113835485	3	2	273	1	0	0	0	0	1	0	0	0	11588	1608	56	2	474	2	PCID2	13	113835485	Missense_Mutation	SNP	T	TCGA-G3-A25T-01A-11D-A16V-10		113835485	1334393	15	39530										
UNC13C	440279	hgsc.bcm.edu	37	chr15	54306377	54306377	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	0.447252747252747	0	0.581428571428571	1	1	0	agggataccatcctcccagaCatatgagagcatggctataa	9	10	0	2			TCGA-G3-A25T-01A-11D-A16V-10	TCGA-G3-A25T-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41840dc1-5ea2-4f01-a0d4-8b65add641c8	ad831284-a522-4712-b7b4-134b92be8125	g.chr15:54306377C>T	ENST00000260323.11	+	1	1277	c.1277C>T	c.(1276-1278)aCa>aTa	p.T426I	UNC13C_ENST00000537900.1_Missense_Mutation_p.T426I|UNC13C_ENST00000545554.1_Missense_Mutation_p.T426I	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	426					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		TCCTCCCAGACATATGAGAGC	0.393																																					p.T426I		Atlas-SNP	.											.	UNC13C	674	.	0			c.C1277T						.						101	97	98					15																	54306377		1861	4098	5959	SO:0001583	missense	440279	exon1			CCCAGACATATGA	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.1277C>T	chr15.hg19:g.54306377C>T	ENSP00000260323:p.Thr426Ile	65.0	0.0		86.0	36.0	NM_001080534	Q0P613|Q8ND48|Q96NP3	Missense_Mutation	SNP	ENST00000260323.11	hg19	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	C	13.68	2.309250	0.40895	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	D;D;D	0.83755	-1.75;-1.76;-1.75	5.64	5.64	0.86602	.	.	.	.	.	D	0.82628	0.5078	L	0.27053	0.805	0.48087	D	0.999588	D	0.58620	0.983	P	0.53490	0.727	T	0.82275	-0.0538	9	0.39692	T	0.17	.	18.6946	0.91596	0.0:1.0:0.0:0.0	.	426	Q8NB66	UN13C_HUMAN	I	426	ENSP00000260323:T426I;ENSP00000438156:T426I;ENSP00000442569:T426I	ENSP00000260323:T426I	T	+	2	0	UNC13C	52093669	1.000000	0.71417	0.987000	0.45799	0.394000	0.30568	6.086000	0.71352	2.665000	0.90641	0.655000	0.94253	ACA	.	.		0.393	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		T	54306377	C	T	54306377	3	4	273	1	0	0	0	0	1	0	0	0	17001	478	17	3	1279	3	UNC13C	15	54306377	Missense_Mutation	SNP	C	TCGA-G3-A25T-01A-11D-A16V-10		54306377	48225015	16	39531										
IDH2	3418	hgsc.bcm.edu	37	chr15	90631837	90631837	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	0.447252747252747	0	0.581428571428571	1	1	0	acctggtcgccatgggcgtgCctgccaatggtgatgggctt	15	11	0	1			TCGA-G3-A25T-01A-11D-A16V-10	TCGA-G3-A25T-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41840dc1-5ea2-4f01-a0d4-8b65add641c8	ad831284-a522-4712-b7b4-134b92be8125	g.chr15:90631837C>G	ENST00000330062.3	-	4	629	c.516G>C	c.(514-516)agG>agC	p.R172S	IDH2_ENST00000540499.2_Missense_Mutation_p.R120S|IDH2_ENST00000539790.1_Missense_Mutation_p.R42S|IDH2_ENST00000559482.1_Intron	NM_002168.2	NP_002159.2	P48735	IDHP_HUMAN	isocitrate dehydrogenase 2 (NADP+), mitochondrial	172					2-oxoglutarate metabolic process (GO:0006103)|carbohydrate metabolic process (GO:0005975)|cellular metabolic process (GO:0044237)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)	p.R172S(17)|p.R172N(1)		biliary_tract(11)|bone(19)|central_nervous_system(107)|endometrium(1)|haematopoietic_and_lymphoid_tissue(953)|large_intestine(8)|lung(5)|skin(5)	1109	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.106)			CATGGGCGTGCCTGCCAATGG	0.637			M		GBM																																p.R172S		Atlas-SNP	.		Dom	yes		15	15q26.1	3418	"socitrate dehydrogenase 2 (NADP+), mitochondrial "		M	IDH2,NS,haematopoietic_neoplasm,-1,1	IDH2	1372	.	18	Substitution - Missense(18)	bone(11)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(2)|biliary_tract(1)|large_intestine(1)	c.G516C						.						85	80	82					15																	90631837		2200	4298	6498	SO:0001583	missense	3418	exon4			GGCGTGCCTGCCA		CCDS10359.1	15q26.1	2014-09-17			ENSG00000182054	ENSG00000182054	1.1.1.42		5383	protein-coding gene	gene with protein product		147650					Standard	NM_001289910		Approved		uc002box.3	P48735	OTTHUMG00000149815	ENST00000330062.3:c.516G>C	chr15.hg19:g.90631837C>G	ENSP00000331897:p.Arg172Ser	132.0	0.0		96.0	41.0	NM_002168	B2R6L6|B4DFL2|Q96GT3	Missense_Mutation	SNP	ENST00000330062.3	hg19	CCDS10359.1	.	.	.	.	.	.	.	.	.	.	C	12.66	2.005845	0.35415	.	.	ENSG00000182054	ENST00000330062;ENST00000539790;ENST00000540499	D;D;D	0.86865	-2.18;-2.18;-2.18	5.93	-3.19	0.05171	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.94112	0.8112	H	0.98487	4.245	0.53005	D	0.999962	D	0.89917	1.0	D	0.91635	0.999	D	0.89382	0.3682	10	0.87932	D	0	.	5.0108	0.14312	0.237:0.2848:0.0:0.4782	.	172	P48735	IDHP_HUMAN	S	172;42;120	ENSP00000331897:R172S;ENSP00000438457:R42S;ENSP00000446147:R120S	ENSP00000331897:R172S	R	-	3	2	IDH2	88432841	0.145000	0.22656	0.004000	0.12327	0.001000	0.01503	-0.449000	0.06812	-0.649000	0.05430	-1.288000	0.01363	AGG	.	.		0.637	IDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313426.1			G	90631837	C	G	90631837	3	3	273	1	0	0	0	0	1	0	0	0	7504	738	26	4	874	4	IDH2	15	90631837	Missense_Mutation	SNP	C	TCGA-G3-A25T-01A-11D-A16V-10	36325460	90631837	11899555	17	39532										
SMG6	23293	hgsc.bcm.edu	37	chr17	2203159	2203159	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	0.447252747252747	0	0.581428571428571	1	1	0	gaatcggttgaggacacagaCacttgcttcttcagtcgtgg	12	9	2	2			TCGA-G3-A25T-01A-11D-A16V-10	TCGA-G3-A25T-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41840dc1-5ea2-4f01-a0d4-8b65add641c8	ad831284-a522-4712-b7b4-134b92be8125	g.chr17:2203159C>A	ENST00000263073.6	-	2	938	c.888G>T	c.(886-888)gtG>gtT	p.V296V	SMG6_ENST00000544865.1_Silent_p.V265V	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	296	Interaction with telomeric DNA.				gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|telomere maintenance (GO:0000723)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|telomeric DNA binding (GO:0042162)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(10)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						AGGACACAGACACTTGCTTCT	0.522																																					p.V296V	Melanoma(59;28 1088 11621 25887 46638 50814)	Atlas-SNP	.											.	SMG6	97	.	0			c.G888T						.						94	84	88					17																	2203159		2203	4300	6503	SO:0001819	synonymous_variant	23293	exon2			CACAGACACTTGC	AB018275	CCDS11016.1, CCDS58498.1	17p13.3	2013-07-02	2013-07-02	2006-02-16	ENSG00000070366	ENSG00000070366			17809	protein-coding gene	gene with protein product	"EST1 telomerase component homolog A (S. cerevisiae)"	610963	"chromosome 17 open reading frame 31", "smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)"	C17orf31		12676087, 12699629	Standard	NM_017575		Approved	KIAA0732, SMG-6, EST1A	uc002fub.1	Q86US8	OTTHUMG00000177578	ENST00000263073.6:c.888G>T	chr17.hg19:g.2203159C>A		56.0	0.0		65.0	19.0	NM_017575	B7Z874|O94837|Q86VH6|Q9UF60	Silent	SNP	ENST00000263073.6	hg19	CCDS11016.1																																																																																			.	.		0.522	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437826.3			A	2203159	C	A	2203159	2	1	273	1	0	0	0	0	0	0	0	1	14812	465	17	3		3	SMG6	17	2203159	Silent	SNP	C	TCGA-G3-A25T-01A-11D-A16V-10		2203159	78992051	18	39533										
ZZEF1	23140	hgsc.bcm.edu	37	chr17	3957431	3957431	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	0.447252747252747	0	0.581428571428571	1	1	0	agggggcaatctcatcacacCcatcacaagagatgtccaca	8	13	3	1			TCGA-G3-A25T-01A-11D-A16V-10	TCGA-G3-A25T-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41840dc1-5ea2-4f01-a0d4-8b65add641c8	ad831284-a522-4712-b7b4-134b92be8125	g.chr17:3957431C>A	ENST00000381638.2	-	34	5478	c.5354G>T	c.(5353-5355)gGg>gTg	p.G1785V	RNA5SP434_ENST00000516647.1_RNA	NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	1785							calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						CTCATCACACCCATCACAAGA	0.438																																					p.G1785V		Atlas-SNP	.											.	ZZEF1	195	.	0			c.G5354T						.						156	132	140					17																	3957431		2203	4300	6503	SO:0001583	missense	23140	exon34			TCACACCCATCAC	BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"Zinc fingers, ZZ-type", "EF-hand domain containing"	29027	protein-coding gene	gene with protein product			"zinc finger, ZZ-type with EF hand domain 1"			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.5354G>T	chr17.hg19:g.3957431C>A	ENSP00000371051:p.Gly1785Val	42.0	0.0		50.0	16.0	NM_015113	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Missense_Mutation	SNP	ENST00000381638.2	hg19	CCDS11043.1	.	.	.	.	.	.	.	.	.	.	C	33	5.244446	0.95272	.	.	ENSG00000074755	ENST00000381638	D	0.91295	-2.82	6.17	6.17	0.99709	Zinc finger, ZZ-type (3);	0.000000	0.85682	D	0.000000	D	0.93822	0.8024	L	0.41710	1.295	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.995;1.0	D	0.93624	0.6950	10	0.87932	D	0	-19.6938	20.8794	0.99867	0.0:1.0:0.0:0.0	.	1785;1785	O43149-2;O43149	.;ZZEF1_HUMAN	V	1785	ENSP00000371051:G1785V	ENSP00000371051:G1785V	G	-	2	0	ZZEF1	3904180	1.000000	0.71417	0.960000	0.40013	0.990000	0.78478	7.441000	0.80485	2.941000	0.99782	0.655000	0.94253	GGG	.	.		0.438	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113		A	3957431	C	A	3957431	3	1	273	1	0	0	0	0	1	0	0	0	18270	623	22	3	3619	3	ZZEF1	17	3957431	Missense_Mutation	SNP	C	TCGA-G3-A25T-01A-11D-A16V-10	1754272	3957431	77237779	19	39534										
MYO18A	399687	hgsc.bcm.edu	37	chr17	27421740	27421740	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	0.447252747252747	0	0.581428571428571	1	1	0	tccttgactttggcctccagGtcccggagctgtttcttgac	10	13	1	2			TCGA-G3-A25T-01A-11D-A16V-10	TCGA-G3-A25T-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41840dc1-5ea2-4f01-a0d4-8b65add641c8	ad831284-a522-4712-b7b4-134b92be8125	g.chr17:27421740G>A	ENST00000527372.1	-	30	4818	c.4638C>T	c.(4636-4638)gaC>gaT	p.D1546D	MYO18A_ENST00000533112.1_Silent_p.D1546D|MYO18A_ENST00000354329.4_Silent_p.D1546D|MYO18A_ENST00000531253.1_Silent_p.D1546D	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	1546					actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			TGGCCTCCAGGTCCCGGAGCT	0.562																																					p.D1546D	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-SNP	.											.	MYO18A	217	.	0			c.C4638T						.						158	153	155					17																	27421740		2032	4190	6222	SO:0001819	synonymous_variant	399687	exon30			CTCCAGGTCCCGG	D86970	CCDS45641.1, CCDS45642.1	17q11.2	2011-09-27			ENSG00000196535	ENSG00000196535		"Myosins / Myosin superfamily : Class XVIII"	31104	protein-coding gene	gene with protein product		610067				12761286	Standard	NM_078471		Approved	KIAA0216, MysPDZ	uc002hdt.1	Q92614	OTTHUMG00000166360	ENST00000527372.1:c.4638C>T	chr17.hg19:g.27421740G>A		145.0	0.0		108.0	33.0	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Silent	SNP	ENST00000527372.1	hg19	CCDS45642.1																																																																																			.	.		0.562	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471		A	27421740	G	A	27421740	2	1	273	1	0	0	0	0	0	0	0	1	10074	1252	44	3		3	MYO18A	17	27421740	Silent	SNP	G	TCGA-G3-A25T-01A-11D-A16V-10	23464309	27421740	53773470	20	39535										
AFG3L2	10939	hgsc.bcm.edu	37	chr18	12329714	12329714	+	Silent	SNP	T	T	C													0.0434782608695652	1	1	0.447252747252747	0	0.581428571428571	1	1	0	gtagatttttccgcaaatggTctggggcccaaaagttcaac							TCGA-G3-A25T-01A-11D-A16V-10	TCGA-G3-A25T-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41840dc1-5ea2-4f01-a0d4-8b65add641c8	ad831284-a522-4712-b7b4-134b92be8125	g.chr18:12329714T>C	ENST00000269143.3	-	17	2475	c.2244A>G	c.(2242-2244)agA>agG	p.R748R	TUBB6_ENST00000591909.1_3'UTR|TUBB6_ENST00000590967.1_Intron	NM_006796.2	NP_006787.2	Q9Y4W6	AFG32_HUMAN	AFG3-like AAA ATPase 2	748					axonogenesis (GO:0007409)|cell death (GO:0008219)|cristae formation (GO:0042407)|mitochondrial fusion (GO:0008053)|mitochondrial protein processing (GO:0034982)|muscle fiber development (GO:0048747)|myelination (GO:0042552)|nerve development (GO:0021675)|neuromuscular junction development (GO:0007528)|regulation of multicellular organism growth (GO:0040014)|righting reflex (GO:0060013)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metalloendopeptidase activity (GO:0004222)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(12)|prostate(3)|skin(1)|stomach(3)|urinary_tract(1)	27					Adenosine triphosphate(DB00171)	CCGCAAATGGTCTGGGGCCCA	0.398																																					p.R748R		Atlas-SNP	.											.	AFG3L2	60	.	0			c.A2244G						.						93	92	92					18																	12329714		2203	4300	6503	SO:0001819	synonymous_variant	10939	exon17			AAATGGTCTGGGG	Y18314	CCDS11859.1	18p11.21	2014-09-17	2013-10-17		ENSG00000141385	ENSG00000141385		"ATPases / AAA-type"	315	protein-coding gene	gene with protein product		604581	"AFG3 (ATPase family gene 3, yeast)-like 2", "spinocerebellar ataxia 28", "AFG3 ATPase family gene 3-like 2 (yeast)", "AFG3 ATPase family gene 3-like 2 (S. cerevisiae)", "AFG3 ATPase family member 3-like 2 (S. cerevisiae)"	SCA28		10395799, 18769991	Standard	NM_006796		Approved	SPAX5	uc002kqz.2	Q9Y4W6	OTTHUMG00000131695	ENST00000269143.3:c.2244A>G	chr18.hg19:g.12329714T>C		91.0	0.0		84.0	36.0	NM_006796	Q6P1L0	Silent	SNP	ENST00000269143.3	hg19	CCDS11859.1																																																																																			.	.		0.398	AFG3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254603.2	NM_006796		C	12329714	T	C	12329714	2	2	273	1	0	0	0	0	0	0	0	1	360	1664	58	2		2	AFG3L2	18	12329714	Silent	SNP	T	TCGA-G3-A25T-01A-11D-A16V-10		12329714	65747534	21	39536	195	3								
AFG3L2	10939	hgsc.bcm.edu	37	chr18	12329717	12329717	+	Frame_Shift_Del	DEL	G	G	-													0.0434782608695652	1	1	0.447252747252747	0	0.581428571428571	1	1	0	gatttttccgcaaatggtctGgggcccaaaagttcaaccat							TCGA-G3-A25T-01A-11D-A16V-10	TCGA-G3-A25T-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41840dc1-5ea2-4f01-a0d4-8b65add641c8	ad831284-a522-4712-b7b4-134b92be8125	g.chr18:12329717delG	ENST00000269143.3	-	17	2472	c.2241delC	c.(2239-2241)cccfs	p.P747fs	TUBB6_ENST00000591909.1_3'UTR|TUBB6_ENST00000590967.1_Intron	NM_006796.2	NP_006787.2	Q9Y4W6	AFG32_HUMAN	AFG3-like AAA ATPase 2	747					axonogenesis (GO:0007409)|cell death (GO:0008219)|cristae formation (GO:0042407)|mitochondrial fusion (GO:0008053)|mitochondrial protein processing (GO:0034982)|muscle fiber development (GO:0048747)|myelination (GO:0042552)|nerve development (GO:0021675)|neuromuscular junction development (GO:0007528)|regulation of multicellular organism growth (GO:0040014)|righting reflex (GO:0060013)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metalloendopeptidase activity (GO:0004222)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(12)|prostate(3)|skin(1)|stomach(3)|urinary_tract(1)	27					Adenosine triphosphate(DB00171)	CAAATGGTCTGGGGCCCAAAA	0.393																																					p.R748fs		Atlas-INDEL	.											.	AFG3L2	60	.	0			c.2242delA						.						91	89	90					18																	12329717		2203	4300	6503	SO:0001589	frameshift_variant	10939	exon17			.	Y18314	CCDS11859.1	18p11.21	2014-09-17	2013-10-17		ENSG00000141385	ENSG00000141385		"ATPases / AAA-type"	315	protein-coding gene	gene with protein product		604581	"AFG3 (ATPase family gene 3, yeast)-like 2", "spinocerebellar ataxia 28", "AFG3 ATPase family gene 3-like 2 (yeast)", "AFG3 ATPase family gene 3-like 2 (S. cerevisiae)", "AFG3 ATPase family member 3-like 2 (S. cerevisiae)"	SCA28		10395799, 18769991	Standard	NM_006796		Approved	SPAX5	uc002kqz.2	Q9Y4W6	OTTHUMG00000131695	ENST00000269143.3:c.2241delC	chr18.hg19:g.12329717delG	ENSP00000269143:p.Pro747fs	90.0	0.0		85.0	31.0	NM_006796	Q6P1L0	Frame_Shift_Del	DEL	ENST00000269143.3	hg19	CCDS11859.1																																																																																			.	.		0.393	AFG3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254603.2	NM_006796		-	12329717	G	-	12329717	7	5	273	1	0	1	0	1	0	0	0	0	360	1335	47	0	156	0	AFG3L2	18	12329717	Frame_Shift_Del	DEL	G	TCGA-G3-A25T-01A-11D-A16V-10	3	12329717	65747531	22	39537	195	3								
AFG3L2	10939	hgsc.bcm.edu	37	chr18	12329718	12329718	+	Frame_Shift_Del	DEL	G	G	-													0.0434782608695652	1	1	0.447252747252747	0	0.581428571428571	1	1	0	atttttccgcaaatggtctgGggcccaaaagttcaaccata							TCGA-G3-A25T-01A-11D-A16V-10	TCGA-G3-A25T-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41840dc1-5ea2-4f01-a0d4-8b65add641c8	ad831284-a522-4712-b7b4-134b92be8125	g.chr18:12329718delG	ENST00000269143.3	-	17	2471	c.2240delC	c.(2239-2241)cccfs	p.P747fs	TUBB6_ENST00000591909.1_3'UTR|TUBB6_ENST00000590967.1_Intron	NM_006796.2	NP_006787.2	Q9Y4W6	AFG32_HUMAN	AFG3-like AAA ATPase 2	747					axonogenesis (GO:0007409)|cell death (GO:0008219)|cristae formation (GO:0042407)|mitochondrial fusion (GO:0008053)|mitochondrial protein processing (GO:0034982)|muscle fiber development (GO:0048747)|myelination (GO:0042552)|nerve development (GO:0021675)|neuromuscular junction development (GO:0007528)|regulation of multicellular organism growth (GO:0040014)|righting reflex (GO:0060013)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metalloendopeptidase activity (GO:0004222)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(12)|prostate(3)|skin(1)|stomach(3)|urinary_tract(1)	27					Adenosine triphosphate(DB00171)	AAATGGTCTGGGGCCCAAAAG	0.393																																					p.P747fs		Pindel	.											.	AFG3L2	60	.	0			c.2241delC						.						90	89	89					18																	12329718		2203	4300	6503	SO:0001589	frameshift_variant	10939	exon17			.	Y18314	CCDS11859.1	18p11.21	2014-09-17	2013-10-17		ENSG00000141385	ENSG00000141385		"ATPases / AAA-type"	315	protein-coding gene	gene with protein product		604581	"AFG3 (ATPase family gene 3, yeast)-like 2", "spinocerebellar ataxia 28", "AFG3 ATPase family gene 3-like 2 (yeast)", "AFG3 ATPase family gene 3-like 2 (S. cerevisiae)", "AFG3 ATPase family member 3-like 2 (S. cerevisiae)"	SCA28		10395799, 18769991	Standard	NM_006796		Approved	SPAX5	uc002kqz.2	Q9Y4W6	OTTHUMG00000131695	ENST00000269143.3:c.2240delC	chr18.hg19:g.12329718delG	ENSP00000269143:p.Pro747fs	90.0	0.0		87.0	25.0	NM_006796	Q6P1L0	Frame_Shift_Del	DEL	ENST00000269143.3	hg19	CCDS11859.1																																																																																			.	.		0.393	AFG3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254603.2	NM_006796		-	12329718	G	-	12329718	7	5	273	1	0	1	0	1	0	0	0	0	360	1232	43	0	157	0	AFG3L2	18	12329718	Frame_Shift_Del	DEL	G	TCGA-G3-A25T-01A-11D-A16V-10	1	12329718	65747530	23	39538	195	3								
ZNF532	55205	hgsc.bcm.edu	37	chr18	56585829	56585829	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	0.447252747252747	0	0.581428571428571	1	1	0	cctcccttgacagttacagtAaagatggagcaaagtccttg	9	10	0	2			TCGA-G3-A25T-01A-11D-A16V-10	TCGA-G3-A25T-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41840dc1-5ea2-4f01-a0d4-8b65add641c8	ad831284-a522-4712-b7b4-134b92be8125	g.chr18:56585829A>G	ENST00000336078.4	+	4	1086	c.310A>G	c.(310-312)Aaa>Gaa	p.K104E	ZNF532_ENST00000591230.1_Missense_Mutation_p.K104E|ZNF532_ENST00000591083.1_Missense_Mutation_p.K104E|ZNF532_ENST00000589288.1_Missense_Mutation_p.K104E|ZNF532_ENST00000591808.1_Missense_Mutation_p.K104E	NM_018181.4	NP_060651.2	Q9HCE3	ZN532_HUMAN	zinc finger protein 532	104					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(14)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(4)|urinary_tract(1)	52						CAGTTACAGTAAAGATGGAGC	0.512																																					p.K104E		Atlas-SNP	.											.	ZNF532	108	.	0			c.A310G						.						86	71	76					18																	56585829		2203	4300	6503	SO:0001583	missense	55205	exon4			TACAGTAAAGATG	AB046849	CCDS11969.1	18q21.32	2005-08-22			ENSG00000074657	ENSG00000074657		"Zinc fingers, C2H2-type"	30940	protein-coding gene	gene with protein product						10997877	Standard	XM_005266723		Approved	FLJ10697	uc002lho.3	Q9HCE3	OTTHUMG00000132759	ENST00000336078.4:c.310A>G	chr18.hg19:g.56585829A>G	ENSP00000338217:p.Lys104Glu	56.0	0.0		73.0	14.0	NM_018181	Q4G0V6|Q7L7Z7|Q96QR7|Q9NVJ6	Missense_Mutation	SNP	ENST00000336078.4	hg19	CCDS11969.1	.	.	.	.	.	.	.	.	.	.	A	14.60	2.582931	0.46006	.	.	ENSG00000074657	ENST00000336078	T	0.01838	4.61	5.47	5.47	0.80525	.	0.053528	0.64402	D	0.000001	T	0.08179	0.0204	M	0.72894	2.215	0.50039	D	0.999847	D	0.57899	0.981	P	0.53224	0.721	T	0.04693	-1.0933	10	0.49607	T	0.09	-0.6041	15.2263	0.73354	1.0:0.0:0.0:0.0	.	104	Q9HCE3	ZN532_HUMAN	E	104	ENSP00000338217:K104E	ENSP00000338217:K104E	K	+	1	0	ZNF532	54736809	1.000000	0.71417	0.382000	0.26119	0.135000	0.20990	8.854000	0.92228	2.071000	0.62044	0.454000	0.30748	AAA	.	.		0.512	ZNF532-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256130.1	NM_018181		G	56585829	A	G	56585829	3	3	273	1	0	0	0	0	1	0	0	0	17987	363	13	2	312	2	ZNF532	18	56585829	Missense_Mutation	SNP	A	TCGA-G3-A25T-01A-11D-A16V-10	44256111	56585829	21491419	24	39539										
PRKD2	25865	hgsc.bcm.edu	37	chr19	47207834	47207834	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	0.447252747252747	0	0.581428571428571	1	1	0	ccagagacgtggatgacaggCgccgtttgcgggccccacta	14	13	0	2			TCGA-G3-A25T-01A-11D-A16V-10	TCGA-G3-A25T-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41840dc1-5ea2-4f01-a0d4-8b65add641c8	ad831284-a522-4712-b7b4-134b92be8125	g.chr19:47207834C>T	ENST00000291281.4	-	4	809	c.584G>A	c.(583-585)cGc>cAc	p.R195H	PRKD2_ENST00000600194.1_Missense_Mutation_p.R38H|PRKD2_ENST00000433867.1_Missense_Mutation_p.R195H|PRKD2_ENST00000601806.1_Missense_Mutation_p.R38H|PRKD2_ENST00000595515.1_Missense_Mutation_p.R195H			Q9BZL6	KPCD2_HUMAN	protein kinase D2	195					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial tube morphogenesis (GO:0061154)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(13)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	41		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000189)|all cancers(93;0.000545)|Epithelial(262;0.0219)|GBM - Glioblastoma multiforme(486;0.0353)		GGATGACAGGCGCCGTTTGCG	0.652											OREG0025578	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R195H		Atlas-SNP	.											.	PRKD2	94	.	0			c.G584A						.						38	43	41					19																	47207834		2203	4300	6503	SO:0001583	missense	25865	exon4			GACAGGCGCCGTT	AF151021	CCDS12689.1, CCDS59401.1	19q13.2	2013-01-10				ENSG00000105287		"Pleckstrin homology (PH) domain containing"	17293	protein-coding gene	gene with protein product		607074				11042152, 11062248	Standard	NM_001079880		Approved	PKD2, HSPC187, DKFZP586E0820	uc002pfj.3	Q9BZL6		ENST00000291281.4:c.584G>A	chr19.hg19:g.47207834C>T	ENSP00000291281:p.Arg195His	31.0	0.0	945	47.0	13.0	NM_016457	Q8TB08|Q9P0T6|Q9Y3X8	Missense_Mutation	SNP	ENST00000291281.4	hg19	CCDS12689.1	.	.	.	.	.	.	.	.	.	.	C	32	5.164073	0.94727	.	.	ENSG00000105287	ENST00000291281;ENST00000433867	T;T	0.69040	-0.37;-0.37	5.4	5.4	0.78164	.	0.163832	0.37761	N	0.001948	T	0.77505	0.4140	M	0.61703	1.905	0.54753	D	0.999985	D;D	0.65815	0.995;0.995	P;P	0.58520	0.775;0.84	T	0.78795	-0.2064	10	0.56958	D	0.05	-37.0929	17.9478	0.89044	0.0:1.0:0.0:0.0	.	195;195	E7ER94;Q9BZL6	.;KPCD2_HUMAN	H	195	ENSP00000291281:R195H;ENSP00000393978:R195H	ENSP00000291281:R195H	R	-	2	0	PRKD2	51899674	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	3.778000	0.55371	2.535000	0.85469	0.313000	0.20887	CGC	.	.		0.652	PRKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466591.1	NM_016457		T	47207834	C	T	47207834	3	4	273	1	0	0	0	0	1	0	0	0	12531	768	27	1	2112	1	PRKD2	19	47207834	Missense_Mutation	SNP	C	TCGA-G3-A25T-01A-11D-A16V-10		47207834	11921149	25	39540										
XRN2	22803	hgsc.bcm.edu	37	chr20	21346075	21346075	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	1	1	0.447252747252747	0	0.581428571428571	1	1	0	ccagtattaattttaaagacCcacagtttgctgaagattac	6	8	0	3			TCGA-G3-A25T-01A-11D-A16V-10	TCGA-G3-A25T-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41840dc1-5ea2-4f01-a0d4-8b65add641c8	ad831284-a522-4712-b7b4-134b92be8125	g.chr20:21346075C>T	ENST00000377191.3	+	25	2367	c.2272C>T	c.(2272-2274)Cca>Tca	p.P758S	XRN2_ENST00000539513.1_Missense_Mutation_p.P704S|XRN2_ENST00000430571.2_Missense_Mutation_p.P682S	NM_012255.3	NP_036387.2	Q9H0D6	XRN2_HUMAN	5'-3' exoribonuclease 2	758					cell growth (GO:0016049)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA catabolic process (GO:0006401)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|RNA processing (GO:0006396)|spermatogenesis (GO:0007283)	aggresome (GO:0016235)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|5'-3' exoribonuclease activity (GO:0004534)|nuclease activity (GO:0004518)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(6)|large_intestine(10)|lung(12)|ovary(1)|skin(5)	39						TTTTAAAGACCCACAGTTTGC	0.308																																					p.P758S		Atlas-SNP	.											.	XRN2	90	.	0			c.C2272T						.						79	79	79					20																	21346075		2203	4299	6502	SO:0001583	missense	22803	exon25			AAAGACCCACAGT	AF064257	CCDS13144.1	20p11.2-p11.1	2011-09-12			ENSG00000088930	ENSG00000088930	3.1.13.-		12836	protein-coding gene	gene with protein product		608851				10409438	Standard	NM_012255		Approved		uc002wsf.1	Q9H0D6	OTTHUMG00000032025	ENST00000377191.3:c.2272C>T	chr20.hg19:g.21346075C>T	ENSP00000366396:p.Pro758Ser	107.0	0.0		93.0	40.0	NM_012255	Q3L8N4|Q6KGZ9|Q9BQL1|Q9NTW0|Q9NXS6|Q9UL53	Missense_Mutation	SNP	ENST00000377191.3	hg19	CCDS13144.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.504704	0.85176	.	.	ENSG00000088930	ENST00000377191;ENST00000430571;ENST00000539513	T;T;T	0.57273	0.5;0.41;0.46	5.56	5.56	0.83823	.	0.048216	0.85682	D	0.000000	T	0.77315	0.4112	M	0.85630	2.765	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80560	-0.1328	10	0.87932	D	0	-8.1355	19.5261	0.95208	0.0:1.0:0.0:0.0	.	758	Q9H0D6	XRN2_HUMAN	S	758;682;704	ENSP00000366396:P758S;ENSP00000413548:P682S;ENSP00000441113:P704S	ENSP00000366396:P758S	P	+	1	0	XRN2	21294075	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.616000	0.74205	2.632000	0.89209	0.655000	0.94253	CCA	.	.		0.308	XRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078273.2	NM_012255		T	21346075	C	T	21346075	3	4	273	1	0	0	0	0	1	0	0	0	17475	623	22	3	2370	3	XRN2	20	21346075	Missense_Mutation	SNP	C	TCGA-G3-A25T-01A-11D-A16V-10		21346075	41679445	26	39541										
FAM47A	158724	hgsc.bcm.edu	37	chrX	34149594	34149594	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0434782608695652	1	1	0.447252747252747	0	0.581428571428571	1	1	0	ttccagcttcctctcagaatCcagtttcagcagctgtcgta	7	13	2	1			TCGA-G3-A25T-01A-11D-A16V-10	TCGA-G3-A25T-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41840dc1-5ea2-4f01-a0d4-8b65add641c8	ad831284-a522-4712-b7b4-134b92be8125	g.chrX:34149594C>A	ENST00000346193.3	-	1	853	c.802G>T	c.(802-804)Gat>Tat	p.D268Y		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	268										NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	97						CTCTCAGAATCCAGTTTCAGC	0.587																																					p.D268Y		Atlas-SNP	.											.	FAM47A	249	.	0			c.G802T						.						31	32	32					X																	34149594		2198	4299	6497	SO:0001583	missense	158724	exon1			CAGAATCCAGTTT	BC026171	CCDS43926.1	Xp21.1	2004-08-09			ENSG00000185448	ENSG00000185448			29962	protein-coding gene	gene with protein product	"similar to hypothetical protein FLJ35782"					12477932	Standard	NM_203408		Approved	MGC27003	uc004ddg.3	Q5JRC9	OTTHUMG00000021339	ENST00000346193.3:c.802G>T	chrX.hg19:g.34149594C>A	ENSP00000345029:p.Asp268Tyr	66.0	0.0		102.0	56.0	NM_203408	A8K8I9|Q8TAA0	Missense_Mutation	SNP	ENST00000346193.3	hg19	CCDS43926.1	.	.	.	.	.	.	.	.	.	.	c	12.20	1.865190	0.32977	.	.	ENSG00000185448	ENST00000346193	T	0.22336	1.96	0.13	0.13	0.14746	.	.	.	.	.	T	0.27349	0.0671	L	0.39898	1.24	0.09310	N	0.999997	D	0.58268	0.982	P	0.58660	0.843	T	0.12656	-1.0539	8	0.59425	D	0.04	.	.	.	.	.	268	Q5JRC9	FA47A_HUMAN	Y	268	ENSP00000345029:D268Y	ENSP00000345029:D268Y	D	-	1	0	FAM47A	34059515	0.766000	0.28496	0.419000	0.26584	0.420000	0.31355	0.421000	0.21280	0.171000	0.19730	0.173000	0.16961	GAT	.	.		0.587	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408		A	34149594	C	A	34149594	3	1	273	1	0	0	0	0	1	0	0	0	5577	855	30	3	1577	3	FAM47A	23	34149594	Missense_Mutation	SNP	C	TCGA-G3-A25T-01A-11D-A16V-10		34149594	121120966	27	39542										
CD1E	913	hgsc.bcm.edu	37	chr1	158325802	158325802	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	acgagacatggtatctccgaGcaaccctggatgtggcggct	13	11	1	1			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr1:158325802G>A	ENST00000368167.3	+	4	1050	c.811G>A	c.(811-813)Gca>Aca	p.A271T	CD1E_ENST00000368154.1_Intron|CD1E_ENST00000452291.2_Missense_Mutation_p.A82T|CD1E_ENST00000368164.3_Intron|CD1E_ENST00000368157.1_Intron|CD1E_ENST00000368161.3_Intron|CD1E_ENST00000368166.3_Missense_Mutation_p.A82T|CD1E_ENST00000368155.3_Intron|CD1E_ENST00000368156.1_Missense_Mutation_p.A181T|CD1E_ENST00000444681.2_Missense_Mutation_p.A172T|CD1E_ENST00000434258.1_Missense_Mutation_p.A269T|CD1E_ENST00000368160.3_Missense_Mutation_p.A271T|CD1E_ENST00000368165.3_Missense_Mutation_p.A181T|CD1E_ENST00000368163.3_Intron	NM_030893.3	NP_112155.2	P15812	CD1E_HUMAN	CD1e molecule	271	Ig-like.				antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(27)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|urinary_tract(1)	49	all_hematologic(112;0.0378)					GTATCTCCGAGCAACCCTGGA	0.607																																					p.A271T		Atlas-SNP	.											.	CD1E	129	.	0			c.G811A						.						100	99	99					1																	158325802		2203	4300	6503	SO:0001583	missense	913	exon4			CTCCGAGCAACCC	AJ289111	CCDS41417.1, CCDS41418.1, CCDS41419.1, CCDS41420.1, CCDS41421.1, CCDS41422.1, CCDS53387.1, CCDS53388.1, CCDS53389.1, CCDS53390.1, CCDS53384.1, CCDS53385.1, CCDS53386.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158488	ENSG00000158488		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	1638	protein-coding gene	gene with protein product		188411	"CD1E antigen, e polypeptide", "CD1e antigen"			10948205	Standard	NM_001042585		Approved		uc001fse.3	P15812	OTTHUMG00000017515	ENST00000368167.3:c.811G>A	chr1.hg19:g.158325802G>A	ENSP00000357149:p.Ala271Thr	92.0	0.0		128.0	41.0	NM_030893	B4DZV3|E7EP01|Q5TDJ9|Q5TDK3|Q5TDK4|Q5TDK5|Q5TDK6|Q5TDK8|Q5TDL1|Q712E4|Q712E5|Q712E6|Q712E7|Q712E8|Q712E9|Q712F0|Q712F1|Q712F2|Q712F3|Q712F4|Q712F5|Q96TD0|Q96TD1|Q9UMM1|Q9Y5M3	Missense_Mutation	SNP	ENST00000368167.3	hg19	CCDS41417.1	.	.	.	.	.	.	.	.	.	.	G	16.79	3.220546	0.58560	.	.	ENSG00000158488	ENST00000434258;ENST00000444681;ENST00000368167;ENST00000452291;ENST00000368165;ENST00000368166;ENST00000368160;ENST00000368156	T;T;T;T;T;T;T;T	0.02863	4.13;4.13;4.13;4.13;4.13;4.13;4.13;4.13	4.38	4.38	0.52667	Immunoglobulin-like (1);MHC class I-like antigen recognition (1);Immunoglobulin C1-set (2);	0.588914	0.14197	N	0.334970	T	0.05364	0.0142	L	0.60012	1.86	0.09310	N	1	P;D;D;P;P;D;P;P;P;B;D	0.61697	0.917;0.985;0.985;0.91;0.657;0.981;0.89;0.798;0.91;0.405;0.99	P;P;P;P;P;P;P;P;P;B;P	0.62885	0.908;0.841;0.841;0.688;0.688;0.851;0.456;0.561;0.688;0.357;0.851	T	0.15009	-1.0452	10	0.72032	D	0.01	-5.0189	12.3045	0.54893	0.0:0.0:1.0:0.0	.	82;172;269;271;172;181;82;271;271;82;181	B4E057;B4E042;E7ET31;A2RRL5;E7EP01;P15812-5;P15812-9;P15812-2;P15812;P15812-8;P15812-6	.;.;.;.;.;.;.;.;CD1E_HUMAN;.;.	T	269;172;271;82;181;82;271;181	ENSP00000401957:A269T;ENSP00000402906:A172T;ENSP00000357149:A271T;ENSP00000416228:A82T;ENSP00000357147:A181T;ENSP00000357148:A82T;ENSP00000357142:A271T;ENSP00000357138:A181T	ENSP00000357138:A181T	A	+	1	0	CD1E	156592426	0.045000	0.20229	0.006000	0.13384	0.565000	0.35776	2.831000	0.48144	2.277000	0.76020	0.563000	0.77884	GCA	.	.		0.607	CD1E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046353.3	NM_030893		A	158325802	G	A	158325802	3	1	274	1	0	0	0	0	1	0	0	0	2980	971	34	3	825	3	CD1E	1	158325802	Missense_Mutation	SNP	G	TCGA-G3-A25U-01A-11D-A16V-10		158325802	90924819	1	39543										
NPHP1	4867	hgsc.bcm.edu	37	chr2	110959033	110959033	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgtcttttattgggttctagAgcttctttcagttggctctc	9	8	5	1			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr2:110959033A>G	ENST00000393272.3	-	2	205	c.108T>C	c.(106-108)gcT>gcC	p.A36A	NPHP1_ENST00000355301.4_Silent_p.A36A|NPHP1_ENST00000417665.1_Silent_p.A36A|NPHP1_ENST00000316534.4_Silent_p.A36A|NPHP1_ENST00000418527.1_Silent_p.A36A|NPHP1_ENST00000445609.2_Silent_p.A36A	NM_000272.3|NM_207181.2	NP_000263.2|NP_997064.2	O15259	NPHP1_HUMAN	nephronophthisis 1 (juvenile)	36					actin cytoskeleton organization (GO:0030036)|cell projection organization (GO:0030030)|cellular protein localization (GO:0034613)|excretion (GO:0007588)|photoreceptor cell outer segment organization (GO:0035845)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|spermatid differentiation (GO:0048515)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|motile cilium (GO:0031514)|photoreceptor connecting cilium (GO:0032391)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(2)	24						TGGGTTCTAGAGCTTCTTTCA	0.313																																					p.A36A		Atlas-SNP	.											.	NPHP1	68	.	0			c.T108C						.						123	114	117					2																	110959033		2203	4300	6503	SO:0001819	synonymous_variant	4867	exon2			TTCTAGAGCTTCT	AF023674	CCDS2086.1, CCDS46384.1, CCDS46385.1, CCDS46386.1	2q13	2014-01-28			ENSG00000144061	ENSG00000144061			7905	protein-coding gene	gene with protein product	"nephrocystin-1"	607100		NPH1			Standard	NM_000272		Approved	JBTS4, SLSN1	uc002tfm.4	O15259	OTTHUMG00000131195	ENST00000393272.3:c.108T>C	chr2.hg19:g.110959033A>G		68.0	0.0		93.0	42.0	NM_207181	O14837	Silent	SNP	ENST00000393272.3	hg19	CCDS46385.1																																																																																			.	.		0.313	NPHP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253919.3	NM_000272		G	110959033	A	G	110959033	2	3	274	1	0	0	0	0	0	0	0	1	10588	291	11	2		2	NPHP1	2	110959033	Silent	SNP	A	TCGA-G3-A25U-01A-11D-A16V-10		110959033	132240340	2	39544										
ERBB4	2066	hgsc.bcm.edu	37	chr2	212615384	212615384	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aagtctggcaatgattttctGtgggtccccagcaacggcca	11	11	2	1			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr2:212615384G>T	ENST00000342788.4	-	5	912	c.602C>A	c.(601-603)aCa>aAa	p.T201K	ERBB4_ENST00000436443.1_Missense_Mutation_p.T201K|ERBB4_ENST00000402597.1_Missense_Mutation_p.T201K|ERBB4_ENST00000484474.1_5'UTR	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	201	Cys-rich.				cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.T201K(1)		NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	ATGATTTTCTGTGGGTCCCCA	0.458										TSP Lung(8;0.080)																											p.T201K		Atlas-SNP	.											ERBB4,NS,carcinoma,0,1	ERBB4	480	.	1	Substitution - Missense(1)	endometrium(1)	c.C602A						.						136	113	121					2																	212615384		2203	4300	6503	SO:0001583	missense	2066	exon5			TTTTCTGTGGGTC	L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.602C>A	chr2.hg19:g.212615384G>T	ENSP00000342235:p.Thr201Lys	32.0	0.0		51.0	24.0	NM_001042599	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	hg19	CCDS2394.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.73|17.73	3.462532|3.462532	0.63513|0.63513	.|.	.|.	ENSG00000178568|ENSG00000178568	ENST00000260943|ENST00000342788;ENST00000436443;ENST00000402597	.|D;D;D	.|0.82081	.|-1.57;-1.57;-1.57	5.58|5.58	5.58|5.58	0.84498|0.84498	.|Growth factor, receptor (1);Furin-like cysteine-rich domain (1);	.|0.211367	.|0.49916	.|D	.|0.000132	T|T	0.69557|0.69557	0.3124|0.3124	N|N	0.08118|0.08118	0|0	0.43559|0.43559	D|D	0.995878|0.995878	.|B;B;B;B;B	.|0.06786	.|0.0;0.001;0.0;0.0;0.0	.|B;B;B;B;B	.|0.09377	.|0.001;0.004;0.001;0.001;0.0	T|T	0.64041|0.64041	-0.6500|-0.6500	5|9	.|.	.|.	.|.	.|.	19.6257|19.6257	0.95677|0.95677	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|201;201;60;201;201	.|Q15303-4;Q15303-2;Q53QS8;Q15303-3;Q15303	.|.;.;.;.;ERBB4_HUMAN	K|K	201|201	.|ENSP00000342235:T201K;ENSP00000403204:T201K;ENSP00000385565:T201K	.|.	Q|T	-|-	1|2	0|0	ERBB4|ERBB4	212323629|212323629	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.980000|0.980000	0.70556|0.70556	5.303000|5.303000	0.65738|0.65738	2.625000|2.625000	0.88918|0.88918	0.650000|0.650000	0.86243|0.86243	CAG|ACA	.	.		0.458	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		T	212615384	G	T	212615384	3	4	274	1	0	0	0	0	1	0	0	0	5211	1377	48	3	3420	3	ERBB4	2	212615384	Missense_Mutation	SNP	G	TCGA-G3-A25U-01A-11D-A16V-10	101656351	212615384	30583989	3	39545										
SATB1	6304	hgsc.bcm.edu	37	chr3	18456693	18456693	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctcactgtggtgtgcgaccaTtgttcgggaggcaagtcttc	13	10	2	0	rs61733671		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr3:18456693T>C	ENST00000338745.6	-	5	2283	c.549A>G	c.(547-549)caA>caG	p.Q183Q	TBC1D5_ENST00000414318.2_Intron|SATB1_ENST00000454909.2_Silent_p.Q183Q|SATB1_ENST00000475083.1_5'UTR|SATB1_ENST00000417717.2_Silent_p.Q183Q	NM_002971.4	NP_002962.1	Q01826	SATB1_HUMAN	SATB homeobox 1	183	PDZ-like dimerization domain.				activated T cell proliferation (GO:0050798)|apoptotic process (GO:0006915)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|epidermis development (GO:0008544)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|reflex (GO:0060004)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(2)|endometrium(6)|large_intestine(4)|lung(10)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	32						TGTGCGACCATTGTTCGGGAG	0.448																																					p.Q183Q		Atlas-SNP	.											.	SATB1	96	.	0			c.A549G						.						114	103	107					3																	18456693		2203	4300	6503	SO:0001819	synonymous_variant	6304	exon5			CGACCATTGTTCG		CCDS2631.1, CCDS56242.1	3p24.3	2011-07-19	2007-02-15		ENSG00000182568	ENSG00000182568		"Homeoboxes / CUT class"	10541	protein-coding gene	gene with protein product		602075	"special AT-rich sequence binding protein 1 (binds to nuclear matrix/scaffold-associating DNA)"			1505028	Standard	NM_002971		Approved		uc003cbj.3	Q01826	OTTHUMG00000129890	ENST00000338745.6:c.549A>G	chr3.hg19:g.18456693T>C		104.0	0.0		105.0	41.0	NM_002971	B3KXF1|C9JTR6|Q59EQ0	Silent	SNP	ENST00000338745.6	hg19	CCDS2631.1																																																																																			.	T|0.987;C|0.013		0.448	SATB1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252138.4	NM_001131010		C	18456693	T	C	18456693	2	2	274	1	0	0	0	0	0	0	0	1	13868	1490	52	2		2	SATB1	3	18456693	Silent	SNP	T	TCGA-G3-A25U-01A-11D-A16V-10		18456693	179565737	4	39546										
NISCH	11188	hgsc.bcm.edu	37	chr3	52513791	52513791	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctggatgacacagtgaccacAgagaaggagctggacactgt	13	9	0	3			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr3:52513791A>G	ENST00000479054.1	+	13	1401	c.1329A>G	c.(1327-1329)acA>acG	p.T443T	NISCH_ENST00000488380.1_Silent_p.T443T|NISCH_ENST00000345716.4_Silent_p.T443T|NISCH_ENST00000420808.2_Silent_p.T443T			Q9Y2I1	NISCH_HUMAN	nischarin	443	Interaction with PAK1. {ECO:0000250}.|Necessary for homooligomerization and targeting to endosomes.				actin cytoskeleton organization (GO:0030036)|apoptotic process (GO:0006915)|glucose metabolic process (GO:0006006)|negative regulation of cell migration (GO:0030336)|norepinephrine secretion (GO:0048243)|Rac protein signal transduction (GO:0016601)|regulation of blood pressure (GO:0008217)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)|plasma membrane (GO:0005886)	G-protein coupled amine receptor activity (GO:0008227)|identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)			NS(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(9)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	33				BRCA - Breast invasive adenocarcinoma(193;1.93e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)|OV - Ovarian serous cystadenocarcinoma(275;0.0577)	Tizanidine(DB00697)	CAGTGACCACAGAGAAGGAGC	0.512																																					p.T443T		Atlas-SNP	.											.	NISCH	97	.	0			c.A1329G						.						84	66	72					3																	52513791		2203	4300	6503	SO:0001819	synonymous_variant	11188	exon12			GACCACAGAGAAG	AF082516	CCDS33767.1, CCDS63651.1, CCDS63652.1	3p21.1	2008-07-18			ENSG00000010322	ENSG00000010322			18006	protein-coding gene	gene with protein product	"imidazoline receptor candidate", "I-1 receptor candidate protein", "imidazoline receptor antisera selected"	615507				11912194, 10882231	Standard	NM_007184		Approved	KIAA0975, I-1, IRAS	uc003ded.4	Q9Y2I1	OTTHUMG00000158571	ENST00000479054.1:c.1329A>G	chr3.hg19:g.52513791A>G		74.0	0.0		91.0	42.0	NM_001276293	C9J245|Q6PGP3|Q6PIB4|Q7L8M3|Q7Z2X6|Q9UES6|Q9UEU4|Q9UFW3	Silent	SNP	ENST00000479054.1	hg19	CCDS33767.1																																																																																			.	.		0.512	NISCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351357.1	NM_007184		G	52513791	A	G	52513791	2	3	274	1	0	0	0	0	0	0	0	1	10441	175	7	2		2	NISCH	3	52513791	Silent	SNP	A	TCGA-G3-A25U-01A-11D-A16V-10	34057098	52513791	145508639	5	39547										
PTPRG	5793	hgsc.bcm.edu	37	chr3	61975392	61975392	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tttagaccagtatgcgcgtgTtggggaagaataccaggaac	13	7	0	2			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr3:61975392T>C	ENST00000474889.1	+	3	661	c.284T>C	c.(283-285)gTt>gCt	p.V95A	PTPRG_ENST00000295874.10_Missense_Mutation_p.V95A	NM_002841.3	NP_002832.3	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	95	Alpha-carbonic anhydrase.				brain development (GO:0007420)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of neuron projection development (GO:0010977)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|liver(2)|lung(15)|ovary(7)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	62				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		TATGCGCGTGTTGGGGAAGAA	0.493																																					p.V95A		Atlas-SNP	.											.	PTPRG	153	.	0			c.T284C						.						119	109	112					3																	61975392		2203	4300	6503	SO:0001583	missense	5793	exon3			CGCGTGTTGGGGA	L09247	CCDS2895.1	3p21-p14	2013-02-11			ENSG00000144724	ENSG00000144724		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9671	protein-coding gene	gene with protein product		176886		PTPG		1711217	Standard	NM_002841		Approved	RPTPG	uc003dlb.3	P23470	OTTHUMG00000158660	ENST00000474889.1:c.284T>C	chr3.hg19:g.61975392T>C	ENSP00000418112:p.Val95Ala	81.0	0.0		88.0	37.0	NM_002841	B2RU12|B7ZLX5|Q15623|Q59EE0|Q68DU5	Missense_Mutation	SNP	ENST00000474889.1	hg19	CCDS2895.1	.	.	.	.	.	.	.	.	.	.	T	18.83	3.707702	0.68615	.	.	ENSG00000144724	ENST00000474889;ENST00000295874	T;T	0.67171	-0.25;-0.25	5.92	5.92	0.95590	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.359047	0.29300	N	0.012560	T	0.66934	0.2840	L	0.52011	1.625	0.52501	D	0.999954	P;P	0.44429	0.835;0.517	B;B	0.43889	0.435;0.226	T	0.71237	-0.4652	10	0.87932	D	0	.	16.3413	0.83082	0.0:0.0:0.0:1.0	.	95;95	P23470-2;P23470	.;PTPRG_HUMAN	A	95	ENSP00000418112:V95A;ENSP00000295874:V95A	ENSP00000295874:V95A	V	+	2	0	PTPRG	61950432	1.000000	0.71417	0.107000	0.21349	0.943000	0.58893	7.642000	0.83385	2.257000	0.74773	0.533000	0.62120	GTT	.	.		0.493	PTPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351674.1	NM_002841		C	61975392	T	C	61975392	3	2	274	1	0	0	0	0	1	0	0	0	12817	1725	60	2	294	2	PTPRG	3	61975392	Missense_Mutation	SNP	T	TCGA-G3-A25U-01A-11D-A16V-10	9461601	61975392	136047038	6	39548										
CEP70	80321	hgsc.bcm.edu	37	chr3	138219253	138219253	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtcatcacctaattctaagaGttcttggaggtttctcacag	8	9	5	1			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr3:138219253G>A	ENST00000264982.3	-	15	1791	c.1525C>T	c.(1525-1527)Ctc>Ttc	p.L509F	CEP70_ENST00000542237.1_Missense_Mutation_p.L489F|CEP70_ENST00000489254.1_Missense_Mutation_p.L357F|CEP70_ENST00000481834.1_Missense_Mutation_p.L509F|CEP70_ENST00000484888.1_Missense_Mutation_p.L509F	NM_024491.2	NP_077817.2	Q8NHQ1	CEP70_HUMAN	centrosomal protein 70kDa	509					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	24						AATTCTAAGAGTTCTTGGAGG	0.318																																					p.L509F		Atlas-SNP	.											.	CEP70	51	.	0			c.C1525T						.						100	112	108					3																	138219253		2203	4300	6503	SO:0001583	missense	80321	exon15			CTAAGAGTTCTTG	AF202146	CCDS3102.1, CCDS75022.1, CCDS75023.1, CCDS75024.1	3q22.3	2014-02-20			ENSG00000114107	ENSG00000114107			29972	protein-coding gene	gene with protein product		614310				14654843	Standard	XM_005247802		Approved	BITE, FLJ13036	uc003esl.3	Q8NHQ1	OTTHUMG00000159891	ENST00000264982.3:c.1525C>T	chr3.hg19:g.138219253G>A	ENSP00000264982:p.Leu509Phe	120.0	0.0		196.0	76.0	NM_024491	B7Z5I8|B7Z7E8|D3DNE9|F5GZX8|Q96B31|Q9H2C3|Q9H2Z1|Q9H940	Missense_Mutation	SNP	ENST00000264982.3	hg19	CCDS3102.1	.	.	.	.	.	.	.	.	.	.	G	16.36	3.100107	0.56183	.	.	ENSG00000114107	ENST00000264982;ENST00000542237;ENST00000489254;ENST00000484888;ENST00000474781;ENST00000481834	T;T;T;T;T;T	0.28255	1.62;1.62;1.62;1.62;1.62;1.62	4.88	3.93	0.45458	Tetratricopeptide repeat-containing (1);	0.326421	0.29838	N	0.011079	T	0.50103	0.1596	M	0.66939	2.045	0.42564	D	0.993153	D;P;D;P	0.69078	0.96;0.904;0.997;0.904	P;P;D;P	0.68192	0.663;0.625;0.956;0.625	T	0.52866	-0.8518	10	0.72032	D	0.01	-0.9042	12.1533	0.54062	0.0:0.0:0.8187:0.1813	.	357;489;509;509	B7Z2D2;F5GZX8;Q8NHQ1-2;Q8NHQ1	.;.;.;CEP70_HUMAN	F	509;489;357;509;491;509	ENSP00000264982:L509F;ENSP00000444128:L489F;ENSP00000417821:L357F;ENSP00000419231:L509F;ENSP00000419833:L491F;ENSP00000417465:L509F	ENSP00000264982:L509F	L	-	1	0	CEP70	139701943	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.310000	0.43708	2.552000	0.86080	0.655000	0.94253	CTC	.	.		0.318	CEP70-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000358001.1	NM_024491		A	138219253	G	A	138219253	3	1	274	1	0	0	0	0	1	0	0	0	3261	1029	36	3	284	3	CEP70	3	138219253	Missense_Mutation	SNP	G	TCGA-G3-A25U-01A-11D-A16V-10	76243861	138219253	59803177	7	39549										
TFDP2	7029	hgsc.bcm.edu	37	chr3	141678612	141678613	+	Nonsense_Mutation	DNP	CC	CC	AA													0	0	1	0	0	0	1	1	0	ctccaggccaaacgacattcCcatccgctttagtacttcta							TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr3:141678612_141678613CC>AA	ENST00000489671.1	-	11	1384_1385	c.954_955GG>TT	c.(952-957)atGGga>atTTga	p.318_319MG>I*	TFDP2_ENST00000310282.6_Nonsense_Mutation_p.258_259MG>I*|TFDP2_ENST00000397991.4_Nonsense_Mutation_p.290_291MG>I*|TFDP2_ENST00000479040.1_Nonsense_Mutation_p.257_258MG>I*|TFDP2_ENST00000499676.2_Nonsense_Mutation_p.258_259MG>I*|TFDP2_ENST00000495310.1_Nonsense_Mutation_p.221_222MG>I*|TFDP2_ENST00000317104.7_Nonsense_Mutation_p.242_243MG>I*|TFDP2_ENST00000486111.1_Nonsense_Mutation_p.258_259MG>I*|TFDP2_ENST00000477292.1_Nonsense_Mutation_p.182_183MG>I*|TFDP2_ENST00000467072.1_Nonsense_Mutation_p.258_259MG>I*			Q14188	TFDP2_HUMAN	transcription factor Dp-2 (E2F dimerization partner 2)	318	DCB2.				gene expression (GO:0010467)|heart development (GO:0007507)|mitotic cell cycle (GO:0000278)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			kidney(1)|upper_aerodigestive_tract(2)	3						AACGACATTCCCATCCGCTTTA	0.421																																					p.G319X|p.M318I		Atlas-SNP	.											.	TFDP2	44	.	0			c.G955T|c.G954T						.																																			SO:0001587	stop_gained	7029	exon11			ACATTCCCATCCG|CATTCCCATCCGC	U18422	CCDS43159.1, CCDS54647.1, CCDS54648.1, CCDS54649.1, CCDS54650.1	3q23	2011-05-24			ENSG00000114126	ENSG00000114126			11751	protein-coding gene	gene with protein product		602160				7784053, 9027491	Standard	NM_001178138		Approved	Dp-2	uc003eun.4	Q14188	OTTHUMG00000164975	ENST00000489671.1:c.954_955delinsAA	chr3.hg19:g.141678612_141678613delinsAA	ENSP00000420616:p.M318_G319delinsI*	68.0|71.0	0.0		60.0	26.0|28.0	NM_001178139	B7Z8C8|B7Z8L5|D3DNG1|E9PFC3|F8WAI2|Q13331|Q14187|Q6R754|Q8WU88|Q9UG28	Nonsense_Mutation|Missense_Mutation	SNP	ENST00000489671.1	hg19	CCDS54650.1																																																																																			.	.		0.421	TFDP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353294.4	NM_006286		AA	141678613	CC	AA	141678612	4	1	274	1	0	0	0	0	0	1	0	0	15813	632	22	3	397	3	TFDP2	3	141678612	Nonsense_Mutation	DNP	CC	TCGA-G3-A25U-01A-11D-A16V-10	3459359	141678612	56343818	8	39550										
SUCNR1	56670	hgsc.bcm.edu	37	chr3	151598552	151598552	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctctgacttagcttttctgtGcaccctccccatgctgataa	6	14	2	2			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr3:151598552G>T	ENST00000362032.5	+	3	326	c.221G>T	c.(220-222)tGc>tTc	p.C74F	RP11-454C18.2_ENST00000483843.2_RNA|RP11-454C18.2_ENST00000475855.1_RNA	NM_033050.4	NP_149039.2	Q9BXA5	SUCR1_HUMAN	succinate receptor 1	74						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	14			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)		Succinic acid(DB00139)	GCTTTTCTGTGCACCCTCCCC	0.423																																					p.C74F		Atlas-SNP	.											.	SUCNR1	31	.	0			c.G221T						.						152	149	150					3																	151598552		2203	4300	6503	SO:0001583	missense	56670	exon3			TTCTGTGCACCCT	AF348078	CCDS3162.1	3q25.1	2012-08-21	2004-07-08	2004-07-09	ENSG00000198829	ENSG00000198829		"GPCR / Class A : Orphans"	4542	protein-coding gene	gene with protein product		606381	"G protein-coupled receptor 91"	GPR91		11273702, 15141213, 17192395	Standard	NM_033050		Approved		uc003ezf.2	Q9BXA5	OTTHUMG00000159880	ENST00000362032.5:c.221G>T	chr3.hg19:g.151598552G>T	ENSP00000355156:p.Cys74Phe	142.0	0.0		162.0	59.0	NM_033050	A8K305|Q8TDQ8	Missense_Mutation	SNP	ENST00000362032.5	hg19	CCDS3162.1	.	.	.	.	.	.	.	.	.	.	G	11.32	1.603049	0.28534	.	.	ENSG00000198829	ENST00000362032	T	0.35789	1.29	5.26	5.26	0.73747	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.50548	0.1622	L	0.33624	1.015	0.47441	D	0.999423	D	0.76494	0.999	D	0.79784	0.993	T	0.39603	-0.9606	10	0.34782	T	0.22	.	19.2413	0.93886	0.0:0.0:1.0:0.0	.	74	Q9BXA5	SUCR1_HUMAN	F	74	ENSP00000355156:C74F	ENSP00000355156:C74F	C	+	2	0	SUCNR1	153081242	1.000000	0.71417	0.999000	0.59377	0.058000	0.15608	4.301000	0.59086	2.625000	0.88918	0.655000	0.94253	TGC	.	.		0.423	SUCNR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357897.2	NM_033050		T	151598552	G	T	151598552	3	4	274	1	0	0	0	0	1	0	0	0	15381	1319	46	3	227	3	SUCNR1	3	151598552	Missense_Mutation	SNP	G	TCGA-G3-A25U-01A-11D-A16V-10	9919940	151598552	46423878	9	39551										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178916692	178916692	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tcctagtagaatgtttactaCcaaatggaatgatagtgact	8	6	0	3			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr3:178916692C>A	ENST00000263967.3	+	2	236	c.79C>A	c.(79-81)Cca>Aca	p.P27T		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	27	PI3K-ABD. {ECO:0000255|PROSITE- ProRule:PRU00877}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	ATGTTTACTACCAAATGGAAT	0.413		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											p.P27T	Colon(199;1504 1750 3362 26421 31210 32040)	Atlas-SNP	.		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	.	PIK3CA	8460	.	0			c.C79A						.						67	66	66					3																	178916692		1853	4089	5942	SO:0001583	missense	5290	exon2			TTACTACCAAATG		CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.79C>A	chr3.hg19:g.178916692C>A	ENSP00000263967:p.Pro27Thr	74.0	0.0		80.0	38.0	NM_006218	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	hg19	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.364380	0.82463	.	.	ENSG00000121879	ENST00000263967;ENST00000468036	D;D	0.91740	-1.97;-2.9	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	D	0.96516	0.8863	M	0.84683	2.71	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96326	0.9240	9	.	.	.	-18.5061	19.267	0.93990	0.0:1.0:0.0:0.0	.	27	P42336	PK3CA_HUMAN	T	27	ENSP00000263967:P27T;ENSP00000417479:P27T	.	P	+	1	0	PIK3CA	180399386	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.394000	0.79862	2.616000	0.88540	0.650000	0.86243	CCA	.	.		0.413	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			A	178916692	C	A	178916692	3	1	274	1	0	0	0	0	1	0	0	0	11922	507	18	3	81	3	PIK3CA	3	178916692	Missense_Mutation	SNP	C	TCGA-G3-A25U-01A-11D-A16V-10	27318140	178916692	19105738	10	39552										
SHROOM3	57619	hgsc.bcm.edu	37	chr4	77357245	77357245	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	acttccacaagcctagtgccAcattaaactctaacacggcc	5	15	1	0			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr4:77357245A>G	ENST00000296043.6	+	1	993	c.40A>G	c.(40-42)Aca>Gca	p.T14A		NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	14					actin cytoskeleton organization (GO:0030036)|apical protein localization (GO:0045176)|cell morphogenesis (GO:0000902)|cellular pigment accumulation (GO:0043482)|columnar/cuboidal epithelial cell development (GO:0002066)|neural tube closure (GO:0001843)|pattern specification process (GO:0007389)|regulation of cell shape (GO:0008360)	adherens junction (GO:0005912)|apical junction complex (GO:0043296)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)				NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(29)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	60			Lung(101;0.0903)			GCCTAGTGCCACATTAAACTC	0.483																																					p.T14A		Atlas-SNP	.											.	SHROOM3	134	.	0			c.A40G						.						174	167	170					4																	77357245		2203	4300	6503	SO:0001583	missense	57619	exon1			AGTGCCACATTAA	AB055660	CCDS3579.2	4q21.1	2009-11-25			ENSG00000138771	ENSG00000138771			30422	protein-coding gene	gene with protein product		604570				10589677, 16615870	Standard	NM_020859		Approved	ShrmL, SHRM, KIAA1481, APXL3	uc011cbx.2	Q8TF72	OTTHUMG00000157075	ENST00000296043.6:c.40A>G	chr4.hg19:g.77357245A>G	ENSP00000296043:p.Thr14Ala	109.0	0.0		88.0	42.0	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Missense_Mutation	SNP	ENST00000296043.6	hg19	CCDS3579.2	.	.	.	.	.	.	.	.	.	.	A	15.25	2.778445	0.49786	.	.	ENSG00000138771	ENST00000296043	T	0.19532	2.14	5.12	-1.69	0.08186	.	1.822020	0.02688	N	0.110299	T	0.11239	0.0274	N	0.16478	0.41	0.09310	N	1	B	0.21452	0.056	B	0.12156	0.007	T	0.21449	-1.0245	10	0.41790	T	0.15	-1.3602	0.3518	0.00350	0.307:0.1287:0.2417:0.3227	.	14	Q8TF72	SHRM3_HUMAN	A	14	ENSP00000296043:T14A	ENSP00000296043:T14A	T	+	1	0	SHROOM3	77576269	0.009000	0.17119	0.182000	0.23118	0.004000	0.04260	-0.211000	0.09332	-0.122000	0.11766	-0.334000	0.08254	ACA	.	.		0.483	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859		G	77357245	A	G	77357245	3	3	274	1	0	0	0	0	1	0	0	0	14310	159	6	2	42	2	SHROOM3	4	77357245	Missense_Mutation	SNP	A	TCGA-G3-A25U-01A-11D-A16V-10		77357245	113797031	11	39553										
SDHA	6389	hgsc.bcm.edu	37	chr5	240575	240575	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cataagaacatcggaactgcGactcagcatgcagaaggtaa	10	9	1	2	rs192818312		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr5:240575G>T	ENST00000264932.6	+	11	1650	c.1535G>T	c.(1534-1536)cGa>cTa	p.R512L	SDHA_ENST00000510361.1_Missense_Mutation_p.R464L|SDHA_ENST00000504309.1_Missense_Mutation_p.R512L	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	512					cellular metabolic process (GO:0044237)|nervous system development (GO:0007399)|oxidation-reduction process (GO:0055114)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|tricarboxylic acid cycle (GO:0006099)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex II (GO:0005749)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|succinate dehydrogenase (ubiquinone) activity (GO:0008177)			NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|liver(2)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	40			Epithelial(17;0.0159)|all cancers(22;0.0236)|OV - Ovarian serous cystadenocarcinoma(19;0.0674)|Lung(60;0.113)		Succinic acid(DB00139)	TCGGAACTGCGACTCAGCATG	0.458									Familial Paragangliomas																												p.R512L		Atlas-SNP	.											.	SDHA	80	.	0			c.G1535T						.						46	51	50					5																	240575		2202	4299	6501	SO:0001583	missense	6389	exon11	Familial Cancer Database	Hereditary Glomus Tumors, Familial Paragangliomas, Hereditary Paragangliomas, type 1-3: PGL1, PGL2, PGL3, incl. Familial Carotid Body Paraganglioma and Sensorineural Hearing Loss	AACTGCGACTCAG	BC001380	CCDS3853.1	5p15	2014-09-17			ENSG00000073578	ENSG00000073578		"Mitochondrial respiratory chain complex / Complex II"	10680	protein-coding gene	gene with protein product		600857		SDH2		7798181	Standard	XM_005248329		Approved	FP, SDHF	uc003jao.4	P31040	OTTHUMG00000090275	ENST00000264932.6:c.1535G>T	chr5.hg19:g.240575G>T	ENSP00000264932:p.Arg512Leu	176.0	0.0		157.0	67.0	NM_004168	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Missense_Mutation	SNP	ENST00000264932.6	hg19	CCDS3853.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	N|N	18.62|18.62	3.662639|3.662639	0.67700|0.67700	.|.	.|.	ENSG00000073578|ENSG00000073578	ENST00000515815|ENST00000264932;ENST00000327872;ENST00000504309;ENST00000510361	.|D;T;D	.|0.83250	.|-1.7;-0.15;-1.7	4.95|4.95	4.95|4.95	0.65309|0.65309	.|Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal (2);Fumarate reductase/succinate dehydrogenase flavoprotein, C-terminal (1);	.|0.000000	.|0.85682	.|U	.|0.000000	D|D	0.93903|0.93903	0.8049|0.8049	H|H	0.96048|0.96048	3.76|3.76	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D	.|0.89917	.|1.0;0.998;1.0;1.0;1.0	.|D;D;D;D;D	.|0.97110	.|0.998;0.97;1.0;0.985;0.991	D|D	0.95671|0.95671	0.8723|0.8723	5|10	.|0.87932	.|D	.|0	.|.	16.0271|16.0271	0.80551|0.80551	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|464;512;106;512;512	.|E9PBJ5;B4DYN5;B3KYA5;D6RFM5;P31040	.|.;.;.;.;DHSA_HUMAN	Y|L	64|512;367;512;464	.|ENSP00000264932:R512L;ENSP00000426514:R512L;ENSP00000427703:R464L	.|ENSP00000264932:R512L	D|R	+|+	1|2	0|0	SDHA|SDHA	293575|293575	1.000000|1.000000	0.71417|0.71417	0.446000|0.446000	0.26920|0.26920	0.521000|0.521000	0.34408|0.34408	9.240000|9.240000	0.95396|0.95396	2.442000|2.442000	0.82660|0.82660	0.650000|0.650000	0.86243|0.86243	GAC|CGA	.	G|0.999;A|0.001		0.458	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168		T	240575	G	T	240575	3	4	274	1	0	0	0	0	1	0	0	0	13978	1058	37	1	1577	1	SDHA	5	240575	Missense_Mutation	SNP	G	TCGA-G3-A25U-01A-11D-A16V-10		240575	180674685	12	39554										
TNPO1	3842	hgsc.bcm.edu	37	chr5	72189531	72189532	+	Splice_Site	INS	-	-	T													0	0	1	0	0	0	1	1	0	catgttaagccttgtataggINStatgaatattttctactgct							TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr5:72189531_72189532insT	ENST00000337273.5	+	18	2569		c.e18+1		TNPO1_ENST00000506351.2_Splice_Site|TNPO1_ENST00000454282.1_Splice_Site|TNPO1_ENST00000523768.1_Splice_Site	NM_002270.3	NP_002261.3	Q92973	TNPO1_HUMAN	transportin 1						gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|protein import into nucleus, translocation (GO:0000060)|RNA metabolic process (GO:0016070)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(6)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	36		Lung NSC(167;0.0053)|Ovarian(174;0.0175)		OV - Ovarian serous cystadenocarcinoma(47;6.14e-54)		CCTTGTATAGGTATGAATATTT	0.327																																					.		Atlas-INDEL	.											.	TNPO1	90	.	0			c.2143+1->T						.																																			SO:0001630	splice_region_variant	3842	exon18			.	U70322	CCDS4016.1, CCDS43329.1	5q13.1	2009-01-12	2004-01-29	2004-01-30	ENSG00000083312	ENSG00000083312		"Importins"	6401	protein-coding gene	gene with protein product	"importin 2"	602901	"karyopherin (importin) beta 2"	KPNB2		8808633, 9144189	Standard	NM_153188		Approved	MIP, TRN, IPO2, MIP1	uc003kci.4	Q92973	OTTHUMG00000100967	ENST00000337273.5:c.2143+1->T	chr5.hg19:g.72189532_72189532dupT		81.0	0.0		74.0	35.0	NM_002270	B4DVC6|Q92957|Q92975	Splice_Site	INS	ENST00000337273.5	hg19	CCDS43329.1																																																																																			.	.		0.327	TNPO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000218577.3	NM_002270	Intron	T	72189532	-	T	72189531	8	5	274	1	0	1	1	0	0	0	1	0	16350	1275	44	0	2214	0	TNPO1	5	72189531	Splice_Site	INS	-	TCGA-G3-A25U-01A-11D-A16V-10	71948956	72189531	108725729	13	39555										
GABRB2	2561	hgsc.bcm.edu	37	chr5	160972296	160972296	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttcatccccacagccacgggGggacctgcaaagcaagacgg	12	14	1	1			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr5:160972296G>A	ENST00000393959.1	-	3	173	c.174C>T	c.(172-174)ccC>ccT	p.P58P	GABRB2_ENST00000517901.1_5'UTR|GABRB2_ENST00000517547.1_5'UTR|GABRB2_ENST00000523730.1_5'Flank|GABRB2_ENST00000353437.6_Silent_p.P58P|GABRB2_ENST00000274547.2_Silent_p.P58P|GABRB2_ENST00000520240.1_Silent_p.P58P			P47870	GBRB2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 2	58					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|GABA-A receptor activity (GO:0004890)|inhibitory extracellular ligand-gated ion channel activity (GO:0005237)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(9)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	26	Renal(175;0.00259)	Medulloblastoma(196;0.021)|all_neural(177;0.0463)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CAGCCACGGGGGGACCTGCAA	0.453																																					p.P58P		Atlas-SNP	.											.	GABRB2	161	.	0			c.C174T						.						55	49	51					5																	160972296		2203	4300	6503	SO:0001819	synonymous_variant	2561	exon4			CACGGGGGGACCT		CCDS4354.1, CCDS4355.1	5q34	2012-06-22			ENSG00000145864	ENSG00000145864		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4082	protein-coding gene	gene with protein product	"GABA(A) receptor, beta 2"	600232				7851879	Standard	NM_000813		Approved		uc003lys.1	P47870	OTTHUMG00000130349	ENST00000393959.1:c.174C>T	chr5.hg19:g.160972296G>A		53.0	0.0		60.0	26.0	NM_021911	A8K115|A8K1A0|D1LYT0|D1LYT1|Q16323|Q4FZB2	Silent	SNP	ENST00000393959.1	hg19	CCDS4355.1																																																																																			.	.		0.453	GABRB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252704.1			A	160972296	G	A	160972296	2	1	274	1	0	0	0	0	0	0	0	1	6175	1219	43	3		3	GABRB2	5	160972296	Silent	SNP	G	TCGA-G3-A25U-01A-11D-A16V-10	88782765	160972296	19942964	14	39556										
CAP2	10486	hgsc.bcm.edu	37	chr6	17463259	17463259	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cacagtgctttccaggcccaGcgggctttccttctgatggc	11	14	1	1			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr6:17463259G>A	ENST00000229922.2	+	4	787	c.255G>A	c.(253-255)caG>caA	p.Q85Q	CAP2_ENST00000489374.1_Silent_p.Q85Q|CAP2_ENST00000493172.1_Intron|CAP2_ENST00000465994.1_Silent_p.Q85Q|CAP2_ENST00000378990.2_Intron	NM_006366.2	NP_006357.1	P40123	CAP2_HUMAN	CAP, adenylate cyclase-associated protein, 2 (yeast)	85					activation of adenylate cyclase activity (GO:0007190)|axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|establishment or maintenance of cell polarity (GO:0007163)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)				breast(3)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(4)|urinary_tract(1)	27	Breast(50;0.0333)|Ovarian(93;0.0386)	all_hematologic(90;0.0466)	all cancers(50;0.194)|Epithelial(50;0.227)			TCCAGGCCCAGCGGGCTTTCC	0.502																																					p.Q85Q		Atlas-SNP	.											.	CAP2	61	.	0			c.G255A						.						90	82	84					6																	17463259		2203	4300	6503	SO:0001819	synonymous_variant	10486	exon4			GGCCCAGCGGGCT	BC008481	CCDS4539.1	6p22.3	2008-02-05			ENSG00000112186	ENSG00000112186			20039	protein-coding gene	gene with protein product						7962207, 8761950	Standard	NM_006366		Approved		uc003ncb.3	P40123	OTTHUMG00000014311	ENST00000229922.2:c.255G>A	chr6.hg19:g.17463259G>A		49.0	0.0		64.0	34.0	NM_006366	B2R5Y3|B7Z1C4|B7Z214|Q6IAY2	Silent	SNP	ENST00000229922.2	hg19	CCDS4539.1																																																																																			.	.		0.502	CAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039952.2			A	17463259	G	A	17463259	2	1	274	1	0	0	0	0	0	0	0	1	2622	962	34	3		3	CAP2	6	17463259	Silent	SNP	G	TCGA-G3-A25U-01A-11D-A16V-10		17463259	153651808	15	39557										
ZNF804B	219578	hgsc.bcm.edu	37	chr7	88963115	88963115	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aggtttgcaaataaagatacAcaccttaccaaggaaaaaga	7	7	0	2			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr7:88963115A>G	ENST00000333190.4	+	4	1428	c.819A>G	c.(817-819)acA>acG	p.T273T		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	273							metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			ATAAAGATACACACCTTACCA	0.358										HNSCC(36;0.09)																											p.T273T		Atlas-SNP	.											.	ZNF804B	322	.	0			c.A819G						.						73	69	70					7																	88963115		2202	4300	6502	SO:0001819	synonymous_variant	219578	exon4			AGATACACACCTT	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"zinc finger 804B"				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.819A>G	chr7.hg19:g.88963115A>G		119.0	0.0		109.0	54.0	NM_181646	B2RTV2|Q7Z714|Q96MN7	Silent	SNP	ENST00000333190.4	hg19	CCDS5613.1																																																																																			.	.		0.358	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646		G	88963115	A	G	88963115	2	3	274	1	0	0	0	0	0	0	0	1	18186	146	6	2		2	ZNF804B	7	88963115	Silent	SNP	A	TCGA-G3-A25U-01A-11D-A16V-10		88963115	70175548	16	39558										
CYP3A5	1577	hgsc.bcm.edu	37	chr7	99247719	99247721	+	In_Frame_Del	DEL	AGG	AGG	-													0	0	1	0	0	0	1	1	0	tgtttctttacaaggtttgaAggagaagttctgaaggactc							TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr7:99247719_99247721delAGG	ENST00000222982.4	-	12	1487_1489	c.1388_1390delCCT	c.(1387-1392)tccttc>ttc	p.S463del	CYP3A5_ENST00000343703.5_In_Frame_Del_p.S453del|CYP3A5_ENST00000339843.2_3'UTR	NM_000777.3	NP_000768.1	P20815	CP3A5_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 5	463					alkaloid catabolic process (GO:0009822)|drug catabolic process (GO:0042737)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxygen binding (GO:0019825)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_epithelial(64;2.77e-08)|Lung NSC(181;0.00396)|all_lung(186;0.00659)|Esophageal squamous(72;0.0166)				ado-trastuzumab emtansine(DB05773)|Alfentanil(DB00802)|Alprazolam(DB00404)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Apixaban(DB06605)|Aprepitant(DB00673)|Argatroban(DB00278)|Aripiprazole(DB01238)|Artemether(DB06697)|Astemizole(DB00637)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Beclomethasone(DB00394)|Boceprevir(DB08873)|Brentuximab vedotin(DB08870)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Carbamazepine(DB00564)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Cilostazol(DB01166)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clonidine(DB00575)|Clopidogrel(DB00758)|Cocaine(DB00907)|Codeine(DB00318)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diltiazem(DB00343)|Disulfiram(DB00822)|Docetaxel(DB01248)|Dolutegravir(DB08930)|Domperidone(DB01184)|Dutasteride(DB01126)|Enzalutamide(DB08899)|Eplerenone(DB00700)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estrone(DB00655)|Ethosuximide(DB00593)|Etoposide(DB00773)|Felodipine(DB01023)|Fentanyl(DB00813)|Finasteride(DB01216)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flutamide(DB00499)|Fluticasone Propionate(DB00588)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gestodene(DB06730)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Indinavir(DB00224)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Levomethadyl Acetate(DB01227)|Lidocaine(DB00281)|Losartan(DB00678)|Lovastatin(DB00227)|Methadone(DB00333)|Midazolam(DB00683)|Mifepristone(DB00834)|Modafinil(DB00745)|Mycophenolate mofetil(DB00688)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ondansetron(DB00904)|Oxazepam(DB00842)|Oxcarbazepine(DB00776)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Pentamidine(DB00738)|Perampanel(DB08883)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Progesterone(DB00396)|Propranolol(DB00571)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinine(DB00468)|Ranitidine(DB00863)|Reserpine(DB00206)|Rifampicin(DB01045)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Rosuvastatin(DB01098)|Salmeterol(DB00938)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Teniposide(DB00444)|Testosterone(DB00624)|Thalidomide(DB01041)|Trazodone(DB00656)|Tretinoin(DB00755)|Triazolam(DB00897)|Troleandomycin(DB01361)|Udenafil(DB06267)|Valproic Acid(DB00313)|Vardenafil(DB00862)|Verapamil(DB00661)|Vincristine(DB00541)|Voriconazole(DB00582)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Ziprasidone(DB00246)|Zolpidem(DB00425)	CAAGGTTTGAAGGAGAAGTTCTG	0.35																																					p.463_464del		Atlas-Indel,Pindel	.											.	CYP3A5	46	.	0			c.1389_1391del						.																																			SO:0001651	inframe_deletion	1577	exon12			.	L26985	CCDS5672.1, CCDS55134.1	7q21.1	2007-12-14	2003-01-14		ENSG00000106258	ENSG00000106258		"Cytochrome P450s"	2638	protein-coding gene	gene with protein product		605325	"cytochrome P450, subfamily IIIA (niphedipine oxidase), polypeptide 5"				Standard	NR_033808		Approved	PCN3, P450PCN3, CP35		P20815	OTTHUMG00000156724	ENST00000222982.4:c.1388_1390delCCT	chr7.hg19:g.99247719_99247721delAGG	ENSP00000222982:p.Ser463del	192.0	0.0		172.0	69.0	NM_000777	A4D289|B7Z5I7|Q53WY8|Q75MV0|Q9HB56	In_Frame_Del	DEL	ENST00000222982.4	hg19	CCDS5672.1																																																																																			.	.		0.35	CYP3A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345469.1			-	99247721	AGG	-	99247719	7	5	274	1	0	1	0	1	0	0	0	0	4182	72	3	0	126	0	CYP3A5	7	99247719	In_Frame_Del	DEL	AGG	TCGA-G3-A25U-01A-11D-A16V-10	10284604	99247719	59890944	17	39559										
C9orf100	84904	hgsc.bcm.edu	37	chr9	35662720	35662720	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gcaccactaacagccagcccTggcgtaggaaccagcgccct	10	17	0	0			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr9:35662720T>A	ENST00000378387.3	-	7	809	c.692A>T	c.(691-693)cAg>cTg	p.Q231L	ARHGEF39_ENST00000490970.1_5'UTR|ARHGEF39_ENST00000378395.2_Missense_Mutation_p.Q195L|ARHGEF39_ENST00000343259.3_Intron	NM_032818.2	NP_116207.2	Q8N4T4	ARG39_HUMAN	Rho guanine nucleotide exchange factor (GEF) 39	231	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				positive regulation of cell migration (GO:0030335)	plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)										CAGCCAGCCCTGGCGTAGGAA	0.592																																					p.Q231L		Atlas-SNP	.											.	.	.	.	0			c.A692T						.						13	14	13					9																	35662720		2183	4256	6439	SO:0001583	missense	84904	exon7			CAGCCCTGGCGTA	AK001187	CCDS6584.2	9p13.3	2012-08-08	2012-08-08	2012-08-08	ENSG00000137135	ENSG00000137135			25909	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 100"	C9orf100		22327280	Standard	XR_242516		Approved	FLJ14642	uc003zxm.1	Q8N4T4	OTTHUMG00000019869	ENST00000378387.3:c.692A>T	chr9.hg19:g.35662720T>A	ENSP00000367638:p.Gln231Leu	57.0	0.0		94.0	34.0	NM_032818	Q49AG0|Q6TPQ2|Q96ST6	Missense_Mutation	SNP	ENST00000378387.3	hg19	CCDS6584.2	.	.	.	.	.	.	.	.	.	.	T	24.1	4.498025	0.85069	.	.	ENSG00000137135	ENST00000378387;ENST00000378395	T;T	0.44881	0.91;0.91	5.94	5.94	0.96194	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.050478	0.85682	D	0.000000	T	0.41903	0.1179	L	0.44542	1.39	0.80722	D	1	D	0.54207	0.965	P	0.46758	0.526	T	0.29671	-1.0004	10	0.45353	T	0.12	-26.927	12.7916	0.57537	0.0:0.0:0.0:1.0	.	231	Q8N4T4	CI100_HUMAN	L	231;195	ENSP00000367638:Q231L;ENSP00000367648:Q195L	ENSP00000367638:Q231L	Q	-	2	0	C9orf100	35652720	1.000000	0.71417	0.998000	0.56505	0.923000	0.55619	5.581000	0.67471	2.275000	0.75901	0.528000	0.53228	CAG	.	.		0.592	ARHGEF39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052330.1	NM_032818		A	35662720	T	A	35662720	3	1	274	1	0	0	0	0	1	0	0	0	2446	1580	55	4	327	4	C9orf100	9	35662720	Missense_Mutation	SNP	T	TCGA-G3-A25U-01A-11D-A16V-10		35662720	105550711	18	39560										
COL15A1	1306	hgsc.bcm.edu	37	chr9	101778304	101778304	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agcagccacaacagaggagcCcctcatcacagctgggggtg	13	13	2	1			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr9:101778304C>T	ENST00000375001.3	+	11	1973	c.1550C>T	c.(1549-1551)cCc>cTc	p.P517L		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	517	4 X tandem repeats.|Nonhelical region 1 (NC1).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				ACAGAGGAGCCCCTCATCACA	0.592																																					p.P517L		Atlas-SNP	.											.	COL15A1	211	.	0			c.C1550T						.						44	45	45					9																	101778304		2203	4300	6503	SO:0001583	missense	1306	exon11			AGGAGCCCCTCAT	L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2192	protein-coding gene	gene with protein product	"collagen type XV proteoglycan"	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.1550C>T	chr9.hg19:g.101778304C>T	ENSP00000364140:p.Pro517Leu	34.0	0.0		51.0	30.0	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Missense_Mutation	SNP	ENST00000375001.3	hg19	CCDS35081.1	.	.	.	.	.	.	.	.	.	.	C	11.19	1.567139	0.28003	.	.	ENSG00000204291	ENST00000375001;ENST00000536083	D	0.90955	-2.76	3.1	3.1	0.35709	.	.	.	.	.	D	0.84356	0.5454	L	0.46157	1.445	0.18873	N	0.999984	P	0.37781	0.608	B	0.29862	0.108	T	0.74902	-0.3506	9	0.34782	T	0.22	-0.6635	9.8268	0.40916	0.0:1.0:0.0:0.0	.	517	P39059	COFA1_HUMAN	L	517;487	ENSP00000364140:P517L	ENSP00000364140:P517L	P	+	2	0	COL15A1	100818125	0.000000	0.05858	0.005000	0.12908	0.024000	0.10985	0.321000	0.19558	1.736000	0.51660	0.650000	0.86243	CCC	.	.		0.592	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855		T	101778304	C	T	101778304	3	4	274	1	0	0	0	0	1	0	0	0	3674	623	22	3	1592	3	COL15A1	9	101778304	Missense_Mutation	SNP	C	TCGA-G3-A25U-01A-11D-A16V-10	66115584	101778304	39435127	19	39561										
HK1	3098	hgsc.bcm.edu	37	chr10	71148962	71148962	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tctttgcaaaggaatttgacCtggacgtggtggctgtggtc	14	7	1	1			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr10:71148962C>T	ENST00000359426.6	+	14	2049	c.1945C>T	c.(1945-1947)Ctg>Ttg	p.L649L	HK1_ENST00000298649.3_Silent_p.L648L|HK1_ENST00000404387.2_Silent_p.L653L|HK1_ENST00000360289.2_Silent_p.L637L|HK1_ENST00000448642.2_Silent_p.L684L	NM_000188.2	NP_000179.2	P19367	HXK1_HUMAN	hexokinase 1	649	Catalytic.|Hexokinase type-1 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cell death (GO:0008219)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(1)|urinary_tract(2)	35						GGAATTTGACCTGGACGTGGT	0.517																																					p.L653L		Atlas-SNP	.											.	HK1	170	.	0			c.C1957T						.						169	129	143					10																	71148962		2203	4300	6503	SO:0001819	synonymous_variant	3098	exon17			TTTGACCTGGACG	M75126	CCDS7289.1, CCDS7290.1, CCDS7291.1, CCDS7292.1	10q22	2014-09-17			ENSG00000156515	ENSG00000156515	2.7.1.1		4922	protein-coding gene	gene with protein product		142600					Standard	NM_033496		Approved		uc001jpi.4	P19367	OTTHUMG00000018380	ENST00000359426.6:c.1945C>T	chr10.hg19:g.71148962C>T		162.0	0.0		57.0	46.0	NM_033498	E9PCK0|O43443|O43444|O75574|Q5VTC3|Q96HC8|Q9NNZ4|Q9NNZ5	Silent	SNP	ENST00000359426.6	hg19	CCDS7292.1																																																																																			.	.		0.517	HK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048429.2	NM_000188		T	71148962	C	T	71148962	2	4	274	1	0	0	0	0	0	0	0	1	7199	680	24	3		3	HK1	10	71148962	Silent	SNP	C	TCGA-G3-A25U-01A-11D-A16V-10		71148962	64385785	20	39562										
HIPK3	10114	hgsc.bcm.edu	37	chr11	33358704	33358704	+	Missense_Mutation	SNP	A	A	T													0	0	1	0	0	0	1	1	0	tccacaagatttttttgcaaAgaaacagatatgtctcattc							TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr11:33358704A>T	ENST00000303296.4	+	4	1610	c.1305A>T	c.(1303-1305)aaA>aaT	p.K435N	HIPK3_ENST00000525975.1_Missense_Mutation_p.K435N|HIPK3_ENST00000379016.3_Missense_Mutation_p.K435N|HIPK3_ENST00000534262.1_3'UTR|HIPK3_ENST00000456517.1_Missense_Mutation_p.K435N	NM_005734.3	NP_005725.3	Q9H422	HIPK3_HUMAN	homeodomain interacting protein kinase 3	435	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|mRNA transcription (GO:0009299)|negative regulation of apoptotic process (GO:0043066)|negative regulation of JUN kinase activity (GO:0043508)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			endometrium(3)|kidney(3)|large_intestine(9)|liver(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	39						TTTTTTGCAAAGAAACAGATA	0.313																																					p.K435N		Atlas-SNP	.											.	HIPK3	92	.	0			c.A1305T						.						66	67	67					11																	33358704		2201	4295	6496	SO:0001583	missense	10114	exon4			TTGCAAAGAAACA	AF004849	CCDS7884.1, CCDS41634.1	11p13	2008-07-18	2001-11-29		ENSG00000110422	ENSG00000110422			4915	protein-coding gene	gene with protein product		604424	"homeodomain-interacting protein kinase 3"			9373137, 9748262	Standard	NM_005734		Approved	PKY, DYRK6, YAK1, FIST3	uc031pzm.1	Q9H422	OTTHUMG00000132269	ENST00000303296.4:c.1305A>T	chr11.hg19:g.33358704A>T	ENSP00000304226:p.Lys435Asn	57.0	0.0		72.0	33.0	NM_001048200	O14632|Q2PBG4|Q2PBG5|Q92632|Q9HAS2	Missense_Mutation	SNP	ENST00000303296.4	hg19	CCDS7884.1	.	.	.	.	.	.	.	.	.	.	A	14.50	2.552904	0.45487	.	.	ENSG00000110422	ENST00000525975;ENST00000303296;ENST00000379016;ENST00000456517	T;T;T;T	0.20332	2.08;2.08;2.08;2.08	4.88	2.53	0.30540	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.090432	0.48286	D	0.000187	T	0.12475	0.0303	N	0.20845	0.615	0.38943	D	0.958193	B;B	0.15141	0.008;0.012	B;B	0.22152	0.022;0.038	T	0.09143	-1.0688	10	0.87932	D	0	.	5.5243	0.16949	0.7032:0.1447:0.1521:0.0	.	435;435	Q9H422-2;Q9H422	.;HIPK3_HUMAN	N	435	ENSP00000431710:K435N;ENSP00000304226:K435N;ENSP00000368301:K435N;ENSP00000398241:K435N	ENSP00000304226:K435N	K	+	3	2	HIPK3	33315280	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	3.372000	0.52387	0.302000	0.22762	-0.371000	0.07208	AAA	.	.		0.313	HIPK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255358.1	NM_005734		T	33358704	A	T	33358704	3	4	274	1	0	0	0	0	1	0	0	0	7127	69	3	4	1315	4	HIPK3	11	33358704	Missense_Mutation	SNP	A	TCGA-G3-A25U-01A-11D-A16V-10		33358704	101647812	21	39563	196	2								
HIPK3	10114	hgsc.bcm.edu	37	chr11	33358706	33358706	+	Missense_Mutation	SNP	A	A	C													0	0	1	0	0	0	1	1	0	cacaagatttttttgcaaagAaacagatatgtctcattctg							TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr11:33358706A>C	ENST00000303296.4	+	4	1612	c.1307A>C	c.(1306-1308)gAa>gCa	p.E436A	HIPK3_ENST00000525975.1_Missense_Mutation_p.E436A|HIPK3_ENST00000379016.3_Missense_Mutation_p.E436A|HIPK3_ENST00000534262.1_3'UTR|HIPK3_ENST00000456517.1_Missense_Mutation_p.E436A	NM_005734.3	NP_005725.3	Q9H422	HIPK3_HUMAN	homeodomain interacting protein kinase 3	436	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|mRNA transcription (GO:0009299)|negative regulation of apoptotic process (GO:0043066)|negative regulation of JUN kinase activity (GO:0043508)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			endometrium(3)|kidney(3)|large_intestine(9)|liver(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	39						TTTTGCAAAGAAACAGATATG	0.308																																					p.E436A		Atlas-SNP	.											.	HIPK3	92	.	0			c.A1307C						.						65	66	65					11																	33358706		2201	4295	6496	SO:0001583	missense	10114	exon4			GCAAAGAAACAGA	AF004849	CCDS7884.1, CCDS41634.1	11p13	2008-07-18	2001-11-29		ENSG00000110422	ENSG00000110422			4915	protein-coding gene	gene with protein product		604424	"homeodomain-interacting protein kinase 3"			9373137, 9748262	Standard	NM_005734		Approved	PKY, DYRK6, YAK1, FIST3	uc031pzm.1	Q9H422	OTTHUMG00000132269	ENST00000303296.4:c.1307A>C	chr11.hg19:g.33358706A>C	ENSP00000304226:p.Glu436Ala	56.0	0.0		71.0	32.0	NM_001048200	O14632|Q2PBG4|Q2PBG5|Q92632|Q9HAS2	Missense_Mutation	SNP	ENST00000303296.4	hg19	CCDS7884.1	.	.	.	.	.	.	.	.	.	.	A	19.21	3.782867	0.70222	.	.	ENSG00000110422	ENST00000525975;ENST00000303296;ENST00000379016;ENST00000456517	T;T;T;T	0.19669	2.13;2.13;2.13;2.13	4.88	4.88	0.63580	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000013	T	0.16342	0.0393	N	0.20986	0.625	0.80722	D	1	B;P	0.35527	0.198;0.507	B;B	0.34346	0.171;0.18	T	0.05767	-1.0865	10	0.72032	D	0.01	.	14.7855	0.69800	1.0:0.0:0.0:0.0	.	436;436	Q9H422-2;Q9H422	.;HIPK3_HUMAN	A	436	ENSP00000431710:E436A;ENSP00000304226:E436A;ENSP00000368301:E436A;ENSP00000398241:E436A	ENSP00000304226:E436A	E	+	2	0	HIPK3	33315282	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	7.426000	0.80270	1.952000	0.56665	0.460000	0.39030	GAA	.	.		0.308	HIPK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255358.1	NM_005734		C	33358706	A	C	33358706	3	2	274	1	0	0	0	0	1	0	0	0	7127	246	9	5	1317	5	HIPK3	11	33358706	Missense_Mutation	SNP	A	TCGA-G3-A25U-01A-11D-A16V-10	2	33358706	101647810	22	39564	196	2								
AHNAK	79026	hgsc.bcm.edu	37	chr11	62290411	62290411	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aggtcagccttgggcaggttCacatccacatctgggccctc	11	14	3	0			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr11:62290411C>A	ENST00000378024.4	-	5	11752	c.11478G>T	c.(11476-11478)gtG>gtT	p.V3826V	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	3826					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				TGGGCAGGTTCACATCCACAT	0.522																																					p.V3826V		Atlas-SNP	.											.	AHNAK	532	.	0			c.G11478T						.						196	204	201					11																	62290411		2202	4296	6498	SO:0001819	synonymous_variant	79026	exon5			CAGGTTCACATCC	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.11478G>T	chr11.hg19:g.62290411C>A		71.0	0.0		81.0	34.0	NM_001620	A1A586	Silent	SNP	ENST00000378024.4	hg19	CCDS31584.1																																																																																			.	.		0.522	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		A	62290411	C	A	62290411	2	1	274	1	0	0	0	0	0	0	0	1	414	813	29	3		3	AHNAK	11	62290411	Silent	SNP	C	TCGA-G3-A25U-01A-11D-A16V-10	28931705	62290411	72716105	23	39565										
C11orf2	738	hgsc.bcm.edu	37	chr11	64878964	64878964	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	acgaagaactcgtgcacttgCtgctggacgaagtggtggcc	14	10	0	1			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr11:64878964C>G	ENST00000279281.3	+	10	2346	c.2254C>G	c.(2254-2256)Ctg>Gtg	p.L752V	VPS51_ENST00000527646.1_3'UTR|AP003068.9_ENST00000528887.1_RNA|TM7SF2_ENST00000279263.7_5'Flank|TM7SF2_ENST00000345348.5_5'Flank|TM7SF2_ENST00000540748.1_5'Flank	NM_013265.2	NP_037397.2	Q9UID3	VPS51_HUMAN	vacuolar protein sorting 51 homolog (S. cerevisiae)	752					autophagy (GO:0006914)|lipid transport (GO:0006869)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	GARP complex (GO:0000938)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)											CGTGCACTTGCTGCTGGACGA	0.632																																					p.L752V		Atlas-SNP	.											.	.	.	.	0			c.C2254G						.						115	85	95					11																	64878964		2201	4297	6498	SO:0001583	missense	738	exon10			CACTTGCTGCTGG	AF024631	CCDS8093.1	11q13.1	2012-07-19	2012-07-19	2012-07-19	ENSG00000149823	ENSG00000149823			1172	protein-coding gene	gene with protein product	"fat-free homolog (zebrafish)"	615738	"chromosome 11 open reading frame 3", "chromosome 11 open reading frame 2"	C11orf3, C11orf2		9286704, 20685960	Standard	NM_013265		Approved	ANG2, ANG3, FFR	uc001ocr.2	Q9UID3	OTTHUMG00000165600	ENST00000279281.3:c.2254C>G	chr11.hg19:g.64878964C>G	ENSP00000279281:p.Leu752Val	83.0	0.0		73.0	28.0	NM_013265	Q6PJV5|Q7L8A6|Q8WZ35|Q96DF4|Q96GR3	Missense_Mutation	SNP	ENST00000279281.3	hg19	CCDS8093.1	.	.	.	.	.	.	.	.	.	.	C	17.45	3.393038	0.62066	.	.	ENSG00000149823	ENST00000279281	.	.	.	5.05	5.05	0.67936	.	0.000000	0.64402	D	0.000001	T	0.80423	0.4620	M	0.83692	2.655	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.81959	-0.0694	9	0.52906	T	0.07	-13.1403	16.005	0.80357	0.0:1.0:0.0:0.0	.	752	Q9UID3	FFR_HUMAN	V	752	.	ENSP00000279281:L752V	L	+	1	2	C11orf2	64635540	1.000000	0.71417	1.000000	0.80357	0.524000	0.34500	2.909000	0.48758	2.647000	0.89833	0.555000	0.69702	CTG	.	.		0.632	VPS51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385217.1	NM_013265		G	64878964	C	G	64878964	3	3	274	1	0	0	0	0	1	0	0	0	1635	796	28	4	2292	4	C11orf2	11	64878964	Missense_Mutation	SNP	C	TCGA-G3-A25U-01A-11D-A16V-10	2588553	64878964	70127552	24	39566										
TULP3	7289	hgsc.bcm.edu	37	chr12	3048495	3048495	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agctgattatatagtcatgcAgtttggacgtgtggcagatg	13	5	1	2			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr12:3048495A>T	ENST00000448120.2	+	11	1265	c.1214A>T	c.(1213-1215)cAg>cTg	p.Q405L	TULP3_ENST00000397132.2_Missense_Mutation_p.Q405L	NM_003324.4	NP_003315.2	O75386	TULP3_HUMAN	tubby like protein 3	405					anterior/posterior pattern specification (GO:0009952)|bone development (GO:0060348)|brain development (GO:0007420)|bronchus morphogenesis (GO:0060434)|central nervous system neuron differentiation (GO:0021953)|embryonic camera-type eye development (GO:0031076)|embryonic digit morphogenesis (GO:0042733)|embryonic neurocranium morphogenesis (GO:0048702)|G-protein coupled receptor signaling pathway (GO:0007186)|ganglion development (GO:0061548)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of transcription, DNA-templated (GO:0006355)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cilium (GO:0005929)|extracellular region (GO:0005576)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	enzyme binding (GO:0019899)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein complex binding (GO:0032403)			endometrium(1)|large_intestine(4)|lung(13)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22			OV - Ovarian serous cystadenocarcinoma(31;0.000818)			ATAGTCATGCAGTTTGGACGT	0.393																																					p.Q405L		Atlas-SNP	.											.	TULP3	45	.	0			c.A1214T						.						301	255	270					12																	3048495		2203	4300	6503	SO:0001583	missense	7289	exon11			TCATGCAGTTTGG	AF045583	CCDS8519.1, CCDS53737.1	12p13	2014-02-21			ENSG00000078246	ENSG00000078246		"Intraflagellar transport homologs"	12425	protein-coding gene	gene with protein product		604730				9828123	Standard	NM_003324		Approved	TUBL3	uc001qlj.2	O75386	OTTHUMG00000168152	ENST00000448120.2:c.1214A>T	chr12.hg19:g.3048495A>T	ENSP00000410051:p.Gln405Leu	150.0	0.0		124.0	51.0	NM_003324	B3KNB7|B7Z6A2|D3DUQ4|F8WBZ9|Q8N5B0	Missense_Mutation	SNP	ENST00000448120.2	hg19	CCDS8519.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.099136	0.76983	.	.	ENSG00000078246	ENST00000228245;ENST00000544943;ENST00000542730;ENST00000448120;ENST00000397132	D;D;D	0.97870	-4.58;-4.58;-4.58	5.64	5.64	0.86602	Tubby, C-terminal (4);	0.000000	0.85682	D	0.000000	D	0.98833	0.9606	M	0.88450	2.955	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	D	0.99793	1.1032	10	0.87932	D	0	-10.6884	15.0316	0.71710	1.0:0.0:0.0:0.0	.	229;405;405	B7Z1E7;O75386;F8WBZ9	.;TULP3_HUMAN;.	L	405;132;229;405;405	ENSP00000442631:Q132L;ENSP00000410051:Q405L;ENSP00000380321:Q405L	ENSP00000228245:Q405L	Q	+	2	0	TULP3	2918756	1.000000	0.71417	1.000000	0.80357	0.523000	0.34469	9.339000	0.96797	2.150000	0.67090	0.402000	0.26972	CAG	.	.		0.393	TULP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398468.1	NM_003324		T	3048495	A	T	3048495	3	4	274	1	0	0	0	0	1	0	0	0	16790	188	7	4	1256	4	TULP3	12	3048495	Missense_Mutation	SNP	A	TCGA-G3-A25U-01A-11D-A16V-10		3048495	130803400	25	39567										
APAF1	317	hgsc.bcm.edu	37	chr12	99117014	99117014	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	atgtatctttctacgaggccAtcaggaaacagtgaaagact	9	8	3	2			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr12:99117014A>G	ENST00000551964.1	+	23	3864	c.3128A>G	c.(3127-3129)cAt>cGt	p.H1043R	APAF1_ENST00000549007.1_Missense_Mutation_p.H1000R|APAF1_ENST00000550527.1_Missense_Mutation_p.H1032R|APAF1_ENST00000357310.1_Missense_Mutation_p.H1000R|APAF1_ENST00000547045.1_Missense_Mutation_p.H1000R|APAF1_ENST00000359972.2_Missense_Mutation_p.H989R|APAF1_ENST00000333991.1_Intron|APAF1_ENST00000339433.3_Missense_Mutation_p.H1000R|APAF1_ENST00000552268.1_Intron	NM_181861.1	NP_863651.1	O14727	APAF_HUMAN	apoptotic peptidase activating factor 1	1043					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|forebrain development (GO:0030900)|intrinsic apoptotic signaling pathway (GO:0097193)|nervous system development (GO:0007399)|neural tube closure (GO:0001843)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|regulation of apoptotic DNA fragmentation (GO:1902510)|regulation of apoptotic process (GO:0042981)|response to G1 DNA damage checkpoint signaling (GO:0072432)	apoptosome (GO:0043293)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(1)	42					Adenosine triphosphate(DB00171)	CTACGAGGCCATCAGGAAACA	0.353																																					p.H1043R		Atlas-SNP	.											.	APAF1	111	.	0			c.A3128G						.						129	133	132					12																	99117014		2203	4300	6503	SO:0001583	missense	317	exon23			GAGGCCATCAGGA	AF013263	CCDS9069.1, CCDS9070.1, CCDS9071.1, CCDS55862.1, CCDS55863.1	12q23	2013-01-10	2006-10-23			ENSG00000120868		"WD repeat domain containing"	576	protein-coding gene	gene with protein product		602233	"apoptotic protease activating factor", "apoptotic peptidase activating factor"			9267021, 10702682	Standard	NM_181861		Approved	CED4, APAF-1	uc001tfz.3	O14727	OTTHUMG00000170214	ENST00000551964.1:c.3128A>G	chr12.hg19:g.99117014A>G	ENSP00000448165:p.His1043Arg	113.0	0.0		123.0	48.0	NM_181861	B2RMX8|O43297|Q7Z438|Q9BXZ6|Q9UBZ5|Q9UGN8|Q9UGN9|Q9UGP0|Q9UJ58|Q9UJ59|Q9UJ60|Q9UJ61|Q9UJ62|Q9UJ63|Q9UJ64|Q9UJ65|Q9UJ66|Q9UJ67|Q9UNC9	Missense_Mutation	SNP	ENST00000551964.1	hg19	CCDS9069.1	.	.	.	.	.	.	.	.	.	.	A	15.42	2.829789	0.50845	.	.	ENSG00000120868	ENST00000551964;ENST00000359972;ENST00000357310;ENST00000339433;ENST00000550527;ENST00000547045;ENST00000549007	T;T;T;T;T;T;T	0.81163	-1.46;-1.46;-1.46;-1.46;-1.46;-1.46;-1.46	5.76	5.76	0.90799	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.091058	0.85682	D	0.000000	D	0.94315	0.8173	H	0.99379	4.54	0.80722	D	1	D;D;D;D;P	0.89917	1.0;0.999;1.0;0.999;0.925	D;D;D;D;P	0.91635	0.998;0.999;0.996;0.975;0.793	D	0.96041	0.9024	10	0.51188	T	0.08	-3.8213	14.6627	0.68885	1.0:0.0:0.0:0.0	.	1000;1000;989;1043;1032	C9JLV4;O14727-4;O14727-3;O14727;O14727-2	.;.;.;APAF_HUMAN;.	R	1043;989;1000;1000;1032;1000;1000	ENSP00000448165:H1043R;ENSP00000353059:H989R;ENSP00000349862:H1000R;ENSP00000341830:H1000R;ENSP00000448449:H1032R;ENSP00000449791:H1000R;ENSP00000448161:H1000R	ENSP00000341830:H1000R	H	+	2	0	APAF1	97641145	1.000000	0.71417	0.999000	0.59377	0.161000	0.22273	7.094000	0.76944	2.186000	0.69663	0.533000	0.62120	CAT	.	.		0.353	APAF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408006.1	NM_181861.1		G	99117014	A	G	99117014	3	3	274	1	0	0	0	0	1	0	0	0	755	217	8	2	3214	2	APAF1	12	99117014	Missense_Mutation	SNP	A	TCGA-G3-A25U-01A-11D-A16V-10	96068519	99117014	34734881	26	39568										
NBEA	26960	hgsc.bcm.edu	37	chr13	35731313	35731313	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gaagattaccgaaatggtctAcaatatcttccggattcttt	7	8	3	1			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr13:35731313A>G	ENST00000400445.3	+	21	3284	c.2750A>G	c.(2749-2751)tAc>tGc	p.Y917C	NBEA_ENST00000310336.4_Missense_Mutation_p.Y917C|NBEA_ENST00000379939.2_Missense_Mutation_p.Y917C|NBEA_ENST00000540320.1_Missense_Mutation_p.Y917C	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	917					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		GAAATGGTCTACAATATCTTC	0.408																																					p.Y917C		Atlas-SNP	.											.	NBEA	340	.	0			c.A2750G						.						115	113	114					13																	35731313		1826	4081	5907	SO:0001583	missense	26960	exon21			TGGTCTACAATAT	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.2750A>G	chr13.hg19:g.35731313A>G	ENSP00000383295:p.Tyr917Cys	111.0	1.0		116.0	109.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	A	19.82	3.898496	0.72639	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336	T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.77280	0.4107	M	0.69248	2.105	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	T	0.79022	-0.1973	10	0.56958	D	0.05	.	15.6702	0.77267	1.0:0.0:0.0:0.0	.	917	Q5T321	.	C	917	ENSP00000440951:Y917C;ENSP00000383295:Y917C;ENSP00000369271:Y917C;ENSP00000308534:Y917C	ENSP00000308534:Y917C	Y	+	2	0	NBEA	34629313	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.287000	0.95975	2.171000	0.68590	0.528000	0.53228	TAC	.	.		0.408	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		G	35731313	A	G	35731313	3	3	274	1	0	0	0	0	1	0	0	0	10196	391	14	2	2832	2	NBEA	13	35731313	Missense_Mutation	SNP	A	TCGA-G3-A25U-01A-11D-A16V-10		35731313	79438565	27	39569										
RB1	5925	hgsc.bcm.edu	37	chr13	48947605	48947606	+	Frame_Shift_Ins	INS	-	-	A													0	0	1	0	0	0	1	1	0	agcaagtgatcaaccttcagINSaaaatctgatttcctatttt							TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr13:48947605_48947606insA	ENST00000267163.4	+	12	1330_1331	c.1192_1193insA	c.(1192-1194)gaafs	p.E398fs		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	398	Domain A.|Pocket; binds T and E1A.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(8)|p.E398L(2)		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(DB00071)|Insulin Regular(DB00030)"	TCAACCTTCAGAAAATCTGATT	0.287		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)																											p.E398fs		Atlas-INDEL	.	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	.,1	RB1	1068	.	25	Whole gene deletion(15)|Unknown(8)|Substitution - Missense(2)	bone(11)|breast(5)|central_nervous_system(2)|lung(2)|adrenal_gland(1)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	c.1192_1193insA						.																																			SO:0001589	frameshift_variant	5925	exon12	Familial Cancer Database		.	M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1196dupA	chr13.hg19:g.48947609_48947609dupA	ENSP00000267163:p.Glu398fs	228.0	0.0		312.0	277.0	NM_000321	A8K5E3|P78499|Q5VW46|Q8IZL4	Frame_Shift_Ins	INS	ENST00000267163.4	hg19	CCDS31973.1																																																																																			.	.		0.287	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			A	48947606	-	A	48947605	7	5	274	1	0	1	1	0	0	0	0	0	13113	943	33	0	1238	0	RB1	13	48947605	Frame_Shift_Ins	INS	-	TCGA-G3-A25U-01A-11D-A16V-10	13216292	48947605	66222273	28	39570										
PPP2R5C	5527	hgsc.bcm.edu	37	chr14	102391540	102391540	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aagtccgagctgcctcaggaCccccacaccaagaaagcctt	8	16	1	1			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr14:102391540C>A	ENST00000334743.5	+	14	1554	c.1506C>A	c.(1504-1506)gaC>gaA	p.D502E	PPP2R5C_ENST00000350249.3_Missense_Mutation_p.D463E|PPP2R5C_ENST00000422945.2_Missense_Mutation_p.D533E|PPP2R5C_ENST00000328724.5_Missense_Mutation_p.D518E	NM_002719.3	NP_002710.2	Q13362	2A5G_HUMAN	protein phosphatase 2, regulatory subunit B', gamma	502					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of cell proliferation (GO:0008285)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	chromosome, centromeric region (GO:0000775)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	20						TGCCTCAGGACCCCCACACCA	0.632																																					p.D533E		Atlas-SNP	.											.	PPP2R5C	74	.	0			c.C1599A						.						93	102	99					14																	102391540		2203	4300	6503	SO:0001583	missense	5527	exon16			TCAGGACCCCCAC	L42375	CCDS9964.1, CCDS9965.1, CCDS45163.1, CCDS53911.1, CCDS53912.1	14q32.31	2010-06-18	2010-04-14		ENSG00000078304	ENSG00000078304		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9311	protein-coding gene	gene with protein product		601645	"protein phosphatase 2, regulatory subunit B (B56), gamma isoform", "protein phosphatase 2, regulatory subunit B', gamma isoform"			7592815	Standard	NM_002719		Approved	B56G, PR61G	uc001ykk.3	Q13362		ENST00000334743.5:c.1506C>A	chr14.hg19:g.102391540C>A	ENSP00000333905:p.Asp502Glu	61.0	0.0		80.0	36.0	NM_001161725	B4DYJ8|B5BUA5|F5GWP3|Q14391|Q15060|Q15174|Q6ZN33	Missense_Mutation	SNP	ENST00000334743.5	hg19	CCDS9964.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.586613	0.86851	.	.	ENSG00000078304	ENST00000422945;ENST00000328724;ENST00000557268;ENST00000350249;ENST00000334743	T;T;T;T;T	0.61510	0.1;0.53;0.1;0.51;0.1	6.17	0.338	0.15974	.	0.000000	0.85682	D	0.000000	T	0.70465	0.3227	M	0.85630	2.765	0.50171	D	0.999854	D;D;D;D	0.71674	0.994;0.966;0.998;0.994	D;D;D;D	0.66847	0.947;0.921;0.931;0.938	T	0.68176	-0.5478	10	0.59425	D	0.04	-9.0671	5.6504	0.17612	0.0:0.5105:0.1548:0.3347	.	533;463;502;518	F5GWP3;Q13362-3;Q13362;Q6ZN33	.;.;2A5G_HUMAN;.	E	533;518;531;463;502	ENSP00000412324:D533E;ENSP00000329009:D518E;ENSP00000450931:D531E;ENSP00000262239:D463E;ENSP00000333905:D502E	ENSP00000329009:D518E	D	+	3	2	PPP2R5C	101461293	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	1.080000	0.30779	0.284000	0.22305	-0.290000	0.09829	GAC	.	.		0.632	PPP2R5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414373.2	NM_002719		A	102391540	C	A	102391540	3	1	274	1	0	0	0	0	1	0	0	0	12406	506	18	3	1953	3	PPP2R5C	14	102391540	Missense_Mutation	SNP	C	TCGA-G3-A25U-01A-11D-A16V-10		102391540	4958000	29	39571										
IL16	3603	hgsc.bcm.edu	37	chr15	81589305	81589305	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	tgccactgctgctaccacagGaagacacagcagggagaagc	12	12	0	2			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr15:81589305G>A	ENST00000302987.4	+	12	1939	c.1939G>A	c.(1939-1941)Gaa>Aaa	p.E647K	IL16_ENST00000394652.2_5'UTR|IL16_ENST00000394660.2_Missense_Mutation_p.E647K			Q14005	IL16_HUMAN	interleukin 16	647					immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						GCTACCACAGGAAGACACAGC	0.602																																					p.E647K		Atlas-SNP	.											.	IL16	254	.	0			c.G1939A						.						35	39	38					15																	81589305		1963	4158	6121	SO:0001583	missense	3603	exon13			CCACAGGAAGACA	U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"Interleukins and interleukin receptors"	5980	protein-coding gene	gene with protein product	"prointerleukin 16", "lymphocyte chemoattractant factor"	603035	"interleukin 16 (lymphocyte chemoattractant factor)"			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.1939G>A	chr15.hg19:g.81589305G>A	ENSP00000302935:p.Glu647Lys	65.0	0.0		46.0	22.0	NM_001172128	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Missense_Mutation	SNP	ENST00000302987.4	hg19	CCDS42069.1	.	.	.	.	.	.	.	.	.	.	G	14.19	2.460644	0.43736	.	.	ENSG00000172349	ENST00000394660;ENST00000355368;ENST00000302987;ENST00000329842;ENST00000394653	T;T	0.11063	2.81;2.81	4.7	4.7	0.59300	.	0.582759	0.14620	N	0.308470	T	0.15912	0.0383	M	0.65975	2.015	0.80722	D	1	B;B;B;B;B	0.26635	0.089;0.155;0.155;0.016;0.027	B;B;B;B;B	0.32864	0.034;0.043;0.154;0.021;0.047	T	0.07083	-1.0791	10	0.10636	T	0.68	.	15.7839	0.78286	0.0:0.0:1.0:0.0	.	141;184;37;647;647	Q6ZTT5;B7Z8M3;B3KY62;Q14005;Q14005-2	.;.;.;IL16_HUMAN;.	K	647;479;647;184;37	ENSP00000378155:E647K;ENSP00000302935:E647K	ENSP00000302935:E647K	E	+	1	0	IL16	79376360	1.000000	0.71417	0.985000	0.45067	0.317000	0.28152	2.648000	0.46647	2.305000	0.77605	0.655000	0.94253	GAA	.	.		0.602	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217		A	81589305	G	A	81589305	3	1	274	1	0	0	0	0	1	0	0	0	7642	1175	41	3	1985	3	IL16	15	81589305	Missense_Mutation	SNP	G	TCGA-G3-A25U-01A-11D-A16V-10		81589305	20942087	30	39572										
STARD5	80765	hgsc.bcm.edu	37	chr15	81615246	81615246	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aggcatgcacttacaggttcCctggaaactccacagatggc	10	12	0	1			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr15:81615246C>A	ENST00000302824.6	-	2	168	c.143G>T	c.(142-144)gGg>gTg	p.G48V	RP11-761I4.3_ENST00000560973.1_RNA|STARD5_ENST00000559913.1_5'UTR|RP11-761I4.3_ENST00000559781.1_RNA	NM_181900.2	NP_871629.1	Q9NSY2	STAR5_HUMAN	StAR-related lipid transfer (START) domain containing 5	48	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				C21-steroid hormone biosynthetic process (GO:0006700)|lipid transport (GO:0006869)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	cytosol (GO:0005829)	lipid binding (GO:0008289)			large_intestine(3)|ovary(1)|skin(1)|stomach(1)	6						TTACAGGTTCCCTGGAAACTC	0.483																																					p.G48V		Atlas-SNP	.											.	STARD5	20	.	0			c.G143T						.						76	76	76					15																	81615246		2203	4300	6503	SO:0001583	missense	80765	exon2			AGGTTCCCTGGAA	AF480304	CCDS10318.1	15q26	2011-09-12	2007-08-16		ENSG00000172345	ENSG00000172345		"StAR-related lipid transfer (START) domain containing"	18065	protein-coding gene	gene with protein product		607050	"START domain containing 5"			12011452	Standard	NM_181900		Approved	MGC10327	uc002bgm.3	Q9NSY2	OTTHUMG00000147342	ENST00000302824.6:c.143G>T	chr15.hg19:g.81615246C>A	ENSP00000304032:p.Gly48Val	69.0	0.0		74.0	43.0	NM_181900	P59094	Missense_Mutation	SNP	ENST00000302824.6	hg19	CCDS10318.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.868363	0.91587	.	.	ENSG00000172345	ENST00000302824	T	0.79247	-1.25	5.4	5.4	0.78164	Lipid-binding START (3);START-like domain (1);	0.000000	0.85682	D	0.000000	D	0.88987	0.6587	M	0.84683	2.71	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86928	0.2071	10	0.25106	T	0.35	-11.9245	18.7698	0.91887	0.0:1.0:0.0:0.0	.	48	Q9NSY2	STAR5_HUMAN	V	48	ENSP00000304032:G48V	ENSP00000304032:G48V	G	-	2	0	STARD5	79402301	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.520000	0.73773	2.542000	0.85734	0.655000	0.94253	GGG	.	.		0.483	STARD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303950.2			A	81615246	C	A	81615246	3	1	274	1	0	0	0	0	1	0	0	0	15275	623	22	3	518	3	STARD5	15	81615246	Missense_Mutation	SNP	C	TCGA-G3-A25U-01A-11D-A16V-10	25941	81615246	20916146	31	39573										
TP53	7157	hgsc.bcm.edu	37	chr17	7577534	7577534	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtgatgatggtgaggatgggCctccggttcatgccgcccat	15	10	1	3	rs28934571		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr17:7577534C>A	ENST00000269305.4	-	7	936	c.747G>T	c.(745-747)agG>agT	p.R249S	TP53_ENST00000455263.2_Missense_Mutation_p.R249S|TP53_ENST00000359597.4_Missense_Mutation_p.R249S|TP53_ENST00000420246.2_Missense_Mutation_p.R249S|TP53_ENST00000445888.2_Missense_Mutation_p.R249S|TP53_ENST00000413465.2_Missense_Mutation_p.R249S|TP53_ENST00000574684.1_5'Flank	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	249	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> G (in sporadic cancers; somatic mutation).|R -> I (in a sporadic cancer; somatic mutation).|R -> K (in sporadic cancers; somatic mutation).|R -> M (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:17224074}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> S (in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; dbSNP:rs28934571). {ECO:0000269|PubMed:1694291, ECO:0000269|PubMed:16959974}.|R -> T (in sporadic cancers; somatic mutation).|R -> W (in sporadic cancers; somatic mutation).|RP -> SA (in a sporadic cancer; somatic mutation).|RP -> SS (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R249S(348)|p.0?(8)|p.R249R(5)|p.?(5)|p.M246_P250delMNRRP(2)|p.R248_P250delRRP(1)|p.R249_P250delRP(1)|p.R249_P250insR(1)|p.R249_P250>SS(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*14(1)|p.R249_T256delRPILTIIT(1)|p.P250fs*14(1)|p.R249_I251delRPI(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TGAGGATGGGCCTCCGGTTCA	0.572		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.R249S	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,right_lower_lobe,carcinoma,-2,1	TP53	33396	.	378	Substitution - Missense(348)|Deletion - In frame(8)|Whole gene deletion(8)|Unknown(5)|Substitution - coding silent(5)|Insertion - Frameshift(1)|Insertion - In frame(1)|Deletion - Frameshift(1)|Complex - compound substitution(1)	liver(240)|lung(44)|upper_aerodigestive_tract(12)|breast(12)|central_nervous_system(10)|stomach(7)|ovary(6)|prostate(6)|cervix(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(5)|biliary_tract(5)|urinary_tract(5)|bone(4)|endometrium(3)|oesophagus(3)|skin(2)|peritoneum(1)|kidney(1)|salivary_gland(1)|pancreas(1)	c.G747T						.						155	113	127					17																	7577534		2203	4300	6503	SO:0001583	missense	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GATGGGCCTCCGG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.747G>T	chr17.hg19:g.7577534C>A	ENSP00000269305:p.Arg249Ser	83.0	0.0		51.0	39.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.344264	0.61073	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D;D	0.99865	-7.29;-7.29;-7.29;-7.29;-7.29;-7.29;-7.29	4.62	-0.0929	0.13654	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99792	0.9912	M	0.92367	3.3	0.50039	D	0.999848	D;D;D;D;D	0.89917	0.996;0.996;0.997;0.99;1.0	D;D;D;D;D	0.79108	0.968;0.966;0.981;0.955;0.992	D	0.98720	1.0708	10	0.72032	D	0.01	-3.0658	3.2479	0.06803	0.1392:0.5551:0.1362:0.1695	rs28934571	249;249;249;249;249	P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;P53_HUMAN;.;.	S	249;249;249;249;249;249;238;117	ENSP00000410739:R249S;ENSP00000352610:R249S;ENSP00000269305:R249S;ENSP00000398846:R249S;ENSP00000391127:R249S;ENSP00000391478:R249S;ENSP00000425104:R117S	ENSP00000269305:R249S	R	-	3	2	TP53	7518259	0.011000	0.17503	0.998000	0.56505	0.783000	0.44284	-1.379000	0.02554	0.253000	0.21552	0.462000	0.41574	AGG	.	.		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577534	C	A	7577534	3	1	274	1	0	0	0	0	1	0	0	0	16396	738	26	3	543	3	TP53	17	7577534	Missense_Mutation	SNP	C	TCGA-G3-A25U-01A-11D-A16V-10		7577534	73617676	32	39574										
MYO18A	399687	hgsc.bcm.edu	37	chr17	27442787	27442787	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	gaagatggctgaggacagctCctccaggctgcagcccagta	13	12	0	2			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr17:27442787C>T	ENST00000527372.1	-	12	2302	c.2122G>A	c.(2122-2124)Gag>Aag	p.E708K	MYO18A_ENST00000533112.1_Missense_Mutation_p.E708K|MYO18A_ENST00000531253.1_Missense_Mutation_p.E708K|MYO18A_ENST00000354329.4_Missense_Mutation_p.E708K	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	708	Myosin motor.				actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			GAGGACAGCTCCTCCAGGCTG	0.642																																					p.E708K	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-SNP	.											.	MYO18A	217	.	0			c.G2122A						.						30	37	35					17																	27442787		2041	4187	6228	SO:0001583	missense	399687	exon12			ACAGCTCCTCCAG	D86970	CCDS45641.1, CCDS45642.1	17q11.2	2011-09-27			ENSG00000196535	ENSG00000196535		"Myosins / Myosin superfamily : Class XVIII"	31104	protein-coding gene	gene with protein product		610067				12761286	Standard	NM_078471		Approved	KIAA0216, MysPDZ	uc002hdt.1	Q92614	OTTHUMG00000166360	ENST00000527372.1:c.2122G>A	chr17.hg19:g.27442787C>T	ENSP00000437073:p.Glu708Lys	54.0	0.0		34.0	15.0	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Missense_Mutation	SNP	ENST00000527372.1	hg19	CCDS45642.1	.	.	.	.	.	.	.	.	.	.	C	37	6.113689	0.97296	.	.	ENSG00000196535	ENST00000354329;ENST00000359450;ENST00000533112;ENST00000531253;ENST00000527372;ENST00000458428	D;D;D;D	0.87887	-2.31;-2.31;-2.31;-2.31	5.84	5.84	0.93424	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.93006	0.7774	M	0.64170	1.965	0.58432	D	0.999998	D;D;D;D;D	0.89917	0.999;0.998;0.998;0.998;1.0	D;D;D;D;D	0.91635	0.966;0.994;0.994;0.994;0.999	D	0.92946	0.6376	10	0.87932	D	0	.	20.1379	0.98040	0.0:1.0:0.0:0.0	.	377;320;708;708;708	Q92614-2;F8W6Y3;Q92614-3;Q92614-4;Q92614	.;.;.;.;MY18A_HUMAN	K	708;708;708;708;708;320	ENSP00000346291:E708K;ENSP00000435932:E708K;ENSP00000434228:E708K;ENSP00000437073:E708K	ENSP00000346291:E708K	E	-	1	0	MYO18A	24466913	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.453000	0.80700	2.779000	0.95612	0.655000	0.94253	GAG	.	.		0.642	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471		T	27442787	C	T	27442787	3	4	274	1	0	0	0	0	1	0	0	0	10074	864	30	3	4166	3	MYO18A	17	27442787	Missense_Mutation	SNP	C	TCGA-G3-A25U-01A-11D-A16V-10	19865253	27442787	53752423	33	39575										
PTPN2	5771	hgsc.bcm.edu	37	chr18	12802149	12802149	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tagaaagttctttccatcgtTtctaggtagggaagagaaat	10	5	2	2			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr18:12802149T>G	ENST00000309660.5	-	8	953	c.860A>C	c.(859-861)aAa>aCa	p.K287T	PTPN2_ENST00000591115.1_Splice_Site_p.K310T|PTPN2_ENST00000591497.1_Splice_Site_p.K258T|PTPN2_ENST00000353319.4_Splice_Site_p.K287T|PTPN2_ENST00000327283.3_Splice_Site_p.K287T	NM_002828.3	NP_002819.2	P17706	PTN2_HUMAN	protein tyrosine phosphatase, non-receptor type 2	287					B cell differentiation (GO:0030183)|cytokine-mediated signaling pathway (GO:0019221)|erythrocyte differentiation (GO:0030218)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemotaxis (GO:0050922)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of inflammatory response (GO:0050728)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of interleukin-2-mediated signaling pathway (GO:1902206)|negative regulation of interleukin-4-mediated signaling pathway (GO:1902215)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|negative regulation of lipid storage (GO:0010888)|negative regulation of macrophage colony-stimulating factor signaling pathway (GO:1902227)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of positive thymic T cell selection (GO:1902233)|negative regulation of prolactin signaling pathway (GO:1902212)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|negative regulation of tyrosine phosphorylation of Stat1 protein (GO:0042512)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|negative regulation of tyrosine phosphorylation of Stat6 protein (GO:0042527)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of gluconeogenesis (GO:0045722)|regulation of hepatocyte growth factor receptor signaling pathway (GO:1902202)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|T cell differentiation (GO:0030217)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|syntaxin binding (GO:0019905)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|prostate(1)|skin(3)	13		Lung NSC(161;8.94e-06)				TTTCCATCGTTTCTAGGTAGG	0.279																																					p.K310T		Atlas-SNP	.											.	PTPN2	37	.	0			c.A929C						.						61	52	55					18																	12802149		2203	4299	6502	SO:0001630	splice_region_variant	5771	exon9			CATCGTTTCTAGG	M25393	CCDS11863.1, CCDS11864.1, CCDS11865.1, CCDS59306.1	18p11.3-p11.2	2011-06-09			ENSG00000175354	ENSG00000175354		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9650	protein-coding gene	gene with protein product		176887		PTPT		2164224	Standard	NM_002828		Approved	TCELLPTP, TC-PTP, TCPTP	uc002krp.3	P17706	OTTHUMG00000131702	ENST00000309660.5:c.859-1A>C	chr18.hg19:g.12802149T>G		66.0	0.0		98.0	51.0	NM_001207013	A8K955|A8MXU3|K7ENG3|Q96AU5|Q96HR2	Missense_Mutation	SNP	ENST00000309660.5	hg19	CCDS11865.1	.	.	.	.	.	.	.	.	.	.	T	15.53	2.860965	0.51482	.	.	ENSG00000175354	ENST00000327283;ENST00000353319;ENST00000341361;ENST00000309660	T;T;T	0.04275	3.67;3.68;3.66	5.52	5.52	0.82312	.	0.000000	0.56097	D	0.000022	T	0.09555	0.0235	M	0.69823	2.125	0.80722	D	1	B;B;B;B;B	0.33135	0.399;0.066;0.107;0.085;0.04	B;B;B;B;B	0.35607	0.206;0.124;0.065;0.032;0.058	T	0.03306	-1.1050	10	0.44086	T	0.13	.	13.6713	0.62427	0.0:0.0:0.0:1.0	.	287;287;264;287;287	P17706;P17706-2;Q59F91;Q96AU5;A8K3N4	PTN2_HUMAN;.;.;.;.	T	287;287;264;287	ENSP00000320298:K287T;ENSP00000320546:K287T;ENSP00000311857:K287T	ENSP00000311857:K287T	K	-	2	0	PTPN2	12792149	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	4.869000	0.63028	2.222000	0.72286	0.455000	0.32223	AAA	.	.		0.279	PTPN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254613.3	NM_002828, NM_080422, NM_080423	Missense_Mutation	G	12802149	T	G	12802149	5	3	274	1	0	0	0	0	0	0	1	0	12798	1855	64	5	421	5	PTPN2	18	12802149	Splice_Site	SNP	T	TCGA-G3-A25U-01A-11D-A16V-10		12802149	65275099	34	39576										
PIN1	5300	hgsc.bcm.edu	37	chr19	9949168	9949168	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gccagtgggagcggcccagcGgcaacagcagcagtggtggc	18	12	0	0			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr19:9949168G>T	ENST00000247970.4	+	2	137	c.115G>T	c.(115-117)Ggc>Tgc	p.G39C	PIN1_ENST00000587625.1_Missense_Mutation_p.G39C|PIN1_ENST00000380889.6_3'UTR|PIN1_ENST00000588695.1_Missense_Mutation_p.G39C	NM_006221.3	NP_006212.1	Q13526	PIN1_HUMAN	peptidylprolyl cis/trans isomerase, NIMA-interacting 1	39	WW. {ECO:0000255|PROSITE- ProRule:PRU00224}.				cell cycle (GO:0007049)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|negative regulation of cell motility (GO:2000146)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)|regulation of cytokinesis (GO:0032465)|regulation of mitosis (GO:0007088)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	GTPase activating protein binding (GO:0032794)|mitogen-activated protein kinase kinase binding (GO:0031434)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|phosphoserine binding (GO:0050815)|phosphothreonine binding (GO:0050816)	p.G39C(1)		skin(3)	3						GCGGCCCAGCGGCAACAGCAG	0.652																																					p.G39C		Atlas-SNP	.											PIN1_ENST00000247970,NS,carcinoma,0,1	PIN1	7	.	1	Substitution - Missense(1)	lung(1)	c.G115T						.						17	19	18					19																	9949168		2201	4298	6499	SO:0001583	missense	5300	exon2			CCCAGCGGCAACA		CCDS12220.1	19p13	2014-09-17	2008-03-25		ENSG00000127445	ENSG00000127445			8988	protein-coding gene	gene with protein product		601052	"protein (peptidyl-prolyl cis/trans isomerase) NIMA-interacting 1"			8606777	Standard	NM_006221		Approved	dod	uc002mml.2	Q13526		ENST00000247970.4:c.115G>T	chr19.hg19:g.9949168G>T	ENSP00000247970:p.Gly39Cys	55.0	0.0		46.0	17.0	NM_006221	A8K4V9|Q53X75	Missense_Mutation	SNP	ENST00000247970.4	hg19	CCDS12220.1	.	.	.	.	.	.	.	.	.	.	G	19.07	3.755544	0.69648	.	.	ENSG00000127445	ENST00000247970;ENST00000424497	T	0.76839	-1.05	3.63	2.59	0.31030	WW/Rsp5/WWP (3);	0.327520	0.27851	N	0.017596	T	0.80969	0.4726	M	0.69185	2.1	0.42263	D	0.992026	D;P;D	0.65815	0.995;0.894;0.983	P;P;P	0.58721	0.769;0.649;0.844	T	0.79351	-0.1839	9	.	.	.	-36.7392	6.9465	0.24522	0.1238:0.0:0.8762:0.0	.	39;39;39	B3KUM4;Q13526;E7EQR5	.;PIN1_HUMAN;.	C	39	ENSP00000247970:G39C	.	G	+	1	0	PIN1	9810168	1.000000	0.71417	0.996000	0.52242	0.968000	0.65278	5.971000	0.70440	1.125000	0.41998	0.555000	0.69702	GGC	.	.		0.652	PIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451107.1			T	9949168	G	T	9949168	3	4	274	1	0	0	0	0	1	0	0	0	11939	1116	39	1	121	1	PIN1	19	9949168	Missense_Mutation	SNP	G	TCGA-G3-A25U-01A-11D-A16V-10		9949168	49179815	35	39577										
ARHGAP33	115703	hgsc.bcm.edu	37	chr19	36272086	36272086	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cgctgctgctccgagttcatTgaggcccacggggtggtgga	16	11	1	1			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr19:36272086T>G	ENST00000007510.4	+	12	1161	c.1017T>G	c.(1015-1017)atT>atG	p.I339M	ARHGAP33_ENST00000378944.5_Missense_Mutation_p.I203M|ARHGAP33_ENST00000314737.5_Missense_Mutation_p.I339M			O14559	RHG33_HUMAN	Rho GTPase activating protein 33	339	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|Rac GTPase activator activity (GO:0030675)			endometrium(7)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	37						CCGAGTTCATTGAGGCCCACG	0.657																																					p.I339M		Atlas-SNP	.											.	ARHGAP33	102	.	0			c.T1017G						.						75	74	74					19																	36272086		2203	4300	6503	SO:0001583	missense	115703	exon12			GTTCATTGAGGCC	AY044864	CCDS12477.1, CCDS54254.1	19q13.13	2011-06-29	2010-02-19	2010-02-19		ENSG00000004777		"Rho GTPase activating proteins"	23085	protein-coding gene	gene with protein product		614902	"sorting nexin 26"	SNX26		12297274, 12461558	Standard	NM_052948		Approved	FLJ39019, TCGAP	uc002obs.2	O14559		ENST00000007510.4:c.1017T>G	chr19.hg19:g.36272086T>G	ENSP00000007510:p.Ile339Met	34.0	0.0		42.0	19.0	NM_052948	O14552|O14560|Q6ZSP6|Q96CP3|Q9NT23	Missense_Mutation	SNP	ENST00000007510.4	hg19		.	.	.	.	.	.	.	.	.	.	T	17.70	3.454980	0.63290	.	.	ENSG00000004777	ENST00000007510;ENST00000314737;ENST00000378944	T;T;T	0.27557	1.66;1.66;1.66	5.3	-4.36	0.03645	.	0.000000	0.85682	D	0.000000	T	0.62732	0.2452	H	0.96604	3.85	0.34950	D	0.751159	D;D	0.89917	0.999;1.0	D;D	0.91635	0.999;0.996	T	0.72584	-0.4249	10	0.87932	D	0	.	13.0487	0.58942	0.1181:0.7333:0.0:0.1486	.	203;339	O14559-10;O14559-11	.;.	M	339;339;203	ENSP00000007510:I339M;ENSP00000320038:I339M;ENSP00000368227:I203M	ENSP00000007510:I339M	I	+	3	3	ARHGAP33	40963926	0.001000	0.12720	0.923000	0.36655	0.973000	0.67179	-1.984000	0.01487	-1.103000	0.03019	-0.366000	0.07423	ATT	.	.		0.657	ARHGAP33-201	KNOWN	basic	protein_coding	protein_coding		NM_052948		G	36272086	T	G	36272086	3	3	274	1	0	0	0	0	1	0	0	0	882	1800	63	5	1063	5	ARHGAP33	19	36272086	Missense_Mutation	SNP	T	TCGA-G3-A25U-01A-11D-A16V-10	26322918	36272086	22856897	36	39578										
FAM123B	139285	hgsc.bcm.edu	37	chrX	63410591	63410591	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	caccccagggcaggccttggTagaatcgactatggtagttg	13	10	0	1			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chrX:63410591T>A	ENST00000330258.3	-	2	2848	c.2576A>T	c.(2575-2577)tAc>tTc	p.Y859F	AMER1_ENST00000374869.3_Intron|AMER1_ENST00000403336.1_Intron	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	859					adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)									CAGGCCTTGGTAGAATCGACT	0.552																																					p.Y859F		Atlas-SNP	.											.	.	.	.	67	Whole gene deletion(67)	kidney(65)|ovary(1)|large_intestine(1)	c.A2576T						.						40	43	42					X																	63410591		2116	4204	6320	SO:0001583	missense	139285	exon2			CCTTGGTAGAATC	AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"-"	26837	protein-coding gene	gene with protein product	"Wilms Tumor on the X", "adenomatous polyposis coli membrane recruitment 1"	300647	"family with sequence similarity 123B"	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.2576A>T	chrX.hg19:g.63410591T>A	ENSP00000329117:p.Tyr859Phe	107.0	0.0		82.0	36.0	NM_152424	A2IB86|Q8N885	Missense_Mutation	SNP	ENST00000330258.3	hg19	CCDS14377.2	.	.	.	.	.	.	.	.	.	.	T	8.304	0.820525	0.16678	.	.	ENSG00000184675	ENST00000330258	T	0.39056	1.1	4.79	0.735	0.18300	.	.	.	.	.	T	0.17323	0.0416	N	0.08118	0	0.80722	D	1	B	0.09022	0.002	B	0.08055	0.003	T	0.08249	-1.0731	8	.	.	.	-0.6102	4.4958	0.11837	0.3703:0.0941:0.0:0.5356	.	859	Q5JTC6	F123B_HUMAN	F	859	ENSP00000329117:Y859F	.	Y	-	2	0	FAM123B	63327316	1.000000	0.71417	0.999000	0.59377	0.932000	0.56968	1.635000	0.37134	0.252000	0.21531	0.430000	0.28490	TAC	.	.		0.552	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		A	63410591	T	A	63410591	3	1	274	1	0	0	0	0	1	0	0	0	5428	1638	57	4	835	4	FAM123B	23	63410591	Missense_Mutation	SNP	T	TCGA-G3-A25U-01A-11D-A16V-10		63410591	91859969	37	39579										
TEX11	56159	hgsc.bcm.edu	37	chrX	70053381	70053383	+	In_Frame_Del	DEL	CAA	CAA	-													0	0	1	0	0	0	1	1	0	accatctgggggagcctcatCaacatatctttacattgcag							TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chrX:70053381_70053383delCAA	ENST00000395889.2	-	9	786_788	c.631_633delTTG	c.(631-633)ttgdel	p.L211del	TEX11_ENST00000344304.3_In_Frame_Del_p.L211del|TEX11_ENST00000374333.2_In_Frame_Del_p.L196del	NM_001003811.1	NP_001003811.1	Q8IYF3	TEX11_HUMAN	testis expressed 11	211					chiasma assembly (GO:0051026)|fertilization (GO:0009566)|male gonad development (GO:0008584)|male meiosis chromosome segregation (GO:0007060)|meiotic gene conversion (GO:0006311)|negative regulation of apoptotic process (GO:0043066)|reciprocal meiotic recombination (GO:0007131)|resolution of meiotic recombination intermediates (GO:0000712)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)				breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(13)|ovary(3)|prostate(3)|skin(3)	48	Renal(35;0.156)					GGAGCCTCATCAACATATCTTTA	0.379																																					p.211_212del		Atlas-Indel,Pindel	.											.	TEX11	132	.	0			c.632_634del						.																																			SO:0001651	inframe_deletion	56159	exon9			.	AF285594	CCDS35323.1, CCDS43968.1	Xp11	2008-02-05	2007-03-13		ENSG00000120498	ENSG00000120498			11733	protein-coding gene	gene with protein product		300311	"testis expressed sequence 11"			11279525	Standard	NM_001003811		Approved	TSGA3, TGC1	uc004dyl.3	Q8IYF3	OTTHUMG00000021782	ENST00000395889.2:c.631_633delTTG	chrX.hg19:g.70053381_70053383delCAA	ENSP00000379226:p.Leu211del	178.0	0.0		172.0	63.0	NM_001003811	A8K8V6|Q5JQQ8|Q96LZ4|Q96M47|Q9BXU6	In_Frame_Del	DEL	ENST00000395889.2	hg19	CCDS35323.1																																																																																			.	.		0.379	TEX11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359072.1			-	70053383	CAA	-	70053381	7	5	274	1	0	1	0	1	0	0	0	0	15789	825	29	0	2281	0	TEX11	23	70053381	In_Frame_Del	DEL	CAA	TCGA-G3-A25U-01A-11D-A16V-10	6642790	70053381	85217179	38	39580										
TNMD	64102	hgsc.bcm.edu	37	chrX	99854571	99854571	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	attgttgtatttactgccgtCgaggcaaccgctattgccgc	10	11	0	0			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chrX:99854571C>A	ENST00000373031.4	+	7	1028	c.811C>A	c.(811-813)Cga>Aga	p.R271R		NM_022144.2	NP_071427.2	Q9H2S6	TNMD_HUMAN	tenomodulin	271					cellular response to BMP stimulus (GO:0071773)|endothelial cell morphogenesis (GO:0001886)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|tendon cell differentiation (GO:0035990)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(7)|skin(1)	16						TTACTGCCGTCGAGGCAACCG	0.478																																					p.R271R		Atlas-SNP	.											.	TNMD	40	.	0			c.C811A						.						86	56	66					X																	99854571		2203	4300	6503	SO:0001819	synonymous_variant	64102	exon7			TGCCGTCGAGGCA	AF191770	CCDS14469.1	Xq21.33-q23	2012-10-10			ENSG00000000005	ENSG00000000005		"BRICHOS domain containing"	17757	protein-coding gene	gene with protein product	"BRICHOS domain containing 4"	300459					Standard	NM_022144		Approved	myodulin, ChM1L, tendin, TEM, BRICD4	uc004efy.4	Q9H2S6	OTTHUMG00000022001	ENST00000373031.4:c.811C>A	chrX.hg19:g.99854571C>A		81.0	0.0		61.0	18.0	NM_022144	Q9HBX0|Q9UJG0	Silent	SNP	ENST00000373031.4	hg19	CCDS14469.1																																																																																			.	.		0.478	TNMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057481.1	NM_022144		A	99854571	C	A	99854571	2	1	274	1	0	0	0	0	0	0	0	1	16337	876	31	1		1	TNMD	23	99854571	Silent	SNP	C	TCGA-G3-A25U-01A-11D-A16V-10	29801190	99854571	55415989	39	39581										
LONRF3	79836	hgsc.bcm.edu	37	chrX	118148215	118148215	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tcatgggattacataactgtGtctatcagcaagcatcattg	8	8	4	0			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chrX:118148215G>A	ENST00000371628.3	+	10	2051	c.2020G>A	c.(2020-2022)Gtc>Atc	p.V674I	LONRF3_ENST00000304778.7_Missense_Mutation_p.V633I|LONRF3_ENST00000472173.1_3'UTR|LONRF3_ENST00000422289.2_Missense_Mutation_p.V418I	NM_001031855.1	NP_001027026.1	Q496Y0	LONF3_HUMAN	LON peptidase N-terminal domain and ring finger 3	674	Lon.						ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	36						ACATAACTGTGTCTATCAGCA	0.448																																					p.V674I		Atlas-SNP	.											.	LONRF3	138	.	0			c.G2020A						.						332	266	288					X																	118148215		2203	4300	6503	SO:0001583	missense	79836	exon10			AACTGTGTCTATC	AK026265	CCDS14575.1, CCDS35374.1, CCDS76014.1	Xq24	2013-01-09	2005-08-19	2005-08-19	ENSG00000175556	ENSG00000175556		"RING-type (C3HC4) zinc fingers"	21152	protein-coding gene	gene with protein product			"ring finger protein 127"	RNF127			Standard	XM_005262476		Approved	FLJ22612	uc004eqw.3	Q496Y0	OTTHUMG00000022262	ENST00000371628.3:c.2020G>A	chrX.hg19:g.118148215G>A	ENSP00000360690:p.Val674Ile	89.0	0.0		127.0	60.0	NM_001031855	Q5JPN6|Q8NB00|Q9H647	Missense_Mutation	SNP	ENST00000371628.3	hg19	CCDS35374.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	33|33	5.224584|5.224584	0.95139|0.95139	.|.	.|.	ENSG00000175556|ENSG00000175556	ENST00000439603|ENST00000365713;ENST00000304778;ENST00000371628;ENST00000422289	T|T;T;T;T	0.40756|0.36340	1.02|1.26;1.26;1.26;1.26	5.7|5.7	5.7|5.7	0.88788|0.88788	.|Peptidase S16, lon N-terminal (1);PUA-like domain (1);	.|0.000000	.|0.64402	.|D	.|0.000001	T|T	0.67785|0.67785	0.2930|0.2930	M|M	0.88310|0.88310	2.945|2.945	0.58432|0.58432	D|D	0.999998|0.999998	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.91635	.|0.995;0.996;0.999	T|T	0.74657|0.74657	-0.3592|-0.3592	7|10	0.56958|0.87932	D|D	0.05|0	-47.094|-47.094	17.6221|17.6221	0.88084|0.88084	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|418;633;674	.|B3KUN7;Q496Y0-2;Q496Y0	.|.;.;LONF3_HUMAN	Y|I	439|633;633;674;418	ENSP00000414519:C439Y|ENSP00000360691:V633I;ENSP00000307732:V633I;ENSP00000360690:V674I;ENSP00000408894:V418I	ENSP00000414519:C439Y|ENSP00000307732:V633I	C|V	+|+	2|1	0|0	LONRF3|LONRF3	118032243|118032243	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.958000|0.958000	0.62258|0.62258	9.869000|9.869000	0.99810|0.99810	2.377000|2.377000	0.81083|0.81083	0.600000|0.600000	0.82982|0.82982	TGT|GTC	.	.		0.448	LONRF3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355124.2	NM_024778		A	118148215	G	A	118148215	3	1	274	1	0	0	0	0	1	0	0	0	8905	1377	48	3	2058	3	LONRF3	23	118148215	Missense_Mutation	SNP	G	TCGA-G3-A25U-01A-11D-A16V-10	18293644	118148215	37122345	40	39582										
KIF1B	23095	hgsc.bcm.edu	37	chr1	10381913	10381913	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	2	1	1.11728395061728	NA	1.11728395061728	0.428571428571429	1	0	tcagtgtggaactgaaaaagAaggtatggagcaggaggaca	15	4	1	2			TCGA-G3-A25V-01A-11D-A16V-10	TCGA-G3-A25V-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4624fd20-e2ad-4826-b606-a694b04e1076	eac002f0-7695-4df1-8ff0-2c5c976279df	g.chr1:10381913A>C	ENST00000377086.1	+	24	2558	c.2356A>C	c.(2356-2358)Aag>Cag	p.K786Q	KIF1B_ENST00000377081.1_Missense_Mutation_p.K786Q|KIF1B_ENST00000263934.6_Missense_Mutation_p.K740Q			O60333	KIF1B_HUMAN	kinesin family member 1B	786					anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		ACTGAAAAAGAAGGTATGGAG	0.502																																					p.K740Q		Atlas-SNP	.											.	KIF1B	242	.	0			c.A2218C						.						54	54	54					1																	10381913		2203	4300	6503	SO:0001583	missense	23095	exon22			AAAAAGAAGGTAT	AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"Kinesins", "Pleckstrin homology (PH) domain containing"	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.2356A>C	chr1.hg19:g.10381913A>C	ENSP00000366290:p.Lys786Gln	63.0	0.0		80.0	19.0	NM_015074	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Missense_Mutation	SNP	ENST00000377086.1	hg19		.	.	.	.	.	.	.	.	.	.	A	17.63	3.436481	0.62955	.	.	ENSG00000054523	ENST00000355249;ENST00000263934;ENST00000377086;ENST00000377081	T;T;T	0.75050	-0.9;-0.9;-0.9	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.76097	0.3940	L	0.28192	0.835	0.80722	D	1	P;P;D;P;P;D	0.76494	0.87;0.609;0.999;0.609;0.765;0.989	B;B;D;B;B;D	0.75020	0.299;0.298;0.926;0.186;0.287;0.985	T	0.70898	-0.4747	10	0.11485	T	0.65	.	15.5286	0.75932	1.0:0.0:0.0:0.0	.	772;746;786;760;786;740	Q4R9M9;Q4R9M7;Q4VXC4;Q4R9M8;O60333;O60333-2	.;.;.;.;KIF1B_HUMAN;.	Q	786;740;786;786	ENSP00000263934:K740Q;ENSP00000366290:K786Q;ENSP00000366284:K786Q	ENSP00000263934:K740Q	K	+	1	0	KIF1B	10304500	1.000000	0.71417	1.000000	0.80357	0.851000	0.48451	5.782000	0.68973	2.120000	0.65058	0.459000	0.35465	AAG	.	.		0.502	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1			C	10381913	A	C	10381913	3	2	275	1	0	0	0	0	1	0	0	0	8293	247	9	5	3789	5	KIF1B	1	10381913	Missense_Mutation	SNP	A	TCGA-G3-A25V-01A-11D-A16V-10		10381913	238868708	1	39583										
ST6GALNAC5	81849	hgsc.bcm.edu	37	chr1	77528691	77528691	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	2	1	1.11728395061728	NA	1.11728395061728	0.428571428571429	1	0	acccttcagtaccttatcatTattatgaaccttttggacct	4	11	2	1			TCGA-G3-A25V-01A-11D-A16V-10	TCGA-G3-A25V-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4624fd20-e2ad-4826-b606-a694b04e1076	eac002f0-7695-4df1-8ff0-2c5c976279df	g.chr1:77528691T>C	ENST00000477717.1	+	5	1046	c.811T>C	c.(811-813)Tat>Cat	p.Y271H		NM_030965.1	NP_112227.1	Q9BVH7	SIA7E_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	271					glycosphingolipid biosynthetic process (GO:0006688)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	integral component of Golgi membrane (GO:0030173)	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity (GO:0001665)|sialyltransferase activity (GO:0008373)			endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	18						ACCTTATCATTATTATGAACC	0.403																																					p.Y271H		Atlas-SNP	.											.	ST6GALNAC5	59	.	0			c.T811C						.						117	117	117					1																	77528691		2203	4300	6503	SO:0001583	missense	81849	exon5			TATCATTATTATG		CCDS673.1	1p31.1	2013-03-01	2005-02-07	2005-02-07	ENSG00000117069	ENSG00000117069		"Sialyltransferases"	19342	protein-coding gene	gene with protein product		610134	"sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) E"	SIAT7E		10521438, 10601645	Standard	NM_030965		Approved	MGC3184, ST6GalNAcV	uc001dhi.3	Q9BVH7	OTTHUMG00000009687	ENST00000477717.1:c.811T>C	chr1.hg19:g.77528691T>C	ENSP00000417583:p.Tyr271His	89.0	0.0		117.0	12.0	NM_030965	B1AK82	Missense_Mutation	SNP	ENST00000477717.1	hg19	CCDS673.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.572262	0.86542	.	.	ENSG00000117069	ENST00000477717;ENST00000438953	T	0.71461	-0.57	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	D	0.87071	0.6086	H	0.94734	3.575	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90710	0.4627	10	0.87932	D	0	-24.81	16.3789	0.83431	0.0:0.0:0.0:1.0	.	271	Q9BVH7	SIA7E_HUMAN	H	271;181	ENSP00000417583:Y271H	ENSP00000406658:Y181H	Y	+	1	0	ST6GALNAC5	77301279	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.649000	0.83500	2.267000	0.75376	0.533000	0.62120	TAT	.	.		0.403	ST6GALNAC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026692.2	NM_030965		C	77528691	T	C	77528691	3	2	275	1	0	0	0	0	1	0	0	0	15242	1754	61	2	829	2	ST6GALNAC5	1	77528691	Missense_Mutation	SNP	T	TCGA-G3-A25V-01A-11D-A16V-10	67146778	77528691	171721930	2	39584										
ELTD1	64123	hgsc.bcm.edu	37	chr1	79356902	79356902	+	Splice_Site	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0689655172413793	2	1	1.11728395061728	NA	1.11728395061728	0.428571428571429	1	0	ctgtaatattcttcttgaatCtaaaaattaaaaaaaggaaa	4	4	3	1			TCGA-G3-A25V-01A-11D-A16V-10	TCGA-G3-A25V-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4624fd20-e2ad-4826-b606-a694b04e1076	eac002f0-7695-4df1-8ff0-2c5c976279df	g.chr1:79356902C>T	ENST00000370742.3	-	15	2074		c.e15-1			NM_022159.3	NP_071442.2	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain containing 1						G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(45)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	69				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)		CTTCTTGAATCTAAAAATTAA	0.259																																					.		Atlas-SNP	.											.	ELTD1	143	.	0			c.2011-1G>A						.						58	53	54					1																	79356902		1783	4039	5822	SO:0001630	splice_region_variant	64123	exon16			TTGAATCTAAAAA	AF192403	CCDS41352.1	1p33-p32	2014-08-08			ENSG00000162618	ENSG00000162618		"-", "GPCR / Class B : Orphans"	20822	protein-coding gene	gene with protein product						11050079	Standard	NM_022159		Approved	ETL	uc001diq.4	Q9HBW9	OTTHUMG00000009738	ENST00000370742.3:c.2011-1G>A	chr1.hg19:g.79356902C>T		181.0	0.0		285.0	40.0	NM_022159	B1AR71|Q5KU34	Splice_Site	SNP	ENST00000370742.3	hg19	CCDS41352.1	.	.	.	.	.	.	.	.	.	.	C	13.17	2.155873	0.38021	.	.	ENSG00000162618	ENST00000370742;ENST00000401034	.	.	.	5.37	5.37	0.77165	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.2948	0.87168	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ELTD1	79129490	1.000000	0.71417	0.997000	0.53966	0.336000	0.28762	6.835000	0.75344	2.516000	0.84829	0.655000	0.94253	.	.	.		0.259	ELTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026859.1	NM_022159	Intron	T	79356902	C	T	79356902	5	4	275	1	0	0	0	0	0	0	1	0	5086	927	32	3	66	3	ELTD1	1	79356902	Splice_Site	SNP	C	TCGA-G3-A25V-01A-11D-A16V-10	1828211	79356902	169893719	3	39585										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103343720	103343720	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0689655172413793	2	1	1.11728395061728	NA	1.11728395061728	0.428571428571429	1	0	tcttttcatagccttttctgGactgtaaaataaagcagaaa	6	7	3	1			TCGA-G3-A25V-01A-11D-A16V-10	TCGA-G3-A25V-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4624fd20-e2ad-4826-b606-a694b04e1076	eac002f0-7695-4df1-8ff0-2c5c976279df	g.chr1:103343720G>T	ENST00000370096.3	-	67	5588	c.5276C>A	c.(5275-5277)tCc>tAc	p.S1759Y	COL11A1_ENST00000358392.2_Splice_Site_p.S1771Y|COL11A1_ENST00000512756.1_Splice_Site_p.S1643Y|COL11A1_ENST00000353414.4_Splice_Site_p.S1720Y	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	1759	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		GCCTTTTCTGGACTGTAAAAT	0.308																																					p.S1771Y		Atlas-SNP	.											.	COL11A1	972	.	0			c.C5312A						.						66	61	62					1																	103343720		2203	4300	6503	SO:0001630	splice_region_variant	1301	exon67			TTTCTGGACTGTA	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.5275-1C>A	chr1.hg19:g.103343720G>T		48.0	0.0		103.0	14.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	hg19	CCDS778.1	.	.	.	.	.	.	.	.	.	.	G	6.270	0.418019	0.11870	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000370090;ENST00000512756	T;T;T;T	0.74002	-0.8;-0.8;-0.8;-0.8	5.36	5.36	0.76844	Fibrillar collagen, C-terminal (4);	0.335856	0.32918	N	0.005489	T	0.54415	0.1857	L	0.34521	1.04	0.39274	D	0.964436	P;P;P;P;P	0.48503	0.794;0.846;0.911;0.873;0.755	P;B;B;P;B	0.45998	0.5;0.367;0.367;0.5;0.367	T	0.53005	-0.8499	10	0.16420	T	0.52	.	12.575	0.56359	0.0752:0.0:0.9248:0.0	.	1643;1720;1771;1759;979	E9PCU0;P12107-3;P12107-2;P12107;F5H5Z5	.;.;.;COBA1_HUMAN;.	Y	1759;1771;1720;979;1643	ENSP00000359114:S1759Y;ENSP00000351163:S1771Y;ENSP00000302551:S1720Y;ENSP00000426533:S1643Y	ENSP00000302551:S1720Y	S	-	2	0	COL11A1	103116308	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.779000	0.62375	2.774000	0.95407	0.655000	0.94253	TCC	.	.		0.308	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630	Missense_Mutation	T	103343720	G	T	103343720	5	4	275	1	0	0	0	0	0	0	1	0	3669	1188	41	3	148	3	COL11A1	1	103343720	Splice_Site	SNP	G	TCGA-G3-A25V-01A-11D-A16V-10	23986818	103343720	145906901	4	39586										
ELK4	2005	hgsc.bcm.edu	37	chr1	205588972	205588972	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	2	1	1.11728395061728	NA	1.11728395061728	0.428571428571429	1	0	actttcacatgacagtcacaCataacctttctaagacaaac	3	12	3	2			TCGA-G3-A25V-01A-11D-A16V-10	TCGA-G3-A25V-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4624fd20-e2ad-4826-b606-a694b04e1076	eac002f0-7695-4df1-8ff0-2c5c976279df	g.chr1:205588972C>T	ENST00000357992.4	-	3	1420				ELK4_ENST00000468523.1_5'Flank|ELK4_ENST00000289703.4_Missense_Mutation_p.C401Y	NM_001973.3	NP_001964.2	P28324	ELK4_HUMAN	ELK4, ETS-domain protein (SRF accessory protein 1)						cell differentiation (GO:0030154)|histone H3 deacetylation (GO:0070932)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)		SLC45A3/ELK4(18)	breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|skin(1)	12	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0908)			GACAGTCACACATAACCTTTC	0.318			T	SLC45A3	prostate																																p.C401Y		Atlas-SNP	.		Dom	yes		1	1q32	2005	"ELK4, ETS-domain protein (SRF accessory protein 1)"		E	.	ELK4	45	.	0			c.G1202A						.						55	55	55					1																	205588972		2203	4300	6503	SO:0001627	intron_variant	2005	exon3			GTCACACATAACC	M85165	CCDS1456.1, CCDS1457.1	1q32	2008-02-05			ENSG00000158711	ENSG00000158711			3326	protein-coding gene	gene with protein product		600246				7851904, 8575773	Standard	NM_001973		Approved	SAP1		P28324	OTTHUMG00000037221	ENST00000357992.4:c.1080+121G>A	chr1.hg19:g.205588972C>T		82.0	0.0		103.0	17.0	NM_021795	P28323|Q6GSJ2	Missense_Mutation	SNP	ENST00000357992.4	hg19	CCDS1456.1	.	.	.	.	.	.	.	.	.	.	C	11.55	1.670708	0.29693	.	.	ENSG00000158711	ENST00000289703	T	0.32515	1.45	5.42	-9.81	0.00487	.	.	.	.	.	T	0.15478	0.0373	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35500	-0.9786	8	0.87932	D	0	.	3.6076	0.08049	0.3214:0.4379:0.1162:0.1245	.	401	P28324-2	.	Y	401	ENSP00000289703:C401Y	ENSP00000289703:C401Y	C	-	2	0	ELK4	203855595	0.000000	0.05858	0.000000	0.03702	0.083000	0.17756	-0.490000	0.06482	-1.803000	0.01242	-1.261000	0.01458	TGT	.	.		0.318	ELK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090615.1	NM_021795		T	205588972	C	T	205588972	1	4	275	0	1	0	0	0	0	0	0	0	5063	478	17	3		3	ELK4	1	205588972	Intron	SNP	C	TCGA-G3-A25V-01A-11D-A16V-10	102245252	205588972	43661649	5	39587										
PGBD2	267002	hgsc.bcm.edu	37	chr1	249211485	249211485	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	2	1	1.11728395061728	NA	1.11728395061728	0.428571428571429	1	0	ttacattttgcagataacaaCgaacttgatgcaagtgatag	8	6	0	3			TCGA-G3-A25V-01A-11D-A16V-10	TCGA-G3-A25V-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4624fd20-e2ad-4826-b606-a694b04e1076	eac002f0-7695-4df1-8ff0-2c5c976279df	g.chr1:249211485C>T	ENST00000329291.5	+	3	849	c.702C>T	c.(700-702)aaC>aaT	p.N234N	PGBD2_ENST00000355360.4_5'UTR|PGBD2_ENST00000539153.1_Silent_p.N231N|PGBD2_ENST00000462488.1_3'UTR	NM_170725.2	NP_733843.1	Q6P3X8	PGBD2_HUMAN	piggyBac transposable element derived 2	234										NS(1)|endometrium(3)|lung(6)|ovary(1)|skin(3)	14	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.012)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			CAGATAACAACGAACTTGATG	0.433																																					p.N234N		Atlas-SNP	.											.	PGBD2	103	.	0			c.C702T						.						109	111	111					1																	249211485		2203	4300	6503	SO:0001819	synonymous_variant	267002	exon3			TAACAACGAACTT	AF229602	CCDS31128.1, CCDS31129.1	1q	2008-02-05			ENSG00000185220	ENSG00000185220			19399	protein-coding gene	gene with protein product							Standard	XM_005270333		Approved		uc001ifh.3	Q6P3X8	OTTHUMG00000040424	ENST00000329291.5:c.702C>T	chr1.hg19:g.249211485C>T		37.0	0.0		42.0	8.0	NM_170725	B3KVR8|Q6MZF8	Silent	SNP	ENST00000329291.5	hg19	CCDS31128.1																																																																																			.	.		0.433	PGBD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000097318.1			T	249211485	C	T	249211485	2	4	275	1	0	0	0	0	0	0	0	1	11790	535	19	1		1	PGBD2	1	249211485	Silent	SNP	C	TCGA-G3-A25V-01A-11D-A16V-10	43622513	249211485	39136	6	39588										
RANBP2	5903	hgsc.bcm.edu	37	chr2	109347859	109347859	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	2	1	1.11728395061728	NA	1.11728395061728	0.428571428571429	1	0	gtaaaaatgatgttactgatGgaagagcaaaatactggctt	10	4	0	3			TCGA-G3-A25V-01A-11D-A16V-10	TCGA-G3-A25V-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4624fd20-e2ad-4826-b606-a694b04e1076	eac002f0-7695-4df1-8ff0-2c5c976279df	g.chr2:109347859G>T	ENST00000283195.6	+	4	460	c.334G>T	c.(334-336)Gga>Tga	p.G112*		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	112					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						TGTTACTGATGGAAGAGCAAA	0.338																																					p.G112X		Atlas-SNP	.											.	RANBP2	488	.	0			c.G334T						.						129	144	139					2																	109347859		2203	4299	6502	SO:0001587	stop_gained	5903	exon4			ACTGATGGAAGAG	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"Tetratricopeptide (TTC) repeat domain containing"	9848	protein-coding gene	gene with protein product		601181	"acute necrotizing encephalopathy 1 (autosomal dominant)"	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.334G>T	chr2.hg19:g.109347859G>T	ENSP00000283195:p.Gly112*	858.0	0.0		841.0	110.0	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Nonsense_Mutation	SNP	ENST00000283195.6	hg19	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	G	33	5.273520	0.95459	.	.	ENSG00000153201	ENST00000409491;ENST00000283195	.	.	.	4.97	4.97	0.65823	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-25.9233	18.5845	0.91183	0.0:0.0:1.0:0.0	.	.	.	.	X	112	.	ENSP00000283195:G112X	G	+	1	0	RANBP2	108714291	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.531000	0.67148	2.477000	0.83638	0.573000	0.79308	GGA	.	.		0.338	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		T	109347859	G	T	109347859	4	4	275	1	0	0	0	0	0	1	0	0	13043	1349	47	3	348	3	RANBP2	2	109347859	Nonsense_Mutation	SNP	G	TCGA-G3-A25V-01A-11D-A16V-10		109347859	133851514	7	39589										
PMS1	5378	hgsc.bcm.edu	37	chr2	190719433	190719433	+	Frame_Shift_Del	DEL	G	G	-													0.0689655172413793	2	1	1.11728395061728	NA	1.11728395061728	0.428571428571429	1	0	aagaccatatagatgagagtGgggaaaatgaggaagaagca							TCGA-G3-A25V-01A-11D-A16V-10	TCGA-G3-A25V-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4624fd20-e2ad-4826-b606-a694b04e1076	eac002f0-7695-4df1-8ff0-2c5c976279df	g.chr2:190719433delG	ENST00000441310.2	+	9	1668	c.1435delG	c.(1435-1437)gggfs	p.G479fs	PMS1_ENST00000432292.3_Frame_Shift_Del_p.G303fs|PMS1_ENST00000447232.2_Frame_Shift_Del_p.G479fs|PMS1_ENST00000421722.1_3'UTR|PMS1_ENST00000409823.3_Frame_Shift_Del_p.G440fs|PMS1_ENST00000418224.3_Frame_Shift_Del_p.G303fs	NM_000534.4	NP_000525.1	P54277	PMS1_HUMAN	PMS1 postmeiotic segregation increased 1 (S. cerevisiae)	479					ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)	MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|mismatched DNA binding (GO:0030983)|single-stranded DNA binding (GO:0003697)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(16)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			OV - Ovarian serous cystadenocarcinoma(117;0.0013)|Epithelial(96;0.0263)|all cancers(119;0.0751)			AGATGAGAGTGGGGAAAATGA	0.388			"Mis, N"			"colorectal, endometrial, ovarian"		Direct reversal of damage;Mismatch excision repair (MMR)																													p.S478fs		Atlas-Indel,Pindel	.	yes	Rec		Hereditary non-polyposis colorectal cancer	2	2q31-q33	5378	PMS1 postmeiotic segregation increased 1 (S. cerevisiae)		E	.	PMS1	78	.	0			c.1434delT						.						48	52	51					2																	190719433		2196	4298	6494	SO:0001589	frameshift_variant	5378	exon9			.		CCDS2302.1, CCDS46473.1, CCDS46474.1, CCDS74615.1	2q31-q33	2014-09-17	2001-11-28		ENSG00000064933	ENSG00000064933			9121	protein-coding gene	gene with protein product		600258	"postmeiotic segregation increased (S. cerevisiae) 1"	PMSL1		8072530	Standard	NM_000534		Approved		uc002urh.4	P54277	OTTHUMG00000132664	ENST00000441310.2:c.1435delG	chr2.hg19:g.190719433delG	ENSP00000406490:p.Gly479fs	87.0	0.0		130.0	14.0	NM_001128144	D3DPI1|Q4VAL4|Q5FBZ3|Q5FBZ6|Q5FBZ8	Frame_Shift_Del	DEL	ENST00000441310.2	hg19	CCDS2302.1																																																																																			.	.		0.388	PMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255918.2			-	190719433	G	-	190719433	7	5	275	1	0	1	0	1	0	0	0	0	12151	1348	47	0	1465	0	PMS1	2	190719433	Frame_Shift_Del	DEL	G	TCGA-G3-A25V-01A-11D-A16V-10	81371574	190719433	52479940	8	39590										
SLC9A10	285335	hgsc.bcm.edu	37	chr3	111996688	111996688	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	2	1	1.11728395061728	NA	1.11728395061728	0.428571428571429	1	0	tataattaaccaaaaagccgGgaattgaaattaaaagtatc	6	5	0	1			TCGA-G3-A25V-01A-11D-A16V-10	TCGA-G3-A25V-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4624fd20-e2ad-4826-b606-a694b04e1076	eac002f0-7695-4df1-8ff0-2c5c976279df	g.chr3:111996688G>A	ENST00000305815.5	-	5	590	c.338C>T	c.(337-339)cCc>cTc	p.P113L	SLC9C1_ENST00000487372.1_Missense_Mutation_p.P113L|SLC9C1_ENST00000467397.1_5'Flank	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	113					cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										CAAAAAGCCGGGAATTGAAAT	0.303																																					p.P113L		Atlas-SNP	.											.	.	.	.	0			c.C338T						.						45	52	50					3																	111996688		2191	4297	6488	SO:0001583	missense	285335	exon5			AAGCCGGGAATTG	AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"Solute carriers"	31401	protein-coding gene	gene with protein product	"sperm-NHE"	612738	"solute carrier family 9, isoform 10", "solute carrier family 9, member 10"	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.338C>T	chr3.hg19:g.111996688G>A	ENSP00000306627:p.Pro113Leu	126.0	0.0		227.0	28.0	NM_183061	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	hg19	CCDS33817.1	.	.	.	.	.	.	.	.	.	.	G	10.55	1.381080	0.24944	.	.	ENSG00000172139	ENST00000305815;ENST00000487372;ENST00000486574	T;T;T	0.19532	2.14;2.14;2.14	5.13	5.13	0.70059	Cation/H+ exchanger (1);	0.000000	0.50627	D	0.000118	T	0.38585	0.1046	L	0.55481	1.735	0.48040	D	0.999571	D;D	0.89917	0.967;1.0	P;D	0.91635	0.752;0.999	T	0.05419	-1.0886	10	0.17369	T	0.5	.	14.0939	0.65008	0.0:0.0:1.0:0.0	.	113;113	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	L	113;113;40	ENSP00000306627:P113L;ENSP00000420688:P113L;ENSP00000417274:P40L	ENSP00000306627:P113L	P	-	2	0	SLC9A10	113479378	1.000000	0.71417	0.923000	0.36655	0.005000	0.04900	4.760000	0.62235	2.375000	0.81037	0.655000	0.94253	CCC	.	.		0.303	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061		A	111996688	G	A	111996688	3	1	275	1	0	0	0	0	1	0	0	0	14725	1232	43	3	3295	3	SLC9A10	3	111996688	Missense_Mutation	SNP	G	TCGA-G3-A25V-01A-11D-A16V-10		111996688	86025742	9	39591										
KBTBD12	166348	hgsc.bcm.edu	37	chr3	127642837	127642838	+	In_Frame_Ins	INS	-	-	TCA													0.0689655172413793	2	1	1.11728395061728	NA	1.11728395061728	0.428571428571429	1	0	cacggaaaacctatttcatcINStcatctcccaagtacggaga							TCGA-G3-A25V-01A-11D-A16V-10	TCGA-G3-A25V-10A-01D-A16V-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4624fd20-e2ad-4826-b606-a694b04e1076	eac002f0-7695-4df1-8ff0-2c5c976279df	g.chr3:127642837_127642838insTCA	ENST00000405109.1	+	2	1400_1401	c.933_934insTCA	c.(934-936)tca>TCAtca	p.312_312S>SS	KBTBD12_ENST00000407609.3_Intron|KBTBD12_ENST00000405256.1_In_Frame_Ins_p.312_312S>SS|KBTBD12_ENST00000343941.4_Intron			Q3ZCT8	KBTBC_HUMAN	kelch repeat and BTB (POZ) domain containing 12	312										endometrium(1)|large_intestine(6)|lung(5)|ovary(1)	13						CCTATTTCATCTCATCTCCCAA	0.411																																					p.I311delinsIS		Atlas-INDEL	.											.	KBTBD12	41	.	0			c.933_934insTCA						.																																			SO:0001652	inframe_insertion	166348	exon1			.		CCDS33848.2	3q21.3	2013-01-08	2009-10-01	2009-10-01	ENSG00000187715	ENSG00000187715		"BTB/POZ domain containing"	25731	protein-coding gene	gene with protein product			"kelch domain containing 6"	KLHDC6			Standard	NM_207335		Approved	FLJ46299	uc010hsr.3	Q3ZCT8	OTTHUMG00000150508	ENST00000405109.1:c.934_936dupTCA	chr3.hg19:g.127642838_127642840dupTCA	ENSP00000385957:p.Ser313dup	127.0	0.0		176.0	24.0	NM_207335	B5MCC6|Q6ZRK1	In_Frame_Ins	INS	ENST00000405109.1	hg19	CCDS33848.2																																																																																			.	.		0.411	KBTBD12-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318682.1	NM_207335		TCA	127642838	-	TCA	127642837	7	5	275	1	0	1	1	0	0	0	0	0	8000	903	32	0	935	0	KBTBD12	3	127642837	In_Frame_Ins	INS	-	TCGA-G3-A25V-01A-11D-A16V-10	15646149	127642837	70379593	10	39592										
GCNT2	2651	hgsc.bcm.edu	37	chr6	10586875	10586875	+	Intron	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	2	1	1.11728395061728	NA	1.11728395061728	0.428571428571429	1	0	agggaaaaatatcaccccagGggtgctgcctcctgaccatg	11	12	1	1			TCGA-G3-A25V-01A-11D-A16V-10	TCGA-G3-A25V-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4624fd20-e2ad-4826-b606-a694b04e1076	eac002f0-7695-4df1-8ff0-2c5c976279df	g.chr6:10586875G>T	ENST00000379597.3	+	2	1481				GCNT2_ENST00000410107.1_Intron|GCNT2_ENST00000265012.4_Missense_Mutation_p.G218V|GCNT2_ENST00000316170.3_Intron|GCNT2_ENST00000495262.1_Intron|GCNT2_ENST00000397423.2_Intron			Q8N0V5	GNT2A_HUMAN	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group)						maintenance of lens transparency (GO:0036438)|negative regulation of cell-substrate adhesion (GO:0010812)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of protein kinase B signaling (GO:0051897)|posttranscriptional regulation of gene expression (GO:0010608)|protein glycosylation (GO:0006486)|transforming growth factor beta receptor signaling pathway (GO:0007179)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)			endometrium(2)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)	12	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)		ATCACCCCAGGGGTGCTGCCT	0.413																																					p.G218V		Atlas-SNP	.											.	GCNT2	123	.	0			c.G653T						.						72	76	75					6																	10586875		2203	4300	6503	SO:0001627	intron_variant	2651	exon1			CCCCAGGGGTGCT	L41605	CCDS4512.1, CCDS4513.1, CCDS34338.1	6p24.2	2014-07-18	2006-02-23		ENSG00000111846	ENSG00000111846	2.4.1.150	"Blood group antigens", "Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	4204	protein-coding gene	gene with protein product	"Ii blood group", "unassigned linkage group 3"	600429	"glucosaminyl (N-acetyl) transferase 5", "glucosaminyl (N-acetyl) transferase 2, I-branching enzyme", "glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (Ii blood group)", "cataract, congenital"	NACGT1, II, GCNT5, CCAT		8449405, 9915862	Standard	NM_145649		Approved	IGNT, NAGCT1, bA421M1.1, bA360O19.2, ULG3	uc003mze.3	Q06430	OTTHUMG00000014244	ENST00000379597.3:c.926-34709G>T	chr6.hg19:g.10586875G>T		91.0	0.0		88.0	16.0	NM_145655		Missense_Mutation	SNP	ENST00000379597.3	hg19	CCDS34338.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.164504	0.78339	.	.	ENSG00000111846	ENST00000265012	T	0.10960	2.82	5.47	5.47	0.80525	.	.	.	.	.	T	0.23133	0.0559	M	0.83774	2.66	0.80722	D	1	P	0.42649	0.786	P	0.51297	0.665	T	0.01212	-1.1417	9	0.87932	D	0	.	19.3314	0.94291	0.0:0.0:1.0:0.0	.	218	Q8NFS9	GNT2C_HUMAN	V	218	ENSP00000265012:G218V	ENSP00000265012:G218V	G	+	2	0	GCNT2	10694861	1.000000	0.71417	0.994000	0.49952	0.956000	0.61745	6.525000	0.73795	2.552000	0.86080	0.655000	0.94253	GGG	.	.		0.413	GCNT2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327912.3	NM_145649		T	10586875	G	T	10586875	1	4	275	0	1	0	0	0	0	0	0	0	6309	1232	43	3		3	GCNT2	6	10586875	Intron	SNP	G	TCGA-G3-A25V-01A-11D-A16V-10		10586875	160528192	11	39593										
GPR116	221395	hgsc.bcm.edu	37	chr6	46847716	46847716	+	Frame_Shift_Del	DEL	A	A	-													0.0689655172413793	2	1	1.11728395061728	NA	1.11728395061728	0.428571428571429	1	0	acaaaacttccttttcacacAccagactgactgtgtcccct							TCGA-G3-A25V-01A-11D-A16V-10	TCGA-G3-A25V-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4624fd20-e2ad-4826-b606-a694b04e1076	eac002f0-7695-4df1-8ff0-2c5c976279df	g.chr6:46847716delA	ENST00000283296.7	-	9	1163	c.875delT	c.(874-876)gtgfs	p.V292fs	GPR116_ENST00000456426.2_Intron|GPR116_ENST00000265417.7_Frame_Shift_Del_p.V292fs|GPR116_ENST00000362015.4_Frame_Shift_Del_p.V292fs	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	292	Ig-like 1.				energy reserve metabolic process (GO:0006112)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|neuropeptide signaling pathway (GO:0007218)|regulation of lipid metabolic process (GO:0019216)|surfactant homeostasis (GO:0043129)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(21)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59			Lung(136;0.192)			CTTTTCACACACCAGACTGAC	0.418																																					p.V292fs	NSCLC(59;410 1274 8751 36715 50546)	Atlas-INDEL	.											.	GPR116	133	.	0			c.876delG						.						149	128	135					6																	46847716		2203	4300	6503	SO:0001589	frameshift_variant	221395	exon9			.	AB018301	CCDS4919.1	6p12.3	2014-08-08			ENSG00000069122	ENSG00000069122		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19030	protein-coding gene	gene with protein product						12435584	Standard	NM_001098518		Approved	DKFZp564O1923, KIAA0758	uc003oyo.3	Q8IZF2	OTTHUMG00000014793	ENST00000283296.7:c.875delT	chr6.hg19:g.46847716delA	ENSP00000283296:p.Val292fs	81.0	0.0		90.0	15.0	NM_015234	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Frame_Shift_Del	DEL	ENST00000283296.7	hg19	CCDS4919.1																																																																																			.	.		0.418	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234		-	46847716	A	-	46847716	7	5	275	1	0	1	0	1	0	0	0	0	6641	159	6	0	3217	0	GPR116	6	46847716	Frame_Shift_Del	DEL	A	TCGA-G3-A25V-01A-11D-A16V-10	36260841	46847716	124267351	12	39594										
EEF1A1	1915	hgsc.bcm.edu	37	chr6	74227628	74227628	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	2	1	1.11728395061728	NA	1.11728395061728	0.428571428571429	1	0	gatgacacccaccgcaactgTctgtctcatatcacgaacag	7	14	3	1			TCGA-G3-A25V-01A-11D-A16V-10	TCGA-G3-A25V-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4624fd20-e2ad-4826-b606-a694b04e1076	eac002f0-7695-4df1-8ff0-2c5c976279df	g.chr6:74227628T>A	ENST00000316292.9	-	7	2285	c.1294A>T	c.(1294-1296)Aca>Tca	p.T432S	EEF1A1_ENST00000309268.6_Missense_Mutation_p.T432S|EEF1A1_ENST00000491404.1_Intron|EEF1A1_ENST00000331523.2_Missense_Mutation_p.T432S	NM_001402.5	NP_001393.1	P68104	EF1A1_HUMAN	eukaryotic translation elongation factor 1 alpha 1	432					cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation elongation factor activity (GO:0003746)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(6)|prostate(2)|skin(3)	18						ACCGCAACTGTCTGTCTCATA	0.403											OREG0003893	type=REGULATORY REGION|Gene=BC038897|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.T432S		Atlas-SNP	.											.	EEF1A1	56	.	0			c.A1294T						.						42	44	43					6																	74227628		2203	4300	6503	SO:0001583	missense	1915	exon8			CAACTGTCTGTCT	BC019669	CCDS4980.1	6q14.1	2010-06-30	2004-11-19		ENSG00000156508	ENSG00000156508			3189	protein-coding gene	gene with protein product		130590	"leukocyte receptor cluster (LRC) member 7"	EF1A, EEF1A, LENG7		8812466, 10941842	Standard	NM_001402		Approved	EE1A1	uc003phj.3	P68104	OTTHUMG00000015031	ENST00000316292.9:c.1294A>T	chr6.hg19:g.74227628T>A	ENSP00000339063:p.Thr432Ser	84.0	0.0	1151	113.0	18.0	NM_001402	P04719|P04720|Q6IQ15	Missense_Mutation	SNP	ENST00000316292.9	hg19	CCDS4980.1	.	.	.	.	.	.	.	.	.	.	T	14.44	2.534829	0.45073	.	.	ENSG00000156508	ENST00000316292;ENST00000309268;ENST00000331523;ENST00000391977	T;T;T	0.56275	0.47;0.47;0.47	4.81	4.81	0.61882	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal (2);Translation elongation factor EFTu/EF1A, C-terminal (2);	0.000000	0.85682	U	0.000000	T	0.54663	0.1872	H	0.95079	3.62	0.80722	D	1	B;B;B	0.18166	0.026;0.026;0.026	B;B;B	0.24541	0.054;0.054;0.054	T	0.66929	-0.5799	10	0.87932	D	0	.	11.932	0.52851	0.0:0.0:0.1449:0.8551	.	432;432;432	P68104;Q6IPS9;Q5VTE0	EF1A1_HUMAN;.;EF1A3_HUMAN	S	432;432;432;411	ENSP00000339063:T432S;ENSP00000339053:T432S;ENSP00000330054:T432S	ENSP00000339053:T432S	T	-	1	0	EEF1A1	74284349	1.000000	0.71417	0.997000	0.53966	0.894000	0.52154	7.617000	0.83032	1.929000	0.55896	0.454000	0.30748	ACA	.	.		0.403	EEF1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041210.2	NM_001402		A	74227628	T	A	74227628	3	1	275	1	0	0	0	0	1	0	0	0	4925	1667	58	4	98	4	EEF1A1	6	74227628	Missense_Mutation	SNP	T	TCGA-G3-A25V-01A-11D-A16V-10	27379912	74227628	96887439	13	39595										
NUP205	23165	hgsc.bcm.edu	37	chr7	135330244	135330244	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	2	1	1.11728395061728	NA	1.11728395061728	0.428571428571429	1	0	gagacctgcctatttattctTtggcgccatctggagtacta	9	10	2	1			TCGA-G3-A25V-01A-11D-A16V-10	TCGA-G3-A25V-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4624fd20-e2ad-4826-b606-a694b04e1076	eac002f0-7695-4df1-8ff0-2c5c976279df	g.chr7:135330244T>G	ENST00000285968.6	+	41	5738	c.5712T>G	c.(5710-5712)ctT>ctG	p.L1904L		NM_015135.2	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	1904					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			breast(4)|central_nervous_system(2)|endometrium(9)|kidney(7)|large_intestine(17)|liver(4)|lung(36)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	93						TATTTATTCTTTGGCGCCATC	0.403											OREG0018343	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L1904L		Atlas-SNP	.											.	NUP205	198	.	0			c.T5712G						.						212	214	213					7																	135330244		2203	4300	6503	SO:0001819	synonymous_variant	23165	exon41			TATTCTTTGGCGC	D86978	CCDS34759.1	7q31.32	2007-03-26	2004-01-06	2004-01-07	ENSG00000155561	ENSG00000155561			18658	protein-coding gene	gene with protein product		614352	"chromosome 7 open reading frame 14"	C7orf14		9039502, 9348540	Standard	NM_015135		Approved	KIAA0225	uc003vsw.3	Q92621	OTTHUMG00000155497	ENST00000285968.6:c.5712T>G	chr7.hg19:g.135330244T>G		125.0	0.0	1617	184.0	23.0	NM_015135	A6H8X3|Q86YC1	Silent	SNP	ENST00000285968.6	hg19	CCDS34759.1																																																																																			.	.		0.403	NUP205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340358.1			G	135330244	T	G	135330244	2	3	275	1	0	0	0	0	0	0	0	1	10768	1828	64	5		5	NUP205	7	135330244	Silent	SNP	T	TCGA-G3-A25V-01A-11D-A16V-10		135330244	23808419	14	39596										
DPP6	1804	hgsc.bcm.edu	37	chr7	154645528	154645528	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0689655172413793	2	1	1.11728395061728	NA	1.11728395061728	0.428571428571429	1	0	tgacggtgcacaacacaacaGataagaaaagtaagtgctct	9	8	1	3			TCGA-G3-A25V-01A-11D-A16V-10	TCGA-G3-A25V-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4624fd20-e2ad-4826-b606-a694b04e1076	eac002f0-7695-4df1-8ff0-2c5c976279df	g.chr7:154645528G>T	ENST00000377770.3	+	17	1846	c.1705G>T	c.(1705-1707)Gat>Tat	p.D569Y	RP11-476H24.1_ENST00000448767.1_RNA|DPP6_ENST00000332007.3_Missense_Mutation_p.D507Y|DPP6_ENST00000404039.1_Missense_Mutation_p.D505Y|DPP6_ENST00000427557.1_Missense_Mutation_p.D462Y			P42658	DPP6_HUMAN	dipeptidyl-peptidase 6	569					cell death (GO:0008219)|neuronal action potential (GO:0019228)|positive regulation of potassium ion transmembrane transport (GO:1901381)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(3)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(35)|pancreas(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	71	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			CAACACAACAGATAAGAAAAG	0.428																																					p.D569Y	NSCLC(125;1384 1783 2490 7422 34254)	Atlas-SNP	.											.	DPP6	383	.	0			c.G1705T						.						170	152	158					7																	154645528		1876	4110	5986	SO:0001583	missense	1804	exon17			ACAACAGATAAGA	M96859	CCDS75682.1, CCDS75683.1, CCDS75684.1	7q36.2	2006-08-07	2006-01-12		ENSG00000130226	ENSG00000130226			3010	protein-coding gene	gene with protein product		126141	"dipeptidylpeptidase VI", "dipeptidylpeptidase 6"			1729689	Standard	XM_006715871		Approved	DPPX	uc003wlk.3	P42658	OTTHUMG00000151511	ENST00000377770.3:c.1705G>T	chr7.hg19:g.154645528G>T	ENSP00000367001:p.Asp569Tyr	145.0	0.0		154.0	41.0	NM_130797		Missense_Mutation	SNP	ENST00000377770.3	hg19		.	.	.	.	.	.	.	.	.	.	G	8.809	0.934762	0.18206	.	.	ENSG00000130226	ENST00000404039;ENST00000377770;ENST00000332007;ENST00000427557	T;T;T;T	0.33438	1.41;1.41;1.41;1.41	4.47	4.47	0.54385	.	0.540503	0.21329	N	0.076326	T	0.32436	0.0829	L	0.59436	1.845	0.48830	D	0.999715	B;B;B;B	0.18013	0.025;0.005;0.002;0.003	B;B;B;B	0.21151	0.033;0.006;0.004;0.003	T	0.12708	-1.0537	10	0.45353	T	0.12	-7.4579	14.1935	0.65654	0.0:0.0:1.0:0.0	.	462;507;569;505	E9PDL2;P42658-2;P42658;E9PF59	.;.;DPP6_HUMAN;.	Y	505;569;507;462	ENSP00000385578:D505Y;ENSP00000367001:D569Y;ENSP00000328226:D507Y;ENSP00000397303:D462Y	ENSP00000328226:D507Y	D	+	1	0	DPP6	154276461	0.971000	0.33674	0.830000	0.32933	0.141000	0.21300	4.143000	0.58051	2.158000	0.67659	0.655000	0.94253	GAT	.	.		0.428	DPP6-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322932.1	NM_130797		T	154645528	G	T	154645528	3	4	275	1	0	0	0	0	1	0	0	0	4732	942	33	3	1887	3	DPP6	7	154645528	Missense_Mutation	SNP	G	TCGA-G3-A25V-01A-11D-A16V-10	19315284	154645528	4493135	15	39597										
PTPDC1	138639	hgsc.bcm.edu	37	chr9	96870207	96870207	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	2	1	1.11728395061728	NA	1.11728395061728	0.428571428571429	1	0	aagaaaaatgacaaaagatgGccctaagcctggcctctagc	9	10	1	3			TCGA-G3-A25V-01A-11D-A16V-10	TCGA-G3-A25V-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4624fd20-e2ad-4826-b606-a694b04e1076	eac002f0-7695-4df1-8ff0-2c5c976279df	g.chr9:96870207G>A	ENST00000375360.3	+	10	2586	c.2246G>A	c.(2245-2247)gGc>gAc	p.G749D	PTPDC1_ENST00000288976.3_Missense_Mutation_p.G801D	NM_001253830.1|NM_177995.2	NP_001240759.1|NP_818931.1	A2A3K4	PTPC1_HUMAN	protein tyrosine phosphatase domain containing 1	749					cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)		protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			endometrium(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	32						ACAAAAGATGGCCCTAAGCCT	0.378																																					p.G803D		Atlas-SNP	.											.	PTPDC1	134	.	0			c.G2408A						.						26	27	27					9																	96870207		2201	4298	6499	SO:0001583	missense	138639	exon9			AAGATGGCCCTAA	BC051654	CCDS6707.1, CCDS6708.1, CCDS75860.1	9q22.32	2011-06-09			ENSG00000158079	ENSG00000158079		"Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"	30184	protein-coding gene	gene with protein product	"protein tyrosine phosphatase PTP9Q22"					14702039	Standard	NM_152422		Approved	PTP9Q22, FLJ37312	uc010mrj.2	A2A3K4	OTTHUMG00000020258	ENST00000375360.3:c.2246G>A	chr9.hg19:g.96870207G>A	ENSP00000364509:p.Gly749Asp	78.0	0.0		131.0	11.0	NM_001253829	Q5T3M4|Q6NXE8|Q8IWM1|Q8N1X4|Q8N9F5	Missense_Mutation	SNP	ENST00000375360.3	hg19	CCDS6707.1	.	.	.	.	.	.	.	.	.	.	G	12.27	1.888815	0.33348	.	.	ENSG00000158079	ENST00000375360;ENST00000288976	T;T	0.16073	2.39;2.37	5.71	1.92	0.25849	.	0.604103	0.18814	N	0.130440	T	0.18215	0.0437	L	0.57536	1.79	0.09310	N	1	B;B;B;B	0.31680	0.335;0.328;0.335;0.083	B;B;B;B	0.34242	0.086;0.178;0.086;0.025	T	0.12426	-1.0548	10	0.59425	D	0.04	-0.8526	9.0699	0.36486	0.2712:0.0:0.7288:0.0	.	803;801;803;749	E7EN59;A2A3K4-2;A8K0X7;A2A3K4	.;.;.;PTPC1_HUMAN	D	749;801	ENSP00000364509:G749D;ENSP00000288976:G801D	ENSP00000288976:G801D	G	+	2	0	PTPDC1	95910028	0.007000	0.16637	0.000000	0.03702	0.682000	0.39822	1.565000	0.36386	0.105000	0.17753	0.650000	0.86243	GGC	.	.		0.378	PTPDC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000215007.1	NM_177995, NM_152422		A	96870207	G	A	96870207	3	1	275	1	0	0	0	0	1	0	0	0	12786	1203	42	3	2522	3	PTPDC1	9	96870207	Missense_Mutation	SNP	G	TCGA-G3-A25V-01A-11D-A16V-10		96870207	44343224	16	39598										
C9orf152	401546	hgsc.bcm.edu	37	chr9	112963511	112963511	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0689655172413793	2	1	1.11728395061728	NA	1.11728395061728	0.428571428571429	1	0	gagggagcctttgatcagatCccacaagcttgcccctatga	10	12	1	3			TCGA-G3-A25V-01A-11D-A16V-10	TCGA-G3-A25V-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4624fd20-e2ad-4826-b606-a694b04e1076	eac002f0-7695-4df1-8ff0-2c5c976279df	g.chr9:112963511C>T	ENST00000400613.4	-	2	1046	c.437G>A	c.(436-438)gGa>gAa	p.G146E	C9orf152_ENST00000473442.1_Intron	NM_001012993.2	NP_001013011.2	Q5JTZ5	CI152_HUMAN	chromosome 9 open reading frame 152	146										NS(1)|endometrium(1)|large_intestine(1)|lung(1)|skin(1)|stomach(1)	6						TTGATCAGATCCCACAAGCTT	0.532																																					p.G146E		Atlas-SNP	.											.	C9orf152	20	.	0			c.G437A						.						206	187	193					9																	112963511		2203	4300	6503	SO:0001583	missense	401546	exon2			TCAGATCCCACAA	BX648620	CCDS35102.2	9q31.3	2012-04-03			ENSG00000188959	ENSG00000188959			31455	protein-coding gene	gene with protein product							Standard	NM_001012993		Approved	bA470J20.2	uc011lwk.2	Q5JTZ5	OTTHUMG00000020478	ENST00000400613.4:c.437G>A	chr9.hg19:g.112963511C>T	ENSP00000383456:p.Gly146Glu	141.0	0.0		106.0	18.0	NM_001012993	A8MWT6	Missense_Mutation	SNP	ENST00000400613.4	hg19	CCDS35102.2	.	.	.	.	.	.	.	.	.	.	C	0.014	-1.594336	0.00857	.	.	ENSG00000188959	ENST00000400613	.	.	.	4.38	-3.56	0.04626	.	0.637853	0.14603	N	0.309514	T	0.12732	0.0309	N	0.12746	0.255	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.20009	-1.0288	9	0.16420	T	0.52	-2.9295	1.55	0.02573	0.1234:0.2292:0.2425:0.4049	.	146	Q5JTZ5	CI152_HUMAN	E	146	.	ENSP00000383456:G146E	G	-	2	0	C9orf152	112003332	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.214000	0.09292	-0.726000	0.04895	-1.845000	0.00574	GGA	.	.		0.532	C9orf152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053602.2	NM_001012993		T	112963511	C	T	112963511	3	4	275	1	0	0	0	0	1	0	0	0	2465	855	30	3	286	3	C9orf152	9	112963511	Missense_Mutation	SNP	C	TCGA-G3-A25V-01A-11D-A16V-10	16093304	112963511	28249920	17	39599										
OR4A5	81318	hgsc.bcm.edu	37	chr11	51411592	51411592	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0689655172413793	2	1	1.11728395061728	NA	1.11728395061728	0.428571428571429	1	0	ataatggtataaaacacagtCatgaacttatcagtaggaaa	7	5	2	1			TCGA-G3-A25V-01A-11D-A16V-10	TCGA-G3-A25V-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4624fd20-e2ad-4826-b606-a694b04e1076	eac002f0-7695-4df1-8ff0-2c5c976279df	g.chr11:51411592C>A	ENST00000319760.6	-	1	856	c.804G>T	c.(802-804)atG>atT	p.M268I		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, member 5	268						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(28)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	49		all_lung(304;0.236)				AAAACACAGTCATGAACTTAT	0.363																																					p.M268I		Atlas-SNP	.											.	OR4A5	116	.	0			c.G804T						.						50	49	49					11																	51411592		2201	4296	6497	SO:0001583	missense	81318	exon1			CACAGTCATGAAC	AB065506	CCDS73289.1	11p11.12	2012-08-09			ENSG00000221840	ENSG00000221840		"GPCR / Class A : Olfactory receptors"	15162	protein-coding gene	gene with protein product							Standard	NM_001005272		Approved		uc001nhi.2	Q8NH83	OTTHUMG00000166764	ENST00000319760.6:c.804G>T	chr11.hg19:g.51411592C>A	ENSP00000367664:p.Met268Ile	71.0	0.0		87.0	16.0	NM_001005272	Q6IF84	Missense_Mutation	SNP	ENST00000319760.6	hg19	CCDS31497.1	.	.	.	.	.	.	.	.	.	.	.	0.003	-2.457979	0.00173	.	.	ENSG00000221840	ENST00000319760	T	0.32753	1.44	2.2	-4.39	0.03611	GPCR, rhodopsin-like superfamily (1);	2.164420	0.02455	N	0.085995	T	0.11495	0.0280	N	0.02181	-0.65	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.20306	-1.0279	10	0.31617	T	0.26	.	4.7661	0.13132	0.5323:0.1613:0.0:0.3064	.	268	Q8NH83	OR4A5_HUMAN	I	268	ENSP00000367664:M268I	ENSP00000367664:M268I	M	-	3	0	OR4A5	51268168	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-3.282000	0.00528	-2.867000	0.00324	0.162000	0.16502	ATG	.	.		0.363	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272		A	51411592	C	A	51411592	3	1	275	1	0	0	0	0	1	0	0	0	11052	826	29	3	147	3	OR4A5	11	51411592	Missense_Mutation	SNP	C	TCGA-G3-A25V-01A-11D-A16V-10		51411592	83594924	18	39600										
GRIA4	2893	hgsc.bcm.edu	37	chr11	105623945	105623945	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	2	1	1.11728395061728	NA	1.11728395061728	0.428571428571429	1	0	ttcctgtatgacacagacagGggtaagtccagtttcttcat	9	9	2	2			TCGA-G3-A25V-01A-11D-A16V-10	TCGA-G3-A25V-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4624fd20-e2ad-4826-b606-a694b04e1076	eac002f0-7695-4df1-8ff0-2c5c976279df	g.chr11:105623945G>T	ENST00000530497.1	+	3	486	c.486G>T	c.(484-486)agG>agT	p.R162S	GRIA4_ENST00000393125.2_Splice_Site_p.R162S|GRIA4_ENST00000393127.2_Splice_Site_p.R162S|GRIA4_ENST00000525187.1_Splice_Site_p.R162S|GRIA4_ENST00000428631.2_Splice_Site_p.R162S|GRIA4_ENST00000282499.5_Splice_Site_p.R162S			P48058	GRIA4_HUMAN	glutamate receptor, ionotropic, AMPA 4	162					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(24)|liver(2)|lung(25)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	82		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)		ACACAGACAGGGGTAAGTCCA	0.393																																					p.R162S		Atlas-SNP	.											.	GRIA4	380	.	0			c.G486T						.						117	106	110					11																	105623945		2202	4299	6501	SO:0001630	splice_region_variant	2893	exon4			AGACAGGGGTAAG	U16129	CCDS8333.1, CCDS41706.1, CCDS41707.1	11q22	2012-08-29	2012-02-03		ENSG00000152578	ENSG00000152578		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4574	protein-coding gene	gene with protein product		138246	"glutamate receptor, ionotrophic, AMPA 4"	GLUR4			Standard	NM_001077244		Approved	GluA4, GLURD	uc001pix.2	P48058	OTTHUMG00000166236	ENST00000530497.1:c.487+1G>T	chr11.hg19:g.105623945G>T		58.0	0.0		59.0	10.0	NM_001077244	Q86XE8	Missense_Mutation	SNP	ENST00000530497.1	hg19	CCDS8333.1	.	.	.	.	.	.	.	.	.	.	G	16.50	3.141628	0.57044	.	.	ENSG00000152578	ENST00000393125;ENST00000282499;ENST00000393127;ENST00000428631;ENST00000531011;ENST00000530497;ENST00000525187	T;T;T;T;T;T;T	0.81415	-1.49;-1.49;-1.49;-1.49;-1.49;-1.49;-1.49	5.75	2.9	0.33743	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.82972	0.5153	L	0.41824	1.3	0.58432	D	0.999999	D;D;D;D	0.89917	0.999;1.0;1.0;0.98	D;D;D;P	0.91635	0.944;0.999;0.999;0.609	T	0.78974	-0.1992	10	0.36615	T	0.2	.	10.0649	0.42297	0.29:0.0:0.71:0.0	.	162;162;192;162	P48058;G3V164;Q59GL7;Q86XE8	GRIA4_HUMAN;.;.;.	S	162	ENSP00000376833:R162S;ENSP00000282499:R162S;ENSP00000376835:R162S;ENSP00000415551:R162S;ENSP00000432443:R162S;ENSP00000435775:R162S;ENSP00000432180:R162S	ENSP00000282499:R162S	R	+	3	2	GRIA4	105129155	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	1.879000	0.39618	0.370000	0.24538	-0.150000	0.13652	AGG	.	.		0.393	GRIA4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388593.1		Missense_Mutation	T	105623945	G	T	105623945	5	4	275	1	0	0	0	0	0	0	1	0	6779	1246	43	3	496	3	GRIA4	11	105623945	Splice_Site	SNP	G	TCGA-G3-A25V-01A-11D-A16V-10	54212353	105623945	29382571	19	39601										
STYK1	55359	hgsc.bcm.edu	37	chr12	10775259	10775259	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	2	1	1.11728395061728	NA	1.11728395061728	0.428571428571429	1	0	agagtcaccatctcatagagCaggatcccaaaagaccagct	8	12	2	3			TCGA-G3-A25V-01A-11D-A16V-10	TCGA-G3-A25V-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4624fd20-e2ad-4826-b606-a694b04e1076	eac002f0-7695-4df1-8ff0-2c5c976279df	g.chr12:10775259C>A	ENST00000075503.3	-	9	1465	c.945G>T	c.(943-945)ctG>ctT	p.L315L		NM_018423.2	NP_060893.2	Q6J9G0	STYK1_HUMAN	serine/threonine/tyrosine kinase 1	315	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)			breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|liver(1)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	26						TCTCATAGAGCAGGATCCCAA	0.378										HNSCC(73;0.22)																											p.L315L		Atlas-SNP	.											.	STYK1	55	.	0			c.G945T						.						153	142	146					12																	10775259		2203	4300	6503	SO:0001819	synonymous_variant	55359	exon9			ATAGAGCAGGATC	AF251059	CCDS8629.1	12p13.2	2005-01-21							18889	protein-coding gene	gene with protein product		611433				12841579	Standard	NM_018423		Approved	SuRTK106, DKFZp761P1010, NOK	uc001qys.2	Q6J9G0		ENST00000075503.3:c.945G>T	chr12.hg19:g.10775259C>A		89.0	0.0		132.0	15.0	NM_018423	B2R9T2|Q52LR3|Q9BXY2|Q9NSH1	Silent	SNP	ENST00000075503.3	hg19	CCDS8629.1																																																																																			.	.		0.378	STYK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399622.1	NM_018423		A	10775259	C	A	10775259	2	1	275	1	0	0	0	0	0	0	0	1	15374	697	25	3		3	STYK1	12	10775259	Silent	SNP	C	TCGA-G3-A25V-01A-11D-A16V-10		10775259	123076636	20	39602										
CAPS2	84698	hgsc.bcm.edu	37	chr12	75692559	75692559	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	2	1	1.11728395061728	NA	1.11728395061728	0.428571428571429	1	0	aataaaaggaagcacatttgTtctagaaagtaaatgaaaaa	7	3	1	2	rs372993486		TCGA-G3-A25V-01A-11D-A16V-10	TCGA-G3-A25V-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4624fd20-e2ad-4826-b606-a694b04e1076	eac002f0-7695-4df1-8ff0-2c5c976279df	g.chr12:75692559T>C	ENST00000409445.3	-	12	1205	c.1009A>G	c.(1009-1011)Aca>Gca	p.T337A	RP11-560G2.1_ENST00000534648.2_RNA|CAPS2_ENST00000393284.3_Splice_Site_p.T105A|CAPS2_ENST00000442339.2_Intron|CAPS2_ENST00000409004.1_5'UTR|CAPS2_ENST00000409799.1_Splice_Site_p.T255A	NM_032606.3	NP_115995.2	Q9BXY5	CAYP2_HUMAN	calcyphosine 2	337							calcium ion binding (GO:0005509)			endometrium(2)|large_intestine(1)|lung(4)|ovary(2)|skin(1)	10						AGCACATTTGTTCTAGAAAGT	0.323																																					p.T337A		Atlas-SNP	.											.	CAPS2	96	.	0			c.A1009G						.						99	97	98					12																	75692559		2203	4299	6502	SO:0001630	splice_region_variant	84698	exon12			CATTTGTTCTAGA	AF251056	CCDS9008.2, CCDS66424.1, CCDS73497.1	12q14.1	2013-01-10	2005-05-09		ENSG00000180881	ENSG00000180881		"EF-hand domain containing"	16471	protein-coding gene	gene with protein product		607724	"calcyphosphine 2"			11846421	Standard	NM_032606		Approved		uc001sxk.4	Q9BXY5	OTTHUMG00000152787	ENST00000409445.3:c.1008-1A>G	chr12.hg19:g.75692559T>C		76.0	0.0		95.0	12.0	NM_032606	Q6PH84|Q8N242|Q8NAY5	Missense_Mutation	SNP	ENST00000409445.3	hg19	CCDS9008.2	.	.	.	.	.	.	.	.	.	.	T	12.75	2.031379	0.35797	.	.	ENSG00000180881	ENST00000409799;ENST00000409445;ENST00000378703;ENST00000393284	D;T;T	0.82619	-1.63;1.87;1.91	5.45	5.45	0.79879	.	0.143817	0.49305	D	0.000152	T	0.79399	0.4439	M	0.65320	2	0.80722	D	1	B;B;B;B	0.34290	0.447;0.019;0.058;0.011	B;B;B;B	0.26202	0.067;0.019;0.013;0.014	T	0.78360	-0.2234	10	0.34782	T	0.22	-14.7626	15.5603	0.76240	0.0:0.0:0.0:1.0	.	105;73;337;255	Q9BXY5-2;Q9BXY5-3;Q9BXY5;B9A061	.;.;CAYP2_HUMAN;.	A	255;337;73;105	ENSP00000386977:T255A;ENSP00000386959:T337A;ENSP00000376963:T105A	ENSP00000367975:T73A	T	-	1	0	CAPS2	73978826	1.000000	0.71417	1.000000	0.80357	0.461000	0.32589	1.392000	0.34486	2.091000	0.63221	0.439000	0.28862	ACA	.	.		0.323	CAPS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000327880.2		Missense_Mutation	C	75692559	T	C	75692559	5	2	275	1	0	0	0	0	0	0	1	0	2640	1739	60	2	692	2	CAPS2	12	75692559	Splice_Site	SNP	T	TCGA-G3-A25V-01A-11D-A16V-10	64917300	75692559	58159336	21	39603										
CSNK1A1L	122011	hgsc.bcm.edu	37	chr13	37678905	37678906	+	Frame_Shift_Ins	INS	-	-	T													0.0689655172413793	2	1	1.11728395061728	NA	1.11728395061728	0.428571428571429	1	0	tggtcctgttgtctctgtacINStttttggccaaaccaaaatc					rs568346753		TCGA-G3-A25V-01A-11D-A16V-10	TCGA-G3-A25V-10A-01D-A16V-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4624fd20-e2ad-4826-b606-a694b04e1076	eac002f0-7695-4df1-8ff0-2c5c976279df	g.chr13:37678905_37678906insT	ENST00000379800.3	-	1	897_898	c.488_489insA	c.(487-489)aagfs	p.K163fs		NM_145203.5	NP_660204.2	Q8N752	KC1AL_HUMAN	casein kinase 1, alpha 1-like	163	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell morphogenesis (GO:0000902)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	37		Lung NSC(96;7.97e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.109)		all cancers(112;3.58e-07)|Epithelial(112;1.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00695)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0407)		TGTCTCTGTACTTTTTGGCCAA	0.421																																					p.K163fs		Atlas-INDEL	.											.	CSNK1A1L	69	.	0			c.489_490insA						.																																			SO:0001589	frameshift_variant	122011	exon1			.	BC028723	CCDS9363.1	13q13.2	2008-02-05			ENSG00000180138	ENSG00000180138			20289	protein-coding gene	gene with protein product							Standard	NM_145203		Approved	MGC33182	uc001uwm.1	Q8N752	OTTHUMG00000016748	ENST00000379800.3:c.489dupA	chr13.hg19:g.37678910_37678910dupT	ENSP00000369126:p.Lys163fs	323.0	0.0		286.0	43.0	NM_145203	Q5T2N2	Frame_Shift_Ins	INS	ENST00000379800.3	hg19	CCDS9363.1																																																																																			.	.		0.421	CSNK1A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044563.1	NM_145203		T	37678906	-	T	37678905	7	5	275	1	0	1	1	0	0	0	0	0	3953	564	20	0	528	0	CSNK1A1L	13	37678905	Frame_Shift_Ins	INS	-	TCGA-G3-A25V-01A-11D-A16V-10		37678905	77490973	22	39604										
OR4L1	122742	hgsc.bcm.edu	37	chr14	20528668	20528668	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	2	1	1.11728395061728	NA	1.11728395061728	0.428571428571429	1	0	tggataattggttttttacaCtccataagccagatagtttt	7	6	0	1			TCGA-G3-A25V-01A-11D-A16V-10	TCGA-G3-A25V-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4624fd20-e2ad-4826-b606-a694b04e1076	eac002f0-7695-4df1-8ff0-2c5c976279df	g.chr14:20528668C>T	ENST00000315683.1	+	1	465	c.465C>T	c.(463-465)caC>caT	p.H155H		NM_001004717.1	NP_001004717.1	Q8NH43	OR4L1_HUMAN	olfactory receptor, family 4, subfamily L, member 1	155						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(16)|ovary(2)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)		GTTTTTTACACTCCATAAGCC	0.398																																					p.H155H		Atlas-SNP	.											.	OR4L1	98	.	0			c.C465T						.						148	138	141					14																	20528668		2203	4300	6503	SO:0001819	synonymous_variant	122742	exon1			TTTACACTCCATA		CCDS32029.1	14q11.2	2013-09-23			ENSG00000176246	ENSG00000176246		"GPCR / Class A : Olfactory receptors"	15356	protein-coding gene	gene with protein product				OR4L2P			Standard	NM_001004717		Approved		uc001vwn.1	Q8NH43	OTTHUMG00000169492	ENST00000315683.1:c.465C>T	chr14.hg19:g.20528668C>T		53.0	0.0		103.0	14.0	NM_001004717	Q6IEZ5	Silent	SNP	ENST00000315683.1	hg19	CCDS32029.1																																																																																			.	.		0.398	OR4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404381.1			T	20528668	C	T	20528668	2	4	275	1	0	0	0	0	0	0	0	1	11083	564	20	3		3	OR4L1	14	20528668	Silent	SNP	C	TCGA-G3-A25V-01A-11D-A16V-10		20528668	86820872	23	39605										
CHD9	80205	hgsc.bcm.edu	37	chr16	53340280	53340280	+	Frame_Shift_Del	DEL	T	T	-													0.0689655172413793	2	1	1.11728395061728	NA	1.11728395061728	0.428571428571429	1	0	cttatatcttacaaggtggaTatatgctggcagcctcgtat							TCGA-G3-A25V-01A-11D-A16V-10	TCGA-G3-A25V-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4624fd20-e2ad-4826-b606-a694b04e1076	eac002f0-7695-4df1-8ff0-2c5c976279df	g.chr16:53340280delT	ENST00000398510.3	+	31	6838	c.6751delT	c.(6751-6753)tatfs	p.Y2251fs	CHD9_ENST00000447540.1_Frame_Shift_Del_p.Y2252fs|CHD9_ENST00000564845.1_Frame_Shift_Del_p.Y2251fs|CHD9_ENST00000566029.1_Frame_Shift_Del_p.Y2251fs			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	2251					cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				ACAAGGTGGATATATGCTGGC	0.393																																					p.G2250fs		Atlas-Indel,Pindel	.											.	CHD9	203	.	0			c.6750delA						.						79	78	79					16																	53340280		1880	4108	5988	SO:0001589	frameshift_variant	80205	exon32			.	AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.6751delT	chr16.hg19:g.53340280delT	ENSP00000381522:p.Tyr2251fs	89.0	0.0		97.0	15.0	NM_025134	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Frame_Shift_Del	DEL	ENST00000398510.3	hg19																																																																																				.	.		0.393	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134		-	53340280	T	-	53340280	7	5	275	1	0	1	0	1	0	0	0	0	3334	1406	49	0	6873	0	CHD9	16	53340280	Frame_Shift_Del	DEL	T	TCGA-G3-A25V-01A-11D-A16V-10		53340280	37014473	24	39606										
TM4SF5	9032	hgsc.bcm.edu	37	chr17	4686278	4686278	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0689655172413793	2	1	1.11728395061728	NA	1.11728395061728	0.428571428571429	1	0	gagatagtactgtgtgggatCcagctggtgaacgcgaccat	14	8	0	2			TCGA-G3-A25V-01A-11D-A16V-10	TCGA-G3-A25V-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4624fd20-e2ad-4826-b606-a694b04e1076	eac002f0-7695-4df1-8ff0-2c5c976279df	g.chr17:4686278C>T	ENST00000270560.3	+	4	556	c.525C>T	c.(523-525)atC>atT	p.I175I		NM_003963.2	NP_003954.2	O14894	T4S5_HUMAN	transmembrane 4 L six family member 5	175						integral component of plasma membrane (GO:0005887)				large_intestine(2)|lung(3)|ovary(1)	6						TGTGTGGGATCCAGCTGGTGA	0.597																																					p.I175I		Atlas-SNP	.											.	TM4SF5	26	.	0			c.C525T						.						123	104	110					17																	4686278		2203	4300	6503	SO:0001819	synonymous_variant	9032	exon4			TGGGATCCAGCTG	AF027204	CCDS11054.1	17p13.3	2007-01-06	2005-03-21		ENSG00000142484	ENSG00000142484			11857	protein-coding gene	gene with protein product		604657	"transmembrane 4 superfamily member 5"			9479038	Standard	NM_003963		Approved		uc002fyw.1	O14894	OTTHUMG00000090776	ENST00000270560.3:c.525C>T	chr17.hg19:g.4686278C>T		106.0	0.0		73.0	20.0	NM_003963	Q17RW9|Q6IB79	Silent	SNP	ENST00000270560.3	hg19	CCDS11054.1																																																																																			.	.		0.597	TM4SF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207558.2			T	4686278	C	T	4686278	2	4	275	1	0	0	0	0	0	0	0	1	15986	845	30	3		3	TM4SF5	17	4686278	Silent	SNP	C	TCGA-G3-A25V-01A-11D-A16V-10		4686278	76508932	25	39607										
TP53	7157	hgsc.bcm.edu	37	chr17	7577531	7577531	+	Frame_Shift_Del	DEL	G	G	-													0.0689655172413793	2	1	1.11728395061728	NA	1.11728395061728	0.428571428571429	1	0	agtgtgatgatggtgaggatGggcctccggttcatgccgcc							TCGA-G3-A25V-01A-11D-A16V-10	TCGA-G3-A25V-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4624fd20-e2ad-4826-b606-a694b04e1076	eac002f0-7695-4df1-8ff0-2c5c976279df	g.chr17:7577531delG	ENST00000269305.4	-	7	939	c.750delC	c.(748-750)cccfs	p.P250fs	TP53_ENST00000455263.2_Frame_Shift_Del_p.P250fs|TP53_ENST00000359597.4_Frame_Shift_Del_p.P250fs|TP53_ENST00000445888.2_Frame_Shift_Del_p.P250fs|TP53_ENST00000413465.2_Frame_Shift_Del_p.P250fs|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Frame_Shift_Del_p.P250fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	250	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		P -> A (in sporadic cancers; somatic mutation).|P -> F (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|P -> H (in sporadic cancers; somatic mutation).|P -> L (in sporadic cancers; somatic mutation).|P -> N (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|P -> Q (in sporadic cancers; somatic mutation).|P -> S (in sporadic cancers; somatic mutation).|P -> T (in sporadic cancers; somatic mutation).|RP -> SA (in a sporadic cancer; somatic mutation).|RP -> SS (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.?(5)|p.P250P(4)|p.P250L(2)|p.M246_P250delMNRRP(2)|p.P250_L252delPIL(2)|p.P250Q(2)|p.N247_P250delNRRP(1)|p.R248_P250delRRP(1)|p.P250_T253delPILT(1)|p.P250_I251insXXXXXX(1)|p.P250_I251insXXXXXXX(1)|p.R249_P250delRP(1)|p.P250_I251insX(1)|p.I251fs*96(1)|p.R249_T256delRPILTIIT(1)|p.R249_I251delRPI(1)|p.I251fs*13(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TGGTGAGGATGGGCCTCCGGT	0.577		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.I251fs	Pancreas(47;798 1329 9957 10801)	Atlas-Indel,Pindel	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,NS,malignant_melanoma,+1,4	TP53	33396	.	36	Deletion - In frame(10)|Whole gene deletion(8)|Unknown(5)|Substitution - Missense(4)|Substitution - coding silent(4)|Insertion - In frame(3)|Insertion - Frameshift(2)	biliary_tract(5)|breast(4)|bone(4)|upper_aerodigestive_tract(3)|large_intestine(3)|stomach(3)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(3)|skin(3)|genital_tract(1)|peritoneum(1)|oesophagus(1)|lung(1)|ovary(1)	c.751delA						.						154	112	126					17																	7577531		2203	4300	6503	SO:0001589	frameshift_variant	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	.	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.750delC	chr17.hg19:g.7577531delG	ENSP00000269305:p.Pro250fs	106.0	0.0		352.0	91.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Del	DEL	ENST00000269305.4	hg19	CCDS11118.1																																																																																			.	.		0.577	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		-	7577531	G	-	7577531	7	5	275	1	0	1	0	1	0	0	0	0	16396	1335	47	0	540	0	TP53	17	7577531	Frame_Shift_Del	DEL	G	TCGA-G3-A25V-01A-11D-A16V-10	2891253	7577531	73617679	26	39608										
MAP2K4	6416	hgsc.bcm.edu	37	chr17	11998923	11998923	+	Frame_Shift_Del	DEL	A	A	-													0.0689655172413793	2	1	1.11728395061728	NA	1.11728395061728	0.428571428571429	1	0	aacagtggatgaaaaagaacAaaaacaacttcttatggatt							TCGA-G3-A25V-01A-11D-A16V-10	TCGA-G3-A25V-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4624fd20-e2ad-4826-b606-a694b04e1076	eac002f0-7695-4df1-8ff0-2c5c976279df	g.chr17:11998923delA	ENST00000353533.5	+	4	488	c.425delA	c.(424-426)caafs	p.Q142fs	MAP2K4_ENST00000415385.3_Frame_Shift_Del_p.Q153fs|MAP2K4_ENST00000581941.1_3'UTR	NM_003010.2	NP_003001.1	P45985	MP2K4_HUMAN	mitogen-activated protein kinase kinase 4	142	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		Q -> L (in a lung squamous cell carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|cellular response to sorbitol (GO:0072709)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of DNA replication (GO:0045740)|positive regulation of neuron apoptotic process (GO:0043525)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|nucleus (GO:0005634)|perikaryon (GO:0043204)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.0?(10)|p.Q142L(1)|p.?(1)		NS(1)|biliary_tract(2)|breast(22)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(26)|lung(15)|ovary(8)|pancreas(11)|skin(3)|stomach(2)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	100		all_cancers(5;0.0413)|Breast(5;0.000625)|all_epithelial(5;0.00978)|all_lung(20;0.0449)|Lung NSC(33;0.163)		Epithelial(2;4.12e-09)|all cancers(2;6.86e-07)|BRCA - Breast invasive adenocarcinoma(2;8.74e-07)|Colorectal(4;5.32e-05)|COAD - Colon adenocarcinoma(4;0.0039)|READ - Rectum adenocarcinoma(10;0.0681)		GAAAAAGAACAAAAACAACTT	0.333			"D, Mis, N"		"pancreatic, breast, colorectal"																																p.Q142fs		Atlas-INDEL	.		Rec	yes		17	17p11.2	6416	mitogen-activated protein kinase kinase 4		E	.	MAP2K4	176	.	12	Whole gene deletion(10)|Substitution - Missense(1)|Unknown(1)	breast(4)|ovary(4)|biliary_tract(1)|large_intestine(1)|lung(1)|pancreas(1)	c.424delC						.						154	146	149					17																	11998923		2203	4300	6503	SO:0001589	frameshift_variant	6416	exon4			.	L36870	CCDS11162.1, CCDS62095.1	17p12	2012-03-23			ENSG00000065559	ENSG00000065559	2.7.12.2	"Mitogen-activated protein kinase cascade / Kinase kinases"	6844	protein-coding gene	gene with protein product		601335		SERK1		7716521	Standard	NM_003010		Approved	MEK4, JNKK1, PRKMK4, MKK4	uc002gnj.3	P45985		ENST00000353533.5:c.425delA	chr17.hg19:g.11998923delA	ENSP00000262445:p.Gln142fs	78.0	0.0		82.0	13.0	NM_003010	B2R7N7|B3KYB2|D3DTS5|Q5U0B8|Q6FHX4|Q6P9H2|Q6PIE6	Frame_Shift_Del	DEL	ENST00000353533.5	hg19	CCDS11162.1																																																																																			.	.		0.333	MAP2K4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441226.1			-	11998923	A	-	11998923	7	5	275	1	0	1	0	1	0	0	0	0	9248	130	5	0	439	0	MAP2K4	17	11998923	Frame_Shift_Del	DEL	A	TCGA-G3-A25V-01A-11D-A16V-10	4421392	11998923	69196287	27	39609										
DSC2	1824	hgsc.bcm.edu	37	chr18	28648117	28648117	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	2	1	1.11728395061728	NA	1.11728395061728	0.428571428571429	1	0	atcctcttccttcatagttaTatgtcaggacatagtcttgg	7	9	4	0			TCGA-G3-A25V-01A-11D-A16V-10	TCGA-G3-A25V-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4624fd20-e2ad-4826-b606-a694b04e1076	eac002f0-7695-4df1-8ff0-2c5c976279df	g.chr18:28648117T>C	ENST00000280904.6	-	16	3013	c.2570A>G	c.(2569-2571)tAt>tGt	p.Y857C	DSC2_ENST00000251081.6_3'UTR	NM_024422.3	NP_077740.1	Q02487	DSC2_HUMAN	desmocollin 2	857					bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell-cardiac muscle cell adhesion (GO:0086042)|cell adhesion (GO:0007155)|cellular response to starvation (GO:0009267)|homophilic cell adhesion (GO:0007156)|regulation of heart rate by cardiac conduction (GO:0086091)|ventricular cardiac muscle cell action potential (GO:0086005)	cell-cell adherens junction (GO:0005913)|cytoplasmic vesicle (GO:0031410)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)	21			OV - Ovarian serous cystadenocarcinoma(10;0.0241)			TTCATAGTTATATGTCAGGAC	0.393																																					p.Y857C		Atlas-SNP	.											.	DSC2	168	.	0			c.A2570G						.						96	85	89					18																	28648117		2203	4300	6503	SO:0001583	missense	1824	exon16			TAGTTATATGTCA	X56807	CCDS11892.1, CCDS11893.1	18q12.1	2014-09-17			ENSG00000134755	ENSG00000134755		"Cadherins / Major cadherins"	3036	protein-coding gene	gene with protein product		125645		DSC3		7774948	Standard	NM_024422		Approved	CDHF2	uc002kwl.4	Q02487	OTTHUMG00000131981	ENST00000280904.6:c.2570A>G	chr18.hg19:g.28648117T>C	ENSP00000280904:p.Tyr857Cys	93.0	0.0		133.0	30.0	NM_024422		Missense_Mutation	SNP	ENST00000280904.6	hg19	CCDS11892.1	.	.	.	.	.	.	.	.	.	.	T	14.40	2.525070	0.44969	.	.	ENSG00000134755	ENST00000280904;ENST00000438199;ENST00000399347	D	0.87809	-2.3	5.87	5.87	0.94306	Cadherin, cytoplasmic domain (1);	0.000000	0.29838	N	0.011069	D	0.95127	0.8421	M	0.92317	3.295	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96037	0.9021	10	0.87932	D	0	.	16.5764	0.84681	0.0:0.0:0.0:1.0	.	857	Q02487	DSC2_HUMAN	C	857;623;870	ENSP00000280904:Y857C	ENSP00000280904:Y857C	Y	-	2	0	DSC2	26902115	1.000000	0.71417	0.061000	0.19648	0.028000	0.11728	3.815000	0.55651	2.371000	0.80710	0.533000	0.62120	TAT	.	.		0.393	DSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254943.1	NM_004949		C	28648117	T	C	28648117	3	2	275	1	0	0	0	0	1	0	0	0	4768	1406	49	2	139	2	DSC2	18	28648117	Missense_Mutation	SNP	T	TCGA-G3-A25V-01A-11D-A16V-10		28648117	49429131	28	39610										
KDM5D	8284	hgsc.bcm.edu	37	chrY	21897301	21897301	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0689655172413793	2	1	1.11728395061728	NA	1.11728395061728	0.428571428571429	1	0	ttagtgcagggctctaggctCaagtgctgcttgagcaatgt	13	8	2	1			TCGA-G3-A25V-01A-11D-A16V-10	TCGA-G3-A25V-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4624fd20-e2ad-4826-b606-a694b04e1076	eac002f0-7695-4df1-8ff0-2c5c976279df	g.chrY:21897301C>T	ENST00000317961.4	-	8	1141	c.870G>A	c.(868-870)ttG>ttA	p.L290L	KDM5D_ENST00000541639.1_Silent_p.L290L|KDM5D_ENST00000382806.2_Silent_p.L233L	NM_004653.4	NP_004644.2	Q9BY66	KDM5D_HUMAN	lysine (K)-specific demethylase 5D	290					histone H3-K4 demethylation (GO:0034720)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-K4 specific) (GO:0032453)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(9)|lung(6)|skin(1)	17					Vitamin C(DB00126)	GCTCTAGGCTCAAGTGCTGCT	0.453																																					p.L290L		Atlas-SNP	.											.	KDM5D	40	.	0			c.G870A						.						119	117	118					Y																	21897301		624	1956	2580	SO:0001819	synonymous_variant	8284	exon8			TAGGCTCAAGTGC	U52191	CCDS14794.1, CCDS55554.1, CCDS55555.1	Yq11	2013-01-28	2009-04-06	2009-04-06	ENSG00000012817	ENSG00000012817		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	11115	protein-coding gene	gene with protein product		426000	"Jumonji, AT rich interactive domain 1D (RBP2-like)", "Smcy homolog, Y-linked (mouse)", "jumonji, AT rich interactive domain 1D"	HYA, HY, SMCY, JARID1D		795123, 8841177	Standard	NM_001146705		Approved	KIAA0234	uc011naz.2	Q9BY66	OTTHUMG00000036508	ENST00000317961.4:c.870G>A	chrY.hg19:g.21897301C>T		39.0	0.0		74.0	21.0	NM_001146705	A2RU19|A6H8V7|B7ZLX1|Q92509|Q92809|Q9HCU1	Silent	SNP	ENST00000317961.4	hg19	CCDS14794.1																																																																																			.	.		0.453	KDM5D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088790.1	NM_004653		T	21897301	C	T	21897301	2	4	275	1	0	0	0	0	0	0	0	1	8145	825	29	3		3	KDM5D	24	21897301	Silent	SNP	C	TCGA-G3-A25V-01A-11D-A16V-10		21897301	37476265	29	39611										
HFE2	148738	hgsc.bcm.edu	37	chr1	145414811	145414811	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	ccaggccagtcccctagtccCaggtcctcccatggcagtcc	9	19	0	0			TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr1:145414811C>T	ENST00000336751.5	+	2	268	c.30C>T	c.(28-30)ccC>ccT	p.P10P	HFE2_ENST00000475797.1_Intron|HFE2_ENST00000357836.5_Intron|HFE2_ENST00000497365.1_Intron	NM_213653.3	NP_998818.1	Q6ZVN8	RGMC_HUMAN	hemochromatosis type 2 (juvenile)	10					axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|iron ion homeostasis (GO:0055072)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)	14	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					CCCCTAGTCCCAGGTCCTCCC	0.582																																					p.P10P		Atlas-SNP	.											.	HFE2	48	.	0			c.C30T						.						96	83	88					1																	145414811		2203	4300	6503	SO:0001819	synonymous_variant	148738	exon2			TAGTCCCAGGTCC	AY372521	CCDS72877.1, CCDS72878.1, CCDS72879.1	1q21.2	2014-06-26			ENSG00000168509	ENSG00000168509			4887	protein-coding gene	gene with protein product	"repulsive guidance molecule c"	608374				10205270, 14647275	Standard	NM_213653		Approved	JH, HFE2A, RGMC, HJV, hemojuvelin, haemojuvelin	uc001eni.2	Q6ZVN8	OTTHUMG00000013748	ENST00000336751.5:c.30C>T	chr1.hg19:g.145414811C>T		60.0	0.0		80.0	22.0	NM_213653	B1ALI7|Q2PQ63|Q6IMF6|Q8NAH2|Q8WVJ5	Silent	SNP	ENST00000336751.5	hg19	CCDS910.1																																																																																			.	.		0.582	HFE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038527.1	NM_145277		T	145414811	C	T	145414811	2	4	276	1	0	0	0	0	0	0	0	1	7091	581	21	3		3	HFE2	1	145414811	Silent	SNP	C	TCGA-G3-A25W-01A-11D-A16V-10		145414811	103835810	1	39612										
CKS1B	1163	hgsc.bcm.edu	37	chr1	154947279	154947279	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	acgacgaggagtttgagtatCggttagtgctggcgcgggag	18	6	0	1			TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr1:154947279C>T	ENST00000308987.5	+	1	105	c.58C>T	c.(58-60)Cga>Tga	p.R20*	CKS1B_ENST00000368436.1_Splice_Site_p.R20*|SHC1_ENST00000368450.1_5'Flank|CKS1B_ENST00000368439.1_5'UTR|MIR4258_ENST00000580920.1_RNA|SHC1_ENST00000368453.4_5'Flank	NM_001826.2	NP_001817.1	P61024	CKS1_HUMAN	CDC28 protein kinase regulatory subunit 1B	20					cell division (GO:0051301)|cell proliferation (GO:0008283)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)	nucleoplasm (GO:0005654)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			breast(1)|large_intestine(1)|lung(1)	3	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			GTTTGAGTATCGGTTAGTGCT	0.537																																					p.R20X		Atlas-SNP	.											.	CKS1B	5	.	0			c.C58T						.						58	50	52					1																	154947279		2203	4300	6503	SO:0001630	splice_region_variant	1163	exon1			GAGTATCGGTTAG	BC007751	CCDS1077.1	1q21.2	2011-04-28	2002-10-07		ENSG00000173207	ENSG00000173207			19083	protein-coding gene	gene with protein product		116900	"CDC28 protein kinase 1B"			2227411	Standard	NM_001826		Approved	ckshs1, CKS1	uc001fgb.3	P61024	OTTHUMG00000037413	ENST00000308987.5:c.59+1C>T	chr1.hg19:g.154947279C>T		133.0	0.0		185.0	53.0	NM_001826	P33551	Nonsense_Mutation	SNP	ENST00000308987.5	hg19	CCDS1077.1	.	.	.	.	.	.	.	.	.	.	C	32	5.191087	0.94923	.	.	ENSG00000173207	ENST00000368436;ENST00000308987	.	.	.	5.26	2.21	0.28008	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.2945	0.60288	0.3965:0.6035:0.0:0.0	.	.	.	.	X	20	.	ENSP00000311083:R20X	R	+	1	2	CKS1B	153213903	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	2.771000	0.47670	0.305000	0.22832	0.591000	0.81541	CGA	.	.		0.537	CKS1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091078.1	NM_001826	Nonsense_Mutation	T	154947279	C	T	154947279	5	4	276	1	0	0	0	0	0	0	1	0	3454	898	31	1	60	1	CKS1B	1	154947279	Splice_Site	SNP	C	TCGA-G3-A25W-01A-11D-A16V-10	9532468	154947279	94303342	2	39613										
IFI16	3428	hgsc.bcm.edu	37	chr1	158984635	158984635	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	gctgacttgatggaagaaaaGttccgaggtgatgctggttt	14	5	0	4			TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr1:158984635G>C	ENST00000295809.7	+	2	420	c.165G>C	c.(163-165)aaG>aaC	p.K55N	IFI16_ENST00000430894.2_Missense_Mutation_p.K59N|IFI16_ENST00000448393.2_Missense_Mutation_p.K55N|IFI16_ENST00000368131.4_Missense_Mutation_p.K55N|IFI16_ENST00000340979.6_Missense_Mutation_p.K55N|IFI16_ENST00000368132.3_Missense_Mutation_p.K55N|IFI16_ENST00000359709.3_Missense_Mutation_p.K55N			Q16666	IF16_HUMAN	interferon, gamma-inducible protein 16	55	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.|Lys-rich.				activation of cysteine-type endopeptidase activity (GO:0097202)|activation of innate immune response (GO:0002218)|autophagy (GO:0006914)|cell proliferation (GO:0008283)|cellular response to glucose starvation (GO:0042149)|cellular response to ionizing radiation (GO:0071479)|defense response to virus (GO:0051607)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|monocyte differentiation (GO:0030224)|myeloid cell differentiation (GO:0030099)|negative regulation of cysteine-type endopeptidase activity (GO:2000117)|negative regulation of DNA binding (GO:0043392)|negative regulation of innate immune response (GO:0045824)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|positive regulation of cytokine production (GO:0001819)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of autophagy (GO:0010506)|regulation of gene expression, epigenetic (GO:0040029)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_hematologic(112;0.0429)					TGGAAGAAAAGTTCCGAGGTG	0.333																																					p.K55N		Atlas-SNP	.											.	IFI16	111	.	0			c.G165C						.						80	85	84					1																	158984635		2203	4300	6503	SO:0001583	missense	3428	exon2			AGAAAAGTTCCGA	M63838	CCDS1180.3, CCDS58039.1	1q22	2008-02-05			ENSG00000163565	ENSG00000163565			5395	protein-coding gene	gene with protein product		147586				1526658, 7959953	Standard	NM_005531		Approved	IFNGIP1, PYHIN2	uc010pis.2	Q16666	OTTHUMG00000037108	ENST00000295809.7:c.165G>C	chr1.hg19:g.158984635G>C	ENSP00000295809:p.Lys55Asn	258.0	0.0		271.0	64.0	NM_001206567	B4DJT8|H3BLV7|Q59GX0|Q5T3W7|Q5T3W8|Q5T3X0|Q5T3X1|Q5T3X2|Q8N9E5|Q8NEQ7|Q96AJ5|Q9UH78	Missense_Mutation	SNP	ENST00000295809.7	hg19		.	.	.	.	.	.	.	.	.	.	.	13.48	2.250355	0.39797	.	.	ENSG00000163565	ENST00000359709;ENST00000426592;ENST00000447473;ENST00000295809;ENST00000340979;ENST00000368131;ENST00000368132;ENST00000430894	T;T;T;T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68	3.27	2.34	0.29019	Pyrin (2);DEATH-like (1);	.	.	.	.	T	0.47673	0.1458	M	0.71206	2.165	0.09310	N	1	D;P;D	0.67145	0.992;0.713;0.996	P;B;P	0.62491	0.903;0.223;0.903	T	0.23833	-1.0177	9	0.62326	D	0.03	.	8.4964	0.33130	0.0:0.2393:0.7607:0.0	.	59;55;55	E7EPR3;Q16666-2;Q16666	.;.;IF16_HUMAN	N	55;55;55;55;55;55;55;59	ENSP00000352740:K55N;ENSP00000406406:K55N;ENSP00000407052:K55N;ENSP00000295809:K55N;ENSP00000342741:K55N;ENSP00000357113:K55N;ENSP00000357114:K55N;ENSP00000394935:K59N	ENSP00000295809:K55N	K	+	3	2	IFI16	157251259	0.020000	0.18652	0.019000	0.16419	0.001000	0.01503	-0.027000	0.12371	0.916000	0.36871	0.555000	0.69702	AAG	.	.		0.333	IFI16-013	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000421720.1	NM_005531		C	158984635	G	C	158984635	3	2	276	1	0	0	0	0	1	0	0	0	7520	1020	36	4	167	4	IFI16	1	158984635	Missense_Mutation	SNP	G	TCGA-G3-A25W-01A-11D-A16V-10	4037356	158984635	90265986	3	39614										
RASAL2	9462	hgsc.bcm.edu	37	chr1	178420786	178420786	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	gttcatctagtgaactgataGaccatcagagcaacctgaaa	8	9	3	5			TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr1:178420786G>A	ENST00000462775.1	+	8	1389	c.1264G>A	c.(1264-1266)Gac>Aac	p.D422N	RASAL2_ENST00000448150.3_Missense_Mutation_p.D552N|RASAL2_ENST00000367649.3_Missense_Mutation_p.D570N	NM_004841.3	NP_004832.1	Q9UJF2	NGAP_HUMAN	RAS protein activator like 2	422	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Ras GTPase activator activity (GO:0005099)			biliary_tract(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(2)|lung(25)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54						TGAACTGATAGACCATCAGAG	0.408																																					p.D570N		Atlas-SNP	.											.	RASAL2	334	.	0			c.G1708A						.						180	170	173					1																	178420786		2203	4300	6503	SO:0001583	missense	9462	exon10			CTGATAGACCATC	AF047711	CCDS1321.1, CCDS1322.1, CCDS1321.2	1q25	2013-01-10			ENSG00000075391	ENSG00000075391		"Pleckstrin homology (PH) domain containing"	9874	protein-coding gene	gene with protein product	"Ras GTPase activating protein-like", "Ras protein activator like 1"	606136				9877179	Standard	NM_004841		Approved	nGAP	uc001glq.3	Q9UJF2	OTTHUMG00000035022	ENST00000462775.1:c.1264G>A	chr1.hg19:g.178420786G>A	ENSP00000420558:p.Asp422Asn	66.0	0.0		54.0	19.0	NM_170692	F8W755|O95174|Q2TB22|Q5TFU9	Missense_Mutation	SNP	ENST00000462775.1	hg19	CCDS1322.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.875079	0.91664	.	.	ENSG00000075391	ENST00000448150;ENST00000367649;ENST00000462775	D;T;D	0.81739	-1.53;2.33;-1.53	5.84	5.84	0.93424	Rho GTPase activation protein (1);Ras GTPase-activating protein (4);	0.109437	0.64402	D	0.000009	T	0.81380	0.4810	N	0.25380	0.74	0.80722	D	1	P;B	0.38863	0.65;0.241	P;B	0.49140	0.601;0.148	T	0.82345	-0.0503	10	0.87932	D	0	.	20.1551	0.98106	0.0:0.0:1.0:0.0	.	422;570	Q9UJF2;F8W755	NGAP_HUMAN;.	N	552;570;422	ENSP00000407768:D552N;ENSP00000356621:D570N;ENSP00000420558:D422N	ENSP00000356621:D570N	D	+	1	0	RASAL2	176687409	1.000000	0.71417	0.988000	0.46212	0.998000	0.95712	9.731000	0.98807	2.760000	0.94817	0.655000	0.94253	GAC	.	.		0.408	RASAL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000084758.3	NM_170692		A	178420786	G	A	178420786	3	1	276	1	0	0	0	0	1	0	0	0	13079	942	33	3	1763	3	RASAL2	1	178420786	Missense_Mutation	SNP	G	TCGA-G3-A25W-01A-11D-A16V-10	19436151	178420786	70829835	4	39615										
APOB	338	hgsc.bcm.edu	37	chr2	21235442	21235442	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	catgactgaatttgatattcGaatctagaaatttgtggcgt	9	5	1	4	rs200708197		TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr2:21235442G>T	ENST00000233242.1	-	26	4425	c.4298C>A	c.(4297-4299)tCg>tAg	p.S1433*		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	1433					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)	p.S1433L(1)		NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTTGATATTCGAATCTAGAAA	0.368																																					p.S1433X		Atlas-SNP	.											APOB,NS,carcinoma,0,2	APOB	761	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4298A						.						83	88	86					2																	21235442		2202	4300	6502	SO:0001587	stop_gained	338	exon26			ATATTCGAATCTA	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.4298C>A	chr2.hg19:g.21235442G>T	ENSP00000233242:p.Ser1433*	73.0	0.0		73.0	20.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Nonsense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	G	45	11.530493	0.99572	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	.	.	.	5.88	5.88	0.94601	.	0.000000	0.56097	D	0.000037	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.2422	0.98381	0.0:0.0:1.0:0.0	.	.	.	.	X	1433	.	ENSP00000233242:S1433X	S	-	2	0	APOB	21088947	1.000000	0.71417	0.987000	0.45799	0.931000	0.56810	8.712000	0.91403	2.782000	0.95742	0.655000	0.94253	TCG	.	G|0.999;A|0.001		0.368	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			T	21235442	G	T	21235442	4	4	276	1	0	0	0	0	0	1	0	0	785	1059	37	1	9409	1	APOB	2	21235442	Nonsense_Mutation	SNP	G	TCGA-G3-A25W-01A-11D-A16V-10		21235442	221963931	5	39616										
REV1	51455	hgsc.bcm.edu	37	chr2	100019252	100019253	+	Frame_Shift_Del	DEL	AG	AG	-													0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	ggcacacctgaagtagaagcAgagagttcttcctgttaaga							TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr2:100019252_100019253delAG	ENST00000258428.3	-	21	3623_3624	c.3395_3396delCT	c.(3394-3396)tctfs	p.S1132fs	REV1_ENST00000465835.1_5'Flank|REV1_ENST00000393445.3_Frame_Shift_Del_p.S1131fs|RP11-527J8.1_ENST00000608144.1_RNA	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)	1132					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|error-prone translesion synthesis (GO:0042276)|response to UV (GO:0009411)	nucleoplasm (GO:0005654)	damaged DNA binding (GO:0003684)|deoxycytidyl transferase activity (GO:0017125)|DNA-directed DNA polymerase activity (GO:0003887)|magnesium ion binding (GO:0000287)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(12)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						AAGTAGAAGCAGAGAGTTCTTC	0.416								Direct reversal of damage																													p.1132_1133del		Atlas-Indel,Pindel	.											.	REV1	100	.	0			c.3396_3397del						.																																			SO:0001589	frameshift_variant	51455	exon21			.	AF206019	CCDS2045.1, CCDS42722.1	2q11.1-q11.2	2012-05-18	2012-05-18	2006-11-07	ENSG00000135945	ENSG00000135945		"DNA polymerases"	14060	protein-coding gene	gene with protein product		606134	"REV1 (yeast homolog)- like", "REV1-like (yeast)", "REV1 homolog (S. cerevisiae)"	REV1L		10536157	Standard	XM_005263968		Approved		uc002tad.3	Q9UBZ9	OTTHUMG00000130636	ENST00000258428.3:c.3395_3396delCT	chr2.hg19:g.100019256_100019257delAG	ENSP00000258428:p.Ser1132fs	31.0	0.0		63.0	21.0	NM_016316	O95941|Q53SI7|Q9C0J4|Q9NUP2	Frame_Shift_Del	DEL	ENST00000258428.3	hg19	CCDS2045.1																																																																																			.	.		0.416	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253123.2	NM_016316		-	100019253	AG	-	100019252	7	5	276	1	0	1	0	1	0	0	0	0	13254	175	7	0	371	0	REV1	2	100019252	Frame_Shift_Del	DEL	AG	TCGA-G3-A25W-01A-11D-A16V-10	78783810	100019252	143180121	6	39617										
MARCO	8685	hgsc.bcm.edu	37	chr2	119739211	119739211	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	tcttaggtttggctggttttCctggagctaaaggagatcaa	12	6	2	1			TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr2:119739211C>T	ENST00000327097.4	+	10	1015	c.880C>T	c.(880-882)Cct>Tct	p.P294S	MARCO_ENST00000541757.1_Missense_Mutation_p.P216S	NM_006770.3	NP_006761.1	Q9UEW3	MARCO_HUMAN	macrophage receptor with collagenous structure	294	Collagen-like.				apoptotic cell clearance (GO:0043277)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)	collagen trimer (GO:0005581)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(12)|lung(37)|ovary(4)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	70						GGCTGGTTTTCCTGGAGCTAA	0.443																																					p.P294S	GBM(8;18 374 7467 11269 32796)	Atlas-SNP	.											.	MARCO	120	.	0			c.C880T						.						75	79	78					2																	119739211		2202	4298	6500	SO:0001583	missense	8685	exon10			GGTTTTCCTGGAG	AF035819	CCDS2124.1	2q14.2	2011-10-11			ENSG00000019169	ENSG00000019169			6895	protein-coding gene	gene with protein product	"scavenger receptor class A, member 2"	604870				9468508, 7867067, 10331948	Standard	NM_006770		Approved	SCARA2	uc002tln.1	Q9UEW3	OTTHUMG00000131400	ENST00000327097.4:c.880C>T	chr2.hg19:g.119739211C>T	ENSP00000318916:p.Pro294Ser	84.0	0.0		89.0	27.0	NM_006770	B4DW79|Q9Y5S3	Missense_Mutation	SNP	ENST00000327097.4	hg19	CCDS2124.1	.	.	.	.	.	.	.	.	.	.	C	9.481	1.098186	0.20552	.	.	ENSG00000019169	ENST00000327097;ENST00000410021;ENST00000541757	D;D	0.93133	-3.17;-3.17	5.2	3.36	0.38483	.	0.329727	0.29692	N	0.011451	D	0.91068	0.7189	M	0.74467	2.265	0.32272	N	0.568704	P	0.36162	0.54	B	0.37346	0.247	D	0.89187	0.3548	9	.	.	.	.	6.1027	0.20057	0.1856:0.7205:0.0:0.0939	.	294	Q9UEW3	MARCO_HUMAN	S	294;294;216	ENSP00000318916:P294S;ENSP00000441769:P216S	.	P	+	1	0	MARCO	119455681	0.868000	0.29978	0.428000	0.26697	0.969000	0.65631	0.880000	0.28159	0.730000	0.32425	0.561000	0.74099	CCT	.	.		0.443	MARCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254190.2	NM_006770		T	119739211	C	T	119739211	3	4	276	1	0	0	0	0	1	0	0	0	9320	855	30	3	918	3	MARCO	2	119739211	Missense_Mutation	SNP	C	TCGA-G3-A25W-01A-11D-A16V-10	19719959	119739211	123460162	7	39618										
TTN	7273	hgsc.bcm.edu	37	chr2	179407524	179407524	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	agtgtgagtttcaactgtgaCacgctctgattctctcagtt	9	9	4	3			TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr2:179407524C>T	ENST00000591111.1	-	298	92358	c.92134G>A	c.(92134-92136)Gtc>Atc	p.V30712I	TTN-AS1_ENST00000586452.1_RNA|RP11-65L3.4_ENST00000604692.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.V32353I|TTN_ENST00000342992.6_Missense_Mutation_p.V29785I|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.V23413I|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.V23480I|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.V23288I|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	30712	Ig-like 138.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCAACTGTGACACGCTCTGAT	0.458																																					p.V32353I		Atlas-SNP	.											.	TTN	18412	.	0			c.G97057A						.						209	199	202					2																	179407524		1965	4156	6121	SO:0001583	missense	7273	exon348			CTGTGACACGCTC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.92134G>A	chr2.hg19:g.179407524C>T	ENSP00000465570:p.Val30712Ile	104.0	0.0		122.0	20.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	12.76	2.035655	0.35893	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27	5.67	3.87	0.44632	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.46092	0.1375	N	0.10618	0.005	0.34369	D	0.691823	B;B;B;B	0.10296	0.003;0.003;0.003;0.003	B;B;B;B	0.10450	0.005;0.005;0.005;0.005	T	0.55289	-0.8164	9	0.87932	D	0	.	10.0264	0.42074	0.0:0.7803:0.0:0.2197	.	23288;23413;23480;30712	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	I	29785;23288;23480;23413;23285	ENSP00000343764:V29785I;ENSP00000434586:V23288I;ENSP00000340554:V23480I;ENSP00000352154:V23413I	ENSP00000340554:V23480I	V	-	1	0	TTN	179115770	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.541000	0.36126	1.402000	0.46780	0.655000	0.94253	GTC	.	.		0.458	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179407524	C	T	179407524	3	4	276	1	0	0	0	0	1	0	0	0	16750	478	17	3	10982	3	TTN	2	179407524	Missense_Mutation	SNP	C	TCGA-G3-A25W-01A-11D-A16V-10	59668313	179407524	63791849	8	39619										
MLPH	79083	hgsc.bcm.edu	37	chr2	238434305	238434305	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	caaggctgagggcctggaggAggctgatactggggcctctg	18	9	1	2			TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr2:238434305A>T	ENST00000264605.3	+	7	1031	c.737A>T	c.(736-738)gAg>gTg	p.E246V	MLPH_ENST00000338530.4_Missense_Mutation_p.E246V|MLPH_ENST00000409373.1_Missense_Mutation_p.E206V|MLPH_ENST00000410032.1_Intron|MLPH_ENST00000445024.2_Missense_Mutation_p.E246V|MLPH_ENST00000468178.1_3'UTR	NM_024101.5	NP_077006.1	Q9BV36	MELPH_HUMAN	melanophilin	246					melanocyte differentiation (GO:0030318)|melanosome localization (GO:0032400)|protein targeting (GO:0006605)	cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|microtubule plus-end (GO:0035371)|stress fiber (GO:0001725)	metal ion binding (GO:0046872)			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)		GGCCTGGAGGAGGCTGATACT	0.632																																					p.E246V		Atlas-SNP	.											.	MLPH	41	.	0			c.A737T						.						50	52	51					2																	238434305		2203	4300	6503	SO:0001583	missense	79083	exon7			TGGAGGAGGCTGA	AY358857	CCDS2518.1, CCDS42836.1, CCDS63172.1, CCDS63173.1	2q37.2	2014-09-17			ENSG00000115648	ENSG00000115648			29643	protein-coding gene	gene with protein product		606526				11980908, 11504925	Standard	NM_024101		Approved	l1Rk3, l(1)-3Rk, Slac-2a, ln, exophilin-3	uc002vwt.3	Q9BV36	OTTHUMG00000133298	ENST00000264605.3:c.737A>T	chr2.hg19:g.238434305A>T	ENSP00000264605:p.Glu246Val	40.0	0.0		52.0	14.0	NM_001042467	B3KSS2|B4DKW7|G5E9G5|Q9HA71	Missense_Mutation	SNP	ENST00000264605.3	hg19	CCDS2518.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.803|9.803	1.180978|1.180978	0.21787|0.21787	.|.	.|.	ENSG00000115648|ENSG00000115648	ENST00000264605;ENST00000445024;ENST00000338530;ENST00000409373|ENST00000437893	T;T;T;T|T	0.33865|0.31247	1.89;1.88;1.68;1.39|1.5	3.24|3.24	2.07|2.07	0.26955|0.26955	.|.	0.533147|.	0.13871|.	U|.	0.357000|.	T|T	0.32224|0.32224	0.0822|0.0822	L|L	0.47190|0.47190	1.495|1.495	0.09310|0.09310	N|N	1|1	D;D;D;D;D;D|.	0.63046|.	0.98;0.966;0.992;0.985;0.981;0.967|.	P;P;P;P;P;P|.	0.57324|.	0.578;0.543;0.818;0.587;0.793;0.547|.	T|T	0.22871|0.22871	-1.0204|-1.0204	10|7	0.66056|0.87932	D|D	0.02|0	-10.8271|-10.8271	7.5003|7.5003	0.27513|0.27513	0.8826:0.0:0.1174:0.0|0.8826:0.0:0.1174:0.0	.|.	246;130;246;206;246;246|.	B4DKW7;Q6UWC1;A8KA64;B8ZZ97;Q9BV36-2;Q9BV36|.	.;.;.;.;.;MELPH_HUMAN|.	V|W	246;246;246;206|53	ENSP00000264605:E246V;ENSP00000414849:E246V;ENSP00000341845:E246V;ENSP00000386780:E206V|ENSP00000412438:R53W	ENSP00000264605:E246V|ENSP00000412438:R53W	E|R	+|+	2|1	0|2	MLPH|MLPH	238099044|238099044	0.015000|0.015000	0.18098|0.18098	0.003000|0.003000	0.11579|0.11579	0.001000|0.001000	0.01503|0.01503	0.929000|0.929000	0.28844|0.28844	0.159000|0.159000	0.19401|0.19401	-1.450000|-1.450000	0.01041|0.01041	GAG|AGG	.	.		0.632	MLPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257083.2	NM_024101		T	238434305	A	T	238434305	3	4	276	1	0	0	0	0	1	0	0	0	9642	304	11	4	759	4	MLPH	2	238434305	Missense_Mutation	SNP	A	TCGA-G3-A25W-01A-11D-A16V-10	59026781	238434305	4765068	9	39620										
UCN2	90226	hgsc.bcm.edu	37	chr3	48600437	48600437	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	gctctctgaggccgcaggtcGgggagtggtctggggagaat	19	8	2	2	rs149022309		TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr3:48600437G>A	ENST00000273610.3	-	2	203	c.121C>T	c.(121-123)Cga>Tga	p.R41*	PFKFB4_ENST00000536104.1_5'Flank|COL7A1_ENST00000470076.1_5'Flank	NM_033199.3	NP_149976.1	Q96RP3	UCN2_HUMAN	urocortin 2	41					cAMP biosynthetic process (GO:0006171)|cell proliferation (GO:0008283)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to hypoxia (GO:0071456)|digestion (GO:0007586)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of gene expression (GO:0010629)|negative regulation of luteinizing hormone secretion (GO:0033685)|response to stress (GO:0006950)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone binding (GO:0042562)|receptor binding (GO:0005102)								BRCA - Breast invasive adenocarcinoma(193;0.000288)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		GCCGCAGGTCGGGGAGTGGTC	0.652																																					p.R41X		Atlas-SNP	.											.	UCN2	4	.	0			c.C121T						.	A	stop/ARG	0,4406		0,0,2203	30	32	32		121	-10.6	0	3	dbSNP_134	32	1,8599	1.2+/-3.3	0,1,4299	yes	stop-gained	UCN2	NM_033199.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		41/113	48600437	1,13005	2203	4300	6503	SO:0001587	stop_gained	90226	exon2			CAGGTCGGGGAGT	AF320560	CCDS2772.1	3p21.3	2013-02-28			ENSG00000145040	ENSG00000145040		"Endogenous ligands"	18414	protein-coding gene	gene with protein product	"prepro-urocortin 2"	605902				11329063	Standard	NM_033199		Approved	UCNI, SRP, URP, UCN-II	uc003cty.1	Q96RP3	OTTHUMG00000133533	ENST00000273610.3:c.121C>T	chr3.hg19:g.48600437G>A	ENSP00000273610:p.Arg41*	74.0	0.0		71.0	17.0	NM_033199	Q9BUG0	Nonsense_Mutation	SNP	ENST00000273610.3	hg19	CCDS2772.1	.	.	.	.	.	.	.	.	.	.	g	8.413	0.844566	0.16963	0.0	1.16E-4	ENSG00000145040	ENST00000273610	.	.	.	5.28	-10.6	0.00265	.	2.567240	0.01439	N	0.015013	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.22706	T	0.39	-3.5288	0.3326	0.00321	0.2654:0.158:0.2353:0.3414	.	.	.	.	X	41	.	ENSP00000273610:R41X	R	-	1	2	UCN2	48575441	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.503000	0.00449	-3.150000	0.00231	-5.056000	0.00002	CGA	.	G|1.000;A|0.000		0.652	UCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257510.1	NM_033199		A	48600437	G	A	48600437	4	1	276	1	0	0	0	0	0	1	0	0	16943	1124	39	1	221	1	UCN2	3	48600437	Nonsense_Mutation	SNP	G	TCGA-G3-A25W-01A-11D-A16V-10		48600437	149421993	10	39621										
RNF123	63891	hgsc.bcm.edu	37	chr3	49738928	49738928	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	ccttgacacccgccagcttcGacgtgctccgctccgtcgtc	9	19	0	1	rs369164501		TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr3:49738928G>T	ENST00000327697.6	+	16	1426	c.1282G>T	c.(1282-1284)Gac>Tac	p.D428Y	RNF123_ENST00000432042.1_Missense_Mutation_p.D282Y	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	428					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		CGCCAGCTTCGACGTGCTCCG	0.632											OREG0015570	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D428Y		Atlas-SNP	.											.	RNF123	100	.	0			c.G1282T						.						52	56	54					3																	49738928		2203	4300	6503	SO:0001583	missense	63891	exon16			AGCTTCGACGTGC	AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"RING-type (C3HC4) zinc fingers"	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891	ENST00000327697.6:c.1282G>T	chr3.hg19:g.49738928G>T	ENSP00000328287:p.Asp428Tyr	32.0	0.0	964	37.0	12.0	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Missense_Mutation	SNP	ENST00000327697.6	hg19	CCDS33758.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.119186	0.77323	.	.	ENSG00000164068	ENST00000327697;ENST00000389066;ENST00000432042	T;T	0.79033	-0.91;-1.23	5.71	5.71	0.89125	.	0.176658	0.47852	D	0.000204	T	0.81744	0.4887	N	0.19112	0.55	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.84283	0.0495	10	0.87932	D	0	-32.0212	18.8457	0.92205	0.0:0.0:1.0:0.0	.	282;428	C9J266;Q5XPI4	.;RN123_HUMAN	Y	428;428;282	ENSP00000328287:D428Y;ENSP00000392443:D282Y	ENSP00000328287:D428Y	D	+	1	0	RNF123	49713932	1.000000	0.71417	0.991000	0.47740	0.200000	0.23975	9.153000	0.94687	2.698000	0.92095	0.561000	0.74099	GAC	.	.		0.632	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064		T	49738928	G	T	49738928	3	4	276	1	0	0	0	0	1	0	0	0	13448	1058	37	1	1340	1	RNF123	3	49738928	Missense_Mutation	SNP	G	TCGA-G3-A25W-01A-11D-A16V-10	1138491	49738928	148283502	11	39622										
GBE1	2632	hgsc.bcm.edu	37	chr3	81548302	81548302	+	Frame_Shift_Del	DEL	A	A	-													0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	attatgttcaaaagcctcagAaaaaaagtcagtgctgtggt							TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr3:81548302delA	ENST00000429644.2	-	15	2654	c.2011delT	c.(2011-2013)tctfs	p.S671fs	GBE1_ENST00000489715.1_Frame_Shift_Del_p.S630fs	NM_000158.3	NP_000149	Q04446	GLGB_HUMAN	glucan (1,4-alpha-), branching enzyme 1	671					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	1,4-alpha-glucan branching enzyme activity (GO:0003844)|cation binding (GO:0043169)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			breast(1)|endometrium(5)|large_intestine(2)|lung(4)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Lung NSC(201;0.0117)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0654)|Epithelial(33;0.00305)|LUSC - Lung squamous cell carcinoma(29;0.00646)|BRCA - Breast invasive adenocarcinoma(55;0.00813)|Lung(72;0.0129)|KIRC - Kidney renal clear cell carcinoma(39;0.212)|Kidney(39;0.247)		AAAGCCTCAGAAAAAAAGTCA	0.363									Glycogen Storage Disease, type IV																												p.S671fs		Pindel	.											.	GBE1	111	.	0			c.2012delC						.						90	85	86					3																	81548302		1835	4094	5929	SO:0001589	frameshift_variant	2632	exon15	Familial Cancer Database	Andersen Disease, Brancher deficiency	.		CCDS54612.1	3p12.2	2013-09-20	2008-08-01		ENSG00000114480	ENSG00000114480	2.4.1.18		4180	protein-coding gene	gene with protein product	"glycogen branching enzyme", "Andersen disease", "glycogen storage disease type IV"	607839				8463281	Standard	NM_000158		Approved		uc021xav.1	Q04446	OTTHUMG00000158978	ENST00000429644.2:c.2011delT	chr3.hg19:g.81548302delA	ENSP00000410833:p.Ser671fs	166.0	0.0		148.0	16.0	NM_000158	B3KWV3|Q96EN0	Frame_Shift_Del	DEL	ENST00000429644.2	hg19	CCDS54612.1																																																																																			.	.		0.363	GBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352760.2			-	81548302	A	-	81548302	7	5	276	1	0	1	0	1	0	0	0	0	6278	246	9	0	105	0	GBE1	3	81548302	Frame_Shift_Del	DEL	A	TCGA-G3-A25W-01A-11D-A16V-10	31809374	81548302	116474128	12	39623										
C4orf51	646603	hgsc.bcm.edu	37	chr4	146650321	146650321	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	tctatctctcctttttatagGcacatcaaatttgggatttt	5	8	3	0			TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr4:146650321G>T	ENST00000438731.1	+	4	367	c.367G>T	c.(367-369)Gca>Tca	p.A123S		NM_001080531.1	NP_001074000.1	C9J302	CD051_HUMAN	chromosome 4 open reading frame 51	123										haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)	6						CTTTTTATAGGCACATCAAAT	0.343																																					p.A123S		Atlas-SNP	.											.	C4orf51	18	.	0			c.G367T						.						109	99	102					4																	146650321		1823	4079	5902	SO:0001630	splice_region_variant	646603	exon4			TTATAGGCACATC		CCDS47140.1	4q31.21	2009-09-09			ENSG00000237136	ENSG00000237136			37264	protein-coding gene	gene with protein product							Standard	NM_001080531		Approved		uc003ikk.3	C9J302	OTTHUMG00000161367	ENST00000438731.1:c.367-1G>T	chr4.hg19:g.146650321G>T		184.0	0.0		199.0	20.0	NM_001080531		Missense_Mutation	SNP	ENST00000438731.1	hg19	CCDS47140.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.10|19.10	3.762600|3.762600	0.69763|0.69763	.|.	.|.	ENSG00000237136|ENSG00000237136	ENST00000438731|ENST00000511965	.|.	.|.	.|.	3.48|3.48	3.48|3.48	0.39840|0.39840	.|.	.|.	.|.	.|.	.|.	T|T	0.32734|0.32734	0.0839|0.0839	N|N	0.24115|0.24115	0.695|0.695	0.28406|0.28406	N|N	0.918429|0.918429	D|.	0.89917|.	1.0|.	D|.	0.72338|.	0.977|.	T|T	0.14699|0.14699	-1.0463|-1.0463	7|5	.|.	.|.	.|.	.|.	10.7797|10.7797	0.46371|0.46371	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	123|.	C9J302|.	CD051_HUMAN|.	S|C	123|82	.|.	.|.	A|W	+|+	1|3	0|0	C4orf51|C4orf51	146869771|146869771	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.371000|0.371000	0.29859|0.29859	1.323000|1.323000	0.33701|0.33701	2.251000|2.251000	0.74343|0.74343	0.585000|0.585000	0.79938|0.79938	GCA|TGG	.	.		0.343	C4orf51-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080531	Missense_Mutation	T	146650321	G	T	146650321	5	4	276	1	0	0	0	0	0	0	1	0	2279	1217	42	3	381	3	C4orf51	4	146650321	Splice_Site	SNP	G	TCGA-G3-A25W-01A-11D-A16V-10		146650321	44503955	13	39624										
DAB2	1601	hgsc.bcm.edu	37	chr5	39376177	39376177	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	gtagatttggtaactggcagGgaaacttgtctgggagctgg	16	5	1	1			TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr5:39376177G>T	ENST00000320816.6	-	13	2636	c.2169C>A	c.(2167-2169)tcC>tcA	p.S723S	DAB2_ENST00000339788.6_Silent_p.S505S|DAB2_ENST00000509337.1_Silent_p.S702S|DAB2_ENST00000545653.1_Silent_p.S702S	NM_001343.3	NP_001334.2	P98082	DAB2_HUMAN	Dab, mitogen-responsive phosphoprotein, homolog 2 (Drosophila)	723	Required for interaction with MYO6. {ECO:0000250}.|Sufficient for interaction with GRB2. {ECO:0000250}.|Sufficient for interaction with SH3KBP1 SH3 domain. {ECO:0000250}.				activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cell morphogenesis involved in differentiation (GO:0000904)|cell proliferation (GO:0008283)|cellular response to transforming growth factor beta stimulus (GO:0071560)|clathrin coat assembly (GO:0048268)|endoderm development (GO:0007492)|excretion (GO:0007588)|in utero embryonic development (GO:0001701)|leading edge cell differentiation (GO:0035026)|membrane organization (GO:0061024)|myeloid cell differentiation (GO:0030099)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of protein binding (GO:0032091)|negative regulation of protein localization to plasma membrane (GO:1903077)|negative regulation of transcription, DNA-templated (GO:0045892)|pinocytosis (GO:0006907)|positive regulation of cell migration (GO:0030335)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of endocytosis (GO:0045807)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of receptor recycling (GO:0001921)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|clathrin coat of coated pit (GO:0030132)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	cargo receptor activity (GO:0038024)|clathrin adaptor activity (GO:0035615)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein C-terminus binding (GO:0008022)|SMAD binding (GO:0046332)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(9)|lung(19)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	47	all_lung(31;0.000197)		Epithelial(62;0.137)			TAACTGGCAGGGAAACTTGTC	0.433																																					p.S723S		Atlas-SNP	.											.	DAB2	124	.	0			c.C2169A						.						100	102	101					5																	39376177		2203	4300	6503	SO:0001819	synonymous_variant	1601	exon13			TGGCAGGGAAACT	U53446	CCDS34149.1, CCDS58946.1	5p13.1	2013-10-03	2013-03-08		ENSG00000153071	ENSG00000153071			2662	protein-coding gene	gene with protein product		601236	"disabled (Drosophila) homolog 2 (mitogen-responsive phosphoprotein)", "disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)"			8660969, 9620555	Standard	NM_001343		Approved	DOC-2	uc003jlx.3	P98082	OTTHUMG00000162043	ENST00000320816.6:c.2169C>A	chr5.hg19:g.39376177G>T		66.0	0.0		77.0	34.0	NM_001343	A6NES5|Q13598|Q9BTY0|Q9UK04	Silent	SNP	ENST00000320816.6	hg19	CCDS34149.1																																																																																			.	.		0.433	DAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367014.1	NM_001343		T	39376177	G	T	39376177	2	4	276	1	0	0	0	0	0	0	0	1	4220	1219	43	3		3	DAB2	5	39376177	Silent	SNP	G	TCGA-G3-A25W-01A-11D-A16V-10		39376177	141539083	14	39625										
RAPGEF6	51735	hgsc.bcm.edu	37	chr5	130841171	130841171	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	tcaacttttccatctggatgActgatttccacagtgccgtt	7	11	2	2			TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr5:130841171A>T	ENST00000509018.1	-	10	1192	c.987T>A	c.(985-987)agT>agA	p.S329R	RAPGEF6_ENST00000296859.6_Missense_Mutation_p.S329R|RAPGEF6_ENST00000507093.1_Missense_Mutation_p.S329R|RAPGEF6_ENST00000308008.6_Missense_Mutation_p.S329R|CTC-432M15.3_ENST00000514667.1_Missense_Mutation_p.S379R|RAPGEF6_ENST00000307984.5_Missense_Mutation_p.S329R|RAPGEF6_ENST00000510071.1_Missense_Mutation_p.S329R|RAPGEF6_ENST00000512052.1_Missense_Mutation_p.S44R	NM_001164386.1|NM_016340.5	NP_001157858.1|NP_057424.3	Q8TEU7	RPGF6_HUMAN	Rap guanine nucleotide exchange factor (GEF) 6	329					positive regulation of GTPase activity (GO:0043547)|Ras protein signal transduction (GO:0007265)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP-dependent protein binding (GO:0030742)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		CATCTGGATGACTGATTTCCA	0.333																																					p.S329R	Melanoma(168;435 1955 13113 13877 23213)	Atlas-SNP	.											.	RAPGEF6	361	.	0			c.T987A						.						80	77	78					5																	130841171		2203	4300	6503	SO:0001583	missense	51735	exon10			TGGATGACTGATT	AF117947	CCDS34225.1, CCDS54897.1, CCDS54898.1, CCDS54899.1, CCDS54900.1	5q31.1	2008-02-05	2004-03-01	2004-03-02	ENSG00000158987	ENSG00000158987			20655	protein-coding gene	gene with protein product		610499	"PDZ domain containing guanine nucleotide exchange factor (GEF) 2"	PDZGEF2		11524421, 12095257	Standard	NM_016340		Approved	RA-GEF-2, PDZ-GEF2	uc010jdi.2	Q8TEU7	OTTHUMG00000162683	ENST00000509018.1:c.987T>A	chr5.hg19:g.130841171A>T	ENSP00000421684:p.Ser329Arg	70.0	0.0		114.0	20.0	NM_001164387	A3KN82|A5PLL6|B7ZML2|E9PDV7|Q8NI21|Q8TEU6|Q96PC1	Missense_Mutation	SNP	ENST00000509018.1	hg19	CCDS34225.1	.	.	.	.	.	.	.	.	.	.	A	18.34	3.603150	0.66445	.	.	ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000217128	ENST00000509018;ENST00000307984;ENST00000507093;ENST00000296859;ENST00000358714;ENST00000512052;ENST00000308008;ENST00000510071;ENST00000514667	D;D;D;D;D;D;D;D	0.92911	-3.13;-3.13;-3.13;-3.13;-3.13;-3.13;-3.13;-3.13	5.67	3.22	0.36961	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.047074	0.85682	D	0.000000	D	0.93200	0.7834	L	0.54323	1.7	0.80722	D	1	B;B;P;D;B;B;B	0.54772	0.145;0.145;0.689;0.968;0.38;0.119;0.227	P;B;P;D;P;B;B	0.67382	0.489;0.18;0.677;0.951;0.687;0.357;0.416	D	0.90978	0.4825	10	0.54805	T	0.06	.	7.4174	0.27053	0.6307:0.0:0.3693:0.0	.	329;329;329;44;379;329;329	A3KN82;B7ZML2;Q8TEU7-2;D6RE77;E9PCH4;Q8TEU7-3;Q8TEU7	.;.;.;.;.;.;RPGF6_HUMAN	R	329;329;329;329;329;44;329;329;379	ENSP00000421684:S329R;ENSP00000309298:S329R;ENSP00000426081:S329R;ENSP00000296859:S329R;ENSP00000426910:S44R;ENSP00000311419:S329R;ENSP00000425389:S329R;ENSP00000426948:S379R	ENSP00000426948:S379R	S	-	3	2	RAPGEF6;FNIP1	130869070	1.000000	0.71417	0.995000	0.50966	0.988000	0.76386	1.444000	0.35068	0.397000	0.25310	0.383000	0.25322	AGT	.	.		0.333	RAPGEF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370059.1	NM_016340		T	130841171	A	T	130841171	3	4	276	1	0	0	0	0	1	0	0	0	13063	272	10	4	4380	4	RAPGEF6	5	130841171	Missense_Mutation	SNP	A	TCGA-G3-A25W-01A-11D-A16V-10	91464994	130841171	50074089	15	39626										
GRXCR2	643226	hgsc.bcm.edu	37	chr5	145246178	145246178	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	agagactcttcctcagcctcCtcttccttctggagaatttt	6	13	4	2			TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr5:145246178C>G	ENST00000377976.1	-	2	449	c.450G>C	c.(448-450)gaG>gaC	p.E150D		NM_001080516.1	NP_001073985.1	A6NFK2	GRCR2_HUMAN	glutaredoxin, cysteine rich 2	150						cell projection (GO:0042995)				breast(1)|endometrium(1)|large_intestine(2)|lung(1)|urinary_tract(2)	7						CCTCAGCCTCCTCTTCCTTCT	0.428																																					p.E150D		Atlas-SNP	.											.	GRXCR2	32	.	0			c.G450C						.						144	140	141					5																	145246178		2203	4300	6503	SO:0001583	missense	643226	exon2			AGCCTCCTCTTCC		CCDS34263.1	5q32	2014-03-14			ENSG00000204928	ENSG00000204928			33862	protein-coding gene	gene with protein product		615762				24619944	Standard	NM_001080516		Approved	DFNB101	uc003lns.1	A6NFK2	OTTHUMG00000163417	ENST00000377976.1:c.450G>C	chr5.hg19:g.145246178C>G	ENSP00000367214:p.Glu150Asp	91.0	0.0		131.0	30.0	NM_001080516		Missense_Mutation	SNP	ENST00000377976.1	hg19	CCDS34263.1	.	.	.	.	.	.	.	.	.	.	C	1.138	-0.650427	0.03506	.	.	ENSG00000204928	ENST00000377976	T	0.24723	1.84	5.43	-0.984	0.10259	.	0.455549	0.24748	N	0.035933	T	0.13372	0.0324	L	0.33485	1.01	0.09310	N	0.999998	B	0.12630	0.006	B	0.13407	0.009	T	0.29027	-1.0025	10	0.15952	T	0.53	-7.8332	4.8326	0.13449	0.0891:0.4514:0.088:0.3715	.	150	A6NFK2	GRCR2_HUMAN	D	150	ENSP00000367214:E150D	ENSP00000367214:E150D	E	-	3	2	GRXCR2	145226371	0.004000	0.15560	0.932000	0.37286	0.162000	0.22319	-0.664000	0.05292	-0.532000	0.06332	-1.587000	0.00848	GAG	.	.		0.428	GRXCR2-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373289.2			G	145246178	C	G	145246178	3	3	276	1	0	0	0	0	1	0	0	0	6822	680	24	4	304	4	GRXCR2	5	145246178	Missense_Mutation	SNP	C	TCGA-G3-A25W-01A-11D-A16V-10	14405007	145246178	35669082	16	39627										
EYS	346007	hgsc.bcm.edu	37	chr6	65300537	65300537	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	aactcaaaatccagagaactAtcacttgggtgaagtttgaa	8	7	2	3			TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr6:65300537A>G	ENST00000370621.3	-	26	5749	c.5223T>C	c.(5221-5223)gaT>gaC	p.D1741D	EYS_ENST00000503581.1_Silent_p.D1741D|EYS_ENST00000370616.2_Silent_p.D1741D			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	1741					detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						CCAGAGAACTATCACTTGGGT	0.343																																					p.D1741D		Atlas-SNP	.											.	EYS	527	.	0			c.T5223C						.						36	33	34					6																	65300537		692	1590	2282	SO:0001819	synonymous_variant	346007	exon26			AGAACTATCACTT		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.5223T>C	chr6.hg19:g.65300537A>G		128.0	0.0		125.0	21.0	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Silent	SNP	ENST00000370621.3	hg19																																																																																				.	.		0.343	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		G	65300537	A	G	65300537	2	3	276	1	0	0	0	0	0	0	0	1	5334	446	16	2		2	EYS	6	65300537	Silent	SNP	A	TCGA-G3-A25W-01A-11D-A16V-10		65300537	105814530	17	39628										
UTRN	7402	hgsc.bcm.edu	37	chr6	144783916	144783916	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	agcaagaatttgatgatgtgCaaggaaagtggaacaagcta	12	4	0	3			TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr6:144783916C>T	ENST00000367545.3	+	22	2980	c.2980C>T	c.(2980-2982)Caa>Taa	p.Q994*		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	994					aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		TGATGATGTGCAAGGAAAGTG	0.378																																					p.Q994X		Atlas-SNP	.											.	UTRN	327	.	0			c.C2980T						.						104	119	114					6																	144783916		2203	4300	6503	SO:0001587	stop_gained	7402	exon22			GATGTGCAAGGAA	AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"utrophin (homologous to dystrophin)"	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.2980C>T	chr6.hg19:g.144783916C>T	ENSP00000356515:p.Gln994*	81.0	0.0		86.0	22.0	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Nonsense_Mutation	SNP	ENST00000367545.3	hg19	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	C	38	7.192009	0.98125	.	.	ENSG00000152818	ENST00000367529;ENST00000367545	.	.	.	5.47	3.54	0.40534	.	0.131201	0.34828	N	0.003641	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	.	10.7754	0.46346	0.1319:0.5824:0.2857:0.0	.	.	.	.	X	994	.	ENSP00000356499:Q994X	Q	+	1	0	UTRN	144825609	0.998000	0.40836	0.963000	0.40424	0.403000	0.30841	1.301000	0.33447	1.237000	0.43756	0.655000	0.94253	CAA	.	.		0.378	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1			T	144783916	C	T	144783916	4	4	276	1	0	0	0	0	0	1	0	0	17118	711	25	3	3066	3	UTRN	6	144783916	Nonsense_Mutation	SNP	C	TCGA-G3-A25W-01A-11D-A16V-10	79483379	144783916	26331151	18	39629										
FSCN1	6624	hgsc.bcm.edu	37	chr7	5645021	5645021	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	aaggtggccatcaaggtgggCgggcgctacctgaagggcga	18	9	1	1	rs568861608		TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr7:5645021C>T	ENST00000382361.3	+	5	1512	c.1398C>T	c.(1396-1398)ggC>ggT	p.G466G	FSCN1_ENST00000340250.6_Silent_p.G445G	NM_003088.3	NP_003079.1	Q16658	FSCN1_HUMAN	fascin actin-bundling protein 1	466					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|cell migration (GO:0016477)|cell motility (GO:0048870)|cell proliferation (GO:0008283)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|invadopodium (GO:0071437)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|drug binding (GO:0008144)|poly(A) RNA binding (GO:0044822)	p.G466G(1)		central_nervous_system(1)|kidney(3)|large_intestine(1)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	9		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;1.21e-13)		TCAAGGTGGGCGGGCGCTACC	0.657													C|||	1	0.000199681	0	0	5008	,	,		16633	0		0	False		,,,				2504	0.001				p.G466G		Atlas-SNP	.											FSCN1,caecum,carcinoma,0,1	FSCN1	29	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1398T						.						52	45	48					7																	5645021		2203	4300	6503	SO:0001819	synonymous_variant	6624	exon5			GGTGGGCGGGCGC	U03057	CCDS5342.1	7p22	2014-02-03	2014-02-03	2002-09-20	ENSG00000075618	ENSG00000075618		"Fascins"	11148	protein-coding gene	gene with protein product	"Singed, drosophila, homolog-like", "actin bundling protein"	602689	"singed (Drosophila)-like (sea urchin fascin homolog like)", "fascin homolog 1, actin-bundling protein (Strongylocentrotus purpuratus)"	SNL		8068206, 10783262	Standard	NM_003088		Approved	p55, FLJ38511	uc003sou.3	Q16658	OTTHUMG00000090599	ENST00000382361.3:c.1398C>T	chr7.hg19:g.5645021C>T		55.0	0.0		50.0	12.0	NM_003088	A6NI89|B2RE97|Q96IC5|Q96IH1|Q9BRF1	Silent	SNP	ENST00000382361.3	hg19	CCDS5342.1																																																																																			.	.		0.657	FSCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207153.3	NM_003088		T	5645021	C	T	5645021	2	4	276	1	0	0	0	0	0	0	0	1	6075	755	27	1		1	FSCN1	7	5645021	Silent	SNP	C	TCGA-G3-A25W-01A-11D-A16V-10		5645021	153493642	19	39630										
METTL2B	55798	hgsc.bcm.edu	37	chr7	128119304	128119304	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	atagacattggctttttaccGaattccctgagctggcacct	8	11	0	2			TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr7:128119304G>A	ENST00000262432.8	+	3	332	c.295G>A	c.(295-297)Gaa>Aaa	p.E99K	METTL2B_ENST00000480046.1_Missense_Mutation_p.E34K|RP11-212P7.3_ENST00000462662.1_RNA	NM_018396.2	NP_060866.2	Q6P1Q9	MET2B_HUMAN	methyltransferase like 2B	99					tRNA methylation (GO:0030488)		tRNA (cytosine) methyltransferase activity (GO:0016427)			breast(1)|cervix(1)|large_intestine(2)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						GCTTTTTACCGAATTCCCTGA	0.378																																					p.E99K		Atlas-SNP	.											.	METTL2B	34	.	0			c.G295A						.						55	57	56					7																	128119304		2202	4297	6499	SO:0001583	missense	55798	exon3			TTTACCGAATTCC	AK002212	CCDS5803.2	7q32.2	2012-06-12	2006-02-09	2006-02-09	ENSG00000165055	ENSG00000165055			18272	protein-coding gene	gene with protein product		607846	"methyltransferase like 2"	METTL2		11738826	Standard	NM_018396		Approved	METL, FLJ11350	uc003vnf.3	Q6P1Q9	OTTHUMG00000143738	ENST00000262432.8:c.295G>A	chr7.hg19:g.128119304G>A	ENSP00000262432:p.Glu99Lys	238.0	0.0		250.0	41.0	NM_018396	B4DZ68|Q0IJ54|Q3B7J1	Missense_Mutation	SNP	ENST00000262432.8	hg19	CCDS5803.2	.	.	.	.	.	.	.	.	.	.	G	16.89	3.248049	0.59103	.	.	ENSG00000165055	ENST00000462662;ENST00000262432;ENST00000480046	T;T;T	0.03951	3.75;3.75;3.75	2.86	1.97	0.26223	.	0.000000	0.85682	D	0.000000	T	0.24624	0.0597	M	0.93854	3.465	0.52501	D	0.999959	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.01583	-1.1319	10	0.87932	D	0	0.0553	7.7593	0.28942	0.1338:0.0:0.8662:0.0	.	34;99	Q6P1Q9-2;Q6P1Q9	.;MTL2B_HUMAN	K	93;99;34	ENSP00000418634:E93K;ENSP00000262432:E99K;ENSP00000418402:E34K	ENSP00000262432:E99K	E	+	1	0	METTL2B	127906540	1.000000	0.71417	0.801000	0.32222	0.494000	0.33585	9.445000	0.97587	0.540000	0.28808	-0.491000	0.04670	GAA	.	.		0.378	METTL2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289817.1	NM_018396		A	128119304	G	A	128119304	3	1	276	1	0	0	0	0	1	0	0	0	9509	1059	37	1	305	1	METTL2B	7	128119304	Missense_Mutation	SNP	G	TCGA-G3-A25W-01A-11D-A16V-10	122474283	128119304	31019359	20	39631										
TRAM1	23471	hgsc.bcm.edu	37	chr8	71499196	71499196	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	ggaaaagaaattcaacaaaaTaatgtagcaccagaagaaca	7	6	1	3			TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr8:71499196T>C	ENST00000262213.2	-	8	849	c.680A>G	c.(679-681)tAt>tGt	p.Y227C	TRAM1_ENST00000521425.1_Missense_Mutation_p.Y141C|TRAM1_ENST00000536748.1_Missense_Mutation_p.Y196C|TRAM1_ENST00000521049.1_5'UTR	NM_014294.5	NP_055109.1	Q15629	TRAM1_HUMAN	translocation associated membrane protein 1	227	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|gene expression (GO:0010467)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)	17			Epithelial(68;0.00679)|all cancers(69;0.0324)|OV - Ovarian serous cystadenocarcinoma(28;0.0509)			TTCAACAAAATAATGTAGCAC	0.323																																					p.Y227C	Ovarian(85;984 1334 5116 12432 40638)	Atlas-SNP	.											.	TRAM1	33	.	0			c.A680G						.						98	93	95					8																	71499196		2203	4300	6503	SO:0001583	missense	23471	exon8			ACAAAATAATGTA	X63679	CCDS6207.1	8q13.1	2004-01-22			ENSG00000067167	ENSG00000067167			20568	protein-coding gene	gene with protein product		605190				1315422	Standard	NM_014294		Approved	TRAM, TRAMP	uc003xyo.2	Q15629	OTTHUMG00000164428	ENST00000262213.2:c.680A>G	chr8.hg19:g.71499196T>C	ENSP00000262213:p.Tyr227Cys	102.0	0.0		114.0	22.0	NM_014294	B4E0K2	Missense_Mutation	SNP	ENST00000262213.2	hg19	CCDS6207.1	.	.	.	.	.	.	.	.	.	.	T	17.64	3.438708	0.62955	.	.	ENSG00000067167	ENST00000521425;ENST00000262213;ENST00000536748	D;D;D	0.85171	-1.95;-1.95;-1.95	5.66	5.66	0.87406	TRAM/LAG1/CLN8 homology domain (3);	0.116921	0.64402	D	0.000011	D	0.89856	0.6836	M	0.89601	3.045	0.80722	D	1	B	0.30563	0.285	B	0.38378	0.272	D	0.89377	0.3679	10	0.49607	T	0.09	-4.0819	15.8852	0.79241	0.0:0.0:0.0:1.0	.	227	Q15629	TRAM1_HUMAN	C	141;227;196	ENSP00000428052:Y141C;ENSP00000262213:Y227C;ENSP00000439359:Y196C	ENSP00000262213:Y227C	Y	-	2	0	TRAM1	71661750	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.163000	0.71880	2.146000	0.66826	0.477000	0.44152	TAT	.	.		0.323	TRAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378738.1	NM_014294		C	71499196	T	C	71499196	3	2	276	1	0	0	0	0	1	0	0	0	16466	1406	49	2	460	2	TRAM1	8	71499196	Missense_Mutation	SNP	T	TCGA-G3-A25W-01A-11D-A16V-10		71499196	74864826	21	39632										
ALDOB	229	hgsc.bcm.edu	37	chr9	104192169	104192169	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	ttgatggaactgtccacagaGaagaggatttctcggaactg	12	7	1	3			TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr9:104192169G>T	ENST00000374855.4	-	3	316	c.192C>A	c.(190-192)ttC>ttA	p.F64L	ALDOB_ENST00000468981.3_5'Flank	NM_000035.3	NP_000026.2	P05062	ALDOB_HUMAN	aldolase B, fructose-bisphosphate	64					carbohydrate metabolic process (GO:0005975)|fructose 1,6-bisphosphate metabolic process (GO:0030388)|fructose catabolic process (GO:0006001)|fructose metabolic process (GO:0006000)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|NADH oxidation (GO:0006116)|positive regulation of ATPase activity (GO:0032781)|small molecule metabolic process (GO:0044281)|vacuolar proton-transporting V-type ATPase complex assembly (GO:0070072)	centriolar satellite (GO:0034451)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)	ATPase binding (GO:0051117)|cytoskeletal protein binding (GO:0008092)|fructose binding (GO:0070061)|fructose-1-phosphate aldolase activity (GO:0061609)|fructose-bisphosphate aldolase activity (GO:0004332)|identical protein binding (GO:0042802)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|liver(1)|lung(5)|prostate(2)|skin(4)|urinary_tract(1)	24		Acute lymphoblastic leukemia(62;0.0559)				TGTCCACAGAGAAGAGGATTT	0.552																																					p.F64L		Atlas-SNP	.											.	ALDOB	69	.	0			c.C192A						.						148	143	145					9																	104192169		2203	4300	6503	SO:0001583	missense	229	exon3			CACAGAGAAGAGG	X01098	CCDS6756.1	9q21.3-q22.2	2008-02-05			ENSG00000136872	ENSG00000136872	4.1.2.13		417	protein-coding gene	gene with protein product		612724					Standard	NM_000035		Approved		uc004bbk.2	P05062	OTTHUMG00000020378	ENST00000374855.4:c.192C>A	chr9.hg19:g.104192169G>T	ENSP00000363988:p.Phe64Leu	126.0	0.0		134.0	33.0	NM_000035	Q13741|Q13742|Q5T7D6	Missense_Mutation	SNP	ENST00000374855.4	hg19	CCDS6756.1	.	.	.	.	.	.	.	.	.	.	G	17.60	3.429806	0.62844	.	.	ENSG00000136872	ENST00000374855;ENST00000430164	D	0.86694	-2.16	5.94	3.1	0.35709	Aldolase-type TIM barrel (1);	0.000000	0.85682	D	0.000000	T	0.81823	0.4904	L	0.39397	1.21	0.80722	D	1	B	0.21688	0.059	B	0.30401	0.115	T	0.75991	-0.3122	10	0.42905	T	0.14	-16.4465	9.6782	0.40054	0.2252:0.0:0.7748:0.0	.	64	P05062	ALDOB_HUMAN	L	64	ENSP00000363988:F64L	ENSP00000363988:F64L	F	-	3	2	ALDOB	103231990	1.000000	0.71417	0.878000	0.34440	0.935000	0.57460	4.157000	0.58144	0.832000	0.34804	0.650000	0.86243	TTC	.	.		0.552	ALDOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053434.2			T	104192169	G	T	104192169	3	4	276	1	0	0	0	0	1	0	0	0	508	933	33	3	930	3	ALDOB	9	104192169	Missense_Mutation	SNP	G	TCGA-G3-A25W-01A-11D-A16V-10		104192169	37021262	22	39633										
HERC4	26091	hgsc.bcm.edu	37	chr10	69726472	69726472	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	ctgctgttggacccagttgaTataatcatttcttatgtcta	7	8	3	1			TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr10:69726472T>C	ENST00000395198.3	-	16	2141	c.1894A>G	c.(1894-1896)Atc>Gtc	p.I632V	HERC4_ENST00000373700.4_Missense_Mutation_p.I632V|HERC4_ENST00000277817.6_Missense_Mutation_p.I522V|HERC4_ENST00000395187.2_3'UTR|HERC4_ENST00000412272.2_Missense_Mutation_p.I632V	NM_022079.2	NP_071362.1	Q5GLZ8	HERC4_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 4	632					cell differentiation (GO:0030154)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	27						ACCCAGTTGATATAATCATTT	0.284																																					p.I632V		Atlas-SNP	.											.	HERC4	78	.	0			c.A1894G						.						97	91	93					10																	69726472		2203	4300	6503	SO:0001583	missense	26091	exon16			AGTTGATATAATC	AY221963	CCDS7274.1, CCDS41533.1, CCDS60541.1, CCDS60542.1	10q21.3	2013-09-20	2012-02-23		ENSG00000148634	ENSG00000148634			24521	protein-coding gene	gene with protein product		609248	"hect domain and RLD 4"			10997877	Standard	NM_022079		Approved	DKFZP564G092, KIAA1593	uc001jng.4	Q5GLZ8	OTTHUMG00000018343	ENST00000395198.3:c.1894A>G	chr10.hg19:g.69726472T>C	ENSP00000378624:p.Ile632Val	120.0	0.0		100.0	17.0	NM_022079	Q5GC98|Q5GC99|Q5GCA0|Q8IXP9|Q9HCH9	Missense_Mutation	SNP	ENST00000395198.3	hg19	CCDS41533.1	.	.	.	.	.	.	.	.	.	.	T	2.943	-0.218442	0.06101	.	.	ENSG00000148634	ENST00000277817;ENST00000412272;ENST00000395198;ENST00000373700	T;T;T;T	0.76060	1.19;0.93;0.94;-0.99	5.16	5.16	0.70880	.	0.218250	0.47852	D	0.000217	T	0.44623	0.1302	N	0.04116	-0.275	0.80722	D	1	B;B;B;B;B;B	0.13594	0.008;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.10450	0.005;0.003;0.0;0.001;0.001;0.001	T	0.45963	-0.9225	10	0.05525	T	0.97	.	6.2043	0.20593	0.1445:0.0795:0.0:0.776	.	632;522;632;482;632;632	Q5GLZ8-3;Q5GLZ8-6;A8K9U4;Q5VXS9;Q5GLZ8-2;Q5GLZ8	.;.;.;.;.;HERC4_HUMAN	V	522;632;632;632	ENSP00000277817:I522V;ENSP00000416504:I632V;ENSP00000378624:I632V;ENSP00000362804:I632V	ENSP00000277817:I522V	I	-	1	0	HERC4	69396478	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.237000	0.43061	2.086000	0.62901	0.374000	0.22700	ATC	.	.		0.284	HERC4-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359262.1	NM_015601		C	69726472	T	C	69726472	3	2	276	1	0	0	0	0	1	0	0	0	7069	1406	49	2	1323	2	HERC4	10	69726472	Missense_Mutation	SNP	T	TCGA-G3-A25W-01A-11D-A16V-10		69726472	65808275	23	39634										
BEST1	7439	hgsc.bcm.edu	37	chr11	61723374	61723376	+	In_Frame_Del	DEL	CAC	CAC	-													0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	ctcatcctgcgcagcgtcagCaccgcagtctacaagcgctt							TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	CAC	CAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr11:61723374_61723376delCAC	ENST00000378043.4	+	4	1075_1077	c.432_434delCAC	c.(430-435)agcacc>agc	p.T145del	BEST1_ENST00000378042.3_In_Frame_Del_p.T85del|BEST1_ENST00000534553.1_In_Frame_Del_p.T39del|BEST1_ENST00000435278.2_In_Frame_Del_p.T145del|BEST1_ENST00000301774.9_5'UTR|BEST1_ENST00000449131.2_In_Frame_Del_p.T85del|BEST1_ENST00000526988.1_In_Frame_Del_p.T39del	NM_004183.3	NP_004174.1	O76090	BEST1_HUMAN	bestrophin 1	145					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|detection of light stimulus involved in visual perception (GO:0050908)|ion transmembrane transport (GO:0034220)|regulation of calcium ion transport (GO:0051924)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	basolateral plasma membrane (GO:0016323)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|skin(2)|urinary_tract(2)	25						GCAGCGTCAGCACCGCAGTCTAC	0.695																																					p.144_145del		Atlas-INDEL	.											.	BEST1	85	.	0			c.431_433del						.																																			SO:0001651	inframe_deletion	7439	exon4			.	AF057170	CCDS31580.1, CCDS44623.1	11q12	2013-02-14	2006-10-18	2006-10-18	ENSG00000167995	ENSG00000167995		"Ion channels / Chloride channels : Calcium activated : Bestrophins"	12703	protein-coding gene	gene with protein product	"Best disease"	607854	"vitelliform macular dystrophy 2"	VMD2		1302019, 17003041	Standard	NM_004183		Approved	BMD, BEST, RP50	uc001nsr.2	O76090	OTTHUMG00000167469	ENST00000378043.4:c.432_434delCAC	chr11.hg19:g.61723374_61723376delCAC	ENSP00000367282:p.Thr145del	24.0	0.0		35.0	13.0	NM_004183	A8K0W6|B7Z3J8|B7Z736|O75904|Q53YQ9|Q8IUR9|Q8IZ80	In_Frame_Del	DEL	ENST00000378043.4	hg19	CCDS31580.1																																																																																			.	.		0.695	BEST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394715.1	NM_004183		-	61723376	CAC	-	61723374	7	5	276	1	0	1	0	1	0	0	0	0	1404	709	25	0	442	0	BEST1	11	61723374	In_Frame_Del	DEL	CAC	TCGA-G3-A25W-01A-11D-A16V-10		61723374	73283142	24	39635										
LRMP	4033	hgsc.bcm.edu	37	chr12	25232338	25232338	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	tatctttttggcagggaataTtcctcactaccattacccag	6	11	2	0			TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr12:25232338T>A	ENST00000354454.3	+	7	907	c.78T>A	c.(76-78)taT>taA	p.Y26*	LRMP_ENST00000547044.1_Nonsense_Mutation_p.Y26*|LRMP_ENST00000548766.1_Nonsense_Mutation_p.Y26*	NM_006152.3	NP_006143.2	Q12912	LRMP_HUMAN	lymphoid-restricted membrane protein	82					immune system process (GO:0002376)|single fertilization (GO:0007338)|vesicle fusion (GO:0006906)|vesicle targeting (GO:0006903)	chromosome (GO:0005694)|cytoskeleton (GO:0005856)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleus (GO:0005634)		p.Y26*(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	19	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Colorectal(261;0.11)					GCAGGGAATATTCCTCACTAC	0.343																																					p.Y26X		Atlas-SNP	.											LRMP,NS,carcinoma,0,1	LRMP	51	.	1	Substitution - Nonsense(1)	kidney(1)	c.T78A						.						194	184	187					12																	25232338		2203	4300	6503	SO:0001587	stop_gained	4033	exon6			GGAATATTCCTCA		CCDS8701.1	12p12.1	2012-05-16			ENSG00000118308	ENSG00000118308			6690	protein-coding gene	gene with protein product		602003				8021504	Standard	NM_006152		Approved	JAW1	uc010sja.2	Q12912	OTTHUMG00000170192	ENST00000354454.3:c.78T>A	chr12.hg19:g.25232338T>A	ENSP00000346442:p.Tyr26*	109.0	0.0		123.0	22.0	NM_001204126	A0AVM2|B4E077|Q8N301	Nonsense_Mutation	SNP	ENST00000354454.3	hg19	CCDS8701.1	.	.	.	.	.	.	.	.	.	.	T	18.41	3.616908	0.66672	.	.	ENSG00000118308	ENST00000550945;ENST00000557489;ENST00000354454;ENST00000548766;ENST00000554942;ENST00000547044	.	.	.	4.82	-1.46	0.08800	.	1.274630	0.05414	N	0.542971	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	1.4078	8.6515	0.34038	0.0:0.48:0.0:0.52	.	.	.	.	X	26	.	ENSP00000346442:Y26X	Y	+	3	2	LRMP	25123605	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.194000	0.17135	-0.333000	0.08476	-0.353000	0.07706	TAT	.	.		0.343	LRMP-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407870.1	NM_006152		A	25232338	T	A	25232338	4	1	276	1	0	0	0	0	0	1	0	0	8959	1500	52	4	88	4	LRMP	12	25232338	Nonsense_Mutation	SNP	T	TCGA-G3-A25W-01A-11D-A16V-10		25232338	108619557	25	39636										
C12orf35	55196	hgsc.bcm.edu	37	chr12	32135645	32135645	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	atgaaaatatgctacttctcGctttgctttcacaggcacgt	7	10	2	1			TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr12:32135645G>A	ENST00000312561.4	+	4	2170	c.1756G>A	c.(1756-1758)Gct>Act	p.A586T	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	586																	GCTACTTCTCGCTTTGCTTTC	0.353																																					p.A586T		Atlas-SNP	.											.	.	.	.	0			c.G1756A						.						38	39	38					12																	32135645		2203	4299	6502	SO:0001583	missense	55196	exon4			CTTCTCGCTTTGC	AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 35"	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.1756G>A	chr12.hg19:g.32135645G>A	ENSP00000310338:p.Ala586Thr	51.0	0.0		51.0	9.0	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Missense_Mutation	SNP	ENST00000312561.4	hg19	CCDS8725.2	.	.	.	.	.	.	.	.	.	.	G	9.285	1.049138	0.19827	.	.	ENSG00000174718	ENST00000312561;ENST00000381054	T;T	0.05925	4.0;3.37	4.46	-2.73	0.05950	.	5.264380	0.00496	N	0.000142	T	0.03053	0.0090	N	0.08118	0	0.09310	N	1	B	0.20780	0.048	B	0.17098	0.017	T	0.33904	-0.9850	9	.	.	.	.	1.4483	0.02369	0.2113:0.397:0.1678:0.2239	.	586	Q9HCM1	CL035_HUMAN	T	586	ENSP00000310338:A586T;ENSP00000370442:A586T	.	A	+	1	0	C12orf35	32026912	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.370000	0.07523	-0.928000	0.03761	-1.339000	0.01253	GCT	.	.		0.353	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169		A	32135645	G	A	32135645	3	1	276	1	0	0	0	0	1	0	0	0	1684	1087	38	1	1758	1	C12orf35	12	32135645	Missense_Mutation	SNP	G	TCGA-G3-A25W-01A-11D-A16V-10	6903307	32135645	101716250	26	39637										
MAPKAPK5	8550	hgsc.bcm.edu	37	chr12	112308091	112308091	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	tcagatagctttggctctgcGgcactgtcacttgttaaaca	9	10	3	1			TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr12:112308091G>A	ENST00000551404.2	+	6	518	c.410G>A	c.(409-411)cGg>cAg	p.R137Q	MAPKAPK5_ENST00000546394.1_3'UTR|MAPKAPK5_ENST00000550735.2_Missense_Mutation_p.R137Q			Q8IW41	MAPK5_HUMAN	mitogen-activated protein kinase-activated protein kinase 5	137	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|MAPK cascade (GO:0000165)|negative regulation of TOR signaling (GO:0032007)|protein autophosphorylation (GO:0046777)|Ras protein signal transduction (GO:0007265)|regulation of translation (GO:0006417)|signal transduction (GO:0007165)|stress-induced premature senescence (GO:0090400)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|lung(11)|ovary(1)	13						TTGGCTCTGCGGCACTGTCAC	0.403																																					p.R137Q		Atlas-SNP	.											.	MAPKAPK5	56	.	0			c.G410A						.						127	113	117					12																	112308091		1873	4102	5975	SO:0001583	missense	8550	exon6			CTCTGCGGCACTG	AF032437	CCDS44975.1, CCDS44976.1	12q24.13	2012-05-30			ENSG00000089022	ENSG00000089022			6889	protein-coding gene	gene with protein product		606723				9628874	Standard	NM_003668		Approved	PRAK	uc001tta.4	Q8IW41	OTTHUMG00000169605	ENST00000551404.2:c.410G>A	chr12.hg19:g.112308091G>A	ENSP00000449381:p.Arg137Gln	149.0	0.0		151.0	27.0	NM_139078	B3KVA5|O60491|Q86X46|Q9BVX9|Q9UG86	Missense_Mutation	SNP	ENST00000551404.2	hg19	CCDS44975.1	.	.	.	.	.	.	.	.	.	.	G	8.256	0.810106	0.16537	.	.	ENSG00000089022	ENST00000550735;ENST00000202788;ENST00000428907;ENST00000551404	T;T	0.64618	-0.11;-0.11	5.6	4.47	0.54385	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.234953	0.44097	N	0.000486	T	0.32346	0.0826	N	0.03891	-0.335	0.28693	N	0.90448	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.09377	0.004;0.0;0.0	T	0.22941	-1.0202	10	0.02654	T	1	.	10.837	0.46694	0.9248:0.0:0.0752:0.0	.	131;137;137	C9J458;Q8IW41;Q8IW41-2	.;MAPK5_HUMAN;.	Q	137	ENSP00000449667:R137Q;ENSP00000449381:R137Q	ENSP00000202788:R137Q	R	+	2	0	MAPKAPK5	110792474	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.081000	0.64444	0.965000	0.38133	-0.469000	0.05056	CGG	.	.		0.403	MAPKAPK5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405019.2	NM_139078		A	112308091	G	A	112308091	3	1	276	1	0	0	0	0	1	0	0	0	9300	1116	39	1	432	1	MAPKAPK5	12	112308091	Missense_Mutation	SNP	G	TCGA-G3-A25W-01A-11D-A16V-10	80172446	112308091	21543804	27	39638										
NCOR2	9612	hgsc.bcm.edu	37	chr12	124835268	124835268	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	gatggtgcccttgtacaggaCgtcagctggcgtgccctgca	14	12	1	0			TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr12:124835268C>T	ENST00000405201.1	-	28	3709	c.3709G>A	c.(3709-3711)Gtc>Atc	p.V1237I	NCOR2_ENST00000429285.2_Missense_Mutation_p.V1227I|NCOR2_ENST00000356219.3_Missense_Mutation_p.V1244I|NCOR2_ENST00000404121.2_Missense_Mutation_p.V798I|NCOR2_ENST00000404621.1_Missense_Mutation_p.V1227I|NCOR2_ENST00000397355.1_Missense_Mutation_p.V1228I			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1245					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		TTGTACAGGACGTCAGCTGGC	0.637																																					p.V1237I		Atlas-SNP	.											.	NCOR2	475	.	0			c.G3709A						.						55	60	58					12																	124835268		2193	4280	6473	SO:0001583	missense	9612	exon30			ACAGGACGTCAGC	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"nuclear receptor co-repressor 2"			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.3709G>A	chr12.hg19:g.124835268C>T	ENSP00000384018:p.Val1237Ile	14.0	0.0		32.0	10.0	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	hg19	CCDS41858.2	.	.	.	.	.	.	.	.	.	.	C	18.66	3.672057	0.67928	.	.	ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000429285;ENST00000458234	T;T;T;T;T;T;T	0.35789	2.06;2.33;2.07;2.33;2.07;2.33;1.29	4.99	4.99	0.66335	.	0.000000	0.64402	D	0.000001	T	0.59046	0.2165	M	0.64997	1.995	0.58432	D	0.999997	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.76071	0.986;0.979;0.987	T	0.62134	-0.6918	10	0.62326	D	0.03	-42.5425	18.2573	0.90023	0.0:1.0:0.0:0.0	.	1227;1228;1237	C9J0Q5;C9J239;C9JFD3	.;.;.	I	1237;1227;1244;1228;1236;798;1227;1245	ENSP00000384018:V1237I;ENSP00000384202:V1227I;ENSP00000348551:V1244I;ENSP00000380513:V1228I;ENSP00000385618:V798I;ENSP00000400281:V1227I;ENSP00000402808:V1245I	ENSP00000348551:V1244I	V	-	1	0	NCOR2	123401221	1.000000	0.71417	0.719000	0.30619	0.656000	0.38851	5.703000	0.68340	2.315000	0.78130	0.478000	0.44815	GTC	.	.		0.637	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312		T	124835268	C	T	124835268	3	4	276	1	0	0	0	0	1	0	0	0	10245	536	19	1	3915	1	NCOR2	12	124835268	Missense_Mutation	SNP	C	TCGA-G3-A25W-01A-11D-A16V-10	12527177	124835268	9016627	28	39639										
ZIC5	85416	hgsc.bcm.edu	37	chr13	100617641	100617641	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	ataataaattctaatgtatcGtccgcacaacttcagggttc	6	9	2	0	rs146570814		TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr13:100617641G>A	ENST00000267294.4	-	2	2215	c.1982C>T	c.(1981-1983)aCg>aTg	p.T661M		NM_033132.3	NP_149123.2	Q96T25	ZIC5_HUMAN	Zic family member 5	661					cell differentiation (GO:0030154)|forebrain development (GO:0030900)|neural tube closure (GO:0001843)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T661M(1)		endometrium(3)|kidney(1)|lung(2)|prostate(1)|skin(2)	9	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					CTAATGTATCGTCCGCACAAC	0.478																																					p.T661M		Atlas-SNP	.											ZIC5,NS,carcinoma,0,2	ZIC5	38	.	1	Substitution - Missense(1)	prostate(1)	c.C1982T						.	G	MET/THR	0,4406		0,0,2203	60	60	60		1982	6.1	1	13	dbSNP_134	60	2,8598	2.2+/-6.3	0,2,4298	yes	missense	ZIC5	NM_033132.3	81	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	possibly-damaging	661/664	100617641	2,13004	2203	4300	6503	SO:0001583	missense	85416	exon2			TGTATCGTCCGCA	AF378304	CCDS9494.2	13q32.2	2013-01-08	2011-05-19		ENSG00000139800	ENSG00000139800		"Zinc fingers, C2H2-type"	20322	protein-coding gene	gene with protein product			"Zic family member 5 (odd-paired homolog, Drosophila)"				Standard	NM_033132		Approved		uc001vom.1	Q96T25	OTTHUMG00000017280	ENST00000267294.4:c.1982C>T	chr13.hg19:g.100617641G>A	ENSP00000267294:p.Thr661Met	60.0	0.0		63.0	13.0	NM_033132	Q5VYB0	Missense_Mutation	SNP	ENST00000267294.4	hg19	CCDS9494.2	.	.	.	.	.	.	.	.	.	.	G	18.42	3.619827	0.66787	0.0	2.33E-4	ENSG00000139800	ENST00000267294	T	0.15718	2.4	6.06	6.06	0.98353	.	.	.	.	.	T	0.18341	0.0440	L	0.36672	1.1	0.40278	D	0.978365	P	0.52577	0.954	B	0.40659	0.336	T	0.00778	-1.1570	9	0.87932	D	0	.	19.3997	0.94623	0.0:0.0:1.0:0.0	.	661	Q96T25	ZIC5_HUMAN	M	661	ENSP00000267294:T661M	ENSP00000267294:T661M	T	-	2	0	ZIC5	99415642	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.533000	0.67160	2.871000	0.98454	0.655000	0.94253	ACG	.	G|1.000;A|0.000		0.478	ZIC5-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000045623.3	NM_033132		A	100617641	G	A	100617641	3	1	276	1	0	0	0	0	1	0	0	0	17697	1145	40	1	13	1	ZIC5	13	100617641	Missense_Mutation	SNP	G	TCGA-G3-A25W-01A-11D-A16V-10		100617641	14552237	29	39640										
SEC23A	10484	hgsc.bcm.edu	37	chr14	39524374	39524374	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	atgagctgtctgtccagccaCctaagcacatctggaccttc	8	14	2	1			TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr14:39524374C>A	ENST00000307712.6	-	14	2149	c.1632G>T	c.(1630-1632)agG>agT	p.R544S	SEC23A_ENST00000536508.1_Missense_Mutation_p.R418S|SEC23A_ENST00000537403.1_Missense_Mutation_p.R342S|SEC23A_ENST00000545328.2_Missense_Mutation_p.R515S	NM_006364.2	NP_006355.2	Q15436	SC23A_HUMAN	Sec23 homolog A (S. cerevisiae)	544					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			kidney(2)|large_intestine(3)|liver(1)|lung(11)|ovary(4)|pancreas(1)|upper_aerodigestive_tract(1)	23	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0151)		TGTCCAGCCACCTAAGCACAT	0.413																																					p.R544S		Atlas-SNP	.											.	SEC23A	73	.	0			c.G1632T						.						137	129	132					14																	39524374		2203	4300	6503	SO:0001583	missense	10484	exon14			CAGCCACCTAAGC	X97064	CCDS9668.1	14q21.1	2008-05-14	2001-11-28		ENSG00000100934	ENSG00000100934			10701	protein-coding gene	gene with protein product		610511	"Sec23 (S. cerevisiae) homolog A"			8898360, 10329445	Standard	NM_006364		Approved		uc001wup.1	Q15436	OTTHUMG00000028812	ENST00000307712.6:c.1632G>T	chr14.hg19:g.39524374C>A	ENSP00000306881:p.Arg544Ser	83.0	0.0		96.0	21.0	NM_006364	B2R5P4|B3KXI2|Q8NE16	Missense_Mutation	SNP	ENST00000307712.6	hg19	CCDS9668.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.095346	0.76870	.	.	ENSG00000100934	ENST00000537403;ENST00000307712;ENST00000536508;ENST00000545328	D;D;D;D	0.89681	-2.55;-2.55;-2.55;-2.55	5.81	-0.68	0.11346	Sec23/Sec24, helical domain (2);	0.180500	0.49305	D	0.000154	D	0.94873	0.8343	H	0.94503	3.545	0.80722	D	1	D;D;D	0.89917	1.0;0.957;0.97	D;P;P	0.80764	0.994;0.877;0.892	D	0.93921	0.7206	10	0.87932	D	0	-19.4958	11.2054	0.48767	0.0:0.5516:0.0:0.4484	.	515;418;544	F5H365;F5H6C4;Q15436	.;.;SC23A_HUMAN	S	342;544;418;515	ENSP00000444193:R342S;ENSP00000306881:R544S;ENSP00000437715:R418S;ENSP00000445393:R515S	ENSP00000306881:R544S	R	-	3	2	SEC23A	38594125	0.266000	0.24112	0.994000	0.49952	0.998000	0.95712	-0.655000	0.05348	-0.116000	0.11893	0.551000	0.68910	AGG	.	.		0.413	SEC23A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276728.2			A	39524374	C	A	39524374	3	1	276	1	0	0	0	0	1	0	0	0	14006	506	18	3	693	3	SEC23A	14	39524374	Missense_Mutation	SNP	C	TCGA-G3-A25W-01A-11D-A16V-10		39524374	67825166	30	39641										
SDCCAG1	9147	hgsc.bcm.edu	37	chr14	50269987	50269987	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	agcttcctgttgtcaaatatTctccagttggtgctgtttta	8	8	2	0			TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr14:50269987T>C	ENST00000298310.5	-	20	2332	c.1883A>G	c.(1882-1884)gAa>gGa	p.E628G	NEMF_ENST00000556925.1_5'UTR|NEMF_ENST00000546046.1_Missense_Mutation_p.E607G|NEMF_ENST00000545773.1_Missense_Mutation_p.E586G			O60524	NEMF_HUMAN	nuclear export mediator factor	628					nuclear export (GO:0051168)	nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(13)|liver(1)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	36						TGTCAAATATTCTCCAGTTGG	0.328																																					p.E628G		Atlas-SNP	.											.	NEMF	79	.	0			c.A1883G						.						130	116	121					14																	50269987		2202	4299	6501	SO:0001583	missense	9147	exon20			AAATATTCTCCAG	AF039687	CCDS9694.1	14q21.3	2012-11-19	2011-01-31	2011-01-31	ENSG00000165525	ENSG00000165525			10663	protein-coding gene	gene with protein product		608378	"serologically defined colon cancer antigen 1"	SDCCAG1		9610721, 10575219	Standard	XR_429334		Approved	NY-CO-1, FLJ10051	uc001wxc.3	O60524	OTTHUMG00000170857	ENST00000298310.5:c.1883A>G	chr14.hg19:g.50269987T>C	ENSP00000298310:p.Glu628Gly	105.0	0.0		105.0	32.0	NM_004713	A0JLQ3|B3KSK1|B4DDL3|B4DHA9|B4E3F3|Q32Q66|Q8WW70|Q9NWG1	Missense_Mutation	SNP	ENST00000298310.5	hg19	CCDS9694.1	.	.	.	.	.	.	.	.	.	.	T	26.5	4.748169	0.89663	.	.	ENSG00000165525	ENST00000298310;ENST00000545773;ENST00000546046;ENST00000534912;ENST00000555970	T;T;T;T	0.59364	0.38;0.37;0.27;0.36	5.79	5.79	0.91817	Domain of unknown function DUF814 (1);	0.000000	0.85682	D	0.000000	T	0.80549	0.4644	M	0.90483	3.12	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.87578	0.986;0.996;0.996;0.998	D	0.83900	0.0289	10	0.54805	T	0.06	-27.6727	15.8372	0.78808	0.0:0.0:0.0:1.0	.	607;603;586;628	O60524-3;O60524-5;O60524-4;O60524	.;.;.;NEMF_HUMAN	G	628;586;607;400;586	ENSP00000298310:E628G;ENSP00000438309:E586G;ENSP00000441016:E607G;ENSP00000452540:E586G	ENSP00000298310:E628G	E	-	2	0	NEMF	49339737	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.913000	0.75759	2.225000	0.72522	0.477000	0.44152	GAA	.	.		0.328	NEMF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410798.1	NM_004713		C	50269987	T	C	50269987	3	2	276	1	0	0	0	0	1	0	0	0	13972	1783	62	2	1403	2	SDCCAG1	14	50269987	Missense_Mutation	SNP	T	TCGA-G3-A25W-01A-11D-A16V-10	10745613	50269987	57079553	31	39642										
TNRC6A	27327	hgsc.bcm.edu	37	chr16	24802369	24802369	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	aaaggctcaaactgccagggGgggtgggaagatgattctgc	16	7	2	2	rs113829020	byFrequency	TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr16:24802369G>A	ENST00000395799.3	+	6	2535	c.2406G>A	c.(2404-2406)ggG>ggA	p.G802G	TNRC6A_ENST00000315183.7_Silent_p.G802G	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	802	Interaction with argonaute family proteins.|Sufficient for interaction with AGO1 and AGO4.				cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		ACTGCCAGGGGGGGTGGGAAG	0.507																																					p.G802G		Atlas-SNP	.											.	TNRC6A	171	.	0			c.G2406A						.						31	33	32					16																	24802369		2196	4298	6494	SO:0001819	synonymous_variant	27327	exon6			CCAGGGGGGGTGG	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"Trinucleotide (CAG) repeat containing"	11969	protein-coding gene	gene with protein product		610739	"trinucleotide repeat containing 6"	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.2406G>A	chr16.hg19:g.24802369G>A		27.0	0.0		24.0	12.0	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Silent	SNP	ENST00000395799.3	hg19	CCDS10624.2																																																																																			.	G|0.997;C|0.003		0.507	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		A	24802369	G	A	24802369	2	1	276	1	0	0	0	0	0	0	0	1	16355	1219	43	3		3	TNRC6A	16	24802369	Silent	SNP	G	TCGA-G3-A25W-01A-11D-A16V-10		24802369	65552384	32	39643										
KIAA0182	23199	hgsc.bcm.edu	37	chr16	85689985	85689997	+	Frame_Shift_Del	DEL	GCGCGAGCGCGAG	GCGCGAGCGCGAG	-													0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	gagctaaggcgggagagggaGcgcgagcgcgagcgcgagcg					rs376448790|rs555079607|rs374136142|rs369286648|rs372901919	byFrequency	TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	GCGCGAGCGCGAG	GCGCGAGCGCGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr16:85689985_85689997delGCGCGAGCGCGAG	ENST00000253458.7	+	7	1202_1214	c.1026_1038delGCGCGAGCGCGAG	c.(1024-1038)gagcgcgagcgcgagfs	p.ERERE342fs	RN7SL381P_ENST00000577658.1_RNA|GSE1_ENST00000393243.1_Frame_Shift_Del_p.ERERE269fs|GSE1_ENST00000405402.2_Frame_Shift_Del_p.ERERE238fs	NM_014615.2	NP_055430.1	Q14687	GSE1_HUMAN	Gse1 coiled-coil protein	342																	gggagagggagcgcgagcgcgagcgcgagcgtg	0.653																																					p.342_346del		Atlas-INDEL	.											.	.	.	.	0			c.1025_1037del						.																																			SO:0001589	frameshift_variant	23199	exon7			.	D80004	CCDS10952.1, CCDS45539.1, CCDS62007.1	16q24.1	2012-12-07	2012-12-07	2012-10-02	ENSG00000131149	ENSG00000131149			28979	protein-coding gene	gene with protein product	"genetic suppressor element 1"		"KIAA0182", "Gse1 coiled-coil protein homolog (mouse)"	KIAA0182		8724849, 8786132	Standard	NM_014615		Approved		uc002fix.4	Q14687	OTTHUMG00000137650	ENST00000253458.7:c.1026_1038delGCGCGAGCGCGAG	chr16.hg19:g.85689985_85689997delGCGCGAGCGCGAG	ENSP00000253458:p.Glu342fs	21.0	0.0		39.0	13.0	NM_014615	D3DUM4|Q8IY61|Q96GA4|Q9BW09	Frame_Shift_Del	DEL	ENST00000253458.7	hg19	CCDS10952.1																																																																																			.	.		0.653	GSE1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325527.1	NM_014615		-	85689997	GCGCGAGCGCGAG	-	85689985	7	5	276	1	0	1	0	1	0	0	0	0	8168	962	34	0	1052	0	KIAA0182	16	85689985	Frame_Shift_Del	DEL	GCGCGAGCGCGAG	TCGA-G3-A25W-01A-11D-A16V-10	60887616	85689985	4664768	33	39644										
RAB34	83871	hgsc.bcm.edu	37	chr17	27041897	27041897	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	tcagtgctgccacacggaagAagaattctcggacattctca	9	11	3	2			TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr17:27041897A>G	ENST00000395245.3	-	9	1252	c.626T>C	c.(625-627)tTc>tCc	p.F209S	RAB34_ENST00000447716.1_Missense_Mutation_p.F266S|RAB34_ENST00000395243.3_Missense_Mutation_p.F201S|RAB34_ENST00000415040.2_Missense_Mutation_p.F187S|RAB34_ENST00000450529.1_Missense_Mutation_p.F201S|RAB34_ENST00000453384.3_Intron|RAB34_ENST00000395242.2_Missense_Mutation_p.F210S|RAB34_ENST00000301043.6_Missense_Mutation_p.F209S|RAB34_ENST00000436730.3_Missense_Mutation_p.F209S	NM_001256281.1|NM_031934.5	NP_001243210.1|NP_114140.4	Q9BZG1	RAB34_HUMAN	RAB34, member RAS oncogene family	209					antigen processing and presentation (GO:0019882)|Golgi to plasma membrane protein transport (GO:0043001)|lysosome localization (GO:0032418)|phagosome maturation (GO:0090382)|phagosome-lysosome fusion (GO:0090385)|protein localization to plasma membrane (GO:0072659)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|Golgi stack (GO:0005795)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|vesicle (GO:0031982)	GTP binding (GO:0005525)			endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|lung(8)|skin(2)	14	Lung NSC(42;0.00431)					CACACGGAAGAAGAATTCTCG	0.577																																					p.F266S	Pancreas(175;216 2049 29940 32498 41589)	Atlas-SNP	.											.	RAB34	44	.	0			c.T797C						.						64	56	59					17																	27041897		2203	4300	6503	SO:0001583	missense	83871	exon10			CGGAAGAAGAATT	AF322067	CCDS11240.1, CCDS45636.1, CCDS54101.1, CCDS58536.1	17q11.2	2008-07-18			ENSG00000109113	ENSG00000109113		"RAB, member RAS oncogene"	16519	protein-coding gene	gene with protein product		610917				12446704	Standard	NM_031934		Approved	RAB39, RAH	uc010was.1	P0DI83	OTTHUMG00000132680	ENST00000395245.3:c.626T>C	chr17.hg19:g.27041897A>G	ENSP00000378666:p.Phe209Ser	26.0	0.0		41.0	12.0	NM_001144943	B4E3A0|E9PEJ9|Q5BJE6|Q8NCJ8|Q96AR4	Missense_Mutation	SNP	ENST00000395245.3	hg19	CCDS11240.1	.	.	.	.	.	.	.	.	.	.	A	14.86	2.661743	0.47572	.	.	ENSG00000109113	ENST00000447716;ENST00000301043;ENST00000395243;ENST00000415040;ENST00000450529;ENST00000395242;ENST00000395245;ENST00000436730;ENST00000430132;ENST00000412625;ENST00000353676	D;D;D;D;D;D;T;D;D	0.84070	-1.8;-1.8;-1.8;-1.8;-1.8;-1.8;-1.24;-1.8;-1.8	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	D	0.93812	0.8021	H	0.96547	3.84	0.48632	D	0.999683	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.999;0.999;0.999;1.0;0.999;0.999	D	0.95526	0.8599	9	0.87932	D	0	-20.8825	14.437	0.67287	1.0:0.0:0.0:0.0	.	187;201;232;224;210;209	E9PEJ9;Q9BZG1-2;C9JI96;B4DNC0;A8MYQ9;Q9BZG1	.;.;.;.;.;RAB34_HUMAN	S	266;209;201;187;224;210;209;232;210;209;209	ENSP00000410403:F266S;ENSP00000301043:F209S;ENSP00000378664:F201S;ENSP00000410279:F187S;ENSP00000378663:F210S;ENSP00000378666:F209S;ENSP00000407953:F210S;ENSP00000398706:F209S;ENSP00000226259:F209S	ENSP00000301043:F209S	F	-	2	0	RAB34	24066024	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.953000	0.93041	2.087000	0.62958	0.460000	0.39030	TTC	.	.		0.577	RAB34-018	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345906.1	NM_031934		G	27041897	A	G	27041897	3	3	276	1	0	0	0	0	1	0	0	0	12939	246	9	2	225	2	RAB34	17	27041897	Missense_Mutation	SNP	A	TCGA-G3-A25W-01A-11D-A16V-10		27041897	54153313	34	39645										
WDR7	23335	hgsc.bcm.edu	37	chr18	54362254	54362254	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	ccttgtcctgctggaattatAgatcagctgagtgtgattcc	10	9	1	3			TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr18:54362254A>G	ENST00000254442.3	+	11	1393	c.1182A>G	c.(1180-1182)atA>atG	p.I394M	WDR7_ENST00000589935.1_Intron|WDR7_ENST00000357574.3_Missense_Mutation_p.I394M	NM_015285.2	NP_056100.2	Q9Y4E6	WDR7_HUMAN	WD repeat domain 7	394					hematopoietic progenitor cell differentiation (GO:0002244)					NS(1)|breast(5)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(37)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	78				Lung(128;0.0238)|Colorectal(16;0.0296)		CTGGAATTATAGATCAGCTGA	0.403																																					p.I394M		Atlas-SNP	.											.	WDR7	166	.	0			c.A1182G						.						109	102	104					18																	54362254		2203	4300	6503	SO:0001583	missense	23335	exon11			AATTATAGATCAG	AB011113	CCDS11962.1, CCDS11963.1	18q21.31	2013-01-09			ENSG00000091157	ENSG00000091157		"WD repeat domain containing"	13490	protein-coding gene	gene with protein product		613473				10828621	Standard	XM_005266674		Approved	KIAA0541, TRAG	uc002lgk.1	Q9Y4E6	OTTHUMG00000132721	ENST00000254442.3:c.1182A>G	chr18.hg19:g.54362254A>G	ENSP00000254442:p.Ile394Met	130.0	0.0		130.0	29.0	NM_052834	A7E2C8|Q86UX5|Q86VP2|Q96PS7	Missense_Mutation	SNP	ENST00000254442.3	hg19	CCDS11962.1	.	.	.	.	.	.	.	.	.	.	A	15.86	2.958476	0.53400	.	.	ENSG00000091157	ENST00000254442;ENST00000357574;ENST00000398311	T;T	0.69175	-0.38;-0.37	5.68	0.0866	0.14447	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);	0.000000	0.85682	D	0.000000	T	0.74861	0.3772	M	0.68593	2.085	0.53688	D	0.99997	D;D	0.71674	0.995;0.998	D;D	0.78314	0.954;0.991	T	0.70299	-0.4910	10	0.44086	T	0.13	.	9.028	0.36241	0.5044:0.3799:0.0:0.1157	.	394;394	Q9Y4E6-2;Q9Y4E6	.;WDR7_HUMAN	M	394	ENSP00000254442:I394M;ENSP00000350187:I394M	ENSP00000254442:I394M	I	+	3	3	WDR7	52513252	0.996000	0.38824	0.996000	0.52242	0.970000	0.65996	0.497000	0.22514	-0.201000	0.10284	0.477000	0.44152	ATA	.	.		0.403	WDR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256062.1			G	54362254	A	G	54362254	3	3	276	1	0	0	0	0	1	0	0	0	17335	410	15	2	1220	2	WDR7	18	54362254	Missense_Mutation	SNP	A	TCGA-G3-A25W-01A-11D-A16V-10		54362254	23714994	35	39646										
FLRT3	23767	hgsc.bcm.edu	37	chr20	14306475	14306475	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	gctatatgcacagttccttgAgaagagcgatccattcctat	8	10	0	2			TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chr20:14306475A>T	ENST00000378053.3	-	2	1934	c.1678T>A	c.(1678-1680)Tca>Aca	p.S560T	FLRT3_ENST00000341420.4_Missense_Mutation_p.S560T|MACROD2_ENST00000217246.4_Intron|MACROD2_ENST00000310348.4_Intron	NM_013281.3	NP_037413.1	Q9NZU0	FLRT3_HUMAN	fibronectin leucine rich transmembrane protein 3	560					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)			breast(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Colorectal(1;0.0464)	COAD - Colon adenocarcinoma(2;0.129)	Colorectal(1;0.0393)		CAGTTCCTTGAGAAGAGCGAT	0.468																																					p.S560T		Atlas-SNP	.											.	FLRT3	67	.	0			c.T1678A						.						149	137	141					20																	14306475		2203	4300	6503	SO:0001583	missense	23767	exon2			TCCTTGAGAAGAG	AF169677	CCDS13121.1	20p11	2013-02-11			ENSG00000125848	ENSG00000125848		"Fibronectin type III domain containing"	3762	protein-coding gene	gene with protein product		604808				10644439	Standard	NM_198391		Approved		uc002wow.2	Q9NZU0	OTTHUMG00000031914	ENST00000378053.3:c.1678T>A	chr20.hg19:g.14306475A>T	ENSP00000367292:p.Ser560Thr	145.0	0.0		154.0	31.0	NM_013281	D3DW20|Q542Z9|Q96K39|Q96K42|Q96KB1|Q9P259	Missense_Mutation	SNP	ENST00000378053.3	hg19	CCDS13121.1	.	.	.	.	.	.	.	.	.	.	A	10.34	1.321824	0.23994	.	.	ENSG00000125848	ENST00000378053;ENST00000341420;ENST00000541882	T;T	0.62364	0.03;0.03	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	T	0.45337	0.1337	N	0.05351	-0.065	0.80722	D	1	B	0.21147	0.052	B	0.27796	0.083	T	0.38714	-0.9648	10	0.22706	T	0.39	-10.4485	16.4781	0.84144	1.0:0.0:0.0:0.0	.	560	Q9NZU0	FLRT3_HUMAN	T	560	ENSP00000367292:S560T;ENSP00000339912:S560T	ENSP00000339912:S560T	S	-	1	0	FLRT3	14254475	1.000000	0.71417	0.999000	0.59377	0.973000	0.67179	9.339000	0.96797	2.288000	0.76882	0.528000	0.53228	TCA	.	.		0.468	FLRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078075.1	NM_013281		T	14306475	A	T	14306475	3	4	276	1	0	0	0	0	1	0	0	0	5948	304	11	4	275	4	FLRT3	20	14306475	Missense_Mutation	SNP	A	TCGA-G3-A25W-01A-11D-A16V-10		14306475	48719045	36	39647										
PASD1	139135	hgsc.bcm.edu	37	chrX	150839639	150839639	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.027027027027027	1	1	0.365909090909091	0	0.418181818181818	1	1	0	ccatccaaaaccagcagaatGcattggaattgatgatggat	9	8	0	3			TCGA-G3-A25W-01A-11D-A16V-10	TCGA-G3-A25W-11A-12D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36e1d9cc-32ec-4a0a-8fb1-c46f058a6fb8	fdc8e770-343e-4c4e-bc1d-99375ea94de4	g.chrX:150839639G>T	ENST00000370357.4	+	12	1446	c.1201G>T	c.(1201-1203)Gca>Tca	p.A401S		NM_173493.2	NP_775764.2	Q8IV76	PASD1_HUMAN	PAS domain containing 1	401						nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(3)|liver(1)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	48	Acute lymphoblastic leukemia(192;6.56e-05)					CCAGCAGAATGCATTGGAATT	0.463																																					p.A401S		Atlas-SNP	.											.	PASD1	286	.	0			c.G1201T						.						195	161	172					X																	150839639		2203	4300	6503	SO:0001583	missense	139135	exon12			CAGAATGCATTGG	AY270020	CCDS35431.1	Xq28	2009-08-06			ENSG00000166049	ENSG00000166049			20686	protein-coding gene	gene with protein product	"cancer/testis antigen 63"					15122589, 15162151	Standard	NM_173493		Approved	CT63	uc004fev.4	Q8IV76	OTTHUMG00000024169	ENST00000370357.4:c.1201G>T	chrX.hg19:g.150839639G>T	ENSP00000359382:p.Ala401Ser	94.0	0.0		109.0	21.0	NM_173493	Q3MNE0|Q69HD7|Q8N7X9	Missense_Mutation	SNP	ENST00000370357.4	hg19	CCDS35431.1	.	.	.	.	.	.	.	.	.	.	G	11.67	1.707719	0.30322	.	.	ENSG00000166049	ENST00000370357	T	0.17370	2.28	3.78	-2.68	0.06041	.	.	.	.	.	T	0.09335	0.0230	L	0.27053	0.805	0.09310	N	1	P	0.37101	0.582	B	0.35688	0.208	T	0.18053	-1.0349	9	0.49607	T	0.09	-35.6315	3.2783	0.06906	0.314:0.0:0.2256:0.4603	.	401	Q8IV76	PASD1_HUMAN	S	401	ENSP00000359382:A401S	ENSP00000359382:A401S	A	+	1	0	PASD1	150590295	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.227000	0.17795	-0.877000	0.04012	0.529000	0.55759	GCA	.	.		0.463	PASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060879.2	NM_173493		T	150839639	G	T	150839639	3	4	276	1	0	0	0	0	1	0	0	0	11480	1319	46	3	1243	3	PASD1	23	150839639	Missense_Mutation	SNP	G	TCGA-G3-A25W-01A-11D-A16V-10		150839639	4430921	37	39648										
BRDT	676	hgsc.bcm.edu	37	chr1	92433718	92433718	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	tgtagcctggagatgacattGttcttatggcacaagctcta	10	8	2	2			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr1:92433718G>T	ENST00000362005.3	+	5	764	c.346G>T	c.(346-348)Gtt>Ttt	p.V116F	BRDT_ENST00000370389.2_Missense_Mutation_p.V43F|BRDT_ENST00000394530.3_Missense_Mutation_p.V70F|BRDT_ENST00000402388.1_Missense_Mutation_p.V116F|BRDT_ENST00000399546.2_Missense_Mutation_p.V116F	NM_001242805.1	NP_001229734	Q58F21	BRDT_HUMAN	bromodomain, testis-specific	116	Bromo 1. {ECO:0000255|PROSITE- ProRule:PRU00035}.				cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|histone displacement (GO:0001207)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|mRNA processing (GO:0006397)|positive regulation of transcription during meiosis (GO:0051039)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(24)|ovary(1)|prostate(4)|skin(2)|stomach(2)|urinary_tract(2)	56		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)		AGATGACATTGTTCTTATGGC	0.368																																					p.V116F		Atlas-SNP	.											.	BRDT	133	.	0			c.G346T						.						103	102	102					1																	92433718		2203	4300	6503	SO:0001583	missense	676	exon4			GACATTGTTCTTA	AF019085	CCDS735.1, CCDS55615.1, CCDS55616.1, CCDS72820.1	1p22.1	2010-12-23			ENSG00000137948	ENSG00000137948			1105	protein-coding gene	gene with protein product	"cancer/testis antigen 9"	602144				9367677	Standard	NM_001726		Approved	BRD6, CT9	uc010osz.2	Q58F21	OTTHUMG00000010113	ENST00000362005.3:c.346G>T	chr1.hg19:g.92433718G>T	ENSP00000354568:p.Val116Phe	58.0	0.0		50.0	16.0	NM_001242806	A6NF68|B7Z811|B7Z890|B7ZAX7|D3DT32|O14789|Q05DQ4|Q6P5T1|Q7Z4A6|Q8IWI6	Missense_Mutation	SNP	ENST00000362005.3	hg19	CCDS735.1	.	.	.	.	.	.	.	.	.	.	G	31	5.058619	0.93846	.	.	ENSG00000137948	ENST00000362005;ENST00000370389;ENST00000399546;ENST00000539070;ENST00000423434;ENST00000394530;ENST00000440509;ENST00000427104;ENST00000448194;ENST00000426141;ENST00000552654;ENST00000402388	T;T;T;T;T;T;T;T;T;T;T	0.32272	1.46;1.46;1.46;1.46;2.16;1.46;1.46;1.46;1.46;1.46;1.46	5.66	5.66	0.87406	Bromodomain (5);	0.000000	0.64402	D	0.000011	T	0.51618	0.1685	M	0.71920	2.185	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.992;0.992;1.0;1.0	T	0.53613	-0.8414	10	0.87932	D	0	-14.6225	19.7538	0.96281	0.0:0.0:1.0:0.0	.	70;70;116;116	B7ZAX7;B7Z811;B7Z890;Q58F21	.;.;.;BRDT_HUMAN	F	116;43;116;116;116;70;116;116;116;116;43;116	ENSP00000354568:V116F;ENSP00000359416:V43F;ENSP00000387822:V116F;ENSP00000396351:V116F;ENSP00000378038:V70F;ENSP00000416714:V116F;ENSP00000400002:V116F;ENSP00000410587:V116F;ENSP00000404969:V116F;ENSP00000446599:V43F;ENSP00000384051:V116F	ENSP00000354568:V116F	V	+	1	0	BRDT	92206306	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.681000	0.98653	2.690000	0.91761	0.655000	0.94253	GTT	.	.		0.368	BRDT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027980.2	NM_207189		T	92433718	G	T	92433718	3	4	277	1	0	0	0	0	1	0	0	0	1510	1377	48	3	356	3	BRDT	1	92433718	Missense_Mutation	SNP	G	TCGA-G3-A25Y-01A-11D-A16V-10		92433718	156816903	1	39649										
SYCP1	6847	hgsc.bcm.edu	37	chr1	115401205	115401205	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	cagagtgtattcaaaactgtAtaaggaggctgaaaagataa	10	4	1	3			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr1:115401205A>G	ENST00000369522.3	+	6	569	c.329A>G	c.(328-330)tAt>tGt	p.Y110C	SYCP1_ENST00000369518.1_Missense_Mutation_p.Y110C	NM_001282541.1|NM_003176.2	NP_001269470.1|NP_003167.2	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1	110					chiasma assembly (GO:0051026)|lateral element assembly (GO:0051878)|meiotic DNA repair synthesis (GO:0000711)|reciprocal meiotic recombination (GO:0007131)|regulation of protein localization (GO:0032880)|sperm chromatin condensation (GO:0035092)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)|male germ cell nucleus (GO:0001673)|transverse filament (GO:0000802)	DNA binding (GO:0003677)		RGS22/SYCP1(2)	NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		TCAAAACTGTATAAGGAGGCT	0.308																																					p.Y110C		Atlas-SNP	.											.	SYCP1	149	.	0			c.A329G						.						66	70	68					1																	115401205		2203	4299	6502	SO:0001583	missense	6847	exon6			AACTGTATAAGGA	D67035	CCDS879.1, CCDS72840.1	1p13-p12	2009-03-12			ENSG00000198765	ENSG00000198765			11487	protein-coding gene	gene with protein product	"cancer/testis antigen 8"	602162				9560255	Standard	XM_005271154		Approved	HOM-TES-14, SCP1, CT8	uc001efr.3	Q15431	OTTHUMG00000012057	ENST00000369522.3:c.329A>G	chr1.hg19:g.115401205A>G	ENSP00000358535:p.Tyr110Cys	204.0	0.0		204.0	88.0	NM_003176	O14963|Q5VXJ6	Missense_Mutation	SNP	ENST00000369522.3	hg19	CCDS879.1	.	.	.	.	.	.	.	.	.	.	A	10.99	1.508092	0.27036	.	.	ENSG00000198765	ENST00000369522;ENST00000536734;ENST00000455987;ENST00000369518	T;T;T	0.58210	0.35;0.35;0.35	5.05	3.92	0.45320	.	0.273076	0.37095	N	0.002259	T	0.55862	0.1947	M	0.62723	1.935	0.34251	D	0.678766	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.60073	-0.7334	10	0.42905	T	0.14	-3.66	11.0156	0.47687	0.8602:0.0:0.0:0.1397	.	110;110	B7ZLS9;Q15431	.;SYCP1_HUMAN	C	110	ENSP00000358535:Y110C;ENSP00000410011:Y110C;ENSP00000358531:Y110C	ENSP00000358531:Y110C	Y	+	2	0	SYCP1	115202728	1.000000	0.71417	0.965000	0.40720	0.064000	0.16182	5.029000	0.64121	0.776000	0.33473	-0.377000	0.06932	TAT	.	.		0.308	SYCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033386.1	NM_003176		G	115401205	A	G	115401205	3	3	277	1	0	0	0	0	1	0	0	0	15446	449	16	2	347	2	SYCP1	1	115401205	Missense_Mutation	SNP	A	TCGA-G3-A25Y-01A-11D-A16V-10	22967487	115401205	133849416	2	39650										
MAN1A2	10905	hgsc.bcm.edu	37	chr1	118035855	118035855	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	cagataaaacagaccatgagGcaagaaagatgtatgatgat	10	5	0	7			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr1:118035855G>T	ENST00000356554.3	+	9	1990	c.1255G>T	c.(1255-1257)Gca>Tca	p.A419S		NM_006699.3	NP_006690.1	O60476	MA1A2_HUMAN	mannosidase, alpha, class 1A, member 2	419					cellular protein metabolic process (GO:0044267)|lung alveolus development (GO:0048286)|N-glycan processing (GO:0006491)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleolus (GO:0005730)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|urinary_tract(1)	27	Lung SC(450;0.225)	all_cancers(81;7.9e-06)|all_epithelial(167;7.39e-07)|all_lung(203;2.84e-06)|Lung NSC(69;1.99e-05)		Lung(183;0.0688)|Kidney(133;0.114)|LUSC - Lung squamous cell carcinoma(189;0.223)|KIRC - Kidney renal clear cell carcinoma(1967;0.237)|Colorectal(144;0.243)		AGACCATGAGGCAAGAAAGAT	0.363																																					p.A419S	Ovarian(33;199 881 8228 13687 31538)	Atlas-SNP	.											.	MAN1A2	50	.	0			c.G1255T						.						142	127	132					1																	118035855		2203	4300	6503	SO:0001583	missense	10905	exon9			CATGAGGCAAGAA	AF027156	CCDS895.1	1p13	2008-02-05			ENSG00000198162	ENSG00000198162			6822	protein-coding gene	gene with protein product		604345				9592125	Standard	NM_006699		Approved	MAN1B	uc001ehd.1	O60476	OTTHUMG00000012149	ENST00000356554.3:c.1255G>T	chr1.hg19:g.118035855G>T	ENSP00000348959:p.Ala419Ser	91.0	0.0		74.0	24.0	NM_006699	Q9H510	Missense_Mutation	SNP	ENST00000356554.3	hg19	CCDS895.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.7|20.7	4.031081|4.031081	0.75504|0.75504	.|.	.|.	ENSG00000198162|ENSG00000198162	ENST00000356554;ENST00000369450|ENST00000449370	T|.	0.72051|.	-0.62|.	5.09|5.09	5.09|5.09	0.68999|0.68999	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.64294|0.64294	0.2585|0.2585	L|L	0.61387|0.61387	1.9|1.9	0.80722|0.80722	D|D	1|1	B;B|.	0.13145|.	0.002;0.007|.	B;B|.	0.20384|.	0.012;0.029|.	T|T	0.63726|0.63726	-0.6572|-0.6572	10|5	0.22706|.	T|.	0.39|.	-15.6666|-15.6666	16.0138|16.0138	0.80422|0.80422	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	183;419|.	A6NLR2;O60476|.	.;MA1A2_HUMAN|.	S|S	419;183|151	ENSP00000348959:A419S|.	ENSP00000348959:A419S|.	A|R	+|+	1|3	0|2	MAN1A2|MAN1A2	117837378|117837378	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.992000|0.992000	0.81027|0.81027	9.313000|9.313000	0.96297|0.96297	2.378000|2.378000	0.81104|0.81104	0.655000|0.655000	0.94253|0.94253	GCA|AGG	.	.		0.363	MAN1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033593.1	NM_006699		T	118035855	G	T	118035855	3	4	277	1	0	0	0	0	1	0	0	0	9220	1203	42	3	1289	3	MAN1A2	1	118035855	Missense_Mutation	SNP	G	TCGA-G3-A25Y-01A-11D-A16V-10	2634650	118035855	131214766	3	39651										
CEP350	9857	hgsc.bcm.edu	37	chr1	179989459	179989459	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	aagaaattagctggggccagCattaactatgggtcagcatg	12	7	1	1			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr1:179989459C>T	ENST00000367607.3	+	12	2968	c.2550C>T	c.(2548-2550)agC>agT	p.S850S		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	850					microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						CTGGGGCCAGCATTAACTATG	0.453																																					p.S850S		Atlas-SNP	.											.	CEP350	418	.	0			c.C2550T						.						146	148	148					1																	179989459		2203	4300	6503	SO:0001819	synonymous_variant	9857	exon12			GGCCAGCATTAAC	AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"centrosome associated protein 350"					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.2550C>T	chr1.hg19:g.179989459C>T		49.0	0.0		81.0	19.0	NM_014810	O75068|Q8TDK3|Q8WY20	Silent	SNP	ENST00000367607.3	hg19	CCDS1336.1																																																																																			.	.		0.453	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810		T	179989459	C	T	179989459	2	4	277	1	0	0	0	0	0	0	0	1	3256	709	25	3		3	CEP350	1	179989459	Silent	SNP	C	TCGA-G3-A25Y-01A-11D-A16V-10	61953604	179989459	69261162	4	39652										
OR2G2	81470	hgsc.bcm.edu	37	chr1	247751732	247751732	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	tttagggttttctgattatcCtcagttacagaaggttctat	8	6	3	2			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr1:247751732C>T	ENST00000320065.1	+	1	71	c.71C>T	c.(70-72)cCt>cTt	p.P24L	RP11-978I15.10_ENST00000435333.1_RNA|RP11-978I15.10_ENST00000446347.1_RNA	NM_001001915.1	NP_001001915.1	Q8NGZ5	OR2G2_HUMAN	olfactory receptor, family 2, subfamily G, member 2	24			P -> A (in dbSNP:rs12737801).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(4)|large_intestine(3)|lung(30)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			TCTGATTATCCTCAGTTACAG	0.418																																					p.P24L		Atlas-SNP	.											.	OR2G2	88	.	0			c.C71T						.						195	188	190					1																	247751732		2203	4300	6503	SO:0001583	missense	81470	exon1			ATTATCCTCAGTT	BK004472	CCDS31092.1	1q44	2012-08-09	2008-05-23		ENSG00000177489	ENSG00000177489		"GPCR / Class A : Olfactory receptors"	15007	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily G, member 2", "olfactory receptor, family 2, subfamily G, member 2 pseudogene"				Standard	NM_001001915		Approved		uc010pyy.2	Q8NGZ5	OTTHUMG00000040575	ENST00000320065.1:c.71C>T	chr1.hg19:g.247751732C>T	ENSP00000326349:p.Pro24Leu	285.0	0.0		372.0	89.0	NM_001001915	Q5JQT2|Q6IEZ0	Missense_Mutation	SNP	ENST00000320065.1	hg19	CCDS31092.1	.	.	.	.	.	.	.	.	.	.	C	15.65	2.897411	0.52121	.	.	ENSG00000177489	ENST00000320065	T	0.00421	7.46	3.79	3.79	0.43588	.	0.000000	0.33235	U	0.005126	T	0.01353	0.0044	M	0.87097	2.86	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.18999	-1.0319	10	0.66056	D	0.02	.	13.2409	0.59995	0.0:1.0:0.0:0.0	.	24	Q8NGZ5	OR2G2_HUMAN	L	24	ENSP00000326349:P24L	ENSP00000326349:P24L	P	+	2	0	OR2G2	245818355	0.000000	0.05858	0.714000	0.30535	0.942000	0.58702	-0.014000	0.12656	1.925000	0.55765	0.591000	0.81541	CCT	.	.		0.418	OR2G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097623.1			T	247751732	C	T	247751732	3	4	277	1	0	0	0	0	1	0	0	0	11007	681	24	3	73	3	OR2G2	1	247751732	Missense_Mutation	SNP	C	TCGA-G3-A25Y-01A-11D-A16V-10	67762273	247751732	1498889	5	39653										
KCNF1	3754	hgsc.bcm.edu	37	chr2	11053487	11053487	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	ccactcctcgggcctgcagaCcctcacctatgccctcaagc	7	20	2	1			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr2:11053487C>T	ENST00000295082.1	+	1	1425	c.935C>T	c.(934-936)aCc>aTc	p.T312I		NM_002236.4	NP_002227.2	Q9H3M0	KCNF1_HUMAN	potassium voltage-gated channel, subfamily F, member 1	312					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)			NS(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(2)|skin(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.128)		GGCCTGCAGACCCTCACCTAT	0.622																																					p.T312I		Atlas-SNP	.											.	KCNF1	70	.	0			c.C935T						.						61	59	60					2																	11053487		2203	4300	6503	SO:0001583	missense	3754	exon1			TGCAGACCCTCAC	AF033382	CCDS1676.1	2p25	2011-07-05			ENSG00000162975	ENSG00000162975		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6246	protein-coding gene	gene with protein product		603787		KCNF		9434767, 16382104	Standard	NM_002236		Approved	Kv5.1, kH1, IK8	uc002rax.3	Q9H3M0	OTTHUMG00000119054	ENST00000295082.1:c.935C>T	chr2.hg19:g.11053487C>T	ENSP00000295082:p.Thr312Ile	60.0	0.0		68.0	19.0	NM_002236	O43527|Q585L3	Missense_Mutation	SNP	ENST00000295082.1	hg19	CCDS1676.1	.	.	.	.	.	.	.	.	.	.	c	17.50	3.404087	0.62288	.	.	ENSG00000162975	ENST00000295082	D	0.98684	-5.07	4.74	4.74	0.60224	Ion transport (1);	0.105772	0.64402	D	0.000005	D	0.96642	0.8904	N	0.11427	0.14	0.80722	D	1	D	0.55605	0.972	P	0.57620	0.824	D	0.94414	0.7634	10	0.02654	T	1	.	18.1029	0.89512	0.0:1.0:0.0:0.0	.	312	Q9H3M0	KCNF1_HUMAN	I	312	ENSP00000295082:T312I	ENSP00000295082:T312I	T	+	2	0	KCNF1	10970938	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.776000	0.85560	2.348000	0.79779	0.556000	0.70494	ACC	.	.		0.622	KCNF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239265.1	NM_002236		T	11053487	C	T	11053487	3	4	277	1	0	0	0	0	1	0	0	0	8035	507	18	3	937	3	KCNF1	2	11053487	Missense_Mutation	SNP	C	TCGA-G3-A25Y-01A-11D-A16V-10		11053487	232145886	6	39654										
CEBPZ	10153	hgsc.bcm.edu	37	chr2	37455644	37455644	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	ttgccttcatccaggtagaaGaggctcccttttgactattc	8	11	1	3			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr2:37455644G>C	ENST00000234170.5	-	2	837	c.692C>G	c.(691-693)tCt>tGt	p.S231C		NM_005760.2	NP_005751.2	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein (C/EBP), zeta	231					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|endometrium(2)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28		all_hematologic(82;0.21)				CCAGGTAGAAGAGGCTCCCTT	0.438																																					p.S231C		Atlas-SNP	.											.	CEBPZ	68	.	0			c.C692G						.						131	134	133					2																	37455644		2203	4300	6503	SO:0001583	missense	10153	exon2			GTAGAAGAGGCTC	M37197	CCDS1787.1	2p22.3	2008-09-03	2008-09-03		ENSG00000115816	ENSG00000115816			24218	protein-coding gene	gene with protein product		612828				2247079, 12534345	Standard	NM_005760		Approved	CBF2, CTF2	uc002rpz.3	Q03701	OTTHUMG00000100960	ENST00000234170.5:c.692C>G	chr2.hg19:g.37455644G>C	ENSP00000234170:p.Ser231Cys	82.0	0.0		122.0	30.0	NM_005760	Q8NE75	Missense_Mutation	SNP	ENST00000234170.5	hg19	CCDS1787.1	.	.	.	.	.	.	.	.	.	.	G	16.21	3.058717	0.55325	.	.	ENSG00000115816	ENST00000234170;ENST00000545744	T	0.02787	4.16	5.45	4.56	0.56223	.	0.235220	0.41294	N	0.000905	T	0.12092	0.0294	M	0.74258	2.255	0.37729	D	0.925204	D	0.89917	1.0	D	0.64144	0.922	T	0.01334	-1.1382	10	0.87932	D	0	.	11.124	0.48306	0.0:0.139:0.7165:0.1444	.	231	Q03701	CEBPZ_HUMAN	C	231	ENSP00000234170:S231C	ENSP00000234170:S231C	S	-	2	0	CEBPZ	37309148	1.000000	0.71417	0.996000	0.52242	0.992000	0.81027	5.406000	0.66357	1.258000	0.44101	0.655000	0.94253	TCT	.	.		0.438	CEBPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218569.2	NM_005760		C	37455644	G	C	37455644	3	2	277	1	0	0	0	0	1	0	0	0	3206	942	33	4	2532	4	CEBPZ	2	37455644	Missense_Mutation	SNP	G	TCGA-G3-A25Y-01A-11D-A16V-10	26402157	37455644	205743729	7	39655										
LY75	4065	hgsc.bcm.edu	37	chr2	160737646	160737646	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	tattgtagggaacatttggcTcattctcatcccaatatgtt	7	8	2	0			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr2:160737646T>A	ENST00000263636.4	-	8	1379	c.1352A>T	c.(1351-1353)gAg>gTg	p.E451V	LY75_ENST00000553424.1_Missense_Mutation_p.E451V|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.E451V|LY75-CD302_ENST00000505052.1_Missense_Mutation_p.E451V|LY75_ENST00000554112.1_Missense_Mutation_p.E451V	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	451	C-type lectin 2. {ECO:0000255|PROSITE- ProRule:PRU00040}.				endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		AACATTTGGCTCATTCTCATC	0.383																																					p.E451V		Atlas-SNP	.											.	LY75	151	.	0			c.A1352T						.						190	171	177					2																	160737646		2203	4300	6503	SO:0001583	missense	4065	exon8			TTTGGCTCATTCT	AF011333	CCDS2211.1	2q24	2011-08-30			ENSG00000054219	ENSG00000054219		"CD molecules", "C-type lectin domain containing"	6729	protein-coding gene	gene with protein product		604524				9553150	Standard	NM_002349		Approved	DEC-205, CLEC13B, CD205		O60449	OTTHUMG00000132025	ENST00000263636.4:c.1352A>T	chr2.hg19:g.160737646T>A	ENSP00000263636:p.Glu451Val	83.0	0.0		119.0	49.0	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	hg19	CCDS2211.1	.	.	.	.	.	.	.	.	.	.	T	26.2	4.717734	0.89205	.	.	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.17054	2.3;2.3;2.3;2.3;2.3	6.16	6.16	0.99307	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.000000	0.35646	N	0.003065	T	0.51075	0.1653	M	0.90252	3.1	0.52501	D	0.999959	D;D;D;D	0.89917	0.998;0.999;1.0;0.999	D;D;D;D	0.78314	0.991;0.985;0.991;0.953	T	0.60464	-0.7258	10	0.87932	D	0	-15.7446	16.4795	0.84153	0.0:0.0:0.0:1.0	.	69;451;451;451	Q59H44;O60449-3;O60449;O60449-2	.;.;LY75_HUMAN;.	V	451	ENSP00000451511:E451V;ENSP00000451446:E451V;ENSP00000263636:E451V;ENSP00000423463:E451V;ENSP00000421035:E451V	ENSP00000423463:E451V	E	-	2	0	LY75;LY75-CD302	160445892	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.166000	0.71896	2.367000	0.80283	0.528000	0.53228	GAG	.	.		0.383	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1			A	160737646	T	A	160737646	3	1	277	1	0	0	0	0	1	0	0	0	9108	1551	54	4	3928	4	LY75	2	160737646	Missense_Mutation	SNP	T	TCGA-G3-A25Y-01A-11D-A16V-10	123282002	160737646	82461727	8	39656										
USP4	7375	hgsc.bcm.edu	37	chr3	49365180	49365180	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	agtttagtagtttattccacGcctcggtagggaccaataca	9	9	0	0	rs536745381		TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr3:49365180G>C	ENST00000265560.4	-	3	345	c.299C>G	c.(298-300)gCg>gGg	p.A100G	USP4_ENST00000415188.1_Missense_Mutation_p.A100G|USP4_ENST00000351842.4_Missense_Mutation_p.A100G|USP4_ENST00000416417.1_Missense_Mutation_p.A100G	NM_003363.3	NP_003354.2	Q13107	UBP4_HUMAN	ubiquitin specific peptidase 4 (proto-oncogene)	100	DUSP. {ECO:0000255|PROSITE- ProRule:PRU00613}.|Necessary for interaction with SART3. {ECO:0000269|PubMed:20595234}.				negative regulation of protein ubiquitination (GO:0031397)|protein deubiquitination (GO:0016579)|protein localization to cell surface (GO:0034394)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	adenosine receptor binding (GO:0031685)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33		Ovarian(412;0.00308)|Myeloproliferative disorder(1037;0.0255)|Hepatocellular(537;0.121)		OV - Ovarian serous cystadenocarcinoma(275;4.74e-26)|Kidney(197;2.22e-07)|KIRC - Kidney renal clear cell carcinoma(197;5.14e-06)|BRCA - Breast invasive adenocarcinoma(193;9.46e-05)		TTTATTCCACGCCTCGGTAGG	0.438																																					p.A100G		Atlas-SNP	.											.	USP4	72	.	0			c.C299G						.						138	125	130					3																	49365180		2203	4300	6503	SO:0001583	missense	7375	exon3			TTCCACGCCTCGG	U20657	CCDS2793.1, CCDS2794.1, CCDS58832.1	3p21.3	2005-10-11	2005-08-08		ENSG00000114316	ENSG00000114316		"Ubiquitin-specific peptidases"	12627	protein-coding gene	gene with protein product		603486	"ubiquitin specific protease 4 (proto-oncogene)"	UNP		12838346, 9464533	Standard	NM_199443		Approved	Unph	uc003cwq.2	Q13107	OTTHUMG00000156825	ENST00000265560.4:c.299C>G	chr3.hg19:g.49365180G>C	ENSP00000265560:p.Ala100Gly	135.0	0.0		167.0	19.0	NM_199443	A8K6Y0|C9IY91|O43452|O43453|Q08AK8	Missense_Mutation	SNP	ENST00000265560.4	hg19	CCDS2793.1	.	.	.	.	.	.	.	.	.	.	G	16.50	3.141378	0.57044	.	.	ENSG00000114316	ENST00000351842;ENST00000265560;ENST00000416417;ENST00000415188	T;T;T	0.35605	1.78;1.9;1.3	6.07	6.07	0.98685	Peptidase C19, ubiquitin-specific peptidase, DUSP domain (3);	0.000000	0.85682	D	0.000000	T	0.41994	0.1183	L	0.41906	1.305	0.80722	D	1	B;B	0.27656	0.137;0.184	B;B	0.41510	0.123;0.359	T	0.12293	-1.0553	10	0.18276	T	0.48	-24.2326	19.2374	0.93866	0.0:0.0:1.0:0.0	.	100;100	Q13107-2;Q13107	.;UBP4_HUMAN	G	100	ENSP00000341028:A100G;ENSP00000265560:A100G;ENSP00000400623:A100G	ENSP00000265560:A100G	A	-	2	0	USP4	49340184	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	7.620000	0.83070	2.885000	0.99019	0.655000	0.94253	GCG	.	.		0.438	USP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346069.1	NM_199443		C	49365180	G	C	49365180	3	2	277	1	0	0	0	0	1	0	0	0	17086	1087	38	4	2672	4	USP4	3	49365180	Missense_Mutation	SNP	G	TCGA-G3-A25Y-01A-11D-A16V-10		49365180	148657250	9	39657										
EGFLAM	133584	hgsc.bcm.edu	37	chr5	38407124	38407124	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	ggtgtggccataatgtcaagGctctttgacatgccttgtga	12	8	2	2			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr5:38407124G>T	ENST00000354891.3	+	8	1369	c.1023G>T	c.(1021-1023)agG>agT	p.R341S	EGFLAM_ENST00000322350.5_Missense_Mutation_p.R341S|EGFLAM_ENST00000397202.2_Intron|EGFLAM_ENST00000336740.6_Missense_Mutation_p.R107S	NM_001205301.1	NP_001192230.1	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G domains	341					extracellular matrix organization (GO:0030198)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|cell junction (GO:0030054)|interstitial matrix (GO:0005614)|synapse (GO:0045202)	glycosaminoglycan binding (GO:0005539)			NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(43)|ovary(1)|pancreas(3)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	85	all_lung(31;0.000385)					TAATGTCAAGGCTCTTTGACA	0.562																																					p.R341S	Colon(62;485 1295 3347 17454)	Atlas-SNP	.											.	EGFLAM	302	.	0			c.G1023T						.						139	130	133					5																	38407124		2203	4300	6503	SO:0001583	missense	133584	exon8			GTCAAGGCTCTTT	AK097549	CCDS3924.1, CCDS3925.1, CCDS47199.1, CCDS56363.1	5p13.2-p13.1	2014-04-03			ENSG00000164318	ENSG00000164318		"Fibronectin type III domain containing"	26810	protein-coding gene	gene with protein product	"pikachurin", "agrin-like"					18641643, 20078962, 22760553	Standard	NM_182801		Approved	FLJ39155, AGRINL, AGRNL, PIKA	uc003jlc.2	Q63HQ2	OTTHUMG00000131139	ENST00000354891.3:c.1023G>T	chr5.hg19:g.38407124G>T	ENSP00000346964:p.Arg341Ser	90.0	0.0		118.0	30.0	NM_001205301	A8K6D7|Q5U643|Q6P3V1|Q8N124|Q8N197|Q8N7Y0|Q8N8N5|Q8NAL2	Missense_Mutation	SNP	ENST00000354891.3	hg19	CCDS56363.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.305185	0.81247	.	.	ENSG00000164318	ENST00000354891;ENST00000322350;ENST00000336740;ENST00000339580	T;T;T	0.80566	0.74;0.57;-1.39	5.91	5.91	0.95273	.	0.052871	0.64402	D	0.000001	D	0.89420	0.6710	M	0.74881	2.28	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.87578	0.998;0.996;0.98	D	0.89304	0.3628	10	0.56958	D	0.05	-0.0346	16.7452	0.85470	0.0:0.1373:0.8627:0.0	.	107;341;341	Q63HQ2-4;Q63HQ2;Q63HQ2-2	.;EGFLA_HUMAN;.	S	341;341;107;107	ENSP00000346964:R341S;ENSP00000313084:R341S;ENSP00000337607:R107S	ENSP00000313084:R341S	R	+	3	2	EGFLAM	38442881	1.000000	0.71417	0.997000	0.53966	0.982000	0.71751	1.358000	0.34102	2.802000	0.96397	0.655000	0.94253	AGG	.	.		0.562	EGFLAM-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367323.1	NM_152403		T	38407124	G	T	38407124	3	4	277	1	0	0	0	0	1	0	0	0	4968	1194	42	3	1067	3	EGFLAM	5	38407124	Missense_Mutation	SNP	G	TCGA-G3-A25Y-01A-11D-A16V-10		38407124	142508136	10	39658										
ITGA1	3672	hgsc.bcm.edu	37	chr5	52233253	52233253	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	tagaaaaagtggatcttttcCaatgccagagcttaagctgt	9	7	1	2			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr5:52233253C>T	ENST00000282588.6	+	24	3445	c.2987C>T	c.(2986-2988)cCa>cTa	p.P996L	CTD-2175A23.1_ENST00000505701.1_RNA|CTD-2175A23.1_ENST00000503559.1_RNA	NM_181501.1	NP_852478.1	P56199	ITA1_HUMAN	integrin, alpha 1	996					activation of MAPK activity (GO:0000187)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular extravasation (GO:0045123)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neutrophil chemotaxis (GO:0030593)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|vasodilation (GO:0042311)	acrosomal vesicle (GO:0001669)|basal part of cell (GO:0045178)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha1-beta1 complex (GO:0034665)|integrin complex (GO:0008305)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)|protein phosphatase binding (GO:0019903)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(19)|ovary(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(810;5.05e-05)|Breast(144;0.0851)				GGATCTTTTCCAATGCCAGAG	0.358																																					p.P996L		Atlas-SNP	.											.	ITGA1	112	.	0			c.C2987T						.						183	177	179					5																	52233253		2203	4300	6503	SO:0001583	missense	3672	exon24			CTTTTCCAATGCC	X68742	CCDS3955.1	5q11.1	2010-03-23			ENSG00000213949	ENSG00000213949		"CD molecules", "Integrins"	6134	protein-coding gene	gene with protein product		192968				8428973, 11937138	Standard	NM_181501		Approved	VLA1, CD49a	uc003jou.3	P56199	OTTHUMG00000131163	ENST00000282588.6:c.2987C>T	chr5.hg19:g.52233253C>T	ENSP00000282588:p.Pro996Leu	143.0	0.0		197.0	73.0	NM_181501	B2RNU0	Missense_Mutation	SNP	ENST00000282588.6	hg19	CCDS3955.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.553746	0.86231	.	.	ENSG00000213949	ENST00000282588	T	0.45276	0.9	5.69	5.69	0.88448	Integrin alpha-2 (1);	0.318638	0.33161	N	0.005211	T	0.59115	0.2170	L	0.52573	1.65	0.80722	D	1	D	0.71674	0.998	D	0.74023	0.982	T	0.55490	-0.8133	10	0.45353	T	0.12	.	16.731	0.85435	0.0:1.0:0.0:0.0	.	996	P56199	ITA1_HUMAN	L	996	ENSP00000282588:P996L	ENSP00000282588:P996L	P	+	2	0	ITGA1	52269010	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	4.586000	0.60984	2.688000	0.91661	0.585000	0.79938	CCA	.	.		0.358	ITGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253855.3	NM_181501		T	52233253	C	T	52233253	3	4	277	1	0	0	0	0	1	0	0	0	7881	594	21	3	3081	3	ITGA1	5	52233253	Missense_Mutation	SNP	C	TCGA-G3-A25Y-01A-11D-A16V-10	13826129	52233253	128682007	11	39659										
SNCAIP	9627	hgsc.bcm.edu	37	chr5	121767681	121767681	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	tagaatggtcagttggagtgCgtacgctggatggtgagcga	17	5	1	2			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr5:121767681C>T	ENST00000261368.8	+	6	1462	c.1200C>T	c.(1198-1200)tgC>tgT	p.C400C	SNCAIP_ENST00000414317.2_Intron|SNCAIP_ENST00000261367.7_Silent_p.C447C|SNCAIP_ENST00000542191.1_5'UTR|SNCAIP_ENST00000503116.2_Silent_p.C447C|SNCAIP_ENST00000379538.3_Silent_p.C34C|SNCAIP_ENST00000379533.2_Silent_p.C447C|SNCAIP_ENST00000379536.2_Silent_p.C340C|SNCAIP_ENST00000504884.2_3'UTR	NM_005460.2	NP_005451.2	Q9Y6H5	SNCAP_HUMAN	synuclein, alpha interacting protein	400					cell death (GO:0008219)|dopamine metabolic process (GO:0042417)|regulation of inclusion body assembly (GO:0090083)|regulation of neurotransmitter secretion (GO:0046928)	cytoplasm (GO:0005737)|neuronal cell body (GO:0043025)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	identical protein binding (GO:0042802)|ubiquitin protein ligase binding (GO:0031625)			NS(3)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(9)|ovary(2)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	39		all_cancers(142;0.00787)|Prostate(80;0.0327)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000625)|Epithelial(69;0.00216)|all cancers(49;0.0232)		AGTTGGAGTGCGTACGCTGGA	0.403																																					p.C400C		Atlas-SNP	.											.	SNCAIP	308	.	0			c.C1200T						.						112	99	103					5																	121767681		2203	4300	6503	SO:0001819	synonymous_variant	9627	exon6			GGAGTGCGTACGC	AF167306	CCDS4131.1, CCDS58964.1	5q23.2	2013-01-10	2008-07-31		ENSG00000064692	ENSG00000064692		"Ankyrin repeat domain containing"	11139	protein-coding gene	gene with protein product	"synphilin"	603779				10319874	Standard	NM_001242935		Approved	SYPH1	uc003ksw.1	Q9Y6H5	OTTHUMG00000128915	ENST00000261368.8:c.1200C>T	chr5.hg19:g.121767681C>T		108.0	0.0		150.0	38.0	NM_005460	D3DSZ1|Q05BS1|Q1PSC2|Q49AC6|Q504U9|Q6L984|Q6L985|Q6L986|Q9HC59	Silent	SNP	ENST00000261368.8	hg19	CCDS4131.1																																																																																			.	.		0.403	SNCAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250888.1			T	121767681	C	T	121767681	2	4	277	1	0	0	0	0	0	0	0	1	14856	776	27	1		1	SNCAIP	5	121767681	Silent	SNP	C	TCGA-G3-A25Y-01A-11D-A16V-10	69534428	121767681	59147579	12	39660										
FAM13B	51306	hgsc.bcm.edu	37	chr5	137284796	137284796	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	ttcatggtctagagaagagcCaaagctttttggaagtgtgt	12	5	2	2			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr5:137284796C>T	ENST00000033079.3	-	17	2393	c.1942G>A	c.(1942-1944)Ggc>Agc	p.G648S	FAM13B_ENST00000425075.2_Missense_Mutation_p.G552S|FAM13B_ENST00000420893.2_Missense_Mutation_p.G648S	NM_016603.2	NP_057687.2	Q9NYF5	FA13B_HUMAN	family with sequence similarity 13, member B	648					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			endometrium(4)|kidney(2)|lung(5)	11						AGAGAAGAGCCAAAGCTTTTT	0.388																																					p.G648S		Atlas-SNP	.											.	FAM13B	46	.	0			c.G1942A						.						175	167	169					5																	137284796		2203	4300	6503	SO:0001583	missense	51306	exon17			AAGAGCCAAAGCT	AF251038	CCDS4195.1, CCDS47269.1, CCDS47270.1	5q31	2011-09-07	2009-01-20	2009-01-20	ENSG00000031003	ENSG00000031003		"Rho GTPase activating proteins"	1335	protein-coding gene	gene with protein product		609371	"chromosome 5 open reading frame 5", "family with sequence similarity 13, member B1"	C5orf5, FAM13B1		11087669, 11161817	Standard	NM_016603		Approved	N61, KHCHP, ARHGAP49	uc003lbz.2	Q9NYF5	OTTHUMG00000129202	ENST00000033079.3:c.1942G>A	chr5.hg19:g.137284796C>T	ENSP00000033079:p.Gly648Ser	150.0	0.0		180.0	19.0	NM_001101800	D3DQB5|G3V0H9|Q3ZCR0|Q6PGQ2|Q9P0I7	Missense_Mutation	SNP	ENST00000033079.3	hg19	CCDS4195.1	.	.	.	.	.	.	.	.	.	.	C	33	5.248572	0.95305	.	.	ENSG00000031003	ENST00000033079;ENST00000425075;ENST00000420893	T;T;T	0.26518	2.89;1.73;2.88	5.06	5.06	0.68205	.	0.255560	0.36628	N	0.002484	T	0.49253	0.1546	L	0.56396	1.775	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.998	D;D;P	0.91635	0.939;0.999;0.871	T	0.45145	-0.9281	10	0.52906	T	0.07	-5.838	18.4225	0.90595	0.0:1.0:0.0:0.0	.	552;648;648	G3V0H9;Q9NYF5-2;Q9NYF5	.;.;FA13B_HUMAN	S	648;552;648	ENSP00000033079:G648S;ENSP00000394669:G552S;ENSP00000388521:G648S	ENSP00000033079:G648S	G	-	1	0	FAM13B	137312695	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.414000	0.80117	2.508000	0.84585	0.650000	0.86243	GGC	.	.		0.388	FAM13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251279.1			T	137284796	C	T	137284796	3	4	277	1	0	0	0	0	1	0	0	0	5458	594	21	3	833	3	FAM13B	5	137284796	Missense_Mutation	SNP	C	TCGA-G3-A25Y-01A-11D-A16V-10	15517115	137284796	43630464	13	39661										
BTNL3	10917	hgsc.bcm.edu	37	chr5	180432823	180432823	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	tatccagcatgcgatgtatgAcgaggaaaaggggactccca	12	9	0	1			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr5:180432823A>C	ENST00000342868.6	+	8	1536	c.1352A>C	c.(1351-1353)gAc>gCc	p.D451A	RNU6-1036P_ENST00000383959.1_RNA	NM_197975.2	NP_932079.1	Q6UXE8	BTNL3_HUMAN	butyrophilin-like 3	451	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(1)|lung(10)|prostate(2)|skin(1)	25	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.00336)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)|all_lung(500;0.248)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000272)			GCGATGTATGACGAGGAAAAG	0.483																																					p.D451A		Atlas-SNP	.											.	BTNL3	55	.	0			c.A1352C						.						68	63	65					5																	180432823		1941	4146	6087	SO:0001583	missense	10917	exon8			TGTATGACGAGGA	AB020625	CCDS47358.1	5q35	2014-01-14			ENSG00000168903	ENSG00000168903		"Immunoglobulin superfamily / V-set domain containing", "Butyrophilins"	1143	protein-coding gene	gene with protein product	"butyrophilin-like receptor"	606192				10429365	Standard	NM_197975		Approved	BTNLR, BTN9.1	uc003mmr.3	Q6UXE8	OTTHUMG00000162091	ENST00000342868.6:c.1352A>C	chr5.hg19:g.180432823A>C	ENSP00000341787:p.Asp451Ala	97.0	0.0		126.0	30.0	NM_197975	Q496L7|Q9Y2C7	Missense_Mutation	SNP	ENST00000342868.6	hg19	CCDS47358.1	.	.	.	.	.	.	.	.	.	.	A	12.02	1.811989	0.32053	.	.	ENSG00000168903	ENST00000342868;ENST00000376852	T	0.60797	0.16	2.37	-0.711	0.11230	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);	.	.	.	.	T	0.45276	0.1334	L	0.52126	1.63	0.09310	N	1	B;B	0.23650	0.089;0.0	B;B	0.25614	0.062;0.0	T	0.43861	-0.9365	9	0.66056	D	0.02	.	2.1176	0.03718	0.5797:0.0:0.1676:0.2527	.	417;451	C9JDC2;Q6UXE8	.;BTNL3_HUMAN	A	451;417	ENSP00000341787:D451A	ENSP00000341787:D451A	D	+	2	0	BTNL3	180365429	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.006000	0.12833	-0.467000	0.06932	0.164000	0.16699	GAC	.	.		0.483	BTNL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367176.2	NM_197975		C	180432823	A	C	180432823	3	2	277	1	0	0	0	0	1	0	0	0	1568	275	10	5	1382	5	BTNL3	5	180432823	Missense_Mutation	SNP	A	TCGA-G3-A25Y-01A-11D-A16V-10	43148027	180432823	482437	14	39662										
PGBD1	84547	hgsc.bcm.edu	37	chr6	28268801	28268801	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	tgtttcccagaaaagagttgGaccaaaagagacattaaacc	8	8	0	3	rs143874020		TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr6:28268801G>C	ENST00000405948.2	+	7	1590	c.1170G>C	c.(1168-1170)tgG>tgC	p.W390C	PGBD1_ENST00000259883.3_Missense_Mutation_p.W390C	NM_001184743.1|NM_032507.3	NP_001171672.1|NP_115896.1	Q96JS3	PGBD1_HUMAN	piggyBac transposable element derived 1	390						membrane (GO:0016020)|nucleus (GO:0005634)	scavenger receptor activity (GO:0005044)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	41						AAAAGAGTTGGACCAAAAGAG	0.413																																					p.W390C		Atlas-SNP	.											.	PGBD1	106	.	0			c.G1170C						.	G	CYS/TRP,CYS/TRP	1,4405	2.1+/-5.4	0,1,2202	65	69	68		1170,1170	4.5	1	6	dbSNP_134	68	0,8600		0,0,4300	no	missense,missense	PGBD1	NM_001184743.1,NM_032507.3	215,215	0,1,6502	CC,CG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	390/810,390/810	28268801	1,13005	2203	4300	6503	SO:0001583	missense	84547	exon7			GAGTTGGACCAAA	D88259	CCDS4648.1	6p22.1	2013-01-09			ENSG00000137338	ENSG00000137338		"-"	19398	protein-coding gene	gene with protein product							Standard	NM_001184743		Approved	HUCEP-4, dJ874C20.4, SCAND4	uc003nkz.3	Q96JS3	OTTHUMG00000014520	ENST00000405948.2:c.1170G>C	chr6.hg19:g.28268801G>C	ENSP00000385213:p.Trp390Cys	44.0	0.0		60.0	24.0	NM_001184743	Q53F43|Q6NTF5|Q8WWS4	Missense_Mutation	SNP	ENST00000405948.2	hg19	CCDS4648.1	.	.	.	.	.	.	.	.	.	.	G	14.70	2.612478	0.46631	2.27E-4	0.0	ENSG00000137338	ENST00000405948;ENST00000259883	T;T	0.02369	4.32;4.32	4.54	4.54	0.55810	.	0.195133	0.25836	N	0.027990	T	0.04724	0.0128	L	0.32530	0.975	0.58432	D	0.999993	D	0.89917	1.0	D	0.75020	0.985	T	0.42799	-0.9430	10	0.87932	D	0	-16.3181	12.9975	0.58654	0.0:0.0:1.0:0.0	.	390	Q96JS3	PGBD1_HUMAN	C	390	ENSP00000385213:W390C;ENSP00000259883:W390C	ENSP00000259883:W390C	W	+	3	0	PGBD1	28376780	0.998000	0.40836	0.976000	0.42696	0.862000	0.49288	4.406000	0.59748	2.521000	0.84997	0.655000	0.94253	TGG	.	G|1.000;C|0.000		0.413	PGBD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040188.2			C	28268801	G	C	28268801	3	2	277	1	0	0	0	0	1	0	0	0	11789	1183	41	4	1192	4	PGBD1	6	28268801	Missense_Mutation	SNP	G	TCGA-G3-A25Y-01A-11D-A16V-10		28268801	142846266	15	39663										
UBE2J1	51465	hgsc.bcm.edu	37	chr6	90047985	90047985	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	agaacctatggctccctctcCttttgttggcataaacccaa	6	13	1	1			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr6:90047985C>T	ENST00000435041.2	-	5	645	c.367G>A	c.(367-369)Gga>Aga	p.G123R		NM_016021.2	NP_057105.2	Q9Y385	UB2J1_HUMAN	ubiquitin-conjugating enzyme E2, J1	123					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)			NS(1)|breast(2)|kidney(1)|large_intestine(2)|lung(11)|stomach(1)	18		all_cancers(76;1.65e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;2.5e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0139)		GCTCCCTCTCCTTTTGTTGGC	0.358																																					p.G123R		Atlas-SNP	.											.	UBE2J1	28	.	0			c.G367A						.						145	146	146					6																	90047985		2203	4300	6503	SO:0001583	missense	51465	exon5			CCTCTCCTTTTGT	AJ245898	CCDS5021.1	6q15	2014-01-28	2012-06-08		ENSG00000198833	ENSG00000198833		"Ubiquitin-conjugating enzymes E2"	17598	protein-coding gene	gene with protein product			"ubiquitin-conjugating enzyme E2, J1 (UBC6 homolog, yeast)"			10708578	Standard	NM_016021		Approved	HSPC153, CGI-76, NCUBE1, UBC6	uc003pnc.3	Q9Y385	OTTHUMG00000016337	ENST00000435041.2:c.367G>A	chr6.hg19:g.90047985C>T	ENSP00000451261:p.Gly123Arg	113.0	0.0		202.0	11.0	NM_016021	A8K3F9|Q53F25|Q5W0N4|Q9BZ32|Q9NQL3|Q9NY66|Q9P011|Q9P0S0|Q9UF10	Missense_Mutation	SNP	ENST00000435041.2	hg19	CCDS5021.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.972914	0.92919	.	.	ENSG00000198833	ENST00000435041;ENST00000536477	T	0.40476	1.03	5.55	5.55	0.83447	Ubiquitin-conjugating enzyme/RWD-like (2);	0.000000	0.85682	D	0.000000	T	0.67804	0.2932	M	0.90483	3.12	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.72798	-0.4184	10	0.52906	T	0.07	-6.3346	19.4946	0.95067	0.0:1.0:0.0:0.0	.	123	Q9Y385	UB2J1_HUMAN	R	123;108	ENSP00000451261:G123R	ENSP00000354684:G123R	G	-	1	0	UBE2J1	90104704	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.440000	0.80464	2.604000	0.88044	0.650000	0.86243	GGA	.	.		0.358	UBE2J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043742.2	NM_016021		T	90047985	C	T	90047985	3	4	277	1	0	0	0	0	1	0	0	0	16875	690	24	3	605	3	UBE2J1	6	90047985	Missense_Mutation	SNP	C	TCGA-G3-A25Y-01A-11D-A16V-10	61779184	90047985	81067082	16	39664										
GPR63	81491	hgsc.bcm.edu	37	chr6	97247241	97247241	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	caacatgtctgcaaaagctaGgctggcaaggaggatgttaa	12	7	1	0			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr6:97247241G>T	ENST00000229955.3	-	2	712	c.367C>A	c.(367-369)Cta>Ata	p.L123I	GPR63_ENST00000417980.1_Missense_Mutation_p.L123I	NM_001143957.2|NM_030784.3	NP_001137429.1|NP_110411.1	Q9BZJ6	GPR63_HUMAN	G protein-coupled receptor 63	123						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			kidney(1)|large_intestine(5)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(76;6.89e-05)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.0618)|Colorectal(196;0.0721)		BRCA - Breast invasive adenocarcinoma(108;0.0912)		GCAAAAGCTAGGCTGGCAAGG	0.438																																					p.L123I		Atlas-SNP	.											.	GPR63	60	.	0			c.C367A						.						84	83	83					6																	97247241		2203	4300	6503	SO:0001583	missense	81491	exon2			AAGCTAGGCTGGC	AF317654	CCDS5036.1	6q16.1-q16.3	2012-08-21			ENSG00000112218	ENSG00000112218		"GPCR / Class A : Orphans"	13302	protein-coding gene	gene with protein product		606915					Standard	NM_030784		Approved	PSP24(beta), PSP24B	uc003pou.3	Q9BZJ6	OTTHUMG00000015245	ENST00000229955.3:c.367C>A	chr6.hg19:g.97247241G>T	ENSP00000229955:p.Leu123Ile	45.0	0.0		55.0	13.0	NM_030784	Q9UJH3	Missense_Mutation	SNP	ENST00000229955.3	hg19	CCDS5036.1	.	.	.	.	.	.	.	.	.	.	G	17.00	3.276635	0.59758	.	.	ENSG00000112218	ENST00000536583;ENST00000417980;ENST00000229955;ENST00000369268	D;D;D	0.91124	-2.79;-2.79;-2.79	5.1	3.26	0.37387	GPCR, rhodopsin-like superfamily (1);	0.093957	0.44483	D	0.000441	D	0.93848	0.8032	H	0.96239	3.79	0.53005	D	0.999963	P	0.52170	0.951	P	0.56514	0.8	D	0.93615	0.6942	10	0.87932	D	0	-1.0651	6.1511	0.20313	0.198:0.0:0.6553:0.1468	.	123	Q9BZJ6	GPR63_HUMAN	I	147;123;123;123	ENSP00000393170:L123I;ENSP00000229955:L123I;ENSP00000358273:L123I	ENSP00000229955:L123I	L	-	1	2	GPR63	97353962	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.864000	0.56024	1.267000	0.44247	0.555000	0.69702	CTA	.	.		0.438	GPR63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041566.2			T	97247241	G	T	97247241	3	4	277	1	0	0	0	0	1	0	0	0	6712	991	35	3	896	3	GPR63	6	97247241	Missense_Mutation	SNP	G	TCGA-G3-A25Y-01A-11D-A16V-10	7199256	97247241	73867826	17	39665										
MAN1A1	4121	hgsc.bcm.edu	37	chr6	119511012	119511012	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	ctctgcgatataagttagtcCgctgctagacttgcggatca	10	10	2	1			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr6:119511012C>T	ENST00000368468.3	-	10	1804	c.1363G>A	c.(1363-1365)Gga>Aga	p.G455R		NM_005907.3	NP_005898.2	P33908	MA1A1_HUMAN	mannosidase, alpha, class 1A, member 1	455					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|mannosidase activity (GO:0015923)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(8)|ovary(2)|prostate(2)|skin(3)	24		all_epithelial(87;0.173)		OV - Ovarian serous cystadenocarcinoma(136;0.0612)|GBM - Glioblastoma multiforme(226;0.0702)|all cancers(137;0.115)		TAAGTTAGTCCGCTGCTAGAC	0.468																																					p.G455R	Ovarian(136;8 1825 12608 33541 47587)	Atlas-SNP	.											MAN1A1,NS,carcinoma,0,2	MAN1A1	77	.	0			c.G1363A						.						73	67	69					6																	119511012		2203	4300	6503	SO:0001583	missense	4121	exon10			TTAGTCCGCTGCT	AK025599	CCDS5122.1	6q22	2008-08-29			ENSG00000111885	ENSG00000111885	3.2.1.113		6821	protein-coding gene	gene with protein product		604344				8223597	Standard	NM_005907		Approved		uc003pym.2	P33908	OTTHUMG00000015472	ENST00000368468.3:c.1363G>A	chr6.hg19:g.119511012C>T	ENSP00000357453:p.Gly455Arg	76.0	1.0		49.0	13.0	NM_005907	E7EU32|Q6P052|Q9NU44|Q9UJI3	Missense_Mutation	SNP	ENST00000368468.3	hg19	CCDS5122.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.763928	0.89932	.	.	ENSG00000111885	ENST00000368468	T	0.71817	-0.6	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	D	0.85630	0.5741	M	0.88031	2.925	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87256	0.2276	10	0.62326	D	0.03	-4.2762	19.4267	0.94743	0.0:1.0:0.0:0.0	.	455	P33908	MA1A1_HUMAN	R	455	ENSP00000357453:G455R	ENSP00000357453:G455R	G	-	1	0	MAN1A1	119552711	1.000000	0.71417	0.115000	0.21578	0.729000	0.41735	7.818000	0.86416	2.596000	0.87737	0.655000	0.94253	GGA	.	.		0.468	MAN1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042015.1	NM_005907		T	119511012	C	T	119511012	3	4	277	1	0	0	0	0	1	0	0	0	9219	661	23	1	614	1	MAN1A1	6	119511012	Missense_Mutation	SNP	C	TCGA-G3-A25Y-01A-11D-A16V-10	22263771	119511012	51604055	18	39666										
THSD7A	221981	hgsc.bcm.edu	37	chr7	11485864	11485864	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	accagttccccacaggttgtGcattatatttgtcacaagga	8	10	1	0			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr7:11485864G>T	ENST00000423059.4	-	13	3139	c.2888C>A	c.(2887-2889)gCa>gAa	p.A963E	AC004538.3_ENST00000445839.1_RNA	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	963	TSP type-1 10. {ECO:0000255|PROSITE- ProRule:PRU00210}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		CACAGGTTGTGCATTATATTT	0.398										HNSCC(18;0.044)																											p.A963E		Atlas-SNP	.											.	THSD7A	219	.	0			c.C2888A						.						213	199	203					7																	11485864		1872	4119	5991	SO:0001583	missense	221981	exon13			GGTTGTGCATTAT		CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.2888C>A	chr7.hg19:g.11485864G>T	ENSP00000406482:p.Ala963Glu	110.0	0.0		142.0	54.0	NM_015204		Missense_Mutation	SNP	ENST00000423059.4	hg19	CCDS47543.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.680427	0.88542	.	.	ENSG00000005108	ENST00000262042;ENST00000423059	T	0.59083	0.29	5.74	4.87	0.63330	.	0.045699	0.85682	D	0.000000	T	0.65913	0.2737	L	0.47716	1.5	0.80722	D	1	D	0.63046	0.992	P	0.61477	0.889	T	0.63102	-0.6712	10	0.29301	T	0.29	.	14.6117	0.68519	0.0698:0.0:0.9302:0.0	.	963	Q9UPZ6	THS7A_HUMAN	E	963	ENSP00000406482:A963E	ENSP00000262042:A963E	A	-	2	0	THSD7A	11452389	1.000000	0.71417	0.867000	0.34043	0.981000	0.71138	8.018000	0.88722	1.434000	0.47414	0.591000	0.81541	GCA	.	.		0.398	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2		T	11485864	G	T	11485864	3	4	277	1	0	0	0	0	1	0	0	0	15894	1319	46	3	2145	3	THSD7A	7	11485864	Missense_Mutation	SNP	G	TCGA-G3-A25Y-01A-11D-A16V-10		11485864	147652799	19	39667										
CCDC136	64753	hgsc.bcm.edu	37	chr7	128449544	128449544	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	actgacagaattgcaggaaaAgtacaaggccagccagaagg	12	8	0	3			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr7:128449544A>T	ENST00000297788.4	+	11	2013	c.1646A>T	c.(1645-1647)aAg>aTg	p.K549M	CCDC136_ENST00000464832.1_Intron|CCDC136_ENST00000487361.1_Intron|CCDC136_ENST00000378685.4_Intron	NM_022742.4	NP_073579	Q96JN2	CC136_HUMAN	coiled-coil domain containing 136	549						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(3)	24						TTGCAGGAAAAGTACAAGGCC	0.587																																					p.K549M		Atlas-SNP	.											.	CCDC136	170	.	0			c.A1646T						.						21	24	23					7																	128449544		2027	4107	6134	SO:0001583	missense	64753	exon11			AGGAAAAGTACAA		CCDS47704.1, CCDS56510.1	7q33	2007-08-01			ENSG00000128596	ENSG00000128596			22225	protein-coding gene	gene with protein product		611902				15112360	Standard	NM_022742		Approved	KIAA1793, NAG6, DKFZP434G156	uc003vnv.2	Q96JN2	OTTHUMG00000158310	ENST00000297788.4:c.1646A>T	chr7.hg19:g.128449544A>T	ENSP00000297788:p.Lys549Met	248.0	0.0		221.0	61.0	NM_022742	A4D1K1|A7MCY7|A8MYA7|Q6ZVK7|Q9H8M3|Q9UFE1	Missense_Mutation	SNP	ENST00000297788.4	hg19	CCDS47704.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.61|18.61	3.660929|3.660929	0.67700|0.67700	.|.	.|.	ENSG00000128596|ENSG00000128596	ENST00000297788;ENST00000397697;ENST00000320524;ENST00000464672|ENST00000494552	T;T|.	0.35789|.	1.29;1.29|.	5.95|5.95	2.06|2.06	0.26882|0.26882	.|.	0.737577|.	0.12983|.	N|.	0.423081|.	T|T	0.24314|0.24314	0.0589|0.0589	L|L	0.34521|0.34521	1.04|1.04	0.20703|0.20703	N|N	0.999869|0.999869	B;B|.	0.33171|.	0.206;0.4|.	B;B|.	0.30855|.	0.085;0.121|.	T|T	0.21484|0.21484	-1.0244|-1.0244	10|5	0.62326|.	D|.	0.03|.	-19.2775|-19.2775	1.5329|1.5329	0.02539|0.02539	0.5498:0.1492:0.0917:0.2092|0.5498:0.1492:0.0917:0.2092	.|.	549;549|.	Q96JN2-2;Q96JN2|.	.;CC136_HUMAN|.	M|C	549;549;549;140|426	ENSP00000297788:K549M;ENSP00000417991:K140M|.	ENSP00000297788:K549M|.	K|S	+|+	2|1	0|0	CCDC136|CCDC136	128236780|128236780	0.332000|0.332000	0.24722|0.24722	0.785000|0.785000	0.31869|0.31869	0.968000|0.968000	0.65278|0.65278	0.640000|0.640000	0.24705|0.24705	0.499000|0.499000	0.27970|0.27970	0.533000|0.533000	0.62120|0.62120	AAG|AGT	.	.		0.587	CCDC136-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350641.1	NM_022742		T	128449544	A	T	128449544	3	4	277	1	0	0	0	0	1	0	0	0	2772	72	3	4	1688	4	CCDC136	7	128449544	Missense_Mutation	SNP	A	TCGA-G3-A25Y-01A-11D-A16V-10	116963680	128449544	30689119	20	39668										
KIAA1432	57589	hgsc.bcm.edu	37	chr9	5742973	5742973	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	gcctttctttatggagtgttTttggagcacagctgatttgt	11	6	1	1			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr9:5742973T>G	ENST00000414202.2	+	9	1197	c.1006T>G	c.(1006-1008)Ttt>Gtt	p.F336V	KIAA1432_ENST00000449720.2_Missense_Mutation_p.F257V|KIAA1432_ENST00000418622.3_Missense_Mutation_p.F257V|KIAA1432_ENST00000381532.2_Missense_Mutation_p.F257V|KIAA1432_ENST00000251879.6_Missense_Mutation_p.F336V	NM_001206557.1|NM_020829.3	NP_001193486.1|NP_065880.2														breast(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(23)|prostate(1)|upper_aerodigestive_tract(1)	45		Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000525)|Lung(218;0.122)		ATGGAGTGTTTTTGGAGCACA	0.368																																					p.F336V		Atlas-SNP	.											.	KIAA1432	97	.	0			c.T1006G						.						178	176	176					9																	5742973		2203	4300	6503	SO:0001583	missense	57589	exon9			AGTGTTTTTGGAG																												ENST00000414202.2:c.1006T>G	chr9.hg19:g.5742973T>G	ENSP00000416696:p.Phe336Val	253.0	0.0		328.0	115.0	NM_001206557		Missense_Mutation	SNP	ENST00000414202.2	hg19	CCDS34982.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.6|25.6	4.657677|4.657677	0.88154|0.88154	.|.	.|.	ENSG00000107036|ENSG00000107036	ENST00000545641|ENST00000251879;ENST00000414202;ENST00000381532;ENST00000418622;ENST00000449720	.|T;T;T;T;T	.|0.56776	.|0.44;0.44;0.44;0.44;0.44	6.17|6.17	6.17|6.17	0.99709|0.99709	.|WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.74084|0.74084	0.3670|0.3670	M|M	0.82716|0.82716	2.605|2.605	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.76494	.|0.999;0.999;0.999	.|D;D;D	.|0.69479	.|0.941;0.957;0.964	T|T	0.74538|0.74538	-0.3632|-0.3632	6|10	.|0.38643	.|T	.|0.18	-24.1883|-24.1883	16.8222|16.8222	0.85835|0.85835	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|257;336;336	.|B7ZM67;Q4ADV7;G5E932	.|.;RIC1_HUMAN;.	C|V	264|336;336;257;257;257	.|ENSP00000251879:F336V;ENSP00000416696:F336V;ENSP00000370943:F257V;ENSP00000402240:F257V;ENSP00000398823:F257V	.|ENSP00000251879:F336V	F|F	+|+	2|1	0|0	KIAA1432|KIAA1432	5732973|5732973	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.838000|0.838000	0.47535|0.47535	7.637000|7.637000	0.83313|0.83313	2.371000|2.371000	0.80710|0.80710	0.533000|0.533000	0.62120|0.62120	TTT|TTT	.	.		0.368	KIAA1432-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051636.3			G	5742973	T	G	5742973	3	3	277	1	0	0	0	0	1	0	0	0	8242	1841	64	5	799	5	KIAA1432	9	5742973	Missense_Mutation	SNP	T	TCGA-G3-A25Y-01A-11D-A16V-10		5742973	135470458	21	39669										
KDM4C	23081	hgsc.bcm.edu	37	chr9	6793123	6793123	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	aaaggagcccatcgtgcgggTcttgcaaaggtgattatcct	12	9	1	1			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr9:6793123T>C	ENST00000381309.3	+	2	700	c.135T>C	c.(133-135)ggT>ggC	p.G45G	KDM4C_ENST00000536108.1_5'UTR|KDM4C_ENST00000543771.1_Silent_p.G45G|KDM4C_ENST00000535193.1_Silent_p.G67G|KDM4C_ENST00000381306.3_Silent_p.G45G|KDM4C_ENST00000401787.3_Silent_p.G45G|KDM4C_ENST00000442236.2_5'UTR|KDM4C_ENST00000489243.1_3'UTR	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	45	JmjN. {ECO:0000255|PROSITE- ProRule:PRU00537}.				histone H3-K9 demethylation (GO:0033169)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	androgen receptor binding (GO:0050681)|dioxygenase activity (GO:0051213)|enzyme binding (GO:0019899)|histone demethylase activity (H3-K9 specific) (GO:0032454)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43						ATCGTGCGGGTCTTGCAAAGG	0.418																																					p.G67G		Atlas-SNP	.											.	KDM4C	186	.	0			c.T201C						.						81	79	80					9																	6793123		2203	4300	6503	SO:0001819	synonymous_variant	23081	exon2			TGCGGGTCTTGCA	AB018323	CCDS6471.1, CCDS55285.1, CCDS55286.1, CCDS55287.1	9p24-p23	2013-01-23	2009-04-06	2009-04-06	ENSG00000107077	ENSG00000107077		"Chromatin-modifying enzymes / K-demethylases", "Tudor domain containing"	17071	protein-coding gene	gene with protein product	"tudor domain containing 14C"	605469	"jumonji domain containing 2C"	JMJD2C		9872452, 15138608	Standard	NM_015061		Approved	GASC1, KIAA0780, TDRD14C	uc003zkh.3	Q9H3R0	OTTHUMG00000019536	ENST00000381309.3:c.135T>C	chr9.hg19:g.6793123T>C		37.0	0.0		74.0	27.0	NM_001146696	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Silent	SNP	ENST00000381309.3	hg19	CCDS6471.1																																																																																			.	.		0.418	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061		C	6793123	T	C	6793123	2	2	277	1	0	0	0	0	0	0	0	1	8139	1654	58	2		2	KDM4C	9	6793123	Silent	SNP	T	TCGA-G3-A25Y-01A-11D-A16V-10	1050150	6793123	134420308	22	39670										
UNC13B	10497	hgsc.bcm.edu	37	chr9	35403876	35403926	+	In_Frame_Del	DEL	GCTGTGCCTGCTGGTGCCCCTTGGGCCGGAAGATCCATATGGATGAGACAG	GCTGTGCCTGCTGGTGCCCCTTGGGCCGGAAGATCCATATGGATGAGACAG	-													0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	ggatgtcacagccaagggcaGctgtgcctgctggtgcccct							TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	GCTGTGCCTGCTGGTGCCCCTTGGGCCGGAAGATCCATATGGATGAGACAG	GCTGTGCCTGCTGGTGCCCCTTGGGCCGGAAGATCCATATGGATGAGACAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr9:35403876_35403926delGCTGTGCCTGCTGGTGCCCCTTGGGCCGGAAGATCCATATGGATGAGACAG	ENST00000378495.3	+	39	4844_4894	c.4622_4672delGCTGTGCCTGCTGGTGCCCCTTGGGCCGGAAGATCCATATGGATGAGACAG	c.(4621-4674)agctgtgcctgctggtgccccttgggccggaagatccatatggatgagacaggc>agc	p.CACWCPLGRKIHMDETG1542del	UNC13B_ENST00000378496.4_In_Frame_Del_p.CACWCPLGRKIHMDETG1561del|ATP8B5P_ENST00000430846.1_RNA|UNC13B_ENST00000396787.1_In_Frame_Del_p.CACWCPLGRKIHMDETG1573del	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)	1542					apoptotic process (GO:0006915)|excretion (GO:0007588)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synaptic vesicle priming (GO:0010808)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|terminal bouton (GO:0043195)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)	p.H1553H(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(16)|liver(2)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			GCCAAGGGCAGCTGTGCCTGCTGGTGCCCCTTGGGCCGGAAGATCCATATGGATGAGACAGGCCTGACCAT	0.55																																					p.1541_1557del		Pindel	.											.	UNC13B	153	.	1	Substitution - coding silent(1)	prostate(1)	c.4621_4671del						.																																			SO:0001651	inframe_deletion	10497	exon39			.	AF020202	CCDS6579.1	9p13.3	2008-05-15	2003-10-17	2003-10-17	ENSG00000198722	ENSG00000198722			12566	protein-coding gene	gene with protein product		605836	"unc-13-like (C. elegans)"	UNC13		9607201	Standard	NM_006377		Approved	hmunc13, Unc13h2	uc003zwq.3	O14795	OTTHUMG00000019856	ENST00000378495.3:c.4622_4672delGCTGTGCCTGCTGGTGCCCCTTGGGCCGGAAGATCCATATGGATGAGACAG	chr9.hg19:g.35403876_35403926delGCTGTGCCTGCTGGTGCCCCTTGGGCCGGAAGATCCATATGGATGAGACAG	ENSP00000367756:p.Cys1542_Gly1558del	63.0	0.0		48.0	15.0	NM_006377	Q5VYM8	In_Frame_Del	DEL	ENST00000378495.3	hg19	CCDS6579.1																																																																																			.	.		0.55	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377		-	35403926	GCTGTGCCTGCTGGTGCCCCTTGGGCCGGAAGATCCATATGGATGAGACAG	-	35403876	7	5	277	1	0	1	0	1	0	0	0	0	17000	971	34	0	4776	0	UNC13B	9	35403876	In_Frame_Del	DEL	GCTGTGCCTGCTGGTGCCCCTTGGGCCGGAAGATCCATATGGATGAGACAG	TCGA-G3-A25Y-01A-11D-A16V-10	28610753	35403876	105809555	23	39671										
RNF20	56254	hgsc.bcm.edu	37	chr9	104315030	104315030	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	atcaaacaattgaagattgaActcaagtaagaaccacattt	5	7	2	4			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr9:104315030A>T	ENST00000389120.3	+	13	1986	c.1896A>T	c.(1894-1896)gaA>gaT	p.E632D	AL591377.1_ENST00000584534.1_RNA	NM_019592.5	NP_062538.5	Q5VTR2	BRE1A_HUMAN	ring finger protein 20, E3 ubiquitin protein ligase	632					histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|negative regulation of cell migration (GO:0030336)|positive regulation of histone methylation (GO:0031062)|positive regulation of transcription, DNA-templated (GO:0045893)|protein polyubiquitination (GO:0000209)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)	HULC complex (GO:0033503)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|ligase activity (GO:0016874)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(6)|large_intestine(7)|lung(23)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_hematologic(171;8.99e-06)|Acute lymphoblastic leukemia(62;0.000365)|Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.88e-19)|STAD - Stomach adenocarcinoma(157;0.00311)		TGAAGATTGAACTCAAGTAAG	0.363																																					p.E632D		Atlas-SNP	.											.	RNF20	110	.	0			c.A1896T						.						52	55	54					9																	104315030		2203	4300	6503	SO:0001583	missense	56254	exon13			GATTGAACTCAAG	AF265230	CCDS35084.1	9q22	2012-02-23	2012-02-23	2008-12-12	ENSG00000155827	ENSG00000155827		"RING-type (C3HC4) zinc fingers"	10062	protein-coding gene	gene with protein product	"BRE1 E3 ubiquitin ligase homolog (S. cerevisiae)"	607699	"ring finger protein 20"			16337599, 12876294, 18832071, 19037095	Standard	NM_019592		Approved	FLJ20382, FLJ11189, KAIA2779, BRE1A, hBRE1, BRE1	uc004bbn.3	Q5VTR2	OTTHUMG00000020385	ENST00000389120.3:c.1896A>T	chr9.hg19:g.104315030A>T	ENSP00000373772:p.Glu632Asp	180.0	0.0		222.0	57.0	NM_019592	A7MCT5|Q2TB34|Q69YL5|Q6P527|Q8N3J4|Q96JD3|Q9H9Y7|Q9HA51|Q9NUR4|Q9NWQ3|Q9NX83	Missense_Mutation	SNP	ENST00000389120.3	hg19	CCDS35084.1	.	.	.	.	.	.	.	.	.	.	A	13.48	2.248373	0.39797	.	.	ENSG00000155827	ENST00000389120	T	0.33865	1.39	6.17	-2.09	0.07232	.	0.043508	0.85682	D	0.000000	T	0.20536	0.0494	L	0.33485	1.01	0.58432	D	0.99999	B	0.26483	0.15	B	0.25405	0.06	T	0.03394	-1.1041	10	0.29301	T	0.29	-23.1248	6.8613	0.24067	0.3312:0.0:0.4641:0.2047	.	632	Q5VTR2	BRE1A_HUMAN	D	632	ENSP00000373772:E632D	ENSP00000373772:E632D	E	+	3	2	RNF20	103354851	0.669000	0.27502	0.998000	0.56505	0.762000	0.43233	-0.184000	0.09698	-0.027000	0.13873	0.533000	0.62120	GAA	.	.		0.363	RNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356402.1	NM_019592		T	104315030	A	T	104315030	3	4	277	1	0	0	0	0	1	0	0	0	13488	40	2	4	1942	4	RNF20	9	104315030	Missense_Mutation	SNP	A	TCGA-G3-A25Y-01A-11D-A16V-10	68911154	104315030	36898401	24	39672										
DYDC1	143241	hgsc.bcm.edu	37	chr10	82098869	82098869	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	tcacctctgaatgtagaataTcttcattcctaactagattt	4	9	4	3			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr10:82098869T>C	ENST00000372204.3	-	6	547	c.383A>G	c.(382-384)gAt>gGt	p.D128G	DYDC1_ENST00000421924.2_Missense_Mutation_p.D128G|DYDC1_ENST00000372202.1_Missense_Mutation_p.D128G	NM_138812.3	NP_620167.1	Q8WWB3	DYDC1_HUMAN	DPY30 domain containing 1	128										kidney(1)|large_intestine(3)|skin(1)	5			Colorectal(32;0.229)			ATGTAGAATATCTTCATTCCT	0.264																																					p.D128G		Atlas-SNP	.											.	DYDC1	15	.	0			c.A383G						.						67	60	62					10																	82098869		2186	4279	6465	SO:0001583	missense	143241	exon5			AGAATATCTTCAT	BC019250	CCDS7366.1	10q22.3	2006-02-01			ENSG00000170788	ENSG00000170788			23460	protein-coding gene	gene with protein product		615154					Standard	NM_138812		Approved	bA36D19.5, DPY30D1	uc031pwj.1	Q8WWB3	OTTHUMG00000018609	ENST00000372204.3:c.383A>G	chr10.hg19:g.82098869T>C	ENSP00000361278:p.Asp128Gly	151.0	0.0		288.0	28.0	NM_001269053	A8K927|Q5QP03|Q5QP04|Q6WNP4|Q6ZU87	Missense_Mutation	SNP	ENST00000372204.3	hg19	CCDS7366.1	.	.	.	.	.	.	.	.	.	.	T	9.869	1.198414	0.22037	.	.	ENSG00000170788	ENST00000372204;ENST00000372202;ENST00000421924;ENST00000454362	.	.	.	4.88	3.74	0.42951	.	0.890365	0.09714	N	0.765370	T	0.19287	0.0463	N	0.08118	0	0.09310	N	1	B;B	0.12630	0.006;0.003	B;B	0.08055	0.003;0.002	T	0.19353	-1.0308	9	0.33141	T	0.24	-7.4756	7.371	0.26802	0.0:0.0983:0.0:0.9017	.	128;128	A8K927;Q8WWB3	.;DYDC1_HUMAN	G	128	.	ENSP00000361276:D128G	D	-	2	0	DYDC1	82088849	0.377000	0.25106	0.092000	0.20876	0.112000	0.19704	1.674000	0.37544	0.989000	0.38761	0.533000	0.62120	GAT	.	.		0.264	DYDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049059.1	NM_138812		C	82098869	T	C	82098869	3	2	277	1	0	0	0	0	1	0	0	0	4840	1435	50	2	162	2	DYDC1	10	82098869	Missense_Mutation	SNP	T	TCGA-G3-A25Y-01A-11D-A16V-10		82098869	53435878	25	39673										
TNKS2	80351	hgsc.bcm.edu	37	chr10	93609319	93609319	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	tcgtaaggaatcttggacttGagcacctaatggatatattt	9	6	1	1	rs556843721		TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr10:93609319G>A	ENST00000371627.4	+	20	3041	c.2662G>A	c.(2662-2664)Gag>Aag	p.E888K		NM_025235.3	NP_079511.1	Q9H2K2	TNKS2_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2	888	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				multicellular organism growth (GO:0035264)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein polyubiquitination (GO:0000209)|regulation of multicellular organism growth (GO:0040014)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			biliary_tract(1)|breast(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	48		Colorectal(252;0.162)				TCTTGGACTTGAGCACCTAAT	0.323													G|||	1	0.000199681	0	0	5008	,	,		18403	0		0	False		,,,				2504	0.001				p.E888K		Atlas-SNP	.											.	TNKS2	103	.	0			c.G2662A						.						114	109	110					10																	93609319		2203	4300	6503	SO:0001583	missense	80351	exon20			GGACTTGAGCACC	AF342982	CCDS7417.1	10q23.3	2013-01-10			ENSG00000107854	ENSG00000107854		"Poly (ADP-ribose) polymerases", "Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	15677	protein-coding gene	gene with protein product		607128					Standard	NM_025235		Approved	TNKL, TANK2, PARP-5b, PARP-5c, PARP5B, PARP5C, pART6	uc001khp.3	Q9H2K2	OTTHUMG00000018747	ENST00000371627.4:c.2662G>A	chr10.hg19:g.93609319G>A	ENSP00000360689:p.Glu888Lys	122.0	0.0		147.0	47.0	NM_025235	B2RBD3|Q9H8F2|Q9HAS4	Missense_Mutation	SNP	ENST00000371627.4	hg19	CCDS7417.1	.	.	.	.	.	.	.	.	.	.	G	35	5.451636	0.96205	.	.	ENSG00000107854	ENST00000371627	D	0.88818	-2.43	5.52	5.52	0.82312	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 2 (1);	0.000000	0.64402	D	0.000017	D	0.92977	0.7765	M	0.87758	2.905	0.80722	D	1	P	0.42161	0.772	P	0.46940	0.532	D	0.93365	0.6730	10	0.54805	T	0.06	.	19.4315	0.94772	0.0:0.0:1.0:0.0	.	888	Q9H2K2	TNKS2_HUMAN	K	888	ENSP00000360689:E888K	ENSP00000360689:E888K	E	+	1	0	TNKS2	93599299	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.954000	0.87848	2.594000	0.87642	0.585000	0.79938	GAG	.	.		0.323	TNKS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049374.1	NM_025235		A	93609319	G	A	93609319	3	1	277	1	0	0	0	0	1	0	0	0	16336	1291	45	3	2740	3	TNKS2	10	93609319	Missense_Mutation	SNP	G	TCGA-G3-A25Y-01A-11D-A16V-10	11510450	93609319	41925428	26	39674										
VAX1	11023	hgsc.bcm.edu	37	chr10	118896079	118896079	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	tccatctccagccgatagagCtgctccgcggtgaaggacgt	12	13	1	2			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr10:118896079C>G	ENST00000369206.5	-	2	332	c.333G>C	c.(331-333)caG>caC	p.Q111H	VAX1_ENST00000277905.2_Missense_Mutation_p.Q111H	NM_001112704.1	NP_001106175.1	Q5SQQ9	VAX1_HUMAN	ventral anterior homeobox 1	111					axon guidance (GO:0007411)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|palate development (GO:0060021)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(1)|lung(8)|ovary(2)	12				all cancers(201;0.0108)		GCCGATAGAGCTGCTCCGCGG	0.647																																					p.Q111H		Atlas-SNP	.											.	VAX1	50	.	0			c.G333C						.						42	39	40					10																	118896079		2203	4300	6503	SO:0001583	missense	11023	exon2			ATAGAGCTGCTCC	AK127095	CCDS7597.1, CCDS44483.1	10q26.11	2011-06-20			ENSG00000148704	ENSG00000148704		"Homeoboxes / ANTP class : NKL subclass"	12660	protein-coding gene	gene with protein product		604294				9636075, 10485894	Standard	NM_199131		Approved		uc009xyx.3	Q5SQQ9	OTTHUMG00000019117	ENST00000369206.5:c.333G>C	chr10.hg19:g.118896079C>G	ENSP00000358207:p.Gln111His	48.0	0.0		46.0	31.0	NM_001112704	B1AVW5|Q6ZSX0	Missense_Mutation	SNP	ENST00000369206.5	hg19	CCDS44483.1	.	.	.	.	.	.	.	.	.	.	C	15.19	2.760083	0.49468	.	.	ENSG00000148704	ENST00000277905;ENST00000369206	D;D	0.98044	-4.68;-4.68	4.03	4.03	0.46877	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99266	0.9744	H	0.98370	4.215	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.83275	0.996;0.995	D	0.98496	1.0612	10	0.87932	D	0	-4.9345	16.3358	0.83060	0.0:1.0:0.0:0.0	.	111;111	Q5SQQ9;Q5SQQ9-2	VAX1_HUMAN;.	H	111	ENSP00000277905:Q111H;ENSP00000358207:Q111H	ENSP00000277905:Q111H	Q	-	3	2	VAX1	118886069	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.499000	0.66937	2.083000	0.62718	0.455000	0.32223	CAG	.	.		0.647	VAX1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050559.3	XM_301242		G	118896079	C	G	118896079	3	3	277	1	0	0	0	0	1	0	0	0	17149	796	28	4	819	4	VAX1	10	118896079	Missense_Mutation	SNP	C	TCGA-G3-A25Y-01A-11D-A16V-10	25286760	118896079	16638668	27	39675										
AHNAK	79026	hgsc.bcm.edu	37	chr11	62293785	62293785	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	ggagatcttgggggctttgaTattcatctctggcatcttga	12	7	4	3			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr11:62293785T>C	ENST00000378024.4	-	5	8378	c.8104A>G	c.(8104-8106)Atc>Gtc	p.I2702V	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	2702					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)	p.I2702F(1)		NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				GGGGCTTTGATATTCATCTCT	0.458																																					p.I2702V		Atlas-SNP	.											AHNAK,colon,carcinoma,+1,1	AHNAK	532	.	1	Substitution - Missense(1)	lung(1)	c.A8104G						.						192	190	191					11																	62293785		2202	4299	6501	SO:0001583	missense	79026	exon5			CTTTGATATTCAT	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.8104A>G	chr11.hg19:g.62293785T>C	ENSP00000367263:p.Ile2702Val	189.0	0.0		212.0	11.0	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	hg19	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	t	2.437	-0.329610	0.05314	.	.	ENSG00000124942	ENST00000378024	T	0.09630	2.96	4.65	-3.77	0.04346	.	.	.	.	.	T	0.05914	0.0154	L	0.38953	1.18	0.09310	N	1	B	0.31009	0.303	B	0.27076	0.076	T	0.43702	-0.9375	9	0.07482	T	0.82	-1.5199	6.7912	0.23701	0.5021:0.0:0.1309:0.367	.	2702	Q09666	AHNK_HUMAN	V	2702	ENSP00000367263:I2702V	ENSP00000367263:I2702V	I	-	1	0	AHNAK	62050361	0.000000	0.05858	0.007000	0.13788	0.768000	0.43524	-5.329000	0.00131	-0.529000	0.06358	0.392000	0.25879	ATC	.	.		0.458	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		C	62293785	T	C	62293785	3	2	277	1	0	0	0	0	1	0	0	0	414	1406	49	2	9688	2	AHNAK	11	62293785	Missense_Mutation	SNP	T	TCGA-G3-A25Y-01A-11D-A16V-10		62293785	72712731	28	39676										
SAPS3	55291	hgsc.bcm.edu	37	chr11	68338555	68338555	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	cgaatacttgaagcctgggaAatgaatgagaagaaacagta	11	5	0	4			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr11:68338555A>C	ENST00000393800.2	+	12	1580	c.1326A>C	c.(1324-1326)gaA>gaC	p.E442D	PPP6R3_ENST00000393799.2_Missense_Mutation_p.E442D|PPP6R3_ENST00000393801.3_Missense_Mutation_p.E442D|PPP6R3_ENST00000534534.1_Missense_Mutation_p.E210D|PPP6R3_ENST00000527403.2_Missense_Mutation_p.E442D|PPP6R3_ENST00000529710.1_Missense_Mutation_p.E391D|PPP6R3_ENST00000524904.1_Missense_Mutation_p.E442D|PPP6R3_ENST00000265636.5_Missense_Mutation_p.E391D|PPP6R3_ENST00000265637.4_Missense_Mutation_p.E442D|PPP6R3_ENST00000524845.1_Missense_Mutation_p.E442D	NM_001164161.1|NM_001164162.1|NM_001164163.1	NP_001157633.1|NP_001157634.1|NP_001157635.1	Q5H9R7	PP6R3_HUMAN	protein phosphatase 6, regulatory subunit 3	442					regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)			breast(2)|endometrium(6)|kidney(3)|large_intestine(10)|liver(2)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						AAGCCTGGGAAATGAATGAGA	0.294																																					p.E442D		Atlas-SNP	.											.	PPP6R3	159	.	0			c.A1326C						.						78	90	86					11																	68338555		2199	4294	6493	SO:0001583	missense	55291	exon12			CTGGGAAATGAAT	AF264779	CCDS8182.1, CCDS53671.1, CCDS53672.1, CCDS53673.1, CCDS53674.1, CCDS53675.1	11q13	2012-04-17	2010-06-28	2010-06-28	ENSG00000110075	ENSG00000110075		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"	1173	protein-coding gene	gene with protein product	"sporulation-induced transcript 4-associated protein"	610879	"chromosome 11 open reading frame 23", "SAPS domain family, member 3"	C11orf23, SAPS3		11401438, 16769727	Standard	NM_018312		Approved	SAPLa, DKFZp781E2374, DKFZp781O2362, DKFZp781E17107, SAP190, SAPL, PP6R3, FLJ11058, FLJ43065, KIAA1558, MGC125711, MGC125712	uc001onv.3	Q5H9R7		ENST00000393800.2:c.1326A>C	chr11.hg19:g.68338555A>C	ENSP00000377389:p.Glu442Asp	61.0	0.0		87.0	19.0	NM_001164162	Q3B7I1|Q3I4Y0|Q3KR35|Q68CR3|Q7L4R8|Q8N3B2|Q96MB2|Q9H2K5|Q9H2K6|Q9HCL4|Q9NUY3	Missense_Mutation	SNP	ENST00000393800.2	hg19	CCDS53672.1	.	.	.	.	.	.	.	.	.	.	A	14.11	2.437276	0.43224	.	.	ENSG00000110075	ENST00000393799;ENST00000393800;ENST00000534534;ENST00000524845;ENST00000265637;ENST00000524904;ENST00000393801;ENST00000265636;ENST00000529710;ENST00000527403;ENST00000534190	T;T;T;T;T;T;T;T;T;T;T	0.27256	1.68;1.68;1.71;1.78;1.78;1.68;1.69;1.73;1.73;1.78;1.77	5.62	-1.36	0.09085	.	0.440687	0.26753	N	0.022672	T	0.15609	0.0376	L	0.43646	1.37	0.26014	N	0.981956	B;B;B;B;B;B;B;B	0.14805	0.0;0.0;0.001;0.011;0.005;0.006;0.002;0.001	B;B;B;B;B;B;B;B	0.26416	0.003;0.003;0.022;0.025;0.041;0.069;0.003;0.008	T	0.13495	-1.0507	10	0.34782	T	0.22	.	0.8448	0.01159	0.1876:0.2696:0.2929:0.2499	.	154;210;391;442;442;442;442;391	B4DYU6;E9PQP7;Q5H9R7-3;Q5H9R7-6;Q5H9R7-2;Q5H9R7;Q5H9R7-5;Q5H9R7-4	.;.;.;.;.;PP6R3_HUMAN;.;.	D	442;442;210;442;442;442;442;391;391;442;178	ENSP00000377388:E442D;ENSP00000377389:E442D;ENSP00000434429:E210D;ENSP00000431415:E442D;ENSP00000265637:E442D;ENSP00000433058:E442D;ENSP00000377390:E442D;ENSP00000265636:E391D;ENSP00000437329:E391D;ENSP00000433565:E442D;ENSP00000436209:E178D	ENSP00000265636:E391D	E	+	3	2	PPP6R3	68095131	0.818000	0.29161	0.991000	0.47740	0.989000	0.77384	-0.047000	0.11963	-0.154000	0.11118	-0.496000	0.04628	GAA	.	.		0.294	PPP6R3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395275.1	NM_018312		C	68338555	A	C	68338555	3	2	277	1	0	0	0	0	1	0	0	0	13853	11	1	5	1364	5	SAPS3	11	68338555	Missense_Mutation	SNP	A	TCGA-G3-A25Y-01A-11D-A16V-10	6044770	68338555	66667961	29	39677										
RPS3	6188	hgsc.bcm.edu	37	chr11	75110602	75110602	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	cggcggcaagatggcagtgcAaatatccaagaagaggaagg	15	7	0	3			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr11:75110602A>G	ENST00000531188.1	+	1	73	c.11A>G	c.(10-12)cAa>cGa	p.Q4R	RPS3_ENST00000530164.1_Missense_Mutation_p.Q4R|RPS3_ENST00000534440.1_Missense_Mutation_p.Q4R|RPS3_ENST00000524851.1_Missense_Mutation_p.Q4R|SNORD15A_ENST00000384214.1_RNA|RPS3_ENST00000527446.1_Missense_Mutation_p.Q4R|RPS3_ENST00000526608.1_Missense_Mutation_p.Q4R|RPS3_ENST00000278572.6_Missense_Mutation_p.Q4R	NM_001005.4|NM_001260506.1|NM_001260507.1	NP_000996.2|NP_001247435.1|NP_001247436.1	P23396	RS3_HUMAN	ribosomal protein S3	4					cellular protein metabolic process (GO:0044267)|cellular response to DNA damage stimulus (GO:0006974)|cytoplasmic translation (GO:0002181)|DNA catabolic process, endonucleolytic (GO:0000737)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|negative regulation of DNA repair (GO:0045738)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of DNA N-glycosylase activity (GO:1902546)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|ruffle membrane (GO:0032587)	damaged DNA binding (GO:0003684)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|enzyme binding (GO:0019899)|iron-sulfur cluster binding (GO:0051536)|mRNA binding (GO:0003729)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase A binding (GO:0051018)|protein kinase binding (GO:0019901)|structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)	6						ATGGCAGTGCAAATATCCAAG	0.662																																					p.Q4R		Atlas-SNP	.											.	RPS3	20	.	0			c.A11G						.						47	49	48					11																	75110602		2200	4293	6493	SO:0001583	missense	6188	exon1			CAGTGCAAATATC		CCDS8236.1, CCDS58161.1	11q13.3-q13.5	2011-04-05				ENSG00000149273		"S ribosomal proteins"	10420	protein-coding gene	gene with protein product	"IMR-90 ribosomal protein S3", "40S ribosomal protein S3"	600454				1712897, 7789996	Standard	NM_001005		Approved	FLJ26283, FLJ27450, MGC87870, S3	uc031qcs.1	P23396		ENST00000531188.1:c.11A>G	chr11.hg19:g.75110602A>G	ENSP00000434643:p.Gln4Arg	110.0	0.0		113.0	31.0	NM_001256802	B2R7N5|J3KN86|Q498B5|Q8NI95	Missense_Mutation	SNP	ENST00000531188.1	hg19	CCDS8236.1	.	.	.	.	.	.	.	.	.	.	a	14.36	2.513561	0.44763	.	.	ENSG00000149273	ENST00000531188;ENST00000530164;ENST00000530689;ENST00000278572;ENST00000534440;ENST00000527446;ENST00000526608;ENST00000527273;ENST00000524851	.	.	.	5.74	4.55	0.56014	.	0.000000	0.85682	D	0.000000	T	0.60431	0.2268	M	0.62266	1.93	0.58432	D	0.999992	B	0.06786	0.001	B	0.27500	0.08	T	0.62905	-0.6755	9	0.72032	D	0.01	-1.5195	10.7726	0.46332	0.8411:0.1589:0.0:0.0	.	4	P23396	RS3_HUMAN	R	4	.	ENSP00000278572:Q4R	Q	+	2	0	RPS3	74788250	1.000000	0.71417	0.949000	0.38748	0.132000	0.20833	6.324000	0.72896	2.194000	0.70268	0.449000	0.29647	CAA	.	.		0.662	RPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384158.2	NM_001005		G	75110602	A	G	75110602	3	3	277	1	0	0	0	0	1	0	0	0	13658	130	5	2	13	2	RPS3	11	75110602	Missense_Mutation	SNP	A	TCGA-G3-A25Y-01A-11D-A16V-10	6772047	75110602	59895914	30	39678										
FAT3	120114	hgsc.bcm.edu	37	chr11	92531317	92531317	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	agatggagacattaatgggaTctttaccataaatccatatt	7	6	1	2			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr11:92531317T>A	ENST00000298047.6	+	9	5155	c.5138T>A	c.(5137-5139)aTc>aAc	p.I1713N	FAT3_ENST00000409404.2_Missense_Mutation_p.I1713N|FAT3_ENST00000525166.1_Missense_Mutation_p.I1563N			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	1713	Cadherin 15. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				ATTAATGGGATCTTTACCATA	0.398										TCGA Ovarian(4;0.039)																											p.I1713N		Atlas-SNP	.											.	FAT3	1822	.	0			c.T5138A						.						108	107	107					11																	92531317		1957	4143	6100	SO:0001583	missense	120114	exon9			ATGGGATCTTTAC	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.5138T>A	chr11.hg19:g.92531317T>A	ENSP00000298047:p.Ile1713Asn	104.0	0.0		149.0	56.0	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	hg19		.	.	.	.	.	.	.	.	.	.	T	12.04	1.818661	0.32145	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.50277	0.75;0.75;0.75	5.93	-2.4	0.06583	.	.	.	.	.	T	0.29458	0.0734	N	0.25485	0.75	0.09310	N	1	B	0.28605	0.217	B	0.24541	0.054	T	0.15206	-1.0445	9	0.30854	T	0.27	.	9.459	0.38772	0.0:0.5162:0.1259:0.3579	.	1713	Q8TDW7-3	.	N	1713;1713;1563	ENSP00000298047:I1713N;ENSP00000387040:I1713N;ENSP00000432586:I1563N	ENSP00000298047:I1713N	I	+	2	0	FAT3	92170965	0.000000	0.05858	0.001000	0.08648	0.809000	0.45718	0.103000	0.15292	-0.421000	0.07416	0.482000	0.46254	ATC	.	.		0.398	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		A	92531317	T	A	92531317	3	1	277	1	0	0	0	0	1	0	0	0	5699	1435	50	4	5172	4	FAT3	11	92531317	Missense_Mutation	SNP	T	TCGA-G3-A25Y-01A-11D-A16V-10	17420715	92531317	42475199	31	39679										
SCN3B	55800	hgsc.bcm.edu	37	chr11	123513234	123513234	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	caaactcaaactcccgggacAcattgcaggtgtagaggcca	10	12	1	1			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr11:123513234A>T	ENST00000392770.2	-	3	1167	c.365T>A	c.(364-366)gTg>gAg	p.V122E	SCN3B_ENST00000299333.3_Missense_Mutation_p.V122E|SCN3B_ENST00000530277.1_Missense_Mutation_p.V122E	NM_018400.3	NP_060870.1	Q9NY72	SCN3B_HUMAN	sodium channel, voltage-gated, type III, beta subunit	122	Ig-like C2-type.				atrial cardiac muscle cell action potential (GO:0086014)|axon guidance (GO:0007411)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|positive regulation of heart rate (GO:0010460)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|ventricular cardiac muscle cell action potential (GO:0086005)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	ion channel binding (GO:0044325)|sodium channel regulator activity (GO:0017080)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(16)|ovary(2)|skin(2)	26		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0227)	Valproic Acid(DB00313)|Zonisamide(DB00909)	CTCCCGGGACACATTGCAGGT	0.602																																					p.V122E		Atlas-SNP	.											.	SCN3B	53	.	0			c.T365A						.						104	96	99					11																	123513234		2202	4299	6501	SO:0001583	missense	55800	exon3			CGGGACACATTGC	AJ243396	CCDS8442.1	11q24.1	2014-09-17	2012-02-28		ENSG00000166257	ENSG00000166257		"Sodium channels", "Voltage-gated ion channels / Sodium channels", "Immunoglobulin superfamily / V-set domain containing"	20665	protein-coding gene	gene with protein product		608214	"sodium channel, voltage-gated, type III, beta"			10688874	Standard	XR_428980		Approved	HSA243396	uc001pzb.1	Q9NY72	OTTHUMG00000166006	ENST00000392770.2:c.365T>A	chr11.hg19:g.123513234A>T	ENSP00000376523:p.Val122Glu	54.0	0.0		71.0	18.0	NM_018400	A5H1I5|Q17RL3|Q9ULR2	Missense_Mutation	SNP	ENST00000392770.2	hg19	CCDS8442.1	.	.	.	.	.	.	.	.	.	.	A	32	5.160704	0.94727	.	.	ENSG00000166257	ENST00000392770;ENST00000299333;ENST00000530277;ENST00000527836	D;D;D;D	0.95690	-3.78;-3.78;-3.78;-3.78	6.03	6.03	0.97812	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.110193	0.64402	D	0.000008	D	0.97430	0.9159	M	0.79805	2.47	0.80722	D	1	D	0.63046	0.992	P	0.62089	0.898	D	0.97985	1.0351	10	0.87932	D	0	-9.7242	16.5655	0.84588	1.0:0.0:0.0:0.0	.	122	Q9NY72	SCN3B_HUMAN	E	122	ENSP00000376523:V122E;ENSP00000299333:V122E;ENSP00000432785:V122E;ENSP00000435554:V122E	ENSP00000299333:V122E	V	-	2	0	SCN3B	123018444	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.285000	0.89914	2.302000	0.77476	0.533000	0.62120	GTG	.	.		0.602	SCN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387412.1	NM_018400		T	123513234	A	T	123513234	3	4	277	1	0	0	0	0	1	0	0	0	13934	159	6	4	294	4	SCN3B	11	123513234	Missense_Mutation	SNP	A	TCGA-G3-A25Y-01A-11D-A16V-10	30981917	123513234	11493282	32	39680										
BAZ2A	11176	hgsc.bcm.edu	37	chr12	56993854	56993854	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	cgagggtctggcgccagacaCgaatgcgaggggtgatctca	16	10	2	2			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr12:56993854C>A	ENST00000551812.1	-	25	5118	c.4925G>T	c.(4924-4926)cGt>cTt	p.R1642L	BAZ2A_ENST00000179765.5_Missense_Mutation_p.R1610L|BAZ2A_ENST00000549884.1_Missense_Mutation_p.R1640L|BAZ2A_ENST00000379441.3_Missense_Mutation_p.R1612L|BAZ2A_ENST00000553222.1_5'Flank	NM_013449.3	NP_038477.2	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	1642					chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA methylation (GO:0006306)|heterochromatin assembly involved in chromatin silencing (GO:0070869)|histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|histone H4 deacetylation (GO:0070933)|histone H4-K20 methylation (GO:0034770)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|nucleolus (GO:0005730)|rDNA heterochromatin (GO:0033553)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|lysine-acetylated histone binding (GO:0070577)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.R1642H(2)		breast(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(15)|urinary_tract(1)	31						GCGCCAGACACGAATGCGAGG	0.572																																					p.R1642L		Atlas-SNP	.											BAZ2A_ENST00000551812,colon,carcinoma,0,2	BAZ2A	263	.	2	Substitution - Missense(2)	large_intestine(2)	c.G4925T						.						81	82	82					12																	56993854		2002	4179	6181	SO:0001583	missense	11176	exon25			CAGACACGAATGC	AB032254	CCDS44924.1, CCDS73483.1	12q13.3	2013-01-28				ENSG00000076108		"Zinc fingers, PHD-type"	962	protein-coding gene	gene with protein product	"TTF-I interacting peptide 5"	605682				10662543, 11532953	Standard	XM_005268596		Approved	KIAA0314, TIP5, WALp3	uc001slq.1	Q9UIF9	OTTHUMG00000170332	ENST00000551812.1:c.4925G>T	chr12.hg19:g.56993854C>A	ENSP00000446880:p.Arg1642Leu	90.0	0.0		73.0	29.0	NM_013449	B3KN66|O00536|O15030|Q68DI8|Q96H26	Missense_Mutation	SNP	ENST00000551812.1	hg19	CCDS44924.1	.	.	.	.	.	.	.	.	.	.	C	29.4	5.001011	0.93227	.	.	ENSG00000076108	ENST00000379441;ENST00000179765;ENST00000551812;ENST00000549787;ENST00000549884	T;T;T;T;T	0.71698	-0.34;-0.34;-0.36;-0.59;-0.36	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.80428	0.4621	L	0.47716	1.5	0.80722	D	1	D;P;B;D	0.89917	0.999;0.524;0.272;1.0	D;P;B;D	0.91635	0.996;0.498;0.302;0.999	T	0.77305	-0.2637	10	0.35671	T	0.21	-14.6921	18.5763	0.91155	0.0:1.0:0.0:0.0	.	1640;1638;1642;1615	F8VU39;Q9UIF9-3;Q9UIF9;Q9UIF9-2	.;.;BAZ2A_HUMAN;.	L	1612;1610;1642;574;1640	ENSP00000368754:R1612L;ENSP00000179765:R1610L;ENSP00000446880:R1642L;ENSP00000448760:R574L;ENSP00000447941:R1640L	ENSP00000179765:R1610L	R	-	2	0	BAZ2A	55280121	1.000000	0.71417	0.962000	0.40283	0.989000	0.77384	5.568000	0.67385	2.763000	0.94921	0.650000	0.86243	CGT	.	.		0.572	BAZ2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408561.1	NM_013449		A	56993854	C	A	56993854	3	1	277	1	0	0	0	0	1	0	0	0	1331	536	19	1	812	1	BAZ2A	12	56993854	Missense_Mutation	SNP	C	TCGA-G3-A25Y-01A-11D-A16V-10		56993854	76858041	33	39681										
UBE2N	7334	hgsc.bcm.edu	37	chr12	93804590	93804590	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	gatcatctggattgggagcaCttaacaaggcctggatcgat	12	8	2	0	rs555116824		TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr12:93804590C>G	ENST00000318066.2	-	3	715	c.338G>C	c.(337-339)aGt>aCt	p.S113T	UBE2N_ENST00000550657.1_3'UTR|UBE2N_ENST00000552442.1_Intron|UBE2N_ENST00000549833.1_Missense_Mutation_p.S50T	NM_003348.3	NP_003339.1	P61088	UBE2N_HUMAN	ubiquitin-conjugating enzyme E2N	113					cellular protein modification process (GO:0006464)|cytokine-mediated signaling pathway (GO:0019221)|DNA double-strand break processing (GO:0000729)|double-strand break repair via homologous recombination (GO:0000724)|Fc-epsilon receptor signaling pathway (GO:0038095)|histone ubiquitination (GO:0016574)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of DNA repair (GO:0045739)|positive regulation of histone modification (GO:0031058)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|postreplication repair (GO:0006301)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of DNA repair (GO:0006282)|regulation of histone ubiquitination (GO:0033182)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|protein complex (GO:0043234)|UBC13-MMS2 complex (GO:0031372)|UBC13-UEV1A complex (GO:0035370)|ubiquitin ligase complex (GO:0000151)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|liver(2)|lung(5)	10						ATTGGGAGCACTTAACAAGGC	0.463								Direct reversal of damage;Rad6 pathway																													p.S113T	Pancreas(197;738 2228 30225 32034 33454)	Atlas-SNP	.											.	UBE2N	20	.	0			c.G338C						.						154	134	141					12																	93804590		2203	4300	6503	SO:0001583	missense	7334	exon3			GGAGCACTTAACA	D83004	CCDS31875.1	12q22	2011-05-19	2011-05-19			ENSG00000177889		"Ubiquitin-conjugating enzymes E2"	12492	protein-coding gene	gene with protein product		603679	"ubiquitin-conjugating enzyme E2N (homologous to yeast UBC13)", "ubiquitin-conjugating enzyme E2N (UBC13 homolog, yeast)"			8902611	Standard	NM_003348		Approved	UbcH-ben, UBC13, MGC8489	uc001tcp.3	P61088	OTTHUMG00000170156	ENST00000318066.2:c.338G>C	chr12.hg19:g.93804590C>G	ENSP00000316176:p.Ser113Thr	147.0	0.0		201.0	24.0	NM_003348	Q16781|Q53Y81	Missense_Mutation	SNP	ENST00000318066.2	hg19	CCDS31875.1	.	.	.	.	.	.	.	.	.	.	C	18.68	3.675421	0.67928	.	.	ENSG00000177889	ENST00000318066;ENST00000549833	T;T	0.37584	1.19;1.19	5.94	5.94	0.96194	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	.	.	.	.	T	0.43500	0.1250	L	0.49699	1.58	0.80722	D	1	P	0.38617	0.64	P	0.45232	0.474	T	0.05750	-1.0866	9	0.16896	T	0.51	.	20.3736	0.98901	0.0:1.0:0.0:0.0	.	113	P61088	UBE2N_HUMAN	T	113;50	ENSP00000316176:S113T;ENSP00000450260:S50T	ENSP00000316176:S113T	S	-	2	0	UBE2N	92328721	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.633000	0.67825	2.820000	0.97059	0.650000	0.86243	AGT	.	.		0.463	UBE2N-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407710.1	NM_003348		G	93804590	C	G	93804590	3	3	277	1	0	0	0	0	1	0	0	0	16881	565	20	4	128	4	UBE2N	12	93804590	Missense_Mutation	SNP	C	TCGA-G3-A25Y-01A-11D-A16V-10	36810736	93804590	40047305	34	39682										
ANO4	121601	hgsc.bcm.edu	37	chr12	101381373	101381373	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	acctaagaagccaatgaggcTggacaaggagacactgccag	12	10	0	3	rs576854824		TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr12:101381373T>A	ENST00000392977.3	+	8	869	c.659T>A	c.(658-660)cTg>cAg	p.L220Q	ANO4_ENST00000538618.1_3'UTR|ANO4_ENST00000392979.3_Missense_Mutation_p.L185Q|ANO4_ENST00000299222.9_5'UTR			Q32M45	ANO4_HUMAN	anoctamin 4	220					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			NS(1)|biliary_tract(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(4)|prostate(5)|skin(7)|stomach(2)|urinary_tract(1)	78						CCAATGAGGCTGGACAAGGAG	0.498										HNSCC(74;0.22)	OREG0022059	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L185Q		Atlas-SNP	.											.	ANO4	183	.	0			c.T554A						.						254	234	241					12																	101381373		2203	4300	6503	SO:0001583	missense	121601	exon7			TGAGGCTGGACAA	AK091540	CCDS31884.1, CCDS66445.1	12q23.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000151572	ENSG00000151572		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	23837	protein-coding gene	gene with protein product		610111	"transmembrane protein 16D"	TMEM16D		12739008, 15067359, 24692353	Standard	NM_178826		Approved	FLJ34221, FLJ34272, FLJ35277	uc001thw.2	Q32M45		ENST00000392977.3:c.659T>A	chr12.hg19:g.101381373T>A	ENSP00000376703:p.Leu220Gln	47.0	0.0	1358	39.0	17.0	NM_178826	Q8NAJ0|Q8NB39|Q8NB53	Missense_Mutation	SNP	ENST00000392977.3	hg19		.	.	.	.	.	.	.	.	.	.	T	17.65	3.442982	0.63067	.	.	ENSG00000151572	ENST00000392979;ENST00000392977	T;T	0.69561	-0.41;-0.41	5.33	5.33	0.75918	.	0.097548	0.42682	D	0.000680	T	0.63873	0.2548	M	0.67953	2.075	0.80722	D	1	P;B	0.39940	0.696;0.343	B;B	0.33799	0.17;0.133	T	0.70472	-0.4862	10	0.72032	D	0.01	.	15.3283	0.74186	0.0:0.0:0.0:1.0	.	220;185	Q32M45;Q32M45-2	ANO4_HUMAN;.	Q	185;220	ENSP00000376705:L185Q;ENSP00000376703:L220Q	ENSP00000376703:L220Q	L	+	2	0	ANO4	99905504	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.817000	0.86213	2.020000	0.59435	0.533000	0.62120	CTG	.	.		0.498	ANO4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409295.1	NM_178826		A	101381373	T	A	101381373	3	1	277	1	0	0	0	0	1	0	0	0	699	1580	55	4	576	4	ANO4	12	101381373	Missense_Mutation	SNP	T	TCGA-G3-A25Y-01A-11D-A16V-10	7576783	101381373	32470522	35	39683										
NCOR2	9612	hgsc.bcm.edu	37	chr12	124821719	124821753	+	Splice_Site	DEL	AGGTGGACCTGGGGGAGGAGAGAAGGCGGTCAGGC	AGGTGGACCTGGGGGAGGAGAGAAGGCGGTCAGGC	-													0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	gcgaacgggtgaggaggtggAggtggacctgggggaggaga					rs373637496|rs368900171		TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	AGGTGGACCTGGGGGAGGAGAGAAGGCGGTCAGGC	AGGTGGACCTGGGGGAGGAGAGAAGGCGGTCAGGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr12:124821719_124821753delAGGTGGACCTGGGGGAGGAGAGAAGGCGGTCAGGC	ENST00000405201.1	-	38	5688_5695	c.5688_5695delGCCTGACCGCCTTCTCTCCTCCCCCAGGTCCACCT	c.(5686-5697)aggcctgaccgc>aggc	p.RPDR1896fs	NCOR2_ENST00000397355.1_Splice_Site_p.RPDR1887fs|NCOR2_ENST00000404621.1_Splice_Site_p.RPDR1886fs|NCOR2_ENST00000429285.2_Splice_Site_p.RPDR1886fs|NCOR2_ENST00000356219.3_Splice_Site_p.RPDR1903fs|NCOR2_ENST00000404121.2_Splice_Site_p.RPDR1457fs			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1907					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		GAGGAGGTGGAGGTGGACCTGGGGGAGGAGAGAAGGCGGTCAGGCAGTCATGGGA	0.647																																					p.1896_1899del		Atlas-Indel,Pindel	.											.	NCOR2	475	.	0			c.5688_5696del						.																																			SO:0001630	splice_region_variant	9612	exon40			.	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"nuclear receptor co-repressor 2"			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.5688-1GCCTGACCGCCTTCTCTCCTCCCCCAGGTCCACCT>-	chr12.hg19:g.124821719_124821753delAGGTGGACCTGGGGGAGGAGAGAAGGCGGTCAGGC		298.0	0.0		129.0	16.0	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	In_Frame_Del	DEL	ENST00000405201.1	hg19	CCDS41858.2																																																																																			.	.		0.647	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312	Frame_Shift_Del	-	124821753	AGGTGGACCTGGGGGAGGAGAGAAGGCGGTCAGGC	-	124821719	8	5	277	1	0	1	0	1	0	0	1	0	10245	304	11	0	1889	0	NCOR2	12	124821719	Splice_Site	DEL	AGGTGGACCTGGGGGAGGAGAGAAGGCGGTCAGGC	TCGA-G3-A25Y-01A-11D-A16V-10	23440346	124821719	9030176	36	39684										
SKA3	221150	hgsc.bcm.edu	37	chr13	21742126	21742126	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	ccttttaacagagctgcttaCcttttattattcctcgcatt	4	11	0	1			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr13:21742126C>A	ENST00000314759.5	-	4	868		c.e4+1		SKA3_ENST00000400018.3_Splice_Site	NM_145061.5	NP_659498.4	Q8IX90	SKA3_HUMAN	spindle and kinetochore associated complex subunit 3						chromosome segregation (GO:0007059)|mitotic nuclear division (GO:0007067)|regulation of microtubule polymerization or depolymerization (GO:0031110)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|spindle microtubule (GO:0005876)				breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						GAGCTGCTTACCTTTTATTAT	0.284																																					.		Atlas-SNP	.											.	SKA3	76	.	0			c.743+1G>T						.						63	58	60					13																	21742126		2203	4297	6500	SO:0001630	splice_region_variant	221150	exon5			TGCTTACCTTTTA	AF361358	CCDS31946.1, CCDS53856.1	13q11	2013-01-17	2009-08-19	2009-08-19	ENSG00000165480	ENSG00000165480			20262	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 3"	C13orf3		19387489, 19289083, 19646878, 19360002	Standard	NM_145061		Approved	MGC4832, RAMA1	uc001unt.3	Q8IX90	OTTHUMG00000016539	ENST00000314759.5:c.743+1G>T	chr13.hg19:g.21742126C>A		65.0	0.0		91.0	8.0	NM_001166017	A2A330|A2A331|B2RBY2|Q5VZV5|Q86WR2|Q8NBG1|Q96D22	Splice_Site	SNP	ENST00000314759.5	hg19	CCDS31946.1	.	.	.	.	.	.	.	.	.	.	C	12.82	2.052163	0.36181	.	.	ENSG00000165480	ENST00000314759;ENST00000400018	.	.	.	5.86	5.86	0.93980	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.6803	0.77364	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SKA3	20640126	1.000000	0.71417	1.000000	0.80357	0.302000	0.27658	4.395000	0.59678	2.777000	0.95525	0.655000	0.94253	.	.	.		0.284	SKA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000272912.1	NM_145061	Intron	A	21742126	C	A	21742126	5	1	277	1	0	0	0	0	0	0	1	0	14369	521	18	3	565	3	SKA3	13	21742126	Splice_Site	SNP	C	TCGA-G3-A25Y-01A-11D-A16V-10		21742126	93427752	37	39685										
CENPJ	55835	hgsc.bcm.edu	37	chr13	25466801	25466801	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	cgcaagcttgtccttcttctCcacctcgaggctgctctcta	7	16	3	0			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr13:25466801C>A	ENST00000381884.4	-	10	3381	c.3196G>T	c.(3196-3198)Gag>Tag	p.E1066*	CENPJ_ENST00000545981.1_Nonsense_Mutation_p.E1066*	NM_018451.4	NP_060921.3	Q9HC77	CENPJ_HUMAN	centromere protein J	1066					cell division (GO:0051301)|centriole replication (GO:0007099)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|microtubule polymerization (GO:0046785)|mitotic cell cycle (GO:0000278)|regulation of centriole replication (GO:0046599)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|gamma-tubulin small complex (GO:0008275)|microtubule (GO:0005874)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|tubulin binding (GO:0015631)			endometrium(5)|kidney(4)|large_intestine(14)|lung(13)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.00793)|Epithelial(112;0.0411)|OV - Ovarian serous cystadenocarcinoma(117;0.139)		TCCTTCTTCTCCACCTCGAGG	0.517																																					p.E1066X		Atlas-SNP	.											.	CENPJ	116	.	0			c.G3196T						.						137	133	135					13																	25466801		2203	4300	6503	SO:0001587	stop_gained	55835	exon10			TCTTCTCCACCTC	AF139625	CCDS9310.1	13q12.12	2013-11-05			ENSG00000151849	ENSG00000151849			17272	protein-coding gene	gene with protein product	"centrosomal P4.1-associated protein"	609279	"microcephaly, primary autosomal recessive 6"	MCPH6		11003675, 22699936	Standard	NM_018451		Approved	CPAP, BM032, LAP, LIP1, Sas-4, SASS4, SCKL4	uc001upt.5	Q9HC77	OTTHUMG00000016595	ENST00000381884.4:c.3196G>T	chr13.hg19:g.25466801C>A	ENSP00000371308:p.Glu1066*	118.0	0.0		175.0	45.0	NM_018451	Q2KHM6|Q5JPD5|Q5T6R5|Q96KS5|Q9C067	Nonsense_Mutation	SNP	ENST00000381884.4	hg19	CCDS9310.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.999|8.999	0.979745|0.979745	0.18812|0.18812	.|.	.|.	ENSG00000151849|ENSG00000151849	ENST00000381884;ENST00000545981;ENST00000445729|ENST00000418179	.|.	.|.	.|.	4.43|4.43	-6.4|-6.4	0.01944|0.01944	.|.	3.307320|.	0.00890|.	N|.	0.002233|.	.|T	.|0.17831	.|0.0428	.|.	.|.	.|.	0.47123|0.47123	A|A	0.999326|0.999326	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.29243	.|-1.0018	.|3	0.10636|.	T|.	0.68|.	.|.	3.1467|3.1467	0.06474|0.06474	0.1362:0.155:0.1234:0.5855|0.1362:0.155:0.1234:0.5855	.|.	.|.	.|.	.|.	X|V	1066|147	.|.	ENSP00000371308:E1066X|.	E|G	-|-	1|2	0|0	CENPJ|CENPJ	24364801|24364801	0.384000|0.384000	0.25164|0.25164	0.000000|0.000000	0.03702|0.03702	0.024000|0.024000	0.10985|0.10985	0.729000|0.729000	0.26028|0.26028	-0.801000|-0.801000	0.04427|0.04427	-0.391000|-0.391000	0.06502|0.06502	GAG|GGA	.	.		0.517	CENPJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044209.1	NM_018451		A	25466801	C	A	25466801	4	1	277	1	0	0	0	0	0	1	0	0	3236	864	30	3	852	3	CENPJ	13	25466801	Nonsense_Mutation	SNP	C	TCGA-G3-A25Y-01A-11D-A16V-10	3724675	25466801	89703077	38	39686										
RB1	5925	hgsc.bcm.edu	37	chr13	48953728	48953728	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	ttttctttttgtttgtttgtAgcgatacaaacttggagttc	8	5	1	0			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr13:48953728A>G	ENST00000267163.4	+	14	1470		c.e14-1			NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1						androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(10)		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(DB00071)|Insulin Regular(DB00030)"	GTTTGTTTGTAGCGATACAAA	0.333		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)																											.		Atlas-SNP	.	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	RB1_ENST00000267163,NS,carcinoma,0,2	RB1	1068	.	25	Whole gene deletion(15)|Unknown(10)	bone(11)|breast(5)|central_nervous_system(2)|lung(2)|adrenal_gland(1)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	c.1333-2A>G	GRCh37	CS030552	RB1	S		.						18	19	19					13																	48953728		2200	4299	6499	SO:0001630	splice_region_variant	5925	exon14	Familial Cancer Database		GTTTGTAGCGATA	M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1333-1A>G	chr13.hg19:g.48953728A>G		109.0	0.0		143.0	48.0	NM_000321	A8K5E3|P78499|Q5VW46|Q8IZL4	Splice_Site	SNP	ENST00000267163.4	hg19	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.605344	0.87157	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	.	.	.	5.74	5.74	0.90152	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0294	0.80567	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	RB1	47851729	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.469000	0.90395	2.185000	0.69588	0.455000	0.32223	.	.	.		0.333	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1		Intron	G	48953728	A	G	48953728	5	3	277	1	0	0	0	0	0	0	1	0	13113	434	15	2	1385	2	RB1	13	48953728	Splice_Site	SNP	A	TCGA-G3-A25Y-01A-11D-A16V-10	23486927	48953728	66216150	39	39687										
LRFN5	145581	hgsc.bcm.edu	37	chr14	42356583	42356583	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	ttgtgaattgttgtggttgaGgcgtctgtccagagaagatg	15	4	1	4			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr14:42356583G>A	ENST00000298119.4	+	3	1944	c.755G>A	c.(754-756)aGg>aAg	p.R252K	LRFN5_ENST00000554171.1_Missense_Mutation_p.R252K|LRFN5_ENST00000554120.1_Missense_Mutation_p.R252K	NM_152447.3	NP_689660.2	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III domain containing 5	252	LRRCT.					integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(67)|ovary(5)|pancreas(3)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(2)	120			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		TTGTGGTTGAGGCGTCTGTCC	0.443										HNSCC(30;0.082)																											p.R252K		Atlas-SNP	.											.	LRFN5	269	.	0			c.G755A						.						171	170	170					14																	42356583		2203	4300	6503	SO:0001583	missense	145581	exon3			GGTTGAGGCGTCT	AK055365	CCDS9678.1	14q21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000165379	ENSG00000165379		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	20360	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 8"	612811	"chromosome 14 open reading frame 146"	C14orf146		16828986	Standard	NM_152447		Approved	FIGLER8, SALM5	uc001wvm.3	Q96NI6	OTTHUMG00000140261	ENST00000298119.4:c.755G>A	chr14.hg19:g.42356583G>A	ENSP00000298119:p.Arg252Lys	65.0	0.0		84.0	9.0	NM_152447	B3KU78|Q86XL2	Missense_Mutation	SNP	ENST00000298119.4	hg19	CCDS9678.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.937910	0.73557	.	.	ENSG00000165379	ENST00000298119;ENST00000554120;ENST00000554171	T;T;T	0.52057	0.68;0.68;0.68	5.69	5.69	0.88448	Cysteine-rich flanking region, C-terminal (1);	0.000000	0.64402	D	0.000006	T	0.67392	0.2888	M	0.66560	2.04	0.58432	D	0.999999	D;P	0.58970	0.984;0.947	D;D	0.69824	0.966;0.925	T	0.67007	-0.5779	10	0.52906	T	0.07	.	17.3157	0.87224	0.0:0.0:1.0:0.0	.	252;252	G3V364;Q96NI6	.;LRFN5_HUMAN	K	252	ENSP00000298119:R252K;ENSP00000451897:R252K;ENSP00000451067:R252K	ENSP00000298119:R252K	R	+	2	0	LRFN5	41426333	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.676000	0.91093	0.557000	0.71058	AGG	.	.		0.443	LRFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276786.1	NM_152447		A	42356583	G	A	42356583	3	1	277	1	0	0	0	0	1	0	0	0	8950	1000	35	3	757	3	LRFN5	14	42356583	Missense_Mutation	SNP	G	TCGA-G3-A25Y-01A-11D-A16V-10		42356583	64992957	40	39688										
IL21R	50615	hgsc.bcm.edu	37	chr16	27460454	27460454	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	gccggcctggatatggacacGtttgacagtggctttgtggg	16	8	0	1	rs56002407	byFrequency	TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr16:27460454G>T	ENST00000337929.3	+	9	1940	c.1467G>T	c.(1465-1467)acG>acT	p.T489T	IL21R_ENST00000395755.1_Silent_p.T489T|IL21R_ENST00000395754.4_Silent_p.T489T|IL21R-AS1_ENST00000563191.1_RNA|IL21R_ENST00000564089.1_Silent_p.T489T	NM_181078.2	NP_851564.1	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor	489					interleukin-21-mediated signaling pathway (GO:0038114)|natural killer cell activation (GO:0030101)	integral component of membrane (GO:0016021)	interleukin-21 receptor activity (GO:0001532)			breast(2)|large_intestine(3)|lung(1)|ovary(2)	8						ATATGGACACGTTTGACAGTG	0.677			T	BCL6	NHL																																p.T511T		Atlas-SNP	.		Dom	yes		16	16p11	50615	interleukin 21 receptor		L	.	IL21R	95	.	0			c.G1533T						.						47	41	43					16																	27460454		2196	4298	6494	SO:0001819	synonymous_variant	50615	exon10			GGACACGTTTGAC	AF254067	CCDS10630.1	16p11	2014-09-17			ENSG00000103522	ENSG00000103522		"Interleukins and interleukin receptors", "CD molecules"	6006	protein-coding gene	gene with protein product		605383				11081504	Standard	NM_181078		Approved	CD360	uc002dos.2	Q9HBE5	OTTHUMG00000131675	ENST00000337929.3:c.1467G>T	chr16.hg19:g.27460454G>T		48.0	0.0		22.0	11.0	NM_181079	A8K9E8|D3DWF7|Q96HZ1|Q9HB91	Silent	SNP	ENST00000337929.3	hg19	CCDS10630.1																																																																																			.	G|0.999;A|0.001		0.677	IL21R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254578.2	NM_181078		T	27460454	G	T	27460454	2	4	277	1	0	0	0	0	0	0	0	1	7680	1132	40	1		1	IL21R	16	27460454	Silent	SNP	G	TCGA-G3-A25Y-01A-11D-A16V-10		27460454	62894299	41	39689										
SLC38A7	55238	hgsc.bcm.edu	37	chr16	58706093	58706093	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	ccatgtcctccgagggatagGacaggagcacgtcaggatcc	13	12	1	0			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr16:58706093G>T	ENST00000570101.1	-	8	1821	c.938C>A	c.(937-939)tCc>tAc	p.S313Y	SLC38A7_ENST00000566953.1_5'UTR|SLC38A7_ENST00000564100.1_Intron|SLC38A7_ENST00000219320.4_Missense_Mutation_p.S313Y|SLC38A7_ENST00000564010.1_Missense_Mutation_p.S224Y			Q9NVC3	S38A7_HUMAN	solute carrier family 38, member 7	313					sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	L-alanine transmembrane transporter activity (GO:0015180)|L-amino acid transmembrane transporter activity (GO:0015179)|L-asparagine transmembrane transporter activity (GO:0015182)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|L-glutamine transmembrane transporter activity (GO:0015186)|L-histidine transmembrane transporter activity (GO:0005290)|L-leucine transmembrane transporter activity (GO:0015190)|L-methionine transmembrane transporter activity (GO:0015191)|L-serine transmembrane transporter activity (GO:0015194)			endometrium(1)|large_intestine(2)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	13						CGAGGGATAGGACAGGAGCAC	0.622																																					p.S313Y		Atlas-SNP	.											.	SLC38A7	26	.	0			c.C938A						.						50	40	43					16																	58706093		2187	4289	6476	SO:0001583	missense	55238	exon9			GGATAGGACAGGA	BC001961	CCDS10800.1	16q21	2013-05-22			ENSG00000103042	ENSG00000103042		"Solute carriers"	25582	protein-coding gene	gene with protein product		614236					Standard	XM_006721229		Approved	FLJ10815	uc002eod.1	Q9NVC3	OTTHUMG00000133491	ENST00000570101.1:c.938C>A	chr16.hg19:g.58706093G>T	ENSP00000454646:p.Ser313Tyr	80.0	0.0		52.0	26.0	NM_018231	Q53GJ9|Q9H9I5	Missense_Mutation	SNP	ENST00000570101.1	hg19	CCDS10800.1	.	.	.	.	.	.	.	.	.	.	G	32	5.151293	0.94645	.	.	ENSG00000103042	ENST00000219320	T	0.02812	4.15	5.36	5.36	0.76844	.	0.110975	0.64402	D	0.000004	T	0.16428	0.0395	M	0.77313	2.365	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	T	0.00215	-1.1911	9	.	.	.	.	18.0759	0.89427	0.0:0.0:1.0:0.0	.	313	Q9NVC3	S38A7_HUMAN	Y	313	ENSP00000219320:S313Y	.	S	-	2	0	SLC38A7	57263594	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	9.360000	0.97119	2.497000	0.84241	0.591000	0.81541	TCC	.	.		0.622	SLC38A7-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422206.2	NM_018231		T	58706093	G	T	58706093	3	4	277	1	0	0	0	0	1	0	0	0	14624	1174	41	3	466	3	SLC38A7	16	58706093	Missense_Mutation	SNP	G	TCGA-G3-A25Y-01A-11D-A16V-10	31245639	58706093	31648660	42	39690										
TMEM106A	113277	hgsc.bcm.edu	37	chr17	41368750	41368750	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	agctaccaagatacgggatgAaaacacatagtgagtacccc	9	10	0	3			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr17:41368750A>C	ENST00000331615.3	+	7	842	c.605A>C	c.(604-606)gAa>gCa	p.E202A	TMEM106A_ENST00000588659.1_Missense_Mutation_p.E202A|LINC00854_ENST00000595400.1_RNA|LINC00854_ENST00000593624.1_RNA|LINC00854_ENST00000427995.1_RNA|TMEM106A_ENST00000541594.1_Missense_Mutation_p.E154A|TMEM106A_ENST00000536052.1_Missense_Mutation_p.E155A	NM_145041.1	NP_659478.1	Q96A25	T106A_HUMAN	transmembrane protein 106A	202						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|endometrium(2)|large_intestine(1)|lung(6)|prostate(1)	11		Breast(137;0.0164)		BRCA - Breast invasive adenocarcinoma(366;0.0917)		ATACGGGATGAAAACACATAG	0.498																																					p.E202A		Atlas-SNP	.											.	TMEM106A	20	.	0			c.A605C						.						256	220	233					17																	41368750		2203	4296	6499	SO:0001583	missense	113277	exon7			GGGATGAAAACAC	AK056132	CCDS11462.1, CCDS74073.1	17q21.31	2012-01-23			ENSG00000184988	ENSG00000184988			28288	protein-coding gene	gene with protein product							Standard	XM_006721658		Approved	MGC20235	uc002idn.1	Q96A25		ENST00000331615.3:c.605A>C	chr17.hg19:g.41368750A>C	ENSP00000330774:p.Glu202Ala	104.0	0.0		151.0	19.0	NM_145041	A8K2X2|B7Z698	Missense_Mutation	SNP	ENST00000331615.3	hg19	CCDS11462.1	.	.	.	.	.	.	.	.	.	.	A	15.41	2.825993	0.50739	.	.	ENSG00000184988	ENST00000331615;ENST00000536052;ENST00000541594	T;T;T	0.24350	1.86;1.86;1.86	5.07	3.99	0.46301	.	0.694941	0.14548	N	0.312806	T	0.41073	0.1143	M	0.80982	2.52	0.31795	N	0.629097	P;P;P	0.51449	0.945;0.818;0.945	P;B;P	0.52672	0.706;0.3;0.706	T	0.50955	-0.8766	10	0.44086	T	0.13	13.3063	8.2242	0.31560	0.9073:0.0:0.0927:0.0	.	155;154;202	B7Z779;B7Z698;Q96A25	.;.;T106A_HUMAN	A	202;155;154	ENSP00000330774:E202A;ENSP00000439835:E155A;ENSP00000439844:E154A	ENSP00000330774:E202A	E	+	2	0	TMEM106A	38724276	0.998000	0.40836	1.000000	0.80357	0.972000	0.66771	2.384000	0.44362	2.028000	0.59812	0.533000	0.62120	GAA	.	.		0.498	TMEM106A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453470.2	NM_145041		C	41368750	A	C	41368750	3	2	277	1	0	0	0	0	1	0	0	0	16035	246	9	5	623	5	TMEM106A	17	41368750	Missense_Mutation	SNP	A	TCGA-G3-A25Y-01A-11D-A16V-10		41368750	39826460	43	39691										
PLEKHM1	9842	hgsc.bcm.edu	37	chr17	43559816	43559835	+	Frame_Shift_Del	DEL	TGGGGGTCCAGTCCATTCTC	TGGGGGTCCAGTCCATTCTC	-													0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	cacctaccgggatggcagccTgggggtccagtccattctcc					rs201283261		TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	TGGGGGTCCAGTCCATTCTC	TGGGGGTCCAGTCCATTCTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr17:43559816_43559835delTGGGGGTCCAGTCCATTCTC	ENST00000430334.3	-	2	149_168	c.16_35delGAGAATGGACTGGACCCCCA	c.(16-36)gagaatggactggacccccagfs	p.ENGLDPQ6fs	PLEKHM1_ENST00000421073.2_Start_Codon_Del	NM_014798.2	NP_055613.1	Q9Y4G2	PKHM1_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 1	6					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(6)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26	Renal(3;0.0405)					GATGGCAGCCTGGGGGTCCAGTCCATTCTCCACCACTGAA	0.582																																					p.6_12del		Pindel	.											.	PLEKHM1	69	.	0			c.17_36del						.																																			SO:0001589	frameshift_variant	9842	exon2			.	X85792	CCDS32671.1	17q21.31	2013-01-11				ENSG00000225190		"Pleckstrin homology (PH) domain containing"	29017	protein-coding gene	gene with protein product		611466				9205841, 12820725	Standard	NM_014798		Approved	KIAA0356	uc002ija.3	Q9Y4G2		ENST00000430334.3:c.16_35delGAGAATGGACTGGACCCCCA	chr17.hg19:g.43559816_43559835delTGGGGGTCCAGTCCATTCTC	ENSP00000389913:p.Glu6fs	140.0	0.0		142.0	10.0	NM_014798	Q6P2R5|Q8TEL9|Q9NPP5|Q9NYA0	Frame_Shift_Del	DEL	ENST00000430334.3	hg19	CCDS32671.1																																																																																			.	.		0.582	PLEKHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444659.1	NM_014798		-	43559835	TGGGGGTCCAGTCCATTCTC	-	43559816	7	5	277	1	0	1	0	1	0	0	0	0	12089	1580	55	0	3179	0	PLEKHM1	17	43559816	Frame_Shift_Del	DEL	TGGGGGTCCAGTCCATTCTC	TCGA-G3-A25Y-01A-11D-A16V-10	2191066	43559816	37635394	44	39692										
SPATA20	64847	hgsc.bcm.edu	37	chr17	48629417	48629417	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	gaggcctcacaggagagtgcGtggctcgagtgggctctgcg	18	10	2	1			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr17:48629417G>A	ENST00000356488.4	+	13	1868	c.1785G>A	c.(1783-1785)gcG>gcA	p.A595A	SPATA20_ENST00000393244.3_Silent_p.A551A|SPATA20_ENST00000511937.1_3'UTR|SPATA20_ENST00000006658.6_Silent_p.A611A	NM_001258372.1	NP_001245301.1	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20	595					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)	catalytic activity (GO:0003824)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;9.38e-09)			AGGAGAGTGCGTGGCTCGAGT	0.657																																					p.A611A		Atlas-SNP	.											.	SPATA20	59	.	0			c.G1833A						.						31	35	33					17																	48629417		2202	4299	6501	SO:0001819	synonymous_variant	64847	exon14			GAGTGCGTGGCTC		CCDS11571.1, CCDS58563.1, CCDS58564.1	17q21.33	2011-03-17			ENSG00000006282	ENSG00000006282			26125	protein-coding gene	gene with protein product	"hypothetical protein FLJ21347"	613939				12477932	Standard	NM_022827		Approved	FLJ21347, SSP411, Tisp78	uc002ird.3	Q8TB22	OTTHUMG00000162162	ENST00000356488.4:c.1785G>A	chr17.hg19:g.48629417G>A		108.0	0.0		121.0	20.0	NM_022827	Q2TA99|Q2XUZ6|Q6P0P1|Q8WVW3|Q9H747	Silent	SNP	ENST00000356488.4	hg19	CCDS58563.1																																																																																			.	.		0.657	SPATA20-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367651.1	NM_022827		A	48629417	G	A	48629417	2	1	277	1	0	0	0	0	0	0	0	1	15021	1132	40	1		1	SPATA20	17	48629417	Silent	SNP	G	TCGA-G3-A25Y-01A-11D-A16V-10	5069601	48629417	32565793	45	39693										
GH2	2689	hgsc.bcm.edu	37	chr17	61957832	61957832	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	ttgtgtcaaacttgctgtagGactgattgaagatctgccca	10	8	2	3			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr17:61957832G>T	ENST00000423893.2	-	5	564	c.503C>A	c.(502-504)tCc>tAc	p.S168Y	GH2_ENST00000332800.7_Silent_p.V252V|GH2_ENST00000449787.2_Missense_Mutation_p.S153Y|GH2_ENST00000456543.2_Missense_Mutation_p.P167T			P01242	SOM2_HUMAN	growth hormone 2	168					JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			breast(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	24						CTTGCTGTAGGACTGATTGAA	0.542																																					p.S168Y		Atlas-SNP	.											.	GH2	73	.	0			c.C503A						.						189	157	168					17																	61957832		2203	4300	6503	SO:0001583	missense	2689	exon5			CTGTAGGACTGAT	J03756	CCDS11647.1, CCDS11648.1, CCDS45757.1, CCDS45758.1	17q22-q24	2014-01-30						"Endogenous ligands"	4262	protein-coding gene	gene with protein product	"placental-specific growth hormone", "placenta-specific growth hormone"	139240				6306568	Standard	NM_002059		Approved	GH-V, GHV, GHL, hGH-V	uc002jcl.2	P01242		ENST00000423893.2:c.503C>A	chr17.hg19:g.61957832G>T	ENSP00000409294:p.Ser168Tyr	216.0	0.0		241.0	48.0	NM_002059	B1A4H5|B1A4H7|O14643|O14644|P09587	Missense_Mutation	SNP	ENST00000423893.2	hg19	CCDS11647.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	11.41|11.41	1.631433|1.631433	0.28978|0.28978	.|.	.|.	ENSG00000136487|ENSG00000136487	ENST00000456543|ENST00000423893;ENST00000449787	D|D;D	0.90844|0.87029	-2.74|-2.2;-2.2	2.74|2.74	2.74|2.74	0.32292|0.32292	.|Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	.|.	.|.	.|.	.|.	D|D	0.88291|0.88291	0.6397|0.6397	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	B|B;B	0.12630|0.26744	0.006|0.158;0.013	B|B;B	0.12156|0.42495	0.007|0.389;0.06	D|D	0.88642|0.88642	0.3176|0.3176	8|8	0.54805|0.87932	T|D	0.06|0	.|.	12.4782|12.4782	0.55827|0.55827	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	167|168;153	O14644|P01242;O14643	.|SOM2_HUMAN;.	T|Y	167|168;153	ENSP00000394122:P167T|ENSP00000409294:S168Y;ENSP00000410618:S153Y	ENSP00000394122:P167T|ENSP00000409294:S168Y	P|S	-|-	1|2	0|0	GH2|GH2	59311564|59311564	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.022000|0.022000	0.10575|0.10575	6.244000|6.244000	0.72391|0.72391	1.531000|1.531000	0.49152|0.49152	0.306000|0.306000	0.20318|0.20318	CCT|TCC	.	.		0.542	GH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417665.1	NM_002059		T	61957832	G	T	61957832	3	4	277	1	0	0	0	0	1	0	0	0	6376	1174	41	3	242	3	GH2	17	61957832	Missense_Mutation	SNP	G	TCGA-G3-A25Y-01A-11D-A16V-10	13328415	61957832	19237378	46	39694										
EVPL	2125	hgsc.bcm.edu	37	chr17	74019605	74019605	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	tctcaatctcctcagcctgcGggtgcttgagccgccgggcc	12	16	3	1			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr17:74019605G>T	ENST00000301607.3	-	3	582	c.329C>A	c.(328-330)cCg>cAg	p.P110Q	EVPL_ENST00000586740.1_Missense_Mutation_p.P110Q	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	110	Globular 1.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						CTCAGCCTGCGGGTGCTTGAG	0.667																																					p.P110Q		Atlas-SNP	.											.	EVPL	155	.	0			c.C329A						.						33	42	39					17																	74019605		2202	4299	6501	SO:0001583	missense	2125	exon3			GCCTGCGGGTGCT	U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.329C>A	chr17.hg19:g.74019605G>T	ENSP00000301607:p.Pro110Gln	65.0	0.0		68.0	23.0	NM_001988	A0AUV5	Missense_Mutation	SNP	ENST00000301607.3	hg19	CCDS11737.1	.	.	.	.	.	.	.	.	.	.	G	19.91	3.914910	0.72983	.	.	ENSG00000167880	ENST00000301607	T	0.66280	-0.2	4.66	3.67	0.42095	.	0.056975	0.64402	D	0.000001	T	0.73992	0.3658	M	0.64170	1.965	0.46701	D	0.999163	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.75505	-0.3294	10	0.87932	D	0	-40.3397	10.5343	0.44994	0.0756:0.1326:0.7918:0.0	.	110;110	B7ZLH8;Q92817	.;EVPL_HUMAN	Q	110	ENSP00000301607:P110Q	ENSP00000301607:P110Q	P	-	2	0	EVPL	71531200	1.000000	0.71417	0.999000	0.59377	0.957000	0.61999	6.067000	0.71193	1.070000	0.40811	0.561000	0.74099	CCG	.	.		0.667	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988		T	74019605	G	T	74019605	3	4	277	1	0	0	0	0	1	0	0	0	5294	1116	39	1	5852	1	EVPL	17	74019605	Missense_Mutation	SNP	G	TCGA-G3-A25Y-01A-11D-A16V-10	12061773	74019605	7175605	47	39695										
GATA6	2627	hgsc.bcm.edu	37	chr18	19780725	19780725	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	cataggcgtcagtctcgcctCgccggccgaagtcacgtcct	11	16	3	0			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr18:19780725C>T	ENST00000269216.3	+	7	2004	c.1727C>T	c.(1726-1728)tCg>tTg	p.S576L	GATA6_ENST00000581694.1_Missense_Mutation_p.S576L|RP11-627G18.1_ENST00000583442.1_RNA	NM_005257.4	NP_005248.2	Q92908	GATA6_HUMAN	GATA binding protein 6	576					blood coagulation (GO:0007596)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac vascular smooth muscle cell differentiation (GO:0060947)|cellular response to BMP stimulus (GO:0071773)|cellular response to gonadotropin stimulus (GO:0071371)|cellular response to hypoxia (GO:0071456)|Clara cell differentiation (GO:0060486)|endodermal cell fate determination (GO:0007493)|in utero embryonic development (GO:0001701)|intestinal epithelial cell differentiation (GO:0060575)|liver development (GO:0001889)|lung saccule development (GO:0060430)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta1 production (GO:0032911)|negative regulation of transforming growth factor beta2 production (GO:0032912)|organ formation (GO:0048645)|outflow tract septum morphogenesis (GO:0003148)|pancreatic A cell differentiation (GO:0003310)|phospholipid metabolic process (GO:0006644)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to growth factor (GO:0070848)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)|tube morphogenesis (GO:0035239)|type B pancreatic cell differentiation (GO:0003309)|Type II pneumocyte differentiation (GO:0060510)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	18	all_cancers(21;0.00271)|all_epithelial(16;7.31e-05)|Ovarian(2;0.116)|Lung NSC(20;0.123)|all_lung(20;0.246)		STAD - Stomach adenocarcinoma(5;0.106)			AGTCTCGCCTCGCCGGCCGAA	0.682																																					p.S576L	Colon(8;48 282 46199 46856)|Melanoma(177;170 2725 12489 26999)	Atlas-SNP	.											.	GATA6	35	.	0			c.C1727T						.						68	52	57					18																	19780725		2203	4300	6503	SO:0001583	missense	2627	exon7			TCGCCTCGCCGGC	U66075	CCDS11872.1	18q11-q12	2013-01-25	2001-11-28		ENSG00000141448	ENSG00000141448		"GATA zinc finger domain containing"	4174	protein-coding gene	gene with protein product		601656	"GATA-binding protein 6"			8975704	Standard	XM_005258248		Approved		uc002ktt.2	Q92908	OTTHUMG00000131767	ENST00000269216.3:c.1727C>T	chr18.hg19:g.19780725C>T	ENSP00000269216:p.Ser576Leu	41.0	0.0		45.0	12.0	NM_005257	B0YJ17|P78327	Missense_Mutation	SNP	ENST00000269216.3	hg19	CCDS11872.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.278368	0.80692	.	.	ENSG00000141448	ENST00000269216	D	0.98075	-4.7	5.81	4.94	0.65067	.	0.295719	0.33057	N	0.005323	D	0.96349	0.8809	M	0.66939	2.045	0.54753	D	0.999981	B	0.24768	0.111	B	0.14578	0.011	D	0.94761	0.7936	10	0.66056	D	0.02	-15.671	14.8494	0.70284	0.0:0.9314:0.0:0.0686	.	576	Q92908	GATA6_HUMAN	L	576	ENSP00000269216:S576L	ENSP00000269216:S576L	S	+	2	0	GATA6	18034723	0.998000	0.40836	0.729000	0.30791	0.967000	0.64934	3.730000	0.55006	1.467000	0.48044	0.655000	0.94253	TCG	.	.		0.682	GATA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254696.1	NM_005257		T	19780725	C	T	19780725	3	4	277	1	0	0	0	0	1	0	0	0	6266	893	31	1	1749	1	GATA6	18	19780725	Missense_Mutation	SNP	C	TCGA-G3-A25Y-01A-11D-A16V-10		19780725	58296523	48	39696										
DOCK6	57572	hgsc.bcm.edu	37	chr19	11339690	11339690	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	gctgctgaccacccactgcaGagccagctcctcgtgaagca	10	16	0	3			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr19:11339690G>A	ENST00000294618.7	-	23	2751	c.2740C>T	c.(2740-2742)Ctg>Ttg	p.L914L	DOCK6_ENST00000319867.7_Silent_p.L253L	NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	914					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(8)|liver(2)|lung(9)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	39						ACCCACTGCAGAGCCAGCTCC	0.647																																					p.L914L		Atlas-SNP	.											.	DOCK6	104	.	0			c.C2740T						.						32	37	35					19																	11339690		2139	4249	6388	SO:0001819	synonymous_variant	57572	exon23			ACTGCAGAGCCAG		CCDS45975.1	19p13.2	2011-08-04			ENSG00000130158	ENSG00000130158			19189	protein-coding gene	gene with protein product		614194				12432077	Standard	NM_020812		Approved	KIAA1395, ZIR1	uc002mqs.5	Q96HP0		ENST00000294618.7:c.2740C>T	chr19.hg19:g.11339690G>A		51.0	0.0		37.0	15.0	NM_020812	A6H8X5|Q7Z7P4|Q9P2F2	Silent	SNP	ENST00000294618.7	hg19	CCDS45975.1																																																																																			.	.		0.647	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812		A	11339690	G	A	11339690	2	1	277	1	0	0	0	0	0	0	0	1	4693	933	33	3		3	DOCK6	19	11339690	Silent	SNP	G	TCGA-G3-A25Y-01A-11D-A16V-10		11339690	47789293	49	39697										
PDGFB	5155	hgsc.bcm.edu	37	chr22	39621841	39621841	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	ccgaatggtcacccgagtttGgggcgttttggctgcacaag	14	10	1	0			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chr22:39621841G>A	ENST00000331163.6	-	6	1400	c.613C>T	c.(613-615)Caa>Taa	p.Q205*	PDGFB_ENST00000381551.4_Nonsense_Mutation_p.Q190*	NM_002608.2	NP_002599.1	P01127	PDGFB_HUMAN	platelet-derived growth factor beta polypeptide	205					actin cytoskeleton organization (GO:0030036)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|blood coagulation (GO:0007596)|blood vessel morphogenesis (GO:0048514)|branching involved in salivary gland morphogenesis (GO:0060445)|cell chemotaxis (GO:0060326)|cell growth (GO:0016049)|cell projection assembly (GO:0030031)|cellular response to growth factor stimulus (GO:0071363)|cellular response to mycophenolic acid (GO:0071506)|DNA replication (GO:0006260)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|extracellular matrix organization (GO:0030198)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|metanephric glomerular endothelium development (GO:0072264)|metanephric glomerular mesangial cell development (GO:0072255)|metanephric glomerular mesangial cell proliferation involved in metanephros development (GO:0072262)|monocyte chemotaxis (GO:0002548)|negative regulation of cell migration (GO:0030336)|negative regulation of phosphatidylinositol biosynthetic process (GO:0010512)|negative regulation of platelet activation (GO:0010544)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|paracrine signaling (GO:0038001)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemotaxis (GO:0050921)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of DNA replication (GO:0045740)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of glomerular filtration (GO:0003104)|positive regulation of glomerular mesangial cell proliferation (GO:0072126)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of metanephric mesenchymal cell migration (GO:2000591)|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|response to wounding (GO:0009611)|substrate-dependent cell migration (GO:0006929)|transforming growth factor beta receptor signaling pathway (GO:0007179)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi membrane (GO:0000139)|platelet alpha granule lumen (GO:0031093)	chemoattractant activity (GO:0042056)|collagen binding (GO:0005518)|growth factor activity (GO:0008083)|identical protein binding (GO:0042802)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|superoxide-generating NADPH oxidase activator activity (GO:0016176)		COL1A1/PDGFB(429)	central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(2)	7	Melanoma(58;0.04)					ACCCGAGTTTGGGGCGTTTTG	0.592			T	COL1A1	DFSP																																p.Q205X		Atlas-SNP	.		Dom	yes		22	22q12.3-q13.1	5155	platelet-derived growth factor beta polypeptide (simian sarcoma viral (v-sis) oncogene homolog)		M	.	PDGFB	91	.	0			c.C613T						.						81	69	73					22																	39621841		2203	4300	6503	SO:0001587	stop_gained	5155	exon6			GAGTTTGGGGCGT		CCDS13987.1, CCDS33650.1	22q13.1	2012-10-02	2011-05-19		ENSG00000100311	ENSG00000100311			8800	protein-coding gene	gene with protein product	"oncogene SIS", "becaplermin"	190040	"platelet-derived growth factor beta polypeptide (simian sarcoma viral (v-sis) oncogene homolog)"	SIS		2991848, 1661670	Standard	NM_002608		Approved	SSV	uc003axf.3	P01127	OTTHUMG00000151029	ENST00000331163.6:c.613C>T	chr22.hg19:g.39621841G>A	ENSP00000330382:p.Gln205*	69.0	0.0		81.0	13.0	NM_002608	G3XAG8|P78431|Q15354|Q6FHE7|Q9UF23	Nonsense_Mutation	SNP	ENST00000331163.6	hg19	CCDS13987.1	.	.	.	.	.	.	.	.	.	.	G	43	10.183253	0.99354	.	.	ENSG00000100311	ENST00000331163;ENST00000381551	.	.	.	5.04	4.01	0.46588	.	0.531612	0.19911	N	0.103299	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25751	T	0.34	-16.7667	11.9389	0.52888	0.0:0.0:0.8258:0.1742	.	.	.	.	X	205;190	.	ENSP00000330382:Q205X	Q	-	1	0	PDGFB	37951787	1.000000	0.71417	0.987000	0.45799	0.934000	0.57294	4.089000	0.57685	1.350000	0.45770	-0.181000	0.13052	CAA	.	.		0.592	PDGFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321043.1	NM_002608		A	39621841	G	A	39621841	4	1	277	1	0	0	0	0	0	1	0	0	11667	1357	47	3	116	3	PDGFB	22	39621841	Nonsense_Mutation	SNP	G	TCGA-G3-A25Y-01A-11D-A16V-10		39621841	11682725	50	39698										
TLR8	51311	hgsc.bcm.edu	37	chrX	12937428	12937428	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	tcaagggctgcaaaatctcaCtaaaataaatctaaaccaca	4	10	3	0			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chrX:12937428C>G	ENST00000218032.6	+	2	356	c.269C>G	c.(268-270)aCt>aGt	p.T90S	TLR8_ENST00000311912.5_Missense_Mutation_p.T108S	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	90					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	CAAAATCTCACTAAAATAAAT	0.418																																					p.T90S		Atlas-SNP	.											.	TLR8	134	.	0			c.C269G						.						113	113	113					X																	12937428		2203	4300	6503	SO:0001583	missense	51311	exon2			ATCTCACTAAAAT	AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"CD molecules"	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.269C>G	chrX.hg19:g.12937428C>G	ENSP00000218032:p.Thr90Ser	112.0	0.0		144.0	49.0	NM_138636	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Missense_Mutation	SNP	ENST00000218032.6	hg19	CCDS14152.1	.	.	.	.	.	.	.	.	.	.	C	14.71	2.615897	0.46631	.	.	ENSG00000101916	ENST00000218032;ENST00000311912	T;T	0.57107	0.42;0.42	5.2	3.41	0.39046	.	0.199084	0.25388	N	0.031036	T	0.57446	0.2054	L	0.45051	1.395	0.09310	N	1	D;D	0.67145	0.982;0.996	P;D	0.66979	0.823;0.948	T	0.47749	-0.9093	10	0.59425	D	0.04	.	4.9567	0.14044	0.1425:0.5564:0.0:0.301	.	90;108	Q9NR97;D1CS70	TLR8_HUMAN;.	S	90;108	ENSP00000218032:T90S;ENSP00000312082:T108S	ENSP00000218032:T90S	T	+	2	0	TLR8	12847349	0.094000	0.21725	0.002000	0.10522	0.908000	0.53690	0.887000	0.28254	0.418000	0.25898	0.523000	0.50628	ACT	.	.		0.418	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610		G	12937428	C	G	12937428	3	3	277	1	0	0	0	0	1	0	0	0	15972	565	20	4	275	4	TLR8	23	12937428	Missense_Mutation	SNP	C	TCGA-G3-A25Y-01A-11D-A16V-10		12937428	142333132	51	39699										
GLUD2	2747	hgsc.bcm.edu	37	chrX	120182439	120182439	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0769230769230769	4	1	1.21188878235858	1.06040268456376	1.27248322147651	0.485714285714286	1	0	gaatgacaccagggtttagaGataaaacatttgttgttcag	10	5	1	2			TCGA-G3-A25Y-01A-11D-A16V-10	TCGA-G3-A25Y-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6b50391f-d890-4ca0-b942-beab0f8bf1c9	9cfc4adf-3fd0-4f1f-b9e1-5f7a6e1469df	g.chrX:120182439G>A	ENST00000328078.1	+	1	978	c.901G>A	c.(901-903)Gat>Aat	p.D301N		NM_012084.3	NP_036216.2	P49448	DHE4_HUMAN	glutamate dehydrogenase 2	301					glutamate biosynthetic process (GO:0006537)|glutamate catabolic process (GO:0006538)|glutamate metabolic process (GO:0006536)|oxidation-reduction process (GO:0055114)	mitochondrion (GO:0005739)	ADP binding (GO:0043531)|glutamate dehydrogenase (NAD+) activity (GO:0004352)|glutamate dehydrogenase [NAD(P)+] activity (GO:0004353)|GTP binding (GO:0005525)|leucine binding (GO:0070728)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|urinary_tract(1)	38						AGGGTTTAGAGATAAAACATT	0.408																																					p.D301N		Atlas-SNP	.											.	GLUD2	89	.	0			c.G901A						.						198	178	185					X																	120182439		2203	4300	6503	SO:0001583	missense	2747	exon1			TTTAGAGATAAAA	U08997	CCDS14603.1	Xq24-q25	2008-02-05	2003-02-24	2003-02-28	ENSG00000182890	ENSG00000182890			4336	protein-coding gene	gene with protein product		300144	"glutamate dehydrogenase pseudogene 1"	GLUDP1		8207021, 9109504	Standard	NM_012084		Approved		uc004eto.3	P49448	OTTHUMG00000022320	ENST00000328078.1:c.901G>A	chrX.hg19:g.120182439G>A	ENSP00000327589:p.Asp301Asn	298.0	0.0		379.0	96.0	NM_012084	B2R8G0|Q9UDQ4	Missense_Mutation	SNP	ENST00000328078.1	hg19	CCDS14603.1	.	.	.	.	.	.	.	.	.	.	G	12.63	1.996636	0.35226	.	.	ENSG00000182890	ENST00000328078	D	0.96522	-4.04	2.3	0.373	0.16178	Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal (2);NAD(P)-binding domain (1);	0.091849	0.64402	D	0.000001	D	0.92041	0.7478	L	0.41124	1.26	0.43593	D	0.995942	B	0.20052	0.041	B	0.27262	0.078	D	0.83479	0.0063	10	0.54805	T	0.06	-2.2924	5.9678	0.19334	0.3085:0.0:0.6915:0.0	.	301	P49448	DHE4_HUMAN	N	301	ENSP00000327589:D301N	ENSP00000327589:D301N	D	+	1	0	GLUD2	120010120	1.000000	0.71417	0.720000	0.30636	0.938000	0.57974	6.619000	0.74219	-0.116000	0.11893	0.472000	0.43445	GAT	.	.		0.408	GLUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058133.1	NM_012084		A	120182439	G	A	120182439	3	1	277	1	0	0	0	0	1	0	0	0	6485	942	33	3	903	3	GLUD2	23	120182439	Missense_Mutation	SNP	G	TCGA-G3-A25Y-01A-11D-A16V-10	107245011	120182439	35088121	52	39700										
CHD5	26038	hgsc.bcm.edu	37	chr1	6196807	6196807	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	ccttggactggttgttcttgAggcggtgggcctcatctacc	13	11	3	1			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr1:6196807A>T	ENST00000262450.3	-	16	2654	c.2555T>A	c.(2554-2556)cTc>cAc	p.L852H	CHD5_ENST00000378021.1_5'UTR	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5	0					tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		GTTGTTCTTGAGGCGGTGGGC	0.657																																					p.L852H		Atlas-SNP	.											.	CHD5	267	.	0			c.T2555A						.						38	41	40					1																	6196807		2203	4300	6503	SO:0001583	missense	26038	exon16			TTCTTGAGGCGGT	AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"Zinc fingers, PHD-type"	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.2555T>A	chr1.hg19:g.6196807A>T	ENSP00000262450:p.Leu852His	80.0	0.0		53.0	17.0	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Missense_Mutation	SNP	ENST00000262450.3	hg19	CCDS57.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.055912	0.76074	.	.	ENSG00000116254	ENST00000262450;ENST00000378006;ENST00000536802;ENST00000538279	D	0.95482	-3.72	4.57	4.57	0.56435	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.56097	D	0.000024	D	0.98321	0.9443	H	0.95043	3.615	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99548	1.0965	10	0.87932	D	0	-28.3778	14.2217	0.65830	1.0:0.0:0.0:0.0	.	852	Q8TDI0	CHD5_HUMAN	H	852;368;260;260	ENSP00000262450:L852H	ENSP00000262450:L852H	L	-	2	0	CHD5	6119394	1.000000	0.71417	1.000000	0.80357	0.841000	0.47740	9.223000	0.95203	1.828000	0.53243	0.260000	0.18958	CTC	.	.		0.657	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557		T	6196807	A	T	6196807	3	4	278	1	0	0	0	0	1	0	0	0	3330	304	11	4	3413	4	CHD5	1	6196807	Missense_Mutation	SNP	A	TCGA-G3-A25Z-01A-11D-A16V-10		6196807	243053814	1	39701										
UBAP2L	9898	hgsc.bcm.edu	37	chr1	154221748	154221748	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	ggaaaggatttggtgatgtcGgtgaagctaaaggcggcagt	17	4	0	2	rs200980910		TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr1:154221748G>T	ENST00000361546.2	+	11	1090	c.1048G>T	c.(1048-1050)Ggt>Tgt	p.G350C	UBAP2L_ENST00000343815.6_Missense_Mutation_p.G350C|UBAP2L_ENST00000428931.1_Missense_Mutation_p.G350C|UBAP2L_ENST00000271877.7_Missense_Mutation_p.G361C			Q14157	UBP2L_HUMAN	ubiquitin associated protein 2-like	350					binding of sperm to zona pellucida (GO:0007339)		poly(A) RNA binding (GO:0044822)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(20)|ovary(1)|prostate(1)|urinary_tract(2)	50	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			TGGTGATGTCGGTGAAGCTAA	0.488																																					p.G350C		Atlas-SNP	.											.	UBAP2L	197	.	0			c.G1048T						.						151	144	146					1																	154221748		2203	4300	6503	SO:0001583	missense	9898	exon12			GATGTCGGTGAAG	BC003170	CCDS1063.1, CCDS44229.1, CCDS72925.1	1q21.3	2008-02-05			ENSG00000143569	ENSG00000143569			29877	protein-coding gene	gene with protein product						8590280, 11230159	Standard	NM_014847		Approved	NICE-4, KIAA0144	uc001fep.4	Q14157	OTTHUMG00000035983	ENST00000361546.2:c.1048G>T	chr1.hg19:g.154221748G>T	ENSP00000355343:p.Gly350Cys	170.0	0.0		231.0	13.0	NM_001127320	B4E0U8|Q5VU75|Q5VU76|Q9BTU3|Q9UGL2|Q9UGL3|Q9UGL4|Q9UGL5	Missense_Mutation	SNP	ENST00000361546.2	hg19	CCDS1063.1	.	.	.	.	.	.	.	.	.	.	G	15.13	2.743326	0.49151	.	.	ENSG00000143569	ENST00000343815;ENST00000428931;ENST00000271877;ENST00000361546	T;T;T;T	0.14391	2.51;2.51;2.53;2.51	5.36	3.5	0.40072	.	0.167732	0.53938	D	0.000055	T	0.20047	0.0482	M	0.62723	1.935	0.58432	D	0.999994	P;D;D;D;D	0.89917	0.945;1.0;1.0;1.0;0.984	P;D;D;D;P	0.79784	0.599;0.993;0.954;0.954;0.79	T	0.01127	-1.1443	10	0.72032	D	0.01	0.1059	9.6731	0.40023	0.1592:0.0:0.8408:0.0	.	264;361;343;350;350	B4DZJ6;F8W726;Q14157-4;Q14157-1;Q14157	.;.;.;.;UBP2L_HUMAN	C	350;350;361;350	ENSP00000345308:G350C;ENSP00000389445:G350C;ENSP00000271877:G361C;ENSP00000355343:G350C	ENSP00000271877:G361C	G	+	1	0	UBAP2L	152488372	1.000000	0.71417	0.559000	0.28332	0.867000	0.49689	3.240000	0.51368	0.828000	0.34709	-0.140000	0.14226	GGT	.	G|1.000;A|0.000		0.488	UBAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087673.1	NM_014847		T	154221748	G	T	154221748	3	4	278	1	0	0	0	0	1	0	0	0	16853	1116	39	1	1090	1	UBAP2L	1	154221748	Missense_Mutation	SNP	G	TCGA-G3-A25Z-01A-11D-A16V-10	148024941	154221748	95028873	2	39702										
TNN	63923	hgsc.bcm.edu	37	chr1	175048705	175048705	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	acggcgagtgcgtgcgcggcGtgtgccagtgccacgaagac	17	12	0	1			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr1:175048705G>A	ENST00000239462.4	+	3	759	c.646G>A	c.(646-648)Gtg>Atg	p.V216M		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	216	EGF-like 2.				axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		CGTGCGCGGCGTGTGCCAGTG	0.687																																					p.V216M		Atlas-SNP	.											TNN,caecum,carcinoma,0,1	TNN	297	.	0			c.G646A						.						17	14	15					1																	175048705		2191	4281	6472	SO:0001583	missense	63923	exon3			CGCGGCGTGTGCC	AK127044	CCDS30943.1	1q23-q24	2013-02-11			ENSG00000120332	ENSG00000120332		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	22942	protein-coding gene	gene with protein product							Standard	NM_022093		Approved		uc001gkl.1	Q9UQP3	OTTHUMG00000034882	ENST00000239462.4:c.646G>A	chr1.hg19:g.175048705G>A	ENSP00000239462:p.Val216Met	55.0	0.0		54.0	26.0	NM_022093	B9EGP3|Q5R360	Missense_Mutation	SNP	ENST00000239462.4	hg19	CCDS30943.1	.	.	.	.	.	.	.	.	.	.	G	8.785	0.929247	0.18131	.	.	ENSG00000120332	ENST00000239462;ENST00000539081	T	0.11277	2.79	4.7	2.79	0.32731	EGF, extracellular (1);	0.547782	0.19947	N	0.102520	T	0.18087	0.0434	M	0.70275	2.135	0.09310	N	1	D;P	0.54964	0.969;0.677	P;B	0.48840	0.592;0.266	T	0.05835	-1.0861	10	0.49607	T	0.09	.	9.8927	0.41300	0.0782:0.1397:0.782:0.0	.	216;216	B3KXB6;Q9UQP3	.;TENN_HUMAN	M	216	ENSP00000239462:V216M	ENSP00000239462:V216M	V	+	1	0	TNN	173315328	0.000000	0.05858	0.030000	0.17652	0.271000	0.26615	0.219000	0.17641	0.497000	0.27926	0.491000	0.48974	GTG	.	.		0.687	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527		A	175048705	G	A	175048705	3	1	278	1	0	0	0	0	1	0	0	0	16338	1145	40	1	652	1	TNN	1	175048705	Missense_Mutation	SNP	G	TCGA-G3-A25Z-01A-11D-A16V-10	20826957	175048705	74201916	3	39703										
CEP350	9857	hgsc.bcm.edu	37	chr1	180064893	180064893	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	atgtgaaacattattggcagTcccccatactgcagaagaag	9	9	0	3			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr1:180064893T>C	ENST00000367607.3	+	35	9165	c.8747T>C	c.(8746-8748)gTc>gCc	p.V2916A	CEP350_ENST00000490141.1_3'UTR	NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	2916					microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						TTATTGGCAGTCCCCCATACT	0.388																																					p.V2916A		Atlas-SNP	.											.	CEP350	418	.	0			c.T8747C						.						100	95	97					1																	180064893		2203	4300	6503	SO:0001583	missense	9857	exon35			TGGCAGTCCCCCA	AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"centrosome associated protein 350"					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.8747T>C	chr1.hg19:g.180064893T>C	ENSP00000356579:p.Val2916Ala	73.0	0.0		140.0	32.0	NM_014810	O75068|Q8TDK3|Q8WY20	Missense_Mutation	SNP	ENST00000367607.3	hg19	CCDS1336.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.471563	0.84533	.	.	ENSG00000135837	ENST00000367607;ENST00000417046	T	0.72615	-0.67	5.98	5.98	0.97165	.	0.167110	0.27802	N	0.017792	D	0.84229	0.5426	M	0.77103	2.36	0.58432	D	0.999995	D;D	0.76494	0.994;0.999	D;D	0.75484	0.97;0.986	D	0.84706	0.0731	9	.	.	.	.	16.4566	0.84019	0.0:0.0:0.0:1.0	.	2916;2916	E7EU22;Q5VT06	.;CE350_HUMAN	A	2916;380	ENSP00000356579:V2916A	.	V	+	2	0	CEP350	178331516	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.519000	0.73768	2.293000	0.77203	0.477000	0.44152	GTC	.	.		0.388	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810		C	180064893	T	C	180064893	3	2	278	1	0	0	0	0	1	0	0	0	3256	1667	58	2	8881	2	CEP350	1	180064893	Missense_Mutation	SNP	T	TCGA-G3-A25Z-01A-11D-A16V-10	5016188	180064893	69185728	4	39704										
PIK3C2B	5287	hgsc.bcm.edu	37	chr1	204438107	204438107	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	ggggcatagtcttgctcctgGccacgggttttccagaggtg	15	10	1	1	rs375951229		TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr1:204438107G>A	ENST00000367187.3	-	3	1380	c.824C>T	c.(823-825)gCc>gTc	p.A275V	PIK3C2B_ENST00000424712.2_Missense_Mutation_p.A275V	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	275	Interaction with GRB2.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			CTTGCTCCTGGCCACGGGTTT	0.622																																					p.A275V		Atlas-SNP	.											.	PIK3C2B	142	.	0			c.C824T						.	G	VAL/ALA	0,4406		0,0,2203	78	87	84		824	5.3	1	1		84	1,8599	1.2+/-3.3	0,1,4299	no	missense	PIK3C2B	NM_002646.3	64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	275/1635	204438107	1,13005	2203	4300	6503	SO:0001583	missense	5287	exon3			CTCCTGGCCACGG	Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"phosphoinositide-3-kinase, class 2, beta polypeptide"			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.824C>T	chr1.hg19:g.204438107G>A	ENSP00000356155:p.Ala275Val	50.0	0.0		67.0	22.0	NM_002646	O95666|Q5SW99	Missense_Mutation	SNP	ENST00000367187.3	hg19	CCDS1446.1	.	.	.	.	.	.	.	.	.	.	G	17.91	3.503912	0.64410	0.0	1.16E-4	ENSG00000133056	ENST00000367187;ENST00000424712	T;T	0.69040	-0.27;-0.37	5.31	5.31	0.75309	.	0.000000	0.56097	D	0.000038	T	0.61739	0.2371	L	0.47716	1.5	0.38246	D	0.941472	B;B	0.23316	0.043;0.083	B;B	0.24541	0.054;0.039	T	0.60480	-0.7255	10	0.31617	T	0.26	.	16.8301	0.85942	0.0:0.0:1.0:0.0	.	275;275	F5GWN5;O00750	.;P3C2B_HUMAN	V	275	ENSP00000356155:A275V;ENSP00000400561:A275V	ENSP00000356155:A275V	A	-	2	0	PIK3C2B	202704730	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	8.776000	0.91776	2.491000	0.84063	0.456000	0.33151	GCC	.	.		0.622	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646		A	204438107	G	A	204438107	3	1	278	1	0	0	0	0	1	0	0	0	11919	1203	42	3	4208	3	PIK3C2B	1	204438107	Missense_Mutation	SNP	G	TCGA-G3-A25Z-01A-11D-A16V-10	24373214	204438107	44812514	5	39705										
IKBKE	9641	hgsc.bcm.edu	37	chr1	206649567	206649567	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	gagaacggcattgtgcatcgCgacatcaagccggggaacat	13	10	1	1			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr1:206649567C>T	ENST00000367120.3	+	6	775	c.402C>T	c.(400-402)cgC>cgT	p.R134R	IKBKE_ENST00000537984.1_Silent_p.R49R	NM_001193322.1|NM_014002.3	NP_001180251.1|NP_054721.1	Q14164	IKKE_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase epsilon	134	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				immune response (GO:0006955)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of type I interferon production (GO:0032480)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein phosphorylation (GO:0006468)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|NF-kappaB-inducing kinase activity (GO:0004704)	p.R134R(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|ovary(3)|skin(2)	32	Breast(84;0.137)					TTGTGCATCGCGACATCAAGC	0.627																																					p.R134R		Atlas-SNP	.											IKBKE,NS,carcinoma,0,2	IKBKE	77	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C402T						.						97	82	87					1																	206649567		2203	4300	6503	SO:0001819	synonymous_variant	9641	exon6			GCATCGCGACATC	AB016590	CCDS30996.1, CCDS53464.1, CCDS73019.1	1q31	2014-05-06			ENSG00000143466				14552	protein-coding gene	gene with protein product		605048				10421793, 10882136	Standard	NM_001193321		Approved	IKKE, IKK-i, KIAA0151	uc001hdz.2	Q14164	OTTHUMG00000184613	ENST00000367120.3:c.402C>T	chr1.hg19:g.206649567C>T		59.0	1.0		64.0	38.0	NM_001193322	D3DT78|Q3B754|Q3KR43|Q5JTS6	Silent	SNP	ENST00000367120.3	hg19	CCDS30996.1																																																																																			.	.		0.627	IKBKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088484.1			T	206649567	C	T	206649567	2	4	278	1	0	0	0	0	0	0	0	1	7621	755	27	1		1	IKBKE	1	206649567	Silent	SNP	C	TCGA-G3-A25Z-01A-11D-A16V-10	2211460	206649567	42601054	6	39706										
RTN4	57142	hgsc.bcm.edu	37	chr2	55254616	55254616	+	Missense_Mutation	SNP	T	T	C													0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	tggctgctccttcaagtccaTattttctgtgaccatggaca							TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr2:55254616T>C	ENST00000337526.6	-	3	862	c.619A>G	c.(619-621)Atg>Gtg	p.M207V	RTN4_ENST00000394611.2_Start_Codon_SNP_p.M1V|RTN4_ENST00000402434.2_Intron|RTN4_ENST00000357376.3_Start_Codon_SNP_p.M1V|RTN4_ENST00000357732.4_Intron|RTN4_ENST00000404909.1_Start_Codon_SNP_p.M1V|RTN4_ENST00000317610.7_Intron|RTN4_ENST00000405240.1_Start_Codon_SNP_p.M1V|RTN4_ENST00000354474.6_Intron	NM_020532.4	NP_065393.1	Q9NQC3	RTN4_HUMAN	reticulon 4	207					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonal fasciculation (GO:0007413)|cardiac epithelial to mesenchymal transition (GO:0060317)|cerebral cortex radial glia guided migration (GO:0021801)|endoplasmic reticulum tubular network organization (GO:0071786)|negative regulation of axon extension (GO:0030517)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell growth (GO:0030308)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of apoptotic process (GO:0042981)|regulation of axonogenesis (GO:0050770)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of cell migration (GO:0030334)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of endoplasmic reticulum membrane (GO:0030176)|intracellular (GO:0005622)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(1)|skin(1)|stomach(1)	36						TTCAAGTCCATATTTTCTGTG	0.428																																					p.M207V		Atlas-SNP	.											.	RTN4	189	.	0			c.A619G						.						72	64	67					2																	55254616		2203	4300	6503	SO:0001583	missense	57142	exon3			AGTCCATATTTTC	AF087901	CCDS1851.1, CCDS1852.1, CCDS42683.1, CCDS42684.1, CCDS42685.1	2p14-p13	2008-05-23			ENSG00000115310	ENSG00000115310			14085	protein-coding gene	gene with protein product		604475				10667797, 10773680	Standard	NM_020532		Approved	NSP-CL, KIAA0886, NOGO, ASY	uc002rye.3	Q9NQC3	OTTHUMG00000129337	ENST00000337526.6:c.619A>G	chr2.hg19:g.55254616T>C	ENSP00000337838:p.Met207Val	22.0	0.0		50.0	16.0	NM_020532	O94962|Q7L7Q5|Q7L7Q6|Q7L7Q8|Q8IUA4|Q96B16|Q9BXG5|Q9H212|Q9H3I3|Q9UQ42|Q9Y293|Q9Y2Y7|Q9Y5U6	Missense_Mutation	SNP	ENST00000337526.6	hg19	CCDS42684.1	.	.	.	.	.	.	.	.	.	.	T	9.944	1.218355	0.22373	.	.	ENSG00000115310	ENST00000405240;ENST00000357376;ENST00000337526;ENST00000394611;ENST00000404909;ENST00000427710	T;T;T;T;T	0.22743	1.94;1.94;2.35;1.94;1.94	5.8	3.46	0.39613	.	2.597800	0.00924	N	0.002621	T	0.21550	0.0519	L	0.55834	1.745	0.80722	D	1	B	0.23128	0.08	B	0.16289	0.015	T	0.35525	-0.9785	10	0.20519	T	0.43	-18.1312	4.5817	0.12262	0.0:0.4456:0.0:0.5544	.	207	Q9NQC3	RTN4_HUMAN	V	1;1;207;1;1;1	ENSP00000384471:M1V;ENSP00000349944:M1V;ENSP00000337838:M207V;ENSP00000378109:M1V;ENSP00000385650:M1V	ENSP00000337838:M207V	M	-	1	0	RTN4	55108120	0.998000	0.40836	1.000000	0.80357	0.991000	0.79684	1.077000	0.30741	1.022000	0.39626	0.455000	0.32223	ATG	.	.		0.428	RTN4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251484.1			C	55254616	T	C	55254616	3	2	278	1	0	0	0	0	1	0	0	0	13743	1406	49	2	3025	2	RTN4	2	55254616	Missense_Mutation	SNP	T	TCGA-G3-A25Z-01A-11D-A16V-10		55254616	187944757	7	39707	197	2								
RTN4	57142	hgsc.bcm.edu	37	chr2	55254618	55254618	+	Missense_Mutation	SNP	T	T	G													0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	gctgctccttcaagtccataTtttctgtgaccatggacaga							TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr2:55254618T>G	ENST00000337526.6	-	3	860	c.617A>C	c.(616-618)aAt>aCt	p.N206T	RTN4_ENST00000394611.2_5'UTR|RTN4_ENST00000402434.2_Intron|RTN4_ENST00000357376.3_5'UTR|RTN4_ENST00000357732.4_Intron|RTN4_ENST00000404909.1_5'UTR|RTN4_ENST00000317610.7_Intron|RTN4_ENST00000405240.1_5'UTR|RTN4_ENST00000354474.6_Intron	NM_020532.4	NP_065393.1	Q9NQC3	RTN4_HUMAN	reticulon 4	206					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonal fasciculation (GO:0007413)|cardiac epithelial to mesenchymal transition (GO:0060317)|cerebral cortex radial glia guided migration (GO:0021801)|endoplasmic reticulum tubular network organization (GO:0071786)|negative regulation of axon extension (GO:0030517)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell growth (GO:0030308)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of apoptotic process (GO:0042981)|regulation of axonogenesis (GO:0050770)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of cell migration (GO:0030334)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of endoplasmic reticulum membrane (GO:0030176)|intracellular (GO:0005622)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(1)|skin(1)|stomach(1)	36						CAAGTCCATATTTTCTGTGAC	0.418																																					p.N206T		Atlas-SNP	.											.	RTN4	189	.	0			c.A617C						.						72	64	66					2																	55254618		2203	4300	6503	SO:0001583	missense	57142	exon3			TCCATATTTTCTG	AF087901	CCDS1851.1, CCDS1852.1, CCDS42683.1, CCDS42684.1, CCDS42685.1	2p14-p13	2008-05-23			ENSG00000115310	ENSG00000115310			14085	protein-coding gene	gene with protein product		604475				10667797, 10773680	Standard	NM_020532		Approved	NSP-CL, KIAA0886, NOGO, ASY	uc002rye.3	Q9NQC3	OTTHUMG00000129337	ENST00000337526.6:c.617A>C	chr2.hg19:g.55254618T>G	ENSP00000337838:p.Asn206Thr	21.0	0.0		49.0	17.0	NM_020532	O94962|Q7L7Q5|Q7L7Q6|Q7L7Q8|Q8IUA4|Q96B16|Q9BXG5|Q9H212|Q9H3I3|Q9UQ42|Q9Y293|Q9Y2Y7|Q9Y5U6	Missense_Mutation	SNP	ENST00000337526.6	hg19	CCDS42684.1	.	.	.	.	.	.	.	.	.	.	T	13.70	2.316775	0.40996	.	.	ENSG00000115310	ENST00000337526	T	0.16457	2.34	5.8	5.8	0.92144	.	1.351150	0.04498	N	0.380799	T	0.14874	0.0359	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.09997	-1.0649	10	0.87932	D	0	0.4404	16.1372	0.81494	0.0:0.0:0.0:1.0	.	206	Q9NQC3	RTN4_HUMAN	T	206	ENSP00000337838:N206T	ENSP00000337838:N206T	N	-	2	0	RTN4	55108122	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.925000	0.48884	2.207000	0.71202	0.455000	0.32223	AAT	.	.		0.418	RTN4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251484.1			G	55254618	T	G	55254618	3	3	278	1	0	0	0	0	1	0	0	0	13743	1493	52	5	3027	5	RTN4	2	55254618	Missense_Mutation	SNP	T	TCGA-G3-A25Z-01A-11D-A16V-10	2	55254618	187944755	8	39708	197	2								
DHRS9	10170	hgsc.bcm.edu	37	chr2	169938117	169938117	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	cttttgggtgctaggcctccTaatcctctgtggttttctgt	10	10	2	0			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr2:169938117T>A	ENST00000327239.4	+	5	1530	c.26T>A	c.(25-27)cTa>cAa	p.L9Q	DHRS9_ENST00000428522.1_Missense_Mutation_p.L9Q|DHRS9_ENST00000412271.1_Missense_Mutation_p.L9Q|DHRS9_ENST00000602501.1_Missense_Mutation_p.L9Q|DHRS9_ENST00000436483.2_Missense_Mutation_p.L9Q|DHRS9_ENST00000432060.2_Missense_Mutation_p.L69Q|DHRS9_ENST00000421653.1_Intron|DHRS9_ENST00000357546.2_Missense_Mutation_p.L9Q	NM_005771.4	NP_005762.2	Q9BPW9	DHRS9_HUMAN	dehydrogenase/reductase (SDR family) member 9	9					9-cis-retinoic acid biosynthetic process (GO:0042904)|androgen metabolic process (GO:0008209)|epithelial cell differentiation (GO:0030855)|progesterone metabolic process (GO:0042448)|retinol metabolic process (GO:0042572)	integral component of endoplasmic reticulum membrane (GO:0030176)	alcohol dehydrogenase (NAD) activity (GO:0004022)|racemase and epimerase activity (GO:0016854)|retinol dehydrogenase activity (GO:0004745)|testosterone dehydrogenase (NAD+) activity (GO:0047035)			breast(1)|endometrium(3)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	13						CTAGGCCTCCTAATCCTCTGT	0.418																																					p.L9Q		Atlas-SNP	.											.	DHRS9	29	.	0			c.T26A						.						105	103	103					2																	169938117		2203	4300	6503	SO:0001583	missense	10170	exon5			GCCTCCTAATCCT	AF067174	CCDS2231.1, CCDS74600.1	2q31.1	2011-09-14			ENSG00000073737	ENSG00000073737		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	16888	protein-coding gene	gene with protein product	"NADP-dependent retinol dehydrogenase/reductase", "3-alpha hydroxysteroid dehydrogenase", "retinol dehydrogenase homolog", "short chain dehydrogenase/reductase family 9C, member 4"	612131				11304534, 11294878, 19027726	Standard	NM_001142270		Approved	RDHL, 3alpha-HSD, RETSDR8, RDH15, SDR9C4	uc010zde.2	Q9BPW9	OTTHUMG00000132180	ENST00000327239.4:c.26T>A	chr2.hg19:g.169938117T>A	ENSP00000316670:p.Leu9Gln	31.0	0.0		50.0	11.0	NM_005771	B7Z416|D3DPC1|Q5RKX1|Q9NRA9|Q9NRB0	Missense_Mutation	SNP	ENST00000327239.4	hg19	CCDS2231.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.941804	0.73557	.	.	ENSG00000073737	ENST00000327239;ENST00000357546;ENST00000432060;ENST00000428522;ENST00000450153;ENST00000436483;ENST00000412271	D;D;D;D;D;D;D	0.86627	-2.03;-2.03;-2.15;-2.03;-1.61;-2.03;-2.03	5.88	5.88	0.94601	.	0.220080	0.39475	N	0.001341	D	0.83640	0.5298	L	0.41492	1.28	0.37890	D	0.930686	P;P	0.39022	0.613;0.655	B;B	0.38264	0.269;0.15	D	0.86609	0.1871	10	0.59425	D	0.04	.	15.9494	0.79820	0.0:0.0:0.0:1.0	.	69;9	B7Z416;Q9BPW9	.;DHRS9_HUMAN	Q	9;9;69;9;9;9;9	ENSP00000316670:L9Q;ENSP00000350154:L9Q;ENSP00000389241:L69Q;ENSP00000388564:L9Q;ENSP00000391214:L9Q;ENSP00000407167:L9Q;ENSP00000407747:L9Q	ENSP00000316670:L9Q	L	+	2	0	DHRS9	169646363	0.952000	0.32445	0.594000	0.28785	0.872000	0.50106	3.204000	0.51082	2.242000	0.73789	0.533000	0.62120	CTA	.	.		0.418	DHRS9-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333612.3	NM_005771		A	169938117	T	A	169938117	3	1	278	1	0	0	0	0	1	0	0	0	4500	1522	53	4	28	4	DHRS9	2	169938117	Missense_Mutation	SNP	T	TCGA-G3-A25Z-01A-11D-A16V-10	114683499	169938117	73261256	9	39709										
TTN	7273	hgsc.bcm.edu	37	chr2	179648462	179648462	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	ctcaccgagaccaaagttggTggagtaacaggaatttcaac	10	9	2	1			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr2:179648462T>C	ENST00000591111.1	-	17	3050	c.2826A>G	c.(2824-2826)ccA>ccG	p.P942P	TTN_ENST00000342175.6_Silent_p.P896P|TTN_ENST00000342992.6_Silent_p.P942P|TTN_ENST00000359218.5_Silent_p.P896P|TTN_ENST00000460472.2_Silent_p.P896P|TTN_ENST00000589042.1_Silent_p.P942P|TTN_ENST00000360870.5_Silent_p.P942P			Q8WZ42	TITIN_HUMAN	titin	33644					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCAAAGTTGGTGGAGTAACAG	0.348																																					p.P942P		Atlas-SNP	.											.	TTN	18412	.	0			c.A2826G						.						88	90	89					2																	179648462		2203	4300	6503	SO:0001819	synonymous_variant	7273	exon17			AGTTGGTGGAGTA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.2826A>G	chr2.hg19:g.179648462T>C		96.0	0.0		161.0	76.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.348	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179648462	T	C	179648462	2	2	278	1	0	0	0	0	0	0	0	1	16750	1683	59	2		2	TTN	2	179648462	Silent	SNP	T	TCGA-G3-A25Z-01A-11D-A16V-10	9710345	179648462	63550911	10	39710										
SLC39A10	57181	hgsc.bcm.edu	37	chr2	196593015	196593015	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	tcagtatgccaataacatcaCactttggatctttgcagtca	6	10	4	0			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr2:196593015C>A	ENST00000409086.3	+	9	2554	c.2279C>A	c.(2278-2280)aCa>aAa	p.T760K	SLC39A10_ENST00000359634.5_Missense_Mutation_p.T760K|SLC39A10_ENST00000541054.1_Missense_Mutation_p.T310K	NM_001127257.1	NP_001120729.1	Q9ULF5	S39AA_HUMAN	solute carrier family 39 (zinc transporter), member 10	760					transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)			breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(16)|pancreas(1)|prostate(1)|skin(2)	34			OV - Ovarian serous cystadenocarcinoma(117;0.221)			AATAACATCACACTTTGGATC	0.408																																					p.T760K		Atlas-SNP	.											.	SLC39A10	89	.	0			c.C2279A						.						253	216	229					2																	196593015		2203	4300	6503	SO:0001583	missense	57181	exon9			ACATCACACTTTG		CCDS33353.1	2q33.1	2013-05-22			ENSG00000196950	ENSG00000196950		"Solute carriers"	20861	protein-coding gene	gene with protein product		608733	"solute carrier family 39 (metal ion transporter), member 10"			12659941	Standard	NM_020342		Approved	KIAA1265, FLJ90515, DKFZp564L2123	uc002utg.4	Q9ULF5	OTTHUMG00000154380	ENST00000409086.3:c.2279C>A	chr2.hg19:g.196593015C>A	ENSP00000386766:p.Thr760Lys	162.0	0.0		315.0	151.0	NM_020342	A8K5C6|B4DGU0|Q3MJA4|Q68CR5|Q6DKH6|Q9Y3Z1	Missense_Mutation	SNP	ENST00000409086.3	hg19	CCDS33353.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.480599	0.84747	.	.	ENSG00000196950	ENST00000409086;ENST00000359634;ENST00000541054	T;T;T	0.50548	0.74;0.74;0.74	5.4	4.53	0.55603	.	0.045219	0.85682	D	0.000000	T	0.63343	0.2503	L	0.59967	1.855	0.80722	D	1	D	0.67145	0.996	D	0.72338	0.977	T	0.64158	-0.6473	10	0.45353	T	0.12	.	14.1635	0.65461	0.0:0.9285:0.0:0.0715	.	760	Q9ULF5	S39AA_HUMAN	K	760;760;310	ENSP00000386766:T760K;ENSP00000352655:T760K;ENSP00000437787:T310K	ENSP00000352655:T760K	T	+	2	0	SLC39A10	196301260	1.000000	0.71417	0.981000	0.43875	0.992000	0.81027	7.604000	0.82830	1.527000	0.49086	0.655000	0.94253	ACA	.	.		0.408	SLC39A10-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335186.1	XM_047707		A	196593015	C	A	196593015	3	1	278	1	0	0	0	0	1	0	0	0	14628	478	17	3	2309	3	SLC39A10	2	196593015	Missense_Mutation	SNP	C	TCGA-G3-A25Z-01A-11D-A16V-10	16944553	196593015	46606358	11	39711										
ABCA12	26154	hgsc.bcm.edu	37	chr2	215843664	215843664	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	gaagtacataaacaagctctCccccaatatcctccttgagg	6	13	1	1			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr2:215843664C>T	ENST00000272895.7	-	32	5060	c.4841G>A	c.(4840-4842)gGa>gAa	p.G1614E	ABCA12_ENST00000389661.4_Missense_Mutation_p.G1296E	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1614					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		AACAAGCTCTCCCCCAATATC	0.498																																					p.G1614E	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											.	ABCA12	368	.	0			c.G4841A						.						158	139	145					2																	215843664		2203	4300	6503	SO:0001583	missense	26154	exon32			AGCTCTCCCCCAA	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.4841G>A	chr2.hg19:g.215843664C>T	ENSP00000272895:p.Gly1614Glu	75.0	0.0		128.0	22.0	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	hg19	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.304121	0.81136	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	T;T	0.62639	0.01;0.01	5.36	5.36	0.76844	.	0.000000	0.64402	D	0.000002	T	0.74152	0.3679	L	0.43554	1.36	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.77004	0.989;0.979	T	0.72944	-0.4138	10	0.45353	T	0.12	.	19.4492	0.94860	0.0:1.0:0.0:0.0	.	1614;1296	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	E	1614;1296	ENSP00000272895:G1614E;ENSP00000374312:G1296E	ENSP00000272895:G1614E	G	-	2	0	ABCA12	215551909	0.995000	0.38212	0.998000	0.56505	0.901000	0.52897	4.063000	0.57499	2.669000	0.90835	0.655000	0.94253	GGA	.	.		0.498	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		T	215843664	C	T	215843664	3	4	278	1	0	0	0	0	1	0	0	0	30	855	30	3	3034	3	ABCA12	2	215843664	Missense_Mutation	SNP	C	TCGA-G3-A25Z-01A-11D-A16V-10	19250649	215843664	27355709	12	39712										
SLC19A3	80704	hgsc.bcm.edu	37	chr2	228563990	228563990	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	cctgctgtgtaggcggccagCgtgacgctcctgcagtagcc	14	14	0	1			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr2:228563990C>A	ENST00000258403.3	-	3	512	c.441G>T	c.(439-441)acG>acT	p.T147T	SLC19A3_ENST00000541617.1_Silent_p.T143T|SLC19A3_ENST00000409287.1_Intron	NM_025243.3	NP_079519.1	Q9BZV2	S19A3_HUMAN	solute carrier family 19 (thiamine transporter), member 3	147					small molecule metabolic process (GO:0044281)|thiamine transmembrane transport (GO:0071934)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	thiamine uptake transmembrane transporter activity (GO:0015403)			breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|skin(3)	30		Renal(207;0.0112)|all_lung(227;0.0335)|Lung NSC(271;0.142)|all_hematologic(139;0.21)|Esophageal squamous(248;0.236)		Epithelial(121;1.58e-10)|all cancers(144;8.55e-08)|Lung(261;0.00948)|LUSC - Lung squamous cell carcinoma(224;0.0125)	L-Cysteine(DB00151)	AGGCGGCCAGCGTGACGCTCC	0.592																																					p.T147T		Atlas-SNP	.											.	SLC19A3	62	.	0			c.G441T						.						85	87	86					2																	228563990		2203	4300	6503	SO:0001819	synonymous_variant	80704	exon3			GGCCAGCGTGACG	AF271633	CCDS2468.1	2q37	2013-07-18	2013-07-18		ENSG00000135917	ENSG00000135917		"Solute carriers"	16266	protein-coding gene	gene with protein product	"thiamine transporter 2"	606152	"solute carrier family 19, member 3"			11136550, 15871139	Standard	XM_005246871		Approved	THTR2	uc002vpi.3	Q9BZV2	OTTHUMG00000133185	ENST00000258403.3:c.441G>T	chr2.hg19:g.228563990C>A		31.0	0.0		43.0	9.0	NM_025243		Silent	SNP	ENST00000258403.3	hg19	CCDS2468.1																																																																																			.	.		0.592	SLC19A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256894.1			A	228563990	C	A	228563990	2	1	278	1	0	0	0	0	0	0	0	1	14445	755	27	1		1	SLC19A3	2	228563990	Silent	SNP	C	TCGA-G3-A25Z-01A-11D-A16V-10	12720326	228563990	14635383	13	39713										
TATDN2	9797	hgsc.bcm.edu	37	chr3	10290922	10290922	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	caaggtcaagcacaactggaGcagcacgtcggaagggtgtc	14	10	1	0			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr3:10290922G>T	ENST00000287652.4	+	2	1089	c.38G>T	c.(37-39)aGc>aTc	p.S13I	TATDN2_ENST00000448281.2_Missense_Mutation_p.S13I|RP11-438J1.1_ENST00000450534.1_5'Flank	NM_014760.3	NP_055575.3	Q93075	TATD2_HUMAN	TatD DNase domain containing 2	13					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|DNA catabolic process (GO:0006308)|endoplasmic reticulum unfolded protein response (GO:0030968)	intracellular organelle (GO:0043229)|nucleoplasm (GO:0005654)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(9)|pancreas(2)|prostate(1)|stomach(2)	28						CACAACTGGAGCAGCACGTCG	0.672																																					p.S13I		Atlas-SNP	.											.	TATDN2	59	.	0			c.G38T						.						48	49	49					3																	10290922		2202	4298	6500	SO:0001583	missense	9797	exon2			ACTGGAGCAGCAC	D86972	CCDS33698.1	3p25.3	2010-11-24			ENSG00000157014	ENSG00000157014			28988	protein-coding gene	gene with protein product						9039502	Standard	NM_014760		Approved	KIAA0218	uc003bvf.3	Q93075	OTTHUMG00000155361	ENST00000287652.4:c.38G>T	chr3.hg19:g.10290922G>T	ENSP00000287652:p.Ser13Ile	52.0	0.0		63.0	13.0	NM_014760	Q3MIL9|Q5BKU0	Missense_Mutation	SNP	ENST00000287652.4	hg19	CCDS33698.1	.	.	.	.	.	.	.	.	.	.	G	19.16	3.773612	0.69992	.	.	ENSG00000157014	ENST00000287652;ENST00000448281	T;T	0.26518	1.73;1.73	3.77	0.848	0.18966	.	.	.	.	.	T	0.18593	0.0446	L	0.51422	1.61	0.24734	N	0.993078	B	0.30068	0.267	B	0.21151	0.033	T	0.24799	-1.0150	9	0.87932	D	0	-3.0134	3.1275	0.06412	0.2332:0.0:0.5569:0.2099	.	13	Q93075	TATD2_HUMAN	I	13	ENSP00000287652:S13I;ENSP00000408736:S13I	ENSP00000287652:S13I	S	+	2	0	TATDN2	10265922	1.000000	0.71417	0.994000	0.49952	0.996000	0.88848	0.970000	0.29383	0.048000	0.15891	0.563000	0.77884	AGC	.	.		0.672	TATDN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339641.1	XM_376203		T	10290922	G	T	10290922	3	4	278	1	0	0	0	0	1	0	0	0	15607	971	34	3	40	3	TATDN2	3	10290922	Missense_Mutation	SNP	G	TCGA-G3-A25Z-01A-11D-A16V-10		10290922	187731508	14	39714										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41275047	41275047	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	tggaaggtctccttgggactCttgttcagcttctgggttca	12	9	5	0			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr3:41275047C>T	ENST00000349496.5	+	9	1493	c.1213C>T	c.(1213-1215)Ctt>Ttt	p.L405F	CTNNB1_ENST00000405570.1_Missense_Mutation_p.L405F|CTNNB1_ENST00000453024.1_Missense_Mutation_p.L398F|CTNNB1_ENST00000396183.3_Missense_Mutation_p.L405F|CTNNB1_ENST00000396185.3_Missense_Mutation_p.L405F	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	405					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CCTTGGGACTCTTGTTCAGCT	0.418		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.L405F	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	.	CTNNB1	4904	.	0			c.C1213T						.						150	143	146					3																	41275047		2203	4300	6503	SO:0001583	missense	1499	exon9	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	GGGACTCTTGTTC	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.1213C>T	chr3.hg19:g.41275047C>T	ENSP00000344456:p.Leu405Phe	56.0	0.0		63.0	18.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	28.7	4.939289	0.92526	.	.	ENSG00000168036	ENST00000405570;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185	T;T;T;T;T	0.78003	-1.14;-1.14;-1.14;-1.14;-1.14	5.86	5.86	0.93980	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.91236	0.7238	M	0.91090	3.175	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.996;0.996	D	0.92265	0.5820	10	0.87932	D	0	-0.542	20.1865	0.98220	0.0:1.0:0.0:0.0	.	333;398;405	B4DSW9;B4DGU4;P35222	.;.;CTNB1_HUMAN	F	405;405;405;398;405	ENSP00000385604:L405F;ENSP00000379486:L405F;ENSP00000344456:L405F;ENSP00000411226:L398F;ENSP00000379488:L405F	ENSP00000344456:L405F	L	+	1	0	CTNNB1	41250051	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.775000	0.95449	0.655000	0.94253	CTT	.	.		0.418	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41275047	C	T	41275047	3	4	278	1	0	0	0	0	1	0	0	0	4018	913	32	3	1243	3	CTNNB1	3	41275047	Missense_Mutation	SNP	C	TCGA-G3-A25Z-01A-11D-A16V-10	30984125	41275047	156747383	15	39715										
STAB1	23166	hgsc.bcm.edu	37	chr3	52549455	52549455	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	ccaggacacacccaggaagaGctgtgtctaccgatctggct	11	13	2	1			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr3:52549455G>T	ENST00000321725.6	+	37	3957	c.3881G>T	c.(3880-3882)aGc>aTc	p.S1294I		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	1294					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)			breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		CCCAGGAAGAGCTGTGTCTAC	0.607																																					p.S1294I		Atlas-SNP	.											.	STAB1	178	.	0			c.G3881T						.						76	71	73					3																	52549455		2202	4300	6502	SO:0001583	missense	23166	exon37			GGAAGAGCTGTGT	AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"MS-1 antigen", "fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1", "common lymphatic endothelial and vascular endothelial receptor-1"	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.3881G>T	chr3.hg19:g.52549455G>T	ENSP00000312946:p.Ser1294Ile	50.0	0.0		35.0	16.0	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Missense_Mutation	SNP	ENST00000321725.6	hg19	CCDS33768.1	.	.	.	.	.	.	.	.	.	.	G	17.02	3.281890	0.59758	.	.	ENSG00000010327	ENST00000321725	T	0.03152	4.03	4.71	3.83	0.44106	.	0.269718	0.34879	N	0.003614	T	0.05593	0.0147	N	0.17474	0.49	0.39755	D	0.971946	D	0.69078	0.997	P	0.62014	0.897	T	0.56890	-0.7904	10	0.20046	T	0.44	-28.4682	8.8676	0.35296	0.1024:0.0:0.8976:0.0	.	1294	Q9NY15	STAB1_HUMAN	I	1294	ENSP00000312946:S1294I	ENSP00000312946:S1294I	S	+	2	0	STAB1	52524495	1.000000	0.71417	1.000000	0.80357	0.843000	0.47879	3.320000	0.51991	1.327000	0.45338	0.563000	0.77884	AGC	.	.		0.607	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136		T	52549455	G	T	52549455	3	4	278	1	0	0	0	0	1	0	0	0	15252	971	34	3	4027	3	STAB1	3	52549455	Missense_Mutation	SNP	G	TCGA-G3-A25Z-01A-11D-A16V-10	11274408	52549455	145472975	16	39716										
C3orf67	200844	hgsc.bcm.edu	37	chr3	58855185	58855185	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	cagtggacggctggcatgatCggttatttttggacccaacg	13	9	0	1			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr3:58855185C>T	ENST00000482387.1	-	5	605	c.509G>A	c.(508-510)cGa>cAa	p.R170Q	RP11-147N17.1_ENST00000463703.1_RNA|RP11-147N17.1_ENST00000493123.1_RNA|RP11-147N17.1_ENST00000482372.1_RNA|RP11-147N17.1_ENST00000492031.1_RNA|C3orf67_ENST00000472469.1_Missense_Mutation_p.R90Q|C3orf67_ENST00000295966.7_Missense_Mutation_p.R170Q			Q6ZVT6	CC067_HUMAN	chromosome 3 open reading frame 67	170										endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(3)|prostate(2)|skin(1)	19		all_cancers(2;0.000156)|all_epithelial(2;0.000493)|Breast(2;0.00446)|all_lung(2;0.074)|Lung NSC(2;0.248)		BRCA - Breast invasive adenocarcinoma(55;5.93e-06)|Kidney(10;0.00155)|KIRC - Kidney renal clear cell carcinoma(10;0.00172)|OV - Ovarian serous cystadenocarcinoma(275;0.23)		CTGGCATGATCGGTTATTTTT	0.368																																					p.R170Q		Atlas-SNP	.											.	C3orf67	45	.	0			c.G509A						.						119	111	114					3																	58855185		2203	4300	6503	SO:0001583	missense	200844	exon9			CATGATCGGTTAT	AK124920	CCDS33776.1	3p14.2	2011-01-25			ENSG00000163689	ENSG00000163689			24763	protein-coding gene	gene with protein product							Standard	NM_198463		Approved	FLJ42117, FLJ42930	uc003dkt.1	Q6ZVT6	OTTHUMG00000159151	ENST00000482387.1:c.509G>A	chr3.hg19:g.58855185C>T	ENSP00000417122:p.Arg170Gln	100.0	0.0		154.0	46.0	NM_198463	B9EKV6|Q6ZV69	Missense_Mutation	SNP	ENST00000482387.1	hg19		.	.	.	.	.	.	.	.	.	.	C	9.809	1.182661	0.21870	.	.	ENSG00000163689	ENST00000295966;ENST00000482387;ENST00000472469	T;T;T	0.51817	0.69;0.69;0.69	5.85	0.366	0.16136	.	0.925114	0.09158	N	0.840614	T	0.19485	0.0468	N	0.03016	-0.435	0.09310	N	1	B;B	0.26876	0.162;0.028	B;B	0.17979	0.02;0.007	T	0.17107	-1.0380	10	0.27785	T	0.31	-0.0162	5.3638	0.16103	0.0:0.5302:0.14:0.3298	.	90;170	C9J3M8;Q6ZVT6-2	.;.	Q	170;170;90	ENSP00000295966:R170Q;ENSP00000417122:R170Q;ENSP00000417271:R90Q	ENSP00000295966:R170Q	R	-	2	0	C3orf67	58830225	0.347000	0.24853	0.000000	0.03702	0.384000	0.30261	-0.026000	0.12392	-0.225000	0.09913	0.655000	0.94253	CGA	.	.		0.368	C3orf67-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000353803.1	NM_198463		T	58855185	C	T	58855185	3	4	278	1	0	0	0	0	1	0	0	0	2243	884	31	1	1214	1	C3orf67	3	58855185	Missense_Mutation	SNP	C	TCGA-G3-A25Z-01A-11D-A16V-10	6305730	58855185	139167245	17	39717										
EPHA6	285220	hgsc.bcm.edu	37	chr3	97202883	97202883	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	tgatccctcaagaattcgtaTtgagagagtcattggggcag	12	7	2	4			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr3:97202883T>C	ENST00000514100.1	+	7	598	c.356T>C	c.(355-357)aTt>aCt	p.I119T	EPHA6_ENST00000389672.5_Missense_Mutation_p.I727T|EPHA6_ENST00000442602.2_Missense_Mutation_p.I93T|EPHA6_ENST00000502694.1_Missense_Mutation_p.I119T	NM_001278300.1	NP_001265229.1	Q9UF33	EPHA6_HUMAN	EPH receptor A6	633	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.					integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(2)|lung(60)|ovary(3)|skin(11)|stomach(5)|upper_aerodigestive_tract(2)	101						AGAATTCGTATTGAGAGAGTC	0.358																																					p.I727T		Atlas-SNP	.											.	EPHA6	439	.	0			c.T2180C						.						95	95	95					3																	97202883		1851	4110	5961	SO:0001583	missense	285220	exon10			TTCGTATTGAGAG	AK092565	CCDS46876.1, CCDS54616.1, CCDS63697.1	3q12.1	2013-02-11	2004-10-28		ENSG00000080224	ENSG00000080224		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	19296	protein-coding gene	gene with protein product		600066				12471243	Standard	NM_001080448		Approved	FLJ35246	uc010how.1	Q9UF33	OTTHUMG00000159208	ENST00000514100.1:c.356T>C	chr3.hg19:g.97202883T>C	ENSP00000421711:p.Ile119Thr	85.0	0.0		93.0	39.0	NM_001080448	D6RAL5	Missense_Mutation	SNP	ENST00000514100.1	hg19		.	.	.	.	.	.	.	.	.	.	T	21.8	4.198363	0.79015	.	.	ENSG00000080224	ENST00000389672;ENST00000514100;ENST00000502694;ENST00000442602	D;D;D;D	0.82984	-1.67;-1.67;-1.67;-1.67	5.42	5.42	0.78866	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	D	0.89389	0.6701	L	0.59967	1.855	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;0.996;1.0	D;D;D;D	0.91635	0.999;0.999;0.99;0.999	D	0.90503	0.4475	9	0.87932	D	0	.	15.5233	0.75881	0.0:0.0:0.0:1.0	.	93;632;119;119	B4DXQ6;Q9UF33;Q9UF33-2;D6RAL5	.;EPHA6_HUMAN;.;.	T	727;119;119;93	ENSP00000374323:I727T;ENSP00000421711:I119T;ENSP00000423950:I119T;ENSP00000403100:I93T	ENSP00000374323:I727T	I	+	2	0	EPHA6	98685573	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.695000	0.84257	2.071000	0.62044	0.454000	0.30748	ATT	.	.		0.358	EPHA6-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000359997.1	NM_001080448		C	97202883	T	C	97202883	3	2	278	1	0	0	0	0	1	0	0	0	5173	1493	52	2	2286	2	EPHA6	3	97202883	Missense_Mutation	SNP	T	TCGA-G3-A25Z-01A-11D-A16V-10	38347698	97202883	100819547	18	39718										
FAM193A	8603	hgsc.bcm.edu	37	chr4	2698242	2698242	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	cggagggtggaggatttgttGcagtttataaatagctccga	14	5	0	0			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr4:2698242G>T	ENST00000324666.5	+	16	2907	c.2556G>T	c.(2554-2556)ttG>ttT	p.L852F	FAM193A_ENST00000545951.1_Missense_Mutation_p.L852F|FAM193A_ENST00000505311.1_Missense_Mutation_p.L852F|FAM193A_ENST00000382839.3_Missense_Mutation_p.L852F|FAM193A_ENST00000502458.1_Missense_Mutation_p.L874F	NM_001256666.1	NP_001243595.1	P78312	F193A_HUMAN	family with sequence similarity 193, member A	852										NS(2)|breast(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(12)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	40						AGGATTTGTTGCAGTTTATAA	0.502																																					p.L874F		Atlas-SNP	.											.	FAM193A	103	.	0			c.G2622T						.						113	107	109					4																	2698242		2203	4300	6503	SO:0001583	missense	8603	exon17			TTTGTTGCAGTTT	AB000459	CCDS33943.1, CCDS58874.1, CCDS58875.1, CCDS58876.1	4p16.3	2009-09-04	2009-09-04	2009-09-04					16822	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 8"	C4orf8		9734812	Standard	NR_046335		Approved	RES4-22	uc010ick.3	P78312		ENST00000324666.5:c.2556G>T	chr4.hg19:g.2698242G>T	ENSP00000324587:p.Leu852Phe	163.0	0.0		190.0	54.0	NM_001256667	B7ZM85|B9EGR0|E9PFA1|O43607|P78311|P78313|Q9UEG8	Missense_Mutation	SNP	ENST00000324666.5	hg19	CCDS58875.1	.	.	.	.	.	.	.	.	.	.	G	19.20	3.781587	0.70222	.	.	ENSG00000125386	ENST00000382839;ENST00000324666;ENST00000545951;ENST00000502458;ENST00000513350	T;T;T;T;T	0.56275	0.58;0.99;0.56;0.58;0.47	5.26	-5.2	0.02823	.	0.077181	0.53938	D	0.000059	T	0.59878	0.2226	M	0.64404	1.975	0.49687	D	0.999815	D;D;D;D;D	0.76494	0.999;0.999;0.999;0.999;0.996	D;D;D;P;P	0.68192	0.956;0.94;0.956;0.9;0.9	T	0.63576	-0.6606	10	0.87932	D	0	-14.2123	9.918	0.41446	0.1826:0.244:0.5734:0.0	.	852;874;852;874;852	B9EGR0;E9PFA1;P78312;B7ZM85;P78312-2	.;.;F193A_HUMAN;.;.	F	852;852;852;874;706	ENSP00000372290:L852F;ENSP00000324587:L852F;ENSP00000443617:L852F;ENSP00000427505:L874F;ENSP00000427260:L706F	ENSP00000324587:L852F	L	+	3	2	FAM193A	2668040	0.916000	0.31088	0.444000	0.26895	0.934000	0.57294	0.095000	0.15127	-0.970000	0.03569	-0.331000	0.08364	TTG	.	.		0.502	FAM193A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360903.1	NM_003704		T	2698242	G	T	2698242	3	4	278	1	0	0	0	0	1	0	0	0	5529	1310	46	3	2610	3	FAM193A	4	2698242	Missense_Mutation	SNP	G	TCGA-G3-A25Z-01A-11D-A16V-10		2698242	188456034	19	39719										
SLC30A9	10463	hgsc.bcm.edu	37	chr4	42065035	42065035	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	aaatatgcgctatatttcttCgctaattagtggtgttggta	9	5	1	0			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr4:42065035C>T	ENST00000264451.7	+	11	1109	c.929C>T	c.(928-930)tCg>tTg	p.S310L		NM_006345.3	NP_006336.3	Q6PML9	ZNT9_HUMAN	solute carrier family 30 (zinc transporter), member 9	310					nucleotide-excision repair (GO:0006289)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|zinc ion transport (GO:0006829)	cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	cation transmembrane transporter activity (GO:0008324)|chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TATATTTCTTCGCTAATTAGT	0.348																																					p.S310L		Atlas-SNP	.											SLC30A9,colon,carcinoma,-1,2	SLC30A9	58	.	0			c.C929T						.						206	198	201					4																	42065035		2203	4300	6503	SO:0001583	missense	10463	exon11			TTTCTTCGCTAAT	AF006621	CCDS3465.1	4p13	2013-05-22	2003-09-09	2003-09-10	ENSG00000014824	ENSG00000014824		"Solute carriers"	1329	protein-coding gene	gene with protein product	"GRIP1-dependent nuclear receptor coactivator"	604604	"chromosome 4 open reading frame 1"	C4orf1		10409434, 11906820	Standard	NM_006345		Approved	HUEL, ZNT9, GAC63	uc003gwl.3	Q6PML9	OTTHUMG00000099387	ENST00000264451.7:c.929C>T	chr4.hg19:g.42065035C>T	ENSP00000264451:p.Ser310Leu	246.0	0.0		411.0	17.0	NM_006345	Q4W5B6|Q7Z5I7|Q8TBB2|Q9Y6R2	Missense_Mutation	SNP	ENST00000264451.7	hg19	CCDS3465.1	.	.	.	.	.	.	.	.	.	.	C	33	5.250466	0.95305	.	.	ENSG00000014824	ENST00000264451;ENST00000536881	T	0.64618	-0.11	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	D	0.86381	0.5919	H	0.95745	3.715	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89697	0.3902	10	0.87932	D	0	-11.8218	19.9859	0.97351	0.0:1.0:0.0:0.0	.	310	Q6PML9	ZNT9_HUMAN	L	310;138	ENSP00000264451:S310L	ENSP00000264451:S310L	S	+	2	0	SLC30A9	41759792	1.000000	0.71417	0.992000	0.48379	0.805000	0.45488	7.818000	0.86416	2.729000	0.93468	0.655000	0.94253	TCG	.	.		0.348	SLC30A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216842.3			T	42065035	C	T	42065035	3	4	278	1	0	0	0	0	1	0	0	0	14577	893	31	1	971	1	SLC30A9	4	42065035	Missense_Mutation	SNP	C	TCGA-G3-A25Z-01A-11D-A16V-10	39366793	42065035	149089241	20	39720										
POLR2B	5431	hgsc.bcm.edu	37	chr4	57860856	57860856	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	atataacaaaaacagtcattAaagaaggtgaagaacaactt	6	5	1	3			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr4:57860856A>G	ENST00000381227.1	+	6	813	c.400A>G	c.(400-402)Aaa>Gaa	p.K134E	POLR2B_ENST00000431623.2_Missense_Mutation_p.K59E|POLR2B_ENST00000314595.5_Missense_Mutation_p.K134E|snoU13_ENST00000459266.1_RNA|POLR2B_ENST00000441246.2_Missense_Mutation_p.K127E			P30876	RPB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide B, 140kDa	134					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonucleoside binding (GO:0032549)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(10)|large_intestine(9)|lung(17)|ovary(2)|prostate(4)|skin(1)	52	Glioma(25;0.08)|all_neural(26;0.181)					AACAGTCATTAAAGAAGGTGA	0.338																																					p.K134E		Atlas-SNP	.											.	POLR2B	108	.	0			c.A400G						.						56	58	57					4																	57860856		2201	4299	6500	SO:0001583	missense	5431	exon5			GTCATTAAAGAAG		CCDS3511.1	4q12	2013-01-21	2002-08-29		ENSG00000047315	ENSG00000047315		"RNA polymerase subunits"	9188	protein-coding gene	gene with protein product		180661	"polymerase (RNA) II (DNA directed) polypeptide B (140kD)"			1518060, 8034326	Standard	NM_000938		Approved	RPB2	uc003hcl.1	P30876	OTTHUMG00000128771	ENST00000381227.1:c.400A>G	chr4.hg19:g.57860856A>G	ENSP00000370625:p.Lys134Glu	54.0	0.0		46.0	29.0	NM_000938	A8K1A8|Q8IZ61	Missense_Mutation	SNP	ENST00000381227.1	hg19	CCDS3511.1	.	.	.	.	.	.	.	.	.	.	A	13.43	2.233700	0.39498	.	.	ENSG00000047315	ENST00000381227;ENST00000431623;ENST00000441246;ENST00000314595	T;T;T;T	0.62639	0.01;0.01;0.01;0.01	5.77	5.77	0.91146	RNA polymerase, beta subunit, protrusion (1);	0.000000	0.85682	D	0.000000	T	0.46833	0.1413	N	0.20483	0.58	0.58432	D	0.999995	B;B	0.12630	0.001;0.006	B;B	0.15870	0.014;0.014	T	0.41360	-0.9513	10	0.12103	T	0.63	.	16.0891	0.81080	1.0:0.0:0.0:0.0	.	59;134	C9J4M6;P30876	.;RPB2_HUMAN	E	134;59;127;134	ENSP00000370625:K134E;ENSP00000391096:K59E;ENSP00000391452:K127E;ENSP00000312735:K134E	ENSP00000312735:K134E	K	+	1	0	POLR2B	57555613	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.268000	0.72552	2.208000	0.71279	0.455000	0.32223	AAA	.	.		0.338	POLR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250692.1	NM_000938		G	57860856	A	G	57860856	3	3	278	1	0	0	0	0	1	0	0	0	12224	363	13	2	418	2	POLR2B	4	57860856	Missense_Mutation	SNP	A	TCGA-G3-A25Z-01A-11D-A16V-10	15795821	57860856	133293420	21	39721										
CAPSL	133690	hgsc.bcm.edu	37	chr5	35910562	35910562	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	ccacctcttctttttccatgAccacagcataatcatttaac	2	14	3	1			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr5:35910562A>T	ENST00000397367.2	-	3	347	c.221T>A	c.(220-222)gTc>gAc	p.V74D	CAPSL_ENST00000397366.1_Missense_Mutation_p.V74D|CAPSL_ENST00000514524.1_Missense_Mutation_p.V74D	NM_144647.3	NP_653248.3	Q8WWF8	CAPSL_HUMAN	calcyphosine-like	74	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.					cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)			central_nervous_system(1)|kidney(1)|large_intestine(5)|lung(10)|skin(1)|urinary_tract(1)	19	all_lung(31;0.000268)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.167)|Colorectal(62;0.202)			TTTTTCCATGACCACAGCATA	0.328																																					p.V74D		Atlas-SNP	.											.	CAPSL	68	.	0			c.T221A						.						98	99	99					5																	35910562		2202	4300	6502	SO:0001583	missense	133690	exon3			TCCATGACCACAG	BC017586	CCDS3912.2	5p13.2	2013-01-10			ENSG00000152611	ENSG00000152611		"EF-hand domain containing"	28375	protein-coding gene	gene with protein product						12477932	Standard	NM_001042625		Approved	MGC26610	uc003jju.1	Q8WWF8	OTTHUMG00000131109	ENST00000397367.2:c.221T>A	chr5.hg19:g.35910562A>T	ENSP00000380524:p.Val74Asp	94.0	0.0		115.0	36.0	NM_144647		Missense_Mutation	SNP	ENST00000397367.2	hg19	CCDS3912.2	.	.	.	.	.	.	.	.	.	.	A	7.610	0.674700	0.14841	.	.	ENSG00000152611	ENST00000397367;ENST00000397366;ENST00000513623;ENST00000514524	T;T;T;T	0.70164	-0.46;-0.46;-0.46;-0.46	5.18	5.18	0.71444	EF-hand-like domain (1);	0.296699	0.36167	N	0.002749	T	0.28764	0.0713	N	0.00268	-1.735	0.54753	D	0.999982	B	0.02656	0.0	B	0.01281	0.0	T	0.44772	-0.9306	10	0.07030	T	0.85	-18.4972	15.0286	0.71687	1.0:0.0:0.0:0.0	.	74	Q8WWF8	CAPSL_HUMAN	D	74	ENSP00000380524:V74D;ENSP00000380523:V74D;ENSP00000424806:V74D;ENSP00000421018:V74D	ENSP00000380523:V74D	V	-	2	0	CAPSL	35946319	1.000000	0.71417	1.000000	0.80357	0.511000	0.34104	3.836000	0.55813	1.959000	0.56917	0.379000	0.24179	GTC	.	.		0.328	CAPSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253772.2	NM_144647		T	35910562	A	T	35910562	3	4	278	1	0	0	0	0	1	0	0	0	2641	275	10	4	417	4	CAPSL	5	35910562	Missense_Mutation	SNP	A	TCGA-G3-A25Z-01A-11D-A16V-10		35910562	145004698	22	39722										
SLC35A4	113829	hgsc.bcm.edu	37	chr5	139947621	139947621	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	gtgtcctgctcgctggtggtCaacgccgtgctctcagcagt	13	13	2	0			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr5:139947621C>A	ENST00000514199.1	+	2	2553	c.867C>A	c.(865-867)gtC>gtA	p.V289V	SLC35A4_ENST00000323146.3_Silent_p.V289V|APBB3_ENST00000507279.1_Intron			Q96G79	S35A4_HUMAN	solute carrier family 35, member A4	289	Leu-rich.					Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	sugar:proton symporter activity (GO:0005351)			endometrium(4)|kidney(2)|large_intestine(3)|lung(4)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGCTGGTGGTCAACGCCGTGC	0.587																																					p.V289V		Atlas-SNP	.											.	SLC35A4	25	.	0			c.C867A						.						72	53	59					5																	139947621		2203	4300	6503	SO:0001819	synonymous_variant	113829	exon3			GGTGGTCAACGCC	AJ420598	CCDS4231.1	5q31.3	2013-05-22			ENSG00000176087	ENSG00000176087		"Solute carriers"	20753	protein-coding gene	gene with protein product							Standard	NM_080670		Approved		uc003lgg.1	Q96G79	OTTHUMG00000129495	ENST00000514199.1:c.867C>A	chr5.hg19:g.139947621C>A		52.0	0.0		61.0	23.0	NM_080670	A8K013	Silent	SNP	ENST00000514199.1	hg19	CCDS4231.1	.	.	.	.	.	.	.	.	.	.	C	6.521	0.464336	0.12402	.	.	ENSG00000176087	ENST00000432254	.	.	.	5.15	5.15	0.70609	.	.	.	.	.	T	0.58148	0.2102	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55560	-0.8122	4	.	.	.	-7.7688	7.9223	0.29854	0.1616:0.757:0.0:0.0813	.	.	.	.	K	110	.	.	Q	+	1	0	SLC35A4	139927805	0.986000	0.35501	1.000000	0.80357	0.963000	0.63663	0.186000	0.16978	2.674000	0.91012	0.555000	0.69702	CAA	.	.		0.587	SLC35A4-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372815.1	NM_080670		A	139947621	C	A	139947621	2	1	278	1	0	0	0	0	0	0	0	1	14588	813	29	3		3	SLC35A4	5	139947621	Silent	SNP	C	TCGA-G3-A25Z-01A-11D-A16V-10	104037059	139947621	40967639	23	39723										
PCDHB16	57717	hgsc.bcm.edu	37	chr5	140563257	140563257	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	tcagcgtttcagatcctgacTccggaaacaatgggaagacg	11	10	2	3	rs377277959		TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr5:140563257T>A	ENST00000361016.2	+	1	2278	c.1123T>A	c.(1123-1125)Tcc>Acc	p.S375T		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	375	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AGATCCTGACTCCGGAAACAA	0.493																																					p.S375T		Atlas-SNP	.											.	PCDHB16	159	.	0			c.T1123A						.	T	THR/SER	1,4405	2.1+/-5.4	0,1,2202	83	86	85		1123	3.3	0.1	5		85	0,8600		0,0,4300	no	missense	PCDHB16	NM_020957.1	58	0,1,6502	AA,AT,TT		0.0,0.0227,0.0077	possibly-damaging	375/777	140563257	1,13005	2203	4300	6503	SO:0001583	missense	57717	exon1			CCTGACTCCGGAA	AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"Cadherins / Protocadherins : Clustered"	14546	other	protocadherin	"cadherin ME1", "protocadherin-3x", "PCDHbeta 16"	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325	ENST00000361016.2:c.1123T>A	chr5.hg19:g.140563257T>A	ENSP00000354293:p.Ser375Thr	77.0	0.0		59.0	26.0	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	hg19	CCDS4251.1	.	.	.	.	.	.	.	.	.	.	T	17.71	3.455974	0.63401	2.27E-4	0.0	ENSG00000196963	ENST00000361016	T	0.01787	4.64	4.47	3.28	0.37604	Cadherin (4);Cadherin-like (1);	0.000000	0.33834	N	0.004517	T	0.06735	0.0172	M	0.89904	3.07	0.27337	N	0.956618	P;P	0.39424	0.532;0.673	B;P	0.44696	0.158;0.458	T	0.02144	-1.1206	10	0.72032	D	0.01	.	11.0225	0.47726	0.0:0.0:0.1566:0.8434	.	65;375	O15199;Q9NRJ7	.;PCDBG_HUMAN	T	375	ENSP00000354293:S375T	ENSP00000354293:S375T	S	+	1	0	PCDHB16	140543441	0.256000	0.24012	0.086000	0.20670	0.949000	0.60115	1.614000	0.36911	0.549000	0.28973	0.482000	0.46254	TCC	.	.		0.493	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957		A	140563257	T	A	140563257	3	1	278	1	0	0	0	0	1	0	0	0	11550	1551	54	4	1125	4	PCDHB16	5	140563257	Missense_Mutation	SNP	T	TCGA-G3-A25Z-01A-11D-A16V-10	615636	140563257	40352003	24	39724										
PGBD1	84547	hgsc.bcm.edu	37	chr6	28269056	28269056	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	tttatgaggcatcctagaagGgaaatgtattgggaagtctc	12	5	1	2			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr6:28269056G>T	ENST00000405948.2	+	7	1845	c.1425G>T	c.(1423-1425)agG>agT	p.R475S	PGBD1_ENST00000259883.3_Missense_Mutation_p.R475S	NM_001184743.1|NM_032507.3	NP_001171672.1|NP_115896.1	Q96JS3	PGBD1_HUMAN	piggyBac transposable element derived 1	475						membrane (GO:0016020)|nucleus (GO:0005634)	scavenger receptor activity (GO:0005044)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	41						ATCCTAGAAGGGAAATGTATT	0.418																																					p.R475S		Atlas-SNP	.											.	PGBD1	106	.	0			c.G1425T						.						158	156	156					6																	28269056		2203	4300	6503	SO:0001583	missense	84547	exon7			TAGAAGGGAAATG	D88259	CCDS4648.1	6p22.1	2013-01-09			ENSG00000137338	ENSG00000137338		"-"	19398	protein-coding gene	gene with protein product							Standard	NM_001184743		Approved	HUCEP-4, dJ874C20.4, SCAND4	uc003nkz.3	Q96JS3	OTTHUMG00000014520	ENST00000405948.2:c.1425G>T	chr6.hg19:g.28269056G>T	ENSP00000385213:p.Arg475Ser	94.0	0.0		129.0	54.0	NM_001184743	Q53F43|Q6NTF5|Q8WWS4	Missense_Mutation	SNP	ENST00000405948.2	hg19	CCDS4648.1	.	.	.	.	.	.	.	.	.	.	G	10.73	1.432087	0.25813	.	.	ENSG00000137338	ENST00000405948;ENST00000259883	T;T	0.17854	2.25;2.25	4.66	0.887	0.19200	.	0.140189	0.33253	N	0.005116	T	0.05914	0.0154	L	0.60455	1.87	0.23809	N	0.996784	B	0.22146	0.065	B	0.32211	0.142	T	0.39901	-0.9591	10	0.22109	T	0.4	-6.7987	6.3282	0.21255	0.414:0.0:0.586:0.0	.	475	Q96JS3	PGBD1_HUMAN	S	475	ENSP00000385213:R475S;ENSP00000259883:R475S	ENSP00000259883:R475S	R	+	3	2	PGBD1	28377035	0.860000	0.29831	0.970000	0.41538	0.987000	0.75469	0.262000	0.18460	0.292000	0.22492	0.655000	0.94253	AGG	.	.		0.418	PGBD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040188.2			T	28269056	G	T	28269056	3	4	278	1	0	0	0	0	1	0	0	0	11789	1223	43	3	1447	3	PGBD1	6	28269056	Missense_Mutation	SNP	G	TCGA-G3-A25Z-01A-11D-A16V-10		28269056	142846011	25	39725										
ABCB1	5243	hgsc.bcm.edu	37	chr7	87214868	87214868	+	Frame_Shift_Del	DEL	T	T	-													0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	atcagatcttctaaatttccTgcatttgcaaagatatctgt							TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr7:87214868delT	ENST00000265724.3	-	5	663	c.246delA	c.(244-246)gcafs	p.A82fs	ABCB1_ENST00000543898.1_Frame_Shift_Del_p.A82fs	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	82	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				drug transmembrane transport (GO:0006855)|G2/M transition of mitotic cell cycle (GO:0000086)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|stem cell proliferation (GO:0072089)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(14)|kidney(9)|large_intestine(14)|lung(48)|ovary(4)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	111	Esophageal squamous(14;0.00164)				Acebutolol(DB01193)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Adenosine triphosphate(DB00171)|ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Albendazole(DB00518)|Alfentanil(DB00802)|Alitretinoin(DB00523)|Amantadine(DB00915)|Aminohippurate(DB00345)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Amsacrine(DB00276)|Apixaban(DB06605)|Arsenic trioxide(DB01169)|Astemizole(DB00637)|Atazanavir(DB01072)|Atenolol(DB00335)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzocaine(DB01086)|Bepridil(DB01244)|Betamethasone(DB00443)|Biperiden(DB00810)|Boceprevir(DB08873)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Bromocriptine(DB01200)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Canagliflozin(DB08907)|Candesartan(DB00796)|Captopril(DB01197)|Carbamazepine(DB00564)|Carfilzomib(DB08889)|Carvedilol(DB01136)|Caspofungin(DB00520)|Chloroquine(DB00608)|Chlorpromazine(DB00477)|Chlorpropamide(DB00672)|Chlorprothixene(DB01239)|Cilazapril(DB01340)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisplatin(DB00515)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Clofazimine(DB00845)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabigatran etexilate(DB06695)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dipyridamole(DB00975)|Docetaxel(DB01248)|Domperidone(DB01184)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Dronedarone(DB04855)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Etravirine(DB06414)|Ezetimibe(DB00973)|Felodipine(DB01023)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fidaxomicin(DB08874)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluticasone furoate(DB08906)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gemcitabine(DB00441)|Glyburide(DB01016)|Gramicidin D(DB00027)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Imatinib(DB00619)|Imipramine(DB00458)|Indacaterol(DB05039)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketoconazole(DB01026)|Lamivudine(DB00709)|Lamotrigine(DB00555)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lenalidomide(DB00480)|Levetiracetam(DB01202)|Levofloxacin(DB01137)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Liothyronine(DB00279)|Liotrix(DB01583)|Lisinopril(DB00722)|Lomitapide(DB08827)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Mannitol(DB00742)|Maprotiline(DB00934)|Mebendazole(DB00643)|Mefloquine(DB00358)|Megestrol acetate(DB00351)|Meprobamate(DB00371)|Methadone(DB00333)|Methotrexate(DB00563)|Methylprednisolone(DB00959)|Metoprolol(DB00264)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mitomycin(DB00305)|Mitoxantrone(DB01204)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nadolol(DB01203)|Naloxone(DB01183)|Naltrexone(DB00704)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Neostigmine(DB01400)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nizatidine(DB00585)|Norethindrone(DB00717)|Olanzapine(DB00334)|Omeprazole(DB00338)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paroxetine(DB00715)|Pazopanib(DB06589)|Perindopril(DB00790)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Pitavastatin(DB08860)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pravastatin(DB00175)|Prazosin(DB00457)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Progesterone(DB00396)|Promethazine(DB01069)|Propafenone(DB01182)|Propranolol(DB00571)|Protriptyline(DB00344)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reboxetine(DB00234)|Regorafenib(DB08896)|Reserpine(DB00206)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Roxithromycin(DB00778)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Scopolamine(DB00747)|Selegiline(DB01037)|Sertraline(DB01104)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|SOFOSBUVIR(DB08934)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Streptozocin(DB00428)|Sulfinpyrazone(DB01138)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telaprevir(DB05521)|Telmisartan(DB00966)|Temsirolimus(DB06287)|Terazosin(DB01162)|Testosterone(DB00624)|Ticagrelor(DB08816)|Timolol(DB00373)|Tolvaptan(DB06212)|Topotecan(DB01030)|Toremifene(DB00539)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Vecuronium(DB01339)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voacamine(DB04877)|Zidovudine(DB00495)	CTAAATTTCCTGCATTTGCAA	0.393																																					p.G83fs		Atlas-INDEL	.											.	ABCB1	263	.	0			c.247delG						.						93	91	92					7																	87214868		2203	4300	6503	SO:0001589	frameshift_variant	5243	exon5			.	M14758	CCDS5608.1	7q21.12	2012-03-14	2004-05-12		ENSG00000085563	ENSG00000085563		"CD molecules", "ATP binding cassette transporters / subfamily B"	40	protein-coding gene	gene with protein product	"multidrug resistance protein 1"	171050	"colchicin sensitivity"	PGY1, MDR1, CLCS		3027054	Standard	NM_000927		Approved	P-gp, CD243, GP170, ABC20	uc003uiz.2	P08183	OTTHUMG00000023393	ENST00000265724.3:c.246delA	chr7.hg19:g.87214868delT	ENSP00000265724:p.Ala82fs	46.0	0.0		40.0	11.0	NM_000927	A8K294|B5AK60|Q12755|Q14812	Frame_Shift_Del	DEL	ENST00000265724.3	hg19	CCDS5608.1																																																																																			.	.		0.393	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2	NM_000927		-	87214868	T	-	87214868	7	5	278	1	0	1	0	1	0	0	0	0	40	1567	55	0	3696	0	ABCB1	7	87214868	Frame_Shift_Del	DEL	T	TCGA-G3-A25Z-01A-11D-A16V-10		87214868	71923795	26	39726										
INTS10	55174	hgsc.bcm.edu	37	chr8	19682357	19682358	+	Frame_Shift_Ins	INS	-	-	A													0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	aatgaaggatctctgcagatINSacatgaacaactttgatagt							TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr8:19682357_19682358insA	ENST00000397977.3	+	8	1278_1279	c.880_881insA	c.(880-882)tacfs	p.Y294fs		NM_018142.2	NP_060612.2	Q9NVR2	INT10_HUMAN	integrator complex subunit 10	294					snRNA processing (GO:0016180)	integrator complex (GO:0032039)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	20				Colorectal(111;0.057)|COAD - Colon adenocarcinoma(73;0.215)		TCTCTGCAGATACATGAACAAC	0.371																																					p.Y294_M295delinsX		Atlas-INDEL	.											.	INTS10	46	.	0			c.880_881insA						.																																			SO:0001589	frameshift_variant	55174	exon8			.	AK001431	CCDS6011.2	8p21.3	2006-04-26	2006-03-15	2006-03-15	ENSG00000104613	ENSG00000104613			25548	protein-coding gene	gene with protein product		611353	"chromosome 8 open reading frame 35"	C8orf35		16239144	Standard	XM_005273558		Approved	FLJ10569, INT10	uc003wzj.3	Q9NVR2	OTTHUMG00000131065	ENST00000397977.3:c.881dupA	chr8.hg19:g.19682358_19682358dupA	ENSP00000381064:p.Tyr294fs	57.0	0.0		64.0	27.0	NM_018142	Q6IA93|Q7L538|Q7L8C8|Q9H3W8	Frame_Shift_Ins	INS	ENST00000397977.3	hg19	CCDS6011.2																																																																																			.	.		0.371	INTS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253724.2	NM_018142		A	19682358	-	A	19682357	7	5	278	1	0	1	1	0	0	0	0	0	7785	1406	49	0	910	0	INTS10	8	19682357	Frame_Shift_Ins	INS	-	TCGA-G3-A25Z-01A-11D-A16V-10		19682357	126681665	27	39727										
PTPN3	5774	hgsc.bcm.edu	37	chr9	112145782	112145782	+	Frame_Shift_Del	DEL	C	C	-													0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	gacactggatgtgaaagccgCcgtggttcatgacgtcgggg							TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr9:112145782delC	ENST00000374541.2	-	23	2407	c.2303delG	c.(2302-2304)ggcfs	p.G769fs	PTPN3_ENST00000412145.1_Frame_Shift_Del_p.G638fs|PTPN3_ENST00000394827.3_Frame_Shift_Del_p.G237fs|PTPN3_ENST00000262539.3_Frame_Shift_Del_p.G615fs|PTPN3_ENST00000446349.1_Frame_Shift_Del_p.G593fs	NM_001145368.1|NM_002829.3	NP_001138840.1|NP_002820.3	P26045	PTN3_HUMAN	protein tyrosine phosphatase, non-receptor type 3	769	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|negative regulation of mitotic cell cycle (GO:0045930)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of membrane depolarization during action potential (GO:0098902)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	ATPase binding (GO:0051117)|phosphotyrosine binding (GO:0001784)|protein tyrosine phosphatase activity (GO:0004725)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	41						GTGAAAGCCGCCGTGGTTCAT	0.587																																					p.G768fs		Atlas-Indel,Pindel	.											.	PTPN3	106	.	0			c.2304delC						.						132	123	126					9																	112145782		2203	4300	6503	SO:0001589	frameshift_variant	5774	exon23			.		CCDS6776.1, CCDS48000.1, CCDS48001.1	9q31	2011-06-09			ENSG00000070159	ENSG00000070159		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9655	protein-coding gene	gene with protein product		176877				1648725	Standard	NM_002829		Approved	PTPH1	uc004bed.2	P26045	OTTHUMG00000020475	ENST00000374541.2:c.2303delG	chr9.hg19:g.112145782delC	ENSP00000363667:p.Gly769fs	60.0	0.0		54.0	18.0	NM_002829	A0AUW9|E7EN99|E9PGU7	Frame_Shift_Del	DEL	ENST00000374541.2	hg19	CCDS6776.1																																																																																			.	.		0.587	PTPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053598.4			-	112145782	C	-	112145782	7	5	278	1	0	1	0	1	0	0	0	0	12804	739	26	0	454	0	PTPN3	9	112145782	Frame_Shift_Del	DEL	C	TCGA-G3-A25Z-01A-11D-A16V-10		112145782	29067649	28	39728										
TOR2A	27433	hgsc.bcm.edu	37	chr9	130494466	130494466	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	tgggccagctcgttgagcacGcagtgccggacgtggtgccg	17	12	0	1	rs370306195		TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr9:130494466G>A	ENST00000373284.5	-	5	859	c.813C>T	c.(811-813)tgC>tgT	p.C271C	TOR2A_ENST00000373281.5_3'UTR|TOR2A_ENST00000458505.3_3'UTR|TOR2A_ENST00000472723.1_5'UTR|TOR2A_ENST00000336067.6_Missense_Mutation_p.R229C	NM_001085347.2	NP_001078816	Q5JU69	TOR2A_HUMAN	torsin family 2, member A	271					chaperone mediated protein folding requiring cofactor (GO:0051085)|protein homooligomerization (GO:0051260)	endoplasmic reticulum lumen (GO:0005788)	ATP binding (GO:0005524)			NS(1)|endometrium(2)	3						CGTTGAGCACGCAGTGCCGGA	0.627													G|||	1	0.000199681	0	0.0014	5008	,	,		19478	0		0	False		,,,				2504	0				p.R229C		Atlas-SNP	.											.	TOR2A	26	.	0			c.C685T						.						59	64	62					9																	130494466		2049	4185	6234	SO:0001819	synonymous_variant	27433	exon4			GAGCACGCAGTGC	AA873275	CCDS6876.1, CCDS43879.1, CCDS48024.1	9q34.11	2010-08-20			ENSG00000160404	ENSG00000160404			11996	protein-coding gene	gene with protein product		608052				10644435	Standard	NM_001085347		Approved	FLJ14771, TORP1	uc004brs.4	Q5JU69	OTTHUMG00000020706	ENST00000373284.5:c.813C>T	chr9.hg19:g.130494466G>A		78.0	0.0		47.0	19.0	NM_001134430	A4FU12|A4FU13|Q3ZCN9|Q3ZCP0|Q5JU68|Q66K87|Q6UXW6|Q8NAN5|Q96SL7	Missense_Mutation	SNP	ENST00000373284.5	hg19	CCDS43879.1	.	.	.	.	.	.	.	.	.	.	G	7.531	0.658710	0.14645	.	.	ENSG00000160404	ENST00000336067	T	0.65732	-0.17	5.63	-11.3	0.00108	.	.	.	.	.	T	0.52158	0.1717	.	.	.	0.80722	D	1	B	0.10296	0.003	B	0.06405	0.002	T	0.47761	-0.9092	8	0.46703	T	0.11	-20.6337	22.6592	0.99974	0.7529:0.0:0.2471:0.0	.	229	Q8N2E6	TOR2X_HUMAN	C	229	ENSP00000338317:R229C	ENSP00000338317:R229C	R	-	1	0	TOR2A	129534287	0.396000	0.25262	0.101000	0.21167	0.359000	0.29487	-0.256000	0.08757	-2.876000	0.00321	-2.075000	0.00382	CGT	.	.		0.627	TOR2A-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054205.1	NM_130459		A	130494466	G	A	130494466	2	1	278	1	0	0	0	0	0	0	0	1	16390	1088	38	1		1	TOR2A	9	130494466	Silent	SNP	G	TCGA-G3-A25Z-01A-11D-A16V-10	18348684	130494466	10718965	29	39729										
ZNF248	57209	hgsc.bcm.edu	37	chr10	38121994	38121994	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	aagctcccaaaaatggtcatCttcattttcctggctgctct	6	12	4	0			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr10:38121994C>G	ENST00000395867.3	-	6	839	c.289G>C	c.(289-291)Gat>Cat	p.D97H	AL135791.1_ENST00000583461.1_RNA|ZNF248_ENST00000374648.3_Missense_Mutation_p.D97H|ZNF248_ENST00000494133.1_5'UTR|ZNF248_ENST00000357328.4_Missense_Mutation_p.D97H	NM_001267605.1|NM_001267606.1|NM_001267607.1|NM_021045.2	NP_001254534.1|NP_001254535.1|NP_001254536.1|NP_066383.1	Q8NDW4	ZN248_HUMAN	zinc finger protein 248	97					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(2)|urinary_tract(1)	20						AAATGGTCATCTTCATTTTCC	0.368																																					p.D97H		Atlas-SNP	.											.	ZNF248	61	.	0			c.G289C						.						81	76	78					10																	38121994		2203	4299	6502	SO:0001583	missense	57209	exon6			GGTCATCTTCATT	AJ491695	CCDS7194.1, CCDS58077.1, CCDS73087.1	10p11.21	2013-01-08			ENSG00000198105	ENSG00000198105		"Zinc fingers, C2H2-type", "-"	13041	protein-coding gene	gene with protein product						12566394	Standard	NM_021045		Approved	bA162G10.3	uc010qeu.2	Q8NDW4	OTTHUMG00000017980	ENST00000395867.3:c.289G>C	chr10.hg19:g.38121994C>G	ENSP00000379208:p.Asp97His	40.0	0.0		76.0	26.0	NM_001267597	Q8NDV8|Q9UMP3	Missense_Mutation	SNP	ENST00000395867.3	hg19	CCDS7194.1	.	.	.	.	.	.	.	.	.	.	C	11.06	1.527193	0.27299	.	.	ENSG00000198105	ENST00000395867;ENST00000374648;ENST00000357328;ENST00000395873	T;T;T;T	0.05649	3.41;5.71;3.41;5.64	4.86	3.95	0.45737	.	0.279280	0.25875	N	0.027726	T	0.13970	0.0338	L	0.55834	1.745	0.35022	D	0.757947	P;D	0.65815	0.855;0.995	B;P	0.57371	0.365;0.819	T	0.11494	-1.0585	10	0.54805	T	0.06	.	9.1437	0.36919	0.0:0.9007:0.0:0.0993	.	97;97	Q8NDW4;Q8NDV8	ZN248_HUMAN;.	H	97	ENSP00000379208:D97H;ENSP00000363778:D97H;ENSP00000349882:D97H;ENSP00000379214:D97H	ENSP00000349882:D97H	D	-	1	0	ZNF248	38162000	0.002000	0.14202	1.000000	0.80357	0.105000	0.19272	1.045000	0.30341	1.413000	0.46997	0.563000	0.77884	GAT	.	.		0.368	ZNF248-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047609.1	NM_021045		G	38121994	C	G	38121994	3	3	278	1	0	0	0	0	1	0	0	0	17808	913	32	4	1454	4	ZNF248	10	38121994	Missense_Mutation	SNP	C	TCGA-G3-A25Z-01A-11D-A16V-10		38121994	97412753	30	39730										
DPYSL4	10570	hgsc.bcm.edu	37	chr10	134018356	134018356	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	tcttcagggtctcaggctgaTgaccacatcgcccgacgcac	10	15	3	2	rs368616410		TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr10:134018356T>C	ENST00000338492.4	+	14	1805	c.1641T>C	c.(1639-1641)gaT>gaC	p.D547D	DPYSL4_ENST00000368629.1_Silent_p.D387D|DPYSL4_ENST00000368627.1_Silent_p.D387D	NM_006426.2	NP_006417.2	O14531	DPYL4_HUMAN	dihydropyrimidinase-like 4	547					axon guidance (GO:0007411)|nervous system development (GO:0007399)|pyrimidine nucleobase catabolic process (GO:0006208)	cytosol (GO:0005829)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		all_cancers(35;4.33e-08)|all_epithelial(44;6.75e-06)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)|Colorectal(31;0.19)		OV - Ovarian serous cystadenocarcinoma(35;7.21e-05)|Epithelial(32;8.01e-05)|all cancers(32;9.29e-05)|BRCA - Breast invasive adenocarcinoma(275;0.206)		CTCAGGCTGATGACCACATCG	0.622																																					p.D547D		Atlas-SNP	.											.	DPYSL4	91	.	0			c.T1641C						.	T		1,4405	2.1+/-5.4	0,1,2202	162	153	156		1641	-3.2	0.8	10		156	0,8600		0,0,4300	no	coding-synonymous	DPYSL4	NM_006426.2		0,1,6502	CC,CT,TT		0.0,0.0227,0.0077		547/573	134018356	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	10570	exon14			GGCTGATGACCAC	AB006713	CCDS7665.1	10q25.2-q26	2008-05-14			ENSG00000151640	ENSG00000151640			3016	protein-coding gene	gene with protein product		608407				8973361, 9652388	Standard	NM_006426		Approved	ULIP4, DRP-4	uc009ybb.3	O14531	OTTHUMG00000019283	ENST00000338492.4:c.1641T>C	chr10.hg19:g.134018356T>C		86.0	0.0		68.0	29.0	NM_006426	B2RMQ1|D3DRG5|O00240|Q5T0Q7	Silent	SNP	ENST00000338492.4	hg19	CCDS7665.1																																																																																			.	.		0.622	DPYSL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051050.2			C	134018356	T	C	134018356	2	2	278	1	0	0	0	0	0	0	0	1	4751	1461	51	2		2	DPYSL4	10	134018356	Silent	SNP	T	TCGA-G3-A25Z-01A-11D-A16V-10	95896362	134018356	1516391	31	39731										
USH1C	10083	hgsc.bcm.edu	37	chr11	17530990	17530990	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	gcctcccagtcctccactggAttgcctgtgtccccagtgcg	10	17	0	0			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr11:17530990A>G	ENST00000318024.4	-	16	1393				USH1C_ENST00000005226.7_Silent_p.N642N|USH1C_ENST00000527720.1_Intron|USH1C_ENST00000529563.1_Intron|USH1C_ENST00000527020.1_Intron	NM_005709.3	NP_005700.2	Q9Y6N9	USH1C_HUMAN	Usher syndrome 1C (autosomal recessive, severe)						auditory receptor cell differentiation (GO:0042491)|equilibrioception (GO:0050957)|G2/M transition of mitotic cell cycle (GO:0000086)|inner ear morphogenesis (GO:0042472)|parallel actin filament bundle assembly (GO:0030046)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	spectrin binding (GO:0030507)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	48						CCTCCACTGGATTGCCTGTGT	0.607																																					p.N642N		Atlas-SNP	.											.	USH1C	157	.	0			c.T1926C						.						86	76	79					11																	17530990		2200	4293	6493	SO:0001627	intron_variant	10083	exon18			CACTGGATTGCCT	AB006955	CCDS7825.1, CCDS31438.1, CCDS73265.1	11p14.3	2013-06-19	2004-05-19		ENSG00000006611	ENSG00000006611			12597	protein-coding gene	gene with protein product	"harmonin"	605242	"deafness, autosomal recessive 18"	DFNB18		10973247, 12107438	Standard	NM_005709		Approved	PDZ73, harmonin, NY-CO-37, NY-CO-38, PDZ-73, AIE-75, PDZD7C	uc001mne.3	Q9Y6N9	OTTHUMG00000166323	ENST00000318024.4:c.1285-7463T>C	chr11.hg19:g.17530990A>G		96.0	0.0		91.0	21.0	NM_153676	A8K423|Q7RTU8|Q96B29|Q9UM04|Q9UM17|Q9UPC3	Silent	SNP	ENST00000318024.4	hg19	CCDS31438.1																																																																																			.	.		0.607	USH1C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389146.1	NM_005709		G	17530990	A	G	17530990	1	3	278	0	1	0	0	0	0	0	0	0	17049	330	12	2		2	USH1C	11	17530990	Intron	SNP	A	TCGA-G3-A25Z-01A-11D-A16V-10		17530990	117475526	32	39732										
TRAF6	7189	hgsc.bcm.edu	37	chr11	36516546	36516546	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	ctgttctctgatgagtatagTattgcagtattcacagatga	9	6	2	4			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr11:36516546T>C	ENST00000526995.1	-	5	904	c.658A>G	c.(658-660)Act>Gct	p.T220A	TRAF6_ENST00000529150.1_5'UTR|TRAF6_ENST00000348124.5_Missense_Mutation_p.T220A	NM_004620.3	NP_004611.1	Q9Y4K3	TRAF6_HUMAN	TNF receptor-associated factor 6, E3 ubiquitin protein ligase	220	Interaction with TAX1BP1.				activation of MAPK activity (GO:0000187)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|activation of protein kinase activity (GO:0032147)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|apoptotic signaling pathway (GO:0097190)|bone resorption (GO:0045453)|cell development (GO:0048468)|cellular response to lipopolysaccharide (GO:0071222)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|JNK cascade (GO:0007254)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|protein autoubiquitination (GO:0051865)|protein complex assembly (GO:0006461)|protein K63-linked ubiquitination (GO:0070534)|protein polyubiquitination (GO:0000209)|regulation of immunoglobulin secretion (GO:0051023)|response to interleukin-1 (GO:0070555)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|lipid particle (GO:0005811)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	histone deacetylase binding (GO:0042826)|ligase activity (GO:0016874)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein kinase B binding (GO:0043422)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(13)|ovary(2)|pancreas(1)	27	all_lung(20;0.211)	all_hematologic(20;0.107)				ATGAGTATAGTATTGCAGTAT	0.259																																					p.T220A		Atlas-SNP	.											.	TRAF6	56	.	0			c.A658G						.						59	65	63					11																	36516546		2201	4283	6484	SO:0001583	missense	7189	exon5			GTATAGTATTGCA		CCDS7901.1	11p12	2013-01-09	2012-02-23		ENSG00000175104	ENSG00000175104		"RING-type (C3HC4) zinc fingers"	12036	protein-coding gene	gene with protein product		602355	"TNF receptor-associated factor 6"			8837778	Standard	NM_004620		Approved	RNF85	uc001mws.2	Q9Y4K3	OTTHUMG00000166391	ENST00000526995.1:c.658A>G	chr11.hg19:g.36516546T>C	ENSP00000433623:p.Thr220Ala	197.0	0.0		354.0	123.0	NM_004620	A6NKI7|A8KAB3|D3DR16|Q8NEH5	Missense_Mutation	SNP	ENST00000526995.1	hg19	CCDS7901.1	.	.	.	.	.	.	.	.	.	.	T	12.50	1.956005	0.34471	.	.	ENSG00000175104	ENST00000526995;ENST00000348124	T;T	0.25414	1.8;1.8	5.6	5.6	0.85130	Zinc finger, TRAF-type (1);TRAF-like (1);	0.086607	0.85682	D	0.000000	T	0.22126	0.0533	L	0.46947	1.48	0.40062	D	0.97591	B	0.32128	0.357	B	0.30316	0.114	T	0.04635	-1.0937	10	0.08179	T	0.78	-13.8274	15.7861	0.78304	0.0:0.0:0.0:1.0	.	220	Q9Y4K3	TRAF6_HUMAN	A	220	ENSP00000433623:T220A;ENSP00000337853:T220A	ENSP00000337853:T220A	T	-	1	0	TRAF6	36473122	1.000000	0.71417	0.974000	0.42286	0.983000	0.72400	3.311000	0.51919	2.129000	0.65627	0.528000	0.53228	ACT	.	.		0.259	TRAF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389530.1	NM_145803		C	36516546	T	C	36516546	3	2	278	1	0	0	0	0	1	0	0	0	16460	1638	57	2	922	2	TRAF6	11	36516546	Missense_Mutation	SNP	T	TCGA-G3-A25Z-01A-11D-A16V-10	18985556	36516546	98489970	33	39733										
GYLTL1B	120071	hgsc.bcm.edu	37	chr11	45948313	45948313	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	aagacccctgctttgagttcCggcagcagcagctcactgtg	11	13	1	2			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr11:45948313C>T	ENST00000531526.1	+	10	1327	c.1216C>T	c.(1216-1218)Cgg>Tgg	p.R406W	GYLTL1B_ENST00000401752.1_Missense_Mutation_p.R406W|GYLTL1B_ENST00000389968.3_Missense_Mutation_p.R133W|GYLTL1B_ENST00000536139.1_Missense_Mutation_p.R375W|GYLTL1B_ENST00000325468.5_Missense_Mutation_p.R406W|GYLTL1B_ENST00000529052.1_Missense_Mutation_p.R375W	NM_152312.3	NP_689525.3	Q8N3Y3	LARG2_HUMAN	glycosyltransferase-like 1B	406					muscle cell cellular homeostasis (GO:0046716)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(2)|endometrium(6)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	22				GBM - Glioblastoma multiforme(35;0.226)		CTTTGAGTTCCGGCAGCAGCA	0.627																																					p.R406W		Atlas-SNP	.											.	GYLTL1B	45	.	0			c.C1216T						.						76	75	75					11																	45948313		2203	4299	6502	SO:0001583	missense	120071	exon10			GAGTTCCGGCAGC		CCDS31473.1	11p11.12	2013-02-22			ENSG00000165905	ENSG00000165905		"Glycosyltransferase family 8 domain containing"	16522	protein-coding gene	gene with protein product		609709				15661757, 15958417	Standard	XM_005252785		Approved	PP5656, FLJ35207, LARGE2	uc001nbv.1	Q8N3Y3	OTTHUMG00000167037	ENST00000531526.1:c.1216C>T	chr11.hg19:g.45948313C>T	ENSP00000432869:p.Arg406Trp	32.0	0.0		34.0	16.0	NM_152312	A6NN75|Q8N8Y6|Q8NAK3|Q8WY62	Missense_Mutation	SNP	ENST00000531526.1	hg19	CCDS31473.1	.	.	.	.	.	.	.	.	.	.	C	32	5.145324	0.94603	.	.	ENSG00000165905	ENST00000529052;ENST00000531526;ENST00000401752;ENST00000389968;ENST00000325468;ENST00000536139;ENST00000534410	T;T;T;D;T;T	0.84070	0.82;0.81;0.81;-1.8;0.81;0.82	5.37	5.37	0.77165	.	0.054698	0.85682	D	0.000000	D	0.90817	0.7116	M	0.79805	2.47	0.80722	D	1	D;D;D	0.89917	1.0;0.998;0.998	P;P;P	0.61275	0.88;0.776;0.886	D	0.91802	0.5452	10	0.72032	D	0.01	-21.1699	19.1135	0.93328	0.0:1.0:0.0:0.0	.	375;375;406	B3KP69;E9PIZ2;Q8N3Y3	.;.;LARG2_HUMAN	W	375;406;406;133;406;375;67	ENSP00000431932:R375W;ENSP00000432869:R406W;ENSP00000385235:R406W;ENSP00000374618:R133W;ENSP00000324570:R406W;ENSP00000445044:R375W	ENSP00000324570:R406W	R	+	1	2	GYLTL1B	45904889	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	7.438000	0.80431	2.528000	0.85240	0.561000	0.74099	CGG	.	.		0.627	GYLTL1B-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392572.1	NM_152312		T	45948313	C	T	45948313	3	4	278	1	0	0	0	0	1	0	0	0	6916	643	23	1	1250	1	GYLTL1B	11	45948313	Missense_Mutation	SNP	C	TCGA-G3-A25Z-01A-11D-A16V-10	9431767	45948313	89058203	34	39734										
OR4C3	256144	hgsc.bcm.edu	37	chr11	48347263	48347263	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	aggtcccacagtgcagatggGagatgcaaagccctctccac	11	13	1	2			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr11:48347263G>A	ENST00000319856.4	+	1	792	c.771G>A	c.(769-771)ggG>ggA	p.G257G		NM_001004702.1	NP_001004702.1	Q8NH37	OR4C3_HUMAN	olfactory receptor, family 4, subfamily C, member 3	230						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(18)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	32						GTGCAGATGGGAGATGCAAAG	0.473																																					p.G257G		Atlas-SNP	.											.	OR4C3	75	.	0			c.G771A						.						261	208	226					11																	48347263		2201	4298	6499	SO:0001819	synonymous_variant	256144	exon1			AGATGGGAGATGC	AB065567	CCDS31489.1	11p11.2	2012-08-09				ENSG00000176547		"GPCR / Class A : Olfactory receptors"	14697	protein-coding gene	gene with protein product							Standard	NM_001004702		Approved		uc010rhv.2	Q8NH37	OTTHUMG00000166579	ENST00000319856.4:c.771G>A	chr11.hg19:g.48347263G>A		183.0	0.0		206.0	21.0	NM_001004702	B2RNF2|Q6IFB3	Silent	SNP	ENST00000319856.4	hg19	CCDS31489.1																																																																																			.	.		0.473	OR4C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390557.1	NM_001004702		A	48347263	G	A	48347263	2	1	278	1	0	0	0	0	0	0	0	1	11059	1161	41	3		3	OR4C3	11	48347263	Silent	SNP	G	TCGA-G3-A25Z-01A-11D-A16V-10	2398950	48347263	86659253	35	39735										
MRPL11	65003	hgsc.bcm.edu	37	chr11	66204833	66204833	+	Frame_Shift_Del	DEL	C	C	-													0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	gccctcacctgtttgccgggCccccttttcaatcccagctg							TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr11:66204833delC	ENST00000310999.7	-	3	394	c.301delG	c.(301-303)gccfs	p.A101fs	MRPL11_ENST00000329819.4_Frame_Shift_Del_p.A101fs|MRPL11_ENST00000430466.2_Frame_Shift_Del_p.A75fs|MRPL11_ENST00000524576.1_5'UTR	NM_016050.3	NP_057134.1	Q9Y3B7	RM11_HUMAN	mitochondrial ribosomal protein L11	101					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(3)|lung(2)|ovary(1)|prostate(1)	7						GTTTGCCGGGCCCCCTTTTCA	0.507																																					p.A101fs		Atlas-INDEL	.											.	MRPL11	25	.	0			c.302delC						.						59	59	59					11																	66204833		2200	4295	6495	SO:0001589	frameshift_variant	65003	exon3			.	AB051338	CCDS8139.1, CCDS8140.1, CCDS44655.1	11q13.2	2012-11-14			ENSG00000174547	ENSG00000174547		"Mitochondrial ribosomal proteins / large subunits"	14042	protein-coding gene	gene with protein product		611826					Standard	XR_247672		Approved		uc001ohz.4	Q9Y3B7	OTTHUMG00000167097	ENST00000310999.7:c.301delG	chr11.hg19:g.66204833delC	ENSP00000308897:p.Ala101fs	75.0	0.0		42.0	12.0	NM_170739	A6NLT0|A8K219|Q32P46|Q96Q73	Frame_Shift_Del	DEL	ENST00000310999.7	hg19	CCDS8139.1																																																																																			.	.		0.507	MRPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393098.2	NM_016050		-	66204833	C	-	66204833	7	5	278	1	0	1	0	1	0	0	0	0	9785	739	26	0	366	0	MRPL11	11	66204833	Frame_Shift_Del	DEL	C	TCGA-G3-A25Z-01A-11D-A16V-10	17857570	66204833	68801683	36	39736										
KRTAP5-7	440050	hgsc.bcm.edu	37	chr11	71238415	71238415	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	tgtggctccggctgtgggggCtgtggctctggctgtggggg	22	8	1	0	rs536333110	byFrequency	TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr11:71238415C>A	ENST00000398536.4	+	1	103	c.69C>A	c.(67-69)ggC>ggA	p.G23G		NM_001012503.1	NP_001012521.1	Q6L8G8	KRA57_HUMAN	keratin associated protein 5-7	23						keratin filament (GO:0045095)				breast(1)|endometrium(1)|kidney(3)|lung(6)|ovary(1)	12						GCTGTGGGGGCTGTGGCTCTG	0.657													c|||	7	0.00139776	0	0.0014	5008	,	,		10887	0.006		0	False		,,,				2504	0				p.G23G		Atlas-SNP	.											.	KRTAP5-7	23	.	0			c.C69A						.						58	76	70					11																	71238415		2193	4285	6478	SO:0001819	synonymous_variant	440050	exon1			TGGGGGCTGTGGC	AB126076	CCDS41682.1	11q13.4	2008-02-05			ENSG00000244411	ENSG00000244411		"Keratin associated proteins"	23602	protein-coding gene	gene with protein product						15144888	Standard	NM_001012503		Approved	KRTAP5.7, KRTAP5-3	uc001oqq.1	Q6L8G8	OTTHUMG00000057570	ENST00000398536.4:c.69C>A	chr11.hg19:g.71238415C>A		107.0	0.0		131.0	12.0	NM_001012503	B2RNM3|Q701N5	Silent	SNP	ENST00000398536.4	hg19	CCDS41682.1																																																																																			.	.		0.657	KRTAP5-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127953.1			A	71238415	C	A	71238415	2	1	278	1	0	0	0	0	0	0	0	1	8575	784	28	3		3	KRTAP5-7	11	71238415	Silent	SNP	C	TCGA-G3-A25Z-01A-11D-A16V-10	5033582	71238415	63768101	37	39737										
BRAP	8315	hgsc.bcm.edu	37	chr12	112093435	112093435	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	gtagattcgctgagattccaGctggcttgttagtaaatatg	11	6	0	2			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr12:112093435G>C	ENST00000327551.6	-	10	1296	c.1156C>G	c.(1156-1158)Ctg>Gtg	p.L386V	BRAP_ENST00000419234.4_Missense_Mutation_p.L416V|BRAP_ENST00000539060.1_Missense_Mutation_p.L237V			Q6UWU4	CF089_HUMAN	BRCA1 associated protein	0					epithelial cell proliferation (GO:0050673)|positive regulation of cell cycle (GO:0045787)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	20						TGAGATTCCAGCTGGCTTGTT	0.383																																					p.L416V	Pancreas(146;846 1904 7830 25130 26065)	Atlas-SNP	.											.	BRAP	42	.	0			c.C1246G						.						155	134	141					12																	112093435		2203	4300	6503	SO:0001583	missense	8315	exon10			ATTCCAGCTGGCT	AF035620	CCDS9154.1	12q24.12	2014-09-11			ENSG00000089234	ENSG00000089234		"RING-type (C3HC4) zinc fingers"	1099	protein-coding gene	gene with protein product	"impedes mitogenic signal propagation", "galectin-2-binding protein"	604986				9497340, 19198608	Standard	XM_005253944		Approved	BRAP2, RNF52, IMP	uc001tsn.4	Q7Z569	OTTHUMG00000169600	ENST00000327551.6:c.1156C>G	chr12.hg19:g.112093435G>C	ENSP00000330813:p.Leu386Val	78.0	0.0		105.0	38.0	NM_006768	B4DTT1|F4NAR0|F4NAR1|Q6ZMG5|Q7Z356|Q8IZ35	Missense_Mutation	SNP	ENST00000327551.6	hg19		.	.	.	.	.	.	.	.	.	.	G	19.68	3.873277	0.72180	.	.	ENSG00000089234	ENST00000419234;ENST00000539060;ENST00000327551;ENST00000547043	T;T;T	0.70164	-0.46;-0.46;-0.46	5.16	4.27	0.50696	.	0.000000	0.85682	D	0.000000	D	0.84000	0.5376	M	0.92459	3.31	0.80722	D	1	P;D	0.69078	0.956;0.997	P;D	0.78314	0.899;0.991	D	0.86081	0.1544	10	0.59425	D	0.04	-10.2253	10.9941	0.47565	0.1504:0.0:0.8496:0.0	.	237;416	B4DRM1;Q7Z569	.;BRAP_HUMAN	V	416;237;386;198	ENSP00000403524:L416V;ENSP00000441659:L237V;ENSP00000330813:L386V	ENSP00000330813:L386V	L	-	1	2	BRAP	110577818	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.188000	0.65093	1.181000	0.42912	0.561000	0.74099	CTG	.	.		0.383	BRAP-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404994.2			C	112093435	G	C	112093435	3	2	278	1	0	0	0	0	1	0	0	0	1499	962	34	4	544	4	BRAP	12	112093435	Missense_Mutation	SNP	G	TCGA-G3-A25Z-01A-11D-A16V-10		112093435	21758460	38	39738										
ZNF10	7556	hgsc.bcm.edu	37	chr12	133733009	133733009	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	tcagacagagcacacatctcAttctgcatcagagaacccat	6	13	4	3			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr12:133733009A>G	ENST00000248211.6	+	5	1399	c.1177A>G	c.(1177-1179)Att>Gtt	p.I393V	ZNF10_ENST00000426665.2_Missense_Mutation_p.I393V|ZNF10_ENST00000402932.2_Missense_Mutation_p.I259V|ZNF268_ENST00000416488.1_Intron|CTD-2140B24.4_ENST00000540096.2_Intron	NM_015394.4	NP_056209.2	P21506	ZNF10_HUMAN	zinc finger protein 10	393					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|prostate(1)|skin(5)|urinary_tract(1)	26	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;1.28e-06)|all_epithelial(31;0.0051)|Lung NSC(355;0.00948)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		CACACATCTCATTCTGCATCA	0.438																																					p.I393V		Atlas-SNP	.											.	ZNF10	58	.	0			c.A1177G						.						161	162	162					12																	133733009		2203	4300	6503	SO:0001583	missense	7556	exon5			CATCTCATTCTGC	X52332, BC024182	CCDS9283.1	12q24.33	2013-01-08	2005-05-22		ENSG00000256223	ENSG00000256223		"Zinc fingers, C2H2-type", "-"	12879	protein-coding gene	gene with protein product		194538	"zinc finger protein 10 (KOX 1)"			7865130, 8262519	Standard	NM_015394		Approved	KOX1	uc001ulq.3	P21506	OTTHUMG00000167944	ENST00000248211.6:c.1177A>G	chr12.hg19:g.133733009A>G	ENSP00000248211:p.Ile393Val	64.0	0.0		66.0	25.0	NM_015394	B2RBS1|Q8TC91	Missense_Mutation	SNP	ENST00000248211.6	hg19	CCDS9283.1	.	.	.	.	.	.	.	.	.	.	A	1.364	-0.588059	0.03799	.	.	ENSG00000256223	ENST00000248211;ENST00000426665;ENST00000402932	T;T;T	0.15017	2.46;2.46;2.46	3.73	1.16	0.20824	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	1.021450	0.07856	N	0.965538	T	0.10165	0.0249	N	0.21282	0.65	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.40608	-0.9554	9	.	.	.	.	4.1126	0.10065	0.6048:0.1785:0.2168:0.0	.	393	P21506	ZNF10_HUMAN	V	393;393;259	ENSP00000248211:I393V;ENSP00000393814:I393V;ENSP00000384893:I259V	.	I	+	1	0	ZNF10	132243082	0.000000	0.05858	0.992000	0.48379	0.994000	0.84299	-0.455000	0.06762	0.109000	0.17891	0.533000	0.62120	ATT	.	.		0.438	ZNF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397182.1	NM_015394		G	133733009	A	G	133733009	3	3	278	1	0	0	0	0	1	0	0	0	17727	217	8	2	1191	2	ZNF10	12	133733009	Missense_Mutation	SNP	A	TCGA-G3-A25Z-01A-11D-A16V-10	21639574	133733009	118886	39	39739										
POMP	51371	hgsc.bcm.edu	37	chr13	29242666	29242666	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	ctgagaaacattcagggtctAtttgctccgctaaaattaca	7	9	2	1	rs560145213		TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr13:29242666A>G	ENST00000380842.4	+	4	300	c.219A>G	c.(217-219)ctA>ctG	p.L73L	POMP_ENST00000460403.1_3'UTR	NM_015932.5	NP_057016.1	Q9Y244	POMP_HUMAN	proteasome maturation protein	73					proteasome assembly (GO:0043248)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)|proteasome complex (GO:0000502)				endometrium(2)|kidney(1)|large_intestine(1)	4		Lung SC(185;0.0367)		all cancers(112;0.141)|OV - Ovarian serous cystadenocarcinoma(117;0.216)		TTCAGGGTCTATTTGCTCCGC	0.373													A|||	1	0.000199681	8e-04	0	5008	,	,		17728	0		0	False		,,,				2504	0				p.L73L		Atlas-SNP	.											.	POMP	15	.	0			c.A219G						.						116	110	112					13																	29242666		2203	4300	6503	SO:0001819	synonymous_variant	51371	exon4			GGGTCTATTTGCT	AF077200	CCDS9331.1	13q12.13	2013-11-11	2006-07-04	2006-07-04	ENSG00000132963	ENSG00000132963			20330	protein-coding gene	gene with protein product	"proteassemblin"	613386	"chromosome 13 open reading frame 12"	C13orf12		11042152	Standard	NM_015932		Approved	HSPC014, UMP1	uc001usf.3	Q9Y244	OTTHUMG00000016652	ENST00000380842.4:c.219A>G	chr13.hg19:g.29242666A>G		68.0	0.0		75.0	19.0	NM_015932	A5HKJ2|D6MXU3|Q9HB69	Silent	SNP	ENST00000380842.4	hg19	CCDS9331.1																																																																																			.	.		0.373	POMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044327.1	NM_015932		G	29242666	A	G	29242666	2	3	278	1	0	0	0	0	0	0	0	1	12253	436	16	2		2	POMP	13	29242666	Silent	SNP	A	TCGA-G3-A25Z-01A-11D-A16V-10		29242666	85927212	40	39740										
NBEA	26960	hgsc.bcm.edu	37	chr13	35756573	35756573	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	tctgatggtttccaagtatcGtgacatattagaaccccaga	8	9	1	4			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr13:35756573G>A	ENST00000400445.3	+	29	5273	c.4739G>A	c.(4738-4740)cGt>cAt	p.R1580H	NBEA_ENST00000540320.1_Missense_Mutation_p.R1580H|NBEA_ENST00000310336.4_Missense_Mutation_p.R1580H|NBEA_ENST00000379939.2_Missense_Mutation_p.R1577H	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	1580					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)		p.R1580H(1)		NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		TCCAAGTATCGTGACATATTA	0.388																																					p.R1580H		Atlas-SNP	.											NBEA,NS,carcinoma,0,1	NBEA	340	.	1	Substitution - Missense(1)	endometrium(1)	c.G4739A						.						133	122	126					13																	35756573		1833	4088	5921	SO:0001583	missense	26960	exon29			AGTATCGTGACAT	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.4739G>A	chr13.hg19:g.35756573G>A	ENSP00000383295:p.Arg1580His	76.0	0.0		184.0	62.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	G	35	5.424444	0.96111	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336;ENST00000422518	T;T;T;T	0.69306	-0.39;-0.38;-0.39;-0.39	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	D	0.83248	0.5213	M	0.77103	2.36	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	D	0.84686	0.0720	10	0.87932	D	0	.	19.6933	0.96010	0.0:0.0:1.0:0.0	.	1580;1577	Q8NFP9;Q5T321	NBEA_HUMAN;.	H	1580;1580;1577;1580;239	ENSP00000440951:R1580H;ENSP00000383295:R1580H;ENSP00000369271:R1577H;ENSP00000308534:R1580H	ENSP00000308534:R1580H	R	+	2	0	NBEA	34654573	1.000000	0.71417	0.999000	0.59377	0.974000	0.67602	9.869000	0.99810	2.651000	0.90000	0.467000	0.42956	CGT	.	.		0.388	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		A	35756573	G	A	35756573	3	1	278	1	0	0	0	0	1	0	0	0	10196	1145	40	1	4853	1	NBEA	13	35756573	Missense_Mutation	SNP	G	TCGA-G3-A25Z-01A-11D-A16V-10	6513907	35756573	79413305	41	39741										
NOVA1	4857	hgsc.bcm.edu	37	chr14	26917336	26917336	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	gagatctgtatccttgcaccAgtcaactcctggtattccac	7	13	2	1			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr14:26917336A>T	ENST00000539517.2	-	5	1670	c.1353T>A	c.(1351-1353)acT>acA	p.T451T	NOVA1_ENST00000465357.2_Silent_p.T427T|NOVA1_ENST00000267422.7_Silent_p.T329T	NM_002515.2	NP_002506.2	P51513	NOVA1_HUMAN	neuro-oncological ventral antigen 1	454	KH 3. {ECO:0000255|PROSITE- ProRule:PRU00117}.				locomotory behavior (GO:0007626)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA metabolic process (GO:0051252)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(265;0.0135)		TCCTTGCACCAGTCAACTCCT	0.453																																					p.T451T		Atlas-SNP	.											.	NOVA1	146	.	0			c.T1353A						.						166	134	145					14																	26917336		2203	4300	6503	SO:0001819	synonymous_variant	4857	exon5			TGCACCAGTCAAC	U04840	CCDS9635.1, CCDS32060.1, CCDS32061.1	14q12	2006-06-09			ENSG00000139910	ENSG00000139910			7886	protein-coding gene	gene with protein product		602157				8558240	Standard	NM_006489		Approved		uc001wpy.3	P51513	OTTHUMG00000029385	ENST00000539517.2:c.1353T>A	chr14.hg19:g.26917336A>T		232.0	0.0		263.0	96.0	NM_002515	A8K0S4|A8K4Q7|D3DS81|D3DS82|Q6B004	Silent	SNP	ENST00000539517.2	hg19	CCDS32061.1																																																																																			.	.		0.453	NOVA1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000073261.3	NM_006491		T	26917336	A	T	26917336	2	4	278	1	0	0	0	0	0	0	0	1	10563	175	7	4		4	NOVA1	14	26917336	Silent	SNP	A	TCGA-G3-A25Z-01A-11D-A16V-10		26917336	80432204	42	39742										
SLC10A1	6554	hgsc.bcm.edu	37	chr14	70252897	70252897	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	aatgagaaccaggaccagtgAtatcacgatgcctttatagg	10	8	1	2			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr14:70252897A>G	ENST00000216540.4	-	2	617	c.484T>C	c.(484-486)Tca>Cca	p.S162P		NM_003049.3	NP_003040.1	Q14973	NTCP_HUMAN	solute carrier family 10 (sodium/bile acid cotransporter), member 1	162					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bile acid:sodium symporter activity (GO:0008508)			NS(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)	14				all cancers(60;0.00228)|BRCA - Breast invasive adenocarcinoma(234;0.0137)|OV - Ovarian serous cystadenocarcinoma(108;0.0226)	Bumetanide(DB00887)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Ethinyl Estradiol(DB00977)|Indomethacin(DB00328)|Liothyronine(DB00279)|Liotrix(DB01583)|Pitavastatin(DB08860)|Probenecid(DB01032)|Progesterone(DB00396)|Testosterone(DB00624)|Ursodeoxycholic acid(DB01586)	AGGACCAGTGATATCACGATG	0.517																																					p.S162P		Atlas-SNP	.											.	SLC10A1	32	.	0			c.T484C						.						236	194	208					14																	70252897		2203	4300	6503	SO:0001583	missense	6554	exon2			CCAGTGATATCAC	L21893	CCDS9797.1	14q24.2	2013-07-18	2013-07-18		ENSG00000100652	ENSG00000100652		"Solute carriers"	10905	protein-coding gene	gene with protein product		182396				8132774	Standard	NM_003049		Approved	NTCP	uc001xlr.2	Q14973	OTTHUMG00000171236	ENST00000216540.4:c.484T>C	chr14.hg19:g.70252897A>G	ENSP00000216540:p.Ser162Pro	70.0	0.0		76.0	36.0	NM_003049	B9EGB6|Q2TU29	Missense_Mutation	SNP	ENST00000216540.4	hg19	CCDS9797.1	.	.	.	.	.	.	.	.	.	.	A	11.60	1.687662	0.29962	.	.	ENSG00000100652	ENST00000216540	T	0.12147	2.71	5.01	5.01	0.66863	.	0.203863	0.42821	D	0.000647	T	0.40297	0.1111	M	0.89353	3.025	0.29023	N	0.88618	D	0.89917	1.0	D	0.76071	0.987	T	0.43909	-0.9362	10	0.48119	T	0.1	-11.5151	10.1438	0.42751	0.8509:0.0:0.0:0.1491	.	162	Q14973	NTCP_HUMAN	P	162	ENSP00000216540:S162P	ENSP00000216540:S162P	S	-	1	0	SLC10A1	69322650	0.465000	0.25815	0.222000	0.23844	0.004000	0.04260	1.097000	0.30988	2.227000	0.72691	0.459000	0.35465	TCA	.	.		0.517	SLC10A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412464.1			G	70252897	A	G	70252897	3	3	278	1	0	0	0	0	1	0	0	0	14388	333	12	2	581	2	SLC10A1	14	70252897	Missense_Mutation	SNP	A	TCGA-G3-A25Z-01A-11D-A16V-10	43335561	70252897	37096643	43	39743										
HERC2	8924	hgsc.bcm.edu	37	chr15	28465614	28465614	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	ccaccagagtcatcctctgtGtccgaatcctctgctgaggg	10	14	3	2			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr15:28465614G>T	ENST00000261609.7	-	37	5937	c.5829C>A	c.(5827-5829)gaC>gaA	p.D1943E		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		CATCCTCTGTGTCCGAATCCT	0.572																																					p.D1943E		Atlas-SNP	.											.	HERC2	501	.	0			c.C5829A						.						140	137	138					15																	28465614		2203	4300	6503	SO:0001583	missense	8924	exon37			CTCTGTGTCCGAA	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.5829C>A	chr15.hg19:g.28465614G>T	ENSP00000261609:p.Asp1943Glu	18.0	0.0		23.0	9.0	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	hg19	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	G	12.29	1.892424	0.33442	.	.	ENSG00000128731	ENST00000261609	T	0.37235	1.21	4.64	3.69	0.42338	.	0.105688	0.64402	D	0.000008	T	0.40498	0.1119	L	0.28274	0.84	0.58432	D	0.999999	D	0.58970	0.984	D	0.68192	0.956	T	0.05209	-1.0899	10	0.11182	T	0.66	.	13.2565	0.60081	0.0788:0.0:0.9212:0.0	.	1943	O95714	HERC2_HUMAN	E	1943	ENSP00000261609:D1943E	ENSP00000261609:D1943E	D	-	3	2	HERC2	26139209	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	4.399000	0.59703	2.411000	0.81874	0.650000	0.86243	GAC	.	.		0.572	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		T	28465614	G	T	28465614	3	4	278	1	0	0	0	0	1	0	0	0	7067	1368	48	3	8903	3	HERC2	15	28465614	Missense_Mutation	SNP	G	TCGA-G3-A25Z-01A-11D-A16V-10		28465614	74065778	44	39744										
SLC12A1	6557	hgsc.bcm.edu	37	chr15	48595052	48595052	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	gtcttactagttagaggaaaTcacaaaaatgtcttgacatt	7	6	3	2			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr15:48595052T>C	ENST00000558405.1	+	26	3284	c.3270T>C	c.(3268-3270)aaT>aaC	p.N1090N	SLC12A1_ENST00000380993.3_Silent_p.N1090N|SLC12A1_ENST00000396577.3_Silent_p.N1090N			Q13621	S12A1_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 1	1090					cell death (GO:0008219)|chemical homeostasis (GO:0048878)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|kidney development (GO:0001822)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:potassium:chloride symporter activity (GO:0008511)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|prostate(2)|skin(1)	59		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Potassium Chloride(DB00761)|Quinethazone(DB01325)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	TTAGAGGAAATCACAAAAATG	0.343																																					p.N1090N		Atlas-SNP	.											.	SLC12A1	243	.	0			c.T3270C						.						86	88	87					15																	48595052		2198	4297	6495	SO:0001819	synonymous_variant	6557	exon27			AGGAAATCACAAA		CCDS10129.2, CCDS53940.1	15q15-q21	2013-07-18	2013-07-18		ENSG00000074803	ENSG00000074803		"Solute carriers"	10910	protein-coding gene	gene with protein product		600839				8640224	Standard	NM_000338		Approved	NKCC2	uc010bem.3	Q13621	OTTHUMG00000131495	ENST00000558405.1:c.3270T>C	chr15.hg19:g.48595052T>C		66.0	0.0		89.0	31.0	NM_001184832	A8JYA2|E9PDW4	Silent	SNP	ENST00000558405.1	hg19	CCDS10129.2																																																																																			.	.		0.343	SLC12A1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417131.1			C	48595052	T	C	48595052	2	2	278	1	0	0	0	0	0	0	0	1	14397	1432	50	2		2	SLC12A1	15	48595052	Silent	SNP	T	TCGA-G3-A25Z-01A-11D-A16V-10	20129438	48595052	53936340	45	39745										
TNFAIP8L3	388121	hgsc.bcm.edu	37	chr15	51397266	51397266	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	cttgtttgtaacgtggcatcCcttgtgccttgggtccctgc	11	12	0	0	rs267604247		TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr15:51397266C>T	ENST00000327536.5	-	1	207	c.108G>A	c.(106-108)agG>agA	p.R36R	RP11-108K3.1_ENST00000559909.1_lincRNA	NM_207381.2	NP_997264.2	Q5GJ75	TP8L3_HUMAN	tumor necrosis factor, alpha-induced protein 8-like 3	36										endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	11				all cancers(107;0.000389)|GBM - Glioblastoma multiforme(94;0.00338)		ACGTGGCATCCCTTGTGCCTT	0.522																																					p.R36R		Atlas-SNP	.											.	TNFAIP8L3	30	.	0			c.G108A						.						277	218	238					15																	51397266		2196	4293	6489	SO:0001819	synonymous_variant	388121	exon1			GGCATCCCTTGTG	AK123281	CCDS32241.1	15q21.2	2005-08-09				ENSG00000183578			20620	protein-coding gene	gene with protein product							Standard	XM_005254367		Approved	FLJ41287	uc001zyy.3	Q5GJ75		ENST00000327536.5:c.108G>A	chr15.hg19:g.51397266C>T		111.0	0.0		126.0	37.0	NM_207381	Q6ZWD1	Silent	SNP	ENST00000327536.5	hg19	CCDS32241.1																																																																																			.	.		0.522	TNFAIP8L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418661.1	NM_207381		T	51397266	C	T	51397266	2	4	278	1	0	0	0	0	0	0	0	1	16294	622	22	3		3	TNFAIP8L3	15	51397266	Silent	SNP	C	TCGA-G3-A25Z-01A-11D-A16V-10	2802214	51397266	51134126	46	39746										
MEGF11	84465	hgsc.bcm.edu	37	chr15	66209210	66209210	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	agccaggggtgcagtggcagGccccgtcctcggcgctgcag	17	14	0	0			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr15:66209210G>A	ENST00000409699.2	-	17	2343	c.2171C>T	c.(2170-2172)gCc>gTc	p.A724V	MEGF11_ENST00000395625.2_Missense_Mutation_p.A649V|MEGF11_ENST00000288745.3_Missense_Mutation_p.A649V|MEGF11_ENST00000360698.4_Missense_Mutation_p.A724V|MEGF11_ENST00000422354.1_Missense_Mutation_p.A724V|MEGF11_ENST00000395614.1_5'UTR|MEGF11_ENST00000478721.1_5'Flank			A6BM72	MEG11_HUMAN	multiple EGF-like-domains 11	724	EGF-like 12. {ECO:0000255|PROSITE- ProRule:PRU00076}.				homotypic cell-cell adhesion (GO:0034109)|retina layer formation (GO:0010842)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	19						GCAGTGGCAGGCCCCGTCCTC	0.667											OREG0023198	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A724V		Atlas-SNP	.											.	MEGF11	70	.	0			c.C2171T						.						20	19	19					15																	66209210		2200	4296	6496	SO:0001583	missense	84465	exon17			TGGCAGGCCCCGT	AB058677	CCDS10213.2	15q22.31	2006-03-31			ENSG00000157890	ENSG00000157890			29635	protein-coding gene	gene with protein product		612454				11347906	Standard	NM_032445		Approved	KIAA1781, DKFZp434L121	uc002apm.2	A6BM72	OTTHUMG00000133175	ENST00000409699.2:c.2171C>T	chr15.hg19:g.66209210G>A	ENSP00000386908:p.Ala724Val	44.0	0.0	1090	81.0	29.0	NM_032445	Q17R86|Q6UXS5|Q8ND91|Q96KG6	Missense_Mutation	SNP	ENST00000409699.2	hg19	CCDS10213.2	.	.	.	.	.	.	.	.	.	.	G	19.31	3.803260	0.70682	.	.	ENSG00000157890	ENST00000409699;ENST00000288745;ENST00000422354;ENST00000395625;ENST00000360698	T;T;T;T;T	0.34072	1.38;1.38;1.38;1.38;1.38	4.66	2.64	0.31445	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.471570	0.15637	U	0.252065	T	0.33498	0.0865	L	0.43598	1.365	0.28218	N	0.92667	P;P	0.48640	0.858;0.913	B;P	0.49528	0.434;0.614	T	0.09250	-1.0683	10	0.25106	T	0.35	.	6.0547	0.19804	0.0983:0.0:0.5198:0.3819	.	724;649	A6BM72;A6BM72-2	MEG11_HUMAN;.	V	724;649;724;649;724	ENSP00000386908:A724V;ENSP00000288745:A649V;ENSP00000414475:A724V;ENSP00000378987:A649V;ENSP00000353919:A724V	ENSP00000288745:A649V	A	-	2	0	MEGF11	63996264	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	6.543000	0.73874	0.971000	0.38288	0.485000	0.47835	GCC	.	.		0.667	MEGF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329307.2	NM_032445		A	66209210	G	A	66209210	3	1	278	1	0	0	0	0	1	0	0	0	9470	1203	42	3	991	3	MEGF11	15	66209210	Missense_Mutation	SNP	G	TCGA-G3-A25Z-01A-11D-A16V-10	14811944	66209210	36322182	47	39747										
TP53	7157	hgsc.bcm.edu	37	chr17	7578271	7578271	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	ttccttccactcggataagaTgctgaggaggggccagacct	12	11	0	3			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr17:7578271T>C	ENST00000269305.4	-	6	767	c.578A>G	c.(577-579)cAt>cGt	p.H193R	TP53_ENST00000574684.1_Intron|TP53_ENST00000445888.2_Missense_Mutation_p.H193R|TP53_ENST00000413465.2_Missense_Mutation_p.H193R|TP53_ENST00000359597.4_Missense_Mutation_p.H193R|TP53_ENST00000420246.2_Missense_Mutation_p.H193R|TP53_ENST00000455263.2_Missense_Mutation_p.H193R	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	193	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		H -> D (in sporadic cancers; somatic mutation).|H -> L (in sporadic cancers; somatic mutation).|H -> N (in sporadic cancers; somatic mutation).|H -> P (in sporadic cancers; somatic mutation).|H -> Q (in sporadic cancers; somatic mutation).|H -> R (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7887414}.|H -> Y (in sporadic cancers; somatic mutation).|QH -> HN (in a sporadic cancer; somatic mutation).|QH -> HY (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.H193R(80)|p.H193L(42)|p.H193P(18)|p.0?(8)|p.?(6)|p.H61R(4)|p.H100R(4)|p.H100L(4)|p.H61L(4)|p.A189_V197delAPPQHLIRV(4)|p.P191_E198>Q(3)|p.H193fs*16(3)|p.P191fs*53(2)|p.H61P(2)|p.H100P(2)|p.A189fs*53(1)|p.P191fs*6(1)|p.H193_I195delHLI(1)|p.P59_E66>Q(1)|p.P191fs*15(1)|p.P98_E105>Q(1)|p.H193_I195>AP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TCGGATAAGATGCTGAGGAGG	0.562		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.H193R	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,carcinoma,0,1	TP53	33396	.	193	Substitution - Missense(160)|Whole gene deletion(8)|Complex - deletion inframe(6)|Unknown(6)|Deletion - In frame(5)|Deletion - Frameshift(4)|Insertion - Frameshift(3)|Complex - frameshift(1)	lung(36)|upper_aerodigestive_tract(26)|ovary(20)|breast(18)|oesophagus(14)|haematopoietic_and_lymphoid_tissue(12)|endometrium(12)|biliary_tract(10)|liver(9)|stomach(7)|central_nervous_system(6)|large_intestine(6)|urinary_tract(5)|skin(5)|bone(4)|pancreas(2)|prostate(1)	c.A578G	GRCh37	CM083194|CM951225	TP53	M		.						97	87	90					17																	7578271		2203	4300	6503	SO:0001583	missense	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	ATAAGATGCTGAG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.578A>G	chr17.hg19:g.7578271T>C	ENSP00000269305:p.His193Arg	79.0	0.0		61.0	35.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	14.03	2.413611	0.42817	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99850	-7.16;-7.16;-7.16;-7.16;-7.16;-7.16;-7.16;-7.16	5.41	4.33	0.51752	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99825	0.9922	M	0.92738	3.34	0.58432	D	0.999992	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D	0.97536	1.0083	10	0.72032	D	0.01	-29.0766	9.707	0.40222	0.0:0.0827:0.0:0.9173	.	154;193;193;100;193;193;193	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	R	193;193;193;193;193;193;182;100;61;100;61	ENSP00000410739:H193R;ENSP00000352610:H193R;ENSP00000269305:H193R;ENSP00000398846:H193R;ENSP00000391127:H193R;ENSP00000391478:H193R;ENSP00000425104:H61R;ENSP00000423862:H100R	ENSP00000269305:H193R	H	-	2	0	TP53	7518996	1.000000	0.71417	0.814000	0.32528	0.023000	0.10783	7.996000	0.88334	1.001000	0.39076	-0.256000	0.11100	CAT	.	.		0.562	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7578271	T	C	7578271	3	2	278	1	0	0	0	0	1	0	0	0	16396	1464	51	2	716	2	TP53	17	7578271	Missense_Mutation	SNP	T	TCGA-G3-A25Z-01A-11D-A16V-10		7578271	73616939	48	39748										
DDX42	11325	hgsc.bcm.edu	37	chr17	61890756	61890756	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	ttttgctggtgacctggtccGgaacttggaaggagccaatc	13	9	0	1			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr17:61890756G>T	ENST00000578681.1	+	16	2445	c.1844G>T	c.(1843-1845)cGg>cTg	p.R615L	DDX42_ENST00000457800.2_Missense_Mutation_p.R615L|DDX42_ENST00000389924.2_Missense_Mutation_p.R615L|DDX42_ENST00000359353.5_Missense_Mutation_p.R496L|DDX42_ENST00000583590.1_Missense_Mutation_p.R615L	NM_007372.2	NP_031398.2	Q86XP3	DDX42_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 42	615	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				protein localization (GO:0008104)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)	46						GACCTGGTCCGGAACTTGGAA	0.522																																					p.R615L		Atlas-SNP	.											.	DDX42	86	.	0			c.G1844T						.						117	95	102					17																	61890756		2203	4300	6503	SO:0001583	missense	11325	exon15			TGGTCCGGAACTT	BC015505	CCDS32704.1	17q23	2014-02-14	2013-05-13			ENSG00000198231		"DEAD-boxes"	18676	protein-coding gene	gene with protein product	"splicing factor 3b, subunit 8"	613369	"DEAD (Asp-Glu-Ala-Asp) box polypeptide 42"			10727850, 16397294	Standard	NM_007372		Approved	RNAHP, RHELP, SF3b125, SF3B8	uc002jbv.3	Q86XP3		ENST00000578681.1:c.1844G>T	chr17.hg19:g.61890756G>T	ENSP00000464050:p.Arg615Leu	87.0	0.0		85.0	23.0	NM_203499	A6NML1|A8KA43|O75619|Q68G51|Q96BK1|Q96HR7|Q9Y3V8	Missense_Mutation	SNP	ENST00000578681.1	hg19	CCDS32704.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.793936	0.90453	.	.	ENSG00000198231	ENST00000389924;ENST00000457800;ENST00000359353	T;T	0.23147	1.92;1.92	5.52	5.52	0.82312	Helicase, C-terminal (1);	0.207947	0.46758	D	0.000280	T	0.42675	0.1213	L	0.35341	1.055	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.74348	0.983;0.94	T	0.27434	-1.0074	10	0.87932	D	0	-11.7694	18.809	0.92050	0.0:0.0:1.0:0.0	.	161;615	B3KV84;Q86XP3	.;DDX42_HUMAN	L	615;615;332	ENSP00000374574:R615L;ENSP00000390121:R615L	ENSP00000352308:R332L	R	+	2	0	DDX42	59244488	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.841000	0.99482	2.764000	0.94973	0.650000	0.86243	CGG	.	.		0.522	DDX42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444368.1	NM_007372		T	61890756	G	T	61890756	3	4	278	1	0	0	0	0	1	0	0	0	4364	1116	39	1	1898	1	DDX42	17	61890756	Missense_Mutation	SNP	G	TCGA-G3-A25Z-01A-11D-A16V-10	54312485	61890756	19304454	49	39749										
YES1	7525	hgsc.bcm.edu	37	chr18	745776	745776	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	ttgtgatatagtatccaccaTtgtcaagtttcctaattttg	6	7	1	1	rs557201481		TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr18:745776T>C	ENST00000584307.1	-	6	826	c.656A>G	c.(655-657)aAt>aGt	p.N219S	YES1_ENST00000577961.1_Missense_Mutation_p.N224S|YES1_ENST00000314574.4_Missense_Mutation_p.N219S			P07947	YES_HUMAN	YES proto-oncogene 1, Src family tyrosine kinase	219	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				blood coagulation (GO:0007596)|cellular protein modification process (GO:0006464)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|glucose transport (GO:0015758)|innate immune response (GO:0045087)|leukocyte migration (GO:0050900)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|regulation of vascular permeability (GO:0043114)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(1)	17					Dasatinib(DB01254)	GTATCCACCATTGTCAAGTTT	0.348													T|||	1	0.000199681	0	0	5008	,	,		17674	0		0	False		,,,				2504	0.001				p.N219S		Atlas-SNP	.											.	YES1	50	.	0			c.A656G						.						163	147	152					18																	745776		2203	4299	6502	SO:0001583	missense	7525	exon6			CCACCATTGTCAA	M15990	CCDS11824.1	18p11.31-p11.21	2014-06-26	2014-06-26		ENSG00000176105	ENSG00000176105		"SH2 domain containing"	12841	protein-coding gene	gene with protein product		164880	"v-yes-1 Yamaguchi sarcoma viral oncogene homolog 1"			2983418	Standard	NM_005433		Approved	Yes, c-yes, HsT441	uc002kky.3	P07947	OTTHUMG00000131472	ENST00000584307.1:c.656A>G	chr18.hg19:g.745776T>C	ENSP00000462468:p.Asn219Ser	103.0	0.0		152.0	62.0	NM_005433	A6NLB3|D3DUH1	Missense_Mutation	SNP	ENST00000584307.1	hg19	CCDS11824.1	.	.	.	.	.	.	.	.	.	.	T	10.42	1.344976	0.24426	.	.	ENSG00000176105	ENST00000359834;ENST00000314574	T	0.26373	1.74	5.7	5.7	0.88788	SH2 motif (4);	0.082383	0.85682	D	0.000000	T	0.20659	0.0497	L	0.31120	0.905	0.49299	D	0.999772	B	0.02656	0.0	B	0.01281	0.0	T	0.04440	-1.0951	10	0.22109	T	0.4	.	15.9666	0.79979	0.0:0.0:0.0:1.0	.	219	P07947	YES_HUMAN	S	219	ENSP00000324740:N219S	ENSP00000324740:N219S	N	-	2	0	YES1	735776	0.969000	0.33509	1.000000	0.80357	0.995000	0.86356	0.517000	0.22832	2.174000	0.68829	0.482000	0.46254	AAT	.	.		0.348	YES1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440827.2	NM_005433		C	745776	T	C	745776	3	2	278	1	0	0	0	0	1	0	0	0	17489	1493	52	2	1003	2	YES1	18	745776	Missense_Mutation	SNP	T	TCGA-G3-A25Z-01A-11D-A16V-10		745776	77331472	50	39750										
ZNF91	7644	hgsc.bcm.edu	37	chr19	23545393	23545393	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	tttgtgcaccttacactcatCcacacttttacaaccttttc	2	14	1	0			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr19:23545393C>A	ENST00000300619.7	-	4	593	c.388G>T	c.(388-390)Gat>Tat	p.D130Y	ZNF91_ENST00000599743.1_Intron|ZNF91_ENST00000397082.2_Missense_Mutation_p.D98Y	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	130					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				TTACACTCATCCACACTTTTA	0.338																																					p.D130Y		Atlas-SNP	.											.	ZNF91	349	.	0			c.G388T						.						76	81	80					19																	23545393		2157	4280	6437	SO:0001583	missense	7644	exon4			ACTCATCCACACT	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"Zinc fingers, C2H2-type", "-"	13166	protein-coding gene	gene with protein product		603971	"zinc finger protein 91 (HPF7, HTF10)"			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.388G>T	chr19.hg19:g.23545393C>A	ENSP00000300619:p.Asp130Tyr	104.0	0.0		130.0	37.0	NM_003430	A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	hg19	CCDS42541.1	.	.	.	.	.	.	.	.	.	.	C	2.880	-0.232000	0.05983	.	.	ENSG00000167232	ENST00000300619;ENST00000397082	T;T	0.05996	3.36;3.36	0.987	-0.984	0.10259	.	.	.	.	.	T	0.15522	0.0374	L	0.61387	1.9	0.09310	N	1	B;D	0.89917	0.291;1.0	B;D	0.74674	0.093;0.984	T	0.12451	-1.0547	9	0.66056	D	0.02	.	3.7254	0.08473	0.0:0.661:0.0:0.339	.	98;130	Q05481-2;Q05481	.;ZNF91_HUMAN	Y	130;98	ENSP00000300619:D130Y;ENSP00000380272:D98Y	ENSP00000300619:D130Y	D	-	1	0	ZNF91	23337233	0.000000	0.05858	0.007000	0.13788	0.322000	0.28314	-0.648000	0.05391	-0.453000	0.07076	0.174000	0.16983	GAT	.	.		0.338	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430		A	23545393	C	A	23545393	3	1	278	1	0	0	0	0	1	0	0	0	18215	855	30	3	3191	3	ZNF91	19	23545393	Missense_Mutation	SNP	C	TCGA-G3-A25Z-01A-11D-A16V-10		23545393	35583590	51	39751										
PCSK2	5126	hgsc.bcm.edu	37	chr20	17208109	17208109	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	cgccaagttgcagcagaacaCggctttggagtccgaaaggt	13	10	0	1			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr20:17208109C>T	ENST00000262545.2	+	1	474	c.159C>T	c.(157-159)caC>caT	p.H53H	PCSK2_ENST00000377899.1_Silent_p.H34H|PCSK2_ENST00000536609.1_Silent_p.H53H	NM_002594.3	NP_002585.2	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2	53					cellular protein metabolic process (GO:0044267)|embryo development (GO:0009790)|enkephalin processing (GO:0034230)|insulin processing (GO:0030070)|islet amyloid polypeptide processing (GO:0034231)|nervous system development (GO:0007399)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)	dendrite (GO:0030425)|extracellular space (GO:0005615)|membrane (GO:0016020)|perikaryon (GO:0043204)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)	p.H53H(1)		breast(2)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|lung(17)|ovary(3)|pancreas(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	53					"""Insulin(DB00071)|Insulin Regular(DB00030)"	CAGCAGAACACGGCTTTGGAG	0.522																																					p.H53H		Atlas-SNP	.											PCSK2,colon,carcinoma,0,2	PCSK2	112	.	1	Substitution - coding silent(1)	lung(1)	c.C159T						.						69	59	63					20																	17208109		2203	4300	6503	SO:0001819	synonymous_variant	5126	exon1			AGAACACGGCTTT	AK312341	CCDS13125.1, CCDS56179.1, CCDS56180.1	20p11.2	2008-08-01			ENSG00000125851	ENSG00000125851			8744	protein-coding gene	gene with protein product	"neuroendocrine convertase 2", "KEX2-like endoprotease 2"	162151		NEC2		1765368	Standard	NM_001201528		Approved	PC2, SPC2	uc002wpm.3	P16519	OTTHUMG00000031941	ENST00000262545.2:c.159C>T	chr20.hg19:g.17208109C>T		80.0	0.0		86.0	33.0	NM_002594	B1ANH9|B4DFQ3|Q14927|Q5JYQ1|Q8IWA8|Q9NQG3|Q9NUG1|Q9UJC6	Silent	SNP	ENST00000262545.2	hg19	CCDS13125.1																																																																																			.	.		0.522	PCSK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078120.2	NM_002594		T	17208109	C	T	17208109	2	4	278	1	0	0	0	0	0	0	0	1	11610	535	19	1		1	PCSK2	20	17208109	Silent	SNP	C	TCGA-G3-A25Z-01A-11D-A16V-10		17208109	45817411	52	39752										
HUNK	30811	hgsc.bcm.edu	37	chr21	33296847	33296847	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	tgtcaccaaaaacctgcggcGagagggtcagatccagcaga	12	11	2	3			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr21:33296847G>A	ENST00000270112.2	+	2	689	c.329G>A	c.(328-330)cGa>cAa	p.R110Q		NM_014586.1	NP_055401.1	P57058	HUNK_HUMAN	hormonally up-regulated Neu-associated kinase	110	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|skin(2)|stomach(1)	30						AACCTGCGGCGAGAGGGTCAG	0.463																																					p.R110Q		Atlas-SNP	.											.	HUNK	74	.	0			c.G329A						.						58	54	55					21																	33296847		2203	4300	6503	SO:0001583	missense	30811	exon2			TGCGGCGAGAGGG	AJ271722	CCDS13610.1	21q22.1	2008-06-05	2008-06-05		ENSG00000142149	ENSG00000142149			13326	protein-coding gene	gene with protein product		606532	"hormonally upregulated Neu-associated kinase"			10662544, 10830953	Standard	NM_014586		Approved		uc002yph.3	P57058	OTTHUMG00000085019	ENST00000270112.2:c.329G>A	chr21.hg19:g.33296847G>A	ENSP00000270112:p.Arg110Gln	38.0	0.0		67.0	18.0	NM_014586		Missense_Mutation	SNP	ENST00000270112.2	hg19	CCDS13610.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.573179	0.86542	.	.	ENSG00000142149	ENST00000270112	T	0.27890	1.64	4.86	4.86	0.63082	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.067411	0.64402	D	0.000017	T	0.52773	0.1755	L	0.55017	1.72	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	T	0.55496	-0.8132	10	0.87932	D	0	-5.5714	18.1961	0.89822	0.0:0.0:1.0:0.0	.	110	P57058	HUNK_HUMAN	Q	110	ENSP00000270112:R110Q	ENSP00000270112:R110Q	R	+	2	0	HUNK	32218718	1.000000	0.71417	0.996000	0.52242	0.534000	0.34807	9.205000	0.95048	2.513000	0.84729	0.650000	0.86243	CGA	.	.		0.463	HUNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192782.1	NM_014586		A	33296847	G	A	33296847	3	1	278	1	0	0	0	0	1	0	0	0	7467	1058	37	1	335	1	HUNK	21	33296847	Missense_Mutation	SNP	G	TCGA-G3-A25Z-01A-11D-A16V-10		33296847	14833048	53	39753										
KRTAP10-12	386685	hgsc.bcm.edu	37	chr21	46117591	46117591	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	gtgtgcccgtctgctgcaagCccatctgctgtgtgcctgtc	12	14	2	0			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr21:46117591C>T	ENST00000400365.3	+	1	505	c.475C>T	c.(475-477)Ccc>Tcc	p.P159S	TSPEAR_ENST00000323084.4_Intron	NM_198699.1	NP_941972.1	P60413	KR10C_HUMAN	keratin associated protein 10-12	159	19 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(8)	9						CTGCTGCAAGCCCATCTGCTG	0.622																																					p.P159S		Atlas-SNP	.											.	KRTAP10-12	21	.	0			c.C475T						.						182	189	187					21																	46117591		2203	4300	6503	SO:0001583	missense	386685	exon1			TGCAAGCCCATCT	AB076364	CCDS42967.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000189169	ENSG00000189169		"Keratin associated proteins"	20533	protein-coding gene	gene with protein product			"keratin associated protein 18-12"	KRTAP18-12			Standard	NM_198699		Approved	KRTAP18.12, KAP10.12	uc002zfw.1	P60413	OTTHUMG00000057629	ENST00000400365.3:c.475C>T	chr21.hg19:g.46117591C>T	ENSP00000383216:p.Pro159Ser	163.0	0.0		107.0	37.0	NM_198699	B2RPA3	Missense_Mutation	SNP	ENST00000400365.3	hg19	CCDS42967.1	.	.	.	.	.	.	.	.	.	.	c	5.764	0.325382	0.10900	.	.	ENSG00000189169	ENST00000400365;ENST00000452870	T	0.01139	5.28	3.64	3.64	0.41730	.	.	.	.	.	T	0.03220	0.0094	L	0.46157	1.445	0.22866	N	0.99863	P	0.52316	0.952	P	0.57371	0.819	T	0.45673	-0.9245	9	0.49607	T	0.09	.	11.1263	0.48320	0.0:1.0:0.0:0.0	.	159	P60413	KR10C_HUMAN	S	159;67	ENSP00000383216:P159S	ENSP00000383216:P159S	P	+	1	0	KRTAP10-12	44942019	0.103000	0.21917	0.045000	0.18777	0.036000	0.12997	1.208000	0.32345	1.707000	0.51288	0.195000	0.17529	CCC	.	.		0.622	KRTAP10-12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128032.1	NM_198699		T	46117591	C	T	46117591	3	4	278	1	0	0	0	0	1	0	0	0	8517	739	26	3	477	3	KRTAP10-12	21	46117591	Missense_Mutation	SNP	C	TCGA-G3-A25Z-01A-11D-A16V-10	12820744	46117591	2012304	54	39754										
PLA2G6	8398	hgsc.bcm.edu	37	chr22	38528998	38528998	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	tgctgttcacgttgcagcccCgtttcagcagcatgcgggcc	12	14	2	0	rs374007706		TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr22:38528998C>T	ENST00000332509.3	-	7	1100	c.917G>A	c.(916-918)cGg>cAg	p.R306Q	PLA2G6_ENST00000402064.1_Missense_Mutation_p.R306Q|PLA2G6_ENST00000335539.3_Missense_Mutation_p.R306Q	NM_003560.2	NP_003551.2	O60733	PLPL9_HUMAN	phospholipase A2, group VI (cytosolic, calcium-independent)	306					cardiolipin acyl-chain remodeling (GO:0035965)|cardiolipin biosynthetic process (GO:0032049)|cell death (GO:0008219)|chemotaxis (GO:0006935)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|glycerophospholipid biosynthetic process (GO:0046474)|innate immune response (GO:0045087)|lipid catabolic process (GO:0016042)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phospholipid metabolic process (GO:0006644)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of ceramide biosynthetic process (GO:2000304)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of exocytosis (GO:0045921)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of vasodilation (GO:0045909)|regulation of store-operated calcium channel activity (GO:1901339)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|urinary bladder smooth muscle contraction (GO:0014832)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipase A2 activity (GO:0004623)			breast(2)|endometrium(6)|kidney(1)|large_intestine(4)|liver(1)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	24	Melanoma(58;0.045)				Quinacrine(DB01103)	GTTGCAGCCCCGTTTCAGCAG	0.667																																					p.R306Q		Atlas-SNP	.											.	PLA2G6	54	.	0			c.G917A						.	C	GLN/ARG,GLN/ARG,GLN/ARG	1,4387		0,1,2193	47	31	37		917,917,917	4.6	1	22		37	1,8579		0,1,4289	no	missense,missense,missense	PLA2G6	NM_001004426.1,NM_001199562.1,NM_003560.2	43,43,43	0,2,6482	TT,TC,CC		0.0117,0.0228,0.0154	probably-damaging,probably-damaging,probably-damaging	306/753,306/753,306/807	38528998	2,12966	2194	4290	6484	SO:0001583	missense	8398	exon7			CAGCCCCGTTTCA	AF064594	CCDS13967.1, CCDS33645.1	22q13.1	2013-01-10			ENSG00000184381	ENSG00000184381	3.1.1.4	"Patatin-like phospholipase domain containing", "Parkinson disease", "Ankyrin repeat domain containing"	9039	protein-coding gene	gene with protein product	"neurodegeneration with brain iron accumulation 2"	603604				9417066, 16799181, 19029121	Standard	NM_001199562		Approved	iPLA2, PNPLA9, PARK14, iPLA2beta, NBIA2	uc003aux.1	O60733	OTTHUMG00000151246	ENST00000332509.3:c.917G>A	chr22.hg19:g.38528998C>T	ENSP00000333142:p.Arg306Gln	57.0	0.0		39.0	17.0	NM_003560	A8K597|B0QYE8|O75645|Q8N452|Q9UG29|Q9UIT0|Q9Y671	Missense_Mutation	SNP	ENST00000332509.3	hg19	CCDS13967.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.4|20.4	3.985681|3.985681	0.74589|0.74589	2.28E-4|2.28E-4	1.17E-4|1.17E-4	ENSG00000184381|ENSG00000184381	ENST00000427114;ENST00000427453;ENST00000452542|ENST00000332509;ENST00000419848;ENST00000335539;ENST00000402064;ENST00000335538;ENST00000396860;ENST00000451461	.|T;T;T	.|0.65549	.|-0.16;-0.16;-0.16	5.56|5.56	4.55|4.55	0.56014|0.56014	.|Ankyrin repeat-containing domain (3);	.|0.312733	.|0.32204	.|N	.|0.006425	T|T	0.65575|0.65575	0.2704|0.2704	L|L	0.45352|0.45352	1.415|1.415	0.09310|0.09310	N|N	1|1	.|D;P;D	.|0.89917	.|1.0;0.942;0.959	.|D;P;B	.|0.65684	.|0.937;0.455;0.347	T|T	0.54827|0.54827	-0.8235|-0.8235	5|10	.|0.22109	.|T	.|0.4	-24.7838|-24.7838	8.5236|8.5236	0.33291|0.33291	0.0:0.8263:0.0:0.1737|0.0:0.8263:0.0:0.1737	.|.	.|271;306;306	.|B7Z6K3;O60733-2;O60733	.|.;.;PA2G6_HUMAN	R|Q	111;58;137|306;167;306;306;234;306;271	.|ENSP00000333142:R306Q;ENSP00000335149:R306Q;ENSP00000386100:R306Q	.|ENSP00000333142:R306Q	G|R	-|-	1|2	0|0	PLA2G6|PLA2G6	36858944|36858944	0.051000|0.051000	0.20477|0.20477	0.998000|0.998000	0.56505|0.56505	0.987000|0.987000	0.75469|0.75469	1.277000|1.277000	0.33167|0.33167	2.620000|2.620000	0.88729|0.88729	0.650000|0.650000	0.86243|0.86243	GGG|CGG	.	.		0.667	PLA2G6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321860.1	NM_001004426		T	38528998	C	T	38528998	3	4	278	1	0	0	0	0	1	0	0	0	12017	652	23	1	1547	1	PLA2G6	22	38528998	Missense_Mutation	SNP	C	TCGA-G3-A25Z-01A-11D-A16V-10		38528998	12775568	55	39755										
MGAT3	4248	hgsc.bcm.edu	37	chr22	39883537	39883537	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	ggtcacgccccaggccagccCcgagccaggaggccctgacc	13	19	1	1			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr22:39883537C>A	ENST00000341184.6	+	2	400	c.185C>A	c.(184-186)cCc>cAc	p.P62H		NM_001098270.1|NM_002409.4	NP_001091740.1|NP_002400.3	Q09327	MGAT3_HUMAN	mannosyl (beta-1,4-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase	62	Pro-rich.				cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-1,4-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0003830)			endometrium(4)|kidney(1)|large_intestine(5)|lung(12)|prostate(1)|skin(1)	24	Melanoma(58;0.04)					CAGGCCAGCCCCGAGCCAGGA	0.677																																					p.P62H		Atlas-SNP	.											.	MGAT3	65	.	0			c.C185A						.						78	87	84					22																	39883537		2203	4300	6503	SO:0001583	missense	4248	exon2			CCAGCCCCGAGCC	D13789	CCDS13994.2	22q13.1	2013-02-25			ENSG00000128268	ENSG00000128268	2.4.1.144	"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	7046	protein-coding gene	gene with protein product		604621				8370666	Standard	NM_002409		Approved	GNT-III	uc010gxy.3	Q09327	OTTHUMG00000030185	ENST00000341184.6:c.185C>A	chr22.hg19:g.39883537C>A	ENSP00000345270:p.Pro62His	60.0	0.0		47.0	18.0	NM_002409	A6NGD0|Q14CK5|Q6IC49|Q9UH32	Missense_Mutation	SNP	ENST00000341184.6	hg19	CCDS13994.2	.	.	.	.	.	.	.	.	.	.	C	16.25	3.069976	0.55539	.	.	ENSG00000128268	ENST00000341184;ENST00000429402;ENST00000418314	.	.	.	5.03	5.03	0.67393	.	0.583594	0.16049	N	0.232060	T	0.57169	0.2035	N	0.24115	0.695	0.42326	D	0.992278	D	0.54047	0.964	P	0.50791	0.65	T	0.63834	-0.6547	9	0.72032	D	0.01	.	18.3612	0.90375	0.0:1.0:0.0:0.0	.	62	Q09327	MGAT3_HUMAN	H	62;62;90	.	ENSP00000345270:P62H	P	+	2	0	MGAT3	38213483	0.991000	0.36638	0.976000	0.42696	0.934000	0.57294	4.146000	0.58072	2.338000	0.79540	0.467000	0.42956	CCC	.	.		0.677	MGAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075039.2	NM_002409		A	39883537	C	A	39883537	3	1	278	1	0	0	0	0	1	0	0	0	9553	623	22	3	187	3	MGAT3	22	39883537	Missense_Mutation	SNP	C	TCGA-G3-A25Z-01A-11D-A16V-10	1354539	39883537	11421029	56	39756										
PPARA	5465	hgsc.bcm.edu	37	chr22	46615711	46615711	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	tccccctccaaaccctagcgAttcgttttggacgaatgcca	7	15	0	0			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chr22:46615711A>C	ENST00000396000.2	+	6	776	c.511A>C	c.(511-513)Att>Ctt	p.I171L	PPARA_ENST00000402126.1_Missense_Mutation_p.I171L|PPARA_ENST00000407236.1_Missense_Mutation_p.I171L|PPARA_ENST00000434345.2_Intron|PPARA_ENST00000262735.5_Missense_Mutation_p.I171L			Q07869	PPARA_HUMAN	peroxisome proliferator-activated receptor alpha	171					behavioral response to nicotine (GO:0035095)|cellular lipid metabolic process (GO:0044255)|circadian regulation of gene expression (GO:0032922)|enamel mineralization (GO:0070166)|epidermis development (GO:0008544)|fatty acid metabolic process (GO:0006631)|fatty acid transport (GO:0015908)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular receptor signaling pathway (GO:0030522)|lipid metabolic process (GO:0006629)|lipoprotein metabolic process (GO:0042157)|negative regulation of appetite (GO:0032099)|negative regulation of blood pressure (GO:0045776)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of glycolytic process (GO:0045820)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of receptor biosynthetic process (GO:0010871)|negative regulation of sequestering of triglyceride (GO:0010891)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular ketone metabolic process by positive regulation of transcription from RNA polymerase II promoter (GO:0072366)|regulation of circadian rhythm (GO:0042752)|regulation of glycolytic by positive regulation of transcription from RNA polymerase II promoter (GO:0072363)|regulation of lipid transport by positive regulation of transcription from RNA polymerase II promoter (GO:0072369)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|wound healing (GO:0042060)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|drug binding (GO:0008144)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|lipid binding (GO:0008289)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|ubiquitin conjugating enzyme binding (GO:0031624)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	15		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00522)	Bezafibrate(DB01393)|Clofibrate(DB00636)|Fenofibrate(DB01039)|Gemfibrozil(DB01241)|Indomethacin(DB00328)	AACCCTAGCGATTCGTTTTGG	0.488																																					p.I171L		Atlas-SNP	.											.	PPARA	36	.	0			c.A511C						.						69	64	66					22																	46615711		2203	4300	6503	SO:0001583	missense	5465	exon6			CTAGCGATTCGTT	L02932	CCDS33669.1	22q12-q13.1	2013-01-16	2006-10-17		ENSG00000186951	ENSG00000186951		"Nuclear hormone receptors"	9232	protein-coding gene	gene with protein product		170998	"peroxisome proliferative activated receptor, alpha"	PPAR		7684926, 10591208	Standard	XM_005261655		Approved	hPPAR, NR1C1	uc003bgx.1	Q07869	OTTHUMG00000150443	ENST00000396000.2:c.511A>C	chr22.hg19:g.46615711A>C	ENSP00000379322:p.Ile171Leu	25.0	0.0		43.0	22.0	NM_001001928	B0G0X3|Q16241|Q6I9S0|Q92486|Q92689|Q9Y3N1	Missense_Mutation	SNP	ENST00000396000.2	hg19	CCDS33669.1	.	.	.	.	.	.	.	.	.	.	A	17.14	3.313025	0.60414	.	.	ENSG00000186951	ENST00000396000;ENST00000262735;ENST00000407236;ENST00000402126	D;D;D;D	0.96200	-3.94;-3.94;-3.94;-3.94	5.51	5.51	0.81932	Nuclear hormone receptor, ligand-binding (1);Zinc finger, nuclear hormone receptor-type (1);	0.000000	0.85682	D	0.000000	D	0.95981	0.8691	M	0.84773	2.715	0.80722	D	1	B;B	0.21905	0.062;0.062	B;B	0.32211	0.142;0.142	D	0.94764	0.7939	10	0.87932	D	0	.	14.8173	0.70045	1.0:0.0:0.0:0.0	.	171;171	F1D8S4;Q07869	.;PPARA_HUMAN	L	171	ENSP00000379322:I171L;ENSP00000262735:I171L;ENSP00000385523:I171L;ENSP00000385246:I171L	ENSP00000262735:I171L	I	+	1	0	PPARA	44994375	1.000000	0.71417	0.928000	0.36995	0.339000	0.28857	9.101000	0.94219	2.082000	0.62665	0.454000	0.30748	ATT	.	.		0.488	PPARA-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318129.3	NM_001001928		C	46615711	A	C	46615711	3	2	278	1	0	0	0	0	1	0	0	0	12306	333	12	5	525	5	PPARA	22	46615711	Missense_Mutation	SNP	A	TCGA-G3-A25Z-01A-11D-A16V-10	6732174	46615711	4688855	57	39757										
GPR34	2857	hgsc.bcm.edu	37	chrX	41555141	41555141	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	tttctgggtattcaccgtaaAagaaattccattcaaattta	5	7	3	1			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chrX:41555141A>G	ENST00000378142.4	+	3	539	c.255A>G	c.(253-255)aaA>aaG	p.K85K	CASK_ENST00000378158.1_Intron|CASK_ENST00000421587.2_Intron|GPR34_ENST00000378138.5_Silent_p.K85K|CASK_ENST00000378154.1_Intron|CASK_ENST00000442742.2_Intron|CASK_ENST00000378163.1_Intron|CASK_ENST00000318588.9_Intron|CASK_ENST00000378166.4_Intron|CASK_ENST00000361962.4_Intron	NM_001097579.1|NM_005300.3	NP_001091048.1|NP_005291.1	Q9UPC5	GPR34_HUMAN	G protein-coupled receptor 34	85					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(1)|large_intestine(6)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	14						TTCACCGTAAAAGAAATTCCA	0.388																																					p.K85K		Atlas-SNP	.											.	GPR34	42	.	0			c.A255G						.						113	104	107					X																	41555141		2203	4300	6503	SO:0001819	synonymous_variant	2857	exon3			CCGTAAAAGAAAT	AF039686	CCDS14258.1	Xp11.4	2012-08-21			ENSG00000171659	ENSG00000171659		"GPCR / Class A : Orphans"	4490	protein-coding gene	gene with protein product		300241				10395919, 10036181	Standard	NM_005300		Approved		uc004dfq.4	Q9UPC5	OTTHUMG00000021375	ENST00000378142.4:c.255A>G	chrX.hg19:g.41555141A>G		49.0	0.0		105.0	50.0	NM_001097579	O95853	Silent	SNP	ENST00000378142.4	hg19	CCDS14258.1																																																																																			.	.		0.388	GPR34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056264.1	NM_005300		G	41555141	A	G	41555141	2	3	278	1	0	0	0	0	0	0	0	1	6697	11	1	2		2	GPR34	23	41555141	Silent	SNP	A	TCGA-G3-A25Z-01A-11D-A16V-10		41555141	113715419	58	39758										
OCRL	4952	hgsc.bcm.edu	37	chrX	128722192	128722192	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	2	1	0.78125	3.90625	0.434027777777778	1	1	0	cccctggaatgcaggaagagCtccagcagatcattgattgt	11	10	1	3			TCGA-G3-A25Z-01A-11D-A16V-10	TCGA-G3-A25Z-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3fd6af37-1d08-48ee-ab7f-162bb2005b98	543bf78c-8771-4841-84c6-cee5677bb250	g.chrX:128722192C>T	ENST00000371113.4	+	21	2458	c.2293C>T	c.(2293-2295)Ctc>Ttc	p.L765F	OCRL_ENST00000357121.5_Missense_Mutation_p.L757F	NM_000276.3	NP_000267.2	Q01968	OCRL_HUMAN	oculocerebrorenal syndrome of Lowe	765	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				cilium assembly (GO:0042384)|in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|lipid metabolic process (GO:0006629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|Golgi-associated vesicle (GO:0005798)|nucleus (GO:0005634)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	inositol phosphate phosphatase activity (GO:0052745)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)			breast(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(24)|ovary(2)|upper_aerodigestive_tract(3)	48						GCAGGAAGAGCTCCAGCAGAT	0.463																																					p.L765F		Atlas-SNP	.											.	OCRL	117	.	0			c.C2293T						.						96	85	89					X																	128722192		2203	4300	6503	SO:0001583	missense	4952	exon21			GAAGAGCTCCAGC	U57627	CCDS35393.1, CCDS35394.1	Xq25	2014-06-18			ENSG00000122126	ENSG00000122126			8108	protein-coding gene	gene with protein product		300535					Standard	NM_001587		Approved	OCRL1	uc004euq.3	Q01968	OTTHUMG00000022706	ENST00000371113.4:c.2293C>T	chrX.hg19:g.128722192C>T	ENSP00000360154:p.Leu765Phe	27.0	0.0		35.0	28.0	NM_000276	A6NKI1|A8KAP2|B7ZLX2|O60800|Q15684|Q15774|Q4VY09|Q4VY10|Q5JQF1|Q5JQF2|Q9UJG5|Q9UMA5	Missense_Mutation	SNP	ENST00000371113.4	hg19	CCDS35393.1	.	.	.	.	.	.	.	.	.	.	C	6.013	0.370877	0.11409	.	.	ENSG00000122126	ENST00000371113;ENST00000357121	T;T	0.20200	2.09;2.09	5.52	3.16	0.36331	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.070421	0.56097	D	0.000035	T	0.24005	0.0581	L	0.28504	0.86	0.53688	D	0.999978	D;B	0.63046	0.992;0.044	P;B	0.62813	0.907;0.04	T	0.09862	-1.0655	10	0.12430	T	0.62	.	7.4919	0.27466	0.0:0.2692:0.0:0.7308	.	757;765	Q01968-2;Q01968	.;OCRL_HUMAN	F	765;757	ENSP00000360154:L765F;ENSP00000349635:L757F	ENSP00000349635:L757F	L	+	1	0	OCRL	128549873	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	0.664000	0.25068	0.252000	0.21531	-0.340000	0.08031	CTC	.	.		0.463	OCRL-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058917.1	NM_000276		T	128722192	C	T	128722192	3	4	278	1	0	0	0	0	1	0	0	0	10832	797	28	3	2375	3	OCRL	23	128722192	Missense_Mutation	SNP	C	TCGA-G3-A25Z-01A-11D-A16V-10	87167051	128722192	26548368	59	39759										
PLEKHN1	84069	hgsc.bcm.edu	37	chr1	909846	909855	+	Frame_Shift_Del	DEL	GGGACCCCGG	GGGACCCCGG	-													0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tcggtcccccaggaggagccGggaccccggctacgaccacc					rs142252262	byFrequency	TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	GGGACCCCGG	GGGACCCCGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:909846_909855delGGGACCCCGG	ENST00000379409.2	+	15	1913_1922	c.1883_1892delGGGACCCCGG	c.(1882-1893)cgggaccccggcfs	p.RDPG628fs	PLEKHN1_ENST00000379407.3_Frame_Shift_Del_p.RDPG541fs|PLEKHN1_ENST00000379410.3_Frame_Shift_Del_p.RDPG576fs			Q494U1	PKHN1_HUMAN	pleckstrin homology domain containing, family N member 1	628										central_nervous_system(1)|endometrium(3)|kidney(1)|lung(2)|skin(1)|urinary_tract(1)	9	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.93e-23)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.00095)|Kidney(185;0.0023)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.199)		AGGAGGAGCCGGGACCCCGGCTACGACCAC	0.629																																					p.576_579del		Atlas-Indel,Pindel	.											.	PLEKHN1	49	.	0			c.1726_1735del						.																																			SO:0001589	frameshift_variant	84069	exon16			.	AL136730	CCDS4.1, CCDS53256.1	1p36.33	2013-01-11			ENSG00000187583	ENSG00000187583		"Pleckstrin homology (PH) domain containing"	25284	protein-coding gene	gene with protein product						11230166	Standard	NM_032129		Approved	DKFZP434H2010	uc001acd.3	Q494U1	OTTHUMG00000040756	ENST00000379409.2:c.1883_1892delGGGACCCCGG	chr1.hg19:g.909846_909855delGGGACCCCGG	ENSP00000368719:p.Arg628fs	75.0	0.0		62.0	16.0	NM_032129	Q494U2|Q5SV98|Q9H0M7	Frame_Shift_Del	DEL	ENST00000379409.2	hg19																																																																																				.	.		0.629	PLEKHN1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000473256.1	NM_032129		-	909855	GGGACCCCGG	-	909846	7	5	279	1	0	1	0	1	0	0	0	0	12092	1116	39	0	1825	0	PLEKHN1	1	909846	Frame_Shift_Del	DEL	GGGACCCCGG	TCGA-G3-A3CG-01A-11D-A20W-10		909846	248340775	1	39760										
MMEL1	79258	hgsc.bcm.edu	37	chr1	2537745	2537745	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	agatgaagaggtcgatgaggAcgcgcctgttgaactgtgag	16	6	0	6			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:2537745A>G	ENST00000378412.3	-	8	853	c.692T>C	c.(691-693)gTc>gCc	p.V231A	MMEL1_ENST00000502556.1_Intron|MMEL1_ENST00000288709.6_Missense_Mutation_p.V222A			Q495T6	MMEL1_HUMAN	membrane metallo-endopeptidase-like 1	231						endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|urinary_tract(1)	27	all_cancers(77;0.000233)|all_epithelial(69;8.55e-05)|all_lung(157;0.0228)|Lung NSC(156;0.0402)|Ovarian(185;0.0634)	all_epithelial(116;1.03e-20)|all_lung(118;5.15e-09)|Lung NSC(185;9.02e-07)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;8.52e-23)|GBM - Glioblastoma multiforme(42;1.49e-08)|Colorectal(212;4.79e-05)|COAD - Colon adenocarcinoma(227;0.000213)|Kidney(185;0.000371)|BRCA - Breast invasive adenocarcinoma(365;0.00219)|KIRC - Kidney renal clear cell carcinoma(229;0.00571)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.131)		GTCGATGAGGACGCGCCTGTT	0.647																																					p.V231A		Atlas-SNP	.											.	MMEL1	64	.	0			c.T692C						.						65	59	61					1																	2537745		2203	4300	6503	SO:0001583	missense	79258	exon8			ATGAGGACGCGCC	AF336981	CCDS30569.1, CCDS30569.2	1p36	2008-02-05			ENSG00000142606	ENSG00000142606			14668	protein-coding gene	gene with protein product			"membrane metallo-endopeptidase-like 2"	MMEL2			Standard	NM_033467		Approved	SEP, NL1, NL2, NEPII	uc001ajy.2	Q495T6	OTTHUMG00000000846	ENST00000378412.3:c.692T>C	chr1.hg19:g.2537745A>G	ENSP00000367668:p.Val231Ala	130.0	0.0		95.0	4.0	NM_033467	B9DI79|Q495T7|Q495T8|Q5SZS6|Q96PH9	Missense_Mutation	SNP	ENST00000378412.3	hg19	CCDS30569.2	.	.	.	.	.	.	.	.	.	.	a	4.482	0.089316	0.08632	.	.	ENSG00000142606	ENST00000288709;ENST00000378412	T;T	0.75154	-0.91;-0.91	4.76	4.76	0.60689	Peptidase M13 (1);	0.495220	0.21506	N	0.073442	T	0.68210	0.2976	L	0.50919	1.6	0.26583	N	0.973333	B	0.19445	0.036	B	0.28465	0.09	T	0.54596	-0.8270	10	0.12103	T	0.63	-33.0256	13.4557	0.61197	1.0:0.0:0.0:0.0	.	231	Q495T6	MMEL1_HUMAN	A	222;231	ENSP00000288709:V222A;ENSP00000367668:V231A	ENSP00000288709:V222A	V	-	2	0	MMEL1	2527605	0.699000	0.27786	0.952000	0.39060	0.936000	0.57629	3.247000	0.51422	1.766000	0.52107	0.523000	0.50628	GTC	.	.		0.647	MMEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002395.2	NM_033467		G	2537745	A	G	2537745	3	3	279	1	0	0	0	0	1	0	0	0	9655	275	10	2	1715	2	MMEL1	1	2537745	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	1627899	2537745	246712876	2	39761										
MEGF6	1953	hgsc.bcm.edu	37	chr1	3414980	3414980	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gccggctgggcagaggcagcGgcccgtgtgcgggtcacaca	18	13	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:3414980G>A	ENST00000356575.4	-	26	3533	c.3307C>T	c.(3307-3309)Cgc>Tgc	p.R1103C	MEGF6_ENST00000294599.4_Missense_Mutation_p.R912C	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	1103	EGF-like 20. {ECO:0000255|PROSITE- ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			cervix(2)|endometrium(3)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105)	all_epithelial(116;7.41e-22)|all_lung(118;8.3e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.78e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.86e-22)|GBM - Glioblastoma multiforme(42;1.96e-12)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000448)|BRCA - Breast invasive adenocarcinoma(365;0.000779)|KIRC - Kidney renal clear cell carcinoma(229;0.00645)|STAD - Stomach adenocarcinoma(132;0.00669)|Lung(427;0.213)		CAGAGGCAGCGGCCCGTGTGC	0.716																																					p.R1103C	Ovarian(73;978 3658)	Atlas-SNP	.											.	MEGF6	91	.	0			c.C3307T						.						4	6	5					1																	3414980		1677	3843	5520	SO:0001583	missense	1953	exon26			GGCAGCGGCCCGT	AB011539	CCDS41237.1	1p36.3	2008-02-05	2006-03-31	2006-03-31	ENSG00000162591	ENSG00000162591			3232	protein-coding gene	gene with protein product		604266	"EGF-like-domain, multiple 3"	EGFL3		9693030	Standard	NM_001409		Approved		uc001akl.3	O75095	OTTHUMG00000000611	ENST00000356575.4:c.3307C>T	chr1.hg19:g.3414980G>A	ENSP00000348982:p.Arg1103Cys	27.0	0.0		46.0	6.0	NM_001409	Q4AC86|Q5VV39	Missense_Mutation	SNP	ENST00000356575.4	hg19	CCDS41237.1	.	.	.	.	.	.	.	.	.	.	G	12.43	1.935285	0.34189	.	.	ENSG00000162591	ENST00000294599;ENST00000356575	T;T	0.63096	-0.02;1.41	3.8	-1.46	0.08800	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.675552	0.14231	U	0.332711	T	0.64649	0.2617	L	0.60845	1.875	0.18873	N	0.999981	D;D	0.62365	0.991;0.989	P;P	0.55615	0.701;0.78	T	0.57860	-0.7738	10	0.49607	T	0.09	-3.2323	8.6585	0.34077	0.0:0.241:0.5041:0.2548	.	1103;912	O75095;O75095-2	MEGF6_HUMAN;.	C	912;1103	ENSP00000294599:R912C;ENSP00000348982:R1103C	ENSP00000294599:R912C	R	-	1	0	MEGF6	3404840	0.002000	0.14202	0.005000	0.12908	0.113000	0.19764	1.208000	0.32345	-0.123000	0.11745	0.205000	0.17691	CGC	.	.		0.716	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409		A	3414980	G	A	3414980	3	1	279	1	0	0	0	0	1	0	0	0	9471	1116	39	1	1366	1	MEGF6	1	3414980	Missense_Mutation	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	877235	3414980	245835641	3	39762										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27102114	27102139	+	Frame_Shift_Del	DEL	CCTGGCAGAGAGCACATGGGCATTAG	CCTGGCAGAGAGCACATGGGCATTAG	-													0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	atgtccctcaagtctggtctCctggcagagagcacatgggc					rs577286634		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	CCTGGCAGAGAGCACATGGGCATTAG	CCTGGCAGAGAGCACATGGGCATTAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:27102114_27102139delCCTGGCAGAGAGCACATGGGCATTAG	ENST00000324856.7	+	19	5411_5436	c.5040_5065delCCTGGCAGAGAGCACATGGGCATTAG	c.(5038-5067)ctcctggcagagagcacatgggcattagatfs	p.LAESTWALD1681fs	ARID1A_ENST00000457599.2_Frame_Shift_Del_p.LAESTWALD1464fs|ARID1A_ENST00000540690.1_Frame_Shift_Del_p.LAESTWALD9fs|ARID1A_ENST00000374152.2_Frame_Shift_Del_p.LAESTWALD1298fs	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1681					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)	p.E1683Q(1)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		AGTCTGGTCTCCTGGCAGAGAGCACATGGGCATTAGATACCATCAA	0.522			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.1680_1688del		Pindel	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	1	Substitution - Missense(1)	urinary_tract(1)	c.5039_5064del						.																																			SO:0001589	frameshift_variant	8289	exon19			.	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.5040_5065delCCTGGCAGAGAGCACATGGGCATTAG	chr1.hg19:g.27102114_27102139delCCTGGCAGAGAGCACATGGGCATTAG	ENSP00000320485:p.Leu1681fs	0.0	0.0		134.0	10.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Del	DEL	ENST00000324856.7	hg19	CCDS285.1																																																																																			.	.		0.522	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		-	27102139	CCTGGCAGAGAGCACATGGGCATTAG	-	27102114	7	5	279	1	0	1	0	1	0	0	0	0	913	842	30	0	5114	0	ARID1A	1	27102114	Frame_Shift_Del	DEL	CCTGGCAGAGAGCACATGGGCATTAG	TCGA-G3-A3CG-01A-11D-A20W-10	23687134	27102114	222148507	4	39763										
ZNF684	127396	hgsc.bcm.edu	37	chr1	41012332	41012332	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cattcaataaaattctgactAtggagagaatccaccattat	5	8	2	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:41012332A>G	ENST00000372699.3	+	5	588	c.337A>G	c.(337-339)Atg>Gtg	p.M113V	ZNF684_ENST00000493756.1_3'UTR	NM_152373.3	NP_689586.3	Q5T5D7	ZN684_HUMAN	zinc finger protein 684	113					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|kidney(2)|lung(3)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	13	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;5.42e-18)			AATTCTGACTATGGAGAGAAT	0.348																																					p.M113V		Atlas-SNP	.											.	ZNF684	37	.	0			c.A337G						.						54	55	55					1																	41012332		2203	4300	6503	SO:0001583	missense	127396	exon5			CTGACTATGGAGA		CCDS454.1	1p34.2	2013-01-08			ENSG00000117010	ENSG00000117010		"Zinc fingers, C2H2-type", "-"	28418	protein-coding gene	gene with protein product	"hypothetical protein MGC27466"					12477932	Standard	NM_152373		Approved	MGC27466	uc001cft.2	Q5T5D7	OTTHUMG00000007359	ENST00000372699.3:c.337A>G	chr1.hg19:g.41012332A>G	ENSP00000361784:p.Met113Val	88.0	0.0		76.0	32.0	NM_152373	Q2NKY4	Missense_Mutation	SNP	ENST00000372699.3	hg19	CCDS454.1	.	.	.	.	.	.	.	.	.	.	A	2.435	-0.329956	0.05314	.	.	ENSG00000117010	ENST00000372699	T	0.04603	3.59	4.21	0.651	0.17817	.	0.854707	0.09813	N	0.752507	T	0.04318	0.0119	L	0.41824	1.3	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48269	-0.9050	10	0.16896	T	0.51	.	6.743	0.23447	0.6716:0.0:0.3284:0.0	.	113	Q5T5D7	ZN684_HUMAN	V	113	ENSP00000361784:M113V	ENSP00000361784:M113V	M	+	1	0	ZNF684	40784919	0.032000	0.19561	0.004000	0.12327	0.960000	0.62799	0.531000	0.23052	0.015000	0.14971	0.533000	0.62120	ATG	.	.		0.348	ZNF684-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019260.3	NM_152373		G	41012332	A	G	41012332	3	3	279	1	0	0	0	0	1	0	0	0	18106	449	16	2	351	2	ZNF684	1	41012332	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	13910218	41012332	208238289	5	39764										
ZMYND12	84217	hgsc.bcm.edu	37	chr1	42914250	42914250	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gctgctggtacagcatcttcGtgtttcccttcaaagaggta	10	10	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:42914250G>A	ENST00000372565.3	-	3	581	c.312C>T	c.(310-312)caC>caT	p.H104H	ZMYND12_ENST00000433602.2_Intron	NM_032257.4	NP_115633.3	Q9H0C1	ZMY12_HUMAN	zinc finger, MYND-type containing 12	104						intracellular (GO:0005622)	metal ion binding (GO:0046872)			NS(1)|endometrium(2)|large_intestine(3)|lung(5)|ovary(2)|prostate(2)|skin(2)	17	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				CAGCATCTTCGTGTTTCCCTT	0.483																																					p.H104H		Atlas-SNP	.											.	ZMYND12	35	.	0			c.C312T						.						114	102	106					1																	42914250		2203	4300	6503	SO:0001819	synonymous_variant	84217	exon3			ATCTTCGTGTTTC	AK057384	CCDS467.1	1p34.1	2008-02-05			ENSG00000066185	ENSG00000066185		"Zinc fingers, MYND-type"	21192	protein-coding gene	gene with protein product						11230166	Standard	NM_032257		Approved	DKFZp434N2435	uc001chj.3	Q9H0C1	OTTHUMG00000007333	ENST00000372565.3:c.312C>T	chr1.hg19:g.42914250G>A		167.0	0.0		151.0	50.0	NM_032257	Q5VUS6|Q8TC87|Q96M51	Silent	SNP	ENST00000372565.3	hg19	CCDS467.1																																																																																			.	.		0.483	ZMYND12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019170.1	NM_032257		A	42914250	G	A	42914250	2	1	279	1	0	0	0	0	0	0	0	1	17722	1136	40	1		1	ZMYND12	1	42914250	Silent	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	1901918	42914250	206336371	6	39765										
C1orf84	23334	hgsc.bcm.edu	37	chr1	43869391	43869391	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	acccgggtcaccttcctggcTtggcagtatcggtttgtcat	11	12	2	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:43869391T>G	ENST00000562955.1	+	3	273	c.273T>G	c.(271-273)gcT>gcG	p.A91A	SZT2_ENST00000372450.4_Silent_p.A89A|SZT2_ENST00000310739.4_Silent_p.A91A	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	91					central nervous system development (GO:0007417)|corpus callosum morphogenesis (GO:0021540)|embryo development (GO:0009790)|pigmentation (GO:0043473)|post-embryonic development (GO:0009791)|regulation of superoxide dismutase activity (GO:1901668)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)				NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						CCTTCCTGGCTTGGCAGTATC	0.562																																					p.A91A		Atlas-SNP	.											.	SZT2	383	.	0			c.T273G						.						171	146	154					1																	43869391		2203	4300	6503	SO:0001819	synonymous_variant	23334	exon3			CCTGGCTTGGCAG	AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198			29040	protein-coding gene	gene with protein product	"seizure threshold 2 homolog A (mouse)", "seizure threshold 2 homolog B (mouse)"	615463	"chromosome 1 open reading frame 84", "KIAA0467"	C1orf84, KIAA0467		9455484	Standard	NM_015284		Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.273T>G	chr1.hg19:g.43869391T>G		127.0	0.0		121.0	40.0	NM_015284	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Silent	SNP	ENST00000562955.1	hg19	CCDS30694.2																																																																																			.	.		0.562	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284		G	43869391	T	G	43869391	2	3	279	1	0	0	0	0	0	0	0	1	2063	1596	56	5		5	C1orf84	1	43869391	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	955141	43869391	205381230	7	39766										
KIAA0467	23334	hgsc.bcm.edu	37	chr1	43896222	43896222	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gacccagagctagaggtagaAtaccgggagagccgtgaatc	14	9	0	5			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:43896222A>G	ENST00000562955.1	+	31	4365	c.4365A>G	c.(4363-4365)gaA>gaG	p.E1455E	SZT2_ENST00000372442.1_Silent_p.E613E	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	1512					central nervous system development (GO:0007417)|corpus callosum morphogenesis (GO:0021540)|embryo development (GO:0009790)|pigmentation (GO:0043473)|post-embryonic development (GO:0009791)|regulation of superoxide dismutase activity (GO:1901668)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)				NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						TAGAGGTAGAATACCGGGAGA	0.542																																					p.E1455E		Atlas-SNP	.											.	SZT2	383	.	0			c.A4365G						.						67	68	68					1																	43896222		2203	4300	6503	SO:0001819	synonymous_variant	23334	exon31			GGTAGAATACCGG	AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198			29040	protein-coding gene	gene with protein product	"seizure threshold 2 homolog A (mouse)", "seizure threshold 2 homolog B (mouse)"	615463	"chromosome 1 open reading frame 84", "KIAA0467"	C1orf84, KIAA0467		9455484	Standard	NM_015284		Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.4365A>G	chr1.hg19:g.43896222A>G		78.0	0.0		76.0	4.0	NM_015284	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Silent	SNP	ENST00000562955.1	hg19	CCDS30694.2																																																																																			.	.		0.542	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284		G	43896222	A	G	43896222	2	3	279	1	0	0	0	0	0	0	0	1	8187	98	4	2		2	KIAA0467	1	43896222	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	26831	43896222	205354399	8	39767										
FAF1	11124	hgsc.bcm.edu	37	chr1	51210403	51210403	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gccttttaacagcattttggAcacaggtatctgaagttcat	8	8	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:51210403A>G	ENST00000396153.2	-	5	863	c.412T>C	c.(412-414)Tcc>Ccc	p.S138P	FAF1_ENST00000371778.4_Missense_Mutation_p.S138P	NM_007051.2	NP_008982.1	Q9UNN5	FAF1_HUMAN	Fas (TNFRSF6) associated factor 1	138					apoptotic process (GO:0006915)|cell death (GO:0008219)|cytoplasmic sequestering of NF-kappaB (GO:0007253)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of protein complex assembly (GO:0031334)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of cell adhesion (GO:0030155)|regulation of protein catabolic process (GO:0042176)|regulation of protein kinase activity (GO:0045859)	CD95 death-inducing signaling complex (GO:0031265)|Cdc48p-Npl4p-Ufd1p AAA ATPase complex (GO:0034098)|cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	heat shock protein binding (GO:0031072)|NF-kappaB binding (GO:0051059)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)	p.0?(2)		breast(2)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|pancreas(2)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)		AGCATTTTGGACACAGGTATC	0.313																																					p.S138P		Atlas-SNP	.											.	FAF1	64	.	2	Whole gene deletion(2)	thyroid(1)|haematopoietic_and_lymphoid_tissue(1)	c.T412C						.						142	137	139					1																	51210403		2203	4299	6502	SO:0001583	missense	11124	exon5			TTTTGGACACAGG	AF132938	CCDS554.1	1p32.3	2012-09-20			ENSG00000185104	ENSG00000185104		"UBX domain containing"	3578	protein-coding gene	gene with protein product	"TNFRSF6-associated factor 1", "UBX domain protein 3A"	604460				10462485	Standard	NM_007051		Approved	CGI-03, hFAF1, HFAF1s, UBXD12, UBXN3A	uc001cse.1	Q9UNN5	OTTHUMG00000007930	ENST00000396153.2:c.412T>C	chr1.hg19:g.51210403A>G	ENSP00000379457:p.Ser138Pro	58.0	0.0		66.0	4.0	NM_007051	Q549F0|Q9UF34|Q9UNT3|Q9Y2Z3	Missense_Mutation	SNP	ENST00000396153.2	hg19	CCDS554.1	.	.	.	.	.	.	.	.	.	.	A	15.26	2.779830	0.49891	.	.	ENSG00000185104	ENST00000396153;ENST00000371778;ENST00000371780;ENST00000543607	.	.	.	5.85	4.52	0.55395	.	0.056613	0.64402	N	0.000001	T	0.50446	0.1616	L	0.44542	1.39	0.80722	D	1	D	0.54601	0.967	P	0.49799	0.622	T	0.46596	-0.9180	9	0.45353	T	0.12	-15.6875	9.0605	0.36431	0.8859:0.0:0.1141:0.0	.	138	Q9UNN5	FAF1_HUMAN	P	138;138;130;138	.	ENSP00000360843:S138P	S	-	1	0	FAF1	50982991	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.853000	0.69496	0.837000	0.34925	0.533000	0.62120	TCC	.	.		0.313	FAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021807.1	NM_007051		G	51210403	A	G	51210403	3	3	279	1	0	0	0	0	1	0	0	0	5374	275	10	2	1600	2	FAF1	1	51210403	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	7314181	51210403	198040218	9	39768										
NRD1	4898	hgsc.bcm.edu	37	chr1	52306079	52306079	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	catcatcttcttcttcttccTccacctcctcttcttcttca	0	18	9	0	rs62648104		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:52306079T>A	ENST00000354831.7	-	2	638	c.449A>T	c.(448-450)gAg>gTg	p.E150V	NRD1_ENST00000544028.1_Missense_Mutation_p.E18V|NRD1_ENST00000539524.1_Missense_Mutation_p.E18V|NRD1_ENST00000352171.7_Missense_Mutation_p.E150V|NRD1_ENST00000485608.1_5'UTR	NM_002525.2	NP_002516.2	O43847	NRDC_HUMAN	nardilysin (N-arginine dibasic convertase)	0	Asp/Glu-rich (highly acidic).|Poly-Glu.				cell migration (GO:0016477)|cell proliferation (GO:0008283)|neuromuscular junction development (GO:0007528)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)	cell surface (GO:0009986)|cytosol (GO:0005829)	epidermal growth factor binding (GO:0048408)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)	27						ttcttcttcctccacctcctc	0.378																																					p.E150V		Atlas-SNP	.											.	NRD1	89	.	0			c.A449T						.						163	138	146					1																	52306079		2203	4300	6503	SO:0001583	missense	4898	exon2			TCTTCCTCCACCT	X93207	CCDS559.1, CCDS41335.1, CCDS55599.1	1p32.2-p32.1	2008-07-18			ENSG00000078618	ENSG00000078618			7995	protein-coding gene	gene with protein product		602651				9581555, 9479496	Standard	NM_002525		Approved	hNRD1, hNRD2	uc001ctc.4	O43847	OTTHUMG00000008278	ENST00000354831.7:c.449A>T	chr1.hg19:g.52306079T>A	ENSP00000346890:p.Glu150Val	216.0	0.0		205.0	19.0	NM_001101662	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	Missense_Mutation	SNP	ENST00000354831.7	hg19	CCDS559.1	.	.	.	.	.	.	.	.	.	.	T	3.056	-0.194350	0.06259	.	.	ENSG00000078618	ENST00000352171;ENST00000354831;ENST00000539524;ENST00000546169;ENST00000544028	T;T;T;T	0.38240	1.31;3.15;1.15;1.22	5.25	2.92	0.33932	Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.525899	0.19688	N	0.108344	T	0.18341	0.0440	N	0.14661	0.345	0.09310	N	1	B;B;B	0.23650	0.062;0.089;0.01	B;B;B	0.17098	0.017;0.007;0.007	T	0.14755	-1.0461	10	0.38643	T	0.18	-0.0317	5.1939	0.15225	0.0:0.1704:0.2022:0.6274	rs62648104	150;150;150	F5H6R2;O43847;B1AKJ5	.;NRDC_HUMAN;.	V	150;150;18;150;18	ENSP00000262679:E150V;ENSP00000346890:E150V;ENSP00000444416:E18V;ENSP00000442262:E18V	ENSP00000262679:E150V	E	-	2	0	NRD1	52078667	0.129000	0.22400	0.012000	0.15200	0.145000	0.21501	0.870000	0.28010	0.317000	0.23160	0.454000	0.30748	GAG	.	T|0.024;A|0.976		0.378	NRD1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023045.1	NM_002525		A	52306079	T	A	52306079	3	1	279	1	0	0	0	0	1	0	0	0	10654	1551	54	4	3338	4	NRD1	1	52306079	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	1095676	52306079	196944542	10	39769										
USP24	23358	hgsc.bcm.edu	37	chr1	55603294	55603294	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tcccactgccagaagtcttcActgtaaggatttgttcatca	7	11	4	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:55603294A>G	ENST00000294383.6	-	28	3094	c.3095T>C	c.(3094-3096)gTg>gCg	p.V1032A	USP24_ENST00000407756.1_Missense_Mutation_p.V872A	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	1032					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						AGAAGTCTTCACTGTAAGGAT	0.448																																					p.V1032A		Atlas-SNP	.											.	USP24	323	.	0			c.T3095C						.						63	63	63					1																	55603294		1861	4108	5969	SO:0001583	missense	23358	exon28			GTCTTCACTGTAA	AB028980	CCDS44154.1, CCDS44154.2	1p32.3	2008-04-11	2005-08-08		ENSG00000162402	ENSG00000162402		"Ubiquitin-specific peptidases"	12623	protein-coding gene	gene with protein product		610569	"ubiquitin specific protease 24"			12838346	Standard	NM_015306		Approved	KIAA1057	uc021onw.1	Q9UPU5	OTTHUMG00000008135	ENST00000294383.6:c.3095T>C	chr1.hg19:g.55603294A>G	ENSP00000294383:p.Val1032Ala	61.0	0.0		60.0	4.0	NM_015306	Q6ZSY2|Q8N2Y4|Q9NXD1	Missense_Mutation	SNP	ENST00000294383.6	hg19	CCDS44154.2	.	.	.	.	.	.	.	.	.	.	A	6.097	0.386217	0.11524	.	.	ENSG00000162402	ENST00000294383;ENST00000407756	T;T	0.49139	0.79;0.79	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.52338	0.1728	L	0.28556	0.865	0.58432	D	0.999998	D	0.67145	0.996	P	0.61070	0.883	T	0.44128	-0.9348	10	0.20519	T	0.43	.	15.9568	0.79893	1.0:0.0:0.0:0.0	.	872	B7WPF4	.	A	1032;872	ENSP00000294383:V1032A;ENSP00000385700:V872A	ENSP00000294383:V1032A	V	-	2	0	USP24	55375882	1.000000	0.71417	0.999000	0.59377	0.501000	0.33797	8.962000	0.93254	2.158000	0.67659	0.460000	0.39030	GTG	.	.		0.448	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2			G	55603294	A	G	55603294	3	3	279	1	0	0	0	0	1	0	0	0	17070	159	6	2	4931	2	USP24	1	55603294	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	3297215	55603294	193647327	11	39770										
C1orf168	199920	hgsc.bcm.edu	37	chr1	57207872	57207872	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ttctttgttttgtagacatcTtcatacagttctctattttc	4	8	4	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:57207872T>C	ENST00000343433.6	-	12	1646	c.1566A>G	c.(1564-1566)gaA>gaG	p.E522E	C1orf168_ENST00000484327.1_5'UTR	NM_001004303.4	NP_001004303.3	Q5VWT5	CA168_HUMAN	chromosome 1 open reading frame 168	522										NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(13)|ovary(3)|skin(6)|stomach(1)|urinary_tract(2)	46						TGTAGACATCTTCATACAGTT	0.313																																					p.E522E		Atlas-SNP	.											C1orf168,NS,carcinoma,0,1	C1orf168	102	.	0			c.A1566G						.						126	122	123					1																	57207872		2201	4300	6501	SO:0001819	synonymous_variant	199920	exon12			GACATCTTCATAC	BX648439	CCDS30729.1	1p32.2	2011-02-22			ENSG00000187889	ENSG00000187889			27295	protein-coding gene	gene with protein product						14702039	Standard	NM_001004303		Approved	RP4-758N20.2, FLJ43208	uc001cym.4	Q5VWT5	OTTHUMG00000008281	ENST00000343433.6:c.1566A>G	chr1.hg19:g.57207872T>C		58.0	0.0		46.0	2.0	NM_001004303	Q63HM3|Q6ZUY6	Silent	SNP	ENST00000343433.6	hg19	CCDS30729.1																																																																																			.	.		0.313	C1orf168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022751.2	NM_001004303		C	57207872	T	C	57207872	2	2	279	1	0	0	0	0	0	0	0	1	2014	1606	56	2		2	C1orf168	1	57207872	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	1604578	57207872	192042749	12	39771										
LRRC7	57554	hgsc.bcm.edu	37	chr1	70509692	70509692	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	catgctgccctatggaggtaTttcagcaatgcatgcaggca	11	10	1	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:70509692T>C	ENST00000035383.5	+	20	3941	c.3911T>C	c.(3910-3912)aTt>aCt	p.I1304T	LRRC7_ENST00000310961.5_Intron|LRRC7_ENST00000415775.2_Missense_Mutation_p.I588T	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	1304						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)				breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						TATGGAGGTATTTCAGCAATG	0.413																																					p.I1304T		Atlas-SNP	.											.	LRRC7	400	.	0			c.T3911C						.						148	132	137					1																	70509692		2203	4300	6503	SO:0001583	missense	57554	exon20			GAGGTATTTCAGC		CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.3911T>C	chr1.hg19:g.70509692T>C	ENSP00000035383:p.Ile1304Thr	102.0	0.0		97.0	4.0	NM_020794	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Missense_Mutation	SNP	ENST00000035383.5	hg19	CCDS645.1	.	.	.	.	.	.	.	.	.	.	T	16.37	3.104198	0.56291	.	.	ENSG00000033122	ENST00000035383;ENST00000415775	T;T	0.35421	1.31;2.41	6.16	6.16	0.99307	.	0.091197	0.47852	D	0.000206	T	0.11836	0.0288	N	0.14661	0.345	0.38445	D	0.946813	B;B	0.26258	0.145;0.01	B;B	0.24006	0.05;0.013	T	0.11397	-1.0589	10	0.20519	T	0.43	.	15.9872	0.80168	0.0:0.0:0.0:1.0	.	588;1304	F8WE45;Q96NW7	.;LRRC7_HUMAN	T	1304;588	ENSP00000035383:I1304T;ENSP00000394867:I588T	ENSP00000035383:I1304T	I	+	2	0	LRRC7	70282280	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.700000	0.54786	2.367000	0.80283	0.528000	0.53228	ATT	.	.		0.413	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794		C	70509692	T	C	70509692	3	2	279	1	0	0	0	0	1	0	0	0	9029	1493	52	2	3989	2	LRRC7	1	70509692	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	13301820	70509692	178740929	13	39772										
ACADM	34	hgsc.bcm.edu	37	chr1	76198378	76198378	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gctactgctcgtaaatttgcCagagaggaaatcatcccagt	9	10	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:76198378C>T	ENST00000370841.4	+	3	605	c.168C>T	c.(166-168)gcC>gcT	p.A56A	ACADM_ENST00000543667.1_5'UTR|ACADM_ENST00000541113.1_Silent_p.A20A|ACADM_ENST00000420607.2_Silent_p.A60A|ACADM_ENST00000370834.5_Silent_p.A56A	NM_000016.4|NM_001127328.1	NP_000007.1|NP_001120800.1	P11310	ACADM_HUMAN	acyl-CoA dehydrogenase, C-4 to C-12 straight chain	56					cardiac muscle cell differentiation (GO:0055007)|carnitine biosynthetic process (GO:0045329)|carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|glycogen biosynthetic process (GO:0005978)|liver development (GO:0001889)|medium-chain fatty acid catabolic process (GO:0051793)|medium-chain fatty acid metabolic process (GO:0051791)|oxidation-reduction process (GO:0055114)|post-embryonic development (GO:0009791)|regulation of gluconeogenesis (GO:0006111)|response to cold (GO:0009409)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	axon (GO:0030424)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|identical protein binding (GO:0042802)|medium-chain-acyl-CoA dehydrogenase activity (GO:0070991)			breast(3)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|skin(1)	18					Flavin adenine dinucleotide(DB03147)	GTAAATTTGCCAGAGAGGAAA	0.328																																					p.A60A		Atlas-SNP	.											.	ACADM	50	.	0			c.C180T						.						95	107	103					1																	76198378		2202	4300	6502	SO:0001819	synonymous_variant	34	exon3			ATTTGCCAGAGAG	M16827	CCDS668.1, CCDS44165.1, CCDS65562.1, CCDS72807.1	1p31	2014-09-17	2010-04-30		ENSG00000117054	ENSG00000117054	1.3.99.3		89	protein-coding gene	gene with protein product		607008	"acyl-Coenzyme A dehydrogenase, C-4 to C-12 straight chain"			3035565	Standard	NM_000016		Approved	MCAD, MCADH, ACAD1	uc009wbp.3	P11310	OTTHUMG00000009784	ENST00000370841.4:c.168C>T	chr1.hg19:g.76198378C>T		154.0	0.0		122.0	35.0	NM_001127328	Q5T4U4|Q9NYF1	Silent	SNP	ENST00000370841.4	hg19	CCDS668.1																																																																																			.	.		0.328	ACADM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026967.1			T	76198378	C	T	76198378	2	4	279	1	0	0	0	0	0	0	0	1	113	581	21	3		3	ACADM	1	76198378	Silent	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	5688686	76198378	173052243	14	39773										
COL24A1	255631	hgsc.bcm.edu	37	chr1	86340381	86340381	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cactgccagcagttccaacaTctccctgaagaaacaaaggg	8	13	1	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:86340381T>C	ENST00000370571.2	-	35	3455	c.3089A>G	c.(3088-3090)gAt>gGt	p.D1030G	COL24A1_ENST00000436319.1_Missense_Mutation_p.D1030G	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	1030	Collagen-like 9.				extracellular matrix organization (GO:0030198)|hematopoietic progenitor cell differentiation (GO:0002244)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			NS(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(9)|liver(1)|lung(56)|ovary(4)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	101				all cancers(265;0.0627)|Epithelial(280;0.0689)		AGTTCCAACATCTCCCTGAAG	0.478																																					p.D1030G		Atlas-SNP	.											.	COL24A1	202	.	0			c.A3089G						.						57	56	56					1																	86340381		1888	4110	5998	SO:0001583	missense	255631	exon35			CCAACATCTCCCT	AF410793	CCDS41353.1	1p22.3-p22.2	2013-01-16			ENSG00000171502	ENSG00000171502		"Collagens"	20821	protein-coding gene	gene with protein product		610025					Standard	NM_152890		Approved		uc001dlj.3	Q17RW2	OTTHUMG00000010629	ENST00000370571.2:c.3089A>G	chr1.hg19:g.86340381T>C	ENSP00000359603:p.Asp1030Gly	115.0	0.0		102.0	6.0	NM_152890	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Missense_Mutation	SNP	ENST00000370571.2	hg19	CCDS41353.1	.	.	.	.	.	.	.	.	.	.	T	12.29	1.893866	0.33442	.	.	ENSG00000171502	ENST00000370571;ENST00000436319	D;D	0.93189	-3.18;-3.18	5.53	5.53	0.82687	.	0.326077	0.17100	N	0.187031	D	0.89431	0.6713	M	0.66439	2.03	0.80722	D	1	B;B	0.29862	0.095;0.259	B;B	0.36922	0.119;0.236	D	0.86591	0.1860	10	0.24483	T	0.36	.	12.0802	0.53667	0.0:0.0:0.0:1.0	.	1030;1030	Q17RW2;Q17RW2-2	COOA1_HUMAN;.	G	1030	ENSP00000359603:D1030G;ENSP00000392531:D1030G	ENSP00000359603:D1030G	D	-	2	0	COL24A1	86112969	0.994000	0.37717	0.997000	0.53966	0.856000	0.48823	2.760000	0.47581	2.100000	0.63781	0.533000	0.62120	GAT	.	.		0.478	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	NM_152890		C	86340381	T	C	86340381	3	2	279	1	0	0	0	0	1	0	0	0	3685	1435	50	2	2159	2	COL24A1	1	86340381	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	10142003	86340381	162910240	15	39774										
KCNA10	3744	hgsc.bcm.edu	37	chr1	111060286	111060286	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gaaagaagatgagcaaccccAactcccgcatggacgccttc	9	14	0	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:111060286A>T	ENST00000369771.2	-	1	1511	c.1124T>A	c.(1123-1125)tTg>tAg	p.L375*		NM_005549.2	NP_005540.1	Q16322	KCA10_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 10	375					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|intracellular cyclic nucleotide activated cation channel activity (GO:0005221)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(3)|skin(1)|urinary_tract(1)	35		all_cancers(81;4.57e-06)|all_epithelial(167;1.52e-05)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0238)|all cancers(265;0.0874)|Colorectal(144;0.103)|Epithelial(280;0.116)|LUSC - Lung squamous cell carcinoma(189;0.134)	Dalfampridine(DB06637)	GAGCAACCCCAACTCCCGCAT	0.542																																					p.L375X		Atlas-SNP	.											.	KCNA10	92	.	0			c.T1124A						.						89	84	86					1																	111060286		2203	4300	6503	SO:0001587	stop_gained	3744	exon1			AACCCCAACTCCC	U96110	CCDS826.1	1p13.1	2012-07-05			ENSG00000143105	ENSG00000143105		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6219	protein-coding gene	gene with protein product		602420				16382104	Standard	NM_005549		Approved	Kv1.8	uc001dzt.1	Q16322	OTTHUMG00000022785	ENST00000369771.2:c.1124T>A	chr1.hg19:g.111060286A>T	ENSP00000358786:p.Leu375*	166.0	0.0		133.0	30.0	NM_005549		Nonsense_Mutation	SNP	ENST00000369771.2	hg19	CCDS826.1	.	.	.	.	.	.	.	.	.	.	A	40	8.092158	0.98648	.	.	ENSG00000143105	ENST00000369771	.	.	.	5.63	5.63	0.86233	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.7125	0.69244	1.0:0.0:0.0:0.0	.	.	.	.	X	375	.	ENSP00000358786:L375X	L	-	2	0	KCNA10	110861809	1.000000	0.71417	0.996000	0.52242	0.946000	0.59487	9.336000	0.96533	2.161000	0.67846	0.456000	0.33151	TTG	.	.		0.542	KCNA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059081.1	NM_005549		T	111060286	A	T	111060286	4	4	279	1	0	0	0	0	0	1	0	0	8011	131	5	4	415	4	KCNA10	1	111060286	Nonsense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	24719905	111060286	138190335	16	39775										
RAP1A	5906	hgsc.bcm.edu	37	chr1	112247050	112247050	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gggccagaatttagcaagacAgtggtgtaactgtgcctttt	12	7	0	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:112247050A>G	ENST00000369709.3	+	6	589	c.410A>G	c.(409-411)cAg>cGg	p.Q137R	RAP1A_ENST00000356415.1_Missense_Mutation_p.Q137R|RAP1A_ENST00000436150.2_Missense_Mutation_p.Q137R|RAP1A_ENST00000494982.1_3'UTR|RAP1A_ENST00000545460.1_Missense_Mutation_p.Q137R	NM_002884.2	NP_002875.1	P62834	RAP1A_HUMAN	RAP1A, member of RAS oncogene family	137					activation of MAPKK activity (GO:0000186)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to nerve growth factor stimulus (GO:1990090)|energy reserve metabolic process (GO:0006112)|establishment of endothelial barrier (GO:0061028)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of vasculogenesis (GO:2001214)|protein transport (GO:0015031)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|guanyl-nucleotide exchange factor complex (GO:0032045)|late endosome (GO:0005770)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|protein complex binding (GO:0032403)|protein transporter activity (GO:0008565)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)			endometrium(1)|large_intestine(2)|lung(3)	6		all_cancers(81;6.79e-06)|all_epithelial(167;2.42e-05)|all_lung(203;0.000105)|Lung NSC(277;0.00021)		Lung(183;0.0183)|Colorectal(144;0.0418)|LUSC - Lung squamous cell carcinoma(189;0.0966)|all cancers(265;0.098)|Epithelial(280;0.0981)|COAD - Colon adenocarcinoma(174;0.141)		TTAGCAAGACAGTGGTGTAAC	0.418																																					p.Q137R		Atlas-SNP	.											.	RAP1A	14	.	0			c.A410G						.						109	101	104					1																	112247050		2203	4300	6503	SO:0001583	missense	5906	exon7			CAAGACAGTGGTG	BC014086	CCDS840.1	1p13.3	2014-05-09			ENSG00000116473	ENSG00000116473			9855	protein-coding gene	gene with protein product		179520				3143720	Standard	XM_006710803		Approved	KREV-1, SMGP21	uc001ebl.3	P62834	OTTHUMG00000011959	ENST00000369709.3:c.410A>G	chr1.hg19:g.112247050A>G	ENSP00000358723:p.Gln137Arg	62.0	0.0		69.0	4.0	NM_001010935	P10113	Missense_Mutation	SNP	ENST00000369709.3	hg19	CCDS840.1	.	.	.	.	.	.	.	.	.	.	A	17.91	3.505479	0.64410	.	.	ENSG00000116473	ENST00000356415;ENST00000369709;ENST00000436150;ENST00000545460	T;T;T;T	0.76448	-1.02;-1.02;-1.02;-1.02	5.92	5.92	0.95590	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.55049	0.1896	N	0.20401	0.57	0.80722	D	1	B	0.02656	0.0	B	0.10450	0.005	T	0.57568	-0.7789	10	0.56958	D	0.05	.	16.0245	0.80532	1.0:0.0:0.0:0.0	.	137	P62834	RAP1A_HUMAN	R	137	ENSP00000348786:Q137R;ENSP00000358723:Q137R;ENSP00000394318:Q137R;ENSP00000443009:Q137R	ENSP00000348786:Q137R	Q	+	2	0	RAP1A	112048573	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.266000	0.75297	0.533000	0.62120	CAG	.	.		0.418	RAP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033071.1	NM_002884		G	112247050	A	G	112247050	3	3	279	1	0	0	0	0	1	0	0	0	13050	188	7	2	428	2	RAP1A	1	112247050	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	1186764	112247050	137003571	17	39776										
CD58	965	hgsc.bcm.edu	37	chr1	117087065	117087065	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gtctaaataaaccctattttTaaaagatgagaaagctctga	6	6	2	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:117087065T>A	ENST00000369489.5	-	2	298	c.232A>T	c.(232-234)Aaa>Taa	p.K78*	CD58_ENST00000369487.3_Nonsense_Mutation_p.K78*|CD58_ENST00000457047.2_Nonsense_Mutation_p.K78*	NM_001779.2	NP_001770.1	P19256	LFA3_HUMAN	CD58 molecule	78	Ig-like.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to interferon-gamma (GO:0071346)|cellular response to tumor necrosis factor (GO:0071356)|heterotypic cell-cell adhesion (GO:0034113)|leukocyte migration (GO:0050900)|positive regulation of interleukin-8 secretion (GO:2000484)|single organismal cell-cell adhesion (GO:0016337)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(3)|urinary_tract(1)	9	Lung SC(450;0.225)	all_cancers(81;0.000363)|all_lung(203;0.000118)|all_epithelial(167;0.000149)|Lung NSC(69;0.000577)		Lung(183;0.0086)|LUSC - Lung squamous cell carcinoma(189;0.0528)|Colorectal(144;0.0775)|all cancers(265;0.109)|Epithelial(280;0.118)|COAD - Colon adenocarcinoma(174;0.121)		ACCCTATTTTTAAAAGATGAG	0.348																																					p.K78X		Atlas-SNP	.											.	CD58	40	.	0			c.A232T						.						77	80	79					1																	117087065		2203	4300	6503	SO:0001587	stop_gained	965	exon2			TATTTTTAAAAGA	BC005930	CCDS888.1, CCDS44199.1	1p13	2008-02-05	2006-03-28		ENSG00000116815	ENSG00000116815		"CD molecules"	1688	protein-coding gene	gene with protein product		153420	"CD58 antigen, (lymphocyte function-associated antigen 3)"	LFA3		9510189	Standard	NM_001144822		Approved		uc001egm.3	P19256	OTTHUMG00000022749	ENST00000369489.5:c.232A>T	chr1.hg19:g.117087065T>A	ENSP00000358501:p.Lys78*	163.0	0.0		183.0	68.0	NM_001144822	A8K7G5|Q5U053|Q6IB65|Q96KI9	Nonsense_Mutation	SNP	ENST00000369489.5	hg19	CCDS888.1	.	.	.	.	.	.	.	.	.	.	T	15.59	2.877464	0.51801	.	.	ENSG00000116815	ENST00000369489;ENST00000457047;ENST00000526981;ENST00000369487	.	.	.	3.71	-7.42	0.01388	.	3.724730	0.00780	N	0.001263	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.0431	0.09760	0.1173:0.4912:0.1476:0.2439	.	.	.	.	X	78;78;50;78	.	ENSP00000358499:K78X	K	-	1	0	CD58	116888588	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.690000	0.00831	-1.926000	0.01061	-0.496000	0.04628	AAA	.	.		0.348	CD58-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059036.1	NM_001779		A	117087065	T	A	117087065	4	1	279	1	0	0	0	0	0	1	0	0	3027	1763	61	4	544	4	CD58	1	117087065	Nonsense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	4840015	117087065	132163556	18	39777										
HIST2H2AB	317772	hgsc.bcm.edu	37	chr1	149859298	149859298	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	aatttccgcggtcaggtactCgaggaccgccgccaggtaca	12	13	1	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:149859298C>A	ENST00000331128.3	-	1	168	c.169G>T	c.(169-171)Gag>Tag	p.E57*	HIST2H2BE_ENST00000369155.2_5'Flank|BOLA1_ENST00000369153.2_5'Flank	NM_175065.2	NP_778235.1	Q8IUE6	H2A2B_HUMAN	histone cluster 2, H2ab	57						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	15	Breast(34;0.0124)|all_hematologic(923;0.127)		STAD - Stomach adenocarcinoma(528;0.133)|LUSC - Lung squamous cell carcinoma(543;0.221)			GTCAGGTACTCGAGGACCGCC	0.662																																					p.E57X		Atlas-SNP	.											HIST2H2AB,NS,carcinoma,0,1	HIST2H2AB	49	.	0			c.G169T						.						44	49	47					1																	149859298		2203	4300	6503	SO:0001587	stop_gained	317772	exon1			GGTACTCGAGGAC	AY131972	CCDS938.1	1q21.2	2011-01-27	2006-10-11		ENSG00000184270	ENSG00000184270		"Histones / Replication-dependent"	20508	protein-coding gene	gene with protein product		615014	"histone 2, H2ab"			12408966	Standard	NM_175065		Approved		uc001ete.3	Q8IUE6	OTTHUMG00000012085	ENST00000331128.3:c.169G>T	chr1.hg19:g.149859298C>A	ENSP00000332790:p.Glu57*	208.0	0.0		349.0	73.0	NM_175065		Nonsense_Mutation	SNP	ENST00000331128.3	hg19	CCDS938.1	.	.	.	.	.	.	.	.	.	.	C	20.0	3.930053	0.73327	.	.	ENSG00000184270	ENST00000331128	.	.	.	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	14.7467	0.69494	0.0:1.0:0.0:0.0	.	.	.	.	X	57	.	ENSP00000332790:E57X	E	-	1	0	HIST2H2AB	148125922	1.000000	0.71417	0.999000	0.59377	0.676000	0.39594	4.977000	0.63792	2.621000	0.88768	0.655000	0.94253	GAG	.	.		0.662	HIST2H2AB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033440.1	NM_175065		A	149859298	C	A	149859298	4	1	279	1	0	0	0	0	0	1	0	0	7186	893	31	1	227	1	HIST2H2AB	1	149859298	Nonsense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	32772233	149859298	99391323	19	39778										
TARS2	80222	hgsc.bcm.edu	37	chr1	150471707	150471707	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	caaaggtccttaaacaggccCtgaaggaatttggagaaccc	10	10	0	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:150471707C>G	ENST00000369064.3	+	13	1589	c.1555C>G	c.(1555-1557)Ctg>Gtg	p.L519V	TARS2_ENST00000463555.1_3'UTR|TARS2_ENST00000438568.2_3'UTR|TARS2_ENST00000369054.2_Missense_Mutation_p.L389V|TARS2_ENST00000606933.1_Missense_Mutation_p.L437V	NM_025150.3	NP_079426.2	Q9BW92	SYTM_HUMAN	threonyl-tRNA synthetase 2, mitochondrial (putative)	519					gene expression (GO:0010467)|mitochondrial threonyl-tRNA aminoacylation (GO:0070159)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|threonine-tRNA ligase activity (GO:0004829)			cervix(1)|endometrium(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	35	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.51e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)		L-Threonine(DB00156)	TAAACAGGCCCTGAAGGAATT	0.453																																					p.L519V		Atlas-SNP	.											.	TARS2	91	.	0			c.C1555G						.						159	160	159					1																	150471707		2203	4300	6503	SO:0001583	missense	80222	exon13			CAGGCCCTGAAGG	BC007824	CCDS952.1, CCDS60251.1, CCDS60252.1	1q21.2	2012-10-26	2007-02-23	2007-02-23	ENSG00000143374	ENSG00000143374	6.1.1.3	"Aminoacyl tRNA synthetases / Class II"	30740	protein-coding gene	gene with protein product	"threonine tRNA ligase 2, mitochondrial"	612805	"threonyl-tRNA synthetase-like 1"	TARSL1			Standard	NM_001271895		Approved	FLJ12528	uc001euq.4	Q9BW92	OTTHUMG00000012809	ENST00000369064.3:c.1555C>G	chr1.hg19:g.150471707C>G	ENSP00000358060:p.Leu519Val	78.0	0.0		116.0	54.0	NM_025150	Q53GW7|Q96I50|Q9H9V2	Missense_Mutation	SNP	ENST00000369064.3	hg19	CCDS952.1	.	.	.	.	.	.	.	.	.	.	C	17.23	3.337235	0.60963	.	.	ENSG00000143374	ENST00000369054;ENST00000369064;ENST00000369051;ENST00000369052	.	.	.	5.28	2.24	0.28232	Aminoacyl-tRNA synthetase, class II (1);	0.000000	0.64402	D	0.000012	T	0.63153	0.2487	M	0.79475	2.455	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.83275	0.996;0.994;0.994	T	0.65602	-0.6128	9	0.87932	D	0	-10.6729	7.4539	0.27255	0.0:0.6927:0.0:0.3073	.	389;244;519	Q9H9V2;E7EVR9;Q9BW92	.;.;SYTM_HUMAN	V	389;519;244;244	.	ENSP00000358047:L244V	L	+	1	2	TARS2	148738331	1.000000	0.71417	0.998000	0.56505	0.640000	0.38277	1.380000	0.34351	0.296000	0.22592	0.655000	0.94253	CTG	.	.		0.453	TARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035847.1	NM_025150		G	150471707	C	G	150471707	3	3	279	1	0	0	0	0	1	0	0	0	15575	680	24	4	1605	4	TARS2	1	150471707	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	612409	150471707	98778914	20	39779										
DENND4B	9909	hgsc.bcm.edu	37	chr1	153907287	153907287	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tgacacctgctcctgctgctGctgctgctgctgctgctgtt	11	14	0	1	rs3835302|rs199597671		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:153907287G>C	ENST00000361217.4	-	18	3140	c.2722C>G	c.(2722-2724)Cag>Gag	p.Q908E	DENND4B_ENST00000474386.1_5'Flank	NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	908	Gln-rich.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab protein signal transduction (GO:0032483)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	36	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			tcctgctgctgctgctgctgc	0.632																																					p.Q908E		Atlas-SNP	.											.	DENND4B	210	.	0			c.C2722G						.						23	27	26					1																	153907287		2184	4281	6465	SO:0001583	missense	9909	exon18			GCTGCTGCTGCTG	AB007945	CCDS44228.1	1q21.3	2012-10-03	2006-01-27	2006-01-27	ENSG00000198837	ENSG00000198837		"DENN/MADD domain containing"	29044	protein-coding gene	gene with protein product			"KIAA0476"	KIAA0476		9455484, 12906859	Standard	NM_014856		Approved		uc001fdd.1	O75064	OTTHUMG00000037157	ENST00000361217.4:c.2722C>G	chr1.hg19:g.153907287G>C	ENSP00000354597:p.Gln908Glu	48.0	0.0		122.0	18.0	NM_014856	Q5T4K0	Missense_Mutation	SNP	ENST00000361217.4	hg19	CCDS44228.1	.	.	.	.	.	.	.	.	.	.	G	1.785	-0.481073	0.04383	.	.	ENSG00000198837	ENST00000361217;ENST00000368646	T;T	0.06294	3.33;3.32	2.67	0.673	0.17941	.	5.053470	0.00166	N	0.000001	T	0.00815	0.0027	N	0.14661	0.345	0.19300	N	0.999977	B	0.02656	0.0	B	0.04013	0.001	T	0.26573	-1.0099	10	0.02654	T	1	-2.4288	3.3651	0.07201	0.1454:0.0:0.5849:0.2697	.	908	O75064	DEN4B_HUMAN	E	908;919	ENSP00000354597:Q908E;ENSP00000357635:Q919E	ENSP00000354597:Q908E	Q	-	1	0	DENND4B	152173911	0.943000	0.32029	0.986000	0.45419	0.760000	0.43138	0.537000	0.23144	0.194000	0.20326	0.271000	0.19318	CAG	.	.		0.632	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806		C	153907287	G	C	153907287	3	2	279	1	0	0	0	0	1	0	0	0	4436	1328	46	4	1812	4	DENND4B	1	153907287	Missense_Mutation	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	3435580	153907287	95343334	21	39780										
ATP8B2	57198	hgsc.bcm.edu	37	chr1	154319146	154319146	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	atcaaccacttcttcatctgGggaagccttgctgtttactt	7	11	4	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:154319146G>T	ENST00000368489.3	+	26	3174	c.3174G>T	c.(3172-3174)tgG>tgT	p.W1058C		NM_020452.3	NP_065185.1	P98198	AT8B2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 2	1044					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)		IL6R/ATP8B2(2)	breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			TCTTCATCTGGGGAAGCCTTG	0.542																																					p.W1058C		Atlas-SNP	.											.	ATP8B2	158	.	0			c.G3174T						.						232	162	186					1																	154319146		2203	4300	6503	SO:0001583	missense	57198	exon26			CATCTGGGGAAGC	AB032963	CCDS1066.1, CCDS41405.1	1q21.3	2012-03-09	2012-03-09		ENSG00000143515	ENSG00000143515		"ATPases / P-type"	13534	protein-coding gene	gene with protein product		605867	"ATPase, class I, type 8B, member 2"			10574461, 11015572	Standard	NM_020452		Approved	ATPID, KIAA1137	uc001fex.3	P98198	OTTHUMG00000035979	ENST00000368489.3:c.3174G>T	chr1.hg19:g.154319146G>T	ENSP00000357475:p.Trp1058Cys	347.0	0.0		518.0	157.0	NM_020452	B4E3P4|Q6NT69|Q7Z486|Q96I43|Q96NQ7	Missense_Mutation	SNP	ENST00000368489.3	hg19	CCDS1066.1	.	.	.	.	.	.	.	.	.	.	G	17.97	3.519083	0.64634	.	.	ENSG00000143515	ENST00000368489	T	0.74526	-0.85	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	D	0.85004	0.5598	M	0.83012	2.62	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	D	0.87026	0.2132	10	0.72032	D	0.01	.	16.7081	0.85377	0.0:0.0:1.0:0.0	.	1058	P98198-3	.	C	1058	ENSP00000357475:W1058C	ENSP00000357475:W1058C	W	+	3	0	ATP8B2	152585770	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	7.799000	0.85936	2.512000	0.84698	0.655000	0.94253	TGG	.	.		0.542	ATP8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087658.2	NM_020452		T	154319146	G	T	154319146	3	4	279	1	0	0	0	0	1	0	0	0	1195	1241	43	3	3406	3	ATP8B2	1	154319146	Missense_Mutation	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	411859	154319146	94931475	22	39781										
TRIM46	80128	hgsc.bcm.edu	37	chr1	155148089	155148089	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ctctcccgcagaactctcccCaagccagaccgcctggaccg	8	20	2	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:155148089C>A	ENST00000334634.4	+	2	291	c.291C>A	c.(289-291)ccC>ccA	p.P97P	TRIM46_ENST00000368383.3_Silent_p.P97P|TRIM46_ENST00000545012.1_Intron|TRIM46_ENST00000392451.2_Silent_p.P97P|TRIM46_ENST00000368382.1_Silent_p.P74P|KRTCAP2_ENST00000490672.1_5'Flank|TRIM46_ENST00000368385.4_Silent_p.P97P|TRIM46_ENST00000543729.1_Silent_p.P104P|KRTCAP2_ENST00000295682.4_5'Flank|RP11-201K10.3_ENST00000473363.2_Intron|TRIM46_ENST00000468878.1_3'UTR	NM_001256601.1|NM_001282378.1	NP_001243530.1|NP_001269307.1	Q7Z4K8	TRI46_HUMAN	tripartite motif containing 46	97						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	29	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;6.62e-10)|all cancers(21;2.68e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			GAACTCTCCCCAAGCCAGACC	0.637																																					p.P97P		Atlas-SNP	.											.	TRIM46	79	.	0			c.C291A						.						36	42	40					1																	155148089		2178	4263	6441	SO:0001819	synonymous_variant	80128	exon2			TCTCCCCAAGCCA		CCDS1097.1, CCDS58033.1, CCDS60285.1, CCDS72932.1, CCDS72931.1	1q22	2013-01-09	2011-01-25		ENSG00000163462	ENSG00000163462		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19019	protein-coding gene	gene with protein product		600986	"tripartite motif-containing 46"				Standard	NM_025058		Approved	FLJ23229, TRIFIC	uc001fhs.2	Q7Z4K8	OTTHUMG00000035680	ENST00000334634.4:c.291C>A	chr1.hg19:g.155148089C>A		56.0	0.0		84.0	31.0	NM_025058	A0AVI6|B1AVQ4|Q5VT60|Q5VT62|Q6NT17|Q6NT41|Q6ZRL7|Q9H5P2	Silent	SNP	ENST00000334634.4	hg19	CCDS1097.1																																																																																			.	.		0.637	TRIM46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086728.1	NM_025058		A	155148089	C	A	155148089	2	1	279	1	0	0	0	0	0	0	0	1	16536	581	21	3		3	TRIM46	1	155148089	Silent	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	828943	155148089	94102532	23	39782										
THBS3	7059	hgsc.bcm.edu	37	chr1	155167449	155167450	+	Splice_Site	INS	-	-	A													0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	caccattgaaggccgtgtatINScctggggtgggggtgggata					rs376682256		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:155167449_155167450insA	ENST00000368378.3	-	20	2323_2324	c.2303_2304insT	c.(2302-2304)gga>ggTa	p.G768fs	RP11-263K19.4_ENST00000454348.1_RNA|THBS3_ENST00000541576.1_Splice_Site_p.G165fs|THBS3_ENST00000486260.1_5'Flank|RP11-263K19.4_ENST00000453136.1_RNA|RP11-263K19.4_ENST00000447623.1_RNA|RP11-263K19.4_ENST00000436772.1_RNA|THBS3_ENST00000541990.1_Splice_Site_p.G297fs|MIR92B_ENST00000607575.1_RNA|RP11-263K19.4_ENST00000422665.1_RNA|THBS3_ENST00000457183.2_Splice_Site_p.G648fs	NM_001252607.1|NM_007112.4	NP_001239536.1|NP_009043.1	P49746	TSP3_HUMAN	thrombospondin 3	768	TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				bone trabecula formation (GO:0060346)|cell-matrix adhesion (GO:0007160)|growth plate cartilage development (GO:0003417)|ossification involved in bone maturation (GO:0043931)	extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(6)|endometrium(4)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(3)	48	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			AGGCCGTGTATCCTGGGGTGGG	0.53																																					p.G768fs		Atlas-INDEL	.											.	THBS3	70	.	0			c.2304_2305insT						.																																			SO:0001630	splice_region_variant	7059	exon20			.	L38969	CCDS1099.1, CCDS58034.1, CCDS72937.1	1q21	2008-02-05			ENSG00000169231	ENSG00000169231			11787	protein-coding gene	gene with protein product		188062				1601886	Standard	NM_007112		Approved		uc001fix.3	P49746	OTTHUMG00000035710	ENST00000368378.3:c.2303-1->T	chr1.hg19:g.155167449_155167450insA		109.0	0.0		158.0	17.0	NM_007112	B1AVR8|B4DQ20|Q8WV34	Frame_Shift_Ins	INS	ENST00000368378.3	hg19	CCDS1099.1																																																																																			.	.		0.53	THBS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086856.1	NM_007112	Frame_Shift_Ins	A	155167450	-	A	155167449	8	5	279	1	0	1	1	0	0	0	1	0	15870	1449	50	0	582	0	THBS3	1	155167449	Splice_Site	INS	-	TCGA-G3-A3CG-01A-11D-A20W-10	19360	155167449	94083172	24	39783	198	2								
THBS3	7059	hgsc.bcm.edu	37	chr1	155167450	155167451	+	Splice_Site	DNP	CC	CC	AT													0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	caccattgaaggccgtgtatCctggggtgggggtgggataa					rs376682256		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:155167450_155167451CC>AT	ENST00000368378.3	-	20	2323	c.2303_2303GG>AT	c.(2302-2304)gGGg>gATgg	p.G768D	RP11-263K19.4_ENST00000454348.1_RNA|THBS3_ENST00000541576.1_Splice_Site_p.G165D|THBS3_ENST00000486260.1_5'Flank|RP11-263K19.4_ENST00000453136.1_RNA|RP11-263K19.4_ENST00000447623.1_RNA|RP11-263K19.4_ENST00000436772.1_RNA|THBS3_ENST00000541990.1_Splice_Site_p.G297D|MIR92B_ENST00000607575.1_RNA|RP11-263K19.4_ENST00000422665.1_RNA|THBS3_ENST00000457183.2_Splice_Site_p.G648D	NM_001252607.1|NM_007112.4	NP_001239536.1|NP_009043.1	P49746	TSP3_HUMAN	thrombospondin 3	768	TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				bone trabecula formation (GO:0060346)|cell-matrix adhesion (GO:0007160)|growth plate cartilage development (GO:0003417)|ossification involved in bone maturation (GO:0043931)	extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(6)|endometrium(4)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(3)	48	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			GGCCGTGTATCCTGGGGTGGGG	0.525																																					p.G768V|.		Atlas-SNP	.											.	THBS3	70	.	0			c.G2303T|c.2303-1G>A						.																																			SO:0001630	splice_region_variant	7059	exon20|exon21			GTGTATCCTGGGG|TGTATCCTGGGGT	L38969	CCDS1099.1, CCDS58034.1, CCDS72937.1	1q21	2008-02-05			ENSG00000169231	ENSG00000169231			11787	protein-coding gene	gene with protein product		188062				1601886	Standard	NM_007112		Approved		uc001fix.3	P49746	OTTHUMG00000035710	ENST00000368378.3:c.2303_2303delinsAT	chr1.hg19:g.155167450_155167451delinsAT		107.0|110.0	0.0		156.0|158.0	18.0	NM_007112	B1AVR8|B4DQ20|Q8WV34	Missense_Mutation|Splice_Site	SNP	ENST00000368378.3	hg19	CCDS1099.1																																																																																			.	.		0.525	THBS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086856.1	NM_007112	Missense_Mutation	AT	155167451	CC	AT	155167450	5	1	279	1	0	0	0	0	0	0	1	0	15870	869	30	3	583	3	THBS3	1	155167450	Splice_Site	DNP	CC	TCGA-G3-A3CG-01A-11D-A20W-10	1	155167450	94083171	25	39784	198	2								
GON4L	54856	hgsc.bcm.edu	37	chr1	155734765	155734765	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tattactgagtccacgaaatActtgagaatattctccagct	6	9	1	2	rs199671178		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:155734765A>G	ENST00000368331.1	-	21	4522				GON4L_ENST00000437809.1_Intron|GON4L_ENST00000361040.5_Missense_Mutation_p.V1500A|GON4L_ENST00000471341.1_5'UTR|GON4L_ENST00000271883.5_Intron	NM_001282858.1|NM_001282860.1	NP_001269787.1|NP_001269789.1	Q3T8J9	GON4L_HUMAN	gon-4-like (C. elegans)						regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	45	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					TCCACGAAATACTTGAGAATA	0.408																																					p.V1500A		Atlas-SNP	.											.	GON4L	392	.	0			c.T4499C						.						79	72	74					1																	155734765		2203	4300	6503	SO:0001627	intron_variant	54856	exon21			CGAAATACTTGAG	AB046826	CCDS1121.1, CCDS44242.1, CCDS60296.1	1q22	2013-10-31	2006-11-08	2006-02-16	ENSG00000116580	ENSG00000116580			25973	protein-coding gene	gene with protein product		610393	"gon-4 homolog (C.elegans)"	GON4		16545939, 21454521	Standard	XM_005245283		Approved	FLJ20203, GON-4	uc001fly.1	Q3T8J9	OTTHUMG00000014106	ENST00000368331.1:c.4473+25T>C	chr1.hg19:g.155734765A>G		259.0	0.0		377.0	63.0	NM_032292	B7ZBL4|Q14C93|Q3T8J8|Q5VYZ5|Q5W0D5|Q6AWA6|Q6P1Q6|Q7Z3L3|Q8IY79|Q9BQI1|Q9HCG6	Missense_Mutation	SNP	ENST00000368331.1	hg19		.	.	.	.	.	.	.	.	.	.	A	12.85	2.062987	0.36373	.	.	ENSG00000116580	ENST00000361040	T	0.14144	2.53	4.79	-2.37	0.06643	.	.	.	.	.	T	0.01489	0.0048	N	0.08118	0	0.09310	N	1	B	0.15930	0.015	B	0.16289	0.015	T	0.45920	-0.9228	9	0.87932	D	0	.	0.4695	0.00529	0.225:0.2692:0.1546:0.3512	.	1500	Q3T8J9-2	.	A	1500	ENSP00000354322:V1500A	ENSP00000354322:V1500A	V	-	2	0	GON4L	154001389	0.000000	0.05858	0.000000	0.03702	0.082000	0.17680	-0.175000	0.09825	-0.617000	0.05664	0.529000	0.55759	GTA	.	A|1.000;T|0.000		0.408	GON4L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_032292		G	155734765	A	G	155734765	1	3	279	0	1	0	0	0	0	0	0	0	6580	391	14	2		2	GON4L	1	155734765	Intron	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	567315	155734765	93515856	26	39785										
FCRL5	83416	hgsc.bcm.edu	37	chr1	157514336	157514336	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gcactggacgtgtaaatggcTctagagagaagaatcacaac	11	8	2	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:157514336T>C	ENST00000361835.3	-	5	717	c.560A>G	c.(559-561)gAg>gGg	p.E187G	FCRL5_ENST00000356953.4_Splice_Site_p.E187G|FCRL5_ENST00000368189.3_Splice_Site_p.E187G|FCRL5_ENST00000368191.3_Splice_Site_p.E102G|FCRL5_ENST00000368190.3_Splice_Site_p.E187G	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	187					negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(45)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	85	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)				TGTAAATGGCTCTAGAGAGAA	0.527																																					p.E187G		Atlas-SNP	.											.	FCRL5	177	.	0			c.A560G						.						74	72	73					1																	157514336		2203	4300	6503	SO:0001630	splice_region_variant	83416	exon5			AATGGCTCTAGAG	AF369794	CCDS1165.1	1q21	2013-01-11			ENSG00000143297	ENSG00000143297		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18508	protein-coding gene	gene with protein product		605877				11027651, 11290337	Standard	NM_031281		Approved	FCRH5, IRTA2, BXMAS1, CD307e	uc009wsm.3	Q96RD9	OTTHUMG00000017481	ENST00000361835.3:c.560-1A>G	chr1.hg19:g.157514336T>C		61.0	0.0		110.0	57.0	NM_031281	A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Missense_Mutation	SNP	ENST00000361835.3	hg19	CCDS1165.1	.	.	.	.	.	.	.	.	.	.	T	12.44	1.939090	0.34189	.	.	ENSG00000143297	ENST00000361835;ENST00000356953;ENST00000368190;ENST00000368191;ENST00000368189	T;T;T;T;T	0.55588	0.52;0.51;0.54;2.82;0.88	4.17	1.79	0.24919	Immunoglobulin-like fold (1);	.	.	.	.	T	0.49321	0.1550	M	0.79614	2.46	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.999;0.989;1.0;0.991	D;D;P;D;D	0.77557	0.988;0.979;0.659;0.99;0.937	T	0.55970	-0.8056	9	0.14252	T	0.57	.	4.3263	0.11041	0.1759:0.1008:0.0:0.7232	.	102;187;187;187;187	F5GXJ2;Q96RD9-3;A6NJE8;Q96RD9-4;Q96RD9	.;.;.;.;FCRL5_HUMAN	G	187;187;187;102;187	ENSP00000354691:E187G;ENSP00000349434:E187G;ENSP00000357173:E187G;ENSP00000357174:E102G;ENSP00000357172:E187G	ENSP00000349434:E187G	E	-	2	0	FCRL5	155780960	0.872000	0.30054	0.395000	0.26283	0.075000	0.17131	1.069000	0.30641	0.171000	0.19730	0.383000	0.25322	GAG	.	.		0.527	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1	NM_031281	Missense_Mutation	C	157514336	T	C	157514336	5	2	279	1	0	0	0	0	0	0	1	0	5806	1565	54	2	2425	2	FCRL5	1	157514336	Splice_Site	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	1779571	157514336	91736285	27	39786										
MAEL	84944	hgsc.bcm.edu	37	chr1	166958707	166958707	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ctgatgccatcccttactgcTcctcagactgggcggtaagg	11	13	1	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:166958707T>C	ENST00000367872.4	+	1	362	c.118T>C	c.(118-120)Tcc>Ccc	p.S40P	MAEL_ENST00000367870.2_Missense_Mutation_p.S40P	NM_032858.1	NP_116247.1	Q96JY0	MAEL_HUMAN	maelstrom spermatogenic transposon silencer	40					cell differentiation (GO:0030154)|cell morphogenesis (GO:0000902)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|piRNA metabolic process (GO:0034587)|regulation of organ growth (GO:0046620)|spermatogenesis (GO:0007283)|synapsis (GO:0007129)	autosome (GO:0030849)|chromatin (GO:0000785)|chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|perinuclear region of cytoplasm (GO:0048471)|piP-body (GO:0071547)|XY body (GO:0001741)	DNA binding (GO:0003677)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(12)|skin(4)	28						CCCTTACTGCTCCTCAGACTG	0.637																																					p.S40P		Atlas-SNP	.											.	MAEL	95	.	0			c.T118C						.						37	33	34					1																	166958707		2201	4296	6497	SO:0001583	missense	84944	exon1			TACTGCTCCTCAG	AK027810, DQ076156	CCDS1257.1, CCDS65712.1, CCDS72975.1	1q24.1	2013-10-11	2012-12-18		ENSG00000143194	ENSG00000143194			25929	protein-coding gene	gene with protein product	"cancer/testis antigen 128", "spermatogenesis associated 35"	611368	"maelstrom homolog (Drosophila)"			19693694, 18694567	Standard	NM_001286378		Approved	FLJ14904, CT128, SPATA35	uc001gdy.1	Q96JY0	OTTHUMG00000034432	ENST00000367872.4:c.118T>C	chr1.hg19:g.166958707T>C	ENSP00000356846:p.Ser40Pro	62.0	0.0		120.0	7.0	NM_032858	B4DY43|E9JVC3|Q49AP9|Q5VZP8|Q9UIW6	Missense_Mutation	SNP	ENST00000367872.4	hg19	CCDS1257.1	.	.	.	.	.	.	.	.	.	.	T	16.40	3.112171	0.56398	.	.	ENSG00000143194	ENST00000367872;ENST00000367870;ENST00000447624	T;T;T	0.24538	1.85;1.85;1.85	5.49	5.49	0.81192	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (1);Domain of unknown function DUF1898 (1);	0.213636	0.33610	N	0.004731	T	0.25419	0.0618	N	0.19112	0.55	0.58432	D	0.999992	D;D	0.76494	0.999;0.999	D;D	0.71870	0.966;0.975	T	0.09930	-1.0652	10	0.56958	D	0.05	.	14.7155	0.69265	0.0:0.0:0.0:1.0	.	40;40	E9JVC3;Q96JY0	.;MAEL_HUMAN	P	40	ENSP00000356846:S40P;ENSP00000356844:S40P;ENSP00000402143:S40P	ENSP00000356844:S40P	S	+	1	0	MAEL	165225331	1.000000	0.71417	0.995000	0.50966	0.197000	0.23852	2.552000	0.45828	2.311000	0.77944	0.533000	0.62120	TCC	.	.		0.637	MAEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083239.1	NM_032858		C	166958707	T	C	166958707	3	2	279	1	0	0	0	0	1	0	0	0	9163	1551	54	2	120	2	MAEL	1	166958707	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	9444371	166958707	82291914	28	39787										
FMO3	2328	hgsc.bcm.edu	37	chr1	171072961	171072961	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ggcagggctagcatttacaaAtcagtcttttccaactcttc	7	11	3	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:171072961A>G	ENST00000367755.4	+	3	279	c.168A>G	c.(166-168)aaA>aaG	p.K56K	FMO3_ENST00000538429.1_Intron|MIR1295A_ENST00000408463.1_RNA|FMO3_ENST00000542847.1_Silent_p.K36K|FMO3_ENST00000392085.2_Silent_p.K56K	NM_001002294.2	NP_001002294.1	P31513	FMO3_HUMAN	flavin containing monooxygenase 3	56					drug metabolic process (GO:0017144)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	amino acid binding (GO:0016597)|flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)|trimethylamine monooxygenase activity (GO:0034899)			endometrium(1)|kidney(1)|large_intestine(12)|lung(12)|skin(1)|stomach(2)|urinary_tract(2)	31	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)				Almotriptan(DB00918)|Cimetidine(DB00501)|Clozapine(DB00363)|Dapsone(DB00250)|Dasatinib(DB01254)|Olanzapine(DB00334)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582)	GCATTTACAAATCAGTCTTTT	0.438																																					p.K56K		Atlas-SNP	.											.	FMO3	73	.	0			c.A168G						.						169	165	167					1																	171072961		2203	4300	6503	SO:0001819	synonymous_variant	2328	exon3			TTACAAATCAGTC	BC032016	CCDS1292.1	1q24.3	2013-10-01			ENSG00000007933	ENSG00000007933	2.6.1.16		3771	protein-coding gene	gene with protein product		136132				8486388, 9417913	Standard	NM_001002294		Approved		uc001ghh.3	P31513	OTTHUMG00000035505	ENST00000367755.4:c.168A>G	chr1.hg19:g.171072961A>G		169.0	0.0		288.0	153.0	NM_006894	B2R816|Q14854|Q8N5N5	Silent	SNP	ENST00000367755.4	hg19	CCDS1292.1																																																																																			.	.		0.438	FMO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086219.1	NM_006894		G	171072961	A	G	171072961	2	3	279	1	0	0	0	0	0	0	0	1	5964	98	4	2		2	FMO3	1	171072961	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	4114254	171072961	78177660	29	39788										
BAT2L2	23215	hgsc.bcm.edu	37	chr1	171511217	171511217	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	agaatgttctacctccaaagAgggaaattgcaaagagaagt	10	6	1	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:171511217A>G	ENST00000338920.4	+	16	4843	c.4606A>G	c.(4606-4608)Agg>Ggg	p.R1536G	PRRC2C_ENST00000426496.2_Missense_Mutation_p.R1536G|PRRC2C_ENST00000367742.3_Missense_Mutation_p.R1538G|PRRC2C_ENST00000392078.3_Missense_Mutation_p.R1538G	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	1536					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										ACCTCCAAAGAGGGAAATTGC	0.423																																					p.R1536G		Atlas-SNP	.											.	.	.	.	0			c.A4606G						.						52	54	54					1																	171511217		2203	4300	6503	SO:0001583	missense	23215	exon16			CCAAAGAGGGAAA	AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"BAT2 domain containing 1", "HLA-B associated transcript 2-like 2"	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.4606A>G	chr1.hg19:g.171511217A>G	ENSP00000343629:p.Arg1536Gly	65.0	0.0		96.0	4.0	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Missense_Mutation	SNP	ENST00000338920.4	hg19	CCDS1296.2	.	.	.	.	.	.	.	.	.	.	A	6.726	0.502601	0.12822	.	.	ENSG00000117523	ENST00000392078;ENST00000451306;ENST00000426496;ENST00000367742;ENST00000338920;ENST00000392080	T;T;T;T	0.03496	3.92;3.91;3.91;3.92	5.87	3.5	0.40072	.	0.000000	0.52532	D	0.000079	T	0.08447	0.0210	M	0.73962	2.25	0.52501	D	0.999956	D	0.89917	1.0	D	0.85130	0.997	T	0.01266	-1.1401	10	0.87932	D	0	.	9.3876	0.38352	0.7512:0.1275:0.0:0.1213	.	1536	Q9Y520-4	.	G	1538;1537;1536;1538;1536;1293	ENSP00000375928:R1538G;ENSP00000410219:R1536G;ENSP00000356716:R1538G;ENSP00000343629:R1536G	ENSP00000343629:R1536G	R	+	1	2	PRRC2C	169777841	1.000000	0.71417	0.977000	0.42913	0.797000	0.45037	2.109000	0.41863	0.451000	0.26802	-0.320000	0.08662	AGG	.	.		0.423	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172		G	171511217	A	G	171511217	3	3	279	1	0	0	0	0	1	0	0	0	1321	295	11	2	4664	2	BAT2L2	1	171511217	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	438256	171511217	77739404	30	39789										
C1orf9	51430	hgsc.bcm.edu	37	chr1	172525148	172525148	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	atctacctcagaaatcactcCaatctcaaagcttgagtaag	5	11	4	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:172525148C>T	ENST00000263688.3	+	4	647	c.428C>T	c.(427-429)cCa>cTa	p.P143L	SUCO_ENST00000367723.4_Missense_Mutation_p.P301L|SUCO_ENST00000608151.1_Missense_Mutation_p.P302L|SUCO_ENST00000610051.1_Missense_Mutation_p.P106L	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor	143					multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)											GAAATCACTCCAATCTCAAAG	0.348																																					p.P143L		Atlas-SNP	.											.	.	.	.	0			c.C428T						.						60	56	58					1																	172525148		2203	4299	6502	SO:0001583	missense	51430	exon4			TCACTCCAATCTC	AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"SUN-like protein 1", "osteopotentia"		"chromosome 1 open reading frame 9"	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839	ENST00000263688.3:c.428C>T	chr1.hg19:g.172525148C>T	ENSP00000263688:p.Pro143Leu	54.0	0.0		96.0	4.0	NM_014283	B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Missense_Mutation	SNP	ENST00000263688.3	hg19	CCDS1303.1	.	.	.	.	.	.	.	.	.	.	C	14.99	2.701198	0.48307	.	.	ENSG00000094975	ENST00000367723;ENST00000263688	.	.	.	5.76	4.83	0.62350	.	0.145724	0.48767	D	0.000164	T	0.28896	0.0717	L	0.32530	0.975	0.49213	D	0.999767	B;B;B;B	0.31318	0.319;0.005;0.012;0.005	B;B;B;B	0.26517	0.07;0.006;0.006;0.003	T	0.13124	-1.0521	9	0.28530	T	0.3	-5.8702	14.095	0.65016	0.1517:0.8482:0.0:0.0	.	106;143;302;143	B4DYM4;B4DZJ3;Q5H945;Q9UBS9	.;.;.;OSPT_HUMAN	L	302;143	.	ENSP00000263688:P143L	P	+	2	0	C1orf9	170791771	1.000000	0.71417	0.951000	0.38953	0.991000	0.79684	3.746000	0.55127	1.527000	0.49086	0.655000	0.94253	CCA	.	.		0.348	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227		T	172525148	C	T	172525148	3	4	279	1	0	0	0	0	1	0	0	0	2069	594	21	3	442	3	C1orf9	1	172525148	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	1013931	172525148	76725473	31	39790										
TNR	7143	hgsc.bcm.edu	37	chr1	175348689	175348689	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	agagataggtcttactcaccTgtcagggtggccctggtggt	14	9	3	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:175348689T>C	ENST00000367674.2	-	9	2670	c.1962A>G	c.(1960-1962)acA>acG	p.T654T	TNR_ENST00000263525.2_Splice_Site_p.T654T			Q92752	TENR_HUMAN	tenascin R	654	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					CTTACTCACCTGTCAGGGTGG	0.532																																					p.T654T		Atlas-SNP	.											.	TNR	399	.	0			c.A1962G						.						75	68	71					1																	175348689		2203	4300	6503	SO:0001630	splice_region_variant	7143	exon9			CTCACCTGTCAGG	X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11953	protein-coding gene	gene with protein product	"restrictin", "janusin"	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.1963+1A>G	chr1.hg19:g.175348689T>C		95.0	0.0		169.0	24.0	NM_003285	C9J563|Q15568|Q5R3G0	Silent	SNP	ENST00000367674.2	hg19	CCDS1318.1																																																																																			.	.		0.532	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285	Silent	C	175348689	T	C	175348689	5	2	279	1	0	0	0	0	0	0	1	0	16353	1594	55	2	2174	2	TNR	1	175348689	Splice_Site	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	2823541	175348689	73901932	32	39791										
C1orf125	126859	hgsc.bcm.edu	37	chr1	179504037	179504037	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gagaagtaaaagaagaagaaGaacaacaagaagaagaagaa	11	2	0	9	rs200097954|rs368406759|rs6425573	byFrequency	TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:179504037G>C	ENST00000367618.3	+	25	3358	c.2971G>C	c.(2971-2973)Gaa>Caa	p.E991Q		NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	991	Glu-rich.		E -> Q (in dbSNP:rs6425573).					p.E991_Q992delEQ(1)		NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(27)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	59						agaagaagaagaacaacaaga	0.318													G|||	14	0.00279553	0	0.0058	5008	,	,		17137	0.002		0.004	False		,,,				2504	0.0041				p.E991Q		Atlas-SNP	.											.	AXDND1	142	.	1	Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	c.G2971C						.						49	51	50					1																	179504037		2152	4286	6438	SO:0001583	missense	126859	exon25			GAAGAAGAACAAC	BX647935	CCDS30948.1	1q25.2	2011-02-18	2011-02-18	2011-02-18	ENSG00000162779	ENSG00000162779			26564	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 125"	C1orf125		14702039	Standard	NM_144696		Approved	FLJ32940	uc001gmo.3	Q5T1B0	OTTHUMG00000035266	ENST00000367618.3:c.2971G>C	chr1.hg19:g.179504037G>C	ENSP00000356590:p.Glu991Gln	193.0	0.0		242.0	10.0	NM_144696	Q6AWB2|Q96LJ3|Q96M01	Missense_Mutation	SNP	ENST00000367618.3	hg19	CCDS30948.1	.	.	.	.	.	.	.	.	.	.	G	9.300	1.052898	0.19907	.	.	ENSG00000162779	ENST00000367618;ENST00000360322;ENST00000434088	T;T	0.19105	2.17;2.17	4.89	-6.02	0.02192	.	0.508747	0.16499	N	0.211773	T	0.08980	0.0222	N	0.24115	0.695	0.09310	N	1	B;B	0.24186	0.099;0.099	B;B	0.10450	0.003;0.005	T	0.15838	-1.0423	10	0.28530	T	0.3	-2.8152	6.1976	0.20557	0.4456:0.3814:0.173:0.0	rs6425573	875;991	E9PCJ4;Q5T1B0	.;AXDN1_HUMAN	Q	991;875;851	ENSP00000356590:E991Q;ENSP00000391716:E851Q	ENSP00000353471:E875Q	E	+	1	0	AXDND1	177770660	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.365000	0.20348	-1.164000	0.02790	-1.047000	0.02352	GAA	.	G|1.000;|0.000		0.318	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	NM_144696		C	179504037	G	C	179504037	3	2	279	1	0	0	0	0	1	0	0	0	1995	943	33	4	3065	4	C1orf125	1	179504037	Missense_Mutation	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	4155348	179504037	69746584	33	39792										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181765974	181765974	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ggtcacccagtgagggcaggTcacagacgcccaacagacag	13	13	2	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:181765974T>C	ENST00000367573.2	+	47	6379	c.6379T>C	c.(6379-6381)Tca>Cca	p.S2127P	CACNA1E_ENST00000367567.4_Missense_Mutation_p.S1691P|CACNA1E_ENST00000358338.5_Missense_Mutation_p.S2016P|CACNA1E_ENST00000367570.1_Missense_Mutation_p.S2084P|CACNA1E_ENST00000357570.5_Missense_Mutation_p.S2078P|CACNA1E_ENST00000360108.3_Missense_Mutation_p.S2108P|CACNA1E_ENST00000526775.1_Missense_Mutation_p.S2065P	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	2127					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						TGAGGGCAGGTCACAGACGCC	0.592																																					p.S2127P		Atlas-SNP	.											.	CACNA1E	778	.	0			c.T6379C						.						19	21	21					1																	181765974		2056	4189	6245	SO:0001583	missense	777	exon47			GGCAGGTCACAGA	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.6379T>C	chr1.hg19:g.181765974T>C	ENSP00000356545:p.Ser2127Pro	110.0	0.0		171.0	7.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	T	19.07	3.755297	0.69648	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.96265	-3.89;-3.89;-3.92;-3.89;-3.96;-3.92;-3.92	5.91	4.72	0.59763	.	0.636360	0.16141	N	0.227721	D	0.95249	0.8459	N	0.19112	0.55	0.38251	D	0.941591	D;P	0.71674	0.998;0.664	P;B	0.62649	0.905;0.277	D	0.94970	0.8116	10	0.51188	T	0.08	.	11.3122	0.49370	0.0:0.0:0.1518:0.8482	.	2065;2084	Q15878-2;Q15878-3	.;.	P	2084;2065;2078;2016;1691;2108;2127	ENSP00000356542:S2084P;ENSP00000434814:S2065P;ENSP00000350183:S2078P;ENSP00000351101:S2016P;ENSP00000356539:S1691P;ENSP00000353222:S2108P;ENSP00000356545:S2127P	ENSP00000350183:S2078P	S	+	1	0	CACNA1E	180032597	0.993000	0.37304	1.000000	0.80357	0.988000	0.76386	1.920000	0.40025	2.254000	0.74563	0.533000	0.62120	TCA	.	.		0.592	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		C	181765974	T	C	181765974	3	2	279	1	0	0	0	0	1	0	0	0	2544	1667	58	2	6432	2	CACNA1E	1	181765974	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	2261937	181765974	67484647	34	39793										
LAMC2	3918	hgsc.bcm.edu	37	chr1	183192335	183192335	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cctttgactaccgtgtggacAgaggaggcagacacccatct	11	12	1	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:183192335A>G	ENST00000264144.4	+	7	894	c.829A>G	c.(829-831)Aga>Gga	p.R277G	LAMC2_ENST00000493293.1_Missense_Mutation_p.R277G	NM_005562.2	NP_005553.2	Q13753	LAMC2_HUMAN	laminin, gamma 2	277	Laminin IV type A. {ECO:0000255|PROSITE- ProRule:PRU00458}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	cell cortex (GO:0005938)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-2 complex (GO:0005607)|laminin-5 complex (GO:0005610)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	heparin binding (GO:0008201)			breast(2)|endometrium(6)|kidney(8)|large_intestine(11)|lung(18)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55						CCGTGTGGACAGAGGAGGCAG	0.488																																					p.R277G		Atlas-SNP	.											.	LAMC2	113	.	0			c.A829G						.						113	109	110					1																	183192335		2203	4300	6503	SO:0001583	missense	3918	exon7			GTGGACAGAGGAG	Z15008	CCDS1352.1, CCDS44285.1	1q25-q31	2013-03-01	2002-08-29		ENSG00000058085	ENSG00000058085		"Laminins"	6493	protein-coding gene	gene with protein product		150292	"laminin, gamma 2 (nicein (100kD), kalinin (105kD), BM600 (100kD), Herlitz junctional epidermolysis bullosa))"	EBR2, LAMB2T, LAMNB2, EBR2A		1383240	Standard	NM_005562		Approved	nicein-100kDa, kalinin-105kDa, BM600-100kDa	uc001gqa.2	Q13753	OTTHUMG00000035520	ENST00000264144.4:c.829A>G	chr1.hg19:g.183192335A>G	ENSP00000264144:p.Arg277Gly	159.0	0.0		200.0	8.0	NM_005562	Q02536|Q02537|Q13752|Q14941|Q14DF7|Q2M1N2|Q5VYE8	Missense_Mutation	SNP	ENST00000264144.4	hg19	CCDS1352.1	.	.	.	.	.	.	.	.	.	.	A	19.75	3.886051	0.72410	.	.	ENSG00000058085	ENST00000493293;ENST00000537180;ENST00000264144	T;T	0.34072	1.38;1.38	5.0	1.26	0.21427	Laminin B type IV (2);Laminin B, subgroup (1);Growth factor, receptor (1);	0.000000	0.64402	D	0.000001	T	0.47930	0.1472	L	0.40543	1.245	0.51233	D	0.999912	D;D	0.89917	1.0;1.0	D;D	0.87578	0.99;0.998	T	0.32402	-0.9908	10	0.38643	T	0.18	.	14.284	0.66232	0.2784:0.7216:0.0:0.0	.	277;277	Q13753;Q13753-2	LAMC2_HUMAN;.	G	277	ENSP00000432063:R277G;ENSP00000264144:R277G	ENSP00000264144:R277G	R	+	1	2	LAMC2	181458958	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.028000	0.30128	0.222000	0.20900	0.459000	0.35465	AGA	.	.		0.488	LAMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086258.1	NM_005562		G	183192335	A	G	183192335	3	3	279	1	0	0	0	0	1	0	0	0	8624	180	7	2	855	2	LAMC2	1	183192335	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	1426361	183192335	66058286	35	39794										
IVNS1ABP	10625	hgsc.bcm.edu	37	chr1	185267396	185267396	+	Missense_Mutation	SNP	A	A	T													0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tgatggcatgagaaccatcaAagccaccacatacaaacagt							TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:185267396A>T	ENST00000367498.3	-	15	2322	c.1700T>A	c.(1699-1701)tTt>tAt	p.F567Y	IVNS1ABP_ENST00000459929.1_5'UTR|IVNS1ABP_ENST00000392007.3_Missense_Mutation_p.F349Y	NM_006469.4	NP_006460.2	Q9Y6Y0	NS1BP_HUMAN	influenza virus NS1A binding protein	567					negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|response to virus (GO:0009615)|RNA splicing (GO:0008380)|transcription from RNA polymerase III promoter (GO:0006383)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|spliceosomal complex (GO:0005681)|transcription factor complex (GO:0005667)				breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|ovary(4)|prostate(2)	29						AGAACCATCAAAGCCACCACA	0.388																																					p.F567Y		Atlas-SNP	.											.	IVNS1ABP	80	.	0			c.T1700A						.						124	108	114					1																	185267396		2203	4300	6503	SO:0001583	missense	10625	exon15			CCATCAAAGCCAC	AB020657	CCDS1368.1	1q25.1-q31.1	2013-01-30			ENSG00000116679	ENSG00000116679		"Kelch-like", "BTB/POZ domain containing"	16951	protein-coding gene	gene with protein product	"kelch-like family member 39"	609209				9696811, 10048485	Standard	NM_006469		Approved	NS1-BP, HSPC068, NS-1, KIAA0850, ND1, KLHL39	uc001grl.3	Q9Y6Y0	OTTHUMG00000035384	ENST00000367498.3:c.1700T>A	chr1.hg19:g.185267396A>T	ENSP00000356468:p.Phe567Tyr	153.0	0.0		170.0	97.0	NM_006469	A8K8R6|Q1G4T6|Q1G4T7|Q5TF75|Q6NW38|Q7LCG2|Q9NZX0|Q9Y480	Missense_Mutation	SNP	ENST00000367498.3	hg19	CCDS1368.1	.	.	.	.	.	.	.	.	.	.	A	15.07	2.724863	0.48833	.	.	ENSG00000116679	ENST00000367498;ENST00000392007	T;T	0.76839	-1.05;-1.05	5.38	5.38	0.77491	Galactose oxidase, beta-propeller (1);	0.000000	0.85682	D	0.000000	T	0.63570	0.2522	N	0.11106	0.095	0.80722	D	1	B;P	0.40398	0.397;0.716	B;B	0.42319	0.093;0.383	T	0.63225	-0.6685	10	0.16420	T	0.52	.	15.6903	0.77446	1.0:0.0:0.0:0.0	.	349;567	A8MVR0;Q9Y6Y0	.;NS1BP_HUMAN	Y	567;349	ENSP00000356468:F567Y;ENSP00000375864:F349Y	ENSP00000356468:F567Y	F	-	2	0	IVNS1ABP	183534019	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.118000	0.94355	2.163000	0.67991	0.460000	0.39030	TTT	.	.		0.388	IVNS1ABP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085774.1	NM_006469		T	185267396	A	T	185267396	3	4	279	1	0	0	0	0	1	0	0	0	7939	14	1	4	232	4	IVNS1ABP	1	185267396	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	2075061	185267396	63983225	36	39795	199	2								
IVNS1ABP	10625	hgsc.bcm.edu	37	chr1	185267406	185267406	+	Missense_Mutation	SNP	A	A	C													0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	agaaccatcaaagccaccacAtacaaacagttttcctaaaa							TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:185267406A>C	ENST00000367498.3	-	15	2312	c.1690T>G	c.(1690-1692)Tgt>Ggt	p.C564G	IVNS1ABP_ENST00000459929.1_5'UTR|IVNS1ABP_ENST00000392007.3_Missense_Mutation_p.C346G	NM_006469.4	NP_006460.2	Q9Y6Y0	NS1BP_HUMAN	influenza virus NS1A binding protein	564					negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|response to virus (GO:0009615)|RNA splicing (GO:0008380)|transcription from RNA polymerase III promoter (GO:0006383)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|spliceosomal complex (GO:0005681)|transcription factor complex (GO:0005667)				breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|ovary(4)|prostate(2)	29						AAGCCACCACATACAAACAGT	0.368																																					p.C564G		Atlas-SNP	.											.	IVNS1ABP	80	.	0			c.T1690G						.						102	90	94					1																	185267406		2203	4300	6503	SO:0001583	missense	10625	exon15			CACCACATACAAA	AB020657	CCDS1368.1	1q25.1-q31.1	2013-01-30			ENSG00000116679	ENSG00000116679		"Kelch-like", "BTB/POZ domain containing"	16951	protein-coding gene	gene with protein product	"kelch-like family member 39"	609209				9696811, 10048485	Standard	NM_006469		Approved	NS1-BP, HSPC068, NS-1, KIAA0850, ND1, KLHL39	uc001grl.3	Q9Y6Y0	OTTHUMG00000035384	ENST00000367498.3:c.1690T>G	chr1.hg19:g.185267406A>C	ENSP00000356468:p.Cys564Gly	140.0	0.0		141.0	81.0	NM_006469	A8K8R6|Q1G4T6|Q1G4T7|Q5TF75|Q6NW38|Q7LCG2|Q9NZX0|Q9Y480	Missense_Mutation	SNP	ENST00000367498.3	hg19	CCDS1368.1	.	.	.	.	.	.	.	.	.	.	A	11.59	1.683858	0.29872	.	.	ENSG00000116679	ENST00000367498;ENST00000392007	T;T	0.78003	-1.14;-1.14	5.38	4.46	0.54185	Galactose oxidase, beta-propeller (1);	0.103773	0.64402	N	0.000004	T	0.77246	0.4102	M	0.73430	2.235	0.35887	D	0.82936	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.78021	-0.2367	10	0.36615	T	0.2	.	15.527	0.75919	0.1446:0.8554:0.0:0.0	.	346;564	A8MVR0;Q9Y6Y0	.;NS1BP_HUMAN	G	564;346	ENSP00000356468:C564G;ENSP00000375864:C346G	ENSP00000356468:C564G	C	-	1	0	IVNS1ABP	183534029	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.809000	0.62591	1.375000	0.46248	-0.445000	0.05633	TGT	.	.		0.368	IVNS1ABP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085774.1	NM_006469		C	185267406	A	C	185267406	3	2	279	1	0	0	0	0	1	0	0	0	7939	217	8	5	242	5	IVNS1ABP	1	185267406	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	10	185267406	63983215	37	39796	199	2								
FAM5C	339479	hgsc.bcm.edu	37	chr1	190067205	190067205	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tttggcaatttggcattaaaCgcctgcagagcagattggat	11	7	0	2	rs562180986		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:190067205C>T	ENST00000367462.3	-	8	2475	c.2244G>A	c.(2242-2244)gcG>gcA	p.A748A	BRINP3_ENST00000534846.1_Silent_p.A646A	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	748					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)											TGGCATTAAACGCCTGCAGAG	0.423																																					p.A748A		Atlas-SNP	.											.	FAM5C	343	.	0			c.G2244A						.						141	138	139					1																	190067205		2203	4300	6503	SO:0001819	synonymous_variant	339479	exon8			ATTAAACGCCTGC	AB111893	CCDS1373.1	1q31.1	2013-09-18	2013-09-18	2013-09-18	ENSG00000162670	ENSG00000162670			22393	protein-coding gene	gene with protein product			"family with sequence similarity 5, member C"	FAM5C		16018821, 15193423	Standard	NM_199051		Approved	DBCCR1L, DBCCR1L1	uc001gse.1	Q76B58	OTTHUMG00000035533	ENST00000367462.3:c.2244G>A	chr1.hg19:g.190067205C>T		131.0	0.0		192.0	24.0	NM_199051	B3KVP1|B7Z260|O95726|Q2M330	Silent	SNP	ENST00000367462.3	hg19	CCDS1373.1																																																																																			.	.		0.423	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086278.1	NM_199051		T	190067205	C	T	190067205	2	4	279	1	0	0	0	0	0	0	0	1	5602	523	19	1		1	FAM5C	1	190067205	Silent	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	4799799	190067205	59183416	38	39797										
LAD1	3898	hgsc.bcm.edu	37	chr1	201356005	201356005	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ctcttctggctccctgcccaCcaagctctcctcctccaggg	7	20	3	0	rs552300739|rs386638482	byFrequency	TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:201356005C>A	ENST00000391967.2	-	3	785	c.484G>T	c.(484-486)Gtg>Ttg	p.V162L	LAD1_ENST00000367313.3_Missense_Mutation_p.V176L	NM_005558.3	NP_005549.2	O00515	LAD1_HUMAN	ladinin 1	162						basement membrane (GO:0005604)	structural molecule activity (GO:0005198)	p.V162M(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(6)|prostate(2)|skin(2)	19						TCCCTGCCCACCAAGCTCTCC	0.582																																					p.V162L		Atlas-SNP	.											LAD1,trunk,malignant_melanoma,0,1	LAD1	42	.	1	Substitution - Missense(1)	skin(1)	c.G484T						.						45	57	53					1																	201356005		2193	4299	6492	SO:0001583	missense	3898	exon3			TGCCCACCAAGCT	U42408	CCDS1410.1	1q25.1-q32.3	2008-02-05			ENSG00000159166	ENSG00000159166			6472	protein-coding gene	gene with protein product		602314				8618013, 9119369	Standard	NM_005558		Approved		uc001gwm.3	O00515	OTTHUMG00000035737	ENST00000391967.2:c.484G>T	chr1.hg19:g.201356005C>A	ENSP00000375829:p.Val162Leu	75.0	0.0		55.0	3.0	NM_005558	O95614|Q96GD8	Missense_Mutation	SNP	ENST00000391967.2	hg19	CCDS1410.1	.	.	.	.	.	.	.	.	.	.	C	9.310	1.055294	0.19907	.	.	ENSG00000159166	ENST00000391967;ENST00000367313	T;T	0.11930	2.74;2.73	5.3	2.34	0.29019	.	1.710450	0.02842	N	0.128020	T	0.09247	0.0228	N	0.08118	0	0.09310	N	1	B;B	0.15141	0.001;0.012	B;B	0.15484	0.003;0.013	T	0.36016	-0.9765	10	0.28530	T	0.3	-0.7378	9.7698	0.40582	0.0:0.8029:0.0:0.1971	.	176;162	E9PDI4;O00515	.;LAD1_HUMAN	L	162;176	ENSP00000375829:V162L;ENSP00000356282:V176L	ENSP00000356282:V176L	V	-	1	0	LAD1	199622628	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.268000	0.18571	0.197000	0.20387	-1.063000	0.02288	GTG	.	.		0.582	LAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086946.1	NM_005558		A	201356005	C	A	201356005	3	1	279	1	0	0	0	0	1	0	0	0	8608	507	18	3	1101	3	LAD1	1	201356005	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	11288800	201356005	47894616	39	39798										
DISP1	84976	hgsc.bcm.edu	37	chr1	223179204	223179204	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gttgtggcagaattgtgagaGtgaagtgcaattctgtggac	15	4	1	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:223179204G>C	ENST00000284476.6	+	8	4629	c.4465G>C	c.(4465-4467)Gtg>Ctg	p.V1489L		NM_032890.3	NP_116279.2	Q96F81	DISP1_HUMAN	dispatched homolog 1 (Drosophila)	1489					determination of left/right symmetry (GO:0007368)|diaphragm development (GO:0060539)|dorsal/ventral pattern formation (GO:0009953)|embryonic pattern specification (GO:0009880)|patched ligand maturation (GO:0007225)|peptide transport (GO:0015833)|protein homotrimerization (GO:0070207)|regulation of protein secretion (GO:0050708)|smoothened signaling pathway (GO:0007224)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)|peptide transporter activity (GO:0015197)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(20)|lung(25)|prostate(4)|skin(1)|stomach(1)|urinary_tract(5)	69				GBM - Glioblastoma multiforme(131;0.102)		AATTGTGAGAGTGAAGTGCAA	0.398																																					p.V1489L		Atlas-SNP	.											.	DISP1	145	.	0			c.G4465C						.						64	61	62					1																	223179204		2203	4300	6503	SO:0001583	missense	84976	exon10			GTGAGAGTGAAGT	AK056569	CCDS1536.1	1q42.12	2008-02-05			ENSG00000154309	ENSG00000154309			19711	protein-coding gene	gene with protein product		607502				10619433	Standard	NM_032890		Approved	DISPA, MGC13130, DKFZP434I0428, MGC16796	uc001hnu.2	Q96F81	OTTHUMG00000037893	ENST00000284476.6:c.4465G>C	chr1.hg19:g.223179204G>C	ENSP00000284476:p.Val1489Leu	215.0	0.0		290.0	43.0	NM_032890	Q8N7C2|Q96I92|Q9H698|Q9H8H9|Q9UFA2	Missense_Mutation	SNP	ENST00000284476.6	hg19	CCDS1536.1	.	.	.	.	.	.	.	.	.	.	G	10.27	1.304313	0.23736	.	.	ENSG00000154309	ENST00000284476	D	0.91686	-2.89	5.42	1.42	0.22433	.	0.763320	0.11881	N	0.520513	D	0.82857	0.5128	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.69756	-0.5059	10	0.41790	T	0.15	-7.6849	3.09	0.06290	0.2012:0.1229:0.5493:0.1266	.	1489	Q96F81	DISP1_HUMAN	L	1489	ENSP00000284476:V1489L	ENSP00000284476:V1489L	V	+	1	0	DISP1	221245827	1.000000	0.71417	0.128000	0.21923	0.956000	0.61745	0.721000	0.25911	0.248000	0.21435	-0.137000	0.14449	GTG	.	.		0.398	DISP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092512.1	NM_032890		C	223179204	G	C	223179204	3	2	279	1	0	0	0	0	1	0	0	0	4541	1029	36	4	4491	4	DISP1	1	223179204	Missense_Mutation	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	21823199	223179204	26071417	40	39799										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228564922	228564922	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	agctgcacgcagcctacctcAgcccccggcacctggtgctc	10	19	1	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:228564922A>G	ENST00000422127.1	+	101	23253	c.23209A>G	c.(23209-23211)Agc>Ggc	p.S7737G	OBSCN_ENST00000366707.4_Missense_Mutation_p.S5371G|OBSCN_ENST00000570156.2_Missense_Mutation_p.S8694G	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	7737	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				AGCCTACCTCAGCCCCCGGCA	0.687																																					p.S8694G		Atlas-SNP	.											.	OBSCN	2142	.	0			c.A26080G						.						11	15	14					1																	228564922		2032	4173	6205	SO:0001583	missense	84033	exon112			TACCTCAGCCCCC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.23209A>G	chr1.hg19:g.228564922A>G	ENSP00000409493:p.Ser7737Gly	34.0	0.0		79.0	4.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.3|24.3	4.516749|4.516749	0.85495|0.85495	.|.	.|.	ENSG00000154358|ENSG00000154358	ENST00000441106|ENST00000422127;ENST00000366707	.|T;T	.|0.66460	.|-0.21;-0.21	4.82|4.82	4.82|4.82	0.62117|0.62117	.|Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.|.	.|.	.|.	.|.	T|T	0.75874|0.75874	0.3909|0.3909	L|L	0.61218|0.61218	1.895|1.895	0.80722|0.80722	D|D	1|1	.|D	.|0.56968	.|0.978	.|P	.|0.57911	.|0.829	T|T	0.79412|0.79412	-0.1814|-0.1814	5|9	.|0.87932	.|D	.|0	.|.	14.3791|14.3791	0.66900|0.66900	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|7737	.|Q5VST9	.|OBSCN_HUMAN	R|G	2353|7737;5371	.|ENSP00000409493:S7737G;ENSP00000355668:S5371G	.|ENSP00000355668:S5371G	Q|S	+|+	2|1	0|0	OBSCN|OBSCN	226631545|226631545	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.817000|0.817000	0.46193|0.46193	7.336000|7.336000	0.79245|0.79245	1.816000|1.816000	0.52996|0.52996	0.260000|0.260000	0.18958|0.18958	CAG|AGC	.	.		0.687	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		G	228564922	A	G	228564922	3	3	279	1	0	0	0	0	1	0	0	0	10821	188	7	2	24817	2	OBSCN	1	228564922	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	5385718	228564922	20685699	41	39800										
OR2W3	343171	hgsc.bcm.edu	37	chr1	248059354	248059355	+	Missense_Mutation	DNP	TC	TC	AT													0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ggggctgtggggtggccaacTccttggccatgtctcctgtg					rs147816311	byFrequency	TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:248059354_248059355TC>AT	ENST00000360358.3	+	1	466_467	c.466_467TC>AT	c.(466-468)TCc>ATc	p.S156I	OR2W3_ENST00000537741.1_Missense_Mutation_p.S156I	NM_001001957.2	NP_001001957.2	Q7Z3T1	OR2W3_HUMAN	olfactory receptor, family 2, subfamily W, member 3	156						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S156F(1)		breast(1)|kidney(2)|large_intestine(2)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)	49	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0319)			GGTGGCCAACTCCTTGGCCATG	0.639																																					p.S156T|p.S156F		Atlas-SNP	.											.|OR2W3,scalp,carcinoma,0,6	OR2W3	113	.	1	Substitution - Missense(1)	skin(1)	c.T466A|c.C467T						.																																			SO:0001583	missense	343171	exon1			GCCAACTCCTTGG|CCAACTCCTTGGC	N75737	CCDS31099.1	1q44	2012-08-09		2004-03-10	ENSG00000238243	ENSG00000238243		"GPCR / Class A : Olfactory receptors"	15021	protein-coding gene	gene with protein product				OR2W8P, OR2W3P		14983052	Standard	NM_001001957		Approved	OST718	uc010pzb.2	Q7Z3T1	OTTHUMG00000040204	Exception_encountered	chr1.hg19:g.248059354_248059355delinsAT	ENSP00000353516:p.Ser156Ile	126.0|123.0	0.0		152.0|145.0	11.0|16.0	NM_001001957	Q6IF06|Q8NG86	Missense_Mutation	SNP	ENST00000360358.3	hg19	CCDS31099.1																																																																																			.	.		0.639	OR2W3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096861.1	NM_001001957		AT	248059355	TC	AT	248059354	3	1	279	1	0	0	0	0	1	0	0	0	11042	1551	54	4	468	4	OR2W3	1	248059354	Missense_Mutation	DNP	TC	TCGA-G3-A3CG-01A-11D-A20W-10	19494432	248059354	1191267	42	39801										
OR2T33	391195	hgsc.bcm.edu	37	chr1	248436937	248436937	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	atgagggaaagttggctcagGaggaagtacatgggcgtgtg	18	4	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr1:248436937G>T	ENST00000318021.2	-	1	201	c.180C>A	c.(178-180)ctC>ctA	p.L60L		NM_001004695.1	NP_001004695.1	Q8NG76	O2T33_HUMAN	olfactory receptor, family 2, subfamily T, member 33	60						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(41)|ovary(1)|prostate(1)|skin(4)	67	all_cancers(71;0.000124)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			GTTGGCTCAGGAGGAAGTACA	0.537																																					p.L60L		Atlas-SNP	.											.	OR2T33	133	.	0			c.C180A						.						83	75	77					1																	248436937		2202	4300	6502	SO:0001819	synonymous_variant	391195	exon1			GCTCAGGAGGAAG		CCDS31109.1	1q44	2012-08-09			ENSG00000177212	ENSG00000177212		"GPCR / Class A : Olfactory receptors"	31255	protein-coding gene	gene with protein product							Standard	NM_001004695		Approved		uc010pzi.2	Q8NG76	OTTHUMG00000040458	ENST00000318021.2:c.180C>A	chr1.hg19:g.248436937G>T		640.0	0.0		1030.0	456.0	NM_001004695	B2RNN0	Silent	SNP	ENST00000318021.2	hg19	CCDS31109.1																																																																																			.	.		0.537	OR2T33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097354.1	NM_001004695		T	248436937	G	T	248436937	2	4	279	1	0	0	0	0	0	0	0	1	11033	1161	41	3		3	OR2T33	1	248436937	Silent	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	377583	248436937	813684	43	39802										
FAM150B	285016	hgsc.bcm.edu	37	chr2	286308	286308	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	acctgtaaggtgttttagaaActtgtccttcatcctcagat	7	9	2	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:286308A>G	ENST00000403610.4	-	3	629	c.289T>C	c.(289-291)Ttt>Ctt	p.F97L	FAM150B_ENST00000344414.5_Missense_Mutation_p.F5L|FAM150B_ENST00000405290.1_Missense_Mutation_p.F5L|AC079779.4_ENST00000427831.1_RNA|FAM150B_ENST00000401503.1_Missense_Mutation_p.F5L	NM_001002919.2	NP_001002919.2	Q6UX46	F150B_HUMAN	family with sequence similarity 150, member B	97						extracellular region (GO:0005576)				breast(1)|kidney(2)	3	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.00175)|Lung NSC(108;0.216)|all_epithelial(98;0.236)		all cancers(51;0.00091)|Epithelial(75;0.00656)|OV - Ovarian serous cystadenocarcinoma(76;0.00954)|GBM - Glioblastoma multiforme(21;0.128)		TGTTTTAGAAACTTGTCCTTC	0.388																																					p.F97L		Atlas-SNP	.											.	FAM150B	12	.	0			c.T289C						.						117	121	120					2																	286308		1868	4096	5964	SO:0001583	missense	285016	exon3			TTAGAAACTTGTC		CCDS46218.1	2p25.3	2008-05-02			ENSG00000189292	ENSG00000189292			27683	protein-coding gene	gene with protein product							Standard	NM_001002919		Approved		uc002qwi.4	Q6UX46	OTTHUMG00000151366	ENST00000403610.4:c.289T>C	chr2.hg19:g.286308A>G	ENSP00000384604:p.Phe97Leu	134.0	0.0		110.0	5.0	NM_001002919	B5MC76	Missense_Mutation	SNP	ENST00000403610.4	hg19	CCDS46218.1	.	.	.	.	.	.	.	.	.	.	A	28.1	4.894894	0.91962	.	.	ENSG00000189292	ENST00000436353;ENST00000403610;ENST00000401503;ENST00000405290;ENST00000344414;ENST00000452023	.	.	.	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.77184	0.4093	M	0.73217	2.22	0.51482	D	0.999923	D	0.71674	0.998	D	0.76071	0.987	T	0.79727	-0.1682	9	0.87932	D	0	.	12.7401	0.57246	1.0:0.0:0.0:0.0	.	97	Q6UX46	F150B_HUMAN	L	37;97;5;5;5;97	.	ENSP00000339565:F5L	F	-	1	0	FAM150B	276308	1.000000	0.71417	0.994000	0.49952	0.958000	0.62258	7.629000	0.83207	2.254000	0.74563	0.533000	0.62120	TTT	.	.		0.388	FAM150B-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322394.2	NM_001002919		G	286308	A	G	286308	3	3	279	1	0	0	0	0	1	0	0	0	5462	43	2	2	185	2	FAM150B	2	286308	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10		286308	242913065	44	39803										
GREB1	9687	hgsc.bcm.edu	37	chr2	11750977	11750977	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	actccccgaagcagtgccccTgcggccacgggctcatggtc	12	17	1	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:11750977T>C	ENST00000381486.2	+	18	3130	c.2830T>C	c.(2830-2832)Tgc>Cgc	p.C944R	GREB1_ENST00000234142.5_Missense_Mutation_p.C944R|GREB1_ENST00000396123.1_5'Flank	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	944						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		GCAGTGCCCCTGCGGCCACGG	0.687																																					p.C944R	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											.	GREB1	308	.	0			c.T2830C						.						32	36	35					2																	11750977		2056	4196	6252	SO:0001583	missense	9687	exon18			TGCCCCTGCGGCC		CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"gene regulated by estrogen in breast cancer"	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.2830T>C	chr2.hg19:g.11750977T>C	ENSP00000370896:p.Cys944Arg	98.0	0.0		100.0	4.0	NM_014668	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	hg19	CCDS42655.1	.	.	.	.	.	.	.	.	.	.	T	9.421	1.082948	0.20309	.	.	ENSG00000196208	ENST00000381486;ENST00000234142	T;T	0.45276	0.9;0.9	5.32	4.16	0.48862	.	0.313960	0.30869	N	0.008715	T	0.30759	0.0775	L	0.40543	1.245	0.47819	D	0.999521	P	0.49090	0.919	B	0.42422	0.387	T	0.07233	-1.0783	10	0.40728	T	0.16	-37.7755	4.4534	0.11631	0.2981:0.0987:0.0:0.6032	.	944	Q4ZG55	GREB1_HUMAN	R	944	ENSP00000370896:C944R;ENSP00000234142:C944R	ENSP00000234142:C944R	C	+	1	0	GREB1	11668428	0.531000	0.26338	1.000000	0.80357	0.977000	0.68977	0.952000	0.29149	0.843000	0.35070	0.460000	0.39030	TGC	.	.		0.687	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668		C	11750977	T	C	11750977	3	2	279	1	0	0	0	0	1	0	0	0	6769	1580	55	2	3004	2	GREB1	2	11750977	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	11464669	11750977	231448396	45	39804										
NBAS	51594	hgsc.bcm.edu	37	chr2	15614223	15614223	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	aagttcctctggtgtcgtggAgcgcaaactcacaaggcggt	13	10	2	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:15614223A>G	ENST00000281513.5	-	15	1592	c.1567T>C	c.(1567-1569)Tcc>Ccc	p.S523P	NBAS_ENST00000441750.1_Missense_Mutation_p.S523P	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	523					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				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						GGTGTCGTGGAGCGCAAACTC	0.433																																					p.S523P		Atlas-SNP	.											.	NBAS	246	.	0			c.T1567C						.						136	132	133					2																	15614223		2203	4300	6503	SO:0001583	missense	51594	exon15			TCGTGGAGCGCAA	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.1567T>C	chr2.hg19:g.15614223A>G	ENSP00000281513:p.Ser523Pro	109.0	0.0		93.0	4.0	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	hg19	CCDS1685.1	.	.	.	.	.	.	.	.	.	.	A	16.44	3.122537	0.56613	.	.	ENSG00000151779	ENST00000441750;ENST00000281513	T;T	0.12147	2.71;2.87	5.89	4.71	0.59529	.	0.052750	0.85682	D	0.000000	T	0.33265	0.0857	M	0.68593	2.085	0.32450	N	0.545564	D	0.76494	0.999	D	0.66196	0.942	T	0.49143	-0.8970	10	0.87932	D	0	.	13.1019	0.59224	0.866:0.134:0.0:0.0	.	523	A2RRP1	NBAS_HUMAN	P	523	ENSP00000413201:S523P;ENSP00000281513:S523P	ENSP00000281513:S523P	S	-	1	0	NBAS	15531674	1.000000	0.71417	0.921000	0.36526	0.712000	0.41017	7.484000	0.81180	1.020000	0.39573	0.533000	0.62120	TCC	.	.		0.433	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		G	15614223	A	G	15614223	3	3	279	1	0	0	0	0	1	0	0	0	10195	304	11	2	5700	2	NBAS	2	15614223	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	3863246	15614223	227585150	46	39805										
ASXL2	55252	hgsc.bcm.edu	37	chr2	25967273	25967273	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tctgttaggactagtgatggAgactggaaaacgagccctgg	14	7	1	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:25967273A>G	ENST00000435504.4	-	13	2226	c.1933T>C	c.(1933-1935)Tcc>Ccc	p.S645P	ASXL2_ENST00000336112.4_Missense_Mutation_p.S617P|ASXL2_ENST00000404843.1_Missense_Mutation_p.S385P|ASXL2_ENST00000272341.4_Missense_Mutation_p.S385P			Q76L83	ASXL2_HUMAN	additional sex combs like transcriptional regulator 2	645					adult heart development (GO:0007512)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of histone H3-K27 trimethylation (GO:1902466)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(7)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(3)	33	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTAGTGATGGAGACTGGAAAA	0.532																																					p.S645P		Atlas-SNP	.											.	ASXL2	217	.	0			c.T1933C						.						59	58	58					2																	25967273		1906	4124	6030	SO:0001583	missense	55252	exon12			TGATGGAGACTGG			2p24.1	2014-06-17	2014-06-17		ENSG00000143970	ENSG00000143970			23805	protein-coding gene	gene with protein product		612991	"additional sex combs like 2 (Drosophila)"			12888926	Standard	NM_018263		Approved	ASXH2, FLJ10898, KIAA1685	uc002rgs.2	Q76L83	OTTHUMG00000152176	ENST00000435504.4:c.1933T>C	chr2.hg19:g.25967273A>G	ENSP00000391447:p.Ser645Pro	87.0	0.0		84.0	4.0	NM_018263	Q53TC9|Q5H9U4|Q76L81|Q86XM1|Q9C0H8|Q9NV67	Missense_Mutation	SNP	ENST00000435504.4	hg19		.	.	.	.	.	.	.	.	.	.	A	14.20	2.465102	0.43839	.	.	ENSG00000143970	ENST00000435504;ENST00000336112;ENST00000404843;ENST00000272341	T;T;T;T	0.54866	0.55;0.55;0.55;0.55	5.9	3.41	0.39046	.	0.241958	0.43416	N	0.000576	T	0.44519	0.1297	M	0.68952	2.095	0.47183	D	0.999347	B;B	0.17465	0.009;0.022	B;B	0.14578	0.009;0.011	T	0.34576	-0.9823	10	0.38643	T	0.18	-6.2615	3.4259	0.07410	0.6508:0.1406:0.0736:0.1349	.	385;645	Q76L83-2;Q76L83	.;ASXL2_HUMAN	P	645;617;385;385	ENSP00000391447:S645P;ENSP00000337250:S617P;ENSP00000383920:S385P;ENSP00000272341:S385P	ENSP00000272341:S385P	S	-	1	0	ASXL2	25820777	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	1.359000	0.34113	0.422000	0.26005	0.460000	0.39030	TCC	.	.		0.532	ASXL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000325593.3	NM_018263		G	25967273	A	G	25967273	3	3	279	1	0	0	0	0	1	0	0	0	1067	304	11	2	2378	2	ASXL2	2	25967273	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	10353050	25967273	217232100	47	39806										
NRBP1	29959	hgsc.bcm.edu	37	chr2	27656275	27656275	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tcagctgcttccccagaggaAgaagaagaaagtgaagatga	12	7	1	7			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:27656275A>T	ENST00000233557.3	+	3	967	c.135A>T	c.(133-135)gaA>gaT	p.E45D	NRBP1_ENST00000379863.3_Missense_Mutation_p.E45D|NRBP1_ENST00000379852.3_Missense_Mutation_p.E45D			Q9UHY1	NRBP_HUMAN	nuclear receptor binding protein 1	45					ER to Golgi vesicle-mediated transport (GO:0006888)|gene expression (GO:0010467)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell projection (GO:0042995)|endomembrane system (GO:0012505)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19	Acute lymphoblastic leukemia(172;0.155)					CCCCAGAGGAAGAAGAAGAAA	0.517																																					p.E45D		Atlas-SNP	.											.	NRBP1	40	.	0			c.A135T						.						82	73	76					2																	27656275		2203	4300	6503	SO:0001583	missense	29959	exon2			AGAGGAAGAAGAA	AF113249	CCDS1753.1	2p23	2008-02-05	2005-12-22	2005-12-22	ENSG00000115216	ENSG00000115216			7993	protein-coding gene	gene with protein product		606010	"nuclear receptor binding protein"	NRBP		10843813, 11956649	Standard	NM_013392		Approved	BCON3, MUDPNP, MADM	uc002rkp.3	Q9UHY1	OTTHUMG00000097789	ENST00000233557.3:c.135A>T	chr2.hg19:g.27656275A>T	ENSP00000233557:p.Glu45Asp	141.0	0.0		115.0	40.0	NM_013392	B3KV40|D6W558|Q53FZ5|Q96SU3	Missense_Mutation	SNP	ENST00000233557.3	hg19	CCDS1753.1	.	.	.	.	.	.	.	.	.	.	A	16.93	3.257682	0.59321	.	.	ENSG00000115216	ENST00000233557;ENST00000421823;ENST00000379852;ENST00000379863;ENST00000419281;ENST00000356442	D;D;D;D;D	0.99176	-5.52;-5.52;-5.52;-5.52;-5.52	5.27	2.9	0.33743	.	0.053822	0.64402	D	0.000001	D	0.96411	0.8829	L	0.45581	1.43	0.42989	D	0.994486	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	D	0.91797	0.5448	10	0.22706	T	0.39	-7.7005	5.947	0.19223	0.7643:0.0:0.2357:0.0	.	45;45	F8W6G1;Q9UHY1	.;NRBP_HUMAN	D	45;25;45;45;45;45	ENSP00000233557:E45D;ENSP00000369181:E45D;ENSP00000369192:E45D;ENSP00000403916:E45D;ENSP00000415406:E45D	ENSP00000233557:E45D	E	+	3	2	NRBP1	27509779	0.887000	0.30362	1.000000	0.80357	0.997000	0.91878	-0.003000	0.12901	0.355000	0.24131	0.460000	0.39030	GAA	.	.		0.517	NRBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215033.1	NM_013392		T	27656275	A	T	27656275	3	4	279	1	0	0	0	0	1	0	0	0	10651	69	3	4	137	4	NRBP1	2	27656275	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	1689002	27656275	215543098	48	39807										
SPAST	6683	hgsc.bcm.edu	37	chr2	32379552	32379552	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ttggaacaaggactttggagAtaccactgtttaaggaaata	10	5	0	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:32379552A>G	ENST00000315285.3	+	17	1963	c.1838A>G	c.(1837-1839)gAt>gGt	p.D613G	SPAST_ENST00000345662.1_Missense_Mutation_p.D581G	NM_014946.3	NP_055761.2			spastin											breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(8)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					GACTTTGGAGATACCACTGTT	0.383																																					p.D613G		Atlas-SNP	.											.	SPAST	61	.	0			c.A1838G						.						91	88	89					2																	32379552		2203	4300	6503	SO:0001583	missense	6683	exon17			TTGGAGATACCAC	AJ246001	CCDS1778.1, CCDS1779.1	2p24-p21	2014-09-17	2005-03-15	2005-03-17	ENSG00000021574	ENSG00000021574		"ATPases / AAA-type"	11233	protein-coding gene	gene with protein product		604277	"spastic paraplegia 4 (autosomal dominant; spastin)"	SPG4		10493830, 10610178	Standard	NM_014946		Approved	FSP2, ADPSP, KIAA1083	uc002roc.3	Q9UBP0	OTTHUMG00000128455	ENST00000315285.3:c.1838A>G	chr2.hg19:g.32379552A>G	ENSP00000320885:p.Asp613Gly	59.0	0.0		85.0	4.0	NM_014946		Missense_Mutation	SNP	ENST00000315285.3	hg19	CCDS1778.1	.	.	.	.	.	.	.	.	.	.	A	19.08	3.757842	0.69648	.	.	ENSG00000021574	ENST00000345662;ENST00000315285	D;D	0.93604	-3.2;-3.25	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	D	0.95532	0.8548	L	0.56340	1.77	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.992	D	0.95184	0.8302	10	0.45353	T	0.12	-5.2438	16.0308	0.80577	1.0:0.0:0.0:0.0	.	581;613	E5KRP6;Q9UBP0	.;SPAST_HUMAN	G	581;613	ENSP00000340817:D581G;ENSP00000320885:D613G	ENSP00000320885:D613G	D	+	2	0	SPAST	32233056	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.336000	0.79245	2.315000	0.78130	0.533000	0.62120	GAT	.	.		0.383	SPAST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250253.1	NM_199436		G	32379552	A	G	32379552	3	3	279	1	0	0	0	0	1	0	0	0	15012	333	12	2	1904	2	SPAST	2	32379552	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	4723277	32379552	210819821	49	39808										
BIRC6	57448	hgsc.bcm.edu	37	chr2	32660588	32660588	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	taacattgaagtggaacaaaAtgggaaaccgtccctggttg	11	7	0	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:32660588A>G	ENST00000421745.2	+	14	3568	c.3434A>G	c.(3433-3435)aAt>aGt	p.N1145S		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	1145					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					GTGGAACAAAATGGGAAACCG	0.378																																					p.N1145S	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.A3434G						.						59	59	59					2																	32660588		2186	4258	6444	SO:0001583	missense	57448	exon14			AACAAAATGGGAA	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.3434A>G	chr2.hg19:g.32660588A>G	ENSP00000393596:p.Asn1145Ser	83.0	0.0		72.0	4.0	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	hg19	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	A	11.70	1.715464	0.30413	.	.	ENSG00000115760	ENST00000421745	T	0.73681	-0.77	5.12	5.12	0.69794	.	0.125895	0.52532	D	0.000067	T	0.60248	0.2254	N	0.24115	0.695	0.51012	D	0.999907	B	0.14012	0.009	B	0.12156	0.007	T	0.55774	-0.8088	10	0.13470	T	0.59	.	14.9376	0.70970	1.0:0.0:0.0:0.0	.	1145	Q9NR09	BIRC6_HUMAN	S	1145	ENSP00000393596:N1145S	ENSP00000393596:N1145S	N	+	2	0	BIRC6	32514092	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.920000	0.75799	1.926000	0.55796	0.460000	0.39030	AAT	.	.		0.378	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		G	32660588	A	G	32660588	3	3	279	1	0	0	0	0	1	0	0	0	1438	101	4	2	3488	2	BIRC6	2	32660588	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	281036	32660588	210538785	50	39809										
OXER1	165140	hgsc.bcm.edu	37	chr2	42991186	42991186	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gagagggagatggagagctcAggttatgaagttccatgggc	17	5	1	4			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:42991186A>G	ENST00000378661.2	-	1	215	c.134T>C	c.(133-135)cTg>cCg	p.L45P		NM_148962.4	NP_683765.1	Q8TDS5	OXER1_HUMAN	oxoeicosanoid (OXE) receptor 1	45					G-protein coupled receptor signaling pathway (GO:0007186)|regulation of cAMP biosynthetic process (GO:0030817)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	5(S)-hydroxyperoxy-6E,8Z,11Z,14Z-icosatetraenoic acid binding (GO:0050648)|5-hydroxy-6E,8Z,11Z,14Z-icosatetraenoic acid binding (GO:0050647)|5-oxo-6E,8Z,11Z,14Z-icosatetraenoic acid binding (GO:0050646)|G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)	10						tggagagCTCAGGTTATGAAG	0.587																																					p.L45P		Atlas-SNP	.											.	OXER1	33	.	0			c.T134C						.						78	66	70					2																	42991186		2203	4300	6503	SO:0001583	missense	165140	exon1			GAGCTCAGGTTAT	AB083055	CCDS1810.1	2p22.1	2012-08-10			ENSG00000162881	ENSG00000162881		"GPCR / Class A : Leukotriene receptors"	24884	protein-coding gene	gene with protein product	"5-oxo-ETE acid G-protein-coupled receptor 1"					12065583, 15001665	Standard	NM_148962		Approved	GPCR, TG1019, GPR170	uc002rss.3	Q8TDS5	OTTHUMG00000128643	ENST00000378661.2:c.134T>C	chr2.hg19:g.42991186A>G	ENSP00000367930:p.Leu45Pro	121.0	0.0		98.0	4.0	NM_148962	Q86WP7|Q8NGW4	Missense_Mutation	SNP	ENST00000378661.2	hg19	CCDS1810.1	.	.	.	.	.	.	.	.	.	.	A	13.55	2.269394	0.40095	.	.	ENSG00000162881	ENST00000378661	T	0.61859	0.07	2.7	0.177	0.15054	.	.	.	.	.	T	0.29914	0.0748	N	0.08118	0	0.42125	D	0.991441	B	0.24963	0.115	B	0.23419	0.046	T	0.09079	-1.0691	9	0.66056	D	0.02	.	2.0564	0.03582	0.5874:0.0:0.1525:0.2601	.	45	Q8TDS5	OXER1_HUMAN	P	45	ENSP00000367930:L45P	ENSP00000367930:L45P	L	-	2	0	OXER1	42844690	0.002000	0.14202	0.327000	0.25402	0.199000	0.23934	0.265000	0.18515	0.031000	0.15407	0.454000	0.30748	CTG	.	.		0.587	OXER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250514.1	NM_148962		G	42991186	A	G	42991186	3	3	279	1	0	0	0	0	1	0	0	0	11340	188	7	2	1141	2	OXER1	2	42991186	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	10330598	42991186	200208187	51	39810										
KIAA1841	84542	hgsc.bcm.edu	37	chr2	61304085	61304085	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gtgatccatgtgtgtgatgaAgcaaaaaacttgaaagaaga	11	4	0	6			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:61304085A>G	ENST00000402291.1	+	6	703	c.462A>G	c.(460-462)gaA>gaG	p.E154E	KIAA1841_ENST00000356719.2_Silent_p.E154E|KIAA1841_ENST00000295031.5_Silent_p.E154E|KIAA1841_ENST00000453873.1_Silent_p.E154E|KIAA1841_ENST00000482513.1_3'UTR	NM_001129993.1	NP_001123465.1	Q6NSI8	K1841_HUMAN	KIAA1841	154										breast(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	25			Epithelial(17;0.193)			TGTGTGATGAAGCAAAAAACT	0.348																																					p.E154E		Atlas-SNP	.											.	KIAA1841	95	.	0			c.A462G						.						59	61	60					2																	61304085		2203	4300	6503	SO:0001819	synonymous_variant	84542	exon6			TGATGAAGCAAAA	BC070104	CCDS1867.1, CCDS46296.1	2p15	2010-06-22			ENSG00000162929	ENSG00000162929			29387	protein-coding gene	gene with protein product						11347906	Standard	NM_032506		Approved		uc002saw.4	Q6NSI8	OTTHUMG00000129421	ENST00000402291.1:c.462A>G	chr2.hg19:g.61304085A>G		137.0	0.0		97.0	4.0	NM_032506	Q49AF0|Q6ZND0|Q96JI6	Silent	SNP	ENST00000402291.1	hg19	CCDS46296.1																																																																																			.	.		0.348	KIAA1841-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325477.1	NM_032506		G	61304085	A	G	61304085	2	3	279	1	0	0	0	0	0	0	0	1	8270	69	3	2		2	KIAA1841	2	61304085	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	18312899	61304085	181895288	52	39811										
ETAA1	54465	hgsc.bcm.edu	37	chr2	67630454	67630454	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tgattcaagagcaaaacaagAggaattatgattttacccag	8	6	1	4			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:67630454A>G	ENST00000272342.5	+	5	770	c.640A>G	c.(640-642)Agg>Ggg	p.R214G	ETAA1_ENST00000462772.1_Intron	NM_019002.3	NP_061875.2	Q9NY74	ETAA1_HUMAN	Ewing tumor-associated antigen 1	214						cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	33						GCAAAACAAGAGGAATTATGA	0.289																																					p.R214G		Atlas-SNP	.											.	ETAA1	88	.	0			c.A640G						.						35	43	40					2																	67630454		2190	4280	6470	SO:0001583	missense	54465	exon5			AACAAGAGGAATT	AJ242682	CCDS1882.1	2p14	2014-02-12	2007-10-04		ENSG00000143971	ENSG00000143971			24648	protein-coding gene	gene with protein product		613196	"Ewing's tumor-associated antigen 1"			16003559	Standard	XM_005264374		Approved	ETAA16	uc002sdz.1	Q9NY74	OTTHUMG00000129545	ENST00000272342.5:c.640A>G	chr2.hg19:g.67630454A>G	ENSP00000272342:p.Arg214Gly	81.0	0.0		70.0	4.0	NM_019002	Q05BT7|Q53SC4	Missense_Mutation	SNP	ENST00000272342.5	hg19	CCDS1882.1	.	.	.	.	.	.	.	.	.	.	A	11.15	1.554375	0.27739	.	.	ENSG00000143971	ENST00000272342	T	0.21734	1.99	6.16	3.84	0.44239	.	0.958429	0.08683	N	0.909222	T	0.21186	0.0510	L	0.57536	1.79	0.09310	N	1	B	0.11235	0.004	B	0.14023	0.01	T	0.29458	-1.0011	10	0.54805	T	0.06	-13.0862	3.7484	0.08556	0.5661:0.2128:0.2211:0.0	.	214	Q9NY74	ETAA1_HUMAN	G	214	ENSP00000272342:R214G	ENSP00000272342:R214G	R	+	1	2	ETAA1	67483958	0.001000	0.12720	0.012000	0.15200	0.510000	0.34073	1.199000	0.32235	1.155000	0.42497	0.528000	0.53228	AGG	.	.		0.289	ETAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251735.1	NM_019002		G	67630454	A	G	67630454	3	3	279	1	0	0	0	0	1	0	0	0	5269	295	11	2	658	2	ETAA1	2	67630454	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	6326369	67630454	175568919	53	39812										
AAK1	22848	hgsc.bcm.edu	37	chr2	69741744	69741744	+	Silent	SNP	T	T	C													0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tgcagggctgtggccagctgTtgctgttgctgttgttgttg							TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:69741744T>C	ENST00000409085.4	-	13	2011	c.1635A>G	c.(1633-1635)caA>caG	p.Q545Q	AAK1_ENST00000406297.3_Silent_p.Q545Q|RN7SL604P_ENST00000492589.2_RNA|AAK1_ENST00000409068.1_Silent_p.Q545Q	NM_014911.3	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1	545	Gln-rich.				endocytosis (GO:0006897)|positive regulation of Notch signaling pathway (GO:0045747)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of clathrin-mediated endocytosis (GO:2000369)|regulation of protein localization (GO:0032880)	cell leading edge (GO:0031252)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extrinsic component of plasma membrane (GO:0019897)|terminal bouton (GO:0043195)	AP-2 adaptor complex binding (GO:0035612)|ATP binding (GO:0005524)|Notch binding (GO:0005112)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)	17						TGGCCAgctgttgctgttgct	0.562																																					p.Q545Q		Atlas-SNP	.											.	AAK1	121	.	0			c.A1635G						.						33	35	34					2																	69741744		2198	4296	6494	SO:0001819	synonymous_variant	22848	exon13			CAGCTGTTGCTGT	AB028971	CCDS1893.2	2p13.3	2012-07-10			ENSG00000115977	ENSG00000115977			19679	protein-coding gene	gene with protein product						11877461, 12471243	Standard	NM_014911		Approved	KIAA1048, DKFZp686K16132	uc002sfp.2	Q2M2I8	OTTHUMG00000129648	ENST00000409085.4:c.1635A>G	chr2.hg19:g.69741744T>C		80.0	0.0		98.0	5.0	NM_014911	Q4ZFZ3|Q53RX6|Q9UPV4	Silent	SNP	ENST00000409085.4	hg19	CCDS1893.2																																																																																			.	.		0.562	AAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251847.4	NM_014911		C	69741744	T	C	69741744	2	2	279	1	0	0	0	0	0	0	0	1	16	1722	60	2		2	AAK1	2	69741744	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	2111290	69741744	173457629	54	39813	200	2								
AAK1	22848	hgsc.bcm.edu	37	chr2	69741753	69741753	+	Silent	SNP	C	C	T													0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gtggccagctgttgctgttgCtgttgttgttgctgctgctg					rs66931661|rs3832159	byFrequency	TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:69741753C>T	ENST00000409085.4	-	13	2002	c.1626G>A	c.(1624-1626)caG>caA	p.Q542Q	AAK1_ENST00000406297.3_Silent_p.Q542Q|RN7SL604P_ENST00000492589.2_RNA|AAK1_ENST00000409068.1_Silent_p.Q542Q	NM_014911.3	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1	542	Gln-rich.				endocytosis (GO:0006897)|positive regulation of Notch signaling pathway (GO:0045747)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of clathrin-mediated endocytosis (GO:2000369)|regulation of protein localization (GO:0032880)	cell leading edge (GO:0031252)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extrinsic component of plasma membrane (GO:0019897)|terminal bouton (GO:0043195)	AP-2 adaptor complex binding (GO:0035612)|ATP binding (GO:0005524)|Notch binding (GO:0005112)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)	17						gttgctgttgctgttgttgtt	0.552																																					p.Q542Q		Atlas-SNP	.											.	AAK1	121	.	0			c.G1626A						.						33	35	34					2																	69741753		2192	4296	6488	SO:0001819	synonymous_variant	22848	exon13			CTGTTGCTGTTGT	AB028971	CCDS1893.2	2p13.3	2012-07-10			ENSG00000115977	ENSG00000115977			19679	protein-coding gene	gene with protein product						11877461, 12471243	Standard	NM_014911		Approved	KIAA1048, DKFZp686K16132	uc002sfp.2	Q2M2I8	OTTHUMG00000129648	ENST00000409085.4:c.1626G>A	chr2.hg19:g.69741753C>T		74.0	0.0		100.0	8.0	NM_014911	Q4ZFZ3|Q53RX6|Q9UPV4	Silent	SNP	ENST00000409085.4	hg19	CCDS1893.2																																																																																			.	.		0.552	AAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251847.4	NM_014911		T	69741753	C	T	69741753	2	4	279	1	0	0	0	0	0	0	0	1	16	796	28	3		3	AAK1	2	69741753	Silent	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	9	69741753	173457620	55	39814	200	2								
DYSF	8291	hgsc.bcm.edu	37	chr2	71708030	71708030	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	taggggtgaagaagagaaccAaagtcatcaagaacagcgtg	13	6	2	4	rs398123764		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:71708030A>T	ENST00000258104.3	+	2	383	c.106A>T	c.(106-108)Aaa>Taa	p.K36*	DYSF_ENST00000409582.3_Nonsense_Mutation_p.K36*|DYSF_ENST00000409651.1_Nonsense_Mutation_p.K37*|DYSF_ENST00000409366.1_Nonsense_Mutation_p.K37*|DYSF_ENST00000394120.2_Nonsense_Mutation_p.K37*|DYSF_ENST00000409744.1_Nonsense_Mutation_p.K37*|DYSF_ENST00000410020.3_Nonsense_Mutation_p.K37*|DYSF_ENST00000429174.2_Nonsense_Mutation_p.K36*|DYSF_ENST00000413539.2_Nonsense_Mutation_p.K36*|DYSF_ENST00000410041.1_Nonsense_Mutation_p.K37*|DYSF_ENST00000409762.1_Nonsense_Mutation_p.K36*	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	36	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						GAAGAGAACCAAAGTCATCAA	0.488																																					p.K37X		Atlas-SNP	.											.	DYSF	536	.	0			c.A109T						.						253	194	214					2																	71708030		2203	4300	6503	SO:0001587	stop_gained	8291	exon2			AGAACCAAAGTCA	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"fer-1-like family member 1"	603009	"limb girdle muscular dystrophy 2B (autosomal recessive)"	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.106A>T	chr2.hg19:g.71708030A>T	ENSP00000258104:p.Lys36*	272.0	0.0		224.0	85.0	NM_001130984	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Nonsense_Mutation	SNP	ENST00000258104.3	hg19	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	A	40	8.153172	0.98680	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	.	.	.	4.43	4.43	0.53597	.	0.195281	0.41396	D	0.000888	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.4719	11.9148	0.52759	1.0:0.0:0.0:0.0	.	.	.	.	X	36;36;36;36;36;37;37;37;37;37;37	.	ENSP00000258104:K36X	K	+	1	0	DYSF	71561538	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.232000	0.78116	1.771000	0.52183	0.454000	0.30748	AAA	.	.		0.488	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494		T	71708030	A	T	71708030	4	4	279	1	0	0	0	0	0	1	0	0	4861	131	5	4	207	4	DYSF	2	71708030	Nonsense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	1966277	71708030	171491343	56	39815										
SMYD5	10322	hgsc.bcm.edu	37	chr2	73449933	73449933	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	acagaggccctctatgaggaAgcagtcagccaggtgagtga	14	9	2	4			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:73449933A>G	ENST00000389501.4	+	7	738	c.693A>G	c.(691-693)gaA>gaG	p.E231E		NM_006062.2	NP_006053.2	Q6GMV2	SMYD5_HUMAN	SMYD family member 5	231	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.						metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)	13						TCTATGAGGAAGCAGTCAGCC	0.552																																					p.E231E		Atlas-SNP	.											.	SMYD5	58	.	0			c.A693G						.						47	42	44					2																	73449933		2203	4300	6503	SO:0001819	synonymous_variant	10322	exon7			TGAGGAAGCAGTC	U50383	CCDS33221.2	2p12	2007-02-09	2003-05-14	2003-05-16	ENSG00000135632	ENSG00000135632		"Zinc fingers, MYND-type"	16258	protein-coding gene	gene with protein product			"retinoic acid induced 15"	RAI15		8754834	Standard	NM_006062		Approved	RRG1, NN8-4AG, ZMYND23	uc002siw.2	Q6GMV2	OTTHUMG00000150482	ENST00000389501.4:c.693A>G	chr2.hg19:g.73449933A>G		83.0	0.0		119.0	6.0	NM_006062	D6W5H3|Q13558	Silent	SNP	ENST00000389501.4	hg19	CCDS33221.2																																																																																			.	.		0.552	SMYD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318301.1	NM_006062		G	73449933	A	G	73449933	2	3	279	1	0	0	0	0	0	0	0	1	14840	69	3	2		2	SMYD5	2	73449933	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	1741903	73449933	169749440	57	39816										
C2orf78	388960	hgsc.bcm.edu	37	chr2	74043271	74043271	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tgcaagttttccatgcactcGggaaaaagatcgatatgaaa	9	7	0	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:74043271G>T	ENST00000409561.1	+	3	2042	c.1921G>T	c.(1921-1923)Ggg>Tgg	p.G641W		NM_001080474.1	NP_001073943.1	A6NCI8	CB078_HUMAN	chromosome 2 open reading frame 78	641								p.G641W(1)|p.G611W(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(21)|ovary(2)|prostate(2)|soft_tissue(1)|urinary_tract(1)	34						CCATGCACTCGGGAAAAAGAT	0.493																																					p.G641W		Atlas-SNP	.											.	C2orf78	150	.	2	Substitution - Missense(2)	lung(2)	c.G1921T						.						59	58	58					2																	74043271		1870	4102	5972	SO:0001583	missense	388960	exon3			GCACTCGGGAAAA	AC092653, AC136006, AK125975	CCDS46338.1	2p13.2	2008-07-18			ENSG00000187833	ENSG00000187833			34349	protein-coding gene	gene with protein product							Standard	NM_001080474		Approved	FLJ43987, hCG1989538, COG5373	uc002sjr.1	A6NCI8	OTTHUMG00000152819	ENST00000409561.1:c.1921G>T	chr2.hg19:g.74043271G>T	ENSP00000387124:p.Gly641Trp	64.0	0.0		53.0	4.0	NM_001080474		Missense_Mutation	SNP	ENST00000409561.1	hg19	CCDS46338.1	.	.	.	.	.	.	.	.	.	.	G	11.28	1.591505	0.28357	.	.	ENSG00000187833	ENST00000409561;ENST00000342345	.	.	.	5.13	3.26	0.37387	.	0.000000	0.49916	D	0.000139	T	0.75064	0.3799	M	0.82323	2.585	0.33274	D	0.561361	D	0.89917	1.0	D	0.97110	1.0	T	0.82061	-0.0644	9	0.87932	D	0	-25.3562	10.6486	0.45634	0.0:0.0:0.6508:0.3492	.	641	A6NCI8	CB078_HUMAN	W	641;611	.	ENSP00000340692:G611W	G	+	1	0	C2orf78	73896779	1.000000	0.71417	0.401000	0.26359	0.002000	0.02628	4.198000	0.58419	0.623000	0.30267	-0.311000	0.09066	GGG	.	.		0.493	C2orf78-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000328083.1	NM_001080474		T	74043271	G	T	74043271	3	4	279	1	0	0	0	0	1	0	0	0	2197	1116	39	1	1931	1	C2orf78	2	74043271	Missense_Mutation	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	593338	74043271	169156102	58	39817										
ZC3H8	84524	hgsc.bcm.edu	37	chr2	112989436	112989436	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ttagccaacaattcttgtgtTtcaggagtcagtggagcatg	11	7	3	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:112989436T>C	ENST00000409573.2	-	7	951	c.822A>G	c.(820-822)gaA>gaG	p.E274E	ZC3H8_ENST00000272570.5_Silent_p.E274E|ZC3H8_ENST00000476902.1_5'UTR			Q8N5P1	ZC3H8_HUMAN	zinc finger CCCH-type containing 8	274					apoptotic process (GO:0006915)|negative regulation of T cell differentiation in thymus (GO:0033085)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|response to antibiotic (GO:0046677)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)|T cell homeostasis (GO:0043029)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)	7						ATTCTTGTGTTTCAGGAGTCA	0.308																																					p.E274E		Atlas-SNP	.											.	ZC3H8	17	.	0			c.A822G						.						101	95	97					2																	112989436		1910	4170	6080	SO:0001819	synonymous_variant	84524	exon7			TTGTGTTTCAGGA	AF334161	CCDS46392.1	2q13	2012-07-05	2005-06-02	2005-06-02	ENSG00000144161	ENSG00000144161		"Zinc fingers, CCCH-type domain containing"	30941	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 8"	ZC3HDC8		12477932	Standard	NM_032494		Approved	Fliz1	uc021vmw.1	Q8N5P1	OTTHUMG00000153270	ENST00000409573.2:c.822A>G	chr2.hg19:g.112989436T>C		43.0	0.0		41.0	4.0	NM_032494	Q9BZ75	Silent	SNP	ENST00000409573.2	hg19	CCDS46392.1																																																																																			.	.		0.308	ZC3H8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330521.3	NM_032494		C	112989436	T	C	112989436	2	2	279	1	0	0	0	0	0	0	0	1	17589	1838	64	2		2	ZC3H8	2	112989436	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	38946165	112989436	130209937	59	39818										
GCA	25801	hgsc.bcm.edu	37	chr2	163216022	163216022	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	agatttctttaggaaaagagAccacttgcaacaagggtctg	10	7	2	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:163216022A>G	ENST00000437150.2	+	7	748	c.587A>G	c.(586-588)gAc>gGc	p.D196G	GCA_ENST00000233612.4_Missense_Mutation_p.D177G|GCA_ENST00000429691.2_Intron	NM_012198.3	NP_036330.1	P28676	GRAN_HUMAN	grancalcin, EF-hand calcium binding protein	196					membrane fusion (GO:0061025)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|lung(4)|ovary(1)	9						AGGAAAAGAGACCACTTGCAA	0.294																																					p.D196G		Atlas-SNP	.											.	GCA	15	.	0			c.A587G						.						72	76	75					2																	163216022		2202	4293	6495	SO:0001583	missense	25801	exon7			AAAGAGACCACTT	M81637	CCDS2218.1	2q24.2	2013-01-10	2001-11-28		ENSG00000115271	ENSG00000115271		"EF-hand domain containing"	15990	protein-coding gene	gene with protein product		607030	"grancalcin, EF-hand calcium-binding protein"			1737748, 1530588, 12804766	Standard	NM_012198		Approved	GCL	uc002ucg.3	P28676	OTTHUMG00000132057	ENST00000437150.2:c.587A>G	chr2.hg19:g.163216022A>G	ENSP00000394842:p.Asp196Gly	105.0	0.0		93.0	4.0	NM_012198	B2R5X3|Q53TB5|Q59EP3	Missense_Mutation	SNP	ENST00000437150.2	hg19	CCDS2218.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.2|22.2	4.264476|4.264476	0.80358|0.80358	.|.	.|.	ENSG00000115271|ENSG00000115271	ENST00000437150;ENST00000233612|ENST00000414723	T;T|.	0.55234|.	0.53;0.53|.	5.12|5.12	5.12|5.12	0.69794|0.69794	EF-hand-like domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.87458|0.87458	0.6182|0.6182	H|H	0.96720|0.96720	3.87|3.87	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	D|D	0.91498|0.91498	0.5217|0.5217	10|5	0.87932|.	D|.	0|.	.|.	14.193|14.193	0.65652|0.65652	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	196|.	P28676|.	GRAN_HUMAN|.	G|A	196;177|109	ENSP00000394842:D196G;ENSP00000233612:D177G|.	ENSP00000233612:D177G|.	D|T	+|+	2|1	0|0	GCA|GCA	162924268|162924268	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.984000|0.984000	0.73092|0.73092	7.907000|7.907000	0.87430|0.87430	2.050000|2.050000	0.60909|0.60909	0.374000|0.374000	0.22700|0.22700	GAC|ACC	.	.		0.294	GCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255080.3	NM_012198		G	163216022	A	G	163216022	3	3	279	1	0	0	0	0	1	0	0	0	6291	275	10	2	613	2	GCA	2	163216022	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	50226586	163216022	79983351	60	39819										
GRB14	2888	hgsc.bcm.edu	37	chr2	165383605	165383605	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tcttctatcccccagttggaTagcacttcaatcaccagttc	5	14	4	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:165383605T>C	ENST00000263915.3	-	4	1060	c.522A>G	c.(520-522)ctA>ctG	p.L174L	GRB14_ENST00000543549.1_Silent_p.L87L	NM_004490.2	NP_004481.2	Q14449	GRB14_HUMAN	growth factor receptor-bound protein 14	174	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				blood coagulation (GO:0007596)|leukocyte migration (GO:0050900)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			breast(3)|endometrium(2)|large_intestine(6)|lung(10)|ovary(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	32						CCCAGTTGGATAGCACTTCAA	0.308																																					p.L174L		Atlas-SNP	.											.	GRB14	73	.	0			c.A522G						.						98	96	97					2																	165383605		2202	4296	6498	SO:0001819	synonymous_variant	2888	exon4			GTTGGATAGCACT		CCDS2222.1	2q22-q24	2013-02-14			ENSG00000115290	ENSG00000115290		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	4565	protein-coding gene	gene with protein product		601524				8812444	Standard	XM_005246477		Approved		uc002ucl.3	Q14449	OTTHUMG00000132135	ENST00000263915.3:c.522A>G	chr2.hg19:g.165383605T>C		64.0	0.0		84.0	4.0	NM_004490	B7Z7F9|Q7Z6I1	Silent	SNP	ENST00000263915.3	hg19	CCDS2222.1																																																																																			.	.		0.308	GRB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255180.2			C	165383605	T	C	165383605	2	2	279	1	0	0	0	0	0	0	0	1	6766	1393	49	2		2	GRB14	2	165383605	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	2167583	165383605	77815768	61	39820										
SCN1A	6323	hgsc.bcm.edu	37	chr2	166911151	166911151	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tcaaaaaaggcacttacgcaAatgtaatgacagtgaaatcg	8	7	1	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:166911151A>G	ENST00000303395.4	-	4	598	c.599T>C	c.(598-600)tTt>tCt	p.F200S	SCN1A_ENST00000375405.3_Missense_Mutation_p.F200S|SCN1A_ENST00000409050.1_Missense_Mutation_p.F200S|AC010127.3_ENST00000595268.1_RNA|AC010127.3_ENST00000599041.1_RNA|AC010127.3_ENST00000595647.1_RNA|SCN1A_ENST00000423058.2_Missense_Mutation_p.F200S			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	200					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CACTTACGCAAATGTAATGAC	0.338																																					p.F200S		Atlas-SNP	.											.	SCN1A	641	.	0			c.T599C						.						64	66	65					2																	166911151		2203	4299	6502	SO:0001583	missense	6323	exon4			TACGCAAATGTAA	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10585	protein-coding gene	gene with protein product		182389	"febrile convulsions 3"	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.599T>C	chr2.hg19:g.166911151A>G	ENSP00000303540:p.Phe200Ser	83.0	0.0		76.0	4.0	NM_001165964	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	hg19	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	A	29.4	5.004521	0.93287	.	.	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.97378	-4.36;-4.36;-4.36;-4.36	5.24	5.24	0.73138	Ion transport (1);	0.000000	0.64402	D	0.000002	D	0.96907	0.8990	L	0.27944	0.81	0.46725	D	0.999176	D;D;D	0.59357	0.972;0.967;0.985	P;P;D	0.74674	0.805;0.866;0.984	D	0.98196	1.0465	10	0.87932	D	0	.	15.4223	0.75022	1.0:0.0:0.0:0.0	.	200;200;200	P35498-2;E9PG49;P35498	.;.;SCN1A_HUMAN	S	200	ENSP00000407030:F200S;ENSP00000303540:F200S;ENSP00000364554:F200S;ENSP00000386312:F200S	ENSP00000303540:F200S	F	-	2	0	SCN1A	166619397	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.226000	0.95229	2.099000	0.63709	0.459000	0.35465	TTT	.	.		0.338	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		G	166911151	A	G	166911151	3	3	279	1	0	0	0	0	1	0	0	0	13929	14	1	2	5522	2	SCN1A	2	166911151	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	1527546	166911151	76288222	62	39821										
LRP2	4036	hgsc.bcm.edu	37	chr2	170013995	170013995	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gcatatattttcagcacatgTtctttcttttcctttatctg	4	9	4	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:170013995T>C	ENST00000263816.3	-	64	12190	c.11905A>G	c.(11905-11907)Aca>Gca	p.T3969A		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	3969	EGF-like 14. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	TCAGCACATGTTCTTTCTTTT	0.378																																					p.T3969A		Atlas-SNP	.											.	LRP2	751	.	0			c.A11905G						.						135	129	131					2																	170013995		2203	4300	6503	SO:0001583	missense	4036	exon64			CACATGTTCTTTC		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.11905A>G	chr2.hg19:g.170013995T>C	ENSP00000263816:p.Thr3969Ala	124.0	0.0		66.0	4.0	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	hg19	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	T	15.26	2.781527	0.49891	.	.	ENSG00000081479	ENST00000263816	D	0.82081	-1.57	5.88	0.246	0.15516	Growth factor, receptor (1);Epidermal growth factor-like (1);	0.220701	0.45361	D	0.000372	T	0.66906	0.2837	N	0.19112	0.55	0.80722	D	1	B	0.31581	0.329	B	0.27380	0.079	T	0.56703	-0.7935	10	0.12103	T	0.63	.	14.6101	0.68510	0.1427:0.0:0.0:0.8573	.	3969	P98164	LRP2_HUMAN	A	3969	ENSP00000263816:T3969A	ENSP00000263816:T3969A	T	-	1	0	LRP2	169722241	1.000000	0.71417	0.922000	0.36590	0.925000	0.55904	1.775000	0.38584	0.092000	0.17331	0.533000	0.62120	ACA	.	.		0.378	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		C	170013995	T	C	170013995	3	2	279	1	0	0	0	0	1	0	0	0	8965	1725	60	2	2126	2	LRP2	2	170013995	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	3102844	170013995	73185378	63	39822										
PPIG	9360	hgsc.bcm.edu	37	chr2	170487422	170487422	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tactgaagagaaatcaaagaAaagaaaaaagaaacatcgga	8	4	1	5			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:170487422A>G	ENST00000260970.3	+	10	906	c.686A>G	c.(685-687)aAa>aGa	p.K229R	PPIG_ENST00000448752.2_Missense_Mutation_p.K229R|PPIG_ENST00000409714.3_Missense_Mutation_p.K214R|PPIG_ENST00000462903.1_Missense_Mutation_p.K229R|PPIG_ENST00000482772.1_3'UTR	NM_004792.2	NP_004783.2	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G (cyclophilin G)	229	Arg/Lys-rich (basic).				protein folding (GO:0006457)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(17)|ovary(2)|stomach(1)|urinary_tract(1)	43					L-Proline(DB00172)	AAATCAAAGAAAAGAAAAAAG	0.363																																					p.K229R		Atlas-SNP	.											.	PPIG	100	.	0			c.A686G						.						47	54	52					2																	170487422		2172	4242	6414	SO:0001583	missense	9360	exon10			CAAAGAAAAGAAA	X99717	CCDS2235.1	2q31.1	2010-07-23	2006-01-12		ENSG00000138398	ENSG00000138398	6.1.1.16		14650	protein-coding gene	gene with protein product	"SR-related CTD-associated factor 10"	606093	"peptidyl-prolyl isomerase G (cyclophilin G)"			8973360, 9153302	Standard	NM_004792		Approved	CARS-Cyp, SRCyp, SCAF10	uc002uez.3	Q13427	OTTHUMG00000132206	ENST00000260970.3:c.686A>G	chr2.hg19:g.170487422A>G	ENSP00000260970:p.Lys229Arg	133.0	0.0		95.0	4.0	NM_004792	D3DPC5|D3DPC6|O00706|Q53R40|Q53SN4|Q96DG9	Missense_Mutation	SNP	ENST00000260970.3	hg19	CCDS2235.1	.	.	.	.	.	.	.	.	.	.	A	14.63	2.592316	0.46214	.	.	ENSG00000138398	ENST00000260970;ENST00000530133;ENST00000433207;ENST00000409714;ENST00000462903;ENST00000448752;ENST00000414307	T;T;T;T;T;T	0.30182	2.18;1.72;2.18;1.54;2.18;1.88	5.74	5.74	0.90152	.	0.422127	0.26507	N	0.023984	T	0.46718	0.1407	L	0.46614	1.455	0.58432	D	0.999996	D;D;D;D;D	0.69078	0.997;0.993;0.993;0.996;0.993	D;D;D;D;D	0.75020	0.985;0.978;0.978;0.981;0.978	T	0.22977	-1.0201	10	0.17832	T	0.49	-4.4455	15.7137	0.77652	1.0:0.0:0.0:0.0	.	225;214;214;229;229	C9JM79;E9PG73;Q2NKQ6;Q13427-2;Q13427	.;.;.;.;PPIG_HUMAN	R	229;229;225;214;229;229;229	ENSP00000260970:K229R;ENSP00000408683:K225R;ENSP00000386245:K214R;ENSP00000435987:K229R;ENSP00000407083:K229R;ENSP00000402222:K229R	ENSP00000260970:K229R	K	+	2	0	PPIG	170195668	1.000000	0.71417	0.990000	0.47175	0.263000	0.26337	7.416000	0.80143	2.168000	0.68352	0.533000	0.62120	AAA	.	.		0.363	PPIG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255264.2			G	170487422	A	G	170487422	3	3	279	1	0	0	0	0	1	0	0	0	12336	14	1	2	716	2	PPIG	2	170487422	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	473427	170487422	72711951	64	39823										
TTN	7273	hgsc.bcm.edu	37	chr2	179399440	179399440	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	aagcctgaagttgtcccctgGtttcagctgacgggcttgac	12	11	1	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:179399440G>A	ENST00000591111.1	-	308	97203	c.96979C>T	c.(96979-96981)Cca>Tca	p.P32327S	TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.P25028S|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.P25095S|TTN_ENST00000460472.2_Missense_Mutation_p.P24903S|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000415561.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.P31400S|TTN-AS1_ENST00000585358.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.P33968S|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000591466.1_RNA			Q8WZ42	TITIN_HUMAN	titin	32327	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTGTCCCCTGGTTTCAGCTGA	0.438																																					p.P33968S		Atlas-SNP	.											.	TTN	18412	.	0			c.C101902T						.						64	62	63					2																	179399440		1891	4122	6013	SO:0001583	missense	7273	exon358			CCCCTGGTTTCAG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.96979C>T	chr2.hg19:g.179399440G>A	ENSP00000465570:p.Pro32327Ser	77.0	0.0		90.0	4.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	19.24	3.788809	0.70337	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.63255	-0.03;-0.03;-0.03;-0.03	6.02	6.02	0.97574	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.72550	0.3474	L	0.31371	0.925	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.998;0.998;0.998	T	0.73994	-0.3807	9	0.87932	D	0	.	20.1323	0.98003	0.0:0.0:1.0:0.0	.	24903;25028;25095;32327	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	S	31400;24903;25095;25028;24900	ENSP00000343764:P31400S;ENSP00000434586:P24903S;ENSP00000340554:P25095S;ENSP00000352154:P25028S	ENSP00000340554:P25095S	P	-	1	0	TTN	179107686	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.837000	0.99465	2.857000	0.98124	0.650000	0.86243	CCA	.	.		0.438	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179399440	G	A	179399440	3	1	279	1	0	0	0	0	1	0	0	0	16750	1261	44	3	6097	3	TTN	2	179399440	Missense_Mutation	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	8912018	179399440	63799933	65	39824										
TTN	7273	hgsc.bcm.edu	37	chr2	179585665	179585665	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	aacctttcactgtcaacgctGtgctgcagctggcgtcacca	9	14	3	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:179585665G>A	ENST00000591111.1	-	77	22354	c.22130C>T	c.(22129-22131)aCa>aTa	p.T7377I	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.T6450I|RP11-171I2.1_ENST00000590024.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.T7694I			Q8WZ42	TITIN_HUMAN	titin	12937	Ig-like 55.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGTCAACGCTGTGCTGCAGCT	0.433																																					p.T7694I		Atlas-SNP	.											.	TTN	18412	.	0			c.C23081T						.						61	61	61					2																	179585665		2026	4203	6229	SO:0001583	missense	7273	exon79			AACGCTGTGCTGC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.22130C>T	chr2.hg19:g.179585665G>A	ENSP00000465570:p.Thr7377Ile	98.0	0.0		99.0	4.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	10.33	1.319538	0.23994	.	.	ENSG00000155657	ENST00000342992	T	0.65178	-0.14	6.16	6.16	0.99307	Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.65260	0.2674	N	0.25426	0.745	0.80722	D	1	P	0.40282	0.711	P	0.49301	0.606	T	0.65865	-0.6064	9	0.87932	D	0	.	20.8598	0.99761	0.0:0.0:1.0:0.0	.	7377	Q8WZ42	TITIN_HUMAN	I	6450	ENSP00000343764:T6450I	ENSP00000343764:T6450I	T	-	2	0	TTN	179293910	0.997000	0.39634	1.000000	0.80357	0.970000	0.65996	2.662000	0.46766	2.937000	0.99478	0.650000	0.86243	ACA	.	.		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179585665	G	A	179585665	3	1	279	1	0	0	0	0	1	0	0	0	16750	1377	48	3	81584	3	TTN	2	179585665	Missense_Mutation	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	186225	179585665	63613708	66	39825										
SSFA2	6744	hgsc.bcm.edu	37	chr2	182780346	182780346	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	atttactcagtataccacacAccatattctgaaatcattgg	4	10	3	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:182780346A>G	ENST00000431877.2	+	11	2158	c.1979A>G	c.(1978-1980)cAc>cGc	p.H660R	SSFA2_ENST00000409001.1_Missense_Mutation_p.H660R|SSFA2_ENST00000320370.7_Missense_Mutation_p.H660R|SSFA2_ENST00000428267.2_Missense_Mutation_p.H507R|SSFA2_ENST00000409136.1_Missense_Mutation_p.H169R	NM_001130445.1	NP_001123917.1	P28290	SSFA2_HUMAN	sperm specific antigen 2	660						cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(18)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	38			OV - Ovarian serous cystadenocarcinoma(117;0.0856)			TATACCACACACCATATTCTG	0.413																																					p.H660R		Atlas-SNP	.											.	SSFA2	130	.	0			c.A1979G						.						80	76	77					2																	182780346		2203	4300	6503	SO:0001583	missense	6744	exon11			CCACACACCATAT	M61199	CCDS2284.1, CCDS46467.1, CCDS74611.1	2q32.1	2012-02-01			ENSG00000138434	ENSG00000138434			11319	protein-coding gene	gene with protein product	"cleavage signal-1 protein", "KRAS-induced actin-interacting protein", "sperm associated antigen 13"	118990				1555770	Standard	XM_005246812		Approved	CS-1, SPAG13, KRAP, KIAA1927	uc002uoh.3	P28290	OTTHUMG00000132584	ENST00000431877.2:c.1979A>G	chr2.hg19:g.182780346A>G	ENSP00000388731:p.His660Arg	108.0	0.0		106.0	6.0	NM_001130445	A8K6T0|Q68DA6|Q7Z7L2|Q8N1L3|Q8N263|Q8N7H2|Q8NEN5|Q96E36|Q96PW1	Missense_Mutation	SNP	ENST00000431877.2	hg19	CCDS46467.1	.	.	.	.	.	.	.	.	.	.	A	16.82	3.227509	0.58668	.	.	ENSG00000138434	ENST00000431877;ENST00000320370;ENST00000409001;ENST00000428267;ENST00000409136	T;T;T;T;T	0.16743	2.59;2.35;2.58;2.59;2.32	5.54	5.54	0.83059	.	0.177650	0.50627	D	0.000110	T	0.43612	0.1255	M	0.73598	2.24	0.45415	D	0.998398	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.85130	0.997;0.996;0.996;0.996;0.996	T	0.41070	-0.9529	10	0.72032	D	0.01	-10.7804	15.683	0.77388	1.0:0.0:0.0:0.0	.	507;169;660;660;660	E7END2;E7EUL7;E9PHV5;P28290;P28290-3	.;.;.;SSFA2_HUMAN;.	R	660;660;660;507;169	ENSP00000388731:H660R;ENSP00000314669:H660R;ENSP00000387319:H660R;ENSP00000409867:H507R;ENSP00000386916:H169R	ENSP00000314669:H660R	H	+	2	0	SSFA2	182488591	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	4.143000	0.58051	2.119000	0.64992	0.454000	0.30748	CAC	.	.		0.413	SSFA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255793.2	NM_006751		G	182780346	A	G	182780346	3	3	279	1	0	0	0	0	1	0	0	0	15198	159	6	2	2021	2	SSFA2	2	182780346	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	3194681	182780346	60419027	67	39826										
ZNF804A	91752	hgsc.bcm.edu	37	chr2	185802216	185802216	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ccactgtaaaaagaacacaaTacttttaaatggacaatcaa	4	8	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:185802216T>C	ENST00000302277.6	+	4	2687	c.2093T>C	c.(2092-2094)aTa>aCa	p.I698T		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	698							metal ion binding (GO:0046872)			NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						AAGAACACAATACTTTTAAAT	0.294																																					p.I698T		Atlas-SNP	.											.	ZNF804A	322	.	0			c.T2093C						.						73	67	69					2																	185802216		2194	4291	6485	SO:0001583	missense	91752	exon4			ACACAATACTTTT	AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.2093T>C	chr2.hg19:g.185802216T>C	ENSP00000303252:p.Ile698Thr	37.0	0.0		47.0	5.0	NM_194250	A7E253|Q6ZN26	Missense_Mutation	SNP	ENST00000302277.6	hg19	CCDS2291.1	.	.	.	.	.	.	.	.	.	.	T	3.795	-0.042847	0.07452	.	.	ENSG00000170396	ENST00000302277	T	0.05258	3.47	5.63	0.374	0.16183	.	1.826620	0.02817	N	0.125135	T	0.04227	0.0117	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40776	-0.9545	10	0.27082	T	0.32	-0.3078	8.4113	0.32644	0.0:0.5963:0.0:0.4037	.	698	Q7Z570	Z804A_HUMAN	T	698	ENSP00000303252:I698T	ENSP00000303252:I698T	I	+	2	0	ZNF804A	185510461	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	0.483000	0.22292	0.077000	0.16863	0.533000	0.62120	ATA	.	.		0.294	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250		C	185802216	T	C	185802216	3	2	279	1	0	0	0	0	1	0	0	0	18185	1406	49	2	2107	2	ZNF804A	2	185802216	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	3021870	185802216	57397157	68	39827										
ITGAV	3685	hgsc.bcm.edu	37	chr2	187531442	187531442	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ctcctttagctcttagctggTcttcgtttcagtgtgcacca	8	12	3	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:187531442T>C	ENST00000261023.3	+	22	2452	c.2178T>C	c.(2176-2178)ggT>ggC	p.G726G	AC017101.10_ENST00000453665.1_RNA|ITGAV_ENST00000374907.3_Silent_p.G690G|ITGAV_ENST00000433736.2_Silent_p.G680G	NM_002210.3	NP_002201	P06756	ITAV_HUMAN	integrin, alpha V	726					angiogenesis (GO:0001525)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|apoptotic cell clearance (GO:0043277)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|endodermal cell differentiation (GO:0035987)|entry of symbiont into host cell by promotion of host phagocytosis (GO:0052066)|ERK1 and ERK2 cascade (GO:0070371)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|negative chemotaxis (GO:0050919)|negative regulation of entry of bacterium into host cell (GO:2000536)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast proliferation (GO:0033690)|regulation of apoptotic cell clearance (GO:2000425)|regulation of phagocytosis (GO:0050764)|substrate adhesion-dependent cell spreading (GO:0034446)|viral entry into host cell (GO:0046718)	alphav-beta3 integrin-IGF-1-IGF1R complex (GO:0035867)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin alphav-beta5 complex (GO:0034684)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	extracellular matrix binding (GO:0050840)|extracellular matrix protein binding (GO:1990430)|fibronectin binding (GO:0001968)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|transforming growth factor beta binding (GO:0050431)|virus receptor activity (GO:0001618)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47			OV - Ovarian serous cystadenocarcinoma(117;0.0185)|Epithelial(96;0.072)|all cancers(119;0.189)	STAD - Stomach adenocarcinoma(3;0.106)|COAD - Colon adenocarcinoma(31;0.108)	Antithymocyte globulin(DB00098)	TCTTAGCTGGTCTTCGTTTCA	0.323																																					p.G726G	Melanoma(58;108 1995 6081)	Atlas-SNP	.											.	ITGAV	124	.	0			c.T2178C						.						100	95	97					2																	187531442		2203	4300	6503	SO:0001819	synonymous_variant	3685	exon22			AGCTGGTCTTCGT		CCDS2292.1, CCDS46470.1, CCDS46471.1	2q31-q32	2012-04-20	2012-04-20		ENSG00000138448	ENSG00000138448		"CD molecules", "Integrins"	6150	protein-coding gene	gene with protein product		193210	"antigen identified by monoclonal antibody L230", "vitronectin receptor", "integrin, alpha V (vitronectin receptor, alpha polypeptide, antigen CD51)"	VNRA, MSK8, VTNR		2454952	Standard	NM_001144999		Approved	CD51	uc002upq.4	P06756	OTTHUMG00000132635	ENST00000261023.3:c.2178T>C	chr2.hg19:g.187531442T>C		73.0	0.0		76.0	4.0	NM_002210	A0AV67|B0LPF4|B7Z883|B7ZLX0|D3DPG8|E7EWZ6|Q53SK4|Q59EB7|Q6LD15	Silent	SNP	ENST00000261023.3	hg19	CCDS2292.1																																																																																			.	.		0.323	ITGAV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255882.2	NM_002210		C	187531442	T	C	187531442	2	2	279	1	0	0	0	0	0	0	0	1	7897	1654	58	2		2	ITGAV	2	187531442	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	1729226	187531442	55667931	69	39828										
MOBKL3	25843	hgsc.bcm.edu	37	chr2	198405093	198405093	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	agagtgaatgccatccagatActtgcactcaaatgacagca	8	10	1	4			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:198405093A>G	ENST00000323303.4	+	5	541	c.286A>G	c.(286-288)Act>Gct	p.T96A	MOB4_ENST00000497443.1_3'UTR|MOB4_ENST00000233892.4_Missense_Mutation_p.T64A|HSPE1-MOB4_ENST00000604458.1_Missense_Mutation_p.T132A|MOB4_ENST00000409916.1_5'UTR|MOB4_ENST00000409360.1_Missense_Mutation_p.T64A|MOB4_ENST00000448447.2_Missense_Mutation_p.T75A	NM_001202485.1|NM_015387.4	NP_001189414.1|NP_056202.2	Q9Y3A3	PHOCN_HUMAN	MOB family member 4, phocein	96					transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	metal ion binding (GO:0046872)										CCATCCAGATACTTGCACTCA	0.274																																					p.T132A		Atlas-SNP	.											.	.	.	.	0			c.A394G						.						33	33	33					2																	198405093		2202	4291	6493	SO:0001583	missense	0	exon6			CCAGATACTTGCA	AF151853	CCDS2321.1, CCDS2322.1, CCDS46480.1	2q33.1	2011-09-28	2011-09-28	2011-09-28	ENSG00000115540	ENSG00000115540		"MOB kinase activators"	17261	protein-coding gene	gene with protein product	"phocein", "phocein, Mob-like protein"	609361	"preimplantation protein 3", "MOB1, Mps One Binder kinase activator-like 3 (yeast)"	PREI3, MOBKL3		17853115, 10810093, 11230166, 11319234	Standard	NM_199482		Approved	MOB3, DKFZP564M112, CGI-95, 2C4D, PHOCN		Q9Y3A3	OTTHUMG00000132748	ENST00000323303.4:c.286A>G	chr2.hg19:g.198405093A>G	ENSP00000315702:p.Thr96Ala	131.0	0.0		99.0	4.0	NM_001202485	B4DML0|Q53SE0|Q7Z4Y6|Q9H2P3|Q9H5J1|Q9Y4T8	Missense_Mutation	SNP	ENST00000323303.4	hg19	CCDS2321.1	.	.	.	.	.	.	.	.	.	.	A	18.54	3.645165	0.67358	.	.	ENSG00000115540	ENST00000233892;ENST00000323303;ENST00000448447;ENST00000409360	.	.	.	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.79581	0.4470	M	0.92122	3.275	0.80722	D	1	B;B	0.20988	0.04;0.05	B;B	0.25987	0.039;0.065	T	0.79841	-0.1633	9	0.72032	D	0.01	.	15.8317	0.78757	1.0:0.0:0.0:0.0	.	75;96	Q9Y3A3-3;Q9Y3A3	.;PHOCN_HUMAN	A	64;96;75;64	.	ENSP00000233892:T64A	T	+	1	0	PHOCN	198113338	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.248000	0.95456	2.136000	0.66102	0.533000	0.62120	ACT	.	.		0.274	MOB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256110.4	NM_015387		G	198405093	A	G	198405093	3	3	279	1	0	0	0	0	1	0	0	0	9696	391	14	2	304	2	MOBKL3	2	198405093	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	10873651	198405093	44794280	70	39829										
CFLAR	8837	hgsc.bcm.edu	37	chr2	202025503	202025503	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ggtggatgggccagcgatgaAgaatgtggaattcaaggctc	16	6	1	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:202025503A>G	ENST00000309955.3	+	9	1657	c.1142A>G	c.(1141-1143)aAg>aGg	p.K381R	CFLAR_ENST00000423241.2_Missense_Mutation_p.K381R|CFLAR_ENST00000479953.2_Missense_Mutation_p.K285R|CFLAR_ENST00000443227.1_Missense_Mutation_p.K285R|CFLAR_ENST00000340870.5_Missense_Mutation_p.K381R|CFLAR_ENST00000355558.4_Intron|CFLAR_ENST00000341582.6_Missense_Mutation_p.K346R|CFLAR-AS1_ENST00000415011.2_RNA|CFLAR_ENST00000457277.1_Missense_Mutation_p.K381R	NM_001202515.1|NM_003879.5	NP_001189444.1|NP_003870.4	O15519	CFLAR_HUMAN	CASP8 and FADD-like apoptosis regulator	381	Interaction with TRAF1 and TRAF2.|Interaction with caspase-3.|Interaction with caspase-8 subunits p18 and p10.|Interaction with caspase-8.|Not proteolytically processed and involved in apoptosis inhibition.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of myoblast fusion (GO:1901740)|positive regulation of catalytic activity (GO:0043085)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of necroptotic process (GO:0060544)|regulation of satellite cell proliferation (GO:0014842)|skeletal muscle atrophy (GO:0014732)|skeletal muscle tissue development (GO:0007519)|skeletal muscle tissue regeneration (GO:0043403)|skeletal myofibril assembly (GO:0014866)|viral process (GO:0016032)	CD95 death-inducing signaling complex (GO:0031265)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|ripoptosome (GO:0097342)	cysteine-type peptidase activity (GO:0008234)|death effector domain binding (GO:0035877)|enzyme activator activity (GO:0008047)|protease binding (GO:0002020)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|stomach(1)	13						CCAGCGATGAAGAATGTGGAA	0.537																																					p.K381R	Pancreas(16;548 657 22190 32864 42338)	Atlas-SNP	.											.	CFLAR	37	.	0			c.A1142G						.						48	50	49					2																	202025503		2203	4300	6503	SO:0001583	missense	8837	exon9			CGATGAAGAATGT	AF005774	CCDS2337.1, CCDS46487.1, CCDS56157.1, CCDS56158.1, CCDS59436.1	2q33-q34	2014-01-30			ENSG00000003402	ENSG00000003402		"Endogenous ligands"	1876	protein-coding gene	gene with protein product		603599		CASP8AP1		9208847, 9217161	Standard	NM_003879		Approved	CASH, Casper, CLARP, FLAME, FLIP, I-FLICE, MRIT, c-FLIP	uc002uxb.4	O15519	OTTHUMG00000132819	ENST00000309955.3:c.1142A>G	chr2.hg19:g.202025503A>G	ENSP00000312455:p.Lys381Arg	101.0	0.0		89.0	4.0	NM_003879	B4DJE0|B7Z9F9|O14673|O14674|O14675|O15137|O15138|O15356|O15510|O43618|O43619|O43620|O60458|O60459|Q53TS6|Q54AF1|Q96TE4|Q9UEW1	Missense_Mutation	SNP	ENST00000309955.3	hg19	CCDS2337.1	.	.	.	.	.	.	.	.	.	.	A	12.73	2.025136	0.35701	.	.	ENSG00000003402	ENST00000309955;ENST00000443227;ENST00000340870;ENST00000343375;ENST00000341582;ENST00000423241;ENST00000457277	T;T;T;T;T;T	0.22539	1.95;1.95;1.95;1.95;1.95;1.95	5.19	-5.55	0.02536	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase precursor p45, core (1);	1.496790	0.03221	N	0.177577	T	0.23886	0.0578	M	0.67953	2.075	0.09310	N	1	B;P;P;P	0.39920	0.134;0.646;0.589;0.695	B;B;B;B	0.43331	0.041;0.292;0.167;0.416	T	0.30563	-0.9974	10	0.21540	T	0.41	-0.0209	6.252	0.20852	0.332:0.358:0.3101:0.0	.	285;381;346;381	O15519-3;O15519-11;O15519-8;O15519	.;.;.;CFLAR_HUMAN	R	381;285;381;267;346;381;381	ENSP00000312455:K381R;ENSP00000413270:K285R;ENSP00000339326:K381R;ENSP00000345807:K346R;ENSP00000399420:K381R;ENSP00000411535:K381R	ENSP00000312455:K381R	K	+	2	0	CFLAR	201733748	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.439000	0.06897	-1.242000	0.02523	-0.375000	0.07067	AAG	.	.		0.537	CFLAR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256276.3	NM_003879		G	202025503	A	G	202025503	3	3	279	1	0	0	0	0	1	0	0	0	3294	72	3	2	1236	2	CFLAR	2	202025503	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	3620410	202025503	41173870	71	39830										
CDK5R2	8941	hgsc.bcm.edu	37	chr2	219825610	219825610	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gccagggacagctgcgcggcCggaaccaagcactggactat	14	13	0	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:219825610C>T	ENST00000302625.4	+	1	1234	c.1068C>T	c.(1066-1068)gcC>gcT	p.A356A	AC097468.7_ENST00000429343.1_RNA	NM_003936.4	NP_003927.1	Q13319	CD5R2_HUMAN	cyclin-dependent kinase 5, regulatory subunit 2 (p39)	356					cerebellum development (GO:0021549)|hippocampus development (GO:0021766)|layer formation in cerebral cortex (GO:0021819)|neuron migration (GO:0001764)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|superior olivary nucleus maturation (GO:0021722)	cyclin-dependent protein kinase 5 holoenzyme complex (GO:0016533)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	cyclin-dependent protein kinase 5 activator activity (GO:0016534)|lipid binding (GO:0008289)			central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(1)|ovary(1)	8		Renal(207;0.0474)		Epithelial(149;9.77e-07)|all cancers(144;0.000167)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GCTGCGCGGCCGGAACCAAGC	0.751																																					p.A356A		Atlas-SNP	.											CDK5R2,right_lower_lobe,carcinoma,0,1	CDK5R2	17	.	0			c.C1068T						.						5	5	5					2																	219825610		1151	2692	3843	SO:0001819	synonymous_variant	8941	exon1			CGCGGCCGGAACC	U34051	CCDS2427.1	2q35	2008-05-22			ENSG00000171450	ENSG00000171450			1776	protein-coding gene	gene with protein product	"neuronal CDK5 activator isoform"	603764				7592934	Standard	NM_003936		Approved	p39nck5ai, P39, NCK5AI	uc002vjf.4	Q13319	OTTHUMG00000133083	ENST00000302625.4:c.1068C>T	chr2.hg19:g.219825610C>T		13.0	0.0		25.0	2.0	NM_003936	Q4ZFW6	Silent	SNP	ENST00000302625.4	hg19	CCDS2427.1																																																																																			.	.		0.751	CDK5R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256728.1	NM_003936		T	219825610	C	T	219825610	2	4	279	1	0	0	0	0	0	0	0	1	3146	639	23	1		1	CDK5R2	2	219825610	Silent	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	17800107	219825610	23373763	72	39831										
CCDC140	151278	hgsc.bcm.edu	37	chr2	223169002	223169002	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gcccgccctaggacacgtacTctcccgacccctcactcttt	6	20	3	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:223169002T>C	ENST00000295226.1	+	2	765	c.381T>C	c.(379-381)acT>acC	p.T127T		NM_153038.1	NP_694583.1	Q96MF4	CC140_HUMAN	coiled-coil domain containing 140	127										endometrium(4)|large_intestine(1)|prostate(1)	6		Renal(207;0.0376)		Epithelial(121;4.03e-10)|all cancers(144;1.8e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GGACACGTACTCTCCCGACCC	0.547																																					p.T127T		Atlas-SNP	.											.	CCDC140	20	.	0			c.T381C						.						23	27	26					2																	223169002		2203	4300	6503	SO:0001819	synonymous_variant	151278	exon2			ACGTACTCTCCCG	AK057009	CCDS2452.1	2q36.1	2008-02-05			ENSG00000163081	ENSG00000163081			26514	protein-coding gene	gene with protein product							Standard	NM_153038		Approved	FLJ32447	uc002vnb.1	Q96MF4	OTTHUMG00000133154	ENST00000295226.1:c.381T>C	chr2.hg19:g.223169002T>C		92.0	0.0		84.0	4.0	NM_153038		Silent	SNP	ENST00000295226.1	hg19	CCDS2452.1																																																																																			.	.		0.547	CCDC140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256854.1	NM_153038		C	223169002	T	C	223169002	2	2	279	1	0	0	0	0	0	0	0	1	2776	1538	54	2		2	CCDC140	2	223169002	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	3343392	223169002	20030371	73	39832										
SP110	3431	hgsc.bcm.edu	37	chr2	231048350	231048350	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	aacagatatctttctcctttTtcttttctaaacacagaatt	2	9	4	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:231048350T>C	ENST00000358662.4	-	12	1364	c.1286A>G	c.(1285-1287)aAa>aGa	p.K429R	SP110_ENST00000540870.1_Missense_Mutation_p.K435R|SP110_ENST00000392048.3_Missense_Mutation_p.K427R|SP110_ENST00000338556.3_Missense_Mutation_p.K131R|SP110_ENST00000258381.6_Missense_Mutation_p.K429R|SP110_ENST00000258382.5_Missense_Mutation_p.K429R	NM_004509.3	NP_004500	Q9HB58	SP110_HUMAN	SP110 nuclear body protein	429					regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			breast(4)|endometrium(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Renal(207;0.0112)|all_lung(227;0.0223)|Lung NSC(271;0.0983)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.169)		Epithelial(121;2.61e-12)|all cancers(144;6.39e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.0097)		TTTCTCCTTTTTCTTTTCTAA	0.363																																					p.K435R		Atlas-SNP	.											.	SP110	105	.	0			c.A1304G						.						141	146	144					2																	231048350		2203	4300	6503	SO:0001583	missense	3431	exon13			TCCTTTTTCTTTT	L22343	CCDS2474.1, CCDS2475.1, CCDS2476.1, CCDS54435.1	2q37.1	2014-09-17	2001-12-19	2001-12-20	ENSG00000135899	ENSG00000135899			5401	protein-coding gene	gene with protein product		604457	"interferon-induced protein 41, 30kD"	IFI41, IFI75		7693701, 10388521	Standard	NM_080424		Approved		uc002vqg.3	Q9HB58	OTTHUMG00000133204	ENST00000358662.4:c.1286A>G	chr2.hg19:g.231048350T>C	ENSP00000351488:p.Lys429Arg	102.0	0.0		76.0	4.0	NM_001185015	B4DVI4|F5H1M1|Q14976|Q14977|Q53TG2|Q8WUZ6|Q9HCT8	Missense_Mutation	SNP	ENST00000358662.4	hg19	CCDS2474.1	.	.	.	.	.	.	.	.	.	.	T	3.923	-0.017702	0.07681	.	.	ENSG00000135899	ENST00000258381;ENST00000358662;ENST00000392048;ENST00000258382;ENST00000540870;ENST00000338556	T;T;T;T;T;T	0.69175	0.87;0.76;-0.38;-0.36;-0.36;2.32	2.56	-3.31	0.04988	.	3.290600	0.01509	N	0.017822	T	0.42653	0.1212	N	0.11427	0.14	0.09310	N	1	B;B;B;B;B	0.14805	0.011;0.001;0.011;0.006;0.011	B;B;B;B;B	0.12837	0.008;0.001;0.008;0.003;0.005	T	0.13229	-1.0517	10	0.25106	T	0.35	.	3.2332	0.06756	0.202:0.3928:0.0:0.4052	.	427;131;435;429;429	G5E9C0;E7ER70;F5H1M1;Q9HB58;Q9HB58-6	.;.;.;SP110_HUMAN;.	R	429;429;427;429;435;131	ENSP00000258381:K429R;ENSP00000351488:K429R;ENSP00000375902:K427R;ENSP00000258382:K429R;ENSP00000439558:K435R;ENSP00000344049:K131R	ENSP00000258381:K429R	K	-	2	0	SP110	230756594	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-0.875000	0.04205	-0.740000	0.04803	-0.388000	0.06559	AAA	.	.		0.363	SP110-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000332414.1	NM_080424		C	231048350	T	C	231048350	3	2	279	1	0	0	0	0	1	0	0	0	14976	1841	64	2	951	2	SP110	2	231048350	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	7879348	231048350	12151023	74	39833										
EFHD1	80303	hgsc.bcm.edu	37	chr2	233546307	233546307	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ctctgcaggtccaagccttgTcatcggccagtaagtttgaa	10	11	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:233546307T>C	ENST00000264059.3	+	4	1075	c.598T>C	c.(598-600)Tca>Cca	p.S200P	snoU13_ENST00000459149.1_RNA|EFHD1_ENST00000410095.1_Missense_Mutation_p.S88P|EFHD1_ENST00000409613.1_Missense_Mutation_p.S104P|EFHD1_ENST00000409708.1_Missense_Mutation_p.S88P	NM_025202.3	NP_079478.1	Q9BUP0	EFHD1_HUMAN	EF-hand domain family, member D1	200					neuron projection development (GO:0031175)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|large_intestine(2)|lung(3)	7		all_hematologic(139;0.0123)|Acute lymphoblastic leukemia(138;0.0182)|Breast(86;0.0199)|Renal(207;0.025)		Epithelial(121;2.08e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00825)|Lung(119;0.0101)		CCAAGCCTTGTCATCGGCCAG	0.562																																					p.S200P		Atlas-SNP	.											.	EFHD1	28	.	0			c.T598C						.						162	147	152					2																	233546307		2203	4300	6503	SO:0001583	missense	80303	exon4			GCCTTGTCATCGG		CCDS2497.1, CCDS58755.1	2q37.1	2014-07-01	2005-01-25		ENSG00000115468	ENSG00000115468		"EF-hand domain containing"	29556	protein-coding gene	gene with protein product	"swiprosin-2"	611617	"EF hand domain containing 1"			21244694	Standard	NM_025202		Approved	FLJ13612	uc002vtc.3	Q9BUP0	OTTHUMG00000133263	ENST00000264059.3:c.598T>C	chr2.hg19:g.233546307T>C	ENSP00000264059:p.Ser200Pro	97.0	0.0		112.0	5.0	NM_025202	B2RD83|E9PFH3|Q9BTF8|Q9H8I2|Q9HBQ0	Missense_Mutation	SNP	ENST00000264059.3	hg19	CCDS2497.1	.	.	.	.	.	.	.	.	.	.	.	14.90	2.674626	0.47781	.	.	ENSG00000115468	ENST00000409613;ENST00000264059;ENST00000540187;ENST00000409708;ENST00000410095	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	5.65	-2.08	0.07254	.	0.172007	0.52532	D	0.000062	T	0.45756	0.1358	M	0.80183	2.485	0.51233	D	0.999912	B;P	0.48016	0.181;0.904	B;P	0.46362	0.092;0.514	T	0.50039	-0.8874	10	0.49607	T	0.09	-1.359	10.6429	0.45602	0.1084:0.0:0.5185:0.3731	.	104;200	E9PFH3;Q9BUP0	.;EFHD1_HUMAN	P	104;200;103;88;88	ENSP00000386556:S104P;ENSP00000264059:S200P;ENSP00000386243:S88P;ENSP00000386685:S88P	ENSP00000264059:S200P	S	+	1	0	EFHD1	233254551	0.943000	0.32029	0.148000	0.22405	0.658000	0.38924	0.416000	0.21198	-0.616000	0.05671	0.477000	0.44152	TCA	.	.		0.562	EFHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257040.2	NM_025202		C	233546307	T	C	233546307	3	2	279	1	0	0	0	0	1	0	0	0	4950	1667	58	2	612	2	EFHD1	2	233546307	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	2497957	233546307	9653066	75	39834										
USP40	55230	hgsc.bcm.edu	37	chr2	234436105	234436105	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tttttcttttatcaaaggtcAaatcccacacgctttctgtt	4	10	4	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:234436105A>G	ENST00000427112.2	-	12	1705	c.1670T>C	c.(1669-1671)tTg>tCg	p.L557S	USP40_ENST00000251722.6_Missense_Mutation_p.L557S|USP40_ENST00000450966.1_Missense_Mutation_p.L569S			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	557					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|endometrium(6)|kidney(5)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		ATCAAAGGTCAAATCCCACAC	0.423																																					p.L569S		Atlas-SNP	.											.	USP40	174	.	0			c.T1706C						.						87	81	83					2																	234436105		1856	4100	5956	SO:0001583	missense	55230	exon12			AAGGTCAAATCCC	AK001647	CCDS46547.1	2q37.1	2005-08-08	2005-08-08		ENSG00000085982	ENSG00000085982		"Ubiquitin-specific peptidases"	20069	protein-coding gene	gene with protein product		610570	"ubiquitin specific protease 40"			12838346	Standard	NM_018218		Approved	FLJ10785	uc010zmr.2	Q9NVE5	OTTHUMG00000153199	ENST00000427112.2:c.1670T>C	chr2.hg19:g.234436105A>G	ENSP00000387898:p.Leu557Ser	82.0	0.0		69.0	4.0	NM_018218	Q6NX38|Q70EL0	Missense_Mutation	SNP	ENST00000427112.2	hg19	CCDS46547.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.296956	0.81025	.	.	ENSG00000085982	ENST00000450966;ENST00000251722;ENST00000427112	T;T;T	0.07908	3.15;3.16;3.16	4.96	4.96	0.65561	.	0.642393	0.14271	N	0.330148	T	0.29355	0.0731	M	0.71581	2.175	0.46437	D	0.999042	D;D	0.89917	1.0;1.0	D;D	0.79108	0.981;0.992	T	0.01185	-1.1425	10	0.87932	D	0	.	14.9203	0.70832	1.0:0.0:0.0:0.0	.	557;569	Q9NVE5;Q9NVE5-3	UBP40_HUMAN;.	S	569;557;557	ENSP00000415434:L569S;ENSP00000251722:L557S;ENSP00000387898:L557S	ENSP00000251722:L557S	L	-	2	0	USP40	234100844	1.000000	0.71417	0.966000	0.40874	0.939000	0.58152	7.015000	0.76387	1.995000	0.58328	0.482000	0.46254	TTG	.	.		0.423	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294		G	234436105	A	G	234436105	3	3	279	1	0	0	0	0	1	0	0	0	17087	131	5	2	2117	2	USP40	2	234436105	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	889798	234436105	8763268	76	39835										
MTERFD2	130916	hgsc.bcm.edu	37	chr2	242035461	242035461	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tcatcattgtcctccgcctcGtcgtcgtcctcatcatcgtc	6	17	4	0	rs548736677|rs112664190|rs376381853	byFrequency	TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr2:242035461G>C	ENST00000391980.2	-	4	1156	c.1098C>G	c.(1096-1098)gaC>gaG	p.D366E	MTERFD2_ENST00000495694.1_Intron|MTERFD2_ENST00000406593.1_Missense_Mutation_p.D178E|MTERFD2_ENST00000464344.2_Intron	NM_182501.3	NP_872307.2	Q7Z6M4	MTEF4_HUMAN		366					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)	rRNA binding (GO:0019843)			endometrium(3)|large_intestine(6)|lung(5)|ovary(1)|skin(2)|urinary_tract(3)	20		all_cancers(19;4.67e-31)|all_epithelial(40;8.67e-13)|Breast(86;0.000141)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;2.47e-32)|all cancers(36;1.79e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.59e-14)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;2.81e-06)|Lung(119;0.000509)|LUSC - Lung squamous cell carcinoma(224;0.00442)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0886)		cctccgcctcgtcgtcgtcct	0.498																																					p.D366E		Atlas-SNP	.											MTERFD2,NS,carcinoma,0,1	MTERFD2	33	.	0			c.C1098G						.						315	235	262					2																	242035461		2203	4300	6503	SO:0001583	missense	130916	exon4			CGCCTCGTCGTCG																												ENST00000391980.2:c.1098C>G	chr2.hg19:g.242035461G>C	ENSP00000375840:p.Asp366Glu	86.0	0.0		111.0	10.0	NM_182501	A8K6K0|Q9P0E0	Missense_Mutation	SNP	ENST00000391980.2	hg19	CCDS2544.1	.	.	.	.	.	.	.	.	.	.	G	4.181	0.032249	0.08101	.	.	ENSG00000122085	ENST00000391980;ENST00000406593	T;T	0.21543	2.0;2.0	1.45	-2.91	0.05631	.	.	.	.	.	T	0.08268	0.0206	N	0.08118	0	0.18873	N	0.999987	B	0.02656	0.0	B	0.01281	0.0	T	0.27673	-1.0067	9	0.87932	D	0	.	1.4038	0.02276	0.1914:0.4333:0.2001:0.1752	.	366	Q7Z6M4	MTER2_HUMAN	E	366;178	ENSP00000375840:D366E;ENSP00000384998:D178E	ENSP00000241527:D366E	D	-	3	2	MTERFD2	241684134	0.000000	0.05858	0.004000	0.12327	0.006000	0.05464	-1.757000	0.01811	-1.172000	0.02762	-1.398000	0.01145	GAC	.	.		0.498	MTERFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323798.4			C	242035461	G	C	242035461	3	2	279	1	0	0	0	0	1	0	0	0	9929	1136	40	4	51	4	MTERFD2	2	242035461	Missense_Mutation	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	7599356	242035461	1163912	77	39836										
ATP2B2	491	hgsc.bcm.edu	37	chr3	10443863	10443863	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cggaccacggtaaatttctgTtcctgctcgatgcggctctg	11	12	2	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr3:10443863T>C	ENST00000352432.4	-	3	636	c.567A>G	c.(565-567)gaA>gaG	p.E189E	ATP2B2_ENST00000397077.1_Silent_p.E189E|ATP2B2_ENST00000343816.4_Silent_p.E189E|ATP2B2_ENST00000360273.2_Silent_p.E189E|ATP2B2_ENST00000383800.4_Silent_p.E189E			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	189					auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						TAAATTTCTGTTCCTGCTCGA	0.557																																					p.E189E	Ovarian(125;1619 1709 15675 19819 38835)	Atlas-SNP	.											.	ATP2B2	304	.	0			c.A567G						.						138	150	146					3																	10443863		2203	4300	6503	SO:0001819	synonymous_variant	491	exon4			TTTCTGTTCCTGC	X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"ATPases / P-type"	815	protein-coding gene	gene with protein product	"plasma membrane Ca2+ pump 2", "plasma membrane calcium-transporting ATPase 2"	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.567A>G	chr3.hg19:g.10443863T>C		98.0	0.0		85.0	4.0	NM_001683	O00766|Q12994|Q16818	Silent	SNP	ENST00000352432.4	hg19	CCDS33701.1																																																																																			.	.		0.557	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683		C	10443863	T	C	10443863	2	2	279	1	0	0	0	0	0	0	0	1	1140	1722	60	2		2	ATP2B2	3	10443863	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10		10443863	187578567	78	39837										
ANKRD28	23243	hgsc.bcm.edu	37	chr3	15727529	15727529	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ccctctatgcaacgctgtccTtccccacttatctttggcat	5	16	2	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr3:15727529T>C	ENST00000399451.2	-	20	2426	c.2059A>G	c.(2059-2061)Agg>Ggg	p.R687G	ANKRD28_ENST00000383777.1_Missense_Mutation_p.R720G|ANKRD28_ENST00000497037.1_5'UTR	NM_001195098.1|NM_001195099.1|NM_015199.3	NP_001182027.1|NP_001182028.1|NP_056014.2	O15084	ANR28_HUMAN	ankyrin repeat domain 28	687						nucleus (GO:0005634)				breast(2)|endometrium(1)|large_intestine(2)|prostate(1)	6						AACGCTGTCCTTCCCCACTTA	0.418																																					p.R687G		Atlas-SNP	.											.	ANKRD28	121	.	0			c.A2059G						.						129	117	121					3																	15727529		2000	4193	6193	SO:0001583	missense	23243	exon20			CTGTCCTTCCCCA	AY367056	CCDS46769.1, CCDS74908.1	3p25.1	2013-01-10			ENSG00000206560	ENSG00000206560		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits", "Ankyrin repeat domain containing"	29024	protein-coding gene	gene with protein product	"phosphatase interactor targeting K protein", "protein phosphatase 6 ankyrin repeat subunit A", "protein phosphatase 1, regulatory subunit 65"	611122				9205841	Standard	NM_015199		Approved	KIAA0379, PITK, PP6-ARS-A, PPP1R65	uc003caj.1	O15084	OTTHUMG00000155379	ENST00000399451.2:c.2059A>G	chr3.hg19:g.15727529T>C	ENSP00000382379:p.Arg687Gly	99.0	0.0		99.0	4.0	NM_015199	B4DES5|Q1WWL4|Q29RW6|Q3B857|Q6ULS0|Q6ZT57	Missense_Mutation	SNP	ENST00000399451.2	hg19	CCDS46769.1	.	.	.	.	.	.	.	.	.	.	T	15.07	2.723080	0.48728	.	.	ENSG00000206560	ENST00000399451;ENST00000383777;ENST00000412318	T;T;T	0.16073	2.37;2.37;2.37	5.61	3.17	0.36434	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.15435	0.0372	L	0.41492	1.28	0.58432	D	0.999998	P;P;P	0.49783	0.851;0.928;0.714	B;B;B	0.42959	0.359;0.403;0.28	T	0.02232	-1.1191	10	0.26408	T	0.33	.	12.9998	0.58667	0.0:0.0:0.4107:0.5893	.	720;717;687	O15084-1;O15084-4;O15084	.;.;ANR28_HUMAN	G	687;720;687	ENSP00000382379:R687G;ENSP00000373287:R720G;ENSP00000397341:R687G	ENSP00000373287:R720G	R	-	1	2	ANKRD28	15702533	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	1.532000	0.36029	0.379000	0.24794	0.460000	0.39030	AGG	.	.		0.418	ANKRD28-003	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339758.1	NM_015199		C	15727529	T	C	15727529	3	2	279	1	0	0	0	0	1	0	0	0	656	1608	56	2	1138	2	ANKRD28	3	15727529	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	5283666	15727529	182294901	79	39838										
SATB1	6304	hgsc.bcm.edu	37	chr3	18438761	18438761	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	atttgcatagtaagtactgtTcacaatggaagaaatcatac	7	6	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr3:18438761T>C	ENST00000338745.6	-	6	2395	c.661A>G	c.(661-663)Aac>Gac	p.N221D	SATB1_ENST00000475083.1_5'UTR|SATB1_ENST00000417717.2_Missense_Mutation_p.N221D|TBC1D5_ENST00000414318.2_Intron|SATB1_ENST00000454909.2_Missense_Mutation_p.N221D	NM_002971.4	NP_002962.1	Q01826	SATB1_HUMAN	SATB homeobox 1	221					activated T cell proliferation (GO:0050798)|apoptotic process (GO:0006915)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|epidermis development (GO:0008544)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|reflex (GO:0060004)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(2)|endometrium(6)|large_intestine(4)|lung(10)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	32						TAAGTACTGTTCACAATGGAA	0.373																																					p.N221D		Atlas-SNP	.											.	SATB1	96	.	0			c.A661G						.						167	153	157					3																	18438761		2203	4300	6503	SO:0001583	missense	6304	exon6			TACTGTTCACAAT		CCDS2631.1, CCDS56242.1	3p24.3	2011-07-19	2007-02-15		ENSG00000182568	ENSG00000182568		"Homeoboxes / CUT class"	10541	protein-coding gene	gene with protein product		602075	"special AT-rich sequence binding protein 1 (binds to nuclear matrix/scaffold-associating DNA)"			1505028	Standard	NM_002971		Approved		uc003cbj.3	Q01826	OTTHUMG00000129890	ENST00000338745.6:c.661A>G	chr3.hg19:g.18438761T>C	ENSP00000341024:p.Asn221Asp	112.0	0.0		96.0	5.0	NM_002971	B3KXF1|C9JTR6|Q59EQ0	Missense_Mutation	SNP	ENST00000338745.6	hg19	CCDS2631.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.337018	0.81801	.	.	ENSG00000182568	ENST00000338745;ENST00000454909;ENST00000417717;ENST00000440737	D;D;D;D	0.82526	-1.62;-1.62;-1.62;-1.62	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	D	0.89904	0.6850	M	0.61703	1.905	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.90461	0.4446	10	0.62326	D	0.03	-16.4015	16.3291	0.83001	0.0:0.0:0.0:1.0	.	221;221	Q01826-2;Q01826	.;SATB1_HUMAN	D	221	ENSP00000341024:N221D;ENSP00000399708:N221D;ENSP00000399518:N221D;ENSP00000402982:N221D	ENSP00000341024:N221D	N	-	1	0	SATB1	18413765	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.013000	0.88655	2.257000	0.74773	0.528000	0.53228	AAC	.	.		0.373	SATB1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252138.4	NM_001131010		C	18438761	T	C	18438761	3	2	279	1	0	0	0	0	1	0	0	0	13868	1783	62	2	1654	2	SATB1	3	18438761	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	2711232	18438761	179583669	80	39839										
SGOL1	151648	hgsc.bcm.edu	37	chr3	20219761	20219761	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tgataaagaatttgatactaAcggtaaatccttcacaaata	5	6	1	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr3:20219761A>G	ENST00000263753.4	-	4	556		c.e4+1		SGOL1_ENST00000421451.1_Splice_Site|SGOL1_ENST00000417364.1_Splice_Site|SGOL1_ENST00000425061.1_Splice_Site|SGOL1_ENST00000443724.1_Splice_Site|SGOL1_ENST00000412868.1_Splice_Site|SGOL1_ENST00000452020.1_Splice_Site|SGOL1_ENST00000437051.1_Splice_Site|SGOL1-AS1_ENST00000448208.1_RNA|SGOL1-AS1_ENST00000441442.1_RNA|SGOL1_ENST00000419233.2_Splice_Site|SGOL1_ENST00000442720.1_Splice_Site|SGOL1_ENST00000383774.1_Splice_Site|SGOL1_ENST00000412997.1_Splice_Site|SGOL1_ENST00000306698.2_Splice_Site|SGOL1_ENST00000429446.3_Splice_Site	NM_001012410.3|NM_001199252.1	NP_001012410.1|NP_001186181.1	Q5FBB7	SGOL1_HUMAN	shugoshin-like 1 (S. pombe)						attachment of spindle microtubules to kinetochore (GO:0008608)|centriole-centriole cohesion (GO:0010457)|chromosome segregation (GO:0007059)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|chromosome, centromeric region (GO:0000775)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)|spindle pole (GO:0000922)	kinase binding (GO:0019900)			kidney(1)|large_intestine(4)|lung(6)|skin(1)|urinary_tract(2)	14						TTTGATACTAACGGTAAATCC	0.303																																					.		Atlas-SNP	.											SGOL1,NS,carcinoma,0,1	SGOL1	55	.	0			c.416+2T>C						.						75	78	77					3																	20219761		2202	4297	6499	SO:0001630	splice_region_variant	151648	exon5			ATACTAACGGTAA	BC001339	CCDS2635.1, CCDS33716.1, CCDS46771.1, CCDS46772.1, CCDS46773.1, CCDS46774.1, CCDS56243.1	3p24.3	2005-07-27			ENSG00000129810	ENSG00000129810			25088	protein-coding gene	gene with protein product		609168				12747765	Standard	NM_001199251		Approved	NY-BR-85	uc003cbu.3	Q5FBB7	OTTHUMG00000130479	ENST00000263753.4:c.416+1T>C	chr3.hg19:g.20219761A>G		44.0	0.0		49.0	2.0	NM_001199254	Q588H5|Q5FBB4|Q5FBB5|Q5FBB6|Q5FBB8|Q8N579|Q8WVL0|Q9BVA8|Q9H275	Splice_Site	SNP	ENST00000263753.4	hg19	CCDS33716.1	.	.	.	.	.	.	.	.	.	.	A	19.45	3.829127	0.71258	.	.	ENSG00000129810	ENST00000306698;ENST00000419233;ENST00000263753;ENST00000383774;ENST00000425061;ENST00000443724;ENST00000421451;ENST00000452020;ENST00000442720;ENST00000412997;ENST00000437051;ENST00000412868;ENST00000429446;ENST00000417364	.	.	.	5.93	5.93	0.95920	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.7684	0.57405	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SGOL1	20194765	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	4.247000	0.58750	2.263000	0.75096	0.533000	0.62120	.	.	.		0.303	SGOL1-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000340498.1	NM_138484	Intron	G	20219761	A	G	20219761	5	3	279	1	0	0	0	0	0	0	1	0	14231	57	2	2	1311	2	SGOL1	3	20219761	Splice_Site	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	1781000	20219761	177802669	81	39840										
OXSR1	9943	hgsc.bcm.edu	37	chr3	38289195	38289195	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	caggttcacaagaaaccaagAtcccaatcagtctagtacta	6	11	3	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr3:38289195A>G	ENST00000446845.1	+	14	1666	c.1294A>G	c.(1294-1296)Atc>Gtc	p.I432V	OXSR1_ENST00000311806.3_Missense_Mutation_p.I432V					oxidative stress responsive 1											skin(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		AGAAACCAAGATCCCAATCAG	0.368																																					p.I432V		Atlas-SNP	.											.	OXSR1	74	.	0			c.A1294G						.						134	118	124					3																	38289195		2203	4300	6503	SO:0001583	missense	9943	exon14			ACCAAGATCCCAA	AB017642	CCDS2675.1	3p22.2	2013-05-17	2013-05-17	2004-11-26	ENSG00000172939	ENSG00000172939			8508	protein-coding gene	gene with protein product		604046	"oxidative-stress responsive 1"	OSR1		10083736	Standard	XM_005265638		Approved	KIAA1101	uc003chy.3	O95747	OTTHUMG00000131084	ENST00000446845.1:c.1294A>G	chr3.hg19:g.38289195A>G	ENSP00000415851:p.Ile432Val	149.0	0.0		113.0	5.0	NM_005109		Missense_Mutation	SNP	ENST00000446845.1	hg19		.	.	.	.	.	.	.	.	.	.	A	2.398	-0.338163	0.05278	.	.	ENSG00000172939	ENST00000446845;ENST00000311806	T;T	0.70749	-0.51;-0.51	5.57	-1.02	0.10135	.	0.501569	0.23489	N	0.047639	T	0.47358	0.1441	N	0.14661	0.345	0.32268	N	0.569284	B	0.02656	0.0	B	0.04013	0.001	T	0.39941	-0.9589	10	0.27082	T	0.32	-4.8448	10.0221	0.42048	0.5459:0.0:0.4541:0.0	.	432	O95747	OXSR1_HUMAN	V	432	ENSP00000415851:I432V;ENSP00000311713:I432V	ENSP00000311713:I432V	I	+	1	0	OXSR1	38264199	0.998000	0.40836	0.998000	0.56505	0.981000	0.71138	0.357000	0.20199	-0.074000	0.12820	-0.256000	0.11100	ATC	.	.		0.368	OXSR1-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000342708.1	NM_005109		G	38289195	A	G	38289195	3	3	279	1	0	0	0	0	1	0	0	0	11345	333	12	2	1348	2	OXSR1	3	38289195	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	18069434	38289195	159733235	82	39841										
TMEM42	131616	hgsc.bcm.edu	37	chr3	44906569	44906569	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gctgtatggagagtgccaggAggtcttgtggtggggaggag	21	4	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr3:44906569A>G	ENST00000302392.4	+	3	433	c.377A>G	c.(376-378)gAg>gGg	p.E126G		NM_144638.1	NP_653239.1	Q69YG0	TMM42_HUMAN	transmembrane protein 42	126						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(1)|urinary_tract(1)	8				BRCA - Breast invasive adenocarcinoma(193;0.00839)|KIRC - Kidney renal clear cell carcinoma(197;0.0461)|Kidney(197;0.0576)		GAGTGCCAGGAGGTCTTGTGG	0.567																																					p.E126G		Atlas-SNP	.											.	TMEM42	15	.	0			c.A377G						.						210	163	179					3																	44906569		2203	4300	6503	SO:0001583	missense	131616	exon3			GCCAGGAGGTCTT	AL834253	CCDS2722.1	3p21.31	2005-01-19			ENSG00000169964	ENSG00000169964			28444	protein-coding gene	gene with protein product						12477932	Standard	NM_144638		Approved	MGC29956	uc003cnz.3	Q69YG0	OTTHUMG00000133092	ENST00000302392.4:c.377A>G	chr3.hg19:g.44906569A>G	ENSP00000306564:p.Glu126Gly	127.0	0.0		143.0	6.0	NM_144638	Q8WUQ6	Missense_Mutation	SNP	ENST00000302392.4	hg19	CCDS2722.1	.	.	.	.	.	.	.	.	.	.	A	12.33	1.906398	0.33628	.	.	ENSG00000169964	ENST00000302392	T	0.67345	-0.26	4.6	0.693	0.18056	.	0.428373	0.21492	N	0.073670	T	0.40979	0.1139	N	0.14661	0.345	0.09310	N	0.999997	B	0.26195	0.144	B	0.21546	0.035	T	0.16276	-1.0408	10	0.25106	T	0.35	-7.2232	5.7447	0.18114	0.4421:0.4541:0.1037:0.0	.	126	Q69YG0	TMM42_HUMAN	G	126	ENSP00000306564:E126G	ENSP00000306564:E126G	E	+	2	0	TMEM42	44881573	1.000000	0.71417	0.948000	0.38648	0.997000	0.91878	2.575000	0.46025	0.267000	0.21916	0.459000	0.35465	GAG	.	.		0.567	TMEM42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256750.2	NM_144638		G	44906569	A	G	44906569	3	3	279	1	0	0	0	0	1	0	0	0	16181	304	11	2	387	2	TMEM42	3	44906569	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	6617374	44906569	153115861	83	39842										
LAMB2	3913	hgsc.bcm.edu	37	chr3	49167709	49167711	+	In_Frame_Del	DEL	AGA	AGA	-													0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gtccttggttgggtcacggtAgaagaagggccgacagagct							TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr3:49167709_49167711delAGA	ENST00000418109.1	-	10	1342_1344	c.1178_1180delTCT	c.(1177-1182)ttctac>tac	p.F393del	LAMB2_ENST00000305544.4_In_Frame_Del_p.F393del	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	393	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		GGGTCACGGTAGAAGAAGGGCCG	0.596																																					p.393_394del		Atlas-Indel,Pindel	.											.	LAMB2	156	.	0			c.1179_1181del						.																																			SO:0001651	inframe_deletion	3913	exon9			.		CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"Laminins"	6487	protein-coding gene	gene with protein product	"laminin S"	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.1178_1180delTCT	chr3.hg19:g.49167712_49167714delAGA	ENSP00000388325:p.Phe393del	151.0	0.0		147.0	33.0	NM_002292	Q16321	In_Frame_Del	DEL	ENST00000418109.1	hg19	CCDS2789.1																																																																																			.	.		0.596	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292		-	49167711	AGA	-	49167709	7	5	279	1	0	1	0	1	0	0	0	0	8620	420	15	0	4312	0	LAMB2	3	49167709	In_Frame_Del	DEL	AGA	TCGA-G3-A3CG-01A-11D-A20W-10	4261140	49167709	148854721	84	39843										
BSN	8927	hgsc.bcm.edu	37	chr3	49693795	49693795	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tgcaccaagtagatttcccaTtgcttccagtgttccacctg	7	13	0	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr3:49693795T>C	ENST00000296452.4	+	5	6920	c.6806T>C	c.(6805-6807)aTt>aCt	p.I2269T		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	2269					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		AGATTTCCCATTGCTTCCAGT	0.607																																					p.I2269T		Atlas-SNP	.											.	BSN	272	.	0			c.T6806C						.						79	81	80					3																	49693795		2203	4300	6503	SO:0001583	missense	8927	exon5			TTCCCATTGCTTC	AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"zinc finger protein 231", "neuronal double zinc finger protein"	604020	"bassoon (presynaptic cytomatrix protein)"	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.6806T>C	chr3.hg19:g.49693795T>C	ENSP00000296452:p.Ile2269Thr	111.0	0.0		85.0	4.0	NM_003458	O43161|Q7LGH3	Missense_Mutation	SNP	ENST00000296452.4	hg19	CCDS2800.1	.	.	.	.	.	.	.	.	.	.	T	3.789	-0.044123	0.07452	.	.	ENSG00000164061	ENST00000296452	T	0.16897	2.31	5.86	4.9	0.64082	.	0.584497	0.18802	N	0.130746	T	0.05135	0.0137	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38329	-0.9666	10	0.14252	T	0.57	-0.0012	6.8536	0.24028	0.0:0.834:0.0:0.166	.	2269	Q9UPA5	BSN_HUMAN	T	2269	ENSP00000296452:I2269T	ENSP00000296452:I2269T	I	+	2	0	BSN	49668799	0.021000	0.18746	0.003000	0.11579	0.973000	0.67179	2.188000	0.42612	1.280000	0.44463	0.533000	0.62120	ATT	.	.		0.607	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458		C	49693795	T	C	49693795	3	2	279	1	0	0	0	0	1	0	0	0	1532	1493	52	2	6824	2	BSN	3	49693795	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	526086	49693795	148328635	85	39844										
ITIH1	3697	hgsc.bcm.edu	37	chr3	52818435	52818435	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tctggaggtcatgtccatggAgaacaacggacgggcccaga	14	10	2	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr3:52818435A>G	ENST00000273283.2	+	11	1373	c.1349A>G	c.(1348-1350)gAg>gGg	p.E450G	ITIH1_ENST00000537050.1_Missense_Mutation_p.E162G|ITIH1_ENST00000542827.1_Missense_Mutation_p.E450G|ITIH1_ENST00000540715.1_Missense_Mutation_p.E308G	NM_002215.3	NP_002206.2	P19827	ITIH1_HUMAN	inter-alpha-trypsin inhibitor heavy chain 1	450	Hyaluronan-binding.|VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				hyaluronan metabolic process (GO:0030212)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(16)|lung(18)|ovary(4)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	52				BRCA - Breast invasive adenocarcinoma(193;7.04e-05)|Kidney(197;0.000659)|KIRC - Kidney renal clear cell carcinoma(197;0.000795)|OV - Ovarian serous cystadenocarcinoma(275;0.0498)		ATGTCCATGGAGAACAACGGA	0.572																																					p.E450G		Atlas-SNP	.											.	ITIH1	108	.	0			c.A1349G						.						115	105	108					3																	52818435		2203	4300	6503	SO:0001583	missense	3697	exon11			CCATGGAGAACAA		CCDS2864.1, CCDS54595.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055957	ENSG00000055957			6166	protein-coding gene	gene with protein product		147270	"inter-alpha (globulin) inhibitor, H1 polypeptide"			1385302, 10100603	Standard	NM_002215		Approved	H1P, IATIH, ITIH	uc003dfs.3	P19827	OTTHUMG00000150312	ENST00000273283.2:c.1349A>G	chr3.hg19:g.52818435A>G	ENSP00000273283:p.Glu450Gly	133.0	0.0		102.0	5.0	NM_002215	A8K9N5|B2RAH9|B7Z558|B7Z8C0|F5H165|F5H7Y8|P78455|Q01746|Q562G1	Missense_Mutation	SNP	ENST00000273283.2	hg19	CCDS2864.1	.	.	.	.	.	.	.	.	.	.	A	28.0	4.886160	0.91814	.	.	ENSG00000055957	ENST00000542827;ENST00000273283;ENST00000540715;ENST00000537050;ENST00000428133	D;D;D;D;T	0.83755	-1.76;-1.76;-1.76;-1.76;3.65	5.19	5.19	0.71726	von Willebrand factor, type A (3);	0.101985	0.64402	D	0.000003	D	0.91610	0.7349	M	0.86178	2.8	0.41792	D	0.989877	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.85130	0.996;0.96;0.997	D	0.93136	0.6537	10	0.87932	D	0	-46.9039	14.8792	0.70519	1.0:0.0:0.0:0.0	.	308;51;450	F5H165;Q9P1C5;P19827	.;.;ITIH1_HUMAN	G	450;450;308;162;3	ENSP00000442584:E450G;ENSP00000273283:E450G;ENSP00000443973:E308G;ENSP00000443847:E162G;ENSP00000395836:E3G	ENSP00000273283:E450G	E	+	2	0	ITIH1	52793475	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.245000	0.89825	2.187000	0.69744	0.482000	0.46254	GAG	.	.		0.572	ITIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317522.1	NM_002215		G	52818435	A	G	52818435	3	3	279	1	0	0	0	0	1	0	0	0	7912	304	11	2	1391	2	ITIH1	3	52818435	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	3124640	52818435	145203995	86	39845										
DCP1A	55802	hgsc.bcm.edu	37	chr3	53324825	53324825	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gagtccttaccgggatggcaCtggcactggataacacctta	11	11	0	0	rs201612547|rs527572883|rs147183966|rs71087075|rs66506434	byFrequency	TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr3:53324825C>A	ENST00000607628.1	-	8	1554	c.1445G>T	c.(1444-1446)aGt>aTt	p.S482I	RN7SL821P_ENST00000579907.1_RNA|DCP1A_ENST00000606822.1_Missense_Mutation_p.S444I|Y_RNA_ENST00000384175.1_RNA|DCP1A_ENST00000480258.1_5'UTR|DCP1A_ENST00000294241.6_Splice_Site	NM_018403.5	NP_060873.4	Q9NPI6	DCP1A_HUMAN	decapping mRNA 1A	480					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	hydrolase activity (GO:0016787)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10				BRCA - Breast invasive adenocarcinoma(193;0.000164)|KIRC - Kidney renal clear cell carcinoma(197;0.00525)|Kidney(197;0.00579)|OV - Ovarian serous cystadenocarcinoma(275;0.0647)		CGGGATGGCACTGGCACTGGA	0.363																																					.		Atlas-SNP	.											.	DCP1A	30	.	0			c.1444+1G>T						.						8	7	7					3																	53324825		1557	3442	4999	SO:0001583	missense	55802	exon9			ATGGCACTGGCAC	AJ275986	CCDS74946.1	3p21.1	2013-05-02	2013-05-02		ENSG00000162290	ENSG00000272886			18714	protein-coding gene	gene with protein product		607010	"DCP1 decapping enzyme homolog A (S. cerevisiae)"				Standard	XM_005278360		Approved	HSA275986, SMIF, SMAD4IP1	uc021wzi.1	Q9NPI6	OTTHUMG00000158193	ENST00000607628.1:c.1445G>T	chr3.hg19:g.53324825C>A	ENSP00000475920:p.Ser482Ile	7.0	0.0		21.0	8.0	NM_018403	B4DHN9|U3KQM8	Splice_Site	SNP	ENST00000607628.1	hg19																																																																																				.	.		0.363	DCP1A-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_018403		A	53324825	C	A	53324825	3	1	279	1	0	0	0	0	1	0	0	0	4300	579	20	3	315	3	DCP1A	3	53324825	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	506390	53324825	144697605	87	39846										
MAGI1	9223	hgsc.bcm.edu	37	chr3	65376936	65376936	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	caggtgggaactcggggagcAcctgtgtgctgtggcttggg	19	8	0	0	rs201132775		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr3:65376936A>G	ENST00000497477.2	-	14	2296	c.2297T>C	c.(2296-2298)gTg>gCg	p.V766A	MAGI1_ENST00000483466.1_Missense_Mutation_p.V766A|MAGI1_ENST00000402939.2_Missense_Mutation_p.V766A|MAGI1_ENST00000330909.8_Missense_Mutation_p.V766A			Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	766					cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|neuron death (GO:0070997)|protein complex assembly (GO:0006461)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	alpha-actinin binding (GO:0051393)|ATP binding (GO:0005524)|protein C-terminus binding (GO:0008022)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|liver(1)|lung(21)|pancreas(1)|skin(5)	51		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		CTCGGGGAGCACCTGTGTGCT	0.547																																					p.V766A		Atlas-SNP	.											.	MAGI1	481	.	0			c.T2297C						.						120	105	110					3																	65376936		2203	4300	6503	SO:0001583	missense	9223	exon14			GGGAGCACCTGTG	AB010894	CCDS33780.1, CCDS33781.1, CCDS2904.1	3p14.1	2009-10-06	2005-05-10	2005-05-10	ENSG00000151276	ENSG00000151276			946	protein-coding gene	gene with protein product		602625	"BAI1-associated protein 1"	BAIAP1		9647739, 9225980	Standard	XM_005265563		Approved	BAP1, MAGI-1, TNRC19, AIP3, WWP3	uc003dmn.3	Q96QZ7	OTTHUMG00000157554	ENST00000497477.2:c.2297T>C	chr3.hg19:g.65376936A>G	ENSP00000424369:p.Val766Ala	129.0	0.0		107.0	5.0	NM_001033057	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	Missense_Mutation	SNP	ENST00000497477.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	4.578|4.578	0.107360|0.107360	0.08780|0.08780	.|.	.|.	ENSG00000151276|ENSG00000151276	ENST00000460329|ENST00000402939;ENST00000330909;ENST00000422949;ENST00000463103;ENST00000483466;ENST00000497477;ENST00000472257	.|T;T;T;T;T;T	.|0.16597	.|2.84;2.44;2.45;2.44;2.33;2.46	5.98|5.98	3.29|3.29	0.37713|0.37713	.|.	.|0.294450	.|0.37178	.|N	.|0.002203	T|T	0.06600|0.06600	0.0169|0.0169	N|N	0.11427|0.11427	0.14|0.14	0.42028|0.42028	D|D	0.991014|0.991014	.|B;B;B;B;B	.|0.09022	.|0.0;0.0;0.001;0.002;0.0	.|B;B;B;B;B	.|0.06405	.|0.001;0.0;0.002;0.002;0.001	T|T	0.22730|0.22730	-1.0208|-1.0208	5|10	.|0.02654	.|T	.|1	-6.8575|-6.8575	7.2112|7.2112	0.25935|0.25935	0.7306:0.1254:0.144:0.0|0.7306:0.1254:0.144:0.0	.|.	.|766;766;766;766;766	.|A8K188;Q96QZ7-4;Q96QZ7-3;Q96QZ7-2;Q96QZ7-5	.|.;.;.;.;.	R|A	647|766;766;662;641;766;766;552	.|ENSP00000385450:V766A;ENSP00000331157:V766A;ENSP00000418177:V641A;ENSP00000420323:V766A;ENSP00000424369:V766A;ENSP00000420796:V552A	.|ENSP00000331157:V766A	C|V	-|-	1|2	0|0	MAGI1|MAGI1	65351976|65351976	0.984000|0.984000	0.35163|0.35163	1.000000|1.000000	0.80357|0.80357	0.946000|0.946000	0.59487|0.59487	0.851000|0.851000	0.27751|0.27751	1.094000|1.094000	0.41399|0.41399	-0.296000|-0.296000	0.09543|0.09543	TGC|GTG	.	A|0.999;C|0.001		0.547	MAGI1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000349132.2	NM_004742		G	65376936	A	G	65376936	3	3	279	1	0	0	0	0	1	0	0	0	9199	159	6	2	2365	2	MAGI1	3	65376936	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	12052111	65376936	132645494	88	39847										
ROBO1	6091	hgsc.bcm.edu	37	chr3	78648068	78648068	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gcctcttggttgtcttcagcTttcagtttcctgtaagagat	9	9	4	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr3:78648068T>C	ENST00000464233.1	-	31	5064	c.4951A>G	c.(4951-4953)Agc>Ggc	p.S1651G	ROBO1_ENST00000466906.1_5'Flank|ROBO1_ENST00000436010.2_Missense_Mutation_p.S1612G|ROBO1_ENST00000495273.1_Missense_Mutation_p.S1606G|ROBO1_ENST00000467549.1_Missense_Mutation_p.S1551G	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	1651					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		TGTCTTCAGCTTTCAGTTTCC	0.318																																					p.S1651G		Atlas-SNP	.											.	ROBO1	833	.	0			c.A4951G						.						185	175	178					3																	78648068		1847	4102	5949	SO:0001583	missense	6091	exon31			TTCAGCTTTCAGT	AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.4951A>G	chr3.hg19:g.78648068T>C	ENSP00000420321:p.Ser1651Gly	129.0	0.0		95.0	4.0	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Missense_Mutation	SNP	ENST00000464233.1	hg19	CCDS54611.1	.	.	.	.	.	.	.	.	.	.	T	13.85	2.358983	0.41801	.	.	ENSG00000169855	ENST00000436010;ENST00000398412;ENST00000464233;ENST00000495273;ENST00000467549	T;T;T;T	0.62232	0.13;0.09;0.1;0.04	5.58	5.58	0.84498	.	.	.	.	.	T	0.66396	0.2785	N	0.19112	0.55	0.47547	D	0.999453	P;P;P;P	0.52577	0.924;0.924;0.924;0.954	P;P;P;D	0.63597	0.827;0.827;0.827;0.916	T	0.71689	-0.4517	9	0.87932	D	0	.	15.7552	0.78018	0.0:0.0:0.0:1.0	.	1651;1606;1551;1612	Q9Y6N7;B2RXI1;E9PD49;Q9Y6N7-4	ROBO1_HUMAN;.;.;.	G	1612;1606;1651;1606;1551	ENSP00000406043:S1612G;ENSP00000420321:S1651G;ENSP00000420637:S1606G;ENSP00000417992:S1551G	ENSP00000381449:S1606G	S	-	1	0	ROBO1	78730758	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.505000	0.66981	2.123000	0.65237	0.454000	0.30748	AGC	.	.		0.318	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		C	78648068	T	C	78648068	3	2	279	1	0	0	0	0	1	0	0	0	13528	1609	56	2	8	2	ROBO1	3	78648068	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	13271132	78648068	119374362	89	39848										
OR5H1	26341	hgsc.bcm.edu	37	chr3	97852336	97852336	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tatgtgggccctgcatctccGcaagcagatgatcaagatat	10	10	2	3	rs138973744		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr3:97852336G>A	ENST00000354565.2	+	1	795	c.795G>A	c.(793-795)ccG>ccA	p.P265P	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005338.1	NP_001005338.1	A6NKK0	OR5H1_HUMAN	olfactory receptor, family 5, subfamily H, member 1	265						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(7)|kidney(8)|large_intestine(3)|lung(13)|ovary(1)|skin(1)	34						CTGCATCTCCGCAAGCAGATG	0.438																																					p.P265P		Atlas-SNP	.											.	OR5H1	71	.	0			c.G795A						.	G		0,4404		0,0,2202	107	115	112		795	-7.1	0	3	dbSNP_134	112	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	OR5H1	NM_001005338.1		0,1,6500	AA,AG,GG		0.0116,0.0,0.0077		265/314	97852336	1,13001	2202	4299	6501	SO:0001819	synonymous_variant	26341	exon1			ATCTCCGCAAGCA	X64988	CCDS33797.1	3q12.1	2012-08-09			ENSG00000231192	ENSG00000231192		"GPCR / Class A : Olfactory receptors"	8346	protein-coding gene	gene with protein product						1370859	Standard	NM_001005338		Approved	HTPCRX14, HSHTPCRX14	uc011bgt.2	A6NKK0	OTTHUMG00000160070	ENST00000354565.2:c.795G>A	chr3.hg19:g.97852336G>A		238.0	0.0		208.0	54.0	NM_001005338		Silent	SNP	ENST00000354565.2	hg19	CCDS33797.1																																																																																			.	G|1.000;A|0.000		0.438	OR5H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359100.2	NM_001005338		A	97852336	G	A	97852336	2	1	279	1	0	0	0	0	0	0	0	1	11168	1074	38	1		1	OR5H1	3	97852336	Silent	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	19204268	97852336	100170094	90	39849										
ALCAM	214	hgsc.bcm.edu	37	chr3	105268982	105268982	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tttttccagacagaggaatcTccttatattaatggcaggta	8	7	1	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr3:105268982T>C	ENST00000306107.5	+	12	1886	c.1386T>C	c.(1384-1386)tcT>tcC	p.S462S	ALCAM_ENST00000486979.2_Silent_p.S411S|ALCAM_ENST00000472644.2_Silent_p.S462S|ALCAM_ENST00000389927.4_Silent_p.S184S	NM_001627.3	NP_001618.2	Q13740	CD166_HUMAN	activated leukocyte cell adhesion molecule	462	Ig-like C2-type 3.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|motor neuron axon guidance (GO:0008045)|signal transduction (GO:0007165)	axon (GO:0030424)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	receptor binding (GO:0005102)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	28						CAGAGGAATCTCCTTATATTA	0.343																																					p.S462S		Atlas-SNP	.											.	ALCAM	71	.	0			c.T1386C						.						97	120	112					3																	105268982		2197	4293	6490	SO:0001819	synonymous_variant	214	exon12			GGAATCTCCTTAT	AK054632	CCDS33810.1, CCDS58841.1	3q13.1	2013-01-29	2002-08-08		ENSG00000170017	ENSG00000170017		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	400	protein-coding gene	gene with protein product		601662	"activated leucocyte cell adhesion molecule"			7760007	Standard	NM_001627		Approved	CD166, MEMD	uc003dvx.3	Q13740	OTTHUMG00000159192	ENST00000306107.5:c.1386T>C	chr3.hg19:g.105268982T>C		71.0	0.0		71.0	4.0	NM_001627	B2RNS3|B4DTU0|O60892|Q1HGM8|Q1HGM9|Q6PEY4|Q6ZS95	Silent	SNP	ENST00000306107.5	hg19	CCDS33810.1	.	.	.	.	.	.	.	.	.	.	T	9.035	0.988369	0.18966	.	.	ENSG00000170017	ENST00000465413	T	0.12361	2.69	5.92	2.23	0.28157	.	0.139656	0.64402	D	0.000008	T	0.16811	0.0404	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.03043	-1.1079	7	0.49607	T	0.09	-15.8998	3.6072	0.08046	0.2623:0.2994:0.0:0.4383	.	.	.	.	P	223	ENSP00000418937:S223P	ENSP00000418937:S223P	S	+	1	0	ALCAM	106751672	0.996000	0.38824	1.000000	0.80357	0.999000	0.98932	0.143000	0.16115	0.489000	0.27749	0.528000	0.53228	TCC	.	.		0.343	ALCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353764.1	NM_001627		C	105268982	T	C	105268982	2	2	279	1	0	0	0	0	0	0	0	1	487	1538	54	2		2	ALCAM	3	105268982	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	7416646	105268982	92753448	91	39850										
PHLDB2	90102	hgsc.bcm.edu	37	chr3	111671430	111671430	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	catttaaagcactttagaagTctggaagaaaggaaaaaaca	8	5	1	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr3:111671430T>C	ENST00000431670.2	+	11	3054	c.2643T>C	c.(2641-2643)agT>agC	p.S881S	PHLDB2_ENST00000495180.1_Intron|PHLDB2_ENST00000481953.1_Silent_p.S838S|PHLDB2_ENST00000412622.1_Silent_p.S838S|PHLDB2_ENST00000393925.3_Silent_p.S881S|PHLDB2_ENST00000393923.3_Silent_p.S865S	NM_001134438.1	NP_001127910.1	Q86SQ0	PHLB2_HUMAN	pleckstrin homology-like domain, family B, member 2	881						cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(8)|lung(23)|ovary(6)|skin(7)|stomach(1)	55						ACTTTAGAAGTCTGGAAGAAA	0.363																																					p.S881S		Atlas-SNP	.											.	PHLDB2	449	.	0			c.T2643C						.						105	106	106					3																	111671430		2203	4300	6503	SO:0001819	synonymous_variant	90102	exon11			TAGAAGTCTGGAA		CCDS2962.1, CCDS46885.1, CCDS46886.1	3q13.13	2013-01-10			ENSG00000144824	ENSG00000144824		"Pleckstrin homology (PH) domain containing"	29573	protein-coding gene	gene with protein product		610298				12376540	Standard	NM_145753		Approved	LL5beta, FLJ21791, LL5b	uc003dyg.3	Q86SQ0	OTTHUMG00000159282	ENST00000431670.2:c.2643T>C	chr3.hg19:g.111671430T>C		47.0	0.0		50.0	4.0	NM_001134439	A5PKZ3|Q59EA8|Q68CY3|Q6NT98|Q8N8U8|Q8NAB1|Q8NCU5	Silent	SNP	ENST00000431670.2	hg19	CCDS46886.1																																																																																			.	.		0.363	PHLDB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354337.1	NM_145753		C	111671430	T	C	111671430	2	2	279	1	0	0	0	0	0	0	0	1	11861	1664	58	2		2	PHLDB2	3	111671430	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	6402448	111671430	86351000	92	39851										
TIGIT	201633	hgsc.bcm.edu	37	chr3	114018526	114018526	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gtcatctgcacagcagtcatCgtggtggtcgcgttgactag	13	10	3	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr3:114018526C>A	ENST00000486257.1	+	4	731	c.474C>A	c.(472-474)atC>atA	p.I158I	TIGIT_ENST00000383671.3_Silent_p.I158I|TIGIT_ENST00000481065.1_Silent_p.I225I			Q495A1	TIGIT_HUMAN	T cell immunoreceptor with Ig and ITIM domains	158					negative regulation of interleukin-12 production (GO:0032695)|negative regulation of T cell activation (GO:0050868)|positive regulation of interleukin-10 production (GO:0032733)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(7)|prostate(1)	17						CAGCAGTCATCGTGGTGGTCG	0.597																																					p.I158I		Atlas-SNP	.											.	TIGIT	42	.	0			c.C474A						.						79	65	70					3																	114018526		2203	4300	6503	SO:0001819	synonymous_variant	201633	exon3			AGTCATCGTGGTG	AK097192	CCDS2980.1	3q13.31	2013-01-11	2008-10-13	2008-10-13	ENSG00000181847	ENSG00000181847		"Immunoglobulin superfamily / V-set domain containing"	26838	protein-coding gene	gene with protein product		612859	"V-set and immunoglobulin domain containing 9", "V-set and transmembrane domain containing 3"	VSIG9, VSTM3		19011627	Standard	NM_173799		Approved	FLJ39873, DKFZp667A205	uc003ebg.2	Q495A1	OTTHUMG00000159331	ENST00000486257.1:c.474C>A	chr3.hg19:g.114018526C>A		75.0	0.0		73.0	5.0	NM_173799	Q495A3|Q5JPD8|Q6MZS2|Q8N877	Silent	SNP	ENST00000486257.1	hg19	CCDS2980.1																																																																																			.	.		0.597	TIGIT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354690.1	NM_173799		A	114018526	C	A	114018526	2	1	279	1	0	0	0	0	0	0	0	1	15917	874	31	1		1	TIGIT	3	114018526	Silent	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	2347096	114018526	84003904	93	39852										
GOLGB1	2804	hgsc.bcm.edu	37	chr3	121411031	121411031	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gattgcctcttccttgccagAaagcaggcttataatctttt	7	10	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr3:121411031A>G	ENST00000340645.5	-	14	7290	c.7165T>C	c.(7165-7167)Tct>Cct	p.S2389P	GOLGB1_ENST00000393667.3_Missense_Mutation_p.S2394P	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	2389					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		TCCTTGCCAGAAAGCAGGCTT	0.428																																					p.S2394P		Atlas-SNP	.											.	GOLGB1	319	.	0			c.T7180C						.						76	77	76					3																	121411031		2203	4300	6503	SO:0001583	missense	2804	exon14			TGCCAGAAAGCAG	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"macrogolgin", "golgi integral membrane protein 1"	602500	"golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1", "golgin B1, golgi integral membrane protein"			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.7165T>C	chr3.hg19:g.121411031A>G	ENSP00000341848:p.Ser2389Pro	107.0	0.0		80.0	4.0	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	hg19	CCDS3004.1	.	.	.	.	.	.	.	.	.	.	A	12.28	1.891885	0.33442	.	.	ENSG00000173230	ENST00000340645;ENST00000393667	T;T	0.30448	1.53;1.53	5.9	4.68	0.58851	.	0.000000	0.64402	D	0.000008	T	0.46268	0.1384	M	0.62723	1.935	0.41423	D	0.98781	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.83275	0.951;0.951;0.996	T	0.41088	-0.9528	10	0.35671	T	0.21	.	6.3569	0.21406	0.6807:0.1631:0.0:0.1562	.	2394;2394;2389	E7EP74;B2ZZ91;Q14789	.;.;GOGB1_HUMAN	P	2389;2394	ENSP00000341848:S2389P;ENSP00000377275:S2394P	ENSP00000341848:S2389P	S	-	1	0	GOLGB1	122893721	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.026000	0.49689	2.254000	0.74563	0.460000	0.39030	TCT	.	.		0.428	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		G	121411031	A	G	121411031	3	3	279	1	0	0	0	0	1	0	0	0	6573	246	9	2	2650	2	GOLGB1	3	121411031	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	7392505	121411031	76611399	94	39853										
SMC4	10051	hgsc.bcm.edu	37	chr3	160148405	160148405	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	agaaaccttcaaaaggcacaAgactctgtcttgcgtacaga	8	10	3	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr3:160148405A>G	ENST00000357388.3	+	19	3265	c.2814A>G	c.(2812-2814)caA>caG	p.Q938Q	SMC4_ENST00000360111.2_Silent_p.Q938Q|RP11-432B6.3_ENST00000483754.1_Intron|SMC4_ENST00000344722.5_Silent_p.Q938Q|SMC4_ENST00000462787.1_Silent_p.Q938Q|SMC4_ENST00000469762.1_Silent_p.Q913Q	NM_001002800.1	NP_001002800.1	Q9NTJ3	SMC4_HUMAN	structural maintenance of chromosomes 4	938					kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)|mitotic sister chromatid segregation (GO:0000070)	condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(15)|lung(20)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			AAAAGGCACAAGACTCTGTCT	0.378																																					p.Q938Q		Atlas-SNP	.											.	SMC4	135	.	0			c.A2814G						.						76	80	78					3																	160148405		2203	4300	6503	SO:0001819	synonymous_variant	10051	exon18			GGCACAAGACTCT	AF092564	CCDS3189.1, CCDS75046.1	3q26.1	2006-07-06	2006-07-06	2006-07-06	ENSG00000113810	ENSG00000113810		"Structural maintenance of chromosomes proteins"	14013	protein-coding gene	gene with protein product		605575	"SMC4 (structural maintenance of chromosomes 4, yeast)-like 1", "SMC4 structural maintenance of chromosomes 4-like 1 (yeast)"	SMC4L1		9789013, 10319587	Standard	NM_005496		Approved	hCAP-C, CAP-C	uc003fdh.3	Q9NTJ3	OTTHUMG00000159006	ENST00000357388.3:c.2814A>G	chr3.hg19:g.160148405A>G		109.0	0.0		78.0	28.0	NM_005496	A6NLT9|D3DNL8|O95752|Q8NDL4|Q9UNT9	Silent	SNP	ENST00000357388.3	hg19	CCDS3189.1																																																																																			.	.		0.378	SMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352862.1			G	160148405	A	G	160148405	2	3	279	1	0	0	0	0	0	0	0	1	14800	69	3	2		2	SMC4	3	160148405	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	38737374	160148405	37874025	95	39854										
GOLIM4	27333	hgsc.bcm.edu	37	chr3	167728183	167728183	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tctcgaacttcttgctcttcTccatcattatttttatcatc	2	12	6	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr3:167728183T>C	ENST00000470487.1	-	16	2654	c.1965A>G	c.(1963-1965)ggA>ggG	p.G655G	GOLIM4_ENST00000309027.4_Silent_p.G627G	NM_014498.3	NP_055313.1	O00461	GOLI4_HUMAN	golgi integral membrane protein 4	655	Glu-rich.				transport (GO:0006810)	cis-Golgi network (GO:0005801)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(5)|endometrium(2)|large_intestine(8)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						CTTGCTCTTCTCCATCATTAT	0.388																																					p.G655G		Atlas-SNP	.											.	GOLIM4	71	.	0			c.A1965G						.						107	107	107					3																	167728183		2203	4300	6503	SO:0001819	synonymous_variant	27333	exon16			CTCTTCTCCATCA	U55853	CCDS3204.1	3q26	2007-07-30	2007-07-30	2007-07-30	ENSG00000173905	ENSG00000173905			15448	protein-coding gene	gene with protein product		606805	"golgi phosphoprotein 4"	GOLPH4		9201717, 15004235	Standard	NM_014498		Approved	GPP130, GIMPC, P138	uc003ffe.2	O00461	OTTHUMG00000158554	ENST00000470487.1:c.1965A>G	chr3.hg19:g.167728183T>C		77.0	0.0		71.0	4.0	NM_014498		Silent	SNP	ENST00000470487.1	hg19	CCDS3204.1																																																																																			.	.		0.388	GOLIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351278.2			C	167728183	T	C	167728183	2	2	279	1	0	0	0	0	0	0	0	1	6574	1538	54	2		2	GOLIM4	3	167728183	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	7579778	167728183	30294247	96	39855										
EHHADH	1962	hgsc.bcm.edu	37	chr3	184910635	184910635	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	agatcagacactctaaaaggTcccattttaaaaccaaactc	4	11	2	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr3:184910635T>C	ENST00000231887.3	-	7	1626	c.1551A>G	c.(1549-1551)ggA>ggG	p.G517G	EHHADH_ENST00000456310.1_Silent_p.G421G|EHHADH-AS1_ENST00000417720.1_RNA	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	517	3-hydroxyacyl-CoA dehydrogenase.				fatty acid beta-oxidation (GO:0006635)|internal protein amino acid acetylation (GO:0006475)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|coenzyme binding (GO:0050662)|dodecenoyl-CoA delta-isomerase activity (GO:0004165)|enoyl-CoA hydratase activity (GO:0004300)|enzyme binding (GO:0019899)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(2)|skin(3)	24	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)			CTCTAAAAGGTCCCATTTTAA	0.458																																					p.G517G		Atlas-SNP	.											.	EHHADH	73	.	0			c.A1551G						.						71	69	70					3																	184910635		2203	4300	6503	SO:0001819	synonymous_variant	1962	exon7			AAAAGGTCCCATT	L07077	CCDS33901.1, CCDS54694.1	3q26.3-q28	2012-07-13	2010-04-30		ENSG00000113790	ENSG00000113790	4.2.1.17, 1.1.1.35, 5.3.3.8		3247	protein-coding gene	gene with protein product		607037	"enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase"	ECHD		8188243	Standard	NM_001966		Approved		uc003fpf.3	Q08426	OTTHUMG00000156698	ENST00000231887.3:c.1551A>G	chr3.hg19:g.184910635T>C		154.0	0.0		143.0	6.0	NM_001966	A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Silent	SNP	ENST00000231887.3	hg19	CCDS33901.1																																																																																			.	.		0.458	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1			C	184910635	T	C	184910635	2	2	279	1	0	0	0	0	0	0	0	1	4984	1654	58	2		2	EHHADH	3	184910635	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	17182452	184910635	13111795	97	39856										
MAP3K13	9175	hgsc.bcm.edu	37	chr3	185146486	185146486	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gctatggggaaccacccttcTcccaagctgctcgaggacca	10	15	1	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr3:185146486T>C	ENST00000265026.3	+	2	451	c.117T>C	c.(115-117)tcT>tcC	p.S39S	MAP3K13_ENST00000443863.1_Intron|MAP3K13_ENST00000535426.1_Intron|MAP3K13_ENST00000446828.1_Intron|MAP3K13_ENST00000424227.1_Silent_p.S39S	NM_004721.4	NP_004712.1			mitogen-activated protein kinase kinase kinase 13											NS(1)|biliary_tract(1)|breast(3)|endometrium(3)|kidney(1)|large_intestine(13)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54	all_cancers(143;7.21e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)			ACCACCCTTCTCCCAAGCTGC	0.532																																					p.S39S		Atlas-SNP	.											.	MAP3K13	209	.	0			c.T117C						.						80	73	75					3																	185146486		2203	4300	6503	SO:0001819	synonymous_variant	9175	exon2			CCCTTCTCCCAAG	BC031677	CCDS3270.1, CCDS56298.1	3q27	2011-06-09			ENSG00000073803	ENSG00000073803		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6852	protein-coding gene	gene with protein product	"leucine zipper-bearing kinase"	604915				9353328	Standard	NM_004721		Approved	LZK, MEKK13	uc003fpi.3	O43283	OTTHUMG00000156673	ENST00000265026.3:c.117T>C	chr3.hg19:g.185146486T>C		98.0	0.0		85.0	4.0	NM_004721		Silent	SNP	ENST00000265026.3	hg19	CCDS3270.1																																																																																			.	.		0.532	MAP3K13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345268.1	NM_004721		C	185146486	T	C	185146486	2	2	279	1	0	0	0	0	0	0	0	1	9256	1538	54	2		2	MAP3K13	3	185146486	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	235851	185146486	12875944	98	39857										
ADD1	118	hgsc.bcm.edu	37	chr4	2906529	2906529	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ccttatcgataccctgctctGagagagaagtctaaaaaata	7	9	2	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr4:2906529G>T	ENST00000398129.1	+	9	1220	c.1200G>T	c.(1198-1200)ctG>ctT	p.L400L	ADD1_ENST00000398123.2_Silent_p.L400L|ADD1_ENST00000503455.2_Silent_p.L400L|ADD1_ENST00000264758.7_Silent_p.L400L|ADD1_ENST00000513328.2_Silent_p.L400L|ADD1_ENST00000398125.1_Silent_p.L400L|ADD1_ENST00000355842.3_Silent_p.L400L|ADD1_ENST00000446856.1_Silent_p.L400L			P35611	ADDA_HUMAN	adducin 1 (alpha)	400					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|barbed-end actin filament capping (GO:0051016)|cell morphogenesis (GO:0000902)|cell volume homeostasis (GO:0006884)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to retinoic acid (GO:0071300)|endoplasmic reticulum unfolded protein response (GO:0030968)|erythrocyte differentiation (GO:0030218)|hemoglobin metabolic process (GO:0020027)|homeostasis of number of cells within a tissue (GO:0048873)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein binding (GO:0032092)	cytosol (GO:0005829)|dendritic spine (GO:0043197)|F-actin capping protein complex (GO:0008290)|focal adhesion (GO:0005925)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|spectrin binding (GO:0030507)|structural molecule activity (GO:0005198)|transcription factor binding (GO:0008134)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		ACCCTGCTCTGAGAGAGAAGT	0.478																																					p.L400L	Esophageal Squamous(71;505 1201 20414 34538 37449)	Atlas-SNP	.											.	ADD1	56	.	0			c.G1200T						.						110	105	106					4																	2906529		2203	4300	6503	SO:0001819	synonymous_variant	118	exon10			TGCTCTGAGAGAG	L07261	CCDS3363.1, CCDS3364.1, CCDS43205.1, CCDS75094.1	4p16.3	2009-04-22			ENSG00000087274	ENSG00000087274			243	protein-coding gene	gene with protein product		102680				1840603	Standard	NM_001119		Approved		uc003gfq.3	P35611	OTTHUMG00000122080	ENST00000398129.1:c.1200G>T	chr4.hg19:g.2906529G>T		174.0	0.0		188.0	40.0	NM_014190	A2A3N8|A2A3P0|B4DI79|D3DVR3|D3DVR4|D3DVR5|Q13734|Q14729|Q16156|Q86XM2|Q9UJB6	Silent	SNP	ENST00000398129.1	hg19	CCDS43205.1	.	.	.	.	.	.	.	.	.	.	G	9.854	1.194444	0.22037	.	.	ENSG00000087274	ENST00000514940	.	.	.	5.35	5.35	0.76521	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-17.542	19.0717	0.93140	0.0:0.0:1.0:0.0	.	.	.	.	L	106	.	.	X	+	2	2	ADD1	2876327	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.705000	0.74644	2.506000	0.84524	0.655000	0.94253	TGA	.	.		0.478	ADD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242840.1	NM_014189		T	2906529	G	T	2906529	2	4	279	1	0	0	0	0	0	0	0	1	304	1277	45	3		3	ADD1	4	2906529	Silent	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10		2906529	188247747	99	39858										
ARAP2	116984	hgsc.bcm.edu	37	chr4	36085011	36085011	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ttgttggaggcttcattttcTttttcactccacgataaaac	6	9	3	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr4:36085011T>C	ENST00000303965.4	-	29	4976	c.4487A>G	c.(4486-4488)aAg>aGg	p.K1496R		NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	1496	PH 5. {ECO:0000255|PROSITE- ProRule:PRU00145}.				regulation of ARF GTPase activity (GO:0032312)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(32)|ovary(2)|pancreas(1)|prostate(3)|skin(7)|urinary_tract(1)	82						CTTCATTTTCTTTTTCACTCC	0.323																																					p.K1496R		Atlas-SNP	.											.	ARAP2	210	.	0			c.A4487G						.						80	75	77					4																	36085011		2201	4298	6499	SO:0001583	missense	116984	exon29			ATTTTCTTTTTCA	AF411982	CCDS3441.1	4p15.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000047365	ENSG00000047365		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16924	protein-coding gene	gene with protein product		606645	"centaurin, delta 1"	CENTD1			Standard	NM_015230		Approved	PARX	uc003gsq.2	Q8WZ64	OTTHUMG00000097811	ENST00000303965.4:c.4487A>G	chr4.hg19:g.36085011T>C	ENSP00000302895:p.Lys1496Arg	111.0	0.0		95.0	4.0	NM_015230	Q4W5D2|Q7Z2L5|Q96L70|Q96P49|Q9Y4E4	Missense_Mutation	SNP	ENST00000303965.4	hg19	CCDS3441.1	.	.	.	.	.	.	.	.	.	.	T	18.68	3.675896	0.67928	.	.	ENSG00000047365	ENST00000303965	T	0.30182	1.54	5.62	5.62	0.85841	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.054333	0.64402	D	0.000001	T	0.31765	0.0807	L	0.51853	1.615	0.35926	D	0.832182	P	0.47034	0.889	B	0.43658	0.426	T	0.38672	-0.9650	10	0.30078	T	0.28	.	13.3428	0.60555	0.0:0.0:0.0:1.0	.	1496	Q8WZ64	ARAP2_HUMAN	R	1496	ENSP00000302895:K1496R	ENSP00000302895:K1496R	K	-	2	0	ARAP2	35761406	1.000000	0.71417	0.999000	0.59377	0.962000	0.63368	4.529000	0.60588	2.132000	0.65825	0.528000	0.53228	AAG	.	.		0.323	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215074.2	NM_015230		C	36085011	T	C	36085011	3	2	279	1	0	0	0	0	1	0	0	0	839	1609	56	2	647	2	ARAP2	4	36085011	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	33178482	36085011	155069265	100	39859										
UBE2K	3093	hgsc.bcm.edu	37	chr4	39747379	39747379	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cccatttttttaggaggaagAtaccaactagagataaaaat	7	6	0	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr4:39747379A>T	ENST00000261427.5	+	3	449	c.165A>T	c.(163-165)agA>agT	p.R55S	UBE2K_ENST00000438068.2_3'UTR|UBE2K_ENST00000295963.6_Missense_Mutation_p.R55S|UBE2K_ENST00000503368.1_Intron|UBE2K_ENST00000445950.2_Missense_Mutation_p.R55S	NM_001111112.1|NM_005339.4	NP_001104582.1|NP_005330.1	P61086	UBE2K_HUMAN	ubiquitin-conjugating enzyme E2K	55					intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|protein K48-linked ubiquitination (GO:0070936)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)			large_intestine(1)|lung(1)|ovary(2)	4						TAGGAGGAAGATACCAACTAG	0.299																																					p.R55S	NSCLC(101;689 1592 16105 29682 31745)	Atlas-SNP	.											.	UBE2K	16	.	0			c.A165T						.						65	66	66					4																	39747379		2202	4292	6494	SO:0001583	missense	3093	exon3			AGGAAGATACCAA	U58522	CCDS33976.1, CCDS47043.1, CCDS47044.1	4p14	2011-05-19	2011-05-19	2007-12-04	ENSG00000078140	ENSG00000078140		"Ubiquitin-conjugating enzymes E2"	4914	protein-coding gene	gene with protein product		602846	"huntingtin interacting protein 2", "ubiquitin-conjugating enzyme E2K (UBC1 homolog, yeast)"	HIP2		8702625, 17873885	Standard	NM_005339		Approved	HYPG, UBC1	uc003guu.4	P61086	OTTHUMG00000160543	ENST00000261427.5:c.165A>T	chr4.hg19:g.39747379A>T	ENSP00000261427:p.Arg55Ser	269.0	1.0		172.0	75.0	NM_005339	A6NJC1|A8K5Y9|B2RDF8|C9JGP1|O54806|P27924|Q16721|Q9CVV9|Q9Y2D3	Missense_Mutation	SNP	ENST00000261427.5	hg19	CCDS33976.1	.	.	.	.	.	.	.	.	.	.	A	11.47	1.647704	0.29336	.	.	ENSG00000078140	ENST00000261427;ENST00000295963;ENST00000510934;ENST00000445950	T;T;T;T	0.36699	1.24;1.24;1.24;1.24	5.57	5.57	0.84162	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.217561	0.56097	D	0.000029	T	0.21468	0.0517	N	0.11313	0.125	0.80722	D	1	B;B;B	0.22983	0.078;0.032;0.055	B;B;B	0.28385	0.089;0.025;0.022	T	0.11891	-1.0569	10	0.22109	T	0.4	-5.8763	11.6249	0.51139	0.9287:0.0:0.0713:0.0	.	55;55;55	B4DIZ2;P61086;C9JGP1	.;UBE2K_HUMAN;.	S	55	ENSP00000261427:R55S;ENSP00000295963:R55S;ENSP00000425301:R55S;ENSP00000390483:R55S	ENSP00000261427:R55S	R	+	3	2	UBE2K	39423774	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	3.554000	0.53720	2.093000	0.63338	0.533000	0.62120	AGA	.	.		0.299	UBE2K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361061.1	NM_005339		T	39747379	A	T	39747379	3	4	279	1	0	0	0	0	1	0	0	0	16877	330	12	4	175	4	UBE2K	4	39747379	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	3662368	39747379	151406897	101	39860										
CWH43	80157	hgsc.bcm.edu	37	chr4	48990546	48990546	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ggaccgatgatctattacttTcctttgcaaacactagaact	6	10	1	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr4:48990546T>C	ENST00000226432.4	+	2	279	c.96T>C	c.(94-96)ttT>ttC	p.F32F	CWH43_ENST00000513409.1_Silent_p.F5F	NM_025087.2	NP_079363.2	Q9H720	PG2IP_HUMAN	cell wall biogenesis 43 C-terminal homolog (S. cerevisiae)	32					GPI anchor biosynthetic process (GO:0006506)	integral component of membrane (GO:0016021)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(26)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43						TCTATTACTTTCCTTTGCAAA	0.353																																					p.F32F		Atlas-SNP	.											.	CWH43	101	.	0			c.T96C						.						126	124	125					4																	48990546		2203	4300	6503	SO:0001819	synonymous_variant	80157	exon2			TTACTTTCCTTTG		CCDS3486.1, CCDS68697.1	4p12-p11	2010-09-21			ENSG00000109182	ENSG00000109182			26133	protein-coding gene	gene with protein product						17714445, 17761529	Standard	NM_025087		Approved	FLJ21511, CWH43-C	uc003gyv.3	Q9H720	OTTHUMG00000128627	ENST00000226432.4:c.96T>C	chr4.hg19:g.48990546T>C		66.0	0.0		91.0	4.0	NM_025087	B2RPD7	Silent	SNP	ENST00000226432.4	hg19	CCDS3486.1																																																																																			.	.		0.353	CWH43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250496.2	NM_025087		C	48990546	T	C	48990546	2	2	279	1	0	0	0	0	0	0	0	1	4075	1780	62	2		2	CWH43	4	48990546	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	9243167	48990546	142163730	102	39861										
CXCL5	6374	hgsc.bcm.edu	37	chr4	74864222	74864222	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gccctggctgcgtcagcagcAgcagcagcaccaacagcgcg	13	16	1	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr4:74864222A>G	ENST00000296027.4	-	1	274	c.77T>C	c.(76-78)cTg>cCg	p.L26P		NM_002994.3	NP_002985.1	P42830	CXCL5_HUMAN	chemokine (C-X-C motif) ligand 5	26					cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|chemotaxis (GO:0006935)|immune response (GO:0006955)|positive regulation of cell proliferation (GO:0008284)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)			endometrium(3)|large_intestine(2)|lung(3)|urinary_tract(1)	9	Breast(15;0.00136)		all cancers(17;0.00273)|Lung(101;0.196)			CGTCAGCAGCAGCAGCAGCAC	0.701																																					p.L26P		Atlas-SNP	.											.	CXCL5	15	.	0			c.T77C						.						14	18	16					4																	74864222		2197	4288	6485	SO:0001583	missense	6374	exon1			AGCAGCAGCAGCA	X78686	CCDS34006.1	4q13.3	2013-02-25	2002-08-22	2002-08-23		ENSG00000163735		"Endogenous ligands"	10642	protein-coding gene	gene with protein product		600324	"small inducible cytokine subfamily B (Cys-X-Cys), member 5 (epithelial-derived neutrophil-activating peptide 78)"	SCYB5		7929219	Standard	NM_002994		Approved	ENA-78	uc003hhk.4	P42830		ENST00000296027.4:c.77T>C	chr4.hg19:g.74864222A>G	ENSP00000296027:p.Leu26Pro	94.0	0.0		144.0	30.0	NM_002994	Q96QE1	Missense_Mutation	SNP	ENST00000296027.4	hg19	CCDS34006.1	.	.	.	.	.	.	.	.	.	.	A	14.14	2.445430	0.43429	.	.	ENSG00000163735	ENST00000296027	.	.	.	3.51	3.51	0.40186	Chemokine interleukin-8-like domain (1);	0.559011	0.17541	N	0.170552	T	0.76948	0.4059	M	0.82056	2.57	0.58432	D	0.999998	D	0.76494	0.999	D	0.85130	0.997	T	0.77653	-0.2507	9	0.72032	D	0.01	.	8.381	0.32472	1.0:0.0:0.0:0.0	.	26	P42830	CXCL5_HUMAN	P	26	.	ENSP00000296027:L26P	L	-	2	0	CXCL5	75083086	0.997000	0.39634	1.000000	0.80357	0.167000	0.22549	1.548000	0.36201	1.470000	0.48102	0.254000	0.18369	CTG	.	.		0.701	CXCL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362749.1	NM_002994		G	74864222	A	G	74864222	3	3	279	1	0	0	0	0	1	0	0	0	4089	188	7	2	283	2	CXCL5	4	74864222	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	25873676	74864222	116290054	103	39862										
BTC	685	hgsc.bcm.edu	37	chr4	75673278	75673278	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	atatttgtctcttcaatatcTtcattgataggagttatatc	5	6	4	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr4:75673278T>C	ENST00000395743.3	-	5	870	c.510A>G	c.(508-510)gaA>gaG	p.E170E		NM_001729.2	NP_001720.1	P35070	BTC_HUMAN	betacellulin	170					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mitosis (GO:0045840)|positive regulation of urine volume (GO:0035810)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)			central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	10			Lung(101;0.219)			CTTCAATATCTTCATTGATAG	0.348																																					p.E170E		Atlas-SNP	.											.	BTC	23	.	0			c.A510G						.						148	150	149					4																	75673278		2201	4299	6500	SO:0001819	synonymous_variant	685	exon5			AATATCTTCATTG	S55606	CCDS3566.1	4q13.3	2012-09-20			ENSG00000174808	ENSG00000174808			1121	protein-coding gene	gene with protein product		600345				8439318, 11522793	Standard	NM_001729		Approved		uc003hig.2	P35070	OTTHUMG00000130107	ENST00000395743.3:c.510A>G	chr4.hg19:g.75673278T>C		93.0	0.0		94.0	4.0	NM_001729	Q96F48	Silent	SNP	ENST00000395743.3	hg19	CCDS3566.1	.	.	.	.	.	.	.	.	.	.	T	0.686	-0.796451	0.02862	.	.	ENSG00000174808	ENST00000512743	.	.	.	4.84	2.39	0.29439	.	.	.	.	.	T	0.46308	0.1386	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33548	-0.9864	4	.	.	.	-35.4688	3.5545	0.07860	0.2117:0.1029:0.0:0.6854	.	.	.	.	R	100	.	.	K	-	2	0	BTC	75892302	1.000000	0.71417	1.000000	0.80357	0.090000	0.18270	0.867000	0.27968	0.885000	0.36088	0.533000	0.62120	AAG	.	.		0.348	BTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252413.1			C	75673278	T	C	75673278	2	2	279	1	0	0	0	0	0	0	0	1	1551	1606	56	2		2	BTC	4	75673278	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	809056	75673278	115480998	104	39863										
RCHY1	25898	hgsc.bcm.edu	37	chr4	76415820	76415820	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	catgttctgatattctgatgGcataggagtctgtgctactt	10	7	3	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr4:76415820G>A	ENST00000324439.5	-	8	1026	c.628C>T	c.(628-630)Cca>Tca	p.P210S	RCHY1_ENST00000514021.1_5'Flank|RCHY1_ENST00000513257.1_Missense_Mutation_p.P201S|RCHY1_ENST00000512706.1_Missense_Mutation_p.P188S|RCHY1_ENST00000380840.2_Missense_Mutation_p.P170S|RCHY1_ENST00000451788.1_3'UTR	NM_001278536.1|NM_001278538.1|NM_001278539.1	NP_001265465.1|NP_001265467.1|NP_001265468.1	Q96PM5	ZN363_HUMAN	ring finger and CHY zinc finger domain containing 1, E3 ubiquitin protein ligase	210					positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|p53 binding (GO:0002039)|protein homodimerization activity (GO:0042803)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(2)|pancreas(1)	3			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			TATTCTGATGGCATAGGAGTC	0.413																																					p.P210S		Atlas-SNP	.											.	RCHY1	17	.	0			c.C628T						.						183	162	169					4																	76415820		2203	4300	6503	SO:0001583	missense	25898	exon8			CTGATGGCATAGG	AF255666	CCDS3567.1, CCDS34012.1, CCDS63990.1, CCDS63991.1, CCDS63992.1	4q21.1-q21.3	2014-02-17	2012-02-23	2004-03-30	ENSG00000163743	ENSG00000163743		"RING-type (C3HC4) zinc fingers"	17479	protein-coding gene	gene with protein product	"androgen-receptor N-terminal-interacting protein", "p53-induced protein with a RING-H2 domain", "zinc finger, CHY-type"	607680	"zinc finger protein 363", "ring finger and CHY zinc finger domain containing 1"	ZNF363		12654245	Standard	NM_015436		Approved	CHIMP, DKFZp586C1620, PRO1996, RNF199, ARNIP, PIRH2, ZCHY	uc003hik.3	Q96PM5	OTTHUMG00000130105	ENST00000324439.5:c.628C>T	chr4.hg19:g.76415820G>A	ENSP00000321239:p.Pro210Ser	185.0	0.0		155.0	70.0	NM_015436	B3KRG3|C7E541|C7E542|C7E543|D3YRV2|E7EMC8|E7ETW5|J3KPI0|Q2KN33|Q59GN7|Q86X26|Q96PR5	Missense_Mutation	SNP	ENST00000324439.5	hg19	CCDS3567.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.715220	0.89112	.	.	ENSG00000163743	ENST00000324439;ENST00000380840;ENST00000512706;ENST00000513257;ENST00000507014	T;T;T	0.34072	1.42;1.38;1.42	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.65133	0.2662	M	0.82716	2.605	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.998	D;D;D;P	0.87578	0.998;0.996;0.998;0.788	T	0.67604	-0.5628	10	0.62326	D	0.03	-21.5011	17.7022	0.88298	0.0:0.0:1.0:0.0	.	161;188;201;210	E7EMC8;E7ETW5;Q96PM5-2;Q96PM5	.;.;.;ZN363_HUMAN	S	210;170;188;201;161	ENSP00000321239:P210S;ENSP00000370220:P170S;ENSP00000423976:P188S	ENSP00000321239:P210S	P	-	1	0	RCHY1	76634844	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.767000	0.85331	2.774000	0.95407	0.650000	0.86243	CCA	.	.		0.413	RCHY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252411.2	NM_015436		A	76415820	G	A	76415820	3	1	279	1	0	0	0	0	1	0	0	0	13192	1203	42	3	165	3	RCHY1	4	76415820	Missense_Mutation	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	742542	76415820	114738456	105	39864										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79387588	79387588	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cattgaggaagggggaaaagAggtgaggggtgaggacactg	20	3	0	4			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr4:79387588A>G	ENST00000264895.6	+	50	7696	c.7256A>G	c.(7255-7257)gAg>gGg	p.E2419G		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	2419					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						GGGGGAAAAGAGGTGAGGGGT	0.502																																					p.E2419G		Atlas-SNP	.											.	FRAS1	779	.	0			c.A7256G						.						38	38	38					4																	79387588		2014	4194	6208	SO:0001630	splice_region_variant	80144	exon50			GAAAAGAGGTGAG	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.7257+1A>G	chr4.hg19:g.79387588A>G		125.0	0.0		143.0	6.0	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000264895.6	hg19	CCDS54771.1	.	.	.	.	.	.	.	.	.	.	A	17.59	3.427987	0.62733	.	.	ENSG00000138759	ENST00000264895	T	0.43688	0.94	4.86	4.86	0.63082	.	0.233432	0.43260	D	0.000584	T	0.37839	0.1018	M	0.68952	2.095	0.80722	D	1	P	0.44627	0.839	B	0.33196	0.159	T	0.39981	-0.9587	10	0.34782	T	0.22	.	14.89	0.70600	1.0:0.0:0.0:0.0	.	2419	E9PHH6	.	G	2419	ENSP00000264895:E2419G	ENSP00000264895:E2419G	E	+	2	0	FRAS1	79606612	1.000000	0.71417	1.000000	0.80357	0.749000	0.42624	8.816000	0.91979	2.174000	0.68829	0.477000	0.44152	GAG	.	.		0.502	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			Missense_Mutation	G	79387588	A	G	79387588	5	3	279	1	0	0	0	0	0	0	1	0	6050	318	11	2	7529	2	FRAS1	4	79387588	Splice_Site	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	2971768	79387588	111766688	106	39865										
SMARCAD1	56916	hgsc.bcm.edu	37	chr4	95197544	95197544	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	agtctgtttcgacggctgaaActtaattacgcaatttttga	8	7	1	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr4:95197544A>G	ENST00000354268.4	+	15	1936	c.1863A>G	c.(1861-1863)aaA>aaG	p.K621K	SMARCAD1_ENST00000509418.1_Silent_p.K191K|SMARCAD1_ENST00000457823.2_Silent_p.K621K			Q9H4L7	SMRCD_HUMAN	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	621	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP-dependent chromatin remodeling (GO:0043044)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|chromosome separation (GO:0051304)|DNA double-strand break processing (GO:0000729)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|nucleotide metabolic process (GO:0009117)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|regulation of DNA recombination (GO:0000018)	heterochromatin (GO:0000792)|nuclear matrix (GO:0016363)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|liver(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44				OV - Ovarian serous cystadenocarcinoma(123;4.33e-08)		GACGGCTGAAACTTAATTACG	0.388																																					p.K621K		Atlas-SNP	.											.	SMARCAD1	97	.	0			c.A1863G						.						104	96	99					4																	95197544		2203	4300	6503	SO:0001819	synonymous_variant	56916	exon15			GCTGAAACTTAAT	AB032948	CCDS3639.1, CCDS47101.1, CCDS58914.1	4q22-q23	2008-02-05			ENSG00000163104	ENSG00000163104			18398	protein-coding gene	gene with protein product		612761				11031099	Standard	NM_001128430		Approved	ETL1, DKFZP762K2015, KIAA1122, DKFZp762K2015	uc003htb.4	Q9H4L7	OTTHUMG00000130971	ENST00000354268.4:c.1863A>G	chr4.hg19:g.95197544A>G		87.0	0.0		73.0	5.0	NM_001128429	B7Z799|Q05D56|Q96SX1|Q9H017|Q9H860|Q9NPU9|Q9ULU7	Silent	SNP	ENST00000354268.4	hg19	CCDS3639.1																																																																																			.	.		0.388	SMARCAD1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253583.1	NM_020159		G	95197544	A	G	95197544	2	3	279	1	0	0	0	0	0	0	0	1	14787	40	2	2		2	SMARCAD1	4	95197544	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	15809956	95197544	95956732	107	39866										
USP53	54532	hgsc.bcm.edu	37	chr4	120188512	120188512	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	agatgttgtctccaaatgcaTtcgatgccactttcagccac	7	12	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr4:120188512T>C	ENST00000274030.6	+	13	2189	c.1010T>C	c.(1009-1011)aTt>aCt	p.I337T	USP53_ENST00000450251.1_Missense_Mutation_p.I337T	NM_019050.2	NP_061923.2			ubiquitin specific peptidase 53											breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(5)|ovary(1)|pancreas(1)|skin(2)|stomach(1)	27						TCCAAATGCATTCGATGCCAC	0.383																																					p.I337T		Atlas-SNP	.											.	USP53	69	.	0			c.T1010C						.						114	107	110					4																	120188512		1935	4144	6079	SO:0001583	missense	54532	exon12			AATGCATTCGATG	BC017382	CCDS43265.1	4q26	2010-05-12	2005-08-08		ENSG00000145390	ENSG00000145390		"Ubiquitin-specific peptidases"	29255	protein-coding gene	gene with protein product			"ubiquitin specific protease 53"			10718198, 14715245	Standard	NM_019050		Approved	KIAA1350	uc003ics.4	Q70EK8	OTTHUMG00000161331	ENST00000274030.6:c.1010T>C	chr4.hg19:g.120188512T>C	ENSP00000274030:p.Ile337Thr	110.0	0.0		97.0	4.0	NM_019050		Missense_Mutation	SNP	ENST00000274030.6	hg19	CCDS43265.1	.	.	.	.	.	.	.	.	.	.	T	9.648	1.140787	0.21205	.	.	ENSG00000145390	ENST00000274030;ENST00000450251	T;T	0.05513	3.43;3.43	6.02	3.32	0.38043	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.241859	0.47852	N	0.000211	T	0.11110	0.0271	L	0.56769	1.78	0.30548	N	0.765736	P	0.39737	0.685	P	0.45406	0.479	T	0.01652	-1.1303	10	0.46703	T	0.11	-4.6224	11.1821	0.48633	0.0:0.143:0.0:0.857	.	337	Q70EK8	UBP53_HUMAN	T	337	ENSP00000274030:I337T;ENSP00000409906:I337T	ENSP00000274030:I337T	I	+	2	0	USP53	120407960	0.996000	0.38824	0.345000	0.25642	0.882000	0.50991	2.977000	0.49297	1.113000	0.41760	0.533000	0.62120	ATT	.	.		0.383	USP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364564.2	XM_052597		C	120188512	T	C	120188512	3	2	279	1	0	0	0	0	1	0	0	0	17099	1493	52	2	1044	2	USP53	4	120188512	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	24990968	120188512	70965764	108	39867										
ADAD1	132612	hgsc.bcm.edu	37	chr4	123332460	123332460	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	attttgtacagaaccaacttCtaatctactcactcttaaac	2	11	4	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr4:123332460C>T	ENST00000296513.2	+	9	1117	c.932C>T	c.(931-933)tCt>tTt	p.S311F	ADAD1_ENST00000388724.2_Missense_Mutation_p.S300F|ADAD1_ENST00000388725.2_Missense_Mutation_p.S293F	NM_139243.3	NP_640336.1	Q96M93	ADAD1_HUMAN	adenosine deaminase domain containing 1 (testis-specific)	311	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				multicellular organismal development (GO:0007275)|RNA processing (GO:0006396)|spermatid development (GO:0007286)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	35						GAACCAACTTCTAATCTACTC	0.323																																					p.S311F		Atlas-SNP	.											ADAD1,NS,carcinoma,0,2	ADAD1	94	.	0			c.C932T						.						86	85	85					4																	123332460		2203	4300	6503	SO:0001583	missense	132612	exon9			CAACTTCTAATCT	AK057303	CCDS34058.1, CCDS54800.1, CCDS54801.1	4q27	2007-05-31			ENSG00000164113	ENSG00000164113			30713	protein-coding gene	gene with protein product		614130				7543294, 9541871	Standard	NM_139243		Approved	Tenr	uc003iep.3	Q96M93	OTTHUMG00000150128	ENST00000296513.2:c.932C>T	chr4.hg19:g.123332460C>T	ENSP00000296513:p.Ser311Phe	344.0	0.0		287.0	35.0	NM_139243	A6NKN4|B7WPB0|D3DNX2|Q8IWG6|Q8NA06	Missense_Mutation	SNP	ENST00000296513.2	hg19	CCDS34058.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.304288	0.81136	.	.	ENSG00000164113	ENST00000296513;ENST00000388724;ENST00000388725	D;D;D	0.93859	-3.3;-3.3;-3.3	5.74	5.74	0.90152	Adenosine deaminase/editase (3);	0.187202	0.47852	D	0.000214	D	0.96194	0.8759	M	0.61703	1.905	0.49051	D	0.999744	D;D	0.76494	0.985;0.999	P;D	0.71870	0.905;0.975	D	0.96120	0.9084	10	0.72032	D	0.01	-22.2588	19.9151	0.97057	0.0:1.0:0.0:0.0	.	300;311	Q96M93-2;Q96M93	.;ADAD1_HUMAN	F	311;300;293	ENSP00000296513:S311F;ENSP00000373376:S300F;ENSP00000373377:S293F	ENSP00000296513:S311F	S	+	2	0	ADAD1	123551910	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.698000	0.74608	2.716000	0.92895	0.591000	0.81541	TCT	.	.		0.323	ADAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316452.1	NM_139243		T	123332460	C	T	123332460	3	4	279	1	0	0	0	0	1	0	0	0	231	913	32	3	958	3	ADAD1	4	123332460	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	3143948	123332460	67821816	109	39868										
PRSS48	345062	hgsc.bcm.edu	37	chr4	152201018	152201018	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gctgcagggcgctggccttgGcaggtcagcctacactttga	14	12	1	1	rs148861921|rs77216366	byFrequency	TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr4:152201018G>T	ENST00000455694.2	+	2	125	c.123G>T	c.(121-123)tgG>tgT	p.W41C	PRSS48_ENST00000441586.2_Intron|SH3D19_ENST00000604030.1_Intron	NM_183375.2	NP_899231.2	Q7RTY5	PRS48_HUMAN	protease, serine, 48	41	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			kidney(1)|large_intestine(2)|lung(2)|prostate(2)|urinary_tract(1)	8						GCTGGCCTTGGCAGGTCAGCC	0.532																																					p.W41C		Atlas-SNP	.											.	PRSS48	91	.	0			c.G123T						.						120	109	113					4																	152201018		2010	4172	6182	SO:0001583	missense	345062	exon2			GCCTTGGCAGGTC	BN000134	CCDS47145.1	4q31.3	2010-05-07			ENSG00000189099	ENSG00000189099		"Serine peptidases / Serine peptidases"	24635	protein-coding gene	gene with protein product						12838346	Standard	NM_183375		Approved	ESSPL	uc011cif.2	Q7RTY5	OTTHUMG00000161673	ENST00000455694.2:c.123G>T	chr4.hg19:g.152201018G>T	ENSP00000401328:p.Trp41Cys	128.0	0.0		135.0	7.0	NM_183375	Q08E82|Q0VAD4	Missense_Mutation	SNP	ENST00000455694.2	hg19	CCDS47145.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	15.45|15.45	2.836560|2.836560	0.50951|0.50951	.|.	.|.	ENSG00000189099|ENSG00000189099	ENST00000530477|ENST00000455694	.|T	.|0.50001	.|0.76	5.01|5.01	5.01|5.01	0.66863|0.66863	.|Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.|0.000000	.|0.30920	.|N	.|0.008611	T|T	0.81513|0.81513	0.4838|0.4838	H|H	0.98965|0.98965	4.385|4.385	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.97110	.|1.0	D|D	0.88620|0.88620	0.3162|0.3162	5|10	.|0.87932	.|D	.|0	.|.	16.2008|16.2008	0.82071|0.82071	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|41	.|Q7RTY5	.|PRS48_HUMAN	V|C	24|41	.|ENSP00000401328:W41C	.|ENSP00000401328:W41C	G|W	+|+	2|3	0|0	PRSS48|PRSS48	152420468|152420468	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.426000|0.426000	0.31534|0.31534	8.605000|8.605000	0.90883|0.90883	2.774000|2.774000	0.95407|0.95407	0.585000|0.585000	0.79938|0.79938	GGC|TGG	.	.		0.532	PRSS48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365685.3	NM_183375		T	152201018	G	T	152201018	3	4	279	1	0	0	0	0	1	0	0	0	12642	1212	42	3	129	3	PRSS48	4	152201018	Missense_Mutation	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	28868558	152201018	38953258	110	39869										
PRSS48	345062	hgsc.bcm.edu	37	chr4	152212524	152212524	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ggacctaacactatacacagAgtaggcactgtagctgaagc	10	10	0	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr4:152212524A>G	ENST00000455694.2	+	5	908	c.906A>G	c.(904-906)agA>agG	p.R302R	PRSS48_ENST00000441586.2_Silent_p.R159R|SH3D19_ENST00000604030.1_Intron	NM_183375.2	NP_899231.2	Q7RTY5	PRS48_HUMAN	protease, serine, 48	302						extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			kidney(1)|large_intestine(2)|lung(2)|prostate(2)|urinary_tract(1)	8						CTATACACAGAGTAGGCACTG	0.507																																					p.R302R		Atlas-SNP	.											.	PRSS48	91	.	0			c.A906G						.						128	115	119					4																	152212524		1964	4164	6128	SO:0001819	synonymous_variant	345062	exon5			ACACAGAGTAGGC	BN000134	CCDS47145.1	4q31.3	2010-05-07			ENSG00000189099	ENSG00000189099		"Serine peptidases / Serine peptidases"	24635	protein-coding gene	gene with protein product						12838346	Standard	NM_183375		Approved	ESSPL	uc011cif.2	Q7RTY5	OTTHUMG00000161673	ENST00000455694.2:c.906A>G	chr4.hg19:g.152212524A>G		175.0	0.0		149.0	6.0	NM_183375	Q08E82|Q0VAD4	Silent	SNP	ENST00000455694.2	hg19	CCDS47145.1	.	.	.	.	.	.	.	.	.	.	A	3.321	-0.138803	0.06669	.	.	ENSG00000189099	ENST00000530477	.	.	.	3.56	2.36	0.29203	.	.	.	.	.	T	0.27278	0.0669	.	.	.	0.21220	N	0.99976	.	.	.	.	.	.	T	0.19484	-1.0304	4	.	.	.	.	5.6283	0.17495	0.8743:0.0:0.1257:0.0	.	.	.	.	G	281	.	.	E	+	2	0	PRSS48	152431974	0.125000	0.22332	0.022000	0.16811	0.653000	0.38743	4.048000	0.57390	0.732000	0.32470	0.260000	0.18958	GAG	.	.		0.507	PRSS48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365685.3	NM_183375		G	152212524	A	G	152212524	2	3	279	1	0	0	0	0	0	0	0	1	12642	301	11	2		2	PRSS48	4	152212524	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	11506	152212524	38941752	111	39870										
PET112L	5188	hgsc.bcm.edu	37	chr4	152593987	152593987	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ggtcctgcatcagttcaagcTgcttttctgaaacaatctgc	8	11	4	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr4:152593987T>A	ENST00000515812.1	-	11	1365	c.1349A>T	c.(1348-1350)cAg>cTg	p.Q450L	PET112_ENST00000263985.6_Missense_Mutation_p.Q491L|RP11-164P12.3_ENST00000514269.1_RNA|PET112_ENST00000507592.1_5'UTR|RP11-164P12.4_ENST00000508664.1_RNA																breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	23						CAGTTCAAGCTGCTTTTCTGA	0.547																																					p.Q491L		Atlas-SNP	.											.	PET112	43	.	0			c.A1472T						.						104	93	97					4																	152593987		2203	4300	6503	SO:0001583	missense	5188	exon12			TCAAGCTGCTTTT																												ENST00000515812.1:c.1349A>T	chr4.hg19:g.152593987T>A	ENSP00000426859:p.Gln450Leu	168.0	0.0		215.0	40.0	NM_004564		Missense_Mutation	SNP	ENST00000515812.1	hg19		.	.	.	.	.	.	.	.	.	.	T	10.85	1.465695	0.26335	.	.	ENSG00000059691	ENST00000263985;ENST00000515812	T;T	0.43688	0.94;0.94	5.84	3.43	0.39272	Asn/Gln amidotransferase (2);	0.769939	0.12567	N	0.457637	T	0.34571	0.0902	L	0.44542	1.39	0.80722	D	1	B	0.27316	0.175	B	0.22152	0.038	T	0.10543	-1.0625	10	0.87932	D	0	-1.5785	8.6127	0.33813	0.0:0.1512:0.0:0.8488	.	491	O75879	GATB_HUMAN	L	491;450	ENSP00000263985:Q491L;ENSP00000426859:Q450L	ENSP00000263985:Q491L	Q	-	2	0	PET112	152813437	0.578000	0.26717	0.773000	0.31616	0.633000	0.38033	1.128000	0.31369	0.478000	0.27488	0.533000	0.62120	CAG	.	.		0.547	PET112-002	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365672.1			A	152593987	T	A	152593987	3	1	279	1	0	0	0	0	1	0	0	0	11743	1580	55	4	209	4	PET112L	4	152593987	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	381463	152593987	38560289	112	39871										
FGB	2244	hgsc.bcm.edu	37	chr4	155490755	155490755	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	aaatggaggactggaaaggaGacaaagtaaaggctcactat	12	5	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr4:155490755G>A	ENST00000302068.4	+	7	1111	c.1048G>A	c.(1048-1050)Gac>Aac	p.D350N	FGB_ENST00000502545.1_Intron|FGB_ENST00000509493.1_Missense_Mutation_p.D131N	NM_005141.4	NP_005132.2	P02675	FIBB_HUMAN	fibrinogen beta chain	350	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|cellular response to interleukin-1 (GO:0071347)|cellular response to leptin stimulus (GO:0044320)|extracellular matrix organization (GO:0030198)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	chaperone binding (GO:0051087)|structural molecule activity (GO:0005198)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(2)|lung(22)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34	all_hematologic(180;0.215)	Renal(120;0.0458)			Sucralfate(DB00364)	CTGGAAAGGAGACAAAGTAAA	0.413																																					p.D350N	NSCLC(106;1133 1613 21870 46110 52656)	Atlas-SNP	.											.	FGB	71	.	0			c.G1048A						.						104	100	101					4																	155490755		2203	4300	6503	SO:0001583	missense	2244	exon7			AAAGGAGACAAAG		CCDS3786.1	4q28	2014-09-17			ENSG00000171564	ENSG00000171564		"Fibrinogen C domain containing", "Endogenous ligands"	3662	protein-coding gene	gene with protein product		134830	"fibrinogen, B beta polypeptide"				Standard	NM_005141		Approved		uc003ioa.4	P02675	OTTHUMG00000150331	ENST00000302068.4:c.1048G>A	chr4.hg19:g.155490755G>A	ENSP00000306099:p.Asp350Asn	91.0	0.0		94.0	5.0	NM_005141	A0JLR9|B2R7G3|Q32Q65|Q3KPF2	Missense_Mutation	SNP	ENST00000302068.4	hg19	CCDS3786.1	.	.	.	.	.	.	.	.	.	.	G	4.258	0.046899	0.08243	.	.	ENSG00000171564	ENST00000302068;ENST00000537843;ENST00000509493	T;T	0.80738	-1.41;-1.41	5.53	5.53	0.82687	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.259259	0.43747	D	0.000540	T	0.70868	0.3273	N	0.05441	-0.05	0.38293	D	0.942754	P;B	0.37636	0.603;0.003	B;B	0.43680	0.427;0.011	T	0.69247	-0.5195	10	0.15499	T	0.54	.	19.8195	0.96586	0.0:0.0:1.0:0.0	.	333;350	B4E1D3;P02675	.;FIBB_HUMAN	N	350;333;131	ENSP00000306099:D350N;ENSP00000426757:D131N	ENSP00000306099:D350N	D	+	1	0	FGB	155710205	0.004000	0.15560	0.835000	0.33067	0.629000	0.37895	1.548000	0.36201	2.756000	0.94617	0.655000	0.94253	GAC	.	.		0.413	FGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317595.1	NM_005141		A	155490755	G	A	155490755	3	1	279	1	0	0	0	0	1	0	0	0	5839	942	33	3	1074	3	FGB	4	155490755	Missense_Mutation	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	2896768	155490755	35663521	113	39872										
TKTL2	84076	hgsc.bcm.edu	37	chr4	164393283	164393283	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	taatggtaaatgggtcgatgAcacggacagaaataccttgt	11	6	0	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr4:164393283A>T	ENST00000280605.3	-	1	1764	c.1604T>A	c.(1603-1605)gTc>gAc	p.V535D		NM_032136.4	NP_115512.3	Q9H0I9	TKTL2_HUMAN	transketolase-like 2	535						cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|transketolase activity (GO:0004802)			breast(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(42)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	70	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				TGGGTCGATGACACGGACAGA	0.488																																					p.V535D		Atlas-SNP	.											.	TKTL2	130	.	0			c.T1604A						.						155	151	152					4																	164393283		2203	4300	6503	SO:0001583	missense	84076	exon1			TCGATGACACGGA	BC028707	CCDS3805.1	4q32.2	2009-10-06			ENSG00000151005	ENSG00000151005			25313	protein-coding gene	gene with protein product	"similar to transketolase"					11230166	Standard	NM_032136		Approved	FLJ32975, DKFZP434L1717	uc003iqp.4	Q9H0I9	OTTHUMG00000161527	ENST00000280605.3:c.1604T>A	chr4.hg19:g.164393283A>T	ENSP00000280605:p.Val535Asp	108.0	0.0		144.0	38.0	NM_032136	A4FVB4|Q8NCT0|Q96M82	Missense_Mutation	SNP	ENST00000280605.3	hg19	CCDS3805.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.053049	0.75960	.	.	ENSG00000151005	ENST00000280605	D	0.94687	-3.49	4.39	4.39	0.52855	Transketolase, C-terminal (1);Transketolase, C-terminal/Pyruvate-ferredoxin oxidoreductase, domain II (1);Transketolase-like, C-terminal (1);	0.073322	0.53938	D	0.000060	D	0.98349	0.9452	H	0.99325	4.515	0.80722	D	1	D	0.76494	0.999	D	0.74674	0.984	D	0.98604	1.0660	10	0.87932	D	0	-20.8496	12.2228	0.54443	1.0:0.0:0.0:0.0	.	535	Q9H0I9	TKTL2_HUMAN	D	535	ENSP00000280605:V535D	ENSP00000280605:V535D	V	-	2	0	TKTL2	164612733	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	8.557000	0.90700	2.216000	0.71823	0.528000	0.53228	GTC	.	.		0.488	TKTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365207.1	NM_032136		T	164393283	A	T	164393283	3	4	279	1	0	0	0	0	1	0	0	0	15951	275	10	4	280	4	TKTL2	4	164393283	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	8902528	164393283	26760993	114	39873										
TRIM60	166655	hgsc.bcm.edu	37	chr4	165962541	165962541	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gataggtctattctctatacTtttaacgattgtttcacaga	6	7	3	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr4:165962541T>C	ENST00000512596.1	+	3	1533	c.1317T>C	c.(1315-1317)acT>acC	p.T439T	TRIM60_ENST00000341062.5_Silent_p.T439T|TRIM60_ENST00000508504.1_Silent_p.T439T	NM_152620.2	NP_689833.1	Q495X7	TRI60_HUMAN	tripartite motif containing 60	439	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.T439T(1)		NS(1)|breast(2)|endometrium(3)|large_intestine(6)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	29	all_hematologic(180;0.221)	Prostate(90;0.0959)|Melanoma(52;0.18)		GBM - Glioblastoma multiforme(119;0.0844)		TTCTCTATACTTTTAACGATT	0.343																																					p.T439T		Atlas-SNP	.											TRIM60,caecum,carcinoma,0,1	TRIM60	73	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1317C						.						65	71	69					4																	165962541		2203	4300	6503	SO:0001819	synonymous_variant	166655	exon4			CTATACTTTTAAC	AK093201	CCDS3808.1	4q32.3	2013-01-09	2011-01-25	2004-11-17	ENSG00000176979	ENSG00000176979		"RING-type (C3HC4) zinc fingers", "Tripartite motif containing / Tripartite motif containing"	21162	protein-coding gene	gene with protein product			"ring finger protein 129", "tripartite motif-containing 60"	RNF129, RNF33			Standard	NM_152620		Approved	FLJ35882	uc003iqy.1	Q495X7	OTTHUMG00000161262	ENST00000512596.1:c.1317T>C	chr4.hg19:g.165962541T>C		60.0	0.0		49.0	2.0	NM_001258025	Q8NA35	Silent	SNP	ENST00000512596.1	hg19	CCDS3808.1																																																																																			.	.		0.343	TRIM60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364325.1	NM_152620		C	165962541	T	C	165962541	2	2	279	1	0	0	0	0	0	0	0	1	16550	1596	56	2		2	TRIM60	4	165962541	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	1569258	165962541	25191735	115	39874										
NEK1	4750	hgsc.bcm.edu	37	chr4	170502055	170502055	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	aaaattcttctgcaataagcTgagattgaaagagaaaaaaa	7	4	2	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr4:170502055T>C	ENST00000439128.2	-	10	1448		c.e10-2		NEK1_ENST00000511633.1_Splice_Site|NEK1_ENST00000510533.1_Splice_Site|NEK1_ENST00000512193.1_Splice_Site|NEK1_ENST00000507142.1_Splice_Site	NM_012224.2	NP_036356.1	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1						cellular response to DNA damage stimulus (GO:0006974)|cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|stomach(1)	45		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)		TGCAATAAGCTGAGATTGAAA	0.294																																					.		Atlas-SNP	.											.	NEK1	203	.	0			c.808-2A>G						.						48	42	44					4																	170502055		1697	3824	5521	SO:0001630	splice_region_variant	4750	exon12			ATAAGCTGAGATT	AB067488	CCDS47162.1, CCDS56348.1, CCDS56349.1, CCDS56350.1, CCDS56351.1	4q32.3	2012-11-15	2012-11-15		ENSG00000137601	ENSG00000137601			7744	protein-coding gene	gene with protein product		604588	"NIMA (never in mitosis gene a)-related kinase 1"			1382974, 8274451	Standard	NM_012224		Approved	NY-REN-55, KIAA1901	uc003isd.2	Q96PY6	OTTHUMG00000160963	ENST00000439128.2:c.808-2A>G	chr4.hg19:g.170502055T>C		88.0	0.0		90.0	4.0	NM_001199397	G5E9Z3|Q05DG5|Q14CB7|Q5H9T1|Q6PIB8|Q96SS2|Q9H6P7|Q9Y594	Splice_Site	SNP	ENST00000439128.2	hg19	CCDS47162.1	.	.	.	.	.	.	.	.	.	.	T	15.68	2.906121	0.52333	.	.	ENSG00000137601	ENST00000439128;ENST00000511633;ENST00000510533;ENST00000507142;ENST00000512193;ENST00000505119	.	.	.	4.9	4.9	0.64082	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.3834	0.60783	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	NEK1	170738630	1.000000	0.71417	0.991000	0.47740	0.714000	0.41099	5.038000	0.64177	1.968000	0.57251	0.528000	0.53228	.	.	.		0.294	NEK1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000363157.3		Intron	C	170502055	T	C	170502055	5	2	279	1	0	0	0	0	0	0	1	0	10330	1594	55	2	3070	2	NEK1	4	170502055	Splice_Site	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	4539514	170502055	20652221	116	39875										
HPGD	3248	hgsc.bcm.edu	37	chr4	175443546	175443546	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	agcagcgcctctgcaaaggcTctgcctatgccctgagccgc	11	16	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr4:175443546T>C	ENST00000296522.6	-	1	503	c.57A>G	c.(55-57)agA>agG	p.R19R	HPGD_ENST00000296521.7_Silent_p.R19R|HPGD_ENST00000542498.1_Silent_p.R19R|HPGD_ENST00000541923.1_5'UTR|HPGD_ENST00000504433.1_Silent_p.R19R|RP11-440I14.2_ENST00000515178.1_lincRNA|HPGD_ENST00000422112.2_Silent_p.R19R|HPGD_ENST00000510901.1_Intron	NM_000860.5|NM_001145816.2|NM_001256301.1|NM_001256307.1	NP_000851.2|NP_001139288.1|NP_001243230.1|NP_001243236.1	P15428	PGDH_HUMAN	hydroxyprostaglandin dehydrogenase 15-(NAD)	19					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|ductus arteriosus closure (GO:0097070)|female pregnancy (GO:0007565)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|negative regulation of cell cycle (GO:0045786)|ovulation (GO:0030728)|parturition (GO:0007567)|prostaglandin metabolic process (GO:0006693)|small molecule metabolic process (GO:0044281)|thrombin receptor signaling pathway (GO:0070493)|transforming growth factor beta receptor signaling pathway (GO:0007179)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	15-hydroxyprostaglandin dehydrogenase (NAD+) activity (GO:0016404)|catalytic activity (GO:0003824)|NAD binding (GO:0051287)|NAD+ binding (GO:0070403)|prostaglandin E receptor activity (GO:0004957)|protein homodimerization activity (GO:0042803)			kidney(1)|lung(3)|prostate(3)	7		Prostate(90;0.00763)|Melanoma(52;0.0179)|Renal(120;0.0376)|Breast(14;0.0991)|all_hematologic(60;0.124)|all_neural(102;0.196)		all cancers(43;2.6e-18)|Epithelial(43;4.19e-16)|OV - Ovarian serous cystadenocarcinoma(60;5.23e-09)|GBM - Glioblastoma multiforme(59;0.00176)|STAD - Stomach adenocarcinoma(60;0.00299)|LUSC - Lung squamous cell carcinoma(193;0.0253)		CTGCAAAGGCTCTGCCTATGC	0.692																																					p.R19R		Atlas-SNP	.											.	HPGD	19	.	0			c.A57G						.						9	10	10					4																	175443546		2188	4271	6459	SO:0001819	synonymous_variant	3248	exon1			AAAGGCTCTGCCT		CCDS3821.1, CCDS54821.1, CCDS58933.1, CCDS58934.1, CCDS58935.1	4q34-q35	2011-09-14			ENSG00000164120	ENSG00000164120	1.1.1.141	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	5154	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 36C, member 1"	601688				19027726	Standard	NM_000860		Approved	SDR36C1	uc003itu.3	P15428	OTTHUMG00000160772	ENST00000296522.6:c.57A>G	chr4.hg19:g.175443546T>C		75.0	0.0		120.0	5.0	NM_000860	B4DTA4|B4DU74|B4DV57|D3DP43|E7EV11|O00749|Q06F08|Q12998	Silent	SNP	ENST00000296522.6	hg19	CCDS3821.1																																																																																			.	.		0.692	HPGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362228.3			C	175443546	T	C	175443546	2	2	279	1	0	0	0	0	0	0	0	1	7343	1548	54	2		2	HPGD	4	175443546	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	4941491	175443546	15710730	117	39876										
PLEKHG4B	153478	hgsc.bcm.edu	37	chr5	155484	155484	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tggaacacttcgctgcaaacTgtgaagaagccatcattttc	8	10	1	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr5:155484T>A	ENST00000283426.6	+	7	1116	c.1066T>A	c.(1066-1068)Tgt>Agt	p.C356S		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	356							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		CGCTGCAAACTGTGAAGAAGC	0.468																																					p.C356S		Atlas-SNP	.											.	PLEKHG4B	167	.	0			c.T1066A						.						93	89	90					5																	155484		2203	4300	6503	SO:0001583	missense	153478	exon7			GCAAACTGTGAAG	BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"Pleckstrin homology (PH) domain containing"	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.1066T>A	chr5.hg19:g.155484T>A	ENSP00000283426:p.Cys356Ser	170.0	0.0		168.0	68.0	NM_052909		Missense_Mutation	SNP	ENST00000283426.6	hg19	CCDS34124.1	.	.	.	.	.	.	.	.	.	.	.	11.06	1.528261	0.27299	.	.	ENSG00000153404	ENST00000283426;ENST00000502646	T;T	0.35421	1.31;2.87	3.65	3.65	0.41850	.	.	.	.	.	T	0.55705	0.1937	M	0.72894	2.215	0.26823	N	0.968753	D	0.89917	1.0	D	0.85130	0.997	T	0.42682	-0.9437	9	0.54805	T	0.06	.	8.7019	0.34332	0.0:0.0:0.0:1.0	.	356	Q96PX9	PKH4B_HUMAN	S	356;270	ENSP00000283426:C356S;ENSP00000422493:C270S	ENSP00000283426:C356S	C	+	1	0	PLEKHG4B	208484	1.000000	0.71417	0.019000	0.16419	0.012000	0.07955	3.648000	0.54410	1.291000	0.44653	0.383000	0.25322	TGT	.	.		0.468	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909		A	155484	T	A	155484	3	1	279	1	0	0	0	0	1	0	0	0	12081	1580	55	4	1092	4	PLEKHG4B	5	155484	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10		155484	180759776	118	39877										
PLEKHG4B	153478	hgsc.bcm.edu	37	chr5	174118	174118	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	caggcggcggaaatctcaggAcacctacattctccaagcaa	9	13	2	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr5:174118A>G	ENST00000283426.6	+	16	3289	c.3239A>G	c.(3238-3240)gAc>gGc	p.D1080G		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	1080	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		AAATCTCAGGACACCTACATT	0.567																																					p.D1080G		Atlas-SNP	.											.	PLEKHG4B	167	.	0			c.A3239G						.						83	68	74					5																	174118		2202	4300	6502	SO:0001583	missense	153478	exon16			CTCAGGACACCTA	BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"Pleckstrin homology (PH) domain containing"	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.3239A>G	chr5.hg19:g.174118A>G	ENSP00000283426:p.Asp1080Gly	107.0	0.0		95.0	4.0	NM_052909		Missense_Mutation	SNP	ENST00000283426.6	hg19	CCDS34124.1	.	.	.	.	.	.	.	.	.	.	A	14.54	2.564941	0.45694	.	.	ENSG00000153404	ENST00000283426	T	0.11277	2.79	3.38	3.38	0.38709	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	.	.	.	.	T	0.30634	0.0771	M	0.84326	2.69	0.40391	D	0.979545	D	0.63880	0.993	D	0.64506	0.926	T	0.10154	-1.0642	9	0.72032	D	0.01	.	9.7664	0.40563	1.0:0.0:0.0:0.0	.	1080	Q96PX9	PKH4B_HUMAN	G	1080	ENSP00000283426:D1080G	ENSP00000283426:D1080G	D	+	2	0	PLEKHG4B	227118	1.000000	0.71417	0.994000	0.49952	0.903000	0.53119	7.351000	0.79395	1.171000	0.42768	0.383000	0.25322	GAC	.	.		0.567	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909		G	174118	A	G	174118	3	3	279	1	0	0	0	0	1	0	0	0	12081	275	10	2	3301	2	PLEKHG4B	5	174118	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	18634	174118	180741142	119	39878										
CDH18	1016	hgsc.bcm.edu	37	chr5	19503117	19503117	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tcaccttcattgtccttcagAgtgaagtttggatttacagg	9	8	3	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr5:19503117A>G	ENST00000507958.1	-	13	2604	c.1614T>C	c.(1612-1614)acT>acC	p.T538T	CDH18_ENST00000511273.1_Silent_p.T538T|CDH18_ENST00000382275.1_Silent_p.T538T|CDH18_ENST00000274170.4_Silent_p.T538T|CDH18_ENST00000506372.1_Silent_p.T538T|CDH18_ENST00000502796.1_Silent_p.T538T			Q13634	CAD18_HUMAN	cadherin 18, type 2	538	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					TGTCCTTCAGAGTGAAGTTTG	0.348																																					p.T538T		Atlas-SNP	.											.	CDH18	561	.	0			c.T1614C						.						113	105	108					5																	19503117		2203	4300	6503	SO:0001819	synonymous_variant	1016	exon11			CTTCAGAGTGAAG	U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"Cadherins / Major cadherins"	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.1614T>C	chr5.hg19:g.19503117A>G		63.0	0.0		73.0	4.0	NM_001167667	A8K0I2|B4DHG6|Q8N5Z2	Silent	SNP	ENST00000507958.1	hg19	CCDS3889.1																																																																																			.	.		0.348	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934		G	19503117	A	G	19503117	2	3	279	1	0	0	0	0	0	0	0	1	3105	291	11	2		2	CDH18	5	19503117	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	19328999	19503117	161412143	120	39879										
ADAMTS12	81792	hgsc.bcm.edu	37	chr5	33684042	33684042	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	atctttgtgtcggccaccacCagtgtctccacccatctctc	6	17	3	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr5:33684042C>A	ENST00000504830.1	-	4	1088	c.753G>T	c.(751-753)ctG>ctT	p.L251L	ADAMTS12_ENST00000352040.3_Silent_p.L251L|ADAMTS12_ENST00000504582.1_5'UTR	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	251	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						CGGCCACCACCAGTGTCTCCA	0.532										HNSCC(64;0.19)																											p.L251L		Atlas-SNP	.											.	ADAMTS12	464	.	0			c.G753T						.						136	125	129					5																	33684042		2203	4300	6503	SO:0001819	synonymous_variant	81792	exon4			CACCACCAGTGTC	AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"ADAM metallopeptidases with thrombospondin type 1 motif"	14605	protein-coding gene	gene with protein product		606184	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.753G>T	chr5.hg19:g.33684042C>A		84.0	0.0		127.0	70.0	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Silent	SNP	ENST00000504830.1	hg19	CCDS34140.1																																																																																			.	.		0.532	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		A	33684042	C	A	33684042	2	1	279	1	0	0	0	0	0	0	0	1	257	581	21	3		3	ADAMTS12	5	33684042	Silent	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	14180925	33684042	147231218	121	39880										
SLC4A9	83697	hgsc.bcm.edu	37	chr5	139739997	139739997	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	agaccctctgctcttcattcAgctgaatgagctgctgggct	10	12	4	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr5:139739997A>G	ENST00000230993.6	+	1	211	c.176A>G	c.(175-177)cAg>cGg	p.Q59R	SLC4A9_ENST00000507527.1_Missense_Mutation_p.Q59R|CTC-329D1.3_ENST00000520443.1_RNA|SLC4A9_ENST00000506757.2_Missense_Mutation_p.Q59R|SLC4A9_ENST00000506545.1_Missense_Mutation_p.Q59R|SLC4A9_ENST00000432095.2_Missense_Mutation_p.Q59R	NM_001258428.1	NP_001245357.1	Q96Q91	B3A4_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 9	59					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)			endometrium(4)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCTTCATTCAGCTGAATGAG	0.612																																					p.Q59R		Atlas-SNP	.											.	SLC4A9	125	.	0			c.A176G						.						20	24	23					5																	139739997		1964	4143	6107	SO:0001583	missense	83697	exon1			TCATTCAGCTGAA	AF313465	CCDS47278.1, CCDS58973.1, CCDS58974.1, CCDS58975.1	5q31.3	2013-05-22			ENSG00000113073	ENSG00000113073		"Solute carriers"	11035	protein-coding gene	gene with protein product		610207				11305939	Standard	NM_031467		Approved	AE4	uc003lfk.2	Q96Q91	OTTHUMG00000163352	ENST00000230993.6:c.176A>G	chr5.hg19:g.139739997A>G	ENSP00000230993:p.Gln59Arg	70.0	0.0		76.0	5.0	NM_001258428	B7ZL63|D3DQD4|D3DQD5|D3DQD6|E9PDK1|Q96RM5|Q9BXF2|Q9BXN3	Missense_Mutation	SNP	ENST00000230993.6	hg19	CCDS58973.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.561322	0.86335	.	.	ENSG00000113073	ENST00000230993;ENST00000506757;ENST00000432095;ENST00000506545;ENST00000507527	T;T;T;T;T	0.79845	-1.31;-1.31;-1.31;-1.31;-1.31	5.18	5.18	0.71444	Bicarbonate transporter, cytoplasmic (1);Phosphotransferase/anion transporter (1);	0.178836	0.38663	N	0.001612	D	0.83815	0.5336	L	0.32530	0.975	0.43222	D	0.995104	D;D;D;D	0.71674	0.993;0.997;0.998;0.998	D;D;D;D	0.80764	0.968;0.983;0.994;0.994	D	0.85599	0.1251	10	0.87932	D	0	.	12.9136	0.58192	1.0:0.0:0.0:0.0	.	59;59;59;59	E9PDK1;Q96Q91;Q96Q91-2;Q96Q91-3	.;B3A4_HUMAN;.;.	R	59	ENSP00000230993:Q59R;ENSP00000424424:Q59R;ENSP00000410056:Q59R;ENSP00000422855:Q59R;ENSP00000427661:Q59R	ENSP00000230993:Q59R	Q	+	2	0	SLC4A9	139720181	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.747000	0.74872	2.171000	0.68590	0.533000	0.62120	CAG	.	.		0.612	SLC4A9-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000372823.1	NM_031467		G	139739997	A	G	139739997	3	3	279	1	0	0	0	0	1	0	0	0	14675	188	7	2	178	2	SLC4A9	5	139739997	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	106055955	139739997	41175263	122	39881										
PCDHB10	56126	hgsc.bcm.edu	37	chr5	140572961	140572961	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	agtcaacgcggaagtatcctAttcattttttgatgcctcag	8	9	3	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr5:140572961A>G	ENST00000239446.4	+	1	1020	c.836A>G	c.(835-837)tAt>tGt	p.Y279C		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	279	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GAAGTATCCTATTCATTTTTT	0.403																																					p.Y279C		Atlas-SNP	.											.	PCDHB10	177	.	0			c.A836G						.						79	84	82					5																	140572961		2203	4300	6503	SO:0001583	missense	56126	exon1			TATCCTATTCATT	AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"Cadherins / Protocadherins : Clustered"	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.836A>G	chr5.hg19:g.140572961A>G	ENSP00000239446:p.Tyr279Cys	82.0	0.0		80.0	6.0	NM_018930	Q96T99	Missense_Mutation	SNP	ENST00000239446.4	hg19	CCDS4252.1	.	.	.	.	.	.	.	.	.	.	A	12.72	2.021846	0.35701	.	.	ENSG00000120324	ENST00000239446	T	0.63255	-0.03	3.41	3.41	0.39046	Cadherin (4);Cadherin-like (1);	.	.	.	.	D	0.84906	0.5576	H	0.97732	4.065	0.48236	D	0.999617	D	0.89917	1.0	D	0.97110	1.0	D	0.89190	0.3550	9	0.87932	D	0	.	12.0382	0.53438	1.0:0.0:0.0:0.0	.	279	Q9UN67	PCDBA_HUMAN	C	279	ENSP00000239446:Y279C	ENSP00000239446:Y279C	Y	+	2	0	PCDHB10	140553145	1.000000	0.71417	0.991000	0.47740	0.174000	0.22865	6.827000	0.75303	1.572000	0.49736	0.454000	0.30748	TAT	.	.		0.403	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930		G	140572961	A	G	140572961	3	3	279	1	0	0	0	0	1	0	0	0	11544	449	16	2	838	2	PCDHB10	5	140572961	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	832964	140572961	40342299	123	39882										
PCDHGC3	5098	hgsc.bcm.edu	37	chr5	140857641	140857641	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cttgatcaaagacaatggggAgccttcgctctccaccactg	9	13	2	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr5:140857641A>G	ENST00000308177.3	+	1	2062	c.1958A>G	c.(1957-1959)gAg>gGg	p.E653G	PCDHGA5_ENST00000518069.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGB1_ENST00000523390.1_Intron|RN7SL68P_ENST00000488078.2_RNA|PCDHGB4_ENST00000519479.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA9_ENST00000573521.1_Intron	NM_002588.2|NM_032402.1	NP_002579.2|NP_115778.1	Q9UN70	PCDGK_HUMAN	protocadherin gamma subfamily C, 3	653	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(2)|urinary_tract(1)	29			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GACAATGGGGAGCCTTCGCTC	0.592											OREG0016865	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E653G		Atlas-SNP	.											.	PCDHGC3	173	.	0			c.A1958G						.						80	87	85					5																	140857641		2203	4300	6503	SO:0001583	missense	5098	exon1			ATGGGGAGCCTTC	AF152337	CCDS4261.1, CCDS75347.1, CCDS75348.1	5q31	2010-01-26			ENSG00000240184	ENSG00000240184		"Cadherins / Protocadherins : Clustered"	8716	other	protocadherin	"cadherin-like 2", "protocadherin 2", "protocadherin 43"	603627		PCDH2		9360932, 8508762	Standard	NM_032402		Approved	PC-43, PC43, PCDH-GAMMA-C3		Q9UN70	OTTHUMG00000129613	ENST00000308177.3:c.1958A>G	chr5.hg19:g.140857641A>G	ENSP00000312070:p.Glu653Gly	64.0	0.0	1659	71.0	4.0	NM_032402	O60622|Q08192|Q9Y5C4	Missense_Mutation	SNP	ENST00000308177.3	hg19	CCDS4261.1	.	.	.	.	.	.	.	.	.	.	A	18.35	3.604889	0.66445	.	.	ENSG00000240184	ENST00000308177	T	0.51071	0.72	5.55	2.99	0.34606	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.57829	0.2080	L	0.49126	1.545	0.22435	N	0.999103	D;P	0.64830	0.994;0.493	D;B	0.64595	0.927;0.116	T	0.43814	-0.9368	9	0.87932	D	0	.	8.7518	0.34620	0.8047:0.128:0.0673:0.0	.	653;653	Q9UN70;Q9UN70-2	PCDGK_HUMAN;.	G	653	ENSP00000312070:E653G	ENSP00000312070:E653G	E	+	2	0	PCDHGC3	140837825	0.017000	0.18338	0.988000	0.46212	0.759000	0.43091	2.606000	0.46291	1.082000	0.41137	0.533000	0.62120	GAG	.	.		0.592	PCDHGC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251808.2	NM_002588		G	140857641	A	G	140857641	3	3	279	1	0	0	0	0	1	0	0	0	11578	304	11	2	1960	2	PCDHGC3	5	140857641	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	284680	140857641	40057619	124	39883										
FBXO38	81545	hgsc.bcm.edu	37	chr5	147788757	147788757	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cttgaagtagatcttggttaCctcatcattactgctgcccg	8	11	3	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr5:147788757C>A	ENST00000340253.5	+	8	1107	c.939C>A	c.(937-939)taC>taA	p.Y313*	FBXO38_ENST00000296701.6_Nonsense_Mutation_p.Y313*|FBXO38_ENST00000513826.1_Nonsense_Mutation_p.Y313*|FBXO38_ENST00000509699.2_3'UTR|FBXO38_ENST00000394370.3_Nonsense_Mutation_p.Y313*			Q6PIJ6	FBX38_HUMAN	F-box protein 38	313					cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)			ATG4C/FBXO38(2)	NS(1)|breast(2)|endometrium(7)|kidney(5)|large_intestine(9)|lung(15)|ovary(5)|prostate(2)|skin(2)|stomach(2)|urinary_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATCTTGGTTACCTCATCATTA	0.358																																					p.Y313X		Atlas-SNP	.											.	FBXO38	115	.	0			c.C939A						.						253	244	247					5																	147788757		2203	4300	6503	SO:0001587	stop_gained	81545	exon8			TGGTTACCTCATC	BC005873	CCDS43384.1, CCDS64285.1	5q33.1	2008-02-05			ENSG00000145868	ENSG00000145868		"F-boxes /  "other""	28844	protein-coding gene	gene with protein product		608533				12477932	Standard	NM_030793		Approved	MOKA, SP329, FLJ13962, Fbx38	uc003lpg.2	Q6PIJ6	OTTHUMG00000129929	ENST00000340253.5:c.939C>A	chr5.hg19:g.147788757C>A	ENSP00000342023:p.Tyr313*	242.0	0.0		276.0	70.0	NM_001271723	Q6PK72|Q7Z2U0|Q86VN3|Q9BXY6|Q9H837|Q9HC40	Nonsense_Mutation	SNP	ENST00000340253.5	hg19		.	.	.	.	.	.	.	.	.	.	C	34	5.409339	0.96072	.	.	ENSG00000145868	ENST00000340253;ENST00000296701;ENST00000394370;ENST00000513826	.	.	.	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.3216	18.0666	0.89392	0.0:1.0:0.0:0.0	.	.	.	.	X	313	.	ENSP00000296701:Y313X	Y	+	3	2	FBXO38	147768950	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.655000	0.61476	2.674000	0.91012	0.655000	0.94253	TAC	.	.		0.358	FBXO38-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000252185.2	NM_030793		A	147788757	C	A	147788757	4	1	279	1	0	0	0	0	0	1	0	0	5754	518	18	3	965	3	FBXO38	5	147788757	Nonsense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	6931116	147788757	33126503	125	39884										
AFAP1L1	134265	hgsc.bcm.edu	37	chr5	148699221	148699221	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ctccagagtcactccggaggCgctgcactatgactacgtgg	12	13	1	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr5:148699221C>T	ENST00000296721.4	+	13	1654	c.1556C>T	c.(1555-1557)gCg>gTg	p.A519V	AFAP1L1_ENST00000515000.1_Missense_Mutation_p.A519V	NM_001146337.1|NM_152406.2	NP_001139809.1|NP_689619.1	Q8TED9	AF1L1_HUMAN	actin filament associated protein 1-like 1	519						cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(10)|ovary(1)|pancreas(1)|skin(2)	26			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACTCCGGAGGCGCTGCACTAT	0.597																																					p.A519V		Atlas-SNP	.											AFAP1L1,NS,carcinoma,0,1	AFAP1L1	86	.	0			c.C1556T						.						80	76	77					5																	148699221		2203	4300	6503	SO:0001583	missense	134265	exon13			CGGAGGCGCTGCA	AK094067	CCDS34274.1, CCDS54932.1	5q33.1	2013-01-10			ENSG00000157510	ENSG00000157510		"Pleckstrin homology (PH) domain containing"	26714	protein-coding gene	gene with protein product		614410					Standard	NM_152406		Approved	FLJ36748	uc003lqh.3	Q8TED9	OTTHUMG00000163441	ENST00000296721.4:c.1556C>T	chr5.hg19:g.148699221C>T	ENSP00000296721:p.Ala519Val	88.0	0.0		111.0	25.0	NM_001146337	Q08AN4|Q08AN5|Q8IW82|Q8N8Z5|Q8N9Q4	Missense_Mutation	SNP	ENST00000296721.4	hg19	CCDS34274.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.908963	0.92107	.	.	ENSG00000157510	ENST00000296721;ENST00000515000	T;T	0.17370	2.28;2.28	5.98	5.98	0.97165	.	0.227351	0.43919	D	0.000516	T	0.42268	0.1195	M	0.68593	2.085	0.80722	D	1	D;D	0.76494	0.997;0.999	D;P	0.64410	0.925;0.883	T	0.05971	-1.0853	10	0.56958	D	0.05	-17.9497	20.4581	0.99154	0.0:1.0:0.0:0.0	.	519;519	Q8TED9-2;Q8TED9	.;AF1L1_HUMAN	V	519	ENSP00000296721:A519V;ENSP00000424427:A519V	ENSP00000296721:A519V	A	+	2	0	AFAP1L1	148679414	1.000000	0.71417	0.968000	0.41197	0.421000	0.31385	7.818000	0.86416	2.835000	0.97688	0.650000	0.86243	GCG	.	.		0.597	AFAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373443.1	NM_152406		T	148699221	C	T	148699221	3	4	279	1	0	0	0	0	1	0	0	0	354	768	27	1	1606	1	AFAP1L1	5	148699221	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	910464	148699221	32216039	126	39885										
NMUR2	56923	hgsc.bcm.edu	37	chr5	151784407	151784407	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gagcaggaccaggaggtcagAgaccgccaggctgaagaggt	17	9	1	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr5:151784407A>T	ENST00000255262.3	-	1	433	c.268T>A	c.(268-270)Tct>Act	p.S90T	NMUR2_ENST00000518933.1_Intron	NM_020167.4	NP_064552.3	Q9GZQ4	NMUR2_HUMAN	neuromedin U receptor 2	90					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|arachidonic acid secretion (GO:0050482)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell-cell signaling (GO:0007267)|central nervous system development (GO:0007417)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|feeding behavior (GO:0007631)|grooming behavior (GO:0007625)|inositol phosphate-mediated signaling (GO:0048016)|neuropeptide signaling pathway (GO:0007218)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|reduction of food intake in response to dietary excess (GO:0002023)|regulation of smooth muscle contraction (GO:0006940)|response to pain (GO:0048265)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|GTP binding (GO:0005525)|intracellular calcium activated chloride channel activity (GO:0005229)|neuromedin U binding (GO:0042924)|neuromedin U receptor activity (GO:0001607)			breast(1)|endometrium(1)|kidney(2)|large_intestine(12)|liver(1)|lung(15)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	44		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)	Kidney(363;0.000106)|KIRC - Kidney renal clear cell carcinoma(527;0.000672)			AGGAGGTCAGAGACCGCCAGG	0.577																																					p.S90T		Atlas-SNP	.											.	NMUR2	111	.	0			c.T268A						.						103	105	105					5																	151784407		2203	4300	6503	SO:0001583	missense	56923	exon1			GGTCAGAGACCGC	AF242874	CCDS4321.1	5q33.1	2012-08-08		2004-05-28	ENSG00000132911	ENSG00000132911		"GPCR / Class A : Neuromedin U receptors"	16454	protein-coding gene	gene with protein product		605108		NMU2R		8940772, 10894543	Standard	NM_020167		Approved		uc003luv.2	Q9GZQ4	OTTHUMG00000130131	ENST00000255262.3:c.268T>A	chr5.hg19:g.151784407A>T	ENSP00000255262:p.Ser90Thr	100.0	0.0		109.0	56.0	NM_020167	Q7LC54|Q96AM5|Q9NRA6	Missense_Mutation	SNP	ENST00000255262.3	hg19	CCDS4321.1	.	.	.	.	.	.	.	.	.	.	A	16.64	3.179685	0.57800	.	.	ENSG00000132911	ENST00000255262	T	0.72725	-0.68	5.54	5.54	0.83059	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000001	D	0.85427	0.5694	M	0.84846	2.72	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.87908	0.2695	10	0.87932	D	0	-17.1613	14.8781	0.70510	1.0:0.0:0.0:0.0	.	90	Q9GZQ4	NMUR2_HUMAN	T	90	ENSP00000255262:S90T	ENSP00000255262:S90T	S	-	1	0	NMUR2	151764600	1.000000	0.71417	0.316000	0.25252	0.145000	0.21501	8.999000	0.93557	2.108000	0.64289	0.533000	0.62120	TCT	.	.		0.577	NMUR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252439.1	NM_020167		T	151784407	A	T	151784407	3	4	279	1	0	0	0	0	1	0	0	0	10516	304	11	4	995	4	NMUR2	5	151784407	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	3085186	151784407	29130853	127	39886										
SH3PXD2B	285590	hgsc.bcm.edu	37	chr5	171780994	171780994	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gagctgtgtacgggtagatgActgtgtacttctcctctgtg	13	8	2	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr5:171780994A>G	ENST00000311601.5	-	9	853	c.683T>C	c.(682-684)gTc>gCc	p.V228A	SH3PXD2B_ENST00000519643.1_Missense_Mutation_p.V228A	NM_001017995.2	NP_001017995.1	A1X283	SPD2B_HUMAN	SH3 and PX domains 2B	228	SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.				adipose tissue development (GO:0060612)|bone development (GO:0060348)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|eye development (GO:0001654)|heart development (GO:0007507)|podosome assembly (GO:0071800)|positive regulation of fat cell differentiation (GO:0045600)|protein localization to membrane (GO:0072657)|skeletal system development (GO:0001501)|superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|podosome (GO:0002102)	phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|SH2 domain binding (GO:0042169)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0207)|all_neural(177;0.0625)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CGGGTAGATGACTGTGTACTT	0.562																																					p.V228A		Atlas-SNP	.											.	SH3PXD2B	91	.	0			c.T683C						.						94	82	86					5																	171780994		2203	4300	6503	SO:0001583	missense	285590	exon9			TAGATGACTGTGT	AK095834	CCDS34291.1	5q35.2	2008-02-05	2006-02-13	2006-02-13	ENSG00000174705	ENSG00000174705			29242	protein-coding gene	gene with protein product		613293	"KIAA1295"	KIAA1295		10718198	Standard	NM_001017995		Approved	FLJ20831	uc003mbr.3	A1X283	OTTHUMG00000163280	ENST00000311601.5:c.683T>C	chr5.hg19:g.171780994A>G	ENSP00000309714:p.Val228Ala	65.0	0.0		108.0	5.0	NM_001017995	B6F0V2|Q9P2Q1	Missense_Mutation	SNP	ENST00000311601.5	hg19	CCDS34291.1	.	.	.	.	.	.	.	.	.	.	A	13.93	2.384861	0.42308	.	.	ENSG00000174705	ENST00000519643;ENST00000311601	T;T	0.09073	3.02;3.02	5.85	5.85	0.93711	Src homology-3 domain (4);	0.065948	0.64402	D	0.000009	T	0.06690	0.0171	N	0.05050	-0.12	0.58432	D	0.999996	B	0.28400	0.21	B	0.37091	0.241	T	0.49960	-0.8883	10	0.39692	T	0.17	-31.9998	14.1823	0.65583	1.0:0.0:0.0:0.0	.	228	A1X283	SPD2B_HUMAN	A	228	ENSP00000430890:V228A;ENSP00000309714:V228A	ENSP00000309714:V228A	V	-	2	0	SH3PXD2B	171713599	1.000000	0.71417	0.997000	0.53966	0.909000	0.53808	4.209000	0.58493	2.233000	0.73108	0.533000	0.62120	GTC	.	.		0.562	SH3PXD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372449.1	NM_017963		G	171780994	A	G	171780994	3	3	279	1	0	0	0	0	1	0	0	0	14272	275	10	2	2072	2	SH3PXD2B	5	171780994	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	19996587	171780994	9134266	128	39887										
ZNF354C	30832	hgsc.bcm.edu	37	chr5	178506491	178506491	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tcaaagaatccatacaggtgAgaaaccctataaatgtagtg	8	7	1	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr5:178506491A>G	ENST00000315475.6	+	5	1364	c.1058A>G	c.(1057-1059)gAg>gGg	p.E353G		NM_014594.1	NP_055409.1	Q86Y25	Z354C_HUMAN	zinc finger protein 354C	353					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|urinary_tract(3)	30	all_cancers(89;0.00065)|all_epithelial(37;0.000153)|Renal(175;0.000159)|Lung NSC(126;0.00175)|all_lung(126;0.00309)	all_cancers(40;0.19)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.247)		CATACAGGTGAGAAACCCTAT	0.418																																					p.E353G		Atlas-SNP	.											.	ZNF354C	77	.	0			c.A1058G						.						125	134	131					5																	178506491		2203	4300	6503	SO:0001583	missense	30832	exon5			CAGGTGAGAAACC		CCDS4443.1	5q35	2013-01-08			ENSG00000177932	ENSG00000177932		"Zinc fingers, C2H2-type", "-"	16736	protein-coding gene	gene with protein product						10786630	Standard	NM_014594		Approved	KID3	uc003mju.3	Q86Y25	OTTHUMG00000130888	ENST00000315475.6:c.1058A>G	chr5.hg19:g.178506491A>G	ENSP00000324064:p.Glu353Gly	48.0	0.0		82.0	4.0	NM_014594	Q6P4P9|Q8NFX1	Missense_Mutation	SNP	ENST00000315475.6	hg19	CCDS4443.1	.	.	.	.	.	.	.	.	.	.	A	19.90	3.913573	0.72983	.	.	ENSG00000177932	ENST00000315475	T	0.27557	1.66	4.04	4.04	0.47022	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.48960	0.1529	L	0.60957	1.885	0.44745	D	0.997748	D	0.89917	1.0	D	0.77004	0.989	T	0.51100	-0.8748	9	0.87932	D	0	-17.7393	11.2691	0.49127	1.0:0.0:0.0:0.0	.	353	Q86Y25	Z354C_HUMAN	G	353	ENSP00000324064:E353G	ENSP00000324064:E353G	E	+	2	0	ZNF354C	178439097	1.000000	0.71417	0.996000	0.52242	0.865000	0.49528	8.743000	0.91592	1.808000	0.52836	0.482000	0.46254	GAG	.	.		0.418	ZNF354C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253473.2			G	178506491	A	G	178506491	3	3	279	1	0	0	0	0	1	0	0	0	17881	304	11	2	1072	2	ZNF354C	5	178506491	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	6725497	178506491	2408769	129	39888										
CNOT6	57472	hgsc.bcm.edu	37	chr5	179956371	179956371	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tggaaagaaatcccactgggCagagcttgaaataagtggta	12	6	0	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr5:179956371C>G	ENST00000393356.1	+	4	519	c.95C>G	c.(94-96)gCa>gGa	p.A32G	CNOT6_ENST00000502447.1_3'UTR|CNOT6_ENST00000261951.4_Missense_Mutation_p.A32G			Q9ULM6	CNOT6_HUMAN	CCR4-NOT transcription complex, subunit 6	32					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|gene silencing by miRNA (GO:0035195)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, no-go decay (GO:0070966)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of ligand-dependent nuclear receptor transcription coactivator activity (GO:2000327)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	exoribonuclease activity (GO:0004532)|metal ion binding (GO:0046872)|poly(A)-specific ribonuclease activity (GO:0004535)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|skin(1)	23	all_cancers(89;3.3e-05)|all_epithelial(37;7.38e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00543)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.023)		TCCCACTGGGCAGAGCTTGAA	0.408																																					p.A32G		Atlas-SNP	.											.	CNOT6	47	.	0			c.C95G						.						70	81	77					5																	179956371		2203	4300	6503	SO:0001583	missense	57472	exon2			ACTGGGCAGAGCT	AB033020	CCDS4455.1	5q35.3	2014-06-17			ENSG00000113300	ENSG00000113300			14099	protein-coding gene	gene with protein product		608951				11889047	Standard	XM_005265953		Approved	CCR4, KIAA1194, Ccr4a	uc003mlx.3	Q9ULM6	OTTHUMG00000130935	ENST00000393356.1:c.95C>G	chr5.hg19:g.179956371C>G	ENSP00000377024:p.Ala32Gly	202.0	0.0		179.0	39.0	NM_015455	A7MD46|D3DWR0	Missense_Mutation	SNP	ENST00000393356.1	hg19	CCDS4455.1	.	.	.	.	.	.	.	.	.	.	C	15.50	2.853025	0.51270	.	.	ENSG00000113300	ENST00000261951;ENST00000393356;ENST00000504343	T;T;T	0.45668	1.49;1.49;0.89	5.91	4.05	0.47172	.	0.050944	0.85682	D	0.000000	T	0.29524	0.0736	L	0.36672	1.1	0.58432	D	0.999999	B	0.20550	0.046	B	0.23275	0.045	T	0.06588	-1.0818	9	.	.	.	-1.465	7.2312	0.26043	0.1344:0.7203:0.0:0.1453	.	32	Q9ULM6	CNOT6_HUMAN	G	32	ENSP00000261951:A32G;ENSP00000377024:A32G;ENSP00000422087:A32G	.	A	+	2	0	CNOT6	179888977	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	2.985000	0.49362	0.757000	0.33036	-0.136000	0.14681	GCA	.	.		0.408	CNOT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253532.1	NM_015455		G	179956371	C	G	179956371	3	3	279	1	0	0	0	0	1	0	0	0	3624	710	25	4	97	4	CNOT6	5	179956371	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	1449880	179956371	958889	130	39889										
RIOK1	83732	hgsc.bcm.edu	37	chr6	7405545	7405545	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gctctttgaatttgtcacagAtccatccattacacatgaga	6	10	2	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr6:7405545A>G	ENST00000379834.2	+	12	1667	c.1160A>G	c.(1159-1161)gAt>gGt	p.D387G		NM_031480.2|NM_153005.1	NP_113668.2|NP_694550.1	Q9BRS2	RIOK1_HUMAN	RIO kinase 1	387	Protein kinase.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	19	Ovarian(93;0.0418)					TTTGTCACAGATCCATCCATT	0.418																																					p.D387G		Atlas-SNP	.											.	RIOK1	36	.	0			c.A1160G						.						96	81	86					6																	7405545		2203	4300	6503	SO:0001583	missense	83732	exon12			TCACAGATCCATC	BC006104	CCDS4500.1	6p24.3	2012-12-10	2012-12-10		ENSG00000124784	ENSG00000124784			18656	protein-coding gene	gene with protein product			"RIO kinase 1 (yeast)"				Standard	NM_031480		Approved	AD034, FLJ30006, bA288G3.1, RRP10	uc003mxn.3	Q9BRS2	OTTHUMG00000014207	ENST00000379834.2:c.1160A>G	chr6.hg19:g.7405545A>G	ENSP00000369162:p.Asp387Gly	92.0	0.0		93.0	4.0	NM_031480	B2RB28|Q8NDC8|Q96NV9	Missense_Mutation	SNP	ENST00000379834.2	hg19	CCDS4500.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.164814	0.78339	.	.	ENSG00000124784	ENST00000379834	T	0.07021	3.23	5.57	5.57	0.84162	RIO kinase (1);	0.000000	0.85682	D	0.000000	T	0.05547	0.0146	L	0.46157	1.445	0.80722	D	1	P	0.36282	0.546	B	0.40602	0.334	T	0.39742	-0.9599	10	0.27785	T	0.31	-27.8533	14.9078	0.70733	1.0:0.0:0.0:0.0	.	387	Q9BRS2	RIOK1_HUMAN	G	387	ENSP00000369162:D387G	ENSP00000369162:D387G	D	+	2	0	RIOK1	7350544	1.000000	0.71417	0.949000	0.38748	0.989000	0.77384	8.546000	0.90661	2.114000	0.64651	0.455000	0.32223	GAT	.	.		0.418	RIOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039780.2	NM_031480		G	7405545	A	G	7405545	3	3	279	1	0	0	0	0	1	0	0	0	13392	333	12	2	1206	2	RIOK1	6	7405545	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10		7405545	163709522	131	39890										
HIST1H2AC	8334	hgsc.bcm.edu	37	chr6	26124631	26124692	+	Frame_Shift_Del	DEL	GTACCTGACCGCCGAGATCCTGGAGCTGGCCGGCAACGCGGCTCGCGACAACAAGAAGACTC	GTACCTGACCGCCGAGATCCTGGAGCTGGCCGGCAACGCGGCTCGCGACAACAAGAAGACTC	-													0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tacctggcggcggtgttagaGtacctgaccgccgagatcct					rs4645|rs148705455|rs144227315	byFrequency	TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	GTACCTGACCGCCGAGATCCTGGAGCTGGCCGGCAACGCGGCTCGCGACAACAAGAAGACTC	GTACCTGACCGCCGAGATCCTGGAGCTGGCCGGCAACGCGGCTCGCGACAACAAGAAGACTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr6:26124631_26124692delGTACCTGACCGCCGAGATCCTGGAGCTGGCCGGCAACGCGGCTCGCGACAACAAGAAGACTC	ENST00000602637.1	+	1	201_262	c.171_232delGTACCTGACCGCCGAGATCCTGGAGCTGGCCGGCAACGCGGCTCGCGACAACAAGAAGACTC	c.(169-234)gagtacctgaccgccgagatcctggagctggccggcaacgcggctcgcgacaacaagaagactcgcfs	p.YLTAEILELAGNAARDNKKTR58fs	HIST1H2BC_ENST00000314332.5_5'Flank|HIST1H2AC_ENST00000377791.2_Frame_Shift_Del_p.YLTAEILELAGNAARDNKKTR58fs|HIST1H2BC_ENST00000396984.1_5'Flank			Q93077	H2A1C_HUMAN	histone cluster 1, H2ac	58						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.A71T(1)		NS(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|lung(5)	12						CGGTGTTAGAGTACCTGACCGCCGAGATCCTGGAGCTGGCCGGCAACGCGGCTCGCGACAACAAGAAGACTCGCATCATCCC	0.649																																					p.57_77del		Pindel	.											HIST1H2AC,NS,carcinoma,0,1	HIST1H2AC	29	.	1	Substitution - Missense(1)	lung(1)	c.170_231del						.																																			SO:0001589	frameshift_variant	8334	exon1			.	Z80778	CCDS4585.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000180573	ENSG00000180573		"Histones / Replication-dependent"	4733	protein-coding gene	gene with protein product		602794	"H2A histone family, member L", "histone 1, H2ac"	H2AFL		9119399, 12408966	Standard	NM_003512		Approved		uc003ngm.3	Q93077	OTTHUMG00000014428	ENST00000602637.1:c.171_232delGTACCTGACCGCCGAGATCCTGGAGCTGGCCGGCAACGCGGCTCGCGACAACAAGAAGACTC	chr6.hg19:g.26124631_26124692delGTACCTGACCGCCGAGATCCTGGAGCTGGCCGGCAACGCGGCTCGCGACAACAAGAAGACTC	ENSP00000473534:p.Tyr58fs	0.0	0.0		210.0	14.0	NM_003512	B2R4F7|O00775|O00776|O00777|O00778|Q540R1	Frame_Shift_Del	DEL	ENST00000602637.1	hg19	CCDS4585.1																																																																																			.	.		0.649	HIST1H2AC-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000468023.1	NM_003512		-	26124692	GTACCTGACCGCCGAGATCCTGGAGCTGGCCGGCAACGCGGCTCGCGACAACAAGAAGACTC	-	26124631	7	5	279	1	0	1	0	1	0	0	0	0	7139	1020	36	0	173	0	HIST1H2AC	6	26124631	Frame_Shift_Del	DEL	GTACCTGACCGCCGAGATCCTGGAGCTGGCCGGCAACGCGGCTCGCGACAACAAGAAGACTC	TCGA-G3-A3CG-01A-11D-A20W-10	18719086	26124631	144990436	132	39891										
PRSS16	10279	hgsc.bcm.edu	37	chr6	27220676	27220676	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	agcacagaacctcaactgtcTggtgtgggtgaccggcagtg	14	10	2	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr6:27220676T>C	ENST00000230582.3	+	9	1113	c.1098T>C	c.(1096-1098)tcT>tcC	p.S366S	PRSS16_ENST00000377456.2_Intron|PRSS16_ENST00000421826.2_Silent_p.S109S	NM_005865.3	NP_005856.1	Q9NQE7	TSSP_HUMAN	protease, serine, 16 (thymus)	366					protein catabolic process (GO:0030163)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|lysosome (GO:0005764)	serine-type peptidase activity (GO:0008236)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	26						CTCAACTGTCTGGTGTGGGTG	0.507																																					p.S366S	NSCLC(178;1118 2105 17078 23587 44429)	Atlas-SNP	.											.	PRSS16	66	.	0			c.T1098C						.						228	184	199					6																	27220676		2203	4300	6503	SO:0001819	synonymous_variant	10279	exon9			ACTGTCTGGTGTG	AF052514	CCDS4623.1	6p21	2010-05-07			ENSG00000112812	ENSG00000112812		"Serine peptidases / Serine peptidases"	9480	protein-coding gene	gene with protein product		607169				10527559	Standard	NM_005865		Approved	TSSP	uc003nja.3	Q9NQE7	OTTHUMG00000016167	ENST00000230582.3:c.1098T>C	chr6.hg19:g.27220676T>C		201.0	0.0		215.0	83.0	NM_005865	O75416	Silent	SNP	ENST00000230582.3	hg19	CCDS4623.1	.	.	.	.	.	.	.	.	.	.	T	7.642	0.681097	0.14907	.	.	ENSG00000112812	ENST00000485993;ENST00000475106	.	.	.	4.26	-8.51	0.00923	.	.	.	.	.	T	0.27559	0.0677	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.53809	-0.8386	5	0.87932	D	0	-2.633	12.6885	0.56962	0.0:0.118:0.1712:0.7107	.	.	.	.	R	119;145	.	ENSP00000396589:W143R	W	+	1	0	PRSS16	27328655	0.000000	0.05858	0.000000	0.03702	0.069000	0.16628	-2.284000	0.01154	-2.793000	0.00355	-2.020000	0.00432	TGG	.	.		0.507	PRSS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043418.2			C	27220676	T	C	27220676	2	2	279	1	0	0	0	0	0	0	0	1	12628	1567	55	2		2	PRSS16	6	27220676	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	1096045	27220676	143894391	133	39892										
GTF2H4	2968	hgsc.bcm.edu	37	chr6	30880224	30880224	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	aggcaatcgccagtggcatcAcagcccagcaggtattccca	10	14	1	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr6:30880224A>G	ENST00000259895.4	+	11	1301	c.1078A>G	c.(1078-1080)Aca>Gca	p.T360A	VARS2_ENST00000416670.2_5'Flank|GTF2H4_ENST00000376316.2_Missense_Mutation_p.T360A|VARS2_ENST00000542001.1_5'Flank|VARS2_ENST00000541562.1_5'Flank|VARS2_ENST00000321897.5_5'Flank	NM_001517.4	NP_001508.1	Q92759	TF2H4_HUMAN	general transcription factor IIH, polypeptide 4, 52kDa	360					7-methylguanosine mRNA capping (GO:0006370)|ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|gene expression (GO:0010467)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	core TFIIH complex (GO:0000439)|holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)	ATP-dependent DNA helicase activity (GO:0004003)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11						CAGTGGCATCACAGCCCAGCA	0.597								Nucleotide excision repair (NER)																													p.T360A		Atlas-SNP	.											.	GTF2H4	38	.	0			c.A1078G						.						94	90	92					6																	30880224		1511	2709	4220	SO:0001583	missense	2968	exon11			GGCATCACAGCCC	Y07595	CCDS34386.1	6p21.3	2012-11-05	2002-08-29		ENSG00000213780	ENSG00000213780		"General transcription factors", "General transcription factor IIH complex subunits"	4658	protein-coding gene	gene with protein product		601760	"general transcription factor IIH, polypeptide 4 (52kD subunit)"			9118947	Standard	NM_001517		Approved	TFB2, TFIIH, P52	uc003nsa.1	Q92759	OTTHUMG00000031043	ENST00000259895.4:c.1078A>G	chr6.hg19:g.30880224A>G	ENSP00000259895:p.Thr360Ala	82.0	0.0		85.0	4.0	NM_001517	B4DTJ5|Q76KU4	Missense_Mutation	SNP	ENST00000259895.4	hg19	CCDS34386.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.283593	0.80803	.	.	ENSG00000213780	ENST00000259895;ENST00000376316	T;T	0.53857	0.6;0.6	5.31	5.31	0.75309	.	0.000000	0.85682	U	0.000000	T	0.64811	0.2632	M	0.85041	2.73	0.80722	D	1	D;D	0.58620	0.983;0.971	P;P	0.60286	0.832;0.872	T	0.71404	-0.4603	10	0.56958	D	0.05	-16.9388	13.2225	0.59896	1.0:0.0:0.0:0.0	.	366;360	B4DNU0;Q92759	.;TF2H4_HUMAN	A	360	ENSP00000259895:T360A;ENSP00000365493:T360A	ENSP00000259895:T360A	T	+	1	0	GTF2H4	30988203	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.692000	0.91284	2.023000	0.59567	0.482000	0.46254	ACA	.	.		0.597	GTF2H4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076044.3	NM_001517		G	30880224	A	G	30880224	3	3	279	1	0	0	0	0	1	0	0	0	6874	159	6	2	1116	2	GTF2H4	6	30880224	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	3659548	30880224	140234843	134	39893										
DPCR1	135656	hgsc.bcm.edu	37	chr6	30917315	30917315	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gagaataccacactattcccAgcagagcctacagaacatgg	8	12	0	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr6:30917315A>G	ENST00000462446.1	+	2	1102	c.1074A>G	c.(1072-1074)ccA>ccG	p.P358P	DPCR1_ENST00000304311.2_5'UTR|HCG21_ENST00000419481.1_RNA			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	349	Thr-rich.					integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						CACTATTCCCAGCAGAGCCTA	0.478																																					p.P358P		Atlas-SNP	.											.	DPCR1	99	.	0			c.A1074G						.						153	135	141					6																	30917315		692	1591	2283	SO:0001819	synonymous_variant	135656	exon2			ATTCCCAGCAGAG	AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.1074A>G	chr6.hg19:g.30917315A>G		108.0	0.0		98.0	4.0	NM_080870	C9IZC0|Q658M7|Q8WYN2	Silent	SNP	ENST00000462446.1	hg19	CCDS4692.2																																																																																			.	.		0.478	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870		G	30917315	A	G	30917315	2	3	279	1	0	0	0	0	0	0	0	1	4714	175	7	2		2	DPCR1	6	30917315	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	37091	30917315	140197752	135	39894										
CDSN	170679	hgsc.bcm.edu	37	chr6	31084902	31084902	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tacttggaagctgctgctgcTgaactgaaagctgctgctgc	12	10	0	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr6:31084902T>C	ENST00000259881.9	+	1	61				CDSN_ENST00000376288.2_Missense_Mutation_p.S164G|PSORS1C1_ENST00000467107.1_3'UTR	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1											kidney(1)|ovary(2)|prostate(1)|skin(1)	5						CTGCTGCTGCTGAACTGAAAG	0.562																																					p.S164G		Atlas-SNP	.											.	CDSN	48	.	0			c.A490G						.						47	50	49					6																	31084902		2203	4300	6503	SO:0001627	intron_variant	1041	exon2			TGCTGCTGAACTG	AB031479	CCDS34390.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204540	ENSG00000204540			17202	protein-coding gene	gene with protein product		613525	"chromosome 6 open reading frame 16"	C6orf16			Standard	NM_014068		Approved	SEEK1	uc003nsl.2	Q9UIG5	OTTHUMG00000031077	ENST00000259881.9:c.-229+2234T>C	chr6.hg19:g.31084902T>C		74.0	0.0		98.0	4.0	NM_001264	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Missense_Mutation	SNP	ENST00000259881.9	hg19	CCDS34390.1	.	.	.	.	.	.	.	.	.	.	T	0.907	-0.720404	0.03182	.	.	ENSG00000204539	ENST00000376288	T	0.06768	3.26	2.38	-3.88	0.04205	.	.	.	.	.	T	0.01156	0.0038	L	0.38175	1.15	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48068	-0.9067	9	0.07990	T	0.79	.	2.8449	0.05540	0.2082:0.3125:0.0:0.4793	.	164	Q15517	CDSN_HUMAN	G	164	ENSP00000365465:S164G	ENSP00000365465:S164G	S	-	1	0	CDSN	31192881	0.455000	0.25736	0.000000	0.03702	0.001000	0.01503	0.273000	0.18662	-0.510000	0.06523	-0.474000	0.04947	AGC	.	.		0.562	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068		C	31084902	T	C	31084902	1	2	279	0	1	0	0	0	0	0	0	0	3181	1580	55	2		2	CDSN	6	31084902	Intron	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	167587	31084902	140030165	136	39895										
FGD2	221472	hgsc.bcm.edu	37	chr6	36982465	36982465	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gctgcccagcactccaatgcAgccatcactgagatggtaag	10	13	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr6:36982465A>G	ENST00000274963.8	+	7	1038	c.867A>G	c.(865-867)gcA>gcG	p.A289A		NM_173558.3	NP_775829.2	Q7Z6J4	FGD2_HUMAN	FYVE, RhoGEF and PH domain containing 2	289	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	25						ACTCCAATGCAGCCATCACTG	0.612																																					p.A289A		Atlas-SNP	.											.	FGD2	65	.	0			c.A867G						.						69	67	68					6																	36982465		2203	4300	6503	SO:0001819	synonymous_variant	221472	exon7			CAATGCAGCCATC	AK097230	CCDS4829.1	6p21.2	2013-01-10	2004-08-24		ENSG00000146192	ENSG00000146192		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	3664	protein-coding gene	gene with protein product		605091	"FGD1 family, member 2"			10458911	Standard	NM_173558		Approved	ZFYVE4	uc010jwp.1	Q7Z6J4	OTTHUMG00000014616	ENST00000274963.8:c.867A>G	chr6.hg19:g.36982465A>G		102.0	0.0		94.0	4.0	NM_173558	Q5T8I1|Q6P6A8|Q6ZNL5|Q8IZ32|Q8N868|Q9H7M2	Silent	SNP	ENST00000274963.8	hg19	CCDS4829.1																																																																																			.	.		0.612	FGD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040398.2	NM_173558		G	36982465	A	G	36982465	2	3	279	1	0	0	0	0	0	0	0	1	5841	175	7	2		2	FGD2	6	36982465	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	5897563	36982465	134132602	137	39896										
KIF6	221458	hgsc.bcm.edu	37	chr6	39513359	39513359	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ggggaaacatttaagtttacCtttaaatgatgaaaacagtg	9	4	0	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr6:39513359C>T	ENST00000287152.7	-	11	1381	c.1287G>A	c.(1285-1287)aaG>aaA	p.K429K	KIF6_ENST00000373216.3_Splice_Site_p.K429K|KIF6_ENST00000538893.1_Splice_Site_p.K429K|KIF6_ENST00000373215.3_Splice_Site_p.K429K|KIF6_ENST00000373213.4_Splice_Site_p.K268K	NM_145027.4	NP_659464.3	Q6ZMV9	KIF6_HUMAN	kinesin family member 6	429					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|male germ cell nucleus (GO:0001673)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(16)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						TTAAGTTTACCTTTAAATGAT	0.378																																					p.K429K		Atlas-SNP	.											.	KIF6	233	.	0			c.G1287A						.						77	74	75					6																	39513359		2203	4300	6503	SO:0001630	splice_region_variant	221458	exon11			GTTTACCTTTAAA	AL832634	CCDS4844.1, CCDS75449.1	6p21.2	2010-03-30			ENSG00000164627	ENSG00000164627		"Kinesins"	21202	protein-coding gene	gene with protein product		613919	"chromosome 6 open reading frame 102"	C6orf102			Standard	NM_145027		Approved	dJ1043E3.1, MGC33317, dJ137F1.4, dJ188D3.1, DKFZp451I2418	uc003oot.2	Q6ZMV9	OTTHUMG00000014648	ENST00000287152.7:c.1287+1G>A	chr6.hg19:g.39513359C>T		81.0	0.0		54.0	21.0	NM_145027	Q2MDE3|Q2MDE4|Q5T8J6|Q6ZWE3|Q86T87|Q8WTV4	Silent	SNP	ENST00000287152.7	hg19	CCDS4844.1	.	.	.	.	.	.	.	.	.	.	C	13.97	2.396884	0.42512	.	.	ENSG00000164627	ENST00000458470	.	.	.	5.56	5.56	0.83823	.	.	.	.	.	T	0.64170	0.2574	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63075	-0.6718	4	.	.	.	.	15.0307	0.71705	0.0:1.0:0.0:0.0	.	.	.	.	K	321	.	.	R	-	2	0	KIF6	39621337	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	4.095000	0.57728	2.609000	0.88269	0.561000	0.74099	AGA	.	.		0.378	KIF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040455.2	NM_145027	Silent	T	39513359	C	T	39513359	5	4	279	1	0	0	0	0	0	0	1	0	8317	695	24	3	1209	3	KIF6	6	39513359	Splice_Site	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	2530894	39513359	131601708	138	39897										
XPO5	57510	hgsc.bcm.edu	37	chr6	43530011	43530011	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gcacacagctgattgcccagCgcacacaacacctgacagag	9	15	0	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr6:43530011C>T	ENST00000265351.7	-	9	1194	c.984G>A	c.(982-984)gcG>gcA	p.A328A	RP3-337H4.10_ENST00000607635.1_RNA	NM_020750.2	NP_065801.1	Q9HAV4	XPO5_HUMAN	exportin 5	328					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(4)|lung(10)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	34	all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243)		all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524)			GATTGCCCAGCGCACACAACA	0.453																																					p.A328A		Atlas-SNP	.											.	XPO5	79	.	0			c.G984A						.						77	88	84					6																	43530011		2097	4247	6344	SO:0001819	synonymous_variant	57510	exon9			GCCCAGCGCACAC	AB033117	CCDS47430.1	6p21.1	2011-04-13			ENSG00000124571	ENSG00000124571		"Exportins"	17675	protein-coding gene	gene with protein product		607845				11777942, 12426392	Standard	NM_020750		Approved	KIAA1291	uc003ovp.3	Q9HAV4	OTTHUMG00000014742	ENST00000265351.7:c.984G>A	chr6.hg19:g.43530011C>T		98.0	0.0		96.0	4.0	NM_020750	Q5JTE6|Q96G48|Q96HN3|Q9BWM6|Q9BZV5|Q9H9M4|Q9NT89|Q9NW39|Q9ULC9	Silent	SNP	ENST00000265351.7	hg19	CCDS47430.1																																																																																			.	.		0.453	XPO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040657.2	NM_020750		T	43530011	C	T	43530011	2	4	279	1	0	0	0	0	0	0	0	1	17462	755	27	1		1	XPO5	6	43530011	Silent	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	4016652	43530011	127585056	139	39898										
PAQR8	85315	hgsc.bcm.edu	37	chr6	52268756	52268756	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	agcaagcagcctggtaccacAccctccagatcctcttcttc	6	17	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr6:52268756A>G	ENST00000442253.2	+	2	919	c.745A>G	c.(745-747)Acc>Gcc	p.T249A	PAQR8_ENST00000360726.3_Missense_Mutation_p.T249A	NM_133367.4	NP_588608.1	Q8TEZ7	MPRB_HUMAN	progestin and adipoQ receptor family member VIII	249					multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|response to steroid hormone (GO:0048545)|steroid hormone mediated signaling pathway (GO:0043401)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)			endometrium(1)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|skin(1)|urinary_tract(2)	17	Lung NSC(77;0.0875)					CTGGTACCACACCCTCCAGAT	0.592																																					p.T249A		Atlas-SNP	.											.	PAQR8	31	.	0			c.A745G						.						109	101	103					6																	52268756		2203	4300	6503	SO:0001583	missense	85315	exon2			TACCACACCCTCC	AF347029	CCDS4941.1	6p12	2012-08-10	2005-05-20	2005-05-20	ENSG00000170915	ENSG00000170915			15708	protein-coding gene	gene with protein product		607780	"chromosome 6 open reading frame 33"	C6orf33		11676489, 12574519	Standard	NM_133367		Approved	LMPB1, MPRB	uc003pao.4	Q8TEZ7	OTTHUMG00000014846	ENST00000442253.2:c.745A>G	chr6.hg19:g.52268756A>G	ENSP00000406197:p.Thr249Ala	105.0	0.0		126.0	6.0	NM_133367	B2RCF6|Q86WL0|Q8N6D3|Q9HD02	Missense_Mutation	SNP	ENST00000442253.2	hg19	CCDS4941.1	.	.	.	.	.	.	.	.	.	.	A	7.385	0.629660	0.14257	.	.	ENSG00000170915	ENST00000442253;ENST00000360726	T;T	0.27720	1.65;1.65	5.64	3.25	0.37280	.	0.267638	0.38663	N	0.001608	T	0.02727	0.0082	N	0.01493	-0.835	0.36975	D	0.894039	B	0.02656	0.0	B	0.06405	0.002	T	0.33548	-0.9864	9	.	.	.	-9.288	4.4167	0.11459	0.7039:0.0:0.1478:0.1483	.	249	Q8TEZ7	MPRB_HUMAN	A	249	ENSP00000406197:T249A;ENSP00000353953:T249A	.	T	+	1	0	PAQR8	52376715	0.867000	0.29959	1.000000	0.80357	0.998000	0.95712	1.213000	0.32407	0.948000	0.37687	0.533000	0.62120	ACC	.	.		0.592	PAQR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040903.2	NM_133367		G	52268756	A	G	52268756	3	3	279	1	0	0	0	0	1	0	0	0	11450	159	6	2	747	2	PAQR8	6	52268756	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	8738745	52268756	118846311	140	39899										
COL12A1	1303	hgsc.bcm.edu	37	chr6	75893787	75893787	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tagccagtcactggactaggAgatggattccaatttagctt	10	8	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr6:75893787A>G	ENST00000322507.8	-	9	1380	c.1071T>C	c.(1069-1071)tcT>tcC	p.S357S	COL12A1_ENST00000345356.6_Intron|COL12A1_ENST00000416123.2_Silent_p.S357S|COL12A1_ENST00000483888.2_Silent_p.S357S	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	357	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						CTGGACTAGGAGATGGATTCC	0.458																																					p.S357S		Atlas-SNP	.											.	COL12A1	385	.	0			c.T1071C						.						72	69	70					6																	75893787		1942	4151	6093	SO:0001819	synonymous_variant	1303	exon9			ACTAGGAGATGGA	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.1071T>C	chr6.hg19:g.75893787A>G		125.0	0.0		90.0	4.0	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Silent	SNP	ENST00000322507.8	hg19	CCDS43482.1																																																																																			.	.		0.458	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		G	75893787	A	G	75893787	2	3	279	1	0	0	0	0	0	0	0	1	3671	291	11	2		2	COL12A1	6	75893787	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	23625031	75893787	95221280	141	39900										
SENP6	26054	hgsc.bcm.edu	37	chr6	76380428	76380428	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tcttccggctgttaatagagCctgtaattgtaagtacatct	8	8	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr6:76380428C>T	ENST00000447266.2	+	11	1862	c.1384C>T	c.(1384-1386)Cct>Tct	p.P462S	SENP6_ENST00000370014.3_Missense_Mutation_p.P462S|SENP6_ENST00000541192.1_Missense_Mutation_p.P58S|SENP6_ENST00000370010.2_Missense_Mutation_p.P455S|SENP6_ENST00000327284.8_Missense_Mutation_p.P455S	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	462					protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				GTTAATAGAGCCTGTAATTGT	0.313																																					p.P462S		Atlas-SNP	.											SENP6_ENST00000447266,caecum,carcinoma,0,2	SENP6	189	.	0			c.C1384T						.						59	49	52					6																	76380428		1813	4077	5890	SO:0001583	missense	26054	exon11			ATAGAGCCTGTAA		CCDS43483.1, CCDS47454.1	6q13-q14.3	2008-02-05	2005-08-17		ENSG00000112701	ENSG00000112701			20944	protein-coding gene	gene with protein product		605003	"SUMO1/sentrin specific protease 6"				Standard	NM_015571		Approved	SUSP1, KIAA0797	uc003pid.4	Q9GZR1	OTTHUMG00000015060	ENST00000447266.2:c.1384C>T	chr6.hg19:g.76380428C>T	ENSP00000402527:p.Pro462Ser	28.0	0.0		29.0	3.0	NM_015571	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Missense_Mutation	SNP	ENST00000447266.2	hg19	CCDS47454.1	.	.	.	.	.	.	.	.	.	.	C	17.82	3.482375	0.63962	.	.	ENSG00000112701	ENST00000370010;ENST00000370014;ENST00000538088;ENST00000327284;ENST00000447266;ENST00000424947;ENST00000541192	T;T;T;T;T;T	0.32515	2.62;2.65;1.45;2.63;1.46;1.47	5.79	5.79	0.91817	.	0.050110	0.85682	D	0.000000	T	0.45637	0.1352	M	0.67953	2.075	0.48511	D	0.999664	P;D;D	0.76494	0.908;0.999;0.998	P;D;D	0.69142	0.465;0.931;0.962	T	0.08006	-1.0743	10	0.24483	T	0.36	-11.7436	20.0411	0.97590	0.0:1.0:0.0:0.0	.	455;462;455	Q9GZR1-2;Q9GZR1;F8W6D9	.;SENP6_HUMAN;.	S	455;462;311;455;462;352;58	ENSP00000359027:P455S;ENSP00000359031:P462S;ENSP00000321820:P455S;ENSP00000402527:P462S;ENSP00000391426:P352S;ENSP00000441715:P58S	ENSP00000321820:P455S	P	+	1	0	SENP6	76437148	1.000000	0.71417	0.998000	0.56505	0.788000	0.44548	5.356000	0.66052	2.739000	0.93911	0.655000	0.94253	CCT	.	.		0.313	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	NM_015571		T	76380428	C	T	76380428	3	4	279	1	0	0	0	0	1	0	0	0	14065	739	26	3	1426	3	SENP6	6	76380428	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	486641	76380428	94734639	142	39901										
ASCC3	10973	hgsc.bcm.edu	37	chr6	101095306	101095306	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cagagcaatttcaaaaagagCacggacaattctagctgcat	8	9	2	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr6:101095306C>T	ENST00000369162.2	-	21	3618	c.3274G>A	c.(3274-3276)Gct>Act	p.A1092T		NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	1092	SEC63 1.				cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		TCAAAAAGAGCACGGACAATT	0.388																																					p.A1092T		Atlas-SNP	.											ASCC3,NS,carcinoma,0,1	ASCC3	205	.	0			c.G3274A						.						76	75	76					6																	101095306		2203	4300	6503	SO:0001583	missense	10973	exon21			AAAGAGCACGGAC	AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"RNA helicase family"	614217	"helicase, ATP binding 1"	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.3274G>A	chr6.hg19:g.101095306C>T	ENSP00000358159:p.Ala1092Thr	71.0	0.0		64.0	3.0	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Missense_Mutation	SNP	ENST00000369162.2	hg19	CCDS5046.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.891861	0.91889	.	.	ENSG00000112249	ENST00000369162	T	0.68624	-0.34	5.83	5.83	0.93111	Sec63 domain (3);	0.000000	0.85682	D	0.000000	D	0.82733	0.5101	M	0.85777	2.775	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	D	0.84347	0.0530	10	0.87932	D	0	.	20.1208	0.97960	0.0:1.0:0.0:0.0	.	1092	Q8N3C0	HELC1_HUMAN	T	1092	ENSP00000358159:A1092T	ENSP00000358159:A1092T	A	-	1	0	ASCC3	101202027	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.869000	0.69613	2.758000	0.94735	0.655000	0.94253	GCT	.	.		0.388	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828		T	101095306	C	T	101095306	3	4	279	1	0	0	0	0	1	0	0	0	1033	710	25	3	3422	3	ASCC3	6	101095306	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	24714878	101095306	70019761	143	39902										
AIM1	202	hgsc.bcm.edu	37	chr6	106967638	106967638	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	agatttacctccaacggccaTgccaaagccacagcatacat	6	14	0	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr6:106967638T>C	ENST00000369066.3	+	2	1818	c.1331T>C	c.(1330-1332)aTg>aCg	p.M444T		NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		CCAACGGCCATGCCAAAGCCA	0.517																																					p.M444T		Atlas-SNP	.											.	AIM1	161	.	0			c.T1331C						.						111	102	105					6																	106967638		2203	4300	6503	SO:0001583	missense	202	exon2			CGGCCATGCCAAA	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"suppression of tumorigenicity 4", "beta-gamma crystallin domain containing 1"	601797	"suppression of tumorigenicity 4 (malignant melanoma)"	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.1331T>C	chr6.hg19:g.106967638T>C	ENSP00000358062:p.Met444Thr	80.0	0.0		92.0	4.0	NM_001624	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000369066.3	hg19	CCDS34506.1	.	.	.	.	.	.	.	.	.	.	T	1.192	-0.634926	0.03584	.	.	ENSG00000112297	ENST00000285105;ENST00000369066	T	0.70164	-0.46	5.16	-10.3	0.00346	.	2.220720	0.02065	N	0.051066	T	0.14657	0.0354	N	0.02011	-0.69	0.09310	N	0.999996	B	0.02656	0.0	B	0.01281	0.0	T	0.10847	-1.0612	10	0.15499	T	0.54	.	15.7313	0.77807	0.0:0.7598:0.1025:0.1377	.	444	Q9Y4K1	AIM1_HUMAN	T	852;444	ENSP00000358062:M444T	ENSP00000285105:M852T	M	+	2	0	AIM1	107074331	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.641000	0.02007	-2.477000	0.00525	-1.054000	0.02325	ATG	.	.		0.517	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1			C	106967638	T	C	106967638	3	2	279	1	0	0	0	0	1	0	0	0	430	1464	51	2	1337	2	AIM1	6	106967638	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	5872332	106967638	64147429	144	39903										
REV3L	5980	hgsc.bcm.edu	37	chr6	111711382	111711382	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	aacaccttccaatattaaagAgctgcaattaaaggatataa	5	7	0	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr6:111711382A>G	ENST00000358835.3	-	7	1118	c.664T>C	c.(664-666)Tct>Cct	p.S222P	REV3L_ENST00000368802.3_Splice_Site_p.S222P|REV3L_ENST00000435970.1_Splice_Site_p.S144P|REV3L_ENST00000368805.1_Splice_Site_p.S222P			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	222					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		AATATTAAAGAGCTGCAATTA	0.318								DNA polymerases (catalytic subunits)																													p.S222P		Atlas-SNP	.											.	REV3L	386	.	0			c.T664C						.						84	82	83					6																	111711382		2203	4300	6503	SO:0001630	splice_region_variant	5980	exon6			TTAAAGAGCTGCA	AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"DNA polymerases"	9968	protein-coding gene	gene with protein product	"polymerase, DNA, zeta"	602776	"REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta", "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.663-1T>C	chr6.hg19:g.111711382A>G		134.0	0.0		104.0	6.0	NM_002912	O43214|Q5TC33	Missense_Mutation	SNP	ENST00000358835.3	hg19	CCDS5091.2	.	.	.	.	.	.	.	.	.	.	A	16.91	3.252267	0.59212	.	.	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970	T;T;T;T	0.01804	4.75;4.75;4.75;4.63	4.85	4.85	0.62838	Ribonuclease H-like (1);	1.343540	0.04556	N	0.390814	T	0.02267	0.0070	L	0.45581	1.43	0.43698	D	0.996156	P	0.46395	0.877	P	0.48524	0.58	T	0.48091	-0.9065	10	0.42905	T	0.14	-10.0183	14.7192	0.69294	1.0:0.0:0.0:0.0	.	222	O60673	DPOLZ_HUMAN	P	222;222;222;144	ENSP00000357792:S222P;ENSP00000357795:S222P;ENSP00000351697:S222P;ENSP00000402003:S144P	ENSP00000351697:S222P	S	-	1	0	REV3L	111818075	1.000000	0.71417	1.000000	0.80357	0.428000	0.31595	6.103000	0.71492	1.939000	0.56221	0.377000	0.23210	TCT	.	.		0.318	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912	Missense_Mutation	G	111711382	A	G	111711382	5	3	279	1	0	0	0	0	0	0	1	0	13255	318	11	2	8836	2	REV3L	6	111711382	Splice_Site	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	4743744	111711382	59403685	145	39904										
VNN1	8876	hgsc.bcm.edu	37	chr6	133035128	133035128	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cctggcagctggctcttgagAcatagaaaagcaaaattgcc	10	10	1	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr6:133035128A>G	ENST00000367928.4	-	1	60	c.47T>C	c.(46-48)gTc>gCc	p.V16A		NM_004666.2	NP_004657.2	O95497	VNN1_HUMAN	vanin 1	16					acute inflammatory response (GO:0002526)|cellular component movement (GO:0006928)|chronic inflammatory response (GO:0002544)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|pantothenate metabolic process (GO:0015939)|positive regulation of T cell differentiation in thymus (GO:0033089)|response to oxidative stress (GO:0006979)|single organismal cell-cell adhesion (GO:0016337)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	GPI anchor binding (GO:0034235)|pantetheine hydrolase activity (GO:0017159)			NS(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)	31	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.0027)|GBM - Glioblastoma multiforme(226;0.0189)		GGCTCTTGAGACATAGAAAAG	0.473																																					p.V16A		Atlas-SNP	.											.	VNN1	69	.	0			c.T47C						.						66	59	61					6																	133035128		2203	4300	6503	SO:0001583	missense	8876	exon1			CTTGAGACATAGA	AJ132099	CCDS5159.1	6q23-q24	2013-02-13			ENSG00000112299	ENSG00000112299	3.5.1.92	"Vanins"	12705	protein-coding gene	gene with protein product		603570				9790769	Standard	NM_004666		Approved	Tiff66	uc003qdo.3	O95497	OTTHUMG00000015587	ENST00000367928.4:c.47T>C	chr6.hg19:g.133035128A>G	ENSP00000356905:p.Val16Ala	80.0	0.0		48.0	4.0	NM_004666	A8K310|Q4JFW6|Q4VAS7|Q4VAS8|Q4VAS9|Q9UF16|Q9UJF4	Missense_Mutation	SNP	ENST00000367928.4	hg19	CCDS5159.1	.	.	.	.	.	.	.	.	.	.	A	3.015	-0.202955	0.06219	.	.	ENSG00000112299	ENST00000367928	D	0.87809	-2.3	5.38	2.67	0.31697	Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (1);	0.481828	0.20504	N	0.091031	T	0.56077	0.1961	L	0.35414	1.06	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.43814	-0.9368	10	0.09338	T	0.73	-12.464	4.7387	0.13001	0.6418:0.166:0.1922:0.0	.	16	O95497	VNN1_HUMAN	A	16	ENSP00000356905:V16A	ENSP00000356905:V16A	V	-	2	0	VNN1	133076821	0.001000	0.12720	0.004000	0.12327	0.006000	0.05464	0.605000	0.24179	0.898000	0.36418	0.454000	0.30748	GTC	.	.		0.473	VNN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042263.1			G	133035128	A	G	133035128	3	3	279	1	0	0	0	0	1	0	0	0	17197	275	10	2	1522	2	VNN1	6	133035128	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	21323746	133035128	38079939	146	39905										
BCLAF1	9774	hgsc.bcm.edu	37	chr6	136599813	136599813	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ttcctctgtacccataaggtCgtctcattcctctattattt	4	12	3	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr6:136599813C>A	ENST00000531224.1	-	4	458	c.206G>T	c.(205-207)cGa>cTa	p.R69L	BCLAF1_ENST00000527759.1_Missense_Mutation_p.R67L|BCLAF1_ENST00000353331.4_Missense_Mutation_p.R67L|BCLAF1_ENST00000527536.1_Missense_Mutation_p.R69L|BCLAF1_ENST00000392348.2_Missense_Mutation_p.R67L|BCLAF1_ENST00000530767.1_Missense_Mutation_p.R69L	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1	69					apoptotic process (GO:0006915)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA-templated transcription, initiation (GO:2000144)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of response to DNA damage stimulus (GO:2001022)|regulation of DNA-templated transcription in response to stress (GO:0043620)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			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)		CCCATAAGGTCGTCTCATTCC	0.433																																					p.R69L	Colon(142;1534 1789 5427 7063 28491)	Atlas-SNP	.											BCLAF1_ENST00000531224,colon,carcinoma,0,1	BCLAF1	203	.	0			c.G206T						.						85	82	83					6																	136599813		2203	4300	6503	SO:0001583	missense	9774	exon4			TAAGGTCGTCTCA	AF249273	CCDS5177.1, CCDS47485.1, CCDS47486.1, CCDS75525.1	6q22-q23	2007-03-02			ENSG00000029363	ENSG00000029363			16863	protein-coding gene	gene with protein product		612588				8724849, 10330179	Standard	NM_001077440		Approved	KIAA0164, BTF	uc003qgx.1	Q9NYF8	OTTHUMG00000033323	ENST00000531224.1:c.206G>T	chr6.hg19:g.136599813C>A	ENSP00000435210:p.Arg69Leu	149.0	0.0		106.0	25.0	NM_014739	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Missense_Mutation	SNP	ENST00000531224.1	hg19	CCDS5177.1	.	.	.	.	.	.	.	.	.	.	C	16.29	3.082433	0.55861	.	.	ENSG00000029363	ENST00000531224;ENST00000353331;ENST00000527536;ENST00000530767;ENST00000527759;ENST00000392348;ENST00000529826	T;T;T;T;T;T;T	0.55588	0.87;0.62;0.67;0.51;0.81;0.62;0.54	5.64	4.78	0.61160	.	0.000000	0.52532	D	0.000064	T	0.39835	0.1093	M	0.64997	1.995	0.80722	D	1	P;B;P;P	0.38455	0.491;0.275;0.491;0.632	B;B;B;B	0.37833	0.204;0.134;0.204;0.259	T	0.50363	-0.8837	10	0.87932	D	0	-4.5909	14.4744	0.67537	0.0:0.9293:0.0:0.0707	.	67;67;69;69	Q9NYF8-2;Q9NYF8-3;Q9NYF8;Q9NYF8-4	.;.;BCLF1_HUMAN;.	L	69;67;69;69;67;67;69	ENSP00000435210:R69L;ENSP00000229446:R67L;ENSP00000435441:R69L;ENSP00000436501:R69L;ENSP00000434826:R67L;ENSP00000376159:R67L;ENSP00000431734:R69L	ENSP00000229446:R67L	R	-	2	0	BCLAF1	136641506	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.655000	0.67981	1.392000	0.46585	0.557000	0.71058	CGA	.	.		0.433	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739		A	136599813	C	A	136599813	3	1	279	1	0	0	0	0	1	0	0	0	1383	884	31	1	2596	1	BCLAF1	6	136599813	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	3564685	136599813	34515254	147	39906										
C6orf211	79624	hgsc.bcm.edu	37	chr6	151775692	151775692	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ctcttttctagatcatttgcAtatcttacaattaaagacag	4	8	4	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr6:151775692A>G	ENST00000367294.3	+	2	310	c.51A>G	c.(49-51)gcA>gcG	p.A17A	C6orf211_ENST00000483931.1_3'UTR|RMND1_ENST00000367303.4_5'Flank|C6orf211_ENST00000545879.1_Intron	NM_024573.1	NP_078849.1	Q9H993	CF211_HUMAN	chromosome 6 open reading frame 211	17										breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(7)	15			BRCA - Breast invasive adenocarcinoma(37;0.183)	OV - Ovarian serous cystadenocarcinoma(155;5.27e-11)		GATCATTTGCATATCTTACAA	0.318																																					p.A17A		Atlas-SNP	.											C6orf211,NS,carcinoma,0,1	C6orf211	30	.	0			c.A51G						.						98	97	97					6																	151775692		2203	4289	6492	SO:0001819	synonymous_variant	79624	exon2			ATTTGCATATCTT	AJ420548	CCDS5233.1, CCDS69224.1	6q25.1	2013-01-07			ENSG00000146476	ENSG00000146476			17872	protein-coding gene	gene with protein product							Standard	NM_001286562		Approved	FLJ12910	uc003qok.1	Q9H993	OTTHUMG00000015838	ENST00000367294.3:c.51A>G	chr6.hg19:g.151775692A>G		100.0	0.0		85.0	4.0	NM_024573	Q96FC6|Q9UFY5	Silent	SNP	ENST00000367294.3	hg19	CCDS5233.1																																																																																			.	.		0.318	C6orf211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042724.1	NM_024573		G	151775692	A	G	151775692	2	3	279	1	0	0	0	0	0	0	0	1	2356	204	8	2		2	C6orf211	6	151775692	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	15175879	151775692	19339375	148	39907										
C6orf97	80129	hgsc.bcm.edu	37	chr6	151917535	151917535	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	agcctcctccggcagaaaatAgcccagctggaggaggagaa	13	11	0	2	rs549058340		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr6:151917535A>G	ENST00000239374.7	+	9	1632	c.1533A>G	c.(1531-1533)atA>atG	p.I511M	CCDC170_ENST00000367290.5_Missense_Mutation_p.I511M	NM_025059.3	NP_079335.2	Q8IYT3	CC170_HUMAN	coiled-coil domain containing 170	511																	GGCAGAAAATAGCCCAGCTGG	0.493																																					p.I511M		Atlas-SNP	.											.	.	.	.	0			c.A1533G						.						53	59	57					6																	151917535		2113	4253	6366	SO:0001583	missense	80129	exon9			GAAAATAGCCCAG	AK026958	CCDS43515.1	6q25.1	2012-03-26	2012-03-26	2012-03-26	ENSG00000120262	ENSG00000120262			21177	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 97"	C6orf97			Standard	NM_025059		Approved	FLJ23305, bA282P11.1	uc003qol.3	Q8IYT3	OTTHUMG00000015839	ENST00000239374.7:c.1533A>G	chr6.hg19:g.151917535A>G	ENSP00000239374:p.Ile511Met	80.0	0.0		51.0	4.0	NM_025059	Q5VXB7|Q6P9E4|Q96KA9|Q9H5M3	Missense_Mutation	SNP	ENST00000239374.7	hg19	CCDS43515.1	.	.	.	.	.	.	.	.	.	.	A	13.54	2.267457	0.40095	.	.	ENSG00000120262	ENST00000239374;ENST00000367290	T;T	0.09445	2.98;2.98	5.63	-7.73	0.01245	.	0.275715	0.35772	N	0.002990	T	0.04407	0.0121	M	0.76574	2.34	0.24200	N	0.995517	P	0.42692	0.787	B	0.42522	0.39	T	0.01185	-1.1425	10	0.48119	T	0.1	-7.639	8.7763	0.34765	0.1923:0.2769:0.0:0.5308	.	511	Q8IYT3	CF097_HUMAN	M	511	ENSP00000239374:I511M;ENSP00000356259:I511M	ENSP00000239374:I511M	I	+	3	3	C6orf97	151959228	0.000000	0.05858	0.144000	0.22314	0.955000	0.61496	-0.645000	0.05409	-1.709000	0.01399	-0.291000	0.09656	ATA	.	.		0.493	CCDC170-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042727.2	NM_025059		G	151917535	A	G	151917535	3	3	279	1	0	0	0	0	1	0	0	0	2376	410	15	2	1567	2	C6orf97	6	151917535	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	141843	151917535	19197532	149	39908										
PLG	5340	hgsc.bcm.edu	37	chr6	161158038	161158038	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ggcaagtcagtcttagaacaAggtaagaacaggcccagaaa	11	8	2	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr6:161158038A>C	ENST00000308192.9	+	14	1864	c.1801A>C	c.(1801-1803)Agg>Cgg	p.R601R		NM_000301.3	NP_000292.1	P00747	PLMN_HUMAN	plasminogen	601	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of fibrinolysis (GO:0051918)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of fibrinolysis (GO:0051919)|tissue remodeling (GO:0048771)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	apolipoprotein binding (GO:0034185)|protein domain specific binding (GO:0019904)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)	59				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Alteplase(DB00009)|Aminocaproic Acid(DB00513)|Anistreplase(DB00029)|Aprotinin(DB06692)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Tranexamic Acid(DB00302)|Urokinase(DB00013)	TCTTAGAACAAGGTAAGAACA	0.512																																					p.R601R		Atlas-SNP	.											.	PLG	150	.	0			c.A1801C						.						68	66	66					6																	161158038		2203	4300	6503	SO:0001630	splice_region_variant	5340	exon14			AGAACAAGGTAAG	M74220	CCDS5279.1, CCDS55074.1	6q26	2012-10-02			ENSG00000122194	ENSG00000122194			9071	protein-coding gene	gene with protein product		173350					Standard	NM_000301		Approved		uc003qtm.4	P00747	OTTHUMG00000015957	ENST00000308192.9:c.1802+1A>C	chr6.hg19:g.161158038A>C		89.0	0.0		60.0	45.0	NM_000301	Q15146|Q5TEH4|Q6PA00	Silent	SNP	ENST00000308192.9	hg19	CCDS5279.1																																																																																			.	.		0.512	PLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042959.2	NM_000301	Silent	C	161158038	A	C	161158038	5	2	279	1	0	0	0	0	0	0	1	0	12095	86	3	5	1859	5	PLG	6	161158038	Splice_Site	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	9240503	161158038	9957029	150	39909										
GPNMB	10457	hgsc.bcm.edu	37	chr7	23313776	23313776	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tctcaaccgtgcaaaagccgTgttcttcccgggaaaccagg	10	13	2	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr7:23313776T>C	ENST00000381990.2	+	11	1813	c.1652T>C	c.(1651-1653)gTg>gCg	p.V551A	GPNMB_ENST00000539136.1_Missense_Mutation_p.V440A|GPNMB_ENST00000258733.4_Missense_Mutation_p.V539A|GPNMB_ENST00000478451.1_3'UTR|GPNMB_ENST00000453162.2_Missense_Mutation_p.V493A	NM_001005340.1|NM_002510.2	NP_001005340.1|NP_002501.1	Q14956	GPNMB_HUMAN	glycoprotein (transmembrane) nmb	551					bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|negative regulation of cell proliferation (GO:0008285)|osteoblast differentiation (GO:0001649)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)			breast(5)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(3)|stomach(2)	41			GBM - Glioblastoma multiforme(13;0.154)			GCAAAAGCCGTGTTCTTCCCG	0.418																																					p.V551A		Atlas-SNP	.											.	GPNMB	88	.	0			c.T1652C						.						90	92	91					7																	23313776		2203	4300	6503	SO:0001583	missense	10457	exon11			AAGCCGTGTTCTT	X76534	CCDS5380.1, CCDS34610.1	7p	2008-07-18			ENSG00000136235	ENSG00000136235			4462	protein-coding gene	gene with protein product	"transmembrane glycoprotein", "glycoprotein NMB", "glycoprotein nmb-like protein", "osteoactivin"	604368				7814155	Standard	NM_002510		Approved	NMB, HGFIN	uc003swc.3	Q14956	OTTHUMG00000022811	ENST00000381990.2:c.1652T>C	chr7.hg19:g.23313776T>C	ENSP00000371420:p.Val551Ala	98.0	0.0		117.0	5.0	NM_001005340	A4D155|Q6UVX1|Q8N1A1	Missense_Mutation	SNP	ENST00000381990.2	hg19	CCDS34610.1	.	.	.	.	.	.	.	.	.	.	T	6.390	0.440007	0.12104	.	.	ENSG00000136235	ENST00000258733;ENST00000435486;ENST00000381990;ENST00000425903;ENST00000539136;ENST00000453162	T;T;T;T	0.14391	2.51;2.54;2.51;2.55	6.07	-6.49	0.01890	.	1.456020	0.04090	N	0.311192	T	0.08088	0.0202	L	0.38175	1.15	0.09310	N	1	B;B;B;B	0.10296	0.002;0.003;0.001;0.001	B;B;B;B	0.11329	0.005;0.006;0.002;0.001	T	0.33879	-0.9851	10	0.13108	T	0.6	0.7629	2.908	0.05727	0.094:0.325:0.1921:0.3888	.	440;493;551;539	F6SKP1;F5GY20;Q14956;Q14956-2	.;.;GPNMB_HUMAN;.	A	539;586;551;434;440;493	ENSP00000258733:V539A;ENSP00000371420:V551A;ENSP00000445266:V440A;ENSP00000405586:V493A	ENSP00000258733:V539A	V	+	2	0	GPNMB	23280301	0.000000	0.05858	0.000000	0.03702	0.067000	0.16453	0.086000	0.14935	-1.241000	0.02526	0.533000	0.62120	GTG	.	.		0.418	GPNMB-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327152.1	NM_001005340		C	23313776	T	C	23313776	3	2	279	1	0	0	0	0	1	0	0	0	6628	1696	59	2	1694	2	GPNMB	7	23313776	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10		23313776	135824887	151	39910										
UPP1	7378	hgsc.bcm.edu	37	chr7	48147063	48147063	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ccgcaatatcgagatggagtCctcggtgtttgccgccatgt	12	11	0	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr7:48147063C>T	ENST00000331803.4	+	9	1375	c.752C>T	c.(751-753)tCc>tTc	p.S251F	UPP1_ENST00000429491.2_Missense_Mutation_p.S114F|UPP1_ENST00000482015.1_3'UTR|UPP1_ENST00000395564.4_Missense_Mutation_p.S251F|UPP1_ENST00000341253.4_Missense_Mutation_p.S251F			Q16831	UPP1_HUMAN	uridine phosphorylase 1	251					cellular response to glucose starvation (GO:0042149)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide catabolic process (GO:0009166)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside salvage (GO:0043097)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)|uridine metabolic process (GO:0046108)	cytosol (GO:0005829)	uridine phosphorylase activity (GO:0004850)			breast(1)|endometrium(2)|large_intestine(1)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	18					Fluorouracil(DB00544)	GAGATGGAGTCCTCGGTGTTT	0.632																																					p.S251F		Atlas-SNP	.											.	UPP1	35	.	0			c.C752T						.						73	67	69					7																	48147063		2203	4300	6503	SO:0001583	missense	7378	exon8			TGGAGTCCTCGGT	AK096167	CCDS5507.1	7p12.3	2012-10-02	2003-08-28	2003-08-29	ENSG00000183696	ENSG00000183696	2.4.2.3		12576	protein-coding gene	gene with protein product		191730	"uridine phosphorylase"	UP		752472, 11807789	Standard	NM_003364		Approved	UPASE, UPP, UDRPASE	uc003toj.3	Q16831	OTTHUMG00000129253	ENST00000331803.4:c.752C>T	chr7.hg19:g.48147063C>T	ENSP00000330032:p.Ser251Phe	102.0	0.0		143.0	31.0	NM_003364	D3DVM4|Q15362	Missense_Mutation	SNP	ENST00000331803.4	hg19	CCDS5507.1	.	.	.	.	.	.	.	.	.	.	C	19.32	3.804604	0.70682	.	.	ENSG00000183696	ENST00000331803;ENST00000341253;ENST00000395564;ENST00000429491	D;D;D;D	0.88586	-2.4;-2.4;-2.4;-2.4	5.59	5.59	0.84812	Nucleoside phosphorylase domain (1);	0.052450	0.85682	D	0.000000	D	0.95953	0.8682	M	0.92219	3.285	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.79784	0.993;0.989	D	0.96640	0.9473	10	0.87932	D	0	-24.6892	18.5698	0.91130	0.0:1.0:0.0:0.0	.	114;251	Q86Y75;Q16831	.;UPP1_HUMAN	F	251;251;251;114	ENSP00000330032:S251F;ENSP00000342878:S251F;ENSP00000378931:S251F;ENSP00000406224:S114F	ENSP00000330032:S251F	S	+	2	0	UPP1	48113588	1.000000	0.71417	0.437000	0.26809	0.114000	0.19823	7.462000	0.80851	2.608000	0.88229	0.650000	0.86243	TCC	.	.		0.632	UPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251360.1	NM_003364		T	48147063	C	T	48147063	3	4	279	1	0	0	0	0	1	0	0	0	17027	855	30	3	774	3	UPP1	7	48147063	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	24833287	48147063	110991600	152	39911										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48317894	48317894	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	catgcaagatttatttaatgCccttctcagggaaacttcaa	6	9	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr7:48317894C>A	ENST00000435803.1	+	18	7127	c.7103C>A	c.(7102-7104)gCc>gAc	p.A2368D		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	2368					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						TTATTTAATGCCCTTCTCAGG	0.308																																					p.A2368D		Atlas-SNP	.											.	ABCA13	1192	.	0			c.C7103A						.						40	40	40					7																	48317894		1803	4069	5872	SO:0001583	missense	154664	exon18			TTAATGCCCTTCT	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.7103C>A	chr7.hg19:g.48317894C>A	ENSP00000411096:p.Ala2368Asp	86.0	0.0		70.0	29.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	C	10.76	1.440374	0.25900	.	.	ENSG00000179869	ENST00000435803	T	0.55760	0.5	4.75	1.32	0.21799	.	1.533400	0.04221	N	0.333578	T	0.44095	0.1277	L	0.44542	1.39	0.09310	N	1	B	0.20052	0.041	B	0.19391	0.025	T	0.39840	-0.9594	10	0.72032	D	0.01	.	2.659	0.05020	0.2212:0.501:0.0:0.2778	.	2368	Q86UQ4	ABCAD_HUMAN	D	2368	ENSP00000411096:A2368D	ENSP00000411096:A2368D	A	+	2	0	ABCA13	48288440	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.498000	0.06420	0.517000	0.28361	0.561000	0.74099	GCC	.	.		0.308	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		A	48317894	C	A	48317894	3	1	279	1	0	0	0	0	1	0	0	0	31	739	26	3	7002	3	ABCA13	7	48317894	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	170831	48317894	110820769	153	39912										
COBL	23242	hgsc.bcm.edu	37	chr7	51097117	51097117	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	acccagcattgttgtttctaTtggaaaacaaccccgaatcc	6	12	1	0	rs376884962		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr7:51097117T>C	ENST00000265136.7	-	10	1841	c.1676A>G	c.(1675-1677)aAt>aGt	p.N559S	COBL_ENST00000395542.2_Missense_Mutation_p.N641S	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	559					actin filament network formation (GO:0051639)|actin filament polymerization (GO:0030041)|collateral sprouting in absence of injury (GO:0048669)|digestive tract development (GO:0048565)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|liver development (GO:0001889)|neural tube closure (GO:0001843)|notochord development (GO:0030903)|positive regulation of dendrite development (GO:1900006)|somite specification (GO:0001757)	actin filament (GO:0005884)|axon (GO:0030424)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic growth cone (GO:0044294)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)			NS(2)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(26)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Glioma(55;0.08)					GTTGTTTCTATTGGAAAACAA	0.527																																					p.N559S	NSCLC(189;2119 2138 12223 30818 34679)	Atlas-SNP	.											.	COBL	167	.	0			c.A1676G						.	T	SER/ASN	0,4406		0,0,2203	71	64	66		1676	4.7	0.1	7		66	1,8599	1.2+/-3.3	0,1,4299	no	missense	COBL	NM_015198.3	46	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	benign	559/1262	51097117	1,13005	2203	4300	6503	SO:0001583	missense	23242	exon10			TTTCTATTGGAAA	AB014533	CCDS34637.1, CCDS75601.1, CCDS75602.1	7p12.2-p12.1	2012-12-07	2012-12-07		ENSG00000106078	ENSG00000106078			22199	protein-coding gene	gene with protein product		610317	"cordon-bleu homolog (mouse)"				Standard	NM_015198		Approved	KIAA0633	uc003tpr.4	O75128	OTTHUMG00000155999	ENST00000265136.7:c.1676A>G	chr7.hg19:g.51097117T>C	ENSP00000265136:p.Asn559Ser	102.0	0.0		142.0	30.0	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Missense_Mutation	SNP	ENST00000265136.7	hg19	CCDS34637.1	.	.	.	.	.	.	.	.	.	.	T	8.495	0.863008	0.17178	0.0	1.16E-4	ENSG00000106078	ENST00000265136;ENST00000445054;ENST00000431948;ENST00000395542;ENST00000457306	T;T;T;T	0.26660	1.72;1.72;1.72;1.72	5.82	4.68	0.58851	.	0.136517	0.33875	N	0.004466	T	0.24084	0.0583	L	0.36672	1.1	0.20074	N	0.999933	P;P;B;B;P	0.49358	0.923;0.923;0.18;0.312;0.791	P;B;B;B;B	0.47470	0.548;0.397;0.054;0.067;0.181	T	0.06752	-1.0809	10	0.29301	T	0.29	.	9.0662	0.36465	0.0:0.0838:0.0:0.9162	.	559;616;559;641;101	O75128-3;O75128-7;O75128;O75128-2;O75128-6	.;.;COBL_HUMAN;.;.	S	559;451;444;641;57	ENSP00000265136:N559S;ENSP00000401204:N451S;ENSP00000413498:N444S;ENSP00000378912:N641S	ENSP00000265136:N559S	N	-	2	0	COBL	51064611	0.997000	0.39634	0.126000	0.21872	0.051000	0.14879	3.135000	0.50546	1.043000	0.40175	0.528000	0.53228	AAT	.	.		0.527	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198		C	51097117	T	C	51097117	3	2	279	1	0	0	0	0	1	0	0	0	3655	1493	52	2	2125	2	COBL	7	51097117	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	2779223	51097117	108041546	154	39913										
PCLO	27445	hgsc.bcm.edu	37	chr7	82581498	82581498	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	caacgggtttttcatcttctAttattttggtcatcacactt	5	9	5	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr7:82581498A>T	ENST00000333891.9	-	5	9108	c.8771T>A	c.(8770-8772)aTa>aAa	p.I2924K	PCLO_ENST00000437081.1_5'Flank|PCLO_ENST00000423517.2_Missense_Mutation_p.I2924K	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TTCATCTTCTATTATTTTGGT	0.433																																					p.I2924K		Atlas-SNP	.											Q9Y6V0-3,colon,carcinoma,-1,3	PCLO	1506	.	0			c.T8771A						.						145	142	143					7																	82581498		1909	4123	6032	SO:0001583	missense	27445	exon5			TCTTCTATTATTT	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.8771T>A	chr7.hg19:g.82581498A>T	ENSP00000334319:p.Ile2924Lys	44.0	0.0		69.0	4.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	A	12.71	2.018568	0.35606	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.19394	2.15;2.16	5.68	5.68	0.88126	.	.	.	.	.	T	0.30696	0.0773	L	0.50333	1.59	0.80722	D	1	P;P	0.46220	0.874;0.874	P;P	0.48227	0.447;0.571	T	0.02758	-1.1114	9	0.87932	D	0	.	15.9242	0.79603	1.0:0.0:0.0:0.0	.	2924;2924	Q9Y6V0-5;Q9Y6V0-6	.;.	K	2855;2924;2924	ENSP00000334319:I2924K;ENSP00000388393:I2924K	ENSP00000334319:I2924K	I	-	2	0	PCLO	82419434	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	6.606000	0.74159	2.152000	0.67230	0.460000	0.39030	ATA	.	.		0.433	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		T	82581498	A	T	82581498	3	4	279	1	0	0	0	0	1	0	0	0	11592	449	16	4	6758	4	PCLO	7	82581498	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	31484381	82581498	76557165	155	39914										
CCDC132	55610	hgsc.bcm.edu	37	chr7	92888896	92888896	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	aggagctattcagttgtgccTtgaatgtcaaaaagctgcca	10	8	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr7:92888896T>C	ENST00000305866.5	+	9	739	c.611T>C	c.(610-612)cTt>cCt	p.L204P	CCDC132_ENST00000251739.5_Missense_Mutation_p.L204P|CCDC132_ENST00000541136.1_Missense_Mutation_p.L15P|CCDC132_ENST00000535481.1_Intron|CCDC132_ENST00000317751.6_5'UTR|CCDC132_ENST00000544910.1_Missense_Mutation_p.L174P	NM_017667.3	NP_060137.2	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132	204						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|lung(5)	8	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)			CAGTTGTGCCTTGAATGTCAA	0.348																																					p.L204P		Atlas-SNP	.											.	CCDC132	136	.	0			c.T611C						.						88	88	88					7																	92888896		2203	4300	6503	SO:0001583	missense	55610	exon9			TGTGCCTTGAATG	AL833112, AK055965, AL832393	CCDS5630.1, CCDS43617.1, CCDS59065.1	7q21.3	2007-07-23			ENSG00000004766	ENSG00000004766			25956	protein-coding gene	gene with protein product						11347906	Standard	NM_024553		Approved	KIAA1861, FLJ20097, DKFZp313I2429	uc003umo.4	Q96JG6	OTTHUMG00000131733	ENST00000305866.5:c.611T>C	chr7.hg19:g.92888896T>C	ENSP00000307666:p.Leu204Pro	56.0	0.0		65.0	4.0	NM_024553	B3KX22|D1MQ00|F5H5U7|Q75N07|Q8WVK3|Q9H5C6	Missense_Mutation	SNP	ENST00000305866.5	hg19	CCDS43617.1	.	.	.	.	.	.	.	.	.	.	T	25.1	4.602384	0.87157	.	.	ENSG00000004766	ENST00000251739;ENST00000305866;ENST00000544910;ENST00000541136	T	0.31769	1.48	5.25	5.25	0.73442	Vacuolar protein sorting-associated protein 54 (1);	0.000000	0.85682	D	0.000000	T	0.53932	0.1827	M	0.74881	2.28	0.80722	D	1	D;D;D	0.71674	0.986;0.998;0.992	P;D;P	0.70016	0.862;0.967;0.898	T	0.52109	-0.8619	10	0.30078	T	0.28	-2.7577	15.4567	0.75321	0.0:0.0:0.0:1.0	.	174;204;204	F5H5U7;Q96JG6;Q96JG6-2	.;CC132_HUMAN;.	P	204;204;174;15	ENSP00000251739:L204P	ENSP00000251739:L204P	L	+	2	0	CCDC132	92726832	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.040000	0.89188	2.109000	0.64355	0.533000	0.62120	CTT	.	.		0.348	CCDC132-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341687.1	NM_017667		C	92888896	T	C	92888896	3	2	279	1	0	0	0	0	1	0	0	0	2769	1609	56	2	645	2	CCDC132	7	92888896	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	10307398	92888896	66249767	156	39915										
CASD1	64921	hgsc.bcm.edu	37	chr7	94167114	94167114	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	accgtgcaaatctgttcatgAaggaaaacaaattttataca	6	7	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr7:94167114A>G	ENST00000297273.4	+	9	1461	c.1174A>G	c.(1174-1176)Aag>Gag	p.K392E		NM_022900.4	NP_075051.4	Q96PB1	CASD1_HUMAN	CAS1 domain containing 1	392						integral component of membrane (GO:0016021)				NS(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(3)|stomach(2)|upper_aerodigestive_tract(1)	31	all_cancers(62;6.71e-10)|all_epithelial(64;5e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			TCTGTTCATGAAGGAAAACAA	0.308																																					p.K392E		Atlas-SNP	.											.	CASD1	70	.	0			c.A1174G						.						85	95	91					7																	94167114		2202	4300	6502	SO:0001583	missense	64921	exon9			TTCATGAAGGAAA	AF355594	CCDS5636.1	7q22	2006-03-09			ENSG00000127995	ENSG00000127995			16014	protein-coding gene	gene with protein product	"chromosome 7 open reading frame 12"	611686				11703667, 11528394	Standard	NM_022900		Approved	FLJ21213, FLJ21879, C7orf12	uc003uni.4	Q96PB1	OTTHUMG00000023356	ENST00000297273.4:c.1174A>G	chr7.hg19:g.94167114A>G	ENSP00000297273:p.Lys392Glu	68.0	0.0		76.0	4.0	NM_022900	B3KW13|O14574|Q3LIE2|Q6P4R4|Q9H6T9|Q9H770	Missense_Mutation	SNP	ENST00000297273.4	hg19	CCDS5636.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.692976	0.88735	.	.	ENSG00000127995	ENST00000297273	T	0.61742	0.08	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.72374	0.3452	L	0.54323	1.7	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.83275	0.996;0.996	T	0.75150	-0.3419	10	0.87932	D	0	.	15.9173	0.79531	1.0:0.0:0.0:0.0	.	392;392	Q8WZ77;Q96PB1	.;CASD1_HUMAN	E	392	ENSP00000297273:K392E	ENSP00000297273:K392E	K	+	1	0	CASD1	94005050	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.093000	0.94163	2.226000	0.72624	0.477000	0.44152	AAG	.	.		0.308	CASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255216.1	NM_022900		G	94167114	A	G	94167114	3	3	279	1	0	0	0	0	1	0	0	0	2666	247	9	2	1208	2	CASD1	7	94167114	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	1278218	94167114	64971549	157	39916										
PTCD1	26024	hgsc.bcm.edu	37	chr7	99021532	99021532	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gttcagcttcctgatggccgCgttgatgagggcactgtaga	14	9	1	4			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr7:99021532C>A	ENST00000292478.4	-	7	2036	c.1786G>T	c.(1786-1788)Gcg>Tcg	p.A596S	PTCD1_ENST00000555673.1_Missense_Mutation_p.A645S|ATP5J2-PTCD1_ENST00000413834.1_Missense_Mutation_p.A645S	NM_015545.3	NP_056360.2	O75127	PTCD1_HUMAN	pentatricopeptide repeat domain 1	596					tRNA 3'-end processing (GO:0042780)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|tRNA binding (GO:0000049)			endometrium(5)|large_intestine(3)|lung(16)|ovary(2)|skin(1)	27	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			CTGATGGCCGCGTTGATGAGG	0.532																																					p.A645S		Atlas-SNP	.											.	.	.	.	0			c.G1933T						.						172	130	145					7																	99021532		2203	4300	6503	SO:0001583	missense	100526740	exon8			TGGCCGCGTTGAT	AB014532	CCDS34691.1	7q22.1	2006-01-27				ENSG00000106246			22198	protein-coding gene	gene with protein product		614774					Standard	NM_015545		Approved	KIAA0632		O75127		ENST00000292478.4:c.1786G>T	chr7.hg19:g.99021532C>A	ENSP00000292478:p.Ala596Ser	216.0	0.0		304.0	132.0	NM_001198879	Q3ZB78|Q66K60|Q9UDV2	Missense_Mutation	SNP	ENST00000292478.4	hg19	CCDS34691.1	.	.	.	.	.	.	.	.	.	.	C	9.888	1.203380	0.22121	.	.	ENSG00000106246;ENSG00000106246;ENSG00000106246;ENSG00000248919	ENST00000292478;ENST00000438524;ENST00000555673;ENST00000413834	T;T;T	0.68025	-0.3;-0.3;-0.3	6.03	4.22	0.49857	.	0.224693	0.47093	D	0.000256	T	0.64994	0.2649	M	0.65975	2.015	0.24711	N	0.993205	P;P	0.47841	0.901;0.589	B;B	0.42495	0.389;0.094	T	0.61242	-0.7102	10	0.39692	T	0.17	-10.651	13.0953	0.59188	0.0:0.8692:0.0:0.1308	.	645;596	G3V325;O75127	.;PTCD1_HUMAN	S	596;378;645;645	ENSP00000292478:A596S;ENSP00000450995:A645S;ENSP00000400168:A645S	ENSP00000400168:A645S	A	-	1	0	ATP5J2-PTCD1;PTCD1	98859468	0.821000	0.29204	0.402000	0.26371	0.013000	0.08279	3.387000	0.52501	1.563000	0.49615	0.655000	0.94253	GCG	.	.		0.532	PTCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336391.1	NM_015545		A	99021532	C	A	99021532	3	1	279	1	0	0	0	0	1	0	0	0	12739	768	27	1	324	1	PTCD1	7	99021532	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	4854418	99021532	60117131	158	39917										
CNPY4	245812	hgsc.bcm.edu	37	chr7	99722198	99722198	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ctggtacttccaccatcaggAgcagcccctacaaaattttc	6	14	1	0	rs569434978		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr7:99722198A>G	ENST00000262932.3	+	5	659	c.527A>G	c.(526-528)gAg>gGg	p.E176G	MBLAC1_ENST00000398075.2_5'Flank|RP11-506M12.1_ENST00000494221.1_RNA|CNPY4_ENST00000480692.1_3'UTR	NM_152755.1	NP_689968.1	Q8N129	CNPY4_HUMAN	canopy FGF signaling regulator 4	176	Glu-rich.					extracellular region (GO:0005576)				breast(2)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	7	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CACCATCAGGAGCAGCCCCTA	0.507													A|||	1	0.000199681	0	0	5008	,	,		19696	0		0	False		,,,				2504	0.001				p.E176G		Atlas-SNP	.											.	CNPY4	18	.	0			c.A527G						.						100	98	99					7																	99722198		2203	4300	6503	SO:0001583	missense	245812	exon5			ATCAGGAGCAGCC	AK075537	CCDS34701.1	7q22.1	2013-07-23	2013-07-23		ENSG00000166997	ENSG00000166997			28631	protein-coding gene	gene with protein product	"protein associated with TLR4"	610047	"canopy 4 homolog (zebrafish)"			12975309	Standard	NM_152755		Approved	MGC40499, PRAT4B	uc003uto.3	Q8N129	OTTHUMG00000154817	ENST00000262932.3:c.527A>G	chr7.hg19:g.99722198A>G	ENSP00000262932:p.Glu176Gly	99.0	0.0		99.0	5.0	NM_152755	Q8WUN9	Missense_Mutation	SNP	ENST00000262932.3	hg19	CCDS34701.1	.	.	.	.	.	.	.	.	.	.	A	16.82	3.229893	0.58777	.	.	ENSG00000166997	ENST00000262932	T	0.37752	1.18	5.94	4.8	0.61643	.	0.155039	0.56097	D	0.000024	T	0.23330	0.0564	N	0.21097	0.63	0.45056	D	0.99807	B	0.10296	0.003	B	0.16289	0.015	T	0.06409	-1.0828	10	0.44086	T	0.13	-17.9226	7.972	0.30132	0.9112:0.0:0.0888:0.0	.	176	Q8N129	CNPY4_HUMAN	G	176	ENSP00000262932:E176G	ENSP00000262932:E176G	E	+	2	0	CNPY4	99560134	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	5.600000	0.67599	2.279000	0.76181	0.459000	0.35465	GAG	.	.		0.507	CNPY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337224.4	NM_152755		G	99722198	A	G	99722198	3	3	279	1	0	0	0	0	1	0	0	0	3632	304	11	2	545	2	CNPY4	7	99722198	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	700666	99722198	59416465	159	39918										
MUC17	140453	hgsc.bcm.edu	37	chr7	100684024	100684024	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ggaagcactccattaacaggTgtgcctgtcagcaccacacc	9	14	1	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr7:100684024T>C	ENST00000306151.4	+	3	9391	c.9327T>C	c.(9325-9327)ggT>ggC	p.G3109G		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	3109	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					CATTAACAGGTGTGCCTGTCA	0.502																																					p.G3109G		Atlas-SNP	.											.	MUC17	804	.	0			c.T9327C						.						278	281	280					7																	100684024		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			AACAGGTGTGCCT	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.9327T>C	chr7.hg19:g.100684024T>C		77.0	0.0		87.0	4.0	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	hg19	CCDS34711.1																																																																																			.	.		0.502	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		C	100684024	T	C	100684024	2	2	279	1	0	0	0	0	0	0	0	1	9983	1683	59	2		2	MUC17	7	100684024	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	961826	100684024	58454639	160	39919										
LRRC17	10234	hgsc.bcm.edu	37	chr7	102575002	102575002	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tctgaacagttgtgtaatgaAgaagaaaaggaacaattgga	11	3	1	4	rs3832497|rs77576273|rs531650613	byFrequency	TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr7:102575002A>T	ENST00000339431.4	+	2	937	c.642A>T	c.(640-642)gaA>gaT	p.E214D	FBXL13_ENST00000456695.1_Intron|FBXL13_ENST00000455112.2_Intron|FBXL13_ENST00000379308.3_Intron|FBXL13_ENST00000313221.4_Intron|FBXL13_ENST00000379306.3_Intron|FBXL13_ENST00000436908.1_Intron|FBXL13_ENST00000379305.3_Intron|FBXL13_ENST00000393772.2_Intron|LRRC17_ENST00000249377.4_Missense_Mutation_p.E214D	NM_001031692.2	NP_001026862.1	Q8N6Y2	LRC17_HUMAN	leucine rich repeat containing 17	214	LRRCT 1.			Missing (in Ref. 2; AAQ89248). {ECO:0000305}.	bone marrow development (GO:0048539)|negative regulation of osteoclast differentiation (GO:0045671)|ossification (GO:0001503)	extracellular space (GO:0005615)				NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	17						TGTGTAATGAAGAAGAAAAGG	0.438																																					p.E214D		Atlas-SNP	.											.	LRRC17	45	.	0			c.A642T						.						19	11	14					7																	102575002		1944	3733	5677	SO:0001583	missense	10234	exon2			TAATGAAGAAGAA	U32907	CCDS5727.1, CCDS34721.1	7q22.1	2009-05-26			ENSG00000128606	ENSG00000128606			16895	protein-coding gene	gene with protein product						8982252, 19336404	Standard	NM_005824		Approved	P37NB, H_RG318M05.3	uc003vau.3	Q8N6Y2	OTTHUMG00000157210	ENST00000339431.4:c.642A>T	chr7.hg19:g.102575002A>T	ENSP00000344242:p.Glu214Asp	3.0	0.0		9.0	4.0	NM_005824	Q13288|Q6UWA7|Q75MG5	Missense_Mutation	SNP	ENST00000339431.4	hg19	CCDS34721.1	.	.	.	.	.	.	.	.	.	.	A	10.68	1.419589	0.25552	.	.	ENSG00000128606	ENST00000339431;ENST00000249377	T;T	0.62639	0.22;0.01	5.28	2.92	0.33932	.	0.000000	0.56097	D	0.000026	T	0.46190	0.1380	L	0.37850	1.14	0.37180	D	0.903456	B;B	0.18013	0.015;0.025	B;B	0.20184	0.012;0.028	T	0.36648	-0.9739	10	0.34782	T	0.22	-31.8822	4.9104	0.13820	0.7178:0.0:0.1465:0.1357	.	214;214	Q8N6Y2;Q8N6Y2-2	LRC17_HUMAN;.	D	214	ENSP00000344242:E214D;ENSP00000249377:E214D	ENSP00000249377:E214D	E	+	3	2	LRRC17	102362238	1.000000	0.71417	0.874000	0.34290	0.990000	0.78478	2.097000	0.41748	0.416000	0.25844	0.460000	0.39030	GAA	.	.		0.438	LRRC17-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347930.1	NM_005824		T	102575002	A	T	102575002	3	4	279	1	0	0	0	0	1	0	0	0	8982	69	3	4	644	4	LRRC17	7	102575002	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	1890978	102575002	56563661	161	39920										
ING3	54556	hgsc.bcm.edu	37	chr7	120607679	120607679	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tctatccacccttacgtcagAtgcctctaaggaaaatacac	5	13	3	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr7:120607679A>G	ENST00000315870.5	+	7	681	c.533A>G	c.(532-534)gAt>gGt	p.D178G	ING3_ENST00000431467.1_Missense_Mutation_p.D163G	NM_019071.2	NP_061944.2	Q9NXR8	ING3_HUMAN	inhibitor of growth family, member 3	178					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|positive regulation of apoptotic process (GO:0043065)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)|Swr1 complex (GO:0000812)	methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(2)|lung(7)|ovary(1)|urinary_tract(1)	12	all_neural(327;0.117)					CTTACGTCAGATGCCTCTAAG	0.323																																					p.D178G		Atlas-SNP	.											.	ING3	36	.	0			c.A533G						.						75	80	79					7																	120607679		2203	4294	6497	SO:0001583	missense	54556	exon7			CGTCAGATGCCTC	AF074968	CCDS5778.1, CCDS35497.1	7q31	2013-01-28			ENSG00000071243	ENSG00000071243		"Zinc fingers, PHD-type"	14587	protein-coding gene	gene with protein product		607493				12080476	Standard	NM_019071		Approved	p47ING3, FLJ20089, Eaf4, MEAF4	uc003vjn.3	Q9NXR8	OTTHUMG00000141270	ENST00000315870.5:c.533A>G	chr7.hg19:g.120607679A>G	ENSP00000320566:p.Asp178Gly	87.0	0.0		73.0	4.0	NM_019071	A8K790|O60394|Q567P3|Q6GMT3|Q7Z762|Q969G0|Q96DT4|Q9HC99|Q9P081	Missense_Mutation	SNP	ENST00000315870.5	hg19	CCDS5778.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.294899	0.81025	.	.	ENSG00000071243	ENST00000315870;ENST00000431467	D;D	0.95238	-3.63;-3.65	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	D	0.96327	0.8802	M	0.68317	2.08	0.80722	D	1	D;D	0.63880	0.993;0.993	D;D	0.74674	0.984;0.956	D	0.94999	0.8141	10	0.19147	T	0.46	-28.0763	16.0084	0.80380	1.0:0.0:0.0:0.0	.	178;178	Q5GRH6;Q9NXR8	.;ING3_HUMAN	G	178;163	ENSP00000320566:D178G;ENSP00000388506:D163G	ENSP00000320566:D178G	D	+	2	0	ING3	120394915	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	8.850000	0.92190	2.180000	0.69256	0.460000	0.39030	GAT	.	.		0.323	ING3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280453.2	NM_019071		G	120607679	A	G	120607679	3	3	279	1	0	0	0	0	1	0	0	0	7746	333	12	2	575	2	ING3	7	120607679	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	18032677	120607679	38530984	162	39921										
GPR37	2861	hgsc.bcm.edu	37	chr7	124387043	124387043	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cgcagtcactagagagcaggTgatggtgaaaagcgtgggca	16	7	1	3	rs553797830		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr7:124387043T>C	ENST00000303921.2	-	2	2028	c.1378A>G	c.(1378-1380)Acc>Gcc	p.T460A		NM_005302.3	NP_005293.1	O15354	GPR37_HUMAN	G protein-coupled receptor 37 (endothelin receptor type B-like)	460					dopamine biosynthetic process (GO:0042416)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotion involved in locomotory behavior (GO:0031987)|positive regulation of dopamine metabolic process (GO:0045964)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|ubiquitin ligase complex (GO:0000151)	G-protein coupled receptor activity (GO:0004930)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						AGAGAGCAGGTGATGGTGAAA	0.478																																					p.T460A		Atlas-SNP	.											.	GPR37	89	.	0			c.A1378G						.						135	119	125					7																	124387043		2203	4300	6503	SO:0001583	missense	2861	exon2			AGCAGGTGATGGT		CCDS5792.1	7q31	2012-08-21			ENSG00000170775	ENSG00000170775		"GPCR / Class A : Orphans"	4494	protein-coding gene	gene with protein product		602583				9339362	Standard	NM_005302		Approved	EDNRBL, hET(B)R-LP, PAELR	uc003vli.4	O15354	OTTHUMG00000157197	ENST00000303921.2:c.1378A>G	chr7.hg19:g.124387043T>C	ENSP00000306449:p.Thr460Ala	59.0	0.0		92.0	4.0	NM_005302	A4D0Y6|O00348|O14768|Q8TD39	Missense_Mutation	SNP	ENST00000303921.2	hg19	CCDS5792.1	.	.	.	.	.	.	.	.	.	.	T	12.05	1.822233	0.32237	.	.	ENSG00000170775	ENST00000303921	T	0.36699	1.24	5.73	5.73	0.89815	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000004	T	0.32675	0.0837	N	0.14661	0.345	0.38511	D	0.948465	B	0.28470	0.213	B	0.41174	0.349	T	0.36237	-0.9756	10	0.42905	T	0.14	-33.7917	15.205	0.73173	0.0:0.0:0.0:1.0	.	460	O15354	GPR37_HUMAN	A	460	ENSP00000306449:T460A	ENSP00000306449:T460A	T	-	1	0	GPR37	124174279	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.958000	0.40402	2.179000	0.69175	0.533000	0.62120	ACC	.	.		0.478	GPR37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347873.1	NM_005302		C	124387043	T	C	124387043	3	2	279	1	0	0	0	0	1	0	0	0	6699	1696	59	2	467	2	GPR37	7	124387043	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	3779364	124387043	34751620	163	39922										
CCDC136	64753	hgsc.bcm.edu	37	chr7	128445480	128445480	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tgacgtcagcagagtctcagActtcagaaatggatttctta	9	8	4	4			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr7:128445480A>G	ENST00000297788.4	+	6	1217	c.850A>G	c.(850-852)Act>Gct	p.T284A	CCDC136_ENST00000378685.4_Missense_Mutation_p.T322A|CCDC136_ENST00000487361.1_Missense_Mutation_p.T284A|CCDC136_ENST00000464832.1_Missense_Mutation_p.T334A	NM_022742.4	NP_073579	Q96JN2	CC136_HUMAN	coiled-coil domain containing 136	284	Glu-rich.					integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(3)	24						AGAGTCTCAGACTTCAGAAAT	0.488																																					p.T322A		Atlas-SNP	.											.	CCDC136	170	.	0			c.A964G						.						87	89	88					7																	128445480		1994	4183	6177	SO:0001583	missense	64753	exon7			TCTCAGACTTCAG		CCDS47704.1, CCDS56510.1	7q33	2007-08-01			ENSG00000128596	ENSG00000128596			22225	protein-coding gene	gene with protein product		611902				15112360	Standard	NM_022742		Approved	KIAA1793, NAG6, DKFZP434G156	uc003vnv.2	Q96JN2	OTTHUMG00000158310	ENST00000297788.4:c.850A>G	chr7.hg19:g.128445480A>G	ENSP00000297788:p.Thr284Ala	65.0	0.0		87.0	5.0	NM_001201372	A4D1K1|A7MCY7|A8MYA7|Q6ZVK7|Q9H8M3|Q9UFE1	Missense_Mutation	SNP	ENST00000297788.4	hg19	CCDS47704.1	.	.	.	.	.	.	.	.	.	.	A	17.54	3.414507	0.62511	.	.	ENSG00000128596	ENST00000378685;ENST00000464832;ENST00000487361;ENST00000297788;ENST00000397697;ENST00000320524	T;T;T;T	0.77750	0.91;0.9;-1.12;1.44	5.65	4.51	0.55191	.	0.483051	0.24282	N	0.039893	T	0.80628	0.4659	L	0.55834	1.745	0.40537	D	0.980982	P;D;D	0.71674	0.506;0.998;0.996	B;D;D	0.80764	0.319;0.994;0.987	T	0.76495	-0.2938	10	0.09843	T	0.71	-10.6722	7.5478	0.27777	0.9066:0.0:0.0934:0.0	.	284;284;322	C9JE17;Q96JN2;Q96JN2-3	.;CC136_HUMAN;.	A	322;334;284;284;284;284	ENSP00000367956:T322A;ENSP00000419515:T334A;ENSP00000420509:T284A;ENSP00000297788:T284A	ENSP00000297788:T284A	T	+	1	0	CCDC136	128232716	1.000000	0.71417	0.999000	0.59377	0.737000	0.42083	3.069000	0.50026	2.155000	0.67459	0.533000	0.62120	ACT	.	.		0.488	CCDC136-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350641.1	NM_022742		G	128445480	A	G	128445480	3	3	279	1	0	0	0	0	1	0	0	0	2772	275	10	2	872	2	CCDC136	7	128445480	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	4058437	128445480	30693183	164	39923										
DGKI	9162	hgsc.bcm.edu	37	chr7	137154364	137154364	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tggggaaggaggtttcatggTcctggaaagagacacacaca	14	7	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr7:137154364T>C	ENST00000288490.5	-	25	2429	c.2429A>G	c.(2428-2430)gAc>gGc	p.D810G	DGKI_ENST00000424189.2_Splice_Site_p.D813G|DGKI_ENST00000446122.1_Splice_Site_p.D792G|DGKI_ENST00000453654.2_Splice_Site_p.D510G	NM_004717.2	NP_004708.1	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	810					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|positive regulation of Ras protein signal transduction (GO:0046579)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of Rap GTPase activity (GO:0032317)	cytoplasm (GO:0005737)|guanyl-nucleotide exchange factor complex (GO:0032045)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(46)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	84						GGTTTCATGGTCCTGGAAAGA	0.532																																					p.D810G		Atlas-SNP	.											.	DGKI	335	.	0			c.A2429G						.						121	107	112					7																	137154364		2203	4300	6503	SO:0001630	splice_region_variant	9162	exon25			TCATGGTCCTGGA	AF061936	CCDS5845.1	7q32.3-q33	2013-01-10			ENSG00000157680	ENSG00000157680		"Ankyrin repeat domain containing"	2855	protein-coding gene	gene with protein product		604072				9830018	Standard	NM_004717		Approved	DGK-IOTA	uc003vtt.3	O75912	OTTHUMG00000155697	ENST00000288490.5:c.2428-1A>G	chr7.hg19:g.137154364T>C		57.0	0.0		91.0	4.0	NM_004717	A4D1Q9|Q9NZ49	Missense_Mutation	SNP	ENST00000288490.5	hg19	CCDS5845.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.459170	0.84317	.	.	ENSG00000157680	ENST00000453654;ENST00000540376;ENST00000424189;ENST00000288490;ENST00000446122	T;T;T	0.36520	1.81;1.25;1.56	5.84	5.84	0.93424	.	0.152963	0.56097	D	0.000021	T	0.42765	0.1217	L	0.54323	1.7	0.80722	D	1	P;P	0.51791	0.948;0.915	P;P	0.46975	0.533;0.468	T	0.32666	-0.9898	10	0.48119	T	0.1	.	16.2108	0.82158	0.0:0.0:0.0:1.0	.	510;810	E9PFX6;O75912	.;DGKI_HUMAN	G	510;758;813;810;792	ENSP00000392161:D510G;ENSP00000288490:D810G;ENSP00000399131:D792G	ENSP00000288490:D810G	D	-	2	0	DGKI	136804904	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.299000	0.65716	2.232000	0.73038	0.533000	0.62120	GAC	.	.		0.532	DGKI-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341286.3	NM_004717	Missense_Mutation	C	137154364	T	C	137154364	5	2	279	1	0	0	0	0	0	0	1	0	4473	1681	58	2	808	2	DGKI	7	137154364	Splice_Site	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	8708884	137154364	21984299	165	39924										
SVOPL	136306	hgsc.bcm.edu	37	chr7	138329500	138329500	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cttcccctccggcatgaccgAgcggttcatcttggcaacgc	10	16	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr7:138329500A>G	ENST00000419765.3	-	8	784	c.751T>C	c.(751-753)Tcg>Ccg	p.S251P	SVOPL_ENST00000436657.1_Missense_Mutation_p.S99P|SVOPL_ENST00000288513.5_Missense_Mutation_p.S99P|SVOPL_ENST00000421622.1_Missense_Mutation_p.S131P	NM_001139456.1	NP_001132928.1	Q8N434	SVOPL_HUMAN	SVOP-like	251						integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	19						GGCATGACCGAGCGGTTCATC	0.607																																					p.S251P		Atlas-SNP	.											.	SVOPL	111	.	0			c.T751C						.						55	55	55					7																	138329500		2203	4300	6503	SO:0001583	missense	136306	exon8			TGACCGAGCGGTT	BC036796	CCDS5848.1, CCDS47721.1	7q34	2011-07-12	2007-04-04		ENSG00000157703	ENSG00000157703			27034	protein-coding gene	gene with protein product		611700	"SV2 related protein homolog (rat)-like"				Standard	NM_001139456		Approved	MGC46715	uc011kqh.2	Q8N434	OTTHUMG00000155870	ENST00000419765.3:c.751T>C	chr7.hg19:g.138329500A>G	ENSP00000405482:p.Ser251Pro	59.0	0.0		85.0	4.0	NM_001139456		Missense_Mutation	SNP	ENST00000419765.3	hg19	CCDS47721.1	.	.	.	.	.	.	.	.	.	.	A	12.51	1.959389	0.34565	.	.	ENSG00000157703	ENST00000288513;ENST00000421622;ENST00000436657;ENST00000419765	T;T;T;T	0.74842	-0.88;-0.88;-0.88;-0.81	5.06	2.63	0.31362	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.381515	0.26560	N	0.023697	T	0.70482	0.3229	L	0.39397	1.21	0.38783	D	0.954818	P;P	0.48911	0.917;0.874	P;P	0.49226	0.603;0.491	T	0.67726	-0.5596	10	0.33141	T	0.24	-8.0477	12.3898	0.55352	0.598:0.402:0.0:0.0	.	251;99	Q8N434;Q8N434-2	SVOPL_HUMAN;.	P	99;131;99;251	ENSP00000288513:S99P;ENSP00000412830:S131P;ENSP00000417018:S99P;ENSP00000405482:S251P	ENSP00000288513:S99P	S	-	1	0	SVOPL	137980040	0.991000	0.36638	0.921000	0.36526	0.120000	0.20174	1.299000	0.33424	0.251000	0.21505	-1.485000	0.00982	TCG	.	.		0.607	SVOPL-005	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342092.4	NM_174959		G	138329500	A	G	138329500	3	3	279	1	0	0	0	0	1	0	0	0	15439	304	11	2	759	2	SVOPL	7	138329500	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	1175136	138329500	20809163	166	39925										
UBN2	254048	hgsc.bcm.edu	37	chr7	138954250	138954250	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	actagtaaaacgtctgaagaAgttacatctcaatgtccagg	8	8	2	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr7:138954250A>G	ENST00000473989.3	+	8	1577	c.1577A>G	c.(1576-1578)aAg>aGg	p.K526R	UBN2_ENST00000288561.8_Missense_Mutation_p.K443R	NM_173569.3	NP_775840.3	Q6ZU65	UBN2_HUMAN	ubinuclein 2	526						extracellular space (GO:0005615)|nucleus (GO:0005634)				NS(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	42						CGTCTGAAGAAGTTACATCTC	0.413																																					p.K526R		Atlas-SNP	.											.	UBN2	90	.	0			c.A1577G						.						101	90	94					7																	138954250		1857	4122	5979	SO:0001583	missense	254048	exon8			TGAAGAAGTTACA	AK098644	CCDS43655.1, CCDS43655.2	7q34	2008-12-08			ENSG00000157741	ENSG00000157741			21931	protein-coding gene	gene with protein product		613841				19029251	Standard	NM_173569		Approved	FLJ25778, KIAA2030	uc011kqr.2	Q6ZU65	OTTHUMG00000157623	ENST00000473989.3:c.1577A>G	chr7.hg19:g.138954250A>G	ENSP00000418648:p.Lys526Arg	52.0	0.0		80.0	4.0	NM_173569	A4D1S2|Q2YDY4|Q6P1K0|Q86XN9|Q8N7D1	Missense_Mutation	SNP	ENST00000473989.3	hg19	CCDS43655.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	26.7|26.7	4.765426|4.765426	0.90020|0.90020	.|.	.|.	ENSG00000157741|ENSG00000157741	ENST00000473989;ENST00000288561|ENST00000483726	T;T|.	0.52057|.	0.68;0.68|.	5.58|5.58	5.58|5.58	0.84498|0.84498	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.70448|0.70448	0.3225|0.3225	L|L	0.56769|0.56769	1.78|1.78	0.58432|0.58432	D|D	0.999999|0.999999	D|.	0.76494|.	0.999|.	D|.	0.81914|.	0.995|.	T|T	0.68949|0.68949	-0.5274|-0.5274	10|5	0.42905|.	T|.	0.14|.	-11.3517|-11.3517	15.7561|15.7561	0.78025|0.78025	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	526|.	Q6ZU65|.	UBN2_HUMAN|.	R|G	526;443|295	ENSP00000418648:K526R;ENSP00000288561:K443R|.	ENSP00000288561:K443R|.	K|S	+|+	2|1	0|0	UBN2|UBN2	138604790|138604790	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.985000|0.985000	0.73830|0.73830	9.307000|9.307000	0.96226|0.96226	2.129000|2.129000	0.65627|0.65627	0.528000|0.528000	0.53228|0.53228	AAG|AGT	.	.		0.413	UBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349272.3	NM_173569		G	138954250	A	G	138954250	3	3	279	1	0	0	0	0	1	0	0	0	16908	72	3	2	1607	2	UBN2	7	138954250	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	624750	138954250	20184413	167	39926										
ZNF786	136051	hgsc.bcm.edu	37	chr7	148768069	148768069	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cttcaggcggaagctcctgtTgcactctgggcactggaagg	14	11	2	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr7:148768069T>C	ENST00000491431.1	-	4	1859	c.1795A>G	c.(1795-1797)Aac>Gac	p.N599D	ZNF786_ENST00000316286.9_Missense_Mutation_p.N513D|ZNF786_ENST00000451334.3_Missense_Mutation_p.N562D	NM_152411.3	NP_689624.2	Q8N393	ZN786_HUMAN	zinc finger protein 786	599					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|cervix(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(2)|skin(2)|soft_tissue(1)|urinary_tract(2)	26	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			AAGCTCCTGTTGCACTCTGGG	0.642																																					p.N599D		Atlas-SNP	.											.	ZNF786	69	.	0			c.A1795G						.						30	33	32					7																	148768069		2192	4291	6483	SO:0001583	missense	136051	exon4			TCCTGTTGCACTC	AK095701, AL834510	CCDS47738.1	7q36.1	2013-01-08			ENSG00000197362	ENSG00000197362		"Zinc fingers, C2H2-type", "-"	21806	protein-coding gene	gene with protein product							Standard	NM_152411		Approved	DKFZp762I137	uc003wfh.2	Q8N393	OTTHUMG00000158975	ENST00000491431.1:c.1795A>G	chr7.hg19:g.148768069T>C	ENSP00000417470:p.Asn599Asp	86.0	0.0		99.0	4.0	NM_152411	A1A568|B4DMI1	Missense_Mutation	SNP	ENST00000491431.1	hg19	CCDS47738.1	.	.	.	.	.	.	.	.	.	.	T	0.003	-2.432512	0.00184	.	.	ENSG00000197362	ENST00000316286;ENST00000491431;ENST00000451334	T;T;T	0.14266	2.52;2.52;2.52	4.71	-0.323	0.12709	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	1.056690	0.07499	N	0.906948	T	0.06781	0.0173	N	0.03253	-0.375	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.40308	-0.9570	10	0.62326	D	0.03	-10.5891	9.4207	0.38550	0.0:0.6495:0.0:0.3505	.	599	Q8N393	ZN786_HUMAN	D	513;599;562	ENSP00000313516:N513D;ENSP00000417470:N599D;ENSP00000404984:N562D	ENSP00000313516:N513D	N	-	1	0	ZNF786	148399002	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-0.068000	0.11561	-0.231000	0.09825	-1.054000	0.02325	AAC	.	.		0.642	ZNF786-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352751.1	NM_152411		C	148768069	T	C	148768069	3	2	279	1	0	0	0	0	1	0	0	0	18173	1812	63	2	557	2	ZNF786	7	148768069	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	9813819	148768069	10370594	168	39927										
SSPO	23145	hgsc.bcm.edu	37	chr7	149523267	149523267	+	RNA	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ccccctgtggtgggggcactAtggagcgacatcggacttgt	15	11	0	0	rs569525128		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr7:149523267A>G	ENST00000378016.2	+	0	14353							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			TGGGGGCACTATGGAGCGACA	0.652													A|||	1	0.000199681	0	0	5008	,	,		19496	0		0.001	False		,,,				2504	0				p.M4784V		Atlas-SNP	.											NM_198455_2,lower_third,carcinoma,0,1	.	.	.	0			c.A14350G						.						37	46	43					7																	149523267		1973	4143	6116			23145	exon101			GGCACTATGGAGC	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		chr7.hg19:g.149523267A>G		49.0	0.0		71.0	3.0	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	hg19																																																																																				.	.		0.652	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				G	149523267	A	G	149523267	1	3	279	0	1	0	0	0	0	0	0	0	15204	449	16	2		2	SSPO	7	149523267	RNA	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	755198	149523267	9615396	169	39928										
FBXO25	26260	hgsc.bcm.edu	37	chr8	408474	408474	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tcatcaccttaggccaggtgAcccccacgttgtatatgctt	8	13	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr8:408474A>G	ENST00000276326.5	+	8	885	c.766A>G	c.(766-768)Acc>Gcc	p.T256A	FBXO25_ENST00000519376.1_3'UTR|FBXO25_ENST00000382824.1_Missense_Mutation_p.T189A|FBXO25_ENST00000350302.3_Missense_Mutation_p.T256A|FBXO25_ENST00000352684.2_Missense_Mutation_p.T189A	NM_183421.1	NP_904357.1	Q8TCJ0	FBX25_HUMAN	F-box protein 25	256	F-box.				protein ubiquitination (GO:0016567)	nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	10		Ovarian(12;0.00965)|Colorectal(14;0.0815)|Myeloproliferative disorder(644;0.116)|all_neural(12;0.122)		Epithelial(5;3.14e-14)|OV - Ovarian serous cystadenocarcinoma(5;1.56e-07)|BRCA - Breast invasive adenocarcinoma(11;1.88e-06)		AGGCCAGGTGACCCCCACGTT	0.507																																					p.T256A		Atlas-SNP	.											.	FBXO25	25	.	0			c.A766G						.						181	144	156					8																	408474		2203	4300	6503	SO:0001583	missense	26260	exon8			CAGGTGACCCCCA	AF174605	CCDS5952.1, CCDS5953.1, CCDS5954.1	8p23.3	2007-03-30	2004-06-15		ENSG00000147364	ENSG00000147364		"F-boxes /  "other""	13596	protein-coding gene	gene with protein product		609098	"F-box only protein 25"			10531035, 10531037	Standard	NM_012173		Approved	FBX25	uc003wox.3	Q8TCJ0	OTTHUMG00000090341	ENST00000276326.5:c.766A>G	chr8.hg19:g.408474A>G	ENSP00000276326:p.Thr256Ala	154.0	0.0		103.0	5.0	NM_183420	Q6PJ83|Q7Z4V4|Q9UKB8	Missense_Mutation	SNP	ENST00000276326.5	hg19	CCDS5953.1	.	.	.	.	.	.	.	.	.	.	A	9.520	1.108057	0.20714	.	.	ENSG00000147364	ENST00000350302;ENST00000352684;ENST00000276326;ENST00000382824	T;T;T;T	0.21932	1.98;1.98;1.98;1.98	4.32	4.32	0.51571	F-box domain, Skp2-like (1);	0.048093	0.85682	D	0.000000	T	0.19886	0.0478	L	0.46741	1.465	0.53688	D	0.999979	P;P;P	0.47106	0.89;0.69;0.69	B;B;B	0.44044	0.225;0.439;0.439	T	0.03453	-1.1035	10	0.13853	T	0.58	-25.7154	11.6929	0.51527	1.0:0.0:0.0:0.0	.	189;256;256	Q8TCJ0-3;Q8TCJ0-2;Q8TCJ0	.;.;FBX25_HUMAN	A	256;189;256;189	ENSP00000342077:T256A;ENSP00000341345:T189A;ENSP00000276326:T256A;ENSP00000372274:T189A	ENSP00000276326:T256A	T	+	1	0	FBXO25	398474	1.000000	0.71417	0.997000	0.53966	0.773000	0.43773	5.522000	0.67092	1.697000	0.51169	0.482000	0.46254	ACC	.	.		0.507	FBXO25-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206710.2	NM_012173		G	408474	A	G	408474	3	3	279	1	0	0	0	0	1	0	0	0	5744	275	10	2	792	2	FBXO25	8	408474	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10		408474	145955548	170	39929										
XKR5	389610	hgsc.bcm.edu	37	chr8	6681155	6681155	+	RNA	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tggcagaagagggcggcccaTggcatggccaggtggcctgg	19	10	0	2	rs539008683		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr8:6681155T>C	ENST00000518724.1	-	0	675							Q6UX68	XKR5_HUMAN	XK, Kell blood group complex subunit-related family, member 5							integral component of membrane (GO:0016021)		p.P175P(1)		endometrium(1)|large_intestine(1)|lung(1)	3			STAD - Stomach adenocarcinoma(24;0.0984)	READ - Rectum adenocarcinoma(644;0.137)|COAD - Colon adenocarcinoma(149;0.166)		GGGCGGCCCATGGCATGGCCA	0.587													T|||	1	0.000199681	0	0	5008	,	,		19137	0.001		0	False		,,,				2504	0				p.P175P		Atlas-SNP	.											XKR5,caecum,carcinoma,0,1	XKR5	20	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A525G						.						24	28	27					8																	6681155		1990	4157	6147			389610	exon4			GGCCCATGGCATG	AY358489		8p23.1	2006-01-12	2006-01-12		ENSG00000186530	ENSG00000275591			20782	protein-coding gene	gene with protein product			"X Kell blood group precursor-related family, member 5"				Standard	NM_207411		Approved		uc022aqv.1	Q6UX68	OTTHUMG00000153652		chr8.hg19:g.6681155T>C		103.0	0.0		71.0	3.0	NM_207411	Q5GH74	Silent	SNP	ENST00000518724.1	hg19																																																																																				.	.		0.587	XKR5-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000331969.2	NM_207411		C	6681155	T	C	6681155	1	2	279	0	1	0	0	0	0	0	0	0	17449	1451	51	2		2	XKR5	8	6681155	RNA	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	6272681	6681155	139682867	171	39930										
TUSC3	7991	hgsc.bcm.edu	37	chr8	15605922	15605922	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tgggcctggtggtcttcttcTtcagttttctactttcaata	8	9	6	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr8:15605922T>C	ENST00000503731.1	+	9	1124	c.976T>C	c.(976-978)Ttc>Ctc	p.F326L	TUSC3_ENST00000506802.1_Intron|TUSC3_ENST00000382020.4_Missense_Mutation_p.F326L	NM_006765.3	NP_006756.2	Q13454	TUSC3_HUMAN	tumor suppressor candidate 3	326					cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cognition (GO:0050890)|magnesium ion transport (GO:0015693)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|oligosaccharyltransferase complex (GO:0008250)	magnesium ion transmembrane transporter activity (GO:0015095)	p.F326V(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(10)|ovary(2)	28				Colorectal(111;0.113)		GGTCTTCTTCTTCAGTTTTCT	0.323																																					p.F326L		Atlas-SNP	.											TUSC3,caecum,carcinoma,0,1	TUSC3	98	.	1	Substitution - Missense(1)	large_intestine(1)	c.T976C						.						247	235	239					8																	15605922		2203	4300	6503	SO:0001583	missense	7991	exon9			TTCTTCTTCAGTT	AK026149	CCDS5993.1, CCDS5994.1	8p22	2010-10-22			ENSG00000104723	ENSG00000104723			30242	protein-coding gene	gene with protein product	"oligosaccharyltransferase 3 homolog A (S. cerevisiae)"	601385				8661104, 10097140	Standard	NM_178234		Approved	MGC13453, N33, OST3A, MRT7	uc003wwt.3	Q13454	OTTHUMG00000094803	ENST00000503731.1:c.976T>C	chr8.hg19:g.15605922T>C	ENSP00000424544:p.Phe326Leu	145.0	0.0		81.0	4.0	NM_178234	A8MSM0|D3DSP2|Q14911|Q14912|Q96FW0	Missense_Mutation	SNP	ENST00000503731.1	hg19	CCDS5994.1	.	.	.	.	.	.	.	.	.	.	T	27.2	4.808692	0.90707	.	.	ENSG00000104723	ENST00000382020;ENST00000503731	T;T	0.78003	-1.14;-1.14	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	D	0.84502	0.5486	L	0.51422	1.61	0.80722	D	1	P;P	0.52577	0.954;0.739	D;P	0.66351	0.943;0.516	D	0.84930	0.0859	10	0.54805	T	0.06	-16.1508	15.7284	0.77780	0.0:0.0:0.0:1.0	.	326;326	Q13454-2;Q13454	.;TUSC3_HUMAN	L	326	ENSP00000371450:F326L;ENSP00000424544:F326L	ENSP00000221167:F326L	F	+	1	0	TUSC3	15650293	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.367000	0.79558	2.371000	0.80710	0.533000	0.62120	TTC	.	.		0.323	TUSC3-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365367.1	NM_006765		C	15605922	T	C	15605922	3	2	279	1	0	0	0	0	1	0	0	0	16793	1609	56	2	1010	2	TUSC3	8	15605922	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	8924767	15605922	130758100	172	39931										
ASAH1	427	hgsc.bcm.edu	37	chr8	17920692	17920692	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tgaccctttgttctttacttAcccaagaaatactccaaaat	3	11	1	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr8:17920692A>G	ENST00000262097.6	-	7	815		c.e7+1		ASAH1_ENST00000314146.10_Splice_Site|ASAH1_ENST00000520781.1_Splice_Site|ASAH1_ENST00000417108.2_Splice_Site|ASAH1_ENST00000381733.4_Splice_Site	NM_177924.3	NP_808592.2	Q13510	ASAH1_HUMAN	N-acylsphingosine amidohydrolase (acid ceramidase) 1						cell death (GO:0008219)|ceramide metabolic process (GO:0006672)|glycosphingolipid metabolic process (GO:0006687)|lung development (GO:0030324)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	catalytic activity (GO:0003824)|ceramidase activity (GO:0017040)			breast(1)|endometrium(2)|large_intestine(4)|lung(2)	9				Colorectal(111;0.0646)|COAD - Colon adenocarcinoma(73;0.228)		TTCTTTACTTACCCAAGAAAT	0.438																																					.		Atlas-SNP	.											.	ASAH1	71	.	0			c.551+2T>C						.						301	299	299					8																	17920692		2203	4300	6503	SO:0001630	splice_region_variant	427	exon8			TTACTTACCCAAG	U70063	CCDS6005.1, CCDS6006.1, CCDS47813.1	8p22	2007-03-27	2002-09-11	2002-09-13	ENSG00000104763	ENSG00000104763			735	protein-coding gene	gene with protein product		613468	"N-acylsphingosine amidohydrolase (acid ceramidase)"	ASAH		8955159, 10610716	Standard	NM_004315		Approved	AC, PHP32, FLJ21558	uc003wyn.2	Q13510	OTTHUMG00000096997	ENST00000262097.6:c.503+1T>C	chr8.hg19:g.17920692A>G		147.0	0.0		82.0	4.0	NM_004315	E9PDS0|Q6W898|Q96AS2	Splice_Site	SNP	ENST00000262097.6	hg19	CCDS6006.1	.	.	.	.	.	.	.	.	.	.	A	16.35	3.097594	0.56075	.	.	ENSG00000104763	ENST00000262097;ENST00000381733;ENST00000520781;ENST00000417108;ENST00000314146	.	.	.	5.03	5.03	0.67393	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4268	0.67220	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ASAH1	17964972	1.000000	0.71417	1.000000	0.80357	0.585000	0.36419	8.076000	0.89503	2.184000	0.69523	0.533000	0.62120	.	.	.		0.438	ASAH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214077.2	NM_004315	Intron	G	17920692	A	G	17920692	5	3	279	1	0	0	0	0	0	0	1	0	1006	405	14	2	714	2	ASAH1	8	17920692	Splice_Site	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	2314770	17920692	128443330	173	39932										
KIF13B	23303	hgsc.bcm.edu	37	chr8	28980143	28980143	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	atataacaggaatgtgtgtcTccatcccaggtactggggtc	11	9	1	0	rs370420261		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr8:28980143T>C	ENST00000524189.1	-	29	3538	c.3500A>G	c.(3499-3501)gAg>gGg	p.E1167G	CTD-2647L4.1_ENST00000523661.1_RNA	NM_015254.3	NP_056069.2	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	1167					metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein targeting (GO:0006605)|regulation of axonogenesis (GO:0050770)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	axon (GO:0030424)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)	p.E1167A(1)		endometrium(6)|kidney(1)|lung(20)|urinary_tract(1)	28		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)		AATGTGTGTCTCCATCCCAGG	0.438																																					p.E1167G		Atlas-SNP	.											KIF13B_ENST00000524189,colon,carcinoma,0,1	KIF13B	192	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3500G						.	T	GLY/GLU	0,3826		0,0,1913	85	79	81		3500	5.3	1	8		81	1,8265		0,1,4132	no	missense	KIF13B	NM_015254.3	98	0,1,6045	CC,CT,TT		0.0121,0.0,0.0083	probably-damaging	1167/1827	28980143	1,12091	1913	4133	6046	SO:0001583	missense	23303	exon29			TGTGTCTCCATCC	AB014539	CCDS55217.1	8p21	2008-07-30				ENSG00000197892		"Kinesins"	14405	protein-coding gene	gene with protein product		607350				9734811, 10859302, 16864656	Standard	NM_015254		Approved	GAKIN, KIAA0639	uc003xhh.4	Q9NQT8		ENST00000524189.1:c.3500A>G	chr8.hg19:g.28980143T>C	ENSP00000427900:p.Glu1167Gly	136.0	0.0		74.0	3.0	NM_015254	B4DGY5|B5MC45|F8VPJ2|O75134|Q9BYJ6	Missense_Mutation	SNP	ENST00000524189.1	hg19	CCDS55217.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.816701	0.90790	0.0	1.21E-4	ENSG00000197892	ENST00000524189	D	0.89050	-2.46	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	D	0.93756	0.8004	M	0.72894	2.215	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94436	0.7654	10	0.87932	D	0	.	15.3683	0.74541	0.0:0.0:0.0:1.0	.	1167	F8VPJ2	.	G	1167	ENSP00000427900:E1167G	ENSP00000427900:E1167G	E	-	2	0	KIF13B	29036062	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.461000	0.80834	2.206000	0.71126	0.528000	0.53228	GAG	.	.		0.438	KIF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376878.1			C	28980143	T	C	28980143	3	2	279	1	0	0	0	0	1	0	0	0	8284	1551	54	2	2028	2	KIF13B	8	28980143	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	11059451	28980143	117383879	174	39933										
TEX15	56154	hgsc.bcm.edu	37	chr8	30705230	30705230	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tatagtctctctgaatgttcTctaatgacactggttcattt	6	8	4	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr8:30705230T>C	ENST00000256246.2	-	1	1378	c.1304A>G	c.(1303-1305)gAg>gGg	p.E435G	TEX15_ENST00000523186.1_5'Flank	NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	435					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)					NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		CTGAATGTTCTCTAATGACAC	0.348																																					p.E435G		Atlas-SNP	.											.	TEX15	350	.	0			c.A1304G						.						148	147	148					8																	30705230		2203	4300	6503	SO:0001583	missense	56154	exon1			ATGTTCTCTAATG	AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"cancer/testis antigen 42"	605795	"testis expressed sequence 15"			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.1304A>G	chr8.hg19:g.30705230T>C	ENSP00000256246:p.Glu435Gly	109.0	0.0		81.0	4.0	NM_031271		Missense_Mutation	SNP	ENST00000256246.2	hg19	CCDS6080.1	.	.	.	.	.	.	.	.	.	.	T	11.92	1.781671	0.31502	.	.	ENSG00000133863	ENST00000256246	T	0.10668	2.85	5.61	1.75	0.24633	.	0.664633	0.13939	N	0.352379	T	0.07503	0.0189	L	0.29908	0.895	0.09310	N	1	B	0.15930	0.015	B	0.18561	0.022	T	0.34502	-0.9826	10	0.87932	D	0	.	3.5494	0.07840	0.1323:0.0737:0.1383:0.6557	.	435	Q9BXT5	TEX15_HUMAN	G	435	ENSP00000256246:E435G	ENSP00000256246:E435G	E	-	2	0	TEX15	30824772	0.002000	0.14202	0.004000	0.12327	0.003000	0.03518	0.335000	0.19806	0.112000	0.17975	-0.297000	0.09499	GAG	.	.		0.348	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			C	30705230	T	C	30705230	3	2	279	1	0	0	0	0	1	0	0	0	15794	1551	54	2	7081	2	TEX15	8	30705230	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	1725087	30705230	115658792	175	39934										
WRN	7486	hgsc.bcm.edu	37	chr8	30938674	30938674	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gaagatggatttgaagatggAgtagaagacaacaaattgaa	12	2	0	6			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr8:30938674A>G	ENST00000298139.5	+	9	1380	c.1131A>G	c.(1129-1131)ggA>ggG	p.G377G		NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN	Werner syndrome, RecQ helicase-like	377					aging (GO:0007568)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to starvation (GO:0009267)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|double-strand break repair (GO:0006302)|multicellular organismal aging (GO:0010259)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleolus to nucleoplasm transport (GO:0032066)|positive regulation of hydrolase activity (GO:0051345)|regulation of apoptotic process (GO:0042981)|regulation of growth rate (GO:0040009)|replication fork processing (GO:0031297)|replicative cell aging (GO:0001302)|response to oxidative stress (GO:0006979)|response to UV-C (GO:0010225)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	3'-5' DNA helicase activity (GO:0043138)|3'-5' exonuclease activity (GO:0008408)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|exonuclease activity (GO:0004527)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|Y-form DNA binding (GO:0000403)			central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(13)|lung(28)|ovary(3)|skin(3)|upper_aerodigestive_tract(3)	60		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		TTGAAGATGGAGTAGAAGACA	0.363			"Mis, N, F, S"			"osteosarcoma, meningioma, others"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome																												p.G377G	Ovarian(18;161 598 2706 14834 27543)	Atlas-SNP	.	yes	Rec		Werner Syndrome	8	8p12-p11.2	7486	Werner syndrome (RECQL2)		"L, E, M, O"	.	WRN	116	.	0			c.A1131G						.						111	113	112					8																	30938674		2203	4300	6503	SO:0001819	synonymous_variant	7486	exon9	Familial Cancer Database	WS, Adult Progeria	AGATGGAGTAGAA		CCDS6082.1	8p12	2014-09-17	2009-03-19		ENSG00000165392	ENSG00000165392			12791	protein-coding gene	gene with protein product		604611	"Werner syndrome"			9288107	Standard	NM_000553		Approved	RECQL2, RECQ3	uc003xio.4	Q14191	OTTHUMG00000163894	ENST00000298139.5:c.1131A>G	chr8.hg19:g.30938674A>G		153.0	0.0		95.0	4.0	NM_000553	A1KYY9	Silent	SNP	ENST00000298139.5	hg19	CCDS6082.1																																																																																			.	.		0.363	WRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376248.1			G	30938674	A	G	30938674	2	3	279	1	0	0	0	0	0	0	0	1	17417	291	11	2		2	WRN	8	30938674	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	233444	30938674	115425348	176	39935										
HOOK3	84376	hgsc.bcm.edu	37	chr8	42812266	42812266	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	aaagaatctcctgtctctgcTggaaatgatgcctatgttga	9	8	2	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr8:42812266T>C	ENST00000307602.4	+	7	698	c.498T>C	c.(496-498)gcT>gcC	p.A166A		NM_032410.3	NP_115786.1	Q86VS8	HOOK3_HUMAN	hook microtubule-tethering protein 3	166					cytoplasmic microtubule organization (GO:0031122)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|Golgi localization (GO:0051645)|interkinetic nuclear migration (GO:0022027)|lysosome organization (GO:0007040)|microtubule anchoring at centrosome (GO:0034454)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|protein localization to centrosome (GO:0071539)|protein transport (GO:0015031)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|FHF complex (GO:0070695)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule organizing center (GO:0005815)|pericentriolar material (GO:0000242)	identical protein binding (GO:0042802)|microtubule binding (GO:0008017)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	31	Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.000105)|Lung NSC(58;0.000419)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)			CTGTCTCTGCTGGAAATGATG	0.308			T	RET	papillary thyroid																																p.A166A		Atlas-SNP	.		Dom	yes		8	8p11.21	84376	hook homolog 3		E	.	HOOK3	71	.	0			c.T498C						.						103	98	100					8																	42812266		2203	4299	6502	SO:0001819	synonymous_variant	84376	exon7			CTCTGCTGGAAAT	AK090540	CCDS6139.1	8p11.21	2013-08-21	2013-08-21		ENSG00000168172	ENSG00000168172			23576	protein-coding gene	gene with protein product		607825	"hook homolog 3 (Drosophila)"			9927460	Standard	NM_032410		Approved	HK3	uc003xpr.3	Q86VS8	OTTHUMG00000165278	ENST00000307602.4:c.498T>C	chr8.hg19:g.42812266T>C		83.0	0.0		84.0	4.0	NM_032410	D3DSY8|Q8NBH0|Q9BY13	Silent	SNP	ENST00000307602.4	hg19	CCDS6139.1																																																																																			.	.		0.308	HOOK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383172.2	NM_032410		C	42812266	T	C	42812266	2	2	279	1	0	0	0	0	0	0	0	1	7293	1567	55	2		2	HOOK3	8	42812266	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	11873592	42812266	103551756	177	39936										
PXDNL	137902	hgsc.bcm.edu	37	chr8	52321315	52321315	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ctcgttggcccggtggtcccCggccaggaaacaggggctct	15	14	1	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr8:52321315C>A	ENST00000356297.4	-	17	2969	c.2869G>T	c.(2869-2871)Ggg>Tgg	p.G957W	PXDNL_ENST00000543296.1_Missense_Mutation_p.G957W	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	957					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				CGGTGGTCCCCGGCCAGGAAA	0.652																																					p.G957W		Atlas-SNP	.											.	PXDNL	414	.	0			c.G2869T						.						12	13	13					8																	52321315		1965	4141	6106	SO:0001583	missense	137902	exon17			GGTCCCCGGCCAG		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"Immunoglobulin superfamily / I-set domain containing"	26359	protein-coding gene	gene with protein product	"polysomal ribonuclease 1 homolog (Xenopus)"	615904	"peroxidasin homolog-like (Drosophila)"			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.2869G>T	chr8.hg19:g.52321315C>A	ENSP00000348645:p.Gly957Trp	118.0	0.0		166.0	32.0	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	hg19	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	C	10.93	1.488586	0.26686	.	.	ENSG00000147485	ENST00000356297;ENST00000543296	D;D	0.94280	-3.39;-3.39	4.16	2.35	0.29111	.	0.120623	0.36972	N	0.002308	D	0.97870	0.9300	H	0.99368	4.535	0.38939	D	0.958116	D	0.89917	1.0	D	0.97110	1.0	D	0.96100	0.9068	10	0.87932	D	0	.	8.2046	0.31446	0.0:0.7973:0.0:0.2027	.	957	A1KZ92	PXDNL_HUMAN	W	957	ENSP00000348645:G957W;ENSP00000444865:G957W	ENSP00000348645:G957W	G	-	1	0	PXDNL	52483868	0.978000	0.34361	0.000000	0.03702	0.005000	0.04900	3.193000	0.50997	0.236000	0.21180	-0.768000	0.03414	GGG	.	.		0.652	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		A	52321315	C	A	52321315	3	1	279	1	0	0	0	0	1	0	0	0	12863	652	23	1	1550	1	PXDNL	8	52321315	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	9509049	52321315	94042707	178	39937										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77690642	77690642	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	aggacaacctcagtgagatcTtttttgttaaagattgccca	8	8	2	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr8:77690642T>C	ENST00000521891.2	+	4	3740	c.3292T>C	c.(3292-3294)Ttt>Ctt	p.F1098L	ZFHX4_ENST00000050961.6_Missense_Mutation_p.F1072L|ZFHX4_ENST00000455469.2_Missense_Mutation_p.F1072L|ZFHX4_ENST00000517683.1_3'UTR|ZFHX4_ENST00000518282.1_Missense_Mutation_p.F1072L	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	1072					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			CAGTGAGATCTTTTTTGTTAA	0.537										HNSCC(33;0.089)																											p.F1098L		Atlas-SNP	.											.	ZFHX4	878	.	0			c.T3292C						.						112	120	117					8																	77690642		1992	4166	6158	SO:0001583	missense	79776	exon4			GAGATCTTTTTTG		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.3292T>C	chr8.hg19:g.77690642T>C	ENSP00000430497:p.Phe1098Leu	82.0	0.0		146.0	6.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	hg19	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	T	13.60	2.284793	0.40394	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.50813	0.73;0.73;0.73;0.73	5.22	5.22	0.72569	.	0.000000	0.45867	U	0.000329	T	0.70771	0.3262	M	0.84326	2.69	0.80722	D	1	D;D;D	0.71674	0.997;0.998;0.998	D;D;D	0.76071	0.97;0.987;0.987	T	0.74870	-0.3517	10	0.56958	D	0.05	.	15.5609	0.76244	0.0:0.0:0.0:1.0	.	1072;1072;1098	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	L	1098;1098;1072;1072;1072	ENSP00000430497:F1098L;ENSP00000399605:F1072L;ENSP00000050961:F1072L;ENSP00000430848:F1072L	ENSP00000050961:F1072L	F	+	1	0	ZFHX4	77853197	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.954000	0.63631	2.320000	0.78422	0.528000	0.53228	TTT	.	.		0.537	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		C	77690642	T	C	77690642	3	2	279	1	0	0	0	0	1	0	0	0	17650	1609	56	2	3302	2	ZFHX4	8	77690642	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	25369327	77690642	68673380	179	39938										
NBN	4683	hgsc.bcm.edu	37	chr8	90960118	90960118	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ttcttcccaatttcattttcTtgctaaagaaataaaataaa	2	7	3	1	rs587782269		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr8:90960118T>C	ENST00000265433.3	-	12	2002	c.1848A>G	c.(1846-1848)caA>caG	p.Q616Q	NBN_ENST00000409330.1_Silent_p.Q534Q	NM_002485.4	NP_002476.2	O60934	NBN_HUMAN	nibrin	616					blastocyst growth (GO:0001832)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|DNA damage checkpoint (GO:0000077)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intrinsic apoptotic signaling pathway (GO:0097193)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mitotic cell cycle checkpoint (GO:0007093)|mitotic G2 DNA damage checkpoint (GO:0007095)|neuromuscular process controlling balance (GO:0050885)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|telomere maintenance (GO:0000723)	Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nuclear inclusion body (GO:0042405)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|replication fork (GO:0005657)|site of double-strand break (GO:0035861)	damaged DNA binding (GO:0003684)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(11;0.0344)			TTTCATTTTCTTGCTAAAGAA	0.289								Homologous recombination																													p.Q616Q		Atlas-SNP	.											.	NBN	86	.	0			c.A1848G						.						53	48	50					8																	90960118		2198	4292	6490	SO:0001819	synonymous_variant	4683	exon12			ATTTTCTTGCTAA	AF058696	CCDS6249.1	8q21-q24	2014-09-17	2005-06-02	2005-06-02	ENSG00000104320	ENSG00000104320			7652	protein-coding gene	gene with protein product		602667	"Nijmegen breakage syndrome 1 (nibrin)"	NBS, NBS1		9590181, 9590180	Standard	XM_005250923		Approved	ATV, AT-V2, AT-V1	uc003yej.1	O60934	OTTHUMG00000153546	ENST00000265433.3:c.1848A>G	chr8.hg19:g.90960118T>C		85.0	0.0		83.0	4.0	NM_002485	B2R626|B2RNC5|O60672|Q32NF7|Q53FM6|Q63HR6|Q7LDM2	Silent	SNP	ENST00000265433.3	hg19	CCDS6249.1																																																																																			.	.		0.289	NBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331583.3	NM_001024688		C	90960118	T	C	90960118	2	2	279	1	0	0	0	0	0	0	0	1	10200	1606	56	2		2	NBN	8	90960118	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	13269476	90960118	55403904	180	39939										
RGS22	26166	hgsc.bcm.edu	37	chr8	101016167	101016167	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ccctcaccttgaagaatgagTctcaagaaactgacggaaat	8	10	2	5			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr8:101016167T>C	ENST00000360863.6	-	17	2808	c.2614A>G	c.(2614-2616)Act>Gct	p.T872A	RGS22_ENST00000519421.1_5'UTR|SNORD77_ENST00000391112.1_RNA|RGS22_ENST00000523437.1_Missense_Mutation_p.T860A|RGS22_ENST00000523287.1_Missense_Mutation_p.T691A	NM_015668.3	NP_056483.3	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22	872	RGS 1. {ECO:0000255|PROSITE- ProRule:PRU00171}.				positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)		RGS22/SYCP1(2)	breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(33)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	68			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			GAAGAATGAGTCTCAAGAAAC	0.323																																					p.T872A		Atlas-SNP	.											.	RGS22	319	.	0			c.A2614G						.						123	113	116					8																	101016167		1843	4086	5929	SO:0001583	missense	26166	exon17			AATGAGTCTCAAG	AY009106	CCDS43758.1, CCDS69521.1, CCDS75775.1	8q22.2	2014-01-21	2007-08-14		ENSG00000132554	ENSG00000132554		"Regulators of G-protein signaling"	24499	protein-coding gene	gene with protein product		615650	"regulator of G-protein signalling 22"				Standard	XM_005250856		Approved	DKFZP434I092, PRTD-NY2, CT145	uc003yjb.1	Q8NE09	OTTHUMG00000164802	ENST00000360863.6:c.2614A>G	chr8.hg19:g.101016167T>C	ENSP00000354109:p.Thr872Ala	65.0	0.0		79.0	6.0	NM_015668	A8K944|Q569L2|Q86Y71|Q9BYZ4|Q9UFN6	Missense_Mutation	SNP	ENST00000360863.6	hg19	CCDS43758.1	.	.	.	.	.	.	.	.	.	.	T	0.763	-0.768655	0.02974	.	.	ENSG00000132554	ENST00000360863;ENST00000427793;ENST00000523287;ENST00000523437;ENST00000517828	T;T;T;T	0.23348	1.91;1.91;1.91;1.91	5.49	0.496	0.16896	Regulator of G protein signalling (3);Regulator of G protein signalling superfamily (1);	0.778208	0.11603	N	0.547526	T	0.06325	0.0163	N	0.00538	-1.39	0.09310	N	0.999999	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.40813	-0.9543	10	0.10377	T	0.69	.	9.1571	0.36998	0.4657:0.4546:0.0:0.0797	.	860;872;691	A8K944;Q8NE09;G3V112	.;RGS22_HUMAN;.	A	872;860;691;860;187	ENSP00000354109:T872A;ENSP00000429382:T691A;ENSP00000428212:T860A;ENSP00000427754:T187A	ENSP00000354109:T872A	T	-	1	0	RGS22	101085343	0.104000	0.21937	0.985000	0.45067	0.767000	0.43475	0.031000	0.13710	0.126000	0.18424	-1.252000	0.01501	ACT	.	.		0.323	RGS22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380365.1	NM_015668		C	101016167	T	C	101016167	3	2	279	1	0	0	0	0	1	0	0	0	13320	1667	58	2	1224	2	RGS22	8	101016167	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	10056049	101016167	45347855	181	39940										
GRHL2	79977	hgsc.bcm.edu	37	chr8	102589654	102589654	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	agagtgtggtgatggtggtcTtcagtgaagacaaaaacaga	14	4	2	5			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr8:102589654T>C	ENST00000251808.3	+	7	1248	c.910T>C	c.(910-912)Ttc>Ctc	p.F304L	GRHL2_ENST00000395927.1_Missense_Mutation_p.F288L	NM_024915.3	NP_079191.2	Q6ISB3	GRHL2_HUMAN	grainyhead-like 2 (Drosophila)	304					brain development (GO:0007420)|camera-type eye development (GO:0043010)|cardiac ventricle morphogenesis (GO:0003208)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digit morphogenesis (GO:0042733)|face development (GO:0060324)|in utero embryonic development (GO:0001701)|lung lobe morphogenesis (GO:0060463)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	all_cancers(14;4.39e-08)|all_epithelial(15;4.09e-10)|Lung NSC(17;7.11e-06)|all_lung(17;1.44e-05)		Epithelial(11;5.81e-09)|all cancers(13;3.81e-07)|OV - Ovarian serous cystadenocarcinoma(57;0.000213)			GATGGTGGTCTTCAGTGAAGA	0.483																																					p.F304L		Atlas-SNP	.											.	GRHL2	68	.	0			c.T910C						.						121	102	109					8																	102589654		2203	4300	6503	SO:0001583	missense	79977	exon7			GTGGTCTTCAGTG	AK023844	CCDS34931.1	8q22.3	2008-02-05	2005-07-11	2005-07-11	ENSG00000083307	ENSG00000083307			2799	protein-coding gene	gene with protein product		608576	"deafness, autosomal dominant 28", "transcription factor CP2-like 3"	DFNA28, TFCP2L3		12393799	Standard	NM_024915		Approved	FLJ13782, BOM	uc010mbu.3	Q6ISB3	OTTHUMG00000149915	ENST00000251808.3:c.910T>C	chr8.hg19:g.102589654T>C	ENSP00000251808:p.Phe304Leu	47.0	0.0		77.0	4.0	NM_024915	A1L303|Q6NT03|Q9H8B8	Missense_Mutation	SNP	ENST00000251808.3	hg19	CCDS34931.1	.	.	.	.	.	.	.	.	.	.	T	32	5.177064	0.94846	.	.	ENSG00000083307	ENST00000251808;ENST00000395927;ENST00000395928	T;T	0.48836	0.8;0.8	5.35	5.35	0.76521	CP2 transcription factor (1);	0.000000	0.85682	D	0.000000	T	0.72220	0.3433	M	0.85710	2.77	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.77797	-0.2453	10	0.87932	D	0	-24.3069	15.645	0.77042	0.0:0.0:0.0:1.0	.	304	Q6ISB3	GRHL2_HUMAN	L	304;288;304	ENSP00000251808:F304L;ENSP00000379260:F288L	ENSP00000251808:F304L	F	+	1	0	GRHL2	102658830	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.997000	0.88414	2.146000	0.66826	0.533000	0.62120	TTC	.	.		0.483	GRHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313882.1	NM_024915		C	102589654	T	C	102589654	3	2	279	1	0	0	0	0	1	0	0	0	6773	1609	56	2	936	2	GRHL2	8	102589654	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	1573487	102589654	43774368	182	39941										
ZFPM2	23414	hgsc.bcm.edu	37	chr8	106456547	106456547	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ggagacagcagaatcagatgGggacacacagtcagagaaac	13	8	2	4	rs374450510		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr8:106456547G>A	ENST00000407775.2	+	3	489	c.239G>A	c.(238-240)gGg>gAg	p.G80E	ZFPM2_ENST00000520492.1_5'UTR	NM_012082.3	NP_036214.2	Q8WW38	FOG2_HUMAN	zinc finger protein, FOG family member 2	80					blood coagulation (GO:0007596)|embryonic organ development (GO:0048568)|gonadal mesoderm development (GO:0007506)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of female gonad development (GO:2000195)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(4)|breast(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(11)|liver(2)|lung(48)|ovary(4)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	99			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			GAATCAGATGGGGACACACAG	0.463																																					p.G80E		Atlas-SNP	.											.	ZFPM2	219	.	0			c.G239A						.						78	83	82					8																	106456547		1938	4156	6094	SO:0001583	missense	23414	exon3			CAGATGGGGACAC	AF119334	CCDS47908.1	8q23	2013-01-10	2012-11-27		ENSG00000169946	ENSG00000169946		"Zinc fingers, C2H2-type", "Zinc fingers, C2HC-type containing"	16700	protein-coding gene	gene with protein product		603693	"zinc finger protein, multitype 2"			9927675, 10438528	Standard	NM_012082		Approved	FOG2, hFOG-2, ZNF89B, ZC2HC11B	uc003ymd.3	Q8WW38	OTTHUMG00000164818	ENST00000407775.2:c.239G>A	chr8.hg19:g.106456547G>A	ENSP00000384179:p.Gly80Glu	61.0	0.0		84.0	4.0	NM_012082	Q32MA6|Q9NPL7|Q9NPS4|Q9UNI5	Missense_Mutation	SNP	ENST00000407775.2	hg19	CCDS47908.1	.	.	.	.	.	.	.	.	.	.	G	11.69	1.714764	0.30413	.	.	ENSG00000169946	ENST00000407775	T	0.17854	2.25	5.87	5.87	0.94306	.	0.293907	0.27851	N	0.017599	T	0.12220	0.0297	N	0.04508	-0.205	0.80722	D	1	D	0.54964	0.969	P	0.46144	0.505	T	0.29792	-1.0000	10	0.17369	T	0.5	.	20.193	0.98233	0.0:0.0:1.0:0.0	.	80	Q8WW38	FOG2_HUMAN	E	80	ENSP00000384179:G80E	ENSP00000384179:G80E	G	+	2	0	ZFPM2	106525723	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.791000	0.55469	2.941000	0.99782	0.655000	0.94253	GGG	.	.		0.463	ZFPM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380614.1			A	106456547	G	A	106456547	3	1	279	1	0	0	0	0	1	0	0	0	17673	1232	43	3	249	3	ZFPM2	8	106456547	Missense_Mutation	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	3866893	106456547	39907475	183	39942										
COL22A1	169044	hgsc.bcm.edu	37	chr8	139890424	139890424	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tgtagcgcacgacccccacaCgggtgcggtcggggcccacc	14	17	0	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr8:139890424C>A	ENST00000303045.6	-	3	673	c.227G>T	c.(226-228)cGt>cTt	p.R76L	COL22A1_ENST00000435777.1_Missense_Mutation_p.R76L	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	76	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			GACCCCCACACGGGTGCGGTC	0.687										HNSCC(7;0.00092)																											p.R76L		Atlas-SNP	.											.	COL22A1	390	.	0			c.G227T						.						14	16	15					8																	139890424		2199	4297	6496	SO:0001583	missense	169044	exon3			CCCACACGGGTGC	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"Collagens"	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.227G>T	chr8.hg19:g.139890424C>A	ENSP00000303153:p.Arg76Leu	44.0	0.0		73.0	22.0	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Missense_Mutation	SNP	ENST00000303045.6	hg19	CCDS6376.1	.	.	.	.	.	.	.	.	.	.	C	35	5.486310	0.96323	.	.	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	D;D	0.86865	-2.18;-2.18	5.28	5.28	0.74379	von Willebrand factor, type A (3);	0.000000	0.48286	U	0.000191	D	0.93413	0.7899	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93351	0.6718	9	.	.	.	.	17.8919	0.88875	0.0:1.0:0.0:0.0	.	76	Q8NFW1	COMA1_HUMAN	L	76	ENSP00000303153:R76L;ENSP00000387655:R76L	.	R	-	2	0	COL22A1	139959606	1.000000	0.71417	0.954000	0.39281	0.984000	0.73092	7.606000	0.82863	2.440000	0.82611	0.585000	0.79938	CGT	.	.		0.687	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257		A	139890424	C	A	139890424	3	1	279	1	0	0	0	0	1	0	0	0	3683	536	19	1	4905	1	COL22A1	8	139890424	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	33433877	139890424	6473598	184	39943										
TSNARE1	203062	hgsc.bcm.edu	37	chr8	143399967	143399967	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gctggcgctggctgcaatggTcttgttggtctcctgctgtg	15	10	2	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr8:143399967T>C	ENST00000307180.3	-	7	1039	c.922A>G	c.(922-924)Acc>Gcc	p.T308A	TSNARE1_ENST00000519651.1_Missense_Mutation_p.T89A|TSNARE1_ENST00000524325.1_Missense_Mutation_p.T308A|TSNARE1_ENST00000518928.1_5'UTR|TSNARE1_ENST00000520166.1_Missense_Mutation_p.T308A	NM_145003.3	NP_659440.2	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1	308					intracellular protein transport (GO:0006886)|synaptic vesicle exocytosis (GO:0016079)	integral component of membrane (GO:0016021)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)			breast(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(6)|ovary(2)|stomach(2)|urinary_tract(1)	20	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					GCTGCAATGGTCTTGTTGGTC	0.667																																					p.T308A		Atlas-SNP	.											.	TSNARE1	59	.	0			c.A922G						.						92	86	88					8																	143399967		2203	4300	6503	SO:0001583	missense	203062	exon7			CAATGGTCTTGTT			8q24.3	2005-08-18							26437	protein-coding gene	gene with protein product						14702039	Standard	XM_005250828		Approved	FLJ31164	uc003ywk.3	Q96NA8		ENST00000307180.3:c.922A>G	chr8.hg19:g.143399967T>C	ENSP00000303437:p.Thr308Ala	65.0	0.0		64.0	4.0	NM_145003	B7ZLB0|Q14D03	Missense_Mutation	SNP	ENST00000307180.3	hg19	CCDS6384.1	.	.	.	.	.	.	.	.	.	.	T	0.056	-1.236321	0.01505	.	.	ENSG00000171045	ENST00000524325;ENST00000307180;ENST00000520166;ENST00000519651	T;T;T;T	0.29655	1.56;1.56;1.56;1.56	4.0	1.44	0.22558	t-SNARE (1);	0.238492	0.20572	U	0.089706	T	0.27063	0.0663	M	0.72894	2.215	0.09310	N	1	B;B;B;B	0.24618	0.064;0.107;0.064;0.064	B;B;B;B	0.20184	0.028;0.021;0.028;0.028	T	0.24584	-1.0156	10	0.20519	T	0.43	.	7.1917	0.25828	0.0:0.2023:0.0:0.7977	.	308;89;308;308	B7ZLB0;E5RHT3;Q96NA8;A0AVG3	.;.;TSNA1_HUMAN;.	A	308;308;308;89	ENSP00000428763:T308A;ENSP00000303437:T308A;ENSP00000427770:T308A;ENSP00000429679:T89A	ENSP00000303437:T308A	T	-	1	0	TSNARE1	143397874	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.277000	0.08502	-0.006000	0.14370	0.533000	0.62120	ACC	.	.		0.667	TSNARE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_145003		C	143399967	T	C	143399967	3	2	279	1	0	0	0	0	1	0	0	0	16645	1667	58	2	647	2	TSNARE1	8	143399967	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	3509543	143399967	2964055	185	39944										
KIFC2	90990	hgsc.bcm.edu	37	chr8	145697525	145697526	+	Frame_Shift_Del	DEL	CT	CT	-													0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cccaccccatcctcagggccCtcctgaggaccccggcatag							TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr8:145697525_145697526delCT	ENST00000301332.2	+	14	1867_1868	c.1490_1491delCT	c.(1489-1491)cctfs	p.P498fs	FOXH1_ENST00000525197.1_5'Flank|KIFC2_ENST00000531423.1_3'UTR|KIFC2_ENST00000301331.5_Frame_Shift_Del_p.P246fs	NM_145754.2	NP_665697.1	Q96AC6	KIFC2_HUMAN	kinesin family member C2	498	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(7)|ovary(3)|prostate(3)|skin(2)|urinary_tract(1)	19	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			CCTCAGGGCCCTCCTGAGGACC	0.678																																					p.497_497del		Atlas-Indel,Pindel	.											.	KIFC2	53	.	0			c.1489_1490del						.																																			SO:0001589	frameshift_variant	90990	exon14			.	AY007121	CCDS6427.1	8q24.3	2007-02-13			ENSG00000167702	ENSG00000167702		"Kinesins"	29530	protein-coding gene	gene with protein product						9115737	Standard	NM_145754		Approved		uc003zcz.3	Q96AC6	OTTHUMG00000165133	ENST00000301332.2:c.1490_1491delCT	chr8.hg19:g.145697525_145697526delCT	ENSP00000301332:p.Pro498fs	98.0	0.0		120.0	31.0	NM_145754	E9PHB2|Q96NN6	Frame_Shift_Del	DEL	ENST00000301332.2	hg19	CCDS6427.1																																																																																			.	.		0.678	KIFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382052.2	NM_145754		-	145697526	CT	-	145697525	7	5	279	1	0	1	0	1	0	0	0	0	8322	681	24	0	1544	0	KIFC2	8	145697525	Frame_Shift_Del	DEL	CT	TCGA-G3-A3CG-01A-11D-A20W-10	2297558	145697525	666497	186	39945										
ZNF7	7553	hgsc.bcm.edu	37	chr8	146067567	146067567	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	accagagaactcacactgggGagaggccctacccttgcaag	11	13	1	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr8:146067567G>A	ENST00000528372.1	+	5	1315	c.1075G>A	c.(1075-1077)Gag>Aag	p.E359K	ZNF7_ENST00000325217.5_Intron|ZNF7_ENST00000525266.1_Intron|ZNF7_ENST00000544249.1_Missense_Mutation_p.E263K|ZNF7_ENST00000446747.2_Missense_Mutation_p.E370K|ZNF7_ENST00000325241.6_Missense_Mutation_p.E359K			P17097	ZNF7_HUMAN	zinc finger protein 7	359					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|ovary(5)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.0812)|Ovarian(118;0.0822)|Acute lymphoblastic leukemia(644;0.143)	Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;2.11e-07)		TCACACTGGGGAGAGGCCCTA	0.557																																					p.E359K		Atlas-SNP	.											ZNF7,NS,carcinoma,-2,1	ZNF7	62	.	0			c.G1075A						.						59	56	57					8																	146067567		2203	4300	6503	SO:0001583	missense	7553	exon5			ACTGGGGAGAGGC	AB209619	CCDS6435.1, CCDS64996.1, CCDS64998.1, CCDS64999.1	8q24	2013-01-08	2006-05-09		ENSG00000147789	ENSG00000147789		"Zinc fingers, C2H2-type", "-"	13139	protein-coding gene	gene with protein product		194531	"zinc finger protein 7 (KOX 4, clone HF.16)"			2106481, 1946370	Standard	NM_003416		Approved	KOX4, HF.16	uc003zeg.4	P17097	OTTHUMG00000165200	ENST00000528372.1:c.1075G>A	chr8.hg19:g.146067567G>A	ENSP00000432724:p.Glu359Lys	59.0	0.0		39.0	2.0	NM_003416	B4DT08|D3DWN6|P17015|Q8N8Y4	Missense_Mutation	SNP	ENST00000528372.1	hg19	CCDS6435.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.028091	0.75390	.	.	ENSG00000147789	ENST00000325241;ENST00000446747;ENST00000544249;ENST00000528372	T;T;T;T	0.24350	1.86;1.86;1.86;1.86	4.89	4.02	0.46733	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.47852	D	0.000212	T	0.33527	0.0866	L	0.56199	1.76	0.80722	D	1	D;D	0.53462	0.96;0.96	P;P	0.53518	0.728;0.728	T	0.04041	-1.0982	9	.	.	.	-30.5563	8.8041	0.34927	0.1751:0.0:0.8249:0.0	.	370;359	B4DT08;P17097	.;ZNF7_HUMAN	K	359;370;263;359	ENSP00000320627:E359K;ENSP00000393260:E370K;ENSP00000439424:E263K;ENSP00000432724:E359K	.	E	+	1	0	ZNF7	146038371	1.000000	0.71417	0.864000	0.33941	0.935000	0.57460	6.848000	0.75409	1.294000	0.44707	0.555000	0.69702	GAG	.	.		0.557	ZNF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382660.1	NM_003416		A	146067567	G	A	146067567	3	1	279	1	0	0	0	0	1	0	0	0	18117	1175	41	3	1089	3	ZNF7	8	146067567	Missense_Mutation	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	370042	146067567	296455	187	39946										
SMARCA2	6595	hgsc.bcm.edu	37	chr9	2039821	2039821	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cagcagcagcagcagcaacaGcagccgcagcagcagccgcc	12	17	0	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr9:2039821G>A	ENST00000382203.1	+	4	920	c.711G>A	c.(709-711)caG>caA	p.Q237Q	SMARCA2_ENST00000491574.1_3'UTR|RP11-264I13.2_ENST00000426860.1_RNA|SMARCA2_ENST00000382194.1_Silent_p.Q237Q|SMARCA2_ENST00000357248.2_Silent_p.Q237Q|SMARCA2_ENST00000349721.2_Silent_p.Q237Q			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	237	Poly-Gln.			Missing (in Ref. 1; CAA51407). {ECO:0000305}.	aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|chromatin remodeling (GO:0006338)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		agcagcaacagcagccgcagc	0.577																																					p.Q237Q		Atlas-SNP	.											SMARCA2_ENST00000349721,caecum,carcinoma,0,2	SMARCA2	313	.	0			c.G711A						.						12	14	13					9																	2039821		2178	4243	6421	SO:0001819	synonymous_variant	6595	exon4			GCAACAGCAGCCG	D26155	CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1	9p24.3	2008-11-11	2006-11-09		ENSG00000080503	ENSG00000080503			11098	protein-coding gene	gene with protein product		600014		SNF2L2		8012116	Standard	NM_003070		Approved	BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2	uc003zhc.3	P51531	OTTHUMG00000019445	ENST00000382203.1:c.711G>A	chr9.hg19:g.2039821G>A		76.0	2.0		77.0	7.0	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Silent	SNP	ENST00000382203.1	hg19	CCDS34977.1																																																																																			.	.		0.577	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070		A	2039821	G	A	2039821	2	1	279	1	0	0	0	0	0	0	0	1	14784	962	34	3		3	SMARCA2	9	2039821	Silent	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10		2039821	139173610	188	39947										
CDC37L1	55664	hgsc.bcm.edu	37	chr9	4688579	4688579	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	aatcagaatcatttatgcaaAaatatgagcaaaaaatcaga	5	5	3	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr9:4688579A>C	ENST00000381854.3	+	3	683	c.481A>C	c.(481-483)Aaa>Caa	p.K161Q	CDC37L1_ENST00000381858.1_Missense_Mutation_p.K161Q	NM_017913.2	NP_060383.2	Q7L3B6	CD37L_HUMAN	cell division cycle 37-like 1	161	Self-association and interaction with Hsp90.|Self-association.					cytoplasm (GO:0005737)				breast(1)|kidney(1)|lung(2)	4	all_hematologic(13;0.137)	Breast(48;0.238)		GBM - Glioblastoma multiforme(50;0.0318)		ATTTATGCAAAAATATGAGCA	0.249																																					p.K161Q		Atlas-SNP	.											.	CDC37L1	19	.	0			c.A481C						.						41	42	42					9																	4688579		2185	4284	6469	SO:0001583	missense	55664	exon3			ATGCAAAAATATG	AK000497	CCDS6454.1	9p24.1	2013-01-17	2013-01-17		ENSG00000106993	ENSG00000106993			17179	protein-coding gene	gene with protein product		610346	"CDC37 cell division cycle 37 homolog (S. cerevisiae)-like 1", "cell division cycle 37 homolog (S. cerevisiae)-like 1"				Standard	NM_017913		Approved	HARC, FLJ20639, CDC37B	uc003zio.3	Q7L3B6	OTTHUMG00000019465	ENST00000381854.3:c.481A>C	chr9.hg19:g.4688579A>C	ENSP00000371278:p.Lys161Gln	176.0	0.0		160.0	53.0	NM_017913	B1AL70|Q9NWS3|Q9NX16	Missense_Mutation	SNP	ENST00000381854.3	hg19	CCDS6454.1	.	.	.	.	.	.	.	.	.	.	A	18.53	3.644849	0.67358	.	.	ENSG00000106993	ENST00000381858;ENST00000381854	T;T	0.48522	0.81;0.81	5.79	5.79	0.91817	Cdc37, Hsp90 binding (1);	0.098323	0.64402	D	0.000002	T	0.58538	0.2129	M	0.79475	2.455	0.54753	D	0.99998	P	0.45283	0.855	P	0.46320	0.512	T	0.64795	-0.6323	10	0.66056	D	0.02	-25.7243	16.123	0.81375	1.0:0.0:0.0:0.0	.	161	Q7L3B6	CD37L_HUMAN	Q	161	ENSP00000371282:K161Q;ENSP00000371278:K161Q	ENSP00000371278:K161Q	K	+	1	0	CDC37L1	4678579	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.473000	0.73572	2.202000	0.70862	0.533000	0.62120	AAA	.	.		0.249	CDC37L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051564.1	NM_017913		C	4688579	A	C	4688579	3	2	279	1	0	0	0	0	1	0	0	0	3071	15	1	5	491	5	CDC37L1	9	4688579	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	2648758	4688579	136524852	189	39948										
KIAA1432	57589	hgsc.bcm.edu	37	chr9	5756332	5756332	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	taatagtatttagagcagacTgttcaatatgcctttacagt	7	6	1	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr9:5756332T>C	ENST00000414202.2	+	16	2004	c.1813T>C	c.(1813-1815)Tgt>Cgt	p.C605R	KIAA1432_ENST00000418622.3_Missense_Mutation_p.C526R|KIAA1432_ENST00000251879.6_Missense_Mutation_p.C605R|KIAA1432_ENST00000381532.2_Missense_Mutation_p.C526R|KIAA1432_ENST00000449720.2_Missense_Mutation_p.C489R	NM_001206557.1|NM_020829.3	NP_001193486.1|NP_065880.2														breast(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(23)|prostate(1)|upper_aerodigestive_tract(1)	45		Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000525)|Lung(218;0.122)		TAGAGCAGACTGTTCAATATG	0.378																																					p.C605R		Atlas-SNP	.											.	KIAA1432	97	.	0			c.T1813C						.						141	135	137					9																	5756332		2203	4300	6503	SO:0001583	missense	57589	exon16			GCAGACTGTTCAA																												ENST00000414202.2:c.1813T>C	chr9.hg19:g.5756332T>C	ENSP00000416696:p.Cys605Arg	82.0	0.0		88.0	4.0	NM_001135920		Missense_Mutation	SNP	ENST00000414202.2	hg19	CCDS34982.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.02|18.02	3.530200|3.530200	0.64860|0.64860	.|.	.|.	ENSG00000107036|ENSG00000107036	ENST00000251879;ENST00000414202;ENST00000381532;ENST00000418622;ENST00000449720|ENST00000545641	.|.	.|.	.|.	5.89|5.89	5.89|5.89	0.94794|0.94794	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72366|0.72366	0.3451|0.3451	M|M	0.63843|0.63843	1.955|1.955	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0|.	D;D;D;D|.	0.76575|.	0.972;0.972;0.98;0.988|.	T|T	0.70974|0.70974	-0.4726|-0.4726	9|5	0.24483|.	T|.	0.36|.	-15.0596|-15.0596	16.3123|16.3123	0.82883|0.82883	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	489;526;605;605|.	B7ZM67;B2RN24;Q4ADV7;G5E932|.	.;.;RIC1_HUMAN;.|.	R|P	605;605;526;526;489|496	.|.	ENSP00000251879:C605R|.	C|L	+|+	1|2	0|0	KIAA1432|KIAA1432	5746332|5746332	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	7.698000|7.698000	0.84413|0.84413	2.254000|2.254000	0.74563|0.74563	0.459000|0.459000	0.35465|0.35465	TGT|CTG	.	.		0.378	KIAA1432-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051636.3			C	5756332	T	C	5756332	3	2	279	1	0	0	0	0	1	0	0	0	8242	1580	55	2	1634	2	KIAA1432	9	5756332	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	1067753	5756332	135457099	190	39949										
KIAA1432	57589	hgsc.bcm.edu	37	chr9	5772583	5772583	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ggtgatgaatgcagtattggTtcagccacagacttgactga	12	7	1	5			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr9:5772583T>C	ENST00000414202.2	+	24	3827	c.3636T>C	c.(3634-3636)ggT>ggC	p.G1212G	KIAA1432_ENST00000418622.3_Silent_p.G1133G|KIAA1432_ENST00000449720.2_Silent_p.G1096G	NM_001206557.1|NM_020829.3	NP_001193486.1|NP_065880.2														breast(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(23)|prostate(1)|upper_aerodigestive_tract(1)	45		Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000525)|Lung(218;0.122)		GCAGTATTGGTTCAGCCACAG	0.393																																					p.G1212G		Atlas-SNP	.											.	KIAA1432	97	.	0			c.T3636C						.						131	119	123					9																	5772583		2203	4300	6503	SO:0001819	synonymous_variant	57589	exon24			TATTGGTTCAGCC																												ENST00000414202.2:c.3636T>C	chr9.hg19:g.5772583T>C		103.0	0.0		92.0	4.0	NM_020829		Silent	SNP	ENST00000414202.2	hg19	CCDS34982.2	.	.	.	.	.	.	.	.	.	.	T	9.659	1.143651	0.21205	.	.	ENSG00000107036	ENST00000545641	.	.	.	5.66	1.89	0.25635	.	.	.	.	.	T	0.51873	0.1700	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.36286	-0.9754	4	.	.	.	-17.5631	5.224	0.15383	0.0:0.1478:0.2903:0.5619	.	.	.	.	L	1104	.	.	F	+	1	0	KIAA1432	5762583	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.049000	0.30392	0.073000	0.16731	0.459000	0.35465	TTC	.	.		0.393	KIAA1432-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051636.3			C	5772583	T	C	5772583	2	2	279	1	0	0	0	0	0	0	0	1	8242	1712	60	2		2	KIAA1432	9	5772583	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	16251	5772583	135440848	191	39950										
TTC39B	158219	hgsc.bcm.edu	37	chr9	15177727	15177727	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tgattgtaacatagttcagcTtgcaagggccgctgtaagtt	11	7	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr9:15177727T>C	ENST00000512701.2	-	18	1845	c.1809A>G	c.(1807-1809)caA>caG	p.Q603Q	TTC39B_ENST00000355694.2_Silent_p.Q537Q|TTC39B_ENST00000380850.4_Silent_p.Q590Q|TTC39B_ENST00000507285.1_Silent_p.Q438Q|TTC39B_ENST00000297615.5_Silent_p.Q534Q|TTC39B_ENST00000507993.1_Silent_p.Q438Q			Q5VTQ0	TT39B_HUMAN	tetratricopeptide repeat domain 39B	603										NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)	21						ATAGTTCAGCTTGCAAGGGCC	0.398																																					p.Q603Q		Atlas-SNP	.											.	TTC39B	83	.	0			c.A1809G						.						141	125	131					9																	15177727		2203	4300	6503	SO:0001819	synonymous_variant	158219	exon18			TTCAGCTTGCAAG	AK091187	CCDS6477.1, CCDS6477.2, CCDS55294.1, CCDS55295.1, CCDS55296.1	9p22.2	2013-01-11	2008-06-23	2008-06-23	ENSG00000155158	ENSG00000155158		"Tetratricopeptide (TTC) repeat domain containing"	23704	protein-coding gene	gene with protein product		613574	"chromosome 9 open reading frame 52"	C9orf52			Standard	NM_001168339		Approved	FLJ33868	uc003zlr.2	Q5VTQ0	OTTHUMG00000019581	ENST00000512701.2:c.1809A>G	chr9.hg19:g.15177727T>C		111.0	0.0		80.0	4.0	NM_152574	A5PLN1|B4DQ10|B4DQX4|B4DW93|Q8IVR7|Q8IXZ6|Q8N267	Silent	SNP	ENST00000512701.2	hg19	CCDS6477.2																																																																																			.	.		0.398	TTC39B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051758.3	NM_152574		C	15177727	T	C	15177727	2	2	279	1	0	0	0	0	0	0	0	1	16723	1606	56	2		2	TTC39B	9	15177727	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	9405144	15177727	126035704	192	39951										
CA9	768	hgsc.bcm.edu	37	chr9	35674185	35674185	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	attcacccagagaggaggatCcacccggagaggaggatcta	13	10	2	2	rs113670057		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr9:35674185C>T	ENST00000378357.4	+	1	333	c.229C>T	c.(229-231)Cca>Tca	p.P77S	RN7SL22P_ENST00000471800.2_RNA	NM_001216.2	NP_001207.2	Q16790	CAH9_HUMAN	carbonic anhydrase IX	77	Proteoglycan-like (PG).				bicarbonate transport (GO:0015701)|cellular response to hypoxia (GO:0071456)|morphogenesis of an epithelium (GO:0002009)|one-carbon metabolic process (GO:0006730)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to drug (GO:0042493)|response to testosterone (GO:0033574)|secretion (GO:0046903)|small molecule metabolic process (GO:0044281)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(3)|lung(5)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	17	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)		Benzthiazide(DB00562)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Zonisamide(DB00909)	AGAGGAGGATCCACCCGGAGA	0.562																																					p.P77S		Atlas-SNP	.											.	CA9	48	.	0			c.C229T						.						58	56	56					9																	35674185		2203	4300	6503	SO:0001583	missense	768	exon1			GAGGATCCACCCG	X66839	CCDS6585.1	9p13.3	2012-08-21			ENSG00000107159	ENSG00000107159		"Carbonic anhydrases"	1383	protein-coding gene	gene with protein product	"carbonic dehydratase", "RCC-associated protein G250"	603179				8661007, 9787087	Standard	NM_001216		Approved	MN, CAIX	uc003zxo.4	Q16790	OTTHUMG00000021029	ENST00000378357.4:c.229C>T	chr9.hg19:g.35674185C>T	ENSP00000367608:p.Pro77Ser	103.0	0.0		87.0	6.0	NM_001216	Q5T4R1	Missense_Mutation	SNP	ENST00000378357.4	hg19	CCDS6585.1	.	.	.	.	.	.	.	.	.	.	C	7.172	0.587818	0.13812	.	.	ENSG00000107159	ENST00000378357;ENST00000544074	T	0.62788	-0.0	3.48	-1.89	0.07689	.	.	.	.	.	T	0.39809	0.1092	N	0.20986	0.625	0.09310	N	1	B;B	0.14012	0.009;0.005	B;B	0.08055	0.003;0.001	T	0.13980	-1.0489	9	0.37606	T	0.19	.	3.0936	0.06302	0.3213:0.2582:0.0:0.4204	.	77;77	F5H404;Q16790	.;CAH9_HUMAN	S	77	ENSP00000367608:P77S	ENSP00000367608:P77S	P	+	1	0	CA9	35664185	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-0.507000	0.06352	-0.820000	0.04318	0.655000	0.94253	CCA	.	C|0.500;T|0.500		0.562	CA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055479.1	NM_001216		T	35674185	C	T	35674185	3	4	279	1	0	0	0	0	1	0	0	0	2526	855	30	3	231	3	CA9	9	35674185	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	20496458	35674185	105539246	193	39952										
CA9	768	hgsc.bcm.edu	37	chr9	35674228	35674228	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tggagaggaggatctacctgGagaggaggatctacctgaag	16	6	2	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr9:35674228G>A	ENST00000378357.4	+	1	376	c.272G>A	c.(271-273)gGa>gAa	p.G91E	RN7SL22P_ENST00000471800.2_RNA	NM_001216.2	NP_001207.2	Q16790	CAH9_HUMAN	carbonic anhydrase IX	91	Proteoglycan-like (PG).				bicarbonate transport (GO:0015701)|cellular response to hypoxia (GO:0071456)|morphogenesis of an epithelium (GO:0002009)|one-carbon metabolic process (GO:0006730)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to drug (GO:0042493)|response to testosterone (GO:0033574)|secretion (GO:0046903)|small molecule metabolic process (GO:0044281)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(3)|lung(5)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	17	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)		Benzthiazide(DB00562)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Zonisamide(DB00909)	GATCTACCTGGAGAGGAGGAT	0.537																																					p.G91E		Atlas-SNP	.											CA9,NS,carcinoma,0,2	CA9	48	.	0			c.G272A						.						61	55	57					9																	35674228		2203	4300	6503	SO:0001583	missense	768	exon1			TACCTGGAGAGGA	X66839	CCDS6585.1	9p13.3	2012-08-21			ENSG00000107159	ENSG00000107159		"Carbonic anhydrases"	1383	protein-coding gene	gene with protein product	"carbonic dehydratase", "RCC-associated protein G250"	603179				8661007, 9787087	Standard	NM_001216		Approved	MN, CAIX	uc003zxo.4	Q16790	OTTHUMG00000021029	ENST00000378357.4:c.272G>A	chr9.hg19:g.35674228G>A	ENSP00000367608:p.Gly91Glu	95.0	0.0		82.0	7.0	NM_001216	Q5T4R1	Missense_Mutation	SNP	ENST00000378357.4	hg19	CCDS6585.1	.	.	.	.	.	.	.	.	.	.	G	7.555	0.663537	0.14710	.	.	ENSG00000107159	ENST00000378357;ENST00000544074	T	0.62788	0.0	3.89	2.97	0.34412	.	.	.	.	.	T	0.43322	0.1242	N	0.17082	0.46	0.09310	N	1	B;B	0.25904	0.137;0.084	B;B	0.25884	0.064;0.029	T	0.34700	-0.9818	9	0.54805	T	0.06	.	6.3978	0.21622	0.2279:0.0:0.7721:0.0	.	91;91	F5H404;Q16790	.;CAH9_HUMAN	E	91	ENSP00000367608:G91E	ENSP00000367608:G91E	G	+	2	0	CA9	35664228	0.211000	0.23529	0.001000	0.08648	0.004000	0.04260	0.310000	0.19356	0.796000	0.33947	0.591000	0.81541	GGA	.	.		0.537	CA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055479.1	NM_001216		A	35674228	G	A	35674228	3	1	279	1	0	0	0	0	1	0	0	0	2526	1174	41	3	274	3	CA9	9	35674228	Missense_Mutation	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	43	35674228	105539203	194	39953										
ZCCHC7	84186	hgsc.bcm.edu	37	chr9	37357124	37357124	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ccttctaagccctttcaccgTtcatcacattaccacacgtc	3	17	4	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr9:37357124T>C	ENST00000336755.5	+	9	1597	c.1491T>C	c.(1489-1491)cgT>cgC	p.R497R	ZCCHC7_ENST00000461038.1_3'UTR|ZCCHC7_ENST00000534928.1_Silent_p.R207R	NM_032226.2	NP_115602.2	Q8N3Z6	ZCHC7_HUMAN	zinc finger, CCHC domain containing 7	497						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	30				GBM - Glioblastoma multiforme(29;0.0137)		CCTTTCACCGTTCATCACATT	0.488																																					p.R497R		Atlas-SNP	.											.	ZCCHC7	56	.	0			c.T1491C						.						70	76	74					9																	37357124		2203	4300	6503	SO:0001819	synonymous_variant	84186	exon9			TCACCGTTCATCA	AK026264	CCDS6608.2	9p13.1	2008-05-02			ENSG00000147905	ENSG00000147905		"Zinc fingers, CCHC domain containing"	26209	protein-coding gene	gene with protein product							Standard	NM_032226		Approved	FLJ22611, AIR1	uc003zzq.3	Q8N3Z6	OTTHUMG00000019915	ENST00000336755.5:c.1491T>C	chr9.hg19:g.37357124T>C		152.0	0.0		95.0	4.0	NM_032226	B2RCI4|D3DRQ0|Q5T0Q8|Q5T0Q9|Q5T0R0|Q8N2M1|Q8N4J2|Q8TBK8|Q9H648|Q9P0F0	Silent	SNP	ENST00000336755.5	hg19	CCDS6608.2																																																																																			.	.		0.488	ZCCHC7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052453.2	NM_032226		C	37357124	T	C	37357124	2	2	279	1	0	0	0	0	0	0	0	1	17608	1712	60	2		2	ZCCHC7	9	37357124	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	1682896	37357124	103856307	195	39954										
FRMPD1	22844	hgsc.bcm.edu	37	chr9	37740139	37740139	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gtggactgcgtactcgaaccTctctctgacaggcgcctggt	12	13	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr9:37740139T>C	ENST00000539465.1	+	15	2207	c.1614T>C	c.(1612-1614)ccT>ccC	p.P538P	FRMPD1_ENST00000536622.1_Silent_p.P360P|RP11-613M10.9_ENST00000540557.1_Intron|FRMPD1_ENST00000377765.3_Silent_p.P538P|FRMPD1_ENST00000541302.1_Silent_p.P407P			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	538						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		TACTCGAACCTCTCTCTGACA	0.572																																					p.P538P		Atlas-SNP	.											.	FRMPD1	237	.	0			c.T1614C						.						76	82	80					9																	37740139		2203	4300	6503	SO:0001819	synonymous_variant	22844	exon15			CGAACCTCTCTCT	AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.1614T>C	chr9.hg19:g.37740139T>C		83.0	0.0		99.0	5.0	NM_014907	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Silent	SNP	ENST00000539465.1	hg19	CCDS6612.1																																																																																			.	.		0.572	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907		C	37740139	T	C	37740139	2	2	279	1	0	0	0	0	0	0	0	1	6065	1538	54	2		2	FRMPD1	9	37740139	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	383015	37740139	103473292	196	39955										
TRPM6	140803	hgsc.bcm.edu	37	chr9	77386643	77386643	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ctgatgtcactcggattcgtTcctcacaactacaattcaca	5	13	3	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr9:77386643T>C	ENST00000360774.1	-	25	3749	c.3512A>G	c.(3511-3513)gAa>gGa	p.E1171G	TRPM6_ENST00000376871.3_Intron|TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000361255.3_Missense_Mutation_p.E1166G|TRPM6_ENST00000449912.2_Missense_Mutation_p.E1166G|TRPM6_ENST00000451710.3_Missense_Mutation_p.E1171G|TRPM6_ENST00000376864.4_Missense_Mutation_p.E1171G	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	1171					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						TCGGATTCGTTCCTCACAACT	0.373																																					p.E1171G		Atlas-SNP	.											.	TRPM6	377	.	0			c.A3512G						.						125	109	115					9																	77386643		2203	4300	6503	SO:0001583	missense	140803	exon25			ATTCGTTCCTCAC	AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"Voltage-gated ion channels / Transient receptor potential cation channels"	17995	protein-coding gene	gene with protein product		607009	"hypomagnesemia, secondary hypocalcemia"	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.3512A>G	chr9.hg19:g.77386643T>C	ENSP00000354006:p.Glu1171Gly	80.0	0.0		88.0	4.0	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	ENST00000360774.1	hg19	CCDS6647.1	.	.	.	.	.	.	.	.	.	.	T	17.02	3.280949	0.59758	.	.	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000449912;ENST00000361255;ENST00000376864;ENST00000312449;ENST00000448641	T;T;T;T;T	0.55760	0.5;0.5;0.5;0.5;0.5	5.23	4.07	0.47477	.	0.233816	0.50627	D	0.000105	T	0.70150	0.3191	M	0.85859	2.78	0.46901	D	0.999242	P;D;P	0.55385	0.85;0.971;0.907	P;P;P	0.58721	0.589;0.844;0.767	T	0.74618	-0.3605	10	0.87932	D	0	.	12.2995	0.54866	0.0:0.0:0.1418:0.8582	.	1171;1166;1166	Q9BX84;Q9BX84-3;Q9BX84-2	TRPM6_HUMAN;.;.	G	1171;1171;1166;1166;1171;834;834	ENSP00000354006:E1171G;ENSP00000407341:E1171G;ENSP00000396672:E1166G;ENSP00000354962:E1166G;ENSP00000366060:E1171G	ENSP00000309693:E834G	E	-	2	0	TRPM6	76576463	1.000000	0.71417	0.164000	0.22755	0.473000	0.32948	3.960000	0.56752	0.808000	0.34231	-0.313000	0.08912	GAA	.	.		0.373	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662		C	77386643	T	C	77386643	3	2	279	1	0	0	0	0	1	0	0	0	16605	1783	62	2	2616	2	TRPM6	9	77386643	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	39646504	77386643	63826788	197	39956										
ZNF367	195828	hgsc.bcm.edu	37	chr9	99180148	99180148	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	agccggggctggtggggatgAgcggcggcggcggctccggc	23	11	0	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr9:99180148A>G	ENST00000375256.4	-	1	463	c.167T>C	c.(166-168)cTc>cCc	p.L56P		NM_153695.3	NP_710162.1	Q7RTV3	ZN367_HUMAN	zinc finger protein 367	56	Pro-rich.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(4)|large_intestine(3)|lung(3)|prostate(1)	12		Acute lymphoblastic leukemia(62;0.0167)				GGTGGGGATGAGCGGCGGCGG	0.716																																					p.L56P		Atlas-SNP	.											.	ZNF367	27	.	0			c.T167C						.						5	7	6					9																	99180148		1985	3966	5951	SO:0001583	missense	195828	exon1			GGGATGAGCGGCG	AK091289	CCDS6718.1	9q22	2008-05-02			ENSG00000165244	ENSG00000165244		"Zinc fingers, C2H2-type"	18320	protein-coding gene	gene with protein product		610160					Standard	NM_153695		Approved	FLJ33970	uc004awf.3	Q7RTV3	OTTHUMG00000020295	ENST00000375256.4:c.167T>C	chr9.hg19:g.99180148A>G	ENSP00000364405:p.Leu56Pro	46.0	0.0		61.0	4.0	NM_153695	Q6Q7C8	Missense_Mutation	SNP	ENST00000375256.4	hg19	CCDS6718.1	.	.	.	.	.	.	.	.	.	.	A	12.87	2.068758	0.36470	.	.	ENSG00000165244	ENST00000375256	T	0.06294	3.32	4.0	2.81	0.32909	.	0.170472	0.39544	N	0.001338	T	0.03783	0.0107	N	0.25647	0.755	0.80722	D	1	B;B	0.11235	0.004;0.002	B;B	0.13407	0.009;0.004	T	0.45411	-0.9263	10	0.22706	T	0.39	-11.934	2.6294	0.04939	0.4982:0.2573:0.2444:0.0	.	56;56	Q7RTV3-2;Q7RTV3	.;ZN367_HUMAN	P	56	ENSP00000364405:L56P	ENSP00000364405:L56P	L	-	2	0	ZNF367	98219969	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	2.237000	0.43061	0.570000	0.29347	0.260000	0.18958	CTC	.	.		0.716	ZNF367-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053266.1			G	99180148	A	G	99180148	3	3	279	1	0	0	0	0	1	0	0	0	17886	304	11	2	905	2	ZNF367	9	99180148	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	21793505	99180148	42033283	198	39957										
RAD23B	5887	hgsc.bcm.edu	37	chr9	110064350	110064350	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gatgatactgctctcaaagaAtataaaattgatgagaaaaa	7	4	1	4			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr9:110064350A>G	ENST00000358015.3	+	3	534	c.183A>G	c.(181-183)gaA>gaG	p.E61E	RAD23B_ENST00000416373.2_5'UTR	NM_001244713.1|NM_002874.4	NP_001231642.1|NP_002865.1	P54727	RD23B_HUMAN	RAD23 homolog B (S. cerevisiae)	61	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				DNA repair (GO:0006281)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage recognition (GO:0000715)|nucleotide-excision repair, DNA damage removal (GO:0000718)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|XPC complex (GO:0071942)	damaged DNA binding (GO:0003684)|polyubiquitin binding (GO:0031593)|single-stranded DNA binding (GO:0003697)			breast(3)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14						CTCTCAAAGAATATAAAATTG	0.294								Direct reversal of damage;Nucleotide excision repair (NER)																													p.E61E		Atlas-SNP	.											.	RAD23B	31	.	0			c.A183G						.						137	143	141					9																	110064350		2203	4298	6501	SO:0001819	synonymous_variant	5887	exon3			CAAAGAATATAAA		CCDS6769.1, CCDS59138.1	9q31.2	2008-07-21	2001-11-28		ENSG00000119318	ENSG00000119318			9813	protein-coding gene	gene with protein product	"XP-C repair complementing protein", "XP-C repair complementing complex 58 kDa"	600062	"RAD23 (S. cerevisiae) homolog B"			7851894, 8168482	Standard	NM_002874		Approved	HHR23B, P58, HR23B	uc004bde.3	P54727	OTTHUMG00000020446	ENST00000358015.3:c.183A>G	chr9.hg19:g.110064350A>G		118.0	0.0		87.0	4.0	NM_002874	B3KWK8|G5E9P0|Q7Z5K8|Q8WUB0	Silent	SNP	ENST00000358015.3	hg19	CCDS6769.1																																																																																			.	.		0.294	RAD23B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053548.1	NM_002874		G	110064350	A	G	110064350	2	3	279	1	0	0	0	0	0	0	0	1	12998	98	4	2		2	RAD23B	9	110064350	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	10884202	110064350	31149081	199	39958										
CTNNAL1	8727	hgsc.bcm.edu	37	chr9	111710491	111710491	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gttgatgaattaaatcctggGaagttttcagtggcccctct	10	8	2	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr9:111710491G>C	ENST00000325551.4	-	15	1945	c.1859C>G	c.(1858-1860)tCc>tGc	p.S620C	CTNNAL1_ENST00000374595.4_Missense_Mutation_p.S620C|CTNNAL1_ENST00000325580.6_Missense_Mutation_p.S536C|FAM206A_ENST00000374624.3_Intron|CTNNAL1_ENST00000374594.1_Missense_Mutation_p.S21C	NM_003798.2	NP_003789.1	Q9UBT7	CTNL1_HUMAN	catenin (cadherin-associated protein), alpha-like 1	620					cell adhesion (GO:0007155)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(4)|urinary_tract(2)	25				STAD - Stomach adenocarcinoma(157;0.0768)		TAAATCCTGGGAAGTTTTCAG	0.303																																					p.S620C		Atlas-SNP	.											CTNNAL1,mucosal,malignant_melanoma,0,1	CTNNAL1	51	.	0			c.C1859G						.						85	86	86					9																	111710491		2203	4300	6503	SO:0001583	missense	8727	exon15			TCCTGGGAAGTTT	AF030233	CCDS6775.1, CCDS69638.1	9q31.2	2008-07-21			ENSG00000119326	ENSG00000119326			2512	protein-coding gene	gene with protein product	"alpha-catulin", "alpha2-catulin"	604785				9806841	Standard	XM_005252291		Approved	CLLP, alpha-CATU	uc004bdo.1	Q9UBT7	OTTHUMG00000020466	ENST00000325551.4:c.1859C>G	chr9.hg19:g.111710491G>C	ENSP00000320434:p.Ser620Cys	22.0	0.0		27.0	2.0	NM_003798	B5BU47|O76084|Q53FQ2|Q5JTQ7|Q5JTQ8|Q9Y401	Missense_Mutation	SNP	ENST00000325551.4	hg19	CCDS6775.1	.	.	.	.	.	.	.	.	.	.	G	16.49	3.136741	0.56936	.	.	ENSG00000119326	ENST00000374595;ENST00000325551;ENST00000325580;ENST00000374594	T;T;T;T	0.47869	1.19;1.19;1.19;0.83	5.03	2.13	0.27403	.	0.202567	0.51477	N	0.000092	T	0.46112	0.1376	L	0.44542	1.39	0.20926	N	0.999822	P;B;P;P;P	0.47034	0.822;0.0;0.822;0.889;0.822	P;B;P;P;P	0.53722	0.733;0.003;0.733;0.69;0.733	T	0.36163	-0.9759	10	0.87932	D	0	-0.0012	3.7267	0.08477	0.0912:0.1651:0.5727:0.171	.	620;536;620;620;620	B2RBI4;Q9UBT7-3;B3KMX6;Q9UBT7-2;Q9UBT7	.;.;.;.;CTNL1_HUMAN	C	620;620;536;21	ENSP00000363723:S620C;ENSP00000320434:S620C;ENSP00000323351:S536C;ENSP00000363722:S21C	ENSP00000320434:S620C	S	-	2	0	CTNNAL1	110750312	1.000000	0.71417	0.993000	0.49108	0.941000	0.58515	4.832000	0.62759	0.149000	0.19098	-0.225000	0.12378	TCC	.	.		0.303	CTNNAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053577.1	NM_003798		C	111710491	G	C	111710491	3	2	279	1	0	0	0	0	1	0	0	0	4017	1174	41	4	365	4	CTNNAL1	9	111710491	Missense_Mutation	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	1646141	111710491	29502940	200	39959										
C9orf84	158401	hgsc.bcm.edu	37	chr9	114454237	114454237	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	aagatagggtccgatacatcTttatttatgaaaccttttgc	7	7	1	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr9:114454237T>C	ENST00000318737.4	-	25	3956	c.3828A>G	c.(3826-3828)aaA>aaG	p.K1276K	C9orf84_ENST00000374287.3_Silent_p.K1276K|C9orf84_ENST00000394777.4_Silent_p.K1202K|C9orf84_ENST00000394779.3_Silent_p.K1237K	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	1276								p.N1275fs*10(1)|p.N1236fs*10(1)		breast(1)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(10)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						CCGATACATCTTTATTTATGA	0.378																																					p.K1276K		Atlas-SNP	.											C9orf84_ENST00000374287,NS,carcinoma,-2,2	C9orf84	207	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.A3828G						.						58	56	57					9																	114454237		2203	4300	6503	SO:0001819	synonymous_variant	158401	exon25			TACATCTTTATTT	AL833535	CCDS6781.3, CCDS43863.1	9q32	2012-03-16			ENSG00000165181	ENSG00000165181			26535	protein-coding gene	gene with protein product							Standard	XM_005251738		Approved	FLJ32779	uc004bfr.3	Q5VXU9	OTTHUMG00000020495	ENST00000318737.4:c.3828A>G	chr9.hg19:g.114454237T>C		37.0	0.0		40.0	3.0	NM_173521	A2A2V3|Q2M1H8|Q96M73	Silent	SNP	ENST00000318737.4	hg19	CCDS6781.3																																																																																			.	.		0.378	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521		C	114454237	T	C	114454237	2	2	279	1	0	0	0	0	0	0	0	1	2502	1606	56	2		2	C9orf84	9	114454237	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	2743746	114454237	26759194	201	39960										
TTLL11	158135	hgsc.bcm.edu	37	chr9	124855592	124855592	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gttgacagcggcagtcaccgCatcgagacggggtccgggaa	16	11	1	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr9:124855592C>A	ENST00000373776.3	-	1	293	c.106G>T	c.(106-108)Gcg>Tcg	p.A36S	TTLL11_ENST00000474723.1_5'Flank|TTLL11_ENST00000321582.5_Missense_Mutation_p.A36S	NM_194252.2	NP_919228.2	Q8NHH1	TTL11_HUMAN	tubulin tyrosine ligase-like family, member 11	36					cellular protein modification process (GO:0006464)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(3)|skin(1)	18						GCAGTCACCGCATCGAGACGG	0.706																																					p.A36S		Atlas-SNP	.											.	TTLL11	67	.	0			c.G106T						.						8	9	9					9																	124855592		1694	3121	4815	SO:0001583	missense	158135	exon1			TCACCGCATCGAG	AF521886	CCDS6834.2, CCDS48012.1	9q34.11	2013-02-14	2005-07-28	2005-07-28	ENSG00000175764	ENSG00000175764		"Tubulin tyrosine ligase-like family"	18113	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 20"	C9orf20		15890843	Standard	NM_001139442		Approved	bA244O19.1	uc011lyl.2	Q8NHH1	OTTHUMG00000020597	ENST00000373776.3:c.106G>T	chr9.hg19:g.124855592C>A	ENSP00000362881:p.Ala36Ser	22.0	0.0		30.0	13.0	NM_001139442		Missense_Mutation	SNP	ENST00000373776.3	hg19	CCDS6834.2	.	.	.	.	.	.	.	.	.	.	C	12.77	2.037068	0.35893	.	.	ENSG00000175764	ENST00000321582;ENST00000373776	T;T	0.10099	3.09;2.91	4.47	3.54	0.40534	.	1.165150	0.06885	U	0.803240	T	0.06416	0.0165	N	0.08118	0	0.22996	N	0.998459	B;B	0.25105	0.115;0.118	B;B	0.22152	0.038;0.029	T	0.40646	-0.9552	9	.	.	.	.	9.3504	0.38133	0.2404:0.7596:0.0:0.0	.	36;36	F8W6M1;Q8NHH1	.;TTL11_HUMAN	S	36	ENSP00000321346:A36S;ENSP00000362881:A36S	.	A	-	1	0	TTLL11	123895413	1.000000	0.71417	0.989000	0.46669	0.220000	0.24768	1.213000	0.32407	1.017000	0.39495	0.561000	0.74099	GCG	.	.		0.706	TTLL11-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053907.1	XM_088486		A	124855592	C	A	124855592	3	1	279	1	0	0	0	0	1	0	0	0	16739	710	25	3	2410	3	TTLL11	9	124855592	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	10401355	124855592	16357839	202	39961										
OR1B1	347169	hgsc.bcm.edu	37	chr9	125391426	125391426	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ccaaagcatagtgcagggggTcacagatggccacatagcga	13	10	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr9:125391426T>C	ENST00000304833.3	-	1	426	c.389A>G	c.(388-390)gAc>gGc	p.D130G	RP11-64P14.7_ENST00000419604.1_RNA|RP11-64P14.7_ENST00000431442.1_RNA	NM_001004450.1	NP_001004450.1	Q8NGR6	OR1B1_HUMAN	olfactory receptor, family 1, subfamily B, member 1	130						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|prostate(1)	16						GTGCAGGGGGTCACAGATGGC	0.512																																					p.D130G		Atlas-SNP	.											.	OR1B1	48	.	0			c.A389G						.						103	85	91					9																	125391426		2203	4300	6503	SO:0001583	missense	347169	exon1			AGGGGGTCACAGA	AC006313	CCDS35126.1	9q33.2	2012-08-09			ENSG00000171484	ENSG00000171484		"GPCR / Class A : Olfactory receptors"	8181	protein-coding gene	gene with protein product							Standard	NM_001004450		Approved	OR9-B	uc011lyz.2	Q8NGR6	OTTHUMG00000020616	ENST00000304833.3:c.389A>G	chr9.hg19:g.125391426T>C	ENSP00000303151:p.Asp130Gly	48.0	0.0		75.0	4.0	NM_001004450	Q6IFN3	Missense_Mutation	SNP	ENST00000304833.3	hg19	CCDS35126.1	.	.	.	.	.	.	.	.	.	.	T	11.40	1.627860	0.28978	.	.	ENSG00000171484	ENST00000304833	T	0.01323	5.01	4.26	4.26	0.50523	GPCR, rhodopsin-like superfamily (1);	0.440723	0.19144	N	0.121609	T	0.01940	0.0061	L	0.38838	1.175	0.31666	N	0.644985	B	0.18013	0.025	B	0.23275	0.045	T	0.06463	-1.0825	10	0.87932	D	0	-4.1565	12.8487	0.57844	0.0:0.0:0.0:1.0	.	130	Q8NGR6	OR1B1_HUMAN	G	130	ENSP00000303151:D130G	ENSP00000303151:D130G	D	-	2	0	OR1B1	124431247	0.397000	0.25270	1.000000	0.80357	0.454000	0.32378	1.739000	0.38217	1.912000	0.55364	0.524000	0.50904	GAC	.	.		0.512	OR1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053947.2	NM_001004450		C	125391426	T	C	125391426	3	2	279	1	0	0	0	0	1	0	0	0	10960	1667	58	2	570	2	OR1B1	9	125391426	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	535834	125391426	15822005	203	39962										
PTGES2	80142	hgsc.bcm.edu	37	chr9	130887595	130887595	+	Silent	SNP	C	C	G													0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	aacttgatctcagccctgcgCacagggttcacctccaccac							TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr9:130887595C>G	ENST00000338961.6	-	2	1149	c.405G>C	c.(403-405)gtG>gtC	p.V135V	PTGES2_ENST00000483625.1_5'UTR|PTGES2_ENST00000277462.5_5'UTR	NM_001256335.1|NM_025072.6	NP_001243264.1|NP_079348.1	Q9H7Z7	PGES2_HUMAN	prostaglandin E synthase 2	135	Glutaredoxin. {ECO:0000255|PROSITE- ProRule:PRU00686}.				cell redox homeostasis (GO:0045454)|positive regulation of transcription, DNA-templated (GO:0045893)|prostaglandin biosynthetic process (GO:0001516)|secretion (GO:0046903)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|electron carrier activity (GO:0009055)|glutathione binding (GO:0043295)|heme binding (GO:0020037)|lyase activity (GO:0016829)|prostaglandin-E synthase activity (GO:0050220)|protein disulfide oxidoreductase activity (GO:0015035)			endometrium(1)|large_intestine(1)|lung(2)	4						CAGCCCTGCGCACAGGGTTCA	0.602																																					p.V135V		Atlas-SNP	.											.	PTGES2	14	.	0			c.G405C						.						78	64	68					9																	130887595		2203	4300	6503	SO:0001819	synonymous_variant	80142	exon2			CCTGCGCACAGGG	AK024100	CCDS6891.1	9q34.12	2008-05-06	2002-06-13	2002-06-14	ENSG00000148334	ENSG00000148334			17822	protein-coding gene	gene with protein product		608152	"chromosome 9 open reading frame 15"	C9orf15		11866447	Standard	NM_025072		Approved	FLJ14038	uc004bti.4	Q9H7Z7	OTTHUMG00000020730	ENST00000338961.6:c.405G>C	chr9.hg19:g.130887595C>G		96.0	0.0		122.0	54.0	NM_025072	Q53EW9|Q5SYV6|Q96GI0|Q96GL2	Silent	SNP	ENST00000338961.6	hg19	CCDS6891.1																																																																																			.	.		0.602	PTGES2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054339.1			G	130887595	C	G	130887595	2	3	279	1	0	0	0	0	0	0	0	1	12760	697	25	4		4	PTGES2	9	130887595	Silent	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	5496169	130887595	10325836	204	39963	201	2								
PTGES2	80142	hgsc.bcm.edu	37	chr9	130887600	130887600	+	Missense_Mutation	SNP	G	G	A													0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gatctcagccctgcgcacagGgttcacctccaccacctggt							TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr9:130887600G>A	ENST00000338961.6	-	2	1144	c.400C>T	c.(400-402)Cct>Tct	p.P134S	PTGES2_ENST00000483625.1_5'UTR|PTGES2_ENST00000277462.5_5'UTR	NM_001256335.1|NM_025072.6	NP_001243264.1|NP_079348.1	Q9H7Z7	PGES2_HUMAN	prostaglandin E synthase 2	134	Glutaredoxin. {ECO:0000255|PROSITE- ProRule:PRU00686}.				cell redox homeostasis (GO:0045454)|positive regulation of transcription, DNA-templated (GO:0045893)|prostaglandin biosynthetic process (GO:0001516)|secretion (GO:0046903)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|electron carrier activity (GO:0009055)|glutathione binding (GO:0043295)|heme binding (GO:0020037)|lyase activity (GO:0016829)|prostaglandin-E synthase activity (GO:0050220)|protein disulfide oxidoreductase activity (GO:0015035)			endometrium(1)|large_intestine(1)|lung(2)	4						CTGCGCACAGGGTTCACCTCC	0.612																																					p.P134S		Atlas-SNP	.											.	PTGES2	14	.	0			c.C400T						.						80	67	71					9																	130887600		2203	4300	6503	SO:0001583	missense	80142	exon2			GCACAGGGTTCAC	AK024100	CCDS6891.1	9q34.12	2008-05-06	2002-06-13	2002-06-14	ENSG00000148334	ENSG00000148334			17822	protein-coding gene	gene with protein product		608152	"chromosome 9 open reading frame 15"	C9orf15		11866447	Standard	NM_025072		Approved	FLJ14038	uc004bti.4	Q9H7Z7	OTTHUMG00000020730	ENST00000338961.6:c.400C>T	chr9.hg19:g.130887600G>A	ENSP00000345341:p.Pro134Ser	95.0	0.0		123.0	55.0	NM_025072	Q53EW9|Q5SYV6|Q96GI0|Q96GL2	Missense_Mutation	SNP	ENST00000338961.6	hg19	CCDS6891.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.503832	0.85176	.	.	ENSG00000148334	ENST00000338961;ENST00000449878	T;T	0.32515	1.45;2.48	4.88	3.98	0.46160	Glutaredoxin (2);Thioredoxin-like fold (2);	0.051838	0.85682	N	0.000000	T	0.53850	0.1822	M	0.74546	2.27	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.57676	-0.7770	10	0.72032	D	0.01	0.3231	12.2012	0.54326	0.083:0.0:0.917:0.0	.	134	Q9H7Z7	PGES2_HUMAN	S	134;99	ENSP00000345341:P134S;ENSP00000411378:P99S	ENSP00000345341:P134S	P	-	1	0	PTGES2	129927421	1.000000	0.71417	0.996000	0.52242	0.980000	0.70556	9.476000	0.97823	1.048000	0.40298	0.561000	0.74099	CCT	.	.		0.612	PTGES2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054339.1			A	130887600	G	A	130887600	3	1	279	1	0	0	0	0	1	0	0	0	12760	1232	43	3	757	3	PTGES2	9	130887600	Missense_Mutation	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	5	130887600	10325831	205	39964	201	2								
SLC27A4	10999	hgsc.bcm.edu	37	chr9	131105476	131105476	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gctggtgctgaaactgccctGgacccaggtgggattctccc	13	13	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr9:131105476G>C	ENST00000300456.4	+	2	182	c.65G>C	c.(64-66)tGg>tCg	p.W22S	SLC27A4_ENST00000372870.1_Silent_p.L49L	NM_005094.3	NP_005085.2	Q6P1M0	S27A4_HUMAN	solute carrier family 27 (fatty acid transporter), member 4	22					fatty acid transport (GO:0015908)|lipid metabolic process (GO:0006629)|long-chain fatty acid import (GO:0044539)|long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty acid transport (GO:0015909)|medium-chain fatty acid transport (GO:0001579)|response to nutrient (GO:0007584)|skin development (GO:0043588)|transmembrane transport (GO:0055085)|transport (GO:0006810)|very long-chain fatty acid catabolic process (GO:0042760)	brush border membrane (GO:0031526)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	fatty acid transporter activity (GO:0015245)|long-chain fatty acid-CoA ligase activity (GO:0004467)|nucleotide binding (GO:0000166)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			autonomic_ganglia(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(2)	13						AAACTGCCCTGGACCCAGGTG	0.582																																					p.W22S	Pancreas(107;1554 2241 10946 12953)	Atlas-SNP	.											.	SLC27A4	41	.	0			c.G65C						.						123	98	107					9																	131105476		2203	4300	6503	SO:0001583	missense	10999	exon2			TGCCCTGGACCCA	AF055899	CCDS6899.1	9q34.13	2013-05-22			ENSG00000167114	ENSG00000167114		"Acyl-CoA synthetase family", "Solute carriers"	10998	protein-coding gene	gene with protein product		604194				9878842	Standard	NM_005094		Approved	FATP4, ACSVL4	uc004but.3	Q6P1M0	OTTHUMG00000020746	ENST00000300456.4:c.65G>C	chr9.hg19:g.131105476G>C	ENSP00000300456:p.Trp22Ser	256.0	1.0		337.0	163.0	NM_005094	A8K2F7|O95186|Q96G53	Missense_Mutation	SNP	ENST00000300456.4	hg19	CCDS6899.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.250123	0.80024	.	.	ENSG00000167114	ENST00000300456	T	0.49139	0.79	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.69504	0.3118	M	0.78049	2.395	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	T	0.71609	-0.4541	10	0.52906	T	0.07	-16.4834	16.3322	0.83039	0.0:0.0:1.0:0.0	.	22	Q6P1M0	S27A4_HUMAN	S	22	ENSP00000300456:W22S	ENSP00000300456:W22S	W	+	2	0	SLC27A4	130145297	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.849000	0.86908	2.522000	0.85027	0.467000	0.42956	TGG	.	.		0.582	SLC27A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054432.2			C	131105476	G	C	131105476	3	2	279	1	0	0	0	0	1	0	0	0	14543	1357	47	4	67	4	SLC27A4	9	131105476	Missense_Mutation	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	217876	131105476	10107955	206	39965										
LRRC8A	56262	hgsc.bcm.edu	37	chr9	131670047	131670047	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	acaaaaagtcatcgaccgtcAgtgaggacgtggaggccacc	12	11	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr9:131670047A>G	ENST00000259324.5	+	3	1127	c.604A>G	c.(604-606)Agt>Ggt	p.S202G	LRRC8A_ENST00000372599.3_Missense_Mutation_p.S202G|LRRC8A_ENST00000372600.4_Missense_Mutation_p.S202G	NM_001127244.1	NP_001120716.1	Q8IWT6	LRC8A_HUMAN	leucine rich repeat containing 8 family, member A	202					anion transport (GO:0006820)|cell volume homeostasis (GO:0006884)|pre-B cell differentiation (GO:0002329)|response to osmotic stress (GO:0006970)	cell surface (GO:0009986)|ion channel complex (GO:0034702)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|skin(3)	28						ATCGACCGTCAGTGAGGACGT	0.617																																					p.S202G		Atlas-SNP	.											.	LRRC8A	69	.	0			c.A604G						.						53	46	48					9																	131670047		2203	4300	6503	SO:0001583	missense	56262	exon3			ACCGTCAGTGAGG	AB037858	CCDS35155.1	9q34.2	2014-09-17	2005-06-29	2005-06-29	ENSG00000136802	ENSG00000136802			19027	protein-coding gene	gene with protein product		608360	"leucine rich repeat containing 8"	LRRC8			Standard	NM_001127244		Approved	KIAA1437, FLJ10337	uc010myp.3	Q8IWT6	OTTHUMG00000020766	ENST00000259324.5:c.604A>G	chr9.hg19:g.131670047A>G	ENSP00000259324:p.Ser202Gly	64.0	0.0		84.0	27.0	NM_001127244	Q6UXM2|Q8NCI0|Q9P2B1	Missense_Mutation	SNP	ENST00000259324.5	hg19	CCDS35155.1	.	.	.	.	.	.	.	.	.	.	A	9.854	1.194382	0.22037	.	.	ENSG00000136802	ENST00000372600;ENST00000372599;ENST00000259324	T;T;T	0.30182	1.54;1.54;1.54	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.31979	0.0814	M	0.61703	1.905	0.53005	D	0.999967	D	0.54964	0.969	B	0.40228	0.323	T	0.20773	-1.0265	10	0.48119	T	0.1	.	14.346	0.66665	1.0:0.0:0.0:0.0	.	202	Q8IWT6	LRC8A_HUMAN	G	202	ENSP00000361682:S202G;ENSP00000361680:S202G;ENSP00000259324:S202G	ENSP00000259324:S202G	S	+	1	0	LRRC8A	130709868	1.000000	0.71417	0.991000	0.47740	0.231000	0.25187	7.576000	0.82467	1.991000	0.58162	0.460000	0.39030	AGT	.	.		0.617	LRRC8A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054516.2	NM_019594		G	131670047	A	G	131670047	3	3	279	1	0	0	0	0	1	0	0	0	9030	188	7	2	606	2	LRRC8A	9	131670047	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	564571	131670047	9543384	207	39966										
UBAC1	10422	hgsc.bcm.edu	37	chr9	138836944	138836944	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ccgtcagctcatctctggccTcctcatcggtggcgctggct	11	16	4	0	rs66767056|rs140946801	byFrequency	TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr9:138836944T>G	ENST00000371756.3	-	7	1023	c.806A>C	c.(805-807)gAg>gCg	p.E269A	UBAC1_ENST00000465873.1_5'UTR	NM_016172.2	NP_057256.2	Q9BSL1	UBAC1_HUMAN	UBA domain containing 1	269				Missing (in Ref. 1; AAD51084). {ECO:0000305}.	protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)		p.E269delE(1)|p.E269fs*6(1)		NS(1)|biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(6)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	25		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.1e-06)|Epithelial(140;7.79e-06)		ATCTCTGGCCTCCTCATCGGT	0.622																																					p.E269A	NSCLC(78;973 1398 27381 29552 42415)	Atlas-SNP	.											.,1	UBAC1	40	.	2	Deletion - Frameshift(1)|Deletion - In frame(1)	stomach(1)|kidney(1)	c.A806C						.						123	88	100					9																	138836944		2203	4296	6499	SO:0001583	missense	10422	exon7			CTGGCCTCCTCAT	AF176796	CCDS35177.1	9q34.3	2008-02-05	2007-04-20	2007-04-20	ENSG00000130560	ENSG00000130560			30221	protein-coding gene	gene with protein product		608129	"ubiquitin associated domain containing 1"	UBADC1		10857748, 8619474	Standard	NM_016172		Approved	GBDR1	uc004cgt.3	Q9BSL1	OTTHUMG00000020920	ENST00000371756.3:c.806A>C	chr9.hg19:g.138836944T>G	ENSP00000360821:p.Glu269Ala	1.0	0.0		21.0	6.0	NM_016172	O75500|Q9UMW7	Missense_Mutation	SNP	ENST00000371756.3	hg19	CCDS35177.1	.	.	.	.	.	.	.	.	.	.	T	13.95	2.388710	0.42308	.	.	ENSG00000130560	ENST00000371756	T	0.26373	1.74	5.38	5.38	0.77491	.	0.419347	0.25786	N	0.028305	T	0.24890	0.0604	L	0.52364	1.645	0.51767	D	0.999939	B	0.30741	0.293	B	0.27608	0.081	T	0.02991	-1.1085	10	0.30854	T	0.27	-40.5679	14.5777	0.68262	0.0:0.0:0.0:1.0	.	269	Q9BSL1	UBAC1_HUMAN	A	269	ENSP00000360821:E269A	ENSP00000360821:E269A	E	-	2	0	UBAC1	137976765	1.000000	0.71417	0.978000	0.43139	0.513000	0.34164	6.970000	0.76099	2.038000	0.60285	0.533000	0.62120	GAG	.	.		0.622	UBAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055034.1	NM_016172		G	138836944	T	G	138836944	3	3	279	1	0	0	0	0	1	0	0	0	16849	1551	54	5	427	5	UBAC1	9	138836944	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	7166897	138836944	2376487	208	39967										
SEC16A	9919	hgsc.bcm.edu	37	chr9	139368633	139368633	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ggtgggccgggggcaagtgcAggcactggctgtggccacgg	21	10	0	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr9:139368633A>G	ENST00000371706.3	-	1	2934	c.2901T>C	c.(2899-2901)ccT>ccC	p.P967P	SEC16A_ENST00000431893.2_Silent_p.P967P|SEC16A_ENST00000290037.6_Silent_p.P967P|SEC16A_ENST00000313050.7_Silent_p.P1145P			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	967	Pro-rich.|Required for endoplasmic reticulum localization.				COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|protein transport (GO:0015031)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)				breast(1)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(15)|lung(14)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)		GGGCAAGTGCAGGCACTGGCT	0.657																																					p.P1145P		Atlas-SNP	.											.	SEC16A	249	.	0			c.T3435C						.						27	33	31					9																	139368633		2052	4182	6234	SO:0001819	synonymous_variant	9919	exon3			AAGTGCAGGCACT	AK074565	CCDS55351.1, CCDS75936.1	9q34.3	2007-06-20	2007-06-20	2007-06-20	ENSG00000148396	ENSG00000148396			29006	protein-coding gene	gene with protein product		612854	"KIAA0310"	KIAA0310		9205841	Standard	NM_014866		Approved	p250	uc004chx.3	O15027	OTTHUMG00000020932	ENST00000371706.3:c.2901T>C	chr9.hg19:g.139368633A>G		74.0	0.0		96.0	4.0	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Silent	SNP	ENST00000371706.3	hg19																																																																																				.	.		0.657	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459		G	139368633	A	G	139368633	2	3	279	1	0	0	0	0	0	0	0	1	14001	175	7	2		2	SEC16A	9	139368633	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	531689	139368633	1844798	209	39968										
DPP7	29952	hgsc.bcm.edu	37	chr9	140008791	140008791	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cacacgtcgccctcgttcccAgtgtagaagaagatgggccc	11	14	0	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr9:140008791A>G	ENST00000371579.2	-	3	229	c.225T>C	c.(223-225)acT>acC	p.T75T		NM_013379.2	NP_037511.2	Q9UHL4	DPP2_HUMAN	dipeptidyl-peptidase 7	75						cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			endometrium(2)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	7	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;4.25e-05)|Epithelial(140;0.000633)		CCTCGTTCCCAGTGTAGAAGA	0.726																																					p.T75T		Atlas-SNP	.											.	DPP7	22	.	0			c.T225C						.						9	11	10					9																	140008791		2111	4150	6261	SO:0001819	synonymous_variant	29952	exon3			GTTCCCAGTGTAG	AF154502	CCDS7030.1	9q34.3	2008-02-05	2006-01-12		ENSG00000176978	ENSG00000176978			14892	protein-coding gene	gene with protein product		610537	"dipeptidylpeptidase 7"			10477574, 11139392	Standard	XM_005266075		Approved	DPPII	uc004clh.3	Q9UHL4	OTTHUMG00000020977	ENST00000371579.2:c.225T>C	chr9.hg19:g.140008791A>G		33.0	0.0		34.0	4.0	NM_013379	A8K7U7|Q5VSF1|Q969X4	Silent	SNP	ENST00000371579.2	hg19	CCDS7030.1	.	.	.	.	.	.	.	.	.	.	A	4.725	0.134791	0.09032	.	.	ENSG00000176978	ENST00000443858	.	.	.	4.04	-8.09	0.01090	.	.	.	.	.	T	0.41971	0.1182	.	.	.	0.51012	D	0.999907	B	0.02656	0.0	B	0.01281	0.0	T	0.44112	-0.9349	7	0.87932	D	0	-14.8968	6.7544	0.23505	0.0925:0.1216:0.5589:0.227	.	99	E7EQS4	.	R	99	.	ENSP00000413492:W99R	W	-	1	0	DPP7	139128612	0.002000	0.14202	0.022000	0.16811	0.278000	0.26855	-2.110000	0.01334	-4.177000	0.00067	-1.251000	0.01509	TGG	.	.		0.726	DPP7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055279.1	NM_013379		G	140008791	A	G	140008791	2	3	279	1	0	0	0	0	0	0	0	1	4733	175	7	2		2	DPP7	9	140008791	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	640158	140008791	1204640	210	39969										
DNAJC1	64215	hgsc.bcm.edu	37	chr10	22209794	22209794	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ctgtgagaataatgaacaagAgtaatgccagctcagcattg	10	7	1	3	rs375039357		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr10:22209794A>G	ENST00000376980.3	-	4	760	c.470T>C	c.(469-471)cTc>cCc	p.L157P	DNAJC1_ENST00000376946.1_3'UTR	NM_022365.3	NP_071760.2	Q96KC8	DNJC1_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 1	157					negative regulation of proteolysis (GO:0045861)|positive regulation of ATPase activity (GO:0032781)|protein folding (GO:0006457)|regulation of protein secretion (GO:0050708)|regulation of translation (GO:0006417)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ATPase activator activity (GO:0001671)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)			cervix(1)|endometrium(1)|large_intestine(2)|lung(13)|skin(2)|upper_aerodigestive_tract(2)	21		Breast(68;0.00869)|Prostate(175;0.0181)|Lung SC(717;0.0262)				AATGAACAAGAGTAATGCCAG	0.408																																					p.L157P		Atlas-SNP	.											.	DNAJC1	42	.	0			c.T470C						.						115	114	114					10																	22209794		2203	4300	6503	SO:0001583	missense	64215	exon4			AACAAGAGTAATG	AK026062	CCDS7136.1	10p11.23	2011-09-02			ENSG00000136770	ENSG00000136770		"Heat shock proteins / DNAJ (HSP40)"	20090	protein-coding gene	gene with protein product		611207					Standard	NM_022365		Approved	DNAJL1, ERdj1, MTJ1	uc001irc.3	Q96KC8	OTTHUMG00000017800	ENST00000376980.3:c.470T>C	chr10.hg19:g.22209794A>G	ENSP00000366179:p.Leu157Pro	83.0	0.0		78.0	4.0	NM_022365	B0YIZ8|Q5VX89|Q9H6B8	Missense_Mutation	SNP	ENST00000376980.3	hg19	CCDS7136.1	.	.	.	.	.	.	.	.	.	.	A	18.95	3.732126	0.69189	.	.	ENSG00000136770	ENST00000376980	T	0.47869	0.83	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.68467	0.3004	M	0.74258	2.255	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.70414	-0.4878	10	0.48119	T	0.1	-3.9148	15.5555	0.76189	1.0:0.0:0.0:0.0	.	157	Q96KC8	DNJC1_HUMAN	P	157	ENSP00000366179:L157P	ENSP00000366179:L157P	L	-	2	0	DNAJC1	22249800	1.000000	0.71417	0.997000	0.53966	0.947000	0.59692	9.232000	0.95325	2.132000	0.65825	0.460000	0.39030	CTC	.	.		0.408	DNAJC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047149.1	NM_022365		G	22209794	A	G	22209794	3	3	279	1	0	0	0	0	1	0	0	0	4630	304	11	2	1230	2	DNAJC1	10	22209794	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10		22209794	113324953	211	39970										
BMI1	648	hgsc.bcm.edu	37	chr10	22618054	22618054	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gcctacatttatacctggagAagggtaagtagcatatctgt	10	7	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr10:22618054A>G	ENST00000376663.3	+	9	1153	c.648A>G	c.(646-648)agA>agG	p.R216R	COMMD3-BMI1_ENST00000602390.1_Silent_p.R359R	NM_005180.8	NP_005171.4	P35226	BMI1_HUMAN	BMI1 proto-oncogene, polycomb ring finger	216	Interaction with E4F1.				chromatin modification (GO:0016568)|hemopoiesis (GO:0030097)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|regulation of gene expression (GO:0010468)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|ubiquitin ligase complex (GO:0000151)	RING-like zinc finger domain binding (GO:0071535)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(2)|urinary_tract(1)	12						ATACCTGGAGAAGGGTAAGTA	0.284																																					p.R359R		Atlas-SNP	.											.	.	.	.	0			c.A1077G						.						104	122	116					10																	22618054		2199	4287	6486	SO:0001819	synonymous_variant	0	exon13			CTGGAGAAGGGTA	BC011652	CCDS7138.1	10p13	2014-06-26	2014-06-26	2006-04-26	ENSG00000168283	ENSG00000168283		"RING-type (C3HC4) zinc fingers", "Polycomb group ring fingers"	1066	protein-coding gene	gene with protein product		164831	"polycomb group ring finger 4", "B lymphoma Mo-MLV insertion region 1 homolog (mouse)"	PCGF4		8268912	Standard	NM_005180		Approved	RNF51		P35226	OTTHUMG00000017807	ENST00000376663.3:c.648A>G	chr10.hg19:g.22618054A>G		53.0	0.0		53.0	4.0	NM_001204062	Q16030|Q5T8Z3|Q96F37	Silent	SNP	ENST00000376663.3	hg19	CCDS7138.1																																																																																			.	.		0.284	BMI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047176.1	NM_005180		G	22618054	A	G	22618054	2	3	279	1	0	0	0	0	0	0	0	1	1455	243	9	2		2	BMI1	10	22618054	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	408260	22618054	112916693	212	39971										
KIAA1217	56243	hgsc.bcm.edu	37	chr10	24669829	24669829	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	caaactgtctcacagtcctcAaccacccagtctgggtgacc	7	16	3	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr10:24669829A>G	ENST00000376454.3	+	3	416	c.386A>G	c.(385-387)cAa>cGa	p.Q129R	KIAA1217_ENST00000458595.1_Missense_Mutation_p.Q129R|KIAA1217_ENST00000376452.3_Missense_Mutation_p.Q129R|KIAA1217_ENST00000376462.1_Missense_Mutation_p.Q49R|KIAA1217_ENST00000430453.2_Missense_Mutation_p.Q50R	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	129					embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						CACAGTCCTCAACCACCCAGT	0.468																																					p.Q129R		Atlas-SNP	.											.	KIAA1217	235	.	0			c.A386G						.						72	77	76					10																	24669829		2203	4300	6503	SO:0001583	missense	56243	exon3			GTCCTCAACCACC	BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"sickle tail"					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.386A>G	chr10.hg19:g.24669829A>G	ENSP00000365637:p.Gln129Arg	58.0	0.0		69.0	4.0	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Missense_Mutation	SNP	ENST00000376454.3	hg19	CCDS31165.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.534638	0.85812	.	.	ENSG00000120549	ENST00000376462;ENST00000376456;ENST00000458595;ENST00000376454;ENST00000376452;ENST00000430453	T;D;T;T;T;T	0.94576	1.31;-3.46;1.3;1.68;1.3;0.7	5.54	5.54	0.83059	.	0.179385	0.49305	D	0.000153	D	0.96907	0.8990	M	0.75777	2.31	0.53005	D	0.999964	D;D;D;D	0.76494	0.996;0.968;0.999;0.993	D;P;D;D	0.75484	0.986;0.504;0.964;0.91	D	0.97456	1.0031	10	0.72032	D	0.01	.	15.6685	0.77255	1.0:0.0:0.0:0.0	.	129;129;129;129	Q5T5P2-7;A6NLF3;Q5T5P2;Q5T5P2-2	.;.;SKT_HUMAN;.	R	49;129;129;129;129;50	ENSP00000365645:Q49R;ENSP00000365639:Q129R;ENSP00000392625:Q129R;ENSP00000365637:Q129R;ENSP00000365635:Q129R;ENSP00000389680:Q50R	ENSP00000365635:Q129R	Q	+	2	0	KIAA1217	24709835	1.000000	0.71417	0.991000	0.47740	0.880000	0.50808	6.281000	0.72632	2.114000	0.64651	0.482000	0.46254	CAA	.	.		0.468	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590		G	24669829	A	G	24669829	3	3	279	1	0	0	0	0	1	0	0	0	8225	130	5	2	396	2	KIAA1217	10	24669829	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	2051775	24669829	110864918	213	39972										
ANKRD26	22852	hgsc.bcm.edu	37	chr10	27294602	27294602	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ttgatttagatttgactcatCagtagaccctagaggggaag	11	6	2	5			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr10:27294602C>T	ENST00000376087.4	-	34	5215	c.5050G>A	c.(5050-5052)Gat>Aat	p.D1684N	ANKRD26_ENST00000436985.2_Missense_Mutation_p.D1700N|ANKRD26_ENST00000376070.3_Missense_Mutation_p.D1241N	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	1683					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						TTTGACTCATCAGTAGACCCT	0.308																																					p.D1684N		Atlas-SNP	.											.	ANKRD26	179	.	0			c.G5050A						.						86	84	85					10																	27294602		1805	4069	5874	SO:0001583	missense	22852	exon34			ACTCATCAGTAGA	AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"Ankyrin repeat domain containing"	29186	protein-coding gene	gene with protein product		610855	"thrombocytopenia 2 (autosomal dominant)"	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.5050G>A	chr10.hg19:g.27294602C>T	ENSP00000365255:p.Asp1684Asn	114.0	0.0		91.0	4.0	NM_014915	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Missense_Mutation	SNP	ENST00000376087.4	hg19	CCDS41499.1	.	.	.	.	.	.	.	.	.	.	C	11.93	1.786773	0.31593	.	.	ENSG00000107890	ENST00000376070;ENST00000376087;ENST00000436985	T;T;T	0.29917	4.03;1.55;1.56	4.88	-1.63	0.08345	.	.	.	.	.	T	0.28599	0.0708	M	0.65498	2.005	0.09310	N	1	B;B;B	0.16396	0.017;0.01;0.002	B;B;B	0.13407	0.009;0.004;0.003	T	0.27806	-1.0063	9	0.33141	T	0.24	.	9.1304	0.36841	0.0:0.3868:0.0:0.6131	.	1684;1683;1700	Q9UPS8-3;Q9UPS8;A1L497	.;ANR26_HUMAN;.	N	1241;1684;1700	ENSP00000365238:D1241N;ENSP00000365255:D1684N;ENSP00000405112:D1700N	ENSP00000365238:D1241N	D	-	1	0	ANKRD26	27334608	0.000000	0.05858	0.000000	0.03702	0.435000	0.31806	-0.251000	0.08818	-0.564000	0.06070	0.313000	0.20887	GAT	.	.		0.308	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1			T	27294602	C	T	27294602	3	4	279	1	0	0	0	0	1	0	0	0	654	826	29	3	86	3	ANKRD26	10	27294602	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	2624773	27294602	108240145	214	39973										
RET	5979	hgsc.bcm.edu	37	chr10	43610012	43610012	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ctcggtgctgctgtctgcctTctgcatccactgctaccaca	8	16	2	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr10:43610012T>C	ENST00000355710.3	+	11	2196	c.1964T>C	c.(1963-1965)tTc>tCc	p.F655S	RET_ENST00000340058.5_Missense_Mutation_p.F655S	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	655					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to retinoic acid (GO:0071300)|embryonic epithelial tube formation (GO:0001838)|enteric nervous system development (GO:0048484)|homophilic cell adhesion (GO:0007156)|innervation (GO:0060384)|lymphocyte migration into lymphoid organs (GO:0097021)|MAPK cascade (GO:0000165)|membrane protein proteolysis (GO:0033619)|neural crest cell migration (GO:0001755)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch morphogenesis (GO:0061146)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell migration (GO:0030335)|positive regulation of cell size (GO:0045793)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of neuron maturation (GO:0014042)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior midgut development (GO:0007497)|protein phosphorylation (GO:0006468)|regulation of axonogenesis (GO:0050770)|regulation of cell adhesion (GO:0030155)|response to drug (GO:0042493)|response to pain (GO:0048265)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ureter maturation (GO:0035799)|ureteric bud development (GO:0001657)	endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		CCDC6/RET(4)|KIF5B/RET(79)	NS(2)|adrenal_gland(26)|breast(5)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|lung(27)|ovary(5)|prostate(3)|skin(1)|thyroid(504)|upper_aerodigestive_tract(1)|urinary_tract(1)	607		Ovarian(717;0.0423)			Cabozantinib(DB08875)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	CTGTCTGCCTTCTGCATCCAC	0.627		1	"T, Mis, N, F"	"H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6"	"medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC"	"medullary thyroid,  papillary thyroid, pheochromocytoma"	Hirschsprung disease		Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma																												p.F655S	Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149)	Atlas-SNP	.	yes	Dom	yes	Multiple endocrine neoplasia 2A/2B	10	10q11.2	5979	ret proto-oncogene	yes	"E, O"	.	RET	916	.	0			c.T1964C						.						186	118	141					10																	43610012		2203	4300	6503	SO:0001583	missense	5979	exon11	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	CTGCCTTCTGCAT	BC004257	CCDS7200.1, CCDS53525.1	10q11.2	2014-09-17	2007-02-16		ENSG00000165731	ENSG00000165731		"Cadherins / Cadherin-related"	9967	protein-coding gene	gene with protein product	"cadherin-related family member 16"	164761	"multiple endocrine neoplasia and medullary thyroid carcinoma 1", "Hirschsprung disease 1"	HSCR1, MEN2A, MTC1, MEN2B		2687772, 1611909	Standard	NM_020975		Approved	PTC, CDHF12, RET51, CDHR16	uc001jal.3	P07949	OTTHUMG00000018024	ENST00000355710.3:c.1964T>C	chr10.hg19:g.43610012T>C	ENSP00000347942:p.Phe655Ser	101.0	0.0		95.0	4.0	NM_020630	A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Missense_Mutation	SNP	ENST00000355710.3	hg19	CCDS7200.1	.	.	.	.	.	.	.	.	.	.	T	17.05	3.289135	0.59976	.	.	ENSG00000165731	ENST00000355710;ENST00000498820;ENST00000340058	T;D;T	0.98914	-1.24;-5.23;-1.36	4.85	3.65	0.41850	.	0.104953	0.64402	D	0.000002	D	0.96962	0.9008	L	0.55481	1.735	0.41743	D	0.989626	B;P;P	0.40875	0.282;0.611;0.731	B;B;P	0.44518	0.205;0.265;0.452	D	0.95033	0.8171	10	0.28530	T	0.3	.	7.8551	0.29478	0.3801:0.0:0.0:0.6199	.	401;655;655	B4DGX8;P07949;P07949-2	.;RET_HUMAN;.	S	655;172;655	ENSP00000347942:F655S;ENSP00000419080:F172S;ENSP00000344798:F655S	ENSP00000344798:F655S	F	+	2	0	RET	42930018	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	5.393000	0.66279	2.038000	0.60285	0.379000	0.24179	TTC	.	.		0.627	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	NM_020975		C	43610012	T	C	43610012	3	2	279	1	0	0	0	0	1	0	0	0	13250	1783	62	2	2006	2	RET	10	43610012	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	16315410	43610012	91924735	215	39974										
SIRT1	23411	hgsc.bcm.edu	37	chr10	69666641	69666641	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	acttcgcaactatacccagaAcatagacacgctggaacagg	8	12	0	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr10:69666641A>G	ENST00000212015.6	+	5	1090	c.1037A>G	c.(1036-1038)aAc>aGc	p.N346S	SIRT1_ENST00000432464.1_Missense_Mutation_p.N51S|SIRT1_ENST00000403579.1_Missense_Mutation_p.N43S|SIRT1_ENST00000406900.1_Missense_Mutation_p.N43S	NM_012238.4	NP_036370.2	Q96EB6	SIR1_HUMAN	sirtuin 1	346	Deacetylase sirtuin-type. {ECO:0000255|PROSITE-ProRule:PRU00236}.|Interaction with CCAR2.				angiogenesis (GO:0001525)|cell aging (GO:0007569)|cellular glucose homeostasis (GO:0001678)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to starvation (GO:0009267)|cellular response to tumor necrosis factor (GO:0071356)|cellular triglyceride homeostasis (GO:0035356)|cholesterol homeostasis (GO:0042632)|chromatin organization (GO:0006325)|chromatin silencing (GO:0006342)|chromatin silencing at rDNA (GO:0000183)|circadian regulation of gene expression (GO:0032922)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|establishment of chromatin silencing (GO:0006343)|fatty acid homeostasis (GO:0055089)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of chromatin silencing (GO:0006344)|methylation-dependent chromatin silencing (GO:0006346)|muscle organ development (GO:0007517)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|negative regulation of cell growth (GO:0030308)|negative regulation of cellular response to testosterone stimulus (GO:2000655)|negative regulation of cellular senescence (GO:2000773)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of helicase activity (GO:0051097)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of neuron death (GO:1901215)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of peptidyl-lysine acetylation (GO:2000757)|negative regulation of phosphorylation (GO:0042326)|negative regulation of prostaglandin biosynthetic process (GO:0031393)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|ovulation from ovarian follicle (GO:0001542)|peptidyl-lysine acetylation (GO:0018394)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular senescence (GO:2000774)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of chromatin silencing (GO:0031937)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of DNA repair (GO:0045739)|positive regulation of histone H3-K9 methylation (GO:0051574)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of macroautophagy (GO:0016239)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein deacetylation (GO:0006476)|protein destabilization (GO:0031648)|protein ubiquitination (GO:0016567)|pyrimidine dimer repair by nucleotide-excision repair (GO:0000720)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cell proliferation (GO:0042127)|regulation of endodeoxyribonuclease activity (GO:0032071)|regulation of glucose metabolic process (GO:0010906)|regulation of mitotic cell cycle (GO:0007346)|regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035358)|regulation of protein import into nucleus, translocation (GO:0033158)|regulation of smooth muscle cell apoptotic process (GO:0034391)|response to hydrogen peroxide (GO:0042542)|response to insulin (GO:0032868)|response to oxidative stress (GO:0006979)|rRNA processing (GO:0006364)|single strand break repair (GO:0000012)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)|triglyceride mobilization (GO:0006642)|viral process (GO:0016032)|white fat cell differentiation (GO:0050872)	chromatin silencing complex (GO:0005677)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear envelope (GO:0005635)|nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|rDNA heterochromatin (GO:0033553)	bHLH transcription factor binding (GO:0043425)|deacetylase activity (GO:0019213)|enzyme binding (GO:0019899)|histone binding (GO:0042393)|histone deacetylase activity (GO:0004407)|HLH domain binding (GO:0043398)|identical protein binding (GO:0042802)|keratin filament binding (GO:1990254)|metal ion binding (GO:0046872)|mitogen-activated protein kinase binding (GO:0051019)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (GO:0017136)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent protein deacetylase activity (GO:0034979)|p53 binding (GO:0002039)|protein C-terminus binding (GO:0008022)|protein deacetylase activity (GO:0033558)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(3)|skin(1)	14						TATACCCAGAACATAGACACG	0.378																																					p.N346S		Atlas-SNP	.											.	SIRT1	38	.	0			c.A1037G						.						91	93	92					10																	69666641		2203	4300	6503	SO:0001583	missense	23411	exon5			CCCAGAACATAGA	AF083106	CCDS7273.1, CCDS44412.1	10q21	2010-06-25	2010-06-25		ENSG00000096717	ENSG00000096717			14929	protein-coding gene	gene with protein product		604479	"sirtuin (silent mating type information regulation 2, S. cerevisiae, homolog) 1", "sirtuin (silent mating type information regulation 2 homolog) 1 (S. cerevisiae)"			10381378	Standard	NM_012238		Approved	SIR2L1	uc001jnd.3	Q96EB6	OTTHUMG00000018340	ENST00000212015.6:c.1037A>G	chr10.hg19:g.69666641A>G	ENSP00000212015:p.Asn346Ser	137.0	0.0		97.0	4.0	NM_012238	Q2XNF6|Q5JVQ0|Q9GZR9|Q9Y6F0	Missense_Mutation	SNP	ENST00000212015.6	hg19	CCDS7273.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.084144	0.76642	.	.	ENSG00000096717	ENST00000212015;ENST00000432464;ENST00000406900;ENST00000403579	T;T;T;T	0.59224	0.28;0.28;0.28;0.28	5.2	4.06	0.47325	.	0.000000	0.85682	D	0.000000	D	0.85522	0.5716	H	0.99705	4.715	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.88266	0.2926	10	0.87932	D	0	-13.129	10.4572	0.44557	0.9219:0.0:0.0781:0.0	.	43;346	B0QZ35;Q96EB6	.;SIRT1_HUMAN	S	346;51;43;43	ENSP00000212015:N346S;ENSP00000409208:N51S;ENSP00000384508:N43S;ENSP00000384063:N43S	ENSP00000212015:N346S	N	+	2	0	SIRT1	69336647	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	8.888000	0.92464	0.814000	0.34374	0.477000	0.44152	AAC	.	.		0.378	SIRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048296.1			G	69666641	A	G	69666641	3	3	279	1	0	0	0	0	1	0	0	0	14352	43	2	2	1055	2	SIRT1	10	69666641	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	26056629	69666641	65868106	216	39975										
TYSND1	219743	hgsc.bcm.edu	37	chr10	71905706	71905706	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	caatggcgcacccttgggcaCggccccgagaggcgacaccg	14	16	0	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr10:71905706C>T	ENST00000287078.6	-	1	636	c.637G>A	c.(637-639)Gtg>Atg	p.V213M	TYSND1_ENST00000494143.1_5'Flank|TYSND1_ENST00000335494.5_Missense_Mutation_p.V213M	NM_173555.2	NP_775826.2	Q2T9J0	TYSD1_HUMAN	trypsin domain containing 1	213					protein homooligomerization (GO:0051260)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of fatty acid beta-oxidation (GO:0031998)	membrane (GO:0016020)|peroxisome (GO:0005777)	identical protein binding (GO:0042802)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(2)|liver(1)|lung(3)|prostate(1)	9						CCCTTGGGCACGGCCCCGAGA	0.692																																					p.V213M		Atlas-SNP	.											.	TYSND1	20	.	0			c.G637A						.						12	14	13					10																	71905706		2155	4213	6368	SO:0001583	missense	219743	exon1			TGGGCACGGCCCC	BC016840	CCDS31213.1, CCDS31214.1	10q22.1	2009-11-06		2006-09-21	ENSG00000156521	ENSG00000156521			28531	protein-coding gene	gene with protein product		611017				17255948	Standard	NM_173555		Approved	MGC34695, NET41	uc001jqr.4	Q2T9J0	OTTHUMG00000018397	ENST00000287078.6:c.637G>A	chr10.hg19:g.71905706C>T	ENSP00000287078:p.Val213Met	44.0	0.0		95.0	4.0	NM_173555	Q5SQT4|Q5SQU1|Q8N6H2|Q96AR5	Missense_Mutation	SNP	ENST00000287078.6	hg19	CCDS31213.1	.	.	.	.	.	.	.	.	.	.	C	11.35	1.613406	0.28712	.	.	ENSG00000156521	ENST00000287078;ENST00000335494	T;T	0.58060	0.36;0.36	3.15	3.15	0.36227	.	0.234002	0.36234	N	0.002717	T	0.52933	0.1765	L	0.44542	1.39	0.30467	N	0.773686	B;D	0.71674	0.411;0.998	B;P	0.58520	0.057;0.84	T	0.54846	-0.8232	10	0.59425	D	0.04	-14.0618	4.7328	0.12974	0.0:0.6504:0.2256:0.124	.	213;213	Q2T9J0-2;Q2T9J0	.;TYSD1_HUMAN	M	213	ENSP00000287078:V213M;ENSP00000335673:V213M	ENSP00000287078:V213M	V	-	1	0	TYSND1	71575712	0.722000	0.28017	0.838000	0.33150	0.546000	0.35178	-0.076000	0.11412	2.045000	0.60652	0.313000	0.20887	GTG	.	.		0.692	TYSND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048483.1	NM_173555		T	71905706	C	T	71905706	3	4	279	1	0	0	0	0	1	0	0	0	16832	536	19	1	1079	1	TYSND1	10	71905706	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	2239065	71905706	63629041	217	39976										
C10orf57	80195	hgsc.bcm.edu	37	chr10	81838495	81838495	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cgacctactttcagcgaggcAgtctgttctggttcacagtc	10	12	4	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr10:81838495A>C	ENST00000372281.3	+	1	70	c.40A>C	c.(40-42)Agt>Cgt	p.S14R	TMEM254_ENST00000372274.1_Missense_Mutation_p.S14R|TMEM254-AS1_ENST00000432070.2_RNA|TMEM254-AS1_ENST00000448729.2_RNA|TMEM254_ENST00000372277.3_Missense_Mutation_p.S14R|TMEM254-AS1_ENST00000412298.1_RNA|TMEM254_ENST00000372275.1_Missense_Mutation_p.S14R	NM_001270372.1|NM_025125.3	NP_001257301.1|NP_079401.2	Q8TBM7	TM254_HUMAN	transmembrane protein 254	14						integral component of membrane (GO:0016021)											TCAGCGAGGCAGTCTGTTCTG	0.637																																					p.S14R		Atlas-SNP	.											.	TMEM254	1	.	0			c.A40C						.						87	71	76					10																	81838495		2202	4300	6502	SO:0001583	missense	80195	exon1			CGAGGCAGTCTGT	BC022252	CCDS7363.1, CCDS58086.1, CCDS58087.1, CCDS73157.1	10q23.1	2012-11-06	2012-11-06	2012-11-06	ENSG00000133678	ENSG00000133678			25804	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 57"	C10orf57		14702039	Standard	NM_025125		Approved	FLJ13263, bA369J21.6	uc010qlw.3	Q8TBM7	OTTHUMG00000018602	ENST00000372281.3:c.40A>C	chr10.hg19:g.81838495A>C	ENSP00000361355:p.Ser14Arg	39.0	0.0		36.0	10.0	NM_001270370	D3DWC8|Q53HP4|Q5JTC0|Q5JTC1|Q6IA45|Q9H8S6	Missense_Mutation	SNP	ENST00000372281.3	hg19	CCDS7363.1	.	.	.	.	.	.	.	.	.	.	A	9.023	0.985388	0.18889	.	.	ENSG00000133678	ENST00000372281;ENST00000372277;ENST00000372275;ENST00000372274	.	.	.	4.76	4.76	0.60689	.	.	.	.	.	T	0.26702	0.0653	N	0.21373	0.66	0.09310	N	0.999999	B;B	0.21606	0.058;0.006	B;B	0.18561	0.022;0.015	T	0.14090	-1.0485	8	0.09843	T	0.71	.	10.8465	0.46746	1.0:0.0:0.0:0.0	.	14;14	Q5JTC0;Q8TBM7	.;CJ057_HUMAN	R	14	.	ENSP00000361348:S14R	S	+	1	0	C10orf57	81828475	0.121000	0.22262	0.118000	0.21660	0.167000	0.22549	2.053000	0.41326	2.137000	0.66172	0.379000	0.24179	AGT	.	.		0.637	TMEM254-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049030.1	NM_025125		C	81838495	A	C	81838495	3	2	279	1	0	0	0	0	1	0	0	0	1611	188	7	5	42	5	C10orf57	10	81838495	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	9932789	81838495	53696252	218	39977										
CYP2C9	1559	hgsc.bcm.edu	37	chr10	96707544	96707544	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ctaattatttagcctcacccTgtgatcccactttcatcctg	4	14	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr10:96707544T>C	ENST00000260682.6	+	4	502	c.490T>C	c.(490-492)Tgt>Cgt	p.C164R		NM_000771.3	NP_000762.2	P11712	CP2C9_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 9	164					arachidonic acid metabolic process (GO:0019369)|cellular amide metabolic process (GO:0043603)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|monocarboxylic acid metabolic process (GO:0032787)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|urea metabolic process (GO:0019627)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	(R)-limonene 6-monooxygenase activity (GO:0052741)|(S)-limonene 6-monooxygenase activity (GO:0018675)|(S)-limonene 7-monooxygenase activity (GO:0018676)|caffeine oxidase activity (GO:0034875)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|steroid hydroxylase activity (GO:0008395)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	34		Colorectal(252;0.0902)		all cancers(201;6.93e-05)	Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Agomelatine(DB06594)|Alosetron(DB00969)|Alprazolam(DB00404)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amprenavir(DB00701)|Anastrozole(DB01217)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Arformoterol(DB01274)|Artemether(DB06697)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Atovaquone(DB01117)|Azelastine(DB00972)|Bexarotene(DB00307)|Bicalutamide(DB01128)|Bortezomib(DB00188)|Bosentan(DB00559)|Brompheniramine(DB00835)|Buprenorphine(DB00921)|Bupropion(DB01156)|Cabozantinib(DB08875)|Caffeine(DB00201)|Candesartan(DB00796)|Capecitabine(DB01101)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Carvedilol(DB01136)|Celecoxib(DB00482)|Chloramphenicol(DB00446)|Chlorpropamide(DB00672)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Cinnarizine(DB00568)|Cisapride(DB00604)|Cisplatin(DB00515)|Clevidipine(DB04920)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Colchicine(DB01394)|Cyclizine(DB01176)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Dapsone(DB00250)|Delavirdine(DB00705)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Diclofenamide(DB01144)|Dicoumarol(DB00266)|Diethylstilbestrol(DB00255)|Diltiazem(DB00343)|Diphenhydramine(DB01075)|Disulfiram(DB00822)|Dolasetron(DB00757)|Donepezil(DB00843)|Dopamine(DB00988)|Dorzolamide(DB00869)|Doxepin(DB01142)|Dronabinol(DB00470)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enzalutamide(DB08899)|Epinephrine(DB00668)|Epoprostenol(DB01240)|Eprosartan(DB00876)|Estradiol(DB00783)|Estrone(DB00655)|Estropipate(DB04574)|Eszopiclone(DB00402)|Ethanol(DB00898)|Etodolac(DB00749)|Etoricoxib(DB01628)|Etravirine(DB06414)|Felodipine(DB01023)|Fenofibrate(DB01039)|Flecainide(DB01195)|Fluconazole(DB00196)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Fluoxetine(DB00472)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Fosphenytoin(DB01320)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Ginkgo biloba(DB01381)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Glyburide(DB01016)|Guanfacine(DB01018)|Haloperidol(DB00502)|Halothane(DB01159)|Hexobarbital(DB01355)|Histamine Phosphate(DB00667)|Human Serum Albumin(DB00062)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Ifosfamide(DB01181)|Imatinib(DB00619)|Indinavir(DB00224)|Indomethacin(DB00328)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Lidocaine(DB00281)|Lopinavir(DB01601)|Loratadine(DB00455)|Lornoxicam(DB06725)|Losartan(DB00678)|Lovastatin(DB00227)|Lumiracoxib(DB01283)|Medroxyprogesterone Acetate(DB00603)|Mefenamic acid(DB00784)|Melatonin(DB01065)|Meloxicam(DB00814)|Mestranol(DB01357)|Methadone(DB00333)|Methazolamide(DB00703)|Methimazole(DB00763)|Methoxyflurane(DB01028)|Metronidazole(DB00916)|Miconazole(DB01110)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Modafinil(DB00745)|Montelukast(DB00471)|Naproxen(DB00788)|Nateglinide(DB00731)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Niclosamide(DB06803)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Ospemifene(DB04938)|Oxaprozin(DB00991)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paramethadione(DB00617)|Paroxetine(DB00715)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phenprocoumon(DB00946)|Phentermine(DB00191)|Phenylbutazone(DB00812)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Prasugrel(DB06209)|Pravastatin(DB00175)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Pyrimethamine(DB00205)|Quazepam(DB01589)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rifapentine(DB01201)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Secobarbital(DB00418)|Selegiline(DB01037)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sitaxentan(DB06268)|Sorafenib(DB00398)|Sulfadiazine(DB00359)|Sulfadimethoxine(DB06150)|Sulfamethizole(DB00576)|Sulfamethoxazole(DB01015)|Sulfamoxole(DB08798)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Sulfapyridine(DB00891)|Sulfinpyrazone(DB01138)|Sulfisoxazole(DB00263)|Suprofen(DB00870)|Tamoxifen(DB00675)|Tapentadol(DB06204)|Temazepam(DB00231)|Teniposide(DB00444)|Tenoxicam(DB00469)|Terbinafine(DB00857)|Testosterone(DB00624)|Thalidomide(DB01041)|Theophylline(DB00277)|Thiamylal(DB01154)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tolbutamide(DB01124)|Tolcapone(DB00323)|Tolterodine(DB01036)|Torasemide(DB00214)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Treprostinil(DB00374)|Tretinoin(DB00755)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Valsartan(DB00177)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vismodegib(DB08828)|Voriconazole(DB00582)|Warfarin(DB00682)|Ximelagatran(DB04898)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Zidovudine(DB00495)|Zileuton(DB00744)|Zolpidem(DB00425)|Zopiclone(DB01198)	AGCCTCACCCTGTGATCCCAC	0.303																																					p.C164R	Ovarian(54;1266 1406 16072 35076)	Atlas-SNP	.											.	CYP2C9	82	.	0			c.T490C						.						121	120	120					10																	96707544		2203	4300	6503	SO:0001583	missense	1559	exon4			TCACCCTGTGATC	M61855	CCDS7437.1	10q24.1	2007-12-14	2003-01-14		ENSG00000138109	ENSG00000138109		"Cytochrome P450s"	2623	protein-coding gene	gene with protein product		601130	"cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 9"	CYP2C10		2009263, 7841444	Standard	NM_000771		Approved	P450IIC9	uc001kka.4	P11712	OTTHUMG00000018805	ENST00000260682.6:c.490T>C	chr10.hg19:g.96707544T>C	ENSP00000260682:p.Cys164Arg	122.0	0.0		91.0	4.0	NM_000771	P11713|Q16756|Q16872|Q5VX92|Q6IRV8|Q8WW80	Missense_Mutation	SNP	ENST00000260682.6	hg19	CCDS7437.1	.	.	.	.	.	.	.	.	.	.	.	11.49	1.653707	0.29425	.	.	ENSG00000138109	ENST00000545448;ENST00000260682	T	0.68479	-0.33	3.33	3.33	0.38152	.	0.157256	0.41396	U	0.000882	T	0.54191	0.1843	N	0.25825	0.765	0.53005	D	0.99996	P;P	0.35242	0.492;0.492	B;B	0.39299	0.296;0.296	T	0.56805	-0.7918	10	0.49607	T	0.09	.	9.9282	0.41505	0.0:0.0:0.0:1.0	.	164;164	Q5VX92;P11712	.;CP2C9_HUMAN	R	164	ENSP00000260682:C164R	ENSP00000260682:C164R	C	+	1	0	CYP2C9	96697534	0.996000	0.38824	0.989000	0.46669	0.888000	0.51559	2.722000	0.47269	1.488000	0.48433	0.402000	0.26972	TGT	.	.		0.303	CYP2C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049501.1	NM_000771		C	96707544	T	C	96707544	3	2	279	1	0	0	0	0	1	0	0	0	4170	1580	55	2	504	2	CYP2C9	10	96707544	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	14869049	96707544	38827203	219	39978										
BLNK	29760	hgsc.bcm.edu	37	chr10	97966769	97966769	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	caaaataatagattttacctTcacaaacacttgaagcattc	3	9	1	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr10:97966769T>C	ENST00000224337.5	-	11	956	c.815A>G	c.(814-816)gAa>gGa	p.E272G	BLNK_ENST00000371176.2_Missense_Mutation_p.E249G|BLNK_ENST00000427367.2_Missense_Mutation_p.E272G|BLNK_ENST00000413476.2_Missense_Mutation_p.E272G	NM_013314.3	NP_037446.1	Q8WV28	BLNK_HUMAN	B-cell linker	272					B cell differentiation (GO:0030183)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|positive regulation of signal transduction (GO:0009967)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|skin(2)|stomach(1)	14		Colorectal(252;0.083)		Epithelial(162;7.89e-08)|all cancers(201;2.27e-06)		GATTTTACCTTCACAAACACT	0.308																																					p.E272G		Atlas-SNP	.											.	BLNK	46	.	0			c.A815G						.						82	86	85					10																	97966769		2203	4300	6503	SO:0001583	missense	29760	exon11			TTACCTTCACAAA	AF068180	CCDS7446.1, CCDS44464.1, CCDS58091.1, CCDS73171.1	10q23.2-q23.33	2014-09-17			ENSG00000095585	ENSG00000095585		"SH2 domain containing"	14211	protein-coding gene	gene with protein product	"B-cell adapter containing a SH2 domain protein", "B-cell activation", "Src homology [SH2] domain-containing leukocyte protein of 65 kD", "B cell adaptor containing SH2 domain"	604515				9697839, 10583958	Standard	NM_013314		Approved	SLP65, Ly57, SLP-65, BLNK-s, BASH, bca	uc001kls.4	Q8WV28	OTTHUMG00000018827	ENST00000224337.5:c.815A>G	chr10.hg19:g.97966769T>C	ENSP00000224337:p.Glu272Gly	114.0	0.0		80.0	4.0	NM_013314	O75498|O75499|Q2MD49	Missense_Mutation	SNP	ENST00000224337.5	hg19	CCDS7446.1	.	.	.	.	.	.	.	.	.	.	T	19.01	3.743738	0.69418	.	.	ENSG00000095585	ENST00000224337;ENST00000371176;ENST00000427367;ENST00000413476;ENST00000537049	.	.	.	5.63	5.63	0.86233	.	0.473283	0.25857	N	0.027858	T	0.68284	0.2984	M	0.62723	1.935	0.41510	D	0.988331	D;D;P;B;P;D	0.69078	0.972;0.997;0.921;0.055;0.872;0.989	P;P;P;B;B;P	0.62298	0.737;0.9;0.626;0.036;0.399;0.759	T	0.65730	-0.6097	9	0.25106	T	0.35	-27.9035	12.5296	0.56106	0.0:0.0:0.0:1.0	.	249;272;249;167;249;272	Q2MD54;Q2MD49;Q8WV28-2;Q2MD59;Q2MD52;Q8WV28	.;.;.;.;.;BLNK_HUMAN	G	272;249;272;272;167	.	ENSP00000224337:E272G	E	-	2	0	BLNK	97956759	1.000000	0.71417	1.000000	0.80357	0.680000	0.39746	3.521000	0.53472	2.281000	0.76405	0.533000	0.62120	GAA	.	.		0.308	BLNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049593.1	NM_013314		C	97966769	T	C	97966769	3	2	279	1	0	0	0	0	1	0	0	0	1447	1783	62	2	583	2	BLNK	10	97966769	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	1259225	97966769	37567978	220	39979										
SLIT1	6585	hgsc.bcm.edu	37	chr10	98824597	98824597	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cgcagagcacggaaggccccTtcctcaatgcagctgatctg	11	14	2	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr10:98824597T>C	ENST00000266058.4	-	6	767	c.522A>G	c.(520-522)gaA>gaG	p.E174E	ARHGAP19-SLIT1_ENST00000453547.2_3'UTR|SLIT1_ENST00000371041.3_Silent_p.E174E|SLIT1_ENST00000371070.4_Silent_p.E174E	NM_003061.2	NP_003052.2	O75093	SLIT1_HUMAN	slit homolog 1 (Drosophila)	174					axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|dorsal/ventral axon guidance (GO:0033563)|establishment of nucleus localization (GO:0040023)|forebrain morphogenesis (GO:0048853)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of synapse assembly (GO:0051964)|retinal ganglion cell axon guidance (GO:0031290)|spinal cord development (GO:0021510)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(37)|ovary(5)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	78		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		GGAAGGCCCCTTCCTCAATGC	0.557																																					p.E174E		Atlas-SNP	.											.	SLIT1	154	.	0			c.A522G						.						182	162	169					10																	98824597		2203	4300	6503	SO:0001819	synonymous_variant	6585	exon6			GGCCCCTTCCTCA	AB011537	CCDS7453.1	10q23.3-q24	2008-08-01	2001-11-28		ENSG00000187122	ENSG00000187122			11085	protein-coding gene	gene with protein product		603742	"slit (Drosophila) homolog 1"	SLIL1		9693030, 9813312	Standard	NM_003061		Approved	slit1, MEGF4, Slit-1, SLIT3	uc001kmw.2	O75093	OTTHUMG00000018843	ENST00000266058.4:c.522A>G	chr10.hg19:g.98824597T>C		70.0	0.0		77.0	4.0	NM_003061	Q5T0V1|Q8WWZ2|Q9UIL7	Silent	SNP	ENST00000266058.4	hg19	CCDS7453.1																																																																																			.	.		0.557	SLIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049636.1	NM_003061		C	98824597	T	C	98824597	2	2	279	1	0	0	0	0	0	0	0	1	14754	1606	56	2		2	SLIT1	10	98824597	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	857828	98824597	36710150	221	39980										
WNT8B	7479	hgsc.bcm.edu	37	chr10	102239648	102239648	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	caggcttacctgatttactcCagcagtgtggcagctggtgc	12	11	0	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr10:102239648C>T	ENST00000343737.5	+	3	248	c.120C>T	c.(118-120)tcC>tcT	p.S40S		NM_003393.3	NP_003384.2	Q93098	WNT8B_HUMAN	wingless-type MMTV integration site family, member 8B	40					cell fate commitment (GO:0045165)|cellular response to retinoic acid (GO:0071300)|determination of dorsal identity (GO:0048263)|gastrulation (GO:0007369)|negative regulation of gene expression (GO:0010629)|nervous system development (GO:0007399)|neuron differentiation (GO:0030182)|positive regulation of gene expression (GO:0010628)|response to estradiol (GO:0032355)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(1)|large_intestine(1)|ovary(1)|skin(1)	4		Colorectal(252;0.117)		Epithelial(162;1.87e-10)|all cancers(201;1.64e-08)		TGATTTACTCCAGCAGTGTGG	0.512																																					p.S40S		Atlas-SNP	.											.	WNT8B	31	.	0			c.C120T						.						113	114	114					10																	102239648		2203	4300	6503	SO:0001819	synonymous_variant	7479	exon3			TTACTCCAGCAGT	X91940	CCDS7494.1	10q24	2003-11-12			ENSG00000075290	ENSG00000075290		"Wingless-type MMTV integration sites"	12789	protein-coding gene	gene with protein product		601396				8661156	Standard	NM_003393		Approved		uc001krb.3	Q93098	OTTHUMG00000018912	ENST00000343737.5:c.120C>T	chr10.hg19:g.102239648C>T		82.0	0.0		71.0	4.0	NM_003393	O00771|Q5VX55|Q8WYK9	Silent	SNP	ENST00000343737.5	hg19	CCDS7494.1																																																																																			.	.		0.512	WNT8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049867.1	NM_003393		T	102239648	C	T	102239648	2	4	279	1	0	0	0	0	0	0	0	1	17412	581	21	3		3	WNT8B	10	102239648	Silent	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	3415051	102239648	33295099	222	39981										
KCNIP2	30819	hgsc.bcm.edu	37	chr10	103588904	103588904	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tgctcctgcagctgctccagAccctcaggccggtgacacac	10	17	1	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr10:103588904A>G	ENST00000356640.2	-	4	551	c.276T>C	c.(274-276)ggT>ggC	p.G92G	KCNIP2_ENST00000461105.1_Silent_p.G107G|KCNIP2_ENST00000370046.1_Silent_p.G42G|KCNIP2_ENST00000343195.4_Silent_p.G42G|KCNIP2_ENST00000353068.3_Silent_p.G42G|KCNIP2-AS1_ENST00000412353.1_RNA|KCNIP2_ENST00000355657.2_5'UTR|KCNIP2_ENST00000348850.5_Silent_p.G47G|KCNIP2_ENST00000358038.3_Silent_p.G74G	NM_014591.4|NM_173191.2	NP_055406.2|NP_775283.1	Q9NS61	KCIP2_HUMAN	Kv channel interacting protein 2	92	EF-hand 1; degenerate. {ECO:0000255|PROSITE-ProRule:PRU00448}.				clustering of voltage-gated potassium channels (GO:0045163)|detection of calcium ion (GO:0005513)|membrane repolarization (GO:0086009)|muscle contraction (GO:0006936)|potassium ion export (GO:0071435)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of cation channel activity (GO:2001257)|regulation of heart contraction (GO:0008016)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|calcium ion binding (GO:0005509)|ER retention sequence binding (GO:0046923)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein N-terminus binding (GO:0047485)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	11		Colorectal(252;0.122)		Epithelial(162;4.93e-09)|all cancers(201;2.63e-07)		GCTGCTCCAGACCCTCAGGCC	0.617																																					p.G107G		Atlas-SNP	.											.	KCNIP2	45	.	0			c.T321C						.						80	65	70					10																	103588904		2203	4300	6503	SO:0001819	synonymous_variant	30819	exon4			CTCCAGACCCTCA		CCDS7521.1, CCDS7522.1, CCDS7523.1, CCDS7524.1, CCDS7525.1, CCDS7526.1, CCDS41562.1	10q24.32	2013-09-20	2001-11-29		ENSG00000120049	ENSG00000120049		"EF-hand domain containing"	15522	protein-coding gene	gene with protein product		604661	"Kv channel-interacting protein 2"			10676964	Standard	NM_173192		Approved	KCHIP2	uc001kuc.3	Q9NS61	OTTHUMG00000018937	ENST00000356640.2:c.276T>C	chr10.hg19:g.103588904A>G		89.0	0.0		65.0	5.0	NM_014591	A6NJE5|A8MQ75|Q3YAC6|Q3YAC8|Q3YAC9|Q7Z6F1|Q96K86|Q96T41|Q96T42|Q96T43|Q96T44|Q9H0N4|Q9HD10|Q9HD11|Q9NS60|Q9NY10|Q9NZI1	Silent	SNP	ENST00000356640.2	hg19	CCDS7522.1	.	.	.	.	.	.	.	.	.	.	A	15.01	2.705257	0.48412	.	.	ENSG00000120049	ENST00000359877;ENST00000434163	T	0.72394	-0.65	5.1	-8.12	0.01078	.	.	.	.	.	T	0.42494	0.1205	.	.	.	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.11012	-1.0605	8	0.21014	T	0.42	.	2.2216	0.03973	0.16:0.1314:0.3619:0.3467	.	14;23	B3KSZ5;Q9NS61-8	.;.	A	14;23	ENSP00000411679:V23A	ENSP00000352940:V14A	V	-	2	0	KCNIP2	103578894	0.692000	0.27719	0.942000	0.38095	0.972000	0.66771	-0.143000	0.10296	-1.077000	0.03121	-0.378000	0.06908	GTC	.	.		0.617	KCNIP2-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049973.1			G	103588904	A	G	103588904	2	3	279	1	0	0	0	0	0	0	0	1	8049	262	10	2		2	KCNIP2	10	103588904	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	1349256	103588904	31945843	223	39982										
MXI1	4601	hgsc.bcm.edu	37	chr10	112038992	112038992	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	aaagttctgattccactaggAccagactgcacccggcacac	8	14	1	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr10:112038992A>G	ENST00000239007.7	+	4	509	c.291A>G	c.(289-291)ggA>ggG	p.G97G	MXI1_ENST00000369612.1_Silent_p.G61G|MXI1_ENST00000361248.4_Silent_p.G51G|MXI1_ENST00000332674.5_Silent_p.G164G|MXI1_ENST00000393134.1_Silent_p.G87G|MXI1_ENST00000485566.1_3'UTR	NM_005962.4	NP_005953.4	P50539	MXI1_HUMAN	MAX interactor 1, dimerization protein	97	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				cytoplasmic sequestering of transcription factor (GO:0042994)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(3)|lung(1)	10		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;1.33e-05)|all cancers(201;0.000277)|BRCA - Breast invasive adenocarcinoma(275;0.127)		TTCCACTAGGACCAGACTGCA	0.423																																					p.G164G		Atlas-SNP	.											.	MXI1	17	.	0			c.A492G						.						132	126	128					10																	112038992		2203	4300	6503	SO:0001819	synonymous_variant	4601	exon4			ACTAGGACCAGAC	BC016678	CCDS7563.1, CCDS7564.2, CCDS31284.1	10q24-q25	2012-11-15	2012-11-15		ENSG00000119950	ENSG00000119950		"MAX dimerization proteins", "Basic helix-loop-helix proteins"	7534	protein-coding gene	gene with protein product		600020	"MAX interacting protein 1", "MAX interactor 1"			7959753	Standard	NM_130439		Approved	MXD2, MAD2, MXI, bHLHc11	uc001kyy.3	P50539	OTTHUMG00000019033	ENST00000239007.7:c.291A>G	chr10.hg19:g.112038992A>G		119.0	0.0		99.0	4.0	NM_130439	B1ANN7|D3DR25|D3DRA9|Q15887|Q6FHW2|Q96E53	Silent	SNP	ENST00000239007.7	hg19	CCDS7564.2																																																																																			.	.		0.423	MXI1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050316.1	NM_130439		G	112038992	A	G	112038992	2	3	279	1	0	0	0	0	0	0	0	1	10011	262	10	2		2	MXI1	10	112038992	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	8450088	112038992	23495755	224	39983										
ABLIM1	3983	hgsc.bcm.edu	37	chr10	116232776	116232804	+	Frame_Shift_Del	DEL	GAAGTGTAGAAAGGCTCATAGGTAATAAG	GAAGTGTAGAAAGGCTCATAGGTAATAAG	-													0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cctgtttgtcatcatagcccGaagtgtagaaaggctcatag					rs369821107		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	GAAGTGTAGAAAGGCTCATAGGTAATAAG	GAAGTGTAGAAAGGCTCATAGGTAATAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr10:116232776_116232804delGAAGTGTAGAAAGGCTCATAGGTAATAAG	ENST00000277895.5	-	10	1304_1332	c.1207_1235delCTTATTACCTATGAGCCTTTCTACACTTC	c.(1207-1236)cttattacctatgagcctttctacacttcgfs	p.LITYEPFYTS403fs	ABLIM1_ENST00000369266.3_Frame_Shift_Del_p.LITYEPFYTS115fs|ABLIM1_ENST00000369252.4_Frame_Shift_Del_p.LITYEPFYTS343fs|ABLIM1_ENST00000392952.3_Frame_Shift_Del_p.LITYEPFYTS115fs|ABLIM1_ENST00000533213.2_Frame_Shift_Del_p.LITYEPFYTS343fs|ABLIM1_ENST00000369253.2_Frame_Shift_Del_p.LITYEPFYTS61fs	NM_002313.5	NP_002304.3	O14639	ABLM1_HUMAN	actin binding LIM protein 1	403					axon guidance (GO:0007411)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|visual perception (GO:0007601)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	30		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)		ATCATAGCCCGAAGTGTAGAAAGGCTCATAGGTAATAAGATCTGGACGT	0.41																																					p.403_412del		Pindel	.											.	ABLIM1	131	.	0			c.1208_1236del						.																																			SO:0001589	frameshift_variant	3983	exon10			.	AF005654	CCDS7590.1, CCDS31289.1	10q25	2008-07-07		2002-09-13	ENSG00000099204	ENSG00000099204			78	protein-coding gene	gene with protein product		602330		LIMAB1, ABLIM		9245787	Standard	NM_002313		Approved	abLIM, limatin	uc021pyw.1	O14639	OTTHUMG00000019088	ENST00000277895.5:c.1207_1235delCTTATTACCTATGAGCCTTTCTACACTTC	chr10.hg19:g.116232776_116232804delGAAGTGTAGAAAGGCTCATAGGTAATAAG	ENSP00000277895:p.Leu403fs	0.0	0.0		53.0	10.0	NM_002313	A6NI16|A6NJ06|A8MXA9|B3KVH2|Q15039|Q5JVV1|Q5JVV2|Q5T6N2|Q5T6N3|Q5T6N5|Q68CQ9|Q9BUP1	Frame_Shift_Del	DEL	ENST00000277895.5	hg19	CCDS7590.1																																																																																			.	.		0.41	ABLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050469.3			-	116232804	GAAGTGTAGAAAGGCTCATAGGTAATAAG	-	116232776	7	5	279	1	0	1	0	1	0	0	0	0	94	1059	37	0	1153	0	ABLIM1	10	116232776	Frame_Shift_Del	DEL	GAAGTGTAGAAAGGCTCATAGGTAATAAG	TCGA-G3-A3CG-01A-11D-A20W-10	4193784	116232776	19301971	225	39984										
ATRNL1	26033	hgsc.bcm.edu	37	chr10	117061550	117061550	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	agtggcaaactgccacctgcTcccgtaagtatttatctaga	8	11	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr10:117061550T>C	ENST00000355044.3	+	17	2941	c.2815T>C	c.(2815-2817)Tcc>Ccc	p.S939P	ATRNL1_ENST00000423111.2_Missense_Mutation_p.S36P|ATRNL1_ENST00000303745.7_5'UTR	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	939	PSI 4.				G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(11)|liver(2)|lung(44)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		TGCCACCTGCTCCCGTAAGTA	0.368																																					p.S939P		Atlas-SNP	.											.	ATRNL1	219	.	0			c.T2815C						.						173	148	156					10																	117061550		2203	4300	6503	SO:0001583	missense	26033	exon17			ACCTGCTCCCGTA	AB011106	CCDS7592.1, CCDS73204.1	10q26	2004-03-04			ENSG00000107518	ENSG00000107518			29063	protein-coding gene	gene with protein product		612869				9628581	Standard	NM_001276282		Approved	KIAA0534, FLJ45344, ALP	uc001lcg.3	Q5VV63	OTTHUMG00000019096	ENST00000355044.3:c.2815T>C	chr10.hg19:g.117061550T>C	ENSP00000347152:p.Ser939Pro	75.0	0.0		67.0	4.0	NM_207303	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Missense_Mutation	SNP	ENST00000355044.3	hg19	CCDS7592.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	8.902|8.902	0.956570|0.956570	0.18507|0.18507	.|.	.|.	ENSG00000107518|ENSG00000107518	ENST00000526373|ENST00000355044;ENST00000423111	.|T;T	.|0.24151	.|2.5;1.87	5.64|5.64	5.64|5.64	0.86602|0.86602	.|.	.|0.261243	.|0.43747	.|D	.|0.000525	T|T	0.11750|0.11750	0.0286|0.0286	N|N	0.02916|0.02916	-0.46|-0.46	0.80722|0.80722	D|D	1|1	.|P;P	.|0.42584	.|0.475;0.784	.|B;B	.|0.38880	.|0.063;0.284	T|T	0.26744|0.26744	-1.0094|-1.0094	5|10	.|0.14252	.|T	.|0.57	-8.0369|-8.0369	15.8593|15.8593	0.79009|0.79009	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|36;939	.|B4DH41;Q5VV63	.|.;ATRN1_HUMAN	P|P	68|939;36	.|ENSP00000347152:S939P;ENSP00000409624:S36P	.|ENSP00000347152:S939P	L|S	+|+	2|1	0|0	ATRNL1|ATRNL1	117051540|117051540	0.989000|0.989000	0.36119|0.36119	1.000000|1.000000	0.80357|0.80357	0.941000|0.941000	0.58515|0.58515	0.911000|0.911000	0.28584|0.28584	2.153000|2.153000	0.67306|0.67306	0.482000|0.482000	0.46254|0.46254	CTC|TCC	.	.		0.368	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349		C	117061550	T	C	117061550	3	2	279	1	0	0	0	0	1	0	0	0	1207	1551	54	2	2881	2	ATRNL1	10	117061550	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	828774	117061550	18473197	226	39985										
EIF3A	8661	hgsc.bcm.edu	37	chr10	120832562	120832562	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ccacttacagcacttaggagAacactacaaagaaaaaaatg	6	9	0	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr10:120832562A>G	ENST00000369144.3	-	4	508	c.381T>C	c.(379-381)gtT>gtC	p.V127V	EIF3A_ENST00000541549.1_Silent_p.V93V	NM_003750.2	NP_003741.1	P56537	IF6_HUMAN	eukaryotic translation initiation factor 3, subunit A	0					mature ribosome assembly (GO:0042256)|ribosomal large subunit biogenesis (GO:0042273)|ribosomal subunit export from nucleus (GO:0000054)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lamin filament (GO:0005638)|nucleus (GO:0005634)	ribosomal large subunit binding (GO:0043023)|ribosome binding (GO:0043022)|translation initiation factor activity (GO:0003743)			endometrium(8)|kidney(4)|large_intestine(14)|lung(22)|prostate(1)|skin(4)|urinary_tract(3)	56		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0236)		CACTTAGGAGAACACTACAAA	0.363																																					p.V127V		Atlas-SNP	.											.	EIF3A	142	.	0			c.T381C						.						56	53	54					10																	120832562		2203	4300	6503	SO:0001819	synonymous_variant	8661	exon4			TAGGAGAACACTA	U78311	CCDS7608.1	10q26.11	2007-08-03	2007-07-27	2007-07-27	ENSG00000107581	ENSG00000107581			3271	protein-coding gene	gene with protein product		602039	"eukaryotic translation initiation factor 3, subunit 10 theta, 150/170kDa"	EIF3, EIF3S10		9054404, 8590280	Standard	NM_003750		Approved	eIF3-theta, eIF3-p170, KIAA0139, eIF3a, TIF32	uc001ldu.3	Q14152	OTTHUMG00000019144	ENST00000369144.3:c.381T>C	chr10.hg19:g.120832562A>G		47.0	0.0		42.0	4.0	NM_003750	B7ZBG9|Q6IBN8|Q96TD5	Silent	SNP	ENST00000369144.3	hg19	CCDS7608.1																																																																																			.	.		0.363	EIF3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050634.1	NM_003750		G	120832562	A	G	120832562	2	3	279	1	0	0	0	0	0	0	0	1	5014	233	9	2		2	EIF3A	10	120832562	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	3771012	120832562	14702185	227	39986										
C10orf119	79892	hgsc.bcm.edu	37	chr10	121595143	121595143	+	Nonsense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gcacggaaggcagcaccgctGagagaaggctgttcatgtac	14	10	1	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr10:121595143G>C	ENST00000360003.3	-	14	1791	c.1622C>G	c.(1621-1623)tCa>tGa	p.S541*	MCMBP_ENST00000369077.3_Nonsense_Mutation_p.S539*|MCMBP_ENST00000466047.1_5'UTR	NM_001256378.1|NM_001256379.1|NM_024834.3	NP_001243307.1|NP_001243308.1|NP_079110.1	Q9BTE3	MCMBP_HUMAN	minichromosome maintenance complex binding protein	541					DNA-dependent DNA replication (GO:0006261)|mitotic nuclear division (GO:0007067)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(2)|skin(2)	21						CAGCACCGCTGAGAGAAGGCT	0.428																																					p.S541X		Atlas-SNP	.											.	MCMBP	49	.	0			c.C1622G						.						121	116	118					10																	121595143		2203	4300	6503	SO:0001587	stop_gained	79892	exon14			ACCGCTGAGAGAA	BC007219	CCDS7617.1, CCDS58099.1	10q26.13	2013-10-11	2011-01-05	2011-01-05	ENSG00000197771	ENSG00000197771			25782	protein-coding gene	gene with protein product		610909	"chromosome 10 open reading frame 119"	C10orf119		17296731	Standard	NM_024834		Approved	FLJ13081, MCM-BP	uc001ler.3	Q9BTE3	OTTHUMG00000019159	ENST00000360003.3:c.1622C>G	chr10.hg19:g.121595143G>C	ENSP00000353098:p.Ser541*	92.0	0.0		83.0	25.0	NM_024834	B3KSP7|Q6IA56|Q9BVT9|Q9H916	Nonsense_Mutation	SNP	ENST00000360003.3	hg19	CCDS7617.1	.	.	.	.	.	.	.	.	.	.	G	37	6.427239	0.97559	.	.	ENSG00000197771	ENST00000360003;ENST00000369077	.	.	.	5.52	4.58	0.56647	.	1.101780	0.06752	N	0.780258	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	-8.4364	16.3692	0.83347	0.0:0.1316:0.8684:0.0	.	.	.	.	X	541;539	.	ENSP00000353098:S541X	S	-	2	0	MCMBP	121585133	0.864000	0.29904	0.393000	0.26258	0.949000	0.60115	3.044000	0.49830	2.601000	0.87937	0.313000	0.20887	TCA	.	.		0.428	MCMBP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050684.1	NM_024834		C	121595143	G	C	121595143	4	2	279	1	0	0	0	0	0	1	0	0	1590	1294	45	4	318	4	C10orf119	10	121595143	Nonsense_Mutation	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	762581	121595143	13939604	228	39987										
ADAM8	101	hgsc.bcm.edu	37	chr10	135085698	135085698	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cgggcaggagccccctcaccTggttcacagcccctgagctg	12	17	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr10:135085698T>C	ENST00000445355.3	-	10	1006	c.956A>G	c.(955-957)cAg>cGg	p.Q319R	ADAM8_ENST00000559180.1_5'Flank|ADAM8_ENST00000485491.2_Splice_Site_p.Q280R|ADAM8_ENST00000415217.3_Splice_Site_p.Q319R	NM_001109.4	NP_001100.3	P78325	ADAM8_HUMAN	ADAM metallopeptidase domain 8	319	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				activation of MAPK activity involved in innate immune response (GO:0035419)|angiogenesis (GO:0001525)|cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|leukocyte migration involved in inflammatory response (GO:0002523)|lymphocyte chemotaxis (GO:0048247)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of bone resorption (GO:0045780)|positive regulation of cell adhesion (GO:0045785)|positive regulation of eosinophil migration (GO:2000418)|positive regulation of fibronectin-dependent thymocyte migration (GO:2000415)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of neutrophil extravasation (GO:2000391)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein processing (GO:0010954)|positive regulation of protein secretion (GO:0050714)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000309)|regulation of cell-cell adhesion (GO:0022407)|single organismal cell-cell adhesion (GO:0016337)	alpha9-beta1 integrin-ADAM8 complex (GO:0071133)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dense core granule membrane (GO:0032127)|integral component of plasma membrane (GO:0005887)|phagolysosome (GO:0032010)|plasma membrane (GO:0005886)|podosome (GO:0002102)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein self-association (GO:0043621)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)	17		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		all cancers(32;7.72e-06)|OV - Ovarian serous cystadenocarcinoma(35;8.23e-06)|Epithelial(32;1.02e-05)		CCCCCTCACCTGGTTCACAGC	0.667																																					p.Q319R		Atlas-SNP	.											.	ADAM8	41	.	0			c.A956G						.						17	16	16					10																	135085698		1999	3965	5964	SO:0001630	splice_region_variant	101	exon10			CTCACCTGGTTCA	D26579	CCDS31319.2, CCDS58102.1, CCDS58103.1	10q26.3	2014-03-20	2005-08-18		ENSG00000151651	ENSG00000151651		"ADAM metallopeptidase domain containing", "CD molecules"	215	protein-coding gene	gene with protein product		602267	"a disintegrin and metalloproteinase domain 8"			9126482	Standard	NM_001109		Approved	CD156, MS2, CD156a	uc021qbe.1	P78325	OTTHUMG00000019309	ENST00000445355.3:c.957+1A>G	chr10.hg19:g.135085698T>C		88.0	0.0		74.0	4.0	NM_001164489	B4DVM6|H0YL36|H0YLR0|H0YN39	Missense_Mutation	SNP	ENST00000445355.3	hg19	CCDS31319.2																																																																																			.	.		0.667	ADAM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051118.4	NM_001109	Missense_Mutation	C	135085698	T	C	135085698	5	2	279	1	0	0	0	0	0	0	1	0	252	1594	55	2	1492	2	ADAM8	10	135085698	Splice_Site	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	13490555	135085698	449049	229	39988										
AP2A2	161	hgsc.bcm.edu	37	chr11	992507	992507	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	agcctgtcccccacaggtgcTgaaggtcgccatcctggctg	12	15	0	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr11:992507T>G	ENST00000448903.2	+	11	1415	c.1274T>G	c.(1273-1275)cTg>cGg	p.L425R	AP2A2_ENST00000332231.5_Missense_Mutation_p.L426R|AP2A2_ENST00000534328.1_Intron	NM_001242837.1|NM_012305.3	NP_001229766.1|NP_036437.1	O94973	AP2A2_HUMAN	adaptor-related protein complex 2, alpha 2 subunit	425					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(2)	21		all_cancers(49;9.46e-06)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.75e-24)|BRCA - Breast invasive adenocarcinoma(625;5.73e-05)|Lung(200;0.0696)|LUSC - Lung squamous cell carcinoma(625;0.082)		CCACAGGTGCTGAAGGTCGCC	0.537																																					p.L426R		Atlas-SNP	.											.	AP2A2	50	.	0			c.T1277G						.						56	52	53					11																	992507		2006	4159	6165	SO:0001583	missense	161	exon11			AGGTGCTGAAGGT	AB020706	CCDS44512.1, CCDS73234.1	11p15.5	2008-07-18			ENSG00000183020	ENSG00000183020			562	protein-coding gene	gene with protein product	"alpha-adaptin C; Huntingtin interacting protein J", "adaptin, alpha B", "clathrin-associated/assembly/adaptor protein, large, alpha 2"	607242		CLAPA2, ADTAB		9700202, 2564002	Standard	NM_012305		Approved	DKFZP564D1864, HYPJ, KIAA0899, HIP9	uc001lst.2	O94973	OTTHUMG00000165627	ENST00000448903.2:c.1274T>G	chr11.hg19:g.992507T>G	ENSP00000413234:p.Leu425Arg	81.0	0.0		100.0	4.0	NM_001242837	O75403|Q53ET1|Q96SI8	Missense_Mutation	SNP	ENST00000448903.2	hg19	CCDS44512.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.173036	0.78452	.	.	ENSG00000183020	ENST00000448903;ENST00000332231;ENST00000448757;ENST00000529125;ENST00000452310	T;T	0.23950	1.88;1.88	3.79	3.79	0.43588	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.64402	D	0.000004	T	0.54663	0.1872	M	0.87900	2.915	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.995;0.997	T	0.64193	-0.6465	10	0.72032	D	0.01	-18.0546	13.232	0.59949	0.0:0.0:0.0:1.0	.	164;426;425	B7Z1Q4;O94973-2;O94973	.;.;AP2A2_HUMAN	R	425;426;426;162;165	ENSP00000413234:L425R;ENSP00000327694:L426R	ENSP00000327694:L426R	L	+	2	0	AP2A2	982507	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	7.707000	0.84623	1.678000	0.50952	0.374000	0.22700	CTG	.	.		0.537	AP2A2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385431.2	NM_012305		G	992507	T	G	992507	3	3	279	1	0	0	0	0	1	0	0	0	740	1580	55	5	1316	5	AP2A2	11	992507	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10		992507	134014009	230	39989										
AP2A2	161	hgsc.bcm.edu	37	chr11	1000575	1000575	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gtggtcgcgcctctcgctccTggctccgaagacaactttgc	11	15	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr11:1000575T>C	ENST00000448903.2	+	15	2241	c.2100T>C	c.(2098-2100)ccT>ccC	p.P700P	AP2A2_ENST00000332231.5_Silent_p.P701P|AP2A2_ENST00000534328.1_Intron|AP2A2_ENST00000525891.1_3'UTR	NM_001242837.1|NM_012305.3	NP_001229766.1|NP_036437.1	O94973	AP2A2_HUMAN	adaptor-related protein complex 2, alpha 2 subunit	700					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(2)	21		all_cancers(49;9.46e-06)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.75e-24)|BRCA - Breast invasive adenocarcinoma(625;5.73e-05)|Lung(200;0.0696)|LUSC - Lung squamous cell carcinoma(625;0.082)		CTCTCGCTCCTGGCTCCGAAG	0.706																																					p.P701P		Atlas-SNP	.											.	AP2A2	50	.	0			c.T2103C						.						9	10	10					11																	1000575		2000	4132	6132	SO:0001819	synonymous_variant	161	exon15			CGCTCCTGGCTCC	AB020706	CCDS44512.1, CCDS73234.1	11p15.5	2008-07-18			ENSG00000183020	ENSG00000183020			562	protein-coding gene	gene with protein product	"alpha-adaptin C; Huntingtin interacting protein J", "adaptin, alpha B", "clathrin-associated/assembly/adaptor protein, large, alpha 2"	607242		CLAPA2, ADTAB		9700202, 2564002	Standard	NM_012305		Approved	DKFZP564D1864, HYPJ, KIAA0899, HIP9	uc001lst.2	O94973	OTTHUMG00000165627	ENST00000448903.2:c.2100T>C	chr11.hg19:g.1000575T>C		20.0	0.0		20.0	4.0	NM_001242837	O75403|Q53ET1|Q96SI8	Silent	SNP	ENST00000448903.2	hg19	CCDS44512.1																																																																																			.	.		0.706	AP2A2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385431.2	NM_012305		C	1000575	T	C	1000575	2	2	279	1	0	0	0	0	0	0	0	1	740	1567	55	2		2	AP2A2	11	1000575	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	8068	1000575	134005941	231	39990										
MUC2	4583	hgsc.bcm.edu	37	chr11	1093299	1093299	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cccatcaccaccaccactacGgtgaccccaaccccaacacc	3	23	1	1	rs113492997		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr11:1093299G>A	ENST00000441003.2	+	30	5145	c.5118G>A	c.(5116-5118)acG>acA	p.T1706T	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Silent_p.T1673T|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ccaccactacggtgaccccaa	0.637																																					p.T1706T		Atlas-SNP	.											.	MUC2	614	.	0			c.G5118A						.																																			SO:0001819	synonymous_variant	4583	exon30			CACTACGGTGACC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5118G>A	chr11.hg19:g.1093299G>A		50.0	0.0		67.0	5.0	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	hg19																																																																																				.	.		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		A	1093299	G	A	1093299	2	1	279	1	0	0	0	0	0	0	0	1	9984	1103	39	1		1	MUC2	11	1093299	Silent	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	92724	1093299	133913217	232	39991										
TRIM34	53840	hgsc.bcm.edu	37	chr11	5664784	5664784	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gccgtgttggggttttcctcGactatgaagcaggcattgtc	13	9	0	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr11:5664784G>A	ENST00000514226.1	+	8	1649	c.1312G>A	c.(1312-1314)Gac>Aac	p.D438N	TRIM34_ENST00000495668.1_3'UTR|TRIM6-TRIM34_ENST00000457787.2_Missense_Mutation_p.D438N|HBG2_ENST00000380259.2_Intron|TRIM6-TRIM34_ENST00000354852.5_Missense_Mutation_p.D792N|TRIM34_ENST00000429814.2_Missense_Mutation_p.D438N	NM_001003827.1	NP_001003827.1	Q9BYJ4	TRI34_HUMAN	tripartite motif containing 34	438	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein trimerization (GO:0070206)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			NS(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	17		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;5.72e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGTTTTCCTCGACTATGAAGC	0.443																																					p.D792N		Atlas-SNP	.											.	TRIM6-TRIM34	68	.	0			c.G2374A						.						124	115	119					11																	5664784		2201	4297	6498	SO:0001583	missense	445372	exon14			TTCCTCGACTATG	AB039902	CCDS31391.1	11p15	2013-01-09	2011-01-25	2001-11-23		ENSG00000258659		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	10063	protein-coding gene	gene with protein product		605684	"tripartite motif-containing 34"	RNF21			Standard	NM_130390		Approved			Q9BYJ4	OTTHUMG00000066892	ENST00000514226.1:c.1312G>A	chr11.hg19:g.5664784G>A	ENSP00000422947:p.Asp438Asn	222.0	0.0		218.0	13.0	NM_001003819	D3DQS7|Q9C016|Q9HCR0|Q9HCR1|Q9HCR2	Missense_Mutation	SNP	ENST00000514226.1	hg19	CCDS31391.1	.	.	.	.	.	.	.	.	.	.	G	16.64	3.180374	0.57800	.	.	ENSG00000258659;ENSG00000258659;ENSG00000258659;ENSG00000258659;ENSG00000258588	ENST00000337072;ENST00000514226;ENST00000429814;ENST00000457787;ENST00000354852	T;T;T;T	0.80214	-1.35;-1.35;-1.35;-1.35	2.99	2.07	0.26955	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.35235	N	0.003360	D	0.85712	0.5760	M	0.81614	2.55	0.25800	N	0.984524	D;D	0.60575	0.973;0.988	D;P	0.63113	0.911;0.832	T	0.75736	-0.3213	10	0.59425	D	0.04	.	5.8549	0.18714	0.1491:0.0:0.8509:0.0	.	438;792	Q9BYJ4;B2RNG4	TRI34_HUMAN;.	N	792;438;438;438;792	ENSP00000422947:D438N;ENSP00000402595:D438N;ENSP00000395982:D438N;ENSP00000346916:D792N	ENSP00000402595:D438N	D	+	1	0	TRIM34;TRIM6-TRIM34	5621360	1.000000	0.71417	0.767000	0.31495	0.577000	0.36160	3.065000	0.49994	0.823000	0.34589	0.467000	0.42956	GAC	.	.		0.443	TRIM34-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143357.2	NM_001003827		A	5664784	G	A	5664784	3	1	279	1	0	0	0	0	1	0	0	0	16523	1058	37	1	1311	1	TRIM34	11	5664784	Missense_Mutation	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	4571485	5664784	129341732	233	39992										
NAV2	89797	hgsc.bcm.edu	37	chr11	20127228	20127228	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ttcccaaggtctggcatcacCtcaaccgcttcctggaggct	9	15	3	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr11:20127228C>T	ENST00000396087.3	+	38	7072	c.6973C>T	c.(6973-6975)Ctc>Ttc	p.L2325F	NAV2_ENST00000527559.2_Missense_Mutation_p.L2254F|NAV2_ENST00000540292.1_Missense_Mutation_p.L2256F|NAV2_ENST00000533917.1_Missense_Mutation_p.L1330F|NAV2_ENST00000396085.1_Missense_Mutation_p.L2269F|NAV2_ENST00000311043.8_Missense_Mutation_p.L1330F|NAV2_ENST00000360655.4_Missense_Mutation_p.L2202F|NAV2_ENST00000349880.4_Missense_Mutation_p.L2266F	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	2325					glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						CTGGCATCACCTCAACCGCTT	0.582																																					p.L2325F		Atlas-SNP	.											.	NAV2	255	.	0			c.C6973T						.						109	100	103					11																	20127228		2203	4300	6503	SO:0001583	missense	89797	exon37			CATCACCTCAACC	AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 2", "retinoic acid inducible gene in neuroblastoma 1", "helicase, APC down-regulated 1"	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.6973C>T	chr11.hg19:g.20127228C>T	ENSP00000379396:p.Leu2325Phe	100.0	0.0		97.0	4.0	NM_001244963	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Missense_Mutation	SNP	ENST00000396087.3	hg19	CCDS58126.1	.	.	.	.	.	.	.	.	.	.	c	31	5.091066	0.94149	.	.	ENSG00000166833	ENST00000360655;ENST00000396085;ENST00000349880;ENST00000396087;ENST00000527559;ENST00000540292;ENST00000533917;ENST00000311043	T;T;T;T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93	5.25	5.25	0.73442	.	0.000000	0.56097	D	0.000032	T	0.68732	0.3033	M	0.84326	2.69	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.91635	0.986;0.997;0.994;0.999	T	0.72137	-0.4381	9	.	.	.	.	18.4317	0.90628	0.0:1.0:0.0:0.0	.	2269;1330;2266;2202	A7E2D6;Q8IVL1-5;Q8IVL1-3;Q8IVL1-4	.;.;.;.	F	2202;2269;2266;2325;2254;2256;1330;1330	ENSP00000353871:L2202F;ENSP00000379394:L2269F;ENSP00000309577:L2266F;ENSP00000379396:L2325F;ENSP00000435395:L2254F;ENSP00000443489:L2256F;ENSP00000437316:L1330F;ENSP00000312169:L1330F	.	L	+	1	0	NAV2	20083804	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.965000	0.63708	2.462000	0.83206	0.655000	0.94253	CTC	.	.		0.582	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117		T	20127228	C	T	20127228	3	4	279	1	0	0	0	0	1	0	0	0	10193	681	24	3	7052	3	NAV2	11	20127228	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	14462444	20127228	114879288	234	39993										
HIPK3	10114	hgsc.bcm.edu	37	chr11	33308364	33308364	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gcgcaagagtgaggagttggAtaatcatagcagcgcaatgc	14	7	1	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr11:33308364A>G	ENST00000303296.4	+	2	709	c.404A>G	c.(403-405)gAt>gGt	p.D135G	HIPK3_ENST00000525975.1_Missense_Mutation_p.D135G|HIPK3_ENST00000456517.1_Missense_Mutation_p.D135G|HIPK3_ENST00000379016.3_Missense_Mutation_p.D135G	NM_005734.3	NP_005725.3	Q9H422	HIPK3_HUMAN	homeodomain interacting protein kinase 3	135					apoptotic process (GO:0006915)|mRNA transcription (GO:0009299)|negative regulation of apoptotic process (GO:0043066)|negative regulation of JUN kinase activity (GO:0043508)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			endometrium(3)|kidney(3)|large_intestine(9)|liver(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	39						GAGGAGTTGGATAATCATAGC	0.502																																					p.D135G		Atlas-SNP	.											.	HIPK3	92	.	0			c.A404G						.						86	73	78					11																	33308364		2202	4298	6500	SO:0001583	missense	10114	exon2			AGTTGGATAATCA	AF004849	CCDS7884.1, CCDS41634.1	11p13	2008-07-18	2001-11-29		ENSG00000110422	ENSG00000110422			4915	protein-coding gene	gene with protein product		604424	"homeodomain-interacting protein kinase 3"			9373137, 9748262	Standard	NM_005734		Approved	PKY, DYRK6, YAK1, FIST3	uc031pzm.1	Q9H422	OTTHUMG00000132269	ENST00000303296.4:c.404A>G	chr11.hg19:g.33308364A>G	ENSP00000304226:p.Asp135Gly	103.0	0.0		93.0	5.0	NM_001048200	O14632|Q2PBG4|Q2PBG5|Q92632|Q9HAS2	Missense_Mutation	SNP	ENST00000303296.4	hg19	CCDS7884.1	.	.	.	.	.	.	.	.	.	.	A	13.37	2.217415	0.39201	.	.	ENSG00000110422	ENST00000525975;ENST00000303296;ENST00000379016;ENST00000456517	T;T;T;T	0.53423	0.65;0.62;0.65;0.65	5.65	5.65	0.86999	.	0.170827	0.41097	D	0.000947	T	0.45438	0.1342	L	0.49126	1.545	0.54753	D	0.999982	B;B	0.06786	0.001;0.001	B;B	0.10450	0.005;0.003	T	0.32666	-0.9898	10	0.45353	T	0.12	.	15.8791	0.79189	1.0:0.0:0.0:0.0	.	135;135	Q9H422-2;Q9H422	.;HIPK3_HUMAN	G	135	ENSP00000431710:D135G;ENSP00000304226:D135G;ENSP00000368301:D135G;ENSP00000398241:D135G	ENSP00000304226:D135G	D	+	2	0	HIPK3	33264940	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	6.308000	0.72820	2.160000	0.67779	0.477000	0.44152	GAT	.	.		0.502	HIPK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255358.1	NM_005734		G	33308364	A	G	33308364	3	3	279	1	0	0	0	0	1	0	0	0	7127	333	12	2	406	2	HIPK3	11	33308364	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	13181136	33308364	101698152	235	39994										
ALKBH3	221120	hgsc.bcm.edu	37	chr11	43940662	43940662	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gggaccttgttaatcatggaAggagcgacacaagctgactg	13	8	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr11:43940662A>G	ENST00000302708.4	+	9	1155	c.744A>G	c.(742-744)gaA>gaG	p.E248E	ALKBH3_ENST00000532410.1_3'UTR|ALKBH3-AS1_ENST00000528285.1_RNA|ALKBH3-AS1_ENST00000499194.1_RNA|RP11-613D13.4_ENST00000526408.1_RNA|ALKBH3-AS1_ENST00000534287.1_RNA|ALKBH3-AS1_ENST00000527960.1_RNA	NM_139178.3	NP_631917.1	Q96Q83	ALKB3_HUMAN	alkB, alkylation repair homolog 3 (E. coli)	248	Fe2OG dioxygenase. {ECO:0000255|PROSITE- ProRule:PRU00805}.				cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA repair (GO:0006281)|oxidative single-stranded DNA demethylation (GO:0035552)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA-N1-methyladenine dioxygenase activity (GO:0043734)|ferrous iron binding (GO:0008198)|L-ascorbic acid binding (GO:0031418)			endometrium(2)|kidney(1)|lung(4)|prostate(1)	8					Vitamin C(DB00126)	TAATCATGGAAGGAGCGACAC	0.423								Direct reversal of damage																													p.E248E		Atlas-SNP	.											.	ALKBH3	33	.	0			c.A744G						.						186	153	164					11																	43940662		2203	4300	6503	SO:0001819	synonymous_variant	221120	exon9			CATGGAAGGAGCG	AB042029	CCDS7906.1	11p11.2	2013-10-11			ENSG00000166199	ENSG00000166199		"Alkylation repair homologs"	30141	protein-coding gene	gene with protein product		610603				22055184	Standard	NM_139178		Approved	DEPC-1	uc001mxs.2	Q96Q83	OTTHUMG00000166417	ENST00000302708.4:c.744A>G	chr11.hg19:g.43940662A>G		66.0	0.0		67.0	4.0	NM_139178	A6NDJ1|Q3SYI0|Q6NX57|Q96BU8	Silent	SNP	ENST00000302708.4	hg19	CCDS7906.1	.	.	.	.	.	.	.	.	.	.	A	9.787	1.176856	0.21704	.	.	ENSG00000166199	ENST00000532129	.	.	.	5.79	0.751	0.18392	.	.	.	.	.	T	0.54498	0.1862	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44711	-0.9310	4	.	.	.	-18.5699	7.5324	0.27691	0.4811:0.0:0.5189:0.0	.	.	.	.	G	118	.	.	R	+	1	2	ALKBH3	43897238	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	0.736000	0.26130	0.127000	0.18452	-0.250000	0.11733	AGG	.	.		0.423	ALKBH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389693.1	NM_139178		G	43940662	A	G	43940662	2	3	279	1	0	0	0	0	0	0	0	1	528	69	3	2		2	ALKBH3	11	43940662	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	10632298	43940662	91065854	236	39995										
PHF21A	51317	hgsc.bcm.edu	37	chr11	45958088	45958088	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tgaacaattgctaaagttccAggccatggaattgcttcttc	8	9	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr11:45958088A>G	ENST00000418153.2	-	16	1837	c.1638T>C	c.(1636-1638)ccT>ccC	p.P546P	PHF21A_ENST00000257821.4_Silent_p.P547P|PHF21A_ENST00000323180.6_Silent_p.P500P|PHF21A_ENST00000527753.1_5'Flank			Q96BD5	PF21A_HUMAN	PHD finger protein 21A	546	Required for transcriptional repression.				blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|suckling behavior (GO:0001967)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(10)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	29						CTAAAGTTCCAGGCCATGGAA	0.368																																					p.P546P		Atlas-SNP	.											.	PHF21A	107	.	0			c.T1638C						.						130	127	128					11																	45958088		2202	4299	6501	SO:0001819	synonymous_variant	51317	exon16			AGTTCCAGGCCAT	AL359593	CCDS31474.1, CCDS44578.1	11p11.2	2013-01-28			ENSG00000135365	ENSG00000135365		"Zinc fingers, PHD-type"	24156	protein-coding gene	gene with protein product		608325				11214970, 12032298	Standard	NM_001101802		Approved	BHC80, KIAA1696, BM-006	uc001ncc.4	Q96BD5	OTTHUMG00000167038	ENST00000418153.2:c.1638T>C	chr11.hg19:g.45958088A>G		80.0	0.0		100.0	4.0	NM_001101802	D3DQP5|Q6AWA2|Q9C0G7|Q9H8V9|Q9HAK6|Q9NZE9	Silent	SNP	ENST00000418153.2	hg19	CCDS44578.1																																																																																			.	.		0.368	PHF21A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392583.1	NM_016621		G	45958088	A	G	45958088	2	3	279	1	0	0	0	0	0	0	0	1	11842	175	7	2		2	PHF21A	11	45958088	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	2017426	45958088	89048428	237	39996										
ARHGAP1	392	hgsc.bcm.edu	37	chr11	46703710	46703710	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gtagtcactctccacgtactGgtccagggtgtgcttcaggt	12	11	3	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr11:46703710G>C	ENST00000311956.4	-	5	437	c.340C>G	c.(340-342)Cag>Gag	p.Q114E		NM_004308.3	NP_004299.1	Q07960	RHG01_HUMAN	Rho GTPase activating protein 1	114	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				positive regulation of signal transduction (GO:0009967)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	Rac GTPase activator activity (GO:0030675)|Rho GTPase activator activity (GO:0005100)|SH3/SH2 adaptor activity (GO:0005070)			endometrium(1)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	11		Lung NSC(402;1.76e-12)|all_lung(304;1.3e-11)		GBM - Glioblastoma multiforme(35;5.17e-06)|BRCA - Breast invasive adenocarcinoma(625;0.00112)|Lung(87;0.153)		TCCACGTACTGGTCCAGGGTG	0.607																																					p.Q114E		Atlas-SNP	.											.	ARHGAP1	27	.	0			c.C340G						.						225	179	195					11																	46703710		2201	4299	6500	SO:0001583	missense	392	exon5			CGTACTGGTCCAG	BC018118	CCDS7922.1	11p11.2	2006-04-11			ENSG00000175220	ENSG00000175220		"Rho GTPase activating proteins"	673	protein-coding gene	gene with protein product		602732				8288572	Standard	NM_004308		Approved	RhoGAP, p50rhoGAP, CDC42GAP, Cdc42GAP	uc001ndd.4	Q07960	OTTHUMG00000166567	ENST00000311956.4:c.340C>G	chr11.hg19:g.46703710G>C	ENSP00000310491:p.Gln114Glu	163.0	0.0		190.0	37.0	NM_004308	D3DQQ6	Missense_Mutation	SNP	ENST00000311956.4	hg19	CCDS7922.1	.	.	.	.	.	.	.	.	.	.	G	15.34	2.805404	0.50315	.	.	ENSG00000175220	ENST00000311956;ENST00000443332;ENST00000525488	T;T	0.60797	0.16;0.16	5.1	5.1	0.69264	Cellular retinaldehyde-binding/triple function, C-terminal (4);	0.052744	0.85682	D	0.000000	T	0.53883	0.1824	L	0.52573	1.65	0.58432	D	0.999998	P	0.38250	0.624	B	0.39465	0.3	T	0.50558	-0.8814	10	0.12103	T	0.63	.	18.5084	0.90907	0.0:0.0:1.0:0.0	.	114	Q07960	RHG01_HUMAN	E	114	ENSP00000310491:Q114E;ENSP00000432794:Q114E	ENSP00000310491:Q114E	Q	-	1	0	ARHGAP1	46660286	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	6.312000	0.72840	2.366000	0.80165	0.491000	0.48974	CAG	.	.		0.607	ARHGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390472.1	NM_004308		C	46703710	G	C	46703710	3	2	279	1	0	0	0	0	1	0	0	0	861	1357	47	4	1015	4	ARHGAP1	11	46703710	Missense_Mutation	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	745622	46703710	88302806	238	39997										
FAM111B	374393	hgsc.bcm.edu	37	chr11	58893058	58893058	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	catgttgtacatcttatggtGggtaaaaacacacatccaag	8	8	1	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr11:58893058G>A	ENST00000343597.3	+	4	1679	c.1488G>A	c.(1486-1488)gtG>gtA	p.V496V	FAM111B_ENST00000529618.1_Silent_p.V466V|FAM111B_ENST00000411426.1_Silent_p.V466V	NM_198947.3	NP_945185.1	Q6SJ93	F111B_HUMAN	family with sequence similarity 111, member B	496							catalytic activity (GO:0003824)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(12)|ovary(3)|pancreas(1)|skin(1)	40						ATCTTATGGTGGGTAAAAACA	0.398																																					p.V496V		Atlas-SNP	.											.	FAM111B	84	.	0			c.G1488A						.						114	112	112					11																	58893058		2201	4290	6491	SO:0001819	synonymous_variant	374393	exon4			TATGGTGGGTAAA	BC062456	CCDS7972.1, CCDS44611.1	11q12.1	2014-03-13			ENSG00000189057	ENSG00000189057			24200	protein-coding gene	gene with protein product		615584				24268661	Standard	NM_198947		Approved	CANP	uc001nnl.3	Q6SJ93	OTTHUMG00000167279	ENST00000343597.3:c.1488G>A	chr11.hg19:g.58893058G>A		240.0	0.0		224.0	54.0	NM_198947	B4E2G2|Q6P661	Silent	SNP	ENST00000343597.3	hg19	CCDS7972.1																																																																																			.	.		0.398	FAM111B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393974.1	NM_198947		A	58893058	G	A	58893058	2	1	279	1	0	0	0	0	0	0	0	1	5405	1335	47	3		3	FAM111B	11	58893058	Silent	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	12189348	58893058	76113458	239	39998										
EML3	256364	hgsc.bcm.edu	37	chr11	62370679	62370679	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cattcccggtctcggctctcAtagcgattcttcagctgctt	8	14	4	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr11:62370679A>G	ENST00000394773.2	-	20	2605	c.2298T>C	c.(2296-2298)taT>taC	p.Y766Y	MTA2_ENST00000278823.2_5'Flank|EML3_ENST00000531557.1_Silent_p.Y549Y|EML3_ENST00000494176.2_Silent_p.Y738Y|RP11-831H9.3_ENST00000532626.1_RNA|EML3_ENST00000529309.1_Silent_p.Y766Y|MTA2_ENST00000527204.1_5'Flank|EML3_ENST00000438258.1_5'Flank|EML3_ENST00000278845.4_Silent_p.Y767Y	NM_153265.2	NP_694997.2	Q32P44	EMAL3_HUMAN	echinoderm microtubule associated protein like 3	766						cytoplasm (GO:0005737)|microtubule (GO:0005874)				biliary_tract(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						CTCGGCTCTCATAGCGATTCT	0.627																																					p.Y766Y		Atlas-SNP	.											.	EML3	61	.	0			c.T2298C						.						105	103	103					11																	62370679		2202	4299	6501	SO:0001819	synonymous_variant	256364	exon20			GCTCTCATAGCGA	AK093146	CCDS8023.2	11q12.3	2013-01-10			ENSG00000149499	ENSG00000149499		"WD repeat domain containing"	26666	protein-coding gene	gene with protein product						15225882, 14744259	Standard	NM_153265		Approved	FLJ35827, ELP95	uc001ntu.1	Q32P44	OTTHUMG00000149817	ENST00000394773.2:c.2298T>C	chr11.hg19:g.62370679A>G		58.0	0.0		84.0	4.0	NM_153265	Q6ZQW7|Q8NA55	Silent	SNP	ENST00000394773.2	hg19	CCDS8023.2	.	.	.	.	.	.	.	.	.	.	A	8.041	0.763806	0.15914	.	.	ENSG00000149499	ENST00000394776	.	.	.	4.78	0.982	0.19762	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-15.9591	7.6462	0.28321	0.7269:0.0:0.2731:0.0	.	.	.	.	R	761	.	.	X	-	1	0	EML3	62127255	0.913000	0.31002	1.000000	0.80357	0.997000	0.91878	0.282000	0.18829	0.150000	0.19136	0.459000	0.35465	TGA	.	.		0.627	EML3-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313432.1	NM_153265		G	62370679	A	G	62370679	2	3	279	1	0	0	0	0	0	0	0	1	5100	224	8	2		2	EML3	11	62370679	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	3477621	62370679	72635837	240	39999										
ATL3	25923	hgsc.bcm.edu	37	chr11	63398635	63398635	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	agtccaaccatacagttgaaCaactgggctacaacctcaag	7	12	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr11:63398635C>T	ENST00000398868.3	-	12	1692	c.1416G>A	c.(1414-1416)ttG>ttA	p.L472L	ATL3_ENST00000332645.4_Silent_p.L499L|ATL3_ENST00000538786.1_Silent_p.L454L	NM_015459.3	NP_056274.3	Q6DD88	ATLA3_HUMAN	atlastin GTPase 3	472					endoplasmic reticulum organization (GO:0007029)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	11						TACAGTTGAACAACTGGGCTA	0.502																																					p.L472L		Atlas-SNP	.											.	ATL3	31	.	0			c.G1416A						.						78	80	79					11																	63398635		1960	4157	6117	SO:0001819	synonymous_variant	25923	exon12			GTTGAACAACTGG		CCDS41663.1, CCDS73309.1	11q13.1	2008-09-17			ENSG00000184743	ENSG00000184743			24526	protein-coding gene	gene with protein product		609369				18270207	Standard	XM_005273891		Approved	DKFZP564J0863	uc001nxk.1	Q6DD88	OTTHUMG00000167854	ENST00000398868.3:c.1416G>A	chr11.hg19:g.63398635C>T		139.0	0.0		177.0	44.0	NM_015459	Q8N7W5|Q9H8Q5|Q9UFL1	Silent	SNP	ENST00000398868.3	hg19	CCDS41663.1																																																																																			.	.		0.502	ATL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396637.1	NM_015459		T	63398635	C	T	63398635	2	4	279	1	0	0	0	0	0	0	0	1	1108	477	17	3		3	ATL3	11	63398635	Silent	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	1027956	63398635	71607881	241	40000										
PLCB3	5331	hgsc.bcm.edu	37	chr11	64023957	64023957	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tgtacccgcccctgcggcccTcccaggcccggctgctcatc	10	21	1	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr11:64023957T>C	ENST00000540288.1	+	9	911	c.808T>C	c.(808-810)Tcc>Ccc	p.S270P	PLCB3_ENST00000279230.6_Missense_Mutation_p.S270P|PLCB3_ENST00000325234.5_Missense_Mutation_p.S203P	NM_000932.2	NP_000923.1	Q01970	PLCB3_HUMAN	phospholipase C, beta 3 (phosphatidylinositol-specific)	270					inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|regulation of systemic arterial blood pressure (GO:0003073)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|urinary_tract(1)	33						CCTGCGGCCCTCCCAGGCCCG	0.637																																					p.S270P		Atlas-SNP	.											.	PLCB3	103	.	0			c.T808C						.						86	105	99					11																	64023957		2200	4295	6495	SO:0001583	missense	5331	exon9			CGGCCCTCCCAGG	Z26649	CCDS8064.1, CCDS53654.1	11q13	2008-03-18			ENSG00000149782	ENSG00000149782	3.1.4.11		9056	protein-coding gene	gene with protein product		600230				7849701	Standard	NM_000932		Approved		uc009ypg.2	Q01970	OTTHUMG00000167816	ENST00000540288.1:c.808T>C	chr11.hg19:g.64023957T>C	ENSP00000443631:p.Ser270Pro	177.0	0.0		248.0	10.0	NM_000932	A5PKZ6|G5E960|Q8N1A4	Missense_Mutation	SNP	ENST00000540288.1	hg19	CCDS8064.1	.	.	.	.	.	.	.	.	.	.	T	18.26	3.583924	0.65992	.	.	ENSG00000149782	ENST00000279230;ENST00000540288;ENST00000325234	T;T;T	0.18960	2.18;2.18;2.18	5.32	4.22	0.49857	Phospholipase C, phosphoinositol-specific, EF-hand-like (1);EF-hand-like domain (1);	0.169628	0.50627	D	0.000105	T	0.18299	0.0439	L	0.34521	1.04	0.39075	D	0.96078	P;P	0.47106	0.89;0.775	B;B	0.44224	0.444;0.318	T	0.02975	-1.1087	10	0.62326	D	0.03	.	9.794	0.40724	0.0:0.0:0.385:0.6149	.	203;270	G5E960;Q01970	.;PLCB3_HUMAN	P	270;270;203	ENSP00000279230:S270P;ENSP00000443631:S270P;ENSP00000324660:S203P	ENSP00000279230:S270P	S	+	1	0	PLCB3	63780533	0.998000	0.40836	1.000000	0.80357	0.958000	0.62258	3.998000	0.57024	2.019000	0.59389	0.459000	0.35465	TCC	.	.		0.637	PLCB3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396405.1			C	64023957	T	C	64023957	3	2	279	1	0	0	0	0	1	0	0	0	12038	1551	54	2	842	2	PLCB3	11	64023957	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	625322	64023957	70982559	242	40001										
KCNK4	50801	hgsc.bcm.edu	37	chr11	64060660	64060660	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tccgtgtgtgagcgaccaggAgctgggcctcctcatcaagg	14	12	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr11:64060660A>G	ENST00000539216.1	+	1	530	c.170A>G	c.(169-171)gAg>gGg	p.E57G	KCNK4_ENST00000539651.1_Intron|KCNK4_ENST00000422670.2_Missense_Mutation_p.E57G|KCNK4_ENST00000538767.1_Intron|KCNK4_ENST00000394525.2_Missense_Mutation_p.E57G|Y_RNA_ENST00000384297.1_RNA|RP11-783K16.10_ENST00000539086.1_RNA			Q9NYG8	KCNK4_HUMAN	potassium channel, subfamily K, member 4	57					potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			breast(2)|large_intestine(2)|lung(3)|prostate(2)|urinary_tract(1)	10						AGCGACCAGGAGCTGGGCCTC	0.682																																					p.E57G		Atlas-SNP	.											.	KCNK4	22	.	0			c.A170G						.						37	33	34					11																	64060660		1832	3455	5287	SO:0001583	missense	50801	exon2			ACCAGGAGCTGGG	AF247042	CCDS8067.1	11q13	2012-03-07			ENSG00000182450	ENSG00000182450		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6279	protein-coding gene	gene with protein product		605720				10767409, 16382106	Standard	NM_033310		Approved	K2p4.1, TRAAK	uc001nzk.1	Q9NYG8	OTTHUMG00000168006	ENST00000539216.1:c.170A>G	chr11.hg19:g.64060660A>G	ENSP00000444948:p.Glu57Gly	106.0	0.0		148.0	6.0	NM_033310	B5TJL1|Q96T94	Missense_Mutation	SNP	ENST00000539216.1	hg19	CCDS8067.1	.	.	.	.	.	.	.	.	.	.	A	14.00	2.404259	0.42613	.	.	ENSG00000182450	ENST00000422670;ENST00000539852;ENST00000394525;ENST00000544845;ENST00000539216	T;T;T	0.18338	2.22;2.22;2.22	4.4	1.79	0.24919	.	0.767534	0.12781	N	0.439687	T	0.14570	0.0352	L	0.52573	1.65	0.09310	N	1	B	0.17667	0.023	B	0.23275	0.045	T	0.28427	-1.0044	10	0.59425	D	0.04	.	3.194	0.06626	0.6281:0.0:0.1979:0.174	.	57	Q9NYG8	KCNK4_HUMAN	G	57;82;57;119;57	ENSP00000402797:E57G;ENSP00000378033:E57G;ENSP00000444948:E57G	ENSP00000378033:E57G	E	+	2	0	KCNK4	63817236	0.243000	0.23878	0.980000	0.43619	0.954000	0.61252	1.457000	0.35212	0.690000	0.31570	0.374000	0.22700	GAG	.	.		0.682	KCNK4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396430.1	NM_033311		G	64060660	A	G	64060660	3	3	279	1	0	0	0	0	1	0	0	0	8077	304	11	2	172	2	KCNK4	11	64060660	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	36703	64060660	70945856	243	40002										
RPS6KB2	6199	hgsc.bcm.edu	37	chr11	67200857	67200857	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gaaaaccatggataagatcaTcaggggcaagctggcactgc	12	9	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr11:67200857T>C	ENST00000312629.5	+	10	890	c.845T>C	c.(844-846)aTc>aCc	p.I282T	AP003419.16_ENST00000535922.1_RNA	NM_003952.2	NP_003943.2	Q9UBS0	KS6B2_HUMAN	ribosomal protein S6 kinase, 70kDa, polypeptide 2	282	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of translational initiation (GO:0045948)|protein kinase B signaling (GO:0043491)|signal transduction (GO:0007165)|translation (GO:0006412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|peptide binding (GO:0042277)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ribosomal protein S6 kinase activity (GO:0004711)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|prostate(3)|salivary_gland(1)|stomach(2)	25			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)			GATAAGATCATCAGGGGCAAG	0.632																																					p.I282T		Atlas-SNP	.											.	RPS6KB2	92	.	0			c.T845C						.						100	112	108					11																	67200857		1963	4135	6098	SO:0001583	missense	6199	exon10			AGATCATCAGGGG	AB019245	CCDS41677.1	11q13.1	2011-04-05	2002-08-29		ENSG00000175634	ENSG00000175634			10437	protein-coding gene	gene with protein product		608939	"ribosomal protein S6 kinase, 70kD, polypeptide 2"			9878560, 9804755	Standard	XM_005274164		Approved	p70S6Kb, P70-BETA, STK14B, KLS	uc001old.3	Q9UBS0	OTTHUMG00000167673	ENST00000312629.5:c.845T>C	chr11.hg19:g.67200857T>C	ENSP00000308413:p.Ile282Thr	54.0	0.0		90.0	4.0	NM_003952	B2RMZ9|B4DML8|O94809|Q9UEC1	Missense_Mutation	SNP	ENST00000312629.5	hg19	CCDS41677.1	.	.	.	.	.	.	.	.	.	.	T	13.43	2.236110	0.39498	.	.	ENSG00000175634	ENST00000312629	T	0.55052	0.54	5.4	4.2	0.49525	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.387293	0.24156	N	0.041030	T	0.41650	0.1168	N	0.17631	0.505	0.80722	D	1	B;B	0.26041	0.07;0.14	B;B	0.34385	0.073;0.181	T	0.46610	-0.9179	10	0.87932	D	0	.	11.7689	0.51947	0.0:0.0:0.1471:0.8529	.	282;282	Q9BRS0;Q9UBS0	.;KS6B2_HUMAN	T	282	ENSP00000308413:I282T	ENSP00000308413:I282T	I	+	2	0	RPS6KB2	66957433	1.000000	0.71417	0.946000	0.38457	0.330000	0.28571	5.687000	0.68219	2.039000	0.60335	0.459000	0.35465	ATC	.	.		0.632	RPS6KB2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395508.1	NM_003952		C	67200857	T	C	67200857	3	2	279	1	0	0	0	0	1	0	0	0	13672	1435	50	2	883	2	RPS6KB2	11	67200857	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	3140197	67200857	67805659	244	40003										
KRTAP5-8	57830	hgsc.bcm.edu	37	chr11	71249121	71249121	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	catgggctgctgtggctgctCtggaggctgtggctccggct	17	11	1	0	rs200585722		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr11:71249121C>G	ENST00000398534.3	+	1	51	c.20C>G	c.(19-21)tCt>tGt	p.S7C		NM_021046.2	NP_066384.2	O75690	KRA58_HUMAN	keratin associated protein 5-8	7						keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|lung(2)|skin(1)|stomach(1)	6						TGTGGCTGCTCTGGAGGCTGT	0.657																																					p.S7C		Atlas-SNP	.											.	KRTAP5-8	28	.	0			c.C20G						.						47	66	60					11																	71249121		2189	4282	6471	SO:0001583	missense	57830	exon1			GCTGCTCTGGAGG	AB126077	CCDS41683.1	11q13.4	2008-02-05			ENSG00000241233	ENSG00000241233		"Keratin associated proteins"	23603	protein-coding gene	gene with protein product						15144888	Standard	NM_021046		Approved	KRTAP5.8, UHSKerB, KRTAP5-2	uc001oqr.1	O75690	OTTHUMG00000057571	ENST00000398534.3:c.20C>G	chr11.hg19:g.71249121C>G	ENSP00000420723:p.Ser7Cys	176.0	0.0		207.0	21.0	NM_021046	Q6L8G7|Q6UTX6	Missense_Mutation	SNP	ENST00000398534.3	hg19	CCDS41683.1	.	.	.	.	.	.	.	.	.	.	c	3.358	-0.131059	0.06753	.	.	ENSG00000241233	ENST00000398534	T	0.01527	4.8	1.57	1.57	0.23409	.	.	.	.	.	T	0.03564	0.0102	M	0.74389	2.26	0.09310	N	1	P	0.39094	0.659	B	0.43225	0.412	T	0.34204	-0.9838	9	0.62326	D	0.03	.	3.9595	0.09404	0.0:0.775:0.0:0.225	.	7	O75690	KRA58_HUMAN	C	7	ENSP00000420723:S7C	ENSP00000420723:S7C	S	+	2	0	KRTAP5-8	70926769	0.030000	0.19436	0.804000	0.32291	0.223000	0.24884	-0.589000	0.05767	1.182000	0.42928	0.514000	0.50259	TCT	.	.		0.657	KRTAP5-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127954.1	NM_021046		G	71249121	C	G	71249121	3	3	279	1	0	0	0	0	1	0	0	0	8576	913	32	4	22	4	KRTAP5-8	11	71249121	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	4048264	71249121	63757395	245	40004										
ARHGEF17	9828	hgsc.bcm.edu	37	chr11	73020389	73020389	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cctcctgctcctcctcctccAtcgccgcctcctatcctgtc	4	23	0	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr11:73020389A>T	ENST00000263674.3	+	1	1056	c.706A>T	c.(706-708)Atc>Ttc	p.I236F	RP11-800A3.7_ENST00000546324.1_RNA	NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	236					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(2)	32						CTCCTCCTCCATCGCCGCCTC	0.677																																					p.I236F		Atlas-SNP	.											.	ARHGEF17	117	.	0			c.A706T						.						12	15	14					11																	73020389		2048	3983	6031	SO:0001583	missense	9828	exon1			TCCTCCATCGCCG	AF378754	CCDS8221.1	11q13.3	2011-11-16			ENSG00000110237	ENSG00000110237		"Rho guanine nucleotide exchange factors"	21726	protein-coding gene	gene with protein product	"Rho-specific guanine-nucleotide exchange factor 164 kDa", "tumor endothelial marker 4"					11559528, 12071859	Standard	NM_014786		Approved	TEM4, KIAA0337, p164-RhoGEF	uc001otu.3	Q96PE2	OTTHUMG00000167971	ENST00000263674.3:c.706A>T	chr11.hg19:g.73020389A>T	ENSP00000263674:p.Ile236Phe	216.0	0.0		268.0	36.0	NM_014786	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Missense_Mutation	SNP	ENST00000263674.3	hg19	CCDS8221.1	.	.	.	.	.	.	.	.	.	.	A	12.21	1.870463	0.33069	.	.	ENSG00000110237	ENST00000263674	T	0.59638	0.25	4.61	0.695	0.18070	.	0.993735	0.08148	N	0.990484	T	0.35480	0.0933	N	0.24115	0.695	0.19775	N	0.999951	P	0.35982	0.531	B	0.24394	0.053	T	0.25117	-1.0141	10	0.54805	T	0.06	-1.1385	5.2264	0.15397	0.6445:0.1573:0.1981:0.0	.	236	Q96PE2	ARHGH_HUMAN	F	236	ENSP00000263674:I236F	ENSP00000263674:I236F	I	+	1	0	ARHGEF17	72698037	0.000000	0.05858	0.765000	0.31456	0.926000	0.56050	-0.104000	0.10923	0.647000	0.30713	0.379000	0.24179	ATC	.	.		0.677	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786		T	73020389	A	T	73020389	3	4	279	1	0	0	0	0	1	0	0	0	900	217	8	4	708	4	ARHGEF17	11	73020389	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	1771268	73020389	61986127	246	40005										
ODZ4	26011	hgsc.bcm.edu	37	chr11	78482151	78482151	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	attcaggtctaaggtacatcTgccgttgccattgcacaacc	8	12	3	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr11:78482151T>A	ENST00000278550.7	-	18	2887	c.2425A>T	c.(2425-2427)Aga>Tga	p.R809*		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	809	EGF-like 8. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										AAGGTACATCTGCCGTTGCCA	0.552																																					p.R809X		Atlas-SNP	.											.	.	.	.	0			c.A2425T						.						55	57	56					11																	78482151		2142	4233	6375	SO:0001587	stop_gained	26011	exon18			TACATCTGCCGTT	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"odz, odd Oz/ten-m homolog 4 (Drosophila)"	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.2425A>T	chr11.hg19:g.78482151T>A	ENSP00000278550:p.Arg809*	111.0	0.0		175.0	35.0	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Nonsense_Mutation	SNP	ENST00000278550.7	hg19	CCDS44688.1	.	.	.	.	.	.	.	.	.	.	T	44	10.732393	0.99458	.	.	ENSG00000149256	ENST00000278550	.	.	.	5.24	4.06	0.47325	.	0.045968	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.4811	0.55842	0.0:0.0:0.1389:0.8611	.	.	.	.	X	809	.	.	R	-	1	2	ODZ4	78159799	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.291000	0.51764	2.200000	0.70718	0.459000	0.35465	AGA	.	.		0.552	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			A	78482151	T	A	78482151	4	1	279	1	0	0	0	0	0	1	0	0	10846	1588	55	4	5952	4	ODZ4	11	78482151	Nonsense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	5461762	78482151	56524365	247	40006										
C11orf82	220042	hgsc.bcm.edu	37	chr11	82644461	82644461	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ggacattgcaactgagattaCcaaaaaatcacaggatattt	7	7	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr11:82644461C>T	ENST00000533655.1	+	6	2293	c.2081C>T	c.(2080-2082)aCc>aTc	p.T694I	C11orf82_ENST00000528759.1_3'UTR|C11orf82_ENST00000525361.1_Intron|C11orf82_ENST00000430323.2_Missense_Mutation_p.T694I|C11orf82_ENST00000329143.3_Missense_Mutation_p.T393I	NM_145018.3	NP_659455.3	Q8IXT1	DDIAS_HUMAN		694					apoptotic process (GO:0006915)|cellular response to cytokine stimulus (GO:0071345)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to hydroperoxide (GO:0071447)|cellular response to UV (GO:0034644)|hemopoiesis (GO:0030097)|mitotic cell cycle arrest (GO:0071850)|negative regulation of fibroblast apoptotic process (GO:2000270)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(17)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	33						ACTGAGATTACCAAAAAATCA	0.373																																					p.T694I		Atlas-SNP	.											.	C11orf82	71	.	0			c.C2081T						.						125	124	125					11																	82644461		2203	4299	6502	SO:0001583	missense	220042	exon6			AGATTACCAAAAA																												ENST00000533655.1:c.2081C>T	chr11.hg19:g.82644461C>T	ENSP00000435421:p.Thr694Ile	80.0	0.0		72.0	34.0	NM_145018	Q96LK6|Q9H856	Missense_Mutation	SNP	ENST00000533655.1	hg19	CCDS8263.1	.	.	.	.	.	.	.	.	.	.	C	11.09	1.535677	0.27475	.	.	ENSG00000165490	ENST00000430323;ENST00000533655;ENST00000329143	T;T;T	0.18338	2.49;2.49;2.22	6.16	2.9	0.33743	.	0.493879	0.21442	N	0.074468	T	0.13628	0.0330	L	0.45581	1.43	0.09310	N	1	B	0.21071	0.051	B	0.16722	0.016	T	0.19549	-1.0302	9	.	.	.	-0.4458	7.5526	0.27806	0.0:0.6471:0.0:0.3529	.	694	Q8IXT1	NOXIN_HUMAN	I	694;694;393	ENSP00000414687:T694I;ENSP00000435421:T694I;ENSP00000329930:T393I	.	T	+	2	0	C11orf82	82322109	0.003000	0.15002	0.060000	0.19600	0.663000	0.39108	0.461000	0.21940	0.946000	0.37632	0.650000	0.86243	ACC	.	.		0.373	C11orf82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391936.1			T	82644461	C	T	82644461	3	4	279	1	0	0	0	0	1	0	0	0	1667	507	18	3	2095	3	C11orf82	11	82644461	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	4162310	82644461	52362055	248	40007										
CCDC67	159989	hgsc.bcm.edu	37	chr11	93088638	93088638	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	aagaaagatgcgggctttggAgacacgattagatcttcggg	14	6	1	4			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr11:93088638A>G	ENST00000298050.3	+	3	231	c.131A>G	c.(130-132)gAg>gGg	p.E44G	CCDC67_ENST00000527307.1_Missense_Mutation_p.E44G|CCDC67_ENST00000530053.1_3'UTR	NM_181645.3	NP_857596.2	Q05D60	DEUP1_HUMAN	coiled-coil domain containing 67	44					cell projection organization (GO:0030030)|de novo centriole assembly (GO:0098535)	cytoplasm (GO:0005737)|deuterosome (GO:0098536)				endometrium(3)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		Acute lymphoblastic leukemia(157;2.35e-05)|all_hematologic(158;0.00824)				CGGGCTTTGGAGACACGATTA	0.393																																					p.E44G		Atlas-SNP	.											.	CCDC67	57	.	0			c.A131G						.						110	110	110					11																	93088638		1876	4099	5975	SO:0001583	missense	159989	exon3			CTTTGGAGACACG	AK058122	CCDS44707.1	11q21	2014-02-20				ENSG00000165325			26344	protein-coding gene	gene with protein product						24240477	Standard	NM_181645		Approved	FLJ25393	uc001pdq.3	Q05D60		ENST00000298050.3:c.131A>G	chr11.hg19:g.93088638A>G	ENSP00000298050:p.Glu44Gly	106.0	0.0		149.0	6.0	NM_181645	Q8NEF1|Q96LL7	Missense_Mutation	SNP	ENST00000298050.3	hg19	CCDS44707.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.716677	0.89205	.	.	ENSG00000165325	ENST00000534747;ENST00000298050;ENST00000532819;ENST00000527307	T;T;T;T	0.24723	1.84;1.84;1.84;1.84	5.54	5.54	0.83059	.	0.000000	0.64402	D	0.000001	T	0.50752	0.1634	M	0.70595	2.14	0.44295	D	0.997164	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.74674	0.984;0.984;0.984	T	0.53995	-0.8359	10	0.72032	D	0.01	.	15.6625	0.77199	1.0:0.0:0.0:0.0	.	44;44;36	Q05D60;E9PJR5;Q6ZRU6	CCD67_HUMAN;.;.	G	44	ENSP00000432111:E44G;ENSP00000298050:E44G;ENSP00000434635:E44G;ENSP00000433002:E44G	ENSP00000298050:E44G	E	+	2	0	CCDC67	92728286	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.336000	0.72954	2.114000	0.64651	0.402000	0.26972	GAG	.	.		0.393	CCDC67-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_181645		G	93088638	A	G	93088638	3	3	279	1	0	0	0	0	1	0	0	0	2841	304	11	2	137	2	CCDC67	11	93088638	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	10444177	93088638	41917878	249	40008										
MAML2	84441	hgsc.bcm.edu	37	chr11	95825422	95825422	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tgctgctgctgctgttgctgCtgttgctgttgggtgtagtg	16	7	0	0	rs200834136		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr11:95825422C>T	ENST00000524717.1	-	2	3057	c.1773G>A	c.(1771-1773)caG>caA	p.Q591Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	591					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				gctgttgctgctgttgctgTT	0.507			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																p.Q591Q		Atlas-SNP	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2	94	.	0			c.G1773A						.						50	54	53					11																	95825422		2171	4250	6421	SO:0001819	synonymous_variant	84441	exon2			TTGCTGCTGTTGC	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"mastermind (Drosophila)-like 2"			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1773G>A	chr11.hg19:g.95825422C>T		152.0	0.0		201.0	12.0	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	hg19	CCDS44714.1																																																																																			.	.		0.507	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			T	95825422	C	T	95825422	2	4	279	1	0	0	0	0	0	0	0	1	9215	796	28	3		3	MAML2	11	95825422	Silent	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	2736784	95825422	39181094	250	40009										
MMP3	4314	hgsc.bcm.edu	37	chr11	102713260	102713260	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	agactttcagagctttctcaAcagcagaatcaacagcatct	6	11	4	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr11:102713260A>T	ENST00000299855.5	-	3	657	c.401T>A	c.(400-402)gTt>gAt	p.V134D		NM_002422.3	NP_002413.1	P08254	MMP3_HUMAN	matrix metallopeptidase 3 (stromelysin 1, progelatinase)	134					cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|positive regulation of oxidative stress-induced cell death (GO:1903209)|proteolysis (GO:0006508)|regulation of cell migration (GO:0030334)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0142)	Marimastat(DB00786)	AGCTTTCTCAACAGCAGAATC	0.398																																					p.V134D		Atlas-SNP	.											.	MMP3	60	.	0			c.T401A						.						114	114	114					11																	102713260		2203	4299	6502	SO:0001583	missense	4314	exon3			TTCTCAACAGCAG	X05232	CCDS8323.1	11q22.3	2012-10-02	2005-08-08		ENSG00000149968	ENSG00000149968	3.4.24.17		7173	protein-coding gene	gene with protein product		185250	"matrix metalloproteinase 3 (stromelysin 1, progelatinase)"	STMY1, STMY			Standard	NM_002422		Approved		uc001phj.1	P08254	OTTHUMG00000048254	ENST00000299855.5:c.401T>A	chr11.hg19:g.102713260A>T	ENSP00000299855:p.Val134Asp	154.0	0.0		178.0	39.0	NM_002422	B2R8B8|Q3B7S0|Q6GRF8	Missense_Mutation	SNP	ENST00000299855.5	hg19	CCDS8323.1	.	.	.	.	.	.	.	.	.	.	A	26.5	4.747933	0.89663	.	.	ENSG00000149968	ENST00000299855	T	0.25085	1.82	6.16	6.16	0.99307	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.697800	0.11566	N	0.551276	T	0.59238	0.2179	M	0.86740	2.835	0.80722	D	1	D	0.76494	0.999	D	0.67103	0.949	T	0.60276	-0.7295	10	0.87932	D	0	.	16.8061	0.85666	1.0:0.0:0.0:0.0	.	134	P08254	MMP3_HUMAN	D	134	ENSP00000299855:V134D	ENSP00000299855:V134D	V	-	2	0	MMP3	102218470	0.986000	0.35501	1.000000	0.80357	0.812000	0.45895	9.307000	0.96226	2.367000	0.80283	0.528000	0.53228	GTT	.	.		0.398	MMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109758.2	NM_002422		T	102713260	A	T	102713260	3	4	279	1	0	0	0	0	1	0	0	0	9675	43	2	4	1064	4	MMP3	11	102713260	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	6887838	102713260	32293256	251	40010										
ALKBH8	91801	hgsc.bcm.edu	37	chr11	107420510	107420510	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	aactgagagaaacgatctcaTcctcaaaagcggaatgtgta	9	8	2	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr11:107420510T>C	ENST00000428149.2	-	7	891	c.740A>G	c.(739-741)gAt>gGt	p.D247G	ALKBH8_ENST00000389568.3_Missense_Mutation_p.D247G|ALKBH8_ENST00000429370.1_Intron|ALKBH8_ENST00000417449.2_Missense_Mutation_p.D250G	NM_138775.2	NP_620130.2	Q96BT7	ALKB8_HUMAN	alkB, alkylation repair homolog 8 (E. coli)	247	Fe2OG dioxygenase. {ECO:0000255|PROSITE- ProRule:PRU00805}.				cellular response to DNA damage stimulus (GO:0006974)|tRNA methylation (GO:0030488)	cytosol (GO:0005829)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|RNA binding (GO:0003723)|tRNA (uracil) methyltransferase activity (GO:0016300)			breast(2)|large_intestine(2)|lung(5)	9		Melanoma(852;0.000288)|Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00301)|all_epithelial(67;0.00512)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.53e-05)|Epithelial(105;0.00029)|all cancers(92;0.00518)		AACGATCTCATCCTCAAAAGC	0.373																																					p.D247G		Atlas-SNP	.											.	ALKBH8	88	.	0			c.A740G						.						119	103	108					11																	107420510		692	1591	2283	SO:0001583	missense	91801	exon7			ATCTCATCCTCAA	AF086489	CCDS8337.2, CCDS73376.1	11q22.3	2013-10-04			ENSG00000137760	ENSG00000137760	2.1.1.229	"Alkylation repair homologs", "RNA binding motif (RRM) containing"	25189	protein-coding gene	gene with protein product		613306				20123966	Standard	NM_138775		Approved	MGC10235	uc009yxp.3	Q96BT7	OTTHUMG00000157008	ENST00000428149.2:c.740A>G	chr11.hg19:g.107420510T>C	ENSP00000415885:p.Asp247Gly	59.0	0.0		91.0	4.0	NM_138775	B1Q2M0|B4DEF6|Q8N989	Missense_Mutation	SNP	ENST00000428149.2	hg19	CCDS8337.2	.	.	.	.	.	.	.	.	.	.	T	21.1	4.090938	0.76756	.	.	ENSG00000137760	ENST00000428149;ENST00000389568;ENST00000417449	T;T;T	0.30182	1.54;1.54;1.54	5.95	5.95	0.96441	Oxoglutarate/iron-dependent oxygenase (2);	0.093564	0.64402	D	0.000001	T	0.36248	0.0960	M	0.68728	2.09	0.80722	D	1	B	0.21606	0.058	B	0.25405	0.06	T	0.09314	-1.0680	10	0.37606	T	0.19	-4.0789	15.6031	0.76639	0.0:0.0:0.0:1.0	.	247	Q96BT7	ALKB8_HUMAN	G	247;247;250	ENSP00000415885:D247G;ENSP00000374219:D247G;ENSP00000397673:D250G	ENSP00000374219:D247G	D	-	2	0	ALKBH8	106925720	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.156000	0.64905	2.277000	0.76020	0.528000	0.53228	GAT	.	.		0.373	ALKBH8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347071.2	NM_138775		C	107420510	T	C	107420510	3	2	279	1	0	0	0	0	1	0	0	0	533	1435	50	2	1278	2	ALKBH8	11	107420510	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	4707250	107420510	27586006	252	40011										
POU2AF1	5450	hgsc.bcm.edu	37	chr11	111224991	111224991	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	aggtgggagccacgcctaaaAgccttccacagagagagtgt	13	10	0	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr11:111224991A>G	ENST00000393067.3	-	5	1280	c.766T>C	c.(766-768)Ttt>Ctt	p.F256L		NM_006235.2	NP_006226.2	Q16633	OBF1_HUMAN	POU class 2 associating factor 1	256					humoral immune response (GO:0006959)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			breast(1)|kidney(2)|lung(2)	5		all_cancers(61;1.36e-12)|all_epithelial(67;1.87e-07)|Melanoma(852;1.46e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|all_neural(223;0.0146)|Medulloblastoma(222;0.0245)|Breast(348;0.0389)		Epithelial(105;1.01e-06)|BRCA - Breast invasive adenocarcinoma(274;3.12e-06)|all cancers(92;1.8e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0364)		CACGCCTAAAAGCCTTCCACA	0.522			T	BCL6	NHL																																p.F256L		Atlas-SNP	.		Dom	yes		11	11q23.1	5450	"POU domain, class 2, associating factor 1 (OBF1)"		L	.	POU2AF1	23	.	0			c.T766C						.						54	46	48					11																	111224991		2201	4297	6498	SO:0001583	missense	5450	exon5			CCTAAAAGCCTTC		CCDS31675.1	11q23.1	2011-06-01	2007-07-13			ENSG00000110777			9211	protein-coding gene	gene with protein product		601206	"POU domain class 2, associating factor 1"			8617501	Standard	NM_006235		Approved	OBF1	uc001plg.4	Q16633		ENST00000393067.3:c.766T>C	chr11.hg19:g.111224991A>G	ENSP00000376786:p.Phe256Leu	103.0	0.0		100.0	4.0	NM_006235	B2R8Z9|Q14983	Missense_Mutation	SNP	ENST00000393067.3	hg19	CCDS31675.1	.	.	.	.	.	.	.	.	.	.	A	16.60	3.168610	0.57584	.	.	ENSG00000110777	ENST00000393067	T	0.33438	1.41	5.07	5.07	0.68467	.	0.067100	0.56097	D	0.000023	T	0.18383	0.0441	L	0.35414	1.06	0.32621	N	0.523283	B	0.12013	0.005	B	0.12837	0.008	T	0.20706	-1.0267	10	0.11485	T	0.65	-36.7508	5.383	0.16201	0.7844:0.0:0.2156:0.0	.	256	Q16633	OBF1_HUMAN	L	256	ENSP00000376786:F256L	ENSP00000376786:F256L	F	-	1	0	POU2AF1	110730201	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	2.798000	0.47884	2.122000	0.65172	0.533000	0.62120	TTT	.	.		0.522	POU2AF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391002.1	NM_006235		G	111224991	A	G	111224991	3	3	279	1	0	0	0	0	1	0	0	0	12279	72	3	2	8	2	POU2AF1	11	111224991	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	3804481	111224991	23781525	253	40012										
NCAM1	4684	hgsc.bcm.edu	37	chr11	112832332	112832363	+	5'UTR	DEL	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	-													0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ccctcccagccagcagattaCaatgctgccaaactaaggat					rs6589347|rs11284059|rs559828324|rs201772924|rs563686839|rs7105734|rs112306738		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr11:112832332_112832363delCATCCCTCCCAGCCAGCAGATTACAATGCTGC	ENST00000533760.1	+	0	243_274				RP11-629G13.1_ENST00000500537.2_RNA|NCAM1_ENST00000397957.4_3'UTR|RP11-629G13.1_ENST00000532002.1_RNA	NM_001242608.1	NP_001229537.1	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		CAGCAGATTACAATGCTGCCAAACTAAGGATTTCATTTGGACTTTGTTTTTC	0.491																																					.		Pindel	.											.	NCAM1	372	.	0			.						.																																			SO:0001623	5_prime_UTR_variant	4684	wholegene			.		CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000533760.1:c.-326CATCCCTCCCAGCCAGCAGATTACAATGCTGC>-	chr11.hg19:g.112832332_112832363delCATCCCTCCCAGCCAGCAGATTACAATGCTGC		0.0	0.0		110.0	33.0	NM_001242607	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Frame_Shift_Del	DEL	ENST00000533760.1	hg19																																																																																				.	.		0.491	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394068.2	NM_000615		-	112832363	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	-	112832332	6	5	279	0	1	1	0	1	0	0	0	0	10211	493	17	0		0	NCAM1	11	112832332	5'UTR	DEL	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	TCGA-G3-A3CG-01A-11D-A20W-10	1607341	112832332	22174184	254	40013										
VWA5A	4013	hgsc.bcm.edu	37	chr11	124013281	124013281	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ggctgcacagcctgccgaggTaagattcaatggaaaaagga	13	8	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr11:124013281T>A	ENST00000456829.2	+	17	2405		c.e17+2		VWA5A_ENST00000392748.1_Splice_Site|VWA5A_ENST00000360334.4_Splice_Site	NM_001130142.1	NP_001123614.1	O00534	VMA5A_HUMAN	von Willebrand factor A domain containing 5A											autonomic_ganglia(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	47						CCTGCCGAGGTAAGATTCAAT	0.423																																					.		Atlas-SNP	.											.	VWA5A	102	.	0			c.2154+2T>A						.						98	93	94					11																	124013281		2201	4299	6500	SO:0001630	splice_region_variant	4013	exon16			CCGAGGTAAGATT	AF002672	CCDS8444.1, CCDS8445.1	11q24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000110002	ENSG00000110002			6658	protein-coding gene	gene with protein product		602929	"loss of heterozygosity, 11, chromosomal region 2, gene A"	LOH11CR2A		9417908, 14504409	Standard	NM_001130142		Approved	BCSC-1	uc001pzt.3	O00534	OTTHUMG00000165971	ENST00000456829.2:c.2154+2T>A	chr11.hg19:g.124013281T>A		49.0	0.0		69.0	4.0	NM_014622	Q6UN19|Q6UN20|Q9BVF8	Splice_Site	SNP	ENST00000456829.2	hg19	CCDS8444.1	.	.	.	.	.	.	.	.	.	.	T	11.76	1.735418	0.30774	.	.	ENSG00000110002	ENST00000456829;ENST00000392748	.	.	.	5.29	5.29	0.74685	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.8862	0.52604	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	VWA5A	123518491	1.000000	0.71417	0.960000	0.40013	0.104000	0.19210	3.817000	0.55668	2.131000	0.65755	0.459000	0.35465	.	.	.		0.423	VWA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387273.1	NM_014622	Intron	A	124013281	T	A	124013281	5	1	279	1	0	0	0	0	0	0	1	0	17257	1652	57	4	2218	4	VWA5A	11	124013281	Splice_Site	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	11180949	124013281	10993235	255	40014										
OR8D2	283160	hgsc.bcm.edu	37	chr11	124189739	124189739	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	agcaacataacggtcatattCcatggctgtcagaaggtagc	10	9	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr11:124189739C>T	ENST00000357438.2	-	1	445	c.355G>A	c.(355-357)Gaa>Aaa	p.E119K		NM_001002918.1	NP_001002918.1	Q9GZM6	OR8D2_HUMAN	olfactory receptor, family 8, subfamily D, member 2	119						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	25		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0525)		CGGTCATATTCCATGGCTGTC	0.418																																					p.E119K		Atlas-SNP	.											OR8D2,NS,lymphoid_neoplasm,0,1	OR8D2	65	.	0			c.G355A						.						85	81	82					11																	124189739		2201	4299	6500	SO:0001583	missense	283160	exon1			CATATTCCATGGC	AF162668	CCDS31707.1	11q24.1	2012-08-09			ENSG00000197263	ENSG00000197263		"GPCR / Class A : Olfactory receptors"	8482	protein-coding gene	gene with protein product							Standard	NM_001002918		Approved		uc010sah.2	Q9GZM6	OTTHUMG00000165978	ENST00000357438.2:c.355G>A	chr11.hg19:g.124189739C>T	ENSP00000350022:p.Glu119Lys	55.0	0.0		45.0	22.0	NM_001002918	B9EH49|Q6IFR0	Missense_Mutation	SNP	ENST00000357438.2	hg19	CCDS31707.1	.	.	.	.	.	.	.	.	.	.	c	12.08	1.829188	0.32329	.	.	ENSG00000197263	ENST00000357438	T	0.36878	1.23	3.73	2.81	0.32909	GPCR, rhodopsin-like superfamily (1);	0.138494	0.32703	N	0.005757	T	0.19846	0.0477	N	0.08118	0	0.32254	N	0.571002	B	0.02656	0.0	B	0.01281	0.0	T	0.19063	-1.0317	10	0.87932	D	0	.	12.0269	0.53375	0.0:0.9107:0.0:0.0893	.	119	Q9GZM6	OR8D2_HUMAN	K	119	ENSP00000350022:E119K	ENSP00000350022:E119K	E	-	1	0	OR8D2	123694949	1.000000	0.71417	0.957000	0.39632	0.199000	0.23934	1.436000	0.34980	1.177000	0.42855	0.530000	0.56133	GAA	.	.		0.418	OR8D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387286.1	NM_001002918		T	124189739	C	T	124189739	3	4	279	1	0	0	0	0	1	0	0	0	11241	864	30	3	583	3	OR8D2	11	124189739	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	176458	124189739	10816777	256	40015										
PRDM10	56980	hgsc.bcm.edu	37	chr11	129825426	129825426	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cctgctgagctgtagcatccTgttggacataagctacctgg	11	11	0	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr11:129825426T>C	ENST00000360871.3	-	4	506	c.275A>G	c.(274-276)cAg>cGg	p.Q92R	PRDM10_ENST00000528746.1_Missense_Mutation_p.Q92R|PRDM10_ENST00000358825.5_Missense_Mutation_p.Q92R	NM_199437.1	NP_955469.1	Q9NQV6	PRD10_HUMAN	PR domain containing 10	92					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			breast(2)|endometrium(6)|kidney(3)|large_intestine(14)|lung(15)|pancreas(2)|skin(1)|stomach(3)|urinary_tract(2)	48	all_hematologic(175;0.0537)	Breast(109;0.000496)|Lung NSC(97;0.000693)|all_lung(97;0.00151)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0174)|Lung(977;0.176)|LUSC - Lung squamous cell carcinoma(976;0.185)		TGTAGCATCCTGTTGGACATA	0.473																																					p.Q92R		Atlas-SNP	.											.	PRDM10	120	.	0			c.A275G						.						156	121	133					11																	129825426		2201	4297	6498	SO:0001583	missense	56980	exon4			GCATCCTGTTGGA	AF275817	CCDS8484.1, CCDS8485.1, CCDS44771.1, CCDS44772.1	11q24.3	2013-01-08			ENSG00000170325	ENSG00000170325		"Zinc fingers, C2H2-type"	13995	protein-coding gene	gene with protein product	"PRDM zinc finger transcription factor", "PR-domain family member 7", "tristanin"					12175877	Standard	NM_020228		Approved	KIAA1231, PFM7, MGC131802	uc001qfm.3	Q9NQV6	OTTHUMG00000165762	ENST00000360871.3:c.275A>G	chr11.hg19:g.129825426T>C	ENSP00000354118:p.Gln92Arg	105.0	0.0		97.0	4.0	NM_020228	B7ZL71|G3XAE5|J3KP23|Q17R90|Q2KHR4|Q863Z2|Q9NXI4|Q9ULI9	Missense_Mutation	SNP	ENST00000360871.3	hg19	CCDS8484.1	.	.	.	.	.	.	.	.	.	.	T	17.19	3.326937	0.60743	.	.	ENSG00000170325	ENST00000358825;ENST00000360871;ENST00000528746;ENST00000531431	T;T;T;T	0.51071	1.09;1.09;2.79;0.72	5.31	5.31	0.75309	.	0.158633	0.44902	D	0.000411	T	0.54498	0.1862	N	0.24115	0.695	0.80722	D	1	D;D;B	0.63046	0.992;0.981;0.281	D;D;B	0.72982	0.979;0.969;0.056	T	0.60100	-0.7329	10	0.87932	D	0	-24.6945	13.8234	0.63336	0.0:0.0:0.0:1.0	.	92;92;92	Q9NQV6-4;G3XAE5;Q9NQV6	.;.;PRD10_HUMAN	R	92	ENSP00000351686:Q92R;ENSP00000354118:Q92R;ENSP00000431262:Q92R;ENSP00000436681:Q92R	ENSP00000351686:Q92R	Q	-	2	0	PRDM10	129330636	1.000000	0.71417	0.999000	0.59377	0.945000	0.59286	7.389000	0.79806	2.013000	0.59113	0.533000	0.62120	CAG	.	.		0.473	PRDM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386076.1	NM_199437		C	129825426	T	C	129825426	3	2	279	1	0	0	0	0	1	0	0	0	12463	1580	55	2	3319	2	PRDM10	11	129825426	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	5635687	129825426	5181090	257	40016										
NCAPD3	23310	hgsc.bcm.edu	37	chr11	134072793	134072793	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ttagatgtctgcctttggtaGgaaaaagctttaaaaaaaaa	8	4	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr11:134072793G>A	ENST00000534548.2	-	13	1597	c.1533C>T	c.(1531-1533)tcC>tcT	p.S511S		NM_015261.2	NP_056076.1	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3	511					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	germinal vesicle (GO:0042585)|membrane (GO:0016020)|nuclear condensin complex (GO:0000799)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)	methylated histone binding (GO:0035064)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)		GCCTTTGGTAGGAAAAAGCTT	0.353																																					p.S511S		Atlas-SNP	.											.	NCAPD3	141	.	0			c.C1533T						.						109	104	106					11																	134072793		2201	4297	6498	SO:0001819	synonymous_variant	23310	exon13			TTGGTAGGAAAAA	AK124878	CCDS31723.1	11q25	2008-02-04			ENSG00000151503	ENSG00000151503			28952	protein-coding gene	gene with protein product		609276				7584044, 8619474, 14532007	Standard	NM_015261		Approved	hCAP-D3, CAP-D3, hHCP-6, KIAA0056, FLJ42888, hcp-6	uc001qhd.1	P42695	OTTHUMG00000167172	ENST00000534548.2:c.1533C>T	chr11.hg19:g.134072793G>A		109.0	0.0		80.0	8.0	NM_015261	A6NFS2|Q4KMQ9	Silent	SNP	ENST00000534548.2	hg19	CCDS31723.1																																																																																			.	.		0.353	NCAPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393575.2	NM_015261		A	134072793	G	A	134072793	2	1	279	1	0	0	0	0	0	0	0	1	10215	987	35	3		3	NCAPD3	11	134072793	Silent	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	4247367	134072793	933723	258	40017										
CSDA	8531	hgsc.bcm.edu	37	chr12	10853935	10853935	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ggagcagggttctcagttggTgcttcacctgccttggccta	13	11	2	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr12:10853935T>C	ENST00000228251.4	-	9	1271	c.1071A>G	c.(1069-1071)gcA>gcG	p.A357A	YBX3_ENST00000546164.1_5'UTR|YBX3_ENST00000279550.7_Silent_p.A288A	NM_003651.4	NP_003642.3	P16989	YBOX3_HUMAN	Y box binding protein 3	357					3'-UTR-mediated mRNA stabilization (GO:0070935)|cellular hyperosmotic response (GO:0071474)|cellular response to tumor necrosis factor (GO:0071356)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress (GO:1902219)|negative regulation of necroptotic process (GO:0060546)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cytoplasmic translation (GO:2000767)|positive regulation of organ growth (GO:0046622)|response to cold (GO:0009409)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|tight junction (GO:0005923)	double-stranded DNA binding (GO:0003690)|mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|Rho GTPase binding (GO:0017048)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)										TCTCAGTTGGTGCTTCACCTG	0.493																																					p.A357A		Atlas-SNP	.											.	CSDA	35	.	0			c.A1071G						.						110	93	99					12																	10853935		2203	4300	6503	SO:0001819	synonymous_variant	8531	exon9			AGTTGGTGCTTCA	L29064	CCDS8630.1, CCDS44831.1	12p13.1	2013-03-13	2013-03-13	2013-03-13	ENSG00000060138	ENSG00000060138			2428	protein-coding gene	gene with protein product	"cold-shock domain containing A1"	603437	"cold shock domain protein A"	CSDA		2977358, 8710501	Standard	NM_003651		Approved	dbpA, ZONAB, CSDA1	uc001qyt.3	P16989	OTTHUMG00000168409	ENST00000228251.4:c.1071A>G	chr12.hg19:g.10853935T>C		86.0	0.0		102.0	5.0	NM_003651	B2RBW6|Q14121|Q969N6|Q96B76	Silent	SNP	ENST00000228251.4	hg19	CCDS8630.1																																																																																			.	.		0.493	YBX3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399628.1	NM_003651		C	10853935	T	C	10853935	2	2	279	1	0	0	0	0	0	0	0	1	3929	1683	59	2		2	CSDA	12	10853935	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10		10853935	122997960	259	40018										
WBP11	51729	hgsc.bcm.edu	37	chr12	14954258	14954258	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	actaatggacacttacgggcTtggtctgtggggttcataaa	12	7	2	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr12:14954258T>C	ENST00000261167.2	-	2	293	c.60A>G	c.(58-60)caA>caG	p.Q20Q	C12orf60_ENST00000330828.2_5'Flank	NM_016312.2	NP_057396.1	Q9Y2W2	WBP11_HUMAN	WW domain binding protein 11	20	Required for nuclear import. {ECO:0000250}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein phosphatase type 1 regulator activity (GO:0008599)|single-stranded DNA binding (GO:0003697)|WW domain binding (GO:0050699)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)	30						ACTTACGGGCTTGGTCTGTGG	0.373																																					p.Q20Q		Atlas-SNP	.											.	WBP11	66	.	0			c.A60G						.						174	166	169					12																	14954258		2203	4300	6503	SO:0001819	synonymous_variant	51729	exon2			ACGGGCTTGGTCT	AB029309	CCDS8666.1	12p12.3	2014-06-13			ENSG00000084463	ENSG00000084463			16461	protein-coding gene	gene with protein product	"splicing factor, PQBP1 and PP1 interacting", "protein phosphatase 1, regulatory subunit 165"					10593949	Standard	NM_016312		Approved	NPWBP, SIPP1, PPP1R165	uc001rci.3	Q9Y2W2	OTTHUMG00000168737	ENST00000261167.2:c.60A>G	chr12.hg19:g.14954258T>C		110.0	0.0		97.0	4.0	NM_016312	Q96AY8	Silent	SNP	ENST00000261167.2	hg19	CCDS8666.1																																																																																			.	.		0.373	WBP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400850.1	NM_016312		C	14954258	T	C	14954258	2	2	279	1	0	0	0	0	0	0	0	1	17273	1606	56	2		2	WBP11	12	14954258	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	4100323	14954258	118897637	260	40019										
PLCZ1	89869	hgsc.bcm.edu	37	chr12	18876412	18876412	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	taatttcttctctgtgcgtgAtaattcgataaattgctcta	6	7	3	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr12:18876412A>G	ENST00000266505.7	-	4	463	c.200T>C	c.(199-201)aTc>aCc	p.I67T	RP11-361I14.2_ENST00000536931.1_RNA|PLCZ1_ENST00000435379.1_Intron|PLCZ1_ENST00000447925.2_Missense_Mutation_p.I65T|PLCZ1_ENST00000539875.1_Intron					phospholipase C, zeta 1											NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	31	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241)					TCTGTGCGTGATAATTCGATA	0.353																																					p.I67T		Atlas-SNP	.											.	PLCZ1	107	.	0			c.T200C						.						91	92	92					12																	18876412		2202	4297	6499	SO:0001583	missense	89869	exon4			TGCGTGATAATTC	AY035866	CCDS8680.1	12p13.31	2013-01-10			ENSG00000139151	ENSG00000139151	3.1.4.11	"EF-hand domain containing"	19218	protein-coding gene	gene with protein product		608075				12117804	Standard	NM_033123		Approved	NYD-SP27, PLCzeta	uc021qvx.2	Q86YW0	OTTHUMG00000168937	ENST00000266505.7:c.200T>C	chr12.hg19:g.18876412A>G	ENSP00000266505:p.Ile67Thr	92.0	0.0		69.0	4.0	NM_033123		Missense_Mutation	SNP	ENST00000266505.7	hg19	CCDS8680.1	.	.	.	.	.	.	.	.	.	.	A	13.24	2.177296	0.38413	.	.	ENSG00000139151	ENST00000266505;ENST00000447925	T;T	0.47177	0.85;0.85	5.02	5.02	0.67125	EF-hand-like domain (1);	0.227351	0.30177	N	0.010240	T	0.55940	0.1952	M	0.64997	1.995	0.58432	D	0.999997	D	0.57899	0.981	P	0.52109	0.69	T	0.61505	-0.7049	10	0.87932	D	0	.	12.472	0.55792	1.0:0.0:0.0:0.0	.	67	Q86YW0	PLCZ1_HUMAN	T	67;65	ENSP00000266505:I67T;ENSP00000402358:I65T	ENSP00000266505:I67T	I	-	2	0	PLCZ1	18767679	0.231000	0.23751	0.913000	0.36048	0.121000	0.20230	5.736000	0.68597	1.884000	0.54569	0.460000	0.39030	ATC	.	.		0.353	PLCZ1-001	KNOWN	NAGNAG_splice_site|non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401667.3	NM_033123		G	18876412	A	G	18876412	3	3	279	1	0	0	0	0	1	0	0	0	12053	333	12	2	1674	2	PLCZ1	12	18876412	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	3922154	18876412	114975483	261	40020										
ITPR2	3709	hgsc.bcm.edu	37	chr12	26647249	26647249	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	acattgatatccccatcttaTctgaatcttgtccagaaaag	5	10	3	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr12:26647249T>A	ENST00000381340.3	-	39	5623	c.5207A>T	c.(5206-5208)gAt>gTt	p.D1736V		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1736					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	CCCCATCTTATCTGAATCTTG	0.323																																					p.D1736V		Atlas-SNP	.											.	ITPR2	270	.	0			c.A5207T						.						88	72	77					12																	26647249		1824	4085	5909	SO:0001583	missense	3709	exon39			ATCTTATCTGAAT	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"Ion channels / Inositol triphosphate receptors"	6181	protein-coding gene	gene with protein product	"cilia and flagella associated protein 48"	600144	"inositol 1,4,5-triphosphate receptor, type 2"			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.5207A>T	chr12.hg19:g.26647249T>A	ENSP00000370744:p.Asp1736Val	54.0	0.0		64.0	19.0	NM_002223	O94773	Missense_Mutation	SNP	ENST00000381340.3	hg19	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	T	14.21	2.468170	0.43839	.	.	ENSG00000123104	ENST00000381340	D	0.89875	-2.58	3.97	3.97	0.46021	.	1.683260	0.02614	N	0.102516	D	0.92541	0.7631	L	0.50333	1.59	0.80722	D	1	D	0.56746	0.977	P	0.60682	0.878	T	0.83357	-0.0000	10	0.33940	T	0.23	.	12.4741	0.55803	0.0:0.0:0.0:1.0	.	1736	Q14571	ITPR2_HUMAN	V	1736	ENSP00000370744:D1736V	ENSP00000370744:D1736V	D	-	2	0	ITPR2	26538516	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.404000	0.79996	2.026000	0.59711	0.482000	0.46254	GAT	.	.		0.323	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		A	26647249	T	A	26647249	3	1	279	1	0	0	0	0	1	0	0	0	7930	1435	50	4	2974	4	ITPR2	12	26647249	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	7770837	26647249	107204646	262	40021										
BICD1	636	hgsc.bcm.edu	37	chr12	32458899	32458899	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gagtgaaccaaacaatgatgAcaaaatgaacggtcatatcc	8	8	1	4			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr12:32458899A>G	ENST00000281474.5	+	4	951	c.848A>G	c.(847-849)gAc>gGc	p.D283G	BICD1_ENST00000548411.1_Missense_Mutation_p.D283G	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	283					anatomical structure morphogenesis (GO:0009653)|intracellular mRNA localization (GO:0008298)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900737)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein localization to organelle (GO:0033365)|regulation of proteinase activated receptor activity (GO:1900276)|RNA processing (GO:0006396)|stress granule assembly (GO:0034063)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|host cell viral assembly compartment (GO:0072517)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	cytoskeletal adaptor activity (GO:0008093)|dynactin binding (GO:0034452)|dynein binding (GO:0045502)|proteinase activated receptor binding (GO:0031871)|Rab GTPase binding (GO:0017137)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			AACAATGATGACAAAATGAAC	0.458																																					p.D283G		Atlas-SNP	.											.	BICD1	89	.	0			c.A848G						.						115	111	112					12																	32458899		2203	4300	6503	SO:0001583	missense	636	exon4			ATGATGACAAAAT	U90028	CCDS8726.1, CCDS44859.1	12p11.2-p11.1	2005-01-13	2001-11-28			ENSG00000151746			1049	protein-coding gene	gene with protein product		602204	"Bicaudal D (Drosophila) homolog 1"			9367685	Standard	NM_001714		Approved		uc001rku.3	Q96G01	OTTHUMG00000169307	ENST00000281474.5:c.848A>G	chr12.hg19:g.32458899A>G	ENSP00000281474:p.Asp283Gly	77.0	0.0		70.0	4.0	NM_001714	A8K2C3|F8W113|O43892|O43893	Missense_Mutation	SNP	ENST00000281474.5	hg19	CCDS8726.1	.	.	.	.	.	.	.	.	.	.	A	15.35	2.808403	0.50421	.	.	ENSG00000151746	ENST00000548411;ENST00000281474	T;T	0.47177	0.85;0.85	4.59	4.59	0.56863	.	0.182670	0.47852	D	0.000216	T	0.47838	0.1467	L	0.53671	1.685	0.80722	D	1	B;B	0.31459	0.13;0.324	B;B	0.37198	0.112;0.243	T	0.49194	-0.8965	10	0.41790	T	0.15	.	14.4981	0.67702	1.0:0.0:0.0:0.0	.	283;283	F8W113;Q96G01	.;BICD1_HUMAN	G	283	ENSP00000446793:D283G;ENSP00000281474:D283G	ENSP00000281474:D283G	D	+	2	0	BICD1	32350166	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.101000	0.76997	2.074000	0.62210	0.529000	0.55759	GAC	.	.		0.458	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403380.1	NM_001714		G	32458899	A	G	32458899	3	3	279	1	0	0	0	0	1	0	0	0	1428	275	10	2	862	2	BICD1	12	32458899	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	5811650	32458899	101392996	263	40022										
DNAJC22	79962	hgsc.bcm.edu	37	chr12	49743308	49743308	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ggcagaaacctttggctcctTcttgaattggttcagcttct	9	10	3	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr12:49743308T>A	ENST00000549441.2	+	3	1857	c.653T>A	c.(652-654)tTc>tAc	p.F218Y	DNAJC22_ENST00000395069.3_Missense_Mutation_p.F218Y			Q8N4W6	DJC22_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 22	218						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|liver(2)|lung(1)|ovary(1)|pancreas(1)	10						TTTGGCTCCTTCTTGAATTGG	0.562																																					p.F218Y		Atlas-SNP	.											.	DNAJC22	29	.	0			c.T653A						.						177	172	174					12																	49743308		2203	4300	6503	SO:0001583	missense	79962	exon2			GCTCCTTCTTGAA	AK055747	CCDS8785.1	12q13.12	2011-09-02		2008-07-08	ENSG00000178401	ENSG00000178401		"Heat shock proteins / DNAJ (HSP40)"	25802	protein-coding gene	gene with protein product	"wurst homolog (Drosophila)"					17558392	Standard	NM_024902		Approved	wus, FLJ13236	uc001rua.3	Q8N4W6		ENST00000549441.2:c.653T>A	chr12.hg19:g.49743308T>A	ENSP00000446830:p.Phe218Tyr	129.0	0.0		121.0	8.0	NM_024902	B3KP54	Missense_Mutation	SNP	ENST00000549441.2	hg19	CCDS8785.1	.	.	.	.	.	.	.	.	.	.	T	17.10	3.302358	0.60195	.	.	ENSG00000178401	ENST00000549441;ENST00000395069	T;T	0.43688	0.94;0.94	4.76	4.76	0.60689	.	0.315552	0.35436	N	0.003206	T	0.40473	0.1118	L	0.51422	1.61	0.41228	D	0.986552	B	0.24721	0.11	B	0.27170	0.077	T	0.41787	-0.9489	10	0.87932	D	0	-7.8231	13.5448	0.61697	0.0:0.0:0.0:1.0	.	218	Q8N4W6	DJC22_HUMAN	Y	218	ENSP00000446830:F218Y;ENSP00000378508:F218Y	ENSP00000378508:F218Y	F	+	2	0	DNAJC22	48029575	0.998000	0.40836	0.987000	0.45799	0.968000	0.65278	5.257000	0.65473	1.900000	0.55004	0.459000	0.35465	TTC	.	.		0.562	DNAJC22-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404302.2	NM_024902		A	49743308	T	A	49743308	3	1	279	1	0	0	0	0	1	0	0	0	4643	1783	62	4	655	4	DNAJC22	12	49743308	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	17284409	49743308	84108587	264	40023										
LARP4	113251	hgsc.bcm.edu	37	chr12	50822863	50822863	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gatctgagttaccaaatataTgatgtttccggtaaacttta	7	6	1	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr12:50822863T>C	ENST00000398473.2	+	3	424	c.312T>C	c.(310-312)taT>taC	p.Y104Y	LARP4_ENST00000518561.1_Silent_p.Y34Y|LARP4_ENST00000429001.3_Silent_p.Y110Y|LARP4_ENST00000293618.8_Silent_p.Y104Y|LARP4_ENST00000522085.1_Silent_p.Y104Y|LARP4_ENST00000518444.1_Silent_p.Y103Y|LARP4_ENST00000347328.5_Silent_p.Y104Y	NM_052879.4|NM_199188.2	NP_443111.4|NP_954658.2	Q71RC2	LARP4_HUMAN	La ribonucleoprotein domain family, member 4	104					cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(1)|skin(2)|urinary_tract(1)	23						ACCAAATATATGATGTTTCCG	0.358																																					p.Y104Y		Atlas-SNP	.											LARP4,caecum,carcinoma,0,1	LARP4	58	.	0			c.T312C						.						108	102	104					12																	50822863		1828	4086	5914	SO:0001819	synonymous_variant	113251	exon3			AATATATGATGTT	AY004310	CCDS41782.1, CCDS44879.1, CCDS44880.1, CCDS44879.2, CCDS53789.1, CCDS53790.1	12q13.12	2005-08-09			ENSG00000161813	ENSG00000161813		"La ribonucleoprotein domain containing"	24320	protein-coding gene	gene with protein product						12477932	Standard	NM_052879		Approved	PP13296	uc001rwp.2	Q71RC2	OTTHUMG00000163724	ENST00000398473.2:c.312T>C	chr12.hg19:g.50822863T>C		52.0	0.0		33.0	2.0	NM_001170808	A8K6T1|E9PDG5|G3XAA8|G5E976|Q5CZ97|Q6ZV14|Q96NF9	Silent	SNP	ENST00000398473.2	hg19	CCDS41782.1																																																																																			.	.		0.358	LARP4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374981.1	NM_052879		C	50822863	T	C	50822863	2	2	279	1	0	0	0	0	0	0	0	1	8639	1471	51	2		2	LARP4	12	50822863	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	1079555	50822863	83029032	265	40024										
SPRYD3	84926	hgsc.bcm.edu	37	chr12	53462069	53462069	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	catccacgatgcttttgcccTtccctaagtactccagcagc	6	16	0	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr12:53462069T>C	ENST00000301463.4	-	7	799	c.713A>G	c.(712-714)aAg>aGg	p.K238R	SPRYD3_ENST00000547837.1_Missense_Mutation_p.K275R	NM_032840.2	NP_116229.1	Q8NCJ5	SPRY3_HUMAN	SPRY domain containing 3	238										central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	17						GCTTTTGCCCTTCCCTAAGTA	0.637																																					p.K238R		Atlas-SNP	.											.	SPRYD3	29	.	0			c.A713G						.						99	99	99					12																	53462069		2203	4300	6503	SO:0001583	missense	84926	exon7			TTGCCCTTCCCTA	AK074694	CCDS8845.1	12q13.13	2006-11-29		2006-02-02		ENSG00000167778			25920	protein-coding gene	gene with protein product						14702039	Standard	NM_032840		Approved	FLJ14800	uc001sbt.2	Q8NCJ5	OTTHUMG00000170101	ENST00000301463.4:c.713A>G	chr12.hg19:g.53462069T>C	ENSP00000301463:p.Lys238Arg	82.0	0.0		73.0	4.0	NM_032840	B9EG99|Q96SK5	Missense_Mutation	SNP	ENST00000301463.4	hg19	CCDS8845.1	.	.	.	.	.	.	.	.	.	.	T	15.19	2.760634	0.49468	.	.	ENSG00000167778	ENST00000301463;ENST00000547837	.	.	.	5.16	5.16	0.70880	.	0.107189	0.64402	D	0.000009	T	0.38427	0.1040	N	0.14661	0.345	0.41277	D	0.986881	B	0.15473	0.013	B	0.12837	0.008	T	0.25257	-1.0137	9	0.14252	T	0.57	.	13.2682	0.60146	0.0:0.0:0.0:1.0	.	238	Q8NCJ5	SPRY3_HUMAN	R	238;275	.	ENSP00000301463:K238R	K	-	2	0	SPRYD3	51748336	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.703000	0.68340	2.082000	0.62665	0.459000	0.35465	AAG	.	.		0.637	SPRYD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407264.1	NM_032840		C	53462069	T	C	53462069	3	2	279	1	0	0	0	0	1	0	0	0	15124	1609	56	2	635	2	SPRYD3	12	53462069	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	2639206	53462069	80389826	266	40025										
MDM2	4193	hgsc.bcm.edu	37	chr12	69207366	69207366	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ccattgcttttgaagttattAaagtctgttggtgcacaaaa	8	6	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr12:69207366A>G	ENST00000393410.1	+	2	114	c.114A>G	c.(112-114)ttA>ttG	p.L38L	MDM2_ENST00000299252.4_Silent_p.L38L|MDM2_ENST00000517852.1_Silent_p.L38L|MDM2_ENST00000393413.3_Intron|MDM2_ENST00000356290.4_Silent_p.L38L|MDM2_ENST00000360430.2_Intron|MDM2_ENST00000545204.1_Intron|MDM2_ENST00000350057.5_Intron|MDM2_ENST00000393412.3_Intron|MDM2_ENST00000462284.1_Silent_p.L44L|MDM2_ENST00000478070.1_Intron|MDM2_ENST00000544561.1_Silent_p.L38L|MDM2_ENST00000348801.2_Intron|MDM2_ENST00000258149.5_Silent_p.L38L|MDM2_ENST00000428863.2_Intron|MDM2_ENST00000258148.7_Silent_p.L44L|MDM2_ENST00000540827.1_Intron			Q00987	MDM2_HUMAN	MDM2 proto-oncogene, E3 ubiquitin protein ligase	38	Necessary for interaction with USP2.|SWIB.				cellular response to acid chemical (GO:0071229)|cellular response to alkaloid (GO:0071312)|cellular response to antibiotic (GO:0071236)|cellular response to estrogen stimulus (GO:0071391)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to UV-C (GO:0071494)|cellular response to vitamin B1 (GO:0071301)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment of protein localization (GO:0045184)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of protein processing (GO:0010955)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-lysine modification (GO:0018205)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein export from nucleus (GO:0046827)|protein complex assembly (GO:0006461)|protein destabilization (GO:0031648)|protein localization to nucleus (GO:0034504)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of protein catabolic process (GO:0042176)|response to antibiotic (GO:0046677)|response to carbohydrate (GO:0009743)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ether (GO:0045472)|response to iron ion (GO:0010039)|response to magnesium ion (GO:0032026)|response to morphine (GO:0043278)|synaptic transmission (GO:0007268)|traversing start control point of mitotic cell cycle (GO:0007089)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|p53 binding (GO:0002039)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.L44L(1)|p.L38L(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(8)|prostate(1)|urinary_tract(1)	19	all_cancers(1;8.46e-121)|all_epithelial(5;3.21e-36)|Lung NSC(4;2.16e-33)|all_lung(4;3.03e-31)|Glioma(1;1.9e-09)|Breast(13;1.59e-06)|all_neural(1;1.03e-05)|Melanoma(1;0.0171)|Renal(347;0.0684)		all cancers(2;8.67e-65)|GBM - Glioblastoma multiforme(2;8.89e-62)|BRCA - Breast invasive adenocarcinoma(5;2.43e-08)|Lung(24;1.5e-05)|LUAD - Lung adenocarcinoma(15;8.5e-05)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143)			TGAAGTTATTAAAGTCTGTTG	0.353			A		"sarcoma, glioma, colorectal, other"																																p.L44L		Atlas-SNP	.		Dom	yes		12	12q15	4193	Mdm2 p53 binding protein homolog		"M, O, E, L"	MDM2_ENST00000462284,bladder,carcinoma,0,2	MDM2	92	.	2	Substitution - coding silent(2)	urinary_tract(2)	c.A132G						.						147	145	146					12																	69207366		1830	4089	5919	SO:0001819	synonymous_variant	4193	exon3			GTTATTAAAGTCT		CCDS8986.2, CCDS61189.1	12q13-q14	2014-06-26	2014-06-26		ENSG00000135679	ENSG00000135679			6973	protein-coding gene	gene with protein product		164785	"mouse double minute 2, human homolog of; p53-binding protein", "Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse)", "Mdm2 p53 binding protein homolog (mouse)"			1614537, 16905769	Standard	NM_002392		Approved	HDM2, MGC5370	uc001sui.4	Q00987	OTTHUMG00000142827	ENST00000393410.1:c.114A>G	chr12.hg19:g.69207366A>G		106.0	0.0		65.0	4.0	NM_002392	A6NL51|A8K2S6|Q13226|Q13297|Q13298|Q13299|Q13300|Q13301|Q53XW0|Q71TW9|Q8WYJ1|Q8WYJ2|Q9UGI3|Q9UMT8	Silent	SNP	ENST00000393410.1	hg19																																																																																				.	.		0.353	MDM2-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000286422.1	NM_006880		G	69207366	A	G	69207366	2	3	279	1	0	0	0	0	0	0	0	1	9422	359	13	2		2	MDM2	12	69207366	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	15745297	69207366	64644529	267	40026										
POC1B	282809	hgsc.bcm.edu	37	chr12	89865461	89865461	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gtttgatcagaacctgctgaAgctatgcatgtaccactagg	10	9	1	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr12:89865461A>G	ENST00000313546.3	-	6	734	c.606T>C	c.(604-606)gcT>gcC	p.A202A	POC1B_ENST00000549504.1_Intron|POC1B_ENST00000393179.4_Silent_p.A72A|POC1B_ENST00000549035.1_Silent_p.A160A|POC1B_ENST00000378528.2_Intron|POC1B_ENST00000541909.1_Silent_p.A72A	NM_172240.2	NP_758440.1	Q8TC44	POC1B_HUMAN	POC1 centriolar protein B	202					cell proliferation (GO:0008283)|cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|spindle pole (GO:0000922)				endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	14						AACCTGCTGAAGCTATGCATG	0.318																																					p.A202A		Atlas-SNP	.											.	POC1B	41	.	0			c.T606C						.						140	133	135					12																	89865461		2203	4300	6503	SO:0001819	synonymous_variant	282809	exon6			TGCTGAAGCTATG	AL832918	CCDS31869.1, CCDS55859.1	12q21.33	2014-05-02	2013-08-21	2010-03-26	ENSG00000139323	ENSG00000139323		"WD repeat domain containing"	30836	protein-coding gene	gene with protein product		614784	"WD repeat domain 51B", "POC1 centriolar protein homolog B (Chlamydomonas)"	WDR51B		19109428	Standard	NM_172240		Approved	TUWD12, FLJ14923		Q8TC44	OTTHUMG00000169944	ENST00000313546.3:c.606T>C	chr12.hg19:g.89865461A>G		83.0	0.0		90.0	4.0	NM_172240	G3V1X0	Silent	SNP	ENST00000313546.3	hg19	CCDS31869.1																																																																																			.	.		0.318	POC1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406637.1	NM_172240		G	89865461	A	G	89865461	2	3	279	1	0	0	0	0	0	0	0	1	12185	59	3	2		2	POC1B	12	89865461	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	20658095	89865461	43986434	268	40027										
POC1B	282809	hgsc.bcm.edu	37	chr12	89885846	89885846	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	atcagctgaaaagtctacacTtcgaactggagctgtatgag	10	8	2	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr12:89885846T>C	ENST00000313546.3	-	4	447	c.319A>G	c.(319-321)Agt>Ggt	p.S107G	POC1B_ENST00000549504.1_5'UTR|POC1B_ENST00000393179.4_5'UTR|POC1B_ENST00000549035.1_Missense_Mutation_p.S65G|POC1B_ENST00000378528.2_5'UTR|POC1B_ENST00000541909.1_5'UTR	NM_172240.2	NP_758440.1	Q8TC44	POC1B_HUMAN	POC1 centriolar protein B	107					cell proliferation (GO:0008283)|cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|spindle pole (GO:0000922)				endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	14						AAGTCTACACTTCGAACTGGA	0.353																																					p.S107G		Atlas-SNP	.											.	POC1B	41	.	0			c.A319G						.						95	94	94					12																	89885846		2203	4300	6503	SO:0001583	missense	282809	exon4			CTACACTTCGAAC	AL832918	CCDS31869.1, CCDS55859.1	12q21.33	2014-05-02	2013-08-21	2010-03-26	ENSG00000139323	ENSG00000139323		"WD repeat domain containing"	30836	protein-coding gene	gene with protein product		614784	"WD repeat domain 51B", "POC1 centriolar protein homolog B (Chlamydomonas)"	WDR51B		19109428	Standard	NM_172240		Approved	TUWD12, FLJ14923		Q8TC44	OTTHUMG00000169944	ENST00000313546.3:c.319A>G	chr12.hg19:g.89885846T>C	ENSP00000323302:p.Ser107Gly	89.0	0.0		82.0	4.0	NM_172240	G3V1X0	Missense_Mutation	SNP	ENST00000313546.3	hg19	CCDS31869.1	.	.	.	.	.	.	.	.	.	.	T	18.77	3.695310	0.68386	.	.	ENSG00000139323	ENST00000313546;ENST00000549035	T;T	0.64618	-0.11;-0.11	5.76	4.62	0.57501	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.080464	0.85682	N	0.000000	T	0.60457	0.2270	L	0.27944	0.81	0.80722	D	1	D	0.61080	0.989	P	0.60173	0.87	T	0.61148	-0.7121	10	0.52906	T	0.07	.	6.4826	0.22071	0.1387:0.0736:0.0:0.7877	.	107	Q8TC44	POC1B_HUMAN	G	107;65	ENSP00000323302:S107G;ENSP00000447916:S65G	ENSP00000323302:S107G	S	-	1	0	POC1B	88409977	1.000000	0.71417	0.999000	0.59377	0.970000	0.65996	3.276000	0.51646	1.024000	0.39682	0.383000	0.25322	AGT	.	.		0.353	POC1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406637.1	NM_172240		C	89885846	T	C	89885846	3	2	279	1	0	0	0	0	1	0	0	0	12185	1609	56	2	1153	2	POC1B	12	89885846	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	20385	89885846	43966049	269	40028										
PLXNC1	10154	hgsc.bcm.edu	37	chr12	94697585	94697585	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gatatcccaacctacaaagaAgaagtaaaatcttattacaa	4	8	1	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr12:94697585A>G	ENST00000258526.4	+	29	4689	c.4440A>G	c.(4438-4440)gaA>gaG	p.E1480E	PLXNC1_ENST00000547057.1_Silent_p.E527E|PLXNC1_ENST00000545312.1_Silent_p.E219E	NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	1480					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(12)|lung(30)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						CCTACAAAGAAGAAGTAAAAT	0.343																																					p.E1480E		Atlas-SNP	.											.	PLXNC1	135	.	0			c.A4440G						.						68	69	69					12																	94697585		2203	4299	6502	SO:0001819	synonymous_variant	10154	exon29			CAAAGAAGAAGTA	AF030339	CCDS9049.1	12q23	2009-04-17				ENSG00000136040		"CD molecules", "Plexins"	9106	protein-coding gene	gene with protein product		604259					Standard	NR_037687		Approved	VESPR, CD232	uc001tdc.3	O60486	OTTHUMG00000170235	ENST00000258526.4:c.4440A>G	chr12.hg19:g.94697585A>G		87.0	0.0		81.0	4.0	NM_005761	Q59H25	Silent	SNP	ENST00000258526.4	hg19	CCDS9049.1																																																																																			.	.		0.343	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2			G	94697585	A	G	94697585	2	3	279	1	0	0	0	0	0	0	0	1	12135	69	3	2		2	PLXNC1	12	94697585	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	4811739	94697585	39154310	270	40029										
APAF1	317	hgsc.bcm.edu	37	chr12	99056329	99056329	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tacaaccagagacaagagtgTtacagattcagtaatgggta	10	6	1	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr12:99056329T>C	ENST00000551964.1	+	6	1542	c.806T>C	c.(805-807)gTt>gCt	p.V269A	APAF1_ENST00000359972.2_Missense_Mutation_p.V258A|APAF1_ENST00000547045.1_Missense_Mutation_p.V269A|APAF1_ENST00000549007.1_Missense_Mutation_p.V269A|APAF1_ENST00000552268.1_Missense_Mutation_p.V269A|APAF1_ENST00000339433.3_Missense_Mutation_p.V269A|APAF1_ENST00000357310.1_Missense_Mutation_p.V269A|APAF1_ENST00000333991.1_Missense_Mutation_p.V269A|APAF1_ENST00000550527.1_Missense_Mutation_p.V258A	NM_181861.1	NP_863651.1	O14727	APAF_HUMAN	apoptotic peptidase activating factor 1	269	NB-ARC.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|forebrain development (GO:0030900)|intrinsic apoptotic signaling pathway (GO:0097193)|nervous system development (GO:0007399)|neural tube closure (GO:0001843)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|regulation of apoptotic DNA fragmentation (GO:1902510)|regulation of apoptotic process (GO:0042981)|response to G1 DNA damage checkpoint signaling (GO:0072432)	apoptosome (GO:0043293)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(1)	42					Adenosine triphosphate(DB00171)	GACAAGAGTGTTACAGATTCA	0.323																																					p.V269A		Atlas-SNP	.											.	APAF1	111	.	0			c.T806C						.						115	111	112					12																	99056329		2203	4300	6503	SO:0001583	missense	317	exon6			AGAGTGTTACAGA	AF013263	CCDS9069.1, CCDS9070.1, CCDS9071.1, CCDS55862.1, CCDS55863.1	12q23	2013-01-10	2006-10-23			ENSG00000120868		"WD repeat domain containing"	576	protein-coding gene	gene with protein product		602233	"apoptotic protease activating factor", "apoptotic peptidase activating factor"			9267021, 10702682	Standard	NM_181861		Approved	CED4, APAF-1	uc001tfz.3	O14727	OTTHUMG00000170214	ENST00000551964.1:c.806T>C	chr12.hg19:g.99056329T>C	ENSP00000448165:p.Val269Ala	110.0	0.0		80.0	4.0	NM_181868	B2RMX8|O43297|Q7Z438|Q9BXZ6|Q9UBZ5|Q9UGN8|Q9UGN9|Q9UGP0|Q9UJ58|Q9UJ59|Q9UJ60|Q9UJ61|Q9UJ62|Q9UJ63|Q9UJ64|Q9UJ65|Q9UJ66|Q9UJ67|Q9UNC9	Missense_Mutation	SNP	ENST00000551964.1	hg19	CCDS9069.1	.	.	.	.	.	.	.	.	.	.	T	19.96	3.923911	0.73213	.	.	ENSG00000120868	ENST00000551964;ENST00000359972;ENST00000357310;ENST00000339433;ENST00000333991;ENST00000552268;ENST00000550527;ENST00000547045;ENST00000549007	D;D;D;D;D;D;D;D;D	0.85171	-1.95;-1.95;-1.95;-1.95;-1.95;-1.95;-1.95;-1.95;-1.95	5.87	4.71	0.59529	NB-ARC (1);	0.056024	0.64402	D	0.000001	D	0.90655	0.7069	M	0.76002	2.32	0.51012	D	0.999903	P;P;D;P;B	0.53745	0.936;0.686;0.962;0.908;0.367	P;P;D;P;B	0.65010	0.847;0.638;0.931;0.855;0.188	D	0.89944	0.4075	10	0.46703	T	0.11	-0.3615	12.4355	0.55596	0.1259:0.0:0.0:0.8741	.	269;269;258;269;258	O14727-6;O14727-4;O14727-3;O14727;O14727-2	.;.;.;APAF_HUMAN;.	A	269;258;269;269;269;269;258;269;269	ENSP00000448165:V269A;ENSP00000353059:V258A;ENSP00000349862:V269A;ENSP00000341830:V269A;ENSP00000334558:V269A;ENSP00000448826:V269A;ENSP00000448449:V258A;ENSP00000449791:V269A;ENSP00000448161:V269A	ENSP00000334558:V269A	V	+	2	0	APAF1	97580460	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.653000	0.83643	1.032000	0.39892	0.533000	0.62120	GTT	.	.		0.323	APAF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408006.1	NM_181861.1		C	99056329	T	C	99056329	3	2	279	1	0	0	0	0	1	0	0	0	755	1725	60	2	824	2	APAF1	12	99056329	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	4358744	99056329	34795566	271	40030										
UHRF1BP1L	23074	hgsc.bcm.edu	37	chr12	100497704	100497704	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	aactcaccaaacagatgggaTgtgttttcagttttgtccat	8	8	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr12:100497704T>C	ENST00000279907.7	-	3	445	c.233A>G	c.(232-234)cAt>cGt	p.H78R	UHRF1BP1L_ENST00000356828.3_Missense_Mutation_p.H78R	NM_015054.1	NP_055869.1	A0JNW5	UH1BL_HUMAN	UHRF1 binding protein 1-like	78										breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(21)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	50						ACAGATGGGATGTGTTTTCAG	0.279																																					p.H78R		Atlas-SNP	.											.	UHRF1BP1L	144	.	0			c.A233G						.						78	83	81					12																	100497704		2203	4293	6496	SO:0001583	missense	23074	exon3			ATGGGATGTGTTT		CCDS31882.1, CCDS31883.1	12q23.1	2011-04-15	2008-08-15		ENSG00000111647	ENSG00000111647			29102	protein-coding gene	gene with protein product							Standard	XM_005268737		Approved	KIAA0701	uc001tgq.3	A0JNW5	OTTHUMG00000170195	ENST00000279907.7:c.233A>G	chr12.hg19:g.100497704T>C	ENSP00000279907:p.His78Arg	149.0	0.0		91.0	4.0	NM_015054	A0PJE5|O75183|Q8NDL1|Q96C30|Q9BTS5|Q9H0F1	Missense_Mutation	SNP	ENST00000279907.7	hg19	CCDS31882.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.794742	0.90453	.	.	ENSG00000111647	ENST00000279907;ENST00000356828	D;D	0.81821	-1.54;-1.54	5.52	5.52	0.82312	.	0.103647	0.64402	D	0.000003	D	0.87192	0.6116	M	0.73598	2.24	0.58432	D	0.999999	B;P	0.46512	0.16;0.879	B;P	0.55260	0.109;0.772	D	0.88521	0.3096	10	0.66056	D	0.02	-6.1829	15.6359	0.76953	0.0:0.0:0.0:1.0	.	78;78	A0JNW5-2;A0JNW5	.;UH1BL_HUMAN	R	78	ENSP00000279907:H78R;ENSP00000349285:H78R	ENSP00000279907:H78R	H	-	2	0	UHRF1BP1L	99021835	1.000000	0.71417	0.999000	0.59377	0.977000	0.68977	6.102000	0.71486	2.090000	0.63153	0.482000	0.46254	CAT	.	.		0.279	UHRF1BP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407875.1	NM_001006947		C	100497704	T	C	100497704	3	2	279	1	0	0	0	0	1	0	0	0	16984	1464	51	2	4261	2	UHRF1BP1L	12	100497704	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	1441375	100497704	33354191	272	40031										
TDG	6996	hgsc.bcm.edu	37	chr12	104379508	104379508	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ttctcttcaaatgggctaagTatggttccctccacatgtgt	8	10	2	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr12:104379508T>C	ENST00000392872.3	+	9	1324		c.e9+2		TDG_ENST00000544861.1_Splice_Site|TDG_ENST00000266775.9_Splice_Site|TDG_ENST00000542036.1_Splice_Site|AC078819.1_ENST00000401157.1_RNA	NM_003211.4	NP_003202.3	Q13569	TDG_HUMAN	thymine-DNA glycosylase						base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|chromatin modification (GO:0016568)|depyrimidination (GO:0045008)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|embryo development (GO:0009790)|mismatch repair (GO:0006298)|negative regulation of chromatin binding (GO:0035562)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression, epigenetic (GO:0040029)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|double-stranded DNA binding (GO:0003690)|mismatched DNA binding (GO:0030983)|protein homodimerization activity (GO:0042803)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|RNA polymerase II transcription cofactor activity (GO:0001104)|structure-specific DNA binding (GO:0043566)			large_intestine(2)|lung(14)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(302;0.00114)		ATGGGCTAAGTATGGTTCCCT	0.413								Base excision repair (BER), DNA glycosylases																													.		Atlas-SNP	.											.	TDG	43	.	0			c.1090+2T>C						.						132	126	128					12																	104379508		2203	4300	6503	SO:0001630	splice_region_variant	6996	exon9			GCTAAGTATGGTT	U51166	CCDS9095.1	12q24.1	2014-05-14			ENSG00000139372	ENSG00000139372	3.2.2.29		11700	protein-coding gene	gene with protein product	"G/T mismatch-specific thymine DNA glycosylase"	601423				8662714, 9299239	Standard	NM_003211		Approved		uc001tkg.3	Q13569	OTTHUMG00000168418	ENST00000392872.3:c.1090+2T>C	chr12.hg19:g.104379508T>C		129.0	0.0		93.0	27.0	NM_003211	Q8IUZ6|Q8IZM3	Splice_Site	SNP	ENST00000392872.3	hg19	CCDS9095.1	.	.	.	.	.	.	.	.	.	.	T	13.32	2.202862	0.38905	.	.	ENSG00000139372	ENST00000392872;ENST00000266775;ENST00000544861;ENST00000542036	.	.	.	5.7	5.7	0.88788	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8048	0.69945	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	TDG	102903638	1.000000	0.71417	0.917000	0.36280	0.314000	0.28054	2.133000	0.42093	2.175000	0.68902	0.533000	0.62120	.	.	.		0.413	TDG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399673.2		Intron	C	104379508	T	C	104379508	5	2	279	1	0	0	0	0	0	0	1	0	15740	1652	57	2	1126	2	TDG	12	104379508	Splice_Site	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	3881804	104379508	29472387	273	40032										
RIC8B	55188	hgsc.bcm.edu	37	chr12	107237670	107237670	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tctaactccagttctcagctTattaaccgaatgttcccgag	6	12	2	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr12:107237670T>C	ENST00000392839.2	+	6	1212	c.1106T>C	c.(1105-1107)tTa>tCa	p.L369S	RIC8B_ENST00000549643.1_Intron|RIC8B_ENST00000392837.4_Missense_Mutation_p.L369S|RIC8B_ENST00000355478.2_Missense_Mutation_p.L329S	NM_018157.2	NP_060627.2	Q9NVN3	RIC8B_HUMAN	RIC8 guanine nucleotide exchange factor B	369					regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	G-protein alpha-subunit binding (GO:0001965)|guanyl-nucleotide exchange factor activity (GO:0005085)			kidney(2)|large_intestine(5)|lung(10)|ovary(1)|urinary_tract(1)	19						GTTCTCAGCTTATTAACCGAA	0.343																																					p.L369S		Atlas-SNP	.											.	RIC8B	51	.	0			c.T1106C						.						109	103	105					12																	107237670		2203	4300	6503	SO:0001583	missense	55188	exon6			TCAGCTTATTAAC	AK128102	CCDS9109.2	12q23.3	2013-08-05	2013-08-05		ENSG00000111785	ENSG00000111785			25555	protein-coding gene	gene with protein product		609147	"resistance to inhibitors of cholinesterase 8 homolog B (C. elegans)"				Standard	XM_005268998		Approved	FLJ10620, hSyn, RIC8	uc001tlx.3	Q9NVN3	OTTHUMG00000144188	ENST00000392839.2:c.1106T>C	chr12.hg19:g.107237670T>C	ENSP00000376583:p.Leu369Ser	49.0	0.0		57.0	4.0	NM_018157	A2RTZ0|Q4G103|Q6ZRN4|Q86WD3	Missense_Mutation	SNP	ENST00000392839.2	hg19	CCDS9109.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.4|25.4	4.633859|4.633859	0.87660|0.87660	.|.	.|.	ENSG00000111785|ENSG00000111785	ENST00000392837;ENST00000392839;ENST00000355478|ENST00000548914	T;T;T|.	0.52295|.	0.67;0.67;0.67|.	5.51|5.51	5.51|5.51	0.81932|0.81932	Synembryn (1);Armadillo-type fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.74921|0.74921	0.3780|0.3780	M|M	0.75777|0.75777	2.31|2.31	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;0.999;1.0|.	D;D;D|.	0.91635|.	0.999;0.999;0.999|.	T|T	0.75789|0.75789	-0.3194|-0.3194	10|5	0.59425|.	D|.	0.04|.	-2.922|-2.922	15.6203|15.6203	0.76802|0.76802	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	329;369;369|.	Q9NVN3-3;Q9NVN3;B7WPL0|.	.;RIC8B_HUMAN;.|.	S|H	369;369;329|194	ENSP00000376582:L369S;ENSP00000376583:L369S;ENSP00000347662:L329S|.	ENSP00000347662:L329S|.	L|Y	+|+	2|1	0|0	RIC8B|RIC8B	105761800|105761800	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.985000|0.985000	0.73830|0.73830	7.796000|7.796000	0.85898|0.85898	2.088000|2.088000	0.63022|0.63022	0.455000|0.455000	0.32223|0.32223	TTA|TAT	.	.		0.343	RIC8B-006	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000291398.2	NM_018157		C	107237670	T	C	107237670	3	2	279	1	0	0	0	0	1	0	0	0	13371	1764	61	2	1128	2	RIC8B	12	107237670	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	2858162	107237670	26614225	274	40033										
MTERFD3	80298	hgsc.bcm.edu	37	chr12	107371779	107371779	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	agaatttcaaagctggtgaaAccttgctcctggagaaattc	9	8	1	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr12:107371779A>G	ENST00000552029.1	-	2	2782	c.714T>C	c.(712-714)ggT>ggC	p.G238G	MTERFD3_ENST00000392830.2_Silent_p.G238G|MTERFD3_ENST00000240050.4_Silent_p.G238G|C12orf23_ENST00000551237.1_Intron			Q49AM1	MTEF2_HUMAN		238					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)	transcription regulatory region DNA binding (GO:0044212)			breast(1)|kidney(1)|large_intestine(2)|lung(3)	7						AGCTGGTGAAACCTTGCTCCT	0.343																																					p.G238G		Atlas-SNP	.											.	MTERFD3	32	.	0			c.T714C						.						57	65	62					12																	107371779		2201	4300	6501	SO:0001819	synonymous_variant	80298	exon3			GGTGAAACCTTGC																												ENST00000552029.1:c.714T>C	chr12.hg19:g.107371779A>G		71.0	0.0		71.0	5.0	NM_001033050	Q53HM2|Q9H4L6|Q9H7Y9	Silent	SNP	ENST00000552029.1	hg19	CCDS9111.1																																																																																			.	.		0.343	MTERFD3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406835.1			G	107371779	A	G	107371779	2	3	279	1	0	0	0	0	0	0	0	1	9930	30	2	2		2	MTERFD3	12	107371779	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	134109	107371779	26480116	275	40034										
ATXN2	6311	hgsc.bcm.edu	37	chr12	111926327	111926327	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tcgtctttctcttgtttacaTgctgggctggaagtctgaac	10	9	3	1	rs138912353		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr12:111926327T>C	ENST00000377617.3	-	15	2834	c.2673A>G	c.(2671-2673)gcA>gcG	p.A891A	ATXN2_ENST00000608853.1_Silent_p.A731A|AC002395.1_ENST00000581907.1_RNA|ATXN2_ENST00000389153.4_Silent_p.A626A|ATXN2_ENST00000550104.1_Silent_p.A891A|ATXN2_ENST00000542287.2_Silent_p.A626A|ATXN2_ENST00000535949.1_Silent_p.A602A	NM_002973.3	NP_002964.3	Q99700	ATX2_HUMAN	ataxin 2	891					cell death (GO:0008219)|cerebellar Purkinje cell differentiation (GO:0021702)|cytoplasmic mRNA processing body assembly (GO:0033962)|homeostasis of number of cells (GO:0048872)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of receptor internalization (GO:0002091)|neuromuscular process (GO:0050905)|neuron projection morphogenesis (GO:0048812)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA transport (GO:0050658)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|trans-Golgi network (GO:0005802)	epidermal growth factor receptor binding (GO:0005154)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37						CTTGTTTACATGCTGGGCTGG	0.453																																					p.A891A		Atlas-SNP	.											.	ATXN2	99	.	0			c.A2673G						.						118	115	116					12																	111926327		2203	4300	6503	SO:0001819	synonymous_variant	6311	exon15			TTTACATGCTGGG	U80749	CCDS31902.1	12q23-q24.1	2014-09-17	2004-08-12	2004-08-13	ENSG00000204842	ENSG00000204842		"Ataxins"	10555	protein-coding gene	gene with protein product	"trinucleotide repeat containing 13"	601517	"spinocerebellar ataxia 2 (olivopontocerebellar ataxia 2, autosomal dominant, ataxin 2)"	SCA2, TNRC13		8358438, 9225980	Standard	NM_002973		Approved	ATX2	uc001tsj.3	Q99700	OTTHUMG00000133475	ENST00000377617.3:c.2673A>G	chr12.hg19:g.111926327T>C		198.0	0.0		181.0	54.0	NM_002973	A6NLD4|Q6ZQZ7|Q99493	Silent	SNP	ENST00000377617.3	hg19	CCDS31902.1																																																																																			.	T|1.000;G|0.000		0.453	ATXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257351.3	NM_002973		C	111926327	T	C	111926327	2	2	279	1	0	0	0	0	0	0	0	1	1211	1451	51	2		2	ATXN2	12	111926327	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	4554548	111926327	21925568	276	40035										
C12orf51	283450	hgsc.bcm.edu	37	chr12	112613662	112613662	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gtcaggtatttttcctcaggGactggtggaaagggttcagt	14	6	3	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr12:112613662G>A	ENST00000430131.2	-	65	11351	c.10206C>T	c.(10204-10206)gtC>gtT	p.V3402V	HECTD4_ENST00000377560.5_Splice_Site_p.V3652V|HECTD4_ENST00000550722.1_Splice_Site_p.V3678V			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	3402					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										TTTCCTCAGGGACTGGTGGAA	0.557																																					p.V3690V		Atlas-SNP	.											.	.	.	.	0			c.C11070T						.						50	53	52					12																	112613662		1982	4162	6144	SO:0001630	splice_region_variant	283450	exon66			CTCAGGGACTGGT	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 51"	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.10205-1C>T	chr12.hg19:g.112613662G>A		176.0	0.0		141.0	34.0	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Silent	SNP	ENST00000430131.2	hg19																																																																																				.	.		0.557	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813	Silent	A	112613662	G	A	112613662	5	1	279	1	0	0	0	0	0	0	1	0	1698	1188	41	3	1828	3	C12orf51	12	112613662	Splice_Site	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	687335	112613662	21238233	277	40036										
PIWIL1	9271	hgsc.bcm.edu	37	chr12	130834496	130834496	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cggctctgaagtcagcttctTagaatactacaggaaggtaa	10	8	3	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr12:130834496T>C	ENST00000245255.3	+	9	1300	c.1028T>C	c.(1027-1029)tTa>tCa	p.L343S		NM_001190971.1|NM_004764.4	NP_001177900.1|NP_004755.2	Q96J94	PIWL1_HUMAN	piwi-like RNA-mediated gene silencing 1	343	PAZ. {ECO:0000255|PROSITE- ProRule:PRU00142}.				gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|mRNA cap binding complex (GO:0005845)|P granule (GO:0043186)|polysome (GO:0005844)	mRNA binding (GO:0003729)|piRNA binding (GO:0034584)|single-stranded RNA binding (GO:0003727)			breast(6)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(26)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	57	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.02e-06)|Epithelial(86;3.85e-05)|all cancers(50;4.65e-05)		GTCAGCTTCTTAGAATACTAC	0.408																																					p.L343S		Atlas-SNP	.											.	PIWIL1	157	.	0			c.T1028C						.						69	72	71					12																	130834496		2203	4300	6503	SO:0001583	missense	9271	exon9			GCTTCTTAGAATA	AF104260	CCDS9268.1	12q24.33	2014-01-21	2013-02-15		ENSG00000125207	ENSG00000125207		"Argonaute/PIWI family"	9007	protein-coding gene	gene with protein product		605571	"piwi (Drosophila)-like 1", "piwi-like 1 (Drosophila)"			9851978, 12906857	Standard	NM_004764		Approved	PIWI, HIWI, CT80.1	uc001uik.3	Q96J94	OTTHUMG00000168382	ENST00000245255.3:c.1028T>C	chr12.hg19:g.130834496T>C	ENSP00000245255:p.Leu343Ser	63.0	0.0		45.0	4.0	NM_004764	A4F266|O95404|Q8NA60|Q8TBY5|Q96JD5	Missense_Mutation	SNP	ENST00000245255.3	hg19	CCDS9268.1	.	.	.	.	.	.	.	.	.	.	T	11.61	1.689917	0.29962	.	.	ENSG00000125207	ENST00000245255	T	0.11063	2.81	5.72	5.72	0.89469	Argonaute/Dicer protein, PAZ (4);	0.376313	0.28338	N	0.015713	T	0.22936	0.0554	L	0.56396	1.775	0.34108	D	0.662673	P;B	0.42161	0.772;0.401	P;B	0.50896	0.653;0.292	T	0.18241	-1.0343	10	0.59425	D	0.04	-17.9593	15.185	0.72993	0.0:0.0:0.0:1.0	.	343;343	Q96J94;Q96J94-2	PIWL1_HUMAN;.	S	343	ENSP00000245255:L343S	ENSP00000245255:L343S	L	+	2	0	PIWIL1	129400449	0.996000	0.38824	0.995000	0.50966	0.071000	0.16799	2.725000	0.47294	2.168000	0.68352	0.460000	0.39030	TTA	.	.		0.408	PIWIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399510.1			C	130834496	T	C	130834496	3	2	279	1	0	0	0	0	1	0	0	0	11966	1764	61	2	1058	2	PIWIL1	12	130834496	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	18220834	130834496	3017399	278	40037										
PARP4	143	hgsc.bcm.edu	37	chr13	25044076	25044076	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gatgaaggcttcgaagccacAcacagcggccttgtcatcca	10	13	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr13:25044076A>G	ENST00000381989.3	-	16	2107	c.2002T>C	c.(2002-2004)Tgt>Cgt	p.C668R		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	668	VIT. {ECO:0000255|PROSITE- ProRule:PRU00801}.				cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		TCGAAGCCACACACAGCGGCC	0.443																																					p.C668R		Atlas-SNP	.											.	PARP4	142	.	0			c.T2002C						.						93	70	78					13																	25044076		2203	4300	6503	SO:0001583	missense	143	exon16			AGCCACACACAGC	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"Poly (ADP-ribose) polymerases"	271	protein-coding gene	gene with protein product	"von Willebrand factor A domain containing 5C"	607519	"ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.2002T>C	chr13.hg19:g.25044076A>G	ENSP00000371419:p.Cys668Arg	75.0	0.0		91.0	4.0	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	hg19	CCDS9307.1	.	.	.	.	.	.	.	.	.	.	A	14.95	2.689320	0.48097	.	.	ENSG00000102699	ENST00000381989	T	0.21031	2.03	3.6	3.6	0.41247	Vault protein inter-alpha-trypsin (2);Vault protein inter-alpha-trypsin, metazoa (1);	0.000000	0.85682	U	0.000000	T	0.43055	0.1230	M	0.88181	2.935	0.80722	D	1	P	0.49307	0.922	P	0.54759	0.76	T	0.50668	-0.8801	10	0.62326	D	0.03	-12.9249	10.4971	0.44783	1.0:0.0:0.0:0.0	.	668	Q9UKK3	PARP4_HUMAN	R	668	ENSP00000371419:C668R	ENSP00000371419:C668R	C	-	1	0	PARP4	23942076	1.000000	0.71417	1.000000	0.80357	0.181000	0.23173	8.057000	0.89457	1.645000	0.50612	0.369000	0.22263	TGT	.	.		0.443	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437		G	25044076	A	G	25044076	3	3	279	1	0	0	0	0	1	0	0	0	11472	159	6	2	3248	2	PARP4	13	25044076	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10		25044076	90125802	279	40038										
RNF6	6049	hgsc.bcm.edu	37	chr13	26788190	26788190	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tggtggaaagattgtcaatcTgctctttggttaaaccacgt	10	7	3	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr13:26788190T>C	ENST00000381588.4	-	5	2581	c.1829A>G	c.(1828-1830)cAg>cGg	p.Q610R	RNF6_ENST00000399762.2_Missense_Mutation_p.Q254R|RNF6_ENST00000381570.3_Missense_Mutation_p.Q610R|RNF6_ENST00000468480.1_Intron|RNF6_ENST00000346166.3_Missense_Mutation_p.Q610R	NM_005977.3	NP_005968.1	Q9Y252	RNF6_HUMAN	ring finger protein (C3H2C3 type) 6	610	Required for polyubiquitination. {ECO:0000250}.				negative regulation of axon extension (GO:0030517)|positive regulation of transcription, DNA-templated (GO:0045893)|protein K27-linked ubiquitination (GO:0044314)|protein K48-linked ubiquitination (GO:0070936)|protein K6-linked ubiquitination (GO:0085020)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)	axon (GO:0030424)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|PML body (GO:0016605)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(1)|large_intestine(9)|lung(3)|ovary(2)|prostate(2)|skin(2)	23	Colorectal(5;0.000442)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.00893)|Epithelial(112;0.0481)|OV - Ovarian serous cystadenocarcinoma(117;0.148)|GBM - Glioblastoma multiforme(144;0.23)|Lung(94;0.245)		ATTGTCAATCTGCTCTTTGGT	0.363																																					p.Q610R		Atlas-SNP	.											.	RNF6	68	.	0			c.A1829G						.						171	162	165					13																	26788190		2203	4300	6503	SO:0001583	missense	6049	exon5			TCAATCTGCTCTT	AJ010346	CCDS9316.1	13q12.2	2013-01-09			ENSG00000127870	ENSG00000127870		"RING-type (C3HC4) zinc fingers"	10069	protein-coding gene	gene with protein product	"RING-H2 protein RNF-6"	604242				10331950	Standard	NM_005977		Approved	DKFZp686P0776	uc001uqq.3	Q9Y252	OTTHUMG00000016614	ENST00000381588.4:c.1829A>G	chr13.hg19:g.26788190T>C	ENSP00000371000:p.Gln610Arg	116.0	0.0		99.0	4.0	NM_183043	B4DDP0|Q5W0H0|Q9BZP5|Q9UF41	Missense_Mutation	SNP	ENST00000381588.4	hg19	CCDS9316.1	.	.	.	.	.	.	.	.	.	.	T	19.79	3.892085	0.72524	.	.	ENSG00000127870	ENST00000346166;ENST00000381588;ENST00000381570;ENST00000399762	T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	T	0.80502	0.4635	M	0.70595	2.14	0.80722	D	1	D;B	0.76494	0.999;0.294	D;B	0.77004	0.989;0.224	T	0.82862	-0.0247	10	0.72032	D	0.01	-15.5422	15.1787	0.72938	0.0:0.0:0.0:1.0	.	254;610	B4DDP0;Q9Y252	.;RNF6_HUMAN	R	610;610;610;254	ENSP00000342121:Q610R;ENSP00000371000:Q610R;ENSP00000370982:Q610R;ENSP00000382665:Q254R	ENSP00000342121:Q610R	Q	-	2	0	RNF6	25686190	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.396000	0.79891	2.230000	0.72887	0.455000	0.32223	CAG	.	.		0.363	RNF6-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044246.2	NM_005977		C	26788190	T	C	26788190	3	2	279	1	0	0	0	0	1	0	0	0	13513	1580	55	2	232	2	RNF6	13	26788190	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	1744114	26788190	88381688	280	40039										
B3GALTL	145173	hgsc.bcm.edu	37	chr13	31822032	31822032	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gaaattcatcttggattttcTtctgtgaagaagagacaaga	9	5	4	4			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr13:31822032T>C	ENST00000343307.4	+	6	537	c.388T>C	c.(388-390)Ttc>Ctc	p.F130L		NM_194318.3	NP_919299.3	Q6Y288	B3GLT_HUMAN	beta 1,3-galactosyltransferase-like	130					fucose metabolic process (GO:0006004)|protein glycosylation (GO:0006486)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19		Lung SC(185;0.0257)		all cancers(112;0.00436)|Epithelial(112;0.0285)|OV - Ovarian serous cystadenocarcinoma(117;0.0512)|GBM - Glioblastoma multiforme(144;0.184)		TTGGATTTTCTTCTGTGAAGA	0.318																																					p.F130L		Atlas-SNP	.											.	B3GALTL	48	.	0			c.T388C						.						48	45	46					13																	31822032		2203	4294	6497	SO:0001583	missense	145173	exon6			ATTTTCTTCTGTG	AB101481	CCDS9341.1	13q12.3	2014-03-24			ENSG00000187676	ENSG00000187676		"Beta 3-glycosyltransferases"	20207	protein-coding gene	gene with protein product		610308				12943678, 16899492, 17032646	Standard	NM_194318		Approved	B3GTL, B3Glc-T	uc010aaz.3	Q6Y288	OTTHUMG00000016688	ENST00000343307.4:c.388T>C	chr13.hg19:g.31822032T>C	ENSP00000343002:p.Phe130Leu	90.0	0.0		85.0	4.0	NM_194318	A8K5F8|Q5W0H2|Q6NUI3	Missense_Mutation	SNP	ENST00000343307.4	hg19	CCDS9341.1	.	.	.	.	.	.	.	.	.	.	T	26.5	4.741703	0.89573	.	.	ENSG00000187676	ENST00000343307	T	0.61392	0.11	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.76723	0.4027	M	0.76838	2.35	0.58432	D	0.999995	D	0.89917	1.0	D	0.97110	1.0	T	0.79588	-0.1741	10	0.66056	D	0.02	-29.8454	15.7471	0.77955	0.0:0.0:0.0:1.0	.	130	Q6Y288	B3GLT_HUMAN	L	130	ENSP00000343002:F130L	ENSP00000343002:F130L	F	+	1	0	B3GALTL	30720032	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.005000	0.63972	2.264000	0.75181	0.533000	0.62120	TTC	.	.		0.318	B3GALTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044396.3	NM_194318		C	31822032	T	C	31822032	3	2	279	1	0	0	0	0	1	0	0	0	1252	1609	56	2	410	2	B3GALTL	13	31822032	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	5033842	31822032	83347846	281	40040										
RCBTB2	1102	hgsc.bcm.edu	37	chr13	49070340	49070340	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tccttacctgtgcatcatacTtcaccgcagccgagagcaga	8	14	2	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr13:49070340T>C	ENST00000344532.3	-	14	1925	c.1502A>G	c.(1501-1503)aAg>aGg	p.K501R	RCBTB2_ENST00000544492.1_Missense_Mutation_p.K227R|RCBTB2_ENST00000430805.2_Missense_Mutation_p.K506R	NM_001268.2	NP_001259.1	O95199	RCBT2_HUMAN	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 2	501	BTB 2. {ECO:0000255|PROSITE- ProRule:PRU00037}.				positive regulation of Ran GTPase activity (GO:0032853)	acrosomal vesicle (GO:0001669)	Ran guanyl-nucleotide exchange factor activity (GO:0005087)			breast(5)|endometrium(3)|kidney(2)|large_intestine(2)|lung(11)|ovary(2)|prostate(3)|skin(3)	31		all_cancers(8;4.86e-71)|all_epithelial(8;2.11e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;2.3e-10)|Lung NSC(96;1.07e-07)|Breast(56;1.53e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.00826)|Myeloproliferative disorder(33;0.0179)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(99;1.8e-09)|LUSC - Lung squamous cell carcinoma(3;0.116)		TGCATCATACTTCACCGCAGC	0.478																																					p.K501R		Atlas-SNP	.											.	RCBTB2	62	.	0			c.A1502G						.						83	78	80					13																	49070340		2203	4300	6503	SO:0001583	missense	1102	exon14			TCATACTTCACCG	AF060219	CCDS9411.1, CCDS73570.1, CCDS73571.1, CCDS73572.1	13q14.3	2013-01-08	2005-05-09	2005-05-09	ENSG00000136161	ENSG00000136161		"BTB/POZ domain containing"	1914	protein-coding gene	gene with protein product		603524	"chromosome condensation 1-like"	CHC1L		9806834	Standard	XM_005266242		Approved		uc001vch.3	O95199	OTTHUMG00000016902	ENST00000344532.3:c.1502A>G	chr13.hg19:g.49070340T>C	ENSP00000345144:p.Lys501Arg	76.0	0.0		69.0	4.0	NM_001268	B2RDW8	Missense_Mutation	SNP	ENST00000344532.3	hg19	CCDS9411.1	.	.	.	.	.	.	.	.	.	.	t	6.933	0.541968	0.13250	.	.	ENSG00000136161	ENST00000344532;ENST00000450343;ENST00000452987;ENST00000430805;ENST00000544492	T;T;T	0.74526	0.05;0.05;-0.85	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.61160	0.2325	N	0.25789	0.76	0.80722	D	1	B;B;B;B	0.21753	0.019;0.001;0.06;0.001	B;B;B;B	0.20384	0.029;0.007;0.018;0.007	T	0.56842	-0.7912	10	0.13108	T	0.6	.	15.0715	0.72040	0.0:0.0:0.0:1.0	.	227;506;453;501	B4E372;B4DWG0;B3KVB1;O95199	.;.;.;RCBT2_HUMAN	R	501;453;506;506;227	ENSP00000345144:K501R;ENSP00000389910:K506R;ENSP00000443862:K227R	ENSP00000345144:K501R	K	-	2	0	RCBTB2	47968341	1.000000	0.71417	0.932000	0.37286	0.040000	0.13550	5.900000	0.69853	2.021000	0.59480	0.456000	0.33151	AAG	.	.		0.478	RCBTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044888.2	NM_001268		C	49070340	T	C	49070340	3	2	279	1	0	0	0	0	1	0	0	0	13187	1609	56	2	161	2	RCBTB2	13	49070340	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	17248308	49070340	66099538	282	40041										
DIAPH3	81624	hgsc.bcm.edu	37	chr13	60557952	60557952	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ctttttcgatatgtgaagtcTggatccattccatctctatg	7	9	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr13:60557952T>C	ENST00000400324.4	-	13	1651	c.1431A>G	c.(1429-1431)ccA>ccG	p.P477P	DIAPH3_ENST00000377908.2_Silent_p.P466P|DIAPH3_ENST00000400319.1_Silent_p.P407P|DIAPH3_ENST00000267215.4_Silent_p.P477P|DIAPH3_ENST00000400330.1_Silent_p.P477P|DIAPH3_ENST00000465066.1_5'UTR|DIAPH3_ENST00000400320.1_Silent_p.P431P	NM_001042517.1|NM_001258366.1	NP_001035982.1|NP_001245295.1	Q9NSV4	DIAP3_HUMAN	diaphanous-related formin 3	477					actin cytoskeleton organization (GO:0030036)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|liver(1)|lung(20)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		ATGTGAAGTCTGGATCCATTC	0.294																																					p.P477P		Atlas-SNP	.											.	DIAPH3	139	.	0			c.A1431G						.						110	104	106					13																	60557952		1822	4075	5897	SO:0001819	synonymous_variant	81624	exon13			GAAGTCTGGATCC	AL137718	CCDS41898.1, CCDS58294.1, CCDS58295.1, CCDS58296.1, CCDS58297.1, CCDS73579.1, CCDS73580.1	13q21.2	2013-05-24	2013-05-24		ENSG00000139734	ENSG00000139734			15480	protein-coding gene	gene with protein product		614567	"diaphanous (Drosophila, homolog) 3", "auditory neuropathy, autosomal dominant 1", "diaphanous homolog 3 (Drosophila)"	AUNA1		14767582, 20624953	Standard	NM_030932		Approved	DRF3, FLJ34705, AN, NSDAN	uc001vht.4	Q9NSV4	OTTHUMG00000017004	ENST00000400324.4:c.1431A>G	chr13.hg19:g.60557952T>C		86.0	0.0		65.0	4.0	NM_001042517	A2A3B8|A2A3B9|A2A3C0|Q18P99|Q18PA0|Q18PA1|Q2KPB6|Q3ZK23|Q5JTP8|Q5T2S7|Q5XKF6|Q6MZF0|Q6NUP0|Q86VS4|Q8NAV4	Silent	SNP	ENST00000400324.4	hg19	CCDS41898.1																																																																																			.	.		0.294	DIAPH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045166.3	NM_001042517		C	60557952	T	C	60557952	2	2	279	1	0	0	0	0	0	0	0	1	4522	1567	55	2		2	DIAPH3	13	60557952	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	11487612	60557952	54611926	283	40042										
ABCC4	10257	hgsc.bcm.edu	37	chr13	95858953	95858953	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ggtggtgaaggtcacaaacaCgatgattttgcttgcactga	12	7	1	3	rs377022090		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr13:95858953C>T	ENST00000376887.4	-	8	1108	c.994G>A	c.(994-996)Gtg>Atg	p.V332M	ABCC4_ENST00000431522.1_Missense_Mutation_p.V332M|ABCC4_ENST00000538287.1_3'UTR|ABCC4_ENST00000412704.1_Missense_Mutation_p.V332M|ABCC4_ENST00000536256.1_Missense_Mutation_p.V257M	NM_005845.3	NP_005836.2	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	332	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				blood coagulation (GO:0007596)|oxidation-reduction process (GO:0055114)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of smooth muscle cell proliferation (GO:0048661)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)	15-hydroxyprostaglandin dehydrogenase (NAD+) activity (GO:0016404)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(1)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cefazolin(DB01327)|Celecoxib(DB00482)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Flurbiprofen(DB00712)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Lamivudine(DB00709)|Leucovorin(DB00650)|Meloxicam(DB00814)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Probenecid(DB01032)|Rosuvastatin(DB01098)|Sildenafil(DB00203)|Sorafenib(DB00398)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tenofovir(DB00300)|Tioguanine(DB00352)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Zidovudine(DB00495)	GTCACAAACACGATGATTTTG	0.517																																					p.V332M		Atlas-SNP	.											.	ABCC4	248	.	0			c.G994A						.	C	MET/VAL,MET/VAL	0,4406		0,0,2203	165	150	155		994,994	1.4	1	13		155	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	ABCC4	NM_001105515.1,NM_005845.3	21,21	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign,benign	332/860,332/1326	95858953	2,13004	2203	4300	6503	SO:0001583	missense	10257	exon8			CAAACACGATGAT	U66682	CCDS9474.1	13q31	2012-03-14			ENSG00000125257	ENSG00000125257		"ATP binding cassette transporters / subfamily C"	55	protein-coding gene	gene with protein product	"canalicular multispecific organic anion transporter (ABC superfamily)", "bA464I2.1 (ATP-binding cassette, sub-family C (CFTR/MRP), member 4)", "multidrug resistance-associated protein 4", "multispecific organic anion transporter B"	605250				8894702, 9661885	Standard	NM_005845		Approved	MRP4, EST170205, MOAT-B, MOATB	uc001vmd.4	O15439	OTTHUMG00000017216	ENST00000376887.4:c.994G>A	chr13.hg19:g.95858953C>T	ENSP00000366084:p.Val332Met	95.0	0.0		76.0	26.0	NM_005845	A9Z1Z7|Q8IVZ4|Q8IZN6|Q8NEW8|Q9Y6J2	Missense_Mutation	SNP	ENST00000376887.4	hg19	CCDS9474.1	.	.	.	.	.	.	.	.	.	.	C	7.493	0.651031	0.14516	0.0	2.33E-4	ENSG00000125257	ENST00000412704;ENST00000376887;ENST00000536256;ENST00000431522	D;D;D;D	0.90504	-2.68;-2.68;-2.68;-2.68	5.43	1.42	0.22433	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.770161	0.12546	N	0.459441	D	0.87485	0.6189	M	0.77103	2.36	0.30143	N	0.803717	B;B;B;B;B	0.26809	0.051;0.1;0.131;0.16;0.147	B;B;B;B;B	0.26693	0.028;0.028;0.04;0.072;0.066	T	0.80890	-0.1180	10	0.52906	T	0.07	.	1.7983	0.03066	0.1178:0.3272:0.3037:0.2513	.	257;332;332;332;332	B7Z3Q7;A8K2Q2;O15439-2;Q8IVZ4;O15439	.;.;.;.;MRP4_HUMAN	M	332;332;257;332	ENSP00000388657:V332M;ENSP00000366084:V332M;ENSP00000442024:V257M;ENSP00000398562:V332M	ENSP00000366084:V332M	V	-	1	0	ABCC4	94656954	0.001000	0.12720	0.989000	0.46669	0.096000	0.18686	-0.721000	0.04963	0.216000	0.20781	0.650000	0.86243	GTG	.	.		0.517	ABCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045478.2	NM_005845		T	95858953	C	T	95858953	3	4	279	1	0	0	0	0	1	0	0	0	55	536	19	1	3128	1	ABCC4	13	95858953	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	35301001	95858953	19310925	284	40043										
UGGT2	55757	hgsc.bcm.edu	37	chr13	96642227	96642227	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	agtatctcaaaatactatacCttgtagttcccagactttca	4	10	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr13:96642227C>T	ENST00000376747.3	-	8	1001	c.931G>A	c.(931-933)Gat>Aat	p.D311N	UGGT2_ENST00000467305.1_5'UTR|UGGT2_ENST00000376714.3_Intron|UGGT2_ENST00000397618.3_Splice_Site_p.D311N	NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	311					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-glucosylation (GO:0097359)	endoplasmic reticulum lumen (GO:0005788)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(17)|lung(20)|ovary(3)|pancreas(1)|prostate(4)|urinary_tract(2)	60						AATACTATACCTTGTAGTTCC	0.294																																					p.D311N		Atlas-SNP	.											.	UGGT2	127	.	0			c.G931A						.						170	171	170					13																	96642227		2203	4294	6497	SO:0001630	splice_region_variant	55757	exon8			CTATACCTTGTAG	AF227906	CCDS9480.1	13q32.1	2009-07-23	2009-07-23	2009-07-23	ENSG00000102595	ENSG00000102595			15664	protein-coding gene	gene with protein product	"UDP-glucose:glycoprotein glucosyltransferase 2"	605898	"UDP-glucose ceramide glucosyltransferase-like 2"	UGCGL2		10694380	Standard	NM_020121		Approved	FLJ11485, HUGT2, FLJ10873, MGC150689, MGC87276, MGC117360	uc001vmt.3	Q9NYU1	OTTHUMG00000017230	ENST00000376747.3:c.931+1G>A	chr13.hg19:g.96642227C>T		54.0	0.0		76.0	23.0	NM_020121	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Missense_Mutation	SNP	ENST00000376747.3	hg19	CCDS9480.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.910784	0.92178	.	.	ENSG00000102595	ENST00000376747;ENST00000397618	T;T	0.41400	1.0;1.0	5.48	5.48	0.80851	.	0.094082	0.64402	N	0.000001	T	0.67543	0.2904	M	0.83483	2.645	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.974	D;D;P	0.66716	0.946;0.946;0.742	T	0.69537	-0.5119	9	.	.	.	-16.4242	18.4851	0.90825	0.0:1.0:0.0:0.0	.	311;311;311	Q2TAA6;E7EMU6;Q9NYU1	.;.;UGGG2_HUMAN	N	311	ENSP00000365938:D311N;ENSP00000380743:D311N	.	D	-	1	0	UGGT2	95440228	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	6.385000	0.73182	2.732000	0.93576	0.591000	0.81541	GAT	.	.		0.294	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121	Missense_Mutation	T	96642227	C	T	96642227	5	4	279	1	0	0	0	0	0	0	1	0	16957	695	24	3	3747	3	UGGT2	13	96642227	Splice_Site	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	783274	96642227	18527651	285	40044										
IPO5	3843	hgsc.bcm.edu	37	chr13	98645235	98645235	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gttccaaagtatttgcgtccTcacttggaagcaactctaca	7	11	2	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr13:98645235T>C	ENST00000490680.1	+	7	824	c.759T>C	c.(757-759)ccT>ccC	p.P253P	IPO5_ENST00000539640.1_Silent_p.P128P|IPO5_ENST00000261574.5_Silent_p.P271P			O00410	IPO5_HUMAN	importin 5	253					cellular response to amino acid stimulus (GO:0071230)|negative regulation of catalytic activity (GO:0043086)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein import into nucleus (GO:0042307)|ribosomal protein import into nucleus (GO:0006610)|viral process (GO:0016032)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	GTPase inhibitor activity (GO:0005095)|poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|Ran GTPase binding (GO:0008536)			breast(2)|endometrium(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	27						ATTTGCGTCCTCACTTGGAAG	0.363																																					p.P271P		Atlas-SNP	.											.	IPO5	90	.	0			c.T813C						.						124	116	119					13																	98645235		2203	4300	6503	SO:0001819	synonymous_variant	3843	exon10			GCGTCCTCACTTG	U72761	CCDS31999.1	13q32.2	2012-05-02	2008-04-15	2008-04-15	ENSG00000065150	ENSG00000065150		"Importins"	6402	protein-coding gene	gene with protein product		602008	"karyopherin (importin) beta 3", "RAN binding protein 5"	KPNB3, RANBP5		9114010, 9271386, 17005651	Standard	NM_002271		Approved	IMB3, MGC2068, Pse1	uc001vne.3	O00410	OTTHUMG00000017244	ENST00000490680.1:c.759T>C	chr13.hg19:g.98645235T>C		97.0	0.0		80.0	4.0	NM_002271	B4DZA0|O15257|Q5T578|Q86XC7	Silent	SNP	ENST00000490680.1	hg19		.	.	.	.	.	.	.	.	.	.	T	10.94	1.492717	0.26774	.	.	ENSG00000065150	ENST00000469360	.	.	.	6.17	3.48	0.39840	.	.	.	.	.	T	0.43875	0.1267	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40117	-0.9580	4	.	.	.	-13.0217	1.223	0.01928	0.2392:0.1519:0.1101:0.4988	.	.	.	.	P	255	.	.	L	+	2	0	IPO5	97443236	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.805000	0.38883	1.161000	0.42604	0.533000	0.62120	CTC	.	.		0.363	IPO5-006	NOVEL	alternative_5_UTR|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000354655.1	NM_002271		C	98645235	T	C	98645235	2	2	279	1	0	0	0	0	0	0	0	1	7805	1538	54	2		2	IPO5	13	98645235	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	2003008	98645235	16524643	286	40045										
MYO16	23026	hgsc.bcm.edu	37	chr13	109661386	109661386	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	accagaatggagttttggacTtttttttccaggtattcata	8	6	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr13:109661386T>C	ENST00000357550.2	+	21	2559	c.2518T>C	c.(2518-2520)Ttt>Ctt	p.F840L	MYO16_ENST00000251041.5_Missense_Mutation_p.F840L|MYO16_ENST00000356711.2_Missense_Mutation_p.F840L|MYO16_ENST00000457511.2_Missense_Mutation_p.F352L	NM_001198950.1	NP_001185879.1			myosin XVI											NS(3)|breast(4)|central_nervous_system(2)|endometrium(10)|kidney(8)|large_intestine(27)|lung(51)|ovary(9)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	121	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			AGTTTTGGACTTTTTTTTCCA	0.353																																					p.F862L		Atlas-SNP	.											.,9	MYO16	285	.	0			c.T2584C						.						69	74	72					13																	109661386		2203	4300	6503	SO:0001583	missense	23026	exon22			TTGGACTTTTTTT		CCDS32008.1, CCDS73598.1	13q33.3	2014-06-12			ENSG00000041515	ENSG00000041515		"Myosins / Myosin superfamily : Class XVI", "Ankyrin repeat domain containing"	29822	protein-coding gene	gene with protein product	"neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 3", "protein phosphatase 1, regulatory subunit 107"	615479				11588169, 17029291, 21946561	Standard	NM_001198950		Approved	MYR8, KIAA0865, Myo16b, NYAP3, PPP1R107	uc001vqt.1	Q9Y6X6	OTTHUMG00000017333	ENST00000357550.2:c.2518T>C	chr13.hg19:g.109661386T>C	ENSP00000350160:p.Phe840Leu	42.0	0.0		28.0	2.0	NM_001198950		Missense_Mutation	SNP	ENST00000357550.2	hg19	CCDS32008.1	.	.	.	.	.	.	.	.	.	.	T	14.74	2.625318	0.46840	.	.	ENSG00000041515	ENST00000356711;ENST00000397258;ENST00000357550;ENST00000251041;ENST00000375857;ENST00000457511	T;T;T;T	0.76186	-1.0;-1.0;-1.0;-1.0	5.66	5.66	0.87406	Myosin head, motor domain (2);	0.000000	0.41938	U	0.000788	T	0.62865	0.2463	N	0.00637	-1.305	0.58432	D	0.999998	D;P;D	0.89917	0.98;0.885;1.0	P;P;D	0.81914	0.689;0.482;0.995	T	0.72253	-0.4347	9	.	.	.	.	15.3717	0.74570	0.0:0.0:0.0:1.0	.	352;840;840	F8W883;Q9Y6X6-2;Q9Y6X6	.;.;MYO16_HUMAN	L	840;840;840;840;628;352	ENSP00000349145:F840L;ENSP00000350160:F840L;ENSP00000251041:F840L;ENSP00000401633:F352L	.	F	+	1	0	MYO16	108459387	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.509000	0.73725	2.278000	0.76064	0.533000	0.62120	TTT	.	.		0.353	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011		C	109661386	T	C	109661386	3	2	279	1	0	0	0	0	1	0	0	0	10073	1609	56	2	2600	2	MYO16	13	109661386	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	11016151	109661386	5508492	287	40046										
TEP1	7011	hgsc.bcm.edu	37	chr14	20853228	20853228	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ggttcaggaactgcatcaccTccatctctgtcacagagcgc	9	14	4	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr14:20853228T>C	ENST00000262715.5	-	21	3063	c.3023A>G	c.(3022-3024)gAg>gGg	p.E1008G	TEP1_ENST00000556935.1_Missense_Mutation_p.E900G|TEP1_ENST00000545983.1_5'Flank	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1008					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		CTGCATCACCTCCATCTCTGT	0.577																																					p.E1008G		Atlas-SNP	.											.	TEP1	224	.	0			c.A3023G						.						112	98	103					14																	20853228		2203	4300	6503	SO:0001583	missense	7011	exon21			ATCACCTCCATCT		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"WD repeat domain containing"	11726	protein-coding gene	gene with protein product	"TROVE domain family, member 1"	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.3023A>G	chr14.hg19:g.20853228T>C	ENSP00000262715:p.Glu1008Gly	64.0	0.0		107.0	5.0	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	hg19	CCDS9548.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.165035	0.78339	.	.	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935	T;T	0.19806	2.12;2.12	4.52	4.52	0.55395	.	0.105694	0.64402	D	0.000007	T	0.48021	0.1477	M	0.84683	2.71	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.83275	0.996;0.996;0.992	T	0.53401	-0.8444	10	0.72032	D	0.01	-21.5764	10.2378	0.43294	0.0:0.0:0.0:1.0	.	900;358;1008	G3V5X7;G3V2A4;Q99973	.;.;TEP1_HUMAN	G	1008;1008;900	ENSP00000262715:E1008G;ENSP00000452574:E900G	ENSP00000262715:E1008G	E	-	2	0	TEP1	19923068	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.360000	0.59455	1.662000	0.50781	0.459000	0.35465	GAG	.	.		0.577	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		C	20853228	T	C	20853228	3	2	279	1	0	0	0	0	1	0	0	0	15774	1551	54	2	5000	2	TEP1	14	20853228	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10		20853228	86496312	288	40047										
ARHGAP5	394	hgsc.bcm.edu	37	chr14	32560165	32560165	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tcatgtcattgaacaaacagAgttcattgatgaccagactt	7	8	3	5			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr14:32560165A>T	ENST00000345122.3	+	2	605	c.290A>T	c.(289-291)gAg>gTg	p.E97V	ARHGAP5_ENST00000432921.1_Missense_Mutation_p.E97V|ARHGAP5_ENST00000539826.2_Missense_Mutation_p.E97V|ARHGAP5_ENST00000433497.1_Intron|ARHGAP5_ENST00000556611.1_Missense_Mutation_p.E97V|ARHGAP5_ENST00000396582.2_Intron	NM_001030055.1	NP_001025226.1	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5	97					cell adhesion (GO:0007155)|GTP catabolic process (GO:0006184)|mammary gland development (GO:0030879)|positive regulation of cell migration (GO:0030335)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell size (GO:0008361)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(10)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(12)|ovary(4)|skin(1)|stomach(1)|urinary_tract(4)	55	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)		GAACAAACAGAGTTCATTGAT	0.373																																					p.E97V	NSCLC(9;77 350 3443 29227 41353)	Atlas-SNP	.											.	ARHGAP5	166	.	0			c.A290T						.						86	85	86					14																	32560165		2202	4299	6501	SO:0001583	missense	394	exon2			AAACAGAGTTCAT	U17032	CCDS32062.1, CCDS45095.1	14q12	2010-02-05						"Rho GTPase activating proteins"	675	protein-coding gene	gene with protein product		602680	"growth factor independent 2"	GFI2		8537347	Standard	XM_005267635		Approved	RhoGAP5, p190-B, p190BRhoGAP	uc001wrn.3	Q13017		ENST00000345122.3:c.290A>T	chr14.hg19:g.32560165A>T	ENSP00000371897:p.Glu97Val	89.0	0.0		68.0	16.0	NM_001173	A1L375|A1L376|A8KAA1|D3DS89|D3DS90|Q05BE8|Q05BU8|Q59ER0|Q6DHZ3	Missense_Mutation	SNP	ENST00000345122.3	hg19	CCDS32062.1	.	.	.	.	.	.	.	.	.	.	A	14.89	2.670382	0.47677	.	.	ENSG00000100852	ENST00000556611;ENST00000539826;ENST00000345122;ENST00000432921;ENST00000556191	T;T;T;T;T	0.51574	2.47;2.47;2.47;2.47;0.7	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.68238	0.2979	M	0.70842	2.15	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.72316	-0.4330	10	0.87932	D	0	.	15.5311	0.75964	1.0:0.0:0.0:0.0	.	97;97	Q13017-2;Q13017	.;RHG05_HUMAN	V	97	ENSP00000452222:E97V;ENSP00000441692:E97V;ENSP00000371897:E97V;ENSP00000393307:E97V;ENSP00000451579:E97V	ENSP00000371897:E97V	E	+	2	0	ARHGAP5	31629916	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.064000	0.61679	0.533000	0.62120	GAG	.	.		0.373	ARHGAP5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409735.1	NM_001030055		T	32560165	A	T	32560165	3	4	279	1	0	0	0	0	1	0	0	0	886	304	11	4	292	4	ARHGAP5	14	32560165	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	11706937	32560165	74789375	289	40048										
C14orf147	171546	hgsc.bcm.edu	37	chr14	34931375	34931375	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tactggtagtagaaccaggaCatctgcttccaggcccgcgc	11	13	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr14:34931375C>T	ENST00000298130.4	-	1	187	c.39G>A	c.(37-39)atG>atA	p.M13I		NM_138288.3	NP_612145.2	Q969W0	SPTSA_HUMAN	serine palmitoyltransferase, small subunit A	13					sphingolipid biosynthetic process (GO:0030148)	integral component of membrane (GO:0016021)|serine C-palmitoyltransferase complex (GO:0017059)											AGAACCAGGACATCTGCTTCC	0.687																																					p.M13I		Atlas-SNP	.											.	.	.	.	0			c.G39A						.						27	25	25					14																	34931375		2203	4296	6499	SO:0001583	missense	171546	exon1			CCAGGACATCTGC	AK001993	CCDS9647.2	14q13.1	2011-07-26	2011-07-26	2011-07-26	ENSG00000165389	ENSG00000165389			20361	protein-coding gene	gene with protein product	"small subunit of serine palmitoyltransferase A"	613540	"chromosome 14 open reading frame 147"	C14orf147		19416851	Standard	NM_138288		Approved	ssSPTa	uc001wsc.3	Q969W0	OTTHUMG00000140212	ENST00000298130.4:c.39G>A	chr14.hg19:g.34931375C>T	ENSP00000298130:p.Met13Ile	120.0	0.0		149.0	25.0	NM_138288	B2RD54|D3DS93|Q8WTZ7	Missense_Mutation	SNP	ENST00000298130.4	hg19	CCDS9647.2	.	.	.	.	.	.	.	.	.	.	c	12.20	1.866132	0.32977	.	.	ENSG00000165389	ENST00000298130	.	.	.	4.02	4.02	0.46733	.	0.061470	0.64402	D	0.000005	T	0.40886	0.1135	.	.	.	0.43313	D	0.995328	B	0.02656	0.0	B	0.04013	0.001	T	0.27123	-1.0083	8	0.10636	T	0.68	-12.7977	16.7074	0.85376	0.0:1.0:0.0:0.0	.	13	Q969W0	SPTSA_HUMAN	I	13	.	ENSP00000298130:M13I	M	-	3	0	SPTSSA	34001126	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	1.610000	0.36869	2.243000	0.73865	0.484000	0.47621	ATG	.	.		0.687	SPTSSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276640.2	NM_138288		T	34931375	C	T	34931375	3	4	279	1	0	0	0	0	1	0	0	0	1752	478	17	3	184	3	C14orf147	14	34931375	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	2371210	34931375	72418165	290	40049										
KTN1	3895	hgsc.bcm.edu	37	chr14	56138558	56138558	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gcaagaagaaaataaatggaAagttaaggtcgatgaatcac	10	4	1	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr14:56138558A>G	ENST00000395314.3	+	37	3562	c.3494A>G	c.(3493-3495)aAa>aGa	p.K1165R	KTN1_ENST00000416613.1_Missense_Mutation_p.K1165R|KTN1_ENST00000395311.1_Missense_Mutation_p.K1142R|KTN1_ENST00000395309.3_Missense_Mutation_p.K1165R|KTN1_ENST00000395308.1_Missense_Mutation_p.K1142R|KTN1_ENST00000554507.1_Missense_Mutation_p.K431R|KTN1_ENST00000555573.1_Missense_Mutation_p.K170R|KTN1_ENST00000438792.2_Missense_Mutation_p.K1136R|KTN1_ENST00000413890.2_Missense_Mutation_p.K1142R	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	1165					microtubule-based movement (GO:0007018)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|large_intestine(8)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	19						AATAAATGGAAAGTTAAGGTC	0.363			T	RET	papillary thryoid																																p.K1165R		Atlas-SNP	.		Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	.	KTN1	147	.	0			c.A3494G						.						85	88	87					14																	56138558		2203	4300	6503	SO:0001583	missense	3895	exon37			AATGGAAAGTTAA		CCDS41957.1, CCDS41958.1, CCDS41959.1	14q22.1	2008-05-02			ENSG00000126777	ENSG00000126777			6467	protein-coding gene	gene with protein product		600381				9605849	Standard	NM_001079521		Approved	KIAA0004, CG1	uc001xcc.3	Q86UP2	OTTHUMG00000140312	ENST00000395314.3:c.3494A>G	chr14.hg19:g.56138558A>G	ENSP00000378725:p.Lys1165Arg	132.0	0.0		99.0	4.0	NM_001079521	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Missense_Mutation	SNP	ENST00000395314.3	hg19	CCDS41957.1	.	.	.	.	.	.	.	.	.	.	A	15.19	2.759499	0.49468	.	.	ENSG00000126777	ENST00000413890;ENST00000395309;ENST00000438792;ENST00000395314;ENST00000395308;ENST00000395311;ENST00000416613;ENST00000554507;ENST00000553624;ENST00000555573	T;T;T;T;T;T;T;T;T;T	0.78707	1.23;1.23;1.23;1.23;1.23;1.23;1.23;-1.2;1.23;-1.2	5.53	5.53	0.82687	.	0.000000	0.56097	D	0.000027	D	0.84261	0.5433	L	0.51914	1.62	0.39711	D	0.971338	D;D;D;D;P;D	0.89917	0.998;0.998;1.0;0.999;0.702;0.998	D;D;D;D;P;D	0.91635	0.998;0.997;0.999;0.996;0.519;0.998	T	0.82542	-0.0405	10	0.25751	T	0.34	-23.2499	15.9509	0.79835	1.0:0.0:0.0:0.0	.	170;1165;431;1136;1142;1165	B7Z6P3;B4DZ88;G3V4Y7;Q86UP2-2;Q17RZ5;Q86UP2	.;.;.;.;.;KTN1_HUMAN	R	1142;1165;1136;1165;1142;1142;1165;431;126;170	ENSP00000394992:K1142R;ENSP00000378720:K1165R;ENSP00000391964:K1136R;ENSP00000378725:K1165R;ENSP00000378719:K1142R;ENSP00000378722:K1142R;ENSP00000388807:K1165R;ENSP00000452073:K431R;ENSP00000452445:K126R;ENSP00000451698:K170R	ENSP00000378719:K1142R	K	+	2	0	KTN1	55208311	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.023000	0.57211	2.225000	0.72522	0.533000	0.62120	AAA	.	.		0.363	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2			G	56138558	A	G	56138558	3	3	279	1	0	0	0	0	1	0	0	0	8594	14	1	2	3636	2	KTN1	14	56138558	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	21207183	56138558	51210982	291	40050										
PELI2	57161	hgsc.bcm.edu	37	chr14	56645115	56645115	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	aagtagatttgccctctacaAgcggcccaaggcaaatggtg	11	10	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr14:56645115A>G	ENST00000267460.4	+	2	426	c.140A>G	c.(139-141)aAg>aGg	p.K47R		NM_021255.2	NP_067078.1	Q9HAT8	PELI2_HUMAN	pellino E3 ubiquitin protein ligase family member 2	47	FHA; atypical.				innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein phosphorylation (GO:0001934)|protein ubiquitination (GO:0016567)|Toll signaling pathway (GO:0008063)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytosol (GO:0005829)	ligase activity (GO:0016874)			kidney(6)|large_intestine(3)|lung(11)|ovary(1)|skin(1)	22						GCCCTCTACAAGCGGCCCAAG	0.507																																					p.K47R		Atlas-SNP	.											.	PELI2	55	.	0			c.A140G						.						118	111	113					14																	56645115		2203	4300	6503	SO:0001583	missense	57161	exon2			TCTACAAGCGGCC	AF302502	CCDS9726.1	14q21	2012-02-23	2012-02-23		ENSG00000139946	ENSG00000139946		"Pellino homologs"	8828	protein-coding gene	gene with protein product		614798	"pellino (Drosophila) homolog 2", "pellino homolog 2 (Drosophila)"			11306823, 12860405	Standard	XM_006720211		Approved		uc001xch.3	Q9HAT8	OTTHUMG00000152336	ENST00000267460.4:c.140A>G	chr14.hg19:g.56645115A>G	ENSP00000267460:p.Lys47Arg	106.0	0.0		91.0	4.0	NM_021255	B2RDY5	Missense_Mutation	SNP	ENST00000267460.4	hg19	CCDS9726.1	.	.	.	.	.	.	.	.	.	.	A	10.55	1.381315	0.24944	.	.	ENSG00000139946	ENST00000267460	T	0.39056	1.1	5.93	4.77	0.60923	.	0.149301	0.56097	D	0.000033	T	0.30198	0.0757	L	0.31207	0.915	0.38229	D	0.940991	B	0.10296	0.003	B	0.11329	0.006	T	0.11817	-1.0572	10	0.17369	T	0.5	-30.7734	12.4374	0.55606	0.8595:0.1405:0.0:0.0	.	47	Q9HAT8	PELI2_HUMAN	R	47	ENSP00000267460:K47R	ENSP00000267460:K47R	K	+	2	0	PELI2	55714868	1.000000	0.71417	0.998000	0.56505	0.761000	0.43186	3.233000	0.51311	1.041000	0.40125	-0.323000	0.08544	AAG	.	.		0.507	PELI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276925.1			G	56645115	A	G	56645115	3	3	279	1	0	0	0	0	1	0	0	0	11731	72	3	2	146	2	PELI2	14	56645115	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	506557	56645115	50704425	292	40051										
C14orf37	145407	hgsc.bcm.edu	37	chr14	58605485	58605485	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	atgtcccaaaccaactccttCctgactttcagttgcaaatg	5	13	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr14:58605485C>T	ENST00000267485.7	-	2	786	c.592G>A	c.(592-594)Gaa>Aaa	p.E198K	C14orf37_ENST00000334342.5_5'UTR	NM_001001872.2	NP_001001872.2	Q86TY3	CN037_HUMAN	chromosome 14 open reading frame 37	198						integral component of membrane (GO:0016021)				breast(7)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|skin(1)	33						CCAACTCCTTCCTGACTTTCA	0.388																																					p.E198K		Atlas-SNP	.											.	C14orf37	87	.	0			c.G592A						.						120	115	117					14																	58605485		2203	4300	6503	SO:0001583	missense	145407	exon2			CTCCTTCCTGACT		CCDS32089.1	14q23.1	2012-09-03			ENSG00000139971	ENSG00000139971			19846	protein-coding gene	gene with protein product							Standard	NM_001001872		Approved		uc001xdc.3	Q86TY3	OTTHUMG00000171173	ENST00000267485.7:c.592G>A	chr14.hg19:g.58605485C>T	ENSP00000267485:p.Glu198Lys	116.0	0.0		94.0	4.0	NM_001001872	A8K8Z8|Q6P5Q1|Q86TY1	Missense_Mutation	SNP	ENST00000267485.7	hg19	CCDS32089.1	.	.	.	.	.	.	.	.	.	.	C	6.009	0.370132	0.11352	.	.	ENSG00000139971	ENST00000267485;ENST00000438670	T	0.32988	1.43	5.76	3.94	0.45596	.	0.852017	0.10635	N	0.651714	T	0.24044	0.0582	L	0.50333	1.59	0.09310	N	0.999997	B;P;B;B	0.34462	0.091;0.454;0.091;0.091	B;B;B;B	0.30572	0.032;0.117;0.032;0.032	T	0.20107	-1.0285	10	0.18276	T	0.48	-0.1043	6.1486	0.20298	0.0:0.6805:0.1543:0.1652	.	236;198;198;198	B4DMS4;Q86TY3-2;A8K990;Q86TY3	.;.;.;CN037_HUMAN	K	198;236	ENSP00000267485:E198K	ENSP00000267485:E198K	E	-	1	0	C14orf37	57675238	0.635000	0.27199	0.731000	0.30826	0.619000	0.37552	1.784000	0.38674	0.787000	0.33731	0.655000	0.94253	GAA	.	.		0.388	C14orf37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412059.1	NM_001001872		T	58605485	C	T	58605485	3	4	279	1	0	0	0	0	1	0	0	0	1773	864	30	3	1760	3	C14orf37	14	58605485	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	1960370	58605485	48744055	293	40052										
PLEKHG3	26030	hgsc.bcm.edu	37	chr14	65208191	65208191	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ggcagcgagaagggcctggcCcggcatggcagtgccacaga	17	12	0	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr14:65208191C>T	ENST00000394691.1	+	16	2103	c.1956C>T	c.(1954-1956)gcC>gcT	p.A652A	PLEKHG3_ENST00000471182.2_Silent_p.A185A|PLEKHG3_ENST00000247226.7_Silent_p.A596A|PLEKHG3_ENST00000484731.2_Silent_p.A157A			A1L390	PKHG3_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 3	652							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(5)|kidney(2)|large_intestine(1)|lung(14)|prostate(2)|skin(3)|urinary_tract(2)	29				all cancers(60;0.00802)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)|BRCA - Breast invasive adenocarcinoma(234;0.0485)		AGGGCCTGGCCCGGCATGGCA	0.652																																					p.A596A		Atlas-SNP	.											.	PLEKHG3	89	.	0			c.C1788T						.						32	38	36					14																	65208191		2203	4300	6503	SO:0001819	synonymous_variant	26030	exon14			CCTGGCCCGGCAT	AB011171	CCDS32098.1	14q23.3	2013-01-10	2004-12-01	2004-12-01	ENSG00000126822	ENSG00000126822		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	20364	protein-coding gene	gene with protein product			"KIAA0599"	KIAA0599			Standard	XM_005267511		Approved	ARHGEF43	uc001xhp.2	A1L390	OTTHUMG00000029671	ENST00000394691.1:c.1956C>T	chr14.hg19:g.65208191C>T		58.0	0.0		61.0	31.0	NM_015549	A1L389|B5MEC9|O60339|Q6GMS3|Q6P4B1|Q7L3S3|Q86SW7|Q8TEF5|Q96EW6|Q9BT82	Silent	SNP	ENST00000394691.1	hg19																																																																																				.	.		0.652	PLEKHG3-010	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000412028.1	NM_015549		T	65208191	C	T	65208191	2	4	279	1	0	0	0	0	0	0	0	1	12079	610	22	3		3	PLEKHG3	14	65208191	Silent	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	6602706	65208191	42141349	294	40053										
GPHN	10243	hgsc.bcm.edu	37	chr14	67243210	67243210	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ggactatatcagcatacaagAtagtaccagatgaaatagaa	8	6	1	4			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr14:67243210A>G	ENST00000315266.5	+	3	1293	c.172A>G	c.(172-174)Ata>Gta	p.I58V	GPHN_ENST00000543237.1_Missense_Mutation_p.I58V|GPHN_ENST00000478722.1_Missense_Mutation_p.I58V|GPHN_ENST00000305960.9_Missense_Mutation_p.I58V|GPHN_ENST00000459628.1_Missense_Mutation_p.I58V	NM_001024218.1	NP_001019389.1	Q9NQX3	GEPH_HUMAN	gephyrin	58	MPT Mo-transferase.				establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycine receptor clustering (GO:0072579)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|molybdopterin adenylyltransferase activity (GO:0061598)|molybdopterin molybdotransferase activity (GO:0061599)|transferase activity (GO:0016740)			large_intestine(8)|liver(1)|ovary(2)|stomach(1)	12		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		AGCATACAAGATAGTACCAGA	0.358			T	MLL	AL																																p.I58V		Atlas-SNP	.		Dom	yes		14	14q24	10243	gephyrin (GPH)		L	.	GPHN	79	.	0			c.A172G						.						164	166	165					14																	67243210		2203	4300	6503	SO:0001583	missense	10243	exon3			TACAAGATAGTAC	AB037806	CCDS9777.1, CCDS32103.1	14q23.3	2008-04-22			ENSG00000171723	ENSG00000171723			15465	protein-coding gene	gene with protein product		603930				1319186, 10325225, 18403029	Standard	XM_005267250		Approved	KIAA1385	uc001xix.3	Q9NQX3	OTTHUMG00000029785	ENST00000315266.5:c.172A>G	chr14.hg19:g.67243210A>G	ENSP00000312771:p.Ile58Val	108.0	0.0		85.0	4.0	NM_001024218	Q9H4E9|Q9P2G2	Missense_Mutation	SNP	ENST00000315266.5	hg19	CCDS32103.1	.	.	.	.	.	.	.	.	.	.	A	15.80	2.939390	0.52972	.	.	ENSG00000171723	ENST00000315266;ENST00000478722;ENST00000459628;ENST00000543237;ENST00000305960	T;T;T;T;T	0.75477	-0.94;-0.94;-0.94;-0.94;-0.94	5.39	5.39	0.77823	Molybdenum cofactor synthesis (1);Molybdopterin binding (4);	0.000000	0.85682	D	0.000000	T	0.66066	0.2752	N	0.04043	-0.29	0.45946	D	0.998775	B;P;B;B;P	0.37083	0.103;0.581;0.015;0.332;0.527	B;P;B;P;B	0.50352	0.271;0.638;0.109;0.45;0.31	T	0.68988	-0.5264	10	0.33141	T	0.24	-11.5435	14.2406	0.65954	1.0:0.0:0.0:0.0	.	58;58;58;58;58	F8W7D6;F5H039;Q9NQX3;Q9NQX3-2;G3V582	.;.;GEPH_HUMAN;.;.	V	58	ENSP00000312771:I58V;ENSP00000417901:I58V;ENSP00000452220:I58V;ENSP00000438404:I58V;ENSP00000303019:I58V	ENSP00000303019:I58V	I	+	1	0	GPHN	66312963	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.492000	0.66893	2.168000	0.68352	0.477000	0.44152	ATA	.	.		0.358	GPHN-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000074299.2	NM_020806		G	67243210	A	G	67243210	3	3	279	1	0	0	0	0	1	0	0	0	6618	333	12	2	182	2	GPHN	14	67243210	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	2035019	67243210	40106330	295	40054										
ZFYVE26	23503	hgsc.bcm.edu	37	chr14	68241773	68241773	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	aactctgctgatggtgatctAgggagggtctcgggatctgc	15	8	4	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr14:68241773A>G	ENST00000347230.4	-	27	5418	c.5280T>C	c.(5278-5280)ccT>ccC	p.P1760P	ZFYVE26_ENST00000555452.1_Silent_p.P1760P	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	1760					cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		ATGGTGATCTAGGGAGGGTCT	0.443																																					p.P1760P		Atlas-SNP	.											.	ZFYVE26	223	.	0			c.T5280C						.						78	73	75					14																	68241773		2203	4300	6503	SO:0001819	synonymous_variant	23503	exon27			TGATCTAGGGAGG	AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"Zinc fingers, FYVE domain containing"	20761	protein-coding gene	gene with protein product	"spastizin", "FYVE-CENT"	612012	"spastic paraplegia 15 (complicated, autosomal recessive)"	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.5280T>C	chr14.hg19:g.68241773A>G		65.0	0.0		79.0	4.0	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Silent	SNP	ENST00000347230.4	hg19	CCDS9788.1																																																																																			.	.		0.443	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346		G	68241773	A	G	68241773	2	3	279	1	0	0	0	0	0	0	0	1	17683	407	15	2		2	ZFYVE26	14	68241773	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	998563	68241773	39107767	296	40055										
C14orf43	91748	hgsc.bcm.edu	37	chr14	74196575	74196575	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gtgatgttggagtagacgggAggggcgatgaaagtgcccgc	19	6	0	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr14:74196575A>C	ENST00000286523.5	-	4	2645	c.1863T>G	c.(1861-1863)ccT>ccG	p.P621P	ELMSAN1_ENST00000394071.2_Silent_p.P621P	NM_194278.3	NP_919254.2	Q6PJG2	EMSA1_HUMAN	ELM2 and Myb/SANT-like domain containing 1	621					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)										AGTAGACGGGAGGGGCGATGA	0.632																																					p.P621P		Atlas-SNP	.											.	.	.	.	0			c.T1863G						.						57	56	56					14																	74196575		2203	4300	6503	SO:0001819	synonymous_variant	91748	exon4			GACGGGAGGGGCG	BF971739	CCDS9819.1	14q24.3	2012-09-25	2012-09-25	2012-09-25	ENSG00000156030	ENSG00000156030			19853	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 117", "chromosome 14 open reading frame 43"	C14orf117, C14orf43			Standard	NM_194278		Approved	LSR68	uc001xou.3	Q6PJG2	OTTHUMG00000150359	ENST00000286523.5:c.1863T>G	chr14.hg19:g.74196575A>C		98.0	0.0		118.0	56.0	NM_194278	Q6PK13|Q6PK59|Q6ZS23	Silent	SNP	ENST00000286523.5	hg19	CCDS9819.1																																																																																			.	.		0.632	ELMSAN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317793.1	NM_194278		C	74196575	A	C	74196575	2	2	279	1	0	0	0	0	0	0	0	1	1776	291	11	5		5	C14orf43	14	74196575	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	5954802	74196575	33152965	297	40056										
PTGR2	145482	hgsc.bcm.edu	37	chr14	74325597	74325597	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	aagagtggtattgaattctcGacctggtatgtatttgcgat	11	5	1	2	rs548709026		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr14:74325597G>A	ENST00000555661.1	+	2	177	c.32G>A	c.(31-33)cGa>cAa	p.R11Q	PTGR2_ENST00000267568.4_Missense_Mutation_p.R11Q|PTGR2_ENST00000553326.1_3'UTR|Y_RNA_ENST00000411368.1_RNA|PTGR2_ENST00000553813.1_5'Flank|RP5-1021I20.4_ENST00000556551.2_Missense_Mutation_p.R11Q|PTGR2_ENST00000555228.1_Missense_Mutation_p.R11Q			Q8N8N7	PTGR2_HUMAN	prostaglandin reductase 2	11					prostaglandin metabolic process (GO:0006693)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	13-prostaglandin reductase activity (GO:0036132)|15-oxoprostaglandin 13-oxidase activity (GO:0047522)			NS(1)|large_intestine(3)|lung(2)|prostate(1)|skin(2)	9					Indomethacin(DB00328)	TTGAATTCTCGACCTGGTATG	0.308																																					p.R11Q	Esophageal Squamous(98;1155 1417 16452 47043 47872)	Atlas-SNP	.											.	PTGR2	21	.	0			c.G32A						.						96	89	92					14																	74325597		2203	4299	6502	SO:0001583	missense	145482	exon2			ATTCTCGACCTGG	AK096410	CCDS9820.1	14q24.1-q24.2	2008-06-04	2008-06-02	2008-06-03		ENSG00000140043			20149	protein-coding gene	gene with protein product		608642	"zinc binding alcohol dehydrogenase domain containing 1"	ZADH1		17449869	Standard	NM_152444		Approved	FLJ39091	uc001xow.3	Q8N8N7		ENST00000555661.1:c.32G>A	chr14.hg19:g.74325597G>A	ENSP00000452280:p.Arg11Gln	118.0	0.0		117.0	5.0	NM_152444	Q3L8A4|Q6MZH8	Missense_Mutation	SNP	ENST00000555661.1	hg19	CCDS9820.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.760884	0.89932	.	.	ENSG00000140043	ENST00000555228;ENST00000555661;ENST00000555976;ENST00000267568	T;T;T;T	0.41400	1.0;1.0;1.0;1.0	4.76	4.76	0.60689	GroES-like (1);	0.132923	0.50627	D	0.000119	T	0.67211	0.2869	M	0.90082	3.085	0.58432	D	0.999999	D	0.89917	1.0	P	0.59703	0.862	T	0.76072	-0.3093	10	0.87932	D	0	-5.6036	15.757	0.78043	0.0:0.0:1.0:0.0	.	11	Q8N8N7	PTGR2_HUMAN	Q	11	ENSP00000450975:R11Q;ENSP00000452280:R11Q;ENSP00000450517:R11Q;ENSP00000267568:R11Q	ENSP00000267568:R11Q	R	+	2	0	PTGR2	73395350	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.141000	0.71744	2.465000	0.83290	0.650000	0.86243	CGA	.	.		0.308	PTGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412575.1			A	74325597	G	A	74325597	3	1	279	1	0	0	0	0	1	0	0	0	12767	1058	37	1	34	1	PTGR2	14	74325597	Missense_Mutation	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	129022	74325597	33023943	298	40057										
MLH3	27030	hgsc.bcm.edu	37	chr14	75513956	75513957	+	Frame_Shift_Del	DEL	AG	AG	-													0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gtagtgattttacaaacatcAgagttctctaagcggttctt							TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr14:75513956_75513957delAG	ENST00000556740.1	-	1	2437_2438	c.2402_2403delCT	c.(2401-2403)tctfs	p.S801fs	MLH3_ENST00000544985.1_5'Flank|MLH3_ENST00000556257.1_Frame_Shift_Del_p.S801fs|MLH3_ENST00000355774.2_Frame_Shift_Del_p.S801fs|MLH3_ENST00000380968.2_5'UTR|MLH3_ENST00000238662.7_Frame_Shift_Del_p.S801fs|MLH3_ENST00000555671.1_5'Flank			Q9UHC1	MLH3_HUMAN	mutL homolog 3	801					ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44				BRCA - Breast invasive adenocarcinoma(234;0.00688)		TACAAACATCAGAGTTCTCTAA	0.416								Mismatch excision repair (MMR)																													p.801_802del		Atlas-Indel,Pindel	.											.	MLH3	200	.	0			c.2403_2404del						.																																			SO:0001589	frameshift_variant	27030	exon2			.	AF195657	CCDS9837.1, CCDS32123.1	14q24.3	2014-09-17	2013-09-12			ENSG00000119684			7128	protein-coding gene	gene with protein product		604395	"mutL (E. coli) homolog 3", "mutL homolog 3 (E. coli)"			10615123	Standard	XR_245681		Approved		uc001xrd.1	Q9UHC1		ENST00000556740.1:c.2402_2403delCT	chr14.hg19:g.75513958_75513959delAG	ENSP00000452316:p.Ser801fs	175.0	0.0		125.0	20.0	NM_014381	P49751|Q56DK9|Q9P292|Q9UHC0	Frame_Shift_Del	DEL	ENST00000556740.1	hg19	CCDS32123.1																																																																																			.	.		0.416	MLH3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415006.1	NM_014381		-	75513957	AG	-	75513956	7	5	279	1	0	1	0	1	0	0	0	0	9627	175	7	0	2006	0	MLH3	14	75513956	Frame_Shift_Del	DEL	AG	TCGA-G3-A3CG-01A-11D-A20W-10	1188359	75513956	31835584	299	40058										
TDP1	55775	hgsc.bcm.edu	37	chr14	90433726	90433726	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tctagtttaactactgctttGacgtggactggctcgtaaaa	9	8	1	1	rs543257445		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr14:90433726G>T	ENST00000335725.4	+	5	869	c.619G>T	c.(619-621)Gac>Tac	p.D207Y	TDP1_ENST00000393454.2_Missense_Mutation_p.D207Y|TDP1_ENST00000555565.1_3'UTR|TDP1_ENST00000357382.3_5'UTR|TDP1_ENST00000393452.3_Missense_Mutation_p.D207Y|TDP1_ENST00000555880.1_Missense_Mutation_p.D207Y	NM_018319.3	NP_060789.2	Q9NUW8	TYDP1_HUMAN	tyrosyl-DNA phosphodiesterase 1	207					cell death (GO:0008219)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	3'-tyrosyl-DNA phosphodiesterase activity (GO:0017005)|double-stranded DNA binding (GO:0003690)|exonuclease activity (GO:0004527)|single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|urinary_tract(1)	25		all_cancers(154;0.185)		COAD - Colon adenocarcinoma(157;0.23)		CTACTGCTTTGACGTGGACTG	0.398								Repair of DNA-protein crosslinks																													p.D207Y		Atlas-SNP	.											.	TDP1	47	.	0			c.G619T						.						189	182	184					14																	90433726		2203	4300	6503	SO:0001583	missense	55775	exon5			TGCTTTGACGTGG	AF182002	CCDS9888.1	14q32.11	2008-08-11				ENSG00000042088			18884	protein-coding gene	gene with protein product		607198				11839309, 12244316	Standard	XM_005267847		Approved	FLJ11090, SCAN1	uc001xxz.3	Q9NUW8		ENST00000335725.4:c.619G>T	chr14.hg19:g.90433726G>T	ENSP00000337353:p.Asp207Tyr	271.0	0.0		197.0	87.0	NM_018319	Q2HXX4|Q86TV8|Q96BK7|Q9NZM7|Q9NZM8	Missense_Mutation	SNP	ENST00000335725.4	hg19	CCDS9888.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.173126	0.78452	.	.	ENSG00000042088	ENST00000393452;ENST00000554180;ENST00000393454;ENST00000553617;ENST00000335725;ENST00000555880	T;T;T;T;T;T	0.62364	0.03;0.03;0.03;0.03;0.03;0.03	5.74	5.74	0.90152	.	0.096464	0.64402	D	0.000001	D	0.85932	0.5812	H	0.94542	3.55	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.994;0.996;0.996	D	0.89152	0.3524	10	0.87932	D	0	-22.7504	19.9403	0.97159	0.0:0.0:1.0:0.0	.	207;207;207	G3V2F4;E7EPD8;Q9NUW8	.;.;TYDP1_HUMAN	Y	207;207;207;108;207;207	ENSP00000377098:D207Y;ENSP00000450872:D207Y;ENSP00000377099:D207Y;ENSP00000450708:D108Y;ENSP00000337353:D207Y;ENSP00000450628:D207Y	ENSP00000337353:D207Y	D	+	1	0	TDP1	89503479	1.000000	0.71417	0.995000	0.50966	0.675000	0.39556	8.846000	0.92159	2.712000	0.92718	0.650000	0.86243	GAC	.	.		0.398	TDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411239.1	NM_018319		T	90433726	G	T	90433726	3	4	279	1	0	0	0	0	1	0	0	0	15743	1290	45	3	629	3	TDP1	14	90433726	Missense_Mutation	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	14919770	90433726	16915814	300	40059										
CPSF2	53981	hgsc.bcm.edu	37	chr14	92624139	92624139	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gtcaagatctggcagagtgcTgtcgcgcctttggtgggaaa	15	8	2	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr14:92624139T>C	ENST00000298875.4	+	13	2017	c.1732T>C	c.(1732-1734)Tgt>Cgt	p.C578R		NM_017437.2	NP_059133.1	Q9P2I0	CPSF2_HUMAN	cleavage and polyadenylation specific factor 2, 100kDa	578					gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)|mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	RNA binding (GO:0003723)			breast(2)|cervix(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	24		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.222)		GGCAGAGTGCTGTCGCGCCTT	0.448																																					p.C578R	Ovarian(78;28 1788 18702 44111)	Atlas-SNP	.											.	CPSF2	63	.	0			c.T1732C						.						76	75	75					14																	92624139		2203	4300	6503	SO:0001583	missense	53981	exon13			GAGTGCTGTCGCG	AB037788	CCDS9902.1	14q31.1	2008-07-28	2002-08-29			ENSG00000165934			2325	protein-coding gene	gene with protein product		606028	"cleavage and polyadenylation specific factor 2, 100kD subunit"			7969155, 11124543	Standard	NM_017437		Approved	KIAA1367	uc001yah.2	Q9P2I0		ENST00000298875.4:c.1732T>C	chr14.hg19:g.92624139T>C	ENSP00000298875:p.Cys578Arg	126.0	0.0		119.0	5.0	NM_017437	B3KME1|Q6NSJ1|Q9H3W7	Missense_Mutation	SNP	ENST00000298875.4	hg19	CCDS9902.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.360930	0.82353	.	.	ENSG00000165934	ENST00000298875	T	0.53206	0.63	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.64416	0.2596	M	0.68317	2.08	0.80722	D	1	D	0.59357	0.985	P	0.59357	0.856	T	0.68135	-0.5489	10	0.87932	D	0	.	16.0499	0.80749	0.0:0.0:0.0:1.0	.	578	Q9P2I0	CPSF2_HUMAN	R	578	ENSP00000298875:C578R	ENSP00000298875:C578R	C	+	1	0	CPSF2	91693892	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	7.946000	0.87746	2.193000	0.70182	0.533000	0.62120	TGT	.	.		0.448	CPSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412123.1			C	92624139	T	C	92624139	3	2	279	1	0	0	0	0	1	0	0	0	3827	1580	55	2	1774	2	CPSF2	14	92624139	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	2190413	92624139	14725401	301	40060										
C14orf177	283598	hgsc.bcm.edu	37	chr14	99182534	99182534	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ttccagtacgactggatgcaTcggaaagagcctggggcaag	14	9	0	1	rs373583218|rs139827156	byFrequency	TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr14:99182534T>C	ENST00000325812.2	+	3	425	c.6T>C	c.(4-6)caT>caC	p.H2H		NM_182560.2	NP_872366.2	Q52M58	CN177_HUMAN	chromosome 14 open reading frame 177	2										endometrium(1)|kidney(1)|large_intestine(1)|lung(10)	13		Melanoma(154;0.128)				ACTGGATGCATCGGAAAGAGC	0.562																																					p.H2H		Atlas-SNP	.											.	C14orf177	37	.	0			c.T6C						.						66	52	57					14																	99182534		2203	4290	6493	SO:0001819	synonymous_variant	283598	exon3			GATGCATCGGAAA	AK098639	CCDS9948.1	14q32.2	2012-05-30			ENSG00000176605	ENSG00000176605			26375	protein-coding gene	gene with protein product						12477932	Standard	NM_182560		Approved	FLJ25773	uc001yfz.2	Q52M58	OTTHUMG00000167745	ENST00000325812.2:c.6T>C	chr14.hg19:g.99182534T>C		0.0	0.0		6.0	5.0	NM_182560	Q8N7D2	Silent	SNP	ENST00000325812.2	hg19	CCDS9948.1																																																																																			.	.		0.562	C14orf177-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396078.1	NM_182560		C	99182534	T	C	99182534	2	2	279	1	0	0	0	0	0	0	0	1	1762	1432	50	2		2	C14orf177	14	99182534	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	6558395	99182534	8167006	302	40061										
TYRO3	7301	hgsc.bcm.edu	37	chr15	41865543	41865543	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cagtgtgtgtggctgacttcGgactctcccggaagatctac	12	11	2	2	rs116540200	byFrequency	TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr15:41865543G>C	ENST00000263798.3	+	17	2247	c.2023G>C	c.(2023-2025)Gga>Cga	p.G675R	TYRO3_ENST00000559066.1_Missense_Mutation_p.G630R	NM_006293.3	NP_006284.2	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase	675	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic cell clearance (GO:0043277)|cell adhesion (GO:0007155)|forebrain cell migration (GO:0021885)|natural killer cell differentiation (GO:0001779)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|neuron cellular homeostasis (GO:0070050)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein autophosphorylation (GO:0046777)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.G675R(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(26)|ovary(3)|prostate(1)	43		all_cancers(109;7.33e-15)|all_epithelial(112;2.8e-12)|Lung NSC(122;3.48e-08)|all_lung(180;1.71e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.31e-18)|GBM - Glioblastoma multiforme(113;9.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.117)		GGCTGACTTCGGACTCTCCCG	0.587																																					p.G675R		Atlas-SNP	.											TYRO3_ENST00000263798,colon,carcinoma,0,3	TYRO3	169	.	1	Substitution - Missense(1)	stomach(1)	c.G2023C						.						192	196	194					15																	41865543		2203	4300	6503	SO:0001583	missense	7301	exon17			GACTTCGGACTCT	D50479	CCDS10080.1	15q15.1-q21.1	2013-02-11			ENSG00000092445	ENSG00000092445	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12446	protein-coding gene	gene with protein product		600341		RSE		7851890	Standard	NM_006293		Approved	Dtk, Brt, Tif, Sky	uc001zof.2	Q06418	OTTHUMG00000130341	ENST00000263798.3:c.2023G>C	chr15.hg19:g.41865543G>C	ENSP00000263798:p.Gly675Arg	112.0	0.0		102.0	35.0	NM_006293	O14953|Q86VR3	Missense_Mutation	SNP	ENST00000263798.3	hg19	CCDS10080.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.525914	0.85600	.	.	ENSG00000092445	ENST00000540218;ENST00000263798	D	0.92858	-3.12	5.55	5.55	0.83447	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.39475	N	0.001347	D	0.97794	0.9276	H	0.97465	4.01	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98903	1.0777	10	0.87932	D	0	-10.6616	19.5084	0.95130	0.0:0.0:1.0:0.0	.	675	Q06418	TYRO3_HUMAN	R	607;675	ENSP00000263798:G675R	ENSP00000263798:G675R	G	+	1	0	TYRO3	39652835	1.000000	0.71417	0.997000	0.53966	0.716000	0.41182	9.869000	0.99810	2.612000	0.88384	0.655000	0.94253	GGA	.	G|0.995;A|0.005		0.587	TYRO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252693.2			C	41865543	G	C	41865543	3	2	279	1	0	0	0	0	1	0	0	0	16829	1117	39	4	2089	4	TYRO3	15	41865543	Missense_Mutation	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10		41865543	60665849	303	40062										
CDAN1	146059	hgsc.bcm.edu	37	chr15	43027504	43027504	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gtcgctgtccttggcagtcaCcatcctccgggcagtgagga	13	13	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr15:43027504C>T	ENST00000356231.3	-	5	1035	c.1012G>A	c.(1012-1014)Gtg>Atg	p.V338M		NM_138477.2	NP_612486.2	Q8IWY9	CDAN1_HUMAN	codanin 1	338					chromatin assembly (GO:0031497)|chromatin organization (GO:0006325)|negative regulation of DNA replication (GO:0008156)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	24		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;2.49e-07)		TTGGCAGTCACCATCCTCCGG	0.498																																					p.V338M		Atlas-SNP	.											.	CDAN1	70	.	0			c.G1012A						.						35	36	36					15																	43027504		2203	4299	6502	SO:0001583	missense	146059	exon5			CAGTCACCATCCT	AF525398	CCDS32209.1	15q15.2	2012-04-25	2012-04-25			ENSG00000140326			1713	protein-coding gene	gene with protein product		607465	"congenital dyserythropoietic anemia, type I"			8634422, 12434312	Standard	XM_005254177		Approved	CDA-I, CDAI	uc001zql.3	Q8IWY9		ENST00000356231.3:c.1012G>A	chr15.hg19:g.43027504C>T	ENSP00000348564:p.Val338Met	53.0	0.0		60.0	4.0	NM_138477	Q6NYD0|Q7Z7L5|Q969N3	Missense_Mutation	SNP	ENST00000356231.3	hg19	CCDS32209.1	.	.	.	.	.	.	.	.	.	.	C	11.58	1.682221	0.29872	.	.	ENSG00000140326	ENST00000356231;ENST00000267892	D	0.86694	-2.16	5.94	2.57	0.30868	.	0.630111	0.16968	N	0.192216	T	0.74344	0.3704	N	0.22421	0.69	0.09310	N	1	B	0.24920	0.114	B	0.21708	0.036	T	0.63189	-0.6693	10	0.49607	T	0.09	-7.1626	2.866	0.05601	0.1811:0.5279:0.1245:0.1665	.	338	Q8IWY9	CDAN1_HUMAN	M	338;336	ENSP00000348564:V338M	ENSP00000267892:V336M	V	-	1	0	CDAN1	40814796	0.475000	0.25894	1.000000	0.80357	0.804000	0.45430	0.410000	0.21098	0.837000	0.34925	0.561000	0.74099	GTG	.	.		0.498	CDAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431103.1	XM_085300		T	43027504	C	T	43027504	3	4	279	1	0	0	0	0	1	0	0	0	3056	507	18	3	2767	3	CDAN1	15	43027504	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	1161961	43027504	59503888	304	40063										
CEP152	22995	hgsc.bcm.edu	37	chr15	49073394	49073394	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	taaaatattctttccataccTggtaactttggattttttcc	4	8	1	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr15:49073394T>C	ENST00000380950.2	-	12	1763	c.1576A>G	c.(1576-1578)Agc>Ggc	p.S526G	CEP152_ENST00000399334.3_Splice_Site_p.S526G|RP11-485O10.2_ENST00000558304.1_RNA|CEP152_ENST00000325747.5_Splice_Site_p.S433G	NM_001194998.1|NM_014985.3	NP_001181927.1|NP_055800.2	O94986	CE152_HUMAN	centrosomal protein 152kDa	526					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)			breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		TTTCCATACCTGGTAACTTTG	0.333																																					p.S526G		Atlas-SNP	.											.	CEP152	145	.	0			c.A1576G						.						79	76	77					15																	49073394		1804	4075	5879	SO:0001630	splice_region_variant	22995	exon12			CATACCTGGTAAC	AB020719	CCDS42033.1, CCDS58361.1	15q21.1	2014-02-20							29298	protein-coding gene	gene with protein product	"asterless"	613529	"microcephaly, primary autosomal recessive 4"	MCPH4		14654843, 21131973	Standard	NM_014985		Approved	KIAA0912, SCKL5	uc001zwz.3	O94986		ENST00000380950.2:c.1577+1A>G	chr15.hg19:g.49073394T>C		108.0	0.0		91.0	4.0	NM_014985	E7ER66|Q17RV1|Q6NTA0	Missense_Mutation	SNP	ENST00000380950.2	hg19	CCDS58361.1	.	.	.	.	.	.	.	.	.	.	T	15.38	2.816179	0.50527	.	.	ENSG00000103995	ENST00000380950;ENST00000325747;ENST00000399334;ENST00000541880	T;T;T	0.80653	-1.4;-1.4;-1.4	5.95	5.95	0.96441	.	0.290154	0.43919	D	0.000517	D	0.87152	0.6106	M	0.67953	2.075	0.37012	D	0.895795	D;D;D	0.76494	0.99;0.987;0.999	P;P;D	0.66602	0.789;0.768;0.945	D	0.86513	0.1811	10	0.21014	T	0.42	-5.2587	16.085	0.81038	0.0:0.0:0.0:1.0	.	433;526;526	O94986-1;E7ER66;O94986	.;.;CE152_HUMAN	G	526;433;526;526	ENSP00000370337:S526G;ENSP00000321000:S433G;ENSP00000382271:S526G	ENSP00000321000:S433G	S	-	1	0	CEP152	46860686	1.000000	0.71417	0.993000	0.49108	0.270000	0.26580	6.324000	0.72896	2.276000	0.75962	0.528000	0.53228	AGC	.	.		0.333	CEP152-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417365.1	NM_014985	Missense_Mutation	C	49073394	T	C	49073394	5	2	279	1	0	0	0	0	0	0	1	0	3250	1594	55	2	3448	2	CEP152	15	49073394	Splice_Site	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	6045890	49073394	53457998	305	40064										
MYO5A	4644	hgsc.bcm.edu	37	chr15	52605952	52605952	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	aatctggatggtttctagtgCgagggaagatgggttgaaag	16	3	2	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr15:52605952C>T	ENST00000399231.3	-	41	5752	c.5509G>A	c.(5509-5511)Gca>Aca	p.A1837T	MYO5A_ENST00000358212.6_Missense_Mutation_p.A1862T|MYO5A_ENST00000399233.2_Missense_Mutation_p.A1834T|MYO5A_ENST00000356338.6_Missense_Mutation_p.A1810T|MYO5A_ENST00000553916.1_Missense_Mutation_p.A1835T	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	1837					actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		GTTTCTAGTGCGAGGGAAGAT	0.488																																					p.A1837T		Atlas-SNP	.											.	MYO5A	145	.	0			c.G5509A						.						115	114	114					15																	52605952		1880	4120	6000	SO:0001583	missense	4644	exon41			CTAGTGCGAGGGA		CCDS42037.1, CCDS45262.1	15q21	2014-09-17	2006-09-29		ENSG00000197535	ENSG00000197535		"Myosins / Myosin superfamily : Class V"	7602	protein-coding gene	gene with protein product	"myosin, heavy polypeptide kinase", "myosin heavy chain 12", "myoxin", "myosin V"	160777	"myosin VA (heavy polypeptide 12, myoxin)"	MYH12		8188282, 8022818	Standard	NM_000259		Approved	MYO5, GS1, MYR12	uc002aby.2	Q9Y4I1	OTTHUMG00000137383	ENST00000399231.3:c.5509G>A	chr15.hg19:g.52605952C>T	ENSP00000382177:p.Ala1837Thr	74.0	0.0		70.0	4.0	NM_000259	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Missense_Mutation	SNP	ENST00000399231.3	hg19	CCDS42037.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.453929	0.84209	.	.	ENSG00000197535	ENST00000399231;ENST00000399229;ENST00000399233;ENST00000356338;ENST00000358212;ENST00000546028;ENST00000553916	D;D;D;D;D	0.86562	-2.08;-2.08;-2.12;-2.14;-2.08	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	D	0.87200	0.6118	N	0.11927	0.2	0.80722	D	1	B;B;D	0.89917	0.366;0.236;1.0	B;B;D	0.87578	0.05;0.024;0.998	T	0.82896	-0.0230	10	0.12430	T	0.62	.	20.1467	0.98079	0.0:1.0:0.0:0.0	.	567;1837;1810	B5LY56;Q9Y4I1;Q9Y4I1-2	.;MYO5A_HUMAN;.	T	1837;1344;1834;1810;1862;1440;1835	ENSP00000382177:A1837T;ENSP00000382179:A1834T;ENSP00000348693:A1810T;ENSP00000350945:A1862T;ENSP00000451109:A1835T	ENSP00000348693:A1810T	A	-	1	0	MYO5A	50393244	1.000000	0.71417	0.103000	0.21229	0.991000	0.79684	7.776000	0.85560	2.838000	0.97847	0.655000	0.94253	GCA	.	.		0.488	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259		T	52605952	C	T	52605952	3	4	279	1	0	0	0	0	1	0	0	0	10087	768	27	1	62	1	MYO5A	15	52605952	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	3532558	52605952	49925440	306	40065										
RNF111	54778	hgsc.bcm.edu	37	chr15	59377873	59377873	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gttagggaactgggaattgaAgctggagtgactgcagctac	15	6	0	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr15:59377873A>G	ENST00000557998.1	+	10	2726	c.2439A>G	c.(2437-2439)gaA>gaG	p.E813E	RNF111_ENST00000561186.1_Silent_p.E822E|RNF111_ENST00000434298.1_Silent_p.E822E|RNF111_ENST00000348370.4_Silent_p.E813E|RNF111_ENST00000559209.1_Silent_p.E822E	NM_001270530.1	NP_001257459.1	Q6ZNA4	RN111_HUMAN	ring finger protein 111	813					gene expression (GO:0010467)|pattern specification process (GO:0007389)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein polyubiquitination (GO:0000209)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|SUMO polymer binding (GO:0032184)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35				all cancers(107;0.194)		TGGGAATTGAAGCTGGAGTGA	0.433																																					p.E822E	NSCLC(72;983 1365 10746 34387 47081)	Atlas-SNP	.											.	RNF111	179	.	0			c.A2466G						.						151	126	135					15																	59377873		2192	4291	6483	SO:0001819	synonymous_variant	54778	exon10			AATTGAAGCTGGA	AL157474	CCDS10169.1, CCDS58365.1, CCDS58366.1	15q21	2013-01-09			ENSG00000157450	ENSG00000157450		"RING-type (C3HC4) zinc fingers"	17384	protein-coding gene	gene with protein product		605840				11298452	Standard	NM_017610		Approved	ARK, Arkadia, FLJ38008, DKFZP761D081	uc002aft.4	Q6ZNA4	OTTHUMG00000132716	ENST00000557998.1:c.2439A>G	chr15.hg19:g.59377873A>G		83.0	0.0		91.0	5.0	NM_001270528	C9JUS4|H0YN55|Q6P9A4|Q6ZMU2|Q7L428|Q7Z346|Q8N1P9|Q8WUA3|Q9NSR1	Silent	SNP	ENST00000557998.1	hg19	CCDS58366.1																																																																																			.	.		0.433	RNF111-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000416012.1	NM_017610		G	59377873	A	G	59377873	2	3	279	1	0	0	0	0	0	0	0	1	13440	69	3	2		2	RNF111	15	59377873	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	6771921	59377873	43153519	307	40066										
RORA	6095	hgsc.bcm.edu	37	chr15	60907095	60907095	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	agctctcaaataacgcacctTttctcaatgcagggagcaga	8	11	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr15:60907095T>C	ENST00000335670.6	-	2	297				RORA_ENST00000309157.4_Missense_Mutation_p.K90R|RP11-219B17.1_ENST00000558235.1_RNA|RORA_ENST00000261523.5_Intron|RP11-219B17.1_ENST00000559824.1_RNA|RORA_ENST00000560004.1_Intron	NM_134261.2	NP_599023.1	P35398	RORA_HUMAN	RAR-related orphan receptor A						angiogenesis (GO:0001525)|cellular response to hypoxia (GO:0071456)|cellular response to sterol (GO:0036315)|cerebellar granule cell precursor proliferation (GO:0021930)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|circadian regulation of gene expression (GO:0032922)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|muscle cell differentiation (GO:0042692)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|nitric oxide biosynthetic process (GO:0006809)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of cholesterol homeostasis (GO:2000188)|regulation of glucose metabolic process (GO:0010906)|regulation of macrophage activation (GO:0043030)|regulation of smoothened signaling pathway (GO:0008589)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription involved in cell fate commitment (GO:0060850)|regulation of transcription, DNA-templated (GO:0006355)|T-helper 17 cell differentiation (GO:0072539)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)|xenobiotic metabolic process (GO:0006805)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	direct ligand regulated sequence-specific DNA binding transcription factor activity (GO:0098531)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|oxysterol binding (GO:0008142)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator binding (GO:0001223)|transcription corepressor binding (GO:0001222)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	21						TAACGCACCTTTTCTCAATGC	0.418																																					p.K90R		Atlas-SNP	.											.	RORA	114	.	0			c.A269G						.						44	40	41					15																	60907095		2203	4300	6503	SO:0001627	intron_variant	6095	exon2			GCACCTTTTCTCA	U04897	CCDS10177.1, CCDS10178.1, CCDS10179.1, CCDS45271.1	15q21-q22	2013-01-16			ENSG00000069667	ENSG00000069667		"Nuclear hormone receptors"	10258	protein-coding gene	gene with protein product		600825				7926749	Standard	NM_134261		Approved	RZRA, ROR1, ROR2, ROR3, NR1F1	uc002agv.3	P35398	OTTHUMG00000132769	ENST00000335670.6:c.196+63760A>G	chr15.hg19:g.60907095T>C		103.0	0.0		77.0	4.0	NM_002943	P35397|P35399|P45445|Q495X4|Q96H83	Missense_Mutation	SNP	ENST00000335670.6	hg19	CCDS10177.1	.	.	.	.	.	.	.	.	.	.	T	0.007	-2.002097	0.00431	.	.	ENSG00000069667	ENST00000309157	D	0.94417	-3.42	3.93	-7.85	0.01192	.	.	.	.	.	T	0.81408	0.4816	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.69312	-0.5178	8	0.08599	T	0.76	.	1.6339	0.02738	0.2235:0.2635:0.3405:0.1726	.	90	P35398-3	.	R	90	ENSP00000309753:K90R	ENSP00000309753:K90R	K	-	2	0	RORA	58694387	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.706000	0.01895	-3.578000	0.00138	-1.339000	0.01253	AAA	.	.		0.418	RORA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256142.2			C	60907095	T	C	60907095	1	2	279	0	1	0	0	0	0	0	0	0	13543	1841	64	2		2	RORA	15	60907095	Intron	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	1529222	60907095	41624297	308	40067										
DAPK2	23604	hgsc.bcm.edu	37	chr15	64263741	64263741	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cttctgggccaggaaatcgaAgagctctcctccagacactc	9	14	2	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr15:64263741A>G	ENST00000457488.1	-	4	364	c.334T>C	c.(334-336)Ttc>Ctc	p.F112L	DAPK2_ENST00000261891.3_Missense_Mutation_p.F112L|DAPK2_ENST00000558069.1_Missense_Mutation_p.F112L|DAPK2_ENST00000558482.1_5'UTR	NM_014326.3	NP_055141.2	Q9UIK4	DAPK2_HUMAN	death-associated protein kinase 2	112	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				anoikis (GO:0043276)|apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|skin(1)|stomach(1)	11				LUAD - Lung adenocarcinoma(2;0.215)		AGGAAATCGAAGAGCTCTCCT	0.562																																					p.F112L		Atlas-SNP	.											.	DAPK2	31	.	0			c.T334C						.						61	55	57					15																	64263741		2203	4300	6503	SO:0001583	missense	23604	exon4			AATCGAAGAGCTC	AB018001	CCDS10188.1	15q22.1	2008-07-18			ENSG00000035664	ENSG00000035664			2675	protein-coding gene	gene with protein product						10376525	Standard	XM_005254265		Approved	DRP-1, MGC119312	uc002amr.3	Q9UIK4	OTTHUMG00000132947	ENST00000457488.1:c.334T>C	chr15.hg19:g.64263741A>G	ENSP00000408277:p.Phe112Leu	83.0	0.0		84.0	4.0	NM_014326	E9JGM7|O75892|Q24JS1	Missense_Mutation	SNP	ENST00000457488.1	hg19	CCDS10188.1	.	.	.	.	.	.	.	.	.	.	A	35	5.467607	0.96257	.	.	ENSG00000035664	ENST00000261891;ENST00000457488	T;T	0.65916	-0.18;-0.18	5.4	5.4	0.78164	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.066090	0.64402	N	0.000012	T	0.71400	0.3335	L	0.37630	1.12	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.83275	0.985;0.996	T	0.74671	-0.3587	10	0.87932	D	0	.	14.9034	0.70699	1.0:0.0:0.0:0.0	.	112;112	E9JGM7;Q9UIK4	.;DAPK2_HUMAN	L	112	ENSP00000261891:F112L;ENSP00000408277:F112L	ENSP00000261891:F112L	F	-	1	0	DAPK2	62050794	1.000000	0.71417	0.995000	0.50966	0.996000	0.88848	9.287000	0.95975	2.176000	0.68965	0.379000	0.24179	TTC	.	.		0.562	DAPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256479.1	NM_014326		G	64263741	A	G	64263741	3	3	279	1	0	0	0	0	1	0	0	0	4238	72	3	2	814	2	DAPK2	15	64263741	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	3356646	64263741	38267651	309	40068										
DPP8	54878	hgsc.bcm.edu	37	chr15	65772582	65772582	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ttatccagatgtctgttgttTcttcatagataattagtggc	8	6	3	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr15:65772582T>C	ENST00000341861.5	-	10	2902	c.1322A>G	c.(1321-1323)gAa>gGa	p.E441G	DPP8_ENST00000339244.5_Intron|DPP8_ENST00000300141.6_Missense_Mutation_p.E425G|DPP8_ENST00000358939.4_Missense_Mutation_p.E425G|DPP8_ENST00000321147.6_Missense_Mutation_p.E441G|DPP8_ENST00000559233.1_Missense_Mutation_p.E441G|DPP8_ENST00000321118.7_Missense_Mutation_p.E441G	NM_197960.2	NP_932064.1	Q6V1X1	DPP8_HUMAN	dipeptidyl-peptidase 8	441					immune response (GO:0006955)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(2)|endometrium(3)|large_intestine(11)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						GTCTGTTGTTTCTTCATAGAT	0.333																																					p.E441G		Atlas-SNP	.											.	DPP8	78	.	0			c.A1322G						.						88	79	82					15																	65772582		2201	4299	6500	SO:0001583	missense	54878	exon11			GTTGTTTCTTCAT	AF221634	CCDS10207.1, CCDS10208.1, CCDS10209.1, CCDS10210.1	15q22	2008-07-18	2006-01-12		ENSG00000074603	ENSG00000074603			16490	protein-coding gene	gene with protein product	"dipeptidyl peptidase VIII", "dipeptidyl peptidase IV-related protein-1", "prolyl dipeptidase DPP8"	606819	"dipeptidylpeptidase 8"			11012666	Standard	XM_005254500		Approved	DP8, DPRP1, MSTP141, FLJ14920, FLJ20283, MGC26191	uc002aox.3	Q6V1X1	OTTHUMG00000133150	ENST00000341861.5:c.1322A>G	chr15.hg19:g.65772582T>C	ENSP00000339208:p.Glu441Gly	84.0	0.0		57.0	4.0	NM_197960	Q7Z4C8|Q7Z4D3|Q7Z4E1|Q8IWG7|Q8NEM5|Q96JX1|Q9HBM2|Q9HBM3|Q9HBM4|Q9HBM5|Q9NXF4	Missense_Mutation	SNP	ENST00000341861.5	hg19	CCDS10207.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.666962	0.88251	.	.	ENSG00000074603	ENST00000341861;ENST00000358939;ENST00000300141;ENST00000321147;ENST00000321118;ENST00000395652	T;T;T;T;T;T	0.38401	1.14;1.14;1.14;1.14;1.14;1.14	5.67	5.67	0.87782	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.65873	0.2733	M	0.87971	2.92	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.78314	0.979;0.991;0.979;0.988	T	0.72830	-0.4174	10	0.87932	D	0	-28.5277	15.9054	0.79423	0.0:0.0:0.0:1.0	.	425;425;441;441	Q6V1X1-3;Q6V1X1-4;Q6V1X1-2;Q6V1X1	.;.;.;DPP8_HUMAN	G	441;425;425;441;441;441	ENSP00000339208:E441G;ENSP00000351817:E425G;ENSP00000300141:E425G;ENSP00000318111:E441G;ENSP00000316373:E441G;ENSP00000379013:E441G	ENSP00000300141:E425G	E	-	2	0	DPP8	63559635	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.163000	0.77524	2.157000	0.67596	0.533000	0.62120	GAA	.	.		0.333	DPP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256847.1	NM_017743		C	65772582	T	C	65772582	3	2	279	1	0	0	0	0	1	0	0	0	4734	1783	62	2	1418	2	DPP8	15	65772582	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	1508841	65772582	36758810	310	40069										
MYO9A	4649	hgsc.bcm.edu	37	chr15	72122595	72122595	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	atcagacacagaaggcaaccGaactacaacaggagacgatg	10	10	1	3	rs371514628		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr15:72122595G>A	ENST00000356056.5	-	40	7367	c.6895C>T	c.(6895-6897)Cgg>Tgg	p.R2299W	MYO9A_ENST00000424560.1_Missense_Mutation_p.R2370W|MYO9A_ENST00000444904.1_Missense_Mutation_p.R2280W|MYO9A_ENST00000564571.1_Missense_Mutation_p.R2299W	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	2299	Tail.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)			NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						GAAGGCAACCGAACTACAACA	0.488																																					p.R2299W		Atlas-SNP	.											MYO9A,colon,carcinoma,0,1	MYO9A	203	.	0			c.C6895T						.	G	TRP/ARG	1,4397	2.1+/-5.4	0,1,2198	134	126	128		6895	3.8	0.1	15		128	1,8593	1.2+/-3.3	0,1,4296	no	missense	MYO9A	NM_006901.2	101	0,2,6494	AA,AG,GG		0.0116,0.0227,0.0154	probably-damaging	2299/2549	72122595	2,12990	2199	4297	6496	SO:0001583	missense	4649	exon40			GCAACCGAACTAC	AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"Myosins / Myosin superfamily : Class IX"	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.6895C>T	chr15.hg19:g.72122595G>A	ENSP00000348349:p.Arg2299Trp	108.0	0.0		86.0	19.0	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	hg19	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	G	18.27	3.587506	0.66105	2.27E-4	1.16E-4	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904	D;D;D	0.85556	-1.99;-2.0;-1.98	4.73	3.79	0.43588	.	.	.	.	.	D	0.84763	0.5544	L	0.60455	1.87	0.09310	N	0.999996	D;D	0.67145	0.996;0.994	B;P	0.46049	0.425;0.502	T	0.77194	-0.2677	9	0.66056	D	0.02	.	13.8244	0.63342	0.0:0.2922:0.7078:0.0	.	2299;2063	B2RTY4;B2RTY4-5	MYO9A_HUMAN;.	W	2299;2370;2280	ENSP00000348349:R2299W;ENSP00000399162:R2370W;ENSP00000398250:R2280W	ENSP00000348349:R2299W	R	-	1	2	MYO9A	69909649	0.995000	0.38212	0.088000	0.20740	0.981000	0.71138	4.128000	0.57951	1.324000	0.45282	0.655000	0.94253	CGG	.	.		0.488	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901		A	72122595	G	A	72122595	3	1	279	1	0	0	0	0	1	0	0	0	10093	1057	37	1	763	1	MYO9A	15	72122595	Missense_Mutation	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	6350013	72122595	30408797	311	40070										
NEIL1	79661	hgsc.bcm.edu	37	chr15	75641528	75641528	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gtgccccgcgaggagctgccAcgccatgcccacctgcgctt	12	18	0	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr15:75641528A>G	ENST00000564784.1	+	3	911	c.282A>G	c.(280-282)ccA>ccG	p.P94P	NEIL1_ENST00000355059.4_Silent_p.P94P|NEIL1_ENST00000567959.1_Intron|NEIL1_ENST00000569035.1_Silent_p.P94P			Q96FI4	NEIL1_HUMAN	nei endonuclease VIII-like 1 (E. coli)	94					base-excision repair (GO:0006284)|negative regulation of nuclease activity (GO:0032074)|nucleotide-excision repair (GO:0006289)|response to oxidative stress (GO:0006979)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|hydrolase activity, acting on glycosyl bonds (GO:0016798)|protein C-terminus binding (GO:0008022)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|large_intestine(4)|lung(4)|ovary(1)	13						AGGAGCTGCCACGCCATGCCC	0.697								Base excision repair (BER), DNA glycosylases																													p.P180P		Atlas-SNP	.											.	NEIL1	36	.	0			c.A540G						.						31	31	31					15																	75641528		2195	4291	6486	SO:0001819	synonymous_variant	79661	exon2			GCTGCCACGCCAT	AK026055	CCDS10278.1	15q33.33	2008-07-18			ENSG00000140398	ENSG00000140398			18448	protein-coding gene	gene with protein product		608844				11904416	Standard	NM_024608		Approved	FLJ22402, hFPG1, NEI1, FPG1	uc002bae.4	Q96FI4	OTTHUMG00000142821	ENST00000564784.1:c.282A>G	chr15.hg19:g.75641528A>G		51.0	0.0		47.0	4.0	NM_001256552	D3DW75|Q6ZRA7|Q86XW7|Q9H6C3	Silent	SNP	ENST00000564784.1	hg19	CCDS10278.1	.	.	.	.	.	.	.	.	.	.	A	7.715	0.696046	0.15106	.	.	ENSG00000140398	ENST00000336572	.	.	.	5.4	-8.43	0.00953	.	.	.	.	.	T	0.48874	0.1524	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58983	-0.7539	5	0.48119	T	0.1	-17.2927	4.304	0.10938	0.1303:0.5039:0.1992:0.1666	.	.	.	.	A	80	.	ENSP00000338328:T80A	T	+	1	0	NEIL1	73428581	0.002000	0.14202	0.646000	0.29493	0.585000	0.36419	-1.219000	0.02973	-1.252000	0.02491	0.459000	0.35465	ACG	.	.		0.697	NEIL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419885.1	NM_024608		G	75641528	A	G	75641528	2	3	279	1	0	0	0	0	0	0	0	1	10327	146	6	2		2	NEIL1	15	75641528	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	3518933	75641528	26889864	312	40071										
AKAP13	11214	hgsc.bcm.edu	37	chr15	86123972	86123972	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	aatatcaaggggaacactgaCtcttccctgcaaagtgtggg	11	9	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr15:86123972C>T	ENST00000394518.2	+	7	2768	c.2673C>T	c.(2671-2673)gaC>gaT	p.D891D	RP11-815J21.2_ENST00000561409.1_RNA|AKAP13_ENST00000361243.2_Silent_p.D891D	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	891					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						GGAACACTGACTCTTCCCTGC	0.512																																					p.D891D	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.C2673T						.						71	70	70					15																	86123972		2202	4299	6501	SO:0001819	synonymous_variant	11214	exon7			CACTGACTCTTCC	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"A-kinase anchor proteins", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	371	protein-coding gene	gene with protein product		604686	"lymphoid blast crisis oncogene"	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.2673C>T	chr15.hg19:g.86123972C>T		92.0	0.0		73.0	10.0	NM_007200	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Silent	SNP	ENST00000394518.2	hg19	CCDS32319.1																																																																																			.	.		0.512	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200		T	86123972	C	T	86123972	2	4	279	1	0	0	0	0	0	0	0	1	449	564	20	3		3	AKAP13	15	86123972	Silent	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	10482444	86123972	16407420	313	40072										
LRRK1	79705	hgsc.bcm.edu	37	chr15	101606304	101606304	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tacatacgcccggtgctgccTccgacaggtctgagcatgac	11	14	1	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr15:101606304T>C	ENST00000388948.3	+	32	6021	c.5662T>C	c.(5662-5664)Tcc>Ccc	p.S1888P	RP11-505E24.2_ENST00000559857.1_RNA|LRRK1_ENST00000284395.5_Missense_Mutation_p.S1885P|LRRK1_ENST00000532145.1_3'UTR	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1											breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			CGGTGCTGCCTCCGACAGGTC	0.617																																					p.S1888P		Atlas-SNP	.											.	LRRK1	310	.	0			c.T5662C						.						98	106	104					15																	101606304		2146	4265	6411	SO:0001583	missense	79705	exon32			GCTGCCTCCGACA	AB058693	CCDS42086.1	15q26.3	2007-01-29			ENSG00000154237	ENSG00000154237			18608	protein-coding gene	gene with protein product		610986				11347906, 14654223	Standard	XM_005254979		Approved	FLJ23119, KIAA1790, Roco1, RIPK6	uc002bwr.3	Q38SD2	OTTHUMG00000165514	ENST00000388948.3:c.5662T>C	chr15.hg19:g.101606304T>C	ENSP00000373600:p.Ser1888Pro	115.0	0.0		116.0	5.0	NM_024652		Missense_Mutation	SNP	ENST00000388948.3	hg19	CCDS42086.1	.	.	.	.	.	.	.	.	.	.	T	5.022	0.189800	0.09547	.	.	ENSG00000154237	ENST00000388948;ENST00000284395;ENST00000529762;ENST00000542170	T;T	0.74526	-0.82;-0.85	5.35	2.98	0.34508	.	0.699658	0.14725	N	0.302133	T	0.64713	0.2623	L	0.48362	1.52	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.51795	-0.8660	10	0.33141	T	0.24	.	8.1976	0.31407	0.0:0.2877:0.0:0.7123	.	1888	Q38SD2	LRRK1_HUMAN	P	1888;1885;579;442	ENSP00000373600:S1888P;ENSP00000284395:S1885P	ENSP00000284395:S1885P	S	+	1	0	LRRK1	99423827	0.001000	0.12720	0.008000	0.14137	0.369000	0.29798	0.437000	0.21543	0.319000	0.23209	0.533000	0.62120	TCC	.	.		0.617	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652		C	101606304	T	C	101606304	3	2	279	1	0	0	0	0	1	0	0	0	9041	1551	54	2	5784	2	LRRK1	15	101606304	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	15482332	101606304	925088	314	40073										
CHSY1	22856	hgsc.bcm.edu	37	chr15	101717856	101717856	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gtccacatcctccagcccccAgccttggatggaaacatcaa	7	16	1	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr15:101717856A>G	ENST00000254190.3	-	3	2621	c.2146T>C	c.(2146-2148)Tgg>Cgg	p.W716R	CHSY1_ENST00000543813.1_5'UTR	NM_014918.4	NP_055733.2	Q86X52	CHSS1_HUMAN	chondroitin sulfate synthase 1	716					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|negative regulation of ossification (GO:0030279)|response to nutrient levels (GO:0031667)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(5)|skin(1)	24	Lung NSC(78;0.00217)|all_lung(78;0.00271)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			TCCAGCCCCCAGCCTTGGATG	0.498																																					p.W716R		Atlas-SNP	.											.	CHSY1	60	.	0			c.T2146C						.						102	104	103					15																	101717856		2203	4300	6503	SO:0001583	missense	22856	exon3			GCCCCCAGCCTTG	AB023207	CCDS10390.1	15q26.3	2013-02-19	2008-01-24	2008-01-24	ENSG00000131873	ENSG00000131873	2.4.1.175, 2.4.1.226	"Beta 3-glycosyltransferases", "Beta 4-glycosyltransferases"	17198	protein-coding gene	gene with protein product		608183	"carbohydrate (chondroitin) synthase 1"			11514575	Standard	NM_014918		Approved	KIAA0990, CSS1	uc021sxt.1	Q86X52	OTTHUMG00000149873	ENST00000254190.3:c.2146T>C	chr15.hg19:g.101717856A>G	ENSP00000254190:p.Trp716Arg	106.0	0.0		88.0	4.0	NM_014918	Q6UX38|Q7LFU5|Q9Y2J5	Missense_Mutation	SNP	ENST00000254190.3	hg19	CCDS10390.1	.	.	.	.	.	.	.	.	.	.	A	19.38	3.815849	0.70912	.	.	ENSG00000131873	ENST00000254190;ENST00000543813	T	0.40476	1.03	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.71643	0.3364	M	0.91354	3.2	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75816	-0.3184	10	0.39692	T	0.17	-32.6771	16.2588	0.82530	1.0:0.0:0.0:0.0	.	716	Q86X52	CHSS1_HUMAN	R	716;444	ENSP00000254190:W716R	ENSP00000254190:W716R	W	-	1	0	CHSY1	99535379	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.107000	0.94261	2.243000	0.73865	0.459000	0.35465	TGG	.	.		0.498	CHSY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313624.1	NM_014918		G	101717856	A	G	101717856	3	3	279	1	0	0	0	0	1	0	0	0	3414	188	7	2	266	2	CHSY1	15	101717856	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	111552	101717856	813536	315	40074										
TARSL2	123283	hgsc.bcm.edu	37	chr15	102224289	102224289	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	attgtttacctgctccactgTgcaaaaaatgtgagcatcgt	8	9	0	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr15:102224289T>A	ENST00000335968.3	-	12	1855	c.1639A>T	c.(1639-1641)Aca>Tca	p.T547S	snoU13_ENST00000458877.1_RNA	NM_152334.2	NP_689547.2	A2RTX5	SYTC2_HUMAN	threonyl-tRNA synthetase-like 2	547					threonyl-tRNA aminoacylation (GO:0006435)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|threonine-tRNA ligase activity (GO:0004829)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(14)|ovary(2)|skin(1)|urinary_tract(1)	29	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000268)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			TGCTCCACTGTGCAAAAAATG	0.473																																					p.T547S		Atlas-SNP	.											.	TARSL2	63	.	0			c.A1639T						.						97	81	87					15																	102224289		2203	4300	6503	SO:0001583	missense	123283	exon12			CCACTGTGCAAAA	AL833188	CCDS10394.1	15q26.3	2008-02-05			ENSG00000185418	ENSG00000185418			24728	protein-coding gene	gene with protein product							Standard	NM_152334		Approved	FLJ25005	uc002bxm.3	A2RTX5	OTTHUMG00000149869	ENST00000335968.3:c.1639A>T	chr15.hg19:g.102224289T>A	ENSP00000338093:p.Thr547Ser	154.0	0.0		153.0	43.0	NM_152334	B2RMP7|Q6B0A1|Q6IS76|Q96LW3|Q96MP4	Missense_Mutation	SNP	ENST00000335968.3	hg19	CCDS10394.1	.	.	.	.	.	.	.	.	.	.	T	15.70	2.911377	0.52439	.	.	ENSG00000185418	ENST00000335968;ENST00000333018;ENST00000539112	T;T	0.68025	-0.3;-0.3	5.46	5.46	0.80206	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (G/ H/ P/ S), conserved domain (1);	0.280684	0.39274	N	0.001410	T	0.66597	0.2805	M	0.76433	2.335	0.36599	D	0.874548	B;B	0.24092	0.002;0.097	B;B	0.22880	0.042;0.028	T	0.70252	-0.4923	10	0.42905	T	0.14	-5.2204	13.4859	0.61366	0.0:0.0:0.0:1.0	.	547;452	A2RTX5;A2RTX5-2	SYTC2_HUMAN;.	S	547;452;547	ENSP00000338093:T547S;ENSP00000439899:T547S	ENSP00000329291:T452S	T	-	1	0	TARSL2	100041812	1.000000	0.71417	0.995000	0.50966	0.996000	0.88848	2.050000	0.41297	2.079000	0.62486	0.482000	0.46254	ACA	.	.		0.473	TARSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313619.3	NM_152334		A	102224289	T	A	102224289	3	1	279	1	0	0	0	0	1	0	0	0	15576	1696	59	4	801	4	TARSL2	15	102224289	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	506433	102224289	307103	316	40075										
SSTR5	6755	hgsc.bcm.edu	37	chr16	1129760	1129760	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tcctctcctacgccaacagcTgtgccaaccccgtcctctac	5	20	2	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr16:1129760T>C	ENST00000293897.4	+	1	980	c.892T>C	c.(892-894)Tgt>Cgt	p.C298R	SSTR5_ENST00000397547.2_Missense_Mutation_p.C298R|SSTR5-AS1_ENST00000569832.1_RNA|SSTR5_ENST00000562758.1_Intron	NM_001053.3	NP_001044.1	P35346	SSR5_HUMAN	somatostatin receptor 5	298					G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose homeostasis (GO:0042593)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cytokinesis (GO:0032467)|regulation of insulin secretion (GO:0050796)|somatostatin signaling pathway (GO:0038170)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			endometrium(2)|lung(5)|prostate(1)|skin(1)	9		Hepatocellular(780;0.00369)			Octreotide(DB00104)|Pasireotide(DB06663)|Vapreotide(DB04894)	CGCCAACAGCTGTGCCAACCC	0.627																																					p.C298R		Atlas-SNP	.											.	SSTR5	36	.	0			c.T892C						.						90	89	89					16																	1129760		2197	4295	6492	SO:0001583	missense	6755	exon2			AACAGCTGTGCCA	D16827	CCDS10429.1	16p13.3	2012-08-08			ENSG00000162009	ENSG00000162009		"GPCR / Class A : Somatostatin receptors"	11334	protein-coding gene	gene with protein product		182455				7607700	Standard	NM_001053		Approved		uc021taf.1	P35346	OTTHUMG00000047842	ENST00000293897.4:c.892T>C	chr16.hg19:g.1129760T>C	ENSP00000293897:p.Cys298Arg	90.0	0.0		110.0	6.0	NM_001172560	P34988|Q541E0|Q9UJI5	Missense_Mutation	SNP	ENST00000293897.4	hg19	CCDS10429.1	.	.	.	.	.	.	.	.	.	.	T	14.59	2.582252	0.46006	.	.	ENSG00000162009	ENST00000397547;ENST00000293897	T;T	0.42131	0.98;0.98	4.76	4.76	0.60689	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.78648	0.4316	H	0.99347	4.525	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.87274	0.2288	10	0.87932	D	0	.	13.4447	0.61134	0.0:0.0:0.0:1.0	.	298	P35346	SSR5_HUMAN	R	298	ENSP00000380680:C298R;ENSP00000293897:C298R	ENSP00000293897:C298R	C	+	1	0	SSTR5	1069761	1.000000	0.71417	0.994000	0.49952	0.068000	0.16541	7.813000	0.86123	1.786000	0.52430	0.459000	0.35465	TGT	.	.		0.627	SSTR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420836.1			C	1129760	T	C	1129760	3	2	279	1	0	0	0	0	1	0	0	0	15216	1580	55	2	894	2	SSTR5	16	1129760	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10		1129760	89224993	317	40076										
C16orf73	254528	hgsc.bcm.edu	37	chr16	1884295	1884295	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	agacaagtttctgcttgcctCagtaggatctgcaagcttgc	10	10	3	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr16:1884295C>T	ENST00000397344.3	-	13	1485	c.1291G>A	c.(1291-1293)Gag>Aag	p.E431K	FAHD1_ENST00000382668.4_Intron|MEIOB_ENST00000325962.3_Missense_Mutation_p.E460K|MEIOB_ENST00000412554.2_Missense_Mutation_p.E460K|FAHD1_ENST00000382666.4_Intron|MEIOB_ENST00000452149.2_Missense_Mutation_p.E431K|MEIOB_ENST00000470044.1_Missense_Mutation_p.E253K	NM_152764.2	NP_689977.2	Q8N635	MEIOB_HUMAN	meiosis specific with OB domains	431					double-strand break repair via homologous recombination (GO:0000724)|female meiosis I (GO:0007144)|fertilization (GO:0009566)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|resolution of meiotic recombination intermediates (GO:0000712)|synapsis (GO:0007129)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|single-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008310)|single-stranded DNA binding (GO:0003697)										CTGCTTGCCTCAGTAGGATCT	0.383																																					p.E460K		Atlas-SNP	.											.	.	.	.	0			c.G1378A						.						103	98	100					16																	1884295		2199	4300	6499	SO:0001583	missense	254528	exon14			TTGCCTCAGTAGG	BC029829	CCDS10449.2, CCDS53983.1	16p13.3	2012-08-13	2012-08-13	2012-08-13	ENSG00000162039	ENSG00000162039			28569	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 73"	C16orf73		12477932	Standard	NM_152764		Approved	MGC35212	uc010uvq.1	Q8N635	OTTHUMG00000128683	ENST00000397344.3:c.1291G>A	chr16.hg19:g.1884295C>T	ENSP00000380504:p.Glu431Lys	102.0	0.0		84.0	4.0	NM_001163560	B1AK39|C9J0S1|Q96RY0	Missense_Mutation	SNP	ENST00000397344.3	hg19	CCDS10449.2	.	.	.	.	.	.	.	.	.	.	C	18.16	3.561340	0.65538	.	.	ENSG00000162039	ENST00000412554;ENST00000452149;ENST00000325962;ENST00000397344	T;T;T;T	0.10860	2.83;2.83;2.83;2.83	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.33411	0.0862	M	0.70595	2.14	0.45607	D	0.998541	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.00534	-1.1684	10	0.42905	T	0.14	.	17.0244	0.86441	0.0:1.0:0.0:0.0	.	460;431	C9J0S1;Q8N635	.;CP073_HUMAN	K	460;431;460;431	ENSP00000390778:E460K;ENSP00000391033:E431K;ENSP00000314484:E460K;ENSP00000380504:E431K	ENSP00000314484:E460K	E	-	1	0	C16orf73	1824296	0.997000	0.39634	0.946000	0.38457	0.071000	0.16799	4.624000	0.61254	2.715000	0.92844	0.585000	0.79938	GAG	.	.		0.383	MEIOB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250580.1	NM_152764		T	1884295	C	T	1884295	3	4	279	1	0	0	0	0	1	0	0	0	1834	835	29	3	41	3	C16orf73	16	1884295	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	754535	1884295	88470458	318	40077										
EMP2	2013	hgsc.bcm.edu	37	chr16	10626827	10626827	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ggtgcaggcgaaggccacccAcgccaggatgtaggagtagc	16	11	0	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr16:10626827A>G	ENST00000359543.3	-	5	648	c.439T>C	c.(439-441)Tgg>Cgg	p.W147R	EMP2_ENST00000536829.1_Missense_Mutation_p.W147R|EMP2_ENST00000566033.1_5'Flank|RP11-27M24.1_ENST00000535363.1_RNA	NM_001424.4	NP_001415.1	P54851	EMP2_HUMAN	epithelial membrane protein 2	147					cell proliferation (GO:0008283)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|regulation of glomerular filtration (GO:0003093)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	integrin binding (GO:0005178)			NS(1)|endometrium(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	6						AAGGCCACCCACGCCAGGATG	0.527																																					p.W147R	GBM(158;2021 2691 14714 39478)	Atlas-SNP	.											.	EMP2	21	.	0			c.T439C						.						144	114	124					16																	10626827		2197	4300	6497	SO:0001583	missense	2013	exon5			CCACCCACGCCAG	U52100	CCDS10541.1	16p13.2	2008-08-01			ENSG00000213853	ENSG00000213853			3334	protein-coding gene	gene with protein product		602334				8996089, 10331954, 16216233	Standard	NM_001424		Approved	XMP	uc002czx.3	P54851	OTTHUMG00000129752	ENST00000359543.3:c.439T>C	chr16.hg19:g.10626827A>G	ENSP00000352540:p.Trp147Arg	60.0	0.0		69.0	4.0	NM_001424	B2R7V6|D3DUF8	Missense_Mutation	SNP	ENST00000359543.3	hg19	CCDS10541.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.294020	0.81025	.	.	ENSG00000213853	ENST00000359543;ENST00000536829	D;D	0.93426	-3.22;-3.22	5.37	4.27	0.50696	.	0.000000	0.85682	U	0.000000	D	0.96725	0.8931	M	0.89214	3.015	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.96464	0.9343	10	0.66056	D	0.02	-8.3053	11.2492	0.49015	0.8631:0.0:0.0:0.1369	.	147	P54851	EMP2_HUMAN	R	147	ENSP00000352540:W147R;ENSP00000445712:W147R	ENSP00000352540:W147R	W	-	1	0	EMP2	10534328	1.000000	0.71417	0.993000	0.49108	0.963000	0.63663	8.779000	0.91792	0.968000	0.38212	0.533000	0.62120	TGG	.	.		0.527	EMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251965.1	NM_001424		G	10626827	A	G	10626827	3	3	279	1	0	0	0	0	1	0	0	0	5104	159	6	2	68	2	EMP2	16	10626827	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	8742532	10626827	79727926	319	40078										
TEKT5	146279	hgsc.bcm.edu	37	chr16	10783830	10783830	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ttttctccacgttgtcatggAccaaatcaatcccaatcctc	4	14	3	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr16:10783830A>G	ENST00000283025.2	-	2	688	c.617T>C	c.(616-618)gTc>gCc	p.V206A	RP11-109M19.1_ENST00000576710.1_RNA	NM_144674.1	NP_653275.1	Q96M29	TEKT5_HUMAN	tektin 5	206						cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)	34						GTTGTCATGGACCAAATCAAT	0.517																																					p.V206A		Atlas-SNP	.											.	TEKT5	66	.	0			c.T617C						.						114	97	103					16																	10783830		2197	4300	6497	SO:0001583	missense	146279	exon2			TCATGGACCAAAT		CCDS10542.1	16p13.13	2014-01-21			ENSG00000153060	ENSG00000153060			26554	protein-coding gene	gene with protein product							Standard	NM_144674		Approved	FLJ32871, CT149	uc002czz.1	Q96M29	OTTHUMG00000129750	ENST00000283025.2:c.617T>C	chr16.hg19:g.10783830A>G	ENSP00000283025:p.Val206Ala	101.0	0.0		98.0	4.0	NM_144674	A1L3Z3	Missense_Mutation	SNP	ENST00000283025.2	hg19	CCDS10542.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.553462	0.86127	.	.	ENSG00000153060	ENST00000283025	T	0.05139	3.49	5.22	5.22	0.72569	.	0.000000	0.56097	D	0.000033	T	0.30978	0.0782	M	0.90082	3.085	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.20107	-1.0285	10	0.87932	D	0	-51.5563	13.3635	0.60669	1.0:0.0:0.0:0.0	.	206	Q96M29	TEKT5_HUMAN	A	206	ENSP00000283025:V206A	ENSP00000283025:V206A	V	-	2	0	TEKT5	10691331	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	8.622000	0.90953	2.088000	0.63022	0.533000	0.62120	GTC	.	.		0.517	TEKT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251963.1	NM_144674		G	10783830	A	G	10783830	3	3	279	1	0	0	0	0	1	0	0	0	15771	275	10	2	864	2	TEKT5	16	10783830	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	157003	10783830	79570923	320	40079										
DCUN1D3	123879	hgsc.bcm.edu	37	chr16	20871607	20871607	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	aatttatcctcttgtttggcTtctgttaagaggctagggaa	10	6	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr16:20871607T>A	ENST00000324344.4	-	3	801	c.516A>T	c.(514-516)gaA>gaT	p.E172D	ERI2_ENST00000564349.1_Intron|DCUN1D3_ENST00000563934.1_Missense_Mutation_p.E172D	NM_173475.2	NP_775746.1	Q8IWE4	DCNL3_HUMAN	DCN1, defective in cullin neddylation 1, domain containing 3	172	DCUN1. {ECO:0000255|PROSITE- ProRule:PRU00574}.				negative regulation of cell growth (GO:0030308)|positive regulation of apoptotic process (GO:0043065)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)	perinuclear region of cytoplasm (GO:0048471)				NS(2)|breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|ovary(2)	14				GBM - Glioblastoma multiforme(48;0.249)		CTTGTTTGGCTTCTGTTAAGA	0.468																																					p.E172D		Atlas-SNP	.											.	DCUN1D3	29	.	0			c.A516T						.						98	99	99					16																	20871607		2201	4300	6501	SO:0001583	missense	123879	exon3			TTTGGCTTCTGTT	BC040442	CCDS10592.1	16p12.3	2013-06-10	2013-06-10		ENSG00000188215	ENSG00000188215			28734	protein-coding gene	gene with protein product			"DCN1, defective in cullin neddylation 1, domain containing 3 (S. cerevisiae)"			15988528	Standard	NM_173475		Approved	MGC48972, FLJ41725, DKFZp686O0290	uc002dhz.3	Q8IWE4	OTTHUMG00000131553	ENST00000324344.4:c.516A>T	chr16.hg19:g.20871607T>A	ENSP00000319482:p.Glu172Asp	71.0	0.0		79.0	4.0	NM_173475	B3KVY4	Missense_Mutation	SNP	ENST00000324344.4	hg19	CCDS10592.1	.	.	.	.	.	.	.	.	.	.	T	13.44	2.237801	0.39598	.	.	ENSG00000188215	ENST00000324344	.	.	.	5.92	5.92	0.95590	Domain of unknown function DUF298 (2);	0.089651	0.85682	D	0.000000	T	0.53594	0.1806	L	0.41079	1.255	0.47621	D	0.999479	B	0.22480	0.07	B	0.24974	0.057	T	0.49485	-0.8935	9	0.29301	T	0.29	-19.5782	12.8313	0.57748	0.0:0.0:0.136:0.864	.	172	Q8IWE4	DCNL3_HUMAN	D	172	.	ENSP00000319482:E172D	E	-	3	2	DCUN1D3	20779108	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.274000	0.51631	2.274000	0.75844	0.533000	0.62120	GAA	.	.		0.468	DCUN1D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254415.2	NM_173475		A	20871607	T	A	20871607	3	1	279	1	0	0	0	0	1	0	0	0	4317	1606	56	4	402	4	DCUN1D3	16	20871607	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	10087777	20871607	69483146	321	40080										
TAOK2	9344	hgsc.bcm.edu	37	chr16	29998852	29998852	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gcatatctcgactctggttgCgggttctgctgcgcctgtca	12	12	4	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr16:29998852C>T	ENST00000308893.4	+	16	4302	c.3259C>T	c.(3259-3261)Cgg>Tgg	p.R1087W	TAOK2_ENST00000416441.2_Missense_Mutation_p.R914W|TAOK2_ENST00000543033.1_Missense_Mutation_p.R974W|TAOK2_ENST00000279394.3_Intron	NM_001252043.1|NM_016151.3	NP_001238972.1|NP_057235.2	Q9UL54	TAOK2_HUMAN	TAO kinase 2	1087					actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|focal adhesion assembly (GO:0048041)|G2 DNA damage checkpoint (GO:0031572)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein targeting to membrane (GO:0006612)|regulation of cell growth (GO:0001558)|regulation of cell shape (GO:0008360)|response to stress (GO:0006950)|stress-activated MAPK cascade (GO:0051403)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleolus (GO:0005730)|nucleus (GO:0005634)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|mitogen-activated protein kinase kinase binding (GO:0031434)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(3)|skin(1)	22						ACTCTGGTTGCGGGTTCTGCT	0.677																																					p.R1087W		Atlas-SNP	.											.	TAOK2	142	.	0			c.C3259T						.						41	51	48					16																	29998852		2196	4299	6495	SO:0001583	missense	9344	exon16			TGGTTGCGGGTTC	AB020688	CCDS10662.1, CCDS10663.1, CCDS58448.1	16p11.2	2008-02-05			ENSG00000149930	ENSG00000149930			16835	protein-coding gene	gene with protein product		613199				10048485, 9786855	Standard	NM_016151		Approved	TAO1, KIAA0881, PSK, PSK1, TAO2, MAP3K17	uc002dva.2	Q9UL54	OTTHUMG00000132111	ENST00000308893.4:c.3259C>T	chr16.hg19:g.29998852C>T	ENSP00000310094:p.Arg1087Trp	76.0	0.0		73.0	31.0	NM_016151	A5PKY1|A7MCZ2|B2RN35|B7ZM88|O94957|Q6UW73|Q7LC09|Q9NSW2	Missense_Mutation	SNP	ENST00000308893.4	hg19	CCDS10663.1	.	.	.	.	.	.	.	.	.	.	C	11.98	1.799342	0.31869	.	.	ENSG00000149930	ENST00000308893;ENST00000543033	T;T	0.75154	-0.86;-0.91	4.8	1.65	0.23941	.	0.342835	0.21289	N	0.077017	T	0.52773	0.1755	N	0.19112	0.55	0.32969	D	0.522131	B;B;B	0.22983	0.002;0.078;0.002	B;B;B	0.18871	0.001;0.023;0.001	T	0.48969	-0.8987	9	.	.	.	.	6.6163	0.22778	0.3142:0.6002:0.0:0.0856	.	1278;914;1087	Q86V37;Q9UL54-3;Q9UL54	.;.;TAOK2_HUMAN	W	1087;974	ENSP00000310094:R1087W;ENSP00000440336:R974W	.	R	+	1	2	TAOK2	29906353	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	1.055000	0.30467	0.208000	0.20626	0.563000	0.77884	CGG	.	.		0.677	TAOK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255152.2	NM_016151		T	29998852	C	T	29998852	3	4	279	1	0	0	0	0	1	0	0	0	15563	759	27	1	3317	1	TAOK2	16	29998852	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	9127245	29998852	60355901	322	40081										
PHKB	5257	hgsc.bcm.edu	37	chr16	47695696	47695696	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tcaaaagagaaggccccaacTtcatcacaaaggaaggtaag	9	9	3	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr16:47695696T>C	ENST00000323584.5	+	23	2287	c.2263T>C	c.(2263-2265)Ttc>Ctc	p.F755L	PHKB_ENST00000566044.1_Missense_Mutation_p.F748L|PHKB_ENST00000299167.8_Missense_Mutation_p.F755L|PHKB_ENST00000455779.1_Missense_Mutation_p.F748L	NM_000293.2	NP_000284.1	Q93100	KPBB_HUMAN	phosphorylase kinase, beta	755					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|liver(1)|lung(18)|ovary(1)|skin(1)	41		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				AGGCCCCAACTTCATCACAAA	0.423																																					p.F755L		Atlas-SNP	.											.	PHKB	298	.	0			c.T2263C						.						113	108	109					16																	47695696		2201	4300	6501	SO:0001583	missense	5257	exon23			CCCAACTTCATCA		CCDS10729.1, CCDS42161.1	16q12-q13	2009-07-10			ENSG00000102893	ENSG00000102893	2.7.11.19		8927	protein-coding gene	gene with protein product		172490					Standard	NM_000293		Approved		uc002eev.4	Q93100	OTTHUMG00000133102	ENST00000323584.5:c.2263T>C	chr16.hg19:g.47695696T>C	ENSP00000313504:p.Phe755Leu	95.0	0.0		82.0	4.0	NM_000293	Q8N4T5	Missense_Mutation	SNP	ENST00000323584.5	hg19	CCDS10729.1	.	.	.	.	.	.	.	.	.	.	T	29.1	4.974914	0.92919	.	.	ENSG00000102893	ENST00000299167;ENST00000455779;ENST00000323584	D;D	0.91011	-2.76;-2.77	6.07	6.07	0.98685	Glycoside hydrolase 15-related (1);	0.097902	0.64402	D	0.000001	D	0.93278	0.7858	M	0.61703	1.905	0.80722	D	1	P;D	0.65815	0.568;0.995	P;P	0.58721	0.627;0.844	D	0.92362	0.5898	10	0.36615	T	0.2	-22.3124	16.6407	0.85098	0.0:0.0:0.0:1.0	.	755;748	Q93100;Q93100-4	KPBB_HUMAN;.	L	748;748;755	ENSP00000414345:F748L;ENSP00000313504:F755L	ENSP00000299167:F748L	F	+	1	0	PHKB	46253197	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.862000	0.69560	2.326000	0.78906	0.533000	0.62120	TTC	.	.		0.423	PHKB-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000430413.1			C	47695696	T	C	47695696	3	2	279	1	0	0	0	0	1	0	0	0	11854	1609	56	2	2412	2	PHKB	16	47695696	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	17696844	47695696	42659057	323	40082										
ABCC12	94160	hgsc.bcm.edu	37	chr16	48120709	48120709	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	agcatctcatcggtgtgactCtcaaagggatccaagttgta	10	9	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr16:48120709C>T	ENST00000311303.3	-	26	4002	c.3657G>A	c.(3655-3657)gaG>gaA	p.E1219E	ABCC12_ENST00000532355.1_5'Flank|ABCC12_ENST00000448542.1_3'UTR|ABCC12_ENST00000416054.1_3'UTR	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	1219	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.					integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|liver(1)|lung(43)|ovary(2)|prostate(3)|skin(7)|urinary_tract(1)	90		all_cancers(37;0.0474)|all_lung(18;0.047)				CGGTGTGACTCTCAAAGGGAT	0.522																																					p.E1219E		Atlas-SNP	.											.	ABCC12	190	.	0			c.G3657A						.						193	193	193					16																	48120709		2201	4300	6501	SO:0001819	synonymous_variant	94160	exon26			GTGACTCTCAAAG	AY040220	CCDS10730.1	16q12.1	2012-03-14			ENSG00000140798	ENSG00000140798		"ATP binding cassette transporters / subfamily C"	14640	protein-coding gene	gene with protein product		607041				11435397, 11483364	Standard	NM_033226		Approved	MRP9	uc002efc.1	Q96J65	OTTHUMG00000133143	ENST00000311303.3:c.3657G>A	chr16.hg19:g.48120709C>T		73.0	0.0		92.0	4.0	NM_033226	Q49AL2|Q8TAF0|Q8TEY2	Silent	SNP	ENST00000311303.3	hg19	CCDS10730.1																																																																																			.	.		0.522	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226		T	48120709	C	T	48120709	2	4	279	1	0	0	0	0	0	0	0	1	52	912	32	3		3	ABCC12	16	48120709	Silent	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	425013	48120709	42234044	324	40083										
CHD9	80205	hgsc.bcm.edu	37	chr16	53338416	53338416	+	Silent	SNP	T	T	A													0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cgatcaggctctagttcttcTtcatcttcatcttgttcttc							TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr16:53338416T>A	ENST00000398510.3	+	30	6585	c.6498T>A	c.(6496-6498)tcT>tcA	p.S2166S	CHD9_ENST00000447540.1_Silent_p.S2166S|CHD9_ENST00000566029.1_Silent_p.S2166S|CHD9_ENST00000564845.1_Silent_p.S2166S			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	2166	Ser-rich.				cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				CTAGttcttcttcatcttcat	0.443																																					p.S2166S		Atlas-SNP	.											.	CHD9	203	.	0			c.T6498A						.						150	141	144					16																	53338416		2098	4200	6298	SO:0001819	synonymous_variant	80205	exon31			TTCTTCTTCATCT	AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.6498T>A	chr16.hg19:g.53338416T>A		271.0	0.0		302.0	21.0	NM_025134	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Silent	SNP	ENST00000398510.3	hg19																																																																																				.	.		0.443	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134		A	53338416	T	A	53338416	2	1	279	1	0	0	0	0	0	0	0	1	3334	1596	56	4		4	CHD9	16	53338416	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	5217707	53338416	37016337	325	40084	202	2								
CHD9	80205	hgsc.bcm.edu	37	chr16	53338419	53338419	+	Silent	SNP	A	A	T													0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tcaggctctagttcttcttcAtcttcatcttgttcttcagc							TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr16:53338419A>T	ENST00000398510.3	+	30	6588	c.6501A>T	c.(6499-6501)tcA>tcT	p.S2167S	CHD9_ENST00000447540.1_Silent_p.S2167S|CHD9_ENST00000566029.1_Silent_p.S2167S|CHD9_ENST00000564845.1_Silent_p.S2167S			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	2167	Ser-rich.				cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				Gttcttcttcatcttcatctt	0.448																																					p.S2167S		Atlas-SNP	.											.	CHD9	203	.	0			c.A6501T						.						153	142	146					16																	53338419		2096	4201	6297	SO:0001819	synonymous_variant	80205	exon31			TTCTTCATCTTCA	AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.6501A>T	chr16.hg19:g.53338419A>T		275.0	0.0		292.0	14.0	NM_025134	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Silent	SNP	ENST00000398510.3	hg19																																																																																				.	.		0.448	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134		T	53338419	A	T	53338419	2	4	279	1	0	0	0	0	0	0	0	1	3334	204	8	4		4	CHD9	16	53338419	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	3	53338419	37016334	326	40085	202	2								
RBL2	5934	hgsc.bcm.edu	37	chr16	53513887	53513887	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	catcagaattctccaacagaActaaacaaagatagaagtaa	5	8	2	4			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr16:53513887A>G	ENST00000262133.6	+	19	3002	c.2865A>G	c.(2863-2865)gaA>gaG	p.E955E	RBL2_ENST00000544545.1_Intron|RBL2_ENST00000379935.4_3'UTR	NM_005611.3	NP_005602.3	Q08999	RBL2_HUMAN	retinoblastoma-like 2	955	Domain B.|Pocket; binds E1A.				chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						CTCCAACAGAACTAAACAAAG	0.343																																					p.E955E		Atlas-SNP	.											.	RBL2	115	.	0			c.A2865G						.						64	67	66					16																	53513887		2198	4300	6498	SO:0001819	synonymous_variant	5934	exon19			AACAGAACTAAAC	X74594	CCDS10748.1	16q12.2	2014-03-11	2014-03-11		ENSG00000103479	ENSG00000103479			9894	protein-coding gene	gene with protein product		180203				8361765, 8643454	Standard	NM_005611		Approved	Rb2, p130	uc002ehi.4	Q08999	OTTHUMG00000133198	ENST00000262133.6:c.2865A>G	chr16.hg19:g.53513887A>G		129.0	0.0		95.0	4.0	NM_005611	B7Z913|Q15073|Q16084|Q8NE70|Q92812	Silent	SNP	ENST00000262133.6	hg19	CCDS10748.1																																																																																			.	.		0.343	RBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256908.3	NM_005611		G	53513887	A	G	53513887	2	3	279	1	0	0	0	0	0	0	0	1	13125	40	2	2		2	RBL2	16	53513887	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	175468	53513887	36840866	327	40086										
NQO1	1728	hgsc.bcm.edu	37	chr16	69748881	69748881	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	acctacccggaagggtccttTgtcatacatggcagcgtaag	11	11	1	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr16:69748881T>C	ENST00000320623.5	-	4	914	c.403A>G	c.(403-405)Aaa>Gaa	p.K135E	NQO1_ENST00000561500.1_Intron|NQO1_ENST00000564043.1_Missense_Mutation_p.K114E|NQO1_ENST00000379046.2_Intron|NQO1_ENST00000379047.3_Missense_Mutation_p.K135E|NQO1_ENST00000439109.2_Intron	NM_000903.2	NP_000894.1	P15559	NQO1_HUMAN	NAD(P)H dehydrogenase, quinone 1	135					aging (GO:0007568)|cellular nitrogen compound metabolic process (GO:0034641)|negative regulation of catalytic activity (GO:0043086)|nitric oxide biosynthetic process (GO:0006809)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cellular amino acid metabolic process (GO:0006521)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to nutrient (GO:0007584)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|synaptic transmission, cholinergic (GO:0007271)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|NAD(P)H dehydrogenase (quinone) activity (GO:0003955)|poly(A) RNA binding (GO:0044822)|superoxide dismutase activity (GO:0004784)			autonomic_ganglia(1)|large_intestine(2)|lung(5)|prostate(1)|stomach(1)	10					Carboplatin(DB00958)|Cisplatin(DB00515)|Dicoumarol(DB00266)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|Menadione(DB00170)|Oxaliplatin(DB00526)|Vitamin E(DB00163)	AAGGGTCCTTTGTCATACATG	0.507																																					p.K135E		Atlas-SNP	.											.	NQO1	21	.	0			c.A403G						.						225	204	211					16																	69748881		2198	4300	6498	SO:0001583	missense	1728	exon4			GTCCTTTGTCATA	M81600	CCDS10883.1, CCDS32471.1, CCDS32472.1, CCDS67067.1	16q12-q22	2012-10-02	2001-11-30	2001-12-07	ENSG00000181019	ENSG00000181019	1.6.5.2		2874	protein-coding gene	gene with protein product		125860	"diaphorase (NADH/NADPH) (cytochrome b-5 reductase)"	NMOR1, DIA4		2843525	Standard	NM_001286137		Approved	DHQU, QR1, DTD	uc002exp.3	P15559	OTTHUMG00000137575	ENST00000320623.5:c.403A>G	chr16.hg19:g.69748881T>C	ENSP00000319788:p.Lys135Glu	89.0	0.0		115.0	5.0	NM_000903	B2R5Y9|B4DNM7|B7ZAD1|Q86UK1	Missense_Mutation	SNP	ENST00000320623.5	hg19	CCDS10883.1	.	.	.	.	.	.	.	.	.	.	T	9.723	1.160176	0.21454	.	.	ENSG00000181019	ENST00000320623;ENST00000379047	T;T	0.09445	2.98;3.17	6.03	4.94	0.65067	Flavodoxin-like fold (1);	0.462649	0.26421	N	0.024476	T	0.05686	0.0149	N	0.11818	0.18	0.25895	N	0.983429	B;B	0.14805	0.011;0.0	B;B	0.15870	0.014;0.002	T	0.39035	-0.9633	9	.	.	.	-5.147	7.6144	0.28150	0.0:0.0737:0.1414:0.7849	.	135;135	B7ZAD1;P15559	.;NQO1_HUMAN	E	135	ENSP00000319788:K135E;ENSP00000368335:K135E	.	K	-	1	0	NQO1	68306382	0.850000	0.29656	0.990000	0.47175	0.632000	0.37999	0.080000	0.14802	1.112000	0.41740	0.454000	0.30748	AAA	.	.		0.507	NQO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268956.2			C	69748881	T	C	69748881	3	2	279	1	0	0	0	0	1	0	0	0	10620	1821	63	2	433	2	NQO1	16	69748881	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	16234994	69748881	20605872	328	40087										
CENPN	55839	hgsc.bcm.edu	37	chr16	81066238	81066238	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ccacagtcaagggacccaggAcccgagcagctggcagaagg	14	13	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr16:81066238A>G	ENST00000393335.3	+	11	1075	c.1001A>G	c.(1000-1002)gAc>gGc	p.D334G	RP11-303E16.3_ENST00000561808.1_RNA|RP11-303E16.2_ENST00000566639.1_RNA|RP11-303E16.3_ENST00000566390.1_RNA	NM_001100625.2	NP_001094095.2	Q96H22	CENPN_HUMAN	centromere protein N	0					CENP-A containing nucleosome assembly (GO:0034080)|chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|large_intestine(5)|lung(4)	10						gggacccaggacccgagcagc	0.393																																					p.D334G		Atlas-SNP	.											.	CENPN	84	.	0			c.A1001G						.						64	67	66					16																	81066238		1862	4102	5964	SO:0001583	missense	55839	exon11			CCCAGGACCCGAG	AK026313	CCDS10931.1, CCDS42199.1, CCDS42200.1, CCDS58482.1, CCDS58483.1	16q23.2	2013-11-05	2006-06-15	2006-06-15	ENSG00000166451	ENSG00000166451			30873	protein-coding gene	gene with protein product		611509	"chromosome 16 open reading frame 60"	C16orf60		16622419	Standard	NM_001100625		Approved	FLJ13607, FLJ22660, BM039	uc002ffy.4	Q96H22	OTTHUMG00000137628	ENST00000393335.3:c.1001A>G	chr16.hg19:g.81066238A>G	ENSP00000377007:p.Asp334Gly	75.0	0.0		59.0	4.0	NM_001100625	A8MZE6|B3KN53|B4DJD1|B4DPY7|C9JJM5|D3DUK8|E7ES30|E7ETS3|Q9NZ83	Missense_Mutation	SNP	ENST00000393335.3	hg19	CCDS42199.1	.	.	.	.	.	.	.	.	.	.	A	7.598	0.672171	0.14776	.	.	ENSG00000166451	ENST00000393335	T	0.27256	1.68	0.559	-1.12	0.09808	.	.	.	.	.	T	0.10551	0.0258	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.24225	-1.0166	8	0.87932	D	0	.	.	.	.	.	334	A8MZE6	.	G	334	ENSP00000377007:D334G	ENSP00000377007:D334G	D	+	2	0	CENPN	79623739	0.022000	0.18835	0.002000	0.10522	0.002000	0.02628	-0.277000	0.08502	-1.216000	0.02607	-1.235000	0.01560	GAC	.	.		0.393	CENPN-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269052.1	NM_018455		G	81066238	A	G	81066238	3	3	279	1	0	0	0	0	1	0	0	0	3240	275	10	2	1214	2	CENPN	16	81066238	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	11317357	81066238	9288515	329	40088										
PKD1L2	114780	hgsc.bcm.edu	37	chr16	81236287	81236287	+	RNA	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	actggttgtgcattcagcaaAcacggtgaattccccaggag	11	10	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr16:81236287A>G	ENST00000525539.1	-	0	960				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						CATTCAGCAAACACGGTGAAT	0.552																																					p.F321L		Atlas-SNP	.											.	PKD1L2	361	.	0			c.T961C						.						58	62	60					16																	81236287		2182	4279	6461			114780	exon6			CAGCAAACACGGT	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		chr16.hg19:g.81236287A>G		85.0	0.0		89.0	4.0	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	hg19		.	.	.	.	.	.	.	.	.	.	A	19.61	3.860740	0.71834	.	.	ENSG00000166473	ENST00000337114	D	0.90444	-2.67	4.74	3.64	0.41730	.	0.328291	0.29900	N	0.010908	D	0.94275	0.8161	.	.	.	0.22851	N	0.998657	D;D	0.76494	0.999;0.983	D;P	0.75484	0.986;0.746	D	0.87774	0.2607	9	0.87932	D	0	-5.9811	10.4851	0.44717	0.9227:0.0:0.0773:0.0	.	321;321	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	L	321	ENSP00000337397:F321L	ENSP00000337397:F321L	F	-	1	0	PKD1L2	79793788	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	2.072000	0.41510	0.771000	0.33359	0.533000	0.62120	TTT	.	.		0.552	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2			G	81236287	A	G	81236287	1	3	279	0	1	0	0	0	0	0	0	0	11974	43	2	2		2	PKD1L2	16	81236287	RNA	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	170049	81236287	9118466	330	40089										
CDH13	1012	hgsc.bcm.edu	37	chr16	83378493	83378493	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gtggagaccactgatgtcaaTggcaaaactctcgaggggcc	13	10	2	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr16:83378493T>C	ENST00000566620.1	+	6	953	c.663T>C	c.(661-663)aaT>aaC	p.N221N	CDH13_ENST00000428848.3_Silent_p.N182N|CDH13_ENST00000268613.10_Silent_p.N268N|CDH13_ENST00000569454.1_3'UTR	NM_001220488.1|NM_001220489.1|NM_001220490.1|NM_001257.4	NP_001207417.1|NP_001207418.1|NP_001207419.1|NP_001248.1	P55290	CAD13_HUMAN	cadherin 13	221	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|endothelial cell migration (GO:0043542)|homophilic cell adhesion (GO:0007156)|keratinocyte proliferation (GO:0043616)|lamellipodium assembly (GO:0030032)|localization within membrane (GO:0051668)|low-density lipoprotein particle mediated signaling (GO:0055096)|mitotic cell cycle (GO:0000278)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell proliferation (GO:0008285)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Rac protein signal transduction (GO:0016601)|regulation of cell growth (GO:0001558)|regulation of endocytosis (GO:0030100)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|Rho protein signal transduction (GO:0007266)|sprouting angiogenesis (GO:0002040)	anchored component of membrane (GO:0031225)|caveola (GO:0005901)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	adiponectin binding (GO:0055100)|cadherin binding (GO:0045296)|calcium ion binding (GO:0005509)|lipoprotein particle binding (GO:0071813)|low-density lipoprotein particle binding (GO:0030169)			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		CTGATGTCAATGGCAAAACTC	0.448																																					p.N268N		Atlas-SNP	.											.	CDH13	97	.	0			c.T804C						.						79	81	81					16																	83378493		1855	4087	5942	SO:0001819	synonymous_variant	1012	exon7			TGTCAATGGCAAA	U59288	CCDS56009.1, CCDS56010.1, CCDS58485.1, CCDS58486.1, CCDS58487.1	16q23.3	2013-08-27	2013-08-27			ENSG00000140945		"Cadherins / Major cadherins"	1753	protein-coding gene	gene with protein product	"T-cadherin", "H-cadherin (heart)"	601364				8673923, 9468307	Standard	NM_001257		Approved	CDHH	uc010vns.2	P55290		ENST00000566620.1:c.663T>C	chr16.hg19:g.83378493T>C		111.0	0.0		99.0	4.0	NM_001220488	A8W476|A8W477|B7Z590|C9JRI6|J3KN62|Q6GTW4|Q8TBX3	Silent	SNP	ENST00000566620.1	hg19	CCDS58486.1																																																																																			.	.		0.448	CDH13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432917.1	NM_001257		C	83378493	T	C	83378493	2	2	279	1	0	0	0	0	0	0	0	1	3101	1461	51	2		2	CDH13	16	83378493	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	2142206	83378493	6976260	331	40090										
ZNF778	197320	hgsc.bcm.edu	37	chr16	89293512	89293512	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	atgggctgcgccacacctgtTgaaatgcatgccgtcaggaa	12	11	1	1	rs376986456		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr16:89293512T>C	ENST00000433976.2	+	6	1064	c.732T>C	c.(730-732)gtT>gtC	p.V244V	RP11-46C24.6_ENST00000563182.1_RNA|ZNF778_ENST00000306502.6_Silent_p.V202V	NM_001201407.1|NM_182531.3	NP_001188336.1|NP_872337.2	Q96MU6	ZN778_HUMAN	zinc finger protein 778	244					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|skin(2)	24				BRCA - Breast invasive adenocarcinoma(80;0.0269)		CCACACCTGTTGAAATGCATG	0.552																																					p.V272V		Atlas-SNP	.											.	ZNF778	67	.	0			c.T816C						.						111	113	112					16																	89293512		2078	4206	6284	SO:0001819	synonymous_variant	197320	exon7			ACCTGTTGAAATG	AK056437	CCDS45550.1, CCDS73928.1	16q24.3	2014-09-17			ENSG00000170100	ENSG00000170100		"Zinc fingers, C2H2-type", "-"	26479	protein-coding gene	gene with protein product							Standard	NM_182531		Approved	FLJ31875	uc021tms.1	Q96MU6		ENST00000433976.2:c.732T>C	chr16.hg19:g.89293512T>C		90.0	0.0		81.0	4.0	NM_001201407	Q08AG0	Silent	SNP	ENST00000433976.2	hg19	CCDS45550.1																																																																																			.	.		0.552	ZNF778-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430383.1	NM_182531		C	89293512	T	C	89293512	2	2	279	1	0	0	0	0	0	0	0	1	18166	1799	63	2		2	ZNF778	16	89293512	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	5915019	89293512	1061241	332	40091										
SPG7	6687	hgsc.bcm.edu	37	chr16	89598432	89598432	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ccacggaggctcaggtgcccTtcctggcgatggccggccca	14	16	1	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr16:89598432T>C	ENST00000268704.2	+	8	1123	c.1108T>C	c.(1108-1110)Ttc>Ctc	p.F370L	RNU7-117P_ENST00000516770.1_RNA|SPG7_ENST00000341316.2_Missense_Mutation_p.F370L	NM_003119.2	NP_003110.1	Q9UQ90	SPG7_HUMAN	spastic paraplegia 7 (pure and complicated autosomal recessive)	370					anterograde axon cargo transport (GO:0008089)|cell death (GO:0008219)|mitochondrion organization (GO:0007005)|nervous system development (GO:0007399)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metalloendopeptidase activity (GO:0004222)|peptidase activity (GO:0008233)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|urinary_tract(1)	20		all_hematologic(23;0.00824)|Colorectal(91;0.102)		all cancers(4;1.39e-07)|OV - Ovarian serous cystadenocarcinoma(4;5.64e-06)|BRCA - Breast invasive adenocarcinoma(80;0.015)		TCAGGTGCCCTTCCTGGCGAT	0.677																																					p.F370L		Atlas-SNP	.											.	SPG7	75	.	0			c.T1108C						.						55	51	52					16																	89598432		2198	4300	6498	SO:0001583	missense	6687	exon8			GTGCCCTTCCTGG	Y16610	CCDS10977.1, CCDS10978.1	16q24.3	2010-04-21	2007-04-23		ENSG00000197912	ENSG00000197912		"ATPases / AAA-type"	11237	protein-coding gene	gene with protein product	"paraplegin"	602783	"cell matrix adhesion regulator"	CMAR		9635427, 9634528	Standard	XM_006721264		Approved	CAR, SPG5C	uc002fnj.3	Q9UQ90	OTTHUMG00000138046	ENST00000268704.2:c.1108T>C	chr16.hg19:g.89598432T>C	ENSP00000268704:p.Phe370Leu	78.0	0.0		81.0	4.0	NM_199367	O75756|Q2TB70|Q58F00|Q96IB0	Missense_Mutation	SNP	ENST00000268704.2	hg19	CCDS10977.1	.	.	.	.	.	.	.	.	.	.	T	32	5.135457	0.94517	.	.	ENSG00000197912	ENST00000268704;ENST00000341316	D;D	0.93307	-3.2;-3.2	5.85	5.85	0.93711	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);Peptidase M41, FtsH (2);	0.043726	0.85682	N	0.000000	D	0.96466	0.8847	M	0.73430	2.235	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96930	0.9680	10	0.87932	D	0	.	16.2946	0.82763	0.0:0.0:0.0:1.0	.	370;370	Q9UQ90;Q9UQ90-2	SPG7_HUMAN;.	L	370	ENSP00000268704:F370L;ENSP00000341157:F370L	ENSP00000268704:F370L	F	+	1	0	SPG7	88125933	1.000000	0.71417	1.000000	0.80357	0.605000	0.37080	7.666000	0.83877	2.253000	0.74438	0.456000	0.33151	TTC	.	.		0.677	SPG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269921.2	NM_003119		C	89598432	T	C	89598432	3	2	279	1	0	0	0	0	1	0	0	0	15059	1609	56	2	1138	2	SPG7	16	89598432	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	304920	89598432	756321	333	40092										
ASGR1	432	hgsc.bcm.edu	37	chr17	7077757	7077757	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tcagacacgaactgcttcacGtggagcagcaggctggagtg	14	10	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr17:7077757G>A	ENST00000269299.3	-	6	777	c.378C>T	c.(376-378)caC>caT	p.H126H	ASGR1_ENST00000380920.4_Silent_p.H25H|ASGR1_ENST00000574388.1_Silent_p.H87H|ASGR1_ENST00000572879.1_De_novo_Start_OutOfFrame	NM_001197216.2|NM_001671.4	NP_001184145.1|NP_001662.1	P07306	ASGR1_HUMAN	asialoglycoprotein receptor 1	126					cellular response to extracellular stimulus (GO:0031668)|receptor-mediated endocytosis (GO:0006898)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	asialoglycoprotein receptor activity (GO:0004873)|carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|skin(1)|urinary_tract(1)	10						ACTGCTTCACGTGGAGCAGCA	0.667																																					p.H126H		Atlas-SNP	.											.	ASGR1	20	.	0			c.C378T						.						29	26	27					17																	7077757		2203	4300	6503	SO:0001819	synonymous_variant	432	exon6			CTTCACGTGGAGC		CCDS11089.1, CCDS56017.1	17p13-p11	2011-08-30			ENSG00000141505	ENSG00000141505		"C-type lectin domain containing"	742	protein-coding gene	gene with protein product		108360					Standard	NM_001671		Approved	CLEC4H1	uc002ges.4	P07306	OTTHUMG00000102159	ENST00000269299.3:c.378C>T	chr17.hg19:g.7077757G>A		194.0	0.0		267.0	90.0	NM_001671	I3L1X1	Silent	SNP	ENST00000269299.3	hg19	CCDS11089.1																																																																																			.	.		0.667	ASGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220004.3	NM_001671		A	7077757	G	A	7077757	2	1	279	1	0	0	0	0	0	0	0	1	1039	1136	40	1		1	ASGR1	17	7077757	Silent	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10		7077757	74117453	334	40093										
NEURL4	84461	hgsc.bcm.edu	37	chr17	7219555	7219555	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	aggttctccaagggcagcggAagggggtcccggggtgtagg	20	8	1	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr17:7219555A>G	ENST00000399464.2	-	29	4591	c.4576T>C	c.(4576-4578)Tcc>Ccc	p.S1526P	NEURL4_ENST00000315614.7_Missense_Mutation_p.S1524P|RP11-542C16.2_ENST00000575474.1_Intron|NEURL4_ENST00000574120.1_5'Flank|GPS2_ENST00000391950.3_5'Flank|GPS2_ENST00000389167.5_5'Flank|NEURL4_ENST00000570460.1_Missense_Mutation_p.S1502P|GPS2_ENST00000380728.2_5'Flank	NM_032442.2	NP_115818.2	Q96JN8	NEUL4_HUMAN	neuralized E3 ubiquitin protein ligase 4	1526						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						AGGGCAGCGGAAGGGGGTCCC	0.637																																					p.S1526P		Atlas-SNP	.											.	NEURL4	192	.	0			c.T4576C						.						49	56	54					17																	7219555		1971	4150	6121	SO:0001583	missense	84461	exon29			CAGCGGAAGGGGG		CCDS42251.1, CCDS42252.1	17p13	2013-10-24	2013-10-24		ENSG00000215041	ENSG00000215041			34410	protein-coding gene	gene with protein product		615865	"neuralized homolog 4 (Drosophila)"			22261722, 22441691	Standard	NM_001005408		Approved	KIAA1787	uc002gga.1	Q96JN8	OTTHUMG00000132319	ENST00000399464.2:c.4576T>C	chr17.hg19:g.7219555A>G	ENSP00000382390:p.Ser1526Pro	71.0	0.0		89.0	4.0	NM_032442	Q6GPI8|Q96IU9|Q9H0B0	Missense_Mutation	SNP	ENST00000399464.2	hg19	CCDS42251.1	.	.	.	.	.	.	.	.	.	.	A	15.38	2.816549	0.50633	.	.	ENSG00000215041	ENST00000315614;ENST00000399464	T;T	0.36340	1.26;1.26	4.78	2.52	0.30459	.	0.298724	0.27558	U	0.018829	T	0.32645	0.0836	M	0.69823	2.125	0.20563	N	0.999881	B;B	0.09022	0.002;0.001	B;B	0.08055	0.003;0.001	T	0.36578	-0.9742	10	0.72032	D	0.01	-12.4952	4.394	0.11355	0.7286:0.0:0.0959:0.1755	.	1524;1526	Q96JN8-2;Q96JN8	.;NEUL4_HUMAN	P	1524;1526	ENSP00000319826:S1524P;ENSP00000382390:S1526P	ENSP00000319826:S1524P	S	-	1	0	NEURL4	7160279	0.997000	0.39634	0.500000	0.27589	0.984000	0.73092	1.949000	0.40313	0.652000	0.30806	0.460000	0.39030	TCC	.	.		0.637	NEURL4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255434.2	NM_032442		G	7219555	A	G	7219555	3	3	279	1	0	0	0	0	1	0	0	0	10356	246	9	2	116	2	NEURL4	17	7219555	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	141798	7219555	73975655	335	40094										
DNAH2	146754	hgsc.bcm.edu	37	chr17	7671282	7671282	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ggaggagaactggaatgagtGgaagactggccggttcctga	17	6	0	4			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr17:7671282G>C	ENST00000572933.1	+	23	5200	c.3740G>C	c.(3739-3741)tGg>tCg	p.W1247S	DNAH2_ENST00000389173.2_Missense_Mutation_p.W1247S			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	1247	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				TGGAATGAGTGGAAGACTGGC	0.562																																					p.W1247S		Atlas-SNP	.											.	DNAH2	498	.	0			c.G3740C						.						65	60	62					17																	7671282		2203	4300	6503	SO:0001583	missense	146754	exon22			ATGAGTGGAAGAC	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.3740G>C	chr17.hg19:g.7671282G>C	ENSP00000458355:p.Trp1247Ser	118.0	0.0		95.0	4.0	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	hg19	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.144790	0.77888	.	.	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.65732	-0.17	4.36	4.36	0.52297	Dynein heavy chain, domain-2 (1);	0.000000	0.64402	D	0.000001	D	0.85128	0.5626	H	0.96547	3.84	0.80722	D	1	D	0.71674	0.998	D	0.77004	0.989	D	0.90339	0.4358	10	0.72032	D	0.01	.	15.6686	0.77255	0.0:0.0:1.0:0.0	.	1247	Q9P225	DYH2_HUMAN	S	1247	ENSP00000373825:W1247S	ENSP00000353818:W1247S	W	+	2	0	DNAH2	7612007	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	8.218000	0.89768	1.966000	0.57179	0.491000	0.48974	TGG	.	.		0.562	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		C	7671282	G	C	7671282	3	2	279	1	0	0	0	0	1	0	0	0	4604	1357	47	4	3826	4	DNAH2	17	7671282	Missense_Mutation	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	451727	7671282	73523928	336	40095										
DNAH2	146754	hgsc.bcm.edu	37	chr17	7671482	7671482	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tgcccccaacttttgctcagGaccgaaactgggaaattatt	8	11	1	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr17:7671482G>T	ENST00000572933.1	+	24	5298	c.3838G>T	c.(3838-3840)Gac>Tac	p.D1280Y	DNAH2_ENST00000389173.2_Splice_Site_p.D1280Y			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	1280	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				TTTTGCTCAGGACCGAAACTG	0.552																																					p.D1280Y		Atlas-SNP	.											.	DNAH2	498	.	0			c.G3838T						.						127	133	131					17																	7671482		2203	4300	6503	SO:0001630	splice_region_variant	146754	exon23			GCTCAGGACCGAA	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.3838-1G>T	chr17.hg19:g.7671482G>T		64.0	0.0		68.0	5.0	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	hg19	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	G	18.78	3.697017	0.68386	.	.	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.62364	0.03	4.26	4.26	0.50523	Dynein heavy chain, domain-2 (1);	0.302454	0.29791	N	0.011187	T	0.78861	0.4350	M	0.89414	3.03	0.80722	D	1	D	0.54964	0.969	P	0.57425	0.82	D	0.83684	0.0173	9	.	.	.	.	15.4504	0.75268	0.0:0.0:1.0:0.0	.	1280	Q9P225	DYH2_HUMAN	Y	1280	ENSP00000373825:D1280Y	.	D	+	1	0	DNAH2	7612207	1.000000	0.71417	1.000000	0.80357	0.553000	0.35397	8.129000	0.89597	1.919000	0.55581	0.561000	0.74099	GAC	.	.		0.552	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877	Missense_Mutation	T	7671482	G	T	7671482	5	4	279	1	0	0	0	0	0	0	1	0	4604	1188	41	3	3928	3	DNAH2	17	7671482	Splice_Site	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	200	7671482	73523728	337	40096										
ALOX12B	242	hgsc.bcm.edu	37	chr17	7984440	7984440	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tcactggtagaagtcctgctTggctctgatctcctcttttc	8	12	4	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr17:7984440T>C	ENST00000319144.4	-	3	678	c.418A>G	c.(418-420)Aag>Gag	p.K140E	AC129492.6_ENST00000399413.3_3'UTR|ALOX12B_ENST00000577351.1_5'Flank	NM_001139.2	NP_001130.1	O75342	LX12B_HUMAN	arachidonate 12-lipoxygenase, 12R type	140	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				arachidonic acid metabolic process (GO:0019369)|ceramide biosynthetic process (GO:0046513)|establishment of skin barrier (GO:0061436)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipoxygenase pathway (GO:0019372)|oxidation-reduction process (GO:0055114)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mucus secretion (GO:0070257)|protein lipidation (GO:0006497)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytosol (GO:0005829)	arachidonate 12-lipoxygenase activity (GO:0004052)|iron ion binding (GO:0005506)|linoleate 9S-lipoxygenase activity (GO:1990136)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|stomach(1)	16						AAGTCCTGCTTGGCTCTGATC	0.627										Multiple Myeloma(8;0.094)																											p.K140E		Atlas-SNP	.											.	ALOX12B	61	.	0			c.A418G						.						79	64	69					17																	7984440		2203	4300	6503	SO:0001583	missense	242	exon3			CCTGCTTGGCTCT	AF038461	CCDS11129.1	17p13.1	2008-03-18			ENSG00000179477	ENSG00000179477	1.13.11.-	"Arachidonate lipoxygenases"	430	protein-coding gene	gene with protein product		603741				9618483	Standard	NM_001139		Approved	12R-LOX	uc002gjy.1	O75342	OTTHUMG00000108180	ENST00000319144.4:c.418A>G	chr17.hg19:g.7984440T>C	ENSP00000315167:p.Lys140Glu	78.0	0.0		83.0	4.0	NM_001139		Missense_Mutation	SNP	ENST00000319144.4	hg19	CCDS11129.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.126026	0.77436	.	.	ENSG00000179477	ENST00000319144	D	0.89810	-2.57	4.13	4.13	0.48395	Lipoxygenase, C-terminal (2);	0.160289	0.53938	D	0.000042	D	0.88288	0.6396	M	0.69358	2.11	0.37884	D	0.930471	P	0.51791	0.948	P	0.45681	0.49	D	0.90661	0.4590	10	0.87932	D	0	-28.3008	11.0749	0.48025	0.0:0.0:0.0:1.0	.	140	O75342	LX12B_HUMAN	E	140	ENSP00000315167:K140E	ENSP00000315167:K140E	K	-	1	0	ALOX12B	7925165	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	2.541000	0.45735	1.874000	0.54306	0.374000	0.22700	AAG	.	.		0.627	ALOX12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226984.3			C	7984440	T	C	7984440	3	2	279	1	0	0	0	0	1	0	0	0	537	1821	63	2	1739	2	ALOX12B	17	7984440	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	312958	7984440	73210770	338	40097										
NCOR1	9611	hgsc.bcm.edu	37	chr17	15935796	15935796	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ttataaggaaactgagttgaGcctgacaaaagaaaaattag	9	4	0	4			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr17:15935796G>C	ENST00000268712.3	-	46	7394	c.7137C>G	c.(7135-7137)ggC>ggG	p.G2379G	NCOR1_ENST00000395851.1_Splice_Site_p.G2276G|NCOR1_ENST00000395857.3_Splice_Site_p.G963G	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	2379	Interaction with C1D. {ECO:0000250}.				CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		ACTGAGTTGAGCCTGACAAAA	0.418																																					p.G2379G		Atlas-SNP	.											.	NCOR1	240	.	0			c.C7137G						.						83	77	79					17																	15935796		2203	4300	6503	SO:0001630	splice_region_variant	9611	exon46			AGTTGAGCCTGAC	AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"thyroid hormone- and retinoic acid receptor-associated corepressor 1", "protein phosphatase 1, regulatory subunit 109"	600849	"nuclear receptor co-repressor 1"			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.7136-1C>G	chr17.hg19:g.15935796G>C		77.0	0.0		49.0	25.0	NM_006311	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Silent	SNP	ENST00000268712.3	hg19	CCDS11175.1																																																																																			.	.		0.418	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311	Silent	C	15935796	G	C	15935796	5	2	279	1	0	0	0	0	0	0	1	0	10244	985	34	4	189	4	NCOR1	17	15935796	Splice_Site	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	7951356	15935796	65259414	339	40098										
NCOR1	9611	hgsc.bcm.edu	37	chr17	15971227	15971227	+	Frame_Shift_Del	DEL	A	A	-													0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ccaggatccaaagccctgtgAaaaggcatggctggatccaa							TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr17:15971227delA	ENST00000268712.3	-	32	4979	c.4722delT	c.(4720-4722)tttfs	p.F1574fs	NCOR1_ENST00000395851.1_Frame_Shift_Del_p.F1590fs|NCOR1_ENST00000395857.3_Frame_Shift_Del_p.F158fs	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	1574	Interaction with C1D. {ECO:0000250}.|Interaction with ETO.				CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		AAGCCCTGTGAAAAGGCATGG	0.468																																					p.H1591fs		Atlas-Indel,Pindel	.											.	NCOR1	240	.	0			c.4771delC						.						60	60	60					17																	15971227		2203	4300	6503	SO:0001589	frameshift_variant	9611	exon31			.	AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"thyroid hormone- and retinoic acid receptor-associated corepressor 1", "protein phosphatase 1, regulatory subunit 109"	600849	"nuclear receptor co-repressor 1"			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.4722delT	chr17.hg19:g.15971227delA	ENSP00000268712:p.Phe1574fs	108.0	0.0		43.0	18.0	NM_001190440	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Frame_Shift_Del	DEL	ENST00000268712.3	hg19	CCDS11175.1																																																																																			.	.		0.468	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		-	15971227	A	-	15971227	7	5	279	1	0	1	0	1	0	0	0	0	10244	243	9	0	2660	0	NCOR1	17	15971227	Frame_Shift_Del	DEL	A	TCGA-G3-A3CG-01A-11D-A20W-10	35431	15971227	65223983	340	40099										
MFAP4	4239	hgsc.bcm.edu	37	chr17	19288768	19288768	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ttgaatctcttctggaaaacCtggagcagagaagatgagac	11	7	2	4			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr17:19288768C>T	ENST00000299610.4	-	4	325		c.e4-1		MFAP4_ENST00000574313.2_5'Flank|MFAP4_ENST00000497081.2_Splice_Site|MFAP4_ENST00000395592.2_Splice_Site	NM_002404.2	NP_002395.1	P55083	MFAP4_HUMAN	microfibrillar-associated protein 4						cell adhesion (GO:0007155)|cellular response to UV-B (GO:0071493)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)|regulation of collagen metabolic process (GO:0010712)|UV protection (GO:0009650)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)				large_intestine(1)|lung(6)|prostate(2)|upper_aerodigestive_tract(1)	10	all_cancers(12;2.87e-05)|all_epithelial(12;0.00114)|Hepatocellular(7;0.00345)|Breast(13;0.206)					TCTGGAAAACCTGGAGCAGAG	0.547																																					.		Atlas-SNP	.											.	MFAP4	33	.	0			c.241-1G>A						.						49	49	49					17																	19288768		2203	4300	6503	SO:0001630	splice_region_variant	4239	exon5			GAAAACCTGGAGC	L38486	CCDS11208.1, CCDS56023.1	17p11.2	2013-02-06			ENSG00000166482	ENSG00000166482		"Fibrinogen C domain containing"	7035	protein-coding gene	gene with protein product	"microfibril-associated glycoprotein 4"	600596				7633408	Standard	NM_001198695		Approved		uc002gvs.3	P55083	OTTHUMG00000059585	ENST00000299610.4:c.241-1G>A	chr17.hg19:g.19288768C>T		119.0	0.0		77.0	4.0	NM_002404	A8KAJ1|A8MVM2|B4E317|Q6P680	Splice_Site	SNP	ENST00000299610.4	hg19	CCDS11208.1	.	.	.	.	.	.	.	.	.	.	c	20.9	4.074187	0.76415	.	.	ENSG00000166482	ENST00000395592;ENST00000299610	.	.	.	5.26	5.26	0.73747	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.4764	0.84133	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MFAP4	19229361	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	6.981000	0.76166	2.760000	0.94817	0.550000	0.68814	.	.	.		0.547	MFAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132493.2	NM_002404	Intron	T	19288768	C	T	19288768	5	4	279	1	0	0	0	0	0	0	1	0	9526	695	24	3	539	3	MFAP4	17	19288768	Splice_Site	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	3317541	19288768	61906442	341	40100										
KCNJ12	3768	hgsc.bcm.edu	37	chr17	21319654	21319654	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ttgagcccgtgctcttcgagGagaagaaccagtacaagatt	11	9	1	4			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr17:21319654G>A	ENST00000583088.1	+	3	1895	c.1000G>A	c.(1000-1002)Gag>Aag	p.E334K	KCNJ12_ENST00000331718.5_Missense_Mutation_p.E334K	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	334				Missing (in Ref. 2; AAC50615). {ECO:0000305}.	muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	GCTCTTCGAGGAGAAGAACCA	0.577										Prostate(3;0.18)																											p.E334K		Atlas-SNP	.											.	.	.	.	0			c.G1000A						.						153	154	154					17																	21319654		2203	4300	6503	SO:0001583	missense	100134444	exon3			TTCGAGGAGAAGA	L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6258	protein-coding gene	gene with protein product		602323	"potassium inwardly-rectifying channel, subfamily J, inhibitor 1"	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.1000G>A	chr17.hg19:g.21319654G>A	ENSP00000463778:p.Glu334Lys	172.0	0.0		152.0	15.0	NM_001194958	O43401|Q15756|Q8NG63	Missense_Mutation	SNP	ENST00000583088.1	hg19	CCDS11219.1	.	.	.	.	.	.	.	.	.	.	G	19.64	3.866216	0.71949	.	.	ENSG00000184185	ENST00000331718	D	0.91686	-2.89	5.76	5.76	0.90799	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.000000	0.85682	D	0.000000	D	0.89884	0.6844	L	0.41632	1.29	0.80722	D	1	B	0.16603	0.018	B	0.17098	0.017	D	0.85181	0.1004	10	0.66056	D	0.02	.	19.9738	0.97296	0.0:0.0:1.0:0.0	.	334	Q14500	IRK12_HUMAN	K	334	ENSP00000328150:E334K	ENSP00000328150:E334K	E	+	1	0	KCNJ12	21260247	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.698000	0.98700	2.732000	0.93576	0.655000	0.94253	GAG	.	.		0.577	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012		A	21319654	G	A	21319654	3	1	279	1	0	0	0	0	1	0	0	0	8055	1175	41	3	1002	3	KCNJ12	17	21319654	Missense_Mutation	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	2030886	21319654	59875556	342	40101										
MYO18A	399687	hgsc.bcm.edu	37	chr17	27421007	27421007	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	agataccttaccttcttctgAcacgactgccgggcctcctc	7	16	2	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr17:27421007A>G	ENST00000527372.1	-	31	4992	c.4812T>C	c.(4810-4812)tgT>tgC	p.C1604C	MYO18A_ENST00000533112.1_Intron|MYO18A_ENST00000529578.1_5'Flank|TIAF1_ENST00000408971.2_5'Flank|MYO18A_ENST00000354329.4_Silent_p.C1604C|MYO18A_ENST00000531253.1_Silent_p.C1604C	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	1604					actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			CCTTCTTCTGACACGACTGCC	0.547																																					p.C1604C	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-SNP	.											.	MYO18A	217	.	0			c.T4812C						.						119	126	124					17																	27421007		2091	4207	6298	SO:0001819	synonymous_variant	399687	exon31			CTTCTGACACGAC	D86970	CCDS45641.1, CCDS45642.1	17q11.2	2011-09-27			ENSG00000196535	ENSG00000196535		"Myosins / Myosin superfamily : Class XVIII"	31104	protein-coding gene	gene with protein product		610067				12761286	Standard	NM_078471		Approved	KIAA0216, MysPDZ	uc002hdt.1	Q92614	OTTHUMG00000166360	ENST00000527372.1:c.4812T>C	chr17.hg19:g.27421007A>G		64.0	0.0		76.0	4.0	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Silent	SNP	ENST00000527372.1	hg19	CCDS45642.1																																																																																			.	.		0.547	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471		G	27421007	A	G	27421007	2	3	279	1	0	0	0	0	0	0	0	1	10074	273	10	2		2	MYO18A	17	27421007	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	6101353	27421007	53774203	343	40102										
C17orf75	64149	hgsc.bcm.edu	37	chr17	30662412	30662412	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ggattgggcatacaacatccTcaaaccagctgctcagatag	9	11	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr17:30662412T>C	ENST00000577809.1	-	6	648	c.599A>G	c.(598-600)gAg>gGg	p.E200G	RP11-227G15.3_ENST00000581915.1_RNA|C17orf75_ENST00000225805.4_Missense_Mutation_p.E200G	NM_022344.3	NP_071739.2	Q9HAS0	NJMU_HUMAN	chromosome 17 open reading frame 75	200										ovary(1)	1		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)			TACAACATCCTCAAACCAGCT	0.408																																					p.E200G		Atlas-SNP	.											.	C17orf75	23	.	0			c.A599G						.						184	180	181					17																	30662412		1904	4120	6024	SO:0001583	missense	64149	exon6			ACATCCTCAAACC	AB062437	CCDS58537.1	17q11.2	2013-01-21			ENSG00000108666	ENSG00000108666			30173	protein-coding gene	gene with protein product							Standard	NM_022344		Approved	NJMU-R1	uc002hhg.3	Q9HAS0		ENST00000577809.1:c.599A>G	chr17.hg19:g.30662412T>C	ENSP00000464275:p.Glu200Gly	118.0	0.0		96.0	4.0	NM_022344	Q7Z2H4	Missense_Mutation	SNP	ENST00000577809.1	hg19	CCDS58537.1	.	.	.	.	.	.	.	.	.	.	T	14.24	2.477737	0.44044	.	.	ENSG00000108666	ENST00000225805	.	.	.	5.68	4.59	0.56863	.	0.046659	0.85682	D	0.000000	T	0.57286	0.2043	M	0.61703	1.905	0.50813	D	0.999895	P	0.35575	0.51	B	0.38428	0.273	T	0.59621	-0.7420	9	0.72032	D	0.01	-19.2621	12.2269	0.54465	0.0:0.0:0.1425:0.8575	.	200	Q9HAS0	NJMU_HUMAN	G	200	.	ENSP00000225805:E200G	E	-	2	0	C17orf75	27686525	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.243000	0.65395	0.958000	0.37956	0.460000	0.39030	GAG	.	.		0.408	C17orf75-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447204.1	NM_022344		C	30662412	T	C	30662412	3	2	279	1	0	0	0	0	1	0	0	0	1882	1551	54	2	611	2	C17orf75	17	30662412	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	3241405	30662412	50532798	344	40103										
TAF15	8148	hgsc.bcm.edu	37	chr17	34171800	34171800	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ggctatggtggagaccgaggAggctatggaggagatcgagg	20	5	0	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr17:34171800A>G	ENST00000588240.1	+	15	1612	c.1497A>G	c.(1495-1497)ggA>ggG	p.G499G	TAF15_ENST00000592237.1_Intron|TAF15_ENST00000311979.3_Silent_p.G496G	NM_003487.3|NM_139215.2	NP_003478.1|NP_631961.1	Q16514	TAF12_HUMAN	TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa	0					chromatin organization (GO:0006325)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of RNA biosynthetic process (GO:2001141)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)		TAF15/NR4A3(33)	lung(1)|ovary(1)|skin(2)|stomach(1)	5		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		gagaccgaggaggctatggag	0.602			T	"TEC, CHN1, ZNF384"	"extraskeletal myxoid chondrosarcomas, ALL"																																p.G499G		Atlas-SNP	.		Dom	yes		17	17q11.1-q11.2	8148	"TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa"		"L, M"	.	TAF15	46	.	0			c.A1497G						.																																			SO:0001819	synonymous_variant	8148	exon15			CCGAGGAGGCTAT	U51334	CCDS32623.1, CCDS59279.1	17q11.1-q11.2	2013-02-12	2002-08-29	2001-12-07		ENSG00000270647		"RNA binding motif (RRM) containing"	11547	protein-coding gene	gene with protein product		601574	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, N, 68kD (RNA-binding protein 56)"	TAF2N		8954779, 9795213	Standard	NM_003487		Approved	hTAFII68, RBP56, Npl3	uc002hkd.4	Q92804		ENST00000588240.1:c.1497A>G	chr17.hg19:g.34171800A>G		74.0	0.0		66.0	5.0	NM_139215	D3DPM5|Q15775|Q5T077	Silent	SNP	ENST00000588240.1	hg19	CCDS32623.1																																																																																			.	.		0.602	TAF15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449134.1	NM_139215		G	34171800	A	G	34171800	2	3	279	1	0	0	0	0	0	0	0	1	15533	291	11	2		2	TAF15	17	34171800	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	3509388	34171800	47023410	345	40104										
TOP2A	7153	hgsc.bcm.edu	37	chr17	38572733	38572733	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	aagtgacttccctatagttaAtgccaacatcttcatcgtaa	5	10	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr17:38572733A>G	ENST00000423485.1	-	3	367	c.209T>C	c.(208-210)aTt>aCt	p.I70T		NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	70					apoptotic chromosome condensation (GO:0030263)|ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA ligation (GO:0006266)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|embryonic cleavage (GO:0040016)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|positive regulation of apoptotic process (GO:0043065)|positive regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral genome replication (GO:0045070)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|DNA-dependent ATPase activity (GO:0008094)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(9)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	39		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	CCTATAGTTAATGCCAACATC	0.308																																					p.I70T		Atlas-SNP	.											.	TOP2A	124	.	0			c.T209C						.						48	44	46					17																	38572733		1825	4069	5894	SO:0001583	missense	7153	exon3			TAGTTAATGCCAA		CCDS45672.1	17q21-q22	2008-08-06	2002-08-29		ENSG00000131747	ENSG00000131747	5.99.1.2		11989	protein-coding gene	gene with protein product		126430	"topoisomerase (DNA) II alpha (170kD)"	TOP2			Standard	NM_001067		Approved		uc002huq.3	P11388	OTTHUMG00000155008	ENST00000423485.1:c.209T>C	chr17.hg19:g.38572733A>G	ENSP00000411532:p.Ile70Thr	138.0	0.0		73.0	4.0	NM_001067	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Missense_Mutation	SNP	ENST00000423485.1	hg19	CCDS45672.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.383077	0.82792	.	.	ENSG00000131747	ENST00000423485;ENST00000269577;ENST00000348049;ENST00000357601	T	0.23552	1.9	4.83	4.83	0.62350	ATPase-like, ATP-binding domain (2);	0.206221	0.42682	D	0.000672	T	0.38348	0.1037	L	0.52126	1.63	0.51233	D	0.999919	B	0.31351	0.32	P	0.46299	0.511	T	0.37454	-0.9705	10	0.87932	D	0	.	14.7218	0.69311	1.0:0.0:0.0:0.0	.	70	P11388	TOP2A_HUMAN	T	70;69;69;70	ENSP00000411532:I70T	ENSP00000269577:I69T	I	-	2	0	TOP2A	35826259	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.201000	0.95017	1.932000	0.55993	0.533000	0.62120	ATT	.	.		0.308	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1			G	38572733	A	G	38572733	3	3	279	1	0	0	0	0	1	0	0	0	16380	101	4	2	4518	2	TOP2A	17	38572733	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	4400933	38572733	42622477	346	40105										
KRT26	353288	hgsc.bcm.edu	37	chr17	38926059	38926059	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ggtttgcagattgcgttttaAttcggtcagctcatttctgg	11	7	3	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr17:38926059A>G	ENST00000335552.4	-	5	964	c.916T>C	c.(916-918)Tta>Cta	p.L306L		NM_181539.4	NP_853517.2			keratin 26											central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(5)	16		Breast(137;0.00526)				TTGCGTTTTAATTCGGTCAGC	0.438																																					p.L306L		Atlas-SNP	.											.	KRT26	49	.	0			c.T916C						.						185	169	175					17																	38926059		2203	4300	6503	SO:0001819	synonymous_variant	353288	exon5			GTTTTAATTCGGT	AJ564205	CCDS11374.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000186393	ENSG00000186393		"-", "Intermediate filaments type I, keratins (acidic)"	30840	protein-coding gene	gene with protein product			"keratin 25B"	KRT25B		16831889	Standard	NM_181539		Approved		uc002hvf.3	Q7Z3Y9	OTTHUMG00000133370	ENST00000335552.4:c.916T>C	chr17.hg19:g.38926059A>G		478.0	0.0		416.0	32.0	NM_181539		Silent	SNP	ENST00000335552.4	hg19	CCDS11374.1																																																																																			.	.		0.438	KRT26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257215.1	NM_181539		G	38926059	A	G	38926059	2	3	279	1	0	0	0	0	0	0	0	1	8472	98	4	2		2	KRT26	17	38926059	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	353326	38926059	42269151	347	40106										
MAPT	4137	hgsc.bcm.edu	37	chr17	44049306	44049306	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tgctaagagcactccaacagCggaaggtgggccccccttca	11	14	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr17:44049306C>T	ENST00000571987.1	+	2	215	c.215C>T	c.(214-216)gCg>gTg	p.A72V	MAPT_ENST00000344290.5_Missense_Mutation_p.A72V|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000574436.1_Missense_Mutation_p.A72V|MAPT_ENST00000535772.1_Missense_Mutation_p.A72V|MAPT_ENST00000446361.3_Intron|MAPT_ENST00000420682.2_Missense_Mutation_p.A72V|MAPT_ENST00000340799.5_Missense_Mutation_p.A72V|MAPT_ENST00000415613.2_Missense_Mutation_p.A72V|MAPT_ENST00000262410.5_Missense_Mutation_p.A72V|MAPT_ENST00000347967.5_Missense_Mutation_p.R8W|MAPT_ENST00000334239.8_Intron|MAPT_ENST00000576518.1_5'Flank|MAPT_ENST00000351559.5_Missense_Mutation_p.A72V|MAPT_ENST00000431008.3_Missense_Mutation_p.A72V			P10636	TAU_HUMAN	microtubule-associated protein tau	72					adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	ACTCCAACAGCGGAAGGTGGG	0.617																																					p.A72V		Atlas-SNP	.											.	MAPT	135	.	0			c.C215T						.						60	53	56					17																	44049306		2203	4300	6503	SO:0001583	missense	4137	exon3			CAACAGCGGAAGG	J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"G protein beta1/gamma2 subunit-interacting factor 1", "microtubule-associated protein tau, isoform 4", "protein phosphatase 1, regulatory subunit 103"	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.215C>T	chr17.hg19:g.44049306C>T	ENSP00000458742:p.Ala72Val	48.0	0.0		52.0	16.0	NM_001123066	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Missense_Mutation	SNP	ENST00000571987.1	hg19	CCDS11501.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.20|10.20	1.283832|1.283832	0.23392|0.23392	.|.	.|.	ENSG00000186868|ENSG00000186868	ENST00000344290;ENST00000262410;ENST00000351559;ENST00000340799;ENST00000535772;ENST00000354326;ENST00000420682;ENST00000415613|ENST00000347967	T;T;T;T;T;T;T|T	0.29142|0.19532	2.74;2.73;2.04;1.58;2.3;1.58;2.74|2.14	5.88|5.88	4.92|4.92	0.64577|0.64577	.|.	0.000000|.	0.44097|.	D|.	0.000498|.	T|T	0.20129|0.20129	0.0484|0.0484	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	N|N	1|1	B;B;B;B;B|.	0.19073|.	0.027;0.014;0.004;0.009;0.033|.	B;B;B;B;B|.	0.20767|.	0.031;0.004;0.005;0.004;0.007|.	T|T	0.15925|0.15925	-1.0420|-1.0420	10|7	0.51188|0.66056	T|D	0.08|0.02	-13.4756|-13.4756	11.2157|11.2157	0.48825|0.48825	0.0:0.9159:0.0:0.0841|0.0:0.9159:0.0:0.0841	.|.	72;72;72;72;72|.	P10636-9;P10636-7;F8WAB2;P10636-8;P10636|.	.;.;.;.;TAU_HUMAN|.	V|W	72|8	ENSP00000340820:A72V;ENSP00000262410:A72V;ENSP00000303214:A72V;ENSP00000340438:A72V;ENSP00000443028:A72V;ENSP00000413056:A72V;ENSP00000410838:A72V|ENSP00000302706:R8W	ENSP00000262410:A72V|ENSP00000302706:R8W	A|R	+|+	2|1	0|2	MAPT|MAPT	41405142|41405142	0.286000|0.286000	0.24305|0.24305	0.211000|0.211000	0.23655|0.23655	0.019000|0.019000	0.09904|0.09904	1.413000|1.413000	0.34725|0.34725	1.500000|1.500000	0.48636|0.48636	-0.263000|-0.263000	0.10527|0.10527	GCG|CGG	.	.		0.617	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835		T	44049306	C	T	44049306	3	4	279	1	0	0	0	0	1	0	0	0	9306	768	27	1	221	1	MAPT	17	44049306	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	5123247	44049306	37145904	348	40107										
ITGB3	3690	hgsc.bcm.edu	37	chr17	45384933	45384933	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cctgctcatctggaaactccTcatcaccatccacgaccgaa	5	17	4	0	rs398122374		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr17:45384933T>C	ENST00000559488.1	+	14	2247	c.2231T>C	c.(2230-2232)cTc>cCc	p.L744P	RP11-290H9.4_ENST00000575039.1_RNA|ITGB3_ENST00000560629.1_Silent_p.P732P|RP11-290H9.4_ENST00000576345.1_RNA|ITGB3_ENST00000435993.2_Missense_Mutation_p.L697P	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	744					activation of protein kinase activity (GO:0032147)|angiogenesis involved in wound healing (GO:0060055)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|mesodermal cell differentiation (GO:0048333)|negative chemotaxis (GO:0050919)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein folding (GO:0006457)|regulation of bone resorption (GO:0045124)|smooth muscle cell migration (GO:0014909)|substrate adhesion-dependent cell spreading (GO:0034446)|tube development (GO:0035295)|viral entry into host cell (GO:0046718)|wound healing (GO:0042060)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|melanosome (GO:0042470)|microvillus membrane (GO:0031528)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|receptor complex (GO:0043235)|ruffle membrane (GO:0032587)	cell adhesion molecule binding (GO:0050839)|extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|identical protein binding (GO:0042802)|platelet-derived growth factor receptor binding (GO:0005161)|protease binding (GO:0002020)|protein disulfide isomerase activity (GO:0003756)|receptor activity (GO:0004872)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	39					Abciximab(DB00054)|Antithymocyte globulin(DB00098)|Eptifibatide(DB00063)|Tirofiban(DB00775)	TGGAAACTCCTCATCACCATC	0.542																																					p.L744P		Atlas-SNP	.											.	ITGB3	157	.	0			c.T2231C						.						84	67	73					17																	45384933		2203	4300	6503	SO:0001583	missense	3690	exon14			AACTCCTCATCAC		CCDS11511.1	17q21.32	2014-09-17			ENSG00000259207	ENSG00000259207		"CD molecules", "Integrins"	6156	protein-coding gene	gene with protein product	"platelet glycoprotein IIIa"	173470		GP3A		2454952	Standard	NM_000212		Approved	CD61, GPIIIa	uc002ilj.3	P05106	OTTHUMG00000171956	ENST00000559488.1:c.2231T>C	chr17.hg19:g.45384933T>C	ENSP00000452786:p.Leu744Pro	127.0	0.0		113.0	5.0	NM_000212	A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Missense_Mutation	SNP	ENST00000559488.1	hg19	CCDS11511.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.592322	0.86953	.	.	ENSG00000178852	ENST00000262017;ENST00000435993	D	0.91843	-2.92	5.48	5.48	0.80851	Integrin beta subunit, cytoplasmic (2);	0.058087	0.64402	D	0.000002	D	0.97052	0.9037	H	0.94503	3.545	0.80722	D	1	D	0.71674	0.998	D	0.74348	0.983	D	0.98091	1.0409	10	0.87932	D	0	.	14.8497	0.70286	0.0:0.0:0.0:1.0	.	744	P05106	ITB3_HUMAN	P	744;697	ENSP00000407801:L697P	ENSP00000262017:L744P	L	+	2	0	C17orf57	42739932	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.182000	0.71995	2.200000	0.70718	0.460000	0.39030	CTC	.	.		0.542	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3	NM_000212		C	45384933	T	C	45384933	3	2	279	1	0	0	0	0	1	0	0	0	7904	1551	54	2	2285	2	ITGB3	17	45384933	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	1335627	45384933	35810277	349	40108										
HOXB13	10481	hgsc.bcm.edu	37	chr17	46805467	46805467	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tggtaactgtccacaggcaaCagggagtcatgtcgcggttc	13	10	1	0	rs199561305		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr17:46805467C>T	ENST00000290295.7	-	1	1073	c.489G>A	c.(487-489)ctG>ctA	p.L163L	PRAC2_ENST00000422730.2_RNA	NM_006361.5	NP_006352.2	Q92826	HXB13_HUMAN	homeobox B13	163					angiogenesis (GO:0001525)|epidermis development (GO:0008544)|epithelial cell maturation involved in prostate gland development (GO:0060743)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|response to testosterone (GO:0033574)|response to wounding (GO:0009611)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|kidney(2)|lung(6)|prostate(1)	11						CCACAGGCAACAGGGAGTCAT	0.582																																					p.L163L		Atlas-SNP	.											.	HOXB13	28	.	0			c.G489A						.						85	81	83					17																	46805467		2203	4300	6503	SO:0001819	synonymous_variant	10481	exon1			AGGCAACAGGGAG	U57052	CCDS11536.1	17q21.32	2014-09-17	2005-12-22		ENSG00000159184	ENSG00000159184		"Homeoboxes / ANTP class : HOXL subclass"	5112	protein-coding gene	gene with protein product		604607	"homeo box B13"			8756292, 9665387	Standard	NM_006361		Approved		uc002ioa.3	Q92826	OTTHUMG00000159900	ENST00000290295.7:c.489G>A	chr17.hg19:g.46805467C>T		104.0	0.0		94.0	4.0	NM_006361	B2R878|Q96QM4|Q99810	Silent	SNP	ENST00000290295.7	hg19	CCDS11536.1																																																																																			.	C|1.000;G|0.000		0.582	HOXB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358087.3	NM_006361		T	46805467	C	T	46805467	2	4	279	1	0	0	0	0	0	0	0	1	7309	465	17	3		3	HOXB13	17	46805467	Silent	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	1420534	46805467	34389743	350	40109										
SCPEP1	59342	hgsc.bcm.edu	37	chr17	55058493	55058493	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gcaaggaagtatgggattatGtgacggtccgcaaggatgcc	15	7	0	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr17:55058493G>A	ENST00000262288.3	+	2	182	c.127G>A	c.(127-129)Gtg>Atg	p.V43M	SCPEP1_ENST00000571898.1_3'UTR|RP5-1107A17.4_ENST00000572877.1_RNA	NM_021626.2	NP_067639.1	Q9HB40	RISC_HUMAN	serine carboxypeptidase 1	43					negative regulation of blood pressure (GO:0045776)|positive regulation of vasodilation (GO:0045909)|retinoic acid metabolic process (GO:0042573)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	serine-type carboxypeptidase activity (GO:0004185)			endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|skin(2)	14	Breast(9;2.86e-08)					ATGGGATTATGTGACGGTCCG	0.502																																					p.V43M		Atlas-SNP	.											.	SCPEP1	35	.	0			c.G127A						.						141	114	123					17																	55058493		2203	4300	6503	SO:0001583	missense	59342	exon2			GATTATGTGACGG	AF282618	CCDS11593.1	17q22	2012-09-20			ENSG00000121064	ENSG00000121064			29507	protein-coding gene	gene with protein product	"retinoid inducible serine carboxypeptidase"					11447226, 12975309	Standard	NM_021626		Approved	RISC	uc002iuv.4	Q9HB40	OTTHUMG00000178129	ENST00000262288.3:c.127G>A	chr17.hg19:g.55058493G>A	ENSP00000262288:p.Val43Met	218.0	0.0		168.0	49.0	NM_021626	Q96A94|Q9H3F0	Missense_Mutation	SNP	ENST00000262288.3	hg19	CCDS11593.1	.	.	.	.	.	.	.	.	.	.	G	17.65	3.441897	0.63067	.	.	ENSG00000121064	ENST00000262288	D	0.88046	-2.33	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	D	0.95446	0.8521	M	0.94021	3.485	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96075	0.9049	10	0.87932	D	0	-22.7715	18.3196	0.90232	0.0:0.0:1.0:0.0	.	43	Q9HB40	RISC_HUMAN	M	43	ENSP00000262288:V43M	ENSP00000262288:V43M	V	+	1	0	SCPEP1	52413492	1.000000	0.71417	0.998000	0.56505	0.023000	0.10783	6.016000	0.70798	2.764000	0.94973	0.655000	0.94253	GTG	.	.		0.502	SCPEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440622.1	NM_021626		A	55058493	G	A	55058493	3	1	279	1	0	0	0	0	1	0	0	0	13950	1377	48	3	133	3	SCPEP1	17	55058493	Missense_Mutation	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	8253026	55058493	26136717	351	40110										
BRIP1	83990	hgsc.bcm.edu	37	chr17	59871069	59871069	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	taatctctttctacaagataTtcagcgtttgcttctaacca	4	10	4	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr17:59871069T>C	ENST00000259008.2	-	10	1629	c.1362A>G	c.(1360-1362)gaA>gaG	p.E454E	BRIP1_ENST00000577598.1_Silent_p.E454E	NM_032043.2	NP_114432.2	Q9BX63	FANCJ_HUMAN	BRCA1 interacting protein C-terminal helicase 1	454					DNA damage checkpoint (GO:0000077)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(9)|kidney(5)|large_intestine(9)|liver(2)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	55						CTACAAGATATTCAGCGTTTG	0.333			"F, N, Mis"			"AML, leukemia, breast"		Involved in tolerance or repair of DNA crosslinks																													p.E454E		Atlas-SNP	.	yes	Rec		"Fanconi anaemia J, breast cancer susceptiblity"	17	17q22	83990	BRCA1 interacting protein C-terminal helicase 1		"L, E"	.	BRIP1	237	.	0			c.A1362G						.						72	68	69					17																	59871069		2203	4297	6500	SO:0001819	synonymous_variant	83990	exon10			AAGATATTCAGCG	AF360549	CCDS11631.1	17q22.2	2014-09-17				ENSG00000136492		"Fanconi anemia, complementation groups"	20473	protein-coding gene	gene with protein product	"BRCA1/BRCA2-associated helicase 1"	605882				11595410, 11301010	Standard	NM_032043		Approved	OF, BACH1, FANCJ	uc002izk.2	Q9BX63		ENST00000259008.2:c.1362A>G	chr17.hg19:g.59871069T>C		68.0	0.0		64.0	5.0	NM_032043	Q3MJE2|Q8NCI5	Silent	SNP	ENST00000259008.2	hg19	CCDS11631.1																																																																																			.	.		0.333	BRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445362.1	NM_032043		C	59871069	T	C	59871069	2	2	279	1	0	0	0	0	0	0	0	1	1516	1490	52	2		2	BRIP1	17	59871069	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	4812576	59871069	21324141	352	40111										
HELZ	9931	hgsc.bcm.edu	37	chr17	65185736	65185736	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gagcaaaggtccatgtctggTgggattttttggtgctgaca	14	6	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr17:65185736T>A	ENST00000358691.5	-	11	999	c.833A>T	c.(832-834)cAc>cTc	p.H278L	HELZ_ENST00000580168.1_Missense_Mutation_p.H278L|HELZ_ENST00000580662.1_5'Flank	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	278						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					CCATGTCTGGTGGGATTTTTT	0.368																																					p.H278L		Atlas-SNP	.											.	HELZ	160	.	0			c.A833T						.						188	170	176					17																	65185736		1887	4104	5991	SO:0001583	missense	9931	exon11			GTCTGGTGGGATT	D29677	CCDS42374.1	17q24.2	2013-01-18			ENSG00000198265	ENSG00000198265		"Zinc fingers, CCCH-type domain containing"	16878	protein-coding gene	gene with protein product	"down-regulated in human cancers"	606699				10471385, 12691822	Standard	NM_014877		Approved	KIAA0054, HUMORF5, DHRC	uc002jfx.4	P42694	OTTHUMG00000179555	ENST00000358691.5:c.833A>T	chr17.hg19:g.65185736T>A	ENSP00000351524:p.His278Leu	195.0	0.0		146.0	35.0	NM_014877	I6L9H4	Missense_Mutation	SNP	ENST00000358691.5	hg19	CCDS42374.1	.	.	.	.	.	.	.	.	.	.	T	10.74	1.436808	0.25900	.	.	ENSG00000198265	ENST00000358691;ENST00000417253	D;T	0.82619	-1.63;1.52	5.06	3.98	0.46160	.	0.157358	0.56097	D	0.000021	T	0.73210	0.3558	L	0.29908	0.895	0.43399	D	0.995522	B;B	0.29481	0.245;0.075	B;B	0.29176	0.099;0.054	T	0.69053	-0.5247	10	0.45353	T	0.12	-10.7043	10.753	0.46219	0.0:0.0754:0.0:0.9246	.	278;278	B7ZLW2;P42694	.;HELZ_HUMAN	L	278	ENSP00000351524:H278L;ENSP00000411144:H278L	ENSP00000351524:H278L	H	-	2	0	HELZ	62616198	1.000000	0.71417	0.980000	0.43619	0.960000	0.62799	5.054000	0.64275	0.893000	0.36288	0.528000	0.53228	CAC	.	.		0.368	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		A	65185736	T	A	65185736	3	1	279	1	0	0	0	0	1	0	0	0	7058	1696	59	4	5087	4	HELZ	17	65185736	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	5314667	65185736	16009474	353	40112										
ABCA6	23460	hgsc.bcm.edu	37	chr17	67085652	67085652	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cactcaattcaaaatttgccTctggaaattctctgtagtgc	6	10	4	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr17:67085652T>C	ENST00000284425.2	-	27	3734	c.3560A>G	c.(3559-3561)gAg>gGg	p.E1187G	ABCA6_ENST00000446604.2_5'UTR	NM_080284.2	NP_525023.2	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 6	1187					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(6)|endometrium(5)|kidney(17)|large_intestine(18)|lung(20)|ovary(3)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	82	Breast(10;5.65e-12)					AAAATTTGCCTCTGGAAATTC	0.378																																					p.E1187G		Atlas-SNP	.											.	ABCA6	210	.	0			c.A3560G						.						121	124	123					17																	67085652		2203	4300	6503	SO:0001583	missense	23460	exon27			TTTGCCTCTGGAA	U66680	CCDS11683.1	17q21	2012-03-14			ENSG00000154262	ENSG00000154262		"ATP binding cassette transporters / subfamily A"	36	protein-coding gene	gene with protein product		612504				8894702	Standard	NM_080284		Approved	EST155051	uc002jhw.1	Q8N139		ENST00000284425.2:c.3560A>G	chr17.hg19:g.67085652T>C	ENSP00000284425:p.Glu1187Gly	66.0	0.0		73.0	4.0	NM_080284	Q6NSH9|Q8N856|Q8WWZ6	Missense_Mutation	SNP	ENST00000284425.2	hg19	CCDS11683.1	.	.	.	.	.	.	.	.	.	.	T	4.336	0.061842	0.08339	.	.	ENSG00000154262	ENST00000284425;ENST00000446604	D	0.86865	-2.18	4.0	1.71	0.24356	.	1.068010	0.07406	N	0.891605	T	0.77678	0.4166	N	0.25647	0.755	0.09310	N	1	B	0.02656	0.0	B	0.10450	0.005	T	0.61931	-0.6961	10	0.36615	T	0.2	.	4.2972	0.10908	0.0:0.1075:0.2023:0.6901	.	1187	Q8N139	ABCA6_HUMAN	G	1187;47	ENSP00000284425:E1187G	ENSP00000284425:E1187G	E	-	2	0	ABCA6	64597247	0.005000	0.15991	0.000000	0.03702	0.003000	0.03518	1.750000	0.38329	0.321000	0.23259	0.533000	0.62120	GAG	.	.		0.378	ABCA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450463.1	NM_080284		C	67085652	T	C	67085652	3	2	279	1	0	0	0	0	1	0	0	0	36	1551	54	2	1345	2	ABCA6	17	67085652	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	1899916	67085652	14109558	354	40113										
ABCA10	10349	hgsc.bcm.edu	37	chr17	67148261	67148261	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	acctgggtaggttctttcatTtttatttctagtaaataatc	6	6	3	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr17:67148261T>C	ENST00000269081.4	-	37	5229	c.4320A>G	c.(4318-4320)aaA>aaG	p.K1440K	ABCA10_ENST00000416101.2_3'UTR|ABCA10_ENST00000519732.1_5'UTR	NM_080282.3	NP_525021.3	Q8WWZ4	ABCAA_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 10	1440	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(34)|ovary(2)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	81	Breast(10;6.95e-12)					GTTCTTTCATTTTTATTTCTA	0.383																																					p.K1440K		Atlas-SNP	.											.	ABCA10	209	.	0			c.A4320G						.						87	92	90					17																	67148261		2203	4300	6503	SO:0001819	synonymous_variant	10349	exon37			TTTCATTTTTATT	AY247065	CCDS11684.1	17q24	2012-03-14			ENSG00000154263	ENSG00000154263		"ATP binding cassette transporters / subfamily A"	30	protein-coding gene	gene with protein product		612508				12821155, 11435397	Standard	NM_080282		Approved	EST698739	uc010dfa.1	Q8WWZ4	OTTHUMG00000164716	ENST00000269081.4:c.4320A>G	chr17.hg19:g.67148261T>C		93.0	0.0		78.0	4.0	NM_080282	C9JZH2|C9K035|Q6PIQ6|Q7Z2I9|Q7Z7P7|Q86TD2	Silent	SNP	ENST00000269081.4	hg19	CCDS11684.1																																																																																			.	.		0.383	ABCA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379881.4	NM_080282		C	67148261	T	C	67148261	2	2	279	1	0	0	0	0	0	0	0	1	29	1838	64	2		2	ABCA10	17	67148261	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	62609	67148261	14046949	355	40114										
TMC8	147138	hgsc.bcm.edu	37	chr17	76129494	76129494	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tcgctgtccccaggccttcaCcaacacctatctcttctacg	5	18	3	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr17:76129494C>T	ENST00000318430.5	+	6	913	c.539C>T	c.(538-540)aCc>aTc	p.T180I	TMC8_ENST00000589691.1_5'UTR|TMC6_ENST00000322914.3_5'Flank	NM_152468.4	NP_689681.2	Q8IU68	TMC8_HUMAN	transmembrane channel-like 8	180					ion transport (GO:0006811)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|regulation of cell growth (GO:0001558)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|zinc ion homeostasis (GO:0055069)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	receptor binding (GO:0005102)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	12			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)|OV - Ovarian serous cystadenocarcinoma(97;0.192)			CAGGCCTTCACCAACACCTAT	0.612																																					p.T180I		Atlas-SNP	.											.	TMC8	44	.	0			c.C539T						.						142	130	134					17																	76129494		2203	4300	6503	SO:0001583	missense	147138	exon6			CCTTCACCAACAC	AY057380	CCDS32749.1	17q25.3	2014-09-17	2005-11-10	2005-11-10	ENSG00000167895	ENSG00000167895			20474	protein-coding gene	gene with protein product		605829	"epidermodysplasia verruciformis 2"	EVER2		12426567	Standard	NM_152468		Approved	EVIN2	uc002jup.2	Q8IU68		ENST00000318430.5:c.539C>T	chr17.hg19:g.76129494C>T	ENSP00000325561:p.Thr180Ile	141.0	0.0		115.0	5.0	NM_152468	Q2YDC0|Q8IWU7|Q8N358|Q8NF04	Missense_Mutation	SNP	ENST00000318430.5	hg19	CCDS32749.1	.	.	.	.	.	.	.	.	.	.	C	4.165	0.029110	0.08054	.	.	ENSG00000167895	ENST00000318430;ENST00000301627	T	0.55588	0.51	4.08	-4.49	0.03504	.	0.666605	0.14835	N	0.295647	T	0.23330	0.0564	N	0.11255	0.115	0.80722	D	1	B	0.10296	0.003	B	0.04013	0.001	T	0.01844	-1.1262	10	0.37606	T	0.19	-9.2058	3.5926	0.07994	0.2071:0.1567:0.4943:0.1419	.	180	Q8IU68	TMC8_HUMAN	I	180	ENSP00000325561:T180I	ENSP00000301627:T180I	T	+	2	0	TMC8	73641089	0.001000	0.12720	0.991000	0.47740	0.443000	0.32047	-0.600000	0.05693	-0.435000	0.07264	-0.311000	0.09066	ACC	.	.		0.612	TMC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436900.3			T	76129494	C	T	76129494	3	4	279	1	0	0	0	0	1	0	0	0	16006	507	18	3	557	3	TMC8	17	76129494	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	8981233	76129494	5065716	356	40115										
DLGAP1	9229	hgsc.bcm.edu	37	chr18	3742408	3742408	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ttggtgatgtgagcaagcctGcagggtccaggctgtccagg	16	9	0	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr18:3742408G>T	ENST00000315677.3	-	6	1872	c.1277C>A	c.(1276-1278)gCa>gAa	p.A426E	DLGAP1_ENST00000400155.1_Missense_Mutation_p.A132E|DLGAP1_ENST00000539435.1_Missense_Mutation_p.A124E|DLGAP1_ENST00000478161.1_5'UTR|DLGAP1_ENST00000400149.3_Missense_Mutation_p.A134E|DLGAP1_ENST00000534970.1_Missense_Mutation_p.A138E|DLGAP1_ENST00000584874.1_Missense_Mutation_p.A426E|DLGAP1_ENST00000515196.2_Missense_Mutation_p.A426E|DLGAP1_ENST00000400145.2_Missense_Mutation_p.A124E|DLGAP1_ENST00000581699.1_Missense_Mutation_p.A132E|DLGAP1_ENST00000400147.2_Missense_Mutation_p.A124E|DLGAP1_ENST00000400150.3_Missense_Mutation_p.A132E|DLGAP1_ENST00000581527.1_Missense_Mutation_p.A426E	NM_004746.3	NP_004737.2	O14490	DLGP1_HUMAN	discs, large (Drosophila) homolog-associated protein 1	426					synaptic transmission (GO:0007268)	cell junction (GO:0030054)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)				breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	56		Colorectal(8;0.0257)				GAGCAAGCCTGCAGGGTCCAG	0.577																																					p.A426E		Atlas-SNP	.											.	DLGAP1	201	.	0			c.C1277A						.						71	64	66					18																	3742408		2203	4300	6503	SO:0001583	missense	9229	exon6			AAGCCTGCAGGGT	AB000277	CCDS11836.1, CCDS42406.1, CCDS56049.1, CCDS56050.1, CCDS56051.1, CCDS56052.1, CCDS56053.1, CCDS74191.1	18p11.3	2008-07-28	2001-11-28		ENSG00000170579	ENSG00000170579			2905	protein-coding gene	gene with protein product		605445	"discs, large (Drosophila) homolog-associated protein 1"			9024696, 9286858	Standard	NM_004746		Approved	GKAP, SAPAP1, DAP-1	uc002kmf.3	O14490	OTTHUMG00000131537	ENST00000315677.3:c.1277C>A	chr18.hg19:g.3742408G>T	ENSP00000316377:p.Ala426Glu	148.0	0.0		125.0	42.0	NM_001242761	A8MWN8|B2RMU8|B7WPA1|B7Z2H2|B7Z2I2|B7Z9Y4|O14489|P78335	Missense_Mutation	SNP	ENST00000315677.3	hg19	CCDS11836.1	.	.	.	.	.	.	.	.	.	.	G	14.43	2.532180	0.45073	.	.	ENSG00000170579	ENST00000315677;ENST00000400147;ENST00000400150;ENST00000400149;ENST00000400155;ENST00000534970;ENST00000539435;ENST00000400145;ENST00000515196	T;T;T;T;T;T;T;T;T	0.21932	1.98;1.98;1.98;1.98;1.98;1.98;1.98;1.98;1.98	4.97	4.09	0.47781	.	0.251600	0.40385	N	0.001105	T	0.25606	0.0623	L	0.56769	1.78	0.38038	D	0.93536	B;B;B;B;B;B;B;B;B	0.28584	0.047;0.112;0.073;0.1;0.167;0.216;0.16;0.005;0.032	B;B;B;B;B;B;B;B;B	0.31337	0.024;0.024;0.028;0.036;0.028;0.079;0.128;0.017;0.062	T	0.16453	-1.0402	10	0.59425	D	0.04	-5.0623	15.125	0.72475	0.0:0.0:0.8571:0.1429	.	426;138;112;132;124;426;124;426;124	B7Z9Y4;B7Z2H2;B7Z2J5;A8MWN8;B7Z2I2;Q6IS01;O14490-3;O14490;O14490-2	.;.;.;.;.;.;.;DLGP1_HUMAN;.	E	426;124;132;134;132;138;124;124;426	ENSP00000316377:A426E;ENSP00000383011:A124E;ENSP00000383014:A132E;ENSP00000383013:A134E;ENSP00000383019:A132E;ENSP00000437817:A138E;ENSP00000446312:A124E;ENSP00000383010:A124E;ENSP00000445973:A426E	ENSP00000316377:A426E	A	-	2	0	DLGAP1	3732408	1.000000	0.71417	0.969000	0.41365	0.980000	0.70556	5.334000	0.65923	1.245000	0.43885	0.516000	0.50304	GCA	.	.		0.577	DLGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254394.4			T	3742408	G	T	3742408	3	4	279	1	0	0	0	0	1	0	0	0	4561	1319	46	3	1688	3	DLGAP1	18	3742408	Missense_Mutation	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10		3742408	74334840	357	40116										
ANKRD30B	374860	hgsc.bcm.edu	37	chr18	14791433	14791433	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cggtttcacagaaggatgtgTatttacccaaagctacacat	8	9	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr18:14791433T>C	ENST00000358984.4	+	16	1948	c.1768T>C	c.(1768-1770)Tat>Cat	p.Y590H	ANKRD30B_ENST00000447268.2_Missense_Mutation_p.Y590H|ANKRD30B_ENST00000579292.1_Intron	NM_001145029.1	NP_001138501.1	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B	590										breast(3)|endometrium(4)|kidney(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	22						GAAGGATGTGTATTTACCCAA	0.284																																					p.Y590H		Atlas-SNP	.											.	ANKRD30B	237	.	0			c.T1768C						.						79	61	67					18																	14791433		692	1584	2276	SO:0001583	missense	374860	exon16			GATGTGTATTTAC	BC028407	CCDS54182.1	18p11.21	2013-01-10			ENSG00000180777	ENSG00000180777		"Ankyrin repeat domain containing"	24165	protein-coding gene	gene with protein product						11280766	Standard	NM_001145029		Approved	NY-BR-1.1	uc010dlo.2	Q9BXX2		ENST00000358984.4:c.1768T>C	chr18.hg19:g.14791433T>C	ENSP00000351875:p.Tyr590His	314.0	0.0		246.0	93.0	NM_001145029	B4DGP1|F8WAG3|Q4G175	Missense_Mutation	SNP	ENST00000358984.4	hg19	CCDS54182.1	.	.	.	.	.	.	.	.	.	.	N	2.726	-0.265509	0.05754	.	.	ENSG00000180777	ENST00000358984;ENST00000447268	T;T	0.05996	3.36;3.36	0.749	-1.5	0.08691	.	.	.	.	.	T	0.01800	0.0057	N	0.01576	-0.805	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.44620	-0.9316	9	0.20046	T	0.44	.	2.1247	0.03735	0.0:0.3053:0.3411:0.3536	.	590	F8WAG3	.	H	590	ENSP00000351875:Y590H;ENSP00000399031:Y590H	ENSP00000351875:Y590H	Y	+	1	0	ANKRD30B	14781433	0.102000	0.21896	0.000000	0.03702	0.002000	0.02628	0.521000	0.22893	-1.031000	0.03308	0.241000	0.17934	TAT	.	.		0.284	ANKRD30B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443557.1	NM_001145029		C	14791433	T	C	14791433	3	2	279	1	0	0	0	0	1	0	0	0	659	1638	57	2	1830	2	ANKRD30B	18	14791433	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	11049025	14791433	63285815	358	40117										
KIAA1012	22878	hgsc.bcm.edu	37	chr18	29446819	29446819	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ctatagcctttacctgtgtgAcatccgggaagagcaccaat	9	11	0	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr18:29446819A>G	ENST00000283351.4	-	18	2918	c.2583T>C	c.(2581-2583)tgT>tgC	p.C861C	TRAPPC8_ENST00000582539.1_Silent_p.C807C	NM_014939.3	NP_055754	Q9Y2L5	TPPC8_HUMAN	trafficking protein particle complex 8	861					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(7)|liver(2)|lung(13)|ovary(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						TACCTGTGTGACATCCGGGAA	0.383																																					p.C861C		Atlas-SNP	.											.	TRAPPC8	126	.	0			c.T2583C						.						145	141	143					18																	29446819		2203	4300	6503	SO:0001819	synonymous_variant	22878	exon18			TGTGTGACATCCG	AB023229	CCDS11901.1	18q12.1	2011-10-10	2010-06-29	2010-06-29	ENSG00000153339	ENSG00000153339		"Trafficking protein particle complex"	29169	protein-coding gene	gene with protein product	"general sporulation gene 1 homolog (S. cerevisiae)"	614136	"KIAA1012"	KIAA1012		10231032, 11230166	Standard	NM_014939		Approved	HsT2706, TRS85, GSG1	uc002kxc.4	Q9Y2L5	OTTHUMG00000132267	ENST00000283351.4:c.2583T>C	chr18.hg19:g.29446819A>G		62.0	0.0		59.0	4.0	NM_014939	A0JP15|B3KME5|Q9H0L2	Silent	SNP	ENST00000283351.4	hg19	CCDS11901.1																																																																																			.	.		0.383	TRAPPC8-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255355.1	NM_014939		G	29446819	A	G	29446819	2	3	279	1	0	0	0	0	0	0	0	1	8213	273	10	2		2	KIAA1012	18	29446819	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	14655386	29446819	48630429	359	40118										
KATNAL2	83473	hgsc.bcm.edu	37	chr18	44626699	44626699	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	atgcggcccgtgaggaagatCtttgatgcacttgaaaatca	11	8	2	4			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr18:44626699C>T	ENST00000245121.5	+	14	1427	c.1233C>T	c.(1231-1233)atC>atT	p.I411I	KATNAL2_ENST00000356157.7_Silent_p.I483I	NM_031303.2	NP_112593.2			katanin p60 subunit A-like 2											central_nervous_system(2)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	27						TGAGGAAGATCTTTGATGCAC	0.493											OREG0024959	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I411I		Atlas-SNP	.											.	KATNAL2	64	.	0			c.C1233T						.						103	92	96					18																	44626699		2203	4300	6503	SO:0001819	synonymous_variant	83473	exon14			GAAGATCTTTGAT	BC034999	CCDS32828.1	18q21.1	2010-04-21			ENSG00000167216	ENSG00000167216		"ATPases / AAA-type"	25387	protein-coding gene	gene with protein product		614697				12477932	Standard	NM_031303		Approved	MGC33211, DKFZP667C165	uc002lco.3	Q8IYT4		ENST00000245121.5:c.1233C>T	chr18.hg19:g.44626699C>T		47.0	0.0	925	36.0	7.0	NM_031303		Silent	SNP	ENST00000245121.5	hg19	CCDS32828.1																																																																																			.	.		0.493	KATNAL2-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446138.2	NM_031303		T	44626699	C	T	44626699	2	4	279	1	0	0	0	0	0	0	0	1	7995	903	32	3		3	KATNAL2	18	44626699	Silent	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	15179880	44626699	33450549	360	40119										
MAPK4	5596	hgsc.bcm.edu	37	chr18	48190780	48190780	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cgtgctgcacagggacctgaAgcccgccaacatcttcatca	9	15	3	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr18:48190780A>G	ENST00000400384.2	+	2	1488	c.452A>G	c.(451-453)aAg>aGg	p.K151R	MAPK4_ENST00000588540.1_Missense_Mutation_p.K151R|MAPK4_ENST00000587823.1_3'UTR|MAPK4_ENST00000540640.1_Intron|MAPK4_ENST00000592595.1_Missense_Mutation_p.K151R	NM_002747.3	NP_002738.2	P31152	MK04_HUMAN	mitogen-activated protein kinase 4	151	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|MAPK cascade (GO:0000165)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)			lung(4)|skin(3)|upper_aerodigestive_tract(1)	8		Colorectal(6;0.0297)		Colorectal(21;0.156)		AGGGACCTGAAGCCCGCCAAC	0.562																																					p.K151R		Atlas-SNP	.											.	MAPK4	75	.	0			c.A452G						.						60	63	62					18																	48190780		2196	4296	6492	SO:0001583	missense	5596	exon2			ACCTGAAGCCCGC	X59727	CCDS42437.1	18q21.1	2012-10-02			ENSG00000141639	ENSG00000141639		"Mitogen-activated protein kinase cascade / Kinases"	6878	protein-coding gene	gene with protein product		176949		PRKM4		8290275	Standard	XM_005258299		Approved	Erk3-related, Erk4	uc002lev.3	P31152	OTTHUMG00000179853	ENST00000400384.2:c.452A>G	chr18.hg19:g.48190780A>G	ENSP00000383234:p.Lys151Arg	93.0	0.0		79.0	4.0	NM_002747	A1A4C4|Q0VG04	Missense_Mutation	SNP	ENST00000400384.2	hg19	CCDS42437.1	.	.	.	.	.	.	.	.	.	.	A	31	5.066309	0.93898	.	.	ENSG00000141639	ENST00000400384	D	0.90900	-2.75	5.87	5.87	0.94306	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000001	D	0.96244	0.8775	M	0.91406	3.205	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.96952	0.9695	10	0.72032	D	0.01	-17.6672	15.2414	0.73474	1.0:0.0:0.0:0.0	.	151;151	Q0VG04;P31152	.;MK04_HUMAN	R	151	ENSP00000383234:K151R	ENSP00000383234:K151R	K	+	2	0	MAPK4	46444778	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.243000	0.73865	0.459000	0.35465	AAG	.	.		0.562	MAPK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448631.2	NM_002747		G	48190780	A	G	48190780	3	3	279	1	0	0	0	0	1	0	0	0	9289	72	3	2	454	2	MAPK4	18	48190780	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	3564081	48190780	29886468	361	40120										
STARD6	147323	hgsc.bcm.edu	37	chr18	51880863	51880863	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tattttcttactgaagttttAaccactttccagcctgatgt	5	9	1	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr18:51880863A>C	ENST00000581310.1	-	4	454	c.81T>G	c.(79-81)gtT>gtG	p.V27V	STARD6_ENST00000580990.2_5'Flank|STARD6_ENST00000584040.1_Silent_p.V27V|STARD6_ENST00000307844.3_Silent_p.V27V|STARD6_ENST00000577499.1_Silent_p.V27V			P59095	STAR6_HUMAN	StAR-related lipid transfer (START) domain containing 6	27	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				lipid transport (GO:0006869)		lipid binding (GO:0008289)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)	8				Colorectal(16;0.021)|READ - Rectum adenocarcinoma(59;0.188)		CTGAAGTTTTAACCACTTTCC	0.289																																					p.V27V		Atlas-SNP	.											.	STARD6	19	.	0			c.T81G						.						65	66	66					18																	51880863		2203	4300	6503	SO:0001819	synonymous_variant	147323	exon1			AGTTTTAACCACT	AF480305	CCDS11955.1	18q21.2	2011-09-12	2007-08-16		ENSG00000174448	ENSG00000174448		"StAR-related lipid transfer (START) domain containing"	18066	protein-coding gene	gene with protein product		607051	"START domain containing 6"			12011452	Standard	NM_139171		Approved		uc010xdt.2	P59095	OTTHUMG00000132702	ENST00000581310.1:c.81T>G	chr18.hg19:g.51880863A>C		192.0	0.0		170.0	55.0	NM_139171		Silent	SNP	ENST00000581310.1	hg19	CCDS11955.1																																																																																			.	.		0.289	STARD6-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256000.3	NM_139171		C	51880863	A	C	51880863	2	2	279	1	0	0	0	0	0	0	0	1	15276	349	13	5		5	STARD6	18	51880863	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	3690083	51880863	26196385	362	40121										
ATP8B1	5205	hgsc.bcm.edu	37	chr18	55351288	55351288	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	catcagtcctatccaccatgActgtgtggcaaactgcgagc	9	13	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr18:55351288A>G	ENST00000283684.4	-	14	1609	c.1610T>C	c.(1609-1611)gTc>gCc	p.V537A	RP11-35G9.5_ENST00000588925.1_RNA|RP11-35G9.3_ENST00000599199.1_RNA|ATP8B1_ENST00000536015.1_Missense_Mutation_p.V537A			O43520	AT8B1_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 1	537					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|drug transmembrane transport (GO:0006855)|inner ear receptor cell development (GO:0060119)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|phospholipid translocation (GO:0045332)|regulation of microvillus assembly (GO:0032534)|sensory perception of sound (GO:0007605)|transmembrane transport (GO:0055085)|vestibulocochlear nerve formation (GO:0021650)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|cardiolipin binding (GO:1901612)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(6)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(19)|ovary(3)|prostate(1)	53		Colorectal(73;0.229)				ATCCACCATGACTGTGTGGCA	0.448																																					p.V537A		Atlas-SNP	.											.	ATP8B1	126	.	0			c.T1610C						.						158	129	139					18																	55351288		2203	4300	6503	SO:0001583	missense	5205	exon15			ACCATGACTGTGT	AF038007	CCDS11965.1	18q21	2010-04-28	2010-04-28		ENSG00000081923	ENSG00000081923		"ATPases / P-type"	3706	protein-coding gene	gene with protein product		602397	"ATPase, Class I, type 8B, member 1", "ATPase, class I, type 8B, member 1"	FIC1, BRIC, PFIC1		9500542, 7655458	Standard	NM_005603		Approved	ATPIC, PFIC	uc002lgw.3	O43520	OTTHUMG00000132739	ENST00000283684.4:c.1610T>C	chr18.hg19:g.55351288A>G	ENSP00000283684:p.Val537Ala	62.0	0.0		93.0	6.0	NM_005603	Q9BTP8	Missense_Mutation	SNP	ENST00000283684.4	hg19	CCDS11965.1	.	.	.	.	.	.	.	.	.	.	A	19.56	3.849782	0.71603	.	.	ENSG00000081923	ENST00000283684;ENST00000536015	T;T	0.70749	-0.51;-0.51	5.81	5.81	0.92471	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.115168	0.56097	D	0.000021	T	0.79417	0.4442	M	0.75264	2.295	0.80722	D	1	P	0.52170	0.951	P	0.53035	0.716	T	0.81304	-0.0993	10	0.54805	T	0.06	.	15.1467	0.72657	1.0:0.0:0.0:0.0	.	537	O43520	AT8B1_HUMAN	A	537	ENSP00000283684:V537A;ENSP00000445359:V537A	ENSP00000283684:V537A	V	-	2	0	ATP8B1	53502286	1.000000	0.71417	1.000000	0.80357	0.274000	0.26718	9.330000	0.96422	2.225000	0.72522	0.379000	0.24179	GTC	.	.		0.448	ATP8B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256097.1	NM_005603		G	55351288	A	G	55351288	3	3	279	1	0	0	0	0	1	0	0	0	1194	275	10	2	2201	2	ATP8B1	18	55351288	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	3470425	55351288	22725960	363	40122										
PTBP1	5725	hgsc.bcm.edu	37	chr19	810762	810762	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ggtccaggccctcattgaccTgcacaaccacgacctcgggg	11	16	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr19:810762T>C	ENST00000349038.4	+	14	1605	c.1532T>C	c.(1531-1533)cTg>cCg	p.L511P	PTBP1_ENST00000350092.4_Missense_Mutation_p.L177P|MIR3187_ENST00000583431.1_RNA|PTBP1_ENST00000394601.4_Missense_Mutation_p.L530P|PTBP1_ENST00000356948.6_Missense_Mutation_p.L537P	NM_031991.3	NP_114368.1	P26599	PTBP1_HUMAN	polypyrimidine tract binding protein 1	511	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|negative regulation of muscle cell differentiation (GO:0051148)|negative regulation of RNA splicing (GO:0033119)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly-pyrimidine tract binding (GO:0008187)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(4)	19		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTCATTGACCTGCACAACCAC	0.677																																					p.L537P		Atlas-SNP	.											.	PTBP1	43	.	0			c.T1610C						.						72	75	74					19																	810762		2203	4300	6503	SO:0001583	missense	5725	exon15			TTGACCTGCACAA	X60648	CCDS32859.1, CCDS42456.1, CCDS45892.1	19p13.3	2013-07-16	2002-01-25	2002-01-25	ENSG00000011304	ENSG00000011304		"RNA binding motif (RRM) containing"	9583	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein I"	600693	"polypyrimidine tract binding protein (heterogeneous nuclear ribonucleoprotein I)"	PTB		1906036, 11024286	Standard	NM_002819		Approved	HNRPI, HNRNP-I, PTB2, PTB3, PTB-1, PTB4, pPTB	uc002lpp.2	P26599		ENST00000349038.4:c.1532T>C	chr19.hg19:g.810762T>C	ENSP00000014112:p.Leu511Pro	56.0	0.0		39.0	4.0	NM_002819	Q9BUQ0	Missense_Mutation	SNP	ENST00000349038.4	hg19	CCDS32859.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.687954	0.88639	.	.	ENSG00000011304	ENST00000356948;ENST00000394601;ENST00000349038;ENST00000350092	T;T;T;T	0.09911	2.93;2.99;2.93;2.93	5.38	5.38	0.77491	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.149797	0.47455	N	0.000239	T	0.42944	0.1225	M	0.92219	3.285	0.80722	D	1	D;D;D;D	0.89917	0.997;0.998;0.996;1.0	D;D;D;D	0.83275	0.996;0.994;0.986;0.996	T	0.55958	-0.8058	10	0.87932	D	0	-25.6391	14.5619	0.68144	0.0:0.0:0.0:1.0	.	177;511;530;537	A6NLN1;P26599;P26599-2;Q9BUQ0	.;PTBP1_HUMAN;.;.	P	537;530;511;177	ENSP00000349428:L537P;ENSP00000408096:L530P;ENSP00000014112:L511P;ENSP00000342332:L177P	ENSP00000014112:L511P	L	+	2	0	PTBP1	761762	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	5.952000	0.70282	2.027000	0.59764	0.533000	0.62120	CTG	.	.		0.677	PTBP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457605.1			C	810762	T	C	810762	3	2	279	1	0	0	0	0	1	0	0	0	12737	1580	55	2	1668	2	PTBP1	19	810762	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10		810762	58318221	364	40123										
MED16	10025	hgsc.bcm.edu	37	chr19	868154	868154	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ggatctgggggtcctgggagAgtggtgtgtggactgcgggc	22	6	1	1	rs372252782		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr19:868154A>G	ENST00000589119.1	-	15	2580	c.2581T>C	c.(2581-2583)Tct>Cct	p.S861P	MED16_ENST00000269814.4_3'UTR|MED16_ENST00000325464.1_Missense_Mutation_p.S861P|MED16_ENST00000312090.6_3'UTR|MED16_ENST00000395808.3_3'UTR			Q9Y2X0	MED16_HUMAN	mediator complex subunit 16	861					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|receptor activity (GO:0004872)|thyroid hormone receptor binding (GO:0046966)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GTCCTGGGAGAGTGGTGTGTG	0.682																																					p.S861P		Atlas-SNP	.											.	MED16	61	.	0			c.T2581C						.		PRO/SER	0,4392		0,0,2196	43	40	41		2581	0.8	0	19		41	1,8593	805.8+/-407.3	0,1,4296	no	missense	MED16	NM_005481.2	74	0,1,6492	GG,GA,AA		0.0116,0.0,0.0077	benign	861/878	868154	1,12985	2196	4297	6493	SO:0001583	missense	10025	exon16			TGGGAGAGTGGTG	AF121228	CCDS12047.1	19p13.3	2013-01-10	2007-07-30	2007-07-30		ENSG00000175221		"WD repeat domain containing"	17556	protein-coding gene	gene with protein product		604062	"thyroid hormone receptor associated protein 5"	THRAP5		10235266, 10198638	Standard	NM_005481		Approved	DRIP92, TRAP95	uc002lqd.1	Q9Y2X0		ENST00000589119.1:c.2581T>C	chr19.hg19:g.868154A>G	ENSP00000464810:p.Ser861Pro	92.0	0.0		80.0	4.0	NM_005481	Q6PJT2|Q96AD4|Q96I35|Q9Y652	Missense_Mutation	SNP	ENST00000589119.1	hg19	CCDS12047.1	.	.	.	.	.	.	.	.	.	.	g	0.007	-2.001328	0.00431	0.0	1.16E-4	ENSG00000175221	ENST00000325464	T	0.34072	1.38	0.84	0.84	0.18912	.	.	.	.	.	T	0.12902	0.0313	N	0.08118	0	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.32188	-0.9916	9	0.02654	T	1	.	3.3086	0.07009	0.3106:0.0:0.6894:0.0	.	861	Q9Y2X0	MED16_HUMAN	P	861	ENSP00000325612:S861P	ENSP00000325612:S861P	S	-	1	0	MED16	819154	0.000000	0.05858	0.002000	0.10522	0.018000	0.09664	0.115000	0.15540	-0.052000	0.13311	-0.370000	0.07254	TCT	.	.		0.682	MED16-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457902.3	NM_005481		G	868154	A	G	868154	3	3	279	1	0	0	0	0	1	0	0	0	9443	304	11	2	56	2	MED16	19	868154	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	57392	868154	58260829	365	40124										
GPX4	22904	hgsc.bcm.edu	37	chr19	1104930	1104930	+	IGR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tcccaagtcccaggacccggTgcgcgcggggcccccacacc	12	20	0	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr19:1104930T>C	ENST00000361757.3	-	0	4922				GPX4_ENST00000589115.1_Intron|GPX4_ENST00000354171.8_Intron	NM_014963.2	NP_055778.2	Q9Y2G9	SBNO2_HUMAN	strawberry notch homolog 2 (Drosophila)						bone mineralization (GO:0030282)|bone trabecula morphogenesis (GO:0061430)|macrophage activation involved in immune response (GO:0002281)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoclast fusion (GO:0072675)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of inflammatory response (GO:0050727)|transcription, DNA-templated (GO:0006351)					NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGGACCCGGTGCGCGCGGGG	0.682																																					.		Atlas-SNP	.											.	GPX4	9	.	0			c.195+2T>C						.						6	9	8					19																	1104930		1705	3878	5583	SO:0001628	intergenic_variant	2879	exon1			ACCCGGTGCGCGC	AK074102	CCDS45894.1, CCDS45895.1	19p13.3	2008-02-05	2006-10-06	2006-10-06		ENSG00000064932			29158	protein-coding gene	gene with protein product		615729	"KIAA0963"	KIAA0963		10231032	Standard	NM_014963		Approved	FLJ00173, Stno, Sno	uc002lrk.4	Q9Y2G9			chr19.hg19:g.1104930T>C		93.0	0.0		88.0	4.0	NM_001039848	A8K8P2|B3KWJ1|O75257|Q3KQX0|Q8TEM0	Splice_Site	SNP	ENST00000361757.3	hg19	CCDS45894.1																																																																																			.	.		0.682	SBNO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458065.2	NM_014963		C	1104930	T	C	1104930	1	2	279	0	1	0	0	0	0	0	0	0	6751	1710	59	2		2	GPX4	19	1104930	IGR	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	236776	1104930	58024053	366	40125										
RAX2	84839	hgsc.bcm.edu	37	chr19	3771558	3771558	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tcaggtaggtgcaccttggcTgccagctcctcacggctgta	12	13	2	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr19:3771558T>C	ENST00000555633.1	-	2	523	c.183A>G	c.(181-183)gcA>gcG	p.A61A	RAX2_ENST00000555978.1_Silent_p.A61A			Q96IS3	RAX2_HUMAN	retina and anterior neural fold homeobox 2	61					regulation of transcription, DNA-templated (GO:0006355)|response to stimulus (GO:0050896)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			large_intestine(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00463)|STAD - Stomach adenocarcinoma(1328;0.18)		GCACCTTGGCTGCCAGCTCCT	0.627																																					p.A61A		Atlas-SNP	.											.	RAX2	4	.	0			c.A183G						.						61	47	52					19																	3771558		2198	4296	6494	SO:0001819	synonymous_variant	84839	exon2			CTTGGCTGCCAGC	AY211277	CCDS12112.1	19p13.3	2013-06-06	2007-08-28	2007-08-28				"Homeoboxes / PRD class"	18286	protein-coding gene	gene with protein product		610362	"retina and anterior neural fold homeobox like 1"	RAXL1			Standard	NM_032753		Approved	MGC15631, ARMD6, CORD11	uc002lys.3	Q96IS3		ENST00000555633.1:c.183A>G	chr19.hg19:g.3771558T>C		62.0	0.0		76.0	4.0	NM_032753		Silent	SNP	ENST00000555633.1	hg19	CCDS12112.1	.	.	.	.	.	.	.	.	.	.	T	11.56	1.676507	0.29783	.	.	ENSG00000173976	ENST00000555978	.	.	.	3.52	-7.04	0.01578	.	.	.	.	.	T	0.34948	0.0915	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.36939	-0.9727	4	.	.	.	.	1.7359	0.02941	0.175:0.1269:0.2512:0.4469	.	.	.	.	G	81	.	.	S	-	1	0	RAX2	3722558	0.350000	0.24878	0.768000	0.31515	0.967000	0.64934	-0.415000	0.07106	-1.728000	0.01366	-1.067000	0.02272	AGC	.	.		0.627	RAX2-001	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411919.2	NM_032753		C	3771558	T	C	3771558	2	2	279	1	0	0	0	0	0	0	0	1	13112	1567	55	2		2	RAX2	19	3771558	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	2666628	3771558	55357425	367	40126										
PLIN4	729359	hgsc.bcm.edu	37	chr19	4510594	4510594	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tcctccctgcctggggcggcCccttgggtgaacgtcgccac	13	17	0	1	rs558381075		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr19:4510594C>T	ENST00000301286.3	-	3	3335	c.3336G>A	c.(3334-3336)ggG>ggA	p.G1112G		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	1112						cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						CTGGGGCGGCCCCTTGGGTGA	0.677																																					p.G1112G		Atlas-SNP	.											.	PLIN4	191	.	0			c.G3336A						.						29	34	32					19																	4510594		2147	4239	6386	SO:0001819	synonymous_variant	729359	exon3			GGCGGCCCCTTGG	AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"Perilipins"	29393	protein-coding gene	gene with protein product		613247	"KIAA1881"	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.3336G>A	chr19.hg19:g.4510594C>T		104.0	0.0		89.0	27.0	NM_001080400	A6NEI2	Silent	SNP	ENST00000301286.3	hg19	CCDS45927.1																																																																																			.	.		0.677	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901		T	4510594	C	T	4510594	2	4	279	1	0	0	0	0	0	0	0	1	12101	610	22	3		3	PLIN4	19	4510594	Silent	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	739036	4510594	54618389	368	40127										
EMR1	2015	hgsc.bcm.edu	37	chr19	6921786	6921786	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	actgatgtgaagggtggaagAtggacatcctttggctgtgt	15	5	0	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr19:6921786A>G	ENST00000312053.4	+	14	1720	c.1683A>G	c.(1681-1683)agA>agG	p.R561R	EMR1_ENST00000250572.8_Silent_p.R561R|EMR1_ENST00000381404.4_Silent_p.R509R|EMR1_ENST00000381407.5_Silent_p.R420R|EMR1_ENST00000450315.3_Silent_p.R384R	NM_001974.4	NP_001965.3	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 1	561	GPS. {ECO:0000255|PROSITE- ProRule:PRU00098}.|Ser/Thr-rich.				cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(8)	62	all_hematologic(4;0.166)					AGGGTGGAAGATGGACATCCT	0.443																																					p.R561R		Atlas-SNP	.											.	EMR1	153	.	0			c.A1683G						.						129	114	119					19																	6921786		2203	4300	6503	SO:0001819	synonymous_variant	2015	exon14			TGGAAGATGGACA	X81479	CCDS12175.1, CCDS58643.1, CCDS58644.1, CCDS58645.1, CCDS58646.1	19p13.3	2014-08-08	2003-11-26					"-", "GPCR / Class B : Orphans"	3336	protein-coding gene	gene with protein product		600493	"egf-like module containing, mucin-like, hormone receptor-like sequence 1"	TM7LN3		7601460, 9500513	Standard	NM_001974		Approved		uc002mfw.4	Q14246		ENST00000312053.4:c.1683A>G	chr19.hg19:g.6921786A>G		111.0	0.0		96.0	4.0	NM_001256253	A6NHV2|B7Z486|B7Z489|E7EPX9|E9PD45|H9KV79|Q2I7G5|Q6ZMN0|Q8NGA7	Silent	SNP	ENST00000312053.4	hg19	CCDS12175.1																																																																																			.	.		0.443	EMR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458485.1			G	6921786	A	G	6921786	2	3	279	1	0	0	0	0	0	0	0	1	5106	330	12	2		2	EMR1	19	6921786	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	2411192	6921786	52207197	369	40128										
ZNF266	10781	hgsc.bcm.edu	37	chr19	9528560	9528560	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cttgttccagccaagagatcAgactgggtttgaagagctga	12	8	1	5			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr19:9528560A>G	ENST00000592904.1	-	3	2135	c.59T>C	c.(58-60)cTg>cCg	p.L20P	ZNF266_ENST00000588933.1_Missense_Mutation_p.L20P|ZNF266_ENST00000361451.2_Missense_Mutation_p.L20P|ZNF266_ENST00000590306.1_Missense_Mutation_p.L20P|ZNF266_ENST00000592292.1_Missense_Mutation_p.L20P|ZNF266_ENST00000588221.1_Missense_Mutation_p.L20P|ZNF266_ENST00000361151.1_Missense_Mutation_p.L20P			Q14584	ZN266_HUMAN	zinc finger protein 266	20	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(2)|large_intestine(11)|lung(8)|ovary(1)|skin(2)|stomach(1)	28						CCAAGAGATCAGACTGGGTTT	0.443																																					p.L20P		Atlas-SNP	.											.	ZNF266	65	.	0			c.T59C						.						186	179	182					19																	9528560		2203	4300	6503	SO:0001583	missense	10781	exon9			GAGATCAGACTGG	X78924	CCDS12213.1	19p13.2	2013-01-08				ENSG00000174652		"Zinc fingers, C2H2-type"	13059	protein-coding gene	gene with protein product		604751				7865130	Standard	NM_006631		Approved	HZF1	uc002mlo.4	Q14584		ENST00000592904.1:c.59T>C	chr19.hg19:g.9528560A>G	ENSP00000466714:p.Leu20Pro	96.0	0.0		91.0	4.0	NM_001271314	A0AV90|A4FU85|Q6IQ07|Q6U8A5|Q8IVG3|Q8WVX1|Q96SX9	Missense_Mutation	SNP	ENST00000592904.1	hg19	CCDS12213.1	.	.	.	.	.	.	.	.	.	.	A	18.57	3.653605	0.67472	.	.	ENSG00000174652	ENST00000361451;ENST00000361151	T;T	0.00976	5.48;5.48	2.41	2.41	0.29592	Krueppel-associated box (2);	.	.	.	.	T	0.04092	0.0114	M	0.78049	2.395	0.09310	N	0.999999	D	0.89917	1.0	D	0.71656	0.974	T	0.27905	-1.0060	9	0.72032	D	0.01	.	6.7472	0.23468	1.0:0.0:0.0:0.0	.	20	Q14584	ZN266_HUMAN	P	20	ENSP00000354680:L20P;ENSP00000355047:L20P	ENSP00000355047:L20P	L	-	2	0	ZNF266	9389560	0.024000	0.19004	0.004000	0.12327	0.978000	0.69477	2.988000	0.49386	1.357000	0.45904	0.482000	0.46254	CTG	.	.		0.443	ZNF266-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449033.1			G	9528560	A	G	9528560	3	3	279	1	0	0	0	0	1	0	0	0	17820	188	7	2	1602	2	ZNF266	19	9528560	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	2606774	9528560	49600423	370	40129										
DNM2	1785	hgsc.bcm.edu	37	chr19	10906847	10906847	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cctggttatccaggagctaaTcaatacagttaggcagtgta	10	8	1	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr19:10906847T>G	ENST00000355667.6	+	10	1387	c.1307T>G	c.(1306-1308)aTc>aGc	p.I436S	DNM2_ENST00000359692.6_Missense_Mutation_p.I436S|DNM2_ENST00000408974.4_Intron|DNM2_ENST00000314646.5_Intron|DNM2_ENST00000585892.1_Missense_Mutation_p.I436S|DNM2_ENST00000389253.4_Intron	NM_001005360.2|NM_001190716.1	NP_001005360.1|NP_001177645.1	P50570	DYN2_HUMAN	dynamin 2	436					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|endocytosis (GO:0006897)|G2/M transition of mitotic cell cycle (GO:0000086)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|nitric oxide metabolic process (GO:0046209)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic vesicle transport (GO:0048489)|transferrin transport (GO:0033572)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	enzyme binding (GO:0019899)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|microtubule binding (GO:0008017)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	42			Epithelial(33;4.17e-05)|all cancers(31;8.48e-05)			CAGGAGCTAATCAATACAGTT	0.532			"F, N, Splice, Mis, O"		ETP ALL																																p.I436S		Atlas-SNP	.		Rec	yes		19	19p13.2	1785	dynamin 2		L	.	DNM2	175	.	0			c.T1307G						.						169	151	157					19																	10906847		2203	4300	6503	SO:0001583	missense	1785	exon10			AGCTAATCAATAC		CCDS32907.1, CCDS32908.1, CCDS45968.1, CCDS45969.1, CCDS59351.1	19p	2014-09-17						"Pleckstrin homology (PH) domain containing"	2974	protein-coding gene	gene with protein product	"dynamin II", "cytoskeletal protein"	602378				7590285, 9143510	Standard	NM_001190716		Approved	DYNII, DYN2, CMTDIB, CMTDI1, DI-CMTB	uc002mps.2	P50570		ENST00000355667.6:c.1307T>G	chr19.hg19:g.10906847T>G	ENSP00000347890:p.Ile436Ser	162.0	0.0		138.0	42.0	NM_004945	A8K1B6|E7EV30|E9PEQ4|K7ESI9|Q5I0Y0|Q7Z5S3|Q9UPH4	Missense_Mutation	SNP	ENST00000355667.6	hg19	CCDS45968.1	.	.	.	.	.	.	.	.	.	.	T	14.24	2.476612	0.44044	.	.	ENSG00000079805	ENST00000355667;ENST00000359692	T;T	0.72505	-0.66;-0.66	4.59	4.59	0.56863	Dynamin central domain (1);Pleckstrin homology-type (1);	.	.	.	.	T	0.68007	0.2954	L	0.42487	1.325	0.80722	D	1	B;B	0.25521	0.128;0.004	B;B	0.38378	0.272;0.026	T	0.65022	-0.6269	9	0.33141	T	0.24	.	12.9716	0.58515	0.0:0.0:0.0:1.0	.	436;436	P50570-2;P50570	.;DYN2_HUMAN	S	436	ENSP00000347890:I436S;ENSP00000352721:I436S	ENSP00000347890:I436S	I	+	2	0	DNM2	10767847	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.268000	0.72552	1.709000	0.51313	0.459000	0.35465	ATC	.	.		0.532	DNM2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452592.1	NM_004945		G	10906847	T	G	10906847	3	3	279	1	0	0	0	0	1	0	0	0	4674	1435	50	5	1345	5	DNM2	19	10906847	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	1378287	10906847	48222136	371	40130										
PIK3R2	5296	hgsc.bcm.edu	37	chr19	18279290	18279290	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cctgttccttctcaggtggcTcacccagaaaggcgcccggc	11	16	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr19:18279290T>C	ENST00000593731.1	+	14	2302	c.1742T>C	c.(1741-1743)cTc>cCc	p.L581P	PIK3R2_ENST00000222254.8_Missense_Mutation_p.L581P			O00459	P85B_HUMAN	phosphoinositide-3-kinase, regulatory subunit 2 (beta)	581					blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)	phosphatidylinositol 3-kinase regulator activity (GO:0035014)|receptor tyrosine kinase binding (GO:0030971)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(3)|pancreas(1)|stomach(1)	24					Isoprenaline(DB01064)	ctcaggtggctcacccagaaa	0.597											OREG0025359	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L581P		Atlas-SNP	.											.	PIK3R2	48	.	0			c.T1742C						.						35	36	36					19																	18279290		2203	4300	6503	SO:0001583	missense	5296	exon14			GGTGGCTCACCCA		CCDS12371.1	19p13.11	2013-03-28	2008-02-04		ENSG00000105647	ENSG00000105647		"SH2 domain containing"	8980	protein-coding gene	gene with protein product		603157				1314371	Standard	NM_005027		Approved	P85B, p85	uc002nia.2	O00459	OTTHUMG00000183383	ENST00000593731.1:c.1742T>C	chr19.hg19:g.18279290T>C	ENSP00000471914:p.Leu581Pro	53.0	0.0	724	54.0	5.0	NM_005027	Q5EAT5|Q9UPH9	Missense_Mutation	SNP	ENST00000593731.1	hg19	CCDS12371.1	.	.	.	.	.	.	.	.	.	.	T	19.09	3.760585	0.69763	.	.	ENSG00000105647	ENST00000222254	T	0.37915	1.17	3.5	3.5	0.40072	.	0.173720	0.38778	N	0.001571	T	0.60051	0.2239	M	0.88842	2.985	0.80722	D	1	D	0.76494	0.999	D	0.63283	0.913	T	0.67654	-0.5615	10	0.87932	D	0	-26.9665	10.4366	0.44439	0.0:0.0:0.0:1.0	.	581	O00459	P85B_HUMAN	P	581	ENSP00000222254:L581P	ENSP00000222254:L581P	L	+	2	0	PIK3R2	18140290	1.000000	0.71417	0.998000	0.56505	0.821000	0.46438	6.768000	0.74980	1.555000	0.49500	0.254000	0.18369	CTC	.	.		0.597	PIK3R2-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000466386.2	NM_005027		C	18279290	T	C	18279290	3	2	279	1	0	0	0	0	1	0	0	0	11928	1551	54	2	1792	2	PIK3R2	19	18279290	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	7372443	18279290	40849693	372	40131										
MLL4	9757	hgsc.bcm.edu	37	chr19	36210419	36210419	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	atgtggcccccagttccctgCgctctgcgctccgatcccag	10	18	1	0	rs567944243		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr19:36210419C>T	ENST00000222270.7	+	2	412	c.412C>T	c.(412-414)Cgc>Tgc	p.R138C	KMT2B_ENST00000341701.1_Missense_Mutation_p.R138C|KMT2B_ENST00000420124.1_Missense_Mutation_p.R138C|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	138					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										CAGTTCCCTGCGCTCTGCGCT	0.567													C|||	1	0.000199681	0	0	5008	,	,		18239	0.001		0	False		,,,				2504	0				p.R138C		Atlas-SNP	.											.	MLL4	229	.	0			c.C412T						.						58	58	58					19																	36210419		1932	4135	6067	SO:0001583	missense	8085	exon2			TCCCTGCGCTCTG	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"Chromatin-modifying enzymes / K-methyltransferases"	15840	protein-coding gene	gene with protein product	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.412C>T	chr19.hg19:g.36210419C>T	ENSP00000222270:p.Arg138Cys	68.0	0.0		51.0	4.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Missense_Mutation	SNP	ENST00000222270.7	hg19	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.964494	0.74131	.	.	ENSG00000105663	ENST00000222270;ENST00000420124;ENST00000341701	D;D;T	0.90732	-2.72;-2.72;0.0	5.35	5.35	0.76521	.	0.000000	0.42548	D	0.000687	D	0.90920	0.7146	N	0.14661	0.345	0.51233	D	0.999912	D	0.89917	1.0	D	0.77557	0.99	D	0.92801	0.6256	10	0.87932	D	0	.	16.5535	0.84478	0.0:1.0:0.0:0.0	.	138	Q9UMN6	MLL4_HUMAN	C	138	ENSP00000222270:R138C;ENSP00000398837:R138C;ENSP00000345761:R138C	ENSP00000222270:R138C	R	+	1	0	AD000671.1	40902259	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.185000	0.58330	2.516000	0.84829	0.561000	0.74099	CGC	.	.		0.567	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727		T	36210419	C	T	36210419	3	4	279	1	0	0	0	0	1	0	0	0	9632	768	27	1	418	1	MLL4	19	36210419	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	17931129	36210419	22918564	373	40132										
ZNF829	374899	hgsc.bcm.edu	37	chr19	37383205	37383205	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gtgagttttgattaaaggtcTttccacatatcttacattcc	6	8	2	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr19:37383205T>C	ENST00000391711.3	-	6	852	c.488A>G	c.(487-489)aAg>aGg	p.K163R	ZNF345_ENST00000432005.2_Intron|ZNF829_ENST00000520965.1_Missense_Mutation_p.K244R|ZNF345_ENST00000526123.1_Intron	NM_001037232.3	NP_001032309.2	Q3KNS6	ZN829_HUMAN	zinc finger protein 829	163					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|large_intestine(11)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			ATTAAAGGTCTTTCCACATAT	0.368																																					p.K244R		Atlas-SNP	.											.	ZNF829	70	.	0			c.A731G						.						75	68	70					19																	37383205		1984	4186	6170	SO:0001583	missense	374899	exon6			AAGGTCTTTCCAC	BC107131	CCDS42557.1, CCDS59380.1	19q13.12	2013-01-08			ENSG00000185869	ENSG00000185869		"Zinc fingers, C2H2-type", "-"	34032	protein-coding gene	gene with protein product							Standard	NM_001037232		Approved	DKFZp779O175	uc021utr.1	Q3KNS6	OTTHUMG00000048161	ENST00000391711.3:c.488A>G	chr19.hg19:g.37383205T>C	ENSP00000429266:p.Lys163Arg	59.0	0.0		60.0	4.0	NM_001171979	Q3KNS7|Q6ZNN0|Q7Z657	Missense_Mutation	SNP	ENST00000391711.3	hg19	CCDS42557.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.948851	0.73787	.	.	ENSG00000185869	ENST00000520965;ENST00000391711	T	0.58060	0.36	3.18	3.18	0.36537	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.52757	0.1754	L	0.46885	1.475	0.27099	N	0.962655	P	0.46621	0.881	P	0.47864	0.559	T	0.48375	-0.9041	9	0.66056	D	0.02	.	11.3524	0.49596	0.0:0.0:0.0:1.0	.	163	Q3KNS6	ZN829_HUMAN	R	163	ENSP00000429266:K163R	ENSP00000429266:K163R	K	-	2	0	ZNF829	42075045	0.306000	0.24490	0.943000	0.38184	0.993000	0.82548	2.730000	0.47335	1.693000	0.51124	0.528000	0.53228	AAG	.	.		0.368	ZNF829-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109575.3	NM_001037232		C	37383205	T	C	37383205	3	2	279	1	0	0	0	0	1	0	0	0	18197	1609	56	2	814	2	ZNF829	19	37383205	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	1172786	37383205	21745778	374	40133										
ZNF404	342908	hgsc.bcm.edu	37	chr19	44384170	44384170	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	agatattcttacccaatgagAccaagttagtataattctcc	5	9	2	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr19:44384170A>G	ENST00000587539.1	-	2	127	c.128T>C	c.(127-129)gTc>gCc	p.V43A	ZNF404_ENST00000588094.1_5'Flank|ZNF404_ENST00000324394.6_Missense_Mutation_p.V41A	NM_001033719.2	NP_001028891.2	Q494X3	ZN404_HUMAN	zinc finger protein 404	43	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|skin(1)|stomach(2)|urinary_tract(1)	17		Prostate(69;0.0352)				ACCCAATGAGACCAAGTTAGT	0.383																																					p.V40A		Atlas-SNP	.											.	ZNF404	46	.	0			c.T119C						.						176	187	183					19																	44384170		2186	4293	6479	SO:0001583	missense	342908	exon1			AATGAGACCAAGT	XM_092027	CCDS59394.1	19q13.31	2013-01-08				ENSG00000176222		"Zinc fingers, C2H2-type", "-"	19417	protein-coding gene	gene with protein product							Standard	NM_001033719		Approved		uc002oxs.5	Q494X3		ENST00000587539.1:c.128T>C	chr19.hg19:g.44384170A>G	ENSP00000466051:p.Val43Ala	76.0	0.0		92.0	4.0	NM_001033719	A4FU30|K7ELF2	Missense_Mutation	SNP	ENST00000587539.1	hg19	CCDS59394.1	.	.	.	.	.	.	.	.	.	.	A	8.638	0.895377	0.17613	.	.	ENSG00000176222	ENST00000324394	T	0.02140	4.43	1.85	0.821	0.18799	Krueppel-associated box (4);	.	.	.	.	T	0.03011	0.0089	M	0.67569	2.06	0.20638	N	0.999877	B	0.12630	0.006	B	0.16289	0.015	T	0.41466	-0.9507	9	0.33940	T	0.23	.	4.1478	0.10224	0.6373:0.0:0.3627:0.0	.	43	Q494X3	ZN404_HUMAN	A	41	ENSP00000319479:V41A	ENSP00000319479:V41A	V	-	2	0	ZNF404	49076010	0.000000	0.05858	0.679000	0.29978	0.988000	0.76386	-0.075000	0.11431	0.214000	0.20742	0.410000	0.27636	GTC	.	.		0.383	ZNF404-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460019.1	NM_001033719		G	44384170	A	G	44384170	3	3	279	1	0	0	0	0	1	0	0	0	17901	275	10	2	1538	2	ZNF404	19	44384170	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	7000965	44384170	14744813	375	40134										
ZFP112	7771	hgsc.bcm.edu	37	chr19	44831614	44831614	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	aaacagaatcttcatttctgTgtagattctctgatgaaggg	9	6	4	4			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr19:44831614T>C	ENST00000337401.4	-	5	2802	c.2714A>G	c.(2713-2715)cAc>cGc	p.H905R	ZNF112_ENST00000354340.4_Missense_Mutation_p.H899R|ZNF112_ENST00000536500.1_Missense_Mutation_p.H922R	NM_001083335.1	NP_001076804.1	Q9UJU3	ZN112_HUMAN	zinc finger protein 112	905					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										TTCATTTCTGTGTAGATTCTC	0.343																																					p.H905R		Atlas-SNP	.											.	ZFP112	219	.	0			c.A2714G						.						51	50	51					19																	44831614		2203	4299	6502	SO:0001583	missense	7771	exon5			TTTCTGTGTAGAT	AF198358		19q13.2	2014-02-06	2012-11-27		ENSG00000062370	ENSG00000062370		"Zinc fingers, C2H2-type"	12892	protein-coding gene	gene with protein product		603994	"zinc finger protein 112 homolog (mouse)", "zinc finger protein 228"	ZFP112, ZNF228			Standard	NM_013380		Approved			Q9UJU3	OTTHUMG00000182357	ENST00000337401.4:c.2714A>G	chr19.hg19:g.44831614T>C	ENSP00000337081:p.His905Arg	79.0	0.0		58.0	4.0	NM_001083335	A4FU53|Q9HCA7	Missense_Mutation	SNP	ENST00000337401.4	hg19	CCDS54276.1	.	.	.	.	.	.	.	.	.	.	T	3.556	-0.090586	0.07053	.	.	ENSG00000062370	ENST00000337401;ENST00000412927;ENST00000354340;ENST00000536500;ENST00000253426	T;T;T	0.05199	3.48;3.48;3.49	4.74	1.15	0.20763	.	0.473653	0.15676	N	0.250140	T	0.02380	0.0073	N	0.03967	-0.31	0.09310	N	1	B;B;B	0.18741	0.017;0.03;0.017	B;B;B	0.10450	0.002;0.005;0.002	T	0.45789	-0.9237	10	0.25106	T	0.35	0.0431	4.3488	0.11146	0.1489:0.1949:0.0:0.6563	.	904;922;905	B4DYT4;F5GWS7;Q9UJU3	.;.;ZF112_HUMAN	R	905;905;899;922;904	ENSP00000337081:H905R;ENSP00000346305:H899R;ENSP00000441990:H922R	ENSP00000253426:H904R	H	-	2	0	ZNF285	49523454	0.005000	0.15991	0.022000	0.16811	0.979000	0.70002	1.614000	0.36911	0.410000	0.25675	0.460000	0.39030	CAC	.	.		0.343	ZNF112-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460744.1	NM_013380		C	44831614	T	C	44831614	3	2	279	1	0	0	0	0	1	0	0	0	17653	1696	59	2	31	2	ZFP112	19	44831614	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	447444	44831614	14297369	376	40135										
CLPTM1	1209	hgsc.bcm.edu	37	chr19	45488528	45488528	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	aaaaccaagaacctgctgacAggagagacagaagcggaccc	11	11	0	4			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr19:45488528A>G	ENST00000337392.5	+	6	789	c.639A>G	c.(637-639)acA>acG	p.T213T	CLPTM1_ENST00000541297.2_Silent_p.T199T|CLPTM1_ENST00000546079.1_Silent_p.T111T|CLPTM1_ENST00000589158.1_3'UTR	NM_001282175.1|NM_001282176.1|NM_001294.2	NP_001269104.1|NP_001269105.1|NP_001285.1	O96005	CLPT1_HUMAN	cleft lip and palate associated transmembrane protein 1	213					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of T cell differentiation in thymus (GO:0033081)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00354)|Epithelial(262;0.187)		ACCTGCTGACAGGAGAGACAG	0.537																																					p.T213T		Atlas-SNP	.											.	CLPTM1	109	.	0			c.A639G						.						102	96	98					19																	45488528		2203	4300	6503	SO:0001819	synonymous_variant	1209	exon6			GCTGACAGGAGAG	AF037339	CCDS12651.1, CCDS74394.1, CCDS74395.1	19q13.3	2008-02-05				ENSG00000104853			2087	protein-coding gene	gene with protein product		604783				9828125	Standard	NM_001294		Approved		uc002pai.3	O96005		ENST00000337392.5:c.639A>G	chr19.hg19:g.45488528A>G		80.0	0.0		75.0	34.0	NM_001294	B3KQH2|B4DDS3|B4E2X9|B7Z9X9|F5H8J3|Q53ET6|Q9BSS5	Silent	SNP	ENST00000337392.5	hg19	CCDS12651.1																																																																																			.	.		0.537	CLPTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453267.1	NM_001294		G	45488528	A	G	45488528	2	3	279	1	0	0	0	0	0	0	0	1	3556	175	7	2		2	CLPTM1	19	45488528	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	656914	45488528	13640455	377	40136										
CD3EAP	10849	hgsc.bcm.edu	37	chr19	45912491	45912492	+	Missense_Mutation	DNP	AG	AG	CC													0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ggcagctcccacatccaccaAgaagaagaagaagaagaaag					rs374686338|rs35729377		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A|G	A|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr19:45912491_45912492AG>CC	ENST00000309424.3	+	3	1753_1754	c.1265_1266AG>CC	c.(1264-1266)aAG>aCC	p.K422T	PPP1R13L_ENST00000418234.2_5'Flank|ERCC1_ENST00000423698.2_3'UTR|ERCC1_ENST00000300853.3_3'UTR|CD3EAP_ENST00000589804.1_Missense_Mutation_p.K424T|ERCC1_ENST00000588738.1_5'Flank	NM_012099.1	NP_036231.1	O15446	RPA34_HUMAN	CD3e molecule, epsilon associated protein	422	Poly-Lys.			Missing (in Ref. 3; AAI08890). {ECO:0000305}.	rRNA transcription (GO:0009303)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|RNA polymerase I transcription factor complex (GO:0000120)	DNA-directed RNA polymerase activity (GO:0003899)|poly(A) RNA binding (GO:0044822)			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)		ACATCCACCaagaagaagaaga	0.554																																					p.K422T|p.K422N		Atlas-SNP	.											.	CD3EAP	27	.	0			c.A1265C|c.G1266C						.																																			SO:0001583	missense	10849	exon3			CCACCAAGAAGAA|CACCAAGAAGAAG	U86751	CCDS12661.1, CCDS74397.1	19q13.3	2008-02-05	2006-03-28			ENSG00000117877			24219	protein-coding gene	gene with protein product	"CD3 epsilon associated protein", "antisense to ERCC 1"	107325	"CD3e antigen, epsilon polypeptide associated protein"			10373416, 9426281, 15226435	Standard	XM_005258425		Approved	ASE-1, CAST, PAF49	uc002pbq.1	O15446		Exception_encountered	chr19.hg19:g.45912491_45912492delinsCC	ENSP00000310966:p.Lys422Thr	51.0	0.0		47.0|50.0	4.0|6.0	NM_012099	Q32N11|Q7Z5U2|Q9UPF6	Missense_Mutation	SNP	ENST00000309424.3	hg19	CCDS12661.1																																																																																			.	.		0.554	CD3EAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459538.1	NM_012099		CC	45912492	AG	CC	45912491	3	2	279	1	0	0	0	0	1	0	0	0	3014	72	3	5	1275	5	CD3EAP	19	45912491	Missense_Mutation	DNP	AG	TCGA-G3-A3CG-01A-11D-A20W-10	423963	45912491	13216492	378	40137										
SYMPK	8189	hgsc.bcm.edu	37	chr19	46319817	46319817	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ctccaagatggtcatgatggAgttagggatgtgagcttgct	14	6	1	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr19:46319817A>G	ENST00000245934.7	-	25	3521	c.3277T>C	c.(3277-3279)Tcc>Ccc	p.S1093P	RSPH6A_ENST00000597055.1_5'Flank|SYMPK_ENST00000598155.1_5'UTR|RSPH6A_ENST00000221538.3_5'Flank	NM_004819.2	NP_004810.2	Q92797	SYMPK_HUMAN	symplekin	1093					cell adhesion (GO:0007155)|mRNA polyadenylation (GO:0006378)|positive regulation of protein dephosphorylation (GO:0035307)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(25)|ovary(1)|urinary_tract(1)	45		all_neural(266;0.0299)|Ovarian(192;0.0308)		OV - Ovarian serous cystadenocarcinoma(262;0.00509)|GBM - Glioblastoma multiforme(486;0.0593)		GTCATGATGGAGTTAGGGATG	0.667																																					p.S1093P		Atlas-SNP	.											.	SYMPK	104	.	0			c.T3277C						.						37	41	40					19																	46319817		2203	4300	6503	SO:0001583	missense	8189	exon25			TGATGGAGTTAGG	U49240	CCDS12676.2	19q13.3	2008-02-05			ENSG00000125755	ENSG00000125755			22935	protein-coding gene	gene with protein product		602388				9330635	Standard	NM_004819		Approved	SYM, SPK	uc002pdn.3	Q92797	OTTHUMG00000150151	ENST00000245934.7:c.3277T>C	chr19.hg19:g.46319817A>G	ENSP00000245934:p.Ser1093Pro	108.0	0.0		106.0	5.0	NM_004819	O00521|O00689|O00733|Q59GT5|Q8N2U5	Missense_Mutation	SNP	ENST00000245934.7	hg19	CCDS12676.2	.	.	.	.	.	.	.	.	.	.	A	17.35	3.368723	0.61624	.	.	ENSG00000125755	ENST00000245934	.	.	.	4.4	4.4	0.53042	.	0.000000	0.85682	D	0.000000	T	0.39462	0.1079	L	0.27053	0.805	0.53688	D	0.999979	P	0.39044	0.656	B	0.39339	0.297	T	0.32561	-0.9902	9	0.45353	T	0.12	.	9.9684	0.41738	1.0:0.0:0.0:0.0	.	1093	Q92797	SYMPK_HUMAN	P	1093	.	ENSP00000245934:S1093P	S	-	1	0	SYMPK	51011657	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.675000	0.84002	1.853000	0.53794	0.454000	0.30748	TCC	.	.		0.667	SYMPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316581.1	NM_004819		G	46319817	A	G	46319817	3	3	279	1	0	0	0	0	1	0	0	0	15454	304	11	2	559	2	SYMPK	19	46319817	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	407326	46319817	12809166	379	40138										
IGFL1	374918	hgsc.bcm.edu	37	chr19	46733725	46733725	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ccttcatggtgaagctgataAaccagaactgcgactcagcc	9	12	2	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr19:46733725A>G	ENST00000437936.1	+	3	297	c.274A>G	c.(274-276)Aac>Gac	p.N92D	AC006262.10_ENST00000597337.1_RNA	NM_198541.1	NP_940943.1	Q6UW32	IGFL1_HUMAN	IGF-like family member 1	92						extracellular space (GO:0005615)				lung(5)	5		Ovarian(192;0.0731)|all_neural(266;0.196)		OV - Ovarian serous cystadenocarcinoma(262;0.00242)|all cancers(93;0.0132)|GBM - Glioblastoma multiforme(486;0.0294)|Epithelial(262;0.201)		GAAGCTGATAAACCAGAACTG	0.597																																					p.N92D		Atlas-SNP	.											.	IGFL1	10	.	0			c.A274G						.						115	116	116					19																	46733725		2049	4212	6261	SO:0001583	missense	374918	exon3			CTGATAAACCAGA	AY359013	CCDS46123.1	19q13.32	2010-06-15			ENSG00000188293	ENSG00000188293			24093	protein-coding gene	gene with protein product		610544				12975309	Standard	NM_198541		Approved	UNQ644	uc002pee.3	Q6UW32		ENST00000437936.1:c.274A>G	chr19.hg19:g.46733725A>G	ENSP00000415823:p.Asn92Asp	82.0	0.0		65.0	4.0	NM_198541		Missense_Mutation	SNP	ENST00000437936.1	hg19	CCDS46123.1	.	.	.	.	.	.	.	.	.	.	A	1.364	-0.587895	0.03799	.	.	ENSG00000188293	ENST00000437936	T	0.23348	1.91	2.61	-1.13	0.09775	.	2.589850	0.02370	N	0.077809	T	0.09069	0.0224	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.23511	-1.0186	10	0.09590	T	0.72	-6.8682	5.3976	0.16278	0.4223:0.0:0.5777:0.0	.	92	Q6UW32	IGFL1_HUMAN	D	92	ENSP00000415823:N92D	ENSP00000415823:N92D	N	+	1	0	IGFL1	51425565	0.001000	0.12720	0.000000	0.03702	0.059000	0.15707	0.076000	0.14712	-0.114000	0.11936	-0.609000	0.04063	AAC	.	.		0.597	IGFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461724.1	NM_198541		G	46733725	A	G	46733725	3	3	279	1	0	0	0	0	1	0	0	0	7595	14	1	2	284	2	IGFL1	19	46733725	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	413908	46733725	12395258	380	40139										
CALM3	808	hgsc.bcm.edu	37	chr19	47111479	47111479	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	aaggaggccttctccctcttTgacaaggatggagatggcac	12	10	2	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr19:47111479T>C	ENST00000291295.9	+	3	259	c.60T>C	c.(58-60)ttT>ttC	p.F20F	CALM3_ENST00000597743.1_Silent_p.F20F|CALM3_ENST00000594523.1_5'UTR|CALM3_ENST00000477244.1_3'UTR|CALM3_ENST00000599839.1_5'UTR|CTB-12A17.3_ENST00000597609.1_RNA|CALM3_ENST00000391918.2_5'UTR|CALM3_ENST00000596362.1_Silent_p.F20F|CALM3_ENST00000598871.1_5'UTR	NM_005184.2	NP_005175.2	P62158	CALM_HUMAN	calmodulin 3 (phosphorylase kinase, delta)	20	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				activation of adenylate cyclase activity (GO:0007190)|activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|carbohydrate metabolic process (GO:0005975)|detection of calcium ion (GO:0005513)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nitric oxide metabolic process (GO:0046209)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cyclic nucleotide metabolic process (GO:0030801)|positive regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051343)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of cytokinesis (GO:0032465)|regulation of heart rate (GO:0002027)|regulation of high voltage-gated calcium channel activity (GO:1901841)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|response to amphetamine (GO:0001975)|response to calcium ion (GO:0051592)|response to corticosterone (GO:0051412)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)|synaptic transmission (GO:0007268)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcomere (GO:0030017)|spindle microtubule (GO:0005876)|spindle pole (GO:0000922)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|N-terminal myristoylation domain binding (GO:0031997)|nitric-oxide synthase regulator activity (GO:0030235)|phospholipase binding (GO:0043274)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|protein phosphatase activator activity (GO:0072542)|protein serine/threonine kinase activator activity (GO:0043539)|thioesterase binding (GO:0031996)|titin binding (GO:0031432)			breast(1)|cervix(2)|endometrium(1)|lung(1)|ovary(1)	6		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000338)|all cancers(93;0.000683)|Epithelial(262;0.0181)|GBM - Glioblastoma multiforme(486;0.0341)	Aprindine(DB01429)|Bepridil(DB01244)|Chlorpromazine(DB00477)|Cinchocaine(DB00527)|Felodipine(DB01023)|Flunarizine(DB04841)|Fluphenazine(DB00623)|Isoflurane(DB00753)|Loperamide(DB00836)|Melatonin(DB01065)|Nicardipine(DB00622)|Nifedipine(DB01115)|Perphenazine(DB00850)|Phenoxybenzamine(DB00925)|Pimozide(DB01100)|Promethazine(DB01069)|Trifluoperazine(DB00831)	TCTCCCTCTTTGACAAGGATG	0.542																																					p.F20F		Atlas-SNP	.											.	CALM3	9	.	0			c.T60C						.						82	70	74					19																	47111479		2203	4300	6503	SO:0001819	synonymous_variant	808	exon3			CCTCTTTGACAAG		CCDS33061.1	19q13.2-q13.3	2013-02-25			ENSG00000160014	ENSG00000160014		"EF-hand domain containing", "Endogenous ligands"	1449	protein-coding gene	gene with protein product	"prepro-calmodulin 3"	114183					Standard	NM_005184		Approved	PHKD	uc002pew.3	P62158	OTTHUMG00000133517	ENST00000291295.9:c.60T>C	chr19.hg19:g.47111479T>C		87.0	0.0		63.0	4.0	NM_005184	P02593|P70667|P99014|Q13942|Q53S29|Q61379|Q61380|Q96HK3	Silent	SNP	ENST00000291295.9	hg19	CCDS33061.1																																																																																			.	.		0.542	CALM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257483.2			C	47111479	T	C	47111479	2	2	279	1	0	0	0	0	0	0	0	1	2588	1809	63	2		2	CALM3	19	47111479	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	377754	47111479	12017504	381	40140										
EHD2	30846	hgsc.bcm.edu	37	chr19	48219967	48219967	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ggagctgtaccgcacgaagcTgctgccgctggaggagcact	15	12	0	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr19:48219967T>A	ENST00000263277.3	+	2	349	c.98T>A	c.(97-99)cTg>cAg	p.L33Q	CTD-2571L23.8_ENST00000599924.1_lincRNA|EHD2_ENST00000538399.1_Intron	NM_014601.3	NP_055416.2	Q9NZN4	EHD2_HUMAN	EH-domain containing 2	33					blood coagulation (GO:0007596)|cortical actin cytoskeleton organization (GO:0030866)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of myoblast fusion (GO:1901741)|protein localization to plasma membrane (GO:0072659)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|nucleic acid binding (GO:0003676)			endometrium(3)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	19		all_cancers(25;6.74e-07)|all_lung(116;2.02e-05)|Lung NSC(112;3.77e-05)|all_epithelial(76;4.89e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		OV - Ovarian serous cystadenocarcinoma(262;0.000336)|all cancers(93;0.000415)|Epithelial(262;0.0132)|GBM - Glioblastoma multiforme(486;0.0537)		CGCACGAAGCTGCTGCCGCTG	0.697																																					p.L33Q		Atlas-SNP	.											.	EHD2	59	.	0			c.T98A						.						29	24	26					19																	48219967		2202	4298	6500	SO:0001583	missense	30846	exon2			CGAAGCTGCTGCC	AF181263	CCDS12704.1	19q13.3	2014-08-12			ENSG00000024422	ENSG00000024422		"EF-hand domain containing"	3243	protein-coding gene	gene with protein product		605890		PAST2		10673336	Standard	NM_014601		Approved		uc002phj.4	Q9NZN4	OTTHUMG00000183266	ENST00000263277.3:c.98T>A	chr19.hg19:g.48219967T>A	ENSP00000263277:p.Leu33Gln	178.0	0.0		135.0	37.0	NM_014601	B2RDH9|B4DNU6|Q96CB6	Missense_Mutation	SNP	ENST00000263277.3	hg19	CCDS12704.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.197260	0.79015	.	.	ENSG00000024422	ENST00000263277;ENST00000539439;ENST00000540364	T	0.25085	1.82	3.88	3.88	0.44766	.	0.000000	0.64402	D	0.000005	T	0.54208	0.1844	M	0.91612	3.225	0.80722	D	1	D	0.69078	0.997	D	0.64687	0.928	T	0.64487	-0.6396	10	0.87932	D	0	-22.9802	10.947	0.47306	0.0:0.0:0.0:1.0	.	33	Q9NZN4	EHD2_HUMAN	Q	33	ENSP00000263277:L33Q	ENSP00000263277:L33Q	L	+	2	0	EHD2	52911779	1.000000	0.71417	1.000000	0.80357	0.822000	0.46500	7.706000	0.84615	1.772000	0.52199	0.418000	0.28097	CTG	.	.		0.697	EHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465851.1			A	48219967	T	A	48219967	3	1	279	1	0	0	0	0	1	0	0	0	4980	1580	55	4	100	4	EHD2	19	48219967	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	1108488	48219967	10909016	382	40141										
SPHK2	56848	hgsc.bcm.edu	37	chr19	49132828	49132828	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gcgccttttcttggccatggAgcgtggtagccacttcagcc	12	13	2	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr19:49132828A>G	ENST00000245222.4	+	7	2129	c.1763A>G	c.(1762-1764)gAg>gGg	p.E588G	SPHK2_ENST00000598088.1_Missense_Mutation_p.E588G|SPHK2_ENST00000599029.1_Missense_Mutation_p.E552G|SPHK2_ENST00000443164.1_Missense_Mutation_p.E650G|SPHK2_ENST00000340932.3_Missense_Mutation_p.E550G|SPHK2_ENST00000599748.1_Missense_Mutation_p.E552G|SPHK2_ENST00000600537.1_Missense_Mutation_p.E529G	NM_001204158.2|NM_001243876.1|NM_020126.4	NP_001191087.1|NP_001230805.1|NP_064511.2	Q9NRA0	SPHK2_HUMAN	sphingosine kinase 2	588					blood vessel development (GO:0001568)|brain development (GO:0007420)|cell proliferation (GO:0008283)|lipid phosphorylation (GO:0046834)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|small molecule metabolic process (GO:0044281)|sphinganine-1-phosphate biosynthetic process (GO:0006669)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	ATP binding (GO:0005524)|D-erythro-sphingosine kinase activity (GO:0017050)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)|Ras GTPase binding (GO:0017016)|sphinganine kinase activity (GO:0008481)			NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	19		all_lung(116;0.000125)|Lung NSC(112;0.000202)|all_epithelial(76;0.000283)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)		TTGGCCATGGAGCGTGGTAGC	0.697																																					p.E588G		Atlas-SNP	.											.	SPHK2	62	.	0			c.A1763G						.						18	16	17					19																	49132828		2192	4292	6484	SO:0001583	missense	56848	exon7			CCATGGAGCGTGG	AF245447	CCDS12727.1, CCDS59404.1, CCDS59405.1, CCDS74414.1	19q13.33	2013-09-20			ENSG00000063176	ENSG00000063176			18859	protein-coding gene	gene with protein product		607092				10751414, 17895250	Standard	NM_020126		Approved		uc002pjs.3	Q9NRA0	OTTHUMG00000183318	ENST00000245222.4:c.1763A>G	chr19.hg19:g.49132828A>G	ENSP00000245222:p.Glu588Gly	46.0	0.0		62.0	4.0	NM_020126	A0T4C8|B4DU87|Q9BRN1|Q9H0Q2|Q9NWU7	Missense_Mutation	SNP	ENST00000245222.4	hg19	CCDS12727.1	.	.	.	.	.	.	.	.	.	.	A	15.56	2.868940	0.51588	.	.	ENSG00000063176	ENST00000245222;ENST00000406269;ENST00000340932;ENST00000443164	T;T;T	0.13901	2.55;2.55;2.55	4.68	4.68	0.58851	.	0.000000	0.85682	D	0.000000	T	0.32255	0.0823	M	0.62016	1.91	0.44388	D	0.997294	D;B;B	0.89917	1.0;0.009;0.018	D;B;B	0.80764	0.994;0.006;0.01	T	0.01776	-1.1276	10	0.45353	T	0.12	-25.7613	12.3792	0.55297	1.0:0.0:0.0:0.0	.	529;650;588	B4DU87;A0T4C8;Q9NRA0	.;.;SPHK2_HUMAN	G	588;561;550;650	ENSP00000245222:E588G;ENSP00000341091:E550G;ENSP00000413369:E650G	ENSP00000245222:E588G	E	+	2	0	SPHK2	53824640	1.000000	0.71417	0.985000	0.45067	0.954000	0.61252	5.472000	0.66768	2.095000	0.63458	0.454000	0.30748	GAG	.	.		0.697	SPHK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466153.1			G	49132828	A	G	49132828	3	3	279	1	0	0	0	0	1	0	0	0	15062	304	11	2	1785	2	SPHK2	19	49132828	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	912861	49132828	9996155	383	40142										
HRC	3270	hgsc.bcm.edu	37	chr19	49657920	49657920	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cctcctcctcctcctcttctCcttcatcatcttccccatca	0	22	6	0	rs200730671		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr19:49657920C>T	ENST00000252825.4	-	1	761	c.575G>A	c.(574-576)gGa>gAa	p.G192E	HRC_ENST00000595625.1_Missense_Mutation_p.G192E	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	192	4 X tandem repeats, acidic.|6 X approximate tandem repeats.				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		ctcctcttcTCCTTCATCATC	0.562																																					p.G192E	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											.	HRC	85	.	0			c.G575A						.						124	98	107					19																	49657920		2203	4300	6503	SO:0001583	missense	3270	exon1			TCTTCTCCTTCAT		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"histidine-rich calcium-binding protein"			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.575G>A	chr19.hg19:g.49657920C>T	ENSP00000252825:p.Gly192Glu	150.0	0.0		137.0	7.0	NM_002152	Q504Y6	Missense_Mutation	SNP	ENST00000252825.4	hg19	CCDS12759.1	.	.	.	.	.	.	.	.	.	.	c	0.009	-1.835792	0.00579	.	.	ENSG00000130528	ENST00000252825;ENST00000434964	T	0.05717	3.4	2.59	-1.01	0.10169	.	.	.	.	.	T	0.02156	0.0067	N	0.03608	-0.345	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.46289	-0.9202	9	0.02654	T	1	4.5523	7.8184	0.29274	0.0:0.7009:0.0:0.2991	.	192	P23327	SRCH_HUMAN	E	192;162	ENSP00000252825:G192E	ENSP00000252825:G192E	G	-	2	0	HRC	54349732	0.005000	0.15991	0.001000	0.08648	0.082000	0.17680	-0.740000	0.04861	-0.145000	0.11294	-0.389000	0.06534	GGA	.	.		0.562	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152		T	49657920	C	T	49657920	3	4	279	1	0	0	0	0	1	0	0	0	7361	855	30	3	1548	3	HRC	19	49657920	Missense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	525092	49657920	9471063	384	40143										
ZNF320	162967	hgsc.bcm.edu	37	chr19	53384894	53384894	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ctttctcacattcttcacatTtgtaaggtttctctccagta	4	11	4	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr19:53384894T>C	ENST00000595635.1	-	8	986	c.485A>G	c.(484-486)aAa>aGa	p.K162R	ZNF320_ENST00000597909.1_Intron|ZNF320_ENST00000600930.1_Intron|ZNF320_ENST00000391781.2_Missense_Mutation_p.K162R	NM_207333.2	NP_997216.2	A2RRD8	ZN320_HUMAN	zinc finger protein 320	162					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(4)|large_intestine(5)|liver(1)|lung(10)|urinary_tract(1)	24				GBM - Glioblastoma multiforme(134;0.0534)		TTCTTCACATTTGTAAGGTTT	0.363																																					p.K162R		Atlas-SNP	.											.	ZNF320	67	.	0			c.A485G						.						74	72	73					19																	53384894		2203	4300	6503	SO:0001583	missense	162967	exon4			TCACATTTGTAAG	AF086262	CCDS33095.1	19q13.41	2014-09-04			ENSG00000182986	ENSG00000182986		"Zinc fingers, C2H2-type", "-"	13842	protein-coding gene	gene with protein product		606427				11536051	Standard	XM_006723059		Approved	ZFPL, DKFZp686G16228	uc002qag.3	A2RRD8	OTTHUMG00000182797	ENST00000595635.1:c.485A>G	chr19.hg19:g.53384894T>C	ENSP00000473091:p.Lys162Arg	96.0	0.0		68.0	4.0	NM_207333	Q8NDR6	Missense_Mutation	SNP	ENST00000595635.1	hg19	CCDS33095.1	.	.	.	.	.	.	.	.	.	.	-	8.068	0.769560	0.15983	.	.	ENSG00000182986	ENST00000391781	T	0.03831	3.79	1.75	0.657	0.17850	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06416	0.0165	L	0.59436	1.845	0.09310	N	1	B	0.29432	0.244	B	0.35727	0.209	T	0.39440	-0.9614	9	0.46703	T	0.11	.	2.9814	0.05954	0.0:0.1661:0.2545:0.5794	.	162	A2RRD8	ZN320_HUMAN	R	162	ENSP00000375660:K162R	ENSP00000375660:K162R	K	-	2	0	ZNF320	58076706	0.000000	0.05858	0.000000	0.03702	0.120000	0.20174	-0.442000	0.06871	-0.011000	0.14247	0.165000	0.16767	AAA	.	.		0.363	ZNF320-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463771.1	NM_207333		C	53384894	T	C	53384894	3	2	279	1	0	0	0	0	1	0	0	0	17854	1841	64	2	1048	2	ZNF320	19	53384894	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	3726974	53384894	5744089	385	40144										
EPS8L1	54869	hgsc.bcm.edu	37	chr19	55591536	55591536	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cactgggcgccatcgtgcgcTgtgacgcggtgatgccaccc	14	15	0	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr19:55591536T>C	ENST00000201647.6	+	6	375	c.319T>C	c.(319-321)Tgt>Cgt	p.C107R	EPS8L1_ENST00000588359.1_5'Flank|EPS8L1_ENST00000540810.1_Missense_Mutation_p.C43R|EPS8L1_ENST00000586329.1_Missense_Mutation_p.C89R|EPS8L1_ENST00000592824.1_3'UTR|EPS8L1_ENST00000245618.5_5'Flank	NM_133180.2	NP_573441.2	Q8TE68	ES8L1_HUMAN	EPS8-like 1	107					positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|T cell receptor binding (GO:0042608)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|prostate(1)	12			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		CATCGTGCGCTGTGACGCGGT	0.657																																					p.C107R	Ovarian(149;255 1863 3636 27051 29647)	Atlas-SNP	.											.	EPS8L1	122	.	0			c.T319C						.						11	9	10					19																	55591536		2111	4132	6243	SO:0001583	missense	54869	exon6			GTGCGCTGTGACG	AK057052	CCDS12914.1, CCDS12915.1	19q13.42	2008-02-05				ENSG00000131037			21295	protein-coding gene	gene with protein product		614987				12620401	Standard	NM_133180		Approved	FLJ20258, DRC3, MGC23164, MGC4642	uc002qis.4	Q8TE68		ENST00000201647.6:c.319T>C	chr19.hg19:g.55591536T>C	ENSP00000201647:p.Cys107Arg	55.0	0.0		70.0	4.0	NM_133180	Q71RE2|Q8NC10|Q96BB7|Q9BSQ2|Q9GZQ2|Q9NXH0	Missense_Mutation	SNP	ENST00000201647.6	hg19	CCDS12914.1	.	.	.	.	.	.	.	.	.	.	T	15.55	2.867061	0.51588	.	.	ENSG00000131037	ENST00000310075;ENST00000201647;ENST00000540810	T;T	0.34072	1.38;1.38	3.87	3.87	0.44632	Pleckstrin homology-type (1);Tensin phosphotyrosine-binding domain (1);	0.127967	0.53938	D	0.000060	T	0.55114	0.1900	M	0.68317	2.08	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;0.999;1.0	T	0.57596	-0.7784	10	0.59425	D	0.04	-28.4198	10.935	0.47241	0.0:0.0:0.0:1.0	.	43;89;107	B4DKV7;Q8TE68-3;Q8TE68	.;.;ES8L1_HUMAN	R	89;107;43	ENSP00000201647:C107R;ENSP00000437541:C43R	ENSP00000201647:C107R	C	+	1	0	EPS8L1	60283348	1.000000	0.71417	0.988000	0.46212	0.132000	0.20833	4.870000	0.63035	1.535000	0.49220	0.397000	0.26171	TGT	.	.		0.657	EPS8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451713.1	NM_017729		C	55591536	T	C	55591536	3	2	279	1	0	0	0	0	1	0	0	0	5197	1580	55	2	337	2	EPS8L1	19	55591536	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	2206642	55591536	3537447	386	40145										
EPS8L1	54869	hgsc.bcm.edu	37	chr19	55592800	55592800	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tcgagcaacgctgactcggcCtccccggacctgggtccccg	12	18	0	1	rs146217963		TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr19:55592800C>A	ENST00000201647.6	+	8	770	c.714C>A	c.(712-714)gcC>gcA	p.A238A	EPS8L1_ENST00000588359.1_Intron|EPS8L1_ENST00000540810.1_Silent_p.A174A|EPS8L1_ENST00000586329.1_Silent_p.A220A|EPS8L1_ENST00000592824.1_3'UTR|EPS8L1_ENST00000245618.5_Silent_p.A111A	NM_133180.2	NP_573441.2	Q8TE68	ES8L1_HUMAN	EPS8-like 1	238					positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|T cell receptor binding (GO:0042608)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|prostate(1)	12			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		CTGACTCGGCCTCCCCGGACC	0.741																																					p.A238A	Ovarian(149;255 1863 3636 27051 29647)	Atlas-SNP	.											.	EPS8L1	122	.	0			c.C714A						.						12	13	12					19																	55592800		2189	4283	6472	SO:0001819	synonymous_variant	54869	exon8			CTCGGCCTCCCCG	AK057052	CCDS12914.1, CCDS12915.1	19q13.42	2008-02-05				ENSG00000131037			21295	protein-coding gene	gene with protein product		614987				12620401	Standard	NM_133180		Approved	FLJ20258, DRC3, MGC23164, MGC4642	uc002qis.4	Q8TE68		ENST00000201647.6:c.714C>A	chr19.hg19:g.55592800C>A		88.0	0.0		95.0	38.0	NM_133180	Q71RE2|Q8NC10|Q96BB7|Q9BSQ2|Q9GZQ2|Q9NXH0	Silent	SNP	ENST00000201647.6	hg19	CCDS12914.1																																																																																			.	C|1.000;G|0.000		0.741	EPS8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451713.1	NM_017729		A	55592800	C	A	55592800	2	1	279	1	0	0	0	0	0	0	0	1	5197	668	24	3		3	EPS8L1	19	55592800	Silent	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	1264	55592800	3536183	387	40146										
HSPBP1	23640	hgsc.bcm.edu	37	chr19	55790905	55790905	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gagccgccgccgccgcccccTgaagagcaaccctgggaggc	14	18	0	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr19:55790905T>G	ENST00000255631.5	-	3	382	c.72A>C	c.(70-72)tcA>tcC	p.S24S	BRSK1_ENST00000590333.1_5'Flank|HSPBP1_ENST00000587922.1_Silent_p.S24S|HSPBP1_ENST00000376343.3_Silent_p.S24S|HSPBP1_ENST00000433386.2_Silent_p.S24S	NM_001130106.1|NM_012267.4	NP_001123578.1|NP_036399.3	Q9NZL4	HPBP1_HUMAN	HSPA (heat shock 70kDa) binding protein, cytoplasmic cochaperone 1	24	Gly-rich.				negative regulation of catalytic activity (GO:0043086)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein folding (GO:0006457)		enzyme inhibitor activity (GO:0004857)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)|urinary_tract(1)	8			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0452)		CGCCGCCCCCTGAAGAGCAAC	0.697																																					p.S24S		Atlas-SNP	.											HSPBP1,NS,carcinoma,0,1	HSPBP1	24	.	0			c.A72C						.						7	10	9					19																	55790905		1698	3669	5367	SO:0001819	synonymous_variant	23640	exon2			GCCCCCTGAAGAG		CCDS33111.1	19q13.42	2008-12-16			ENSG00000133265	ENSG00000133265			24989	protein-coding gene	gene with protein product	"hsp70 interacting protein", "Hsp70 binding protein 1"	612939				10786638, 9830037	Standard	NM_001130106		Approved	HspBP1, FES1	uc002qkd.3	Q9NZL4		ENST00000255631.5:c.72A>C	chr19.hg19:g.55790905T>G		8.0	0.0		7.0	3.0	NM_012267	B3KQP0|B4DG11|O95351|Q6ZNU5	Silent	SNP	ENST00000255631.5	hg19	CCDS33111.1																																																																																			.	.		0.697	HSPBP1-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452670.1	NM_012267		G	55790905	T	G	55790905	2	3	279	1	0	0	0	0	0	0	0	1	7435	1567	55	5		5	HSPBP1	19	55790905	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	198105	55790905	3338078	388	40147										
ZNF787	126208	hgsc.bcm.edu	37	chr19	56599440	56599440	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	caccgcccgcccgcggcctcGtcgtcgtcgtcgtcctcctc	10	22	0	0	rs5828672|rs71696054	byFrequency	TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr19:56599440G>C	ENST00000270459.3	-	3	1219	c.1101C>G	c.(1099-1101)gaC>gaG	p.D367E		NM_001002836.2	NP_001002836	Q6DD87	ZN787_HUMAN	zinc finger protein 787	367					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|lung(2)|pancreas(1)	5		Colorectal(82;3.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0559)		CCGCGGCCTCGTCGTCGTCGT	0.781																																					p.D367E		Atlas-SNP	.											.	ZNF787	20	.	0			c.C1101G						.						1	1	1					19																	56599440		975	2269	3244	SO:0001583	missense	126208	exon3			GGCCTCGTCGTCG	BC077728, AF000560	CCDS42634.1	19q13.42	2013-01-08				ENSG00000142409		"Zinc fingers, C2H2-type"	26998	protein-coding gene	gene with protein product							Standard	NM_001002836		Approved		uc010eth.1	Q6DD87		ENST00000270459.3:c.1101C>G	chr19.hg19:g.56599440G>C	ENSP00000270459:p.Asp367Glu	2.0	0.0		5.0	5.0	NM_001002836	O00455	Missense_Mutation	SNP	ENST00000270459.3	hg19	CCDS42634.1	.	.	.	.	.	.	.	.	.	.	g	0.250	-1.007020	0.02112	.	.	ENSG00000142409	ENST00000270459	T	0.06687	3.27	3.12	-3.97	0.04094	.	.	.	.	.	T	0.05868	0.0153	N	0.19112	0.55	0.09310	N	0.999997	.	.	.	.	.	.	T	0.42103	-0.9471	7	0.59425	D	0.04	-5.5942	6.3674	0.21463	0.2259:0.5191:0.2551:0.0	.	.	.	.	E	367	ENSP00000270459:D367E	ENSP00000270459:D367E	D	-	3	2	ZNF787	61291252	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-4.144000	0.00286	-0.645000	0.05458	-0.742000	0.03525	GAC	.	.		0.781	ZNF787-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457498.1	NM_001002836		C	56599440	G	C	56599440	3	2	279	1	0	0	0	0	1	0	0	0	18174	1136	40	4	54	4	ZNF787	19	56599440	Missense_Mutation	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	808535	56599440	2529543	389	40148										
ZNF582	147948	hgsc.bcm.edu	37	chr19	56896375	56896375	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	atgatcatctgatggaaatgTctgtctggatttccctgttg	10	7	4	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr19:56896375T>C	ENST00000301310.4	-	5	569	c.411A>G	c.(409-411)agA>agG	p.R137R	AC006116.12_ENST00000589671.1_RNA|ZNF582_ENST00000586929.1_Silent_p.R137R	NM_144690.1	NP_653291.1	Q96NG8	ZN582_HUMAN	zinc finger protein 582	137					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0547)		GATGGAAATGTCTGTCTGGAT	0.383																																					p.R137R	Ovarian(183;1887 2032 4349 30507 51343)	Atlas-SNP	.											.	ZNF582	56	.	0			c.A411G						.						163	161	162					19																	56896375		2203	4300	6503	SO:0001819	synonymous_variant	147948	exon5			GAAATGTCTGTCT	AK055489	CCDS33121.1	19q13.43	2013-07-15			ENSG00000018869	ENSG00000018869		"Zinc fingers, C2H2-type", "-"	26421	protein-coding gene	gene with protein product		615600				12477932	Standard	NM_144690		Approved	FLJ30927	uc002qmz.1	Q96NG8	OTTHUMG00000181939	ENST00000301310.4:c.411A>G	chr19.hg19:g.56896375T>C		112.0	0.0		96.0	4.0	NM_144690	B4DQZ9|B7Z9R3|Q6PJT6	Silent	SNP	ENST00000301310.4	hg19	CCDS33121.1																																																																																			.	.		0.383	ZNF582-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458387.2	NM_144690		C	56896375	T	C	56896375	2	2	279	1	0	0	0	0	0	0	0	1	18029	1664	58	2		2	ZNF582	19	56896375	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	296935	56896375	2232608	390	40149										
TASP1	55617	hgsc.bcm.edu	37	chr20	13539657	13539657	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tttcaaacaccacctgacctTctcacttgattgtcttcttt	3	13	4	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr20:13539657T>C	ENST00000337743.4	-	8	793	c.673A>G	c.(673-675)Aag>Gag	p.K225E	TASP1_ENST00000539805.1_Intron|TASP1_ENST00000480436.1_5'UTR	NM_017714.2	NP_060184.2	Q9H6P5	TASP1_HUMAN	taspase, threonine aspartase, 1	225					positive regulation of transcription, DNA-templated (GO:0045893)		threonine-type endopeptidase activity (GO:0004298)			NS(1)|breast(1)|endometrium(2)|large_intestine(11)|liver(1)|lung(11)|stomach(2)|urinary_tract(2)	31						CACCTGACCTTCTCACTTGAT	0.343																																					p.K225E		Atlas-SNP	.											.	TASP1	52	.	0			c.A673G						.						173	164	167					20																	13539657		2203	4298	6501	SO:0001583	missense	55617	exon8			TGACCTTCTCACT	AK000219	CCDS13116.1	20p12	2005-10-15	2005-10-15	2005-10-15	ENSG00000089123	ENSG00000089123	3.4.25.-		15859	protein-coding gene	gene with protein product		608270	"chromosome 20 open reading frame 13"	C20orf13		14636557	Standard	XR_430268		Approved	FLJ20212, dJ585I14.2	uc002woi.3	Q9H6P5	OTTHUMG00000031904	ENST00000337743.4:c.673A>G	chr20.hg19:g.13539657T>C	ENSP00000338624:p.Lys225Glu	100.0	0.0		95.0	4.0	NM_017714	B7Z690|B7Z963|Q5TDU9|Q9BQN0|Q9NQ08|Q9NTS6|Q9NXJ2	Missense_Mutation	SNP	ENST00000337743.4	hg19	CCDS13116.1	.	.	.	.	.	.	.	.	.	.	T	11.19	1.566176	0.27915	.	.	ENSG00000089123	ENST00000378157;ENST00000337743;ENST00000455532	D;D	0.86956	-2.19;-2.19	5.54	5.54	0.83059	.	0.142108	0.64402	D	0.000008	T	0.77198	0.4095	N	0.25647	0.755	0.80722	D	1	B;B	0.18610	0.029;0.017	B;B	0.15870	0.014;0.006	T	0.70726	-0.4793	10	0.06236	T	0.91	-11.8352	13.6177	0.62120	0.0:0.0:0.0:1.0	.	225;202	Q9H6P5;Q5JWM4	TASP1_HUMAN;.	E	202;225;202	ENSP00000338624:K225E;ENSP00000400580:K202E	ENSP00000338624:K225E	K	-	1	0	TASP1	13487657	1.000000	0.71417	1.000000	0.80357	0.558000	0.35554	6.485000	0.73625	2.105000	0.64084	0.482000	0.46254	AAG	.	.		0.343	TASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078041.2	NM_017714		C	13539657	T	C	13539657	3	2	279	1	0	0	0	0	1	0	0	0	15604	1792	62	2	617	2	TASP1	20	13539657	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10		13539657	49485863	391	40150										
CST5	1473	hgsc.bcm.edu	37	chr20	23860147	23860147	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	catccttattaatgaccttgTtgtactcgctgatggcaaag	8	9	0	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr20:23860147T>C	ENST00000304710.4	-	1	240	c.167A>G	c.(166-168)aAc>aGc	p.N56S		NM_001900.4	NP_001891.2	P28325	CYTD_HUMAN	cystatin D	56					negative regulation of endopeptidase activity (GO:0010951)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|kidney(1)|large_intestine(1)|lung(6)|skin(1)|stomach(1)	11						AATGACCTTGTTGTACTCGCT	0.577																																					p.N56S		Atlas-SNP	.											.	CST5	24	.	0			c.A167G						.						230	211	217					20																	23860147		2203	4300	6503	SO:0001583	missense	1473	exon1			ACCTTGTTGTACT		CCDS13162.1	20p11.21	2008-04-15			ENSG00000170367	ENSG00000170367			2477	protein-coding gene	gene with protein product		123858				1939105	Standard	NM_001900		Approved		uc002wtr.1	P28325	OTTHUMG00000032089	ENST00000304710.4:c.167A>G	chr20.hg19:g.23860147T>C	ENSP00000307132:p.Asn56Ser	96.0	0.0		89.0	4.0	NM_001900	Q5JRF5|Q9UCA0	Missense_Mutation	SNP	ENST00000304710.4	hg19	CCDS13162.1	.	.	.	.	.	.	.	.	.	.	t	12.26	1.885247	0.33255	.	.	ENSG00000170367	ENST00000304710	T	0.55234	0.53	1.99	1.99	0.26369	Proteinase inhibitor I25, cystatin (2);	0.000000	0.85682	D	0.000000	T	0.72755	0.3500	M	0.92268	3.29	0.09310	N	1	D	0.89917	1.0	D	0.80764	0.994	T	0.60939	-0.7163	10	0.66056	D	0.02	.	5.9639	0.19315	0.0:0.0:0.0:1.0	.	56	P28325	CYTD_HUMAN	S	56	ENSP00000307132:N56S	ENSP00000307132:N56S	N	-	2	0	CST5	23808147	0.962000	0.33011	0.004000	0.12327	0.001000	0.01503	2.037000	0.41174	1.163000	0.42636	0.368000	0.22195	AAC	.	.		0.577	CST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078355.2	NM_001900		C	23860147	T	C	23860147	3	2	279	1	0	0	0	0	1	0	0	0	3977	1725	60	2	273	2	CST5	20	23860147	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	10320490	23860147	39165373	392	40151										
ACSS1	84532	hgsc.bcm.edu	37	chr20	25004120	25004120	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	acctgctccagcgggacgtcCagatcccccatgtggacctt	10	16	0	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr20:25004120C>T	ENST00000323482.4	-	4	868	c.789G>A	c.(787-789)ctG>ctA	p.L263L	ACSS1_ENST00000537502.1_Silent_p.L180L|ACSS1_ENST00000432802.2_Silent_p.L263L|ACSS1_ENST00000542618.1_Silent_p.L142L	NM_001252675.1|NM_032501.3	NP_001239604.1|NP_115890.2	Q9NUB1	ACS2L_HUMAN	acyl-CoA synthetase short-chain family member 1	263					acetate biosynthetic process (GO:0019413)|acetyl-CoA biosynthetic process (GO:0006085)|acetyl-CoA biosynthetic process from acetate (GO:0019427)|ethanol oxidation (GO:0006069)|propionate biosynthetic process (GO:0019542)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	mitochondrial matrix (GO:0005759)	acetate-CoA ligase activity (GO:0003987)|AMP binding (GO:0016208)|ATP binding (GO:0005524)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	26					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	GCGGGACGTCCAGATCCCCCA	0.557																																					p.L263L		Atlas-SNP	.											.	ACSS1	46	.	0			c.G789A						.						117	87	97					20																	25004120		2203	4300	6503	SO:0001819	synonymous_variant	84532	exon4			GACGTCCAGATCC		CCDS13167.1, CCDS58764.1, CCDS58765.1	20p11.23-p11.21	2012-07-13	2005-09-08	2005-09-08	ENSG00000154930	ENSG00000154930	6.2.1.1	"Acyl-CoA synthetase family"	16091	protein-coding gene	gene with protein product		614355	"acetyl-Coenzyme A synthetase 2 (AMP forming)-like"	ACAS2L			Standard	NM_032501		Approved	dJ568C11.3, AceCS2L, MGC33843	uc002wub.3	Q9NUB1	OTTHUMG00000032112	ENST00000323482.4:c.789G>A	chr20.hg19:g.25004120C>T		80.0	0.0		66.0	4.0	NM_001252677	B3KXL2|B4DJZ3|D3DW48|F5H6F4|F8W7Y1|Q5TF42|Q8IV99|Q8N234|Q96JI1|Q96JX6|Q9NU28	Silent	SNP	ENST00000323482.4	hg19	CCDS13167.1																																																																																			.	.		0.557	ACSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078386.2	NM_032501		T	25004120	C	T	25004120	2	4	279	1	0	0	0	0	0	0	0	1	188	581	21	3		3	ACSS1	20	25004120	Silent	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	1143973	25004120	38021400	393	40152										
NINL	22981	hgsc.bcm.edu	37	chr20	25434263	25434263	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cttcagcagcaggtcggactTcgtgttcttttcaaactaga	9	10	3	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr20:25434263T>C	ENST00000278886.6	-	24	4046	c.3973A>G	c.(3973-3975)Aag>Gag	p.K1325E	NINL_ENST00000422516.1_Missense_Mutation_p.K976E|NINL_ENST00000464285.1_5'UTR	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	1325					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|microtubule (GO:0005874)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(13)|lung(25)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	57						AGGTCGGACTTCGTGTTCTTT	0.557																																					p.K1325E		Atlas-SNP	.											.	NINL	148	.	0			c.A3973G						.						74	64	67					20																	25434263		2203	4300	6503	SO:0001583	missense	22981	exon24			CGGACTTCGTGTT		CCDS33452.1	20p11.22-p11.1	2013-01-10			ENSG00000101004	ENSG00000101004		"EF-hand domain containing"	29163	protein-coding gene	gene with protein product	"ninein-like protein"	609580				10231032	Standard	XM_005260678		Approved	KIAA0980, NLP	uc002wux.1	Q9Y2I6	OTTHUMG00000032127	ENST00000278886.6:c.3973A>G	chr20.hg19:g.25434263T>C	ENSP00000278886:p.Lys1325Glu	122.0	0.0		95.0	4.0	NM_025176	A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	Missense_Mutation	SNP	ENST00000278886.6	hg19	CCDS33452.1	.	.	.	.	.	.	.	.	.	.	T	14.49	2.551679	0.45487	.	.	ENSG00000101004	ENST00000278886;ENST00000422516	T;T	0.39229	1.09;1.09	4.89	3.78	0.43462	.	0.233607	0.33916	N	0.004429	T	0.47746	0.1462	L	0.57536	1.79	0.19300	N	0.999974	D;P;P	0.55385	0.971;0.593;0.952	P;B;P	0.50860	0.651;0.29;0.652	T	0.42396	-0.9454	10	0.72032	D	0.01	-14.3263	11.0363	0.47802	0.0:0.0:0.1671:0.8329	.	976;1325;116	Q9Y2I6-2;Q9Y2I6;Q9HAD5	.;NINL_HUMAN;.	E	1325;976	ENSP00000278886:K1325E;ENSP00000410431:K976E	ENSP00000278886:K1325E	K	-	1	0	NINL	25382263	0.887000	0.30362	0.001000	0.08648	0.123000	0.20343	2.010000	0.40913	0.881000	0.35993	0.533000	0.62120	AAG	.	.		0.557	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078445.3	NM_025176		C	25434263	T	C	25434263	3	2	279	1	0	0	0	0	1	0	0	0	10429	1792	62	2	179	2	NINL	20	25434263	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	430143	25434263	37591257	394	40153										
RALGAPB	57148	hgsc.bcm.edu	37	chr20	37202799	37202799	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tttcttttcttaagatctacAactcttgaaaaagaagttcc	4	8	4	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr20:37202799A>G	ENST00000262879.6	+	29	4433	c.4149A>G	c.(4147-4149)acA>acG	p.T1383T	RALGAPB_ENST00000397042.3_Silent_p.T1380T|RALGAPB_ENST00000490114.1_3'UTR|RALGAPB_ENST00000397038.1_Silent_p.T1162T|RALGAPB_ENST00000397040.1_Silent_p.T1383T			Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit (non-catalytic)	1383	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)|Ral protein signal transduction (GO:0032484)|regulation of exocyst localization (GO:0060178)		protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(29)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						TAAGATCTACAACTCTTGAAA	0.388																																					p.T1383T		Atlas-SNP	.											.	RALGAPB	134	.	0			c.A4149G						.						58	66	63					20																	37202799		2203	4300	6503	SO:0001819	synonymous_variant	57148	exon29			ATCTACAACTCTT	AB033045	CCDS13305.1, CCDS63272.1	20q11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000170471	ENSG00000170471			29221	protein-coding gene	gene with protein product			"KIAA1219"	KIAA1219		19520869	Standard	XM_005260462		Approved	DKFZp781M2411, RalGAPbeta	uc002xiw.3	Q86X10	OTTHUMG00000140270	ENST00000262879.6:c.4149A>G	chr20.hg19:g.37202799A>G		126.0	0.0		81.0	4.0	NM_020336	A2A2E8|A2A2E9|Q5TG31|Q8N3D1|Q8WWC0|Q9H3X8|Q9UJR1|Q9ULK1|Q9Y3G9	Silent	SNP	ENST00000262879.6	hg19	CCDS13305.1																																																																																			.	.		0.388	RALGAPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079191.1	NM_020336		G	37202799	A	G	37202799	2	3	279	1	0	0	0	0	0	0	0	1	13030	117	5	2		2	RALGAPB	20	37202799	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	11768536	37202799	25822721	395	40154										
FAM65C	140876	hgsc.bcm.edu	37	chr20	49221180	49221180	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tgccccgggaaggctcactcAccaggtagtatctctcccgg	11	15	3	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr20:49221180A>G	ENST00000327979.2	-	12	1486		c.e12+1		FAM65C_ENST00000535356.1_Splice_Site|FAM65C_ENST00000045083.2_Splice_Site			Q96MK2	FA65C_HUMAN	family with sequence similarity 65, member C											endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|liver(1)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						AGGCTCACTCACCAGGTAGTA	0.657																																					.		Atlas-SNP	.											.	FAM65C	87	.	0			c.1074+2T>C						.						41	43	43					20																	49221180		2203	4300	6503	SO:0001630	splice_region_variant	140876	exon13			TCACTCACCAGGT	AL133230	CCDS13431.2	20q13.13	2011-11-24	2008-06-13	2008-06-13	ENSG00000042062	ENSG00000042062			16168	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 175", "chromosome 20 open reading frame 176"	C20orf175, C20orf176			Standard	XM_005260294		Approved	dJ530I15.2, dJ530I15.3	uc002xvm.3	Q96MK2	OTTHUMG00000032724	ENST00000327979.2:c.1074+1T>C	chr20.hg19:g.49221180A>G		66.0	0.0		58.0	4.0	NM_080829	Q5QPB6|Q9NQQ2	Splice_Site	SNP	ENST00000327979.2	hg19	CCDS13431.2	.	.	.	.	.	.	.	.	.	.	A	17.61	3.432285	0.62844	.	.	ENSG00000042062	ENST00000327979;ENST00000045083;ENST00000535356	.	.	.	4.33	4.33	0.51752	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.7827	0.57487	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	FAM65C	48654587	1.000000	0.71417	1.000000	0.80357	0.704000	0.40688	7.861000	0.87004	1.727000	0.51537	0.459000	0.35465	.	.	.		0.657	FAM65C-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257962.1		Intron	G	49221180	A	G	49221180	5	3	279	1	0	0	0	0	0	0	1	0	5609	173	6	2	1808	2	FAM65C	20	49221180	Splice_Site	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	12018381	49221180	13804340	396	40155										
HSPA13	6782	hgsc.bcm.edu	37	chr21	15748106	15748106	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ccataggccatagctgctgcTgtgggttcatttattaccct	9	11	1	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr21:15748106T>C	ENST00000285667.3	-	4	682	c.615A>G	c.(613-615)acA>acG	p.T205T	HSPA13_ENST00000478035.1_5'Flank|HSPA13_ENST00000544452.1_5'UTR	NM_006948.4	NP_008879.3	P48723	HSP13_HUMAN	heat shock protein 70kDa family, member 13	205						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	ATP binding (GO:0005524)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	13						TAGCTGCTGCTGTGGGTTCAT	0.438																																					p.T205T		Atlas-SNP	.											.	HSPA13	44	.	0			c.A615G						.						118	110	113					21																	15748106		2203	4300	6503	SO:0001819	synonymous_variant	6782	exon4			TGCTGCTGTGGGT		CCDS13567.1	21q11.1	2011-09-02	2008-06-17	2008-06-17	ENSG00000155304	ENSG00000155304		"Heat shock proteins / HSP70"	11375	protein-coding gene	gene with protein product		601100	"stress 70 protein chaperone, microsome-associated, 60kD", "stress 70 protein chaperone, microsome-associated, 60kDa"	STCH		8825657	Standard	NM_006948		Approved		uc002yjt.3	P48723	OTTHUMG00000074261	ENST00000285667.3:c.615A>G	chr21.hg19:g.15748106T>C		104.0	0.0		91.0	4.0	NM_006948	B2R616|Q8NE40	Silent	SNP	ENST00000285667.3	hg19	CCDS13567.1																																																																																			.	.		0.438	HSPA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157815.1			C	15748106	T	C	15748106	2	2	279	1	0	0	0	0	0	0	0	1	7415	1567	55	2		2	HSPA13	21	15748106	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10		15748106	32381789	397	40156										
N6AMT1	29104	hgsc.bcm.edu	37	chr21	30248785	30248785	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gcagtggttccttgcagaccTtttgtcttcattattttcaa	7	9	3	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr21:30248785T>C	ENST00000303775.5	-	6	592	c.567A>G	c.(565-567)aaA>aaG	p.K189K	N6AMT1_ENST00000351429.3_Silent_p.K161K	NM_013240.4	NP_037372	Q9Y5N5	HEMK2_HUMAN	N-6 adenine-specific DNA methyltransferase 1 (putative)	189					positive regulation of cell growth (GO:0030307)|protein methylation (GO:0006479)	protein complex (GO:0043234)	nucleic acid binding (GO:0003676)|protein methyltransferase activity (GO:0008276)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(2)	12						CTTGCAGACCTTTTGTCTTCA	0.363																																					p.K189K		Atlas-SNP	.											.	N6AMT1	31	.	0			c.A567G						.						147	130	136					21																	30248785		2203	4300	6503	SO:0001819	synonymous_variant	29104	exon6			CAGACCTTTTGTC	AF139682	CCDS33525.1, CCDS33526.1	21q21.3	2006-12-14	2006-12-14	2006-12-14	ENSG00000156239	ENSG00000156239	2.1.1.72		16021	protein-coding gene	gene with protein product		614553	"chromosome 21 open reading frame 127", "HemK methyltransferase family member 2"	C21orf127, HEMK2			Standard	NM_013240		Approved	PRED28, N6AMT, MTQ2	uc002ymo.2	Q9Y5N5	OTTHUMG00000078750	ENST00000303775.5:c.567A>G	chr21.hg19:g.30248785T>C		67.0	0.0		90.0	4.0	NM_013240	Q96F73	Silent	SNP	ENST00000303775.5	hg19	CCDS33526.1																																																																																			.	.		0.363	N6AMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171738.1	NM_013240		C	30248785	T	C	30248785	2	2	279	1	0	0	0	0	0	0	0	1	10123	1606	56	2		2	N6AMT1	21	30248785	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	14500679	30248785	17881110	398	40157										
GRIK1	2897	hgsc.bcm.edu	37	chr21	31015285	31015285	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	catcgtacatcagagccgctTcagtctgtggaggaaaacac	10	11	3	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr21:31015285T>C	ENST00000399907.1	-	7	1370	c.959A>G	c.(958-960)gAa>gGa	p.E320G	GRIK1_ENST00000535441.1_Missense_Mutation_p.E320G|GRIK1_ENST00000399909.1_Missense_Mutation_p.E320G|GRIK1_ENST00000389124.2_Missense_Mutation_p.E320G|GRIK1_ENST00000399914.1_Missense_Mutation_p.E320G|GRIK1_ENST00000327783.4_Missense_Mutation_p.E320G|GRIK1_ENST00000389125.3_Missense_Mutation_p.E320G|GRIK1_ENST00000309434.7_Missense_Mutation_p.E320G|GRIK1_ENST00000472429.1_5'UTR|GRIK1_ENST00000399913.1_Missense_Mutation_p.E320G	NM_000830.3	NP_000821.1	P39086	GRIK1_HUMAN	glutamate receptor, ionotropic, kainate 1	320					adult behavior (GO:0030534)|behavioral response to pain (GO:0048266)|central nervous system development (GO:0007417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|nervous system development (GO:0007399)|positive regulation of gamma-aminobutyric acid secretion (GO:0014054)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(18)|ovary(1)|prostate(4)|skin(1)|stomach(1)|urinary_tract(1)	45					Topiramate(DB00273)	CAGAGCCGCTTCAGTCTGTGG	0.507																																					p.E320G		Atlas-SNP	.											.	GRIK1	293	.	0			c.A959G						.						111	98	103					21																	31015285		2203	4300	6503	SO:0001583	missense	2897	exon7			GCCGCTTCAGTCT		CCDS33530.1, CCDS42913.1	21q22	2012-08-29			ENSG00000171189	ENSG00000171189		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4579	protein-coding gene	gene with protein product		138245		GLUR5		8468067	Standard	XM_005260942		Approved	GluK1	uc002yno.1	P39086	OTTHUMG00000078879	ENST00000399907.1:c.959A>G	chr21.hg19:g.31015285T>C	ENSP00000382791:p.Glu320Gly	91.0	0.0		97.0	4.0	NM_175611	Q13001|Q86SU9	Missense_Mutation	SNP	ENST00000399907.1	hg19	CCDS42913.1	.	.	.	.	.	.	.	.	.	.	T	17.92	3.507044	0.64410	.	.	ENSG00000171189	ENST00000327783;ENST00000389125;ENST00000399913;ENST00000399914;ENST00000535441;ENST00000541508;ENST00000389124;ENST00000399907;ENST00000399909;ENST00000309434	T;T;T;T;T;T;T;T;T	0.23754	1.89;1.89;1.89;1.89;1.89;1.89;1.89;1.89;1.89	5.33	4.16	0.48862	Extracellular ligand-binding receptor (1);	0.048109	0.85682	D	0.000000	T	0.36690	0.0976	M	0.62723	1.935	0.58432	D	0.999996	B;B;P;B;B;B	0.42620	0.318;0.155;0.785;0.318;0.155;0.234	B;B;P;B;B;B	0.49012	0.297;0.297;0.598;0.297;0.297;0.197	T	0.15122	-1.0448	10	0.62326	D	0.03	.	12.2112	0.54381	0.0:0.0:0.1427:0.8573	.	320;320;320;320;320;320	E7EPY9;E9PD61;E7EPZ0;B7Z3V7;P39086;P39086-2	.;.;.;.;GRIK1_HUMAN;.	G	320;320;320;320;320;264;320;320;320;320	ENSP00000327687:E320G;ENSP00000373777:E320G;ENSP00000382797:E320G;ENSP00000382798:E320G;ENSP00000446326:E320G;ENSP00000373776:E320G;ENSP00000382791:E320G;ENSP00000382793:E320G;ENSP00000311646:E320G	ENSP00000311646:E320G	E	-	2	0	GRIK1	29937156	1.000000	0.71417	0.914000	0.36105	0.970000	0.65996	4.585000	0.60977	1.011000	0.39340	0.533000	0.62120	GAA	.	.		0.507	GRIK1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171979.1			C	31015285	T	C	31015285	3	2	279	1	0	0	0	0	1	0	0	0	6782	1783	62	2	2001	2	GRIK1	21	31015285	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	766500	31015285	17114610	399	40158										
DNAJC28	54943	hgsc.bcm.edu	37	chr21	34860754	34860754	+	Nonsense_Mutation	SNP	A	A	C													0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tggtcaggatgggaacaattAaattaaaatcattaattcgc					rs139852262|rs3834674	byFrequency	TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr21:34860754A>C	ENST00000314399.3	-	2	1385	c.947T>G	c.(946-948)tTa>tGa	p.L316*	DNAJC28_ENST00000402202.1_Nonsense_Mutation_p.L316*|DNAJC28_ENST00000381947.3_Nonsense_Mutation_p.L316*	NM_017833.3	NP_060303.2	Q9NX36	DJC28_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 28	316				LIVPILTRQKVHFDAQKEIVRAQKIYETLIKTKEVTDRNPN NLDQGEGEKTPEIKKGFLNWMNLWKFIKIRSF -> CSHPD QAKSPF (in Ref. 2; BAA91185). {ECO:0000305}.				p.L316*(2)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(5)|skin(1)|urinary_tract(1)	18						GGGAACAATTAAATTAAAATC	0.338																																					p.L316X		Atlas-SNP	.											DNAJC28,NS,carcinoma,0,2	DNAJC28	47	.	2	Substitution - Nonsense(2)	lung(2)	c.T947G						.						78	64	69					21																	34860754		2203	4291	6494	SO:0001587	stop_gained	54943	exon2			ACAATTAAATTAA	AK000468	CCDS13626.1	21q22.11	2011-09-02	2008-06-17	2008-06-17	ENSG00000177692	ENSG00000177692		"Heat shock proteins / DNAJ (HSP40)"	1297	protein-coding gene	gene with protein product	"Orf28"		"chromosome 21 open reading frame 55"	C21orf55			Standard	NM_017833		Approved	C21orf78	uc002yrw.3	Q9NX36	OTTHUMG00000065531	ENST00000314399.3:c.947T>G	chr21.hg19:g.34860754A>C	ENSP00000320303:p.Leu316*	9.0	1.0		19.0	4.0	NM_001040192	D3DSF2	Nonsense_Mutation	SNP	ENST00000314399.3	hg19	CCDS13626.1	.	.	.	.	.	.	.	.	.	.	A	38	7.162118	0.98107	.	.	ENSG00000177692	ENST00000381947;ENST00000314399;ENST00000402202	.	.	.	5.09	5.09	0.68999	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.8259	14.8401	0.70217	1.0:0.0:0.0:0.0	.	.	.	.	X	316	.	ENSP00000320303:L316X	L	-	2	0	DNAJC28	33782624	1.000000	0.71417	0.993000	0.49108	0.986000	0.74619	8.254000	0.89844	2.050000	0.60909	0.528000	0.53228	TTA	.	.		0.338	DNAJC28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140454.3			C	34860754	A	C	34860754	4	2	279	1	0	0	0	0	0	1	0	0	4648	372	13	5	223	5	DNAJC28	21	34860754	Nonsense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	3845469	34860754	13269141	400	40159	203	2								
DNAJC28	54943	hgsc.bcm.edu	37	chr21	34860757	34860757	+	Missense_Mutation	SNP	T	T	A													0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tcaggatgggaacaattaaaTtaaaatcattaattcgcttg							TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr21:34860757T>A	ENST00000314399.3	-	2	1382	c.944A>T	c.(943-945)aAt>aTt	p.N315I	DNAJC28_ENST00000402202.1_Missense_Mutation_p.N315I|DNAJC28_ENST00000381947.3_Missense_Mutation_p.N315I	NM_017833.3	NP_060303.2	Q9NX36	DJC28_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 28	315										endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(5)|skin(1)|urinary_tract(1)	18						AACAATTAAATTAAAATCATT	0.348																																					p.N315I		Atlas-SNP	.											.	DNAJC28	47	.	0			c.A944T						.						83	79	80					21																	34860757		2203	4300	6503	SO:0001583	missense	54943	exon2			ATTAAATTAAAAT	AK000468	CCDS13626.1	21q22.11	2011-09-02	2008-06-17	2008-06-17	ENSG00000177692	ENSG00000177692		"Heat shock proteins / DNAJ (HSP40)"	1297	protein-coding gene	gene with protein product	"Orf28"		"chromosome 21 open reading frame 55"	C21orf55			Standard	NM_017833		Approved	C21orf78	uc002yrw.3	Q9NX36	OTTHUMG00000065531	ENST00000314399.3:c.944A>T	chr21.hg19:g.34860757T>A	ENSP00000320303:p.Asn315Ile	145.0	0.0		97.0	9.0	NM_001040192	D3DSF2	Missense_Mutation	SNP	ENST00000314399.3	hg19	CCDS13626.1	.	.	.	.	.	.	.	.	.	.	T	19.95	3.921477	0.73213	.	.	ENSG00000177692	ENST00000381947;ENST00000314399;ENST00000402202	.	.	.	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	T	0.79816	0.4511	M	0.80183	2.485	0.53688	D	0.999979	D	0.89917	1.0	D	0.87578	0.998	T	0.83136	-0.0111	9	0.87932	D	0	-25.7443	14.8401	0.70217	0.0:0.0:0.0:1.0	.	315	Q9NX36	DJC28_HUMAN	I	315	.	ENSP00000320303:N315I	N	-	2	0	DNAJC28	33782627	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.094000	0.76944	2.050000	0.60909	0.528000	0.53228	AAT	.	.		0.348	DNAJC28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140454.3			A	34860757	T	A	34860757	3	1	279	1	0	0	0	0	1	0	0	0	4648	1493	52	4	226	4	DNAJC28	21	34860757	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	3	34860757	13269138	401	40160	203	2								
MYO18B	84700	hgsc.bcm.edu	37	chr22	26157091	26157091	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	atcacgcctcgccctgtgggAgcagaaggaaagtgacactc	12	12	1	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr22:26157091A>G	ENST00000407587.2	+	2	201	c.32A>G	c.(31-33)gAg>gGg	p.E11G	MYO18B_ENST00000335473.7_Missense_Mutation_p.E11G|MYO18B_ENST00000536101.1_Missense_Mutation_p.E11G			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	11						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						GCCCTGTGGGAGCAGAAGGAA	0.597																																					p.E11G		Atlas-SNP	.											.	MYO18B	322	.	0			c.A32G						.						98	100	99					22																	26157091		2188	4276	6464	SO:0001583	missense	84700	exon2			TGTGGGAGCAGAA	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.32A>G	chr22.hg19:g.26157091A>G	ENSP00000386096:p.Glu11Gly	75.0	0.0		107.0	5.0	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	hg19		.	.	.	.	.	.	.	.	.	.	A	22.5	4.299248	0.81025	.	.	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.91996	-2.93;-2.93;-2.95	5.3	5.3	0.74995	.	0.000000	0.36665	N	0.002474	D	0.94532	0.8239	L	0.59436	1.845	0.33699	D	0.614359	D	0.89917	1.0	D	0.87578	0.998	D	0.96838	0.9616	10	0.87932	D	0	.	11.635	0.51198	1.0:0.0:0.0:0.0	.	11	F5GYU7	.	G	11	ENSP00000441229:E11G;ENSP00000334563:E11G;ENSP00000386096:E11G	ENSP00000334563:E11G	E	+	2	0	MYO18B	24487091	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.910000	0.63321	2.012000	0.59069	0.482000	0.46254	GAG	.	.		0.597	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		G	26157091	A	G	26157091	3	3	279	1	0	0	0	0	1	0	0	0	10075	304	11	2	34	2	MYO18B	22	26157091	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10		26157091	25147475	402	40161										
BAIAP2L2	80115	hgsc.bcm.edu	37	chr22	38482394	38482394	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	cccagtactccgagggtgctAtggagttgcccggccggtcc	14	14	0	0	rs371997714|rs66500630	byFrequency	TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr22:38482394A>G	ENST00000381669.3	-	12	1466	c.1322T>C	c.(1321-1323)aTa>aCa	p.I441T	SLC16A8_ENST00000469516.1_5'Flank	NM_025045.4	NP_079321.3	Q6UXY1	BI2L2_HUMAN	BAI1-associated protein 2-like 2	441					filopodium assembly (GO:0046847)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|signal transduction (GO:0007165)	cell-cell contact zone (GO:0044291)|cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	phospholipid binding (GO:0005543)			large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)	8	Melanoma(58;0.045)					CGAGGGTGCTATGGAGTTGCC	0.677																																					p.I441T		Atlas-SNP	.											.	BAIAP2L2	39	.	0			c.T1322C						.						16	17	17					22																	38482394		2030	3883	5913	SO:0001583	missense	80115	exon12			GGTGCTATGGAGT	BC015619	CCDS43018.1	22q13.1	2005-02-09			ENSG00000128298	ENSG00000128298			26203	protein-coding gene	gene with protein product							Standard	NM_025045		Approved	FLJ22582	uc003auw.3	Q6UXY1	OTTHUMG00000151197	ENST00000381669.3:c.1322T>C	chr22.hg19:g.38482394A>G	ENSP00000371085:p.Ile441Thr	88.0	0.0		87.0	10.0	NM_025045	B0QYE2|Q96BG7	Missense_Mutation	SNP	ENST00000381669.3	hg19	CCDS43018.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	0.203|0.203	-1.043386|-1.043386	0.01997|0.01997	.|.	.|.	ENSG00000128298|ENSG00000128298	ENST00000402500|ENST00000381669;ENST00000428572	.|T	.|0.43688	.|0.94	4.42|4.42	1.07|1.07	0.20283|0.20283	.|.	.|1.241170	.|0.05585	.|N	.|0.573669	.|T	.|0.21103	.|0.0508	N|N	0.03084|0.03084	-0.415|-0.415	0.09310|0.09310	N|N	1|1	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	.|T	.|0.20806	.|-1.0264	.|10	.|0.25106	.|T	.|0.35	.|-17.1778	8.3981|8.3981	0.32570|0.32570	0.2569:0.0:0.7431:0.0|0.2569:0.0:0.7431:0.0	.|.	.|441	.|Q6UXY1	.|BI2L2_HUMAN	.|T	-1|441;132	.|ENSP00000410074:I132T	.|ENSP00000371085:I441T	.|I	-|-	.|2	.|0	BAIAP2L2|BAIAP2L2	36812340|36812340	0.001000|0.001000	0.12720|0.12720	0.292000|0.292000	0.24919|0.24919	0.859000|0.859000	0.49053|0.49053	1.072000|1.072000	0.30678|0.30678	0.322000|0.322000	0.23283|0.23283	-0.414000|-0.414000	0.06135|0.06135	.|ATA	.	.		0.677	BAIAP2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321727.1	NM_025045		G	38482394	A	G	38482394	3	3	279	1	0	0	0	0	1	0	0	0	1303	449	16	2	279	2	BAIAP2L2	22	38482394	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	12325303	38482394	12822172	403	40162										
PACSIN2	11252	hgsc.bcm.edu	37	chr22	43308052	43308052	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	agaagctgtcgctggacactTctactccaacggaatcatca	8	12	3	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr22:43308052T>C	ENST00000263246.3	-	2	236	c.35A>G	c.(34-36)gAa>gGa	p.E12G	PACSIN2_ENST00000407585.1_Missense_Mutation_p.E12G|PACSIN2_ENST00000402229.1_Missense_Mutation_p.E12G|PACSIN2_ENST00000337959.4_Missense_Mutation_p.E12G|PACSIN2_ENST00000403744.3_Missense_Mutation_p.E12G	NM_001184970.1	NP_001171899.1	Q9UNF0	PACN2_HUMAN	protein kinase C and casein kinase substrate in neurons 2	12	F-BAR domain.|FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.				actin cytoskeleton organization (GO:0030036)|caveola assembly (GO:0070836)|caveolin-mediated endocytosis (GO:0072584)|cell projection morphogenesis (GO:0048858)|membrane tubulation (GO:0097320)|negative regulation of endocytosis (GO:0045806)|protein localization to endosome (GO:0036010)	caveola (GO:0005901)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|recycling endosome membrane (GO:0055038)	identical protein binding (GO:0042802)|phosphatidic acid binding (GO:0070300)|transporter activity (GO:0005215)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)	19		Glioma(61;0.222)				GCTGGACACTTCTACTCCAAC	0.473																																					p.E12G		Atlas-SNP	.											.	PACSIN2	48	.	0			c.A35G						.						81	80	80					22																	43308052		1903	4108	6011	SO:0001583	missense	11252	exon2			GACACTTCTACTC	AF128536	CCDS43023.1, CCDS54536.1	22q13.2-q13.33	2009-05-08			ENSG00000100266	ENSG00000100266			8571	protein-coding gene	gene with protein product	"syndapin II"	604960				10431838, 11082044	Standard	NM_007229		Approved	SDPII	uc003bdg.4	Q9UNF0	OTTHUMG00000150701	ENST00000263246.3:c.35A>G	chr22.hg19:g.43308052T>C	ENSP00000263246:p.Glu12Gly	54.0	0.0		63.0	4.0	NM_007229	O95921|Q96HV9|Q9H0D3|Q9NPN1|Q9Y4V2	Missense_Mutation	SNP	ENST00000263246.3	hg19	CCDS43023.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.441397	0.83993	.	.	ENSG00000100266	ENST00000263246;ENST00000337959;ENST00000407585;ENST00000403744;ENST00000402229;ENST00000453643;ENST00000418133;ENST00000422336;ENST00000453079	T;T;T;T;T;T;T;T	0.50277	1.41;1.36;1.36;1.41;1.41;0.75;0.75;0.75	5.65	5.65	0.86999	Fps/Fes/Fer/CIP4 homology (1);	0.049079	0.85682	D	0.000000	T	0.46795	0.1411	L	0.47716	1.5	0.51767	D	0.99993	P;P	0.45348	0.682;0.856	B;P	0.45639	0.307;0.488	T	0.45056	-0.9287	10	0.48119	T	0.1	-1.1225	12.1892	0.54261	0.0:0.0:0.0:1.0	.	12;12	Q6FIA3;Q9UNF0	.;PACN2_HUMAN	G	12	ENSP00000263246:E12G;ENSP00000338379:E12G;ENSP00000385952:E12G;ENSP00000385372:E12G;ENSP00000385040:E12G;ENSP00000398573:E12G;ENSP00000396816:E12G;ENSP00000403435:E12G	ENSP00000263246:E12G	E	-	2	0	PACSIN2	41637996	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.083000	0.57643	2.371000	0.80710	0.533000	0.62120	GAA	.	.		0.473	PACSIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319665.1	NM_007229		C	43308052	T	C	43308052	3	2	279	1	0	0	0	0	1	0	0	0	11384	1783	62	2	1465	2	PACSIN2	22	43308052	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	4825658	43308052	7996514	404	40163										
PNPLA5	150379	hgsc.bcm.edu	37	chr22	44283472	44283472	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ctgtgggactgccacctaccAcgtctctccaggaacctcag	9	16	2	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr22:44283472A>G	ENST00000597664.1	-	5	891	c.762T>C	c.(760-762)cgT>cgC	p.R254R	PNPLA5_ENST00000381198.2_Splice_Site_p.R140R|PNPLA5_ENST00000216177.4_Splice_Site_p.R254R|PNPLA5_ENST00000593866.1_Splice_Site_p.R140R			Q7Z6Z6	PLPL5_HUMAN	patatin-like phospholipase domain containing 5	254					lipid catabolic process (GO:0016042)		hydrolase activity (GO:0016787)			endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	16		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				GCCACCTACCACGTCTCTCCA	0.602																																					p.R254R		Atlas-SNP	.											.	PNPLA5	46	.	0			c.T762C						.						133	82	99					22																	44283472		2203	4300	6503	SO:0001630	splice_region_variant	150379	exon5			CCTACCACGTCTC	Z97055	CCDS14053.1, CCDS54537.1	22q13.31	2009-01-12			ENSG00000100341	ENSG00000100341		"Patatin-like phospholipase domain containing"	24888	protein-coding gene	gene with protein product		611589				16799181, 19029121	Standard	NM_138814		Approved	dJ388M5.4, GS2L	uc003beg.3	Q7Z6Z6	OTTHUMG00000030779	ENST00000597664.1:c.763+1T>C	chr22.hg19:g.44283472A>G		64.0	0.0		94.0	4.0	NM_138814	B1AHL8|B3KPR1|Q6ZST0	Silent	SNP	ENST00000597664.1	hg19																																																																																				.	.		0.602	PNPLA5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000075667.4	NM_138814	Silent	G	44283472	A	G	44283472	5	3	279	1	0	0	0	0	0	0	1	0	12177	173	6	2	547	2	PNPLA5	22	44283472	Splice_Site	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	975420	44283472	7021094	405	40164										
PKDREJ	10343	hgsc.bcm.edu	37	chr22	46654318	46654318	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ggtttattcgttctgaagccTgacaggagtataattttaga	10	5	1	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr22:46654318T>C	ENST00000253255.5	-	1	4901	c.4902A>G	c.(4900-4902)tcA>tcG	p.S1634S		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	1634					acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		TTCTGAAGCCTGACAGGAGTA	0.398																																					p.S1634S		Atlas-SNP	.											.	PKDREJ	195	.	0			c.A4902G						.						84	82	82					22																	46654318		2203	4300	6503	SO:0001819	synonymous_variant	10343	exon1			GAAGCCTGACAGG	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like", "polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like", "polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.4902A>G	chr22.hg19:g.46654318T>C		105.0	0.0		90.0	4.0	NM_006071	B1AJY3|O95850	Silent	SNP	ENST00000253255.5	hg19	CCDS14073.1																																																																																			.	.		0.398	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071		C	46654318	T	C	46654318	2	2	279	1	0	0	0	0	0	0	0	1	11979	1567	55	2		2	PKDREJ	22	46654318	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	2370846	46654318	4650248	406	40165										
SAPS2	9701	hgsc.bcm.edu	37	chr22	50854528	50854528	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ttttctctttcagtggctgaAtgaagagaaggtcatccaga	10	7	3	4			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr22:50854528A>G	ENST00000216061.5	+	7	930	c.560A>G	c.(559-561)aAt>aGt	p.N187S	PPP6R2_ENST00000395744.3_Missense_Mutation_p.N187S|PPP6R2_ENST00000395741.3_Missense_Mutation_p.N187S|PPP6R2_ENST00000359139.3_Missense_Mutation_p.N187S			O75170	PP6R2_HUMAN	protein phosphatase 6, regulatory subunit 2	187						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	22						CAGTGGCTGAATGAAGAGAAG	0.512																																					p.N187S		Atlas-SNP	.											.	PPP6R2	71	.	0			c.A560G						.						135	119	125					22																	50854528		2203	4300	6503	SO:0001583	missense	9701	exon6			GGCTGAATGAAGA	AB014585	CCDS33681.1, CCDS56235.1, CCDS56236.1, CCDS74881.1	22q13.33	2012-04-17	2010-06-28	2010-06-28	ENSG00000100239	ENSG00000100239		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"	19253	protein-coding gene	gene with protein product		610877	"KIAA0685", "SAPS domain family, member 2"	KIAA0685, SAPS2		16769727	Standard	NM_014678		Approved	dJ579N16.1, SAP190	uc003blc.3	O75170	OTTHUMG00000150199	ENST00000216061.5:c.560A>G	chr22.hg19:g.50854528A>G	ENSP00000216061:p.Asn187Ser	103.0	0.0		100.0	27.0	NM_001242898	A6PVG3|B7Z7T3|Q5U5P3|Q7Z2L2|Q7Z5G5|Q7Z731|Q9UGB9	Missense_Mutation	SNP	ENST00000216061.5	hg19		.	.	.	.	.	.	.	.	.	.	A	20.4	3.990861	0.74703	.	.	ENSG00000100239	ENST00000359139;ENST00000395741;ENST00000395744;ENST00000216061	T;T;T;T	0.28666	1.6;1.6;1.6;1.6	5.5	5.5	0.81552	.	0.084250	0.85682	D	0.000000	T	0.58395	0.2119	M	0.85197	2.74	0.54753	D	0.999986	D;D;D;D;D	0.69078	0.997;0.997;0.984;0.997;0.984	D;D;D;D;P	0.68483	0.93;0.958;0.92;0.93;0.891	T	0.65660	-0.6114	10	0.87932	D	0	-10.9755	13.5452	0.61699	1.0:0.0:0.0:0.0	.	187;187;187;187;187	O75170-5;O75170;O75170-3;O75170-4;O75170-2	.;PP6R2_HUMAN;.;.;.	S	187	ENSP00000352051:N187S;ENSP00000379090:N187S;ENSP00000379093:N187S;ENSP00000216061:N187S	ENSP00000216061:N187S	N	+	2	0	PPP6R2	49201394	1.000000	0.71417	0.995000	0.50966	0.522000	0.34438	6.908000	0.75730	2.093000	0.63338	0.374000	0.22700	AAT	.	.		0.512	PPP6R2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316809.1	NM_014678		G	50854528	A	G	50854528	3	3	279	1	0	0	0	0	1	0	0	0	13852	101	4	2	574	2	SAPS2	22	50854528	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	4200210	50854528	450038	407	40166										
ODF3B	440836	hgsc.bcm.edu	37	chr22	50969184	50969184	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gccctggcttccgagtgttgTcttgggggagcgaagtccgc	16	11	1	0			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chr22:50969184T>C	ENST00000428989.2	-	5	637	c.638A>G	c.(637-639)gAc>gGc	p.D213G	TYMP_ENST00000395678.3_5'Flank|TYMP_ENST00000252029.3_5'Flank|ODF3B_ENST00000329363.4_Missense_Mutation_p.D213G|ODF3B_ENST00000403326.1_Missense_Mutation_p.D145G|TYMP_ENST00000395681.1_5'Flank|TYMP_ENST00000395680.1_5'Flank|ODF3B_ENST00000401779.1_Silent_p.R189R|ODF3B_ENST00000405135.1_Silent_p.R228R			A8MYP8	ODF3B_HUMAN	outer dense fiber of sperm tails 3B	213										lung(2)	2						CCGAGTGTTGTCTTGGGGGAG	0.667																																					p.D213G		Atlas-SNP	.											.	ODF3B	6	.	0			c.A638G						.						16	19	18					22																	50969184		1923	4109	6032	SO:0001583	missense	440836	exon6			GTGTTGTCTTGGG		CCDS43039.1	22q13.33	2008-10-24			ENSG00000177989	ENSG00000177989			34388	protein-coding gene	gene with protein product							Standard	NM_001014440		Approved		uc003bmh.2	A8MYP8	OTTHUMG00000150334	ENST00000428989.2:c.638A>G	chr22.hg19:g.50969184T>C	ENSP00000390712:p.Asp213Gly	54.0	0.0		86.0	4.0	NM_001014440	A0PK18	Missense_Mutation	SNP	ENST00000428989.2	hg19	CCDS43039.1	.	.	.	.	.	.	.	.	.	.	T	10.22	1.291132	0.23564	.	.	ENSG00000177989	ENST00000329363;ENST00000403326;ENST00000428989	T;T;T	0.34275	1.37;1.37;1.37	5.14	4.1	0.47936	.	.	.	.	.	T	0.32912	0.0845	M	0.64630	1.985	0.26183	N	0.979709	B	0.06786	0.001	B	0.08055	0.003	T	0.23762	-1.0179	9	0.28530	T	0.3	-1.0048	6.9715	0.24652	0.0:0.1055:0.0:0.8945	.	213	A8MYP8	ODF3B_HUMAN	G	213;145;213	ENSP00000382804:D213G;ENSP00000385123:D145G;ENSP00000390712:D213G	ENSP00000382804:D213G	D	-	2	0	ODF3B	49316050	0.658000	0.27402	0.162000	0.22713	0.120000	0.20174	1.333000	0.33816	0.986000	0.38683	0.459000	0.35465	GAC	.	.		0.667	ODF3B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317626.2			C	50969184	T	C	50969184	3	2	279	1	0	0	0	0	1	0	0	0	10839	1667	58	2	131	2	ODF3B	22	50969184	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	114656	50969184	335382	408	40167										
PHEX	5251	hgsc.bcm.edu	37	chrX	22237189	22237189	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gctataggagtaattgtcggAcatgaatttacacatggatt	10	5	0	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chrX:22237189A>G	ENST00000379374.4	+	17	2302	c.1737A>G	c.(1735-1737)ggA>ggG	p.G579G	PHEX_ENST00000535894.1_Silent_p.G482G|PHEX_ENST00000537599.1_Silent_p.G579G|PHEX_ENST00000418858.3_Silent_p.G282G	NM_000444.4	NP_000435.3	P78562	PHEX_HUMAN	phosphate regulating endopeptidase homolog, X-linked	579			G -> R (in XLHR). {ECO:0000269|PubMed:9097956, ECO:0000269|PubMed:9199930, ECO:0000269|PubMed:9768674}.|G -> V (in XLHR). {ECO:0000269|PubMed:9106524}.		bone mineralization (GO:0030282)|cell-cell signaling (GO:0007267)|cellular protein modification process (GO:0006464)|organophosphate metabolic process (GO:0019637)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|cervix(2)|endometrium(2)|large_intestine(12)|liver(1)|lung(19)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	42						TAATTGTCGGACATGAATTTA	0.313																																					p.G579G		Atlas-SNP	.											.	PHEX	95	.	0			c.A1737G						.						165	145	152					X																	22237189		2203	4299	6502	SO:0001819	synonymous_variant	5251	exon17			TGTCGGACATGAA	U82970	CCDS14204.1	Xp22.2-p22.1	2008-07-31	2008-07-31		ENSG00000102174	ENSG00000102174			8918	protein-coding gene	gene with protein product		300550	"phosphate regulating gene with homologies to endopeptidases on the X chromosome (hypophosphatemia, vitamin D resistant rickets)"	HYP, HPDR		7550339, 9070861	Standard	NM_000444		Approved	PEX, HPDR1, HYP1, XLH	uc004dah.3	P78562	OTTHUMG00000021241	ENST00000379374.4:c.1737A>G	chrX.hg19:g.22237189A>G		48.0	0.0		72.0	4.0	NM_000444	O00678|Q13646|Q2M325|Q93032|Q99827	Silent	SNP	ENST00000379374.4	hg19	CCDS14204.1																																																																																			.	.		0.313	PHEX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056035.1	NM_000444		G	22237189	A	G	22237189	2	3	279	1	0	0	0	0	0	0	0	1	11828	262	10	2		2	PHEX	23	22237189	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10		22237189	133033371	409	40168										
PHEX	5251	hgsc.bcm.edu	37	chrX	22265970	22265970	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tgacatatcgtttttcagggTcaatggtgcaattagtaact	9	6	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chrX:22265970T>C	ENST00000379374.4	+	22	2715	c.2150T>C	c.(2149-2151)gTc>gCc	p.V717A	PHEX_ENST00000535894.1_Missense_Mutation_p.V620A|PHEX_ENST00000537599.1_Silent_p.G691G|PHEX_ENST00000418858.3_Missense_Mutation_p.V420A	NM_000444.4	NP_000435.3	P78562	PHEX_HUMAN	phosphate regulating endopeptidase homolog, X-linked	717					bone mineralization (GO:0030282)|cell-cell signaling (GO:0007267)|cellular protein modification process (GO:0006464)|organophosphate metabolic process (GO:0019637)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|cervix(2)|endometrium(2)|large_intestine(12)|liver(1)|lung(19)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	42						TTTTTCAGGGTCAATGGTGCA	0.403																																					p.V717A		Atlas-SNP	.											.	PHEX	95	.	0			c.T2150C						.						91	79	83					X																	22265970		2203	4300	6503	SO:0001583	missense	5251	exon22			TCAGGGTCAATGG	U82970	CCDS14204.1	Xp22.2-p22.1	2008-07-31	2008-07-31		ENSG00000102174	ENSG00000102174			8918	protein-coding gene	gene with protein product		300550	"phosphate regulating gene with homologies to endopeptidases on the X chromosome (hypophosphatemia, vitamin D resistant rickets)"	HYP, HPDR		7550339, 9070861	Standard	NM_000444		Approved	PEX, HPDR1, HYP1, XLH	uc004dah.3	P78562	OTTHUMG00000021241	ENST00000379374.4:c.2150T>C	chrX.hg19:g.22265970T>C	ENSP00000368682:p.Val717Ala	67.0	0.0		96.0	4.0	NM_000444	O00678|Q13646|Q2M325|Q93032|Q99827	Missense_Mutation	SNP	ENST00000379374.4	hg19	CCDS14204.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.573189	0.86542	.	.	ENSG00000102174	ENST00000379374;ENST00000535894;ENST00000418858	D;D;D	0.87571	-2.27;-2.27;-2.27	5.59	5.59	0.84812	Peptidase M13, neprilysin, C-terminal (1);Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.89093	0.6617	L	0.53780	1.695	0.80722	D	1	D	0.56968	0.978	P	0.54815	0.761	D	0.89316	0.3636	10	0.52906	T	0.07	.	13.0096	0.58724	0.0:0.0:0.0:1.0	.	717	P78562	PHEX_HUMAN	A	717;620;420	ENSP00000368682:V717A;ENSP00000439418:V620A;ENSP00000443531:V420A	ENSP00000368682:V717A	V	+	2	0	PHEX	22175891	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	6.220000	0.72237	1.873000	0.54277	0.486000	0.48141	GTC	.	.		0.403	PHEX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056035.1	NM_000444		C	22265970	T	C	22265970	3	2	279	1	0	0	0	0	1	0	0	0	11828	1667	58	2	2236	2	PHEX	23	22265970	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	28781	22265970	133004590	410	40169										
TAB3	257397	hgsc.bcm.edu	37	chrX	30864763	30864763	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	atcttgtcatttcctcaggcTagtaagaaaggacccaaaat	7	9	3	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chrX:30864763T>C	ENST00000378933.1	-	5	1888		c.e5-2		TAB3_ENST00000288422.2_Splice_Site|TAB3_ENST00000378930.3_Splice_Site|TAB3_ENST00000378932.2_Splice_Site|TAB3_ENST00000378928.1_Splice_Site	NM_152787.3	NP_690000.2	Q8N5C8	TAB3_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 3						activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|skin(1)	27						TTCCTCAGGCTAGTAAGAAAG	0.373																																					.	Pancreas(164;1598 1985 29022 43301 49529)	Atlas-SNP	.											.	TAB3	82	.	0			c.1711-2A>G						.						160	133	142					X																	30864763		2202	4300	6502	SO:0001630	splice_region_variant	257397	exon9			TCAGGCTAGTAAG	AY331591	CCDS14226.1	Xp21.2	2010-02-05	2010-02-05	2010-02-05	ENSG00000157625	ENSG00000157625			30681	protein-coding gene	gene with protein product	"TAK1 binding protein 3"	300480	"mitogen-activated protein kinase kinase kinase 7 interacting protein 3"	MAP3K7IP3		14633987, 14670075	Standard	XM_005274482		Approved		uc004dcj.3	Q8N5C8	OTTHUMG00000021329	ENST00000378933.1:c.1711-2A>G	chrX.hg19:g.30864763T>C		64.0	0.0		72.0	4.0	NM_152787	A6NDD9|Q6VQR0	Splice_Site	SNP	ENST00000378933.1	hg19	CCDS14226.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.980496	0.74474	.	.	ENSG00000157625	ENST00000378933;ENST00000378930;ENST00000288422;ENST00000378932;ENST00000378928	.	.	.	5.14	5.14	0.70334	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.1015	0.65059	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	TAB3	30774684	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.678000	0.84035	1.707000	0.51288	0.437000	0.28790	.	.	.		0.373	TAB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056173.1	NM_152787	Intron	C	30864763	T	C	30864763	5	2	279	1	0	0	0	0	0	0	1	0	15512	1536	53	2	445	2	TAB3	23	30864763	Splice_Site	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	8598793	30864763	124405797	411	40170										
RP2	6102	hgsc.bcm.edu	37	chrX	46713254	46713254	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tatcaaatttggatgttttcAatggtactatcctgaattag	7	5	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chrX:46713254A>G	ENST00000218340.3	+	2	607	c.446A>G	c.(445-447)cAa>cGa	p.Q149R		NM_006915.2	NP_008846.2	O75695	XRP2_HUMAN	retinitis pigmentosa 2 (X-linked recessive)	149	C-CAP/cofactor C-like. {ECO:0000255|PROSITE-ProRule:PRU00659}.				cell morphogenesis (GO:0000902)|CTP biosynthetic process (GO:0006241)|cytoskeleton organization (GO:0007010)|GTP biosynthetic process (GO:0006183)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|protein transport (GO:0015031)|UTP biosynthetic process (GO:0006228)|visual perception (GO:0007601)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|periciliary membrane compartment (GO:1990075)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|GTPase activator activity (GO:0005096)|nucleoside diphosphate kinase activity (GO:0004550)|unfolded protein binding (GO:0051082)			NS(1)|large_intestine(4)|lung(5)|stomach(1)	11						GGATGTTTTCAATGGTACTAT	0.388																																					p.Q149R		Atlas-SNP	.											.	RP2	37	.	0			c.A446G						.						109	100	103					X																	46713254		2203	4300	6503	SO:0001583	missense	6102	exon2			GTTTTCAATGGTA	AJ007590	CCDS14270.1	Xp11.3	2013-01-08			ENSG00000102218	ENSG00000102218			10274	protein-coding gene	gene with protein product		300757				6325945, 9697692, 19852809	Standard	NM_006915		Approved	TBCCD2, NME10, NM23-H10	uc004dgw.4	O75695	OTTHUMG00000021430	ENST00000218340.3:c.446A>G	chrX.hg19:g.46713254A>G	ENSP00000218340:p.Gln149Arg	57.0	0.0		77.0	4.0	NM_006915	Q86XJ7|Q9NU67	Missense_Mutation	SNP	ENST00000218340.3	hg19	CCDS14270.1	.	.	.	.	.	.	.	.	.	.	A	14.00	2.404954	0.42613	.	.	ENSG00000102218	ENST00000218340	D	0.86366	-2.11	5.62	5.62	0.85841	Tubulin binding cofactor C (1);C-CAP/cofactor C-like domain (1);	0.050000	0.85682	D	0.000000	T	0.79941	0.4533	L	0.28014	0.82	0.58432	D	0.999999	P	0.40032	0.699	B	0.38378	0.272	T	0.78216	-0.2290	10	0.23302	T	0.38	-20.1065	14.8103	0.69989	1.0:0.0:0.0:0.0	.	149	O75695	XRP2_HUMAN	R	149	ENSP00000218340:Q149R	ENSP00000218340:Q149R	Q	+	2	0	RP2	46598198	1.000000	0.71417	0.958000	0.39756	0.991000	0.79684	8.820000	0.92003	1.879000	0.54435	0.417000	0.27973	CAA	.	.		0.388	RP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056375.1	NM_006915		G	46713254	A	G	46713254	3	3	279	1	0	0	0	0	1	0	0	0	13549	130	5	2	452	2	RP2	23	46713254	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	15848491	46713254	108557306	412	40171										
HDAC6	10013	hgsc.bcm.edu	37	chrX	48661291	48661291	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	ttcacagaagcgaaatattaAaaagggagccgttccccgct	9	10	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chrX:48661291A>G	ENST00000334136.5	+	3	285	c.107A>G	c.(106-108)aAa>aGa	p.K36R	HDAC6_ENST00000444343.2_Missense_Mutation_p.K50R|HDAC6_ENST00000413163.2_5'UTR|HDAC6_ENST00000469223.1_3'UTR|HDAC6_ENST00000376619.2_Missense_Mutation_p.K36R			Q9UBN7	HDAC6_HUMAN	histone deacetylase 6	36					aggresome assembly (GO:0070842)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to misfolded protein (GO:0071218)|cellular response to topologically incorrect protein (GO:0035967)|histone deacetylation (GO:0016575)|Hsp90 deacetylation (GO:0070846)|intracellular protein transport (GO:0006886)|lysosome localization (GO:0032418)|macroautophagy (GO:0016236)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of oxidoreductase activity (GO:0051354)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of proteolysis (GO:0045861)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of chaperone-mediated protein complex assembly (GO:0090035)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of hydrogen peroxide-mediated programmed cell death (GO:1901300)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of signal transduction (GO:0009967)|protein complex disassembly (GO:0043241)|protein deacetylation (GO:0006476)|protein polyubiquitination (GO:0000209)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of establishment of protein localization (GO:0070201)|regulation of gene expression, epigenetic (GO:0040029)|regulation of microtubule-based movement (GO:0060632)|regulation of receptor activity (GO:0010469)|response to growth factor (GO:0070848)|response to misfolded protein (GO:0051788)|response to organic substance (GO:0010033)|response to toxic substance (GO:0009636)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	aggresome (GO:0016235)|axon (GO:0030424)|caveola (GO:0005901)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|dendrite (GO:0030425)|histone deacetylase complex (GO:0000118)|inclusion body (GO:0016234)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)	alpha-tubulin binding (GO:0043014)|beta-catenin binding (GO:0008013)|core promoter binding (GO:0001047)|dynein complex binding (GO:0070840)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|Hsp90 protein binding (GO:0051879)|microtubule binding (GO:0008017)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|polyubiquitin binding (GO:0031593)|tau protein binding (GO:0048156)|tubulin deacetylase activity (GO:0042903)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|kidney(5)|large_intestine(8)|lung(9)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	40					Vorinostat(DB02546)	CGAAATATTAAAAAGGGAGCC	0.527																																					p.K36R	Pancreas(112;205 1675 2305 8976 15959)	Atlas-SNP	.											.	HDAC6	111	.	0			c.A107G						.						40	36	37					X																	48661291		2202	4300	6502	SO:0001583	missense	10013	exon3			ATATTAAAAAGGG	AF132609	CCDS14306.1	Xp11.23	2014-06-12			ENSG00000094631	ENSG00000094631			14064	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 90"	300272				10220385, 10048485	Standard	NM_006044		Approved	KIAA0901, JM21, HD6, FLJ16239, PPP1R90	uc004dks.1	Q9UBN7	OTTHUMG00000034496	ENST00000334136.5:c.107A>G	chrX.hg19:g.48661291A>G	ENSP00000334061:p.Lys36Arg	57.0	0.0		85.0	57.0	NM_006044	O94975|Q6NT75|Q7L3E5|Q96CY0	Missense_Mutation	SNP	ENST00000334136.5	hg19	CCDS14306.1	.	.	.	.	.	.	.	.	.	.	A	13.22	2.170859	0.38315	.	.	ENSG00000094631	ENST00000423941;ENST00000438518;ENST00000376643;ENST00000444343;ENST00000376610;ENST00000334136;ENST00000376619;ENST00000436813;ENST00000441703;ENST00000426196;ENST00000443563;ENST00000440653	T;T;T	0.60548	0.18;0.2;0.2	4.42	3.28	0.37604	.	0.335207	0.25469	N	0.030452	T	0.55816	0.1944	N	0.24115	0.695	0.40731	D	0.982747	B;D;B	0.69078	0.057;0.997;0.27	B;D;B	0.75020	0.023;0.985;0.147	T	0.52313	-0.8592	10	0.26408	T	0.33	-18.528	6.9838	0.24718	0.8855:0.0:0.1145:0.0	.	26;36;36	B4DZN1;Q9UBN7;Q9BRX7	.;HDAC6_HUMAN;.	R	36;36;36;50;36;36;36;36;36;36;36;36	ENSP00000398566:K50R;ENSP00000334061:K36R;ENSP00000365804:K36R	ENSP00000334061:K36R	K	+	2	0	HDAC6	48546235	0.997000	0.39634	0.648000	0.29521	0.765000	0.43378	2.972000	0.49256	1.744000	0.51775	0.486000	0.48141	AAA	.	.		0.527	HDAC6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083394.2	NM_006044		G	48661291	A	G	48661291	3	3	279	1	0	0	0	0	1	0	0	0	7020	14	1	2	113	2	HDAC6	23	48661291	Missense_Mutation	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	1948037	48661291	106609269	413	40172										
HUWE1	10075	hgsc.bcm.edu	37	chrX	53591670	53591670	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tcctcctcctgcacttctgcTtccccaggctcgcctgaaac	6	19	1	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chrX:53591670T>C	ENST00000342160.3	-	50	7351	c.6894A>G	c.(6892-6894)gaA>gaG	p.E2298E	HUWE1_ENST00000262854.6_Silent_p.E2298E			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	2298	Glu-rich.				base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						GCACTTCTGCTTCCCCAGGCT	0.517																																					p.E2298E		Atlas-SNP	.											.	HUWE1	724	.	0			c.A6894G						.						149	105	120					X																	53591670		2203	4300	6503	SO:0001819	synonymous_variant	10075	exon51			TTCTGCTTCCCCA	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"HECT, UBA and WWE domain containing 1"			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.6894A>G	chrX.hg19:g.53591670T>C		70.0	0.0		97.0	4.0	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Silent	SNP	ENST00000342160.3	hg19	CCDS35301.1	.	.	.	.	.	.	.	.	.	.	T	6.323	0.427651	0.11987	.	.	ENSG00000086758	ENST00000427052	.	.	.	5.44	1.88	0.25563	.	.	.	.	.	T	0.56108	0.1963	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50048	-0.8873	4	.	.	.	.	8.2131	0.31494	0.0:0.244:0.0:0.756	.	.	.	.	G	1332	.	.	S	-	1	0	HUWE1	53608395	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.038000	0.30254	0.712000	0.32039	0.417000	0.27973	AGC	.	.		0.517	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		C	53591670	T	C	53591670	2	2	279	1	0	0	0	0	0	0	0	1	7470	1606	56	2		2	HUWE1	23	53591670	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	4930379	53591670	101678890	414	40173										
ACRC	93953	hgsc.bcm.edu	37	chrX	70823976	70823976	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gacagcagtgatgattcggaAgcttccgacgacagcagtga	13	9	0	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chrX:70823976A>G	ENST00000373695.1	+	7	1386	c.849A>G	c.(847-849)gaA>gaG	p.E283E	ACRC_ENST00000373696.3_Silent_p.E283E			Q96QF7	ACRC_HUMAN	acidic repeat containing	283	Asp/Ser-rich.					nucleus (GO:0005634)				autonomic_ganglia(1)|breast(1)|endometrium(15)|kidney(4)|large_intestine(4)|lung(20)|ovary(5)|prostate(1)|skin(2)|stomach(1)	54	Renal(35;0.156)					ATGATTCGGAAGCTTCCGACG	0.542																																					p.E283E		Atlas-SNP	.											.	ACRC	110	.	0			c.A849G						.						106	103	104					X																	70823976		2203	4300	6503	SO:0001819	synonymous_variant	93953	exon8			TTCGGAAGCTTCC	AJ311392	CCDS35326.1	Xq13.1	2010-08-05			ENSG00000147174	ENSG00000147174			15805	protein-coding gene	gene with protein product		300369					Standard	NM_052957		Approved		uc004eae.2	Q96QF7	OTTHUMG00000033327	ENST00000373695.1:c.849A>G	chrX.hg19:g.70823976A>G		39.0	0.0		90.0	4.0	NM_052957	B9EG62	Silent	SNP	ENST00000373695.1	hg19	CCDS35326.1																																																																																			.	.		0.542	ACRC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081856.1			G	70823976	A	G	70823976	2	3	279	1	0	0	0	0	0	0	0	1	171	69	3	2		2	ACRC	23	70823976	Silent	SNP	A	TCGA-G3-A3CG-01A-11D-A20W-10	17232306	70823976	84446584	415	40174										
NKAP	79576	hgsc.bcm.edu	37	chrX	119059318	119059318	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tcatcagcactgtagatctgGttctcttttcgcagtcgcac	8	12	4	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chrX:119059318G>T	ENST00000371410.3	-	9	1279	c.1113C>A	c.(1111-1113)aaC>aaA	p.N371K	RP3-327A19.5_ENST00000455986.1_RNA|AC002477.1_ENST00000581061.1_RNA|NKAP_ENST00000477789.1_5'UTR	NM_024528.3	NP_078804.2	Q8N5F7	NKAP_HUMAN	NFKB activating protein	371	Necessary for interaction with HDAC3 and transcriptional repression.				granulocyte differentiation (GO:0030851)|hematopoietic stem cell proliferation (GO:0071425)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|stem cell maintenance (GO:0019827)|T cell differentiation in thymus (GO:0033077)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)	20						TGTAGATCTGGTTCTCTTTTC	0.418																																					p.N371K		Atlas-SNP	.											.	NKAP	53	.	0			c.C1113A						.						138	125	129					X																	119059318		2203	4300	6503	SO:0001583	missense	79576	exon9			GATCTGGTTCTCT	BC012770	CCDS14592.1	Xq24	2010-07-20			ENSG00000101882	ENSG00000101882			29873	protein-coding gene	gene with protein product	"NF kappaB activating protein"	300766				14550261	Standard	NM_024528		Approved	FLJ22626	uc004esh.3	Q8N5F7	OTTHUMG00000022284	ENST00000371410.3:c.1113C>A	chrX.hg19:g.119059318G>T	ENSP00000360464:p.Asn371Lys	60.0	0.0		103.0	81.0	NM_024528	Q6IPW6|Q96BQ2|Q9H638	Missense_Mutation	SNP	ENST00000371410.3	hg19	CCDS14592.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.030201	0.93575	.	.	ENSG00000101882	ENST00000371410	T	0.24538	1.85	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.56863	0.2014	M	0.83384	2.64	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.62455	-0.6851	10	0.87932	D	0	-26.6892	17.8402	0.88713	0.0:0.0:1.0:0.0	.	371	Q8N5F7	NKAP_HUMAN	K	371	ENSP00000360464:N371K	ENSP00000360464:N371K	N	-	3	2	NKAP	118943346	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.792000	0.99085	2.432000	0.82394	0.600000	0.82982	AAC	.	.		0.418	NKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058072.1	NM_024528		T	119059318	G	T	119059318	3	4	279	1	0	0	0	0	1	0	0	0	10448	1252	44	3	138	3	NKAP	23	119059318	Missense_Mutation	SNP	G	TCGA-G3-A3CG-01A-11D-A20W-10	48235342	119059318	36211242	416	40175										
MCF2	4168	hgsc.bcm.edu	37	chrX	138699701	138699701	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gagtttatgcattttgaaggTcctgctgagttgtatccgtt	11	6	0	2			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chrX:138699701T>C	ENST00000370576.4	-	8	1179	c.970A>G	c.(970-972)Acc>Gcc	p.T324A	MCF2_ENST00000414978.1_Missense_Mutation_p.T384A|MCF2_ENST00000370578.4_Missense_Mutation_p.T469A|MCF2_ENST00000519895.1_Missense_Mutation_p.T384A|MCF2_ENST00000370573.4_Missense_Mutation_p.T324A|MCF2_ENST00000536274.1_Missense_Mutation_p.T285A|MCF2_ENST00000338585.6_Missense_Mutation_p.T324A|MCF2_ENST00000483690.1_5'Flank|MCF2_ENST00000520602.1_Missense_Mutation_p.T384A	NM_001171879.1|NM_005369.4	NP_001165350.1|NP_005360.3	P10911	MCF2_HUMAN	MCF.2 cell line derived transforming sequence	324					apoptotic signaling pathway (GO:0097190)|dendrite development (GO:0016358)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(15)|lung(34)|pancreas(1)|pleura(1)|prostate(1)	62	Acute lymphoblastic leukemia(192;0.000127)					ATTTTGAAGGTCCTGCTGAGT	0.393																																					p.T384A		Atlas-SNP	.											.	MCF2	432	.	0			c.A1150G						.						202	160	174					X																	138699701		2203	4300	6503	SO:0001583	missense	4168	exon11			TGAAGGTCCTGCT		CCDS14667.1, CCDS48175.1, CCDS55514.1, CCDS55515.1, CCDS55516.1, CCDS55517.1	Xq26.3-q27.1	2012-07-24			ENSG00000101977	ENSG00000101977		"Rho guanine nucleotide exchange factors"	6940	protein-coding gene	gene with protein product	"Oncogene MCF2 (oncogene DBL)"	311030				2577874, 1611909	Standard	NM_001099855		Approved	DBL, ARHGEF21	uc011mwo.1	P10911	OTTHUMG00000022537	ENST00000370576.4:c.970A>G	chrX.hg19:g.138699701T>C	ENSP00000359608:p.Thr324Ala	78.0	0.0		105.0	5.0	NM_001171876	B7Z3Y5|B7Z869|B7ZAV1|E9PH77|F5H091|P14919|Q5JYJ2|Q5JYJ3|Q5JYJ4|Q8IUF3|Q8IUF4|Q9UJB3	Missense_Mutation	SNP	ENST00000370576.4	hg19	CCDS14667.1	.	.	.	.	.	.	.	.	.	.	T	12.19	1.862957	0.32884	.	.	ENSG00000101977	ENST00000520602;ENST00000370576;ENST00000536274;ENST00000370578;ENST00000414978;ENST00000519895;ENST00000370573;ENST00000338585	T;T;T;T;T;T;T;T	0.36340	1.44;1.34;1.26;1.41;1.44;1.49;1.38;1.41	5.98	4.83	0.62350	.	0.235047	0.50627	D	0.000118	T	0.27594	0.0678	L	0.35414	1.06	0.27522	N	0.951357	B;B;B;B;B;B;B;B	0.20052	0.0;0.024;0.0;0.0;0.001;0.0;0.041;0.0	B;B;B;B;B;B;B;B	0.25987	0.004;0.029;0.004;0.003;0.004;0.005;0.065;0.004	T	0.19516	-1.0303	10	0.23302	T	0.38	.	10.1445	0.42755	0.0:0.078:0.0:0.922	.	384;469;285;324;324;469;324;324	E9PH77;B7Z3Z2;F5H091;B2R9S6;P10911-2;Q5JYJ7;P10911-4;P10911	.;.;.;.;.;.;.;MCF2_HUMAN	A	384;324;285;469;384;384;324;324	ENSP00000427745:T384A;ENSP00000359608:T324A;ENSP00000438155:T285A;ENSP00000359610:T469A;ENSP00000397055:T384A;ENSP00000430276:T384A;ENSP00000359605:T324A;ENSP00000342204:T324A	ENSP00000342204:T324A	T	-	1	0	MCF2	138527367	1.000000	0.71417	0.998000	0.56505	0.978000	0.69477	1.987000	0.40687	0.873000	0.35799	0.441000	0.28932	ACC	.	.		0.393	MCF2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058560.1	NM_005369		C	138699701	T	C	138699701	3	2	279	1	0	0	0	0	1	0	0	0	9387	1667	58	2	1959	2	MCF2	23	138699701	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	19640383	138699701	16570859	417	40176										
SLITRK4	139065	hgsc.bcm.edu	37	chrX	142716432	142716432	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	tagatcttgttcaaagctgtTtgctcctcaaggacctgtag	9	9	3	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chrX:142716432T>C	ENST00000381779.4	-	2	2718	c.2493A>G	c.(2491-2493)caA>caG	p.Q831Q	SLITRK4_ENST00000338017.4_Silent_p.Q831Q|SLITRK4_ENST00000356928.1_Silent_p.Q831Q	NM_001184749.2|NM_001184750.1|NM_173078.4	NP_001171678.1|NP_001171679.1|NP_775101.1	Q8IW52	SLIK4_HUMAN	SLIT and NTRK-like family, member 4	831						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(27)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	60	Acute lymphoblastic leukemia(192;6.56e-05)					TCAAAGCTGTTTGCTCCTCAA	0.388																																					p.Q831Q		Atlas-SNP	.											.	SLITRK4	162	.	0			c.A2493G						.						101	89	93					X																	142716432		2203	4300	6503	SO:0001819	synonymous_variant	139065	exon2			AGCTGTTTGCTCC	BC040986	CCDS14679.1	Xq27.3	2004-06-23			ENSG00000179542	ENSG00000179542			23502	protein-coding gene	gene with protein product		300562				14557068	Standard	NM_001184749		Approved	DKFZp547M2010	uc004fby.3	Q8IW52	OTTHUMG00000022580	ENST00000381779.4:c.2493A>G	chrX.hg19:g.142716432T>C		67.0	0.0		75.0	4.0	NM_001184750	Q5JXG3|Q8TCM8|Q96DL3	Silent	SNP	ENST00000381779.4	hg19	CCDS14679.1																																																																																			.	.		0.388	SLITRK4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058617.1	NM_173078		C	142716432	T	C	142716432	2	2	279	1	0	0	0	0	0	0	0	1	14760	1838	64	2		2	SLITRK4	23	142716432	Silent	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10	4016731	142716432	12554128	418	40177										
ZNF185	7739	hgsc.bcm.edu	37	chrX	152113989	152113989	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gatctgagcaacttgtcagaCgagagagttgtggcagcagg	15	7	2	3			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chrX:152113989C>T	ENST00000370268.4	+	16	1424	c.1387C>T	c.(1387-1389)Cga>Tga	p.R463*	ZNF185_ENST00000324823.6_Nonsense_Mutation_p.R231*|ZNF185_ENST00000318504.7_Nonsense_Mutation_p.R404*|ZNF185_ENST00000535861.1_Nonsense_Mutation_p.R495*|ZNF185_ENST00000449285.2_Nonsense_Mutation_p.R464*|ZNF185_ENST00000370270.2_Nonsense_Mutation_p.R495*|ZNF185_ENST00000454925.1_Nonsense_Mutation_p.R101*|ZNF185_ENST00000318529.8_Nonsense_Mutation_p.R242*|ZNF185_ENST00000539731.1_Nonsense_Mutation_p.R466*			O15231	ZN185_HUMAN	zinc finger protein 185 (LIM domain)	463						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(3)	12	Acute lymphoblastic leukemia(192;6.56e-05)					ACTTGTCAGACGAGAGAGTTG	0.607																																					p.R495X		Atlas-SNP	.											.	ZNF185	92	.	0			c.C1483T						.						27	31	30					X																	152113989		2062	4176	6238	SO:0001587	stop_gained	7739	exon17			GTCAGACGAGAGA	AK056517	CCDS48184.1, CCDS55528.1, CCDS55529.1, CCDS55530.1, CCDS55531.1, CCDS55532.1, CCDS69832.1	Xq28	2012-08-08			ENSG00000147394	ENSG00000147394		"Zinc fingers, C2H2-type"	12976	protein-coding gene	gene with protein product		300381				9268636	Standard	NM_001178106		Approved		uc011myg.2	O15231	OTTHUMG00000024187	ENST00000370268.4:c.1387C>T	chrX.hg19:g.152113989C>T	ENSP00000359291:p.Arg463*	42.0	0.0		93.0	5.0	NM_001178106	A4FTV3|A6NME5|B4DLE9|B7Z771|B8K2L9|B8K2M0|B8K2M1|B8K2M2|E9PFR6|F5GXF7|F5GZL4|F8W8V7|H0Y4M8|O00345|Q8N1R8|Q9NSD2	Nonsense_Mutation	SNP	ENST00000370268.4	hg19	CCDS48184.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.84|12.84	2.057940|2.057940	0.36277|0.36277	.|.	.|.	ENSG00000147394|ENSG00000147394	ENST00000535861;ENST00000539731;ENST00000449285;ENST00000318504;ENST00000535156;ENST00000324823;ENST00000433245;ENST00000370268;ENST00000318529;ENST00000370270;ENST00000436731|ENST00000426821	.|.	.|.	.|.	2.54|2.54	-2.02|-2.02	0.07388|0.07388	.|.	572.326000|.	0.01289|.	U|.	0.009945|.	.|T	.|0.30230	.|0.0758	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.39563	.|-0.9608	.|3	0.27785|.	T|.	0.31|.	.|.	6.2702|6.2702	0.20951|0.20951	0.0:0.3018:0.5631:0.1352|0.0:0.3018:0.5631:0.1352	.|.	.|.	.|.	.|.	X|M	495;466;464;404;298;231;329;463;242;226;168|248	.|.	ENSP00000312782:R404X|.	R|T	+|+	1|2	2|0	ZNF185|ZNF185	151864645|151864645	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-1.372000|-1.372000	0.02570|0.02570	-0.660000|-0.660000	0.05352|0.05352	-0.435000|-0.435000	0.05868|0.05868	CGA|ACG	.	.		0.607	ZNF185-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000377480.1	NM_007150		T	152113989	C	T	152113989	4	4	279	1	0	0	0	0	0	1	0	0	17767	528	19	1	1693	1	ZNF185	23	152113989	Nonsense_Mutation	SNP	C	TCGA-G3-A3CG-01A-11D-A20W-10	9397557	152113989	3156571	419	40178										
UTY	7404	hgsc.bcm.edu	37	chrY	15448106	15448106	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0217391304347826	9	1	0.733827493261456	1.25566037735849	0.607577601947657	0.386996904024768	1	0	gagtgagatgttcattcgccTtcttaataccagtgctagtt	9	8	2	1			TCGA-G3-A3CG-01A-11D-A20W-10	TCGA-G3-A3CG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe8bcb2-95a5-43cc-97e1-ee6c7ed87731	d9577f26-985f-433d-becb-50301258d4d6	g.chrY:15448106T>C	ENST00000331397.4	-	16	2887	c.1880A>G	c.(1879-1881)aAg>aGg	p.K627R	UTY_ENST00000538878.1_Missense_Mutation_p.K594R|UTY_ENST00000545955.1_Missense_Mutation_p.K702R|UTY_ENST00000537580.1_Missense_Mutation_p.K548R|UTY_ENST00000382896.4_Missense_Mutation_p.K672R|UTY_ENST00000540140.1_Missense_Mutation_p.K624R|UTY_ENST00000329134.5_Missense_Mutation_p.K627R|UTY_ENST00000362096.4_Missense_Mutation_p.K627R	NM_001258267.1|NM_007125.4	NP_001245196.1|NP_009056.3	O14607	UTY_HUMAN	ubiquitously transcribed tetratricopeptide repeat containing, Y-linked	627					regulation of gene expression (GO:0010468)	nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)			kidney(1)|lung(6)	7						TTCATTCGCCTTCTTAATACC	0.478																																					p.K724R	Colon(103;1740 2135 40732 45171)	Atlas-SNP	.											.	UTY	45	.	0			c.A2171G						.						99	91	93					Y																	15448106		607	1974	2581	SO:0001583	missense	7404	exon18			TTCGCCTTCTTAA	AF000994	CCDS14783.1, CCDS14784.1, CCDS14785.1, CCDS59184.1, CCDS76073.1, CCDS76074.1, CCDS76075.1, CCDS76076.1, CCDS76077.1, CCDS76078.1, CCDS76079.1	Yq11.221	2013-11-04	2012-11-15		ENSG00000183878	ENSG00000183878		"Tetratricopeptide (TTC) repeat domain containing"	12638	protein-coding gene	gene with protein product		400009	"ubiquitously transcribed tetratricopeptide repeat gene, Y chromosome", "ubiquitously transcribed tetratricopeptide repeat gene, Y-linked"			8944031, 9499428	Standard	NM_182659		Approved	KDM6AL	uc022ckf.2	O14607	OTTHUMG00000036319	ENST00000331397.4:c.1880A>G	chrY.hg19:g.15448106T>C	ENSP00000328939:p.Lys627Arg	113.0	0.0		93.0	4.0	NM_001258249	A8K9Z3|E1U199|E1U1A0|F5H4V7|F8W8R7|O14608	Missense_Mutation	SNP	ENST00000331397.4	hg19	CCDS14783.1																																																																																			.	.		0.478	UTY-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000088394.1	NM_182660		C	15448106	T	C	15448106	3	2	279	1	0	0	0	0	1	0	0	0	17122	1609	56	2	2478	2	UTY	24	15448106	Missense_Mutation	SNP	T	TCGA-G3-A3CG-01A-11D-A20W-10		15448106	43925460	420	40179										
TMEM51	55092	hgsc.bcm.edu	37	chr1	15541828	15541828	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	gctgctgctgctttctatctGcctgagtatcagggataaga	11	9	3	2	rs529430855		TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr1:15541828G>A	ENST00000428417.1	+	2	691	c.245G>A	c.(244-246)tGc>tAc	p.C82Y	TMEM51_ENST00000400796.3_Missense_Mutation_p.C82Y|TMEM51_ENST00000434578.2_Missense_Mutation_p.C82Y|TMEM51_ENST00000376008.2_Missense_Mutation_p.C82Y|TMEM51_ENST00000376014.3_Missense_Mutation_p.C82Y	NM_001136217.1	NP_001129689.1	Q9NW97	TMM51_HUMAN	transmembrane protein 51	82						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(3)|large_intestine(2)|lung(5)|prostate(2)	14		Renal(390;0.00145)|Breast(348;0.00186)|Colorectal(325;0.00215)|all_lung(284;0.00459)|Lung NSC(340;0.0104)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;2.07e-06)|COAD - Colon adenocarcinoma(227;7.14e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000175)|KIRC - Kidney renal clear cell carcinoma(229;0.00141)|STAD - Stomach adenocarcinoma(313;0.00644)|READ - Rectum adenocarcinoma(331;0.0751)		CTTTCTATCTGCCTGAGTATC	0.632																																					p.C82Y		Atlas-SNP	.											.	TMEM51	28	.	0			c.G245A						.						77	69	72					1																	15541828		2203	4300	6503	SO:0001583	missense	55092	exon2			CTATCTGCCTGAG	AK098467	CCDS154.1	1p36.21	2008-02-05	2005-05-22	2005-05-22	ENSG00000171729	ENSG00000171729			25488	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 72"	C1orf72		12477932	Standard	NM_018022		Approved	FLJ10199	uc001avx.3	Q9NW97	OTTHUMG00000002046	ENST00000428417.1:c.245G>A	chr1.hg19:g.15541828G>A	ENSP00000394899:p.Cys82Tyr	41.0	0.0		36.0	11.0	NM_018022	A8K819	Missense_Mutation	SNP	ENST00000428417.1	hg19	CCDS154.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.163419	0.78226	.	.	ENSG00000171729	ENST00000428417;ENST00000376014;ENST00000451326;ENST00000434578;ENST00000400796;ENST00000376008;ENST00000303840	T;T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02;1.02	5.43	5.43	0.79202	.	0.042207	0.85682	D	0.000000	T	0.65491	0.2696	M	0.70275	2.135	0.58432	D	0.999998	D;D	0.76494	0.999;0.999	D;D	0.76071	0.987;0.987	T	0.68398	-0.5419	10	0.87932	D	0	-9.7527	18.2265	0.89918	0.0:0.0:1.0:0.0	.	82;82	Q9BSA0;Q9NW97	.;TMM51_HUMAN	Y	82	ENSP00000394899:C82Y;ENSP00000365182:C82Y;ENSP00000412298:C82Y;ENSP00000409665:C82Y;ENSP00000383600:C82Y;ENSP00000365176:C82Y	ENSP00000303666:C82Y	C	+	2	0	TMEM51	15414415	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.696000	0.68287	2.564000	0.86499	0.655000	0.94253	TGC	.	.		0.632	TMEM51-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005699.3	NM_018022		A	15541828	G	A	15541828	3	1	280	1	0	0	0	0	1	0	0	0	16192	1319	46	3	247	3	TMEM51	1	15541828	Missense_Mutation	SNP	G	TCGA-G3-A3CH-01A-11D-A22F-10		15541828	233708793	1	40180										
PAPPA2	60676	hgsc.bcm.edu	37	chr1	176564726	176564726	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	tgctttgaccctgactcaccCaagaggtaagggactgggat	12	10	1	3			TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr1:176564726C>T	ENST00000367662.3	+	3	3150	c.1986C>T	c.(1984-1986)ccC>ccT	p.P662P	PAPPA2_ENST00000367661.3_Silent_p.P662P	NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	662	Metalloprotease.				bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						CTGACTCACCCAAGAGGTAAG	0.498																																					p.P662P		Atlas-SNP	.											.	PAPPA2	665	.	0			c.C1986T						.						40	44	43					1																	176564726		2135	4241	6376	SO:0001819	synonymous_variant	60676	exon3			CTCACCCAAGAGG	BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"placenta-specific 3"	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.1986C>T	chr1.hg19:g.176564726C>T		39.0	0.0		39.0	14.0	NM_021936	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Silent	SNP	ENST00000367662.3	hg19	CCDS41438.1																																																																																			.	.		0.498	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1			T	176564726	C	T	176564726	2	4	280	1	0	0	0	0	0	0	0	1	11442	581	21	3		3	PAPPA2	1	176564726	Silent	SNP	C	TCGA-G3-A3CH-01A-11D-A22F-10	161022898	176564726	72685895	2	40181										
LYST	1130	hgsc.bcm.edu	37	chr1	235937265	235937265	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	tcattcatataaataatatcTtcaccacagcatccttcaag	2	11	5	0			TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr1:235937265T>A	ENST00000389794.3	-	19	5835	c.5661A>T	c.(5659-5661)gaA>gaT	p.E1887D	LYST_ENST00000536965.1_3'UTR|LYST_ENST00000389793.2_Missense_Mutation_p.E1887D			Q99698	LYST_HUMAN	lysosomal trafficking regulator	1887					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			AAATAATATCTTCACCACAGC	0.323																																					p.E1887D		Atlas-SNP	.											.	LYST	370	.	0			c.A5661T						.						89	90	90					1																	235937265		2202	4298	6500	SO:0001583	missense	1130	exon19			AATATCTTCACCA	U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"WD repeat domain containing"	1968	protein-coding gene	gene with protein product		606897	"Chediak-Higashi syndrome 1"	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.5661A>T	chr1.hg19:g.235937265T>A	ENSP00000374444:p.Glu1887Asp	216.0	0.0		277.0	87.0	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Missense_Mutation	SNP	ENST00000389794.3	hg19	CCDS31062.1	.	.	.	.	.	.	.	.	.	.	T	12.48	1.950107	0.34377	.	.	ENSG00000143669	ENST00000389794;ENST00000389793	T;T	0.62639	0.01;0.01	5.32	1.82	0.25136	.	0.207580	0.49305	D	0.000147	T	0.49321	0.1550	L	0.57536	1.79	0.80722	D	1	B	0.16166	0.016	B	0.13407	0.009	T	0.28106	-1.0054	10	0.22109	T	0.4	.	4.2983	0.10913	0.1767:0.4044:0.0:0.4189	.	1887	Q99698	LYST_HUMAN	D	1887	ENSP00000374444:E1887D;ENSP00000374443:E1887D	ENSP00000374443:E1887D	E	-	3	2	LYST	234003888	1.000000	0.71417	0.982000	0.44146	0.702000	0.40608	0.615000	0.24329	0.356000	0.24157	0.477000	0.44152	GAA	.	.		0.323	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			A	235937265	T	A	235937265	3	1	280	1	0	0	0	0	1	0	0	0	9137	1606	56	4	5884	4	LYST	1	235937265	Missense_Mutation	SNP	T	TCGA-G3-A3CH-01A-11D-A22F-10	59372539	235937265	13313356	3	40182										
OR6F1	343169	hgsc.bcm.edu	37	chr1	247875185	247875185	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	cttacttccttattacgaagCgtatagatgaaggggtttaa	9	6	0	2			TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr1:247875185C>T	ENST00000302084.2	-	1	920	c.873G>A	c.(871-873)acG>acA	p.T291T	RP11-634B7.4_ENST00000449298.1_RNA	NM_001005286.1	NP_001005286.1	Q8NGZ6	OR6F1_HUMAN	olfactory receptor, family 6, subfamily F, member 1	291						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(1)|large_intestine(5)|lung(34)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)	47	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.0168)			TATTACGAAGCGTATAGATGA	0.438																																					p.T291T		Atlas-SNP	.											OR6F1,NS,carcinoma,0,2	OR6F1	88	.	0			c.G873A						.						126	125	125					1																	247875185		2203	4300	6503	SO:0001819	synonymous_variant	343169	exon1			ACGAAGCGTATAG	BK004460	CCDS31095.1	1q44	2012-08-09			ENSG00000169214	ENSG00000169214		"GPCR / Class A : Olfactory receptors"	15027	protein-coding gene	gene with protein product							Standard	NM_001005286		Approved	OST731	uc001idj.1	Q8NGZ6	OTTHUMG00000040213	ENST00000302084.2:c.873G>A	chr1.hg19:g.247875185C>T		55.0	0.0		61.0	19.0	NM_001005286	B2RNV6|Q6IF02|Q96R39	Silent	SNP	ENST00000302084.2	hg19	CCDS31095.1																																																																																			.	.		0.438	OR6F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096870.1	NM_001005286		T	247875185	C	T	247875185	2	4	280	1	0	0	0	0	0	0	0	1	11210	755	27	1		1	OR6F1	1	247875185	Silent	SNP	C	TCGA-G3-A3CH-01A-11D-A22F-10	11937920	247875185	1375436	4	40183										
SNTG2	54221	hgsc.bcm.edu	37	chr2	1241722	1241722	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	tgggatcctccggttttacaCagcccaggatggcaccgact	11	13	0	0	rs530642242		TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr2:1241722C>G	ENST00000308624.5	+	10	911	c.782C>G	c.(781-783)aCa>aGa	p.T261R	SNTG2_ENST00000407292.1_Missense_Mutation_p.T134R	NM_018968.3	NP_061841.2	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2	261					central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|syntrophin complex (GO:0016013)	PDZ domain binding (GO:0030165)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		CGGTTTTACACAGCCCAGGAT	0.622																																					p.T261R		Atlas-SNP	.											.	SNTG2	125	.	0			c.C782G						.						40	45	43					2																	1241722		2195	4297	6492	SO:0001583	missense	54221	exon10			TTTACACAGCCCA	AJ003029	CCDS46220.1	2p25	2008-05-23			ENSG00000172554	ENSG00000172554			13741	protein-coding gene	gene with protein product		608715				10747910	Standard	NM_018968		Approved	SYN5, G2SYN	uc002qwq.3	Q9NY99	OTTHUMG00000151370	ENST00000308624.5:c.782C>G	chr2.hg19:g.1241722C>G	ENSP00000311837:p.Thr261Arg	30.0	0.0		37.0	10.0	NM_018968	Q05AH5	Missense_Mutation	SNP	ENST00000308624.5	hg19	CCDS46220.1	.	.	.	.	.	.	.	.	.	.	C	13.86	2.361665	0.41801	.	.	ENSG00000172554	ENST00000308624;ENST00000407292	T;T	0.55588	0.51;0.51	4.68	4.68	0.58851	.	0.052895	0.85682	D	0.000000	T	0.69396	0.3106	M	0.70595	2.14	0.53688	D	0.999973	D;D	0.76494	0.999;0.998	D;P	0.65987	0.94;0.873	T	0.71938	-0.4441	10	0.51188	T	0.08	.	15.457	0.75325	0.0:1.0:0.0:0.0	.	134;261	Q9NY99-2;Q9NY99	.;SNTG2_HUMAN	R	261;134	ENSP00000311837:T261R;ENSP00000385020:T134R	ENSP00000311837:T261R	T	+	2	0	SNTG2	1224273	0.999000	0.42202	0.009000	0.14445	0.051000	0.14879	5.719000	0.68462	2.298000	0.77334	0.655000	0.94253	ACA	.	.		0.622	SNTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322454.1	NM_018968		G	1241722	C	G	1241722	3	3	280	1	0	0	0	0	1	0	0	0	14890	478	17	4	820	4	SNTG2	2	1241722	Missense_Mutation	SNP	C	TCGA-G3-A3CH-01A-11D-A22F-10		1241722	241957651	5	40184										
CRIM1	51232	hgsc.bcm.edu	37	chr2	36739445	36739445	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	gcacggctgtgacatctgtcGctgtaagaaatgtccagagc	12	10	1	3			TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr2:36739445G>A	ENST00000280527.2	+	10	2055	c.1688G>A	c.(1687-1689)cGc>cAc	p.R563H	RP11-78I14.1_ENST00000609765.1_RNA	NM_016441.2	NP_057525.1	Q9NZV1	CRIM1_HUMAN	cysteine rich transmembrane BMP regulator 1 (chordin-like)	563	Antistasin-like 3. {ECO:0000255|PROSITE- ProRule:PRU00582}.				insulin-like growth factor receptor signaling pathway (GO:0048009)|nervous system development (GO:0007399)|regulation of cell growth (GO:0001558)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	insulin-like growth factor-activated receptor activity (GO:0005010)|PDZ domain binding (GO:0030165)|serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(15)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	45		all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154)				GACATCTGTCGCTGTAAGAAA	0.463																																					p.R563H		Atlas-SNP	.											.	CRIM1	88	.	0			c.G1688A						.						145	142	143					2																	36739445		2203	4300	6503	SO:0001583	missense	51232	exon10			TCTGTCGCTGTAA	AF168681	CCDS1783.1	2p21	2010-06-29	2005-07-25		ENSG00000150938	ENSG00000150938			2359	protein-coding gene	gene with protein product		606189	"cysteine-rich motor neuron 1"	S52		10642437	Standard	NM_016441		Approved		uc002rpd.3	Q9NZV1	OTTHUMG00000099419	ENST00000280527.2:c.1688G>A	chr2.hg19:g.36739445G>A	ENSP00000280527:p.Arg563His	129.0	0.0		144.0	7.0	NM_016441	Q2M2G4|Q59GH0|Q7LCQ5|Q9H318	Missense_Mutation	SNP	ENST00000280527.2	hg19	CCDS1783.1	.	.	.	.	.	.	.	.	.	.	G	34	5.345885	0.95807	.	.	ENSG00000150938	ENST00000280527	T	0.04917	3.53	5.61	5.61	0.85477	Proteinase inhibitor I14/I15, hirudin/antistatin (1);Proteinase inhibitor I15, antistasin (1);Proteinase inhibitor I15, antistasin-like (2);	0.000000	0.85682	D	0.000000	T	0.27900	0.0687	M	0.78801	2.425	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.00164	-1.1968	10	0.42905	T	0.14	-37.1378	18.9896	0.92786	0.0:0.0:1.0:0.0	.	563	Q9NZV1	CRIM1_HUMAN	H	563	ENSP00000280527:R563H	ENSP00000280527:R563H	R	+	2	0	CRIM1	36592949	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	9.813000	0.99286	2.793000	0.96121	0.655000	0.94253	CGC	.	.		0.463	CRIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216878.2	NM_016441		A	36739445	G	A	36739445	3	1	280	1	0	0	0	0	1	0	0	0	3875	1087	38	1	1726	1	CRIM1	2	36739445	Missense_Mutation	SNP	G	TCGA-G3-A3CH-01A-11D-A22F-10	35497723	36739445	206459928	6	40185										
HEATR5B	54497	hgsc.bcm.edu	37	chr2	37306331	37306331	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	tcattgcatttatcaagtgtCtgaaaaactgtgaaagtatc	7	6	3	2			TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr2:37306331C>A	ENST00000233099.5	-	3	365	c.270G>T	c.(268-270)caG>caT	p.Q90H	HEATR5B_ENST00000354531.2_Missense_Mutation_p.Q90H	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	90						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				TATCAAGTGTCTGAAAAACTG	0.373																																					p.Q90H		Atlas-SNP	.											.	HEATR5B	185	.	0			c.G270T						.						81	76	78					2																	37306331		2201	4298	6499	SO:0001583	missense	54497	exon3			AAGTGTCTGAAAA	AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.270G>T	chr2.hg19:g.37306331C>A	ENSP00000233099:p.Gln90His	139.0	0.0		155.0	51.0	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Missense_Mutation	SNP	ENST00000233099.5	hg19	CCDS33181.1	.	.	.	.	.	.	.	.	.	.	C	17.06	3.292860	0.60086	.	.	ENSG00000008869	ENST00000233099;ENST00000354531;ENST00000424416	T;T	0.08546	3.08;3.08	5.88	2.18	0.27775	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.16769	0.0403	L	0.47716	1.5	0.48395	D	0.999646	D	0.63880	0.993	P	0.62649	0.905	T	0.00350	-1.1797	10	0.72032	D	0.01	-17.0384	8.749	0.34605	0.0:0.4622:0.0:0.5378	.	90	Q9P2D3	HTR5B_HUMAN	H	90	ENSP00000233099:Q90H;ENSP00000346531:Q90H	ENSP00000233099:Q90H	Q	-	3	2	HEATR5B	37159835	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	0.949000	0.29109	0.129000	0.18514	-0.302000	0.09304	CAG	.	.		0.373	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024		A	37306331	C	A	37306331	3	1	280	1	0	0	0	0	1	0	0	0	7041	912	32	3	6081	3	HEATR5B	2	37306331	Missense_Mutation	SNP	C	TCGA-G3-A3CH-01A-11D-A22F-10	566886	37306331	205893042	7	40186										
SPHKAP	80309	hgsc.bcm.edu	37	chr2	228884827	228884827	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	cctgggtggctccctttagcTgtttactttccaaaacattg	8	11	0	0			TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr2:228884827T>A	ENST00000392056.3	-	7	789	c.743A>T	c.(742-744)cAg>cTg	p.Q248L	SPHKAP_ENST00000344657.5_Missense_Mutation_p.Q248L	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	248						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)			NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		TCCCTTTAGCTGTTTACTTTC	0.378																																					p.Q248L		Atlas-SNP	.											.	SPHKAP	750	.	0			c.A743T						.						118	126	123					2																	228884827		2203	4300	6503	SO:0001583	missense	80309	exon7			TTTAGCTGTTTAC		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"A-kinase anchor proteins"	30619	protein-coding gene	gene with protein product	"sphingosine kinase type 1-interacting protein"	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.743A>T	chr2.hg19:g.228884827T>A	ENSP00000375909:p.Gln248Leu	134.0	0.0		177.0	52.0	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	hg19	CCDS46537.1	.	.	.	.	.	.	.	.	.	.	T	9.850	1.193385	0.22037	.	.	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.12255	2.7;2.7	5.72	3.21	0.36854	.	0.358525	0.31347	N	0.007815	T	0.08223	0.0205	N	0.22421	0.69	0.24619	N	0.993687	B;P	0.35226	0.081;0.491	B;B	0.32465	0.021;0.146	T	0.22208	-1.0223	10	0.56958	D	0.05	.	6.2306	0.20732	0.141:0.0762:0.0:0.7828	.	248;248	Q2M3C7;Q2M3C7-2	SPKAP_HUMAN;.	L	248	ENSP00000375909:Q248L;ENSP00000339886:Q248L	ENSP00000339886:Q248L	Q	-	2	0	SPHKAP	228593071	0.474000	0.25886	0.640000	0.29408	0.167000	0.22549	0.339000	0.19875	0.379000	0.24794	0.533000	0.62120	CAG	.	.		0.378	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623		A	228884827	T	A	228884827	3	1	280	1	0	0	0	0	1	0	0	0	15063	1580	55	4	4383	4	SPHKAP	2	228884827	Missense_Mutation	SNP	T	TCGA-G3-A3CH-01A-11D-A22F-10	191578496	228884827	14314546	8	40187										
SHQ1	55164	hgsc.bcm.edu	37	chr3	72890225	72890225	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	ttgcaacactcctgatcgtaAgtttccaaatccatagtggc	7	11	0	1			TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr3:72890225A>T	ENST00000325599.8	-	4	596	c.457T>A	c.(457-459)Tta>Ata	p.L153I	SHQ1_ENST00000463369.1_Missense_Mutation_p.L125I	NM_018130.2	NP_060600.2	Q6PI26	SHQ1_HUMAN	SHQ1, H/ACA ribonucleoprotein assembly factor	153					negative regulation of rRNA processing (GO:2000233)|positive regulation of apoptotic process (GO:0043065)|ribonucleoprotein complex assembly (GO:0022618)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	27		Prostate(10;0.00482)|Lung NSC(201;0.0339)|Myeloproliferative disorder(1037;0.204)		BRCA - Breast invasive adenocarcinoma(55;9.68e-05)|Epithelial(33;0.000563)|LUSC - Lung squamous cell carcinoma(21;0.00229)|Lung(16;0.00688)|KIRC - Kidney renal clear cell carcinoma(39;0.018)|Kidney(39;0.0213)		CCTGATCGTAAGTTTCCAAAT	0.393																																					p.L153I		Atlas-SNP	.											.	SHQ1	60	.	0			c.T457A						.						181	171	175					3																	72890225		2203	4300	6503	SO:0001583	missense	55164	exon4			ATCGTAAGTTTCC	BC025270	CCDS33788.1	3p13	2013-01-08	2013-01-08		ENSG00000144736	ENSG00000144736			25543	protein-coding gene	gene with protein product		613663	"SHQ1 homolog (S. cerevisiae)"			12477932	Standard	NM_018130		Approved	FLJ10539, Shq1p	uc003dpf.3	Q6PI26	OTTHUMG00000158814	ENST00000325599.8:c.457T>A	chr3.hg19:g.72890225A>T	ENSP00000315182:p.Leu153Ile	132.0	0.0		153.0	59.0	NM_018130	B4DL05|Q6MZJ4|Q7Z748|Q9H7E5|Q9NVS8	Missense_Mutation	SNP	ENST00000325599.8	hg19	CCDS33788.1	.	.	.	.	.	.	.	.	.	.	A	17.51	3.406835	0.62399	.	.	ENSG00000144736	ENST00000325599;ENST00000463369;ENST00000482785	T;T;T	0.47869	0.83;0.83;0.83	5.27	1.01	0.19927	.	0.350898	0.25753	N	0.028527	T	0.57681	0.2070	M	0.72894	2.215	0.24490	N	0.994305	D	0.69078	0.997	P	0.62560	0.904	T	0.49652	-0.8917	10	0.30854	T	0.27	-2.5829	8.937	0.35706	0.6128:0.0:0.3872:0.0	.	153	Q6PI26	SHQ1_HUMAN	I	153;125;64	ENSP00000315182:L153I;ENSP00000417452:L125I;ENSP00000418398:L64I	ENSP00000315182:L153I	L	-	1	2	SHQ1	72972915	0.987000	0.35691	0.312000	0.25196	0.868000	0.49771	1.615000	0.36922	0.267000	0.21916	0.477000	0.44152	TTA	.	.		0.393	SHQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352310.1	NM_018130		T	72890225	A	T	72890225	3	4	280	1	0	0	0	0	1	0	0	0	14307	69	3	4	1308	4	SHQ1	3	72890225	Missense_Mutation	SNP	A	TCGA-G3-A3CH-01A-11D-A22F-10		72890225	125132205	9	40188										
COL6A6	131873	hgsc.bcm.edu	37	chr3	130354582	130354582	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	gtggtccaggagagactgggCtgaagggagctagaggcaaa	18	6	0	3			TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr3:130354582C>A	ENST00000358511.6	+	27	5099	c.5068C>A	c.(5068-5070)Ctg>Atg	p.L1690M	COL6A6_ENST00000453409.2_Missense_Mutation_p.L1690M	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	1690	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						AGAGACTGGGCTGAAGGGAGC	0.373																																					p.L1690M		Atlas-SNP	.											.	COL6A6	497	.	0			c.C5068A						.						88	91	90					3																	130354582		1880	4093	5973	SO:0001583	missense	131873	exon27			ACTGGGCTGAAGG	AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.5068C>A	chr3.hg19:g.130354582C>A	ENSP00000351310:p.Leu1690Met	53.0	0.0		58.0	25.0	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	hg19	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	C	13.65	2.300853	0.40694	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	D;D	0.83755	-1.76;-1.76	5.41	5.41	0.78517	.	.	.	.	.	T	0.71970	0.3403	N	0.21617	0.685	0.22500	N	0.999049	B	0.33379	0.41	B	0.25405	0.06	T	0.63373	-0.6652	9	0.34782	T	0.22	.	14.6899	0.69076	0.0:1.0:0.0:0.0	.	1690	A6NMZ7	CO6A6_HUMAN	M	1690	ENSP00000351310:L1690M;ENSP00000399236:L1690M	ENSP00000351310:L1690M	L	+	1	2	COL6A6	131837272	0.948000	0.32251	0.992000	0.48379	0.582000	0.36321	1.631000	0.37092	2.531000	0.85337	0.655000	0.94253	CTG	.	.		0.373	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		A	130354582	C	A	130354582	3	1	280	1	0	0	0	0	1	0	0	0	3705	796	28	3	5174	3	COL6A6	3	130354582	Missense_Mutation	SNP	C	TCGA-G3-A3CH-01A-11D-A22F-10	57464357	130354582	67667848	10	40189										
KY	339855	hgsc.bcm.edu	37	chr3	134366278	134366278	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	aaggaaaaagagaatttaccGtgaaagtcatttccttctaa	7	6	2	2			TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr3:134366278G>A	ENST00000423778.2	-	2	259	c.198C>T	c.(196-198)caC>caT	p.H66H	KY_ENST00000508956.1_Splice_Site_p.H66H|KY_ENST00000503669.1_Splice_Site_p.H66H	NM_178554.4	NP_848649.3	Q8NBH2	KY_HUMAN	kyphoscoliosis peptidase	66					muscle organ development (GO:0007517)|neuromuscular junction development (GO:0007528)	cytoskeleton (GO:0005856)|Z disc (GO:0030018)	peptidase activity (GO:0008233)			central_nervous_system(1)|endometrium(3)|kidney(1)|lung(12)|ovary(2)|upper_aerodigestive_tract(2)	21						AGAATTTACCGTGAAAGTCAT	0.388																																					p.H66H		Atlas-SNP	.											KY_ENST00000423778,NS,carcinoma,0,2	KY	92	.	0			c.C198T						.						91	89	89					3																	134366278		1834	4084	5918	SO:0001630	splice_region_variant	339855	exon2			TTTACCGTGAAAG	AK090526	CCDS46920.1	3q22.1	2010-11-23			ENSG00000174611	ENSG00000174611			26576	protein-coding gene	gene with protein product		605739					Standard	NM_178554		Approved	FLJ33207	uc010hty.3	Q8NBH2	OTTHUMG00000159788	ENST00000423778.2:c.199+1C>T	chr3.hg19:g.134366278G>A		76.0	0.0		62.0	16.0	NM_178554	B7Z1S4|Q6ZT15	Silent	SNP	ENST00000423778.2	hg19	CCDS46920.1																																																																																			.	.		0.388	KY-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357320.1	NM_178554	Silent	A	134366278	G	A	134366278	5	1	280	1	0	0	0	0	0	0	1	0	8595	1159	40	1	1827	1	KY	3	134366278	Splice_Site	SNP	G	TCGA-G3-A3CH-01A-11D-A22F-10	4011696	134366278	63656152	11	40190										
PSMD2	5708	hgsc.bcm.edu	37	chr3	184020202	184020202	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	tgagaactcagccctactgcGttgtgccctgggtgtgttcc	12	12	1	1	rs11545182		TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr3:184020202G>A	ENST00000310118.4	+	6	1307	c.749G>A	c.(748-750)cGt>cAt	p.R250H	PSMD2_ENST00000439383.1_Missense_Mutation_p.R120H|EIF2B5_ENST00000444495.1_Intron|PSMD2_ENST00000435761.1_Missense_Mutation_p.R91H	NM_002808.3	NP_002799.3	Q13200	PSMD2_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 2	250					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(5)|liver(1)|lung(12)|prostate(3)|upper_aerodigestive_tract(2)	27	all_cancers(143;1.54e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		Bortezomib(DB00188)	GCCCTACTGCGTTGTGCCCTG	0.468																																					p.R250H	Colon(24;313 636 6917 9932 15554)	Atlas-SNP	.											.	PSMD2	56	.	0			c.G749A						.						137	124	128					3																	184020202		2203	4300	6503	SO:0001583	missense	5708	exon6			TACTGCGTTGTGC	AK095245	CCDS3258.1, CCDS63853.1, CCDS63854.1	3q27.3	2008-05-22			ENSG00000175166	ENSG00000175166		"Proteasome (prosome, macropain) subunits"	9559	protein-coding gene	gene with protein product		606223				8774743	Standard	NM_002808		Approved	S2, P97, TRAP2, MGC14274, Rpn1	uc003fnn.1	Q13200	OTTHUMG00000156796	ENST00000310118.4:c.749G>A	chr3.hg19:g.184020202G>A	ENSP00000310129:p.Arg250His	111.0	0.0		111.0	31.0	NM_002808	B4DX07|B4DXY1|E7EW34|E9PCS3|Q12932|Q15321|Q53XQ4|Q96I12	Missense_Mutation	SNP	ENST00000310118.4	hg19	CCDS3258.1	.	.	.	.	.	.	.	.	.	.	G	16.13	3.035150	0.54896	.	.	ENSG00000175166	ENST00000310118;ENST00000417952;ENST00000538096;ENST00000435761;ENST00000439383	T;T;T	0.22336	1.96;1.96;1.96	5.46	5.46	0.80206	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.17916	0.0430	L	0.39085	1.19	0.58432	D	0.999999	B;P	0.37708	0.004;0.606	B;B	0.32289	0.002;0.143	T	0.01786	-1.1274	10	0.46703	T	0.11	-12.0332	16.5504	0.84471	0.0:0.13:0.87:0.0	.	91;250	E9PCS3;Q13200	.;PSMD2_HUMAN	H	250;175;242;91;120	ENSP00000310129:R250H;ENSP00000402618:R91H;ENSP00000416028:R120H	ENSP00000310129:R250H	R	+	2	0	PSMD2	185502896	1.000000	0.71417	0.995000	0.50966	0.993000	0.82548	4.672000	0.61597	2.845000	0.97973	0.603000	0.83216	CGT	.	G|1.000;|0.000		0.468	PSMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345843.1	NM_002808		A	184020202	G	A	184020202	3	1	280	1	0	0	0	0	1	0	0	0	12710	1145	40	1	771	1	PSMD2	3	184020202	Missense_Mutation	SNP	G	TCGA-G3-A3CH-01A-11D-A22F-10	49653924	184020202	14002228	12	40191										
USP38	84640	hgsc.bcm.edu	37	chr4	144135683	144135683	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	ttgtggttcactctggtataTcctctgaaagtgggcattac	10	8	3	1			TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr4:144135683T>C	ENST00000307017.4	+	9	3060	c.2554T>C	c.(2554-2556)Tcc>Ccc	p.S852P	USP38_ENST00000510377.1_Missense_Mutation_p.S852P	NM_032557.5	NP_115946.2	Q8NB14	UBP38_HUMAN	ubiquitin specific peptidase 38	852	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	33	all_hematologic(180;0.158)					CTCTGGTATATCCTCTGAAAG	0.423																																					p.S852P		Atlas-SNP	.											.	USP38	92	.	0			c.T2554C						.						100	93	96					4																	144135683		2203	4300	6503	SO:0001583	missense	84640	exon9			GGTATATCCTCTG	AF211481	CCDS3758.1	4q31.1	2008-02-05	2005-08-08		ENSG00000170185	ENSG00000170185		"Ubiquitin-specific peptidases"	20067	protein-coding gene	gene with protein product			"ubiquitin specific protease 38"			12838346	Standard	NM_032557		Approved	KIAA1891, HP43.8KD	uc003ijb.3	Q8NB14	OTTHUMG00000161420	ENST00000307017.4:c.2554T>C	chr4.hg19:g.144135683T>C	ENSP00000303434:p.Ser852Pro	103.0	0.0		133.0	6.0	NM_032557	B3KX93|Q3ZCV1|Q8NDF5|Q96DK6|Q96PZ6|Q9BY55	Missense_Mutation	SNP	ENST00000307017.4	hg19	CCDS3758.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.070254	0.76301	.	.	ENSG00000170185	ENST00000510377;ENST00000307017	T;T	0.77750	-1.12;-1.12	5.48	5.48	0.80851	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site (1);Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	D	0.90106	0.6909	M	0.90483	3.12	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.92163	0.5737	10	0.87932	D	0	-9.3991	15.8623	0.79035	0.0:0.0:0.0:1.0	.	852;852	Q8NB14;Q3ZCV1	UBP38_HUMAN;.	P	852	ENSP00000427647:S852P;ENSP00000303434:S852P	ENSP00000303434:S852P	S	+	1	0	USP38	144355133	1.000000	0.71417	0.947000	0.38551	0.993000	0.82548	7.798000	0.85924	2.205000	0.71048	0.482000	0.46254	TCC	.	.		0.423	USP38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364869.1	NM_032557		C	144135683	T	C	144135683	3	2	280	1	0	0	0	0	1	0	0	0	17084	1435	50	2	2588	2	USP38	4	144135683	Missense_Mutation	SNP	T	TCGA-G3-A3CH-01A-11D-A22F-10		144135683	47018593	13	40192										
USP38	84640	hgsc.bcm.edu	37	chr4	144135888	144135888	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	gtttttatttaatgacagtaGagtgacatttacttcatttc	6	5	1	3			TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr4:144135888G>T	ENST00000307017.4	+	9	3265	c.2759G>T	c.(2758-2760)aGa>aTa	p.R920I	USP38_ENST00000510377.1_Missense_Mutation_p.R920I	NM_032557.5	NP_115946.2	Q8NB14	UBP38_HUMAN	ubiquitin specific peptidase 38	920	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	33	all_hematologic(180;0.158)					AATGACAGTAGAGTGACATTT	0.348																																					p.R920I		Atlas-SNP	.											.	USP38	92	.	0			c.G2759T						.						71	74	73					4																	144135888		2203	4300	6503	SO:0001583	missense	84640	exon9			ACAGTAGAGTGAC	AF211481	CCDS3758.1	4q31.1	2008-02-05	2005-08-08		ENSG00000170185	ENSG00000170185		"Ubiquitin-specific peptidases"	20067	protein-coding gene	gene with protein product			"ubiquitin specific protease 38"			12838346	Standard	NM_032557		Approved	KIAA1891, HP43.8KD	uc003ijb.3	Q8NB14	OTTHUMG00000161420	ENST00000307017.4:c.2759G>T	chr4.hg19:g.144135888G>T	ENSP00000303434:p.Arg920Ile	172.0	0.0		217.0	76.0	NM_032557	B3KX93|Q3ZCV1|Q8NDF5|Q96DK6|Q96PZ6|Q9BY55	Missense_Mutation	SNP	ENST00000307017.4	hg19	CCDS3758.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.622055	0.87460	.	.	ENSG00000170185	ENST00000510377;ENST00000307017	T;T	0.32515	1.45;1.45	5.88	5.88	0.94601	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.53594	0.1806	L	0.50847	1.595	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.49790	-0.8902	10	0.66056	D	0.02	-10.7871	20.2187	0.98312	0.0:0.0:1.0:0.0	.	920;920	Q8NB14;Q3ZCV1	UBP38_HUMAN;.	I	920	ENSP00000427647:R920I;ENSP00000303434:R920I	ENSP00000303434:R920I	R	+	2	0	USP38	144355338	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.780000	0.95670	0.655000	0.94253	AGA	.	.		0.348	USP38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364869.1	NM_032557		T	144135888	G	T	144135888	3	4	280	1	0	0	0	0	1	0	0	0	17084	942	33	3	2793	3	USP38	4	144135888	Missense_Mutation	SNP	G	TCGA-G3-A3CH-01A-11D-A22F-10	205	144135888	47018388	14	40193										
LRRC14B	389257	hgsc.bcm.edu	37	chr5	192439	192439	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	acctacgcctccactcccgaCggcgaggaccccctcctcgc	8	22	0	0	rs369014987	byFrequency	TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr5:192439C>T	ENST00000328278.3	+	1	814	c.786C>T	c.(784-786)gaC>gaT	p.D262D		NM_001080478.1	NP_001073947.1	A6NHZ5	LR14B_HUMAN	leucine rich repeat containing 14B	262										endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)|upper_aerodigestive_tract(2)	10						CCACTCCCGACGGCGAGGACC	0.682													C|||	10	0.00199681	0.0076	0	5008	,	,		15181	0		0	False		,,,				2504	0				p.D262D		Atlas-SNP	.											.	LRRC14B	30	.	0			c.C786T						.	C		8,4182		0,8,2087	11	14	13		786	-2.1	0	5		13	1,8433		0,1,4216	no	coding-synonymous	LRRC14B	NM_001080478.1		0,9,6303	TT,TC,CC		0.0119,0.1909,0.0713		262/515	192439	9,12615	2095	4217	6312	SO:0001819	synonymous_variant	389257	exon1			TCCCGACGGCGAG		CCDS47184.1	5p15.33	2010-02-17			ENSG00000185028	ENSG00000185028			37268	protein-coding gene	gene with protein product							Standard	NM_001080478		Approved		uc003jal.1	A6NHZ5	OTTHUMG00000161578	ENST00000328278.3:c.786C>T	chr5.hg19:g.192439C>T		76.0	0.0		69.0	21.0	NM_001080478		Silent	SNP	ENST00000328278.3	hg19	CCDS47184.1																																																																																			.	.		0.682	LRRC14B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000365393.2	NM_001080478		T	192439	C	T	192439	2	4	280	1	0	0	0	0	0	0	0	1	8978	535	19	1		1	LRRC14B	5	192439	Silent	SNP	C	TCGA-G3-A3CH-01A-11D-A22F-10		192439	180722821	15	40194										
HIVEP1	3096	hgsc.bcm.edu	37	chr6	12121666	12121666	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	aatgtgataggtgactttttGctacaggacagatctgcaga	11	6	1	4			TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr6:12121666G>A	ENST00000379388.2	+	4	1970	c.1638G>A	c.(1636-1638)ttG>ttA	p.L546L		NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	546					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				GTGACTTTTTGCTACAGGACA	0.438																																					p.L546L		Atlas-SNP	.											.	HIVEP1	242	.	0			c.G1638A						.						55	52	53					6																	12121666		2001	4175	6176	SO:0001819	synonymous_variant	3096	exon4			CTTTTTGCTACAG	J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"Zinc fingers, C2H2-type"	4920	protein-coding gene	gene with protein product		194540	"human immunodeficiency virus type I enhancer-binding protein 1", "zinc finger protein 40"	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.1638G>A	chr6.hg19:g.12121666G>A		62.0	0.0		65.0	21.0	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Silent	SNP	ENST00000379388.2	hg19	CCDS43426.1																																																																																			.	.		0.438	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114		A	12121666	G	A	12121666	2	1	280	1	0	0	0	0	0	0	0	1	7195	1310	46	3		3	HIVEP1	6	12121666	Silent	SNP	G	TCGA-G3-A3CH-01A-11D-A22F-10		12121666	158993401	16	40195										
MDC1	9656	hgsc.bcm.edu	37	chr6	30673414	30673414	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	cccctagtaacctgagatgtGggctcagaggtgacaggctg	14	10	1	3			TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr6:30673414G>A	ENST00000376406.3	-	10	4193	c.3546C>T	c.(3544-3546)ccC>ccT	p.P1182P	MDC1_ENST00000376405.2_Silent_p.P918P|MDC1-AS1_ENST00000442150.1_RNA	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	1182	Interaction with the PRKDC complex.|Pro-rich.			Missing (in Ref. 2; CAH18685). {ECO:0000305}.	DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intra-S DNA damage checkpoint (GO:0031573)	chromosome (GO:0005694)|focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	FHA domain binding (GO:0070975)|protein C-terminus binding (GO:0008022)			breast(2)|kidney(1)|ovary(1)	4						CCTGAGATGTGGGCTCAGAGG	0.567								Other conserved DNA damage response genes																													p.P1182P		Atlas-SNP	.											.	MDC1	218	.	0			c.C3546T						.						156	172	167					6																	30673414		2203	4300	6503	SO:0001819	synonymous_variant	9656	exon10			AGATGTGGGCTCA	D79992	CCDS34384.1	6p21.3	2010-02-17	2009-06-12		ENSG00000137337	ENSG00000137337			21163	protein-coding gene	gene with protein product		607593				10975465, 12607005	Standard	NM_014641		Approved	NFBD1, KIAA0170, Em:AB023051.5	uc003nrg.4	Q14676	OTTHUMG00000031075	ENST00000376406.3:c.3546C>T	chr6.hg19:g.30673414G>A		240.0	0.0		265.0	82.0	NM_014641	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Silent	SNP	ENST00000376406.3	hg19	CCDS34384.1	.	.	.	.	.	.	.	.	.	.	G	4.863	0.160387	0.09287	.	.	ENSG00000137337	ENST00000417033	.	.	.	3.62	3.62	0.41486	.	.	.	.	.	T	0.47857	0.1468	.	.	.	0.35888	D	0.829475	.	.	.	.	.	.	T	0.47995	-0.9073	4	.	.	.	-0.4572	11.0187	0.47705	0.0:0.0:1.0:0.0	.	.	.	.	Y	243	.	.	H	-	1	0	MDC1	30781393	0.000000	0.05858	0.015000	0.15790	0.150000	0.21749	-0.049000	0.11924	2.061000	0.61500	0.478000	0.44815	CAC	.	.		0.567	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641		A	30673414	G	A	30673414	2	1	280	1	0	0	0	0	0	0	0	1	9412	1335	47	3		3	MDC1	6	30673414	Silent	SNP	G	TCGA-G3-A3CH-01A-11D-A22F-10	18551748	30673414	140441653	17	40196										
PPT2	9374	hgsc.bcm.edu	37	chr6	32130607	32130607	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	tatctgcgggattcttttggGttgaagactctattggcccg	12	8	3	2			TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr6:32130607G>A	ENST00000324816.6	+	9	1357	c.789G>A	c.(787-789)ggG>ggA	p.G263G	PPT2_ENST00000375137.2_Silent_p.G263G|PPT2_ENST00000395523.1_Silent_p.G263G|PPT2_ENST00000375143.2_Silent_p.G263G|PPT2_ENST00000445576.2_Intron|PPT2_ENST00000361568.2_Silent_p.G269G|PPT2_ENST00000437001.2_Intron|EGFL8_ENST00000333845.6_5'Flank|PPT2-EGFL8_ENST00000422437.1_Intron|EGFL8_ENST00000395512.1_5'Flank|PPT2-EGFL8_ENST00000453656.2_Intron			Q9UMR5	PPT2_HUMAN	palmitoyl-protein thioesterase 2	263					cellular protein modification process (GO:0006464)|macromolecule depalmitoylation (GO:0098734)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	palmitoyl hydrolase activity (GO:0098599)|palmitoyl-(protein) hydrolase activity (GO:0008474)|thiolester hydrolase activity (GO:0016790)			NS(1)|endometrium(2)|large_intestine(2)|lung(10)|prostate(1)|urinary_tract(1)	17						ATTCTTTTGGGTTGAAGACTC	0.542																																					p.G269G		Atlas-SNP	.											.	PPT2	19	.	0			c.G807A						.						113	123	120					6																	32130607		2203	4300	6503	SO:0001819	synonymous_variant	9374	exon9			TTTTGGGTTGAAG	AF020543	CCDS4740.1, CCDS4742.1	6p21.3	2012-07-02			ENSG00000221988	ENSG00000221988	3.1.2.22		9326	protein-coding gene	gene with protein product		603298				9341199, 10051407	Standard	NM_138717		Approved		uc003nzw.3	Q9UMR5	OTTHUMG00000031257	ENST00000324816.6:c.789G>A	chr6.hg19:g.32130607G>A		140.0	0.0		142.0	37.0	NM_138717	A2ABC9|A2ABD1|A2ARM7|A2BFH7|A2BFH9|A2BFI2|A8K9L4|B0S868|G8JLE1|O14799|Q0P6K0|Q5JP13|Q5JP14|Q5JQF0|Q5SSX4|Q5SSX5|Q5SSX6|Q5STJ4|Q5STJ5|Q5STJ6|Q6FI80|Q99945	Silent	SNP	ENST00000324816.6	hg19	CCDS4742.1																																																																																			.	.		0.542	PPT2-207	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076552.4	NM_138717		A	32130607	G	A	32130607	2	1	280	1	0	0	0	0	0	0	0	1	12424	1248	44	3		3	PPT2	6	32130607	Silent	SNP	G	TCGA-G3-A3CH-01A-11D-A22F-10	1457193	32130607	138984460	18	40197										
EYS	346007	hgsc.bcm.edu	37	chr6	65612308	65612308	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	tttctgtacctgaaattgttGaccatatcttcacagtcacc	5	11	4	2			TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr6:65612308G>A	ENST00000370621.3	-	17	3253	c.2727C>T	c.(2725-2727)gtC>gtT	p.V909V	EYS_ENST00000370616.2_Silent_p.V909V|EYS_ENST00000503581.1_Silent_p.V909V			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	909	EGF-like 13. {ECO:0000255|PROSITE- ProRule:PRU00076}.				detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						TGAAATTGTTGACCATATCTT	0.333																																					p.V909V		Atlas-SNP	.											.	EYS	527	.	0			c.C2727T						.						149	123	131					6																	65612308		692	1591	2283	SO:0001819	synonymous_variant	346007	exon17			ATTGTTGACCATA		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.2727C>T	chr6.hg19:g.65612308G>A		103.0	0.0		109.0	43.0	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Silent	SNP	ENST00000370621.3	hg19																																																																																				.	.		0.333	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		A	65612308	G	A	65612308	2	1	280	1	0	0	0	0	0	0	0	1	5334	1277	45	3		3	EYS	6	65612308	Silent	SNP	G	TCGA-G3-A3CH-01A-11D-A22F-10	33481701	65612308	105502759	19	40198										
MOSPD3	64598	hgsc.bcm.edu	37	chr7	100211234	100211234	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	ctccattctgagagccccagCgtacccccttgagcttcagg	9	16	2	2			TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr7:100211234C>T	ENST00000393950.2	+	3	698	c.416C>T	c.(415-417)gCg>gTg	p.A139V	MOSPD3_ENST00000223054.4_Missense_Mutation_p.A139V|MOSPD3_ENST00000379527.2_Missense_Mutation_p.A139V|MOSPD3_ENST00000424091.2_Missense_Mutation_p.A129V	NM_023948.4	NP_076438.1	O75425	MSPD3_HUMAN	motile sperm domain containing 3	139	MSP. {ECO:0000255|PROSITE- ProRule:PRU00132}.				heart development (GO:0007507)	integral component of membrane (GO:0016021)	structural molecule activity (GO:0005198)	p.A139V(1)		breast(1)|kidney(3)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	16	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					AGAGCCCCAGCGTACCCCCTT	0.627																																					p.A139V		Atlas-SNP	.											MOSPD3,NS,carcinoma,0,1	MOSPD3	29	.	1	Substitution - Missense(1)	prostate(1)	c.C416T						.						64	59	61					7																	100211234		2203	4300	6503	SO:0001583	missense	64598	exon4			CCCCAGCGTACCC	BC011653	CCDS5701.1, CCDS47662.1	7q22	2009-11-06			ENSG00000106330	ENSG00000106330			25078	protein-coding gene	gene with protein product		609125				15533722	Standard	XM_005250531		Approved	CDS3, NET30	uc003uvs.3	O75425	OTTHUMG00000159599	ENST00000393950.2:c.416C>T	chr7.hg19:g.100211234C>T	ENSP00000377522:p.Ala139Val	54.0	0.0		66.0	25.0	NM_001040098	A4D2D1|A6NG17|C9JE89|D6W5W1|O75423|O75424	Missense_Mutation	SNP	ENST00000393950.2	hg19	CCDS5701.1	.	.	.	.	.	.	.	.	.	.	C	12.65	2.002850	0.35320	.	.	ENSG00000106330	ENST00000223054;ENST00000493970;ENST00000379527;ENST00000393950;ENST00000424091;ENST00000393953	.	.	.	4.28	3.4	0.38934	.	0.157917	0.30269	N	0.010008	T	0.19127	0.0459	N	0.22421	0.69	0.09310	N	0.99999	B;B	0.27971	0.059;0.196	B;B	0.17098	0.005;0.017	T	0.11227	-1.0596	9	0.22109	T	0.4	-8.9796	6.7813	0.23648	0.0:0.7963:0.0:0.2037	.	129;139	C9JE89;O75425	.;MSPD3_HUMAN	V	139;139;139;139;129;125	.	ENSP00000223054:A139V	A	+	2	0	MOSPD3	100049170	0.847000	0.29606	0.326000	0.25389	0.694000	0.40290	3.232000	0.51302	1.400000	0.46741	0.563000	0.77884	GCG	.	.		0.627	MOSPD3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356395.1	NM_023948		T	100211234	C	T	100211234	3	4	280	1	0	0	0	0	1	0	0	0	9726	768	27	1	426	1	MOSPD3	7	100211234	Missense_Mutation	SNP	C	TCGA-G3-A3CH-01A-11D-A22F-10		100211234	58927429	20	40199										
FBXL6	26233	hgsc.bcm.edu	37	chr8	145580146	145580146	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	tggtccgggagccacccctcGtcccggaggcttgggcagcc	15	16	0	0			TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr8:145580146G>C	ENST00000331890.5	-	7	1103	c.1039C>G	c.(1039-1041)Cga>Gga	p.R347G	SLC52A2_ENST00000532887.1_5'Flank|FBXL6_ENST00000526524.1_5'UTR|SLC52A2_ENST00000530047.1_5'Flank|FBXL6_ENST00000455319.2_Missense_Mutation_p.R341G|SLC52A2_ENST00000526752.1_5'Flank|SLC52A2_ENST00000540505.1_5'Flank|TMEM249_ENST00000531225.1_5'Flank|SLC52A2_ENST00000527078.1_5'Flank|TMEM249_ENST00000398633.3_5'Flank|SLC52A2_ENST00000402965.1_5'Flank|SLC52A2_ENST00000329994.2_5'Flank	NM_012162.2	NP_036294.2	Q8N531	FBXL6_HUMAN	F-box and leucine-rich repeat protein 6	347					protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)		ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|lung(3)|ovary(1)	5	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;4.43e-40)|Epithelial(56;1.48e-39)|all cancers(56;1.49e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0441)|Colorectal(110;0.055)			GCCACCCCTCGTCCCGGAGGC	0.647																																					p.R347G		Atlas-SNP	.											.	FBXL6	26	.	0			c.C1039G						.						33	39	37					8																	145580146		2202	4300	6502	SO:0001583	missense	26233	exon7			CCCCTCGTCCCGG	AF174592	CCDS6422.1, CCDS47942.1	8q24.3	2011-06-09			ENSG00000182325	ENSG00000182325		"F-boxes / Leucine-rich repeats"	13603	protein-coding gene	gene with protein product		609076				10531035, 10531037	Standard	NM_012162		Approved	FBL6	uc003zcb.3	Q8N531	OTTHUMG00000165169	ENST00000331890.5:c.1039C>G	chr8.hg19:g.145580146G>C	ENSP00000330098:p.Arg347Gly	70.0	0.0		75.0	25.0	NM_012162	Q53G43|Q9H5W9|Q9UKC7	Missense_Mutation	SNP	ENST00000331890.5	hg19	CCDS6422.1	.	.	.	.	.	.	.	.	.	.	G	2.895	-0.228891	0.06022	.	.	ENSG00000182325	ENST00000455319;ENST00000331890	T;T	0.16324	5.47;2.35	4.92	2.02	0.26589	.	0.247112	0.33610	N	0.004728	T	0.14098	0.0341	L	0.50333	1.59	0.09310	N	1	B;B	0.32396	0.253;0.369	B;B	0.32211	0.033;0.142	T	0.16364	-1.0405	10	0.59425	D	0.04	-7.1819	5.6088	0.17394	0.0943:0.0:0.5587:0.347	.	347;341	Q8N531;Q8N531-2	FBXL6_HUMAN;.	G	341;347	ENSP00000403873:R341G;ENSP00000330098:R347G	ENSP00000330098:R347G	R	-	1	2	FBXL6	145550954	0.000000	0.05858	0.001000	0.08648	0.015000	0.08874	0.305000	0.19254	0.092000	0.17331	0.563000	0.77884	CGA	.	.		0.647	FBXL6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382413.1	NM_024555		C	145580146	G	C	145580146	3	2	280	1	0	0	0	0	1	0	0	0	5731	1153	40	4	592	4	FBXL6	8	145580146	Missense_Mutation	SNP	G	TCGA-G3-A3CH-01A-11D-A22F-10		145580146	783876	21	40200										
SPAG8	4882	hgsc.bcm.edu	37	chr9	35810300	35810300	+	IGR	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	aggttgctcctggcggtagtCgtgaggctgtgagggagggt	20	6	0	2			TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr9:35810300C>G	ENST00000342694.2	+	0	3686				SPAG8_ENST00000484764.1_Intron|HINT2_ENST00000474908.1_5'Flank|SPAG8_ENST00000479751.1_5'UTR|SPAG8_ENST00000396638.2_Missense_Mutation_p.D403H|SPAG8_ENST00000340291.2_Missense_Mutation_p.D403H|AL133410.1_ENST00000582432.1_RNA	NM_003995.3	NP_003986.2	P20594	ANPRB_HUMAN	natriuretic peptide receptor 2						bone development (GO:0060348)|cell surface receptor signaling pathway (GO:0007166)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cGMP biosynthetic process (GO:0006182)|intracellular signal transduction (GO:0035556)|negative regulation of meiotic cell cycle (GO:0051447)|negative regulation of oocyte maturation (GO:1900194)|ossification (GO:0001503)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|signal transduction (GO:0007165)|single organism reproductive process (GO:0044702)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(2)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)		Erythrityl Tetranitrate(DB01613)|Nesiritide(DB04899)	TGGCGGTAGTCGTGAGGCTGT	0.612																																					p.D403H		Atlas-SNP	.											.	SPAG8	67	.	0			c.G1207C						.						156	153	154					9																	35810300		2203	4300	6503	SO:0001628	intergenic_variant	26206	exon6			GGTAGTCGTGAGG	AJ005282	CCDS6590.1	9p21-p12	2014-03-03	2014-03-03		ENSG00000159899	ENSG00000159899			7944	protein-coding gene	gene with protein product	"guanylate cyclase B"	108961	"acromesomelic dysplasia, Maroteaux type", "atrionatriuretic peptide receptor B", "natriuretic peptide receptor B"	ANPRB, NPRB, AMDM		9634515, 15146390	Standard	XM_005251478		Approved	GUCY2B, ANPb	uc003zyd.3	P20594	OTTHUMG00000019871		chr9.hg19:g.35810300C>G		86.0	0.0		67.0	21.0	NM_001039592	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	Missense_Mutation	SNP	ENST00000342694.2	hg19	CCDS6590.1	.	.	.	.	.	.	.	.	.	.	C	15.44	2.834243	0.50951	.	.	ENSG00000137098	ENST00000340291;ENST00000396638	T;T	0.36878	1.23;1.26	5.42	3.31	0.37934	.	0.268766	0.31051	N	0.008350	T	0.45013	0.1321	L	0.47716	1.5	0.34920	D	0.748328	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.56147	-0.8027	10	0.66056	D	0.02	-24.3527	3.6592	0.08232	0.2407:0.6096:0.0:0.1497	.	403;403	E9PDV6;Q99932-2	.;.	H	403	ENSP00000340982:D403H;ENSP00000379878:D403H	ENSP00000340982:D403H	D	-	1	0	SPAG8	35800300	0.306000	0.24490	0.996000	0.52242	0.814000	0.46013	0.504000	0.22626	2.542000	0.85734	0.655000	0.94253	GAC	.	.		0.612	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1			G	35810300	C	G	35810300	1	3	280	0	1	0	0	0	0	0	0	0	14999	884	31	4		4	SPAG8	9	35810300	IGR	SNP	C	TCGA-G3-A3CH-01A-11D-A22F-10		35810300	105403131	22	40201										
GRIN1	2902	hgsc.bcm.edu	37	chr9	140057102	140057102	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	tgtgggccggctttgccatgAtcatcgtggcctcctacacc	11	14	1	1			TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr9:140057102A>G	ENST00000371561.3	+	14	3021	c.1924A>G	c.(1924-1926)Atc>Gtc	p.I642V	GRIN1_ENST00000315048.3_Missense_Mutation_p.I642V|GRIN1_ENST00000371559.4_Missense_Mutation_p.I642V|GRIN1_ENST00000371560.3_Missense_Mutation_p.I663V|GRIN1_ENST00000371555.4_Missense_Mutation_p.I663V|GRIN1_ENST00000350902.5_Missense_Mutation_p.I642V|GRIN1_ENST00000471122.1_3'UTR|GRIN1_ENST00000371546.4_Missense_Mutation_p.I663V|GRIN1_ENST00000371553.3_Missense_Mutation_p.I663V|GRIN1_ENST00000371550.4_Missense_Mutation_p.I642V	NM_007327.3	NP_015566.1	Q05586	NMDZ1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 1	642					adult locomotory behavior (GO:0008344)|calcium ion homeostasis (GO:0055074)|calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular calcium ion homeostasis (GO:0006874)|cellular response to manganese ion (GO:0071287)|cerebral cortex development (GO:0021987)|conditioned taste aversion (GO:0001661)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|male mating behavior (GO:0060179)|negative regulation of neuron apoptotic process (GO:0043524)|olfactory learning (GO:0008355)|pons maturation (GO:0021586)|positive regulation of apoptotic process (GO:0043065)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prepulse inhibition (GO:0060134)|propylene metabolic process (GO:0018964)|protein tetramerization (GO:0051262)|regulation of axonogenesis (GO:0050770)|regulation of dendrite morphogenesis (GO:0048814)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of membrane potential (GO:0042391)|regulation of respiratory gaseous exchange (GO:0043576)|regulation of synapse assembly (GO:0051963)|respiratory gaseous exchange (GO:0007585)|response to amphetamine (GO:0001975)|response to calcium ion (GO:0051592)|response to ethanol (GO:0045471)|response to fungicide (GO:0060992)|response to morphine (GO:0043278)|rhythmic process (GO:0048511)|sensory perception of pain (GO:0019233)|social behavior (GO:0035176)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)|synaptic cleft (GO:0043083)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate binding (GO:0016595)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|voltage-gated cation channel activity (GO:0022843)			NS(1)|breast(1)|endometrium(1)|kidney(1)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;6.87e-05)|Epithelial(140;0.00095)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CTTTGCCATGATCATCGTGGC	0.697																																					p.I663V	NSCLC(113;717 1653 2089 20474 37618)	Atlas-SNP	.											.	GRIN1	51	.	0			c.A1987G						.						20	24	22					9																	140057102		2199	4297	6496	SO:0001583	missense	2902	exon15			GCCATGATCATCG		CCDS7031.1, CCDS7032.1, CCDS43910.1, CCDS55354.1, CCDS55355.1	9q34.3	2013-01-11			ENSG00000176884	ENSG00000176884		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4584	protein-coding gene	gene with protein product		138249	"N-methyl-D-aspartate receptor subunit NR1"	NMDAR1		1350383	Standard	NM_000832		Approved	GluN1	uc004cln.3	Q05586	OTTHUMG00000020976	ENST00000371561.3:c.1924A>G	chr9.hg19:g.140057102A>G	ENSP00000360616:p.Ile642Val	19.0	0.0		25.0	11.0	NM_001185091	A6NLK7|A6NLR1|C9K0X1|P35437|Q12867|Q12868|Q5VSF3|Q5VSF4|Q5VSF5|Q5VSF6|Q5VSF7|Q5VSF8|Q9UPF8|Q9UPF9	Missense_Mutation	SNP	ENST00000371561.3	hg19	CCDS7031.1	.	.	.	.	.	.	.	.	.	.	a	21.3	4.125299	0.77436	.	.	ENSG00000176884	ENST00000371561;ENST00000315048;ENST00000350902;ENST00000371550;ENST00000371546;ENST00000371555;ENST00000371553;ENST00000371559;ENST00000371560	T;T;T;T;T;T;T;T;T	0.56103	0.48;0.48;0.48;0.48;0.48;0.48;0.48;0.48;0.48	4.54	4.54	0.55810	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.000000	0.85682	D	0.000000	T	0.66479	0.2793	L	0.53249	1.67	0.80722	D	1	D;D;D;D;D;D	0.67145	0.996;0.977;0.995;0.995;0.996;0.994	D;P;D;D;D;D	0.80764	0.994;0.836;0.99;0.99;0.994;0.953	T	0.69847	-0.5034	10	0.87932	D	0	.	12.7363	0.57225	1.0:0.0:0.0:0.0	.	663;663;642;642;642;642	Q5VSF4;Q5VSF5;Q05586-2;Q05586-3;Q05586;A2AVK2	.;.;.;.;NMDZ1_HUMAN;.	V	642;642;642;642;663;663;663;642;663	ENSP00000360616:I642V;ENSP00000316696:I642V;ENSP00000316915:I642V;ENSP00000360605:I642V;ENSP00000360601:I663V;ENSP00000360610:I663V;ENSP00000360608:I663V;ENSP00000360614:I642V;ENSP00000360615:I663V	ENSP00000316696:I642V	I	+	1	0	GRIN1	139176923	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	7.077000	0.76814	1.700000	0.51204	0.370000	0.22315	ATC	.	.		0.697	GRIN1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055267.3	NM_007327		G	140057102	A	G	140057102	3	3	280	1	0	0	0	0	1	0	0	0	6787	333	12	2	2045	2	GRIN1	9	140057102	Missense_Mutation	SNP	A	TCGA-G3-A3CH-01A-11D-A22F-10	104246802	140057102	1156329	23	40202										
PHYHIPL	84457	hgsc.bcm.edu	37	chr10	61005153	61005174	+	Frame_Shift_Del	DEL	GACCTGTACAGAAGAAGATGGG	GACCTGTACAGAAGAAGATGGG	-													0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	tctaaggataataaatttttGacctgtacagaagaagatgg					rs200012194		TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	GACCTGTACAGAAGAAGATGGG	GACCTGTACAGAAGAAGATGGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr10:61005153_61005174delGACCTGTACAGAAGAAGATGGG	ENST00000373880.4	+	5	1197_1218	c.933_954delGACCTGTACAGAAGAAGATGGG	c.(931-954)ttgacctgtacagaagaagatgggfs	p.LTCTEEDG311fs	PHYHIPL_ENST00000373878.3_Frame_Shift_Del_p.LTCTEEDG285fs	NM_032439.3	NP_115815.2	Q96FC7	PHIPL_HUMAN	phytanoyl-CoA 2-hydroxylase interacting protein-like	311						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)				NS(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|liver(2)|lung(3)|skin(1)|urinary_tract(1)	18						ATAAATTTTTGACCTGTACAGAAGAAGATGGGGTGCTGGTTT	0.428																																					p.311_318del		Atlas-Indel,Pindel	.											.	PHYHIPL	44	.	0			c.932_953del						.																																			SO:0001589	frameshift_variant	84457	exon5			.	AL834339	CCDS7254.1, CCDS44405.1	10q21.1	2013-02-11	2006-01-09		ENSG00000165443	ENSG00000165443		"Fibronectin type III domain containing"	29378	protein-coding gene	gene with protein product			"phytanoyl-CoA hydroxylase interacting protein-like"			11347906	Standard	NM_032439		Approved	KIAA1796, Em:AC025038.1	uc001jkk.4	Q96FC7	OTTHUMG00000018276	ENST00000373880.4:c.933_954delGACCTGTACAGAAGAAGATGGG	chr10.hg19:g.61005153_61005174delGACCTGTACAGAAGAAGATGGG	ENSP00000362987:p.Leu311fs	129.0	0.0		89.0	12.0	NM_032439	B7WP61|Q68DF3|Q6UXY3|Q8N3W3|Q96JM9|Q96NP7	Frame_Shift_Del	DEL	ENST00000373880.4	hg19	CCDS7254.1																																																																																			.	.		0.428	PHYHIPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048156.1	NM_032439		-	61005174	GACCTGTACAGAAGAAGATGGG	-	61005153	7	5	280	1	0	1	0	1	0	0	0	0	11876	1281	45	0	983	0	PHYHIPL	10	61005153	Frame_Shift_Del	DEL	GACCTGTACAGAAGAAGATGGG	TCGA-G3-A3CH-01A-11D-A22F-10		61005153	74529594	24	40203										
TIAL1	7073	hgsc.bcm.edu	37	chr10	121342007	121342008	+	Frame_Shift_Del	DEL	TG	TG	-													0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	ctcccattcatagcagctaaTgcagcagctgcatctctgtg							TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr10:121342007_121342008delTG	ENST00000436547.2	-	3	235_236	c.191_192delCA	c.(190-192)gcafs	p.A64fs	TIAL1_ENST00000369092.4_5'UTR|TIAL1_ENST00000369093.2_Frame_Shift_Del_p.A81fs	NM_003252.3	NP_003243.1	Q01085	TIAR_HUMAN	TIA1 cytotoxic granule-associated RNA binding protein-like 1	64	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				apoptotic process (GO:0006915)|defense response (GO:0006952)|germ cell development (GO:0007281)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell division (GO:0017145)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(3)|ovary(1)	13		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.00239)|BRCA - Breast invasive adenocarcinoma(275;0.0932)		TAGCAGCTAATGCAGCAGCTGC	0.371																																					p.81_82del		Atlas-INDEL	.											.	TIAL1	47	.	0			c.243_244del						.																																			SO:0001589	frameshift_variant	7073	exon3			.	AL833106	CCDS7613.1, CCDS31295.1	10q	2013-02-12	2001-11-28		ENSG00000151923	ENSG00000151923		"RNA binding motif (RRM) containing"	11804	protein-coding gene	gene with protein product		603413	"TIA1 cytotoxic granule-associated RNA-binding protein-like 1"			1326761	Standard	XM_005270108		Approved	TIAR	uc001lej.1	Q01085	OTTHUMG00000019156	ENST00000436547.2:c.191_192delCA	chr10.hg19:g.121342007_121342008delTG	ENSP00000394902:p.Ala64fs	163.0	0.0		152.0	46.0	NM_001033925	A8K3T0|A8K4L9	Frame_Shift_Del	DEL	ENST00000436547.2	hg19	CCDS7613.1																																																																																			.	.		0.371	TIAL1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050672.2	NM_022333, NM_003252		-	121342008	TG	-	121342007	7	5	280	1	0	1	0	1	0	0	0	0	15904	1451	51	0	975	0	TIAL1	10	121342007	Frame_Shift_Del	DEL	TG	TCGA-G3-A3CH-01A-11D-A22F-10	60336854	121342007	14192740	25	40204	204	3								
TIAL1	7073	hgsc.bcm.edu	37	chr10	121342010	121342010	+	Frame_Shift_Del	DEL	A	A	-													0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	ccattcatagcagctaatgcAgcagctgcatctctgtgttc							TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr10:121342010delA	ENST00000436547.2	-	3	233	c.189delT	c.(187-189)gctfs	p.A64fs	TIAL1_ENST00000369092.4_5'UTR|TIAL1_ENST00000369093.2_Frame_Shift_Del_p.A81fs	NM_003252.3	NP_003243.1	Q01085	TIAR_HUMAN	TIA1 cytotoxic granule-associated RNA binding protein-like 1	64	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				apoptotic process (GO:0006915)|defense response (GO:0006952)|germ cell development (GO:0007281)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell division (GO:0017145)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(3)|ovary(1)	13		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.00239)|BRCA - Breast invasive adenocarcinoma(275;0.0932)		CAGCTAATGCAGCAGCTGCAT	0.383																																					p.A81fs		Atlas-INDEL	.											.	TIAL1	47	.	0			c.241delG						.						118	127	124					10																	121342010		2203	4300	6503	SO:0001589	frameshift_variant	7073	exon3			.	AL833106	CCDS7613.1, CCDS31295.1	10q	2013-02-12	2001-11-28		ENSG00000151923	ENSG00000151923		"RNA binding motif (RRM) containing"	11804	protein-coding gene	gene with protein product		603413	"TIA1 cytotoxic granule-associated RNA-binding protein-like 1"			1326761	Standard	XM_005270108		Approved	TIAR	uc001lej.1	Q01085	OTTHUMG00000019156	ENST00000436547.2:c.189delT	chr10.hg19:g.121342010delA	ENSP00000394902:p.Ala64fs	163.0	0.0		151.0	46.0	NM_001033925	A8K3T0|A8K4L9	Frame_Shift_Del	DEL	ENST00000436547.2	hg19	CCDS7613.1																																																																																			.	.		0.383	TIAL1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050672.2	NM_022333, NM_003252		-	121342010	A	-	121342010	7	5	280	1	0	1	0	1	0	0	0	0	15904	175	7	0	978	0	TIAL1	10	121342010	Frame_Shift_Del	DEL	A	TCGA-G3-A3CH-01A-11D-A22F-10	3	121342010	14192737	26	40205	204	3								
TIAL1	7073	hgsc.bcm.edu	37	chr10	121342011	121342013	+	In_Frame_Del	DEL	GCA	GCA	-													0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	cattcatagcagctaatgcaGcagctgcatctctgtgttca							TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	GCA	GCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr10:121342011_121342013delGCA	ENST00000436547.2	-	3	230_232	c.186_188delTGC	c.(184-189)gctgct>gct	p.62_63AA>A	TIAL1_ENST00000369092.4_5'UTR|TIAL1_ENST00000369093.2_In_Frame_Del_p.79_80AA>A	NM_003252.3	NP_003243.1	Q01085	TIAR_HUMAN	TIA1 cytotoxic granule-associated RNA binding protein-like 1	62	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				apoptotic process (GO:0006915)|defense response (GO:0006952)|germ cell development (GO:0007281)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell division (GO:0017145)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(3)|ovary(1)	13		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.00239)|BRCA - Breast invasive adenocarcinoma(275;0.0932)		AGCTAATGCAGCAGCTGCATCTC	0.379																																					p.80_80del		Pindel	.											.	TIAL1	47	.	0			c.238_240del						.																																			SO:0001651	inframe_deletion	7073	exon3			.	AL833106	CCDS7613.1, CCDS31295.1	10q	2013-02-12	2001-11-28		ENSG00000151923	ENSG00000151923		"RNA binding motif (RRM) containing"	11804	protein-coding gene	gene with protein product		603413	"TIA1 cytotoxic granule-associated RNA-binding protein-like 1"			1326761	Standard	XM_005270108		Approved	TIAR	uc001lej.1	Q01085	OTTHUMG00000019156	ENST00000436547.2:c.186_188delTGC	chr10.hg19:g.121342011_121342013delGCA	ENSP00000394902:p.Ala64del	163.0	0.0		151.0	41.0	NM_001033925	A8K3T0|A8K4L9	In_Frame_Del	DEL	ENST00000436547.2	hg19	CCDS7613.1																																																																																			.	.		0.379	TIAL1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050672.2	NM_022333, NM_003252		-	121342013	GCA	-	121342011	7	5	280	1	0	1	0	1	0	0	0	0	15904	971	34	0	979	0	TIAL1	10	121342011	In_Frame_Del	DEL	GCA	TCGA-G3-A3CH-01A-11D-A22F-10	1	121342011	14192736	27	40206	204	3								
OR51I1	390063	hgsc.bcm.edu	37	chr11	5462320	5462320	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	ccagacccatagccaatataCggttgtgagtgagcacagtg	11	10	0	3	rs138548705		TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr11:5462320C>T	ENST00000380211.1	-	1	424	c.425G>A	c.(424-426)cGt>cAt	p.R142H	HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron	NM_001005288.2	NP_001005288.1	Q9H343	O51I1_HUMAN	olfactory receptor, family 51, subfamily I, member 1	142					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	30		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AGCCAATATACGGTTGTGAGT	0.478													C|||	1	0.000199681	0	0.0014	5008	,	,		24090	0		0	False		,,,				2504	0				p.R142H		Atlas-SNP	.											OR51I1,NS,carcinoma,-1,1	OR51I1	66	.	0			c.G425A						.	C	HIS/ARG	1,4401	2.1+/-5.4	0,1,2200	137	107	117		425	3.7	0.3	11	dbSNP_134	117	0,8594		0,0,4297	no	missense	OR51I1	NM_001005288.2	29	0,1,6497	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	142/315	5462320	1,12995	2201	4297	6498	SO:0001583	missense	390063	exon1			AATATACGGTTGT	BK004429	CCDS31382.1	11p15.4	2012-08-09			ENSG00000167359	ENSG00000167359		"GPCR / Class A : Olfactory receptors"	15200	protein-coding gene	gene with protein product							Standard	NM_001005288		Approved		uc010qze.2	Q9H343	OTTHUMG00000066908	ENST00000380211.1:c.425G>A	chr11.hg19:g.5462320C>T	ENSP00000369559:p.Arg142His	83.0	1.0		92.0	36.0	NM_001005288	B9EKW2|Q6IF33	Missense_Mutation	SNP	ENST00000380211.1	hg19	CCDS31382.1	.	.	.	.	.	.	.	.	.	.	C	11.85	1.760391	0.31137	2.27E-4	0.0	ENSG00000167359	ENST00000317283;ENST00000321307;ENST00000380211	T	0.39592	1.07	5.74	3.69	0.42338	GPCR, rhodopsin-like superfamily (1);	0.243881	0.29059	N	0.013271	T	0.56202	0.1969	M	0.81614	2.55	0.09310	N	1	D	0.63880	0.993	P	0.55087	0.768	T	0.50180	-0.8858	10	0.40728	T	0.16	.	12.1837	0.54226	0.2579:0.7421:0.0:0.0	.	142	Q9H343	O51I1_HUMAN	H	127;139;142	ENSP00000369559:R142H	ENSP00000348350:R127H	R	-	2	0	OR51I1	5418896	0.000000	0.05858	0.339000	0.25562	0.128000	0.20619	-1.648000	0.01995	2.742000	0.94016	0.551000	0.68910	CGT	.	C|1.000;T|0.000		0.478	OR51I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143399.1	NM_001005288		T	5462320	C	T	5462320	3	4	280	1	0	0	0	0	1	0	0	0	11109	536	19	1	523	1	OR51I1	11	5462320	Missense_Mutation	SNP	C	TCGA-G3-A3CH-01A-11D-A22F-10		5462320	129544196	28	40207										
LYVE1	10894	hgsc.bcm.edu	37	chr11	10580711	10580711	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	tttgcttggactcttggactCttctgggtttttatcagttt	9	7	4	0			TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr11:10580711C>T	ENST00000256178.3	-	6	1074	c.916G>A	c.(916-918)Gag>Aag	p.E306K	LYVE1_ENST00000531706.1_5'Flank|MRVI1-AS1_ENST00000529829.1_RNA|MRVI1-AS1_ENST00000529979.1_RNA|LYVE1_ENST00000529598.1_Missense_Mutation_p.E202K	NM_006691.3	NP_006682.2	Q9Y5Y7	LYVE1_HUMAN	lymphatic vessel endothelial hyaluronan receptor 1	306					anatomical structure morphogenesis (GO:0009653)|carbohydrate metabolic process (GO:0005975)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|response to wounding (GO:0009611)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	8				all cancers(16;7.22e-08)|Epithelial(150;1.03e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0609)		CTCTTGGACTCTTCTGGGTTT	0.438																																					p.E306K		Atlas-SNP	.											.	LYVE1	19	.	0			c.G916A						.						307	282	291					11																	10580711		2201	4294	6495	SO:0001583	missense	10894	exon6			TGGACTCTTCTGG	AF118108	CCDS7804.1	11p15	2008-02-05	2007-06-26	2007-06-26		ENSG00000133800			14687	protein-coding gene	gene with protein product		605702	"extracellular link domain containing 1"	XLKD1		10037799, 12554094	Standard	NM_006691		Approved	LYVE-1	uc001miv.2	Q9Y5Y7		ENST00000256178.3:c.916G>A	chr11.hg19:g.10580711C>T	ENSP00000256178:p.Glu306Lys	327.0	0.0		344.0	104.0	NM_006691	Q8TC18|Q9UNF4	Missense_Mutation	SNP	ENST00000256178.3	hg19	CCDS7804.1	.	.	.	.	.	.	.	.	.	.	C	33	5.275007	0.95459	.	.	ENSG00000133800	ENST00000256178;ENST00000529598	T;T	0.37752	2.88;1.18	6.02	6.02	0.97574	.	0.134638	0.51477	D	0.000097	T	0.58337	0.2115	M	0.71581	2.175	0.52099	D	0.999942	D;D	0.63046	0.992;0.986	P;P	0.61592	0.891;0.78	T	0.58618	-0.7605	10	0.72032	D	0.01	-10.1708	17.4575	0.87611	0.0:1.0:0.0:0.0	.	202;306	F2Z296;Q9Y5Y7	.;LYVE1_HUMAN	K	306;202	ENSP00000256178:E306K;ENSP00000436016:E202K	ENSP00000256178:E306K	E	-	1	0	LYVE1	10537287	1.000000	0.71417	0.993000	0.49108	0.942000	0.58702	4.151000	0.58105	2.865000	0.98341	0.655000	0.94253	GAG	.	.		0.438	LYVE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385893.1	NM_016164		T	10580711	C	T	10580711	3	4	280	1	0	0	0	0	1	0	0	0	9138	922	32	3	56	3	LYVE1	11	10580711	Missense_Mutation	SNP	C	TCGA-G3-A3CH-01A-11D-A22F-10	5118391	10580711	124425805	29	40208										
CEP290	80184	hgsc.bcm.edu	37	chr12	88478474	88478474	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	gcaattttcaatgtgtggtgAgattttggttccatctcttt	9	6	2	1			TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr12:88478474A>C	ENST00000552810.1	-	35	4936	c.4593T>G	c.(4591-4593)tcT>tcG	p.S1531S	CEP290_ENST00000547691.2_Silent_p.S591S|CEP290_ENST00000397838.3_Silent_p.S591S|CEP290_ENST00000309041.7_Silent_p.S1533S	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	1531					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						ATGTGTGGTGAGATTTTGGTT	0.383																																					p.S1531S		Atlas-SNP	.											.	CEP290	195	.	0			c.T4593G						.						214	202	206					12																	88478474		1876	4112	5988	SO:0001819	synonymous_variant	80184	exon35			GTGGTGAGATTTT	AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"Joubert syndrome 5", "nephrocystin-6", "cancer/testis antigen 87", "POC3 centriolar protein homolog (Chlamydomonas)", "Meckel syndrome, type 4"	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.4593T>G	chr12.hg19:g.88478474A>C		151.0	0.0		178.0	62.0	NM_025114	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Silent	SNP	ENST00000552810.1	hg19	CCDS55858.1																																																																																			.	.		0.383	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		C	88478474	A	C	88478474	2	2	280	1	0	0	0	0	0	0	0	1	3255	291	11	5		5	CEP290	12	88478474	Silent	SNP	A	TCGA-G3-A3CH-01A-11D-A22F-10		88478474	45373421	30	40209										
ANO4	121601	hgsc.bcm.edu	37	chr12	101333093	101333093	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	tgtatttactttggttctagTggccaaggatgtcaatattc	9	6	2	0			TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr12:101333093T>A	ENST00000392977.3	+	4	371	c.161T>A	c.(160-162)aTg>aAg	p.M54K	ANO4_ENST00000392979.3_Splice_Site_p.V19E|ANO4_ENST00000299222.9_5'UTR|ANO4_ENST00000538618.1_Splice_Site_p.M220K			Q32M45	ANO4_HUMAN	anoctamin 4	54					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			NS(1)|biliary_tract(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(4)|prostate(5)|skin(7)|stomach(2)|urinary_tract(1)	78						TTGGTTCTAGTGGCCAAGGAT	0.378										HNSCC(74;0.22)																											p.V19E		Atlas-SNP	.											.	ANO4	183	.	0			c.T56A						.						111	110	110					12																	101333093		2203	4300	6503	SO:0001630	splice_region_variant	121601	exon3			TTCTAGTGGCCAA	AK091540	CCDS31884.1, CCDS66445.1	12q23.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000151572	ENSG00000151572		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	23837	protein-coding gene	gene with protein product		610111	"transmembrane protein 16D"	TMEM16D		12739008, 15067359, 24692353	Standard	NM_178826		Approved	FLJ34221, FLJ34272, FLJ35277	uc001thw.2	Q32M45		ENST00000392977.3:c.161-1T>A	chr12.hg19:g.101333093T>A		165.0	0.0		171.0	37.0	NM_178826	Q8NAJ0|Q8NB39|Q8NB53	Missense_Mutation	SNP	ENST00000392977.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.88|14.88	2.667839|2.667839	0.47677|0.47677	.|.	.|.	ENSG00000151572|ENSG00000151572	ENST00000538618;ENST00000392977|ENST00000392979	T;T|T	0.39592|0.35973	1.07;1.07|1.28	5.54|5.54	5.54|5.54	0.83059|0.83059	.|.	.|0.563867	.|0.17673	.|N	.|0.165919	T|T	0.14442|0.14442	0.0349|0.0349	N|N	0.02011|0.02011	-0.69|-0.69	0.80722|0.80722	D|D	1|1	B|B	0.12630|0.02656	0.006|0.0	B|B	0.15052|0.04013	0.012|0.001	T|T	0.17167|0.17167	-1.0378|-1.0378	8|9	.|.	.|.	.|.	.|.	10.8653|10.8653	0.46851|0.46851	0.1405:0.0:0.0:0.8595|0.1405:0.0:0.0:0.8595	.|.	54|19	Q32M45|Q32M45-2	ANO4_HUMAN|.	K|E	220;54|19	ENSP00000443751:M220K;ENSP00000376703:M54K|ENSP00000376705:V19E	.|.	M|V	+|+	2|2	0|0	ANO4|ANO4	99857224|99857224	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.940000|0.940000	0.58332|0.58332	2.980000|2.980000	0.49321|0.49321	2.115000|2.115000	0.64714|0.64714	0.528000|0.528000	0.53228|0.53228	ATG|GTG	.	.		0.378	ANO4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409295.1	NM_178826	Missense_Mutation	A	101333093	T	A	101333093	5	1	280	1	0	0	0	0	0	0	1	0	699	1710	59	4	62	4	ANO4	12	101333093	Splice_Site	SNP	T	TCGA-G3-A3CH-01A-11D-A22F-10	12854619	101333093	32518802	31	40210										
RB1	5925	hgsc.bcm.edu	37	chr13	48954378	48954378	+	Splice_Site	DEL	G	G	-													0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	tgtaatggccacatatagcaGtaagttaaattttcataaat							TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr13:48954378delG	ENST00000267163.4	+	16	1636		c.e16+1			NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1						androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(9)		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(DB00071)|Insulin Regular(DB00030)"	ACATATAGCAGTAAGTTAAAT	0.338		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)																											p.R500fs		Atlas-Indel,Pindel	.	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	RB1,NS,carcinoma,0,1	RB1	1068	.	24	Whole gene deletion(15)|Unknown(9)	bone(11)|breast(5)|central_nervous_system(2)|adrenal_gland(1)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)|lung(1)	c.1498delA						.						43	46	45					13																	48954378		2201	4299	6500	SO:0001630	splice_region_variant	5925	exon16	Familial Cancer Database		.	M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1498+1G>-	chr13.hg19:g.48954378delG		116.0	0.0		107.0	55.0	NM_000321	A8K5E3|P78499|Q5VW46|Q8IZL4	Frame_Shift_Del	DEL	ENST00000267163.4	hg19	CCDS31973.1																																																																																			.	.		0.338	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1		Intron	-	48954378	G	-	48954378	8	5	280	1	0	1	0	1	0	0	1	0	13113	1043	36	0	1561	0	RB1	13	48954378	Splice_Site	DEL	G	TCGA-G3-A3CH-01A-11D-A22F-10		48954378	66215500	32	40211										
MEX3B	84206	hgsc.bcm.edu	37	chr15	82336764	82336765	+	Missense_Mutation	DNP	GC	GC	TT													0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	ttgggcggcccaggcaccgcGccgttgagtgccgtgttctt							TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr15:82336764_82336765GC>TT	ENST00000329713.4	-	2	881_882	c.446_447GC>AA	c.(445-447)gGC>gAA	p.G149E	MEX3B_ENST00000558133.1_3'UTR|AC026956.1_ENST00000410589.1_RNA	NM_032246.4	NP_115622.2	Q6ZN04	MEX3B_HUMAN	mex-3 RNA binding family member B	149					protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|upper_aerodigestive_tract(1)	19						CAGGCACCGCGCCGTTGAGTGC	0.658																																					p.G149G|p.G149D		Atlas-SNP	.											.	MEX3B	50	.	0			c.C447A|c.G446A						.																																			SO:0001583	missense	84206	exon2			CACCGCGCCGTTG|ACCGCGCCGTTGA	AK131424	CCDS10319.1	15q25.1	2013-08-21	2013-08-21	2007-07-18	ENSG00000183496	ENSG00000183496		"RING-type (C3HC4) zinc fingers", "Mex-3 homologs"	25297	protein-coding gene	gene with protein product		611008	"ring finger and KH domain containing 3", "mex-3 homolog B (C. elegans)"	RKHD3		11230166, 17267406	Standard	NM_032246		Approved	DKFZp434J0617, RNF195	uc002bgq.2	Q6ZN04	OTTHUMG00000147356	ENST00000329713.4:c.446_447delinsTT	chr15.hg19:g.82336764_82336765delinsTT	ENSP00000329918:p.Gly149Glu	60.0|61.0	0.0		30.0	17.0	NM_032246	Q4G0W1|Q8IVG2|Q9H0J0	Silent|Missense_Mutation	SNP	ENST00000329713.4	hg19	CCDS10319.1																																																																																			.	.		0.658	MEX3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304000.1	XM_290645		TT	82336765	GC	TT	82336764	3	4	280	1	0	0	0	0	1	0	0	0	9519	1074	38	1	1266	1	MEX3B	15	82336764	Missense_Mutation	DNP	GC	TCGA-G3-A3CH-01A-11D-A22F-10		82336764	20194628	33	40212										
C16orf90	646174	hgsc.bcm.edu	37	chr16	3543984	3543984	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	ctgggtccatgctggaactgGaagctgaggaaagaggagag	17	6	0	3			TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr16:3543984G>A	ENST00000437192.3	-	3	406	c.404C>T	c.(403-405)tCc>tTc	p.S135F	LA16c-306E5.3_ENST00000574423.2_RNA	NM_001080524.1	NP_001073993.1	A8MZG2	CP090_HUMAN	chromosome 16 open reading frame 90	125										large_intestine(1)	1						GCTGGAACTGGAAGCTGAGGA	0.612																																					p.S135F		Atlas-SNP	.											.	C16orf90	16	.	0			c.C404T						.						21	21	21					16																	3543984		1906	4120	6026	SO:0001583	missense	646174	exon3			GAACTGGAAGCTG		CCDS45397.1	16p13.3	2009-01-29			ENSG00000215131	ENSG00000215131			34455	protein-coding gene	gene with protein product							Standard	NM_001080524		Approved	LOC646174	uc002cvi.3	A8MZG2	OTTHUMG00000154627	ENST00000437192.3:c.404C>T	chr16.hg19:g.3543984G>A	ENSP00000401335:p.Ser135Phe	22.0	0.0		21.0	8.0	NM_001080524		Missense_Mutation	SNP	ENST00000437192.3	hg19	CCDS45397.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.989072	0.74589	.	.	ENSG00000215131	ENST00000437192	.	.	.	5.55	5.55	0.83447	.	1.166210	0.06877	U	0.801728	T	0.79435	0.4445	M	0.67953	2.075	0.36210	D	0.85129	D	0.71674	0.998	D	0.70935	0.971	T	0.71484	-0.4579	8	.	.	.	-16.9115	15.0163	0.71588	0.0:0.0:1.0:0.0	.	135	A8MZG2-2	.	F	135	.	.	S	-	2	0	C16orf90	3483985	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.091000	0.50199	2.621000	0.88768	0.655000	0.94253	TCC	.	.		0.612	C16orf90-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346319.2	NM_001080524		A	3543984	G	A	3543984	3	1	280	1	0	0	0	0	1	0	0	0	1845	1174	41	3	148	3	C16orf90	16	3543984	Missense_Mutation	SNP	G	TCGA-G3-A3CH-01A-11D-A22F-10		3543984	86810769	34	40213										
BRD7	29117	hgsc.bcm.edu	37	chr16	50357553	50357553	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	cttttgttaaaacatccagtAaactatctgccatgacatac	4	10	1	1			TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr16:50357553A>T	ENST00000394688.3	-	12	1547	c.1388T>A	c.(1387-1389)tTa>tAa	p.L463*	BRD7_ENST00000394689.2_Nonsense_Mutation_p.L463*			Q9NPI1	BRD7_HUMAN	bromodomain containing 7	463					cell cycle (GO:0007049)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|prostate(2)|urinary_tract(2)	22		all_cancers(37;0.0127)				AACATCCAGTAAACTATCTGC	0.418																																					p.L463X		Atlas-SNP	.											.	BRD7	61	.	0			c.T1388A						.						130	109	116					16																	50357553		2198	4300	6498	SO:0001587	stop_gained	29117	exon12			TCCAGTAAACTAT	AF213969	CCDS10742.1, CCDS54007.1	16q12.1	2008-11-18	2002-01-14		ENSG00000166164	ENSG00000166164			14310	protein-coding gene	gene with protein product			"bromodomain-containing 7"			10526152, 18809673	Standard	NM_013263		Approved	CELTIX1, BP75	uc002ege.2	Q9NPI1	OTTHUMG00000133170	ENST00000394688.3:c.1388T>A	chr16.hg19:g.50357553A>T	ENSP00000378180:p.Leu463*	107.0	0.0		103.0	55.0	NM_013263	Q4VC09|Q8N2L9|Q96KA4|Q9BV48|Q9UH59	Nonsense_Mutation	SNP	ENST00000394688.3	hg19	CCDS10742.1	.	.	.	.	.	.	.	.	.	.	A	38	6.977248	0.97975	.	.	ENSG00000166164	ENST00000394688;ENST00000394689	.	.	.	5.63	5.63	0.86233	.	0.244591	0.35646	N	0.003080	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.7803	15.8266	0.78711	1.0:0.0:0.0:0.0	.	.	.	.	X	463	.	ENSP00000378180:L463X	L	-	2	0	BRD7	48915054	1.000000	0.71417	0.951000	0.38953	0.718000	0.41266	8.678000	0.91211	2.141000	0.66446	0.533000	0.62120	TTA	.	.		0.418	BRD7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256874.3	NM_013263		T	50357553	A	T	50357553	4	4	280	1	0	0	0	0	0	1	0	0	1507	372	13	4	594	4	BRD7	16	50357553	Nonsense_Mutation	SNP	A	TCGA-G3-A3CH-01A-11D-A22F-10	46813569	50357553	39997200	35	40214										
BCL2	596	hgsc.bcm.edu	37	chr18	60795937	60795937	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	gcagagtcttcagagacagcCaggagaaatcaaacagaggc	12	9	3	4			TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr18:60795937C>T	ENST00000398117.1	-	2	2102	c.641G>A	c.(640-642)tGg>tAg	p.W214*	BCL2_ENST00000590515.1_5'UTR|BCL2_ENST00000333681.4_Nonsense_Mutation_p.W214*	NM_000633.2	NP_000624.2	P10415	BCL2_HUMAN	B-cell CLL/lymphoma 2	214					actin filament organization (GO:0007015)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|axonogenesis (GO:0007409)|B cell homeostasis (GO:0001782)|B cell lineage commitment (GO:0002326)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|behavioral fear response (GO:0001662)|branching involved in ureteric bud morphogenesis (GO:0001658)|CD8-positive, alpha-beta T cell lineage commitment (GO:0043375)|cell aging (GO:0007569)|cell growth (GO:0016049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to organic substance (GO:0071310)|cochlear nucleus development (GO:0021747)|defense response to virus (GO:0051607)|developmental growth (GO:0048589)|digestive tract morphogenesis (GO:0048546)|ear development (GO:0043583)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|female pregnancy (GO:0007565)|focal adhesion assembly (GO:0048041)|gland morphogenesis (GO:0022612)|glomerulus development (GO:0032835)|hair follicle morphogenesis (GO:0031069)|homeostasis of number of cells within a tissue (GO:0048873)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|melanin metabolic process (GO:0006582)|melanocyte differentiation (GO:0030318)|mesenchymal cell development (GO:0014031)|metanephros development (GO:0001656)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of autophagy (GO:0010507)|negative regulation of calcium ion transport into cytosol (GO:0010523)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cellular pH reduction (GO:0032848)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of mitochondrial depolarization (GO:0051902)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of myeloid cell apoptotic process (GO:0033033)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of retinal cell programmed cell death (GO:0046671)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|oocyte development (GO:0048599)|organ growth (GO:0035265)|ossification (GO:0001503)|ovarian follicle development (GO:0001541)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|pigment granule organization (GO:0048753)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of catalytic activity (GO:0043085)|positive regulation of cell growth (GO:0030307)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron maturation (GO:0014042)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of skeletal muscle fiber development (GO:0048743)|positive regulation of smooth muscle cell migration (GO:0014911)|post-embryonic development (GO:0009791)|protein dephosphorylation (GO:0006470)|protein polyubiquitination (GO:0000209)|reactive oxygen species metabolic process (GO:0072593)|regulation of calcium ion transport (GO:0051924)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glycoprotein biosynthetic process (GO:0010559)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of nitrogen utilization (GO:0006808)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|regulation of protein stability (GO:0031647)|regulation of transmembrane transporter activity (GO:0022898)|regulation of viral genome replication (GO:0045069)|release of cytochrome c from mitochondria (GO:0001836)|renal system process (GO:0003014)|response to acid chemical (GO:0001101)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to gamma radiation (GO:0010332)|response to glucocorticoid (GO:0051384)|response to hydrogen peroxide (GO:0042542)|response to iron ion (GO:0010039)|response to ischemia (GO:0002931)|response to nicotine (GO:0035094)|response to radiation (GO:0009314)|response to toxic substance (GO:0009636)|response to UV-B (GO:0010224)|single organismal cell-cell adhesion (GO:0016337)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|myelin sheath (GO:0043209)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|pore complex (GO:0046930)	BH3 domain binding (GO:0051434)|channel activity (GO:0015267)|channel inhibitor activity (GO:0016248)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(106)|kidney(1)|large_intestine(1)|lung(3)	113		all_hematologic(56;1.18e-20)|Prostate(75;0.0872)		Lung(128;0.0234)|READ - Rectum adenocarcinoma(59;0.0935)	Docetaxel(DB01248)|Ibuprofen(DB01050)|Paclitaxel(DB01229)|Rasagiline(DB01367)	CAGAGACAGCCAGGAGAAATC	0.542			T	IGH@	"NHL, CLL"																																p.W214X		Atlas-SNP	.		Dom	yes		18	18q21.3	596	B-cell CLL/lymphoma 2		L	.	BCL2	272	.	0			c.G641A						.						51	48	49					18																	60795937		2203	4300	6503	SO:0001587	stop_gained	596	exon3			GACAGCCAGGAGA	M14745	CCDS11981.1, CCDS45882.1	18q21.3	2014-03-07			ENSG00000171791	ENSG00000171791		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	990	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 50"	151430					Standard	XM_006722523		Approved	Bcl-2, PPP1R50	uc002lit.1	P10415	OTTHUMG00000132791	ENST00000398117.1:c.641G>A	chr18.hg19:g.60795937C>T	ENSP00000381185:p.Trp214*	76.0	0.0		96.0	36.0	NM_000633	C9JHD5|P10416|Q13842|Q16197	Nonsense_Mutation	SNP	ENST00000398117.1	hg19	CCDS11981.1	.	.	.	.	.	.	.	.	.	.	C	40	8.139537	0.98672	.	.	ENSG00000171791	ENST00000398117;ENST00000333681	.	.	.	5.15	5.15	0.70609	.	0.071604	0.64402	D	0.000011	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	-5.6122	17.999	0.89193	0.0:1.0:0.0:0.0	.	.	.	.	X	214	.	ENSP00000329623:W214X	W	-	2	0	BCL2	58946917	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.050000	0.64251	2.550000	0.86006	0.655000	0.94253	TGG	.	.		0.542	BCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256199.1	NM_000633, NM_000657		T	60795937	C	T	60795937	4	4	280	1	0	0	0	0	0	1	0	0	1365	595	21	3	82	3	BCL2	18	60795937	Nonsense_Mutation	SNP	C	TCGA-G3-A3CH-01A-11D-A22F-10		60795937	17281311	36	40215										
OR1I1	126370	hgsc.bcm.edu	37	chr19	15198366	15198366	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	tcatacacacctgcctcatgGctcaactgaccttctgcgcc	6	17	4	1			TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr19:15198366G>A	ENST00000209540.2	+	1	576	c.490G>A	c.(490-492)Gct>Act	p.A164T		NM_001004713.1	NP_001004713.1	O60431	OR1I1_HUMAN	olfactory receptor, family 1, subfamily I, member 1	164						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(3)|ovary(2)|stomach(2)	20						CTGCCTCATGGCTCAACTGAC	0.567																																					p.A164T		Atlas-SNP	.											.	OR1I1	58	.	0			c.G490A						.						108	101	103					19																	15198366		2203	4300	6503	SO:0001583	missense	126370	exon1			CTCATGGCTCAAC	AC004794	CCDS32937.1	19p13.1	2012-08-09				ENSG00000094661		"GPCR / Class A : Olfactory receptors"	8207	protein-coding gene	gene with protein product							Standard	NM_001004713		Approved	OR1I1P, OR19-20, OR1I1Q	uc010xoe.2	O60431		ENST00000209540.2:c.490G>A	chr19.hg19:g.15198366G>A	ENSP00000209540:p.Ala164Thr	88.0	0.0		69.0	9.0	NM_001004713	Q96R92	Missense_Mutation	SNP	ENST00000209540.2	hg19	CCDS32937.1	.	.	.	.	.	.	.	.	.	.	G	6.270	0.417960	0.11870	.	.	ENSG00000094661	ENST00000209540	T	0.00076	8.76	4.79	2.6	0.31112	GPCR, rhodopsin-like superfamily (1);	0.268945	0.19455	U	0.113848	T	0.00109	0.0003	N	0.14661	0.345	0.09310	N	1	B	0.24258	0.1	B	0.28991	0.097	T	0.06463	-1.0825	10	0.37606	T	0.19	.	7.3758	0.26827	0.0901:0.0:0.7427:0.1672	.	164	O60431	OR1I1_HUMAN	T	164	ENSP00000209540:A164T	ENSP00000209540:A164T	A	+	1	0	OR1I1	15059366	0.000000	0.05858	0.596000	0.28811	0.437000	0.31866	-0.126000	0.10563	0.597000	0.29811	0.555000	0.69702	GCT	.	.		0.567	OR1I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465665.1			A	15198366	G	A	15198366	3	1	280	1	0	0	0	0	1	0	0	0	10967	1203	42	3	492	3	OR1I1	19	15198366	Missense_Mutation	SNP	G	TCGA-G3-A3CH-01A-11D-A22F-10		15198366	43930617	37	40216										
KIAA1683	80726	hgsc.bcm.edu	37	chr19	18368567	18368567	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	agtgccgggcttggtcccggCgggtgctgtagccgcgccag	18	13	0	0			TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr19:18368567C>T	ENST00000600328.3	-	4	3159	c.2966G>A	c.(2965-2967)cGc>cAc	p.R989H	PDE4C_ENST00000596647.1_5'Flank|PDE4C_ENST00000355502.3_5'Flank|KIAA1683_ENST00000392413.4_Missense_Mutation_p.R1176H|KIAA1683_ENST00000600359.3_Missense_Mutation_p.R943H			Q9H0B3	K1683_HUMAN	KIAA1683	989	IQ 4. {ECO:0000255|PROSITE- ProRule:PRU00116}.					mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						TTGGTCCCGGCGGGTGCTGTA	0.677																																					p.R1176H		Atlas-SNP	.											KIAA1683_ENST00000392413,colon,carcinoma,0,2	KIAA1683	190	.	0			c.G3527A						.						21	26	24					19																	18368567		2079	4078	6157	SO:0001583	missense	80726	exon4			TCCCGGCGGGTGC	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.2966G>A	chr19.hg19:g.18368567C>T	ENSP00000470780:p.Arg989His	40.0	0.0		11.0	4.0	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Missense_Mutation	SNP	ENST00000600328.3	hg19	CCDS32958.1	.	.	.	.	.	.	.	.	.	.	C	18.87	3.715173	0.68844	.	.	ENSG00000130518	ENST00000392413;ENST00000359737;ENST00000427634;ENST00000392412;ENST00000411671	T;T;T	0.65549	-0.16;-0.16;-0.16	3.54	3.54	0.40534	.	0.000000	0.33253	N	0.005102	T	0.81550	0.4846	M	0.92412	3.305	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.72937	-0.4140	10	0.54805	T	0.06	-22.7126	11.3138	0.49379	0.0:1.0:0.0:0.0	.	1176;989	E9PDE0;Q9H0B3	.;K1683_HUMAN	H	1176;989;943;253;603	ENSP00000376213:R1176H;ENSP00000352774:R989H;ENSP00000404501:R943H	ENSP00000352774:R989H	R	-	2	0	KIAA1683	18229567	0.503000	0.26115	0.048000	0.18961	0.170000	0.22686	1.663000	0.37429	1.935000	0.56089	0.313000	0.20887	CGC	.	.		0.677	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3			T	18368567	C	T	18368567	3	4	280	1	0	0	0	0	1	0	0	0	8260	768	27	1	580	1	KIAA1683	19	18368567	Missense_Mutation	SNP	C	TCGA-G3-A3CH-01A-11D-A22F-10	3170201	18368567	40760416	38	40217										
UMODL1	89766	hgsc.bcm.edu	37	chr21	43529725	43529725	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	actgctcaccggctgcctggTgcatcaacctggagggctcc	12	15	2	0			TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chr21:43529725T>A	ENST00000408910.2	+	10	1573	c.1573T>A	c.(1573-1575)Tgc>Agc	p.C525S	C21orf128_ENST00000329015.2_5'Flank|UMODL1_ENST00000400427.1_Missense_Mutation_p.C453S|UMODL1_ENST00000400424.2_Missense_Mutation_p.C453S|UMODL1_ENST00000408989.2_Missense_Mutation_p.C525S	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	525	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				adipose tissue development (GO:0060612)|cellular response to gonadotropin-releasing hormone (GO:0097211)|multicellular organismal reproductive process (GO:0048609)|regulation of apoptotic process (GO:0042981)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|peptidase inhibitor activity (GO:0030414)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(22)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	47						GGCTGCCTGGTGCATCAACCT	0.642																																					p.C525S	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.T1573A						.						59	72	68					21																	43529725		2050	4178	6228	SO:0001583	missense	89766	exon10			GCCTGGTGCATCA		CCDS42935.1, CCDS42936.1, CCDS56214.1, CCDS56215.1	21q22.3	2008-07-04			ENSG00000177398	ENSG00000177398			12560	protein-coding gene	gene with protein product	"olfactorin"	613859				16026467	Standard	NM_173568		Approved		uc002zag.1	Q5DID0	OTTHUMG00000086788	ENST00000408910.2:c.1573T>A	chr21.hg19:g.43529725T>A	ENSP00000386147:p.Cys525Ser	24.0	0.0		14.0	8.0	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Missense_Mutation	SNP	ENST00000408910.2	hg19	CCDS42936.1	.	.	.	.	.	.	.	.	.	.	T	14.00	2.403961	0.42613	.	.	ENSG00000177398	ENST00000400427;ENST00000400424;ENST00000408989;ENST00000408910	D;D;D;D	0.99429	-5.75;-5.89;-5.75;-5.89	3.23	3.23	0.37069	EGF-like calcium-binding, conserved site (1);Epidermal growth factor-like (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.45126	D	0.000400	D	0.99582	0.9849	H	0.96430	3.82	0.51482	D	0.999929	D;D	0.89917	0.999;1.0	D;D	0.97110	0.999;1.0	D	0.98490	1.0609	10	0.87932	D	0	-25.068	8.2316	0.31601	0.0:0.0:0.0:1.0	.	525;525	Q5DID0-2;Q5DID0	.;UROL1_HUMAN	S	453;453;525;525	ENSP00000383279:C453S;ENSP00000383276:C453S;ENSP00000386126:C525S;ENSP00000386147:C525S	ENSP00000383276:C453S	C	+	1	0	UMODL1	42402794	1.000000	0.71417	0.858000	0.33744	0.253000	0.25986	3.453000	0.52978	1.722000	0.51474	0.533000	0.62120	TGC	.	.		0.642	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2			A	43529725	T	A	43529725	3	1	280	1	0	0	0	0	1	0	0	0	16995	1696	59	4	1611	4	UMODL1	21	43529725	Missense_Mutation	SNP	T	TCGA-G3-A3CH-01A-11D-A22F-10		43529725	4600170	39	40218										
LPAR4	2846	hgsc.bcm.edu	37	chrX	78010878	78010878	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0526315789473684	2	1	0.631292517006803	0	0.736507936507937	0.428571428571429	1	0	cctagtcctcagtggcggtaTttcagcctctttgttttcca	8	12	3	0			TCGA-G3-A3CH-01A-11D-A22F-10	TCGA-G3-A3CH-11A-11D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f57d294a-3b16-45e5-a1ff-1eaae9229aee	cd23964a-9449-49ed-a1db-32a3dfb922bb	g.chrX:78010878T>C	ENST00000435339.3	+	2	898	c.512T>C	c.(511-513)aTt>aCt	p.I171T		NM_005296.2	NP_005287.1	Q99677	LPAR4_HUMAN	lysophosphatidic acid receptor 4	171					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)			breast(3)|endometrium(3)|kidney(4)|large_intestine(4)|lung(16)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	38						AGTGGCGGTATTTCAGCCTCT	0.458																																					p.I171T		Atlas-SNP	.											.	LPAR4	83	.	0			c.T512C						.						120	85	97					X																	78010878		2203	4300	6503	SO:0001583	missense	2846	exon2			GCGGTATTTCAGC	U90322	CCDS14441.1	Xq21.1	2012-08-08	2008-04-11	2008-04-11	ENSG00000147145	ENSG00000147145		"GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"	4478	protein-coding gene	gene with protein product		300086	"G protein-coupled receptor 23"	GPR23			Standard	NM_005296		Approved	P2Y9, P2Y5-LIKE, P2RY9, LPA4	uc010nme.3	Q99677	OTTHUMG00000021895	ENST00000435339.3:c.512T>C	chrX.hg19:g.78010878T>C	ENSP00000408205:p.Ile171Thr	75.0	0.0		88.0	4.0	NM_005296	B2RAC7|O15132|Q502U9|Q6NSP5	Missense_Mutation	SNP	ENST00000435339.3	hg19	CCDS14441.1	.	.	.	.	.	.	.	.	.	.	T	10.90	1.482326	0.26598	.	.	ENSG00000147145	ENST00000435339;ENST00000373301	T;T	0.72835	-0.69;-0.69	4.2	4.2	0.49525	GPCR, rhodopsin-like superfamily (1);	0.117281	0.56097	D	0.000027	T	0.55257	0.1909	N	0.25031	0.7	0.49582	D	0.999807	B	0.25007	0.116	B	0.24006	0.05	T	0.53408	-0.8443	10	0.36615	T	0.2	.	11.3699	0.49694	0.0:0.0:0.0:1.0	.	171	Q99677	LPAR4_HUMAN	T	171	ENSP00000408205:I171T;ENSP00000362398:I171T	ENSP00000362398:I171T	I	+	2	0	LPAR4	77897534	1.000000	0.71417	1.000000	0.80357	0.829000	0.46940	5.721000	0.68477	1.558000	0.49541	0.339000	0.21740	ATT	.	.		0.458	LPAR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057322.2	NM_005296		C	78010878	T	C	78010878	3	2	280	1	0	0	0	0	1	0	0	0	8916	1493	52	2	514	2	LPAR4	23	78010878	Missense_Mutation	SNP	T	TCGA-G3-A3CH-01A-11D-A22F-10		78010878	77259682	40	40219										
PPAP2B	8613	hgsc.bcm.edu	37	chr1	56989987	56989987	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.133333333333333	2	1	2.10884353741497	0	2.46031746031746	0.333333333333333	1	0	ctgtcatcacctctgcatctGtagttctgaatgtagccttc	7	12	5	1			TCGA-G3-A3CI-01A-11D-A20W-10	TCGA-G3-A3CI-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03de17c7-1318-460c-966a-477083e6fbc1	4a2e4e6a-8fef-4c74-968b-c0e269634c4f	g.chr1:56989987G>A	ENST00000371250.3	-	3	1088	c.537C>T	c.(535-537)taC>taT	p.Y179Y		NM_003713.4	NP_003704.3	O14495	LPP3_HUMAN	phosphatidic acid phosphatase type 2B	179					Bergmann glial cell differentiation (GO:0060020)|blood vessel development (GO:0001568)|canonical Wnt signaling pathway involved in positive regulation of cell-cell adhesion (GO:0044329)|canonical Wnt signaling pathway involved in positive regulation of endothelial cell migration (GO:0044328)|canonical Wnt signaling pathway involved in positive regulation of wound healing (GO:0044330)|dephosphorylation (GO:0016311)|gastrulation with mouth forming second (GO:0001702)|germ cell migration (GO:0008354)|homotypic cell-cell adhesion (GO:0034109)|lipid metabolic process (GO:0006629)|negative regulation of protein phosphorylation (GO:0001933)|phospholipid metabolic process (GO:0006644)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein stabilization (GO:0050821)|regulation of sphingolipid mediated signaling pathway (GO:1902068)|regulation of Wnt signaling pathway (GO:0030111)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	adherens junction (GO:0005912)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lipid phosphatase activity (GO:0042577)|phosphatidate phosphatase activity (GO:0008195)|phosphoprotein phosphatase activity (GO:0004721)|sphingosine-1-phosphate phosphatase activity (GO:0042392)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	17						CTCTGCATCTGTAGTTCTGAA	0.532																																					p.Y179Y		Atlas-SNP	.											.	PPAP2B	30	.	0			c.C537T						.						138	134	136					1																	56989987		2203	4300	6503	SO:0001819	synonymous_variant	8613	exon3			GCATCTGTAGTTC	AB000889	CCDS604.1	1p32.2	2009-05-27			ENSG00000162407	ENSG00000162407	3.1.3.4		9229	protein-coding gene	gene with protein product		607125				9305923	Standard	NM_003713		Approved	PAP-2b, LPP3	uc001cyj.2	O14495	OTTHUMG00000008160	ENST00000371250.3:c.537C>T	chr1.hg19:g.56989987G>A		232.0	0.0		118.0	23.0	NM_003713	B2R651|D3DQ52|Q5U0F7|Q96GW0|Q99782	Silent	SNP	ENST00000371250.3	hg19	CCDS604.1																																																																																			.	.		0.532	PPAP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022334.2	NM_003713		A	56989987	G	A	56989987	2	1	281	1	0	0	0	0	0	0	0	1	12300	1372	48	3		3	PPAP2B	1	56989987	Silent	SNP	G	TCGA-G3-A3CI-01A-11D-A20W-10		56989987	192260634	1	40220										
CR1	1378	hgsc.bcm.edu	37	chr1	207787833	207787833	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.133333333333333	2	1	2.10884353741497	0	2.46031746031746	0.333333333333333	1	0	agcagtgttccagtgtgtgaAcgtgagtagaaagaactatg	13	5	0	4			TCGA-G3-A3CI-01A-11D-A20W-10	TCGA-G3-A3CI-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03de17c7-1318-460c-966a-477083e6fbc1	4a2e4e6a-8fef-4c74-968b-c0e269634c4f	g.chr1:207787833A>C	ENST00000367049.4	+	40	6660	c.6660A>C	c.(6658-6660)gaA>gaC	p.E2220D	CR1_ENST00000367052.1_Splice_Site_p.E1770D|CR1_ENST00000367053.1_Splice_Site_p.E1770D|CR1_ENST00000367051.1_Splice_Site_p.E1770D|CR1_ENST00000400960.2_Splice_Site_p.E1770D	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1770					complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						CAGTGTGTGAACGTGAGTAGA	0.403																																					p.E2220D		Atlas-SNP	.											.	CR1	354	.	0			c.A6660C						.						129	121	123					1																	207787833		1888	4127	6015	SO:0001630	splice_region_variant	1378	exon40			GTGTGAACGTGAG	Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"CD molecules", "Blood group antigens", "Complement system"	2334	protein-coding gene	gene with protein product		120620	"complement component (3b/4b) receptor 1, including Knops blood group system"			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.6661+1A>C	chr1.hg19:g.207787833A>C		201.0	0.0		143.0	27.0	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Missense_Mutation	SNP	ENST00000367049.4	hg19	CCDS44308.1	.	.	.	.	.	.	.	.	.	.	A	16.87	3.243171	0.58995	.	.	ENSG00000203710	ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000367049	T;T;T;T;T	0.25912	1.77;1.77;1.77;1.77;1.77	4.29	1.95	0.26073	Complement control module (2);Sushi/SCR/CCP (1);	.	.	.	.	T	0.43897	0.1268	M	0.81497	2.545	0.21473	N	0.999673	D;D	0.76494	0.999;0.997	D;D	0.75020	0.985;0.977	T	0.34925	-0.9809	9	0.14656	T	0.56	.	6.0899	0.19989	0.7817:0.0:0.2183:0.0	.	1770;2220	P17927;E9PDY4	CR1_HUMAN;.	D	1770;1770;1770;1770;2220	ENSP00000356019:E1770D;ENSP00000356018:E1770D;ENSP00000356020:E1770D;ENSP00000383744:E1770D;ENSP00000356016:E2220D	ENSP00000356016:E2220D	E	+	3	2	CR1	205854456	0.989000	0.36119	0.998000	0.56505	0.893000	0.52053	0.675000	0.25232	0.274000	0.22072	0.358000	0.22013	GAA	.	.		0.403	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573	Missense_Mutation	C	207787833	A	C	207787833	5	2	281	1	0	0	0	0	0	0	1	0	3842	57	2	5	6818	5	CR1	1	207787833	Splice_Site	SNP	A	TCGA-G3-A3CI-01A-11D-A20W-10	150797846	207787833	41462788	2	40221										
APOB	338	hgsc.bcm.edu	37	chr2	21249790	21249790	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.133333333333333	2	1	2.10884353741497	0	2.46031746031746	0.333333333333333	1	0	ggaaaaatccttgcttcccaAaaagagcttccaatgttggc	8	10	0	1			TCGA-G3-A3CI-01A-11D-A20W-10	TCGA-G3-A3CI-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03de17c7-1318-460c-966a-477083e6fbc1	4a2e4e6a-8fef-4c74-968b-c0e269634c4f	g.chr2:21249790A>G	ENST00000233242.1	-	15	2241	c.2114T>C	c.(2113-2115)tTt>tCt	p.F705S	APOB_ENST00000399256.4_Missense_Mutation_p.F705S	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	705					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTGCTTCCCAAAAAGAGCTTC	0.418																																					p.F705S		Atlas-SNP	.											.	APOB	761	.	0			c.T2114C						.						95	94	94					2																	21249790		2203	4300	6503	SO:0001583	missense	338	exon15			TTCCCAAAAAGAG	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.2114T>C	chr2.hg19:g.21249790A>G	ENSP00000233242:p.Phe705Ser	239.0	0.0		140.0	22.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	A	28.1	4.892049	0.91889	.	.	ENSG00000084674	ENST00000233242;ENST00000535079;ENST00000399256	T;T	0.25414	1.8;1.8	5.7	5.7	0.88788	Lipid transport protein, beta-sheet shell (1);Vitellinogen, open beta-sheet (1);	0.000000	0.85682	D	0.000000	T	0.55909	0.1950	M	0.82923	2.615	0.54753	D	0.999986	D	0.89917	1.0	D	0.97110	1.0	T	0.62072	-0.6931	10	0.87932	D	0	.	16.2838	0.82709	1.0:0.0:0.0:0.0	.	705	P04114	APOB_HUMAN	S	705	ENSP00000233242:F705S;ENSP00000382200:F705S	ENSP00000233242:F705S	F	-	2	0	APOB	21103295	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.896000	0.92521	2.308000	0.77769	0.533000	0.62120	TTT	.	.		0.418	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			G	21249790	A	G	21249790	3	3	281	1	0	0	0	0	1	0	0	0	785	14	1	2	11637	2	APOB	2	21249790	Missense_Mutation	SNP	A	TCGA-G3-A3CI-01A-11D-A20W-10		21249790	221949583	3	40222										
DNAH6	1768	hgsc.bcm.edu	37	chr2	84972221	84972221	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.133333333333333	2	1	2.10884353741497	0	2.46031746031746	0.333333333333333	1	0	caggatcttttgagacttatAttaacccacagaaatgggaa	8	7	1	2			TCGA-G3-A3CI-01A-11D-A20W-10	TCGA-G3-A3CI-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03de17c7-1318-460c-966a-477083e6fbc1	4a2e4e6a-8fef-4c74-968b-c0e269634c4f	g.chr2:84972221A>G	ENST00000237449.6	+	62	10368	c.10360A>G	c.(10360-10362)Att>Gtt	p.I3454V	DNAH6_ENST00000389394.3_Missense_Mutation_p.I3454V			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	3454					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						TGAGACTTATATTAACCCACA	0.313																																					p.I3454V		Atlas-SNP	.											.	DNAH6	194	.	0			c.A10360G						.						79	70	73					2																	84972221		692	1591	2283	SO:0001583	missense	1768	exon63			ACTTATATTAACC	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.10360A>G	chr2.hg19:g.84972221A>G	ENSP00000237449:p.Ile3454Val	122.0	0.0		79.0	22.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	hg19	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	A	8.787	0.929599	0.18131	.	.	ENSG00000115423	ENST00000389394;ENST00000237449	T;T	0.68624	-0.34;-0.34	5.51	4.34	0.51931	Dynein heavy chain (1);	0.358848	0.26828	N	0.022300	T	0.45875	0.1364	N	0.16903	0.455	0.80722	D	1	B;B	0.22003	0.063;0.003	B;B	0.19666	0.026;0.02	T	0.23583	-1.0184	10	0.12430	T	0.62	.	9.6915	0.40131	0.8253:0.1747:0.0:0.0	.	3454;213	Q9C0G6;Q9C0G6-2	DYH6_HUMAN;.	V	3454	ENSP00000374045:I3454V;ENSP00000237449:I3454V	ENSP00000237449:I3454V	I	+	1	0	DNAH6	84825732	0.990000	0.36364	0.944000	0.38274	0.923000	0.55619	3.218000	0.51192	0.923000	0.37045	0.460000	0.39030	ATT	.	.		0.313	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		G	84972221	A	G	84972221	3	3	281	1	0	0	0	0	1	0	0	0	4607	449	16	2	10606	2	DNAH6	2	84972221	Missense_Mutation	SNP	A	TCGA-G3-A3CI-01A-11D-A20W-10	63722431	84972221	158227152	4	40223										
NEB	4703	hgsc.bcm.edu	37	chr2	152466364	152466364	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.133333333333333	2	1	2.10884353741497	0	2.46031746031746	0.333333333333333	1	0	cttttttgcttggataatgtCgttttgatccggcatgcatg	10	7	0	1			TCGA-G3-A3CI-01A-11D-A20W-10	TCGA-G3-A3CI-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03de17c7-1318-460c-966a-477083e6fbc1	4a2e4e6a-8fef-4c74-968b-c0e269634c4f	g.chr2:152466364C>G	ENST00000172853.10	-	77	11707	c.11560G>C	c.(11560-11562)Gac>Cac	p.D3854H	NEB_ENST00000603639.1_Missense_Mutation_p.D4097H|NEB_ENST00000397345.3_Missense_Mutation_p.D4097H|NEB_ENST00000604864.1_Missense_Mutation_p.D4097H|NEB_ENST00000427231.2_Missense_Mutation_p.D4097H|NEB_ENST00000409198.1_Missense_Mutation_p.D3854H			P20929	NEBU_HUMAN	nebulin	3854					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TGGATAATGTCGTTTTGATCC	0.433																																					p.D4097H		Atlas-SNP	.											NEB_ENST00000427231,NS,carcinoma,0,3	NEB	1697	.	0			c.G12289C						.						223	208	213					2																	152466364		1960	4149	6109	SO:0001583	missense	4703	exon81			TAATGTCGTTTTG	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.11560G>C	chr2.hg19:g.152466364C>G	ENSP00000172853:p.Asp3854His	132.0	0.0		111.0	9.0	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	hg19		.	.	.	.	.	.	.	.	.	.	C	24.0	4.481740	0.84747	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.51817	0.69;0.69;0.69;0.69	5.55	5.55	0.83447	.	0.043254	0.85682	D	0.000000	T	0.75932	0.3917	M	0.89601	3.045	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.79329	-0.1848	10	0.56958	D	0.05	.	19.8667	0.96806	0.0:1.0:0.0:0.0	.	3854	P20929	NEBU_HUMAN	H	3854;4097;4097;3854	ENSP00000386259:D3854H;ENSP00000380505:D4097H;ENSP00000416578:D4097H;ENSP00000172853:D3854H	ENSP00000172853:D3854H	D	-	1	0	NEB	152174610	1.000000	0.71417	0.992000	0.48379	0.994000	0.84299	4.802000	0.62539	2.773000	0.95371	0.655000	0.94253	GAC	.	.		0.433	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		G	152466364	C	G	152466364	3	3	281	1	0	0	0	0	1	0	0	0	10311	884	31	4	13805	4	NEB	2	152466364	Missense_Mutation	SNP	C	TCGA-G3-A3CI-01A-11D-A20W-10	67494143	152466364	90733009	5	40224										
NCEH1	57552	hgsc.bcm.edu	37	chr3	172365871	172365871	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.133333333333333	2	1	2.10884353741497	0	2.46031746031746	0.333333333333333	1	0	aaaattcagtgccagcaggtGatggctcagtcccaggtagt	12	9	2	1			TCGA-G3-A3CI-01A-11D-A20W-10	TCGA-G3-A3CI-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03de17c7-1318-460c-966a-477083e6fbc1	4a2e4e6a-8fef-4c74-968b-c0e269634c4f	g.chr3:172365871G>A	ENST00000475381.1	-	2	405	c.172C>T	c.(172-174)Cac>Tac	p.H58Y	NCEH1_ENST00000538775.1_Missense_Mutation_p.H90Y|NCEH1_ENST00000543711.1_Intron|NCEH1_ENST00000273512.3_Missense_Mutation_p.H90Y			Q6PIU2	NCEH1_HUMAN	neutral cholesterol ester hydrolase 1	58				H -> R (in Ref. 2; BAH13028). {ECO:0000305}.	lipid catabolic process (GO:0016042)|protein dephosphorylation (GO:0006470)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carboxylic ester hydrolase activity (GO:0052689)|phosphate ion binding (GO:0042301)|serine hydrolase activity (GO:0017171)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|prostate(1)|skin(1)	15						GCCAGCAGGTGATGGCTCAGT	0.522																																					p.H90Y		Atlas-SNP	.											.	NCEH1	63	.	0			c.C268T						.						68	69	69					3																	172365871		2203	4300	6503	SO:0001583	missense	57552	exon2			GCAGGTGATGGCT	AB037784	CCDS54681.1, CCDS54682.1	3q26.31	2009-07-23	2009-07-23	2009-07-23	ENSG00000144959	ENSG00000144959			29260	protein-coding gene	gene with protein product		613234	"arylacetamide deacetylase-like 1"	AADACL1		10718198	Standard	NM_001146276		Approved	KIAA1363, NCEH	uc011bpx.2	Q6PIU2	OTTHUMG00000156872	ENST00000475381.1:c.172C>T	chr3.hg19:g.172365871G>A	ENSP00000418571:p.His58Tyr	149.0	0.0		81.0	16.0	NM_020792	B7Z2K4|B7Z3A1|B7Z5U2|B7Z906|B7ZAW6|F5H7K4|Q86WZ1|Q9P2I4	Missense_Mutation	SNP	ENST00000475381.1	hg19		.	.	.	.	.	.	.	.	.	.	G	9.731	1.162359	0.21538	.	.	ENSG00000144959	ENST00000475381;ENST00000538775;ENST00000273512	T;T;T	0.04234	3.68;3.69;3.67	5.96	5.96	0.96718	.	0.350311	0.34507	N	0.003917	T	0.05273	0.0140	L	0.31926	0.97	0.80722	D	1	B;B	0.12630	0.006;0.002	B;B	0.15052	0.012;0.005	T	0.26643	-1.0097	10	0.02654	T	1	-22.2593	20.422	0.99049	0.0:0.0:1.0:0.0	.	90;58	F5H7K4;Q6PIU2	.;NCEH1_HUMAN	Y	58;90;90	ENSP00000418571:H58Y;ENSP00000442464:H90Y;ENSP00000273512:H90Y	ENSP00000273512:H90Y	H	-	1	0	NCEH1	173848565	1.000000	0.71417	0.993000	0.49108	0.961000	0.63080	5.955000	0.70306	2.832000	0.97577	0.655000	0.94253	CAC	.	.		0.522	NCEH1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000346367.3	NM_020792		A	172365871	G	A	172365871	3	1	281	1	0	0	0	0	1	0	0	0	10224	1290	45	3	1094	3	NCEH1	3	172365871	Missense_Mutation	SNP	G	TCGA-G3-A3CI-01A-11D-A20W-10		172365871	25656559	6	40225										
NUP214	8021	hgsc.bcm.edu	37	chr9	134053778	134053778	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.133333333333333	2	1	2.10884353741497	0	2.46031746031746	0.333333333333333	1	0	aattgaagaataaccctgcaAccccttctacagccatgggg	8	12	1	2			TCGA-G3-A3CI-01A-11D-A20W-10	TCGA-G3-A3CI-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03de17c7-1318-460c-966a-477083e6fbc1	4a2e4e6a-8fef-4c74-968b-c0e269634c4f	g.chr9:134053778A>G	ENST00000359428.5	+	24	3544	c.3400A>G	c.(3400-3402)Acc>Gcc	p.T1134A	NUP214_ENST00000411637.2_Missense_Mutation_p.T1124A|NUP214_ENST00000451030.1_Missense_Mutation_p.T1135A			P35658	NU214_HUMAN	nucleoporin 214kDa	1134	11 X 5 AA approximate repeats.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		TAACCCTGCAACCCCTTCTAC	0.483			T	"DEK, SET, ABL1"	"AML, T-ALL"						OREG0019558	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T1134A	Pancreas(4;24 48 25510 30394 32571)	Atlas-SNP	.		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.	NUP214	166	.	0			c.A3400G						.						112	95	101					9																	134053778		2203	4300	6503	SO:0001583	missense	8021	exon24			CCTGCAACCCCTT	X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"nuclear pore complex protein Nup214", "CAN protein, putative oncogene"	114350	"nucleoporin 214kD (CAIN)"			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.3400A>G	chr9.hg19:g.134053778A>G	ENSP00000352400:p.Thr1134Ala	88.0	0.0	1607	53.0	18.0	NM_005085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Missense_Mutation	SNP	ENST00000359428.5	hg19	CCDS6940.1	.	.	.	.	.	.	.	.	.	.	A	0.638	-0.814402	0.02798	.	.	ENSG00000126883	ENST00000359428;ENST00000411637;ENST00000451030;ENST00000541375;ENST00000540899;ENST00000438605	T;T;T	0.29917	1.55;1.55;1.55	5.51	-5.68	0.02436	.	0.990981	0.08185	N	0.984862	T	0.09158	0.0226	N	0.08118	0	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.001;0.001	T	0.33240	-0.9876	10	0.02654	T	1	-0.348	2.6701	0.05065	0.4094:0.3081:0.1836:0.0989	.	1123;728;1124;1134	P35658-2;Q5JUP9;P35658-4;P35658	.;.;.;NU214_HUMAN	A	1134;1124;1135;1123;728;563	ENSP00000352400:T1134A;ENSP00000396576:T1124A;ENSP00000405014:T1135A	ENSP00000352400:T1134A	T	+	1	0	NUP214	133043599	0.000000	0.05858	0.000000	0.03702	0.118000	0.20060	-0.851000	0.04313	-0.942000	0.03695	-0.379000	0.06801	ACC	.	.		0.483	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085		G	134053778	A	G	134053778	3	3	281	1	0	0	0	0	1	0	0	0	10771	43	2	2	3494	2	NUP214	9	134053778	Missense_Mutation	SNP	A	TCGA-G3-A3CI-01A-11D-A20W-10		134053778	7159653	7	40226										
ARL5B	221079	hgsc.bcm.edu	37	chr10	18964121	18964121	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.133333333333333	2	1	2.10884353741497	0	2.46031746031746	0.333333333333333	1	0	tgccaaggtctagagtggatGacctcccggattggtgtgag	15	8	1	3			TCGA-G3-A3CI-01A-11D-A20W-10	TCGA-G3-A3CI-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03de17c7-1318-460c-966a-477083e6fbc1	4a2e4e6a-8fef-4c74-968b-c0e269634c4f	g.chr10:18964121G>A	ENST00000377275.3	+	6	749	c.516G>A	c.(514-516)atG>atA	p.M172I		NM_178815.3	NP_848930.1	Q96KC2	ARL5B_HUMAN	ADP-ribosylation factor-like 5B	172					small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)			lung(1)|ovary(1)	2						TAGAGTGGATGACCTCCCGGA	0.338																																					p.M172I		Atlas-SNP	.											.	ARL5B	12	.	0			c.G516A						.						159	153	155					10																	18964121		2203	4300	6503	SO:0001583	missense	221079	exon6			GTGGATGACCTCC	AF494061	CCDS7131.1	10p13	2014-05-09	2005-11-03	2005-11-03	ENSG00000165997	ENSG00000165997		"ADP-ribosylation factors-like", "ADP-ribosylation factors"	23052	protein-coding gene	gene with protein product		608909	"ADP-ribosylation factor-like 8"	ARL8		12853149	Standard	XM_005252400		Approved		uc001iqd.1	Q96KC2	OTTHUMG00000017765	ENST00000377275.3:c.516G>A	chr10.hg19:g.18964121G>A	ENSP00000366487:p.Met172Ile	172.0	0.0		109.0	22.0	NM_178815		Missense_Mutation	SNP	ENST00000377275.3	hg19	CCDS7131.1	.	.	.	.	.	.	.	.	.	.	G	13.85	2.359737	0.41801	.	.	ENSG00000165997	ENST00000377275	T	0.79554	-1.28	6.16	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.63745	0.2537	N	0.03050	-0.425	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.61505	-0.7049	10	0.87932	D	0	-29.7788	16.8211	0.85746	0.0:0.0:0.8703:0.1297	.	172	Q96KC2	ARL5B_HUMAN	I	172	ENSP00000366487:M172I	ENSP00000366487:M172I	M	+	3	0	ARL5B	19004127	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.018000	0.88722	1.580000	0.49851	0.650000	0.86243	ATG	.	.		0.338	ARL5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047078.1	NM_178815		A	18964121	G	A	18964121	3	1	281	1	0	0	0	0	1	0	0	0	940	1290	45	3	538	3	ARL5B	10	18964121	Missense_Mutation	SNP	G	TCGA-G3-A3CI-01A-11D-A20W-10		18964121	116570626	8	40227										
SLC22A12	116085	hgsc.bcm.edu	37	chr11	64367214	64367214	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.133333333333333	2	1	2.10884353741497	0	2.46031746031746	0.333333333333333	1	0	gccctgggcagcaacatcttCctgctccaaatgttcattgg	9	13	2	0			TCGA-G3-A3CI-01A-11D-A20W-10	TCGA-G3-A3CI-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03de17c7-1318-460c-966a-477083e6fbc1	4a2e4e6a-8fef-4c74-968b-c0e269634c4f	g.chr11:64367214C>T	ENST00000377574.1	+	7	1884	c.1137C>T	c.(1135-1137)ttC>ttT	p.F379F	SLC22A12_ENST00000377572.1_Silent_p.F271F|SLC22A12_ENST00000377567.2_Silent_p.F271F|SLC22A12_ENST00000336464.7_Silent_p.F345F|SLC22A12_ENST00000473690.1_Silent_p.F158F	NM_144585.2	NP_653186.2	Q96S37	S22AC_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 12	379					cellular homeostasis (GO:0019725)|response to drug (GO:0042493)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|urate transmembrane transporter activity (GO:0015143)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27					Losartan(DB00678)|Probenecid(DB01032)	GCAACATCTTCCTGCTCCAAA	0.662																																					p.F379F		Atlas-SNP	.											.	SLC22A12	68	.	0			c.C1137T						.						53	49	50					11																	64367214		2201	4297	6498	SO:0001819	synonymous_variant	116085	exon7			CATCTTCCTGCTC	AB071863	CCDS8075.1, CCDS60835.1, CCDS60836.1	11q13.1	2013-05-22	2008-01-11		ENSG00000197891	ENSG00000197891		"Solute carriers"	17989	protein-coding gene	gene with protein product		607096	"solute carrier family 22 (organic anion/cation transporter), member 12"			12024214	Standard	NM_144585		Approved	OAT4L, RST, URAT1	uc009yps.2	Q96S37	OTTHUMG00000045213	ENST00000377574.1:c.1137C>T	chr11.hg19:g.64367214C>T		304.0	0.0		120.0	27.0	NM_144585	B7WPG1|G3XAN7|Q19PF7|Q19PF8|Q19PF9|Q19PG0|Q6UXW3|Q96DT2	Silent	SNP	ENST00000377574.1	hg19	CCDS8075.1																																																																																			.	.		0.662	SLC22A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104966.2	NM_144585		T	64367214	C	T	64367214	2	4	281	1	0	0	0	0	0	0	0	1	14458	854	30	3		3	SLC22A12	11	64367214	Silent	SNP	C	TCGA-G3-A3CI-01A-11D-A20W-10		64367214	70639302	9	40228										
ADCY4	196883	hgsc.bcm.edu	37	chr14	24802167	24802167	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.133333333333333	2	1	2.10884353741497	0	2.46031746031746	0.333333333333333	1	0	cagcgcgcacagcacagtggTcaggaagctcgggtctgagg	16	11	2	1			TCGA-G3-A3CI-01A-11D-A20W-10	TCGA-G3-A3CI-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03de17c7-1318-460c-966a-477083e6fbc1	4a2e4e6a-8fef-4c74-968b-c0e269634c4f	g.chr14:24802167T>C	ENST00000310677.4	-	3	300	c.187A>G	c.(187-189)Acc>Gcc	p.T63A	ADCY4_ENST00000396747.3_5'UTR|ADCY4_ENST00000554068.2_Missense_Mutation_p.T63A|ADCY4_ENST00000558563.1_5'UTR|ADCY4_ENST00000418030.2_Missense_Mutation_p.T63A|RP11-934B9.3_ENST00000555591.1_Missense_Mutation_p.D129G	NM_001198568.1|NM_001198592.1|NM_139247.3	NP_001185497.1|NP_001185521.1|NP_640340.2	Q8NFM4	ADCY4_HUMAN	adenylate cyclase 4	63					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(265;0.0192)		AGCACAGTGGTCAGGAAGCTC	0.637											OREG0022624	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T63A		Atlas-SNP	.											.	ADCY4	86	.	0			c.A187G						.						28	37	34					14																	24802167		2203	4300	6503	SO:0001583	missense	196883	exon3			CAGTGGTCAGGAA	AF497516	CCDS9627.1	14q11.2	2013-02-04			ENSG00000129467	ENSG00000129467	4.6.1.1	"Adenylate cyclases"	235	protein-coding gene	gene with protein product		600292				7766992	Standard	NM_001198592		Approved	AC4	uc001woy.3	Q8NFM4	OTTHUMG00000029347	ENST00000310677.4:c.187A>G	chr14.hg19:g.24802167T>C	ENSP00000312126:p.Thr63Ala	174.0	0.0	774	63.0	12.0	NM_001198592	B3KV74|D3DS75|Q17R40|Q6ZTM6|Q96ML7	Missense_Mutation	SNP	ENST00000310677.4	hg19	CCDS9627.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.53|17.53	3.412633|3.412633	0.62511|0.62511	.|.	.|.	ENSG00000258973|ENSG00000129467	ENST00000555591|ENST00000310677;ENST00000554068;ENST00000418030	.|T;T;T	.|0.74842	.|-0.88;-0.88;-0.88	5.66|5.66	-1.06|-1.06	0.10002|0.10002	.|.	.|0.706766	.|0.12860	.|N	.|0.433237	T|T	0.39937|0.39937	0.1097|0.1097	N|N	0.02011|0.02011	-0.69|-0.69	0.80722|0.80722	D|D	1|1	.|B;B	.|0.14805	.|0.011;0.0	.|B;B	.|0.14023	.|0.01;0.001	T|T	0.14924|0.14924	-1.0455|-1.0455	5|10	.|0.13470	.|T	.|0.59	.|.	5.3003|5.3003	0.15773|0.15773	0.1456:0.4096:0.0:0.4448|0.1456:0.4096:0.0:0.4448	.|.	.|63;63	.|G3V258;Q8NFM4	.|.;ADCY4_HUMAN	G|A	129|63	.|ENSP00000312126:T63A;ENSP00000452250:T63A;ENSP00000393177:T63A	.|ENSP00000312126:T63A	D|T	-|-	2|1	0|0	RP11-934B9.3|ADCY4	23872007|23872007	0.429000|0.429000	0.25530|0.25530	0.998000|0.998000	0.56505|0.56505	0.988000|0.988000	0.76386|0.76386	-0.503000|-0.503000	0.06383|0.06383	0.112000|0.112000	0.17975|0.17975	0.454000|0.454000	0.30748|0.30748	GAC|ACC	.	.		0.637	ADCY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073200.4			C	24802167	T	C	24802167	3	2	281	1	0	0	0	0	1	0	0	0	296	1667	58	2	3142	2	ADCY4	14	24802167	Missense_Mutation	SNP	T	TCGA-G3-A3CI-01A-11D-A20W-10		24802167	82547373	10	40229										
SMOC1	64093	hgsc.bcm.edu	37	chr14	70490056	70490056	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.133333333333333	2	1	2.10884353741497	0	2.46031746031746	0.333333333333333	1	0	agcgctacgtgaagaagaaaGccaagcccaagaaatgtgcc	11	10	0	4			TCGA-G3-A3CI-01A-11D-A20W-10	TCGA-G3-A3CI-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03de17c7-1318-460c-966a-477083e6fbc1	4a2e4e6a-8fef-4c74-968b-c0e269634c4f	g.chr14:70490056G>A	ENST00000381280.4	+	11	1436	c.1183G>A	c.(1183-1185)Gcc>Acc	p.A395T	SMOC1_ENST00000361956.3_Missense_Mutation_p.A395T	NM_001034852.2|NM_022137.5	NP_001030024.1|NP_071420.1	Q9H4F8	SMOC1_HUMAN	SPARC related modular calcium binding 1	395					cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|eye development (GO:0001654)|limb development (GO:0060173)|positive regulation of cell-substrate adhesion (GO:0010811)|regulation of osteoblast differentiation (GO:0045667)|signal transduction (GO:0007165)	basement membrane (GO:0005604)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	21				all cancers(60;0.00417)|BRCA - Breast invasive adenocarcinoma(234;0.0119)|OV - Ovarian serous cystadenocarcinoma(108;0.028)		GAAGAAGAAAGCCAAGCCCAA	0.527																																					p.A395T		Atlas-SNP	.											.	SMOC1	61	.	0			c.G1183A						.						167	152	157					14																	70490056		2203	4300	6503	SO:0001583	missense	64093	exon11			AAGAAAGCCAAGC	AJ249900	CCDS9798.1, CCDS32110.1	14q24.1	2010-08-05			ENSG00000198732	ENSG00000198732			20318	protein-coding gene	gene with protein product		608488				12130637	Standard	NM_001034852		Approved		uc001xlt.2	Q9H4F8		ENST00000381280.4:c.1183G>A	chr14.hg19:g.70490056G>A	ENSP00000370680:p.Ala395Thr	195.0	0.0		100.0	19.0	NM_001034852	A8K1S3|B2R7P5|Q96F78	Missense_Mutation	SNP	ENST00000381280.4	hg19	CCDS9798.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.054462	0.75960	.	.	ENSG00000198732	ENST00000361956;ENST00000381280	T;T	0.57107	0.42;0.42	5.34	4.44	0.53790	SPARC/Testican, calcium-binding domain (1);EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.54902	0.1887	N	0.22421	0.69	0.58432	D	0.999996	D;P	0.58970	0.984;0.626	P;B	0.61201	0.885;0.393	T	0.51293	-0.8724	10	0.23891	T	0.37	-22.3305	15.7082	0.77602	0.0:0.0:0.862:0.138	.	395;395	Q9H4F8-2;Q9H4F8	.;SMOC1_HUMAN	T	395	ENSP00000355110:A395T;ENSP00000370680:A395T	ENSP00000355110:A395T	A	+	1	0	SMOC1	69559809	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.540000	0.73861	1.352000	0.45808	0.655000	0.94253	GCC	.	.		0.527	SMOC1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000412467.1			A	70490056	G	A	70490056	3	1	281	1	0	0	0	0	1	0	0	0	14816	971	34	3	1225	3	SMOC1	14	70490056	Missense_Mutation	SNP	G	TCGA-G3-A3CI-01A-11D-A20W-10	45687889	70490056	36859484	11	40230										
OR1E2	8388	hgsc.bcm.edu	37	chr17	3336389	3336389	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.133333333333333	2	1	2.10884353741497	0	2.46031746031746	0.333333333333333	1	0	acagagaggtgggagccacaAgtagagaaggccttgcagat	15	7	0	3			TCGA-G3-A3CI-01A-11D-A20W-10	TCGA-G3-A3CI-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03de17c7-1318-460c-966a-477083e6fbc1	4a2e4e6a-8fef-4c74-968b-c0e269634c4f	g.chr17:3336389A>T	ENST00000248384.1	-	1	746	c.747T>A	c.(745-747)acT>acA	p.T249T		NM_003554.1	NP_003545.1	P47887	OR1E2_HUMAN	olfactory receptor, family 1, subfamily E, member 2	249					sensory perception of chemical stimulus (GO:0007606)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)|receptor activity (GO:0004872)			endometrium(3)|large_intestine(3)|lung(3)	9						GGGAGCCACAAGTAGAGAAGG	0.473																																					p.T249T		Atlas-SNP	.											.	OR1E2	25	.	0			c.T747A						.						68	67	67					17																	3336389		2203	4300	6503	SO:0001819	synonymous_variant	8388	exon1			GCCACAAGTAGAG	U04686	CCDS11026.1	17p13.3	2012-08-09			ENSG00000127780	ENSG00000127780		"GPCR / Class A : Olfactory receptors"	8190	protein-coding gene	gene with protein product				OR1E4		8004088, 9500546	Standard	NM_003554		Approved	OR17-93, OR17-135	uc010vre.2	P47887	OTTHUMG00000090651	ENST00000248384.1:c.747T>A	chr17.hg19:g.3336389A>T		178.0	0.0		119.0	23.0	NM_003554	O43877|O95632|Q0VAD5|Q0VAD6|Q9UL13	Silent	SNP	ENST00000248384.1	hg19	CCDS11026.1																																																																																			.	.		0.473	OR1E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207311.1			T	3336389	A	T	3336389	2	4	281	1	0	0	0	0	0	0	0	1	10964	59	3	4		4	OR1E2	17	3336389	Silent	SNP	A	TCGA-G3-A3CI-01A-11D-A20W-10		3336389	77858821	12	40231										
CACNG8	59283	hgsc.bcm.edu	37	chr19	54483251	54483251	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.133333333333333	2	1	2.10884353741497	0	2.46031746031746	0.333333333333333	1	0	ctgggcgcagggatcctgttCgtggcagcaggtgagaggca	18	9	0	1	rs374385020		TCGA-G3-A3CI-01A-11D-A20W-10	TCGA-G3-A3CI-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03de17c7-1318-460c-966a-477083e6fbc1	4a2e4e6a-8fef-4c74-968b-c0e269634c4f	g.chr19:54483251C>T	ENST00000270458.2	+	3	601	c.498C>T	c.(496-498)ttC>ttT	p.F166F	MIR935_ENST00000401179.1_RNA	NM_031895.5	NP_114101	Q8WXS5	CCG8_HUMAN	calcium channel, voltage-dependent, gamma subunit 8	166					calcium ion transport (GO:0006816)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			kidney(1)|large_intestine(3)|lung(8)|urinary_tract(1)	13	all_cancers(19;0.0385)|all_epithelial(19;0.0207)|all_lung(19;0.145)|Lung NSC(19;0.168)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.162)		GGATCCTGTTCGTGGCAGCAG	0.677																																					p.F166F		Atlas-SNP	.											.	CACNG8	29	.	0			c.C498T						.	C		1,4403		0,1,2201	30	31	31		498	1.3	1	19		31	0,8596		0,0,4298	no	coding-synonymous	CACNG8	NM_031895.5		0,1,6499	TT,TC,CC		0.0,0.0227,0.0077		166/426	54483251	1,12999	2202	4298	6500	SO:0001819	synonymous_variant	59283	exon3			CCTGTTCGTGGCA	AF288388	CCDS33104.1	19q13.4	2008-05-02			ENSG00000142408	ENSG00000142408		"Calcium channel subunits"	13628	protein-coding gene	gene with protein product		606900				11170751	Standard	NM_031895		Approved		uc002qcs.2	Q8WXS5	OTTHUMG00000064908	ENST00000270458.2:c.498C>T	chr19.hg19:g.54483251C>T		93.0	0.0		59.0	4.0	NM_031895	Q9BXT0|Q9BY23	Silent	SNP	ENST00000270458.2	hg19	CCDS33104.1																																																																																			.	.		0.677	CACNG8-001	KNOWN	non_ATG_start|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139361.3			T	54483251	C	T	54483251	2	4	281	1	0	0	0	0	0	0	0	1	2565	883	31	1		1	CACNG8	19	54483251	Silent	SNP	C	TCGA-G3-A3CI-01A-11D-A20W-10		54483251	4645732	13	40232										
USP29	57663	hgsc.bcm.edu	37	chr19	57640050	57640050	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.133333333333333	2	1	2.10884353741497	0	2.46031746031746	0.333333333333333	1	0	tacataaagaaaggatgataTctctaaaggtatgtggattc	9	4	1	2			TCGA-G3-A3CI-01A-11D-A20W-10	TCGA-G3-A3CI-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03de17c7-1318-460c-966a-477083e6fbc1	4a2e4e6a-8fef-4c74-968b-c0e269634c4f	g.chr19:57640050T>A	ENST00000254181.4	+	4	461	c.7T>A	c.(7-9)Tct>Act	p.S3T	USP29_ENST00000598197.1_Missense_Mutation_p.S3T	NM_020903.2	NP_065954.1	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	3					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			breast(3)|endometrium(4)|kidney(3)|large_intestine(15)|lung(47)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		AAGGATGATATCTCTAAAGGT	0.333																																					p.S3T		Atlas-SNP	.											.	USP29	186	.	0			c.T7A						.						40	41	41					19																	57640050		2203	4300	6503	SO:0001583	missense	57663	exon4			ATGATATCTCTAA		CCDS33124.1	19q13.4	2008-06-23	2005-08-08			ENSG00000131864		"Ubiquitin-specific peptidases"	18563	protein-coding gene	gene with protein product		609546	"ubiquitin specific protease 29"			12838346	Standard	NM_020903		Approved		uc002qny.3	Q9HBJ7		ENST00000254181.4:c.7T>A	chr19.hg19:g.57640050T>A	ENSP00000254181:p.Ser3Thr	173.0	0.0		75.0	17.0	NM_020903		Missense_Mutation	SNP	ENST00000254181.4	hg19	CCDS33124.1	.	.	.	.	.	.	.	.	.	.	T	4.596	0.110769	0.08780	.	.	ENSG00000131864	ENST00000254181	T	0.47869	0.83	2.55	-1.61	0.08399	.	1.298900	0.05959	U	0.640204	T	0.23014	0.0556	N	0.11427	0.14	0.09310	N	1	B	0.27229	0.172	B	0.16289	0.015	T	0.12863	-1.0531	10	0.18276	T	0.48	-0.9375	5.6961	0.17857	0.0:0.4567:0.0:0.5433	.	3	Q9HBJ7	UBP29_HUMAN	T	3	ENSP00000254181:S3T	ENSP00000254181:S3T	S	+	1	0	USP29	62331862	0.000000	0.05858	0.000000	0.03702	0.067000	0.16453	-0.245000	0.08890	-0.275000	0.09219	-0.326000	0.08463	TCT	.	.		0.333	USP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465075.1			A	57640050	T	A	57640050	3	1	281	1	0	0	0	0	1	0	0	0	17074	1435	50	4	9	4	USP29	19	57640050	Missense_Mutation	SNP	T	TCGA-G3-A3CI-01A-11D-A20W-10	3156799	57640050	1488933	14	40233										
TRPM2	7226	hgsc.bcm.edu	37	chr21	45833800	45833800	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.133333333333333	2	1	2.10884353741497	0	2.46031746031746	0.333333333333333	1	0	acttcaacccggagcactgcAgccccaatggcaccgacccc	8	19	1	0			TCGA-G3-A3CI-01A-11D-A20W-10	TCGA-G3-A3CI-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	03de17c7-1318-460c-966a-477083e6fbc1	4a2e4e6a-8fef-4c74-968b-c0e269634c4f	g.chr21:45833800A>T	ENST00000397928.1	+	20	3434	c.2989A>T	c.(2989-2991)Agc>Tgc	p.S997C	AP001065.2_ENST00000423310.1_RNA|TRPM2_ENST00000300482.5_Missense_Mutation_p.S997C|TRPM2_ENST00000300481.9_Missense_Mutation_p.S977C|TRPM2_ENST00000397932.2_Missense_Mutation_p.S997C|AP001065.2_ENST00000456880.1_RNA|TRPM2_ENST00000498430.1_3'UTR	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	997					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)			breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						GGAGCACTGCAGCCCCAATGG	0.632																																					p.S997C		Atlas-SNP	.											.	TRPM2	196	.	0			c.A2989T						.						172	178	176					21																	45833800		2203	4300	6503	SO:0001583	missense	7226	exon20			CACTGCAGCCCCA	AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"Voltage-gated ion channels / Transient receptor potential cation channels", "Nudix motif containing"	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.2989A>T	chr21.hg19:g.45833800A>T	ENSP00000381023:p.Ser997Cys	163.0	0.0		83.0	16.0	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Missense_Mutation	SNP	ENST00000397928.1	hg19	CCDS13710.1	.	.	.	.	.	.	.	.	.	.	A	26.7	4.764643	0.89932	.	.	ENSG00000142185	ENST00000300482;ENST00000397928;ENST00000300481;ENST00000397932	T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18	4.78	4.78	0.61160	Ion transport (1);	0.000000	0.85682	D	0.000000	T	0.80571	0.4648	M	0.84846	2.72	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.995;0.995;0.995	D	0.84254	0.0479	10	0.72032	D	0.01	-34.9615	14.6241	0.68608	1.0:0.0:0.0:0.0	.	997;783;997	E9PGK7;Q5KTC1;O94759	.;.;TRPM2_HUMAN	C	997;997;977;997	ENSP00000300482:S997C;ENSP00000381023:S997C;ENSP00000300481:S977C;ENSP00000381026:S997C	ENSP00000300481:S977C	S	+	1	0	TRPM2	44658228	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	8.645000	0.91049	1.923000	0.55706	0.482000	0.46254	AGC	.	.		0.632	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307		T	45833800	A	T	45833800	3	4	281	1	0	0	0	0	1	0	0	0	16601	188	7	4	3067	4	TRPM2	21	45833800	Missense_Mutation	SNP	A	TCGA-G3-A3CI-01A-11D-A20W-10		45833800	2296095	15	40234										
TAS1R3	83756	hgsc.bcm.edu	37	chr1	1267320	1267320	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cttcttcctcatgccccaggTgggcgccccccaccatcacc	7	21	3	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:1267320T>G	ENST00000339381.5	+	2	524		c.e2+2			NM_152228.1	NP_689414	Q7RTX0	TS1R3_HUMAN	taste receptor, type 1, member 3						detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			kidney(2)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.88e-21)|Colorectal(212;0.000157)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00251)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.146)		ATGCCCCAGGTGGGCGCCCCC	0.662																																					.		Atlas-SNP	.											.	TAS1R3	39	.	0			c.492+2T>G						.						25	31	29					1																	1267320		2190	4264	6454	SO:0001630	splice_region_variant	83756	exon2			CCCAGGTGGGCGC	AC026283	CCDS30556.1	1p36	2012-08-22			ENSG00000169962	ENSG00000169962		"Taste receptors / Type 1", "GPCR / Unclassified : Taste receptors"	15661	protein-coding gene	gene with protein product		605865				11319557	Standard	XM_006710939		Approved	T1R3	uc010nyk.2	Q7RTX0	OTTHUMG00000003071	ENST00000339381.5:c.492+2T>G	chr1.hg19:g.1267320T>G		325.0	0.0		206.0	9.0	NM_152228	Q5TA49|Q8NGW9	Splice_Site	SNP	ENST00000339381.5	hg19	CCDS30556.1	.	.	.	.	.	.	.	.	.	.	T	9.811	1.183254	0.21870	.	.	ENSG00000169962	ENST00000339381	.	.	.	4.75	4.75	0.60458	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.429	0.44395	0.0:0.0:0.1637:0.8363	.	.	.	.	.	-1	.	.	.	+	.	.	TAS1R3	1257183	1.000000	0.71417	0.949000	0.38748	0.337000	0.28794	7.860000	0.86993	1.790000	0.52503	0.459000	0.35465	.	.	.		0.662	TAS1R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008493.1		Intron	G	1267320	T	G	1267320	5	3	282	1	0	0	0	0	0	0	1	0	15579	1710	59	5	500	5	TAS1R3	1	1267320	Splice_Site	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10		1267320	247983301	1	40235										
ATAD3B	83858	hgsc.bcm.edu	37	chr1	1431107	1431107	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tttaggatatgctcctggatGgggactgggctgtgcccagg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:1431107delG	ENST00000308647.7	+	16	1973	c.1857delG	c.(1855-1857)atgfs	p.M619fs		NM_031921.4	NP_114127.3	Q5T9A4	ATD3B_HUMAN	ATPase family, AAA domain containing 3B	619						mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(2)|urinary_tract(1)	10	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		GCTCCTGGATGGGGACTGGGC	0.667																																					p.M619fs		Atlas-INDEL	.											.	ATAD3B	68	.	0			c.1856delT						.						40	41	41					1																	1431107		2201	4300	6501	SO:0001589	frameshift_variant	83858	exon16			.	AL834179	CCDS30.1	1p36.33	2010-04-21		2007-02-08	ENSG00000160072	ENSG00000160072		"ATPases / AAA-type"	24007	protein-coding gene	gene with protein product		612317				10574462	Standard	XM_005244806		Approved	TOB3, KIAA1273	uc001afv.3	Q5T9A4	OTTHUMG00000000577	ENST00000308647.7:c.1857delG	chr1.hg19:g.1431107delG	ENSP00000311766:p.Met619fs	324.0	0.0		225.0	14.0	NM_031921	A8K3H1|Q6ZRB5|Q9BUK4|Q9ULE7	Frame_Shift_Del	DEL	ENST00000308647.7	hg19	CCDS30.1																																																																																			.	.		0.667	ATAD3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001369.2	NM_031921		-	1431107	G	-	1431107	7	5	282	1	0	1	0	1	0	0	0	0	1074	1348	47	0	1919	0	ATAD3B	1	1431107	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	163787	1431107	247819514	2	40236										
CALML6	163688	hgsc.bcm.edu	37	chr1	1848432	1848432	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggtacgtgctaatgaacgcaGgggagcccctcaacgaggtg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:1848432delG	ENST00000307786.3	+	5	872	c.418delG	c.(418-420)gggfs	p.G140fs	CALML6_ENST00000462293.1_3'UTR	NM_138705.2	NP_619650.2	Q8TD86	CALL6_HUMAN	calmodulin-like 6	140	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(1)|kidney(1)|lung(1)|prostate(2)	7	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.61e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.94e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.83e-23)|GBM - Glioblastoma multiforme(42;3.23e-08)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00437)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)		AATGAACGCAGGGGAGCCCCT	0.667																																					p.A139fs		Atlas-INDEL	.											.	CALML6	18	.	0			c.417delA						.						72	62	65					1																	1848432		2203	4298	6501	SO:0001589	frameshift_variant	163688	exon5			.	AF490905	CCDS30566.1	1p36.33	2013-01-10			ENSG00000169885	ENSG00000169885		"EF-hand domain containing"	24193	protein-coding gene	gene with protein product		610171					Standard	NM_138705		Approved	CAGLP	uc001aih.1	Q8TD86	OTTHUMG00000000943	ENST00000307786.3:c.418delG	chr1.hg19:g.1848432delG	ENSP00000304643:p.Gly140fs	146.0	0.0		126.0	10.0	NM_138705	A2A2M3|Q6Q2C4	Frame_Shift_Del	DEL	ENST00000307786.3	hg19	CCDS30566.1																																																																																			.	.		0.667	CALML6-004	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276929.1	NM_138705		-	1848432	G	-	1848432	7	5	282	1	0	1	0	1	0	0	0	0	2592	1000	35	0	436	0	CALML6	1	1848432	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	417325	1848432	247402189	3	40237										
PANK4	55229	hgsc.bcm.edu	37	chr1	2441359	2441359	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagcagcagcctctcttcctGgagcgcagagctgccagata	11	14	1	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:2441359G>C	ENST00000378466.3	-	18	2062	c.2050C>G	c.(2050-2052)Cag>Gag	p.Q684E	PANK4_ENST00000435556.3_Missense_Mutation_p.Q645E	NM_018216.1	NP_060686.1	Q9NVE7	PANK4_HUMAN	pantothenate kinase 4	684			Q -> R (in dbSNP:rs2494620). {ECO:0000269|Ref.2}.		coenzyme A biosynthetic process (GO:0015937)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)			breast(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	23	all_cancers(77;0.000158)|all_epithelial(69;8.01e-05)|all_lung(157;0.0212)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.18e-20)|all_lung(118;1.67e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;1.54e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.95e-23)|GBM - Glioblastoma multiforme(42;2.81e-08)|Colorectal(212;4.25e-05)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.00445)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.201)		CTCTCTTCCTGGAGCGCAGAG	0.657																																					p.Q684E		Atlas-SNP	.											PANK4,NS,lymphoid_neoplasm,+1,1	PANK4	64	.	0			c.C2050G						.						46	54	52					1																	2441359		2198	4296	6494	SO:0001583	missense	55229	exon18			CTTCCTGGAGCGC	AK001644	CCDS42.1	1p36.32	2008-02-05			ENSG00000157881	ENSG00000157881			19366	protein-coding gene	gene with protein product		606162				11479594	Standard	XR_241034		Approved	FLJ10782	uc001ajm.1	Q9NVE7	OTTHUMG00000000791	ENST00000378466.3:c.2050C>G	chr1.hg19:g.2441359G>C	ENSP00000367727:p.Gln684Glu	231.0	0.0		189.0	0.0	NM_018216	B9DI84|Q53EU3|Q5TA84|Q7RTX3|Q9H3X5	Missense_Mutation	SNP	ENST00000378466.3	hg19	CCDS42.1	.	.	.	.	.	.	.	.	.	.	G	0.133	-1.111755	0.01813	.	.	ENSG00000157881	ENST00000378466;ENST00000435556	T;T	0.06068	3.35;3.35	5.03	-5.43	0.02632	Domain of unknown function DUF89 (2);	0.544208	0.20048	N	0.100373	T	0.01661	0.0053	N	0.03050	-0.425	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.38156	-0.9674	10	0.02654	T	1	-0.009	8.3957	0.32555	0.0:0.2361:0.5253:0.2386	.	645;684	E9PHT6;Q9NVE7	.;PANK4_HUMAN	E	684;645	ENSP00000367727:Q684E;ENSP00000421433:Q645E	ENSP00000367727:Q684E	Q	-	1	0	PANK4	2431219	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.211000	0.17474	-1.004000	0.03421	-0.397000	0.06425	CAG	.	.		0.657	PANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002082.1			C	2441359	G	C	2441359	3	2	282	1	0	0	0	0	1	0	0	0	11428	1357	47	4	279	4	PANK4	1	2441359	Missense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	592927	2441359	246809262	4	40238										
ICMT	23463	hgsc.bcm.edu	37	chr1	6293699	6293699	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaacaatgacagggagcacaTgtacctatttaaagacaaaa	8	7	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:6293699T>C	ENST00000343813.5	-	3	317	c.289A>G	c.(289-291)Atg>Gtg	p.M97V	LINC00337_ENST00000441724.1_RNA	NM_012405.3	NP_036537.1	O60725	ICMT_HUMAN	isoprenylcysteine carboxyl methyltransferase	97					C-terminal protein methylation (GO:0006481)|cellular protein modification process (GO:0006464)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|multicellular organism growth (GO:0035264)|positive regulation of cell proliferation (GO:0008284)|protein targeting to membrane (GO:0006612)|regulation of Ras protein signal transduction (GO:0046578)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	cAMP response element binding protein binding (GO:0008140)|protein C-terminal carboxyl O-methyltransferase activity (GO:0003880)|protein C-terminal S-isoprenylcysteine carboxyl O-methyltransferase activity (GO:0004671)			NS(1)|endometrium(2)	3	Ovarian(185;0.0634)	all_cancers(23;5.85e-39)|all_epithelial(116;2.4e-22)|all_lung(118;2.65e-08)|Lung NSC(185;6.45e-07)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000688)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211)		Epithelial(90;5.52e-38)|GBM - Glioblastoma multiforme(13;6.51e-32)|OV - Ovarian serous cystadenocarcinoma(86;3.03e-19)|Colorectal(212;7.08e-08)|COAD - Colon adenocarcinoma(227;8.35e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(365;0.00109)|STAD - Stomach adenocarcinoma(132;0.00313)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)		AGGGAGCACATGTACCTATTT	0.423																																					p.M97V		Atlas-SNP	.											.	ICMT	13	.	0			c.A289G						.						77	74	75					1																	6293699		2203	4300	6503	SO:0001583	missense	23463	exon3			AGCACATGTACCT	AF064084	CCDS61.1	1p36	2010-04-29			ENSG00000116237	ENSG00000116237	2.1.1.100		5350	protein-coding gene	gene with protein product	"protein-S-isoprenylcysteine O-methyltransferase"	605851				9614111, 10441503	Standard	XM_005263437		Approved	PCCMT, HSTE14, PPMT	uc001amk.3	O60725	OTTHUMG00000001254	ENST00000343813.5:c.289A>G	chr1.hg19:g.6293699T>C	ENSP00000343552:p.Met97Val	120.0	0.0		95.0	4.0	NM_012405	Q6FHT0	Missense_Mutation	SNP	ENST00000343813.5	hg19	CCDS61.1	.	.	.	.	.	.	.	.	.	.	T	3.940	-0.014327	0.07681	.	.	ENSG00000116237	ENST00000343813;ENST00000535068	.	.	.	5.83	4.69	0.59074	.	0.090275	0.85682	N	0.000000	T	0.39145	0.1067	L	0.31926	0.97	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.15178	-1.0446	9	0.10636	T	0.68	.	6.0053	0.19542	0.0:0.2443:0.0:0.7557	.	97	O60725	ICMT_HUMAN	V	97;1	.	ENSP00000343552:M97V	M	-	1	0	ICMT	6216286	1.000000	0.71417	0.983000	0.44433	0.968000	0.65278	3.181000	0.50903	1.013000	0.39391	0.533000	0.62120	ATG	.	.		0.423	ICMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003681.1	NM_012405		C	6293699	T	C	6293699	3	2	282	1	0	0	0	0	1	0	0	0	7494	1464	51	2	577	2	ICMT	1	6293699	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3852340	6293699	242956922	5	40239										
PLEKHG5	57449	hgsc.bcm.edu	37	chr1	6536010	6536010	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccctttgccatccacagagcTctcctcctcctcctcctcca	3	22	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:6536010T>C	ENST00000400915.3	-	4	364	c.298A>G	c.(298-300)Agc>Ggc	p.S100G	PLEKHG5_ENST00000377740.3_Missense_Mutation_p.S121G|PLEKHG5_ENST00000535355.1_Missense_Mutation_p.S113G|PLEKHG5_ENST00000377748.1_Missense_Mutation_p.S121G|PLEKHG5_ENST00000537245.1_Missense_Mutation_p.S123G|PLEKHG5_ENST00000400913.1_Missense_Mutation_p.S44G|PLEKHG5_ENST00000377728.3_Missense_Mutation_p.S44G|PLEKHG5_ENST00000377725.1_Missense_Mutation_p.S44G|PLEKHG5_ENST00000340850.5_Missense_Mutation_p.S44G|PLEKHG5_ENST00000377737.2_Missense_Mutation_p.S44G|PLEKHG5_ENST00000544978.1_Missense_Mutation_p.S44G|PLEKHG5_ENST00000377732.1_Missense_Mutation_p.S81G	NM_001042663.1	NP_001036128.1	O94827	PKHG5_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 5	100					apoptotic signaling pathway (GO:0097190)|endothelial cell chemotaxis (GO:0035767)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			liver(1)	1	Ovarian(185;0.02)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;5.51e-35)|GBM - Glioblastoma multiforme(13;3.57e-27)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00159)|READ - Rectum adenocarcinoma(331;0.0419)		TCCACAGAGCTCTCCTCCTCC	0.632											OREG0013041	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S123G		Atlas-SNP	.											.,1	PLEKHG5	66	.	0			c.A367G						.						108	107	107					1																	6536010		2203	4300	6503	SO:0001583	missense	57449	exon4			CAGAGCTCTCCTC	AK024676	CCDS79.1, CCDS41240.1, CCDS41241.1, CCDS57967.1, CCDS57968.1, CCDS57969.1	1p36.31	2014-09-17		2005-08-09	ENSG00000171680	ENSG00000171680		"Pleckstrin homology (PH) domain containing"	29105	protein-coding gene	gene with protein product	"synectin-binding guanine exchange factor"	611101				17564964	Standard	NM_001042663		Approved	KIAA0720, Syx, GEF720, Tech	uc010nzr.1	O94827	OTTHUMG00000000905	ENST00000400915.3:c.298A>G	chr1.hg19:g.6536010T>C	ENSP00000383706:p.Ser100Gly	167.0	0.0	634	93.0	4.0	NM_001265592	B3KU07|B7Z2M3|B7Z5X2|F5GZ21|F5H1I0|Q5SY17|Q5T8W5|Q5T8W9|Q6ZNM0|Q7Z436|Q86YD8|Q96BS1	Missense_Mutation	SNP	ENST00000400915.3	hg19	CCDS41241.1	.	.	.	.	.	.	.	.	.	.	T	2.162	-0.391982	0.04932	.	.	ENSG00000171680	ENST00000377748;ENST00000340850;ENST00000400913;ENST00000400915;ENST00000377740;ENST00000377732;ENST00000377728;ENST00000377725;ENST00000535355;ENST00000377737;ENST00000537245;ENST00000544978	T;T;T;T;T;T;T;T;T;T;T;T	0.70045	-0.43;-0.43;-0.43;-0.4;-0.37;-0.39;-0.43;-0.41;-0.39;-0.43;-0.45;-0.41	4.44	-1.08	0.09936	.	0.345630	0.27060	N	0.021124	T	0.30135	0.0755	N	0.01482	-0.84	0.09310	N	1	B;B;B;B;B	0.06786	0.001;0.0;0.0;0.001;0.0	B;B;B;B;B	0.04013	0.001;0.0;0.001;0.001;0.0	T	0.21211	-1.0252	10	0.25751	T	0.34	-9.0471	5.98	0.19401	0.1808:0.6279:0.0:0.1913	.	113;44;121;121;100	F5GZ21;O94827-4;Q5SY18;O94827-2;O94827	.;.;.;.;PKHG5_HUMAN	G	121;44;44;100;121;81;44;44;113;44;123;44	ENSP00000366977:S121G;ENSP00000344570:S44G;ENSP00000383704:S44G;ENSP00000383706:S100G;ENSP00000366969:S121G;ENSP00000366961:S81G;ENSP00000366957:S44G;ENSP00000366954:S44G;ENSP00000441445:S113G;ENSP00000366966:S44G;ENSP00000439625:S123G;ENSP00000437710:S44G	ENSP00000344570:S44G	S	-	1	0	PLEKHG5	6458597	0.012000	0.17670	0.002000	0.10522	0.079000	0.17450	0.231000	0.17872	-0.311000	0.08754	0.260000	0.18958	AGC	.	.		0.632	PLEKHG5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002631.1	NM_020631		C	6536010	T	C	6536010	3	2	282	1	0	0	0	0	1	0	0	0	12082	1551	54	2	2966	2	PLEKHG5	1	6536010	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	242311	6536010	242714611	6	40240										
ENO1	2023	hgsc.bcm.edu	37	chr1	8926380	8926380	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gggagcaaacccgccttcatCccccacattggtggcatctt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:8926380delC	ENST00000234590.4	-	7	744	c.625delG	c.(625-627)gatfs	p.D209fs		NM_001428.3	NP_001419.1	P06733	ENOA_HUMAN	enolase 1, (alpha)	209	Required for repression of c-myc promoter activity.				carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|negative regulation of cell growth (GO:0030308)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|response to virus (GO:0009615)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|phosphopyruvate hydratase complex (GO:0000015)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|phosphopyruvate hydratase activity (GO:0004634)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	10	Ovarian(185;0.0661)|all_lung(157;0.127)	all_epithelial(116;2.54e-20)|all_lung(118;2.99e-06)|Lung NSC(185;6.25e-06)|Renal(390;0.000147)|Breast(348;0.00086)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;2.42e-07)|COAD - Colon adenocarcinoma(227;2.78e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.00177)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|READ - Rectum adenocarcinoma(331;0.0642)		CCGCCTTCATCCCCCACATTG	0.542																																					p.D209fs	Esophageal Squamous(21;302 608 19946 22210 33560)	Atlas-INDEL	.											.	ENO1	38	.	0			c.626delA						.						116	111	113					1																	8926380		2203	4300	6503	SO:0001589	frameshift_variant	2023	exon7			.	BC022545	CCDS97.1	1p36.2	2010-03-11			ENSG00000074800	ENSG00000074800	4.2.1.11		3350	protein-coding gene	gene with protein product		172430		ENO1L1, MPB1		9653645, 9691177	Standard	NM_001428		Approved	PPH, MBP-1	uc001apj.2	P06733	OTTHUMG00000001773	ENST00000234590.4:c.625delG	chr1.hg19:g.8926380delC	ENSP00000234590:p.Asp209fs	190.0	0.0		118.0	10.0	NM_001428	B2RD59|P22712|Q16704|Q4TUS4|Q53FT9|Q53HR3|Q658M5|Q6GMP2|Q71V37|Q7Z3V6|Q8WU71|Q96GV1|Q9BT62|Q9UCH6|Q9UM55	Frame_Shift_Del	DEL	ENST00000234590.4	hg19	CCDS97.1																																																																																			.	.		0.542	ENO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004945.1	NM_001428		-	8926380	C	-	8926380	7	5	282	1	0	1	0	1	0	0	0	0	5123	855	30	0	703	0	ENO1	1	8926380	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	2390370	8926380	240324241	7	40241										
CLSTN1	22883	hgsc.bcm.edu	37	chr1	9790636	9790636	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cgttctgggggtcgccctgcTccccctcctcctcctcgctg	10	20	1	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:9790636T>C	ENST00000377298.4	-	19	3668	c.2876A>G	c.(2875-2877)gAg>gGg	p.E959G	CLSTN1_ENST00000377288.3_Missense_Mutation_p.E940G|CLSTN1_ENST00000361311.4_Missense_Mutation_p.E949G|CLSTN1_ENST00000477264.1_5'UTR	NM_001009566.1	NP_001009566.1	O94985	CSTN1_HUMAN	calsyntenin 1	959	Glu-rich (highly acidic).				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	beta-amyloid binding (GO:0001540)|calcium ion binding (GO:0005509)|kinesin binding (GO:0019894)|X11-like protein binding (GO:0042988)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(9)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	36	all_lung(157;0.222)	all_lung(284;4.03e-05)|Lung NSC(185;6.93e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;8.36e-08)|COAD - Colon adenocarcinoma(227;1.93e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|STAD - Stomach adenocarcinoma(132;0.00644)|READ - Rectum adenocarcinoma(331;0.0419)		GTCGCCCTGCTCCCCCTCCTC	0.647																																					p.E959G		Atlas-SNP	.											.	CLSTN1	88	.	0			c.A2876G						.						98	81	87					1																	9790636		2203	4300	6503	SO:0001583	missense	22883	exon19			CCCTGCTCCCCCT	AB020718	CCDS105.1, CCDS30580.1	1p36.22	2011-07-01			ENSG00000171603	ENSG00000171603		"Cadherins / Cadherin-related"	17447	protein-coding gene	gene with protein product	"cadherin-related family member 12"	611321				10048485	Standard	XM_005263432		Approved	CSTN1, KIAA0911, CDHR12	uc001aqh.3	O94985	OTTHUMG00000001451	ENST00000377298.4:c.2876A>G	chr1.hg19:g.9790636T>C	ENSP00000366513:p.Glu959Gly	83.0	0.0		93.0	4.0	NM_001009566	A8K183|Q5SR52|Q5UE58|Q71MN0|Q8N4K9	Missense_Mutation	SNP	ENST00000377298.4	hg19	CCDS30580.1	.	.	.	.	.	.	.	.	.	.	T	9.798	1.179632	0.21787	.	.	ENSG00000171603	ENST00000377298;ENST00000361311;ENST00000435891;ENST00000377288;ENST00000539822	T;T;T;T	0.05649	3.41;3.41;3.41;3.41	5.19	-1.11	0.09840	.	0.347275	0.28706	N	0.014410	T	0.03434	0.0099	N	0.24115	0.695	0.44619	D	0.997595	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.47724	-0.9095	10	0.24483	T	0.36	-10.8934	5.5378	0.17021	0.0:0.3988:0.1509:0.4503	.	940;949;959;314	B4E3Q1;O94985-2;O94985;B3KMD3	.;.;CSTN1_HUMAN;.	G	959;949;760;940;940	ENSP00000366513:E959G;ENSP00000354997:E949G;ENSP00000401934:E760G;ENSP00000366502:E940G	ENSP00000354997:E949G	E	-	2	0	CLSTN1	9713223	0.998000	0.40836	0.067000	0.19924	0.690000	0.40134	0.820000	0.27323	-0.157000	0.11059	0.533000	0.62120	GAG	.	.		0.647	CLSTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004239.1			C	9790636	T	C	9790636	3	2	282	1	0	0	0	0	1	0	0	0	3563	1551	54	2	73	2	CLSTN1	1	9790636	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	864256	9790636	239459985	8	40242										
VPS13D	55187	hgsc.bcm.edu	37	chr1	12336449	12336449	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agactccgtaatgaatttaaCccagagcattgtgttgttgg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:12336449delC	ENST00000358136.3	+	19	2934	c.2804delC	c.(2803-2805)accfs	p.T935fs	VPS13D_ENST00000356315.4_Frame_Shift_Del_p.T935fs	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		ATGAATTTAACCCAGAGCATT	0.478											OREG0013110	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T935fs		Atlas-INDEL	.											.	VPS13D	316	.	0			c.2803delA						.						49	51	50					1																	12336449		2203	4300	6503	SO:0001589	frameshift_variant	55187	exon19			.	AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"vacuolar protein sorting 13D (yeast)"				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.2804delC	chr1.hg19:g.12336449delC	ENSP00000350854:p.Thr935fs	174.0	0.0	679	125.0	11.0	NM_015378		Frame_Shift_Del	DEL	ENST00000358136.3	hg19	CCDS30588.1																																																																																			.	.		0.478	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		-	12336449	C	-	12336449	7	5	282	1	0	1	0	1	0	0	0	0	17207	507	18	0	2874	0	VPS13D	1	12336449	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	2545813	12336449	236914172	9	40243										
VPS13D	55187	hgsc.bcm.edu	37	chr1	12414184	12414184	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttgctaccctgtgaacttgaTttttatgttaaaggaatgcc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:12414184delT	ENST00000358136.3	+	47	9715	c.9585delT	c.(9583-9585)gatfs	p.D3195fs	VPS13D_ENST00000356315.4_Frame_Shift_Del_p.D3170fs	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		GTGAACTTGATTTTTATGTTA	0.438																																					p.D3195fs		Atlas-INDEL	.											.	VPS13D	316	.	0			c.9584delA						.						113	110	111					1																	12414184		2203	4300	6503	SO:0001589	frameshift_variant	55187	exon47			.	AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"vacuolar protein sorting 13D (yeast)"				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.9585delT	chr1.hg19:g.12414184delT	ENSP00000350854:p.Asp3195fs	271.0	0.0		195.0	14.0	NM_015378		Frame_Shift_Del	DEL	ENST00000358136.3	hg19	CCDS30588.1																																																																																			.	.		0.438	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		-	12414184	T	-	12414184	7	5	282	1	0	1	0	1	0	0	0	0	17207	1490	52	0	9767	0	VPS13D	1	12414184	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	77735	12414184	236836437	10	40244										
ZBTB17	7709	hgsc.bcm.edu	37	chr1	16270914	16270914	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gccgcagtagtcgcactggtAgggcttctcgccgctgtgca	14	13	1	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:16270914A>G	ENST00000375743.4	-	9	1484	c.1252T>C	c.(1252-1254)Tac>Cac	p.Y418H	ZBTB17_ENST00000375733.2_Missense_Mutation_p.Y418H|ZBTB17_ENST00000448462.2_Missense_Mutation_p.Y355H|ZBTB17_ENST00000537142.1_Missense_Mutation_p.Y336H|ZBTB17_ENST00000479282.1_5'Flank	NM_003443.2	NP_003434.2	Q13105	ZBT17_HUMAN	zinc finger and BTB domain containing 17	418					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|ectoderm development (GO:0007398)|endoplasmic reticulum unfolded protein response (GO:0030968)|gastrulation with mouth forming second (GO:0001702)|negative regulation of cell cycle (GO:0045786)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(4)|large_intestine(1)|lung(4)|ovary(2)|prostate(2)	15		Colorectal(325;0.000257)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|Colorectal(212;4.12e-07)|COAD - Colon adenocarcinoma(227;2.43e-05)|BRCA - Breast invasive adenocarcinoma(304;9.97e-05)|Kidney(64;0.000182)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0649)		TCGCACTGGTAGGGCTTCTCG	0.662																																					p.Y418H		Atlas-SNP	.											.	ZBTB17	45	.	0			c.T1252C						.						57	52	54					1																	16270914		2191	4290	6481	SO:0001583	missense	7709	exon9			ACTGGTAGGGCTT	U20647	CCDS165.1, CCDS55576.1, CCDS72712.1	1p36.13	2013-01-08	2004-07-16	2004-07-16	ENSG00000116809	ENSG00000116809		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	12936	protein-coding gene	gene with protein product		604084	"zinc finger protein 151 (pHZ-67)", "zinc finger protein 60"	ZNF151, ZNF60			Standard	NM_003443		Approved	MIZ1, pHZ-67	uc001axl.4	Q13105	OTTHUMG00000009377	ENST00000375743.4:c.1252T>C	chr1.hg19:g.16270914A>G	ENSP00000364895:p.Tyr418His	183.0	0.0		146.0	6.0	NM_003443	A0AV07|B4DXB4|B7ZLQ9|F5H411|Q15932|Q5JYB2|Q9NUC9	Missense_Mutation	SNP	ENST00000375743.4	hg19	CCDS165.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	23.9|23.9	4.468063|4.468063	0.84533|0.84533	.|.	.|.	ENSG00000116809|ENSG00000116809	ENST00000375729|ENST00000375743;ENST00000375733;ENST00000444654;ENST00000537142;ENST00000444358;ENST00000448462	.|T;T;T;T	.|0.21734	.|1.99;1.99;1.99;1.99	5.46|5.46	5.46|5.46	0.80206|0.80206	.|Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.|0.000000	.|0.64402	.|D	.|0.000001	T|T	0.41994|0.41994	0.1183|0.1183	L|L	0.49455|0.49455	1.56|1.56	0.58432|0.58432	D|D	0.999997|0.999997	.|D;D;D;D;D	.|0.89917	.|0.999;0.999;1.0;1.0;1.0	.|D;D;D;D;D	.|0.91635	.|0.992;0.997;0.997;0.999;0.99	T|T	0.29579|0.29579	-1.0007|-1.0007	6|10	0.87932|0.87932	D|D	0|0	.|.	15.5311|15.5311	0.75964|0.75964	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|374;355;418;336;418	.|B4DYU5;E7EPQ4;Q13105-2;F5H411;Q13105	.|.;.;.;.;ZBT17_HUMAN	P|H	3|418;418;337;336;4;355	.|ENSP00000364895:Y418H;ENSP00000364885:Y418H;ENSP00000438529:Y336H;ENSP00000391002:Y355H	ENSP00000364881:L3P|ENSP00000364885:Y418H	L|Y	-|-	2|1	0|0	ZBTB17|ZBTB17	16143501|16143501	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.605000|0.605000	0.37080|0.37080	9.232000|9.232000	0.95325|0.95325	2.064000|2.064000	0.61679|0.61679	0.533000|0.533000	0.62120|0.62120	CTA|TAC	.	.		0.662	ZBTB17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025998.1	NM_003443		G	16270914	A	G	16270914	3	3	282	1	0	0	0	0	1	0	0	0	17542	420	15	2	1191	2	ZBTB17	1	16270914	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	3856730	16270914	232979707	11	40245										
ATP13A2	23400	hgsc.bcm.edu	37	chr1	17312586	17312586	+	3'UTR	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cccagggtgggggtggtctcGggggaggagtgtagacagtc					rs189334432	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:17312586delG	ENST00000326735.8	-	0	3706				ATP13A2_ENST00000341676.5_Frame_Shift_Del_p.P1124fs|RP1-37C10.3_ENST00000446261.1_RNA|ATP13A2_ENST00000452699.1_3'UTR			Q9NQ11	AT132_HUMAN	ATPase type 13A2						cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		GGGTGGTCTCGGGGGAGGAGT	0.647																																					p.P1124fs		Atlas-INDEL	.											.	ATP13A2	85	.	0			c.3372delG						.						50	54	53					1																	17312586		692	1591	2283	SO:0001624	3_prime_UTR_variant	23400	exon27			.	AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"ATPases / P-type", "Parkinson disease"	30213	protein-coding gene	gene with protein product		610513	"Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.*130C>-	chr1.hg19:g.17312586delG		247.0	0.0		160.0	10.0	NM_001141974	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Frame_Shift_Del	DEL	ENST00000326735.8	hg19	CCDS175.1																																																																																			.	.		0.647	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089		-	17312586	G	-	17312586	6	5	282	0	1	1	0	1	0	0	0	0	1124	1116	39	0		0	ATP13A2	1	17312586	3'UTR	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1041672	17312586	231938035	12	40246										
ATP13A2	23400	hgsc.bcm.edu	37	chr1	17314703	17314703	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgtacttgaagacgctgaacGaagtgtcaagggaacagcgc	13	8	1	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:17314703G>T	ENST00000326735.8	-	25	2822	c.2789C>A	c.(2788-2790)tCg>tAg	p.S930*	ATP13A2_ENST00000341676.5_Nonsense_Mutation_p.S886*|RP1-37C10.3_ENST00000446261.1_RNA|ATP13A2_ENST00000452699.1_Nonsense_Mutation_p.S925*			Q9NQ11	AT132_HUMAN	ATPase type 13A2	930					cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		GACGCTGAACGAAGTGTCAAG	0.607																																					p.S930X		Atlas-SNP	.											ATP13A2,NS,carcinoma,0,1	ATP13A2	85	.	0			c.C2789A						.						140	125	130					1																	17314703		2203	4300	6503	SO:0001587	stop_gained	23400	exon25			CTGAACGAAGTGT	AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"ATPases / P-type", "Parkinson disease"	30213	protein-coding gene	gene with protein product		610513	"Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.2789C>A	chr1.hg19:g.17314703G>T	ENSP00000327214:p.Ser930*	260.0	0.0		198.0	0.0	NM_022089	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Nonsense_Mutation	SNP	ENST00000326735.8	hg19	CCDS175.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.026541	0.93518	.	.	ENSG00000159363	ENST00000326735;ENST00000341676;ENST00000452699;ENST00000502418	.	.	.	5.51	4.59	0.56863	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-17.1612	10.0451	0.42182	0.0932:0.0:0.9068:0.0	.	.	.	.	X	930;886;925;126	.	ENSP00000327214:S930X	S	-	2	0	ATP13A2	17187290	1.000000	0.71417	0.185000	0.23176	0.726000	0.41606	9.375000	0.97178	1.326000	0.45319	0.561000	0.74099	TCG	.	.		0.607	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089		T	17314703	G	T	17314703	4	4	282	1	0	0	0	0	0	1	0	0	1124	1059	37	1	1009	1	ATP13A2	1	17314703	Nonsense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	2117	17314703	231935918	13	40247										
PLA2G2D	26279	hgsc.bcm.edu	37	chr1	20442055	20442055	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	taatagtccttgtagatgctGcacccctgggtcttcaggtg	11	10	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:20442055G>C	ENST00000375105.3	-	3	295	c.237C>G	c.(235-237)tgC>tgG	p.C79W		NM_012400.2	NP_036532.1	Q9UNK4	PA2GD_HUMAN	phospholipase A2, group IID	79					glycerophospholipid biosynthetic process (GO:0046474)|inflammatory response (GO:0006954)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)	p.C79C(1)		endometrium(1)|lung(2)	3		Colorectal(325;0.000147)|Renal(390;0.000469)|Lung NSC(340;0.00412)|all_lung(284;0.00419)|Breast(348;0.00526)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.15e-05)|BRCA - Breast invasive adenocarcinoma(304;8.01e-05)|Kidney(64;0.000175)|GBM - Glioblastoma multiforme(114;0.000798)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		TGTAGATGCTGCACCCCTGGG	0.582										Multiple Myeloma(11;0.12)																											p.C79W	Melanoma(60;742 1548 31762 39240)	Atlas-SNP	.											PLA2G2D,NS,carcinoma,0,1	PLA2G2D	7	.	1	Substitution - coding silent(1)	lung(1)	c.C237G						.																																			SO:0001583	missense	26279	exon3			GATGCTGCACCCC	AF112982	CCDS203.1, CCDS72721.1	1p36.12	2008-09-19			ENSG00000117215	ENSG00000117215	3.1.1.4		9033	protein-coding gene	gene with protein product		605630				10455175	Standard	NM_012400		Approved	sPLA2S	uc001bcz.4	Q9UNK4	OTTHUMG00000002701	ENST00000375105.3:c.237C>G	chr1.hg19:g.20442055G>C	ENSP00000364246:p.Cys79Trp	234.0	0.0		225.0	0.0	NM_012400	A8K2Z1|B1AEL9|Q9UK01	Missense_Mutation	SNP	ENST00000375105.3	hg19	CCDS203.1	.	.	.	.	.	.	.	.	.	.	G	13.45	2.239625	0.39598	.	.	ENSG00000117215	ENST00000375105	T	0.37584	1.19	5.6	-0.0442	0.13856	Phospholipase A2 (3);	0.000000	0.64402	D	0.000008	T	0.63165	0.2488	M	0.93720	3.45	0.25014	N	0.99139	D	0.89917	1.0	D	0.97110	1.0	T	0.55885	-0.8070	10	0.87932	D	0	-26.6937	8.4483	0.32856	0.4766:0.0:0.5234:0.0	.	79	Q9UNK4	PA2GD_HUMAN	W	79	ENSP00000364246:C79W	ENSP00000364246:C79W	C	-	3	2	PLA2G2D	20314642	0.138000	0.22547	0.008000	0.14137	0.002000	0.02628	0.124000	0.15728	-0.023000	0.13963	-0.234000	0.12200	TGC	.	.		0.582	PLA2G2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007683.1			C	20442055	G	C	20442055	3	2	282	1	0	0	0	0	1	0	0	0	12006	1311	46	4	208	4	PLA2G2D	1	20442055	Missense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	3127352	20442055	228808566	14	40248										
HP1BP3	50809	hgsc.bcm.edu	37	chr1	21097452	21097452	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gactcctctatttaattctcTtttcagtgcttgtttaagga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:21097452delT	ENST00000312239.5	-	6	764	c.625delA	c.(625-627)agafs	p.R209fs	HP1BP3_ENST00000375003.2_Frame_Shift_Del_p.R57fs	NM_016287.3	NP_057371.2	Q5SSJ5	HP1B3_HUMAN	heterochromatin protein 1, binding protein 3	209	H15 1. {ECO:0000255|PROSITE- ProRule:PRU00837}.				nucleosome assembly (GO:0006334)	nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(5)|prostate(2)|skin(2)|urinary_tract(1)	16		all_lung(284;6.55e-06)|Lung NSC(340;6.59e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.26e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00015)|GBM - Glioblastoma multiforme(114;0.000521)|Kidney(64;0.000529)|STAD - Stomach adenocarcinoma(196;0.00311)|KIRC - Kidney renal clear cell carcinoma(64;0.00687)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.201)		TTTAATTCTCTTTTCAGTGCT	0.358																																					p.R209fs		Atlas-INDEL	.											.	HP1BP3	47	.	0			c.626delG						.						165	157	160					1																	21097452		2203	4300	6503	SO:0001589	frameshift_variant	50809	exon6			.	BC053327	CCDS30621.1	1p36.12	2008-02-05			ENSG00000127483	ENSG00000127483			24973	protein-coding gene	gene with protein product						12477932	Standard	NM_016287		Approved	HP1-BP74	uc001bdw.1	Q5SSJ5	OTTHUMG00000002622	ENST00000312239.5:c.625delA	chr1.hg19:g.21097452delT	ENSP00000312625:p.Arg209fs	222.0	0.0		133.0	10.0	NM_016287	A6NI71|A8K5D7|B3KMZ8|B4E210|Q05BI0|Q5SSJ6|Q5SWC6|Q6PIM9|Q8NDF0|Q9UHY0	Frame_Shift_Del	DEL	ENST00000312239.5	hg19	CCDS30621.1																																																																																			.	.		0.358	HP1BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007457.2	NM_016287		-	21097452	T	-	21097452	7	5	282	1	0	1	0	1	0	0	0	0	7337	1617	56	0	1068	0	HP1BP3	1	21097452	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	655397	21097452	228153169	15	40249										
ECE1	1889	hgsc.bcm.edu	37	chr1	21564732	21564732	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caaaacttccagcgaggaagAcaggtctggaaaacacaagt	10	9	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:21564732A>G	ENST00000374893.6	-	11	1358	c.1284T>C	c.(1282-1284)tgT>tgC	p.C428C	ECE1_ENST00000264205.6_Silent_p.C425C|ECE1_ENST00000436918.2_Silent_p.C428C|ECE1_ENST00000528294.1_5'UTR|ECE1_ENST00000415912.2_Silent_p.C412C|ECE1_ENST00000357071.4_Silent_p.C416C	NM_001397.2	NP_001388.1	P42892	ECE1_HUMAN	endothelin converting enzyme 1	428					bradykinin catabolic process (GO:0010815)|calcitonin catabolic process (GO:0010816)|ear development (GO:0043583)|embryonic digit morphogenesis (GO:0042733)|endothelin maturation (GO:0034959)|heart development (GO:0007507)|hormone catabolic process (GO:0042447)|peptide hormone processing (GO:0016486)|pharyngeal system development (GO:0060037)|positive regulation of receptor recycling (GO:0001921)|protein processing (GO:0016485)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|substance P catabolic process (GO:0010814)	early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intrinsic component of endosome membrane (GO:0031302)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)|Weibel-Palade body (GO:0033093)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|peptide hormone binding (GO:0017046)|protein homodimerization activity (GO:0042803)			endometrium(5)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)	25		Lung NSC(340;1.14e-05)|all_lung(284;1.23e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00147)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0183)|OV - Ovarian serous cystadenocarcinoma(117;4.83e-27)|COAD - Colon adenocarcinoma(152;1.36e-06)|GBM - Glioblastoma multiforme(114;1.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000162)|STAD - Stomach adenocarcinoma(196;0.00326)|KIRC - Kidney renal clear cell carcinoma(1967;0.00755)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.206)		AGCGAGGAAGACAGGTCTGGA	0.562																																					p.C428C		Atlas-SNP	.											.	ECE1	76	.	0			c.T1284C						.						55	50	52					1																	21564732		2203	4300	6503	SO:0001819	synonymous_variant	1889	exon11			AGGAAGACAGGTC	D49471	CCDS215.1, CCDS44081.1, CCDS44082.1, CCDS44083.1	1p36.1	2008-02-05			ENSG00000117298	ENSG00000117298			3146	protein-coding gene	gene with protein product		600423		ECE		7805846, 7864876, 17592116	Standard	NM_001397		Approved		uc001bei.2	P42892	OTTHUMG00000002625	ENST00000374893.6:c.1284T>C	chr1.hg19:g.21564732A>G		107.0	0.0		67.0	4.0	NM_001397	A8K3P1|B4E291|Q14217|Q17RN5|Q2Z2K8|Q58GE7|Q5THM5|Q5THM7|Q5THM8|Q9UJQ6|Q9UPF4|Q9UPM4|Q9Y501	Silent	SNP	ENST00000374893.6	hg19	CCDS215.1																																																																																			.	.		0.562	ECE1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007470.2	NM_001397		G	21564732	A	G	21564732	2	3	282	1	0	0	0	0	0	0	0	1	4891	273	10	2		2	ECE1	1	21564732	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	467280	21564732	227685889	16	40250										
USP48	84196	hgsc.bcm.edu	37	chr1	22056297	22056297	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gttcctttgccacacttgggTttacgtgtctgagacttaga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:22056297delT	ENST00000308271.9	-	10	1848	c.1200delA	c.(1198-1200)aaafs	p.K400fs	USP48_ENST00000529637.1_Frame_Shift_Del_p.K399fs|USP48_ENST00000400301.1_Frame_Shift_Del_p.K400fs|USP48_ENST00000421625.2_Frame_Shift_Del_p.K400fs	NM_032236.5	NP_115612.4	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 48	400	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			NS(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(14)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)		CACACTTGGGTTTACGTGTCT	0.403																																					p.P401fs		Atlas-INDEL	.											.	USP48	91	.	0			c.1201delC						.						186	173	178					1																	22056297		2203	4300	6503	SO:0001589	frameshift_variant	84196	exon10			.	AF502942	CCDS30623.1, CCDS44084.1	1p36.12	2008-02-05	2005-08-08	2004-04-07	ENSG00000090686	ENSG00000090686		"Ubiquitin-specific peptidases"	18533	protein-coding gene	gene with protein product			"ubiquitin specific protease 31", "ubiquitin specific protease 48"	USP31		12838346	Standard	XM_005246009		Approved	FLJ23277, FLJ11328, FLJ20103, FLJ23054, MGC14879	uc001bfb.3	Q86UV5	OTTHUMG00000007798	ENST00000308271.9:c.1200delA	chr1.hg19:g.22056297delT	ENSP00000309262:p.Lys400fs	214.0	0.0		152.0	10.0	NM_001032730	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Frame_Shift_Del	DEL	ENST00000308271.9	hg19	CCDS30623.1																																																																																			.	.		0.403	USP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021372.1	NM_032236		-	22056297	T	-	22056297	7	5	282	1	0	1	0	1	0	0	0	0	17094	1722	60	0	1987	0	USP48	1	22056297	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	491565	22056297	227194324	17	40251										
EPHA8	2046	hgsc.bcm.edu	37	chr1	22927800	22927800	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccctgtgcctcaggtgcccaCcccctgccttcgtccggagc					rs571732433		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:22927800delC	ENST00000166244.3	+	16	2809	c.2737delC	c.(2737-2739)cccfs	p.P914fs		NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8	914					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		CAGGTGCCCACCCCCTGCCTT	0.697																																					p.P912fs		Atlas-INDEL	.											.	EPHA8	221	.	0			c.2736delA						.						36	41	40					1																	22927800		2176	4230	6406	SO:0001589	frameshift_variant	2046	exon16			.	BC038796	CCDS225.1, CCDS30626.1	1p36.12	2013-02-11	2004-10-28		ENSG00000070886	ENSG00000070886	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3391	protein-coding gene	gene with protein product		176945	"EphA8"	EEK		1648701	Standard	NM_001006943		Approved	Hek3	uc001bfx.1	P29322	OTTHUMG00000002892	ENST00000166244.3:c.2737delC	chr1.hg19:g.22927800delC	ENSP00000166244:p.Pro914fs	271.0	0.0		222.0	14.0	NM_020526	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Frame_Shift_Del	DEL	ENST00000166244.3	hg19	CCDS225.1																																																																																			.	.		0.697	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526		-	22927800	C	-	22927800	7	5	282	1	0	1	0	1	0	0	0	0	5175	507	18	0	2972	0	EPHA8	1	22927800	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	871503	22927800	226322821	18	40252										
SRRM1	10250	hgsc.bcm.edu	37	chr1	24996012	24996012	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atcaccccaaagaaggcagtCcccgtctccaagtactaggc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:24996012delC	ENST00000323848.9	+	14	2453	c.2138delC	c.(2137-2139)tccfs	p.S713fs	SRRM1_ENST00000447431.2_Frame_Shift_Del_p.S725fs|SRRM1_ENST00000374389.4_Frame_Shift_Del_p.S722fs|SRRM1_ENST00000479034.1_3'UTR|snoU13_ENST00000459464.1_RNA	NM_005839.3	NP_005830.2	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1	713	Arg-rich.|Pro-rich.|Ser-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	36		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;1.01e-24)|Colorectal(126;5.95e-08)|COAD - Colon adenocarcinoma(152;3.24e-06)|GBM - Glioblastoma multiforme(114;0.000148)|BRCA - Breast invasive adenocarcinoma(304;0.00177)|KIRC - Kidney renal clear cell carcinoma(1967;0.00348)|STAD - Stomach adenocarcinoma(196;0.00483)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		AGAAGGCAGTCCCCGTCTCCA	0.498																																					p.S713fs	Ovarian(68;897 1494 3282 17478)	Atlas-INDEL	.											.	SRRM1	81	.	0			c.2137delT						.						40	39	39					1																	24996012		2203	4297	6500	SO:0001589	frameshift_variant	10250	exon14			.	AF048977	CCDS255.1	1p36	2010-04-22			ENSG00000133226	ENSG00000133226			16638	protein-coding gene	gene with protein product	"Ser/Arg-related nuclear matrix protein", "plenty of prolines 101-like"	605975				9531537	Standard	NM_005839		Approved	SRM160, POP101, MGC39488	uc001bjm.3	Q8IYB3	OTTHUMG00000003320	ENST00000323848.9:c.2138delC	chr1.hg19:g.24996012delC	ENSP00000326261:p.Ser713fs	198.0	0.0		126.0	10.0	NM_005839	O60585|Q5VVN4	Frame_Shift_Del	DEL	ENST00000323848.9	hg19	CCDS255.1																																																																																			.	.		0.498	SRRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009292.2	NM_005839		-	24996012	C	-	24996012	7	5	282	1	0	1	0	1	0	0	0	0	15183	855	30	0	2192	0	SRRM1	1	24996012	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	2068212	24996012	224254609	19	40253										
TMEM50A	23585	hgsc.bcm.edu	37	chr1	25683316	25683316	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tataccctggaattgctgtaTttttccagaatgccttcatc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:25683316delT	ENST00000374358.4	+	6	953	c.400delT	c.(400-402)tttfs	p.F135fs	TMEM50A_ENST00000480937.1_3'UTR	NM_014313.3	NP_055128.1	O95807	TM50A_HUMAN	transmembrane protein 50A	135						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(3)|lung(1)	6		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;3.47e-27)|Colorectal(126;1.1e-08)|COAD - Colon adenocarcinoma(152;7.48e-07)|STAD - Stomach adenocarcinoma(196;0.00035)|BRCA - Breast invasive adenocarcinoma(304;0.00047)|KIRC - Kidney renal clear cell carcinoma(1967;0.000755)|GBM - Glioblastoma multiforme(114;0.00106)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.204)		AATTGCTGTATTTTTCCAGAA	0.274																																					p.V133fs		Atlas-INDEL	.											.	TMEM50A	17	.	0			c.399delA						.						158	142	147					1																	25683316		2201	4298	6499	SO:0001589	frameshift_variant	23585	exon6			.	AY071927	CCDS264.1	1p36.11	2008-02-05			ENSG00000183726	ENSG00000183726			30590	protein-coding gene	gene with protein product	"small membrane protein 1"	605348				10938938, 10845894	Standard	NM_014313		Approved	SMP1	uc001bke.3	O95807	OTTHUMG00000007651	ENST00000374358.4:c.400delT	chr1.hg19:g.25683316delT	ENSP00000363478:p.Phe135fs	185.0	0.0		170.0	11.0	NM_014313		Frame_Shift_Del	DEL	ENST00000374358.4	hg19	CCDS264.1																																																																																			.	.		0.274	TMEM50A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020313.1			-	25683316	T	-	25683316	7	5	282	1	0	1	0	1	0	0	0	0	16190	1493	52	0	418	0	TMEM50A	1	25683316	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	687304	25683316	223567305	20	40254										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27092724	27092724	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttccttaggccgccaggctaCcccaatatgaatcaaggggg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:27092724delC	ENST00000324856.7	+	9	3116	c.2745delC	c.(2743-2745)tacfs	p.Y915fs	ARID1A_ENST00000457599.2_Frame_Shift_Del_p.Y915fs|ARID1A_ENST00000374152.2_Frame_Shift_Del_p.Y532fs|RN7SL501P_ENST00000578818.1_RNA	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	915					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		CGCCAGGCTACCCCAATATGA	0.473			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.Y915fs		Atlas-INDEL	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.2744delA						.						82	81	81					1																	27092724		2203	4300	6503	SO:0001589	frameshift_variant	8289	exon9			.	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.2745delC	chr1.hg19:g.27092724delC	ENSP00000320485:p.Tyr915fs	207.0	0.0		146.0	10.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Del	DEL	ENST00000324856.7	hg19	CCDS285.1																																																																																			.	.		0.473	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		-	27092724	C	-	27092724	7	5	282	1	0	1	0	1	0	0	0	0	913	518	18	0	2779	0	ARID1A	1	27092724	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1409408	27092724	222157897	21	40255										
TMEM200B	399474	hgsc.bcm.edu	37	chr1	29447542	29447542	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tggggccccaaggaggagctCcccaaggcccagatccagag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:29447542delC	ENST00000420504.2	-	2	956	c.799delG	c.(799-801)gagfs	p.E267fs	TMEM200B_ENST00000521452.1_Frame_Shift_Del_p.E267fs	NM_001171868.1	NP_001165339.1	Q69YZ2	T200B_HUMAN	transmembrane protein 200B	267						integral component of membrane (GO:0016021)				ovary(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.00765)|Lung NSC(340;0.0153)|all_lung(284;0.0173)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;7.32e-08)|COAD - Colon adenocarcinoma(152;4.92e-06)|STAD - Stomach adenocarcinoma(196;0.00618)|BRCA - Breast invasive adenocarcinoma(304;0.0501)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.126)		AGGAGGAGCTCCCCAAGGCCC	0.632																																					p.E267fs		Atlas-INDEL	.											.	TMEM200B	9	.	0			c.800delA						.						25	27	26					1																	29447542		2202	4300	6502	SO:0001589	frameshift_variant	399474	exon2			.		CCDS30658.1	1p35	2007-12-18			ENSG00000253304	ENSG00000253304			33785	protein-coding gene	gene with protein product						15722956	Standard	NM_001003682		Approved	TTMB	uc001brn.2	Q69YZ2	OTTHUMG00000003658	ENST00000420504.2:c.799delG	chr1.hg19:g.29447542delC	ENSP00000428544:p.Glu267fs	240.0	0.0		195.0	12.0	NM_001171868	Q6P2G8|Q6P2Q5	Frame_Shift_Del	DEL	ENST00000420504.2	hg19	CCDS30658.1																																																																																			.	.		0.632	TMEM200B-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010377.2	NM_001003682		-	29447542	C	-	29447542	7	5	282	1	0	1	0	1	0	0	0	0	16139	864	30	0	128	0	TMEM200B	1	29447542	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	2354818	29447542	219803079	22	40256	205	2								
TMEM200B	399474	hgsc.bcm.edu	37	chr1	29447550	29447550	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caaggaggagctccccaaggCccagatccagagacttggaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:29447550delC	ENST00000420504.2	-	2	948	c.791delG	c.(790-792)ggcfs	p.G264fs	TMEM200B_ENST00000521452.1_Frame_Shift_Del_p.G264fs	NM_001171868.1	NP_001165339.1	Q69YZ2	T200B_HUMAN	transmembrane protein 200B	264						integral component of membrane (GO:0016021)				ovary(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.00765)|Lung NSC(340;0.0153)|all_lung(284;0.0173)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;7.32e-08)|COAD - Colon adenocarcinoma(152;4.92e-06)|STAD - Stomach adenocarcinoma(196;0.00618)|BRCA - Breast invasive adenocarcinoma(304;0.0501)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.126)		CTCCCCAAGGCCCAGATCCAG	0.637																																					p.G264fs		Atlas-INDEL	.											.	TMEM200B	9	.	0			c.792delC						.						26	28	28					1																	29447550		2203	4300	6503	SO:0001589	frameshift_variant	399474	exon2			.		CCDS30658.1	1p35	2007-12-18			ENSG00000253304	ENSG00000253304			33785	protein-coding gene	gene with protein product						15722956	Standard	NM_001003682		Approved	TTMB	uc001brn.2	Q69YZ2	OTTHUMG00000003658	ENST00000420504.2:c.791delG	chr1.hg19:g.29447550delC	ENSP00000428544:p.Gly264fs	236.0	0.0		192.0	12.0	NM_001171868	Q6P2G8|Q6P2Q5	Frame_Shift_Del	DEL	ENST00000420504.2	hg19	CCDS30658.1																																																																																			.	.		0.637	TMEM200B-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010377.2	NM_001003682		-	29447550	C	-	29447550	7	5	282	1	0	1	0	1	0	0	0	0	16139	739	26	0	136	0	TMEM200B	1	29447550	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	8	29447550	219803071	23	40257	205	2								
PUM1	9698	hgsc.bcm.edu	37	chr1	31418315	31418315	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caagacatggccatctagttCccgaaccatctcattctaat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:31418315delC	ENST00000257075.5	-	18	2959	c.2866delG	c.(2866-2868)gaafs	p.E956fs	PUM1_ENST00000423018.2_Frame_Shift_Del_p.E814fs|PUM1_ENST00000373741.4_Frame_Shift_Del_p.E994fs|PUM1_ENST00000426105.2_Frame_Shift_Del_p.E958fs|PUM1_ENST00000424085.2_Frame_Shift_Del_p.E714fs|PUM1_ENST00000373742.2_Frame_Shift_Del_p.E897fs|PUM1_ENST00000373747.3_Frame_Shift_Del_p.E959fs|PUM1_ENST00000440538.2_Frame_Shift_Del_p.E932fs	NM_014676.2	NP_055491.1	Q14671	PUM1_HUMAN	pumilio RNA-binding family member 1	956	PUM-HD. {ECO:0000255|PROSITE- ProRule:PRU00318}.				membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(17)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)		CCATCTAGTTCCCGAACCATC	0.403																																					p.E958fs		Atlas-INDEL	.											.	PUM1	107	.	0			c.2873delA						.						93	84	87					1																	31418315		2203	4300	6503	SO:0001589	frameshift_variant	9698	exon18			.	AF315592	CCDS338.1, CCDS44099.1	1p35.2	2013-09-02	2013-09-02		ENSG00000134644	ENSG00000134644			14957	protein-coding gene	gene with protein product		607204	"pumilio (Drosophila) homolog 1", "pumilio homolog 1 (Drosophila)"				Standard	NM_001020658		Approved	PUMH1, KIAA0099	uc001bsh.1	Q14671	OTTHUMG00000003795	ENST00000257075.5:c.2866delG	chr1.hg19:g.31418315delC	ENSP00000257075:p.Glu956fs	199.0	0.0		136.0	10.0	NM_001020658	A8K6W4|B4DG92|D3DPN3|E9PCJ0|Q53HH5|Q5VXY7|Q9HAN1	Frame_Shift_Del	DEL	ENST00000257075.5	hg19	CCDS338.1																																																																																			.	.		0.403	PUM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000010671.1			-	31418315	C	-	31418315	7	5	282	1	0	1	0	1	0	0	0	0	12840	864	30	0	714	0	PUM1	1	31418315	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1970765	31418315	217832306	24	40258										
NKAIN1	79570	hgsc.bcm.edu	37	chr1	31656681	31656681	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tactgccaggaagatctgcaGggcgctgctgagggcttcaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:31656681delG	ENST00000373736.2	-	4	460	c.454delC	c.(454-456)ctgfs	p.L152fs	NKAIN1_ENST00000263693.1_Frame_Shift_Del_p.L108fs|NKAIN1_ENST00000528449.1_5'Flank|NKAIN1_ENST00000398657.2_Frame_Shift_Del_p.L81fs	NM_024522.2	NP_078798.2	Q4KMZ8	NKAI1_HUMAN	Na+/K+ transporting ATPase interacting 1	152						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(1)|kidney(2)|ovary(1)|prostate(1)	7		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)|Breast(348;0.141)|all_neural(195;0.146)|Medulloblastoma(700;0.151)		STAD - Stomach adenocarcinoma(196;0.0184)|READ - Rectum adenocarcinoma(331;0.148)		AAGATCTGCAGGGCGCTGCTG	0.577																																					p.L152fs		Atlas-INDEL	.											.	NKAIN1	21	.	0			c.455delT						.						136	130	132					1																	31656681		2203	4300	6503	SO:0001589	frameshift_variant	79570	exon4			.	AK022712	CCDS339.1, CCDS339.2	1p35.2	2010-06-25	2007-10-04	2007-10-04	ENSG00000084628	ENSG00000084628		"Na+/K+ transporting ATPase interacting"	25743	protein-coding gene	gene with protein product		612871	"family with sequence similarity 77, member C"	FAM77C		17606467	Standard	NM_024522		Approved	FLJ12650	uc010ogd.2	Q4KMZ8	OTTHUMG00000003788	ENST00000373736.2:c.454delC	chr1.hg19:g.31656681delG	ENSP00000362841:p.Leu152fs	217.0	0.0		171.0	12.0	NM_024522	A2VDJ3|B7Z5F5|B7Z5W9|Q9H9M7	Frame_Shift_Del	DEL	ENST00000373736.2	hg19	CCDS339.2																																																																																			.	.		0.577	NKAIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010655.2	NM_024522		-	31656681	G	-	31656681	7	5	282	1	0	1	0	1	0	0	0	0	10444	991	35	0	185	0	NKAIN1	1	31656681	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	238366	31656681	217593940	25	40259										
COL16A1	1307	hgsc.bcm.edu	37	chr1	32134408	32134408	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccagcttcttcttaccggctCccccttgtctccagtcaggc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:32134408delC	ENST00000373672.3	-	50	3760	c.3244delG	c.(3244-3246)gagfs	p.E1082fs	COL16A1_ENST00000271069.6_Frame_Shift_Del_p.E1082fs	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	1082	Triple-helical region 2 (COL2) with 2 imperfections.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female pregnancy (GO:0007565)|integrin-mediated signaling pathway (GO:0007229)	collagen type XVI trimer (GO:0005597)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(15)|ovary(8)|prostate(4)	48		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		CTTACCGGCTCCCCCTTGTCT	0.607																																					p.E1082fs	Colon(143;498 1786 21362 25193 36625)	Atlas-INDEL	.											.	COL16A1	137	.	0			c.3245delA						.						68	72	71					1																	32134408		1909	4112	6021	SO:0001589	frameshift_variant	1307	exon50			.	M92642	CCDS41297.1	1p35-p34	2013-01-16			ENSG00000084636	ENSG00000084636		"Collagens"	2193	protein-coding gene	gene with protein product		120326				1631157	Standard	NM_001856		Approved		uc001btk.1	Q07092	OTTHUMG00000003883	ENST00000373672.3:c.3244delG	chr1.hg19:g.32134408delC	ENSP00000362776:p.Glu1082fs	192.0	0.0		132.0	10.0	NM_001856	Q16593|Q59F89|Q71RG9	Frame_Shift_Del	DEL	ENST00000373672.3	hg19	CCDS41297.1																																																																																			.	.		0.607	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856		-	32134408	C	-	32134408	7	5	282	1	0	1	0	1	0	0	0	0	3675	864	30	0	1658	0	COL16A1	1	32134408	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	477727	32134408	217116213	26	40260										
COL16A1	1307	hgsc.bcm.edu	37	chr1	32136240	32136240	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caacagcaccaggaaaacctGgggggccctggtgggagaaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:32136240delG	ENST00000373672.3	-	49	3674	c.3158delC	c.(3157-3159)ccafs	p.P1053fs	COL16A1_ENST00000271069.6_Frame_Shift_Del_p.P1053fs	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	1053	Collagen-like 6.|Triple-helical region 2 (COL2) with 2 imperfections.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female pregnancy (GO:0007565)|integrin-mediated signaling pathway (GO:0007229)	collagen type XVI trimer (GO:0005597)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(15)|ovary(8)|prostate(4)	48		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		AGGAAAACCTGGGGGGCCCTG	0.637																																					p.P1053fs	Colon(143;498 1786 21362 25193 36625)	Atlas-INDEL	.											.	COL16A1	137	.	0			c.3159delA						.						8	12	11					1																	32136240		1542	3202	4744	SO:0001589	frameshift_variant	1307	exon49			.	M92642	CCDS41297.1	1p35-p34	2013-01-16			ENSG00000084636	ENSG00000084636		"Collagens"	2193	protein-coding gene	gene with protein product		120326				1631157	Standard	NM_001856		Approved		uc001btk.1	Q07092	OTTHUMG00000003883	ENST00000373672.3:c.3158delC	chr1.hg19:g.32136240delG	ENSP00000362776:p.Pro1053fs	187.0	0.0		193.0	12.0	NM_001856	Q16593|Q59F89|Q71RG9	Frame_Shift_Del	DEL	ENST00000373672.3	hg19	CCDS41297.1																																																																																			.	.		0.637	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856		-	32136240	G	-	32136240	7	5	282	1	0	1	0	1	0	0	0	0	3675	1348	47	0	1748	0	COL16A1	1	32136240	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1832	32136240	217114381	27	40261										
TMEM39B	55116	hgsc.bcm.edu	37	chr1	32542775	32542775	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cccgacccaggcctctcagaGggggaaggtctccctctttc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:32542775delG	ENST00000336294.5	+	5	592	c.446delG	c.(445-447)aggfs	p.R149fs	TMEM39B_ENST00000373634.4_Intron|TMEM39B_ENST00000487305.1_3'UTR|TMEM39B_ENST00000427288.1_Frame_Shift_Del_p.R34fs|TMEM39B_ENST00000456834.2_Intron	NM_018056.2	NP_060526.2	Q9GZU3	TM39B_HUMAN	transmembrane protein 39B	149						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|lung(5)|ovary(1)|prostate(2)	11		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				GCCTCTCAGAGGGGGAAGGTC	0.622																																					p.R149fs		Atlas-INDEL	.											.	TMEM39B	66	.	0			c.445delA						.						128	116	120					1																	32542775		2203	4300	6503	SO:0001589	frameshift_variant	55116	exon5			.	AL136695	CCDS351.2	1p35.1	2008-02-05			ENSG00000121775	ENSG00000121775			25510	protein-coding gene	gene with protein product						12477932	Standard	NM_018056		Approved	FLJ10315	uc010ogv.2	Q9GZU3	OTTHUMG00000004020	ENST00000336294.5:c.446delG	chr1.hg19:g.32542775delG	ENSP00000338165:p.Arg149fs	225.0	0.0		152.0	11.0	NM_018056	B4DKN8|B4DQE6|B4DTN8|D3DPP4|Q6IA44	Frame_Shift_Del	DEL	ENST00000336294.5	hg19	CCDS351.2																																																																																			.	.		0.622	TMEM39B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011489.2	NM_018056		-	32542775	G	-	32542775	7	5	282	1	0	1	0	1	0	0	0	0	16177	1000	35	0	464	0	TMEM39B	1	32542775	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	406535	32542775	216707846	28	40262										
LCK	3932	hgsc.bcm.edu	37	chr1	32742265	32742265	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cctgaagcagggcagcatgtCcccggacgccttcctggccg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:32742265delC	ENST00000336890.5	+	9	980	c.842delC	c.(841-843)tccfs	p.S281fs	LCK_ENST00000373564.3_Frame_Shift_Del_p.S288fs|LCK_ENST00000333070.4_Frame_Shift_Del_p.S281fs	NM_005356.3	NP_005347.3	P06239	LCK_HUMAN	LCK proto-oncogene, Src family tyrosine kinase	281	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|aging (GO:0007568)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular zinc ion homeostasis (GO:0006882)|dephosphorylation (GO:0016311)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hemopoiesis (GO:0030097)|innate immune response (GO:0045087)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of gene expression (GO:0010628)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|positive regulation of uterine smooth muscle contraction (GO:0070474)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of defense response to virus by virus (GO:0050690)|regulation of lymphocyte activation (GO:0051249)|release of sequestered calcium ion into cytosol (GO:0051209)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to zinc ion (GO:0010043)|T cell costimulation (GO:0031295)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|pericentriolar material (GO:0000242)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|ATP binding (GO:0005524)|ATPase binding (GO:0051117)|CD4 receptor binding (GO:0042609)|CD8 receptor binding (GO:0042610)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine kinase activity (GO:0004713)|SH2 domain binding (GO:0042169)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	37		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.212)			Dasatinib(DB01254)|Ponatinib(DB08901)	GGCAGCATGTCCCCGGACGCC	0.632			T	TRB@	T-ALL																																p.S281fs		Atlas-INDEL	.		Dom	yes		1	1p35-p34.3	3932	lymphocyte-specific protein tyrosine kinase		L	.	LCK	124	.	0			c.841delT						.						86	73	78					1																	32742265		2203	4300	6503	SO:0001589	frameshift_variant	3932	exon9			.	M36881	CCDS359.1	1p34.3	2014-09-17	2014-06-25		ENSG00000182866	ENSG00000182866	2.7.10.1	"SH2 domain containing"	6524	protein-coding gene	gene with protein product		153390	"lymphocyte-specific protein tyrosine kinase"			2787474	Standard	XM_005270862		Approved		uc001buy.3	P06239	OTTHUMG00000007463	ENST00000336890.5:c.842delC	chr1.hg19:g.32742265delC	ENSP00000337825:p.Ser281fs	229.0	0.0		161.0	10.0	NM_005356	D3DPP8|P07100|Q12850|Q13152|Q5TDH8|Q5TDH9|Q7RTZ3|Q96DW4|Q9NYT8	Frame_Shift_Del	DEL	ENST00000336890.5	hg19	CCDS359.1																																																																																			.	.		0.632	LCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019616.4	NM_005356		-	32742265	C	-	32742265	7	5	282	1	0	1	0	1	0	0	0	0	8685	855	30	0	872	0	LCK	1	32742265	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	199490	32742265	216508356	29	40263										
SYNC	81493	hgsc.bcm.edu	37	chr1	33147421	33147421	+	3'UTR	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgctaagaagttttttgctgTttccgggttacagatttggc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:33147421delT	ENST00000409190.3	-	0	1937				SYNC_ENST00000373484.3_Frame_Shift_Del_p.T467fs|RBBP4_ENST00000373493.5_3'UTR	NM_030786.2	NP_110413	Q9H7C4	SYNCI_HUMAN	syncoilin, intermediate filament protein						intermediate filament-based process (GO:0045103)	cytosol (GO:0005829)|intermediate filament (GO:0005882)|neuromuscular junction (GO:0031594)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	structural molecule activity (GO:0005198)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	12						TTTTTTGCTGTTTCCGGGTTA	0.403																																					p.T467fs		Atlas-INDEL	.											.	SYNC	36	.	0			c.1400delC						.						131	116	121					1																	33147421		2203	4299	6502	SO:0001624	3_prime_UTR_variant	81493	exon4			.	AK024707	CCDS367.2, CCDS53294.1	1p35.1	2013-01-16	2008-09-19	2008-09-19	ENSG00000162520	ENSG00000162520		"Intermediate filaments type III"	28897	protein-coding gene	gene with protein product		611750	"syncoilin, intermediate filament 1"	SYNC1		11053421	Standard	NM_030786		Approved	SYNCOILIN	uc001bvt.2	Q9H7C4	OTTHUMG00000008087	ENST00000409190.3:c.*30A>-	chr1.hg19:g.33147421delT		292.0	0.0		238.0	15.0	NM_001161708	B4DNK8|B4DY58|C9IY41	Frame_Shift_Del	DEL	ENST00000409190.3	hg19	CCDS367.2																																																																																			.	.		0.403	SYNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022129.3	NM_030786		-	33147421	T	-	33147421	6	5	282	0	1	1	0	1	0	0	0	0	15458	1725	60	0		0	SYNC	1	33147421	3'UTR	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	405156	33147421	216103200	30	40264										
ZNF362	149076	hgsc.bcm.edu	37	chr1	33745933	33745933	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagggccacggcctgcttggCccccccaagtccgaacgcgg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:33745933delC	ENST00000539719.1	+	5	728	c.558delC	c.(556-558)ggcfs	p.G186fs	ZNF362_ENST00000373428.5_Frame_Shift_Del_p.G186fs	NM_152493.2	NP_689706.2	Q5T0B9	ZN362_HUMAN	zinc finger protein 362	186					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(1)|large_intestine(4)|lung(2)	10		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				GCCTGCTTGGCCCCCCCAAGT	0.657																																					p.G186fs	Pancreas(162;1431 2676 35353 38425)	Pindel	.											.	ZNF362	31	.	0			c.557delG						.						42	41	41					1																	33745933		2203	4300	6503	SO:0001589	frameshift_variant	149076	exon5			.		CCDS377.1	1p35.1	2013-01-08			ENSG00000160094	ENSG00000160094		"Zinc fingers, C2H2-type"	18079	protein-coding gene	gene with protein product	"rotund homolog (Drosophila)"						Standard	NM_152493		Approved	FLJ25476, lin-29, RN	uc001bxc.1	Q5T0B9	OTTHUMG00000004124	ENST00000539719.1:c.558delC	chr1.hg19:g.33745933delC	ENSP00000446335:p.Gly186fs	264.0	0.0		231.0	10.0	NM_152493	Q8WYU4	Frame_Shift_Del	DEL	ENST00000539719.1	hg19	CCDS377.1																																																																																			.	.		0.657	ZNF362-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011857.2	NM_152493		-	33745933	C	-	33745933	7	5	282	1	0	1	0	1	0	0	0	0	17883	726	26	0	572	0	ZNF362	1	33745933	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	598512	33745933	215504688	31	40265										
HMGB4	127540	hgsc.bcm.edu	37	chr1	34329847	34329847	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atgtctcttcttacgttcacTttttgctgaattacagaaac							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:34329847delT	ENST00000522796.1	+	4	1960	c.55delT	c.(55-57)tttfs	p.F19fs	HMGB4_ENST00000519684.1_Frame_Shift_Del_p.F19fs|HMGB4_ENST00000425537.1_Intron|CSMD2_ENST00000373381.4_Intron			Q8WW32	HMGB4_HUMAN	high mobility group box 4	19						chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(1)|large_intestine(1)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	12		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				TTACGTTCACTTTTTGCTGAA	0.393																																					p.H18fs		Atlas-INDEL	.											.	HMGB4	27	.	0			c.54delC						.						83	87	85					1																	34329847		2203	4300	6503	SO:0001589	frameshift_variant	127540	exon2			.		CCDS30668.1	1p35.1	2011-07-01	2011-04-05		ENSG00000176256	ENSG00000176256		"High-mobility group / Canonical"	24954	protein-coding gene	gene with protein product			"high-mobility group box 4"				Standard	NR_033264		Approved	FLJ40388	uc001bxp.3	Q8WW32	OTTHUMG00000013143	ENST00000522796.1:c.55delT	chr1.hg19:g.34329847delT	ENSP00000430919:p.Phe19fs	263.0	0.0		159.0	10.0	NM_145205	B2R4X7|Q0QWA4	Frame_Shift_Del	DEL	ENST00000522796.1	hg19	CCDS30668.1																																																																																			.	.		0.393	HMGB4-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375773.1	NM_145205		-	34329847	T	-	34329847	7	5	282	1	0	1	0	1	0	0	0	0	7237	1609	56	0	57	0	HMGB4	1	34329847	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	583914	34329847	214920774	32	40266										
OSCP1	127700	hgsc.bcm.edu	37	chr1	36888410	36888410	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	actcggtctccataaagttcAaaagaaccttctttgggtgc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:36888410delA	ENST00000356637.5	-	7	801	c.738delT	c.(736-738)tttfs	p.F246fs	OSCP1_ENST00000495222.1_5'UTR|OSCP1_ENST00000433045.2_Frame_Shift_Del_p.F191fs|OSCP1_ENST00000235532.5_Frame_Shift_Del_p.F236fs|OSCP1_ENST00000315643.9_Frame_Shift_Del_p.F246fs			Q8WVF1	OSCP1_HUMAN	organic solute carrier partner 1	246					transport (GO:0006810)	plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	22						CATAAAGTTCAAAAGAACCTT	0.388																																					p.E237fs		Atlas-INDEL	.											.	OSCP1	48	.	0			c.709delG						.						139	126	131					1																	36888410		2203	4300	6503	SO:0001589	frameshift_variant	127700	exon6			.		CCDS409.1, CCDS410.1, CCDS409.2	1p34.3	2009-07-06	2009-07-06	2009-07-06	ENSG00000116885	ENSG00000116885			29971	protein-coding gene	gene with protein product	"oxidored nitro domain containing protein"	608854	"chromosome 1 open reading frame 102"	C1orf102		12477932	Standard	NM_145047		Approved	NOR1	uc001caq.3	Q8WVF1	OTTHUMG00000008139	ENST00000356637.5:c.738delT	chr1.hg19:g.36888410delA	ENSP00000349052:p.Phe246fs	243.0	0.0		197.0	12.0	NM_145047	A6NHM5|A6NHS9|A6NIN9|Q4AEJ0|Q8N7G2|Q8TDF1	Frame_Shift_Del	DEL	ENST00000356637.5	hg19																																																																																				.	.		0.388	OSCP1-010	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000389759.1	NM_145047		-	36888410	A	-	36888410	7	5	282	1	0	1	0	1	0	0	0	0	11295	127	5	0	451	0	OSCP1	1	36888410	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2558563	36888410	212362211	33	40267										
PPT1	5538	hgsc.bcm.edu	37	chr1	40555118	40555118	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tggagtacgccccagcattcAgtgtttttcggatgaagtca	11	9	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:40555118A>G	ENST00000433473.3	-	5	964	c.500T>C	c.(499-501)cTg>cCg	p.L167P	PPT1_ENST00000449045.2_Missense_Mutation_p.L64P	NM_000310.3	NP_000301.1	P50897	PPT1_HUMAN	palmitoyl-protein thioesterase 1	167					adult locomotory behavior (GO:0008344)|associative learning (GO:0008306)|brain development (GO:0007420)|cell death (GO:0008219)|cellular protein catabolic process (GO:0044257)|cofactor metabolic process (GO:0051186)|cofactor transport (GO:0051181)|grooming behavior (GO:0007625)|lipid catabolic process (GO:0016042)|lysosomal lumen acidification (GO:0007042)|membrane raft organization (GO:0031579)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)|neuron development (GO:0048666)|neurotransmitter secretion (GO:0007269)|pinocytosis (GO:0006907)|positive regulation of pinocytosis (GO:0048549)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein catabolic process (GO:0030163)|protein depalmitoylation (GO:0002084)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|regulation of phospholipase A2 activity (GO:0032429)|regulation of synapse structure and activity (GO:0050803)|sphingolipid catabolic process (GO:0030149)|visual perception (GO:0007601)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)	palmitoyl-(protein) hydrolase activity (GO:0008474)|palmitoyl-CoA hydrolase activity (GO:0016290)			endometrium(5)|large_intestine(1)|lung(3)|ovary(1)|stomach(1)	11	Lung NSC(20;3.43e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1e-18)|Epithelial(16;3.6e-17)|all cancers(16;1.1e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			CCCAGCATTCAGTGTTTTTCG	0.453																																					p.L167P		Atlas-SNP	.											.	PPT1	18	.	0			c.T500C						.						146	133	138					1																	40555118		2203	4300	6503	SO:0001583	missense	5538	exon5			GCATTCAGTGTTT	U44772	CCDS447.1, CCDS44119.1	1p32	2014-09-17	2008-07-31		ENSG00000131238	ENSG00000131238	3.1.2.22		9325	protein-coding gene	gene with protein product	"ceroid-lipofuscinosis, neuronal 1, infantile"	600722		PPT		7637805, 8325646	Standard	NM_000310		Approved	CLN1, INCL	uc001cfb.2	P50897	OTTHUMG00000004495	ENST00000433473.3:c.500T>C	chr1.hg19:g.40555118A>G	ENSP00000394863:p.Leu167Pro	171.0	0.0		146.0	6.0	NM_000310	B4DY24|Q6FGQ4	Missense_Mutation	SNP	ENST00000433473.3	hg19	CCDS447.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.332784	0.81801	.	.	ENSG00000131238	ENST00000433473;ENST00000449045;ENST00000439754;ENST00000372779	D;D;D;D	0.97831	-4.56;-4.56;-4.56;-4.56	4.82	4.82	0.62117	.	0.000000	0.85682	D	0.000000	D	0.98991	0.9656	H	0.94964	3.605	0.80722	D	1	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.97110	1.0;0.98;0.975	D	0.99474	1.0946	10	0.87932	D	0	-14.266	13.3546	0.60621	1.0:0.0:0.0:0.0	.	64;117;167	P50897-2;B4DWU3;P50897	.;.;PPT1_HUMAN	P	167;64;62;196	ENSP00000394863:L167P;ENSP00000392293:L64P;ENSP00000403207:L62P;ENSP00000361865:L196P	ENSP00000361865:L196P	L	-	2	0	PPT1	40327705	1.000000	0.71417	0.943000	0.38184	0.973000	0.67179	8.254000	0.89844	2.019000	0.59389	0.528000	0.53228	CTG	.	.		0.453	PPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000013126.2	NM_000310		G	40555118	A	G	40555118	3	3	282	1	0	0	0	0	1	0	0	0	12423	188	7	2	440	2	PPT1	1	40555118	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	3666708	40555118	208695503	34	40268										
HIVEP3	59269	hgsc.bcm.edu	37	chr1	41978825	41978825	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tggagacccacaagggagagCgcccatgccccttcctgggt					rs2483689	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:41978825delC	ENST00000372583.1	-	8	6952	c.6067delG	c.(6067-6069)gctfs	p.A2023fs	HIVEP3_ENST00000372584.1_Frame_Shift_Del_p.A2023fs|HIVEP3_ENST00000247584.5_Frame_Shift_Del_p.A2023fs|HIVEP3_ENST00000460604.1_5'UTR|HIVEP3_ENST00000429157.2_Frame_Shift_Del_p.A2023fs	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	2023			A -> P (in dbSNP:rs2483689). {ECO:0000269|PubMed:10997877, ECO:0000269|PubMed:11161801, ECO:0000269|PubMed:15489334}.		positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				CAAGGGAGAGCGCCCATGCCC	0.637																																					p.A2023fs		Atlas-INDEL	.											.	HIVEP3	235	.	0			c.6068delC						.						40	47	44					1																	41978825		2203	4300	6503	SO:0001589	frameshift_variant	59269	exon8			.	AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"Zinc fingers, C2H2-type"	13561	protein-coding gene	gene with protein product	"kappabinding protein-1"	606649	"human immunodeficiency virus type I enhancer-binding protein 3"			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.6067delG	chr1.hg19:g.41978825delC	ENSP00000361664:p.Ala2023fs	222.0	0.0		194.0	12.0	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Frame_Shift_Del	DEL	ENST00000372583.1	hg19	CCDS463.1																																																																																			.	.		0.637	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503		-	41978825	C	-	41978825	7	5	282	1	0	1	0	1	0	0	0	0	7197	768	27	0	1161	0	HIVEP3	1	41978825	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1423707	41978825	207271796	35	40269										
KIAA0467	23334	hgsc.bcm.edu	37	chr1	43893038	43893038	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gggattggagtggggctcccAgtctgaaagatctaggagga	17	6	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:43893038A>G	ENST00000562955.1	+	24	3349	c.3349A>G	c.(3349-3351)Agt>Ggt	p.S1117G	SZT2_ENST00000372442.1_Missense_Mutation_p.S275G	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	1174					central nervous system development (GO:0007417)|corpus callosum morphogenesis (GO:0021540)|embryo development (GO:0009790)|pigmentation (GO:0043473)|post-embryonic development (GO:0009791)|regulation of superoxide dismutase activity (GO:1901668)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)				NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						TGGGGCTCCCAGTCTGAAAGA	0.567																																					p.S1117G		Atlas-SNP	.											.	SZT2	383	.	0			c.A3349G						.						63	65	64					1																	43893038		2203	4300	6503	SO:0001583	missense	23334	exon24			GCTCCCAGTCTGA	AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198			29040	protein-coding gene	gene with protein product	"seizure threshold 2 homolog A (mouse)", "seizure threshold 2 homolog B (mouse)"	615463	"chromosome 1 open reading frame 84", "KIAA0467"	C1orf84, KIAA0467		9455484	Standard	NM_015284		Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.3349A>G	chr1.hg19:g.43893038A>G	ENSP00000457168:p.Ser1117Gly	125.0	0.0		98.0	4.0	NM_015284	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Missense_Mutation	SNP	ENST00000562955.1	hg19	CCDS30694.2	.	.	.	.	.	.	.	.	.	.	A	10.96	1.499087	0.26861	.	.	ENSG00000198198	ENST00000372442	.	.	.	5.79	5.79	0.91817	.	0.505466	0.22867	N	0.054669	T	0.45094	0.1325	L	0.54323	1.7	0.09310	N	1	B	0.18741	0.03	B	0.21917	0.037	T	0.38757	-0.9646	9	0.44086	T	0.13	.	12.5272	0.56093	1.0:0.0:0.0:0.0	.	1117	Q5T011-5	.	G	275	.	ENSP00000361519:S275G	S	+	1	0	SZT2	43665625	0.254000	0.23992	0.063000	0.19743	0.295000	0.27426	1.297000	0.33400	2.207000	0.71202	0.533000	0.62120	AGT	.	.		0.567	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284		G	43893038	A	G	43893038	3	3	282	1	0	0	0	0	1	0	0	0	8187	188	7	2	853	2	KIAA0467	1	43893038	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1914213	43893038	205357583	36	40270										
KIAA0467	23334	hgsc.bcm.edu	37	chr1	43912809	43912809	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tggcccaccaccctgacggaCcccactttggccgcaatcac							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:43912809delC	ENST00000562955.1	+	65	9085	c.9085delC	c.(9085-9087)cccfs	p.P3029fs	SZT2-AS1_ENST00000396885.2_RNA|SZT2_ENST00000372442.1_Frame_Shift_Del_p.P2187fs	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	3086					central nervous system development (GO:0007417)|corpus callosum morphogenesis (GO:0021540)|embryo development (GO:0009790)|pigmentation (GO:0043473)|post-embryonic development (GO:0009791)|regulation of superoxide dismutase activity (GO:1901668)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)				NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						CCCTGACGGACCCCACTTTGG	0.607																																					p.G3028fs		Atlas-INDEL	.											.	SZT2	383	.	0			c.9084delA						.						106	76	86					1																	43912809		2203	4300	6503	SO:0001589	frameshift_variant	23334	exon65			.	AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198			29040	protein-coding gene	gene with protein product	"seizure threshold 2 homolog A (mouse)", "seizure threshold 2 homolog B (mouse)"	615463	"chromosome 1 open reading frame 84", "KIAA0467"	C1orf84, KIAA0467		9455484	Standard	NM_015284		Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.9085delC	chr1.hg19:g.43912809delC	ENSP00000457168:p.Pro3029fs	278.0	0.0		211.0	14.0	NM_015284	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Frame_Shift_Del	DEL	ENST00000562955.1	hg19	CCDS30694.2																																																																																			.	.		0.607	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284		-	43912809	C	-	43912809	7	5	282	1	0	1	0	1	0	0	0	0	8187	507	18	0	6753	0	KIAA0467	1	43912809	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	19771	43912809	205337812	37	40271										
KIF2C	11004	hgsc.bcm.edu	37	chr1	45226265	45226265	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gttcctgctgcccccacaggAgtgcatcagggccctgggac	13	15	1	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:45226265A>G	ENST00000372224.4	+	16	1687	c.1574A>G	c.(1573-1575)gAg>gGg	p.E525G	RP11-269F19.2_ENST00000440985.1_RNA|RP11-269F19.2_ENST00000428791.1_RNA|KIF2C_ENST00000372222.3_Splice_Site_p.E412G|KIF2C_ENST00000372218.4_Splice_Site_p.E484G|KIF2C_ENST00000372217.1_Splice_Site_p.E471G	NM_006845.3	NP_006836.2	Q99661	KIF2C_HUMAN	kinesin family member 2C	525	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|microtubule motor activity (GO:0003777)|microtubule plus-end binding (GO:0051010)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(16)|ovary(1)|skin(1)|urinary_tract(1)	34	Acute lymphoblastic leukemia(166;0.155)					CCCCCACAGGAGTGCATCAGG	0.597																																					p.E525G		Atlas-SNP	.											.	KIF2C	68	.	0			c.A1574G						.						81	73	75					1																	45226265		2203	4300	6503	SO:0001630	splice_region_variant	11004	exon16			CACAGGAGTGCAT	U63743	CCDS512.1, CCDS72774.1	1p34.1	2014-01-21	2003-01-13	2003-01-17	ENSG00000142945	ENSG00000142945		"Kinesins"	6393	protein-coding gene	gene with protein product		604538	"kinesin-like 6 (mitotic centromere-associated kinesin)"	KNSL6		9434124	Standard	NM_006845		Approved	MCAK, CT139	uc001cmg.4	Q99661	OTTHUMG00000008416	ENST00000372224.4:c.1573-1A>G	chr1.hg19:g.45226265A>G		87.0	0.0		80.0	4.0	NM_006845	B3ITR9|Q5JR88|Q6ICU1|Q96C18|Q96HB8|Q9BWV8	Missense_Mutation	SNP	ENST00000372224.4	hg19	CCDS512.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.3|21.3	4.131478|4.131478	0.77549|0.77549	.|.	.|.	ENSG00000142945|ENSG00000142945	ENST00000372224;ENST00000372218;ENST00000372222;ENST00000372217|ENST00000423289	T;T;T;T|.	0.17370|.	2.28;2.28;2.28;2.28|.	5.66|5.66	5.66|5.66	0.87406|0.87406	Kinesin, motor domain (3);|.	0.118870|.	0.64402|.	D|.	0.000011|.	T|T	0.80417|0.80417	0.4619|0.4619	M|M	0.87617|0.87617	2.895|2.895	0.80722|0.80722	D|D	1|1	P;D;P|.	0.54772|.	0.949;0.968;0.949|.	D;P;D|.	0.66497|.	0.944;0.801;0.944|.	T|T	0.83227|0.83227	-0.0065|-0.0065	10|5	0.87932|.	D|.	0|.	.|.	16.1884|16.1884	0.81971|0.81971	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	484;471;525|.	B7Z6Q6;Q99661-2;Q99661|.	.;.;KIF2C_HUMAN|.	G|G	525;484;412;471|3	ENSP00000361298:E525G;ENSP00000361292:E484G;ENSP00000361296:E412G;ENSP00000361291:E471G|.	ENSP00000361291:E471G|.	E|S	+|+	2|1	0|0	KIF2C|KIF2C	44998852|44998852	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.495000|0.495000	0.33615|0.33615	9.267000|9.267000	0.95665|0.95665	2.285000|2.285000	0.76669|0.76669	0.528000|0.528000	0.53228|0.53228	GAG|AGT	.	.		0.597	KIF2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023180.1	NM_006845	Missense_Mutation	G	45226265	A	G	45226265	5	3	282	1	0	0	0	0	0	0	1	0	8308	318	11	2	1636	2	KIF2C	1	45226265	Splice_Site	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1313456	45226265	204024356	38	40272										
PTCH2	8643	hgsc.bcm.edu	37	chr1	45293130	45293130	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggggtgcctgggtggccggtGggggcagcaccgccttgagg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:45293130delG	ENST00000372192.3	-	15	2445	c.2315delC	c.(2314-2316)ccafs	p.P773fs	PTCH2_ENST00000447098.2_Frame_Shift_Del_p.P773fs	NM_003738.4	NP_003729.3	Q9Y6C5	PTC2_HUMAN	patched 2	773					epidermis development (GO:0008544)|hair cycle (GO:0042633)|negative regulation of smoothened signaling pathway (GO:0045879)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|smoothened binding (GO:0005119)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(19)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	50	Acute lymphoblastic leukemia(166;0.155)					GGTGGCCGGTGGGGGCAGCAC	0.662									Basal Cell Nevus syndrome																												p.P772fs		Atlas-INDEL	.											.	PTCH2	96	.	0			c.2316delA						.						46	56	53					1																	45293130		2203	4300	6503	SO:0001589	frameshift_variant	8643	exon15	Familial Cancer Database	Gorlin syndrome, Gorlin-Golz syndrome, Naevoid Basal Cell Carcinoma syndrome, NBCCS	.	AF091501	CCDS516.1, CCDS53312.1	1p34.1	2010-06-24	2010-06-24		ENSG00000117425	ENSG00000117425			9586	protein-coding gene	gene with protein product		603673	"patched (Drosophila) homolog 2", "patched homolog 2 (Drosophila)"			9811851, 9931336	Standard	NM_003738		Approved		uc010olf.2	Q9Y6C5	OTTHUMG00000008490	ENST00000372192.3:c.2315delC	chr1.hg19:g.45293130delG	ENSP00000361266:p.Pro773fs	241.0	0.0		189.0	13.0	NM_003738	O95341|O95856|Q53Z57|Q5QP87|Q6UX14	Frame_Shift_Del	DEL	ENST00000372192.3	hg19	CCDS516.1																																																																																			.	.		0.662	PTCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023428.4	NM_003738		-	45293130	G	-	45293130	7	5	282	1	0	1	0	1	0	0	0	0	12743	1348	47	0	1348	0	PTCH2	1	45293130	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	66865	45293130	203957491	39	40273										
PTCH2	8643	hgsc.bcm.edu	37	chr1	45296538	45296538	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acctgcctgctgtgatggttGggggcactaggtgggcagtg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:45296538delG	ENST00000372192.3	-	6	925	c.795delC	c.(793-795)cccfs	p.P265fs	PTCH2_ENST00000447098.2_Frame_Shift_Del_p.P265fs	NM_003738.4	NP_003729.3	Q9Y6C5	PTC2_HUMAN	patched 2	265					epidermis development (GO:0008544)|hair cycle (GO:0042633)|negative regulation of smoothened signaling pathway (GO:0045879)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|smoothened binding (GO:0005119)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(19)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	50	Acute lymphoblastic leukemia(166;0.155)					TGTGATGGTTGGGGGCACTAG	0.622									Basal Cell Nevus syndrome																												p.N266fs		Atlas-INDEL	.											.	PTCH2	96	.	0			c.796delA						.						49	51	50					1																	45296538		2203	4300	6503	SO:0001589	frameshift_variant	8643	exon6	Familial Cancer Database	Gorlin syndrome, Gorlin-Golz syndrome, Naevoid Basal Cell Carcinoma syndrome, NBCCS	.	AF091501	CCDS516.1, CCDS53312.1	1p34.1	2010-06-24	2010-06-24		ENSG00000117425	ENSG00000117425			9586	protein-coding gene	gene with protein product		603673	"patched (Drosophila) homolog 2", "patched homolog 2 (Drosophila)"			9811851, 9931336	Standard	NM_003738		Approved		uc010olf.2	Q9Y6C5	OTTHUMG00000008490	ENST00000372192.3:c.795delC	chr1.hg19:g.45296538delG	ENSP00000361266:p.Pro265fs	241.0	0.0		163.0	11.0	NM_003738	O95341|O95856|Q53Z57|Q5QP87|Q6UX14	Frame_Shift_Del	DEL	ENST00000372192.3	hg19	CCDS516.1																																																																																			.	.		0.622	PTCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023428.4	NM_003738		-	45296538	G	-	45296538	7	5	282	1	0	1	0	1	0	0	0	0	12743	1335	47	0	2904	0	PTCH2	1	45296538	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	3408	45296538	203954083	40	40274										
NASP	4678	hgsc.bcm.edu	37	chr1	46073041	46073041	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggtttatgacgccatgggagAaaaagaagaagccaaaaaaa					rs35351400		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:46073041delA	ENST00000350030.3	+	6	545	c.458delA	c.(457-459)gaafs	p.E153fs	NASP_ENST00000372052.4_Intron|NASP_ENST00000402363.3_Frame_Shift_Del_p.E155fs|NASP_ENST00000537798.1_Frame_Shift_Del_p.E89fs|NASP_ENST00000351223.3_Intron	NM_002482.3	NP_002473.2	P49321	NASP_HUMAN	nuclear autoantigenic sperm protein (histone-binding)	153	Glu-rich (acidic).				blastocyst development (GO:0001824)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone exchange (GO:0043486)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	Hsp90 protein binding (GO:0051879)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	17	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.211)					GCCATGGGAGAAAAAGAAGAA	0.393																																					p.E153fs		Atlas-INDEL	.											.	NASP	77	.	0			c.457delG						.						56	55	56					1																	46073041		2203	4300	6503	SO:0001589	frameshift_variant	4678	exon6			.	M97856	CCDS524.1, CCDS525.1, CCDS55597.1	1p34.1	2013-01-10			ENSG00000132780	ENSG00000132780		"Tetratricopeptide (TTC) repeat domain containing"	7644	protein-coding gene	gene with protein product		603185				1426632	Standard	NM_002482		Approved	FLB7527, FLJ31599, FLJ35510, MGC19722, MGC20372, MGC2297, DKFZp547F162, PRO1999	uc001coi.2	P49321	OTTHUMG00000007826	ENST00000350030.3:c.458delA	chr1.hg19:g.46073041delA	ENSP00000255120:p.Glu153fs	165.0	0.0		146.0	10.0	NM_002482	A8K6H2|B4DQP3|D3DQ07|F5H3J2|Q53GW5|Q5T622|Q5T625|Q96A69|Q9BTW2	Frame_Shift_Del	DEL	ENST00000350030.3	hg19	CCDS524.1																																																																																			.	.		0.393	NASP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021533.2	NM_002482		-	46073041	A	-	46073041	7	5	282	1	0	1	0	1	0	0	0	0	10181	246	9	0	557	0	NASP	1	46073041	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	776503	46073041	203177580	41	40275										
GPBP1L1	60313	hgsc.bcm.edu	37	chr1	46120968	46120968	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctgggtaggtgctctccgtgTttttcgaaggtggcagtagg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:46120968delT	ENST00000290795.3	-	4	1305	c.84delA	c.(82-84)aaafs	p.K28fs	GPBP1L1_ENST00000355105.3_Frame_Shift_Del_p.K28fs			Q9HC44	GPBL1_HUMAN	GC-rich promoter binding protein 1-like 1	28					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)		GPBP1L1/MAST2_ENST00000361297(2)	breast(1)|endometrium(2)|large_intestine(4)|lung(10)|ovary(1)|skin(2)|stomach(1)	21	Acute lymphoblastic leukemia(166;0.155)					GCTCTCCGTGTTTTTCGAAGG	0.428																																					p.H29fs		Atlas-INDEL	.											.	GPBP1L1	43	.	0			c.85delC						.						143	138	140					1																	46120968		2203	4300	6503	SO:0001589	frameshift_variant	60313	exon5			.		CCDS528.1	1p34.1	2008-02-05			ENSG00000159592	ENSG00000159592			28843	protein-coding gene	gene with protein product						12477932	Standard	NM_021639		Approved	SP192	uc001coq.3	Q9HC44	OTTHUMG00000040990	ENST00000290795.3:c.84delA	chr1.hg19:g.46120968delT	ENSP00000290795:p.Lys28fs	325.0	0.0		238.0	15.0	NM_021639	D3DQ10|Q9H751	Frame_Shift_Del	DEL	ENST00000290795.3	hg19	CCDS528.1																																																																																			.	.		0.428	GPBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098375.1	NM_021639		-	46120968	T	-	46120968	7	5	282	1	0	1	0	1	0	0	0	0	6604	1722	60	0	1376	0	GPBP1L1	1	46120968	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	47927	46120968	203129653	42	40276										
MAST2	23139	hgsc.bcm.edu	37	chr1	46290243	46290243	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggagaggaaacctggccagcTctctatcgggtaaatatctg	12	9	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:46290243T>C	ENST00000361297.2	+	2	599	c.316T>C	c.(316-318)Tct>Cct	p.S106P	MAST2_ENST00000372009.2_Missense_Mutation_p.S106P	NM_015112.2	NP_055927.2			microtubule associated serine/threonine kinase 2											breast(1)|lung(3)|ovary(5)|stomach(2)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					CCTGGCCAGCTCTCTATCGGG	0.368																																					p.S106P		Atlas-SNP	.											.	MAST2	136	.	0			c.T316C						.						145	130	135					1																	46290243		1851	4093	5944	SO:0001583	missense	23139	exon2			GCCAGCTCTCTAT	AB047005	CCDS41326.1	1p34.1	2008-02-05			ENSG00000086015	ENSG00000086015			19035	protein-coding gene	gene with protein product		612257					Standard	NM_015112		Approved	MAST205, KIAA0807	uc001cov.3	Q6P0Q8	OTTHUMG00000008007	ENST00000361297.2:c.316T>C	chr1.hg19:g.46290243T>C	ENSP00000354671:p.Ser106Pro	165.0	0.0		95.0	4.0	NM_015112		Missense_Mutation	SNP	ENST00000361297.2	hg19	CCDS41326.1	.	.	.	.	.	.	.	.	.	.	T	15.60	2.882221	0.51908	.	.	ENSG00000086015	ENST00000361297;ENST00000372009	T;T	0.66099	-0.15;-0.19	5.39	4.2	0.49525	.	0.000000	0.45126	D	0.000394	T	0.56499	0.1989	L	0.38175	1.15	0.34464	D	0.702027	D;D	0.56035	0.974;0.974	P;P	0.45913	0.497;0.497	T	0.72040	-0.4410	10	0.66056	D	0.02	-0.4891	13.6487	0.62297	0.0:0.0:0.1375:0.8625	.	106;106	E7ERL6;Q6P0Q8	.;MAST2_HUMAN	P	106	ENSP00000354671:S106P;ENSP00000361079:S106P	ENSP00000354671:S106P	S	+	1	0	MAST2	46062830	1.000000	0.71417	0.993000	0.49108	0.934000	0.57294	3.754000	0.55189	2.048000	0.60808	0.533000	0.62120	TCT	.	.		0.368	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112		C	46290243	T	C	46290243	3	2	282	1	0	0	0	0	1	0	0	0	9334	1551	54	2	322	2	MAST2	1	46290243	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	169275	46290243	202960378	43	40277										
PIK3R3	8503	hgsc.bcm.edu	37	chr1	46531807	46531807	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgagagtggtattcttgcagTtttttacctactgcatcaat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:46531807delT	ENST00000262741.5	-	5	1229	c.540delA	c.(538-540)aaafs	p.K180fs	PIK3R3_ENST00000340332.6_Frame_Shift_Del_p.K144fs|PIK3R3_ENST00000420542.1_Frame_Shift_Del_p.K180fs|PIK3R3_ENST00000540385.1_Frame_Shift_Del_p.K226fs|PIK3R3_ENST00000354242.4_Frame_Shift_Del_p.K180fs|PIK3R3_ENST00000423209.1_Frame_Shift_Del_p.K180fs|PIK3R3_ENST00000372006.1_Frame_Shift_Del_p.K180fs	NM_003629.3	NP_003620.3	Q92569	P55G_HUMAN	phosphoinositide-3-kinase, regulatory subunit 3 (gamma)	180					insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)			endometrium(1)|large_intestine(5)|lung(6)|prostate(2)	14	Acute lymphoblastic leukemia(166;0.155)				Isoprenaline(DB01064)	ATTCTTGCAGTTTTTTACCTA	0.318																																					p.L181fs		Atlas-INDEL	.											.	PIK3R3	41	.	0			c.541delC						.						149	133	138					1																	46531807		2201	4296	6497	SO:0001589	frameshift_variant	8503	exon5			.	BC021622	CCDS529.1	1p34.1	2013-02-14	2008-02-04		ENSG00000117461	ENSG00000117461		"SH2 domain containing"	8981	protein-coding gene	gene with protein product		606076				9524259	Standard	NM_003629		Approved	p55	uc001cpb.4	Q92569	OTTHUMG00000008096	ENST00000262741.5:c.540delA	chr1.hg19:g.46531807delT	ENSP00000262741:p.Lys180fs	259.0	0.0		187.0	14.0	NM_003629	B2R9C1|D3DQ12|O60482|Q5T4P1|Q5T4P2	Frame_Shift_Del	DEL	ENST00000262741.5	hg19	CCDS529.1																																																																																			.	.		0.318	PIK3R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022171.1	NM_003629		-	46531807	T	-	46531807	7	5	282	1	0	1	0	1	0	0	0	0	11929	1722	60	0	869	0	PIK3R3	1	46531807	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	241564	46531807	202718814	44	40278										
CYP4B1	1580	hgsc.bcm.edu	37	chr1	47284400	47284400	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctctggacccctcacggctgCccatcaagatgccccagctt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:47284400delC	ENST00000271153.4	+	12	1486	c.1450delC	c.(1450-1452)cccfs	p.P484fs	CYP4B1_ENST00000452782.2_Frame_Shift_Del_p.P322fs|CYP4B1_ENST00000371923.4_Frame_Shift_Del_p.P485fs|CYP4B1_ENST00000371919.4_Frame_Shift_Del_p.P470fs			P13584	CP4B1_HUMAN	cytochrome P450, family 4, subfamily B, polypeptide 1	484					biphenyl metabolic process (GO:0018879)|exogenous drug catabolic process (GO:0042738)|fluorene metabolic process (GO:0018917)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|fluorene oxygenase activity (GO:0018585)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	36	Acute lymphoblastic leukemia(166;0.155)				Midazolam(DB00683)|Phenobarbital(DB01174)|Thiamine(DB00152)	CTCACGGCTGCCCATCAAGAT	0.567																																					p.L484fs		Atlas-INDEL	.											.	CYP4B1	81	.	0			c.1452delG						.						144	127	132					1																	47284400		2203	4300	6503	SO:0001589	frameshift_variant	1580	exon12			.	BC017758	CCDS542.1, CCDS41328.1	1p33	2013-11-11	2003-01-14		ENSG00000142973	ENSG00000142973		"Cytochrome P450s"	2644	protein-coding gene	gene with protein product		124075	"cytochrome P450, subfamily IVB, polypeptide 1"				Standard	NM_000779		Approved		uc001cqn.4	P13584	OTTHUMG00000007984	ENST00000271153.4:c.1450delC	chr1.hg19:g.47284400delC	ENSP00000271153:p.Pro484fs	245.0	0.0		166.0	10.0	NM_001099772	Q1HBI2|Q8TD85|Q8WWF2|Q8WWU9|Q8WWV0	Frame_Shift_Del	DEL	ENST00000271153.4	hg19	CCDS542.1																																																																																			.	.		0.567	CYP4B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021911.1	NM_000779		-	47284400	C	-	47284400	7	5	282	1	0	1	0	1	0	0	0	0	4187	739	26	0	1499	0	CYP4B1	1	47284400	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	752593	47284400	201966221	45	40279										
ZFYVE9	9372	hgsc.bcm.edu	37	chr1	52705235	52705235	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aagccaggtttacattcaccAaaaggaggcatcactgcaga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:52705235delA	ENST00000371591.1	+	3	2277	c.2146delA	c.(2146-2148)aaafs	p.K716fs	ZFYVE9_ENST00000287727.3_Frame_Shift_Del_p.K716fs|ZFYVE9_ENST00000357206.2_Frame_Shift_Del_p.K716fs	NM_004799.2|NM_007324.2	NP_004790.2|NP_015563.2	O95405	ZFYV9_HUMAN	zinc finger, FYVE domain containing 9	716					endocytosis (GO:0006897)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|SMAD protein complex assembly (GO:0007183)|SMAD protein import into nucleus (GO:0007184)|transforming growth factor beta receptor signaling pathway (GO:0007179)	early endosome (GO:0005769)|early endosome membrane (GO:0031901)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|serine-type peptidase activity (GO:0008236)			breast(1)|central_nervous_system(4)|endometrium(3)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	53						TACATTCACCAAAAGGAGGCA	0.443																																					p.T715fs		Atlas-INDEL	.											.	ZFYVE9	131	.	0			c.2145delC						.						53	53	53					1																	52705235		2203	4299	6502	SO:0001589	frameshift_variant	9372	exon4			.	AF104304	CCDS563.1, CCDS564.1	1p32.3	2014-06-13	2004-05-21	2004-05-26	ENSG00000157077	ENSG00000157077		"Zinc fingers, FYVE domain containing"	6775	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 173"	603755	"MAD, mothers against decapentaplegic homolog (Drosophila) interacting protein, receptor activation anchor"	MADHIP		9865696	Standard	NM_007324		Approved	SMADIP, SARA, PPP1R173	uc001cto.4	O95405	OTTHUMG00000008061	ENST00000371591.1:c.2146delA	chr1.hg19:g.52705235delA	ENSP00000360647:p.Lys716fs	223.0	0.0		155.0	11.0	NM_007324	Q5T0F6|Q5T0F7|Q9UNE1|Q9Y5R7	Frame_Shift_Del	DEL	ENST00000371591.1	hg19	CCDS563.1																																																																																			.	.		0.443	ZFYVE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022083.1	NM_007324		-	52705235	A	-	52705235	7	5	282	1	0	1	0	1	0	0	0	0	17686	131	5	0	2152	0	ZFYVE9	1	52705235	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	5420835	52705235	196545386	46	40280										
CC2D1B	200014	hgsc.bcm.edu	37	chr1	52822693	52822693	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctcttgttgctccagaagcaTtttttgcagctgggcataca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:52822693delT	ENST00000371586.2	-	16	2014	c.1876delA	c.(1876-1878)atgfs	p.M626fs	CC2D1B_ENST00000438831.1_Start_Codon_Del|CC2D1B_ENST00000460261.1_5'UTR|CC2D1B_ENST00000284376.3_Frame_Shift_Del_p.M620fs	NM_032449.2	NP_115825.1	Q5T0F9	C2D1B_HUMAN	coiled-coil and C2 domain containing 1B	626						nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(1)|large_intestine(6)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	27						TCCAGAAGCATTTTTTGCAGC	0.592																																					p.M626fs		Atlas-INDEL	.											.	CC2D1B	73	.	0			c.1877delT						.						76	73	74					1																	52822693		2191	4294	6485	SO:0001589	frameshift_variant	200014	exon16			.	AB058739	CCDS30714.1	1p32.3	2008-02-05			ENSG00000154222	ENSG00000154222			29386	protein-coding gene	gene with protein product						11347906	Standard	NM_032449		Approved	KIAA1836	uc001ctq.2	Q5T0F9	OTTHUMG00000008102	ENST00000371586.2:c.1876delA	chr1.hg19:g.52822693delT	ENSP00000360642:p.Met626fs	282.0	0.0		214.0	13.0	NM_032449	Q49AE8|Q5T0F8|Q5T0G0|Q6ZNQ1|Q96AP3|Q96I04|Q96JJ1	Frame_Shift_Del	DEL	ENST00000371586.2	hg19	CCDS30714.1																																																																																			.	.		0.592	CC2D1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000022189.1	NM_032449		-	52822693	T	-	52822693	7	5	282	1	0	1	0	1	0	0	0	0	2729	1493	52	0	736	0	CC2D1B	1	52822693	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	117458	52822693	196427928	47	40281										
ZCCHC11	23318	hgsc.bcm.edu	37	chr1	52891114	52891114	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aggccacgaagctgggacaaGggggaaatggggacgcggtg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:52891114delG	ENST00000371544.3	-	29	5036	c.4774delC	c.(4774-4776)cttfs	p.L1592fs	ZCCHC11_ENST00000257177.4_Frame_Shift_Del_p.L1593fs	NM_001009881.2|NM_015269.2	NP_001009881.1|NP_056084.1	Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11	1592	Pro-rich.				cytokine production (GO:0001816)|miRNA catabolic process (GO:0010587)|miRNA metabolic process (GO:0010586)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|pre-miRNA processing (GO:0031054)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|RNA 3'-end processing (GO:0031123)|stem cell maintenance (GO:0019827)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(17)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	58						GCTGGGACAAGGGGGAAATGG	0.483																																					p.L1593fs		Atlas-INDEL	.											.	ZCCHC11	151	.	0			c.4778delT						.						84	84	84					1																	52891114		2203	4300	6503	SO:0001589	frameshift_variant	23318	exon29			.	D83776	CCDS30715.1, CCDS30716.1	1p32.3	2014-03-05			ENSG00000134744	ENSG00000134744		"Zinc fingers, CCHC domain containing"	28981	protein-coding gene	gene with protein product	"TUTase4"	613692				8724849, 12239557	Standard	NM_015269		Approved	KIAA0191, PAPD3, TUT4	uc001cty.2	Q5TAX3	OTTHUMG00000008200	ENST00000371544.3:c.4774delC	chr1.hg19:g.52891114delG	ENSP00000360599:p.Leu1592fs	224.0	0.0		145.0	11.0	NM_001009881	A2RRP0|B7Z8J5|D3DQ35|Q12764|Q5TAX2|Q5TAX4|Q86XZ3	Frame_Shift_Del	DEL	ENST00000371544.3	hg19	CCDS30716.1																																																																																			.	.		0.483	ZCCHC11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022462.1	XM_038288		-	52891114	G	-	52891114	7	5	282	1	0	1	0	1	0	0	0	0	17595	1000	35	0	168	0	ZCCHC11	1	52891114	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	68421	52891114	196359507	48	40282										
ZYG11B	79699	hgsc.bcm.edu	37	chr1	53287272	53287272	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atgggaggccacctccctgtAaaaaacagccccaagccaga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:53287272delA	ENST00000294353.6	+	14	2351	c.2206delA	c.(2206-2208)aaafs	p.K737fs	ZYG11B_ENST00000443756.2_Frame_Shift_Del_p.K667fs	NM_024646.2	NP_078922.1	Q9C0D3	ZY11B_HUMAN	zyg-11 family member B, cell cycle regulator	737										breast(1)|endometrium(1)|kidney(6)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	30						ACCTCCCTGTAAAAAACAGCC	0.433																																					p.C735X		Atlas-INDEL	.											.	ZYG11B	61	.	0			c.2205delT						.						67	66	66					1																	53287272		2203	4300	6503	SO:0001589	frameshift_variant	79699	exon14			.	AB051517	CCDS30717.1	1p32.3	2013-01-17	2012-12-10	2005-07-11	ENSG00000162378	ENSG00000162378		"ZYG11 cell cycle regulator family"	25820	protein-coding gene	gene with protein product			"zyg-11 homolog (C. elegans)", "zyg-11 homolog B (C. elegans)"	ZYG11		11214970	Standard	NM_024646		Approved	FLJ13456	uc001cuj.3	Q9C0D3	OTTHUMG00000008938	ENST00000294353.6:c.2206delA	chr1.hg19:g.53287272delA	ENSP00000294353:p.Lys737fs	276.0	0.0		222.0	15.0	NM_024646	Q8N2X3|Q9H8L8	Frame_Shift_Del	DEL	ENST00000294353.6	hg19	CCDS30717.1																																																																																			.	.		0.433	ZYG11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024749.1	NM_024646		-	53287272	A	-	53287272	7	5	282	1	0	1	0	1	0	0	0	0	18268	363	13	0	2260	0	ZYG11B	1	53287272	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	396158	53287272	195963349	49	40283										
USP24	23358	hgsc.bcm.edu	37	chr1	55608747	55608747	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atcaggtgattccatggctaTtttccaaatgaaatccattc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:55608747delT	ENST00000294383.6	-	22	2484	c.2485delA	c.(2485-2487)atafs	p.I829fs	USP24_ENST00000407756.1_Frame_Shift_Del_p.I669fs	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	829					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						TCCATGGCTATTTTCCAAATG	0.289																																					p.I829fs		Atlas-INDEL	.											.	USP24	323	.	0			c.2486delT						.						51	45	47					1																	55608747		1776	4000	5776	SO:0001589	frameshift_variant	23358	exon22			.	AB028980	CCDS44154.1, CCDS44154.2	1p32.3	2008-04-11	2005-08-08		ENSG00000162402	ENSG00000162402		"Ubiquitin-specific peptidases"	12623	protein-coding gene	gene with protein product		610569	"ubiquitin specific protease 24"			12838346	Standard	NM_015306		Approved	KIAA1057	uc021onw.1	Q9UPU5	OTTHUMG00000008135	ENST00000294383.6:c.2485delA	chr1.hg19:g.55608747delT	ENSP00000294383:p.Ile829fs	284.0	0.0		193.0	12.0	NM_015306	Q6ZSY2|Q8N2Y4|Q9NXD1	Frame_Shift_Del	DEL	ENST00000294383.6	hg19	CCDS44154.2																																																																																			.	.		0.289	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2			-	55608747	T	-	55608747	7	5	282	1	0	1	0	1	0	0	0	0	17070	1493	52	0	5565	0	USP24	1	55608747	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2321475	55608747	193641874	50	40284										
MYSM1	114803	hgsc.bcm.edu	37	chr1	59137586	59137586	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaagatttaacaggtctgccTttttcctcttctcttctttt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:59137586delT	ENST00000472487.1	-	12	1656	c.1617delA	c.(1615-1617)aaafs	p.K539fs	MYSM1_ENST00000493821.1_5'UTR	NM_001085487.2	NP_001078956.1	Q5VVJ2	MYSM1_HUMAN	Myb-like, SWIRM and MPN domains 1	539					chromatin remodeling (GO:0006338)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(6)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(7;9.36e-06)					CAGGTCTGCCTTTTTCCTCTT	0.343																																					p.G540fs		Atlas-INDEL	.											.	MYSM1	50	.	0			c.1618delG						.						132	120	124					1																	59137586		1824	4092	5916	SO:0001589	frameshift_variant	114803	exon12			.	AB067502	CCDS41343.1	1p32.1	2009-02-11	2009-02-11		ENSG00000162601	ENSG00000162601			29401	protein-coding gene	gene with protein product		612176				11572484, 17428495, 17707232	Standard	NM_001085487		Approved	KIAA1915	uc009wab.2	Q5VVJ2	OTTHUMG00000009533	ENST00000472487.1:c.1617delA	chr1.hg19:g.59137586delT	ENSP00000418734:p.Lys539fs	277.0	0.0		164.0	10.0	NM_001085487	A8KA54|B3KX65|Q68DD3|Q6AI53|Q7Z3G8|Q96PX3	Frame_Shift_Del	DEL	ENST00000472487.1	hg19	CCDS41343.1																																																																																			.	.		0.343	MYSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026343.2	XM_055481		-	59137586	T	-	59137586	7	5	282	1	0	1	0	1	0	0	0	0	10110	1606	56	0	905	0	MYSM1	1	59137586	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3528839	59137586	190113035	51	40285										
HOOK1	51361	hgsc.bcm.edu	37	chr1	60325886	60325886	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtttattcgactgcaacatgAaaataagatgcttcgcttac							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:60325886delA	ENST00000371208.3	+	15	1675	c.1418delA	c.(1417-1419)gaafs	p.E473fs	HOOK1_ENST00000395561.2_Frame_Shift_Del_p.E431fs|HOOK1_ENST00000465876.1_3'UTR	NM_015888.4	NP_056972.1	Q9UJC3	HOOK1_HUMAN	hook microtubule-tethering protein 1	473	Sufficient for interaction with microtubules.				early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)|spermatid development (GO:0007286)	FHF complex (GO:0070695)|microtubule (GO:0005874)	identical protein binding (GO:0042802)			biliary_tract(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|urinary_tract(1)	29	all_cancers(7;0.000129)					CTGCAACATGAAAATAAGATG	0.333																																					p.E473fs		Atlas-INDEL	.											.	HOOK1	54	.	0			c.1417delG						.						95	98	97					1																	60325886		2203	4300	6503	SO:0001589	frameshift_variant	51361	exon15			.	AF044923	CCDS612.1	1p32.1	2013-08-21	2013-08-21		ENSG00000134709	ENSG00000134709			19884	protein-coding gene	gene with protein product		607820	"hook homolog 1 (Drosophila)"			9927460	Standard	XM_005270922		Approved	HK1	uc001czo.3	Q9UJC3	OTTHUMG00000008990	ENST00000371208.3:c.1418delA	chr1.hg19:g.60325886delA	ENSP00000360252:p.Glu473fs	217.0	0.0		178.0	15.0	NM_015888	A8K8E9|A8MU44|B4DX15|O60561|Q5TG44	Frame_Shift_Del	DEL	ENST00000371208.3	hg19	CCDS612.1																																																																																			.	.		0.333	HOOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024934.1	NM_015888		-	60325886	A	-	60325886	7	5	282	1	0	1	0	1	0	0	0	0	7291	246	9	0	1476	0	HOOK1	1	60325886	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1188300	60325886	188924735	52	40286										
INADL	10207	hgsc.bcm.edu	37	chr1	62586958	62586958	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gagtttcagatccttcccagAaaaattcaggtattacacgg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:62586958delA	ENST00000371158.2	+	38	5110	c.4996delA	c.(4996-4998)aaafs	p.K1666fs	INADL_ENST00000472512.1_3'UTR	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1666					cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						TCCTTCCCAGAAAAATTCAGG	0.408																																					p.Q1665fs		Atlas-INDEL	.											.	INADL	179	.	0			c.4995delG						.			1,3747		0,1,1873	66	69	68			-5	0	1		69	0,7928		0,0,3964	no	frameshift	INADL	NM_176877.2		0,1,5837	A1A1,A1R,RR		0.0,0.0267,0.0086			62586958	1,11675	1946	4153	6099	SO:0001589	frameshift_variant	10207	exon38			.	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.4996delA	chr1.hg19:g.62586958delA	ENSP00000360200:p.Lys1666fs	219.0	0.0		159.0	11.0	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Frame_Shift_Del	DEL	ENST00000371158.2	hg19	CCDS617.2																																																																																			.	.		0.408	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		-	62586958	A	-	62586958	7	5	282	1	0	1	0	1	0	0	0	0	7740	247	9	0	5142	0	INADL	1	62586958	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2261072	62586958	186663663	53	40287										
JAK1	3716	hgsc.bcm.edu	37	chr1	65309771	65309771	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atcagcgtcttgtctttcaaGgggatctcgccattgtagca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:65309771delG	ENST00000342505.4	-	17	2627	c.2379delC	c.(2377-2379)cccfs	p.P793fs	JAK1_ENST00000465376.1_5'UTR	NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	793	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	TGTCTTTCAAGGGGATCTCGC	0.557			Mis		ALL																																p.L794X		Atlas-INDEL	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	.	JAK1	209	.	0			c.2380delT						.						128	131	130					1																	65309771		2030	4203	6233	SO:0001589	frameshift_variant	3716	exon17			.	M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.2379delC	chr1.hg19:g.65309771delG	ENSP00000343204:p.Pro793fs	241.0	0.0		150.0	10.0	NM_002227	Q59GQ2|Q9UD26	Frame_Shift_Del	DEL	ENST00000342505.4	hg19	CCDS41346.1																																																																																			.	.		0.557	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227		-	65309771	G	-	65309771	7	5	282	1	0	1	0	1	0	0	0	0	7946	987	35	0	1121	0	JAK1	1	65309771	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	2722813	65309771	183940850	54	40288										
PDE4B	5142	hgsc.bcm.edu	37	chr1	66458806	66458806	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcattcggcagcgtcgtcgcTtcactgtggctcatacatgg	12	12	2	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:66458806T>C	ENST00000329654.4	+	3	468				PDE4B_ENST00000423207.2_Missense_Mutation_p.F73L|PDE4B_ENST00000371049.3_Intron	NM_001037341.1	NP_001032418.1	Q07343	PDE4B_HUMAN	phosphodiesterase 4B, cAMP-specific						cAMP catabolic process (GO:0006198)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to lipopolysaccharide (GO:0071222)|leukocyte migration (GO:0050900)|negative regulation of relaxation of cardiac muscle (GO:1901898)|neutrophil chemotaxis (GO:0030593)|neutrophil homeostasis (GO:0001780)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of high voltage-gated calcium channel activity (GO:1901841)|T cell receptor signaling pathway (GO:0050852)	cell periphery (GO:0071944)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	37					Adenosine monophosphate(DB00131)|Amrinone(DB01427)|Caffeine(DB00201)|Dyphylline(DB00651)|Enprofylline(DB00824)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Papaverine(DB01113)|Pentoxifylline(DB00806)|Roflumilast(DB01656)|Theobromine(DB01412)|Theophylline(DB00277)	GCGTCGTCGCTTCACTGTGGC	0.438																																					p.F73L		Atlas-SNP	.											.	PDE4B	231	.	0			c.T217C						.						68	64	66					1																	66458806		2203	4300	6503	SO:0001627	intron_variant	5142	exon1			CGTCGCTTCACTG	L20971	CCDS632.1, CCDS30742.1, CCDS30743.1, CCDS72802.1	1p31	2010-06-24	2010-06-24		ENSG00000184588	ENSG00000184588		"Phosphodiesterases"	8781	protein-coding gene	gene with protein product	"phosphodiesterase E4 dunce homolog (Drosophila)"	600127	"phosphodiesterase 4B, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E4)", "phosphodiesterase 4B, cAMP-specific (phosphodiesterase E4 dunce homolog, Drosophila)"	DPDE4			Standard	XM_005270925		Approved		uc001dco.3	Q07343	OTTHUMG00000009088	ENST00000329654.4:c.281+74288T>C	chr1.hg19:g.66458806T>C		142.0	0.0		89.0	4.0	NM_001037340	A5YW33|O15443|Q13945|Q5TEK4|Q5TEK5|Q5TEK6	Missense_Mutation	SNP	ENST00000329654.4	hg19	CCDS632.1	.	.	.	.	.	.	.	.	.	.	T	14.81	2.646020	0.47258	.	.	ENSG00000184588	ENST00000423207	T	0.68025	-0.3	5.52	5.52	0.82312	.	.	.	.	.	T	0.67468	0.2896	M	0.61703	1.905	0.80722	D	1	P	0.49447	0.924	P	0.60682	0.878	T	0.65467	-0.6161	9	0.11182	T	0.66	.	15.8108	0.78561	0.0:0.0:0.0:1.0	.	78	Q59GM8	.	L	73	ENSP00000392947:F73L	ENSP00000392947:F73L	F	+	1	0	PDE4B	66231394	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.471000	0.80985	2.320000	0.78422	0.528000	0.53228	TTC	.	.		0.438	PDE4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025188.3	NM_002600		C	66458806	T	C	66458806	1	2	282	0	1	0	0	0	0	0	0	0	11649	1609	56	2		2	PDE4B	1	66458806	Intron	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1149035	66458806	182791815	55	40289										
PDE4B	5142	hgsc.bcm.edu	37	chr1	66831430	66831430	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gatcatcctggagtctccaaTcagtttctcatcaacacaag	6	12	5	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:66831430T>C	ENST00000329654.4	+	13	1552	c.1365T>C	c.(1363-1365)aaT>aaC	p.N455N	PDE4B_ENST00000480109.2_Silent_p.N222N|PDE4B_ENST00000371045.5_Silent_p.N283N|PDE4B_ENST00000423207.2_Silent_p.N440N|PDE4B_ENST00000371049.3_Silent_p.N455N	NM_001037341.1	NP_001032418.1	Q07343	PDE4B_HUMAN	phosphodiesterase 4B, cAMP-specific	455					cAMP catabolic process (GO:0006198)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to lipopolysaccharide (GO:0071222)|leukocyte migration (GO:0050900)|negative regulation of relaxation of cardiac muscle (GO:1901898)|neutrophil chemotaxis (GO:0030593)|neutrophil homeostasis (GO:0001780)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of high voltage-gated calcium channel activity (GO:1901841)|T cell receptor signaling pathway (GO:0050852)	cell periphery (GO:0071944)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	37					Adenosine monophosphate(DB00131)|Amrinone(DB01427)|Caffeine(DB00201)|Dyphylline(DB00651)|Enprofylline(DB00824)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Papaverine(DB01113)|Pentoxifylline(DB00806)|Roflumilast(DB01656)|Theobromine(DB01412)|Theophylline(DB00277)	GAGTCTCCAATCAGTTTCTCA	0.413																																					p.N455N		Atlas-SNP	.											.	PDE4B	231	.	0			c.T1365C						.						105	98	100					1																	66831430		2203	4300	6503	SO:0001819	synonymous_variant	5142	exon13			CTCCAATCAGTTT	L20971	CCDS632.1, CCDS30742.1, CCDS30743.1, CCDS72802.1	1p31	2010-06-24	2010-06-24		ENSG00000184588	ENSG00000184588		"Phosphodiesterases"	8781	protein-coding gene	gene with protein product	"phosphodiesterase E4 dunce homolog (Drosophila)"	600127	"phosphodiesterase 4B, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E4)", "phosphodiesterase 4B, cAMP-specific (phosphodiesterase E4 dunce homolog, Drosophila)"	DPDE4			Standard	XM_005270925		Approved		uc001dco.3	Q07343	OTTHUMG00000009088	ENST00000329654.4:c.1365T>C	chr1.hg19:g.66831430T>C		106.0	0.0		96.0	5.0	NM_001037341	A5YW33|O15443|Q13945|Q5TEK4|Q5TEK5|Q5TEK6	Silent	SNP	ENST00000329654.4	hg19	CCDS632.1																																																																																			.	.		0.413	PDE4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025188.3	NM_002600		C	66831430	T	C	66831430	2	2	282	1	0	0	0	0	0	0	0	1	11649	1432	50	2		2	PDE4B	1	66831430	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	372624	66831430	182419191	56	40290										
TCTEX1D1	200132	hgsc.bcm.edu	37	chr1	67236141	67236141	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctctcgccttacagttcagaTggaaaacacctatcagttgg	8	11	3	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:67236141T>C	ENST00000282670.2	+	3	319	c.191T>C	c.(190-192)aTg>aCg	p.M64T	TCTEX1D1_ENST00000491611.1_3'UTR	NM_152665.2	NP_689878.2	Q8N7M0	TC1D1_HUMAN	Tctex1 domain containing 1	64										large_intestine(2)|lung(10)|skin(1)	13						ACAGTTCAGATGGAAAACACC	0.348																																					p.M64T		Atlas-SNP	.											.	TCTEX1D1	27	.	0			c.T191C						.						186	179	182					1																	67236141		2203	4300	6503	SO:0001583	missense	200132	exon3			TTCAGATGGAAAA	AK098192	CCDS633.1	1p31.2	2008-02-05			ENSG00000152760	ENSG00000152760			26882	protein-coding gene	gene with protein product							Standard	NM_152665		Approved	FLJ40873	uc001dcv.3	Q8N7M0	OTTHUMG00000009162	ENST00000282670.2:c.191T>C	chr1.hg19:g.67236141T>C	ENSP00000282670:p.Met64Thr	111.0	0.0		97.0	4.0	NM_152665	Q06YR9|Q5VYE1	Missense_Mutation	SNP	ENST00000282670.2	hg19	CCDS633.1	.	.	.	.	.	.	.	.	.	.	T	16.75	3.210431	0.58343	.	.	ENSG00000152760	ENST00000282670	T	0.14516	2.5	6.06	6.06	0.98353	.	0.120357	0.85682	D	0.000000	T	0.08802	0.0218	M	0.70275	2.135	0.58432	D	0.999999	P	0.36683	0.565	B	0.29440	0.102	T	0.05162	-1.0902	10	0.33141	T	0.24	0.0027	15.6071	0.76682	0.0:0.0:0.0:1.0	.	64	Q8N7M0	TC1D1_HUMAN	T	64	ENSP00000282670:M64T	ENSP00000282670:M64T	M	+	2	0	TCTEX1D1	67008729	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	6.361000	0.73070	2.323000	0.78572	0.528000	0.53228	ATG	.	.		0.348	TCTEX1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025399.2	NM_152665		C	67236141	T	C	67236141	3	2	282	1	0	0	0	0	1	0	0	0	15734	1464	51	2	197	2	TCTEX1D1	1	67236141	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	404711	67236141	182014480	57	40291										
WDR78	79819	hgsc.bcm.edu	37	chr1	67292680	67292680	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cccaatctgcagaacagcttAaaaatacatcatgacaaaat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:67292680delA	ENST00000371026.3	-	15	2217	c.2162delT	c.(2161-2163)ttafs	p.L721fs	WDR78_ENST00000431318.1_Frame_Shift_Del_p.L434fs|RP11-342H21.2_ENST00000456389.1_RNA	NM_024763.4	NP_079039.4	Q5VTH9	WDR78_HUMAN	WD repeat domain 78	721					hematopoietic progenitor cell differentiation (GO:0002244)					NS(1)|endometrium(3)|kidney(6)|large_intestine(6)|lung(10)|ovary(3)|skin(3)	32						AGAACAGCTTAAAAATACATC	0.328																																					p.L721fs		Atlas-INDEL	.											.	WDR78	102	.	0			c.2163delA						.						130	133	132					1																	67292680		2203	4300	6503	SO:0001589	frameshift_variant	79819	exon15			.	BX648840	CCDS635.1, CCDS44157.1	1p31.2	2014-02-21	2013-02-19	2013-02-19	ENSG00000152763	ENSG00000152763		"WD repeat domain containing"	26252	protein-coding gene	gene with protein product						21953912	Standard	NM_207014		Approved	DIC4, FLJ23129	uc001dcx.3	Q5VTH9	OTTHUMG00000009165	ENST00000371026.3:c.2162delT	chr1.hg19:g.67292680delA	ENSP00000360065:p.Leu721fs	461.0	0.0		360.0	24.0	NM_024763	A8K9W5|B5MDT3|H7BY80|Q5VTI0|Q8N5G5|Q9H5R9|Q9UF44	Frame_Shift_Del	DEL	ENST00000371026.3	hg19	CCDS635.1																																																																																			.	.		0.328	WDR78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025404.1	NM_024763		-	67292680	A	-	67292680	7	5	282	1	0	1	0	1	0	0	0	0	17343	372	13	0	396	0	WDR78	1	67292680	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	56539	67292680	181957941	58	40292										
RPE65	6121	hgsc.bcm.edu	37	chr1	68905279	68905279	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggcttgaatcggtcactgcaGgggaattgtacaacgatctc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:68905279delG	ENST00000262340.5	-	7	743	c.690delC	c.(688-690)cccfs	p.P230fs		NM_000329.2	NP_000320.1	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein 65kDa	230					cellular response to electrical stimulus (GO:0071257)|detection of light stimulus involved in visual perception (GO:0050908)|insulin receptor signaling pathway (GO:0008286)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin gene expression (GO:0007468)|retina homeostasis (GO:0001895)|retina morphogenesis in camera-type eye (GO:0060042)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity (GO:0052885)|all-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity (GO:0052884)|metal ion binding (GO:0046872)|retinal isomerase activity (GO:0004744)			central_nervous_system(1)|kidney(3)|large_intestine(12)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	35						GGTCACTGCAGGGGAATTGTA	0.378																																					p.C231fs		Atlas-INDEL	.											.	RPE65	87	.	0			c.691delT						.						188	180	183					1																	68905279		2203	4300	6503	SO:0001589	frameshift_variant	6121	exon7			.	U18991	CCDS643.1	1p31	2014-05-13	2002-08-29		ENSG00000116745	ENSG00000116745	3.1.1.64		10294	protein-coding gene	gene with protein product	"retinol isomerase", "all-trans-retinyl-palmitate hydrolase", "retinoid isomerohydrolase", "BCO family, member 3"	180069	"retinal pigment epithelium-specific protein (65kD)"	RP20		8340400	Standard	XM_006710811		Approved	LCA2, rd12, BCO3	uc001dei.1	Q16518	OTTHUMG00000009208	ENST00000262340.5:c.690delC	chr1.hg19:g.68905279delG	ENSP00000262340:p.Pro230fs	231.0	0.0		145.0	10.0	NM_000329	A8K1L0|Q5T9U3	Frame_Shift_Del	DEL	ENST00000262340.5	hg19	CCDS643.1																																																																																			.	.		0.378	RPE65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025509.1	NM_000329		-	68905279	G	-	68905279	7	5	282	1	0	1	0	1	0	0	0	0	13560	987	35	0	943	0	RPE65	1	68905279	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1612599	68905279	180345342	59	40293										
ZRANB2	9406	hgsc.bcm.edu	37	chr1	71532574	71532574	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgatgaacttgaataagatcTttttcgtggggaagaagagc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:71532574delT	ENST00000370920.3	-	9	1115	c.814delA	c.(814-816)agafs	p.R272fs	ZRANB2_ENST00000254821.6_Frame_Shift_Del_p.R272fs|ZRANB2_ENST00000477096.1_5'UTR|MIR186_ENST00000384988.1_RNA|ZRANB2-AS1_ENST00000450461.1_RNA|ZRANB2-AS1_ENST00000426999.1_RNA	NM_203350.2	NP_976225.1	O95218	ZRAB2_HUMAN	zinc finger, RAN-binding domain containing 2	272	Required for nuclear targeting.				mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(4)|ovary(2)|stomach(1)	15						GAATAAGATCTTTTTCGTGGG	0.388																																					p.R272fs		Atlas-INDEL	.											ZRANB2_ENST00000370920,colon,carcinoma,0,2	ZRANB2	75	.	0			c.815delG						.						83	83	83					1																	71532574		2203	4300	6503	SO:0001589	frameshift_variant	9406	exon9			.	AF065391	CCDS659.1, CCDS660.1	1p31	2008-02-05	2006-06-28	2006-06-28	ENSG00000132485	ENSG00000132485		"Zinc fingers, RAN-binding domain containing"	13058	protein-coding gene	gene with protein product		604347	"zinc finger protein 265"	ZNF265		9931435	Standard	NM_005455		Approved	ZIS, ZIS1, ZIS2	uc001dft.3	O95218	OTTHUMG00000009660	ENST00000370920.3:c.814delA	chr1.hg19:g.71532574delT	ENSP00000359958:p.Arg272fs	231.0	0.0		163.0	11.0	NM_005455	D3DQ75|Q53GS3|Q59F92|Q5VV33|Q5VV34|Q8IXN6|Q9UP63	Frame_Shift_Del	DEL	ENST00000370920.3	hg19	CCDS659.1																																																																																			.	.		0.388	ZRANB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026636.1	NM_203350		-	71532574	T	-	71532574	7	5	282	1	0	1	0	1	0	0	0	0	18238	1617	56	0	224	0	ZRANB2	1	71532574	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2627295	71532574	177718047	60	40294										
TNNI3K	100526835	hgsc.bcm.edu	37	chr1	74901809	74901809	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gggcatgctgtggtggcagaTtttggaggtgagatacccca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:74901809delT	ENST00000370899.3	+	20	2158	c.2121delT	c.(2119-2121)gatfs	p.D707fs	FPGT-TNNI3K_ENST00000557284.2_Frame_Shift_Del_p.D720fs|TNNI3K_ENST00000370891.2_Frame_Shift_Del_p.D707fs|TNNI3K_ENST00000326637.3_Frame_Shift_Del_p.D606fs	NM_001199327.1	NP_001186256			FPGT-TNNI3K readthrough																		TGGTGGCAGATTTTGGAGGTG	0.373																																					p.D707fs		Atlas-INDEL	.											.	.	.	.	0			c.2120delA						.						139	127	131					1																	74901809		2203	4300	6503	SO:0001589	frameshift_variant	100526835	exon20			.			1p31.3	2014-03-14			ENSG00000259030	ENSG00000259030			42952	other	readthrough							Standard	NM_001112808		Approved		uc001dge.2		OTTHUMG00000166281	ENST00000370899.3:c.2121delT	chr1.hg19:g.74901809delT	ENSP00000359936:p.Asp707fs	272.0	0.0		235.0	16.0	NM_001199327		Frame_Shift_Del	DEL	ENST00000370899.3	hg19																																																																																				.	.		0.373	FPGT-TNNI3K-003	NOVEL	basic|appris_candidate|readthrough_transcript|exp_conf	protein_coding	protein_coding	OTTHUMT00000026438.3			-	74901809	T	-	74901809	7	5	282	1	0	1	0	1	0	0	0	0	16344	1490	52	0	2243	0	TNNI3K	1	74901809	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3369235	74901809	174348812	61	40295										
TYW3	127253	hgsc.bcm.edu	37	chr1	75229675	75229675	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	actcatcatatattcataagAaaaaaagaaacccagaaaaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:75229675delA	ENST00000370867.3	+	6	747	c.658delA	c.(658-660)aaafs	p.K221fs	TYW3_ENST00000479111.1_Frame_Shift_Del_p.K101fs|TYW3_ENST00000457880.2_Frame_Shift_Del_p.K188fs|TYW3_ENST00000421739.2_Frame_Shift_Del_p.K137fs|TYW3_ENST00000467646.1_3'UTR	NM_138467.2	NP_612476.1	Q6IPR3	TYW3_HUMAN	tRNA-yW synthesizing protein 3 homolog (S. cerevisiae)	221					tRNA processing (GO:0008033)		methyltransferase activity (GO:0008168)			central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|ovary(2)|prostate(1)|skin(1)	15						TATTCATAAGAAAAAAAGAAA	0.343																																					p.K219fs		Atlas-INDEL	.											.	TYW3	36	.	0			c.657delG						.						81	87	85					1																	75229675		2203	4300	6503	SO:0001589	frameshift_variant	127253	exon6			.	BX647591	CCDS666.1, CCDS53334.1	1p31.1	2008-02-05	2006-05-25	2006-05-25	ENSG00000162623	ENSG00000162623			24757	protein-coding gene	gene with protein product		611245	"chromosome 1 open reading frame 171"	C1orf171		17150819	Standard	NM_138467		Approved	FLJ40918	uc001dgn.3	Q6IPR3	OTTHUMG00000009641	ENST00000370867.3:c.658delA	chr1.hg19:g.75229675delA	ENSP00000359904:p.Lys221fs	288.0	0.0		243.0	17.0	NM_138467	B4DSP9|E9PGR7|Q5HYJ0|Q8N7L1	Frame_Shift_Del	DEL	ENST00000370867.3	hg19	CCDS666.1																																																																																			.	.		0.343	TYW3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026573.1	NM_138467		-	75229675	A	-	75229675	7	5	282	1	0	1	0	1	0	0	0	0	16835	247	9	0	680	0	TYW3	1	75229675	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	327866	75229675	174020946	62	40296										
MSH4	4438	hgsc.bcm.edu	37	chr1	76269449	76269449	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaacaaaagagcttatgcagAaaacacagttgcatcaaatt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:76269449delA	ENST00000263187.3	+	2	382	c.278delA	c.(277-279)gaafs	p.E93fs		NM_002440.3	NP_002431.2	O15457	MSH4_HUMAN	mutS homolog 4	93					ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|female gamete generation (GO:0007292)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|ovarian follicle development (GO:0001541)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	47						GCTTATGCAGAAAACACAGTT	0.303								Mismatch excision repair (MMR)																													p.E93fs		Atlas-INDEL	.											.	MSH4	147	.	0			c.277delG						.						60	62	61					1																	76269449		2203	4300	6503	SO:0001589	frameshift_variant	4438	exon2			.	U89293	CCDS670.1	1p31	2013-09-12	2013-09-12		ENSG00000057468	ENSG00000057468			7327	protein-coding gene	gene with protein product		602105	"mutS (E. coli) homolog 4", "mutS homolog 4 (E. coli)"			9299235	Standard	NM_002440		Approved		uc001dhd.2	O15457	OTTHUMG00000009788	ENST00000263187.3:c.278delA	chr1.hg19:g.76269449delA	ENSP00000263187:p.Glu93fs	168.0	0.0		147.0	10.0	NM_002440	Q5T4U6|Q8NEB3|Q9UNP8	Frame_Shift_Del	DEL	ENST00000263187.3	hg19	CCDS670.1																																																																																			.	.		0.303	MSH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026983.1	NM_002440		-	76269449	A	-	76269449	7	5	282	1	0	1	0	1	0	0	0	0	9881	246	9	0	284	0	MSH4	1	76269449	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1039774	76269449	172981172	63	40297										
NEXN	91624	hgsc.bcm.edu	37	chr1	78401592	78401592	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggagtggctctattcaagctAaaaacctaaaaagcaagttt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:78401592delA	ENST00000334785.7	+	11	1520	c.1336delA	c.(1336-1338)aaafs	p.K446fs	NEXN_ENST00000330010.8_Frame_Shift_Del_p.K382fs|NEXN_ENST00000480732.2_3'UTR|NEXN_ENST00000457030.1_Frame_Shift_Del_p.K432fs	NM_144573.3	NP_653174.3			nexilin (F actin binding protein)											breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30				Colorectal(170;0.114)		TATTCAAGCTAAAAACCTAAA	0.323																																					p.A445fs		Atlas-INDEL	.											.	NEXN	77	.	0			c.1335delT						.						56	56	56					1																	78401592		1790	4059	5849	SO:0001589	frameshift_variant	91624	exon11			.	AK057954	CCDS41351.1, CCDS53335.1	1p31.1	2014-09-17			ENSG00000162614	ENSG00000162614		"Immunoglobulin superfamily / I-set domain containing"	29557	protein-coding gene	gene with protein product		613121				12053183, 8227983	Standard	NM_144573		Approved	nexilin, NELIN	uc001dic.4	Q0ZGT2	OTTHUMG00000040533	ENST00000334785.7:c.1336delA	chr1.hg19:g.78401592delA	ENSP00000333938:p.Lys446fs	265.0	0.0		193.0	12.0	NM_144573		Frame_Shift_Del	DEL	ENST00000334785.7	hg19	CCDS41351.1																																																																																			.	.		0.323	NEXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097549.1	NM_144573		-	78401592	A	-	78401592	7	5	282	1	0	1	0	1	0	0	0	0	10364	363	13	0	1374	0	NEXN	1	78401592	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2132143	78401592	170849029	64	40298										
PRKACB	5567	hgsc.bcm.edu	37	chr1	84679946	84679946	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aagaatggtgtcagtgatatAaaaactcacaagtggtttgc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:84679946delA	ENST00000370689.2	+	9	1140	c.876delA	c.(874-876)atafs	p.I292fs	PRKACB_ENST00000370685.3_Frame_Shift_Del_p.I339fs|PRKACB_ENST00000370682.3_Frame_Shift_Del_p.I296fs|PRKACB_ENST00000394839.2_Frame_Shift_Del_p.I262fs|PRKACB_ENST00000394838.2_Frame_Shift_Del_p.I299fs	NM_001242862.1|NM_002731.2	NP_001229791.1|NP_002722.1	P22694	KAPCB_HUMAN	protein kinase, cAMP-dependent, catalytic, beta	292	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|carbohydrate metabolic process (GO:0005975)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|negative regulation of meiotic cell cycle (GO:0051447)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|regulation of protein processing (GO:0070613)|response to clozapine (GO:0097338)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|triglyceride catabolic process (GO:0019433)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)|magnesium ion binding (GO:0000287)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(2)|kidney(1)|lung(11)|ovary(1)	16				all cancers(265;0.00536)|Epithelial(280;0.0161)|OV - Ovarian serous cystadenocarcinoma(397;0.141)		TCAGTGATATAAAAACTCACA	0.388																																					p.I339fs		Atlas-INDEL	.											.	PRKACB	174	.	0			c.1016delT						.						85	85	85					1																	84679946		2203	4300	6503	SO:0001589	frameshift_variant	5567	exon9			.	BC035058	CCDS691.1, CCDS692.1, CCDS693.1, CCDS55610.1, CCDS55611.1, CCDS72812.1, CCDS72813.1, CCDS72814.1, CCDS72815.1, CCDS72816.1	1p36.1	2012-10-02			ENSG00000142875	ENSG00000142875	2.7.11.1		9381	protein-coding gene	gene with protein product		176892					Standard	XM_005271016		Approved	PKACb	uc001djl.3	P22694	OTTHUMG00000009975	ENST00000370689.2:c.876delA	chr1.hg19:g.84679946delA	ENSP00000359723:p.Ile292fs	165.0	0.0		131.0	13.0	NM_182948	B1APG4|B4DKB0|B4E2Q1|Q14VH1|Q59GC0|Q5BNE9|Q5BNF0|Q5BNF1|Q5BNF2|Q5BNF3|Q5CZ92|Q5T1K3|Q7Z3M1|Q8IYR5|Q8IZQ0|Q96B09	Frame_Shift_Del	DEL	ENST00000370689.2	hg19	CCDS691.1																																																																																			.	.		0.388	PRKACB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027641.1	NM_182948		-	84679946	A	-	84679946	7	5	282	1	0	1	0	1	0	0	0	0	12510	352	13	0	1114	0	PRKACB	1	84679946	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	6278354	84679946	164570675	65	40299										
SSX2IP	117178	hgsc.bcm.edu	37	chr1	85127951	85127951	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaagaagagaaatcatttccTttttcatttgttgaagaacc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:85127951delT	ENST00000342203.3	-	8	1120	c.857delA	c.(856-858)aagfs	p.K286fs	SSX2IP_ENST00000437941.2_Frame_Shift_Del_p.K259fs|SSX2IP_ENST00000370612.4_Frame_Shift_Del_p.K286fs|SSX2IP_ENST00000605755.1_Frame_Shift_Del_p.K259fs|SSX2IP_ENST00000603677.1_Intron	NM_001166293.1|NM_001166294.1|NM_014021.3	NP_001159765.1|NP_001159766.1|NP_054740.3	Q9Y2D8	ADIP_HUMAN	synovial sarcoma, X breakpoint 2 interacting protein	286					cell adhesion (GO:0007155)|centrosome organization (GO:0051297)|regulation of cell motility (GO:2000145)|regulation of Rac protein signal transduction (GO:0035020)	cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|centriolar satellite (GO:0034451)|nucleus (GO:0005634)|protein complex (GO:0043234)				endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|urinary_tract(1)	19				all cancers(265;0.0053)|Epithelial(280;0.0214)|OV - Ovarian serous cystadenocarcinoma(397;0.173)		AATCATTTCCTTTTTCATTTG	0.333																																					p.K286fs		Atlas-INDEL	.											.	SSX2IP	53	.	0			c.858delG						.						156	175	169					1																	85127951		2203	4300	6503	SO:0001589	frameshift_variant	117178	exon8			.		CCDS699.1, CCDS53337.1	1p22.3	2008-02-05			ENSG00000117155	ENSG00000117155			16509	protein-coding gene	gene with protein product		608690					Standard	NM_014021		Approved		uc001dkj.3	Q9Y2D8	OTTHUMG00000009926	ENST00000342203.3:c.857delA	chr1.hg19:g.85127951delT	ENSP00000340279:p.Lys286fs	177.0	0.0		146.0	10.0	NM_001166293	A8K8W0|B4DFE3|D3DT13|J3KR02|Q6P2P8|Q6ULS1|Q7L168|Q9UIX0	Frame_Shift_Del	DEL	ENST00000342203.3	hg19	CCDS699.1																																																																																			.	.		0.333	SSX2IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027469.1	NM_014021		-	85127951	T	-	85127951	7	5	282	1	0	1	0	1	0	0	0	0	15219	1609	56	0	1015	0	SSX2IP	1	85127951	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	448005	85127951	164122670	66	40300										
SYDE2	84144	hgsc.bcm.edu	37	chr1	85648623	85648623	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aatatcagtatgatgaacttCtcggcagttatatttagaca	7	6	2	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:85648623C>T	ENST00000341460.5	-	3	1751	c.1702G>A	c.(1702-1704)Gaa>Aaa	p.E568K		NM_032184.1	NP_115560.1	Q5VT97	SYDE2_HUMAN	synapse defective 1, Rho GTPase, homolog 2 (C. elegans)	568					activation of Rho GTPase activity (GO:0032862)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)	20				all cancers(265;0.0126)|Epithelial(280;0.0336)		TGATGAACTTCTCGGCAGTTA	0.403																																					p.E568K		Atlas-SNP	.											.	SYDE2	135	.	0			c.G1702A						.						165	162	163					1																	85648623		1843	4098	5941	SO:0001583	missense	84144	exon3			GAACTTCTCGGCA	AL834286	CCDS44169.1	1p22.3	2008-02-05		2005-08-09	ENSG00000097096	ENSG00000097096			25841	protein-coding gene	gene with protein product							Standard	NM_032184		Approved	FLJ13815	uc009wcm.3	Q5VT97	OTTHUMG00000009956	ENST00000341460.5:c.1702G>A	chr1.hg19:g.85648623C>T	ENSP00000340594:p.Glu568Lys	183.0	0.0		122.0	5.0	NM_032184	Q5VT96|Q8NDB8|Q9H8A6	Missense_Mutation	SNP	ENST00000341460.5	hg19	CCDS44169.1	.	.	.	.	.	.	.	.	.	.	C	11.51	1.660920	0.29515	.	.	ENSG00000097096	ENST00000341460	T	0.08984	3.03	5.41	4.5	0.54988	.	0.288725	0.37136	N	0.002222	T	0.03477	0.0100	L	0.51422	1.61	0.23016	N	0.998423	B;B	0.33379	0.41;0.002	B;B	0.26614	0.071;0.005	T	0.19484	-1.0304	10	0.52906	T	0.07	.	13.9668	0.64213	0.0:0.9269:0.0:0.0731	.	568;568	Q5VT97;Q5VT97-2	SYDE2_HUMAN;.	K	568	ENSP00000340594:E568K	ENSP00000340594:E568K	E	-	1	0	SYDE2	85421211	0.979000	0.34478	0.985000	0.45067	0.416000	0.31233	2.532000	0.45659	1.306000	0.44926	0.650000	0.86243	GAA	.	.		0.403	SYDE2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127989.2			T	85648623	C	T	85648623	3	4	282	1	0	0	0	0	1	0	0	0	15451	922	32	3	1902	3	SYDE2	1	85648623	Missense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	520672	85648623	163601998	67	40301										
COL24A1	255631	hgsc.bcm.edu	37	chr1	86196292	86196292	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcagttttgagatgaggaagTttttgtacttcaatcactgg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:86196292delT	ENST00000370571.2	-	60	5448	c.5082delA	c.(5080-5082)aaafs	p.K1694fs	COL24A1_ENST00000436319.1_Frame_Shift_Del_p.K1673fs	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	1694	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				extracellular matrix organization (GO:0030198)|hematopoietic progenitor cell differentiation (GO:0002244)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			NS(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(9)|liver(1)|lung(56)|ovary(4)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	101				all cancers(265;0.0627)|Epithelial(280;0.0689)		GATGAGGAAGTTTTTGTACTT	0.383																																					p.L1695fs		Atlas-INDEL	.											.	COL24A1	202	.	0			c.5083delC						.						144	135	138					1																	86196292		1864	4096	5960	SO:0001589	frameshift_variant	255631	exon60			.	AF410793	CCDS41353.1	1p22.3-p22.2	2013-01-16			ENSG00000171502	ENSG00000171502		"Collagens"	20821	protein-coding gene	gene with protein product		610025					Standard	NM_152890		Approved		uc001dlj.3	Q17RW2	OTTHUMG00000010629	ENST00000370571.2:c.5082delA	chr1.hg19:g.86196292delT	ENSP00000359603:p.Lys1694fs	204.0	0.0		164.0	10.0	NM_152890	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Frame_Shift_Del	DEL	ENST00000370571.2	hg19	CCDS41353.1																																																																																			.	.		0.383	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	NM_152890		-	86196292	T	-	86196292	7	5	282	1	0	1	0	1	0	0	0	0	3685	1722	60	0	66	0	COL24A1	1	86196292	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	547669	86196292	163054329	68	40302										
COL24A1	255631	hgsc.bcm.edu	37	chr1	86313395	86313395	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cttaggaccacttttcccaaTttttccaggaggacctctgc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:86313395delT	ENST00000370571.2	-	39	3781	c.3415delA	c.(3415-3417)attfs	p.I1139fs	COL24A1_ENST00000436319.1_Frame_Shift_Del_p.I1139fs	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	1139	Collagen-like 11.				extracellular matrix organization (GO:0030198)|hematopoietic progenitor cell differentiation (GO:0002244)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			NS(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(9)|liver(1)|lung(56)|ovary(4)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	101				all cancers(265;0.0627)|Epithelial(280;0.0689)		CTTTTCCCAATTTTTCCAGGA	0.443																																					p.I1139fs		Atlas-INDEL	.											.	COL24A1	202	.	0			c.3416delT						.						148	139	142					1																	86313395		1872	4092	5964	SO:0001589	frameshift_variant	255631	exon39			.	AF410793	CCDS41353.1	1p22.3-p22.2	2013-01-16			ENSG00000171502	ENSG00000171502		"Collagens"	20821	protein-coding gene	gene with protein product		610025					Standard	NM_152890		Approved		uc001dlj.3	Q17RW2	OTTHUMG00000010629	ENST00000370571.2:c.3415delA	chr1.hg19:g.86313395delT	ENSP00000359603:p.Ile1139fs	209.0	0.0		178.0	11.0	NM_152890	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Frame_Shift_Del	DEL	ENST00000370571.2	hg19	CCDS41353.1																																																																																			.	.		0.443	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	NM_152890		-	86313395	T	-	86313395	7	5	282	1	0	1	0	1	0	0	0	0	3685	1493	52	0	1817	0	COL24A1	1	86313395	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	117103	86313395	162937226	69	40303										
CLCA1	1179	hgsc.bcm.edu	37	chr1	86957003	86957003	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aacaatggcctcattgatgcTtttggggccctttcatcagg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:86957003delT	ENST00000234701.3	+	10	1764	c.1413delT	c.(1411-1413)gctfs	p.A471fs	CLCA1_ENST00000394711.1_Frame_Shift_Del_p.A471fs			A8K7I4	CLCA1_HUMAN	chloride channel accessory 1	471	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				calcium ion transport (GO:0006816)|cellular response to hypoxia (GO:0071456)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|zymogen granule membrane (GO:0042589)	chloride channel activity (GO:0005254)			NS(1)|breast(3)|endometrium(1)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Lung NSC(277;0.239)		all cancers(265;0.0249)|Epithelial(280;0.0476)		TCATTGATGCTTTTGGGGCCC	0.388																																					p.A471fs		Atlas-INDEL	.											.	CLCA1	109	.	0			c.1412delC						.						126	124	124					1																	86957003		2203	4300	6503	SO:0001589	frameshift_variant	1179	exon9			.		CCDS709.1	1p22.3	2012-02-26	2009-01-29		ENSG00000016490	ENSG00000016490			2015	protein-coding gene	gene with protein product		603906	"chloride channel, calcium activated, family member 1", "chloride channel regulator 1"			9828122	Standard	NM_001285		Approved	CaCC, CLCRG1	uc001dlt.3	A8K7I4	OTTHUMG00000010254	ENST00000234701.3:c.1413delT	chr1.hg19:g.86957003delT	ENSP00000234701:p.Ala471fs	242.0	0.0		169.0	13.0	NM_001285	B2RAV5|O95151|Q5TDF4|Q9UNF6|Q9UPC6	Frame_Shift_Del	DEL	ENST00000234701.3	hg19	CCDS709.1																																																																																			.	.		0.388	CLCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028277.1	NM_001285		-	86957003	T	-	86957003	7	5	282	1	0	1	0	1	0	0	0	0	3459	1596	56	0	1447	0	CLCA1	1	86957003	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	643608	86957003	162293618	70	40304										
BTBD8	284697	hgsc.bcm.edu	37	chr1	92568057	92568057	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tattcatcaaacagaaacatAaaaaactatgaagaggaaat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:92568057delA	ENST00000342818.3	+	3	611	c.375delA	c.(373-375)atafs	p.I125fs	BTBD8_ENST00000540648.1_Frame_Shift_Del_p.I125fs|BTBD8_ENST00000370382.3_Frame_Shift_Del_p.I125fs	NM_183242.3	NP_899065.2	Q5XKL5	BTBD8_HUMAN	BTB (POZ) domain containing 8	125	BTB 1. {ECO:0000255|PROSITE- ProRule:PRU00037}.					nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)	16		all_lung(203;0.0484)|Lung NSC(277;0.126)|Glioma(108;0.222)		all cancers(265;0.0153)|Epithelial(280;0.0982)		ACAGAAACATAAAAAACTATG	0.269																																					p.I125fs		Atlas-INDEL	.											.	BTBD8	32	.	0			c.374delT						.						37	37	37					1																	92568057		2201	4297	6498	SO:0001589	frameshift_variant	284697	exon3			.	AY346333	CCDS737.1	1p22.1	2013-01-08			ENSG00000189195	ENSG00000189195		"BTB/POZ domain containing"	21019	protein-coding gene	gene with protein product						14654994	Standard	NM_183242		Approved		uc001doo.3	Q5XKL5	OTTHUMG00000010289	ENST00000342818.3:c.375delA	chr1.hg19:g.92568057delA	ENSP00000343686:p.Ile125fs	180.0	0.0		150.0	12.0	NM_183242	Q6V9S5	Frame_Shift_Del	DEL	ENST00000342818.3	hg19	CCDS737.1																																																																																			.	.		0.269	BTBD8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028372.1	NM_183242		-	92568057	A	-	92568057	7	5	282	1	0	1	0	1	0	0	0	0	1549	352	13	0	385	0	BTBD8	1	92568057	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	5611054	92568057	156682564	71	40305										
PALMD	54873	hgsc.bcm.edu	37	chr1	100154982	100154982	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaattcttcacccacttgtcAggaggacgaggaagatgtca	11	9	4	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:100154982A>G	ENST00000263174.4	+	7	1541	c.1166A>G	c.(1165-1167)cAg>cGg	p.Q389R	PALMD_ENST00000605497.1_Missense_Mutation_p.Q389R	NM_017734.4	NP_060204.1	Q9NP74	PALMD_HUMAN	palmdelphin	389					regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|membrane (GO:0016020)				central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(8)|ovary(6)|pancreas(1)|prostate(2)	31		all_epithelial(167;0.000813)|all_lung(203;0.0214)|Lung NSC(277;0.0216)		Epithelial(280;0.067)|all cancers(265;0.117)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)		CCCACTTGTCAGGAGGACGAG	0.463																																					p.Q389R		Atlas-SNP	.											PALMD,colon,carcinoma,0,1	PALMD	64	.	0			c.A1166G						.						57	49	52					1																	100154982		2203	4299	6502	SO:0001583	missense	54873	exon7			CTTGTCAGGAGGA	AJ312214	CCDS758.1	1p22-p21	2008-07-18			ENSG00000099260	ENSG00000099260			15846	protein-coding gene	gene with protein product		610182		C1orf11		11478809	Standard	NM_017734		Approved	FLJ20271, PALML	uc001dsg.3	Q9NP74	OTTHUMG00000010764	ENST00000263174.4:c.1166A>G	chr1.hg19:g.100154982A>G	ENSP00000263174:p.Gln389Arg	181.0	0.0		120.0	5.0	NM_017734	Q9H7E6|Q9NPM5|Q9NPM6|Q9NPS0	Missense_Mutation	SNP	ENST00000263174.4	hg19	CCDS758.1	.	.	.	.	.	.	.	.	.	.	A	5.924	0.354610	0.11239	.	.	ENSG00000099260	ENST00000263174	T	0.18016	2.24	5.56	4.44	0.53790	.	0.803312	0.11781	N	0.530179	T	0.05090	0.0136	M	0.63428	1.95	0.26273	N	0.978398	B;P	0.41848	0.351;0.763	B;B	0.35182	0.197;0.165	T	0.38156	-0.9674	10	0.27082	T	0.32	-6.4421	2.0465	0.03561	0.5408:0.1453:0.0783:0.2356	.	389;309	Q9NP74;Q9NP74-2	PALMD_HUMAN;.	R	389	ENSP00000263174:Q389R	ENSP00000263174:Q389R	Q	+	2	0	PALMD	99927570	0.174000	0.23070	0.998000	0.56505	0.299000	0.27559	0.882000	0.28186	0.946000	0.37632	0.460000	0.39030	CAG	.	.		0.463	PALMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029672.1	NM_017734		G	100154982	A	G	100154982	3	3	282	1	0	0	0	0	1	0	0	0	11420	188	7	2	1192	2	PALMD	1	100154982	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	7586925	100154982	149095639	72	40306										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103364549	103364549	+	Splice_Site	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cacctgcagctccaggaggaCcctatagacataagatttat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:103364549delC	ENST00000370096.3	-	55	4400	c.4088delG	c.(4087-4089)ggt>gt	p.G1363fs	COL11A1_ENST00000353414.4_Splice_Site_p.G1324fs|COL11A1_ENST00000512756.1_Splice_Site_p.G1247fs|COL11A1_ENST00000358392.2_Splice_Site_p.G1375fs	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	1363	Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		TCCAGGAGGACCCTATAGACA	0.279																																					p.G1375fs		Atlas-INDEL	.											.	COL11A1	972	.	0			c.4125delT						.						41	42	42					1																	103364549		2201	4297	6498	SO:0001630	splice_region_variant	1301	exon55			.	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.4087-1G>-	chr1.hg19:g.103364549delC		174.0	0.0		171.0	13.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Frame_Shift_Del	DEL	ENST00000370096.3	hg19	CCDS778.1																																																																																			.	.		0.279	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630	Frame_Shift_Del	-	103364549	C	-	103364549	8	5	282	1	0	1	0	1	0	0	1	0	3669	521	18	0	1384	0	COL11A1	1	103364549	Splice_Site	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	3209567	103364549	145886072	73	40307										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103461421	103461421	+	Splice_Site	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctaaacaattaaattttaccTtttcacctttagatcccttg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:103461421delT	ENST00000370096.3	-	28	2651	c.2339delA	c.(2338-2340)aag>ag	p.K780fs	COL11A1_ENST00000353414.4_Splice_Site_p.K741fs|COL11A1_ENST00000512756.1_Splice_Site_p.K664fs|COL11A1_ENST00000358392.2_Splice_Site_p.K792fs	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	780	Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		AAATTTTACCTTTTCACCTTT	0.269																																					p.K792fs		Atlas-INDEL	.											.	COL11A1	972	.	0			c.2376delG						.						68	76	73					1																	103461421		2202	4290	6492	SO:0001630	splice_region_variant	1301	exon28			.	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.2340+1A>-	chr1.hg19:g.103461421delT		232.0	0.0		163.0	10.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Frame_Shift_Del	DEL	ENST00000370096.3	hg19	CCDS778.1																																																																																			.	.		0.269	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630	Frame_Shift_Del	-	103461421	T	-	103461421	8	5	282	1	0	1	0	1	0	0	1	0	3669	1623	56	0	3241	0	COL11A1	1	103461421	Splice_Site	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	96872	103461421	145789200	74	40308										
AKNAD1	254268	hgsc.bcm.edu	37	chr1	109369920	109369920	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gccctttttctccacgttttGcttcctaaaaaaaggtgcat	6	11	1	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:109369920G>T	ENST00000370001.3	-	11	2111	c.1843C>A	c.(1843-1845)Caa>Aaa	p.Q615K	AKNAD1_ENST00000369995.3_Missense_Mutation_p.Q615K|AKNAD1_ENST00000369994.1_Missense_Mutation_p.Q585K|AKNAD1_ENST00000357393.4_Missense_Mutation_p.Q322K	NM_152763.4	NP_689976.2	Q5T1N1	AKND1_HUMAN	AKNA domain containing 1	615						cytoplasm (GO:0005737)				breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|prostate(6)|skin(3)|stomach(2)	32						TCCACGTTTTGCTTCCTAAAA	0.363																																					p.Q615K		Atlas-SNP	.											.	AKNAD1	83	.	0			c.C1843A						.						144	149	148					1																	109369920		2203	4299	6502	SO:0001583	missense	254268	exon11			CGTTTTGCTTCCT	AK095517	CCDS791.2	1p13.3	2009-10-29	2009-10-29	2009-10-29	ENSG00000162641	ENSG00000162641			28398	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 62"	C1orf62			Standard	NM_152763		Approved	MGC26989	uc001dwa.4	Q5T1N1	OTTHUMG00000011231	ENST00000370001.3:c.1843C>A	chr1.hg19:g.109369920G>T	ENSP00000359018:p.Gln615Lys	70.0	0.0		61.0	4.0	NM_152763	B9EK62|Q5T1N0|Q8N990|Q8NCN9	Missense_Mutation	SNP	ENST00000370001.3	hg19	CCDS791.2	.	.	.	.	.	.	.	.	.	.	G	10.91	1.483286	0.26598	.	.	ENSG00000162641	ENST00000370001;ENST00000357393;ENST00000369994;ENST00000369995	T;T;T;T	0.20069	2.1;2.1;2.1;2.1	5.0	3.12	0.35913	.	0.665053	0.13262	N	0.401240	T	0.07098	0.0180	L	0.46157	1.445	0.09310	N	1	B;B	0.26635	0.155;0.084	B;B	0.22386	0.039;0.039	T	0.27297	-1.0078	10	0.52906	T	0.07	-2.3218	6.9745	0.24666	0.0941:0.1884:0.7175:0.0	.	322;615	B4DET8;Q5T1N1	.;AKND1_HUMAN	K	615;322;585;615	ENSP00000359018:Q615K;ENSP00000349968:Q322K;ENSP00000359011:Q585K;ENSP00000359012:Q615K	ENSP00000349968:Q322K	Q	-	1	0	AKNAD1	109171443	1.000000	0.71417	0.170000	0.22879	0.000000	0.00434	2.655000	0.46707	0.807000	0.34208	-0.258000	0.10820	CAA	.	.		0.363	AKNAD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030923.2	NM_152763		T	109369920	G	T	109369920	3	4	282	1	0	0	0	0	1	0	0	0	464	1328	46	3	691	3	AKNAD1	1	109369920	Missense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	5908499	109369920	139880701	75	40309										
AKNAD1	254268	hgsc.bcm.edu	37	chr1	109395035	109395035	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cattgtttctctttctcgtcTtttttgttggcagcattttc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:109395035delT	ENST00000370001.3	-	2	520	c.252delA	c.(250-252)aaafs	p.K84fs	AKNAD1_ENST00000369995.3_Frame_Shift_Del_p.K84fs|AKNAD1_ENST00000369994.1_Frame_Shift_Del_p.K84fs|AKNAD1_ENST00000357393.4_Intron	NM_152763.4	NP_689976.2	Q5T1N1	AKND1_HUMAN	AKNA domain containing 1	84						cytoplasm (GO:0005737)				breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|prostate(6)|skin(3)|stomach(2)	32						CTTTCTCGTCTTTTTTGTTGG	0.403																																					p.D85fs		Atlas-INDEL	.											.,1	AKNAD1	83	.	0			c.253delG						.						122	117	118					1																	109395035		2203	4300	6503	SO:0001589	frameshift_variant	254268	exon2			.	AK095517	CCDS791.2	1p13.3	2009-10-29	2009-10-29	2009-10-29	ENSG00000162641	ENSG00000162641			28398	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 62"	C1orf62			Standard	NM_152763		Approved	MGC26989	uc001dwa.4	Q5T1N1	OTTHUMG00000011231	ENST00000370001.3:c.252delA	chr1.hg19:g.109395035delT	ENSP00000359018:p.Lys84fs	271.0	0.0		198.0	13.0	NM_152763	B9EK62|Q5T1N0|Q8N990|Q8NCN9	Frame_Shift_Del	DEL	ENST00000370001.3	hg19	CCDS791.2																																																																																			.	.		0.403	AKNAD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030923.2	NM_152763		-	109395035	T	-	109395035	7	5	282	1	0	1	0	1	0	0	0	0	464	1606	56	0	2318	0	AKNAD1	1	109395035	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	25115	109395035	139855586	76	40310										
DDX20	11218	hgsc.bcm.edu	37	chr1	112305374	112305374	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cattggattgggagacatacAtgcatcggattgggagagct	14	6	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:112305374A>G	ENST00000369702.4	+	9	1800	c.1180A>G	c.(1180-1182)Atg>Gtg	p.M394V	DDX20_ENST00000475700.1_5'UTR|DDX20_ENST00000536167.1_3'UTR	NM_007204.4	NP_009135.4	Q9UHI6	DDX20_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	394	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oogenesis (GO:0048477)|positive regulation of apoptotic process (GO:0043065)|regulation of steroid biosynthetic process (GO:0050810)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|spliceosomal snRNP assembly (GO:0000387)|spliceosomal tri-snRNP complex assembly (GO:0000244)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)|transcriptional repressor complex (GO:0017053)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)			endometrium(3)|kidney(7)|large_intestine(6)|lung(3)|pancreas(1)|prostate(1)	21		all_cancers(81;1.06e-05)|all_epithelial(167;7.36e-06)|all_lung(203;2.44e-05)|Lung NSC(69;4.15e-05)		Lung(183;0.0234)|Colorectal(144;0.0282)|all cancers(265;0.0614)|Epithelial(280;0.0999)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GGAGACATACATGCATCGGAT	0.403																																					p.M394V		Atlas-SNP	.											.	DDX20	50	.	0			c.A1180G						.						160	159	159					1																	112305374		2203	4300	6503	SO:0001583	missense	11218	exon9			ACATACATGCATC	AF106019	CCDS842.1	1p21.1-p13.2	2008-02-05	2003-06-13		ENSG00000064703	ENSG00000064703		"DEAD-boxes"	2743	protein-coding gene	gene with protein product		606168	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 20, 103kD"			10383418	Standard	NM_007204		Approved	DP103, GEMIN3	uc001ebs.3	Q9UHI6	OTTHUMG00000011956	ENST00000369702.4:c.1180A>G	chr1.hg19:g.112305374A>G	ENSP00000358716:p.Met394Val	103.0	0.0		79.0	4.0	NM_007204	B4DWV7|Q96F72|Q9NVM3|Q9UF59|Q9UIY0|Q9Y659	Missense_Mutation	SNP	ENST00000369702.4	hg19	CCDS842.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.975185	0.74360	.	.	ENSG00000064703	ENST00000369702	T	0.73681	-0.77	5.64	5.64	0.86602	Helicase, C-terminal (3);	0.037568	0.85682	D	0.000000	T	0.41465	0.1160	N	0.00471	-1.455	0.80722	D	1	B	0.29766	0.256	B	0.42112	0.376	T	0.64453	-0.6404	10	0.87932	D	0	-24.0728	15.5302	0.75952	1.0:0.0:0.0:0.0	.	394	Q9UHI6	DDX20_HUMAN	V	394	ENSP00000358716:M394V	ENSP00000358716:M394V	M	+	1	0	DDX20	112106897	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	7.154000	0.77437	2.145000	0.66743	0.533000	0.62120	ATG	.	.		0.403	DDX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033063.2	NM_007204		G	112305374	A	G	112305374	3	3	282	1	0	0	0	0	1	0	0	0	4350	217	8	2	1214	2	DDX20	1	112305374	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2910339	112305374	136945247	77	40311										
AP4B1	10717	hgsc.bcm.edu	37	chr1	114442999	114442999	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agttcaatacttcagcctggCcccattggtccagttttgac							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:114442999delC	ENST00000369569.1	-	5	921	c.641delG	c.(640-642)ggcfs	p.G214fs	AP4B1-AS1_ENST00000419536.1_RNA|AP4B1_ENST00000369567.1_Frame_Shift_Del_p.G46fs|AP4B1_ENST00000369566.3_Frame_Shift_Del_p.G121fs|AP4B1_ENST00000256658.4_Frame_Shift_Del_p.G214fs|AP4B1_ENST00000462591.1_5'Flank	NM_001253852.1	NP_001240781.1	Q9Y6B7	AP4B1_HUMAN	adaptor-related protein complex 4, beta 1 subunit	214					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|coated pit (GO:0005905)|trans-Golgi network (GO:0005802)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|ovary(3)|prostate(3)	25	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.1e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTCAGCCTGGCCCCATTGGTC	0.418																																					p.G214fs		Atlas-INDEL	.											.	AP4B1	72	.	0			c.642delC						.						62	57	59					1																	114442999		2203	4300	6503	SO:0001589	frameshift_variant	10717	exon6			.	AF092094	CCDS865.1	1p13.2	2012-03-30			ENSG00000134262	ENSG00000134262			572	protein-coding gene	gene with protein product	"beta 4 subunit of AP-4"	607245	"spastic paraplegia 47"	SPG47		10066790	Standard	NM_006594		Approved	BETA-4	uc001eeb.3	Q9Y6B7	OTTHUMG00000011943	ENST00000369569.1:c.641delG	chr1.hg19:g.114442999delC	ENSP00000358582:p.Gly214fs	238.0	0.0		188.0	13.0	NM_006594	B7Z4X3|Q59EJ4|Q96CL6	Frame_Shift_Del	DEL	ENST00000369569.1	hg19	CCDS865.1																																																																																			.	.		0.418	AP4B1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033037.1	NM_006594		-	114442999	C	-	114442999	7	5	282	1	0	1	0	1	0	0	0	0	751	739	26	0	1602	0	AP4B1	1	114442999	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	2137625	114442999	134807622	78	40312										
HIPK1	204851	hgsc.bcm.edu	37	chr1	114515848	114515848	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcatctgtatacgtatgctgCcccgacttctgctgctgcac							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:114515848delC	ENST00000369558.1	+	16	3579	c.3347delC	c.(3346-3348)gccfs	p.A1116fs	HIPK1_ENST00000369555.2_Frame_Shift_Del_p.A1071fs|HIPK1_ENST00000369554.2_Frame_Shift_Del_p.A1071fs|HIPK1_ENST00000369561.4_Frame_Shift_Del_p.A1082fs|HIPK1_ENST00000340480.4_Frame_Shift_Del_p.A742fs|HIPK1_ENST00000369553.1_Frame_Shift_Del_p.A722fs|HIPK1_ENST00000426820.2_Frame_Shift_Del_p.A1116fs|HIPK1_ENST00000406344.1_Frame_Shift_Del_p.A722fs			Q86Z02	HIPK1_HUMAN	homeodomain interacting protein kinase 1	1116					anterior/posterior pattern specification (GO:0009952)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|neuron differentiation (GO:0030182)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|retina layer formation (GO:0010842)|smoothened signaling pathway (GO:0007224)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(15)|ovary(4)|prostate(2)	39	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		ACGTATGCTGCCCCGACTTCT	0.602																																					p.A1116fs		Atlas-INDEL	.											.	HIPK1	195	.	0			c.3346delG						.						175	156	163					1																	114515848		2203	4300	6503	SO:0001589	frameshift_variant	204851	exon16			.	AB089957	CCDS867.1, CCDS868.1, CCDS869.1, CCDS41370.1	1p13.1	2008-02-05			ENSG00000163349	ENSG00000163349			19006	protein-coding gene	gene with protein product		608003					Standard	NM_198268		Approved	KIAA0630, Myak, MGC26642, Nbak2, MGC33446, MGC33548	uc001eem.3	Q86Z02	OTTHUMG00000011983	ENST00000369558.1:c.3347delC	chr1.hg19:g.114515848delC	ENSP00000358571:p.Ala1116fs	203.0	0.0		162.0	11.0	NM_198268	A6NJ34|O75125|Q5SQL2|Q5SQL4|Q5SQL5|Q8IYD7|Q8NDN5|Q8NEB6|Q8TBZ1	Frame_Shift_Del	DEL	ENST00000369558.1	hg19	CCDS867.1																																																																																			.	.		0.602	HIPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000033127.1	NM_198268		-	114515848	C	-	114515848	7	5	282	1	0	1	0	1	0	0	0	0	7125	739	26	0	3507	0	HIPK1	1	114515848	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	72849	114515848	134734773	79	40313										
OLFML3	56944	hgsc.bcm.edu	37	chr1	114524304	114524304	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	catgccagcctccgctataaCccccgagaacgccagctcta							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:114524304delC	ENST00000320334.4	+	3	1208	c.1134delC	c.(1132-1134)aacfs	p.N378fs	OLFML3_ENST00000393300.2_Frame_Shift_Del_p.N358fs|OLFML3_ENST00000491700.1_3'UTR|OLFML3_ENST00000369551.1_Frame_Shift_Del_p.N358fs	NM_020190.2	NP_064575.1	Q9NRN5	OLFL3_HUMAN	olfactomedin-like 3	378	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				multicellular organismal development (GO:0007275)	extracellular region (GO:0005576)|vesicle (GO:0031982)				breast(1)|endometrium(2)|large_intestine(3)|lung(3)|prostate(2)|skin(2)|urinary_tract(1)	14	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TCCGCTATAACCCCCGAGAAC	0.562																																					p.N378fs		Atlas-INDEL	.											.	OLFML3	42	.	0			c.1133delA						.						50	50	50					1																	114524304		2203	4300	6503	SO:0001589	frameshift_variant	56944	exon3			.	AF201945	CCDS870.1, CCDS65618.1, CCDS72839.1	1p13.1	2008-02-05			ENSG00000116774	ENSG00000116774			24956	protein-coding gene	gene with protein product		610088					Standard	NM_001286353		Approved	HNOEL-iso, OLF44	uc001eer.1	Q9NRN5	OTTHUMG00000011980	ENST00000320334.4:c.1134delC	chr1.hg19:g.114524304delC	ENSP00000322273:p.Asn378fs	214.0	0.0		181.0	11.0	NM_020190	Q53FR1|Q53HV9|Q5SQL6|Q69AX9|Q8NBJ2	Frame_Shift_Del	DEL	ENST00000320334.4	hg19	CCDS870.1																																																																																			.	.		0.562	OLFML3-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033119.1	NM_020190		-	114524304	C	-	114524304	7	5	282	1	0	1	0	1	0	0	0	0	10868	506	18	0	1144	0	OLFML3	1	114524304	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	8456	114524304	134726317	80	40314										
DENND2C	163259	hgsc.bcm.edu	37	chr1	115144134	115144134	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcattctccactcacctttgAaaaaagattgaagcagccta							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:115144134delA	ENST00000393274.1	-	13	2435	c.1810delT	c.(1810-1812)tcafs	p.S604fs	DENND2C_ENST00000393277.1_Frame_Shift_Del_p.S604fs|DENND2C_ENST00000481894.1_5'UTR|DENND2C_ENST00000393276.3_Frame_Shift_Del_p.S547fs	NM_001256404.1	NP_001243333.1	Q68D51	DEN2C_HUMAN	DENN/MADD domain containing 2C	604	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|breast(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|skin(3)	37	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		CTCACCTTTGAAAAAAGATTG	0.388																																					p.S604X		Atlas-INDEL	.											.	DENND2C	105	.	0			c.1811delC						.						215	230	225					1																	115144134		2203	4300	6503	SO:0001589	frameshift_variant	163259	exon13			.		CCDS875.1, CCDS58018.1	1p13.2-p13.1	2012-10-03			ENSG00000175984	ENSG00000175984		"DENN/MADD domain containing"	24748	protein-coding gene	gene with protein product							Standard	NM_198459		Approved	FLJ37099, DKFZp686G0351, DKFZp779P1149, dJ1156J9.1, RP5-1156J9.1	uc001efd.1	Q68D51	OTTHUMG00000011893	ENST00000393274.1:c.1810delT	chr1.hg19:g.115144134delA	ENSP00000376955:p.Ser604fs	374.0	0.0		259.0	16.0	NM_001256404	B1AL26|Q5TCX6|Q6P3R3	Frame_Shift_Del	DEL	ENST00000393274.1	hg19	CCDS58018.1																																																																																			.	.		0.388	DENND2C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000314822.1	NM_198459		-	115144134	A	-	115144134	7	5	282	1	0	1	0	1	0	0	0	0	4432	246	9	0	1012	0	DENND2C	1	115144134	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	619830	115144134	134106487	81	40315										
SIKE1	80143	hgsc.bcm.edu	37	chr1	115321811	115321811	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	actggttcagcatccaccgcTtttttagcaaccattaactg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:115321811delT	ENST00000060969.5	-	3	429	c.360delA	c.(358-360)aaafs	p.K120fs	SIKE1_ENST00000506320.1_5'UTR|SIKE1_ENST00000369528.5_Frame_Shift_Del_p.K124fs			Q9BRV8	SIKE1_HUMAN	suppressor of IKBKE 1	120					innate immune response (GO:0045087)	cytosol (GO:0005829)				endometrium(1)|kidney(2)|large_intestine(1)|lung(2)	6						CATCCACCGCTTTTTTAGCAA	0.398																																					p.A125fs		Atlas-INDEL	.											.	SIKE1	12	.	0			c.373delG						.						172	172	172					1																	115321811		2203	4300	6503	SO:0001589	frameshift_variant	80143	exon3			.	AK024821	CCDS878.1, CCDS41371.1	1p13.1	2009-08-13			ENSG00000052723	ENSG00000052723			26119	protein-coding gene	gene with protein product	"suppressor of IKK epsilon"	611656				16281057	Standard	NM_025073		Approved	FLJ21168, SIKE	uc001efp.4	Q9BRV8	OTTHUMG00000012061	ENST00000060969.5:c.360delA	chr1.hg19:g.115321811delT	ENSP00000060969:p.Lys120fs	195.0	0.0		150.0	11.0	NM_001102396	Q5TEZ7|Q5TEZ9|Q68DZ4|Q9H778	Frame_Shift_Del	DEL	ENST00000060969.5	hg19	CCDS878.1																																																																																			.	.		0.398	SIKE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033401.1	NM_025073		-	115321811	T	-	115321811	7	5	282	1	0	1	0	1	0	0	0	0	14335	1606	56	0	275	0	SIKE1	1	115321811	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	177677	115321811	133928810	82	40316										
SPAG17	200162	hgsc.bcm.edu	37	chr1	118583387	118583387	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtcttttccacttcaatctgCcccccatcagaaggatacag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:118583387delC	ENST00000336338.5	-	22	3197	c.3132delG	c.(3130-3132)gggfs	p.G1044fs		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1044						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		CTTCAATCTGCCCCCCATCAG	0.368																																					p.Q1045fs		Atlas-INDEL	.											SPAG17,mouth,carcinoma,0,1	SPAG17	263	.	0			c.3133delC						.						131	112	118					1																	118583387		2203	4300	6503	SO:0001589	frameshift_variant	200162	exon22			.		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.3132delG	chr1.hg19:g.118583387delC	ENSP00000337804:p.Gly1044fs	284.0	0.0		200.0	13.0	NM_206996	Q8NAZ1|Q9NT21	Frame_Shift_Del	DEL	ENST00000336338.5	hg19	CCDS899.1																																																																																			.	.		0.368	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		-	118583387	C	-	118583387	7	5	282	1	0	1	0	1	0	0	0	0	14994	726	26	0	3647	0	SPAG17	1	118583387	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	3261576	118583387	130667234	83	40317										
NBPF7	343505	hgsc.bcm.edu	37	chr1	120378829	120378829	+	IGR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tctcttcagactcctgcagcTtcctgatgagccagacagga	9	13	2	4			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:120378829T>C								REG4 (24546 upstream) : ADAM30 (57326 downstream)																							CTCCTGCAGCTTCCTGATGAG	0.493																																					p.K306R		Atlas-SNP	.											.	NBPF7	46	.	0			c.A917G						.						46	47	46					1																	120378829		1970	4183	6153	SO:0001628	intergenic_variant	343505	exon7			TGCAGCTTCCTGA																													chr1.hg19:g.120378829T>C		106.0	0.0		81.0	4.0	NM_001047980		Missense_Mutation	SNP		hg19																																																																																				.	.	0	0.493									C	120378829	T	C	120378829	1	2	282	0	1	0	0	0	0	0	0	0	10207	1609	56	2		2	NBPF7	1	120378829	IGR	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1795442	120378829	128871792	84	40318										
NOTCH2	4853	hgsc.bcm.edu	37	chr1	120468081	120468081	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccatggtgagagaacagtcaCccccatcccactggcaggca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:120468081delC	ENST00000256646.2	-	25	4577	c.4358delG	c.(4357-4359)ggtfs	p.G1453fs	NOTCH2_ENST00000493703.1_5'Flank	NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	1453	Negative regulatory region (NRR).				apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		AGAACAGTCACCCCCATCCCA	0.582			"N, F, Mis"		"marginal zone lymphoma, DLBCL"				Alagille Syndrome																												p.G1453fs		Atlas-INDEL	.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	.	NOTCH2	348	.	0			c.4359delT						.						78	77	77					1																	120468081		2203	4300	6503	SO:0001589	frameshift_variant	4853	exon25	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	.	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"Ankyrin repeat domain containing"	7882	protein-coding gene	gene with protein product		600275	"Notch (Drosophila) homolog 2", "Notch homolog 2 (Drosophila)"			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.4358delG	chr1.hg19:g.120468081delC	ENSP00000256646:p.Gly1453fs	236.0	0.0		151.0	10.0	NM_024408	Q5T3X7|Q99734|Q9H240	Frame_Shift_Del	DEL	ENST00000256646.2	hg19	CCDS908.1																																																																																			.	.		0.582	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408		-	120468081	C	-	120468081	7	5	282	1	0	1	0	1	0	0	0	0	10557	507	18	0	3097	0	NOTCH2	1	120468081	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	89252	120468081	128782540	85	40319										
BCL9	607	hgsc.bcm.edu	37	chr1	147091647	147091647	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccagggagccagatgcgcctCcctggatttgcaggcatgat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:147091647delC	ENST00000234739.3	+	8	2426	c.1686delC	c.(1684-1686)ctcfs	p.L562fs		NM_004326.2	NP_004317.2	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	562	Pro-rich.				canonical Wnt signaling pathway (GO:0060070)|myotube differentiation involved in skeletal muscle regeneration (GO:0014908)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)		p.L562L(1)		breast(1)|large_intestine(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	7	all_hematologic(923;0.115)					AGATGCGCCTCCCTGGATTTG	0.557			T	"IGH@, IGL@"	B-ALL																																p.L562fs		Atlas-INDEL	.		Dom	yes		1	1q21	607	B-cell CLL/lymphoma 9		L	.	BCL9	150	.	1	Substitution - coding silent(1)	kidney(1)	c.1685delT						.						67	73	71					1																	147091647		2203	4300	6503	SO:0001589	frameshift_variant	607	exon8			.	Y13620	CCDS30833.1	1q21	2008-02-05			ENSG00000116128	ENSG00000116128			1008	protein-coding gene	gene with protein product		602597				9490669	Standard	NM_004326		Approved		uc001epq.3	O00512	OTTHUMG00000014031	ENST00000234739.3:c.1686delC	chr1.hg19:g.147091647delC	ENSP00000234739:p.Leu562fs	121.0	0.0		163.0	10.0	NM_004326	Q5T489	Frame_Shift_Del	DEL	ENST00000234739.3	hg19	CCDS30833.1																																																																																			.	.		0.557	BCL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039468.1	NM_004326		-	147091647	C	-	147091647	7	5	282	1	0	1	0	1	0	0	0	0	1381	842	30	0	1704	0	BCL9	1	147091647	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	26623566	147091647	102158974	86	40320										
HIST2H2AC	8338	hgsc.bcm.edu	37	chr1	149858905	149858905	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	accgaaagccacaaagccaaAagcaaataaatgcagacaaa	6	10	0	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:149858905A>G	ENST00000331380.2	+	1	381	c.381A>G	c.(379-381)aaA>aaG	p.K127K	BOLA1_ENST00000369153.2_5'Flank|HIST2H2BE_ENST00000369155.2_5'Flank	NM_003517.2	NP_003508.1	Q16777	H2A2C_HUMAN	histone cluster 2, H2ac	127						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(11)|ovary(1)|skin(1)	20	Breast(34;0.0124)|all_hematologic(923;0.127)		STAD - Stomach adenocarcinoma(528;0.133)|LUSC - Lung squamous cell carcinoma(543;0.221)			ACAAAGCCAAAAGCAAATAAA	0.463																																					p.K127K		Atlas-SNP	.											.	HIST2H2AC	75	.	0			c.A381G						.						67	71	70					1																	149858905		2203	4300	6503	SO:0001819	synonymous_variant	8338	exon1			AGCCAAAAGCAAA	AY131973	CCDS937.1	1q21.2	2011-01-27	2006-10-11	2003-02-21	ENSG00000184260	ENSG00000184260		"Histones / Replication-dependent"	4738	protein-coding gene	gene with protein product		602797	"H2A histone family, member Q", "histone 2, H2ac"	H2A, H2AFQ		1469070, 9439656, 12408966	Standard	NM_003517		Approved	H2A/q	uc001etd.3	Q16777	OTTHUMG00000035825	ENST00000331380.2:c.381A>G	chr1.hg19:g.149858905A>G		281.0	0.0		394.0	78.0	NM_003517	Q6DRA7|Q8IUE5	Silent	SNP	ENST00000331380.2	hg19	CCDS937.1																																																																																			.	.		0.463	HIST2H2AC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087128.1	NM_003517		G	149858905	A	G	149858905	2	3	282	1	0	0	0	0	0	0	0	1	7187	11	1	2		2	HIST2H2AC	1	149858905	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2767258	149858905	99391716	87	40321										
OTUD7B	56957	hgsc.bcm.edu	37	chr1	149936173	149936173	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	attctgctgtgtctgctgccAcctccagcgccttttcaacg	8	15	3	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:149936173A>G	ENST00000369135.4	-	6	1000	c.706T>C	c.(706-708)Tgg>Cgg	p.W236R	OTUD7B_ENST00000479905.1_5'UTR	NM_020205.2	NP_064590.2	Q6GQQ9	OTU7B_HUMAN	OTU deubiquitinase 7B	236	Catalytic.|OTU. {ECO:0000255|PROSITE- ProRule:PRU00139}.|TRAF-binding.				mucosal immune response (GO:0002385)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|DNA binding (GO:0003677)|Lys48-specific deubiquitinase activity (GO:1990380)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(18)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39	Breast(34;0.0009)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.247)			GTCTGCTGCCACCTCCAGCGC	0.532																																					p.W236R		Atlas-SNP	.											.	OTUD7B	76	.	0			c.T706C						.						108	119	115					1																	149936173		2108	4247	6355	SO:0001583	missense	56957	exon6			GCTGCCACCTCCA	AJ293573	CCDS72903.1	1q21.2	2014-02-24	2014-02-24	2006-07-07	ENSG00000163113	ENSG00000264522		"OTU domain containing"	16683	protein-coding gene	gene with protein product		611748	"zinc finger, A20 domain containing 1", "OTU domain containing 7B"	ZA20D1		11463333, 23827681	Standard	NM_020205		Approved	CEZANNE	uc001etn.3	Q6GQQ9	OTTHUMG00000012291	ENST00000369135.4:c.706T>C	chr1.hg19:g.149936173A>G	ENSP00000358131:p.Trp236Arg	70.0	0.0		94.0	4.0	NM_020205	B7Z643|D3DUZ8|Q5SZ60|Q8WWA7|Q9NQ53|Q9UFF4	Missense_Mutation	SNP	ENST00000369135.4	hg19	CCDS41389.1	.	.	.	.	.	.	.	.	.	.	A	19.56	3.850341	0.71719	.	.	ENSG00000163113	ENST00000369135;ENST00000543330;ENST00000417191	T;T	0.33438	1.41;1.5	4.87	4.87	0.63330	Ovarian tumour, otubain (2);	0.119404	0.64402	D	0.000009	T	0.39036	0.1063	L	0.56340	1.77	0.80722	D	1	D;D	0.76494	0.999;0.994	D;D	0.72982	0.979;0.968	T	0.13442	-1.0509	9	.	.	.	-8.913	13.7243	0.62748	1.0:0.0:0.0:0.0	.	236;236	B7Z643;Q6GQQ9	.;OTU7B_HUMAN	R	236	ENSP00000358131:W236R;ENSP00000408231:W236R	.	W	-	1	0	OTUD7B	148202797	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.654000	0.91092	2.178000	0.69098	0.533000	0.62120	TGG	.	.		0.532	OTUD7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034146.3	NM_020205		G	149936173	A	G	149936173	3	3	282	1	0	0	0	0	1	0	0	0	11328	159	6	2	1853	2	OTUD7B	1	149936173	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	77268	149936173	99314448	88	40322										
PLEKHO1	51177	hgsc.bcm.edu	37	chr1	150129661	150129661	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctcccgccgccccccaacaaGgggacacctaatggctgtgg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:150129661delG	ENST00000369124.4	+	5	784	c.506delG	c.(505-507)aggfs	p.R169fs	PLEKHO1_ENST00000369126.1_Intron|PLEKHO1_ENST00000479194.1_3'UTR|PLEKHO1_ENST00000025469.6_Intron	NM_016274.4	NP_057358.2	Q53GL0	PKHO1_HUMAN	pleckstrin homology domain containing, family O member 1	169	Interaction with ATM, CKIP, IFP35 and NMI.|Interaction with capping proteins (CPs).					cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|skin(2)	22	Lung NSC(24;7.78e-28)|Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			CCCCCAACAAGGGGACACCTA	0.522																																					p.R169fs		Atlas-INDEL	.											.	PLEKHO1	37	.	0			c.505delA						.						82	69	74					1																	150129661		2203	4300	6503	SO:0001589	frameshift_variant	51177	exon5			.	AF073836	CCDS945.1	1q21.2	2013-01-10			ENSG00000023902	ENSG00000023902		"Pleckstrin homology (PH) domain containing"	24310	protein-coding gene	gene with protein product		608335				10799509	Standard	NM_016274		Approved	CKIP-1, OC120	uc001ett.3	Q53GL0	OTTHUMG00000012510	ENST00000369124.4:c.506delG	chr1.hg19:g.150129661delG	ENSP00000358120:p.Arg169fs	130.0	0.0		141.0	10.0	NM_016274	Q336K5|Q8IZ51|Q9NRV3|Q9UL48	Frame_Shift_Del	DEL	ENST00000369124.4	hg19	CCDS945.1																																																																																			.	.		0.522	PLEKHO1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034962.1	NM_016274		-	150129661	G	-	150129661	7	5	282	1	0	1	0	1	0	0	0	0	12093	1000	35	0	524	0	PLEKHO1	1	150129661	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	193488	150129661	99120960	89	40323										
ADAMTSL4	54507	hgsc.bcm.edu	37	chr1	150531054	150531054	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtgcgtcaggccccccgcagCcccccagcagagaggcctgt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:150531054delC	ENST00000369038.2	+	13	2689	c.2488delC	c.(2488-2490)cccfs	p.P831fs	ADAMTSL4_ENST00000369039.5_Frame_Shift_Del_p.P854fs|RP11-54A4.2_ENST00000442435.2_RNA|ADAMTSL4_ENST00000271643.4_Frame_Shift_Del_p.P831fs|ADAMTSL4_ENST00000369041.5_Frame_Shift_Del_p.P831fs			Q6UY14	ATL4_HUMAN	ADAMTS-like 4	831	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|positive regulation of apoptotic process (GO:0043065)	interstitial matrix (GO:0005614)	metalloendopeptidase activity (GO:0004222)|protease binding (GO:0002020)			breast(1)|cervix(1)|endometrium(6)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(3)	32	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			CCCCCCGCAGCCCCCCAGCAG	0.657																																					p.Q829fs		Atlas-INDEL	.											.	ADAMTSL4	101	.	0			c.2487delG						.						56	62	60					1																	150531054		2203	4300	6503	SO:0001589	frameshift_variant	54507	exon15			.	BC027478	CCDS955.1, CCDS30852.1, CCDS72908.1	1q21.2	2008-02-05	2005-12-01	2005-12-01	ENSG00000143382	ENSG00000143382			19706	protein-coding gene	gene with protein product		610113	"thrombospondin repeat containing 1"	TSRC1		12706885	Standard	NM_019032		Approved	DKFZP434K1772	uc001eux.3	Q6UY14	OTTHUMG00000034863	ENST00000369038.2:c.2488delC	chr1.hg19:g.150531054delC	ENSP00000358034:p.Pro831fs	201.0	0.0		219.0	14.0	NM_019032	B2RTT0|F8WAD0|Q5T5F7|Q6IPM6|Q8N643|Q9HBS6	Frame_Shift_Del	DEL	ENST00000369038.2	hg19	CCDS955.1																																																																																			.	.		0.657	ADAMTSL4-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084395.4	NM_019032		-	150531054	C	-	150531054	7	5	282	1	0	1	0	1	0	0	0	0	277	739	26	0	2538	0	ADAMTSL4	1	150531054	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	401393	150531054	98719567	90	40324										
FAM63A	55793	hgsc.bcm.edu	37	chr1	150974245	150974245	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atgtgatcacttccttctgcGgggggagcttcacctggagg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:150974245delG	ENST00000361936.5	-	4	1421	c.467delC	c.(466-468)ccgfs	p.P156fs	FAM63A_ENST00000470877.1_5'UTR|FAM63A_ENST00000493834.2_Frame_Shift_Del_p.P61fs|FAM63A_ENST00000361738.6_Frame_Shift_Del_p.P204fs|FAM63A_ENST00000312210.5_Frame_Shift_Del_p.P14fs	NM_018379.4	NP_060849	Q8N5J2	FA63A_HUMAN	family with sequence similarity 63, member A	156						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(3)|large_intestine(4)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			TTCCTTCTGCGGGGGGAGCTT	0.562																																					p.P204fs		Atlas-INDEL	.											.	FAM63A	42	.	0			c.612delG						.						60	54	56					1																	150974245		2203	4300	6503	SO:0001589	frameshift_variant	55793	exon4			.	BC032321	CCDS976.1, CCDS30854.1, CCDS53361.1, CCDS55635.1	1q21.2	2008-02-05			ENSG00000143409	ENSG00000143409			25648	protein-coding gene	gene with protein product						10718198	Standard	NM_001040217		Approved	FLJ11280	uc010pcn.2	Q8N5J2	OTTHUMG00000035061	ENST00000361936.5:c.467delC	chr1.hg19:g.150974245delG	ENSP00000354814:p.Pro156fs	179.0	0.0		192.0	15.0	NM_001163258	B3KWP4|B3KWV8|B4DXF2|B4E1S4|D3DV09|J3KP53|Q5SZF0|Q9NUL9|Q9P2F7	Frame_Shift_Del	DEL	ENST00000361936.5	hg19	CCDS976.1																																																																																			.	.		0.562	FAM63A-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411753.1	NM_018379		-	150974245	G	-	150974245	7	5	282	1	0	1	0	1	0	0	0	0	5604	1116	39	0	974	0	FAM63A	1	150974245	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	443191	150974245	98276376	91	40325										
LCE2D	353141	hgsc.bcm.edu	37	chr1	152636615	152636615	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaaaccagcagcagtgccagCcccctcccaaatgtcctccc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:152636615delC	ENST00000368784.1	+	2	89	c.34delC	c.(34-36)cccfs	p.P14fs		NM_178430.2	NP_848517.1	Q5TA82	LCE2D_HUMAN	late cornified envelope 2D	14	Cys-rich.				keratinization (GO:0031424)					large_intestine(1)|lung(7)|prostate(2)	10	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCAGTGCCAGCCCCCTCCCAA	0.493																																					p.Q11fs		Atlas-INDEL	.											.	LCE2D	26	.	0			c.33delG						.						106	112	110					1																	152636615		2203	4300	6503	SO:0001589	frameshift_variant	353141	exon2			.	BI670513	CCDS1018.1	1q21.3	2008-02-05	2004-10-11	2004-10-15	ENSG00000187223	ENSG00000187223		"Late cornified envelopes"	16518	protein-coding gene	gene with protein product		612612	"small proline rich-like (epidermal differentiation complex) 1A"	SPRL1A		11698679	Standard	NM_178430		Approved	LEP12	uc001fag.4	Q5TA82	OTTHUMG00000014400	ENST00000368784.1:c.34delC	chr1.hg19:g.152636615delC	ENSP00000357773:p.Pro14fs	181.0	0.0		266.0	16.0	NM_178430	A1L4M8	Frame_Shift_Del	DEL	ENST00000368784.1	hg19	CCDS1018.1																																																																																			.	.		0.493	LCE2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040058.1	NM_178430		-	152636615	C	-	152636615	7	5	282	1	0	1	0	1	0	0	0	0	8677	739	26	0	36	0	LCE2D	1	152636615	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1662370	152636615	96614006	92	40326										
LCE1E	353135	hgsc.bcm.edu	37	chr1	152760075	152760075	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gactgctgcagccagccctcAgggggctccagctgctgtgg					rs201660535	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:152760075delA	ENST00000368770.3	+	2	353	c.300delA	c.(298-300)tcafs	p.S100fs	LCE1E_ENST00000368771.1_Frame_Shift_Del_p.S100fs	NM_178353.1	NP_848130.1	Q5T753	LCE1E_HUMAN	late cornified envelope 1E	100	Cys-rich.				keratinization (GO:0031424)					lung(5)|stomach(1)	6	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCCAGCCCTCAGGGGGCTCCA	0.642																																					p.S100X		Atlas-INDEL	.											.	LCE1E	26	.	0			c.299delC						.						36	52	47					1																	152760075		2104	4254	6358	SO:0001589	frameshift_variant	353135	exon2			.	BC038391	CCDS1024.1	1q21.3	2008-02-05			ENSG00000186226	ENSG00000186226		"Late cornified envelopes"	29466	protein-coding gene	gene with protein product		612607				11698679	Standard	NM_178353		Approved	LEP5	uc001fan.3	Q5T753	OTTHUMG00000012405	ENST00000368770.3:c.300delA	chr1.hg19:g.152760075delA	ENSP00000357759:p.Ser100fs	123.0	0.0		207.0	16.0	NM_178353	D3DV30	Frame_Shift_Del	DEL	ENST00000368770.3	hg19	CCDS1024.1																																																																																			.	.		0.642	LCE1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034525.1	NM_178353		-	152760075	A	-	152760075	7	5	282	1	0	1	0	1	0	0	0	0	8672	175	7	0	302	0	LCE1E	1	152760075	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	123460	152760075	96490546	93	40327										
SSR2	6746	hgsc.bcm.edu	37	chr1	155979390	155979390	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gctggagtaccacaatagcaGggggatgccgatggagggaa					rs531493503		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:155979390delG	ENST00000295702.4	-	6	564	c.493delC	c.(493-495)ctgfs	p.L167fs	SSR2_ENST00000529008.1_3'UTR|SSR2_ENST00000496742.1_3'UTR|SSR2_ENST00000480567.1_Frame_Shift_Del_p.L167fs	NM_003145.3	NP_003136.1	P43308	SSRB_HUMAN	signal sequence receptor, beta (translocon-associated protein beta)	167					cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|gene expression (GO:0010467)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|stomach(1)	10	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					CACAATAGCAGGGGGATGCCG	0.517																																					p.L165fs		Atlas-INDEL	.											.	SSR2	20	.	0			c.494delT						.						125	115	118					1																	155979390		2203	4300	6503	SO:0001589	frameshift_variant	6746	exon6			.	BC000341	CCDS1126.1	1q21-q23	2008-02-05			ENSG00000163479	ENSG00000163479			11324	protein-coding gene	gene with protein product		600867				7789174	Standard	NM_003145		Approved	TLAP, TRAPB	uc001fmx.3	P43308	OTTHUMG00000017456	ENST00000295702.4:c.493delC	chr1.hg19:g.155979390delG	ENSP00000295702:p.Leu167fs	246.0	0.0		287.0	18.0	NM_003145	B2R9K9|D3DVA7|Q53HI0|Q5VY95|Q5VY96|Q6IB31|Q9BWE4	Frame_Shift_Del	DEL	ENST00000295702.4	hg19	CCDS1126.1																																																																																			.	.		0.517	SSR2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046172.2	NM_003145		-	155979390	G	-	155979390	7	5	282	1	0	1	0	1	0	0	0	0	15206	991	35	0	62	0	SSR2	1	155979390	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	3219315	155979390	93271231	94	40328										
MEF2D	4209	hgsc.bcm.edu	37	chr1	156446904	156446904	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgctgtgggtaggtgggggtGgagacttggcagggatgacc	21	5	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:156446904G>C	ENST00000348159.4	-	7	1235	c.755C>G	c.(754-756)cCa>cGa	p.P252R	MEF2D_ENST00000353795.3_Missense_Mutation_p.P206R|MEF2D_ENST00000340875.5_Missense_Mutation_p.P251R|MEF2D_ENST00000360595.3_Missense_Mutation_p.P252R|MEF2D_ENST00000368240.2_Missense_Mutation_p.P252R|MEF2D_ENST00000464356.2_Missense_Mutation_p.P251R	NM_005920.2	NP_005911.1	Q14814	MEF2D_HUMAN	myocyte enhancer factor 2D	252	Poly-Pro.				adult heart development (GO:0007512)|apoptotic process (GO:0006915)|chondrocyte differentiation (GO:0002062)|endochondral ossification (GO:0001958)|muscle organ development (GO:0007517)|nervous system development (GO:0007399)|osteoblast differentiation (GO:0001649)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|histone deacetylase binding (GO:0042826)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	15	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					AGGTGGGGGTGGAGACTTGGC	0.607																																					p.P252R		Atlas-SNP	.											MEF2D,colon,adenoma,0,1	MEF2D	43	.	0			c.C755G						.						83	76	78					1																	156446904		2203	4300	6503	SO:0001583	missense	4209	exon7			GGGGGTGGAGACT	BC054520	CCDS1143.1, CCDS60304.1	1q12-q23	2008-02-05	2007-04-24		ENSG00000116604	ENSG00000116604		"Myocyte enhancer factors"	6997	protein-coding gene	gene with protein product		600663				8269842	Standard	NM_005920		Approved		uc001fpb.4	Q14814	OTTHUMG00000033095	ENST00000348159.4:c.755C>G	chr1.hg19:g.156446904G>C	ENSP00000271555:p.Pro252Arg	185.0	0.0		351.0	0.0	NM_005920	D3DVC0|Q14815|Q5T9U5|Q5T9U6	Missense_Mutation	SNP	ENST00000348159.4	hg19	CCDS1143.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.004510	0.93287	.	.	ENSG00000116604	ENST00000348159;ENST00000340875;ENST00000368240;ENST00000353795;ENST00000360595;ENST00000454816	T;T;T;T;T;T	0.34667	1.35;1.35;1.35;1.35;1.35;1.35	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.57227	0.2039	M	0.81497	2.545	0.80722	D	1	D;D;D	0.76494	0.999;0.997;0.995	D;D;D	0.71870	0.968;0.909;0.975	T	0.61941	-0.6959	10	0.72032	D	0.01	-12.8772	18.1525	0.89678	0.0:0.0:1.0:0.0	.	257;252;252	Q4LE66;Q14814;Q14814-4	.;MEF2D_HUMAN;.	R	252;251;252;206;252;251	ENSP00000271555:P252R;ENSP00000343159:P251R;ENSP00000357223:P252R;ENSP00000344705:P206R;ENSP00000353803:P252R;ENSP00000388505:P251R	ENSP00000343159:P251R	P	-	2	0	MEF2D	154713528	1.000000	0.71417	0.994000	0.49952	0.982000	0.71751	9.238000	0.95380	2.626000	0.88956	0.655000	0.94253	CCA	.	.		0.607	MEF2D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080562.2	NM_005920		C	156446904	G	C	156446904	3	2	282	1	0	0	0	0	1	0	0	0	9467	1348	47	4	834	4	MEF2D	1	156446904	Missense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	467514	156446904	92803717	95	40329										
IQGAP3	128239	hgsc.bcm.edu	37	chr1	156503821	156503821	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cctgtgcgtgttgaccagctCccccacggtgatgtacacca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:156503821delC	ENST00000361170.2	-	30	3863	c.3853delG	c.(3853-3855)gagfs	p.E1285fs		NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	1285					activation of MAPK activity (GO:0000187)|cellular response to organic substance (GO:0071310)|ERK1 and ERK2 cascade (GO:0070371)|G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|Ras protein signal transduction (GO:0007265)|regulation of cell size (GO:0008361)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)	Ras GTPase activator activity (GO:0005099)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(14)|lung(29)|ovary(5)|prostate(5)|skin(5)|urinary_tract(3)	75	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TTGACCAGCTCCCCCACGGTG	0.612																																					p.E1285fs		Atlas-INDEL	.											.	IQGAP3	146	.	0			c.3854delA						.						134	112	119					1																	156503821		2203	4300	6503	SO:0001589	frameshift_variant	128239	exon30			.	AY253300	CCDS1144.1	1q21.3	2008-02-05			ENSG00000183856	ENSG00000183856			20669	protein-coding gene	gene with protein product							Standard	NM_178229		Approved		uc001fpf.3	Q86VI3	OTTHUMG00000033114	ENST00000361170.2:c.3853delG	chr1.hg19:g.156503821delC	ENSP00000354451:p.Glu1285fs	127.0	0.0		168.0	11.0	NM_178229	Q5T3H8	Frame_Shift_Del	DEL	ENST00000361170.2	hg19	CCDS1144.1																																																																																			.	.		0.612	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229		-	156503821	C	-	156503821	7	5	282	1	0	1	0	1	0	0	0	0	7825	864	30	0	1078	0	IQGAP3	1	156503821	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	56917	156503821	92746800	96	40330										
ARHGAP30	257106	hgsc.bcm.edu	37	chr1	161017601	161017601	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcaggaacctggggttctctGgggggcagactaagacgact							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:161017601delG	ENST00000368013.3	-	12	3530	c.3210delC	c.(3208-3210)cccfs	p.P1070fs	ARHGAP30_ENST00000368015.1_Frame_Shift_Del_p.P893fs|USF1_ENST00000435396.1_5'Flank|ARHGAP30_ENST00000368016.3_Frame_Shift_Del_p.P859fs|USF1_ENST00000368020.1_5'Flank|USF1_ENST00000368021.3_5'Flank	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30	1070					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)			breast(2)|cervix(3)|endometrium(4)|kidney(2)|large_intestine(4)|lung(6)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			GGGGTTCTCTGGGGGGCAGAC	0.567																																					p.R1071fs		Atlas-INDEL	.											.	ARHGAP30	105	.	0			c.3211delA						.						68	75	72					1																	161017601		2203	4300	6503	SO:0001589	frameshift_variant	257106	exon12			.	AL832852	CCDS1215.1, CCDS30918.1, CCDS72958.1	1q23.3	2011-06-29			ENSG00000186517	ENSG00000186517		"Rho GTPase activating proteins"	27414	protein-coding gene	gene with protein product		614264					Standard	NM_001287602		Approved	FLJ00267	uc001fxl.3	Q7Z6I6	OTTHUMG00000031477	ENST00000368013.3:c.3210delC	chr1.hg19:g.161017601delG	ENSP00000356992:p.Pro1070fs	116.0	0.0		203.0	13.0	NM_001025598	Q5SY52|Q5SY53|Q5SY54|Q6ZML6|Q7Z3J8|Q86XI7	Frame_Shift_Del	DEL	ENST00000368013.3	hg19	CCDS30918.1																																																																																			.	.		0.567	ARHGAP30-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077090.2	NM_181720		-	161017601	G	-	161017601	7	5	282	1	0	1	0	1	0	0	0	0	879	1335	47	0	99	0	ARHGAP30	1	161017601	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	4513780	161017601	88233020	97	40331										
KLHDC9	126823	hgsc.bcm.edu	37	chr1	161068399	161068399	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gccagtggcgcgggacgcgcTtttggctagagctttccatt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:161068399delT	ENST00000368011.4	+	1	216	c.74delT	c.(73-75)cttfs	p.L26fs	KLHDC9_ENST00000490724.2_Intron|PFDN2_ENST00000468311.1_5'Flank|KLHDC9_ENST00000392192.2_Frame_Shift_Del_p.L26fs	NM_152366.4	NP_689579.3	Q8NEP7	KLDC9_HUMAN	kelch domain containing 9	26										lung(5)|upper_aerodigestive_tract(1)	6	all_cancers(52;1.28e-19)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			CGGGACGCGCTTTTGGCTAGA	0.692																																					p.L25fs		Atlas-INDEL	.											.	KLHDC9	16	.	0			c.73delC						.						25	25	25					1																	161068399		2203	4300	6503	SO:0001589	frameshift_variant	126823	exon1			.	BC022077	CCDS30919.1, CCDS41425.1	1q23.3	2008-02-05			ENSG00000162755	ENSG00000162755			28489	protein-coding gene	gene with protein product	"kelch/ankyrin repeat containing cyclin A1 interacting protein"					15159402	Standard	NM_152366		Approved	KARCA1	uc001fxr.3	Q8NEP7	OTTHUMG00000031479	ENST00000368011.4:c.74delT	chr1.hg19:g.161068399delT	ENSP00000356990:p.Leu26fs	209.0	0.0		224.0	15.0	NM_152366	Q5SY56|Q6NXT9|Q6PKN4|Q8N5E1|Q8NA16	Frame_Shift_Del	DEL	ENST00000368011.4	hg19	CCDS30919.1																																																																																			.	.		0.692	KLHDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077092.1	NM_152366		-	161068399	T	-	161068399	7	5	282	1	0	1	0	1	0	0	0	0	8373	1609	56	0	76	0	KLHDC9	1	161068399	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	50798	161068399	88182222	98	40332										
ATF6	22926	hgsc.bcm.edu	37	chr1	161816357	161816357	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	catcagatggtattatccagAaaaacagctacaggtaagat					rs368810553		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:161816357delA	ENST00000367942.3	+	10	1373	c.1306delA	c.(1306-1308)aaafs	p.K436fs	ATF6_ENST00000476437.1_3'UTR	NM_007348.3	NP_031374.2	P18850	ATF6A_HUMAN	activating transcription factor 6	436					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response (GO:0006990)|protein folding (GO:0006457)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to stress (GO:0006950)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(14)|ovary(3)|skin(1)|stomach(1)	34	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.00953)		Pseudoephedrine(DB00852)	TATTATCCAGAAAAACAGCTA	0.403																																					p.Q435fs		Atlas-INDEL	.											ATF6,NS,carcinoma,0,1	ATF6	84	.	0			c.1305delG						.						117	110	112					1																	161816357		2203	4300	6503	SO:0001589	frameshift_variant	22926	exon10			.	AB015856	CCDS1235.1	1q22-q23	2013-01-10			ENSG00000118217	ENSG00000118217		"basic leucine zipper proteins"	791	protein-coding gene	gene with protein product	"activating transcription factor 6 alpha"	605537				9837962, 9271374, 11256944	Standard	NM_007348		Approved	ATF6A	uc001gbs.3	P18850	OTTHUMG00000023961	ENST00000367942.3:c.1306delA	chr1.hg19:g.161816357delA	ENSP00000356919:p.Lys436fs	144.0	0.0		181.0	11.0	NM_007348	O15139|Q5VW62|Q6IPB5|Q9UEC9	Frame_Shift_Del	DEL	ENST00000367942.3	hg19	CCDS1235.1																																																																																			.	.		0.403	ATF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060304.2	NM_007348		-	161816357	A	-	161816357	7	5	282	1	0	1	0	1	0	0	0	0	1084	247	9	0	1344	0	ATF6	1	161816357	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	747958	161816357	87434264	99	40333										
C1orf156	92342	hgsc.bcm.edu	37	chr1	169762228	169762228	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaccctcccttgaatgcagtTatacctagtaaacctgatcc	6	13	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:169762228T>G	ENST00000310392.4	-	2	962	c.609A>C	c.(607-609)atA>atC	p.I203I	METTL18_ENST00000303469.2_Silent_p.I203I|C1orf112_ENST00000359326.4_5'Flank|C1orf112_ENST00000286031.6_5'Flank|C1orf112_ENST00000456684.1_5'Flank|C1orf112_ENST00000413811.2_5'Flank|C1orf112_ENST00000498289.1_Intron	NM_033418.2	NP_219486.1	O95568	MET18_HUMAN	methyltransferase like 18	203						cytoplasm (GO:0005737)	protein methyltransferase activity (GO:0008276)			kidney(1)|large_intestine(3)|lung(4)	8						TGAATGCAGTTATACCTAGTA	0.383																																					p.I203I		Atlas-SNP	.											.	METTL18	23	.	0			c.A609C						.						126	129	128					1																	169762228		2203	4299	6502	SO:0001819	synonymous_variant	92342	exon2			TGCAGTTATACCT	AL035369	CCDS1284.1	1q24.2	2013-10-11	2011-03-02	2011-03-02	ENSG00000171806	ENSG00000171806			28793	protein-coding gene	gene with protein product	"histidine protein methyltransferase 1"	615255	"chromosome 1 open reading frame 156"	C1orf156		20864530	Standard	NM_033418		Approved	MGC9084, AsTP2, HPM1	uc001ggn.4	O95568	OTTHUMG00000035813	ENST00000310392.4:c.609A>C	chr1.hg19:g.169762228T>G		208.0	0.0		291.0	54.0	NM_033418	B2R9T5	Silent	SNP	ENST00000310392.4	hg19	CCDS1284.1																																																																																			.	.		0.383	METTL18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087109.1	NM_033418		G	169762228	T	G	169762228	2	3	282	1	0	0	0	0	0	0	0	1	2008	1744	61	5		5	C1orf156	1	169762228	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	7945871	169762228	79488393	100	40334										
SEC16B	89866	hgsc.bcm.edu	37	chr1	177913790	177913790	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cctcagttgttgcaaatttcAaaaactcttgactaaaacca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:177913790delA	ENST00000308284.6	-	15	1876	c.1787delT	c.(1786-1788)ttgfs	p.L596fs	RP4-798P15.3_ENST00000354921.3_RNA	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	596					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|peroxisome fission (GO:0016559)|peroxisome organization (GO:0007031)|positive regulation of gene expression (GO:0010628)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endoplasmic reticulum (GO:0070972)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)				central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)|stomach(1)	35						TGCAAATTTCAAAAACTCTTG	0.468																																					p.L596fs		Atlas-INDEL	.											.	SEC16B	92	.	0			c.1788delG						.						109	112	111					1																	177913790		1877	4110	5987	SO:0001589	frameshift_variant	89866	exon15			.	AK090411	CCDS44281.1	1q25.2	2012-10-08	2007-06-20	2007-06-20	ENSG00000120341	ENSG00000120341			30301	protein-coding gene	gene with protein product	"regucalcin gene promotor region related protein"	612855	"leucine zipper transcription regulator 2"	LZTR2		11572484, 11605020	Standard	NM_033127		Approved	RGPR, PGPR-p117	uc001gli.1	Q96JE7	OTTHUMG00000167206	ENST00000308284.6:c.1787delT	chr1.hg19:g.177913790delA	ENSP00000308339:p.Leu596fs	105.0	0.0		131.0	11.0	NM_033127	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Frame_Shift_Del	DEL	ENST00000308284.6	hg19	CCDS44281.1																																																																																			.	.		0.468	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127		-	177913790	A	-	177913790	7	5	282	1	0	1	0	1	0	0	0	0	14002	131	5	0	1443	0	SEC16B	1	177913790	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	8151562	177913790	71336831	101	40335										
RALGPS2	55103	hgsc.bcm.edu	37	chr1	178780494	178780494	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	attcttcatgctcaaacattAaaaattagagcagaagtttt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:178780494delA	ENST00000367635.3	+	6	680	c.342delA	c.(340-342)ttafs	p.L114fs	RALGPS2_ENST00000367634.2_Frame_Shift_Del_p.L114fs	NM_152663.3	NP_689876.2	Q86X27	RGPS2_HUMAN	Ral GEF with PH domain and SH3 binding motif 2	114	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						CTCAAACATTAAAAATTAGAG	0.249																																					p.L114X		Atlas-INDEL	.											.	RALGPS2	69	.	0			c.341delT						.						60	71	67					1																	178780494		2202	4280	6482	SO:0001589	frameshift_variant	55103	exon6			.	AK098470	CCDS1325.1, CCDS65733.1	1q24	2013-01-11			ENSG00000116191	ENSG00000116191		"Pleckstrin homology (PH) domain containing"	30279	protein-coding gene	gene with protein product						10747847, 12102558	Standard	NM_152663		Approved	KIAA0351, FLJ10244, FLJ25604	uc001glz.3	Q86X27	OTTHUMG00000035076	ENST00000367635.3:c.342delA	chr1.hg19:g.178780494delA	ENSP00000356607:p.Leu114fs	200.0	0.0		309.0	19.0	NM_152663	B7Z7B1|Q5T5Z1|Q5VZ67|Q9NW78	Frame_Shift_Del	DEL	ENST00000367635.3	hg19	CCDS1325.1																																																																																			.	.		0.249	RALGPS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084926.2	NM_152663		-	178780494	A	-	178780494	7	5	282	1	0	1	0	1	0	0	0	0	13033	359	13	0	360	0	RALGPS2	1	178780494	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	866704	178780494	70470127	102	40336										
MR1	3140	hgsc.bcm.edu	37	chr1	181003146	181003146	+	Start_Codon_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cccggaaagagaaggactatGggggaactgatggcgttcct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:181003146delG	ENST00000367580.5	+	0	8				MR1_ENST00000367579.3_Start_Codon_Del|MR1_ENST00000434571.2_Start_Codon_Del|MR1_ENST00000438435.2_3'UTR|MR1_ENST00000282990.6_Start_Codon_Del	NM_001531.2	NP_001522.1	Q95460	HMR1_HUMAN	major histocompatibility complex, class I-related						antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	MHC class I receptor activity (GO:0032393)|peptide antigen binding (GO:0042605)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	18					Antithymocyte globulin(DB00098)	GAAGGACTATGGGGGAACTGA	0.488																																					p.M1fs	Colon(174;1412 1962 45296 46549 47110)	Atlas-INDEL	.											.	MR1	46	.	0			c.2delT						.						116	101	106					1																	181003146		2203	4300	6503	SO:0001582	initiator_codon_variant	3140	exon2			.	AF010446	CCDS1342.1, CCDS53440.1, CCDS53441.1, CCDS53442.1	1q25.3	2013-01-11	2003-03-05	2003-03-07	ENSG00000153029	ENSG00000153029		"Immunoglobulin superfamily / C1-set domain containing"	4975	protein-coding gene	gene with protein product		600764	"major histocompatibility complex, class I-like sequence"	HLALS		7624800, 9784382	Standard	NM_001194999		Approved		uc001goq.2	Q95460	OTTHUMG00000035175		chr1.hg19:g.181003146delG		174.0	0.0		173.0	13.0	NM_001195035	A8K2V9|B4E3B1|O97985|O97986|Q53GM1|Q95HB8|Q9MY23|Q9NPL2|Q9TQB3|Q9TQB9|Q9TQK3	Frame_Shift_Del	DEL	ENST00000367580.5	hg19	CCDS1342.1																																																																																			.	.		0.488	MR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085134.2	NM_001531		-	181003146	G	-	181003146	7	5	282	1	0	1	0	1	0	0	0	0	9761	1348	47	0	5	0	MR1	1	181003146	Start_Codon_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	2222652	181003146	68247475	103	40337										
EDEM3	80267	hgsc.bcm.edu	37	chr1	184680896	184680896	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gacagctcttatccaccacaTttttcaagggctcacgaata							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:184680896delT	ENST00000318130.8	-	15	1918	c.1652delA	c.(1651-1653)aatfs	p.N551fs	EDEM3_ENST00000367512.3_Frame_Shift_Del_p.N508fs|EDEM3_ENST00000466392.1_5'Flank	NM_025191.3	NP_079467.3	Q9BZQ6	EDEM3_HUMAN	ER degradation enhancer, mannosidase alpha-like 3	551					cellular protein metabolic process (GO:0044267)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|glycoprotein endo-alpha-1,2-mannosidase activity (GO:0004569)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						ATCCACCACATTTTTCAAGGG	0.363																																					p.N551fs		Atlas-INDEL	.											.	EDEM3	63	.	0			c.1653delT						.						116	108	110					1																	184680896		2203	4300	6503	SO:0001589	frameshift_variant	80267	exon15			.	AF288393	CCDS1363.2	1q25	2008-02-05	2006-03-31	2006-03-31	ENSG00000116406	ENSG00000116406			16787	protein-coding gene	gene with protein product		610214	"chromosome 1 open reading frame 22"	C1orf22		15537790, 15579471	Standard	NM_025191		Approved		uc010pok.2	Q9BZQ6	OTTHUMG00000035387	ENST00000318130.8:c.1652delA	chr1.hg19:g.184680896delT	ENSP00000318147:p.Asn551fs	130.0	0.0		163.0	11.0	NM_025191	B2RCH6|B7ZLZ2|Q0VGM5|Q5TEZ0|Q9HCW1|Q9UFV7	Frame_Shift_Del	DEL	ENST00000318130.8	hg19	CCDS1363.2																																																																																			.	.		0.363	EDEM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085785.3	NM_025191		-	184680896	T	-	184680896	7	5	282	1	0	1	0	1	0	0	0	0	4915	1493	52	0	1170	0	EDEM3	1	184680896	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3677750	184680896	64569725	104	40338										
C1orf26	54823	hgsc.bcm.edu	37	chr1	185143640	185143640	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtccttcttcaaatggaactAaaaaagacatacataaatgt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:185143640delA	ENST00000367500.4	+	5	526	c.361delA	c.(361-363)aaafs	p.K122fs	SWT1_ENST00000367501.3_Frame_Shift_Del_p.K122fs	NM_017673.6	NP_060143.4	Q5T5J6	SWT1_HUMAN	SWT1 RNA endoribonuclease homolog (S. cerevisiae)	122										breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(16)|ovary(1)|prostate(1)|urinary_tract(1)	41						AAATGGAACTAAAAAAGACAT	0.323																																					p.T120fs		Atlas-INDEL	.											.	SWT1	88	.	0			c.360delT						.						40	41	40					1																	185143640		2203	4300	6503	SO:0001589	frameshift_variant	54823	exon5			.	AF288392	CCDS1367.1	1q25	2013-08-29	2011-01-24	2011-01-24	ENSG00000116668	ENSG00000116668			16785	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 26"	C1orf26		11318611, 19127978, 23768067	Standard	NM_017673		Approved	FLJ20121, HsSwt1	uc001grg.4	Q5T5J6	OTTHUMG00000035390	ENST00000367500.4:c.361delA	chr1.hg19:g.185143640delA	ENSP00000356470:p.Lys122fs	207.0	0.0		238.0	15.0	NM_017673	Q8NEK9|Q9BZQ7|Q9NXQ0	Frame_Shift_Del	DEL	ENST00000367500.4	hg19	CCDS1367.1																																																																																			.	.		0.323	SWT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085790.1	NM_017673		-	185143640	A	-	185143640	7	5	282	1	0	1	0	1	0	0	0	0	2037	363	13	0	375	0	C1orf26	1	185143640	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	462744	185143640	64106981	105	40339										
C1orf26	54823	hgsc.bcm.edu	37	chr1	185175808	185175808	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tacatttactacagtgctttAaaaaacattggttggctgta							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:185175808delA	ENST00000367500.4	+	13	2050	c.1885delA	c.(1885-1887)aaafs	p.K630fs	SWT1_ENST00000367501.3_Frame_Shift_Del_p.K630fs	NM_017673.6	NP_060143.4	Q5T5J6	SWT1_HUMAN	SWT1 RNA endoribonuclease homolog (S. cerevisiae)	630										breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(16)|ovary(1)|prostate(1)|urinary_tract(1)	41						ACAGTGCTTTAAAAAACATTG	0.313																																					p.F628fs		Atlas-INDEL	.											.	SWT1	88	.	0			c.1884delT						.						67	70	69					1																	185175808		2202	4295	6497	SO:0001589	frameshift_variant	54823	exon13			.	AF288392	CCDS1367.1	1q25	2013-08-29	2011-01-24	2011-01-24	ENSG00000116668	ENSG00000116668			16785	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 26"	C1orf26		11318611, 19127978, 23768067	Standard	NM_017673		Approved	FLJ20121, HsSwt1	uc001grg.4	Q5T5J6	OTTHUMG00000035390	ENST00000367500.4:c.1885delA	chr1.hg19:g.185175808delA	ENSP00000356470:p.Lys630fs	158.0	0.0		181.0	11.0	NM_017673	Q8NEK9|Q9BZQ7|Q9NXQ0	Frame_Shift_Del	DEL	ENST00000367500.4	hg19	CCDS1367.1																																																																																			.	.		0.313	SWT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085790.1	NM_017673		-	185175808	A	-	185175808	7	5	282	1	0	1	0	1	0	0	0	0	2037	363	13	0	1931	0	C1orf26	1	185175808	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	32168	185175808	64074813	106	40340										
PRG4	10216	hgsc.bcm.edu	37	chr1	186282017	186282017	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acggctatgattactatgccTtttctaaaggtaaggtatta							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:186282017delT	ENST00000445192.2	+	12	4153	c.4108delT	c.(4108-4110)tttfs	p.F1370fs	PRG4_ENST00000367486.3_Frame_Shift_Del_p.F1327fs|PRG4_ENST00000367484.3_Frame_Shift_Del_p.F899fs|PRG4_ENST00000367485.4_Frame_Shift_Del_p.F1277fs|PRG4_ENST00000367483.4_Frame_Shift_Del_p.F1329fs|RNU6-1240P_ENST00000365155.1_RNA|TPR_ENST00000367478.4_3'UTR	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	1370					cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						TTACTATGCCTTTTCTAAAGG	0.383																																					p.A1369fs		Atlas-INDEL	.											.	PRG4	259	.	0			c.4107delC						.						100	94	96					1																	186282017		2203	4300	6503	SO:0001589	frameshift_variant	10216	exon12			.	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"lubricin", "megakaryocyte stimulating factor", "articular superficial zone protein", "Jacobs camptodactyly-arthropathy-pericarditis syndrome", "camptodactyly, arthropathy, coxa vara, pericarditis syndrome", "bG174L6.2 (MSF: megakaryocyte stimulating factor )"	604283	"proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.4108delT	chr1.hg19:g.186282017delT	ENSP00000399679:p.Phe1370fs	147.0	0.0		193.0	13.0	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Frame_Shift_Del	DEL	ENST00000445192.2	hg19	CCDS1369.1																																																																																			.	.		0.383	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807		-	186282017	T	-	186282017	7	5	282	1	0	1	0	1	0	0	0	0	12493	1609	56	0	4150	0	PRG4	1	186282017	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1106209	186282017	62968604	107	40341										
CFH	3075	hgsc.bcm.edu	37	chr1	196697534	196697534	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	attatacttgaggaacatttAaaaaacaagaaggaattcga					rs551215138		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:196697534delA	ENST00000367429.4	+	15	2535	c.2295delA	c.(2293-2295)ttafs	p.L765fs		NM_000186.3	NP_000177.2	P08603	CFAH_HUMAN	complement factor H	765	Sushi 13. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)			NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						AGGAACATTTAAAAAACAAGA	0.279																																					p.L765X		Atlas-INDEL	.											.	CFH	251	.	0			c.2294delT						.						48	47	47					1																	196697534		2203	4298	6501	SO:0001589	frameshift_variant	3075	exon15			.	Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971		"Complement system"	4883	protein-coding gene	gene with protein product	"beta-1H", "H factor 2 (complement)", "age-related maculopathy susceptibility 1"	134370	"H factor 1 (complement)"	HF, HF1, HF2		2889480, 2963625	Standard	NM_000186		Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000367429.4:c.2295delA	chr1.hg19:g.196697534delA	ENSP00000356399:p.Leu765fs	137.0	0.0		191.0	12.0	NM_000186	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Frame_Shift_Del	DEL	ENST00000367429.4	hg19	CCDS1385.1																																																																																			.	.		0.279	CFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086412.2	NM_000186		-	196697534	A	-	196697534	7	5	282	1	0	1	0	1	0	0	0	0	3285	359	13	0	2371	0	CFH	1	196697534	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	10415517	196697534	52553087	108	40342										
ASPM	259266	hgsc.bcm.edu	37	chr1	197056087	197056087	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aatacggtcaacaactttggAcctacttcgtacatcctaca	5	12	1	0	rs200083138		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:197056087A>G	ENST00000367409.4	-	27	10433	c.10177T>C	c.(10177-10179)Tcc>Ccc	p.S3393P	ASPM_ENST00000367408.1_Missense_Mutation_p.S1058P|ASPM_ENST00000294732.7_Missense_Mutation_p.S1808P	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	3393					developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						ACAACTTTGGACCTACTTCGT	0.269																																					p.S3393P		Atlas-SNP	.											ASPM,caecum,carcinoma,0,1	ASPM	444	.	0			c.T10177C						.						63	63	63					1																	197056087		2203	4297	6500	SO:0001583	missense	259266	exon27			CTTTGGACCTACT	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"microcephaly, primary autosomal recessive 5", "asp (abnormal spindle)-like, microcephaly associated (Drosophila)"	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.10177T>C	chr1.hg19:g.197056087A>G	ENSP00000356379:p.Ser3393Pro	82.0	0.0		100.0	4.0	NM_018136	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	hg19	CCDS1389.1	.	.	.	.	.	.	.	.	.	.	A	13.40	2.226779	0.39399	.	.	ENSG00000066279	ENST00000367409;ENST00000294732;ENST00000367408	T;T;T	0.56103	0.48;1.73;1.41	5.76	0.131	0.14755	.	0.110888	0.64402	N	0.000008	T	0.22322	0.0538	N	0.03608	-0.345	0.23425	N	0.997702	B;B	0.12630	0.001;0.006	B;B	0.12837	0.002;0.008	T	0.11941	-1.0567	10	0.30078	T	0.28	.	5.2057	0.15289	0.3084:0.1907:0.5009:0.0	.	1808;3393	Q4G1H1;Q8IZT6	.;ASPM_HUMAN	P	3393;1808;1058	ENSP00000356379:S3393P;ENSP00000294732:S1808P;ENSP00000356378:S1058P	ENSP00000294732:S1808P	S	-	1	0	ASPM	195322710	0.643000	0.27269	0.954000	0.39281	0.607000	0.37147	0.998000	0.29744	0.041000	0.15688	0.533000	0.62120	TCC	.	A|1.000;C|0.000		0.269	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136		G	197056087	A	G	197056087	3	3	282	1	0	0	0	0	1	0	0	0	1056	275	10	2	264	2	ASPM	1	197056087	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	358553	197056087	52194534	109	40343										
PTPRC	5788	hgsc.bcm.edu	37	chr1	198717290	198717290	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcacattggaaatcaagaagAaaataaaagtaaaaacagga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:198717290delA	ENST00000367376.2	+	27	3065	c.2894delA	c.(2893-2895)gaafs	p.E965fs	PTPRC_ENST00000348564.6_Frame_Shift_Del_p.E806fs|PTPRC_ENST00000442510.2_Frame_Shift_Del_p.E967fs|PTPRC_ENST00000352140.3_Frame_Shift_Del_p.E917fs|PTPRC_ENST00000594404.1_Frame_Shift_Del_p.E804fs	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	965	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axon guidance (GO:0007411)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|bone marrow development (GO:0048539)|cell cycle phase transition (GO:0044770)|cell surface receptor signaling pathway (GO:0007166)|defense response to virus (GO:0051607)|dephosphorylation (GO:0016311)|hematopoietic progenitor cell differentiation (GO:0002244)|immunoglobulin biosynthetic process (GO:0002378)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of antigen receptor-mediated signaling pathway (GO:0050857)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of T cell proliferation (GO:0042102)|protein dephosphorylation (GO:0006470)|regulation of cell cycle (GO:0051726)|release of sequestered calcium ion into cytosol (GO:0051209)|stem cell development (GO:0048864)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			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						AATCAAGAAGAAAATAAAAGT	0.269																																					p.E967fs		Atlas-INDEL	.											.	PTPRC	229	.	0			c.2899delG						.						21	21	21					1																	198717290		2050	4177	6227	SO:0001589	frameshift_variant	5788	exon27			.	Y00062	CCDS1397.1, CCDS1398.1, CCDS44291.1, CCDS1397.2, CCDS1398.2, CCDS44291.2	1q31-q32	2014-09-17			ENSG00000081237	ENSG00000081237		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9666	protein-coding gene	gene with protein product		151460		CD45		2169617	Standard	NM_001267798		Approved	LCA, T200, GP180	uc001gur.2	P08575	OTTHUMG00000035702	ENST00000367376.2:c.2894delA	chr1.hg19:g.198717290delA	ENSP00000356346:p.Glu965fs	95.0	0.0		134.0	11.0	NM_002838	A8K7W6|Q16614|Q9H0Y6	Frame_Shift_Del	DEL	ENST00000367376.2	hg19																																																																																				.	.		0.269	PTPRC-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding				-	198717290	A	-	198717290	7	5	282	1	0	1	0	1	0	0	0	0	12812	246	9	0	3007	0	PTPRC	1	198717290	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1661203	198717290	50533331	110	40344										
KIF21B	23046	hgsc.bcm.edu	37	chr1	200974546	200974546	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggctgtggtgcgggacagggCcccctgcttcaggcactgga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:200974546delC	ENST00000422435.2	-	5	938	c.622delG	c.(622-624)gccfs	p.A208fs	KIF21B_ENST00000332129.2_Frame_Shift_Del_p.A208fs|KIF21B_ENST00000461742.2_Frame_Shift_Del_p.A208fs|KIF21B_ENST00000360529.5_Frame_Shift_Del_p.A208fs	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	208	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						CGGGACAGGGCCCCCTGCTTC	0.622																																					p.A208fs		Atlas-INDEL	.											.	KIF21B	208	.	0			c.623delC						.						103	94	97					1																	200974546		2203	4300	6503	SO:0001589	frameshift_variant	23046	exon5			.	BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"Kinesins", "WD repeat domain containing"	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.622delG	chr1.hg19:g.200974546delC	ENSP00000411831:p.Ala208fs	137.0	0.0		212.0	14.0	NM_017596	B2RP62|B7ZMI0|Q5T4J3	Frame_Shift_Del	DEL	ENST00000422435.2	hg19	CCDS58056.1																																																																																			.	.		0.622	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332		-	200974546	C	-	200974546	7	5	282	1	0	1	0	1	0	0	0	0	8298	739	26	0	4372	0	KIF21B	1	200974546	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	2257256	200974546	48276075	111	40345										
DSTYK	25778	hgsc.bcm.edu	37	chr1	205180473	205180473	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cgccgcccgtgagggaggagAgacaagtgtggttgtgggag	20	7	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:205180473A>G	ENST00000367162.3	-	1	221	c.191T>C	c.(190-192)cTc>cCc	p.L64P	DSTYK_ENST00000367160.4_Missense_Mutation_p.L64P|DSTYK_ENST00000367161.3_Missense_Mutation_p.L64P	NM_015375.2	NP_056190.1	Q6XUX3	DUSTY_HUMAN	dual serine/threonine and tyrosine protein kinase	64					cellular response to fibroblast growth factor stimulus (GO:0044344)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of kinase activity (GO:0033674)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(2)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(2)	14						GAGGGAGGAGAGACAAGTGTG	0.692																																					p.L64P		Atlas-SNP	.											.	DSTYK	87	.	0			c.T191C						.						28	26	27					1																	205180473		2202	4300	6502	SO:0001583	missense	25778	exon1			GAGGAGAGACAAG	AF068286	CCDS1451.1, CCDS1452.1	1q32	2008-12-18	2008-12-18	2008-12-18	ENSG00000133059	ENSG00000133059			29043	protein-coding gene	gene with protein product		612666	"receptor interacting protein kinase 5"	RIPK5		15178406	Standard	NM_015375		Approved	KIAA0472, DustyPK, RIP5	uc001hbw.3	Q6XUX3	OTTHUMG00000037102	ENST00000367162.3:c.191T>C	chr1.hg19:g.205180473A>G	ENSP00000356130:p.Leu64Pro	67.0	0.0		54.0	4.0	NM_199462	B7ZL64|O75060|Q17R94|Q5RKT0|Q6IN87|Q6P997|Q86Y03|Q9P1S5	Missense_Mutation	SNP	ENST00000367162.3	hg19	CCDS1451.1	.	.	.	.	.	.	.	.	.	.	A	0.965	-0.702055	0.03255	.	.	ENSG00000133059	ENST00000367160;ENST00000367161;ENST00000367162	T;T;T	0.78126	-0.66;-1.08;-1.15	4.42	3.51	0.40186	.	0.329127	0.25887	N	0.027644	T	0.43277	0.1240	N	0.00707	-1.245	0.40637	D	0.981912	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.28839	-1.0031	10	0.18276	T	0.48	-6.8449	8.2263	0.31570	0.1914:0.0:0.8086:0.0	.	64;64	Q6XUX3-2;Q6XUX3	.;DUSTY_HUMAN	P	64	ENSP00000356128:L64P;ENSP00000356129:L64P;ENSP00000356130:L64P	ENSP00000356128:L64P	L	-	2	0	DSTYK	203447096	0.995000	0.38212	0.982000	0.44146	0.567000	0.35839	1.630000	0.37081	1.094000	0.41399	-0.232000	0.12228	CTC	.	.		0.692	DSTYK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090345.1	NM_015375		G	205180473	A	G	205180473	3	3	282	1	0	0	0	0	1	0	0	0	4787	304	11	2	2650	2	DSTYK	1	205180473	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	4205927	205180473	44070148	112	40346										
SLC30A1	7779	hgsc.bcm.edu	37	chr1	211751711	211751711	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaagatggcgttcaccagagCccccattacctcggctcgga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:211751711delC	ENST00000367001.4	-	1	373	c.244delG	c.(244-246)gctfs	p.A82fs		NM_021194.2	NP_067017.2	Q9Y6M5	ZNT1_HUMAN	solute carrier family 30 (zinc transporter), member 1	82					cadmium ion transmembrane transport (GO:0070574)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|cellular zinc ion homeostasis (GO:0006882)|detoxification of cadmium ion (GO:0071585)|in utero embryonic development (GO:0001701)|negative regulation of calcium ion import (GO:0090281)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of zinc ion transmembrane import (GO:0071584)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)	calcium channel inhibitor activity (GO:0019855)|zinc ion transmembrane transporter activity (GO:0005385)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(1)|ovary(3)|prostate(1)	11				OV - Ovarian serous cystadenocarcinoma(81;0.00535)|GBM - Glioblastoma multiforme(131;0.051)|all cancers(67;0.0604)|Epithelial(68;0.0978)		TTCACCAGAGCCCCCATTACC	0.667																																					p.A82fs		Atlas-INDEL	.											.	SLC30A1	27	.	0			c.245delC						.						39	48	45					1																	211751711		2203	4300	6503	SO:0001589	frameshift_variant	7779	exon1			.	AF323590	CCDS1499.1	1q32.3	2013-05-22			ENSG00000170385	ENSG00000170385		"Solute carriers"	11012	protein-coding gene	gene with protein product		609521		ZNT1			Standard	NM_021194		Approved	ZRC1	uc001hio.1	Q9Y6M5	OTTHUMG00000036995	ENST00000367001.4:c.244delG	chr1.hg19:g.211751711delC	ENSP00000355968:p.Ala82fs	152.0	0.0		166.0	10.0	NM_021194	Q0VAK9|Q9BZF6	Frame_Shift_Del	DEL	ENST00000367001.4	hg19	CCDS1499.1																																																																																			.	.		0.667	SLC30A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104738.2			-	211751711	C	-	211751711	7	5	282	1	0	1	0	1	0	0	0	0	14568	739	26	0	1287	0	SLC30A1	1	211751711	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	6571238	211751711	37498910	113	40347										
FAM71A	149647	hgsc.bcm.edu	37	chr1	212799568	212799568	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgaaagccgccacaaaacaaGgggagacaagattgcccaaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:212799568delG	ENST00000294829.3	+	1	1780	c.1349delG	c.(1348-1350)aggfs	p.R450fs	RP11-338C15.5_ENST00000427949.1_RNA	NM_153606.3	NP_705834.2	Q8IYT1	FA71A_HUMAN	family with sequence similarity 71, member A	450						nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(7)|liver(1)|lung(12)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(81;0.00631)|all cancers(67;0.00981)|GBM - Glioblastoma multiforme(131;0.0715)|Epithelial(68;0.094)		CACAAAACAAGGGGAGACAAG	0.562																																					p.R450fs		Atlas-INDEL	.											.	FAM71A	87	.	0			c.1348delA						.						62	77	72					1																	212799568		2203	4300	6503	SO:0001589	frameshift_variant	149647	exon1			.		CCDS1507.1	1q32.3	2008-02-05			ENSG00000162771	ENSG00000162771			26541	protein-coding gene	gene with protein product						12477932	Standard	NM_153606		Approved	FLJ32796	uc010pth.1	Q8IYT1	OTTHUMG00000041084	ENST00000294829.3:c.1349delG	chr1.hg19:g.212799568delG	ENSP00000294829:p.Arg450fs	107.0	0.0		141.0	12.0	NM_153606	Q5VTZ1	Frame_Shift_Del	DEL	ENST00000294829.3	hg19	CCDS1507.1																																																																																			.	.		0.562	FAM71A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098529.1	NM_153606		-	212799568	G	-	212799568	7	5	282	1	0	1	0	1	0	0	0	0	5615	1000	35	0	1351	0	FAM71A	1	212799568	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1047857	212799568	36451053	114	40348										
FLVCR1	28982	hgsc.bcm.edu	37	chr1	213068596	213068596	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acagaccaagaaccaaaaacGgttatgttgtccaagcagtc	8	10	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:213068596G>T	ENST00000366971.4	+	10	1830	c.1632G>T	c.(1630-1632)acG>acT	p.T544T	FLVCR1_ENST00000483790.1_3'UTR	NM_014053.3	NP_054772.1	Q9Y5Y0	FLVC1_HUMAN	feline leukemia virus subgroup C cellular receptor 1	544			T -> M (in dbSNP:rs3207090). {ECO:0000269|PubMed:15489334}.		blood vessel development (GO:0001568)|cell death (GO:0008219)|cellular iron ion homeostasis (GO:0006879)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|erythrocyte differentiation (GO:0030218)|erythrocyte maturation (GO:0043249)|head morphogenesis (GO:0060323)|heme export (GO:0097037)|heme transport (GO:0015886)|in utero embryonic development (GO:0001701)|mitochondrial transport (GO:0006839)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|regulation of organ growth (GO:0046620)|spleen development (GO:0048536)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	heme transporter activity (GO:0015232)|transporter activity (GO:0005215)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(2)	12				OV - Ovarian serous cystadenocarcinoma(81;0.00733)|all cancers(67;0.013)|GBM - Glioblastoma multiforme(131;0.0845)|Epithelial(68;0.11)		AACCAAAAACGGTTATGTTGT	0.383																																					p.T544T	Esophageal Squamous(199;2235 2952 19233 26256)	Atlas-SNP	.											FLVCR1,rectum,carcinoma,+1,1	FLVCR1	31	.	0			c.G1632T						.						119	109	113					1																	213068596		2203	4300	6503	SO:0001819	synonymous_variant	28982	exon10			AAAAACGGTTATG	AF118637	CCDS1510.1	1q32.3	2014-05-30			ENSG00000162769	ENSG00000162769		"Solute carriers"	24682	protein-coding gene	gene with protein product		609144	"ataxia, posterior column 1, with retinitis pigmentosa"	AXPC1		10400745, 10648427, 21070897	Standard	NM_014053		Approved	FLVCR, MFSD7B, PCA	uc001hjt.3	Q9Y5Y0	OTTHUMG00000036924	ENST00000366971.4:c.1632G>T	chr1.hg19:g.213068596G>T		216.0	0.0		246.0	0.0	NM_014053	Q1HE16|Q86XY9|Q9NVR9	Silent	SNP	ENST00000366971.4	hg19	CCDS1510.1	.	.	.	.	.	.	.	.	.	.	G	0.014	-1.571189	0.00895	.	.	ENSG00000162769	ENST00000419102	.	.	.	4.7	-9.39	0.00619	.	.	.	.	.	T	0.14270	0.0345	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.13335	-1.0513	4	.	.	.	-16.4378	0.9914	0.01458	0.4041:0.1528:0.2673:0.1757	.	.	.	.	L	343	.	.	R	+	2	0	FLVCR1	211135219	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-2.028000	0.01431	-2.726000	0.00386	-2.213000	0.00299	CGG	.	.		0.383	FLVCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089678.2	NM_014053		T	213068596	G	T	213068596	2	4	282	1	0	0	0	0	0	0	0	1	5953	1103	39	1		1	FLVCR1	1	213068596	Silent	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	269028	213068596	36182025	115	40349										
PROX1	5629	hgsc.bcm.edu	37	chr1	214209037	214209037	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctcagatcacattacgggagTttttcaatgccattatcgca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:214209037delT	ENST00000366958.4	+	5	2682	c.2074delT	c.(2074-2076)tttfs	p.F693fs	PROX1_ENST00000498508.2_Frame_Shift_Del_p.F693fs|PROX1_ENST00000261454.4_Frame_Shift_Del_p.F693fs|PROX1_ENST00000435016.1_Frame_Shift_Del_p.F693fs	NM_001270616.1	NP_001257545.1	Q92786	PROX1_HUMAN	prospero homeobox 1	693	Prospero-like.				aorta smooth muscle tissue morphogenesis (GO:0060414)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|brain development (GO:0007420)|cell fate determination (GO:0001709)|cerebellar granule cell differentiation (GO:0021707)|dentate gyrus development (GO:0021542)|dorsal spinal cord development (GO:0021516)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocardium formation (GO:0060214)|hepatocyte cell migration (GO:0002194)|hepatocyte differentiation (GO:0070365)|hepatocyte proliferation (GO:0072574)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|lens fiber cell morphogenesis (GO:0070309)|liver development (GO:0001889)|lung development (GO:0030324)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|negative regulation of bile acid biosynthetic process (GO:0070858)|negative regulation of cell proliferation (GO:0008285)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|olfactory placode formation (GO:0030910)|optic placode formation involved in camera-type eye formation (GO:0046619)|otic placode formation (GO:0043049)|pancreas development (GO:0031016)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell cycle checkpoint (GO:1901978)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of forebrain neuron differentiation (GO:2000979)|positive regulation of heart growth (GO:0060421)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of gene expression (GO:0010468)|regulation of transcription involved in lymphatic endothelial cell fate commitment (GO:0060849)|response to nutrient levels (GO:0031667)|retina morphogenesis in camera-type eye (GO:0060042)|skeletal muscle thin filament assembly (GO:0030240)|venous blood vessel morphogenesis (GO:0048845)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular cardiac myofibril assembly (GO:0055005)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DBD domain binding (GO:0050692)|DNA binding (GO:0003677)|LBD domain binding (GO:0050693)|ligand-dependent nuclear receptor binding (GO:0016922)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|prostate(2)|skin(4)	47				OV - Ovarian serous cystadenocarcinoma(81;0.0179)|all cancers(67;0.0488)|GBM - Glioblastoma multiforme(131;0.188)|Epithelial(68;0.219)		ATTACGGGAGTTTTTCAATGC	0.423																																					p.E691fs		Atlas-INDEL	.											.	PROX1	124	.	0			c.2073delG						.						87	81	83					1																	214209037		2203	4300	6503	SO:0001589	frameshift_variant	5629	exon5			.	U44060	CCDS31021.1	1q41	2011-06-20	2007-06-01		ENSG00000117707	ENSG00000117707		"Homeoboxes / PROS class"	9459	protein-coding gene	gene with protein product		601546	"prospero-related homeobox 1"			8812486	Standard	NM_002763		Approved		uc001hkg.2	Q92786	OTTHUMG00000036946	ENST00000366958.4:c.2074delT	chr1.hg19:g.214209037delT	ENSP00000355925:p.Phe693fs	249.0	0.0		267.0	17.0	NM_001270616	A6NK29|A8K2B1|Q5SW76|Q8TB91	Frame_Shift_Del	DEL	ENST00000366958.4	hg19	CCDS31021.1																																																																																			.	.		0.423	PROX1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089727.6	NM_002763		-	214209037	T	-	214209037	7	5	282	1	0	1	0	1	0	0	0	0	12572	1725	60	0	2088	0	PROX1	1	214209037	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1140441	214209037	35041584	116	40350										
KCNK2	3776	hgsc.bcm.edu	37	chr1	215297991	215297991	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgcagcaaatagtggcagcaAtaaatgcagggattataccg	11	7	0	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:215297991A>G	ENST00000444842.2	+	3	523	c.373A>G	c.(373-375)Ata>Gta	p.I125V	KCNK2_ENST00000391895.2_Missense_Mutation_p.I121V|KCNK2_ENST00000391894.2_Missense_Mutation_p.I110V	NM_001017425.2|NM_014217.3	NP_001017425.2|NP_055032.1	O95069	KCNK2_HUMAN	potassium channel, subfamily K, member 2	125					G-protein coupled receptor signaling pathway (GO:0007186)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	outward rectifier potassium channel activity (GO:0015271)|potassium channel inhibitor activity (GO:0019870)|potassium ion leak channel activity (GO:0022841)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|upper_aerodigestive_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(81;0.0399)|all cancers(67;0.0556)|GBM - Glioblastoma multiforme(131;0.068)	Dofetilide(DB00204)|Dronedarone(DB04855)	AGTGGCAGCAATAAATGCAGG	0.388																																					p.I125V		Atlas-SNP	.											.	KCNK2	135	.	0			c.A373G						.						138	136	137					1																	215297991		2203	4300	6503	SO:0001583	missense	3776	exon3			GCAGCAATAAATG	AF004711	CCDS31024.1, CCDS41466.1, CCDS41467.1	1q41	2012-03-07			ENSG00000082482	ENSG00000082482		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6277	protein-coding gene	gene with protein product		603219				9721223, 16382106	Standard	NM_001017424		Approved	K2p2.1, TREK-1	uc001hkr.4	O95069	OTTHUMG00000037017	ENST00000444842.2:c.373A>G	chr1.hg19:g.215297991A>G	ENSP00000394033:p.Ile125Val	310.0	0.0		389.0	106.0	NM_001017425	A1Z1V3|A8K618|B2RCS4|B7ZL56|D3DTA5|Q5DP47|Q5DP48|Q9NRT2|Q9UNE3	Missense_Mutation	SNP	ENST00000444842.2	hg19	CCDS41467.1	.	.	.	.	.	.	.	.	.	.	A	7.878	0.729600	0.15507	.	.	ENSG00000082482	ENST00000391895;ENST00000478774;ENST00000391894;ENST00000444842;ENST00000457122	T;T;T;T;T	0.20069	2.1;2.29;2.11;2.1;2.55	5.91	3.6	0.41247	Ion transport 2 (1);	0.140469	0.64402	N	0.000005	T	0.11623	0.0283	N	0.17278	0.47	0.42989	D	0.994483	B;B;B	0.14012	0.001;0.009;0.003	B;B;B	0.14023	0.006;0.01;0.006	T	0.13737	-1.0498	10	0.14252	T	0.57	.	10.2248	0.43218	0.8663:0.0:0.1337:0.0	.	110;125;121	O95069-2;O95069;O95069-3	.;KCNK2_HUMAN;.	V	121;69;110;125;69	ENSP00000375765:I121V;ENSP00000420569:I69V;ENSP00000375764:I110V;ENSP00000394033:I125V;ENSP00000413460:I69V	ENSP00000375764:I110V	I	+	1	0	KCNK2	213364614	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.845000	0.55880	0.502000	0.28037	0.524000	0.50904	ATA	.	.		0.388	KCNK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089856.2	NM_014217		G	215297991	A	G	215297991	3	3	282	1	0	0	0	0	1	0	0	0	8075	101	4	2	426	2	KCNK2	1	215297991	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1088954	215297991	33952630	117	40351										
USH2A	7399	hgsc.bcm.edu	37	chr1	216019331	216019331	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtttgaggtagcagaactccAaaaaagtgtgtaatattcaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:216019331delA	ENST00000307340.3	-	45	9276	c.8890delT	c.(8890-8892)tggfs	p.W2964fs	USH2A_ENST00000366943.2_Frame_Shift_Del_p.W2964fs	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	2964	Fibronectin type-III 16. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			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)		GCAGAACTCCAAAAAAGTGTG	0.398										HNSCC(13;0.011)																											p.W2964X		Atlas-INDEL	.											.	USH2A	1168	.	0			c.8891delG						.						85	84	84					1																	216019331		2203	4300	6503	SO:0001589	frameshift_variant	7399	exon45			.	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.8890delT	chr1.hg19:g.216019331delA	ENSP00000305941:p.Trp2964fs	189.0	0.0		215.0	14.0	NM_206933	Q5VVM9|Q6S362|Q9NS27	Frame_Shift_Del	DEL	ENST00000307340.3	hg19	CCDS31025.1																																																																																			.	.		0.398	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		-	216019331	A	-	216019331	7	5	282	1	0	1	0	1	0	0	0	0	17051	130	5	0	6830	0	USH2A	1	216019331	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	721340	216019331	33231290	118	40352										
MOSC1	64757	hgsc.bcm.edu	37	chr1	220960447	220960447	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcgccggcggctgctgcagcAggtgggcacagtggcgcagc	19	13	0	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:220960447A>G	ENST00000366910.5	+	1	347	c.161A>G	c.(160-162)cAg>cGg	p.Q54R		NM_022746.3	NP_073583.3	Q5VT66	MARC1_HUMAN	mitochondrial amidoxime reducing component 1	54					detoxification of nitrogen compound (GO:0051410)|nitrate metabolic process (GO:0042126)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	molybdenum ion binding (GO:0030151)|molybdopterin cofactor binding (GO:0043546)|nitrate reductase activity (GO:0008940)|pyridoxal phosphate binding (GO:0030170)										CTGCTGCAGCAGGTGGGCACA	0.751																																					p.Q54R		Atlas-SNP	.											.	.	.	.	0			c.A161G						.						7	7	7					1																	220960447		2015	4019	6034	SO:0001583	missense	64757	exon1			TGCAGCAGGTGGG	AK026043	CCDS1526.1	1q41	2011-11-02	2011-11-02	2011-11-02	ENSG00000186205	ENSG00000186205			26189	protein-coding gene	gene with protein product		614126	"MOCO sulphurase C-terminal domain containing 1"	MOSC1		11886751	Standard	NM_022746		Approved	FLJ22390	uc001hms.3	Q5VT66	OTTHUMG00000037353	ENST00000366910.5:c.161A>G	chr1.hg19:g.220960447A>G	ENSP00000355877:p.Gln54Arg	52.0	0.0		50.0	5.0	NM_022746	A8K447|B2D078|Q5VVS9|Q5VVT0|Q5VVT1|Q8N9P5|Q96FN8|Q9H6C7	Missense_Mutation	SNP	ENST00000366910.5	hg19	CCDS1526.1	.	.	.	.	.	.	.	.	.	.	A	7.969	0.748572	0.15710	.	.	ENSG00000186205	ENST00000366910	T	0.22134	1.97	4.13	4.13	0.48395	Pyruvate kinase-like, insert domain (1);	0.409866	0.19939	N	0.102686	T	0.08758	0.0217	N	0.08118	0	0.29995	N	0.816538	B;B	0.26081	0.141;0.031	B;B	0.21151	0.033;0.022	T	0.21042	-1.0257	10	0.15066	T	0.55	-15.0579	6.8898	0.24222	0.8435:0.0:0.1565:0.0	.	54;54	Q5VT66-2;Q5VT66	.;MOSC1_HUMAN	R	54	ENSP00000355877:Q54R	ENSP00000355877:Q54R	Q	+	2	0	MOSC1	219027070	1.000000	0.71417	1.000000	0.80357	0.394000	0.30568	1.491000	0.35583	1.490000	0.48466	0.254000	0.18369	CAG	.	.		0.751	MARC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090904.1	NM_022746		G	220960447	A	G	220960447	3	3	282	1	0	0	0	0	1	0	0	0	9722	188	7	2	163	2	MOSC1	1	220960447	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	4941116	220960447	28290174	119	40353										
PARP1	142	hgsc.bcm.edu	37	chr1	226570841	226570841	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gggggaatatacggtcctgtTttttaaccttcaatttcttg	9	7	2	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:226570841T>C	ENST00000366794.5	-	8	1198	c.1055A>G	c.(1054-1056)aAa>aGa	p.K352R		NM_001618.3	NP_001609.2	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase 1	352					base-excision repair (GO:0006284)|cellular response to insulin stimulus (GO:0032869)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|gene expression (GO:0010467)|macrophage differentiation (GO:0030225)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|protein ADP-ribosylation (GO:0006471)|protein autoprocessing (GO:0016540)|protein poly-ADP-ribosylation (GO:0070212)|regulation of growth rate (GO:0040009)|signal transduction involved in regulation of gene expression (GO:0023019)|telomere maintenance (GO:0000723)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NAD binding (GO:0051287)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(4)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	44	Breast(184;0.133)			GBM - Glioblastoma multiforme(131;0.0531)		ACGGTCCTGTTTTTTAACCTT	0.502								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA																													p.K352R		Atlas-SNP	.											PARP1,NS,carcinoma,0,1	PARP1	100	.	0			c.A1055G						.						115	143	134					1																	226570841		2203	4300	6503	SO:0001583	missense	142	exon8			TCCTGTTTTTTAA	BC037545	CCDS1554.1	1q41-q42	2010-02-16	2008-07-28	2004-08-26	ENSG00000143799	ENSG00000143799	2.4.2.30	"Poly (ADP-ribose) polymerases"	270	protein-coding gene	gene with protein product		173870	"ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)", "poly (ADP-ribose) polymerase family, member 1"	PPOL, ADPRT		10964595	Standard	NM_001618		Approved	PARP	uc001hqd.4	P09874	OTTHUMG00000037556	ENST00000366794.5:c.1055A>G	chr1.hg19:g.226570841T>C	ENSP00000355759:p.Lys352Arg	129.0	0.0		191.0	0.0	NM_001618	B1ANJ4|Q8IUZ9	Missense_Mutation	SNP	ENST00000366794.5	hg19	CCDS1554.1	.	.	.	.	.	.	.	.	.	.	T	8.952	0.968513	0.18659	.	.	ENSG00000143799	ENST00000366794	T	0.10192	2.9	5.27	2.95	0.34219	.	0.147960	0.64402	N	0.000015	T	0.04724	0.0128	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.42258	-0.9462	10	0.15952	T	0.53	-10.5467	7.8417	0.29402	0.0:0.2327:0.0:0.7673	.	352	P09874	PARP1_HUMAN	R	352	ENSP00000355759:K352R	ENSP00000355759:K352R	K	-	2	0	PARP1	224637464	0.897000	0.30589	0.987000	0.45799	0.573000	0.36030	0.922000	0.28734	0.323000	0.23307	0.459000	0.35465	AAA	.	.		0.502	PARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091519.1	NM_001618		C	226570841	T	C	226570841	3	2	282	1	0	0	0	0	1	0	0	0	11463	1841	64	2	2053	2	PARP1	1	226570841	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	5610394	226570841	22679780	120	40354										
PSEN2	5664	hgsc.bcm.edu	37	chr1	227073343	227073343	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cgtcatcgtggttatgaccaTcttcttggtggtgctctaca	10	10	4	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:227073343T>C	ENST00000366783.3	+	6	897	c.461T>C	c.(460-462)aTc>aCc	p.I154T	PSEN2_ENST00000472139.2_Missense_Mutation_p.I10T|PSEN2_ENST00000391872.2_Missense_Mutation_p.I187T|PSEN2_ENST00000366782.1_Missense_Mutation_p.I187T|PSEN2_ENST00000340188.4_Missense_Mutation_p.I154T|PSEN2_ENST00000422240.2_Missense_Mutation_p.I154T	NM_000447.2|NM_012486.2	NP_000438.2|NP_036618.2	P49810	PSN2_HUMAN	presenilin 2	154					amyloid precursor protein catabolic process (GO:0042987)|anagen (GO:0042640)|apoptotic signaling pathway (GO:0097190)|beta-amyloid metabolic process (GO:0050435)|brain morphogenesis (GO:0048854)|calcium ion transport (GO:0006816)|cardiac muscle contraction (GO:0060048)|cell fate specification (GO:0001708)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic limb morphogenesis (GO:0030326)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|forebrain development (GO:0030900)|hematopoietic progenitor cell differentiation (GO:0002244)|intracellular signal transduction (GO:0035556)|locomotion (GO:0040011)|lung alveolus development (GO:0048286)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|memory (GO:0007613)|myeloid leukocyte differentiation (GO:0002573)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of protein binding (GO:0032091)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of protein phosphorylation (GO:0001933)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|positive regulation of coagulation (GO:0050820)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein processing (GO:0016485)|protein transport (GO:0015031)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of synaptic plasticity (GO:0048167)|response to hypoxia (GO:0001666)|somitogenesis (GO:0001756)|T cell activation involved in immune response (GO:0002286)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cell cortex (GO:0005938)|cell surface (GO:0009986)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|ciliary rootlet (GO:0035253)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|kinetochore (GO:0000776)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nuclear inner membrane (GO:0005637)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|Z disc (GO:0030018)	aspartic-type endopeptidase activity (GO:0004190)|endopeptidase activity (GO:0004175)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|urinary_tract(1)	20		Prostate(94;0.0771)				GTTATGACCATCTTCTTGGTG	0.602																																					p.I154T		Atlas-SNP	.											.	PSEN2	55	.	0			c.T461C						.						213	141	165					1																	227073343		2203	4300	6503	SO:0001583	missense	5664	exon6			TGACCATCTTCTT	BC006365	CCDS1556.1, CCDS44324.1	1q42.13	2014-09-17	2014-02-24		ENSG00000143801	ENSG00000143801			9509	protein-coding gene	gene with protein product		600759	"Alzheimer disease 4"	AD4		7638621	Standard	NM_000447		Approved	AD3L, STM2, PS2	uc009xeo.1	P49810	OTTHUMG00000037563	ENST00000366783.3:c.461T>C	chr1.hg19:g.227073343T>C	ENSP00000355747:p.Ile154Thr	93.0	0.0		142.0	6.0	NM_012486	A8K8D4|B1AP21|Q96P32	Missense_Mutation	SNP	ENST00000366783.3	hg19	CCDS1556.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.478244	0.84747	.	.	ENSG00000143801	ENST00000366783;ENST00000340188;ENST00000422240;ENST00000366782;ENST00000391872;ENST00000472139	D;D;D;D;D;D	0.99552	-6.15;-6.15;-6.15;-6.15;-6.15;-6.15	5.27	5.27	0.74061	.	0.106621	0.64402	D	0.000007	D	0.99211	0.9726	L	0.56124	1.755	0.58432	D	0.999999	B;D	0.57571	0.11;0.98	B;P	0.55260	0.215;0.772	D	0.99047	1.0826	10	0.87932	D	0	.	15.1959	0.73088	0.0:0.0:0.0:1.0	.	154;154	A8K8D4;P49810	.;PSN2_HUMAN	T	154;154;154;187;187;10	ENSP00000355747:I154T;ENSP00000339860:I154T;ENSP00000403737:I154T;ENSP00000355746:I187T;ENSP00000375745:I187T;ENSP00000427806:I10T	ENSP00000339860:I154T	I	+	2	0	PSEN2	225139966	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.007000	0.70731	2.011000	0.59026	0.454000	0.30748	ATC	.	.		0.602	PSEN2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000091539.1	NM_000447		C	227073343	T	C	227073343	3	2	282	1	0	0	0	0	1	0	0	0	12663	1435	50	2	471	2	PSEN2	1	227073343	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	502502	227073343	22177278	121	40355										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228434468	228434468	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gggagtacacctgtgaggctGggggccagcggctctccttc	16	12	1	1	rs372487722		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:228434468G>C	ENST00000422127.1	+	13	4041	c.3997G>C	c.(3997-3999)Ggg>Cgg	p.G1333R	OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000570156.2_Missense_Mutation_p.G1425R|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000284548.11_Missense_Mutation_p.G1333R	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1333	Ig-like 13.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)	p.G1334fs*37(2)		NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CTGTGAGGCTGGGGGCCAGCG	0.592																																					p.G1425R		Atlas-SNP	.											.,2	OBSCN	2142	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.G4273C						.						71	80	77					1																	228434468		2004	4180	6184	SO:0001583	missense	84033	exon14			GAGGCTGGGGGCC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.3997G>C	chr1.hg19:g.228434468G>C	ENSP00000409493:p.Gly1333Arg	339.0	1.0		371.0	0.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	.	7.104	0.574764	0.13623	.	.	ENSG00000154358	ENST00000284548;ENST00000422127	T;T	0.11930	2.73;2.73	5.07	4.15	0.48705	Immunoglobulin subtype (1);	0.070770	0.53938	D	0.000044	T	0.17408	0.0418	L	0.49256	1.55	0.80722	D	1	P;D	0.54964	0.536;0.969	B;P	0.46796	0.398;0.527	T	0.01162	-1.1432	10	0.48119	T	0.1	.	11.4416	0.50100	0.1512:0.0:0.8488:0.0	.	1333;1333	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	R	1333	ENSP00000284548:G1333R;ENSP00000409493:G1333R	ENSP00000284548:G1333R	G	+	1	0	OBSCN	226501091	1.000000	0.71417	0.896000	0.35187	0.062000	0.15995	5.366000	0.66122	1.115000	0.41800	0.557000	0.71058	GGG	.	.		0.592	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		C	228434468	G	C	228434468	3	2	282	1	0	0	0	0	1	0	0	0	10821	1348	47	4	4043	4	OBSCN	1	228434468	Missense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1361125	228434468	20816153	122	40356										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228560756	228560756	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggcctccgtggagcacatctCccggatcctgaagggcaggc	14	14	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:228560756C>G	ENST00000422127.1	+	94	22321	c.22277C>G	c.(22276-22278)tCc>tGc	p.S7426C	OBSCN_ENST00000570156.2_Missense_Mutation_p.S8383C|OBSCN_ENST00000366707.4_Missense_Mutation_p.S5060C	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	7426					apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GAGCACATCTCCCGGATCCTG	0.637																																					p.S8383C		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C25148G						.						21	25	23					1																	228560756		2070	4184	6254	SO:0001583	missense	84033	exon105			ACATCTCCCGGAT	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.22277C>G	chr1.hg19:g.228560756C>G	ENSP00000409493:p.Ser7426Cys	125.0	0.0		183.0	40.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.799630	0.90538	.	.	ENSG00000154358	ENST00000422127;ENST00000366707	T;T	0.79033	-1.14;-1.23	5.44	5.44	0.79542	.	.	.	.	.	D	0.82388	0.5026	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.81618	-0.0851	9	0.39692	T	0.17	.	16.4183	0.83750	0.0:1.0:0.0:0.0	.	7426	Q5VST9	OBSCN_HUMAN	C	7426;5060	ENSP00000409493:S7426C;ENSP00000355668:S5060C	ENSP00000355668:S5060C	S	+	2	0	OBSCN	226627379	1.000000	0.71417	1.000000	0.80357	0.769000	0.43574	4.248000	0.58760	2.550000	0.86006	0.462000	0.41574	TCC	.	.		0.637	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		G	228560756	C	G	228560756	3	3	282	1	0	0	0	0	1	0	0	0	10821	855	30	4	23857	4	OBSCN	1	228560756	Missense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	126288	228560756	20689865	123	40357										
COG2	22796	hgsc.bcm.edu	37	chr1	230800279	230800279	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcggtcagttgagaaaattgAaaaaatcttaaactctcaaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:230800279delA	ENST00000366669.4	+	5	546	c.431delA	c.(430-432)gaafs	p.E144fs	COG2_ENST00000535166.1_Frame_Shift_Del_p.E28fs|COG2_ENST00000534989.1_Frame_Shift_Del_p.E85fs|COG2_ENST00000366668.3_Frame_Shift_Del_p.E144fs	NM_001145036.1|NM_007357.2	NP_001138508.1|NP_031383.1	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2	144					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	cytosol (GO:0005829)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|Golgi transport complex (GO:0017119)	protein transporter activity (GO:0008565)			NS(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|urinary_tract(3)	27	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				GAGAAAATTGAAAAAATCTTA	0.269																																					p.E144fs		Atlas-INDEL	.											.	COG2	61	.	0			c.430delG						.						28	30	29					1																	230800279		2196	4274	6470	SO:0001589	frameshift_variant	22796	exon5			.	Z34975	CCDS1584.1, CCDS44329.1	1q42.2	2008-02-05	2002-05-28	2002-05-31	ENSG00000135775	ENSG00000135775		"Components of oligomeric golgi complex"	6546	protein-coding gene	gene with protein product		606974	"low density lipoprotein receptor defect C complementing"	LDLC		7962052	Standard	NM_007357		Approved		uc001htw.3	Q14746	OTTHUMG00000037753	ENST00000366669.4:c.431delA	chr1.hg19:g.230800279delA	ENSP00000355629:p.Glu144fs	173.0	0.0		269.0	18.0	NM_007357	Q86U99	Frame_Shift_Del	DEL	ENST00000366669.4	hg19	CCDS1584.1																																																																																			.	.		0.269	COG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092087.1	NM_007357		-	230800279	A	-	230800279	7	5	282	1	0	1	0	1	0	0	0	0	3660	246	9	0	449	0	COG2	1	230800279	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2239523	230800279	18450342	124	40358										
C1orf131	128061	hgsc.bcm.edu	37	chr1	231362561	231362561	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccttgtaattcacataactcTttttaggaggctgtaatgaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:231362561delT	ENST00000366649.2	-	5	642	c.617delA	c.(616-618)aagfs	p.K206fs	C1orf131_ENST00000366651.3_Frame_Shift_Del_p.K205fs|C1orf131_ENST00000318906.2_Frame_Shift_Del_p.K206fs			Q8NDD1	CA131_HUMAN	chromosome 1 open reading frame 131	206	Lys-rich.						poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(1)	8	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)				CACATAACTCTTTTTAGGAGG	0.373																																					p.K206fs		Atlas-INDEL	.											.	C1orf131	30	.	0			c.618delG						.						125	131	129					1																	231362561		2203	4300	6503	SO:0001589	frameshift_variant	128061	exon5			.	BC062353	CCDS1591.2, CCDS73049.1	1q42.2	2012-06-27			ENSG00000143633	ENSG00000143633			25332	protein-coding gene	gene with protein product						12975309	Standard	XM_005273051		Approved	DKFZp547B1713	uc001hul.3	Q8NDD1	OTTHUMG00000038023	ENST00000366649.2:c.617delA	chr1.hg19:g.231362561delT	ENSP00000355609:p.Lys206fs	123.0	0.0		214.0	16.0	NM_152379	Q5TBI0|Q5TBI1|Q6P6B4|Q7Z6H5|Q8N432|Q96NM6	Frame_Shift_Del	DEL	ENST00000366649.2	hg19	CCDS1591.2																																																																																			.	.		0.373	C1orf131-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092864.1	NM_152379		-	231362561	T	-	231362561	7	5	282	1	0	1	0	1	0	0	0	0	2000	1609	56	0	276	0	C1orf131	1	231362561	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	562282	231362561	17888060	125	40359										
PCNXL2	80003	hgsc.bcm.edu	37	chr1	233334767	233334767	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgtaaacagccgaggttatcCcagacacagctggaacacaa	9	11	0	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:233334767C>A	ENST00000258229.9	-	15	3218	c.2984G>T	c.(2983-2985)gGg>gTg	p.G995V	PCNXL2_ENST00000488780.2_Missense_Mutation_p.G128V	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	995						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				CGAGGTTATCCCAGACACAGC	0.502																																					p.G995V		Atlas-SNP	.											.	PCNXL2	204	.	0			c.G2984T						.						18	19	18					1																	233334767		1969	4160	6129	SO:0001583	missense	80003	exon15			GTTATCCCAGACA	AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749			8736	protein-coding gene	gene with protein product			"pecanex (Drosophila)-like 2"			12477932	Standard	NM_014801		Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.2984G>T	chr1.hg19:g.233334767C>A	ENSP00000258229:p.Gly995Val	399.0	0.0		468.0	304.0	NM_014801	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Missense_Mutation	SNP	ENST00000258229.9	hg19	CCDS44335.1	.	.	.	.	.	.	.	.	.	.	C	17.36	3.368733	0.61624	.	.	ENSG00000135749	ENST00000258229;ENST00000488780;ENST00000518351	T;T	0.46819	2.95;0.86	5.33	5.33	0.75918	.	.	.	.	.	T	0.66973	0.2844	M	0.64997	1.995	0.80722	D	1	D	0.71674	0.998	D	0.68621	0.959	T	0.68447	-0.5406	9	0.59425	D	0.04	.	19.0247	0.92927	0.0:1.0:0.0:0.0	.	995	A6NKB5	PCX2_HUMAN	V	995;128;164	ENSP00000258229:G995V;ENSP00000429231:G164V	ENSP00000258229:G995V	G	-	2	0	PCNXL2	231401390	0.998000	0.40836	0.912000	0.35992	0.178000	0.23041	6.539000	0.73856	2.512000	0.84698	0.591000	0.81541	GGG	.	.		0.502	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092480.3	NM_014801		A	233334767	C	A	233334767	3	1	282	1	0	0	0	0	1	0	0	0	11601	623	22	3	3509	3	PCNXL2	1	233334767	Missense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1972206	233334767	15915854	126	40360										
LYST	1130	hgsc.bcm.edu	37	chr1	235887447	235887447	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aatttcttcatatgtccaggAaaatgatgctggttccaact							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:235887447delA	ENST00000389794.3	-	39	9370	c.9196delT	c.(9196-9198)tccfs	p.S3066fs	LYST_ENST00000389793.2_Frame_Shift_Del_p.S3066fs|LYST_ENST00000473037.1_5'UTR			Q99698	LYST_HUMAN	lysosomal trafficking regulator	3066					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			TATGTCCAGGAAAATGATGCT	0.338																																					p.S3066fs		Atlas-INDEL	.											.	LYST	370	.	0			c.9197delC						.						89	88	88					1																	235887447		2203	4300	6503	SO:0001589	frameshift_variant	1130	exon39			.	U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"WD repeat domain containing"	1968	protein-coding gene	gene with protein product		606897	"Chediak-Higashi syndrome 1"	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.9196delT	chr1.hg19:g.235887447delA	ENSP00000374444:p.Ser3066fs	191.0	0.0		291.0	18.0	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Frame_Shift_Del	DEL	ENST00000389794.3	hg19	CCDS31062.1																																																																																			.	.		0.338	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			-	235887447	A	-	235887447	7	5	282	1	0	1	0	1	0	0	0	0	9137	246	9	0	2269	0	LYST	1	235887447	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2552680	235887447	13363174	127	40361										
LYST	1130	hgsc.bcm.edu	37	chr1	235964220	235964220	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctttctgcctaataattttcAaaaaactctcaaatacatgg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:235964220delA	ENST00000389794.3	-	9	4064	c.3890delT	c.(3889-3891)ttgfs	p.L1297fs	LYST_ENST00000536965.1_Frame_Shift_Del_p.L1297fs|LYST_ENST00000389793.2_Frame_Shift_Del_p.L1297fs			Q99698	LYST_HUMAN	lysosomal trafficking regulator	1297					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			AATAATTTTCAAAAAACTCTC	0.318																																					p.L1297fs		Atlas-INDEL	.											.	LYST	370	.	0			c.3891delG						.						54	54	54					1																	235964220		2203	4300	6503	SO:0001589	frameshift_variant	1130	exon9			.	U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"WD repeat domain containing"	1968	protein-coding gene	gene with protein product		606897	"Chediak-Higashi syndrome 1"	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.3890delT	chr1.hg19:g.235964220delA	ENSP00000374444:p.Leu1297fs	136.0	0.0		151.0	12.0	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Frame_Shift_Del	DEL	ENST00000389794.3	hg19	CCDS31062.1																																																																																			.	.		0.318	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			-	235964220	A	-	235964220	7	5	282	1	0	1	0	1	0	0	0	0	9137	131	5	0	7695	0	LYST	1	235964220	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	76773	235964220	13286401	128	40362										
RYR2	6262	hgsc.bcm.edu	37	chr1	237778080	237778080	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gctggtgaggaagaagccaaGgggggcaagcggcccaagga					rs202117250		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:237778080delG	ENST00000366574.2	+	37	5969	c.5652delG	c.(5650-5652)aagfs	p.K1884fs	RYR2_ENST00000542537.1_Frame_Shift_Del_p.K1868fs|RYR2_ENST00000360064.6_Frame_Shift_Del_p.K1882fs	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1884	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)	p.K1882N(1)		NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			AAGAAGCCAAGGGGGGCAAGC	0.512																																					p.K1884fs		Atlas-INDEL	.											.	RYR2	1273	.	1	Substitution - Missense(1)	lung(1)	c.5651delA						.						45	48	47					1																	237778080		2000	4162	6162	SO:0001589	frameshift_variant	6262	exon37			.	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.5652delG	chr1.hg19:g.237778080delG	ENSP00000355533:p.Lys1884fs	154.0	0.0		182.0	13.0	NM_001035	Q15411|Q546N8|Q5T3P2	Frame_Shift_Del	DEL	ENST00000366574.2	hg19	CCDS55691.1																																																																																			.	.		0.512	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		-	237778080	G	-	237778080	7	5	282	1	0	1	0	1	0	0	0	0	13784	991	35	0	5798	0	RYR2	1	237778080	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1813860	237778080	11472541	129	40363										
HNRNPU	3192	hgsc.bcm.edu	37	chr1	245027581	245027581	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcagctccgacaccttcagcTtttttacattaacaggcgag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:245027581delT	ENST00000283179.9	-	1	192	c.29delA	c.(28-30)aagfs	p.K10fs	HNRNPU_ENST00000444376.2_Frame_Shift_Del_p.K10fs|RP11-11N7.4_ENST00000610145.1_lincRNA			Q00839	HNRPU_HUMAN	heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A)	10	Asp/Glu-rich (acidic).|SAP. {ECO:0000255|PROSITE- ProRule:PRU00186}.				CRD-mediated mRNA stabilization (GO:0070934)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasmic ribonucleoprotein granule (GO:0036464)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|endometrium(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20	all_cancers(71;6.97e-06)|all_epithelial(71;0.000104)|all_neural(11;0.0269)|Breast(184;0.0545)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0989)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.00868)			CACCTTCAGCTTTTTTACATT	0.597																																					p.K10fs	NSCLC(33;911 1010 3329 23631 49995)	Atlas-INDEL	.											.	HNRNPU	64	.	0			c.30delG						.						25	29	27					1																	245027581		2201	4295	6496	SO:0001589	frameshift_variant	3192	exon1			.	X65488	CCDS31081.1, CCDS41479.1	1q44	2011-10-24		2007-08-16	ENSG00000153187	ENSG00000153187			5048	protein-coding gene	gene with protein product		602869		HNRPU		7509195, 8068679	Standard	NM_031844		Approved	SAF-A, hnRNPU	uc001iaz.1	Q00839	OTTHUMG00000040396	ENST00000283179.9:c.29delA	chr1.hg19:g.245027581delT	ENSP00000283179:p.Lys10fs	267.0	0.0		316.0	19.0	NM_004501	O75507|Q8N174|Q96HY9|Q9BQ09	Frame_Shift_Del	DEL	ENST00000283179.9	hg19	CCDS41479.1																																																																																			.	.		0.597	HNRNPU-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000097163.3	NM_031844		-	245027581	T	-	245027581	7	5	282	1	0	1	0	1	0	0	0	0	7282	1609	56	0	2504	0	HNRNPU	1	245027581	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	7249501	245027581	4223040	130	40364										
KIF26B	55083	hgsc.bcm.edu	37	chr1	245775272	245775272	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggatggagaagagcgggaaaGggggaagtaagtcggccact							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:245775272delG	ENST00000407071.2	+	9	2532	c.2092delG	c.(2092-2094)gggfs	p.G699fs	KIF26B_ENST00000366518.4_Frame_Shift_Del_p.G318fs|RP11-522M21.2_ENST00000418402.1_RNA	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	699	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			GAGCGGGAAAGGGGGAAGTAA	0.577																																					p.K697fs		Atlas-INDEL	.											.	KIF26B	343	.	0			c.2091delA						.						52	60	57					1																	245775272		2074	4192	6266	SO:0001589	frameshift_variant	55083	exon9			.	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"Kinesins"	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.2092delG	chr1.hg19:g.245775272delG	ENSP00000385545:p.Gly699fs	122.0	0.0		200.0	12.0	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Frame_Shift_Del	DEL	ENST00000407071.2	hg19	CCDS44342.1																																																																																			.	.		0.577	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354		-	245775272	G	-	245775272	7	5	282	1	0	1	0	1	0	0	0	0	8304	1000	35	0	2126	0	KIF26B	1	245775272	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	747691	245775272	3475349	131	40365										
KIF26B	55083	hgsc.bcm.edu	37	chr1	245848940	245848940	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gagctcaccgacaacgagggCcccccagactttgtccctat					rs190318015	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:245848940delC	ENST00000407071.2	+	12	3095	c.2655delC	c.(2653-2655)ggcfs	p.G885fs	KIF26B_ENST00000366518.4_Frame_Shift_Del_p.G504fs	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	885					establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			ACAACGAGGGCCCCCCAGACT	0.662																																					p.G885fs		Atlas-INDEL	.											.	KIF26B	343	.	0			c.2654delG						.						32	36	34					1																	245848940		2010	4149	6159	SO:0001589	frameshift_variant	55083	exon12			.	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"Kinesins"	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.2655delC	chr1.hg19:g.245848940delC	ENSP00000385545:p.Gly885fs	238.0	0.0		341.0	21.0	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Frame_Shift_Del	DEL	ENST00000407071.2	hg19	CCDS44342.1																																																																																			.	.		0.662	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354		-	245848940	C	-	245848940	7	5	282	1	0	1	0	1	0	0	0	0	8304	726	26	0	2701	0	KIF26B	1	245848940	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	73668	245848940	3401681	132	40366										
KIF26B	55083	hgsc.bcm.edu	37	chr1	245849535	245849535	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cggagtacaagccacccagcTctccttcccagagatgcaaa	8	15	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:245849535T>C	ENST00000407071.2	+	12	3690	c.3250T>C	c.(3250-3252)Tct>Cct	p.S1084P	KIF26B_ENST00000366518.4_Missense_Mutation_p.S703P	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	1084					establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			GCCACCCAGCTCTCCTTCCCA	0.657																																					p.S1084P		Atlas-SNP	.											.	KIF26B	343	.	0			c.T3250C						.						46	53	51					1																	245849535		1957	4157	6114	SO:0001583	missense	55083	exon12			CCCAGCTCTCCTT	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"Kinesins"	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.3250T>C	chr1.hg19:g.245849535T>C	ENSP00000385545:p.Ser1084Pro	245.0	0.0		326.0	16.0	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Missense_Mutation	SNP	ENST00000407071.2	hg19	CCDS44342.1	.	.	.	.	.	.	.	.	.	.	T	16.31	3.088282	0.55968	.	.	ENSG00000162849	ENST00000407071;ENST00000366518;ENST00000413001	T;T	0.80480	-1.38;-1.37	5.77	5.77	0.91146	.	.	.	.	.	T	0.81508	0.4837	M	0.77616	2.38	0.58432	D	0.999999	P;P	0.42409	0.779;0.779	B;B	0.39805	0.141;0.31	T	0.82194	-0.0578	9	0.38643	T	0.18	.	16.0977	0.81139	0.0:0.0:0.0:1.0	.	703;1084	B7WPD9;Q2KJY2	.;KI26B_HUMAN	P	1084;703;700	ENSP00000385545:S1084P;ENSP00000355475:S703P	ENSP00000355475:S703P	S	+	1	0	KIF26B	243916158	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	7.794000	0.85869	2.215000	0.71742	0.459000	0.35465	TCT	.	.		0.657	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354		C	245849535	T	C	245849535	3	2	282	1	0	0	0	0	1	0	0	0	8304	1551	54	2	3296	2	KIF26B	1	245849535	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	595	245849535	3401086	133	40367										
OR2C3	81472	hgsc.bcm.edu	37	chr1	247695757	247695757	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtttctagtgagggtcgtgtGgagaagcccaggaggacaaa	16	6	1	2	rs61746303|rs386641879	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:247695757G>C	ENST00000366487.3	-	2	418	c.57C>G	c.(55-57)tcC>tcG	p.S19S	GCSAML_ENST00000366491.2_Intron|GCSAML_ENST00000366489.1_Intron|GCSAML_ENST00000527541.1_Intron|GCSAML_ENST00000527084.1_Intron|GCSAML_ENST00000366490.3_Intron|GCSAML_ENST00000463359.1_Intron|GCSAML_ENST00000531662.1_Intron	NM_198074.4	NP_932340	Q8N628	OR2C3_HUMAN	olfactory receptor, family 2, subfamily C, member 3	19						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S19S(1)|p.S18S(1)		breast(1)|endometrium(5)|large_intestine(2)|lung(31)|ovary(1)|prostate(1)|skin(2)	43	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0242)	OV - Ovarian serous cystadenocarcinoma(106;0.0241)			AGGGTCGTGTGGAGAAGCCCA	0.488																																					p.S19S		Atlas-SNP	.											OR2C3,NS,carcinoma,0,2	OR2C3	92	.	2	Substitution - coding silent(2)	prostate(2)	c.C57G						.						78	73	74					1																	247695757		2203	4300	6503	SO:0001819	synonymous_variant	81472	exon2			TCGTGTGGAGAAG	BC030717	CCDS1634.2	1q44	2014-02-19	2002-02-28		ENSG00000196242	ENSG00000196242		"GPCR / Class A : Olfactory receptors"	15005	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily C, member 4"	OR2C4, OR2C5P			Standard	NM_198074		Approved	OST742	uc009xgy.3	Q8N628	OTTHUMG00000040579	ENST00000366487.3:c.57C>G	chr1.hg19:g.247695757G>C		235.0	0.0		280.0	0.0	NM_198074	Q5JQS4|Q6IEZ1|Q8NGW7	Silent	SNP	ENST00000366487.3	hg19	CCDS1634.2																																																																																			.	G|0.996;A|0.004		0.488	OR2C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097626.2	NM_198074		C	247695757	G	C	247695757	2	2	282	1	0	0	0	0	0	0	0	1	11002	1335	47	4		4	OR2C3	1	247695757	Silent	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1846222	247695757	1554864	134	40368										
OR2T4	127074	hgsc.bcm.edu	37	chr1	248525054	248525054	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gacaatccaaacatccagcaCtactttgtgtggtcattttt	6	10	1	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:248525054C>T	ENST00000366475.1	+	1	172	c.172C>T	c.(172-174)Cta>Tta	p.L58L		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	58						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			ACATCCAGCACTACTTTGTGT	0.488																																					p.L58L		Atlas-SNP	.											OR2T4,NS,carcinoma,0,1	OR2T4	126	.	0			c.C172T						.						174	171	172					1																	248525054		2203	4300	6503	SO:0001819	synonymous_variant	127074	exon1			CCAGCACTACTTT	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"GPCR / Class A : Olfactory receptors"	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.172C>T	chr1.hg19:g.248525054C>T		437.0	0.0		535.0	0.0	NM_001004696	Q6IEZ8	Silent	SNP	ENST00000366475.1	hg19	CCDS31113.1																																																																																			.	.		0.488	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696		T	248525054	C	T	248525054	2	4	282	1	0	0	0	0	0	0	0	1	11036	564	20	3		3	OR2T4	1	248525054	Silent	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	829297	248525054	725567	135	40369										
OR2T35	403244	hgsc.bcm.edu	37	chr1	248801642	248801642	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctctgggaggaaccacatctCcctagtactttcctcagagc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:248801642delC	ENST00000317450.3	-	1	917	c.918delG	c.(916-918)gggfs	p.G306fs		NM_001001827.1	NP_001001827.1	Q8NGX2	O2T35_HUMAN	olfactory receptor, family 2, subfamily T, member 35	306						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|skin(1)	6	all_cancers(71;2.04e-05)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			AACCACATCTCCCTAGTACTT	0.537																																					p.R307fs		Atlas-INDEL	.											.	OR2T35	19	.	0			c.919delA						.						12	4	7					1																	248801642		1964	2979	4943	SO:0001589	frameshift_variant	403244	exon1			.	BK004475	CCDS31123.1	1q44	2012-08-09			ENSG00000177151	ENSG00000177151		"GPCR / Class A : Olfactory receptors"	31257	protein-coding gene	gene with protein product							Standard	NM_001001827		Approved		uc001ies.1	Q8NGX2	OTTHUMG00000040380	ENST00000317450.3:c.918delG	chr1.hg19:g.248801642delC	ENSP00000324369:p.Gly306fs	116.0	0.0		160.0	10.0	NM_001001827	Q6IEY7	Frame_Shift_Del	DEL	ENST00000317450.3	hg19	CCDS31123.1																																																																																			.	.		0.537	OR2T35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097130.1	NM_001001827		-	248801642	C	-	248801642	7	5	282	1	0	1	0	1	0	0	0	0	11035	842	30	0	57	0	OR2T35	1	248801642	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	276588	248801642	448979	136	40370										
PGBD2	267002	hgsc.bcm.edu	37	chr1	249211954	249211954	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	taaaagaccccaaagaactgAaaaaaatgaagaggggttca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:249211954delA	ENST00000329291.5	+	3	1318	c.1171delA	c.(1171-1173)aaafs	p.K392fs	PGBD2_ENST00000355360.4_Frame_Shift_Del_p.K141fs|PGBD2_ENST00000539153.1_Frame_Shift_Del_p.K389fs	NM_170725.2	NP_733843.1	Q6P3X8	PGBD2_HUMAN	piggyBac transposable element derived 2	392										NS(1)|endometrium(3)|lung(6)|ovary(1)|skin(3)	14	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.012)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			CAAAGAACTGAAAAAAATGAA	0.463																																					p.L390fs		Atlas-INDEL	.											.	PGBD2	103	.	0			c.1170delG						.						59	64	62					1																	249211954		2203	4300	6503	SO:0001589	frameshift_variant	267002	exon3			.	AF229602	CCDS31128.1, CCDS31129.1	1q	2008-02-05			ENSG00000185220	ENSG00000185220			19399	protein-coding gene	gene with protein product							Standard	XM_005270333		Approved		uc001ifh.3	Q6P3X8	OTTHUMG00000040424	ENST00000329291.5:c.1171delA	chr1.hg19:g.249211954delA	ENSP00000331643:p.Lys392fs	158.0	0.0		229.0	14.0	NM_170725	B3KVR8|Q6MZF8	Frame_Shift_Del	DEL	ENST00000329291.5	hg19	CCDS31128.1																																																																																			.	.		0.463	PGBD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000097318.1			-	249211954	A	-	249211954	7	5	282	1	0	1	0	1	0	0	0	0	11790	247	9	0	1177	0	PGBD2	1	249211954	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	410312	249211954	38667	137	40371										
ACP1	52	hgsc.bcm.edu	37	chr2	277054	277054	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acttgggagctatgatccacAaaaacaacttattattgaag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:277054delA	ENST00000272065.5	+	5	461	c.368delA	c.(367-369)caafs	p.Q123fs	ACP1_ENST00000484464.1_3'UTR|ACP1_ENST00000272067.6_Frame_Shift_Del_p.Q123fs	NM_004300.3	NP_004291.1	P24666	PPAC_HUMAN	acid phosphatase 1, soluble	123						cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|extracellular vesicular exosome (GO:0070062)	acid phosphatase activity (GO:0003993)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)			endometrium(1)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	12	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.00175)|Lung NSC(108;0.216)|all_epithelial(98;0.236)		all cancers(51;0.000391)|Epithelial(75;0.00281)|OV - Ovarian serous cystadenocarcinoma(76;0.00542)|GBM - Glioblastoma multiforme(21;0.127)	Adenine(DB00173)	TATGATCCACAAAAACAACTT	0.303																																					p.Q123fs		Atlas-INDEL	.											.	ACP1	42	.	0			c.367delC						.						70	72	72					2																	277054		2203	4300	6503	SO:0001589	frameshift_variant	52	exon5			.	M87546	CCDS1639.1, CCDS1640.1, CCDS46217.1	2p25	2011-06-09			ENSG00000143727	ENSG00000143727	3.1.3.2	"Protein tyrosine phosphatases / Class II Cys-based PTPs"	122	protein-coding gene	gene with protein product		171500					Standard	NM_001040649		Approved		uc002qwf.3	P24666	OTTHUMG00000086933	ENST00000272065.5:c.368delA	chr2.hg19:g.277054delA	ENSP00000272065:p.Gln123fs	279.0	0.0		171.0	11.0	NM_007099	A8K1L9|B5MCC7|P24667|Q16035|Q16036|Q16725|Q3KQX8|Q53RU0	Frame_Shift_Del	DEL	ENST00000272065.5	hg19	CCDS1639.1																																																																																			.	.		0.303	ACP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195862.3			-	277054	A	-	277054	7	5	282	1	0	1	0	1	0	0	0	0	162	130	5	0	541	0	ACP1	2	277054	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10		277054	242922319	138	40372										
TAF1B	9014	hgsc.bcm.edu	37	chr2	10045015	10045015	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctgactacgaggacatctacAaaaaaacagtagaagttgga	9	7	1	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:10045015A>T	ENST00000263663.5	+	9	1023	c.835A>T	c.(835-837)Aaa>Taa	p.K279*	TAF1B_ENST00000396242.3_Nonsense_Mutation_p.K24*	NM_005680.2	NP_005671	Q53T94	TAF1B_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa	279	C-terminal cyclin fold.				gene expression (GO:0010467)|RNA polymerase I transcriptional preinitiation complex assembly at the promoter for the nuclear large rRNA transcript (GO:0001189)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RNA polymerase I core factor complex (GO:0070860)	metal ion binding (GO:0046872)|RNA polymerase I CORE element sequence-specific DNA binding (GO:0001164)|RNA polymerase I CORE element sequence-specific DNA binding transcription factor recruiting transcription factor activity (GO:0001187)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TBP-class protein binding (GO:0017025)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	14	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					GGACATCTACAAAAAAACAGT	0.328																																					p.K279X		Atlas-SNP	.											TAF1B,NS,carcinoma,0,1	TAF1B	62	.	0			c.A835T						.						75	65	68					2																	10045015		2203	4300	6503	SO:0001587	stop_gained	9014	exon9			ATCTACAAAAAAA	L39061	CCDS33143.1	2p25	2008-06-02	2002-08-29		ENSG00000115750	ENSG00000115750			11533	protein-coding gene	gene with protein product		604904	"TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kD"			7801123	Standard	NM_005680		Approved	TAFI63, SL1, RAF1B, RAFI63	uc002qzz.3	Q53T94	OTTHUMG00000151673	ENST00000263663.5:c.835A>T	chr2.hg19:g.10045015A>T	ENSP00000263663:p.Lys279*	85.0	0.0		83.0	0.0	NM_005680	B4DI42|F8WD72|Q15574|Q8WVC3	Nonsense_Mutation	SNP	ENST00000263663.5	hg19	CCDS33143.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.648783	0.87958	.	.	ENSG00000115750	ENST00000263663;ENST00000396242	.	.	.	5.46	0.00658	0.14068	.	0.641420	0.17120	N	0.186264	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-14.238	2.8251	0.05483	0.6069:0.1237:0.1497:0.1198	.	.	.	.	X	279;24	.	.	K	+	1	0	TAF1B	9962466	0.964000	0.33143	0.630000	0.29268	0.414000	0.31173	0.565000	0.23578	0.355000	0.24131	0.383000	0.25322	AAA	.	.		0.328	TAF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323426.2	NM_005680		T	10045015	A	T	10045015	4	4	282	1	0	0	0	0	0	1	0	0	15535	131	5	4	869	4	TAF1B	2	10045015	Nonsense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	9767961	10045015	233154358	139	40373										
SMC6	79677	hgsc.bcm.edu	37	chr2	17888597	17888597	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagtaaaagcttctctacaaTttttgggtggcttttgggac							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:17888597delT	ENST00000448223.2	-	18	2164	c.1895delA	c.(1894-1896)aatfs	p.N632fs	SMC6_ENST00000381272.4_Frame_Shift_Del_p.N658fs|SMC6_ENST00000402989.1_Frame_Shift_Del_p.N632fs|SMC6_ENST00000351948.4_Frame_Shift_Del_p.N632fs	NM_001142286.1	NP_001135758.1	Q96SB8	SMC6_HUMAN	structural maintenance of chromosomes 6	632	Flexible hinge.				cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|intracellular (GO:0005622)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			NS(1)|biliary_tract(1)|breast(6)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TTCTCTACAATTTTTGGGTGG	0.338																																					p.N632fs		Atlas-INDEL	.											.	SMC6	102	.	0			c.1896delT						.						101	99	100					2																	17888597		2203	4300	6503	SO:0001589	frameshift_variant	79677	exon18			.	AJ310551	CCDS1690.1	2p24.3	2008-02-05	2006-07-06	2006-07-06	ENSG00000163029	ENSG00000163029		"Structural maintenance of chromosomes proteins"	20466	protein-coding gene	gene with protein product		609387	"SMC6 structural maintenance of chromosomes 6-like 1 (yeast)"	SMC6L1		11230166	Standard	NM_024624		Approved	FLJ22116	uc002rcn.3	Q96SB8	OTTHUMG00000090675	ENST00000448223.2:c.1895delA	chr2.hg19:g.17888597delT	ENSP00000404092:p.Asn632fs	234.0	0.0		179.0	16.0	NM_001142286	A8K8Q6|D6W518|Q05BV4|Q9H0X3|Q9H6M0	Frame_Shift_Del	DEL	ENST00000448223.2	hg19	CCDS1690.1																																																																																			.	.		0.338	SMC6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207359.1	NM_024624		-	17888597	T	-	17888597	7	5	282	1	0	1	0	1	0	0	0	0	14802	1493	52	0	1424	0	SMC6	2	17888597	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	7843582	17888597	225310776	140	40374										
APOB	338	hgsc.bcm.edu	37	chr2	21235238	21235238	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccctctgacaagacaggccaTatgtgcctttagcatagaac	8	12	1	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:21235238T>C	ENST00000233242.1	-	26	4629	c.4502A>G	c.(4501-4503)tAt>tGt	p.Y1501C		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	1501					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGACAGGCCATATGTGCCTTT	0.458																																					p.Y1501C		Atlas-SNP	.											.	APOB	761	.	0			c.A4502G						.						144	137	140					2																	21235238		2203	4300	6503	SO:0001583	missense	338	exon26			AGGCCATATGTGC	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.4502A>G	chr2.hg19:g.21235238T>C	ENSP00000233242:p.Tyr1501Cys	260.0	0.0		190.0	77.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	T	10.21	1.286329	0.23478	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.00840	5.63	5.88	3.47	0.39725	.	0.243265	0.29139	N	0.013031	T	0.02727	0.0082	L	0.56769	1.78	0.26805	N	0.969117	D	0.71674	0.998	P	0.60173	0.87	T	0.31724	-0.9933	10	0.72032	D	0.01	.	7.505	0.27540	0.1345:0.0681:0.0:0.7974	.	1501	P04114	APOB_HUMAN	C	1501	ENSP00000233242:Y1501C	ENSP00000233242:Y1501C	Y	-	2	0	APOB	21088743	0.677000	0.27577	0.007000	0.13788	0.036000	0.12997	1.291000	0.33330	0.458000	0.26988	0.533000	0.62120	TAT	.	.		0.458	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			C	21235238	T	C	21235238	3	2	282	1	0	0	0	0	1	0	0	0	785	1406	49	2	9205	2	APOB	2	21235238	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3346641	21235238	221964135	141	40375										
ATAD2B	54454	hgsc.bcm.edu	37	chr2	24008915	24008915	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acctcttcaatatccaccggTttgctgaagatgttaaagcg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:24008915delT	ENST00000238789.5	-	21	3298	c.2955delA	c.(2953-2955)aaafs	p.K985fs	ATAD2B_ENST00000474583.1_5'UTR	NM_001242338.1|NM_017552.2	NP_001229267.1|NP_060022.1	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B	985	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TATCCACCGGTTTGCTGAAGA	0.398																																					p.P986fs		Atlas-INDEL	.											.	ATAD2B	110	.	0			c.2956delC						.						71	66	68					2																	24008915		1878	4104	5982	SO:0001589	frameshift_variant	54454	exon21			.	AB033066	CCDS46227.1	2p24.1-p23.3	2010-04-21		2007-02-08	ENSG00000119778	ENSG00000119778		"ATPases / AAA-type"	29230	protein-coding gene	gene with protein product		615347					Standard	XM_005264372		Approved	KIAA1240	uc002rek.4	Q9ULI0	OTTHUMG00000151902	ENST00000238789.5:c.2955delA	chr2.hg19:g.24008915delT	ENSP00000238789:p.Lys985fs	204.0	0.0		182.0	11.0	NM_017552	B9ZVQ5|Q6ZNA6|Q8N9E7	Frame_Shift_Del	DEL	ENST00000238789.5	hg19	CCDS46227.1																																																																																			.	.		0.398	ATAD2B-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324333.1	NM_017552		-	24008915	T	-	24008915	7	5	282	1	0	1	0	1	0	0	0	0	1072	1722	60	0	1453	0	ATAD2B	2	24008915	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2773677	24008915	219190458	142	40376										
ATAD2B	54454	hgsc.bcm.edu	37	chr2	24042637	24042637	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	attgtaaaatgaaggtagggTttatgtatagcagcagatga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:24042637delT	ENST00000238789.5	-	17	2590	c.2247delA	c.(2245-2247)aaafs	p.K749fs	ATAD2B_ENST00000474583.1_5'UTR	NM_001242338.1|NM_017552.2	NP_001229267.1|NP_060022.1	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B	749						nucleus (GO:0005634)	ATP binding (GO:0005524)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GAAGGTAGGGTTTATGTATAG	0.294																																					p.P750fs		Atlas-Indel,Pindel	.											.	ATAD2B	110	.	0			c.2248delC						.						124	114	117					2																	24042637		1852	4095	5947	SO:0001589	frameshift_variant	54454	exon17			.	AB033066	CCDS46227.1	2p24.1-p23.3	2010-04-21		2007-02-08	ENSG00000119778	ENSG00000119778		"ATPases / AAA-type"	29230	protein-coding gene	gene with protein product		615347					Standard	XM_005264372		Approved	KIAA1240	uc002rek.4	Q9ULI0	OTTHUMG00000151902	ENST00000238789.5:c.2247delA	chr2.hg19:g.24042637delT	ENSP00000238789:p.Lys749fs	121.0	0.0		86.0	23.0	NM_017552	B9ZVQ5|Q6ZNA6|Q8N9E7	Frame_Shift_Del	DEL	ENST00000238789.5	hg19	CCDS46227.1																																																																																			.	.		0.294	ATAD2B-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324333.1	NM_017552		-	24042637	T	-	24042637	7	5	282	1	0	1	0	1	0	0	0	0	1072	1722	60	0	2177	0	ATAD2B	2	24042637	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	33722	24042637	219156736	143	40377										
PFN4	375189	hgsc.bcm.edu	37	chr2	24345390	24345390	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gagggtgtctaacaataagcTctgcaaatggctcatgttcc	10	9	3	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:24345390T>C	ENST00000313213.4	-	2	387	c.16A>G	c.(16-18)Agc>Ggc	p.S6G	FAM228B_ENST00000407625.1_5'Flank|PFN4_ENST00000465360.1_Intron|FAM228B_ENST00000420135.2_5'Flank|RP11-507M3.1_ENST00000584973.1_5'Flank	NM_199346.1	NP_955378.1	Q8NHR9	PROF4_HUMAN	profilin family, member 4	6					actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	lipid binding (GO:0008289)			breast(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AACAATAAGCTCTGCAAATGG	0.463																																					p.S6G		Atlas-SNP	.											.	PFN4	16	.	0			c.A16G						.						140	140	140					2																	24345390		2203	4300	6503	SO:0001583	missense	375189	exon2			ATAAGCTCTGCAA	BC029523	CCDS1709.1	2p24.1	2008-02-05			ENSG00000176732	ENSG00000176732			31103	protein-coding gene	gene with protein product							Standard	NM_199346		Approved		uc002rfa.1	Q8NHR9	OTTHUMG00000090816	ENST00000313213.4:c.16A>G	chr2.hg19:g.24345390T>C	ENSP00000322170:p.Ser6Gly	234.0	0.0		164.0	8.0	NM_199346	Q53TL9	Missense_Mutation	SNP	ENST00000313213.4	hg19	CCDS1709.1	.	.	.	.	.	.	.	.	.	.	T	10.82	1.459562	0.26248	.	.	ENSG00000176732	ENST00000313213;ENST00000436622	.	.	.	5.05	5.05	0.67936	.	0.551999	0.17529	N	0.170944	T	0.29321	0.0730	N	0.22421	0.69	0.21762	N	0.999558	B	0.13145	0.007	B	0.14578	0.011	T	0.12192	-1.0557	9	0.30078	T	0.28	-2.0685	11.5184	0.50536	0.0:0.0:0.0:1.0	.	6	Q8NHR9	PROF4_HUMAN	G	6	.	ENSP00000322170:S6G	S	-	1	0	PFN4	24198894	0.105000	0.21958	0.900000	0.35374	0.746000	0.42486	2.027000	0.41078	2.043000	0.60533	0.459000	0.35465	AGC	.	.		0.463	PFN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207617.2	NM_199346		C	24345390	T	C	24345390	3	2	282	1	0	0	0	0	1	0	0	0	11779	1551	54	2	389	2	PFN4	2	24345390	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	302753	24345390	218853983	144	40378										
DNMT3A	1788	hgsc.bcm.edu	37	chr2	25467083	25467083	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccgggagggccagtcctctcGccgccgcagcagcccgtagg	15	17	1	0	rs568207978		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:25467083G>T	ENST00000264709.3	-	15	2129	c.1792C>A	c.(1792-1794)Cga>Aga	p.R598R	DNMT3A_ENST00000402667.1_Silent_p.R375R|DNMT3A_ENST00000380746.4_Silent_p.R409R|DNMT3A_ENST00000321117.5_Silent_p.R598R|DNMT3A_ENST00000474887.1_5'UTR	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	598	ADD. {ECO:0000255|PROSITE- ProRule:PRU00865}.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)	p.R598*(2)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CAGTCCTCTCGCCGCCGCAGC	0.647			"Mis, F, N, S"		AML																																p.R598R		Atlas-SNP	.		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	DNMT3A,NS,haematopoietic_neoplasm,0,4	DNMT3A	1807	.	2	Substitution - Nonsense(2)	haematopoietic_and_lymphoid_tissue(2)	c.C1792A						.						29	34	33					2																	25467083		2203	4299	6502	SO:0001819	synonymous_variant	1788	exon15			CCTCTCGCCGCCG		CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.1792C>A	chr2.hg19:g.25467083G>T		217.0	1.0		189.0	0.0	NM_175629	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Silent	SNP	ENST00000264709.3	hg19	CCDS33157.1																																																																																			.	.		0.647	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	NM_022552		T	25467083	G	T	25467083	2	4	282	1	0	0	0	0	0	0	0	1	4678	1095	38	1		1	DNMT3A	2	25467083	Silent	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1121693	25467083	217732290	145	40379										
ASXL2	55252	hgsc.bcm.edu	37	chr2	26029194	26029194	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	attgcattcaggcatgcaagAggagaagtcccactgcaaaa	10	9	1	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:26029194A>G	ENST00000435504.4	-	4	449	c.156T>C	c.(154-156)ccT>ccC	p.P52P	ASXL2_ENST00000272341.4_5'UTR|ASXL2_ENST00000497092.1_5'UTR|ASXL2_ENST00000336112.4_Silent_p.P24P			Q76L83	ASXL2_HUMAN	additional sex combs like transcriptional regulator 2	52					adult heart development (GO:0007512)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of histone H3-K27 trimethylation (GO:1902466)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(7)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(3)	33	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGCATGCAAGAGGAGAAGTCC	0.373																																					p.P52P		Atlas-SNP	.											.	ASXL2	217	.	0			c.T156C						.						45	43	44					2																	26029194		1899	4122	6021	SO:0001819	synonymous_variant	55252	exon3			TGCAAGAGGAGAA			2p24.1	2014-06-17	2014-06-17		ENSG00000143970	ENSG00000143970			23805	protein-coding gene	gene with protein product		612991	"additional sex combs like 2 (Drosophila)"			12888926	Standard	NM_018263		Approved	ASXH2, FLJ10898, KIAA1685	uc002rgs.2	Q76L83	OTTHUMG00000152176	ENST00000435504.4:c.156T>C	chr2.hg19:g.26029194A>G		159.0	0.0		107.0	6.0	NM_018263	Q53TC9|Q5H9U4|Q76L81|Q86XM1|Q9C0H8|Q9NV67	Silent	SNP	ENST00000435504.4	hg19																																																																																				.	.		0.373	ASXL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000325593.3	NM_018263		G	26029194	A	G	26029194	2	3	282	1	0	0	0	0	0	0	0	1	1067	291	11	2		2	ASXL2	2	26029194	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	562111	26029194	217170179	146	40380										
RAB10	10890	hgsc.bcm.edu	37	chr2	26350743	26350743	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caagggagcatggtattaggTtttttgagactagtgcaaaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:26350743delT	ENST00000264710.4	+	5	941	c.442delT	c.(442-444)tttfs	p.F149fs	RAB10_ENST00000462003.1_3'UTR	NM_016131.4	NP_057215.3	P61026	RAB10_HUMAN	RAB10, member RAS oncogene family	149					antigen processing and presentation (GO:0019882)|axonogenesis (GO:0007409)|basolateral protein localization (GO:0061467)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum tubular network organization (GO:0071786)|endosomal transport (GO:0016197)|establishment of neuroblast polarity (GO:0045200)|establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|establishment of protein localization to membrane (GO:0090150)|Golgi to plasma membrane protein transport (GO:0043001)|Golgi to plasma membrane transport (GO:0006893)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|polarized epithelial cell differentiation (GO:0030859)|protein localization to plasma membrane (GO:0072659)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum tubular network (GO:0071782)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|insulin-responsive compartment (GO:0032593)|primary cilium (GO:0072372)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			lung(2)|ovary(1)	3	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGGTATTAGGTTTTTTGAGAC	0.348																																					p.R147fs		Atlas-INDEL	.											.	RAB10	14	.	0			c.441delG						.						168	161	163					2																	26350743		2203	4300	6503	SO:0001589	frameshift_variant	10890	exon5			.	AF106681	CCDS1720.1	2p23.3	2008-05-21			ENSG00000084733	ENSG00000084733		"RAB, member RAS oncogene"	9759	protein-coding gene	gene with protein product	"ras-related GTP-binding protein"	612672				7688123	Standard	NM_016131		Approved		uc002rgv.3	P61026	OTTHUMG00000094796	ENST00000264710.4:c.442delT	chr2.hg19:g.26350743delT	ENSP00000264710:p.Phe149fs	199.0	0.0		166.0	11.0	NM_016131	D6W538|O88386|Q6IA52|Q9D7X6|Q9H0T3	Frame_Shift_Del	DEL	ENST00000264710.4	hg19	CCDS1720.1																																																																																			.	.		0.348	RAB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211610.1	NM_016131		-	26350743	T	-	26350743	7	5	282	1	0	1	0	1	0	0	0	0	12905	1725	60	0	460	0	RAB10	2	26350743	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	321549	26350743	216848630	147	40381										
ZNF513	130557	hgsc.bcm.edu	37	chr2	27603076	27603076	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcaaatcactctccaataccAgggccccgggtccttcgtcg	9	16	2	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:27603076A>G	ENST00000323703.6	-	2	293	c.95T>C	c.(94-96)cTg>cCg	p.L32P	ZNF513_ENST00000491924.1_5'Flank|ZNF513_ENST00000407879.1_5'UTR	NM_144631.5	NP_653232.3	Q8N8E2	ZN513_HUMAN	zinc finger protein 513	32					regulation of transcription, DNA-templated (GO:0006355)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription regulatory region DNA binding (GO:0044212)			endometrium(5)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)	17	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTCCAATACCAGGGCCCCGGG	0.577																																					p.L32P		Atlas-SNP	.											.	ZNF513	45	.	0			c.T95C						.						85	92	90					2																	27603076		2203	4300	6503	SO:0001583	missense	130557	exon2			AATACCAGGGCCC	AL833946	CCDS1751.1, CCDS56114.1	2p23.3	2014-01-28			ENSG00000163795	ENSG00000163795		"Zinc fingers, C2H2-type"	26498	protein-coding gene	gene with protein product		613598				12477932	Standard	NM_001201459		Approved	FLJ32203, RP58	uc002rkk.3	Q8N8E2	OTTHUMG00000097783	ENST00000323703.6:c.95T>C	chr2.hg19:g.27603076A>G	ENSP00000318373:p.Leu32Pro	121.0	0.0		101.0	5.0	NM_144631	A8K3S5|B7WP71|Q3ZCU1|Q68CJ1|Q86UZ3|Q8NDL8|Q96ML3	Missense_Mutation	SNP	ENST00000323703.6	hg19	CCDS1751.1	.	.	.	.	.	.	.	.	.	.	A	19.79	3.893132	0.72524	.	.	ENSG00000163795	ENST00000323703	T	0.19669	2.13	3.84	3.84	0.44239	.	0.000000	0.34088	N	0.004275	T	0.30230	0.0758	L	0.29908	0.895	0.80722	D	1	D	0.71674	0.998	D	0.79784	0.993	T	0.03193	-1.1062	10	0.56958	D	0.05	-3.2129	9.2058	0.37289	1.0:0.0:0.0:0.0	.	32	Q8N8E2	ZN513_HUMAN	P	32	ENSP00000318373:L32P	ENSP00000318373:L32P	L	-	2	0	ZNF513	27456580	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.946000	0.75953	1.746000	0.51805	0.413000	0.27773	CTG	.	.		0.577	ZNF513-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215026.2	NM_144631		G	27603076	A	G	27603076	3	3	282	1	0	0	0	0	1	0	0	0	17973	188	7	2	1542	2	ZNF513	2	27603076	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1252333	27603076	215596297	148	40382										
IFT172	26160	hgsc.bcm.edu	37	chr2	27707958	27707958	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aattttagtggaatcaggagAaaaagccatgcccttcacca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:27707958delA	ENST00000260570.3	-	3	326	c.223delT	c.(223-225)tctfs	p.S75fs	IFT172_ENST00000416524.2_Frame_Shift_Del_p.S54fs|IFT172_ENST00000359466.6_Frame_Shift_Del_p.S75fs	NM_015662.1	NP_056477.1	Q9UG01	IF172_HUMAN	intraflagellar transport 172	75					bone development (GO:0060348)|brain development (GO:0007420)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|epidermis development (GO:0008544)|heart looping (GO:0001947)|hindgut development (GO:0061525)|left/right axis specification (GO:0070986)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)	axoneme (GO:0005930)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|sperm midpiece (GO:0097225)|sperm principal piece (GO:0097228)|vesicle (GO:0031982)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(17)|lung(17)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	43	Acute lymphoblastic leukemia(172;0.155)					GAATCAGGAGAAAAAGCCATG	0.373																																					p.S75fs		Atlas-INDEL	.											.	IFT172	119	.	0			c.224delC						.						157	157	157					2																	27707958		2203	4300	6503	SO:0001589	frameshift_variant	26160	exon3			.	AB033005	CCDS1755.1	2p23.3	2014-07-03	2014-07-03		ENSG00000138002	ENSG00000138002		"Intraflagellar transport homologs", "WD repeat domain containing"	30391	protein-coding gene	gene with protein product	"wimple homolog"	607386	"intraflagellar transport 172 homolog (Chlamydomonas)"			10788441, 10574461, 24140113	Standard	XM_005264254		Approved	SLB, wim, osm-1, NPHP17	uc002rku.3	Q9UG01	OTTHUMG00000128425	ENST00000260570.3:c.223delT	chr2.hg19:g.27707958delA	ENSP00000260570:p.Ser75fs	254.0	0.0		213.0	13.0	NM_015662	A5PKZ0|B2RNU5|Q86X44|Q96HW4|Q9UFJ9|Q9ULP1	Frame_Shift_Del	DEL	ENST00000260570.3	hg19	CCDS1755.1																																																																																			.	.		0.373	IFT172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250213.2	NM_015662		-	27707958	A	-	27707958	7	5	282	1	0	1	0	1	0	0	0	0	7566	246	9	0	5210	0	IFT172	2	27707958	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	104882	27707958	215491415	149	40383										
C2orf16	84226	hgsc.bcm.edu	37	chr2	27800546	27800546	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gagttgacttctaagtcaggAgtgcaggtagagaaaacttt	12	5	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:27800546A>G	ENST00000408964.2	+	1	1158	c.1107A>G	c.(1105-1107)ggA>ggG	p.G369G		NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	369						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					CTAAGTCAGGAGTGCAGGTAG	0.463																																					p.G369G		Atlas-SNP	.											.	C2orf16	357	.	0			c.A1107G						.						67	65	66					2																	27800546		1912	4123	6035	SO:0001819	synonymous_variant	84226	exon1			GTCAGGAGTGCAG	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"P-S-E-R-S-H-H-S repeats containing"						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.1107A>G	chr2.hg19:g.27800546A>G		82.0	0.0		75.0	4.0	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Silent	SNP	ENST00000408964.2	hg19	CCDS42666.1																																																																																			.	.		0.463	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266		G	27800546	A	G	27800546	2	3	282	1	0	0	0	0	0	0	0	1	2159	291	11	2		2	C2orf16	2	27800546	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	92588	27800546	215398827	150	40384										
PLB1	151056	hgsc.bcm.edu	37	chr2	28820879	28820879	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcactccctacagtgcaggaGgggacggctccctggagaat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:28820879delG	ENST00000327757.5	+	34	2373	c.2329delG	c.(2329-2331)gggfs	p.G777fs	PLB1_ENST00000422425.2_Frame_Shift_Del_p.G766fs	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	777	4 X 308-326 AA approximate repeats.				glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(31)|ovary(6)|prostate(1)|skin(7)|stomach(2)	69	Acute lymphoblastic leukemia(172;0.155)					CAGTGCAGGAGGGGACGGCTC	0.527																																					p.G776fs		Atlas-INDEL	.											.	PLB1	255	.	0			c.2328delA						.						118	100	106					2																	28820879		2203	4300	6503	SO:0001589	frameshift_variant	151056	exon34			.		CCDS33168.1, CCDS54340.1	2p23.3	2014-03-14			ENSG00000163803	ENSG00000163803	3.1.1.4, 3.1.1.5		30041	protein-coding gene	gene with protein product		610179				12150957	Standard	NM_153021		Approved	PLB, FLJ30866	uc002rmb.2	Q6P1J6	OTTHUMG00000152014	ENST00000327757.5:c.2329delG	chr2.hg19:g.28820879delG	ENSP00000330442:p.Gly777fs	225.0	0.0		177.0	11.0	NM_153021	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Frame_Shift_Del	DEL	ENST00000327757.5	hg19	CCDS33168.1																																																																																			.	.		0.527	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2			-	28820879	G	-	28820879	7	5	282	1	0	1	0	1	0	0	0	0	12033	1000	35	0	2496	0	PLB1	2	28820879	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1020333	28820879	214378494	151	40385										
CAPN13	92291	hgsc.bcm.edu	37	chr2	30987138	30987138	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caccagggcatcctcgaggaAgccatagtgcagatcggaat	12	11	0	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:30987138A>G	ENST00000295055.8	-	6	735	c.559T>C	c.(559-561)Ttc>Ctc	p.F187L	CAPN13_ENST00000465960.2_5'UTR|CAPN13_ENST00000534090.2_Missense_Mutation_p.F187L	NM_144575.2	NP_653176.2	Q6MZZ7	CAN13_HUMAN	calpain 13	187	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	30	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					TCCTCGAGGAAGCCATAGTGC	0.582																																					p.F187L		Atlas-SNP	.											.	CAPN13	70	.	0			c.T559C						.						53	55	54					2																	30987138		2092	4212	6304	SO:0001583	missense	92291	exon6			CGAGGAAGCCATA		CCDS46252.1	2p22-p21	2008-02-05			ENSG00000162949	ENSG00000162949			16663	protein-coding gene	gene with protein product		610228				11675017	Standard	NM_144575		Approved	FLJ23523	uc021vfm.1	Q6MZZ7	OTTHUMG00000152053	ENST00000295055.8:c.559T>C	chr2.hg19:g.30987138A>G	ENSP00000295055:p.Phe187Leu	168.0	0.0		96.0	5.0	NM_144575	Q17RF0|Q580X1|Q8TE80	Missense_Mutation	SNP	ENST00000295055.8	hg19	CCDS46252.1	.	.	.	.	.	.	.	.	.	.	A	11.72	1.722535	0.30503	.	.	ENSG00000162949	ENST00000295055;ENST00000534090	T;T	0.15256	2.44;2.44	5.22	-0.408	0.12381	Peptidase C2, calpain, catalytic domain (3);	0.812208	0.11609	N	0.546995	T	0.08980	0.0222	N	0.21583	0.68	0.19300	N	0.999976	B	0.31351	0.32	B	0.31390	0.129	T	0.38693	-0.9649	10	0.17369	T	0.5	.	5.478	0.16706	0.6284:0.0:0.2399:0.1317	.	187	Q6MZZ7	CAN13_HUMAN	L	187	ENSP00000295055:F187L;ENSP00000431298:F187L	ENSP00000295055:F187L	F	-	1	0	CAPN13	30840642	0.243000	0.23878	0.988000	0.46212	0.208000	0.24298	0.287000	0.18920	0.301000	0.22738	0.379000	0.24179	TTC	.	.		0.582	CAPN13-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325101.2	NM_144575		G	30987138	A	G	30987138	3	3	282	1	0	0	0	0	1	0	0	0	2628	72	3	2	1518	2	CAPN13	2	30987138	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2166259	30987138	212212235	152	40386										
XDH	7498	hgsc.bcm.edu	37	chr2	31588960	31588960	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtttgctggaacccccaacaTttttgcaacaaagctctgtg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:31588960delT	ENST00000379416.3	-	22	2386	c.2338delA	c.(2338-2340)atgfs	p.M780fs		NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	780					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|lactation (GO:0007595)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of gene expression (GO:0010629)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|negative regulation of vasculogenesis (GO:2001213)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)|xanthine catabolic process (GO:0009115)	cytosol (GO:0005829)|extracellular space (GO:0005615)|peroxisome (GO:0005777)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|protein homodimerization activity (GO:0042803)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)|xanthine oxidase activity (GO:0004855)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(31)|ovary(1)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(1)	74	Acute lymphoblastic leukemia(172;0.155)				Aldesleukin(DB00041)|Allopurinol(DB00437)|Azathioprine(DB00993)|Carboplatin(DB00958)|Carvedilol(DB01136)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|L-Carnitine(DB00583)|Menadione(DB00170)|Mercaptopurine(DB01033)|Nitrofural(DB00336)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Spermine(DB00127)|Trifluoperazine(DB00831)	ACCCCCAACATTTTTGCAACA	0.507																																					p.M780fs	Colon(66;682 1445 30109 40147)	Atlas-INDEL	.											.	XDH	191	.	0			c.2339delT						.						127	122	124					2																	31588960		2203	4300	6503	SO:0001589	frameshift_variant	7498	exon22			.	D11456	CCDS1775.1	2p23.1	2009-07-10	2003-03-20		ENSG00000158125	ENSG00000158125	1.17.1.4		12805	protein-coding gene	gene with protein product		607633	"xanthene dehydrogenase"			8224915	Standard	NM_000379		Approved	XOR, XO	uc002rnv.1	P47989	OTTHUMG00000099385	ENST00000379416.3:c.2338delA	chr2.hg19:g.31588960delT	ENSP00000368727:p.Met780fs	181.0	0.0		134.0	10.0	NM_000379	Q16681|Q16712|Q4PJ16	Frame_Shift_Del	DEL	ENST00000379416.3	hg19	CCDS1775.1																																																																																			.	.		0.507	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379		-	31588960	T	-	31588960	7	5	282	1	0	1	0	1	0	0	0	0	17441	1493	52	0	1723	0	XDH	2	31588960	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	601822	31588960	211610413	153	40387										
SPAST	6683	hgsc.bcm.edu	37	chr2	32340780	32340780	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tatcctttaagggtactccgAaaacaaataggacaaataaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:32340780delA	ENST00000315285.3	+	6	1005	c.880delA	c.(880-882)aaafs	p.K294fs	SPAST_ENST00000345662.1_Frame_Shift_Del_p.K262fs	NM_014946.3	NP_055761.2			spastin											breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(8)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					GGGTACTCCGAAAACAAATAG	0.323																																					p.P293fs		Atlas-INDEL	.											.	SPAST	61	.	0			c.879delG						.						62	68	66					2																	32340780		2202	4299	6501	SO:0001589	frameshift_variant	6683	exon6			.	AJ246001	CCDS1778.1, CCDS1779.1	2p24-p21	2014-09-17	2005-03-15	2005-03-17	ENSG00000021574	ENSG00000021574		"ATPases / AAA-type"	11233	protein-coding gene	gene with protein product		604277	"spastic paraplegia 4 (autosomal dominant; spastin)"	SPG4		10493830, 10610178	Standard	NM_014946		Approved	FSP2, ADPSP, KIAA1083	uc002roc.3	Q9UBP0	OTTHUMG00000128455	ENST00000315285.3:c.880delA	chr2.hg19:g.32340780delA	ENSP00000320885:p.Lys294fs	171.0	0.0		150.0	10.0	NM_014946		Frame_Shift_Del	DEL	ENST00000315285.3	hg19	CCDS1778.1																																																																																			.	.		0.323	SPAST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250253.1	NM_199436		-	32340780	A	-	32340780	7	5	282	1	0	1	0	1	0	0	0	0	15012	247	9	0	902	0	SPAST	2	32340780	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	751820	32340780	210858593	154	40388										
YIPF4	84272	hgsc.bcm.edu	37	chr2	32503243	32503243	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agatgcagcctccgggcccgCccccggcctatgcccccact							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:32503243delC	ENST00000238831.4	+	1	265	c.19delC	c.(19-21)cccfs	p.P8fs		NM_032312.3	NP_115688.1	Q9BSR8	YIPF4_HUMAN	Yip1 domain family, member 4	8						endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)				kidney(2)|lung(3)|prostate(3)|skin(1)	9	Acute lymphoblastic leukemia(172;0.155)					TCCGGGCCCGCCCCCGGCCTA	0.716																																					p.P6fs		Atlas-INDEL	.											.,1	YIPF4	23	.	0			c.18delG						.						7	8	8					2																	32503243		2162	4234	6396	SO:0001589	frameshift_variant	84272	exon1			.	AK098486	CCDS1781.1	2p22.3	2008-02-05			ENSG00000119820	ENSG00000119820		"Yip1 domain family"	28145	protein-coding gene	gene with protein product						12477932	Standard	NM_032312		Approved	MGC11061, FinGER4	uc002rok.3	Q9BSR8	OTTHUMG00000128452	ENST00000238831.4:c.19delC	chr2.hg19:g.32503243delC	ENSP00000238831:p.Pro8fs	184.0	0.0		124.0	10.0	NM_032312		Frame_Shift_Del	DEL	ENST00000238831.4	hg19	CCDS1781.1																																																																																			.	.		0.716	YIPF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250250.3	NM_032312		-	32503243	C	-	32503243	7	5	282	1	0	1	0	1	0	0	0	0	17495	739	26	0	21	0	YIPF4	2	32503243	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	162463	32503243	210696130	155	40389										
SLC3A1	6519	hgsc.bcm.edu	37	chr2	44513251	44513251	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	catcagtttatgaaagagcaAcctgatttaaatttccgcaa	6	8	1	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:44513251A>G	ENST00000260649.6	+	4	922	c.846A>G	c.(844-846)caA>caG	p.Q282Q	SLC3A1_ENST00000409380.1_Silent_p.Q4Q|SLC3A1_ENST00000409387.1_Silent_p.Q282Q|SLC3A1_ENST00000409741.1_Silent_p.Q282Q|SLC3A1_ENST00000410056.3_Silent_p.Q282Q|SLC3A1_ENST00000409229.3_Silent_p.Q282Q	NM_000341.3	NP_000332.2	Q07837	SLC31_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 1	282					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|basic amino acid transport (GO:0015802)|carbohydrate metabolic process (GO:0005975)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)|vacuolar membrane (GO:0005774)	amino acid transmembrane transporter activity (GO:0015171)|basic amino acid transmembrane transporter activity (GO:0015174)|catalytic activity (GO:0003824)|cation binding (GO:0043169)|L-cystine transmembrane transporter activity (GO:0015184)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(3)	26		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)			L-Cystine(DB00138)	TGAAAGAGCAACCTGATTTAA	0.358																																					p.Q282Q		Atlas-SNP	.											.	SLC3A1	62	.	0			c.A846G						.						128	127	127					2																	44513251		2203	4300	6503	SO:0001819	synonymous_variant	6519	exon4			AGAGCAACCTGAT		CCDS1819.1	2p16.3	2013-07-19	2013-07-19		ENSG00000138079	ENSG00000138079		"Solute carriers"	11025	protein-coding gene	gene with protein product		104614	"solute carrier family 3 (cystine, dibasic and neutral amino acid transporters, activator of cystine, dibasic and neutral amino acid transport), member 1"			8486766, 9186880	Standard	NM_000341		Approved	CSNU1, D2H, RBAT, ATR1, NBAT	uc002ruc.4	Q07837	OTTHUMG00000128759	ENST00000260649.6:c.846A>G	chr2.hg19:g.44513251A>G		128.0	0.0		99.0	4.0	NM_000341	A8K0S1|O00658|Q15295|Q4J6B4|Q4J6B5|Q4J6B6|Q4J6B7|Q4J6B8|Q4J6B9|Q52M92|Q52M94	Silent	SNP	ENST00000260649.6	hg19	CCDS1819.1																																																																																			.	.		0.358	SLC3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250676.1	NM_000341		G	44513251	A	G	44513251	2	3	282	1	0	0	0	0	0	0	0	1	14641	40	2	2		2	SLC3A1	2	44513251	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	12010008	44513251	198686122	156	40390										
MSH2	4436	hgsc.bcm.edu	37	chr2	47630437	47630437	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gccgaccaccacagtgcgccTtttcgaccggggcgacttct					rs63751056		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:47630437delT	ENST00000233146.2	+	1	330	c.107delT	c.(106-108)cttfs	p.L36fs	MSH2_ENST00000406134.1_Frame_Shift_Del_p.L36fs|MSH2_ENST00000543555.1_Intron	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2	36					ATP catabolic process (GO:0006200)|B cell differentiation (GO:0030183)|B cell mediated immunity (GO:0019724)|cell cycle arrest (GO:0007050)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|intra-S DNA damage checkpoint (GO:0031573)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|isotype switching (GO:0045190)|maintenance of DNA repeat elements (GO:0043570)|male gonad development (GO:0008584)|meiotic gene conversion (GO:0006311)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reciprocal meiotic recombination (GO:0045128)|oxidative phosphorylation (GO:0006119)|positive regulation of helicase activity (GO:0051096)|postreplication repair (GO:0006301)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSalpha complex (GO:0032301)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|guanine/thymine mispair binding (GO:0032137)|heteroduplex DNA loop binding (GO:0000404)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|Y-form DNA binding (GO:0000403)	p.0?(2)|p.?(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(5)|large_intestine(50)|lung(18)|ovary(5)|prostate(2)|skin(3)|small_intestine(1)|stomach(2)|urinary_tract(1)	112		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			ACAGTGCGCCTTTTCGACCGG	0.667			"D, Mis, N, F, S"		"colorectal, endometrial, ovarian"	"colorectal, endometrial, ovarian"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.L36fs		Atlas-INDEL	.	yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p22-p21	4436	mutS homolog 2 (E. coli)		E	.	MSH2	198	.	3	Whole gene deletion(2)|Unknown(1)	haematopoietic_and_lymphoid_tissue(3)	c.106delC						.						14	15	15					2																	47630437		2196	4294	6490	SO:0001589	frameshift_variant	4436	exon1	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	.	U03911	CCDS1834.1, CCDS58709.1	2p21	2014-09-17	2013-09-12		ENSG00000095002	ENSG00000095002			7325	protein-coding gene	gene with protein product		609309	"mutS (E. coli) homolog 2 (colon cancer, nonpolyposis type 1)", "mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)"	COCA1		8484120, 9843200	Standard	NM_000251		Approved	HNPCC, HNPCC1	uc002rvy.2	P43246	OTTHUMG00000128861	ENST00000233146.2:c.107delT	chr2.hg19:g.47630437delT	ENSP00000233146:p.Leu36fs	239.0	0.0		206.0	13.0	NM_000251	B4E2Z2|O75488	Frame_Shift_Del	DEL	ENST00000233146.2	hg19	CCDS1834.1																																																																																			.	.		0.667	MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3			-	47630437	T	-	47630437	7	5	282	1	0	1	0	1	0	0	0	0	9879	1609	56	0	109	0	MSH2	2	47630437	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3117186	47630437	195568936	157	40391										
FBXO11	80204	hgsc.bcm.edu	37	chr2	48066828	48066828	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgttcttttcggcaaaagagTttttctacgaagttggtatg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:48066828delT	ENST00000403359.3	-	2	385	c.313delA	c.(313-315)actfs	p.T105fs	FBXO11_ENST00000480038.1_5'UTR|FBXO11_ENST00000316377.4_Frame_Shift_Del_p.T21fs|FBXO11_ENST00000378314.3_5'UTR|FBXO11_ENST00000402508.1_Frame_Shift_Del_p.T21fs	NM_001190274.1	NP_001177203.1	Q86XK2	FBX11_HUMAN	F-box protein 11	105					cellular protein modification process (GO:0006464)|peptidyl-arginine N-methylation (GO:0035246)|protein ubiquitination (GO:0016567)|sensory perception of sound (GO:0007605)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	protein-arginine N-methyltransferase activity (GO:0016274)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.0?(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	26		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GGCAAAAGAGTTTTTCTACGA	0.368			"Mis, F, D"		DLBCL																																p.T105fs		Atlas-INDEL	.		Rec	yes		2	2p16.3	80204	F-box protein 11		L	.	FBXO11	127	.	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.314delC						.						133	124	127					2																	48066828		2203	4300	6503	SO:0001589	frameshift_variant	80204	exon2			.	AF174599	CCDS1837.1, CCDS54357.1	2p16.3	2014-01-29	2008-06-23	2008-06-23	ENSG00000138081	ENSG00000138081		"Ubiquitin protein ligase E3 component n-recognins", "F-boxes /  "other""	13590	protein-coding gene	gene with protein product	"ubiquitin protein ligase E3 component n-recognin 6"	607871	"F-box only protein 11"			10531035, 16487488, 18162545	Standard	NM_025133		Approved	FBX11, UBR6	uc002rwe.3	Q86XK2	OTTHUMG00000129130	ENST00000403359.3:c.313delA	chr2.hg19:g.48066828delT	ENSP00000384823:p.Thr105fs	185.0	0.0		128.0	10.0	NM_001190274	A1L491|Q52ZP1|Q53EP7|Q53RT5|Q8IXG3|Q96E90|Q9H6V8|Q9H9L1|Q9NR14|Q9UFK1|Q9UHI1|Q9UKC2	Frame_Shift_Del	DEL	ENST00000403359.3	hg19	CCDS54357.1																																																																																			.	.		0.368	FBXO11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251181.3	NM_012167, NM_018693, NM_025133		-	48066828	T	-	48066828	7	5	282	1	0	1	0	1	0	0	0	0	5735	1725	60	0	2648	0	FBXO11	2	48066828	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	436391	48066828	195132545	158	40392										
FBXO11	80204	hgsc.bcm.edu	37	chr2	48066902	48066902	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caaccatatctgcaggcacaTcatcatctgttataaacaaa	4	11	4	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:48066902T>C	ENST00000403359.3	-	2	311	c.239A>G	c.(238-240)gAt>gGt	p.D80G	FBXO11_ENST00000480038.1_5'UTR|FBXO11_ENST00000316377.4_5'UTR|FBXO11_ENST00000378314.3_5'UTR|FBXO11_ENST00000402508.1_5'UTR	NM_001190274.1	NP_001177203.1	Q86XK2	FBX11_HUMAN	F-box protein 11	80					cellular protein modification process (GO:0006464)|peptidyl-arginine N-methylation (GO:0035246)|protein ubiquitination (GO:0016567)|sensory perception of sound (GO:0007605)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	protein-arginine N-methyltransferase activity (GO:0016274)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.0?(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	26		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TGCAGGCACATCATCATCTGT	0.353			"Mis, F, D"		DLBCL																																p.D80G		Atlas-SNP	.		Rec	yes		2	2p16.3	80204	F-box protein 11		L	.	FBXO11	127	.	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.A239G						.						94	87	90					2																	48066902		2203	4300	6503	SO:0001583	missense	80204	exon2			GGCACATCATCAT	AF174599	CCDS1837.1, CCDS54357.1	2p16.3	2014-01-29	2008-06-23	2008-06-23	ENSG00000138081	ENSG00000138081		"Ubiquitin protein ligase E3 component n-recognins", "F-boxes /  "other""	13590	protein-coding gene	gene with protein product	"ubiquitin protein ligase E3 component n-recognin 6"	607871	"F-box only protein 11"			10531035, 16487488, 18162545	Standard	NM_025133		Approved	FBX11, UBR6	uc002rwe.3	Q86XK2	OTTHUMG00000129130	ENST00000403359.3:c.239A>G	chr2.hg19:g.48066902T>C	ENSP00000384823:p.Asp80Gly	123.0	0.0		79.0	4.0	NM_001190274	A1L491|Q52ZP1|Q53EP7|Q53RT5|Q8IXG3|Q96E90|Q9H6V8|Q9H9L1|Q9NR14|Q9UFK1|Q9UHI1|Q9UKC2	Missense_Mutation	SNP	ENST00000403359.3	hg19	CCDS54357.1	.	.	.	.	.	.	.	.	.	.	T	12.89	2.072929	0.36566	.	.	ENSG00000138081	ENST00000403359	T	0.49139	0.79	5.34	4.15	0.48705	.	.	.	.	.	T	0.29423	0.0733	N	0.08118	0	0.80722	D	1	.	.	.	.	.	.	T	0.06954	-1.0798	7	0.20519	T	0.43	-24.1546	10.2135	0.43156	0.1528:0.0:0.0:0.8472	.	.	.	.	G	80	ENSP00000384823:D80G	ENSP00000384823:D80G	D	-	2	0	FBXO11	47920406	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.012000	0.76366	0.925000	0.37094	0.455000	0.32223	GAT	.	.		0.353	FBXO11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251181.3	NM_012167, NM_018693, NM_025133		C	48066902	T	C	48066902	3	2	282	1	0	0	0	0	1	0	0	0	5735	1435	50	2	2722	2	FBXO11	2	48066902	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	74	48066902	195132471	159	40393										
PSME4	23198	hgsc.bcm.edu	37	chr2	54197809	54197809	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctagccgctccgcgtagggcAgcagcttgttgtagacgatc	13	12	0	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:54197809A>G	ENST00000404125.1	-	1	168	c.113T>C	c.(112-114)cTg>cCg	p.L38P	ACYP2_ENST00000607452.1_5'Flank|ACYP2_ENST00000422521.2_5'Flank|ACYP2_ENST00000606082.1_5'Flank	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	38					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|spermatoproteasome complex (GO:1990111)	lysine-acetylated histone binding (GO:0070577)|peptidase activator activity (GO:0016504)			breast(5)|endometrium(8)|kidney(1)|large_intestine(11)|lung(26)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(2)	60			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			CGCGTAGGGCAGCAGCTTGTT	0.716																																					p.L38P		Atlas-SNP	.											.	PSME4	247	.	0			c.T113C						.						9	11	11					2																	54197809		690	1586	2276	SO:0001583	missense	23198	exon1			TAGGGCAGCAGCT	D38521	CCDS33197.2	2p16.1	2003-04-14			ENSG00000068878	ENSG00000068878		"Proteasome (prosome, macropain) subunits"	20635	protein-coding gene	gene with protein product		607705				7584044, 12093752	Standard	NM_014614		Approved	PA200, KIAA0077	uc002rxp.2	Q14997	OTTHUMG00000151852	ENST00000404125.1:c.113T>C	chr2.hg19:g.54197809A>G	ENSP00000384211:p.Leu38Pro	126.0	0.0		94.0	6.0	NM_014614	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Missense_Mutation	SNP	ENST00000404125.1	hg19	CCDS33197.2	.	.	.	.	.	.	.	.	.	.	a	26.7	4.762560	0.89932	.	.	ENSG00000068878	ENST00000404125	T	0.61742	0.08	3.55	3.55	0.40652	.	.	.	.	.	T	0.75598	0.3871	M	0.84219	2.685	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.79586	-0.1742	9	0.87932	D	0	.	11.9294	0.52837	1.0:0.0:0.0:0.0	.	38	Q14997	PSME4_HUMAN	P	38	ENSP00000384211:L38P	ENSP00000374643:L38P	L	-	2	0	PSME4	54051313	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.361000	0.90098	1.469000	0.48083	0.451000	0.29950	CTG	.	.		0.716	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158		G	54197809	A	G	54197809	3	3	282	1	0	0	0	0	1	0	0	0	12721	188	7	2	5602	2	PSME4	2	54197809	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	6130907	54197809	189001564	160	40394										
TSPYL6	388951	hgsc.bcm.edu	37	chr2	54482889	54482889	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttcagactccgacctccctgCcccacaggtttctagagcct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:54482889delC	ENST00000317802.7	-	1	520	c.400delG	c.(400-402)gcafs	p.A134fs	ACYP2_ENST00000394666.3_Intron|ACYP2_ENST00000607452.1_Intron|ACYP2_ENST00000303536.4_Intron|ACYP2_ENST00000606865.1_Intron	NM_001003937.2	NP_001003937.2	Q8N831	TSYL6_HUMAN	TSPY-like 6	134					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(1)|ovary(1)|skin(1)|stomach(2)	20						GACCTCCCTGCCCCACAGGTT	0.602																																					p.A134fs		Atlas-INDEL	.											.	TSPYL6	54	.	0			c.401delC						.						61	65	64					2																	54482889		2093	4231	6324	SO:0001589	frameshift_variant	388951	exon1			.	AK097417	CCDS42682.1	2p16.3	2007-10-22			ENSG00000178021	ENSG00000178021			14521	protein-coding gene	gene with protein product							Standard	NM_001003937		Approved		uc002rxr.2	Q8N831	OTTHUMG00000151823	ENST00000317802.7:c.400delG	chr2.hg19:g.54482889delC	ENSP00000417919:p.Ala134fs	116.0	0.0		104.0	10.0	NM_001003937	Q6NUJ3	Frame_Shift_Del	DEL	ENST00000317802.7	hg19	CCDS42682.1																																																																																			.	.		0.602	TSPYL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324069.3	XM_371494		-	54482889	C	-	54482889	7	5	282	1	0	1	0	1	0	0	0	0	16678	739	26	0	836	0	TSPYL6	2	54482889	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	285080	54482889	188716484	161	40395										
SPTBN1	6711	hgsc.bcm.edu	37	chr2	54858486	54858486	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaccgaggctgagaagctgcTcacgcagcacgagaacatca	12	12	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:54858486T>C	ENST00000356805.4	+	16	3583	c.3302T>C	c.(3301-3303)cTc>cCc	p.L1101P	SPTBN1_ENST00000333896.5_Missense_Mutation_p.L1088P	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	1101					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			GAGAAGCTGCTCACGCAGCAC	0.582																																					p.L1101P		Atlas-SNP	.											.	SPTBN1	378	.	0			c.T3302C						.						146	121	130					2																	54858486		2203	4300	6503	SO:0001583	missense	6711	exon16			AGCTGCTCACGCA		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"Pleckstrin homology (PH) domain containing"	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.3302T>C	chr2.hg19:g.54858486T>C	ENSP00000349259:p.Leu1101Pro	205.0	0.0		138.0	6.0	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Missense_Mutation	SNP	ENST00000356805.4	hg19	CCDS33198.1	.	.	.	.	.	.	.	.	.	.	T	16.82	3.227677	0.58668	.	.	ENSG00000115306	ENST00000356805;ENST00000333896	T;T	0.50277	0.75;0.75	5.56	5.56	0.83823	.	0.134965	0.52532	D	0.000079	T	0.70570	0.3239	M	0.80616	2.505	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.81914	0.985;0.995	T	0.75473	-0.3305	10	0.87932	D	0	.	15.727	0.77770	0.0:0.0:0.0:1.0	.	1088;1101	Q01082-3;Q01082	.;SPTB2_HUMAN	P	1101;1088	ENSP00000349259:L1101P;ENSP00000334156:L1088P	ENSP00000334156:L1088P	L	+	2	0	SPTBN1	54711990	1.000000	0.71417	0.996000	0.52242	0.225000	0.24961	7.991000	0.88244	2.118000	0.64928	0.533000	0.62120	CTC	.	.		0.582	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			C	54858486	T	C	54858486	3	2	282	1	0	0	0	0	1	0	0	0	15134	1551	54	2	3473	2	SPTBN1	2	54858486	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	375597	54858486	188340887	162	40396										
RPS27A	6233	hgsc.bcm.edu	37	chr2	55461316	55461316	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagctggaagatggacgtacTttgtctgactacaatattca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:55461316delT	ENST00000272317.6	+	4	489	c.165delT	c.(163-165)actfs	p.T55fs	CLHC1_ENST00000406076.1_5'Flank|CLHC1_ENST00000401408.1_5'Flank|RPS27A_ENST00000402285.3_Frame_Shift_Del_p.T55fs|RPS27A_ENST00000404735.1_Frame_Shift_Del_p.T55fs|CLHC1_ENST00000407122.1_5'Flank|CLHC1_ENST00000494539.1_5'Flank|CLHC1_ENST00000406437.2_5'Flank	NM_002954.5	NP_002945.1	P62979	RS27A_HUMAN	ribosomal protein S27a	55	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				activation of MAPK activity (GO:0000187)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|viral transcription (GO:0019083)|virion assembly (GO:0019068)	cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|small ribosomal subunit (GO:0015935)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			cervix(1)|ovary(1)|urinary_tract(1)	3						ATGGACGTACTTTGTCTGACT	0.353																																					p.T55fs		Atlas-INDEL	.											.	RPS27A	12	.	0			c.164delC						.						84	87	86					2																	55461316		2203	4300	6503	SO:0001589	frameshift_variant	6233	exon4			.	AB007163	CCDS33202.1	2p16	2011-04-06			ENSG00000143947	ENSG00000143947		"S ribosomal proteins"	10417	protein-coding gene	gene with protein product	"ubiquitin carboxyl extension protein 80"	191343				9582194	Standard	NM_001135592		Approved	UBCEP80, Uba80, S27A	uc010yow.2	P62979	OTTHUMG00000151919	ENST00000272317.6:c.165delT	chr2.hg19:g.55461316delT	ENSP00000272317:p.Thr55fs	329.0	0.0		249.0	16.0	NM_001135592	P02248|P02249|P02250|P14798|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BQ77|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Frame_Shift_Del	DEL	ENST00000272317.6	hg19	CCDS33202.1																																																																																			.	.		0.353	RPS27A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324423.15			-	55461316	T	-	55461316	7	5	282	1	0	1	0	1	0	0	0	0	13654	1596	56	0	175	0	RPS27A	2	55461316	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	602830	55461316	187738057	163	40397										
MTIF2	4528	hgsc.bcm.edu	37	chr2	55473549	55473549	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atctgctttcaattctaacaTttctgcaagagcaactgttg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:55473549delT	ENST00000263629.4	-	10	1345	c.1030delA	c.(1030-1032)atgfs	p.M344fs	MTIF2_ENST00000394600.3_Frame_Shift_Del_p.M344fs|MTIF2_ENST00000403721.1_Frame_Shift_Del_p.M344fs	NM_002453.2	NP_002444.2	P46199	IF2M_HUMAN	mitochondrial translational initiation factor 2	344	tr-type G.				formation of translation initiation complex (GO:0001732)|regulation of translational initiation (GO:0006446)|ribosome disassembly (GO:0032790)	mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	24						AATTCTAACATTTCTGCAAGA	0.373																																					p.M344fs		Atlas-INDEL	.											.	MTIF2	64	.	0			c.1031delT						.						167	152	157					2																	55473549		2203	4300	6503	SO:0001589	frameshift_variant	4528	exon10			.	L34600	CCDS1853.1	2p16.1	2008-02-05			ENSG00000085760	ENSG00000085760			7441	protein-coding gene	gene with protein product		603766				9925935, 7829522	Standard	XM_005264335		Approved	IF-2mt	uc002ryo.3	P46199	OTTHUMG00000129338	ENST00000263629.4:c.1030delA	chr2.hg19:g.55473549delT	ENSP00000263629:p.Met344fs	252.0	0.0		143.0	11.0	NM_002453	D6W5D0	Frame_Shift_Del	DEL	ENST00000263629.4	hg19	CCDS1853.1																																																																																			.	.		0.373	MTIF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251486.4	NM_002453		-	55473549	T	-	55473549	7	5	282	1	0	1	0	1	0	0	0	0	9943	1493	52	0	1181	0	MTIF2	2	55473549	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	12233	55473549	187725824	164	40398										
CCDC88A	55704	hgsc.bcm.edu	37	chr2	55536323	55536323	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aggaggagatgggtcataaaAtttgtattgatccataattt	10	3	1	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:55536323A>C	ENST00000436346.1	-	24	4988	c.4147T>G	c.(4147-4149)Ttt>Gtt	p.F1383V	CCDC88A_ENST00000413716.2_Missense_Mutation_p.F1382V|AC012358.8_ENST00000366287.4_RNA|CCDC88A_ENST00000263630.8_Missense_Mutation_p.F1383V|CCDC88A_ENST00000336838.6_Missense_Mutation_p.F1382V|CCDC88A_ENST00000422883.2_Missense_Mutation_p.F6V	NM_001135597.1|NM_001254943.1	NP_001129069.1|NP_001241872.1	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A	1383					activation of protein kinase B activity (GO:0032148)|cell migration (GO:0016477)|DNA replication (GO:0006260)|lamellipodium assembly (GO:0030032)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell proliferation (GO:0042127)|regulation of DNA replication (GO:0006275)|regulation of neuron projection development (GO:0010975)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|microtubule binding (GO:0008017)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)|protein kinase B binding (GO:0043422)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(22)|lung(23)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	69						GGGTCATAAAATTTGTATTGA	0.289																																					p.F1383V		Atlas-SNP	.											.	CCDC88A	336	.	0			c.T4147G						.						46	47	47					2																	55536323		2197	4283	6480	SO:0001583	missense	55704	exon24			CATAAAATTTGTA	AB033038, AF112218	CCDS33203.1, CCDS46288.1, CCDS58710.1	2p16.3	2013-03-13	2007-05-31	2007-05-31	ENSG00000115355	ENSG00000115355			25523	protein-coding gene	gene with protein product	"Galpha-interacting vesicle-associated protein", "Akt-phosphorylation enhancer", "girdin", "girders of actin filaments"	609736	"KIAA1212"	KIAA1212		15749703, 15753085	Standard	NM_001135597		Approved	FLJ10392, APE, GIV, HkRP1, GRDN	uc002ryv.2	Q3V6T2	OTTHUMG00000151915	ENST00000436346.1:c.4147T>G	chr2.hg19:g.55536323A>C	ENSP00000410608:p.Phe1383Val	187.0	0.0		195.0	83.0	NM_018084	A1IGE7|B7ZM78|C9JG83|Q53SF1|Q581G3|Q5HYD0|Q7Z339|Q7Z3C5	Missense_Mutation	SNP	ENST00000436346.1	hg19		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	A|A|A	24.0|24.0|24.0	4.481486|4.481486|4.481486	0.84747|0.84747|0.84747	.|.|.	.|.|.	ENSG00000115355|ENSG00000115355|ENSG00000115355	ENST00000336838;ENST00000263630;ENST00000436346;ENST00000422883;ENST00000412148;ENST00000413716;ENST00000426576|ENST00000456975|ENST00000444458	T;T;T;T;T;T|.|.	0.58210|.|.	0.35;0.35;0.35;0.35;0.35;0.35|.|.	5.84|5.84|5.84	5.84|5.84|5.84	0.93424|0.93424|0.93424	.|.|.	0.000000|.|.	0.49916|.|.	U|.|.	0.000140|.|.	T|T|T	0.76248|0.76248|0.76248	0.3961|0.3961|0.3961	M|M|M	0.76838|0.76838|0.76838	2.35|2.35|2.35	0.37274|0.37274|0.37274	D|D|D	0.907559|0.907559|0.907559	D;D;D;D;P;D;D|.|.	0.89917|.|.	0.987;0.997;0.992;1.0;0.931;0.992;0.99|.|.	P;D;P;D;P;D;P|.|.	0.85130|.|.	0.893;0.99;0.844;0.997;0.782;0.925;0.897|.|.	T|T|T	0.80329|0.80329|0.80329	-0.1428|-0.1428|-0.1428	10|5|5	0.31617|.|.	T|.|.	0.26|.|.	-17.7153|-17.7153|-17.7153	16.2055|16.2055|16.2055	0.82126|0.82126|0.82126	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.|.	1382;1383;1328;6;1383;1382;1382|.|.	B7ZM78;Q3V6T2-2;D6W5D1;B3KW94;Q3V6T2;Q3V6T2-3;Q3V6T2-4|.|.	.;.;.;.;GRDN_HUMAN;.;.|.|.	V|S|K	1382;1383;1383;6;428;1382;558|363|7	ENSP00000338728:F1382V;ENSP00000263630:F1383V;ENSP00000410608:F1383V;ENSP00000390012:F428V;ENSP00000404431:F1382V;ENSP00000405080:F558V|.|.	ENSP00000263630:F1383V|.|.	F|I|N	-|-|-	1|2|3	0|0|2	CCDC88A|CCDC88A|CCDC88A	55389827|55389827|55389827	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.991000|0.991000|0.991000	0.79684|0.79684|0.79684	9.210000|9.210000|9.210000	0.95106|0.95106|0.95106	2.226000|2.226000|2.226000	0.72624|0.72624|0.72624	0.482000|0.482000|0.482000	0.46254|0.46254|0.46254	TTT|ATT|AAT	.	.		0.289	CCDC88A-203	KNOWN	basic	protein_coding	protein_coding		NM_017571		C	55536323	A	C	55536323	3	2	282	1	0	0	0	0	1	0	0	0	2865	101	4	5	1504	5	CCDC88A	2	55536323	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	62774	55536323	187663050	165	40399										
PNPT1	87178	hgsc.bcm.edu	37	chr2	55887311	55887311	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cctcgtagtgcagcatgaaaTttttatcttttatcccacta							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:55887311delT	ENST00000447944.2	-	15	1351	c.1265delA	c.(1264-1266)aatfs	p.N422fs		NM_033109.3	NP_149100.2	Q8TCS8	PNPT1_HUMAN	polyribonucleotide nucleotidyltransferase 1	422					cellular response to interferon-beta (GO:0035458)|cellular response to oxidative stress (GO:0034599)|mitochondrial mRNA catabolic process (GO:0000958)|mitochondrial mRNA polyadenylation (GO:0097222)|mitochondrial RNA 3'-end processing (GO:0000965)|mitochondrial RNA 5'-end processing (GO:0000964)|mitochondrial RNA catabolic process (GO:0000957)|mitochondrion morphogenesis (GO:0070584)|mitotic cell cycle arrest (GO:0071850)|mRNA catabolic process (GO:0006402)|negative regulation of growth (GO:0045926)|nuclear polyadenylation-dependent mRNA catabolic process (GO:0071042)|positive regulation of miRNA catabolic process (GO:2000627)|positive regulation of mitochondrial RNA catabolic process (GO:0000962)|positive regulation of mRNA catabolic process (GO:0061014)|protein homooligomerization (GO:0051260)|protein homotrimerization (GO:0070207)|regulation of cellular respiration (GO:0043457)|regulation of cellular senescence (GO:2000772)|RNA catabolic process (GO:0006401)|RNA import into mitochondrion (GO:0035927)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|RNA polyadenylation (GO:0043631)|rRNA import into mitochondrion (GO:0035928)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrial degradosome (GO:0045025)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)	3'-5'-exoribonuclease activity (GO:0000175)|miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|polyribonucleotide nucleotidyltransferase activity (GO:0004654)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(9)|skin(2)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			CAGCATGAAATTTTTATCTTT	0.284																																					p.N422fs		Atlas-INDEL	.											.	PNPT1	68	.	0			c.1266delT						.						16	17	17					2																	55887311		2157	4260	6417	SO:0001589	frameshift_variant	87178	exon15			.	BC053660	CCDS1856.1	2p15	2013-01-08			ENSG00000138035	ENSG00000138035			23166	protein-coding gene	gene with protein product	"polynucleotide phosphorylase", "3'-5' RNA exonuclease"	610316	"deafness, autosomal recessive 70"	DFNB70		12419256	Standard	NM_033109		Approved	PNPase, OLD35, old-35	uc002rzf.3	Q8TCS8	OTTHUMG00000129335	ENST00000447944.2:c.1265delA	chr2.hg19:g.55887311delT	ENSP00000400646:p.Asn422fs	123.0	0.0		155.0	10.0	NM_033109	Q53SU0|Q68CN1|Q7Z7D1|Q8IWX1|Q96T05|Q9BRU3|Q9BVX0	Frame_Shift_Del	DEL	ENST00000447944.2	hg19	CCDS1856.1																																																																																			.	.		0.284	PNPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251481.2	NM_033109		-	55887311	T	-	55887311	7	5	282	1	0	1	0	1	0	0	0	0	12182	1493	52	0	1142	0	PNPT1	2	55887311	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	350988	55887311	187312062	166	40400										
EHBP1	23301	hgsc.bcm.edu	37	chr2	62991489	62991489	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cattgaaatcactgtaacacTttttaaggtaagttccattt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:62991489delT	ENST00000263991.5	+	4	733	c.251delT	c.(250-252)cttfs	p.L84fs	EHBP1_ENST00000405289.1_Frame_Shift_Del_p.L84fs|EHBP1_ENST00000431489.1_Frame_Shift_Del_p.L84fs|EHBP1_ENST00000405015.3_Frame_Shift_Del_p.L84fs|EHBP1_ENST00000354487.3_Frame_Shift_Del_p.L84fs	NM_015252.3	NP_056067.2	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1	84						cytoplasm (GO:0005737)|membrane (GO:0016020)				biliary_tract(1)|breast(3)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(22)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	47	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			ACTGTAACACTTTTTAAGGTA	0.348																																					p.L84fs		Atlas-INDEL	.											.	EHBP1	127	.	0			c.250delC						.						106	103	104					2																	62991489		2203	4300	6503	SO:0001589	frameshift_variant	23301	exon4			.	AL833968	CCDS1872.1, CCDS46299.1, CCDS46300.1	2p15	2008-02-05			ENSG00000115504	ENSG00000115504			29144	protein-coding gene	gene with protein product		609922				10048485	Standard	NM_015252		Approved	KIAA0903, NACSIN	uc002sby.3	Q8NDI1	OTTHUMG00000129453	ENST00000263991.5:c.251delT	chr2.hg19:g.62991489delT	ENSP00000263991:p.Leu84fs	262.0	0.0		164.0	10.0	NM_001142616	O94977|Q53TG7|Q53TV6|Q580X2|Q6NX72|Q6PIT3|Q6QNV2|Q9NWI9	Frame_Shift_Del	DEL	ENST00000263991.5	hg19	CCDS1872.1																																																																																			.	.		0.348	EHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251616.1	NM_015252		-	62991489	T	-	62991489	7	5	282	1	0	1	0	1	0	0	0	0	4977	1609	56	0	261	0	EHBP1	2	62991489	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	7104178	62991489	180207884	167	40401										
UGP2	7360	hgsc.bcm.edu	37	chr2	64084969	64084969	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttctattttcacagcacaccAaaaaagacctggatggattt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:64084969delA	ENST00000337130.5	+	3	630	c.154delA	c.(154-156)aaafs	p.K53fs	UGP2_ENST00000394417.2_Frame_Shift_Del_p.K42fs|UGP2_ENST00000445915.2_Frame_Shift_Del_p.K62fs|UGP2_ENST00000467648.2_Frame_Shift_Del_p.K42fs|UGP2_ENST00000487469.1_Intron	NM_006759.3	NP_006750.3	Q16851	UGPA_HUMAN	UDP-glucose pyrophosphorylase 2	53					carbohydrate metabolic process (GO:0005975)|cellular glucuronidation (GO:0052695)|glucose 1-phosphate metabolic process (GO:0019255)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|small molecule metabolic process (GO:0044281)|UDP-glucose metabolic process (GO:0006011)|UDP-glucuronate biosynthetic process (GO:0006065)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	glucose binding (GO:0005536)|metal ion binding (GO:0046872)|pyrimidine ribonucleotide binding (GO:0032557)|UTP:glucose-1-phosphate uridylyltransferase activity (GO:0003983)			endometrium(2)|kidney(1)|large_intestine(8)|lung(6)|prostate(1)	18						ACAGCACACCAAAAAAGACCT	0.358																																					p.T51fs		Atlas-INDEL	.											.	UGP2	38	.	0			c.153delC						.						161	191	181					2																	64084969		2203	4300	6503	SO:0001589	frameshift_variant	7360	exon3			.		CCDS1875.1, CCDS42690.1	2p14-p13	2012-10-02			ENSG00000169764	ENSG00000169764	2.7.7.9		12527	protein-coding gene	gene with protein product		191760	"UDP-glucose pyrophosphorylase 1"	UGP1			Standard	NM_006759		Approved	UGPP1	uc002scm.3	Q16851	OTTHUMG00000129513	ENST00000337130.5:c.154delA	chr2.hg19:g.64084969delA	ENSP00000338703:p.Lys53fs	134.0	0.0		106.0	10.0	NM_006759	Q07131|Q0P6K2|Q86Y81|Q9BU15	Frame_Shift_Del	DEL	ENST00000337130.5	hg19	CCDS1875.1																																																																																			.	.		0.358	UGP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251688.1	NM_006759		-	64084969	A	-	64084969	7	5	282	1	0	1	0	1	0	0	0	0	16958	131	5	0	164	0	UGP2	2	64084969	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1093480	64084969	179114404	168	40402										
MEIS1	4211	hgsc.bcm.edu	37	chr2	66667704	66667704	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttgtatttagattcgcgcagAaaaacctctattttcttcta							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:66667704delA	ENST00000272369.9	+	4	849	c.392delA	c.(391-393)gaafs	p.E131fs	MEIS1_ENST00000407092.2_Frame_Shift_Del_p.E131fs|MEIS1_ENST00000488550.1_Frame_Shift_Del_p.E131fs|MEIS1_ENST00000444274.2_Frame_Shift_Del_p.E99fs|MEIS1_ENST00000398506.2_Frame_Shift_Del_p.E129fs|MEIS1-AS1_ENST00000454595.1_RNA|MEIS1_ENST00000560281.2_Frame_Shift_Del_p.E131fs|MEIS1_ENST00000495021.2_Frame_Shift_Del_p.E66fs|MEIS1-AS2_ENST00000439433.1_RNA	NM_002398.2	NP_002389.1	O00470	MEIS1_HUMAN	Meis homeobox 1	131					angiogenesis (GO:0001525)|definitive hemopoiesis (GO:0060216)|lens morphogenesis in camera-type eye (GO:0002089)|megakaryocyte development (GO:0035855)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of neuron differentiation (GO:0045665)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(10)|prostate(2)|skin(1)|urinary_tract(1)	24						ATTCGCGCAGAAAAACCTCTA	0.493																																					p.E131fs		Atlas-INDEL	.											.	MEIS1	52	.	0			c.391delG						.						87	88	87					2																	66667704		1801	4064	5865	SO:0001589	frameshift_variant	4211	exon4			.		CCDS46309.1	2p14	2011-06-20	2007-02-15		ENSG00000143995	ENSG00000143995		"Homeoboxes / TALE class"	7000	protein-coding gene	gene with protein product		601739	"Meis1 (mouse) homolog", "Meis1, myeloid ecotropic viral integration site 1 homolog (mouse)"			7565694	Standard	NM_002398		Approved		uc002sdu.3	O00470	OTTHUMG00000150714	ENST00000272369.9:c.392delA	chr2.hg19:g.66667704delA	ENSP00000272369:p.Glu131fs	345.0	0.0		256.0	18.0	NM_002398	A8MV50	Frame_Shift_Del	DEL	ENST00000272369.9	hg19	CCDS46309.1																																																																																			.	.		0.493	MEIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319725.4	NM_002398		-	66667704	A	-	66667704	7	5	282	1	0	1	0	1	0	0	0	0	9476	246	9	0	406	0	MEIS1	2	66667704	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2582735	66667704	176531669	169	40403										
CYP26B1	56603	hgsc.bcm.edu	37	chr2	72359653	72359653	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cgcgcctggctgaagcgatcGgggtcgaacacgttcacgtc					rs150438812		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:72359653delG	ENST00000001146.2	-	6	1445	c.1242delC	c.(1240-1242)cccfs	p.P414fs	CYP26B1_ENST00000412253.1_Frame_Shift_Del_p.P223fs|CYP26B1_ENST00000546307.1_Frame_Shift_Del_p.P339fs	NM_001277742.1|NM_019885.2	NP_001264671.1|NP_063938.1	Q9NR63	CP26B_HUMAN	cytochrome P450, family 26, subfamily B, polypeptide 1	414					bone morphogenesis (GO:0060349)|cell fate determination (GO:0001709)|cellular response to retinoic acid (GO:0071300)|cornification (GO:0070268)|embryonic limb morphogenesis (GO:0030326)|establishment of skin barrier (GO:0061436)|male meiosis (GO:0007140)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|oxidation-reduction process (GO:0055114)|positive regulation of gene expression (GO:0010628)|positive regulation of tongue muscle cell differentiation (GO:2001037)|proximal/distal pattern formation (GO:0009954)|retinoic acid catabolic process (GO:0034653)|retinoic acid receptor signaling pathway (GO:0048384)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|tongue morphogenesis (GO:0043587)|vitamin metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|retinoic acid 4-hydroxylase activity (GO:0008401)|retinoic acid binding (GO:0001972)			breast(1)|kidney(3)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)	28						TGAAGCGATCGGGGTCGAACA	0.617																																					p.D415fs		Atlas-INDEL	.											CYP26B1,NS,carcinoma,0,1	CYP26B1	73	.	0			c.1243delG						.						56	49	51					2																	72359653		2203	4300	6503	SO:0001589	frameshift_variant	56603	exon6			.		CCDS1919.1, CCDS62934.1	2p12	2006-11-24			ENSG00000003137	ENSG00000003137		"Cytochrome P450s"	20581	protein-coding gene	gene with protein product		605207				10545224	Standard	NM_019885		Approved	P450RAI-2	uc002sih.2	Q9NR63	OTTHUMG00000129756	ENST00000001146.2:c.1242delC	chr2.hg19:g.72359653delG	ENSP00000001146:p.Pro414fs	290.0	0.0		202.0	14.0	NM_019885	B2R8M7|B7Z2K6|B7Z2P4|B7Z3B8|E4W5W7|Q32MC0|Q53TW1|Q9NP41	Frame_Shift_Del	DEL	ENST00000001146.2	hg19	CCDS1919.1																																																																																			.	.		0.617	CYP26B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251969.1	NM_019885		-	72359653	G	-	72359653	7	5	282	1	0	1	0	1	0	0	0	0	4158	1103	39	0	300	0	CYP26B1	2	72359653	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	5691949	72359653	170839720	170	40404										
CCT7	10574	hgsc.bcm.edu	37	chr2	73471802	73471802	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcgatgatttgctgcagcttAaaatgattggaatcaagaag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:73471802delA	ENST00000258091.5	+	6	718	c.577delA	c.(577-579)aaafs	p.K193fs	CCT7_ENST00000538797.1_Frame_Shift_Del_p.K65fs|CCT7_ENST00000539919.1_Frame_Shift_Del_p.K149fs|CCT7_ENST00000473786.1_3'UTR|CCT7_ENST00000537131.1_Frame_Shift_Del_p.K93fs|CCT7_ENST00000540468.1_Frame_Shift_Del_p.K106fs|CCT7_ENST00000398422.2_Intron	NM_006429.3	NP_006420.1	Q99832	TCPH_HUMAN	chaperonin containing TCP1, subunit 7 (eta)	193					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|unfolded protein binding (GO:0051082)			breast(1)|cervix(1)|endometrium(1)|lung(3)|stomach(1)	7						GCTGCAGCTTAAAATGATTGG	0.498																																					p.L192fs		Atlas-INDEL	.											.	CCT7	60	.	0			c.576delT						.						62	61	62					2																	73471802		2031	4189	6220	SO:0001589	frameshift_variant	10574	exon6			.	AF026292	CCDS42696.1, CCDS46336.1, CCDS54366.1, CCDS54367.1	2p13.2	2011-09-02			ENSG00000135624	ENSG00000135624		"Heat Shock Proteins / Chaperonins"	1622	protein-coding gene	gene with protein product		605140				9819444	Standard	NM_006429		Approved	Ccth, Nip7-1	uc002siz.3	Q99832	OTTHUMG00000152765	ENST00000258091.5:c.577delA	chr2.hg19:g.73471802delA	ENSP00000258091:p.Lys193fs	241.0	0.0		169.0	11.0	NM_006429	A8K7E6|A8MWI8|B7WNW9|B7Z4T9|B7Z4Z7|O14871|Q6FI26	Frame_Shift_Del	DEL	ENST00000258091.5	hg19	CCDS46336.1																																																																																			.	.		0.498	CCT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327714.2			-	73471802	A	-	73471802	7	5	282	1	0	1	0	1	0	0	0	0	2961	363	13	0	599	0	CCT7	2	73471802	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1112149	73471802	169727571	171	40405										
TCF7L1	83439	hgsc.bcm.edu	37	chr2	85531091	85531091	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cccggagctgtcggacaaatCccccaccccctcggctggct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:85531091delC	ENST00000282111.3	+	6	1007	c.732delC	c.(730-732)atcfs	p.I244fs		NM_031283.2	NP_112573.1	Q9HCS4	TF7L1_HUMAN	transcription factor 7-like 1 (T-cell specific, HMG-box)	244	Pro-rich.				anterior/posterior axis specification, embryo (GO:0008595)|axial mesoderm morphogenesis (GO:0048319)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|chromatin organization (GO:0006325)|generation of neurons (GO:0048699)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|skin(4)|upper_aerodigestive_tract(1)	18						TCGGACAAATCCCCCACCCCC	0.632																																					p.I244fs		Atlas-INDEL	.											.	TCF7L1	44	.	0			c.731delT						.						103	97	99					2																	85531091		2203	4300	6503	SO:0001589	frameshift_variant	83439	exon6			.	X62870	CCDS1971.1	2p11.2	2008-02-05			ENSG00000152284	ENSG00000152284			11640	protein-coding gene	gene with protein product		604652		TCF3		1741298, 11085512	Standard	NM_031283		Approved		uc002soy.3	Q9HCS4	OTTHUMG00000130026	ENST00000282111.3:c.732delC	chr2.hg19:g.85531091delC	ENSP00000282111:p.Ile244fs	190.0	0.0		159.0	10.0	NM_031283	Q53R97|Q6PD70|Q9NP00	Frame_Shift_Del	DEL	ENST00000282111.3	hg19	CCDS1971.1																																																																																			.	.		0.632	TCF7L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252301.2	NM_031283		-	85531091	C	-	85531091	7	5	282	1	0	1	0	1	0	0	0	0	15712	845	30	0	754	0	TCF7L1	2	85531091	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	12059289	85531091	157668282	172	40406										
POLR1A	25885	hgsc.bcm.edu	37	chr2	86259442	86259442	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggcatcagaggcatcggcgtCcccctcctcagcttcagcat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:86259442delC	ENST00000263857.6	-	29	4603	c.4225delG	c.(4225-4227)gacfs	p.D1409fs	POLR1A_ENST00000409681.1_Frame_Shift_Del_p.D1409fs			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	1409					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						GCATCGGCGTCCCCCTCCTCA	0.582																																					p.D1409fs		Pindel	.											.	POLR1A	137	.	0			c.4226delA						.						166	180	175					2																	86259442		2123	4233	6356	SO:0001589	frameshift_variant	25885	exon29			.	AK025568	CCDS42706.1	2p11.2	2013-01-21			ENSG00000068654	ENSG00000068654		"RNA polymerase subunits"	17264	protein-coding gene	gene with protein product						9236775	Standard	NM_015425		Approved	DKFZP586M0122, FLJ21915, RPO1-4, RPA1	uc002sqs.3	O95602	OTTHUMG00000153165	ENST00000263857.6:c.4225delG	chr2.hg19:g.86259442delC	ENSP00000263857:p.Asp1409fs	283.0	0.0		243.0	10.0	NM_015425	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Frame_Shift_Del	DEL	ENST00000263857.6	hg19	CCDS42706.1																																																																																			.	.		0.582	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425		-	86259442	C	-	86259442	7	5	282	1	0	1	0	1	0	0	0	0	12218	855	30	0	961	0	POLR1A	2	86259442	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	728351	86259442	156939931	173	40407										
IMMT	10989	hgsc.bcm.edu	37	chr2	86385804	86385804	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cttggaccaccagctcatgaTactgagatacaaccttagcc	7	13	1	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:86385804T>C	ENST00000410111.3	-	10	1460	c.1073A>G	c.(1072-1074)tAt>tGt	p.Y358C	IMMT_ENST00000254636.5_Missense_Mutation_p.Y259C|IMMT_ENST00000409051.2_Missense_Mutation_p.Y311C|IMMT_ENST00000449247.2_Missense_Mutation_p.Y347C|IMMT_ENST00000442664.2_Missense_Mutation_p.Y357C|Y_RNA_ENST00000363371.1_RNA|IMMT_ENST00000490238.1_5'UTR	NM_001100169.1|NM_001100170.1|NM_006839.2	NP_001093639.1|NP_001093640.1|NP_006830.2	Q16891	MIC60_HUMAN	inner membrane protein, mitochondrial	358					mitochondrial calcium ion homeostasis (GO:0051560)|response to cold (GO:0009409)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						CAGCTCATGATACTGAGATAC	0.438																																					p.Y358C		Atlas-SNP	.											.	IMMT	65	.	0			c.A1073G						.						60	55	57					2																	86385804		1879	4124	6003	SO:0001583	missense	10989	exon10			TCATGATACTGAG	D21094	CCDS46355.1, CCDS46356.1, CCDS46357.1	2p11.2	2011-10-04	2010-04-29		ENSG00000132305	ENSG00000132305			6047	protein-coding gene	gene with protein product	"mitofilin", "mitochondrial inner membrane organizing system 2"	600378	"inner membrane protein, mitochondrial (mitofilin)"			9168817, 8039717	Standard	NM_001100169		Approved	P87, P89, HMP, MINOS2	uc002sqz.4	Q16891	OTTHUMG00000153170	ENST00000410111.3:c.1073A>G	chr2.hg19:g.86385804T>C	ENSP00000387262:p.Tyr358Cys	173.0	0.0		136.0	58.0	NM_006839	B1H0U5|B2R5N6|Q14539|Q15092|Q68D41|Q69HW5|Q6IBL0|Q7Z3X1|Q8TAJ5|Q9P0V2	Missense_Mutation	SNP	ENST00000410111.3	hg19	CCDS46355.1	.	.	.	.	.	.	.	.	.	.	T	26.2	4.715540	0.89112	.	.	ENSG00000132305	ENST00000254636;ENST00000449247;ENST00000410111;ENST00000442664;ENST00000409051;ENST00000545283;ENST00000377310	T;T;T;T;T	0.36520	1.25;1.25;1.25;1.25;1.25	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.63153	0.2487	M	0.81341	2.54	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0	T	0.66122	-0.6002	10	0.51188	T	0.08	-11.236	16.0709	0.80928	0.0:0.0:0.0:1.0	.	311;346;326;260;347;326;358	B9A067;B4DKR1;F8W9I1;B4DS66;Q16891-2;Q16891-3;Q16891	.;.;.;.;.;.;IMMT_HUMAN	C	259;347;358;357;311;347;326	ENSP00000254636:Y259C;ENSP00000396899:Y347C;ENSP00000387262:Y358C;ENSP00000407788:Y357C;ENSP00000387227:Y311C	ENSP00000254636:Y259C	Y	-	2	0	IMMT	86239315	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.519000	0.81809	2.198000	0.70561	0.528000	0.53228	TAT	.	.		0.438	IMMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329909.2	NM_006839		C	86385804	T	C	86385804	3	2	282	1	0	0	0	0	1	0	0	0	7727	1406	49	2	1227	2	IMMT	2	86385804	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	126362	86385804	156813569	174	40408										
FAHD2A	51011	hgsc.bcm.edu	37	chr2	96078466	96078466	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggatgtcatcctaactgggaCccccccaggtgtcggtgtat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:96078466delC	ENST00000233379.4	+	7	989	c.836delC	c.(835-837)accfs	p.T279fs	FAHD2A_ENST00000447036.1_Frame_Shift_Del_p.T279fs	NM_016044.2	NP_057128.2	Q96GK7	FAH2A_HUMAN	fumarylacetoacetate hydrolase domain containing 2A	279							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|lung(3)|ovary(1)	8						CTAACTGGGACCCCCCCAGGT	0.562																																					p.T279fs		Atlas-INDEL	.											.,1	FAHD2A	25	.	0			c.835delA						.						43	43	43					2																	96078466		2203	4298	6501	SO:0001589	frameshift_variant	51011	exon7			.	AF151863	CCDS2014.1	2q11.2	2008-02-05			ENSG00000115042	ENSG00000115042			24252	protein-coding gene	gene with protein product							Standard	NM_016044		Approved	CGI-105	uc002sur.3	Q96GK7	OTTHUMG00000130397	ENST00000233379.4:c.836delC	chr2.hg19:g.96078466delC	ENSP00000233379:p.Thr279fs	293.0	0.0		214.0	14.0	NM_016044	Q9Y3B0	Frame_Shift_Del	DEL	ENST00000233379.4	hg19	CCDS2014.1																																																																																			.	.		0.562	FAHD2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252778.1	NM_016044		-	96078466	C	-	96078466	7	5	282	1	0	1	0	1	0	0	0	0	5378	507	18	0	858	0	FAHD2A	2	96078466	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	9692662	96078466	147120907	175	40409										
CNNM4	26504	hgsc.bcm.edu	37	chr2	97427712	97427712	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccattagcaagctcctggacTtttttctgggccaggagatt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:97427712delT	ENST00000377075.2	+	1	1074	c.976delT	c.(976-978)tttfs	p.F327fs		NM_020184.3	NP_064569.3	Q6P4Q7	CNNM4_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 4	327	DUF21.				biomineral tissue development (GO:0031214)|ion transport (GO:0006811)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)			breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)	20						GCTCCTGGACTTTTTTCTGGG	0.512																																					p.D325fs		Atlas-INDEL	.											.	CNNM4	48	.	0			c.975delC						.						94	98	96					2																	97427712		2203	4300	6503	SO:0001589	frameshift_variant	26504	exon1			.	AB046812	CCDS2024.2	2q11.2	2014-08-08	2014-08-07		ENSG00000158158	ENSG00000158158			105	protein-coding gene	gene with protein product		607805	"cyclin M4"	ACDP4		21393841, 24194943	Standard	XM_005263914		Approved	KIAA1592	uc002swx.3	Q6P4Q7	OTTHUMG00000130532	ENST00000377075.2:c.976delT	chr2.hg19:g.97427712delT	ENSP00000366275:p.Phe327fs	215.0	0.0		198.0	13.0	NM_020184	B7Z1U0|C7SQM3|C7SQM4|C7SQM5|Q53RE5|Q9H9G3|Q9HCI0|Q9NRN1	Frame_Shift_Del	DEL	ENST00000377075.2	hg19	CCDS2024.2																																																																																			.	.		0.512	CNNM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252954.1	NM_020184		-	97427712	T	-	97427712	7	5	282	1	0	1	0	1	0	0	0	0	3617	1609	56	0	978	0	CNNM4	2	97427712	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1349246	97427712	145771661	176	40410										
VWA3B	200403	hgsc.bcm.edu	37	chr2	98828460	98828460	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgataaagaaacacaggcaaTctaccttctgaccgatggga	9	9	2	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:98828460T>C	ENST00000477737.1	+	13	2009	c.1805T>C	c.(1804-1806)aTc>aCc	p.I602T	VWA3B_ENST00000435344.1_Missense_Mutation_p.I602T|VWA3B_ENST00000451075.2_Missense_Mutation_p.I452T	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	602	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.									NS(3)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						ACACAGGCAATCTACCTTCTG	0.478																																					p.I602T		Atlas-SNP	.											.	VWA3B	138	.	0			c.T1805C						.						100	99	99					2																	98828460		1871	4111	5982	SO:0001583	missense	200403	exon13			AGGCAATCTACCT	AL832761	CCDS42718.1	2q11.2	2008-02-05			ENSG00000168658	ENSG00000168658			28385	protein-coding gene	gene with protein product						12477932	Standard	NM_144992		Approved	DKFZp686F2227, MGC26733	uc002syo.3	Q502W6	OTTHUMG00000153104	ENST00000477737.1:c.1805T>C	chr2.hg19:g.98828460T>C	ENSP00000417955:p.Ile602Thr	148.0	0.0		111.0	5.0	NM_144992	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Missense_Mutation	SNP	ENST00000477737.1	hg19	CCDS42718.1	.	.	.	.	.	.	.	.	.	.	T	15.66	2.898203	0.52227	.	.	ENSG00000168658	ENST00000435344;ENST00000477737;ENST00000451075	T;T;T	0.80994	-1.44;1.66;-1.44	5.4	5.4	0.78164	von Willebrand factor, type A (3);	0.000000	0.85682	D	0.000000	D	0.89733	0.6800	M	0.83312	2.635	0.32177	N	0.580877	D;D;D;D	0.89917	0.999;1.0;1.0;0.999	D;D;D;D	0.87578	0.996;0.997;0.992;0.998	D	0.92042	0.5641	10	0.87932	D	0	.	13.3675	0.60694	0.0:0.0:0.0:1.0	.	452;602;602;602	B7Z7Q7;Q502W6;Q502W6-8;Q502W6-6	.;VWA3B_HUMAN;.;.	T	602;602;452	ENSP00000401959:I602T;ENSP00000417955:I602T;ENSP00000389463:I452T	ENSP00000388158:I602T	I	+	2	0	VWA3B	98194892	1.000000	0.71417	0.994000	0.49952	0.235000	0.25334	5.137000	0.64789	2.212000	0.71576	0.391000	0.25812	ATC	.	.		0.478	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992		C	98828460	T	C	98828460	3	2	282	1	0	0	0	0	1	0	0	0	17256	1435	50	2	1851	2	VWA3B	2	98828460	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1400748	98828460	144370913	177	40411										
CREG2	200407	hgsc.bcm.edu	37	chr2	102000039	102000039	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggcagcatcagcgaggccatGgggttcttcatcagatcagc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:102000039delG	ENST00000324768.5	-	2	704	c.567delC	c.(565-567)cccfs	p.P189fs	CREG2_ENST00000495455.1_5'UTR	NM_153836.3	NP_722578.1	Q8IUH2	CREG2_HUMAN	cellular repressor of E1A-stimulated genes 2	189						endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)	FMN binding (GO:0010181)|oxidoreductase activity (GO:0016491)			endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	10						GCGAGGCCATGGGGTTCTTCA	0.552																																					p.M190fs		Atlas-INDEL	.											.	CREG2	21	.	0			c.568delA						.						71	68	69					2																	102000039		2203	4300	6503	SO:0001589	frameshift_variant	200407	exon2			.	AB046109	CCDS2052.1	2q12.1	2007-08-01			ENSG00000175874	ENSG00000175874			14272	protein-coding gene	gene with protein product						12408961	Standard	NM_153836		Approved		uc002tba.2	Q8IUH2	OTTHUMG00000130692	ENST00000324768.5:c.567delC	chr2.hg19:g.102000039delG	ENSP00000315203:p.Pro189fs	130.0	0.0		89.0	10.0	NM_153836	Q86X03|Q8N540|Q8N9E3	Frame_Shift_Del	DEL	ENST00000324768.5	hg19	CCDS2052.1																																																																																			.	.		0.552	CREG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253188.2	NM_153836		-	102000039	G	-	102000039	7	5	282	1	0	1	0	1	0	0	0	0	3867	1335	47	0	317	0	CREG2	2	102000039	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	3171579	102000039	141199334	178	40412										
IL18R1	8809	hgsc.bcm.edu	37	chr2	103013192	103013192	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cttgccccaatcactaaagcTtttgaaatctcacagagttc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:103013192delT	ENST00000409599.1	+	12	1828	c.1472delT	c.(1471-1473)cttfs	p.L492fs	IL18R1_ENST00000233957.1_Frame_Shift_Del_p.L492fs			Q13478	IL18R_HUMAN	interleukin 18 receptor 1	492	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				immune response (GO:0006955)|natural killer cell activation (GO:0030101)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|signal transduction (GO:0007165)|T-helper 1 cell differentiation (GO:0045063)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-18 receptor activity (GO:0042008)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34						TCACTAAAGCTTTTGAAATCT	0.358																																					p.L491fs		Atlas-INDEL	.											.	IL18R1	72	.	0			c.1471delC						.						90	96	94					2																	103013192		2203	4300	6503	SO:0001589	frameshift_variant	8809	exon10			.	U43672	CCDS2060.1	2q12	2013-01-29			ENSG00000115604	ENSG00000115604		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5988	protein-coding gene	gene with protein product		604494				8626725, 10191101	Standard	NM_003855		Approved	IL1RRP, IL-1Rrp, CD218a	uc010fiy.3	Q13478	OTTHUMG00000130780	ENST00000409599.1:c.1472delT	chr2.hg19:g.103013192delT	ENSP00000387211:p.Leu492fs	449.0	0.0		307.0	21.0	NM_003855	B2R9Y5|Q52LC9	Frame_Shift_Del	DEL	ENST00000409599.1	hg19	CCDS2060.1																																																																																			.	.		0.358	IL18R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253294.2	NM_003855		-	103013192	T	-	103013192	7	5	282	1	0	1	0	1	0	0	0	0	7656	1609	56	0	1510	0	IL18R1	2	103013192	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1013153	103013192	140186181	179	40413										
SLC9A2	6549	hgsc.bcm.edu	37	chr2	103300596	103300596	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gttttctttctttgcaggtgTttttgtcctgactcaggtca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:103300596delT	ENST00000233969.2	+	5	1368	c.1226delT	c.(1225-1227)gttfs	p.V409fs		NM_003048.3	NP_003039.2	Q9UBY0	SL9A2_HUMAN	solute carrier family 9, subfamily A (NHE2, cation proton antiporter 2), member 2	409					ion transport (GO:0006811)|protein localization (GO:0008104)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			breast(5)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42						TTTGCAGGTGTTTTTGTCCTG	0.453																																					p.V409fs		Atlas-INDEL	.											.	SLC9A2	112	.	0			c.1225delG						.						96	86	89					2																	103300596		2203	4300	6503	SO:0001589	frameshift_variant	6549	exon5			.		CCDS2062.1	2q11.2	2013-05-22	2012-03-22		ENSG00000115616	ENSG00000115616		"Solute carriers"	11072	protein-coding gene	gene with protein product		600530	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 2", "solute carrier family 9 (sodium/hydrogen exchanger), member 2"	NHE2			Standard	NM_003048		Approved		uc002tca.3	Q9UBY0	OTTHUMG00000130778	ENST00000233969.2:c.1226delT	chr2.hg19:g.103300596delT	ENSP00000233969:p.Val409fs	268.0	0.0		177.0	11.0	NM_003048	B2RMS2	Frame_Shift_Del	DEL	ENST00000233969.2	hg19	CCDS2062.1																																																																																			.	.		0.453	SLC9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253292.2			-	103300596	T	-	103300596	7	5	282	1	0	1	0	1	0	0	0	0	14727	1725	60	0	1244	0	SLC9A2	2	103300596	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	287404	103300596	139898777	180	40414										
CCDC138	165055	hgsc.bcm.edu	37	chr2	109473308	109473308	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gacttgaagacagaagaaggAaaaaccttgtttttggagta							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:109473308delA	ENST00000295124.4	+	13	1635	c.1575delA	c.(1573-1575)ggafs	p.G525fs	CCDC138_ENST00000412964.2_Frame_Shift_Del_p.G525fs	NM_144978.1	NP_659415.1	Q96M89	CC138_HUMAN	coiled-coil domain containing 138	525										endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	14						CAGAAGAAGGAAAAACCTTGT	0.373																																					p.G525fs		Atlas-INDEL	.											.	CCDC138	49	.	0			c.1574delG						.						190	196	194					2																	109473308		2203	4300	6503	SO:0001589	frameshift_variant	165055	exon13			.	AK057307	CCDS2080.1	2q13	2008-02-05			ENSG00000163006	ENSG00000163006			26531	protein-coding gene	gene with protein product						12477932	Standard	NM_144978		Approved	FLJ32745	uc002ten.1	Q96M89	OTTHUMG00000130980	ENST00000295124.4:c.1575delA	chr2.hg19:g.109473308delA	ENSP00000295124:p.Gly525fs	231.0	0.0		137.0	11.0	NM_144978	Q05DF1|Q4ZG07|Q53TE1|Q6ZUY5|Q86VL7	Frame_Shift_Del	DEL	ENST00000295124.4	hg19	CCDS2080.1																																																																																			.	.		0.373	CCDC138-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253593.1	NM_144978		-	109473308	A	-	109473308	7	5	282	1	0	1	0	1	0	0	0	0	2774	233	9	0	1625	0	CCDC138	2	109473308	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	6172712	109473308	133726065	181	40415										
NPHP1	4867	hgsc.bcm.edu	37	chr2	110881425	110881425	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	taggtctgctctgaaaggtcAaaaggttcatgaactccgtc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:110881425delA	ENST00000393272.3	-	20	2239	c.2142delT	c.(2140-2142)tttfs	p.F714fs	NPHP1_ENST00000417665.1_Frame_Shift_Del_p.F693fs|NPHP1_ENST00000445609.2_Frame_Shift_Del_p.F659fs|AC013268.1_ENST00000390802.1_RNA|NPHP1_ENST00000316534.4_Frame_Shift_Del_p.F715fs|NPHP1_ENST00000355301.4_Frame_Shift_Del_p.F596fs	NM_000272.3|NM_207181.2	NP_000263.2|NP_997064.2	O15259	NPHP1_HUMAN	nephronophthisis 1 (juvenile)	714					actin cytoskeleton organization (GO:0030036)|cell projection organization (GO:0030030)|cellular protein localization (GO:0034613)|excretion (GO:0007588)|photoreceptor cell outer segment organization (GO:0035845)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|spermatid differentiation (GO:0048515)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|motile cilium (GO:0031514)|photoreceptor connecting cilium (GO:0032391)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)	p.F715L(1)		autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(2)	24						CTGAAAGGTCAAAAGGTTCAT	0.502																																					p.D716fs		Atlas-INDEL	.											.	NPHP1	68	.	1	Substitution - Missense(1)	lung(1)	c.2146delG						.						105	93	97					2																	110881425		2203	4300	6503	SO:0001589	frameshift_variant	4867	exon20			.	AF023674	CCDS2086.1, CCDS46384.1, CCDS46385.1, CCDS46386.1	2q13	2014-01-28			ENSG00000144061	ENSG00000144061			7905	protein-coding gene	gene with protein product	"nephrocystin-1"	607100		NPH1			Standard	NM_000272		Approved	JBTS4, SLSN1	uc002tfm.4	O15259	OTTHUMG00000131195	ENST00000393272.3:c.2142delT	chr2.hg19:g.110881425delA	ENSP00000376953:p.Phe714fs	248.0	0.0		157.0	10.0	NM_000272	O14837	Frame_Shift_Del	DEL	ENST00000393272.3	hg19	CCDS46385.1																																																																																			.	.		0.502	NPHP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253919.3	NM_000272		-	110881425	A	-	110881425	7	5	282	1	0	1	0	1	0	0	0	0	10588	127	5	0	60	0	NPHP1	2	110881425	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1408117	110881425	132317948	182	40416										
PSD4	23550	hgsc.bcm.edu	37	chr2	113950863	113950863	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tccaggccttggtgctcagtGgggagactcaggaacgggag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:113950863delG	ENST00000245796.6	+	8	2143	c.1948delG	c.(1948-1950)gggfs	p.G650fs	PSD4_ENST00000441564.3_Frame_Shift_Del_p.G622fs	NM_012455.2	NP_036587.2	Q8NDX1	PSD4_HUMAN	pleckstrin and Sec7 domain containing 4	650	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			cervix(1)|endometrium(2)|large_intestine(4)|lung(13)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						GGTGCTCAGTGGGGAGACTCA	0.617																																					p.S649fs		Atlas-INDEL	.											.	PSD4	74	.	0			c.1947delT						.						62	67	66					2																	113950863		2203	4300	6503	SO:0001589	frameshift_variant	23550	exon8			.	U63127	CCDS33276.1	2q13	2013-01-10			ENSG00000125637	ENSG00000125637		"Pleckstrin homology (PH) domain containing"	19096	protein-coding gene	gene with protein product		614442				12082148	Standard	XM_005263634		Approved	TIC, EFA6B	uc002tjc.3	Q8NDX1	OTTHUMG00000153339	ENST00000245796.6:c.1948delG	chr2.hg19:g.113950863delG	ENSP00000245796:p.Gly650fs	182.0	0.0		165.0	10.0	NM_012455	A6NEG7|A8K1Y0|O95621|Q4ZG34|Q6GPH8|Q8IYP4	Frame_Shift_Del	DEL	ENST00000245796.6	hg19	CCDS33276.1																																																																																			.	.		0.617	PSD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330789.1	NM_012455		-	113950863	G	-	113950863	7	5	282	1	0	1	0	1	0	0	0	0	12661	1348	47	0	1974	0	PSD4	2	113950863	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	3069438	113950863	129248510	183	40417										
SLC35F5	80255	hgsc.bcm.edu	37	chr2	114493428	114493428	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cttgatatgacaaatttgccAaaaaccactaaagaaaaaga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:114493428delA	ENST00000245680.2	-	8	1171	c.758delT	c.(757-759)ttgfs	p.L253fs		NM_025181.2	NP_079457.2	Q8WV83	S35F5_HUMAN	solute carrier family 35, member F5	253	EamA.				transport (GO:0006810)	integral component of membrane (GO:0016021)				endometrium(1)|kidney(4)|large_intestine(2)|lung(7)|ovary(2)|prostate(3)|skin(1)	20						CAAATTTGCCAAAAACCACTA	0.313																																					p.L253fs		Atlas-INDEL	.											.	SLC35F5	60	.	0			c.759delG						.						36	36	36					2																	114493428		2202	4292	6494	SO:0001589	frameshift_variant	80255	exon8			.	AF529364	CCDS2119.1	2q14.1	2013-05-22			ENSG00000115084	ENSG00000115084		"Solute carriers"	23617	protein-coding gene	gene with protein product							Standard	XM_005263799		Approved	FLJ22004	uc002tku.1	Q8WV83	OTTHUMG00000131361	ENST00000245680.2:c.758delT	chr2.hg19:g.114493428delA	ENSP00000245680:p.Leu253fs	277.0	0.0		203.0	14.0	NM_025181	Q9H6P8|Q9H7D8	Frame_Shift_Del	DEL	ENST00000245680.2	hg19	CCDS2119.1																																																																																			.	.		0.313	SLC35F5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254150.1	NM_025181		-	114493428	A	-	114493428	7	5	282	1	0	1	0	1	0	0	0	0	14607	131	5	0	845	0	SLC35F5	2	114493428	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	542565	114493428	128705945	184	40418										
SLC35F5	80255	hgsc.bcm.edu	37	chr2	114512776	114512776	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aggaagcaacccatatcacaTcaacaagcagaagaataaca	6	10	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:114512776T>C	ENST00000245680.2	-	3	652	c.239A>G	c.(238-240)gAt>gGt	p.D80G	SLC35F5_ENST00000409342.1_Missense_Mutation_p.D74G	NM_025181.2	NP_079457.2	Q8WV83	S35F5_HUMAN	solute carrier family 35, member F5	80					transport (GO:0006810)	integral component of membrane (GO:0016021)				endometrium(1)|kidney(4)|large_intestine(2)|lung(7)|ovary(2)|prostate(3)|skin(1)	20						CCATATCACATCAACAAGCAG	0.423																																					p.D80G		Atlas-SNP	.											.	SLC35F5	60	.	0			c.A239G						.						87	83	84					2																	114512776		2203	4300	6503	SO:0001583	missense	80255	exon3			ATCACATCAACAA	AF529364	CCDS2119.1	2q14.1	2013-05-22			ENSG00000115084	ENSG00000115084		"Solute carriers"	23617	protein-coding gene	gene with protein product							Standard	XM_005263799		Approved	FLJ22004	uc002tku.1	Q8WV83	OTTHUMG00000131361	ENST00000245680.2:c.239A>G	chr2.hg19:g.114512776T>C	ENSP00000245680:p.Asp80Gly	129.0	0.0		95.0	4.0	NM_025181	Q9H6P8|Q9H7D8	Missense_Mutation	SNP	ENST00000245680.2	hg19	CCDS2119.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.411181	0.83340	.	.	ENSG00000115084	ENST00000245680;ENST00000409106;ENST00000409342	T;T	0.48201	0.82;0.83	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.63733	0.2536	L	0.56199	1.76	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;0.993	D;D;D	0.85130	0.996;0.997;0.984	T	0.66380	-0.5938	10	0.72032	D	0.01	-17.5576	13.9127	0.63878	0.0:0.0:0.0:1.0	.	80;74;80	B2RDY0;B8ZZV6;Q8WV83	.;.;S35F5_HUMAN	G	80;74;74	ENSP00000245680:D80G;ENSP00000386754:D74G	ENSP00000245680:D80G	D	-	2	0	SLC35F5	114229246	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.978000	0.76147	2.209000	0.71365	0.533000	0.62120	GAT	.	.		0.423	SLC35F5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254150.1	NM_025181		C	114512776	T	C	114512776	3	2	282	1	0	0	0	0	1	0	0	0	14607	1435	50	2	1384	2	SLC35F5	2	114512776	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	19348	114512776	128686597	185	40419										
CNTNAP5	129684	hgsc.bcm.edu	37	chr2	125261880	125261880	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gttttccagggcaatgtcacTttttcctgctccgaaccaca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:125261880delT	ENST00000431078.1	+	8	1435	c.1071delT	c.(1069-1071)actfs	p.T357fs		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	357	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		GCAATGTCACTTTTTCCTGCT	0.463																																					p.T357fs		Atlas-INDEL	.											.	CNTNAP5	405	.	0			c.1070delC						.						119	106	110					2																	125261880		1866	4114	5980	SO:0001589	frameshift_variant	129684	exon8			.	AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.1071delT	chr2.hg19:g.125261880delT	ENSP00000399013:p.Thr357fs	223.0	0.0		173.0	12.0	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Frame_Shift_Del	DEL	ENST00000431078.1	hg19	CCDS46401.1																																																																																			.	.		0.463	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			-	125261880	T	-	125261880	7	5	282	1	0	1	0	1	0	0	0	0	3652	1596	56	0	1101	0	CNTNAP5	2	125261880	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	10749104	125261880	117937493	186	40420										
BIN1	274	hgsc.bcm.edu	37	chr2	127821169	127821169	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgctcatctccttgtggaagTtttcctccaggcccgcgatg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:127821169delT	ENST00000316724.5	-	9	1163	c.752delA	c.(751-753)aacfs	p.N251fs	BIN1_ENST00000352848.3_Frame_Shift_Del_p.N220fs|BIN1_ENST00000393040.3_Frame_Shift_Del_p.N220fs|BIN1_ENST00000409400.1_Frame_Shift_Del_p.N220fs|BIN1_ENST00000346226.3_Frame_Shift_Del_p.N220fs|BIN1_ENST00000393041.3_Frame_Shift_Del_p.N220fs|BIN1_ENST00000376113.2_Frame_Shift_Del_p.N220fs|BIN1_ENST00000466111.1_5'UTR|BIN1_ENST00000357970.3_Frame_Shift_Del_p.N251fs|BIN1_ENST00000259238.4_Frame_Shift_Del_p.N220fs|BIN1_ENST00000348750.4_Frame_Shift_Del_p.N220fs|BIN1_ENST00000351659.3_Frame_Shift_Del_p.N251fs	NM_139343.2	NP_647593.1	O00499	BIN1_HUMAN	bridging integrator 1	251	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|lipid tube assembly (GO:0060988)|muscle cell differentiation (GO:0042692)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of endocytosis (GO:0045807)|positive regulation of GTPase activity (GO:0043547)|regulation of cell cycle arrest (GO:0071156)|regulation of neuron differentiation (GO:0045664)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|axon initial segment (GO:0043194)|axon terminus (GO:0043679)|cerebellar mossy fiber (GO:0044300)|cytoplasm (GO:0005737)|I band (GO:0031674)|lipid tube (GO:0060987)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)|T-tubule (GO:0030315)|varicosity (GO:0043196)|Z disc (GO:0030018)	identical protein binding (GO:0042802)|tau protein binding (GO:0048156)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(3)|skin(3)	24	Colorectal(110;0.0831)			BRCA - Breast invasive adenocarcinoma(221;0.073)		CTTGTGGAAGTTTTCCTCCAG	0.632																																					p.N251fs		Atlas-INDEL	.											.	BIN1	85	.	0			c.753delC						.						94	70	78					2																	127821169		2203	4300	6503	SO:0001589	frameshift_variant	274	exon9			.	U68485	CCDS2137.1, CCDS2138.1, CCDS2139.1, CCDS2140.1, CCDS2141.1, CCDS2142.1, CCDS2143.1, CCDS42743.1, CCDS42744.1, CCDS46403.1	2q14	2014-09-17			ENSG00000136717	ENSG00000136717			1052	protein-coding gene	gene with protein product	"amphiphysin II"	601248		AMPHL		8725406, 8782822, 17676042	Standard	NM_004305		Approved	SH3P9, AMPH2	uc002tns.2	O00499	OTTHUMG00000131465	ENST00000316724.5:c.752delA	chr2.hg19:g.127821169delT	ENSP00000316779:p.Asn251fs	198.0	0.0		155.0	10.0	NM_139343	O00297|O00545|O43867|O60552|O60553|O60554|O60555|O75514|O75515|O75516|O75517|O75518|Q659B7|Q92944|Q99688	Frame_Shift_Del	DEL	ENST00000316724.5	hg19	CCDS2138.1																																																																																			.	.		0.632	BIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254298.2	NM_139343		-	127821169	T	-	127821169	7	5	282	1	0	1	0	1	0	0	0	0	1432	1725	60	0	1122	0	BIN1	2	127821169	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2559289	127821169	115378204	187	40421										
MYO7B	4648	hgsc.bcm.edu	37	chr2	128345986	128345986	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggcttcctggagaagaaccgAgacgtgctgagcacagatat	13	9	0	5			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:128345986A>G	ENST00000409816.2	+	14	1742	c.1710A>G	c.(1708-1710)cgA>cgG	p.R570R	MYO7B_ENST00000389524.4_Silent_p.R570R|MYO7B_ENST00000428314.1_Silent_p.R570R			Q6PIF6	MYO7B_HUMAN	myosin VIIB	570	Myosin motor.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		AGAAGAACCGAGACGTGCTGA	0.557																																					p.R570R		Atlas-SNP	.											.	MYO7B	359	.	0			c.A1710G						.						49	54	53					2																	128345986		1975	4152	6127	SO:0001819	synonymous_variant	4648	exon15			GAACCGAGACGTG		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"Myosins / Myosin superfamily : Class VII"	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.1710A>G	chr2.hg19:g.128345986A>G		81.0	0.0		75.0	4.0	NM_001080527	Q14786|Q8TEE1	Silent	SNP	ENST00000409816.2	hg19	CCDS46405.1																																																																																			.	.		0.557	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001		G	128345986	A	G	128345986	2	3	282	1	0	0	0	0	0	0	0	1	10092	291	11	2		2	MYO7B	2	128345986	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	524817	128345986	114853387	188	40422										
FAM123C	205147	hgsc.bcm.edu	37	chr2	131520663	131520663	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aggggacagacagggaccaaTcccggctggacacagctggg					rs1905235	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:131520663delT	ENST00000423981.1	+	2	1128	c.1018delT	c.(1018-1020)tccfs	p.S340fs	AMER3_ENST00000321420.4_Frame_Shift_Del_p.S340fs	NM_001105193.1|NM_001105194.1|NM_001105195.1|NM_152698.2	NP_001098663.1|NP_001098664.1|NP_001098665.1|NP_689911.2	Q8N944	AMER3_HUMAN	APC membrane recruitment protein 3	340			S -> P (in dbSNP:rs1905235). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15815621}.		Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	lipid binding (GO:0008289)										CAGGGACCAATCCCGGCTGGA	0.667																																					p.Q339fs		Atlas-INDEL	.											.	.	.	.	0			c.1017delA						.						32	37	36					2																	131520663		2203	4300	6503	SO:0001589	frameshift_variant	205147	exon2			.	AK095696	CCDS2164.1	2q21.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000178171	ENSG00000178171		"-"	26771	protein-coding gene	gene with protein product			"family with sequence similarity 123C"	FAM123C		20843316	Standard	NM_001105195		Approved	FLJ38377	uc002trw.2	Q8N944	OTTHUMG00000131637	ENST00000423981.1:c.1018delT	chr2.hg19:g.131520663delT	ENSP00000392700:p.Ser340fs	221.0	0.0		157.0	10.0	NM_001105195	B7ZLH6	Frame_Shift_Del	DEL	ENST00000423981.1	hg19	CCDS2164.1																																																																																			.	.		0.667	AMER3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254531.3	NM_152698		-	131520663	T	-	131520663	7	5	282	1	0	1	0	1	0	0	0	0	5429	1435	50	0	1020	0	FAM123C	2	131520663	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3174677	131520663	111678710	189	40423										
PLEKHB2	55041	hgsc.bcm.edu	37	chr2	131884342	131884342	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acaattagtctttgtgcagaAagcacagatgattgcttgta	9	6	1	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:131884342A>G	ENST00000403716.1	+	4	836	c.276A>G	c.(274-276)gaA>gaG	p.E92E	PLEKHB2_ENST00000303908.3_Silent_p.E92E|PLEKHB2_ENST00000409279.1_Silent_p.E92E|PLEKHB2_ENST00000234115.6_Silent_p.E92E|PLEKHB2_ENST00000439822.2_Silent_p.E92E|PLEKHB2_ENST00000409612.1_Silent_p.E92E|PLEKHB2_ENST00000404460.1_Silent_p.E92E|PLEKHB2_ENST00000438882.2_Silent_p.E92E|PLEKHB2_ENST00000409158.1_Silent_p.E92E|PLEKHB2_ENST00000538982.1_Silent_p.E44E	NM_001100623.1|NM_001267062.1|NM_001267063.1|NM_001267064.1|NM_001267065.1|NM_001267066.1|NM_017958.2	NP_001094093.1|NP_001253991.1|NP_001253992.1|NP_001253993.1|NP_001253994.1|NP_001253995.1|NP_060428.2	Q96CS7	PKHB2_HUMAN	pleckstrin homology domain containing, family B (evectins) member 2	92	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.					endosome (GO:0005768)|membrane (GO:0016020)				large_intestine(1)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				BRCA - Breast invasive adenocarcinoma(221;0.0828)		TTTGTGCAGAAAGCACAGATG	0.343																																					p.E92E		Atlas-SNP	.											.	PLEKHB2	47	.	0			c.A276G						.						109	108	108					2																	131884342		2203	4300	6503	SO:0001819	synonymous_variant	55041	exon4			TGCAGAAAGCACA		CCDS2166.1, CCDS46413.1, CCDS58729.1, CCDS58730.1, CCDS74576.1, CCDS74577.1	2q22.1	2013-01-10			ENSG00000115762	ENSG00000115762		"Pleckstrin homology (PH) domain containing"	19236	protein-coding gene	gene with protein product						10200314	Standard	NM_017958		Approved	EVT2, FLJ20783	uc031rpd.1	Q96CS7	OTTHUMG00000131656	ENST00000403716.1:c.276A>G	chr2.hg19:g.131884342A>G		102.0	0.0		93.0	36.0	NM_001267062	B4DF08|B4DZ66|B8ZZN1|Q53FF1|Q53TH7|Q86W37|Q9BV75|Q9NWK1	Silent	SNP	ENST00000403716.1	hg19	CCDS46413.1																																																																																			.	.		0.343	PLEKHB2-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331304.2	NM_017958		G	131884342	A	G	131884342	2	3	282	1	0	0	0	0	0	0	0	1	12074	11	1	2		2	PLEKHB2	2	131884342	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	363679	131884342	111315031	190	40424										
TUBA3D	113457	hgsc.bcm.edu	37	chr2	132238225	132238225	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggcctgctgcatgttgtacaGgggggacgtggtccccaaag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:132238225delG	ENST00000321253.6	+	4	1066	c.959delG	c.(958-960)aggfs	p.R320fs		NM_080386.3	NP_525125.2	Q13748	TBA3C_HUMAN	tubulin, alpha 3d	320					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	32				BRCA - Breast invasive adenocarcinoma(221;0.13)		ATGTTGTACAGGGGGGACGTG	0.567																																					p.R320fs	Ovarian(137;2059 2432 35543 39401)	Atlas-INDEL	.											.	TUBA3D	60	.	0			c.958delA						.						126	130	129					2																	132238225		2203	4300	6503	SO:0001589	frameshift_variant	113457	exon4			.	K03460	CCDS33290.1	2q21.1	2007-03-16			ENSG00000075886	ENSG00000075886		"Tubulins"	24071	protein-coding gene	gene with protein product	"alpha-tubulin isotype H2-alpha"					3785200	Standard	NM_080386		Approved	H2-ALPHA	uc002tsu.4	Q13748	OTTHUMG00000153600	ENST00000321253.6:c.959delG	chr2.hg19:g.132238225delG	ENSP00000326042:p.Arg320fs	418.0	0.0		243.0	15.0	NM_080386	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Frame_Shift_Del	DEL	ENST00000321253.6	hg19	CCDS33290.1																																																																																			.	.		0.567	TUBA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331800.2	NM_080386		-	132238225	G	-	132238225	7	5	282	1	0	1	0	1	0	0	0	0	16762	1000	35	0	973	0	TUBA3D	2	132238225	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	353883	132238225	110961148	191	40425										
MGAT5	4249	hgsc.bcm.edu	37	chr2	135107494	135107494	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggaatctgaaccctcagcagTtttataccatgttccgtgag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:135107494delT	ENST00000409645.1	+	10	1483	c.1231delT	c.(1231-1233)tttfs	p.F411fs	MGAT5_ENST00000281923.2_Frame_Shift_Del_p.F411fs			Q09328	MGT5A_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase	411					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|liver(1)|lung(18)|ovary(3)|pancreas(1)|skin(3)	36				BRCA - Breast invasive adenocarcinoma(221;0.0964)		CCCTCAGCAGTTTTATACCAT	0.413																																					p.Q410fs		Atlas-INDEL	.											.	MGAT5	84	.	0			c.1230delG						.						135	130	132					2																	135107494		2203	4300	6503	SO:0001589	frameshift_variant	4249	exon9			.	D17716	CCDS2171.1	2q21	2013-02-25			ENSG00000152127	ENSG00000152127	2.4.1.155	"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	7049	protein-coding gene	gene with protein product		601774				8292036	Standard	NM_002410		Approved	GNT-V	uc002ttw.4	Q09328	OTTHUMG00000131681	ENST00000409645.1:c.1231delT	chr2.hg19:g.135107494delT	ENSP00000386377:p.Phe411fs	198.0	0.0		129.0	11.0	NM_002410	D3DP70	Frame_Shift_Del	DEL	ENST00000409645.1	hg19	CCDS2171.1																																																																																			.	.		0.413	MGAT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254584.3	NM_002410		-	135107494	T	-	135107494	7	5	282	1	0	1	0	1	0	0	0	0	9557	1725	60	0	1265	0	MGAT5	2	135107494	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2869269	135107494	108091879	192	40426										
CCNT2	905	hgsc.bcm.edu	37	chr2	135712007	135712007	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tatatcctctcacaactctgTttttaaccatcccttacccc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:135712007delT	ENST00000264157.5	+	9	2012	c.1982delT	c.(1981-1983)gttfs	p.V661fs	CCNT2_ENST00000295238.6_Intron|CCNT2_ENST00000537343.1_Intron	NM_001241.3|NM_058241.2	NP_001232.1|NP_490595.1	O60583	CCNT2_HUMAN	cyclin T2	661					cell cycle (GO:0007049)|cell division (GO:0051301)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(2)|kidney(3)|large_intestine(10)|lung(6)|ovary(2)|prostate(1)|skin(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.107)		CACAACTCTGTTTTTAACCAT	0.483																																					p.V661fs		Atlas-INDEL	.											.	CCNT2	98	.	0			c.1981delG						.						188	176	180					2																	135712007		2203	4300	6503	SO:0001589	frameshift_variant	905	exon9			.	AF048731	CCDS2174.1, CCDS2175.1	2q21.3	2010-11-15			ENSG00000082258	ENSG00000082258			1600	protein-coding gene	gene with protein product		603862				9499409, 10465067	Standard	NM_001241		Approved		uc002tuc.2	O60583	OTTHUMG00000131712	ENST00000264157.5:c.1982delT	chr2.hg19:g.135712007delT	ENSP00000264157:p.Val661fs	263.0	0.0		207.0	14.0	NM_058241	A8KA48|D3DP73|D3DP74|O60582|Q29R66|Q53SR4|Q5I1Y0	Frame_Shift_Del	DEL	ENST00000264157.5	hg19	CCDS2174.1																																																																																			.	.		0.483	CCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254629.1	NM_058241		-	135712007	T	-	135712007	7	5	282	1	0	1	0	1	0	0	0	0	2937	1725	60	0	2016	0	CCNT2	2	135712007	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	604513	135712007	107487366	193	40427										
ZRANB3	84083	hgsc.bcm.edu	37	chr2	135985575	135985575	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tggatatggttgaggctatcTatttgcataactattaaaat	8	4	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:135985575T>C	ENST00000264159.6	-	14	2081	c.1965A>G	c.(1963-1965)atA>atG	p.I655M	ZRANB3_ENST00000412849.1_5'UTR|ZRANB3_ENST00000401392.1_Missense_Mutation_p.I655M|ZRANB3_ENST00000536680.1_Missense_Mutation_p.I655M	NM_032143.2	NP_115519.2	Q5FWF4	ZRAB3_HUMAN	zinc finger, RAN-binding domain containing 3	655					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|DNA rewinding (GO:0036292)|DNA strand renaturation (GO:0000733)|negative regulation of DNA recombination (GO:0045910)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to UV (GO:0009411)	nuclear replication fork (GO:0043596)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|endodeoxyribonuclease activity (GO:0004520)|helicase activity (GO:0004386)|K63-linked polyubiquitin binding (GO:0070530)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|upper_aerodigestive_tract(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.135)		TGAGGCTATCTATTTGCATAA	0.284																																					p.I655M		Atlas-SNP	.											.	ZRANB3	109	.	0			c.A1965G						.						45	35	38					2																	135985575		1576	3543	5119	SO:0001583	missense	84083	exon14			GCTATCTATTTGC	AL136824	CCDS46419.1, CCDS67963.1, CCDS74580.1	2q21.3	2013-05-13			ENSG00000121988	ENSG00000121988		"Zinc fingers, RAN-binding domain containing"	25249	protein-coding gene	gene with protein product						11230166	Standard	XM_005263809		Approved	DKFZP434B1727	uc002tum.3	Q5FWF4	OTTHUMG00000150475	ENST00000264159.6:c.1965A>G	chr2.hg19:g.135985575T>C	ENSP00000264159:p.Ile655Met	92.0	0.0		104.0	37.0	NM_032143	B3KYA1|B4E375|B5MDI3|D3DP76|E9PBP0|Q53SM1|Q6P2C4|Q8N1P4|Q9H0E8	Missense_Mutation	SNP	ENST00000264159.6	hg19	CCDS46419.1	.	.	.	.	.	.	.	.	.	.	T	7.579	0.668435	0.14776	.	.	ENSG00000121988	ENST00000538542;ENST00000283060;ENST00000401392;ENST00000264159;ENST00000536680	D;D;D	0.90676	-2.71;-2.71;-2.7	4.45	4.45	0.53987	.	0.393053	0.24568	N	0.037409	T	0.77363	0.4119	N	0.08118	0	0.22571	N	0.998979	P;P	0.41345	0.63;0.746	B;B	0.33196	0.076;0.159	T	0.72057	-0.4405	10	0.48119	T	0.1	-8.633	10.2931	0.43608	0.0:0.0:0.0:1.0	.	655;655	Q5FWF4;Q5FWF4-3	ZRAB3_HUMAN;.	M	120;120;655;655;655	ENSP00000383979:I655M;ENSP00000264159:I655M;ENSP00000441320:I655M	ENSP00000264159:I655M	I	-	3	3	ZRANB3	135702045	0.802000	0.28943	0.359000	0.25824	0.351000	0.29236	1.326000	0.33735	1.987000	0.57996	0.454000	0.30748	ATA	.	.		0.284	ZRANB3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318254.1	NM_032143		C	135985575	T	C	135985575	3	2	282	1	0	0	0	0	1	0	0	0	18239	1512	53	2	1306	2	ZRANB3	2	135985575	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	273568	135985575	107213798	194	40428										
UBXN4	23190	hgsc.bcm.edu	37	chr2	136540331	136540331	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cgtatcagggaaccagtgagAaaaagagtgctggaaaaacg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:136540331delA	ENST00000272638.9	+	13	1712	c.1401delA	c.(1399-1401)agafs	p.R467fs	UBXN4_ENST00000490163.1_3'UTR	NM_014607.3	NP_055422.1	Q92575	UBXN4_HUMAN	UBX domain protein 4	467					response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)				NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	24						AACCAGTGAGAAAAAGAGTGC	0.383																																					p.R467fs		Atlas-INDEL	.											.	UBXN4	54	.	0			c.1400delG						.						167	169	168					2																	136540331		1822	4080	5902	SO:0001589	frameshift_variant	23190	exon13			.	D87684	CCDS42761.1	2q21.3-q22.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000144224	ENSG00000144224		"UBX domain containing"	14860	protein-coding gene	gene with protein product	"erasin"	611216	"UBX domain-containing 2", "UBX domain containing 2"	UBXDC1, UBXD2		16968747	Standard	NM_014607		Approved	KIAA0242	uc002tur.3	Q92575	OTTHUMG00000153577	ENST00000272638.9:c.1401delA	chr2.hg19:g.136540331delA	ENSP00000272638:p.Arg467fs	163.0	0.0		128.0	10.0	NM_014607	A8K9W4|Q4ZG56|Q8IYM5	Frame_Shift_Del	DEL	ENST00000272638.9	hg19	CCDS42761.1																																																																																			.	.		0.383	UBXN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331696.1	NM_014607		-	136540331	A	-	136540331	7	5	282	1	0	1	0	1	0	0	0	0	16931	243	9	0	1451	0	UBXN4	2	136540331	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	554756	136540331	106659042	195	40429										
RBM43	375287	hgsc.bcm.edu	37	chr2	152107693	152107693	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tttgcattgtttggctgagaAccaacttgaatgctttttag	9	6	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:152107693A>G	ENST00000331426.5	-	4	952	c.801T>C	c.(799-801)ggT>ggC	p.G267G		NM_198557.2	NP_940959.1	Q6ZSC3	RBM43_HUMAN	RNA binding motif protein 43	267							nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(2)|large_intestine(3)|lung(2)|ovary(1)	8				BRCA - Breast invasive adenocarcinoma(221;0.131)		TTGGCTGAGAACCAACTTGAA	0.363																																					p.G267G		Atlas-SNP	.											.	RBM43	35	.	0			c.T801C						.						85	81	83					2																	152107693		2203	4300	6503	SO:0001819	synonymous_variant	375287	exon4			CTGAGAACCAACT	AK127552	CCDS2191.1	2q23.3	2007-01-30	2007-01-30	2007-01-30	ENSG00000184898	ENSG00000184898		"RNA binding motif (RRM) containing"	24790	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 38"	C2orf38			Standard	NM_198557		Approved	FLJ45645	uc002txh.3	Q6ZSC3	OTTHUMG00000131866	ENST00000331426.5:c.801T>C	chr2.hg19:g.152107693A>G		152.0	0.0		96.0	4.0	NM_198557	B2RMT5	Silent	SNP	ENST00000331426.5	hg19	CCDS2191.1																																																																																			.	.		0.363	RBM43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254816.2	NM_198557		G	152107693	A	G	152107693	2	3	282	1	0	0	0	0	0	0	0	1	13152	30	2	2		2	RBM43	2	152107693	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	15567362	152107693	91091680	196	40430										
PKP4	8502	hgsc.bcm.edu	37	chr2	159499020	159499020	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtgtaggttagggggaatcaAgcatctggttgaccttctgg	15	6	3	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:159499020A>G	ENST00000389759.3	+	11	1830	c.1718A>G	c.(1717-1719)aAg>aGg	p.K573R	PKP4_ENST00000389757.3_Missense_Mutation_p.K573R	NM_003628.3	NP_003619.2	Q99569	PKP4_HUMAN	plakophilin 4	573					cell-cell junction assembly (GO:0007043)|cell-cell signaling (GO:0007267)|positive regulation of cytokinesis (GO:0032467)|positive regulation of gene expression (GO:0010628)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell adhesion (GO:0030155)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|desmosome (GO:0030057)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)				breast(2)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(21)|ovary(6)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	61						GGGGGAATCAAGCATCTGGTT	0.418										HNSCC(62;0.18)																											p.K573R		Atlas-SNP	.											.	PKP4	133	.	0			c.A1718G						.						110	112	111					2																	159499020		2203	4300	6503	SO:0001583	missense	8502	exon11			GAATCAAGCATCT	X81889	CCDS33305.1, CCDS33306.1	2q24.1	2013-02-14			ENSG00000144283	ENSG00000144283		"Armadillo repeat containing"	9026	protein-coding gene	gene with protein product		604276				9342840, 8937994	Standard	NM_003628		Approved	p0071	uc002tzv.3	Q99569	OTTHUMG00000153969	ENST00000389759.3:c.1718A>G	chr2.hg19:g.159499020A>G	ENSP00000374409:p.Lys573Arg	130.0	0.0		123.0	42.0	NM_001005476	Q86W91	Missense_Mutation	SNP	ENST00000389759.3	hg19	CCDS33305.1	.	.	.	.	.	.	.	.	.	.	A	14.97	2.693650	0.48202	.	.	ENSG00000144283	ENST00000428353;ENST00000389757;ENST00000389759;ENST00000389756	T;T	0.68765	-0.35;-0.35	5.87	5.87	0.94306	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.55705	0.1937	N	0.12182	0.205	0.49299	D	0.999776	B;B;B;B;B	0.32302	0.363;0.107;0.073;0.053;0.313	B;B;B;B;B	0.38194	0.267;0.078;0.031;0.039;0.137	T	0.60434	-0.7264	10	0.56958	D	0.05	-16.9594	16.2813	0.82687	1.0:0.0:0.0:0.0	.	425;528;573;573;424	Q6LCG8;Q4W5T8;Q99569-2;Q99569;F8W7E2	.;.;.;PKP4_HUMAN;.	R	424;573;573;61	ENSP00000374407:K573R;ENSP00000374409:K573R	ENSP00000374406:K61R	K	+	2	0	PKP4	159207266	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.100000	0.71473	2.244000	0.73946	0.533000	0.62120	AAG	.	.		0.418	PKP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333250.1			G	159499020	A	G	159499020	3	3	282	1	0	0	0	0	1	0	0	0	11996	72	3	2	1756	2	PKP4	2	159499020	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	7391327	159499020	83700353	197	40431										
CD302	9936	hgsc.bcm.edu	37	chr2	160628476	160628476	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtgaaacgagaatcagaatgTtttttgtacaggaaccaaat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:160628476delT	ENST00000259053.4	-	6	628	c.585delA	c.(583-585)aaafs	p.K195fs	LY75-CD302_ENST00000504764.1_Frame_Shift_Del_p.K1836fs|CD302_ENST00000429078.2_Frame_Shift_Del_p.K137fs|LY75-CD302_ENST00000505052.1_Frame_Shift_Del_p.K1780fs|LY75_ENST00000554112.1_Frame_Shift_Del_p.K1836fs|LY75_ENST00000553424.1_Frame_Shift_Del_p.K1780fs|CD302_ENST00000480212.1_5'UTR	NM_001198764.1|NM_014880.4	NP_001185693.1|NP_055695.2	Q8IX05	CD302_HUMAN	CD302 molecule	195					phagocytosis (GO:0006909)	cell cortex (GO:0005938)|filopodium (GO:0030175)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|prostate(1)|skin(1)	11						AATCAGAATGTTTTTTGTACA	0.368																																					p.H1837fs		Atlas-INDEL	.											.	.	.	.	0			c.5509delC						.						104	107	106					2																	160628476		2203	4300	6503	SO:0001589	frameshift_variant	100526664	exon39			.	AY314007	CCDS33308.1, CCDS56139.1, CCDS74595.1	2q24.2	2011-08-30	2006-03-28		ENSG00000241399	ENSG00000241399		"CD molecules", "C-type lectin domain containing"	30843	protein-coding gene	gene with protein product	"C-type lectin domain family 13, member A"	612246	"CD302 antigen"			7584026, 7584028	Standard	NM_014880		Approved	DCL-1, KIAA0022, BIMLEC, CLEC13A		Q8IX05	OTTHUMG00000154080	ENST00000259053.4:c.585delA	chr2.hg19:g.160628476delT	ENSP00000259053:p.Lys195fs	230.0	0.0		189.0	12.0	NM_001198759	A8K5G4|B4E2T9|Q15009	Frame_Shift_Del	DEL	ENST00000259053.4	hg19	CCDS33308.1																																																																																			.	.		0.368	CD302-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333760.1	NM_014880		-	160628476	T	-	160628476	7	5	282	1	0	1	0	1	0	0	0	0	3005	1722	60	0	117	0	CD302	2	160628476	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1129456	160628476	82570897	198	40432										
SCN1A	6323	hgsc.bcm.edu	37	chr2	166903299	166903299	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cctgagctgcctcctgttgcTttttaagctgttcaatcatc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:166903299delT	ENST00000303395.4	-	9	1357	c.1358delA	c.(1357-1359)aagfs	p.K453fs	SCN1A_ENST00000423058.2_Frame_Shift_Del_p.K453fs|SCN1A_ENST00000375405.3_Frame_Shift_Del_p.K453fs|SCN1A_ENST00000409050.1_Frame_Shift_Del_p.K453fs|AC010127.3_ENST00000595647.1_RNA|AC010127.3_ENST00000595268.1_RNA|AC010127.3_ENST00000599041.1_RNA			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	453					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CTCCTGTTGCTTTTTAAGCTG	0.468																																					p.K453fs		Atlas-INDEL	.											.	SCN1A	641	.	0			c.1359delG						.						104	92	96					2																	166903299		2203	4300	6503	SO:0001589	frameshift_variant	6323	exon9			.	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10585	protein-coding gene	gene with protein product		182389	"febrile convulsions 3"	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.1358delA	chr2.hg19:g.166903299delT	ENSP00000303540:p.Lys453fs	244.0	0.0		172.0	12.0	NM_001165964	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Frame_Shift_Del	DEL	ENST00000303395.4	hg19	CCDS54413.1																																																																																			.	.		0.468	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		-	166903299	T	-	166903299	7	5	282	1	0	1	0	1	0	0	0	0	13929	1609	56	0	4743	0	SCN1A	2	166903299	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	6274823	166903299	76296074	199	40433										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168103504	168103504	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aagaaattataaaaggtaacAtgctagccacactcaagtca	6	8	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:168103504A>G	ENST00000409195.1	+	9	5691	c.5602A>G	c.(5602-5604)Atg>Gtg	p.M1868V	XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.M1646V|XIRP2_ENST00000295237.9_Missense_Mutation_p.M1868V|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409043.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1693					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AAAAGGTAACATGCTAGCCAC	0.378																																					p.M1868V		Atlas-SNP	.											.	XIRP2	914	.	0			c.A5602G						.						74	67	69					2																	168103504		1873	4107	5980	SO:0001583	missense	129446	exon9			GGTAACATGCTAG	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.5602A>G	chr2.hg19:g.168103504A>G	ENSP00000386840:p.Met1868Val	77.0	0.0		87.0	4.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	hg19	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	A	2.510	-0.313082	0.05422	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.02301	4.35;4.35;4.36	5.46	4.27	0.50696	.	0.520995	0.23169	N	0.051148	T	0.02807	0.0084	L	0.57536	1.79	0.24198	N	0.995521	B;B;B	0.24920	0.07;0.114;0.003	B;B;B	0.20955	0.014;0.032;0.009	T	0.43589	-0.9382	10	0.19590	T	0.45	-0.0097	7.2509	0.26148	0.7042:0.151:0.0:0.1447	.	1693;1693;1646	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	V	1868;1868;1646	ENSP00000386840:M1868V;ENSP00000295237:M1868V;ENSP00000387255:M1646V	ENSP00000295237:M1868V	M	+	1	0	XIRP2	167811750	0.918000	0.31147	0.480000	0.27341	0.287000	0.27160	2.351000	0.44071	0.963000	0.38082	0.528000	0.53228	ATG	.	.		0.378	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		G	168103504	A	G	168103504	3	3	282	1	0	0	0	0	1	0	0	0	17445	217	8	2	5632	2	XIRP2	2	168103504	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1200205	168103504	75095869	200	40434										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168108333	168108333	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gattcacctaaagaagtaagAaaaaattttcaaaagacgtg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:168108333delA	ENST00000409195.1	+	9	10520	c.10431delA	c.(10429-10431)agafs	p.R3477fs	XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409273.1_Frame_Shift_Del_p.R3255fs|XIRP2_ENST00000295237.9_Frame_Shift_Del_p.R3477fs|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409043.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	3302					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AAGAAGTAAGAAAAAATTTTC	0.433																																					p.R3477fs		Atlas-INDEL	.											.,1	XIRP2	914	.	0			c.10430delG						.						58	59	58					2																	168108333		1856	4087	5943	SO:0001589	frameshift_variant	129446	exon9			.	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.10431delA	chr2.hg19:g.168108333delA	ENSP00000386840:p.Arg3477fs	208.0	0.0		175.0	11.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Frame_Shift_Del	DEL	ENST00000409195.1	hg19	CCDS42769.1																																																																																			.	.		0.433	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		-	168108333	A	-	168108333	7	5	282	1	0	1	0	1	0	0	0	0	17445	243	9	0	10461	0	XIRP2	2	168108333	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	4829	168108333	75091040	201	40435										
FASTKD1	79675	hgsc.bcm.edu	37	chr2	170428277	170428277	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggtctctgacatactcagcaTtttttaacaggctggtcttc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:170428277delT	ENST00000453153.2	-	2	609	c.263delA	c.(262-264)aatfs	p.N88fs	FASTKD1_ENST00000453929.2_Frame_Shift_Del_p.N88fs	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	88					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(5)|large_intestine(10)|lung(9)|ovary(4)|prostate(3)	37						ATACTCAGCATTTTTTAACAG	0.343																																					p.N88fs		Atlas-INDEL	.											.	FASTKD1	86	.	0			c.264delT						.						93	87	89					2																	170428277		2203	4300	6503	SO:0001589	frameshift_variant	79675	exon2			.	AL832058	CCDS33318.1, CCDS63051.1	2q31.1	2008-02-05			ENSG00000138399	ENSG00000138399			26150	protein-coding gene	gene with protein product						11347906	Standard	NM_024622		Approved	FLJ21901	uc002uev.4	Q53R41	OTTHUMG00000154953	ENST00000453153.2:c.263delA	chr2.hg19:g.170428277delT	ENSP00000400513:p.Asn88fs	269.0	0.0		227.0	14.0	NM_024622	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Frame_Shift_Del	DEL	ENST00000453153.2	hg19	CCDS33318.1																																																																																			.	.		0.343	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	NM_024622		-	170428277	T	-	170428277	7	5	282	1	0	1	0	1	0	0	0	0	5693	1493	52	0	2336	0	FASTKD1	2	170428277	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2319944	170428277	72771096	202	40436										
GAD1	2571	hgsc.bcm.edu	37	chr2	171715334	171715334	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cctgagcacacaaacgtctgTttttggtatattccacaaag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:171715334delT	ENST00000358196.3	+	16	2092	c.1542delT	c.(1540-1542)tgtfs	p.C514fs		NM_000817.2	NP_000808.2	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 (brain, 67kDa)	514					gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate catabolic process (GO:0006538)|glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|protein-pyridoxal-5-phosphate linkage (GO:0018352)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(15)|ovary(1)|urinary_tract(2)	35						CAAACGTCTGTTTTTGGTATA	0.428																																					p.C514fs		Atlas-INDEL	.											.	GAD1	79	.	0			c.1541delG						.						85	85	85					2																	171715334		2203	4300	6503	SO:0001589	frameshift_variant	2571	exon16			.		CCDS2239.1, CCDS2240.1	2q31	2008-02-05	2002-08-29		ENSG00000128683	ENSG00000128683	4.1.1.15		4092	protein-coding gene	gene with protein product		605363	"glutamate decarboxylase 1 (brain, 67kD)"	GAD		1549570	Standard	XM_005246443		Approved		uc002ugi.3	Q99259	OTTHUMG00000044175	ENST00000358196.3:c.1542delT	chr2.hg19:g.171715334delT	ENSP00000350928:p.Cys514fs	242.0	0.0		182.0	12.0	NM_000817	Q49AK1|Q53TQ7|Q9BU91|Q9UHH4	Frame_Shift_Del	DEL	ENST00000358196.3	hg19	CCDS2239.1																																																																																			.	.		0.428	GAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102664.2			-	171715334	T	-	171715334	7	5	282	1	0	1	0	1	0	0	0	0	6187	1731	60	0	1641	0	GAD1	2	171715334	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1287057	171715334	71484039	203	40437										
TLK1	9874	hgsc.bcm.edu	37	chr2	171923383	171923383	+	Intron	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttttcaaatcatacaagaatAaaacagccatttagaacaac							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:171923383delA	ENST00000431350.2	-	4	735				TLK1_ENST00000521943.1_Intron|TLK1_ENST00000360843.3_Intron|TLK1_ENST00000486857.1_Intron|TLK1_ENST00000434911.2_Frame_Shift_Del_p.L4fs|TLK1_ENST00000442919.2_Intron			Q9UKI8	TLK1_HUMAN	tousled-like kinase 1						cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of chromatin assembly or disassembly (GO:0001672)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|liver(3)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	33						ATACAAGAATAAAACAGCCAT	0.323																																					p.L4fs		Atlas-INDEL	.											.	TLK1	134	.	0			c.12delA						.						27	25	26					2																	171923383		1520	3492	5012	SO:0001627	intron_variant	9874	exon1			.	AB004885	CCDS2241.1, CCDS46447.1, CCDS46448.1	2q31.1	2010-04-19			ENSG00000198586	ENSG00000198586			11841	protein-coding gene	gene with protein product		608438				9427565, 12660173	Standard	NM_012290		Approved	KIAA0137, PKU-BETA	uc002ugp.2	Q9UKI8	OTTHUMG00000132243	ENST00000431350.2:c.331-5717T>-	chr2.hg19:g.171923383delA		229.0	0.0		167.0	11.0	NM_001136555	B3KR15|B4DX87|Q14150|Q8N591|Q9NYH2|Q9Y4F6	Frame_Shift_Del	DEL	ENST00000431350.2	hg19	CCDS2241.1																																																																																			.	.		0.323	TLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255314.1	NM_012290		-	171923383	A	-	171923383	6	5	282	0	1	1	0	1	0	0	0	0	15958	372	13	0		0	TLK1	2	171923383	Intron	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	208049	171923383	71275990	204	40438										
RAPGEF4	11069	hgsc.bcm.edu	37	chr2	173866030	173866030	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctttattatgatgcactgtgTttttatgccaaatacccagc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:173866030delT	ENST00000397081.3	+	17	1759	c.1616delT	c.(1615-1617)gttfs	p.V539fs	RAPGEF4_ENST00000539331.1_Frame_Shift_Del_p.V386fs|RAPGEF4_ENST00000538974.1_Frame_Shift_Del_p.V368fs|RAPGEF4_ENST00000397087.3_Frame_Shift_Del_p.V395fs|RAPGEF4_ENST00000540783.1_Frame_Shift_Del_p.V386fs|RAPGEF4_ENST00000264111.6_Frame_Shift_Del_p.V538fs|RAPGEF4_ENST00000409036.1_Frame_Shift_Del_p.V539fs|RAPGEF4_ENST00000535187.1_Frame_Shift_Del_p.V319fs	NM_007023.3	NP_008954.2	Q8WZA2	RPGF4_HUMAN	Rap guanine nucleotide exchange factor (GEF) 4	539	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				blood coagulation (GO:0007596)|calcium ion-dependent exocytosis (GO:0017156)|cAMP-mediated signaling (GO:0019933)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|insulin secretion (GO:0030073)|platelet activation (GO:0030168)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of exocytosis (GO:0017157)|regulation of insulin secretion (GO:0050796)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase regulator activity (GO:0008603)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			breast(1)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(14)|lung(13)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47			OV - Ovarian serous cystadenocarcinoma(117;0.194)			ATGCACTGTGTTTTTATGCCA	0.408																																					p.V539fs		Atlas-INDEL	.											.	RAPGEF4	103	.	0			c.1615delG						.						189	166	173					2																	173866030		1826	4086	5912	SO:0001589	frameshift_variant	11069	exon17			.	U78516	CCDS42775.1, CCDS42776.1, CCDS63060.1, CCDS63061.1, CCDS74604.1	2q31-q32	2008-02-05	2004-03-26		ENSG00000091428	ENSG00000091428			16626	protein-coding gene	gene with protein product	"cAMP-regulated guanine nucleotide exchange factor II", " exchange protein directly activated by cAMP 2"	606058	"RAP guanine-nucleotide-exchange factor (GEF) 4"			10777494, 9856955	Standard	NM_007023		Approved	cAMP-GEFII, CGEF2	uc002uhv.4	Q8WZA2	OTTHUMG00000133677	ENST00000397081.3:c.1616delT	chr2.hg19:g.173866030delT	ENSP00000380271:p.Val539fs	215.0	0.0		118.0	10.0	NM_007023	B2R7R3|B7Z283|B7Z3T6|B7Z912|O95636|Q8IXK6|Q8TAA4	Frame_Shift_Del	DEL	ENST00000397081.3	hg19	CCDS42775.1																																																																																			.	.		0.408	RAPGEF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257864.2	NM_007023		-	173866030	T	-	173866030	7	5	282	1	0	1	0	1	0	0	0	0	13061	1725	60	0	1698	0	RAPGEF4	2	173866030	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1942647	173866030	69333343	205	40439										
CHRNA1	1134	hgsc.bcm.edu	37	chr2	175622346	175622346	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cttttctgaaggaatgtgaaTttttttcacaccgccatagt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:175622346delT	ENST00000261007.5	-	5	433	c.367delA	c.(367-369)attfs	p.I123fs	CHRNA1_ENST00000348749.5_Frame_Shift_Del_p.I98fs|CHRNA1_ENST00000409219.1_Frame_Shift_Del_p.I98fs|CHRNA1_ENST00000409542.1_Intron|CHRNA1_ENST00000409323.1_Frame_Shift_Del_p.I98fs|AC018890.6_ENST00000442996.1_RNA	NM_001039523.2	NP_001034612.1	P02708	ACHA_HUMAN	cholinergic receptor, nicotinic, alpha 1 (muscle)	123					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|muscle cell cellular homeostasis (GO:0046716)|musculoskeletal movement (GO:0050881)|neuromuscular junction development (GO:0007528)|neuromuscular process (GO:0050905)|neuromuscular synaptic transmission (GO:0007274)|neuron cellular homeostasis (GO:0070050)|neuronal action potential (GO:0019228)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue growth (GO:0048630)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cell surface (GO:0009986)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ion channel activity (GO:0005216)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(3)|prostate(3)|skin(4)	37					Galantamine(DB00674)	GGAATGTGAATTTTTTTCACA	0.443																																					p.I123fs		Atlas-INDEL	.											.	CHRNA1	92	.	0			c.368delT						.						83	81	82					2																	175622346		2203	4300	6503	SO:0001589	frameshift_variant	1134	exon5			.	Y00762	CCDS2261.1, CCDS33331.1	2q31.1	2012-02-11	2006-02-01		ENSG00000138435	ENSG00000138435		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1955	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 1 (muscle)"	100690	"cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle)"	CHRNA			Standard	NM_001039523		Approved		uc002uje.2	P02708	OTTHUMG00000132357	ENST00000261007.5:c.367delA	chr2.hg19:g.175622346delT	ENSP00000261007:p.Ile123fs	253.0	0.0		179.0	11.0	NM_001039523	B4DRV6|D3DPE8	Frame_Shift_Del	DEL	ENST00000261007.5	hg19	CCDS33331.1																																																																																			.	.		0.443	CHRNA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000334116.1			-	175622346	T	-	175622346	7	5	282	1	0	1	0	1	0	0	0	0	3383	1493	52	0	1105	0	CHRNA1	2	175622346	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1756316	175622346	67577027	206	40440										
CHN1	1123	hgsc.bcm.edu	37	chr2	175666522	175666522	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	catgaagggtttccaattgcTcatccggatccataatttct	7	10	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:175666522T>C	ENST00000409900.3	-	12	1434	c.1121A>G	c.(1120-1122)gAg>gGg	p.E374G	CHN1_ENST00000409597.1_Missense_Mutation_p.E190G|CHN1_ENST00000488080.1_5'UTR|CHN1_ENST00000409156.3_Missense_Mutation_p.E348G|CHN1_ENST00000295497.7_Missense_Mutation_p.E249G	NM_001822.5	NP_001813.1	P15882	CHIN_HUMAN	chimerin 1	374	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				ephrin receptor signaling pathway (GO:0048013)|motor neuron axon guidance (GO:0008045)|positive regulation of signal transduction (GO:0009967)|regulation of axonogenesis (GO:0050770)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(117;0.226)			TTCCAATTGCTCATCCGGATC	0.408			T	TAF15	extraskeletal myxoid chondrosarcoma																																p.E374G		Atlas-SNP	.		Dom	yes		2	2q31-q32.1	1123	chimerin (chimaerin) 1		M	.	CHN1	67	.	0			c.A1121G						.						177	175	176					2																	175666522		1933	4142	6075	SO:0001583	missense	1123	exon12			AATTGCTCATCCG		CCDS46454.1, CCDS46455.1, CCDS56147.1	2q31-q32.1	2013-02-14	2012-10-17		ENSG00000128656	ENSG00000128656		"Rho GTPase activating proteins", "SH2 domain containing"	1943	protein-coding gene	gene with protein product	"Chimerin 1 (GTPase-activating protein, rho, 2)", "chimaerin 1"	118423	"Duane retraction syndrome 2", "chimerin (chimaerin) 1"	CHN, DURS2		2299665, 15013773, 18653847	Standard	NM_001822		Approved	RhoGAP2, ARHGAP2, n-chimerin	uc002uji.3	P15882	OTTHUMG00000154225	ENST00000409900.3:c.1121A>G	chr2.hg19:g.175666522T>C	ENSP00000386741:p.Glu374Gly	151.0	0.0		131.0	7.0	NM_001822	A8K1M6|B3KNU6|B4DV19|Q53SD6|Q53SH5|Q96FB0	Missense_Mutation	SNP	ENST00000409900.3	hg19	CCDS46455.1	.	.	.	.	.	.	.	.	.	.	T	18.55	3.648972	0.67358	.	.	ENSG00000128656	ENST00000409900;ENST00000295497;ENST00000409597;ENST00000409156;ENST00000409089;ENST00000444394	T;T;T;T;T;T	0.22945	1.93;1.93;1.93;1.93;1.93;1.93	5.42	5.42	0.78866	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.094279	0.64402	D	0.000001	T	0.28034	0.0691	M	0.63208	1.945	0.80722	D	1	B;B;B	0.15930	0.015;0.009;0.007	B;B;B	0.17979	0.02;0.012;0.007	T	0.06698	-1.0812	10	0.56958	D	0.05	.	11.0068	0.47639	0.0:0.0:0.1558:0.8442	.	348;374;249	B4DV19;P15882;P15882-2	.;CHIN_HUMAN;.	G	374;249;190;348;166;149	ENSP00000386741:E374G;ENSP00000295497:E249G;ENSP00000386469:E190G;ENSP00000386470:E348G;ENSP00000386322:E166G;ENSP00000411911:E149G	ENSP00000295497:E249G	E	-	2	0	CHN1	175374768	1.000000	0.71417	0.991000	0.47740	0.996000	0.88848	6.193000	0.72075	2.173000	0.68751	0.482000	0.46254	GAG	.	.		0.408	CHN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334453.1	NM_001822		C	175666522	T	C	175666522	3	2	282	1	0	0	0	0	1	0	0	0	3364	1551	54	2	266	2	CHN1	2	175666522	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	44176	175666522	67532851	207	40441										
TTN	7273	hgsc.bcm.edu	37	chr2	179485563	179485563	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctgagggtgtagactaggtcTttttggagaatgatgtattt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:179485563delT	ENST00000591111.1	-	197	41075	c.40851delA	c.(40849-40851)aaafs	p.K13617fs	TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Frame_Shift_Del_p.K12690fs|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Frame_Shift_Del_p.K6318fs|TTN-AS1_ENST00000604956.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000460472.2_Frame_Shift_Del_p.K6193fs|TTN_ENST00000589042.1_Frame_Shift_Del_p.K15258fs|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000342175.6_Frame_Shift_Del_p.K6385fs|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13617	Ig-like 92.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGACTAGGTCTTTTTGGAGAA	0.368																																					p.D15259fs		Atlas-INDEL	.											.	TTN	18412	.	0			c.45775delG						.						172	167	168					2																	179485563		1870	4093	5963	SO:0001589	frameshift_variant	7273	exon247			.	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.40851delA	chr2.hg19:g.179485563delT	ENSP00000465570:p.Lys13617fs	244.0	0.0		154.0	10.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Frame_Shift_Del	DEL	ENST00000591111.1	hg19																																																																																				.	.		0.368	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		-	179485563	T	-	179485563	7	5	282	1	0	1	0	1	0	0	0	0	16750	1606	56	0	62383	0	TTN	2	179485563	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3819041	179485563	63713810	208	40442										
TTN	7273	hgsc.bcm.edu	37	chr2	179600364	179600364	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgctattttatcttcaaaacAgatcttataatctttccctg	3	9	4	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:179600364A>G	ENST00000591111.1	-	48	14082	c.13858T>C	c.(13858-13860)Tgt>Cgt	p.C4620R	TTN_ENST00000342992.6_Missense_Mutation_p.C3693R|TTN-AS1_ENST00000582847.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.C4937R|TTN_ENST00000342175.6_Intron			Q8WZ42	TITIN_HUMAN	titin	12372	Ig-like 26.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCTTCAAAACAGATCTTATAA	0.433																																					p.C4937R		Atlas-SNP	.											.	TTN	18412	.	0			c.T14809C						.						73	71	72					2																	179600364		1838	4081	5919	SO:0001583	missense	7273	exon50			CAAAACAGATCTT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.13858T>C	chr2.hg19:g.179600364A>G	ENSP00000465570:p.Cys4620Arg	116.0	0.0		121.0	6.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	9.169	1.020586	0.19433	.	.	ENSG00000155657	ENST00000342992	T	0.64803	-0.12	5.77	4.55	0.56014	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.60919	0.2306	M	0.66939	2.045	0.80722	D	1	B	0.13145	0.007	B	0.21151	0.033	T	0.63571	-0.6607	9	0.87932	D	0	.	12.1032	0.53796	0.8715:0.0:0.0:0.1285	.	4620	Q8WZ42	TITIN_HUMAN	R	3693	ENSP00000343764:C3693R	ENSP00000343764:C3693R	C	-	1	0	TTN	179308609	1.000000	0.71417	0.998000	0.56505	0.930000	0.56654	3.947000	0.56652	2.326000	0.78906	0.533000	0.62120	TGT	.	.		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179600364	A	G	179600364	3	3	282	1	0	0	0	0	1	0	0	0	16750	188	7	2	89972	2	TTN	2	179600364	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	114801	179600364	63599009	209	40443										
ITGA4	3676	hgsc.bcm.edu	37	chr2	182339748	182339748	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gagagagacaatcagtggttGggggtcacactttccagaca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:182339748delG	ENST00000397033.2	+	3	811	c.381delG	c.(379-381)ttgfs	p.L127fs	ITGA4_ENST00000339307.4_Frame_Shift_Del_p.L127fs|ITGA4_ENST00000478440.1_3'UTR	NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	127					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|chorio-allantoic fusion (GO:0060710)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|face development (GO:0060324)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|negative regulation of protein homodimerization activity (GO:0090074)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha4-beta7 complex (GO:0034669)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)|Tinzaparin(DB06822)	ATCAGTGGTTGGGGGTCACAC	0.438																																					p.L127fs		Atlas-INDEL	.											.	ITGA4	142	.	0			c.380delT						.						92	92	92					2																	182339748		1899	4127	6026	SO:0001589	frameshift_variant	3676	exon3			.		CCDS42788.1	2q31-q32	2010-03-23			ENSG00000115232	ENSG00000115232		"CD molecules", "Integrins"	6140	protein-coding gene	gene with protein product		192975		CD49D		1537388	Standard	NM_000885		Approved	CD49d	uc002unu.3	P13612	OTTHUMG00000154212	ENST00000397033.2:c.381delG	chr2.hg19:g.182339748delG	ENSP00000380227:p.Leu127fs	322.0	0.0		250.0	15.0	NM_000885	D3DPG4|Q7Z4L6	Frame_Shift_Del	DEL	ENST00000397033.2	hg19	CCDS42788.1																																																																																			.	.		0.438	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1			-	182339748	G	-	182339748	7	5	282	1	0	1	0	1	0	0	0	0	7887	1339	47	0	391	0	ITGA4	2	182339748	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	2739384	182339748	60859625	210	40444										
CERKL	375298	hgsc.bcm.edu	37	chr2	182430832	182430832	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttaagcagtgacagagcgtgCccttcatattccattactat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:182430832delC	ENST00000339098.5	-	4	629	c.630delG	c.(628-630)gggfs	p.G210fs	CERKL_ENST00000479558.1_5'UTR|CERKL_ENST00000374969.2_Intron|CERKL_ENST00000374970.2_Intron|CERKL_ENST00000410087.3_Frame_Shift_Del_p.G210fs|CERKL_ENST00000409440.3_Frame_Shift_Del_p.G166fs			Q49MI3	CERKL_HUMAN	ceramide kinase-like	210	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.			G -> E (in Ref. 2; CAG26977). {ECO:0000305}.	negative regulation of apoptotic process (GO:0043066)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(13)|ovary(3)|skin(3)	32			OV - Ovarian serous cystadenocarcinoma(117;0.088)			ACAGAGCGTGCCCTTCATATT	0.308																																					p.H211fs		Atlas-INDEL	.											.	CERKL	138	.	0			c.631delC						.						82	77	79					2																	182430832		1830	4098	5928	SO:0001589	frameshift_variant	375298	exon4			.	BC020465	CCDS33340.1, CCDS33341.1, CCDS42789.1, CCDS46466.1, CCDS54425.1	2q31.3	2005-01-04			ENSG00000188452	ENSG00000188452			21699	protein-coding gene	gene with protein product			"retinitis pigmentosa 26 (autosomal recessive)"	RP26		14681825	Standard	NR_027689		Approved		uc002uny.3	Q49MI3	OTTHUMG00000154315	ENST00000339098.5:c.630delG	chr2.hg19:g.182430832delC	ENSP00000341159:p.Gly210fs	318.0	0.0		265.0	17.0	NM_001030311	B2RPL2|B4DEY1|Q49MH9|Q49MI0|Q49MI1|Q49MI2|Q5DVJ2|Q5DVJ4|Q5DVJ5|Q6UZF6|Q6ZP59	Frame_Shift_Del	DEL	ENST00000339098.5	hg19	CCDS42789.1																																																																																			.	.		0.308	CERKL-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334811.1			-	182430832	C	-	182430832	7	5	282	1	0	1	0	1	0	0	0	0	3270	726	26	0	1090	0	CERKL	2	182430832	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	91084	182430832	60768541	211	40445										
DNAJC10	54431	hgsc.bcm.edu	37	chr2	183582853	183582865	+	Frame_Shift_Del	DEL	TTGAAAAGGATCA	TTGAAAAGGATCA	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aagatgactatatcagagacTtgaaaaggatcattctctgt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	TTGAAAAGGATCA	TTGAAAAGGATCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:183582853_183582865delTTGAAAAGGATCA	ENST00000264065.7	+	3	455_467	c.40_52delTTGAAAAGGATCA	c.(40-54)ttgaaaaggatcattfs	p.LKRII14fs	DNAJC10_ENST00000469118.1_Intron|DNAJC10_ENST00000537515.1_Frame_Shift_Del_p.LKRII14fs	NM_018981.1	NP_061854.1	Q8IXB1	DJC10_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 10	14					cell redox homeostasis (GO:0045454)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of ATPase activity (GO:0032781)|protein folding in endoplasmic reticulum (GO:0034975)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum chaperone complex (GO:0034663)|endoplasmic reticulum lumen (GO:0005788)|membrane (GO:0016020)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|chaperone binding (GO:0051087)|disulfide oxidoreductase activity (GO:0015036)|Hsp70 protein binding (GO:0030544)|misfolded protein binding (GO:0051787)|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor (GO:0016671)|protein disulfide oxidoreductase activity (GO:0015035)			breast(3)|endometrium(1)|kidney(4)|large_intestine(7)|lung(15)|ovary(1)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			TATCAGAGACTTGAAAAGGATCATTCTCTGTTT	0.366																																					p.13_17del	Pancreas(56;860 1183 25669 35822 48585)	Atlas-INDEL	.											.	DNAJC10	76	.	0			c.39_51del						.																																			SO:0001589	frameshift_variant	54431	exon3			.		CCDS33345.1, CCDS74613.1	2q32.1	2011-11-23			ENSG00000077232	ENSG00000077232		"Heat shock proteins / DNAJ (HSP40)", "Protein disulfide isomerases"	24637	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 19"	607987				12411443, 12446677	Standard	NM_018981		Approved	ERdj5, PDIA19	uc002uow.2	Q8IXB1	OTTHUMG00000154209	ENST00000264065.7:c.40_52delTTGAAAAGGATCA	chr2.hg19:g.183582853_183582865delTTGAAAAGGATCA	ENSP00000264065:p.Leu14fs	156.0	0.0		79.0	13.0	NM_001271581	Q17RJ6|Q3B7W8|Q4ZG06|Q53QT7|Q6UWZ6|Q86T61|Q8NC82|Q8TD87|Q96K38|Q96K44|Q96K54|Q9NSY6	Frame_Shift_Del	DEL	ENST00000264065.7	hg19	CCDS33345.1																																																																																			.	.		0.366	DNAJC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334418.2	NM_018981		-	183582865	TTGAAAAGGATCA	-	183582853	7	5	282	1	0	1	0	1	0	0	0	0	4631	1606	56	0	42	0	DNAJC10	2	183582853	Frame_Shift_Del	DEL	TTGAAAAGGATCA	TCGA-G3-A3CJ-01A-11D-A20W-10	1152021	183582853	59616520	212	40446										
NCKAP1	10787	hgsc.bcm.edu	37	chr2	183822266	183822266	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cccctttcttaccagtctgcTtttttgatttcttattcact							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:183822266delT	ENST00000361354.4	-	19	2312	c.1940delA	c.(1939-1941)aagfs	p.K647fs	NCKAP1_ENST00000360982.2_Frame_Shift_Del_p.K653fs	NM_013436.3	NP_038464.1	Q9Y2A7	NCKP1_HUMAN	NCK-associated protein 1	647					apical protein localization (GO:0045176)|apoptotic process (GO:0006915)|basal protein localization (GO:0045175)|central nervous system development (GO:0007417)|embryonic body morphogenesis (GO:0010172)|embryonic foregut morphogenesis (GO:0048617)|embryonic heart tube development (GO:0035050)|endoderm development (GO:0007492)|establishment or maintenance of actin cytoskeleton polarity (GO:0030950)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|mesodermal cell migration (GO:0008078)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|paraxial mesoderm morphogenesis (GO:0048340)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|positive regulation of lamellipodium assembly (GO:0010592)|protein stabilization (GO:0050821)|Rac protein signal transduction (GO:0016601)|regulation of protein localization (GO:0032880)|somitogenesis (GO:0001756)|zygotic determination of anterior/posterior axis, embryo (GO:0007354)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|SCAR complex (GO:0031209)	protein complex binding (GO:0032403)			breast(3)|cervix(2)|endometrium(3)|kidney(4)|large_intestine(11)|lung(16)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			ACCAGTCTGCTTTTTTGATTT	0.378																																					p.K653fs		Atlas-INDEL	.											.	NCKAP1	105	.	0			c.1959delG						.						172	154	160					2																	183822266		2203	4300	6503	SO:0001589	frameshift_variant	10787	exon20			.	AB014509	CCDS2287.1, CCDS2288.1	2q32	2009-08-14			ENSG00000061676	ENSG00000061676			7666	protein-coding gene	gene with protein product		604891				10673335, 12181570, 9344857	Standard	NM_013436		Approved	Nap1, HEM2, NAP125	uc002upb.4	Q9Y2A7	OTTHUMG00000132623	ENST00000361354.4:c.1940delA	chr2.hg19:g.183822266delT	ENSP00000355348:p.Lys647fs	243.0	0.0		190.0	14.0	NM_205842	O60329|Q53QN5|Q53S94|Q53Y35	Frame_Shift_Del	DEL	ENST00000361354.4	hg19	CCDS2287.1																																																																																			.	.		0.378	NCKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255867.2	NM_205842		-	183822266	T	-	183822266	7	5	282	1	0	1	0	1	0	0	0	0	10230	1609	56	0	1498	0	NCKAP1	2	183822266	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	239413	183822266	59377107	213	40447										
TFPI	7035	hgsc.bcm.edu	37	chr2	188349646	188349646	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctgttttgtctgattgttatAaaaatacctggtaatataac							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:188349646delA	ENST00000233156.3	-	5	721	c.427delT	c.(427-429)tatfs	p.Y143fs	AC007319.1_ENST00000453517.1_RNA|TFPI_ENST00000339091.4_Frame_Shift_Del_p.Y143fs|AC007319.1_ENST00000412276.1_RNA|TFPI_ENST00000409676.1_Frame_Shift_Del_p.Y143fs|TFPI_ENST00000392365.1_Frame_Shift_Del_p.Y143fs	NM_006287.4	NP_006278.1	P10646	TFPI1_HUMAN	tissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor)	143	BPTI/Kunitz inhibitor 2. {ECO:0000255|PROSITE-ProRule:PRU00031}.				blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|negative regulation of endopeptidase activity (GO:0010951)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.0554)		Coagulation factor VIIa(DB00036)|Dalteparin(DB06779)	TGATTGTTATAAAAATACCTG	0.343																																					p.Y143fs		Atlas-INDEL	.											.	TFPI	66	.	0			c.428delA						.						93	92	92					2																	188349646		2202	4296	6498	SO:0001589	frameshift_variant	7035	exon5			.		CCDS2294.1, CCDS33349.1	2q32	2008-06-02			ENSG00000003436	ENSG00000003436			11760	protein-coding gene	gene with protein product	"extrinsic pathway inhibitor"	152310		LACI		1993173	Standard	XM_005246818		Approved	EPI, TFI, TFPI1	uc002upy.3	P10646	OTTHUMG00000132634	ENST00000233156.3:c.427delT	chr2.hg19:g.188349646delA	ENSP00000233156:p.Tyr143fs	246.0	0.0		165.0	10.0	NM_001032281	O95103|Q53TS4	Frame_Shift_Del	DEL	ENST00000233156.3	hg19	CCDS2294.1																																																																																			.	.		0.343	TFPI-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255881.1	NM_006287		-	188349646	A	-	188349646	7	5	282	1	0	1	0	1	0	0	0	0	15823	362	13	0	635	0	TFPI	2	188349646	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	4527380	188349646	54849727	214	40448										
ANKAR	150709	hgsc.bcm.edu	37	chr2	190585478	190585478	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgtgagagaacataaaggccTcccatatcttatcagatttc	7	9	2	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:190585478T>C	ENST00000520309.1	+	12	2688	c.2600T>C	c.(2599-2601)cTc>cCc	p.L867P	ANKAR_ENST00000431575.2_Missense_Mutation_p.L796P|ANKAR_ENST00000281412.6_Missense_Mutation_p.L631P|ANKAR_ENST00000313581.4_Missense_Mutation_p.L867P|ANKAR_ENST00000438402.2_Missense_Mutation_p.L867P	NM_144708.3	NP_653309.3	Q7Z5J8	ANKAR_HUMAN	ankyrin and armadillo repeat containing	867						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|liver(2)|lung(16)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(2)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00156)|Epithelial(96;0.0256)|all cancers(119;0.0744)			CATAAAGGCCTCCCATATCTT	0.328																																					p.L867P		Atlas-SNP	.											.	ANKAR	184	.	0			c.T2600C						.						194	216	208					2																	190585478		2203	4300	6503	SO:0001583	missense	150709	exon12			AAGGCCTCCCATA	AJ549812	CCDS33351.1, CCDS33351.2	2q32.2	2013-02-14			ENSG00000151687	ENSG00000151687		"Ankyrin repeat domain containing", "Armadillo repeat containing"	26350	protein-coding gene	gene with protein product		609803				15110750	Standard	NM_144708		Approved	FLJ25415	uc002uqw.2	Q7Z5J8	OTTHUMG00000154398	ENST00000520309.1:c.2600T>C	chr2.hg19:g.190585478T>C	ENSP00000427882:p.Leu867Pro	75.0	0.0		69.0	5.0	NM_144708	Q3ZCS6|Q4G0M2|Q6ZU02	Missense_Mutation	SNP	ENST00000520309.1	hg19	CCDS33351.2	.	.	.	.	.	.	.	.	.	.	T	14.97	2.694602	0.48202	.	.	ENSG00000151687	ENST00000520309;ENST00000313581;ENST00000438402;ENST00000431575;ENST00000281412	T;T;T;T;T	0.38722	1.12;1.12;1.12;1.12;1.12	4.84	4.84	0.62591	.	0.360162	0.25275	N	0.031844	T	0.39436	0.1078	N	0.19112	0.55	0.53688	D	0.99997	.	.	.	.	.	.	T	0.40421	-0.9564	8	0.66056	D	0.02	-3.9671	13.541	0.61674	0.0:0.0:0.0:1.0	.	.	.	.	P	867;867;867;796;631	ENSP00000427882:L867P;ENSP00000313513:L867P;ENSP00000397243:L867P;ENSP00000393043:L796P;ENSP00000281412:L631P	ENSP00000281412:L631P	L	+	2	0	ANKAR	190293723	1.000000	0.71417	0.920000	0.36463	0.223000	0.24884	3.763000	0.55257	2.054000	0.61138	0.533000	0.62120	CTC	.	.		0.328	ANKAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335045.3	NM_144708		C	190585478	T	C	190585478	3	2	282	1	0	0	0	0	1	0	0	0	623	1551	54	2	2642	2	ANKAR	2	190585478	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2235832	190585478	52613895	215	40449										
PMS1	5378	hgsc.bcm.edu	37	chr2	190719401	190719401	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cgttaagcacacccagtcagAaaatggcaataaagaccata							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:190719401delA	ENST00000441310.2	+	9	1636	c.1403delA	c.(1402-1404)gaafs	p.E468fs	PMS1_ENST00000447232.2_Frame_Shift_Del_p.E468fs|PMS1_ENST00000409823.3_Frame_Shift_Del_p.E429fs|PMS1_ENST00000421722.1_3'UTR|PMS1_ENST00000432292.3_Frame_Shift_Del_p.E292fs|PMS1_ENST00000418224.3_Frame_Shift_Del_p.E292fs	NM_000534.4	NP_000525.1	P54277	PMS1_HUMAN	PMS1 postmeiotic segregation increased 1 (S. cerevisiae)	468					ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)	MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|mismatched DNA binding (GO:0030983)|single-stranded DNA binding (GO:0003697)	p.N469fs*7(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(16)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			OV - Ovarian serous cystadenocarcinoma(117;0.0013)|Epithelial(96;0.0263)|all cancers(119;0.0751)			ACCCAGTCAGAAAATGGCAAT	0.403			"Mis, N"			"colorectal, endometrial, ovarian"		Direct reversal of damage;Mismatch excision repair (MMR)																													p.E468fs		Atlas-INDEL	.	yes	Rec		Hereditary non-polyposis colorectal cancer	2	2q31-q33	5378	PMS1 postmeiotic segregation increased 1 (S. cerevisiae)		E	.	PMS1	78	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1402delG						.						54	58	56					2																	190719401		2202	4297	6499	SO:0001589	frameshift_variant	5378	exon9			.		CCDS2302.1, CCDS46473.1, CCDS46474.1, CCDS74615.1	2q31-q33	2014-09-17	2001-11-28		ENSG00000064933	ENSG00000064933			9121	protein-coding gene	gene with protein product		600258	"postmeiotic segregation increased (S. cerevisiae) 1"	PMSL1		8072530	Standard	NM_000534		Approved		uc002urh.4	P54277	OTTHUMG00000132664	ENST00000441310.2:c.1403delA	chr2.hg19:g.190719401delA	ENSP00000406490:p.Glu468fs	169.0	0.0		121.0	10.0	NM_001128144	D3DPI1|Q4VAL4|Q5FBZ3|Q5FBZ6|Q5FBZ8	Frame_Shift_Del	DEL	ENST00000441310.2	hg19	CCDS2302.1																																																																																			.	.		0.403	PMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255918.2			-	190719401	A	-	190719401	7	5	282	1	0	1	0	1	0	0	0	0	12151	246	9	0	1433	0	PMS1	2	190719401	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	133923	190719401	52479972	216	40450										
GLS	2744	hgsc.bcm.edu	37	chr2	191769844	191769844	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tatgtgcatcgatatgttggAaaagagccgagtggactaag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:191769844delA	ENST00000320717.3	+	6	1188	c.930delA	c.(928-930)ggafs	p.G310fs	GLS_ENST00000338435.4_Frame_Shift_Del_p.G310fs	NM_014905.4	NP_055720.3	O94925	GLSK_HUMAN	glutaminase	310					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate biosynthetic process (GO:0006537)|glutamate secretion (GO:0014047)|glutamine catabolic process (GO:0006543)|neurotransmitter secretion (GO:0007269)|protein homotetramerization (GO:0051289)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|small molecule metabolic process (GO:0044281)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	glutaminase activity (GO:0004359)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	16			OV - Ovarian serous cystadenocarcinoma(117;0.00625)|Epithelial(96;0.0744)|all cancers(119;0.181)		L-Glutamine(DB00130)	GATATGTTGGAAAAGAGCCGA	0.338																																					p.G310fs		Atlas-INDEL	.											.	GLS	47	.	0			c.929delG						.						125	124	124					2																	191769844		2203	4300	6503	SO:0001589	frameshift_variant	2744	exon6			.	AB020645	CCDS2308.1, CCDS58744.1	2q32-q34	2013-01-10			ENSG00000115419	ENSG00000115419	3.5.1.2	"Ankyrin repeat domain containing"	4331	protein-coding gene	gene with protein product		138280				10048485	Standard	NM_014905		Approved	KIAA0838, GLS1	uc002usf.3	O94925	OTTHUMG00000132701	ENST00000320717.3:c.930delA	chr2.hg19:g.191769844delA	ENSP00000317379:p.Gly310fs	222.0	0.0		147.0	11.0	NM_001256310	Q9UL05|Q9UL06|Q9UL07|Q9UN40	Frame_Shift_Del	DEL	ENST00000320717.3	hg19	CCDS2308.1																																																																																			.	.		0.338	GLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255999.2			-	191769844	A	-	191769844	7	5	282	1	0	1	0	1	0	0	0	0	6471	233	9	0	952	0	GLS	2	191769844	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1050443	191769844	51429529	217	40451										
STAT1	6772	hgsc.bcm.edu	37	chr2	191862950	191862950	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agtaaataactacctttctcTtattgtcaagcattaaatac	3	8	2	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:191862950T>C	ENST00000361099.3	-	8	1013	c.626A>G	c.(625-627)aAg>aGg	p.K209R	STAT1_ENST00000409465.1_Missense_Mutation_p.K209R|STAT1_ENST00000392322.3_Missense_Mutation_p.K209R|STAT1_ENST00000540176.1_Intron|STAT1_ENST00000392323.2_Missense_Mutation_p.K211R	NM_007315.3	NP_009330.1	P42224	STAT1_HUMAN	signal transducer and activator of transcription 1, 91kDa	209					apoptotic process (GO:0006915)|blood circulation (GO:0008015)|cellular response to insulin stimulus (GO:0032869)|cellular response to interferon-beta (GO:0035458)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchymal cell proliferation involved in metanephros development (GO:0072136)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of macrophage fusion (GO:0034240)|negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003340)|negative regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072308)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|renal tubule development (GO:0061326)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|transcription from RNA polymerase II promoter (GO:0006366)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|tumor necrosis factor receptor binding (GO:0005164)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			OV - Ovarian serous cystadenocarcinoma(117;0.00434)|Epithelial(96;0.0555)|all cancers(119;0.141)			TACCTTTCTCTTATTGTCAAG	0.348																																					p.K209R		Atlas-SNP	.											.	STAT1	93	.	0			c.A626G						.						139	132	134					2																	191862950		2202	4297	6499	SO:0001583	missense	6772	exon8			TTTCTCTTATTGT		CCDS2309.1, CCDS42793.1	2q32.2-q32.3	2014-09-17	2002-08-29		ENSG00000115415	ENSG00000115415		"SH2 domain containing"	11362	protein-coding gene	gene with protein product	"transcription factor ISGF-3 components p91/p84"	600555	"signal transducer and activator of transcription 1, 91kD"			7885841	Standard	NM_139266		Approved	STAT91, ISGF-3	uc002usj.2	P42224	OTTHUMG00000132699	ENST00000361099.3:c.626A>G	chr2.hg19:g.191862950T>C	ENSP00000354394:p.Lys209Arg	128.0	0.0		69.0	4.0	NM_007315	A8K989|B2RCA0|D2KFR8|D3DPI7|Q53S88|Q53XW4|Q68D00|Q9UDL5	Missense_Mutation	SNP	ENST00000361099.3	hg19	CCDS2309.1	.	.	.	.	.	.	.	.	.	.	T	10.06	1.247059	0.22796	.	.	ENSG00000115415	ENST00000361099;ENST00000409465;ENST00000392322;ENST00000392323;ENST00000544783	T;T;T;T	0.61274	0.12;0.12;0.12;0.12	4.89	4.89	0.63831	STAT transcription factor, all-alpha (2);STAT transcription factor, coiled coil (1);	0.043563	0.85682	D	0.000000	T	0.47893	0.1470	L	0.58354	1.805	0.80722	D	1	B;B	0.14805	0.011;0.009	B;B	0.21151	0.033;0.02	T	0.39583	-0.9607	10	0.15066	T	0.55	-38.7538	6.6173	0.22784	0.1386:0.077:0.0:0.7844	.	209;209	P42224-2;P42224	.;STAT1_HUMAN	R	209;209;209;211;117	ENSP00000354394:K209R;ENSP00000386244:K209R;ENSP00000376136:K209R;ENSP00000376137:K211R	ENSP00000354394:K209R	K	-	2	0	STAT1	191571195	1.000000	0.71417	0.992000	0.48379	0.679000	0.39708	3.548000	0.53670	2.052000	0.61016	0.533000	0.62120	AAG	.	.		0.348	STAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255997.3	NM_007315		C	191862950	T	C	191862950	3	2	282	1	0	0	0	0	1	0	0	0	15279	1609	56	2	1702	2	STAT1	2	191862950	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	93106	191862950	51336423	218	40452										
SGOL2	151246	hgsc.bcm.edu	37	chr2	201436349	201436349	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttcagatgtcgatattggggAaaagattgaaaacaggacag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:201436349delA	ENST00000357799.4	+	7	1378	c.1280delA	c.(1279-1281)gaafs	p.E427fs		NM_001160033.1|NM_001160046.1|NM_152524.5	NP_001153505.1|NP_001153518.1|NP_689737.4	Q562F6	SGOL2_HUMAN	shugoshin-like 2 (S. pombe)	427					meiotic sister chromatid cohesion, centromeric (GO:0051754)|mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)				NS(2)|breast(2)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	46						GATATTGGGGAAAAGATTGAA	0.378																																					p.E427fs		Atlas-INDEL	.											.	SGOL2	126	.	0			c.1279delG						.						79	77	77					2																	201436349		1831	4078	5909	SO:0001589	frameshift_variant	151246	exon7			.	AY094614	CCDS42796.1	2q33.2	2008-02-05			ENSG00000163535	ENSG00000163535			30812	protein-coding gene	gene with protein product		612425					Standard	NM_001160046		Approved	TRIPIN, FLJ25211	uc002uvw.2	Q562F6	OTTHUMG00000154535	ENST00000357799.4:c.1280delA	chr2.hg19:g.201436349delA	ENSP00000350447:p.Glu427fs	216.0	0.0		179.0	11.0	NM_001160046	Q53RR9|Q53T20|Q86XY4|Q8IWK2|Q8IZK1|Q8N1Q5|Q96LQ3	Frame_Shift_Del	DEL	ENST00000357799.4	hg19	CCDS42796.1																																																																																			.	.		0.378	SGOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335834.1	NM_152524		-	201436349	A	-	201436349	7	5	282	1	0	1	0	1	0	0	0	0	14232	246	9	0	1302	0	SGOL2	2	201436349	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	9573399	201436349	41763024	219	40453										
TRAK2	66008	hgsc.bcm.edu	37	chr2	202245603	202245603	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tctcagctggtcgagaggccAaaaaattttcagagagatgc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:202245603delA	ENST00000332624.3	-	16	2836	c.2408delT	c.(2407-2409)ttgfs	p.L803fs		NM_015049.2	NP_055864.2	O60296	TRAK2_HUMAN	trafficking protein, kinesin binding 2	803					protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|endosome (GO:0005768)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GABA receptor binding (GO:0050811)|receptor binding (GO:0005102)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	23						TCGAGAGGCCAAAAAATTTTC	0.512																																					p.L803fs		Atlas-INDEL	.											.	TRAK2	62	.	0			c.2409delG						.						85	86	86					2																	202245603		2203	4300	6503	SO:0001589	frameshift_variant	66008	exon16			.	AB038951	CCDS2347.1	2q33.1	2012-03-05	2005-12-13	2005-12-13	ENSG00000115993	ENSG00000115993			13206	protein-coding gene	gene with protein product	"gamma-aminobutyric acid(A) receptor-interacting factor", "milton homolog 2 (Drosophila)", "O-linked N-acetylglucosamine transferase interacting protein 98"	607334	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 3"	ALS2CR3		11161814, 16380713, 20230862	Standard	NM_015049		Approved	CALS-C, KIAA0549, GRIF-1, OIP98, MILT2	uc002uyb.4	O60296	OTTHUMG00000132822	ENST00000332624.3:c.2408delT	chr2.hg19:g.202245603delA	ENSP00000328875:p.Leu803fs	243.0	0.0		156.0	10.0	NM_015049	E7EV21|Q8WVH7|Q96NS2|Q9C0K5|Q9C0K6	Frame_Shift_Del	DEL	ENST00000332624.3	hg19	CCDS2347.1																																																																																			.	.		0.512	TRAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256284.3	NM_015049		-	202245603	A	-	202245603	7	5	282	1	0	1	0	1	0	0	0	0	16465	131	5	0	340	0	TRAK2	2	202245603	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	809254	202245603	40953770	220	40454										
ALS2CR4	65062	hgsc.bcm.edu	37	chr2	202501540	202501540	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtgctctttgagttctttagTtgatggctcattgccctcag	10	9	4	2	rs376226585		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:202501540T>A	ENST00000409883.2	-	5	321	c.205A>T	c.(205-207)Act>Tct	p.T69S	TMEM237_ENST00000409444.2_Missense_Mutation_p.T61S	NM_001044385.2	NP_001037850.1	Q96Q45	TM237_HUMAN	transmembrane protein 237	69					cilium assembly (GO:0042384)|regulation of Wnt signaling pathway (GO:0030111)	ciliary transition zone (GO:0035869)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(2)|kidney(1)|large_intestine(1)|lung(3)	7						AGTTCTTTAGTTGATGGCTCA	0.438																																					p.T69S		Atlas-SNP	.											.	TMEM237	21	.	0			c.A205T						.	T	SER/THR,SER/THR	0,3676		0,0,1838	63	59	60		181,205	0.4	0.5	2		60	1,8177		0,1,4088	no	missense,missense	TMEM237	NM_152388.2,NM_001044385.1	58,58	0,1,5926	AA,AT,TT		0.0122,0.0,0.0084	benign,benign	61/401,69/409	202501540	1,11853	1838	4089	5927	SO:0001583	missense	65062	exon4			CTTTAGTTGATGG	AB053301	CCDS46489.1, CCDS46490.1	2q33	2012-05-08	2011-05-20	2011-05-20	ENSG00000155755	ENSG00000155755			14432	protein-coding gene	gene with protein product		614423	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 4"	ALS2CR4		11586298, 20375344	Standard	NM_001044385		Approved	JBTS14	uc021vvg.2	Q96Q45	OTTHUMG00000154526	ENST00000409883.2:c.205A>T	chr2.hg19:g.202501540T>A	ENSP00000386264:p.Thr69Ser	53.0	0.0		44.0	19.0	NM_001044385	B4E1R8|B4E2R8|E9PAR8|E9PBF8|E9PG24|E9PGX0|Q53TS9|Q53TT2|Q7Z3B6|Q8IZ18|Q8NBF8|Q96CY1	Missense_Mutation	SNP	ENST00000409883.2	hg19	CCDS46489.1	.	.	.	.	.	.	.	.	.	.	T	8.241	0.806894	0.16467	0.0	1.22E-4	ENSG00000155755	ENST00000409444;ENST00000409883;ENST00000435876;ENST00000426684	T;T	0.44083	0.93;0.93	5.27	0.376	0.16193	.	0.122859	0.53938	N	0.000044	T	0.26557	0.0649	L	0.39397	1.21	0.09310	N	1	B;B	0.12013	0.005;0.0	B;B	0.09377	0.004;0.003	T	0.11348	-1.0591	10	0.33141	T	0.24	-3.1583	4.4306	0.11525	0.1405:0.3118:0.0:0.5477	.	69;93	E9PAR8;Q96Q45	.;TM237_HUMAN	S	61;69;69;91	ENSP00000387203:T61S;ENSP00000386264:T69S	ENSP00000387203:T61S	T	-	1	0	TMEM237	202209785	0.966000	0.33281	0.460000	0.27093	0.309000	0.27889	0.146000	0.16180	-0.071000	0.12886	0.528000	0.53228	ACT	.	.		0.438	TMEM237-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335753.1	NM_152388		A	202501540	T	A	202501540	3	1	282	1	0	0	0	0	1	0	0	0	554	1725	60	4	1057	4	ALS2CR4	2	202501540	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	255937	202501540	40697833	221	40455										
FAM117B	150864	hgsc.bcm.edu	37	chr2	203630172	203630172	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtctgttctatgtctaggccAaaacagcttcatgaaatccc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:203630172delA	ENST00000392238.2	+	8	1455	c.1455delA	c.(1453-1455)ccafs	p.P485fs	FAM117B_ENST00000303116.6_Frame_Shift_Del_p.P241fs			Q6P1L5	F117B_HUMAN	family with sequence similarity 117, member B	485										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)	17						TGTCTAGGCCAAAACAGCTTC	0.343																																					p.P485fs		Atlas-INDEL	.											.	FAM117B	73	.	0			c.1454delC						.						90	94	93					2																	203630172		2203	4300	6503	SO:0001589	frameshift_variant	150864	exon8			.	AB053315	CCDS33362.1, CCDS33362.2	2q33	2008-08-18	2008-08-18	2008-08-18	ENSG00000138439	ENSG00000138439			14440	protein-coding gene	gene with protein product			"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 13"	ALS2CR13		11586298	Standard	NM_173511		Approved	FLJ38771	uc010zhx.2	Q6P1L5	OTTHUMG00000154550	ENST00000392238.2:c.1455delA	chr2.hg19:g.203630172delA	ENSP00000376071:p.Pro485fs	163.0	0.0		140.0	10.0	NM_173511	Q53QZ5|Q585T9|Q8N8W1|Q96Q34	Frame_Shift_Del	DEL	ENST00000392238.2	hg19	CCDS33362.2																																																																																			.	.		0.343	FAM117B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335888.3	NM_173511		-	203630172	A	-	203630172	7	5	282	1	0	1	0	1	0	0	0	0	5415	117	5	0	1485	0	FAM117B	2	203630172	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1128632	203630172	39569201	222	40456										
PARD3B	117583	hgsc.bcm.edu	37	chr2	206305272	206305272	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atgtctttagatctccatctCcccctcgagctggaccattt					rs201407485		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:206305272delC	ENST00000406610.2	+	20	3127	c.2920delC	c.(2920-2922)cccfs	p.P975fs	PARD3B_ENST00000349953.3_Intron|PARD3B_ENST00000358768.2_Frame_Shift_Del_p.P913fs|PARD3B_ENST00000351153.1_Frame_Shift_Del_p.P906fs	NM_057177.6|NM_152526.5|NM_205863.3	NP_476518.4|NP_689739.4|NP_995585.2	Q8TEW8	PAR3L_HUMAN	par-3 family cell polarity regulator beta	975					cell cycle (GO:0007049)|cell division (GO:0051301)	membrane (GO:0016020)|tight junction (GO:0005923)				breast(1)|endometrium(9)|kidney(2)|large_intestine(6)|liver(4)|lung(33)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	65		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		ATCTCCATCTCCCCCTCGAGC	0.483																																					p.S911fs		Atlas-INDEL	.											.	PARD3B	314	.	0			c.2733delT						.						137	140	139					2																	206305272		2007	4146	6153	SO:0001589	frameshift_variant	117583	exon19			.	AB053321	CCDS42804.1, CCDS42805.1, CCDS42806.1	2q33.3	2013-08-28	2013-08-28	2006-09-28	ENSG00000116117	ENSG00000116117			14446	protein-coding gene	gene with protein product			"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 19", "par-3 partitioning defective 3 homolog B (C. elegans)"	ALS2CR19		11586298, 12459187	Standard	NM_057177		Approved	Par3L, PAR3beta	uc002vap.2	Q8TEW8	OTTHUMG00000154562	ENST00000406610.2:c.2920delC	chr2.hg19:g.206305272delC	ENSP00000385848:p.Pro975fs	293.0	0.0		210.0	14.0	NM_152526	E9PE87|Q8IUC7|Q8IUC9|Q96DK9|Q96N09|Q96NX6|Q96NX7|Q96Q29	Frame_Shift_Del	DEL	ENST00000406610.2	hg19																																																																																				.	.		0.483	PARD3B-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000335992.1	NM_057177		-	206305272	C	-	206305272	7	5	282	1	0	1	0	1	0	0	0	0	11453	855	30	0	2998	0	PARD3B	2	206305272	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	2675100	206305272	36894101	223	40457										
ZDBF2	57683	hgsc.bcm.edu	37	chr2	207175038	207175038	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agcagagaggcctcctaagcAaaaggggcgtgtggcttctc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:207175038delA	ENST00000374423.3	+	5	6172	c.5786delA	c.(5785-5787)caafs	p.Q1929fs		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1929							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						CCTCCTAAGCAAAAGGGGCGT	0.428																																					p.Q1929fs		Atlas-INDEL	.											.	ZDBF2	531	.	0			c.5785delC						.						69	69	69					2																	207175038		1957	4154	6111	SO:0001589	frameshift_variant	57683	exon5			.	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"Zinc fingers, DBF-type"	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.5786delA	chr2.hg19:g.207175038delA	ENSP00000363545:p.Gln1929fs	261.0	0.0		177.0	11.0	NM_020923	Q6ZNP7|Q6ZSN8	Frame_Shift_Del	DEL	ENST00000374423.3	hg19	CCDS46501.1																																																																																			.	.		0.428	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		-	207175038	A	-	207175038	7	5	282	1	0	1	0	1	0	0	0	0	17614	130	5	0	5796	0	ZDBF2	2	207175038	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	869766	207175038	36024335	224	40458										
MAP2	4133	hgsc.bcm.edu	37	chr2	210543360	210543360	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtagcagtcctgaaaggtgaAcaagagaaagaagctcaaca	11	7	1	4			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:210543360A>G	ENST00000360351.4	+	5	833	c.327A>G	c.(325-327)gaA>gaG	p.E109E	MAP2_ENST00000392194.1_Silent_p.E109E|MAP2_ENST00000361559.4_Silent_p.E109E|MAP2_ENST00000447185.1_Silent_p.E109E|MAP2_ENST00000199940.6_Silent_p.E109E	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	109					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	TGAAAGGTGAACAAGAGAAAG	0.423																																					p.E109E	Pancreas(27;423 979 28787 29963)	Atlas-SNP	.											.	MAP2	372	.	0			c.A327G						.						121	114	116					2																	210543360		2203	4300	6503	SO:0001819	synonymous_variant	4133	exon6			AGGTGAACAAGAG		CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"A-kinase anchor proteins"	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.327A>G	chr2.hg19:g.210543360A>G		127.0	0.0		80.0	4.0	NM_001039538	Q17S04|Q8IUX2|Q99975|Q99976	Silent	SNP	ENST00000360351.4	hg19	CCDS2384.1																																																																																			.	.		0.423	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538		G	210543360	A	G	210543360	2	3	282	1	0	0	0	0	0	0	0	1	9244	40	2	2		2	MAP2	2	210543360	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	3368322	210543360	32656013	225	40459										
MAP2	4133	hgsc.bcm.edu	37	chr2	210558065	210558065	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cctcagaggcaatgaccttaCccaaagatgctcacattcca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:210558065delC	ENST00000360351.4	+	7	1677	c.1171delC	c.(1171-1173)cccfs	p.P391fs	MAP2_ENST00000392194.1_Intron|MAP2_ENST00000361559.4_Intron|MAP2_ENST00000447185.1_Frame_Shift_Del_p.P387fs|MAP2_ENST00000199940.6_Intron	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	391					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	AATGACCTTACCCAAAGATGC	0.448																																					p.L390fs	Pancreas(27;423 979 28787 29963)	Atlas-INDEL	.											.	MAP2	372	.	0			c.1170delA						.						64	65	65					2																	210558065		2203	4300	6503	SO:0001589	frameshift_variant	4133	exon7			.		CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"A-kinase anchor proteins"	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.1171delC	chr2.hg19:g.210558065delC	ENSP00000353508:p.Pro391fs	260.0	0.0		182.0	11.0	NM_002374	Q17S04|Q8IUX2|Q99975|Q99976	Frame_Shift_Del	DEL	ENST00000360351.4	hg19	CCDS2384.1																																																																																			.	.		0.448	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538		-	210558065	C	-	210558065	7	5	282	1	0	1	0	1	0	0	0	0	9244	507	18	0	1185	0	MAP2	2	210558065	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	14705	210558065	32641308	226	40460										
TNS1	7145	hgsc.bcm.edu	37	chr2	218674974	218674974	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttcaggtgaccactcacctgCcccttgtttcagcaggtctg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:218674974delC	ENST00000171887.4	-	29	5241	c.4789delG	c.(4789-4791)gcafs	p.A1598fs	TNS1_ENST00000419504.1_Frame_Shift_Del_p.A1584fs|TNS1_ENST00000430930.1_Frame_Shift_Del_p.A1577fs	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1598					cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		CACTCACCTGCCCCTTGTTTC	0.547																																					p.A1597fs		Atlas-INDEL	.											.	TNS1	251	.	0			c.4790delC						.						105	100	102					2																	218674974		2203	4300	6503	SO:0001589	frameshift_variant	7145	exon29			.	AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	11973	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 155"	600076	"tensin", "matrix-remodelling associated 6"	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.4789delG	chr2.hg19:g.218674974delC	ENSP00000171887:p.Ala1598fs	224.0	0.0		158.0	13.0	NM_022648	Q4ZG71|Q6IPI5	Frame_Shift_Del	DEL	ENST00000171887.4	hg19	CCDS2407.1																																																																																			.	.		0.547	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		-	218674974	C	-	218674974	7	5	282	1	0	1	0	1	0	0	0	0	16358	739	26	0	438	0	TNS1	2	218674974	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	8116909	218674974	24524399	227	40461										
ZNF142	7701	hgsc.bcm.edu	37	chr2	219509322	219509322	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtcccaggttcgtgacctggCccctcaggtcgggctgacag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:219509322delC	ENST00000449707.1	-	8	2338	c.1917delG	c.(1915-1917)gggfs	p.G639fs	ZNF142_ENST00000411696.2_Frame_Shift_Del_p.G639fs	NM_001105537.1	NP_001099007.1	P52746	ZN142_HUMAN	zinc finger protein 142	639					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(7)|endometrium(7)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38		Renal(207;0.0474)		Epithelial(149;5.21e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		CGTGACCTGGCCCCTCAGGTC	0.632																																					p.P640fs	Colon(170;867 1942 8995 15834 18053)	Atlas-INDEL	.											.	ZNF142	190	.	0			c.1918delC						.						35	38	37					2																	219509322		1989	4145	6134	SO:0001589	frameshift_variant	7701	exon8			.	U09849	CCDS42817.1	2q35	2013-01-08	2006-06-13		ENSG00000115568	ENSG00000115568		"Zinc fingers, C2H2-type"	12927	protein-coding gene	gene with protein product		604083	"zinc finger protein 142 (clone pHZ-49)"				Standard	NM_001105537		Approved	KIAA0236, pHZ-49	uc002vin.4	P52746	OTTHUMG00000154736	ENST00000449707.1:c.1917delG	chr2.hg19:g.219509322delC	ENSP00000408643:p.Gly639fs	179.0	0.0		158.0	11.0	NM_001105537	Q92510	Frame_Shift_Del	DEL	ENST00000449707.1	hg19	CCDS42817.1																																																																																			.	.		0.632	ZNF142-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336833.1	NM_005081		-	219509322	C	-	219509322	7	5	282	1	0	1	0	1	0	0	0	0	17746	726	26	0	3158	0	ZNF142	2	219509322	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	834348	219509322	23690051	228	40462										
TTLL4	9654	hgsc.bcm.edu	37	chr2	219617891	219617891	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggttccacatgggagttgtcTctgattctgctccagtggtg	13	9	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:219617891T>C	ENST00000392102.1	+	18	3581	c.3241T>C	c.(3241-3243)Tct>Cct	p.S1081P	TTLL4_ENST00000457313.1_Missense_Mutation_p.S916P|TTLL4_ENST00000442769.1_Missense_Mutation_p.S1017P|TTLL4_ENST00000258398.4_Missense_Mutation_p.S1081P	NM_014640.4	NP_055455.3	Q14679	TTLL4_HUMAN	tubulin tyrosine ligase-like family, member 4	1081					protein polyglutamylation (GO:0018095)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)|tubulin binding (GO:0015631)			endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	39		Renal(207;0.0915)		Epithelial(149;5.03e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0101)		GGGAGTTGTCTCTGATTCTGC	0.527																																					p.S1081P	GBM(172;1818 2053 15407 20943 49753)	Atlas-SNP	.											.	TTLL4	96	.	0			c.T3241C						.						227	214	218					2																	219617891		2203	4300	6503	SO:0001583	missense	9654	exon18			GTTGTCTCTGATT		CCDS2422.1	2p24.3-p24.1	2013-02-14			ENSG00000135912	ENSG00000135912		"Tubulin tyrosine ligase-like family"	28976	protein-coding gene	gene with protein product						11054573	Standard	NM_014640		Approved	KIAA0173	uc002viy.3	Q14679	OTTHUMG00000133081	ENST00000392102.1:c.3241T>C	chr2.hg19:g.219617891T>C	ENSP00000375951:p.Ser1081Pro	268.0	0.0		195.0	8.0	NM_014640	A8K6V5|Q8WW29	Missense_Mutation	SNP	ENST00000392102.1	hg19	CCDS2422.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.96|14.96	2.691596|2.691596	0.48097|0.48097	.|.	.|.	ENSG00000135912|ENSG00000135912	ENST00000436668|ENST00000457313;ENST00000392102;ENST00000442769;ENST00000258398	.|T;T;T;T	.|0.04502	.|3.82;4.05;3.61;4.05	5.17|5.17	2.78|2.78	0.32641|0.32641	.|.	.|0.558082	.|0.18504	.|N	.|0.139256	T|T	0.05640|0.05640	0.0148|0.0148	M|M	0.68952|0.68952	2.095|2.095	0.26038|0.26038	N|N	0.981642|0.981642	.|B;D;B	.|0.54601	.|0.337;0.967;0.026	.|B;B;B	.|0.40329	.|0.133;0.326;0.008	T|T	0.35251|0.35251	-0.9796|-0.9796	5|10	.|0.39692	.|T	.|0.17	.|.	4.1007|4.1007	0.10012|0.10012	0.3445:0.0872:0.0:0.5683|0.3445:0.0872:0.0:0.5683	.|.	.|916;1017;1081	.|E9PH58;E7EX20;Q14679	.|.;.;TTLL4_HUMAN	P|P	183|916;1081;1017;1081	.|ENSP00000393332:S916P;ENSP00000375951:S1081P;ENSP00000396555:S1017P;ENSP00000258398:S1081P	.|ENSP00000258398:S1081P	L|S	+|+	2|1	0|0	TTLL4|TTLL4	219326135|219326135	0.122000|0.122000	0.22280|0.22280	0.992000|0.992000	0.48379|0.48379	0.996000|0.996000	0.88848|0.88848	0.705000|0.705000	0.25675|0.25675	0.420000|0.420000	0.25954|0.25954	0.533000|0.533000	0.62120|0.62120	CTC|TCT	.	.		0.527	TTLL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256726.1	NM_014640		C	219617891	T	C	219617891	3	2	282	1	0	0	0	0	1	0	0	0	16744	1551	54	2	3303	2	TTLL4	2	219617891	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	108569	219617891	23581482	229	40463										
GMPPA	29926	hgsc.bcm.edu	37	chr2	220364899	220364899	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaccattgtttcctgtggcaGgggtccctatgatccaacac							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:220364899delG	ENST00000358215.3	+	3	466	c.97delG	c.(97-99)gggfs	p.G33fs	GMPPA_ENST00000313597.5_Frame_Shift_Del_p.G33fs|GMPPA_ENST00000373908.1_Frame_Shift_Del_p.G33fs|RP11-316O14.1_ENST00000601508.1_RNA|AC053503.11_ENST00000429882.1_RNA|GMPPA_ENST00000373917.3_Frame_Shift_Del_p.G33fs|GMPPA_ENST00000341142.3_Frame_Shift_Del_p.G33fs	NM_205847.2	NP_995319.1	Q96IJ6	GMPPA_HUMAN	GDP-mannose pyrophosphorylase A	33					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotidyltransferase activity (GO:0016779)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(6)|prostate(1)|skin(1)	20		Renal(207;0.0183)		Epithelial(149;3.82e-10)|all cancers(144;6.25e-08)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00807)|READ - Rectum adenocarcinoma(5;0.148)		TCCTGTGGCAGGGGTCCCTAT	0.537																																					p.A32fs		Atlas-INDEL	.											.	GMPPA	50	.	0			c.96delA						.						76	61	66					2																	220364899		2203	4299	6502	SO:0001589	frameshift_variant	29926	exon3			.	AF135422	CCDS2441.1	2q36.1	2008-02-05			ENSG00000144591	ENSG00000144591			22923	protein-coding gene	gene with protein product		615495					Standard	NM_205847		Approved		uc002vlr.3	Q96IJ6	OTTHUMG00000058922	ENST00000358215.3:c.97delG	chr2.hg19:g.220364899delG	ENSP00000350949:p.Gly33fs	239.0	0.0		152.0	11.0	NM_205847	A6NJ74|A8K3Q6|B3KMT4|Q53GI0|Q9NWC3|Q9Y5P5	Frame_Shift_Del	DEL	ENST00000358215.3	hg19	CCDS2441.1																																																																																			.	.		0.537	GMPPA-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130230.1	NM_013335		-	220364899	G	-	220364899	7	5	282	1	0	1	0	1	0	0	0	0	6502	1000	35	0	103	0	GMPPA	2	220364899	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	747008	220364899	22834474	230	40464										
CHPF	79586	hgsc.bcm.edu	37	chr2	220405010	220405010	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaggggccggcggcctccctGgggggtcagtgcctccagct					rs538123825		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:220405010delG	ENST00000243776.6	-	4	1671	c.1423delC	c.(1423-1425)cagfs	p.Q475fs	CHPF_ENST00000535926.1_Frame_Shift_Del_p.Q313fs	NM_024536.5	NP_078812	Q8IZ52	CHSS2_HUMAN	chondroitin polymerizing factor	475					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)	21		Renal(207;0.0183)		Epithelial(149;3.02e-08)|all cancers(144;3.41e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		CGGCCTCCCTGGGGGGTCAGT	0.662																																					p.Q475fs		Atlas-INDEL	.											.	CHPF	56	.	0			c.1424delA						.						26	29	28					2																	220405010		2203	4296	6499	SO:0001589	frameshift_variant	79586	exon4			.	BC008878	CCDS2443.1, CCDS56169.1	2q35	2014-02-12			ENSG00000123989	ENSG00000123989	2.4.1.175, 2.4.1.226	"Beta 3-glycosyltransferases", "Beta 4-glycosyltransferases"	24291	protein-coding gene	gene with protein product	"chondroitin sulfate synthase 2"	610405				11230166, 12716890	Standard	NM_024536		Approved	CSS2, CHSY2	uc002vmc.4	Q8IZ52	OTTHUMG00000058929	ENST00000243776.6:c.1423delC	chr2.hg19:g.220405010delG	ENSP00000243776:p.Gln475fs	317.0	0.0		214.0	15.0	NM_024536	B4DXU0|Q6UXD6|Q7L4G1|Q9H0F8|Q9H618	Frame_Shift_Del	DEL	ENST00000243776.6	hg19	CCDS2443.1																																																																																			.	.		0.662	CHPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130268.1	NM_024536		-	220405010	G	-	220405010	7	5	282	1	0	1	0	1	0	0	0	0	3370	1357	47	0	908	0	CHPF	2	220405010	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	40111	220405010	22794363	231	40465										
IRS1	3667	hgsc.bcm.edu	37	chr2	227659975	227659975	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cacagtttggctggctccttGggggctcccccaagctcccc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:227659975delG	ENST00000305123.5	-	1	4500	c.3480delC	c.(3478-3480)cccfs	p.P1160fs	IRS1_ENST00000498335.1_5'Flank	NM_005544.2	NP_005535.1	P35568	IRS1_HUMAN	insulin receptor substrate 1	1160					cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid catabolic process (GO:0016042)|mammary gland development (GO:0030879)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein kinase B signaling (GO:0043491)|protein localization to nucleus (GO:0034504)|regulation of gene expression (GO:0010468)|response to insulin (GO:0032868)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)	caveola (GO:0005901)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|insulin receptor complex (GO:0005899)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein kinase C binding (GO:0005080)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.P1160P(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(10)|lung(33)|ovary(6)|pancreas(1)|prostate(1)|urinary_tract(2)	69		Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23)		Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137)		CTGGCTCCTTGGGGGCTCCCC	0.582																																					p.K1161fs		Atlas-INDEL	.											.	IRS1	141	.	1	Substitution - coding silent(1)	breast(1)	c.3481delA						.						50	59	56					2																	227659975		2203	4300	6503	SO:0001589	frameshift_variant	3667	exon1			.		CCDS2463.1	2q36	2013-01-10			ENSG00000169047	ENSG00000169047		"Pleckstrin homology (PH) domain containing"	6125	protein-coding gene	gene with protein product		147545				1648180	Standard	NM_005544		Approved	HIRS-1	uc002voh.4	P35568	OTTHUMG00000133179	ENST00000305123.5:c.3480delC	chr2.hg19:g.227659975delG	ENSP00000304895:p.Pro1160fs	162.0	0.0		112.0	10.0	NM_005544		Frame_Shift_Del	DEL	ENST00000305123.5	hg19	CCDS2463.1																																																																																			.	.		0.582	IRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256886.3	NM_005544		-	227659975	G	-	227659975	7	5	282	1	0	1	0	1	0	0	0	0	7849	1335	47	0	252	0	IRS1	2	227659975	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	7254965	227659975	15539398	232	40466										
TM4SF20	79853	hgsc.bcm.edu	37	chr2	228243963	228243963	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gctgaatccattgcaggatgTccatccttcgcagcaggtca	10	12	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:228243963T>C	ENST00000304568.3	-	1	59	c.22A>G	c.(22-24)Aca>Gca	p.T8A		NM_024795.3	NP_079071.2	Q53R12	T4S20_HUMAN	transmembrane 4 L six family member 20	8						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|kidney(2)|large_intestine(1)|lung(4)|stomach(2)	10		Renal(207;0.025)|all_lung(227;0.123)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;3.8e-11)|all cancers(144;2.57e-08)|Lung(261;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0115)		TTGCAGGATGTCCATCCTTCG	0.468																																					p.T8A		Atlas-SNP	.											.	TM4SF20	24	.	0			c.A22G						.						111	109	110					2																	228243963		2203	4300	6503	SO:0001583	missense	79853	exon1			AGGATGTCCATCC	AK026453	CCDS2466.1	2q36.3	2008-02-05			ENSG00000168955	ENSG00000168955			26230	protein-coding gene	gene with protein product		615404				12975309	Standard	NM_024795		Approved	FLJ22800, TCCE518	uc002vpb.2	Q53R12	OTTHUMG00000133187	ENST00000304568.3:c.22A>G	chr2.hg19:g.228243963T>C	ENSP00000303028:p.Thr8Ala	157.0	0.0		115.0	5.0	NM_024795	B2RP42|Q5U609|Q6UWS1|Q9H5X9	Missense_Mutation	SNP	ENST00000304568.3	hg19	CCDS2466.1	.	.	.	.	.	.	.	.	.	.	T	15.42	2.827170	0.50739	.	.	ENSG00000168955	ENST00000304568;ENST00000449706	T	0.27402	1.67	5.77	5.77	0.91146	.	0.083182	0.51477	D	0.000093	T	0.34687	0.0906	L	0.28556	0.865	0.36193	D	0.850231	D	0.76494	0.999	D	0.79784	0.993	T	0.35699	-0.9778	10	0.02654	T	1	-21.5116	9.352	0.38145	0.1595:0.0:0.0:0.8405	.	8	Q53R12	T4S20_HUMAN	A	8	ENSP00000303028:T8A	ENSP00000303028:T8A	T	-	1	0	TM4SF20	227952207	1.000000	0.71417	0.999000	0.59377	0.905000	0.53344	2.974000	0.49272	2.194000	0.70268	0.482000	0.46254	ACA	.	.		0.468	TM4SF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256896.2	NM_024795		C	228243963	T	C	228243963	3	2	282	1	0	0	0	0	1	0	0	0	15984	1667	58	2	683	2	TM4SF20	2	228243963	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	583988	228243963	14955410	233	40467										
FBXO36	130888	hgsc.bcm.edu	37	chr2	230841022	230841022	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcaacaaaacctggagaagcAaaagaaacccatgaagactt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:230841022delA	ENST00000283946.3	+	2	180	c.162delA	c.(160-162)gcafs	p.A54fs	FBXO36_ENST00000373652.3_Frame_Shift_Del_p.A23fs|RNU6-1027P_ENST00000383998.1_RNA|FBXO36_ENST00000409992.1_Frame_Shift_Del_p.A54fs	NM_174899.4	NP_777559.3	Q8NEA4	FBX36_HUMAN	F-box protein 36	54										endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	7		Renal(207;0.0112)|all_lung(227;0.0179)|Lung NSC(271;0.0804)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;7.56e-14)|all cancers(144;7.74e-11)|Lung(119;0.00488)|LUSC - Lung squamous cell carcinoma(224;0.008)		CTGGAGAAGCAAAAGAAACCC	0.338																																					p.A54fs		Atlas-INDEL	.											.	FBXO36	22	.	0			c.161delC						.						67	69	68					2																	230841022		2203	4300	6503	SO:0001589	frameshift_variant	130888	exon2			.	BC033935	CCDS2472.1	2q37.1	2008-02-05	2004-06-15		ENSG00000153832	ENSG00000153832		"F-boxes /  "other""	27020	protein-coding gene	gene with protein product		609105	"F-box only protein 36"			12477932	Standard	NM_174899		Approved	Fbx36, FLJ37592	uc002vqa.3	Q8NEA4	OTTHUMG00000133206	ENST00000283946.3:c.162delA	chr2.hg19:g.230841022delA	ENSP00000283946:p.Ala54fs	218.0	0.0		150.0	10.0	NM_174899	B3KVQ6|Q53TE6|Q8WWD4	Frame_Shift_Del	DEL	ENST00000283946.3	hg19	CCDS2472.1																																																																																			.	.		0.338	FBXO36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256919.2	NM_174899		-	230841022	A	-	230841022	7	5	282	1	0	1	0	1	0	0	0	0	5753	117	5	0	168	0	FBXO36	2	230841022	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2597059	230841022	12358351	234	40468										
CAB39	51719	hgsc.bcm.edu	37	chr2	231657931	231657931	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gattgtattcctaatagggcAaaaaagacgtggctcaaatt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:231657931delA	ENST00000258418.5	+	4	712	c.283delA	c.(283-285)aaafs	p.K96fs	CAB39_ENST00000409788.3_Frame_Shift_Del_p.K96fs|CAB39_ENST00000410084.3_Frame_Shift_Del_p.K96fs	NM_016289.3	NP_057373.1	Q9Y376	CAB39_HUMAN	calcium binding protein 39	96					activation of protein kinase activity (GO:0032147)|cell cycle arrest (GO:0007050)|cellular hypotonic response (GO:0071476)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of rubidium ion transmembrane transporter activity (GO:2000687)|negative regulation of rubidium ion transport (GO:2000681)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein heterooligomerization (GO:0051291)|signal transduction by phosphorylation (GO:0023014)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	kinase binding (GO:0019900)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activator activity (GO:0043539)			central_nervous_system(1)|large_intestine(1)|skin(1)	3		all_lung(227;4.63e-07)|all_hematologic(139;1.83e-06)|Lung NSC(271;2.11e-05)|Acute lymphoblastic leukemia(138;5.51e-05)|Hepatocellular(293;0.0207)|Lung SC(224;0.187)		all cancers(144;1.64e-12)|Epithelial(121;5.29e-11)|LUSC - Lung squamous cell carcinoma(224;0.0154)|Lung(119;0.0177)|COAD - Colon adenocarcinoma(134;0.226)		CTAATAGGGCAAAAAAGACGT	0.358																																					p.G94fs		Atlas-INDEL	.											.	CAB39	30	.	0			c.282delC						.						119	117	118					2																	231657931		2203	4300	6503	SO:0001589	frameshift_variant	51719	exon4			.	AF113536	CCDS2478.1	2q37.1	2008-02-05			ENSG00000135932	ENSG00000135932			20292	protein-coding gene	gene with protein product		612174					Standard	NM_016289		Approved	CGI-66, MO25	uc002vqx.3	Q9Y376	OTTHUMG00000133220	ENST00000258418.5:c.283delA	chr2.hg19:g.231657931delA	ENSP00000258418:p.Lys96fs	271.0	0.0		177.0	15.0	NM_001130850	A8K8L7	Frame_Shift_Del	DEL	ENST00000258418.5	hg19	CCDS2478.1																																																																																			.	.		0.358	CAB39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256955.2	NM_016289		-	231657931	A	-	231657931	7	5	282	1	0	1	0	1	0	0	0	0	2527	131	5	0	293	0	CAB39	2	231657931	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	816909	231657931	11541442	235	40469										
ATG16L1	55054	hgsc.bcm.edu	37	chr2	234178690	234178690	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaagagcttgcagaagcagcAaaggaacctctaccagtcga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:234178690delA	ENST00000392017.4	+	6	941	c.684delA	c.(682-684)gcafs	p.A228fs	ATG16L1_ENST00000347464.5_Frame_Shift_Del_p.A84fs|ATG16L1_ENST00000373525.5_Frame_Shift_Del_p.A84fs|ATG16L1_ENST00000498620.1_3'UTR|ATG16L1_ENST00000392018.1_Frame_Shift_Del_p.A228fs|ATG16L1_ENST00000392020.4_Frame_Shift_Del_p.A228fs	NM_001190266.1|NM_001190267.1|NM_030803.6	NP_001177195.1|NP_001177196.1|NP_110430.5	Q676U5	A16L1_HUMAN	autophagy related 16-like 1 (S. cerevisiae)	228	WIPI2-binding. {ECO:0000269|PubMed:24954904}.				autophagic vacuole assembly (GO:0000045)|negative stranded viral RNA replication (GO:0039689)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)	autophagic vacuole (GO:0005776)|autophagic vacuole membrane (GO:0000421)|axoneme (GO:0005930)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(7)|prostate(3)|skin(1)	25		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0539)		Epithelial(121;1.53e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000379)|LUSC - Lung squamous cell carcinoma(224;0.00619)|Lung(119;0.00732)|GBM - Glioblastoma multiforme(43;0.11)		CAGAAGCAGCAAAGGAACCTC	0.388																																					p.A228fs		Atlas-INDEL	.											.	ATG16L1	83	.	0			c.683delC						.						77	92	87					2																	234178690		2203	4300	6503	SO:0001589	frameshift_variant	55054	exon6			.	AK000897	CCDS2502.2, CCDS2503.2, CCDS54438.1	2q37.1	2014-02-12	2012-06-06	2005-09-13	ENSG00000085978	ENSG00000085978		"WD repeat domain containing"	21498	protein-coding gene	gene with protein product		610767	"APG16 autophagy 16-like (S. cerevisiae)", "ATG16 autophagy related 16-like (S. cerevisiae)", "ATG16 autophagy related 16-like 1 (S. cerevisiae)"	APG16L, ATG16L			Standard	NM_017974		Approved	WDR30, FLJ10035, ATG16A	uc002vty.3	Q676U5	OTTHUMG00000133619	ENST00000392017.4:c.684delA	chr2.hg19:g.234178690delA	ENSP00000375872:p.Ala228fs	287.0	0.0		249.0	15.0	NM_017974	A3EXK9|A3EXL0|B6ZDH0|Q6IPN1|Q6UXW4|Q6ZVZ5|Q8NCY2|Q96JV5|Q9H619	Frame_Shift_Del	DEL	ENST00000392017.4	hg19	CCDS2503.2																																																																																			.	.		0.388	ATG16L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257069.2	NM_017974		-	234178690	A	-	234178690	7	5	282	1	0	1	0	1	0	0	0	0	1091	117	5	0	706	0	ATG16L1	2	234178690	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2520759	234178690	9020683	236	40470										
DGKD	8527	hgsc.bcm.edu	37	chr2	234368500	234368500	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gccagggtacattcggattgTccacaagaaccgggcacaga	12	11	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:234368500T>C	ENST00000264057.2	+	23	2804	c.2792T>C	c.(2791-2793)gTc>gCc	p.V931A	DGKD_ENST00000409813.3_Missense_Mutation_p.V887A	NM_152879.2	NP_690618.2	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa	931					blood coagulation (GO:0007596)|cell growth (GO:0016049)|diacylglycerol metabolic process (GO:0046339)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|multicellular organismal development (GO:0007275)|platelet activation (GO:0030168)|protein homooligomerization (GO:0051260)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein transport (GO:0015031)|response to organic substance (GO:0010033)|second-messenger-mediated signaling (GO:0019932)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol binding (GO:0019992)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(13)|lung(15)|ovary(1)|pancreas(1)|skin(1)	38		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Phosphatidylserine(DB00144)	ATTCGGATTGTCCACAAGAAC	0.632																																					p.V931A		Atlas-SNP	.											.	DGKD	106	.	0			c.T2792C						.						68	60	63					2																	234368500		2203	4300	6503	SO:0001583	missense	8527	exon23			GGATTGTCCACAA	D63479	CCDS2504.1, CCDS46546.1	2q37	2013-01-10	2002-08-29		ENSG00000077044	ENSG00000077044		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	2851	protein-coding gene	gene with protein product	"diglyceride kinase"	601826	"diacylglycerol kinase, delta (130kD)"			8626538, 12810723	Standard	NM_003648		Approved	KIAA0145, DGKdelta	uc002vui.1	Q16760	OTTHUMG00000133290	ENST00000264057.2:c.2792T>C	chr2.hg19:g.234368500T>C	ENSP00000264057:p.Val931Ala	163.0	0.0		117.0	5.0	NM_152879	Q14158|Q6PK55|Q8NG53	Missense_Mutation	SNP	ENST00000264057.2	hg19	CCDS2504.1	.	.	.	.	.	.	.	.	.	.	T	13.04	2.118733	0.37436	.	.	ENSG00000077044	ENST00000264057;ENST00000409813	T;T	0.42513	0.97;0.97	4.35	3.15	0.36227	.	0.802743	0.11222	N	0.586553	T	0.44603	0.1301	M	0.73962	2.25	0.09310	N	1	B;B	0.22146	0.029;0.065	B;B	0.28991	0.068;0.097	T	0.40905	-0.9538	10	0.18710	T	0.47	.	11.1441	0.48419	0.0:0.0:0.1548:0.8452	.	887;931	Q16760-2;Q16760	.;DGKD_HUMAN	A	931;887	ENSP00000264057:V931A;ENSP00000386455:V887A	ENSP00000264057:V931A	V	+	2	0	DGKD	234033239	0.989000	0.36119	0.088000	0.20740	0.949000	0.60115	3.992000	0.56980	0.786000	0.33708	0.379000	0.24179	GTC	.	.		0.632	DGKD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257072.2	NM_003648		C	234368500	T	C	234368500	3	2	282	1	0	0	0	0	1	0	0	0	4469	1667	58	2	2906	2	DGKD	2	234368500	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	189810	234368500	8830873	237	40471										
UGT1A5	54579	hgsc.bcm.edu	37	chr2	234622350	234622350	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgcaagccttgcctctgagcTttttcagagagaggtgtcag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:234622350delT	ENST00000373414.3	+	1	713	c.713delT	c.(712-714)cttfs	p.L238fs	UGT1A9_ENST00000354728.4_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A6_ENST00000480628.1_Intron|UGT1A1_ENST00000608381.1_Frame_Shift_Del_p.L238fs			P35504	UD15_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A5	238						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			cervix(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|skin(3)|urinary_tract(1)	22		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;4.51e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000523)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.00645)		GCCTCTGAGCTTTTTCAGAGA	0.527																																					p.L238fs		Atlas-INDEL	.											.	UGT1A5	66	.	0			c.712delC						.						225	217	220					2																	234622350		2203	4300	6503	SO:0001589	frameshift_variant	54579	exon1			.	M84129	CCDS33404.1	2q37	2010-03-05	2005-07-20		ENSG00000240224	ENSG00000240224		"UDP glucuronosyltransferases"	12537	other	complex locus constituent		606430	"UDP glycosyltransferase 1 family, polypeptide A5"			9295054, 1339448	Standard	NM_019078		Approved	UGT1E		P35504	OTTHUMG00000059120	ENST00000373414.3:c.713delT	chr2.hg19:g.234622350delT	ENSP00000362513:p.Leu238fs	328.0	0.0		198.0	13.0	NM_019078	B8K294	Frame_Shift_Del	DEL	ENST00000373414.3	hg19	CCDS33404.1																																																																																			.	.		0.527	UGT1A5-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130985.1	NM_019078		-	234622350	T	-	234622350	7	5	282	1	0	1	0	1	0	0	0	0	16963	1609	56	0	715	0	UGT1A5	2	234622350	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	253850	234622350	8577023	238	40472										
UGT1A3	54659	hgsc.bcm.edu	37	chr2	234638491	234638492	+	Frame_Shift_Del	DEL	AG	AG	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccttgcctctgagctttttcAgagagaggtgtcagtggtgg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:234638491_234638492delAG	ENST00000482026.1	+	1	738_739	c.719_720delAG	c.(718-720)cagfs	p.Q240fs	UGT1A9_ENST00000354728.4_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A1_ENST00000609767.1_Frame_Shift_Del_p.Q240fs|UGT1A4_ENST00000373409.3_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A6_ENST00000480628.1_Intron|UGT1A5_ENST00000373414.3_Intron|UGT1A1_ENST00000608381.1_Intron			P35503	UD13_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A3	240					cellular glucuronidation (GO:0052695)|flavonoid glucuronidation (GO:0052696)|metabolic process (GO:0008152)|retinoic acid metabolic process (GO:0042573)|xenobiotic glucuronidation (GO:0052697)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|UDP-glycosyltransferase activity (GO:0008194)			breast(2)|endometrium(7)|kidney(18)|large_intestine(6)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	46		Breast(86;0.000765)|all_lung(227;0.00266)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0456)|Lung SC(224;0.128)		Epithelial(121;2.4e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000476)|Lung(119;0.00243)|LUSC - Lung squamous cell carcinoma(224;0.00599)	Atorvastatin(DB01076)|Candesartan(DB00796)|Cyproheptadine(DB00434)|Eltrombopag(DB06210)|Etodolac(DB00749)|Ezetimibe(DB00973)|Ezogabine(DB04953)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Irbesartan(DB01029)|Lamotrigine(DB00555)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Pitavastatin(DB08860)|Simvastatin(DB00641)|Valproic Acid(DB00313)	GAGCTTTTTCAGAGAGAGGTGT	0.505																																					p.240_240del		Atlas-Indel,Pindel	.											.	UGT1A3	91	.	0			c.718_719del						.																																			SO:0001589	frameshift_variant	54659	exon1			.	M84127	CCDS2509.1	2q37	2010-03-05	2005-07-20		ENSG00000243135	ENSG00000243135		"UDP glucuronosyltransferases"	12535	other	complex locus constituent		606428	"UDP glycosyltransferase 1 family, polypeptide A3"			9295054, 1339448, 11434514	Standard	NM_019093		Approved	UGT1C		P35503	OTTHUMG00000059118	ENST00000482026.1:c.719_720delAG	chr2.hg19:g.234638497_234638498delAG	ENSP00000418532:p.Gln240fs	473.0	0.0		327.0	72.0	NM_019093	B8K287	Frame_Shift_Del	DEL	ENST00000482026.1	hg19	CCDS2509.1																																																																																			.	.		0.505	UGT1A3-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130983.1	NM_019093		-	234638492	AG	-	234638491	7	5	282	1	0	1	0	1	0	0	0	0	16961	188	7	0	721	0	UGT1A3	2	234638491	Frame_Shift_Del	DEL	AG	TCGA-G3-A3CJ-01A-11D-A20W-10	16141	234638491	8560882	239	40473										
COL6A3	1293	hgsc.bcm.edu	37	chr2	238273019	238273019	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggcggaggttctcagatgctCtgtgtaaatcagccagatct	12	9	4	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:238273019C>T	ENST00000295550.4	-	13	6343	c.5891G>A	c.(5890-5892)aGa>aAa	p.R1964K	COL6A3_ENST00000347401.3_Missense_Mutation_p.R1763K|COL6A3_ENST00000409809.1_Missense_Mutation_p.R1758K|COL6A3_ENST00000346358.4_Missense_Mutation_p.R1764K|COL6A3_ENST00000353578.4_Missense_Mutation_p.R1758K|COL6A3_ENST00000472056.1_Missense_Mutation_p.R1357K	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1964	Nonhelical region.|VWFA 10. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		CTCAGATGCTCTGTGTAAATC	0.473																																					p.R1964K		Atlas-SNP	.											.	COL6A3	608	.	0			c.G5891A						.						121	108	112					2																	238273019		2203	4300	6503	SO:0001583	missense	1293	exon13			GATGCTCTGTGTA	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.5891G>A	chr2.hg19:g.238273019C>T	ENSP00000295550:p.Arg1964Lys	120.0	0.0		91.0	4.0	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	hg19	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	11.48	1.650292	0.29336	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	T;T;T;T;T;T	0.36878	1.23;1.23;1.23;1.23;1.23;1.23	5.62	-2.49	0.06403	von Willebrand factor, type A (2);	0.738576	0.11875	N	0.521021	T	0.21267	0.0512	L	0.41710	1.295	0.09310	N	1	B;B;B	0.24721	0.11;0.035;0.0	B;B;B	0.19666	0.026;0.018;0.0	T	0.34650	-0.9820	10	0.08837	T	0.75	.	7.5818	0.27970	0.0:0.3077:0.1993:0.493	.	1357;1758;1964	E9PFQ6;P12111-2;P12111	.;.;CO6A3_HUMAN	K	1964;1763;1758;1357;1758;1764	ENSP00000295550:R1964K;ENSP00000315609:R1763K;ENSP00000315873:R1758K;ENSP00000418285:R1357K;ENSP00000386844:R1758K;ENSP00000295546:R1764K	ENSP00000295550:R1964K	R	-	2	0	COL6A3	237937758	0.000000	0.05858	0.079000	0.20413	0.696000	0.40369	-1.679000	0.01940	-0.193000	0.10415	0.650000	0.86243	AGA	.	.		0.473	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		T	238273019	C	T	238273019	3	4	282	1	0	0	0	0	1	0	0	0	3703	913	32	3	3770	3	COL6A3	2	238273019	Missense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	3634528	238273019	4926354	240	40474										
COL6A3	1293	hgsc.bcm.edu	37	chr2	238285701	238285701	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cggctgccagcagacttcacAaaaatgtacctctgtgcata							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:238285701delA	ENST00000295550.4	-	7	3236	c.2784delT	c.(2782-2784)tttfs	p.F928fs	COL6A3_ENST00000347401.3_Frame_Shift_Del_p.F727fs|COL6A3_ENST00000409809.1_Frame_Shift_Del_p.F722fs|COL6A3_ENST00000346358.4_Frame_Shift_Del_p.F728fs|COL6A3_ENST00000392004.3_Frame_Shift_Del_p.F722fs|COL6A3_ENST00000392003.2_Frame_Shift_Del_p.F521fs|COL6A3_ENST00000353578.4_Frame_Shift_Del_p.F722fs|COL6A3_ENST00000472056.1_Frame_Shift_Del_p.F321fs	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	928	Nonhelical region.|VWFA 5. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		CAGACTTCACAAAAATGTACC	0.537																																					p.V929X		Atlas-INDEL	.											.	COL6A3	608	.	0			c.2785delG						.						85	73	77					2																	238285701		2203	4300	6503	SO:0001589	frameshift_variant	1293	exon7			.	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.2784delT	chr2.hg19:g.238285701delA	ENSP00000295550:p.Phe928fs	233.0	0.0		154.0	11.0	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Frame_Shift_Del	DEL	ENST00000295550.4	hg19	CCDS33412.1																																																																																			.	.		0.537	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		-	238285701	A	-	238285701	7	5	282	1	0	1	0	1	0	0	0	0	3703	127	5	0	6948	0	COL6A3	2	238285701	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	12682	238285701	4913672	241	40475										
ANO7	50636	hgsc.bcm.edu	37	chr2	242129532	242129532	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	accgtcctgatcgatgtgagCccccctgaggcagagaagag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:242129532delC	ENST00000274979.8	+	2	319	c.216delC	c.(214-216)agcfs	p.S72fs	ANO7_ENST00000402430.3_Frame_Shift_Del_p.S72fs|ANO7_ENST00000402530.3_Frame_Shift_Del_p.S72fs	NM_001001891.3	NP_001001891.2	Q6IWH7	ANO7_HUMAN	anoctamin 7	72					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(14)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	32						TCGATGTGAGCCCCCCTGAGG	0.662																																					p.S72fs		Atlas-INDEL	.											.	ANO7	136	.	0			c.215delG						.						36	34	35					2																	242129532		2199	4287	6486	SO:0001589	frameshift_variant	50636	exon2			.	AY617079	CCDS33423.1, CCDS46563.1	2q37.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000146205	ENSG00000146205		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	31677	protein-coding gene	gene with protein product		605096	"transmembrane protein 16G"	PCANAP5, TMEM16G		14981236, 15375614, 24692353	Standard	NM_001001891		Approved	NGEP, PCANAP5L, IPCA-5	uc002wax.2	Q6IWH7	OTTHUMG00000151702	ENST00000274979.8:c.216delC	chr2.hg19:g.242129532delC	ENSP00000274979:p.Ser72fs	319.0	0.0		231.0	14.0	NM_001001666	Q6IWH6	Frame_Shift_Del	DEL	ENST00000274979.8	hg19	CCDS33423.1																																																																																			.	.		0.662	ANO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323509.1	NM_001001891		-	242129532	C	-	242129532	7	5	282	1	0	1	0	1	0	0	0	0	702	738	26	0	222	0	ANO7	2	242129532	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	3843831	242129532	1069841	242	40476										
SEPT2	4735	hgsc.bcm.edu	37	chr2	242275390	242275390	+	Splice_Site	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	taagtttgtttcttttctagAaaaaattgaaagaactgtcc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:242275390delA	ENST00000391973.2	+	5	746	c.218delA	c.(217-219)gaa>ga	p.E73fs	SEPT2_ENST00000401990.1_Splice_Site_p.E83fs|SEPT2_ENST00000407971.1_Splice_Site_p.E33fs|SEPT2_ENST00000402092.2_Splice_Site_p.E73fs|SEPT2_ENST00000391971.2_Splice_Site_p.E73fs|SEPT2_ENST00000360051.3_Splice_Site_p.E73fs	NM_006155.1	NP_006146.1	Q15019	SEPT2_HUMAN	septin 2	73	Septin-type G.				cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|neuron projection development (GO:0031175)|regulation of L-glutamate transport (GO:0002036)|regulation of protein localization (GO:0032880)|smoothened signaling pathway (GO:0007224)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|ciliary membrane (GO:0060170)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|exocyst (GO:0000145)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|septin complex (GO:0031105)|synapse (GO:0045202)	enzyme regulator activity (GO:0030234)|GTP binding (GO:0005525)			central_nervous_system(2)|endometrium(1)|large_intestine(4)|lung(3)|skin(2)	12		all_cancers(19;7.62e-41)|all_epithelial(40;1.71e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.24e-34)|all cancers(36;7.15e-32)|OV - Ovarian serous cystadenocarcinoma(60;1.21e-15)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;3.16e-06)|Lung(119;7.81e-05)|LUSC - Lung squamous cell carcinoma(224;0.000742)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0889)		TCTTTTCTAGAAAAAATTGAA	0.433																																					.		Atlas-INDEL	.											.	SEPT2	33	.	0			c.218-1A>-						.						66	69	68					2																	242275390		2203	4300	6503	SO:0001630	splice_region_variant	4735	exon5			.	D28540	CCDS2548.1, CCDS63195.1, CCDS74682.1	2q37.3	2013-01-21	2005-01-11	2005-01-12	ENSG00000168385	ENSG00000168385		"Septins"	7729	protein-coding gene	gene with protein product		601506	"neural precursor cell expressed, developmentally down-regulated 5"	DIFF6, NEDD5		8697812	Standard	XM_005247011		Approved	KIAA0158, hNedd5, Pnutl3	uc002wbd.3	Q15019	OTTHUMG00000133394	ENST00000391973.2:c.218-1A>-	chr2.hg19:g.242275390delA		207.0	0.0		143.0	13.0	NM_006155	B4DGE8|Q14132|Q53QU3|Q8IUK9|Q96CB0	Splice_Site	DEL	ENST00000391973.2	hg19	CCDS2548.1																																																																																			.	.		0.433	SEPT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323177.3	NM_006155	Frame_Shift_Del	-	242275390	A	-	242275390	8	5	282	1	0	1	0	1	0	0	1	0	14079	260	9	0	232	0	SEPT2	2	242275390	Splice_Site	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	145858	242275390	923983	243	40477										
C2orf85	285093	hgsc.bcm.edu	37	chr2	242814476	242814476	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gggattcagtggccatgcctGggggcaaaggcttcccggtg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:242814476delG	ENST00000343216.3	+	2	797	c.769delG	c.(769-771)gggfs	p.G258fs		NM_173821.2	NP_776182.2																					GGCCATGCCTGGGGGCAAAGG	0.667																																					p.P256fs		Atlas-INDEL	.											.	.	.	.	0			c.768delT						.						29	33	32					2																	242814476		1905	4115	6020	SO:0001589	frameshift_variant	285093	exon2			.																												ENST00000343216.3:c.769delG	chr2.hg19:g.242814476delG	ENSP00000345374:p.Gly258fs	224.0	0.0		156.0	10.0	NM_173821		Frame_Shift_Del	DEL	ENST00000343216.3	hg19	CCDS42843.1																																																																																			.	.		0.667	CXXC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322310.1			-	242814476	G	-	242814476	7	5	282	1	0	1	0	1	0	0	0	0	2202	1348	47	0	775	0	C2orf85	2	242814476	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	539086	242814476	384897	244	40478										
CNTN6	27255	hgsc.bcm.edu	37	chr3	1414128	1414128	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gatgtcatagacttaaaaaaAggagtggctcattttgaaag	10	4	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:1414128A>G	ENST00000446702.2	+	13	2265	c.1638A>G	c.(1636-1638)aaA>aaG	p.K546K	CNTN6_ENST00000350110.2_Silent_p.K546K|CNTN6_ENST00000539053.1_Silent_p.K474K			Q9UQ52	CNTN6_HUMAN	contactin 6	546	Ig-like C2-type 6.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		ACTTAAAAAAAGGAGTGGCTC	0.368																																					p.K546K		Atlas-SNP	.											.	CNTN6	245	.	0			c.A1638G						.						106	107	107					3																	1414128		2203	4300	6503	SO:0001819	synonymous_variant	27255	exon13			AAAAAAAGGAGTG	AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	2176	protein-coding gene	gene with protein product	"neural adhesion molecule"	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.1638A>G	chr3.hg19:g.1414128A>G		99.0	0.0		74.0	4.0	NM_014461	Q2KHM2	Silent	SNP	ENST00000446702.2	hg19	CCDS2557.1																																																																																			.	.		0.368	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461		G	1414128	A	G	1414128	2	3	282	1	0	0	0	0	0	0	0	1	3647	69	3	2		2	CNTN6	3	1414128	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10		1414128	196608302	245	40479										
CNTN6	27255	hgsc.bcm.edu	37	chr3	1427450	1427450	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gctgggacagggccctcaagCcccccagtcaatgttaccac					rs201612169		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:1427450delC	ENST00000446702.2	+	20	3300	c.2673delC	c.(2671-2673)agcfs	p.S891fs	CNTN6_ENST00000350110.2_Frame_Shift_Del_p.S891fs|CNTN6_ENST00000539053.1_Frame_Shift_Del_p.S819fs			Q9UQ52	CNTN6_HUMAN	contactin 6	891	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		GGCCCTCAAGCCCCCCAGTCA	0.453																																					p.S891fs		Atlas-INDEL	.											.,1	CNTN6	245	.	0			c.2672delG						.						144	143	144					3																	1427450		2203	4300	6503	SO:0001589	frameshift_variant	27255	exon20			.	AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	2176	protein-coding gene	gene with protein product	"neural adhesion molecule"	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.2673delC	chr3.hg19:g.1427450delC	ENSP00000407822:p.Ser891fs	203.0	0.0		150.0	11.0	NM_014461	Q2KHM2	Frame_Shift_Del	DEL	ENST00000446702.2	hg19	CCDS2557.1																																																																																			.	.		0.453	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461		-	1427450	C	-	1427450	7	5	282	1	0	1	0	1	0	0	0	0	3647	738	26	0	2747	0	CNTN6	3	1427450	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	13322	1427450	196594980	246	40480										
SUMF1	285362	hgsc.bcm.edu	37	chr3	4403894	4403894	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttcgaagcagagctatcaggTgtgttctggctccgagcagc	13	10	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:4403894T>C	ENST00000272902.5	-	9	1094	c.1059A>G	c.(1057-1059)acA>acG	p.T353T	SUMF1_ENST00000534863.1_Intron|SUMF1_ENST00000458465.2_Silent_p.T221T|SUMF1_ENST00000405420.2_Silent_p.T333T|SUMF1_ENST00000383843.5_Silent_p.T328T	NM_182760.3	NP_877437.2	Q8NBK3	SUMF1_HUMAN	sulfatase modifying factor 1	353	Interaction with sulfatases.				cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)	metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)			breast(1)|endometrium(1)|large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(3)	13		Melanoma(143;0.068)|Colorectal(144;0.233)		Epithelial(13;0.0147)|OV - Ovarian serous cystadenocarcinoma(96;0.0444)|all cancers(10;0.0549)		AGCTATCAGGTGTGTTCTGGC	0.532																																					p.T353T		Atlas-SNP	.											.	SUMF1	23	.	0			c.A1059G						.						89	81	84					3																	4403894		2203	4300	6503	SO:0001819	synonymous_variant	285362	exon9			ATCAGGTGTGTTC	BC017005	CCDS2564.1, CCDS54548.1, CCDS54549.1	3p26.1	2009-07-23			ENSG00000144455	ENSG00000144455			20376	protein-coding gene	gene with protein product		607939				12757705, 12757706	Standard	NM_182760		Approved	FGE, UNQ3037	uc003bpz.2	Q8NBK3	OTTHUMG00000090269	ENST00000272902.5:c.1059A>G	chr3.hg19:g.4403894T>C		131.0	0.0		96.0	4.0	NM_182760	B4DXK5|B7XD05|E9PGL0|G5E9B0|Q0VAC6|Q0VAC7|Q2NL78|Q53ZE4|Q6UY39|Q96AK5|Q96DK8	Silent	SNP	ENST00000272902.5	hg19	CCDS2564.1																																																																																			.	.		0.532	SUMF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206591.2	NM_182760		C	4403894	T	C	4403894	2	2	282	1	0	0	0	0	0	0	0	1	15400	1683	59	2		2	SUMF1	3	4403894	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2976444	4403894	193618536	247	40481										
TADA3	10474	hgsc.bcm.edu	37	chr3	9827071	9827071	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gattctttcccagacatgtcAggaataggagaatcctccat	8	10	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:9827071A>G	ENST00000301964.2	-	7	1407	c.849T>C	c.(847-849)ccT>ccC	p.P283P	TADA3_ENST00000343450.2_Silent_p.P283P|TADA3_ENST00000440161.1_Silent_p.P283P	NM_006354.2	NP_006345.1	O75528	TADA3_HUMAN	transcriptional adaptor 3	283					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|intracellular estrogen receptor signaling pathway (GO:0030520)|mitotic nuclear division (GO:0007067)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of histone deacetylation (GO:0031063)|regulation of protein phosphorylation (GO:0001932)|regulation of protein stability (GO:0031647)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of tubulin deacetylation (GO:0090043)|transcription, DNA-templated (GO:0006351)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|intracellular (GO:0005622)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|STAGA complex (GO:0030914)|transcription factor TFTC complex (GO:0033276)	ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	16						CAGACATGTCAGGAATAGGAG	0.483																																					p.P283P		Atlas-SNP	.											.	TADA3	36	.	0			c.T849C						.						88	86	87					3																	9827071		2203	4300	6503	SO:0001819	synonymous_variant	10474	exon7			CATGTCAGGAATA	AF069733	CCDS2583.1, CCDS2584.1	3p25.3	2010-08-13	2009-10-02	2009-10-02	ENSG00000171148	ENSG00000171148			19422	protein-coding gene	gene with protein product		602945	"transcriptional adaptor 3 (NGG1 homolog, yeast)-like"	TADA3L		9674425, 11707411	Standard	NM_006354		Approved	FLJ20221, FLJ21329, ADA3, hADA3, NGG1	uc010hcn.2	O75528	OTTHUMG00000128440	ENST00000301964.2:c.849T>C	chr3.hg19:g.9827071A>G		155.0	0.0		123.0	5.0	NM_133480	Q6FI83|Q9UFS2	Silent	SNP	ENST00000301964.2	hg19	CCDS2583.1																																																																																			.	.		0.483	TADA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250236.1			G	9827071	A	G	9827071	2	3	282	1	0	0	0	0	0	0	0	1	15527	175	7	2		2	TADA3	3	9827071	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	5423177	9827071	188195359	248	40482										
CRELD1	78987	hgsc.bcm.edu	37	chr3	9984844	9984844	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctggctatcagcaggtgggcTccaagtgtctcggtgagtct	14	10	3	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:9984844T>C	ENST00000383811.3	+	8	1500	c.901T>C	c.(901-903)Tcc>Ccc	p.S301P	CRELD1_ENST00000489674.1_3'UTR|CRELD1_ENST00000397170.3_Missense_Mutation_p.S301P|CRELD1_ENST00000326434.5_Missense_Mutation_p.S301P|CRELD1_ENST00000452070.1_Missense_Mutation_p.S301P	NM_015513.4	NP_056328	Q96HD1	CREL1_HUMAN	cysteine-rich with EGF-like domains 1	301					cardiac septum development (GO:0003279)|endocardial cushion development (GO:0003197)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)|urinary_tract(1)	14						GCAGGTGGGCTCCAAGTGTCT	0.607																																					p.S301P		Atlas-SNP	.											.	CRELD1	48	.	0			c.T901C						.						50	50	50					3																	9984844		2203	4300	6503	SO:0001583	missense	78987	exon9			GTGGGCTCCAAGT	AF452623	CCDS2593.1, CCDS33693.1	3p25.3	2005-12-08	2004-02-13		ENSG00000163703	ENSG00000163703			14630	protein-coding gene	gene with protein product		607170	"atrioventricular septal defect 2"	AVSD2		10922384, 12137942	Standard	NM_015513		Approved		uc003buf.3	Q96HD1	OTTHUMG00000128653	ENST00000383811.3:c.901T>C	chr3.hg19:g.9984844T>C	ENSP00000373322:p.Ser301Pro	204.0	0.0		157.0	7.0	NM_001077415	A8MX90|B2RAA9|Q6I9X5|Q8NFT4|Q9Y409	Missense_Mutation	SNP	ENST00000383811.3	hg19	CCDS2593.1	.	.	.	.	.	.	.	.	.	.	T	17.45	3.392787	0.62066	.	.	ENSG00000163703	ENST00000397170;ENST00000383811;ENST00000452070;ENST00000326434	D;D;D;D	0.87966	-2.32;-2.32;-2.32;-2.32	4.67	3.56	0.40772	Growth factor, receptor (1);	0.244831	0.39834	N	0.001255	T	0.80369	0.4610	N	0.21240	0.645	0.33581	D	0.599836	P;P	0.51933	0.855;0.949	B;P	0.48454	0.36;0.578	T	0.82384	-0.0484	9	.	.	.	.	8.403	0.32597	0.0:0.0:0.3872:0.6128	.	301;301	Q96HD1;Q96HD1-2	CREL1_HUMAN;.	P	301	ENSP00000380355:S301P;ENSP00000373322:S301P;ENSP00000393643:S301P;ENSP00000321856:S301P	.	S	+	1	0	CRELD1	9959844	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.774000	0.68906	1.734000	0.51633	0.459000	0.35465	TCC	.	.		0.607	CRELD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250533.1	NM_015513		C	9984844	T	C	9984844	3	2	282	1	0	0	0	0	1	0	0	0	3868	1551	54	2	931	2	CRELD1	3	9984844	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	157773	9984844	188037586	249	40483										
TMEM43	79188	hgsc.bcm.edu	37	chr3	14174380	14174380	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gagcagacactgaatggaggTcagaaatcatcaacagcaaa	10	8	3	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:14174380T>C	ENST00000306077.4	+	6	711	c.457T>C	c.(457-459)Tca>Cca	p.S153P	RP11-434D12.1_ENST00000608606.1_5'Flank	NM_024334.2	NP_077310.1	Q9BTV4	TMM43_HUMAN	transmembrane protein 43	153					nuclear membrane organization (GO:0071763)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|cervix(3)|endometrium(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(2)	19						TGAATGGAGGTCAGAAATCAT	0.562																																					p.S153P		Atlas-SNP	.											.	TMEM43	33	.	0			c.T457C						.						85	87	86					3																	14174380		2203	4300	6503	SO:0001583	missense	79188	exon6			TGGAGGTCAGAAA	BC008054	CCDS2618.1	3p25.1	2014-09-17			ENSG00000170876	ENSG00000170876			28472	protein-coding gene	gene with protein product		612048	"arrhythmogenic right ventricular dysplasia 5"	ARVD5		11230166, 18313022	Standard	NM_024334		Approved	MGC3222, DKFZp586G1919, LUMA	uc003byk.2	Q9BTV4	OTTHUMG00000129802	ENST00000306077.4:c.457T>C	chr3.hg19:g.14174380T>C	ENSP00000303992:p.Ser153Pro	228.0	0.0		138.0	8.0	NM_024334	Q7L4N5|Q8NC30|Q96A63|Q96F19|Q96JX0|Q9H076	Missense_Mutation	SNP	ENST00000306077.4	hg19	CCDS2618.1	.	.	.	.	.	.	.	.	.	.	T	17.50	3.405530	0.62288	.	.	ENSG00000170876	ENST00000306077	T	0.40476	1.03	5.08	3.84	0.44239	.	0.138505	0.50627	D	0.000118	T	0.32164	0.0820	L	0.39898	1.24	0.47778	D	0.99951	P;P	0.39326	0.668;0.473	B;B	0.38712	0.233;0.28	T	0.14671	-1.0464	10	0.54805	T	0.06	-10.7548	7.6526	0.28356	0.0:0.0761:0.1408:0.7832	.	83;153	Q8TEP9;Q9BTV4	.;TMM43_HUMAN	P	153	ENSP00000303992:S153P	ENSP00000303992:S153P	S	+	1	0	TMEM43	14149381	1.000000	0.71417	0.997000	0.53966	0.922000	0.55478	3.222000	0.51223	1.900000	0.55004	0.482000	0.46254	TCA	.	.		0.562	TMEM43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252030.2	NM_024334		C	14174380	T	C	14174380	3	2	282	1	0	0	0	0	1	0	0	0	16182	1667	58	2	479	2	TMEM43	3	14174380	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	4189536	14174380	183848050	250	40484										
C3orf19	51244	hgsc.bcm.edu	37	chr3	14708332	14708332	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttttattagtcctgctaatgAaaaaaccctattatctgaag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:14708332delA	ENST00000383794.3	+	7	675	c.602delA	c.(601-603)gaafs	p.E201fs	CCDC174_ENST00000303688.7_Frame_Shift_Del_p.E201fs	NM_016474.4	NP_057558.3	Q6PII3	CC174_HUMAN	coiled-coil domain containing 174	201						cytoplasm (GO:0005737)|nucleus (GO:0005634)											CCTGCTAATGAAAAAACCCTA	0.418																																					p.E201fs		Atlas-INDEL	.											.	.	.	.	0			c.601delG						.						133	155	147					3																	14708332		2203	4300	6503	SO:0001589	frameshift_variant	51244	exon7			.	AF151046	CCDS2620.2	3p25.1	2012-09-20	2012-09-20	2012-09-20	ENSG00000154781	ENSG00000154781			28033	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 19"	C3orf19		11042152	Standard	NM_016474		Approved	FLJ33839	uc003byw.3	Q6PII3	OTTHUMG00000129837	ENST00000383794.3:c.602delA	chr3.hg19:g.14708332delA	ENSP00000373304:p.Glu201fs	228.0	0.0		153.0	10.0	NM_016474	Q96CS5	Frame_Shift_Del	DEL	ENST00000383794.3	hg19	CCDS2620.2																																																																																			.	.		0.418	CCDC174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252077.2	NM_016474		-	14708332	A	-	14708332	7	5	282	1	0	1	0	1	0	0	0	0	2214	246	9	0	628	0	C3orf19	3	14708332	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	533952	14708332	183314098	251	40485										
ZFYVE20	64145	hgsc.bcm.edu	37	chr3	15132024	15132024	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttcaacaacctgtcctttgcTtttttagccttctggacaag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:15132024delT	ENST00000253699.3	-	5	784	c.171delA	c.(169-171)aaafs	p.K57fs	ZFYVE20_ENST00000476527.2_Frame_Shift_Del_p.K57fs|ZFYVE20_ENST00000449964.2_5'UTR|ZFYVE20_ENST00000435849.3_Frame_Shift_Del_p.K57fs	NM_022340.2	NP_071735.2	Q9H1K0	RBNS5_HUMAN	zinc finger, FYVE domain containing 20	57					blood coagulation (GO:0007596)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	endosome (GO:0005768)|endosome membrane (GO:0010008)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|skin(3)|stomach(1)|urinary_tract(2)	26						TGTCCTTTGCTTTTTTAGCCT	0.408																																					p.A58fs		Atlas-INDEL	.											.	ZFYVE20	61	.	0			c.172delG						.						181	155	164					3																	15132024		2203	4300	6503	SO:0001589	frameshift_variant	64145	exon5			.	AY009133	CCDS2623.1	3p25.1	2014-01-15			ENSG00000131381	ENSG00000131381		"Zinc fingers, FYVE domain containing"	20759	protein-coding gene	gene with protein product		609511				11062261	Standard	XR_427283		Approved	Rabenosyn-5	uc003bzm.1	Q9H1K0	OTTHUMG00000129860	ENST00000253699.3:c.171delA	chr3.hg19:g.15132024delT	ENSP00000253699:p.Lys57fs	219.0	0.0		184.0	13.0	NM_022340	B4DWY8|C9J4P5|Q3KP30|Q59EY8|Q8NAQ1	Frame_Shift_Del	DEL	ENST00000253699.3	hg19	CCDS2623.1																																																																																			.	.		0.408	ZFYVE20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252102.2	NM_022340		-	15132024	T	-	15132024	7	5	282	1	0	1	0	1	0	0	0	0	17681	1606	56	0	2223	0	ZFYVE20	3	15132024	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	423692	15132024	182890406	252	40486										
SH3BP5	9467	hgsc.bcm.edu	37	chr3	15311265	15311265	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcctgccaggcggagtcgaaCtgccgcttgtcatcctccag	11	15	1	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:15311265C>T	ENST00000383791.3	-	4	670	c.450G>A	c.(448-450)caG>caA	p.Q150Q	SH3BP5_ENST00000465894.2_5'Flank|SH3BP5_ENST00000253688.5_5'UTR|SH3BP5_ENST00000426925.1_5'UTR|SH3BP5_ENST00000408919.3_5'UTR	NM_004844.4	NP_004835.2	O60239	3BP5_HUMAN	SH3-domain binding protein 5 (BTK-associated)	150					intracellular signal transduction (GO:0035556)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	protein kinase inhibitor activity (GO:0004860)			NS(1)|endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	12						CGGAGTCGAACTGCCGCTTGT	0.652																																					p.Q150Q		Atlas-SNP	.											.	SH3BP5	32	.	0			c.G450A						.						88	88	88					3																	15311265		2203	4300	6503	SO:0001819	synonymous_variant	9467	exon4			GTCGAACTGCCGC	AB005047	CCDS2625.2, CCDS43055.1	3p24.3	2008-07-10			ENSG00000131370	ENSG00000131370			10827	protein-coding gene	gene with protein product	"SH3 binding protein"	605612				9571151, 10339589	Standard	NM_004844		Approved	Sab	uc003bzp.2	O60239	OTTHUMG00000129859	ENST00000383791.3:c.450G>A	chr3.hg19:g.15311265C>T		166.0	0.0		135.0	6.0	NM_004844	B3KQW6|Q5JWV9	Silent	SNP	ENST00000383791.3	hg19	CCDS2625.2																																																																																			.	.		0.652	SH3BP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340740.2	NM_004844		T	15311265	C	T	15311265	2	4	282	1	0	0	0	0	0	0	0	1	14262	564	20	3		3	SH3BP5	3	15311265	Silent	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	179241	15311265	182711165	253	40487										
RARB	5915	hgsc.bcm.edu	37	chr3	25470337	25470337	+	Intron	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctctcaaagcatgcttcagtGgattgacccaaaccgaatgg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:25470337delG	ENST00000404969.1	+	2	178				RARB_ENST00000330688.4_Frame_Shift_Del_p.G39fs|RARB_ENST00000462272.1_3'UTR|RARB_ENST00000437042.2_Intron			P10826	RARB_HUMAN	retinoic acid receptor, beta						embryonic digestive tract development (GO:0048566)|embryonic eye morphogenesis (GO:0048048)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|glandular epithelial cell development (GO:0002068)|growth plate cartilage development (GO:0003417)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of myelination (GO:0031641)|retinal pigment epithelium development (GO:0003406)|signal transduction (GO:0007165)|striatum development (GO:0021756)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ureteric bud development (GO:0001657)|ventricular cardiac muscle cell differentiation (GO:0055012)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|drug binding (GO:0008144)|retinoic acid receptor activity (GO:0003708)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(3)|kidney(1)|large_intestine(10)|lung(11)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	28					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Tamibarotene(DB04942)|Tazarotene(DB00799)	ATGCTTCAGTGGATTGACCCA	0.458																																					p.S38fs		Atlas-INDEL	.											.	RARB	123	.	0			c.114delT						.						149	126	134					3																	25470337		2203	4300	6503	SO:0001627	intron_variant	5915	exon1			.	Y00291	CCDS2642.1, CCDS46775.1	3p24	2013-01-16			ENSG00000077092	ENSG00000077092		"Nuclear hormone receptors"	9865	protein-coding gene	gene with protein product		180220					Standard	NM_016152		Approved	HAP, NR1B2, RRB2	uc003cdh.3	P10826	OTTHUMG00000130480	ENST00000404969.1:c.179-32347G>-	chr3.hg19:g.25470337delG		213.0	0.0		142.0	10.0	NM_000965	P12891|Q00989|Q15298|Q9UN48	Frame_Shift_Del	DEL	ENST00000404969.1	hg19																																																																																				.	.		0.458	RARB-201	KNOWN	basic	protein_coding	protein_coding		NM_000965, NM_016152		-	25470337	G	-	25470337	6	5	282	0	1	1	0	1	0	0	0	0	13068	1349	47	0		0	RARB	3	25470337	Intron	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	10159072	25470337	172552093	254	40488										
SLC4A7	9497	hgsc.bcm.edu	37	chr3	27439766	27439766	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaaaaacaagatgacacaccAaaagagcacatctggaatat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:27439766delA	ENST00000295736.5	-	17	2549	c.2479delT	c.(2479-2481)tggfs	p.W827fs	SLC4A7_ENST00000454389.1_Frame_Shift_Del_p.W836fs|SLC4A7_ENST00000428386.1_Frame_Shift_Del_p.W703fs|SLC4A7_ENST00000445684.1_Frame_Shift_Del_p.W823fs|SLC4A7_ENST00000435667.2_Frame_Shift_Del_p.W712fs|SLC4A7_ENST00000455077.1_Frame_Shift_Del_p.W708fs|SLC4A7_ENST00000437179.1_Frame_Shift_Del_p.W708fs|SLC4A7_ENST00000388777.4_Frame_Shift_Del_p.W377fs|SLC4A7_ENST00000425128.2_3'UTR|SLC4A7_ENST00000446700.1_Frame_Shift_Del_p.W819fs|SLC4A7_ENST00000440156.1_Frame_Shift_Del_p.W823fs	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	827					auditory receptor cell development (GO:0060117)|bicarbonate transport (GO:0015701)|cochlear nucleus development (GO:0021747)|ion transport (GO:0006811)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal cell programmed cell death (GO:0046666)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(9)|ovary(4)|skin(1)	38					Sodium bicarbonate(DB01390)	ATGACACACCAAAAGAGCACA	0.368																																					p.W827fs		Atlas-INDEL	.											.	SLC4A7	119	.	0			c.2480delG						.						116	117	117					3																	27439766		2203	4300	6503	SO:0001589	frameshift_variant	9497	exon17			.	AB012130	CCDS33721.1, CCDS58819.1, CCDS58820.1	3p24.1	2013-05-22			ENSG00000033867	ENSG00000033867		"Solute carriers"	11033	protein-coding gene	gene with protein product		603353		SLC4A6		10198178, 9610397	Standard	NM_003615		Approved	NBC3, SBC2	uc003cdv.4	Q9Y6M7	OTTHUMG00000155679	ENST00000295736.5:c.2479delT	chr3.hg19:g.27439766delA	ENSP00000295736:p.Trp827fs	241.0	0.0		183.0	11.0	NM_003615	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Frame_Shift_Del	DEL	ENST00000295736.5	hg19	CCDS33721.1																																																																																			.	.		0.368	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615		-	27439766	A	-	27439766	7	5	282	1	0	1	0	1	0	0	0	0	14673	130	5	0	1201	0	SLC4A7	3	27439766	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1969429	27439766	170582664	255	40489										
GOLGA4	2803	hgsc.bcm.edu	37	chr3	37366955	37366955	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gagtttgaaatcttcacatgAaaaaagtaacaaaagcctag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:37366955delA	ENST00000361924.2	+	14	3952	c.3578delA	c.(3577-3579)gaafs	p.E1193fs	GOLGA4_ENST00000356847.4_Frame_Shift_Del_p.E1215fs|GOLGA4_ENST00000444882.1_Intron	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	1193	Glu-rich.				Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						TCTTCACATGAAAAAAGTAAC	0.393																																					p.E1215fs		Atlas-INDEL	.											.	GOLGA4	173	.	0			c.3643delG						.						36	39	38					3																	37366955		2201	4296	6497	SO:0001589	frameshift_variant	2803	exon15			.	U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"golgin 245"	602509	"golgi autoantigen, golgin subfamily a, 4"			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.3578delA	chr3.hg19:g.37366955delA	ENSP00000354486:p.Glu1193fs	288.0	0.0		233.0	15.0	NM_001172713	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Frame_Shift_Del	DEL	ENST00000361924.2	hg19	CCDS2666.1																																																																																			.	.		0.393	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078		-	37366955	A	-	37366955	7	5	282	1	0	1	0	1	0	0	0	0	6563	246	9	0	3702	0	GOLGA4	3	37366955	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	9927189	37366955	160655475	256	40490										
SCN10A	6336	hgsc.bcm.edu	37	chr3	38793861	38793861	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccccacccagcagcagagagCcccgatggctttcgtggtct					rs556526024		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:38793861delC	ENST00000449082.2	-	11	1603	c.1604delG	c.(1603-1605)ggcfs	p.G535fs		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	535					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	CAGCAGAGAGCCCCGATGGCT	0.597																																					p.G535fs		Atlas-INDEL	.											.	SCN10A	359	.	0			c.1605delC						.						62	68	66					3																	38793861		2203	4300	6503	SO:0001589	frameshift_variant	6336	exon11			.	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10582	protein-coding gene	gene with protein product		604427	"sodium channel, voltage-gated, type X, alpha polypeptide"			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.1604delG	chr3.hg19:g.38793861delC	ENSP00000390600:p.Gly535fs	193.0	0.0		127.0	10.0	NM_006514	A6NDQ1	Frame_Shift_Del	DEL	ENST00000449082.2	hg19	CCDS33736.1																																																																																			.	.		0.597	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		-	38793861	C	-	38793861	7	5	282	1	0	1	0	1	0	0	0	0	13927	739	26	0	4334	0	SCN10A	3	38793861	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1426906	38793861	159228569	257	40491										
XIRP1	165904	hgsc.bcm.edu	37	chr3	39227535	39227535	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccatcctgaattgtcacccaCcccccaggcagccctctggg					rs575108313		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:39227535delC	ENST00000340369.3	-	2	3630	c.3402delG	c.(3400-3402)gggfs	p.G1134fs	XIRP1_ENST00000421646.1_Intron|XIRP1_ENST00000396251.1_Intron	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	1134					cardiac muscle cell development (GO:0055013)|negative regulation of cell proliferation (GO:0008285)|regulation of membrane potential (GO:0042391)|sarcomere organization (GO:0045214)	fascia adherens (GO:0005916)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(14)|lung(22)|ovary(4)|pancreas(1)|prostate(2)|skin(6)	71				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		TTGTCACCCACCCCCCAGGCA	0.607																																					p.W1135fs		Atlas-INDEL	.											.	XIRP1	173	.	0			c.3403delT						.						67	70	69					3																	39227535		2203	4300	6503	SO:0001589	frameshift_variant	165904	exon2			.	AW755250	CCDS2683.1, CCDS56245.1	3p21.33	2008-02-05	2007-06-27	2007-06-27	ENSG00000168334	ENSG00000168334			14301	protein-coding gene	gene with protein product		609777	"cardiomyopathy associated 1"	CMYA1		12203715, 15454575	Standard	NM_001198621		Approved	DKFZp451D042, Xin	uc003cjk.2	Q702N8	OTTHUMG00000131297	ENST00000340369.3:c.3402delG	chr3.hg19:g.39227535delC	ENSP00000343140:p.Gly1134fs	222.0	0.0		164.0	11.0	NM_194293	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Frame_Shift_Del	DEL	ENST00000340369.3	hg19	CCDS2683.1																																																																																			.	.		0.607	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522		-	39227535	C	-	39227535	7	5	282	1	0	1	0	1	0	0	0	0	17444	494	18	0	2133	0	XIRP1	3	39227535	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	433674	39227535	158794895	258	40492										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266104	41266104	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acagtcttacctggactctgGaatccattctggtgccacta	8	12	3	0	rs28931589|rs121913416		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:41266104G>T	ENST00000349496.5	+	3	381	c.101G>T	c.(100-102)gGa>gTa	p.G34V	CTNNB1_ENST00000396185.3_Missense_Mutation_p.G34V|CTNNB1_ENST00000405570.1_Missense_Mutation_p.G34V|CTNNB1_ENST00000453024.1_Missense_Mutation_p.G27V|CTNNB1_ENST00000396183.3_Missense_Mutation_p.G34V	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	34			G -> E (in PTR). {ECO:0000269|PubMed:10192393}.|G -> R (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|G -> V (in hepatoblastoma; dbSNP:rs28931589). {ECO:0000269|PubMed:9927029}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.G34E(73)|p.G34V(72)|p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.D32_H36>D(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.D32fs*9(1)|p.A5_T40del(1)|p.S29_H36del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.GIHS34?(1)|p.A5_I35del(1)|p.D32_H36del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CTGGACTCTGGAATCCATTCT	0.488	G34E(AGS_STOMACH)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.G34V	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,0,161	CTNNB1	4904	.	276	Substitution - Missense(145)|Deletion - In frame(105)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(146)|endometrium(30)|large_intestine(27)|stomach(21)|central_nervous_system(20)|skin(8)|pancreas(8)|ovary(6)|small_intestine(2)|lung(2)|adrenal_gland(1)|haematopoietic_and_lymphoid_tissue(1)|biliary_tract(1)|pituitary(1)|prostate(1)|bone(1)	c.G101T						.						93	78	83					3																	41266104		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	ACTCTGGAATCCA	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.101G>T	chr3.hg19:g.41266104G>T	ENSP00000344456:p.Gly34Val	491.0	0.0		299.0	112.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.450603	0.84101	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.53206	0.63;0.63;0.63;0.63;0.63;0.63;0.63;0.63;0.63	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.72053	0.3413	M	0.79258	2.445	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74188	-0.3746	10	0.87932	D	0	-31.2232	19.9596	0.97236	0.0:0.0:1.0:0.0	rs28931589	34	P35222	CTNB1_HUMAN	V	27;34;34;34;34;27;34;34;34	ENSP00000400508:G27V;ENSP00000385604:G34V;ENSP00000412219:G34V;ENSP00000379486:G34V;ENSP00000344456:G34V;ENSP00000411226:G27V;ENSP00000379488:G34V;ENSP00000409302:G34V;ENSP00000401599:G34V	ENSP00000344456:G34V	G	+	2	0	CTNNB1	41241108	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.726000	0.93360	0.655000	0.94253	GGA	.	.		0.488	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41266104	G	T	41266104	3	4	282	1	0	0	0	0	1	0	0	0	4018	1174	41	3	107	3	CTNNB1	3	41266104	Missense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	2038569	41266104	156756326	259	40493										
ABHD5	51099	hgsc.bcm.edu	37	chr3	43753215	43753215	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caacagggttaatcatctcaTtttagtggagccttggggtt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:43753215delT	ENST00000458276.2	+	4	644	c.521delT	c.(520-522)attfs	p.I174fs		NM_016006.4	NP_057090.2	Q8WTS1	ABHD5_HUMAN	abhydrolase domain containing 5	174					cell differentiation (GO:0030154)|fatty acid metabolic process (GO:0006631)|negative regulation of sequestering of triglyceride (GO:0010891)|phosphatidic acid biosynthetic process (GO:0006654)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of triglyceride catabolic process (GO:0010898)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|nucleus (GO:0005634)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)|lysophosphatidic acid acyltransferase activity (GO:0042171)			kidney(3)|large_intestine(2)|liver(2)|lung(5)|ovary(1)|skin(1)	14		Renal(3;0.0134)		KIRC - Kidney renal clear cell carcinoma(197;0.0546)|Kidney(197;0.0687)		AATCATCTCATTTTAGTGGAG	0.408																																					p.I174fs		Atlas-INDEL	.											.	ABHD5	33	.	0			c.520delA						.						102	96	98					3																	43753215		2203	4300	6503	SO:0001589	frameshift_variant	51099	exon4			.	AF007132	CCDS2711.1	3p21.33	2012-05-16			ENSG00000011198	ENSG00000011198		"Abhydrolase domain containing"	21396	protein-coding gene	gene with protein product		604780				11590543, 18606822	Standard	NM_016006		Approved	CGI-58, NCIE2	uc003cmx.3	Q8WTS1	OTTHUMG00000133039	ENST00000458276.2:c.521delT	chr3.hg19:g.43753215delT	ENSP00000390849:p.Ile174fs	211.0	0.0		151.0	11.0	NM_016006	B2R9K0|Q9Y369	Frame_Shift_Del	DEL	ENST00000458276.2	hg19	CCDS2711.1																																																																																			.	.		0.408	ABHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256644.2	NM_016006		-	43753215	T	-	43753215	7	5	282	1	0	1	0	1	0	0	0	0	85	1493	52	0	535	0	ABHD5	3	43753215	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2487111	43753215	154269215	260	40494										
KIF15	56992	hgsc.bcm.edu	37	chr3	44816769	44816769	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgaaggtgatgccatcaaagTttttgtgcgaattcgtcctc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:44816769delT	ENST00000326047.4	+	3	235	c.86delT	c.(85-87)gttfs	p.V29fs		NM_020242.2	NP_064627.1	Q9NS87	KIF15_HUMAN	kinesin family member 15	29	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|plus-end kinesin complex (GO:0005873)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(5)	36				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)		GCCATCAAAGTTTTTGTGCGA	0.418																																					p.V29fs		Atlas-INDEL	.											.	KIF15	103	.	0			c.85delG						.						146	133	137					3																	44816769		2203	4300	6503	SO:0001589	frameshift_variant	56992	exon3			.	AB035898	CCDS33744.1	3p21.31	2008-03-03	2005-03-15	2005-03-17	ENSG00000163808	ENSG00000163808		"Kinesins"	17273	protein-coding gene	gene with protein product			"kinesin-like 7"	KNSL7		10878014	Standard	NM_020242		Approved	HKLP2, NY-BR-62	uc003cnx.4	Q9NS87	OTTHUMG00000156307	ENST00000326047.4:c.86delT	chr3.hg19:g.44816769delT	ENSP00000324020:p.Val29fs	212.0	0.0		167.0	11.0	NM_020242	Q17RV9|Q69YL6|Q96JX7|Q9H280	Frame_Shift_Del	DEL	ENST00000326047.4	hg19	CCDS33744.1																																																																																			.	.		0.418	KIF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343831.2			-	44816769	T	-	44816769	7	5	282	1	0	1	0	1	0	0	0	0	8286	1725	60	0	96	0	KIF15	3	44816769	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1063554	44816769	153205661	261	40495										
XCR1	2829	hgsc.bcm.edu	37	chr3	46062566	46062566	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caggtgtgtgcggaacttgaCccccacgaagacatagagca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:46062566delC	ENST00000309285.3	-	2	1230	c.874delG	c.(874-876)gtcfs	p.V292fs	XCR1_ENST00000542109.1_Frame_Shift_Del_p.V292fs	NM_001024644.1	NP_001019815.1	P46094	XCR1_HUMAN	chemokine (C motif) receptor 1	292					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|inflammatory response (GO:0006954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|release of sequestered calcium ion into cytosol (GO:0051209)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)			NS(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|prostate(2)	14				BRCA - Breast invasive adenocarcinoma(193;0.00113)|KIRC - Kidney renal clear cell carcinoma(197;0.0172)|Kidney(197;0.0203)		CGGAACTTGACCCCCACGAAG	0.607																																					p.V292fs		Atlas-INDEL	.											.	XCR1	51	.	0			c.875delT						.						75	78	77					3																	46062566		2203	4300	6503	SO:0001589	frameshift_variant	2829	exon2			.		CCDS2736.1	3p21.3-p21.1	2012-11-19	2006-01-13	2002-08-23	ENSG00000173578	ENSG00000173578		"GPCR / Class A : Chemokine receptors : X-C motif"	1625	protein-coding gene	gene with protein product		600552	"chemokine (C motif) XC receptor 1"	GPR5, CCXCR1		7832990, 10400311	Standard	NM_005283		Approved		uc003cpf.3	P46094	OTTHUMG00000133449	ENST00000309285.3:c.874delG	chr3.hg19:g.46062566delC	ENSP00000310405:p.Val292fs	428.0	0.0		263.0	18.0	NM_001024644		Frame_Shift_Del	DEL	ENST00000309285.3	hg19	CCDS2736.1																																																																																			.	.		0.607	XCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257322.2			-	46062566	C	-	46062566	7	5	282	1	0	1	0	1	0	0	0	0	17440	507	18	0	131	0	XCR1	3	46062566	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1245797	46062566	151959864	262	40496										
CCR5	1234	hgsc.bcm.edu	37	chr3	46414409	46414409	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acaagatggattatcaagtgTcaagtccaatctatgacatc	7	8	3	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:46414409T>C	ENST00000292303.4	+	2	162	c.16T>C	c.(16-18)Tca>Cca	p.S6P	RP11-24F11.2_ENST00000451485.1_RNA|CCR5_ENST00000343801.4_Missense_Mutation_p.S6P|CCR5_ENST00000445772.1_Missense_Mutation_p.S6P	NM_001100168.1	NP_001093638.1	P51681	CCR5_HUMAN	chemokine (C-C motif) receptor 5 (gene/pseudogene)	6					calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|entry into host cell (GO:0030260)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|MAPK cascade (GO:0000165)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to cholesterol (GO:0070723)|signaling (GO:0023052)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|C-C chemokine binding (GO:0019957)|C-C chemokine receptor activity (GO:0016493)|chemokine (C-C motif) ligand 5 binding (GO:0071791)|chemokine receptor activity (GO:0004950)|coreceptor activity (GO:0015026)|phosphatidylinositol phospholipase C activity (GO:0004435)			central_nervous_system(1)|large_intestine(2)|lung(13)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20				BRCA - Breast invasive adenocarcinoma(193;0.00112)|KIRC - Kidney renal clear cell carcinoma(197;0.017)|Kidney(197;0.02)	Maraviroc(DB04835)	TTATCAAGTGTCAAGTCCAAT	0.408																																					p.S6P		Atlas-SNP	.											.	CCR5	128	.	0			c.T16C						.						108	116	113					3																	46414409		2203	4296	6499	SO:0001583	missense	1234	exon3			CAAGTGTCAAGTC		CCDS2739.1	3p21	2012-08-08	2012-01-23		ENSG00000160791	ENSG00000160791		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1606	protein-coding gene	gene with protein product		601373	"chemokine (C-C motif) receptor 5"	CMKBR5		8639485	Standard	NM_001100168		Approved	CKR-5, CC-CKR-5, CKR5, CD195, IDDM22	uc003cpo.4	P51681	OTTHUMG00000133481	ENST00000292303.4:c.16T>C	chr3.hg19:g.46414409T>C	ENSP00000292303:p.Ser6Pro	107.0	0.0		83.0	5.0	NM_000579	O14692|O14693|O14695|O14696|O14697|O14698|O14699|O14700|O14701|O14702|O14703|O14704|O14705|O14706|O14707|O14708|O15538|Q9UPA4	Missense_Mutation	SNP	ENST00000292303.4	hg19	CCDS2739.1	.	.	.	.	.	.	.	.	.	.	T	17.55	3.417258	0.62622	.	.	ENSG00000160791	ENST00000343801;ENST00000292303;ENST00000445772	T;T;T	0.71222	-0.55;-0.55;-0.55	5.16	-10.3	0.00346	.	0.662303	0.12189	U	0.491419	T	0.42268	0.1195	N	0.20401	0.57	0.09310	N	1	B	0.34226	0.443	B	0.34301	0.179	T	0.35871	-0.9771	10	0.31617	T	0.26	.	3.9897	0.09532	0.141:0.0818:0.1953:0.5819	.	6	P51681	CCR5_HUMAN	P	6	ENSP00000343985:S6P;ENSP00000292303:S6P;ENSP00000404881:S6P	ENSP00000292303:S6P	S	+	1	0	CCR5	46389413	0.000000	0.05858	0.000000	0.03702	0.866000	0.49608	-4.085000	0.00298	-3.515000	0.00149	0.459000	0.35465	TCA	.	.		0.408	CCR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257377.2	NM_000579		C	46414409	T	C	46414409	3	2	282	1	0	0	0	0	1	0	0	0	2946	1667	58	2	18	2	CCR5	3	46414409	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	351843	46414409	151608021	263	40497										
SCAP	22937	hgsc.bcm.edu	37	chr3	47459317	47459317	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cactgtcccggcgctgcctgCtgggggccaggagggcggag	19	13	0	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:47459317C>T	ENST00000265565.5	-	17	2860		c.e17-1		SCAP_ENST00000545718.1_Intron|SCAP_ENST00000465628.1_5'Flank|SCAP_ENST00000441517.2_Intron	NM_012235.2	NP_036367.2	Q12770	SCAP_HUMAN	SREBF chaperone						aging (GO:0007568)|cholesterol metabolic process (GO:0008203)|negative regulation of cholesterol biosynthetic process (GO:0045541)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|regulation of fatty acid biosynthetic process (GO:0042304)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)	unfolded protein binding (GO:0051082)			endometrium(4)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	26				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)		GCGCTGCCTGCTGGGGGCCAg	0.716																																					.	Pancreas(149;978 1908 29304 37806 46700)	Atlas-SNP	.											.	SCAP	88	.	0			c.2448-1G>A						.						12	14	14					3																	47459317		1788	3567	5355	SO:0001630	splice_region_variant	22937	exon18			TGCCTGCTGGGGG	BC020987	CCDS2755.2	3p21.31	2013-01-10			ENSG00000114650	ENSG00000114650		"WD repeat domain containing"	30634	protein-coding gene	gene with protein product	"SREBP cleavage activating protein"	601510				8898195, 8724849, 10570913	Standard	XM_005264967		Approved	KIAA0199	uc003crh.1	Q12770	OTTHUMG00000125539	ENST00000265565.5:c.2448-1G>A	chr3.hg19:g.47459317C>T		102.0	0.0		85.0	4.0	NM_012235	Q8N2E0|Q8WUA1	Splice_Site	SNP	ENST00000265565.5	hg19	CCDS2755.2	.	.	.	.	.	.	.	.	.	.	C	18.66	3.671428	0.67814	.	.	ENSG00000114650	ENST00000265565;ENST00000383739	.	.	.	4.62	-0.573	0.11742	.	.	.	.	.	.	.	.	.	.	.	0.36060	D	0.841372	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1.7192	0.02908	0.1395:0.2827:0.3706:0.2073	.	.	.	.	.	-1	.	.	.	-	.	.	SCAP	47434321	0.270000	0.24152	0.199000	0.23439	0.951000	0.60555	0.542000	0.23222	0.195000	0.20347	0.550000	0.68814	.	.	.		0.716	SCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246872.2	NM_012235	Intron	T	47459317	C	T	47459317	5	4	282	1	0	0	0	0	0	0	1	0	13892	811	28	3	1420	3	SCAP	3	47459317	Splice_Site	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1044908	47459317	150563113	264	40498										
SMARCC1	6599	hgsc.bcm.edu	37	chr3	47727630	47727630	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cccaaggtcaactgatcgacTctgatcacctttggcaggat	9	12	3	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:47727630T>C	ENST00000254480.5	-	14	1413	c.1294A>G	c.(1294-1296)Agt>Ggt	p.S432G	SMARCC1_ENST00000425518.1_5'UTR	NM_003074.3	NP_003065.3	Q92922	SMRC1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1	432					ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|insulin receptor signaling pathway (GO:0008286)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|XY body (GO:0001741)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|protein N-terminus binding (GO:0047485)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(5)|kidney(2)|large_intestine(3)|lung(15)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33				BRCA - Breast invasive adenocarcinoma(193;7.47e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)		ACTGATCGACTCTGATCACCT	0.368																																					p.S432G		Atlas-SNP	.											.	SMARCC1	85	.	0			c.A1294G						.						150	129	136					3																	47727630		2203	4300	6503	SO:0001583	missense	6599	exon14			ATCGACTCTGATC	U66615	CCDS2758.1	3p21.31	2008-05-15			ENSG00000173473	ENSG00000173473			11104	protein-coding gene	gene with protein product		601732				8804307	Standard	NM_003074		Approved	BAF155, SRG3, Rsc8, CRACC1	uc003crq.2	Q92922	OTTHUMG00000133519	ENST00000254480.5:c.1294A>G	chr3.hg19:g.47727630T>C	ENSP00000254480:p.Ser432Gly	119.0	0.0		133.0	6.0	NM_003074	Q17RS0|Q6P172|Q8IWH2	Missense_Mutation	SNP	ENST00000254480.5	hg19	CCDS2758.1	.	.	.	.	.	.	.	.	.	.	T	11.85	1.761401	0.31228	.	.	ENSG00000173473	ENST00000254480	T	0.46451	0.87	5.84	5.84	0.93424	.	0.115587	0.85682	N	0.000000	T	0.32315	0.0825	N	0.25332	0.735	0.44352	D	0.997241	B	0.02656	0.0	B	0.04013	0.001	T	0.06058	-1.0848	10	0.32370	T	0.25	-9.119	15.1063	0.72324	0.0:0.0:0.0:1.0	.	432	Q92922	SMRC1_HUMAN	G	432	ENSP00000254480:S432G	ENSP00000254480:S432G	S	-	1	0	SMARCC1	47702634	0.998000	0.40836	0.996000	0.52242	0.390000	0.30446	2.761000	0.47589	2.240000	0.73641	0.514000	0.50259	AGT	.	.		0.368	SMARCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257491.1			C	47727630	T	C	47727630	3	2	282	1	0	0	0	0	1	0	0	0	14790	1551	54	2	2083	2	SMARCC1	3	47727630	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	268313	47727630	150294800	265	40499										
PLXNB1	5364	hgsc.bcm.edu	37	chr3	48457527	48457527	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cattcagggtgagacgggtgCccccagctctggggccgcgg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:48457527delC	ENST00000358536.4	-	18	3799	c.3530delG	c.(3529-3531)ggcfs	p.G1177fs	PLXNB1_ENST00000465117.1_5'Flank|PLXNB1_ENST00000296440.6_Frame_Shift_Del_p.G1177fs|PLXNB1_ENST00000456774.1_Frame_Shift_Del_p.G994fs|PLXNB1_ENST00000448774.2_Intron|PLXNB1_ENST00000358459.4_Frame_Shift_Del_p.G994fs	NM_002673.4	NP_002664.2	O43157	PLXB1_HUMAN	plexin B1	1177	IPT/TIG 2.				axon guidance (GO:0007411)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast proliferation (GO:0033689)|neuron projection morphogenesis (GO:0048812)|ossification involved in bone maturation (GO:0043931)|positive regulation of axonogenesis (GO:0050772)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	GTPase activating protein binding (GO:0032794)|receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		GAGACGGGTGCCCCCAGCTCT	0.622																																					p.G1177fs		Atlas-INDEL	.											.	PLXNB1	150	.	0			c.3531delC						.						20	22	21					3																	48457527		2197	4298	6495	SO:0001589	frameshift_variant	5364	exon18			.	X87904	CCDS2765.1	3p21.31	2008-07-18			ENSG00000164050	ENSG00000164050		"Plexins"	9103	protein-coding gene	gene with protein product		601053		PLXN5		8570614, 11035813	Standard	XM_005265234		Approved	SEP, KIAA0407	uc003csw.2	O43157	OTTHUMG00000133527	ENST00000358536.4:c.3530delG	chr3.hg19:g.48457527delC	ENSP00000351338:p.Gly1177fs	260.0	0.0		182.0	13.0	NM_001130082	A6H8Y2|Q6NY20|Q9UIV7|Q9UJ92|Q9UJ93	Frame_Shift_Del	DEL	ENST00000358536.4	hg19	CCDS2765.1																																																																																			.	.		0.622	PLXNB1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344454.1	NM_002673		-	48457527	C	-	48457527	7	5	282	1	0	1	0	1	0	0	0	0	12132	739	26	0	2961	0	PLXNB1	3	48457527	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	729897	48457527	149564903	266	40500										
COL7A1	1294	hgsc.bcm.edu	37	chr3	48608294	48608294	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgctgttcccagcccctcacCcgctctccactagggcctgg	9	19	2	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:48608294C>T	ENST00000328333.8	-	94	7379	c.7272G>A	c.(7270-7272)cgG>cgA	p.R2424R	COL7A1_ENST00000454817.1_Splice_Site_p.R2392R	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	2424	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		AGCCCCTCACCCGCTCTCCAC	0.662																																					p.R2424R		Atlas-SNP	.											.	COL7A1	320	.	0			c.G7272A						.						34	28	30					3																	48608294		2202	4300	6502	SO:0001630	splice_region_variant	1294	exon94			CCTCACCCGCTCT	L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"Collagens", "Fibronectin type III domain containing"	2214	protein-coding gene	gene with protein product	"collagen VII, alpha-1 polypeptide", "LC collagen"	120120	"epidermolysis bullosa, dystrophic, dominant and recessive"	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.7272+1G>A	chr3.hg19:g.48608294C>T		210.0	0.0		173.0	74.0	NM_000094	Q14054|Q16507	Silent	SNP	ENST00000328333.8	hg19	CCDS2773.1																																																																																			.	.		0.662	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094	Silent	T	48608294	C	T	48608294	5	4	282	1	0	0	0	0	0	0	1	0	3706	637	22	3	1662	3	COL7A1	3	48608294	Splice_Site	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	150767	48608294	149414136	267	40501										
APEH	327	hgsc.bcm.edu	37	chr3	49714427	49714427	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctgcagtacccatctctgatCccccatcaccaatgcagcca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:49714427delC	ENST00000296456.5	+	10	1369	c.969delC	c.(967-969)atcfs	p.I323fs	APEH_ENST00000438011.1_Frame_Shift_Del_p.I323fs	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase	323					beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		CATCTCTGATCCCCCATCACC	0.602																																					p.I323fs		Atlas-INDEL	.											.	APEH	45	.	0			c.968delT						.						83	72	76					3																	49714427		2203	4300	6503	SO:0001589	frameshift_variant	327	exon10			.	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"acylaminoacyl-peptidase"	102645	"N-acylaminoacyl-peptide hydrolase"	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882	ENST00000296456.5:c.969delC	chr3.hg19:g.49714427delC	ENSP00000296456:p.Ile323fs	279.0	0.0		194.0	13.0	NM_001640	Q9BQ33|Q9P0Y2	Frame_Shift_Del	DEL	ENST00000296456.5	hg19	CCDS2801.1																																																																																			.	.		0.602	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2			-	49714427	C	-	49714427	7	5	282	1	0	1	0	1	0	0	0	0	768	845	30	0	1007	0	APEH	3	49714427	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1106133	49714427	148308003	268	40502										
MST1	327	hgsc.bcm.edu	37	chr3	49722913	49722913	+	IGR	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caactcctaacctggggggtCcaggattgatggcggctggt	15	10	0	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:49722913C>T	ENST00000296456.5	+	0	3220				MST1_ENST00000494828.2_5'Flank|MST1_ENST00000383728.3_3'UTR|MST1_ENST00000449682.2_Missense_Mutation_p.D472N|AC099668.5_ENST00000563780.1_RNA	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase						beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		CCTGGGGGGTCCAGGATTGAT	0.592																																					p.D472N		Atlas-SNP	.											.	MST1	84	.	0			c.G1414A						.						29	32	31					3																	49722913		2202	4299	6501	SO:0001628	intergenic_variant	4485	exon12			GGGGGTCCAGGAT	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"acylaminoacyl-peptidase"	102645	"N-acylaminoacyl-peptide hydrolase"	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882		chr3.hg19:g.49722913C>T		366.0	0.0		421.0	22.0	NM_020998	Q9BQ33|Q9P0Y2	Missense_Mutation	SNP	ENST00000296456.5	hg19	CCDS2801.1	.	.	.	.	.	.	.	.	.	.	C	10.90	1.481708	0.26598	.	.	ENSG00000173531	ENST00000449682	T	0.79940	-1.32	4.78	2.98	0.34508	.	0.707688	0.11995	N	0.509451	T	0.60392	0.2265	N	0.08118	0	0.80722	D	1	B	0.21753	0.06	B	0.26094	0.066	T	0.44436	-0.9328	10	0.10636	T	0.68	.	8.1354	0.31052	0.0:0.8059:0.0:0.1941	.	472	G3XAK1	.	N	472	ENSP00000414287:D472N	ENSP00000414287:D472N	D	-	1	0	MST1	49697917	1.000000	0.71417	0.995000	0.50966	0.784000	0.44337	3.079000	0.50104	0.689000	0.31550	0.655000	0.94253	GAC	.	.		0.592	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2			T	49722913	C	T	49722913	1	4	282	0	1	0	0	0	0	0	0	0	9899	855	30	3		3	MST1	3	49722913	IGR	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	8486	49722913	148299517	269	40503										
RNF123	63891	hgsc.bcm.edu	37	chr3	49740083	49740083	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagaacatgcccatgctctgCccccctgagtacatggtctg					rs188127966		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:49740083delC	ENST00000327697.6	+	20	1791	c.1647delC	c.(1645-1647)tgcfs	p.C549fs	RNF123_ENST00000432042.1_Frame_Shift_Del_p.C403fs	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	549					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		CCATGCTCTGCCCCCCTGAGT	0.552																																					p.C549fs		Atlas-INDEL	.											.	RNF123	100	.	0			c.1646delG						.						245	199	214					3																	49740083		2203	4300	6503	SO:0001589	frameshift_variant	63891	exon20			.	AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"RING-type (C3HC4) zinc fingers"	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891	ENST00000327697.6:c.1647delC	chr3.hg19:g.49740083delC	ENSP00000328287:p.Cys549fs	250.0	0.0		180.0	11.0	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Frame_Shift_Del	DEL	ENST00000327697.6	hg19	CCDS33758.1																																																																																			.	.		0.552	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064		-	49740083	C	-	49740083	7	5	282	1	0	1	0	1	0	0	0	0	13448	747	26	0	1721	0	RNF123	3	49740083	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	17170	49740083	148282347	270	40504										
SEMA3F	6405	hgsc.bcm.edu	37	chr3	50225339	50225339	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgtccatgagcgccccgccaCccccaggcgcaggcccccca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:50225339delC	ENST00000002829.3	+	19	2633	c.2149delC	c.(2149-2151)cccfs	p.P718fs	SEMA3F_ENST00000413852.1_Frame_Shift_Del_p.P619fs|SEMA3F_ENST00000434342.1_Frame_Shift_Del_p.P687fs	NM_004186.3	NP_004177.3	Q13275	SEM3F_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F	718					axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|negative regulation of axon extension involved in axon guidance (GO:0048843)|nerve development (GO:0021675)|neural crest cell migration (GO:0001755)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sympathetic ganglion development (GO:0061549)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	extracellular space (GO:0005615)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|receptor activity (GO:0004872)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(2)	17				BRCA - Breast invasive adenocarcinoma(193;0.00013)|KIRC - Kidney renal clear cell carcinoma(197;0.00599)|Kidney(197;0.00688)		CGCCCCGCCACCCCCAGGCGC	0.647																																					p.P716fs		Atlas-INDEL	.											.	SEMA3F	62	.	0			c.2148delA						.						18	18	18					3																	50225339		2201	4296	6497	SO:0001589	frameshift_variant	6405	exon19			.	U33920	CCDS2811.1	3p21.3	2013-01-11			ENSG00000001617	ENSG00000001617		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10728	protein-coding gene	gene with protein product	"sema IV"	601124				8786119, 8649831	Standard	NM_004186		Approved	SEMAK, Sema4	uc003cyj.3	Q13275	OTTHUMG00000156806	ENST00000002829.3:c.2149delC	chr3.hg19:g.50225339delC	ENSP00000002829:p.Pro718fs	315.0	0.0		261.0	16.0	NM_004186	C9JQ85|Q13274|Q13372|Q15704|Q6GTR4	Frame_Shift_Del	DEL	ENST00000002829.3	hg19	CCDS2811.1																																																																																			.	.		0.647	SEMA3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345929.1	NM_004186		-	50225339	C	-	50225339	7	5	282	1	0	1	0	1	0	0	0	0	14044	507	18	0	2219	0	SEMA3F	3	50225339	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	485256	50225339	147797091	271	40505										
DNAH1	25981	hgsc.bcm.edu	37	chr3	52430409	52430409	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagggacttccgcctctggcTcaccagcctgcccagcaaca	9	18	2	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:52430409T>C	ENST00000420323.2	+	71	11546	c.11285T>C	c.(11284-11286)cTc>cCc	p.L3762P		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	3827	AAA 6. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		CGCCTCTGGCTCACCAGCCTG	0.622																																					p.L3762P		Atlas-SNP	.											.	DNAH1	534	.	0			c.T11285C						.						27	31	30					3																	52430409		2092	4214	6306	SO:0001583	missense	25981	exon71			TCTGGCTCACCAG	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.11285T>C	chr3.hg19:g.52430409T>C	ENSP00000401514:p.Leu3762Pro	120.0	0.0		76.0	5.0	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	hg19	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	T	18.28	3.588217	0.66105	.	.	ENSG00000114841	ENST00000420323;ENST00000273600	T	0.20069	2.1	4.35	4.35	0.52113	.	0.000000	0.64402	D	0.000011	T	0.64692	0.2621	H	0.99104	4.43	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.80487	-0.1361	10	0.87932	D	0	.	13.7114	0.62670	0.0:0.0:0.0:1.0	.	3762;3827	C9JXH6;Q9P2D7-2	.;.	P	3762;515	ENSP00000401514:L3762P	ENSP00000273600:L515P	L	+	2	0	DNAH1	52405449	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.757000	0.68766	1.831000	0.53308	0.402000	0.26972	CTC	.	.		0.622	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		C	52430409	T	C	52430409	3	2	282	1	0	0	0	0	1	0	0	0	4599	1551	54	2	11563	2	DNAH1	3	52430409	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2205070	52430409	145592021	272	40506										
NISCH	11188	hgsc.bcm.edu	37	chr3	52524124	52524124	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agctgaggcacctcatgtggTcctcggtggtgttctaccag	13	11	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:52524124T>C	ENST00000479054.1	+	19	3562	c.3490T>C	c.(3490-3492)Tcc>Ccc	p.S1164P	NISCH_ENST00000345716.4_Missense_Mutation_p.S1164P			Q9Y2I1	NISCH_HUMAN	nischarin	1164					actin cytoskeleton organization (GO:0030036)|apoptotic process (GO:0006915)|glucose metabolic process (GO:0006006)|negative regulation of cell migration (GO:0030336)|norepinephrine secretion (GO:0048243)|Rac protein signal transduction (GO:0016601)|regulation of blood pressure (GO:0008217)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)|plasma membrane (GO:0005886)	G-protein coupled amine receptor activity (GO:0008227)|identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)			NS(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(9)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	33				BRCA - Breast invasive adenocarcinoma(193;1.93e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)|OV - Ovarian serous cystadenocarcinoma(275;0.0577)	Tizanidine(DB00697)	CCTCATGTGGTCCTCGGTGGT	0.622																																					p.S1164P		Atlas-SNP	.											.	NISCH	97	.	0			c.T3490C						.						76	60	65					3																	52524124		2203	4300	6503	SO:0001583	missense	11188	exon18			ATGTGGTCCTCGG	AF082516	CCDS33767.1, CCDS63651.1, CCDS63652.1	3p21.1	2008-07-18			ENSG00000010322	ENSG00000010322			18006	protein-coding gene	gene with protein product	"imidazoline receptor candidate", "I-1 receptor candidate protein", "imidazoline receptor antisera selected"	615507				11912194, 10882231	Standard	NM_007184		Approved	KIAA0975, I-1, IRAS	uc003ded.4	Q9Y2I1	OTTHUMG00000158571	ENST00000479054.1:c.3490T>C	chr3.hg19:g.52524124T>C	ENSP00000418232:p.Ser1164Pro	173.0	0.0		124.0	5.0	NM_007184	C9J245|Q6PGP3|Q6PIB4|Q7L8M3|Q7Z2X6|Q9UES6|Q9UEU4|Q9UFW3	Missense_Mutation	SNP	ENST00000479054.1	hg19	CCDS33767.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.170001	0.78452	.	.	ENSG00000010322	ENST00000479054;ENST00000345716;ENST00000414197	T;T	0.10382	2.88;2.88	5.18	5.18	0.71444	.	0.248715	0.36740	N	0.002423	T	0.09202	0.0227	L	0.27053	0.805	0.31244	N	0.694856	P	0.36789	0.57	B	0.36959	0.237	T	0.04946	-1.0916	10	0.72032	D	0.01	-15.1695	11.088	0.48099	0.0:0.0:0.1549:0.8451	.	1164	Q9Y2I1	NISCH_HUMAN	P	1164;1164;508	ENSP00000418232:S1164P;ENSP00000339958:S1164P	ENSP00000339958:S1164P	S	+	1	0	NISCH	52499164	1.000000	0.71417	0.999000	0.59377	0.970000	0.65996	3.096000	0.50243	1.969000	0.57287	0.459000	0.35465	TCC	.	.		0.622	NISCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351357.1	NM_007184		C	52524124	T	C	52524124	3	2	282	1	0	0	0	0	1	0	0	0	10441	1667	58	2	3560	2	NISCH	3	52524124	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	93715	52524124	145498306	273	40507										
RFT1	91869	hgsc.bcm.edu	37	chr3	53126003	53126003	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtctctgtgaggaatgctgtCccgagagttgctcccagaca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:53126003delC	ENST00000296292.3	-	13	1603	c.1542delG	c.(1540-1542)gggfs	p.G514fs	RFT1_ENST00000394738.3_Frame_Shift_Del_p.G475fs|RP11-894J14.5_ENST00000607203.1_Intron	NM_052859.3	NP_443091.1	Q96AA3	RFT1_HUMAN	RFT1 homolog (S. cerevisiae)	514					carbohydrate transport (GO:0008643)|cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	integral component of membrane (GO:0016021)	lipid transporter activity (GO:0005319)			NS(1)|breast(1)|kidney(1)|lung(5)|skin(2)|urinary_tract(2)	12				BRCA - Breast invasive adenocarcinoma(193;6.98e-05)|Kidney(197;0.0017)|KIRC - Kidney renal clear cell carcinoma(197;0.00192)|OV - Ovarian serous cystadenocarcinoma(275;0.104)		GGAATGCTGTCCCGAGAGTTG	0.552																																					p.T515fs		Atlas-INDEL	.											.	RFT1	34	.	0			c.1543delA						.						114	98	103					3																	53126003		2203	4300	6503	SO:0001589	frameshift_variant	91869	exon13			.	AJ318099	CCDS2869.1	3p21.1	2014-02-06	2005-01-26		ENSG00000163933	ENSG00000163933			30220	protein-coding gene	gene with protein product	"congenital disorder of glycosylation 1N"	611908	"RFT1, requiring fifty three 1 homolog (S. cerevisiae)"			12477932	Standard	NM_052859		Approved	CDG1N	uc003dgj.3	Q96AA3	OTTHUMG00000074035	ENST00000296292.3:c.1542delG	chr3.hg19:g.53126003delC	ENSP00000296292:p.Gly514fs	300.0	0.0		209.0	13.0	NM_052859	Q96J03	Frame_Shift_Del	DEL	ENST00000296292.3	hg19	CCDS2869.1																																																																																			.	.		0.552	RFT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157136.2	NM_052859		-	53126003	C	-	53126003	7	5	282	1	0	1	0	1	0	0	0	0	13272	842	30	0	87	0	RFT1	3	53126003	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	601879	53126003	144896427	274	40508										
CHDH	55349	hgsc.bcm.edu	37	chr3	53855776	53855776	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agagttgatggcacctccacTcagaatcacctccttgctgg	9	13	2	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:53855776T>C	ENST00000315251.6	-	5	1320	c.883A>G	c.(883-885)Agt>Ggt	p.S295G		NM_018397.4	NP_060867.2	Q8NE62	CHDH_HUMAN	choline dehydrogenase	295					glycine betaine biosynthetic process from choline (GO:0019285)	mitochondrial inner membrane (GO:0005743)	choline dehydrogenase activity (GO:0008812)|flavin adenine dinucleotide binding (GO:0050660)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	17		Hepatocellular(537;0.152)		BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)	Choline(DB00122)	GCACCTCCACTCAGAATCACC	0.567																																					p.S295G		Atlas-SNP	.											.	CHDH	34	.	0			c.A883G						.						116	107	110					3																	53855776		2203	4300	6503	SO:0001583	missense	55349	exon5			CTCCACTCAGAAT	AJ272267	CCDS2873.1	3p21	2004-11-24			ENSG00000016391	ENSG00000016391	1.1.99.1		24288	protein-coding gene	gene with protein product							Standard	NM_018397		Approved		uc003dgz.3	Q8NE62	OTTHUMG00000158281	ENST00000315251.6:c.883A>G	chr3.hg19:g.53855776T>C	ENSP00000319851:p.Ser295Gly	133.0	0.0		92.0	4.0	NM_018397	Q9NY17	Missense_Mutation	SNP	ENST00000315251.6	hg19	CCDS2873.1	.	.	.	.	.	.	.	.	.	.	T	28.2	4.900201	0.92035	.	.	ENSG00000016391	ENST00000315251	T	0.69040	-0.37	5.6	5.6	0.85130	Glucose-methanol-choline oxidoreductase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.83691	0.5309	M	0.90870	3.155	0.80722	D	1	D	0.56035	0.974	P	0.61070	0.883	D	0.86520	0.1815	10	0.49607	T	0.09	-24.8983	15.8023	0.78463	0.0:0.0:0.0:1.0	.	295	Q8NE62	CHDH_HUMAN	G	295	ENSP00000319851:S295G	ENSP00000319851:S295G	S	-	1	0	CHDH	53830816	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	3.748000	0.55142	2.137000	0.66172	0.533000	0.62120	AGT	.	.		0.567	CHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350567.2	NM_018397		C	53855776	T	C	53855776	3	2	282	1	0	0	0	0	1	0	0	0	3335	1551	54	2	921	2	CHDH	3	53855776	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	729773	53855776	144166654	275	40509										
SPATA12	353324	hgsc.bcm.edu	37	chr3	57107744	57107744	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgtccagttctgctctgactTgtgggtccaccttagaaaag	10	10	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:57107744T>C	ENST00000334325.1	+	2	697	c.22T>C	c.(22-24)Tgt>Cgt	p.C8R	ARHGEF3_ENST00000338458.4_Intron	NM_181727.1	NP_859078.1	Q7Z6I5	SPT12_HUMAN	spermatogenesis associated 12	8										large_intestine(2)|lung(1)	3				KIRC - Kidney renal clear cell carcinoma(284;0.0111)|Kidney(284;0.0129)		TGCTCTGACTTGTGGGTCCAC	0.547																																					p.C8R		Atlas-SNP	.											.	SPATA12	9	.	0			c.T22C						.						43	43	43					3																	57107744		2203	4300	6503	SO:0001583	missense	353324	exon2			CTGACTTGTGGGT	AY221117	CCDS2879.1	3p21.2	2012-09-19			ENSG00000186451	ENSG00000186451			23221	protein-coding gene	gene with protein product		609869				22981541, 17251597	Standard	NM_181727		Approved		uc003dij.1	Q7Z6I5	OTTHUMG00000158862	ENST00000334325.1:c.22T>C	chr3.hg19:g.57107744T>C	ENSP00000335392:p.Cys8Arg	108.0	0.0		59.0	4.0	NM_181727	A0AVA8|B2RMW1	Missense_Mutation	SNP	ENST00000334325.1	hg19	CCDS2879.1	.	.	.	.	.	.	.	.	.	.	T	8.868	0.948493	0.18356	.	.	ENSG00000186451	ENST00000334325	.	.	.	3.11	0.529	0.17095	.	.	.	.	.	T	0.25644	0.0624	N	0.08118	0	0.09310	N	1	D	0.69078	0.997	P	0.62184	0.899	T	0.10636	-1.0621	8	0.87932	D	0	.	3.678	0.08299	0.2232:0.0:0.2312:0.5455	.	8	Q7Z6I5	SPT12_HUMAN	R	8	.	ENSP00000335392:C8R	C	+	1	0	SPATA12	57082784	0.004000	0.15560	0.006000	0.13384	0.165000	0.22458	0.158000	0.16422	0.106000	0.17784	-0.460000	0.05396	TGT	.	.		0.547	SPATA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352457.2	NM_181727		C	57107744	T	C	57107744	3	2	282	1	0	0	0	0	1	0	0	0	15014	1812	63	2	24	2	SPATA12	3	57107744	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3251968	57107744	140914686	276	40510										
DNAH12	201625	hgsc.bcm.edu	37	chr3	57456205	57456205	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgccacttcaaaacaaaattAaaaaacttctgatagggctc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:57456205delA	ENST00000351747.2	-	16	2250	c.2070delT	c.(2068-2070)tttfs	p.F690fs	snoU13_ENST00000459308.1_RNA|DNAH12_ENST00000389536.4_Frame_Shift_Del_p.F690fs	NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	690	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						AAACAAAATTAAAAAACTTCT	0.274																																					p.N691fs		Atlas-INDEL	.											.	DNAH12	182	.	0			c.2071delA						.						66	53	57					3																	57456205		692	1585	2277	SO:0001589	frameshift_variant	201625	exon16			.	U53532, AK126276	CCDS33771.1	3p21.1	2009-02-04	2006-09-04		ENSG00000174844	ENSG00000174844		"Axonemal dyneins"	2943	protein-coding gene	gene with protein product		603340	"dynein, axonemal, heavy polypeptide 12", "dynein heavy chain domain 2", "dynein heavy domain 2", "dynein, axonemal, heavy chain 12-like", "dynein, axonemal, heavy chain 7-like"	DNHD2, DNAH12L, DNAH7L		8812413, 8666668	Standard	NM_198564		Approved	DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290	uc003dit.2	Q6ZR08	OTTHUMG00000158598	ENST00000351747.2:c.2070delT	chr3.hg19:g.57456205delA	ENSP00000295937:p.Phe690fs	262.0	0.0		228.0	14.0	NM_178504	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Frame_Shift_Del	DEL	ENST00000351747.2	hg19																																																																																				.	.		0.274	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504		-	57456205	A	-	57456205	7	5	282	1	0	1	0	1	0	0	0	0	4602	359	13	0	7384	0	DNAH12	3	57456205	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	348461	57456205	140566225	277	40511										
SNTN	132203	hgsc.bcm.edu	37	chr3	63645488	63645488	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgactctgatggtaaacttgAaaaagctattgccaaagatc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:63645488delA	ENST00000343837.3	+	3	253	c.233delA	c.(232-234)gaafs	p.E78fs	SNTN_ENST00000496807.1_Frame_Shift_Del_p.E74fs	NM_001080537.1	NP_001074006.1	A6NMZ2	SNTAN_HUMAN	sentan, cilia apical structure protein	78						cilium (GO:0005929)	calcium ion binding (GO:0005509)			endometrium(2)|ovary(1)	3						GGTAAACTTGAAAAAGCTATT	0.413																																					p.E78fs		Atlas-INDEL	.											.	SNTN	17	.	0			c.232delG						.						126	125	125					3																	63645488		2203	4300	6503	SO:0001589	frameshift_variant	132203	exon3			.	AK126350	CCDS33779.1	3p14.2	2009-03-10	2009-03-10		ENSG00000188817	ENSG00000188817			33706	protein-coding gene	gene with protein product	"S100A-like protein"					18829862	Standard	NM_001080537		Approved	FLJ44379, S100AL	uc003dlr.3	A6NMZ2	OTTHUMG00000158766	ENST00000343837.3:c.233delA	chr3.hg19:g.63645488delA	ENSP00000341442:p.Glu78fs	206.0	0.0		161.0	10.0	NM_001080537	B7FF65	Frame_Shift_Del	DEL	ENST00000343837.3	hg19	CCDS33779.1																																																																																			.	.		0.413	SNTN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352094.1	NM_001080537		-	63645488	A	-	63645488	7	5	282	1	0	1	0	1	0	0	0	0	14891	246	9	0	243	0	SNTN	3	63645488	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	6189283	63645488	134376942	278	40512										
ADAMTS9	56999	hgsc.bcm.edu	37	chr3	64619493	64619493	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcttctgcttgagacatggcTccgtgttgcaggacttaaat	11	9	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:64619493T>C	ENST00000498707.1	-	13	2261	c.1919A>G	c.(1918-1920)gAg>gGg	p.E640G	ADAMTS9_ENST00000295903.4_Missense_Mutation_p.E612G	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	640	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				glycoprotein catabolic process (GO:0006516)|multicellular organismal development (GO:0007275)|positive regulation of melanocyte differentiation (GO:0045636)|protein transport (GO:0015031)|proteolysis (GO:0006508)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(17)|liver(4)|lung(43)|ovary(3)|prostate(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	100		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		GAGACATGGCTCCGTGTTGCA	0.438																																					p.E640G		Atlas-SNP	.											.	ADAMTS9	206	.	0			c.A1919G						.						131	114	120					3																	64619493		2203	4300	6503	SO:0001583	missense	56999	exon13			CATGGCTCCGTGT	AF261918	CCDS2903.1	3p14.1	2008-05-15	2005-08-19		ENSG00000163638	ENSG00000163638		"ADAM metallopeptidases with thrombospondin type 1 motif"	13202	protein-coding gene	gene with protein product		605421	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 9"			10936055	Standard	NM_182920		Approved	KIAA1312	uc003dmg.3	Q9P2N4	OTTHUMG00000158722	ENST00000498707.1:c.1919A>G	chr3.hg19:g.64619493T>C	ENSP00000418735:p.Glu640Gly	138.0	0.0		106.0	5.0	NM_182920	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	Missense_Mutation	SNP	ENST00000498707.1	hg19	CCDS2903.1	.	.	.	.	.	.	.	.	.	.	T	32	5.119479	0.94385	.	.	ENSG00000163638	ENST00000295903;ENST00000498707	T;T	0.03745	3.82;3.82	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.13756	0.0333	L	0.47078	1.49	0.80722	D	1	D;D;D;D	0.89917	0.994;0.995;1.0;0.987	D;D;D;P	0.91635	0.96;0.948;0.999;0.867	T	0.00505	-1.1700	10	0.66056	D	0.02	.	15.6399	0.76989	0.0:0.0:0.0:1.0	.	612;640;640;640	B7ZVX9;Q9P2N4-2;Q9P2N4-1;Q9P2N4	.;.;.;ATS9_HUMAN	G	612;640	ENSP00000295903:E612G;ENSP00000418735:E640G	ENSP00000295903:E612G	E	-	2	0	ADAMTS9	64594533	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	7.698000	0.84413	2.103000	0.63969	0.533000	0.62120	GAG	.	.		0.438	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351891.1			C	64619493	T	C	64619493	3	2	282	1	0	0	0	0	1	0	0	0	273	1551	54	2	3996	2	ADAMTS9	3	64619493	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	974005	64619493	133402937	279	40513										
SUCLG2	8801	hgsc.bcm.edu	37	chr3	67570955	67570955	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccacctcttcaatgtcgacgCccccctgggggctgcccacc					rs527536615		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:67570955delC	ENST00000307227.5	-	5	548	c.521delG	c.(520-522)ggcfs	p.G174fs	SUCLG2_ENST00000492795.1_Frame_Shift_Del_p.G174fs|SUCLG2_ENST00000493112.1_Frame_Shift_Del_p.G174fs	NM_003848.3	NP_003839.2	Q96I99	SUCB2_HUMAN	succinate-CoA ligase, GDP-forming, beta subunit	174	ATP-grasp.			GV -> RS (in Ref. 4; AAC64397). {ECO:0000305}.	cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|succinyl-CoA metabolic process (GO:0006104)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|succinate-CoA ligase complex (GDP-forming) (GO:0045244)	ATP binding (GO:0005524)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|succinate-CoA ligase (GDP-forming) activity (GO:0004776)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(3)|skin(1)	10		Renal(2;0.00294)|Lung NSC(201;0.012)|Hepatocellular(537;0.121)		BRCA - Breast invasive adenocarcinoma(55;3.53e-05)|Epithelial(33;0.000153)	Succinic acid(DB00139)	AATGTCGACGCCCCCCTGGGG	0.502																																					p.G174fs		Pindel	.											.	SUCLG2	95	.	0			c.522delC						.						67	70	69					3																	67570955		1823	4072	5895	SO:0001589	frameshift_variant	8801	exon5			.	AF058954	CCDS43104.1, CCDS54605.1	3p14.3	2004-05-17			ENSG00000172340	ENSG00000172340	6.2.1.4		11450	protein-coding gene	gene with protein product		603922				9765291	Standard	NM_001177599		Approved		uc003dna.4	Q96I99	OTTHUMG00000158740	ENST00000307227.5:c.521delG	chr3.hg19:g.67570955delC	ENSP00000307432:p.Gly174fs	342.0	0.0		242.0	11.0	NM_001177599	C9JVT2|O95195|Q6NUH7|Q86VX8|Q8WUQ1	Frame_Shift_Del	DEL	ENST00000307227.5	hg19	CCDS43104.1																																																																																			.	.		0.502	SUCLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351993.1	NM_003848		-	67570955	C	-	67570955	7	5	282	1	0	1	0	1	0	0	0	0	15380	739	26	0	949	0	SUCLG2	3	67570955	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	2951462	67570955	130451475	280	40514										
LMOD3	56203	hgsc.bcm.edu	37	chr3	69171278	69171278	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aggtgacaggaactcgttccTcttccagcatgcgcctggat	11	12	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:69171278T>C	ENST00000420581.2	-	1	439	c.260A>G	c.(259-261)gAg>gGg	p.E87G	LMOD3_ENST00000489031.1_Missense_Mutation_p.E87G|LMOD3_ENST00000475434.1_Missense_Mutation_p.E87G	NM_198271.3	NP_938012.2	Q0VAK6	LMOD3_HUMAN	leiomodin 3 (fetal)	87	Glu-rich.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(1)	13		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.88e-05)|Epithelial(33;0.000839)|LUSC - Lung squamous cell carcinoma(21;0.0119)|Lung(16;0.0191)|KIRC - Kidney renal clear cell carcinoma(39;0.205)|Kidney(39;0.24)		AACTCGTTCCTCTTCCAGCAT	0.458																																					p.E87G		Atlas-SNP	.											.	LMOD3	92	.	0			c.A260G						.						74	70	71					3																	69171278		1895	4115	6010	SO:0001583	missense	56203	exon1			CGTTCCTCTTCCA	AK096900	CCDS46862.1	3p14.1	2003-03-07			ENSG00000163380	ENSG00000163380			6649	protein-coding gene	gene with protein product							Standard	NM_198271		Approved		uc003dns.2	Q0VAK6	OTTHUMG00000158774	ENST00000420581.2:c.260A>G	chr3.hg19:g.69171278T>C	ENSP00000414670:p.Glu87Gly	183.0	0.0		98.0	4.0	NM_198271	B4DT85|Q0JTT2|Q5JPG6|Q8IUK4|Q96LS4	Missense_Mutation	SNP	ENST00000420581.2	hg19	CCDS46862.1	.	.	.	.	.	.	.	.	.	.	T	14.70	2.613497	0.46631	.	.	ENSG00000163380	ENST00000420581;ENST00000489031;ENST00000475434	T;T;T	0.36157	1.27;1.27;1.27	5.69	5.69	0.88448	.	0.047464	0.85682	D	0.000000	T	0.30355	0.0762	N	0.17082	0.46	0.40794	D	0.98328	P	0.43938	0.822	P	0.44477	0.451	T	0.11817	-1.0572	10	0.45353	T	0.12	-22.6551	15.9428	0.79771	0.0:0.0:0.0:1.0	.	87	Q0VAK6	LMOD3_HUMAN	G	87	ENSP00000414670:E87G;ENSP00000417210:E87G;ENSP00000418645:E87G	ENSP00000414670:E87G	E	-	2	0	LMOD3	69253968	1.000000	0.71417	0.930000	0.37139	0.228000	0.25075	8.040000	0.89188	2.182000	0.69389	0.482000	0.46254	GAG	.	.		0.458	LMOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352138.1	XM_067529		C	69171278	T	C	69171278	3	2	282	1	0	0	0	0	1	0	0	0	8867	1551	54	2	1434	2	LMOD3	3	69171278	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1600323	69171278	128851152	281	40515										
CNTN3	5067	hgsc.bcm.edu	37	chr3	74385778	74385778	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agctttagtcacattggctaTtttgagtcctccatcgttta							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:74385778delT	ENST00000263665.6	-	11	1423	c.1396delA	c.(1396-1398)atafs	p.I466fs		NM_020872.1	NP_065923.1	Q9P232	CNTN3_HUMAN	contactin 3 (plasmacytoma associated)	466	Ig-like C2-type 5.				cell adhesion (GO:0007155)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(39)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	83		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		ACATTGGCTATTTTGAGTCCT	0.338																																					p.I466fs		Atlas-INDEL	.											.	CNTN3	174	.	0			c.1397delT						.						109	93	99					3																	74385778		2203	4299	6502	SO:0001589	frameshift_variant	5067	exon11			.	AB040929	CCDS33790.1	3p12.3	2013-02-11			ENSG00000113805	ENSG00000113805		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2173	protein-coding gene	gene with protein product		601325		PANG		8661054, 8586965	Standard	XM_005264757		Approved	BIG-1	uc003dpm.1	Q9P232	OTTHUMG00000158813	ENST00000263665.6:c.1396delA	chr3.hg19:g.74385778delT	ENSP00000263665:p.Ile466fs	228.0	0.0		219.0	14.0	NM_020872	B9EK50|Q9H039	Frame_Shift_Del	DEL	ENST00000263665.6	hg19	CCDS33790.1																																																																																			.	.		0.338	CNTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352306.1	NM_020872		-	74385778	T	-	74385778	7	5	282	1	0	1	0	1	0	0	0	0	3644	1493	52	0	1738	0	CNTN3	3	74385778	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	5214500	74385778	123636652	282	40516										
C3orf38	285237	hgsc.bcm.edu	37	chr3	88205437	88205437	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaagaatttctttttctcagCcccaacctagattcacatgg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:88205437delC	ENST00000318887.3	+	3	952	c.642delC	c.(640-642)agcfs	p.S214fs	C3orf38_ENST00000486971.1_3'UTR	NM_173824.3	NP_776185.2	Q5JPI3	CC038_HUMAN	chromosome 3 open reading frame 38	214					apoptotic process (GO:0006915)					breast(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	12		Lung NSC(201;0.17)		UCEC - Uterine corpus endometrioid carcinoma (27;0.194)|LUSC - Lung squamous cell carcinoma(29;0.00353)|Lung(72;0.00661)		TTTTTCTCAGCCCCAACCTAG	0.433																																					p.S214fs		Atlas-INDEL	.											.	C3orf38	29	.	0			c.641delG						.						133	128	130					3																	88205437		2203	4300	6503	SO:0001589	frameshift_variant	285237	exon3			.	AL832398	CCDS2921.1, CCDS2921.2	3p11.1	2011-01-25			ENSG00000179021	ENSG00000179021			28384	protein-coding gene	gene with protein product						12477932	Standard	NM_173824		Approved	MGC26717	uc003dqw.3	Q5JPI3	OTTHUMG00000155752	ENST00000318887.3:c.642delC	chr3.hg19:g.88205437delC	ENSP00000322469:p.Ser214fs	189.0	0.0		143.0	10.0	NM_173824	B2R8X6|Q8TC85	Frame_Shift_Del	DEL	ENST00000318887.3	hg19	CCDS2921.2																																																																																			.	.		0.433	C3orf38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341513.1	NM_173824		-	88205437	C	-	88205437	7	5	282	1	0	1	0	1	0	0	0	0	2230	738	26	0	652	0	C3orf38	3	88205437	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	13819659	88205437	109816993	283	40517										
CRYBG3	131544	hgsc.bcm.edu	37	chr3	97596406	97596406	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgaaaaccagtcctcttctgTtttatcccttctccagtcag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:97596406delT	ENST00000182096.4	+	1	588	c.524delT	c.(523-525)gttfs	p.V175fs		NM_153605.3	NP_705833.3	Q68DQ2	CRBG3_HUMAN	beta-gamma crystallin domain containing 3	2123							carbohydrate binding (GO:0030246)			breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(10)|stomach(1)|upper_aerodigestive_tract(2)	32						TCCTCTTCTGTTTTATCCCTT	0.473																																					p.V2123fs		Atlas-INDEL	.											.	CRYBG3	86	.	0			c.6367delG						.						57	57	57					3																	97596406		1983	4174	6157	SO:0001589	frameshift_variant	131544	exon4			.			3q11.2	2008-09-30			ENSG00000080200	ENSG00000080200			34427	protein-coding gene	gene with protein product							Standard	NM_153605		Approved	DKFZp667G2110	uc021xbn.2	Q68DQ2	OTTHUMG00000159187	ENST00000182096.4:c.524delT	chr3.hg19:g.97596406delT	ENSP00000182096:p.Val175fs	173.0	0.0		154.0	10.0	NM_153605	B4DLE8|F6VHI2|Q4G0V8|Q7Z4R9|Q86VD0|Q8N262|Q8N7F1|Q8NDQ8	Frame_Shift_Del	DEL	ENST00000182096.4	hg19																																																																																				.	.		0.473	CRYBG3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353751.1	NM_153605		-	97596406	T	-	97596406	7	5	282	1	0	1	0	1	0	0	0	0	3915	1725	60	0	526	0	CRYBG3	3	97596406	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	9390969	97596406	100426024	284	40518										
MINA	84864	hgsc.bcm.edu	37	chr3	97666254	97666254	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggacaatgtggtctttaaacTgcagtctcactacactgtcc	8	11	2	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:97666254T>C	ENST00000333396.7	-	8	1682	c.1100A>G	c.(1099-1101)cAg>cGg	p.Q367R	MINA_ENST00000394198.2_Missense_Mutation_p.Q367R|MINA_ENST00000360258.4_Missense_Mutation_p.Q366R	NM_001042533.2|NM_032778.5	NP_001035998.1|NP_116167.3			MYC induced nuclear antigen											breast(2)|endometrium(1)|large_intestine(1)|lung(8)|ovary(1)	13						GTCTTTAAACTGCAGTCTCAC	0.448																																					p.Q367R		Atlas-SNP	.											.	MINA	39	.	0			c.A1100G						.						148	140	143					3																	97666254		2203	4300	6503	SO:0001583	missense	84864	exon8			TTAAACTGCAGTC	AB083189	CCDS2929.1, CCDS43114.1	3q22.1	2005-07-22			ENSG00000170854	ENSG00000170854			19441	protein-coding gene	gene with protein product		612049				12091391	Standard	NM_001042533		Approved	MINA53, FLJ14393, mdig	uc003dsb.1	Q8IUF8	OTTHUMG00000160107	ENST00000333396.7:c.1100A>G	chr3.hg19:g.97666254T>C	ENSP00000328251:p.Gln367Arg	113.0	0.0		107.0	5.0	NM_001042533		Missense_Mutation	SNP	ENST00000333396.7	hg19	CCDS43114.1	.	.	.	.	.	.	.	.	.	.	T	1.645	-0.515518	0.04200	.	.	ENSG00000170854	ENST00000442492;ENST00000333396;ENST00000394198;ENST00000360258	T;T;T	0.10860	2.83;2.83;2.84	5.92	0.536	0.17138	.	0.635091	0.16760	N	0.200679	T	0.08582	0.0213	L	0.45228	1.405	0.42485	D	0.992872	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.001	T	0.24764	-1.0151	10	0.15952	T	0.53	-8.4277	9.9583	0.41680	0.0:0.373:0.0:0.627	.	366;367	Q8IUF8-4;Q8IUF8	.;MINA_HUMAN	R	113;367;367;366	ENSP00000328251:Q367R;ENSP00000377748:Q367R;ENSP00000353395:Q366R	ENSP00000328251:Q367R	Q	-	2	0	MINA	99148944	0.779000	0.28652	0.246000	0.24233	0.130000	0.20726	0.988000	0.29616	0.165000	0.19558	0.533000	0.62120	CAG	.	.		0.448	MINA-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359244.3	NM_032778		C	97666254	T	C	97666254	3	2	282	1	0	0	0	0	1	0	0	0	9595	1580	55	2	309	2	MINA	3	97666254	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	69848	97666254	100356176	285	40519										
FILIP1L	11259	hgsc.bcm.edu	37	chr3	99568351	99568351	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atgtattcatgaattttctcTtttaatgcatccacttctct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:99568351delT	ENST00000354552.3	-	5	2639	c.2169delA	c.(2167-2169)aaafs	p.K723fs	CMSS1_ENST00000421999.2_Intron|FILIP1L_ENST00000383694.2_Frame_Shift_Del_p.K483fs|FILIP1L_ENST00000476723.1_Intron|CMSS1_ENST00000496116.1_Intron|FILIP1L_ENST00000471562.1_Frame_Shift_Del_p.K483fs|FILIP1L_ENST00000331335.5_Frame_Shift_Del_p.K723fs|FILIP1L_ENST00000487087.1_Frame_Shift_Del_p.K299fs	NM_182909.2	NP_878913.2	Q4L180	FIL1L_HUMAN	filamin A interacting protein 1-like	723						cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	35						GAATTTTCTCTTTTAATGCAT	0.403																																					p.E724fs		Atlas-INDEL	.											.	FILIP1L	154	.	0			c.2170delG						.						167	147	153					3																	99568351		1858	4092	5950	SO:0001589	frameshift_variant	11259	exon5			.		CCDS43117.1, CCDS43118.1, CCDS43119.1, CCDS63700.1, CCDS74969.1	3q12.1	2011-10-21			ENSG00000168386	ENSG00000168386			24589	protein-coding gene	gene with protein product	"downregulated in ovarian cancer 1", "GPBP-interacting protein of 130 kDa"	612993				8314147, 15935955, 21832087	Standard	NM_001282793		Approved	DOC-1, GIP130	uc003dtm.3	Q4L180	OTTHUMG00000159055	ENST00000354552.3:c.2169delA	chr3.hg19:g.99568351delT	ENSP00000346560:p.Lys723fs	355.0	0.0		199.0	12.0	NM_001042459	B2CNV7|B2CNV8|Q13597|Q2YDY5|Q6KFX5|Q6KFX6|Q6KFX7|Q8IUM3|Q8N6Z0	Frame_Shift_Del	DEL	ENST00000354552.3	hg19	CCDS43117.1																																																																																			.	.		0.403	FILIP1L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353069.1	NM_014890		-	99568351	T	-	99568351	7	5	282	1	0	1	0	1	0	0	0	0	5903	1606	56	0	1267	0	FILIP1L	3	99568351	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1902097	99568351	98454079	286	40520										
SENP7	57337	hgsc.bcm.edu	37	chr3	101051684	101051684	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acgagtccatgttcttactcTtttatgtcttctctgtgcca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:101051684delT	ENST00000394095.2	-	18	2556	c.2503delA	c.(2503-2505)agafs	p.R835fs	SENP7_ENST00000394094.2_Frame_Shift_Del_p.R770fs|SENP7_ENST00000394091.1_Frame_Shift_Del_p.R671fs|SENP7_ENST00000358203.3_Frame_Shift_Del_p.R671fs|SENP7_ENST00000394085.3_Frame_Shift_Del_p.R23fs|SENP7_ENST00000348610.3_Frame_Shift_Del_p.R802fs|SENP7_ENST00000314261.7_Frame_Shift_Del_p.R769fs	NM_001282802.1|NM_020654.3	NP_001269731.1|NP_065705.3	Q9BQF6	SENP7_HUMAN	SUMO1/sentrin specific peptidase 7	835	Protease.					intracellular (GO:0005622)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)			breast(2)|endometrium(1)|kidney(1)|large_intestine(16)|lung(15)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						GTTCTTACTCTTTTATGTCTT	0.279																																					p.R835fs		Atlas-INDEL	.											.	SENP7	170	.	0			c.2504delG						.						101	100	100					3																	101051684		2203	4275	6478	SO:0001589	frameshift_variant	57337	exon18			.		CCDS2941.2, CCDS43121.1, CCDS63704.1, CCDS63705.1, CCDS63706.1	3q12	2008-02-05	2005-08-17		ENSG00000138468	ENSG00000138468			30402	protein-coding gene	gene with protein product		612846	"SUMO1/sentrin specific protease 7"			11214970, 11230166	Standard	NM_001282802		Approved		uc003dut.3	Q9BQF6	OTTHUMG00000149927	ENST00000394095.2:c.2503delA	chr3.hg19:g.101051684delT	ENSP00000377655:p.Arg835fs	264.0	0.0		223.0	15.0	NM_020654	A1L3A5|A8MW39|B7WNW8|Q7Z3F4|Q96PS5|Q9C0F6|Q9HBT5	Frame_Shift_Del	DEL	ENST00000394095.2	hg19	CCDS2941.2																																																																																			.	.		0.279	SENP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313957.2	NM_020654		-	101051684	T	-	101051684	7	5	282	1	0	1	0	1	0	0	0	0	14066	1617	56	0	677	0	SENP7	3	101051684	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1483333	101051684	96970746	287	40521										
MYH15	22989	hgsc.bcm.edu	37	chr3	108182059	108182059	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cattaaggaggtctttgttcTtttccagccaaccactgata					rs202235922		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:108182059delT	ENST00000273353.3	-	17	1879	c.1823delA	c.(1822-1824)aagfs	p.K608fs	MYH15_ENST00000495753.2_5'Flank	NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	608	Myosin motor.					cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						GTCTTTGTTCTTTTCCAGCCA	0.383																																					p.K608fs		Atlas-INDEL	.											.	MYH15	223	.	0			c.1824delG						.						165	155	158					3																	108182059		1826	4085	5911	SO:0001589	frameshift_variant	22989	exon17			.	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"Myosins / Myosin superfamily : Class II"	31073	protein-coding gene	gene with protein product		609929	"myosin, heavy polypeptide 15"			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.1823delA	chr3.hg19:g.108182059delT	ENSP00000273353:p.Lys608fs	276.0	0.0		191.0	12.0	NM_014981		Frame_Shift_Del	DEL	ENST00000273353.3	hg19	CCDS43127.1																																																																																			.	.		0.383	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988		-	108182059	T	-	108182059	7	5	282	1	0	1	0	1	0	0	0	0	10043	1609	56	0	4121	0	MYH15	3	108182059	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	7130375	108182059	89840371	288	40522										
PVRL3	25945	hgsc.bcm.edu	37	chr3	110841052	110841052	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tctcaaatgtaatgctgatgCaaatccaccacccttcaaat	4	12	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:110841052C>A	ENST00000485303.1	+	4	1159	c.884C>A	c.(883-885)gCa>gAa	p.A295E	PVRL3_ENST00000493615.1_Missense_Mutation_p.A272E|PVRL3_ENST00000319792.3_Missense_Mutation_p.A295E	NM_001243286.1|NM_015480.2	NP_001230215.1|NP_056295.1	Q9NQS3	PVRL3_HUMAN	poliovirus receptor-related 3	295	Ig-like C2-type 2.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|fertilization (GO:0009566)|homophilic cell adhesion (GO:0007156)|lens morphogenesis in camera-type eye (GO:0002089)|retina morphogenesis in camera-type eye (GO:0060042)|single organismal cell-cell adhesion (GO:0016337)	apical junction complex (GO:0043296)|cell-cell adherens junction (GO:0005913)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	cell adhesion molecule binding (GO:0050839)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(3)	19						AATGCTGATGCAAATCCACCA	0.343																																					p.A295E		Atlas-SNP	.											.	PVRL3	78	.	0			c.C884A						.						85	83	84					3																	110841052		2203	4300	6503	SO:0001583	missense	25945	exon4			CTGATGCAAATCC	AF282874	CCDS2957.1, CCDS58842.1, CCDS58843.1	3q13	2013-01-29			ENSG00000177707	ENSG00000177707		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17664	protein-coding gene	gene with protein product		607147				11024295	Standard	NM_015480		Approved	nectin-3, PPR3, PVRR3, DKFZP566B0846, CDw113, CD113	uc003dxt.2	Q9NQS3	OTTHUMG00000159239	ENST00000485303.1:c.884C>A	chr3.hg19:g.110841052C>A	ENSP00000418070:p.Ala295Glu	183.0	0.0		117.0	6.0	NM_001243286	E9PFR0|Q6NVZ3|Q8NC05|Q8WVU4|Q9BVA9|Q9Y412	Missense_Mutation	SNP	ENST00000485303.1	hg19	CCDS2957.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.1|25.1	4.603856|4.603856	0.87157|0.87157	.|.	.|.	ENSG00000177707|ENSG00000177707	ENST00000485303;ENST00000319792;ENST00000493615|ENST00000486596	T;T;T|.	0.15603|.	2.41;2.41;2.41|.	5.67|5.67	5.67|5.67	0.87782|0.87782	Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	0.145674|.	0.64402|.	D|.	0.000011|.	T|.	0.77260|.	0.4104|.	M|M	0.78223|0.78223	2.4|2.4	0.58432|0.58432	D|D	0.999999|0.999999	D;D|.	0.89917|.	1.0;0.998|.	D;D|.	0.75020|.	0.985;0.93|.	T|.	0.77008|.	-0.2747|.	10|.	0.72032|.	D|.	0.01|.	.|.	17.2528|17.2528	0.87047|0.87047	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	272;295|.	E9PFR0;Q9NQS3|.	.;PVRL3_HUMAN|.	E|X	295;295;272|195	ENSP00000418070:A295E;ENSP00000321514:A295E;ENSP00000420579:A272E|.	ENSP00000321514:A295E|.	A|C	+|+	2|3	0|2	PVRL3|PVRL3	112323742|112323742	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	6.778000|6.778000	0.75043|0.75043	2.680000|2.680000	0.91292|0.91292	0.484000|0.484000	0.47621|0.47621	GCA|TGC	.	.		0.343	PVRL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354045.1	NM_015480		A	110841052	C	A	110841052	3	1	282	1	0	0	0	0	1	0	0	0	12856	710	25	3	898	3	PVRL3	3	110841052	Missense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	2658993	110841052	87181378	289	40523										
PVRL3	25945	hgsc.bcm.edu	37	chr3	110852954	110852954	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atggattattatgaagatctAaaaatgggaatgaagtttgt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:110852954delA	ENST00000485303.1	+	6	1817	c.1542delA	c.(1540-1542)ctafs	p.L514fs	PVRL3_ENST00000493615.1_Intron	NM_001243286.1|NM_015480.2	NP_001230215.1|NP_056295.1	Q9NQS3	PVRL3_HUMAN	poliovirus receptor-related 3	514					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|fertilization (GO:0009566)|homophilic cell adhesion (GO:0007156)|lens morphogenesis in camera-type eye (GO:0002089)|retina morphogenesis in camera-type eye (GO:0060042)|single organismal cell-cell adhesion (GO:0016337)	apical junction complex (GO:0043296)|cell-cell adherens junction (GO:0005913)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	cell adhesion molecule binding (GO:0050839)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(3)	19						ATGAAGATCTAAAAATGGGAA	0.343																																					p.L514fs		Atlas-INDEL	.											.	PVRL3	78	.	0			c.1541delT						.						58	60	59					3																	110852954		2203	4294	6497	SO:0001589	frameshift_variant	25945	exon6			.	AF282874	CCDS2957.1, CCDS58842.1, CCDS58843.1	3q13	2013-01-29			ENSG00000177707	ENSG00000177707		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17664	protein-coding gene	gene with protein product		607147				11024295	Standard	NM_015480		Approved	nectin-3, PPR3, PVRR3, DKFZP566B0846, CDw113, CD113	uc003dxt.2	Q9NQS3	OTTHUMG00000159239	ENST00000485303.1:c.1542delA	chr3.hg19:g.110852954delA	ENSP00000418070:p.Leu514fs	234.0	0.0		171.0	11.0	NM_015480	E9PFR0|Q6NVZ3|Q8NC05|Q8WVU4|Q9BVA9|Q9Y412	Frame_Shift_Del	DEL	ENST00000485303.1	hg19	CCDS2957.1																																																																																			.	.		0.343	PVRL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354045.1	NM_015480		-	110852954	A	-	110852954	7	5	282	1	0	1	0	1	0	0	0	0	12856	349	13	0	1564	0	PVRL3	3	110852954	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	11902	110852954	87169476	290	40524										
FBXO40	51725	hgsc.bcm.edu	37	chr3	121341494	121341494	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctccagtgtgctttggaaagAgaactcaaaggccacgtcat	10	10	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:121341494A>G	ENST00000338040.4	+	3	1632	c.1218A>G	c.(1216-1218)agA>agG	p.R406R		NM_016298.3	NP_057382.2	Q9UH90	FBX40_HUMAN	F-box protein 40	406					muscle cell differentiation (GO:0042692)	cytoplasm (GO:0005737)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(11)|lung(19)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	46				GBM - Glioblastoma multiforme(114;0.189)		CTTTGGAAAGAGAACTCAAAG	0.463																																					p.R406R		Atlas-SNP	.											.	FBXO40	108	.	0			c.A1218G						.						116	112	113					3																	121341494		2203	4300	6503	SO:0001819	synonymous_variant	51725	exon3			GGAAAGAGAACTC	AF204674	CCDS33835.1	3q21.1	2004-08-24			ENSG00000163833	ENSG00000163833		"F-boxes /  "other""	29816	protein-coding gene	gene with protein product		609107				10574462	Standard	NM_016298		Approved	KIAA1195, Fbx40	uc003eeg.2	Q9UH90	OTTHUMG00000159410	ENST00000338040.4:c.1218A>G	chr3.hg19:g.121341494A>G		178.0	0.0		123.0	5.0	NM_016298	B2RAX7|Q32M70|Q9ULM5	Silent	SNP	ENST00000338040.4	hg19	CCDS33835.1																																																																																			.	.		0.463	FBXO40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355158.1	NM_016298		G	121341494	A	G	121341494	2	3	282	1	0	0	0	0	0	0	0	1	5757	301	11	2		2	FBXO40	3	121341494	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	10488540	121341494	76680936	291	40525										
PARP9	83666	hgsc.bcm.edu	37	chr3	122274440	122274440	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctactgtcttaatgtgagtaTttttatagatgacataattc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:122274440delT	ENST00000360356.2	-	4	910	c.683delA	c.(682-684)aatfs	p.N228fs	PARP9_ENST00000492382.1_Intron|PARP9_ENST00000471785.1_Frame_Shift_Del_p.N193fs|PARP9_ENST00000477522.2_Frame_Shift_Del_p.N193fs|PARP9_ENST00000462315.1_Frame_Shift_Del_p.N193fs	NM_001146102.1|NM_031458.2	NP_001139574.1|NP_113646.2	Q8IXQ6	PARP9_HUMAN	poly (ADP-ribose) polymerase family, member 9	228	Macro 1. {ECO:0000255|PROSITE- ProRule:PRU00490}.				cell migration (GO:0016477)|double-strand break repair (GO:0006302)|regulation of response to interferon-gamma (GO:0060330)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	34				GBM - Glioblastoma multiforme(114;0.0519)		AATGTGAGTATTTTTATAGAT	0.423																																					p.N228fs		Atlas-INDEL	.											.	PARP9	72	.	0			c.684delT						.						67	68	68					3																	122274440		2203	4300	6503	SO:0001589	frameshift_variant	83666	exon4			.	AF307339	CCDS3014.1, CCDS54633.1, CCDS54634.1	3q13-q21	2010-02-16			ENSG00000138496	ENSG00000138496		"Poly (ADP-ribose) polymerases"	24118	protein-coding gene	gene with protein product		612065				11110709	Standard	NM_031458		Approved	BAL, BAL1	uc003efi.3	Q8IXQ6	OTTHUMG00000159522	ENST00000360356.2:c.683delA	chr3.hg19:g.122274440delT	ENSP00000353512:p.Asn228fs	179.0	0.0		162.0	10.0	NM_001146102	A8KA94|B2R8S9|E9PFM7|Q8TCP3|Q9BZL8|Q9BZL9	Frame_Shift_Del	DEL	ENST00000360356.2	hg19	CCDS3014.1																																																																																			.	.		0.423	PARP9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355957.1	NM_031458		-	122274440	T	-	122274440	7	5	282	1	0	1	0	1	0	0	0	0	11475	1493	52	0	1966	0	PARP9	3	122274440	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	932946	122274440	75747990	292	40526										
DIRC2	84925	hgsc.bcm.edu	37	chr3	122514376	122514376	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cgttcatgtggctcctggacAagagaggtgaggggtcgcgg	18	8	1	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:122514376A>G	ENST00000261038.5	+	1	735	c.337A>G	c.(337-339)Aag>Gag	p.K113E	HSPBAP1_ENST00000383659.1_5'Flank|HSPBAP1_ENST00000465044.1_5'Flank|HSPBAP1_ENST00000306103.2_5'Flank	NM_032839.2	NP_116228.1	Q96SL1	DIRC2_HUMAN	disrupted in renal carcinoma 2	113					transport (GO:0006810)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)				endometrium(2)|large_intestine(1)|lung(14)|prostate(1)	18				GBM - Glioblastoma multiforme(114;0.0614)		GCTCCTGGACAAGAGAGGTGA	0.721																																					p.K113E		Atlas-SNP	.											.	DIRC2	25	.	0			c.A337G						.						14	16	16					3																	122514376		2201	4297	6498	SO:0001583	missense	84925	exon1			CTGGACAAGAGAG	AK027690	CCDS3018.1	3q21.1	2013-05-22			ENSG00000138463	ENSG00000138463		"Solute carriers"	16628	protein-coding gene	gene with protein product	"renal cell carcinoma 4", "disrupted in renal cancer protein 2"	602773				11912179	Standard	NM_032839		Approved	FLJ14784, RCC4	uc003efw.4	Q96SL1	OTTHUMG00000159553	ENST00000261038.5:c.337A>G	chr3.hg19:g.122514376A>G	ENSP00000261038:p.Lys113Glu	54.0	0.0		35.0	4.0	NM_032839	A8K561|Q8NBX9	Missense_Mutation	SNP	ENST00000261038.5	hg19	CCDS3018.1	.	.	.	.	.	.	.	.	.	.	A	18.73	3.685459	0.68157	.	.	ENSG00000138463	ENST00000261038	T	0.61510	0.1	4.63	3.43	0.39272	Major facilitator superfamily domain, general substrate transporter (1);	0.107793	0.64402	D	0.000007	T	0.42086	0.1187	L	0.46157	1.445	0.58432	D	0.999998	B	0.29988	0.264	B	0.20184	0.028	T	0.22556	-1.0213	10	0.14656	T	0.56	.	8.4917	0.33104	0.9085:0.0:0.0915:0.0	.	113	Q96SL1	DIRC2_HUMAN	E	113	ENSP00000261038:K113E	ENSP00000261038:K113E	K	+	1	0	DIRC2	123997066	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.281000	0.72632	1.931000	0.55961	0.454000	0.30748	AAG	.	.		0.721	DIRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356180.2	NM_032839		G	122514376	A	G	122514376	3	3	282	1	0	0	0	0	1	0	0	0	4536	131	5	2	339	2	DIRC2	3	122514376	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	239936	122514376	75508054	293	40527										
PDIA5	10954	hgsc.bcm.edu	37	chr3	122869147	122869147	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acaagcgtgttgcacctggtGggggacaacttccgggagac					rs114278681	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:122869147delG	ENST00000316218.7	+	14	1304	c.1209delG	c.(1207-1209)gtgfs	p.V403fs	PDIA5_ENST00000467157.1_3'UTR	NM_006810.3	NP_006801.1	Q14554	PDIA5_HUMAN	protein disulfide isomerase family A, member 5	403	Thioredoxin 3. {ECO:0000255|PROSITE- ProRule:PRU00691}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|oxidation-reduction process (GO:0055114)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	oxidoreductase activity (GO:0016491)|protein disulfide isomerase activity (GO:0003756)			breast(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	21				GBM - Glioblastoma multiforme(114;0.0427)		TGCACCTGGTGGGGGACAACT	0.602																																					p.V403fs		Atlas-INDEL	.											.	PDIA5	66	.	0			c.1208delT						.						89	84	85					3																	122869147		2203	4300	6503	SO:0001589	frameshift_variant	10954	exon14			.	AK054963	CCDS3020.1	3q21.1	2009-11-20	2005-06-29		ENSG00000065485	ENSG00000065485	5.3.4.1	"Protein disulfide isomerases"	24811	protein-coding gene	gene with protein product			"protein disulfide isomerase-associated 5"			7556671	Standard	NM_006810		Approved	PDIR, FLJ30401	uc003egc.2	Q14554	OTTHUMG00000159558	ENST00000316218.7:c.1209delG	chr3.hg19:g.122869147delG	ENSP00000323313:p.Val403fs	141.0	0.0		144.0	10.0	NM_006810	D3DN95|Q9BV43	Frame_Shift_Del	DEL	ENST00000316218.7	hg19	CCDS3020.1																																																																																			.	.		0.602	PDIA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356192.1	NM_006810		-	122869147	G	-	122869147	7	5	282	1	0	1	0	1	0	0	0	0	11680	1335	47	0	1263	0	PDIA5	3	122869147	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	354771	122869147	75153283	294	40528										
PTPLB	201562	hgsc.bcm.edu	37	chr3	123219490	123219490	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcagagctgcatatattgtgAgcagttctcctgacactccc	9	12	1	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:123219490A>G	ENST00000383657.5	-	6	711	c.554T>C	c.(553-555)cTc>cCc	p.L185P		NM_198402.3	NP_940684.1	Q6Y1H2	HACD2_HUMAN	protein tyrosine phosphatase-like (proline instead of catalytic arginine), member b	185					fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	lyase activity (GO:0016829)			kidney(2)	2				GBM - Glioblastoma multiforme(114;0.1)		ATATATTGTGAGCAGTTCTCC	0.393																																					p.L185P		Atlas-SNP	.											.	PTPLB	11	.	0			c.T554C						.						107	107	107					3																	123219490		1896	4120	6016	SO:0001583	missense	201562	exon6			ATTGTGAGCAGTT	AK074605	CCDS46895.1	3q21.1	2010-04-30			ENSG00000206527	ENSG00000206527			9640	protein-coding gene	gene with protein product		615939				15024066	Standard	NM_198402		Approved		uc003egj.2	Q6Y1H2	OTTHUMG00000159529	ENST00000383657.5:c.554T>C	chr3.hg19:g.123219490A>G	ENSP00000373153:p.Leu185Pro	150.0	0.0		131.0	6.0	NM_198402		Missense_Mutation	SNP	ENST00000383657.5	hg19	CCDS46895.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.404168	0.83230	.	.	ENSG00000206527	ENST00000383657;ENST00000469317	T;T	0.33865	1.39;1.39	5.91	5.91	0.95273	.	0.126462	0.53938	D	0.000044	T	0.59238	0.2179	M	0.68593	2.085	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	T	0.59392	-0.7463	10	0.49607	T	0.09	-17.1207	16.3483	0.83171	1.0:0.0:0.0:0.0	.	185	Q6Y1H2	HACD2_HUMAN	P	185;74	ENSP00000373153:L185P;ENSP00000419237:L74P	ENSP00000373153:L185P	L	-	2	0	PTPLB	124702180	1.000000	0.71417	0.943000	0.38184	0.896000	0.52359	9.339000	0.96797	2.254000	0.74563	0.533000	0.62120	CTC	.	.		0.393	PTPLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356021.3	NM_198402		G	123219490	A	G	123219490	3	3	282	1	0	0	0	0	1	0	0	0	12790	304	11	2	218	2	PTPLB	3	123219490	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	350343	123219490	74802940	295	40529										
KALRN	8997	hgsc.bcm.edu	37	chr3	124174076	124174076	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gctggccgatagctttgtggAaaaaggccacattcatgcca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:124174076delA	ENST00000240874.3	+	22	3756	c.3599delA	c.(3598-3600)gaafs	p.E1200fs	KALRN_ENST00000360013.3_Frame_Shift_Del_p.E1200fs|KALRN_ENST00000460856.1_Frame_Shift_Del_p.E1191fs	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1200					apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						AGCTTTGTGGAAAAAGGCCAC	0.468																																					p.E1200fs		Atlas-INDEL	.											.	KALRN	556	.	0			c.3598delG						.						129	119	122					3																	124174076		2203	4300	6503	SO:0001589	frameshift_variant	8997	exon22			.	U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	4814	protein-coding gene	gene with protein product	"serine/threonine kinase with Dbl and pleckstrin homology domains"	604605	"huntingtin-associated protein interacting protein (duo)"	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000240874.3:c.3599delA	chr3.hg19:g.124174076delA	ENSP00000240874:p.Glu1200fs	173.0	0.0		140.0	10.0	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Frame_Shift_Del	DEL	ENST00000240874.3	hg19	CCDS3027.1																																																																																			.	.		0.468	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947		-	124174076	A	-	124174076	7	5	282	1	0	1	0	1	0	0	0	0	7984	246	9	0	3685	0	KALRN	3	124174076	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	954586	124174076	73848354	296	40530										
MUC13	56667	hgsc.bcm.edu	37	chr3	124646629	124646629	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaactatgtgtactaattatGgggggagcaggtgtaggaat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:124646629delG	ENST00000311075.3	-	2	299	c.261delC	c.(259-261)cccfs	p.P87fs	MUC13_ENST00000497378.1_5'Flank	NM_033049.3	NP_149038	Q9H3R2	MUC13_HUMAN	mucin 13, cell surface associated	88	Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(1)|skin(1)|stomach(1)	18						TACTAATTATGGGGGGAGCAG	0.438																																					p.I88X		Atlas-INDEL	.											.	MUC13	57	.	0			c.262delA						.						229	231	230					3																	124646629		2203	4300	6503	SO:0001589	frameshift_variant	56667	exon2			.	AF286113		3q21.2	2007-01-17	2006-03-14		ENSG00000173702	ENSG00000173702		"Mucins"	7511	protein-coding gene	gene with protein product		612181	"down-regulated in colon cancer 1", "mucin 13, epithelial transmembrane"	DRCC1		11278439	Standard	NM_033049		Approved		uc003ehq.2	Q9H3R2	OTTHUMG00000159484	ENST00000311075.3:c.261delC	chr3.hg19:g.124646629delG	ENSP00000312235:p.Pro87fs	257.0	0.0		244.0	15.0	NM_033049	Q6UWD9|Q9NXT5	Frame_Shift_Del	DEL	ENST00000311075.3	hg19																																																																																				.	.		0.438	MUC13-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000355714.1	NM_033049		-	124646629	G	-	124646629	7	5	282	1	0	1	0	1	0	0	0	0	9980	1335	47	0	1314	0	MUC13	3	124646629	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	472553	124646629	73375801	297	40531										
HEG1	57493	hgsc.bcm.edu	37	chr3	124746183	124746183	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccaaagcaggaagaaaggacGggctccaagccgaagtggtg	15	9	0	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:124746183G>A	ENST00000311127.4	-	3	846	c.779C>T	c.(778-780)cCg>cTg	p.P260L		NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	260					cardiac atrium morphogenesis (GO:0003209)|cell-cell junction assembly (GO:0007043)|endothelial cell morphogenesis (GO:0001886)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|lymph circulation (GO:0003017)|lymph vessel development (GO:0001945)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|post-embryonic development (GO:0009791)|regulation of body fluid levels (GO:0050878)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|ventricular septum development (GO:0003281)	cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(24)|ovary(2)|urinary_tract(4)	47						AAGAAAGGACGGGCTCCAAGC	0.552																																					p.P260L		Atlas-SNP	.											HEG1,NS,carcinoma,0,1	HEG1	109	.	0			c.C779T						.						61	65	64					3																	124746183		1997	4157	6154	SO:0001583	missense	57493	exon3			AAGGACGGGCTCC	AK074987	CCDS46898.1	3q21.2	2013-03-08	2013-03-08		ENSG00000173706	ENSG00000173706			29227	protein-coding gene	gene with protein product	"heart of glass"	614182	"HEG homolog 1 (zebrafish)"			10574462, 19151727, 23007647	Standard	NM_020733		Approved	KIAA1237, HEG	uc003ehs.4	Q9ULI3	OTTHUMG00000159486	ENST00000311127.4:c.779C>T	chr3.hg19:g.124746183G>A	ENSP00000311502:p.Pro260Leu	300.0	0.0		219.0	0.0	NM_020733	Q6NX66|Q8NC40|Q9BSV0	Missense_Mutation	SNP	ENST00000311127.4	hg19	CCDS46898.1	.	.	.	.	.	.	.	.	.	.	G	9.000	0.979900	0.18812	.	.	ENSG00000173706	ENST00000311127	T	0.42513	0.97	4.78	-0.6	0.11642	.	.	.	.	.	T	0.21145	0.0509	N	0.22421	0.69	0.09310	N	1	P;B	0.36660	0.564;0.429	B;B	0.26770	0.073;0.024	T	0.10222	-1.0639	9	0.59425	D	0.04	.	4.7733	0.13166	0.0:0.1765:0.3183:0.5051	.	260;260	Q9ULI3-2;Q9ULI3	.;HEG1_HUMAN	L	260	ENSP00000311502:P260L	ENSP00000311502:P260L	P	-	2	0	HEG1	126228873	0.013000	0.17824	0.000000	0.03702	0.002000	0.02628	0.444000	0.21661	-0.166000	0.10890	-1.036000	0.02392	CCG	.	.		0.552	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386		A	124746183	G	A	124746183	3	1	282	1	0	0	0	0	1	0	0	0	7053	1116	39	1	3426	1	HEG1	3	124746183	Missense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	99554	124746183	73276247	298	40532										
KLF15	28999	hgsc.bcm.edu	37	chr3	126071137	126071137	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tggggccatcaggcgtggggCccccacctgggccctgggca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:126071137delC	ENST00000296233.3	-	2	859	c.629delG	c.(628-630)ggcfs	p.G210fs	KLF15_ENST00000509675.1_5'Flank	NM_014079.3	NP_054798.1	Q9UIH9	KLF15_HUMAN	Kruppel-like factor 15	210					cardiac muscle hypertrophy in response to stress (GO:0014898)|cellular response to peptide (GO:1901653)|glial cell differentiation (GO:0010001)|glomerular visceral epithelial cell differentiation (GO:0072112)|glucose transport (GO:0015758)|negative regulation of peptidyl-lysine acetylation (GO:2000757)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|lung(7)|ovary(2)|skin(2)	12				GBM - Glioblastoma multiforme(114;0.147)		AGGCGTGGGGCCCCCACCTGG	0.687																																					p.G210fs		Atlas-INDEL	.											.	KLF15	40	.	0			c.630delC						.						21	22	21					3																	126071137		2198	4299	6497	SO:0001589	frameshift_variant	28999	exon2			.	AB029254	CCDS3036.1	3q21.3	2013-01-08			ENSG00000163884	ENSG00000163884		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	14536	protein-coding gene	gene with protein product	"kidney-enriched Kruppel-like factor"	606465				10982849	Standard	NM_014079		Approved	KKLF	uc011bkk.1	Q9UIH9	OTTHUMG00000162689	ENST00000296233.3:c.629delG	chr3.hg19:g.126071137delC	ENSP00000296233:p.Gly210fs	182.0	0.0		144.0	10.0	NM_014079		Frame_Shift_Del	DEL	ENST00000296233.3	hg19	CCDS3036.1																																																																																			.	.		0.687	KLF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370096.1	NM_014079		-	126071137	C	-	126071137	7	5	282	1	0	1	0	1	0	0	0	0	8352	739	26	0	629	0	KLF15	3	126071137	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1324954	126071137	71951293	299	40533										
KBTBD12	166348	hgsc.bcm.edu	37	chr3	127642893	127642893	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtgtactggtgttgtcatggAaaataatactataattgtgg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:127642893delA	ENST00000405109.1	+	2	1456	c.989delA	c.(988-990)gaafs	p.E330fs	KBTBD12_ENST00000343941.4_Intron|KBTBD12_ENST00000407609.3_Intron|KBTBD12_ENST00000405256.1_Frame_Shift_Del_p.E330fs			Q3ZCT8	KBTBC_HUMAN	kelch repeat and BTB (POZ) domain containing 12	330										endometrium(1)|large_intestine(6)|lung(5)|ovary(1)	13						GTTGTCATGGAAAATAATACT	0.383																																					p.E330fs		Atlas-INDEL	.											.	KBTBD12	41	.	0			c.988delG						.						126	123	124					3																	127642893		1889	4097	5986	SO:0001589	frameshift_variant	166348	exon1			.		CCDS33848.2	3q21.3	2013-01-08	2009-10-01	2009-10-01	ENSG00000187715	ENSG00000187715		"BTB/POZ domain containing"	25731	protein-coding gene	gene with protein product			"kelch domain containing 6"	KLHDC6			Standard	NM_207335		Approved	FLJ46299	uc010hsr.3	Q3ZCT8	OTTHUMG00000150508	ENST00000405109.1:c.989delA	chr3.hg19:g.127642893delA	ENSP00000385957:p.Glu330fs	177.0	0.0		108.0	11.0	NM_207335	B5MCC6|Q6ZRK1	Frame_Shift_Del	DEL	ENST00000405109.1	hg19	CCDS33848.2																																																																																			.	.		0.383	KBTBD12-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318682.1	NM_207335		-	127642893	A	-	127642893	7	5	282	1	0	1	0	1	0	0	0	0	8000	246	9	0	991	0	KBTBD12	3	127642893	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1571756	127642893	70379537	300	40534										
PIK3R4	30849	hgsc.bcm.edu	37	chr3	130435361	130435361	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtctgaacaagctagtaataTctttagacctcaaagcataa	6	8	3	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:130435361T>C	ENST00000356763.3	-	9	2767	c.2210A>G	c.(2209-2211)gAt>gGt	p.D737G		NM_014602.2	NP_055417.1	Q99570	PI3R4_HUMAN	phosphoinositide-3-kinase, regulatory subunit 4	737					innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	axoneme (GO:0005930)|cytosol (GO:0005829)|late endosome (GO:0005770)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(6)|large_intestine(16)|lung(28)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	77						GCTAGTAATATCTTTAGACCT	0.393																																					p.D737G		Atlas-SNP	.											.	PIK3R4	145	.	0			c.A2210G						.						74	75	74					3																	130435361		2203	4300	6503	SO:0001583	missense	30849	exon9			GTAATATCTTTAG	Y08991	CCDS3067.1	3q22.1	2013-01-10	2008-02-04		ENSG00000196455	ENSG00000196455		"WD repeat domain containing"	8982	protein-coding gene	gene with protein product		602610				8999962	Standard	NM_014602		Approved	VPS15, p150	uc003enj.3	Q99570	OTTHUMG00000159645	ENST00000356763.3:c.2210A>G	chr3.hg19:g.130435361T>C	ENSP00000349205:p.Asp737Gly	143.0	0.0		116.0	5.0	NM_014602	Q2TBF4	Missense_Mutation	SNP	ENST00000356763.3	hg19	CCDS3067.1	.	.	.	.	.	.	.	.	.	.	T	18.92	3.726274	0.69074	.	.	ENSG00000196455	ENST00000356763;ENST00000508273;ENST00000507330;ENST00000512430	T;T;T;T	0.46819	0.86;0.86;0.86;0.86	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	T	0.59676	0.2211	L	0.56769	1.78	0.80722	D	1	D	0.62365	0.991	P	0.59546	0.859	T	0.57021	-0.7882	10	0.28530	T	0.3	-27.2617	14.9134	0.70776	0.0:0.0:0.0:1.0	.	737	Q99570	PI3R4_HUMAN	G	737;96;96;96	ENSP00000349205:D737G;ENSP00000427302:D96G;ENSP00000424274:D96G;ENSP00000422767:D96G	ENSP00000349205:D737G	D	-	2	0	PIK3R4	131918051	1.000000	0.71417	0.996000	0.52242	0.958000	0.62258	7.698000	0.84413	1.929000	0.55896	0.533000	0.62120	GAT	.	.		0.393	PIK3R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356668.1	NM_014602		C	130435361	T	C	130435361	3	2	282	1	0	0	0	0	1	0	0	0	11930	1435	50	2	1914	2	PIK3R4	3	130435361	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2792468	130435361	67587069	301	40535										
ATP2C1	27032	hgsc.bcm.edu	37	chr3	130694322	130694322	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaggcacgcatgggctcagcGggactcagaggtaaggctat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:130694322delG	ENST00000510168.1	+	18	2110	c.1560delG	c.(1558-1560)gcgfs	p.A520fs	ATP2C1_ENST00000508532.1_Frame_Shift_Del_p.A520fs|ATP2C1_ENST00000507488.2_Frame_Shift_Del_p.A504fs|ATP2C1_ENST00000504948.1_Frame_Shift_Del_p.A504fs|ATP2C1_ENST00000328560.8_Frame_Shift_Del_p.A520fs|ATP2C1_ENST00000422190.2_Frame_Shift_Del_p.A520fs|ATP2C1_ENST00000359644.3_Frame_Shift_Del_p.A520fs|ATP2C1_ENST00000513801.1_Frame_Shift_Del_p.A504fs|ATP2C1_ENST00000533801.2_Frame_Shift_Del_p.A515fs|ATP2C1_ENST00000393221.4_Frame_Shift_Del_p.A554fs|ATP2C1_ENST00000504381.1_Frame_Shift_Del_p.A465fs|ATP2C1_ENST00000428331.2_Frame_Shift_Del_p.A520fs|ATP2C1_ENST00000505330.1_Frame_Shift_Del_p.A504fs			P98194	AT2C1_HUMAN	ATPase, Ca++ transporting, type 2C, member 1	520					actin cytoskeleton reorganization (GO:0031532)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cellular calcium ion homeostasis (GO:0006874)|cellular manganese ion homeostasis (GO:0030026)|epidermis development (GO:0008544)|Golgi calcium ion homeostasis (GO:0032468)|Golgi calcium ion transport (GO:0032472)|ion transmembrane transport (GO:0034220)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-transporting ATPase activity (GO:0005388)|manganese ion binding (GO:0030145)|manganese-transporting ATPase activity (GO:0015410)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(15)|prostate(2)|skin(2)|urinary_tract(1)	39					Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	TGGGCTCAGCGGGACTCAGAG	0.478									Hailey-Hailey disease																												p.A554fs	Esophageal Squamous(99;456 1443 27647 34099 42636)	Atlas-INDEL	.											.	ATP2C1	94	.	0			c.1661delC						.						89	78	82					3																	130694322		2203	4300	6503	SO:0001589	frameshift_variant	27032	exon17	Familial Cancer Database	HHD, Familial Benign Chronic Pemphigus, Benign Familial Pemphigus	.	AF181120	CCDS33856.1, CCDS46912.1, CCDS46913.1, CCDS46914.1, CCDS56278.1, CCDS56279.1, CCDS56280.1, CCDS56281.1, CCDS75006.1	3q21.3	2012-10-22			ENSG00000017260	ENSG00000017260	3.6.3.8	"ATPases / P-type"	13211	protein-coding gene	gene with protein product	"secretory pathway Ca2+/Mn2+ ATPase 1", "calcium-transporting ATPase type 2C member 1"	604384	"benign chronic pemphigus (Hailey-Hailey disease)"	BCPM		10615129, 10767338	Standard	NM_001001485		Approved	KIAA1347, ATP2C1A, PMR1, SPCA1	uc011bli.2	P98194	OTTHUMG00000136802	ENST00000510168.1:c.1560delG	chr3.hg19:g.130694322delG	ENSP00000427461:p.Ala520fs	296.0	0.0		178.0	11.0	NM_001199181	B2RAT7|B4DSW3|B7Z3X9|G3XAH8|G8JLN9|O76005|Q86V72|Q86V73|Q8N6V1|Q8NCJ7	Frame_Shift_Del	DEL	ENST00000510168.1	hg19	CCDS46914.1																																																																																			.	.		0.478	ATP2C1-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356648.2	NM_001001486		-	130694322	G	-	130694322	7	5	282	1	0	1	0	1	0	0	0	0	1143	1103	39	0	1626	0	ATP2C1	3	130694322	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	258961	130694322	67328108	302	40536										
DNAJC13	23317	hgsc.bcm.edu	37	chr3	132175174	132175174	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aacccataaaggtcagcgatGggggttactcagcatgcctg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:132175174delG	ENST00000260818.6	+	10	1276	c.1028delG	c.(1027-1029)tggfs	p.W343fs	DNAJC13_ENST00000486798.1_3'UTR	NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	343					osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						GGTCAGCGATGGGGGTTACTC	0.413																																					p.W343fs		Atlas-INDEL	.											.	DNAJC13	253	.	0			c.1027delT						.						87	83	85					3																	132175174		2203	4300	6503	SO:0001589	frameshift_variant	23317	exon10			.	AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"Heat shock proteins / DNAJ (HSP40)"	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.1028delG	chr3.hg19:g.132175174delG	ENSP00000260818:p.Trp343fs	243.0	0.0		162.0	10.0	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Frame_Shift_Del	DEL	ENST00000260818.6	hg19	CCDS33857.1																																																																																			.	.		0.413	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268		-	132175174	G	-	132175174	7	5	282	1	0	1	0	1	0	0	0	0	4634	1357	47	0	1062	0	DNAJC13	3	132175174	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1480852	132175174	65847256	303	40537										
CDV3	55573	hgsc.bcm.edu	37	chr3	133306780	133306780	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gctttgaagtagtaagacacAaaaatagaggtagggatgag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:133306780delA	ENST00000264993.3	+	5	982	c.667delA	c.(667-669)aaafs	p.K223fs	CDV3_ENST00000508481.1_Frame_Shift_Del_p.K121fs|CDV3_ENST00000420115.2_3'UTR|CDV3_ENST00000515421.1_Intron	NM_001134422.1|NM_001282763.1|NM_017548.4	NP_001127894.1|NP_001269692.1|NP_060018.1	Q9UKY7	CDV3_HUMAN	CDV3 homolog (mouse)	223					cell proliferation (GO:0008283)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)				kidney(3)|lung(1)|prostate(1)	5						AGTAAGACACAAAAATAGAGG	0.358																																					p.H222fs		Atlas-INDEL	.											.	CDV3	22	.	0			c.666delC						.						75	83	81					3																	133306780		2201	4300	6501	SO:0001589	frameshift_variant	55573	exon5			.	AK096865	CCDS3079.1, CCDS46917.1, CCDS46918.1, CCDS75013.1, CCDS75014.1, CCDS75015.1	3q22.1	2008-02-05			ENSG00000091527	ENSG00000091527			26928	protein-coding gene	gene with protein product						10497265	Standard	NM_017548		Approved	H41	uc003epq.3	Q9UKY7	OTTHUMG00000159764	ENST00000264993.3:c.667delA	chr3.hg19:g.133306780delA	ENSP00000264993:p.Lys223fs	328.0	0.0		267.0	17.0	NM_017548	B3KUC2|Q96IP9	Frame_Shift_Del	DEL	ENST00000264993.3	hg19	CCDS3079.1																																																																																			.	.		0.358	CDV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357203.1	NM_017548		-	133306780	A	-	133306780	7	5	282	1	0	1	0	1	0	0	0	0	3183	131	5	0	705	0	CDV3	3	133306780	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1131606	133306780	64715650	304	40538										
SLCO2A1	6578	hgsc.bcm.edu	37	chr3	133672591	133672591	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agccggtccaaatacagagaTggcaaataagatggctggaa	12	7	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:133672591T>C	ENST00000310926.4	-	5	913	c.640A>G	c.(640-642)Atc>Gtc	p.I214V	SLCO2A1_ENST00000493729.1_Missense_Mutation_p.I138V|SLCO2A1_ENST00000478651.1_5'Flank	NM_005630.2	NP_005621.2	Q92959	SO2A1_HUMAN	solute carrier organic anion transporter family, member 2A1	214					lipid transport (GO:0006869)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lipid transporter activity (GO:0005319)|prostaglandin transmembrane transporter activity (GO:0015132)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(2)|stomach(2)	30					Alprostadil(DB00770)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Furosemide(DB00695)|Iloprost(DB01088)|Phenobarbital(DB01174)|Pyruvic acid(DB00119)	AATACAGAGATGGCAAATAAG	0.517																																					p.I214V		Atlas-SNP	.											.	SLCO2A1	72	.	0			c.A640G						.						89	87	88					3																	133672591		2203	4300	6503	SO:0001583	missense	6578	exon5			CAGAGATGGCAAA		CCDS3084.1	3q21	2013-05-22	2003-11-25	2003-11-26	ENSG00000174640	ENSG00000174640		"Solute carriers"	10955	protein-coding gene	gene with protein product		601460	"solute carrier family 21 (prostaglandin transporter), member 2", "matrin F/G 1"	SLC21A2, MATR1		8787677, 9618293	Standard	NM_005630		Approved	PGT, OATP2A1	uc003eqa.4	Q92959	OTTHUMG00000159745	ENST00000310926.4:c.640A>G	chr3.hg19:g.133672591T>C	ENSP00000311291:p.Ile214Val	160.0	0.0		98.0	4.0	NM_005630	Q86V98|Q8IUN2	Missense_Mutation	SNP	ENST00000310926.4	hg19	CCDS3084.1	.	.	.	.	.	.	.	.	.	.	T	5.812	0.334093	0.11013	.	.	ENSG00000174640	ENST00000310926;ENST00000493729	T;T	0.58060	0.36;0.36	5.52	5.52	0.82312	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.057645	0.64402	D	0.000002	T	0.29491	0.0735	N	0.11201	0.11	0.46185	D	0.998915	B;B;B	0.31640	0.088;0.333;0.057	B;B;B	0.34991	0.086;0.193;0.045	T	0.24404	-1.0161	10	0.02654	T	1	.	10.0564	0.42248	0.0:0.0749:0.0:0.9251	.	214;138;214	F8W9W8;E7EU40;Q92959	.;.;SO2A1_HUMAN	V	214;138	ENSP00000311291:I214V;ENSP00000418893:I138V	ENSP00000311291:I214V	I	-	1	0	SLCO2A1	135155281	1.000000	0.71417	0.996000	0.52242	0.987000	0.75469	3.583000	0.53928	2.091000	0.63221	0.459000	0.35465	ATC	.	.		0.517	SLCO2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357131.1	NM_005630		C	133672591	T	C	133672591	3	2	282	1	0	0	0	0	1	0	0	0	14741	1464	51	2	1331	2	SLCO2A1	3	133672591	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	365811	133672591	64349839	305	40539										
AMOTL2	51421	hgsc.bcm.edu	37	chr3	134084701	134084701	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	catgtcctgactgccggcctGggcctcctgtgtcttgcttg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:134084701delG	ENST00000422605.2	-	5	1403	c.1237delC	c.(1237-1239)cagfs	p.Q413fs	AMOTL2_ENST00000513145.1_Frame_Shift_Del_p.Q413fs|AMOTL2_ENST00000514516.1_Frame_Shift_Del_p.Q471fs|AMOTL2_ENST00000511759.1_5'Flank|AMOTL2_ENST00000249883.5_Frame_Shift_Del_p.Q413fs			Q9Y2J4	AMOL2_HUMAN	angiomotin like 2	413					hippo signaling (GO:0035329)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|tight junction (GO:0005923)				endometrium(8)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	19						CTGCCGGCCTGGGCCTCCTGT	0.567																																					p.Q413fs		Atlas-INDEL	.											.	AMOTL2	52	.	0			c.1238delA						.						94	91	92					3																	134084701		2203	4300	6503	SO:0001589	frameshift_variant	51421	exon5			.	AF175966	CCDS33860.1, CCDS63783.1, CCDS63784.1	3q21-q22	2008-07-18			ENSG00000114019	ENSG00000114019			17812	protein-coding gene	gene with protein product	"Leman coiled-coil protein", "angiomotin-like protein 2"	614658					Standard	NM_016201		Approved	LCCP	uc003eqg.1	Q9Y2J4	OTTHUMG00000159777	ENST00000422605.2:c.1237delC	chr3.hg19:g.134084701delG	ENSP00000409999:p.Gln413fs	218.0	0.0		154.0	11.0	NM_016201	A8K6F1|B7Z5Q1|E9PHW3|Q53EP1|Q96F99|Q9UKB4	Frame_Shift_Del	DEL	ENST00000422605.2	hg19																																																																																				.	.		0.567	AMOTL2-014	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000358149.1	NM_016201		-	134084701	G	-	134084701	7	5	282	1	0	1	0	1	0	0	0	0	584	1357	47	0	1129	0	AMOTL2	3	134084701	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	412110	134084701	63937729	306	40540										
PPP2R3A	5523	hgsc.bcm.edu	37	chr3	135720746	135720746	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttgaaaaactcaaaaactctAaccatgcagcttacagaaag	5	9	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:135720746A>G	ENST00000264977.3	+	2	1023	c.406A>G	c.(406-408)Aac>Gac	p.N136D	PPP2R3A_ENST00000490467.1_Intron	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	136					eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein catabolic process (GO:0045732)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|somite development (GO:0061053)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						CAAAAACTCTAACCATGCAGC	0.363																																					p.N136D		Atlas-SNP	.											.	PPP2R3A	114	.	0			c.A406G						.						62	63	62					3																	135720746		2203	4300	6503	SO:0001583	missense	5523	exon2			AACTCTAACCATG	L12146	CCDS3087.1, CCDS3088.1, CCDS54642.1	3q22.2-q22.3	2013-01-10	2010-06-18	2002-04-26	ENSG00000073711	ENSG00000073711	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "EF-hand domain containing"	9307	protein-coding gene	gene with protein product		604944	"protein phosphatase 2 (formerly 2A), regulatory subunit B'' (PR 72), alpha isoform and (PR 130), beta isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha"	PPP2R3		8392071	Standard	NM_002718		Approved		uc003eqv.2	Q06190	OTTHUMG00000159766	ENST00000264977.3:c.406A>G	chr3.hg19:g.135720746A>G	ENSP00000264977:p.Asn136Asp	98.0	0.0		71.0	4.0	NM_002718	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Missense_Mutation	SNP	ENST00000264977.3	hg19	CCDS3087.1	.	.	.	.	.	.	.	.	.	.	A	14.86	2.662071	0.47572	.	.	ENSG00000073711	ENST00000264977	T	0.13778	2.56	5.81	4.63	0.57726	.	0.118979	0.56097	D	0.000026	T	0.17492	0.0420	L	0.54323	1.7	0.80722	D	1	P	0.52842	0.956	P	0.45071	0.468	T	0.00920	-1.1514	10	0.72032	D	0.01	.	11.2123	0.48806	0.7066:0.2934:0.0:0.0	.	136	Q06190	P2R3A_HUMAN	D	136	ENSP00000264977:N136D	ENSP00000264977:N136D	N	+	1	0	PPP2R3A	137203436	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.963000	0.76055	0.992000	0.38840	0.533000	0.62120	AAC	.	.		0.363	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718		G	135720746	A	G	135720746	3	3	282	1	0	0	0	0	1	0	0	0	12400	362	13	2	408	2	PPP2R3A	3	135720746	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1636045	135720746	62301684	307	40541										
DZIP1L	199221	hgsc.bcm.edu	37	chr3	137787113	137787113	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	catggctctgacgagttggtGggggtggctctgccggtgtg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:137787113delG	ENST00000327532.2	-	13	2074	c.1712delC	c.(1711-1713)ccafs	p.P572fs	DZIP1L_ENST00000488595.1_5'Flank	NM_173543.2	NP_775814.2	Q8IYY4	DZI1L_HUMAN	DAZ interacting zinc finger protein 1-like	572					cilium assembly (GO:0042384)	ciliary basal body (GO:0036064)	metal ion binding (GO:0046872)			breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(2)|prostate(1)|skin(1)	35						ACGAGTTGGTGGGGGTGGCTC	0.667																																					p.P571fs		Atlas-INDEL	.											.	DZIP1L	88	.	0			c.1713delA						.						56	66	62					3																	137787113		2203	4300	6503	SO:0001589	frameshift_variant	199221	exon13			.	AK057406	CCDS3096.1, CCDS54645.1	3q22.3	2013-05-22	2013-05-22		ENSG00000158163	ENSG00000158163			26551	protein-coding gene	gene with protein product			"DAZ interacting protein 1-like"			12477932	Standard	NM_173543		Approved	FLJ32844, DZIP2	uc003erq.3	Q8IYY4	OTTHUMG00000159819	ENST00000327532.2:c.1712delC	chr3.hg19:g.137787113delG	ENSP00000332148:p.Pro572fs	258.0	0.0		191.0	13.0	NM_173543	C9JUG5|Q96M38	Frame_Shift_Del	DEL	ENST00000327532.2	hg19	CCDS3096.1																																																																																			.	.		0.667	DZIP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357548.1	NM_173543		-	137787113	G	-	137787113	7	5	282	1	0	1	0	1	0	0	0	0	4866	1348	47	0	607	0	DZIP1L	3	137787113	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	2066367	137787113	60235317	308	40542										
PIK3CB	5291	hgsc.bcm.edu	37	chr3	138461437	138461437	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaacagctacgatgagctttCccccataaagtttatcttct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:138461437delC	ENST00000477593.1	-	4	657	c.584delG	c.(583-585)ggafs	p.G195fs	PIK3CB_ENST00000289153.2_Frame_Shift_Del_p.G195fs			P42338	PK3CB_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit beta	195	PI3K-RBD. {ECO:0000255|PROSITE- ProRule:PRU00879}.				activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|embryonic cleavage (GO:0040016)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of autophagy (GO:0010508)|regulation of cell-matrix adhesion (GO:0001952)|regulation of clathrin-mediated endocytosis (GO:2000369)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	41					Caffeine(DB00201)	GATGAGCTTTCCCCCATAAAG	0.353																																					p.G195fs		Atlas-INDEL	.											.	PIK3CB	103	.	0			c.585delA						.						99	94	96					3																	138461437		2203	4300	6503	SO:0001589	frameshift_variant	5291	exon3			.		CCDS3104.1	3q22.3	2013-09-19	2012-07-13		ENSG00000051382	ENSG00000051382	2.7.1.153		8976	protein-coding gene	gene with protein product		602925	"phosphoinositide-3-kinase, catalytic, beta polypeptide"	PIK3C1		8246984	Standard	NM_006219		Approved		uc011bmq.3	P42338	OTTHUMG00000159893	ENST00000477593.1:c.584delG	chr3.hg19:g.138461437delC	ENSP00000418143:p.Gly195fs	216.0	0.0		151.0	12.0	NM_006219	D3DNF0|Q24JU2	Frame_Shift_Del	DEL	ENST00000477593.1	hg19	CCDS3104.1																																																																																			.	.		0.353	PIK3CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358019.1			-	138461437	C	-	138461437	7	5	282	1	0	1	0	1	0	0	0	0	11923	855	30	0	2706	0	PIK3CB	3	138461437	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	674324	138461437	59560993	309	40543										
TFDP2	7029	hgsc.bcm.edu	37	chr3	141678659	141678659	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	catggatctcaaaggtgttgTcaaaattgaaaagatactca	8	6	3	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:141678659T>C	ENST00000489671.1	-	11	1338	c.908A>G	c.(907-909)gAc>gGc	p.D303G	TFDP2_ENST00000495310.1_Missense_Mutation_p.D206G|TFDP2_ENST00000499676.2_Missense_Mutation_p.D243G|TFDP2_ENST00000486111.1_Missense_Mutation_p.D243G|TFDP2_ENST00000317104.7_Missense_Mutation_p.D227G|TFDP2_ENST00000477292.1_Missense_Mutation_p.D167G|TFDP2_ENST00000397991.4_Missense_Mutation_p.D275G|TFDP2_ENST00000310282.6_Missense_Mutation_p.D243G|TFDP2_ENST00000467072.1_Missense_Mutation_p.D243G|TFDP2_ENST00000479040.1_Missense_Mutation_p.D242G			Q14188	TFDP2_HUMAN	transcription factor Dp-2 (E2F dimerization partner 2)	303	DCB2.				gene expression (GO:0010467)|heart development (GO:0007507)|mitotic cell cycle (GO:0000278)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			kidney(1)|upper_aerodigestive_tract(2)	3						AAAGGTGTTGTCAAAATTGAA	0.403																																					p.D303G		Atlas-SNP	.											.	TFDP2	44	.	0			c.A908G						.						101	95	97					3																	141678659		1943	4172	6115	SO:0001583	missense	7029	exon11			GTGTTGTCAAAAT	U18422	CCDS43159.1, CCDS54647.1, CCDS54648.1, CCDS54649.1, CCDS54650.1	3q23	2011-05-24			ENSG00000114126	ENSG00000114126			11751	protein-coding gene	gene with protein product		602160				7784053, 9027491	Standard	NM_001178138		Approved	Dp-2	uc003eun.4	Q14188	OTTHUMG00000164975	ENST00000489671.1:c.908A>G	chr3.hg19:g.141678659T>C	ENSP00000420616:p.Asp303Gly	163.0	0.0		114.0	5.0	NM_001178139	B7Z8C8|B7Z8L5|D3DNG1|E9PFC3|F8WAI2|Q13331|Q14187|Q6R754|Q8WU88|Q9UG28	Missense_Mutation	SNP	ENST00000489671.1	hg19	CCDS54650.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	29.5|29.5	5.009075|5.009075	0.93346|0.93346	.|.	.|.	ENSG00000114126|ENSG00000114126	ENST00000499676;ENST00000489671;ENST00000486111;ENST00000477292;ENST00000495310;ENST00000467072;ENST00000317104;ENST00000310282;ENST00000479040;ENST00000397991;ENST00000467667|ENST00000474279	T;T;T;T;T;T;T;T;T;T;T|.	0.49432|.	1.77;1.73;1.77;0.8;0.78;1.77;1.79;1.77;1.76;1.74;1.36|.	5.69|5.69	5.69|5.69	0.88448|0.88448	Transcription factor DP, C-terminal (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|.	0.83266|.	0.5217|.	M|M	0.89478|0.89478	3.035|3.035	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	0.999;1.0;0.999|.	D;D;D|.	0.97110|.	0.995;1.0;0.998|.	D|.	0.86263|.	0.1656|.	10|.	0.72032|.	D|.	0.01|.	-8.9532|-8.9532	15.944|15.944	0.79779|0.79779	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	206;303;243|.	B7Z8L5;Q14188;Q14188-5|.	.;TFDP2_HUMAN;.|.	G|W	243;303;243;167;206;243;227;243;242;275;243|16	ENSP00000439782:D243G;ENSP00000420616:D303G;ENSP00000420599:D243G;ENSP00000418971:D167G;ENSP00000419036:D206G;ENSP00000418590:D243G;ENSP00000315668:D227G;ENSP00000309622:D243G;ENSP00000417585:D242G;ENSP00000381078:D275G;ENSP00000417726:D243G|.	ENSP00000309622:D243G|.	D|X	-|-	2|3	0|0	TFDP2|TFDP2	143161349|143161349	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.973000|0.973000	0.67179|0.67179	7.539000|7.539000	0.82063|0.82063	2.170000|2.170000	0.68504|0.68504	0.379000|0.379000	0.24179|0.24179	GAC|TGA	.	.		0.403	TFDP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353294.4	NM_006286		C	141678659	T	C	141678659	3	2	282	1	0	0	0	0	1	0	0	0	15813	1667	58	2	444	2	TFDP2	3	141678659	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3217222	141678659	56343771	310	40544										
GK5	256356	hgsc.bcm.edu	37	chr3	141896386	141896386	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atcctccaaacttttggccaTtttttcagtctcagcagcat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:141896386delT	ENST00000392993.2	-	12	1232	c.1081delA	c.(1081-1083)atgfs	p.M361fs		NM_001039547.2	NP_001034636.1	Q6ZS86	GLPK5_HUMAN	glycerol kinase 5 (putative)	361					glycerol catabolic process (GO:0019563)		ATP binding (GO:0005524)|glycerol kinase activity (GO:0004370)			kidney(1)|large_intestine(1)|lung(7)|urinary_tract(1)	10						CTTTTGGCCATTTTTTCAGTC	0.338																																					p.M361fs		Atlas-INDEL	.											.,1	GK5	45	.	0			c.1082delT						.						115	123	121					3																	141896386		2203	4300	6503	SO:0001589	frameshift_variant	256356	exon12			.	BX648681	CCDS33871.1	3q23	2014-02-12	2006-09-21		ENSG00000175066	ENSG00000175066		"Glycerol kinases"	28635	protein-coding gene	gene with protein product						12477932	Standard	NM_001039547		Approved	MGC40579	uc003euq.2	Q6ZS86	OTTHUMG00000133572	ENST00000392993.2:c.1081delA	chr3.hg19:g.141896386delT	ENSP00000418001:p.Met361fs	269.0	0.0		191.0	12.0	NM_001039547	B2R9I2|D3DNG2|Q8N2A7|Q8N5E6	Frame_Shift_Del	DEL	ENST00000392993.2	hg19	CCDS33871.1																																																																																			.	.		0.338	GK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353999.1	NM_001039547		-	141896386	T	-	141896386	7	5	282	1	0	1	0	1	0	0	0	0	6430	1493	52	0	528	0	GK5	3	141896386	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	217727	141896386	56126044	311	40545										
TRPC1	7220	hgsc.bcm.edu	37	chr3	142443550	142443550	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaatacgctgaatgagaagcTtttcttgctggcgtgcgaca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:142443550delT	ENST00000476941.1	+	1	635	c.149delT	c.(148-150)cttfs	p.L50fs	TRPC1_ENST00000273482.6_Frame_Shift_Del_p.L50fs	NM_001251845.1	NP_001238774.1	P48995	TRPC1_HUMAN	transient receptor potential cation channel, subfamily C, member 1	50					axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|response to calcium ion (GO:0051592)|saliva secretion (GO:0046541)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|sarcomere (GO:0030017)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|inositol 1,4,5 trisphosphate binding (GO:0070679)|ion channel binding (GO:0044325)|store-operated calcium channel activity (GO:0015279)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(2)|stomach(3)|urinary_tract(1)	37						AATGAGAAGCTTTTCTTGCTG	0.572																																					p.L50fs		Atlas-INDEL	.											.	TRPC1	82	.	0			c.148delC						.						154	132	139					3																	142443550		2203	4300	6503	SO:0001589	frameshift_variant	7220	exon1			.	X89066	CCDS3126.1, CCDS58856.1	3q23	2011-12-14			ENSG00000144935	ENSG00000144935		"Voltage-gated ion channels / Transient receptor potential cation channels"	12333	protein-coding gene	gene with protein product		602343				7568191, 16382100	Standard	NM_001251845		Approved	HTRP-1	uc003evc.3	P48995	OTTHUMG00000159301	ENST00000476941.1:c.149delT	chr3.hg19:g.142443550delT	ENSP00000419313:p.Leu50fs	168.0	0.0		121.0	10.0	NM_001251845	Q14CE4	Frame_Shift_Del	DEL	ENST00000476941.1	hg19	CCDS58856.1																																																																																			.	.		0.572	TRPC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354520.1	NM_003304		-	142443550	T	-	142443550	7	5	282	1	0	1	0	1	0	0	0	0	16593	1609	56	0	151	0	TRPC1	3	142443550	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	547164	142443550	55578880	312	40546										
MED12L	116931	hgsc.bcm.edu	37	chr3	151107817	151107817	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cctcctaattactcgcctatCtcctcccaaatgatgcacca	3	17	1	1	rs541597798		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:151107817C>A	ENST00000474524.1	+	36	5435	c.5397C>A	c.(5395-5397)atC>atA	p.I1799I	MED12L_ENST00000273432.4_Silent_p.I1659I	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	1799						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			ACTCGCCTATCTCCTCCCAAA	0.463																																					p.I1799I		Atlas-SNP	.											.	MED12L	271	.	0			c.C5397A						.						175	171	172					3																	151107817		2203	4300	6503	SO:0001819	synonymous_variant	116931	exon36			GCCTATCTCCTCC	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.5397C>A	chr3.hg19:g.151107817C>A		166.0	0.0		86.0	32.0	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Silent	SNP	ENST00000474524.1	hg19	CCDS33876.1																																																																																			.	.		0.463	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002		A	151107817	C	A	151107817	2	1	282	1	0	0	0	0	0	0	0	1	9438	903	32	3		3	MED12L	3	151107817	Silent	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	8664267	151107817	46914613	313	40547										
IGSF10	285313	hgsc.bcm.edu	37	chr3	151164709	151164709	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctatatgggctgataatccgCccccttccgccaattttcct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:151164709delC	ENST00000282466.3	-	4	3059	c.3060delG	c.(3058-3060)gggfs	p.G1020fs		NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	1020					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TGATAATCCGCCCCCTTCCGC	0.473																																					p.R1021fs		Atlas-INDEL	.											.	IGSF10	279	.	0			c.3061delC						.						75	77	77					3																	151164709		2203	4300	6503	SO:0001589	frameshift_variant	285313	exon4			.	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"Immunoglobulin superfamily / I-set domain containing"	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.3060delG	chr3.hg19:g.151164709delC	ENSP00000282466:p.Gly1020fs	157.0	0.0		149.0	10.0	NM_178822	Q86YJ9|Q8N772|Q8NA84	Frame_Shift_Del	DEL	ENST00000282466.3	hg19	CCDS3160.1																																																																																			.	.		0.473	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822		-	151164709	C	-	151164709	7	5	282	1	0	1	0	1	0	0	0	0	7606	726	26	0	4871	0	IGSF10	3	151164709	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	56892	151164709	46857721	314	40548										
PLCH1	23007	hgsc.bcm.edu	37	chr3	155199916	155199916	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	accagccacgagaagtattaGgggatccaggcaggttgctt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:155199916delG	ENST00000340059.7	-	23	3922	c.3923delC	c.(3922-3924)cctfs	p.P1308fs	PLCH1_ENST00000460012.1_Frame_Shift_Del_p.P1270fs|PLCH1_ENST00000494598.1_Intron|PLCH1_ENST00000414191.1_Frame_Shift_Del_p.P1270fs|PLCH1_ENST00000447496.2_3'UTR|PLCH1_ENST00000334686.6_Frame_Shift_Del_p.P1270fs	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	1308					inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phosphatidylinositol-mediated signaling (GO:0048015)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase C activity (GO:0050429)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			NS(3)|breast(3)|endometrium(9)|kidney(4)|large_intestine(20)|lung(45)|ovary(2)|prostate(5)|skin(8)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	107			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			AGAAGTATTAGGGGATCCAGG	0.498																																					p.P1308fs		Atlas-INDEL	.											.	PLCH1	406	.	0			c.3924delT						.						122	124	123					3																	155199916		2203	4300	6503	SO:0001589	frameshift_variant	23007	exon23			.	AB028992	CCDS33881.1, CCDS46939.1, CCDS46940.1	3q25	2013-01-10	2006-03-16	2006-03-16	ENSG00000114805	ENSG00000114805	3.1.4.11	"EF-hand domain containing"	29185	protein-coding gene	gene with protein product		612835	"phospholipase C-like 3"	PLCL3		15702972	Standard	NM_014996		Approved	KIAA1069, MGC117152, DKFZp434C1372, PLCeta1	uc021xge.1	Q4KWH8	OTTHUMG00000158477	ENST00000340059.7:c.3923delC	chr3.hg19:g.155199916delG	ENSP00000345988:p.Pro1308fs	243.0	0.0		198.0	13.0	NM_001130960	Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	Frame_Shift_Del	DEL	ENST00000340059.7	hg19	CCDS46939.1																																																																																			.	.		0.498	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351125.1	NM_014996		-	155199916	G	-	155199916	7	5	282	1	0	1	0	1	0	0	0	0	12046	1000	35	0	1162	0	PLCH1	3	155199916	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	4035207	155199916	42822514	315	40549										
LEKR1	389170	hgsc.bcm.edu	37	chr3	156745953	156745953	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggaagtgaccactcttaaagAaaaacttcacaaatcccata							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:156745953delA	ENST00000470811.1	+	13	1853	c.518delA	c.(517-519)gaafs	p.E173fs	LEKR1_ENST00000356539.4_Frame_Shift_Del_p.E477fs			Q6ZMV7	LEKR1_HUMAN	leucine, glutamate and lysine rich 1	173										breast(1)|large_intestine(5)|lung(3)|ovary(1)|skin(1)	11			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			ACTCTTAAAGAAAAACTTCAC	0.343																																					p.E477fs		Atlas-INDEL	.											LEKR1_ENST00000356539,NS,carcinoma,0,2	LEKR1	66	.	0			c.1429delG						.						59	62	61					3																	156745953		2202	4300	6502	SO:0001589	frameshift_variant	389170	exon12			.	AK131473	CCDS54660.1	3q25.31	2014-02-12	2008-02-21		ENSG00000197980	ENSG00000197980			33765	protein-coding gene	gene with protein product		613536					Standard	NM_001004316		Approved	FLJ16641	uc021xgh.1	Q6ZMV7	OTTHUMG00000160130	ENST00000470811.1:c.518delA	chr3.hg19:g.156745953delA	ENSP00000418214:p.Glu173fs	219.0	0.0		154.0	13.0	NM_001004316		Frame_Shift_Del	DEL	ENST00000470811.1	hg19																																																																																				.	.		0.343	LEKR1-010	KNOWN	upstream_ATG|basic	protein_coding	protein_coding	OTTHUMT00000351625.3	NM_001004316		-	156745953	A	-	156745953	7	5	282	1	0	1	0	1	0	0	0	0	8726	246	9	0	1472	0	LEKR1	3	156745953	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1546037	156745953	41276477	316	40550										
MFSD1	64747	hgsc.bcm.edu	37	chr3	158524843	158524843	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaacagatggggcacaatcaTttttagctgctttgtttgca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:158524843delT	ENST00000264266.8	+	4	406	c.344delT	c.(343-345)attfs	p.I115fs	MFSD1_ENST00000415822.2_Frame_Shift_Del_p.I164fs|MFSD1_ENST00000392813.4_Frame_Shift_Del_p.I125fs			Q9H3U5	MFSD1_HUMAN	major facilitator superfamily domain containing 1	115					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	26			Lung(72;0.00372)|LUSC - Lung squamous cell carcinoma(72;0.00523)			GGCACAATCATTTTTAGCTGC	0.308																																					p.I164fs	Pancreas(62;1186 1654 36636 37908)	Atlas-INDEL	.											.	MFSD1	88	.	0			c.490delA						.						112	104	107					3																	158524843		2203	4299	6502	SO:0001589	frameshift_variant	64747	exon4			.	BC017661	CCDS3185.1, CCDS3185.2, CCDS54666.1	3q25.32	2005-11-17			ENSG00000118855	ENSG00000118855			25874	protein-coding gene	gene with protein product							Standard	NM_022736		Approved	FLJ14153, UG0581B09	uc003fcl.2	Q9H3U5	OTTHUMG00000158835	ENST00000264266.8:c.344delT	chr3.hg19:g.158524843delT	ENSP00000264266:p.Ile115fs	378.0	0.0		269.0	17.0	NM_022736	B4DGJ8|B4DMR8|B4DU49|B4DWU1|C9JS94|J3KQL7|Q05C07|Q5XKJ1|Q8IVS1|Q8IXG4|Q9H7X1	Frame_Shift_Del	DEL	ENST00000264266.8	hg19																																																																																				.	.		0.308	MFSD1-018	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470730.1	NM_022736		-	158524843	T	-	158524843	7	5	282	1	0	1	0	1	0	0	0	0	9536	1493	52	0	505	0	MFSD1	3	158524843	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1778890	158524843	39497587	317	40551										
IL12A	3592	hgsc.bcm.edu	37	chr3	159710910	159710910	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtttaccattggaattaaccAaggtataaaggattttcctc	7	7	0	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:159710910A>G	ENST00000305579.2	+	3	683	c.376A>G	c.(376-378)Aag>Gag	p.K126E	IL12A-AS1_ENST00000497452.1_RNA|IL12A_ENST00000480787.1_Intron|IL12A_ENST00000466512.1_Missense_Mutation_p.K126E	NM_000882.3	NP_000873.2	P29459	IL12A_HUMAN	interleukin 12A	92					cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|defense response to Gram-positive bacterium (GO:0050830)|defense response to protozoan (GO:0042832)|extrinsic apoptotic signaling pathway (GO:0097191)|immune response (GO:0006955)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cell adhesion (GO:0045785)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of mononuclear cell proliferation (GO:0032946)|positive regulation of natural killer cell activation (GO:0032816)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|positive regulation of NK T cell activation (GO:0051135)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat4 protein (GO:0042520)|response to lipopolysaccharide (GO:0032496)|response to UV-B (GO:0010224)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|interleukin-12 complex (GO:0043514)	interleukin-12 beta subunit binding (GO:0042163)|interleukin-12 receptor binding (GO:0005143)|interleukin-27 binding (GO:0045513)|protein heterodimerization activity (GO:0046982)			endometrium(3)|kidney(1)|large_intestine(1)|lung(4)	9			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			GGAATTAACCAAGGTATAAAG	0.383																																					p.K126E		Atlas-SNP	.											.	IL12A	23	.	0			c.A376G						.						62	68	66					3																	159710910		2202	4300	6502	SO:0001583	missense	3592	exon3			TTAACCAAGGTAT	M65271	CCDS3187.1	3q25.33	2014-04-04	2014-04-04		ENSG00000168811	ENSG00000168811		"Interleukins and interleukin receptors"	5969	protein-coding gene	gene with protein product	"natural killer cell stimulatory factor 1, 35 kD subunit", "cytotoxic lymphocyte maturation factor 1, p35", "interleukin 12, p35", "IL-12, subunit p35", "NF cell stimulatory factor chain 1", "interleukin-12 alpha chain", "IL35 subunit"	161560	"interleukin 12A (natural killer cell stimulatory factor 1, cytotoxic lymphocyte maturation factor 1, p35)"	NKSF1		1673147	Standard	NM_000882		Approved	CLMF, IL-12A, p35, NFSK	uc003fcx.3	P29459	OTTHUMG00000158942	ENST00000305579.2:c.376A>G	chr3.hg19:g.159710910A>G	ENSP00000303231:p.Lys126Glu	153.0	0.0		100.0	4.0	NM_000882	Q96QZ1	Missense_Mutation	SNP	ENST00000305579.2	hg19	CCDS3187.1	.	.	.	.	.	.	.	.	.	.	A	9.831	1.188533	0.21954	.	.	ENSG00000168811	ENST00000305579;ENST00000466512	.	.	.	5.66	0.495	0.16890	.	1.000120	0.08080	N	1.000000	T	0.34077	0.0885	L	0.47190	1.495	0.09310	N	1	B	0.21225	0.053	B	0.18871	0.023	T	0.33189	-0.9878	9	0.56958	D	0.05	-1.0851	5.5477	0.17073	0.5923:0.2909:0.1168:0.0	.	126	O60595	.	E	126	.	ENSP00000303231:K126E	K	+	1	0	IL12A	161193604	0.007000	0.16637	0.019000	0.16419	0.399000	0.30720	0.482000	0.22276	-0.134000	0.11516	0.460000	0.39030	AAG	.	.		0.383	IL12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352602.2	NM_000882		G	159710910	A	G	159710910	3	3	282	1	0	0	0	0	1	0	0	0	7633	131	5	2	386	2	IL12A	3	159710910	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1186067	159710910	38311520	318	40552										
SI	6476	hgsc.bcm.edu	37	chr3	164700065	164700065	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cttcattaaaaggaagcgaaTttttatttccgttatacgtt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:164700065delT	ENST00000264382.3	-	47	5443	c.5381delA	c.(5380-5382)aatfs	p.N1794fs		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	1794	Sucrase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)			NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	AGGAAGCGAATTTTTATTTCC	0.343										HNSCC(35;0.089)																											p.N1794fs		Atlas-INDEL	.											.	SI	500	.	0			c.5382delT						.						117	112	114					3																	164700065		2202	4299	6501	SO:0001589	frameshift_variant	6476	exon47			.	X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"Oligosaccharide alpha-1,6-glucosidase"	609845	"sucrase-isomaltase"			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.5381delA	chr3.hg19:g.164700065delT	ENSP00000264382:p.Asn1794fs	194.0	0.0		147.0	10.0	NM_001041	A2RUC3|Q1JQ80|Q1RMC2	Frame_Shift_Del	DEL	ENST00000264382.3	hg19	CCDS3196.1																																																																																			.	.		0.343	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041		-	164700065	T	-	164700065	7	5	282	1	0	1	0	1	0	0	0	0	14312	1493	52	0	110	0	SI	3	164700065	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	4989155	164700065	33322365	319	40553										
SI	6476	hgsc.bcm.edu	37	chr3	164710135	164710135	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gggtaaccataaatgctggaCcccataagaactgcttgaat					rs371948467		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:164710135delC	ENST00000264382.3	-	42	4954	c.4892delG	c.(4891-4893)ggtfs	p.G1631fs		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	1631	Sucrase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)			NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	AAATGCTGGACCCCATAAGAA	0.318										HNSCC(35;0.089)																											p.G1631fs		Atlas-INDEL	.											.	SI	500	.	0			c.4893delT						.						57	60	59					3																	164710135		2202	4300	6502	SO:0001589	frameshift_variant	6476	exon42			.	X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"Oligosaccharide alpha-1,6-glucosidase"	609845	"sucrase-isomaltase"			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.4892delG	chr3.hg19:g.164710135delC	ENSP00000264382:p.Gly1631fs	189.0	0.0		170.0	12.0	NM_001041	A2RUC3|Q1JQ80|Q1RMC2	Frame_Shift_Del	DEL	ENST00000264382.3	hg19	CCDS3196.1																																																																																			.	.		0.318	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041		-	164710135	C	-	164710135	7	5	282	1	0	1	0	1	0	0	0	0	14312	507	18	0	619	0	SI	3	164710135	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	10070	164710135	33312295	320	40554										
TNIK	23043	hgsc.bcm.edu	37	chr3	170801981	170801981	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agtatttctgagttgaatcgTttcttgtattttctgatttc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:170801981delT	ENST00000436636.2	-	26	3476	c.3132delA	c.(3130-3132)aaafs	p.K1044fs	TNIK_ENST00000470834.1_Frame_Shift_Del_p.K1007fs|TNIK_ENST00000538048.1_Frame_Shift_Del_p.K996fs|TNIK_ENST00000460047.1_Frame_Shift_Del_p.K981fs|TNIK_ENST00000284483.8_Frame_Shift_Del_p.K1036fs|TNIK_ENST00000488470.1_Frame_Shift_Del_p.K989fs|TNIK_ENST00000341852.6_Frame_Shift_Del_p.K960fs|TNIK_ENST00000475336.1_Frame_Shift_Del_p.K952fs|TNIK_ENST00000357327.5_Frame_Shift_Del_p.K1015fs|TNIK_ENST00000369326.5_Frame_Shift_Del_p.K1022fs	NM_015028.2	NP_055843.1	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase	1044	Mediates interaction with NEDD4.				actin cytoskeleton reorganization (GO:0031532)|activation of JNKK activity (GO:0007256)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite morphogenesis (GO:0048814)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(22)|ovary(5)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)	62	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			AGTTGAATCGTTTCTTGTATT	0.373																																					p.R1045fs		Atlas-INDEL	.											TNIK_ENST00000436636,NS,carcinoma,0,2	TNIK	313	.	0			c.3133delC						.						105	96	99					3																	170801981		1845	4082	5927	SO:0001589	frameshift_variant	23043	exon26			.	AF172264	CCDS46956.1, CCDS54673.1, CCDS54674.1, CCDS54675.1, CCDS54676.1, CCDS54677.1, CCDS54678.1, CCDS54679.1	3q26.31	2008-01-23			ENSG00000154310	ENSG00000154310			30765	protein-coding gene	gene with protein product		610005				9628581, 10521462	Standard	NR_027767		Approved	KIAA0551	uc003fhh.2	Q9UKE5	OTTHUMG00000159036	ENST00000436636.2:c.3132delA	chr3.hg19:g.170801981delT	ENSP00000399511:p.Lys1044fs	230.0	0.0		203.0	13.0	NM_015028	A7E2A3|A8K4U1|D3DNQ6|O60298|Q8WUY7|Q9UKD8|Q9UKD9|Q9UKE0|Q9UKE1|Q9UKE2|Q9UKE3|Q9UKE4	Frame_Shift_Del	DEL	ENST00000436636.2	hg19	CCDS46956.1																																																																																			.	.		0.373	TNIK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352973.2	XM_039796		-	170801981	T	-	170801981	7	5	282	1	0	1	0	1	0	0	0	0	16328	1722	60	0	982	0	TNIK	3	170801981	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	6091846	170801981	27220449	321	40555										
MFN1	55669	hgsc.bcm.edu	37	chr3	179085315	179085315	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agaagcacagaatcgtatctTctttgtttcagcaaaggaag	9	7	3	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:179085315T>C	ENST00000471841.1	+	8	968	c.842T>C	c.(841-843)tTc>tCc	p.F281S	MFN1_ENST00000263969.5_Missense_Mutation_p.F281S|MFN1_ENST00000280653.7_Missense_Mutation_p.F281S	NM_033540.2	NP_284941	Q8IWA4	MFN1_HUMAN	mitofusin 1	281	Dynamin-type G.				mitochondrial fusion (GO:0008053)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(14)|ovary(3)|prostate(1)|urinary_tract(1)	31	all_cancers(143;1.67e-16)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.00225)|BRCA - Breast invasive adenocarcinoma(182;0.0923)			AATCGTATCTTCTTTGTTTCA	0.398																																					p.F281S		Atlas-SNP	.											.	MFN1	72	.	0			c.T842C						.						73	72	72					3																	179085315		2203	4300	6503	SO:0001583	missense	55669	exon8			GTATCTTCTTTGT	AF054986	CCDS3228.1	3q26.32	2006-12-13			ENSG00000171109	ENSG00000171109			18262	protein-coding gene	gene with protein product		608506				8358434, 11181170	Standard	NM_033540		Approved	FLJ20693	uc003fjs.3	Q8IWA4	OTTHUMG00000157385	ENST00000471841.1:c.842T>C	chr3.hg19:g.179085315T>C	ENSP00000420617:p.Phe281Ser	147.0	0.0		100.0	4.0	NM_033540	B2RAR1|D3DNR6|O15323|O60639|Q9BZB5|Q9NWQ2	Missense_Mutation	SNP	ENST00000471841.1	hg19	CCDS3228.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.015741	0.75161	.	.	ENSG00000171109	ENST00000471841;ENST00000280653;ENST00000539169;ENST00000263969;ENST00000474903	D;D;D;D	0.97256	-3.86;-3.86;-3.86;-4.31	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	D	0.98538	0.9512	M	0.87682	2.9	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.997;0.998;0.998	D	0.99751	1.1018	10	0.87932	D	0	-14.039	15.4952	0.75643	0.0:0.0:0.0:1.0	.	281;309;281	Q8IWA4-3;Q4AEJ4;Q8IWA4	.;.;MFN1_HUMAN	S	281;281;281;281;144	ENSP00000420617:F281S;ENSP00000280653:F281S;ENSP00000263969:F281S;ENSP00000419926:F144S	ENSP00000263969:F281S	F	+	2	0	MFN1	180568009	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.649000	0.83500	2.065000	0.61736	0.533000	0.62120	TTC	.	.		0.398	MFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348654.2	NM_017927		C	179085315	T	C	179085315	3	2	282	1	0	0	0	0	1	0	0	0	9532	1783	62	2	868	2	MFN1	3	179085315	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	8283334	179085315	18937115	322	40556										
TTC14	151613	hgsc.bcm.edu	37	chr3	180326508	180326508	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaaatctttggaattaagagAaaaacaagctgaaaaggaag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:180326508delA	ENST00000296015.4	+	11	1442	c.1310delA	c.(1309-1311)gaafs	p.E437fs	TTC14_ENST00000382584.4_Frame_Shift_Del_p.E437fs|TTC14_ENST00000412756.2_3'UTR|TTC14_ENST00000465625.1_3'UTR	NM_133462.3	NP_597719.1	Q96N46	TTC14_HUMAN	tetratricopeptide repeat domain 14	437							RNA binding (GO:0003723)			endometrium(3)|kidney(5)|large_intestine(9)|lung(24)|ovary(2)|pancreas(1)|skin(1)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			GAATTAAGAGAAAAACAAGCT	0.323																																					p.E437fs		Atlas-INDEL	.											.	TTC14	112	.	0			c.1309delG						.						20	21	20					3																	180326508		2198	4284	6482	SO:0001589	frameshift_variant	151613	exon11			.	AB075860	CCDS3237.1, CCDS46963.1, CCDS75055.1	3q27.2	2013-01-10			ENSG00000163728	ENSG00000163728		"Tetratricopeptide (TTC) repeat domain containing"	24697	protein-coding gene	gene with protein product						11853319	Standard	NM_001042601		Approved	FLJ00166, KIAA1980	uc003fkk.3	Q96N46	OTTHUMG00000157859	ENST00000296015.4:c.1310delA	chr3.hg19:g.180326508delA	ENSP00000296015:p.Glu437fs	239.0	0.0		183.0	11.0	NM_133462	G5E9X0|Q6UWJ7|Q8TF22	Frame_Shift_Del	DEL	ENST00000296015.4	hg19	CCDS3237.1																																																																																			.	.		0.323	TTC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349786.1	NM_133462		-	180326508	A	-	180326508	7	5	282	1	0	1	0	1	0	0	0	0	16696	246	9	0	1382	0	TTC14	3	180326508	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1241193	180326508	17695922	323	40557										
OPA1	4976	hgsc.bcm.edu	37	chr3	193332740	193332740	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggctaccagcctcgcaggaaTttttggccagcaagattagc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:193332740delT	ENST00000392438.3	+	2	495	c.261delT	c.(259-261)aatfs	p.N87fs	OPA1_ENST00000487986.1_3'UTR|OPA1_ENST00000361510.2_Frame_Shift_Del_p.N87fs|OPA1_ENST00000361715.2_Frame_Shift_Del_p.N87fs|OPA1_ENST00000361908.3_Frame_Shift_Del_p.N87fs|OPA1_ENST00000361828.2_Frame_Shift_Del_p.N87fs|OPA1_ENST00000361150.2_Frame_Shift_Del_p.N87fs	NM_015560.2	NP_056375.2	O60313	OPA1_HUMAN	optic atrophy 1 (autosomal dominant)	87					apoptotic process (GO:0006915)|axon transport of mitochondrion (GO:0019896)|cellular senescence (GO:0090398)|GTP catabolic process (GO:0006184)|inner mitochondrial membrane organization (GO:0007007)|mitochondrial fission (GO:0000266)|mitochondrial fusion (GO:0008053)|mitochondrion organization (GO:0007005)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|neural tube closure (GO:0001843)|visual perception (GO:0007601)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial crista (GO:0030061)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)			breast(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(4)|lung(15)|upper_aerodigestive_tract(1)|urinary_tract(2)	31	all_cancers(143;9.56e-09)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;9.19e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000162)		CTCGCAGGAATTTTTGGCCAG	0.428																																					p.N87fs		Atlas-INDEL	.											.	OPA1	79	.	0			c.260delA						.						49	48	48					3																	193332740		2203	4300	6503	SO:0001589	frameshift_variant	4976	exon2			.	AB011139	CCDS33917.1, CCDS43186.1	3q29	2014-09-17			ENSG00000198836	ENSG00000198836			8140	protein-coding gene	gene with protein product	"mitochondrial dynamin-like GTPase", "dynamin-like guanosine triphosphatase", "Dynamin-like 120 kDa protein, mitochondrial"	605290				9490303	Standard	NM_015560		Approved	NTG, KIAA0567, FLJ12460, NPG, MGM1	uc003ftg.3	O60313	OTTHUMG00000149897	ENST00000392438.3:c.261delT	chr3.hg19:g.193332740delT	ENSP00000376233:p.Asn87fs	240.0	0.0		175.0	11.0	NM_130832	D3DNW4	Frame_Shift_Del	DEL	ENST00000392438.3	hg19	CCDS43186.1																																																																																			.	.		0.428	OPA1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313812.2	NM_130837		-	193332740	T	-	193332740	7	5	282	1	0	1	0	1	0	0	0	0	10880	1490	52	0	267	0	OPA1	3	193332740	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	13006232	193332740	4689690	324	40558										
ATP13A3	79572	hgsc.bcm.edu	37	chr3	194175043	194175043	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tatggacataaccacaatagCtagagcatagtaatagtatt	7	6	0	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:194175043C>T	ENST00000439040.1	-	9	1500	c.709G>A	c.(709-711)Gct>Act	p.A237T	ATP13A3_ENST00000256031.4_Missense_Mutation_p.A237T			Q9H7F0	AT133_HUMAN	ATPase type 13A3	237						integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			NS(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	24	all_cancers(143;6.01e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	OV - Ovarian serous cystadenocarcinoma(49;3.83e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;5.98e-05)		ACCACAATAGCTAGAGCATAG	0.318																																					p.A237T		Atlas-SNP	.											.	ATP13A3	94	.	0			c.G709A						.						96	88	90					3																	194175043		1862	4099	5961	SO:0001583	missense	79572	exon8			CAATAGCTAGAGC	AJ306929	CCDS43187.1	3q29	2010-04-20			ENSG00000133657	ENSG00000133657		"ATPases / P-type"	24113	protein-coding gene	gene with protein product	"ATPase family homolog up regulated in senescence cells"	610232				11867234	Standard	NM_024524		Approved	AFURS1	uc003fty.4	Q9H7F0	OTTHUMG00000156034	ENST00000439040.1:c.709G>A	chr3.hg19:g.194175043C>T	ENSP00000416508:p.Ala237Thr	107.0	0.0		80.0	4.0	NM_024524	Q8NC11|Q96KS1	Missense_Mutation	SNP	ENST00000439040.1	hg19	CCDS43187.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.804402	0.90623	.	.	ENSG00000133657	ENST00000439040;ENST00000256031	D;D	0.89343	-2.5;-2.5	5.51	4.64	0.57946	.	0.114749	0.64402	D	0.000016	D	0.94820	0.8327	M	0.88105	2.93	0.53005	D	0.999965	D	0.63880	0.993	D	0.70487	0.969	D	0.94252	0.7494	10	0.31617	T	0.26	-7.8778	16.3875	0.83521	0.0:0.8681:0.1319:0.0	.	237	Q9H7F0	AT133_HUMAN	T	237	ENSP00000416508:A237T;ENSP00000256031:A237T	ENSP00000256031:A237T	A	-	1	0	ATP13A3	195656332	0.998000	0.40836	0.996000	0.52242	0.997000	0.91878	3.938000	0.56583	1.308000	0.44962	0.650000	0.86243	GCT	.	.		0.318	ATP13A3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342799.2	NM_024524		T	194175043	C	T	194175043	3	4	282	1	0	0	0	0	1	0	0	0	1125	797	28	3	3071	3	ATP13A3	3	194175043	Missense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	842303	194175043	3847387	325	40559										
NCBP2	22916	hgsc.bcm.edu	37	chr3	196664445	196664445	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agcctgcgtcccagtctgtgCgaatgattcggtcatccaga	11	12	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:196664445C>T	ENST00000321256.5	-	3	428	c.335G>A	c.(334-336)cGc>cAc	p.R112H	NCBP2_ENST00000452404.2_Missense_Mutation_p.R94H|NCBP2_ENST00000447325.1_Missense_Mutation_p.R42H|NCBP2_ENST00000467803.1_5'UTR|NCBP2_ENST00000427641.2_Missense_Mutation_p.R59H|NCBP2-AS1_ENST00000447775.1_RNA|NCBP2_ENST00000422610.1_Missense_Mutation_p.R42H	NM_007362.3	NP_031388.2	P52298	NCBP2_HUMAN	nuclear cap binding protein subunit 2, 20kDa	112	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.|mRNA cap-binding.				7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA cis splicing, via spliceosome (GO:0045292)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of RNA export from nucleus (GO:0046833)|positive regulation of viral transcription (GO:0050434)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|snRNA export from nucleus (GO:0006408)|spliceosomal snRNP assembly (GO:0000387)|termination of RNA polymerase II transcription (GO:0006369)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mRNA cap binding complex (GO:0005845)|nuclear cap binding complex (GO:0005846)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA 7-methylguanosine cap binding (GO:0000340)|RNA cap binding (GO:0000339)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	5	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.42e-24)|all cancers(36;2.27e-22)|OV - Ovarian serous cystadenocarcinoma(49;4.13e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00551)		CCAGTCTGTGCGAATGATTCG	0.537																																					p.R112H		Atlas-SNP	.											.	NCBP2	12	.	0			c.G335A						.						119	106	110					3																	196664445		2203	4300	6503	SO:0001583	missense	22916	exon3			TCTGTGCGAATGA	D59253	CCDS3323.1, CCDS46986.1	3q29	2013-02-12	2002-08-29		ENSG00000114503	ENSG00000114503		"RNA binding motif (RRM) containing"	7659	protein-coding gene	gene with protein product		605133	"nuclear cap binding protein subunit 2, 20kD"			7478990, 7651522, 8682299	Standard	NM_001042540		Approved	NIP1, CBP20, Cbc2	uc003fxd.1	P52298	OTTHUMG00000155520	ENST00000321256.5:c.335G>A	chr3.hg19:g.196664445C>T	ENSP00000326806:p.Arg112His	99.0	0.0		73.0	4.0	NM_007362	B2RE91|B4DMK7|E9PAR5|Q14924|Q2TS50	Missense_Mutation	SNP	ENST00000321256.5	hg19	CCDS3323.1	.	.	.	.	.	.	.	.	.	.	C	33	5.260365	0.95368	.	.	ENSG00000114503	ENST00000447325;ENST00000321256;ENST00000427641;ENST00000452404;ENST00000422610;ENST00000411704	T;T;T;T;T;T	0.76448	-1.02;-1.02;-1.02;-1.02;-1.02;-1.02	4.96	4.96	0.65561	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	D	0.87281	0.6138	M	0.72576	2.205	0.80722	D	1	B;D;P	0.89917	0.226;1.0;0.654	B;D;B	0.97110	0.04;1.0;0.067	D	0.86708	0.1934	10	0.46703	T	0.11	.	17.7697	0.88487	0.0:1.0:0.0:0.0	.	94;59;112	P52298-2;E9PAR5;P52298	.;.;NCBP2_HUMAN	H	42;112;59;94;42;42	ENSP00000413518:R42H;ENSP00000326806:R112H;ENSP00000397619:R59H;ENSP00000412785:R94H;ENSP00000394105:R42H;ENSP00000389315:R42H	ENSP00000326806:R112H	R	-	2	0	NCBP2	198148842	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.518000	0.81795	2.767000	0.95098	0.655000	0.94253	CGC	.	.		0.537	NCBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340470.2	NM_007362		T	196664445	C	T	196664445	3	4	282	1	0	0	0	0	1	0	0	0	10221	768	27	1	143	1	NCBP2	3	196664445	Missense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	2489402	196664445	1357985	326	40560										
FGFR3	2261	hgsc.bcm.edu	37	chr4	1803669	1803669	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aggtgtacagtgacgcacagCcccacatccagtggctcaag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:1803669delC	ENST00000260795.2	+	6	949	c.847delC	c.(847-849)cccfs	p.P283fs	FGFR3_ENST00000340107.4_Frame_Shift_Del_p.P283fs|FGFR3_ENST00000481110.2_Frame_Shift_Del_p.P283fs|FGFR3_ENST00000474521.1_3'UTR|FGFR3_ENST00000352904.1_Frame_Shift_Del_p.P283fs|FGFR3_ENST00000412135.2_Frame_Shift_Del_p.P283fs|FGFR3_ENST00000440486.2_Frame_Shift_Del_p.P283fs			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	283	Ig-like C2-type 3.				alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)	p.P283S(1)		NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	TGACGCACAGCCCCACATCCA	0.672		1	"Mis, T"	"IGH@, ETV6"	"bladder, MM, T-cell lymphoma"		"Hypochondroplasia, Thanatophoric dysplasia"		Saethre-Chotzen syndrome;Muenke syndrome																												p.Q282fs		Atlas-INDEL	.		Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"L, E"	.	FGFR3	3320	.	1	Substitution - Missense(1)	urinary_tract(1)	c.846delG						.						50	44	46					4																	1803669		2203	4299	6502	SO:0001589	frameshift_variant	2261	exon7	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	.	M64347	CCDS3353.1, CCDS3354.1, CCDS54706.1	4p16.3	2013-01-11	2008-08-01		ENSG00000068078	ENSG00000068078		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3690	protein-coding gene	gene with protein product		134934	"achondroplasia, thanatophoric dwarfism"	ACH		1847508	Standard	NM_000142		Approved	CEK2, JTK4, CD333	uc003gdu.2	P22607	OTTHUMG00000121148	ENST00000260795.2:c.847delC	chr4.hg19:g.1803669delC	ENSP00000260795:p.Pro283fs	234.0	0.0		148.0	11.0	NM_001163213	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Frame_Shift_Del	DEL	ENST00000260795.2	hg19	CCDS3353.1																																																																																			.	.		0.672	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142		-	1803669	C	-	1803669	7	5	282	1	0	1	0	1	0	0	0	0	5875	739	26	0	869	0	FGFR3	4	1803669	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10		1803669	189350607	327	40561										
FAM193A	8603	hgsc.bcm.edu	37	chr4	2659604	2659604	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caaagaagattcattgaagaAcaggtaagcttgtcaataag	9	5	2	4			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:2659604A>G	ENST00000324666.5	+	6	864	c.513A>G	c.(511-513)gaA>gaG	p.E171E	FAM193A_ENST00000382839.3_Silent_p.E171E|FAM193A_ENST00000502458.1_Silent_p.E195E|FAM193A_ENST00000545951.1_Silent_p.E171E|FAM193A_ENST00000505311.1_Silent_p.E171E	NM_001256666.1	NP_001243595.1	P78312	F193A_HUMAN	family with sequence similarity 193, member A	171										NS(2)|breast(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(12)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	40						TCATTGAAGAACAGGTAAGCT	0.378																																					p.E195E		Atlas-SNP	.											.	FAM193A	103	.	0			c.A585G						.						120	130	126					4																	2659604		2203	4300	6503	SO:0001819	synonymous_variant	8603	exon7			TGAAGAACAGGTA	AB000459	CCDS33943.1, CCDS58874.1, CCDS58875.1, CCDS58876.1	4p16.3	2009-09-04	2009-09-04	2009-09-04					16822	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 8"	C4orf8		9734812	Standard	NR_046335		Approved	RES4-22	uc010ick.3	P78312		ENST00000324666.5:c.513A>G	chr4.hg19:g.2659604A>G		93.0	0.0		71.0	4.0	NM_001256667	B7ZM85|B9EGR0|E9PFA1|O43607|P78311|P78313|Q9UEG8	Silent	SNP	ENST00000324666.5	hg19	CCDS58875.1																																																																																			.	.		0.378	FAM193A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360903.1	NM_003704		G	2659604	A	G	2659604	2	3	282	1	0	0	0	0	0	0	0	1	5529	40	2	2		2	FAM193A	4	2659604	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	855935	2659604	188494672	328	40562										
ZNF518B	85460	hgsc.bcm.edu	37	chr4	10447095	10447095	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tttggaatacaaactacatcTttttggtattcctttggttc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:10447095delT	ENST00000326756.3	-	3	1296	c.858delA	c.(856-858)aaafs	p.K286fs		NM_053042.2	NP_444270.2	Q9C0D4	Z518B_HUMAN	zinc finger protein 518B	286					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	42						AAACTACATCTTTTTGGTATT	0.358																																					p.D287fs		Atlas-INDEL	.											ZNF518B,mouth,carcinoma,0,1	ZNF518B	116	.	0			c.859delG						.						183	180	181					4																	10447095		2203	4300	6503	SO:0001589	frameshift_variant	85460	exon3			.	AB051516	CCDS33960.1	4p16.1	2007-12-07				ENSG00000178163		"Zinc fingers, C2H2-type"	29365	protein-coding gene	gene with protein product						11214970	Standard	XM_005248193		Approved	KIAA1729	uc003gmn.3	Q9C0D4		ENST00000326756.3:c.858delA	chr4.hg19:g.10447095delT	ENSP00000317614:p.Lys286fs	167.0	0.0		164.0	13.0	NM_053042	Q96LN8	Frame_Shift_Del	DEL	ENST00000326756.3	hg19	CCDS33960.1																																																																																			.	.		0.358	ZNF518B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359040.1	NM_053042		-	10447095	T	-	10447095	7	5	282	1	0	1	0	1	0	0	0	0	17978	1606	56	0	2370	0	ZNF518B	4	10447095	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	7787491	10447095	180707181	329	40563										
GPR125	166647	hgsc.bcm.edu	37	chr4	22439915	22439915	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgtttaccaccctctctggaGgacagtactgtgcagaactc	9	12	1	1	rs147843055		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:22439915G>C	ENST00000334304.5	-	8	1318	c.1049C>G	c.(1048-1050)cCt>cGt	p.P350R	GPR125_ENST00000502482.1_Missense_Mutation_p.P350R|GPR125_ENST00000282943.5_5'UTR|GPR125_ENST00000508133.1_Missense_Mutation_p.P124R	NM_145290.3	NP_660333.2	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125	350					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(33)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	56		Breast(46;0.198)				CCTCTCTGGAGGACAGTACTG	0.448																																					p.P350R		Atlas-SNP	.											GPR125,colon,carcinoma,0,2	GPR125	118	.	0			c.C1049G						.						164	144	150					4																	22439915		2203	4300	6503	SO:0001583	missense	166647	exon8			TCTGGAGGACAGT	AK095866	CCDS33964.1	4p15.31	2014-08-08			ENSG00000152990	ENSG00000152990		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / I-set domain containing"	13839	protein-coding gene	gene with protein product		612303				12565841	Standard	NM_145290		Approved	FLJ38547, PGR21	uc003gqm.2	Q8IWK6	OTTHUMG00000160926	ENST00000334304.5:c.1049C>G	chr4.hg19:g.22439915G>C	ENSP00000334952:p.Pro350Arg	346.0	0.0		256.0	0.0	NM_145290	Q6UXK9|Q86SQ5|Q8TC55	Missense_Mutation	SNP	ENST00000334304.5	hg19	CCDS33964.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.150664	0.78001	.	.	ENSG00000152990	ENST00000334304;ENST00000508133;ENST00000502482;ENST00000514129	T;T;T	0.55413	0.52;0.52;0.52	5.6	5.6	0.85130	GPCR, family 2, extracellular hormone receptor domain (1);	0.054916	0.85682	D	0.000000	T	0.72415	0.3457	M	0.69823	2.125	0.54753	D	0.999983	D;D;D;P	0.65815	0.995;0.983;0.962;0.912	D;P;P;P	0.65443	0.935;0.905;0.605;0.611	T	0.74680	-0.3584	10	0.87932	D	0	-24.3783	19.618	0.95643	0.0:0.0:1.0:0.0	.	225;350;124;350	Q8IWK6-3;Q8IWK6-2;Q8IWK6-4;Q8IWK6	.;.;.;GP125_HUMAN	R	350;124;350;86	ENSP00000334952:P350R;ENSP00000422606:P124R;ENSP00000421006:P350R	ENSP00000334952:P350R	P	-	2	0	GPR125	22049013	1.000000	0.71417	0.991000	0.47740	0.989000	0.77384	4.196000	0.58407	2.635000	0.89317	0.650000	0.86243	CCT	.	.		0.448	GPR125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362960.3			C	22439915	G	C	22439915	3	2	282	1	0	0	0	0	1	0	0	0	6647	1000	35	4	2964	4	GPR125	4	22439915	Missense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	11992820	22439915	168714361	330	40564										
ANAPC4	29945	hgsc.bcm.edu	37	chr4	25390352	25390352	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cttctagctatagcaacaccTcaaaaatatttaggtaagat	5	8	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:25390352T>C	ENST00000315368.3	+	6	599	c.457T>C	c.(457-459)Tca>Cca	p.S153P	ANAPC4_ENST00000510092.1_Missense_Mutation_p.S153P	NM_013367.2	NP_037499.2	Q9UJX5	APC4_HUMAN	anaphase promoting complex subunit 4	153					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)	27		Breast(46;0.0503)				TAGCAACACCTCAAAAATATT	0.289																																					p.S153P		Atlas-SNP	.											.	ANAPC4	61	.	0			c.T457C						.						83	91	88					4																	25390352		2200	4290	6490	SO:0001583	missense	29945	exon6			AACACCTCAAAAA	AF191338	CCDS3434.1, CCDS68684.1	4p15.31	2011-06-15			ENSG00000053900	ENSG00000053900		"Anaphase promoting complex subunits"	19990	protein-coding gene	gene with protein product		606947				6180011	Standard	NM_013367		Approved	APC4	uc003gro.3	Q9UJX5	OTTHUMG00000097753	ENST00000315368.3:c.457T>C	chr4.hg19:g.25390352T>C	ENSP00000318775:p.Ser153Pro	128.0	0.0		100.0	5.0	NM_013367	A8K8H1|E9PCR4|Q6PCC6|Q9NSH6	Missense_Mutation	SNP	ENST00000315368.3	hg19	CCDS3434.1	.	.	.	.	.	.	.	.	.	.	T	15.58	2.875571	0.51695	.	.	ENSG00000053900	ENST00000315368;ENST00000510092;ENST00000505991	T;T	0.35605	1.3;1.3	5.8	4.68	0.58851	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.122787	0.56097	D	0.000037	T	0.33206	0.0855	L	0.38175	1.15	0.47621	D	0.999478	D	0.54397	0.966	P	0.47299	0.543	T	0.05037	-1.0910	10	0.42905	T	0.14	-15.9934	10.9841	0.47513	0.0:0.0:0.3892:0.6108	.	153	Q9UJX5	APC4_HUMAN	P	153	ENSP00000318775:S153P;ENSP00000426654:S153P	ENSP00000318775:S153P	S	+	1	0	ANAPC4	24999450	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.687000	0.61708	2.212000	0.71576	0.528000	0.53228	TCA	.	.		0.289	ANAPC4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214986.1	NM_013367		C	25390352	T	C	25390352	3	2	282	1	0	0	0	0	1	0	0	0	604	1551	54	2	475	2	ANAPC4	4	25390352	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2950437	25390352	165763924	331	40565										
STIM2	57620	hgsc.bcm.edu	37	chr4	26997053	26997053	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tggttgatagagtttgttgaActaccccaatatgagaagaa	10	5	0	5			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:26997053A>G	ENST00000467011.1	+	4	875	c.450A>G	c.(448-450)gaA>gaG	p.E150E	STIM2_ENST00000465503.1_Silent_p.E150E|STIM2_ENST00000237364.5_Silent_p.E237E|STIM2_ENST00000467087.1_Silent_p.E150E|STIM2_ENST00000412829.2_Silent_p.E237E|STIM2_ENST00000382009.3_Silent_p.E237E	NM_001169117.1	NP_001162588	Q9P246	STIM2_HUMAN	stromal interaction molecule 2	150	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				activation of store-operated calcium channel activity (GO:0032237)|calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|positive regulation of calcium ion transport (GO:0051928)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|store-operated calcium channel activity (GO:0015279)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	25		Breast(46;0.0503)				AGTTTGTTGAACTACCCCAAT	0.393																																					p.E150E		Atlas-SNP	.											.	STIM2	77	.	0			c.A450G						.						132	141	138					4																	26997053		2203	4300	6503	SO:0001819	synonymous_variant	57620	exon4			TGTTGAACTACCC	AB040915	CCDS3440.1, CCDS3440.2, CCDS54751.1, CCDS54752.1	4p15.2	2013-01-10			ENSG00000109689	ENSG00000109689		"Sterile alpha motif (SAM) domain containing"	19205	protein-coding gene	gene with protein product		610841				11463338	Standard	NM_020860		Approved		uc003gsh.4	Q9P246	OTTHUMG00000097805	ENST00000467011.1:c.450A>G	chr4.hg19:g.26997053A>G		145.0	0.0		95.0	4.0	NM_001169118	A6H8L7|B7ZVY0|Q96BF1|Q9BQH2|Q9H8R1	Silent	SNP	ENST00000467011.1	hg19	CCDS54752.1																																																																																			.	.		0.393	STIM2-003	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000356861.1	NM_020860		G	26997053	A	G	26997053	2	3	282	1	0	0	0	0	0	0	0	1	15299	40	2	2		2	STIM2	4	26997053	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1606701	26997053	164157223	332	40566										
ARAP2	116984	hgsc.bcm.edu	37	chr4	36148950	36148950	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	accaagagtaaaacatccagTttttccccattttgaaccat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:36148950delT	ENST00000303965.4	-	19	3720	c.3231delA	c.(3229-3231)aaafs	p.K1077fs		NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	1077	PH 4. {ECO:0000255|PROSITE- ProRule:PRU00145}.				regulation of ARF GTPase activity (GO:0032312)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(32)|ovary(2)|pancreas(1)|prostate(3)|skin(7)|urinary_tract(1)	82						AAACATCCAGTTTTTCCCCAT	0.348																																					p.L1078fs		Atlas-INDEL	.											.	ARAP2	210	.	0			c.3232delC						.						97	109	105					4																	36148950		2202	4298	6500	SO:0001589	frameshift_variant	116984	exon19			.	AF411982	CCDS3441.1	4p15.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000047365	ENSG00000047365		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16924	protein-coding gene	gene with protein product		606645	"centaurin, delta 1"	CENTD1			Standard	NM_015230		Approved	PARX	uc003gsq.2	Q8WZ64	OTTHUMG00000097811	ENST00000303965.4:c.3231delA	chr4.hg19:g.36148950delT	ENSP00000302895:p.Lys1077fs	252.0	0.0		225.0	16.0	NM_015230	Q4W5D2|Q7Z2L5|Q96L70|Q96P49|Q9Y4E4	Frame_Shift_Del	DEL	ENST00000303965.4	hg19	CCDS3441.1																																																																																			.	.		0.348	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215074.2	NM_015230		-	36148950	T	-	36148950	7	5	282	1	0	1	0	1	0	0	0	0	839	1722	60	0	1943	0	ARAP2	4	36148950	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	9151897	36148950	155005326	333	40567										
TLR10	81793	hgsc.bcm.edu	37	chr4	38776490	38776490	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atagaaccgatgtcttagcaTtttctaaactaagatttcgt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:38776490delT	ENST00000308973.4	-	4	1327	c.722delA	c.(721-723)aatfs	p.N241fs	TLR10_ENST00000506111.1_Frame_Shift_Del_p.N241fs|TLR10_ENST00000508334.1_Frame_Shift_Del_p.N241fs|TLR10_ENST00000361424.2_Frame_Shift_Del_p.N241fs|TLR10_ENST00000507953.1_5'Flank	NM_001017388.2|NM_001195107.1|NM_030956.3	NP_001017388.1|NP_001182036.1|NP_112218.2	Q9BXR5	TLR10_HUMAN	toll-like receptor 10	241			N -> H (in dbSNP:rs11096957). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of inflammatory response (GO:0050729)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(2)	25						TGTCTTAGCATTTTCTAAACT	0.323																																					p.N241fs		Atlas-INDEL	.											.	TLR10	87	.	0			c.723delT						.						61	60	60					4																	38776490		2203	4300	6503	SO:0001589	frameshift_variant	81793	exon4			.	AF296673	CCDS3445.1	4p14	2009-11-23			ENSG00000174123	ENSG00000174123		"CD molecules"	15634	protein-coding gene	gene with protein product		606270				11267672	Standard	NM_030956		Approved	CD290	uc003gtk.3	Q9BXR5	OTTHUMG00000128578	ENST00000308973.4:c.722delA	chr4.hg19:g.38776490delT	ENSP00000308925:p.Asn241fs	129.0	0.0		120.0	10.0	NM_030956	A8K7L1|B3Y668|D1CS21|D1CS22|Q32MI7|Q32MI8|Q5FWG4|Q6UXL3	Frame_Shift_Del	DEL	ENST00000308973.4	hg19	CCDS3445.1																																																																																			.	.		0.323	TLR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250430.1			-	38776490	T	-	38776490	7	5	282	1	0	1	0	1	0	0	0	0	15965	1493	52	0	1717	0	TLR10	4	38776490	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2627540	38776490	152377786	334	40568										
TLR1	7096	hgsc.bcm.edu	37	chr4	38799868	38799868	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aattctttgtttgtggggaaCacaatgtgcagactctcagt	10	7	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:38799868C>G	ENST00000502213.2	-	3	814	c.585G>C	c.(583-585)gtG>gtC	p.V195V	TLR1_ENST00000308979.2_Silent_p.V195V			Q15399	TLR1_HUMAN	toll-like receptor 1	195					cellular response to triacyl bacterial lipopeptide (GO:0071727)|detection of triacyl bacterial lipopeptide (GO:0042495)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|toll-like receptor 1 signaling pathway (GO:0034130)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)	protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(2)	28						TTGTGGGGAACACAATGTGCA	0.398																																					p.V195V	GBM(5;216 373 40795 46382)	Atlas-SNP	.											.	TLR1	70	.	0			c.G585C						.						63	63	63					4																	38799868		2203	4300	6503	SO:0001819	synonymous_variant	7096	exon4			GGGGAACACAATG	U88540	CCDS33973.1	4p14	2008-02-05				ENSG00000174125		"CD molecules"	11847	protein-coding gene	gene with protein product		601194				9435236, 7584026	Standard	NM_003263		Approved	rsc786, KIAA0012, CD281	uc003gtl.3	Q15399		ENST00000502213.2:c.585G>C	chr4.hg19:g.38799868C>G		190.0	0.0		146.0	63.0	NM_003263	D1CS39|D1CS41|O15452|Q32MK3|Q32MK4|Q9UG90	Silent	SNP	ENST00000502213.2	hg19	CCDS33973.1																																																																																			.	.		0.398	TLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360510.3			G	38799868	C	G	38799868	2	3	282	1	0	0	0	0	0	0	0	1	15964	465	17	4		4	TLR1	4	38799868	Silent	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	23378	38799868	152354408	335	40569										
TLR6	10333	hgsc.bcm.edu	37	chr4	38831040	38831040	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tctggttccaactattatgaTcataaggcaaacaaaatgga	7	7	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:38831040T>C	ENST00000381950.1	-	1	120	c.55A>G	c.(55-57)Atc>Gtc	p.I19V	TLR6_ENST00000436693.2_Missense_Mutation_p.I19V			Q9Y2C9	TLR6_HUMAN	toll-like receptor 6	19					activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to diacyl bacterial lipopeptide (GO:0071726)|defense response to bacterium (GO:0042742)|detection of diacyl bacterial lipopeptide (GO:0042496)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|nitric oxide metabolic process (GO:0046209)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of JUN kinase activity (GO:0043507)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 6 signaling pathway (GO:0034150)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Toll-like receptor 2-Toll-like receptor 6 protein complex (GO:0035355)	diacyl lipopeptide binding (GO:0042498)|lipopeptide binding (GO:0071723)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						ACTATTATGATCATAAGGCAA	0.393																																					p.I19V		Atlas-SNP	.											.	TLR6	67	.	0			c.A55G						.						105	110	109					4																	38831040		2203	4300	6503	SO:0001583	missense	10333	exon2			TTATGATCATAAG		CCDS3446.1	4p16.1	2009-11-23			ENSG00000174130	ENSG00000174130		"CD molecules"	16711	protein-coding gene	gene with protein product		605403				10231569	Standard	NM_006068		Approved	CD286	uc010ifg.2	Q9Y2C9	OTTHUMG00000128579	ENST00000381950.1:c.55A>G	chr4.hg19:g.38831040T>C	ENSP00000371376:p.Ile19Val	100.0	0.0		74.0	4.0	NM_006068	B3Y640|B6CH35|B6RFS4|B6RFS5|Q2NKL3	Missense_Mutation	SNP	ENST00000381950.1	hg19	CCDS3446.1	.	.	.	.	.	.	.	.	.	.	T	0.406	-0.916001	0.02415	.	.	ENSG00000174130	ENST00000436693;ENST00000381950;ENST00000508542;ENST00000508254;ENST00000514655	T;T;T;T	0.28895	3.19;3.19;1.59;2.04	5.55	-1.15	0.09709	.	0.860892	0.10174	N	0.706691	T	0.13586	0.0329	N	0.20685	0.6	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.35351	-0.9792	10	0.05351	T	0.99	.	5.8338	0.18594	0.1544:0.3217:0.0:0.5239	.	19	Q9Y2C9	TLR6_HUMAN	V	19	ENSP00000389600:I19V;ENSP00000371376:I19V;ENSP00000424718:I19V;ENSP00000423326:I19V	ENSP00000371376:I19V	I	-	1	0	TLR6	38507435	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-0.268000	0.08607	-0.130000	0.11599	0.459000	0.35465	ATC	.	.		0.393	TLR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250431.1			C	38831040	T	C	38831040	3	2	282	1	0	0	0	0	1	0	0	0	15970	1435	50	2	2339	2	TLR6	4	38831040	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	31172	38831040	152323236	336	40570										
WDR19	57728	hgsc.bcm.edu	37	chr4	39280220	39280220	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gattaaacgctgctcagctgAaaaagatttcagactgtacc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:39280220delA	ENST00000399820.3	+	36	4133	c.3979delA	c.(3979-3981)aaafs	p.K1328fs	WDR19_ENST00000288634.7_Frame_Shift_Del_p.K1168fs	NM_025132.3	NP_079408.3	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19	1328					ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium assembly (GO:0042384)|digestive system development (GO:0055123)|ear morphogenesis (GO:0042471)|embryonic camera-type eye development (GO:0031076)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|intraciliary retrograde transport (GO:0035721)|myotome development (GO:0061055)|neurological system process (GO:0050877)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|motile cilium (GO:0031514)|nonmotile primary cilium (GO:0031513)|photoreceptor connecting cilium (GO:0032391)				large_intestine(1)	1						TGCTCAGCTGAAAAAGATTTC	0.483																																					p.L1326fs		Atlas-INDEL	.											.	WDR19	96	.	0			c.3978delG						.						84	82	82					4																	39280220		2022	4178	6200	SO:0001589	frameshift_variant	57728	exon36			.	AB046858, AY029257	CCDS47042.1	4p14	2014-02-21			ENSG00000157796	ENSG00000157796		"WD repeat domain containing", "Intraflagellar transport homologs"	18340	protein-coding gene	gene with protein product	"intraflagellar transport 144 homolog (Chlamydomonas)"	608151				12906858, 22019273	Standard	XM_005262658		Approved	Pwdmp, KIAA1638, FLJ23127, ORF26, DYF-2, Oseg6, IFT144, NPHP13	uc003gtv.3	Q8NEZ3	OTTHUMG00000160466	ENST00000399820.3:c.3979delA	chr4.hg19:g.39280220delA	ENSP00000382717:p.Lys1328fs	235.0	0.0		183.0	11.0	NM_025132	B5MEF2|Q8N5B4|Q9H5S0|Q9HCD4	Frame_Shift_Del	DEL	ENST00000399820.3	hg19	CCDS47042.1																																																																																			.	.		0.483	WDR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360689.1			-	39280220	A	-	39280220	7	5	282	1	0	1	0	1	0	0	0	0	17294	247	9	0	4121	0	WDR19	4	39280220	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	449180	39280220	151874056	337	40571										
RFC1	5981	hgsc.bcm.edu	37	chr4	39322284	39322284	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttcatctgaaacttgtgctgTttttactaggaagaaagaaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:39322284delT	ENST00000381897.1	-	9	947	c.814delA	c.(814-816)acafs	p.T272fs	RFC1_ENST00000418436.1_5'UTR|RFC1_ENST00000349703.2_Frame_Shift_Del_p.T272fs	NM_001204747.1|NM_002913.4	NP_001191676.1|NP_002904.3	P35251	RFC1_HUMAN	replication factor C (activator 1) 1, 145kDa	272					DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription, DNA-templated (GO:0045893)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|telomere maintenance via telomerase (GO:0007004)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	cell junction (GO:0030054)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA clamp loader activity (GO:0003689)|double-stranded DNA binding (GO:0003690)|enzyme activator activity (GO:0008047)|sequence-specific DNA binding (GO:0043565)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16						ACTTGTGCTGTTTTTACTAGG	0.323																																					p.T272fs	Colon(109;59 1555 12203 17579 39824)|Esophageal Squamous(18;360 542 16186 28570 51157)	Atlas-INDEL	.											.	RFC1	114	.	0			c.815delC						.						82	78	80					4																	39322284		2203	4298	6501	SO:0001589	frameshift_variant	5981	exon9			.	L23320	CCDS3450.1, CCDS56329.1	4p14-p13	2010-04-21	2002-08-29		ENSG00000035928	ENSG00000035928		"ATPases / AAA-type"	9969	protein-coding gene	gene with protein product		102579	"replication factor C (activator 1) 1 (145kD)"			8114700	Standard	NM_002913		Approved	A1, PO-GA, RFC140, MHCBFB	uc003gty.2	P35251	OTTHUMG00000099363	ENST00000381897.1:c.814delA	chr4.hg19:g.39322284delT	ENSP00000371321:p.Thr272fs	191.0	0.0		150.0	10.0	NM_002913	A8K6E7|Q5XKF5|Q6PKU0|Q86V41|Q86V46	Frame_Shift_Del	DEL	ENST00000381897.1	hg19	CCDS56329.1																																																																																			.	.		0.323	RFC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216808.1	NM_002913		-	39322284	T	-	39322284	7	5	282	1	0	1	0	1	0	0	0	0	13259	1725	60	0	2697	0	RFC1	4	39322284	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	42064	39322284	151831992	338	40572										
FIP1L1	81608	hgsc.bcm.edu	37	chr4	54294251	54294251	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	attttagcaaaccacctccgTttttccctccaggagctcct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:54294251delT	ENST00000337488.6	+	13	1269	c.1075delT	c.(1075-1077)tttfs	p.F360fs	FIP1L1_ENST00000507166.1_Intron|FIP1L1_ENST00000507922.1_Frame_Shift_Del_p.F345fs|FIP1L1_ENST00000306932.6_Frame_Shift_Del_p.F286fs|FIP1L1_ENST00000358575.5_Frame_Shift_Del_p.F345fs	NM_030917.3	NP_112179.2	Q6UN15	FIP1_HUMAN	factor interacting with PAPOLA and CPSF1	360	Pro-rich.				mRNA processing (GO:0006397)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			large_intestine(3)|liver(1)|ovary(1)|skin(1)	6			GBM - Glioblastoma multiforme(3;3.31e-36)|LUSC - Lung squamous cell carcinoma(32;0.0134)			ACCACCTCCGTTTTTCCCTCC	0.463			T	PDGFRA	idiopathic hypereosinophilic syndrome																																p.P358fs		Atlas-INDEL	.		Dom	yes		4	4q12	81608	FIP1 like 1 (S. cerevisiae)		L	.	FIP1L1	60	.	0			c.1074delG						.						106	103	104					4																	54294251		2203	4300	6503	SO:0001589	frameshift_variant	81608	exon13			.	AF161429	CCDS3491.1, CCDS47055.1, CCDS47056.1	4q12	2013-06-18	2013-06-18		ENSG00000145216	ENSG00000145216			19124	protein-coding gene	gene with protein product		607686	"FIP1 like 1 (S. cerevisiae)", "FIP1L1 cleavage and polyadenylation specific factor subunit"			11230166, 14749727	Standard	NM_030917		Approved	DKFZp586K0717, FIP1	uc003hae.3	Q6UN15	OTTHUMG00000128701	ENST00000337488.6:c.1075delT	chr4.hg19:g.54294251delT	ENSP00000336752:p.Phe360fs	278.0	0.0		192.0	15.0	NM_030917	B4DIR3|G3XAD6|Q0VGE0|Q499Y4|Q49AU3|Q7Z608|Q8WVN3|Q96F80|Q9H077	Frame_Shift_Del	DEL	ENST00000337488.6	hg19	CCDS3491.1																																																																																			.	.		0.463	FIP1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250602.1	NM_030917		-	54294251	T	-	54294251	7	5	282	1	0	1	0	1	0	0	0	0	5904	1725	60	0	1125	0	FIP1L1	4	54294251	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	14971967	54294251	136860025	339	40573										
FIP1L1	81608	hgsc.bcm.edu	37	chr4	54319252	54319252	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agaaagagaacgcaccagagAgagagagagggagcgtgatc	16	6	0	6			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:54319252A>G	ENST00000337488.6	+	16	1645	c.1451A>G	c.(1450-1452)gAg>gGg	p.E484G	FIP1L1_ENST00000507166.1_Intron|FIP1L1_ENST00000306932.6_Missense_Mutation_p.E410G|FIP1L1_ENST00000358575.5_Missense_Mutation_p.E478G	NM_030917.3	NP_112179.2	Q6UN15	FIP1_HUMAN	factor interacting with PAPOLA and CPSF1	484	Arg-rich.|Glu-rich.|Sufficient for interaction with CPSF1 and CSTF3.				mRNA processing (GO:0006397)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			large_intestine(3)|liver(1)|ovary(1)|skin(1)	6			GBM - Glioblastoma multiforme(3;3.31e-36)|LUSC - Lung squamous cell carcinoma(32;0.0134)			CGCACCAGAGAGAGAGAGAGG	0.458			T	PDGFRA	idiopathic hypereosinophilic syndrome																																p.E484G		Atlas-SNP	.		Dom	yes		4	4q12	81608	FIP1 like 1 (S. cerevisiae)		L	.	FIP1L1	60	.	0			c.A1451G						.						74	65	68					4																	54319252		2203	4300	6503	SO:0001583	missense	81608	exon16			CCAGAGAGAGAGA	AF161429	CCDS3491.1, CCDS47055.1, CCDS47056.1	4q12	2013-06-18	2013-06-18		ENSG00000145216	ENSG00000145216			19124	protein-coding gene	gene with protein product		607686	"FIP1 like 1 (S. cerevisiae)", "FIP1L1 cleavage and polyadenylation specific factor subunit"			11230166, 14749727	Standard	NM_030917		Approved	DKFZp586K0717, FIP1	uc003hae.3	Q6UN15	OTTHUMG00000128701	ENST00000337488.6:c.1451A>G	chr4.hg19:g.54319252A>G	ENSP00000336752:p.Glu484Gly	171.0	0.0		82.0	4.0	NM_030917	B4DIR3|G3XAD6|Q0VGE0|Q499Y4|Q49AU3|Q7Z608|Q8WVN3|Q96F80|Q9H077	Missense_Mutation	SNP	ENST00000337488.6	hg19	CCDS3491.1	.	.	.	.	.	.	.	.	.	.	A	19.31	3.803115	0.70682	.	.	ENSG00000145216	ENST00000337488;ENST00000358575;ENST00000306932;ENST00000504094	T;T;T	0.07114	3.22;3.22;3.22	5.33	5.33	0.75918	.	0.085280	0.49916	D	0.000138	T	0.09024	0.0223	L	0.52573	1.65	0.80722	D	1	P;P;P;B	0.40731	0.59;0.608;0.728;0.231	B;B;B;B	0.36186	0.16;0.077;0.219;0.081	T	0.31194	-0.9952	10	0.14656	T	0.56	-17.5152	15.2591	0.73606	1.0:0.0:0.0:0.0	.	478;478;410;484	G3XAD6;B4DIR3;Q6UN15-3;Q6UN15	.;.;.;FIP1_HUMAN	G	484;478;410;141	ENSP00000336752:E484G;ENSP00000351383:E478G;ENSP00000302993:E410G	ENSP00000302993:E410G	E	+	2	0	FIP1L1	54014009	1.000000	0.71417	0.989000	0.46669	0.997000	0.91878	7.089000	0.76909	2.134000	0.65973	0.533000	0.62120	GAG	.	.		0.458	FIP1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250602.1	NM_030917		G	54319252	A	G	54319252	3	3	282	1	0	0	0	0	1	0	0	0	5904	304	11	2	1544	2	FIP1L1	4	54319252	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	25001	54319252	136835024	340	40574										
KIT	3815	hgsc.bcm.edu	37	chr4	55565881	55565881	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttcacagtgacgtgcacaatAaaagatgtgtctagttctgt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:55565881delA	ENST00000288135.5	+	4	802	c.705delA	c.(703-705)atafs	p.I235fs		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	235	Ig-like C2-type 3.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CGTGCACAATAAAAGATGTGT	0.428		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																												p.I235fs		Atlas-INDEL	.	yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	.	KIT	7396	.	0			c.704delT						.						185	171	176					4																	55565881		2203	4300	6503	SO:0001589	frameshift_variant	3815	exon4	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	.	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.705delA	chr4.hg19:g.55565881delA	ENSP00000288135:p.Ile235fs	227.0	0.0		151.0	10.0	NM_000222	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Frame_Shift_Del	DEL	ENST00000288135.5	hg19	CCDS3496.1																																																																																			.	.		0.428	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			-	55565881	A	-	55565881	7	5	282	1	0	1	0	1	0	0	0	0	8338	352	13	0	719	0	KIT	4	55565881	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1246629	55565881	135588395	341	40575										
KIT	3815	hgsc.bcm.edu	37	chr4	55594207	55594207	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tttgacagaacgggaagcccTcatgtctgaactcaaagtcc	9	11	3	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:55594207T>C	ENST00000288135.5	+	13	2007	c.1910T>C	c.(1909-1911)cTc>cCc	p.L637P		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	637	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CGGGAAGCCCTCATGTCTGAA	0.453		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																												p.L637P		Atlas-SNP	.	yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	KIT,NS,carcinoma,0,1	KIT	7396	.	0			c.T1910C						.						139	127	131					4																	55594207		2203	4300	6503	SO:0001583	missense	3815	exon13	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	AAGCCCTCATGTC	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.1910T>C	chr4.hg19:g.55594207T>C	ENSP00000288135:p.Leu637Pro	286.0	0.0		164.0	7.0	NM_000222	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	hg19	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.174152	0.78452	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	D;D	0.85339	-1.97;-1.97	6.06	6.06	0.98353	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.48767	D	0.000173	D	0.93400	0.7895	M	0.86502	2.82	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.94277	0.7516	10	0.87932	D	0	.	16.6093	0.84858	0.0:0.0:0.0:1.0	.	144;633;637	D5MAV8;P10721-2;P10721	.;.;KIT_HUMAN	P	637;633	ENSP00000288135:L637P;ENSP00000390987:L633P	ENSP00000288135:L637P	L	+	2	0	KIT	55288964	1.000000	0.71417	0.983000	0.44433	0.651000	0.38670	7.963000	0.87922	2.324000	0.78689	0.533000	0.62120	CTC	.	.		0.453	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			C	55594207	T	C	55594207	3	2	282	1	0	0	0	0	1	0	0	0	8338	1551	54	2	1960	2	KIT	4	55594207	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	28326	55594207	135560069	342	40576										
CEP135	9662	hgsc.bcm.edu	37	chr4	56841104	56841104	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tacaagttatagcgcacgtgAaaaaagttcaatatttagaa					rs34965077		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:56841104delA	ENST00000257287.4	+	11	1566	c.1442delA	c.(1441-1443)gaafs	p.E481fs		NM_025009.4	NP_079285.2	Q66GS9	CP135_HUMAN	centrosomal protein 135kDa	481					centriole replication (GO:0007099)|centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)	protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(26)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	50	Glioma(25;0.08)|all_neural(26;0.101)					AGCGCACGTGAAAAAAGTTCA	0.313																																					p.E481fs		Atlas-INDEL	.											CEP135,NS,carcinoma,0,1	CEP135	115	.	0			c.1441delG						.						62	63	62					4																	56841104		2203	4300	6503	SO:0001589	frameshift_variant	9662	exon11			.	AB014535	CCDS33986.1	4q12	2014-02-20	2005-12-02	2005-12-02	ENSG00000174799	ENSG00000174799			29086	protein-coding gene	gene with protein product		611423	"KIAA0635", "centrosomal protein 4"	KIAA0635, CEP4		9734811, 14654843	Standard	NM_025009		Approved	FLJ13621	uc003hbi.4	Q66GS9	OTTHUMG00000160748	ENST00000257287.4:c.1442delA	chr4.hg19:g.56841104delA	ENSP00000257287:p.Glu481fs	173.0	0.0		141.0	10.0	NM_025009	B2RMY0|O75130|Q58F25|Q9H8H7	Frame_Shift_Del	DEL	ENST00000257287.4	hg19	CCDS33986.1																																																																																			.	.		0.313	CEP135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362092.2	NM_025009		-	56841104	A	-	56841104	7	5	282	1	0	1	0	1	0	0	0	0	3249	246	9	0	1480	0	CEP135	4	56841104	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1246897	56841104	134313172	343	40577										
POLR2B	5431	hgsc.bcm.edu	37	chr4	57871855	57871855	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaacaagagattggatcttgCtgggccgctgcttgcattct	11	9	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:57871855C>T	ENST00000381227.1	+	10	1600	c.1187C>T	c.(1186-1188)gCt>gTt	p.A396V	POLR2B_ENST00000431623.2_Missense_Mutation_p.A321V|RNU6-998P_ENST00000515894.1_RNA|POLR2B_ENST00000314595.5_Missense_Mutation_p.A396V|POLR2B_ENST00000441246.2_Missense_Mutation_p.A389V			P30876	RPB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide B, 140kDa	396					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonucleoside binding (GO:0032549)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(10)|large_intestine(9)|lung(17)|ovary(2)|prostate(4)|skin(1)	52	Glioma(25;0.08)|all_neural(26;0.181)					TTGGATCTTGCTGGGCCGCTG	0.373																																					p.A396V		Atlas-SNP	.											.	POLR2B	108	.	0			c.C1187T						.						90	90	90					4																	57871855		2203	4300	6503	SO:0001583	missense	5431	exon9			ATCTTGCTGGGCC		CCDS3511.1	4q12	2013-01-21	2002-08-29		ENSG00000047315	ENSG00000047315		"RNA polymerase subunits"	9188	protein-coding gene	gene with protein product		180661	"polymerase (RNA) II (DNA directed) polypeptide B (140kD)"			1518060, 8034326	Standard	NM_000938		Approved	RPB2	uc003hcl.1	P30876	OTTHUMG00000128771	ENST00000381227.1:c.1187C>T	chr4.hg19:g.57871855C>T	ENSP00000370625:p.Ala396Val	83.0	0.0		103.0	5.0	NM_000938	A8K1A8|Q8IZ61	Missense_Mutation	SNP	ENST00000381227.1	hg19	CCDS3511.1	.	.	.	.	.	.	.	.	.	.	C	36	5.645050	0.96704	.	.	ENSG00000047315	ENST00000381227;ENST00000431623;ENST00000441246;ENST00000314595	T;T;T;T	0.76578	-1.03;-1.03;-1.03;-1.03	5.46	5.46	0.80206	RNA polymerase, beta subunit, protrusion (1);	0.000000	0.85682	D	0.000000	D	0.88735	0.6517	M	0.83603	2.65	0.80722	D	1	P;P	0.46621	0.881;0.881	P;P	0.61003	0.882;0.882	D	0.89240	0.3583	10	0.66056	D	0.02	.	19.6697	0.95907	0.0:1.0:0.0:0.0	.	321;396	C9J4M6;P30876	.;RPB2_HUMAN	V	396;321;389;396	ENSP00000370625:A396V;ENSP00000391096:A321V;ENSP00000391452:A389V;ENSP00000312735:A396V	ENSP00000312735:A396V	A	+	2	0	POLR2B	57566612	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	7.776000	0.85560	2.724000	0.93272	0.650000	0.86243	GCT	.	.		0.373	POLR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250692.1	NM_000938		T	57871855	C	T	57871855	3	4	282	1	0	0	0	0	1	0	0	0	12224	797	28	3	1221	3	POLR2B	4	57871855	Missense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1030751	57871855	133282421	344	40578										
POLR2B	5431	hgsc.bcm.edu	37	chr4	57883331	57883331	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agtagcttattgttccacatAtacacactgtgagattcatc	6	9	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:57883331A>G	ENST00000381227.1	+	16	2491	c.2078A>G	c.(2077-2079)tAt>tGt	p.Y693C	POLR2B_ENST00000431623.2_Missense_Mutation_p.Y618C|POLR2B_ENST00000314595.5_Missense_Mutation_p.Y693C|POLR2B_ENST00000441246.2_Missense_Mutation_p.Y686C			P30876	RPB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide B, 140kDa	693					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonucleoside binding (GO:0032549)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(10)|large_intestine(9)|lung(17)|ovary(2)|prostate(4)|skin(1)	52	Glioma(25;0.08)|all_neural(26;0.181)					TGTTCCACATATACACACTGT	0.408																																					p.Y693C		Atlas-SNP	.											.	POLR2B	108	.	0			c.A2078G						.						324	298	307					4																	57883331		2203	4300	6503	SO:0001583	missense	5431	exon15			CCACATATACACA		CCDS3511.1	4q12	2013-01-21	2002-08-29		ENSG00000047315	ENSG00000047315		"RNA polymerase subunits"	9188	protein-coding gene	gene with protein product		180661	"polymerase (RNA) II (DNA directed) polypeptide B (140kD)"			1518060, 8034326	Standard	NM_000938		Approved	RPB2	uc003hcl.1	P30876	OTTHUMG00000128771	ENST00000381227.1:c.2078A>G	chr4.hg19:g.57883331A>G	ENSP00000370625:p.Tyr693Cys	440.0	1.0		357.0	154.0	NM_000938	A8K1A8|Q8IZ61	Missense_Mutation	SNP	ENST00000381227.1	hg19	CCDS3511.1	.	.	.	.	.	.	.	.	.	.	A	19.18	3.776910	0.70107	.	.	ENSG00000047315	ENST00000381227;ENST00000431623;ENST00000441246;ENST00000314595	T;T;T;T	0.78126	-1.15;-1.15;-1.15;-1.15	4.91	4.91	0.64330	RNA polymerase Rpb2, domain 5 (1);	0.000000	0.85682	D	0.000000	D	0.90473	0.7016	H	0.94345	3.525	0.80722	D	1	D;D	0.69078	0.993;0.997	D;D	0.66351	0.943;0.943	D	0.93205	0.6595	10	0.87932	D	0	.	14.828	0.70128	1.0:0.0:0.0:0.0	.	618;693	C9J4M6;P30876	.;RPB2_HUMAN	C	693;618;686;693	ENSP00000370625:Y693C;ENSP00000391096:Y618C;ENSP00000391452:Y686C;ENSP00000312735:Y693C	ENSP00000312735:Y693C	Y	+	2	0	POLR2B	57578088	1.000000	0.71417	0.151000	0.22473	0.886000	0.51366	9.283000	0.95860	1.956000	0.56807	0.379000	0.24179	TAT	.	.		0.408	POLR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250692.1	NM_000938		G	57883331	A	G	57883331	3	3	282	1	0	0	0	0	1	0	0	0	12224	449	16	2	2136	2	POLR2B	4	57883331	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	11476	57883331	133270945	345	40579										
EPHA5	2044	hgsc.bcm.edu	37	chr4	66467573	66467573	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgtcgtaccacagaagggcaTtttttatagtatacacgcac							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:66467573delT	ENST00000273854.3	-	3	1296	c.696delA	c.(694-696)aaafs	p.K232fs	EPHA5_ENST00000432638.2_Frame_Shift_Del_p.K232fs|EPHA5_ENST00000511294.1_Frame_Shift_Del_p.K232fs|EPHA5_ENST00000354839.4_Frame_Shift_Del_p.K232fs	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	232	Cys-rich.|Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						CAGAAGGGCATTTTTTATAGT	0.448										TSP Lung(17;0.13)																											p.C233fs		Atlas-INDEL	.											.	EPHA5	315	.	0			c.697delT						.						68	66	67					4																	66467573		2203	4300	6503	SO:0001589	frameshift_variant	2044	exon3			.	L36644	CCDS3513.1, CCDS3514.1, CCDS75131.1, CCDS75132.1, CCDS75133.1	4q13.1	2013-02-11	2004-10-28		ENSG00000145242	ENSG00000145242		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3389	protein-coding gene	gene with protein product		600004	"EphA5"			9267020, 7528718	Standard	NM_004439		Approved	Hek7, TYRO4, CEK7, EHK1	uc003hcy.3	P54756	OTTHUMG00000129273	ENST00000273854.3:c.696delA	chr4.hg19:g.66467573delT	ENSP00000273854:p.Lys232fs	175.0	0.0		128.0	10.0	NM_182472	Q7Z3F2	Frame_Shift_Del	DEL	ENST00000273854.3	hg19	CCDS3513.1																																																																																			.	.		0.448	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439		-	66467573	T	-	66467573	7	5	282	1	0	1	0	1	0	0	0	0	5172	1490	52	0	2481	0	EPHA5	4	66467573	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	8584242	66467573	124686703	346	40580										
CENPC1	1060	hgsc.bcm.edu	37	chr4	68374713	68374713	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctgccttttaagtggaatagTttttttcctaatattcttag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:68374713delT	ENST00000273853.6	-	10	1973	c.1723delA	c.(1723-1725)actfs	p.T575fs		NM_001812.2	NP_001803.2	Q03188	CENPC_HUMAN	centromere protein C	575					chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	centromeric DNA binding (GO:0019237)|DNA binding (GO:0003677)										AGTGGAATAGTTTTTTTCCTA	0.343																																					p.T575fs		Atlas-INDEL	.											.	CENPC1	66	.	0			c.1724delC						.						145	132	136					4																	68374713		1822	4072	5894	SO:0001589	frameshift_variant	1060	exon10			.	M95724	CCDS47063.1	4q13.2	2013-11-05	2013-07-03	2013-07-03	ENSG00000145241	ENSG00000145241			1854	protein-coding gene	gene with protein product		117141	"centromere protein C 1"	CENPC1		7959789	Standard	XR_245245		Approved	CENP-C, hcp-4, MIF2	uc003hdd.1	Q03188	OTTHUMG00000160735	ENST00000273853.6:c.1723delA	chr4.hg19:g.68374713delT	ENSP00000273853:p.Thr575fs	208.0	0.0		205.0	13.0	NM_001812	Q8IW27|Q9P0M5	Frame_Shift_Del	DEL	ENST00000273853.6	hg19	CCDS47063.1																																																																																			.	.		0.343	CENPC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362001.2			-	68374713	T	-	68374713	7	5	282	1	0	1	0	1	0	0	0	0	3231	1725	60	0	1148	0	CENPC1	4	68374713	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1907140	68374713	122779563	347	40581										
YTHDC1	91746	hgsc.bcm.edu	37	chr4	69195927	69195927	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tttttattcttaccttgaaaTtttccactctctctgacaga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:69195927delT	ENST00000344157.4	-	8	1559	c.1224delA	c.(1222-1224)aaafs	p.K408fs	YTHDC1_ENST00000579690.1_Frame_Shift_Del_p.K408fs|YTHDC1_ENST00000355665.3_Frame_Shift_Del_p.K390fs	NM_001031732.2	NP_001026902.1	Q96MU7	YTDC1_HUMAN	YTH domain containing 1	408	YTH. {ECO:0000255|PROSITE- ProRule:PRU00225}.				mRNA splice site selection (GO:0006376)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	30						TACCTTGAAATTTTCCACTCT	0.294																																					p.F409fs		Atlas-INDEL	.											.	YTHDC1	81	.	0			c.1225delT						.						23	24	23					4																	69195927		2186	4275	6461	SO:0001589	frameshift_variant	91746	exon8			.	AK098515	CCDS3522.2, CCDS33992.1	4q13.3	2009-01-14			ENSG00000083896	ENSG00000083896			30626	protein-coding gene	gene with protein product						12368078, 10564280	Standard	XM_005265706		Approved	YT521, KIAA1966, YT521-B	uc003hdx.3	Q96MU7	OTTHUMG00000129306	ENST00000344157.4:c.1224delA	chr4.hg19:g.69195927delT	ENSP00000339245:p.Lys408fs	149.0	0.0		185.0	12.0	NM_001031732	Q4W5Q3|Q7Z622|Q8TF35	Frame_Shift_Del	DEL	ENST00000344157.4	hg19	CCDS33992.1																																																																																			.	.		0.294	YTHDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251437.1	NM_133370		-	69195927	T	-	69195927	7	5	282	1	0	1	0	1	0	0	0	0	17511	1490	52	0	999	0	YTHDC1	4	69195927	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	821214	69195927	121958349	348	40582										
UGT2B28	54490	hgsc.bcm.edu	37	chr4	70156317	70156317	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	catccaatcctaggtcttccAaaaaccagagcttttataac							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:70156317delA	ENST00000335568.5	+	5	1100	c.1098delA	c.(1096-1098)ccafs	p.P366fs	UGT2B28_ENST00000511240.1_Intron	NM_053039.1	NP_444267.1	Q9BY64	UDB28_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B28	366					metabolic process (GO:0008152)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	31						TAGGTCTTCCAAAAACCAGAG	0.383																																					p.P366fs		Atlas-INDEL	.											.	UGT2B28	101	.	0			c.1097delC						.						53	55	54					4																	70156317		1999	4190	6189	SO:0001589	frameshift_variant	54490	exon5			.	AF177272	CCDS3528.1, CCDS56330.1	4q13.3	2011-02-09	2005-07-20		ENSG00000135226	ENSG00000135226		"UDP glucuronosyltransferases"	13479	protein-coding gene	gene with protein product		606497	"UDP glycosyltransferase 2 family, polypeptide B28"			11300766	Standard	NM_053039		Approved		uc003hej.3	Q9BY64	OTTHUMG00000129401	ENST00000335568.5:c.1098delA	chr4.hg19:g.70156317delA	ENSP00000334276:p.Pro366fs	210.0	0.0		185.0	12.0	NM_053039	B5BUM0|Q9BY62|Q9BY63	Frame_Shift_Del	DEL	ENST00000335568.5	hg19	CCDS3528.1																																																																																			.	.		0.383	UGT2B28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251557.2	NM_053039		-	70156317	A	-	70156317	7	5	282	1	0	1	0	1	0	0	0	0	16975	117	5	0	1116	0	UGT2B28	4	70156317	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	960390	70156317	120997959	349	40583										
PROL1	58503	hgsc.bcm.edu	37	chr4	71275514	71275514	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atacaacaatcaccacaaatCcccccaccactgcaacagca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:71275514delC	ENST00000399575.2	+	3	643	c.469delC	c.(469-471)cccfs	p.P158fs	PROL1_ENST00000514338.1_3'UTR	NM_021225.4	NP_067048.4	Q99935	PROL1_HUMAN	proline rich, lacrimal 1	158	Thr-rich.				negative regulation of endopeptidase activity (GO:0010951)|regulation of sensory perception of pain (GO:0051930)|retina homeostasis (GO:0001895)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	endopeptidase inhibitor activity (GO:0004866)|peptidase inhibitor activity (GO:0030414)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|skin(3)	15		all_hematologic(202;0.196)				CACCACAAATCCCCCCACCAC	0.468																																					p.N156fs		Atlas-INDEL	.											.	PROL1	46	.	0			c.468delT						.						162	197	185					4																	71275514		2030	4195	6225	SO:0001589	frameshift_variant	58503	exon3			.	S83198	CCDS43235.1	4q13.3	2011-10-28	2005-02-07		ENSG00000171199	ENSG00000171199			17279	protein-coding gene	gene with protein product		608936	"proline rich 1"			8670737	Standard	NM_021225		Approved	BPLP, PRL1, opiorphin	uc003hfi.3	Q99935	OTTHUMG00000160845	ENST00000399575.2:c.469delC	chr4.hg19:g.71275514delC	ENSP00000382485:p.Pro158fs	456.0	0.0		291.0	24.0	NM_021225	A8MZ07|P85047	Frame_Shift_Del	DEL	ENST00000399575.2	hg19	CCDS43235.1																																																																																			.	.		0.468	PROL1-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000362639.1	NM_021225		-	71275514	C	-	71275514	7	5	282	1	0	1	0	1	0	0	0	0	12566	855	30	0	475	0	PROL1	4	71275514	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1119197	71275514	119878762	350	40584										
ENAM	10117	hgsc.bcm.edu	37	chr4	71501578	71501578	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccatttggaaatgggctattCccctatcaacaaccaccatg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:71501578delC	ENST00000396073.3	+	7	782	c.501delC	c.(499-501)ttcfs	p.F167fs		NM_031889.2	NP_114095.2	Q9NRM1	ENAM_HUMAN	enamelin	167					amelogenesis (GO:0097186)|biomineral tissue development (GO:0031214)	proteinaceous extracellular matrix (GO:0005578)				haematopoietic_and_lymphoid_tissue(1)|ovary(3)|upper_aerodigestive_tract(2)	6			Lung(101;0.235)			ATGGGCTATTCCCCTATCAAC	0.308																																					p.F167fs		Atlas-INDEL	.											.	ENAM	140	.	0			c.500delT						.						129	141	137					4																	71501578		2203	4296	6499	SO:0001589	frameshift_variant	10117	exon7			.	AF125373	CCDS3544.2	4q13.3	2008-02-05			ENSG00000132464	ENSG00000132464			3344	protein-coding gene	gene with protein product		606585	"amelogenesis imperfecta 2, hypocalcification (autosomal dominant)"	AIH2		11978766	Standard	NM_031889		Approved		uc011caw.1	Q9NRM1	OTTHUMG00000129914	ENST00000396073.3:c.501delC	chr4.hg19:g.71501578delC	ENSP00000379383:p.Phe167fs	210.0	0.0		142.0	11.0	NM_031889	Q17RI5|Q9H3D1	Frame_Shift_Del	DEL	ENST00000396073.3	hg19	CCDS3544.2																																																																																			.	.		0.308	ENAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252166.3	NM_031889		-	71501578	C	-	71501578	7	5	282	1	0	1	0	1	0	0	0	0	5114	854	30	0	523	0	ENAM	4	71501578	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	226064	71501578	119652698	351	40585										
SLC4A4	8671	hgsc.bcm.edu	37	chr4	72102334	72102334	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggacagaggggcttccttccTcaagcatgtgtgtgatgaag	14	8	1	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:72102334T>C	ENST00000264485.5	+	2	158	c.41T>C	c.(40-42)cTc>cCc	p.L14P	SLC4A4_ENST00000351898.6_Missense_Mutation_p.L14P|SLC4A4_ENST00000425175.1_Missense_Mutation_p.L14P	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4	14					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	58			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)		Sodium bicarbonate(DB01390)	GCTTCCTTCCTCAAGCATGTG	0.423																																					p.L14P		Atlas-SNP	.											.	SLC4A4	269	.	0			c.T41C						.						116	118	117					4																	72102334		1887	4108	5995	SO:0001583	missense	8671	exon2			CCTTCCTCAAGCA	AF007216	CCDS3549.1, CCDS43236.1, CCDS47071.1	4q13.3	2013-07-19	2013-07-19		ENSG00000080493	ENSG00000080493		"Solute carriers"	11030	protein-coding gene	gene with protein product		603345	"solute carrier family 4, sodium bicarbonate cotransporter, member 4"	SLC4A5		9235899, 9651366	Standard	NM_001098484		Approved	NBC1, HNBC1, NBC2, pNBC, hhNMC	uc010iic.3	Q9Y6R1	OTTHUMG00000129907	ENST00000264485.5:c.41T>C	chr4.hg19:g.72102334T>C	ENSP00000264485:p.Leu14Pro	127.0	0.0		91.0	4.0	NM_001098484	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Missense_Mutation	SNP	ENST00000264485.5	hg19	CCDS43236.1	.	.	.	.	.	.	.	.	.	.	T	17.42	3.384766	0.61956	.	.	ENSG00000080493	ENST00000264485;ENST00000425175;ENST00000351898	T;T;T	0.78924	-1.22;-1.22;-0.85	5.82	5.82	0.92795	.	0.262393	0.39341	N	0.001382	D	0.85301	0.5665	M	0.74881	2.28	0.80722	D	1	P;D;P	0.59767	0.835;0.986;0.898	B;P;P	0.57152	0.445;0.814;0.451	D	0.86055	0.1528	10	0.49607	T	0.09	.	16.1832	0.81925	0.0:0.0:0.0:1.0	.	14;14;14	A5JJ20;Q9Y6R1-4;Q9Y6R1	.;.;S4A4_HUMAN	P	14	ENSP00000264485:L14P;ENSP00000393557:L14P;ENSP00000307349:L14P	ENSP00000264485:L14P	L	+	2	0	SLC4A4	72321198	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.002000	0.70693	2.228000	0.72767	0.533000	0.62120	CTC	.	.		0.423	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759		C	72102334	T	C	72102334	3	2	282	1	0	0	0	0	1	0	0	0	14671	1551	54	2	43	2	SLC4A4	4	72102334	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	600756	72102334	119051942	352	40586										
ADAMTS3	9508	hgsc.bcm.edu	37	chr4	73205236	73205236	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcattagggtcaggaggtagTtttggacgtgctctttgcca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:73205236delT	ENST00000286657.4	-	5	872	c.836delA	c.(835-837)aacfs	p.N279fs		NM_014243.2	NP_055058.2	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 3	279	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|protein processing (GO:0016485)|vascular endothelial growth factor production (GO:0010573)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(33)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	76			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CAGGAGGTAGTTTTGGACGTG	0.443																																					p.N279fs	NSCLC(168;1941 2048 2918 13048 43078)	Atlas-INDEL	.											.	ADAMTS3	164	.	0			c.837delC						.						310	318	315					4																	73205236		2203	4300	6503	SO:0001589	frameshift_variant	9508	exon5			.	AB002364	CCDS3553.1	4q21	2008-07-29	2005-08-19		ENSG00000156140	ENSG00000156140	3.4.24.-	"ADAM metallopeptidases with thrombospondin type 1 motif"	219	protein-coding gene	gene with protein product		605011	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3"			10094461	Standard	NM_014243		Approved	KIAA0366, ADAMTS-4	uc003hgk.2	O15072	OTTHUMG00000129912	ENST00000286657.4:c.836delA	chr4.hg19:g.73205236delT	ENSP00000286657:p.Asn279fs	236.0	0.0		181.0	11.0	NM_014243	A1L3U9|Q9BXZ8	Frame_Shift_Del	DEL	ENST00000286657.4	hg19	CCDS3553.1																																																																																			.	.		0.443	ADAMTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252164.2			-	73205236	T	-	73205236	7	5	282	1	0	1	0	1	0	0	0	0	267	1725	60	0	2853	0	ADAMTS3	4	73205236	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1102902	73205236	117949040	353	40587										
ADAMTS3	9508	hgsc.bcm.edu	37	chr4	73414286	73414286	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tagtctgcaaaggctctgttCtccggattctatacgtagca					rs788908	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:73414286delC	ENST00000286657.4	-	3	449	c.413delG	c.(412-414)agafs	p.R138fs	ADAMTS3_ENST00000505193.1_5'UTR	NM_014243.2	NP_055058.2	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 3	138			R -> K (in dbSNP:rs788908). {ECO:0000269|PubMed:11408482, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9205841}.		collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|protein processing (GO:0016485)|vascular endothelial growth factor production (GO:0010573)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(33)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	76			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			AGGCTCTGTTCTCCGGATTCT	0.493																																					p.R138fs	NSCLC(168;1941 2048 2918 13048 43078)	Atlas-INDEL	.											.	ADAMTS3	164	.	0			c.414delA						.						227	223	224					4																	73414286		2203	4300	6503	SO:0001589	frameshift_variant	9508	exon3			.	AB002364	CCDS3553.1	4q21	2008-07-29	2005-08-19		ENSG00000156140	ENSG00000156140	3.4.24.-	"ADAM metallopeptidases with thrombospondin type 1 motif"	219	protein-coding gene	gene with protein product		605011	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3"			10094461	Standard	NM_014243		Approved	KIAA0366, ADAMTS-4	uc003hgk.2	O15072	OTTHUMG00000129912	ENST00000286657.4:c.413delG	chr4.hg19:g.73414286delC	ENSP00000286657:p.Arg138fs	257.0	0.0		173.0	11.0	NM_014243	A1L3U9|Q9BXZ8	Frame_Shift_Del	DEL	ENST00000286657.4	hg19	CCDS3553.1																																																																																			.	.		0.493	ADAMTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252164.2			-	73414286	C	-	73414286	7	5	282	1	0	1	0	1	0	0	0	0	267	913	32	0	3284	0	ADAMTS3	4	73414286	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	209050	73414286	117739990	354	40588										
ALB	213	hgsc.bcm.edu	37	chr4	74282071	74282071	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gagtacaaattccagaatgcGtaagtaatttttattgactg	8	5	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:74282071G>A	ENST00000503124.1	+	8	1046		c.e8+1		ALB_ENST00000295897.4_Splice_Site|ALB_ENST00000401494.3_Splice_Site|ALB_ENST00000509063.1_Splice_Site|ALB_ENST00000415165.2_Splice_Site|ALB_ENST00000505649.1_Splice_Site			Q8TES7	FBF1_HUMAN	albumin						apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TCCAGAATGCGTAAGTAATTT	0.294																																					.		Atlas-SNP	.											ALB,NS,carcinoma,+1,1	ALB	132	.	0			c.1289+1G>A						.						37	37	37					4																	74282071		2202	4298	6500	SO:0001630	splice_region_variant	213	exon10			GAATGCGTAAGTA	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.839+1G>A	chr4.hg19:g.74282071G>A		118.0	0.0		111.0	41.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Splice_Site	SNP	ENST00000503124.1	hg19		.	.	.	.	.	.	.	.	.	.	G	11.43	1.637194	0.29157	.	.	ENSG00000163631	ENST00000295897;ENST00000415165;ENST00000329326;ENST00000503124;ENST00000509063;ENST00000401494;ENST00000430202;ENST00000511370	.	.	.	5.74	4.89	0.63831	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8057	0.69952	0.0:0.0:0.8546:0.1454	.	.	.	.	.	-1	.	.	.	+	.	.	ALB	74500935	1.000000	0.71417	0.547000	0.28179	0.272000	0.26649	3.923000	0.56469	1.414000	0.47017	0.591000	0.81541	.	.	.		0.294	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477	Intron	A	74282071	G	A	74282071	5	1	282	1	0	0	0	0	0	0	1	0	486	1159	40	1	1328	1	ALB	4	74282071	Splice_Site	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	867785	74282071	116872205	355	40589										
G3BP2	9908	hgsc.bcm.edu	37	chr4	76572284	76572284	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caacaaaaagttgatgactaTctggatagcgaattattcta	7	6	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:76572284T>C	ENST00000359707.4	-	10	1771	c.986A>G	c.(985-987)gAt>gGt	p.D329G	G3BP2_ENST00000395719.3_Missense_Mutation_p.D329G|G3BP2_ENST00000357854.3_Missense_Mutation_p.D296G	NM_203505.2	NP_987101.1	Q9UN86	G3BP2_HUMAN	GTPase activating protein (SH3 domain) binding protein 2	329					cytoplasmic sequestering of NF-kappaB (GO:0007253)|mRNA transport (GO:0051028)|Ras protein signal transduction (GO:0007265)	cytoplasm (GO:0005737)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|receptor signaling complex scaffold activity (GO:0030159)			breast(3)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	27			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			TTGATGACTATCTGGATAGCG	0.343																																					p.D329G		Atlas-SNP	.											.	G3BP2	52	.	0			c.A986G						.						101	100	101					4																	76572284		2203	4299	6502	SO:0001583	missense	9908	exon10			TGACTATCTGGAT	AB014560	CCDS3571.1, CCDS3572.1	4q21.1	2013-02-12	2006-11-01		ENSG00000138757	ENSG00000138757		"RNA binding motif (RRM) containing"	30291	protein-coding gene	gene with protein product	"Ras-GTPase activating protein SH3 domain-binding protein 2"					9734811, 9575347	Standard	NM_203504		Approved	KIAA0660	uc003his.3	Q9UN86	OTTHUMG00000130097	ENST00000359707.4:c.986A>G	chr4.hg19:g.76572284T>C	ENSP00000352738:p.Asp329Gly	137.0	0.0		118.0	5.0	NM_012297	A8K6X1|O60606|O75149|Q9UPA1	Missense_Mutation	SNP	ENST00000359707.4	hg19	CCDS3571.1	.	.	.	.	.	.	.	.	.	.	T	28.8	4.953458	0.92660	.	.	ENSG00000138757	ENST00000395719;ENST00000359707;ENST00000357854	T;T;T	0.74632	-0.86;-0.86;-0.86	6.04	6.04	0.98038	Nucleotide-binding, alpha-beta plait (1);	0.000000	0.85682	D	0.000000	D	0.85660	0.5748	M	0.71206	2.165	0.80722	D	1	D;D	0.67145	0.996;0.991	D;D	0.77557	0.99;0.979	D	0.86994	0.2112	10	0.87932	D	0	.	16.5763	0.84648	0.0:0.0:0.0:1.0	.	296;329	Q9UN86-2;Q9UN86	.;G3BP2_HUMAN	G	329;329;296	ENSP00000379069:D329G;ENSP00000352738:D329G;ENSP00000350518:D296G	ENSP00000350518:D296G	D	-	2	0	G3BP2	76791308	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.698000	0.84413	2.317000	0.78254	0.459000	0.35465	GAT	.	.		0.343	G3BP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252399.2	NM_012297		C	76572284	T	C	76572284	3	2	282	1	0	0	0	0	1	0	0	0	6150	1435	50	2	474	2	G3BP2	4	76572284	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2290213	76572284	114581992	356	40590										
CNOT6L	246175	hgsc.bcm.edu	37	chr4	78652675	78652675	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggttaaattccactgtatgcTtctgcaccaatgtaaatcta	6	9	2	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:78652675T>C	ENST00000504123.1	-	9	1020	c.890A>G	c.(889-891)aAg>aGg	p.K297R	CNOT6L_ENST00000264903.4_Missense_Mutation_p.K297R			Q96LI5	CNO6L_HUMAN	CCR4-NOT transcription complex, subunit 6-like	297	Nuclease domain.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA destabilization (GO:0061157)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A)-specific ribonuclease activity (GO:0004535)			kidney(1)|large_intestine(1)|lung(6)|urinary_tract(1)	9						CACTGTATGCTTCTGCACCAA	0.363																																					p.K297R		Atlas-SNP	.											.	CNOT6L	57	.	0			c.A890G						.						84	82	82					4																	78652675		2105	4268	6373	SO:0001583	missense	246175	exon9			GTATGCTTCTGCA	AL133112	CCDS68731.1	4q13.3	2014-06-17				ENSG00000138767			18042	protein-coding gene	gene with protein product							Standard	NM_144571		Approved	DKFZp434K098, Ccr4b	uc003hks.3	Q96LI5		ENST00000504123.1:c.890A>G	chr4.hg19:g.78652675T>C	ENSP00000424896:p.Lys297Arg	144.0	0.0		96.0	4.0	NM_144571	Q9UF92	Missense_Mutation	SNP	ENST00000504123.1	hg19		.	.	.	.	.	.	.	.	.	.	T	19.25	3.790975	0.70452	.	.	ENSG00000138767	ENST00000504123;ENST00000264903;ENST00000512485;ENST00000505983	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.86	5.86	0.93980	Endonuclease/exonuclease/phosphatase (2);	0.000000	0.85682	D	0.000000	T	0.75510	0.3859	L	0.42529	1.33	0.80722	D	1	P;B	0.40834	0.73;0.242	B;B	0.42555	0.391;0.16	T	0.77778	-0.2460	10	0.59425	D	0.04	-4.0875	16.2526	0.82494	0.0:0.0:0.0:1.0	.	270;297	Q96LI5-2;Q96LI5	.;CNO6L_HUMAN	R	297;297;304;72	ENSP00000424896:K297R;ENSP00000264903:K297R;ENSP00000425571:K304R;ENSP00000426320:K72R	ENSP00000264903:K297R	K	-	2	0	CNOT6L	78871699	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.040000	0.89188	2.241000	0.73720	0.482000	0.46254	AAG	.	.		0.363	CNOT6L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000362515.1			C	78652675	T	C	78652675	3	2	282	1	0	0	0	0	1	0	0	0	3625	1609	56	2	793	2	CNOT6L	4	78652675	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2080391	78652675	112501601	357	40591										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79458204	79458204	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaacaaaatcttaattctgcTtacaaactccagctggagaa	6	9	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:79458204T>C	ENST00000264895.6	+	72	11588	c.11148T>C	c.(11146-11148)gcT>gcC	p.A3716A		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3712					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						TTAATTCTGCTTACAAACTCC	0.408																																					p.A3716A		Atlas-SNP	.											.	FRAS1	779	.	0			c.T11148C						.						134	133	133					4																	79458204		1825	4088	5913	SO:0001819	synonymous_variant	80144	exon72			TTCTGCTTACAAA	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.11148T>C	chr4.hg19:g.79458204T>C		149.0	0.0		96.0	4.0	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000264895.6	hg19	CCDS54771.1																																																																																			.	.		0.408	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	79458204	T	C	79458204	2	2	282	1	0	0	0	0	0	0	0	1	6050	1596	56	2		2	FRAS1	4	79458204	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	805529	79458204	111696072	358	40592										
BMP2K	55589	hgsc.bcm.edu	37	chr4	79768365	79768365	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tacaactctgtcatacagagCccctgaaatgatcaaccttt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:79768365delC	ENST00000335016.5	+	6	858	c.692delC	c.(691-693)gccfs	p.A231fs	BMP2K_ENST00000502871.1_Frame_Shift_Del_p.A231fs	NM_198892.1	NP_942595.1	Q9NSY1	BMP2K_HUMAN	BMP2 inducible kinase	231	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				regulation of bone mineralization (GO:0030500)	nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatase regulator activity (GO:0019208)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	13						TCATACAGAGCCCCTGAAATG	0.378																																					p.A231fs		Atlas-INDEL	.											.	BMP2K	169	.	0			c.691delG						.						51	51	51					4																	79768365		2202	4300	6502	SO:0001589	frameshift_variant	55589	exon6			.	AB015331	CCDS34019.1, CCDS47083.1	4q21.21	2008-05-15			ENSG00000138756	ENSG00000138756			18041	protein-coding gene	gene with protein product							Standard	NM_017593		Approved	DKFZp434K0614, BIKe	uc003hlk.3	Q9NSY1	OTTHUMG00000160900	ENST00000335016.5:c.692delC	chr4.hg19:g.79768365delC	ENSP00000334836:p.Ala231fs	245.0	0.0		159.0	14.0	NM_017593	O94791|Q4W5H2|Q8IYF2|Q8N2G7|Q8NHG9|Q9NTG8	Frame_Shift_Del	DEL	ENST00000335016.5	hg19	CCDS47083.1																																																																																			.	.		0.378	BMP2K-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_017593		-	79768365	C	-	79768365	7	5	282	1	0	1	0	1	0	0	0	0	1460	739	26	0	714	0	BMP2K	4	79768365	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	310161	79768365	111385911	359	40593										
PRKG2	5593	hgsc.bcm.edu	37	chr4	82027025	82027025	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tatcttcctgggaaaatccaTtttttcaattcctttgagaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:82027025delT	ENST00000395578.1	-	16	2121	c.2005delA	c.(2005-2007)atgfs	p.M669fs	PRKG2_ENST00000264399.1_Frame_Shift_Del_p.M669fs|PRKG2_ENST00000418486.2_Frame_Shift_Del_p.M640fs|PRKG2_ENST00000509169.1_5'UTR|PRKG2_ENST00000545647.1_Frame_Shift_Del_p.M249fs			Q13237	KGP2_HUMAN	protein kinase, cGMP-dependent, type II	669	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood coagulation (GO:0007596)|circadian regulation of gene expression (GO:0032922)|nitric oxide metabolic process (GO:0046209)|protein phosphorylation (GO:0006468)|regulation of nitric-oxide synthase activity (GO:0050999)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)|protein kinase activity (GO:0004672)			NS(1)|breast(4)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	37						GGAAAATCCATTTTTTCAATT	0.413																																					p.M669fs		Atlas-INDEL	.											.	PRKG2	195	.	0			c.2006delT						.						129	123	125					4																	82027025		2203	4300	6503	SO:0001589	frameshift_variant	5593	exon15			.	X94612	CCDS3589.1, CCDS75150.1	4q13.1-q21.1	2009-07-10			ENSG00000138669	ENSG00000138669	2.7.11.1		9416	protein-coding gene	gene with protein product		601591				7498513	Standard	XM_005263126		Approved	cGKII, PRKGR2	uc003hmh.2	Q13237	OTTHUMG00000130296	ENST00000395578.1:c.2005delA	chr4.hg19:g.82027025delT	ENSP00000378945:p.Met669fs	227.0	0.0		164.0	10.0	NM_006259	B4DMX3|E7EPE6|O00125|O60916	Frame_Shift_Del	DEL	ENST00000395578.1	hg19	CCDS3589.1																																																																																			.	.		0.413	PRKG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252639.1	NM_006259		-	82027025	T	-	82027025	7	5	282	1	0	1	0	1	0	0	0	0	12535	1493	52	0	299	0	PRKG2	4	82027025	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2258660	82027025	109127251	360	40594										
HELQ	113510	hgsc.bcm.edu	37	chr4	84358058	84358058	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gctagggtagatgtgcaggtAaaaagacagagcactcctgt					rs375051270		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:84358058delA	ENST00000295488.3	-	9	2163	c.2001delT	c.(1999-2001)tttfs	p.F667fs	HELQ_ENST00000510985.1_Frame_Shift_Del_p.F600fs	NM_133636.2	NP_598375	Q8TDG4	HELQ_HUMAN	helicase, POLQ-like	667	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				double-strand break repair via homologous recombination (GO:0000724)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(17)|ovary(2)|skin(2)	38						ATGTGCAGGTAAAAAGACAGA	0.478								Other identified genes with known or suspected DNA repair function																													p.T668fs		Atlas-INDEL	.											.	HELQ	95	.	0			c.2002delA						.						99	93	95					4																	84358058		2203	4300	6503	SO:0001589	frameshift_variant	113510	exon9			.	AF436845	CCDS3603.1, CCDS75158.1	4q21.23	2009-02-26			ENSG00000163312	ENSG00000163312			18536	protein-coding gene	gene with protein product		606769				11751861	Standard	XM_005262711		Approved	Hel308	uc003hom.3	Q8TDG4	OTTHUMG00000130423	ENST00000295488.3:c.2001delT	chr4.hg19:g.84358058delA	ENSP00000295488:p.Phe667fs	234.0	0.0		163.0	10.0	NM_133636	Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7	Frame_Shift_Del	DEL	ENST00000295488.3	hg19	CCDS3603.1																																																																																			.	.		0.478	HELQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252810.1	NM_133636		-	84358058	A	-	84358058	7	5	282	1	0	1	0	1	0	0	0	0	7056	359	13	0	1344	0	HELQ	4	84358058	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2331033	84358058	106796218	361	40595										
MAPK10	5602	hgsc.bcm.edu	37	chr4	86985490	86985490	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggcgtcgtccactgatattcTttttgctgggtcaatcacta							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:86985490delT	ENST00000359221.3	-	11	1565	c.1039delA	c.(1039-1041)agafs	p.R347fs	MAPK10_ENST00000449047.2_Frame_Shift_Del_p.R202fs|MAPK10_ENST00000361569.2_Frame_Shift_Del_p.R347fs|MAPK10_ENST00000395161.2_Frame_Shift_Del_p.R347fs|MAPK10_ENST00000395160.3_Frame_Shift_Del_p.R202fs|MAPK10_ENST00000395169.3_Frame_Shift_Del_p.R309fs|MAPK10_ENST00000395157.3_Frame_Shift_Del_p.R202fs|MAPK10_ENST00000395166.1_Frame_Shift_Del_p.R309fs			P53779	MK10_HUMAN	mitogen-activated protein kinase 10	347	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|JUN phosphorylation (GO:0007258)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|JUN kinase activity (GO:0004705)|MAP kinase kinase activity (GO:0004708)			breast(1)|central_nervous_system(1)|stomach(1)	3		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.243)		OV - Ovarian serous cystadenocarcinoma(123;0.002)		ACTGATATTCTTTTTGCTGGG	0.433																																					p.R347fs		Atlas-INDEL	.											.	MAPK10	106	.	0			c.1040delG						.						175	160	165					4																	86985490		2203	4300	6503	SO:0001589	frameshift_variant	5602	exon11			.	U07620	CCDS3612.1, CCDS3613.1, CCDS34026.1, CCDS43247.1	4q22-q23	2011-06-09			ENSG00000109339	ENSG00000109339	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinases"	6872	protein-coding gene	gene with protein product		602897		PRKM10		8654373, 12436199	Standard	NM_002753		Approved	JNK3, p493F12, p54bSAPK	uc003hpt.3	P53779	OTTHUMG00000130604	ENST00000359221.3:c.1039delA	chr4.hg19:g.86985490delT	ENSP00000352157:p.Arg347fs	225.0	0.0		176.0	11.0	NM_138982	A6NFS3|A6NG28|B3KQ94|Q15707|Q49AP1	Frame_Shift_Del	DEL	ENST00000359221.3	hg19	CCDS34026.1																																																																																			.	.		0.433	MAPK10-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000361363.2			-	86985490	T	-	86985490	7	5	282	1	0	1	0	1	0	0	0	0	9281	1617	56	0	376	0	MAPK10	4	86985490	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2627432	86985490	104168786	362	40596										
PTPN13	5783	hgsc.bcm.edu	37	chr4	87735675	87735675	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtcttcaagcagaagaagagCaaaaacagcagcctcagctt	9	10	3	3	rs373179030		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:87735675C>A	ENST00000411767.2	+	48	7492	c.7429C>A	c.(7429-7431)Caa>Aaa	p.Q2477K	PTPN13_ENST00000316707.6_Missense_Mutation_p.Q2286K|PTPN13_ENST00000427191.2_Missense_Mutation_p.Q2458K|PTPN13_ENST00000436978.1_Missense_Mutation_p.Q2482K|PTPN13_ENST00000511467.1_Missense_Mutation_p.Q2482K			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	2477					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		AGAAGAAGAGCAAAAACAGCA	0.413																																					p.Q2482K		Atlas-SNP	.											.	PTPN13	203	.	0			c.C7444A						.						90	84	86					4																	87735675		1880	4115	5995	SO:0001583	missense	5783	exon48			GAAGAGCAAAAAC		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.7429C>A	chr4.hg19:g.87735675C>A	ENSP00000407249:p.Gln2477Lys	565.0	0.0		397.0	185.0	NM_080685	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	hg19	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	C	14.56	2.572041	0.45798	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T;T	0.52295	0.67;0.7;0.78;0.67;0.7	5.64	4.79	0.61399	.	0.353216	0.21743	N	0.069799	T	0.26666	0.0652	N	0.04508	-0.205	0.24922	N	0.991978	B;B;B;B	0.12630	0.006;0.006;0.004;0.006	B;B;B;B	0.10450	0.005;0.005;0.002;0.005	T	0.18116	-1.0347	10	0.46703	T	0.11	.	11.7022	0.51577	0.1389:0.7275:0.1336:0.0	.	2286;2458;2477;2482	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	K	2458;2482;2286;2477;2482;2426	ENSP00000408368:Q2458K;ENSP00000394794:Q2482K;ENSP00000322675:Q2286K;ENSP00000407249:Q2477K;ENSP00000426626:Q2482K	ENSP00000322675:Q2286K	Q	+	1	0	PTPN13	87954699	0.945000	0.32115	0.339000	0.25562	0.917000	0.54804	2.537000	0.45702	1.510000	0.48803	0.563000	0.77884	CAA	.	.		0.413	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			A	87735675	C	A	87735675	3	1	282	1	0	0	0	0	1	0	0	0	12795	711	25	3	7630	3	PTPN13	4	87735675	Missense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	750185	87735675	103418601	363	40597										
AFF1	4299	hgsc.bcm.edu	37	chr4	88053466	88053466	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acatggcgatgtttcgttgtAaaaaagacatagcaataaag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:88053466delA	ENST00000307808.6	+	18	3616	c.3196delA	c.(3196-3198)aaafs	p.K1067fs	AFF1_ENST00000395146.4_Frame_Shift_Del_p.K1074fs|AFF1_ENST00000544085.1_Frame_Shift_Del_p.K705fs	NM_005935.2	NP_005926.1	P51825	AFF1_HUMAN	AF4/FMR2 family, member 1	1067					positive regulation of transcription, DNA-templated (GO:0045893)	transcription elongation factor complex (GO:0008023)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|large_intestine(2)	3		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)		GTTTCGTTGTAAAAAAGACAT	0.413																																					p.C1072X		Atlas-INDEL	.											.	AFF1	102	.	0			c.3216delT						.						115	107	110					4																	88053466		2203	4300	6503	SO:0001589	frameshift_variant	4299	exon19			.	L22179	CCDS3616.1, CCDS54775.1	4q21.3	2009-08-04	2005-06-27	2005-06-27	ENSG00000172493	ENSG00000172493			7135	protein-coding gene	gene with protein product		159557	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 2", "pre-B-cell monocytic leukemia partner 1"	PBM1, MLLT2		7689231, 1423625, 8353274	Standard	NM_005935		Approved	AF-4, AF4	uc011ccz.2	P51825	OTTHUMG00000130603	ENST00000307808.6:c.3196delA	chr4.hg19:g.88053466delA	ENSP00000305689:p.Lys1067fs	330.0	0.0		220.0	14.0	NM_001166693	B4DTU1|E9PBM3	Frame_Shift_Del	DEL	ENST00000307808.6	hg19	CCDS3616.1																																																																																			.	.		0.413	AFF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253053.3	NM_005935		-	88053466	A	-	88053466	7	5	282	1	0	1	0	1	0	0	0	0	356	363	13	0	3308	0	AFF1	4	88053466	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	317791	88053466	103100810	364	40598										
HERC3	8916	hgsc.bcm.edu	37	chr4	89601295	89601295	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccggtggtgttacaaaggaaTtttttcttttgctgttaaaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:89601295delT	ENST00000402738.1	+	20	2487	c.2248delT	c.(2248-2250)tttfs	p.F751fs	HERC3_ENST00000264345.3_Frame_Shift_Del_p.F751fs|HERC3_ENST00000543130.1_Frame_Shift_Del_p.F195fs	NM_001271602.1|NM_014606.1	NP_001258531.1|NP_055421.1	Q15034	HERC3_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 3	751					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|prostate(2)|skin(2)	45				OV - Ovarian serous cystadenocarcinoma(123;0.000319)		TACAAAGGAATTTTTTCTTTT	0.343																																					p.E749fs		Atlas-INDEL	.											.	HERC3	82	.	0			c.2247delA						.						102	106	105					4																	89601295		2203	4300	6503	SO:0001589	frameshift_variant	8916	exon20			.	D25215	CCDS34028.1	4q21	2012-02-23	2012-02-23		ENSG00000138641	ENSG00000138641			4876	protein-coding gene	gene with protein product		605200	"hect domain and RLD 3"			10702688	Standard	NM_014606		Approved	KIAA0032	uc003hrw.2	Q15034	OTTHUMG00000150436	ENST00000402738.1:c.2248delT	chr4.hg19:g.89601295delT	ENSP00000385684:p.Phe751fs	124.0	0.0		99.0	13.0	NM_014606	A8K1S5|Q8IXX3	Frame_Shift_Del	DEL	ENST00000402738.1	hg19	CCDS34028.1																																																																																			.	.		0.343	HERC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318081.2	NM_014606		-	89601295	T	-	89601295	7	5	282	1	0	1	0	1	0	0	0	0	7068	1493	52	0	2318	0	HERC3	4	89601295	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1547829	89601295	101552981	365	40599										
SMARCAD1	56916	hgsc.bcm.edu	37	chr4	95162076	95162076	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggtggtgggcccaggaaaagAaaattatcttcttcttcaga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:95162076delA	ENST00000354268.4	+	6	697	c.624delA	c.(622-624)agafs	p.R208fs	SMARCAD1_ENST00000457823.2_Frame_Shift_Del_p.R208fs			Q9H4L7	SMRCD_HUMAN	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	208					ATP-dependent chromatin remodeling (GO:0043044)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|chromosome separation (GO:0051304)|DNA double-strand break processing (GO:0000729)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|nucleotide metabolic process (GO:0009117)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|regulation of DNA recombination (GO:0000018)	heterochromatin (GO:0000792)|nuclear matrix (GO:0016363)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|liver(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44				OV - Ovarian serous cystadenocarcinoma(123;4.33e-08)		CCAGGAAAAGAAAATTATCTT	0.323																																					p.R208fs		Atlas-INDEL	.											.	SMARCAD1	97	.	0			c.623delG						.						64	66	65					4																	95162076		2203	4299	6502	SO:0001589	frameshift_variant	56916	exon6			.	AB032948	CCDS3639.1, CCDS47101.1, CCDS58914.1	4q22-q23	2008-02-05			ENSG00000163104	ENSG00000163104			18398	protein-coding gene	gene with protein product		612761				11031099	Standard	NM_001128430		Approved	ETL1, DKFZP762K2015, KIAA1122, DKFZp762K2015	uc003htb.4	Q9H4L7	OTTHUMG00000130971	ENST00000354268.4:c.624delA	chr4.hg19:g.95162076delA	ENSP00000346217:p.Arg208fs	278.0	0.0		189.0	12.0	NM_001128429	B7Z799|Q05D56|Q96SX1|Q9H017|Q9H860|Q9NPU9|Q9ULU7	Frame_Shift_Del	DEL	ENST00000354268.4	hg19	CCDS3639.1																																																																																			.	.		0.323	SMARCAD1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253583.1	NM_020159		-	95162076	A	-	95162076	7	5	282	1	0	1	0	1	0	0	0	0	14787	243	9	0	642	0	SMARCAD1	4	95162076	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	5560781	95162076	95992200	366	40600										
ADH7	131	hgsc.bcm.edu	37	chr4	100348965	100348965	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agcagcgccatatccagtggAaaacccacagccaattaaac							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:100348965delA	ENST00000209665.4	-	5	805	c.565delT	c.(565-567)tccfs	p.S189fs	ADH7_ENST00000437033.2_Frame_Shift_Del_p.S177fs|ADH7_ENST00000482593.1_Frame_Shift_Del_p.S120fs|ADH7_ENST00000476959.1_Frame_Shift_Del_p.S197fs	NM_000673.4	NP_000664.2	P40394	ADH7_HUMAN	alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide	189					ethanol catabolic process (GO:0006068)|ethanol oxidation (GO:0006069)|extracellular negative regulation of signal transduction (GO:1900116)|fatty acid omega-oxidation (GO:0010430)|oxidation-reduction process (GO:0055114)|response to bacterium (GO:0009617)|response to ethanol (GO:0045471)|retinoic acid metabolic process (GO:0042573)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular region (GO:0005576)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|aldehyde oxidase activity (GO:0004031)|ethanol binding (GO:0035276)|receptor antagonist activity (GO:0048019)|retinol binding (GO:0019841)|retinol dehydrogenase activity (GO:0004745)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|large_intestine(4)|lung(11)|skin(1)	19				OV - Ovarian serous cystadenocarcinoma(123;1.75e-08)		TATCCAGTGGAAAACCCACAG	0.408																																					p.S197fs		Atlas-INDEL	.											.	ADH7	76	.	0			c.590delC						.						104	94	98					4																	100348965		2203	4300	6503	SO:0001589	frameshift_variant	131	exon5			.	X76342	CCDS34034.1, CCDS54781.1	4q23-q24	2008-02-05			ENSG00000196344	ENSG00000196344	1.1.1.1	"Alcohol dehydrogenases"	256	protein-coding gene	gene with protein product		600086				8195208	Standard	NM_000673		Approved	ADH-4	uc021xqj.1	P40394	OTTHUMG00000159318	ENST00000209665.4:c.565delT	chr4.hg19:g.100348965delA	ENSP00000209665:p.Ser189fs	223.0	0.0		144.0	10.0	NM_001166504	A2RRB6|A8MVN9|B2R760|B4DWV6|Q13713	Frame_Shift_Del	DEL	ENST00000209665.4	hg19	CCDS34034.1																																																																																			.	.		0.408	ADH7-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_000673		-	100348965	A	-	100348965	7	5	282	1	0	1	0	1	0	0	0	0	313	246	9	0	615	0	ADH7	4	100348965	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	5186889	100348965	90805311	367	40601										
EGF	1950	hgsc.bcm.edu	37	chr4	110925702	110925702	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaacccaaagaatccttatgAggagtcgagcagagatgtga	11	7	0	4			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:110925702A>G	ENST00000265171.5	+	22	3660	c.3215A>G	c.(3214-3216)gAg>gGg	p.E1072G	EGF_ENST00000509793.1_Missense_Mutation_p.E1030G|EGF_ENST00000503392.1_Missense_Mutation_p.E1031G	NM_001178130.1|NM_001963.4	NP_001171601.1|NP_001954.2	P01133	EGF_HUMAN	epidermal growth factor	1072					activation of MAPKK activity (GO:0000186)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|branching morphogenesis of an epithelial tube (GO:0048754)|DNA replication (GO:0006260)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mammary gland alveolus development (GO:0060749)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of secretion (GO:0051048)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)|positive regulation of DNA binding (GO:0043388)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of calcium ion import (GO:0090279)|regulation of protein localization to cell surface (GO:2000008)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(1)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sucralfate(DB00364)	AATCCTTATGAGGAGTCGAGC	0.468																																					p.E1072G		Atlas-SNP	.											.	EGF	113	.	0			c.A3215G						.						123	122	123					4																	110925702		2203	4300	6503	SO:0001583	missense	1950	exon22			CTTATGAGGAGTC	X04571	CCDS3689.1, CCDS54794.1, CCDS54795.1	4q25	2012-10-02	2010-05-11		ENSG00000138798	ENSG00000138798			3229	protein-coding gene	gene with protein product		131530	"epidermal growth factor (beta-urogastrone)"				Standard	NM_001963		Approved		uc003hzy.4	P01133	OTTHUMG00000132044	ENST00000265171.5:c.3215A>G	chr4.hg19:g.110925702A>G	ENSP00000265171:p.Glu1072Gly	117.0	0.0		73.0	4.0	NM_001963	B4DRK7|E7EVD2|E9PBF0|Q52LZ6	Missense_Mutation	SNP	ENST00000265171.5	hg19	CCDS3689.1	.	.	.	.	.	.	.	.	.	.	A	8.949	0.967629	0.18659	.	.	ENSG00000138798	ENST00000509793;ENST00000265171;ENST00000503392	D;D;D	0.89415	-2.51;-2.43;-2.13	4.2	4.2	0.49525	.	0.596165	0.15279	N	0.270820	T	0.79540	0.4463	L	0.32530	0.975	0.25845	N	0.984007	P;P;P	0.44734	0.842;0.763;0.651	B;B;B	0.30855	0.057;0.121;0.057	T	0.74705	-0.3575	10	0.72032	D	0.01	.	9.8422	0.41006	1.0:0.0:0.0:0.0	.	1031;1030;1072	E7EVD2;P01133-2;P01133	.;.;EGF_HUMAN	G	1030;1072;1031	ENSP00000424316:E1030G;ENSP00000265171:E1072G;ENSP00000421384:E1031G	ENSP00000265171:E1072G	E	+	2	0	EGF	111145151	0.993000	0.37304	0.924000	0.36721	0.002000	0.02628	2.581000	0.46077	1.874000	0.54306	0.528000	0.53228	GAG	.	.		0.468	EGF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255065.1			G	110925702	A	G	110925702	3	3	282	1	0	0	0	0	1	0	0	0	4964	304	11	2	3301	2	EGF	4	110925702	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	10576737	110925702	80228574	368	40602										
ALPK1	80216	hgsc.bcm.edu	37	chr4	113353286	113353286	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gggcaactgctcgacagcatGgatgttccctgcacaaatgg	12	11	0	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:113353286G>C	ENST00000458497.1	+	11	2862	c.2583G>C	c.(2581-2583)atG>atC	p.M861I	ALPK1_ENST00000504176.2_Missense_Mutation_p.M783I|ALPK1_ENST00000177648.9_Missense_Mutation_p.M861I	NM_001102406.1|NM_025144.3	NP_001095876.1|NP_079420.3	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	861			M -> T (in dbSNP:rs11726117). {ECO:0000269|PubMed:10021370, ECO:0000269|PubMed:10819331, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17344846, ECO:0000269|Ref.5}.				ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.T861T(1)		NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(20)|ovary(6)|prostate(2)|urinary_tract(1)	53		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		TCGACAGCATGGATGTTCCCT	0.572																																					p.M861I		Atlas-SNP	.											ALPK1,NS,carcinoma,0,1	ALPK1	125	.	1	Substitution - coding silent(1)	endometrium(1)	c.G2583C						.						55	52	53					4																	113353286		2203	4300	6503	SO:0001583	missense	80216	exon11			CAGCATGGATGTT	AY044164	CCDS3697.1, CCDS58923.1	4q26	2008-02-05			ENSG00000073331	ENSG00000073331			20917	protein-coding gene	gene with protein product	"lymphocyte alpha-kinase"	607347				10021370, 10819331	Standard	NM_025144		Approved	Lak, FLJ22670, KIAA1527	uc003ian.4	Q96QP1	OTTHUMG00000132911	ENST00000458497.1:c.2583G>C	chr4.hg19:g.113353286G>C	ENSP00000398048:p.Met861Ile	198.0	0.0		128.0	0.0	NM_001102406	B4E3G1|F5H138|Q68CI9|Q6P9F9|Q6ZNK4|Q9P201	Missense_Mutation	SNP	ENST00000458497.1	hg19	CCDS3697.1	.	.	.	.	.	.	.	.	.	.	G	8.375	0.836138	0.16891	.	.	ENSG00000073331	ENST00000458497;ENST00000177648;ENST00000504176	T;T;T	0.02280	4.43;4.43;4.36	4.81	-5.27	0.02763	.	0.519792	0.18510	N	0.139088	T	0.01222	0.0040	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42172	-0.9467	10	0.56958	D	0.05	0.2401	10.3661	0.44024	0.3425:0.0952:0.5623:0.0	.	783;861	F5H138;Q96QP1	.;ALPK1_HUMAN	I	861;861;783	ENSP00000398048:M861I;ENSP00000177648:M861I;ENSP00000426044:M783I	ENSP00000177648:M861I	M	+	3	0	ALPK1	113572735	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.844000	0.04345	-1.052000	0.03222	-0.150000	0.13652	ATG	.	.		0.572	ALPK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256421.2	NM_025144		C	113353286	G	C	113353286	3	2	282	1	0	0	0	0	1	0	0	0	544	1348	47	4	2617	4	ALPK1	4	113353286	Missense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	2427584	113353286	77800990	369	40603										
USP53	54532	hgsc.bcm.edu	37	chr4	120192499	120192499	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccaatctggatcacctcctgCcccaaatggttttaaacaac							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:120192499delC	ENST00000274030.6	+	16	2663	c.1484delC	c.(1483-1485)gccfs	p.A495fs	USP53_ENST00000450251.1_Frame_Shift_Del_p.A495fs	NM_019050.2	NP_061923.2			ubiquitin specific peptidase 53											breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(5)|ovary(1)|pancreas(1)|skin(2)|stomach(1)	27						TCACCTCCTGCCCCAAATGGT	0.378																																					p.A495fs		Atlas-INDEL	.											.	USP53	69	.	0			c.1483delG						.						68	64	65					4																	120192499		1846	4098	5944	SO:0001589	frameshift_variant	54532	exon15			.	BC017382	CCDS43265.1	4q26	2010-05-12	2005-08-08		ENSG00000145390	ENSG00000145390		"Ubiquitin-specific peptidases"	29255	protein-coding gene	gene with protein product			"ubiquitin specific protease 53"			10718198, 14715245	Standard	NM_019050		Approved	KIAA1350	uc003ics.4	Q70EK8	OTTHUMG00000161331	ENST00000274030.6:c.1484delC	chr4.hg19:g.120192499delC	ENSP00000274030:p.Ala495fs	166.0	0.0		142.0	11.0	NM_019050		Frame_Shift_Del	DEL	ENST00000274030.6	hg19	CCDS43265.1																																																																																			.	.		0.378	USP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364564.2	XM_052597		-	120192499	C	-	120192499	7	5	282	1	0	1	0	1	0	0	0	0	17099	739	26	0	1530	0	USP53	4	120192499	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	6839213	120192499	70961777	370	40604										
QRFPR	84109	hgsc.bcm.edu	37	chr4	122253996	122253996	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctggctattttggacatttcTtttccatgaatagttcgaag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:122253996delT	ENST00000394427.2	-	4	1188	c.777delA	c.(775-777)aaafs	p.K259fs	QRFPR_ENST00000334383.5_Intron	NM_198179.2	NP_937822.2	Q96P65	QRFPR_HUMAN	pyroglutamylated RFamide peptide receptor	259				VILFLLPLMVMLILYSKIGYELWIKKRVGDGSVLRTIHGKE MSKIAR -> SSSSSCLLW (in Ref. 1; AAL26488). {ECO:0000305}.	G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide Y receptor activity (GO:0004983)			endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(2)|skin(3)|stomach(1)	28						TGGACATTTCTTTTCCATGAA	0.358																																					p.E260fs		Atlas-INDEL	.											QRFPR,NS,carcinoma,0,1	QRFPR	65	.	0			c.778delG						.						72	70	71					4																	122253996		2203	4300	6503	SO:0001589	frameshift_variant	84109	exon4			.	AF411117	CCDS3719.1	4q27	2012-08-10	2008-12-18	2008-12-18	ENSG00000186867	ENSG00000186867		"GPCR / Class A : RF amide peptide receptors"	15565	protein-coding gene	gene with protein product		606925	"G protein-coupled receptor 103"	GPR103		11574155	Standard	NM_198179		Approved		uc010inj.1	Q96P65	OTTHUMG00000133036	ENST00000394427.2:c.777delA	chr4.hg19:g.122253996delT	ENSP00000377948:p.Lys259fs	300.0	0.0		221.0	15.0	NM_198179		Frame_Shift_Del	DEL	ENST00000394427.2	hg19	CCDS3719.1																																																																																			.	.		0.358	QRFPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256641.2	NM_198179		-	122253996	T	-	122253996	7	5	282	1	0	1	0	1	0	0	0	0	12893	1606	56	0	530	0	QRFPR	4	122253996	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2061497	122253996	68900280	371	40605										
EXOSC9	5393	hgsc.bcm.edu	37	chr4	122723068	122723068	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgctgcattgtggaacttggAaaaacaaggtaacaggattt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:122723068delA	ENST00000243498.5	+	2	261	c.153delA	c.(151-153)ggafs	p.G51fs	EXOSC9_ENST00000379663.3_Frame_Shift_Del_p.G51fs|EXOSC9_ENST00000512454.1_Frame_Shift_Del_p.G35fs|EXOSC9_ENST00000509980.1_3'UTR	NM_005033.2	NP_005024.2	Q06265	EXOS9_HUMAN	exosome component 9	51	ARE binding.				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|immune response (GO:0006955)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear polyadenylation-dependent rRNA catabolic process (GO:0071035)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of cell growth (GO:0030307)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|intermediate filament cytoskeleton (GO:0045111)|nuclear exosome (RNase complex) (GO:0000176)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|AU-rich element binding (GO:0017091)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|urinary_tract(1)	16						TGGAACTTGGAAAAACAAGGT	0.388																																					p.G51fs		Atlas-INDEL	.											.	EXOSC9	51	.	0			c.152delG						.						103	93	96					4																	122723068		2203	4300	6503	SO:0001589	frameshift_variant	5393	exon2			.	M58460	CCDS3722.2, CCDS34057.1	4q27	2010-05-07	2004-06-16	2004-06-18	ENSG00000123737	ENSG00000123737	3.1.13.-		9137	protein-coding gene	gene with protein product	"polymyositis/scleroderma autoantigen 1 (75kD)"	606180	"polymyositis/scleroderma autoantigen 1, 75kDa"	PMSCL1			Standard	XR_427545		Approved	PM/Scl-75, Rrp45p, RRP45, p5, p6	uc003idz.3	Q06265	OTTHUMG00000128783	ENST00000243498.5:c.153delA	chr4.hg19:g.122723068delA	ENSP00000243498:p.Gly51fs	293.0	0.0		180.0	11.0	NM_001034194	Q12883|Q4W5P5|Q86Y41|Q86Y48	Frame_Shift_Del	DEL	ENST00000243498.5	hg19	CCDS3722.2																																																																																			.	.		0.388	EXOSC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250708.2	NM_005033		-	122723068	A	-	122723068	7	5	282	1	0	1	0	1	0	0	0	0	5323	233	9	0	159	0	EXOSC9	4	122723068	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	469072	122723068	68431208	372	40606										
EXOSC9	5393	hgsc.bcm.edu	37	chr4	122737569	122737569	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgaagaagaagaaatgatcaTtttggaaccagacaagaatc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:122737569delT	ENST00000243498.5	+	11	1310	c.1202delT	c.(1201-1203)attfs	p.I401fs	EXOSC9_ENST00000379663.3_Frame_Shift_Del_p.I418fs|EXOSC9_ENST00000512454.1_Frame_Shift_Del_p.I385fs	NM_005033.2	NP_005024.2	Q06265	EXOS9_HUMAN	exosome component 9	401					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|immune response (GO:0006955)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear polyadenylation-dependent rRNA catabolic process (GO:0071035)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of cell growth (GO:0030307)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|intermediate filament cytoskeleton (GO:0045111)|nuclear exosome (RNase complex) (GO:0000176)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|AU-rich element binding (GO:0017091)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|urinary_tract(1)	16						GAAATGATCATTTTGGAACCA	0.284																																					p.I418fs		Atlas-INDEL	.											.	EXOSC9	51	.	0			c.1252delA						.						71	80	77					4																	122737569		2199	4294	6493	SO:0001589	frameshift_variant	5393	exon12			.	M58460	CCDS3722.2, CCDS34057.1	4q27	2010-05-07	2004-06-16	2004-06-18	ENSG00000123737	ENSG00000123737	3.1.13.-		9137	protein-coding gene	gene with protein product	"polymyositis/scleroderma autoantigen 1 (75kD)"	606180	"polymyositis/scleroderma autoantigen 1, 75kDa"	PMSCL1			Standard	XR_427545		Approved	PM/Scl-75, Rrp45p, RRP45, p5, p6	uc003idz.3	Q06265	OTTHUMG00000128783	ENST00000243498.5:c.1202delT	chr4.hg19:g.122737569delT	ENSP00000243498:p.Ile401fs	274.0	0.0		261.0	20.0	NM_001034194	Q12883|Q4W5P5|Q86Y41|Q86Y48	Frame_Shift_Del	DEL	ENST00000243498.5	hg19	CCDS3722.2																																																																																			.	.		0.284	EXOSC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250708.2	NM_005033		-	122737569	T	-	122737569	7	5	282	1	0	1	0	1	0	0	0	0	5323	1493	52	0	1299	0	EXOSC9	4	122737569	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	14501	122737569	68416707	373	40607										
SPRY1	10252	hgsc.bcm.edu	37	chr4	124323536	124323536	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acctgtgtatgggagccatgTctttatttttaccttgctta	8	8	1	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:124323536T>C	ENST00000394339.2	+	2	1130	c.790T>C	c.(790-792)Tct>Cct	p.S264P	SPRY1_ENST00000339241.1_Missense_Mutation_p.S264P	NM_001258039.1|NM_005841.2	NP_001244968.1|NP_005832.1	O43609	SPY1_HUMAN	sprouty homolog 1, antagonist of FGF signaling (Drosophila)	264	Cys-rich.|SPR. {ECO:0000255|PROSITE- ProRule:PRU00572}.				epidermal growth factor receptor signaling pathway (GO:0007173)|multicellular organismal development (GO:0007275)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)	cytosol (GO:0005829)|plasma membrane (GO:0005886)				NS(1)|large_intestine(4)|lung(2)|ovary(1)|skin(3)	11						GGGAGCCATGTCTTTATTTTT	0.483																																					p.S264P		Atlas-SNP	.											.	SPRY1	28	.	0			c.T790C						.						239	203	215					4																	124323536		2203	4300	6503	SO:0001583	missense	10252	exon2			GCCATGTCTTTAT	AF041037	CCDS3731.1	4q	2009-04-17	2001-11-28		ENSG00000164056	ENSG00000164056			11269	protein-coding gene	gene with protein product		602465	"sprouty (Drosophila) homolog 1 (antagonist of FGF signaling)"			9458049, 15962011	Standard	NM_001258038		Approved	hSPRY1	uc003ifa.4	O43609	OTTHUMG00000133071	ENST00000394339.2:c.790T>C	chr4.hg19:g.124323536T>C	ENSP00000377871:p.Ser264Pro	155.0	0.0		98.0	4.0	NM_001258039	D3DNX6|Q6PNE0	Missense_Mutation	SNP	ENST00000394339.2	hg19	CCDS3731.1	.	.	.	.	.	.	.	.	.	.	T	15.57	2.873713	0.51695	.	.	ENSG00000164056	ENST00000339241;ENST00000394339	T;T	0.72282	-0.64;-0.64	4.61	0.355	0.16069	.	0.237030	0.35739	N	0.003003	T	0.74764	0.3759	M	0.80616	2.505	0.52501	D	0.999952	P	0.49783	0.928	P	0.49387	0.609	T	0.76537	-0.2923	9	.	.	.	-5.6009	12.2445	0.54561	0.0:0.0:0.3998:0.6002	.	264	O43609	SPY1_HUMAN	P	264	ENSP00000343785:S264P;ENSP00000377871:S264P	.	S	+	1	0	SPRY1	124542986	1.000000	0.71417	0.940000	0.37924	0.982000	0.71751	2.656000	0.46716	0.321000	0.23259	0.459000	0.35465	TCT	.	.		0.483	SPRY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256711.1			C	124323536	T	C	124323536	3	2	282	1	0	0	0	0	1	0	0	0	15120	1667	58	2	792	2	SPRY1	4	124323536	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1585967	124323536	66830740	374	40608										
SCLT1	132320	hgsc.bcm.edu	37	chr4	129873978	129873978	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaaatttgtatattacattgTtttttggtgtttgcaacctg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:129873978delT	ENST00000281142.5	-	14	1667	c.1164delA	c.(1162-1164)aaafs	p.K388fs	SCLT1_ENST00000503215.1_Intron|SCLT1_ENST00000434680.1_Intron|SCLT1_ENST00000502495.1_5'UTR|SCLT1_ENST00000439369.2_Intron	NM_144643.2	NP_653244.2	Q96NL6	SCLT1_HUMAN	sodium channel and clathrin linker 1	388					cilium assembly (GO:0042384)|clustering of voltage-gated sodium channels (GO:0045162)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|clathrin complex (GO:0071439)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule cytoskeleton (GO:0015630)	sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|stomach(1)	29						TATTACATTGTTTTTTGGTGT	0.254																																					p.Q389fs		Atlas-INDEL	.											.	SCLT1	136	.	0			c.1165delC						.						118	121	120					4																	129873978		2200	4296	6496	SO:0001589	frameshift_variant	132320	exon14			.	AK055217	CCDS3740.1	4q28.2	2008-05-02			ENSG00000151466	ENSG00000151466			26406	protein-coding gene	gene with protein product		611399				15797711	Standard	XM_005262732		Approved	hCAP-1A, FLJ30655	uc003igp.2	Q96NL6	OTTHUMG00000133346	ENST00000281142.5:c.1164delA	chr4.hg19:g.129873978delT	ENSP00000281142:p.Lys388fs	227.0	0.0		175.0	17.0	NM_144643	A4QN04|Q0VAH2|Q6P2M4	Frame_Shift_Del	DEL	ENST00000281142.5	hg19	CCDS3740.1																																																																																			.	.		0.254	SCLT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257176.2	NM_144643		-	129873978	T	-	129873978	7	5	282	1	0	1	0	1	0	0	0	0	13921	1722	60	0	934	0	SCLT1	4	129873978	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	5550442	129873978	61280298	375	40609										
NAA15	80155	hgsc.bcm.edu	37	chr4	140270718	140270718	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggcctattacaaaggcttggAaaaagcactcaagccaggta							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:140270718delA	ENST00000296543.5	+	7	1117	c.794delA	c.(793-795)gaafs	p.E265fs	NAA15_ENST00000398947.1_Frame_Shift_Del_p.E265fs|NAA15_ENST00000480277.2_3'UTR	NM_057175.3	NP_476516.1	Q9BXJ9	NAA15_HUMAN	N(alpha)-acetyltransferase 15, NatA auxiliary subunit	265					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|N-terminal protein amino acid acetylation (GO:0006474)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|NatA complex (GO:0031415)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	N-acetyltransferase activity (GO:0008080)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)			NS(1)|endometrium(3)|large_intestine(7)|liver(2)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						AAAGGCTTGGAAAAAGCACTC	0.333																																					p.E265fs		Atlas-INDEL	.											.	NAA15	88	.	0			c.793delG						.						49	46	47					4																	140270718		1798	4073	5871	SO:0001589	frameshift_variant	80155	exon7			.	AY039242	CCDS43270.1	4q31.1	2010-01-14	2010-01-14	2010-01-14	ENSG00000164134	ENSG00000164134		"N(alpha)-acetyltransferase subunits"	30782	protein-coding gene	gene with protein product		608000	"NMDA receptor regulated 1"	NARG1		12140756, 11478804, 19660095	Standard	XM_005263236		Approved	TBDN100, NATH, FLJ13340	uc003ihu.1	Q9BXJ9	OTTHUMG00000137363	ENST00000296543.5:c.794delA	chr4.hg19:g.140270718delA	ENSP00000296543:p.Glu265fs	218.0	0.0		162.0	11.0	NM_057175	D3DNY6|Q52LG9|Q8IWH4|Q8NEV2|Q9H8P6	Frame_Shift_Del	DEL	ENST00000296543.5	hg19	CCDS43270.1																																																																																			.	.		0.333	NAA15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000267839.2	NM_057175		-	140270718	A	-	140270718	7	5	282	1	0	1	0	1	0	0	0	0	10127	246	9	0	820	0	NAA15	4	140270718	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	10396740	140270718	50883558	376	40610										
MAB21L2	10586	hgsc.bcm.edu	37	chr4	151505172	151505172	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcgacctctttcagggcaagCcccattcggccctggagagc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:151505172delC	ENST00000317605.4	+	1	2096	c.991delC	c.(991-993)cccfs	p.P331fs	RP11-1336O20.2_ENST00000507934.1_RNA|LRBA_ENST00000503716.1_5'Flank|LRBA_ENST00000507224.1_Intron|LRBA_ENST00000357115.3_Intron|LRBA_ENST00000510413.1_Intron|LRBA_ENST00000535741.1_Intron	NM_006439.4	NP_006430.1	Q9Y586	MB212_HUMAN	mab-21-like 2 (C. elegans)	331					camera-type eye development (GO:0043010)|embryonic body morphogenesis (GO:0010172)|eye development (GO:0001654)|nervous system development (GO:0007399)|positive regulation of cell proliferation (GO:0008284)	nucleus (GO:0005634)				breast(2)|endometrium(6)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|skin(2)	21	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.159)		TCAGGGCAAGCCCCATTCGGC	0.607																																					p.K330fs		Atlas-INDEL	.											.	MAB21L2	53	.	0			c.990delG						.						52	50	51					4																	151505172		2203	4300	6503	SO:0001589	frameshift_variant	10586	exon1			.	AF155219	CCDS3774.1	4q31.3	2013-10-22	2001-11-28		ENSG00000181541	ENSG00000181541			6758	protein-coding gene	gene with protein product		604357	"mab-21 (C. elegans)-like 2"				Standard	NM_006439		Approved		uc003ilw.3	Q9Y586	OTTHUMG00000161442	ENST00000317605.4:c.991delC	chr4.hg19:g.151505172delC	ENSP00000324701:p.Pro331fs	183.0	0.0		129.0	10.0	NM_006439	B3KP37|Q9HBA7	Frame_Shift_Del	DEL	ENST00000317605.4	hg19	CCDS3774.1																																																																																			.	.		0.607	MAB21L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364937.1	NM_006439		-	151505172	C	-	151505172	7	5	282	1	0	1	0	1	0	0	0	0	9151	739	26	0	993	0	MAB21L2	4	151505172	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	11234454	151505172	39649104	377	40611										
LRBA	987	hgsc.bcm.edu	37	chr4	151789357	151789357	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctgttttctctactgttattAaaaagtttaatcatgtcaga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:151789357delA	ENST00000357115.3	-	21	2793	c.2550delT	c.(2548-2550)tttfs	p.F850fs	LRBA_ENST00000507224.1_Frame_Shift_Del_p.F850fs|LRBA_ENST00000510413.1_Frame_Shift_Del_p.F850fs|LRBA_ENST00000535741.1_Frame_Shift_Del_p.F850fs	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	850						cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					TACTGTTATTAAAAAGTTTAA	0.358																																					p.N851fs		Atlas-INDEL	.											.	LRBA	253	.	0			c.2551delA						.						73	78	76					4																	151789357		2203	4300	6503	SO:0001589	frameshift_variant	987	exon21			.	AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"WD repeat domain containing"	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.2550delT	chr4.hg19:g.151789357delA	ENSP00000349629:p.Phe850fs	215.0	0.0		161.0	10.0	NM_006726	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Frame_Shift_Del	DEL	ENST00000357115.3	hg19	CCDS3773.1																																																																																			.	.		0.358	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			-	151789357	A	-	151789357	7	5	282	1	0	1	0	1	0	0	0	0	8940	359	13	0	6193	0	LRBA	4	151789357	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	284185	151789357	39364919	378	40612										
FGA	2243	hgsc.bcm.edu	37	chr4	155511792	155511792	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaaaagggccatacccatgcTgtgcccaccacacttaggac	9	14	0	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:155511792T>C	ENST00000302053.3	-	1	126	c.48A>G	c.(46-48)acA>acG	p.T16T	FGA_ENST00000403106.3_Silent_p.T16T	NM_000508.3	NP_000499.1	P02671	FIBA_HUMAN	fibrinogen alpha chain	16					blood coagulation (GO:0007596)|blood coagulation, common pathway (GO:0072377)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|extracellular matrix organization (GO:0030198)|negative regulation of blood coagulation, common pathway (GO:2000261)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	structural molecule activity (GO:0005198)			NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	73	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)	ATACCCATGCTGTGCCCACCA	0.498																																					p.T16T	NSCLC(143;340 1922 20892 22370 48145)	Atlas-SNP	.											.	FGA	179	.	0			c.A48G						.						73	54	61					4																	155511792		2197	4278	6475	SO:0001819	synonymous_variant	2243	exon1			CCATGCTGTGCCC		CCDS3787.1, CCDS47152.1	4q28	2014-09-17			ENSG00000171560	ENSG00000171560		"Fibrinogen C domain containing", "Endogenous ligands"	3661	protein-coding gene	gene with protein product		134820	"fibrinogen, A alpha polypeptide"				Standard	NM_000508		Approved		uc003iod.1	P02671	OTTHUMG00000150330	ENST00000302053.3:c.48A>G	chr4.hg19:g.155511792T>C		119.0	0.0		100.0	4.0	NM_000508	A8K3E4|D3DP14|D3DP15|Q4QQH7|Q9BX62|Q9UCH2	Silent	SNP	ENST00000302053.3	hg19	CCDS3787.1																																																																																			.	.		0.498	FGA-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317593.1	NM_000508		C	155511792	T	C	155511792	2	2	282	1	0	0	0	0	0	0	0	1	5838	1567	55	2		2	FGA	4	155511792	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3722435	155511792	35642484	379	40613										
RBM46	166863	hgsc.bcm.edu	37	chr4	155720297	155720297	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcagattagtccaaattctgAaaatctgattgtgtttgcta							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:155720297delA	ENST00000281722.3	+	4	1218	c.983delA	c.(982-984)gaafs	p.E328fs	RBM46_ENST00000510397.1_Frame_Shift_Del_p.E328fs|RBM46_ENST00000514866.1_Frame_Shift_Del_p.E328fs	NM_144979.3	NP_659416.1	Q8TBY0	RBM46_HUMAN	RNA binding motif protein 46	328							nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(7)|skin(3)|urinary_tract(2)	26	all_hematologic(180;0.24)	Renal(120;0.0854)				CCAAATTCTGAAAATCTGATT	0.413																																					p.E328fs		Atlas-INDEL	.											.	RBM46	76	.	0			c.982delG						.						64	68	67					4																	155720297		2203	4300	6503	SO:0001589	frameshift_variant	166863	exon4			.	BC028588	CCDS3790.1, CCDS64085.1, CCDS64086.1	4q32.1	2013-02-12				ENSG00000151962		"RNA binding motif (RRM) containing"	28401	protein-coding gene	gene with protein product	"cancer/testis antigen 68"					12477932	Standard	NM_144979		Approved	MGC27016, CT68	uc003ioo.4	Q8TBY0		ENST00000281722.3:c.983delA	chr4.hg19:g.155720297delA	ENSP00000281722:p.Glu328fs	226.0	0.0		198.0	12.0	NM_144979	B3KWU8|B4DZ27	Frame_Shift_Del	DEL	ENST00000281722.3	hg19	CCDS3790.1																																																																																			.	.		0.413	RBM46-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365259.1	NM_144979		-	155720297	A	-	155720297	7	5	282	1	0	1	0	1	0	0	0	0	13155	246	9	0	993	0	RBM46	4	155720297	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	208505	155720297	35433979	380	40614										
ACCN5	51802	hgsc.bcm.edu	37	chr4	156763391	156763391	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaggcacacatccacattgcTtttttatgtgctgggctttg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:156763391delT	ENST00000537611.2	-	6	1023	c.977delA	c.(976-978)aagfs	p.K326fs		NM_017419.2	NP_059115.1	Q9NY37	ASIC5_HUMAN	acid-sensing (proton-gated) ion channel family member 5	326					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrogen ion channel activity (GO:0015252)|ligand-gated sodium channel activity (GO:0015280)										TCCACATTGCTTTTTTATGTG	0.418																																					p.K326fs		Atlas-INDEL	.											.	.	.	.	0			c.978delG						.						142	136	138					4																	156763391		2203	4300	6503	SO:0001589	frameshift_variant	51802	exon6			.	AJ252011	CCDS3793.1	4q32.1	2012-10-03	2012-03-02	2012-03-02	ENSG00000256394	ENSG00000256394			17537	protein-coding gene	gene with protein product			"amiloride-sensitive cation channel 5, intestinal"	ACCN5		10767424	Standard	NM_017419		Approved	INAC, HINAC	uc003ipe.1	Q9NY37	OTTHUMG00000161941	ENST00000537611.2:c.977delA	chr4.hg19:g.156763391delT	ENSP00000442477:p.Lys326fs	214.0	0.0		182.0	11.0	NM_017419		Frame_Shift_Del	DEL	ENST00000537611.2	hg19	CCDS3793.1																																																																																			.	.		0.418	ASIC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366464.1			-	156763391	T	-	156763391	7	5	282	1	0	1	0	1	0	0	0	0	132	1609	56	0	560	0	ACCN5	4	156763391	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1043094	156763391	34390885	381	40615										
SORBS2	8470	hgsc.bcm.edu	37	chr4	186598269	186598273	+	Intron	DEL	TCCTG	TCCTG	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gctgtttgtggctttcaagaTcctgtcctgaaaggggagct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	TCCTG	TCCTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:186598269_186598273delTCCTG	ENST00000284776.7	-	4	465				SORBS2_ENST00000448662.2_Intron|SORBS2_ENST00000319471.9_Intron|SORBS2_ENST00000437304.2_Frame_Shift_Del_p.QD124fs|SORBS2_ENST00000355634.5_Intron|SORBS2_ENST00000431808.1_Intron|SORBS2_ENST00000393528.3_Intron|SORBS2_ENST00000449407.2_Intron|RP11-626E13.1_ENST00000447277.1_RNA	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2						actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		GCTTTCAAGATCCTGTCCTGAAAGG	0.498																																					p.124_125del	Esophageal Squamous(153;41 2433 9491 36028)	Atlas-Indel,Pindel	.											.	SORBS2	300	.	0			c.371_375del						.																																			SO:0001627	intron_variant	8470	exon5			.		CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556			24098	protein-coding gene	gene with protein product	"Arg/Abl interacting protein"					9211900, 9872452	Standard	NM_021069		Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000284776.7:c.44+1303CAGGA>-	chr4.hg19:g.186598274_186598278delTCCTG		167.0	0.0		126.0	41.0	NM_001145673	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Frame_Shift_Del	DEL	ENST00000284776.7	hg19	CCDS3845.1																																																																																			.	.		0.498	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603		-	186598273	TCCTG	-	186598269	6	5	282	0	1	1	0	1	0	0	0	0	14943	1435	50	0		0	SORBS2	4	186598269	Intron	DEL	TCCTG	TCGA-G3-A3CJ-01A-11D-A20W-10	29834878	186598269	4556007	382	40616										
TLR3	7098	hgsc.bcm.edu	37	chr4	186998188	186998188	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccaactcaatccagaaaattAaaaataatccctttgtcaag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:186998188delA	ENST00000296795.3	+	2	519	c.415delA	c.(415-417)aaafs	p.K139fs		NM_003265.2	NP_003256.1	O15455	TLR3_HUMAN	toll-like receptor 3	139					activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to drug (GO:0035690)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|cellular response to interferon-gamma (GO:0071346)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|detection of virus (GO:0009597)|extrinsic apoptotic signaling pathway (GO:0097191)|hyperosmotic response (GO:0006972)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|microglial cell activation involved in immune response (GO:0002282)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic signaling pathway (GO:0097527)|negative regulation of osteoclast differentiation (GO:0045671)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of chemokine production (GO:0032722)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type III interferon production (GO:0034346)|response to exogenous dsRNA (GO:0043330)|signal transduction (GO:0007165)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	double-stranded RNA binding (GO:0003725)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(5)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	29		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.47e-11)|BRCA - Breast invasive adenocarcinoma(30;1.14e-05)|GBM - Glioblastoma multiforme(59;0.000107)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.16)		CCAGAAAATTAAAAATAATCC	0.353																																					p.I138fs		Atlas-INDEL	.											.	TLR3	83	.	0			c.414delT						.						36	38	37					4																	186998188		2203	4300	6503	SO:0001589	frameshift_variant	7098	exon2			.	U88879	CCDS3846.1	4q35	2014-09-17				ENSG00000164342		"CD molecules"	11849	protein-coding gene	gene with protein product		603029				9435236	Standard	NM_003265		Approved	CD283	uc003iyq.3	O15455		ENST00000296795.3:c.415delA	chr4.hg19:g.186998188delA	ENSP00000296795:p.Lys139fs	150.0	0.0		119.0	10.0	NM_003265	B2RAI7|B7Z7K0|E6Y0F0|E6Y0F1|E9PGH4|Q4VAL2|Q504W0	Frame_Shift_Del	DEL	ENST00000296795.3	hg19	CCDS3846.1																																																																																			.	.		0.353	TLR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360313.4			-	186998188	A	-	186998188	7	5	282	1	0	1	0	1	0	0	0	0	15967	363	13	0	417	0	TLR3	4	186998188	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	399919	186998188	4156088	383	40617										
CYP4V2	285440	hgsc.bcm.edu	37	chr4	187130116	187130116	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cgcctttttccttctgttccTttatttgcccgtagtgttag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:187130116delT	ENST00000378802.4	+	9	1492	c.1188delT	c.(1186-1188)cctfs	p.P396fs	CYP4V2_ENST00000502665.1_3'UTR	NM_207352.3	NP_997235.3	Q6ZWL3	CP4V2_HUMAN	cytochrome P450, family 4, subfamily V, polypeptide 2	396					fatty acid omega-oxidation (GO:0010430)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|skin(1)|stomach(2)	20		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.33e-10)|BRCA - Breast invasive adenocarcinoma(30;3.84e-05)|GBM - Glioblastoma multiforme(59;0.000132)|STAD - Stomach adenocarcinoma(60;0.000293)|LUSC - Lung squamous cell carcinoma(40;0.00242)|READ - Rectum adenocarcinoma(43;0.17)		CTTCTGTTCCTTTATTTGCCC	0.448																																					p.P396fs		Atlas-INDEL	.											.	CYP4V2	49	.	0			c.1187delC						.						179	169	172					4																	187130116		2203	4300	6503	SO:0001589	frameshift_variant	285440	exon9			.	AK022114	CCDS34119.1	4q35.2	2004-07-05			ENSG00000145476	ENSG00000145476		"Cytochrome P450s"	23198	protein-coding gene	gene with protein product		608614				15042513	Standard	NM_207352		Approved	CYP4AH1	uc003iyw.4	Q6ZWL3	OTTHUMG00000160379	ENST00000378802.4:c.1188delT	chr4.hg19:g.187130116delT	ENSP00000368079:p.Pro396fs	236.0	0.0		161.0	10.0	NM_207352	B7U6W2|Q6ZTM4	Frame_Shift_Del	DEL	ENST00000378802.4	hg19	CCDS34119.1																																																																																			.	.		0.448	CYP4V2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360398.1	XM_209612		-	187130116	T	-	187130116	7	5	282	1	0	1	0	1	0	0	0	0	4194	1596	56	0	1222	0	CYP4V2	4	187130116	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	131928	187130116	4024160	384	40618										
FAT1	2195	hgsc.bcm.edu	37	chr4	187510197	187510197	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagctgcggggaagtcttctGggggtggaggaaaatcactt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:187510197delG	ENST00000441802.2	-	27	13525	c.13316delC	c.(13315-13317)ccafs	p.P4439fs		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	4439					actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						GAAGTCTTCTGGGGGTGGAGG	0.537										HNSCC(5;0.00058)																											p.P4439fs	Colon(197;1040 2055 4143 4984 49344)	Atlas-INDEL	.											.	FAT1	500	.	0			c.13317delA						.						217	223	221					4																	187510197		1989	4144	6133	SO:0001589	frameshift_variant	2195	exon27			.	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.13316delC	chr4.hg19:g.187510197delG	ENSP00000406229:p.Pro4439fs	224.0	0.0		229.0	15.0	NM_005245		Frame_Shift_Del	DEL	ENST00000441802.2	hg19	CCDS47177.1																																																																																			.	.		0.537	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		-	187510197	G	-	187510197	7	5	282	1	0	1	0	1	0	0	0	0	5697	1348	47	0	454	0	FAT1	4	187510197	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	380081	187510197	3644079	385	40619										
FAT1	2195	hgsc.bcm.edu	37	chr4	187541324	187541324	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aggtgtcaagctcaaattgcTttttcagtgaaatttcaccc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:187541324delT	ENST00000441802.2	-	10	6625	c.6416delA	c.(6415-6417)aagfs	p.K2139fs		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2139	Cadherin 19. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						CTCAAATTGCTTTTTCAGTGA	0.428										HNSCC(5;0.00058)																											p.K2139fs	Colon(197;1040 2055 4143 4984 49344)	Atlas-INDEL	.											.	FAT1	500	.	0			c.6417delG						.						79	75	76					4																	187541324		1857	4112	5969	SO:0001589	frameshift_variant	2195	exon10			.	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.6416delA	chr4.hg19:g.187541324delT	ENSP00000406229:p.Lys2139fs	177.0	0.0		168.0	11.0	NM_005245		Frame_Shift_Del	DEL	ENST00000441802.2	hg19	CCDS47177.1																																																																																			.	.		0.428	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		-	187541324	T	-	187541324	7	5	282	1	0	1	0	1	0	0	0	0	5697	1609	56	0	7422	0	FAT1	4	187541324	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	31127	187541324	3612952	386	40620										
PLEKHG4B	153478	hgsc.bcm.edu	37	chr5	163580	163580	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctgtggcagcatgccaggagCcccccggtcactcagagccg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:163580delC	ENST00000283426.6	+	11	2375	c.2325delC	c.(2323-2325)agcfs	p.S775fs		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	775							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		ATGCCAGGAGCCCCCCGGTCA	0.652																																					p.S775fs		Atlas-INDEL	.											.	PLEKHG4B	167	.	0			c.2324delG						.						25	28	27					5																	163580		2200	4300	6500	SO:0001589	frameshift_variant	153478	exon11			.	BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"Pleckstrin homology (PH) domain containing"	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.2325delC	chr5.hg19:g.163580delC	ENSP00000283426:p.Ser775fs	167.0	0.0		193.0	12.0	NM_052909		Frame_Shift_Del	DEL	ENST00000283426.6	hg19	CCDS34124.1																																																																																			.	.		0.652	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909		-	163580	C	-	163580	7	5	282	1	0	1	0	1	0	0	0	0	12081	738	26	0	2367	0	PLEKHG4B	5	163580	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10		163580	180751680	387	40621										
SLC12A7	10723	hgsc.bcm.edu	37	chr5	1078065	1078065	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gagccgatgacgatgacccaGggggagggccaggccagcat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:1078065delG	ENST00000264930.5	-	12	1555	c.1512delC	c.(1510-1512)cccfs	p.P504fs		NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	504					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	CGATGACCCAGGGGGAGGGCC	0.701																																					p.W505fs		Atlas-INDEL	.											.	SLC12A7	97	.	0			c.1513delT						.						20	23	22					5																	1078065		2179	4286	6465	SO:0001589	frameshift_variant	10723	exon12			.	AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504		"Solute carriers"	10915	protein-coding gene	gene with protein product		604879				10347194	Standard	NM_006598		Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.1512delC	chr5.hg19:g.1078065delG	ENSP00000264930:p.Pro504fs	173.0	0.0		189.0	13.0	NM_006598	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Frame_Shift_Del	DEL	ENST00000264930.5	hg19	CCDS34129.1																																																																																			.	.		0.701	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598		-	1078065	G	-	1078065	7	5	282	1	0	1	0	1	0	0	0	0	14403	987	35	0	1791	0	SLC12A7	5	1078065	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	914485	1078065	179837195	388	40622										
FASTKD3	79072	hgsc.bcm.edu	37	chr5	7867919	7867919	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gactctcctcatttttaacaTtttgttcaagcctgtcgcag					rs79525539	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:7867919delT	ENST00000264669.5	-	2	414	c.278delA	c.(277-279)aatfs	p.N93fs	FASTKD3_ENST00000513658.1_Intron|MTRR_ENST00000341013.6_5'Flank|MTRR_ENST00000440940.2_5'Flank|MTRR_ENST00000502509.1_Intron|MTRR_ENST00000264668.2_5'Flank	NM_024091.3	NP_076996.2	Q14CZ7	FAKD3_HUMAN	FAST kinase domains 3	93					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						ATTTTTAACATTTTGTTCAAG	0.413																																					p.N93fs		Atlas-INDEL	.											.	FASTKD3	88	.	0			c.279delT						.						67	65	66					5																	7867919		2203	4300	6503	SO:0001589	frameshift_variant	79072	exon2			.	AK026927	CCDS3873.1	5p15.31	2008-02-05			ENSG00000124279	ENSG00000124279			28758	protein-coding gene	gene with protein product						12477932	Standard	NM_024091		Approved	MGC5297, FLJ23274	uc003jeb.3	Q14CZ7	OTTHUMG00000131029	ENST00000264669.5:c.278delA	chr5.hg19:g.7867919delT	ENSP00000264669:p.Asn93fs	196.0	0.0		151.0	10.0	NM_024091	Q9BVD3	Frame_Shift_Del	DEL	ENST00000264669.5	hg19	CCDS3873.1																																																																																			.	.		0.413	FASTKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253673.1	NM_024091		-	7867919	T	-	7867919	7	5	282	1	0	1	0	1	0	0	0	0	5695	1493	52	0	1734	0	FASTKD3	5	7867919	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	6789854	7867919	173047341	389	40623										
FASTKD3	79072	hgsc.bcm.edu	37	chr5	7868134	7868134	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttattttttaaagcagccagAgctctatgcatctgaaaatc	6	8	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:7868134A>G	ENST00000264669.5	-	2	199	c.63T>C	c.(61-63)gcT>gcC	p.A21A	FASTKD3_ENST00000513658.1_Intron|MTRR_ENST00000341013.6_5'Flank|MTRR_ENST00000440940.2_5'Flank|MTRR_ENST00000502509.1_Intron|MTRR_ENST00000264668.2_5'Flank	NM_024091.3	NP_076996.2	Q14CZ7	FAKD3_HUMAN	FAST kinase domains 3	21					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						AAGCAGCCAGAGCTCTATGCA	0.388																																					p.A21A		Atlas-SNP	.											.	FASTKD3	88	.	0			c.T63C						.						65	73	70					5																	7868134		2203	4300	6503	SO:0001819	synonymous_variant	79072	exon2			AGCCAGAGCTCTA	AK026927	CCDS3873.1	5p15.31	2008-02-05			ENSG00000124279	ENSG00000124279			28758	protein-coding gene	gene with protein product						12477932	Standard	NM_024091		Approved	MGC5297, FLJ23274	uc003jeb.3	Q14CZ7	OTTHUMG00000131029	ENST00000264669.5:c.63T>C	chr5.hg19:g.7868134A>G		103.0	0.0		98.0	4.0	NM_024091	Q9BVD3	Silent	SNP	ENST00000264669.5	hg19	CCDS3873.1																																																																																			.	.		0.388	FASTKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253673.1	NM_024091		G	7868134	A	G	7868134	2	3	282	1	0	0	0	0	0	0	0	1	5695	291	11	2		2	FASTKD3	5	7868134	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	215	7868134	173047126	390	40624										
FAM173B	134145	hgsc.bcm.edu	37	chr5	10236710	10236710	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccaactgctgtgaaccctttCttcgcagccgctatgacctg	8	15	1	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:10236710C>T	ENST00000511437.1	-	3	336	c.324G>A	c.(322-324)aaG>aaA	p.K108K	FAM173B_ENST00000280330.8_5'UTR|FAM173B_ENST00000510052.1_5'UTR|FAM173B_ENST00000510047.1_Silent_p.K108K	NM_199133.3	NP_954584.2	Q6P4H8	F173B_HUMAN	family with sequence similarity 173, member B	108						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	16						TGAACCCTTTCTTCGCAGCCG	0.403																																					p.K108K		Atlas-SNP	.											.	FAM173B	24	.	0			c.G324A						.						80	78	78					5																	10236710		1856	4111	5967	SO:0001819	synonymous_variant	134145	exon3			CCCTTTCTTCGCA		CCDS43301.1, CCDS58942.1	5p15.2	2008-08-08			ENSG00000150756	ENSG00000150756			27029	protein-coding gene	gene with protein product						12477932	Standard	NM_199133		Approved		uc003jeo.3	Q6P4H8	OTTHUMG00000161771	ENST00000511437.1:c.324G>A	chr5.hg19:g.10236710C>T		101.0	0.0		91.0	4.0	NM_199133	B4DT41|B4DXK2|E9PBZ4	Silent	SNP	ENST00000511437.1	hg19	CCDS43301.1																																																																																			.	.		0.403	FAM173B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000366048.2	NM_199133		T	10236710	C	T	10236710	2	4	282	1	0	0	0	0	0	0	0	1	5499	912	32	3		3	FAM173B	5	10236710	Silent	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	2368576	10236710	170678550	391	40625										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13864702	13864702	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caatgatcttcttcaggtccAaaaaagcctgccagtccttc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:13864702delA	ENST00000265104.4	-	28	4504	c.4400delT	c.(4399-4401)ttgfs	p.L1467fs	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1467	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CTTCAGGTCCAAAAAAGCCTG	0.498									Kartagener syndrome																												p.L1467fs		Atlas-INDEL	.											.	DNAH5	868	.	0			c.4401delG						.						57	57	57					5																	13864702		2203	4300	6503	SO:0001589	frameshift_variant	1767	exon28	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	.	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.4400delT	chr5.hg19:g.13864702delA	ENSP00000265104:p.Leu1467fs	215.0	0.0		152.0	10.0	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Frame_Shift_Del	DEL	ENST00000265104.4	hg19	CCDS3882.1																																																																																			.	.		0.498	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		-	13864702	A	-	13864702	7	5	282	1	0	1	0	1	0	0	0	0	4606	131	5	0	9682	0	DNAH5	5	13864702	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	3627992	13864702	167050558	392	40626										
TRIO	7204	hgsc.bcm.edu	37	chr5	14286982	14286982	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgttttctttctctgcagcgAggaggtctgcaagcgtggct	13	9	3	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:14286982A>G	ENST00000344204.4	+	4	374	c.350A>G	c.(349-351)gAg>gGg	p.E117G	TRIO_ENST00000537187.1_Missense_Mutation_p.E117G|TRIO_ENST00000509967.2_Missense_Mutation_p.E68G	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	117	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118	Lung NSC(4;0.000742)					CTCTGCAGCGAGGAGGTCTGC	0.587																																					p.E117G		Atlas-SNP	.											.	TRIO	305	.	0			c.A350G						.						97	82	87					5																	14286982		2203	4300	6503	SO:0001583	missense	7204	exon4			GCAGCGAGGAGGT	AF091395	CCDS3883.1	5p14-p15.1	2013-01-11	2012-07-12		ENSG00000038382	ENSG00000038382		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing"	12303	protein-coding gene	gene with protein product		601893	"triple functional domain (PTPRF interacting)"			8643598	Standard	NM_007118		Approved	ARHGEF23	uc003jff.3	O75962	OTTHUMG00000131057	ENST00000344204.4:c.350A>G	chr5.hg19:g.14286982A>G	ENSP00000339299:p.Glu117Gly	132.0	0.0		98.0	4.0	NM_007118	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Missense_Mutation	SNP	ENST00000344204.4	hg19	CCDS3883.1	.	.	.	.	.	.	.	.	.	.	A	18.99	3.739618	0.69304	.	.	ENSG00000038382	ENST00000344204;ENST00000537187;ENST00000509967	T;T;T	0.65916	-0.18;-0.18;-0.18	5.56	5.56	0.83823	Cellular retinaldehyde-binding/triple function, C-terminal (4);	0.000000	0.85682	D	0.000000	T	0.79441	0.4446	M	0.79926	2.475	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.995	T	0.78826	-0.2051	10	0.32370	T	0.25	.	15.711	0.77626	1.0:0.0:0.0:0.0	.	68;117	F5H228;O75962	.;TRIO_HUMAN	G	117;117;68	ENSP00000339299:E117G;ENSP00000446348:E117G;ENSP00000445592:E68G	ENSP00000339299:E117G	E	+	2	0	TRIO	14339982	1.000000	0.71417	0.995000	0.50966	0.652000	0.38707	9.339000	0.96797	2.118000	0.64928	0.482000	0.46254	GAG	.	.		0.587	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118		G	14286982	A	G	14286982	3	3	282	1	0	0	0	0	1	0	0	0	16567	304	11	2	364	2	TRIO	5	14286982	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	422280	14286982	166628278	393	40627										
CDH10	1008	hgsc.bcm.edu	37	chr5	24509876	24509876	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aacggggatctacatgggtgTtttctgcttcgactttcaga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:24509876delT	ENST00000264463.4	-	7	1562	c.1055delA	c.(1054-1056)aacfs	p.N352fs		NM_006727.3	NP_006718.2	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 (T2-cadherin)	352	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(29)|lung(111)|ovary(6)|pancreas(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)	185				STAD - Stomach adenocarcinoma(35;0.0556)		TACATGGGTGTTTTCTGCTTC	0.363										HNSCC(23;0.051)																											p.N352fs		Atlas-INDEL	.											.	CDH10	391	.	0			c.1056delC						.						70	72	72					5																	24509876		2203	4300	6503	SO:0001589	frameshift_variant	1008	exon7			.	AF039747	CCDS3892.1	5p14.2	2010-01-26			ENSG00000040731	ENSG00000040731		"Cadherins / Major cadherins"	1749	protein-coding gene	gene with protein product		604555				2059658	Standard	NM_006727		Approved		uc003jgr.2	Q9Y6N8	OTTHUMG00000090667	ENST00000264463.4:c.1055delA	chr5.hg19:g.24509876delT	ENSP00000264463:p.Asn352fs	147.0	0.0		117.0	10.0	NM_006727	Q9ULB3	Frame_Shift_Del	DEL	ENST00000264463.4	hg19	CCDS3892.1																																																																																			.	.		0.363	CDH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207345.2	NM_006727		-	24509876	T	-	24509876	7	5	282	1	0	1	0	1	0	0	0	0	3098	1725	60	0	1335	0	CDH10	5	24509876	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	10222894	24509876	156405384	394	40628										
SKP2	6502	hgsc.bcm.edu	37	chr5	36170455	36170455	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tctttttccagtactctcgcAaaaaactcaaatttagtgcg					rs142374565	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:36170455delA	ENST00000274255.6	+	6	877	c.681delA	c.(679-681)gcafs	p.A227fs	SKP2_ENST00000508514.1_Intron|SKP2_ENST00000546211.1_Frame_Shift_Del_p.A13fs|SKP2_ENST00000274254.5_Frame_Shift_Del_p.A227fs	NM_005983.3	NP_005974.2	Q13309	SKP2_HUMAN	S-phase kinase-associated protein 2, E3 ubiquitin protein ligase	227					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|cellular response to cell-matrix adhesion (GO:0071460)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein polyubiquitination (GO:0000209)|regulation of cell cycle (GO:0051726)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)	identical protein binding (GO:0042802)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(2)|ovary(1)	4	all_lung(31;5.63e-05)		Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			GTACTCTCGCAAAAAACTCAA	0.398																																					p.A227fs		Atlas-INDEL	.											.	SKP2	70	.	0			c.680delC						.						126	120	122					5																	36170455		2203	4299	6502	SO:0001589	frameshift_variant	6502	exon6			.	U33761	CCDS3915.1, CCDS3916.1, CCDS58944.1	5p13	2012-02-23	2012-02-23		ENSG00000145604	ENSG00000145604		"F-boxes / Leucine-rich repeats"	10901	protein-coding gene	gene with protein product		601436	"S-phase kinase-associated protein 2 (p45)"			8646875	Standard	NM_005983		Approved	FBXL1, FBL1, p45	uc003jkc.2	Q13309	OTTHUMG00000131106	ENST00000274255.6:c.681delA	chr5.hg19:g.36170455delA	ENSP00000274255:p.Ala227fs	239.0	0.0		195.0	12.0	NM_032637	A8K5E0|B4DJT4|Q8TDZ0|Q8TDZ1|Q9BV69	Frame_Shift_Del	DEL	ENST00000274255.6	hg19	CCDS3916.1																																																																																			.	.		0.398	SKP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253769.2	NM_005983		-	36170455	A	-	36170455	7	5	282	1	0	1	0	1	0	0	0	0	14377	117	5	0	703	0	SKP2	5	36170455	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	11660579	36170455	144744805	395	40629										
C5orf42	65250	hgsc.bcm.edu	37	chr5	37153894	37153894	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tggggaaatcctgttctatgTtttcagcaatgttctgtatt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:37153894delT	ENST00000508244.1	-	40	8252	c.8159delA	c.(8158-8160)aacfs	p.N2720fs	C5orf42_ENST00000425232.2_Frame_Shift_Del_p.N2720fs|C5orf42_ENST00000274258.7_Frame_Shift_Del_p.N1618fs			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	2720						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			CTGTTCTATGTTTTCAGCAAT	0.398																																					p.N2720fs		Atlas-INDEL	.											.	C5orf42	422	.	0			c.8160delC						.						98	89	92					5																	37153894		2203	4300	6503	SO:0001589	frameshift_variant	65250	exon41			.		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.8159delA	chr5.hg19:g.37153894delT	ENSP00000421690:p.Asn2720fs	179.0	0.0		164.0	10.0	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Frame_Shift_Del	DEL	ENST00000508244.1	hg19	CCDS34146.2																																																																																			.	.		0.398	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		-	37153894	T	-	37153894	7	5	282	1	0	1	0	1	0	0	0	0	2303	1725	60	0	1482	0	C5orf42	5	37153894	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	983439	37153894	143761366	396	40630										
OSMR	9180	hgsc.bcm.edu	37	chr5	38917660	38917660	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aatttcagctccctcagaggCccctgatgtctggagaattg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:38917660delC	ENST00000274276.3	+	10	1700	c.1298delC	c.(1297-1299)gccfs	p.A433fs		NM_003999.2	NP_003990.1	Q99650	OSMR_HUMAN	oncostatin M receptor	433	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	oncostatin-M receptor complex (GO:0005900)	growth factor binding (GO:0019838)|oncostatin-M receptor activity (GO:0004924)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(8)|lung(20)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	46	all_lung(31;0.000365)					CCCTCAGAGGCCCCTGATGTC	0.418																																					p.A433fs		Atlas-INDEL	.											.	OSMR	133	.	0			c.1297delG						.						115	114	114					5																	38917660		2203	4300	6503	SO:0001589	frameshift_variant	9180	exon10			.	U60805	CCDS3928.1, CCDS54847.1	5p13.2	2013-02-11			ENSG00000145623	ENSG00000145623		"Fibronectin type III domain containing"	8507	protein-coding gene	gene with protein product		601743				8999038	Standard	NM_001168355		Approved	OSMRB	uc003jln.2	Q99650	OTTHUMG00000090811	ENST00000274276.3:c.1298delC	chr5.hg19:g.38917660delC	ENSP00000274276:p.Ala433fs	228.0	0.0		173.0	11.0	NM_003999	Q6P4E8|Q96QJ6	Frame_Shift_Del	DEL	ENST00000274276.3	hg19	CCDS3928.1																																																																																			.	.		0.418	OSMR-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000207609.2	NM_003999		-	38917660	C	-	38917660	7	5	282	1	0	1	0	1	0	0	0	0	11301	739	26	0	1370	0	OSMR	5	38917660	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1763766	38917660	141997600	397	40631										
DAB2	1601	hgsc.bcm.edu	37	chr5	39377168	39377168	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtgccacagatgcagaagggCcccagacaacaggcactgga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:39377168delC	ENST00000320816.6	-	12	2188	c.1721delG	c.(1720-1722)ggcfs	p.G574fs	DAB2_ENST00000509337.1_Frame_Shift_Del_p.G553fs|DAB2_ENST00000339788.6_Frame_Shift_Del_p.G356fs|DAB2_ENST00000545653.1_Frame_Shift_Del_p.G553fs	NM_001343.3	NP_001334.2	P98082	DAB2_HUMAN	Dab, mitogen-responsive phosphoprotein, homolog 2 (Drosophila)	574					activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cell morphogenesis involved in differentiation (GO:0000904)|cell proliferation (GO:0008283)|cellular response to transforming growth factor beta stimulus (GO:0071560)|clathrin coat assembly (GO:0048268)|endoderm development (GO:0007492)|excretion (GO:0007588)|in utero embryonic development (GO:0001701)|leading edge cell differentiation (GO:0035026)|membrane organization (GO:0061024)|myeloid cell differentiation (GO:0030099)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of protein binding (GO:0032091)|negative regulation of protein localization to plasma membrane (GO:1903077)|negative regulation of transcription, DNA-templated (GO:0045892)|pinocytosis (GO:0006907)|positive regulation of cell migration (GO:0030335)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of endocytosis (GO:0045807)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of receptor recycling (GO:0001921)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|clathrin coat of coated pit (GO:0030132)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	cargo receptor activity (GO:0038024)|clathrin adaptor activity (GO:0035615)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein C-terminus binding (GO:0008022)|SMAD binding (GO:0046332)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(9)|lung(19)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	47	all_lung(31;0.000197)		Epithelial(62;0.137)			TGCAGAAGGGCCCCAGACAAC	0.527											OREG0016586	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G574fs		Atlas-INDEL	.											.	DAB2	124	.	0			c.1722delC						.						70	75	73					5																	39377168		2203	4300	6503	SO:0001589	frameshift_variant	1601	exon12			.	U53446	CCDS34149.1, CCDS58946.1	5p13.1	2013-10-03	2013-03-08		ENSG00000153071	ENSG00000153071			2662	protein-coding gene	gene with protein product		601236	"disabled (Drosophila) homolog 2 (mitogen-responsive phosphoprotein)", "disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)"			8660969, 9620555	Standard	NM_001343		Approved	DOC-2	uc003jlx.3	P98082	OTTHUMG00000162043	ENST00000320816.6:c.1721delG	chr5.hg19:g.39377168delC	ENSP00000313391:p.Gly574fs	251.0	0.0	885	192.0	12.0	NM_001343	A6NES5|Q13598|Q9BTY0|Q9UK04	Frame_Shift_Del	DEL	ENST00000320816.6	hg19	CCDS34149.1																																																																																			.	.		0.527	DAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367014.1	NM_001343		-	39377168	C	-	39377168	7	5	282	1	0	1	0	1	0	0	0	0	4220	739	26	0	603	0	DAB2	5	39377168	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	459508	39377168	141538092	398	40632										
PARP8	79668	hgsc.bcm.edu	37	chr5	50129819	50129819	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tttttggaatttagtcacagAaaaaaggacagcaatcccaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:50129819delA	ENST00000281631.5	+	24	2472	c.2314delA	c.(2314-2316)aaafs	p.K773fs	PARP8_ENST00000505697.2_Frame_Shift_Del_p.K773fs|PARP8_ENST00000503750.2_Frame_Shift_Del_p.K731fs|PARP8_ENST00000505554.1_Frame_Shift_Del_p.K752fs|PARP8_ENST00000514342.2_Splice_Site_p.K484fs|PARP8_ENST00000514067.2_Frame_Shift_Del_p.K731fs|PARP8_ENST00000511363.2_3'UTR	NM_001178056.1|NM_024615.3	NP_001171527.1|NP_078891.2	Q8N3A8	PARP8_HUMAN	poly (ADP-ribose) polymerase family, member 8	773	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.					intracellular (GO:0005622)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(23)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Lung NSC(810;0.0305)|Breast(144;0.222)				TTAGTCACAGAAAAAAGGACA	0.328																																					p.Q771fs		Atlas-INDEL	.											.	PARP8	93	.	0			c.2313delG						.						76	78	77					5																	50129819		2203	4300	6503	SO:0001589	frameshift_variant	79668	exon25			.	AL834477	CCDS3954.1, CCDS54849.1	5q11.2	2010-02-16			ENSG00000151883	ENSG00000151883		"Poly (ADP-ribose) polymerases"	26124	protein-coding gene	gene with protein product						15273990	Standard	NM_001178055		Approved	FLJ21308, pART16	uc003joo.3	Q8N3A8	OTTHUMG00000096969	ENST00000281631.5:c.2314delA	chr5.hg19:g.50129819delA	ENSP00000281631:p.Lys773fs	242.0	0.0		157.0	11.0	NM_001178055	Q3KRB7|Q6DHZ1|Q9H754	Frame_Shift_Del	DEL	ENST00000281631.5	hg19	CCDS3954.1																																																																																			.	.		0.328	PARP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214035.3	NM_024615		-	50129819	A	-	50129819	7	5	282	1	0	1	0	1	0	0	0	0	11474	247	9	0	2408	0	PARP8	5	50129819	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	10752651	50129819	130785441	399	40633										
HSPB3	8988	hgsc.bcm.edu	37	chr5	53751734	53751734	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atgctttatatgcactgcctGggccaaccatcgtggacctg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:53751734delG	ENST00000302005.1	+	1	290	c.115delG	c.(115-117)gggfs	p.G39fs		NM_006308.2	NP_006299.1	Q12988	HSPB3_HUMAN	heat shock 27kDa protein 3	39					cell death (GO:0008219)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|large_intestine(4)|prostate(3)	8		Lung NSC(810;0.00104)				TGCACTGCCTGGGCCAACCAT	0.547																																					p.P38fs		Atlas-INDEL	.											.	HSPB3	17	.	0			c.114delT						.						74	71	72					5																	53751734		2203	4300	6503	SO:0001589	frameshift_variant	8988	exon1			.	Y17782	CCDS3961.1	5q11.2	2011-09-02	2002-08-29		ENSG00000169271	ENSG00000169271		"Heat shock proteins / HSPB"	5248	protein-coding gene	gene with protein product		604624	"heat shock 27kD protein 3"			8972725, 9858786	Standard	NM_006308		Approved	HSPL27	uc003jph.2	Q12988	OTTHUMG00000096995	ENST00000302005.1:c.115delG	chr5.hg19:g.53751734delG	ENSP00000303394:p.Gly39fs	201.0	0.0		147.0	11.0	NM_006308		Frame_Shift_Del	DEL	ENST00000302005.1	hg19	CCDS3961.1																																																																																			.	.		0.547	HSPB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214074.2			-	53751734	G	-	53751734	7	5	282	1	0	1	0	1	0	0	0	0	7430	1348	47	0	117	0	HSPB3	5	53751734	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	3621915	53751734	127163526	400	40634										
CDC20B	166979	hgsc.bcm.edu	37	chr5	54424346	54424346	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aagtgagacttaagtctatgTtttcaatcccattgtggttc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:54424346delT	ENST00000381375.2	-	7	942	c.797delA	c.(796-798)aacfs	p.N266fs	CDC20B_ENST00000322374.6_Frame_Shift_Del_p.N266fs|CDC20B_ENST00000334206.5_Frame_Shift_Del_p.N266fs|CDC20B_ENST00000296733.1_Frame_Shift_Del_p.N266fs			Q86Y33	CD20B_HUMAN	cell division cycle 20B	266										kidney(1)|large_intestine(5)|lung(7)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	19		Lung NSC(810;0.000744)|Breast(144;0.159)|Prostate(74;0.194)	LUSC - Lung squamous cell carcinoma(15;0.225)			TAAGTCTATGTTTTCAATCCC	0.448																																					p.N266fs		Atlas-INDEL	.											.	CDC20B	61	.	0			c.798delC						.						160	162	161					5																	54424346		2203	4300	6503	SO:0001589	frameshift_variant	166979	exon7			.	AB086378	CCDS3966.1, CCDS47207.1, CCDS54852.1	5q11.2	2013-01-17	2013-01-17		ENSG00000164287	ENSG00000164287		"WD repeat domain containing"	24222	protein-coding gene	gene with protein product			"CDC20 cell division cycle 20 homolog B (S. cerevisiae)", "cell division cycle 20 homolog B (S. cerevisiae)"				Standard	NM_152623		Approved	FLJ37927	uc003jpo.2	Q86Y33	OTTHUMG00000131185	ENST00000381375.2:c.797delA	chr5.hg19:g.54424346delT	ENSP00000370781:p.Asn266fs	262.0	0.0		171.0	11.0	NM_001145734	B7WNV8|B9EGL8|C9J6X8|C9JHE9|C9JKL5|Q86Y31|Q86Y32|Q8IUZ8|Q8N1S1|Q8NG56	Frame_Shift_Del	DEL	ENST00000381375.2	hg19	CCDS54852.1																																																																																			.	.		0.448	CDC20B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369715.1	NM_152623		-	54424346	T	-	54424346	7	5	282	1	0	1	0	1	0	0	0	0	3062	1725	60	0	786	0	CDC20B	5	54424346	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	672612	54424346	126490914	401	40635										
DHX29	54505	hgsc.bcm.edu	37	chr5	54565369	54565369	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atttaattcacaagctccaaTttttcggagcaaattcattg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:54565369delT	ENST00000251636.5	-	21	3314	c.3166delA	c.(3166-3168)attfs	p.I1056fs	RP11-506H20.1_ENST00000506435.1_RNA	NM_019030.2	NP_061903.2	Q7Z478	DHX29_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 29	1056						eukaryotic 43S preinitiation complex (GO:0016282)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|translation initiation factor activity (GO:0003743)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|lung(6)|ovary(4)|prostate(1)|skin(3)|urinary_tract(2)	46		Lung NSC(810;4.08e-05)|Breast(144;0.0544)|Prostate(74;0.183)				CAAGCTCCAATTTTTCGGAGC	0.428																																					p.I1056fs		Atlas-INDEL	.											.	DHX29	116	.	0			c.3167delT						.						95	86	89					5																	54565369		2203	4300	6503	SO:0001589	frameshift_variant	54505	exon21			.	AY036974	CCDS34158.1	5q11.2	2008-02-05	2003-06-13	2003-06-20	ENSG00000067248	ENSG00000067248		"DEAH-boxes"	15815	protein-coding gene	gene with protein product		612720	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 29"	DDX29			Standard	XM_005248544		Approved		uc003jpx.3	Q7Z478	OTTHUMG00000162313	ENST00000251636.5:c.3166delA	chr5.hg19:g.54565369delT	ENSP00000251636:p.Ile1056fs	242.0	0.0		181.0	11.0	NM_019030	O75549|Q63HN0|Q63HN3|Q8IWW2|Q8N3A1|Q9UMH2	Frame_Shift_Del	DEL	ENST00000251636.5	hg19	CCDS34158.1																																																																																			.	.		0.428	DHX29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368532.1	NM_019030		-	54565369	T	-	54565369	7	5	282	1	0	1	0	1	0	0	0	0	4505	1493	52	0	971	0	DHX29	5	54565369	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	141023	54565369	126349891	402	40636										
GAPT	202309	hgsc.bcm.edu	37	chr5	57790552	57790552	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgtactaaaacattcttgggCccccgcatcattggcttaag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:57790552delC	ENST00000396776.2	+	3	651	c.189delC	c.(187-189)ggcfs	p.G63fs	GAPT_ENST00000318469.2_Frame_Shift_Del_p.G63fs	NM_152687.2	NP_689900.1	Q8N292	GAPT_HUMAN	GRB2-binding adaptor protein, transmembrane	63					B cell activation (GO:0042113)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|endometrium(2)|large_intestine(1)|lung(2)|skin(1)	7						CATTCTTGGGCCCCCGCATCA	0.448																																					p.G63fs		Pindel	.											.	GAPT	21	.	0			c.188delG						.						60	61	61					5																	57790552		2203	4300	6503	SO:0001589	frameshift_variant	202309	exon3			.	AK090960	CCDS3975.1	5q11.2	2011-11-01	2008-10-07	2008-10-07	ENSG00000175857	ENSG00000175857			26588	protein-coding gene	gene with protein product	"GRB2-binding transmembrane adaptor"		"chromosome 5 open reading frame 29"	C5orf29			Standard	NM_152687		Approved	FLJ33641	uc003jro.1	Q8N292	OTTHUMG00000131219	ENST00000396776.2:c.189delC	chr5.hg19:g.57790552delC	ENSP00000379997:p.Gly63fs	230.0	0.0		186.0	10.0	NM_152687		Frame_Shift_Del	DEL	ENST00000396776.2	hg19	CCDS3975.1																																																																																			.	.		0.448	GAPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253963.1	NM_152687		-	57790552	C	-	57790552	7	5	282	1	0	1	0	1	0	0	0	0	6246	726	26	0	191	0	GAPT	5	57790552	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	3225183	57790552	123124708	403	40637										
ERBB2IP	55914	hgsc.bcm.edu	37	chr5	65374265	65374265	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttctaggctaatggctacagTtttataaatattgaacatgg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:65374265delT	ENST00000284037.5	+	26	4535	c.4146delT	c.(4144-4146)agtfs	p.S1382fs	ERBB2IP_ENST00000506030.1_Frame_Shift_Del_p.S1389fs|ERBB2IP_ENST00000380935.1_Frame_Shift_Del_p.S1272fs|ERBB2IP_ENST00000511297.1_Frame_Shift_Del_p.S1337fs|ERBB2IP_ENST00000416865.2_Frame_Shift_Del_p.S580fs|ERBB2IP_ENST00000380939.2_Frame_Shift_Del_p.S1330fs|ERBB2IP_ENST00000380943.2_Frame_Shift_Del_p.S1341fs|ERBB2IP_ENST00000380936.1_Frame_Shift_Del_p.S1310fs|ERBB2IP_ENST00000380938.2_Frame_Shift_Del_p.S1316fs|ERBB2IP_ENST00000503913.1_3'UTR|ERBB2IP_ENST00000508515.1_Frame_Shift_Del_p.S1272fs	NM_001253697.1	NP_001240626.1	Q96RT1	LAP2_HUMAN	erbb2 interacting protein	1382	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				basal protein localization (GO:0045175)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell growth (GO:0016049)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|signal transduction (GO:0007165)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|hemidesmosome (GO:0030056)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ErbB-2 class receptor binding (GO:0005176)|integrin binding (GO:0005178)|structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|skin(2)	36		Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191)		ATGGCTACAGTTTTATAAATA	0.333																																					p.S1389fs		Atlas-INDEL	.											.	ERBB2IP	120	.	0			c.4166delG						.						54	56	55					5																	65374265		2203	4300	6503	SO:0001589	frameshift_variant	55914	exon26			.		CCDS3990.1, CCDS34172.1, CCDS58951.1, CCDS58952.1, CCDS58953.1, CCDS58954.1	5p14.3-q12.3	2008-07-18	2001-11-29		ENSG00000112851	ENSG00000112851			15842	protein-coding gene	gene with protein product	"densin-180-like protein", "ERBB2-interacting protein"	606944	"erbb2-interacting protein"			10574462, 10878805	Standard	NM_001253697		Approved	ERBIN, LAP2	uc011cqx.2	Q96RT1	OTTHUMG00000097808	ENST00000284037.5:c.4146delT	chr5.hg19:g.65374265delT	ENSP00000284037:p.Ser1382fs	309.0	0.0		216.0	13.0	NM_001253699	A0AVR1|B4E3F1|B7ZLV9|E7EQW9|E9PCR8|Q1RMD0|Q86W38|Q9NR18|Q9NW48|Q9ULJ5	Frame_Shift_Del	DEL	ENST00000284037.5	hg19	CCDS58953.1																																																																																			.	.		0.333	ERBB2IP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215070.1	NM_018695		-	65374265	T	-	65374265	7	5	282	1	0	1	0	1	0	0	0	0	5209	1722	60	0	4113	0	ERBB2IP	5	65374265	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	7583713	65374265	115540995	404	40638										
RAD17	5884	hgsc.bcm.edu	37	chr5	68687769	68687769	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggtttttgaaaatcaagaggTccaagctattggtggcaaag	12	5	1	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:68687769T>C	ENST00000509734.1	+	12	1829	c.1151T>C	c.(1150-1152)gTc>gCc	p.V384A	RAD17_ENST00000504177.1_Intron|RAD17_ENST00000361732.2_Missense_Mutation_p.V373A|RAD17_ENST00000358030.2_Missense_Mutation_p.V208A|RAD17_ENST00000282891.6_Missense_Mutation_p.V287A|RAD17_ENST00000380774.3_Missense_Mutation_p.V384A|RAD17_ENST00000345306.6_Missense_Mutation_p.V373A|RAD17_ENST00000354312.3_Missense_Mutation_p.V373A|RAD17_ENST00000305138.4_Missense_Mutation_p.V373A|RAD17_ENST00000354868.5_Missense_Mutation_p.V373A|RAD17_ENST00000521422.1_Missense_Mutation_p.V208A			O75943	RAD17_HUMAN	RAD17 homolog (S. pombe)	384					cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of DNA replication (GO:0008156)|regulation of phosphorylation (GO:0042325)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)						Lung NSC(167;5.19e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;9.36e-57)|Epithelial(20;1.21e-52)|all cancers(19;3.34e-48)|Lung(70;0.0183)		AATCAAGAGGTCCAAGCTATT	0.333								Other conserved DNA damage response genes																													p.V384A		Atlas-SNP	.											.	RAD17	49	.	0			c.T1151C						.						64	74	71					5																	68687769		2203	4299	6502	SO:0001583	missense	5884	exon10			AAGAGGTCCAAGC	AF085736	CCDS4003.1, CCDS4004.1, CCDS4005.1, CCDS47226.1	5q13	2010-09-24	2001-11-28		ENSG00000152942	ENSG00000152942			9807	protein-coding gene	gene with protein product		603139	"RAD1 (S. pombe) homolog"			9869296, 9660800	Standard	NM_133343		Approved	Rad24, RAD17Sp, CCYC	uc003jwo.3	O75943	OTTHUMG00000099357	ENST00000509734.1:c.1151T>C	chr5.hg19:g.68687769T>C	ENSP00000426191:p.Val384Ala	233.0	0.0		184.0	8.0	NM_133339	A8K8X2|D3DWA5|O75714|Q7Z3S4|Q9UNK7|Q9UNR7|Q9UNR8|Q9UPF5	Missense_Mutation	SNP	ENST00000509734.1	hg19	CCDS4003.1	.	.	.	.	.	.	.	.	.	.	T	9.057	0.993456	0.19043	.	.	ENSG00000152942	ENST00000361732;ENST00000509734;ENST00000354868;ENST00000521422;ENST00000354312;ENST00000345306;ENST00000305138;ENST00000282891;ENST00000358030;ENST00000380774	T;T;T;T;T;T;T;T;T;T	0.23950	1.88;1.88;1.88;1.88;1.88;1.88;1.88;1.88;1.88;1.88	5.24	2.79	0.32731	.	0.791975	0.12301	N	0.481067	T	0.16128	0.0388	N	0.21097	0.63	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.001	T	0.31166	-0.9953	10	0.21540	T	0.41	-22.5517	8.9953	0.36048	0.0:0.1565:0.0:0.8435	.	384;287;373	O75943;O75943-4;O75943-2	RAD17_HUMAN;.;.	A	373;384;373;208;373;373;373;287;208;384	ENSP00000355226:V373A;ENSP00000426191:V384A;ENSP00000346938:V373A;ENSP00000427743:V208A;ENSP00000346271:V373A;ENSP00000311227:V373A;ENSP00000303134:V373A;ENSP00000282891:V287A;ENSP00000350725:V208A;ENSP00000370151:V384A	ENSP00000282891:V287A	V	+	2	0	RAD17	68723525	0.069000	0.21087	0.487000	0.27428	0.996000	0.88848	1.580000	0.36547	0.299000	0.22661	0.528000	0.53228	GTC	.	.		0.333	RAD17-008	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369171.1	NM_133344		C	68687769	T	C	68687769	3	2	282	1	0	0	0	0	1	0	0	0	12994	1667	58	2	1202	2	RAD17	5	68687769	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3313504	68687769	112227491	405	40639										
PTCD2	79810	hgsc.bcm.edu	37	chr5	71648518	71648518	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaaaacctgataaagactctAaaaaatgctgcagaaggaaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:71648518delA	ENST00000380639.5	+	9	895	c.879delA	c.(877-879)ctafs	p.L293fs	PTCD2_ENST00000536805.1_Frame_Shift_Del_p.L121fs|PTCD2_ENST00000543322.1_3'UTR|PTCD2_ENST00000503868.1_Frame_Shift_Del_p.L184fs|PTCD2_ENST00000460837.2_3'UTR	NM_024754.3	NP_079030.3	Q8WV60	PTCD2_HUMAN	pentatricopeptide repeat domain 2	293					kidney development (GO:0001822)|liver development (GO:0001889)|mitochondrion organization (GO:0007005)|mRNA processing (GO:0006397)|muscle fiber development (GO:0048747)|regulation of mRNA processing (GO:0050684)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(6)|lung(1)|skin(1)	11		Lung NSC(167;0.00237)|Ovarian(174;0.0175)|Prostate(461;0.141)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.73e-53)		TAAAGACTCTAAAAAATGCTG	0.348																																					p.L293fs		Atlas-INDEL	.											.	PTCD2	31	.	0			c.878delT						.						74	76	75					5																	71648518		2203	4300	6503	SO:0001589	frameshift_variant	79810	exon9			.	BC018720	CCDS4014.2, CCDS68891.1, CCDS68892.1, CCDS75258.1	5q13.2	2008-02-05			ENSG00000049883	ENSG00000049883			25734	protein-coding gene	gene with protein product		615484				12477932	Standard	XM_005248601		Approved	FLJ12598	uc003kcb.3	Q8WV60	OTTHUMG00000100953	ENST00000380639.5:c.879delA	chr5.hg19:g.71648518delA	ENSP00000370013:p.Leu293fs	301.0	0.0		199.0	12.0	NM_024754	B7Z5D0|B7Z8L7|E9PFV7|Q6IA65|Q9H9R0	Frame_Shift_Del	DEL	ENST00000380639.5	hg19	CCDS4014.2																																																																																			.	.		0.348	PTCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218562.6	NM_024754		-	71648518	A	-	71648518	7	5	282	1	0	1	0	1	0	0	0	0	12740	349	13	0	913	0	PTCD2	5	71648518	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2960749	71648518	109266742	406	40640										
POC5	134359	hgsc.bcm.edu	37	chr5	74998581	74998581	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagctaaaagatgtgaactgAaaaaatccatgactgggtga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:74998581delA	ENST00000428202.2	-	5	551	c.362delT	c.(361-363)ttcfs	p.F121fs	POC5_ENST00000504862.1_5'UTR|POC5_ENST00000380475.2_Frame_Shift_Del_p.F4fs|POC5_ENST00000510798.1_Frame_Shift_Del_p.F4fs|POC5_ENST00000514838.2_Frame_Shift_Del_p.F93fs|POC5_ENST00000446329.2_Frame_Shift_Del_p.F96fs	NM_001099271.1	NP_001092741.1	Q8NA72	POC5_HUMAN	POC5 centriolar protein	121					cell cycle (GO:0007049)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						ATGTGAACTGAAAAAATCCAT	0.388																																					p.F121fs		Atlas-INDEL	.											.	POC5	82	.	0			c.363delC						.						93	96	95					5																	74998581		1994	4182	6176	SO:0001589	frameshift_variant	134359	exon5			.	AK093098	CCDS47236.1, CCDS47237.1	5q13.3	2013-08-05	2013-08-05	2010-03-26	ENSG00000152359	ENSG00000152359			26658	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 37", "POC5 centriolar protein homolog (Chlamydomonas)"	C5orf37		19349582	Standard	NM_152408		Approved	FLJ35779, MGC120442, MGC120443, MGC120444, hPOC5	uc003keh.4	Q8NA72	OTTHUMG00000162487	ENST00000428202.2:c.362delT	chr5.hg19:g.74998581delA	ENSP00000410216:p.Phe121fs	258.0	0.0		173.0	15.0	NM_001099271	B4DJG7|Q494X7|Q494X9|Q6P085	Frame_Shift_Del	DEL	ENST00000428202.2	hg19	CCDS47236.1																																																																																			.	.		0.388	POC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369124.1	NM_152408		-	74998581	A	-	74998581	7	5	282	1	0	1	0	1	0	0	0	0	12186	246	9	0	1397	0	POC5	5	74998581	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	3350063	74998581	105916679	407	40641										
F2R	2149	hgsc.bcm.edu	37	chr5	76029269	76029269	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtgggcagttgatggcaagtAaaatggatacctgctctagt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:76029269delA	ENST00000319211.4	+	2	1484	c.1219delA	c.(1219-1221)aaafs	p.K407fs		NM_001992.3	NP_001983.2	P25116	PAR1_HUMAN	coagulation factor II (thrombin) receptor	407					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPKK activity (GO:0000186)|anatomical structure morphogenesis (GO:0009653)|blood coagulation (GO:0007596)|connective tissue replacement involved in inflammatory response wound healing (GO:0002248)|establishment of synaptic specificity at neuromuscular junction (GO:0007529)|G-protein coupled receptor signaling pathway (GO:0007186)|homeostasis of number of cells within a tissue (GO:0048873)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glomerular filtration (GO:0003105)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of renin secretion into blood stream (GO:1900134)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|platelet activation (GO:0030168)|platelet dense granule organization (GO:0060155)|positive regulation of blood coagulation (GO:0030194)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of Rho protein signal transduction (GO:0035025)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vasoconstriction (GO:0045907)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of blood coagulation (GO:0030193)|regulation of interleukin-1 beta production (GO:0032651)|regulation of sensory perception of pain (GO:0051930)|release of sequestered calcium ion into cytosol (GO:0051209)|response to lipopolysaccharide (GO:0032496)|response to wounding (GO:0009611)|STAT protein import into nucleus (GO:0007262)|tyrosine phosphorylation of STAT protein (GO:0007260)	caveola (GO:0005901)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|platelet dense tubular network (GO:0031094)|postsynaptic membrane (GO:0045211)	G-protein alpha-subunit binding (GO:0001965)|G-protein beta-subunit binding (GO:0031681)|G-protein coupled receptor activity (GO:0004930)|receptor binding (GO:0005102)|thrombin receptor activity (GO:0015057)			NS(1)|breast(1)|endometrium(3)|kidney(1)|lung(7)|ovary(3)	16		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Prostate(461;0.00955)|Ovarian(174;0.0129)		all cancers(79;4.43e-43)	Streptokinase(DB00086)	GATGGCAAGTAAAATGGATAC	0.413																																					p.S406fs		Atlas-INDEL	.											.	F2R	58	.	0			c.1218delT						.						81	86	85					5																	76029269		2203	4300	6503	SO:0001589	frameshift_variant	2149	exon2			.	M62424	CCDS4032.1	5q13	2012-08-08			ENSG00000181104	ENSG00000181104		"GPCR / Class A : Protease activated receptors"	3537	protein-coding gene	gene with protein product		187930				8395910	Standard	NM_001992		Approved	TR, CF2R, PAR1, PAR-1	uc003ken.4	P25116	OTTHUMG00000131299	ENST00000319211.4:c.1219delA	chr5.hg19:g.76029269delA	ENSP00000321326:p.Lys407fs	325.0	0.0		202.0	13.0	NM_001992	Q53XV0|Q96RF7|Q9BUN4	Frame_Shift_Del	DEL	ENST00000319211.4	hg19	CCDS4032.1																																																																																			.	.		0.413	F2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254068.2			-	76029269	A	-	76029269	7	5	282	1	0	1	0	1	0	0	0	0	5345	363	13	0	1225	0	F2R	5	76029269	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1030688	76029269	104885991	408	40642										
ZFYVE16	9765	hgsc.bcm.edu	37	chr5	79769620	79769620	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	attacaaggatttccaagtgAaaaaataaaactggaagcag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:79769620delA	ENST00000338008.5	+	16	4415	c.4235delA	c.(4234-4236)gaafs	p.E1412fs	ZFYVE16_ENST00000510158.1_Frame_Shift_Del_p.E1412fs|ZFYVE16_ENST00000505560.1_Frame_Shift_Del_p.E1412fs	NM_001284236.1|NM_014733.3	NP_001271165.1|NP_055548	Q7Z3T8	ZFY16_HUMAN	zinc finger, FYVE domain containing 16	1412					BMP signaling pathway (GO:0030509)|endosomal transport (GO:0016197)|protein targeting to lysosome (GO:0006622)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)|vesicle organization (GO:0016050)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|early endosome membrane (GO:0031901)|intracellular membrane-bounded organelle (GO:0043231)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein transporter activity (GO:0008565)			breast(4)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|liver(1)|lung(6)|ovary(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.6e-46)|Epithelial(54;2.02e-41)|all cancers(79;5.05e-36)		TTTCCAAGTGAAAAAATAAAA	0.313																																					p.E1412fs	Melanoma(150;1452 1854 16018 17851 37292)	Atlas-INDEL	.											.	ZFYVE16	100	.	0			c.4234delG						.						60	67	65					5																	79769620		2203	4300	6503	SO:0001589	frameshift_variant	9765	exon17			.	AB002303	CCDS4050.1	5q14.1	2012-09-20			ENSG00000039319	ENSG00000039319		"Zinc fingers, FYVE domain containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	20756	protein-coding gene	gene with protein product	"endofin", "protein phosphatase 1, regulatory subunit 69"	608880				11546807	Standard	NM_014733		Approved	KIAA0305, PPP1R69	uc003kgq.4	Q7Z3T8	OTTHUMG00000108178	ENST00000338008.5:c.4235delA	chr5.hg19:g.79769620delA	ENSP00000337159:p.Glu1412fs	206.0	0.0		167.0	12.0	NM_001105251	O15023|Q5H9U2|Q7LAU7|Q86T69|Q8N5L3|Q8NEK3	Frame_Shift_Del	DEL	ENST00000338008.5	hg19	CCDS4050.1																																																																																			.	.		0.313	ZFYVE16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226982.2	NM_014733		-	79769620	A	-	79769620	7	5	282	1	0	1	0	1	0	0	0	0	17679	246	9	0	4293	0	ZFYVE16	5	79769620	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	3740351	79769620	101145640	409	40643										
ACOT12	134526	hgsc.bcm.edu	37	chr5	80640756	80640756	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acgtgatgagattttccttaTcatcagcagcattgtaaatg	8	7	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:80640756T>C	ENST00000307624.3	-	8	906	c.878A>G	c.(877-879)gAt>gGt	p.D293G	ACOT12_ENST00000508234.1_5'Flank	NM_130767.2	NP_570123.1	Q8WYK0	ACO12_HUMAN	acyl-CoA thioesterase 12	293	Acyl coenzyme A hydrolase 2.				acetyl-CoA metabolic process (GO:0006084)|acyl-CoA metabolic process (GO:0006637)|fatty acid metabolic process (GO:0006631)|pyruvate metabolic process (GO:0006090)	cytosol (GO:0005829)	acetyl-CoA hydrolase activity (GO:0003986)|ATP binding (GO:0005524)|carboxylic ester hydrolase activity (GO:0052689)|lipid binding (GO:0008289)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)	23		Lung NSC(167;0.0176)|all_lung(232;0.0205)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;1.37e-45)|Epithelial(54;1.25e-39)|all cancers(79;5.01e-34)		ATTTTCCTTATCATCAGCAGC	0.478																																					p.D293G		Atlas-SNP	.											.	ACOT12	57	.	0			c.A878G						.						137	133	134					5																	80640756		2203	4300	6503	SO:0001583	missense	134526	exon8			TCCTTATCATCAG	AB078619	CCDS4055.1	5q14.1	2011-09-13			ENSG00000172497	ENSG00000172497		"Acyl CoA thioesterases", "StAR-related lipid transfer (START) domain containing"	24436	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 15"	614315				16103133, 16940157	Standard	NM_130767		Approved	Cach, THEAL, STARD15	uc003khl.4	Q8WYK0	OTTHUMG00000131305	ENST00000307624.3:c.878A>G	chr5.hg19:g.80640756T>C	ENSP00000303246:p.Asp293Gly	167.0	0.0		101.0	5.0	NM_130767	B3KVK9|Q5FWE9	Missense_Mutation	SNP	ENST00000307624.3	hg19	CCDS4055.1	.	.	.	.	.	.	.	.	.	.	T	8.370	0.835206	0.16820	.	.	ENSG00000172497	ENST00000307624	T	0.32515	1.45	5.46	4.27	0.50696	.	0.734758	0.13829	N	0.359880	T	0.29945	0.0749	M	0.67700	2.07	0.09310	N	0.999997	B	0.16396	0.017	B	0.13407	0.009	T	0.25047	-1.0143	10	0.34782	T	0.22	-0.9437	6.4229	0.21754	0.0:0.0809:0.1599:0.7592	.	293	Q8WYK0	ACO12_HUMAN	G	293	ENSP00000303246:D293G	ENSP00000303246:D293G	D	-	2	0	ACOT12	80676512	0.193000	0.23313	0.023000	0.16930	0.756000	0.42949	2.254000	0.43214	0.882000	0.36016	0.418000	0.28097	GAT	.	.		0.478	ACOT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254074.1	NM_130767		C	80640756	T	C	80640756	3	2	282	1	0	0	0	0	1	0	0	0	150	1435	50	2	821	2	ACOT12	5	80640756	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	871136	80640756	100274504	410	40644										
ATP6AP1L	92270	hgsc.bcm.edu	37	chr5	81613888	81613888	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcctcctccttctcgccagcTtttctgatcggcctggcaat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:81613888delT	ENST00000380167.4	+	10	1769	c.444delT	c.(442-444)gctfs	p.A148fs	ATP6AP1L_ENST00000508366.1_Intron|ATP6AP1L_ENST00000439350.1_Frame_Shift_Del_p.A148fs			Q52LC2	VAS1L_HUMAN	ATPase, H+ transporting, lysosomal accessory protein 1-like	148					ATP hydrolysis coupled proton transport (GO:0015991)	integral component of membrane (GO:0016021)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	12						TCTCGCCAGCTTTTCTGATCG	0.537																																					p.A148fs		Atlas-INDEL	.											.	ATP6AP1L	29	.	0			c.443delC						.						96	84	88					5																	81613888		2203	4300	6503	SO:0001589	frameshift_variant	92270	exon4			.	AK022625	CCDS34196.1	5q14.2	2010-03-10				ENSG00000205464			28091	protein-coding gene	gene with protein product							Standard	XR_112744		Approved		uc003khw.3	Q52LC2		ENST00000380167.4:c.444delT	chr5.hg19:g.81613888delT	ENSP00000369513:p.Ala148fs	236.0	0.0		159.0	10.0	NM_001017971		Frame_Shift_Del	DEL	ENST00000380167.4	hg19	CCDS34196.1																																																																																			.	.		0.537	ATP6AP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369562.3	NM_001017971		-	81613888	T	-	81613888	7	5	282	1	0	1	0	1	0	0	0	0	1166	1596	56	0	458	0	ATP6AP1L	5	81613888	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	973132	81613888	99301372	411	40645										
MCTP1	79772	hgsc.bcm.edu	37	chr5	94353090	94353090	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cctcctcgatctcgagcagcTaaactttgaccccttcttaa	5	15	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:94353090T>C	ENST00000515393.1	-	2	818	c.819A>G	c.(817-819)ttA>ttG	p.L273L	MCTP1_ENST00000429576.2_Silent_p.L52L|MCTP1_ENST00000312216.8_Silent_p.L52L|MCTP1_ENST00000505208.1_Silent_p.L52L	NM_024717.4	NP_078993.4	Q6DN14	MCTP1_HUMAN	multiple C2 domains, transmembrane 1	273	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(13)|liver(2)|lung(13)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	41		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)		CTCGAGCAGCTAAACTTTGAC	0.418																																					p.L273L		Atlas-SNP	.											.	MCTP1	110	.	0			c.A819G						.						155	145	148					5																	94353090		2203	4300	6503	SO:0001819	synonymous_variant	79772	exon2			AGCAGCTAAACTT		CCDS34203.1, CCDS47247.1, CCDS75275.1	5q15	2008-02-05			ENSG00000175471	ENSG00000175471			26183	protein-coding gene	gene with protein product						15528213	Standard	XM_005272082		Approved	FLJ22344	uc003kkx.2	Q6DN14	OTTHUMG00000162742	ENST00000515393.1:c.819A>G	chr5.hg19:g.94353090T>C		107.0	0.0		109.0	5.0	NM_024717	Q6DN13|Q8N2W1|Q8NBA2|Q96LX0|Q9H6E8	Silent	SNP	ENST00000515393.1	hg19	CCDS34203.1	.	.	.	.	.	.	.	.	.	.	T	10.03	1.237812	0.22711	.	.	ENSG00000175471	ENST00000503301	.	.	.	5.79	5.79	0.91817	.	.	.	.	.	T	0.70395	0.3219	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.69544	-0.5117	4	.	.	.	-8.8561	13.651	0.62310	0.0:0.0:0.0:1.0	.	.	.	.	G	82	.	.	S	-	1	0	MCTP1	94378846	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.437000	0.59955	2.213000	0.71641	0.533000	0.62120	AGC	.	.		0.418	MCTP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370280.3	NM_024717		C	94353090	T	C	94353090	2	2	282	1	0	0	0	0	0	0	0	1	9409	1519	53	2		2	MCTP1	5	94353090	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	12739202	94353090	86562170	412	40646										
RHOBTB3	22836	hgsc.bcm.edu	37	chr5	95099309	95099309	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gagaaagttaaatgcattttAaaaacaccaggaaaggtaag					rs539979625		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:95099309delA	ENST00000379982.3	+	7	1654	c.1146delA	c.(1144-1146)ttafs	p.L382fs	GLRX_ENST00000508780.1_Intron	NM_014899.3	NP_055714.3	O94955	RHBT3_HUMAN	Rho-related BTB domain containing 3	382					ATP catabolic process (GO:0006200)|retrograde transport, endosome to Golgi (GO:0042147)|small GTPase mediated signal transduction (GO:0007264)	Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|GTP binding (GO:0005525)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|skin(1)	16		all_cancers(142;2.58e-06)|all_epithelial(76;4.19e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0164)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.79e-16)		AATGCATTTTAAAAACACCAG	0.328																																					p.L382X		Atlas-INDEL	.											.	RHOBTB3	43	.	0			c.1145delT						.						85	88	87					5																	95099309		2203	4299	6502	SO:0001589	frameshift_variant	22836	exon7			.	AB020685	CCDS4077.1	5q15	2014-05-09			ENSG00000164292	ENSG00000164292		"BTB/POZ domain containing"	18757	protein-coding gene	gene with protein product		607353				11222756, 17035353	Standard	NM_014899		Approved	KIAA0878	uc003klm.3	O94955	OTTHUMG00000121171	ENST00000379982.3:c.1146delA	chr5.hg19:g.95099309delA	ENSP00000369318:p.Leu382fs	219.0	0.0		172.0	11.0	NM_014899	A0PJA4|A8K1W9|Q8IW06	Frame_Shift_Del	DEL	ENST00000379982.3	hg19	CCDS4077.1																																																																																			.	.		0.328	RHOBTB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241658.1	NM_014899		-	95099309	A	-	95099309	7	5	282	1	0	1	0	1	0	0	0	0	13350	359	13	0	1172	0	RHOBTB3	5	95099309	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	746219	95099309	85815951	413	40647										
ERAP1	51752	hgsc.bcm.edu	37	chr5	96139154	96139154	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgcttttgtaaaatccgtggAaagtctccgaaagattgcca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:96139154delA	ENST00000443439.2	-	2	542	c.476delT	c.(475-477)ttcfs	p.F159fs	CTD-2260A17.3_ENST00000606346.1_RNA|CTD-2260A17.3_ENST00000606656.1_RNA|ERAP1_ENST00000296754.3_Frame_Shift_Del_p.F159fs	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	159					angiogenesis (GO:0001525)|antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|fat cell differentiation (GO:0045444)|membrane protein ectodomain proteolysis (GO:0006509)|positive regulation of angiogenesis (GO:0045766)|regulation of blood pressure (GO:0008217)|regulation of innate immune response (GO:0045088)|response to bacterium (GO:0009617)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|interleukin-1, Type II receptor binding (GO:0005151)|interleukin-6 receptor binding (GO:0005138)|metalloexopeptidase activity (GO:0008235)|zinc ion binding (GO:0008270)			endometrium(7)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|stomach(2)	19		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)		AAATCCGTGGAAAGTCTCCGA	0.483																																					p.F159fs		Atlas-INDEL	.											.	ERAP1	59	.	0			c.477delC						.						76	81	79					5																	96139154		2203	4300	6503	SO:0001589	frameshift_variant	51752	exon2			.	AB011097	CCDS4085.1, CCDS47250.1	5q15	2014-04-07			ENSG00000164307	ENSG00000164307			18173	protein-coding gene	gene with protein product	"aminopeptidase regulator of TNFR1 shedding", "adipocyte-derived leucine aminopeptidase", "puromycin-insensitive leucyl-specific aminopeptidase"	606832				10220586, 12189246, 16286653	Standard	NM_001198541		Approved	ARTS-1, A-LAP, PILS-AP, KIAA0525, ERAAP1	uc003kml.3	Q9NZ08	OTTHUMG00000128721	ENST00000443439.2:c.476delT	chr5.hg19:g.96139154delA	ENSP00000406304:p.Phe159fs	227.0	0.0		173.0	11.0	NM_001198541	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Frame_Shift_Del	DEL	ENST00000443439.2	hg19	CCDS47250.1																																																																																			.	.		0.483	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442		-	96139154	A	-	96139154	7	5	282	1	0	1	0	1	0	0	0	0	5205	246	9	0	2454	0	ERAP1	5	96139154	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1039845	96139154	84776106	414	40648										
LNPEP	4012	hgsc.bcm.edu	37	chr5	96341897	96341897	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttatacaacaagagagattcTttttaaatatgaagcctgaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:96341897delT	ENST00000231368.5	+	10	2598	c.1906delT	c.(1906-1908)tttfs	p.F636fs	LNPEP_ENST00000395770.3_Frame_Shift_Del_p.F622fs	NM_005575.2	NP_005566.2	Q9UIQ6	LCAP_HUMAN	leucyl/cystinyl aminopeptidase	636					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-cell signaling (GO:0007267)|female pregnancy (GO:0007565)|membrane organization (GO:0061024)|protein catabolic process (GO:0030163)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|early endosome lumen (GO:0031905)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	34		all_cancers(142;7e-07)|all_epithelial(76;9.52e-10)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0269)|Breast(839;0.244)		COAD - Colon adenocarcinoma(37;0.072)		AGAGAGATTCTTTTTAAATAT	0.358																																					p.F635fs		Atlas-INDEL	.											LNPEP,caecum,carcinoma,0,1	LNPEP	80	.	0			c.1905delC						.						73	80	78					5																	96341897		2202	4296	6498	SO:0001589	frameshift_variant	4012	exon10			.	D50810	CCDS4087.1, CCDS43346.1	5q15	2011-07-25			ENSG00000113441	ENSG00000113441	3.4.11.3		6656	protein-coding gene	gene with protein product	"cystinyl aminopeptidase", "placental leucine aminopeptidase"	151300				8550619	Standard	NM_175920		Approved	CAP, PLAP, P-LAP	uc003kmw.1	Q9UIQ6	OTTHUMG00000128719	ENST00000231368.5:c.1906delT	chr5.hg19:g.96341897delT	ENSP00000231368:p.Phe636fs	188.0	0.0		165.0	10.0	NM_005575	O00769|Q15145|Q59H76|Q9TNQ2|Q9TNQ3|Q9UIQ7	Frame_Shift_Del	DEL	ENST00000231368.5	hg19	CCDS4087.1																																																																																			.	.		0.358	LNPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250624.1	NM_005575		-	96341897	T	-	96341897	7	5	282	1	0	1	0	1	0	0	0	0	8873	1609	56	0	1944	0	LNPEP	5	96341897	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	202743	96341897	84573363	415	40649										
CHD1	1105	hgsc.bcm.edu	37	chr5	98232103	98232103	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaatgagatcgtctgtattgTttttccaaggcccatttcat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:98232103delT	ENST00000284049.3	-	11	1686	c.1537delA	c.(1537-1539)acafs	p.T513fs		NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	513	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	49		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	GTCTGTATTGTTTTTCCAAGG	0.338																																					p.T513fs		Atlas-INDEL	.											.	CHD1	137	.	0			c.1538delC						.						81	86	84					5																	98232103		2203	4300	6503	SO:0001589	frameshift_variant	1105	exon11			.	AF006513	CCDS34204.1	5q15-q21	2008-07-18			ENSG00000153922	ENSG00000153922			1915	protein-coding gene	gene with protein product		602118				8460153, 9326634	Standard	XM_005271866		Approved		uc003knf.3	O14646	OTTHUMG00000162744	ENST00000284049.3:c.1537delA	chr5.hg19:g.98232103delT	ENSP00000284049:p.Thr513fs	206.0	0.0		167.0	11.0	NM_001270	Q17RZ3	Frame_Shift_Del	DEL	ENST00000284049.3	hg19	CCDS34204.1																																																																																			.	.		0.338	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270		-	98232103	T	-	98232103	7	5	282	1	0	1	0	1	0	0	0	0	3325	1725	60	0	3695	0	CHD1	5	98232103	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1890206	98232103	82683157	416	40650										
SLCO4C1	353189	hgsc.bcm.edu	37	chr5	101595975	101595975	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atttcacatctgcattactaTtactctgatgagcctgggaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:101595975delT	ENST00000310954.6	-	6	1356	c.1070delA	c.(1069-1071)aatfs	p.N357fs		NM_180991.4	NP_851322.3			solute carrier organic anion transporter family, member 4C1											breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	50		all_cancers(142;1.86e-08)|all_epithelial(76;5.24e-12)|Prostate(80;0.00124)|Colorectal(57;0.00332)|Ovarian(225;0.024)|Lung NSC(167;0.0402)|all_lung(232;0.0486)		Epithelial(69;4.07e-14)|COAD - Colon adenocarcinoma(37;0.00986)		TGCATTACTATTACTCTGATG	0.274																																					p.N357fs		Atlas-INDEL	.											.	SLCO4C1	113	.	0			c.1071delT						.						45	45	45					5																	101595975		2200	4296	6496	SO:0001589	frameshift_variant	353189	exon6			.	AY273896	CCDS34205.1	5q21	2013-05-22	2003-11-25		ENSG00000173930	ENSG00000173930		"Solute carriers"	23612	protein-coding gene	gene with protein product		609013					Standard	NM_180991		Approved	SLC21A20, OATP4C1, OATPX, OATP-H	uc003knm.3	Q6ZQN7	OTTHUMG00000162757	ENST00000310954.6:c.1070delA	chr5.hg19:g.101595975delT	ENSP00000309741:p.Asn357fs	242.0	0.0		180.0	11.0	NM_180991		Frame_Shift_Del	DEL	ENST00000310954.6	hg19	CCDS34205.1																																																																																			.	.		0.274	SLCO4C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370332.1	NM_180991		-	101595975	T	-	101595975	7	5	282	1	0	1	0	1	0	0	0	0	14745	1493	52	0	1136	0	SLCO4C1	5	101595975	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3363872	101595975	79319285	417	40651										
NUDT12	83594	hgsc.bcm.edu	37	chr5	102895020	102895020	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtagtgttttgctaaaataaTtttcacattcttccacttca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:102895020delT	ENST00000230792.2	-	3	452	c.356delA	c.(355-357)aatfs	p.N119fs	NUDT12_ENST00000507423.1_Frame_Shift_Del_p.N101fs	NM_031438.2	NP_113626.1	Q9BQG2	NUD12_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 12	119					NAD catabolic process (GO:0019677)|NADP catabolic process (GO:0006742)	nucleus (GO:0005634)|peroxisome (GO:0005777)	metal ion binding (GO:0046872)|NAD+ diphosphatase activity (GO:0000210)|NADH pyrophosphatase activity (GO:0035529)			endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|urinary_tract(1)	12		all_cancers(142;6.38e-08)|all_epithelial(76;1.99e-10)|Prostate(80;0.0138)|Lung NSC(167;0.0212)|Colorectal(57;0.0247)|all_lung(232;0.0283)|Ovarian(225;0.0423)		Epithelial(69;9.3e-13)|COAD - Colon adenocarcinoma(37;0.0221)		GCTAAAATAATTTTCACATTC	0.378																																					p.N119fs		Atlas-INDEL	.											.	NUDT12	27	.	0			c.357delT						.						61	65	63					5																	102895020		2202	4299	6501	SO:0001589	frameshift_variant	83594	exon3			.	AL136592	CCDS4096.1, CCDS75284.1	5q15	2013-01-10			ENSG00000112874	ENSG00000112874		"Nudix motif containing", "Ankyrin repeat domain containing"	18826	protein-coding gene	gene with protein product	"nucleoside diphosphate linked moiety X-type motif 12"	609232				11230166	Standard	XM_005272095		Approved	DKFZP761I172	uc003koi.3	Q9BQG2	OTTHUMG00000128739	ENST00000230792.2:c.356delA	chr5.hg19:g.102895020delT	ENSP00000230792:p.Asn119fs	172.0	0.0		164.0	10.0	NM_031438	B3KUW2|Q8TAL7	Frame_Shift_Del	DEL	ENST00000230792.2	hg19	CCDS4096.1																																																																																			.	.		0.378	NUDT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250650.1	NM_031438		-	102895020	T	-	102895020	7	5	282	1	0	1	0	1	0	0	0	0	10737	1493	52	0	1052	0	NUDT12	5	102895020	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1299045	102895020	78020240	418	40652										
CAMK4	814	hgsc.bcm.edu	37	chr5	110820086	110820086	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aagactgtggaggaggcagcAgctcccagagaagggcaagg	17	8	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:110820086A>G	ENST00000282356.4	+	11	1742	c.1344A>G	c.(1342-1344)gcA>gcG	p.A448A	CAMK4_ENST00000512890.1_3'UTR|CAMK4_ENST00000512453.1_Silent_p.A448A	NM_001744.4	NP_001735.1	Q16566	KCC4_HUMAN	calcium/calmodulin-dependent protein kinase IV	448					activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|long-term memory (GO:0007616)|myeloid dendritic cell differentiation (GO:0043011)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleocytoplasmic transport (GO:0006913)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of osteoclast differentiation (GO:0045670)|regulation of T cell differentiation in thymus (GO:0033081)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(3)|prostate(2)|skin(1)|urinary_tract(1)	30		all_cancers(142;1.49e-05)|all_epithelial(76;1.82e-07)|Prostate(80;0.00964)|all_lung(232;0.0181)|Lung NSC(167;0.0298)|Ovarian(225;0.0446)|Colorectal(57;0.0478)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;3.79e-08)|Epithelial(69;5.29e-08)|all cancers(49;1.1e-05)|COAD - Colon adenocarcinoma(37;0.109)		AGGAGGCAGCAGCTCCCAGAG	0.532																																					p.A448A		Atlas-SNP	.											.	CAMK4	77	.	0			c.A1344G						.						53	53	53					5																	110820086		2202	4300	6502	SO:0001819	synonymous_variant	814	exon11			GGCAGCAGCTCCC	D30742	CCDS4103.1	5q22.1	2012-09-20			ENSG00000152495	ENSG00000152495	2.7.11.17		1464	protein-coding gene	gene with protein product	"brain Ca++-calmodulin-dependent protein kinase type IV", "calcium/calmodulin-dependent protein kinase type IV catalytic chain", "CAM kinase IV", "CAM kinase- GR"	114080				2536634	Standard	NM_001744		Approved	CaMK-GR	uc003kpf.3	Q16566	OTTHUMG00000128792	ENST00000282356.4:c.1344A>G	chr5.hg19:g.110820086A>G		107.0	0.0		80.0	4.0	NM_001744	D3DSZ7	Silent	SNP	ENST00000282356.4	hg19	CCDS4103.1																																																																																			.	.		0.532	CAMK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250719.2	NM_001744		G	110820086	A	G	110820086	2	3	282	1	0	0	0	0	0	0	0	1	2607	175	7	2		2	CAMK4	5	110820086	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	7925066	110820086	70095174	419	40653										
PPIC	5480	hgsc.bcm.edu	37	chr5	122364469	122364469	+	Splice_Site	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggaaaaatgcaaagacgttaCccccagtgccatctccagtg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:122364469delC	ENST00000306442.4	-	3	441		c.e3+1			NM_000943.4	NP_000934.1	P45877	PPIC_HUMAN	peptidylprolyl isomerase C (cyclophilin C)						protein folding (GO:0006457)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	6		all_cancers(142;0.0168)|Prostate(80;0.0322)|Lung NSC(810;0.102)|all_lung(232;0.163)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	OV - Ovarian serous cystadenocarcinoma(64;0.000331)|Epithelial(69;0.000553)|all cancers(49;0.00505)	L-Proline(DB00172)	AAAGACGTTACCCCCAGTGCC	0.413																																					.	Ovarian(99;690 1502 20765 45543 49568)	Atlas-INDEL	.											.	PPIC	18	.	0			c.325+2G>-						.						135	107	116					5																	122364469		2203	4300	6503	SO:0001630	splice_region_variant	5480	exon4			.	S71018	CCDS4133.1	5q23.2	2008-02-05			ENSG00000168938	ENSG00000168938	5.2.1.8		9256	protein-coding gene	gene with protein product		123842				1383094, 8031755	Standard	NM_000943		Approved	CYPC	uc003kth.3	P45877	OTTHUMG00000128921	ENST00000306442.4:c.325+1G>-	chr5.hg19:g.122364469delC		211.0	0.0		164.0	10.0	NM_000943	A4LBB5	Splice_Site	DEL	ENST00000306442.4	hg19	CCDS4133.1																																																																																			.	.		0.413	PPIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250898.2	NM_000943	Intron	-	122364469	C	-	122364469	8	5	282	1	0	1	0	1	0	0	1	0	12332	521	18	0	324	0	PPIC	5	122364469	Splice_Site	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	11544383	122364469	58550791	420	40654										
MEGF10	84466	hgsc.bcm.edu	37	chr5	126792818	126792818	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aatatgtccttggttatcacAgaacctacagtgagtgttgt	9	7	1	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:126792818A>G	ENST00000274473.6	+	26	3499		c.e26-1		MEGF10_ENST00000503335.2_Splice_Site	NM_032446.2	NP_115822.1	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10						homotypic cell-cell adhesion (GO:0034109)|muscle cell development (GO:0055001)|recognition of apoptotic cell (GO:0043654)|regulation of muscle cell differentiation (GO:0051147)|regulation of skeletal muscle tissue development (GO:0048641)|skeletal muscle satellite cell activation (GO:0014719)|skeletal muscle satellite cell differentiation (GO:0014816)|skeletal muscle satellite cell proliferation (GO:0014841)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(28)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	68		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)		TGGTTATCACAGAACCTACAG	0.383																																					.		Atlas-SNP	.											.	MEGF10	152	.	0			c.3233-2A>G						.						95	84	88					5																	126792818		2203	4300	6503	SO:0001630	splice_region_variant	84466	exon25			TATCACAGAACCT	AK021631	CCDS4142.1	5q33	2008-02-05			ENSG00000145794	ENSG00000145794			29634	protein-coding gene	gene with protein product		612453				11347906	Standard	NM_032446		Approved	KIAA1780	uc003kui.4	Q96KG7	OTTHUMG00000128984	ENST00000274473.6:c.3233-1A>G	chr5.hg19:g.126792818A>G		156.0	0.0		91.0	4.0	NM_001256545	Q68DE5|Q8WUL3	Splice_Site	SNP	ENST00000274473.6	hg19	CCDS4142.1	.	.	.	.	.	.	.	.	.	.	A	19.52	3.843575	0.71488	.	.	ENSG00000145794	ENST00000503335;ENST00000274473	.	.	.	5.77	5.77	0.91146	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0879	0.81070	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MEGF10	126820717	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	8.725000	0.91468	2.197000	0.70478	0.455000	0.32223	.	.	.		0.383	MEGF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250973.2	NM_032446	Intron	G	126792818	A	G	126792818	5	3	282	1	0	0	0	0	0	0	1	0	9469	202	7	2	3325	2	MEGF10	5	126792818	Splice_Site	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	4428349	126792818	54122442	421	40655										
ADAMTS19	171019	hgsc.bcm.edu	37	chr5	128864241	128864241	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atatattgggcatcatggagAaaaaatgctagagagttttt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:128864241delA	ENST00000274487.4	+	6	1326	c.1181delA	c.(1180-1182)gaafs	p.E394fs	CTC-575N7.1_ENST00000503616.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	394	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		CATCATGGAGAAAAAATGCTA	0.353																																					p.E394fs		Atlas-INDEL	.											.	ADAMTS19	216	.	0			c.1180delG						.						67	71	70					5																	128864241		2203	4300	6503	SO:0001589	frameshift_variant	171019	exon6			.	AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"ADAM metallopeptidases with thrombospondin type 1 motif"	17111	protein-coding gene	gene with protein product		607513	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.1181delA	chr5.hg19:g.128864241delA	ENSP00000274487:p.Glu394fs	234.0	0.0		179.0	11.0	NM_133638		Frame_Shift_Del	DEL	ENST00000274487.4	hg19	CCDS4146.1																																																																																			.	.		0.353	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638		-	128864241	A	-	128864241	7	5	282	1	0	1	0	1	0	0	0	0	264	246	9	0	1203	0	ADAMTS19	5	128864241	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2071423	128864241	52051019	422	40656										
RAPGEF6	51735	hgsc.bcm.edu	37	chr5	130766663	130766663	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggtgctctccaatactctctGtttaactgtcccatagtttg	7	11	2	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:130766663G>C	ENST00000509018.1	-	26	4559	c.4354C>G	c.(4354-4356)Cag>Gag	p.Q1452E	RAPGEF6_ENST00000307984.5_Missense_Mutation_p.Q1465E|RAPGEF6_ENST00000296859.6_Missense_Mutation_p.Q1460E|RAPGEF6_ENST00000507093.1_Missense_Mutation_p.Q1460E|CTC-432M15.3_ENST00000514667.1_Missense_Mutation_p.Q1502E	NM_001164386.1|NM_016340.5	NP_001157858.1|NP_057424.3	Q8TEU7	RPGF6_HUMAN	Rap guanine nucleotide exchange factor (GEF) 6	1452			Q -> R (in dbSNP:rs1291602). {ECO:0000269|PubMed:11524421, ECO:0000269|PubMed:12581858, ECO:0000269|Ref.2}.		positive regulation of GTPase activity (GO:0043547)|Ras protein signal transduction (GO:0007265)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP-dependent protein binding (GO:0030742)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)	p.Q1452*(1)|p.Q1465*(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		AATACTCTCTGTTTAACTGTC	0.463																																					p.Q1465E	Melanoma(168;435 1955 13113 13877 23213)	Atlas-SNP	.											RAPGEF6_ENST00000509018,NS,carcinoma,0,2	RAPGEF6	361	.	2	Substitution - Nonsense(2)	prostate(2)	c.C4393G						.						145	151	149					5																	130766663		2203	4300	6503	SO:0001583	missense	51735	exon28			CTCTCTGTTTAAC	AF117947	CCDS34225.1, CCDS54897.1, CCDS54898.1, CCDS54899.1, CCDS54900.1	5q31.1	2008-02-05	2004-03-01	2004-03-02	ENSG00000158987	ENSG00000158987			20655	protein-coding gene	gene with protein product		610499	"PDZ domain containing guanine nucleotide exchange factor (GEF) 2"	PDZGEF2		11524421, 12095257	Standard	NM_016340		Approved	RA-GEF-2, PDZ-GEF2	uc010jdi.2	Q8TEU7	OTTHUMG00000162683	ENST00000509018.1:c.4354C>G	chr5.hg19:g.130766663G>C	ENSP00000421684:p.Gln1452Glu	270.0	0.0		197.0	0.0	NM_001164387	A3KN82|A5PLL6|B7ZML2|E9PDV7|Q8NI21|Q8TEU6|Q96PC1	Missense_Mutation	SNP	ENST00000509018.1	hg19	CCDS34225.1	.	.	.	.	.	.	.	.	.	.	G	13.17	2.158025	0.38119	.	.	ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000217128	ENST00000509018;ENST00000307984;ENST00000507093;ENST00000296859;ENST00000358714;ENST00000514667	T;T;T;T;T	0.23754	1.99;1.89;1.89;1.99;2.07	5.22	2.19	0.27852	.	0.112278	0.64402	D	0.000013	T	0.14700	0.0355	N	0.08118	0	0.80722	D	1	B;B;B;B;B	0.06786	0.001;0.0;0.0;0.0;0.0	B;B;B;B;B	0.10450	0.005;0.0;0.0;0.001;0.0	T	0.08186	-1.0734	10	0.72032	D	0.01	.	14.5329	0.67939	0.0:0.0:0.6233:0.3767	.	1460;1460;1502;1465;1452	A3KN82;B7ZML2;E9PCH4;Q8TEU7-3;Q8TEU7	.;.;.;.;RPGF6_HUMAN	E	1452;1465;1460;1460;1465;1502	ENSP00000421684:Q1452E;ENSP00000309298:Q1465E;ENSP00000426081:Q1460E;ENSP00000296859:Q1460E;ENSP00000426948:Q1502E	ENSP00000426948:Q1502E	Q	-	1	0	RAPGEF6;FNIP1	130794562	1.000000	0.71417	0.995000	0.50966	0.850000	0.48378	4.611000	0.61162	0.654000	0.30846	0.655000	0.94253	CAG	.	.		0.463	RAPGEF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370059.1	NM_016340		C	130766663	G	C	130766663	3	2	282	1	0	0	0	0	1	0	0	0	13063	1386	48	4	463	4	RAPGEF6	5	130766663	Missense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1902422	130766663	50148597	423	40657										
RAD50	10111	hgsc.bcm.edu	37	chr5	131977933	131977933	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtaatcactcatgatgaagaTtttgtggagcttttaggacg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:131977933delT	ENST00000265335.6	+	25	4203	c.3816delT	c.(3814-3816)gatfs	p.D1272fs	AC004041.2_ENST00000457489.1_RNA|AC004041.2_ENST00000435042.1_RNA|RAD50_ENST00000378823.3_Frame_Shift_Del_p.D1133fs|AC004041.2_ENST00000458509.1_RNA|AC004041.2_ENST00000417516.1_RNA			Q92878	RAD50_HUMAN	RAD50 homolog (S. cerevisiae)	1272					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|reciprocal meiotic recombination (GO:0007131)|regulation of mitotic recombination (GO:0000019)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	membrane (GO:0016020)|Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|nuclease activity (GO:0004518)|protein binding, bridging (GO:0030674)|zinc ion binding (GO:0008270)			breast(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		all_cancers(142;0.0368)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			ATGATGAAGATTTTGTGGAGC	0.363								Homologous recombination																													p.D1272fs		Atlas-INDEL	.											.	RAD50	246	.	0			c.3815delA						.						111	111	111					5																	131977933		2203	4300	6503	SO:0001589	frameshift_variant	10111	exon25			.	Z75311	CCDS34233.1	5q23-q31	2008-05-30	2001-11-28		ENSG00000113522	ENSG00000113522			9816	protein-coding gene	gene with protein product		604040	"RAD50 (S. cerevisiae) homolog"			8756642, 9705271	Standard	NM_005732		Approved	hRad50, RAD50-2	uc003kxi.3	Q92878	OTTHUMG00000059613	ENST00000265335.6:c.3816delT	chr5.hg19:g.131977933delT	ENSP00000265335:p.Asp1272fs	270.0	0.0		185.0	12.0	NM_005732	B9EGF5|O43254|Q6GMT7|Q6P5X3|Q9UP86	Frame_Shift_Del	DEL	ENST00000265335.6	hg19	CCDS34233.1																																																																																			.	.		0.363	RAD50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132566.5	NM_005732		-	131977933	T	-	131977933	7	5	282	1	0	1	0	1	0	0	0	0	12999	1490	52	0	3914	0	RAD50	5	131977933	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1211270	131977933	48937327	424	40658										
HSPA4	3308	hgsc.bcm.edu	37	chr5	132432855	132432855	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cataatatttattctcagggTaagatgatcatgcaggataa	8	5	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:132432855T>C	ENST00000304858.2	+	15	2095	c.1806T>C	c.(1804-1806)ggT>ggC	p.G602G		NM_002154.3	NP_002145.3	P34932	HSP74_HUMAN	heat shock 70kDa protein 4	602					chaperone-mediated protein complex assembly (GO:0051131)|protein import into mitochondrial outer membrane (GO:0045040)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|stomach(1)	32			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			ATTCTCAGGGTAAGATGATCA	0.348																																					p.G602G	Colon(114;1299 1588 6063 12302 48757)	Atlas-SNP	.											.	HSPA4	68	.	0			c.T1806C						.						113	112	112					5																	132432855		2203	4300	6503	SO:0001819	synonymous_variant	3308	exon15			TCAGGGTAAGATG	AB023420	CCDS4166.1	5q31.1	2011-09-07	2002-08-29		ENSG00000170606	ENSG00000170606		"Heat shock proteins / HSP70"	5237	protein-coding gene	gene with protein product	"hsp70 RY"	601113	"heat shock 70kD protein 4"			8335910	Standard	NM_002154		Approved	HS24/P52, HSPH2	uc003kyj.3	P34932	OTTHUMG00000129012	ENST00000304858.2:c.1806T>C	chr5.hg19:g.132432855T>C		115.0	0.0		114.0	5.0	NM_002154	O95756|Q2TAL4|Q9BUK9	Silent	SNP	ENST00000304858.2	hg19	CCDS4166.1																																																																																			.	.		0.348	HSPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251011.1	NM_002154, NM_198431		C	132432855	T	C	132432855	2	2	282	1	0	0	0	0	0	0	0	1	7421	1625	57	2		2	HSPA4	5	132432855	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	454922	132432855	48482405	425	40659										
KIF20A	10112	hgsc.bcm.edu	37	chr5	137522908	137522908	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tccaaggccaggtttctgccAaaaagcgccttggtaccaac					rs17234961	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:137522908delA	ENST00000394894.3	+	19	2705	c.2479delA	c.(2479-2481)aaafs	p.K828fs	KIF20A_ENST00000508792.1_Frame_Shift_Del_p.K810fs	NM_005733.2	NP_005724.1	O95235	KI20A_HUMAN	kinesin family member 20A	828	Globular. {ECO:0000255}.				ATP catabolic process (GO:0006200)|cytokinesis (GO:0000910)|metabolic process (GO:0008152)|microtubule bundle formation (GO:0001578)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)|transporter activity (GO:0005215)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|liver(2)|lung(9)|prostate(2)|upper_aerodigestive_tract(1)	27			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			GGTTTCTGCCAAAAAGCGCCT	0.473																																					p.A826fs		Atlas-INDEL	.											.	KIF20A	53	.	0			c.2478delC						.						91	88	89					5																	137522908		2203	4300	6503	SO:0001589	frameshift_variant	10112	exon19			.	AF070672	CCDS4199.1	5q31	2008-02-05	2003-01-13	2003-01-17	ENSG00000112984	ENSG00000112984		"Kinesins"	9787	protein-coding gene	gene with protein product		605664	"RAB6 interacting, kinesin-like (rabkinesin6)"	RAB6KIFL		11416179, 10806357	Standard	NM_005733		Approved		uc003lcj.3	O95235	OTTHUMG00000129195	ENST00000394894.3:c.2479delA	chr5.hg19:g.137522908delA	ENSP00000378356:p.Lys828fs	175.0	0.0		139.0	10.0	NM_005733	B4DL79|D3DQB6	Frame_Shift_Del	DEL	ENST00000394894.3	hg19	CCDS4199.1																																																																																			.	.		0.473	KIF20A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251272.1	NM_005733		-	137522908	A	-	137522908	7	5	282	1	0	1	0	1	0	0	0	0	8295	131	5	0	2549	0	KIF20A	5	137522908	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	5090053	137522908	43392352	426	40660										
MATR3	9782	hgsc.bcm.edu	37	chr5	138657644	138657644	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caatggttgaccattgtttgAaaaaagccctttggtttcag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:138657644delA	ENST00000394805.3	+	10	1995	c.1660delA	c.(1660-1662)aaafs	p.K555fs	MATR3_ENST00000394800.2_Frame_Shift_Del_p.K555fs|MATR3_ENST00000510056.1_Frame_Shift_Del_p.K555fs|MATR3_ENST00000502929.1_Frame_Shift_Del_p.K555fs|MATR3_ENST00000504203.1_Frame_Shift_Del_p.K217fs|MATR3_ENST00000502499.1_Frame_Shift_Del_p.K217fs|MATR3_ENST00000361059.2_Frame_Shift_Del_p.K555fs|MATR3_ENST00000503811.1_Frame_Shift_Del_p.K267fs|MATR3_ENST00000509990.1_Frame_Shift_Del_p.K555fs	NM_001194955.1|NM_018834.5	NP_001181884.1|NP_061322.2	P43243	MATR3_HUMAN	matrin 3	555	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cell death (GO:0008219)	membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|kidney(4)|large_intestine(6)|lung(9)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	29			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CCATTGTTTGAAAAAAGCCCT	0.353																																					p.L553fs		Atlas-INDEL	.											.	MATR3	85	.	0			c.1659delG						.						133	133	133					5																	138657644		2203	4300	6503	SO:0001589	frameshift_variant	9782	exon10			.	M63483	CCDS4210.1, CCDS54908.1, CCDS75316.1	5q31.3	2010-08-12			ENSG00000015479	ENSG00000015479			6912	protein-coding gene	gene with protein product		164015	"myopathy, distal 2"	MPD2		2033075, 19344878	Standard	NM_018834		Approved	KIAA0723, MGC9105, VCPDM	uc003ldx.3	P43243	OTTHUMG00000129229	ENST00000394805.3:c.1660delA	chr5.hg19:g.138657644delA	ENSP00000378284:p.Lys555fs	152.0	0.0		135.0	10.0	NM_018834	B7ZAV5|D3DQC3|Q9UHW0|Q9UQ27	Frame_Shift_Del	DEL	ENST00000394805.3	hg19	CCDS4210.1																																																																																			.	.		0.353	MATR3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251324.2	NM_018834		-	138657644	A	-	138657644	7	5	282	1	0	1	0	1	0	0	0	0	9346	247	9	0	1694	0	MATR3	5	138657644	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1134736	138657644	42257616	427	40661										
ANKHD1	54882	hgsc.bcm.edu	37	chr5	139864753	139864753	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ataatgatcatacagtagtgTcgctggcatgtgcaggaggc	13	7	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:139864753T>C	ENST00000360839.2	+	12	2072	c.1918T>C	c.(1918-1920)Tcg>Ccg	p.S640P	ANKHD1-EIF4EBP3_ENST00000532219.1_Missense_Mutation_p.S640P|ANKHD1_ENST00000297183.6_Missense_Mutation_p.S640P	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	640						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TACAGTAGTGTCGCTGGCATG	0.448																																					p.S640P		Atlas-SNP	.											.	ANKHD1	233	.	0			c.T1918C						.						102	92	95					5																	139864753		2203	4300	6503	SO:0001583	missense	54882	exon12			GTAGTGTCGCTGG	AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503		"Ankyrin repeat domain containing"	24714	protein-coding gene	gene with protein product		610500				10470851, 11230166, 16098192	Standard	NM_017747		Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.1918T>C	chr5.hg19:g.139864753T>C	ENSP00000354085:p.Ser640Pro	166.0	0.0		140.0	8.0	NM_017747	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Missense_Mutation	SNP	ENST00000360839.2	hg19	CCDS4225.1	.	.	.	.	.	.	.	.	.	.	T	28.3	4.908170	0.92107	.	.	ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000254996	ENST00000360839;ENST00000422011;ENST00000297183;ENST00000253810;ENST00000310356;ENST00000235510;ENST00000421134;ENST00000412116;ENST00000532219	T;T;T;T;T	0.65916	-0.01;-0.01;-0.18;-0.18;-0.01	5.17	5.17	0.71159	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.77412	0.4126	M	0.66439	2.03	0.80722	D	1	D;D;D;D	0.76494	0.997;0.999;0.997;0.997	D;D;D;D	0.83275	0.991;0.996;0.995;0.995	T	0.80101	-0.1523	10	0.72032	D	0.01	.	15.2896	0.73857	0.0:0.0:0.0:1.0	.	640;659;640;640	Q8IWZ3-4;E9PDP5;Q8IWZ2;Q8IWZ3	.;.;.;ANKH1_HUMAN	P	640;673;640;640;174;120;659;46;640	ENSP00000354085:S640P;ENSP00000297183:S640P;ENSP00000394489:S659P;ENSP00000405602:S46P;ENSP00000432016:S640P	ENSP00000432016:S640P	S	+	1	0	ANKHD1-EIF4EBP3;ANKHD1	139844937	1.000000	0.71417	0.997000	0.53966	0.958000	0.62258	7.976000	0.88070	2.071000	0.62044	0.379000	0.24179	TCG	.	.		0.448	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747		C	139864753	T	C	139864753	3	2	282	1	0	0	0	0	1	0	0	0	628	1667	58	2	2070	2	ANKHD1	5	139864753	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1207109	139864753	41050507	428	40662										
PCDHA6	56142	hgsc.bcm.edu	37	chr5	140209711	140209711	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtggccaggctccaaaggcgTcatcacgggcgtcggtgggc	17	12	2	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:140209711T>C	ENST00000529310.1	+	1	2149	c.2035T>C	c.(2035-2037)Tca>Cca	p.S679P	PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018909.2|NM_031848.2|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6	679					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(42)|prostate(8)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	89			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCAAAGGCGTCATCACGGGC	0.677																																					p.S679P		Atlas-SNP	.											.	PCDHA6	442	.	0			c.T2035C						.						38	44	42					5																	140209711		2199	4298	6497	SO:0001583	missense	56142	exon1			AAGGCGTCATCAC	AF152484	CCDS47281.1, CCDS47282.1	5q31	2010-11-26			ENSG00000081842	ENSG00000081842		"Cadherins / Protocadherins : Clustered"	8672	other	complex locus constituent	"KIAA0345-like 8"	606312		CNRS2		10380929, 10662547	Standard	NM_018909		Approved	CNR2, CRNR2, PCDH-ALPHA6		Q9UN73	OTTHUMG00000163353	ENST00000529310.1:c.2035T>C	chr5.hg19:g.140209711T>C	ENSP00000433378:p.Ser679Pro	233.0	0.0		133.0	6.0	NM_018909	O75283|Q9NRT8	Missense_Mutation	SNP	ENST00000529310.1	hg19	CCDS47281.1	.	.	.	.	.	.	.	.	.	.	T	8.428	0.847962	0.17034	.	.	ENSG00000081842	ENST00000529310	T	0.52754	0.65	3.98	3.98	0.46160	.	0.268055	0.19503	U	0.112681	T	0.40222	0.1108	L	0.58810	1.83	0.20821	N	0.999844	B;B	0.17667	0.023;0.005	B;B	0.25291	0.059;0.006	T	0.26189	-1.0110	10	0.36615	T	0.2	.	4.3124	0.10977	0.0:0.1066:0.2058:0.6876	.	679;679	Q9UN73-3;Q9UN73	.;PCDA6_HUMAN	P	679	ENSP00000433378:S679P	ENSP00000433378:S679P	S	+	1	0	PCDHA6	140189895	0.059000	0.20769	0.010000	0.14722	0.007000	0.05969	1.420000	0.34804	1.798000	0.52647	0.254000	0.18369	TCA	.	.		0.677	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372829.3	NM_018909		C	140209711	T	C	140209711	3	2	282	1	0	0	0	0	1	0	0	0	11537	1667	58	2	2037	2	PCDHA6	5	140209711	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	344958	140209711	40705549	429	40663										
PCDHB1	29930	hgsc.bcm.edu	37	chr5	140433196	140433196	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agtgatcttcattatacatgTctaccaaaagattaaatata	4	6	3	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:140433196T>C	ENST00000306549.3	+	1	2218	c.2141T>C	c.(2140-2142)gTc>gCc	p.V714A		NM_013340.2	NP_037472.2	Q9Y5F3	PCDB1_HUMAN	protocadherin beta 1	714					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|liver(1)|lung(13)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	53			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ATTATACATGTCTACCAAAAG	0.348																																					p.V714A		Atlas-SNP	.											.	PCDHB1	148	.	0			c.T2141C						.						104	108	106					5																	140433196		2203	4300	6503	SO:0001583	missense	29930	exon1			TACATGTCTACCA	AF152488	CCDS4243.1	5q31	2010-01-26			ENSG00000171815	ENSG00000171815		"Cadherins / Protocadherins : Clustered"	8680	other	protocadherin		606327				10380929	Standard	NM_013340		Approved	PCDH-BETA1	uc003lik.1	Q9Y5F3	OTTHUMG00000129627	ENST00000306549.3:c.2141T>C	chr5.hg19:g.140433196T>C	ENSP00000307234:p.Val714Ala	165.0	0.0		142.0	7.0	NM_013340	Q2M257	Missense_Mutation	SNP	ENST00000306549.3	hg19	CCDS4243.1	.	.	.	.	.	.	.	.	.	.	T	10.88	1.474182	0.26423	.	.	ENSG00000171815	ENST00000306549	T	0.14391	2.51	5.91	5.91	0.95273	.	0.461817	0.17620	N	0.167760	T	0.09024	0.0223	N	0.08118	0	0.20638	N	0.99987	B	0.16396	0.017	B	0.11329	0.006	T	0.26189	-1.0110	10	0.87932	D	0	.	13.7272	0.62765	0.0:0.0:0.0:1.0	.	714	Q9Y5F3	PCDB1_HUMAN	A	714	ENSP00000307234:V714A	ENSP00000307234:V714A	V	+	2	0	PCDHB1	140413380	0.922000	0.31269	0.996000	0.52242	0.876000	0.50452	2.997000	0.49457	2.269000	0.75478	0.533000	0.62120	GTC	.	.		0.348	PCDHB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251822.2	NM_013340		C	140433196	T	C	140433196	3	2	282	1	0	0	0	0	1	0	0	0	11543	1667	58	2	2143	2	PCDHB1	5	140433196	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	223485	140433196	40482064	430	40664										
PCDHB14	56122	hgsc.bcm.edu	37	chr5	140603423	140603423	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttttggaaaaccctttacagTtttttcggtttgagctgtgt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:140603423delT	ENST00000239449.4	+	1	346	c.346delT	c.(346-348)tttfs	p.F117fs	PCDHB14_ENST00000515856.2_Intron	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	117	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(21)|ovary(2)|prostate(3)|skin(6)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCCTTTACAGTTTTTTCGGTT	0.423																																					p.Q115fs	Ovarian(141;50 1831 27899 33809 37648)	Atlas-INDEL	.											.	PCDHB14	132	.	0			c.345delG						.						92	103	99					5																	140603423		2203	4299	6502	SO:0001589	frameshift_variant	56122	exon1			.	AF152493	CCDS4256.1	5q31	2010-01-26			ENSG00000120327	ENSG00000120327		"Cadherins / Protocadherins : Clustered"	8685	other	protocadherin		606340				10380929	Standard	NM_018934		Approved	PCDH-BETA14	uc003ljb.3	Q9Y5E9	OTTHUMG00000129619	ENST00000239449.4:c.346delT	chr5.hg19:g.140603423delT	ENSP00000239449:p.Phe117fs	225.0	0.0		192.0	12.0	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Frame_Shift_Del	DEL	ENST00000239449.4	hg19	CCDS4256.1																																																																																			.	.		0.423	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934		-	140603423	T	-	140603423	7	5	282	1	0	1	0	1	0	0	0	0	11548	1725	60	0	348	0	PCDHB14	5	140603423	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	170227	140603423	40311837	431	40665										
PCDHGA2	56113	hgsc.bcm.edu	37	chr5	140720687	140720687	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgttgctggcgcacaggctgCggcgctggcacaagtcacgc	15	13	1	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:140720687C>T	ENST00000394576.2	+	1	2149	c.2149C>T	c.(2149-2151)Cgg>Tgg	p.R717W	PCDHGA3_ENST00000253812.6_5'Flank|PCDHGA1_ENST00000517417.1_Intron	NM_018915.2	NP_061738.1	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2	717					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(32)|ovary(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCACAGGCTGCGGCGCTGGCA	0.642																																					p.R717W		Atlas-SNP	.											.	PCDHGA2	205	.	0			c.C2149T						.						84	88	87					5																	140720687		2203	4300	6503	SO:0001583	missense	56113	exon1			AGGCTGCGGCGCT	AF152508	CCDS47289.1	5q31	2011-03-28			ENSG00000081853	ENSG00000081853		"Cadherins / Protocadherins : Clustered"	8700	other	protocadherin		606289				10380929	Standard	NM_018915		Approved	PCDH-GAMMA-A2		Q9Y5H1	OTTHUMG00000163679	ENST00000394576.2:c.2149C>T	chr5.hg19:g.140720687C>T	ENSP00000378077:p.Arg717Trp	399.0	0.0		342.0	132.0	NM_018915	Q52LL6|Q9Y5D5	Missense_Mutation	SNP	ENST00000394576.2	hg19	CCDS47289.1	.	.	.	.	.	.	.	.	.	.	.	11.29	1.594846	0.28445	.	.	ENSG00000081853	ENST00000394576	T	0.17054	2.3	4.88	-5.05	0.02955	.	0.000000	0.38548	U	0.001643	T	0.16685	0.0401	M	0.66560	2.04	0.19775	N	0.99995	B;B	0.31599	0.33;0.107	B;B	0.33750	0.169;0.03	T	0.19063	-1.0317	10	0.49607	T	0.09	.	12.2431	0.54555	0.4631:0.4704:0.0:0.0665	.	717;717	Q9Y5H1-2;Q9Y5H1	.;PCDG2_HUMAN	W	717	ENSP00000378077:R717W	ENSP00000378077:R717W	R	+	1	2	PCDHGA2	140700871	0.000000	0.05858	0.691000	0.30163	0.028000	0.11728	-0.359000	0.07632	-0.673000	0.05259	0.306000	0.20318	CGG	.	.		0.642	PCDHGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374738.1	NM_018915		T	140720687	C	T	140720687	3	4	282	1	0	0	0	0	1	0	0	0	11563	759	27	1	2151	1	PCDHGA2	5	140720687	Missense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	117264	140720687	40194573	432	40666										
PCDHGB2	56103	hgsc.bcm.edu	37	chr5	140741739	140741739	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccagacctcagcgaccgccgGgagccctctgacccccaggc	11	20	2	2	rs576630104		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:140741739G>C	ENST00000522605.1	+	1	2037	c.2037G>C	c.(2035-2037)cgG>cgC	p.R679R	PCDHGA2_ENST00000394576.2_Intron|PCDHGA5_ENST00000518069.1_5'Flank|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018923.2|NM_032096.1	NP_061746.1|NP_115267.1	Q9Y5G2	PCDGE_HUMAN	protocadherin gamma subfamily B, 2	679					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGACCGCCGGGAGCCCTCTG	0.597																																					p.R679R		Atlas-SNP	.											PCDHGB2_ENST00000522605,NS,carcinoma,+1,1	PCDHGB2	196	.	0			c.G2037C						.						61	65	63					5																	140741739		2021	4177	6198	SO:0001819	synonymous_variant	56103	exon1			CCGCCGGGAGCCC	AF152331	CCDS54924.1, CCDS75332.1	5q31	2010-01-26				ENSG00000253910		"Cadherins / Protocadherins : Clustered"	8709	other	protocadherin		606300				10380929	Standard	NM_018923		Approved	PCDH-GAMMA-B2		Q9Y5G2		ENST00000522605.1:c.2037G>C	chr5.hg19:g.140741739G>C		257.0	1.0		183.0	0.0	NM_018923	Q3MIJ3|Q9UN65	Silent	SNP	ENST00000522605.1	hg19	CCDS54924.1																																																																																			.	.		0.597	PCDHGB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374741.1	NM_018923		C	140741739	G	C	140741739	2	2	282	1	0	0	0	0	0	0	0	1	11572	1219	43	4		4	PCDHGB2	5	140741739	Silent	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	21052	140741739	40173521	433	40667										
CAMK2A	815	hgsc.bcm.edu	37	chr5	149629865	149629865	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcatgcaggatgccacggtgGagcggtgctggaggaagtag	19	7	0	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:149629865G>T	ENST00000348628.6	-	11	1489	c.824C>A	c.(823-825)tCc>tAc	p.S275Y	CAMK2A_ENST00000398376.3_Missense_Mutation_p.S275Y	NM_015981.3|NM_171825.2	NP_057065.2|NP_741960.1	Q9UQM7	KCC2A_HUMAN	calcium/calmodulin-dependent protein kinase II alpha	275					calcium ion transport (GO:0006816)|cytokine-mediated signaling pathway (GO:0019221)|G1/S transition of mitotic cell cycle (GO:0000082)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of neurotransmitter secretion (GO:0046928)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|kinase activity (GO:0016301)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|skin(1)|stomach(1)	15		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGCCACGGTGGAGCGGTGCTG	0.587																																					p.S275Y		Atlas-SNP	.											.	CAMK2A	42	.	0			c.C824A						.						73	73	73					5																	149629865		2132	4259	6391	SO:0001583	missense	815	exon11			ACGGTGGAGCGGT	AB023185	CCDS43386.1, CCDS43387.1	5q32	2013-09-20	2008-10-30		ENSG00000070808	ENSG00000070808	2.7.11.17		1460	protein-coding gene	gene with protein product	"CaM-kinase II alpha chain", "calcium/calmodulin-dependent protein kinase II alpha-B subunit", "CaM kinase II alpha subunit", "CaMK-II alpha subunit", "calcium/calmodulin-dependent protein kinase type II alpha chain"	114078	"calcium/calmodulin-dependent protein kinase (CaM kinase) II alpha"	CAMKA		10231032, 3475713	Standard	NM_015981		Approved	KIAA0968, CaMKIINalpha	uc003lrt.2	Q9UQM7	OTTHUMG00000134281	ENST00000348628.6:c.824C>A	chr5.hg19:g.149629865G>T	ENSP00000261793:p.Ser275Tyr	106.0	0.0		77.0	26.0	NM_171825	Q9UL21|Q9Y2H4|Q9Y352	Missense_Mutation	SNP	ENST00000348628.6	hg19	CCDS43386.1	.	.	.	.	.	.	.	.	.	.	G	33	5.201341	0.94997	.	.	ENSG00000070808	ENST00000348628;ENST00000398376	T;T	0.69306	-0.37;-0.39	5.38	5.38	0.77491	Protein kinase-like domain (1);	0.075620	0.53938	D	0.000047	T	0.81725	0.4883	M	0.82323	2.585	0.80722	D	1	D;D;D	0.58268	0.982;0.981;0.969	P;P;P	0.58331	0.837;0.822;0.692	D	0.84634	0.0691	10	0.87932	D	0	.	19.1203	0.93360	0.0:0.0:1.0:0.0	.	275;275;275	Q9UQM7-2;Q9UQM7;A8K161	.;KCC2A_HUMAN;.	Y	275	ENSP00000261793:S275Y;ENSP00000381412:S275Y	ENSP00000261793:S275Y	S	-	2	0	CAMK2A	149610058	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	9.750000	0.98875	2.539000	0.85634	0.655000	0.94253	TCC	.	.		0.587	CAMK2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258869.2	NM_015981		T	149629865	G	T	149629865	3	4	282	1	0	0	0	0	1	0	0	0	2601	1174	41	3	681	3	CAMK2A	5	149629865	Missense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	8888126	149629865	31285395	434	40668										
FAM71B	153745	hgsc.bcm.edu	37	chr5	156592606	156592606	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gttgtcttcgggtggtgcgtCcccagatagaagtgttgggg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:156592606delC	ENST00000302938.4	-	1	669	c.574delG	c.(574-576)gacfs	p.D192fs		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	192						nucleus (GO:0005634)				NS(3)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(32)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GGTGGTGCGTCCCCAGATAGA	0.507																																					p.D192fs		Atlas-INDEL	.											.	FAM71B	145	.	0			c.575delA						.						200	201	200					5																	156592606		2203	4300	6503	SO:0001589	frameshift_variant	153745	exon1			.		CCDS4335.1	5q33.3	2005-08-09			ENSG00000170613	ENSG00000170613			28397	protein-coding gene	gene with protein product						12477932	Standard	NM_130899		Approved	MGC26988	uc003lwn.3	Q8TC56	OTTHUMG00000130246	ENST00000302938.4:c.574delG	chr5.hg19:g.156592606delC	ENSP00000305596:p.Asp192fs	354.0	0.0		212.0	14.0	NM_130899	Q1EDD9|Q8TC64|Q96LY8	Frame_Shift_Del	DEL	ENST00000302938.4	hg19	CCDS4335.1																																																																																			.	.		0.507	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252570.2	NM_130899		-	156592606	C	-	156592606	7	5	282	1	0	1	0	1	0	0	0	0	5616	855	30	0	1251	0	FAM71B	5	156592606	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	6962741	156592606	24322654	435	40669										
CYFIP2	26999	hgsc.bcm.edu	37	chr5	156721858	156721858	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cctggcgcagctgttcccggGccattcccaggtgagactgt	13	14	0	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:156721858G>C	ENST00000347377.6	+	4	705	c.274G>C	c.(274-276)Gcc>Ccc	p.A92P	CYFIP2_ENST00000377576.3_Missense_Mutation_p.A92P|CYFIP2_ENST00000521420.1_Intron|CYFIP2_ENST00000522463.1_Intron|CYFIP2_ENST00000541131.1_Intron|CYFIP2_ENST00000442283.2_5'UTR|CYFIP2_ENST00000318218.6_Missense_Mutation_p.A92P	NM_001037332.2	NP_001032409.2			cytoplasmic FMR1 interacting protein 2											breast(1)|endometrium(12)|kidney(2)|lung(23)	38	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CTGTTCCCGGGCCATTCCCAG	0.527																																					p.A92P		Atlas-SNP	.											.	CYFIP2	354	.	0			c.G274C						.						116	125	122					5																	156721858		2145	4280	6425	SO:0001583	missense	26999	exon4			TCCCGGGCCATTC	AF160973	CCDS75364.1	5q34	2008-07-18				ENSG00000055163			13760	protein-coding gene	gene with protein product	"p53 inducible protein"	606323				11438699	Standard	NM_001037333		Approved	PIR121	uc021ygm.1	Q96F07		ENST00000347377.6:c.274G>C	chr5.hg19:g.156721858G>C	ENSP00000313567:p.Ala92Pro	329.0	0.0		225.0	10.0	NM_001037332		Missense_Mutation	SNP	ENST00000347377.6	hg19		.	.	.	.	.	.	.	.	.	.	G	32	5.153806	0.94645	.	.	ENSG00000055163	ENST00000318218;ENST00000347377;ENST00000377576	T;T;T	0.44482	0.92;0.92;0.92	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	T	0.69958	0.3169	M	0.88310	2.945	0.80722	D	1	P;D;P	0.67145	0.943;0.996;0.909	P;D;P	0.67548	0.49;0.952;0.665	T	0.77552	-0.2545	10	0.72032	D	0.01	-10.9957	18.1684	0.89736	0.0:0.0:1.0:0.0	.	92;92;92	E7EVF4;Q96F07-2;Q96F07	.;.;CYFP2_HUMAN	P	92	ENSP00000325817:A92P;ENSP00000313567:A92P;ENSP00000366799:A92P	ENSP00000325817:A92P	A	+	1	0	CYFIP2	156654436	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.769000	0.98969	2.285000	0.76669	0.563000	0.77884	GCC	.	.		0.527	CYFIP2-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001037332		C	156721858	G	C	156721858	3	2	282	1	0	0	0	0	1	0	0	0	4140	1203	42	4	284	4	CYFIP2	5	156721858	Missense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	129252	156721858	24193402	436	40670										
THG1L	54974	hgsc.bcm.edu	37	chr5	157160024	157160024	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acagctttgtgttcaagcggAaaaccaattggtttaaaaga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:157160024delA	ENST00000231198.7	+	2	584	c.340delA	c.(340-342)aaafs	p.K114fs	AC026407.1_ENST00000599823.1_Frame_Shift_Del_p.F57fs	NM_017872.3	NP_060342.2	Q9NWX6	THG1_HUMAN	tRNA-histidine guanylyltransferase 1-like (S. cerevisiae)	114					protein homotetramerization (GO:0051289)|tRNA modification (GO:0006400)|tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|tRNA binding (GO:0000049)|tRNA guanylyltransferase activity (GO:0008193)			NS(1)|central_nervous_system(2)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)|skin(1)	13	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GTTCAAGCGGAAAACCAATTG	0.423																																					p.R113fs		Atlas-INDEL	.											.	THG1L	31	.	0			c.339delG						.						157	141	147					5																	157160024		2203	4300	6503	SO:0001589	frameshift_variant	54974	exon2			.	AK223119	CCDS4341.1	5q33.3	2008-02-05			ENSG00000113272	ENSG00000113272			26053	protein-coding gene	gene with protein product	"interphase cytoplasmic foci protein 45"					11230166	Standard	XM_005265939		Approved	ICF45, FLJ11601, FLJ20546	uc003lxd.3	Q9NWX6	OTTHUMG00000130254	ENST00000231198.7:c.340delA	chr5.hg19:g.157160024delA	ENSP00000231198:p.Lys114fs	247.0	0.0		171.0	11.0	NM_017872	D3DQJ5|Q53G12|Q7L5R3|Q9H0S2	Frame_Shift_Del	DEL	ENST00000231198.7	hg19	CCDS4341.1																																																																																			.	.		0.423	THG1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252579.2	NM_017872		-	157160024	A	-	157160024	7	5	282	1	0	1	0	1	0	0	0	0	15876	247	9	0	346	0	THG1L	5	157160024	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	438166	157160024	23755236	437	40671										
GABRG2	2566	hgsc.bcm.edu	37	chr5	161569294	161569294	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtgtctttctggatcaataaGgatgctgttccagccagaac	10	9	3	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:161569294G>A	ENST00000361925.4	+	7	1114	c.894G>A	c.(892-894)aaG>aaA	p.K298K	GABRG2_ENST00000356592.3_Silent_p.K298K|GABRG2_ENST00000393933.4_Silent_p.K203K|GABRG2_ENST00000414552.2_Silent_p.K338K			P18507	GBRG2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 2	298					adult behavior (GO:0030534)|cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|post-embryonic development (GO:0009791)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|GABA-A receptor complex (GO:1902711)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(15)|lung(24)|ovary(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	62	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GGATCAATAAGGATGCTGTTC	0.403																																					p.K338K		Atlas-SNP	.											.	GABRG2	142	.	0			c.G1014A						.						218	183	195					5																	161569294		2203	4300	6503	SO:0001819	synonymous_variant	2566	exon8			CAATAAGGATGCT		CCDS4358.1, CCDS4359.1, CCDS47333.1	5q34	2012-06-22			ENSG00000113327	ENSG00000113327		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4087	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma 2"	137164					Standard	NM_198904		Approved		uc010jjc.3	P18507	OTTHUMG00000130350	ENST00000361925.4:c.894G>A	chr5.hg19:g.161569294G>A		240.0	0.0		167.0	63.0	NM_198903	F5HB82|Q6GRL6|Q6PCC3|Q9UDB3|Q9UN15	Silent	SNP	ENST00000361925.4	hg19	CCDS4358.1																																																																																			.	.		0.403	GABRG2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252706.1			A	161569294	G	A	161569294	2	1	282	1	0	0	0	0	0	0	0	1	6180	991	35	3		3	GABRG2	5	161569294	Silent	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	4409270	161569294	19345966	438	40672										
FOXI1	2299	hgsc.bcm.edu	37	chr5	169533034	169533034	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tccccagcatcggccaggagCcccccgagatgaacctctac							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:169533034delC	ENST00000306268.6	+	1	134	c.73delC	c.(73-75)cccfs	p.P26fs	FOXI1_ENST00000449804.2_Frame_Shift_Del_p.P26fs			Q12951	FOXI1_HUMAN	forkhead box I1	26	Pro-rich.				embryo development (GO:0009790)|inner ear morphogenesis (GO:0042472)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	Renal(175;0.000159)|Lung NSC(126;0.0267)|all_lung(126;0.04)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CGGCCAGGAGCCCCCCGAGAT	0.697									Pendred syndrome																												p.E24fs		Atlas-INDEL	.											.	FOXI1	70	.	0			c.72delG						.						24	28	26					5																	169533034		2203	4298	6501	SO:0001589	frameshift_variant	2299	exon1	Familial Cancer Database	Goiter-Deafness syndrome	.	BC029778	CCDS4372.1, CCDS47337.1	5q34	2008-02-05			ENSG00000168269	ENSG00000168269		"Forkhead boxes"	3815	protein-coding gene	gene with protein product		601093		FKHL10		7957066, 8825632	Standard	NM_144769		Approved	FREAC6	uc003mai.4	Q12951	OTTHUMG00000130436	ENST00000306268.6:c.73delC	chr5.hg19:g.169533034delC	ENSP00000304286:p.Pro26fs	411.0	0.0		283.0	17.0	NM_012188	Q14518|Q66SR7|Q8N6L8	Frame_Shift_Del	DEL	ENST00000306268.6	hg19	CCDS4372.1																																																																																			.	.		0.697	FOXI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252827.2	NM_144769, NM_012188		-	169533034	C	-	169533034	7	5	282	1	0	1	0	1	0	0	0	0	6017	739	26	0	75	0	FOXI1	5	169533034	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	7963740	169533034	11382226	439	40673										
KCNIP1	30820	hgsc.bcm.edu	37	chr5	170145819	170145819	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccatcggcccgagggactggAgcagctcgaggcccagacca	14	15	0	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:170145819A>G	ENST00000411494.1	+	3	152	c.152A>G	c.(151-153)gAg>gGg	p.E51G	KCNIP1_ENST00000328939.4_Missense_Mutation_p.E40G|KCNIP1_ENST00000377360.4_Missense_Mutation_p.E49G|KCNIP1_ENST00000434108.1_Missense_Mutation_p.E40G|KCNIP1_ENST00000520740.1_Missense_Mutation_p.E12G|KCNIP1_ENST00000390656.4_Missense_Mutation_p.E40G			Q9NZI2	KCIP1_HUMAN	Kv channel interacting protein 1	51	EF-hand 1; degenerate. {ECO:0000255|PROSITE-ProRule:PRU00448}.				detection of calcium ion (GO:0005513)|positive regulation of action potential (GO:0045760)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|potassium channel complex (GO:0034705)	calcium ion binding (GO:0005509)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|voltage-gated ion channel activity (GO:0005244)			autonomic_ganglia(1)|large_intestine(7)|lung(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	18	Renal(175;0.000159)|Lung NSC(126;0.0191)|all_lung(126;0.0297)	Medulloblastoma(196;0.0109)|all_neural(177;0.0177)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GAGGGACTGGAGCAGCTCGAG	0.552																																					p.E51G		Atlas-SNP	.											.	KCNIP1	66	.	0			c.A152G						.						61	57	59					5																	170145819		2203	4300	6503	SO:0001583	missense	30820	exon3			GACTGGAGCAGCT	AF199597	CCDS34285.1, CCDS34286.1, CCDS4374.1, CCDS64312.1, CCDS64313.1	5q35	2013-01-10			ENSG00000182132	ENSG00000182132		"EF-hand domain containing"	15521	protein-coding gene	gene with protein product		604660				10676964	Standard	NM_001278339		Approved	KCHIP1	uc003map.3	Q9NZI2	OTTHUMG00000130442	ENST00000411494.1:c.152A>G	chr5.hg19:g.170145819A>G	ENSP00000395323:p.Glu51Gly	190.0	0.0		144.0	6.0	NM_001034837	B7Z7B4|Q3YAD0|Q3YAD1|Q3YAD2|Q3YAD3|Q5U822	Missense_Mutation	SNP	ENST00000411494.1	hg19	CCDS34286.1	.	.	.	.	.	.	.	.	.	.	A	29.0	4.970494	0.92919	.	.	ENSG00000182132	ENST00000377360;ENST00000328939;ENST00000390656;ENST00000520740;ENST00000434108;ENST00000411494	T;T;T;T;T;T	0.24538	1.85;1.85;1.85;1.85;1.85;1.85	5.59	5.59	0.84812	EF-hand-like domain (1);	0.191271	0.56097	D	0.000039	T	0.45135	0.1327	M	0.88640	2.97	0.80722	D	1	P;P;P;P	0.49635	0.862;0.838;0.926;0.577	P;P;B;B	0.48400	0.576;0.519;0.393;0.305	T	0.54984	-0.8211	9	.	.	.	.	13.7125	0.62675	1.0:0.0:0.0:0.0	.	40;40;51;49	Q3YAD0;Q3YAD2;Q9NZI2;Q3YAD3	.;.;KCIP1_HUMAN;.	G	49;40;40;12;40;51	ENSP00000366577:E49G;ENSP00000329686:E40G;ENSP00000375071:E40G;ENSP00000431102:E12G;ENSP00000414886:E40G;ENSP00000395323:E51G	.	E	+	2	0	KCNIP1	170078397	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.904000	0.92590	2.117000	0.64856	0.533000	0.62120	GAG	.	.		0.552	KCNIP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000371760.1			G	170145819	A	G	170145819	3	3	282	1	0	0	0	0	1	0	0	0	8048	304	11	2	254	2	KCNIP1	5	170145819	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	612785	170145819	10769441	440	40674										
GPRIN1	114787	hgsc.bcm.edu	37	chr5	176025442	176025442	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tacttccagcagatatggggTcctcccttctggaggacacc	10	13	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:176025442T>C	ENST00000303991.4	-	2	1571	c.1394A>G	c.(1393-1395)gAc>gGc	p.D465G		NM_052899.2	NP_443131.2	Q7Z2K8	GRIN1_HUMAN	G protein regulated inducer of neurite outgrowth 1	465					neuron projection development (GO:0031175)	cell projection (GO:0042995)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGATATGGGGTCCTCCCTTCT	0.532																																					p.D465G		Atlas-SNP	.											.	GPRIN1	77	.	0			c.A1394G						.						94	105	101					5																	176025442		2201	4299	6500	SO:0001583	missense	114787	exon2			ATGGGGTCCTCCC	AB067480	CCDS4405.1	5q35.2	2008-02-05			ENSG00000169258	ENSG00000169258			24835	protein-coding gene	gene with protein product		611239				11572484	Standard	NM_052899		Approved	GRIN1, KIAA1893	uc003meo.1	Q7Z2K8	OTTHUMG00000130659	ENST00000303991.4:c.1394A>G	chr5.hg19:g.176025442T>C	ENSP00000305839:p.Asp465Gly	183.0	0.0		119.0	5.0	NM_052899	C9JM70|Q8ND74|Q96PZ4	Missense_Mutation	SNP	ENST00000303991.4	hg19	CCDS4405.1	.	.	.	.	.	.	.	.	.	.	T	15.11	2.736476	0.49045	.	.	ENSG00000169258	ENST00000303991;ENST00000335532	T	0.12774	2.65	5.04	2.61	0.31194	.	0.907068	0.09103	N	0.848199	T	0.14056	0.0340	M	0.64997	1.995	0.09310	N	1	B	0.21225	0.053	B	0.23419	0.046	T	0.40887	-0.9539	10	0.26408	T	0.33	0.1413	3.3295	0.07079	0.1702:0.1836:0.0:0.6462	.	465	Q7Z2K8	GRIN1_HUMAN	G	465	ENSP00000305839:D465G	ENSP00000305839:D465G	D	-	2	0	GPRIN1	175958048	0.001000	0.12720	0.020000	0.16555	0.273000	0.26683	0.917000	0.28665	0.262000	0.21774	0.374000	0.22700	GAC	.	.		0.532	GPRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253149.1	NM_052899		C	176025442	T	C	176025442	3	2	282	1	0	0	0	0	1	0	0	0	6738	1667	58	2	1636	2	GPRIN1	5	176025442	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	5879623	176025442	4889818	441	40675										
FGFR4	2264	hgsc.bcm.edu	37	chr5	176518005	176518005	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agtacctgcggggaacaccgTcaagttccgctgtccagctg	12	13	1	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:176518005T>C	ENST00000292408.4	+	5	748	c.503T>C	c.(502-504)gTc>gCc	p.V168A	FGFR4_ENST00000393637.1_Missense_Mutation_p.V168A|FGFR4_ENST00000292410.3_Missense_Mutation_p.V168A|FGFR4_ENST00000393648.2_Missense_Mutation_p.V168A|FGFR4_ENST00000502906.1_Missense_Mutation_p.V168A	NM_002011.3|NM_213647.1	NP_002002.3|NP_998812.1	P22455	FGFR4_HUMAN	fibroblast growth factor receptor 4	168	Ig-like C2-type 2.				alveolar secondary septum development (GO:0061144)|cell migration (GO:0016477)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphate ion homeostasis (GO:0055062)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of proteolysis (GO:0045862)|protein autophosphorylation (GO:0046777)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cholesterol homeostasis (GO:2000188)|regulation of extracellular matrix disassembly (GO:0010715)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein tyrosine kinase activity (GO:0004713)	p.V168D(2)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	34	all_cancers(89;5.93e-05)|Renal(175;0.000269)|Lung NSC(126;0.0088)|all_lung(126;0.0142)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Palifermin(DB00039)|Ponatinib(DB08901)	GGGAACACCGTCAAGTTCCGC	0.612										TSP Lung(9;0.080)																											p.V168A		Atlas-SNP	.											FGFR4_ENST00000292408,bladder,carcinoma,0,2	FGFR4	174	.	2	Substitution - Missense(2)	urinary_tract(2)	c.T503C						.						95	76	82					5																	176518005		2203	4300	6503	SO:0001583	missense	2264	exon4			ACACCGTCAAGTT	AF202063	CCDS4410.1, CCDS4411.1	5q35.2	2013-09-19			ENSG00000160867	ENSG00000160867		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3691	protein-coding gene	gene with protein product		134935					Standard	XM_005265837		Approved	JTK2, CD334	uc003mfm.3	P22455	OTTHUMG00000151523	ENST00000292408.4:c.503T>C	chr5.hg19:g.176518005T>C	ENSP00000292408:p.Val168Ala	126.0	1.0		98.0	4.0	NM_022963	G3JVM2|G3JVM5|G3JVM7|G3JVM9|O43785|Q14309|Q71TW8|Q8TDA0|Q96KE5	Missense_Mutation	SNP	ENST00000292408.4	hg19	CCDS4410.1	.	.	.	.	.	.	.	.	.	.	T	17.12	3.309399	0.60414	.	.	ENSG00000160867	ENST00000292408;ENST00000503708;ENST00000393648;ENST00000502906;ENST00000292410;ENST00000393637;ENST00000377207	T;T;T;T;T;T	0.67345	1.44;-0.26;1.44;1.44;1.44;1.44	4.74	4.74	0.60224	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.122935	0.53938	D	0.000046	T	0.72036	0.3411	L	0.31845	0.965	0.50171	D	0.999851	D;D;P;P	0.65815	0.994;0.995;0.604;0.942	D;D;B;P	0.66716	0.94;0.946;0.269;0.569	T	0.74601	-0.3611	10	0.56958	D	0.05	.	14.0727	0.64870	0.0:0.0:0.0:1.0	.	168;168;168;168	B5A965;B4DVP5;P22455-2;P22455	.;.;.;FGFR4_HUMAN	A	168;168;168;168;168;168;280	ENSP00000292408:V168A;ENSP00000424905:V168A;ENSP00000377259:V168A;ENSP00000424960:V168A;ENSP00000292410:V168A;ENSP00000377254:V168A	ENSP00000292408:V168A	V	+	2	0	FGFR4	176450611	1.000000	0.71417	0.804000	0.32291	0.776000	0.43924	7.825000	0.86693	1.999000	0.58509	0.459000	0.35465	GTC	.	.		0.612	FGFR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253410.1			C	176518005	T	C	176518005	3	2	282	1	0	0	0	0	1	0	0	0	5876	1667	58	2	517	2	FGFR4	5	176518005	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	492563	176518005	4397255	442	40676										
PDLIM7	9260	hgsc.bcm.edu	37	chr5	176918124	176918124	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gccgctgcttgctggcatctGggaccagcggtcggagcggc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:176918124delG	ENST00000355841.2	-	6	488	c.422delC	c.(421-423)ccafs	p.P141fs	PDLIM7_ENST00000356618.4_Frame_Shift_Del_p.P141fs|PDLIM7_ENST00000359895.2_Frame_Shift_Del_p.P107fs|PDLIM7_ENST00000355572.2_Frame_Shift_Del_p.P141fs|PDLIM7_ENST00000393551.1_Frame_Shift_Del_p.P141fs	NM_005451.3	NP_005442.2	Q9NR12	PDLI7_HUMAN	PDZ and LIM domain 7 (enigma)	141					actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of osteoblast differentiation (GO:0045669)|receptor-mediated endocytosis (GO:0006898)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ruffle (GO:0001726)|stress fiber (GO:0001725)	zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	10	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCTGGCATCTGGGACCAGCGG	0.682																																					p.P141fs		Atlas-INDEL	.											.	PDLIM7	32	.	0			c.423delA						.						14	18	17					5																	176918124		2202	4298	6500	SO:0001589	frameshift_variant	9260	exon6			.	BC001093	CCDS4422.1, CCDS4423.1, CCDS4424.1	5q35.3	2008-02-05			ENSG00000196923	ENSG00000196923			22958	protein-coding gene	gene with protein product		605903				11874232	Standard	NM_005451		Approved	ENIGMA	uc003mhc.1	Q9NR12	OTTHUMG00000130853	ENST00000355841.2:c.422delC	chr5.hg19:g.176918124delG	ENSP00000348099:p.Pro141fs	221.0	0.0		153.0	10.0	NM_213636	Q14250|Q5XG82|Q6NVZ5|Q96C91|Q9BXB8|Q9BXB9	Frame_Shift_Del	DEL	ENST00000355841.2	hg19	CCDS4422.1																																																																																			.	.		0.682	PDLIM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253423.1	NM_005451		-	176918124	G	-	176918124	7	5	282	1	0	1	0	1	0	0	0	0	11693	1348	47	0	1084	0	PDLIM7	5	176918124	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	400119	176918124	3997136	443	40677										
HNRNPH1	3187	hgsc.bcm.edu	37	chr5	179044644	179044644	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tctcacagggttgagcggtgAaaaaaactacaacacaaggc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:179044644delA	ENST00000356731.5	-	8	2463	c.928delT	c.(928-930)tcafs	p.S310fs	HNRNPH1_ENST00000511300.2_Frame_Shift_Del_p.S40fs|HNRNPH1_ENST00000393432.4_Frame_Shift_Del_p.S310fs|HNRNPH1_ENST00000510411.1_Frame_Shift_Del_p.S310fs|HNRNPH1_ENST00000329433.6_Frame_Shift_Del_p.S310fs|HNRNPH1_ENST00000442819.2_Frame_Shift_Del_p.S310fs|HNRNPH1_ENST00000524180.1_5'Flank			P31943	HNRH1_HUMAN	heterogeneous nuclear ribonucleoprotein H1 (H)	310	2 X 16 AA Gly-rich approximate repeats.|RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA splicing (GO:0043484)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(4)|skin(1)	14						TTGAGCGGTGAAAAAAACTAC	0.383																																					p.S310fs		Atlas-INDEL	.											.	HNRNPH1	62	.	0			c.929delC						.						80	79	80					5																	179044644		2203	4300	6503	SO:0001589	frameshift_variant	3187	exon9			.	BC001348	CCDS4446.1	5q35.3	2013-02-12		2008-04-18	ENSG00000169045	ENSG00000169045		"RNA binding motif (RRM) containing"	5041	protein-coding gene	gene with protein product		601035		HNRPH1		7499401	Standard	NM_005520		Approved	hnRNPH	uc003mkf.5	P31943	OTTHUMG00000130908	ENST00000356731.5:c.928delT	chr5.hg19:g.179044644delA	ENSP00000349168:p.Ser310fs	280.0	0.0		204.0	15.0	NM_001257293	B3KW86|D3DWQ2|Q6IBM4	Frame_Shift_Del	DEL	ENST00000356731.5	hg19	CCDS4446.1																																																																																			.	.		0.383	HNRNPH1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253497.3	NM_005520		-	179044644	A	-	179044644	7	5	282	1	0	1	0	1	0	0	0	0	7275	246	9	0	441	0	HNRNPH1	5	179044644	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2126520	179044644	1870616	444	40678										
EXOC2	55770	hgsc.bcm.edu	37	chr6	564874	564874	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccttactcaccttaaaatcaTtttgtctttgccttacattc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:564874delT	ENST00000230449.4	-	14	1634	c.1499delA	c.(1498-1500)aatfs	p.N500fs	EXOC2_ENST00000448181.3_Frame_Shift_Del_p.N95fs	NM_018303.5	NP_060773.3	Q96KP1	EXOC2_HUMAN	exocyst complex component 2	500					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|liver(1)|lung(16)|ovary(4)|pancreas(1)|prostate(2)	46	Ovarian(93;0.0733)	Breast(5;0.0014)|all_lung(73;0.0697)|all_hematologic(90;0.0897)		OV - Ovarian serous cystadenocarcinoma(45;0.0507)|BRCA - Breast invasive adenocarcinoma(62;0.14)		CTTAAAATCATTTTGTCTTTG	0.328																																					p.N500fs		Atlas-INDEL	.											.	EXOC2	81	.	0			c.1500delT						.						203	193	196					6																	564874		2203	4300	6503	SO:0001589	frameshift_variant	55770	exon14			.	AJ420556	CCDS34327.1	6p25.3	2013-01-22	2005-11-01	2005-11-01	ENSG00000112685	ENSG00000112685			24968	protein-coding gene	gene with protein product		615329	"SEC5-like 1 (S. cerevisiae)"	SEC5L1		12575951, 12459492	Standard	NM_018303		Approved	FLJ11026, Sec5p	uc003mtd.4	Q96KP1	OTTHUMG00000137437	ENST00000230449.4:c.1499delA	chr6.hg19:g.564874delT	ENSP00000230449:p.Asn500fs	375.0	0.0		261.0	16.0	NM_018303	B2RBE6|Q5JPC8|Q96AN6|Q9NUZ8|Q9UJM7	Frame_Shift_Del	DEL	ENST00000230449.4	hg19	CCDS34327.1																																																																																			.	.		0.328	EXOC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039627.1	NM_018303		-	564874	T	-	564874	7	5	282	1	0	1	0	1	0	0	0	0	5304	1493	52	0	1335	0	EXOC2	6	564874	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10		564874	170550193	445	40679										
RREB1	6239	hgsc.bcm.edu	37	chr6	7232097	7232097	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccccactgtccccgggttttCccttgggccagctccctaca					rs552152051		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:7232097delC	ENST00000349384.6	+	10	4079	c.3765delC	c.(3763-3765)ttcfs	p.F1255fs	RREB1_ENST00000379938.2_Frame_Shift_Del_p.F1255fs|RREB1_ENST00000334984.6_Frame_Shift_Del_p.F1255fs|RREB1_ENST00000379933.3_Frame_Shift_Del_p.F1255fs	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	1255					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				CCCGGGTTTTCCCTTGGGCCA	0.617																																					p.F1255fs		Atlas-INDEL	.											.	RREB1	242	.	0			c.3764delT						.						54	40	45					6																	7232097		2203	4300	6503	SO:0001589	frameshift_variant	6239	exon10			.	U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"Zinc fingers, C2H2-type"	10449	protein-coding gene	gene with protein product	"hindsight homolog (drosophila)"	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.3765delC	chr6.hg19:g.7232097delC	ENSP00000305560:p.Phe1255fs	246.0	0.0		180.0	11.0	NM_001003700	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Frame_Shift_Del	DEL	ENST00000349384.6	hg19	CCDS34336.1																																																																																			.	.		0.617	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1			-	7232097	C	-	7232097	7	5	282	1	0	1	0	1	0	0	0	0	13694	854	30	0	3791	0	RREB1	6	7232097	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	6667223	7232097	163882970	446	40680										
RREB1	6239	hgsc.bcm.edu	37	chr6	7246876	7246876	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggaggagcatggcactgaggAgagcactggggacgccgacg	19	9	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:7246876A>G	ENST00000349384.6	+	11	4342	c.4028A>G	c.(4027-4029)gAg>gGg	p.E1343G	RREB1_ENST00000379938.2_Missense_Mutation_p.E1398G|RREB1_ENST00000334984.6_Intron|RREB1_ENST00000379933.3_Missense_Mutation_p.E1343G	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	1343					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				GGCACTGAGGAGAGCACTGGG	0.682																																					p.E1398G		Atlas-SNP	.											.	RREB1	242	.	0			c.A4193G						.						53	50	51					6																	7246876		2177	4273	6450	SO:0001583	missense	6239	exon12			CTGAGGAGAGCAC	U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"Zinc fingers, C2H2-type"	10449	protein-coding gene	gene with protein product	"hindsight homolog (drosophila)"	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.4028A>G	chr6.hg19:g.7246876A>G	ENSP00000305560:p.Glu1343Gly	97.0	0.0		45.0	5.0	NM_001003699	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Missense_Mutation	SNP	ENST00000349384.6	hg19	CCDS34336.1	.	.	.	.	.	.	.	.	.	.	A	14.75	2.629142	0.46944	.	.	ENSG00000124782	ENST00000379933;ENST00000379938;ENST00000349384	T;T;T	0.11169	2.8;2.83;2.8	5.14	2.7	0.31948	.	.	.	.	.	T	0.05456	0.0144	M	0.68593	2.085	0.58432	D	0.999997	P;P	0.38504	0.501;0.634	B;B	0.36766	0.116;0.232	T	0.12993	-1.0526	9	0.72032	D	0.01	-4.7087	6.988	0.24739	0.7947:0.0:0.0726:0.1327	.	1343;1398	Q92766;Q92766-2	RREB1_HUMAN;.	G	1343;1398;1343	ENSP00000369265:E1343G;ENSP00000369270:E1398G;ENSP00000305560:E1343G	ENSP00000305560:E1343G	E	+	2	0	RREB1	7191875	0.979000	0.34478	0.378000	0.26068	0.088000	0.18126	2.496000	0.45346	0.281000	0.22233	0.459000	0.35465	GAG	.	.		0.682	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1			G	7246876	A	G	7246876	3	3	282	1	0	0	0	0	1	0	0	0	13694	304	11	2	4227	2	RREB1	6	7246876	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	14779	7246876	163868191	447	40681										
DSP	1832	hgsc.bcm.edu	37	chr6	7574928	7574928	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	actgctccaggctattctccAaacagaagacatgttaaagg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:7574928delA	ENST00000379802.3	+	17	2677	c.2336delA	c.(2335-2337)caafs	p.Q779fs	DSP_ENST00000418664.2_Frame_Shift_Del_p.Q779fs	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	779	Globular 1.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		GCTATTCTCCAAACAGAAGAC	0.453																																					p.Q779fs		Atlas-INDEL	.											.	DSP	306	.	0			c.2335delC						.						128	120	123					6																	7574928		2203	4300	6503	SO:0001589	frameshift_variant	1832	exon17			.	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"desmoplakin (DPI, DPII)"			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.2336delA	chr6.hg19:g.7574928delA	ENSP00000369129:p.Gln779fs	216.0	0.0		134.0	10.0	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Frame_Shift_Del	DEL	ENST00000379802.3	hg19	CCDS4501.1																																																																																			.	.		0.453	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		-	7574928	A	-	7574928	7	5	282	1	0	1	0	1	0	0	0	0	4783	130	5	0	2402	0	DSP	6	7574928	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	328052	7574928	163540139	448	40682										
DSP	1832	hgsc.bcm.edu	37	chr6	7585185	7585185	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttgctgacatgatctccttgAaaaatggtgtcggcaccagc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:7585185delA	ENST00000379802.3	+	24	8031	c.7690delA	c.(7690-7692)aaafs	p.K2564fs	DSP_ENST00000418664.2_Frame_Shift_Del_p.K1965fs	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	2564	Globular 2.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		GATCTCCTTGAAAAATGGTGT	0.478																																					p.L2563fs		Atlas-INDEL	.											.	DSP	306	.	0			c.7689delG						.						95	92	93					6																	7585185		2203	4300	6503	SO:0001589	frameshift_variant	1832	exon24			.	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"desmoplakin (DPI, DPII)"			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.7690delA	chr6.hg19:g.7585185delA	ENSP00000369129:p.Lys2564fs	211.0	0.0		186.0	13.0	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Frame_Shift_Del	DEL	ENST00000379802.3	hg19	CCDS4501.1																																																																																			.	.		0.478	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		-	7585185	A	-	7585185	7	5	282	1	0	1	0	1	0	0	0	0	4783	247	9	0	7784	0	DSP	6	7585185	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	10257	7585185	163529882	449	40683										
GCNT2	2651	hgsc.bcm.edu	37	chr6	10586407	10586407	+	Intron	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aatgccagtctttttgtgggAaaatatattaccatcacctt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:10586407delA	ENST00000379597.3	+	2	1481				GCNT2_ENST00000495262.1_Intron|GCNT2_ENST00000316170.3_Intron|GCNT2_ENST00000397423.2_Intron|GCNT2_ENST00000265012.4_Frame_Shift_Del_p.E62fs|GCNT2_ENST00000410107.1_Intron			Q8N0V5	GNT2A_HUMAN	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group)						maintenance of lens transparency (GO:0036438)|negative regulation of cell-substrate adhesion (GO:0010812)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of protein kinase B signaling (GO:0051897)|posttranscriptional regulation of gene expression (GO:0010608)|protein glycosylation (GO:0006486)|transforming growth factor beta receptor signaling pathway (GO:0007179)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)			endometrium(2)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)	12	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)		TTTTTGTGGGAAAATATATTA	0.438																																					p.E62fs		Atlas-INDEL	.											.	GCNT2	123	.	0			c.184delG						.						163	161	162					6																	10586407		2203	4300	6503	SO:0001627	intron_variant	2651	exon1			.	L41605	CCDS4512.1, CCDS4513.1, CCDS34338.1	6p24.2	2014-07-18	2006-02-23		ENSG00000111846	ENSG00000111846	2.4.1.150	"Blood group antigens", "Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	4204	protein-coding gene	gene with protein product	"Ii blood group", "unassigned linkage group 3"	600429	"glucosaminyl (N-acetyl) transferase 5", "glucosaminyl (N-acetyl) transferase 2, I-branching enzyme", "glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (Ii blood group)", "cataract, congenital"	NACGT1, II, GCNT5, CCAT		8449405, 9915862	Standard	NM_145649		Approved	IGNT, NAGCT1, bA421M1.1, bA360O19.2, ULG3	uc003mze.3	Q06430	OTTHUMG00000014244	ENST00000379597.3:c.926-35177A>-	chr6.hg19:g.10586407delA		247.0	0.0		158.0	10.0	NM_145655		Frame_Shift_Del	DEL	ENST00000379597.3	hg19	CCDS34338.1																																																																																			.	.		0.438	GCNT2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327912.3	NM_145649		-	10586407	A	-	10586407	6	5	282	0	1	1	0	1	0	0	0	0	6309	246	9	0		0	GCNT2	6	10586407	Intron	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	3001222	10586407	160528660	450	40684										
SYCP2L	221711	hgsc.bcm.edu	37	chr6	10942722	10942722	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcctcactcactgagtgagcTctcttccttgaagcactcag	7	14	4	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:10942722T>C	ENST00000283141.6	+	22	2140	c.1844T>C	c.(1843-1845)cTc>cCc	p.L615P		NM_001040274.2	NP_001035364.2	Q5T4T6	SYC2L_HUMAN	synaptonemal complex protein 2-like	615						nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	36	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)	Epithelial(50;0.239)			CTGAGTGAGCTCTCTTCCTTG	0.348																																					p.L615P		Atlas-SNP	.											.	SYCP2L	101	.	0			c.T1844C						.						47	43	44					6																	10942722		1834	4085	5919	SO:0001583	missense	221711	exon22			GTGAGCTCTCTTC	AK128130	CCDS43423.1	6p24.2	2008-11-06	2007-07-02	2007-07-02	ENSG00000153157	ENSG00000153157			21537	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 177"	C6orf177			Standard	NM_001040274		Approved	dJ62D2.1, NO145	uc003mzo.3	Q5T4T6	OTTHUMG00000014250	ENST00000283141.6:c.1844T>C	chr6.hg19:g.10942722T>C	ENSP00000283141:p.Leu615Pro	95.0	0.0		74.0	4.0	NM_001040274	A6NDS5|Q08GK5|Q6ZRM2|Q96EJ2	Missense_Mutation	SNP	ENST00000283141.6	hg19	CCDS43423.1	.	.	.	.	.	.	.	.	.	.	T	10.04	1.242314	0.22796	.	.	ENSG00000153157	ENST00000283141	T	0.22134	1.97	4.27	-2.85	0.05734	.	1.111370	0.06908	N	0.807156	T	0.04048	0.0113	L	0.29908	0.895	0.09310	N	1	B	0.14805	0.011	B	0.14578	0.011	T	0.43653	-0.9378	10	0.34782	T	0.22	-1.4292	4.4828	0.11774	0.0:0.282:0.322:0.396	.	615	Q5T4T6	SYC2L_HUMAN	P	615	ENSP00000283141:L615P	ENSP00000283141:L615P	L	+	2	0	SYCP2L	11050708	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.092000	0.15066	-0.479000	0.06813	0.533000	0.62120	CTC	.	.		0.348	SYCP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039845.3	NM_194299		C	10942722	T	C	10942722	3	2	282	1	0	0	0	0	1	0	0	0	15448	1551	54	2	1930	2	SYCP2L	6	10942722	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	356315	10942722	160172345	451	40685										
CD83	9308	hgsc.bcm.edu	37	chr6	14131848	14131848	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcaaaatggttctttcgacgCccccaatgaaaggccctatt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:14131848delC	ENST00000379153.3	+	3	422	c.251delC	c.(250-252)gccfs	p.A84fs		NM_001040280.1|NM_001251901.1|NM_004233.3	NP_001035370.1|NP_001238830.1|NP_004224.1	Q01151	CD83_HUMAN	CD83 molecule	84	Ig-like V-type.				defense response (GO:0006952)|humoral immune response (GO:0006959)|negative regulation of interleukin-4 production (GO:0032713)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-2 production (GO:0032743)|response to organic cyclic compound (GO:0014070)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)	12	Breast(50;0.00245)|Ovarian(93;0.137)	all_hematologic(90;0.117)				TCTTTCGACGCCCCCAATGAA	0.547																																					p.A84fs		Atlas-INDEL	.											CD83,NS,carcinoma,-1,1	CD83	23	.	0			c.250delG						.						130	121	124					6																	14131848		2203	4300	6503	SO:0001589	frameshift_variant	9308	exon3			.	Z11697	CCDS4532.1, CCDS75403.1	6p23	2013-01-11	2006-03-31		ENSG00000112149	ENSG00000112149		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	1703	protein-coding gene	gene with protein product		604534	"CD83 antigen (activated B lymphocytes, immunoglobulin superfamily)", "CD83 molecule "			1378080, 8422464	Standard	NM_001251901		Approved	HB15, BL11	uc003nbi.3	Q01151	OTTHUMG00000014283	ENST00000379153.3:c.251delC	chr6.hg19:g.14131848delC	ENSP00000368450:p.Ala84fs	209.0	0.0		144.0	11.0	NM_004233	Q5THX9	Frame_Shift_Del	DEL	ENST00000379153.3	hg19	CCDS4532.1																																																																																			.	.		0.547	CD83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039916.1			-	14131848	C	-	14131848	7	5	282	1	0	1	0	1	0	0	0	0	3043	739	26	0	261	0	CD83	6	14131848	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	3189126	14131848	156983219	452	40686										
ATXN1	6310	hgsc.bcm.edu	37	chr6	16327823	16327823	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	actggttctgctgggctggtGggggggaccccggggtgatg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:16327823delG	ENST00000244769.4	-	8	1655	c.719delC	c.(718-720)ccafs	p.P241fs	ATXN1_ENST00000436367.1_Frame_Shift_Del_p.P241fs	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	241					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				CTGGGCTGGTGGGGGGGACCC	0.677																																					p.P240fs		Atlas-INDEL	.											.	ATXN1	117	.	0			c.720delA						.																																			SO:0001589	frameshift_variant	6310	exon8			.	X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"Ataxins"	10548	protein-coding gene	gene with protein product		601556	"spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.719delC	chr6.hg19:g.16327823delG	ENSP00000244769:p.Pro241fs	187.0	0.0		179.0	11.0	NM_000332	Q17S02|Q9UJG2|Q9Y4J1	Frame_Shift_Del	DEL	ENST00000244769.4	hg19	CCDS34342.1																																																																																			.	.		0.677	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332		-	16327823	G	-	16327823	7	5	282	1	0	1	0	1	0	0	0	0	1209	1348	47	0	1736	0	ATXN1	6	16327823	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	2195975	16327823	154787244	453	40687										
FAM8A1	51439	hgsc.bcm.edu	37	chr6	17608468	17608468	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aagaatttttcaattgcttcTtttttccctgctttcatcac							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:17608468delT	ENST00000259963.3	+	5	1195	c.1140delT	c.(1138-1140)tctfs	p.S380fs		NM_016255.2	NP_057339.1	Q9UBU6	FA8A1_HUMAN	family with sequence similarity 8, member A1	380	RDD.					integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)|lung(3)	6	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.143)	all cancers(50;0.176)|Epithelial(50;0.204)			CAATTGCTTCTTTTTTCCCTG	0.343																																					p.S380fs		Atlas-INDEL	.											.	FAM8A1	26	.	0			c.1139delC						.						148	148	148					6																	17608468		2203	4300	6503	SO:0001589	frameshift_variant	51439	exon5			.	AF097027	CCDS4540.1	6p23	2010-11-22			ENSG00000137414	ENSG00000137414			16372	protein-coding gene	gene with protein product						11707071	Standard	NM_016255		Approved	AHCP	uc003ncc.3	Q9UBU6	OTTHUMG00000014309	ENST00000259963.3:c.1140delT	chr6.hg19:g.17608468delT	ENSP00000259963:p.Ser380fs	211.0	0.0		172.0	11.0	NM_016255	B2R725	Frame_Shift_Del	DEL	ENST00000259963.3	hg19	CCDS4540.1																																																																																			.	.		0.343	FAM8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039950.1			-	17608468	T	-	17608468	7	5	282	1	0	1	0	1	0	0	0	0	5657	1596	56	0	1158	0	FAM8A1	6	17608468	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1280645	17608468	153506599	454	40688										
KIAA0319	9856	hgsc.bcm.edu	37	chr6	24596508	24596508	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tctgatatcctcaggtgagtCcccccagatccccgaggggg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:24596508delC	ENST00000378214.3	-	3	918	c.394delG	c.(394-396)gacfs	p.D132fs	KIAA0319_ENST00000430948.2_Frame_Shift_Del_p.D87fs|KIAA0319_ENST00000535378.1_Frame_Shift_Del_p.D123fs|KIAA0319_ENST00000543707.1_Frame_Shift_Del_p.D132fs|KIAA0319_ENST00000537886.1_Frame_Shift_Del_p.D132fs	NM_001168375.1|NM_014809.3	NP_001161847.1|NP_055624.2	Q5VV43	K0319_HUMAN	KIAA0319	132					negative regulation of dendrite development (GO:2000171)|neuron migration (GO:0001764)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|endometrium(6)|kidney(3)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	53						TCAGGTGAGTCCCCCCAGATC	0.547																																					p.D132fs		Atlas-INDEL	.											.	KIAA0319	117	.	0			c.395delA						.						70	77	75					6																	24596508		2203	4300	6503	SO:0001589	frameshift_variant	9856	exon3			.	AB002317	CCDS34348.1, CCDS54969.1, CCDS54970.1, CCDS54971.1, CCDS75409.1	6p22.3	2013-12-13			ENSG00000137261	ENSG00000137261			21580	protein-coding gene	gene with protein product	"neuronal migration"	609269				9205841, 15514892	Standard	NM_014809		Approved	NMIG	uc003neh.1	Q5VV43	OTTHUMG00000014358	ENST00000378214.3:c.394delG	chr6.hg19:g.24596508delC	ENSP00000367459:p.Asp132fs	140.0	0.0		124.0	10.0	NM_001168375	A7MD37|B2RTU7|B4DHA7|B4DK75|B7ZML3|F5H123|Q9UJC8|Q9Y4G7	Frame_Shift_Del	DEL	ENST00000378214.3	hg19	CCDS34348.1																																																																																			.	.		0.547	KIAA0319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040009.1	NM_014809		-	24596508	C	-	24596508	7	5	282	1	0	1	0	1	0	0	0	0	8177	855	30	0	2900	0	KIAA0319	6	24596508	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	6988040	24596508	146518559	455	40689										
KIAA0319	9856	hgsc.bcm.edu	37	chr6	24596529	24596529	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cccccagatccccgagggggAgcccctgttcagcatcatgt	11	16	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:24596529A>G	ENST00000378214.3	-	3	897	c.373T>C	c.(373-375)Tcc>Ccc	p.S125P	KIAA0319_ENST00000430948.2_Missense_Mutation_p.S80P|KIAA0319_ENST00000535378.1_Missense_Mutation_p.S116P|KIAA0319_ENST00000543707.1_Missense_Mutation_p.S125P|KIAA0319_ENST00000537886.1_Missense_Mutation_p.S125P	NM_001168375.1|NM_014809.3	NP_001161847.1|NP_055624.2	Q5VV43	K0319_HUMAN	KIAA0319	125					negative regulation of dendrite development (GO:2000171)|neuron migration (GO:0001764)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|endometrium(6)|kidney(3)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	53						CCCGAGGGGGAGCCCCTGTTC	0.552																																					p.S125P		Atlas-SNP	.											KIAA0319,NS,adenocarcinoma,0,1	KIAA0319	117	.	0			c.T373C						.						63	72	69					6																	24596529		2203	4300	6503	SO:0001583	missense	9856	exon3			AGGGGGAGCCCCT	AB002317	CCDS34348.1, CCDS54969.1, CCDS54970.1, CCDS54971.1, CCDS75409.1	6p22.3	2013-12-13			ENSG00000137261	ENSG00000137261			21580	protein-coding gene	gene with protein product	"neuronal migration"	609269				9205841, 15514892	Standard	NM_014809		Approved	NMIG	uc003neh.1	Q5VV43	OTTHUMG00000014358	ENST00000378214.3:c.373T>C	chr6.hg19:g.24596529A>G	ENSP00000367459:p.Ser125Pro	170.0	2.0		139.0	6.0	NM_001168377	A7MD37|B2RTU7|B4DHA7|B4DK75|B7ZML3|F5H123|Q9UJC8|Q9Y4G7	Missense_Mutation	SNP	ENST00000378214.3	hg19	CCDS34348.1	.	.	.	.	.	.	.	.	.	.	A	8.735	0.917681	0.17982	.	.	ENSG00000137261	ENST00000537886;ENST00000535378;ENST00000430948;ENST00000378214;ENST00000543707	T;T;T;T;T	0.07327	3.2;3.2;3.2;3.2;3.2	4.43	-3.03	0.05429	.	0.306847	0.23146	N	0.051405	T	0.01320	0.0043	L	0.27053	0.805	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.09377	0.004;0.004;0.002	T	0.43621	-0.9380	10	0.32370	T	0.25	-0.0397	5.2005	0.15262	0.3908:0.2699:0.3393:0.0	.	125;116;125	F5H123;Q5VV43-2;Q5VV43	.;.;K0319_HUMAN	P	125;116;80;125;125	ENSP00000439700:S125P;ENSP00000442403:S116P;ENSP00000401086:S80P;ENSP00000367459:S125P;ENSP00000437656:S125P	ENSP00000367459:S125P	S	-	1	0	KIAA0319	24704508	0.000000	0.05858	0.000000	0.03702	0.775000	0.43874	-0.048000	0.11944	-0.573000	0.05998	0.421000	0.28195	TCC	.	.		0.552	KIAA0319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040009.1	NM_014809		G	24596529	A	G	24596529	3	3	282	1	0	0	0	0	1	0	0	0	8177	304	11	2	2921	2	KIAA0319	6	24596529	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	21	24596529	146518538	456	40690										
SLC17A2	10246	hgsc.bcm.edu	37	chr6	25917264	25917264	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgcacgggtgatgcatggggTcatcataaatcactgtgaac	12	8	3	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:25917264T>C	ENST00000265425.3	-	6	721	c.701A>G	c.(700-702)gAc>gGc	p.D234G	SLC17A2_ENST00000377850.3_Missense_Mutation_p.D234G|SLC17A2_ENST00000360488.3_Missense_Mutation_p.D234G			O00624	NPT3_HUMAN	solute carrier family 17, member 2	234					phosphate ion transmembrane transport (GO:0035435)|phosphate-containing compound metabolic process (GO:0006796)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	sodium:phosphate symporter activity (GO:0005436)			endometrium(3)|kidney(1)|large_intestine(9)|lung(12)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	31						ATGCATGGGGTCATCATAAAT	0.483																																					p.D234G		Atlas-SNP	.											.	SLC17A2	70	.	0			c.A701G						.						142	119	127					6																	25917264		2203	4300	6503	SO:0001583	missense	10246	exon7			ATGGGGTCATCAT	U90544	CCDS4567.1, CCDS69060.1	6p22.2	2013-07-18	2013-07-18		ENSG00000112337	ENSG00000112337		"Solute carriers"	10930	protein-coding gene	gene with protein product		611049	"solute carrier family 17 (sodium phosphate), member 2"			9149941	Standard	NM_001286123		Approved	NPT3	uc003nfl.3	O00624	OTTHUMG00000014413	ENST00000265425.3:c.701A>G	chr6.hg19:g.25917264T>C	ENSP00000265425:p.Asp234Gly	150.0	0.0		124.0	5.0	NM_005835	A6NK81|A6NLD6|Q5TB84|Q76P85	Missense_Mutation	SNP	ENST00000265425.3	hg19		.	.	.	.	.	.	.	.	.	.	T	18.83	3.708161	0.68615	.	.	ENSG00000112337	ENST00000360488;ENST00000377850;ENST00000265425	T;T;T	0.58797	0.31;0.31;0.31	4.65	4.65	0.58169	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.64402	D	0.000013	T	0.67767	0.2928	M	0.80183	2.485	0.35035	D	0.759147	D;D;D	0.89917	1.0;0.996;0.999	D;D;D	0.77004	0.989;0.959;0.982	T	0.73395	-0.3996	10	0.54805	T	0.06	.	10.6641	0.45719	0.0:0.0:0.0:1.0	.	234;234;234	O00624;A6NK81;O00624-2	NPT3_HUMAN;.;.	G	234	ENSP00000353677:D234G;ENSP00000367081:D234G;ENSP00000265425:D234G	ENSP00000265425:D234G	D	-	2	0	SLC17A2	26025243	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.632000	0.54287	2.067000	0.61834	0.460000	0.39030	GAC	.	.		0.483	SLC17A2-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040075.1			C	25917264	T	C	25917264	3	2	282	1	0	0	0	0	1	0	0	0	14432	1667	58	2	629	2	SLC17A2	6	25917264	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1320735	25917264	145197803	457	40691										
HIST1H1C	3006	hgsc.bcm.edu	37	chr6	26056377	26056377	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	accggtgcctttcgtttgcaCcagagtgcccttgctcacca	9	15	1	1	rs186228942		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:26056377C>T	ENST00000343677.2	-	1	322	c.280G>A	c.(280-282)Gtg>Atg	p.V94M		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	94	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(4)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	34						TTCGTTTGCACCAGAGTGCCC	0.537																																					p.V94M		Atlas-SNP	.											.	HIST1H1C	80	.	0			c.G280A						.						108	113	111					6																	26056377		2203	4300	6503	SO:0001583	missense	3006	exon1			TTTGCACCAGAGT	X57129	CCDS4577.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000187837	ENSG00000187837		"Histones / Replication-dependent"	4716	protein-coding gene	gene with protein product		142710	"H1 histone family, member 2", "histone 1, H1c"	H1F2		2759094, 12408966	Standard	NM_005319		Approved	H1.2, H1s-1, H1c	uc003nfw.3	P16403	OTTHUMG00000016140	ENST00000343677.2:c.280G>A	chr6.hg19:g.26056377C>T	ENSP00000339566:p.Val94Met	318.0	1.0		240.0	103.0	NM_005319	A8K4I2	Missense_Mutation	SNP	ENST00000343677.2	hg19	CCDS4577.1	.	.	.	.	.	.	.	.	.	.	C	17.76	3.468828	0.63625	.	.	ENSG00000187837	ENST00000343677	T	0.09817	2.94	5.63	5.63	0.86233	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.210714	0.39909	N	0.001234	T	0.34308	0.0893	M	0.93328	3.405	0.58432	D	0.999999	D	0.71674	0.998	D	0.77004	0.989	T	0.38308	-0.9667	10	0.87932	D	0	-29.6342	12.3739	0.55269	0.0:0.9231:0.0:0.0768	.	94	P16403	H12_HUMAN	M	94	ENSP00000339566:V94M	ENSP00000339566:V94M	V	-	1	0	HIST1H1C	26164356	1.000000	0.71417	1.000000	0.80357	0.282000	0.26991	2.516000	0.45520	2.814000	0.96858	0.655000	0.94253	GTG	.	C|1.000;G|0.000		0.537	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319		T	26056377	C	T	26056377	3	4	282	1	0	0	0	0	1	0	0	0	7133	507	18	3	365	3	HIST1H1C	6	26056377	Missense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	139113	26056377	145058690	458	40692										
HIST1H4G	8369	hgsc.bcm.edu	37	chr6	26246913	26246913	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cttaaccgccaaagccttacAgggttcttccctggcgtttg	9	13	1	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:26246913A>G	ENST00000244537.4	-	1	346	c.293T>C	c.(292-294)cTg>cCg	p.L98P		NM_003547.2	NP_003538.1	Q99525	H4G_HUMAN	histone cluster 1, H4g	98						nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(1)|large_intestine(1)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	7		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)				AAAGCCTTACAGGGTTCTTCC	0.562																																					p.L98P		Atlas-SNP	.											.	HIST1H4G	18	.	0			c.T293C						.						53	44	47					6																	26246913		2203	4300	6503	SO:0001583	missense	8369	exon1			CCTTACAGGGTTC	Z80788	CCDS4599.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000124578	ENSG00000275663		"Histones / Replication-dependent"	4792	protein-coding gene	gene with protein product		602832	"H4 histone family, member L", "histone 1, H4g"	H4FL		9119399, 12408966	Standard	NM_003547		Approved	H4/l	uc003nhf.3	Q99525	OTTHUMG00000014444	ENST00000244537.4:c.293T>C	chr6.hg19:g.26246913A>G	ENSP00000244537:p.Leu98Pro	138.0	0.0		115.0	40.0	NM_003547		Missense_Mutation	SNP	ENST00000244537.4	hg19	CCDS4599.1	.	.	.	.	.	.	.	.	.	.	.	9.569	1.120585	0.20877	.	.	ENSG00000124578	ENST00000244537	.	.	.	3.05	3.05	0.35203	Histone-fold (1);	.	.	.	.	T	0.70290	0.3207	.	.	.	0.58432	D	0.999995	D	0.89917	1.0	D	0.70227	0.968	T	0.75133	-0.3425	7	0.87932	D	0	.	11.2158	0.48825	1.0:0.0:0.0:0.0	.	98	Q99525	H4G_HUMAN	P	98	.	ENSP00000244537:L98P	L	-	2	0	HIST1H4G	26354892	1.000000	0.71417	0.853000	0.33588	0.003000	0.03518	8.352000	0.90075	1.376000	0.46267	0.321000	0.21382	CTG	.	.		0.562	HIST1H4G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040107.1	NM_003547		G	26246913	A	G	26246913	3	3	282	1	0	0	0	0	1	0	0	0	7180	188	7	2	7	2	HIST1H4G	6	26246913	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	190536	26246913	144868154	459	40693										
ZNF323	64288	hgsc.bcm.edu	37	chr6	28295184	28295184	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttcttgaaattggtggaggcAaaaagattcatatctgagct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:28295184delA	ENST00000414429.1	-	7	1411	c.508delT	c.(508-510)tgcfs	p.C170fs	ZSCAN31_ENST00000344279.6_Frame_Shift_Del_p.C170fs|ZSCAN31_ENST00000481934.1_5'Flank|ZSCAN31_ENST00000396838.2_Frame_Shift_Del_p.C170fs|ZSCAN31_ENST00000439158.1_Frame_Shift_Del_p.C170fs|ZSCAN31_ENST00000446474.1_Frame_Shift_Del_p.C11fs			Q96LW9	ZSC31_HUMAN	zinc finger and SCAN domain containing 31	170					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TGGTGGAGGCAAAAAGATTCA	0.458																																					p.C170fs		Atlas-INDEL	.											.	.	.	.	0			c.509delG						.		,,,	2,4262		1,0,2131	201	176	185		,,,	-3.2	0	6		183	23,8231		11,1,4115	no	frameshift,frameshift,frameshift,frameshift	ZNF323	NM_145909.2,NM_030899.4,NM_001135216.1,NM_001135215.1	,,,	12,1,6246	A1A1,A1R,RR		0.2787,0.0469,0.1997	,,,	,,,	28295184	25,12493	2203	4300	6503	SO:0001589	frameshift_variant	64288	exon3			.		CCDS4649.1, CCDS59001.1	6p	2013-01-09	2013-01-08	2013-01-08	ENSG00000235109	ENSG00000235109		"-", "Zinc fingers, C2H2-type"	14097	protein-coding gene	gene with protein product		610794	"zinc finger protein 310 pseudogene", "zinc finger protein 323"	ZNF310P, ZNF323			Standard	NM_001135216		Approved		uc003nla.3	Q96LW9	OTTHUMG00000014518	ENST00000414429.1:c.508delT	chr6.hg19:g.28295184delA	ENSP00000390076:p.Cys170fs	195.0	0.0		143.0	12.0	NM_030899	Q6P178|Q8WWS5	Frame_Shift_Del	DEL	ENST00000414429.1	hg19	CCDS4649.1																																																																																			.	.		0.458	ZSCAN31-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346804.1	NM_030899		-	28295184	A	-	28295184	7	5	282	1	0	1	0	1	0	0	0	0	17858	130	5	0	720	0	ZNF323	6	28295184	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2048271	28295184	142819883	460	40694										
TRIM27	5987	hgsc.bcm.edu	37	chr6	28887983	28887983	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtgatacagctgctcaaactCccaaacaatcttctccctct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:28887983delC	ENST00000377199.3	-	3	909	c.553delG	c.(553-555)gagfs	p.E185fs	TRIM27_ENST00000377194.3_Frame_Shift_Del_p.E185fs|TRIM27_ENST00000498117.1_5'UTR	NM_006510.4	NP_006501.1	P14373	TRI27_HUMAN	tripartite motif containing 27	185					Arp2/3 complex-mediated actin nucleation (GO:0034314)|cell proliferation (GO:0008283)|innate immune response (GO:0045087)|interferon-gamma secretion (GO:0072643)|negative regulation of adaptive immune response (GO:0002820)|negative regulation of calcium ion import (GO:0090281)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of interleukin-2 secretion (GO:1900041)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein K63-linked ubiquitination (GO:0070534)|protein trimerization (GO:0070206)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(6)|ovary(1)	10						TGCTCAAACTCCCAAACAATC	0.493			T	RET	papillary thyroid																																p.E185fs		Atlas-INDEL	.		Dom	yes		6	6p22	5987	tripartite motif-containing 27		E	.	TRIM27	26	.	0			c.554delA						.						172	162	166					6																	28887983		2203	4300	6503	SO:0001589	frameshift_variant	5987	exon3			.	Z58939	CCDS4654.1	6p22	2013-01-09	2011-01-25	2006-09-26	ENSG00000204713	ENSG00000204713		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	9975	protein-coding gene	gene with protein product		602165	"ret finger protein", "tripartite motif-containing 27"	RFP		8114113	Standard	NM_006510		Approved	RNF76	uc003nlr.3	P14373	OTTHUMG00000031215	ENST00000377199.3:c.553delG	chr6.hg19:g.28887983delC	ENSP00000366404:p.Glu185fs	249.0	0.0		181.0	11.0	NM_006510	A2BE15|Q5RJA8|Q5ST26|Q6LA73|Q6NXR9|Q9BZY6|Q9UJL3	Frame_Shift_Del	DEL	ENST00000377199.3	hg19	CCDS4654.1																																																																																			.	.		0.493	TRIM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076442.2	NM_030950		-	28887983	C	-	28887983	7	5	282	1	0	1	0	1	0	0	0	0	16516	864	30	0	1012	0	TRIM27	6	28887983	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	592799	28887983	142227084	461	40695										
ZFP57	4340	hgsc.bcm.edu	37	chr6	29640726	29640726	+	IGR	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gctaaaagtcaaagaacaatGggggcaacagaagacattga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:29640726delG	ENST00000376917.3	+	0	2160				ZFP57_ENST00000488757.1_Frame_Shift_Del_p.H388fs|ZFP57_ENST00000376883.1_Frame_Shift_Del_p.H368fs|ZFP57_ENST00000376881.3_Frame_Shift_Del_p.H368fs	NM_002433.4|NM_206809.3	NP_002424.3|NP_996532.2	Q16653	MOG_HUMAN	myelin oligodendrocyte glycoprotein						cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|positive regulation of MyD88-dependent toll-like receptor signaling pathway (GO:0034126)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)|skin(2)	19						AAAGAACAATGGGGGCAACAG	0.517																																					p.H388fs		Atlas-INDEL	.											.	ZFP57	80	.	0			c.1163delA						.						325	353	344					6																	29640726		1267	2556	3823	SO:0001628	intergenic_variant	346171	exon4			.		CCDS4667.1, CCDS34366.1, CCDS34367.1, CCDS34368.1, CCDS34369.1, CCDS34370.1, CCDS47394.1, CCDS47395.1, CCDS47395.2, CCDS54977.1	6p22.1	2014-01-16			ENSG00000204655	ENSG00000204655		"Immunoglobulin superfamily / V-set domain containing", "Butyrophilins"	7197	protein-coding gene	gene with protein product		159465					Standard	NM_002433		Approved	BTN6, BTNL11	uc003nne.3	Q16653	OTTHUMG00000031099		chr6.hg19:g.29640726delG		232.0	0.0		160.0	11.0	NM_001109809	A6NDR4|A6NNJ9|A8MY31|B0UZR9|E9PGF0|F8W9D5|O00713|O00714|O00715|Q13054|Q13055|Q14855|Q29ZN8|Q56UY0|Q5JNX7|Q5JNY1|Q5JNY2|Q5JNY4|Q5SSB5|Q5SSB6|Q5STL9|Q5STM0|Q5STM1|Q5STM2|Q5STM5|Q5SUK5|Q5SUK7|Q5SUK8|Q5SUK9|Q5SUL0|Q5SUL1|Q8IYG5|Q92891|Q92892|Q92893|Q92894|Q92895|Q93053|Q96KU9|Q96KV0|Q96KV1|Q99605	Frame_Shift_Del	DEL	ENST00000376917.3	hg19	CCDS34370.1																																																																																			.	.		0.517	MOG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076160.3	NM_002433		-	29640726	G	-	29640726	6	5	282	0	1	1	0	1	0	0	0	0	17666	1348	47	0		0	ZFP57	6	29640726	IGR	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	752743	29640726	141474341	462	40696										
HLA-A	3105	hgsc.bcm.edu	37	chr6	29910372	29910372	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	accctcctcctgctactctcGggggccctggccctgaccca					rs200905772|rs41548119	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:29910372delG	ENST00000396634.1	+	3	383	c.42delG	c.(40-42)tcgfs	p.S14fs	HLA-A_ENST00000376802.2_Frame_Shift_Del_p.S14fs|HLA-A_ENST00000376809.5_Frame_Shift_Del_p.S14fs|HLA-A_ENST00000376806.5_Frame_Shift_Del_p.S14fs			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	14					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						TGCTACTCTCGGGGGCCCTGG	0.706									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)																											p.S14fs		Atlas-INDEL	.											.	HLA-A	89	.	0			c.41delC						.																																			SO:0001589	frameshift_variant	3105	exon1	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	.	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.42delG	chr6.hg19:g.29910372delG	ENSP00000379873:p.Ser14fs	292.0	0.0		200.0	16.0	NM_002116	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Frame_Shift_Del	DEL	ENST00000396634.1	hg19	CCDS34373.1																																																																																			.	.		0.706	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116		-	29910372	G	-	29910372	7	5	282	1	0	1	0	1	0	0	0	0	7204	1103	39	0	44	0	HLA-A	6	29910372	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	269646	29910372	141204695	463	40697										
HLA-E	3133	hgsc.bcm.edu	37	chr6	30458916	30458916	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tctgactcttcccctcagagCccccaaagacacacgtgact							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:30458916delC	ENST00000376630.4	+	4	678	c.613delC	c.(613-615)cccfs	p.P206fs		NM_005516.5	NP_005507.3	P13747	HLAE_HUMAN	major histocompatibility complex, class I, E	206	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of endogenous peptide antigen via MHC class Ib (GO:0002476)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of natural killer cell mediated immunity (GO:0002717)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protection from natural killer cell mediated cytotoxicity (GO:0042270)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	MHC class I protein binding (GO:0042288)|peptide antigen binding (GO:0042605)			breast(2)|central_nervous_system(4)|endometrium(1)|kidney(3)|large_intestine(2)|lung(1)|ovary(3)|skin(1)|urinary_tract(1)	18						CCCCTCAGAGCCCCCAAAGAC	0.552																																					p.E204fs		Atlas-INDEL	.											.	HLA-E	35	.	0			c.612delG						.						115	135	127					6																	30458916		1511	2709	4220	SO:0001589	frameshift_variant	3133	exon4			.	M20022	CCDS34379.1	6p21.3	2013-01-11			ENSG00000204592	ENSG00000204592		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4962	protein-coding gene	gene with protein product		143010				3131426	Standard	NM_005516		Approved		uc003nqg.3	P13747	OTTHUMG00000031155	ENST00000376630.4:c.613delC	chr6.hg19:g.30458916delC	ENSP00000365817:p.Pro206fs	283.0	0.0		174.0	11.0	NM_005516	Q30169|Q9BT83|Q9GIY7|Q9GIY8	Frame_Shift_Del	DEL	ENST00000376630.4	hg19	CCDS34379.1																																																																																			.	.		0.552	HLA-E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076282.2	NM_005516		-	30458916	C	-	30458916	7	5	282	1	0	1	0	1	0	0	0	0	7219	739	26	0	627	0	HLA-E	6	30458916	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	548544	30458916	140656151	464	40698										
VARS2	57176	hgsc.bcm.edu	37	chr6	30890972	30890972	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cttcgctttatcctcaatgcTttaggggagaaatttgtgcc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:30890972delT	ENST00000321897.5	+	23	2909	c.2277delT	c.(2275-2277)gctfs	p.A759fs	VARS2_ENST00000541562.1_Frame_Shift_Del_p.A789fs|VARS2_ENST00000416670.2_Frame_Shift_Del_p.A759fs|VARS2_ENST00000476162.1_3'UTR|VARS2_ENST00000542001.1_Frame_Shift_Del_p.A619fs			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	759					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						TCCTCAATGCTTTAGGGGAGA	0.532																																					p.A789fs		Atlas-INDEL	.											.	VARS2	60	.	0			c.2366delC						.						108	121	116					6																	30890972		1510	2708	4218	SO:0001589	frameshift_variant	57176	exon24			.	AB067472	CCDS34387.1, CCDS54980.1	6p21.33	2012-10-26	2012-10-26	2007-02-23	ENSG00000137411	ENSG00000137411	6.1.1.9	"Aminoacyl tRNA synthetases / Class I"	21642	protein-coding gene	gene with protein product	"valine tRNA ligase 2, mitochondrial"	612802	"valyl-tRNA synthetase 2-like", "valyl-tRNA synthetase like", "valyl-tRNA synthetase 2, mitochondrial (putative)"	VARS2L, VARSL		1898367, 11572484, 18400783	Standard	NM_001167734		Approved	DKFZP434L1435, KIAA1885, G7a	uc011dmz.2	Q5ST30	OTTHUMG00000031263	ENST00000321897.5:c.2277delT	chr6.hg19:g.30890972delT	ENSP00000316092:p.Ala759fs	261.0	0.0		159.0	12.0	NM_001167734	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Frame_Shift_Del	DEL	ENST00000321897.5	hg19	CCDS34387.1																																																																																			.	.		0.532	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442		-	30890972	T	-	30890972	7	5	282	1	0	1	0	1	0	0	0	0	17139	1596	56	0	2461	0	VARS2	6	30890972	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	432056	30890972	140224095	465	40699										
BAT2	7916	hgsc.bcm.edu	37	chr6	31602310	31602310	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tggatggagcccctgagtccTtttgaggatgtggctggcac							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:31602310delT	ENST00000376033.2	+	20	5145	c.4911delT	c.(4909-4911)cctfs	p.P1637fs	PRRC2A_ENST00000376007.4_Frame_Shift_Del_p.P1637fs	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1637	4 X 57 AA type A repeats.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						CCCTGAGTCCTTTTGAGGATG	0.572																																					p.P1637fs		Atlas-INDEL	.											.	PRRC2A	152	.	0			c.4910delC						.						35	32	33					6																	31602310		1511	2708	4219	SO:0001589	frameshift_variant	7916	exon20			.	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"HLA-B associated transcript 2"	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.4911delT	chr6.hg19:g.31602310delT	ENSP00000365201:p.Pro1637fs	125.0	0.0		110.0	10.0	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Frame_Shift_Del	DEL	ENST00000376033.2	hg19	CCDS4708.1																																																																																			.	.		0.572	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686		-	31602310	T	-	31602310	7	5	282	1	0	1	0	1	0	0	0	0	1319	1596	56	0	4985	0	BAT2	6	31602310	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	711338	31602310	139512757	466	40700										
BAT4	7918	hgsc.bcm.edu	37	chr6	31630338	31630338	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccctcagcagcagtttgaagCccgggctggagatgggcacc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:31630338delC	ENST00000375906.1	-	4	1460	c.776delG	c.(775-777)ggcfs	p.G259fs	GPANK1_ENST00000375895.2_Frame_Shift_Del_p.G259fs|CSNK2B_ENST00000375885.4_5'Flank|GPANK1_ENST00000375900.4_Frame_Shift_Del_p.G259fs|C6orf47_ENST00000375911.1_5'Flank|GPANK1_ENST00000375893.2_Frame_Shift_Del_p.G259fs|GPANK1_ENST00000375896.4_Frame_Shift_Del_p.G259fs|C6orf47-AS1_ENST00000422049.1_RNA|Y_RNA_ENST00000364337.1_RNA	NM_001199237.1	NP_001186166.1	O95872	GPAN1_HUMAN	G patch domain and ankyrin repeats 1	259	G-patch. {ECO:0000255|PROSITE- ProRule:PRU00092}.						nucleic acid binding (GO:0003676)			central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(7)	12						CAGTTTGAAGCCCGGGCTGGA	0.647																																					p.G259fs		Atlas-INDEL	.											.	GPANK1	19	.	0			c.777delC						.						39	48	45					6																	31630338		1511	2708	4219	SO:0001589	frameshift_variant	7918	exon4			.		CCDS4711.1	6p21.3	2013-01-28	2010-11-24	2010-11-24	ENSG00000204438	ENSG00000204438		"Ankyrin repeat domain containing", "G patch domain containing"	13920	protein-coding gene	gene with protein product	"G patch domain containing 10", "ankyrin repeat domain 59"	142610	"HLA-B associated transcript 4"	BAT4		2911734, 2813433	Standard	NM_001199237		Approved	G5, D6S54E, GPATCH10, ANKRD59	uc021yuu.1	O95872	OTTHUMG00000031174	ENST00000375906.1:c.776delG	chr6.hg19:g.31630338delC	ENSP00000365071:p.Gly259fs	225.0	0.0		167.0	11.0	NM_001199238	A6NG25|B0UXA2|Q5SQ49	Frame_Shift_Del	DEL	ENST00000375906.1	hg19	CCDS4711.1																																																																																			.	.		0.647	GPANK1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144445.2	NM_033177		-	31630338	C	-	31630338	7	5	282	1	0	1	0	1	0	0	0	0	1323	739	26	0	298	0	BAT4	6	31630338	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	28028	31630338	139484729	467	40701										
EHMT2	10919	hgsc.bcm.edu	37	chr6	31850734	31850734	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atgagcacgcctggttacacTcgaaaatcagcggaggctca	11	11	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:31850734T>C	ENST00000375537.4	-	24	3053	c.3047A>G	c.(3046-3048)gAg>gGg	p.E1016G	EHMT2_ENST00000480912.1_5'UTR|EHMT2_ENST00000395728.3_Missense_Mutation_p.E1073G|EHMT2_ENST00000375528.4_Missense_Mutation_p.E1039G|EHMT2_ENST00000375530.4_Missense_Mutation_p.E982G|EHMT2-AS1_ENST00000434689.1_RNA	NM_006709.3	NP_006700.3	Q96KQ7	EHMT2_HUMAN	euchromatic histone-lysine N-methyltransferase 2	1016	Pre-SET. {ECO:0000255|PROSITE- ProRule:PRU00157}.				DNA methylation (GO:0006306)|DNA methylation on cytosine within a CG sequence (GO:0010424)|fertilization (GO:0009566)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ growth (GO:0035265)|peptidyl-lysine dimethylation (GO:0018027)|regulation of DNA replication (GO:0006275)|spermatid development (GO:0007286)|synaptonemal complex assembly (GO:0007130)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)	21						CTGGTTACACTCGAAAATCAG	0.572																																					p.E1016G		Atlas-SNP	.											.	EHMT2	45	.	0			c.A3047G						.						71	71	71					6																	31850734		1511	2709	4220	SO:0001583	missense	10919	exon24			TTACACTCGAAAA	AF134726	CCDS4725.1, CCDS4726.1, CCDS75425.1	6p21.3	2013-01-10	2004-03-22	2005-06-09	ENSG00000204371	ENSG00000204371	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases", "Ankyrin repeat domain containing"	14129	protein-coding gene	gene with protein product		604599	"chromosome 6 open reading frame 30", "HLA-B associated transcript 8"	C6orf30, BAT8		8457211, 11316813	Standard	XM_005274833		Approved	G9A, Em:AF134726.3, NG36/G9a, KMT1C	uc003nxz.1	Q96KQ7	OTTHUMG00000031180	ENST00000375537.4:c.3047A>G	chr6.hg19:g.31850734T>C	ENSP00000364687:p.Glu1016Gly	128.0	0.0		92.0	4.0	NM_006709	B0UZY2|Q14349|Q5JP83|Q5JQ92|Q5JQA1|Q5JQG3|Q6PK06|Q96MH5|Q96QD0|Q9UQL8|Q9Y331	Missense_Mutation	SNP	ENST00000375537.4	hg19	CCDS4725.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.324471	0.81580	.	.	ENSG00000204371	ENST00000395728;ENST00000375528;ENST00000375530;ENST00000375537;ENST00000442298	D;D;D;D	0.86694	-2.16;-2.16;-2.16;-2.16	4.24	4.24	0.50183	Pre-SET zinc-binding sub-group (1);Pre-SET domain (2);	0.000000	0.85682	D	0.000000	D	0.95178	0.8437	H	0.97896	4.1	0.58432	D	0.999993	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.96364	0.9268	10	0.87932	D	0	.	12.4856	0.55871	0.0:0.0:0.0:1.0	.	1039;982;1016;837	A2ABF8;Q96KQ7-2;Q96KQ7;Q59FM7	.;.;EHMT2_HUMAN;.	G	1073;1039;982;1016;837	ENSP00000379078:E1073G;ENSP00000364678:E1039G;ENSP00000364680:E982G;ENSP00000364687:E1016G	ENSP00000364678:E1039G	E	-	2	0	EHMT2	31958713	1.000000	0.71417	0.998000	0.56505	0.830000	0.47004	7.629000	0.83207	1.787000	0.52448	0.459000	0.35465	GAG	.	.		0.572	EHMT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076355.5	NM_006709		C	31850734	T	C	31850734	3	2	282	1	0	0	0	0	1	0	0	0	4986	1551	54	2	605	2	EHMT2	6	31850734	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	220396	31850734	139264333	468	40702										
C2	717	hgsc.bcm.edu	37	chr6	31903769	31903769	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagagcccaaagtcctcatgTctgtcctgaacgacaactcc	7	15	2	2	rs541199729		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:31903769T>C	ENST00000299367.5	+	7	1195	c.919T>C	c.(919-921)Tct>Cct	p.S307P	CFB_ENST00000556679.1_Intron|C2_ENST00000442278.2_Missense_Mutation_p.S175P|CFB_ENST00000456570.1_Intron|C2_ENST00000469372.1_Missense_Mutation_p.S61P|CFB_ENST00000477310.1_Intron|C2_ENST00000452323.2_Intron	NM_000063.4	NP_000054.2	P06681	CO2_HUMAN	complement component 2	307	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|positive regulation of apoptotic cell clearance (GO:2000427)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)|skin(2)|urinary_tract(2)	27		Ovarian(999;0.00965)		LUAD - Lung adenocarcinoma(999;0.247)		AGTCCTCATGTCTGTCCTGAA	0.502																																					p.S307P		Atlas-SNP	.											.	C2	50	.	0			c.T919C						.						110	98	102					6																	31903769		1511	2709	4220	SO:0001583	missense	717	exon7			CTCATGTCTGTCC		CCDS4728.1, CCDS54991.1, CCDS56416.1, CCDS75427.1, CCDS75428.1	6p21.3	2014-09-17			ENSG00000166278	ENSG00000166278		"Complement system"	1248	protein-coding gene	gene with protein product		613927					Standard	NM_001145903		Approved		uc011hbs.1	P06681	OTTHUMG00000031190	ENST00000299367.5:c.919T>C	chr6.hg19:g.31903769T>C	ENSP00000299367:p.Ser307Pro	124.0	0.0		93.0	4.0	NM_000063	B4DPF3|B4DV20|E9PFN7|O19694|Q13904	Missense_Mutation	SNP	ENST00000299367.5	hg19	CCDS4728.1	.	.	.	.	.	.	.	.	.	.	T	14.52	2.561228	0.45590	.	.	ENSG00000166278	ENST00000469372;ENST00000497706;ENST00000432397;ENST00000299367;ENST00000442278	T;T;T;T	0.76968	-1.06;-1.06;-1.06;-1.06	5.73	5.73	0.89815	von Willebrand factor, type A (3);	0.000000	0.38605	N	0.001621	T	0.81559	0.4848	.	.	.	0.80722	D	1	P;B;B;P;D	0.76494	0.895;0.281;0.442;0.863;0.999	B;B;B;P;D	0.72075	0.444;0.128;0.199;0.504;0.976	T	0.82078	-0.0635	9	0.38643	T	0.18	-17.5078	10.1003	0.42499	0.0:0.0:0.1682:0.8318	.	278;61;175;307;94	B4DV48;B4DQI1;E9PFN7;P06681;E9PDZ0	.;.;.;CO2_HUMAN;.	P	61;94;94;307;175	ENSP00000418923:S61P;ENSP00000417482:S94P;ENSP00000299367:S307P;ENSP00000395683:S175P	ENSP00000299367:S307P	S	+	1	0	C2	32011748	0.867000	0.29959	0.996000	0.52242	0.502000	0.33828	0.659000	0.24994	2.188000	0.69820	0.383000	0.25322	TCT	.	.		0.502	C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076379.9			C	31903769	T	C	31903769	3	2	282	1	0	0	0	0	1	0	0	0	2076	1667	58	2	1022	2	C2	6	31903769	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	53035	31903769	139211298	469	40703										
TNXB	7148	hgsc.bcm.edu	37	chr6	32036432	32036432	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcccccaggcgaggcttgatGgggggctcgggggttgcggt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:32036432delG	ENST00000375244.3	-	17	6156	c.5955delC	c.(5953-5955)cccfs	p.P1985fs	TNXB_ENST00000375247.2_Frame_Shift_Del_p.P1985fs			P22105	TENX_HUMAN	tenascin XB	2067	Fibronectin type-III 12. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						GAGGCTTGATGGGGGGCTCGG	0.632																																					p.I1986fs		Atlas-INDEL	.											.	TNXB	553	.	0			c.5956delA						.						44	50	48					6																	32036432		1943	4133	6076	SO:0001589	frameshift_variant	7148	exon17			.	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.5955delC	chr6.hg19:g.32036432delG	ENSP00000364393:p.Pro1985fs	215.0	0.0		190.0	12.0	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Frame_Shift_Del	DEL	ENST00000375244.3	hg19																																																																																				.	.		0.632	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		-	32036432	G	-	32036432	7	5	282	1	0	1	0	1	0	0	0	0	16361	1335	47	0	8870	0	TNXB	6	32036432	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	132663	32036432	139078635	470	40704										
TNXB	7148	hgsc.bcm.edu	37	chr6	32038147	32038147	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggggtctgtcacccacagctCcccaaggcggggtggggccc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:32038147delC	ENST00000375244.3	-	14	5236	c.5035delG	c.(5035-5037)gagfs	p.E1679fs	TNXB_ENST00000375247.2_Frame_Shift_Del_p.E1679fs			P22105	TENX_HUMAN	tenascin XB	1761	Fibronectin type-III 9. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						ACCCACAGCTCCCCAAGGCGG	0.582																																					p.E1679fs		Atlas-INDEL	.											.	TNXB	553	.	0			c.5036delA						.						15	17	16					6																	32038147		1915	4106	6021	SO:0001589	frameshift_variant	7148	exon14			.	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.5035delG	chr6.hg19:g.32038147delC	ENSP00000364393:p.Glu1679fs	186.0	0.0		179.0	11.0	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Frame_Shift_Del	DEL	ENST00000375244.3	hg19																																																																																				.	.		0.582	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		-	32038147	C	-	32038147	7	5	282	1	0	1	0	1	0	0	0	0	16361	864	30	0	9802	0	TNXB	6	32038147	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1715	32038147	139076920	471	40705										
NOTCH4	4855	hgsc.bcm.edu	37	chr6	32169107	32169107	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccagggcaaacagctgctggTctagggctggggggctcagt	17	10	2	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:32169107T>C	ENST00000375023.3	-	22	4064	c.3926A>G	c.(3925-3927)gAc>gGc	p.D1309G		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	1309					cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						CAGCTGCTGGTCTAGGGCTGG	0.637																																					p.D1309G		Atlas-SNP	.											.	NOTCH4	201	.	0			c.A3926G						.						37	41	39					6																	32169107		1508	2709	4217	SO:0001583	missense	4855	exon22			TGCTGGTCTAGGG		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"Ankyrin repeat domain containing"	7884	protein-coding gene	gene with protein product		164951	"Notch (Drosophila) homolog 4", "Notch homolog 4 (Drosophila)"	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.3926A>G	chr6.hg19:g.32169107T>C	ENSP00000364163:p.Asp1309Gly	129.0	0.0		93.0	4.0	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Missense_Mutation	SNP	ENST00000375023.3	hg19	CCDS34420.1	.	.	.	.	.	.	.	.	.	.	T	10.62	1.402555	0.25291	.	.	ENSG00000204301	ENST00000375023	T	0.81163	-1.46	4.37	4.37	0.52481	.	0.364566	0.19536	N	0.111902	T	0.57080	0.2029	L	0.27053	0.805	0.80722	D	1	B	0.14012	0.009	B	0.20184	0.028	T	0.58853	-0.7563	10	0.40728	T	0.16	.	11.615	0.51083	0.0:0.0:0.0:1.0	.	1309	Q99466	NOTC4_HUMAN	G	1309	ENSP00000364163:D1309G	ENSP00000364163:D1309G	D	-	2	0	NOTCH4	32277085	0.998000	0.40836	0.999000	0.59377	0.651000	0.38670	3.197000	0.51028	1.862000	0.54008	0.374000	0.22700	GAC	.	.		0.637	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2			C	32169107	T	C	32169107	3	2	282	1	0	0	0	0	1	0	0	0	10560	1667	58	2	2121	2	NOTCH4	6	32169107	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	130960	32169107	138945960	472	40706										
COL11A2	1302	hgsc.bcm.edu	37	chr6	33136315	33136315	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctcgctttccaagtggccctGggggtccattctccccggtg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:33136315delG	ENST00000374708.4	-	52	3941	c.3683delC	c.(3682-3684)ccafs	p.P1228fs	COL11A2_ENST00000374713.1_Frame_Shift_Del_p.P1267fs|COL11A2_ENST00000477772.1_Intron|COL11A2_ENST00000395197.1_Frame_Shift_Del_p.P1254fs|COL11A2_ENST00000361917.1_Frame_Shift_Del_p.P1207fs|COL11A2_ENST00000374714.1_Frame_Shift_Del_p.P1288fs|COL11A2_ENST00000357486.1_Frame_Shift_Del_p.P1293fs|COL11A2_ENST00000374712.1_Frame_Shift_Del_p.P1233fs|COL11A2_ENST00000341947.2_Frame_Shift_Del_p.P1314fs	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	1314	Triple-helical region.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						AAGTGGCCCTGGGGGTCCATT	0.632																																					p.P1314fs	Melanoma(1;90 116 3946 5341 17093)	Atlas-INDEL	.											.	COL11A2	124	.	0			c.3942delA						.						52	48	49					6																	33136315		1511	2709	4220	SO:0001589	frameshift_variant	1302	exon54			.	U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"Collagens"	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000374708.4:c.3683delC	chr6.hg19:g.33136315delG	ENSP00000363840:p.Pro1228fs	142.0	0.0		119.0	10.0	NM_080680	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Frame_Shift_Del	DEL	ENST00000374708.4	hg19	CCDS43452.1																																																																																			.	.		0.632	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2			-	33136315	G	-	33136315	7	5	282	1	0	1	0	1	0	0	0	0	3670	1348	47	0	1321	0	COL11A2	6	33136315	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	967208	33136315	137978752	473	40707										
SLC39A7	7922	hgsc.bcm.edu	37	chr6	33169107	33169107	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggcttctggtggctggactcGggggtcatgacgacctgcac							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:33169107delG	ENST00000374677.3	+	1	458	c.85delG	c.(85-87)gggfs	p.G30fs	RXRB_ENST00000413614.2_5'Flank|RNY4P10_ENST00000365571.1_RNA|RXRB_ENST00000374685.4_5'Flank|RXRB_ENST00000374680.3_5'Flank|SLC39A7_ENST00000374675.3_Frame_Shift_Del_p.G30fs|RXRB_ENST00000544186.1_5'Flank	NM_006979.2	NP_008910.2	Q92504	S39A7_HUMAN	solute carrier family 39 (zinc transporter), member 7	30	His-rich.				transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metal ion transmembrane transporter activity (GO:0046873)			NS(1)|breast(3)|endometrium(2)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						GGCTGGACTCGGGGGTCATGA	0.647																																					p.L28fs		Atlas-INDEL	.											.	SLC39A7	32	.	0			c.84delC						.						57	66	63					6																	33169107		2069	4211	6280	SO:0001589	frameshift_variant	7922	exon2			.	AF117221	CCDS43453.1	6p21.3	2014-01-28		2003-10-27	ENSG00000112473	ENSG00000112473		"Solute carriers"	4927	protein-coding gene	gene with protein product		601416	"HLA class II region expressed gene KE4"	HKE4		8812499, 1855816, 19246244, 15705588	Standard	NM_006979		Approved	H2-KE4, D6S2244E, KE4, RING5, ZIP7	uc003odf.3	Q92504	OTTHUMG00000031238	ENST00000374677.3:c.85delG	chr6.hg19:g.33169107delG	ENSP00000363809:p.Gly30fs	204.0	0.0		157.0	11.0	NM_001077516	B0UXF6|Q5STP8|Q9UIQ0	Frame_Shift_Del	DEL	ENST00000374677.3	hg19	CCDS43453.1																																																																																			.	.		0.647	SLC39A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076499.2	NM_006979		-	33169107	G	-	33169107	7	5	282	1	0	1	0	1	0	0	0	0	14638	1116	39	0	87	0	SLC39A7	6	33169107	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	32792	33169107	137945960	474	40708										
RING1	6015	hgsc.bcm.edu	37	chr6	33180112	33180112	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaccctggagctggtgaatgAgaaattctggaaggtgtccc	14	8	1	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:33180112A>G	ENST00000374656.4	+	7	1365	c.1157A>G	c.(1156-1158)gAg>gGg	p.E386G	RING1_ENST00000478431.1_3'UTR	NM_002931.3	NP_002922.2	Q06587	RING1_HUMAN	ring finger protein 1	386	Necessary for interaction with CBX2. {ECO:0000250}.				anterior/posterior pattern specification (GO:0009952)|camera-type eye morphogenesis (GO:0048593)|histone H2A monoubiquitination (GO:0035518)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(5)|large_intestine(1)|lung(3)|ovary(2)|prostate(2)|skin(4)	17						CTGGTGAATGAGAAATTCTGG	0.557																																					p.E386G		Atlas-SNP	.											.	RING1	40	.	0			c.A1157G						.						28	24	26					6																	33180112		1507	2706	4213	SO:0001583	missense	6015	exon7			TGAATGAGAAATT		CCDS34424.1	6p21.3	2013-01-09			ENSG00000204227	ENSG00000204227		"RING-type (C3HC4) zinc fingers"	10018	protein-coding gene	gene with protein product		602045				1906426	Standard	NM_002931		Approved	RNF1	uc003odk.3	Q06587	OTTHUMG00000031278	ENST00000374656.4:c.1157A>G	chr6.hg19:g.33180112A>G	ENSP00000363787:p.Glu386Gly	191.0	0.0		154.0	7.0	NM_002931	A8JZZ0|Q5JP96|Q5SQW2|Q86V19	Missense_Mutation	SNP	ENST00000374656.4	hg19	CCDS34424.1	.	.	.	.	.	.	.	.	.	.	A	13.12	2.142262	0.37825	.	.	ENSG00000204227	ENST00000374656	D	0.88354	-2.37	4.92	4.92	0.64577	.	0.000000	0.85682	D	0.000000	D	0.89532	0.6742	L	0.43152	1.355	0.51767	D	0.99993	D	0.71674	0.998	D	0.70227	0.968	D	0.91220	0.5006	10	0.87932	D	0	-17.1428	12.5707	0.56334	1.0:0.0:0.0:0.0	.	386	Q06587	RING1_HUMAN	G	386	ENSP00000363787:E386G	ENSP00000363787:E386G	E	+	2	0	RING1	33288090	1.000000	0.71417	0.995000	0.50966	0.025000	0.11179	8.207000	0.89746	2.046000	0.60703	0.523000	0.50628	GAG	.	.		0.557	RING1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076609.2			G	33180112	A	G	33180112	3	3	282	1	0	0	0	0	1	0	0	0	13389	304	11	2	1179	2	RING1	6	33180112	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	11005	33180112	137934955	475	40709										
SYNGAP1	8831	hgsc.bcm.edu	37	chr6	33388070	33388070	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtctcgagcctccatccatcGggggagcatccccgcgatgt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:33388070delG	ENST00000418600.2	+	1	130	c.29delG	c.(28-30)cggfs	p.R10fs	CUTA_ENST00000607266.1_5'Flank|CUTA_ENST00000492510.1_5'Flank|CUTA_ENST00000374496.3_5'Flank|SYNGAP1_ENST00000293748.5_Frame_Shift_Del_p.R10fs|CUTA_ENST00000374500.5_5'Flank|CUTA_ENST00000488034.1_5'Flank|CUTA_ENST00000494751.1_5'Flank|CUTA_ENST00000488478.1_5'Flank|CUTA_ENST00000440279.3_5'Flank	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	10					dendrite development (GO:0016358)|negative regulation of axonogenesis (GO:0050771)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|pattern specification process (GO:0007389)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|receptor clustering (GO:0043113)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of MAPK cascade (GO:0043408)|regulation of synapse structure and activity (GO:0050803)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Rab GTPase activator activity (GO:0005097)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(15)|ovary(7)|pancreas(1)|stomach(1)|urinary_tract(1)	43						TCCATCCATCGGGGGAGCATC	0.682																																					p.R10fs		Atlas-INDEL	.											.	SYNGAP1	202	.	0			c.28delC						.						4	3	3					6																	33388070		1493	2602	4095	SO:0001589	frameshift_variant	8831	exon1			.	AB067525	CCDS34434.2	6p21.3	2010-06-25	2010-06-25		ENSG00000197283	ENSG00000197283			11497	protein-coding gene	gene with protein product		603384	"synaptic Ras GTPase activating protein 1 homolog (rat)"			9581761, 18323856	Standard	NM_006772		Approved	SYNGAP, RASA5, KIAA1938	uc011dri.2	Q96PV0	OTTHUMG00000031096	ENST00000418600.2:c.29delG	chr6.hg19:g.33388070delG	ENSP00000403636:p.Arg10fs	264.0	0.0		193.0	13.0	NM_006772	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Frame_Shift_Del	DEL	ENST00000418600.2	hg19	CCDS34434.2																																																																																			.	.		0.682	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407		-	33388070	G	-	33388070	7	5	282	1	0	1	0	1	0	0	0	0	15462	1116	39	0	31	0	SYNGAP1	6	33388070	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	207958	33388070	137726997	476	40710										
FANCE	2178	hgsc.bcm.edu	37	chr6	35425715	35425715	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gttagagggattggaggatgCccccccagttgagctacagc					rs587778337		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:35425715delC	ENST00000229769.2	+	4	1108	c.923delC	c.(922-924)gccfs	p.A308fs		NM_021922.2	NP_068741.1	Q9HB96	FANCE_HUMAN	Fanconi anemia, complementation group E	308	Interaction with FANCC.				DNA repair (GO:0006281)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|ovary(1)|skin(2)	13						TTGGAGGATGCCCCCCCAGTT	0.542			"N, F, S"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.A308fs		Atlas-INDEL	.	yes	Rec		Fanconi anaemia E	6	6p21-p22	2178	"Fanconi anemia, complementation group E"		L	.,2	FANCE	45	.	0			c.922delG						.						77	74	75					6																	35425715		2203	4300	6503	SO:0001589	frameshift_variant	2178	exon4	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	.	AF265210	CCDS4805.1	6p22-p21	2014-09-17			ENSG00000112039	ENSG00000112039		"Fanconi anemia, complementation groups"	3586	protein-coding gene	gene with protein product		613976		FACE		7662964, 11001585	Standard	XM_005248885		Approved	FAE	uc003oko.1	Q9HB96	OTTHUMG00000014565	ENST00000229769.2:c.923delC	chr6.hg19:g.35425715delC	ENSP00000229769:p.Ala308fs	173.0	0.0		150.0	10.0	NM_021922	A8K907|Q4ZGH2	Frame_Shift_Del	DEL	ENST00000229769.2	hg19	CCDS4805.1																																																																																			.	.		0.542	FANCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040282.1			-	35425715	C	-	35425715	7	5	282	1	0	1	0	1	0	0	0	0	5674	739	26	0	937	0	FANCE	6	35425715	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	2037645	35425715	135689352	477	40711										
MDGA1	266727	hgsc.bcm.edu	37	chr6	37605207	37605207	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agctgtgggctggactggcaGggggctccactgcccggcat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:37605207delG	ENST00000434837.3	-	17	3983	c.2805delC	c.(2803-2805)cccfs	p.P935fs	MDGA1_ENST00000297153.7_Frame_Shift_Del_p.P939fs	NM_153487.3	NP_705691.1	Q8NFP4	MDGA1_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 1	935					brain development (GO:0007420)|cerebral cortex radially oriented cell migration (GO:0021799)|neuron migration (GO:0001764)|spinal cord association neuron differentiation (GO:0021527)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)				central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	38						TGGACTGGCAGGGGGCTCCAC	0.657																																					p.C936fs		Atlas-INDEL	.											.	MDGA1	104	.	0			c.2806delT						.						36	41	39					6																	37605207		2028	4189	6217	SO:0001589	frameshift_variant	266727	exon17			.	AF478693	CCDS47417.1	6p21	2013-01-29			ENSG00000112139	ENSG00000112139		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19267	protein-coding gene	gene with protein product		609626				15922729, 15019943	Standard	NM_153487		Approved	GPIM, MAMDC3	uc003onu.1	Q8NFP4	OTTHUMG00000014626	ENST00000434837.3:c.2805delC	chr6.hg19:g.37605207delG	ENSP00000402584:p.Pro935fs	284.0	0.0		210.0	13.0	NM_153487	A6NHG0|Q8NBE3	Frame_Shift_Del	DEL	ENST00000434837.3	hg19	CCDS47417.1																																																																																			.	.		0.657	MDGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040419.3			-	37605207	G	-	37605207	7	5	282	1	0	1	0	1	0	0	0	0	9415	987	35	0	66	0	MDGA1	6	37605207	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	2179492	37605207	133509860	478	40712										
TFEB	7942	hgsc.bcm.edu	37	chr6	41655721	41655721	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caccagggaggctgtgacctGggggtcgctgctgtacacat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:41655721delG	ENST00000230323.4	-	6	896	c.595delC	c.(595-597)cagfs	p.Q199fs	TFEB_ENST00000403298.4_Frame_Shift_Del_p.Q199fs|TFEB_ENST00000394283.1_Frame_Shift_Del_p.Q199fs|TFEB_ENST00000358871.2_Frame_Shift_Del_p.Q213fs|TFEB_ENST00000373033.1_Frame_Shift_Del_p.Q199fs|TFEB_ENST00000420312.1_Frame_Shift_Del_p.Q114fs	NM_001271945.1|NM_007162.2	NP_001258874.1|NP_009093.1	P19484	TFEB_HUMAN	transcription factor EB	199					autophagy (GO:0006914)|embryonic placenta development (GO:0001892)|humoral immune response (GO:0006959)|lysosome organization (GO:0007040)|positive regulation of autophagy (GO:0010508)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	11	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;7.61e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)			GCTGTGACCTGGGGGTCGCTG	0.657			T	ALPHA	renal (childhood epithelioid)																																p.Q213fs		Atlas-INDEL	.		Dom	yes		6	6p21	7942	transcription factor EB		"E,M"	.	TFEB	37	.	0			c.638delA						.						65	65	65					6																	41655721		2203	4300	6503	SO:0001589	frameshift_variant	7942	exon5			.	M33782	CCDS4858.1, CCDS64424.1, CCDS64425.1	6p21	2013-05-21			ENSG00000112561	ENSG00000112561		"Basic helix-loop-helix proteins"	11753	protein-coding gene	gene with protein product		600744				2115126	Standard	NM_007162		Approved	TCFEB, bHLHe35	uc003oqu.2	P19484	OTTHUMG00000014684	ENST00000230323.4:c.595delC	chr6.hg19:g.41655721delG	ENSP00000230323:p.Gln199fs	253.0	0.0		205.0	14.0	NM_001167827	Q709B3|Q7Z6P9|Q9BRJ5|Q9UJD8	Frame_Shift_Del	DEL	ENST00000230323.4	hg19	CCDS4858.1																																																																																			.	.		0.657	TFEB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040522.3			-	41655721	G	-	41655721	7	5	282	1	0	1	0	1	0	0	0	0	15816	1357	47	0	855	0	TFEB	6	41655721	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	4050514	41655721	129459346	479	40713										
PGC	5225	hgsc.bcm.edu	37	chr6	41708310	41708310	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgtacaggctgctatccacaCccccaaagacaaccgctccc					rs572661097		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:41708310delC	ENST00000373025.3	-	6	748	c.686delG	c.(685-687)ggtfs	p.G229fs		NM_002630.3	NP_002621.1	P20142	PEPC_HUMAN	progastricsin (pepsinogen C)	229					digestion (GO:0007586)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|skin(1)	16	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;0.000132)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)			GCTATCCACACCCCCAAAGAC	0.602																																					p.G229fs		Atlas-INDEL	.											.	PGC	56	.	0			c.687delT						.						103	103	103					6																	41708310		2203	4300	6503	SO:0001589	frameshift_variant	5225	exon6			.		CCDS4859.1, CCDS55000.1	6p21.1	2012-10-02			ENSG00000096088	ENSG00000096088	3.4.23.3		8890	protein-coding gene	gene with protein product		169740					Standard	NM_002630		Approved		uc003ora.2	P20142	OTTHUMG00000014683	ENST00000373025.3:c.686delG	chr6.hg19:g.41708310delC	ENSP00000362116:p.Gly229fs	153.0	0.0		147.0	13.0	NM_002630	B4DVZ3|Q5T3D7|Q5T3D8	Frame_Shift_Del	DEL	ENST00000373025.3	hg19	CCDS4859.1																																																																																			.	.		0.602	PGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040521.2			-	41708310	C	-	41708310	7	5	282	1	0	1	0	1	0	0	0	0	11794	507	18	0	496	0	PGC	6	41708310	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	52589	41708310	129406757	480	40714										
UBR2	23304	hgsc.bcm.edu	37	chr6	42620286	42620286	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtttgcaagcctggttaacaTtttgcagtcagatgtcatgt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:42620286delT	ENST00000372899.1	+	25	2930	c.2672delT	c.(2671-2673)attfs	p.I891fs	UBR2_ENST00000372901.1_Frame_Shift_Del_p.I891fs|UBR2_ENST00000372883.3_Frame_Shift_Del_p.I395fs	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	891					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			CTGGTTAACATTTTGCAGTCA	0.448																																					p.I891fs		Atlas-INDEL	.											.	UBR2	134	.	0			c.2671delA						.						237	206	217					6																	42620286		2203	4300	6503	SO:0001589	frameshift_variant	23304	exon25			.	BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"Ubiquitin protein ligase E3 component n-recognins"	21289	protein-coding gene	gene with protein product		609134	"chromosome 6 open reading frame 133"	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.2672delT	chr6.hg19:g.42620286delT	ENSP00000361990:p.Ile891fs	240.0	0.0		183.0	13.0	NM_015255	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Frame_Shift_Del	DEL	ENST00000372899.1	hg19	CCDS4870.1																																																																																			.	.		0.448	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255		-	42620286	T	-	42620286	7	5	282	1	0	1	0	1	0	0	0	0	16917	1493	52	0	2916	0	UBR2	6	42620286	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	911976	42620286	128494781	481	40715										
SRF	6722	hgsc.bcm.edu	37	chr6	43143627	43143627	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcagcagtgccaatgggactGtgctgaagagtacaggcagc	14	9	1	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:43143627G>A	ENST00000265354.4	+	3	1322	c.964G>A	c.(964-966)Gtg>Atg	p.V322M	SRF_ENST00000457278.2_Missense_Mutation_p.V118M	NM_003131.2	NP_003122.1	P11831	SRF_HUMAN	serum response factor (c-fos serum response element-binding transcription factor)	322					angiogenesis involved in wound healing (GO:0060055)|associative learning (GO:0008306)|cardiac myofibril assembly (GO:0055003)|cardiac vascular smooth muscle cell differentiation (GO:0060947)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-matrix adhesion (GO:0007160)|cellular response to glucose stimulus (GO:0071333)|cellular senescence (GO:0090398)|contractile actin filament bundle assembly (GO:0030038)|developmental growth (GO:0048589)|dorsal aorta morphogenesis (GO:0035912)|epithelial cell-cell adhesion (GO:0090136)|epithelial structure maintenance (GO:0010669)|erythrocyte development (GO:0048821)|eyelid development in camera-type eye (GO:0061029)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula formation (GO:0060347)|hematopoietic stem cell differentiation (GO:0060218)|hippocampus development (GO:0021766)|long term synaptic depression (GO:0060292)|long-term memory (GO:0007616)|megakaryocyte development (GO:0035855)|mesoderm formation (GO:0001707)|morphogenesis of an epithelial sheet (GO:0002011)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|neuron development (GO:0048666)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|patterning of blood vessels (GO:0001569)|platelet activation (GO:0030168)|platelet formation (GO:0030220)|positive regulation of cell differentiation (GO:0045597)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription by glucose (GO:0046016)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription via serum response element binding (GO:0010735)|positive thymic T cell selection (GO:0045059)|primitive streak formation (GO:0090009)|regulation of cell adhesion (GO:0030155)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of water loss via skin (GO:0033561)|response to cytokine (GO:0034097)|response to hormone (GO:0009725)|response to hypoxia (GO:0001666)|response to toxic substance (GO:0009636)|sarcomere organization (GO:0045214)|skin morphogenesis (GO:0043589)|stress fiber assembly (GO:0043149)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)|tight junction assembly (GO:0070830)|transcription from RNA polymerase II promoter (GO:0006366)|trophectodermal cell differentiation (GO:0001829)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|serum response element binding (GO:0010736)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)	12			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.011)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)			CAATGGGACTGTGCTGAAGAG	0.612																																					p.V322M		Atlas-SNP	.											.	SRF	24	.	0			c.G964A						.						114	101	106					6																	43143627		2203	4300	6503	SO:0001583	missense	6722	exon3			GGGACTGTGCTGA	J03161	CCDS4889.1	6p	2008-02-05			ENSG00000112658	ENSG00000112658			11291	protein-coding gene	gene with protein product		600589				3203386	Standard	NM_003131		Approved	MCM1	uc003oui.3	P11831	OTTHUMG00000014722	ENST00000265354.4:c.964G>A	chr6.hg19:g.43143627G>A	ENSP00000265354:p.Val322Met	146.0	0.0		100.0	4.0	NM_003131	Q5T648	Missense_Mutation	SNP	ENST00000265354.4	hg19	CCDS4889.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.316191	0.81469	.	.	ENSG00000112658	ENST00000265354;ENST00000457278	D	0.84800	-1.9	4.82	4.82	0.62117	.	0.000000	0.85682	D	0.000000	D	0.84611	0.5510	L	0.47716	1.5	0.80722	D	1	D	0.59357	0.985	P	0.54060	0.741	D	0.86513	0.1811	10	0.62326	D	0.03	-4.0164	17.8792	0.88835	0.0:0.0:1.0:0.0	.	322	P11831	SRF_HUMAN	M	322;118	ENSP00000265354:V322M	ENSP00000265354:V322M	V	+	1	0	SRF	43251605	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	6.244000	0.72391	2.203000	0.70933	0.462000	0.41574	GTG	.	.		0.612	SRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040581.1	NM_003131		A	43143627	G	A	43143627	3	1	282	1	0	0	0	0	1	0	0	0	15158	1377	48	3	974	3	SRF	6	43143627	Missense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	523341	43143627	127971440	482	40716										
SLC29A1	2030	hgsc.bcm.edu	37	chr6	44197187	44197187	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggaacgctgctcccgtggaaTtttttcatgacggccactca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:44197187delT	ENST00000393841.1	+	4	581	c.90delT	c.(88-90)aatfs	p.N30fs	SLC29A1_ENST00000371713.1_Frame_Shift_Del_p.N30fs|SLC29A1_ENST00000371724.1_Frame_Shift_Del_p.N30fs|SLC29A1_ENST00000313248.7_Frame_Shift_Del_p.N109fs|SLC29A1_ENST00000371740.5_Frame_Shift_Del_p.N30fs|SLC29A1_ENST00000371731.1_Frame_Shift_Del_p.N30fs|SLC29A1_ENST00000393844.1_Frame_Shift_Del_p.N30fs|SLC29A1_ENST00000371755.3_Frame_Shift_Del_p.N30fs|SLC29A1_ENST00000427851.2_Frame_Shift_Del_p.N30fs|SLC29A1_ENST00000371708.1_Frame_Shift_Del_p.N30fs	NM_001078177.1	NP_001071645.1	Q99808	S29A1_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 1	30					cellular response to glucose stimulus (GO:0071333)|cellular response to hypoxia (GO:0071456)|lactation (GO:0007595)|nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|sleep (GO:0030431)|transmembrane transport (GO:0055085)|uridine transport (GO:0015862)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside transmembrane transporter activity (GO:0005337)			endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(2)	17	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)		Cytarabine(DB00987)|Didanosine(DB00900)|Fludarabine(DB01073)|Fluorouracil(DB00544)|Gemcitabine(DB00441)|Mercaptopurine(DB01033)|Pemetrexed(DB00642)|Ribavirin(DB00811)|Zalcitabine(DB00943)	TCCCGTGGAATTTTTTCATGA	0.557																																					p.N30fs		Pindel	.											.	SLC29A1	45	.	0			c.89delA						.						161	153	156					6																	44197187		2203	4300	6503	SO:0001589	frameshift_variant	2030	exon3			.	U81375	CCDS4908.1	6p21.1	2013-07-17	2013-07-17		ENSG00000112759	ENSG00000112759		"Solute carriers"	11003	protein-coding gene	gene with protein product		602193	"solute carrier family 29 (nucleoside transporters), member 1"	ENT1		8986748, 9344680	Standard	NM_004955		Approved		uc003owy.2	Q99808	OTTHUMG00000014759	ENST00000393841.1:c.90delT	chr6.hg19:g.44197187delT	ENSP00000377424:p.Asn30fs	371.0	0.0		282.0	12.0	NM_004955	B3KQV7|B3KQY5|Q5T9W9|Q9UJY2	Frame_Shift_Del	DEL	ENST00000393841.1	hg19	CCDS4908.1																																																																																			.	.		0.557	SLC29A1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040721.1			-	44197187	T	-	44197187	7	5	282	1	0	1	0	1	0	0	0	0	14549	1490	52	0	96	0	SLC29A1	6	44197187	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1053560	44197187	126917880	483	40717										
SLC29A1	2030	hgsc.bcm.edu	37	chr6	44199193	44199193	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	actctatcaaagccatcctgAaaaatgtacgtaggggaggt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:44199193delA	ENST00000393841.1	+	10	1350	c.859delA	c.(859-861)aaafs	p.K287fs	SLC29A1_ENST00000371713.1_Frame_Shift_Del_p.K287fs|SLC29A1_ENST00000371724.1_Frame_Shift_Del_p.K287fs|SLC29A1_ENST00000472176.1_3'UTR|SLC29A1_ENST00000313248.7_Frame_Shift_Del_p.K366fs|SLC29A1_ENST00000371740.5_Frame_Shift_Del_p.K287fs|SLC29A1_ENST00000371731.1_Frame_Shift_Del_p.K287fs|SLC29A1_ENST00000393844.1_Frame_Shift_Del_p.K287fs|SLC29A1_ENST00000371755.3_Frame_Shift_Del_p.K287fs|SLC29A1_ENST00000427851.2_Frame_Shift_Del_p.K287fs|SLC29A1_ENST00000371708.1_Frame_Shift_Del_p.K287fs	NM_001078177.1	NP_001071645.1	Q99808	S29A1_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 1	287					cellular response to glucose stimulus (GO:0071333)|cellular response to hypoxia (GO:0071456)|lactation (GO:0007595)|nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|sleep (GO:0030431)|transmembrane transport (GO:0055085)|uridine transport (GO:0015862)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside transmembrane transporter activity (GO:0005337)			endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(2)	17	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)		Cytarabine(DB00987)|Didanosine(DB00900)|Fludarabine(DB01073)|Fluorouracil(DB00544)|Gemcitabine(DB00441)|Mercaptopurine(DB01033)|Pemetrexed(DB00642)|Ribavirin(DB00811)|Zalcitabine(DB00943)	AGCCATCCTGAAAAATGTACG	0.522																																					p.L286fs		Atlas-INDEL	.											.	SLC29A1	45	.	0			c.858delG						.						106	86	93					6																	44199193		2203	4300	6503	SO:0001589	frameshift_variant	2030	exon10			.	U81375	CCDS4908.1	6p21.1	2013-07-17	2013-07-17		ENSG00000112759	ENSG00000112759		"Solute carriers"	11003	protein-coding gene	gene with protein product		602193	"solute carrier family 29 (nucleoside transporters), member 1"	ENT1		8986748, 9344680	Standard	NM_004955		Approved		uc003owy.2	Q99808	OTTHUMG00000014759	ENST00000393841.1:c.859delA	chr6.hg19:g.44199193delA	ENSP00000377424:p.Lys287fs	153.0	0.0		173.0	11.0	NM_001078175	B3KQV7|B3KQY5|Q5T9W9|Q9UJY2	Frame_Shift_Del	DEL	ENST00000393841.1	hg19	CCDS4908.1																																																																																			.	.		0.522	SLC29A1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040721.1			-	44199193	A	-	44199193	7	5	282	1	0	1	0	1	0	0	0	0	14549	247	9	0	889	0	SLC29A1	6	44199193	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2006	44199193	126915874	484	40718										
PKHD1	5314	hgsc.bcm.edu	37	chr6	51503672	51503672	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggagaagtgacagtaaaaatAaagtgccagtttgacccaga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:51503672delA	ENST00000371117.3	-	64	11756	c.11481delT	c.(11479-11481)tttfs	p.F3827fs		NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3827					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					CAGTAAAAATAAAGTGCCAGT	0.353																																					p.I3828fs		Atlas-INDEL	.											.	PKHD1	927	.	0			c.11482delA						.						149	153	152					6																	51503672		2203	4300	6503	SO:0001589	frameshift_variant	5314	exon64			.	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.11481delT	chr6.hg19:g.51503672delA	ENSP00000360158:p.Phe3827fs	210.0	0.0		165.0	10.0	NM_138694	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Frame_Shift_Del	DEL	ENST00000371117.3	hg19	CCDS4935.1																																																																																			.	.		0.353	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		-	51503672	A	-	51503672	7	5	282	1	0	1	0	1	0	0	0	0	11980	359	13	0	759	0	PKHD1	6	51503672	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	7304479	51503672	119611395	485	40719										
PKHD1	5314	hgsc.bcm.edu	37	chr6	51927342	51927342	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aggttgtccttcctgtgaccAaaacccaaatggagaactgg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:51927342delA	ENST00000371117.3	-	14	1368	c.1093delT	c.(1093-1095)tggfs	p.W365fs	PKHD1_ENST00000340994.4_Frame_Shift_Del_p.W365fs|AL590391.1_ENST00000408630.2_RNA	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	365					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					TCCTGTGACCAAAACCCAAAT	0.488																																					p.W365fs		Atlas-INDEL	.											.	PKHD1	927	.	0			c.1094delG						.						151	140	143					6																	51927342		2203	4300	6503	SO:0001589	frameshift_variant	5314	exon14			.	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.1093delT	chr6.hg19:g.51927342delA	ENSP00000360158:p.Trp365fs	216.0	0.0		162.0	10.0	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Frame_Shift_Del	DEL	ENST00000371117.3	hg19	CCDS4935.1																																																																																			.	.		0.488	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		-	51927342	A	-	51927342	7	5	282	1	0	1	0	1	0	0	0	0	11980	130	5	0	11386	0	PKHD1	6	51927342	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	423670	51927342	119187725	486	40720										
FAM83B	222584	hgsc.bcm.edu	37	chr6	54806060	54806060	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaagaaggaagttaagggttCcccaagttttttgaaaaagg					rs200345393	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:54806060delC	ENST00000306858.7	+	5	2407	c.2291delC	c.(2290-2292)tccfs	p.S764fs	RP3-523K23.2_ENST00000562834.1_RNA	NM_001010872.1	NP_001010872.1	Q5T0W9	FA83B_HUMAN	family with sequence similarity 83, member B	764										autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(28)|ovary(6)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	71	Lung NSC(77;0.0178)|Renal(3;0.122)					GTTAAGGGTTCCCCAAGTTTT	0.373																																					p.S764fs		Atlas-INDEL	.											.	FAM83B	186	.	0			c.2290delT						.						56	59	58					6																	54806060		2203	4300	6503	SO:0001589	frameshift_variant	222584	exon5			.	AK055204	CCDS34479.1	6p12.1	2014-03-13	2006-03-23	2006-03-23	ENSG00000168143	ENSG00000168143			21357	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 143"	C6orf143		22886302	Standard	NM_001010872		Approved	FLJ30642	uc003pck.4	Q5T0W9	OTTHUMG00000014899	ENST00000306858.7:c.2291delC	chr6.hg19:g.54806060delC	ENSP00000304078:p.Ser764fs	126.0	0.0		77.0	10.0	NM_001010872	Q2M1P3|Q96DQ2	Frame_Shift_Del	DEL	ENST00000306858.7	hg19	CCDS34479.1																																																																																			.	.		0.373	FAM83B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040994.1	XM_294139		-	54806060	C	-	54806060	7	5	282	1	0	1	0	1	0	0	0	0	5642	855	30	0	2305	0	FAM83B	6	54806060	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	2878718	54806060	116309007	487	40721										
DST	667	hgsc.bcm.edu	37	chr6	56340988	56340988	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tttcacctcttcgatctcctGggggatgacttctttatcct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:56340988delG	ENST00000361203.3	-	87	20870	c.20863delC	c.(20863-20865)cagfs	p.Q6955fs	DST_ENST00000244364.6_Frame_Shift_Del_p.Q4652fs|DST_ENST00000446842.2_Frame_Shift_Del_p.Q6740fs|DST_ENST00000370788.2_Frame_Shift_Del_p.Q4869fs|DST_ENST00000370769.4_Frame_Shift_Del_p.Q7066fs|DST_ENST00000421834.2_Frame_Shift_Del_p.Q4978fs|DST_ENST00000370754.5_Frame_Shift_Del_p.Q7244fs|DST_ENST00000312431.6_3'UTR			Q03001	DYST_HUMAN	dystonin	6953					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TCGATCTCCTGGGGGATGACT	0.408																																					p.Q4652fs		Atlas-INDEL	.											.	DST	1427	.	0			c.13955delA						.						90	86	87					6																	56340988		1898	4112	6010	SO:0001589	frameshift_variant	667	exon73			.	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.20863delC	chr6.hg19:g.56340988delG	ENSP00000354508:p.Gln6955fs	198.0	0.0		153.0	11.0	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Frame_Shift_Del	DEL	ENST00000361203.3	hg19																																																																																				.	.		0.408	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		-	56340988	G	-	56340988	7	5	282	1	0	1	0	1	0	0	0	0	4785	1357	47	0	1609	0	DST	6	56340988	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1534928	56340988	114774079	488	40722										
PHF3	23469	hgsc.bcm.edu	37	chr6	64404551	64404551	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctagctcctcttcgtaagatGggacaaccagttttacctcg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:64404551delG	ENST00000262043.3	+	6	2917	c.2577delG	c.(2575-2577)atgfs	p.M859fs	PHF3_ENST00000393387.1_Frame_Shift_Del_p.M859fs			Q92576	PHF3_HUMAN	PHD finger protein 3	859					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(7)|cervix(2)|endometrium(8)|kidney(7)|large_intestine(18)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(6)	75	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			TTCGTAAGATGGGACAACCAG	0.383																																					p.M859fs	GBM(135;136 1820 29512 34071 46235)	Atlas-INDEL	.											.	PHF3	191	.	0			c.2576delT						.						100	113	108					6																	64404551		2202	4300	6502	SO:0001589	frameshift_variant	23469	exon5			.	AF091622	CCDS4966.1	6q12	2013-09-24			ENSG00000118482	ENSG00000118482		"Zinc fingers, PHD-type"	8921	protein-coding gene	gene with protein product		607789				11856869	Standard	XM_005248701		Approved		uc003pep.1	Q92576	OTTHUMG00000014952	ENST00000262043.3:c.2577delG	chr6.hg19:g.64404551delG	ENSP00000262043:p.Met859fs	215.0	0.0		164.0	11.0	NM_015153	A3KFI8|Q14CR5|Q5CZI1|Q5T1T6|Q9NQ16|Q9UI45	Frame_Shift_Del	DEL	ENST00000262043.3	hg19	CCDS4966.1																																																																																			.	.		0.383	PHF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041086.2			-	64404551	G	-	64404551	7	5	282	1	0	1	0	1	0	0	0	0	11845	1348	47	0	2595	0	PHF3	6	64404551	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	8063563	64404551	106710516	489	40723										
EYS	346007	hgsc.bcm.edu	37	chr6	65016918	65016918	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggatggaatgaaagatctccAgttatttatttctataactt	7	5	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:65016918A>G	ENST00000370621.3	-	30	6662	c.6136T>C	c.(6136-6138)Tgg>Cgg	p.W2046R	EYS_ENST00000503581.1_Missense_Mutation_p.W2046R|EYS_ENST00000370616.2_Missense_Mutation_p.W2046R			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	2046	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						AAAGATCTCCAGTTATTTATT	0.338																																					p.W2046R		Atlas-SNP	.											.	EYS	527	.	0			c.T6136C						.						198	162	173					6																	65016918		692	1588	2280	SO:0001583	missense	346007	exon30			ATCTCCAGTTATT		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.6136T>C	chr6.hg19:g.65016918A>G	ENSP00000359655:p.Trp2046Arg	80.0	0.0		64.0	5.0	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	hg19		.	.	.	.	.	.	.	.	.	.	A	12.57	1.978562	0.34942	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	T;T;T	0.66099	-0.19;-0.19;-0.19	5.2	-3.76	0.04359	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);	.	.	.	.	T	0.14184	0.0343	N	0.08118	0	0.09310	N	0.999999	B;B	0.32160	0.358;0.244	B;B	0.30495	0.116;0.054	T	0.15925	-1.0420	9	0.23891	T	0.37	.	6.4241	0.21760	0.2192:0.3184:0.4624:0.0	.	2046;2046	Q5T1H1-1;Q5T1H1	.;EYS_HUMAN	R	2046	ENSP00000424243:W2046R;ENSP00000359655:W2046R;ENSP00000359650:W2046R	ENSP00000359650:W2046R	W	-	1	0	EYS	65074877	0.001000	0.12720	0.001000	0.08648	0.453000	0.32348	-0.257000	0.08745	-0.582000	0.05929	-0.316000	0.08728	TGG	.	.		0.338	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		G	65016918	A	G	65016918	3	3	282	1	0	0	0	0	1	0	0	0	5334	188	7	2	3354	2	EYS	6	65016918	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	612367	65016918	106098149	490	40724										
EYS	346007	hgsc.bcm.edu	37	chr6	65301367	65301367	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttcttcaatatcctcttgagCccccctagagacaactggag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:65301367delC	ENST00000370621.3	-	26	4919	c.4393delG	c.(4393-4395)gctfs	p.A1465fs	EYS_ENST00000503581.1_Frame_Shift_Del_p.A1465fs|EYS_ENST00000370616.2_Frame_Shift_Del_p.A1465fs			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	1465					detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						TCCTCTTGAGCCCCCCTAGAG	0.463																																					p.A1465fs		Atlas-INDEL	.											EYS_ENST00000370621,NS,carcinoma,0,1	EYS	527	.	0			c.4394delC						.						53	54	54					6																	65301367		692	1591	2283	SO:0001589	frameshift_variant	346007	exon26			.		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.4393delG	chr6.hg19:g.65301367delC	ENSP00000359655:p.Ala1465fs	266.0	0.0		157.0	10.0	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Frame_Shift_Del	DEL	ENST00000370621.3	hg19																																																																																				.	.		0.463	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		-	65301367	C	-	65301367	7	5	282	1	0	1	0	1	0	0	0	0	5334	739	26	0	4958	0	EYS	6	65301367	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	284449	65301367	105813700	491	40725										
EYS	346007	hgsc.bcm.edu	37	chr6	66054028	66054028	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgcagtttgcagccagaaagAaataggcatcaataacccct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:66054028delA	ENST00000370621.3	-	10	2028	c.1502delT	c.(1501-1503)ttcfs	p.F502fs	EYS_ENST00000370618.3_Frame_Shift_Del_p.F502fs|EYS_ENST00000342421.5_Frame_Shift_Del_p.F502fs|EYS_ENST00000503581.1_Frame_Shift_Del_p.F502fs|EYS_ENST00000370616.2_Frame_Shift_Del_p.F502fs|EYS_ENST00000393380.2_Frame_Shift_Del_p.F502fs			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	502					detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						AGCCAGAAAGAAATAGGCATC	0.358																																					p.F501fs		Atlas-INDEL	.											EYS_ENST00000370621,NS,carcinoma,0,2	EYS	527	.	0			c.1503delC						.						100	100	100					6																	66054028		2203	4300	6503	SO:0001589	frameshift_variant	346007	exon10			.		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.1502delT	chr6.hg19:g.66054028delA	ENSP00000359655:p.Phe502fs	217.0	0.0		170.0	11.0	NM_001142801	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Frame_Shift_Del	DEL	ENST00000370621.3	hg19																																																																																				.	.		0.358	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		-	66054028	A	-	66054028	7	5	282	1	0	1	0	1	0	0	0	0	5334	246	9	0	8030	0	EYS	6	66054028	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	752661	66054028	105061039	492	40726										
EYS	346007	hgsc.bcm.edu	37	chr6	66200486	66200486	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtatacatatgcattttttaCctgaaaattgctcatcacat	4	8	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:66200486C>A	ENST00000370621.3	-	5	1389		c.e5+1		EYS_ENST00000370618.3_Splice_Site|EYS_ENST00000342421.5_Splice_Site|EYS_ENST00000503581.1_Splice_Site|EYS_ENST00000370616.2_Splice_Site|EYS_ENST00000393380.2_Splice_Site			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)						detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						GCATTTTTTACCTGAAAATTG	0.274																																					.		Atlas-SNP	.											.	EYS	527	.	0			c.862+1G>T						.						58	53	55					6																	66200486		2203	4294	6497	SO:0001630	splice_region_variant	346007	exon6			TTTTTACCTGAAA		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.862+1G>T	chr6.hg19:g.66200486C>A		468.0	0.0		372.0	15.0	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Splice_Site	SNP	ENST00000370621.3	hg19		.	.	.	.	.	.	.	.	.	.	C	7.600	0.672484	0.14776	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616;ENST00000393380;ENST00000342421;ENST00000370618	.	.	.	4.54	2.52	0.30459	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.0309	0.19679	0.2503:0.6524:0.0:0.0973	.	.	.	.	.	-1	.	.	.	-	.	.	EYS	66257207	1.000000	0.71417	0.035000	0.18076	0.300000	0.27592	3.082000	0.50128	0.302000	0.22762	0.655000	0.94253	.	.	.		0.274	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	Intron	A	66200486	C	A	66200486	5	1	282	1	0	0	0	0	0	0	1	0	5334	521	18	3	8689	3	EYS	6	66200486	Splice_Site	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	146458	66200486	104914581	493	40727										
LMBRD1	55788	hgsc.bcm.edu	37	chr6	70411386	70411386	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggattactcaggttagctccAaaaattatgaaaccagaatc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:70411386delA	ENST00000370577.3	-	11	1261	c.1032delT	c.(1030-1032)tttfs	p.F344fs	LMBRD1_ENST00000370570.1_Frame_Shift_Del_p.F271fs	NM_018368.3	NP_060838.3	Q9NUN5	LMBD1_HUMAN	LMBR1 domain containing 1	344					cobalamin metabolic process (GO:0009235)|insulin receptor internalization (GO:0038016)|negative regulation of glucose import (GO:0046325)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein kinase B signaling (GO:0051898)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	clathrin-coated endocytic vesicle (GO:0045334)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cobalamin binding (GO:0031419)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)	31						GGTTAGCTCCAAAAATTATGA	0.274																																					p.G345fs		Atlas-INDEL	.											LMBRD1,NS,carcinoma,0,1	LMBRD1	61	.	0			c.1033delG						.						57	58	57					6																	70411386		2199	4290	6489	SO:0001589	frameshift_variant	55788	exon11			.	AF113224	CCDS4969.1	6q13	2011-05-12	2005-07-25	2005-07-25	ENSG00000168216	ENSG00000168216			23038	protein-coding gene	gene with protein product		612625	"chromosome 6 open reading frame 209"	C6orf209		19136951	Standard	NM_018368		Approved	FLJ11240, bA810I22.1, cblF	uc003pfa.3	Q9NUN5	OTTHUMG00000014985	ENST00000370577.3:c.1032delT	chr6.hg19:g.70411386delA	ENSP00000359609:p.Phe344fs	209.0	0.0		148.0	10.0	NM_018368	A8K204|E1P531|Q5VUN6|Q86Y70|Q96FW4|Q9BY56|Q9NZD6	Frame_Shift_Del	DEL	ENST00000370577.3	hg19	CCDS4969.1																																																																																			.	.		0.274	LMBRD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041124.1	NM_018368		-	70411386	A	-	70411386	7	5	282	1	0	1	0	1	0	0	0	0	8851	127	5	0	614	0	LMBRD1	6	70411386	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	4210900	70411386	100703681	494	40728										
LMBRD1	55788	hgsc.bcm.edu	37	chr6	70500277	70500277	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gataagtgcaattgctagagAaaaaattgctgttatggtgg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:70500277delA	ENST00000370577.3	-	2	386	c.157delT	c.(157-159)tctfs	p.S53fs	LMBRD1_ENST00000370570.1_5'UTR	NM_018368.3	NP_060838.3	Q9NUN5	LMBD1_HUMAN	LMBR1 domain containing 1	53					cobalamin metabolic process (GO:0009235)|insulin receptor internalization (GO:0038016)|negative regulation of glucose import (GO:0046325)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein kinase B signaling (GO:0051898)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	clathrin-coated endocytic vesicle (GO:0045334)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cobalamin binding (GO:0031419)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)	31						ATTGCTAGAGAAAAAATTGCT	0.343																																					p.S53fs		Atlas-INDEL	.											LMBRD1,NS,carcinoma,0,1	LMBRD1	61	.	0			c.158delC						.						121	128	126					6																	70500277		2203	4300	6503	SO:0001589	frameshift_variant	55788	exon2			.	AF113224	CCDS4969.1	6q13	2011-05-12	2005-07-25	2005-07-25	ENSG00000168216	ENSG00000168216			23038	protein-coding gene	gene with protein product		612625	"chromosome 6 open reading frame 209"	C6orf209		19136951	Standard	NM_018368		Approved	FLJ11240, bA810I22.1, cblF	uc003pfa.3	Q9NUN5	OTTHUMG00000014985	ENST00000370577.3:c.157delT	chr6.hg19:g.70500277delA	ENSP00000359609:p.Ser53fs	186.0	0.0		123.0	10.0	NM_018368	A8K204|E1P531|Q5VUN6|Q86Y70|Q96FW4|Q9BY56|Q9NZD6	Frame_Shift_Del	DEL	ENST00000370577.3	hg19	CCDS4969.1																																																																																			.	.		0.343	LMBRD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041124.1	NM_018368		-	70500277	A	-	70500277	7	5	282	1	0	1	0	1	0	0	0	0	8851	246	9	0	1525	0	LMBRD1	6	70500277	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	88891	70500277	100614790	495	40729										
OGFRL1	79627	hgsc.bcm.edu	37	chr6	72011155	72011155	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggtgagcttggatatgaaagTtttaaatctcctcttgtaaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:72011155delT	ENST00000370435.4	+	7	893	c.759delT	c.(757-759)agtfs	p.S253fs	RP11-154D6.1_ENST00000586030.1_RNA|RP11-154D6.1_ENST00000412751.1_RNA|RP11-154D6.1_ENST00000423255.1_RNA|RP11-154D6.1_ENST00000587253.1_RNA|RP11-154D6.1_ENST00000588612.1_RNA|RP11-154D6.1_ENST00000587397.1_RNA|RP3-331H24.5_ENST00000602823.1_lincRNA|RP11-154D6.1_ENST00000432050.1_RNA|RP11-154D6.1_ENST00000450998.1_RNA|RP11-154D6.1_ENST00000585882.1_RNA|RP11-154D6.1_ENST00000587036.1_RNA|RP11-154D6.1_ENST00000586232.1_RNA|RP11-154D6.1_ENST00000591156.1_RNA	NM_024576.3	NP_078852.3	Q5TC84	OGRL1_HUMAN	opioid growth factor receptor-like 1	253						membrane (GO:0016020)	receptor activity (GO:0004872)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|upper_aerodigestive_tract(1)	13						GATATGAAAGTTTTAAATCTC	0.353																																					p.S253fs		Atlas-INDEL	.											.	OGFRL1	44	.	0			c.758delG						.						142	164	156					6																	72011155		2203	4300	6503	SO:0001589	frameshift_variant	79627	exon7			.		CCDS34482.1	6q13	2008-02-05			ENSG00000119900	ENSG00000119900			21378	protein-coding gene	gene with protein product							Standard	NM_024576		Approved	dJ331H24.1	uc003pfx.1	Q5TC84	OTTHUMG00000015000	ENST00000370435.4:c.759delT	chr6.hg19:g.72011155delT	ENSP00000359464:p.Ser253fs	176.0	0.0		156.0	12.0	NM_024576	Q2TAC1|Q8NEQ4|Q9H7B5	Frame_Shift_Del	DEL	ENST00000370435.4	hg19	CCDS34482.1																																																																																			.	.		0.353	OGFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041153.2	NM_024576		-	72011155	T	-	72011155	7	5	282	1	0	1	0	1	0	0	0	0	10853	1722	60	0	785	0	OGFRL1	6	72011155	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1510878	72011155	99103912	496	40730										
RIMS1	22999	hgsc.bcm.edu	37	chr6	73102485	73102485	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaccagcccagcttgttggcCgccaaacccttgccacccct	8	19	0	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:73102485C>T	ENST00000521978.1	+	31	4591	c.4591C>T	c.(4591-4593)Cgc>Tgc	p.R1531C	RIMS1_ENST00000523963.1_Missense_Mutation_p.R656C|RIMS1_ENST00000491071.2_Missense_Mutation_p.R1354C|RIMS1_ENST00000520567.1_Missense_Mutation_p.R1181C|RIMS1_ENST00000431478.2_3'UTR|RIMS1_ENST00000348717.5_Missense_Mutation_p.R1314C|RIMS1_ENST00000264839.7_Missense_Mutation_p.R1380C|RIMS1_ENST00000538414.1_Missense_Mutation_p.R337C|RIMS1_ENST00000425662.2_Missense_Mutation_p.R599C|RIMS1_ENST00000517960.1_Missense_Mutation_p.R1314C|RIMS1_ENST00000518273.1_Missense_Mutation_p.R1210C|RIMS1_ENST00000517827.1_Missense_Mutation_p.R665C|RIMS1_ENST00000401910.3_Missense_Mutation_p.R851C|RIMS1_ENST00000414192.2_Missense_Mutation_p.R58C|RIMS1_ENST00000522291.1_Missense_Mutation_p.R1130C	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	1531					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				GCTTGTTGGCCGCCAAACCCT	0.388																																					p.R1531C		Atlas-SNP	.											RIMS1,rectum,carcinoma,0,1	RIMS1	278	.	0			c.C4591T						.						86	82	83					6																	73102485		1840	4103	5943	SO:0001583	missense	22999	exon31			GTTGGCCGCCAAA	AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"Rab3-interacting molecule"	606629	"RAB3 interacting protein 2"	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.4591C>T	chr6.hg19:g.73102485C>T	ENSP00000428417:p.Arg1531Cys	143.0	0.0		80.0	33.0	NM_014989	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Missense_Mutation	SNP	ENST00000521978.1	hg19	CCDS47449.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.72|18.72	3.683389|3.683389	0.68157|0.68157	.|.	.|.	ENSG00000079841|ENSG00000079841	ENST00000517433|ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978;ENST00000401910;ENST00000523963;ENST00000425662;ENST00000453976;ENST00000517827;ENST00000370420;ENST00000538414;ENST00000414192	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.43294	.|0.95;2.12;2.05;2.13;2.32;2.35;2.35;2.0;2.07;2.34;2.26;1.41;2.26;1.71;1.67;1.96	5.5|5.5	2.56|2.56	0.30785|0.30785	.|.	.|0.000000	.|0.64402	.|D	.|0.000020	T|T	0.58552|0.58552	0.2130|0.2130	M|M	0.84683|0.84683	2.71|2.71	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D;D;D;D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;0.998;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D;D;D;D;D;D;D;D;D	.|0.97110	.|0.999;0.996;0.992;0.969;0.996;0.998;0.994;1.0;0.995;0.996;0.979;0.998;0.979	T|T	0.69000|0.69000	-0.5261|-0.5261	5|10	.|0.87932	.|D	.|0	-10.7348|-10.7348	14.3795|14.3795	0.66902|0.66902	0.467:0.533:0.0:0.0|0.467:0.533:0.0:0.0	.|.	.|155;337;665;656;1380;851;1130;434;1210;1314;607;1354;1531	.|B7Z6K9;B7Z7W2;B7Z3S3;E9PHF5;E9PHR1;E9PF48;E7EX08;Q5JY22;E7ERQ1;E7ENC2;Q5JY21;C9JNW6;Q86UR5	.|.;.;.;.;.;.;.;.;.;.;.;.;RIMS1_HUMAN	L|C	876|1354;1380;1354;1314;1210;1130;1380;1314;1210;1181;1130;1531;851;656;599;696;665;579;337;58	.|ENSP00000430101:R1354C;ENSP00000275037:R1314C;ENSP00000264839:R1380C;ENSP00000429959:R1314C;ENSP00000430408:R1210C;ENSP00000430502:R1181C;ENSP00000430932:R1130C;ENSP00000428417:R1531C;ENSP00000385649:R851C;ENSP00000428328:R656C;ENSP00000411235:R599C;ENSP00000389503:R696C;ENSP00000428367:R665C;ENSP00000359448:R579C;ENSP00000439730:R337C;ENSP00000402273:R58C	.|ENSP00000264839:R1380C	P|R	+|+	2|1	0|0	RIMS1|RIMS1	73159206|73159206	0.877000|0.877000	0.30153|0.30153	0.998000|0.998000	0.56505|0.56505	0.984000|0.984000	0.73092|0.73092	1.520000|1.520000	0.35899|0.35899	0.646000|0.646000	0.30693|0.30693	0.591000|0.591000	0.81541|0.81541	CCG|CGC	.	.		0.388	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1			T	73102485	C	T	73102485	3	4	282	1	0	0	0	0	1	0	0	0	13382	652	23	1	4876	1	RIMS1	6	73102485	Missense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1091330	73102485	98012582	497	40731										
CD109	135228	hgsc.bcm.edu	37	chr6	74502402	74502402	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cctcattgattcggatgcctTatggctgtggtgaacagaac	11	9	1	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:74502402T>C	ENST00000287097.5	+	23	2867	c.2755T>C	c.(2755-2757)Tat>Cat	p.Y919H	CD109_ENST00000437994.2_Missense_Mutation_p.Y919H|CD109_ENST00000474094.1_3'UTR|CD109_ENST00000422508.2_Missense_Mutation_p.Y842H			Q6YHK3	CD109_HUMAN	CD109 molecule	919					negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TCGGATGCCTTATGGCTGTGG	0.358																																					p.Y919H		Atlas-SNP	.											.	CD109	170	.	0			c.T2755C						.						164	147	153					6																	74502402		2203	4300	6503	SO:0001583	missense	135228	exon23			ATGCCTTATGGCT	AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"CD molecules"	21685	protein-coding gene	gene with protein product		608859	"CD109 antigen (Gov platelet alloantigens)"			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.2755T>C	chr6.hg19:g.74502402T>C	ENSP00000287097:p.Tyr919His	106.0	0.0		99.0	4.0	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Missense_Mutation	SNP	ENST00000287097.5	hg19	CCDS4982.1	.	.	.	.	.	.	.	.	.	.	T	16.65	3.182865	0.57800	.	.	ENSG00000156535	ENST00000437994;ENST00000422508;ENST00000287097	T;T;T	0.54675	0.56;0.56;0.56	5.87	3.49	0.39957	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);Alpha-2-macroglobulin, thiol-ester bond-forming (1);Alpha-2-macroglobulin, conserved site (1);	0.280178	0.36034	N	0.002822	T	0.34832	0.0911	L	0.56280	1.765	0.38385	D	0.945239	B;P;P	0.45569	0.313;0.861;0.607	B;B;B	0.42738	0.14;0.396;0.385	T	0.29792	-1.0000	10	0.87932	D	0	.	10.4107	0.44291	0.0:0.1319:0.0:0.8681	.	842;919;919	Q6YHK3-2;Q6YHK3-4;Q6YHK3	.;.;CD109_HUMAN	H	919;842;919	ENSP00000388062:Y919H;ENSP00000404475:Y842H;ENSP00000287097:Y919H	ENSP00000287097:Y919H	Y	+	1	0	CD109	74559123	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	3.388000	0.52509	0.569000	0.29329	0.533000	0.62120	TAT	.	.		0.358	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493		C	74502402	T	C	74502402	3	2	282	1	0	0	0	0	1	0	0	0	2965	1754	61	2	2845	2	CD109	6	74502402	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1399917	74502402	96612665	498	40732										
SENP6	26054	hgsc.bcm.edu	37	chr6	76312282	76312282	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggtagcgcaggggagattacTtttctggaaggtacgtctgt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:76312282delT	ENST00000447266.2	+	1	520	c.42delT	c.(40-42)actfs	p.T14fs	SENP6_ENST00000370014.3_Frame_Shift_Del_p.T14fs|SENP6_ENST00000327284.8_Frame_Shift_Del_p.T14fs|SENP6_ENST00000370010.2_Frame_Shift_Del_p.T14fs	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	14					protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				GGGAGATTACTTTTCTGGAAG	0.607																																					p.T14fs		Atlas-INDEL	.											.	SENP6	189	.	0			c.41delC						.						32	38	36					6																	76312282		1764	3787	5551	SO:0001589	frameshift_variant	26054	exon1			.		CCDS43483.1, CCDS47454.1	6q13-q14.3	2008-02-05	2005-08-17		ENSG00000112701	ENSG00000112701			20944	protein-coding gene	gene with protein product		605003	"SUMO1/sentrin specific protease 6"				Standard	NM_015571		Approved	SUSP1, KIAA0797	uc003pid.4	Q9GZR1	OTTHUMG00000015060	ENST00000447266.2:c.42delT	chr6.hg19:g.76312282delT	ENSP00000402527:p.Thr14fs	204.0	0.0		159.0	10.0	NM_015571	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Frame_Shift_Del	DEL	ENST00000447266.2	hg19	CCDS47454.1																																																																																			.	.		0.607	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	NM_015571		-	76312282	T	-	76312282	7	5	282	1	0	1	0	1	0	0	0	0	14065	1596	56	0	44	0	SENP6	6	76312282	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1809880	76312282	94802785	499	40733										
LCA5	167691	hgsc.bcm.edu	37	chr6	80223315	80223315	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttcattctgcaactcattgaTttttagcagtcttgcagaca					rs576105476	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:80223315delT	ENST00000392959.1	-	4	945	c.334delA	c.(334-336)atcfs	p.I112fs	LCA5_ENST00000467898.3_Frame_Shift_Del_p.I112fs|LCA5_ENST00000369846.4_Frame_Shift_Del_p.I112fs	NM_181714.3	NP_859065.2	Q86VQ0	LCA5_HUMAN	Leber congenital amaurosis 5	112					intraciliary transport (GO:0042073)|photoreceptor cell maintenance (GO:0045494)|protein transport (GO:0015031)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein complex binding (GO:0032403)			haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	32		all_cancers(76;3.32e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0176)		BRCA - Breast invasive adenocarcinoma(397;0.0657)		AACTCATTGATTTTTAGCAGT	0.418																																					p.I112fs		Atlas-INDEL	.											.	LCA5	71	.	0			c.335delT						.						98	105	103					6																	80223315		2203	4298	6501	SO:0001589	frameshift_variant	167691	exon3			.		CCDS4990.1	6q14	2014-01-28			ENSG00000135338	ENSG00000135338			31923	protein-coding gene	gene with protein product	"lebercilin"	611408	"chromosome 6 open reading frame 152"	C6orf152		10631161, 17546029	Standard	NM_181714		Approved		uc003pix.3	Q86VQ0	OTTHUMG00000015080	ENST00000392959.1:c.334delA	chr6.hg19:g.80223315delT	ENSP00000376686:p.Ile112fs	216.0	0.0		148.0	10.0	NM_001122769	E1P542|Q9BWX7	Frame_Shift_Del	DEL	ENST00000392959.1	hg19	CCDS4990.1																																																																																			.	.		0.418	LCA5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259269.1	NM_181714		-	80223315	T	-	80223315	7	5	282	1	0	1	0	1	0	0	0	0	8665	1493	52	0	1783	0	LCA5	6	80223315	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3911033	80223315	90891752	500	40734										
IBTK	25998	hgsc.bcm.edu	37	chr6	82910419	82910419	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aatgactcttctatccattgCtggaatctgcagaattgaag	8	8	3	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:82910419C>T	ENST00000306270.7	-	20	3346	c.2797G>A	c.(2797-2799)Gca>Aca	p.A933T	IBTK_ENST00000510291.1_Missense_Mutation_p.A933T|IBTK_ENST00000503631.1_Missense_Mutation_p.A732T	NM_015525.2	NP_056340.2	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton agammaglobulinemia tyrosine kinase	933					negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein tyrosine kinase activity (GO:0061099)|release of sequestered calcium ion into cytosol (GO:0051209)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine kinase inhibitor activity (GO:0030292)			central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(10)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	54		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)		CTATCCATTGCTGGAATCTGC	0.308																																					p.A933T		Atlas-SNP	.											.	IBTK	128	.	0			c.G2797A						.						75	72	73					6																	82910419		2203	4300	6503	SO:0001583	missense	25998	exon20			CCATTGCTGGAAT	AF235049	CCDS34490.1, CCDS75486.1	6q14.3	2013-01-10	2003-10-06	2003-10-08	ENSG00000005700	ENSG00000005700		"BTB/POZ domain containing", "Ankyrin repeat domain containing"	17853	protein-coding gene	gene with protein product		606457	"Bruton agammaglobulinemia tyrosine kinase inhibitor"	BTKI		11577348	Standard	XM_006715453		Approved	DKFZP564B116, BTBD26	uc003pjl.1	Q9P2D0	OTTHUMG00000015102	ENST00000306270.7:c.2797G>A	chr6.hg19:g.82910419C>T	ENSP00000305721:p.Ala933Thr	157.0	0.0		100.0	4.0	NM_015525	Q2QKU2|Q2QKU3|Q2QKU4|Q5TFD7|Q5TFD9|Q8IUQ9|Q8IUY7|Q8TAI4|Q9HBI8|Q9Y3T8	Missense_Mutation	SNP	ENST00000306270.7	hg19	CCDS34490.1	.	.	.	.	.	.	.	.	.	.	C	16.26	3.072175	0.55646	.	.	ENSG00000005700	ENST00000306270;ENST00000503631;ENST00000510291	T;T;T	0.33216	1.8;1.42;1.8	5.83	5.83	0.93111	.	0.105207	0.64402	D	0.000004	T	0.24928	0.0605	M	0.64997	1.995	0.53005	D	0.999963	B;B;P;P	0.44521	0.13;0.349;0.837;0.54	B;B;P;B	0.46172	0.139;0.159;0.506;0.21	T	0.02398	-1.1165	10	0.15066	T	0.55	-10.9631	15.5776	0.76404	0.0:0.8629:0.1371:0.0	.	732;933;933;933	E9PDR5;E7EPI0;Q9P2D0-2;Q9P2D0	.;.;.;IBTK_HUMAN	T	933;732;933	ENSP00000305721:A933T;ENSP00000422762:A732T;ENSP00000426405:A933T	ENSP00000305721:A933T	A	-	1	0	IBTK	82967138	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.013000	0.64023	2.741000	0.93983	0.655000	0.94253	GCA	.	.		0.308	IBTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041337.2	NM_015525		T	82910419	C	T	82910419	3	4	282	1	0	0	0	0	1	0	0	0	7485	797	28	3	1304	3	IBTK	6	82910419	Missense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	2687104	82910419	88204648	501	40735										
IBTK	25998	hgsc.bcm.edu	37	chr6	82949918	82949918	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aacacaatcaatatgtccatAaaaaatgcttctgtgcaatg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:82949918delA	ENST00000306270.7	-	2	835	c.286delT	c.(286-288)tatfs	p.Y96fs	IBTK_ENST00000510291.1_Frame_Shift_Del_p.Y96fs|IBTK_ENST00000503631.1_Frame_Shift_Del_p.Y96fs	NM_015525.2	NP_056340.2	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton agammaglobulinemia tyrosine kinase	96					negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein tyrosine kinase activity (GO:0061099)|release of sequestered calcium ion into cytosol (GO:0051209)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine kinase inhibitor activity (GO:0030292)			central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(10)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	54		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)		ATATGTCCATAAAAAATGCTT	0.333																																					p.Y96fs		Atlas-INDEL	.											.	IBTK	128	.	0			c.287delA						.						130	118	122					6																	82949918		2203	4300	6503	SO:0001589	frameshift_variant	25998	exon2			.	AF235049	CCDS34490.1, CCDS75486.1	6q14.3	2013-01-10	2003-10-06	2003-10-08	ENSG00000005700	ENSG00000005700		"BTB/POZ domain containing", "Ankyrin repeat domain containing"	17853	protein-coding gene	gene with protein product		606457	"Bruton agammaglobulinemia tyrosine kinase inhibitor"	BTKI		11577348	Standard	XM_006715453		Approved	DKFZP564B116, BTBD26	uc003pjl.1	Q9P2D0	OTTHUMG00000015102	ENST00000306270.7:c.286delT	chr6.hg19:g.82949918delA	ENSP00000305721:p.Tyr96fs	222.0	0.0		171.0	11.0	NM_015525	Q2QKU2|Q2QKU3|Q2QKU4|Q5TFD7|Q5TFD9|Q8IUQ9|Q8IUY7|Q8TAI4|Q9HBI8|Q9Y3T8	Frame_Shift_Del	DEL	ENST00000306270.7	hg19	CCDS34490.1																																																																																			.	.		0.333	IBTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041337.2	NM_015525		-	82949918	A	-	82949918	7	5	282	1	0	1	0	1	0	0	0	0	7485	362	13	0	3887	0	IBTK	6	82949918	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	39499	82949918	88165149	502	40736										
DOPEY1	23033	hgsc.bcm.edu	37	chr6	83839069	83839069	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggacagaaattcacaaggagAtgtaaaagagaaaaacataa	9	4	1	3	rs370284003		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:83839069A>G	ENST00000349129.2	+	16	2443	c.2183A>G	c.(2182-2184)gAt>gGt	p.D728G	DOPEY1_ENST00000237163.5_Missense_Mutation_p.D709G|DOPEY1_ENST00000369739.3_Missense_Mutation_p.D719G	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	728					protein transport (GO:0015031)					breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(16)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	67		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		TCACAAGGAGATGTAAAAGAG	0.403																																					p.D728G		Atlas-SNP	.											.	DOPEY1	190	.	0			c.A2183G						.	A	GLY/ASP,GLY/ASP	0,4406		0,0,2203	79	77	77		2183,2156	4.5	1	6		77	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	DOPEY1	NM_015018.3,NM_001199942.1	94,94	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign,benign	728/2466,719/2477	83839069	1,13005	2203	4300	6503	SO:0001583	missense	23033	exon16			AAGGAGATGTAAA	AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097			21194	protein-coding gene	gene with protein product			"KIAA1117"	KIAA1117		16301316, 16303751, 10931277	Standard	NM_015018		Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365	ENST00000349129.2:c.2183A>G	chr6.hg19:g.83839069A>G	ENSP00000195654:p.Asp728Gly	168.0	0.0		121.0	5.0	NM_015018	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Missense_Mutation	SNP	ENST00000349129.2	hg19	CCDS4996.1	.	.	.	.	.	.	.	.	.	.	A	12.99	2.103880	0.37145	0.0	1.16E-4	ENSG00000083097	ENST00000349129;ENST00000237163;ENST00000369739	T;T	0.23950	1.88;1.88	5.68	4.52	0.55395	.	0.247012	0.39083	N	0.001461	T	0.08891	0.0220	L	0.39633	1.23	0.80722	D	1	B;B;B	0.14012	0.009;0.003;0.0	B;B;B	0.10450	0.005;0.003;0.002	T	0.08868	-1.0701	10	0.18710	T	0.47	.	11.7905	0.52068	0.9311:0.0:0.0689:0.0	.	619;719;728	E1P545;B2RWN9;Q5JWR5	.;.;DOP1_HUMAN	G	728;709;709	ENSP00000195654:D728G;ENSP00000237163:D709G	ENSP00000237163:D709G	D	+	2	0	DOPEY1	83895788	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	3.138000	0.50570	0.972000	0.38314	0.528000	0.53228	GAT	.	.		0.403	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018		G	83839069	A	G	83839069	3	3	282	1	0	0	0	0	1	0	0	0	4709	333	12	2	2237	2	DOPEY1	6	83839069	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	889151	83839069	87275998	503	40737										
KIAA1009	22832	hgsc.bcm.edu	37	chr6	84930848	84930848	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttcatctcttttttagattgTctagctgttttgtctgaatt	6	6	4	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:84930848T>C	ENST00000403245.3	-	3	213	c.99A>G	c.(97-99)agA>agG	p.R33R	KIAA1009_ENST00000257766.4_5'UTR	NM_014895.2	NP_055710.2														breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	43		all_cancers(76;1.5e-06)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00258)		BRCA - Breast invasive adenocarcinoma(397;0.089)		TTTTAGATTGTCTAGCTGTTT	0.294																																					p.R33R		Atlas-SNP	.											.	KIAA1009	119	.	0			c.A99G						.						189	176	180					6																	84930848		1814	4074	5888	SO:0001819	synonymous_variant	22832	exon3			AGATTGTCTAGCT																												ENST00000403245.3:c.99A>G	chr6.hg19:g.84930848T>C		178.0	0.0		115.0	5.0	NM_014895		Silent	SNP	ENST00000403245.3	hg19	CCDS34494.2																																																																																			.	.		0.294	KIAA1009-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317315.1			C	84930848	T	C	84930848	2	2	282	1	0	0	0	0	0	0	0	1	8212	1664	58	2		2	KIAA1009	6	84930848	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1091779	84930848	86184219	504	40738										
SNX14	57231	hgsc.bcm.edu	37	chr6	86259455	86259455	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttatacctgcagtctgttgcTttaggaggcaaaatataagg	10	6	1	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:86259455T>C	ENST00000314673.3	-	8	953	c.777A>G	c.(775-777)aaA>aaG	p.K259K	SNX14_ENST00000369627.2_Silent_p.K259K|SNX14_ENST00000513865.1_Silent_p.K259K|SNX14_ENST00000508980.1_5'UTR|SNX14_ENST00000505648.1_Silent_p.K207K|SNX14_ENST00000346348.3_Silent_p.K215K	NM_153816.3	NP_722523.1	Q9Y5W7	SNX14_HUMAN	sorting nexin 14	259	PXA. {ECO:0000255|PROSITE- ProRule:PRU00147, ECO:0000255|PROSITE- ProRule:PRU00553}.				protein transport (GO:0015031)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	integral component of membrane (GO:0016021)	phosphatidylinositol binding (GO:0035091)			NS(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(11)|skin(1)	22		all_cancers(76;4.83e-07)|Acute lymphoblastic leukemia(125;3.3e-08)|Prostate(29;2.55e-07)|all_hematologic(105;3.66e-05)|all_epithelial(107;0.000695)|Lung NSC(302;0.197)|all_lung(197;0.24)		BRCA - Breast invasive adenocarcinoma(108;0.0423)		AGTCTGTTGCTTTAGGAGGCA	0.338																																					p.K259K		Atlas-SNP	.											.	SNX14	58	.	0			c.A777G						.						67	69	69					6																	86259455		2203	4299	6502	SO:0001819	synonymous_variant	57231	exon8			TGTTGCTTTAGGA	AF121863	CCDS5003.1, CCDS5004.1, CCDS75490.1	6q15	2008-10-22			ENSG00000135317	ENSG00000135317		"Sorting nexins"	14977	protein-coding gene	gene with protein product						11485546, 11736640	Standard	XM_005248738		Approved	RGS-PX2	uc003pkr.3	Q9Y5W7	OTTHUMG00000015140	ENST00000314673.3:c.777A>G	chr6.hg19:g.86259455T>C		94.0	0.0		73.0	4.0	NM_153816	B4DI55|Q4VBR3|Q5TCF9|Q5TCG0|Q6NUI7|Q6PI37|Q9BSD1	Silent	SNP	ENST00000314673.3	hg19	CCDS5004.1																																																																																			.	.		0.338	SNX14-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041393.2	NM_153816		C	86259455	T	C	86259455	2	2	282	1	0	0	0	0	0	0	0	1	14900	1606	56	2		2	SNX14	6	86259455	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1328607	86259455	84855612	505	40739										
ZNF292	23036	hgsc.bcm.edu	37	chr6	87970226	87970226	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gctcatttgattcgtccaagAagattaacaccaggccagga	9	10	1	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:87970226A>G	ENST00000369577.3	+	8	6922	c.6879A>G	c.(6877-6879)agA>agG	p.R2293R	ZNF292_ENST00000339907.4_Silent_p.R2288R	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	2293						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		TTCGTCCAAGAAGATTAACAC	0.428																																					p.R2293R		Atlas-SNP	.											.	ZNF292	479	.	0			c.A6879G						.						53	52	52					6																	87970226		1855	4097	5952	SO:0001819	synonymous_variant	23036	exon8			TCCAAGAAGATTA	AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"Zinc fingers, C2H2-type"	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.6879A>G	chr6.hg19:g.87970226A>G		99.0	0.0		85.0	4.0	NM_015021	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Silent	SNP	ENST00000369577.3	hg19	CCDS47457.1																																																																																			.	.		0.428	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021		G	87970226	A	G	87970226	2	3	282	1	0	0	0	0	0	0	0	1	17841	243	9	2		2	ZNF292	6	87970226	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1710771	87970226	83144841	506	40740										
SFRS13B	135295	hgsc.bcm.edu	37	chr6	89827583	89827583	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctgatgaacagggaggtgttGgggggcctcgtgtagcgaga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:89827583delG	ENST00000452027.2	-	1	217	c.24delC	c.(22-24)cccfs	p.P8fs		NM_080743.4	NP_542781.3	Q8WXF0	SRS12_HUMAN	serine/arginine-rich splicing factor 12	8					cytoplasmic transport (GO:0016482)|mRNA 5'-splice site recognition (GO:0000395)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|spliceosomal tri-snRNP complex assembly (GO:0000244)	nucleoplasm (GO:0005654)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RS domain binding (GO:0050733)|unfolded protein binding (GO:0051082)			autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(4)	8						GGGAGGTGTTGGGGGGCCTCG	0.711																																					p.N9fs		Atlas-INDEL	.											.	SRSF12	17	.	0			c.25delA						.						19	27	24					6																	89827583		2035	4179	6214	SO:0001589	frameshift_variant	135295	exon1			.	AF449428	CCDS47459.1	6q16.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000154548	ENSG00000154548		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	21220	protein-coding gene	gene with protein product	"splicing factor, arginine/serine-rich 19", "SR splicing factor 12"		"splicing factor, arginine/serine-rich 13B"	SFRS13B		11684676, 20516191	Standard	NM_080743		Approved	SRrp35, SFRS19	uc021zcq.1	Q8WXF0	OTTHUMG00000015192	ENST00000452027.2:c.24delC	chr6.hg19:g.89827583delG	ENSP00000414302:p.Pro8fs	250.0	0.0		140.0	11.0	NM_080743	B2RA22|Q5T7K0|Q8WW25	Frame_Shift_Del	DEL	ENST00000452027.2	hg19	CCDS47459.1																																																																																			.	.		0.711	SRSF12-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041474.2	NM_080743		-	89827583	G	-	89827583	7	5	282	1	0	1	0	1	0	0	0	0	14184	1335	47	0	781	0	SFRS13B	6	89827583	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1857357	89827583	81287484	507	40741										
BACH2	60468	hgsc.bcm.edu	37	chr6	90660586	90660586	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagagagcctccaacccaggCcccctgaggggcgaccccat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:90660586delC	ENST00000257749.4	-	7	1946	c.1239delG	c.(1237-1239)gggfs	p.G413fs	BACH2_ENST00000343122.3_Frame_Shift_Del_p.G413fs|RP3-512E2.2_ENST00000445838.1_RNA|BACH2_ENST00000537989.1_Frame_Shift_Del_p.G413fs|RP3-512E2.2_ENST00000413986.1_RNA	NM_021813.2	NP_068585.1	Q9BYV9	BACH2_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 2	413						cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	45		all_cancers(76;7.37e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.0063)		BRCA - Breast invasive adenocarcinoma(108;0.0799)		CCAACCCAGGCCCCCTGAGGG	0.582																																					p.P414fs		Atlas-INDEL	.											.	BACH2	224	.	0			c.1240delC						.						26	28	27					6																	90660586		2138	4210	6348	SO:0001589	frameshift_variant	60468	exon7			.	AL121787	CCDS5026.1	6q15	2013-01-10			ENSG00000112182	ENSG00000112182		"BTB/POZ domain containing", "basic leucine zipper proteins"	14078	protein-coding gene	gene with protein product		605394				10949928, 12829606	Standard	NM_001170794		Approved	BTBD25	uc003pnw.3	Q9BYV9	OTTHUMG00000015216	ENST00000257749.4:c.1239delG	chr6.hg19:g.90660586delC	ENSP00000257749:p.Gly413fs	187.0	0.0		149.0	10.0	NM_021813	E1P518|Q59H70|Q5T793|Q9NTS5	Frame_Shift_Del	DEL	ENST00000257749.4	hg19	CCDS5026.1																																																																																			.	.		0.582	BACH2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041522.2	NM_021813		-	90660586	C	-	90660586	7	5	282	1	0	1	0	1	0	0	0	0	1284	726	26	0	1298	0	BACH2	6	90660586	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	833003	90660586	80454481	508	40742										
FBXL4	26235	hgsc.bcm.edu	37	chr6	99328458	99328458	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	actgcctaaactgaggtgctGaagctctgaacagaagttca	10	9	2	4			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:99328458G>T	ENST00000369244.2	-	8	1788	c.1360C>A	c.(1360-1362)Cag>Aag	p.Q454K	FBXL4_ENST00000229971.1_Missense_Mutation_p.Q454K	NM_001278716.1	NP_001265645.1	Q9UKA2	FBXL4_HUMAN	F-box and leucine-rich repeat protein 4	454					ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(4)|prostate(3)|skin(2)	18		all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197)		BRCA - Breast invasive adenocarcinoma(108;0.0413)		CTGAGGTGCTGAAGCTCTGAA	0.393																																					p.Q454K		Atlas-SNP	.											.	FBXL4	54	.	0			c.C1360A						.						109	92	98					6																	99328458		2203	4300	6503	SO:0001583	missense	26235	exon7			GGTGCTGAAGCTC	AF176699	CCDS5041.1	6q16.1-q16.3	2011-06-09			ENSG00000112234	ENSG00000112234		"F-boxes / Leucine-rich repeats"	13601	protein-coding gene	gene with protein product		605654				10531035	Standard	NM_012160		Approved	FBL4, FBL5	uc003ppf.1	Q9UKA2	OTTHUMG00000015259	ENST00000369244.2:c.1360C>A	chr6.hg19:g.99328458G>T	ENSP00000358247:p.Gln454Lys	78.0	0.0		76.0	29.0	NM_012160	B2R7Q5|E1P530|O95919|Q5BJH0|Q9UJU0	Missense_Mutation	SNP	ENST00000369244.2	hg19	CCDS5041.1	.	.	.	.	.	.	.	.	.	.	G	8.948	0.967438	0.18659	.	.	ENSG00000112234	ENST00000369244;ENST00000229971	T;T	0.17213	2.29;2.29	5.58	5.58	0.84498	.	0.104710	0.64402	D	0.000003	T	0.05181	0.0138	L	0.28192	0.835	0.45607	D	0.998547	B	0.06786	0.001	B	0.08055	0.003	T	0.27571	-1.0070	10	0.16896	T	0.51	.	12.8495	0.57850	0.0744:0.0:0.9256:0.0	.	454	Q9UKA2	FBXL4_HUMAN	K	454	ENSP00000358247:Q454K;ENSP00000229971:Q454K	ENSP00000229971:Q454K	Q	-	1	0	FBXL4	99435179	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.673000	0.61604	2.650000	0.89964	0.591000	0.81541	CAG	.	.		0.393	FBXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041587.2			T	99328458	G	T	99328458	3	4	282	1	0	0	0	0	1	0	0	0	5729	1299	45	3	517	3	FBXL4	6	99328458	Missense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	8667872	99328458	71786609	509	40743										
ASCC3	10973	hgsc.bcm.edu	37	chr6	100960741	100960741	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	actaagtcatcccacgagccTttaacacttatgccaacatt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:100960741delT	ENST00000369162.2	-	40	6473	c.6129delA	c.(6127-6129)aaafs	p.K2043fs		NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	2043	SEC63 2.				cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		CCCACGAGCCTTTAACACTTA	0.373																																					p.G2044fs		Atlas-INDEL	.											.	ASCC3	205	.	0			c.6130delG						.						119	98	105					6																	100960741		2203	4300	6503	SO:0001589	frameshift_variant	10973	exon40			.	AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"RNA helicase family"	614217	"helicase, ATP binding 1"	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.6129delA	chr6.hg19:g.100960741delT	ENSP00000358159:p.Lys2043fs	196.0	0.0		172.0	11.0	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Frame_Shift_Del	DEL	ENST00000369162.2	hg19	CCDS5046.1																																																																																			.	.		0.373	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828		-	100960741	T	-	100960741	7	5	282	1	0	1	0	1	0	0	0	0	1033	1606	56	0	491	0	ASCC3	6	100960741	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1632283	100960741	70154326	510	40744										
ASCC3	10973	hgsc.bcm.edu	37	chr6	101086535	101086535	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctaattcagctgcaacagtcTttcccgatccagtaggtgct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:101086535delT	ENST00000369162.2	-	25	4408	c.4064delA	c.(4063-4065)aagfs	p.K1355fs		NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	1355	Helicase ATP-binding 2. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		TGCAACAGTCTTTCCCGATCC	0.373																																					p.K1355fs		Atlas-INDEL	.											.	ASCC3	205	.	0			c.4065delG						.						136	124	128					6																	101086535		2203	4300	6503	SO:0001589	frameshift_variant	10973	exon25			.	AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"RNA helicase family"	614217	"helicase, ATP binding 1"	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.4064delA	chr6.hg19:g.101086535delT	ENSP00000358159:p.Lys1355fs	233.0	0.0		165.0	11.0	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Frame_Shift_Del	DEL	ENST00000369162.2	hg19	CCDS5046.1																																																																																			.	.		0.373	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828		-	101086535	T	-	101086535	7	5	282	1	0	1	0	1	0	0	0	0	1033	1609	56	0	2616	0	ASCC3	6	101086535	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	125794	101086535	70028532	511	40745										
HACE1	57531	hgsc.bcm.edu	37	chr6	105198277	105198277	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgaacatatgaaagccctgtAaaaaagcattgatctgaggc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:105198277delA	ENST00000262903.4	-	20	2558	c.2282delT	c.(2281-2283)ttafs	p.L761fs	HACE1_ENST00000517995.1_5'UTR|HACE1_ENST00000369125.2_Frame_Shift_Del_p.L546fs	NM_020771.3	NP_065822.2	Q8IYU2	HACE1_HUMAN	HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1	761	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cell cycle (GO:0007049)|Golgi organization (GO:0007030)|membrane fusion (GO:0061025)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|Rac protein signal transduction (GO:0016601)|regulation of cell migration (GO:0030334)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Rab GTPase binding (GO:0017137)|Rac GTPase binding (GO:0048365)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	44		all_cancers(87;6.89e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0216)|Colorectal(196;0.202)		BRCA - Breast invasive adenocarcinoma(108;0.122)|Epithelial(106;0.204)		AAAGCCCTGTAAAAAAGCATT	0.383																																					p.L761fs		Atlas-INDEL	.											.	HACE1	96	.	0			c.2283delA						.						110	104	106					6																	105198277		2203	4300	6503	SO:0001589	frameshift_variant	57531	exon20			.	BC034982	CCDS5050.1	6q21	2013-01-10	2012-02-23		ENSG00000085382	ENSG00000085382		"Ankyrin repeat domain containing"	21033	protein-coding gene	gene with protein product		610876				10718198	Standard	NM_020771		Approved	KIAA1320	uc003pqu.1	Q8IYU2	OTTHUMG00000015287	ENST00000262903.4:c.2282delT	chr6.hg19:g.105198277delA	ENSP00000262903:p.Leu761fs	245.0	0.0		146.0	10.0	NM_020771	A8K6U5|B3KY89|B4DFM6|B4DTQ4|B7Z9X6|E9PGP0|Q5VU99|Q5VUA0|Q8ND12|Q9P2M6	Frame_Shift_Del	DEL	ENST00000262903.4	hg19	CCDS5050.1																																																																																			.	.		0.383	HACE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041643.2	XM_045095		-	105198277	A	-	105198277	7	5	282	1	0	1	0	1	0	0	0	0	6949	372	13	0	467	0	HACE1	6	105198277	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	4111742	105198277	65916790	512	40746										
AIM1	202	hgsc.bcm.edu	37	chr6	106967099	106967099	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aatccatttagccagccagtTcacaaaggcaacactgccac	6	14	1	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:106967099T>C	ENST00000369066.3	+	2	1279	c.792T>C	c.(790-792)gtT>gtC	p.V264V		NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		GCCAGCCAGTTCACAAAGGCA	0.448																																					p.V264V		Atlas-SNP	.											.	AIM1	161	.	0			c.T792C						.						58	56	57					6																	106967099		2203	4300	6503	SO:0001819	synonymous_variant	202	exon2			GCCAGTTCACAAA	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"suppression of tumorigenicity 4", "beta-gamma crystallin domain containing 1"	601797	"suppression of tumorigenicity 4 (malignant melanoma)"	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.792T>C	chr6.hg19:g.106967099T>C		62.0	0.0		57.0	4.0	NM_001624	Q6P2P0|Q9BTM3	Silent	SNP	ENST00000369066.3	hg19	CCDS34506.1																																																																																			.	.		0.448	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1			C	106967099	T	C	106967099	2	2	282	1	0	0	0	0	0	0	0	1	430	1770	62	2		2	AIM1	6	106967099	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1768822	106967099	64147968	513	40747										
FYN	2534	hgsc.bcm.edu	37	chr6	112021336	112021336	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cttccccaaactgcccatttCccagtctcttgatcaactgc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:112021336delC	ENST00000354650.3	-	9	1439	c.833delG	c.(832-834)ggafs	p.G278fs	FYN_ENST00000229471.4_Intron|FYN_ENST00000368667.2_Frame_Shift_Del_p.G278fs|FYN_ENST00000538466.1_Intron|FYN_ENST00000476769.2_5'UTR|FYN_ENST00000229470.5_Intron|FYN_ENST00000368678.4_Intron|FYN_ENST00000368682.3_Intron|FYN_ENST00000356013.2_Intron	NM_002037.5	NP_002028.1	P06241	FYN_HUMAN	FYN proto-oncogene, Src family tyrosine kinase	278	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activated T cell proliferation (GO:0050798)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|cellular response to peptide hormone stimulus (GO:0071375)|dendrite morphogenesis (GO:0048813)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|feeding behavior (GO:0007631)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|leukocyte migration (GO:0050900)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein localization to nucleus (GO:1900182)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of defense response to virus by virus (GO:0050690)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|glycoprotein binding (GO:0001948)|growth factor receptor binding (GO:0070851)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(17)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	30		all_cancers(87;1.37e-05)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00125)|Colorectal(196;0.0211)		all cancers(137;0.0451)|OV - Ovarian serous cystadenocarcinoma(136;0.0476)|Epithelial(106;0.102)	Dasatinib(DB01254)	CTGCCCATTTCCCAGTCTCTT	0.478																																					p.G278fs		Atlas-INDEL	.											.	FYN	108	.	0			c.834delA						.						137	138	138					6																	112021336		2203	4300	6503	SO:0001589	frameshift_variant	2534	exon9			.	AK056699	CCDS5094.1, CCDS5095.1, CCDS5096.1	6q21	2014-06-25	2014-06-25		ENSG00000010810	ENSG00000010810		"SH2 domain containing"	4037	protein-coding gene	gene with protein product		137025	"FYN oncogene related to SRC, FGR, YES"			3526330	Standard	NM_002037		Approved	SYN, SLK, MGC45350	uc003pvh.3	P06241	OTTHUMG00000016305	ENST00000354650.3:c.833delG	chr6.hg19:g.112021336delC	ENSP00000346671:p.Gly278fs	193.0	0.0		169.0	12.0	NM_002037	B5BU57|E1P557|H0UI48|Q16248|Q5R3A6|Q5R3A7|Q8N5D7	Frame_Shift_Del	DEL	ENST00000354650.3	hg19	CCDS5094.1																																																																																			.	.		0.478	FYN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043655.1			-	112021336	C	-	112021336	7	5	282	1	0	1	0	1	0	0	0	0	6134	855	30	0	964	0	FYN	6	112021336	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	5054237	112021336	59093731	514	40748										
TUBE1	51175	hgsc.bcm.edu	37	chr6	112397152	112397152	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agaattacctcgttaggttgAggagcaaatttgccacaatg	10	7	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:112397152A>G	ENST00000368662.5	-	8	878	c.800T>C	c.(799-801)cTc>cCc	p.L267P	TUBE1_ENST00000604814.1_5'UTR	NM_016262.4	NP_057346.1	Q9UJT0	TBE_HUMAN	tubulin, epsilon 1	267					centrosome cycle (GO:0007098)|protein polymerization (GO:0051258)	microtubule (GO:0005874)|pericentriolar material (GO:0000242)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			cervix(1)|endometrium(2)|large_intestine(5)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	12		all_cancers(87;0.0101)|all_hematologic(75;0.000258)|Colorectal(196;0.0466)|all_epithelial(87;0.1)		all cancers(137;0.0217)|OV - Ovarian serous cystadenocarcinoma(136;0.0613)|Epithelial(106;0.0636)|GBM - Glioblastoma multiforme(226;0.0972)|BRCA - Breast invasive adenocarcinoma(108;0.246)	Vinblastine(DB00570)	CGTTAGGTTGAGGAGCAAATT	0.348																																					p.L267P		Atlas-SNP	.											.	TUBE1	49	.	0			c.T800C						.						111	117	115					6																	112397152		2203	4300	6503	SO:0001583	missense	51175	exon8			AGGTTGAGGAGCA	AF201334	CCDS5100.1	6q21	2005-11-03			ENSG00000074935	ENSG00000074935		"Tubulins"	20775	protein-coding gene	gene with protein product		607345				10620804	Standard	NM_016262		Approved	dJ142L7.2, FLJ22589, TUBE	uc003pvq.3	Q9UJT0	OTTHUMG00000015382	ENST00000368662.5:c.800T>C	chr6.hg19:g.112397152A>G	ENSP00000357651:p.Leu267Pro	163.0	0.0		122.0	5.0	NM_016262	Q5H8W8|Q8NEG3	Missense_Mutation	SNP	ENST00000368662.5	hg19	CCDS5100.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.198864	0.79015	.	.	ENSG00000074935	ENST00000368662	T	0.68903	-0.36	5.7	5.7	0.88788	Tubulin/FtsZ, GTPase domain (3);	0.000000	0.85682	D	0.000000	T	0.74520	0.3727	L	0.56396	1.775	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.77859	-0.2431	10	0.66056	D	0.02	.	15.9692	0.79998	1.0:0.0:0.0:0.0	.	267	Q9UJT0	TBE_HUMAN	P	267	ENSP00000357651:L267P	ENSP00000357651:L267P	L	-	2	0	TUBE1	112503845	1.000000	0.71417	0.996000	0.52242	0.987000	0.75469	8.968000	0.93407	2.162000	0.67917	0.528000	0.53228	CTC	.	.		0.348	TUBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041867.1	NM_016262		G	112397152	A	G	112397152	3	3	282	1	0	0	0	0	1	0	0	0	16778	304	11	2	647	2	TUBE1	6	112397152	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	375816	112397152	58717915	515	40749										
HS3ST5	222537	hgsc.bcm.edu	37	chr6	114378787	114378787	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctggttcttactgctttgtaTtttgtgttcacttcgcatgt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:114378787delT	ENST00000312719.5	-	5	1863	c.675delA	c.(673-675)aaafs	p.K225fs	RP3-399L15.3_ENST00000519270.1_RNA|HS3ST5_ENST00000411826.1_Frame_Shift_Del_p.K225fs|RP3-399L15.3_ENST00000523087.1_RNA|RP3-399L15.3_ENST00000519104.1_RNA			Q8IZT8	HS3S5_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	225					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|negative regulation of coagulation (GO:0050819)|protein sulfation (GO:0006477)|regulation of viral entry into host cell (GO:0046596)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)			breast(4)|endometrium(2)|kidney(1)|large_intestine(7)|lung(17)|ovary(1)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	41		all_cancers(87;0.0587)|Colorectal(196;0.0676)|all_epithelial(87;0.154)		OV - Ovarian serous cystadenocarcinoma(136;0.00937)|all cancers(137;0.0117)|Epithelial(106;0.0274)|GBM - Glioblastoma multiforme(226;0.143)		CTGCTTTGTATTTTGTGTTCA	0.413																																					p.Y226fs		Atlas-INDEL	.											.	HS3ST5	80	.	0			c.676delT						.						285	284	284					6																	114378787		2203	4300	6503	SO:0001589	frameshift_variant	222537	exon2			.	AF503292	CCDS34517.1	6q21	2011-11-16			ENSG00000249853	ENSG00000249853		"Sulfotransferases, membrane-bound"	19419	protein-coding gene	gene with protein product		609407				12138164	Standard	NM_153612		Approved	3-OST-5	uc003pwg.4	Q8IZT8	OTTHUMG00000015412	ENST00000312719.5:c.675delA	chr6.hg19:g.114378787delT	ENSP00000427888:p.Lys225fs	401.0	0.0		330.0	21.0	NM_153612	A8K1J2|Q52LI2|Q8N285	Frame_Shift_Del	DEL	ENST00000312719.5	hg19	CCDS34517.1																																																																																			.	.		0.413	HS3ST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041911.2	NM_153612		-	114378787	T	-	114378787	7	5	282	1	0	1	0	1	0	0	0	0	7377	1490	52	0	369	0	HS3ST5	6	114378787	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1981635	114378787	56736280	516	40750										
TSPYL1	7259	hgsc.bcm.edu	37	chr6	116600132	116600132	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cctaatcatggcggacaactGggggtggtttcgaaaagcag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:116600132delG	ENST00000368608.3	-	1	934	c.862delC	c.(862-864)cagfs	p.Q288fs	RP1-93H18.1_ENST00000449314.1_lincRNA|DSE_ENST00000540275.1_Intron|DSE_ENST00000452085.3_5'Flank	NM_003309.3	NP_003300.1	Q9H0U9	TSYL1_HUMAN	TSPY-like 1	288					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)	enzyme binding (GO:0019899)			breast(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(3)|urinary_tract(1)	11		all_cancers(87;0.0144)|all_epithelial(87;0.021)|Colorectal(196;0.234)		all cancers(137;0.0235)|OV - Ovarian serous cystadenocarcinoma(136;0.0469)|GBM - Glioblastoma multiforme(226;0.0503)|Epithelial(106;0.094)		GCGGACAACTGGGGGTGGTTT	0.502																																					p.Q288fs		Atlas-INDEL	.											.	TSPYL1	28	.	0			c.863delA						.						126	130	129					6																	116600132		2203	4300	6503	SO:0001589	frameshift_variant	7259	exon1			.	AF042181	CCDS34518.1	6q22.1	2014-09-17	2004-04-05	2004-04-07	ENSG00000189241	ENSG00000189241			12382	protein-coding gene	gene with protein product		604714	"TSPY-like"	TSPYL		9730615	Standard	NM_003309		Approved		uc003pwp.4	Q9H0U9	OTTHUMG00000015427	ENST00000368608.3:c.862delC	chr6.hg19:g.116600132delG	ENSP00000357597:p.Gln288fs	203.0	0.0		165.0	11.0	NM_003309	O75885|Q5TFE6	Frame_Shift_Del	DEL	ENST00000368608.3	hg19	CCDS34518.1																																																																																			.	.		0.502	TSPYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041929.1			-	116600132	G	-	116600132	7	5	282	1	0	1	0	1	0	0	0	0	16674	1357	47	0	455	0	TSPYL1	6	116600132	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	2221345	116600132	54514935	517	40751										
HINT3	135114	hgsc.bcm.edu	37	chr6	126288056	126288056	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaggacctaatttgcttcaaAgatatcaaaccagcagcaac	7	10	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:126288056A>G	ENST00000229633.5	+	2	422	c.225A>G	c.(223-225)aaA>aaG	p.K75K		NM_138571.4	NP_612638.3	Q9NQE9	HINT3_HUMAN	histidine triad nucleotide binding protein 3	75	HIT. {ECO:0000255|PROSITE- ProRule:PRU00464}.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	hydrolase activity (GO:0016787)|nucleotide binding (GO:0000166)			endometrium(1)|large_intestine(1)|lung(1)|stomach(1)	4				UCEC - Uterine corpus endometrioid carcinoma (4;0.153)|GBM - Glioblastoma multiforme(226;0.0321)		TTTGCTTCAAAGATATCAAAC	0.333																																					p.K75K		Atlas-SNP	.											.	HINT3	14	.	0			c.A225G						.						106	100	102					6																	126288056		2203	4300	6503	SO:0001819	synonymous_variant	135114	exon2			CTTCAAAGATATC	AK057688	CCDS5133.1	6q22.33	2007-12-04			ENSG00000111911	ENSG00000111911			18468	protein-coding gene	gene with protein product		609998				11805111	Standard	NM_138571		Approved	FLJ33126	uc003qal.4	Q9NQE9	OTTHUMG00000015514	ENST00000229633.5:c.225A>G	chr6.hg19:g.126288056A>G		97.0	0.0		70.0	4.0	NM_138571	B3KQ91|Q8N0Y9	Silent	SNP	ENST00000229633.5	hg19	CCDS5133.1																																																																																			.	.		0.333	HINT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042090.1	NM_138571		G	126288056	A	G	126288056	2	3	282	1	0	0	0	0	0	0	0	1	7122	69	3	2		2	HINT3	6	126288056	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	9687924	126288056	44827011	518	40752										
TRMT11	60487	hgsc.bcm.edu	37	chr6	126332450	126332450	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aggaccagatgaaaacattaGggccaatcttcgtcaatatg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:126332450delG	ENST00000334379.5	+	9	933	c.812delG	c.(811-813)aggfs	p.R271fs	TRMT11_ENST00000368332.3_Frame_Shift_Del_p.R271fs	NM_001031712.2	NP_001026882.2	Q7Z4G4	TRM11_HUMAN	tRNA methyltransferase 11 homolog (S. cerevisiae)	271					tRNA processing (GO:0008033)		methyltransferase activity (GO:0008168)|tRNA binding (GO:0000049)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				GBM - Glioblastoma multiforme(226;0.0356)		GAAAACATTAGGGCCAATCTT	0.398																																					p.R271fs		Atlas-INDEL	.											.	TRMT11	43	.	0			c.811delA						.						104	84	91					6																	126332450		2203	4300	6503	SO:0001589	frameshift_variant	60487	exon9			.	AF182423	CCDS35496.1	6q11.1-q22.33	2009-06-15	2006-11-28	2006-11-28	ENSG00000066651	ENSG00000066651			21080	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 75"	C6orf75			Standard	XM_006715546		Approved	MDS024, dJ187J11.2, TRM11, TRMT11-1	uc003qam.3	Q7Z4G4	OTTHUMG00000015515	ENST00000334379.5:c.812delG	chr6.hg19:g.126332450delG	ENSP00000333934:p.Arg271fs	165.0	0.0		140.0	10.0	NM_001031712	E1P570|Q5JY11|Q6PGQ5|Q9HC13	Frame_Shift_Del	DEL	ENST00000334379.5	hg19	CCDS35496.1																																																																																			.	.		0.398	TRMT11-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_021820		-	126332450	G	-	126332450	7	5	282	1	0	1	0	1	0	0	0	0	16577	1000	35	0	846	0	TRMT11	6	126332450	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	44394	126332450	44782617	519	40753										
LAMA2	3908	hgsc.bcm.edu	37	chr6	129636958	129636958	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caatctatttcgaggctcggGaagaaacaggtttctctaca	9	9	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:129636958G>T	ENST00000421865.2	+	26	3836	c.3787G>T	c.(3787-3789)Gaa>Taa	p.E1263*		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	1263	Laminin IV type A 2. {ECO:0000255|PROSITE-ProRule:PRU00458}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		CGAGGCTCGGGAAGAAACAGG	0.418																																					p.E1263X		Atlas-SNP	.											LAMA2,right_upper_lobe,carcinoma,0,1	LAMA2	481	.	0			c.G3787T						.						109	110	109					6																	129636958		2203	4300	6503	SO:0001587	stop_gained	3908	exon26			GCTCGGGAAGAAA	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"Laminins"	6482	protein-coding gene	gene with protein product	"merosin", "congenital muscular dystrophy"	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.3787G>T	chr6.hg19:g.129636958G>T	ENSP00000400365:p.Glu1263*	70.0	0.0		69.0	30.0	NM_000426	Q14736|Q5VUM2|Q93022	Nonsense_Mutation	SNP	ENST00000421865.2	hg19	CCDS5138.1	.	.	.	.	.	.	.	.	.	.	G	44	10.630437	0.99440	.	.	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865	.	.	.	5.55	5.55	0.83447	.	0.178129	0.49305	D	0.000142	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22109	T	0.4	.	19.8741	0.96863	0.0:0.0:1.0:0.0	.	.	.	.	X	1263	.	ENSP00000346769:E1263X	E	+	1	0	LAMA2	129678651	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	9.416000	0.97383	2.761000	0.94854	0.655000	0.94253	GAA	.	.		0.418	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			T	129636958	G	T	129636958	4	4	282	1	0	0	0	0	0	1	0	0	8615	1175	41	3	3889	3	LAMA2	6	129636958	Nonsense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	3304508	129636958	41478109	520	40754										
ENPP3	5169	hgsc.bcm.edu	37	chr6	132061522	132061522	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caacgtggagagctgtcctgTgagtatgctttgggagggtc	16	7	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:132061522T>A	ENST00000414305.1	+	25	2785		c.e25+2		ENPP3_ENST00000358229.5_Splice_Site|ENPP3_ENST00000357639.3_Splice_Site			O14638	ENPP3_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 3						immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)	metal ion binding (GO:0046872)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0252)|OV - Ovarian serous cystadenocarcinoma(155;0.0511)		AGCTGTCCTGTGAGTATGCTT	0.478																																					.		Atlas-SNP	.											.	ENPP3	117	.	0			c.2457+2T>A						.						97	88	91					6																	132061522		2203	4300	6503	SO:0001630	splice_region_variant	5169	exon24			GTCCTGTGAGTAT	AF005632	CCDS5148.1	6q22	2010-06-23			ENSG00000154269	ENSG00000154269	3.1.4.1, 3.6.1.9	"CD molecules"	3358	protein-coding gene	gene with protein product		602182		PDNP3		9344668	Standard	NM_005021		Approved	PD-IBETA, gp130RB13-6, B10, CD203c	uc003qcv.3	O14638	OTTHUMG00000016292	ENST00000414305.1:c.2457+2T>A	chr6.hg19:g.132061522T>A		145.0	0.0		83.0	4.0	NM_005021	Q5JTL3	Splice_Site	SNP	ENST00000414305.1	hg19	CCDS5148.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.687161	0.88639	.	.	ENSG00000154269	ENST00000414305;ENST00000357639	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.2988	0.82793	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	ENPP3	132103215	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.337000	0.72958	2.311000	0.77944	0.533000	0.62120	.	.	.		0.478	ENPP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043627.2		Intron	A	132061522	T	A	132061522	5	1	282	1	0	0	0	0	0	0	1	0	5133	1710	59	4	2553	4	ENPP3	6	132061522	Splice_Site	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2424564	132061522	39053545	521	40755										
MYB	4602	hgsc.bcm.edu	37	chr6	135518299	135518299	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gacccacccaaggtcttaccTcctgcaaggcacagcacaat	7	16	1	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:135518299T>C	ENST00000367814.4	+	9	1389				MYB_ENST00000527615.1_Intron|MYB_ENST00000531845.1_Intron|MYB_ENST00000533624.1_Intron|MYB_ENST00000528774.1_Silent_p.P465P|MYB_ENST00000525369.1_Intron|MYB-AS1_ENST00000455534.1_RNA|MYB_ENST00000442647.2_Intron|MYB_ENST00000341911.5_Silent_p.P468P|MYB_ENST00000534044.1_Intron|MYB_ENST00000534121.1_Silent_p.P452P|MYB_ENST00000316528.8_Intron	NM_001161659.1|NM_005375.2	NP_001155131.1|NP_005366.2	P10242	MYB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog						B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|chromatin remodeling (GO:0006338)|embryonic digestive tract development (GO:0048566)|G1/S transition of mitotic cell cycle (GO:0000082)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 methylation (GO:0051574)|positive regulation of T-helper cell differentiation (GO:0045624)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|thymus development (GO:0048538)	nuclear matrix (GO:0016363)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(4)|endometrium(1)|kidney(2)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	all_epithelial(2;0.109)|Breast(56;0.158)|Colorectal(23;0.221)	Lung NSC(302;3.08e-05)|Ovarian(999;0.208)		OV - Ovarian serous cystadenocarcinoma(155;0.0079)|GBM - Glioblastoma multiforme(68;0.0117)		AGGTCTTACCTCCTGCAAGGC	0.517			T	NFIB	adenoid cystic carcinoma																																p.P468P		Atlas-SNP	.		Dom	yes		6	6q22-23	4602	v-myb myeloblastosis viral oncogene homolog		E	.	MYB	137	.	0			c.T1404C						.						126	111	116					6																	135518299		1568	3582	5150	SO:0001627	intron_variant	4602	exon10			CTTACCTCCTGCA		CCDS5174.1, CCDS47481.1, CCDS47482.1, CCDS55058.1, CCDS55059.1, CCDS55060.1, CCDS55061.1, CCDS55062.1	6q22-q23	2013-07-09	2013-07-09		ENSG00000118513	ENSG00000118513			7545	protein-coding gene	gene with protein product		189990				17599807	Standard	NM_001130172		Approved	c-myb	uc003qfh.3	P10242	OTTHUMG00000015629	ENST00000367814.4:c.1203+1159T>C	chr6.hg19:g.135518299T>C		170.0	0.0		99.0	6.0	NM_001130173	E9PI07|E9PLZ5|E9PNA4|E9PNL6|E9PRS2|P78391|P78392|P78525|P78526|Q14023|Q14024|Q708E4|Q708E7|Q9UE83	Silent	SNP	ENST00000367814.4	hg19	CCDS5174.1																																																																																			.	.		0.517	MYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042347.4			C	135518299	T	C	135518299	1	2	282	0	1	0	0	0	0	0	0	0	10016	1538	54	2		2	MYB	6	135518299	Intron	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3456777	135518299	35596768	522	40756										
AHI1	54806	hgsc.bcm.edu	37	chr6	135768254	135768254	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcacaatgcactggtttaccTttttcctcctgaagagccat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:135768254delT	ENST00000367800.4	-	11	1887	c.1671delA	c.(1669-1671)aaafs	p.K557fs	AHI1_ENST00000327035.6_Frame_Shift_Del_p.K557fs|AHI1_ENST00000457866.2_Frame_Shift_Del_p.K557fs	NM_001134830.1	NP_001128302.1	Q8N157	AHI1_HUMAN	Abelson helper integration site 1	557					cellular protein localization (GO:0034613)|central nervous system development (GO:0007417)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|cloaca development (GO:0035844)|heart looping (GO:0001947)|hindbrain development (GO:0030902)|Kupffer's vesicle development (GO:0070121)|left/right axis specification (GO:0070986)|morphogenesis of a polarized epithelium (GO:0001738)|negative regulation of apoptotic process (GO:0043066)|otic vesicle development (GO:0071599)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of polarized epithelial cell differentiation (GO:0030862)|positive regulation of receptor internalization (GO:0002092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pronephric duct morphogenesis (GO:0039023)|pronephric nephron tubule morphogenesis (GO:0039008)|protein localization to organelle (GO:0033365)|regulation of behavior (GO:0050795)|retina layer formation (GO:0010842)|specification of axis polarity (GO:0065001)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vesicle targeting (GO:0006903)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|nonmotile primary cilium (GO:0031513)|photoreceptor outer segment (GO:0001750)|primary cilium (GO:0072372)|TCTN-B9D complex (GO:0036038)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(18)|ovary(1)	37	Breast(56;0.239)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00904)|OV - Ovarian serous cystadenocarcinoma(155;0.00991)		CTGGTTTACCTTTTTCCTCCT	0.373																																					p.G558fs		Atlas-INDEL	.											.	AHI1	81	.	0			c.1672delG						.						169	161	164					6																	135768254		1878	4118	5996	SO:0001589	frameshift_variant	54806	exon12			.	AJ459824	CCDS47483.1, CCDS47484.1	6q23.2	2013-01-10	2005-11-29		ENSG00000135541	ENSG00000135541		"WD repeat domain containing"	21575	protein-coding gene	gene with protein product	"Jouberin"	608894	"Abelson helper integration site"			15060101, 16240161	Standard	NM_017651		Approved	FLJ20069, ORF1, JBTS3	uc003qgj.3	Q8N157	OTTHUMG00000015631	ENST00000367800.4:c.1671delA	chr6.hg19:g.135768254delT	ENSP00000356774:p.Lys557fs	208.0	0.0		161.0	10.0	NM_001134832	E1P584|Q4FD35|Q504T3|Q5TCP9|Q6P098|Q6PIT6|Q8NDX0|Q9H0H2	Frame_Shift_Del	DEL	ENST00000367800.4	hg19	CCDS47483.1																																																																																			.	.		0.373	AHI1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391948.1	NM_017651		-	135768254	T	-	135768254	7	5	282	1	0	1	0	1	0	0	0	0	413	1606	56	0	2044	0	AHI1	6	135768254	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	249955	135768254	35346813	523	40757										
AHI1	54806	hgsc.bcm.edu	37	chr6	135811800	135811800	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctgacaagttttttcttcagTtttttcttttcacgcattag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:135811800delT	ENST00000367800.4	-	3	312	c.96delA	c.(94-96)aaafs	p.K32fs	AHI1_ENST00000531527.1_5'Flank|AHI1_ENST00000327035.6_Frame_Shift_Del_p.K32fs|AHI1_ENST00000534469.1_Frame_Shift_Del_p.K32fs|AHI1_ENST00000367798.2_Frame_Shift_Del_p.K32fs|AHI1_ENST00000528103.1_Frame_Shift_Del_p.K32fs|AHI1_ENST00000488690.2_Frame_Shift_Del_p.K32fs|AHI1_ENST00000457866.2_Frame_Shift_Del_p.K32fs	NM_001134830.1	NP_001128302.1	Q8N157	AHI1_HUMAN	Abelson helper integration site 1	32					cellular protein localization (GO:0034613)|central nervous system development (GO:0007417)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|cloaca development (GO:0035844)|heart looping (GO:0001947)|hindbrain development (GO:0030902)|Kupffer's vesicle development (GO:0070121)|left/right axis specification (GO:0070986)|morphogenesis of a polarized epithelium (GO:0001738)|negative regulation of apoptotic process (GO:0043066)|otic vesicle development (GO:0071599)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of polarized epithelial cell differentiation (GO:0030862)|positive regulation of receptor internalization (GO:0002092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pronephric duct morphogenesis (GO:0039023)|pronephric nephron tubule morphogenesis (GO:0039008)|protein localization to organelle (GO:0033365)|regulation of behavior (GO:0050795)|retina layer formation (GO:0010842)|specification of axis polarity (GO:0065001)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vesicle targeting (GO:0006903)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|nonmotile primary cilium (GO:0031513)|photoreceptor outer segment (GO:0001750)|primary cilium (GO:0072372)|TCTN-B9D complex (GO:0036038)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(18)|ovary(1)	37	Breast(56;0.239)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00904)|OV - Ovarian serous cystadenocarcinoma(155;0.00991)		TTTTCTTCAGTTTTTTCTTTT	0.348																																					p.L33X		Atlas-INDEL	.											.	AHI1	81	.	0			c.97delC						.						205	189	194					6																	135811800		1823	4073	5896	SO:0001589	frameshift_variant	54806	exon4			.	AJ459824	CCDS47483.1, CCDS47484.1	6q23.2	2013-01-10	2005-11-29		ENSG00000135541	ENSG00000135541		"WD repeat domain containing"	21575	protein-coding gene	gene with protein product	"Jouberin"	608894	"Abelson helper integration site"			15060101, 16240161	Standard	NM_017651		Approved	FLJ20069, ORF1, JBTS3	uc003qgj.3	Q8N157	OTTHUMG00000015631	ENST00000367800.4:c.96delA	chr6.hg19:g.135811800delT	ENSP00000356774:p.Lys32fs	277.0	0.0		212.0	13.0	NM_001134832	E1P584|Q4FD35|Q504T3|Q5TCP9|Q6P098|Q6PIT6|Q8NDX0|Q9H0H2	Frame_Shift_Del	DEL	ENST00000367800.4	hg19	CCDS47483.1																																																																																			.	.		0.348	AHI1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391948.1	NM_017651		-	135811800	T	-	135811800	7	5	282	1	0	1	0	1	0	0	0	0	413	1722	60	0	3651	0	AHI1	6	135811800	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	43546	135811800	35303267	524	40758										
TNFAIP3	7128	hgsc.bcm.edu	37	chr6	138200242	138200242	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cctcctccagcctcagcaccAgcctccctccttcctgtcac	4	23	2	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:138200242A>G	ENST00000237289.4	+	7	1726	c.1660A>G	c.(1660-1662)Agc>Ggc	p.S554G		NM_001270507.1|NM_001270508.1|NM_006290.3	NP_001257436.1|NP_001257437.1|NP_006281.1	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3	554	Interaction with TNIP1. {ECO:0000250}.				apoptotic process (GO:0006915)|B-1 B cell homeostasis (GO:0001922)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of B cell activation (GO:0050869)|negative regulation of bone resorption (GO:0045779)|negative regulation of CD40 signaling pathway (GO:2000349)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast proliferation (GO:0090291)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 3 signaling pathway (GO:0034140)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of protein catabolic process (GO:0045732)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked deubiquitination (GO:0070536)|protein oligomerization (GO:0051259)|regulation of defense response to virus by host (GO:0050691)|regulation of germinal center formation (GO:0002634)|regulation of vascular wound healing (GO:0061043)|response to molecule of bacterial origin (GO:0002237)|tolerance induction to lipopolysaccharide (GO:0072573)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|protease binding (GO:0002020)|protein self-association (GO:0043621)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.0?(25)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(196)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	225	Breast(32;0.135)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468)		CCTCAGCACCAGCCTCCCTCC	0.597			"D, N, F"		"marginal zone B-cell lymphomas, Hodgkin's lymphoma, primary mediastinal B cell lymphoma"																																p.S554G	GBM(130;153 1739 22295 28918 47987)	Atlas-SNP	.		Rec	yes		6	6q23	7128	"tumor necrosis factor, alpha-induced protein 3"		L	.	TNFAIP3	340	.	25	Whole gene deletion(25)	haematopoietic_and_lymphoid_tissue(25)	c.A1660G						.						81	87	85					6																	138200242		2203	4300	6503	SO:0001583	missense	7128	exon7			AGCACCAGCCTCC	M59465	CCDS5187.1	6q23-q25	2013-01-21			ENSG00000118503	ENSG00000118503		"OTU domain containing"	11896	protein-coding gene	gene with protein product		191163				2118515	Standard	NM_006290		Approved	A20, OTUD7C	uc031spw.1	P21580	OTTHUMG00000015664	ENST00000237289.4:c.1660A>G	chr6.hg19:g.138200242A>G	ENSP00000237289:p.Ser554Gly	112.0	0.0		81.0	5.0	NM_001270507	B2R767|E1P588|Q2HIX9|Q5VXQ7|Q9NSR6	Missense_Mutation	SNP	ENST00000237289.4	hg19	CCDS5187.1	.	.	.	.	.	.	.	.	.	.	A	3.758	-0.050162	0.07407	.	.	ENSG00000118503	ENST00000237289;ENST00000535574;ENST00000544646	T	0.22945	1.93	5.73	-0.857	0.10693	.	0.615493	0.17661	N	0.166309	T	0.05960	0.0155	L	0.27053	0.805	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.35748	-0.9776	10	0.41790	T	0.15	-2.6623	10.9605	0.47383	0.5957:0.0:0.4043:0.0	.	554	P21580	TNAP3_HUMAN	G	554	ENSP00000237289:S554G	ENSP00000237289:S554G	S	+	1	0	TNFAIP3	138241935	0.118000	0.22208	0.000000	0.03702	0.008000	0.06430	0.670000	0.25157	-0.362000	0.08113	-0.441000	0.05720	AGC	.	.		0.597	TNFAIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042414.1			G	138200242	A	G	138200242	3	3	282	1	0	0	0	0	1	0	0	0	16289	188	7	2	1682	2	TNFAIP3	6	138200242	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2388442	138200242	32914825	525	40759										
KIAA1244	57221	hgsc.bcm.edu	37	chr6	138584101	138584101	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctcagaacacacgccgtgggAgtcagggaacgagaggagcc	15	11	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:138584101A>G	ENST00000251691.4	+	12	1647	c.1481A>G	c.(1480-1482)gAg>gGg	p.E494G		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		ACGCCGTGGGAGTCAGGGAAC	0.592																																					p.E494G		Atlas-SNP	.											.	KIAA1244	236	.	0			c.A1481G						.						51	39	44					6																	138584101		2203	4299	6502	SO:0001583	missense	57221	exon12			CGTGGGAGTCAGG	AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	21213	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 33"		"chromosome 6 open reading frame 92"	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.1481A>G	chr6.hg19:g.138584101A>G	ENSP00000251691:p.Glu494Gly	127.0	0.0		63.0	4.0	NM_020340		Missense_Mutation	SNP	ENST00000251691.4	hg19	CCDS5189.2	.	.	.	.	.	.	.	.	.	.	A	14.44	2.537338	0.45176	.	.	ENSG00000112379	ENST00000251691	T	0.21734	1.99	5.52	4.36	0.52297	.	0.693905	0.13313	N	0.397288	T	0.07458	0.0188	L	0.27053	0.805	0.41433	D	0.98787	B	0.12013	0.005	B	0.11329	0.006	T	0.06023	-1.0850	10	0.72032	D	0.01	-30.105	11.088	0.48099	0.9276:0.0:0.0724:0.0	.	494	Q5TH69	BIG3_HUMAN	G	494	ENSP00000251691:E494G	ENSP00000251691:E494G	E	+	2	0	KIAA1244	138625794	1.000000	0.71417	0.992000	0.48379	0.826000	0.46750	5.935000	0.70145	0.927000	0.37143	0.533000	0.62120	GAG	.	.		0.592	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340		G	138584101	A	G	138584101	3	3	282	1	0	0	0	0	1	0	0	0	8226	304	11	2	1527	2	KIAA1244	6	138584101	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	383859	138584101	32530966	526	40760										
ECT2L	345930	hgsc.bcm.edu	37	chr6	139159510	139159510	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tttgtccaagactggttttcAgaaaggatgcaagtggccaa	11	7	1	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:139159510A>G	ENST00000423192.1	+	4	362	c.201A>G	c.(199-201)tcA>tcG	p.S67S	ECT2L_ENST00000367682.2_Silent_p.S67S|ECT2L_ENST00000541398.1_5'UTR			Q008S8	ECT2L_HUMAN	epithelial cell transforming 2 like	67							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			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						ACTGGTTTTCAGAAAGGATGC	0.348			"N, Splice, Mis"		ETP ALL																																p.S67S		Atlas-SNP	.		Rec	yes		6	6q24.1	345930	epithelial cell transforming sequence 2 oncogene-like		L	.	ECT2L	75	.	0			c.A201G						.						101	95	97					6																	139159510		1827	4085	5912	SO:0001819	synonymous_variant	345930	exon4			GTTTTCAGAAAGG		CCDS43508.1	6q24.1	2014-03-11	2014-03-11		ENSG00000203734	ENSG00000203734		"Rho guanine nucleotide exchange factors", "F-boxes /  "other""	21118	protein-coding gene	gene with protein product	"lung specific F-box and DH domain containing protein", "F-box protein 49"		"chromosome 6 open reading frame 91", "epithelial cell transforming sequence 2 oncogene-like"	C6orf91			Standard	NM_001077706		Approved	ARHGEF32, FBXO49, LFDH	uc021zfx.1	Q008S8	OTTHUMG00000015679	ENST00000423192.1:c.201A>G	chr6.hg19:g.139159510A>G		213.0	0.0		154.0	7.0	NM_001195037	B2RUV6|Q5JWK2|Q5JWK3|Q5JWK4	Silent	SNP	ENST00000423192.1	hg19	CCDS43508.1																																																																																			.	.		0.348	ECT2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042441.3	NM_001077706		G	139159510	A	G	139159510	2	3	282	1	0	0	0	0	0	0	0	1	4904	175	7	2		2	ECT2L	6	139159510	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	575409	139159510	31955557	527	40761										
SHPRH	257218	hgsc.bcm.edu	37	chr6	146248366	146248366	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttttcctttgtgttcctccgAggagcgcaacacttctctgt	8	12	1	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:146248366A>G	ENST00000367505.2	-	15	3424	c.3160T>C	c.(3160-3162)Tcg>Ccg	p.S1054P	SHPRH_ENST00000367503.3_Missense_Mutation_p.S1063P|SHPRH_ENST00000275233.7_Missense_Mutation_p.S1054P|SHPRH_ENST00000438092.2_Missense_Mutation_p.S1063P			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	1054					DNA repair (GO:0006281)|nucleosome assembly (GO:0006334)|protein polyubiquitination (GO:0000209)	nucleosome (GO:0000786)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1)	79		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		TGTTCCTCCGAGGAGCGCAAC	0.338																																					p.S1063P		Atlas-SNP	.											.	SHPRH	169	.	0			c.T3187C						.						137	119	124					6																	146248366		1851	4096	5947	SO:0001583	missense	257218	exon15			CCTCCGAGGAGCG	AB095943	CCDS43513.1, CCDS47496.1, CCDS43513.2	6q24.2	2012-02-23	2012-02-23		ENSG00000146414	ENSG00000146414		"RING-type (C3HC4) zinc fingers"	19336	protein-coding gene	gene with protein product		608048	"SNF2 histone linker PHD RING helicase"			12837266	Standard	NM_001042683		Approved	FLJ90837, KIAA2023, bA545I5.2	uc003qlf.3	Q149N8	OTTHUMG00000015750	ENST00000367505.2:c.3160T>C	chr6.hg19:g.146248366A>G	ENSP00000356475:p.Ser1054Pro	153.0	0.0		118.0	10.0	NM_173082	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Missense_Mutation	SNP	ENST00000367505.2	hg19	CCDS43513.2	.	.	.	.	.	.	.	.	.	.	A	24.4	4.522569	0.85600	.	.	ENSG00000146414	ENST00000367505;ENST00000367503;ENST00000438092;ENST00000275233	T;T;T;T	0.74842	-0.86;-0.88;-0.87;-0.86	5.55	5.55	0.83447	.	0.000000	0.64402	D	0.000001	T	0.81264	0.4786	M	0.64997	1.995	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.996;0.998	T	0.82307	-0.0522	10	0.51188	T	0.08	-19.8107	15.9985	0.80270	1.0:0.0:0.0:0.0	.	1054;1063	Q149N8;Q149N8-4	SHPRH_HUMAN;.	P	1054;1063;1063;1054	ENSP00000356475:S1054P;ENSP00000356473:S1063P;ENSP00000412797:S1063P;ENSP00000275233:S1054P	ENSP00000275233:S1054P	S	-	1	0	SHPRH	146290059	1.000000	0.71417	0.992000	0.48379	0.928000	0.56348	8.933000	0.92911	2.233000	0.73108	0.455000	0.32223	TCG	.	.		0.338	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082		G	146248366	A	G	146248366	3	3	282	1	0	0	0	0	1	0	0	0	14306	304	11	2	1972	2	SHPRH	6	146248366	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	7088856	146248366	24866701	528	40762										
STXBP5	134957	hgsc.bcm.edu	37	chr6	147648266	147648266	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttttcctattcccagggtggTttttggcaattgcaatggca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:147648266delT	ENST00000321680.6	+	18	1934	c.1934delT	c.(1933-1935)gttfs	p.V645fs	STXBP5_ENST00000179882.6_Frame_Shift_Del_p.V316fs|STXBP5_ENST00000367481.3_Frame_Shift_Del_p.V645fs|STXBP5_ENST00000367480.3_Frame_Shift_Del_p.V645fs	NM_001127715.2	NP_001121187.1	Q5T5C0	STXB5_HUMAN	syntaxin binding protein 5 (tomosyn)	645					exocytosis (GO:0006887)|negative regulation of exocytosis (GO:0045920)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|synapse (GO:0045202)	syntaxin-1 binding (GO:0017075)			breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(21)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	42		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.77e-09)|GBM - Glioblastoma multiforme(68;0.0694)		CCCAGGGTGGTTTTTGGCAAT	0.388																																					p.V645fs		Atlas-INDEL	.											.	STXBP5	163	.	0			c.1933delG						.						155	145	149					6																	147648266		2203	4300	6503	SO:0001589	frameshift_variant	134957	exon18			.	AK055484	CCDS5211.1, CCDS47499.1	6q24.3	2013-01-10			ENSG00000164506	ENSG00000164506		"WD repeat domain containing"	19665	protein-coding gene	gene with protein product		604586				9620695, 14767561	Standard	NM_139244		Approved	tomosyn, LLGL3	uc010khz.2	Q5T5C0	OTTHUMG00000015766	ENST00000321680.6:c.1934delT	chr6.hg19:g.147648266delT	ENSP00000321826:p.Val645fs	198.0	0.0		140.0	12.0	NM_139244	Q14DF3|Q5T5C1|Q5T5C2|Q8NBG8|Q96NG9	Frame_Shift_Del	DEL	ENST00000321680.6	hg19	CCDS47499.1																																																																																			.	.		0.388	STXBP5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042606.1			-	147648266	T	-	147648266	7	5	282	1	0	1	0	1	0	0	0	0	15371	1725	60	0	2004	0	STXBP5	6	147648266	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1399900	147648266	23466801	529	40763										
FBXO5	26271	hgsc.bcm.edu	37	chr6	153296240	153296240	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	taggatttcgttttgcattcTtttttaatgttgaacaaacc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:153296240delT	ENST00000229758.3	-	2	678	c.620delA	c.(619-621)aagfs	p.K207fs	FBXO5_ENST00000477822.1_5'Flank|FBXO5_ENST00000367241.3_Frame_Shift_Del_p.K161fs	NM_012177.3	NP_036309.1	Q9UKT4	FBX5_HUMAN	F-box protein 5	207	Interaction with EVI5.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|G1/S transition of mitotic cell cycle (GO:0000082)|inhibition of mitotic anaphase-promoting complex activity (GO:0060565)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|microtubule polymerization (GO:0046785)|mitotic cell cycle (GO:0000278)|negative regulation of meiosis (GO:0045835)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|oocyte maturation (GO:0001556)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|spindle assembly involved in female meiosis I (GO:0007057)|vesicle organization (GO:0016050)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)	15		Ovarian(120;0.125)		OV - Ovarian serous cystadenocarcinoma(155;4.38e-10)|BRCA - Breast invasive adenocarcinoma(81;0.0893)		TTTTGCATTCTTTTTTAATGT	0.373																																					p.K207fs	NSCLC(121;372 1757 17721 17977 29669)	Atlas-INDEL	.											.	FBXO5	40	.	0			c.621delG						.						90	94	93					6																	153296240		2203	4300	6503	SO:0001589	frameshift_variant	26271	exon2			.	AF129535	CCDS5242.1, CCDS47501.1	6q25-q26	2008-02-05	2004-06-15		ENSG00000112029	ENSG00000112029		"F-boxes /  "other""	13584	protein-coding gene	gene with protein product		606013	"F-box only protein 5"			10531035, 10531037	Standard	NM_012177		Approved	FBX5, Fbxo31, EMI1	uc003qpg.3	Q9UKT4	OTTHUMG00000015854	ENST00000229758.3:c.620delA	chr6.hg19:g.153296240delT	ENSP00000229758:p.Lys207fs	243.0	0.0		148.0	11.0	NM_012177	B3KNX5|Q5TF47|Q8WV29|Q9UGC8	Frame_Shift_Del	DEL	ENST00000229758.3	hg19	CCDS5242.1																																																																																			.	.		0.373	FBXO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042757.1			-	153296240	T	-	153296240	7	5	282	1	0	1	0	1	0	0	0	0	5766	1609	56	0	739	0	FBXO5	6	153296240	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	5647974	153296240	17818827	530	40764										
TIAM2	26230	hgsc.bcm.edu	37	chr6	155565153	155565153	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	attttctttcaggatttgagCtgcctctttgaattatactt	6	7	3	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:155565153C>T	ENST00000461783.3	+	19	4630	c.3357C>T	c.(3355-3357)agC>agT	p.S1119S	TIAM2_ENST00000528391.2_Silent_p.S455S|TIAM2_ENST00000360366.4_Silent_p.S1143S|TIAM2_ENST00000275246.7_Silent_p.S44S|TIAM2_ENST00000318981.5_Silent_p.S1119S|TIAM2_ENST00000529824.2_Silent_p.S1119S|TIAM2_ENST00000367174.2_Silent_p.S495S|TIAM2_ENST00000456877.2_Silent_p.S431S|TIAM2_ENST00000456144.1_Silent_p.S1119S			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	1119	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|cellular lipid metabolic process (GO:0044255)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(20)|lung(21)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	65		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		AGGATTTGAGCTGCCTCTTTG	0.433																																					p.S1119S		Atlas-SNP	.											.	TIAM2	161	.	0			c.C3357T						.						156	151	153					6																	155565153		2203	4300	6503	SO:0001819	synonymous_variant	26230	exon16			TTTGAGCTGCCTC		CCDS34558.1, CCDS34559.1	6q25	2013-01-10			ENSG00000146426	ENSG00000146426		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11806	protein-coding gene	gene with protein product		604709				10512681	Standard	NM_012454		Approved	STEF	uc003qqe.3	Q8IVF5	OTTHUMG00000015880	ENST00000461783.3:c.3357C>T	chr6.hg19:g.155565153C>T		149.0	0.0		101.0	6.0	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Silent	SNP	ENST00000461783.3	hg19	CCDS34558.1																																																																																			.	.		0.433	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454		T	155565153	C	T	155565153	2	4	282	1	0	0	0	0	0	0	0	1	15906	796	28	3		3	TIAM2	6	155565153	Silent	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	2268913	155565153	15549914	531	40765										
CLDN20	49861	hgsc.bcm.edu	37	chr6	155596902	155596902	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctttcatcctggccttatctGgggtctctggagtgctcaca	10	12	4	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:155596902G>C	ENST00000367165.3	+	2	429	c.49G>C	c.(49-51)Ggg>Cgg	p.G17R	TFB1M_ENST00000367166.4_Intron	NM_001001346.3	NP_001001346.1	P56880	CLD20_HUMAN	claudin 20	17					calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)	p.G17R(1)		endometrium(1)|lung(2)	3				OV - Ovarian serous cystadenocarcinoma(155;7.82e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0114)		GGCCTTATCTGGGGTCTCTGG	0.493																																					p.G17R		Atlas-SNP	.											CLDN20,NS,carcinoma,0,1	CLDN20	10	.	1	Substitution - Missense(1)	endometrium(1)	c.G49C						.						99	103	102					6																	155596902		2203	4300	6503	SO:0001583	missense	49861	exon2			TTATCTGGGGTCT	BC020838	CCDS5249.1	6q25	2008-08-01			ENSG00000171217	ENSG00000171217		"Claudins"	2042	protein-coding gene	gene with protein product						16836752	Standard	NM_001001346		Approved		uc003qql.2	P56880	OTTHUMG00000015882	ENST00000367165.3:c.49G>C	chr6.hg19:g.155596902G>C	ENSP00000356133:p.Gly17Arg	285.0	0.0		216.0	0.0	NM_001001346		Missense_Mutation	SNP	ENST00000367165.3	hg19	CCDS5249.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.001899	0.93227	.	.	ENSG00000171217	ENST00000367165	D	0.89681	-2.55	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	D	0.96476	0.8850	H	0.96547	3.84	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97406	0.9999	10	0.87932	D	0	.	19.451	0.94867	0.0:0.0:1.0:0.0	.	17	P56880	CLD20_HUMAN	R	17	ENSP00000356133:G17R	ENSP00000356133:G17R	G	+	1	0	CLDN20	155638594	1.000000	0.71417	0.942000	0.38095	0.906000	0.53458	9.624000	0.98398	2.593000	0.87608	0.655000	0.94253	GGG	.	.		0.493	CLDN20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042818.1	NM_001001346		C	155596902	G	C	155596902	3	2	282	1	0	0	0	0	1	0	0	0	3484	1348	47	4	51	4	CLDN20	6	155596902	Missense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	31749	155596902	15518165	532	40766										
TFB1M	51106	hgsc.bcm.edu	37	chr6	155619614	155619614	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tacccaaaagcactcaccatCttcccagggtcttttaagac	5	14	3	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:155619614C>T	ENST00000367166.4	-	3	446	c.391G>A	c.(391-393)Gat>Aat	p.D131N		NM_016020.3	NP_057104.2	Q8WVM0	TFB1M_HUMAN	transcription factor B1, mitochondrial	131					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	mitochondrial nucleoid (GO:0042645)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|rRNA (adenine-N6,N6-)-dimethyltransferase activity (GO:0000179)			lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;1.48e-12)|BRCA - Breast invasive adenocarcinoma(81;0.0131)		CACTCACCATCTTCCCAGGGT	0.318																																					p.D131N		Atlas-SNP	.											.	TFB1M	30	.	0			c.G391A						.						69	67	68					6																	155619614		2203	4300	6503	SO:0001583	missense	51106	exon3			CACCATCTTCCCA	AF151833	CCDS5248.1	6q25.1-q25.3	2011-01-28			ENSG00000029639	ENSG00000029639			17037	protein-coding gene	gene with protein product	"dimethyladenosine transferase 1, mitochondrial"	607033				10810093, 11809803	Standard	NM_016020		Approved	mtTFB, CGI-75	uc003qqj.4	Q8WVM0	OTTHUMG00000015881	ENST00000367166.4:c.391G>A	chr6.hg19:g.155619614C>T	ENSP00000356134:p.Asp131Asn	56.0	0.0		63.0	4.0	NM_016020	Q05DR0|Q9Y384	Missense_Mutation	SNP	ENST00000367166.4	hg19	CCDS5248.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.082067	0.76528	.	.	ENSG00000029639	ENST00000367166	T	0.36157	1.27	5.65	5.65	0.86999	Ribosomal RNA adenine methylase transferase, N-terminal (1);	0.094410	0.64402	D	0.000001	T	0.36580	0.0972	M	0.65975	2.015	0.58432	D	0.999998	P	0.37548	0.599	P	0.44673	0.457	T	0.06162	-1.0842	10	0.23302	T	0.38	.	20.0781	0.97751	0.0:1.0:0.0:0.0	.	131	Q8WVM0	TFB1M_HUMAN	N	131	ENSP00000356134:D131N	ENSP00000356134:D131N	D	-	1	0	TFB1M	155661306	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	5.415000	0.66411	2.817000	0.96982	0.563000	0.77884	GAT	.	.		0.318	TFB1M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042809.1			T	155619614	C	T	155619614	3	4	282	1	0	0	0	0	1	0	0	0	15808	913	32	3	669	3	TFB1M	6	155619614	Missense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	22712	155619614	15495453	533	40767										
ARID1B	57492	hgsc.bcm.edu	37	chr6	157511264	157511264	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gactccaaacgccccctaccAgcagggcatgagcatgcccg	10	17	0	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:157511264A>G	ENST00000350026.5	+	14	3744	c.3743A>G	c.(3742-3744)cAg>cGg	p.Q1248R	ARID1B_ENST00000275248.4_Missense_Mutation_p.Q1243R|ARID1B_ENST00000346085.5_Missense_Mutation_p.Q1261R|ARID1B_ENST00000367148.1_Missense_Mutation_p.Q1301R	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1248					chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		GCCCCCTACCAGCAGGGCATG	0.547																																					p.Q1261R		Atlas-SNP	.											.	ARID1B	320	.	0			c.A3782G						.						111	110	110					6																	157511264		2203	4296	6499	SO:0001583	missense	57492	exon15			CCTACCAGCAGGG	AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"-"	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.3743A>G	chr6.hg19:g.157511264A>G	ENSP00000055163:p.Gln1248Arg	123.0	0.0		92.0	4.0	NM_020732	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Missense_Mutation	SNP	ENST00000350026.5	hg19	CCDS5251.2	.	.	.	.	.	.	.	.	.	.	A	17.80	3.477210	0.63849	.	.	ENSG00000049618	ENST00000346085;ENST00000350026;ENST00000367148;ENST00000275248;ENST00000414678	T;T;T;T;T	0.02472	4.5;4.45;4.58;4.6;4.28	5.95	4.77	0.60923	.	0.000000	0.85682	D	0.000000	T	0.03011	0.0089	L	0.54323	1.7	0.58432	D	0.999994	P;P;P	0.50272	0.89;0.933;0.933	B;P;P	0.49829	0.419;0.623;0.623	T	0.51052	-0.8754	10	0.48119	T	0.1	.	12.363	0.55213	0.8735:0.0:0.0:0.1265	.	1248;1261;1243	Q8NFD5;Q8NFD5-2;G3XAA0	ARI1B_HUMAN;.;.	R	1261;1248;1301;1243;770	ENSP00000344546:Q1261R;ENSP00000055163:Q1248R;ENSP00000356116:Q1301R;ENSP00000275248:Q1243R;ENSP00000412835:Q770R	ENSP00000275248:Q1243R	Q	+	2	0	ARID1B	157552956	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.962000	0.93254	1.037000	0.40024	0.533000	0.62120	CAG	.	.		0.547	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732		G	157511264	A	G	157511264	3	3	282	1	0	0	0	0	1	0	0	0	914	188	7	2	3840	2	ARID1B	6	157511264	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1891650	157511264	13603803	534	40768										
TULP4	56995	hgsc.bcm.edu	37	chr6	158915819	158915819	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcaggtcacgtctaatatctGgggaaccaaatttaagattg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:158915819delG	ENST00000367097.3	+	11	3168	c.1811delG	c.(1810-1812)tggfs	p.W604fs	TULP4_ENST00000367094.2_Frame_Shift_Del_p.W604fs	NM_020245.4	NP_064630.2	Q9NRJ4	TULP4_HUMAN	tubby like protein 4	604					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(7)|kidney(2)|large_intestine(15)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)		TCTAATATCTGGGGAACCAAA	0.433																																					p.W604fs		Atlas-INDEL	.											.	TULP4	137	.	0			c.1810delT						.						138	123	128					6																	158915819		2203	4300	6503	SO:0001589	frameshift_variant	56995	exon11			.		CCDS34561.1, CCDS34562.1	6q25-q26	2013-01-10			ENSG00000130338	ENSG00000130338		"WD repeat domain containing"	15530	protein-coding gene	gene with protein product						11595174	Standard	NM_020245		Approved	TUSP, KIAA1397	uc003qrf.3	Q9NRJ4	OTTHUMG00000015910	ENST00000367097.3:c.1811delG	chr6.hg19:g.158915819delG	ENSP00000356064:p.Trp604fs	291.0	0.0		169.0	11.0	NM_001007466	Q5T3M2|Q5T3M3|Q9HD22|Q9P2F0	Frame_Shift_Del	DEL	ENST00000367097.3	hg19	CCDS34561.1																																																																																			.	.		0.433	TULP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042869.1	NM_020245		-	158915819	G	-	158915819	7	5	282	1	0	1	0	1	0	0	0	0	16791	1357	47	0	1853	0	TULP4	6	158915819	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1404555	158915819	12199248	535	40769										
TULP4	56995	hgsc.bcm.edu	37	chr6	158923160	158923160	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggacgcagtggtctttagtgCcccccaggaggtccaggtga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:158923160delC	ENST00000367097.3	+	13	3822	c.2465delC	c.(2464-2466)gccfs	p.A822fs	TULP4_ENST00000367094.2_Intron	NM_020245.4	NP_064630.2	Q9NRJ4	TULP4_HUMAN	tubby like protein 4	822					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(7)|kidney(2)|large_intestine(15)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)		GTCTTTAGTGCCCCCCAGGAG	0.672																																					p.A822fs		Atlas-INDEL	.											.,1	TULP4	137	.	0			c.2464delG						.																																			SO:0001589	frameshift_variant	56995	exon13			.		CCDS34561.1, CCDS34562.1	6q25-q26	2013-01-10			ENSG00000130338	ENSG00000130338		"WD repeat domain containing"	15530	protein-coding gene	gene with protein product						11595174	Standard	NM_020245		Approved	TUSP, KIAA1397	uc003qrf.3	Q9NRJ4	OTTHUMG00000015910	ENST00000367097.3:c.2465delC	chr6.hg19:g.158923160delC	ENSP00000356064:p.Ala822fs	176.0	0.0		147.0	11.0	NM_020245	Q5T3M2|Q5T3M3|Q9HD22|Q9P2F0	Frame_Shift_Del	DEL	ENST00000367097.3	hg19	CCDS34561.1																																																																																			.	.		0.672	TULP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042869.1	NM_020245		-	158923160	C	-	158923160	7	5	282	1	0	1	0	1	0	0	0	0	16791	739	26	0	2515	0	TULP4	6	158923160	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	7341	158923160	12191907	536	40770										
PNLDC1	154197	hgsc.bcm.edu	37	chr6	160230045	160230045	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggaatttgtccctgcttttcAggtggtagtgaagaaagtga	13	5	1	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:160230045A>G	ENST00000610273.1	+	9	777		c.e9-1		PNLDC1_ENST00000392167.3_Splice_Site	NM_001271862.1|NM_173516.1	NP_001258791.1|NP_775787.1	Q8NA58	PNDC1_HUMAN	poly(A)-specific ribonuclease (PARN)-like domain containing 1							integral component of membrane (GO:0016021)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(9)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	31		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;1.55e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		CCTGCTTTTCAGGTGGTAGTG	0.433																																					.		Atlas-SNP	.											.	PNLDC1	66	.	0			c.607-2A>G						.						123	128	127					6																	160230045		2203	4300	6503	SO:0001630	splice_region_variant	154197	exon9			CTTTTCAGGTGGT	AK097559	CCDS5271.1, CCDS5271.2, CCDS64561.1	6q25.3	2008-02-05			ENSG00000146453	ENSG00000146453			21185	protein-coding gene	gene with protein product							Standard	NM_001271862		Approved	FLJ40240, dJ195P10.2	uc003qsy.2	Q8NA58	OTTHUMG00000015941	ENST00000610273.1:c.607-1A>G	chr6.hg19:g.160230045A>G		172.0	0.0		115.0	5.0	NM_173516	Q5TAP7|Q8N7X5	Splice_Site	SNP	ENST00000610273.1	hg19	CCDS5271.1	.	.	.	.	.	.	.	.	.	.	A	10.58	1.388903	0.25118	.	.	ENSG00000146453	ENST00000275275;ENST00000392167	.	.	.	5.46	-3.5	0.04710	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.4397	0.32808	0.3707:0.5298:0.0995:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PNLDC1	160150035	1.000000	0.71417	0.415000	0.26534	0.397000	0.30659	5.586000	0.67503	-0.422000	0.07405	0.533000	0.62120	.	.	.		0.433	PNLDC1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_173516	Intron	G	160230045	A	G	160230045	5	3	282	1	0	0	0	0	0	0	1	0	12157	202	7	2	635	2	PNLDC1	6	160230045	Splice_Site	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1306885	160230045	10885022	537	40771										
MAP3K4	4216	hgsc.bcm.edu	37	chr6	161455391	161455391	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agaatctttatggtacctctCcccccagcacacctcgacag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:161455391delC	ENST00000392142.4	+	2	401	c.253delC	c.(253-255)cccfs	p.P86fs	MAP3K4_ENST00000366919.2_Frame_Shift_Del_p.P86fs|MAP3K4_ENST00000348824.7_Frame_Shift_Del_p.P86fs|MAP3K4_ENST00000366920.2_Frame_Shift_Del_p.P86fs|MAP3K4_ENST00000446500.1_3'UTR	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	86					activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		TGGTACCTCTCCCCCCAGCAC	0.473																																					p.S84fs		Atlas-INDEL	.											.	MAP3K4	364	.	0			c.252delT						.						90	87	88					6																	161455391		2203	4300	6503	SO:0001589	frameshift_variant	4216	exon2			.	AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.253delC	chr6.hg19:g.161455391delC	ENSP00000375986:p.Pro86fs	195.0	0.0		157.0	10.0	NM_006724	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Frame_Shift_Del	DEL	ENST00000392142.4	hg19	CCDS34565.1																																																																																			.	.		0.473	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3			-	161455391	C	-	161455391	7	5	282	1	0	1	0	1	0	0	0	0	9261	855	30	0	259	0	MAP3K4	6	161455391	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1225346	161455391	9659676	538	40772										
MAP3K4	4216	hgsc.bcm.edu	37	chr6	161532936	161532936	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttggatgttcagtaaagctcAaaaacaatgcccagaccatg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:161532936delA	ENST00000392142.4	+	24	4613	c.4465delA	c.(4465-4467)aaafs	p.K1489fs	MAP3K4_ENST00000366919.2_Frame_Shift_Del_p.K1439fs|MAP3K4_ENST00000348824.7_Frame_Shift_Del_p.K1435fs|MAP3K4_ENST00000366920.2_Frame_Shift_Del_p.K1485fs	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	1489	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		AGTAAAGCTCAAAAACAATGC	0.468																																					p.L1488fs		Atlas-INDEL	.											.	MAP3K4	364	.	0			c.4464delC						.						202	187	192					6																	161532936		2203	4300	6503	SO:0001589	frameshift_variant	4216	exon24			.	AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.4465delA	chr6.hg19:g.161532936delA	ENSP00000375986:p.Lys1489fs	392.0	0.0		298.0	18.0	NM_005922	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Frame_Shift_Del	DEL	ENST00000392142.4	hg19	CCDS34565.1																																																																																			.	.		0.468	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3			-	161532936	A	-	161532936	7	5	282	1	0	1	0	1	0	0	0	0	9261	131	5	0	4559	0	MAP3K4	6	161532936	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	77545	161532936	9582131	539	40773										
T	6862	hgsc.bcm.edu	37	chr6	166580213	166580213	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcgcctgcggctccggcttgCcccccggcacccattccccg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:166580213delC	ENST00000296946.2	-	3	806	c.338delG	c.(337-339)ggcfs	p.G113fs	T_ENST00000366871.3_Frame_Shift_Del_p.G113fs	NM_003181.3	NP_003172.1	O15178	BRAC_HUMAN	T, brachyury homolog (mouse)	113					anterior/posterior axis specification, embryo (GO:0008595)|BMP signaling pathway (GO:0030509)|bone morphogenesis (GO:0060349)|canonical Wnt signaling pathway (GO:0060070)|determination of heart left/right asymmetry (GO:0061371)|embryonic skeletal system development (GO:0048706)|heart morphogenesis (GO:0003007)|mesoderm development (GO:0007498)|mesoderm migration involved in gastrulation (GO:0007509)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate morphogenesis (GO:0001839)|neural tube closure (GO:0001843)|notochord formation (GO:0014028)|penetration of zona pellucida (GO:0007341)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|signal transduction (GO:0007165)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|somitogenesis (GO:0001756)|transcription from RNA polymerase II promoter (GO:0006366)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(23)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	39		Prostate(117;4.48e-07)|Ovarian(120;1.78e-06)|Breast(66;2.54e-06)|Lung SC(201;0.0225)|Esophageal squamous(34;0.0559)		OV - Ovarian serous cystadenocarcinoma(33;1.09e-113)|GBM - Glioblastoma multiforme(31;1.51e-108)|BRCA - Breast invasive adenocarcinoma(81;8.45e-09)|LUAD - Lung adenocarcinoma(999;0.0407)		CTCCGGCTTGCCCCCCGGCAC	0.657									Chordoma, Familial Clustering of																												p.G113fs		Atlas-INDEL	.											.	T	77	.	0			c.339delC						.						46	48	47					6																	166580213		2203	4300	6503	SO:0001589	frameshift_variant	6862	exon3	Familial Cancer Database		.	AJ001699	CCDS5290.1, CCDS59045.1	6q27	2011-06-13	2001-11-28		ENSG00000164458	ENSG00000164458		"T-boxes"	11515	protein-coding gene	gene with protein product		601397	"T brachyury (mouse) homolog"			8963900	Standard	NM_003181		Approved		uc003quu.2	O15178	OTTHUMG00000015991	ENST00000296946.2:c.338delG	chr6.hg19:g.166580213delC	ENSP00000296946:p.Gly113fs	188.0	0.0		143.0	10.0	NM_001270484	E7ERD6|Q4KMP4	Frame_Shift_Del	DEL	ENST00000296946.2	hg19	CCDS5290.1																																																																																			.	.		0.657	T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043037.2	NM_003181		-	166580213	C	-	166580213	7	5	282	1	0	1	0	1	0	0	0	0	15503	739	26	0	997	0	T	6	166580213	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	5047277	166580213	4534854	540	40774										
TTLL2	83887	hgsc.bcm.edu	37	chr6	167755064	167755064	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agcaggcaactttgttcttgTttttcctttcaatgaagcaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:167755064delT	ENST00000239587.5	+	3	1764	c.1676delT	c.(1675-1677)gttfs	p.V559fs		NM_031949.4	NP_114155.4	Q9BWV7	TTLL2_HUMAN	tubulin tyrosine ligase-like family, member 2	559			V -> I (in dbSNP:rs34931196).		cellular protein modification process (GO:0006464)		ligase activity (GO:0016874)			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(66;7.8e-06)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		TTTGTTCTTGTTTTTCCTTTC	0.468																																					p.V559fs		Atlas-INDEL	.											.	TTLL2	82	.	0			c.1675delG						.						92	89	90					6																	167755064		2203	4300	6503	SO:0001589	frameshift_variant	83887	exon3			.	AK093039	CCDS5301.1	6q27	2013-02-14		2004-01-14	ENSG00000120440	ENSG00000120440		"Tubulin tyrosine ligase-like family"	21211	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 104"	C6orf104		11054573	Standard	XM_006715572		Approved	NYD-TSPG, dJ366N23.3	uc003qvs.1	Q9BWV7	OTTHUMG00000016023	ENST00000239587.5:c.1676delT	chr6.hg19:g.167755064delT	ENSP00000239587:p.Val559fs	233.0	0.0		186.0	12.0	NM_031949	B2RB11|B3KS77|Q7Z6R8|Q86X22	Frame_Shift_Del	DEL	ENST00000239587.5	hg19	CCDS5301.1																																																																																			.	.		0.468	TTLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043127.3	NM_031949		-	167755064	T	-	167755064	7	5	282	1	0	1	0	1	0	0	0	0	16742	1725	60	0	1686	0	TTLL2	6	167755064	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1174851	167755064	3360003	541	40775										
FAM120B	84498	hgsc.bcm.edu	37	chr6	170639584	170639584	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aggagtggtttgtgtatcctGggaacccactgaggcacccg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:170639584delG	ENST00000476287.1	+	4	2071	c.1963delG	c.(1963-1965)gggfs	p.G655fs	MIR4644_ENST00000579929.1_RNA|FAM120B_ENST00000537664.1_Frame_Shift_Del_p.G678fs|FAM120B_ENST00000540480.1_Frame_Shift_Del_p.G667fs|FAM120B_ENST00000252510.9_5'UTR	NM_032448.1	NP_115824.1	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	655					cell differentiation (GO:0030154)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(2)	44		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)		TGTGTATCCTGGGAACCCACT	0.522																																					p.P654fs		Atlas-INDEL	.											.	FAM120B	108	.	0			c.1962delT						.						155	141	146					6																	170639584		2203	4300	6503	SO:0001589	frameshift_variant	84498	exon4			.	AB058741	CCDS5314.1, CCDS75555.1	6q27	2011-04-13	2006-07-04	2006-07-04	ENSG00000112584	ENSG00000112584			21109	protein-coding gene	gene with protein product	"PPARgamma constitutive coactivator 1", "constitutive coactivator of PPAR-gamma"	612266	"KIAA1838"	KIAA1838		14585507	Standard	NM_032448		Approved	PGCC1, CCPG	uc003qxp.3	Q96EK7	OTTHUMG00000016080	ENST00000476287.1:c.1963delG	chr6.hg19:g.170639584delG	ENSP00000417970:p.Gly655fs	342.0	0.0		222.0	14.0	NM_032448	B4DL34|Q86V68|Q96JI9	Frame_Shift_Del	DEL	ENST00000476287.1	hg19	CCDS5314.1																																																																																			.	.		0.522	FAM120B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000043259.2	NM_032448		-	170639584	G	-	170639584	7	5	282	1	0	1	0	1	0	0	0	0	5422	1348	47	0	1973	0	FAM120B	6	170639584	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	2884520	170639584	475483	542	40776										
PDCD2	5134	hgsc.bcm.edu	37	chr6	170892201	170892201	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccacaacctcaggcataatcTcatcttctgtttctattaca	3	13	5	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:170892201T>C	ENST00000541970.1	-	3	680	c.602A>G	c.(601-603)gAg>gGg	p.E201G	PDCD2_ENST00000453163.2_Missense_Mutation_p.E201G|PDCD2_ENST00000443345.2_Missense_Mutation_p.E168G|PDCD2_ENST00000542896.1_Missense_Mutation_p.E201G|PDCD2_ENST00000537445.1_Missense_Mutation_p.E168G|PDCD2_ENST00000392090.2_Missense_Mutation_p.E168G	NM_001199462.1|NM_002598.3	NP_001186391.1|NP_002589.2	Q16342	PDCD2_HUMAN	programmed cell death 2	201					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|large_intestine(1)|lung(5)	9		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;6.91e-23)|BRCA - Breast invasive adenocarcinoma(81;4.82e-06)|GBM - Glioblastoma multiforme(31;0.142)		AGGCATAATCTCATCTTCTGT	0.358																																					p.E201G	Colon(60;1476 1726 39478)	Atlas-SNP	.											.	PDCD2	13	.	0			c.A602G						.						126	124	125					6																	170892201		2203	4300	6503	SO:0001583	missense	5134	exon3			ATAATCTCATCTT	AJ420535	CCDS5316.1, CCDS47521.1, CCDS56460.1, CCDS56461.1, CCDS56462.1, CCDS75557.1	6q27	2008-02-05			ENSG00000071994	ENSG00000071994		"Zinc fingers, MYND-type"	8762	protein-coding gene	gene with protein product		600866				7606924	Standard	NM_002598		Approved	ZMYND7, RP8	uc003qxw.3	Q16342	OTTHUMG00000016083	ENST00000541970.1:c.602A>G	chr6.hg19:g.170892201T>C	ENSP00000439467:p.Glu201Gly	145.0	0.0		109.0	5.0	NM_002598	E9PCU7|F5GYS7|Q58HM9|Q58HN0|Q9UH12	Missense_Mutation	SNP	ENST00000541970.1	hg19	CCDS5316.1	.	.	.	.	.	.	.	.	.	.	.	11.52	1.664237	0.29604	.	.	ENSG00000071994	ENST00000541970;ENST00000392090;ENST00000542896;ENST00000453163;ENST00000537445;ENST00000443345	.	.	.	4.12	2.91	0.33838	Programmed cell death protein 2, C-terminal (1);	1.107890	0.06556	N	0.745960	T	0.32793	0.0841	M	0.67700	2.07	0.31291	N	0.689384	B;B;B;B;B;B;B	0.22414	0.006;0.011;0.012;0.012;0.069;0.006;0.006	B;B;B;B;B;B;B	0.23419	0.004;0.009;0.004;0.006;0.046;0.033;0.038	T	0.22452	-1.0216	8	.	.	.	-31.6789	9.5721	0.39433	0.0:0.0865:0.0:0.9135	.	150;168;201;168;201;201;168	Q7Z6S7;F5GYS7;E9PCU7;Q58HM9;F5H4V9;Q16342;Q58HN0	.;.;.;.;.;PDCD2_HUMAN;.	G	201;168;201;201;168;168	.	.	E	-	2	0	PDCD2	170734126	0.045000	0.20229	0.029000	0.17559	0.013000	0.08279	1.263000	0.33004	0.699000	0.31761	0.455000	0.32223	GAG	.	.		0.358	PDCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043269.2	NM_002598		C	170892201	T	C	170892201	3	2	282	1	0	0	0	0	1	0	0	0	11628	1551	54	2	477	2	PDCD2	6	170892201	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	252617	170892201	222866	543	40777										
SUN1	23353	hgsc.bcm.edu	37	chr7	881594	881594	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcttcttagaacaacaaaacAgcgcagaagcacaaacaaat	5	10	2	2	rs78842948	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:881594A>G	ENST00000405266.1	+	3	302	c.278A>G	c.(277-279)cAg>cGg	p.Q93R	SUN1_ENST00000456758.2_Missense_Mutation_p.Q151R|SUN1_ENST00000401592.1_Missense_Mutation_p.Q93R|SUN1_ENST00000403868.1_Missense_Mutation_p.Q93R|SUN1_ENST00000457378.2_Missense_Mutation_p.Q114R|SUN1_ENST00000469755.1_3'UTR|SUN1_ENST00000452783.2_Missense_Mutation_p.Q93R|SUN1_ENST00000425407.2_Missense_Mutation_p.Q43R|SUN1_ENST00000389574.3_Missense_Mutation_p.Q43R			O94901	SUN1_HUMAN	Sad1 and UNC84 domain containing 1	93	LMNA-binding.				cytoskeletal anchoring at nuclear membrane (GO:0090286)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)	acrosomal membrane (GO:0002080)|integral component of nuclear inner membrane (GO:0005639)|nuclear envelope (GO:0005635)|SUN-KASH complex (GO:0034993)				NS(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(17)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						ACAACAAAACAGCGCAGAAGC	0.423																																					p.Q114R		Atlas-SNP	.											.	SUN1	157	.	0			c.A341G						.						85	82	83					7																	881594		1952	4150	6102	SO:0001583	missense	23353	exon5			CAAAACAGCGCAG	AF202724	CCDS43533.1, CCDS47525.1, CCDS55078.1, CCDS55079.1, CCDS55080.1	7p22.3	2010-01-27	2010-01-27	2010-01-27	ENSG00000164828	ENSG00000164828			18587	protein-coding gene	gene with protein product	"Sad1 unc-84 domain protein 1"	607723	"unc-84 homolog A (C. elegans)"	UNC84A		11593002	Standard	NM_001130965		Approved	KIAA0810, FLJ12407	uc021zym.1	O94901	OTTHUMG00000151426	ENST00000405266.1:c.278A>G	chr7.hg19:g.881594A>G	ENSP00000384116:p.Gln93Arg	81.0	0.0		88.0	4.0	NM_001171945	A5PL20|B3KMV7|B4DZF7|B7WNY4|B7WP53|E9PDU4|E9PF23|F8WD13|Q96CZ7|Q9HA14|Q9UH98	Missense_Mutation	SNP	ENST00000405266.1	hg19		.	.	.	.	.	.	.	.	.	.	A	12.40	1.925821	0.34002	.	.	ENSG00000164828	ENST00000456758;ENST00000389574;ENST00000457378;ENST00000452783;ENST00000435699;ENST00000439679;ENST00000457598;ENST00000421580;ENST00000405266;ENST00000401592;ENST00000403868;ENST00000297445;ENST00000425407;ENST00000450881	T;T;T;T;T;T;T;T;T;T;T;T;T	0.47177	0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85	5.68	4.49	0.54785	.	1.930510	0.01867	N	0.036993	T	0.71434	0.3339	M	0.72894	2.215	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.998;0.992;0.998;0.999	D;D;D;D;D	0.79784	0.977;0.975;0.912;0.993;0.961	T	0.37934	-0.9684	10	0.38643	T	0.18	-22.4615	12.4432	0.55637	0.8595:0.1405:0.0:0.0	.	93;93;114;43;93	E9PDU4;E9PF23;F8WD13;O94901-5;O94901-3	.;.;.;.;.	R	151;43;114;93;93;93;93;93;93;93;93;93;43;68	ENSP00000388743:Q151R;ENSP00000374225:Q43R;ENSP00000395952:Q114R;ENSP00000413439:Q93R;ENSP00000388430:Q93R;ENSP00000413188:Q93R;ENSP00000404965:Q93R;ENSP00000394381:Q93R;ENSP00000384116:Q93R;ENSP00000384015:Q93R;ENSP00000383947:Q93R;ENSP00000392309:Q43R;ENSP00000392595:Q68R	ENSP00000297445:Q93R	Q	+	2	0	SUN1	848120	0.998000	0.40836	0.039000	0.18376	0.049000	0.14656	6.021000	0.70832	0.945000	0.37605	0.533000	0.62120	CAG	.	A|0.983;C|0.017		0.423	SUN1-001	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000322566.1	NM_025154		G	881594	A	G	881594	3	3	282	1	0	0	0	0	1	0	0	0	15406	188	7	2	355	2	SUN1	7	881594	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10		881594	158257069	544	40778										
INTS1	26173	hgsc.bcm.edu	37	chr7	1517412	1517412	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccaccgtccgcacccggcttCcccccagccaggggctcctc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:1517412delC	ENST00000404767.3	-	34	4876	c.4791delG	c.(4789-4791)gggfs	p.G1597fs	INTS1_ENST00000389470.4_Frame_Shift_Del_p.G1796fs	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1	1597					inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	62		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		CACCCGGCTTCCCCCCAGCCA	0.697																																					p.K1598fs		Atlas-INDEL	.											.	INTS1	145	.	0			c.4792delA						.						22	28	26					7																	1517412		2046	4170	6216	SO:0001589	frameshift_variant	26173	exon34			.	AB037861	CCDS47526.1	7p22.3	2009-11-06			ENSG00000164880	ENSG00000164880			24555	protein-coding gene	gene with protein product		611345				16239144	Standard	NM_001080453		Approved	DKFZp586J0619, KIAA1440, INT1, NET28	uc003skn.2	Q8N201	OTTHUMG00000151449	ENST00000404767.3:c.4791delG	chr7.hg19:g.1517412delC	ENSP00000385722:p.Gly1597fs	177.0	0.0		195.0	13.0	NM_001080453	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Frame_Shift_Del	DEL	ENST00000404767.3	hg19	CCDS47526.1																																																																																			.	.		0.697	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1			-	1517412	C	-	1517412	7	5	282	1	0	1	0	1	0	0	0	0	7784	842	30	0	1841	0	INTS1	7	1517412	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	635818	1517412	157621251	545	40779										
COL28A1	340267	hgsc.bcm.edu	37	chr7	7480482	7480482	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttcctttgctccctttcttgCcttcgtcaccctaacaaaat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:7480482delC	ENST00000399429.3	-	21	1801	c.1661delG	c.(1660-1662)ggcfs	p.G554fs		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	554	Collagen-like 5.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.G554V(1)		cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		CCCTTTCTTGCCTTCGTCACC	0.443																																					p.G554fs		Atlas-INDEL	.											.	COL28A1	113	.	1	Substitution - Missense(1)	lung(1)	c.1662delC						.						150	141	144					7																	7480482		1845	4094	5939	SO:0001589	frameshift_variant	340267	exon21			.	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"Collagens"	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.1661delG	chr7.hg19:g.7480482delC	ENSP00000382356:p.Gly554fs	77.0	0.0		154.0	10.0	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Frame_Shift_Del	DEL	ENST00000399429.3	hg19	CCDS43553.1																																																																																			.	.		0.443	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763		-	7480482	C	-	7480482	7	5	282	1	0	1	0	1	0	0	0	0	3688	739	26	0	1776	0	COL28A1	7	7480482	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	5963070	7480482	151658181	546	40780										
COL28A1	340267	hgsc.bcm.edu	37	chr7	7559697	7559697	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctgtttattcatttaccgggTttccttttggtcctcgctca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:7559697delT	ENST00000399429.3	-	6	949	c.809delA	c.(808-810)aacfs	p.N270fs		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	270	Collagen-like 1.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		ATTTACCGGGTTTCCTTTTGG	0.318																																					p.N270fs		Atlas-INDEL	.											.	COL28A1	113	.	0			c.810delC						.						80	74	76					7																	7559697		1801	4073	5874	SO:0001589	frameshift_variant	340267	exon6			.	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"Collagens"	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.809delA	chr7.hg19:g.7559697delT	ENSP00000382356:p.Asn270fs	140.0	0.0		231.0	15.0	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Frame_Shift_Del	DEL	ENST00000399429.3	hg19	CCDS43553.1																																																																																			.	.		0.318	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763		-	7559697	T	-	7559697	7	5	282	1	0	1	0	1	0	0	0	0	3688	1725	60	0	2688	0	COL28A1	7	7559697	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	79215	7559697	151578966	547	40781										
THSD7A	221981	hgsc.bcm.edu	37	chr7	11468622	11468622	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggccttcctccattatatggTttttcacgcagccatttaga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:11468622delT	ENST00000423059.4	-	14	3446	c.3195delA	c.(3193-3195)aaafs	p.K1065fs	AC004538.3_ENST00000445839.1_RNA	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	1065	TSP type-1 11. {ECO:0000255|PROSITE- ProRule:PRU00210}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		CATTATATGGTTTTTCACGCA	0.478										HNSCC(18;0.044)																											p.P1066fs		Atlas-INDEL	.											.	THSD7A	219	.	0			c.3196delC						.						250	243	245					7																	11468622		2016	4174	6190	SO:0001589	frameshift_variant	221981	exon14			.		CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.3195delA	chr7.hg19:g.11468622delT	ENSP00000406482:p.Lys1065fs	282.0	0.0		343.0	21.0	NM_015204		Frame_Shift_Del	DEL	ENST00000423059.4	hg19	CCDS47543.1																																																																																			.	.		0.478	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2		-	11468622	T	-	11468622	7	5	282	1	0	1	0	1	0	0	0	0	15894	1722	60	0	1834	0	THSD7A	7	11468622	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3908925	11468622	147670041	548	40782										
CCDC126	90693	hgsc.bcm.edu	37	chr7	23650955	23650955	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atgttttttacaatctcaagAaaaaatatgtcccagaaatt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:23650955delA	ENST00000307471.3	+	3	478	c.21delA	c.(19-21)agafs	p.R7fs	CCDC126_ENST00000486109.1_3'UTR|CCDC126_ENST00000410069.1_Frame_Shift_Del_p.R7fs|CCDC126_ENST00000409765.1_Frame_Shift_Del_p.R7fs	NM_138771.3	NP_620126.2	Q96EE4	CC126_HUMAN	coiled-coil domain containing 126	7					protein N-linked glycosylation (GO:0006487)	extracellular region (GO:0005576)|membrane (GO:0016020)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)			endometrium(3)|kidney(1)|large_intestine(1)|ovary(1)|skin(1)	7						CAATCTCAAGAAAAAATATGT	0.323																																					p.R7fs		Atlas-INDEL	.											.	CCDC126	16	.	0			c.20delG						.						76	78	77					7																	23650955		2203	4300	6503	SO:0001589	frameshift_variant	90693	exon3			.	BC012427	CCDS5384.1	7p15.3	2006-08-15			ENSG00000169193	ENSG00000169193			22398	protein-coding gene	gene with protein product						12477932	Standard	NM_138771		Approved	FLJ23031	uc003swl.3	Q96EE4	OTTHUMG00000128461	ENST00000307471.3:c.21delA	chr7.hg19:g.23650955delA	ENSP00000304355:p.Arg7fs	164.0	0.0		229.0	15.0	NM_138771	A8K1J6|Q6UWP1|Q75MQ6	Frame_Shift_Del	DEL	ENST00000307471.3	hg19	CCDS5384.1																																																																																			.	.		0.323	CCDC126-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250259.1	NM_138771		-	23650955	A	-	23650955	7	5	282	1	0	1	0	1	0	0	0	0	2764	243	9	0	23	0	CCDC126	7	23650955	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	12182333	23650955	135487708	549	40783										
HOXA7	3204	hgsc.bcm.edu	37	chr7	27194547	27194547	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctcattcctcctcgtcttccTcttcttcatcatcgtcctcc	2	19	6	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:27194547T>C	ENST00000242159.3	-	2	807	c.674A>G	c.(673-675)gAg>gGg	p.E225G	RP1-170O19.22_ENST00000467897.2_RNA|RP1-170O19.23_ENST00000498652.1_RNA|HOXA-AS3_ENST00000524304.1_RNA|HOXA-AS3_ENST00000518848.1_RNA|HOXA-AS3_ENST00000521197.1_RNA|HOXA-AS3_ENST00000518947.2_RNA|HOXA-AS3_ENST00000521231.1_RNA|HOXA7_ENST00000523796.2_5'UTR	NM_006896.3	NP_008827.2	P31268	HXA7_HUMAN	homeobox A7	225	Asp/Glu-rich (highly acidic).|Poly-Glu.				angiogenesis (GO:0001525)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of monocyte differentiation (GO:0045656)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(3)|large_intestine(1)|lung(10)|prostate(1)|urinary_tract(1)	16						ctcgtcttcctcttcttcatc	0.617																																					p.E225G		Atlas-SNP	.											.	HOXA7	34	.	0			c.A674G						.						49	55	53					7																	27194547		2202	4299	6501	SO:0001583	missense	3204	exon2			TCTTCCTCTTCTT		CCDS5408.1	7p15.2	2011-06-20	2005-12-22		ENSG00000122592	ENSG00000122592		"Homeoboxes / ANTP class : HOXL subclass"	5108	protein-coding gene	gene with protein product		142950	"homeo box A7"	HOX1A, HOX1		1973146, 1358459	Standard	NM_006896		Approved		uc003sys.3	P31268	OTTHUMG00000023217	ENST00000242159.3:c.674A>G	chr7.hg19:g.27194547T>C	ENSP00000242159:p.Glu225Gly	147.0	0.0		169.0	7.0	NM_006896	A4D191|O43368|O43486|O95655|Q9NSC8|Q9UDM1	Missense_Mutation	SNP	ENST00000242159.3	hg19	CCDS5408.1	.	.	.	.	.	.	.	.	.	.	T	12.79	2.042103	0.35989	.	.	ENSG00000122592	ENST00000242159	D	0.91843	-2.92	4.49	4.49	0.54785	.	0.389458	0.24544	N	0.037601	T	0.82176	0.4980	N	0.08118	0	0.38086	D	0.936825	B	0.17667	0.023	B	0.16289	0.015	T	0.78193	-0.2299	10	0.23891	T	0.37	.	12.3864	0.55335	0.0:0.0:0.0:1.0	.	225	P31268	HXA7_HUMAN	G	225	ENSP00000242159:E225G	ENSP00000242159:E225G	E	-	2	0	HOXA7	27161072	0.999000	0.42202	0.584000	0.28653	0.377000	0.30045	5.326000	0.65875	1.667000	0.50832	0.379000	0.24179	GAG	.	.		0.617	HOXA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358695.1			C	27194547	T	C	27194547	3	2	282	1	0	0	0	0	1	0	0	0	7306	1551	54	2	22	2	HOXA7	7	27194547	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3543592	27194547	131944116	550	40784										
ADCYAP1R1	117	hgsc.bcm.edu	37	chr7	31132336	31132336	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagacatgggaggcaatgagTccagcatctacttgtaagta	11	8	1	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:31132336T>C	ENST00000304166.4	+	13	1322	c.1033T>C	c.(1033-1035)Tcc>Ccc	p.S345P	ADCYAP1R1_ENST00000409489.1_Missense_Mutation_p.S345P|ADCYAP1R1_ENST00000409363.1_Missense_Mutation_p.S324P|ADCYAP1R1_ENST00000396211.2_Missense_Mutation_p.S345P	NM_001118.4|NM_001199635.1|NM_001199636.1	NP_001109.2|NP_001186564.1|NP_001186565.1	P41586	PACR_HUMAN	adenylate cyclase activating polypeptide 1 (pituitary) receptor type I	345					activation of adenylate cyclase activity (GO:0007190)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)|vasoactive intestinal polypeptide receptor activity (GO:0004999)			endometrium(1)|large_intestine(4)|liver(2)|lung(24)|ovary(1)|skin(2)|stomach(1)	35						AGGCAATGAGTCCAGCATCTA	0.478																																					p.S345P	Ovarian(44;225 1186 2158 11092)	Atlas-SNP	.											.	ADCYAP1R1	78	.	0			c.T1033C						.						103	95	98					7																	31132336		2203	4300	6503	SO:0001583	missense	117	exon13			AATGAGTCCAGCA		CCDS5433.1, CCDS56480.1, CCDS56481.1	7p14.3	2012-09-20			ENSG00000078549	ENSG00000078549		"GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"	242	protein-coding gene	gene with protein product	"PACAP receptor 1"	102981				7902709	Standard	NM_001199635		Approved	PAC1, PACAPR, PAC1R	uc003tcg.3	P41586	OTTHUMG00000023884	ENST00000304166.4:c.1033T>C	chr7.hg19:g.31132336T>C	ENSP00000306620:p.Ser345Pro	165.0	0.0		180.0	8.0	NM_001118	A8K1Y1|B7ZLA7|B8ZZK3|Q17S10	Missense_Mutation	SNP	ENST00000304166.4	hg19	CCDS5433.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	26.5|26.5	4.744555|4.744555	0.89663|0.89663	.|.	.|.	ENSG00000078549|ENSG00000078549	ENST00000304166;ENST00000381667;ENST00000409363;ENST00000396211;ENST00000409489|ENST00000436116	T;T;T;T|.	0.46819|.	1.14;1.11;0.86;1.13|.	5.72|5.72	5.72|5.72	0.89469|0.89469	GPCR, family 2-like (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.70780|0.70780	0.3263|0.3263	M|M	0.61703|0.61703	1.905|1.905	0.80722|0.80722	D|D	1|1	P;D;D;P;D|.	0.76494|.	0.78;0.983;0.999;0.953;0.983|.	B;P;D;P;P|.	0.81914|.	0.377;0.88;0.995;0.808;0.88|.	T|T	0.69687|0.69687	-0.5078|-0.5078	10|5	0.66056|.	D|.	0.02|.	.|.	14.2607|14.2607	0.66083|0.66083	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	345;345;345;324;345|.	B7ZLA7;Q17S10;E9PFU5;B8ZZK3;P41586|.	.;.;.;.;PACR_HUMAN|.	P|A	345;116;324;345;345|61	ENSP00000306620:S345P;ENSP00000387335:S324P;ENSP00000379514:S345P;ENSP00000386395:S345P|.	ENSP00000306620:S345P|.	S|V	+|+	1|2	0|0	ADCYAP1R1|ADCYAP1R1	31098861|31098861	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	4.673000|4.673000	0.61604|0.61604	2.317000|2.317000	0.78254|0.78254	0.460000|0.460000	0.39030|0.39030	TCC|GTC	.	.		0.478	ADCYAP1R1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000215041.3	NM_001118		C	31132336	T	C	31132336	3	2	282	1	0	0	0	0	1	0	0	0	303	1667	58	2	1079	2	ADCYAP1R1	7	31132336	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3937789	31132336	128006327	551	40785										
NEUROD6	63974	hgsc.bcm.edu	37	chr7	31378032	31378032	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aatgcatgccgtaattgtaaTttttaccatagtccaaggtt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:31378032delT	ENST00000297142.3	-	2	1173	c.851delA	c.(850-852)aatfs	p.N284fs		NM_022728.2	NP_073565.2	Q96NK8	NDF6_HUMAN	neuronal differentiation 6	284					cell differentiation (GO:0030154)|dentate gyrus development (GO:0021542)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	32						GTAATTGTAATTTTTACCATA	0.502																																					p.N284fs		Atlas-INDEL	.											.	NEUROD6	84	.	0			c.852delT						.						93	93	93					7																	31378032		2203	4300	6503	SO:0001589	frameshift_variant	63974	exon2			.	AF248954	CCDS5434.1	7p15.1	2013-05-21	2012-02-22		ENSG00000164600	ENSG00000164600		"Basic helix-loop-helix proteins"	13804	protein-coding gene	gene with protein product		611513	"neurogenic differentiation 6"			12357074	Standard	NM_022728		Approved	Atoh2, NEX1M, Math-2, bHLHa2, Nex1	uc003tch.4	Q96NK8	OTTHUMG00000022865	ENST00000297142.3:c.851delA	chr7.hg19:g.31378032delT	ENSP00000297142:p.Asn284fs	121.0	0.0		157.0	10.0	NM_022728	Q548T9|Q9H3H6	Frame_Shift_Del	DEL	ENST00000297142.3	hg19	CCDS5434.1																																																																																			.	.		0.502	NEUROD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215050.1	NM_022728		-	31378032	T	-	31378032	7	5	282	1	0	1	0	1	0	0	0	0	10360	1493	52	0	166	0	NEUROD6	7	31378032	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	245696	31378032	127760631	552	40786										
DPY19L1	23333	hgsc.bcm.edu	37	chr7	35057514	35057514	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	catttcagtgcgaaaagccaTctccctttccaatgttgaga	7	11	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:35057514T>C	ENST00000310974.4	-	3	316	c.172A>G	c.(172-174)Atg>Gtg	p.M58V		NM_015283.1	NP_056098.1	Q2PZI1	D19L1_HUMAN	dpy-19-like 1 (C. elegans)	58						integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity, transferring glycosyl groups (GO:0016757)			endometrium(3)|kidney(5)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	31						CGAAAAGCCATCTCCCTTTCC	0.303																																					p.M58V		Atlas-SNP	.											.	DPY19L1	56	.	0			c.A172G						.						80	79	79					7																	35057514		1969	4205	6174	SO:0001583	missense	23333	exon3			AAGCCATCTCCCT	AB020684	CCDS43567.1	7p14.3-p14.2	2006-04-26			ENSG00000173852	ENSG00000173852			22205	protein-coding gene	gene with protein product		613892					Standard	NM_015283		Approved	KIAA0877	uc003tem.4	Q2PZI1	OTTHUMG00000154888	ENST00000310974.4:c.172A>G	chr7.hg19:g.35057514T>C	ENSP00000308695:p.Met58Val	86.0	0.0		103.0	6.0	NM_015283	O94954|Q4G151	Missense_Mutation	SNP	ENST00000310974.4	hg19	CCDS43567.1	.	.	.	.	.	.	.	.	.	.	T	17.75	3.465948	0.63625	.	.	ENSG00000173852	ENST00000310974	T	0.55930	0.49	5.22	5.22	0.72569	.	0.000000	0.85682	U	0.000000	T	0.72898	0.3518	M	0.80183	2.485	0.58432	D	0.999997	P	0.50156	0.932	D	0.67103	0.949	T	0.76732	-0.2851	10	0.66056	D	0.02	-18.7281	14.5697	0.68203	0.0:0.0:0.0:1.0	.	58	Q2PZI1	D19L1_HUMAN	V	58	ENSP00000308695:M58V	ENSP00000308695:M58V	M	-	1	0	DPY19L1	35024039	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.459000	0.80802	2.102000	0.63906	0.477000	0.44152	ATG	.	.		0.303	DPY19L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337506.1			C	35057514	T	C	35057514	3	2	282	1	0	0	0	0	1	0	0	0	4742	1435	50	2	1935	2	DPY19L1	7	35057514	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3679482	35057514	124081149	553	40787										
ELMO1	9844	hgsc.bcm.edu	37	chr7	37172765	37172765	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcatcttggtggtgcttggcAaagtacagcatgttgtccag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:37172765delA	ENST00000310758.4	-	14	1808	c.1161delT	c.(1159-1161)tttfs	p.F387fs	ELMO1_ENST00000442504.1_Frame_Shift_Del_p.F387fs|ELMO1_ENST00000448602.1_Frame_Shift_Del_p.F387fs|ELMO1_ENST00000341056.3_Frame_Shift_Del_p.F89fs	NM_001206480.1|NM_014800.10	NP_001193409.1|NP_055615.8	Q92556	ELMO1_HUMAN	engulfment and cell motility 1	387	ELMO. {ECO:0000255|PROSITE- ProRule:PRU00664}.				actin cytoskeleton organization (GO:0030036)|apoptotic process (GO:0006915)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|phagocytosis, engulfment (GO:0006911)|Rac protein signal transduction (GO:0016601)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(28)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	58						GGTGCTTGGCAAAGTACAGCA	0.438																																					p.A388fs		Atlas-INDEL	.											.	ELMO1	141	.	0			c.1162delG						.						169	143	152					7																	37172765		2203	4300	6503	SO:0001589	frameshift_variant	9844	exon14			.	AF398885	CCDS5449.1, CCDS5450.1	7p14.1	2012-07-10	2006-01-20		ENSG00000155849	ENSG00000155849		"Engulfment and cell motility proteins"	16286	protein-coding gene	gene with protein product		606420	"engulfment and cell motility 1 (ced-12 homolog, C. elegans)"			11595183	Standard	NM_001039459		Approved	KIAA0281, CED12, ELMO-1, CED-12	uc003tfk.2	Q92556	OTTHUMG00000023701	ENST00000310758.4:c.1161delT	chr7.hg19:g.37172765delA	ENSP00000312185:p.Phe387fs	141.0	0.0		175.0	11.0	NM_014800	A4D1X6|Q29R79|Q6ZTJ0|Q96PB0|Q9H0I1	Frame_Shift_Del	DEL	ENST00000310758.4	hg19	CCDS5449.1																																																																																			.	.		0.438	ELMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219830.4	NM_130442		-	37172765	A	-	37172765	7	5	282	1	0	1	0	1	0	0	0	0	5067	127	5	0	1058	0	ELMO1	7	37172765	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2115251	37172765	121965898	554	40788										
EPDR1	54749	hgsc.bcm.edu	37	chr7	37988590	37988590	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttgaagaccagtactccatcGgggggcctcaggagcagatc	13	11	1	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:37988590G>T	ENST00000199448.4	+	2	797	c.418G>T	c.(418-420)Ggg>Tgg	p.G140W	EPDR1_ENST00000476620.1_Missense_Mutation_p.G38W|EPDR1_ENST00000559325.1_Missense_Mutation_p.G260W|EPDR1_ENST00000423717.1_Intron|EPDR1_ENST00000425345.1_Missense_Mutation_p.G79W	NM_017549.4	NP_060019.2	Q9UM22	EPDR1_HUMAN	ependymin related 1	140					cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|large_intestine(2)|lung(9)|ovary(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	22						GTACTCCATCGGGGGGCCTCA	0.512																																					p.G140W		Atlas-SNP	.											EPDR1,NS,carcinoma,0,1	EPDR1	48	.	0			c.G418T						.						89	88	88					7																	37988590		2203	4300	6503	SO:0001583	missense	54749	exon2			TCCATCGGGGGGC	BC018299	CCDS5454.1, CCDS5454.2, CCDS59051.1, CCDS59052.1	7p14.1	2013-07-31	2013-07-31		ENSG00000086289	ENSG00000086289			17572	protein-coding gene	gene with protein product			"ependymin related protein 1 (zebrafish)"			11749721, 11248421	Standard	NM_001242946		Approved	MERP-1, MERP1, UCC1, EPDR	uc003tfp.4	Q9UM22	OTTHUMG00000102187	ENST00000199448.4:c.418G>T	chr7.hg19:g.37988590G>T	ENSP00000199448:p.Gly140Trp	136.0	0.0		182.0	0.0	NM_017549	A8K4C0|C9JYS3|Q06BL0|Q99M77	Missense_Mutation	SNP	ENST00000199448.4	hg19	CCDS5454.2	.	.	.	.	.	.	.	.	.	.	G	27.6	4.842274	0.91197	.	.	ENSG00000086289	ENST00000476620;ENST00000199448;ENST00000425345	.	.	.	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	D	0.82986	0.5156	M	0.81942	2.565	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.85000	0.0899	9	0.87932	D	0	-22.3895	17.7611	0.88465	0.0:0.0:1.0:0.0	.	79;260	C9JYS3;A4D1W8	.;.	W	38;260;79	.	ENSP00000199448:G260W	G	+	1	0	EPDR1	37955115	1.000000	0.71417	0.994000	0.49952	0.971000	0.66376	9.657000	0.98554	2.729000	0.93468	0.655000	0.94253	GGG	.	.		0.512	EPDR1-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220037.3	NM_017549		T	37988590	G	T	37988590	3	4	282	1	0	0	0	0	1	0	0	0	5165	1116	39	1	784	1	EPDR1	7	37988590	Missense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	815825	37988590	121150073	555	40789										
URGCP	55665	hgsc.bcm.edu	37	chr7	43917420	43917420	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccccgagatgaactcctgcaCccccgaggagggatcatggc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:43917420delC	ENST00000453200.1	-	6	2135	c.1642delG	c.(1642-1644)gtgfs	p.V548fs	URGCP_ENST00000447717.3_Frame_Shift_Del_p.V505fs|URGCP_ENST00000223341.7_Frame_Shift_Del_p.V505fs|URGCP-MRPS24_ENST00000603700.1_Intron|URGCP_ENST00000443736.1_Frame_Shift_Del_p.V505fs|URGCP_ENST00000336086.6_Frame_Shift_Del_p.V505fs|URGCP_ENST00000402306.3_Frame_Shift_Del_p.V539fs|URGCP_ENST00000497914.1_5'UTR			Q8TCY9	URGCP_HUMAN	upregulator of cell proliferation	548					cell cycle (GO:0007049)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|liver(1)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						AACTCCTGCACCCCCGAGGAG	0.652																																					p.V548fs		Atlas-INDEL	.											.	URGCP	170	.	0			c.1643delT						.						34	39	37					7																	43917420		2038	4172	6210	SO:0001589	frameshift_variant	55665	exon6			.		CCDS43572.1, CCDS47577.1, CCDS47578.1	7p13	2010-02-17			ENSG00000106608	ENSG00000106608			30890	protein-coding gene	gene with protein product	"up-regulated gene 4"	610337				10819331, 12082552	Standard	NM_017920		Approved	URG4, KIAA1507, FLJ20654, DKFZp666G166, DKFZp686O0457	uc003tiw.3	Q8TCY9	OTTHUMG00000155245	ENST00000453200.1:c.1642delG	chr7.hg19:g.43917420delC	ENSP00000396918:p.Val548fs	182.0	0.0		197.0	12.0	NM_001077663	E9PFF6|Q658M4|Q68DH6|Q6MZZ5|Q8WV98|Q9NWR7|Q9P221	Frame_Shift_Del	DEL	ENST00000453200.1	hg19	CCDS47578.1																																																																																			.	.		0.652	URGCP-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338995.1	NM_001077664		-	43917420	C	-	43917420	7	5	282	1	0	1	0	1	0	0	0	0	17041	507	18	0	1157	0	URGCP	7	43917420	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	5928830	43917420	115221243	556	40790										
NUDCD3	23386	hgsc.bcm.edu	37	chr7	44425624	44425624	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tggtcattaaaactgcacagCccccggggagatgttgaaca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:44425624delC	ENST00000355451.7	-	6	1351	c.1072delG	c.(1072-1074)gctfs	p.A358fs	NUDCD3_ENST00000460110.1_5'UTR	NM_015332.3	NP_056147.2	Q8IVD9	NUDC3_HUMAN	NudC domain containing 3	358										endometrium(2)|large_intestine(1)|lung(3)|skin(1)	7						AACTGCACAGCCCCCGGGGAG	0.577																																					p.A358fs		Atlas-INDEL	.											.	NUDCD3	20	.	0			c.1073delC						.						68	63	64					7																	44425624		2203	4300	6503	SO:0001589	frameshift_variant	23386	exon6			.	BC003691	CCDS5490.2	7p13-p12	2005-03-18			ENSG00000015676	ENSG00000015676			22208	protein-coding gene	gene with protein product		610296					Standard	NM_015332		Approved	KIAA1068	uc003tkz.3	Q8IVD9	OTTHUMG00000129174	ENST00000355451.7:c.1072delG	chr7.hg19:g.44425624delC	ENSP00000347626:p.Ala358fs	124.0	0.0		183.0	11.0	NM_015332	Q9BTI3|Q9H7W9|Q9UPT4	Frame_Shift_Del	DEL	ENST00000355451.7	hg19	CCDS5490.2																																																																																			.	.		0.577	NUDCD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251248.3	NM_015332		-	44425624	C	-	44425624	7	5	282	1	0	1	0	1	0	0	0	0	10733	739	26	0	17	0	NUDCD3	7	44425624	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	508204	44425624	114713039	557	40791										
ZMIZ2	83637	hgsc.bcm.edu	37	chr7	44806215	44806215	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctgccacaggcgtgatggggCcccccagcatgtctggagcc					rs199813267		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:44806215delC	ENST00000309315.4	+	18	2731	c.2608delC	c.(2608-2610)cccfs	p.P871fs	ZMIZ2_ENST00000413916.1_Frame_Shift_Del_p.P813fs|ZMIZ2_ENST00000433667.1_Frame_Shift_Del_p.P839fs|ZMIZ2_ENST00000463931.1_3'UTR|ZMIZ2_ENST00000265346.7_Frame_Shift_Del_p.P845fs|ZMIZ2_ENST00000441627.1_Frame_Shift_Del_p.P871fs	NM_031449.3	NP_113637.3	Q8NF64	ZMIZ2_HUMAN	zinc finger, MIZ-type containing 2	871	Pro-rich.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|zinc ion binding (GO:0008270)			breast(3)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						CGTGATGGGGCCCCCCAGCAT	0.672																																					p.G869fs	NSCLC(20;604 852 1948 16908 50522)	Atlas-INDEL	.											ZMIZ2,colon,carcinoma,0,1	ZMIZ2	82	.	0			c.2607delG						.						29	34	32					7																	44806215		1852	4090	5942	SO:0001589	frameshift_variant	83637	exon18			.	AK090415	CCDS43576.1, CCDS43577.1, CCDS75591.1	7p13	2009-11-06			ENSG00000122515	ENSG00000122515		"Zinc fingers, MIZ-type"	22229	protein-coding gene	gene with protein product		611196					Standard	XM_005249866		Approved	KIAA1886, hZIMP7, ZIMP7, DKFZp761I2123, NET27	uc003tlr.3	Q8NF64	OTTHUMG00000155817	ENST00000309315.4:c.2608delC	chr7.hg19:g.44806215delC	ENSP00000311778:p.Pro871fs	109.0	0.0		170.0	12.0	NM_031449	A4D2K7|D3DVL1|O94790|Q0VGB4|Q659A8|Q6JKL5|Q8WTX8|Q96Q01|Q9BQH7	Frame_Shift_Del	DEL	ENST00000309315.4	hg19	CCDS43576.1																																																																																			.	.		0.672	ZMIZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341790.1	NM_031449		-	44806215	C	-	44806215	7	5	282	1	0	1	0	1	0	0	0	0	17712	739	26	0	2674	0	ZMIZ2	7	44806215	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	380591	44806215	114332448	558	40792										
NCF1	653361	hgsc.bcm.edu	37	chr7	74202414	74202414	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggcccaacgccagatcaagcGgggggcgccgccccgcaggt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:74202414delG	ENST00000289473.4	+	9	957	c.887delG	c.(886-888)cggfs	p.R296fs		NM_000265.4	NP_000256.4	P14598	NCF1_HUMAN	neutrophil cytosolic factor 1	296	Arg/Lys-rich (highly basic).				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular defense response (GO:0006968)|hydrogen peroxide biosynthetic process (GO:0050665)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|leukotriene metabolic process (GO:0006691)|negative regulation of smooth muscle contraction (GO:0045986)|neutrophil mediated killing of fungus (GO:0070947)|neutrophil mediated killing of gram-positive bacterium (GO:0070946)|oxidation-reduction process (GO:0055114)|phagosome maturation (GO:0090382)|protein targeting to membrane (GO:0006612)|respiratory burst (GO:0045730)|respiratory burst involved in defense response (GO:0002679)|response to yeast (GO:0001878)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of membrane (GO:0019898)|Golgi apparatus (GO:0005794)|NADPH oxidase complex (GO:0043020)|neuronal cell body (GO:0043025)|phagolysosome (GO:0032010)|rough endoplasmic reticulum (GO:0005791)	electron carrier activity (GO:0009055)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|SH3 domain binding (GO:0017124)|superoxide-generating NADPH oxidase activity (GO:0016175)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|skin(3)	10					Dextromethorphan(DB00514)	CAGATCAAGCGGGGGGCGCCG	0.667																																					p.R296fs		Atlas-INDEL	.											.,1	NCF1	26	.	0			c.886delC						.						1	1	1					7																	74202414		219	155	374	SO:0001589	frameshift_variant	653361	exon9			.	M25665	CCDS34657.1	7q11.23	2014-09-17	2008-07-31		ENSG00000158517	ENSG00000158517			7660	protein-coding gene	gene with protein product	"NADPH oxidase organizer 2", "chronic granulomatous disease, autosomal 1"	608512	"neutrophil cytosolic factor 1 (47kD, chronic granulomatous disease, autosomal 1)"				Standard	NM_000265		Approved	p47phox, NOXO2, NCF1A, SH3PXD1A	uc022aft.1	P14598	OTTHUMG00000149965	ENST00000289473.4:c.887delG	chr7.hg19:g.74202414delG	ENSP00000289473:p.Arg296fs	221.0	0.0		158.0	11.0	NM_000265	A6NEH2|A8K7S9|O43842|Q2PP07|Q53FR5|Q9BU90|Q9BXI7|Q9BXI8|Q9UDV9|Q9UMU2	Frame_Shift_Del	DEL	ENST00000289473.4	hg19	CCDS34657.1																																																																																			.	.		0.667	NCF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314560.1	NM_000265		-	74202414	G	-	74202414	7	5	282	1	0	1	0	1	0	0	0	0	10225	1116	39	0	921	0	NCF1	7	74202414	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	29396199	74202414	84936249	559	40793										
ABCB4	5244	hgsc.bcm.edu	37	chr7	87079305	87079305	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tttccagctctttgttctggCccccgaaagctatcacagtc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:87079305delC	ENST00000265723.4	-	8	923	c.812delG	c.(811-813)ggcfs	p.G271fs	ABCB4_ENST00000359206.3_Frame_Shift_Del_p.G271fs|ABCB4_ENST00000545634.1_Frame_Shift_Del_p.G271fs|ABCB4_ENST00000358400.3_Frame_Shift_Del_p.G271fs|ABCB4_ENST00000453593.1_Frame_Shift_Del_p.G271fs	NM_000443.3|NM_018849.2	NP_000434.1|NP_061337.1	P21439	MDR3_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 4	271	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular lipid metabolic process (GO:0044255)|lipid metabolic process (GO:0006629)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|xenobiotic-transporting ATPase activity (GO:0008559)			breast(5)|endometrium(7)|kidney(2)|large_intestine(15)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				Colchicine(DB01394)|Etravirine(DB06414)|Silodosin(DB06207)	TTTGTTCTGGCCCCCGAAAGC	0.468																																					p.G271fs		Atlas-INDEL	.											.	ABCB4	177	.	0			c.813delC						.						117	97	104					7																	87079305		2203	4300	6503	SO:0001589	frameshift_variant	5244	exon8			.	M23234	CCDS5605.1, CCDS5606.1, CCDS5607.1	7q21	2012-03-14			ENSG00000005471	ENSG00000005471		"ATP binding cassette transporters / subfamily B"	45	protein-coding gene	gene with protein product		171060		PGY3, MDR3		2892668, 11313316	Standard	NM_018850		Approved	MDR2, PFIC-3, GBD1	uc003uiv.1	P21439	OTTHUMG00000023396	ENST00000265723.4:c.812delG	chr7.hg19:g.87079305delC	ENSP00000265723:p.Gly271fs	305.0	0.0		297.0	18.0	NM_018849	A0A2V7|A4D1D3|A4D1D4|A4D1D5|D6W5P3|D6W5P4|Q14813	Frame_Shift_Del	DEL	ENST00000265723.4	hg19	CCDS5606.1																																																																																			.	.		0.468	ABCB4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000336083.1	NM_000443		-	87079305	C	-	87079305	7	5	282	1	0	1	0	1	0	0	0	0	43	739	26	0	3132	0	ABCB4	7	87079305	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	12876891	87079305	72059358	560	40794										
PON1	5444	hgsc.bcm.edu	37	chr7	94935617	94935617	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cttcaatggagttaaagtccAattagcatgcttttcataca	6	8	2	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:94935617A>G	ENST00000222381.3	-	7	991	c.760T>C	c.(760-762)Tgg>Cgg	p.W254R	PON1_ENST00000542556.1_Missense_Mutation_p.W254R	NM_000446.5	NP_000437.3	P27169	PON1_HUMAN	paraoxonase 1	254					aromatic compound catabolic process (GO:0019439)|carboxylic acid catabolic process (GO:0046395)|dephosphorylation (GO:0016311)|organophosphate catabolic process (GO:0046434)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of binding (GO:0051099)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of transporter activity (GO:0032411)|response to external stimulus (GO:0009605)|response to toxic substance (GO:0009636)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|intracellular membrane-bounded organelle (GO:0043231)|spherical high-density lipoprotein particle (GO:0034366)	aryldialkylphosphatase activity (GO:0004063)|arylesterase activity (GO:0004064)|calcium ion binding (GO:0005509)|phospholipid binding (GO:0005543)|protein homodimerization activity (GO:0042803)			autonomic_ganglia(1)|endometrium(2)|large_intestine(6)|lung(11)|pancreas(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	27	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0031)		Cefazolin(DB01327)	GTTAAAGTCCAATTAGCATGC	0.323																																					p.W254R	GBM(119;715 1622 17358 22490 33240)	Atlas-SNP	.											.	PON1	55	.	0			c.T760C						.						148	146	146					7																	94935617		2203	4300	6503	SO:0001583	missense	5444	exon7			AAGTCCAATTAGC	AF539592	CCDS5638.1	7q21.3	2014-03-14			ENSG00000005421	ENSG00000005421	3.1.1.2	"Paraoxonases"	9204	protein-coding gene	gene with protein product	"esterase A", "arylesterase 1"	168820		PON		8661009, 15450851	Standard	NM_000446		Approved	ESA	uc003uns.3	P27169	OTTHUMG00000153894	ENST00000222381.3:c.760T>C	chr7.hg19:g.94935617A>G	ENSP00000222381:p.Trp254Arg	109.0	0.0		119.0	5.0	NM_000446	B2RA40|Q16052|Q6B0J6|Q9UCB1	Missense_Mutation	SNP	ENST00000222381.3	hg19	CCDS5638.1	.	.	.	.	.	.	.	.	.	.	A	9.485	1.099095	0.20552	.	.	ENSG00000005421	ENST00000222381;ENST00000542556	T;T	0.39787	1.06;1.06	4.83	3.6	0.41247	Six-bladed beta-propeller, TolB-like (1);	0.272271	0.42053	D	0.000771	T	0.44829	0.1312	M	0.84683	2.71	0.42629	D	0.993372	B;B	0.22211	0.066;0.014	B;B	0.14023	0.01;0.004	T	0.45818	-0.9235	10	0.23891	T	0.37	-8.365	12.2817	0.54767	0.8593:0.1407:0.0:0.0	.	254;254	F5H4W9;P27169	.;PON1_HUMAN	R	254	ENSP00000222381:W254R;ENSP00000444854:W254R	ENSP00000222381:W254R	W	-	1	0	PON1	94773553	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.489000	0.45285	2.156000	0.67533	0.459000	0.35465	TGG	.	.		0.323	PON1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000332865.2	NM_000446		G	94935617	A	G	94935617	3	3	282	1	0	0	0	0	1	0	0	0	12257	130	5	2	319	2	PON1	7	94935617	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	7856312	94935617	64203046	561	40795										
PON2	5445	hgsc.bcm.edu	37	chr7	95035443	95035443	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ataaaaacctctgacgagggAggattgttcgggtcatacac	11	8	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:95035443A>G	ENST00000222572.3	-	8	1140	c.894T>C	c.(892-894)ccT>ccC	p.P298P	PON2_ENST00000433091.2_Silent_p.P286P|PON2_ENST00000483292.1_5'UTR|PON2_ENST00000536183.1_Silent_p.P319P			Q15165	PON2_HUMAN	paraoxonase 2	298					aromatic compound catabolic process (GO:0019439)|response to oxidative stress (GO:0006979)	extracellular region (GO:0005576)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arylesterase activity (GO:0004064)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|prostate(1)	9	all_cancers(62;9.35e-11)|all_epithelial(64;3.37e-09)		STAD - Stomach adenocarcinoma(171;0.0151)			CTGACGAGGGAGGATTGTTCG	0.378																																					p.P298P	GBM(42;803 823 13649 23368 31463)	Atlas-SNP	.											.	PON2	32	.	0			c.T894C						.						103	105	104					7																	95035443		2203	4300	6503	SO:0001819	synonymous_variant	5445	exon8			CGAGGGAGGATTG	M63012, AF001601	CCDS5640.1, CCDS47644.1	7q21.3	2014-03-14			ENSG00000105854	ENSG00000105854	3.1.1.2	"Paraoxonases"	9205	protein-coding gene	gene with protein product	"paraoxonase nirs", "arylesterase 2"	602447				8661009, 9714608	Standard	XM_005250453		Approved		uc003unv.3	Q15165	OTTHUMG00000153948	ENST00000222572.3:c.894T>C	chr7.hg19:g.95035443A>G		72.0	0.0		56.0	4.0	NM_000305	A4D1H7|B2RCP9|B4DJD5|O15114|O15115|O75856|Q5FBX7|Q86YL0	Silent	SNP	ENST00000222572.3	hg19	CCDS5640.1																																																																																			.	.		0.378	PON2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333142.1	NM_000305		G	95035443	A	G	95035443	2	3	282	1	0	0	0	0	0	0	0	1	12258	291	11	2		2	PON2	7	95035443	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	99826	95035443	64103220	562	40796										
LMTK2	22853	hgsc.bcm.edu	37	chr7	97821054	97821054	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggtcgactttgaacagcagtGgaacgctctgaagccgaaca	12	10	1	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:97821054G>A	ENST00000297293.5	+	11	1570	c.1277G>A	c.(1276-1278)tGg>tAg	p.W426*		NM_014916.3	NP_055731.2	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2	426					early endosome to late endosome transport (GO:0045022)|endocytic recycling (GO:0032456)|negative regulation of catalytic activity (GO:0043086)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor recycling (GO:0001881)|transferrin transport (GO:0033572)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|myosin VI binding (GO:0070853)|protein phosphatase inhibitor activity (GO:0004864)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|pancreas(2)|skin(2)|stomach(3)	59	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)					GAACAGCAGTGGAACGCTCTG	0.562																																					p.W426X		Atlas-SNP	.											.	LMTK2	228	.	0			c.G1277A						.						95	82	87					7																	97821054		2203	4300	6503	SO:0001587	stop_gained	22853	exon11			AGCAGTGGAACGC	AB029002	CCDS5654.1	7q22.1	2014-06-12			ENSG00000164715	ENSG00000164715			17880	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 100"	610989				15005709	Standard	NM_014916		Approved	KIAA1079, KPI2, KPI-2, cprk, LMR2, BREK, AATYK2, PPP1R100	uc003upd.2	Q8IWU2	OTTHUMG00000154256	ENST00000297293.5:c.1277G>A	chr7.hg19:g.97821054G>A	ENSP00000297293:p.Trp426*	220.0	1.0		218.0	110.0	NM_014916	A4D272|Q75MG7|Q9UPS3	Nonsense_Mutation	SNP	ENST00000297293.5	hg19	CCDS5654.1	.	.	.	.	.	.	.	.	.	.	G	40	8.350838	0.98772	.	.	ENSG00000164715	ENST00000297293	.	.	.	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.551	0.91065	0.0:0.0:1.0:0.0	.	.	.	.	X	426	.	ENSP00000297293:W426X	W	+	2	0	LMTK2	97658990	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	9.420000	0.97426	2.710000	0.92621	0.655000	0.94253	TGG	.	.		0.562	LMTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334560.1	NM_014916		A	97821054	G	A	97821054	4	1	282	1	0	0	0	0	0	1	0	0	8868	1357	47	3	1319	3	LMTK2	7	97821054	Nonsense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	2785611	97821054	61317609	563	40797										
BHLHA15	168620	hgsc.bcm.edu	37	chr7	97841927	97841927	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caggccctgcgtgaagtcatCccccacgtgcgcgcggacaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:97841927delC	ENST00000609256.1	+	2	432	c.306delC	c.(304-306)atcfs	p.I102fs	BHLHA15_ENST00000314018.2_Frame_Shift_Del_p.I102fs			Q7RTS1	BHA15_HUMAN	basic helix-loop-helix family, member a15	102	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				calcium-mediated signaling (GO:0019722)|cell maturation (GO:0048469)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|Golgi organization (GO:0007030)|intracellular distribution of mitochondria (GO:0048312)|mitochondrial calcium ion transport (GO:0006851)	nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)										GTGAAGTCATCCCCCACGTGC	0.602																																					p.I102fs		Atlas-INDEL	.											.	BHLHA15	11	.	0			c.305delT						.						64	48	53					7																	97841927		2200	4297	6497	SO:0001589	frameshift_variant	168620	exon1			.	BK000276	CCDS5655.1	7q21.3	2009-01-12	2009-01-12	2009-01-12	ENSG00000180535	ENSG00000180535		"Basic helix-loop-helix proteins"	22265	protein-coding gene	gene with protein product		608606	"basic helix-loop-helix domain containing, class B, 8"	BHLHB8		14516699, 18557763	Standard	NM_177455		Approved	MIST1, bHLHa15	uc003upf.1	Q7RTS1	OTTHUMG00000154289	ENST00000609256.1:c.306delC	chr7.hg19:g.97841927delC	ENSP00000476312:p.Ile102fs	218.0	0.0		209.0	13.0	NM_177455	A4D271|Q14DE4	Frame_Shift_Del	DEL	ENST00000609256.1	hg19	CCDS5655.1																																																																																			.	.		0.602	BHLHA15-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472733.1	NM_177455		-	97841927	C	-	97841927	7	5	282	1	0	1	0	1	0	0	0	0	1419	845	30	0	308	0	BHLHA15	7	97841927	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	20873	97841927	61296736	564	40798										
TMEM130	222865	hgsc.bcm.edu	37	chr7	98460876	98460876	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcttgccagtaagcaccagcGgggtgtggatccagtggaag					rs369651719		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:98460876delG	ENST00000416379.2	-	2	237	c.233delC	c.(232-234)ccgfs	p.P78fs	TMEM130_ENST00000450876.1_5'UTR|TMEM130_ENST00000546258.1_Frame_Shift_Del_p.P59fs|TMEM130_ENST00000345589.4_Intron|TMEM130_ENST00000339375.4_Frame_Shift_Del_p.P78fs			Q8N3G9	TM130_HUMAN	transmembrane protein 130	78						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	25	all_cancers(62;4.05e-09)|all_epithelial(64;2.62e-09)|Lung NSC(181;0.01)|all_lung(186;0.0115)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			AAGCACCAGCGGGGTGTGGAT	0.662																																					p.P78fs		Atlas-INDEL	.											.	TMEM130	54	.	0			c.234delG						.						59	58	58					7																	98460876		2203	4300	6503	SO:0001589	frameshift_variant	222865	exon2			.		CCDS5658.1, CCDS47649.1, CCDS47650.1	7q22.1	2006-03-09			ENSG00000166448	ENSG00000166448			25429	protein-coding gene	gene with protein product						12975309	Standard	NM_152913		Approved	DKFZp761L1417, FLJ42643	uc003upo.3	Q8N3G9	OTTHUMG00000154419	ENST00000416379.2:c.233delC	chr7.hg19:g.98460876delG	ENSP00000413163:p.Pro78fs	180.0	0.0		174.0	12.0	NM_152913	A4D266|B7Z364|Q8IY46|Q8N0W9|Q8N3R2	Frame_Shift_Del	DEL	ENST00000416379.2	hg19	CCDS47650.1																																																																																			.	.		0.662	TMEM130-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000380713.1	NM_152913		-	98460876	G	-	98460876	7	5	282	1	0	1	0	1	0	0	0	0	16058	1116	39	0	1102	0	TMEM130	7	98460876	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	618949	98460876	60677787	565	40799										
ZNF394	84124	hgsc.bcm.edu	37	chr7	99091600	99091600	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cacatttcagacaggtgtacGgcttctcgcctgtgtgtgtc	11	11	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:99091600G>T	ENST00000337673.6	-	3	1441	c.1238C>A	c.(1237-1239)cCg>cAg	p.P413Q	ZNF394_ENST00000426306.2_3'UTR|ZNF394_ENST00000394177.3_5'Flank|ZNF789_ENST00000494186.1_Intron|ZNF789_ENST00000493485.1_Intron	NM_032164.2	NP_115540.2	Q53GI3	ZN394_HUMAN	zinc finger protein 394	413					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(5)|stomach(1)|urinary_tract(1)	16	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					ACAGGTGTACGGCTTCTCGCC	0.498																																					p.P413Q	Ovarian(24;589 697 9939 12704 40742)	Atlas-SNP	.											ZNF394,NS,carcinoma,0,1	ZNF394	48	.	0			c.C1238A						.						101	101	101					7																	99091600		2203	4300	6503	SO:0001583	missense	84124	exon3			GTGTACGGCTTCT	BC025241	CCDS5666.1	7q22.1	2014-01-28			ENSG00000160908	ENSG00000160908		"Zinc fingers, C2H2-type", "-", "-", "-"	18832	protein-coding gene	gene with protein product							Standard	NM_032164		Approved	ZKSCAN14, FLJ12298, ZSCAN46	uc003uqs.3	Q53GI3	OTTHUMG00000154660	ENST00000337673.6:c.1238C>A	chr7.hg19:g.99091600G>T	ENSP00000337363:p.Pro413Gln	285.0	0.0		288.0	0.0	NM_032164	A4D281|Q05DA6|Q6P5X9|Q8TB27|Q9HA37|Q9UD51	Missense_Mutation	SNP	ENST00000337673.6	hg19	CCDS5666.1	.	.	.	.	.	.	.	.	.	.	G	15.49	2.849151	0.51270	.	.	ENSG00000160908	ENST00000337673	T	0.28454	1.61	3.54	3.54	0.40534	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.151199	0.31542	N	0.007463	T	0.51907	0.1702	M	0.69463	2.115	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.57124	-0.7865	10	0.87932	D	0	.	13.4733	0.61292	0.0:0.0:1.0:0.0	.	413	Q53GI3	ZN394_HUMAN	Q	413	ENSP00000337363:P413Q	ENSP00000337363:P413Q	P	-	2	0	ZNF394	98929536	1.000000	0.71417	0.454000	0.27019	0.160000	0.22226	5.811000	0.69187	2.287000	0.76781	0.650000	0.86243	CCG	.	.		0.498	ZNF394-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336498.1	NM_032164		T	99091600	G	T	99091600	3	4	282	1	0	0	0	0	1	0	0	0	17895	1116	39	1	451	1	ZNF394	7	99091600	Missense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	630724	99091600	60047063	566	40800										
MLL5	55904	hgsc.bcm.edu	37	chr7	104745930	104745930	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gagaagaatgagaagacaggAaaaccttcagatggcctttc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:104745930delA	ENST00000311117.3	+	18	2786	c.2241delA	c.(2239-2241)ggafs	p.G747fs	KMT2E_ENST00000334877.4_Frame_Shift_Del_p.G747fs|CTB-152G17.6_ENST00000607968.1_RNA|KMT2E_ENST00000257745.4_Frame_Shift_Del_p.G747fs|KMT2E_ENST00000334914.7_5'UTR	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	747					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)										AGAAGACAGGAAAACCTTCAG	0.378																																					p.G747fs		Atlas-INDEL	.											.	MLL5	173	.	0			c.2240delG						.						89	90	90					7																	104745930		2203	4300	6503	SO:0001589	frameshift_variant	55904	exon18			.	AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	18541	protein-coding gene	gene with protein product		608444	"myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.2241delA	chr7.hg19:g.104745930delA	ENSP00000312379:p.Gly747fs	106.0	0.0		132.0	10.0	NM_182931	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Frame_Shift_Del	DEL	ENST00000311117.3	hg19	CCDS34723.1																																																																																			.	.		0.378	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1			-	104745930	A	-	104745930	7	5	282	1	0	1	0	1	0	0	0	0	9633	233	9	0	2303	0	MLL5	7	104745930	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	5654330	104745930	54392733	567	40801										
CDHR3	222256	hgsc.bcm.edu	37	chr7	105658335	105658335	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cgagccactgataaagacctCccccagagcagcctcctgta							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:105658335delC	ENST00000317716.9	+	12	1550	c.1470delC	c.(1468-1470)ctcfs	p.L490fs	CDHR3_ENST00000470188.1_Intron|CDHR3_ENST00000542731.1_Frame_Shift_Del_p.L490fs|CDHR3_ENST00000343407.5_Intron|CDHR3_ENST00000478080.1_Frame_Shift_Del_p.L402fs	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	490	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						ATAAAGACCTCCCCCAGAGCA	0.517																																					p.L490fs		Atlas-INDEL	.											.	CDHR3	153	.	0			c.1469delT						.						33	36	35					7																	105658335		1888	4103	5991	SO:0001589	frameshift_variant	222256	exon12			.	AK126338	CCDS47684.1, CCDS75651.1	7q22.2	2011-07-01			ENSG00000128536	ENSG00000128536		"Cadherins / Cadherin-related"	26308	protein-coding gene	gene with protein product		615610					Standard	NM_152750		Approved	FLJ44366, FLJ23834, CDH28	uc003vdl.4	Q6ZTQ4	OTTHUMG00000157520	ENST00000317716.9:c.1470delC	chr7.hg19:g.105658335delC	ENSP00000325954:p.Leu490fs	141.0	0.0		135.0	11.0	NM_152750	Q8TCI7	Frame_Shift_Del	DEL	ENST00000317716.9	hg19	CCDS47684.1																																																																																			.	.		0.517	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	NM_152750		-	105658335	C	-	105658335	7	5	282	1	0	1	0	1	0	0	0	0	3122	842	30	0	1516	0	CDHR3	7	105658335	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	912405	105658335	53480328	568	40802										
LAMB1	3912	hgsc.bcm.edu	37	chr7	107564717	107564717	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atttgcttgagctaaaagagTttttgcttcattttgtagca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:107564717delT	ENST00000222399.6	-	33	5412	c.5182delA	c.(5182-5184)actfs	p.T1728fs	LAMB1_ENST00000393561.1_Frame_Shift_Del_p.T1752fs	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	1728	Domain I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|neuron projection development (GO:0031175)|neuronal-glial interaction involved in cerebral cortex radial glia guided migration (GO:0021812)|odontogenesis (GO:0042476)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell proliferation (GO:0050679)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-2 complex (GO:0005607)|laminin-8 complex (GO:0043257)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)|structural molecule activity (GO:0005198)			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						GCTAAAAGAGTTTTTGCTTCA	0.338																																					p.T1728fs		Atlas-INDEL	.											.	LAMB1	185	.	0			c.5183delC						.						91	91	91					7																	107564717		2203	4300	6503	SO:0001589	frameshift_variant	3912	exon33			.	M61916	CCDS5750.1	7q22	2013-03-01			ENSG00000091136	ENSG00000091136		"Laminins"	6486	protein-coding gene	gene with protein product		150240	"cutis laxa with marfanoid phenotype"	CLM		2563160, 2704655, 1864606	Standard	NM_002291		Approved		uc003vew.2	P07942	OTTHUMG00000149966	ENST00000222399.6:c.5182delA	chr7.hg19:g.107564717delT	ENSP00000222399:p.Thr1728fs	223.0	0.0		246.0	16.0	NM_002291	Q14D91	Frame_Shift_Del	DEL	ENST00000222399.6	hg19	CCDS5750.1																																																																																			.	.		0.338	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291		-	107564717	T	-	107564717	7	5	282	1	0	1	0	1	0	0	0	0	8619	1725	60	0	186	0	LAMB1	7	107564717	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1906382	107564717	51573946	569	40803										
DOCK4	9732	hgsc.bcm.edu	37	chr7	111448882	111448882	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cttttcctcacttacctaggTtttgccacatgctgaaaatt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:111448882delT	ENST00000437633.1	-	30	3417	c.3161delA	c.(3160-3162)aacfs	p.N1054fs	DOCK4_ENST00000428084.1_Frame_Shift_Del_p.N1054fs|DOCK4-AS1_ENST00000452714.1_RNA	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	1054					cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				CTTACCTAGGTTTTGCCACAT	0.413																																					p.N1054fs		Atlas-INDEL	.											.	DOCK4	365	.	0			c.3162delC						.						116	104	108					7																	111448882		1898	4124	6022	SO:0001589	frameshift_variant	9732	exon30			.		CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.3161delA	chr7.hg19:g.111448882delT	ENSP00000404179:p.Asn1054fs	288.0	0.0		253.0	16.0	NM_014705	O14584|O94824|Q8NB45	Frame_Shift_Del	DEL	ENST00000437633.1	hg19	CCDS47688.1																																																																																			.	.		0.413	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705		-	111448882	T	-	111448882	7	5	282	1	0	1	0	1	0	0	0	0	4691	1725	60	0	2831	0	DOCK4	7	111448882	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3884165	111448882	47689781	570	40804										
TMEM168	64418	hgsc.bcm.edu	37	chr7	112424114	112424114	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgcaaattcttccacggtacAaaaagggtttccatctttca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:112424114delA	ENST00000312814.6	-	2	1327	c.767delT	c.(766-768)ttgfs	p.L256fs	TMEM168_ENST00000454074.1_Frame_Shift_Del_p.L256fs	NM_022484.4	NP_071929.3	Q9H0V1	TM168_HUMAN	transmembrane protein 168	256						integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(2)|stomach(1)	32						TCCACGGTACAAAAAGGGTTT	0.363																																					p.L256fs		Atlas-INDEL	.											.	TMEM168	84	.	0			c.768delG						.						123	137	132					7																	112424114		2202	4299	6501	SO:0001589	frameshift_variant	64418	exon2			.		CCDS5757.1	7q31.32	2006-08-08			ENSG00000146802	ENSG00000146802			25826	protein-coding gene	gene with protein product						12477932	Standard	XM_005250527		Approved	DKFZp564C012,FLJ13576	uc003vgn.3	Q9H0V1	OTTHUMG00000155188	ENST00000312814.6:c.767delT	chr7.hg19:g.112424114delA	ENSP00000323068:p.Leu256fs	113.0	0.0		154.0	11.0	NM_022484	A4D0T9|B4DDS0|Q8NEK4|Q9H8J2	Frame_Shift_Del	DEL	ENST00000312814.6	hg19	CCDS5757.1																																																																																			.	.		0.363	TMEM168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338696.4	NM_022484		-	112424114	A	-	112424114	7	5	282	1	0	1	0	1	0	0	0	0	16098	131	5	0	1342	0	TMEM168	7	112424114	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	975232	112424114	46714549	571	40805										
WNT2	7472	hgsc.bcm.edu	37	chr7	116962981	116962981	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caccatgaagagttgacctcGggggtgagccaggtcaagag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:116962981delG	ENST00000265441.3	-	1	362	c.63delC	c.(61-63)cccfs	p.P21fs	AC002465.2_ENST00000436097.1_RNA	NM_003391.2	NP_003382.1	P09544	WNT2_HUMAN	wingless-type MMTV integration site family member 2	21					atrial cardiac muscle tissue morphogenesis (GO:0055009)|canonical Wnt signaling pathway (GO:0060070)|cardiac epithelial to mesenchymal transition (GO:0060317)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|iris morphogenesis (GO:0061072)|labyrinthine layer blood vessel development (GO:0060716)|lens development in camera-type eye (GO:0002088)|lung development (GO:0030324)|lung induction (GO:0060492)|mammary gland epithelium development (GO:0061180)|neuron differentiation (GO:0030182)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)			breast(2)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|ovary(3)|prostate(1)|skin(2)	31	all_epithelial(6;2.24e-06)|Lung NSC(10;0.000936)|all_lung(10;0.00109)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		AGTTGACCTCGGGGGTGAGCC	0.602																																					p.E22fs		Atlas-INDEL	.											.	WNT2	56	.	0			c.64delG						.						79	79	79					7																	116962981		2203	4300	6503	SO:0001589	frameshift_variant	7472	exon1			.	X07876	CCDS5771.1	7q31	2013-02-28			ENSG00000105989	ENSG00000105989		"Wingless-type MMTV integration sites", "Endogenous ligands"	12780	protein-coding gene	gene with protein product	"secreted growth factor"	147870		INT1L1		2971536	Standard	NM_003391		Approved	IRP	uc003viz.3	P09544	OTTHUMG00000023428	ENST00000265441.3:c.63delC	chr7.hg19:g.116962981delG	ENSP00000265441:p.Pro21fs	102.0	0.0		105.0	10.0	NM_003391	A4D0V1|Q75N05|Q9UDP9	Frame_Shift_Del	DEL	ENST00000265441.3	hg19	CCDS5771.1																																																																																			.	.		0.602	WNT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059749.3	NM_003391		-	116962981	G	-	116962981	7	5	282	1	0	1	0	1	0	0	0	0	17401	1103	39	0	1039	0	WNT2	7	116962981	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	4538867	116962981	42175682	572	40806										
KCND2	3751	hgsc.bcm.edu	37	chr7	120372995	120372995	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaaaaccatagcagggaagaTttttggttctatctgttcgc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:120372995delT	ENST00000331113.4	+	2	2119	c.1154delT	c.(1153-1155)attfs	p.I385fs		NM_012281.2	NP_036413.1	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 2	385					action potential (GO:0001508)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)			NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(35)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	75	all_neural(327;0.117)				Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458)	GCAGGGAAGATTTTTGGTTCT	0.398																																					p.I385fs		Atlas-INDEL	.											.	KCND2	194	.	0			c.1153delA						.						177	161	166					7																	120372995		2203	4300	6503	SO:0001589	frameshift_variant	3751	exon2			.	AJ010969	CCDS5776.1	7q31	2012-07-05			ENSG00000184408	ENSG00000184408		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6238	protein-coding gene	gene with protein product		605410				10551270, 16382104	Standard	NM_012281		Approved	Kv4.2, RK5, KIAA1044	uc003vjj.1	Q9NZV8	OTTHUMG00000156989	ENST00000331113.4:c.1154delT	chr7.hg19:g.120372995delT	ENSP00000333496:p.Ile385fs	291.0	0.0		264.0	18.0	NM_012281	O95012|O95021|Q2TBD3|Q9UBY7|Q9UN98|Q9UNH9	Frame_Shift_Del	DEL	ENST00000331113.4	hg19	CCDS5776.1																																																																																			.	.		0.398	KCND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346996.1	NM_012281		-	120372995	T	-	120372995	7	5	282	1	0	1	0	1	0	0	0	0	8028	1493	52	0	1160	0	KCND2	7	120372995	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3410014	120372995	38765668	573	40807										
TSPAN12	23554	hgsc.bcm.edu	37	chr7	120450526	120450526	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtagcacttacctctctctgAaaaaaattccaagcatgagt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:120450526delA	ENST00000222747.3	-	6	1066	c.459delT	c.(457-459)tttfs	p.F153fs	TSPAN12_ENST00000415871.1_Frame_Shift_Del_p.F153fs	NM_012338.3	NP_036470.1	O95859	TSN12_HUMAN	tetraspanin 12	153					angiogenesis (GO:0001525)|cell surface receptor signaling pathway (GO:0007166)|regulation of angiogenesis (GO:0045765)|retina layer formation (GO:0010842)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				endometrium(3)|kidney(1)|lung(4)|ovary(1)|skin(1)	10	all_neural(327;0.117)					CCTCTCTCTGAAAAAAATTCC	0.398																																					p.Q154fs		Atlas-INDEL	.											.	TSPAN12	25	.	0			c.460delC						.						118	113	115					7																	120450526		2203	4300	6503	SO:0001589	frameshift_variant	23554	exon6			.	AF124522	CCDS5777.1	7q31.31	2013-02-14	2005-03-21	2005-03-21	ENSG00000106025	ENSG00000106025		"Tetraspanins"	21641	protein-coding gene	gene with protein product		613138	"transmembrane 4 superfamily member 12"	TM4SF12			Standard	NM_012338		Approved	NET-2	uc003vjk.3	O95859	OTTHUMG00000156980	ENST00000222747.3:c.459delT	chr7.hg19:g.120450526delA	ENSP00000222747:p.Phe153fs	164.0	0.0		154.0	11.0	NM_012338	A4D0V8|B4DRG6|Q549U9|Q8N5Y0	Frame_Shift_Del	DEL	ENST00000222747.3	hg19	CCDS5777.1																																																																																			.	.		0.398	TSPAN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346951.1	NM_012338		-	120450526	A	-	120450526	7	5	282	1	0	1	0	1	0	0	0	0	16651	243	9	0	470	0	TSPAN12	7	120450526	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	77531	120450526	38688137	574	40808										
PTPRZ1	5803	hgsc.bcm.edu	37	chr7	121650545	121650545	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgaagccaagactaaccgatCcccaacaagaggaagtgaat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:121650545delC	ENST00000393386.2	+	12	1856	c.1445delC	c.(1444-1446)tccfs	p.S482fs	PTPRZ1_ENST00000449182.1_Frame_Shift_Del_p.S482fs	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	482					axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						ACTAACCGATCCCCAACAAGA	0.413																																					p.S482fs		Atlas-INDEL	.											.	PTPRZ1	605	.	0			c.1444delT						.						126	110	115					7																	121650545		2203	4300	6503	SO:0001589	frameshift_variant	5803	exon12			.	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.1445delC	chr7.hg19:g.121650545delC	ENSP00000377047:p.Ser482fs	184.0	0.0		194.0	12.0	NM_001206838	A4D0W5|C9JFM0|O76043|Q9UDR6	Frame_Shift_Del	DEL	ENST00000393386.2	hg19	CCDS34740.1																																																																																			.	.		0.413	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		-	121650545	C	-	121650545	7	5	282	1	0	1	0	1	0	0	0	0	12829	855	30	0	1491	0	PTPRZ1	7	121650545	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1200019	121650545	37488118	575	40809										
PAX4	5078	hgsc.bcm.edu	37	chr7	127252045	127252045	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cccttggtacagtcagccccTgggaagcacctataaaatga	9	12	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:127252045T>C	ENST00000341640.2	-	7	906	c.701A>G	c.(700-702)cAg>cGg	p.Q234R	PAX4_ENST00000378740.2_Missense_Mutation_p.Q234R|PAX4_ENST00000463946.1_Missense_Mutation_p.Q232R|PAX4_ENST00000338516.3_Intron	NM_006193.2	NP_006184.2	O43316	PAX4_HUMAN	paired box 4	242					cell differentiation (GO:0030154)|circadian rhythm (GO:0007623)|endocrine pancreas development (GO:0031018)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|positive regulation of cell differentiation (GO:0045597)|response to cAMP (GO:0051591)|response to drug (GO:0042493)|retina development in camera-type eye (GO:0060041)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)			cervix(1)|kidney(2)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35						AGTCAGCCCCTGGGAAGCACC	0.552																																					p.Q234R	Ovarian(113;737 1605 7858 27720 34092)	Atlas-SNP	.											.	PAX4	66	.	0			c.A701G						.						59	55	56					7																	127252045		2203	4300	6503	SO:0001583	missense	5078	exon7			AGCCCCTGGGAAG		CCDS5797.1	7q32.1	2011-06-20	2007-07-12		ENSG00000106331	ENSG00000106331		"Paired boxes", "Homeoboxes / PRD class"	8618	protein-coding gene	gene with protein product		167413	"paired box gene 4"				Standard	NM_006193		Approved	MODY9	uc010lld.1	O43316	OTTHUMG00000157562	ENST00000341640.2:c.701A>G	chr7.hg19:g.127252045T>C	ENSP00000339906:p.Gln234Arg	87.0	0.0		93.0	4.0	NM_006193	O95161|Q6B0H0	Missense_Mutation	SNP	ENST00000341640.2	hg19	CCDS5797.1	.	.	.	.	.	.	.	.	.	.	T	12.62	1.992062	0.35131	.	.	ENSG00000106331	ENST00000341640;ENST00000378740;ENST00000463946	D;D	0.94092	-3.35;-3.2	5.27	4.11	0.48088	.	6.684740	0.00496	N	0.000141	D	0.90400	0.6995	L	0.43152	1.355	0.80722	D	1	B;B;B;B	0.12630	0.006;0.002;0.003;0.006	B;B;B;B	0.15052	0.006;0.002;0.002;0.012	T	0.69094	-0.5236	10	0.13853	T	0.58	.	8.1187	0.30959	0.0:0.0925:0.0:0.9075	.	234;232;242;232	O43316-4;Q1W386;O43316;G3V4Q1	.;.;PAX4_HUMAN;.	R	234;242;232	ENSP00000339906:Q234R;ENSP00000451923:Q232R	ENSP00000339906:Q234R	Q	-	2	0	PAX4	127039281	0.754000	0.28360	0.932000	0.37286	0.567000	0.35839	0.501000	0.22578	0.946000	0.37632	0.533000	0.62120	CAG	.	.		0.552	PAX4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349165.1			C	127252045	T	C	127252045	3	2	282	1	0	0	0	0	1	0	0	0	11490	1580	55	2	342	2	PAX4	7	127252045	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	5601500	127252045	31886618	576	40810										
CALD1	800	hgsc.bcm.edu	37	chr7	134618168	134618168	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtgatggtggaagagaaaacAactgaaagccaggaggaaac							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:134618168delA	ENST00000361675.2	+	5	877	c.648delA	c.(646-648)acafs	p.T217fs	CALD1_ENST00000422748.1_Intron|CALD1_ENST00000543443.1_Intron|CALD1_ENST00000424922.1_Intron|CALD1_ENST00000361388.2_Intron|CALD1_ENST00000417172.1_Intron|CALD1_ENST00000495522.1_Intron|CALD1_ENST00000361901.2_Intron|CALD1_ENST00000393118.2_Intron			Q05682	CALD1_HUMAN	caldesmon 1	217					cellular component movement (GO:0006928)|muscle contraction (GO:0006936)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|calmodulin binding (GO:0005516)|tropomyosin binding (GO:0005523)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(15)|lung(10)	43						aagagaaAACAACTGAAAGCC	0.453																																					p.T216fs		Atlas-INDEL	.											.	CALD1	150	.	0			c.647delC						.						81	76	78					7																	134618168		2203	4300	6503	SO:0001589	frameshift_variant	800	exon5			.	M64110	CCDS5834.1, CCDS5835.1, CCDS5836.1, CCDS47716.1, CCDS47717.1, CCDS5836.2	7q33	2007-04-23			ENSG00000122786	ENSG00000122786			1441	protein-coding gene	gene with protein product		114213				1885618	Standard	NM_004342		Approved	CDM, H-CAD, L-CAD	uc003vrz.3	Q05682	OTTHUMG00000155407	ENST00000361675.2:c.648delA	chr7.hg19:g.134618168delA	ENSP00000354826:p.Thr217fs	111.0	0.0		142.0	10.0	NM_033138	A8K0X1|Q13978|Q13979|Q14741|Q14742|Q9UD91	Frame_Shift_Del	DEL	ENST00000361675.2	hg19	CCDS5835.1																																																																																			.	.		0.453	CALD1-005	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339939.1	NM_033138		-	134618168	A	-	134618168	7	5	282	1	0	1	0	1	0	0	0	0	2583	117	5	0	715	0	CALD1	7	134618168	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	7366123	134618168	24520495	577	40811										
CNOT4	4850	hgsc.bcm.edu	37	chr7	135106990	135106990	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cactagccaaatgtttgcgaTtttctgatattttctgtttt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:135106990delT	ENST00000315544.5	-	3	566	c.287delA	c.(286-288)aatfs	p.N96fs	CNOT4_ENST00000428680.2_Frame_Shift_Del_p.N96fs|CNOT4_ENST00000361528.4_Frame_Shift_Del_p.N96fs|CNOT4_ENST00000541284.1_Frame_Shift_Del_p.N96fs|CNOT4_ENST00000356162.4_Frame_Shift_Del_p.N96fs|CNOT4_ENST00000451834.1_Frame_Shift_Del_p.N96fs|CNOT4_ENST00000414802.1_Frame_Shift_Del_p.N96fs|CNOT4_ENST00000423368.2_Frame_Shift_Del_p.N96fs	NM_001190848.1	NP_001177777.1	O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	96					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|protein autoubiquitination (GO:0051865)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)	22						ATGTTTGCGATTTTCTGATAT	0.403																																					p.N96fs	Ovarian(51;766 1130 5502 35047 50875)	Atlas-INDEL	.											.	CNOT4	146	.	0			c.288delT						.						182	167	172					7																	135106990		1845	4085	5930	SO:0001589	frameshift_variant	4850	exon3			.	AF180475	CCDS43650.1, CCDS47719.1, CCDS55164.1, CCDS55165.1, CCDS55166.1, CCDS55167.1	7q33	2013-09-19			ENSG00000080802	ENSG00000080802		"RNA binding motif (RRM) containing"	7880	protein-coding gene	gene with protein product		604911		NOT4		10637334	Standard	NM_013316		Approved	CLONE243, NOT4H	uc011kpy.2	O95628	OTTHUMG00000155568	ENST00000315544.5:c.287delA	chr7.hg19:g.135106990delT	ENSP00000326731:p.Asn96fs	246.0	0.0		239.0	16.0	NM_001190850	B7Z6I4|E7ET38|F8VQP3|O95339|O95627|Q8IYM7|Q8NCL0|Q9NPQ1|Q9NZN6	Frame_Shift_Del	DEL	ENST00000315544.5	hg19	CCDS55166.1																																																																																			.	.		0.403	CNOT4-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_013316		-	135106990	T	-	135106990	7	5	282	1	0	1	0	1	0	0	0	0	3623	1493	52	0	1773	0	CNOT4	7	135106990	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	488822	135106990	24031673	578	40812										
PDIA4	9601	hgsc.bcm.edu	37	chr7	148702444	148702444	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tccttggccacctctaggacTttgctccgccaaaactgagt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:148702444delT	ENST00000286091.4	-	9	1543	c.1311delA	c.(1309-1311)aaafs	p.K437fs		NM_004911.4	NP_004902.1	P13667	PDIA4_HUMAN	protein disulfide isomerase family A, member 4	437					cell redox homeostasis (GO:0045454)|chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein secretion (GO:0009306)|response to endoplasmic reticulum stress (GO:0034976)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)	poly(A) RNA binding (GO:0044822)|protein disulfide isomerase activity (GO:0003756)			large_intestine(6)|lung(15)|ovary(2)|prostate(1)	24	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00385)			CCTCTAGGACTTTGCTCCGCC	0.582											OREG0018420	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V438fs		Atlas-INDEL	.											.	PDIA4	57	.	0			c.1312delG						.						92	81	85					7																	148702444		2203	4300	6503	SO:0001589	frameshift_variant	9601	exon9			.	BC001928	CCDS5893.1	7q35	2009-11-20	2005-06-29		ENSG00000155660	ENSG00000155660	5.3.4.1	"Protein disulfide isomerases"	30167	protein-coding gene	gene with protein product			"protein disulfide isomerase-associated 4"			2549034, 2002068	Standard	NM_004911		Approved	ERP70, ERP72	uc003wff.2	P13667	OTTHUMG00000150248	ENST00000286091.4:c.1311delA	chr7.hg19:g.148702444delT	ENSP00000286091:p.Lys437fs	145.0	0.0	1719	154.0	10.0	NM_004911	A8K4K6|Q549T6	Frame_Shift_Del	DEL	ENST00000286091.4	hg19	CCDS5893.1																																																																																			.	.		0.582	PDIA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317077.1	NM_004911		-	148702444	T	-	148702444	7	5	282	1	0	1	0	1	0	0	0	0	11679	1606	56	0	634	0	PDIA4	7	148702444	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	13595454	148702444	10436219	579	40813										
ZNF425	155054	hgsc.bcm.edu	37	chr7	148800796	148800796	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccttccacactcatcacaagAaaaaggcctctccccactgt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:148800796delA	ENST00000378061.2	-	4	2299	c.2167delT	c.(2167-2169)tctfs	p.S723fs		NM_001001661.2	NP_001001661.1	Q6IV72	ZN425_HUMAN	zinc finger protein 425	723					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(6)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	50	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			TCATCACAAGAAAAAGGCCTC	0.577																																					p.S723fs		Atlas-INDEL	.											.	ZNF425	99	.	0			c.2168delC						.						75	67	70					7																	148800796		2203	4300	6503	SO:0001589	frameshift_variant	155054	exon4			.	AK056498	CCDS34773.1	7q36.1	2013-01-08			ENSG00000204947	ENSG00000204947		"Zinc fingers, C2H2-type", "-"	20690	protein-coding gene	gene with protein product							Standard	NM_001001661		Approved		uc003wfj.3	Q6IV72	OTTHUMG00000158971	ENST00000378061.2:c.2167delT	chr7.hg19:g.148800796delA	ENSP00000367300:p.Ser723fs	173.0	0.0		182.0	11.0	NM_001001661	B3KPM1|Q08AG3	Frame_Shift_Del	DEL	ENST00000378061.2	hg19	CCDS34773.1																																																																																			.	.		0.577	ZNF425-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352726.1	XM_088140		-	148800796	A	-	148800796	7	5	282	1	0	1	0	1	0	0	0	0	17914	246	9	0	95	0	ZNF425	7	148800796	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	98352	148800796	10337867	580	40814										
ZNF746	155061	hgsc.bcm.edu	37	chr7	149172419	149172419	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggggaaggagctgccctggcTttcccaggctccttcctggg	15	13	0	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:149172419T>C	ENST00000340622.3	-	7	1271	c.991A>G	c.(991-993)Agc>Ggc	p.S331G	ZNF746_ENST00000458143.2_Missense_Mutation_p.S332G			Q6NUN9	ZN746_HUMAN	zinc finger protein 746	331					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neuron death (GO:1901216)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			CTGCCCTGGCTTTCCCAGGCT	0.652																																					p.S332G		Atlas-SNP	.											.	ZNF746	68	.	0			c.A994G						.						36	39	38					7																	149172419		2203	4300	6503	SO:0001583	missense	155061	exon7			CCTGGCTTTCCCA	AK055975	CCDS5897.1, CCDS55180.1	7q36.1	2013-01-08			ENSG00000181220	ENSG00000181220		"Zinc fingers, C2H2-type", "-"	21948	protein-coding gene	gene with protein product		613914					Standard	NM_152557		Approved	FLJ31413	uc010lpi.2	Q6NUN9	OTTHUMG00000158972	ENST00000340622.3:c.991A>G	chr7.hg19:g.149172419T>C	ENSP00000345140:p.Ser331Gly	59.0	0.0		90.0	4.0	NM_001163474	A8K6Z9|Q6ZRF9	Missense_Mutation	SNP	ENST00000340622.3	hg19	CCDS5897.1	.	.	.	.	.	.	.	.	.	.	T	13.08	2.131117	0.37630	.	.	ENSG00000181220	ENST00000340622;ENST00000458143	T;T	0.09350	3.02;2.99	4.74	3.56	0.40772	.	1.078000	0.07210	N	0.858969	T	0.05364	0.0142	N	0.08118	0	0.09310	N	1	B;B	0.24426	0.103;0.063	B;B	0.21917	0.037;0.016	T	0.45716	-0.9242	10	0.16896	T	0.51	-18.1524	4.0703	0.09879	0.1824:0.0969:0.0:0.7207	.	332;331	Q6NUN9-2;Q6NUN9	.;ZN746_HUMAN	G	331;332	ENSP00000345140:S331G;ENSP00000395007:S332G	ENSP00000345140:S331G	S	-	1	0	ZNF746	148803352	0.002000	0.14202	0.711000	0.30485	0.962000	0.63368	1.391000	0.34475	0.644000	0.30656	0.460000	0.39030	AGC	.	.		0.652	ZNF746-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352730.1	NM_152557		C	149172419	T	C	149172419	3	2	282	1	0	0	0	0	1	0	0	0	18144	1609	56	2	947	2	ZNF746	7	149172419	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	371623	149172419	9966244	581	40815										
KRBA1	84626	hgsc.bcm.edu	37	chr7	149420823	149420824	+	Splice_Site	DNP	AG	AG	TA													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaacatgttcctttttccttAgtgaagaccgaggcggtttc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A|G	A|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:149420823_149420824AG>TA	ENST00000485033.2	+	7	772		c.e7-1		KRBA1_ENST00000319551.8_Splice_Site|KRBA1_ENST00000479560.1_Splice_Site|KRBA1_ENST00000255992.10_Splice_Site			A5PL33	KRBA1_HUMAN	KRAB-A domain containing 1											breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(17)|ovary(1)|prostate(1)	27	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CTTTTTCCTTAGTGAAGACCGA	0.559																																					.		Atlas-SNP	.											.	KRBA1	68	.	0			c.773-2A>T|c.773-1G>A						.																																			SO:0001630	splice_region_variant	84626	exon8			TTCCTTAGTGAAG|TCCTTAGTGAAGA	AB058765	CCDS75674.1	7q36	2014-02-12	2006-08-15		ENSG00000133619	ENSG00000133619		"-"	22228	protein-coding gene	gene with protein product			"KRAB A domain containing 1"				Standard	NM_001290187		Approved	KIAA1862	uc003wfz.3	A5PL33	OTTHUMG00000157886	Exception_encountered	chr7.hg19:g.149420823_149420824delinsTA		144.0|147.0	0.0		126.0|128.0	9.0|8.0	NM_032534	A7E2F5|E7ENE9|Q8N4X0|Q96JG5	Splice_Site	SNP	ENST00000485033.2	hg19																																																																																				.	.		0.559	KRBA1-004	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000349841.3	NM_032534	Intron	TA	149420824	AG	TA	149420823	5	4	282	1	0	0	0	0	0	0	1	0	8448	434	15	4	797	4	KRBA1	7	149420823	Splice_Site	DNP	AG	TCGA-G3-A3CJ-01A-11D-A20W-10	248404	149420823	9717840	582	40816										
SSPO	23145	hgsc.bcm.edu	37	chr7	149486904	149486904	+	RNA	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caagtcccctggccagcgccAgccctggtgagtctcctgga	12	16	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:149486904A>G	ENST00000378016.2	+	0	4678							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GGCCAGCGCCAGCCCTGGTGA	0.657																																					p.S1560G		Atlas-SNP	.											.	.	.	.	0			c.A4678G						.						16	18	18					7																	149486904		1919	4115	6034			23145	exon31			AGCGCCAGCCCTG	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		chr7.hg19:g.149486904A>G		104.0	0.0		114.0	5.0	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	hg19																																																																																				.	.		0.657	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				G	149486904	A	G	149486904	1	3	282	0	1	0	0	0	0	0	0	0	15204	188	7	2		2	SSPO	7	149486904	RNA	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	66081	149486904	9651759	583	40817										
SSPO	23145	hgsc.bcm.edu	37	chr7	149489415	149489415	+	RNA	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgcccagaagggcaggtgctGggcagcgaggggtggtgtgt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:149489415delG	ENST00000378016.2	+	0	5568							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GGCAGGTGCTGGGCAGCGAGG	0.692																																					p.L1856fs		Atlas-INDEL	.											.	.	.	.	0			c.5567delT						.						12	19	17					7																	149489415		2021	4180	6201			23145	exon37			.	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		chr7.hg19:g.149489415delG		129.0	0.0		169.0	11.0	NM_198455	Q76B61	Frame_Shift_Del	DEL	ENST00000378016.2	hg19																																																																																				.	.		0.692	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				-	149489415	G	-	149489415	6	5	282	0	1	1	0	1	0	0	0	0	15204	1335	47	0		0	SSPO	7	149489415	RNA	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	2511	149489415	9649248	584	40818										
ABCB8	11194	hgsc.bcm.edu	37	chr7	150742395	150742395	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggacagcggccccaccgcccAaaaagccagaaggccccagg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:150742395delA	ENST00000297504.6	+	17	2233	c.2167delA	c.(2167-2169)aaafs	p.K724fs	ABCB8_ENST00000356058.4_3'UTR|ABCB8_ENST00000542328.1_Frame_Shift_Del_p.K619fs|ASIC3_ENST00000357922.4_5'Flank|ABCB8_ENST00000498578.1_Frame_Shift_Del_p.K682fs|ABCB8_ENST00000358849.4_Frame_Shift_Del_p.K707fs			Q9NUT2	ABCB8_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 8	724					transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Doxorubicin(DB00997)	CCCACCGCCCAAAAAGCCAGA	0.652																																					p.P705fs		Atlas-INDEL	.											.	ABCB8	65	.	0			c.2115delC						.						43	42	42					7																	150742395		2203	4300	6503	SO:0001589	frameshift_variant	11194	exon16			.	AF047690	CCDS5913.1, CCDS64798.1, CCDS64799.1, CCDS64800.1	7q36.1	2012-05-16			ENSG00000197150	ENSG00000197150		"ATP binding cassette transporters / subfamily B"	49	protein-coding gene	gene with protein product	"mitochondrial ABC protein"	605464				8894702	Standard	NM_001282291		Approved	EST328128, M-ABC1, MABC1	uc003wik.4	Q9NUT2	OTTHUMG00000158686	ENST00000297504.6:c.2167delA	chr7.hg19:g.150742395delA	ENSP00000297504:p.Lys724fs	132.0	0.0		159.0	10.0	NM_007188	A5D8W3|B2RBL8|B3KND2|B4DG02|G3XAP3|O95787|Q53GM0	Frame_Shift_Del	DEL	ENST00000297504.6	hg19																																																																																				.	.		0.652	ABCB8-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351733.2	NM_007188		-	150742395	A	-	150742395	7	5	282	1	0	1	0	1	0	0	0	0	47	131	5	0	2178	0	ABCB8	7	150742395	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1252980	150742395	8396268	585	40819										
FASTK	10922	hgsc.bcm.edu	37	chr7	150775131	150775131	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gggcataaactgctgttccaGgggcaggtagttcagtcgcc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:150775131delG	ENST00000297532.6	-	5	951	c.874delC	c.(874-876)ctgfs	p.L292fs	FASTK_ENST00000482571.1_Frame_Shift_Del_p.L265fs|FASTK_ENST00000540185.1_Frame_Shift_Del_p.P151fs|FASTK_ENST00000353841.2_Frame_Shift_Del_p.L151fs|RP11-148K1.12_ENST00000485974.1_RNA|FASTK_ENST00000489884.1_5'UTR	NM_006712.4	NP_006703.1	Q14296	FASTK_HUMAN	Fas-activated serine/threonine kinase	292					apoptotic signaling pathway (GO:0097190)|protein phosphorylation (GO:0006468)|regulation of RNA splicing (GO:0043484)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|Fas-activated serine/threonine kinase activity (GO:0033867)|protein serine/threonine kinase activity (GO:0004674)			lung(4)|stomach(2)	6			OV - Ovarian serous cystadenocarcinoma(82;0.00989)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)|LUSC - Lung squamous cell carcinoma(290;0.0718)|Lung(243;0.138)		TGCTGTTCCAGGGGCAGGTAG	0.542																																					p.L292fs		Atlas-INDEL	.											.	FASTK	29	.	0			c.875delT						.						94	97	96					7																	150775131		2203	4300	6503	SO:0001589	frameshift_variant	10922	exon5			.		CCDS5918.1, CCDS5919.1, CCDS59088.1	7q35	2006-07-06			ENSG00000164896	ENSG00000164896			24676	protein-coding gene	gene with protein product		606965				7544399, 15572676	Standard	NM_006712		Approved	FAST	uc003wix.2	Q14296	OTTHUMG00000158694	ENST00000297532.6:c.874delC	chr7.hg19:g.150775131delG	ENSP00000297532:p.Leu292fs	196.0	0.0		187.0	12.0	NM_006712	A8K867|F8VTW9|Q59EM8|Q8IVA0	Frame_Shift_Del	DEL	ENST00000297532.6	hg19	CCDS5918.1																																																																																			.	.		0.542	FASTK-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351832.2	NM_006712		-	150775131	G	-	150775131	7	5	282	1	0	1	0	1	0	0	0	0	5692	991	35	0	799	0	FASTK	7	150775131	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	32736	150775131	8363532	586	40820										
ABCF2	10061	hgsc.bcm.edu	37	chr7	150923507	150923507	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gagctttggcagcctccttcTttttggctgccttcttcttg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:150923507delT	ENST00000287844.2	-	2	147	c.38delA	c.(37-39)aagfs	p.K14fs	ABCF2_ENST00000222388.2_Frame_Shift_Del_p.K14fs	NM_007189.1	NP_009120.1	Q9UG63	ABCF2_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 2	14					transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|large_intestine(4)|lung(15)|ovary(1)|skin(2)	24			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		AGCCTCCTTCTTTTTGGCTGC	0.512																																					p.K13fs		Atlas-INDEL	.											.	ABCF2	54	.	0			c.39delG						.						119	115	116					7																	150923507		2203	4300	6503	SO:0001589	frameshift_variant	10061	exon2			.	AJ005016	CCDS5922.1, CCDS5923.1	7q36.1	2012-03-14			ENSG00000033050	ENSG00000033050		"ATP binding cassette transporters / subfamily F"	71	protein-coding gene	gene with protein product		612510				8894702	Standard	NM_007189		Approved	EST133090, ABC28, M-ABC1, HUSSY-18	uc003wjo.1	Q9UG63	OTTHUMG00000154570	ENST00000287844.2:c.38delA	chr7.hg19:g.150923507delT	ENSP00000287844:p.Lys14fs	202.0	0.0		202.0	13.0	NM_005692	O60864|Q75MJ0|Q75MJ1|Q96TE8	Frame_Shift_Del	DEL	ENST00000287844.2	hg19	CCDS5923.1																																																																																			.	.		0.512	ABCF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336086.1	NM_005692		-	150923507	T	-	150923507	7	5	282	1	0	1	0	1	0	0	0	0	66	1609	56	0	1930	0	ABCF2	7	150923507	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	148376	150923507	8215156	587	40821										
GALNTL5	168391	hgsc.bcm.edu	37	chr7	151704993	151704993	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagtatgacaaggatatggaTttttggggaagagaaaattt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:151704993delT	ENST00000392800.2	+	7	1244	c.990delT	c.(988-990)gatfs	p.D330fs	GALNTL5_ENST00000431418.2_Frame_Shift_Del_p.D330fs|GALNTL5_ENST00000483959.1_3'UTR	NM_145292.3	NP_660335.2	Q7Z4T8	GLTL5_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 5	330	Catalytic subdomain B.				spermatid development (GO:0007286)	endosome (GO:0005768)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(11)|ovary(2)|prostate(2)|skin(3)	32	all_neural(206;0.187)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00427)	UCEC - Uterine corpus endometrioid carcinoma (81;0.18)|BRCA - Breast invasive adenocarcinoma(188;0.166)		AGGATATGGATTTTTGGGGAA	0.343																																					p.D330fs		Atlas-INDEL	.											.	GALNTL5	87	.	0			c.989delA						.						106	109	108					7																	151704993		2203	4300	6503	SO:0001589	frameshift_variant	168391	exon7			.	AF440400	CCDS5929.1	7q36.2	2014-03-13	2014-03-13	2004-07-28	ENSG00000106648	ENSG00000106648		"Glycosyltransferase family 2 domain containing"	21725	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase-like 5"	615133	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15", "UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 5"	GALNT15			Standard	NM_145292		Approved	GalNAc-T5L	uc003wkp.3	Q7Z4T8	OTTHUMG00000157306	ENST00000392800.2:c.990delT	chr7.hg19:g.151704993delT	ENSP00000376548:p.Asp330fs	173.0	0.0		155.0	10.0	NM_145292	Q75KN2|Q75MD3|Q8NCV4|Q8WW05|Q9UDR9	Frame_Shift_Del	DEL	ENST00000392800.2	hg19	CCDS5929.1																																																																																			.	.		0.343	GALNTL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348395.1	NM_145292		-	151704993	T	-	151704993	7	5	282	1	0	1	0	1	0	0	0	0	6232	1490	52	0	1012	0	GALNTL5	7	151704993	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	781486	151704993	7433670	588	40822										
MLL3	58508	hgsc.bcm.edu	37	chr7	151859254	151859254	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtttattatcctttgtacagTcatcttctgaacaaatactg	5	8	3	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:151859254T>C	ENST00000262189.6	-	43	11626	c.11408A>G	c.(11407-11409)gAc>gGc	p.D3803G	KMT2C_ENST00000355193.2_Missense_Mutation_p.D3803G	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	3803					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										CTTTGTACAGTCATCTTCTGA	0.338																																					p.D3803G		Atlas-SNP	.											.	MLL3	1564	.	0			c.A11408G						.						43	47	45					7																	151859254		2202	4300	6502	SO:0001583	missense	58508	exon43			GTACAGTCATCTT	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.11408A>G	chr7.hg19:g.151859254T>C	ENSP00000262189:p.Asp3803Gly	166.0	0.0		147.0	6.0	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	hg19	CCDS5931.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	8.998|8.998	0.979427|0.979427	0.18812|0.18812	.|.	.|.	ENSG00000055609|ENSG00000055609	ENST00000262189;ENST00000355193;ENST00000424877|ENST00000360104	D;D;D|.	0.88586|.	-1.73;-1.69;-2.4|.	5.21|5.21	0.807|0.807	0.18714|0.18714	.|.	0.613334|.	0.13625|.	U|.	0.374139|.	T|.	0.24547|.	0.0595|.	L|L	0.36672|0.36672	1.1|1.1	0.09310|0.09310	N|N	0.999999|0.999999	B;B;B|.	0.20887|.	0.049;0.0;0.0|.	B;B;B|.	0.19148|.	0.024;0.0;0.0|.	T|.	0.23547|.	-1.0185|.	10|.	0.44086|.	T|.	0.13|.	.|.	1.6582|1.6582	0.02786|0.02786	0.13:0.1826:0.1352:0.5521|0.13:0.1826:0.1352:0.5521	.|.	3803;2864;3803|.	Q8NEZ4;Q8NEZ4-2;Q8NEZ4-3|.	MLL3_HUMAN;.;.|.	G|W	3803;3803;389|1308	ENSP00000262189:D3803G;ENSP00000347325:D3803G;ENSP00000410411:D389G|.	ENSP00000262189:D3803G|.	D|X	-|-	2|3	0|0	MLL3|MLL3	151490187|151490187	0.919000|0.919000	0.31177|0.31177	0.000000|0.000000	0.03702|0.03702	0.976000|0.976000	0.68499|0.68499	2.319000|2.319000	0.43788|0.43788	-0.037000|-0.037000	0.13646|0.13646	0.528000|0.528000	0.53228|0.53228	GAC|TGA	.	.		0.338	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			C	151859254	T	C	151859254	3	2	282	1	0	0	0	0	1	0	0	0	9631	1667	58	2	3395	2	MLL3	7	151859254	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	154261	151859254	7279409	589	40823										
DPP6	1804	hgsc.bcm.edu	37	chr7	154263979	154263979	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tccagatagagagtatgcacTtttttcatacaatgtggaac							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:154263979delT	ENST00000377770.3	+	5	746	c.605delT	c.(604-606)cttfs	p.L202fs	DPP6_ENST00000404039.1_Frame_Shift_Del_p.L138fs|DPP6_ENST00000496611.1_3'UTR|DPP6_ENST00000427557.1_Frame_Shift_Del_p.L140fs|DPP6_ENST00000332007.3_Frame_Shift_Del_p.L140fs|DPP6_ENST00000406326.1_Frame_Shift_Del_p.L202fs			P42658	DPP6_HUMAN	dipeptidyl-peptidase 6	202					cell death (GO:0008219)|neuronal action potential (GO:0019228)|positive regulation of potassium ion transmembrane transport (GO:1901381)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(3)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(35)|pancreas(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	71	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			GAGTATGCACTTTTTTCATAC	0.294																																					p.L202fs	NSCLC(125;1384 1783 2490 7422 34254)	Atlas-INDEL	.											.	DPP6	383	.	0			c.604delC						.						86	86	86					7																	154263979		1802	4062	5864	SO:0001589	frameshift_variant	1804	exon5			.	M96859	CCDS75682.1, CCDS75683.1, CCDS75684.1	7q36.2	2006-08-07	2006-01-12		ENSG00000130226	ENSG00000130226			3010	protein-coding gene	gene with protein product		126141	"dipeptidylpeptidase VI", "dipeptidylpeptidase 6"			1729689	Standard	XM_006715871		Approved	DPPX	uc003wlk.3	P42658	OTTHUMG00000151511	ENST00000377770.3:c.605delT	chr7.hg19:g.154263979delT	ENSP00000367001:p.Leu202fs	115.0	0.0		139.0	10.0	NM_130797		Frame_Shift_Del	DEL	ENST00000377770.3	hg19																																																																																				.	.		0.294	DPP6-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322932.1	NM_130797		-	154263979	T	-	154263979	7	5	282	1	0	1	0	1	0	0	0	0	4732	1609	56	0	739	0	DPP6	7	154263979	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2404725	154263979	4874684	590	40824										
PAXIP1	22976	hgsc.bcm.edu	37	chr7	154768002	154768002	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aacccagtcaggagtcacaaTtttaatacttgctcgcttta							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:154768002delT	ENST00000404141.1	-	6	632	c.478delA	c.(478-480)attfs	p.I160fs	PAXIP1_ENST00000473219.1_5'UTR|PAXIP1_ENST00000397192.1_Frame_Shift_Del_p.I160fs			Q6ZW49	PAXI1_HUMAN	PAX interacting (with transcription-activation domain) protein 1	160	BRCT 2. {ECO:0000255|PROSITE- ProRule:PRU00033}.|Interaction with PAGR1. {ECO:0000250}.				adipose tissue development (GO:0060612)|chorion development (GO:0060717)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|endothelial cell migration (GO:0043542)|histone H3-K4 methylation (GO:0051568)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K36 methylation (GO:0000416)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of isotype switching (GO:0045830)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	33	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0296)	UCEC - Uterine corpus endometrioid carcinoma (81;0.178)		GGAGTCACAATTTTAATACTT	0.368																																					p.I160fs		Atlas-INDEL	.											.	PAXIP1	150	.	0			c.479delT						.						79	77	78					7																	154768002		1859	4119	5978	SO:0001589	frameshift_variant	22976	exon6			.	U80735	CCDS47753.1	7q36	2007-07-06	2005-04-05	2005-04-05	ENSG00000157212	ENSG00000157212			8624	protein-coding gene	gene with protein product		608254	"PAX transcription activation domain interacting protein 1 like"	PAXIP1L		9225980	Standard	XM_005249539		Approved	CAGF29, CAGF28, TNRC2, PTIP	uc022aqf.1	Q6ZW49	OTTHUMG00000151322	ENST00000404141.1:c.478delA	chr7.hg19:g.154768002delT	ENSP00000384048:p.Ile160fs	195.0	0.0		177.0	12.0	NM_007349	O15404|Q6N099|Q6ZWH9|Q7Z315|Q86UN0|Q8N4P9|Q96HP2	Frame_Shift_Del	DEL	ENST00000404141.1	hg19	CCDS47753.1																																																																																			.	.		0.368	PAXIP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322223.1	NM_007349		-	154768002	T	-	154768002	7	5	282	1	0	1	0	1	0	0	0	0	11496	1493	52	0	2795	0	PAXIP1	7	154768002	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	504023	154768002	4370661	591	40825										
RBM33	155435	hgsc.bcm.edu	37	chr7	155537920	155537920	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tccaggtgcacaggtcagacAaaatgtgaagaacagacttc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:155537920delA	ENST00000401878.3	+	14	2801	c.2603delA	c.(2602-2604)caafs	p.Q868fs	RBM33_ENST00000341148.3_5'Flank	NM_053043.2	NP_444271.2	Q96EV2	RBM33_HUMAN	RNA binding motif protein 33	868							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	27	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)		CAGGTCAGACAAAATGTGAAG	0.498																																					p.Q868fs		Atlas-INDEL	.											.	RBM33	157	.	0			c.2602delC						.						54	45	48					7																	155537920		2203	4300	6503	SO:0001589	frameshift_variant	155435	exon14			.	AL832196	CCDS5941.2	7q36.3	2013-02-12			ENSG00000184863	ENSG00000184863		"RNA binding motif (RRM) containing"	27223	protein-coding gene	gene with protein product			"proline rich 8"	PRR8			Standard	NM_053043		Approved	DKFZp686F102, MGC20460, DKFZp434D1319	uc010lqk.1	Q96EV2	OTTHUMG00000150260	ENST00000401878.3:c.2603delA	chr7.hg19:g.155537920delA	ENSP00000384160:p.Gln868fs	258.0	0.0		225.0	15.0	NM_053043	A4D244|B5MC24|Q52LF5|Q75LN9|Q75ML5|Q9NSV0	Frame_Shift_Del	DEL	ENST00000401878.3	hg19	CCDS5941.2																																																																																			.	.		0.498	RBM33-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317225.3	NM_001008408		-	155537920	A	-	155537920	7	5	282	1	0	1	0	1	0	0	0	0	13145	130	5	0	2657	0	RBM33	7	155537920	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	769918	155537920	3600743	592	40826										
NOM1	64434	hgsc.bcm.edu	37	chr7	156755794	156755794	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acgggtcgctggtggattgtGgggtccgcctggagtggggc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:156755794delG	ENST00000275820.3	+	6	1851	c.1836delG	c.(1834-1836)gtgfs	p.V612fs		NM_138400.1	NP_612409.1	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	612						nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(4)|large_intestine(9)|lung(7)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	31	Ovarian(565;0.218)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)		GGTGGATTGTGGGGTCCGCCT	0.622																																					p.V612fs		Atlas-INDEL	.											.	NOM1	73	.	0			c.1835delT						.						53	46	48					7																	156755794		2203	4300	6503	SO:0001589	frameshift_variant	64434	exon6			.	AF107455	CCDS34787.1	7q36.3	2014-06-13	2005-03-30	2005-03-30	ENSG00000146909	ENSG00000146909			13244	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 113"	611269	"chromosome 7 open reading frame 3"	C7orf3		10329000	Standard	XM_005249560		Approved	SGD1, PPP1R113	uc003wmy.3	Q5C9Z4	OTTHUMG00000152639	ENST00000275820.3:c.1836delG	chr7.hg19:g.156755794delG	ENSP00000275820:p.Val612fs	129.0	0.0		155.0	12.0	NM_138400	Q96I08	Frame_Shift_Del	DEL	ENST00000275820.3	hg19	CCDS34787.1																																																																																			.	.		0.622	NOM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327098.1	NM_138400		-	156755794	G	-	156755794	7	5	282	1	0	1	0	1	0	0	0	0	10539	1335	47	0	1858	0	NOM1	7	156755794	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1217874	156755794	2382869	593	40827										
DLGAP2	9228	hgsc.bcm.edu	37	chr8	1497492	1497492	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccggagggcaagccccggccCggcatgagcagctggtggag	18	13	0	1	rs375164454		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:1497492C>T	ENST00000421627.2	+	2	767	c.633C>T	c.(631-633)ccC>ccT	p.P211P		NM_004745.3	NP_004736.2	Q9P1A6	DLGP2_HUMAN	discs, large (Drosophila) homolog-associated protein 2	290					neuron-neuron synaptic transmission (GO:0007270)	cell junction (GO:0030054)|neurofilament (GO:0005883)|postsynaptic membrane (GO:0045211)				breast(1)|endometrium(6)|lung(31)|prostate(3)	41		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)		AGCCCCGGCCCGGCATGAGCA	0.706																																					p.P211P		Atlas-SNP	.											.	DLGAP2	292	.	0			c.C633T						.	C		1,4383		0,1,2191	27	38	34		633	-10.8	0	8		34	0,8584		0,0,4292	no	coding-synonymous	DLGAP2	NM_004745.3		0,1,6483	TT,TC,CC		0.0,0.0228,0.0077		211/976	1497492	1,12967	2192	4292	6484	SO:0001819	synonymous_variant	9228	exon2			CCGGCCCGGCATG	AB000275	CCDS47760.1, CCDS75689.1	8p23	2007-12-06	2001-11-28		ENSG00000198010	ENSG00000198010			2906	protein-coding gene	gene with protein product		605438	"discs, large (Drosophila) homolog-associated protein 2"			9286858, 10854099	Standard	NM_004745		Approved	DAP-2	uc003wpl.4	Q9P1A6	OTTHUMG00000163599	ENST00000421627.2:c.633C>T	chr8.hg19:g.1497492C>T		103.0	0.0		61.0	42.0	NM_004745	A1QCF8|A1QCF9|A5D8Y2|O14488|O14664|Q9P1A7	Silent	SNP	ENST00000421627.2	hg19	CCDS47760.1	.	.	.	.	.	.	.	.	.	.	C	0.053	-1.245796	0.01481	2.28E-4	0.0	ENSG00000198010	ENST00000520901	T	0.39592	1.07	5.42	-10.8	0.00216	.	0.299402	0.37715	N	0.001974	T	0.40473	0.1118	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.69544	-0.5117	7	0.87932	D	0	-3.4284	7.252	0.26154	0.0744:0.2286:0.5326:0.1644	.	.	.	.	L	228	ENSP00000430563:P228L	ENSP00000430563:P228L	P	+	2	0	DLGAP2	1484899	0.181000	0.23161	0.000000	0.03702	0.004000	0.04260	-0.751000	0.04803	-2.976000	0.00284	-2.530000	0.00182	CCG	.	.		0.706	DLGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374478.1	NM_004745		T	1497492	C	T	1497492	2	4	282	1	0	0	0	0	0	0	0	1	4562	639	23	1		1	DLGAP2	8	1497492	Silent	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10		1497492	144866530	594	40828										
ERI1	90459	hgsc.bcm.edu	37	chr8	8865648	8865648	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctaagctttcagaattcaagCttgaaactaggtaattaaaa	6	6	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:8865648C>G	ENST00000523898.1	+	3	956	c.277C>G	c.(277-279)Ctt>Gtt	p.L93V	ERI1_ENST00000250263.7_Missense_Mutation_p.L93V|ERI1_ENST00000519292.1_Missense_Mutation_p.L93V			Q8IV48	ERI1_HUMAN	exoribonuclease 1	93	SAP. {ECO:0000255|PROSITE- ProRule:PRU00186}.				gene silencing by RNA (GO:0031047)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|rRNA 3'-end processing (GO:0031125)	cytoplasm (GO:0005737)|histone pre-mRNA 3'end processing complex (GO:0071204)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|histone pre-mRNA stem-loop binding (GO:0071207)|metal ion binding (GO:0046872)|ribosome binding (GO:0043022)|rRNA binding (GO:0019843)			NS(1)|endometrium(2)|large_intestine(1)|lung(6)|prostate(1)	11						AGAATTCAAGCTTGAAACTAG	0.294																																					p.L93V		Atlas-SNP	.											.	ERI1	20	.	0			c.C277G						.						35	37	37					8																	8865648		2203	4297	6500	SO:0001583	missense	90459	exon2			TTCAAGCTTGAAA	BC035279	CCDS5972.1	8p23.1	2008-12-16	2008-12-16	2008-12-16	ENSG00000104626	ENSG00000104626		"Enhanced RNAi three prime mRNA exonucleases"	23994	protein-coding gene	gene with protein product	"exoribonuclease 1", "enhanced RNAi three prime mRNA exonuclease homolog 1 (C.elegans)"	608739	"three prime histone mRNA exonuclease 1"	THEX1		14536070	Standard	NM_153332		Approved	3'HEXO	uc003wsk.2	Q8IV48	OTTHUMG00000129328	ENST00000523898.1:c.277C>G	chr8.hg19:g.8865648C>G	ENSP00000429615:p.Leu93Val	77.0	0.0		50.0	31.0	NM_153332	A8K4U7|Q9NSX3	Missense_Mutation	SNP	ENST00000523898.1	hg19	CCDS5972.1	.	.	.	.	.	.	.	.	.	.	C	19.46	3.831148	0.71258	.	.	ENSG00000104626	ENST00000523898;ENST00000250263;ENST00000519292	T;T;T	0.53857	0.6;0.6;0.6	4.82	4.82	0.62117	DNA-binding SAP (3);	0.000000	0.85682	D	0.000000	T	0.58821	0.2149	L	0.59436	1.845	0.80722	D	1	P	0.34684	0.463	B	0.42959	0.403	T	0.62483	-0.6845	10	0.54805	T	0.06	-21.7298	17.2738	0.87109	0.0:1.0:0.0:0.0	.	93	Q8IV48	ERI1_HUMAN	V	93	ENSP00000429615:L93V;ENSP00000250263:L93V;ENSP00000430190:L93V	ENSP00000250263:L93V	L	+	1	0	ERI1	8903058	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.304000	0.78882	2.374000	0.81015	0.563000	0.77884	CTT	.	.		0.294	ERI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251471.2	NM_153332		G	8865648	C	G	8865648	3	3	282	1	0	0	0	0	1	0	0	0	5229	797	28	4	283	4	ERI1	8	8865648	Missense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	7368156	8865648	137498374	595	40829										
RP1L1	94137	hgsc.bcm.edu	37	chr8	10467809	10467809	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctcattggtggcacaagcgcAggctcgggcgttcaagaagg	15	10	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:10467809A>G	ENST00000382483.3	-	4	4022	c.3799T>C	c.(3799-3801)Tgc>Cgc	p.C1267R		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1267					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		GCACAAGCGCAGGCTCGGGCG	0.522																																					p.C1267R		Atlas-SNP	.											.	RP1L1	453	.	0			c.T3799C						.						119	121	120					8																	10467809		2047	4193	6240	SO:0001583	missense	94137	exon4			AAGCGCAGGCTCG	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.3799T>C	chr8.hg19:g.10467809A>G	ENSP00000371923:p.Cys1267Arg	272.0	0.0		116.0	5.0	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	hg19	CCDS43708.1	.	.	.	.	.	.	.	.	.	.	A	4.797	0.148143	0.09134	.	.	ENSG00000183638	ENST00000382483	T	0.03982	3.74	3.1	-4.57	0.03421	.	1.137500	0.06901	N	0.805886	T	0.01800	0.0057	N	0.08118	0	0.09310	N	1	B	0.16603	0.018	B	0.06405	0.002	T	0.46020	-0.9221	10	0.05620	T	0.96	4.8821	4.0931	0.09978	0.2682:0.1845:0.0:0.5473	.	1267	A6NKC6	.	R	1267	ENSP00000371923:C1267R	ENSP00000371923:C1267R	C	-	1	0	RP1L1	10505219	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.287000	0.02785	-0.484000	0.06763	0.260000	0.18958	TGC	.	.		0.522	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			G	10467809	A	G	10467809	3	3	282	1	0	0	0	0	1	0	0	0	13548	188	7	2	3407	2	RP1L1	8	10467809	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1602161	10467809	135896213	596	40830										
EFHA2	286097	hgsc.bcm.edu	37	chr8	16939226	16939226	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gatttcttacacagaatatcTttttcttttatgtattttaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:16939226delT	ENST00000318063.5	+	5	713	c.671delT	c.(670-672)cttfs	p.L224fs		NM_181723.2	NP_859074.1	Q86XE3	MICU3_HUMAN	mitochondrial calcium uptake family, member 3	224						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)										ACAGAATATCTTTTTCTTTTA	0.259																																					p.L224fs		Atlas-INDEL	.											.	EFHA2	60	.	0			c.670delC						.						34	32	33					8																	16939226		1995	3915	5910	SO:0001589	frameshift_variant	286097	exon5			.	BC032868	CCDS5999.1	8p22	2013-03-26	2013-03-26	2013-03-14	ENSG00000155970	ENSG00000155970		"EF-hand domain containing"	27820	protein-coding gene	gene with protein product		610633	"EF hand domain family A2", "EF-hand domain family, member A2"	EFHA2		23409044	Standard	NM_181723		Approved	DKFZp313A0139	uc003wxd.2	Q86XE3	OTTHUMG00000096965	ENST00000318063.5:c.671delT	chr8.hg19:g.16939226delT	ENSP00000321455:p.Leu224fs	171.0	0.0		110.0	13.0	NM_181723	Q8IYZ3	Frame_Shift_Del	DEL	ENST00000318063.5	hg19	CCDS5999.1																																																																																			.	.		0.259	MICU3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214031.1	NM_181723		-	16939226	T	-	16939226	7	5	282	1	0	1	0	1	0	0	0	0	4946	1609	56	0	689	0	EFHA2	8	16939226	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	6471417	16939226	129424796	597	40831										
SLC7A2	6542	hgsc.bcm.edu	37	chr8	17417985	17417985	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgcggaccctcttctgccccTcccttctgccaacacagcag	7	19	3	0	rs536330311		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:17417985T>C	ENST00000494857.1	+	10	1665	c.1447T>C	c.(1447-1449)Tcc>Ccc	p.S483P	SLC7A2_ENST00000470360.1_Missense_Mutation_p.S522P|SLC7A2_ENST00000522656.1_Missense_Mutation_p.S483P|SLC7A2_ENST00000398090.3_Missense_Mutation_p.S522P|SLC7A2_ENST00000004531.10_Missense_Mutation_p.S523P	NM_001008539.3	NP_001008539.3	P52569	CTR2_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	483					amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|macrophage activation (GO:0042116)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide production involved in inflammatory response (GO:0002537)|regulation of inflammatory response (GO:0050727)|regulation of macrophage activation (GO:0043030)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	basic amino acid transmembrane transporter activity (GO:0015174)|high-affinity arginine transmembrane transporter activity (GO:0005289)|L-lysine transmembrane transporter activity (GO:0015189)|L-ornithine transmembrane transporter activity (GO:0000064)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(4)|lung(8)|ovary(2)|skin(1)|stomach(1)	25				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	L-Lysine(DB00123)|L-Ornithine(DB00129)	CTTCTGCCCCTCCCTTCTGCC	0.537																																					p.S523P		Atlas-SNP	.											.	SLC7A2	157	.	0			c.T1567C						.						151	137	142					8																	17417985		2203	4300	6503	SO:0001583	missense	6542	exon9			TGCCCCTCCCTTC	D29990	CCDS6002.2, CCDS34852.1, CCDS55203.1	8p22	2013-05-22			ENSG00000003989	ENSG00000003989		"Solute carriers"	11060	protein-coding gene	gene with protein product		601872		ATRC2		8954799	Standard	NM_001164771		Approved	CAT-2, HCAT2	uc011kye.2	P52569	OTTHUMG00000130819	ENST00000494857.1:c.1447T>C	chr8.hg19:g.17417985T>C	ENSP00000419140:p.Ser483Pro	207.0	0.0		93.0	5.0	NM_001164771	B7ZL54|O15291|O15292|Q14CQ6|Q6NSZ7|Q86TC6	Missense_Mutation	SNP	ENST00000494857.1	hg19	CCDS34852.1	.	.	.	.	.	.	.	.	.	.	t	9.214	1.031615	0.19590	.	.	ENSG00000003989	ENST00000494857;ENST00000522656;ENST00000470360;ENST00000004531;ENST00000398090	D;D;D;D;D	0.88664	-2.25;-2.25;-2.41;-2.27;-2.41	5.27	4.12	0.48240	.	0.103983	0.64402	D	0.000002	T	0.78489	0.4291	N	0.20483	0.58	0.29014	N	0.886682	B;B;B	0.09022	0.002;0.0;0.001	B;B;B	0.08055	0.003;0.003;0.002	T	0.68413	-0.5415	10	0.41790	T	0.15	.	6.4963	0.22144	0.1391:0.0726:0.0:0.7883	.	523;522;483	P52569-3;P52569-2;P52569	.;.;CTR2_HUMAN	P	483;483;522;523;522	ENSP00000419140:S483P;ENSP00000430464:S483P;ENSP00000419873:S522P;ENSP00000004531:S523P;ENSP00000381164:S522P	ENSP00000004531:S523P	S	+	1	0	SLC7A2	17462277	1.000000	0.71417	0.861000	0.33841	0.111000	0.19643	1.921000	0.40035	0.954000	0.37851	-0.257000	0.10917	TCC	.	.		0.537	SLC7A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253367.3	NM_003046		C	17417985	T	C	17417985	3	2	282	1	0	0	0	0	1	0	0	0	14712	1551	54	2	1742	2	SLC7A2	8	17417985	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	478759	17417985	128946037	598	40832										
PCM1	5108	hgsc.bcm.edu	37	chr8	17829875	17829875	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aagaggaggtggaaagcagtAggacaccatggttatatgaa	14	4	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:17829875A>G	ENST00000519253.1	+	23	3873	c.3622A>G	c.(3622-3624)Agg>Ggg	p.R1208G	PCM1_ENST00000327578.8_5'Flank|PCM1_ENST00000524226.1_Missense_Mutation_p.R1209G|PCM1_ENST00000325083.8_Missense_Mutation_p.R1208G			Q15154	PCM1_HUMAN	pericentriolar material 1	1208					centrosome organization (GO:0051297)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|interkinetic nuclear migration (GO:0022027)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|microtubule anchoring (GO:0034453)|microtubule anchoring at centrosome (GO:0034454)|mitotic cell cycle (GO:0000278)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|positive regulation of intracellular protein transport (GO:0090316)|protein localization to centrosome (GO:0071539)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|pericentriolar material (GO:0000242)|protein complex (GO:0043234)	identical protein binding (GO:0042802)		PCM1/JAK2(30)	breast(4)|endometrium(8)|kidney(5)|large_intestine(16)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	48				Colorectal(111;0.0789)		GGAAAGCAGTAGGACACCATG	0.343			T	"RET, JAK2"	"papillary thyroid, CML, MPD"																																p.R1208G		Atlas-SNP	.		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"E, L"	.	PCM1	120	.	0			c.A3622G						.						65	61	62					8																	17829875		1852	4086	5938	SO:0001583	missense	5108	exon23			AGCAGTAGGACAC		CCDS47812.1	8p22-p21.3	2008-08-08			ENSG00000078674	ENSG00000078674			8727	protein-coding gene	gene with protein product		600299				8120099, 15659651	Standard	NM_006197		Approved	PTC4	uc003wyi.4	Q15154	OTTHUMG00000163699	ENST00000519253.1:c.3622A>G	chr8.hg19:g.17829875A>G	ENSP00000431099:p.Arg1208Gly	182.0	0.0		95.0	5.0	NM_006197	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Missense_Mutation	SNP	ENST00000519253.1	hg19		.	.	.	.	.	.	.	.	.	.	A	15.59	2.879702	0.51801	.	.	ENSG00000078674	ENST00000325083;ENST00000519253;ENST00000524226	T;T;T	0.55234	0.53;0.53;0.53	5.37	4.15	0.48705	.	0.409562	0.30704	N	0.009046	T	0.47173	0.1431	L	0.44542	1.39	0.80722	D	1	B;B;B;B	0.34329	0.449;0.277;0.449;0.277	B;B;B;B	0.37091	0.241;0.116;0.241;0.116	T	0.53563	-0.8421	10	0.59425	D	0.04	-9.7344	12.9826	0.58572	0.8661:0.1339:0.0:0.0	.	70;1208;1209;1208	B4DJ00;E7ETA6;E7EV56;Q15154	.;.;.;PCM1_HUMAN	G	1208;1208;1209	ENSP00000327077:R1208G;ENSP00000431099:R1208G;ENSP00000430521:R1209G	ENSP00000327077:R1208G	R	+	1	2	PCM1	17874155	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.016000	0.49607	2.171000	0.68590	0.402000	0.26972	AGG	.	.		0.343	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197		G	17829875	A	G	17829875	3	3	282	1	0	0	0	0	1	0	0	0	11593	411	15	2	3704	2	PCM1	8	17829875	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	411890	17829875	128534147	599	40833										
SH2D4A	63898	hgsc.bcm.edu	37	chr8	19190562	19190562	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agataaaccctatgatgtgcTctgtaatgaaattattgctg	8	6	1	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:19190562T>C	ENST00000265807.3	+	3	689	c.278T>C	c.(277-279)cTc>cCc	p.L93P	SH2D4A_ENST00000519207.1_Missense_Mutation_p.L93P|SH2D4A_ENST00000518040.1_Missense_Mutation_p.L48P	NM_001174160.1|NM_022071.3	NP_001167631.1|NP_071354.2	Q9H788	SH24A_HUMAN	SH2 domain containing 4A	93					negative regulation of phosphatase activity (GO:0010923)	cytoplasm (GO:0005737)	phosphatase binding (GO:0019902)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|stomach(1)	16				Colorectal(111;0.0732)		TATGATGTGCTCTGTAATGAA	0.473																																					p.L93P		Atlas-SNP	.											.	SH2D4A	49	.	0			c.T278C						.						124	121	122					8																	19190562		2203	4300	6503	SO:0001583	missense	63898	exon3			ATGTGCTCTGTAA	AY190323	CCDS6009.1, CCDS55206.1	8p21	2013-02-14			ENSG00000104611	ENSG00000104611		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "SH2 domain containing"	26102	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 38"	614968					Standard	NM_022071		Approved	FLJ20967, SH2A, PPP1R38	uc003wzc.3	Q9H788	OTTHUMG00000097005	ENST00000265807.3:c.278T>C	chr8.hg19:g.19190562T>C	ENSP00000265807:p.Leu93Pro	142.0	0.0		63.0	4.0	NM_022071	B4DDR1|Q5XKC1|Q6NXE9|Q86YM2|Q96C88|Q9H7F7	Missense_Mutation	SNP	ENST00000265807.3	hg19	CCDS6009.1	.	.	.	.	.	.	.	.	.	.	T	10.40	1.339888	0.24339	.	.	ENSG00000104611	ENST00000265807;ENST00000518040;ENST00000519207;ENST00000523736	T;T;T;T	0.15256	2.44;2.44;2.44;2.44	5.58	4.43	0.53597	.	0.242085	0.34802	N	0.003679	T	0.18383	0.0441	L	0.56769	1.78	0.58432	D	0.999999	B;B	0.18461	0.028;0.009	B;B	0.15870	0.014;0.01	T	0.02596	-1.1136	10	0.87932	D	0	.	9.6753	0.40037	0.0:0.0825:0.0:0.9175	.	48;93	B4DDR1;Q9H788	.;SH24A_HUMAN	P	93;48;93;79	ENSP00000265807:L93P;ENSP00000429482:L48P;ENSP00000428684:L93P;ENSP00000428048:L79P	ENSP00000265807:L93P	L	+	2	0	SH2D4A	19234842	1.000000	0.71417	0.994000	0.49952	0.207000	0.24258	4.409000	0.59768	0.954000	0.37851	0.374000	0.22700	CTC	.	.		0.473	SH2D4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214094.1	NM_022071		C	19190562	T	C	19190562	3	2	282	1	0	0	0	0	1	0	0	0	14250	1551	54	2	334	2	SH2D4A	8	19190562	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1360687	19190562	127173460	600	40834										
CDCA2	157313	hgsc.bcm.edu	37	chr8	25325868	25325868	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aggaaaagtaattggtctccAgatattcaatattgatacag	8	5	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:25325868A>G	ENST00000330560.3	+	6	1151	c.674A>G	c.(673-675)cAg>cGg	p.Q225R	CDCA2_ENST00000380665.3_Missense_Mutation_p.Q210R	NM_152562.2	NP_689775.2	Q69YH5	CDCA2_HUMAN	cell division cycle associated 2	225					mitotic nuclear division (GO:0007067)|positive regulation of protein dephosphorylation (GO:0035307)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(3)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(7)|lung(10)|ovary(1)|prostate(3)	35		all_cancers(63;0.0378)|Ovarian(32;0.000878)|all_epithelial(46;0.0162)|Breast(100;0.0164)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.022)|Epithelial(17;1.37e-11)|Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0443)		ATTGGTCTCCAGATATTCAAT	0.403																																					p.Q225R		Atlas-SNP	.											.	CDCA2	78	.	0			c.A674G						.						117	120	119					8																	25325868		2203	4300	6503	SO:0001583	missense	157313	exon6			GTCTCCAGATATT	BG354575	CCDS6049.1	8p21.2	2014-06-12			ENSG00000184661	ENSG00000184661			14623	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 81"					12188893, 16492807	Standard	NM_152562		Approved	Repo-Man, PPP1R81	uc003xep.1	Q69YH5	OTTHUMG00000099429	ENST00000330560.3:c.674A>G	chr8.hg19:g.25325868A>G	ENSP00000328228:p.Gln225Arg	145.0	0.0		71.0	4.0	NM_152562	Q3SX74|Q4G0W0|Q5RKN0|Q69YI4|Q6P464|Q8N7C1	Missense_Mutation	SNP	ENST00000330560.3	hg19	CCDS6049.1	.	.	.	.	.	.	.	.	.	.	A	10.20	1.285250	0.23478	.	.	ENSG00000184661	ENST00000330560;ENST00000380665	T;T	0.32515	1.45;1.45	5.05	1.32	0.21799	.	1.721060	0.02819	N	0.125391	T	0.18341	0.0440	N	0.22421	0.69	0.09310	N	1	B;B;B	0.26809	0.019;0.16;0.16	B;B;B	0.26770	0.022;0.073;0.073	T	0.12863	-1.0531	10	0.07644	T	0.81	0.848	3.2514	0.06815	0.6428:0.0:0.186:0.1712	.	225;210;225	B7Z5Q5;E9PEI0;Q69YH5	.;.;CDCA2_HUMAN	R	225;210	ENSP00000328228:Q225R;ENSP00000370040:Q210R	ENSP00000328228:Q225R	Q	+	2	0	CDCA2	25381785	0.007000	0.16637	0.005000	0.12908	0.014000	0.08584	0.711000	0.25764	0.083000	0.17047	0.529000	0.55759	CAG	.	.		0.403	CDCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216891.3	NM_152562		G	25325868	A	G	25325868	3	3	282	1	0	0	0	0	1	0	0	0	3088	188	7	2	692	2	CDCA2	8	25325868	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	6135306	25325868	121038154	601	40835										
PPP2R2A	5520	hgsc.bcm.edu	37	chr8	26211994	26211994	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttcattttagaacaaaatccAgtctcatagcagaggagaat	7	7	2	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:26211994A>G	ENST00000380737.3	+	4	520	c.191A>G	c.(190-192)cAg>cGg	p.Q64R	PPP2R2A_ENST00000315985.7_Missense_Mutation_p.Q74R	NM_002717.3	NP_002708.1	P63151	2ABA_HUMAN	protein phosphatase 2, regulatory subunit B, alpha	64					G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope reassembly (GO:0007084)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|response to morphine (GO:0043278)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			kidney(1)|large_intestine(2)|ovary(1)	4		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)		AACAAAATCCAGTCTCATAGC	0.313																																					p.Q74R		Atlas-SNP	.											.	PPP2R2A	44	.	0			c.A221G						.						74	77	76					8																	26211994		2203	4300	6503	SO:0001583	missense	5520	exon4			AAATCCAGTCTCA	M64929	CCDS34867.1, CCDS55213.1	8p21.2	2013-01-10	2010-04-14		ENSG00000221914	ENSG00000221914	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "WD repeat domain containing"	9304	protein-coding gene	gene with protein product	"PP2A subunit B isoform alpha"	604941	"protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), alpha isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B, alpha isoform"			1849734	Standard	NM_001177591		Approved	PR52A, PR55A, B55A		P63151	OTTHUMG00000163850	ENST00000380737.3:c.191A>G	chr8.hg19:g.26211994A>G	ENSP00000370113:p.Gln64Arg	162.0	0.0		68.0	4.0	NM_001177591	B2RBU8|B4E1T7|P50409|Q00007	Missense_Mutation	SNP	ENST00000380737.3	hg19	CCDS34867.1	.	.	.	.	.	.	.	.	.	.	A	9.582	1.123757	0.20959	.	.	ENSG00000221914	ENST00000380737;ENST00000315985	T;T	0.29655	1.57;1.56	5.97	4.75	0.60458	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.163914	0.41396	U	0.000887	T	0.08802	0.0218	N	0.00538	-1.39	0.37224	D	0.905387	B;B	0.02656	0.0;0.0	B;B	0.08055	0.001;0.003	T	0.24225	-1.0166	10	0.12103	T	0.63	-5.53	11.8334	0.52309	0.7323:0.2677:0.0:0.0	.	74;64	B4E1T7;P63151	.;2ABA_HUMAN	R	64;74	ENSP00000370113:Q64R;ENSP00000325074:Q74R	ENSP00000325074:Q74R	Q	+	2	0	PPP2R2A	26267911	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.241000	0.51376	2.285000	0.76669	0.528000	0.53228	CAG	.	.		0.313	PPP2R2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375954.2	NM_002717		G	26211994	A	G	26211994	3	3	282	1	0	0	0	0	1	0	0	0	12396	188	7	2	246	2	PPP2R2A	8	26211994	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	886126	26211994	120152028	602	40836										
MAK16	84549	hgsc.bcm.edu	37	chr8	33346292	33346292	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaggttatagaacgagcggcTtttcctcggcgtctctggga	13	9	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:33346292T>C	ENST00000360128.6	+	4	673	c.216T>C	c.(214-216)gcT>gcC	p.A72A	TTI2_ENST00000519356.1_Intron	NM_032509.3	NP_115898.2	Q9BXY0	MAK16_HUMAN	MAK16 homolog (S. cerevisiae)	72						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|urinary_tract(1)	8						AACGAGCGGCTTTTCCTCGGC	0.418																																					p.A72A		Atlas-SNP	.											.	MAK16	25	.	0			c.T216C						.						84	82	83					8																	33346292		2203	4300	6503	SO:0001819	synonymous_variant	84549	exon4			AGCGGCTTTTCCT	AF251062	CCDS6089.1	8p12	2011-10-13	2008-06-04	2008-06-04	ENSG00000198042	ENSG00000198042		"RNA binding motif (RRM) containing"	13703	protein-coding gene	gene with protein product			"RNA binding motif protein 13"	RBM13			Standard	NM_032509		Approved	MAK16L	uc003xjj.3	Q9BXY0	OTTHUMG00000163957	ENST00000360128.6:c.216T>C	chr8.hg19:g.33346292T>C		159.0	0.0		75.0	4.0	NM_032509	B2RB44|Q5U5T1|Q86UC4|Q96SY6	Silent	SNP	ENST00000360128.6	hg19	CCDS6089.1																																																																																			.	.		0.418	MAK16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376559.3	NM_032509		C	33346292	T	C	33346292	2	2	282	1	0	0	0	0	0	0	0	1	9207	1596	56	2		2	MAK16	8	33346292	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	7134298	33346292	113017730	603	40837										
WHSC1L1	54904	hgsc.bcm.edu	37	chr8	38148152	38148153	+	Missense_Mutation	DNP	TC	TC	AG													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atgtttaaggccctggatgtTcagtggcacagacctggggt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:38148152_38148153TC>AG	ENST00000317025.8	-	17	3475_3476	c.2958_2959GA>CT	c.(2956-2961)ctGAac>ctCTac	p.N987Y	WHSC1L1_ENST00000527502.1_Missense_Mutation_p.N987Y|WHSC1L1_ENST00000433384.2_Missense_Mutation_p.N938Y	NM_023034.1	NP_075447.1	Q9BZ95	NSD3_HUMAN	Wolf-Hirschhorn syndrome candidate 1-like 1	987	PWWP 2. {ECO:0000255|PROSITE- ProRule:PRU00162}.				histone lysine methylation (GO:0034968)|histone methylation (GO:0016571)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)			CCCTGGATGTTCAGTGGCACAG	0.455			T	NUP98	AML																																p.N987Y|p.L986L		Atlas-SNP	.		Dom	yes		8	8p12	54904	Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3)		L	.	WHSC1L1	137	.	0			c.A2959T|c.G2958C						.																																			SO:0001583	missense	54904	exon17			GGATGTTCAGTGG|GATGTTCAGTGGC	AF332469	CCDS6105.1, CCDS43729.1	8p11.2	2013-05-20			ENSG00000147548	ENSG00000147548			12767	protein-coding gene	gene with protein product		607083				10802047, 23269674	Standard	NM_023034		Approved	FLJ20353, NSD3	uc003xli.3	Q9BZ95		ENST00000317025.8:c.2958_2959delinsAG	chr8.hg19:g.38148152_38148153delinsAG	ENSP00000313983:p.Asn987Tyr	173.0|174.0	0.0		149.0|148.0	53.0|52.0	NM_023034	B7ZL11|D3DSX1|Q1RMD3|Q3B796|Q6ZSA5|Q9BYU8|Q9BYU9|Q9H2M8|Q9H9W9|Q9NXA6	Missense_Mutation|Silent	SNP	ENST00000317025.8	hg19	CCDS43729.1																																																																																			.	.		0.455	WHSC1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381924.3	NM_023034		AG	38148153	TC	AG	38148152	3	1	282	1	0	0	0	0	1	0	0	0	17378	1783	62	4	1386	4	WHSC1L1	8	38148152	Missense_Mutation	DNP	TC	TCGA-G3-A3CJ-01A-11D-A20W-10	4801860	38148152	108215870	604	40838										
MYST3	7994	hgsc.bcm.edu	37	chr8	41791683	41791683	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcttctgcatattagcatctAaaaaagactcttgaacacca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:41791683delA	ENST00000396930.3	-	18	4598	c.4055delT	c.(4054-4056)ttafs	p.L1352fs	KAT6A_ENST00000265713.2_Frame_Shift_Del_p.L1352fs|KAT6A_ENST00000406337.1_Frame_Shift_Del_p.L1352fs	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	1352					aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										ATTAGCATCTAAAAAAGACTC	0.493																																					p.L1352fs		Atlas-INDEL	.											.	.	.	.	0			c.4056delA						.						149	152	151					8																	41791683		2203	4300	6503	SO:0001589	frameshift_variant	7994	exon17			.	U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	13013	protein-coding gene	gene with protein product	"Monocytic leukemia zinc finger protein"	601408	"runt-related transcription factor binding protein 2", "MYST histone acetyltransferase (monocytic leukemia) 3"	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.4055delT	chr8.hg19:g.41791683delA	ENSP00000380136:p.Leu1352fs	217.0	0.0		155.0	10.0	NM_006766	Q76L81	Frame_Shift_Del	DEL	ENST00000396930.3	hg19	CCDS6124.1																																																																																			.	.		0.493	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766		-	41791683	A	-	41791683	7	5	282	1	0	1	0	1	0	0	0	0	10113	372	13	0	1963	0	MYST3	8	41791683	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	3643531	41791683	104572339	605	40839										
MYST3	7994	hgsc.bcm.edu	37	chr8	41792228	41792228	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cgactcaacttaaatcctggTtttcgaccaggtcttttctt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:41792228delT	ENST00000396930.3	-	18	4053	c.3510delA	c.(3508-3510)aaafs	p.K1170fs	KAT6A_ENST00000265713.2_Frame_Shift_Del_p.K1170fs|KAT6A_ENST00000406337.1_Frame_Shift_Del_p.K1170fs	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	1170					aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										TAAATCCTGGTTTTCGACCAG	0.463																																					p.P1171fs		Atlas-INDEL	.											.	.	.	.	0			c.3511delC						.						149	152	151					8																	41792228		2203	4300	6503	SO:0001589	frameshift_variant	7994	exon17			.	U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	13013	protein-coding gene	gene with protein product	"Monocytic leukemia zinc finger protein"	601408	"runt-related transcription factor binding protein 2", "MYST histone acetyltransferase (monocytic leukemia) 3"	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.3510delA	chr8.hg19:g.41792228delT	ENSP00000380136:p.Lys1170fs	252.0	0.0		194.0	14.0	NM_006766	Q76L81	Frame_Shift_Del	DEL	ENST00000396930.3	hg19	CCDS6124.1																																																																																			.	.		0.463	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766		-	41792228	T	-	41792228	7	5	282	1	0	1	0	1	0	0	0	0	10113	1722	60	0	2508	0	MYST3	8	41792228	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	545	41792228	104571794	606	40840										
PXDNL	137902	hgsc.bcm.edu	37	chr8	52321457	52321457	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggcaccgaagggtctctgagAgcctgggattcccgctccga	14	13	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:52321457A>G	ENST00000356297.4	-	17	2827	c.2727T>C	c.(2725-2727)gcT>gcC	p.A909A	PXDNL_ENST00000543296.1_Silent_p.A909A	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	909					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				GGTCTCTGAGAGCCTGGGATT	0.587																																					p.A909A		Atlas-SNP	.											.	PXDNL	414	.	0			c.T2727C						.						36	41	39					8																	52321457		1962	4138	6100	SO:0001819	synonymous_variant	137902	exon17			TCTGAGAGCCTGG		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"Immunoglobulin superfamily / I-set domain containing"	26359	protein-coding gene	gene with protein product	"polysomal ribonuclease 1 homolog (Xenopus)"	615904	"peroxidasin homolog-like (Drosophila)"			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.2727T>C	chr8.hg19:g.52321457A>G		66.0	0.0		92.0	5.0	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Silent	SNP	ENST00000356297.4	hg19	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	A	0.362	-0.938952	0.02340	.	.	ENSG00000147485	ENST00000522933	.	.	.	4.17	-8.15	0.01065	.	.	.	.	.	T	0.16041	0.0386	.	.	.	0.29347	N	0.865632	.	.	.	.	.	.	T	0.29912	-0.9996	4	.	.	.	.	2.0469	0.03562	0.1763:0.4275:0.1848:0.2115	.	.	.	.	P	28	.	.	L	-	2	0	PXDNL	52484010	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	-0.916000	0.04029	-0.713000	0.04981	-0.250000	0.11733	CTC	.	.		0.587	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		G	52321457	A	G	52321457	2	3	282	1	0	0	0	0	0	0	0	1	12863	291	11	2		2	PXDNL	8	52321457	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	10529229	52321457	94042565	607	40841										
LYPLA1	10434	hgsc.bcm.edu	37	chr8	55014376	55014376	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcggggttgacatgttattgCcgcacatacaccgcctcagc	11	13	1	1	rs568447147		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:55014376C>T	ENST00000316963.3	-	1	201	c.8G>A	c.(7-9)gGc>gAc	p.G3D	LYPLA1_ENST00000522007.1_Missense_Mutation_p.G3D|LYPLA1_ENST00000519926.1_5'UTR|LYPLA1_ENST00000343231.6_Missense_Mutation_p.G3D	NM_001279360.1|NM_006330.2	NP_001266289.1|NP_006321.1	O75608	LYPA1_HUMAN	lysophospholipase I	3					fatty acid metabolic process (GO:0006631)|negative regulation of Golgi to plasma membrane protein transport (GO:0042997)|nitric oxide metabolic process (GO:0046209)|protein depalmitoylation (GO:0002084)|regulation of nitric-oxide synthase activity (GO:0050999)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	lysophospholipase activity (GO:0004622)|palmitoyl-(protein) hydrolase activity (GO:0008474)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(3)	6		Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;8.48e-07)|Epithelial(17;9.29e-05)|all cancers(17;0.000689)			CATGTTATTGCCGCACATACA	0.736													C|||	1	0.000199681	0	0	5008	,	,		6889	0		0.001	False		,,,				2504	0				p.G3D		Atlas-SNP	.											.	LYPLA1	15	.	0			c.G8A						.						13	11	12					8																	55014376		2182	4262	6444	SO:0001583	missense	10434	exon1			TTATTGCCGCACA	AF081281	CCDS6157.1, CCDS64899.1, CCDS75738.1, CCDS75739.1	8q11.23-q12.1	2008-05-15			ENSG00000120992	ENSG00000120992	3.1.1.5		6737	protein-coding gene	gene with protein product		605599				10064899	Standard	NM_006330		Approved	LPL1	uc003xry.3	O75608	OTTHUMG00000164313	ENST00000316963.3:c.8G>A	chr8.hg19:g.55014376C>T	ENSP00000320043:p.Gly3Asp	170.0	0.0		137.0	6.0	NM_006330	O43202|Q9UQF9	Missense_Mutation	SNP	ENST00000316963.3	hg19	CCDS6157.1	.	.	.	.	.	.	.	.	.	.	C	15.44	2.835586	0.50951	.	.	ENSG00000120992	ENST00000316963;ENST00000523751;ENST00000343231;ENST00000518546;ENST00000522007;ENST00000519926;ENST00000517297;ENST00000521898	T;T;T	0.36520	1.55;1.25;1.37	3.72	3.72	0.42706	.	0.175026	0.49305	D	0.000144	T	0.32882	0.0844	L	0.40543	1.245	0.48452	D	0.999654	B	0.18968	0.032	B	0.29440	0.102	T	0.30880	-0.9963	10	0.87932	D	0	0.0601	12.5131	0.56017	0.0:1.0:0.0:0.0	.	3	O75608	LYPA1_HUMAN	D	3	ENSP00000320043:G3D;ENSP00000344477:G3D;ENSP00000428729:G3D	ENSP00000320043:G3D	G	-	2	0	LYPLA1	55176929	1.000000	0.71417	0.995000	0.50966	0.392000	0.30506	5.456000	0.66665	1.905000	0.55150	0.305000	0.20034	GGC	.	.		0.736	LYPLA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378238.1			T	55014376	C	T	55014376	3	4	282	1	0	0	0	0	1	0	0	0	9125	739	26	3	720	3	LYPLA1	8	55014376	Missense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	2692919	55014376	91349646	608	40842										
TGS1	96764	hgsc.bcm.edu	37	chr8	56711514	56711514	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gttaataaaccaatggatgaAgaagcatcacaggaatcatc	8	7	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:56711514A>G	ENST00000260129.5	+	8	2061	c.1584A>G	c.(1582-1584)gaA>gaG	p.E528E		NM_024831.6	NP_079107.6	Q96RS0	TGS1_HUMAN	trimethylguanosine synthase 1	528					7-methylguanosine cap hypermethylation (GO:0036261)|7-methylguanosine RNA capping (GO:0009452)|cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|regulation of transcription, DNA-templated (GO:0006355)|ribonucleoprotein complex biogenesis (GO:0022613)|ribonucleoprotein complex import into nucleus (GO:0071167)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)	RNA trimethylguanosine synthase activity (GO:0071164)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		all_lung(136;0.119)|all_epithelial(80;0.125)|Lung NSC(129;0.147)	Epithelial(17;0.00027)|all cancers(17;0.00251)			CAATGGATGAAGAAGCATCAC	0.378																																					p.E528E	Esophageal Squamous(34;275 823 4842 34837 48447)	Atlas-SNP	.											.	TGS1	66	.	0			c.A1584G						.						88	76	80					8																	56711514		2203	4300	6503	SO:0001819	synonymous_variant	96764	exon8			GGATGAAGAAGCA	AY028423	CCDS34894.1	8q11	2010-06-25	2010-06-25	2006-11-27	ENSG00000137574	ENSG00000137574	2.1.1.-		17843	protein-coding gene	gene with protein product		606461	"nuclear receptor coactivator 6 interacting protein", "trimethylguanosine synthase homolog (S. cerevisiae)"	NCOA6IP		11517327, 11983179, 19307714	Standard	NM_024831		Approved	PIMT	uc003xsj.4	Q96RS0	OTTHUMG00000164294	ENST00000260129.5:c.1584A>G	chr8.hg19:g.56711514A>G		55.0	0.0		76.0	4.0	NM_024831	A6NJQ5|Q5GH23|Q8TDG9|Q96QU3|Q9H5V3	Silent	SNP	ENST00000260129.5	hg19	CCDS34894.1																																																																																			.	.		0.378	TGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378152.1	NM_024831		G	56711514	A	G	56711514	2	3	282	1	0	0	0	0	0	0	0	1	15852	69	3	2		2	TGS1	8	56711514	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1697138	56711514	89652508	609	40843										
ARFGEF1	10565	hgsc.bcm.edu	37	chr8	68130371	68130371	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gttgttgtcatccattcagcTttctggggaaaaaagtcatt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:68130371delT	ENST00000262215.3	-	31	4730	c.4341delA	c.(4339-4341)aaafs	p.K1447fs	ARFGEF1_ENST00000520381.1_Frame_Shift_Del_p.K901fs|ARFGEF1_ENST00000518230.1_Frame_Shift_Del_p.K285fs	NM_006421.4	NP_006412.2	Q9Y6D6	BIG1_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)	1447					endomembrane system organization (GO:0010256)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein glycosylation in Golgi (GO:0090284)|positive regulation of wound healing (GO:0090303)|protein transport (GO:0015031)|regulation of ARF protein signal transduction (GO:0032012)|regulation of establishment of cell polarity (GO:2000114)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|small nuclear ribonucleoprotein complex (GO:0030532)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|guanyl-nucleotide exchange factor activity (GO:0005085)|myosin binding (GO:0017022)|protein kinase A regulatory subunit binding (GO:0034237)			breast(1)|endometrium(14)|kidney(4)|large_intestine(17)|lung(20)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)			TCCATTCAGCTTTCTGGGGAA	0.274																																					p.A1448fs		Atlas-INDEL	.											.	ARFGEF1	196	.	0			c.4342delG						.						85	74	78					8																	68130371		2203	4300	6503	SO:0001589	frameshift_variant	10565	exon31			.	AF084520	CCDS6199.1	8q13	2011-08-18	2011-08-18		ENSG00000066777	ENSG00000066777			15772	protein-coding gene	gene with protein product		604141				10212200, 8917509	Standard	NM_006421		Approved	DKFZP434L057, BIG1, ARFGEP1, p200	uc003xxo.2	Q9Y6D6	OTTHUMG00000164626	ENST00000262215.3:c.4341delA	chr8.hg19:g.68130371delT	ENSP00000262215:p.Lys1447fs	194.0	0.0		179.0	13.0	NM_006421	Q9NV46|Q9UFV2|Q9UNL0	Frame_Shift_Del	DEL	ENST00000262215.3	hg19	CCDS6199.1																																																																																			.	.		0.274	ARFGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379441.4	NM_006421		-	68130371	T	-	68130371	7	5	282	1	0	1	0	1	0	0	0	0	852	1606	56	0	1244	0	ARFGEF1	8	68130371	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	11418857	68130371	78233651	610	40844										
PREX2	80243	hgsc.bcm.edu	37	chr8	68995503	68995503	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	catggaagtcgggaaaaagaTttttgctattaatggtgacc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:68995503delT	ENST00000288368.4	+	18	2184	c.1907delT	c.(1906-1908)attfs	p.I636fs	PREX2_ENST00000529398.1_3'UTR|RP11-403D15.2_ENST00000526901.1_RNA	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	636	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						GGGAAAAAGATTTTTGCTATT	0.318																																					p.I636fs		Atlas-INDEL	.											.	PREX2	614	.	0			c.1906delA						.						93	94	93					8																	68995503		2203	4300	6503	SO:0001589	frameshift_variant	80243	exon18			.	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.1907delT	chr8.hg19:g.68995503delT	ENSP00000288368:p.Ile636fs	157.0	0.0		159.0	10.0	NM_025170	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Frame_Shift_Del	DEL	ENST00000288368.4	hg19	CCDS6201.1																																																																																			.	.		0.318	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		-	68995503	T	-	68995503	7	5	282	1	0	1	0	1	0	0	0	0	12489	1493	52	0	1977	0	PREX2	8	68995503	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	865132	68995503	77368519	611	40845										
SULF1	23213	hgsc.bcm.edu	37	chr8	70488249	70488249	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cgagaaagattatggaacatGggggggccaccttcatcaat					rs201774043		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:70488249delG	ENST00000260128.4	+	6	934	c.217delG	c.(217-219)gggfs	p.G74fs	SULF1_ENST00000402687.4_Frame_Shift_Del_p.G74fs|SULF1_ENST00000458141.2_Frame_Shift_Del_p.G74fs|SULF1_ENST00000419716.3_Frame_Shift_Del_p.G74fs	NM_015170.2	NP_055985.2	Q8IWU6	SULF1_HUMAN	sulfatase 1	74					apoptotic process (GO:0006915)|bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of prostatic bud formation (GO:0060686)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|central_nervous_system(3)|endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)			TATGGAACATGGGGGGGCCAC	0.493																																					p.H72fs		Atlas-INDEL	.											.,1	SULF1	153	.	0			c.216delT						.						109	89	96					8																	70488249		2203	4300	6503	SO:0001589	frameshift_variant	23213	exon6			.	AB029000	CCDS6204.1	8q13.2	2014-09-11			ENSG00000137573	ENSG00000137573			20391	protein-coding gene	gene with protein product		610012				12368295	Standard	NM_015170		Approved	KIAA1077, SULF-1	uc003xyd.2	Q8IWU6	OTTHUMG00000164466	ENST00000260128.4:c.217delG	chr8.hg19:g.70488249delG	ENSP00000260128:p.Gly74fs	164.0	0.0		199.0	13.0	NM_001128205	Q86YV8|Q8NCA2|Q9UPS5	Frame_Shift_Del	DEL	ENST00000260128.4	hg19	CCDS6204.1																																																																																			.	.		0.493	SULF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378885.2	NM_015170		-	70488249	G	-	70488249	7	5	282	1	0	1	0	1	0	0	0	0	15385	1348	47	0	223	0	SULF1	8	70488249	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1492746	70488249	75875773	612	40846										
TRPA1	8989	hgsc.bcm.edu	37	chr8	72951124	72951124	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtatctagtatttctgaatgAtcactagtttcattgatgat	7	5	4	4			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:72951124A>G	ENST00000262209.4	-	19	2478	c.2271T>C	c.(2269-2271)gaT>gaC	p.D757D	TRPA1_ENST00000519720.1_5'UTR|RP11-383H13.1_ENST00000524152.1_Intron|RP11-383H13.1_ENST00000457356.4_Intron|RP11-383H13.1_ENST00000537896.1_Intron	NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	757					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	TTTCTGAATGATCACTAGTTT	0.308																																					p.D757D		Atlas-SNP	.											.	TRPA1	256	.	0			c.T2271C						.						87	83	84					8																	72951124		2203	4300	6503	SO:0001819	synonymous_variant	8989	exon19			TGAATGATCACTA	Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	497	protein-coding gene	gene with protein product		604775	"ankyrin-like with transmembrane domains 1"	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.2271T>C	chr8.hg19:g.72951124A>G		87.0	0.0		95.0	4.0	NM_007332	A6NIN6	Silent	SNP	ENST00000262209.4	hg19	CCDS34908.1																																																																																			.	.		0.308	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332		G	72951124	A	G	72951124	2	3	282	1	0	0	0	0	0	0	0	1	16592	330	12	2		2	TRPA1	8	72951124	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2462875	72951124	73412898	613	40847										
KCNB2	9312	hgsc.bcm.edu	37	chr8	73480466	73480466	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcgagagcgagaaggagaagAgtttgataatacctgctgcc	14	7	0	5			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:73480466A>G	ENST00000523207.1	+	2	1085	c.497A>G	c.(496-498)gAg>gGg	p.E166G		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	166					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	GAAGGAGAAGAGTTTGATAAT	0.453																																					p.E166G		Atlas-SNP	.											.	KCNB2	228	.	0			c.A497G						.						125	133	131					8																	73480466		2203	4300	6503	SO:0001583	missense	9312	exon2			GAGAAGAGTTTGA	U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.497A>G	chr8.hg19:g.73480466A>G	ENSP00000430846:p.Glu166Gly	118.0	0.0		110.0	5.0	NM_004770	Q7Z7D0|Q9BXD3	Missense_Mutation	SNP	ENST00000523207.1	hg19	CCDS6209.1	.	.	.	.	.	.	.	.	.	.	A	16.85	3.236890	0.58886	.	.	ENSG00000182674	ENST00000523207	D	0.97480	-4.4	6.07	6.07	0.98685	.	0.000000	0.33834	U	0.004516	D	0.95166	0.8433	L	0.43923	1.385	0.51012	D	0.9999	B	0.28801	0.223	B	0.30716	0.119	D	0.93452	0.6803	10	0.45353	T	0.12	.	16.3141	0.82909	1.0:0.0:0.0:0.0	.	166	Q92953	KCNB2_HUMAN	G	166	ENSP00000430846:E166G	ENSP00000430846:E166G	E	+	2	0	KCNB2	73643020	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	9.339000	0.96797	2.326000	0.78906	0.533000	0.62120	GAG	.	.		0.453	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770		G	73480466	A	G	73480466	3	3	282	1	0	0	0	0	1	0	0	0	8022	304	11	2	499	2	KCNB2	8	73480466	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	529342	73480466	72883556	614	40848										
FABP12	646486	hgsc.bcm.edu	37	chr8	82441805	82441805	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtactgatggtcacagtgggTtttgccaaacggcccagttt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:82441805delT	ENST00000360464.4	-	2	176	c.114delA	c.(112-114)aaafs	p.K38fs	RP11-257P3.3_ENST00000523380.1_RNA	NM_001105281.1	NP_001098751.1	A6NFH5	FBP12_HUMAN	fatty acid binding protein 12	38							lipid binding (GO:0008289)|transporter activity (GO:0005215)			large_intestine(1)|lung(3)	4						TCACAGTGGGTTTTGCCAAAC	0.373																																					p.P39fs		Atlas-INDEL	.											.	FABP12	20	.	0			c.115delC						.						97	91	93					8																	82441805		1845	4092	5937	SO:0001589	frameshift_variant	646486	exon2			.		CCDS47882.1	8q21.13	2013-03-01			ENSG00000197416	ENSG00000197416		"Fatty acid binding protein family"	34524	protein-coding gene	gene with protein product						18786628	Standard	NM_001105281		Approved		uc011lfp.2	A6NFH5	OTTHUMG00000164679	ENST00000360464.4:c.114delA	chr8.hg19:g.82441805delT	ENSP00000353650:p.Lys38fs	173.0	0.0		175.0	11.0	NM_001105281	B7SUN0	Frame_Shift_Del	DEL	ENST00000360464.4	hg19	CCDS47882.1																																																																																			.	.		0.373	FABP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379720.1	NM_001105281		-	82441805	T	-	82441805	7	5	282	1	0	1	0	1	0	0	0	0	5361	1722	60	0	318	0	FABP12	8	82441805	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	8961339	82441805	63922217	615	40849										
MMP16	4325	hgsc.bcm.edu	37	chr8	89179946	89179946	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tggctcatctgagtcaaaatGggtatctcctccaattcctg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:89179946delG	ENST00000286614.6	-	4	942	c.661delC	c.(661-663)catfs	p.H221fs	MMP16_ENST00000544227.1_5'UTR	NM_005941.4	NP_005932.2	P51512	MMP16_HUMAN	matrix metallopeptidase 16 (membrane-inserted)	221					chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)	Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(51)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	81					Marimastat(DB00786)	GAGTCAAAATGGGTATCTCCT	0.408																																					p.H221fs		Atlas-INDEL	.											.	MMP16	176	.	0			c.662delA						.						94	81	86					8																	89179946		2203	4300	6503	SO:0001589	frameshift_variant	4325	exon4			.	D85511	CCDS6246.1	8q21	2009-01-09	2005-08-08		ENSG00000156103	ENSG00000156103			7162	protein-coding gene	gene with protein product		602262	"matrix metalloproteinase 16 (membrane-inserted)", "chromosome 8 open reading frame 57"	C8orf57		7559440	Standard	NM_005941		Approved	MT3-MMP, DKFZp761D112	uc003yeb.4	P51512	OTTHUMG00000163769	ENST00000286614.6:c.661delC	chr8.hg19:g.89179946delG	ENSP00000286614:p.His221fs	166.0	0.0		194.0	14.0	NM_005941	B2RAN7|Q14824|Q52H48	Frame_Shift_Del	DEL	ENST00000286614.6	hg19	CCDS6246.1																																																																																			.	.		0.408	MMP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375304.2	NM_005941		-	89179946	G	-	89179946	7	5	282	1	0	1	0	1	0	0	0	0	9664	1348	47	0	1346	0	MMP16	8	89179946	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	6738141	89179946	57184076	616	40850										
RAD54B	25788	hgsc.bcm.edu	37	chr8	95390864	95390864	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tccatactctagacattgccTatagaaaataagtgagaatt	6	7	1	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:95390864T>C	ENST00000336148.5	-	13	2372		c.e13-2			NM_012415.3	NP_036547.1	Q9Y620	RA54B_HUMAN	RAD54 homolog B (S. cerevisiae)						ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|double-strand break repair via homologous recombination (GO:0000724)|mitotic recombination (GO:0006312)|reciprocal meiotic recombination (GO:0007131)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|RNA helicase activity (GO:0003724)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(10)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(36;4.5e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00217)			AGACATTGCCTATAGAAAATA	0.348								Direct reversal of damage;Homologous recombination																													.		Atlas-SNP	.											.	RAD54B	88	.	0			c.1696-2A>G						.						73	74	74					8																	95390864		2203	4299	6502	SO:0001630	splice_region_variant	25788	exon12			ATTGCCTATAGAA	AF112481	CCDS6262.1, CCDS56546.1, CCDS75768.1	8q22.1	2014-08-08			ENSG00000197275	ENSG00000197275			17228	protein-coding gene	gene with protein product		604289				10362364, 10851248	Standard	NM_012415		Approved	RDH54	uc003ygk.3	Q9Y620	OTTHUMG00000133658	ENST00000336148.5:c.2248-2A>G	chr8.hg19:g.95390864T>C		101.0	0.0		97.0	28.0	NM_001205263	F6WBS8	Splice_Site	SNP	ENST00000336148.5	hg19	CCDS6262.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.560588	0.86335	.	.	ENSG00000197275	ENST00000336148;ENST00000546218	.	.	.	5.57	5.57	0.84162	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7397	0.77882	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	RAD54B	95460040	1.000000	0.71417	0.982000	0.44146	0.982000	0.71751	7.582000	0.82546	2.121000	0.65114	0.533000	0.62120	.	.	.		0.348	RAD54B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257806.3	NM_012415	Intron	C	95390864	T	C	95390864	5	2	282	1	0	0	0	0	0	0	1	0	13007	1536	53	2	498	2	RAD54B	8	95390864	Splice_Site	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	6210918	95390864	50973158	617	40851										
INTS8	55656	hgsc.bcm.edu	37	chr8	95877744	95877744	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	catgttatagcttggacagcTtttagcagctacatgcaaag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:95877744delT	ENST00000523731.1	+	17	2220	c.2087delT	c.(2086-2088)cttfs	p.L697fs	INTS8_ENST00000520845.1_Intron|INTS8_ENST00000447247.1_Frame_Shift_Del_p.L697fs	NM_017864.2	NP_060334.2	Q75QN2	INT8_HUMAN	integrator complex subunit 8	697					snRNA processing (GO:0016180)	integrator complex (GO:0032039)				breast(3)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	28	Breast(36;1.05e-06)					CTTGGACAGCTTTTAGCAGCT	0.398																																					p.L696fs		Atlas-INDEL	.											.	INTS8	92	.	0			c.2086delC						.						99	94	96					8																	95877744		2203	4300	6503	SO:0001589	frameshift_variant	55656	exon17			.	AK091278	CCDS34925.1	8q22.1	2007-05-03	2006-03-15	2006-03-15	ENSG00000164941	ENSG00000164941			26048	protein-coding gene	gene with protein product		611351	"chromosome 8 open reading frame 52"	C8orf52		16239144	Standard	NM_017864		Approved	FLJ20530, INT8, MGC131633	uc003yhb.4	Q75QN2	OTTHUMG00000164695	ENST00000523731.1:c.2087delT	chr8.hg19:g.95877744delT	ENSP00000430338:p.Leu697fs	230.0	0.0		291.0	18.0	NM_017864	B2RN92|Q5RKZ3|Q6P1R5|Q7Z314|Q9NVS6|Q9NWY7	Frame_Shift_Del	DEL	ENST00000523731.1	hg19	CCDS34925.1																																																																																			.	.		0.398	INTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379794.1	NM_017864		-	95877744	T	-	95877744	7	5	282	1	0	1	0	1	0	0	0	0	7793	1609	56	0	2153	0	INTS8	8	95877744	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	486880	95877744	50486278	618	40852										
SPAG1	6674	hgsc.bcm.edu	37	chr8	101237506	101237506	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctgcaagcttggcatccggcAaaagagatgatctcaaaaca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:101237506delA	ENST00000388798.2	+	14	1985	c.1794delA	c.(1792-1794)gcafs	p.A598fs	SPAG1_ENST00000523302.1_3'UTR|SPAG1_ENST00000251809.3_Frame_Shift_Del_p.A598fs	NM_003114.4	NP_003105.2	Q07617	SPAG1_HUMAN	sperm associated antigen 1	598					axonemal dynein complex assembly (GO:0070286)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	all_cancers(14;2.35e-05)|all_epithelial(15;5.2e-08)|Lung NSC(17;0.000283)|all_lung(17;0.000823)	Breast(495;0.195)	Epithelial(11;1.12e-09)|all cancers(13;1.26e-07)|OV - Ovarian serous cystadenocarcinoma(57;4.37e-05)|STAD - Stomach adenocarcinoma(118;0.0525)	KIRC - Kidney renal clear cell carcinoma(542;0.00178)|READ - Rectum adenocarcinoma(644;0.236)		GGCATCCGGCAAAAGAGATGA	0.522																																					p.A598fs		Atlas-INDEL	.											.	SPAG1	80	.	0			c.1793delC						.						56	52	54					8																	101237506		2203	4300	6503	SO:0001589	frameshift_variant	6674	exon14			.	AF311312	CCDS34930.1	8q22	2014-01-21			ENSG00000104450	ENSG00000104450		"Tetratricopeptide (TTC) repeat domain containing"	11212	protein-coding gene	gene with protein product		603395				16368546	Standard	NM_172218		Approved	SP75, FLJ32920, HSD-3.8, TPIS, CT140	uc003yjh.2	Q07617	OTTHUMG00000164706	ENST00000388798.2:c.1794delA	chr8.hg19:g.101237506delA	ENSP00000373450:p.Ala598fs	156.0	0.0		166.0	11.0	NM_172218	A6NP70|B3KQ58|G3XAM3|Q7Z5G1	Frame_Shift_Del	DEL	ENST00000388798.2	hg19	CCDS34930.1																																																																																			.	.		0.522	SPAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379853.2	NM_172218		-	101237506	A	-	101237506	7	5	282	1	0	1	0	1	0	0	0	0	14990	117	5	0	1844	0	SPAG1	8	101237506	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	5359762	101237506	45126516	619	40853										
SPAG1	6674	hgsc.bcm.edu	37	chr8	101252868	101252868	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caccaaaagatttgccgatgTttttaagtaacaaacttgaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:101252868delT	ENST00000388798.2	+	18	2709	c.2518delT	c.(2518-2520)tttfs	p.F840fs	SPAG1_ENST00000251809.3_Frame_Shift_Del_p.F840fs	NM_003114.4	NP_003105.2	Q07617	SPAG1_HUMAN	sperm associated antigen 1	840					axonemal dynein complex assembly (GO:0070286)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	all_cancers(14;2.35e-05)|all_epithelial(15;5.2e-08)|Lung NSC(17;0.000283)|all_lung(17;0.000823)	Breast(495;0.195)	Epithelial(11;1.12e-09)|all cancers(13;1.26e-07)|OV - Ovarian serous cystadenocarcinoma(57;4.37e-05)|STAD - Stomach adenocarcinoma(118;0.0525)	KIRC - Kidney renal clear cell carcinoma(542;0.00178)|READ - Rectum adenocarcinoma(644;0.236)		TTTGCCGATGTTTTTAAGTAA	0.373																																					p.M839fs		Atlas-INDEL	.											.	SPAG1	80	.	0			c.2517delG						.						78	74	75					8																	101252868		2203	4300	6503	SO:0001589	frameshift_variant	6674	exon18			.	AF311312	CCDS34930.1	8q22	2014-01-21			ENSG00000104450	ENSG00000104450		"Tetratricopeptide (TTC) repeat domain containing"	11212	protein-coding gene	gene with protein product		603395				16368546	Standard	NM_172218		Approved	SP75, FLJ32920, HSD-3.8, TPIS, CT140	uc003yjh.2	Q07617	OTTHUMG00000164706	ENST00000388798.2:c.2518delT	chr8.hg19:g.101252868delT	ENSP00000373450:p.Phe840fs	216.0	0.0		236.0	18.0	NM_172218	A6NP70|B3KQ58|G3XAM3|Q7Z5G1	Frame_Shift_Del	DEL	ENST00000388798.2	hg19	CCDS34930.1																																																																																			.	.		0.373	SPAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379853.2	NM_172218		-	101252868	T	-	101252868	7	5	282	1	0	1	0	1	0	0	0	0	14990	1725	60	0	2584	0	SPAG1	8	101252868	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	15362	101252868	45111154	620	40854										
OXR1	55074	hgsc.bcm.edu	37	chr8	107726147	107726147	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaacctggatttatagtagtAaaaaagattgaggagtctga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:107726147delA	ENST00000442977.2	+	10	1992	c.1893delA	c.(1891-1893)gtafs	p.V631fs	OXR1_ENST00000312046.6_Frame_Shift_Del_p.V623fs|OXR1_ENST00000452423.2_Frame_Shift_Del_p.V120fs|OXR1_ENST00000531443.1_Frame_Shift_Del_p.V630fs|OXR1_ENST00000445937.1_Frame_Shift_Del_p.V630fs|OXR1_ENST00000517566.2_Frame_Shift_Del_p.V630fs	NM_001198532.1	NP_001185461.1	Q8N573	OXR1_HUMAN	oxidation resistance 1	631					adult walking behavior (GO:0007628)|cellular response to hydroperoxide (GO:0071447)|negative regulation of neuron apoptotic process (GO:0043524)|response to oxidative stress (GO:0006979)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)	oxidoreductase activity (GO:0016491)			NS(2)|breast(2)|endometrium(2)|large_intestine(9)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	31			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)			TTATAGTAGTAAAAAAGATTG	0.378																																					p.V631fs		Atlas-INDEL	.											.	OXR1	190	.	0			c.1892delT						.						83	89	87					8																	107726147		2203	4300	6503	SO:0001589	frameshift_variant	55074	exon10			.	AF309387	CCDS6304.2, CCDS47909.1, CCDS56547.1, CCDS56548.1, CCDS56549.1, CCDS56550.1	8q23	2013-03-14			ENSG00000164830	ENSG00000164830			15822	protein-coding gene	gene with protein product	"TBC/LysM-associated domain containing 3"	605609				11114193	Standard	NM_181354		Approved	TLDC3	uc011lht.2	Q8N573	OTTHUMG00000167682	ENST00000442977.2:c.1893delA	chr8.hg19:g.107726147delA	ENSP00000405424:p.Val631fs	245.0	0.0		223.0	14.0	NM_001198532	A6NK11|A8KA34|B3KXL1|B7Z402|B7Z8N5|D3HIS6|Q3LIB5|Q6ZVK9|Q8N8V0|Q9H266|Q9NWC7	Frame_Shift_Del	DEL	ENST00000442977.2	hg19	CCDS56548.1																																																																																			.	.		0.378	OXR1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_181354		-	107726147	A	-	107726147	7	5	282	1	0	1	0	1	0	0	0	0	11343	349	13	0	2131	0	OXR1	8	107726147	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	6473279	107726147	38637875	621	40855										
COL14A1	7373	hgsc.bcm.edu	37	chr8	121170404	121170404	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggttaagatataatgtaataTctcatgacagtatacagatt	7	4	1	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:121170404T>C	ENST00000297848.3	+	3	394	c.124T>C	c.(124-126)Tct>Cct	p.S42P	COL14A1_ENST00000309791.4_Missense_Mutation_p.S42P|COL14A1_ENST00000537875.1_Missense_Mutation_p.S42P|COL14A1_ENST00000247781.3_Missense_Mutation_p.S42P|COL14A1_ENST00000432943.2_3'UTR	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1											NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			TAATGTAATATCTCATGACAG	0.343																																					p.S42P		Atlas-SNP	.											.	COL14A1	292	.	0			c.T124C						.						69	69	69					8																	121170404		2203	4300	6503	SO:0001583	missense	7373	exon3			GTAATATCTCATG		CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"Collagens", "Fibronectin type III domain containing"	2191	protein-coding gene	gene with protein product		120324	"undulin"	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.124T>C	chr8.hg19:g.121170404T>C	ENSP00000297848:p.Ser42Pro	152.0	0.0		121.0	5.0	NM_021110		Missense_Mutation	SNP	ENST00000297848.3	hg19	CCDS34938.1	.	.	.	.	.	.	.	.	.	.	T	19.45	3.829968	0.71258	.	.	ENSG00000187955	ENST00000537875;ENST00000309791;ENST00000297848;ENST00000247781	T;T;T;T	0.59772	3.42;3.42;0.24;0.24	5.38	4.16	0.48862	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.424919	0.25109	N	0.033077	T	0.54287	0.1849	L	0.43152	1.355	0.33108	D	0.540153	D	0.53619	0.961	P	0.51324	0.666	T	0.66905	-0.5805	10	0.72032	D	0.01	.	5.4167	0.16378	0.2514:0.0:0.1447:0.6039	.	42	Q05707	COEA1_HUMAN	P	42	ENSP00000443974:S42P;ENSP00000311809:S42P;ENSP00000297848:S42P;ENSP00000247781:S42P	ENSP00000247781:S42P	S	+	1	0	COL14A1	121239585	0.996000	0.38824	0.959000	0.39883	0.992000	0.81027	1.589000	0.36644	2.035000	0.60131	0.528000	0.53228	TCT	.	.		0.343	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		C	121170404	T	C	121170404	3	2	282	1	0	0	0	0	1	0	0	0	3673	1435	50	2	130	2	COL14A1	8	121170404	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	13444257	121170404	25193618	622	40856										
MTBP	27085	hgsc.bcm.edu	37	chr8	121528183	121528183	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agatattgcttggatgaccgAaaagctttggaaagagatgg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:121528183delA	ENST00000305949.1	+	18	2043	c.1998delA	c.(1996-1998)cgafs	p.R666fs		NM_022045.4	NP_071328.2	Q96DY7	MTBP_HUMAN	MDM2 binding protein	666	Interaction with MDM2. {ECO:0000250}.				cell cycle arrest (GO:0007050)|mitotic spindle checkpoint (GO:0071174)|negative regulation of cell proliferation (GO:0008285)|protein localization to kinetochore (GO:0034501)|traversing start control point of mitotic cell cycle (GO:0007089)	chromatin (GO:0000785)|kinetochore (GO:0000776)				NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	Lung NSC(37;5.68e-08)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)			TGGATGACCGAAAAGCTTTGG	0.388																																					p.R666fs		Atlas-INDEL	.											MTBP,colon,carcinoma,0,1	MTBP	77	.	0			c.1997delG						.						85	84	84					8																	121528183		2203	4299	6502	SO:0001589	frameshift_variant	27085	exon18			.		CCDS6333.1	8q24.1-q24.2	2014-03-03	2014-03-03		ENSG00000172167	ENSG00000172167			7417	protein-coding gene	gene with protein product		605927	"MDM2 (mouse double minute 2)-binding protein, 104kD", "Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse) binding protein, 104kDa"			10906133, 11060448	Standard	NM_022045		Approved		uc003ypc.2	Q96DY7	OTTHUMG00000165040	ENST00000305949.1:c.1998delA	chr8.hg19:g.121528183delA	ENSP00000303398:p.Arg666fs	167.0	0.0		177.0	11.0	NM_022045	B4DUR5|Q9HA89	Frame_Shift_Del	DEL	ENST00000305949.1	hg19	CCDS6333.1																																																																																			.	.		0.388	MTBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381530.1	NM_022045		-	121528183	A	-	121528183	7	5	282	1	0	1	0	1	0	0	0	0	9921	233	9	0	2068	0	MTBP	8	121528183	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	357779	121528183	24835839	623	40857										
DERL1	79139	hgsc.bcm.edu	37	chr8	124031435	124031435	+	Splice_Site	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gacaggacaaaaacacttacAaaaactgaggtgtggataga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:124031435delA	ENST00000259512.4	-	7	917	c.617delT	c.(616-618)ttg>tg	p.L206fs	DERL1_ENST00000519018.1_Splice_Site_p.L106fs|DERL1_ENST00000523036.1_Splice_Site_p.L106fs|RP11-557C18.3_ENST00000521258.1_RNA|DERL1_ENST00000405944.3_Splice_Site_p.L186fs|DERL1_ENST00000419562.2_Splice_Site_p.L106fs	NM_001134671.2|NM_024295.5	NP_001128143.1|NP_077271.1	Q9BUN8	DERL1_HUMAN	derlin 1	206					endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|establishment of protein localization (GO:0045184)|intracellular transport of viral protein in host cell (GO:0019060)|response to unfolded protein (GO:0006986)|retrograde protein transport, ER to cytosol (GO:0030970)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|Hrd1p ubiquitin ligase complex (GO:0000836)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)	MHC class I protein binding (GO:0042288)|receptor activity (GO:0004872)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)	8	Lung NSC(37;1.06e-09)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)			AAACACTTACAAAAACTGAGG	0.398																																					.		Atlas-INDEL	.											.	DERL1	27	.	0			c.557+1T>-						.						92	87	89					8																	124031435		2203	4300	6503	SO:0001630	splice_region_variant	79139	exon8			.	BC002457	CCDS6337.1, CCDS47915.1	8q24.13	2012-02-01	2012-02-01		ENSG00000136986	ENSG00000136986			28454	protein-coding gene	gene with protein product		608813	"Der1-like domain family, member 1"			12975309, 15215855	Standard	NM_024295		Approved	MGC3067, PRO2577, FLJ13784, DER1, DER-1, derlin-1	uc003ypl.3	Q9BUN8	OTTHUMG00000165080	ENST00000259512.4:c.617+1T>-	chr8.hg19:g.124031435delA		216.0	0.0		182.0	11.0	NM_001134671	B3KW41|E9PH19	Splice_Site	DEL	ENST00000259512.4	hg19	CCDS6337.1																																																																																			.	.		0.398	DERL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381714.2	NM_024295	Frame_Shift_Del	-	124031435	A	-	124031435	8	5	282	1	0	1	0	1	0	0	1	0	4448	144	5	0	146	0	DERL1	8	124031435	Splice_Site	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2503252	124031435	22332587	624	40858										
ZHX1	11244	hgsc.bcm.edu	37	chr8	124266657	124266657	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	taccttgtgtcactaaaccaTtttttaatctctcctttcgt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:124266657delT	ENST00000522655.1	-	3	2070	c.1530delA	c.(1528-1530)aaafs	p.K510fs	ZHX1_ENST00000297857.2_Frame_Shift_Del_p.K510fs|ZHX1_ENST00000522595.1_5'Flank|ZHX1-C8ORF76_ENST00000357082.4_Intron|ZHX1_ENST00000395571.3_Frame_Shift_Del_p.K510fs			Q9UKY1	ZHX1_HUMAN	zinc fingers and homeoboxes 1	510	Required for interaction with NFYA.				cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(37;1.25e-09)|Ovarian(258;0.0154)		STAD - Stomach adenocarcinoma(47;0.00527)			CACTAAACCATTTTTTAATCT	0.348																																					p.W511fs		Atlas-INDEL	.											.	ZHX1	89	.	0			c.1531delT						.						122	124	124					8																	124266657		2203	4300	6503	SO:0001589	frameshift_variant	11244	exon3			.	AF106862	CCDS6342.1	8q24.13	2012-03-09	2004-01-23		ENSG00000165156	ENSG00000165156		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	12871	protein-coding gene	gene with protein product		604764	"zinc-fingers and homeoboxes 1"			10441475	Standard	NM_001017926		Approved		uc003yqe.3	Q9UKY1	OTTHUMG00000165088	ENST00000522655.1:c.1530delA	chr8.hg19:g.124266657delT	ENSP00000428821:p.Lys510fs	192.0	0.0		210.0	14.0	NM_001017926	Q8IWD8	Frame_Shift_Del	DEL	ENST00000522655.1	hg19	CCDS6342.1																																																																																			.	.		0.348	ZHX1-003	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000381759.1			-	124266657	T	-	124266657	7	5	282	1	0	1	0	1	0	0	0	0	17690	1490	52	0	1095	0	ZHX1	8	124266657	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	235222	124266657	22097365	625	40859										
FER1L6	654463	hgsc.bcm.edu	37	chr8	125110040	125110040	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcccagatacgaattgagagTgaccatctggaacactgaag	10	9	1	4			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:125110040T>G	ENST00000522917.1	+	37	5005	c.4799T>G	c.(4798-4800)gTg>gGg	p.V1600G	FER1L6_ENST00000399018.1_Missense_Mutation_p.V1600G|FER1L6-AS2_ENST00000520031.1_RNA	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	1600	C2 6. {ECO:0000255|PROSITE- ProRule:PRU00041}.					integral component of membrane (GO:0016021)				NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			GAATTGAGAGTGACCATCTGG	0.418																																					p.V1600G		Atlas-SNP	.											.	FER1L6	268	.	0			c.T4799G						.						104	98	100					8																	125110040		1998	4174	6172	SO:0001583	missense	654463	exon37			TGAGAGTGACCAT	AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"fer-1-like 6 (C. elegans)"				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.4799T>G	chr8.hg19:g.125110040T>G	ENSP00000428280:p.Val1600Gly	147.0	0.0		123.0	5.0	NM_001039112		Missense_Mutation	SNP	ENST00000522917.1	hg19	CCDS43767.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.278294	0.80692	.	.	ENSG00000214814	ENST00000522917;ENST00000399018	D;D	0.97791	-4.54;-4.54	5.5	5.5	0.81552	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.249821	0.33732	U	0.004615	D	0.98635	0.9543	H	0.94423	3.535	0.80722	D	1	P	0.37038	0.579	P	0.47118	0.538	D	0.99872	1.1098	10	0.87932	D	0	-12.879	15.9545	0.79876	0.0:0.0:0.0:1.0	.	1600	Q2WGJ9	FR1L6_HUMAN	G	1600	ENSP00000428280:V1600G;ENSP00000381982:V1600G	ENSP00000381982:V1600G	V	+	2	0	FER1L6	125179221	1.000000	0.71417	0.997000	0.53966	0.937000	0.57800	7.972000	0.88022	2.228000	0.72767	0.529000	0.55759	GTG	.	.		0.418	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112		G	125110040	T	G	125110040	3	3	282	1	0	0	0	0	1	0	0	0	5823	1696	59	5	4941	5	FER1L6	8	125110040	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	843383	125110040	21253982	626	40860										
ZFAT	57623	hgsc.bcm.edu	37	chr8	135533127	135533127	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccatacttaaaaaaattaccTcccacttggggtctccatca	4	13	2	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:135533127T>C	ENST00000377838.3	-	13	3407	c.3233A>G	c.(3232-3234)gAg>gGg	p.E1078G	ZFAT_ENST00000520356.1_Splice_Site_p.E1066G|ZFAT_ENST00000523399.1_Splice_Site_p.E1016G|ZFAT_ENST00000517307.1_5'UTR|ZFAT_ENST00000520727.1_Splice_Site_p.E1066G|ZFAT_ENST00000429442.2_Splice_Site_p.E1066G|ZFAT_ENST00000520214.1_Splice_Site_p.E1066G	NM_001174157.1|NM_020863.3	NP_001167628.1|NP_065914.2	Q9P243	ZFAT_HUMAN	zinc finger and AT hook domain containing	1078					hematopoietic progenitor cell differentiation (GO:0002244)|spongiotrophoblast layer development (GO:0060712)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(9)|large_intestine(8)|lung(16)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)			AAAAATTACCTCCCACTTGGG	0.413																																					p.E1078G		Atlas-SNP	.											.	ZFAT	265	.	0			c.A3233G						.						55	53	53					8																	135533127		1831	4080	5911	SO:0001630	splice_region_variant	57623	exon13			ATTACCTCCCACT	BC025423	CCDS43768.1, CCDS47924.1, CCDS43768.2, CCDS55275.1, CCDS55276.1	8q24.23	2008-06-05	2008-01-25	2008-01-25	ENSG00000066827	ENSG00000066827		"Zinc fingers, C2H2-type"	19899	protein-coding gene	gene with protein product		610931	"zinc finger protein 406"	ZNF406, ZFAT1		10819331, 18329245	Standard	NM_020863		Approved	KIAA1485	uc003yup.3	Q9P243	OTTHUMG00000164321	ENST00000377838.3:c.3234+1A>G	chr8.hg19:g.135533127T>C		130.0	0.0		143.0	7.0	NM_020863	B7ZL15|E9PER3|Q3MIM5|Q6PJ01|Q75PJ6|Q75PJ7|Q75PJ9|Q86X64	Missense_Mutation	SNP	ENST00000377838.3	hg19	CCDS47924.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.655457	0.88056	.	.	ENSG00000066827	ENST00000520356;ENST00000520727;ENST00000429442;ENST00000377838;ENST00000520214;ENST00000318135;ENST00000523399	T;T;T;T;T;T	0.11277	2.89;2.8;2.81;2.79;2.8;2.81	5.53	5.53	0.82687	.	0.116019	0.56097	D	0.000027	T	0.21227	0.0511	L	0.29908	0.895	0.51233	D	0.999912	D;D;D;D	0.89917	0.999;0.999;0.999;1.0	D;D;D;D	0.83275	0.986;0.994;0.951;0.996	T	0.02813	-1.1107	10	0.30078	T	0.28	-39.7844	14.5267	0.67894	0.0:0.0:0.0:1.0	.	197;1016;1066;1078	B7Z741;E9PER3;E9PBN4;Q9P243	.;.;.;ZFAT_HUMAN	G	1066;1066;1066;1078;1066;965;1016	ENSP00000427879:E1066G;ENSP00000427831:E1066G;ENSP00000394501:E1066G;ENSP00000367069:E1078G;ENSP00000428483:E1066G;ENSP00000429091:E1016G	ENSP00000326997:E965G	E	-	2	0	ZFAT	135602309	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.468000	0.73551	2.113000	0.64589	0.524000	0.50904	GAG	.	.		0.413	ZFAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378272.1	NM_001029939	Missense_Mutation	C	135533127	T	C	135533127	5	2	282	1	0	0	0	0	0	0	1	0	17647	1565	54	2	514	2	ZFAT	8	135533127	Splice_Site	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	10423087	135533127	10830895	627	40861										
FAM135B	51059	hgsc.bcm.edu	37	chr8	139151232	139151232	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgggggaaaccactgacctgTtttttggcttagttggtaga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:139151232delT	ENST00000395297.1	-	18	4068	c.3898delA	c.(3898-3900)acafs	p.T1300fs		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	1300										NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			CACTGACCTGTTTTTTGGCTT	0.443										HNSCC(54;0.14)																											p.T1300fs		Atlas-INDEL	.											LOC51059,NS,carcinoma,0,2	FAM135B	423	.	0			c.3899delC						.						108	106	106					8																	139151232		1879	4112	5991	SO:0001589	frameshift_variant	51059	exon18			.	AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.3898delA	chr8.hg19:g.139151232delT	ENSP00000378710:p.Thr1300fs	200.0	0.0		197.0	15.0	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Frame_Shift_Del	DEL	ENST00000395297.1	hg19	CCDS6375.2																																																																																			.	.		0.443	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912		-	139151232	T	-	139151232	7	5	282	1	0	1	0	1	0	0	0	0	5454	1725	60	0	334	0	FAM135B	8	139151232	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3618105	139151232	7212790	628	40862										
COL22A1	169044	hgsc.bcm.edu	37	chr8	139672699	139672699	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cggcttgccaggaggccctcTttctcctggatttcctggtg	12	13	2	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:139672699T>C	ENST00000303045.6	-	44	3711	c.3265A>G	c.(3265-3267)Aga>Gga	p.R1089G	COL22A1_ENST00000341807.4_5'UTR|COL22A1_ENST00000435777.1_Missense_Mutation_p.R1069G	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	1089	Collagen-like 9.|Gly-rich.|Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			GGAGGCCCTCTTTCTCCTGGA	0.458										HNSCC(7;0.00092)																											p.R1089G		Atlas-SNP	.											.	COL22A1	390	.	0			c.A3265G						.						67	57	61					8																	139672699		2203	4300	6503	SO:0001583	missense	169044	exon44			GCCCTCTTTCTCC	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"Collagens"	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.3265A>G	chr8.hg19:g.139672699T>C	ENSP00000303153:p.Arg1089Gly	151.0	0.0		163.0	9.0	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Missense_Mutation	SNP	ENST00000303045.6	hg19	CCDS6376.1	.	.	.	.	.	.	.	.	.	.	T	14.50	2.555107	0.45487	.	.	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	D;D	0.96073	-3.64;-3.9	4.83	4.83	0.62350	.	0.000000	0.52532	U	0.000065	D	0.97133	0.9063	M	0.82630	2.6	0.38530	D	0.948947	D;D	0.62365	0.989;0.991	D;D	0.78314	0.985;0.991	D	0.96645	0.9477	10	0.24483	T	0.36	.	10.9608	0.47385	0.0:0.0:0.0:1.0	.	1069;1089	Q8NFW1-2;Q8NFW1	.;COMA1_HUMAN	G	1089;1069;782	ENSP00000303153:R1089G;ENSP00000387655:R1069G	ENSP00000303153:R1089G	R	-	1	2	COL22A1	139741881	1.000000	0.71417	1.000000	0.80357	0.841000	0.47740	1.666000	0.37460	2.162000	0.67917	0.450000	0.29827	AGA	.	.		0.458	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257		C	139672699	T	C	139672699	3	2	282	1	0	0	0	0	1	0	0	0	3683	1617	56	2	1703	2	COL22A1	8	139672699	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	521467	139672699	6691323	629	40863										
ARC	23237	hgsc.bcm.edu	37	chr8	143694836	143694836	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcaggaactccttcttgaacTccacccagttcttcacggag	8	14	3	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:143694836T>C	ENST00000356613.2	-	1	1997	c.797A>G	c.(796-798)gAg>gGg	p.E266G	ARC_ENST00000581404.1_5'Flank	NM_015193.4	NP_056008.1	O60936	NOL3_HUMAN	activity-regulated cytoskeleton-associated protein	0					apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of gene expression (GO:0010468)|response to hypoxia (GO:0001666)|response to injury involved in regulation of muscle adaptation (GO:0014876)|RNA splicing (GO:0008380)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|sarcoplasm (GO:0016528)	identical protein binding (GO:0042802)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(3)|upper_aerodigestive_tract(1)	13	all_cancers(97;3.55e-12)|all_epithelial(106;1.03e-08)|Lung NSC(106;0.000353)|all_lung(105;0.00092)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;0.0279)				CTTCTTGAACTCCACCCAGTT	0.622																																					p.E266G		Atlas-SNP	.											.	ARC	34	.	0			c.A797G						.						43	45	44					8																	143694836		2203	4299	6502	SO:0001583	missense	23237	exon1			TTGAACTCCACCC	AF193421	CCDS34950.1	8q24.3	2008-08-01			ENSG00000198576	ENSG00000198576			648	protein-coding gene	gene with protein product		612461				10970730, 17466953	Standard	NM_015193		Approved	KIAA0278, Arg3.1	uc003ywn.2	Q7LC44	OTTHUMG00000134310	ENST00000356613.2:c.797A>G	chr8.hg19:g.143694836T>C	ENSP00000349022:p.Glu266Gly	115.0	0.0		117.0	7.0	NM_015193	B4DFL0|O60937	Missense_Mutation	SNP	ENST00000356613.2	hg19	CCDS34950.1	.	.	.	.	.	.	.	.	.	.	T	19.84	3.901245	0.72754	.	.	ENSG00000198576	ENST00000356613	.	.	.	4.92	4.92	0.64577	.	0.000000	0.47455	U	0.000223	T	0.49795	0.1578	N	0.19112	0.55	0.38121	D	0.937841	D	0.54964	0.969	P	0.53313	0.723	T	0.59043	-0.7528	9	0.59425	D	0.04	-17.5234	13.7151	0.62691	0.0:0.0:0.0:1.0	.	266	Q7LC44	ARC_HUMAN	G	266	.	ENSP00000349022:E266G	E	-	2	0	ARC	143691838	0.958000	0.32768	1.000000	0.80357	0.993000	0.82548	1.921000	0.40035	1.840000	0.53500	0.379000	0.24179	GAG	.	.		0.622	ARC-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259274.2			C	143694836	T	C	143694836	3	2	282	1	0	0	0	0	1	0	0	0	841	1551	54	2	397	2	ARC	8	143694836	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	4022137	143694836	2669186	630	40864										
MAPK15	225689	hgsc.bcm.edu	37	chr8	144801240	144801240	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcccgctccctgggcgacctCcccgaggggcctgaggacca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:144801240delC	ENST00000338033.4	+	6	614	c.495delC	c.(493-495)ctcfs	p.L165fs	RP11-429J17.5_ENST00000527908.1_RNA|MAPK15_ENST00000395108.2_Frame_Shift_Del_p.L165fs|MAPK15_ENST00000395107.4_Frame_Shift_Del_p.L182fs	NM_139021.2	NP_620590.2	Q8TD08	MK15_HUMAN	mitogen-activated protein kinase 15	165	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				MAPK cascade (GO:0000165)|negative regulation of DNA replication (GO:0008156)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|response to estradiol (GO:0032355)	extracellular region (GO:0005576)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|SH3 domain binding (GO:0017124)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|stomach(1)	12	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			TGGGCGACCTCCCCGAGGGGC	0.642																																					p.L165fs		Atlas-INDEL	.											.	MAPK15	32	.	0			c.494delT						.						29	28	28					8																	144801240		2199	4297	6496	SO:0001589	frameshift_variant	225689	exon6			.	AY065978	CCDS6409.2	8q24.3	2011-06-09			ENSG00000181085	ENSG00000181085		"Mitogen-activated protein kinase cascade / Kinases"	24667	protein-coding gene	gene with protein product	"extracellular signal regulated kinase 8"					11875070	Standard	XM_006716528		Approved	ERK8, ERK7	uc003yzj.3	Q8TD08	OTTHUMG00000146450	ENST00000338033.4:c.495delC	chr8.hg19:g.144801240delC	ENSP00000337691:p.Leu165fs	137.0	0.0		143.0	10.0	NM_139021	Q2TCF9|Q8N362	Frame_Shift_Del	DEL	ENST00000338033.4	hg19	CCDS6409.2																																																																																			.	.		0.642	MAPK15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000300348.1	NM_139021		-	144801240	C	-	144801240	7	5	282	1	0	1	0	1	0	0	0	0	9286	842	30	0	517	0	MAPK15	8	144801240	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1106404	144801240	1562782	631	40865										
EPPK1	83481	hgsc.bcm.edu	37	chr8	144946981	144946981	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tggacctccagccagctctgCcccagggccctgtccacaac							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:144946981delC	ENST00000525985.1	-	2	512	c.441delG	c.(439-441)gggfs	p.G147fs				P58107	EPIPL_HUMAN	epiplakin 1	147						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GCCAGCTCTGCCCCAGGGCCC	0.697																																					p.Q148fs		Atlas-INDEL	.											.	EPPK1	199	.	0			c.442delC						.						15	18	17					8																	144946981		1905	4054	5959	SO:0001589	frameshift_variant	83481	exon1			.	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"epidermal autoantigen 450K"	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.441delG	chr8.hg19:g.144946981delC	ENSP00000436337:p.Gly147fs	191.0	0.0		172.0	11.0	NM_031308	Q76E58|Q9NSU9	Frame_Shift_Del	DEL	ENST00000525985.1	hg19																																																																																				.	.		0.697	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		-	144946981	C	-	144946981	7	5	282	1	0	1	0	1	0	0	0	0	5192	726	26	0	6825	0	EPPK1	8	144946981	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	145741	144946981	1417041	632	40866										
ADCK5	203054	hgsc.bcm.edu	37	chr8	145617320	145617320	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cggaaaggcccggacgggaaAgcggagctggtgctgctgga	19	9	0	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:145617320A>G	ENST00000308860.6	+	11	1169	c.1125A>G	c.(1123-1125)aaA>aaG	p.K375K	CPSF1_ENST00000531727.1_5'Flank|MIR939_ENST00000401314.1_RNA	NM_174922.3	NP_777582.4	Q3MIX3	ADCK5_HUMAN	aarF domain containing kinase 5	375	Protein kinase.					integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|lung(2)|prostate(2)|skin(1)|stomach(2)	8	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;8.96e-41)|Epithelial(56;4.08e-40)|all cancers(56;4.51e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			CGGACGGGAAAGCGGAGCTGG	0.667																																					p.K375K		Atlas-SNP	.											.	ADCK5	36	.	0			c.A1125G						.						24	27	26					8																	145617320		2189	4296	6485	SO:0001819	synonymous_variant	203054	exon11			CGGGAAAGCGGAG	BC032402	CCDS34965.1, CCDS34965.2	8q24.3	2004-07-06			ENSG00000173137	ENSG00000173137			21738	protein-coding gene	gene with protein product							Standard	NM_174922		Approved	FLJ35454	uc003zch.3	Q3MIX3	OTTHUMG00000165190	ENST00000308860.6:c.1125A>G	chr8.hg19:g.145617320A>G		100.0	0.0		128.0	6.0	NM_174922	B3KS46|Q5U4P1|Q6P2S4|Q8N5V3	Silent	SNP	ENST00000308860.6	hg19	CCDS34965.1																																																																																			.	.		0.667	ADCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382556.2	NM_174922		G	145617320	A	G	145617320	2	3	282	1	0	0	0	0	0	0	0	1	291	69	3	2		2	ADCK5	8	145617320	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	670339	145617320	746702	633	40867										
KIFC2	90990	hgsc.bcm.edu	37	chr8	145692926	145692926	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcagtcccaggcgagccactGggggatgagacccagggaca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:145692926delG	ENST00000301332.2	+	5	905	c.528delG	c.(526-528)ctgfs	p.L176fs	CYHR1_ENST00000438911.2_5'Flank|KIFC2_ENST00000301331.5_5'Flank|CYHR1_ENST00000306145.5_5'Flank|CTD-2517M22.16_ENST00000525461.1_RNA|CYHR1_ENST00000424149.2_5'Flank|CYHR1_ENST00000403000.2_5'Flank	NM_145754.2	NP_665697.1	Q96AC6	KIFC2_HUMAN	kinesin family member C2	176					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(7)|ovary(3)|prostate(3)|skin(2)|urinary_tract(1)	19	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			GCGAGCCACTGGGGGATGAGA	0.627											OREG0019057	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L176fs		Atlas-INDEL	.											.	KIFC2	53	.	0			c.527delT						.						63	67	66					8																	145692926		2202	4300	6502	SO:0001589	frameshift_variant	90990	exon5			.	AY007121	CCDS6427.1	8q24.3	2007-02-13			ENSG00000167702	ENSG00000167702		"Kinesins"	29530	protein-coding gene	gene with protein product						9115737	Standard	NM_145754		Approved		uc003zcz.3	Q96AC6	OTTHUMG00000165133	ENST00000301332.2:c.528delG	chr8.hg19:g.145692926delG	ENSP00000301332:p.Leu176fs	146.0	0.0	1696	161.0	10.0	NM_145754	E9PHB2|Q96NN6	Frame_Shift_Del	DEL	ENST00000301332.2	hg19	CCDS6427.1																																																																																			.	.		0.627	KIFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382052.2	NM_145754		-	145692926	G	-	145692926	7	5	282	1	0	1	0	1	0	0	0	0	8322	1335	47	0	546	0	KIFC2	8	145692926	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	75606	145692926	671096	634	40868										
ARHGAP39	80728	hgsc.bcm.edu	37	chr8	145759584	145759584	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggcatacgtgcttatcgccaCccctggaaaggaaaggggcc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:145759584delC	ENST00000276826.5	-	6	2725	c.2524delG	c.(2524-2526)gtgfs	p.V842fs	ARHGAP39_ENST00000540274.1_Frame_Shift_Del_p.V842fs|ARHGAP39_ENST00000377307.2_Frame_Shift_Del_p.V873fs			Q9C0H5	RHG39_HUMAN	Rho GTPase activating protein 39	842	MyTH4. {ECO:0000255|PROSITE- ProRule:PRU00359}.				axon guidance (GO:0007411)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	22						CTTATCGCCACCCCTGGAAAG	0.647																																					p.V873fs		Atlas-INDEL	.											.	ARHGAP39	80	.	0			c.2618delT						.						95	90	91					8																	145759584		2203	4300	6503	SO:0001589	frameshift_variant	80728	exon9			.		CCDS34971.1	8q24.3	2011-06-29			ENSG00000147799	ENSG00000147799		"Rho GTPase activating proteins"	29351	protein-coding gene	gene with protein product	"RhoGAP93B homolog (Drosophila)", "crossGAP homolog (Drosophila)"	615880				15755809	Standard	XM_005272344		Approved	KIAA1688, Vilse, CrGAP	uc003zds.1	Q9C0H5	OTTHUMG00000165182	ENST00000276826.5:c.2524delG	chr8.hg19:g.145759584delC	ENSP00000276826:p.Val842fs	233.0	0.0		235.0	15.0	NM_025251	B4E1I1	Frame_Shift_Del	DEL	ENST00000276826.5	hg19																																																																																				.	.		0.647	ARHGAP39-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382509.1			-	145759584	C	-	145759584	7	5	282	1	0	1	0	1	0	0	0	0	884	507	18	0	747	0	ARHGAP39	8	145759584	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	66658	145759584	604438	635	40869										
DMRT3	58524	hgsc.bcm.edu	37	chr9	977116	977116	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gccgcaaccatggcgtcctgTcctggctcaagggccacaag	12	15	1	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:977116T>C	ENST00000190165.2	+	1	153	c.115T>C	c.(115-117)Tcc>Ccc	p.S39P		NM_021240.2	NP_067063.1	Q9NQL9	DMRT3_HUMAN	doublesex and mab-3 related transcription factor 3	39					adult walking behavior (GO:0007628)|male sex differentiation (GO:0046661)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|sex differentiation (GO:0007548)|transcription, DNA-templated (GO:0006351)|transmission of nerve impulse (GO:0019226)|ventral spinal cord interneuron specification (GO:0021521)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	26		all_lung(10;1.39e-08)|Lung NSC(10;1.42e-08)		Lung(218;0.0196)		TGGCGTCCTGTCCTGGCTCAA	0.682																																					p.S39P		Atlas-SNP	.											.	DMRT3	83	.	0			c.T115C						.						23	19	21					9																	977116		2200	4299	6499	SO:0001583	missense	58524	exon1			GTCCTGTCCTGGC	AJ301581	CCDS6443.1	9p24.3	2008-07-21	2001-12-17	2001-12-07	ENSG00000064218	ENSG00000064218			13909	protein-coding gene	gene with protein product	"testis-specific protein"	614754	"DMRT-like family A3"	DMRTA3		11543627, 10729223	Standard	NM_021240		Approved		uc003zgw.2	Q9NQL9	OTTHUMG00000019436	ENST00000190165.2:c.115T>C	chr9.hg19:g.977116T>C	ENSP00000190165:p.Ser39Pro	168.0	0.0		94.0	4.0	NM_021240	Q7LA03|Q7LCH8|Q96SC7|Q9NRQ9	Missense_Mutation	SNP	ENST00000190165.2	hg19	CCDS6443.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.438993	0.83885	.	.	ENSG00000064218	ENST00000190165	T	0.29655	1.56	3.75	3.75	0.43078	DM DNA-binding (6);	0.000000	0.85682	D	0.000000	T	0.63792	0.2541	M	0.93375	3.41	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	T	0.74281	-0.3716	10	0.87932	D	0	-27.9163	12.7597	0.57356	0.0:0.0:0.0:1.0	.	39	Q9NQL9	DMRT3_HUMAN	P	39	ENSP00000190165:S39P	ENSP00000190165:S39P	S	+	1	0	DMRT3	967116	1.000000	0.71417	1.000000	0.80357	0.867000	0.49689	4.136000	0.58004	1.465000	0.48006	0.379000	0.24179	TCC	.	.		0.682	DMRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051490.1	NM_021240		C	977116	T	C	977116	3	2	282	1	0	0	0	0	1	0	0	0	4589	1667	58	2	117	2	DMRT3	9	977116	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10		977116	140236315	636	40870										
KIAA0020	9933	hgsc.bcm.edu	37	chr9	2834151	2834151	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgaagtcatcccatttgggcTtcttggctgctgattctagt	10	9	3	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:2834151T>C	ENST00000397885.2	-	4	526	c.320A>G	c.(319-321)aAg>aGg	p.K107R		NM_014878.4	NP_055693.4	Q15397	K0020_HUMAN	KIAA0020	107						endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(50;0.0319)		CCATTTGGGCTTCTTGGCTGC	0.348																																					p.K107R		Atlas-SNP	.											.	KIAA0020	56	.	0			c.A320G						.						68	69	69					9																	2834151		2202	4300	6502	SO:0001583	missense	9933	exon4			TTGGGCTTCTTGG	AL832239	CCDS6448.2	9p24.2	2012-11-29			ENSG00000080608	ENSG00000080608			29676	protein-coding gene	gene with protein product	"penguin homolog (Drosophila)", "minor histocompatibility antigen HA-8"	609960				7584026, 7584028, 21266351	Standard	NM_014878		Approved	XTP5, PEN, PUF6, hPUF-A, HA-8	uc003zhp.1	Q15397	OTTHUMG00000019450	ENST00000397885.2:c.320A>G	chr9.hg19:g.2834151T>C	ENSP00000380982:p.Lys107Arg	112.0	0.0		96.0	4.0	NM_014878	A8K804|Q547G7|Q5SZY9|Q6IB47|Q96B27|Q96L78|Q96L79|Q96L80	Missense_Mutation	SNP	ENST00000397885.2	hg19	CCDS6448.2	.	.	.	.	.	.	.	.	.	.	T	16.16	3.044148	0.55110	.	.	ENSG00000080608	ENST00000397885	T	0.29655	1.56	5.54	4.41	0.53225	.	0.000000	0.85682	D	0.000000	T	0.50973	0.1647	M	0.74389	2.26	0.58432	D	0.999997	D	0.71674	0.998	D	0.63793	0.918	T	0.51888	-0.8648	10	0.54805	T	0.06	-2.1886	11.3176	0.49401	0.0:0.0711:0.0:0.9289	.	107	Q15397	K0020_HUMAN	R	107	ENSP00000380982:K107R	ENSP00000380982:K107R	K	-	2	0	KIAA0020	2824151	1.000000	0.71417	0.993000	0.49108	0.596000	0.36781	6.420000	0.73349	0.944000	0.37579	-0.250000	0.11733	AAG	.	.		0.348	KIAA0020-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051529.3	NM_014878		C	2834151	T	C	2834151	3	2	282	1	0	0	0	0	1	0	0	0	8161	1609	56	2	1686	2	KIAA0020	9	2834151	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1857035	2834151	138379280	637	40871										
JAK2	3717	hgsc.bcm.edu	37	chr9	5077574	5077574	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagttggcatgggccatgcaTtttctagtaagtagtacaac							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:5077574delT	ENST00000381652.3	+	15	2480	c.1986delT	c.(1984-1986)catfs	p.H662fs	JAK2_ENST00000539801.1_Frame_Shift_Del_p.H662fs|AL161450.1_ENST00000601793.1_Intron|JAK2_ENST00000544510.1_Frame_Shift_Del_p.H513fs	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	662	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)		BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	GGGCCATGCATTTTCTAGTAA	0.244		1	"T, Mis, O"	"ETV6, PCM1, BCR"	"ALL, AML, MPD,  CML"				Polycythemia Vera, Familial																												p.H662fs		Atlas-INDEL	.		Dom	yes		9	9p24	3717	Janus kinase 2		L	.	JAK2	35466	.	0			c.1985delA						.						19	22	21					9																	5077574		2120	4217	6337	SO:0001589	frameshift_variant	3717	exon15	Familial Cancer Database		.		CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"SH2 domain containing"	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.1986delT	chr9.hg19:g.5077574delT	ENSP00000371067:p.His662fs	122.0	0.0		164.0	10.0	NM_004972	O14636|O75297	Frame_Shift_Del	DEL	ENST00000381652.3	hg19	CCDS6457.1																																																																																			.	.		0.244	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1			-	5077574	T	-	5077574	7	5	282	1	0	1	0	1	0	0	0	0	7947	1490	52	0	2036	0	JAK2	9	5077574	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2243423	5077574	136135857	638	40872										
RANBP6	26953	hgsc.bcm.edu	37	chr9	6015153	6015153	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caacttcccatagaaccacaTttttggagtagattgaatca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:6015153delT	ENST00000259569.5	-	1	465	c.455delA	c.(454-456)aatfs	p.N152fs	RANBP6_ENST00000485372.1_Intron	NM_001243202.1|NM_001243203.1|NM_012416.3	NP_001230131.1|NP_001230132.1|NP_036548.1	O60518	RNBP6_HUMAN	RAN binding protein 6	152					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(5)|large_intestine(8)|lung(9)|ovary(7)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	51		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00522)|Lung(218;0.101)		TAGAACCACATTTTTGGAGTA	0.438																																					p.N152fs		Atlas-INDEL	.											.	RANBP6	127	.	0			c.456delT						.						52	53	53					9																	6015153		2203	4300	6503	SO:0001589	frameshift_variant	26953	exon1			.	AF039023	CCDS6467.1	9p24.1	2008-03-26			ENSG00000137040	ENSG00000137040			9851	protein-coding gene	gene with protein product							Standard	NM_001243202		Approved		uc003zjr.3	O60518	OTTHUMG00000019512	ENST00000259569.5:c.455delA	chr9.hg19:g.6015153delT	ENSP00000259569:p.Asn152fs	181.0	0.0		159.0	10.0	NM_012416	Q5T7X4|Q7Z3V2|Q96E78	Frame_Shift_Del	DEL	ENST00000259569.5	hg19	CCDS6467.1																																																																																			.	.		0.438	RANBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051650.1	NM_012416		-	6015153	T	-	6015153	7	5	282	1	0	1	0	1	0	0	0	0	13046	1493	52	0	2866	0	RANBP6	9	6015153	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	937579	6015153	135198278	639	40873										
MPDZ	8777	hgsc.bcm.edu	37	chr9	13123168	13123168	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcaccagcagcgtgtctgaaCccccaacgatgctcaggccc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:13123168delC	ENST00000319217.7	-	36	5184	c.4937delG	c.(4936-4938)ggtfs	p.G1646fs	MPDZ_ENST00000541093.1_5'UTR|MPDZ_ENST00000546205.1_Frame_Shift_Del_p.G1660fs|MPDZ_ENST00000538841.1_Frame_Shift_Del_p.G505fs|MPDZ_ENST00000536827.1_Frame_Shift_Del_p.G1613fs|MPDZ_ENST00000541718.1_Frame_Shift_Del_p.G1646fs|MPDZ_ENST00000381015.4_Frame_Shift_Del_p.G1646fs|MPDZ_ENST00000447879.1_Frame_Shift_Del_p.G1613fs|MPDZ_ENST00000381022.2_Frame_Shift_Del_p.G1646fs	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	1646	PDZ 10. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		CGTGTCTGAACCCCCAACGAT	0.557																																					p.G1646fs		Atlas-INDEL	.											.	MPDZ	324	.	0			c.4938delT						.						50	52	52					9																	13123168		1939	4140	6079	SO:0001589	frameshift_variant	8777	exon36			.	AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.4937delG	chr9.hg19:g.13123168delC	ENSP00000320006:p.Gly1646fs	202.0	0.0		145.0	10.0	NM_003829	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Frame_Shift_Del	DEL	ENST00000319217.7	hg19																																																																																				.	.		0.557	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829		-	13123168	C	-	13123168	7	5	282	1	0	1	0	1	0	0	0	0	9731	507	18	0	1232	0	MPDZ	9	13123168	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	7108015	13123168	128090263	640	40874										
RPS6	6194	hgsc.bcm.edu	37	chr9	19378464	19378464	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgctagctcttttggggcccAggcggcgaggcactgtagta	15	10	1	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:19378464A>G	ENST00000380394.4	-	4	456	c.398T>C	c.(397-399)cTg>cCg	p.L133P	RP11-513M16.8_ENST00000609982.1_RNA|RPS6_ENST00000498815.1_5'Flank|RPS6_ENST00000315377.4_Missense_Mutation_p.L102P|RPS6_ENST00000380384.1_Missense_Mutation_p.L102P	NM_001010.2	NP_001001.2	P62753	RS6_HUMAN	ribosomal protein S6	133					activation-induced cell death of T cells (GO:0006924)|cellular protein metabolic process (GO:0044267)|erythrocyte development (GO:0048821)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation (GO:0007369)|gene expression (GO:0010467)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|oogenesis stage (GO:0022605)|placenta development (GO:0001890)|positive regulation of apoptotic process (GO:0043065)|ribosomal small subunit assembly (GO:0000028)|ribosomal small subunit biogenesis (GO:0042274)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|T cell differentiation in thymus (GO:0033077)|T cell proliferation involved in immune response (GO:0002309)|TOR signaling (GO:0031929)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|dendrite (GO:0030425)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|small ribosomal subunit (GO:0015935)	poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural constituent of ribosome (GO:0003735)			endometrium(3)|lung(2)|ovary(1)|urinary_tract(1)	7		Colorectal(97;3.46e-05)|Myeloproliferative disorder(762;0.0255)		Lung(42;0.161)|LUSC - Lung squamous cell carcinoma(42;0.234)		TTTGGGGCCCAGGCGGCGAGG	0.418																																					p.L133P		Atlas-SNP	.											.	RPS6	25	.	0			c.T398C						.						67	68	68					9																	19378464		2203	4300	6503	SO:0001583	missense	6194	exon4			GGGCCCAGGCGGC		CCDS6492.1	9p21	2011-04-05			ENSG00000137154	ENSG00000137154		"S ribosomal proteins"	10429	protein-coding gene	gene with protein product	"40S ribosomal protein S6", "phosphoprotein NP33"	180460				1577483	Standard	NM_001010		Approved	S6	uc003znv.1	P62753	OTTHUMG00000019642	ENST00000380394.4:c.398T>C	chr9.hg19:g.19378464A>G	ENSP00000369757:p.Leu133Pro	139.0	0.0		105.0	5.0	NM_001010	P08227|P10660|Q4VBY7|Q8N6Z7	Missense_Mutation	SNP	ENST00000380394.4	hg19	CCDS6492.1	.	.	.	.	.	.	.	.	.	.	A	17.05	3.289660	0.59976	.	.	ENSG00000137154	ENST00000380394;ENST00000380384;ENST00000315377	T;T;T	0.54675	0.57;0.56;0.56	5.32	5.32	0.75619	.	0.000000	0.64402	D	0.000001	T	0.74824	0.3767	M	0.84948	2.725	0.80722	D	1	D;B	0.89917	1.0;0.366	D;B	0.74348	0.983;0.25	T	0.78725	-0.2092	9	.	.	.	-10.2462	15.5723	0.76349	1.0:0.0:0.0:0.0	.	102;133	A2A3R5;P62753	.;RS6_HUMAN	P	133;102;102	ENSP00000369757:L133P;ENSP00000369745:L102P;ENSP00000369743:L102P	.	L	-	2	0	RPS6	19368464	1.000000	0.71417	1.000000	0.80357	0.459000	0.32528	9.190000	0.94934	2.139000	0.66308	0.533000	0.62120	CTG	.	.		0.418	RPS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051858.1	NM_001010		G	19378464	A	G	19378464	3	3	282	1	0	0	0	0	1	0	0	0	13664	188	7	2	363	2	RPS6	9	19378464	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	6255296	19378464	121834967	641	40875										
IFNA16	3449	hgsc.bcm.edu	37	chr9	21216773	21216773	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcctttttgcaagtttgttgAaaaagagaaggatctcatga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:21216773delA	ENST00000380216.1	-	1	537	c.532delT	c.(532-534)tcafs	p.S178fs		NM_002173.2	NP_002164.1	P05015	IFN16_HUMAN	interferon, alpha 16	178					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)	13				Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.116)		AAGTTTGTTGAAAAAGAGAAG	0.368																																					p.S178X		Atlas-INDEL	.											.	IFNA16	27	.	0			c.533delC						.						211	203	205					9																	21216773		2203	4300	6503	SO:0001589	frameshift_variant	3449	exon1			.		CCDS34996.1	9p22	2010-12-10			ENSG00000147885	ENSG00000147885		"Interferons"	5421	protein-coding gene	gene with protein product		147580				1385305	Standard	NM_002173		Approved	IFN-alphaO	uc003zor.1	P05015	OTTHUMG00000019663	ENST00000380216.1:c.532delT	chr9.hg19:g.21216773delA	ENSP00000369564:p.Ser178fs	448.0	0.0		312.0	22.0	NM_002173	Q5VV12	Frame_Shift_Del	DEL	ENST00000380216.1	hg19	CCDS34996.1																																																																																			.	.		0.368	IFNA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051892.1	NM_002173		-	21216773	A	-	21216773	7	5	282	1	0	1	0	1	0	0	0	0	7544	246	9	0	41	0	IFNA16	9	21216773	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1838309	21216773	119996658	642	40876										
IFNA17	3451	hgsc.bcm.edu	37	chr9	21227622	21227622	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttcaatccttcctccttaatAttttttgcaagtttgttgaa					rs9298814	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:21227622delA	ENST00000413767.2	-	1	599	c.551delT	c.(550-552)atafs	p.I184fs		NM_021268.2	NP_067091.1	P01571	IFN17_HUMAN	interferon, alpha 17	184			I -> R (in dbSNP:rs9298814). {ECO:0000269|PubMed:3767336, ECO:0000269|PubMed:4008999, ECO:0000269|PubMed:9712362}.		adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			breast(1)|endometrium(2)|lung(4)|ovary(1)|skin(1)	9				Lung(24;2.13e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.116)		CCTCCTTAATATTTTTTGCAA	0.378																																					p.I184fs		Atlas-INDEL	.											.	IFNA17	17	.	0			c.552delA	GRCh37	CM041015	IFNA17	M	rs9298814	.						112	143	133					9																	21227622		2197	4296	6493	SO:0001589	frameshift_variant	3451	exon1			.		CCDS6500.1	9p22	2010-12-10			ENSG00000234829	ENSG00000234829		"Interferons"	5422	protein-coding gene	gene with protein product		147583				1385305	Standard	NM_021268		Approved	LEIF2C1, IFN-alphaI	uc003zos.1	P01571	OTTHUMG00000019667	ENST00000413767.2:c.551delT	chr9.hg19:g.21227622delA	ENSP00000411940:p.Ile184fs	426.0	0.0		344.0	24.0	NM_021268	Q14639|Q4KMT4|Q5VZ53|Q7M4Q4	Frame_Shift_Del	DEL	ENST00000413767.2	hg19	CCDS6500.1																																																																																			.	.		0.378	IFNA17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051896.1	NM_021268		-	21227622	A	-	21227622	7	5	282	1	0	1	0	1	0	0	0	0	7545	449	16	0	22	0	IFNA17	9	21227622	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	10849	21227622	119985809	643	40877										
TEK	7010	hgsc.bcm.edu	37	chr9	27169606	27169606	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaaacctcttcacctcggccTtcaccaggctgatagtccgg	9	15	3	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:27169606T>C	ENST00000380036.4	+	4	1049	c.607T>C	c.(607-609)Ttc>Ctc	p.F203L	TEK_ENST00000406359.4_Missense_Mutation_p.F203L|TEK_ENST00000519097.1_Missense_Mutation_p.F99L	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	203					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	CACCTCGGCCTTCACCAGGCT	0.473																																					p.F203L		Atlas-SNP	.											TEK_ENST00000380036,colon,carcinoma,0,4	TEK	250	.	0			c.T607C						.						105	97	100					9																	27169606		2203	4300	6503	SO:0001583	missense	7010	exon4			TCGGCCTTCACCA	L06139	CCDS6519.1, CCDS75825.1	9p21	2013-02-11	2008-07-31		ENSG00000120156	ENSG00000120156		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	11724	protein-coding gene	gene with protein product		600221	"venous malformations, multiple cutaneous and mucosal"	VMCM		1312667, 7833915	Standard	XM_005251561		Approved	TIE2, TIE-2, VMCM1, CD202b	uc003zqi.4	Q02763	OTTHUMG00000019712	ENST00000380036.4:c.607T>C	chr9.hg19:g.27169606T>C	ENSP00000369375:p.Phe203Leu	101.0	0.0		82.0	4.0	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Missense_Mutation	SNP	ENST00000380036.4	hg19	CCDS6519.1	.	.	.	.	.	.	.	.	.	.	T	19.77	3.888708	0.72524	.	.	ENSG00000120156	ENST00000519097;ENST00000380036;ENST00000346448;ENST00000406359;ENST00000519080	T;T;T;T	0.71103	-0.51;-0.5;-0.54;3.11	5.48	5.48	0.80851	Immunoglobulin-like fold (1);	0.123114	0.37348	N	0.002137	T	0.61185	0.2327	L	0.35487	1.065	0.40886	D	0.984034	B;P;P;P;P;P	0.48640	0.243;0.821;0.913;0.646;0.646;0.688	B;B;B;B;B;B	0.41036	0.066;0.346;0.234;0.091;0.158;0.157	T	0.62987	-0.6737	10	0.31617	T	0.26	.	15.5207	0.75862	0.0:0.0:0.0:1.0	.	99;236;203;56;203;203	E7EWI2;Q59HG2;B5A953;E5RIV9;B4DHD3;Q02763	.;.;.;.;.;TIE2_HUMAN	L	99;203;203;203;56	ENSP00000430686:F99L;ENSP00000369375:F203L;ENSP00000383977:F203L;ENSP00000428337:F56L	ENSP00000343716:F203L	F	+	1	0	TEK	27159606	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.758000	0.55220	2.211000	0.71520	0.459000	0.35465	TTC	.	.		0.473	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3			C	27169606	T	C	27169606	3	2	282	1	0	0	0	0	1	0	0	0	15766	1609	56	2	621	2	TEK	9	27169606	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	5941984	27169606	114043825	644	40878										
ACO1	48	hgsc.bcm.edu	37	chr9	32418340	32418340	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcccagtggggttcccaggcTtttcacaacatgcggattat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:32418340delT	ENST00000309951.6	+	6	627	c.489delT	c.(487-489)gctfs	p.A163fs	ACO1_ENST00000541043.1_Frame_Shift_Del_p.A64fs|ACO1_ENST00000379923.1_Frame_Shift_Del_p.A163fs	NM_002197.2	NP_002188.1	P21399	ACOC_HUMAN	aconitase 1, soluble	163					cellular iron ion homeostasis (GO:0006879)|citrate metabolic process (GO:0006101)|intestinal absorption (GO:0050892)|post-embryonic development (GO:0009791)|regulation of translation (GO:0006417)|response to iron(II) ion (GO:0010040)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|endometrium(7)|kidney(5)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	30			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)		GTTCCCAGGCTTTTCACAACA	0.463																																					p.A163fs		Atlas-INDEL	.											.	ACO1	149	.	0			c.488delC						.						67	70	69					9																	32418340		2203	4300	6503	SO:0001589	frameshift_variant	48	exon6			.	M58510	CCDS6525.1	9p21.1	2013-05-21			ENSG00000122729	ENSG00000122729	4.2.1.3		117	protein-coding gene	gene with protein product	"aconitate hydratase, cytoplasmic"	100880		IREB1		2172968, 2771641	Standard	NM_002197		Approved	IRP1, IREBP	uc003zqw.4	P21399	OTTHUMG00000019740	ENST00000309951.6:c.489delT	chr9.hg19:g.32418340delT	ENSP00000309477:p.Ala163fs	252.0	0.0		193.0	12.0	NM_002197	D3DRK7|Q14652|Q5VZA7	Frame_Shift_Del	DEL	ENST00000309951.6	hg19	CCDS6525.1																																																																																			.	.		0.463	ACO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051998.3	NM_002197		-	32418340	T	-	32418340	7	5	282	1	0	1	0	1	0	0	0	0	146	1596	56	0	507	0	ACO1	9	32418340	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	5248734	32418340	108795091	645	40879										
NFX1	4799	hgsc.bcm.edu	37	chr9	33307273	33307273	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tagaaagaaacagcctggccAggactgcccacattcctgta	9	12	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:33307273A>G	ENST00000379540.3	+	5	1414	c.1352A>G	c.(1351-1353)cAg>cGg	p.Q451R	NFX1_ENST00000379521.4_Missense_Mutation_p.Q451R|NFX1_ENST00000318524.6_Missense_Mutation_p.Q451R	NM_002504.4	NP_002495.2	Q12986	NFX1_HUMAN	nuclear transcription factor, X-box binding 1	451					inflammatory response (GO:0006954)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25			LUSC - Lung squamous cell carcinoma(29;0.00506)	GBM - Glioblastoma multiforme(74;0.224)		CAGCCTGGCCAGGACTGCCCA	0.458																																					p.Q451R		Atlas-SNP	.											.	NFX1	85	.	0			c.A1352G						.						151	147	148					9																	33307273		2203	4300	6503	SO:0001583	missense	4799	exon5			CTGGCCAGGACTG	U19759	CCDS6538.1, CCDS6539.1, CCDS6540.1	9p12	2013-12-13			ENSG00000086102	ENSG00000086102			7803	protein-coding gene	gene with protein product		603255				7964459, 2511169	Standard	NM_002504		Approved	NFX2, MGC20369, Tex42, TEG-42	uc003zsq.3	Q12986	OTTHUMG00000019772	ENST00000379540.3:c.1352A>G	chr9.hg19:g.33307273A>G	ENSP00000368856:p.Gln451Arg	207.0	0.0		128.0	6.0	NM_147134	A8K6H8|Q5VXW6|Q96EL5|Q9BXI1	Missense_Mutation	SNP	ENST00000379540.3	hg19	CCDS6538.1	.	.	.	.	.	.	.	.	.	.	A	10.65	1.408916	0.25378	.	.	ENSG00000086102	ENST00000379540;ENST00000379521;ENST00000536210;ENST00000318524	T;T;T	0.41400	1.0;1.0;1.0	5.47	5.47	0.80525	.	0.208500	0.41194	D	0.000927	T	0.40398	0.1115	L	0.41824	1.3	0.23769	N	0.996897	D;D;P;D;B	0.63880	0.993;0.976;0.88;0.986;0.139	P;B;B;P;B	0.52646	0.705;0.274;0.424;0.561;0.176	T	0.25502	-1.0130	10	0.15499	T	0.54	-4.8251	8.9071	0.35530	0.8338:0.0:0.0:0.1662	.	451;335;451;451;451	F5GXD0;A0JLR2;Q12986;Q12986-2;Q12986-3	.;.;NFX1_HUMAN;.;.	R	451	ENSP00000368856:Q451R;ENSP00000368836:Q451R;ENSP00000317695:Q451R	ENSP00000317695:Q451R	Q	+	2	0	NFX1	33297273	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.683000	0.37638	2.092000	0.63282	0.477000	0.44152	CAG	.	.		0.458	NFX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052069.1			G	33307273	A	G	33307273	3	3	282	1	0	0	0	0	1	0	0	0	10396	188	7	2	1370	2	NFX1	9	33307273	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	888933	33307273	107906158	646	40880										
AQP3	360	hgsc.bcm.edu	37	chr9	33442208	33442208	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccaccaccaatgctggccggTcctggggggacagacactca	12	15	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:33442208T>C	ENST00000297991.4	-	6	792	c.712A>G	c.(712-714)Acc>Gcc	p.T238A	AQP3_ENST00000493581.1_5'UTR	NM_004925.4	NP_004916.1	Q92482	AQP3_HUMAN	aquaporin 3 (Gill blood group)	238					excretion (GO:0007588)|odontogenesis (GO:0042476)|positive regulation of immune system process (GO:0002684)|regulation of keratinocyte differentiation (GO:0045616)|renal water absorption (GO:0070295)|response to calcium ion (GO:0051592)|response to retinoic acid (GO:0032526)|response to vitamin D (GO:0033280)|transmembrane transport (GO:0055085)|transport (GO:0006810)|urea transport (GO:0015840)|water transport (GO:0006833)	basolateral plasma membrane (GO:0016323)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycerol channel activity (GO:0015254)|transporter activity (GO:0005215)|water channel activity (GO:0015250)			endometrium(2)|large_intestine(3)|lung(2)|ovary(1)	8			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.0899)		TGCTGGCCGGTCCTGGGGGGA	0.642																																					p.T238A		Atlas-SNP	.											.	AQP3	18	.	0			c.A712G						.						21	23	22					9																	33442208		2192	4282	6474	SO:0001630	splice_region_variant	360	exon6			GGCCGGTCCTGGG		CCDS6542.1	9p13	2014-07-18	2006-02-23		ENSG00000165272	ENSG00000165272		"Ion channels / Aquaporins", "Blood group antigens"	636	protein-coding gene	gene with protein product	"Gill blood group"	600170	"aquaporin 3", "aquaporin 3 (GIL blood group)"			7558005	Standard	NM_004925		Approved	GIL	uc003zsx.3	Q92482	OTTHUMG00000019769	ENST00000297991.4:c.711-1A>G	chr9.hg19:g.33442208T>C		121.0	0.0		105.0	5.0	NM_004925	A8K843|B2RE16|D3DRL3|O00108|Q6FGT2|Q6FGW6	Missense_Mutation	SNP	ENST00000297991.4	hg19	CCDS6542.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	1.905|1.905	-0.452141|-0.452141	0.04540|0.04540	.|.	.|.	ENSG00000165272|ENSG00000165272	ENST00000343952|ENST00000297991	.|T	.|0.10288	.|2.89	5.59|5.59	5.59|5.59	0.84812|0.84812	.|Aquaporin-like (2);	.|0.132399	.|0.50627	.|D	.|0.000101	T|T	0.02418|0.02418	0.0074|0.0074	N|N	0.00566|0.00566	-1.37|-1.37	0.37308|0.37308	D|D	0.909006|0.909006	B|B	0.06786|0.11235	0.001|0.004	B|B	0.01281|0.13407	0.0|0.009	T|T	0.33394|0.33394	-0.9870|-0.9870	8|10	0.46703|0.02654	T|T	0.11|1	-9.2426|-9.2426	7.9441|7.9441	0.29976|0.29976	0.0:0.1963:0.0:0.8037|0.0:0.1963:0.0:0.8037	.|.	165|238	C9JAH5|Q92482	.|AQP3_HUMAN	G|A	165|238	.|ENSP00000297991:T238A	ENSP00000339229:D165G|ENSP00000297991:T238A	D|T	-|-	2|1	0|0	AQP3|AQP3	33432208|33432208	0.443000|0.443000	0.25641|0.25641	1.000000|1.000000	0.80357|0.80357	0.758000|0.758000	0.43043|0.43043	1.577000|1.577000	0.36515|0.36515	2.125000|2.125000	0.65367|0.65367	0.460000|0.460000	0.39030|0.39030	GAC|ACC	.	.		0.642	AQP3-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052055.1	NM_004925	Missense_Mutation	C	33442208	T	C	33442208	5	2	282	1	0	0	0	0	0	0	1	0	827	1681	58	2	170	2	AQP3	9	33442208	Splice_Site	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	134935	33442208	107771223	647	40881										
NOL6	65083	hgsc.bcm.edu	37	chr9	33469208	33469208	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caccagggcctgctcaccatCccctgcaggactctgccctc					rs192128071	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:33469208delC	ENST00000379471.2	-	6	946	c.859delG	c.(859-861)gatfs	p.D287fs	NOL6_ENST00000455041.2_Frame_Shift_Del_p.D227fs|NOL6_ENST00000464829.1_5'UTR			Q9H6R4	NOL6_HUMAN	nucleolar protein 6 (RNA-associated)	287					rRNA processing (GO:0006364)	condensed nuclear chromosome (GO:0000794)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|skin(2)	27			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.152)		TGCTCACCATCCCCTGCAGGA	0.612																																					p.D287fs		Atlas-INDEL	.											.	NOL6	85	.	0			c.860delA						.						102	100	101					9																	33469208		2203	4300	6503	SO:0001589	frameshift_variant	65083	exon6			.	AF361079	CCDS6543.1, CCDS6544.1	9p12	2013-02-22	2013-02-22		ENSG00000165271	ENSG00000165271			19910	protein-coding gene	gene with protein product		611532	"nucleolar protein family 6 (RNA-associated)"			11895476, 15590835	Standard	NM_022917		Approved	bA311H10.1, Nrap, FLJ21959, MGC14896, MGC14921, MGC20838, UTP22	uc003zsz.3	Q9H6R4	OTTHUMG00000000394	ENST00000379471.2:c.859delG	chr9.hg19:g.33469208delC	ENSP00000368784:p.Asp287fs	211.0	0.0		165.0	10.0	NM_022917	Q5T5M3|Q5T5M4|Q7L4G6|Q8N6I0|Q8TEY9|Q8TEZ0|Q8TEZ1|Q9H675	Frame_Shift_Del	DEL	ENST00000379471.2	hg19																																																																																				.	.		0.612	NOL6-005	NOVEL	non_canonical_TEC|basic	protein_coding	protein_coding	OTTHUMT00000001019.2	NM_022917		-	33469208	C	-	33469208	7	5	282	1	0	1	0	1	0	0	0	0	10534	855	30	0	2665	0	NOL6	9	33469208	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	27000	33469208	107744223	648	40882										
UBAP2	55833	hgsc.bcm.edu	37	chr9	33971700	33971700	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttcccaaactactagctttgTcccacacacatctgtagatg	5	13	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:33971700T>C	ENST00000379238.1	-	8	745	c.628A>G	c.(628-630)Aca>Gca	p.T210A	UBAP2_ENST00000449054.1_Missense_Mutation_p.T210A|UBAP2_ENST00000379239.4_Intron|UBAP2_ENST00000418786.2_Intron|UBAP2_ENST00000360802.1_Missense_Mutation_p.T210A|UBAP2_ENST00000539807.1_Intron					ubiquitin associated protein 2											endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(13)|ovary(3)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)		ACTAGCTTTGTCCCACACACA	0.388																																					p.T210A		Atlas-SNP	.											.	UBAP2	82	.	0			c.A628G						.						133	131	132					9																	33971700		2203	4300	6503	SO:0001583	missense	55833	exon8			GCTTTGTCCCACA	AB040924	CCDS6547.1, CCDS75828.1	9p11.2	2008-02-05			ENSG00000137073	ENSG00000137073			14185	protein-coding gene	gene with protein product						8871400	Standard	NM_018449		Approved	KIAA1491, bA176F3.5, FLJ22435	uc003ztq.1	Q5T6F2	OTTHUMG00000000427	ENST00000379238.1:c.628A>G	chr9.hg19:g.33971700T>C	ENSP00000368540:p.Thr210Ala	180.0	0.0		132.0	6.0	NM_018449		Missense_Mutation	SNP	ENST00000379238.1	hg19	CCDS6547.1	.	.	.	.	.	.	.	.	.	.	T	12.66	2.005458	0.35415	.	.	ENSG00000137073	ENST00000379238;ENST00000449054;ENST00000360802;ENST00000379260;ENST00000421278	T;T;T	0.11495	2.77;2.77;2.77	5.63	0.293	0.15742	.	0.431234	0.24757	N	0.035851	T	0.04543	0.0124	N	0.25485	0.75	0.80722	D	1	B;P	0.39391	0.374;0.671	B;B	0.33254	0.16;0.145	T	0.50259	-0.8849	10	0.13470	T	0.59	-3.0822	3.4001	0.07320	0.1741:0.3316:0.0:0.4944	.	135;210	F5H4D5;Q5T6F2	.;UBAP2_HUMAN	A	210;210;210;150;86	ENSP00000368540:T210A;ENSP00000416932:T210A;ENSP00000354039:T210A	ENSP00000354039:T210A	T	-	1	0	UBAP2	33961700	0.926000	0.31397	0.963000	0.40424	0.900000	0.52787	0.502000	0.22594	0.019000	0.15079	0.528000	0.53228	ACA	.	.		0.388	UBAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001071.1	NM_018449		C	33971700	T	C	33971700	3	2	282	1	0	0	0	0	1	0	0	0	16852	1667	58	2	2819	2	UBAP2	9	33971700	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	502492	33971700	107241731	649	40883										
KIAA1045	23349	hgsc.bcm.edu	37	chr9	34976586	34976586	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccgccaccaagcagccaagcGgggggaccgtgacagggccc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:34976586delG	ENST00000242315.3	+	5	780	c.698delG	c.(697-699)cggfs	p.R233fs	KIAA1045_ENST00000544237.1_Frame_Shift_Del_p.R233fs|KIAA1045_ENST00000476115.2_3'UTR	NM_015297.1	NP_056112.1	Q9UPV7	K1045_HUMAN	KIAA1045	233							metal ion binding (GO:0046872)	p.R233Q(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19			LUSC - Lung squamous cell carcinoma(32;0.00575)			GCAGCCAAGCGGGGGGACCGT	0.632																																					p.R233fs		Atlas-INDEL	.											.	KIAA1045	60	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.697delC						.						41	49	46					9																	34976586		2073	4191	6264	SO:0001589	frameshift_variant	23349	exon5			.	AB028968	CCDS43796.1	9p13.2	2008-02-05			ENSG00000122733	ENSG00000122733			29180	protein-coding gene	gene with protein product						10470851	Standard	NM_015297		Approved		uc003zvr.3	Q9UPV7	OTTHUMG00000019844	ENST00000242315.3:c.698delG	chr9.hg19:g.34976586delG	ENSP00000242315:p.Arg233fs	170.0	0.0		110.0	11.0	NM_015297	B7Z253|Q58FE9|Q5T662	Frame_Shift_Del	DEL	ENST00000242315.3	hg19	CCDS43796.1																																																																																			.	.		0.632	KIAA1045-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052256.2	XM_048592		-	34976586	G	-	34976586	7	5	282	1	0	1	0	1	0	0	0	0	8216	1116	39	0	712	0	KIAA1045	9	34976586	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1004886	34976586	106236845	650	40884										
C9orf131	138724	hgsc.bcm.edu	37	chr9	35042287	35042287	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaggacctgcttggggctaaGggggatatggggcttctctg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:35042287delG	ENST00000312292.5	+	1	83	c.36delG	c.(34-36)aagfs	p.K12fs	C9orf131_ENST00000354479.5_Intron|C9orf131_ENST00000421362.2_Intron	NM_001040410.1|NM_203299.2	NP_001035500.1|NP_976044.2	Q5VYM1	CI131_HUMAN	chromosome 9 open reading frame 131	12										cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(23)|prostate(2)|skin(2)|stomach(1)	39	all_epithelial(49;0.22)		LUSC - Lung squamous cell carcinoma(32;0.00117)|Lung(28;0.00309)			TTGGGGCTAAGGGGGATATGG	0.547																																					p.K12fs		Atlas-INDEL	.											.	C9orf131	71	.	0			c.35delA						.						45	43	44					9																	35042287		2203	4300	6503	SO:0001589	frameshift_variant	138724	exon1			.	BC045643	CCDS6572.2, CCDS47961.1, CCDS47962.1	9p13.3	2008-02-05			ENSG00000174038	ENSG00000174038			31418	protein-coding gene	gene with protein product							Standard	NM_001287391		Approved	MGC41945	uc003zvw.3	Q5VYM1	OTTHUMG00000019853	ENST00000312292.5:c.36delG	chr9.hg19:g.35042287delG	ENSP00000308279:p.Lys12fs	170.0	0.0		148.0	11.0	NM_001040410	A6NLE6|E9PB26|Q86XC6|Q9UF74	Frame_Shift_Del	DEL	ENST00000312292.5	hg19	CCDS6572.2																																																																																			.	.		0.547	C9orf131-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052283.5	NM_203299		-	35042287	G	-	35042287	7	5	282	1	0	1	0	1	0	0	0	0	2459	991	35	0	54	0	C9orf131	9	35042287	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	65701	35042287	106171144	651	40885										
FANCG	2189	hgsc.bcm.edu	37	chr9	35078176	35078176	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctctagtaacaaggccaggtCcccaagacggtcagcactca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:35078176delC	ENST00000378643.3	-	4	963	c.472delG	c.(472-474)gacfs	p.D158fs	FANCG_ENST00000476212.1_5'Flank	NM_004629.1	NP_004620.1	O15287	FANCG_HUMAN	Fanconi anemia, complementation group G	158					cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|mitochondrion organization (GO:0007005)|ovarian follicle development (GO:0001541)|response to radiation (GO:0009314)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	damaged DNA binding (GO:0003684)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(7)|ovary(2)|prostate(3)|stomach(1)	28			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			AAGGCCAGGTCCCCAAGACGG	0.592			"Mis, N, F, S"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks																													p.D158fs		Atlas-INDEL	.	yes	Rec		Fanconi anaemia G	9	9p13	2189	"Fanconi anemia, complementation group G"		L	.	FANCG	56	.	0			c.473delA						.						74	78	77					9																	35078176		2203	4300	6503	SO:0001589	frameshift_variant	2189	exon4			.	AJ007669	CCDS6574.1	9p13	2014-09-17			ENSG00000221829	ENSG00000221829		"Fanconi anemia, complementation groups"	3588	protein-coding gene	gene with protein product	"DNA repair protein XRCC9", "X-ray repair, complementing defective, in Chinese hamster, 9", "X-ray repair complementing defective repair in Chinese hamster cells 9"	602956		XRCC9		9256465, 9382107	Standard	NM_004629		Approved	FAG	uc003zwb.1	O15287	OTTHUMG00000019850	ENST00000378643.3:c.472delG	chr9.hg19:g.35078176delC	ENSP00000367910:p.Asp158fs	272.0	0.0		172.0	11.0	NM_004629		Frame_Shift_Del	DEL	ENST00000378643.3	hg19	CCDS6574.1																																																																																			.	.		0.592	FANCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052269.1	NM_004629		-	35078176	C	-	35078176	7	5	282	1	0	1	0	1	0	0	0	0	5676	855	30	0	1440	0	FANCG	9	35078176	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	35889	35078176	106135255	652	40886										
RUSC2	9853	hgsc.bcm.edu	37	chr9	35557957	35557957	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtggacctcattgtggctcaTtttggcacaagccgggatcc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:35557957delT	ENST00000455600.1	+	6	3599	c.3030delT	c.(3028-3030)catfs	p.H1010fs		NM_001135999.1	NP_001129471	Q8N2Y8	RUSC2_HUMAN	RUN and SH3 domain containing 2	1010						cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)	Rab GTPase binding (GO:0017137)			NS(1)|breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(4)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32			Lung(28;0.000837)|LUSC - Lung squamous cell carcinoma(32;0.00109)|STAD - Stomach adenocarcinoma(86;0.194)			TTGTGGCTCATTTTGGCACAA	0.557																																					p.H1010fs		Atlas-INDEL	.											.	RUSC2	88	.	0			c.3029delA						.						156	134	141					9																	35557957		2203	4300	6503	SO:0001589	frameshift_variant	9853	exon6			.	AB002373	CCDS35008.1	9p13.2	2003-12-02			ENSG00000198853	ENSG00000198853			23625	protein-coding gene	gene with protein product		611053				9205841	Standard	NM_001135999		Approved	KIAA0375	uc003zww.3	Q8N2Y8	OTTHUMG00000019861	ENST00000455600.1:c.3030delT	chr9.hg19:g.35557957delT	ENSP00000393922:p.His1010fs	204.0	0.0		148.0	10.0	NM_014806	A2RU62|A7E2A9|O15080|Q5W134|Q641Q6|Q6P1W7	Frame_Shift_Del	DEL	ENST00000455600.1	hg19	CCDS35008.1																																																																																			.	.		0.557	RUSC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052309.1	XM_048462		-	35557957	T	-	35557957	7	5	282	1	0	1	0	1	0	0	0	0	13766	1490	52	0	3048	0	RUSC2	9	35557957	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	479781	35557957	105655474	653	40887										
OR13J1	392309	hgsc.bcm.edu	37	chr9	35870002	35870002	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccggtggctcatgagcacgtGgtacctgagtggctggcaga	16	10	1	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:35870002G>C	ENST00000377981.2	-	1	459	c.397C>G	c.(397-399)Cac>Gac	p.H133D		NM_001004487.1	NP_001004487.1	Q8NGT2	O13J1_HUMAN	olfactory receptor, family 13, subfamily J, member 1	133			H -> R (in dbSNP:rs7044405).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.H133Y(1)		central_nervous_system(1)|large_intestine(1)|lung(3)|skin(1)	6	all_epithelial(49;0.169)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00494)|STAD - Stomach adenocarcinoma(86;0.194)			ATGAGCACGTGGTACCTGAGT	0.622																																					p.H133D		Atlas-SNP	.											OR13J1,colon,carcinoma,0,1	OR13J1	37	.	1	Substitution - Missense(1)	large_intestine(1)	c.C397G						.																																			SO:0001583	missense	392309	exon1			GCACGTGGTACCT		CCDS35011.1	9p13.3	2013-09-24			ENSG00000168828	ENSG00000168828		"GPCR / Class A : Olfactory receptors"	15108	protein-coding gene	gene with protein product							Standard	NM_001004487		Approved		uc011lph.2	Q8NGT2	OTTHUMG00000019879	ENST00000377981.2:c.397C>G	chr9.hg19:g.35870002G>C	ENSP00000367219:p.His133Asp	209.0	0.0		135.0	0.0	NM_001004487	B2RN66|Q6IF20|Q96R40	Missense_Mutation	SNP	ENST00000377981.2	hg19	CCDS35011.1	.	.	.	.	.	.	.	.	.	.	G	12.13	1.846178	0.32606	.	.	ENSG00000168828	ENST00000377981	T	0.01323	5.01	4.62	3.71	0.42584	GPCR, rhodopsin-like superfamily (1);	0.112691	0.40302	N	0.001130	T	0.01558	0.0050	L	0.29908	0.895	0.19775	N	0.999955	B	0.26195	0.144	B	0.19391	0.025	T	0.45614	-0.9249	10	0.62326	D	0.03	.	12.4119	0.55471	0.0:0.0:0.8305:0.1695	.	133	Q8NGT2	O13J1_HUMAN	D	133	ENSP00000367219:H133D	ENSP00000367219:H133D	H	-	1	0	OR13J1	35860002	0.000000	0.05858	0.894000	0.35097	0.540000	0.34992	-0.698000	0.05092	1.527000	0.49086	0.650000	0.86243	CAC	.	.		0.622	OR13J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052381.1			C	35870002	G	C	35870002	3	2	282	1	0	0	0	0	1	0	0	0	10953	1348	47	4	544	4	OR13J1	9	35870002	Missense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	312045	35870002	105343429	654	40888										
FAM122A	116224	hgsc.bcm.edu	37	chr9	71395729	71395729	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctgaatatcagccaaagagaTttttccagggcatcaccaac							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:71395729delT	ENST00000394264.3	+	1	766	c.649delT	c.(649-651)tttfs	p.F218fs	PIP5K1B_ENST00000265382.3_Intron|PIP5K1B_ENST00000541509.1_Intron	NM_138333.3	NP_612206.3	Q96E09	F122A_HUMAN	family with sequence similarity 122A	218										endometrium(1)|lung(2)	3						GCCAAAGAGATTTTTCCAGGG	0.458																																					p.R216fs		Atlas-INDEL	.											.	FAM122A	14	.	0			c.648delA						.						113	110	111					9																	71395729		2203	4300	6503	SO:0001589	frameshift_variant	116224	exon1			.	AK126379	CCDS6623.1	9q21.13	2011-02-10	2006-07-11	2006-07-11	ENSG00000187866	ENSG00000187866			23490	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 42"	C9orf42		12477932	Standard	NM_138333		Approved	MGC17347	uc004agw.1	Q96E09	OTTHUMG00000019971	ENST00000394264.3:c.649delT	chr9.hg19:g.71395729delT	ENSP00000377807:p.Phe218fs	227.0	0.0		165.0	11.0	NM_138333		Frame_Shift_Del	DEL	ENST00000394264.3	hg19	CCDS6623.1																																																																																			.	.		0.458	FAM122A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052556.1	NM_138333		-	71395729	T	-	71395729	7	5	282	1	0	1	0	1	0	0	0	0	5424	1493	52	0	651	0	FAM122A	9	71395729	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	35525727	71395729	69817702	655	40889										
PTAR1	375743	hgsc.bcm.edu	37	chr9	72338481	72338481	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaaaactggcggtagtgaaaTccactgtggtctgaaacgtg	12	7	1	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:72338481T>C	ENST00000340434.4	-	6	711	c.708A>G	c.(706-708)ggA>ggG	p.G236G	PTAR1_ENST00000377200.5_Silent_p.G157G	NM_001099666.1	NP_001093136.1	Q7Z6K3	PTAR1_HUMAN	protein prenyltransferase alpha subunit repeat containing 1	236					protein prenylation (GO:0018342)		protein prenyltransferase activity (GO:0008318)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)	5						GGTAGTGAAATCCACTGTGGT	0.398																																					p.G236G		Atlas-SNP	.											.	PTAR1	46	.	0			c.A708G						.						98	92	94					9																	72338481		1853	4110	5963	SO:0001819	synonymous_variant	375743	exon6			GTGAAATCCACTG	BC053622	CCDS47978.1	9q21.13	2008-10-01			ENSG00000188647	ENSG00000188647		"Prenyltransferase alpha subunit repeat containing"	30449	protein-coding gene	gene with protein product						12477932	Standard	NM_001099666		Approved		uc004ahj.4	Q7Z6K3	OTTHUMG00000019982	ENST00000340434.4:c.708A>G	chr9.hg19:g.72338481T>C		234.0	0.0		143.0	6.0	NM_001099666	Q5T7V5|Q5T7V6	Silent	SNP	ENST00000340434.4	hg19	CCDS47978.1	.	.	.	.	.	.	.	.	.	.	T	3.965	-0.009517	0.07727	.	.	ENSG00000188647	ENST00000415701	.	.	.	5.69	3.27	0.37495	.	.	.	.	.	T	0.57330	0.2046	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50268	-0.8848	4	.	.	.	-9.3541	7.9037	0.29750	0.1228:0.0668:0.0:0.8104	.	.	.	.	V	3	.	.	I	-	1	0	PTAR1	71528301	1.000000	0.71417	1.000000	0.80357	0.427000	0.31564	2.074000	0.41529	0.466000	0.27193	-0.290000	0.09829	ATT	.	.		0.398	PTAR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052582.4	NM_001099666		C	72338481	T	C	72338481	2	2	282	1	0	0	0	0	0	0	0	1	12736	1422	50	2		2	PTAR1	9	72338481	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	942752	72338481	68874950	656	40890										
KLF9	687	hgsc.bcm.edu	37	chr9	73028126	73028126	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcagtaatccttccaggtgtCccccgggtcaccgtgctcct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:73028126delC	ENST00000377126.2	-	1	1414	c.154delG	c.(154-156)gacfs	p.D52fs		NM_001206.2	NP_001197.1	Q13886	KLF9_HUMAN	Kruppel-like factor 9	52					cellular response to thyroid hormone stimulus (GO:0097067)|embryo implantation (GO:0007566)|progesterone receptor signaling pathway (GO:0050847)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(3)|lung(1)|prostate(2)|urinary_tract(1)	9						TTCCAGGTGTCCCCCGGGTCA	0.647																																					p.D52fs		Atlas-INDEL	.											.	KLF9	16	.	0			c.155delA						.						75	56	62					9																	73028126		2203	4300	6503	SO:0001589	frameshift_variant	687	exon1			.	BC069431	CCDS6633.1	9q21.11	2013-01-08	2004-11-29	2004-12-01	ENSG00000119138	ENSG00000119138		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	1123	protein-coding gene	gene with protein product		602902	"basic transcription element binding protein 1"	BTEB1		1356762	Standard	NM_001206		Approved		uc004aht.3	Q13886	OTTHUMG00000019991	ENST00000377126.2:c.154delG	chr9.hg19:g.73028126delC	ENSP00000366330:p.Asp52fs	245.0	0.0		150.0	11.0	NM_001206	B2R943|Q16196	Frame_Shift_Del	DEL	ENST00000377126.2	hg19	CCDS6633.1																																																																																			.	.		0.647	KLF9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052602.1	NM_001206		-	73028126	C	-	73028126	7	5	282	1	0	1	0	1	0	0	0	0	8362	855	30	0	588	0	KLF9	9	73028126	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	689645	73028126	68185305	657	40891										
TMEM2	23670	hgsc.bcm.edu	37	chr9	74347404	74347404	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tctcatgtctacaccgtctaTgatctcacccatgtgcagga	7	13	4	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:74347404T>C	ENST00000377044.4	-	7	1965	c.1426A>G	c.(1426-1428)Ata>Gta	p.I476V	TMEM2_ENST00000377066.5_Missense_Mutation_p.I413V	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	476					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		ACACCGTCTATGATCTCACCC	0.418																																					p.I476V		Atlas-SNP	.											.	TMEM2	112	.	0			c.A1426G						.						94	85	88					9																	74347404		2203	4300	6503	SO:0001583	missense	23670	exon7			CGTCTATGATCTC		CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.1426A>G	chr9.hg19:g.74347404T>C	ENSP00000366243:p.Ile476Val	174.0	0.0		112.0	41.0	NM_013390	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Missense_Mutation	SNP	ENST00000377044.4	hg19	CCDS6638.1	.	.	.	.	.	.	.	.	.	.	T	5.804	0.332631	0.10956	.	.	ENSG00000135048	ENST00000377044;ENST00000377066	D;T	0.92752	-3.1;-0.55	5.54	-6.81	0.01704	Pectin lyase fold/virulence factor (1);	0.763445	0.13367	N	0.393239	T	0.77745	0.4176	N	0.05158	-0.105	0.23162	N	0.998199	B;B	0.02656	0.0;0.0	B;B	0.08055	0.001;0.003	T	0.62455	-0.6851	10	0.27082	T	0.32	.	11.4444	0.50114	0.0:0.5174:0.1002:0.3824	.	476;413	Q9UHN6;Q9UHN6-2	TMEM2_HUMAN;.	V	476;413	ENSP00000366243:I476V;ENSP00000366266:I413V	ENSP00000366243:I476V	I	-	1	0	TMEM2	73537224	0.002000	0.14202	0.704000	0.30370	0.992000	0.81027	-0.542000	0.06091	-1.195000	0.02680	-0.263000	0.10527	ATA	.	.		0.418	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390		C	74347404	T	C	74347404	3	2	282	1	0	0	0	0	1	0	0	0	16136	1464	51	2	2797	2	TMEM2	9	74347404	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1319278	74347404	66866027	658	40892										
GDA	9615	hgsc.bcm.edu	37	chr9	74860174	74860174	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttgacctgttttatggggacTtttttggtgatatttctgag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:74860174delT	ENST00000358399.3	+	12	1339	c.1246delT	c.(1246-1248)tttfs	p.F417fs	GDA_ENST00000545168.1_Frame_Shift_Del_p.F343fs|GDA_ENST00000376986.1_Frame_Shift_Del_p.F339fs|GDA_ENST00000238018.4_Frame_Shift_Del_p.F417fs|GDA_ENST00000376989.3_Frame_Shift_Del_p.F356fs	NM_001242505.2|NM_001242506.2|NM_004293.4	NP_001229434.1|NP_001229435.1|NP_004284.1	Q9Y2T3	GUAD_HUMAN	guanine deaminase	417					guanine catabolic process (GO:0006147)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	guanine deaminase activity (GO:0008892)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(1)|kidney(1)|large_intestine(1)|lung(20)|ovary(2)|skin(2)|urinary_tract(1)	32		Myeloproliferative disorder(762;0.0122)		Lung(182;0.0583)		TTATGGGGACTTTTTTGGTGA	0.378																																					p.D415fs		Atlas-INDEL	.											.	GDA	113	.	0			c.1245delC						.						148	146	146					9																	74860174		2203	4300	6503	SO:0001589	frameshift_variant	9615	exon12			.	AF095286	CCDS6641.1, CCDS56576.1, CCDS56577.1	9q21.13	2008-05-14			ENSG00000119125	ENSG00000119125			4212	protein-coding gene	gene with protein product		139260				10075721, 3966794	Standard	NM_001242507		Approved		uc004air.3	Q9Y2T3	OTTHUMG00000020005	ENST00000358399.3:c.1246delT	chr9.hg19:g.74860174delT	ENSP00000351170:p.Phe417fs	147.0	0.0		131.0	13.0	NM_001242505	B4DTY5|Q5SZC7|Q9H335|Q9ULG2	Frame_Shift_Del	DEL	ENST00000358399.3	hg19	CCDS6641.1																																																																																			.	.		0.378	GDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052633.1			-	74860174	T	-	74860174	7	5	282	1	0	1	0	1	0	0	0	0	6314	1609	56	0	1292	0	GDA	9	74860174	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	512770	74860174	66353257	659	40893										
RORB	6096	hgsc.bcm.edu	37	chr9	77249628	77249628	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtttaattgacagaacgaacAgaaaccgttgccaacactgc	8	10	0	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:77249628A>G	ENST00000396204.2	+	3	208	c.208A>G	c.(208-210)Aga>Gga	p.R70G	RORB_ENST00000376896.3_Missense_Mutation_p.R59G			Q92753	RORB_HUMAN	RAR-related orphan receptor B	70					amacrine cell differentiation (GO:0035881)|cellular response to retinoic acid (GO:0071300)|eye photoreceptor cell development (GO:0042462)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|rhythmic process (GO:0048511)|transcription initiation from RNA polymerase II promoter (GO:0006367)|visual perception (GO:0007601)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(2)|large_intestine(4)|lung(1)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	12					Melatonin(DB01065)	CAGAACGAACAGAAACCGTTG	0.448																																					p.R59G		Atlas-SNP	.											RORB_ENST00000376896,NS,carcinoma,0,1	RORB	89	.	0			c.A175G						.						82	76	78					9																	77249628		2203	4300	6503	SO:0001583	missense	6096	exon3			ACGAACAGAAACC	Y08639	CCDS6646.1	9q22	2013-01-16			ENSG00000198963	ENSG00000198963		"Nuclear hormone receptors"	10259	protein-coding gene	gene with protein product		601972				7926749	Standard	NM_006914		Approved	RZRB, NR1F2, ROR-BETA	uc004ajh.3	Q92753	OTTHUMG00000020026	ENST00000396204.2:c.208A>G	chr9.hg19:g.77249628A>G	ENSP00000379507:p.Arg70Gly	128.0	0.0		95.0	5.0	NM_006914	Q8WX73	Missense_Mutation	SNP	ENST00000396204.2	hg19		.	.	.	.	.	.	.	.	.	.	A	22.0	4.227069	0.79576	.	.	ENSG00000198963	ENST00000376896;ENST00000396204	D;D	0.98987	-5.3;-5.3	5.82	4.65	0.58169	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (4);	0.000000	0.85682	D	0.000000	D	0.99441	0.9802	H	0.95004	3.61	0.80722	D	1	D;D	0.89917	1.0;0.988	D;D	0.97110	1.0;0.959	D	0.98501	1.0614	10	0.87932	D	0	.	13.0159	0.58757	0.8653:0.1347:0.0:0.0	.	70;59	Q92753;Q58EY0	RORB_HUMAN;.	G	59;70	ENSP00000366093:R59G;ENSP00000379507:R70G	ENSP00000366093:R59G	R	+	1	2	RORB	76439448	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.180000	0.50895	0.992000	0.38840	0.533000	0.62120	AGA	.	.		0.448	RORB-201	KNOWN	basic	protein_coding	protein_coding				G	77249628	A	G	77249628	3	3	282	1	0	0	0	0	1	0	0	0	13544	180	7	2	185	2	RORB	9	77249628	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2389454	77249628	63963803	660	40894										
ZCCHC6	79670	hgsc.bcm.edu	37	chr9	88960648	88960648	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caaatgcaatggattcaattAaaacatcacagagtctgcag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:88960648delA	ENST00000375963.3	-	4	927	c.755delT	c.(754-756)ttafs	p.L252fs	ZCCHC6_ENST00000375961.2_Frame_Shift_Del_p.L252fs|ZCCHC6_ENST00000375948.1_5'Flank|ZCCHC6_ENST00000375947.1_Frame_Shift_Del_p.L85fs|ZCCHC6_ENST00000277141.6_5'UTR|ZCCHC6_ENST00000375960.2_Frame_Shift_Del_p.L252fs	NM_001185059.1|NM_024617.3	NP_001171988.1|NP_078893.2	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6	252					RNA 3'-end processing (GO:0031123)		poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	46						GGATTCAATTAAAACATCACA	0.353																																					p.L252fs		Atlas-INDEL	.											.	ZCCHC6	105	.	0			c.756delA						.						184	169	174					9																	88960648		2203	4300	6503	SO:0001589	frameshift_variant	79670	exon4			.	AL832026	CCDS35057.1, CCDS55323.1	9q21	2014-03-05			ENSG00000083223	ENSG00000083223		"Zinc fingers, CCHC domain containing"	25817	protein-coding gene	gene with protein product	"TUTase7"					11214970	Standard	NM_001185059		Approved	KIAA1711, FLJ13409, PAPD6, TUT7	uc004aoq.3	Q5VYS8	OTTHUMG00000020137	ENST00000375963.3:c.755delT	chr9.hg19:g.88960648delA	ENSP00000365130:p.Leu252fs	255.0	0.0		169.0	11.0	NM_024617	Q5H9T0|Q5VYS5|Q5VYS7|Q658Z9|Q659A2|Q6MZJ3|Q8N5F0|Q96N57|Q96NE8|Q9C0F2|Q9H8M6	Frame_Shift_Del	DEL	ENST00000375963.3	hg19	CCDS35057.1																																																																																			.	.		0.353	ZCCHC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052918.1	NM_024617		-	88960648	A	-	88960648	7	5	282	1	0	1	0	1	0	0	0	0	17607	372	13	0	3828	0	ZCCHC6	9	88960648	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	11711020	88960648	52252783	661	40895										
ROR2	4920	hgsc.bcm.edu	37	chr9	94493324	94493324	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctcagggaagtctgtgctggAcaggtggtggctgtgggggt	20	6	2	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:94493324A>G	ENST00000375708.3	-	7	1249	c.1051T>C	c.(1051-1053)Tcc>Ccc	p.S351P	ROR2_ENST00000550066.1_5'UTR|ROR2_ENST00000375715.1_Missense_Mutation_p.S211P	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	351	Kringle. {ECO:0000255|PROSITE- ProRule:PRU00121}.				cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|embryonic genitalia morphogenesis (GO:0030538)|inner ear morphogenesis (GO:0042472)|JNK cascade (GO:0007254)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	clathrin-coated endocytic vesicle membrane (GO:0030669)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						TCTGTGCTGGACAGGTGGTGG	0.627																																					p.S351P		Atlas-SNP	.											.	ROR2	167	.	0			c.T1051C						.						58	60	59					9																	94493324		2203	4300	6503	SO:0001583	missense	4920	exon7			TGCTGGACAGGTG	M97639	CCDS6691.1	9q22	2013-01-11			ENSG00000169071	ENSG00000169071		"Immunoglobulin superfamily / I-set domain containing"	10257	protein-coding gene	gene with protein product		602337		NTRKR2, BDB, BDB1		1334494, 10700182	Standard	NM_004560		Approved		uc004arj.2	Q01974	OTTHUMG00000020211	ENST00000375708.3:c.1051T>C	chr9.hg19:g.94493324A>G	ENSP00000364860:p.Ser351Pro	176.0	0.0		124.0	5.0	NM_004560	Q59GF5|Q5SPI5|Q9HAY7|Q9HB61	Missense_Mutation	SNP	ENST00000375708.3	hg19	CCDS6691.1	.	.	.	.	.	.	.	.	.	.	A	5.865	0.343745	0.11126	.	.	ENSG00000169071	ENST00000375715;ENST00000375708	T;T	0.62941	-0.01;-0.01	3.81	2.64	0.31445	Kringle (4);Kringle-like fold (1);	0.636870	0.12806	U	0.437586	T	0.47488	0.1448	L	0.31926	0.97	0.41468	D	0.988086	B;B;B	0.16603	0.001;0.018;0.005	B;B;B	0.18871	0.009;0.023;0.014	T	0.24764	-1.0151	10	0.22706	T	0.39	.	8.3068	0.32047	0.4804:0.0:0.0:0.5196	.	351;351;211	A1L4F5;Q01974;B1APY4	.;ROR2_HUMAN;.	P	211;351	ENSP00000364867:S211P;ENSP00000364860:S351P	ENSP00000364860:S351P	S	-	1	0	ROR2	93533145	0.861000	0.29849	0.539000	0.28077	0.660000	0.38997	0.756000	0.26419	0.614000	0.30107	0.459000	0.35465	TCC	.	.		0.627	ROR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053040.1			G	94493324	A	G	94493324	3	3	282	1	0	0	0	0	1	0	0	0	13542	275	10	2	1792	2	ROR2	9	94493324	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	5532676	94493324	46720107	662	40896										
IPPK	64768	hgsc.bcm.edu	37	chr9	95432235	95432235	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttattgccctctccgtggtaCccccattcattctcgtccat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:95432235delC	ENST00000287996.3	-	1	312	c.36delG	c.(34-36)gggfs	p.G12fs		NM_022755.5	NP_073592.1	Q9H8X2	IPPK_HUMAN	inositol 1,3,4,5,6-pentakisphosphate 2-kinase	12					inositol phosphate metabolic process (GO:0043647)|inositol phosphorylation (GO:0052746)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|inositol pentakisphosphate 2-kinase activity (GO:0035299)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(2)|urinary_tract(1)	15						CTCCGTGGTACCCCCATTCAT	0.697																																					p.Y13fs		Atlas-INDEL	.											.	IPPK	34	.	0			c.37delT						.						134	104	114					9																	95432235		2203	4300	6503	SO:0001589	frameshift_variant	64768	exon1			.	AK023225	CCDS6699.1	9q22.31	2010-12-02	2005-10-20	2005-10-20	ENSG00000127080	ENSG00000127080			14645	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 12"	C9orf12		12084730	Standard	NM_022755		Approved	INSP5K2, FLJ13163, IP5K, IPK1	uc004asl.1	Q9H8X2	OTTHUMG00000020231	ENST00000287996.3:c.36delG	chr9.hg19:g.95432235delC	ENSP00000287996:p.Gly12fs	167.0	0.0		105.0	10.0	NM_022755	Q5T9F7|Q9H7V8	Frame_Shift_Del	DEL	ENST00000287996.3	hg19	CCDS6699.1																																																																																			.	.		0.697	IPPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053101.1	NM_022755		-	95432235	C	-	95432235	7	5	282	1	0	1	0	1	0	0	0	0	7810	494	18	0	1491	0	IPPK	9	95432235	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	938911	95432235	45781196	663	40897										
HIATL1	84641	hgsc.bcm.edu	37	chr9	97213759	97213759	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcataggttttggatctgttAaaattgcagcattcatagct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:97213759delA	ENST00000375344.3	+	8	1134	c.865delA	c.(865-867)aaafs	p.K289fs	HIATL1_ENST00000428393.2_Frame_Shift_Del_p.K224fs	NM_032558.2	NP_115947.2	Q5SR56	HIAL1_HUMAN	hippocampus abundant transcript-like 1	289					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|pancreas(1)	11		Acute lymphoblastic leukemia(62;0.136)				TGGATCTGTTAAAATTGCAGC	0.254																																					p.V288fs	Pancreas(77;1260 1915 1973 10423)	Atlas-INDEL	.											.	HIATL1	31	.	0			c.864delT						.						82	86	85					9																	97213759		2203	4300	6503	SO:0001589	frameshift_variant	84641	exon8			.	AK027659	CCDS6710.2	9q22.32	2009-12-04			ENSG00000148110	ENSG00000148110			23376	protein-coding gene	gene with protein product							Standard	XM_005252277		Approved	FLJ14753	uc004aur.3	Q5SR56	OTTHUMG00000020265	ENST00000375344.3:c.865delA	chr9.hg19:g.97213759delA	ENSP00000364493:p.Lys289fs	193.0	0.0		154.0	12.0	NM_032558	B4DUE6|E9PD58|Q3KQT4|Q53GU5|Q8WU95|Q96SM4	Frame_Shift_Del	DEL	ENST00000375344.3	hg19	CCDS6710.2																																																																																			.	.		0.254	HIATL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053184.1	NM_032558		-	97213759	A	-	97213759	7	5	282	1	0	1	0	1	0	0	0	0	7107	363	13	0	895	0	HIATL1	9	97213759	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1781524	97213759	43999672	664	40898										
FBP1	2203	hgsc.bcm.edu	37	chr9	97369188	97369188	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggctgtagattttacctttcTtttttatcttcacatccttg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:97369188delT	ENST00000375326.4	-	5	810	c.614delA	c.(613-615)aagfs	p.K206fs	FBP1_ENST00000415431.1_Frame_Shift_Del_p.K206fs	NM_000507.3	NP_000498.2	P09467	F16P1_HUMAN	fructose-1,6-bisphosphatase 1	206					carbohydrate metabolic process (GO:0005975)|cellular response to drug (GO:0035690)|cellular response to magnesium ion (GO:0071286)|dephosphorylation (GO:0016311)|fructose 6-phosphate metabolic process (GO:0006002)|fructose metabolic process (GO:0006000)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|negative regulation of cell growth (GO:0030308)|negative regulation of glycolytic process (GO:0045820)|negative regulation of Ras protein signal transduction (GO:0046580)|protein homotetramerization (GO:0051289)|regulation of gluconeogenesis (GO:0006111)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	AMP binding (GO:0016208)|fructose 1,6-bisphosphate 1-phosphatase activity (GO:0042132)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|monosaccharide binding (GO:0048029)			kidney(1)|liver(1)|lung(1)	3		Acute lymphoblastic leukemia(62;0.136)			Adenosine monophosphate(DB00131)	TTTACCTTTCTTTTTTATCTT	0.502																																					p.K205fs	Ovarian(142;590 2466 25593 44496)	Atlas-INDEL	.											.	FBP1	13	.	0			c.615delG						.						148	137	141					9																	97369188		2203	4300	6503	SO:0001589	frameshift_variant	2203	exon5			.	M19922	CCDS6712.1	9q22.3	2012-08-13			ENSG00000165140	ENSG00000165140	3.1.3.11		3606	protein-coding gene	gene with protein product		611570		FBP		8387495	Standard	NM_000507		Approved		uc004auw.4	P09467	OTTHUMG00000020268	ENST00000375326.4:c.614delA	chr9.hg19:g.97369188delT	ENSP00000364475:p.Lys206fs	326.0	0.0		216.0	15.0	NM_000507	O75571|Q53F94|Q96E46	Frame_Shift_Del	DEL	ENST00000375326.4	hg19	CCDS6712.1																																																																																			.	.		0.502	FBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053187.1	NM_000507		-	97369188	T	-	97369188	7	5	282	1	0	1	0	1	0	0	0	0	5713	1609	56	0	414	0	FBP1	9	97369188	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	155429	97369188	43844243	665	40899										
TDRD7	23424	hgsc.bcm.edu	37	chr9	100203999	100203999	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctcctgcctcttacacttatAaaatggatgaggttcaaaat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:100203999delA	ENST00000355295.4	+	6	992	c.697delA	c.(697-699)aaafs	p.K233fs	TDRD7_ENST00000422139.2_Frame_Shift_Del_p.K159fs	NM_014290.2	NP_055105.2	Q8NHU6	TDRD7_HUMAN	tudor domain containing 7	233	HTH OST-type 2. {ECO:0000255|PROSITE- ProRule:PRU00975}.				germ cell development (GO:0007281)|lens fiber cell differentiation (GO:0070306)|lens morphogenesis in camera-type eye (GO:0002089)|posttranscriptional regulation of gene expression (GO:0010608)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|P granule (GO:0043186)|ribonucleoprotein granule (GO:0035770)	mRNA binding (GO:0003729)			endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Acute lymphoblastic leukemia(62;0.158)				TTACACTTATAAAATGGATGA	0.284																																					p.Y232X		Atlas-INDEL	.											.	TDRD7	78	.	0			c.696delT						.						63	64	64					9																	100203999		2203	4300	6503	SO:0001589	frameshift_variant	23424	exon6			.	AB025254	CCDS6725.1	9q22.33	2013-01-23			ENSG00000196116	ENSG00000196116		"Tudor domain containing"	30831	protein-coding gene	gene with protein product		611258				21436445	Standard	NM_014290		Approved	PCTAIRE2BP	uc004axj.3	Q8NHU6	OTTHUMG00000020326	ENST00000355295.4:c.697delA	chr9.hg19:g.100203999delA	ENSP00000347444:p.Lys233fs	238.0	0.0		191.0	12.0	NM_014290	A6NCI6|B2RBX3|B4DG99|B4DXF7|E7EQD4|Q5VV27|Q96JT1|Q9UFF0|Q9Y2M3	Frame_Shift_Del	DEL	ENST00000355295.4	hg19	CCDS6725.1																																																																																			.	.		0.284	TDRD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053322.1	NM_014290		-	100203999	A	-	100203999	7	5	282	1	0	1	0	1	0	0	0	0	15750	363	13	0	715	0	TDRD7	9	100203999	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2834811	100203999	41009432	666	40900										
C9orf156	51531	hgsc.bcm.edu	37	chr9	100672289	100672289	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tctcggcatgaggagtaaacCgcacttctaaagtggccaca	10	11	2	1	rs371444295		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:100672289C>T	ENST00000375119.3	-	4	1095	c.1019G>A	c.(1018-1020)cGg>cAg	p.R340Q	C9orf156_ENST00000478126.1_5'UTR	NM_016481.3	NP_057565.3	Q9BU70	NAP1_HUMAN	chromosome 9 open reading frame 156	340					viral process (GO:0016032)		hydrolase activity (GO:0016787)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|prostate(1)|skin(1)	13		Acute lymphoblastic leukemia(62;0.158)				AGGAGTAAACCGCACTTCTAA	0.532																																					p.R340Q		Atlas-SNP	.											.	C9orf156	35	.	0			c.G1019A						.	C	GLN/ARG	0,4406		0,0,2203	43	41	42		1019	5	1	9		42	1,8599		0,1,4299	no	missense	C9orf156	NM_016481.3	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	340/442	100672289	1,13005	2203	4300	6503	SO:0001583	missense	51531	exon4			GTAAACCGCACTT	AK023069	CCDS6730.1	9q31.1	2011-03-02			ENSG00000136932	ENSG00000136932			30967	protein-coding gene	gene with protein product	"Nef (lentivirus myristoylated factor) associated protein 1"						Standard	NM_016481		Approved	HSPC219, NAP1	uc004axv.1	Q9BU70	OTTHUMG00000021007	ENST00000375119.3:c.1019G>A	chr9.hg19:g.100672289C>T	ENSP00000364260:p.Arg340Gln	92.0	0.0		75.0	4.0	NM_016481	Q5T113|Q86SK0|Q9NXJ7|Q9P0Q7	Missense_Mutation	SNP	ENST00000375119.3	hg19	CCDS6730.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.037893	0.93630	0.0	1.16E-4	ENSG00000136932	ENST00000375119;ENST00000375118	T;T	0.42131	0.98;0.98	5.03	5.03	0.67393	Uncharacterised domain UPF0066, YaeB-like domain (1);	0.000000	0.85682	D	0.000000	T	0.59569	0.2203	L	0.52573	1.65	0.58432	D	0.999993	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.61426	-0.7065	10	0.66056	D	0.02	-19.1885	16.2258	0.82288	0.0:1.0:0.0:0.0	.	194;340	Q5T114;Q9BU70	.;NAP1_HUMAN	Q	340;194	ENSP00000364260:R340Q;ENSP00000364259:R194Q	ENSP00000364259:R194Q	R	-	2	0	C9orf156	99712110	1.000000	0.71417	0.997000	0.53966	0.926000	0.56050	5.451000	0.66632	2.503000	0.84419	0.563000	0.77884	CGG	.	.		0.532	C9orf156-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055401.1	NM_016481		T	100672289	C	T	100672289	3	4	282	1	0	0	0	0	1	0	0	0	2467	652	23	1	314	1	C9orf156	9	100672289	Missense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	468290	100672289	40541142	667	40901										
CORO2A	7464	hgsc.bcm.edu	37	chr9	100890927	100890927	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggagatgggctcgatgaggcTtttggttgtgatcagcttgt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:100890927delT	ENST00000343933.5	-	9	1299	c.1042delA	c.(1042-1044)agcfs	p.S348fs	CORO2A_ENST00000375077.4_Frame_Shift_Del_p.S348fs	NM_003389.3	NP_003380.3	Q92828	COR2A_HUMAN	coronin, actin binding protein, 2A	348					actin cytoskeleton organization (GO:0030036)|intracellular signal transduction (GO:0035556)	actin cytoskeleton (GO:0015629)|transcriptional repressor complex (GO:0017053)	actin filament binding (GO:0051015)			endometrium(2)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|skin(4)|urinary_tract(1)	26		Acute lymphoblastic leukemia(62;0.0559)				TCGATGAGGCTTTTGGTTGTG	0.592																																					p.S348fs		Atlas-INDEL	.											.	CORO2A	54	.	0			c.1043delG						.						119	106	110					9																	100890927		2203	4300	6503	SO:0001589	frameshift_variant	7464	exon9			.	U57057	CCDS6735.1	9q22.3	2013-01-10	2001-11-28		ENSG00000106789	ENSG00000106789		"Coronins", "WD repeat domain containing"	2255	protein-coding gene	gene with protein product	"coronin 2A", "coronin-like protein B", "WD protein IR10", "WD-repeat protein 2"	602159	"coronin, actin-binding protein, 2A"			8985118	Standard	NM_052820		Approved	IR10, WDR2	uc004aym.3	Q92828	OTTHUMG00000020340	ENST00000343933.5:c.1042delA	chr9.hg19:g.100890927delT	ENSP00000343746:p.Ser348fs	203.0	0.0		178.0	12.0	NM_003389	Q5TBR5|Q92829|Q9BWS5	Frame_Shift_Del	DEL	ENST00000343933.5	hg19	CCDS6735.1																																																																																			.	.		0.592	CORO2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053357.1	NM_003389		-	100890927	T	-	100890927	7	5	282	1	0	1	0	1	0	0	0	0	3758	1609	56	0	551	0	CORO2A	9	100890927	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	218638	100890927	40322504	668	40902										
TBC1D2	55357	hgsc.bcm.edu	37	chr9	100973055	100973055	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tggcttcgtcccccagggccTcctgcagccttctcagaccg	10	18	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:100973055T>C	ENST00000375064.1	-	8	1594	c.1556A>G	c.(1555-1557)gAg>gGg	p.E519G	TBC1D2_ENST00000493589.2_Intron|TBC1D2_ENST00000375066.5_Missense_Mutation_p.E519G|TBC1D2_ENST00000375063.1_Missense_Mutation_p.E59G|TBC1D2_ENST00000342112.5_Missense_Mutation_p.E301G	NM_001267571.1	NP_001254500.1	Q9BYX2	TBD2A_HUMAN	TBC1 domain family, member 2	519					positive regulation of Rab GTPase activity (GO:0032851)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)	cadherin binding (GO:0045296)|Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.55e-37)		CCCCAGGGCCTCCTGCAGCCT	0.617																																					p.E519G		Atlas-SNP	.											.	TBC1D2	70	.	0			c.A1556G						.						36	28	31					9																	100973055		2191	4282	6473	SO:0001583	missense	55357	exon8			AGGGCCTCCTGCA	AY026527	CCDS35080.1, CCDS59137.1, CCDS75865.1	9q22.32	2011-11-30			ENSG00000095383	ENSG00000095383			18026	protein-coding gene	gene with protein product	"prostate antigen recognized and identified by SEREX"	609871					Standard	NM_018421		Approved	PARIS1, TBC1D2A, Armus	uc011lvb.2	Q9BYX2	OTTHUMG00000020343	ENST00000375064.1:c.1556A>G	chr9.hg19:g.100973055T>C	ENSP00000364205:p.Glu519Gly	294.0	0.0		195.0	8.0	NM_001267571	B3KWD1|B4DQ05|B9A6J7|Q59EU0|Q5TBQ5|Q6IPC7|Q7L1K8|Q8WYT1|Q9H6A2|Q9NSH4	Missense_Mutation	SNP	ENST00000375064.1	hg19		.	.	.	.	.	.	.	.	.	.	T	12.51	1.959198	0.34565	.	.	ENSG00000095383	ENST00000375064;ENST00000375066;ENST00000342112;ENST00000375063	T;T;T;T	0.09630	3.26;2.96;3.39;3.02	5.6	4.42	0.53409	.	0.157654	0.56097	D	0.000030	T	0.15262	0.0368	M	0.62723	1.935	0.38741	D	0.953895	P;P	0.46142	0.799;0.873	B;P	0.47346	0.343;0.544	T	0.03969	-1.0988	10	0.45353	T	0.12	.	6.0753	0.19911	0.0:0.0812:0.319:0.5998	.	519;519	Q9BYX2;Q9BYX2-2	TBD2A_HUMAN;.	G	519;519;301;59	ENSP00000364205:E519G;ENSP00000364207:E519G;ENSP00000341567:E301G;ENSP00000364203:E59G	ENSP00000341567:E301G	E	-	2	0	TBC1D2	100012876	1.000000	0.71417	0.988000	0.46212	0.441000	0.31987	2.750000	0.47500	0.901000	0.36495	0.460000	0.39030	GAG	.	.		0.617	TBC1D2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000053366.1	NM_018421		C	100973055	T	C	100973055	3	2	282	1	0	0	0	0	1	0	0	0	15623	1551	54	2	1221	2	TBC1D2	9	100973055	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	82128	100973055	40240376	669	40903										
GALNT12	79695	hgsc.bcm.edu	37	chr9	101606479	101606479	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctgtacctctgtcatgggatGggccagaatcaggtaggtat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:101606479delG	ENST00000375011.3	+	8	1446	c.1446delG	c.(1444-1446)atgfs	p.M482fs		NM_024642.4	NP_078918.3	Q8IXK2	GLT12_HUMAN	polypeptide N-acetylgalactosaminyltransferase 12	482	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(1)|endometrium(2)|large_intestine(3)|lung(8)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	17		Acute lymphoblastic leukemia(62;0.0559)				GTCATGGGATGGGCCAGAATC	0.383																																					p.M482fs		Atlas-INDEL	.											.	GALNT12	37	.	0			c.1445delT						.						91	83	86					9																	101606479		2203	4300	6503	SO:0001589	frameshift_variant	79695	exon8			.	AB078146	CCDS6737.1	9q22.33	2014-03-13	2014-03-13		ENSG00000119514	ENSG00000119514	2.4.1.41	"Glycosyltransferase family 2 domain containing"	19877	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 12"	610290	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 12 (GalNAc-T12)"			12135769	Standard	NM_024642		Approved	GalNAc-T12	uc004ayz.3	Q8IXK2	OTTHUMG00000020348	ENST00000375011.3:c.1446delG	chr9.hg19:g.101606479delG	ENSP00000364150:p.Met482fs	249.0	0.0		149.0	10.0	NM_024642	Q5TCF7|Q8NG54|Q96CT9|Q9H771	Frame_Shift_Del	DEL	ENST00000375011.3	hg19	CCDS6737.1																																																																																			.	.		0.383	GALNT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053382.1	NM_024642		-	101606479	G	-	101606479	7	5	282	1	0	1	0	1	0	0	0	0	6218	1348	47	0	1476	0	GALNT12	9	101606479	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	633424	101606479	39606952	670	40904										
AKAP2	11217	hgsc.bcm.edu	37	chr9	112898992	112898992	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gccccagctccacaaccagcTcacggtgttcttcccgagat	8	17	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:112898992T>C	ENST00000259318.7	+	2	682	c.475T>C	c.(475-477)Tca>Cca	p.S159P	AKAP2_ENST00000555236.1_Missense_Mutation_p.S390P|PALM2-AKAP2_ENST00000374530.3_Missense_Mutation_p.S390P|AKAP2_ENST00000510514.5_Missense_Mutation_p.S390P|AKAP2_ENST00000374525.1_Missense_Mutation_p.S248P|PALM2-AKAP2_ENST00000302798.7_Missense_Mutation_p.S390P|AKAP2_ENST00000434623.2_Missense_Mutation_p.S248P	NM_001136562.2	NP_001130034.1	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2	159										breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	33						CACAACCAGCTCACGGTGTTC	0.577																																					p.S390P		Atlas-SNP	.											.	PALM2-AKAP2	117	.	0			c.T1168C						.						72	66	68					9																	112898992		2203	4300	6503	SO:0001583	missense	445815	exon8			ACCAGCTCACGGT	AB023137	CCDS43861.1, CCDS48003.1, CCDS56581.1	9q31.3	2009-10-16			ENSG00000241978	ENSG00000241978		"A-kinase anchor proteins"	372	protein-coding gene	gene with protein product	"protein kinase A2"	604582		PRKA2		10231032	Standard	NM_001136562		Approved	AKAP-KL, KIAA0920, DKFZp564L0716		Q9Y2D5	OTTHUMG00000156811	ENST00000259318.7:c.475T>C	chr9.hg19:g.112898992T>C	ENSP00000259318:p.Ser159Pro	240.0	0.0		159.0	7.0	NM_007203	B1ALX9|B2RTU4|B3KQ00|B4DTZ2|B7ZW07|B9EJB5|Q9UG26	Missense_Mutation	SNP	ENST00000259318.7	hg19	CCDS48003.1	.	.	.	.	.	.	.	.	.	.	T	12.37	1.917242	0.33815	.	.	ENSG00000157654;ENSG00000157654;ENSG00000241978;ENSG00000241978;ENSG00000241978;ENSG00000241978;ENSG00000241978;ENSG00000241978	ENST00000374530;ENST00000302798;ENST00000555236;ENST00000510514;ENST00000434623;ENST00000374525;ENST00000480388;ENST00000259318	T;T;T;T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95;0.95;0.95;0.95	5.85	5.85	0.93711	.	0.168137	0.42420	D	0.000711	T	0.62660	0.2446	M	0.63843	1.955	0.49130	D	0.999753	D;D;P;D;D;P;P;B	0.89917	0.999;1.0;0.615;1.0;0.999;0.946;0.946;0.355	D;D;B;D;D;P;P;B	0.85130	0.981;0.997;0.142;0.997;0.994;0.507;0.507;0.142	T	0.64922	-0.6293	10	0.66056	D	0.02	-12.0597	15.4167	0.74974	0.0:0.0:0.0:1.0	.	159;248;242;248;249;390;390;208	Q9Y2D5;Q9Y2D5-7;B4E2K2;Q9Y2D5-5;B1ALY1;Q9Y2D5-6;Q9Y2D5-4;C9JVY5	AKAP2_HUMAN;.;.;.;.;.;.;.	P	390;390;390;390;248;248;208;159	ENSP00000363654:S390P;ENSP00000305861:S390P;ENSP00000451476:S390P;ENSP00000421522:S390P;ENSP00000404782:S248P;ENSP00000363649:S248P;ENSP00000419268:S208P;ENSP00000259318:S159P	ENSP00000259318:S159P	S	+	1	0	PALM2-AKAP2;AKAP2	111938813	1.000000	0.71417	0.997000	0.53966	0.021000	0.10359	4.002000	0.57053	2.232000	0.73038	0.533000	0.62120	TCA	.	.		0.577	AKAP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346067.3	NM_001004065		C	112898992	T	C	112898992	3	2	282	1	0	0	0	0	1	0	0	0	451	1551	54	2	748	2	AKAP2	9	112898992	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	11292513	112898992	28314439	671	40905										
MUSK	4593	hgsc.bcm.edu	37	chr9	113457797	113457797	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agtgtcttggataaagggagAcagccctctcagggtaagtg	14	7	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:113457797A>G	ENST00000374448.4	+	4	607	c.473A>G	c.(472-474)gAc>gGc	p.D158G	MUSK_ENST00000189978.5_Missense_Mutation_p.D158G|MUSK_ENST00000416899.2_Missense_Mutation_p.D158G|MUSK_ENST00000374439.1_Missense_Mutation_p.D40G|MUSK_ENST00000374440.3_Missense_Mutation_p.D40G	NM_001166281.1|NM_005592.3	NP_001159753.1|NP_005583.1	O15146	MUSK_HUMAN	muscle, skeletal, receptor tyrosine kinase	158	Ig-like 2.				cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|memory (GO:0007613)|multicellular organismal development (GO:0007275)|neuromuscular junction development (GO:0007528)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein geranylgeranylation (GO:2000541)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(23)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	49						ATAAAGGGAGACAGCCCTCTC	0.353																																					p.D158G		Atlas-SNP	.											.	MUSK	112	.	0			c.A473G						.						56	50	52					9																	113457797		1820	4063	5883	SO:0001583	missense	4593	exon4			AGGGAGACAGCCC	AF006464	CCDS48005.1, CCDS75874.1	9q31.3-q32	2013-01-29			ENSG00000030304	ENSG00000030304		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7525	protein-coding gene	gene with protein product		601296				7546737	Standard	NM_005592		Approved		uc022blv.1	O15146	OTTHUMG00000020485	ENST00000374448.4:c.473A>G	chr9.hg19:g.113457797A>G	ENSP00000363571:p.Asp158Gly	115.0	0.0		89.0	4.0	NM_001166281	Q32MJ8|Q32MJ9|Q5VZW7|Q5VZW8	Missense_Mutation	SNP	ENST00000374448.4	hg19	CCDS48005.1	.	.	.	.	.	.	.	.	.	.	A	19.19	3.779688	0.70107	.	.	ENSG00000030304	ENST00000189978;ENST00000374448;ENST00000543335;ENST00000374447;ENST00000545907;ENST00000374440;ENST00000416899;ENST00000374439	T;T;T	0.19250	2.16;2.16;2.16	5.97	5.97	0.96955	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.195954	0.53938	D	0.000057	T	0.20861	0.0502	N	0.03948	-0.315	0.51233	D	0.999911	P;D	0.61697	0.847;0.99	P;P	0.59221	0.794;0.854	T	0.34477	-0.9827	10	0.39692	T	0.17	.	15.6346	0.76941	1.0:0.0:0.0:0.0	.	158;158	O15146;F5H6T2	MUSK_HUMAN;.	G	158;158;158;158;158;40;158;40	ENSP00000363571:D158G;ENSP00000363563:D40G;ENSP00000363562:D40G	ENSP00000189978:D158G	D	+	2	0	MUSK	112497618	1.000000	0.71417	0.921000	0.36526	0.820000	0.46376	8.010000	0.88615	2.285000	0.76669	0.477000	0.44152	GAC	.	.		0.353	MUSK-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				G	113457797	A	G	113457797	3	3	282	1	0	0	0	0	1	0	0	0	9998	275	10	2	487	2	MUSK	9	113457797	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	558805	113457797	27755634	672	40906										
C9orf84	158401	hgsc.bcm.edu	37	chr9	114453859	114453859	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gattccttgtctcctgagttAaatgaagattcatggtgcct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:114453859delA	ENST00000318737.4	-	25	4334	c.4206delT	c.(4204-4206)tttfs	p.F1402fs	C9orf84_ENST00000394777.4_Frame_Shift_Del_p.F1328fs|C9orf84_ENST00000374287.3_Frame_Shift_Del_p.F1402fs|C9orf84_ENST00000394779.3_Frame_Shift_Del_p.F1363fs	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	1402										breast(1)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(10)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						CTCCTGAGTTAAATGAAGATT	0.303																																					p.N1403fs		Atlas-INDEL	.											.	C9orf84	207	.	0			c.4207delA						.						88	89	89					9																	114453859		2203	4300	6503	SO:0001589	frameshift_variant	158401	exon25			.	AL833535	CCDS6781.3, CCDS43863.1	9q32	2012-03-16			ENSG00000165181	ENSG00000165181			26535	protein-coding gene	gene with protein product							Standard	XM_005251738		Approved	FLJ32779	uc004bfr.3	Q5VXU9	OTTHUMG00000020495	ENST00000318737.4:c.4206delT	chr9.hg19:g.114453859delA	ENSP00000322108:p.Phe1402fs	228.0	0.0		172.0	11.0	NM_173521	A2A2V3|Q2M1H8|Q96M73	Frame_Shift_Del	DEL	ENST00000318737.4	hg19	CCDS6781.3																																																																																			.	.		0.303	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521		-	114453859	A	-	114453859	7	5	282	1	0	1	0	1	0	0	0	0	2502	359	13	0	136	0	C9orf84	9	114453859	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	996062	114453859	26759572	673	40907										
TLR4	7099	hgsc.bcm.edu	37	chr9	120476424	120476424	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtatggtagaggtgaaaacaTctatgatgcctttgttatct	10	5	2	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:120476424T>C	ENST00000355622.6	+	3	2119	c.2018T>C	c.(2017-2019)aTc>aCc	p.I673T	TLR4_ENST00000472304.1_3'UTR|TLR4_ENST00000394487.4_Missense_Mutation_p.I633T	NM_138554.4|NM_138557.2	NP_612564.1|NP_612567.1	O00206	TLR4_HUMAN	toll-like receptor 4	673	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				activation of MAPK activity (GO:0000187)|B cell proliferation involved in immune response (GO:0002322)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|detection of fungus (GO:0016046)|detection of lipopolysaccharide (GO:0032497)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|innate immune response (GO:0045087)|interferon-gamma production (GO:0032609)|intestinal epithelial structure maintenance (GO:0060729)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-23 production (GO:0032707)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of tumor necrosis factor production (GO:0032720)|nitric oxide production involved in inflammatory response (GO:0002537)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine production (GO:0032722)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 production (GO:0032732)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070430)|positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070434)|positive regulation of platelet activation (GO:0010572)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cytokine secretion (GO:0050707)|response to lipopolysaccharide (GO:0032496)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|lipopolysaccharide receptor complex (GO:0046696)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(66)|ovary(4)|pancreas(1)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	103					Naloxone(DB01183)	GGTGAAAACATCTATGATGCC	0.423																																					p.I673T		Atlas-SNP	.											.	TLR4	220	.	0			c.T2018C						.						127	116	120					9																	120476424		2203	4300	6503	SO:0001583	missense	7099	exon3			AAAACATCTATGA	U88880	CCDS6818.1	9q33.1	2013-01-23			ENSG00000136869	ENSG00000136869		"CD molecules"	11850	protein-coding gene	gene with protein product		603030				9435236, 9237759	Standard	NM_138554		Approved	hToll, CD284, TLR-4, ARMD10	uc004bjz.4	O00206	OTTHUMG00000021046	ENST00000355622.6:c.2018T>C	chr9.hg19:g.120476424T>C	ENSP00000363089:p.Ile673Thr	125.0	0.0		93.0	4.0	NM_138554	A8K1Y8|A9XLP9|A9XLQ0|A9XLQ1|B4E194|D1CS52|D1CS53|Q5VZI8|Q5VZI9|Q9UK78|Q9UM57	Missense_Mutation	SNP	ENST00000355622.6	hg19	CCDS6818.1	.	.	.	.	.	.	.	.	.	.	T	0.004	-2.360984	0.00214	.	.	ENSG00000136869	ENST00000394487;ENST00000355622	T;T	0.02345	4.33;4.33	6.03	-3.2	0.05156	Toll/interleukin-1 receptor homology (TIR) domain (3);	0.952331	0.08833	N	0.887012	T	0.01189	0.0039	N	0.01464	-0.85	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.46456	-0.9190	10	0.02654	T	1	.	15.6154	0.76764	0.0:0.4039:0.0:0.5961	.	673	O00206	TLR4_HUMAN	T	633;673	ENSP00000377997:I633T;ENSP00000363089:I673T	ENSP00000363089:I673T	I	+	2	0	TLR4	119516245	0.000000	0.05858	0.002000	0.10522	0.310000	0.27922	-0.787000	0.04618	-0.621000	0.05633	-0.854000	0.03029	ATC	.	.		0.423	TLR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055549.3	NM_138554		C	120476424	T	C	120476424	3	2	282	1	0	0	0	0	1	0	0	0	15968	1435	50	2	2028	2	TLR4	9	120476424	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	6022565	120476424	20737007	674	40908										
OR1N2	138882	hgsc.bcm.edu	37	chr9	125316423	125316423	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggtaaactttttgtcagtggAaaaacattctttttatgatt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:125316423delA	ENST00000373688.2	+	1	1033	c.975delA	c.(973-975)ggafs	p.G325fs		NM_001004457.1	NP_001004457.1	Q8NGR9	OR1N2_HUMAN	olfactory receptor, family 1, subfamily N, member 2	325						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(3)	26						TTGTCAGTGGAAAAACATTCT	0.388																																					p.G325fs		Atlas-INDEL	.											.	OR1N2	51	.	0			c.974delG						.						84	86	85					9																	125316423		2202	4300	6502	SO:0001589	frameshift_variant	138882	exon1			.		CCDS35123.1	9q33.2	2013-09-20			ENSG00000171501	ENSG00000171501		"GPCR / Class A : Olfactory receptors"	15111	protein-coding gene	gene with protein product							Standard	NM_001004457		Approved		uc011lyx.2	Q8NGR9	OTTHUMG00000020607	ENST00000373688.2:c.975delA	chr9.hg19:g.125316423delA	ENSP00000362792:p.Gly325fs	223.0	0.0		159.0	10.0	NM_001004457	A3KFM2|B2RNY4|Q6IF17|Q96RA3	Frame_Shift_Del	DEL	ENST00000373688.2	hg19	CCDS35123.1																																																																																			.	.		0.388	OR1N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053937.2			-	125316423	A	-	125316423	7	5	282	1	0	1	0	1	0	0	0	0	10979	233	9	0	977	0	OR1N2	9	125316423	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	4839999	125316423	15897008	675	40909										
RABGAP1	23637	hgsc.bcm.edu	37	chr9	125772702	125772702	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tatgcttggaaagtgaatcaGaaagagagaggaggaaaact	13	3	1	4			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:125772702G>C	ENST00000373647.4	+	11	1578	c.1444G>C	c.(1444-1446)Gaa>Caa	p.E482Q		NM_012197.3	NP_036329.3	Q9Y3P9	RBGP1_HUMAN	RAB GTPase activating protein 1	482					cell cycle (GO:0007049)|positive regulation of GTPase activity (GO:0043547)|regulation of GTP catabolic process (GO:0033124)	centrosome (GO:0005813)|cytosol (GO:0005829)|microtubule associated complex (GO:0005875)	DNA binding (GO:0003677)|GTPase activator activity (GO:0005096)|Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)|tubulin binding (GO:0015631)			breast(3)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|prostate(4)|stomach(3)|upper_aerodigestive_tract(1)	41						AAGTGAATCAGAAAGAGAGAG	0.383																																					p.E482Q		Atlas-SNP	.											.	RABGAP1	164	.	0			c.G1444C						.						108	103	105					9																	125772702		2203	4300	6503	SO:0001583	missense	23637	exon11			GAATCAGAAAGAG	AJ011679	CCDS6848.2	9q34.11	2013-07-09			ENSG00000011454	ENSG00000011454			17155	protein-coding gene	gene with protein product	"rab6 GTPase activating protein (GAP and centrosome-associated)", "TBC1 domain family, member 11"	615882				10202141	Standard	NM_012197		Approved	GAPCenA, TBC1D11	uc011lzh.2	Q9Y3P9	OTTHUMG00000020633	ENST00000373647.4:c.1444G>C	chr9.hg19:g.125772702G>C	ENSP00000362751:p.Glu482Gln	84.0	0.0		75.0	31.0	NM_012197	B9A6L2|Q05CW2|Q6ZMY1|Q9HA28|Q9P0E2|Q9UG67	Missense_Mutation	SNP	ENST00000373647.4	hg19	CCDS6848.2	.	.	.	.	.	.	.	.	.	.	G	19.71	3.878331	0.72294	.	.	ENSG00000011454	ENST00000373647	T	0.06608	3.28	5.71	5.71	0.89125	.	0.059702	0.64402	D	0.000004	T	0.08268	0.0206	L	0.38953	1.18	0.80722	D	1	B	0.26672	0.156	B	0.21546	0.035	T	0.23226	-1.0194	10	0.42905	T	0.14	-19.9126	19.85	0.96736	0.0:0.0:1.0:0.0	.	482	Q9Y3P9	RBGP1_HUMAN	Q	482	ENSP00000362751:E482Q	ENSP00000362751:E482Q	E	+	1	0	RABGAP1	124812523	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.842000	0.92136	2.697000	0.92050	0.563000	0.77884	GAA	.	.		0.383	RABGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053976.3	NM_012197		C	125772702	G	C	125772702	3	2	282	1	0	0	0	0	1	0	0	0	12979	943	33	4	1482	4	RABGAP1	9	125772702	Missense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	456279	125772702	15440729	676	40910										
TTC16	158248	hgsc.bcm.edu	37	chr9	130493103	130493103	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccacccagggccagaggcagAgccttagcaagactgagccc	12	15	0	4			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:130493103A>G	ENST00000373289.3	+	14	2121	c.2041A>G	c.(2041-2043)Agc>Ggc	p.S681G	TOR2A_ENST00000472723.1_5'Flank|TTC16_ENST00000489226.1_3'UTR	NM_144965.1	NP_659402.1	Q8NEE8	TTC16_HUMAN	tetratricopeptide repeat domain 16	681										central_nervous_system(2)|endometrium(3)|lung(7)|ovary(3)|pancreas(2)|prostate(4)|skin(1)	22						CCAGAGGCAGAGCCTTAGCAA	0.572																																					p.S681G		Atlas-SNP	.											.	TTC16	55	.	0			c.A2041G						.						83	80	81					9																	130493103		2203	4300	6503	SO:0001583	missense	158248	exon14			AGGCAGAGCCTTA	AK057342	CCDS6875.1	9q34.13	2013-01-10			ENSG00000167094	ENSG00000167094		"Tetratricopeptide (TTC) repeat domain containing"	26536	protein-coding gene	gene with protein product						12477932	Standard	NM_144965		Approved	FLJ32780	uc004brq.1	Q8NEE8	OTTHUMG00000020711	ENST00000373289.3:c.2041A>G	chr9.hg19:g.130493103A>G	ENSP00000362386:p.Ser681Gly	225.0	0.0		171.0	7.0	NM_144965	B4DYG4|B5ME24|Q5JU66|Q96M72	Missense_Mutation	SNP	ENST00000373289.3	hg19	CCDS6875.1	.	.	.	.	.	.	.	.	.	.	A	7.686	0.690133	0.15039	.	.	ENSG00000167094	ENST00000373289	T	0.15952	2.38	3.28	3.28	0.37604	.	1.504790	0.03898	N	0.279859	T	0.10121	0.0248	N	0.04335	-0.225	0.40408	D	0.979728	B;B	0.12630	0.006;0.006	B;B	0.09377	0.004;0.004	T	0.18085	-1.0348	10	0.46703	T	0.11	-1.2238	8.3034	0.32027	1.0:0.0:0.0:0.0	.	668;681	B4DZ42;Q8NEE8	.;TTC16_HUMAN	G	681	ENSP00000362386:S681G	ENSP00000362386:S681G	S	+	1	0	TTC16	129532924	0.087000	0.21565	0.044000	0.18714	0.096000	0.18686	0.942000	0.29017	1.744000	0.51775	0.358000	0.22013	AGC	.	.		0.572	TTC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054224.1	NM_144965		G	130493103	A	G	130493103	3	3	282	1	0	0	0	0	1	0	0	0	16698	304	11	2	2095	2	TTC16	9	130493103	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	4720401	130493103	10720328	677	40911										
SH2D3C	10044	hgsc.bcm.edu	37	chr9	130536685	130536685	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctgatggaagctgaggatcgTctcagagtgaaggaccgagg	16	7	1	4			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:130536685T>C	ENST00000314830.8	-	2	212	c.99A>G	c.(97-99)agA>agG	p.R33R	SH2D3C_ENST00000471939.1_5'Flank|SH2D3C_ENST00000373277.4_5'Flank	NM_170600.2	NP_733745.1	Q8N5H7	SH2D3_HUMAN	SH2 domain containing 3C	33					JNK cascade (GO:0007254)|positive regulation of signal transduction (GO:0009967)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						CTGAGGATCGTCTCAGAGTGA	0.532																																					p.R33R		Atlas-SNP	.											.	SH2D3C	102	.	0			c.A99G						.						64	60	61					9																	130536685		2203	4300	6503	SO:0001819	synonymous_variant	10044	exon2			GGATCGTCTCAGA	AF124251	CCDS6877.1, CCDS6878.1, CCDS48026.1, CCDS48028.1, CCDS59145.1	9q33.1-q33.3	2013-02-14	2002-01-14		ENSG00000095370	ENSG00000095370		"SH2 domain containing"	16884	protein-coding gene	gene with protein product		604722	"SH2 domain-containing 3C"			10187783	Standard	NM_170600		Approved	NSP3	uc004bsc.3	Q8N5H7	OTTHUMG00000020717	ENST00000314830.8:c.99A>G	chr9.hg19:g.130536685T>C		132.0	0.0		117.0	5.0	NM_170600	A8K5S8|E9PG48|Q5HYE5|Q5JU31|Q6UY42|Q8N6X3|Q9Y2X5	Silent	SNP	ENST00000314830.8	hg19	CCDS6877.1																																																																																			.	.		0.532	SH2D3C-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054264.1	NM_005489		C	130536685	T	C	130536685	2	2	282	1	0	0	0	0	0	0	0	1	14249	1664	58	2		2	SH2D3C	9	130536685	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	43582	130536685	10676746	678	40912										
ENG	2022	hgsc.bcm.edu	37	chr9	130592021	130592021	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gatgcaggaagacactgctgTttacactgaggaccagaagc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:130592021delT	ENST00000373203.4	-	3	705	c.305delA	c.(304-306)aacfs	p.N102fs	Y_RNA_ENST00000410489.1_RNA|ENG_ENST00000344849.3_Frame_Shift_Del_p.N102fs	NM_000118.2|NM_001114753.1|NM_001278138.1	NP_000109.1|NP_001108225.1|NP_001265067.1	P17813	EGLN_HUMAN	endoglin	102	Required for interaction with EGL.				artery morphogenesis (GO:0048844)|BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|cell migration involved in endocardial cushion formation (GO:0003273)|cell motility (GO:0048870)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|chronological cell aging (GO:0001300)|detection of hypoxia (GO:0070483)|extracellular matrix constituent secretion (GO:0070278)|extracellular matrix disassembly (GO:0022617)|heart looping (GO:0001947)|intracellular signal transduction (GO:0035556)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|patterning of blood vessels (GO:0001569)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of gene expression (GO:0010628)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell adhesion (GO:0030155)|regulation of cell proliferation (GO:0042127)|regulation of phosphorylation (GO:0042325)|regulation of transcription, DNA-templated (GO:0006355)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to corticosteroid (GO:0031960)|response to hypoxia (GO:0001666)|response to statin (GO:0036273)|response to transforming growth factor beta (GO:0071559)|smooth muscle tissue development (GO:0048745)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|wound healing (GO:0042060)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endothelial microparticle (GO:0072563)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|transforming growth factor beta receptor homodimeric complex (GO:0070022)	activin binding (GO:0048185)|galactose binding (GO:0005534)|glycosaminoglycan binding (GO:0005539)|protein homodimerization activity (GO:0042803)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor, cytoplasmic mediator activity (GO:0005072)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane signaling receptor activity (GO:0004888)|type I transforming growth factor beta receptor binding (GO:0034713)|type II transforming growth factor beta receptor binding (GO:0005114)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	17						GACACTGCTGTTTACACTGAG	0.612									Juvenile Polyposis;Hereditary Hemorrhagic Telangiectasia																												p.N102fs		Atlas-INDEL	.											.	ENG	44	.	0			c.306delC						.						125	103	111					9																	130592021		2203	4300	6503	SO:0001589	frameshift_variant	2022	exon3	Familial Cancer Database	incl.: Juvenile Polyposis of the Stomach;HHT, Rendu-Osler-Weber disease, incl.: Pulmonary arteriovenous malformations, hypertrophic osteoarthropathy and juvenile polyposis,	.	AF035753	CCDS6880.1, CCDS48029.1, CCDS75906.1	9q34.11	2014-09-17	2008-09-04		ENSG00000106991	ENSG00000106991		"CD molecules"	3349	protein-coding gene	gene with protein product		131195	"Osler-Rendu-Weber syndrome 1"	ORW1, ORW		8404038, 10548503	Standard	NM_001278138		Approved	END, HHT1, CD105	uc031tfe.1	P17813	OTTHUMG00000020723	ENST00000373203.4:c.305delA	chr9.hg19:g.130592021delT	ENSP00000362299:p.Asn102fs	204.0	0.0		157.0	10.0	NM_001114753	Q14248|Q14926|Q5T9C0	Frame_Shift_Del	DEL	ENST00000373203.4	hg19	CCDS48029.1																																																																																			.	.		0.612	ENG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054313.1			-	130592021	T	-	130592021	7	5	282	1	0	1	0	1	0	0	0	0	5119	1725	60	0	1749	0	ENG	9	130592021	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	55336	130592021	10621410	679	40913										
NUP188	23511	hgsc.bcm.edu	37	chr9	131745770	131745770	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caggtctggactgatcttcgTcacacaggttttttaccatt	8	10	3	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:131745770T>C	ENST00000372577.2	+	19	1923	c.1902T>C	c.(1900-1902)cgT>cgC	p.R634R		NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	634					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				breast(2)|central_nervous_system(3)|endometrium(6)|kidney(4)|large_intestine(9)|lung(20)|ovary(6)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	60						CTGATCTTCGTCACACAGGTT	0.473																																					p.R634R		Atlas-SNP	.											.	NUP188	140	.	0			c.T1902C						.						122	94	104					9																	131745770		2203	4300	6503	SO:0001819	synonymous_variant	23511	exon19			TCTTCGTCACACA	D79991	CCDS35156.1	9q34.13	2014-01-28	2004-03-19	2004-03-24	ENSG00000095319	ENSG00000095319			17859	protein-coding gene	gene with protein product		615587	"KIAA0169"	KIAA0169		11029043	Standard	NM_015354		Approved		uc004bws.2	Q5SRE5	OTTHUMG00000020768	ENST00000372577.2:c.1902T>C	chr9.hg19:g.131745770T>C		167.0	0.0		99.0	4.0	NM_015354	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Silent	SNP	ENST00000372577.2	hg19	CCDS35156.1																																																																																			.	.		0.473	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2			C	131745770	T	C	131745770	2	2	282	1	0	0	0	0	0	0	0	1	10767	1654	58	2		2	NUP188	9	131745770	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1153749	131745770	9467661	680	40914										
C9orf50	375759	hgsc.bcm.edu	37	chr9	132377810	132377810	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcgttgtgtcctgcagggtcTcgtcagcgaatcgcacccgg	14	13	2	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:132377810T>C	ENST00000372478.4	-	4	1034	c.833A>G	c.(832-834)gAg>gGg	p.E278G	NTMT1_ENST00000372486.1_Intron	NM_199350.3	NP_955382.3	Q5SZB4	CI050_HUMAN	chromosome 9 open reading frame 50	278										central_nervous_system(1)|endometrium(4)|large_intestine(2)|ovary(1)|skin(1)|urinary_tract(1)	10		Ovarian(14;0.00556)				CTGCAGGGTCTCGTCAGCGAA	0.647																																					p.E278G		Atlas-SNP	.											.	C9orf50	25	.	0			c.A833G						.						71	61	65					9																	132377810		2203	4300	6503	SO:0001583	missense	375759	exon4			AGGGTCTCGTCAG	AK093122	CCDS35159.1	9q34.2	2012-03-15			ENSG00000179058	ENSG00000179058			23677	protein-coding gene	gene with protein product							Standard	NM_199350		Approved	FLJ35803	uc004byc.4	Q5SZB4	OTTHUMG00000020786	ENST00000372478.4:c.833A>G	chr9.hg19:g.132377810T>C	ENSP00000361556:p.Glu278Gly	105.0	0.0		88.0	4.0	NM_199350	Q2M1I2|Q8NA65	Missense_Mutation	SNP	ENST00000372478.4	hg19	CCDS35159.1	.	.	.	.	.	.	.	.	.	.	t	12.96	2.093219	0.36952	.	.	ENSG00000179058	ENST00000372478	T	0.38887	1.11	3.17	3.17	0.36434	.	0.000000	0.38217	N	0.001765	T	0.48786	0.1519	L	0.36672	1.1	0.29947	N	0.820566	D	0.89917	1.0	D	0.87578	0.998	T	0.40232	-0.9574	10	0.45353	T	0.12	-29.485	8.1854	0.31335	0.0:0.0:0.0:1.0	.	278	Q5SZB4	CI050_HUMAN	G	278	ENSP00000361556:E278G	ENSP00000361556:E278G	E	-	2	0	C9orf50	131417631	1.000000	0.71417	0.913000	0.36048	0.665000	0.39181	3.256000	0.51492	1.692000	0.51112	0.357000	0.21978	GAG	.	.		0.647	C9orf50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054593.1	NM_199350		C	132377810	T	C	132377810	3	2	282	1	0	0	0	0	1	0	0	0	2489	1551	54	2	478	2	C9orf50	9	132377810	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	632040	132377810	8835621	681	40915										
FIBCD1	84929	hgsc.bcm.edu	37	chr9	133799700	133799700	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttgttgcggggccggcccagCccccggtccctctgcagggc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:133799700delC	ENST00000372338.4	-	3	878	c.636delG	c.(634-636)gggfs	p.G212fs	FIBCD1_ENST00000372337.2_Frame_Shift_Del_p.G54fs|FIBCD1_ENST00000253018.4_Frame_Shift_Del_p.G54fs|FIBCD1_ENST00000448616.1_Frame_Shift_Del_p.G212fs	NM_032843.4	NP_116232.3	Q8N539	FBCD1_HUMAN	fibrinogen C domain containing 1	212						integral component of membrane (GO:0016021)|membrane (GO:0016020)	chitin binding (GO:0008061)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(3)|lung(2)|prostate(5)|urinary_tract(1)	12	all_hematologic(7;0.0028)			OV - Ovarian serous cystadenocarcinoma(145;3.52e-05)|Epithelial(140;0.00019)		GCCGGCCCAGCCCCCGGTCCC	0.706																																					p.L213fs		Atlas-INDEL	.											.	FIBCD1	34	.	0			c.637delC						.						10	14	12					9																	133799700		2191	4286	6477	SO:0001589	frameshift_variant	84929	exon3			.	AK027716	CCDS6937.1	9q34.2	2013-02-06			ENSG00000130720	ENSG00000130720		"Fibrinogen C domain containing"	25922	protein-coding gene	gene with protein product		613357				12975309	Standard	NM_001145106		Approved	FLJ14810	uc004bzz.3	Q8N539	OTTHUMG00000020814	ENST00000372338.4:c.636delG	chr9.hg19:g.133799700delC	ENSP00000361413:p.Gly212fs	185.0	0.0		131.0	12.0	NM_032843	A3KFK0|Q6UXK6|Q96SJ7	Frame_Shift_Del	DEL	ENST00000372338.4	hg19	CCDS6937.1																																																																																			.	.		0.706	FIBCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054687.2	NM_032843		-	133799700	C	-	133799700	7	5	282	1	0	1	0	1	0	0	0	0	5892	726	26	0	769	0	FIBCD1	9	133799700	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1421890	133799700	7413731	682	40916										
CEL	1056	hgsc.bcm.edu	37	chr9	135939849	135939849	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cgtcaataagaagctcggccTcctgggtgactctgtggaca	12	11	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:135939849T>C	ENST00000372080.4	+	2	150	c.134T>C	c.(133-135)cTc>cCc	p.L45P	CEL_ENST00000351304.7_Missense_Mutation_p.L42P	NM_001807.3	NP_001798.2	P19835	CEL_HUMAN	carboxyl ester lipase	42	Heparin-binding.				cholesterol catabolic process (GO:0006707)|fatty acid catabolic process (GO:0009062)|intestinal cholesterol absorption (GO:0030299)|intestinal lipid catabolic process (GO:0044258)|lipid digestion (GO:0044241)|lipid metabolic process (GO:0006629)|pancreatic juice secretion (GO:0030157)|protein esterification (GO:0018350)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	acylglycerol lipase activity (GO:0047372)|catalytic activity (GO:0003824)|heparin binding (GO:0008201)|hydrolase activity (GO:0016787)|sterol esterase activity (GO:0004771)|triglyceride lipase activity (GO:0004806)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|pancreas(2)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;1.03e-40)|Epithelial(140;3.58e-37)|GBM - Glioblastoma multiforme(294;0.00164)|READ - Rectum adenocarcinoma(205;0.196)		AAGCTCGGCCTCCTGGGTGAC	0.627																																					p.L45P		Atlas-SNP	.											.	CEL	71	.	0			c.T134C						.						93	105	101					9																	135939849		2059	4198	6257	SO:0001583	missense	1056	exon2			TCGGCCTCCTGGG	M54994	CCDS43896.1	9q34.3	2013-03-13	2013-03-13		ENSG00000170835	ENSG00000170835	3.1.1.3, 3.1.1.13		1848	protein-coding gene	gene with protein product	"bile salt-stimulated lipase"	114840				1676983	Standard	NM_001807		Approved	BSSL, MODY8	uc010naa.2	P19835	OTTHUMG00000020855	ENST00000372080.4:c.134T>C	chr9.hg19:g.135939849T>C	ENSP00000361151:p.Leu45Pro	212.0	0.0		127.0	7.0	NM_001807	Q16398|Q5T7U7|Q9UCH1|Q9UP41	Missense_Mutation	SNP	ENST00000372080.4	hg19	CCDS43896.1	.	.	.	.	.	.	.	.	.	.	T	17.41	3.381891	0.61845	.	.	ENSG00000170835	ENST00000372080;ENST00000351304;ENST00000303626	T;T	0.66815	-0.23;-0.23	4.97	3.83	0.44106	Carboxylesterase, type B (1);	0.232505	0.43110	D	0.000606	T	0.73361	0.3577	L	0.42686	1.345	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.73814	-0.3864	10	0.87932	D	0	.	9.7227	0.40313	0.0:0.0832:0.0:0.9168	.	42	P19835	CEL_HUMAN	P	45;42;45	ENSP00000361151:L45P;ENSP00000342217:L42P	ENSP00000304021:L45P	L	+	2	0	CEL	134929670	1.000000	0.71417	0.979000	0.43373	0.500000	0.33767	4.346000	0.59367	0.853000	0.35312	0.459000	0.35465	CTC	.	.		0.627	CEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054823.1			C	135939849	T	C	135939849	3	2	282	1	0	0	0	0	1	0	0	0	3211	1551	54	2	140	2	CEL	9	135939849	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2140149	135939849	5273582	683	40917										
REXO4	57109	hgsc.bcm.edu	37	chr9	136272192	136272192	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcattgctgcctgggcatccTgaatctagacgacatgaaac	9	11	2	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:136272192T>C	ENST00000371942.3	-	8	1353	c.1154A>G	c.(1153-1155)cAg>cGg	p.Q385R	REXO4_ENST00000371935.2_Missense_Mutation_p.Q213R	NM_020385.2	NP_065118.2	Q9GZR2	REXO4_HUMAN	REX4, RNA exonuclease 4 homolog (S. cerevisiae)	385	Exonuclease.				regulation of transcription, DNA-templated (GO:0006355)	nucleolus (GO:0005730)|nucleus (GO:0005634)	exonuclease activity (GO:0004527)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(4)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	15				OV - Ovarian serous cystadenocarcinoma(145;8.58e-08)|Epithelial(140;9.55e-07)|all cancers(34;1.05e-05)		CTGGGCATCCTGAATCTAGAC	0.592											OREG0019587	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q385R		Atlas-SNP	.											.	REXO4	27	.	0			c.A1154G						.						149	115	126					9																	136272192		2203	4300	6503	SO:0001583	missense	57109	exon8			GCATCCTGAATCT	AF273304	CCDS6969.1, CCDS65179.1	9q34	2008-02-05	2005-08-22	2005-08-22	ENSG00000148300	ENSG00000148300			12820	protein-coding gene	gene with protein product		602930	"Xenopus prevents mitotic catatrophe 2 homolog", "XPMC2 prevents mitotic catastrophe 2 homolog (Xenopus laevis)"	XPMC2H		9325058	Standard	NM_020385		Approved		uc004cdm.3	Q9GZR2	OTTHUMG00000020870	ENST00000371942.3:c.1154A>G	chr9.hg19:g.136272192T>C	ENSP00000361010:p.Gln385Arg	165.0	0.0	1624	100.0	4.0	NM_020385	B2RAT2|Q5T8S4|Q5T8S5|Q5T8S6|Q9GZW3	Missense_Mutation	SNP	ENST00000371942.3	hg19	CCDS6969.1	.	.	.	.	.	.	.	.	.	.	T	14.08	2.429097	0.43122	.	.	ENSG00000148300	ENST00000371942;ENST00000371935;ENST00000454825	T;T;T	0.22336	1.96;1.96;1.96	5.27	5.27	0.74061	Exonuclease (1);Exonuclease, RNase T/DNA polymerase III (1);Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.47340	0.1440	M	0.86573	2.825	0.49389	D	0.999783	B;P	0.46859	0.064;0.885	B;P	0.58130	0.159;0.833	T	0.54642	-0.8263	10	0.87932	D	0	.	12.9216	0.58234	0.0:0.0:0.0:1.0	.	213;385	Q9GZR2-2;Q9GZR2	.;REXO4_HUMAN	R	385;213;213	ENSP00000361010:Q385R;ENSP00000361003:Q213R;ENSP00000394229:Q213R	ENSP00000361003:Q213R	Q	-	2	0	REXO4	135262013	1.000000	0.71417	0.866000	0.34008	0.092000	0.18411	7.238000	0.78173	1.984000	0.57885	0.459000	0.35465	CAG	.	.		0.592	REXO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054899.1			C	136272192	T	C	136272192	3	2	282	1	0	0	0	0	1	0	0	0	13258	1580	55	2	118	2	REXO4	9	136272192	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	332343	136272192	4941239	684	40918										
MAN1B1	11253	hgsc.bcm.edu	37	chr9	139994268	139994268	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtccaggtccttcagtgagtGgtttggcctcggtctcacac							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:139994268delG	ENST00000371589.4	+	6	924	c.851delG	c.(850-852)tggfs	p.W284fs	MAN1B1_ENST00000474902.1_5'UTR	NM_016219.4	NP_057303.2	Q9UKM7	MA1B1_HUMAN	mannosidase, alpha, class 1B, member 1	284					cellular protein metabolic process (GO:0044267)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum quality control compartment (GO:0044322)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			autonomic_ganglia(1)|central_nervous_system(2)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(2)	14	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;3.08e-05)|Epithelial(140;0.000513)		TTCAGTGAGTGGTTTGGCCTC	0.572																																					p.W284fs		Atlas-INDEL	.											.	MAN1B1	40	.	0			c.850delT						.						219	171	187					9																	139994268		2203	4300	6503	SO:0001589	frameshift_variant	11253	exon6			.	AF145732	CCDS7029.1	9q34.3	2014-05-27			ENSG00000177239	ENSG00000177239			6823	protein-coding gene	gene with protein product	"endoplasmic reticulum alpha-mannosidase 1", "alpha 1,2-mannosidase", "endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase 1", "ER alpha 1,2-mannosidase", "Man9GlcNAc2-specific processing alpha-mannosidase"	604346				10409699, 10521544	Standard	NM_016219		Approved	MANA-ER, MRT15	uc004cld.3	Q9UKM7	OTTHUMG00000020978	ENST00000371589.4:c.851delG	chr9.hg19:g.139994268delG	ENSP00000360645:p.Trp284fs	207.0	0.0		174.0	11.0	NM_016219	Q5VSG3|Q9BRS9|Q9Y5K7	Frame_Shift_Del	DEL	ENST00000371589.4	hg19	CCDS7029.1																																																																																			.	.		0.572	MAN1B1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055294.2	NM_016219		-	139994268	G	-	139994268	7	5	282	1	0	1	0	1	0	0	0	0	9221	1357	47	0	873	0	MAN1B1	9	139994268	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	3722076	139994268	1219163	685	40919										
NELF	26012	hgsc.bcm.edu	37	chr9	140350938	140350938	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aggtacgaatagggatgtcgTctaagagagacaaaaaggag	14	4	1	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:140350938T>C	ENST00000371475.3	-	4	860	c.629A>G	c.(628-630)gAc>gGc	p.D210G	NSMF_ENST00000371474.3_Splice_Site_p.D210G|NSMF_ENST00000371468.1_5'Flank|NSMF_ENST00000541195.1_5'Flank|NSMF_ENST00000265663.7_Splice_Site_p.D210G|NSMF_ENST00000371482.1_5'Flank|NSMF_ENST00000339554.3_Splice_Site_p.D9G|NSMF_ENST00000484316.1_5'Flank|NSMF_ENST00000371472.2_Splice_Site_p.D210G|NSMF_ENST00000371473.3_Splice_Site_p.D210G|NSMF_ENST00000392812.4_Splice_Site_p.D210G|NSMF_ENST00000437259.1_Splice_Site_p.D210G	NM_001130969.1	NP_001124441.1	Q6X4W1	NSMF_HUMAN	NMDA receptor synaptonuclear signaling and neuronal migration factor	210	Necessary and sufficient to elicit dendritic processes and synaptic contacts. {ECO:0000250}.				cellular response to amino acid stimulus (GO:0071230)|cellular response to electrical stimulus (GO:0071257)|cellular response to gonadotropin stimulus (GO:0071371)|positive regulation of neuron migration (GO:2001224)|positive regulation of protein dephosphorylation (GO:0035307)|regulation of dendrite morphogenesis (GO:0048814)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuronal synaptic plasticity (GO:0048168)	apical dendrite (GO:0097440)|cell junction (GO:0030054)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|membrane (GO:0016020)|neuron projection (GO:0043005)|nuclear envelope (GO:0005635)|nuclear euchromatin (GO:0005719)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	calcium-dependent protein binding (GO:0048306)										AGGGATGTCGTCTAAGAGAGA	0.542																																					p.D210G		Atlas-SNP	.											.	NSMF	3	.	0			c.A629G						.						116	124	122					9																	140350938		2203	4300	6503	SO:0001630	splice_region_variant	26012	exon4			ATGTCGTCTAAGA		CCDS7044.1, CCDS48067.1, CCDS48068.1, CCDS48069.1, CCDS55357.1	9q34.3	2013-01-14	2013-01-14	2013-01-14	ENSG00000165802	ENSG00000165802			29843	protein-coding gene	gene with protein product		608137	"nasal embryonic LHRH factor"	NELF		11230166, 10898796	Standard	NM_015537		Approved		uc004cna.3	Q6X4W1	OTTHUMG00000020989	ENST00000371475.3:c.629-1A>G	chr9.hg19:g.140350938T>C		127.0	0.0		92.0	5.0	NM_001130970	Q2TB96|Q6X4V7|Q6X4V8|Q6X4V9|Q8N2M2|Q96SY1|Q9NPM4|Q9NPP3|Q9NPS3	Missense_Mutation	SNP	ENST00000371475.3	hg19	CCDS48069.1	.	.	.	.	.	.	.	.	.	.	T	10.28	1.306273	0.23736	.	.	ENSG00000165802	ENST00000339554;ENST00000371475;ENST00000265663;ENST00000437259;ENST00000392812;ENST00000371474;ENST00000371473;ENST00000371472	T;T;T;T;T;T;T;T	0.50277	0.82;0.81;0.78;0.76;0.76;0.75;0.79;0.78	4.55	4.55	0.56014	.	0.217452	0.36665	N	0.002473	T	0.32585	0.0834	N	0.19112	0.55	0.80722	D	1	B;B;B;B;B	0.32781	0.384;0.222;0.384;0.183;0.183	B;B;B;B;B	0.30572	0.117;0.086;0.117;0.058;0.058	T	0.17745	-1.0359	10	0.41790	T	0.15	.	13.0745	0.59079	0.0:0.0:0.0:1.0	.	210;210;210;210;210	Q6X4W1-3;Q2TB96;Q6X4W1-4;Q6X4W1;Q6X4W1-2	.;.;.;NELF_HUMAN;.	G	9;210;210;210;210;210;210;210	ENSP00000342966:D9G;ENSP00000360530:D210G;ENSP00000265663:D210G;ENSP00000412007:D210G;ENSP00000376559:D210G;ENSP00000360529:D210G;ENSP00000360528:D210G;ENSP00000360527:D210G	ENSP00000265663:D210G	D	-	2	0	NELF	139470759	1.000000	0.71417	0.963000	0.40424	0.026000	0.11368	4.678000	0.61641	1.686000	0.51046	0.379000	0.24179	GAC	.	.		0.542	NSMF-204	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015537	Missense_Mutation	C	140350938	T	C	140350938	5	2	282	1	0	0	0	0	0	0	1	0	10341	1681	58	2	1025	2	NELF	9	140350938	Splice_Site	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	356670	140350938	862493	686	40920										
EHMT1	79813	hgsc.bcm.edu	37	chr9	140611475	140611475	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cttcctggaggggctggcaaAggcaggactccaagcgcttt	14	11	0	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:140611475A>G	ENST00000460843.1	+	3	510	c.483A>G	c.(481-483)aaA>aaG	p.K161K	EHMT1_ENST00000334856.6_Silent_p.K130K|EHMT1_ENST00000371394.2_3'UTR|EHMT1_ENST00000462484.1_Silent_p.K161K	NM_024757.4	NP_079033.4	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	161					chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|embryo development (GO:0009790)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|methyltransferase activity (GO:0008168)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		GGGCTGGCAAAGGCAGGACTC	0.647																																					p.K161K		Atlas-SNP	.											.	EHMT1	196	.	0			c.A483G						.						40	42	41					9																	140611475		2203	4299	6502	SO:0001819	synonymous_variant	79813	exon3			TGGCAAAGGCAGG	AY083210	CCDS7050.1, CCDS7050.2, CCDS56595.1	9q34.3	2013-09-20			ENSG00000181090	ENSG00000181090	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases", "Ankyrin repeat domain containing"	24650	protein-coding gene	gene with protein product		607001	"euchromatic histone methyltransferase 1"			11347906, 12004135	Standard	NM_024757		Approved	Eu-HMTase1, FLJ12879, KIAA1876, bA188C12.1, KMT1D	uc011mfc.2	Q9H9B1	OTTHUMG00000020995	ENST00000460843.1:c.483A>G	chr9.hg19:g.140611475A>G		69.0	0.0		54.0	4.0	NM_001145527	B1AQ58|B1AQ59|Q86X08|Q8TCN7|Q96F53|Q96JF1|Q96KH4	Silent	SNP	ENST00000460843.1	hg19	CCDS7050.2																																																																																			.	.		0.647	EHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055371.2	NM_024757		G	140611475	A	G	140611475	2	3	282	1	0	0	0	0	0	0	0	1	4985	69	3	2		2	EHMT1	9	140611475	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	260537	140611475	601956	687	40921										
LARP4B	23185	hgsc.bcm.edu	37	chr10	876909	876909	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttatctcctttaaatagtgcTtctacttcctacaggaaata	4	9	2	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:876909T>C	ENST00000316157.3	-	8	799	c.759A>G	c.(757-759)gaA>gaG	p.E253E		NM_015155.1	NP_055970.1	Q92615	LAR4B_HUMAN	La ribonucleoprotein domain family, member 4B	253	RRM.				positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)	p.E253D(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(2)|skin(2)|urinary_tract(2)	38						TAAATAGTGCTTCTACTTCCT	0.284																																					p.E253E		Atlas-SNP	.											LARP4B,colon,carcinoma,0,2	LARP4B	110	.	1	Substitution - Missense(1)	lung(1)	c.A759G						.						69	77	75					10																	876909		2201	4298	6499	SO:0001819	synonymous_variant	23185	exon9			TAGTGCTTCTACT	D86971	CCDS31131.1	10p15.3	2011-08-24	2009-06-09	2009-06-09	ENSG00000107929	ENSG00000107929		"La ribonucleoprotein domain containing"	28987	protein-coding gene	gene with protein product			"KIAA0217", "La ribonucleoprotein domain family, member 5"	KIAA0217, LARP5		9039502, 20573744	Standard	NM_015155		Approved		uc031ptb.1	Q92615	OTTHUMG00000017534	ENST00000316157.3:c.759A>G	chr10.hg19:g.876909T>C		93.0	0.0		60.0	3.0	NM_015155	A7MD20|Q5T3R3|Q5T3R4|Q5T3R5|Q68CY4	Silent	SNP	ENST00000316157.3	hg19	CCDS31131.1																																																																																			.	.		0.284	LARP4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046395.2	NM_015155		C	876909	T	C	876909	2	2	282	1	0	0	0	0	0	0	0	1	8640	1606	56	2		2	LARP4B	10	876909	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10		876909	134657838	688	40922										
IDI1	3422	hgsc.bcm.edu	37	chr10	1087256	1087256	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttaatttcaccactggctgcTtttttcagaagttcttttag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:1087256delT	ENST00000381344.3	-	5	892	c.726delA	c.(724-726)aaafs	p.K242fs	IDI2-AS1_ENST00000428780.2_RNA|IDI2-AS1_ENST00000420381.1_RNA|IDI2-AS1_ENST00000536039.1_RNA|RNU7-163P_ENST00000459467.1_RNA|IDI1_ENST00000491735.1_5'UTR|IDI2-AS1_ENST00000437374.1_RNA	NM_004508.2	NP_004499.2	Q13907	IDI1_HUMAN	isopentenyl-diphosphate delta isomerase 1	185					cholesterol biosynthetic process (GO:0006695)|dimethylallyl diphosphate biosynthetic process (GO:0050992)|isoprenoid biosynthetic process (GO:0008299)|response to stilbenoid (GO:0035634)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)	hydrolase activity (GO:0016787)|isopentenyl-diphosphate delta-isomerase activity (GO:0004452)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|metal ion binding (GO:0046872)			large_intestine(3)|lung(2)|prostate(1)	6		all_epithelial(10;0.107)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.221)	Epithelial(11;0.0972)		CACTGGCTGCTTTTTTCAGAA	0.333																																					p.A243fs		Atlas-INDEL	.											.,1	IDI1	22	.	0			c.727delG						.						82	82	82					10																	1087256		2202	4297	6499	SO:0001589	frameshift_variant	3422	exon5			.	BC006999	CCDS7056.1	10p15.3	2003-11-12	2005-07-25		ENSG00000067064	ENSG00000067064	5.3.3.2		5387	protein-coding gene	gene with protein product	"IPP isomerase"	604055	"isopentenyl-diphosphate delta isomerase"			8020941	Standard	NM_004508		Approved		uc001iga.3	Q13907	OTTHUMG00000017536	ENST00000381344.3:c.726delA	chr10.hg19:g.1087256delT	ENSP00000370748:p.Lys242fs	255.0	0.0		219.0	14.0	NM_004508	B4E155|Q32Q13|Q53GQ6|Q86U81|Q8WUX8|Q96IZ4|Q9BQ74	Frame_Shift_Del	DEL	ENST00000381344.3	hg19	CCDS7056.1																																																																																			.	.		0.333	IDI1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046409.2	NM_004508		-	1087256	T	-	1087256	7	5	282	1	0	1	0	1	0	0	0	0	7508	1606	56	0	132	0	IDI1	10	1087256	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	210347	1087256	134447491	689	40923										
WDR37	22884	hgsc.bcm.edu	37	chr10	1170240	1170240	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cggtgaaagtctgggacttgAaaaatatgagatcccccatt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:1170240delA	ENST00000358220.1	+	12	1330	c.1186delA	c.(1186-1188)aaafs	p.K396fs	WDR37_ENST00000263150.4_Frame_Shift_Del_p.K396fs|WDR37_ENST00000482165.1_3'UTR			Q9Y2I8	WDR37_HUMAN	WD repeat domain 37	396										breast(2)|endometrium(2)|kidney(1)|lung(9)|prostate(2)|skin(1)	17		all_epithelial(10;0.0449)|Colorectal(49;0.142)		Epithelial(11;0.134)		CTGGGACTTGAAAAATATGAG	0.473																																					p.L395fs		Atlas-INDEL	.											.	WDR37	52	.	0			c.1185delG						.						136	122	127					10																	1170240		2203	4300	6503	SO:0001589	frameshift_variant	22884	exon12			.	AB023199	CCDS7057.1	10p15.3	2013-01-09			ENSG00000047056	ENSG00000047056		"WD repeat domain containing"	31406	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_014023		Approved	KIAA0982	uc001igf.1	Q9Y2I8	OTTHUMG00000017540	ENST00000358220.1:c.1186delA	chr10.hg19:g.1170240delA	ENSP00000350954:p.Lys396fs	140.0	0.0		117.0	11.0	NM_014023	A8K976|D3DRQ7|Q5SW03|Q8WVG2|Q9NTJ6	Frame_Shift_Del	DEL	ENST00000358220.1	hg19	CCDS7057.1																																																																																			.	.		0.473	WDR37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046418.1	NM_014023		-	1170240	A	-	1170240	7	5	282	1	0	1	0	1	0	0	0	0	17306	247	9	0	1228	0	WDR37	10	1170240	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	82984	1170240	134364507	690	40924										
PFKP	5214	hgsc.bcm.edu	37	chr10	3155593	3155593	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aacgtagctgtcatcaacgtGggggcacccgcggctgggat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:3155593delG	ENST00000381125.4	+	13	1330	c.1254delG	c.(1252-1254)gtgfs	p.V418fs	PFKP_ENST00000381075.2_Frame_Shift_Del_p.V410fs	NM_002627.4	NP_002618.1	Q01813	PFKAP_HUMAN	phosphofructokinase, platelet	418	C-terminal regulatory PFK domain 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 6-phosphate metabolic process (GO:0006002)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein complex binding (GO:0032403)			breast(2)|central_nervous_system(4)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)		TCATCAACGTGGGGGCACCCG	0.597																																					p.V418fs		Atlas-INDEL	.											.	PFKP	182	.	0			c.1253delT						.						43	38	40					10																	3155593		2203	4300	6503	SO:0001589	frameshift_variant	5214	exon13			.	AK092597	CCDS7059.1, CCDS55698.1	10p15.3-p15.2	2006-08-25			ENSG00000067057	ENSG00000067057	2.7.1.11		8878	protein-coding gene	gene with protein product	"Phosphofructokinase, platelet type"	171840					Standard	NM_002627		Approved	PFK-C, PFKF	uc001igp.3	Q01813	OTTHUMG00000017556	ENST00000381125.4:c.1254delG	chr10.hg19:g.3155593delG	ENSP00000370517:p.Val418fs	163.0	0.0		146.0	12.0	NM_002627	B3KS15|Q5VSR7|Q5VSR8	Frame_Shift_Del	DEL	ENST00000381125.4	hg19	CCDS7059.1																																																																																			.	.		0.597	PFKP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046454.1	NM_002627		-	3155593	G	-	3155593	7	5	282	1	0	1	0	1	0	0	0	0	11775	1335	47	0	1304	0	PFKP	10	3155593	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1985353	3155593	132379154	691	40925										
PITRM1	10531	hgsc.bcm.edu	37	chr10	3199171	3199171	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaaattttggattttcctgcAggcactgtctgaatttagct	8	7	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:3199171A>G	ENST00000224949.4	-	13	1467	c.1433T>C	c.(1432-1434)cTg>cCg	p.L478P	PITRM1-AS1_ENST00000601046.1_RNA|PITRM1-AS1_ENST00000598280.1_RNA|PITRM1_ENST00000380989.2_Missense_Mutation_p.L478P|PITRM1_ENST00000451104.2_Missense_Mutation_p.L446P|PITRM1_ENST00000380994.1_Missense_Mutation_p.L36P			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	478					positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						ATTTTCCTGCAGGCACTGTCT	0.353																																					p.L478P		Atlas-SNP	.											.	PITRM1	109	.	0			c.T1433C						.						64	56	59					10																	3199171		1817	4077	5894	SO:0001583	missense	10531	exon13			TCCTGCAGGCACT	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"PreP peptidasome"		"pitrilysin metalloproteinase 1"			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.1433T>C	chr10.hg19:g.3199171A>G	ENSP00000224949:p.Leu478Pro	138.0	0.0		93.0	4.0	NM_014889	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Missense_Mutation	SNP	ENST00000224949.4	hg19	CCDS59208.1	.	.	.	.	.	.	.	.	.	.	a	20.2	3.944531	0.73672	.	.	ENSG00000107959	ENST00000224949;ENST00000380980;ENST00000380989;ENST00000380994;ENST00000451104	T;T;T;T	0.12774	2.65;2.65;2.65;2.65	5.49	5.49	0.81192	Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.000000	0.85682	D	0.000000	T	0.41026	0.1141	M	0.83953	2.67	0.80722	D	1	D;P;D;D;D;D	0.63046	0.984;0.932;0.992;0.987;0.987;0.987	P;P;D;D;D;D	0.68621	0.827;0.702;0.959;0.927;0.927;0.927	T	0.39742	-0.9599	10	0.66056	D	0.02	-26.133	15.8835	0.79222	1.0:0.0:0.0:0.0	.	471;446;478;478;478;471	E9PDX6;E7ES23;Q5JRX3-2;C9JSL2;Q5JRX3;B4DH07	.;.;.;.;PREP_HUMAN;.	P	478;471;478;36;446	ENSP00000224949:L478P;ENSP00000370377:L478P;ENSP00000370382:L36P;ENSP00000401201:L446P	ENSP00000224949:L478P	L	-	2	0	PITRM1	3189171	1.000000	0.71417	0.842000	0.33263	0.765000	0.43378	8.601000	0.90864	2.212000	0.71576	0.460000	0.39030	CTG	.	.		0.353	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2			G	3199171	A	G	3199171	3	3	282	1	0	0	0	0	1	0	0	0	11962	188	7	2	1740	2	PITRM1	10	3199171	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	43578	3199171	132335576	692	40926										
ITIH5	80760	hgsc.bcm.edu	37	chr10	7618714	7618714	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tctccatcgcctccaggcctGgggcttcctgtgacatcttt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:7618714delG	ENST00000256861.6	-	10	1758	c.1680delC	c.(1678-1680)cccfs	p.P560fs	ITIH5_ENST00000298441.6_Frame_Shift_Del_p.P346fs|ITIH5_ENST00000397145.2_Frame_Shift_Del_p.P560fs|ITIH5_ENST00000446830.2_Frame_Shift_Del_p.P342fs|ITIH5_ENST00000397146.2_Frame_Shift_Del_p.P560fs|ITIH5_ENST00000434980.1_5'UTR	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	560					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						CTCCAGGCCTGGGGCTTCCTG	0.577																																					p.R561fs		Atlas-INDEL	.											.	ITIH5	343	.	0			c.1681delA						.						59	58	58					10																	7618714		2203	4300	6503	SO:0001589	frameshift_variant	80760	exon10			.			10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"inter-alpha (globulin) inhibitor H5"			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.1680delC	chr10.hg19:g.7618714delG	ENSP00000256861:p.Pro560fs	219.0	0.0		144.0	11.0	NM_001001851	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Frame_Shift_Del	DEL	ENST00000256861.6	hg19																																																																																				.	.		0.577	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569		-	7618714	G	-	7618714	7	5	282	1	0	1	0	1	0	0	0	0	7916	1335	47	0	1291	0	ITIH5	10	7618714	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	4419543	7618714	127916033	693	40927										
UPF2	26019	hgsc.bcm.edu	37	chr10	11997384	11997384	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gagccatcaggattaacaccAaatgaggtaaaagaatacag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:11997384delA	ENST00000356352.2	-	13	3170	c.2697delT	c.(2695-2697)tttfs	p.F899fs	UPF2_ENST00000357604.5_Frame_Shift_Del_p.F899fs|UPF2_ENST00000397053.2_Frame_Shift_Del_p.F899fs			Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog (yeast)	899	MIF4G 3.|Sufficient for interaction with EIF4A1 and EIF1.|Sufficient for interaction with UPF3A and UPF3B.				gene expression (GO:0010467)|liver development (GO:0001889)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|organ regeneration (GO:0031100)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(14)|lung(17)|ovary(2)|skin(3)|urinary_tract(2)	56		Renal(717;0.228)				GATTAACACCAAATGAGGTAA	0.438																																					p.G900fs		Atlas-INDEL	.											.	UPF2	111	.	0			c.2698delG						.						79	72	75					10																	11997384		2203	4300	6503	SO:0001589	frameshift_variant	26019	exon14			.	AB037829	CCDS7086.1	10p14-p13	2011-06-21			ENSG00000151461	ENSG00000151461			17854	protein-coding gene	gene with protein product	"smg-3 homolog, nonsense mediated mRNA decay factor (C. elegans)"	605529				11073994, 11113196	Standard	NM_080599		Approved	RENT2, DKFZP434D222, KIAA1408, smg-3	uc001ilb.3	Q9HAU5	OTTHUMG00000017678	ENST00000356352.2:c.2697delT	chr10.hg19:g.11997384delA	ENSP00000348708:p.Phe899fs	202.0	0.0		127.0	10.0	NM_080599	A6NLJ5|D3DRS0|Q14BM1|Q5W0J4|Q8N8U1|Q9H1J2|Q9NWL1|Q9P2D9|Q9Y4M9	Frame_Shift_Del	DEL	ENST00000356352.2	hg19	CCDS7086.1																																																																																			.	.		0.438	UPF2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046783.1			-	11997384	A	-	11997384	7	5	282	1	0	1	0	1	0	0	0	0	17019	127	5	0	1157	0	UPF2	10	11997384	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	4378670	11997384	123537363	694	40928										
FAM171A1	221061	hgsc.bcm.edu	37	chr10	15255681	15255681	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggcctgggaagacaggggctGgggctggatctgtgaggacg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:15255681delG	ENST00000378116.4	-	8	1912	c.1906delC	c.(1906-1908)cagfs	p.Q636fs	FAM171A1_ENST00000477161.1_5'Flank	NM_001010924.1	NP_001010924.1	Q5VUB5	F1711_HUMAN	family with sequence similarity 171, member A1	636						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(6)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	52						GACAGGGGCTGGGGCTGGATC	0.612																																					p.Q636fs		Atlas-INDEL	.											.	FAM171A1	252	.	0			c.1907delA						.						50	59	56					10																	15255681		2203	4300	6503	SO:0001589	frameshift_variant	221061	exon8			.	AK022946	CCDS31154.1	10p13	2008-06-16	2008-06-16	2008-06-16	ENSG00000148468	ENSG00000148468			23522	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 38"	C10orf38			Standard	NM_001010924		Approved	FLJ12884	uc001iob.3	Q5VUB5	OTTHUMG00000017732	ENST00000378116.4:c.1906delC	chr10.hg19:g.15255681delG	ENSP00000367356:p.Gln636fs	205.0	0.0		165.0	10.0	NM_001010924	D3DRT9|Q32M49|Q8N4I0	Frame_Shift_Del	DEL	ENST00000378116.4	hg19	CCDS31154.1																																																																																			.	.		0.612	FAM171A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046984.1	XM_167709		-	15255681	G	-	15255681	7	5	282	1	0	1	0	1	0	0	0	0	5495	1357	47	0	770	0	FAM171A1	10	15255681	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	3258297	15255681	120279066	695	40929										
VIM	7431	hgsc.bcm.edu	37	chr10	17278320	17278320	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tctggattcactccctctggTtgatacccactcaaaaagga	7	12	4	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:17278320T>C	ENST00000224237.5	+	8	1446	c.1301T>C	c.(1300-1302)gTt>gCt	p.V434A	RP11-124N14.3_ENST00000456355.1_RNA|VIM_ENST00000544301.1_Missense_Mutation_p.V434A			P08670	VIME_HUMAN	vimentin	434	Tail.				apoptotic process (GO:0006915)|astrocyte development (GO:0014002)|Bergmann glial cell differentiation (GO:0060020)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular component movement (GO:0006928)|intermediate filament organization (GO:0045109)|lens fiber cell development (GO:0070307)|muscle filament sliding (GO:0030049)|negative regulation of neuron projection development (GO:0010977)|positive regulation of gene expression (GO:0010628)|viral process (GO:0016032)	cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|neuron projection (GO:0043005)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	double-stranded RNA binding (GO:0003725)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(2)|lung(18)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CTCCCTCTGGTTGATACCCAC	0.363																																					p.V434A		Atlas-SNP	.											.	VIM	71	.	0			c.T1301C						.						151	167	161					10																	17278320		2203	4300	6503	SO:0001583	missense	7431	exon9			CTCTGGTTGATAC	M14144	CCDS7120.1	10p13	2013-01-16			ENSG00000026025	ENSG00000026025		"Intermediate filaments type III"	12692	protein-coding gene	gene with protein product		193060					Standard	NM_003380		Approved		uc001iou.2	P08670	OTTHUMG00000017744	ENST00000224237.5:c.1301T>C	chr10.hg19:g.17278320T>C	ENSP00000224237:p.Val434Ala	103.0	0.0		85.0	4.0	NM_003380	B0YJC2|D3DRU4|Q15867|Q15868|Q15869|Q548L2|Q6LER9|Q8N850|Q96ML2|Q9NTM3	Missense_Mutation	SNP	ENST00000224237.5	hg19	CCDS7120.1	.	.	.	.	.	.	.	.	.	.	T	9.246	1.039461	0.19669	.	.	ENSG00000026025	ENST00000544301;ENST00000224237	D;D	0.96992	-4.2;-4.2	6.01	6.01	0.97437	.	0.000000	0.41938	D	0.000785	D	0.90714	0.7086	N	0.05441	-0.05	0.48288	D	0.999624	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	D	0.86699	0.1928	10	0.25106	T	0.35	.	16.5319	0.84362	0.0:0.0:0.0:1.0	.	434;434	Q53HU8;P08670	.;VIME_HUMAN	A	434	ENSP00000446007:V434A;ENSP00000224237:V434A	ENSP00000224237:V434A	V	+	2	0	VIM	17318326	0.999000	0.42202	0.984000	0.44739	0.724000	0.41520	2.999000	0.49473	2.295000	0.77249	0.523000	0.50628	GTT	.	.		0.363	VIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047015.1	NM_003380		C	17278320	T	C	17278320	3	2	282	1	0	0	0	0	1	0	0	0	17181	1725	60	2	1331	2	VIM	10	17278320	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2022639	17278320	118256427	696	40930										
SLC39A12	221074	hgsc.bcm.edu	37	chr10	18331679	18331679	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cacaacgaccctggatgatgTttctcctgcaaaactttgga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:18331679delT	ENST00000377369.2	+	13	2266	c.1993delT	c.(1993-1995)tttfs	p.F665fs	SLC39A12_ENST00000377371.3_Frame_Shift_Del_p.F664fs|SLC39A12_ENST00000539911.1_Frame_Shift_Del_p.F531fs|SLC39A12_ENST00000377374.4_Frame_Shift_Del_p.F628fs	NM_001145195.1|NM_001282733.1|NM_001282734.1	NP_001138667.1|NP_001269662.1|NP_001269663.1	Q504Y0	S39AC_HUMAN	solute carrier family 39 (zinc transporter), member 12	665					regulation of microtubule polymerization (GO:0031113)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)|zinc ion transmembrane import (GO:0071578)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	zinc ion transmembrane transporter activity (GO:0005385)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(5)|lung(38)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	60						CTGGATGATGTTTCTCCTGCA	0.358																																					p.M664fs		Atlas-INDEL	.											.	SLC39A12	181	.	0			c.1992delG						.						117	112	114					10																	18331679		2203	4300	6503	SO:0001589	frameshift_variant	221074	exon13			.		CCDS7124.1, CCDS44362.1, CCDS60493.1, CCDS60494.1	10p12.33	2013-05-22			ENSG00000148482	ENSG00000148482		"Solute carriers"	20860	protein-coding gene	gene with protein product		608734	"solute carrier family 39 (metal ion transporter), member 12"			12659941	Standard	NM_152725		Approved	FLJ30499	uc001ipo.2	Q504Y0	OTTHUMG00000017759	ENST00000377369.2:c.1993delT	chr10.hg19:g.18331679delT	ENSP00000366586:p.Phe665fs	151.0	0.0		146.0	10.0	NM_001145195	B7ZL35|C9JJL4|Q49AN8|Q4G0L3|Q5VWV8|Q5VWV9|Q6NZY5|Q96NN4	Frame_Shift_Del	DEL	ENST00000377369.2	hg19	CCDS44362.1																																																																																			.	.		0.358	SLC39A12-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_152725		-	18331679	T	-	18331679	7	5	282	1	0	1	0	1	0	0	0	0	14630	1725	60	0	2039	0	SLC39A12	10	18331679	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1053359	18331679	117203068	697	40931										
CACNB2	783	hgsc.bcm.edu	37	chr10	18439889	18439889	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcatctgatactacctcaaaTagttttgttcgccaggtaag	7	9	3	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:18439889T>C	ENST00000324631.7	+	2	258	c.198T>C	c.(196-198)aaT>aaC	p.N66N	CACNB2_ENST00000377331.2_Silent_p.N38N|CACNB2_ENST00000352115.6_Silent_p.N66N|CACNB2_ENST00000282343.8_Silent_p.N38N|CACNB2_ENST00000377328.1_Silent_p.N66N|CACNB2_ENST00000467034.1_3'UTR	NM_201593.2|NM_201596.2	NP_963887.2|NP_963890.2	Q08289	CACB2_HUMAN	calcium channel, voltage-dependent, beta 2 subunit	66					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|neuromuscular junction development (GO:0007528)|positive regulation of calcium ion transport (GO:0051928)|synaptic transmission (GO:0007268)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|voltage-gated calcium channel complex (GO:0005891)	calcium channel activity (GO:0005262)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(12)|prostate(1)|skin(3)|stomach(2)	31					Amlodipine(DB00381)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CTACCTCAAATAGTTTTGTTC	0.313																																					p.N66N		Atlas-SNP	.											.	CACNB2	220	.	0			c.T198C						.						131	138	135					10																	18439889		2203	4300	6503	SO:0001819	synonymous_variant	783	exon2			CTCAAATAGTTTT	U95019	CCDS7125.1, CCDS7126.1, CCDS7127.1, CCDS7128.1, CCDS7129.1, CCDS41493.1, CCDS41494.1	10p12	2014-09-17			ENSG00000165995	ENSG00000165995		"Calcium channel subunits"	1402	protein-coding gene	gene with protein product		600003		MYSB, CACNLB2		9254841, 8494331	Standard	NM_201596		Approved		uc001ipr.2	Q08289	OTTHUMG00000017764	ENST00000324631.7:c.198T>C	chr10.hg19:g.18439889T>C		169.0	0.0		127.0	48.0	NM_201597	A6PVM5|A6PVM7|A6PVM8|O00304|Q5QJ99|Q5QJA0|Q5VVG9|Q5VVH0|Q5VWV6|Q6TME1|Q6TME2|Q6TME3|Q8WX81|Q96NZ3|Q96NZ4|Q96NZ5|Q9BWU2|Q9HD32|Q9Y340|Q9Y341	Silent	SNP	ENST00000324631.7	hg19	CCDS7125.1																																																																																			.	.		0.313	CACNB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047072.2	NM_000724		C	18439889	T	C	18439889	2	2	282	1	0	0	0	0	0	0	0	1	2555	1403	49	2		2	CACNB2	10	18439889	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	108210	18439889	117094858	698	40932										
NEBL	10529	hgsc.bcm.edu	37	chr10	21178796	21178796	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagaaataaaagcaccgataTtttttacatggtttagcata							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:21178796delT	ENST00000377122.4	-	3	632	c.236delA	c.(235-237)aatfs	p.N79fs	NEBL_ENST00000417816.2_Intron|NEBL_ENST00000377159.4_Intron|NEBL_ENST00000377119.1_Frame_Shift_Del_p.N79fs	NM_006393.2	NP_006384.1	O76041	NEBL_HUMAN	nebulette	79					cardiac muscle thin filament assembly (GO:0071691)	extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|cytoskeletal protein binding (GO:0008092)|filamin binding (GO:0031005)|structural constituent of muscle (GO:0008307)|tropomyosin binding (GO:0005523)			NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						AGCACCGATATTTTTTACATG	0.313																																					p.N79fs		Atlas-INDEL	.											.	NEBL	199	.	0			c.237delT						.						92	95	94					10																	21178796		2202	4300	6502	SO:0001589	frameshift_variant	10529	exon3			.	Y16241	CCDS7133.1, CCDS7134.1	10p12	2014-09-17			ENSG00000078114	ENSG00000078114			16932	protein-coding gene	gene with protein product		605491				9733644, 10470015	Standard	NM_213569		Approved		uc001iqi.3	O76041	OTTHUMG00000017788	ENST00000377122.4:c.236delA	chr10.hg19:g.21178796delT	ENSP00000366326:p.Asn79fs	217.0	0.0		159.0	11.0	NM_006393	B0YJ45|Q2TBD0|Q70I54|Q9UIC4	Frame_Shift_Del	DEL	ENST00000377122.4	hg19	CCDS7134.1																																																																																			.	.		0.313	NEBL-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047113.1	NM_006393		-	21178796	T	-	21178796	7	5	282	1	0	1	0	1	0	0	0	0	10312	1493	52	0	2912	0	NEBL	10	21178796	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2738907	21178796	114355951	699	40933										
PTF1A	256297	hgsc.bcm.edu	37	chr10	23482645	23482645	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctgtccagggtccccctcccCcagcgaccctgattatggcc	9	19	0	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:23482645C>T	ENST00000376504.3	+	2	1001	c.797C>T	c.(796-798)cCc>cTc	p.P266L		NM_178161.2	NP_835455.1	Q7RTS3	PTF1A_HUMAN	pancreas specific transcription factor, 1a	266					amacrine cell differentiation (GO:0035881)|cerebellum development (GO:0021549)|embryo development (GO:0009790)|endocrine pancreas development (GO:0031018)|exocrine pancreas development (GO:0031017)|neuron fate commitment (GO:0048663)|pancreas development (GO:0031016)|regulation of neural retina development (GO:0061074)|regulation of transcription, DNA-templated (GO:0006355)|retina layer formation (GO:0010842)|retinoic acid receptor signaling pathway (GO:0048384)|tissue development (GO:0009888)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)			endometrium(1)|large_intestine(1)|lung(3)|pancreas(1)|skin(1)	7						TCCCCCTCCCCCAGCGACCCT	0.502																																					p.P266L		Atlas-SNP	.											.	PTF1A	24	.	0			c.C797T						.						158	180	172					10																	23482645		2203	4300	6503	SO:0001583	missense	256297	exon2			CCTCCCCCAGCGA	BK000272	CCDS7143.1	10p12.31	2013-05-21			ENSG00000168267	ENSG00000168267		"Basic helix-loop-helix proteins"	23734	protein-coding gene	gene with protein product		607194				8703005	Standard	NM_178161		Approved	PTF1-p48, bHLHa29	uc001irp.3	Q7RTS3	OTTHUMG00000017815	ENST00000376504.3:c.797C>T	chr10.hg19:g.23482645C>T	ENSP00000365687:p.Pro266Leu	148.0	0.0		100.0	4.0	NM_178161	Q9HC25	Missense_Mutation	SNP	ENST00000376504.3	hg19	CCDS7143.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.090143	0.76756	.	.	ENSG00000168267	ENST00000376504	D	0.95069	-3.6	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	D	0.96688	0.8919	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.96683	0.9505	10	0.59425	D	0.04	-8.961	19.2737	0.94021	0.0:1.0:0.0:0.0	.	266	Q7RTS3	PTF1A_HUMAN	L	266	ENSP00000365687:P266L	ENSP00000365687:P266L	P	+	2	0	PTF1A	23522651	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	7.367000	0.79558	2.649000	0.89929	0.555000	0.69702	CCC	.	.		0.502	PTF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047210.1	NM_178161		T	23482645	C	T	23482645	3	4	282	1	0	0	0	0	1	0	0	0	12752	623	22	3	803	3	PTF1A	10	23482645	Missense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	2303849	23482645	112052102	700	40934										
APBB1IP	54518	hgsc.bcm.edu	37	chr10	26802473	26802473	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttcttatttcatcagagaggTtttttgaagaccatgaaaat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:26802473delT	ENST00000376236.4	+	8	1152	c.697delT	c.(697-699)tttfs	p.F234fs		NM_019043.3	NP_061916.3	Q7Z5R6	AB1IP_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	234	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				blood coagulation (GO:0007596)|platelet activation (GO:0030168)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(27)|skin(7)|upper_aerodigestive_tract(1)	45						ATCAGAGAGGTTTTTTGAAGA	0.343																																					p.R232fs		Atlas-INDEL	.											.	APBB1IP	117	.	0			c.696delG						.						67	72	70					10																	26802473		2203	4300	6503	SO:0001589	frameshift_variant	54518	exon8			.	AB085852	CCDS31167.1	10p12.1	2013-01-10			ENSG00000077420	ENSG00000077420		"Pleckstrin homology (PH) domain containing"	17379	protein-coding gene	gene with protein product	"Rap1-GTP-interacting adaptor molecule"	609036				9407065	Standard	NM_019043		Approved	INAG1, RIAM	uc001iss.3	Q7Z5R6	OTTHUMG00000017841	ENST00000376236.4:c.697delT	chr10.hg19:g.26802473delT	ENSP00000365411:p.Phe234fs	270.0	0.0		156.0	10.0	NM_019043	Q8IWS8|Q8IYL7|Q8IZZ7	Frame_Shift_Del	DEL	ENST00000376236.4	hg19	CCDS31167.1																																																																																			.	.		0.343	APBB1IP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047270.1	NM_019043		-	26802473	T	-	26802473	7	5	282	1	0	1	0	1	0	0	0	0	760	1725	60	0	719	0	APBB1IP	10	26802473	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3319828	26802473	108732274	701	40935										
ANKRD26	22852	hgsc.bcm.edu	37	chr10	27322293	27322293	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagctagttcttgttgaagtTgtctcacaacaacctgataa	7	9	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:27322293T>C	ENST00000376087.4	-	25	3833	c.3668A>G	c.(3667-3669)cAa>cGa	p.Q1223R	ANKRD26_ENST00000376070.3_Missense_Mutation_p.Q780R|ANKRD26_ENST00000436985.2_Missense_Mutation_p.Q1239R	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	1222					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						TTGTTGAAGTTGTCTCACAAC	0.284																																					p.Q1223R		Atlas-SNP	.											.	ANKRD26	179	.	0			c.A3668G						.						141	127	131					10																	27322293		1840	4094	5934	SO:0001583	missense	22852	exon25			TGAAGTTGTCTCA	AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"Ankyrin repeat domain containing"	29186	protein-coding gene	gene with protein product		610855	"thrombocytopenia 2 (autosomal dominant)"	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.3668A>G	chr10.hg19:g.27322293T>C	ENSP00000365255:p.Gln1223Arg	110.0	0.0		81.0	4.0	NM_014915	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Missense_Mutation	SNP	ENST00000376087.4	hg19	CCDS41499.1	.	.	.	.	.	.	.	.	.	.	T	18.79	3.698455	0.68386	.	.	ENSG00000107890	ENST00000376070;ENST00000376087;ENST00000436985	T;T;T	0.77489	3.65;-1.1;-1.1	5.41	4.27	0.50696	.	0.000000	0.51477	D	0.000088	T	0.69913	0.3164	L	0.56124	1.755	0.32221	N	0.575286	P;B;P	0.39480	0.582;0.447;0.675	B;B;B	0.34722	0.188;0.092;0.13	T	0.76061	-0.3097	10	0.72032	D	0.01	.	9.5387	0.39237	0.0:0.0841:0.0:0.9159	.	1223;1222;1239	Q9UPS8-3;Q9UPS8;A1L497	.;ANR26_HUMAN;.	R	780;1223;1239	ENSP00000365238:Q780R;ENSP00000365255:Q1223R;ENSP00000405112:Q1239R	ENSP00000365238:Q780R	Q	-	2	0	ANKRD26	27362299	1.000000	0.71417	0.996000	0.52242	0.988000	0.76386	6.695000	0.74593	0.917000	0.36895	0.477000	0.44152	CAA	.	.		0.284	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1			C	27322293	T	C	27322293	3	2	282	1	0	0	0	0	1	0	0	0	654	1812	63	2	1504	2	ANKRD26	10	27322293	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	519820	27322293	108212454	702	40936										
ANKRD26	22852	hgsc.bcm.edu	37	chr10	27337888	27337888	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tccatttcattatttctgtgTtttttcctttcttcttcaac							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:27337888delT	ENST00000376087.4	-	17	1821	c.1656delA	c.(1654-1656)aaafs	p.K552fs	ANKRD26_ENST00000376070.3_Frame_Shift_Del_p.K109fs|ANKRD26_ENST00000436985.2_Frame_Shift_Del_p.K568fs	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	552					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						TATTTCTGTGTTTTTTCCTTT	0.279																																					p.H553fs		Atlas-INDEL	.											.	ANKRD26	179	.	0			c.1657delC						.						145	133	137					10																	27337888		1896	4120	6016	SO:0001589	frameshift_variant	22852	exon17			.	AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"Ankyrin repeat domain containing"	29186	protein-coding gene	gene with protein product		610855	"thrombocytopenia 2 (autosomal dominant)"	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.1656delA	chr10.hg19:g.27337888delT	ENSP00000365255:p.Lys552fs	270.0	0.0		198.0	15.0	NM_014915	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Frame_Shift_Del	DEL	ENST00000376087.4	hg19	CCDS41499.1																																																																																			.	.		0.279	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1			-	27337888	T	-	27337888	7	5	282	1	0	1	0	1	0	0	0	0	654	1722	60	0	3548	0	ANKRD26	10	27337888	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	15595	27337888	108196859	703	40937										
PTCHD3	374308	hgsc.bcm.edu	37	chr10	27688005	27688005	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acattgtacagacctaaaagAgctcataatccctgtatata	5	9	1	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:27688005A>G	ENST00000438700.3	-	4	1639	c.1522T>C	c.(1522-1524)Tct>Cct	p.S508P		NM_001034842.3	NP_001030014.2	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	508	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|sperm midpiece (GO:0097225)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	55						GACCTAAAAGAGCTCATAATC	0.393																																					p.S508P		Atlas-SNP	.											.	PTCHD3	140	.	0			c.T1522C						.						98	90	93					10																	27688005		2203	4300	6503	SO:0001583	missense	374308	exon4			TAAAAGAGCTCAT	AK126025	CCDS31173.1	10p12.1	2006-05-26			ENSG00000182077	ENSG00000182077			24776	protein-coding gene	gene with protein product		611791					Standard	NM_001034842		Approved	FLJ44037, PTR	uc001itu.2	Q3KNS1	OTTHUMG00000017860	ENST00000438700.3:c.1522T>C	chr10.hg19:g.27688005A>G	ENSP00000417658:p.Ser508Pro	131.0	0.0		113.0	5.0	NM_001034842	I3L499|Q6ZU28	Missense_Mutation	SNP	ENST00000438700.3	hg19	CCDS31173.1	.	.	.	.	.	.	.	.	.	.	A	0.427	-0.905089	0.02453	.	.	ENSG00000182077	ENST00000438700	D	0.83992	-1.79	4.08	2.93	0.34026	Sterol-sensing domain (1);	0.564710	0.19601	N	0.110392	T	0.68284	0.2984	L	0.31371	0.925	0.26782	N	0.969579	B	0.13145	0.007	B	0.17433	0.018	T	0.51156	-0.8741	10	0.19147	T	0.46	-10.37	4.2472	0.10677	0.634:0.1749:0.1911:0.0	.	508	Q3KNS1	PTHD3_HUMAN	P	508	ENSP00000417658:S508P	ENSP00000417658:S508P	S	-	1	0	PTCHD3	27728011	0.347000	0.24853	0.994000	0.49952	0.142000	0.21351	0.242000	0.18087	0.609000	0.30018	0.397000	0.26171	TCT	.	.		0.393	PTCHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047325.3	XM_370541		G	27688005	A	G	27688005	3	3	282	1	0	0	0	0	1	0	0	0	12746	304	11	2	785	2	PTCHD3	10	27688005	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	350117	27688005	107846742	704	40938										
ZEB1	6935	hgsc.bcm.edu	37	chr10	31809977	31809977	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aagctgagaagcctgagtccTctgtttcatcagctactgga	10	10	3	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:31809977T>C	ENST00000320985.10	+	7	1824	c.1714T>C	c.(1714-1716)Tct>Cct	p.S572P	ZEB1_ENST00000446923.2_Missense_Mutation_p.S556P|ZEB1_ENST00000361642.5_Missense_Mutation_p.S573P|ZEB1_ENST00000559858.1_3'UTR|ZEB1_ENST00000542815.3_Missense_Mutation_p.S505P|ZEB1_ENST00000560721.2_Missense_Mutation_p.S552P			P37275	ZEB1_HUMAN	zinc finger E-box binding homeobox 1	572					cartilage development (GO:0051216)|cell proliferation (GO:0008283)|cellular response to amino acid stimulus (GO:0071230)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cochlea morphogenesis (GO:0090103)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain development (GO:0030900)|immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pattern specification process (GO:0007389)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of mesenchymal cell proliferation (GO:0010464)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of T cell differentiation in thymus (GO:0033081)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to activity (GO:0014823)|response to nutrient levels (GO:0031667)|semicircular canal morphogenesis (GO:0048752)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(38)|ovary(3)|skin(6)|upper_aerodigestive_tract(4)	77		Prostate(175;0.0156)				GCCTGAGTCCTCTGTTTCATC	0.448																																					p.S573P	Ovarian(40;423 959 14296 36701 49589)	Atlas-SNP	.											.	ZEB1	173	.	0			c.T1717C						.						76	76	76					10																	31809977		2203	4300	6503	SO:0001583	missense	6935	exon7			GAGTCCTCTGTTT	AK091478	CCDS7169.1, CCDS44370.1, CCDS53505.1, CCDS53506.1, CCDS53507.1	10p11.22	2014-02-14	2007-02-15	2007-02-15	ENSG00000148516	ENSG00000148516		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	11642	protein-coding gene	gene with protein product		189909	"transcription factor 8 (represses interleukin 2 expression)", "posterior polymorphous corneal dystrophy 3"	TCF8, PPCD3		1427828, 1840704, 15384081, 16252232	Standard	NM_001128128		Approved	BZP, ZEB, AREB6, NIL-2-A, Zfhep, Zfhx1a, FECD6	uc001ivu.4	P37275	OTTHUMG00000017907	ENST00000320985.10:c.1714T>C	chr10.hg19:g.31809977T>C	ENSP00000319248:p.Ser572Pro	107.0	0.0		114.0	5.0	NM_001174096	B4DJV0|B4DUW9|E9PCM7|F5H4I8|Q12924|Q13800|Q2KJ05|Q5T968|Q5VZ84|Q8NB68	Missense_Mutation	SNP	ENST00000320985.10	hg19	CCDS7169.1	.	.	.	.	.	.	.	.	.	.	T	6.365	0.435363	0.12045	.	.	ENSG00000148516	ENST00000542879;ENST00000537225;ENST00000361642;ENST00000546250;ENST00000542815;ENST00000320985;ENST00000437844;ENST00000541037;ENST00000543514;ENST00000446923	T;T;T;T;T	0.12569	2.97;2.67;2.71;2.67;2.72	5.45	1.41	0.22369	.	0.719450	0.13046	N	0.418161	T	0.04318	0.0119	N	0.02011	-0.69	0.31820	N	0.626042	B;B;B;B;B;B;B;B	0.09022	0.002;0.0;0.001;0.0;0.0;0.002;0.0;0.0	B;B;B;B;B;B;B;B	0.15052	0.012;0.001;0.002;0.001;0.0;0.005;0.001;0.001	T	0.29181	-1.0020	10	0.30078	T	0.28	-7.9253	4.0274	0.09693	0.0:0.2953:0.3971:0.3076	.	505;572;556;572;572;552;573;572	F5H4I8;F5H1R1;E9PCM7;B2RBI8;A0JLS9;Q5VZ84;Q2KJ05;P37275	.;.;.;.;.;.;.;ZEB1_HUMAN	P	354;572;573;572;505;572;552;431;463;556	ENSP00000444282:S354P;ENSP00000354487:S573P;ENSP00000444891:S505P;ENSP00000319248:S572P;ENSP00000391612:S556P	ENSP00000319248:S572P	S	+	1	0	ZEB1	31849983	0.999000	0.42202	0.397000	0.26308	0.820000	0.46376	1.027000	0.30115	0.442000	0.26555	0.533000	0.62120	TCT	.	.		0.448	ZEB1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419083.2	NM_030751		C	31809977	T	C	31809977	3	2	282	1	0	0	0	0	1	0	0	0	17638	1551	54	2	1754	2	ZEB1	10	31809977	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	4121972	31809977	103724770	705	40939										
CUL2	8453	hgsc.bcm.edu	37	chr10	35328009	35328009	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	catcttttaatctacctagaAcctataaaaatattttctta	1	8	3	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:35328009A>G	ENST00000374748.1	-	10	1029	c.716T>C	c.(715-717)gTt>gCt	p.V239A	CUL2_ENST00000537177.1_Splice_Site_p.V258A|CUL2_ENST00000374742.1_Splice_Site_p.V239A|CUL2_ENST00000374746.1_Splice_Site_p.V239A|CUL2_ENST00000374749.3_Splice_Site_p.V239A|CUL2_ENST00000602371.1_Splice_Site_p.V182A|CUL2_ENST00000374751.3_Splice_Site_p.V239A			Q13617	CUL2_HUMAN	cullin 2	239					cell cycle arrest (GO:0007050)|cellular response to hypoxia (GO:0071456)|G1/S transition of mitotic cell cycle (GO:0000082)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	Cul2-RING ubiquitin ligase complex (GO:0031462)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|VCB complex (GO:0030891)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|prostate(2)|skin(1)|urinary_tract(2)	31						TCTACCTAGAACCTATAAAAA	0.313																																					p.V258A		Atlas-SNP	.											.	CUL2	63	.	0			c.T773C						.						61	58	59					10																	35328009		2202	4293	6495	SO:0001630	splice_region_variant	8453	exon9			CCTAGAACCTATA	U83410	CCDS7179.1, CCDS73086.1	10p11.2	2011-05-24			ENSG00000108094	ENSG00000108094			2552	protein-coding gene	gene with protein product		603135				8681378	Standard	NM_003591		Approved		uc021ppa.1	Q13617	OTTHUMG00000017950	ENST00000374748.1:c.715-1T>C	chr10.hg19:g.35328009A>G		82.0	0.0		82.0	4.0	NM_001198778	B3KT95|B7Z6K8|D3DRY6|G3V1S2|O00200|Q5T2B6|Q9UNF9	Missense_Mutation	SNP	ENST00000374748.1	hg19	CCDS7179.1	.	.	.	.	.	.	.	.	.	.	A	15.03	2.711983	0.48517	.	.	ENSG00000108094	ENST00000374751;ENST00000374748;ENST00000374746;ENST00000374749;ENST00000374754;ENST00000374742;ENST00000537177	T;T;T;T;T;T	0.29655	1.56;1.56;1.56;1.56;1.56;1.56	5.44	5.44	0.79542	Cullin, N-terminal (1);Cullin repeat-like-containing domain (1);	0.052061	0.85682	D	0.000000	T	0.22244	0.0536	N	0.16743	0.435	0.80722	D	1	B;B;B	0.25105	0.078;0.118;0.044	B;B;B	0.31547	0.103;0.081;0.132	T	0.07947	-1.0746	10	0.15499	T	0.54	-25.6801	15.7856	0.78300	1.0:0.0:0.0:0.0	.	239;258;239	Q5T2B5;G3V1S2;Q13617	.;.;CUL2_HUMAN	A	239;239;239;239;182;239;258	ENSP00000363883:V239A;ENSP00000363880:V239A;ENSP00000363878:V239A;ENSP00000363881:V239A;ENSP00000363874:V239A;ENSP00000444856:V258A	ENSP00000363874:V239A	V	-	2	0	CUL2	35368015	1.000000	0.71417	1.000000	0.80357	0.545000	0.35147	9.339000	0.96797	2.186000	0.69663	0.455000	0.32223	GTT	.	.		0.313	CUL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047538.1	NM_003591	Missense_Mutation	G	35328009	A	G	35328009	5	3	282	1	0	0	0	0	0	0	1	0	4057	57	2	2	1573	2	CUL2	10	35328009	Splice_Site	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	3518032	35328009	100206738	706	40940										
ANKRD30A	91074	hgsc.bcm.edu	37	chr10	37508232	37508232	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tagaggcagaaattgaatcaCaccatcctagactggcttct	8	10	2	4			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:37508232C>A	ENST00000602533.1	+	34	3523	c.3424C>A	c.(3424-3426)Cac>Aac	p.H1142N	ANKRD30A_ENST00000361713.1_Missense_Mutation_p.H1142N|ANKRD30A_ENST00000374660.1_Missense_Mutation_p.H1261N			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	1198					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						AATTGAATCACACCATCCTAG	0.393																																					p.H1142N		Atlas-SNP	.											.	ANKRD30A	448	.	0			c.C3424A						.						68	66	67					10																	37508232		1867	4098	5965	SO:0001583	missense	91074	exon34			GAATCACACCATC	AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"Ankyrin repeat domain containing"	17234	protein-coding gene	gene with protein product	"breast cancer antigen NY-BR-1"	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.3424C>A	chr10.hg19:g.37508232C>A	ENSP00000473551:p.His1142Asn	244.0	0.0		164.0	54.0	NM_052997	Q5W025	Missense_Mutation	SNP	ENST00000602533.1	hg19		.	.	.	.	.	.	.	.	.	.	c	0.428	-0.904682	0.02453	.	.	ENSG00000148513	ENST00000361713;ENST00000374660	T;T	0.13778	2.56;2.56	2.81	0.189	0.15119	.	.	.	.	.	T	0.09862	0.0242	L	0.40543	1.245	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.34625	-0.9821	9	0.66056	D	0.02	.	2.4956	0.04621	0.4258:0.1339:0.0:0.4403	.	1198	Q9BXX3	AN30A_HUMAN	N	1142;1261	ENSP00000354432:H1142N;ENSP00000363792:H1261N	ENSP00000354432:H1142N	H	+	1	0	ANKRD30A	37548238	0.803000	0.28956	0.051000	0.19133	0.001000	0.01503	1.569000	0.36428	-0.172000	0.10779	-1.930000	0.00511	CAC	.	.		0.393	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997		A	37508232	C	A	37508232	3	1	282	1	0	0	0	0	1	0	0	0	658	478	17	3	3558	3	ANKRD30A	10	37508232	Missense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	2180223	37508232	98026515	707	40941										
ZNF25	219749	hgsc.bcm.edu	37	chr10	38241944	38241944	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaattttctgatgtcttatgAggtcttcatttttagagaaa	8	4	4	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:38241944A>G	ENST00000302609.7	-	6	694	c.482T>C	c.(481-483)cTc>cCc	p.L161P	AL117337.1_ENST00000582458.1_RNA|ZNF25_ENST00000374633.1_5'UTR	NM_145011.2	NP_659448.1	P17030	ZNF25_HUMAN	zinc finger protein 25	161					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		all_neural(218;0.0218)|Breast(68;0.0389)|Ovarian(717;0.0443)|Renal(717;0.157)				ATGTCTTATGAGGTCTTCATT	0.368																																					p.L161P		Atlas-SNP	.											.	ZNF25	66	.	0			c.T482C						.						149	154	152					10																	38241944		2203	4300	6503	SO:0001583	missense	219749	exon6			CTTATGAGGTCTT	AK056452	CCDS7195.1	10p11.2	2013-01-08	2006-05-10		ENSG00000175395	ENSG00000175395		"Zinc fingers, C2H2-type", "-"	13043	protein-coding gene	gene with protein product		194528	"zinc finger protein 25 (KOX 19)"			1639412, 8464732	Standard	NM_145011		Approved	KOX19, FLJ31890, Zfp9	uc001ize.1	P17030	OTTHUMG00000019344	ENST00000302609.7:c.482T>C	chr10.hg19:g.38241944A>G	ENSP00000302222:p.Leu161Pro	119.0	0.0		87.0	4.0	NM_145011	A9Z1X5|Q8IYE3|Q8NDD6|Q96MU2	Missense_Mutation	SNP	ENST00000302609.7	hg19	CCDS7195.1	.	.	.	.	.	.	.	.	.	.	A	14.29	2.491627	0.44249	.	.	ENSG00000175395	ENST00000302609;ENST00000374633	T	0.75260	-0.92	4.84	4.84	0.62591	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.188994	0.26258	N	0.025417	D	0.86364	0.5915	M	0.91406	3.205	0.45172	D	0.998184	D	0.61080	0.989	P	0.59056	0.851	D	0.89201	0.3557	10	0.72032	D	0.01	-13.3187	12.7429	0.57264	1.0:0.0:0.0:0.0	.	161	P17030	ZNF25_HUMAN	P	161;125	ENSP00000302222:L161P	ENSP00000302222:L161P	L	-	2	0	ZNF25	38281950	0.989000	0.36119	0.695000	0.30226	0.391000	0.30476	4.591000	0.61019	2.172000	0.68678	0.524000	0.50904	CTC	.	.		0.368	ZNF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051214.1	NM_145011, NM_006966		G	38241944	A	G	38241944	3	3	282	1	0	0	0	0	1	0	0	0	17809	304	11	2	892	2	ZNF25	10	38241944	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	733712	38241944	97292803	708	40942										
ZNF33A	7581	hgsc.bcm.edu	37	chr10	38344315	38344315	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgtaatgcgtgtgggaaaacTttttgccagaaatctgacct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:38344315delT	ENST00000458705.2	+	5	1418	c.1260delT	c.(1258-1260)actfs	p.T420fs	ZNF33A_ENST00000307441.9_Frame_Shift_Del_p.T420fs|ZNF33A_ENST00000374618.3_Frame_Shift_Del_p.T421fs|ZNF33A_ENST00000469037.2_Intron|ZNF33A_ENST00000432900.2_Frame_Shift_Del_p.T427fs			Q06730	ZN33A_HUMAN	zinc finger protein 33A	420					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(2)|large_intestine(8)|liver(2)|lung(27)|ovary(2)|prostate(1)|skin(2)	46						GTGGGAAAACTTTTTGCCAGA	0.438																																					p.T421fs		Atlas-INDEL	.											.	ZNF33A	103	.	0			c.1262delC						.		,	0,4264		0,0,2132	100	102	101		,	1.4	1	10		102	1,8253		0,1,4126	no	frameshift,frameshift	ZNF33A	NM_006974.2,NM_006954.1	,	0,1,6258	A1A1,A1R,RR		0.0121,0.0,0.0080	,	,	38344315	1,12517	2203	4300	6503	SO:0001589	frameshift_variant	7581	exon5			.	D31763	CCDS31182.1, CCDS60514.1, CCDS73088.1, CCDS73089.1	10p11.2	2013-01-08	2005-03-18		ENSG00000189180	ENSG00000189180		"Zinc fingers, C2H2-type", "-"	13096	protein-coding gene	gene with protein product	"zinc finger and ZAK associated protein with KRAB domain"	194521	"zinc finger protein 33a (KOX 31)", "zinc finger protein 11A"	ZNF33, ZNF11A		2014798, 8464732	Standard	NM_006974		Approved	KOX5, KOX31, KIAA0065, FLJ23404, ZZAPK	uc031pui.1	Q06730	OTTHUMG00000017983	ENST00000458705.2:c.1260delT	chr10.hg19:g.38344315delT	ENSP00000387713:p.Thr420fs	164.0	0.0		152.0	10.0	NM_006954	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Frame_Shift_Del	DEL	ENST00000458705.2	hg19	CCDS31182.1																																																																																			.	.		0.438	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974		-	38344315	T	-	38344315	7	5	282	1	0	1	0	1	0	0	0	0	17869	1596	56	0	1277	0	ZNF33A	10	38344315	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	102371	38344315	97190432	709	40943										
ZNF37A	7587	hgsc.bcm.edu	37	chr10	38407552	38407552	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caccagagaactcatataagAcagaaaccctatggatgtaa	7	9	1	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:38407552A>G	ENST00000361085.5	+	7	1818	c.1473A>G	c.(1471-1473)agA>agG	p.R491R	ZNF37A_ENST00000351773.3_Silent_p.R491R	NM_001178101.1|NM_003421.2	NP_001171572.1|NP_003412.1	P17032	ZN37A_HUMAN	zinc finger protein 37A	491					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(13)|prostate(1)	28						CTCATATAAGACAGAAACCCT	0.408																																					p.R491R		Atlas-SNP	.											.	ZNF37A	118	.	0			c.A1473G						.						59	60	59					10																	38407552		2203	4300	6503	SO:0001819	synonymous_variant	7587	exon7			TATAAGACAGAAA	X69115	CCDS31183.1	10p11.2	2013-01-08	2006-05-11		ENSG00000075407	ENSG00000075407		"Zinc fingers, C2H2-type", "-"	13102	protein-coding gene	gene with protein product			"zinc finger protein 37a (KOX 21)"			2014798, 8464732	Standard	NM_001178101		Approved	KOX21, ZNF37	uc001izl.3	P17032	OTTHUMG00000017990	ENST00000361085.5:c.1473A>G	chr10.hg19:g.38407552A>G		129.0	0.0		81.0	4.0	NM_003421	B3KRQ3|D3DRZ3|Q96B88	Silent	SNP	ENST00000361085.5	hg19	CCDS31183.1																																																																																			.	.		0.408	ZNF37A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047624.2	NM_003421		G	38407552	A	G	38407552	2	3	282	1	0	0	0	0	0	0	0	1	17887	272	10	2		2	ZNF37A	10	38407552	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	63237	38407552	97127195	710	40944										
CXCL12	6387	hgsc.bcm.edu	37	chr10	44871433	44871433	+	Intron	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttctcttcttctgtcgcttcTtttttcctatcttttctttt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:44871433delT	ENST00000374429.2	-	4	353				AL137026.1_ENST00000593376.1_5'Flank|CXCL12_ENST00000395795.4_Intron|CXCL12_ENST00000374426.2_Frame_Shift_Del_p.K106fs|CXCL12_ENST00000496375.1_5'Flank|CXCL12_ENST00000395793.3_Intron	NM_000609.5|NM_001277990.1	NP_000600.1|NP_001264919.1	P48061	SDF1_HUMAN	chemokine (C-X-C motif) ligand 12						adult locomotory behavior (GO:0008344)|ameboidal cell migration (GO:0001667)|blood circulation (GO:0008015)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cellular calcium ion homeostasis (GO:0006874)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|germ cell development (GO:0007281)|germ cell migration (GO:0008354)|immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|motor neuron axon guidance (GO:0008045)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of leukocyte apoptotic process (GO:2000107)|negative regulation of leukocyte tethering or rolling (GO:1903237)|neuron migration (GO:0001764)|organ regeneration (GO:0031100)|patterning of blood vessels (GO:0001569)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cell adhesion (GO:0045785)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of T cell migration (GO:2000406)|regulation of actin polymerization or depolymerization (GO:0008064)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to peptide hormone (GO:0043434)|response to radiation (GO:0009314)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation (GO:0042098)|telencephalon cell migration (GO:0022029)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	chemokine activity (GO:0008009)|chemokine receptor binding (GO:0042379)|CXCR chemokine receptor binding (GO:0045236)|receptor binding (GO:0005102)			endometrium(1)|large_intestine(1)|lung(3)|skin(1)	6					Tinzaparin(DB06822)	CTGTCGCTTCTTTTTTCCTAT	0.398																																					p.K105fs		Atlas-INDEL	.											.	CXCL12	37	.	0			c.315delG						.						308	316	313					10																	44871433		2203	4298	6501	SO:0001627	intron_variant	6387	exon4			.	L36033	CCDS7207.1, CCDS31186.1, CCDS44373.1, CCDS53527.1, CCDS60518.1	10q11.1	2013-02-28	2010-05-11	2002-08-23	ENSG00000107562	ENSG00000107562		"Endogenous ligands"	10672	protein-coding gene	gene with protein product		600835	"stromal cell-derived factor 1"	SDF1A, SDF1B, SDF1		7490086	Standard	NM_001033886		Approved	SCYB12, SDF-1a, SDF-1b, PBSF, TLSF-a, TLSF-b, TPAR1	uc021ppm.1	P48061	OTTHUMG00000018054	ENST00000374429.2:c.267-2642A>-	chr10.hg19:g.44871433delT		301.0	0.0		224.0	15.0	NM_001033886	B2R4G0|E7EVL0|H7BYN8|Q2L985|Q2L986|Q2L988|Q5IT36|Q6ICW0|Q9H554	Frame_Shift_Del	DEL	ENST00000374429.2	hg19	CCDS44373.1																																																																																			.	.		0.398	CXCL12-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047738.2	NM_000609		-	44871433	T	-	44871433	6	5	282	0	1	1	0	1	0	0	0	0	4082	1609	56	0		0	CXCL12	10	44871433	Intron	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	6463881	44871433	90663314	711	40945										
MARCH8	220972	hgsc.bcm.edu	37	chr10	45954578	45954578	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gagaactcacctgttgcctgCccctgcttgatctcctcagc					rs201346647		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:45954578delC	ENST00000319836.3	-	6	1310	c.561delG	c.(559-561)gggfs	p.G187fs	MARCH8_ENST00000395769.2_Frame_Shift_Del_p.G187fs|MARCH8_ENST00000395771.3_Frame_Shift_Del_p.G187fs|MARCH8_ENST00000453424.2_Frame_Shift_Del_p.G469fs|MARCH8_ENST00000476962.1_5'UTR	NM_145021.4	NP_659458.2	Q5T0T0	MARH8_HUMAN	membrane-associated ring finger (C3HC4) 8, E3 ubiquitin protein ligase	187					immune system process (GO:0002376)|protein polyubiquitination (GO:0000209)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(5)|lung(4)	12						CTGTTGCCTGCCCCTGCTTGA	0.532																																					p.Q188fs	NSCLC(102;658 1594 2173 16344 34808)	Atlas-INDEL	.											.	MARCH8	29	.	0			c.562delC						.						143	114	124					10																	45954578		2203	4300	6503	SO:0001589	frameshift_variant	220972	exon6			.	AL833316	CCDS7213.1, CCDS60519.1	10q11.22	2013-01-09	2012-02-23	2005-01-27	ENSG00000165406	ENSG00000165406		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	23356	protein-coding gene	gene with protein product		613335	"c-mir, cellular modulator of immune recognition", "membrane-associated ring finger (C3HC4) 8"	MIR		12582153, 14722266	Standard	XM_005271804		Approved	c-MIR, MARCH-VIII, RNF178	uc001jch.2	Q5T0T0	OTTHUMG00000019345	ENST00000319836.3:c.561delG	chr10.hg19:g.45954578delC	ENSP00000317087:p.Gly187fs	196.0	0.0		126.0	10.0	NM_001002266	B2R8E7|H0Y7C6|Q5T0S8|Q8TC72	Frame_Shift_Del	DEL	ENST00000319836.3	hg19	CCDS7213.1																																																																																			.	.		0.532	MARCH8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051217.1	NM_145021		-	45954578	C	-	45954578	7	5	282	1	0	1	0	1	0	0	0	0	9316	726	26	0	322	0	MARCH8	10	45954578	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1083145	45954578	89580169	712	40946										
FRMPD2	143162	hgsc.bcm.edu	37	chr10	49448531	49448531	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tttcctccacaactcttttcTccacctgggggtcaagtgca	7	14	3	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:49448531T>C	ENST00000374201.3	-	6	874	c.572A>G	c.(571-573)gAg>gGg	p.E191G	FRMPD2_ENST00000407470.4_Missense_Mutation_p.E160G|FRMPD2_ENST00000305531.3_Missense_Mutation_p.E167G	NM_001018071.3|NM_001042512.2	NP_001018081|NP_001035977.2	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2	191	KIND. {ECO:0000255|PROSITE- ProRule:PRU00709}.				tight junction assembly (GO:0070830)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)	1-phosphatidylinositol binding (GO:0005545)			NS(2)|autonomic_ganglia(2)|breast(5)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(15)|lung(24)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	66				Kidney(211;0.201)		AACTCTTTTCTCCACCTGGGG	0.532																																					p.E191G		Atlas-SNP	.											.	FRMPD2	157	.	0			c.A572G						.						63	57	59					10																	49448531		2203	4300	6503	SO:0001583	missense	143162	exon6			CTTTTCTCCACCT	AK123038	CCDS31195.1	10q11	2010-10-13			ENSG00000170324	ENSG00000170324			28572	protein-coding gene	gene with protein product		613323	"PDZ domain containing 5C"	PDZD5C, PDZK5C			Standard	NM_001018071		Approved	MGC35285	uc001jdv.3	Q68DX3	OTTHUMG00000018171	ENST00000374201.3:c.572A>G	chr10.hg19:g.49448531T>C	ENSP00000363317:p.Glu191Gly	122.0	0.0		61.0	4.0	NM_001018071	B7WNW0|B7ZML5|Q2VY07|Q6GMQ9|Q6ZN38|Q6ZWI2|Q8N5T9	Missense_Mutation	SNP	ENST00000374201.3	hg19	CCDS31195.1	.	.	.	.	.	.	.	.	.	.	T	12.28	1.890484	0.33348	.	.	ENSG00000170324	ENST00000374201;ENST00000305531;ENST00000407470	T;T;T	0.35236	1.32;1.32;1.32	4.37	3.23	0.37069	KIND (2);	.	.	.	.	T	0.27765	0.0683	L	0.38531	1.155	0.28214	N	0.9268	B;B;B	0.24043	0.096;0.034;0.096	B;B;B	0.25614	0.062;0.02;0.062	T	0.22521	-1.0214	9	0.56958	D	0.05	.	6.7008	0.23225	0.0:0.108:0.0:0.892	.	167;191;160	Q68DX3-2;Q68DX3;F8WCT2	.;FRPD2_HUMAN;.	G	191;167;160	ENSP00000363317:E191G;ENSP00000307079:E167G;ENSP00000384339:E160G	ENSP00000307079:E167G	E	-	2	0	FRMPD2	49118537	0.970000	0.33590	0.989000	0.46669	0.745000	0.42441	1.365000	0.34182	0.834000	0.34852	0.533000	0.62120	GAG	.	.		0.532	FRMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047923.3	NM_152428		C	49448531	T	C	49448531	3	2	282	1	0	0	0	0	1	0	0	0	6066	1551	54	2	3453	2	FRMPD2	10	49448531	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3493953	49448531	86086216	713	40947										
HERC4	26091	hgsc.bcm.edu	37	chr10	69785411	69785412	+	Missense_Mutation	DNP	CC	CC	AA													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	actgaccataccctccagctCcaaaagtaaacactccacct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:69785411_69785412CC>AA	ENST00000395198.3	-	8	1046_1047	c.799_800GG>TT	c.(799-801)GGa>TTa	p.G267L	HERC4_ENST00000395187.2_3'UTR|HERC4_ENST00000412272.2_Missense_Mutation_p.G267L|HERC4_ENST00000373700.4_Missense_Mutation_p.G267L|HERC4_ENST00000277817.6_Missense_Mutation_p.G157L	NM_022079.2	NP_071362.1	Q5GLZ8	HERC4_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 4	267					cell differentiation (GO:0030154)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	27						CCCTCCAGCTCCAAAAGTAAAC	0.371																																					p.G267V|p.G267X		Atlas-SNP	.											.	HERC4	78	.	0			c.G800T|c.G799T						.																																			SO:0001583	missense	26091	exon8			CCAGCTCCAAAAG|CAGCTCCAAAAGT	AY221963	CCDS7274.1, CCDS41533.1, CCDS60541.1, CCDS60542.1	10q21.3	2013-09-20	2012-02-23		ENSG00000148634	ENSG00000148634			24521	protein-coding gene	gene with protein product		609248	"hect domain and RLD 4"			10997877	Standard	NM_022079		Approved	DKFZP564G092, KIAA1593	uc001jng.4	Q5GLZ8	OTTHUMG00000018343	ENST00000395198.3:c.799_800delinsAA	chr10.hg19:g.69785411_69785412delinsAA	ENSP00000378624:p.Gly267Leu	133.0|132.0	0.0		106.0|101.0	47.0|42.0	NM_022079	Q5GC98|Q5GC99|Q5GCA0|Q8IXP9|Q9HCH9	Missense_Mutation|Nonsense_Mutation	SNP	ENST00000395198.3	hg19	CCDS41533.1																																																																																			.	.		0.371	HERC4-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359262.1	NM_015601		AA	69785412	CC	AA	69785411	3	1	282	1	0	0	0	0	1	0	0	0	7069	855	30	3	2449	3	HERC4	10	69785411	Missense_Mutation	DNP	CC	TCGA-G3-A3CJ-01A-11D-A20W-10	20336880	69785411	65749336	714	40948										
STOX1	219736	hgsc.bcm.edu	37	chr10	70646243	70646243	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caggaaatgagaaaacatttCccacaaaagttccaactttt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:70646243delC	ENST00000298596.6	+	3	2774	c.2691delC	c.(2689-2691)ttcfs	p.F897fs	STOX1_ENST00000421961.2_Frame_Shift_Del_p.F787fs|STOX1_ENST00000399169.4_Frame_Shift_Del_p.F897fs|STOX1_ENST00000399162.2_Intron|STOX1_ENST00000399165.4_Intron	NM_152709.4	NP_689922.3	Q6ZVD7	STOX1_HUMAN	storkhead box 1	897						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|prostate(1)|skin(3)	28						GAAAACATTTCCCACAAAAGT	0.428																																					p.F897fs		Atlas-INDEL	.											.	STOX1	75	.	0			c.2690delT						.						65	68	67					10																	70646243		2082	4252	6334	SO:0001589	frameshift_variant	219736	exon3			.	AK057891	CCDS41535.1, CCDS44416.1, CCDS44417.1	10q22.1	2005-11-29	2005-04-04	2005-04-04	ENSG00000165730	ENSG00000165730			23508	protein-coding gene	gene with protein product		609397	"chromosome 10 open reading frame 24"	C10orf24			Standard	NM_152709		Approved	FLJ25162	uc001joq.3	Q6ZVD7	OTTHUMG00000018367	ENST00000298596.6:c.2691delC	chr10.hg19:g.70646243delC	ENSP00000298596:p.Phe897fs	135.0	0.0		112.0	10.0	NM_152709	A2A3Q9|A5D6Y7|B0QZA4|B0QZA5|B0QZA6|Q4F8Q6|Q5I946|Q5I947|Q5I948|Q5VX38|Q5VX39|Q6ZRY3|Q96LR3|Q96LS0	Frame_Shift_Del	DEL	ENST00000298596.6	hg19	CCDS41535.1																																																																																			.	.		0.428	STOX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276849.3	NM_152709		-	70646243	C	-	70646243	7	5	282	1	0	1	0	1	0	0	0	0	15334	854	30	0	2701	0	STOX1	10	70646243	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	860832	70646243	64888504	715	40949										
PPA1	5464	hgsc.bcm.edu	37	chr10	71969413	71969413	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acagtagcttctaagtagccAggtttcagccgtttgacatc	9	10	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:71969413A>G	ENST00000373232.3	-	7	639	c.540T>C	c.(538-540)ccT>ccC	p.P180P		NM_021129.3	NP_066952.1	Q15181	IPYR_HUMAN	pyrophosphatase (inorganic) 1	180					diphosphate metabolic process (GO:0071344)|gene expression (GO:0010467)|phosphate-containing compound metabolic process (GO:0006796)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	inorganic diphosphatase activity (GO:0004427)|magnesium ion binding (GO:0000287)			breast(2)|endometrium(1)|large_intestine(2)|lung(3)|skin(2)	10						CTAAGTAGCCAGGTTTCAGCC	0.348																																					p.P180P		Atlas-SNP	.											.	PPA1	24	.	0			c.T540C						.						104	107	106					10																	71969413		2203	4300	6503	SO:0001819	synonymous_variant	5464	exon7			GTAGCCAGGTTTC	AF154065	CCDS7299.1	10q11.1-q24	2012-10-02	2005-10-07	2005-10-07	ENSG00000180817	ENSG00000180817	3.6.1.1		9226	protein-coding gene	gene with protein product	"cytosolic inorganic pyrophosphatase", "inorganic pyrophosphatase 1", "pyrophosphate phospho-hydrolase"	179030	"pyrophosphatase (inorganic)"	PP		10542310, 975879	Standard	NM_021129		Approved	SID6-8061, Ppase, IOPPP, PP1	uc001jqv.1	Q15181	OTTHUMG00000018399	ENST00000373232.3:c.540T>C	chr10.hg19:g.71969413A>G		318.0	0.0		245.0	18.0	NM_021129	Q2M348|Q5SQT7|Q6P7P4|Q9UQJ5|Q9Y5B1	Silent	SNP	ENST00000373232.3	hg19	CCDS7299.1																																																																																			.	.		0.348	PPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048490.2	NM_021129		G	71969413	A	G	71969413	2	3	282	1	0	0	0	0	0	0	0	1	12295	175	7	2		2	PPA1	10	71969413	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1323170	71969413	63565334	716	40950										
ADAMTS14	140766	hgsc.bcm.edu	37	chr10	72500743	72500743	+	Splice_Site	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tttctctgtgtctgtcccagCccagcctatggaggccgcct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:72500743delC	ENST00000373207.1	+	12	1749	c.1749delC	c.(1747-1749)tcc>tc	p.S583fs	ADAMTS14_ENST00000373208.1_Splice_Site_p.S586fs	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	583	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						TCTGTCCCAGCCCAGCCTATG	0.617																																					.		Atlas-INDEL	.											.	ADAMTS14	148	.	0			c.1758-1C>-						.						54	47	49					10																	72500743		2203	4300	6503	SO:0001630	splice_region_variant	140766	exon12			.	AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"ADAM metallopeptidases with thrombospondin type 1 motif"	14899	protein-coding gene	gene with protein product		607506	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.1749-1C>-	chr10.hg19:g.72500743delC		265.0	0.0		162.0	10.0	NM_139155	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Splice_Site	DEL	ENST00000373207.1	hg19	CCDS7306.1																																																																																			.	.		0.617	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722	Frame_Shift_Del	-	72500743	C	-	72500743	8	5	282	1	0	1	0	1	0	0	1	0	259	753	26	0	1804	0	ADAMTS14	10	72500743	Splice_Site	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	531330	72500743	63034004	717	40951										
UNC5B	219699	hgsc.bcm.edu	37	chr10	73059012	73059012	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gagtgagatgctggtggctgTggccaccgacggggactgct	18	9	0	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:73059012T>C	ENST00000335350.6	+	17	3232	c.2816T>C	c.(2815-2817)gTg>gCg	p.V939A	UNC5B_ENST00000373192.4_Missense_Mutation_p.V928A	NM_170744.4	NP_734465.2	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B (C. elegans)	939	Death.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(4)|skin(4)	49						CTGGTGGCTGTGGCCACCGAC	0.662																																					p.V939A		Atlas-SNP	.											.	UNC5B	123	.	0			c.T2816C						.						118	116	117					10																	73059012		2203	4300	6503	SO:0001583	missense	219699	exon17			TGGCTGTGGCCAC	AB096256	CCDS7309.1, CCDS58083.1	10q22.2	2013-01-11	2001-11-28		ENSG00000107731	ENSG00000107731		"Immunoglobulin superfamily / I-set domain containing"	12568	protein-coding gene	gene with protein product		607870	"unc5 (C.elegans homolog) b"				Standard	NM_170744		Approved	UNC5H2, p53RDL1	uc001jro.3	Q8IZJ1	OTTHUMG00000018422	ENST00000335350.6:c.2816T>C	chr10.hg19:g.73059012T>C	ENSP00000334329:p.Val939Ala	134.0	0.0		100.0	4.0	NM_170744	Q5T3R9|Q5T3S0|Q86SN3|Q8N1Y2|Q9H9F3	Missense_Mutation	SNP	ENST00000335350.6	hg19	CCDS7309.1	.	.	.	.	.	.	.	.	.	.	T	16.55	3.154050	0.57259	.	.	ENSG00000107731	ENST00000335350;ENST00000373192	T;T	0.49432	0.84;0.78	5.62	5.62	0.85841	Death (1);DEATH-like (2);	0.086033	0.85682	D	0.000000	T	0.30230	0.0758	N	0.04018	-0.295	0.47037	D	0.999298	B;B	0.21071	0.041;0.051	B;B	0.26614	0.043;0.071	T	0.12528	-1.0544	10	0.39692	T	0.17	-22.5639	15.8325	0.78764	0.0:0.0:0.0:1.0	.	928;939	Q8IZJ1-2;Q8IZJ1	.;UNC5B_HUMAN	A	939;928	ENSP00000334329:V939A;ENSP00000362288:V928A	ENSP00000334329:V939A	V	+	2	0	UNC5B	72729018	1.000000	0.71417	1.000000	0.80357	0.808000	0.45660	8.040000	0.89188	2.145000	0.66743	0.254000	0.18369	GTG	.	.		0.662	UNC5B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048541.1	NM_170744		C	73059012	T	C	73059012	3	2	282	1	0	0	0	0	1	0	0	0	17007	1696	59	2	2882	2	UNC5B	10	73059012	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	558269	73059012	62475735	718	40952										
CHST3	9469	hgsc.bcm.edu	37	chr10	73767478	73767478	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctccagccgctccctgtgcgAggaccccgtctgtacgccct	10	19	1	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:73767478A>G	ENST00000373115.4	+	3	1126	c.689A>G	c.(688-690)gAg>gGg	p.E230G		NM_004273.4	NP_004264.2	Q7LGC8	CHST3_HUMAN	carbohydrate (chondroitin 6) sulfotransferase 3	230					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)|T cell homeostasis (GO:0043029)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin 6-sulfotransferase activity (GO:0008459)|proteoglycan sulfotransferase activity (GO:0050698)|sulfotransferase activity (GO:0008146)			endometrium(1)|lung(5)	6						TCCCTGTGCGAGGACCCCGTC	0.652																																					p.E230G		Atlas-SNP	.											.	CHST3	36	.	0			c.A689G						.						17	16	16					10																	73767478		2197	4286	6483	SO:0001583	missense	9469	exon3			TGTGCGAGGACCC	AB017915	CCDS7312.1	10q22.1	2007-03-14			ENSG00000122863	ENSG00000122863		"Sulfotransferases, membrane-bound"	1971	protein-coding gene	gene with protein product		603799				9883891, 9714738	Standard	NM_004273		Approved	C6ST, C6ST1	uc001jsn.3	Q7LGC8	OTTHUMG00000018431	ENST00000373115.4:c.689A>G	chr10.hg19:g.73767478A>G	ENSP00000362207:p.Glu230Gly	122.0	0.0		81.0	6.0	NM_004273	O75099|Q52M30	Missense_Mutation	SNP	ENST00000373115.4	hg19	CCDS7312.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.566975	0.86439	.	.	ENSG00000122863	ENST00000373115	D	0.96491	-4.03	5.68	5.68	0.88126	Sulfotransferase domain (1);	0.000000	0.85682	D	0.000000	D	0.97536	0.9193	M	0.64997	1.995	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.98107	1.0418	10	0.62326	D	0.03	-35.8093	15.1166	0.72407	1.0:0.0:0.0:0.0	.	230	Q7LGC8	CHST3_HUMAN	G	230	ENSP00000362207:E230G	ENSP00000362207:E230G	E	+	2	0	CHST3	73437484	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.166000	0.64965	2.179000	0.69175	0.459000	0.35465	GAG	.	.		0.652	CHST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048563.1	NM_004273		G	73767478	A	G	73767478	3	3	282	1	0	0	0	0	1	0	0	0	3407	304	11	2	695	2	CHST3	10	73767478	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	708466	73767478	61767269	719	40953										
DNAJB12	54788	hgsc.bcm.edu	37	chr10	74104834	74104834	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	catgggttgtgtctgtgggtGggggttggtcaccggcagtc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:74104834delG	ENST00000444643.2	-	2	517	c.185delC	c.(184-186)ccafs	p.P63fs	DNAJB12_ENST00000338820.3_Frame_Shift_Del_p.P97fs|DNAJB12_ENST00000394903.2_Frame_Shift_Del_p.P97fs|DNAJB12_ENST00000461919.1_Intron			Q9NXW2	DJB12_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 12	63						integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|skin(1)	4						GTCTGTGGGTGGGGGTTGGTC	0.597																																					p.P96fs		Atlas-INDEL	.											.	DNAJB12	22	.	0			c.288delA						.						135	145	142					10																	74104834		2203	4300	6503	SO:0001589	frameshift_variant	54788	exon2			.	AK000034	CCDS7316.2	10q22	2011-09-02			ENSG00000148719	ENSG00000148719		"Heat shock proteins / DNAJ (HSP40)"	14891	protein-coding gene	gene with protein product		608376				11147971	Standard	NM_001002762		Approved	DJ10, FLJ20027	uc001jta.2	Q9NXW2	OTTHUMG00000018436	ENST00000444643.2:c.185delC	chr10.hg19:g.74104834delG	ENSP00000403313:p.Pro63fs	167.0	0.0		155.0	10.0	NM_017626	B7Z7I3|Q9H6H0	Frame_Shift_Del	DEL	ENST00000444643.2	hg19																																																																																				.	.		0.597	DNAJB12-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048581.2			-	74104834	G	-	74104834	7	5	282	1	0	1	0	1	0	0	0	0	4619	1348	47	0	970	0	DNAJB12	10	74104834	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	337356	74104834	61429913	720	40954										
MYOZ1	58529	hgsc.bcm.edu	37	chr10	75394369	75394369	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgctgatcagagccatactgTccggcagagccactgccccc	10	16	1	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:75394369T>C	ENST00000359322.4	-	4	739	c.375A>G	c.(373-375)ggA>ggG	p.G125G		NM_021245.3	NP_067068.1			myozenin 1											central_nervous_system(1)|large_intestine(5)|lung(2)|ovary(2)|skin(2)	12	Prostate(51;0.0112)					AGCCATACTGTCCGGCAGAGC	0.657																																					p.G125G		Atlas-SNP	.											.	MYOZ1	24	.	0			c.A375G						.						65	65	65					10																	75394369		2203	4300	6503	SO:0001819	synonymous_variant	58529	exon4			ATACTGTCCGGCA	AF240633	CCDS7330.1	10q22.1	2008-07-03	2002-01-10	2002-01-11	ENSG00000177791	ENSG00000177791			13752	protein-coding gene	gene with protein product	"calsarcin-2"	605603	"myozenin"	MYOZ		11171996, 10984498	Standard	NM_021245		Approved	FATZ, CS-2	uc001jur.4	Q9NP98	OTTHUMG00000018466	ENST00000359322.4:c.375A>G	chr10.hg19:g.75394369T>C		169.0	0.0		120.0	5.0	NM_021245		Silent	SNP	ENST00000359322.4	hg19	CCDS7330.1																																																																																			.	.		0.657	MYOZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048654.1			C	75394369	T	C	75394369	2	2	282	1	0	0	0	0	0	0	0	1	10104	1654	58	2		2	MYOZ1	10	75394369	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1289535	75394369	60140378	721	40955										
PLAU	414236	hgsc.bcm.edu	37	chr10	75673438	75673438	+	Intron	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggccatctacaggaggcaccGggggggctctgtcacctacg					rs549461157	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:75673438delG	ENST00000409178.1	-	3	268				C10orf55_ENST00000412307.2_Intron|PLAU_ENST00000446342.1_Frame_Shift_Del_p.R184fs|PLAU_ENST00000372764.3_Frame_Shift_Del_p.R201fs|PLAU_ENST00000372762.4_Frame_Shift_Del_p.R165fs|PLAU_ENST00000494287.1_3'UTR	NM_001001791.2	NP_001001791.2	Q5SWW7	CJ055_HUMAN	chromosome 10 open reading frame 55											endometrium(1)	1	Prostate(51;0.0112)					AGGAGGCACCGGGGGGGCTCT	0.587																																					p.R201fs		Atlas-Indel,Pindel	.											.,1	PLAU	47	.	0			c.601delC						.		,,	17,4245		5,7,2119					,,	2	0.9			66	27,8227		11,5,4111	no	frameshift,frameshift,intron	PLAU,C10orf55	NM_002658.3,NM_001145031.1,NM_001001791.2	,,	16,12,6230	A1A1,A1R,RR		0.3271,0.3989,0.3516	,,	,,		44,12472				SO:0001627	intron_variant	5328	exon7			.		CCDS53541.1	10q22.2	2012-05-24			ENSG00000222047	ENSG00000222047			31008	protein-coding gene	gene with protein product							Standard	NM_001001791		Approved	bA417O11.3	uc001jvz.2	Q5SWW7	OTTHUMG00000018496	ENST00000409178.1:c.73-605C>-	chr10.hg19:g.75673438delG		282.0	0.0		215.0	13.0	NM_002658	Q3KRG4|Q8NAK4	Frame_Shift_Del	DEL	ENST00000409178.1	hg19	CCDS53541.1																																																																																			.	.		0.587	C10orf55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048746.1	NM_001001791		-	75673438	G	-	75673438	6	5	282	0	1	1	0	1	0	0	0	0	12031	1116	39	0		0	PLAU	10	75673438	Intron	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	279069	75673438	59861309	722	40956										
ADK	132	hgsc.bcm.edu	37	chr10	76153962	76153962	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcattgggatagataaatttGgggagatcctgaagagaaaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:76153962delG	ENST00000286621.2	+	5	387	c.337delG	c.(337-339)gggfs	p.G113fs	ADK_ENST00000372734.3_Frame_Shift_Del_p.G96fs|ADK_ENST00000541550.1_Frame_Shift_Del_p.G78fs|ADK_ENST00000539909.1_Frame_Shift_Del_p.G113fs	NM_006721.3	NP_006712.2	P55263	ADK_HUMAN	adenosine kinase	113					adenosine metabolic process (GO:0046085)|AMP salvage (GO:0044209)|circadian regulation of gene expression (GO:0032922)|dATP biosynthetic process (GO:0006175)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of T cell proliferation (GO:0042102)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|ribonucleoside monophosphate biosynthetic process (GO:0009156)|small molecule metabolic process (GO:0044281)|type B pancreatic cell proliferation (GO:0044342)	cytosol (GO:0005829)|nucleus (GO:0005634)	adenosine kinase activity (GO:0004001)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)|poly(A) RNA binding (GO:0044822)			breast(1)|large_intestine(2)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	8	Prostate(51;0.0112)|Ovarian(15;0.148)				Abacavir(DB01048)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Adenosine(DB00640)|Ribavirin(DB00811)	AGATAAATTTGGGGAGATCCT	0.428																																					p.F112fs		Atlas-INDEL	.											.	ADK	28	.	0			c.336delT						.						120	124	123					10																	76153962		2203	4300	6503	SO:0001589	frameshift_variant	132	exon5			.	U50196	CCDS7343.1, CCDS7344.1, CCDS55716.1, CCDS55717.1	10q22.2	2006-02-21			ENSG00000156110	ENSG00000156110	2.7.1.20		257	protein-coding gene	gene with protein product	"adenosine 5'-phosphotransferase"	102750				8577746	Standard	NM_001123		Approved	AK	uc001jwi.3	P55263	OTTHUMG00000018506	ENST00000286621.2:c.337delG	chr10.hg19:g.76153962delG	ENSP00000286621:p.Gly113fs	239.0	0.0		137.0	10.0	NM_001202450	B7Z783|B7Z800|O00741|O00742|Q16710|Q5JQ10|Q5JQ11|Q9BTN2	Frame_Shift_Del	DEL	ENST00000286621.2	hg19	CCDS7343.1																																																																																			.	.		0.428	ADK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048763.1	NM_001123, NM_006721		-	76153962	G	-	76153962	7	5	282	1	0	1	0	1	0	0	0	0	320	1348	47	0	373	0	ADK	10	76153962	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	480524	76153962	59380785	723	40957										
TSPAN14	81619	hgsc.bcm.edu	37	chr10	82271995	82271995	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agccgagagaagtgcggggtCcccttctcctgctgcgtgcc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:82271995delC	ENST00000429989.3	+	6	769	c.546delC	c.(544-546)gtcfs	p.V182fs	TSPAN14_ENST00000372164.3_Frame_Shift_Del_p.V165fs|TSPAN14_ENST00000372158.1_Frame_Shift_Del_p.V182fs|TSPAN14_ENST00000481124.1_Frame_Shift_Del_p.V59fs|TSPAN14_ENST00000372156.1_Frame_Shift_Del_p.V182fs|TSPAN14_ENST00000341863.6_Frame_Shift_Del_p.V125fs	NM_030927.2	NP_112189.2	Q8NG11	TSN14_HUMAN	tetraspanin 14	182					establishment of protein localization to plasma membrane (GO:0090002)|positive regulation of Notch signaling pathway (GO:0045747)|protein maturation (GO:0051604)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	enzyme binding (GO:0019899)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	7			Colorectal(32;0.229)			AGTGCGGGGTCCCCTTCTCCT	0.612																																					p.V182fs		Atlas-INDEL	.											.	TSPAN14	29	.	0			c.545delT						.						77	74	75					10																	82271995		2203	4300	6503	SO:0001589	frameshift_variant	81619	exon6			.	AF311903	CCDS7369.1, CCDS44448.1	10q23.1	2013-02-14	2005-03-21	2005-03-21	ENSG00000108219	ENSG00000108219		"Tetraspanins"	23303	protein-coding gene	gene with protein product			"transmembrane 4 superfamily member 14"	TM4SF14		11230166	Standard	NM_030927		Approved	DC-TM4F2, MGC11352	uc001kcj.4	Q8NG11	OTTHUMG00000018615	ENST00000429989.3:c.546delC	chr10.hg19:g.82271995delC	ENSP00000396270:p.Val182fs	233.0	0.0		166.0	10.0	NM_030927	A6NHE1|B4DHY6|D3DWD7|D3DWD8|Q567U7|Q9BU34|Q9H0U1	Frame_Shift_Del	DEL	ENST00000429989.3	hg19	CCDS7369.1																																																																																			.	.		0.612	TSPAN14-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049081.2	NM_030927		-	82271995	C	-	82271995	7	5	282	1	0	1	0	1	0	0	0	0	16653	842	30	0	564	0	TSPAN14	10	82271995	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	6118033	82271995	53262752	724	40958										
HECTD2	143279	hgsc.bcm.edu	37	chr10	93221940	93221940	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtatgataccttacttaataCtgtaagtattatgacatgca	6	6	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:93221940C>T	ENST00000298068.5	+	5	693	c.599C>T	c.(598-600)aCt>aTt	p.T200I	HECTD2_ENST00000446394.1_Splice_Site_p.T200I|HECTD2_ENST00000371681.4_Missense_Mutation_p.T200I|HECTD2_ENST00000536715.1_5'UTR	NM_182765.3	NP_877497	Q5U5R9	HECD2_HUMAN	HECT domain containing E3 ubiquitin protein ligase 2	200					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|endometrium(2)|kidney(4)|large_intestine(10)|lung(7)|skin(1)|urinary_tract(1)	27						TTACTTAATACTGTAAGTATT	0.318																																					p.T200I	NSCLC(12;376 469 1699 39910 41417)	Atlas-SNP	.											.	HECTD2	60	.	0			c.C599T						.						170	169	169					10																	93221940		2203	4292	6495	SO:0001630	splice_region_variant	143279	exon5			TTAATACTGTAAG	AK094625	CCDS7414.1, CCDS7415.1, CCDS60591.1	10q23.32	2013-09-20	2012-02-23		ENSG00000165338	ENSG00000165338			26736	protein-coding gene	gene with protein product			"HECT domain containing 2"			8619474, 9110174	Standard	NM_001284274		Approved	FLJ37306	uc001khl.2	Q5U5R9	OTTHUMG00000018742	ENST00000298068.5:c.600+1C>T	chr10.hg19:g.93221940C>T		124.0	0.0		95.0	4.0	NM_173497	Q5VZ97|Q5VZ98|Q5VZ99|Q8N1X7|Q8TCP5	Missense_Mutation	SNP	ENST00000298068.5	hg19	CCDS7414.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.065920	0.76187	.	.	ENSG00000165338	ENST00000446394;ENST00000371681;ENST00000298068	T;T;T	0.55052	1.24;0.54;1.25	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.69369	0.3103	M	0.62723	1.935	0.80722	D	1	B;P;D	0.89917	0.179;0.483;1.0	B;B;D	0.83275	0.057;0.057;0.996	T	0.62053	-0.6935	10	0.15952	T	0.53	.	19.1506	0.93487	0.0:1.0:0.0:0.0	.	200;200;200	E7ERR3;Q5U5R9;Q5VZ98	.;HECD2_HUMAN;.	I	200	ENSP00000401023:T200I;ENSP00000360746:T200I;ENSP00000298068:T200I	ENSP00000298068:T200I	T	+	2	0	HECTD2	93211920	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	6.488000	0.73637	2.637000	0.89404	0.555000	0.69702	ACT	.	.		0.318	HECTD2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098620.1		Missense_Mutation	T	93221940	C	T	93221940	5	4	282	1	0	0	0	0	0	0	1	0	7049	579	20	3	617	3	HECTD2	10	93221940	Splice_Site	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	10949945	93221940	42312807	725	40959										
MARCH5	54708	hgsc.bcm.edu	37	chr10	94110929	94110929	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atttacgacaggcacaccgcAaaattctgaattatccagaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:94110929delA	ENST00000358935.2	+	6	1134	c.802delA	c.(802-804)aaafs	p.K268fs		NM_017824.4	NP_060294.1	Q9NX47	MARH5_HUMAN	membrane-associated ring finger (C3HC4) 5	268					negative regulation of cell aging (GO:0090344)|positive regulation of mitochondrial fission (GO:0090141)|protein autoubiquitination (GO:0051865)|protein localization to mitochondrion (GO:0070585)|protein polyubiquitination (GO:0000209)|regulation of mitochondrial fission (GO:0090140)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	GTPase binding (GO:0051020)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(1)|lung(3)|skin(1)|urinary_tract(1)	9						GGCACACCGCAAAATTCTGAA	0.358																																					p.R267fs		Atlas-INDEL	.											.	MARCH5	28	.	0			c.801delC						.						81	78	79					10																	94110929		2203	4300	6503	SO:0001589	frameshift_variant	54708	exon6			.	BC015480	CCDS7420.1	10q23.32-q23.33	2013-01-09	2005-01-26	2005-01-27	ENSG00000198060	ENSG00000198060		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	26025	protein-coding gene	gene with protein product		610637	"ring finger protein 153"	RNF153		14722266	Standard	XM_005269923		Approved	FLJ20445, MARCH-V	uc001khx.1	Q9NX47	OTTHUMG00000018757	ENST00000358935.2:c.802delA	chr10.hg19:g.94110929delA	ENSP00000351813:p.Lys268fs	206.0	0.0		166.0	10.0	NM_017824		Frame_Shift_Del	DEL	ENST00000358935.2	hg19	CCDS7420.1																																																																																			.	.		0.358	MARCH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049388.1	NM_017824		-	94110929	A	-	94110929	7	5	282	1	0	1	0	1	0	0	0	0	9313	131	5	0	824	0	MARCH5	10	94110929	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	888989	94110929	41423818	726	40960										
LGI1	9211	hgsc.bcm.edu	37	chr10	95552602	95552602	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaagacatctactgcgaaggCcccccagaatacaagaagcg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:95552602delC	ENST00000371418.4	+	6	866	c.606delC	c.(604-606)ggcfs	p.G202fs	LGI1_ENST00000542308.1_Frame_Shift_Del_p.G154fs|LGI1_ENST00000371413.3_Frame_Shift_Del_p.G202fs	NM_005097.2	NP_005088.1	O95970	LGI1_HUMAN	leucine-rich, glioma inactivated 1	202	LRRCT.				axon guidance (GO:0007411)|cell proliferation (GO:0008283)|nervous system development (GO:0007399)|neuron projection development (GO:0031175)|positive regulation of cell growth (GO:0030307)|positive regulation of synaptic transmission (GO:0050806)|protein homooligomerization (GO:0051260)	cell junction (GO:0030054)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|synapse (GO:0045202)	receptor binding (GO:0005102)	p.E205fs*9(1)		central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(18)|ovary(2)|skin(1)	29		Colorectal(252;0.124)				ACTGCGAAGGCCCCCCAGAAT	0.418																																					p.G202fs		Atlas-INDEL	.											.,1	LGI1	69	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.605delG						.						133	135	134					10																	95552602		2203	4300	6503	SO:0001589	frameshift_variant	9211	exon6			.	AF055636	CCDS7431.1	10q24	2008-08-01	2002-06-05		ENSG00000108231	ENSG00000108231			6572	protein-coding gene	gene with protein product		604619	"epilepsy, partial"	EPT		9879993, 11978770, 15079011	Standard	NM_005097		Approved	IB1099, ETL1, EPITEMPIN	uc001kjc.4	O95970	OTTHUMG00000018777	ENST00000371418.4:c.606delC	chr10.hg19:g.95552602delC	ENSP00000360472:p.Gly202fs	231.0	0.0		177.0	12.0	NM_005097	A8K0Z1|B4E1S0|Q5W001|Q5W002|Q8NI23|Q96LF5	Frame_Shift_Del	DEL	ENST00000371418.4	hg19	CCDS7431.1																																																																																			.	.		0.418	LGI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049445.1	NM_005097		-	95552602	C	-	95552602	7	5	282	1	0	1	0	1	0	0	0	0	8760	726	26	0	628	0	LGI1	10	95552602	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1441673	95552602	39982145	727	40961										
TBC1D12	23232	hgsc.bcm.edu	37	chr10	96269902	96269902	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	attaattaagttggacatatCccgtacatttccatctctct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:96269902delC	ENST00000225235.4	+	8	1765	c.1655delC	c.(1654-1656)tccfs	p.S552fs	TBC1D12_ENST00000485048.1_3'UTR	NM_015188.1	NP_056003.1	O60347	TBC12_HUMAN	TBC1 domain family, member 12	552	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						Rab GTPase activator activity (GO:0005097)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(2)	20		Colorectal(252;0.0429)				TTGGACATATCCCGTACATTT	0.373																																					p.S552fs		Atlas-INDEL	.											.	TBC1D12	51	.	0			c.1654delT						.						178	165	169					10																	96269902		1847	4099	5946	SO:0001589	frameshift_variant	23232	exon8			.	AB011180	CCDS41553.1	10q23.33	2013-09-20			ENSG00000108239	ENSG00000108239			29082	protein-coding gene	gene with protein product						9628581	Standard	NM_015188		Approved	KIAA0608	uc001kjr.2	O60347	OTTHUMG00000018794	ENST00000225235.4:c.1655delC	chr10.hg19:g.96269902delC	ENSP00000225235:p.Ser552fs	184.0	0.0		148.0	11.0	NM_015188	Q5VYA6|Q8WX26|Q8WX59|Q9UG83	Frame_Shift_Del	DEL	ENST00000225235.4	hg19	CCDS41553.1																																																																																			.	.		0.373	TBC1D12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049482.2			-	96269902	C	-	96269902	7	5	282	1	0	1	0	1	0	0	0	0	15616	855	30	0	1685	0	TBC1D12	10	96269902	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	717300	96269902	39264845	728	40962										
ENTPD1	953	hgsc.bcm.edu	37	chr10	97620281	97620281	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaacttgacatcagagaaagTctctcaggaaaaggtgactg	10	7	3	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:97620281T>C	ENST00000371205.4	+	8	1413	c.1130T>C	c.(1129-1131)gTc>gCc	p.V377A	ENTPD1_ENST00000371203.5_Missense_Mutation_p.V239A|ENTPD1_ENST00000371207.3_Missense_Mutation_p.V389A|ENTPD1-AS1_ENST00000416301.1_RNA|ENTPD1_ENST00000539125.1_Missense_Mutation_p.V239A|RP11-248J23.7_ENST00000491114.1_5'Flank|RP11-429G19.3_ENST00000433113.1_RNA|ENTPD1_ENST00000453258.2_Missense_Mutation_p.V384A|ENTPD1-AS1_ENST00000451364.1_RNA|ENTPD1_ENST00000543964.1_Missense_Mutation_p.V269A			P49961	ENTP1_HUMAN	ectonucleoside triphosphate diphosphohydrolase 1	377					ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|purine ribonucleoside diphosphate catabolic process (GO:0009181)	basal lamina (GO:0005605)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|nucleoside-diphosphatase activity (GO:0017110)|nucleoside-triphosphatase activity (GO:0017111)			cervix(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(3)|prostate(1)|skin(1)	16		Colorectal(252;0.0821)		Epithelial(162;1.31e-07)|all cancers(201;5.33e-06)		TCAGAGAAAGTCTCTCAGGAA	0.438																																					p.V389A		Atlas-SNP	.											.	ENTPD1	44	.	0			c.T1166C						.						122	111	115					10																	97620281		2203	4300	6503	SO:0001583	missense	953	exon8			AGAAAGTCTCTCA	S73813	CCDS7444.1, CCDS53556.1, CCDS53557.1, CCDS53558.1, CCDS41554.1	10q24.1	2014-03-03			ENSG00000138185	ENSG00000138185		"CD molecules"	3363	protein-coding gene	gene with protein product		601752		CD39		9226376, 24482476	Standard	NM_001098175		Approved	NTPDase-1, ATPDase, SPG64	uc010qoj.2	P49961	OTTHUMG00000018818	ENST00000371205.4:c.1130T>C	chr10.hg19:g.97620281T>C	ENSP00000360248:p.Val377Ala	149.0	0.0		119.0	6.0	NM_001164178	A9Z1X8|B4DWB9|B4E1X1|B7Z599|G3XAF6|Q5T561|Q5T562|Q86VV3|Q9UQQ9|Q9Y3Q9	Missense_Mutation	SNP	ENST00000371205.4	hg19	CCDS7444.1	.	.	.	.	.	.	.	.	.	.	T	9.275	1.046689	0.19748	.	.	ENSG00000138185	ENST00000453258;ENST00000371207;ENST00000543964;ENST00000539125;ENST00000371203;ENST00000371205	T;T;T;T;T;T	0.10960	2.82;2.82;2.82;2.82;2.82;2.82	4.08	-2.59	0.06209	.	4.928260	0.00166	N	0.000012	T	0.08268	0.0206	L	0.41415	1.275	0.09310	N	1	B;B;B;B	0.27192	0.171;0.141;0.108;0.171	B;B;B;B	0.27796	0.083;0.05;0.061;0.083	T	0.25433	-1.0132	10	0.25751	T	0.34	2.8227	0.4026	0.00428	0.2858:0.1259:0.2138:0.3745	.	389;389;384;377	B4DWB9;G3XAF6;P49961-2;P49961	.;.;.;ENTP1_HUMAN	A	384;389;269;239;239;377	ENSP00000390955:V384A;ENSP00000360250:V389A;ENSP00000442968:V269A;ENSP00000440027:V239A;ENSP00000360246:V239A;ENSP00000360248:V377A	ENSP00000360246:V239A	V	+	2	0	ENTPD1	97610271	0.000000	0.05858	0.000000	0.03702	0.165000	0.22458	-0.614000	0.05604	-0.143000	0.11334	0.455000	0.32223	GTC	.	.		0.438	ENTPD1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049566.1	NM_001776		C	97620281	T	C	97620281	3	2	282	1	0	0	0	0	1	0	0	0	5140	1667	58	2	1257	2	ENTPD1	10	97620281	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1350379	97620281	37914466	729	40963										
SLIT1	6585	hgsc.bcm.edu	37	chr10	98766401	98766401	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gccctggtccacacagttggCcccattctggcactcagtcc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:98766401delC	ENST00000266058.4	-	32	3663	c.3418delG	c.(3418-3420)gccfs	p.A1140fs	ARHGAP19-SLIT1_ENST00000453547.2_3'UTR|SLIT1_ENST00000371070.4_Frame_Shift_Del_p.A1140fs	NM_003061.2	NP_003052.2	O75093	SLIT1_HUMAN	slit homolog 1 (Drosophila)	1140	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|dorsal/ventral axon guidance (GO:0033563)|establishment of nucleus localization (GO:0040023)|forebrain morphogenesis (GO:0048853)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of synapse assembly (GO:0051964)|retinal ganglion cell axon guidance (GO:0031290)|spinal cord development (GO:0021510)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(37)|ovary(5)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	78		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		ACACAGTTGGCCCCATTCTGG	0.592																																					p.A1140fs		Atlas-INDEL	.											.	SLIT1	154	.	0			c.3419delC						.						49	41	44					10																	98766401		2203	4300	6503	SO:0001589	frameshift_variant	6585	exon32			.	AB011537	CCDS7453.1	10q23.3-q24	2008-08-01	2001-11-28		ENSG00000187122	ENSG00000187122			11085	protein-coding gene	gene with protein product		603742	"slit (Drosophila) homolog 1"	SLIL1		9693030, 9813312	Standard	NM_003061		Approved	slit1, MEGF4, Slit-1, SLIT3	uc001kmw.2	O75093	OTTHUMG00000018843	ENST00000266058.4:c.3418delG	chr10.hg19:g.98766401delC	ENSP00000266058:p.Ala1140fs	190.0	0.0		137.0	10.0	NM_003061	Q5T0V1|Q8WWZ2|Q9UIL7	Frame_Shift_Del	DEL	ENST00000266058.4	hg19	CCDS7453.1																																																																																			.	.		0.592	SLIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049636.1	NM_003061		-	98766401	C	-	98766401	7	5	282	1	0	1	0	1	0	0	0	0	14754	739	26	0	1210	0	SLIT1	10	98766401	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1146120	98766401	36768346	730	40964										
ANKRD2	26287	hgsc.bcm.edu	37	chr10	99337615	99337615	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cttgctggtgctggaggatgAgaagcaccacggggctcaga	16	9	1	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:99337615A>G	ENST00000307518.5	+	2	494	c.227A>G	c.(226-228)gAg>gGg	p.E76G	ANKRD2_ENST00000298808.5_Missense_Mutation_p.E76G|ANKRD2_ENST00000455090.1_Missense_Mutation_p.E49G|ANKRD2_ENST00000370655.1_Missense_Mutation_p.E49G			Q9GZV1	ANKR2_HUMAN	ankyrin repeat domain 2 (stretch responsive muscle)	76	May mediate interaction with PML, p53/TP53 and YBX1.				muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|skeletal muscle cell differentiation (GO:0035914)	cytosol (GO:0005829)|euchromatin (GO:0000791)|I band (GO:0031674)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	protein kinase B binding (GO:0043422)|structural constituent of muscle (GO:0008307)			breast(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|stomach(1)	7		all_hematologic(284;1.95e-06)|Colorectal(252;0.0163)		Epithelial(162;1.18e-94)|all cancers(201;9.31e-86)|BRCA - Breast invasive adenocarcinoma(275;0.0233)|STAD - Stomach adenocarcinoma(243;0.181)|KIRC - Kidney renal clear cell carcinoma(50;0.206)|Kidney(138;0.241)		CTGGAGGATGAGAAGCACCAC	0.612																																					p.E76G		Atlas-SNP	.											ANKRD2,NS,carcinoma,0,1	ANKRD2	27	.	0			c.A227G						.						52	40	44					10																	99337615		2199	4290	6489	SO:0001583	missense	26287	exon2			AGGATGAGAAGCA	AJ304805	CCDS7466.1, CCDS44468.1	10q23	2013-01-10			ENSG00000165887	ENSG00000165887		"Ankyrin repeat domain containing"	495	protein-coding gene	gene with protein product		610734				10873377, 15136035, 15677738	Standard	NM_001129981		Approved	ARPP	uc001knw.3	Q9GZV1	OTTHUMG00000018860	ENST00000307518.5:c.227A>G	chr10.hg19:g.99337615A>G	ENSP00000306163:p.Glu76Gly	77.0	0.0		70.0	3.0	NM_001129981	Q3B778|Q5T456|Q70EZ9|Q8WUD7|Q96MG0|Q9NQC9	Missense_Mutation	SNP	ENST00000307518.5	hg19	CCDS7466.1	.	.	.	.	.	.	.	.	.	.	A	19.93	3.918878	0.73098	.	.	ENSG00000165887	ENST00000307518;ENST00000298808;ENST00000370655;ENST00000455090	T;T;T;T	0.56941	0.7;0.46;0.62;0.43	4.65	4.65	0.58169	.	0.082483	0.50627	D	0.000101	T	0.58409	0.2120	L	0.34521	1.04	0.36324	D	0.858415	B;D	0.71674	0.079;0.998	B;D	0.78314	0.051;0.991	T	0.60367	-0.7277	10	0.21540	T	0.41	-39.2181	12.4609	0.55731	1.0:0.0:0.0:0.0	.	76;76	Q9GZV1-2;Q9GZV1	.;ANKR2_HUMAN	G	76;76;49;49	ENSP00000306163:E76G;ENSP00000298808:E76G;ENSP00000359689:E49G;ENSP00000403114:E49G	ENSP00000298808:E76G	E	+	2	0	ANKRD2	99327605	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.984000	0.63838	1.949000	0.56562	0.459000	0.35465	GAG	.	.		0.612	ANKRD2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				G	99337615	A	G	99337615	3	3	282	1	0	0	0	0	1	0	0	0	647	304	11	2	233	2	ANKRD2	10	99337615	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	571214	99337615	36197132	731	40965										
CHUK	1147	hgsc.bcm.edu	37	chr10	101953091	101953091	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccacacatgacagagaatgaTcatgttctgctgaagtcggg	11	9	2	4			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:101953091T>C	ENST00000370397.7	-	19	2158	c.2072A>G	c.(2071-2073)gAt>gGt	p.D691G	RP11-316M21.7_ENST00000443919.1_RNA|CHUK_ENST00000590930.1_5'UTR	NM_001278.3	NP_001269.3	O15111	IKKA_HUMAN	conserved helix-loop-helix ubiquitous kinase	691					anatomical structure morphogenesis (GO:0009653)|cellular response to tumor necrosis factor (GO:0071356)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|morphogenesis of an epithelial sheet (GO:0002011)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hydroperoxide (GO:0033194)|response to lipopolysaccharide (GO:0032496)|response to toxic substance (GO:0009636)|response to virus (GO:0009615)|Rho protein signal transduction (GO:0007266)|skeletal muscle contraction (GO:0003009)|striated muscle cell differentiation (GO:0051146)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|scaffold protein binding (GO:0097110)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(9)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	27		Colorectal(252;0.117)		Epithelial(162;2.05e-10)|all cancers(201;1.91e-08)	Acetylcysteine(DB06151)|Aminosalicylic Acid(DB00233)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	CAGAGAATGATCATGTTCTGC	0.483																																					p.D691G	Ovarian(159;52 1904 10536 35305 37148)	Atlas-SNP	.											.	CHUK	71	.	0			c.A2072G						.						133	114	121					10																	101953091		2203	4300	6503	SO:0001583	missense	1147	exon19			GAATGATCATGTT	AF009225	CCDS7488.1	10q24-q25	2008-08-01			ENSG00000213341	ENSG00000213341			1974	protein-coding gene	gene with protein product		600664		TCF16		7558004, 16902410	Standard	XR_246062		Approved	IKK1, IKK-alpha, IkBKA, NFKBIKA, IKKA	uc001kqp.3	O15111	OTTHUMG00000018899	ENST00000370397.7:c.2072A>G	chr10.hg19:g.101953091T>C	ENSP00000359424:p.Asp691Gly	130.0	0.0		86.0	4.0	NM_001278	O14666|Q13132|Q5W0I4|Q92467	Missense_Mutation	SNP	ENST00000370397.7	hg19	CCDS7488.1	.	.	.	.	.	.	.	.	.	.	T	11.86	1.763857	0.31228	.	.	ENSG00000213341	ENST00000370397	T	0.71934	-0.61	5.84	3.36	0.38483	.	0.281692	0.40554	N	0.001065	T	0.45155	0.1328	N	0.08118	0	0.22424	N	0.999111	B	0.02656	0.0	B	0.01281	0.0	T	0.22661	-1.0210	10	0.44086	T	0.13	-12.4824	5.6874	0.17811	0.1534:0.0:0.2492:0.5974	.	691	O15111	IKKA_HUMAN	G	691	ENSP00000359424:D691G	ENSP00000359424:D691G	D	-	2	0	CHUK	101943081	0.068000	0.21057	1.000000	0.80357	0.926000	0.56050	0.249000	0.18216	2.230000	0.72887	0.528000	0.53228	GAT	.	.		0.483	CHUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049836.1	NM_001278		C	101953091	T	C	101953091	3	2	282	1	0	0	0	0	1	0	0	0	3418	1435	50	2	177	2	CHUK	10	101953091	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2615476	101953091	33581656	732	40966										
CHUK	1147	hgsc.bcm.edu	37	chr10	101964874	101964874	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aagagcctgctatagtcttcTtttagtccagacacatagtg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:101964874delT	ENST00000370397.7	-	12	1400	c.1314delA	c.(1312-1314)aaafs	p.K438fs		NM_001278.3	NP_001269.3	O15111	IKKA_HUMAN	conserved helix-loop-helix ubiquitous kinase	438					anatomical structure morphogenesis (GO:0009653)|cellular response to tumor necrosis factor (GO:0071356)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|morphogenesis of an epithelial sheet (GO:0002011)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hydroperoxide (GO:0033194)|response to lipopolysaccharide (GO:0032496)|response to toxic substance (GO:0009636)|response to virus (GO:0009615)|Rho protein signal transduction (GO:0007266)|skeletal muscle contraction (GO:0003009)|striated muscle cell differentiation (GO:0051146)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|scaffold protein binding (GO:0097110)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(9)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	27		Colorectal(252;0.117)		Epithelial(162;2.05e-10)|all cancers(201;1.91e-08)	Acetylcysteine(DB06151)|Aminosalicylic Acid(DB00233)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	TATAGTCTTCTTTTAGTCCAG	0.398																																					p.E439fs	Ovarian(159;52 1904 10536 35305 37148)	Atlas-INDEL	.											.	CHUK	71	.	0			c.1315delG						.						194	170	178					10																	101964874		2203	4300	6503	SO:0001589	frameshift_variant	1147	exon12			.	AF009225	CCDS7488.1	10q24-q25	2008-08-01			ENSG00000213341	ENSG00000213341			1974	protein-coding gene	gene with protein product		600664		TCF16		7558004, 16902410	Standard	XR_246062		Approved	IKK1, IKK-alpha, IkBKA, NFKBIKA, IKKA	uc001kqp.3	O15111	OTTHUMG00000018899	ENST00000370397.7:c.1314delA	chr10.hg19:g.101964874delT	ENSP00000359424:p.Lys438fs	207.0	0.0		174.0	12.0	NM_001278	O14666|Q13132|Q5W0I4|Q92467	Frame_Shift_Del	DEL	ENST00000370397.7	hg19	CCDS7488.1																																																																																			.	.		0.398	CHUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049836.1	NM_001278		-	101964874	T	-	101964874	7	5	282	1	0	1	0	1	0	0	0	0	3418	1606	56	0	963	0	CHUK	10	101964874	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	11783	101964874	33569873	733	40967										
SEC31B	25956	hgsc.bcm.edu	37	chr10	102249484	102249484	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttcctctggaggtttcccctGggggctggggcttctttcca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:102249484delG	ENST00000370345.3	-	22	3097	c.3000delC	c.(2998-3000)cccfs	p.P1000fs		NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	1000	Pro-rich.				protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|vesicle coat (GO:0030120)				NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(3)|lung(17)|ovary(1)|urinary_tract(1)	36		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)		GGTTTCCCCTGGGGGCTGGGG	0.458																																					p.R1001fs		Atlas-INDEL	.											.	SEC31B	84	.	0			c.3001delA						.						80	84	83					10																	102249484		2203	4300	6503	SO:0001589	frameshift_variant	25956	exon22			.	AF274863	CCDS7495.1	10q24.32	2013-01-10	2006-10-05	2006-09-07	ENSG00000075826	ENSG00000075826		"WD repeat domain containing"	23197	protein-coding gene	gene with protein product		610258	"SEC31-like 2 (S. cerevisiae)"	SEC31L2		16495487	Standard	NM_015490		Approved	SEC31B-1, DKFZP434M183	uc001krc.1	Q9NQW1	OTTHUMG00000019342	ENST00000370345.3:c.3000delC	chr10.hg19:g.102249484delG	ENSP00000359370:p.Pro1000fs	178.0	0.0		142.0	10.0	NM_015490	B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Frame_Shift_Del	DEL	ENST00000370345.3	hg19	CCDS7495.1																																																																																			.	.		0.458	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	NM_015490		-	102249484	G	-	102249484	7	5	282	1	0	1	0	1	0	0	0	0	14014	1335	47	0	559	0	SEC31B	10	102249484	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	284610	102249484	33285263	734	40968										
PDCD11	22984	hgsc.bcm.edu	37	chr10	105160237	105160237	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aagttgaaaatcgaaaagagAgaaagcagcaagtccgcaag	11	6	0	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:105160237A>G	ENST00000369797.3	+	3	280	c.186A>G	c.(184-186)agA>agG	p.R62R		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	62					mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	64		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		TCGAAAAGAGAGAAAGCAGCA	0.398																																					p.R62R		Atlas-SNP	.											.	PDCD11	160	.	0			c.A186G						.						118	129	126					10																	105160237		2203	4300	6503	SO:0001819	synonymous_variant	22984	exon3			AAAGAGAGAAAGC	D80007	CCDS31276.1	10q24.32	2010-07-06			ENSG00000148843	ENSG00000148843			13408	protein-coding gene	gene with protein product		612333				10229231	Standard	XM_005269647		Approved	KIAA0185, ALG-4, RRP5	uc001kwy.1	Q14690	OTTHUMG00000018988	ENST00000369797.3:c.186A>G	chr10.hg19:g.105160237A>G		88.0	0.0		86.0	4.0	NM_014976	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Silent	SNP	ENST00000369797.3	hg19	CCDS31276.1																																																																																			.	.		0.398	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1			G	105160237	A	G	105160237	2	3	282	1	0	0	0	0	0	0	0	1	11626	301	11	2		2	PDCD11	10	105160237	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2910753	105160237	30374510	735	40969										
GSTO1	9446	hgsc.bcm.edu	37	chr10	106022766	106022766	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttggtaggaagctttattagAagccaaaataaagaagacta	9	4	0	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:106022766A>G	ENST00000369713.5	+	4	590	c.396A>G	c.(394-396)agA>agG	p.R132R	GSTO1_ENST00000493946.1_3'UTR|GSTO1_ENST00000369710.4_Intron|GSTO1_ENST00000539281.1_Silent_p.R104R	NM_004832.2	NP_004823.1	P78417	GSTO1_HUMAN	glutathione S-transferase omega 1	132	GST C-terminal.				cellular response to arsenic-containing substance (GO:0071243)|glutathione derivative biosynthetic process (GO:1901687)|L-ascorbic acid metabolic process (GO:0019852)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|positive regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014810)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|small molecule metabolic process (GO:0044281)|xenobiotic catabolic process (GO:0042178)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glutathione dehydrogenase (ascorbate) activity (GO:0045174)|glutathione transferase activity (GO:0004364)|methylarsonate reductase activity (GO:0050610)|oxidoreductase activity (GO:0016491)			large_intestine(1)|lung(1)|stomach(1)	3		Colorectal(252;0.102)|Breast(234;0.122)		Epithelial(162;8.07e-10)|all cancers(201;2.72e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0147)	Glutathione(DB00143)|Vitamin E(DB00163)	GCTTTATTAGAAGCCAAAATA	0.363																																					p.R132R		Atlas-SNP	.											.	GSTO1	14	.	0			c.A396G						.						85	82	83					10																	106022766		2203	4300	6503	SO:0001819	synonymous_variant	9446	exon4			TATTAGAAGCCAA	AF212303	CCDS7555.1, CCDS53572.1, CCDS53573.1	10q25.1	2012-06-21			ENSG00000148834	ENSG00000148834	2.5.1.18, 1.8.5.1, 1.20.4.2	"Glutathione S-transferases / Soluble"	13312	protein-coding gene	gene with protein product		605482				10783391, 12618591	Standard	NM_004832		Approved	GSTTLp28, P28	uc001kya.3	P78417	OTTHUMG00000019001	ENST00000369713.5:c.396A>G	chr10.hg19:g.106022766A>G		94.0	0.0		80.0	4.0	NM_004832	D3DRA3|F5H7H0|Q5TA03|Q7Z3T2	Silent	SNP	ENST00000369713.5	hg19	CCDS7555.1																																																																																			.	.		0.363	GSTO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050193.1	NM_004832		G	106022766	A	G	106022766	2	3	282	1	0	0	0	0	0	0	0	1	6851	243	9	2		2	GSTO1	10	106022766	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	862529	106022766	29511981	736	40970										
GPAM	57678	hgsc.bcm.edu	37	chr10	113941524	113941524	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aacatctattgtaccaagggTcagtgcagattcatccatgt	8	9	3	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:113941524T>C	ENST00000348367.4	-	3	216	c.19A>G	c.(19-21)Acc>Gcc	p.T7A	GPAM_ENST00000369425.1_Missense_Mutation_p.T7A|GPAM_ENST00000480130.1_5'UTR|GPAM_ENST00000423155.1_Missense_Mutation_p.T7A			Q9HCL2	GPAT1_HUMAN	glycerol-3-phosphate acyltransferase, mitochondrial	7					acyl-CoA metabolic process (GO:0006637)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|defense response to virus (GO:0051607)|fatty acid homeostasis (GO:0055089)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|interleukin-2 secretion (GO:0070970)|negative regulation of activation-induced cell death of T cells (GO:0070236)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of multicellular organism growth (GO:0040018)|regulation of cytokine secretion (GO:0050707)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			breast(2)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Epithelial(162;0.0306)|all cancers(201;0.123)		GTACCAAGGGTCAGTGCAGAT	0.363																																					p.T7A	Ovarian(161;1017 2606 18293 52943)	Atlas-SNP	.											.	GPAM	68	.	0			c.A19G						.						180	156	164					10																	113941524		2203	4300	6503	SO:0001583	missense	57678	exon3			CAAGGGTCAGTGC	AL832464	CCDS7570.1	10q25.3	2009-07-15			ENSG00000119927	ENSG00000119927			24865	protein-coding gene	gene with protein product	"glycerol-3-phosphate acyltransferase 1, mitochondrial"	602395				10997877, 8369314	Standard	NM_020918		Approved	KIAA1560, MGC26846, GPAT1	uc001kzp.3	Q9HCL2	OTTHUMG00000019055	ENST00000348367.4:c.19A>G	chr10.hg19:g.113941524T>C	ENSP00000265276:p.Thr7Ala	163.0	0.0		136.0	7.0	NM_001244949	Q5VW51|Q86TA3	Missense_Mutation	SNP	ENST00000348367.4	hg19	CCDS7570.1	.	.	.	.	.	.	.	.	.	.	T	14.80	2.642276	0.47153	.	.	ENSG00000119927	ENST00000348367;ENST00000423155;ENST00000369425	T;T;T	0.32988	1.43;1.43;1.43	5.79	3.31	0.37934	.	0.488693	0.23422	N	0.048360	T	0.19805	0.0476	N	0.22421	0.69	0.24770	N	0.992871	B;B	0.13594	0.008;0.008	B;B	0.15484	0.013;0.013	T	0.17501	-1.0367	10	0.62326	D	0.03	-15.2378	8.5001	0.33152	0.4922:0.0:0.0:0.5078	.	7;7	Q5VW52;Q9HCL2	.;GPAT1_HUMAN	A	7	ENSP00000265276:T7A;ENSP00000409242:T7A;ENSP00000358433:T7A	ENSP00000265276:T7A	T	-	1	0	GPAM	113931514	1.000000	0.71417	0.997000	0.53966	0.959000	0.62525	2.320000	0.43797	0.987000	0.38709	0.460000	0.39030	ACC	.	.		0.363	GPAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050377.1	NM_020918		C	113941524	T	C	113941524	3	2	282	1	0	0	0	0	1	0	0	0	6596	1667	58	2	2547	2	GPAM	10	113941524	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	7918758	113941524	21593223	737	40971										
HABP2	3026	hgsc.bcm.edu	37	chr10	115343043	115343043	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaaagaagaatttcatgagcAgagctttagggtggagaaga	14	3	1	6			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:115343043A>G	ENST00000351270.3	+	10	1259	c.1163A>G	c.(1162-1164)cAg>cGg	p.Q388R	HABP2_ENST00000541666.1_3'UTR|HABP2_ENST00000542051.1_Missense_Mutation_p.Q362R	NM_004132.3	NP_004123.1	Q14520	HABP2_HUMAN	hyaluronan binding protein 2	388	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	glycosaminoglycan binding (GO:0005539)|serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	23		Colorectal(252;0.0233)|Breast(234;0.0672)		Epithelial(162;0.00319)|all cancers(201;0.0112)	Hyaluronan(DB08818)	TTTCATGAGCAGAGCTTTAGG	0.438																																					p.Q388R		Atlas-SNP	.											.	HABP2	52	.	0			c.A1163G						.						114	114	114					10																	115343043		2203	4300	6503	SO:0001583	missense	3026	exon10			ATGAGCAGAGCTT		CCDS7577.1, CCDS53579.1	10q25.3	2008-08-01	2001-11-28		ENSG00000148702	ENSG00000148702			4798	protein-coding gene	gene with protein product	"plasma hyaluronan binding protein", "factor VII activating protein"	603924	"hyaluronan-binding protein 2"			8827452, 12437095	Standard	NM_004132		Approved	HABP, PHBP, HGFAL, FSAP	uc001lai.4	Q14520	OTTHUMG00000019073	ENST00000351270.3:c.1163A>G	chr10.hg19:g.115343043A>G	ENSP00000277903:p.Gln388Arg	225.0	0.0		175.0	7.0	NM_004132	A8K467|B7Z8U5|F5H5M6|O00663	Missense_Mutation	SNP	ENST00000351270.3	hg19	CCDS7577.1	.	.	.	.	.	.	.	.	.	.	A	18.15	3.559846	0.65538	.	.	ENSG00000148702	ENST00000542051;ENST00000351270	D;D	0.90261	-2.64;-2.64	6.06	6.06	0.98353	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.85682	D	0.000000	D	0.94371	0.8190	M	0.62209	1.925	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94696	0.7878	10	0.72032	D	0.01	.	15.1865	0.73006	1.0:0.0:0.0:0.0	.	388	Q14520	HABP2_HUMAN	R	362;388	ENSP00000443283:Q362R;ENSP00000277903:Q388R	ENSP00000277903:Q388R	Q	+	2	0	HABP2	115333033	1.000000	0.71417	1.000000	0.80357	0.169000	0.22640	7.424000	0.80242	2.315000	0.78130	0.533000	0.62120	CAG	.	.		0.438	HABP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050428.1	NM_004132		G	115343043	A	G	115343043	3	3	282	1	0	0	0	0	1	0	0	0	6947	188	7	2	1201	2	HABP2	10	115343043	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1401519	115343043	20191704	738	40972										
C10orf81	79949	hgsc.bcm.edu	37	chr10	115529653	115529653	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcaccaagaaatggtctccaAgacaaggtaatggggctcac	10	10	3	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:115529653A>G	ENST00000369310.3	+	6	1090	c.528A>G	c.(526-528)caA>caG	p.Q176Q	PLEKHS1_ENST00000361048.1_Silent_p.Q182Q|PLEKHS1_ENST00000369312.4_Silent_p.Q94Q|PLEKHS1_ENST00000354462.3_5'Flank|PLEKHS1_ENST00000369309.1_5'Flank	NM_182601.1	NP_872407.1	Q5SXH7	PKHS1_HUMAN	pleckstrin homology domain containing, family S member 1	176																	ATGGTCTCCAAGACAAGGTAA	0.483																																					p.Q182Q		Atlas-SNP	.											.	PLEKHS1	19	.	0			c.A546G						.						107	103	105					10																	115529653		2203	4300	6503	SO:0001819	synonymous_variant	79949	exon7			TCTCCAAGACAAG	AK027190	CCDS7583.1, CCDS53580.1, CCDS53581.1	10q26.11	2013-01-11	2012-05-31	2012-05-31	ENSG00000148735	ENSG00000148735		"Pleckstrin homology (PH) domain containing"	26285	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 81"	C10orf81		12477932	Standard	NM_024889		Approved	FLJ23537, bA211N11.2	uc001lat.2	Q5SXH7	OTTHUMG00000019074	ENST00000369310.3:c.528A>G	chr10.hg19:g.115529653A>G		92.0	0.0		60.0	4.0	NM_024889	A8KA02|B3KX00|B6EDE1|Q5SXH8|Q5SXI0|Q6ZQR5|Q8NE42|Q9H5D9	Silent	SNP	ENST00000369310.3	hg19	CCDS53580.1																																																																																			.	.		0.483	PLEKHS1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050432.1	NM_024889		G	115529653	A	G	115529653	2	3	282	1	0	0	0	0	0	0	0	1	1621	69	3	2		2	C10orf81	10	115529653	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	186610	115529653	20005094	739	40973										
PNLIPRP1	5407	hgsc.bcm.edu	37	chr10	118365014	118365014	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgtgataaatccaaccctccCcaaagtgggtgccaccaaga	8	13	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:118365014C>T	ENST00000528052.1	+	12	1360	c.1289C>T	c.(1288-1290)cCc>cTc	p.P430L	PNLIPRP1_ENST00000358834.4_Missense_Mutation_p.P430L|PNLIPRP1_ENST00000534537.1_Missense_Mutation_p.P430L			P54315	LIPR1_HUMAN	pancreatic lipase-related protein 1	430	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				lipid metabolic process (GO:0006629)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|triglyceride lipase activity (GO:0004806)			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)		CCAACCCTCCCCAAAGTGGGT	0.428																																					p.P430L		Atlas-SNP	.											.	PNLIPRP1	82	.	0			c.C1289T						.						94	98	96					10																	118365014		2203	4300	6503	SO:0001583	missense	5407	exon12			CCCTCCCCAAAGT	BC025784	CCDS7595.1	10q26.12	2006-07-04			ENSG00000187021	ENSG00000187021			9156	protein-coding gene	gene with protein product		604422				1379598	Standard	NM_006229		Approved	PLRP1	uc001lco.1	P54315	OTTHUMG00000019109	ENST00000528052.1:c.1289C>T	chr10.hg19:g.118365014C>T	ENSP00000433933:p.Pro430Leu	212.0	0.0		132.0	6.0	NM_006229	Q68D83|Q68DR6|Q8TAU2|Q9BS82	Missense_Mutation	SNP	ENST00000528052.1	hg19	CCDS7595.1	.	.	.	.	.	.	.	.	.	.	c	19.30	3.800491	0.70567	.	.	ENSG00000187021	ENST00000358834;ENST00000528052;ENST00000534537	T;T;T	0.68181	-0.31;-0.31;-0.31	5.67	5.67	0.87782	Lipoxygenase, LH2 (4);Lipase/lipooxygenase, PLAT/LH2 (1);	0.000000	0.85682	D	0.000000	D	0.84669	0.5523	M	0.86651	2.83	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	D	0.86705	0.1932	10	0.72032	D	0.01	-16.5524	18.5642	0.91112	0.0:1.0:0.0:0.0	.	430	P54315	LIPR1_HUMAN	L	430	ENSP00000351695:P430L;ENSP00000433933:P430L;ENSP00000434159:P430L	ENSP00000351695:P430L	P	+	2	0	PNLIPRP1	118355004	0.997000	0.39634	1.000000	0.80357	0.988000	0.76386	3.369000	0.52365	2.657000	0.90304	0.645000	0.84053	CCC	.	.		0.428	PNLIPRP1-011	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384633.1	NM_006229		T	118365014	C	T	118365014	3	4	282	1	0	0	0	0	1	0	0	0	12159	623	22	3	1331	3	PNLIPRP1	10	118365014	Missense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	2835361	118365014	17169733	740	40974										
C10orf46	143384	hgsc.bcm.edu	37	chr10	120514243	120514243	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccatcatcgcctcgtagctgCccccctcctcctcttccatg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:120514243delC	ENST00000369151.3	-	1	515	c.32delG	c.(31-33)ggcfs	p.G11fs	CACUL1_ENST00000340214.4_Frame_Shift_Del_p.G11fs	NM_153810.4	NP_722517.3	Q86Y37	CACL1_HUMAN	CDK2-associated, cullin domain 1	11					G1/S transition of mitotic cell cycle (GO:0000082)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase activity (GO:0045860)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)	protein kinase binding (GO:0019901)										CTCGTAGCTGCCCCCCTCCTC	0.711																																					p.G11fs		Atlas-INDEL	.											.	.	.	.	0			c.33delC						.						58	69	66					10																	120514243		2033	4172	6205	SO:0001589	frameshift_variant	143384	exon1			.	AK097728	CCDS41570.1	10q26.13	2012-06-12	2012-06-12	2012-06-12	ENSG00000151893	ENSG00000151893			23727	protein-coding gene	gene with protein product	"Cdk-Associated Cullin1"		"chromosome 10 open reading frame 46"	C10orf46		19829063	Standard	NM_153810		Approved	FLJ40409, MGC33215, CAC1	uc001lds.1	Q86Y37	OTTHUMG00000019138	ENST00000369151.3:c.32delG	chr10.hg19:g.120514243delC	ENSP00000358147:p.Gly11fs	477.0	0.0		285.0	19.0	NM_153810	Q5XPL7|Q8IY11|Q8N7S4	Frame_Shift_Del	DEL	ENST00000369151.3	hg19	CCDS41570.1																																																																																			.	.		0.711	CACUL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050612.2	NM_153810		-	120514243	C	-	120514243	7	5	282	1	0	1	0	1	0	0	0	0	1606	739	26	0	1113	0	C10orf46	10	120514243	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	2149229	120514243	15020504	741	40975										
SEC23IP	11196	hgsc.bcm.edu	37	chr10	121675303	121675303	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctcaaattgctgcggacacaTttcaagaaatctttagatga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:121675303delT	ENST00000369075.3	+	8	1518	c.1446delT	c.(1444-1446)catfs	p.H482fs	SEC23IP_ENST00000543134.1_Frame_Shift_Del_p.H271fs	NM_007190.3	NP_009121.1	Q9Y6Y8	S23IP_HUMAN	SEC23 interacting protein	482					acrosome assembly (GO:0001675)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|single fertilization (GO:0007338)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear endoplasmic reticulum (GO:0097038)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	36		Lung NSC(174;0.109)|all_lung(145;0.142)|all_neural(114;0.234)		all cancers(201;0.00515)		TGCGGACACATTTCAAGAAAT	0.398																																					p.H482fs		Atlas-INDEL	.											.	SEC23IP	100	.	0			c.1445delA						.						114	115	115					10																	121675303		2203	4300	6503	SO:0001589	frameshift_variant	11196	exon8			.	AB019435	CCDS7618.1	10q26.11-q26.12	2013-01-10			ENSG00000107651	ENSG00000107651		"Sterile alpha motif (SAM) domain containing"	17018	protein-coding gene	gene with protein product						10400679	Standard	NM_007190		Approved	p125	uc001leu.2	Q9Y6Y8	OTTHUMG00000019161	ENST00000369075.3:c.1446delT	chr10.hg19:g.121675303delT	ENSP00000358071:p.His482fs	107.0	0.0		99.0	10.0	NM_007190	D3DRD2|Q8IXH5|Q9BUK5	Frame_Shift_Del	DEL	ENST00000369075.3	hg19	CCDS7618.1																																																																																			.	.		0.398	SEC23IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050688.1			-	121675303	T	-	121675303	7	5	282	1	0	1	0	1	0	0	0	0	14008	1490	52	0	1476	0	SEC23IP	10	121675303	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1161060	121675303	13859444	742	40976										
TACC2	10579	hgsc.bcm.edu	37	chr10	123970853	123970853	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccctgaggaggccaaagatgAaaaagacacccgagaaactt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:123970853delA	ENST00000369005.1	+	9	7253	c.6913delA	c.(6913-6915)aaafs	p.K2306fs	TACC2_ENST00000369000.1_Frame_Shift_Del_p.K10fs|TACC2_ENST00000368999.1_Frame_Shift_Del_p.K384fs|TACC2_ENST00000358010.1_Frame_Shift_Del_p.K452fs|TACC2_ENST00000360561.3_Frame_Shift_Del_p.K384fs|TACC2_ENST00000515603.1_Frame_Shift_Del_p.K2261fs|TACC2_ENST00000369001.1_Frame_Shift_Del_p.K10fs|TACC2_ENST00000334433.3_Frame_Shift_Del_p.K2306fs|TACC2_ENST00000369004.3_Frame_Shift_Del_p.K384fs|TACC2_ENST00000513429.1_Frame_Shift_Del_p.K452fs|TACC2_ENST00000453444.2_Frame_Shift_Del_p.K2310fs|TACC2_ENST00000515273.1_Frame_Shift_Del_p.K2310fs|TACC2_ENST00000260733.3_Frame_Shift_Del_p.K384fs	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	2306					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				GCCAAAGATGAAAAAGACACC	0.498																																					p.M2304fs		Atlas-INDEL	.											.	TACC2	271	.	0			c.6912delG						.						95	98	97					10																	123970853		2203	4300	6503	SO:0001589	frameshift_variant	10579	exon9			.	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.6913delA	chr10.hg19:g.123970853delA	ENSP00000358001:p.Lys2306fs	243.0	0.0		244.0	15.0	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Frame_Shift_Del	DEL	ENST00000369005.1	hg19	CCDS7626.1																																																																																			.	.		0.498	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1			-	123970853	A	-	123970853	7	5	282	1	0	1	0	1	0	0	0	0	15517	247	9	0	7015	0	TACC2	10	123970853	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2295550	123970853	11563894	743	40977										
TACC2	10579	hgsc.bcm.edu	37	chr10	123985931	123985931	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttgtaccttatgtttgacacTtctcaggagagccctgtcaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:123985931delT	ENST00000369005.1	+	13	7999	c.7659delT	c.(7657-7659)actfs	p.T2553fs	TACC2_ENST00000369000.1_Frame_Shift_Del_p.T253fs|TACC2_ENST00000368999.1_Frame_Shift_Del_p.T643fs|TACC2_ENST00000358010.1_Frame_Shift_Del_p.T699fs|TACC2_ENST00000360561.3_Frame_Shift_Del_p.T631fs|TACC2_ENST00000515603.1_Frame_Shift_Del_p.T2508fs|TACC2_ENST00000369001.1_Frame_Shift_Del_p.T257fs|TACC2_ENST00000334433.3_Frame_Shift_Del_p.T2553fs|TACC2_ENST00000369004.3_Frame_Shift_Del_p.T643fs|TACC2_ENST00000513429.1_Frame_Shift_Del_p.T699fs|TACC2_ENST00000453444.2_Frame_Shift_Del_p.T2557fs|TACC2_ENST00000515273.1_Frame_Shift_Del_p.T2557fs|TACC2_ENST00000260733.3_Frame_Shift_Del_p.T631fs	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	2553					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				TGTTTGACACTTCTCAGGAGA	0.522																																					p.T2553fs		Atlas-INDEL	.											.	TACC2	271	.	0			c.7658delC						.						160	124	136					10																	123985931		2203	4300	6503	SO:0001589	frameshift_variant	10579	exon13			.	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.7659delT	chr10.hg19:g.123985931delT	ENSP00000358001:p.Thr2553fs	224.0	0.0		145.0	10.0	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Frame_Shift_Del	DEL	ENST00000369005.1	hg19	CCDS7626.1																																																																																			.	.		0.522	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1			-	123985931	T	-	123985931	7	5	282	1	0	1	0	1	0	0	0	0	15517	1596	56	0	7777	0	TACC2	10	123985931	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	15078	123985931	11548816	744	40978										
C10orf120	399814	hgsc.bcm.edu	37	chr10	124457833	124457833	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aatcacctttgctgtccataTtttttctaggggtacacaaa					rs569498958		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:124457833delT	ENST00000329446.4	-	3	455	c.424delA	c.(424-426)atafs	p.I142fs		NM_001010912.1	NP_001010912.1	Q5SQS8	CJ120_HUMAN	chromosome 10 open reading frame 120	142										endometrium(1)|kidney(1)|large_intestine(6)|lung(9)|skin(2)|stomach(1)|urinary_tract(1)	21		all_neural(114;0.169)|Glioma(114;0.222)				GCTGTCCATATTTTTTCTAGG	0.458																																					p.I142fs		Atlas-INDEL	.											C10orf120,NS,carcinoma,0,1	C10orf120	55	.	0			c.425delT						.						117	122	121					10																	124457833		2203	4300	6503	SO:0001589	frameshift_variant	399814	exon3			.		CCDS31302.1	10q26.13	2012-06-12			ENSG00000183559	ENSG00000183559			25707	protein-coding gene	gene with protein product							Standard	NM_001010912		Approved	bA318C4.1	uc001lgn.3	Q5SQS8	OTTHUMG00000019187	ENST00000329446.4:c.424delA	chr10.hg19:g.124457833delT	ENSP00000331012:p.Ile142fs	133.0	0.0		135.0	10.0	NM_001010912	B2RU17	Frame_Shift_Del	DEL	ENST00000329446.4	hg19	CCDS31302.1																																																																																			.	.		0.458	C10orf120-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050803.1	NM_001010912		-	124457833	T	-	124457833	7	5	282	1	0	1	0	1	0	0	0	0	1592	1493	52	0	587	0	C10orf120	10	124457833	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	471902	124457833	11076914	745	40979										
FAM175B	23172	hgsc.bcm.edu	37	chr10	126519940	126519940	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agtgtgtgcagatgttgaaaAgagtgagcgagttgttgaat	15	2	0	5			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:126519940A>G	ENST00000298492.5	+	8	731	c.686A>G	c.(685-687)aAg>aGg	p.K229R		NM_032182.3	NP_115558.3	Q15018	F175B_HUMAN	family with sequence similarity 175, member B	229					cellular response to freezing (GO:0071497)	BRISC complex (GO:0070552)|cytoplasm (GO:0005737)	polyubiquitin binding (GO:0031593)			NS(1)	1						GATGTTGAAAAGAGTGAGCGA	0.383																																					p.K229R		Atlas-SNP	.											.	FAM175B	39	.	0			c.A686G						.						98	84	89					10																	126519940		2203	4300	6503	SO:0001583	missense	23172	exon8			TTGAAAAGAGTGA	D63877	CCDS31308.2	10q26.2	2013-01-24	2008-07-02	2008-07-02	ENSG00000165660	ENSG00000165660			28975	protein-coding gene	gene with protein product	"Abraxas brother"	611144	"KIAA0157"	KIAA0157		8590280	Standard	NM_032182		Approved	Em:AC068896.4, ABRO1	uc001lib.4	Q15018	OTTHUMG00000019218	ENST00000298492.5:c.686A>G	chr10.hg19:g.126519940A>G	ENSP00000298492:p.Lys229Arg	94.0	0.0		85.0	4.0	NM_032182	B4DKR2|Q96H11	Missense_Mutation	SNP	ENST00000298492.5	hg19	CCDS31308.2	.	.	.	.	.	.	.	.	.	.	A	28.5	4.924392	0.92319	.	.	ENSG00000165660	ENST00000298492	T	0.48522	0.81	5.7	5.7	0.88788	.	0.100317	0.64402	D	0.000001	T	0.45677	0.1354	L	0.29908	0.895	0.52099	D	0.999941	P	0.51933	0.949	P	0.48952	0.596	T	0.32322	-0.9911	10	0.32370	T	0.25	-52.1624	15.9745	0.80049	1.0:0.0:0.0:0.0	.	229	Q15018	F175B_HUMAN	R	229	ENSP00000298492:K229R	ENSP00000298492:K229R	K	+	2	0	FAM175B	126509930	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.114000	0.77103	2.168000	0.68352	0.533000	0.62120	AAG	.	.		0.383	FAM175B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050891.2	NM_032182		G	126519940	A	G	126519940	3	3	282	1	0	0	0	0	1	0	0	0	5503	72	3	2	716	2	FAM175B	10	126519940	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2062107	126519940	9014807	746	40980										
PTPRE	5791	hgsc.bcm.edu	37	chr10	129861413	129861413	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcaaaagtctgcgaccatcgTcatgttaacaaacttgaaag	8	9	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:129861413T>C	ENST00000254667.3	+	10	971	c.692T>C	c.(691-693)gTc>gCc	p.V231A	PTPRE_ENST00000419012.2_Missense_Mutation_p.V231A|PTPRE_ENST00000306042.5_Missense_Mutation_p.V173A|PTPRE_ENST00000430713.2_3'UTR	NM_006504.4	NP_006495.1	P23469	PTPRE_HUMAN	protein tyrosine phosphatase, receptor type, E	231	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of insulin receptor signaling pathway (GO:0046627)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of mast cell activation (GO:0033003)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	22		all_epithelial(44;1.66e-05)|all_lung(145;0.00456)|Lung NSC(174;0.0066)|all_neural(114;0.0936)|Colorectal(57;0.141)|Breast(234;0.166)|Melanoma(40;0.203)			Alendronate(DB00630)	GCGACCATCGTCATGTTAACA	0.498																																					p.V231A	Colon(52;977 1184 20575 41685)	Atlas-SNP	.											.	PTPRE	132	.	0			c.T692C						.						110	99	103					10																	129861413		2203	4300	6503	SO:0001583	missense	5791	exon10			CCATCGTCATGTT	AF406557	CCDS7657.1, CCDS7658.1	10q26	2011-06-09			ENSG00000132334	ENSG00000132334		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9669	protein-coding gene	gene with protein product		600926				8595895	Standard	NM_130435		Approved	PTPE	uc001lkb.3	P23469	OTTHUMG00000019254	ENST00000254667.3:c.692T>C	chr10.hg19:g.129861413T>C	ENSP00000254667:p.Val231Ala	150.0	0.0		101.0	5.0	NM_006504	Q13345|Q5VWH3|Q5VWH4|Q96KQ6	Missense_Mutation	SNP	ENST00000254667.3	hg19	CCDS7657.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.450301	0.84101	.	.	ENSG00000132334	ENST00000254667;ENST00000439034;ENST00000419012;ENST00000306042	T;T;T	0.23147	1.92;1.92;1.92	4.44	4.44	0.53790	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.64402	U	0.000002	T	0.51176	0.1659	M	0.76938	2.355	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.996;1.0;1.0;1.0	T	0.57359	-0.7825	10	0.87932	D	0	.	13.3688	0.60701	0.0:0.0:0.0:1.0	.	209;231;173;231	F5H0X4;Q5VWH4;P23469-2;P23469	.;.;.;PTPRE_HUMAN	A	231;209;231;173	ENSP00000254667:V231A;ENSP00000402337:V231A;ENSP00000303350:V173A	ENSP00000254667:V231A	V	+	2	0	PTPRE	129751403	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	7.577000	0.82486	1.999000	0.58509	0.460000	0.39030	GTC	.	.		0.498	PTPRE-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050990.1			C	129861413	T	C	129861413	3	2	282	1	0	0	0	0	1	0	0	0	12815	1667	58	2	761	2	PTPRE	10	129861413	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3341473	129861413	5673334	747	40981										
ADAM8	101	hgsc.bcm.edu	37	chr10	135089017	135089017	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gggcagagctcggcggactcGggggcctggcagacgccacg					rs201802022	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:135089017delG	ENST00000445355.3	-	2	171	c.121delC	c.(121-123)cgafs	p.R41fs	ADAM8_ENST00000485491.2_Intron|ADAM8_ENST00000559180.1_5'UTR|ADAM8_ENST00000415217.3_Frame_Shift_Del_p.R41fs	NM_001109.4	NP_001100.3	P78325	ADAM8_HUMAN	ADAM metallopeptidase domain 8	41					activation of MAPK activity involved in innate immune response (GO:0035419)|angiogenesis (GO:0001525)|cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|leukocyte migration involved in inflammatory response (GO:0002523)|lymphocyte chemotaxis (GO:0048247)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of bone resorption (GO:0045780)|positive regulation of cell adhesion (GO:0045785)|positive regulation of eosinophil migration (GO:2000418)|positive regulation of fibronectin-dependent thymocyte migration (GO:2000415)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of neutrophil extravasation (GO:2000391)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein processing (GO:0010954)|positive regulation of protein secretion (GO:0050714)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000309)|regulation of cell-cell adhesion (GO:0022407)|single organismal cell-cell adhesion (GO:0016337)	alpha9-beta1 integrin-ADAM8 complex (GO:0071133)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dense core granule membrane (GO:0032127)|integral component of plasma membrane (GO:0005887)|phagolysosome (GO:0032010)|plasma membrane (GO:0005886)|podosome (GO:0002102)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein self-association (GO:0043621)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)	17		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		all cancers(32;7.72e-06)|OV - Ovarian serous cystadenocarcinoma(35;8.23e-06)|Epithelial(32;1.02e-05)		CGGCGGACTCGGGGGCCTGGC	0.652																																					p.R41fs		Atlas-INDEL	.											.	ADAM8	41	.	0			c.122delG						.						11	13	13					10																	135089017		2093	4162	6255	SO:0001589	frameshift_variant	101	exon2			.	D26579	CCDS31319.2, CCDS58102.1, CCDS58103.1	10q26.3	2014-03-20	2005-08-18		ENSG00000151651	ENSG00000151651		"ADAM metallopeptidase domain containing", "CD molecules"	215	protein-coding gene	gene with protein product		602267	"a disintegrin and metalloproteinase domain 8"			9126482	Standard	NM_001109		Approved	CD156, MS2, CD156a	uc021qbe.1	P78325	OTTHUMG00000019309	ENST00000445355.3:c.121delC	chr10.hg19:g.135089017delG	ENSP00000453302:p.Arg41fs	299.0	0.0		247.0	16.0	NM_001164489	B4DVM6|H0YL36|H0YLR0|H0YN39	Frame_Shift_Del	DEL	ENST00000445355.3	hg19	CCDS31319.2																																																																																			.	.		0.652	ADAM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051118.4	NM_001109		-	135089017	G	-	135089017	7	5	282	1	0	1	0	1	0	0	0	0	252	1124	39	0	2359	0	ADAM8	10	135089017	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	5227604	135089017	445730	748	40982										
PKP3	11187	hgsc.bcm.edu	37	chr11	397014	397014	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	catgagcgcggtggggttggGagccgggccgactatgacac	18	10	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:397014G>A	ENST00000331563.2	+	3	589	c.513G>A	c.(511-513)ggG>ggA	p.G171G		NM_007183.2	NP_009114.1	Q9Y446	PKP3_HUMAN	plakophilin 3	171					desmosome assembly (GO:0002159)|establishment of protein localization to plasma membrane (GO:0090002)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|desmosome (GO:0030057)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)			breast(1)|central_nervous_system(1)|endometrium(3)|lung(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_cancers(49;3.02e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GTGGGGTTGGGAGCCGGGCCG	0.731																																					p.G171G		Atlas-SNP	.											.	PKP3	36	.	0			c.G513A						.						20	23	22					11																	397014		2190	4283	6473	SO:0001819	synonymous_variant	11187	exon3			GGTTGGGAGCCGG	Z98265	CCDS7695.1	11p15	2013-02-14			ENSG00000184363	ENSG00000184363		"Armadillo repeat containing"	9025	protein-coding gene	gene with protein product		605561				10374265	Standard	XM_005252760		Approved		uc001lpc.3	Q9Y446	OTTHUMG00000119068	ENST00000331563.2:c.513G>A	chr11.hg19:g.397014G>A		37.0	0.0		40.0	17.0	NM_007183	F8J390|Q53EX8	Silent	SNP	ENST00000331563.2	hg19	CCDS7695.1																																																																																			.	.		0.731	PKP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239281.1	NM_007183		A	397014	G	A	397014	2	1	282	1	0	0	0	0	0	0	0	1	11995	1161	41	3		3	PKP3	11	397014	Silent	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10		397014	134609502	749	40983										
ANO9	338440	hgsc.bcm.edu	37	chr11	418960	418960	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccttggtgtggaagacggacAggctgtggttgacgtagccc	16	9	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:418960A>G	ENST00000332826.6	-	21	2048	c.1964T>C	c.(1963-1965)cTg>cCg	p.L655P	SIGIRR_ENST00000382520.2_5'Flank|SIGIRR_ENST00000332725.3_5'Flank|SIGIRR_ENST00000397632.3_5'Flank	NM_001012302.2	NP_001012302	A1A5B4	ANO9_HUMAN	anoctamin 9	655					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|negative regulation of intracellular calcium activated chloride channel activity (GO:1902939)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)			central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|lung(5)|ovary(1)|prostate(4)|skin(4)	21						GAAGACGGACAGGCTGTGGTT	0.612																																					p.L655P		Atlas-SNP	.											.	ANO9	61	.	0			c.T1964C						.						170	151	157					11																	418960		2203	4300	6503	SO:0001583	missense	338440	exon21			ACGGACAGGCTGT	U33271	CCDS31326.1	11p15.5	2014-04-09	2008-08-28	2008-08-28	ENSG00000185101	ENSG00000185101		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	20679	protein-coding gene	gene with protein product			"tumor protein p53 inducible protein 5", "transmembrane protein 16J"	TP53I5, TMEM16J		9305847, 24692353	Standard	NM_001012302		Approved	PIG5	uc001lpi.2	A1A5B4	OTTHUMG00000165446	ENST00000332826.6:c.1964T>C	chr11.hg19:g.418960A>G	ENSP00000332788:p.Leu655Pro	177.0	0.0		157.0	7.0	NM_001012302	B3KUC4|B4E134|Q8TEN4	Missense_Mutation	SNP	ENST00000332826.6	hg19	CCDS31326.1	.	.	.	.	.	.	.	.	.	.	a	21.1	4.104828	0.77096	.	.	ENSG00000185101	ENST00000332826	D	0.82803	-1.65	4.44	4.44	0.53790	.	0.000000	0.53938	D	0.000046	D	0.93135	0.7814	H	0.94964	3.605	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.94890	0.8047	10	0.87932	D	0	.	14.0161	0.64525	1.0:0.0:0.0:0.0	.	356;655	A1A5B4-2;A1A5B4	.;ANO9_HUMAN	P	655	ENSP00000332788:L655P	ENSP00000332788:L655P	L	-	2	0	ANO9	408960	1.000000	0.71417	0.980000	0.43619	0.751000	0.42716	6.142000	0.71750	1.796000	0.52611	0.391000	0.25812	CTG	.	.		0.612	ANO9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384116.1	NM_001012302		G	418960	A	G	418960	3	3	282	1	0	0	0	0	1	0	0	0	704	188	7	2	396	2	ANO9	11	418960	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	21946	418960	134587556	750	40984										
PTDSS2	81490	hgsc.bcm.edu	37	chr11	488548	488548	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtggatcatggacgtgctcgTctgcaacgggctgggcatct	15	10	3	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:488548T>C	ENST00000308020.5	+	8	931	c.755T>C	c.(754-756)gTc>gCc	p.V252A		NM_030783.1	NP_110410.1	Q9BVG9	PTSS2_HUMAN	phosphatidylserine synthase 2	252					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylserine biosynthetic process (GO:0006659)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	CDP-diacylglycerol-serine O-phosphatidyltransferase activity (GO:0003882)			autonomic_ganglia(1)|breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(1)	9		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;2.76e-26)|Epithelial(43;2.56e-25)|OV - Ovarian serous cystadenocarcinoma(40;7.54e-20)|BRCA - Breast invasive adenocarcinoma(625;8.76e-05)|Lung(200;0.0407)|LUSC - Lung squamous cell carcinoma(625;0.0735)	Phosphatidylserine(DB00144)	GACGTGCTCGTCTGCAACGGG	0.622																																					p.V252A		Atlas-SNP	.											.	PTDSS2	27	.	0			c.T755C						.						106	89	95					11																	488548		2203	4300	6503	SO:0001583	missense	81490	exon8			TGCTCGTCTGCAA	BC001210	CCDS7696.1	11p15	2008-05-02			ENSG00000174915	ENSG00000174915			15463	protein-coding gene	gene with protein product		612793				14984733	Standard	NM_030783		Approved	PSS2	uc001lpj.3	Q9BVG9	OTTHUMG00000119087	ENST00000308020.5:c.755T>C	chr11.hg19:g.488548T>C	ENSP00000308258:p.Val252Ala	151.0	0.0		119.0	5.0	NM_030783		Missense_Mutation	SNP	ENST00000308020.5	hg19	CCDS7696.1	.	.	.	.	.	.	.	.	.	.	T	17.50	3.404288	0.62288	.	.	ENSG00000174915	ENST00000308020	.	.	.	4.33	4.33	0.51752	.	0.568705	0.16126	N	0.228405	T	0.61553	0.2356	M	0.64170	1.965	0.53688	D	0.999976	B	0.32918	0.39	B	0.34536	0.185	T	0.66131	-0.6000	9	0.62326	D	0.03	-12.7402	13.9771	0.64279	0.0:0.0:0.0:1.0	.	252	Q9BVG9	PTSS2_HUMAN	A	252	.	ENSP00000308258:V252A	V	+	2	0	PTDSS2	478548	1.000000	0.71417	0.860000	0.33809	0.703000	0.40648	7.668000	0.83897	1.973000	0.57446	0.459000	0.35465	GTC	.	.		0.622	PTDSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239301.2			C	488548	T	C	488548	3	2	282	1	0	0	0	0	1	0	0	0	12749	1667	58	2	785	2	PTDSS2	11	488548	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	69588	488548	134517968	751	40985										
PTDSS2	81490	hgsc.bcm.edu	37	chr11	489639	489639	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgaagtttgtgctgtggatgCccccggagcactacctggtc					rs143446343		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:489639delC	ENST00000308020.5	+	10	1197	c.1021delC	c.(1021-1023)cccfs	p.P342fs		NM_030783.1	NP_110410.1	Q9BVG9	PTSS2_HUMAN	phosphatidylserine synthase 2	342					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylserine biosynthetic process (GO:0006659)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	CDP-diacylglycerol-serine O-phosphatidyltransferase activity (GO:0003882)			autonomic_ganglia(1)|breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(1)	9		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;2.76e-26)|Epithelial(43;2.56e-25)|OV - Ovarian serous cystadenocarcinoma(40;7.54e-20)|BRCA - Breast invasive adenocarcinoma(625;8.76e-05)|Lung(200;0.0407)|LUSC - Lung squamous cell carcinoma(625;0.0735)	Phosphatidylserine(DB00144)	GCTGTGGATGCCCCCGGAGCA	0.622																																					p.M340fs		Atlas-INDEL	.											.	PTDSS2	27	.	0			c.1020delG						.																																			SO:0001589	frameshift_variant	81490	exon10			.	BC001210	CCDS7696.1	11p15	2008-05-02			ENSG00000174915	ENSG00000174915			15463	protein-coding gene	gene with protein product		612793				14984733	Standard	NM_030783		Approved	PSS2	uc001lpj.3	Q9BVG9	OTTHUMG00000119087	ENST00000308020.5:c.1021delC	chr11.hg19:g.489639delC	ENSP00000308258:p.Pro342fs	259.0	0.0		179.0	11.0	NM_030783		Frame_Shift_Del	DEL	ENST00000308020.5	hg19	CCDS7696.1																																																																																			.	.		0.622	PTDSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239301.2			-	489639	C	-	489639	7	5	282	1	0	1	0	1	0	0	0	0	12749	739	26	0	1059	0	PTDSS2	11	489639	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1091	489639	134516877	752	40986										
EPS8L2	64787	hgsc.bcm.edu	37	chr11	721655	721655	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcaagcagctgaaccagcggAaaaaggggaagaagaagggc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:721655delA	ENST00000533256.1	+	11	1234	c.859delA	c.(859-861)aaafs	p.K288fs	EPS8L2_ENST00000318562.8_Frame_Shift_Del_p.K288fs|EPS8L2_ENST00000530636.1_Frame_Shift_Del_p.K288fs|AP006621.9_ENST00000527021.2_RNA|EPS8L2_ENST00000526198.1_Frame_Shift_Del_p.K304fs			Q9H6S3	ES8L2_HUMAN	EPS8-like 2	288					positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	actin binding (GO:0003779)	p.K290fs*22(1)		NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|pancreas(1)|prostate(2)|soft_tissue(1)|urinary_tract(1)	13		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;4.37e-27)|Epithelial(43;2.81e-26)|OV - Ovarian serous cystadenocarcinoma(40;1.33e-20)|BRCA - Breast invasive adenocarcinoma(625;4.29e-05)|Lung(200;0.0582)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GAACCAGCGGAAAAAGGGGAA	0.652																																					p.R286fs		Atlas-INDEL	.											.,1	EPS8L2	42	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.858delG						.						33	44	40					11																	721655		2196	4288	6484	SO:0001589	frameshift_variant	64787	exon10			.	AF318331	CCDS31328.1	11p15.5	2008-02-05				ENSG00000177106			21296	protein-coding gene	gene with protein product		614988				12620401	Standard	NM_022772		Approved	FLJ21935, FLJ22171, MGC3088	uc001lqt.3	Q9H6S3		ENST00000533256.1:c.859delA	chr11.hg19:g.721655delA	ENSP00000435585:p.Lys288fs	312.0	0.0		248.0	15.0	NM_022772	B3KSX1|B7ZKL3|Q53GM8|Q8WYW7|Q96K06|Q9H6K9	Frame_Shift_Del	DEL	ENST00000533256.1	hg19	CCDS31328.1																																																																																			.	.		0.652	EPS8L2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382344.1	NM_022772		-	721655	A	-	721655	7	5	282	1	0	1	0	1	0	0	0	0	5198	247	9	0	893	0	EPS8L2	11	721655	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	232016	721655	134284861	753	40987										
TALDO1	6888	hgsc.bcm.edu	37	chr11	759019	759019	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tttggagcagaaatactaaaGaagattccgggccgagtatc	11	7	0	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:759019G>T	ENST00000319006.3	+	3	444	c.291G>T	c.(289-291)aaG>aaT	p.K97N	TALDO1_ENST00000528097.1_Missense_Mutation_p.K97N			P37837	TALDO_HUMAN	transaldolase 1	97					carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|fructose 6-phosphate metabolic process (GO:0006002)|glyceraldehyde-3-phosphate metabolic process (GO:0019682)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, non-oxidative branch (GO:0009052)|small molecule metabolic process (GO:0044281)|xylulose biosynthetic process (GO:0005999)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	monosaccharide binding (GO:0048029)|sedoheptulose-7-phosphate:D-glyceraldehyde-3-phosphate glyceronetransferase activity (GO:0004801)			breast(1)|kidney(2)|large_intestine(5)|lung(4)|prostate(2)	14		all_cancers(49;1.13e-08)|all_epithelial(84;2.95e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.159)|all_lung(207;0.198)		all cancers(45;4.66e-26)|Epithelial(43;2.97e-25)|OV - Ovarian serous cystadenocarcinoma(40;1.48e-19)|BRCA - Breast invasive adenocarcinoma(625;4.41e-05)|Lung(200;0.0595)|LUSC - Lung squamous cell carcinoma(625;0.0712)		AAATACTAAAGAAGATTCCGG	0.443																																					p.K97N		Atlas-SNP	.											.	TALDO1	25	.	0			c.G291T						.						134	144	141					11																	759019		2203	4300	6503	SO:0001583	missense	6888	exon3			ACTAAAGAAGATT		CCDS7712.1	11p15.5-p15.4	2009-12-02			ENSG00000177156	ENSG00000177156	2.2.1.2		11559	protein-coding gene	gene with protein product		602063				9339383	Standard	NM_006755		Approved		uc001lqz.3	P37837	OTTHUMG00000133318	ENST00000319006.3:c.291G>T	chr11.hg19:g.759019G>T	ENSP00000321259:p.Lys97Asn	160.0	0.0		121.0	48.0	NM_006755	B2R8M2|O00751|Q8WV32|Q8WZ45	Missense_Mutation	SNP	ENST00000319006.3	hg19	CCDS7712.1	.	.	.	.	.	.	.	.	.	.	G	33	5.207784	0.95033	.	.	ENSG00000177156	ENST00000319006;ENST00000528097	D;D	0.86230	-2.09;-2.09	4.9	4.9	0.64082	Aldolase-type TIM barrel (1);	0.000000	0.85682	D	0.000000	D	0.88706	0.6509	M	0.70275	2.135	0.80722	D	1	P;B	0.35363	0.497;0.339	B;B	0.40982	0.345;0.236	D	0.89509	0.3770	10	0.59425	D	0.04	-16.3143	17.2585	0.87064	0.0:0.0:1.0:0.0	.	97;97	F2Z393;P37837	.;TALDO_HUMAN	N	97	ENSP00000321259:K97N;ENSP00000437098:K97N	ENSP00000321259:K97N	K	+	3	2	TALDO1	749019	1.000000	0.71417	0.999000	0.59377	0.979000	0.70002	6.731000	0.74785	2.437000	0.82529	0.561000	0.74099	AAG	.	.		0.443	TALDO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257116.1	NM_006755		T	759019	G	T	759019	3	4	282	1	0	0	0	0	1	0	0	0	15558	933	33	3	301	3	TALDO1	11	759019	Missense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	37364	759019	134247497	754	40988										
MUC6	4588	hgsc.bcm.edu	37	chr11	1024954	1024954	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtctgtcacgaagctcacgtCcccgcacagcgggctctcct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:1024954delC	ENST00000421673.2	-	24	3165	c.3115delG	c.(3115-3117)gacfs	p.D1039fs		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1039	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AAGCTCACGTCCCCGCACAGC	0.622																																					p.D1039fs		Atlas-INDEL	.											.	MUC6	408	.	0			c.3116delA						.						40	48	46					11																	1024954		2124	4232	6356	SO:0001589	frameshift_variant	4588	exon24			.	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"Mucins"	7517	protein-coding gene	gene with protein product		158374	"mucin 6, gastric"			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.3115delG	chr11.hg19:g.1024954delC	ENSP00000406861:p.Asp1039fs	260.0	0.0		199.0	12.0	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Frame_Shift_Del	DEL	ENST00000421673.2	hg19	CCDS44513.1																																																																																			.	.		0.622	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540		-	1024954	C	-	1024954	7	5	282	1	0	1	0	1	0	0	0	0	9989	855	30	0	4244	0	MUC6	11	1024954	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	265935	1024954	133981562	755	40989										
MUC5B	727897	hgsc.bcm.edu	37	chr11	1276641	1276641	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctgagtgccacaaccttgtgCccccgggcccattcttcaac							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:1276641delC	ENST00000529681.1	+	37	15977	c.15919delC	c.(15919-15921)cccfs	p.P5308fs	MUC5B_ENST00000447027.1_Frame_Shift_Del_p.P5311fs	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	5308					cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CAACCTTGTGCCCCCGGGCCC	0.687																																					p.V5306fs		Atlas-INDEL	.											.	MUC5B	473	.	0			c.15918delG						.						24	26	26					11																	1276641		1993	4153	6146	SO:0001589	frameshift_variant	727897	exon37			.	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.15919delC	chr11.hg19:g.1276641delC	ENSP00000436812:p.Pro5308fs	249.0	0.0		142.0	10.0	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Frame_Shift_Del	DEL	ENST00000529681.1	hg19	CCDS44515.2																																																																																			.	.		0.687	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		-	1276641	C	-	1276641	7	5	282	1	0	1	0	1	0	0	0	0	9988	739	26	0	16074	0	MUC5B	11	1276641	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	251687	1276641	133729875	756	40990										
BRSK2	9024	hgsc.bcm.edu	37	chr11	1477640	1477640	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cgggccgagtacaaggccacGggggggccagccgtgttcca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:1477640delG	ENST00000528841.1	+	17	2115	c.1731delG	c.(1729-1731)acgfs	p.T577fs	BRSK2_ENST00000526678.1_Frame_Shift_Del_p.T599fs|BRSK2_ENST00000528710.1_Frame_Shift_Del_p.T517fs|BRSK2_ENST00000382179.1_Frame_Shift_Del_p.T623fs|BRSK2_ENST00000308230.5_Frame_Shift_Del_p.T599fs|BRSK2_ENST00000544817.1_Frame_Shift_Del_p.T272fs|BRSK2_ENST00000531197.1_Frame_Shift_Del_p.T577fs|BRSK2_ENST00000308219.9_Frame_Shift_Del_p.T577fs			Q8IWQ3	BRSK2_HUMAN	BR serine/threonine kinase 2	577					actin cytoskeleton reorganization (GO:0031532)|axonogenesis (GO:0007409)|establishment of cell polarity (GO:0030010)|exocytosis (GO:0006887)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mitotic nuclear division (GO:0007067)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			endometrium(4)|large_intestine(1)|lung(5)	10		all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00144)|Lung(200;0.0713)|LUSC - Lung squamous cell carcinoma(625;0.0842)		ACAAGGCCACGGGGGGGCCAG	0.622																																					p.T623fs		Atlas-INDEL	.											.,2	BRSK2	97	.	0			c.1868delC						.																																			SO:0001589	frameshift_variant	9024	exon17			.	AF020089	CCDS41590.1, CCDS58106.1, CCDS58107.1, CCDS58108.1, CCDS60696.1	11p15.5	2008-02-05	2003-09-11	2005-01-27	ENSG00000174672	ENSG00000174672			11405	protein-coding gene	gene with protein product	"serine/threonine kinase 29"	609236	"chromsosome 11 open reading frame 7"	C11orf7, STK29		9852686, 9929968	Standard	NM_001256629		Approved	PEN11B	uc001ltm.4	Q8IWQ3	OTTHUMG00000167089	ENST00000528841.1:c.1731delG	chr11.hg19:g.1477640delG	ENSP00000432000:p.Thr577fs	209.0	0.0		147.0	10.0	NM_001256630	B3KVE9|E9PLM7|O60843|O95099|Q5J5B4|Q6ZMQ4|Q8TB60	Frame_Shift_Del	DEL	ENST00000528841.1	hg19	CCDS58107.1																																																																																			.	.		0.622	BRSK2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393033.1	NM_003957		-	1477640	G	-	1477640	7	5	282	1	0	1	0	1	0	0	0	0	1526	1103	39	0	1797	0	BRSK2	11	1477640	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	200999	1477640	133528876	757	40991										
LSP1	4046	hgsc.bcm.edu	37	chr11	1902755	1902755	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gagcagcggcagcagcacgaGggggcgcagggcgccttgga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:1902755delG	ENST00000311604.3	+	3	460	c.285delG	c.(283-285)gagfs	p.E95fs	LSP1_ENST00000405957.2_Frame_Shift_Del_p.E33fs|LSP1_ENST00000406638.2_Frame_Shift_Del_p.E33fs|LSP1_ENST00000485341.1_3'UTR|LSP1_ENST00000381775.1_Frame_Shift_Del_p.E223fs	NM_002339.2	NP_002330.1	P33241	LSP1_HUMAN	lymphocyte-specific protein 1	95					cellular component movement (GO:0006928)|cellular defense response (GO:0006968)|chemotaxis (GO:0006935)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|signal transducer activity (GO:0004871)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	16		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|Lung(200;0.0729)|LUSC - Lung squamous cell carcinoma(625;0.0856)		AGCAGCACGAGGGGGCGCAGG	0.701																																					p.E223fs		Atlas-INDEL	.											.	LSP1	59	.	0			c.668delA						.						16	18	17					11																	1902755		2173	4239	6412	SO:0001589	frameshift_variant	4046	exon4			.	M33552	CCDS31334.1, CCDS31335.1, CCDS58110.1	11p15.5	2008-02-05			ENSG00000130592	ENSG00000130592			6707	protein-coding gene	gene with protein product		153432				2174784	Standard	NM_001242932		Approved	WP34	uc001luj.3	P33241	OTTHUMG00000012252	ENST00000311604.3:c.285delG	chr11.hg19:g.1902755delG	ENSP00000308383:p.Glu95fs	253.0	0.0		197.0	14.0	NM_001242932	B3KPP1|B3KRR6|E9PBV6|E9PFP3|Q16096|Q53H48|Q6FHM3|Q9BUY8	Frame_Shift_Del	DEL	ENST00000311604.3	hg19	CCDS31334.1																																																																																			.	.		0.701	LSP1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034045.3	NM_002339		-	1902755	G	-	1902755	7	5	282	1	0	1	0	1	0	0	0	0	9072	991	35	0	295	0	LSP1	11	1902755	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	425115	1902755	133103761	758	40992										
MMP26	56547	hgsc.bcm.edu	37	chr11	5010948	5010948	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccaggagacacaaacacagcTcctgcaacaattccatcgga	7	14	0	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:5010948T>C	ENST00000380390.1	+	3	386	c.170T>C	c.(169-171)cTc>cCc	p.L57P	MMP26_ENST00000477339.1_3'UTR|MMP26_ENST00000300762.1_Missense_Mutation_p.L57P			Q9NRE1	MMP26_HUMAN	matrix metallopeptidase 26	57					collagen catabolic process (GO:0030574)|proteolysis (GO:0006508)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(11)|pancreas(1)|skin(3)|stomach(1)	22		Medulloblastoma(188;0.0025)|Breast(177;0.0204)|all_neural(188;0.0227)		Epithelial(150;1.33e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0287)|LUSC - Lung squamous cell carcinoma(625;0.191)	Marimastat(DB00786)	CAAACACAGCTCCTGCAACAA	0.507																																					p.L57P		Atlas-SNP	.											.	MMP26	49	.	0			c.T170C						.						75	60	65					11																	5010948		2201	4298	6499	SO:0001583	missense	56547	exon2			CACAGCTCCTGCA	AF230354	CCDS7752.1	11p15	2008-07-18	2005-08-08		ENSG00000167346	ENSG00000167346	3.4.24.1		14249	protein-coding gene	gene with protein product	"matrilysin 2"	605470	"matrix metalloproteinase 26"			10801841, 10824119	Standard	NM_021801		Approved	endometase, MGC126590, MGC126592	uc001lzv.3	Q9NRE1	OTTHUMG00000066442	ENST00000380390.1:c.170T>C	chr11.hg19:g.5010948T>C	ENSP00000369753:p.Leu57Pro	91.0	0.0		60.0	4.0	NM_021801	Q3MJ78|Q9GZS2|Q9NR87	Missense_Mutation	SNP	ENST00000380390.1	hg19	CCDS7752.1	.	.	.	.	.	.	.	.	.	.	T	9.028	0.986513	0.18889	.	.	ENSG00000167346	ENST00000380390;ENST00000300762	T;T	0.38240	1.15;1.15	3.73	2.55	0.30701	Metallopeptidase, catalytic domain (1);	0.630671	0.12428	U	0.469764	T	0.24774	0.0601	L	0.46157	1.445	0.36742	D	0.88227	P	0.46277	0.875	B	0.34652	0.187	T	0.22417	-1.0217	10	0.87932	D	0	-0.3599	4.33	0.11059	0.2016:0.0:0.2086:0.5898	.	57	Q9NRE1	MMP26_HUMAN	P	57	ENSP00000369753:L57P;ENSP00000300762:L57P	ENSP00000300762:L57P	L	+	2	0	MMP26	4967524	0.007000	0.16637	0.008000	0.14137	0.350000	0.29205	-0.116000	0.10724	0.304000	0.22809	0.455000	0.32223	CTC	.	.		0.507	MMP26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142058.3	NM_021801		C	5010948	T	C	5010948	3	2	282	1	0	0	0	0	1	0	0	0	9672	1551	54	2	176	2	MMP26	11	5010948	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3108193	5010948	129995568	759	40993										
OR52B6	340980	hgsc.bcm.edu	37	chr11	5602667	5602667	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctccttgagcacctgcactaTtgccagatcaatatcattgc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:5602667delT	ENST00000345043.2	+	1	561	c.561delT	c.(559-561)tatfs	p.Y187fs	HBG2_ENST00000380259.2_Intron|AC015691.13_ENST00000394793.2_RNA	NM_001005162.2	NP_001005162.2	Q8NGF0	O52B6_HUMAN	olfactory receptor, family 52, subfamily B, member 6	187						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|lung(7)|ovary(1)|prostate(1)	12		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;3.56e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ACCTGCACTATTGCCAGATCA	0.478																																					p.Y187fs		Atlas-INDEL	.											.	OR52B6	37	.	0			c.560delA						.						196	201	199					11																	5602667		2185	4289	6474	SO:0001589	frameshift_variant	340980	exon1			.	AB065858	CCDS41611.1	11p15.4	2012-08-09			ENSG00000187747	ENSG00000187747		"GPCR / Class A : Olfactory receptors"	15211	protein-coding gene	gene with protein product							Standard	NM_001005162		Approved		uc010qzi.2	Q8NGF0	OTTHUMG00000066906	ENST00000345043.2:c.561delT	chr11.hg19:g.5602667delT	ENSP00000341581:p.Tyr187fs	201.0	0.0		152.0	10.0	NM_001005162	Q6IFI7	Frame_Shift_Del	DEL	ENST00000345043.2	hg19	CCDS41611.1																																																																																			.	.		0.478	OR52B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143397.1	NM_001005162		-	5602667	T	-	5602667	7	5	282	1	0	1	0	1	0	0	0	0	11122	1500	52	0	563	0	OR52B6	11	5602667	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	591719	5602667	129403849	760	40994										
FAM160A2	84067	hgsc.bcm.edu	37	chr11	6245706	6245706	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaggtatacggtgcccagggCcccgggaggccagtctgctc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:6245706delC	ENST00000449352.2	-	2	304	c.41delG	c.(40-42)ggcfs	p.G14fs	FAM160A2_ENST00000265978.4_Frame_Shift_Del_p.G14fs|FAM160A2_ENST00000524416.1_Frame_Shift_Del_p.G14fs			Q8N612	F16A2_HUMAN	family with sequence similarity 160, member A2	14					early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|protein transport (GO:0015031)	FHF complex (GO:0070695)				NS(1)|endometrium(3)|kidney(2)|large_intestine(7)|liver(1)|lung(14)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						GTGCCCAGGGCCCCGGGAGGC	0.597																																					p.G14fs		Atlas-INDEL	.											.	FAM160A2	100	.	0			c.42delC						.						72	68	69					11																	6245706		2201	4296	6497	SO:0001589	frameshift_variant	84067	exon2			.		CCDS7760.1, CCDS44530.1	11p15.4	2008-06-05	2008-06-05	2008-06-05	ENSG00000051009	ENSG00000051009			25378	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 56"	C11orf56		11230166, 11214970	Standard	NM_001098794		Approved	FLJ22665, KIAA1759, DKFZP566M1046	uc001mck.4	Q8N612	OTTHUMG00000133379	ENST00000449352.2:c.41delG	chr11.hg19:g.6245706delC	ENSP00000416918:p.Gly14fs	209.0	0.0		160.0	11.0	NM_032127	Q9C0A4|Q9H0N3|Q9H624	Frame_Shift_Del	DEL	ENST00000449352.2	hg19	CCDS44530.1																																																																																			.	.		0.597	FAM160A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383759.1	NM_032127		-	6245706	C	-	6245706	7	5	282	1	0	1	0	1	0	0	0	0	5474	739	26	0	2963	0	FAM160A2	11	6245706	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	643039	6245706	128760810	761	40995										
APBB1	322	hgsc.bcm.edu	37	chr11	6416867	6416867	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gccgtgccacagactcagcaGggggtgctgggaggcaggag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:6416867delG	ENST00000609360.1	-	15	2129	c.2030delC	c.(2029-2031)cctfs	p.P677fs	APBB1_ENST00000609331.1_Frame_Shift_Del_p.P442fs|APBB1_ENST00000608394.1_Frame_Shift_Del_p.P418fs|APBB1_ENST00000299402.6_Frame_Shift_Del_p.P675fs|APBB1_ENST00000311051.3_Frame_Shift_Del_p.P675fs|APBB1_ENST00000389906.2_Frame_Shift_Del_p.P677fs|APBB1_ENST00000608704.1_Frame_Shift_Del_p.P418fs|APBB1_ENST00000530885.1_Frame_Shift_Del_p.P455fs|APBB1_ENST00000526240.1_5'UTR|APBB1_ENST00000608655.1_Frame_Shift_Del_p.P457fs|APBB1_ENST00000608645.1_Frame_Shift_Del_p.P418fs|APBB1_ENST00000529519.1_Frame_Shift_Del_p.P202fs	NM_001164.3	NP_001155.1	O00213	APBB1_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 1 (Fe65)	677	PID 2. {ECO:0000255|PROSITE- ProRule:PRU00148}.				apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|histone H4 acetylation (GO:0043967)|negative regulation of cell growth (GO:0030308)|negative regulation of thymidylate synthase biosynthetic process (GO:0050760)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|proline-rich region binding (GO:0070064)|transcription factor binding (GO:0008134)			breast(4)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|prostate(2)|skin(1)|urinary_tract(1)	24		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;6.49e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)		AGACTCAGCAGGGGGTGCTGG	0.662																																					p.P677fs	GBM(147;1810 2556 5672 39622)	Atlas-INDEL	.											.	APBB1	73	.	0			c.2031delT						.						33	32	32					11																	6416867		2201	4295	6496	SO:0001589	frameshift_variant	322	exon14			.	L77864	CCDS31410.1, CCDS58114.1, CCDS66015.1, CCDS66016.1, CCDS66017.1, CCDS66018.1	11p15	2008-02-01				ENSG00000166313			581	protein-coding gene	gene with protein product		602709		RIR		8955346, 8894693	Standard	NM_001164		Approved	Fe65	uc001mcy.1	O00213		ENST00000609360.1:c.2030delC	chr11.hg19:g.6416867delG	ENSP00000477213:p.Pro677fs	166.0	0.0		139.0	11.0	NM_001164	A1E379|A6NH82|A6NL69|B7Z1J5|B7Z1J6|B7Z2Y0|D3DQT2|Q7Z324|Q96A93|V9GYK0|V9GYT4	Frame_Shift_Del	DEL	ENST00000609360.1	hg19																																																																																				.	.		0.662	APBB1-023	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471831.1	NM_001164		-	6416867	G	-	6416867	7	5	282	1	0	1	0	1	0	0	0	0	759	1000	35	0	106	0	APBB1	11	6416867	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	171161	6416867	128589649	762	40996										
DNHD1	144132	hgsc.bcm.edu	37	chr11	6568378	6568378	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcagtgtaacaacatgggccAaaagaggcagacagaggaat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:6568378delA	ENST00000527990.2	+	19	6209	c.6209delA	c.(6208-6210)caafs	p.Q2070fs	DNHD1_ENST00000254579.6_Frame_Shift_Del_p.Q2070fs			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	2070					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		AACATGGGCCAAAAGAGGCAG	0.547																																					p.Q2070fs		Atlas-INDEL	.											.	DNHD1	198	.	0			c.6208delC						.						124	141	136					11																	6568378		692	1591	2283	SO:0001589	frameshift_variant	144132	exon21			.	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 47", "dynein heavy chain domain 1-like", "coiled-coil domain containing 35"	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.6209delA	chr11.hg19:g.6568378delA	ENSP00000436180:p.Gln2070fs	225.0	0.0		163.0	12.0	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Frame_Shift_Del	DEL	ENST00000527990.2	hg19	CCDS44532.1																																																																																			.	.		0.547	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666		-	6568378	A	-	6568378	7	5	282	1	0	1	0	1	0	0	0	0	4670	130	5	0	6292	0	DNHD1	11	6568378	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	151511	6568378	128438138	763	40997										
C11orf17	56672	hgsc.bcm.edu	37	chr11	8938845	8938845	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tctcttcagagaaaagacagAaaaaagacatcccttggtcc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:8938845delA	ENST00000309377.4	+	5	510	c.420delA	c.(418-420)agafs	p.R140fs	AKIP1_ENST00000525005.1_Frame_Shift_Del_p.R140fs|AKIP1_ENST00000396648.2_Frame_Shift_Del_p.R113fs|AKIP1_ENST00000299576.5_Frame_Shift_Del_p.R113fs|AKIP1_ENST00000529876.1_Frame_Shift_Del_p.R113fs|AKIP1_ENST00000534506.1_Frame_Shift_Del_p.R113fs|AKIP1_ENST00000309357.4_Intron|AKIP1_ENST00000534147.1_Frame_Shift_Del_p.R140fs	NM_020642.3	NP_065693.2	Q9NQ31	AKIP1_HUMAN	A kinase (PRKA) interacting protein 1	140					substrate adhesion-dependent cell spreading (GO:0034446)	nucleus (GO:0005634)				kidney(1)|large_intestine(2)|lung(2)	5						GAAAAGACAGAAAAAAGACAT	0.443																																					p.R140fs		Atlas-INDEL	.											.	AKIP1	9	.	0			c.419delG						.						91	77	82					11																	8938845		2201	4296	6497	SO:0001589	frameshift_variant	56672	exon5			.	AF512007	CCDS7793.1, CCDS55743.1, CCDS55744.1	11p15.3	2011-04-18	2011-04-18	2011-04-18	ENSG00000166452	ENSG00000166452			1170	protein-coding gene	gene with protein product		609191	"chromosome 11 open reading frame 17"	C11orf17		20562110, 18178962, 15630084	Standard	NM_020642		Approved	BCA3	uc001mgx.3	Q9NQ31	OTTHUMG00000165653	ENST00000309377.4:c.420delA	chr11.hg19:g.8938845delA	ENSP00000310459:p.Arg140fs	210.0	0.0		163.0	11.0	NM_020642	Q8NBS2|Q8TAC6|Q8TAD3|Q8TAE0	Frame_Shift_Del	DEL	ENST00000309377.4	hg19	CCDS7793.1																																																																																			.	.		0.443	AKIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000385615.1	NM_020642		-	8938845	A	-	8938845	7	5	282	1	0	1	0	1	0	0	0	0	1634	243	9	0	434	0	C11orf17	11	8938845	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2370467	8938845	126067671	764	40998										
USP47	55031	hgsc.bcm.edu	37	chr11	11970052	11970052	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttagactggggagagcacttAaaaaaggagaatacagagtt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:11970052delA	ENST00000399455.2	+	23	3475	c.3355delA	c.(3355-3357)aaafs	p.K1120fs	USP47_ENST00000339865.5_Frame_Shift_Del_p.K1032fs|USP47_ENST00000527733.1_Frame_Shift_Del_p.K1100fs|USP47_ENST00000539466.1_5'UTR	NM_001282659.1	NP_001269588.1	Q96K76	UBP47_HUMAN	ubiquitin specific peptidase 47	1120					base-excision repair (GO:0006284)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of G2/M transition of mitotic cell cycle (GO:0010972)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell growth (GO:0030307)|response to drug (GO:0042493)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	ubiquitin-specific protease activity (GO:0004843)|WD40-repeat domain binding (GO:0071987)			breast(4)|endometrium(7)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46				Epithelial(150;0.000339)		GAGAGCACTTAAAAAAGGAGA	0.308																																					p.L1030fs		Atlas-INDEL	.											.	USP47	91	.	0			c.3090delT						.						52	53	53					11																	11970052		1801	4053	5854	SO:0001589	frameshift_variant	55031	exon21			.	AK027362	CCDS41619.1, CCDS60725.1	11p15.2	2008-02-05	2005-08-08		ENSG00000170242	ENSG00000170242		"Ubiquitin-specific peptidases"	20076	protein-coding gene	gene with protein product		614460	"Trf (TATA binding protein-related factor)-proximal homolog (Drosophila)", "ubiquitin specific protease 47"			12838346	Standard	XM_005252997		Approved		uc001mjr.3	Q96K76	OTTHUMG00000165685	ENST00000399455.2:c.3355delA	chr11.hg19:g.11970052delA	ENSP00000382382:p.Lys1120fs	162.0	0.0		159.0	10.0	NM_017944	B3KXF5|E9PM46|Q658U0|Q86Y73|Q8TEP6|Q9BWI0|Q9NWN1	Frame_Shift_Del	DEL	ENST00000399455.2	hg19																																																																																				.	.		0.308	USP47-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000385853.2	NM_017944		-	11970052	A	-	11970052	7	5	282	1	0	1	0	1	0	0	0	0	17093	363	13	0	3173	0	USP47	11	11970052	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	3031207	11970052	123036464	765	40999										
MICALCL	84953	hgsc.bcm.edu	37	chr11	12315123	12315123	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tctagatgacagcttctgagCccctctcgcaagtctcgaga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:12315123delC	ENST00000256186.2	+	3	436	c.145delC	c.(145-147)cccfs	p.P49fs		NM_032867.2	NP_116256.2	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	49	Ser-rich.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	mitogen-activated protein kinase binding (GO:0051019)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(5)|lung(5)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	30				Epithelial(150;0.00177)		AGCTTCTGAGCCCCTCTCGCA	0.458																																					p.E48fs		Atlas-INDEL	.											.	MICALCL	59	.	0			c.144delG						.						111	112	111					11																	12315123		1869	4102	5971	SO:0001589	frameshift_variant	84953	exon3			.	BK000463	CCDS41620.1	11p15.3	2005-11-01			ENSG00000133808	ENSG00000133808			25933	protein-coding gene	gene with protein product		612355				12110185	Standard	NM_032867		Approved	FLJ14966	uc001mkg.1	Q6ZW33	OTTHUMG00000165777	ENST00000256186.2:c.145delC	chr11.hg19:g.12315123delC	ENSP00000256186:p.Pro49fs	137.0	0.0		142.0	10.0	NM_032867	Q7RTP7|Q96JU6	Frame_Shift_Del	DEL	ENST00000256186.2	hg19	CCDS41620.1																																																																																			.	.		0.458	MICALCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386164.1	NM_032867		-	12315123	C	-	12315123	7	5	282	1	0	1	0	1	0	0	0	0	9581	739	26	0	151	0	MICALCL	11	12315123	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	345071	12315123	122691393	766	41000										
PIK3C2A	5286	hgsc.bcm.edu	37	chr11	17139207	17139207	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	actgtacatcatgcagggcaTctttgagaagcctaatacag	9	9	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:17139207T>C	ENST00000265970.7	-	18	3046	c.3047A>G	c.(3046-3048)gAt>gGt	p.D1016G	PIK3C2A_ENST00000531428.1_Intron|PIK3C2A_ENST00000540361.1_Missense_Mutation_p.D636G|RNU6-593P_ENST00000364716.1_RNA	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	1016	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|exocytosis (GO:0006887)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|small molecule metabolic process (GO:0044281)|vascular smooth muscle contraction (GO:0014829)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol binding (GO:0035091)			central_nervous_system(4)|endometrium(5)|kidney(5)|large_intestine(7)|lung(24)|ovary(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	58						ATGCAGGGCATCTTTGAGAAG	0.398																																					p.D1016G		Atlas-SNP	.											.	PIK3C2A	148	.	0			c.A3047G						.						84	78	80					11																	17139207		2200	4293	6493	SO:0001583	missense	5286	exon18			AGGGCATCTTTGA	Y13367	CCDS7824.1	11p15.5-p14	2012-07-13	2012-07-13			ENSG00000011405	2.7.1.154		8971	protein-coding gene	gene with protein product		603601	"phosphoinositide-3-kinase, class 2, alpha polypeptide"			9337861	Standard	NM_002645		Approved	PI3K-C2alpha	uc001mmq.4	O00443		ENST00000265970.7:c.3047A>G	chr11.hg19:g.17139207T>C	ENSP00000265970:p.Asp1016Gly	149.0	0.0		102.0	5.0	NM_002645	B0LPH2|B4E2G4|Q14CQ9	Missense_Mutation	SNP	ENST00000265970.7	hg19	CCDS7824.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.227565	0.79576	.	.	ENSG00000011405	ENST00000265970;ENST00000540361	T;T	0.62498	0.02;0.02	5.15	5.15	0.70609	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.094057	0.64402	D	0.000001	T	0.77405	0.4125	M	0.72479	2.2	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.77749	-0.2471	10	0.41790	T	0.15	-13.8277	14.9612	0.71158	0.0:0.0:0.0:1.0	.	1016	O00443	P3C2A_HUMAN	G	1016;636	ENSP00000265970:D1016G;ENSP00000438687:D636G	ENSP00000265970:D1016G	D	-	2	0	PIK3C2A	17095783	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	5.601000	0.67606	1.946000	0.56461	0.477000	0.44152	GAT	.	.		0.398	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645		C	17139207	T	C	17139207	3	2	282	1	0	0	0	0	1	0	0	0	11918	1435	50	2	2073	2	PIK3C2A	11	17139207	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	4824084	17139207	117867309	767	41001										
SERGEF	26297	hgsc.bcm.edu	37	chr11	18014534	18014534	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cacacattgctttagaattcTctagacctacaaaagaaaaa	4	9	1	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:18014534T>C	ENST00000265965.5	-	7	780	c.629A>G	c.(628-630)gAg>gGg	p.E210G	SERGEF_ENST00000532265.1_Missense_Mutation_p.E96G|SERGEF_ENST00000528200.1_Missense_Mutation_p.E210G	NM_012139.2	NP_036271.1	Q9UGK8	SRGEF_HUMAN	secretion regulating guanine nucleotide exchange factor	210					negative regulation of protein secretion (GO:0050709)|positive regulation of Ran GTPase activity (GO:0032853)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)	Ran guanyl-nucleotide exchange factor activity (GO:0005087)			autonomic_ganglia(1)|central_nervous_system(1)|large_intestine(5)|lung(5)	12						TTTAGAATTCTCTAGACCTAC	0.448																																					p.E210G		Atlas-SNP	.											.	SERGEF	38	.	0			c.A629G						.						105	96	99					11																	18014534		2200	4293	6493	SO:0001583	missense	26297	exon7			GAATTCTCTAGAC	AJ243950	CCDS7828.1	11p14.3	2006-03-09			ENSG00000129158	ENSG00000129158			17499	protein-coding gene	gene with protein product		606051				10571079, 12459492	Standard	NM_012139		Approved	DelGEF, Gnefr	uc001mnm.3	Q9UGK8	OTTHUMG00000166420	ENST00000265965.5:c.629A>G	chr11.hg19:g.18014534T>C	ENSP00000265965:p.Glu210Gly	160.0	0.0		86.0	4.0	NM_012139	Q9UGK9	Missense_Mutation	SNP	ENST00000265965.5	hg19	CCDS7828.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.31|18.31	3.595681|3.595681	0.66219|0.66219	.|.	.|.	ENSG00000129158|ENSG00000129158	ENST00000265965;ENST00000528200;ENST00000525920;ENST00000532265;ENST00000529728;ENST00000530613;ENST00000532389|ENST00000529151	T;T;T;T;T;T;T|.	0.80824|.	-1.42;-1.42;-1.42;-1.42;-1.42;-1.42;-1.42|.	5.19|5.19	4.07|4.07	0.47477|0.47477	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);|.	0.404705|.	0.27797|.	N|.	0.017805|.	T|T	0.66479|0.66479	0.2793|0.2793	M|M	0.77103|0.77103	2.36|2.36	0.34629|0.34629	D|D	0.71943|0.71943	D;B;D;D|.	0.59357|.	0.968;0.005;0.967;0.985|.	P;B;P;P|.	0.53518|.	0.476;0.005;0.676;0.728|.	T|T	0.74575|0.74575	-0.3620|-0.3620	10|5	0.27082|.	T|.	0.32|.	-19.7625|-19.7625	8.7695|8.7695	0.34724|0.34724	0.0:0.0868:0.0:0.9132|0.0:0.0868:0.0:0.9132	.|.	96;96;210;210|.	B4DFC0;E9PMV6;Q9UGK8-2;Q9UGK8|.	.;.;.;SRGEF_HUMAN|.	G|G	210;210;80;96;96;96;96|74	ENSP00000265965:E210G;ENSP00000434188:E210G;ENSP00000436648:E80G;ENSP00000431314:E96G;ENSP00000437297:E96G;ENSP00000436080:E96G;ENSP00000435898:E96G|.	ENSP00000265965:E210G|.	E|R	-|-	2|1	0|2	SERGEF|SERGEF	17971110|17971110	1.000000|1.000000	0.71417|0.71417	0.990000|0.990000	0.47175|0.47175	0.987000|0.987000	0.75469|0.75469	2.201000|2.201000	0.42734|0.42734	1.111000|1.111000	0.41721|0.41721	0.533000|0.533000	0.62120|0.62120	GAG|AGA	.	.		0.448	SERGEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389538.1	NM_012139		C	18014534	T	C	18014534	3	2	282	1	0	0	0	0	1	0	0	0	14092	1551	54	2	767	2	SERGEF	11	18014534	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	875327	18014534	116991982	768	41002										
CCDC73	493860	hgsc.bcm.edu	37	chr11	32739625	32739625	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctaatcatattactcaccttTtgccatttaagttcctgtgt	4	10	2	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:32739625T>C	ENST00000335185.5	-	3	247	c.204A>G	c.(202-204)caA>caG	p.Q68Q	CCDC73_ENST00000531481.1_Silent_p.Q68Q|CCDC73_ENST00000534415.1_5'UTR	NM_001008391.2	NP_001008392.2	Q6ZRK6	CCD73_HUMAN	coiled-coil domain containing 73	68										NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	51	Breast(20;0.112)					taCTCACCTTTTGCCATTTAA	0.398																																					p.E68E		Atlas-SNP	.											.	CCDC73	136	.	0			c.A204G						.						151	154	153					11																	32739625		1863	4107	5970	SO:0001819	synonymous_variant	493860	exon3			CACCTTTTGCCAT	AK128159	CCDS41630.1	11p13	2006-02-11			ENSG00000186714	ENSG00000186714			23261	protein-coding gene	gene with protein product		612328					Standard	NM_001008391		Approved	NY-SAR-79	uc001mtv.4	Q6ZRK6	OTTHUMG00000166279	ENST00000335185.5:c.204A>G	chr11.hg19:g.32739625T>C		63.0	0.0		45.0	5.0	NM_001008391	Q6P5Q7|Q6ZMW0|Q86WE7	Silent	SNP	ENST00000335185.5	hg19	CCDS41630.1																																																																																			.	.		0.398	CCDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388874.2	NM_001008391		C	32739625	T	C	32739625	2	2	282	1	0	0	0	0	0	0	0	1	2848	1838	64	2		2	CCDC73	11	32739625	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	14725091	32739625	102266891	769	41003										
CSTF3	1479	hgsc.bcm.edu	37	chr11	33121158	33121158	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gggaaggaacacttactcccTtttctgcgagcagtttactt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:33121158delT	ENST00000323959.4	-	11	1071	c.932delA	c.(931-933)aagfs	p.K311fs	TCP11L1_ENST00000324357.9_Intron	NM_001326.2	NP_001317.1	Q12996	CSTF3_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit 3, 77kDa	311					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|prostate(1)|skin(1)|stomach(1)	19						ACTTACTCCCTTTTCTGCGAG	0.388																																					p.K311fs		Atlas-INDEL	.											.	CSTF3	59	.	0			c.933delG						.						75	71	73					11																	33121158		2202	4298	6500	SO:0001589	frameshift_variant	1479	exon11			.	U15782	CCDS7883.1, CCDS44563.1, CCDS44564.1	11p13	2007-01-05	2002-08-29		ENSG00000176102	ENSG00000176102			2485	protein-coding gene	gene with protein product		600367	"cleavage stimulation factor, 3' pre-RNA, subunit 3, 77kD"			7984242	Standard	XM_006718154		Approved	CstF-77	uc001muh.3	Q12996	OTTHUMG00000166268	ENST00000323959.4:c.932delA	chr11.hg19:g.33121158delT	ENSP00000315791:p.Lys311fs	324.0	0.0		248.0	16.0	NM_001326	A8K471|D3DR04|E9PB40|Q32P22|Q96FQ8|Q96QD6|Q96QK4	Frame_Shift_Del	DEL	ENST00000323959.4	hg19	CCDS7883.1																																																																																			.	.		0.388	CSTF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388801.1	NM_001326		-	33121158	T	-	33121158	7	5	282	1	0	1	0	1	0	0	0	0	3988	1609	56	0	1265	0	CSTF3	11	33121158	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	381533	33121158	101885358	770	41004										
PHF21A	51317	hgsc.bcm.edu	37	chr11	45992680	45992680	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggcttaccagagtgactgtgTtttttgccacaatttggaca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:45992680delT	ENST00000418153.2	-	7	798	c.599delA	c.(598-600)aacfs	p.N200fs	PHF21A_ENST00000257821.4_Frame_Shift_Del_p.N200fs|PHF21A_ENST00000323180.6_Frame_Shift_Del_p.N200fs			Q96BD5	PF21A_HUMAN	PHD finger protein 21A	200					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|suckling behavior (GO:0001967)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(10)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	29						AGTGACTGTGTTTTTTGCCAC	0.507																																					p.N200fs		Atlas-INDEL	.											.	PHF21A	107	.	0			c.600delC						.						104	84	91					11																	45992680		2202	4299	6501	SO:0001589	frameshift_variant	51317	exon7			.	AL359593	CCDS31474.1, CCDS44578.1	11p11.2	2013-01-28			ENSG00000135365	ENSG00000135365		"Zinc fingers, PHD-type"	24156	protein-coding gene	gene with protein product		608325				11214970, 12032298	Standard	NM_001101802		Approved	BHC80, KIAA1696, BM-006	uc001ncc.4	Q96BD5	OTTHUMG00000167038	ENST00000418153.2:c.599delA	chr11.hg19:g.45992680delT	ENSP00000398824:p.Asn200fs	392.0	0.0		264.0	17.0	NM_016621	D3DQP5|Q6AWA2|Q9C0G7|Q9H8V9|Q9HAK6|Q9NZE9	Frame_Shift_Del	DEL	ENST00000418153.2	hg19	CCDS44578.1																																																																																			.	.		0.507	PHF21A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392583.1	NM_016621		-	45992680	T	-	45992680	7	5	282	1	0	1	0	1	0	0	0	0	11842	1725	60	0	1521	0	PHF21A	11	45992680	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	12871522	45992680	89013836	771	41005										
KIAA0652	9776	hgsc.bcm.edu	37	chr11	46670721	46670721	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gctggaaatatggtgtcttgAaatgaatgaaaagtaagtgc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:46670721delA	ENST00000434074.1	+	5	994	c.305delA	c.(304-306)gaafs	p.E102fs	ATG13_ENST00000451945.1_Frame_Shift_Del_p.E102fs|ATG13_ENST00000312040.4_Frame_Shift_Del_p.E102fs|ATG13_ENST00000530500.1_Frame_Shift_Del_p.E23fs|ATG13_ENST00000529655.1_Frame_Shift_Del_p.E102fs|ATG13_ENST00000526508.1_Frame_Shift_Del_p.E102fs|ATG13_ENST00000528494.1_Frame_Shift_Del_p.E102fs|ATG13_ENST00000359513.4_Frame_Shift_Del_p.E102fs|ATG13_ENST00000524625.1_Frame_Shift_Del_p.E102fs	NM_001205120.1	NP_001192049.1	O75143	ATG13_HUMAN	autophagy related 13	102					autophagic vacuole assembly (GO:0000045)	ATG1/UKL1 signaling complex (GO:0034273)|cytosol (GO:0005829)|pre-autophagosomal structure (GO:0000407)|ULK1-ATG13-FIP200 complex (GO:0070969)	protein kinase binding (GO:0019901)	p.M103fs*1(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|prostate(1)|skin(1)	15						TGGTGTCTTGAAATGAATGAA	0.358																																					p.E102fs		Atlas-INDEL	.											ATG13_ENST00000528494,NS,carcinoma,0,2	ATG13	60	.	1	Deletion - Frameshift(1)	central_nervous_system(1)	c.304delG						.						265	237	246					11																	46670721		2201	4299	6500	SO:0001589	frameshift_variant	9776	exon6			.	AB014552	CCDS7921.1, CCDS44582.1, CCDS55760.1, CCDS55761.1	11p11.2	2014-02-12	2012-06-06	2010-06-29	ENSG00000175224	ENSG00000175224			29091	protein-coding gene	gene with protein product		615088	"KIAA0652", "ATG13 autophagy related 13 homolog (S. cerevisiae)"	KIAA0652		15169610, 18339812, 17204848	Standard	NM_001205120		Approved		uc001nda.3	O75143	OTTHUMG00000166538	ENST00000434074.1:c.305delA	chr11.hg19:g.46670721delA	ENSP00000400642:p.Glu102fs	265.0	0.0		192.0	12.0	NM_001142673	B4DFI4|D3DQQ1|D3DQQ2|E9PQZ8|Q53EN6|Q9BRL3|Q9H8B0	Frame_Shift_Del	DEL	ENST00000434074.1	hg19	CCDS44582.1																																																																																			.	.		0.358	ATG13-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390300.2	NM_014741		-	46670721	A	-	46670721	7	5	282	1	0	1	0	1	0	0	0	0	8197	246	9	0	319	0	KIAA0652	11	46670721	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	678041	46670721	88335795	772	41006										
DDB2	1643	hgsc.bcm.edu	37	chr11	47259439	47259439	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttgtgggccgatacccagatCctaatttcaaaagttgtacc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:47259439delC	ENST00000256996.4	+	8	1270	c.1075delC	c.(1075-1077)cctfs	p.P359fs	DDB2_ENST00000378600.3_Frame_Shift_Del_p.P170fs|DDB2_ENST00000378603.3_Frame_Shift_Del_p.P295fs|DDB2_ENST00000378601.3_3'UTR|ACP2_ENST00000525230.1_5'Flank	NM_000107.2	NP_000098.1	Q92466	DDB2_HUMAN	damage-specific DNA binding protein 2, 48kDa	359					DNA repair (GO:0006281)|histone H2A monoubiquitination (GO:0035518)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|protein autoubiquitination (GO:0051865)|protein polyubiquitination (GO:0000209)|pyrimidine dimer repair (GO:0006290)|response to UV (GO:0009411)|UV-damage excision repair (GO:0070914)	Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|nucleoplasm (GO:0005654)|protein complex (GO:0043234)	damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(1)	17						ATACCCAGATCCTAATTTCAA	0.488			"Mis, N"			"skin basal cell, skin squamous cell, melanoma"		Direct reversal of damage;Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.D358fs		Atlas-INDEL	.	yes	Rec		Xeroderma pigmentosum (E)	11	11p12	1643	damage-specific DNA binding protein 2		E	.	DDB2	31	.	0			c.1074delT						.						115	110	112					11																	47259439		2201	4298	6499	SO:0001589	frameshift_variant	1643	exon8	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	.		CCDS7927.1, CCDS73284.1	11p12-p11	2014-09-17	2002-08-29			ENSG00000134574		"WD repeat domain containing"	2718	protein-coding gene	gene with protein product	"xeroderma pigmentosum group E protein", "UV-damaged DNA-binding protein 2", "DDB p48 subunit"	600811	"damage-specific DNA binding protein 2 (48kD)"			8407967, 8530102	Standard	NM_000107		Approved	DDBB, UV-DDB2, FLJ34321	uc001neb.2	Q92466		ENST00000256996.4:c.1075delC	chr11.hg19:g.47259439delC	ENSP00000256996:p.Pro359fs	232.0	0.0		122.0	10.0	NM_000107	B2R875|Q76E54|Q76E55|Q76E56|Q76E57	Frame_Shift_Del	DEL	ENST00000256996.4	hg19	CCDS7927.1																																																																																			.	.		0.488	DDB2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000107		-	47259439	C	-	47259439	7	5	282	1	0	1	0	1	0	0	0	0	4326	855	30	0	1105	0	DDB2	11	47259439	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	588718	47259439	87747077	773	41007										
AGBL2	79841	hgsc.bcm.edu	37	chr11	47721054	47721054	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctcctacaatctctggtaccTtttcatttcctttaggctga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:47721054delT	ENST00000525123.1	-	8	923	c.638delA	c.(637-639)aagfs	p.K213fs	AGBL2_ENST00000528244.1_Frame_Shift_Del_p.K175fs|AGBL2_ENST00000298861.4_Frame_Shift_Del_p.K213fs|AGBL2_ENST00000357610.3_Frame_Shift_Del_p.K213fs|AGBL2_ENST00000529712.1_5'UTR	NM_024783.3	NP_079059.2	Q5U5Z8	CBPC2_HUMAN	ATP/GTP binding protein-like 2	213						cytosol (GO:0005829)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)	34						CTCTGGTACCTTTTCATTTCC	0.338																																					p.K213fs		Atlas-INDEL	.											.	AGBL2	73	.	0			c.639delG						.						170	164	166					11																	47721054		2201	4298	6499	SO:0001589	frameshift_variant	79841	exon8			.		CCDS7944.1	11p11.2	2014-06-23			ENSG00000165923	ENSG00000165923			26296	protein-coding gene	gene with protein product	"cytoplasmic carboxypeptidase 2"					12738998, 21303978	Standard	NM_024783		Approved	FLJ23598, CCP2	uc001ngg.3	Q5U5Z8	OTTHUMG00000165368	ENST00000525123.1:c.638delA	chr11.hg19:g.47721054delT	ENSP00000435582:p.Lys213fs	198.0	0.0		149.0	10.0	NM_024783	A8MPX2|Q53FV5|Q8IV57|Q9H5C0	Frame_Shift_Del	DEL	ENST00000525123.1	hg19	CCDS7944.1																																																																																			.	.		0.338	AGBL2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383726.2	NM_024783		-	47721054	T	-	47721054	7	5	282	1	0	1	0	1	0	0	0	0	376	1609	56	0	2118	0	AGBL2	11	47721054	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	461615	47721054	87285462	774	41008										
OR4C46	119749	hgsc.bcm.edu	37	chr11	51515445	51515445	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgccagcccatcactggggtCccccatgtacctttccctgg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:51515445delC	ENST00000328188.1	+	1	164	c.164delC	c.(163-165)tccfs	p.S55fs		NM_001004703.1	NP_001004703.1	A6NHA9	O4C46_HUMAN	olfactory receptor, family 4, subfamily C, member 46	55						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(5)|large_intestine(5)|lung(31)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	48						TCACTGGGGTCCCCCATGTAC	0.448																																					p.S55fs		Atlas-INDEL	.											.	OR4C46	96	.	0			c.163delT						.						232	227	229					11																	51515445		2201	4296	6497	SO:0001589	frameshift_variant	119749	exon1			.		CCDS73288.1	11p11.12	2012-08-09			ENSG00000185926	ENSG00000185926		"GPCR / Class A : Olfactory receptors"	31271	protein-coding gene	gene with protein product		614273					Standard	NM_001004703		Approved		uc010ric.2	A6NHA9	OTTHUMG00000166705	ENST00000328188.1:c.164delC	chr11.hg19:g.51515445delC	ENSP00000329056:p.Ser55fs	301.0	0.0		199.0	13.0	NM_001004703		Frame_Shift_Del	DEL	ENST00000328188.1	hg19	CCDS31498.1																																																																																			.	.		0.448	OR4C46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391155.1	NM_001004703		-	51515445	C	-	51515445	7	5	282	1	0	1	0	1	0	0	0	0	11060	855	30	0	166	0	OR4C46	11	51515445	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	3794391	51515445	83491071	775	41009										
OR4A15	81328	hgsc.bcm.edu	37	chr11	55135387	55135387	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttctgacaaataatctcaaaTttatcactgacccttttgtt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:55135387delT	ENST00000314706.3	+	1	28	c.28delT	c.(28-30)tttfs	p.F10fs		NM_001005275.1	NP_001005275.1	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A, member 15	10						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(48)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	71						TAATCTCAAATTTATCACTGA	0.413																																					p.K9fs		Atlas-INDEL	.											.	OR4A15	161	.	0			c.27delA						.						54	47	49					11																	55135387		2201	4296	6497	SO:0001589	frameshift_variant	81328	exon1			.	AB065776	CCDS31500.1	11q11	2012-08-09			ENSG00000181958	ENSG00000181958		"GPCR / Class A : Olfactory receptors"	15152	protein-coding gene	gene with protein product							Standard	NM_001005275		Approved		uc010rif.2	Q8NGL6	OTTHUMG00000166711	ENST00000314706.3:c.28delT	chr11.hg19:g.55135387delT	ENSP00000325065:p.Phe10fs	188.0	0.0		156.0	10.0	NM_001005275	Q6IFL4|Q96R65	Frame_Shift_Del	DEL	ENST00000314706.3	hg19	CCDS31500.1																																																																																			.	.		0.413	OR4A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391161.1	NM_001005275		-	55135387	T	-	55135387	7	5	282	1	0	1	0	1	0	0	0	0	11049	1493	52	0	30	0	OR4A15	11	55135387	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3619942	55135387	79871129	776	41010										
OR5T2	219464	hgsc.bcm.edu	37	chr11	55999651	55999651	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aacatttttttcattgagtcTtttacatctttgttcctcaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:55999651delT	ENST00000313264.4	-	1	1086	c.1011delA	c.(1009-1011)aaafs	p.K337fs		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	337						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(3)	41	Esophageal squamous(21;0.00448)					TCATTGAGTCTTTTACATCTT	0.338																																					p.D338fs		Atlas-INDEL	.											.	OR5T2	107	.	0			c.1012delG						.						71	68	69					11																	55999651		2201	4296	6497	SO:0001589	frameshift_variant	219464	exon1			.	AB065838	CCDS31523.1	11q11	2012-08-09			ENSG00000181718	ENSG00000181718		"GPCR / Class A : Olfactory receptors"	15296	protein-coding gene	gene with protein product							Standard	NM_001004746		Approved		uc010rjc.2	Q8NGG2	OTTHUMG00000166851	ENST00000313264.4:c.1011delA	chr11.hg19:g.55999651delT	ENSP00000323688:p.Lys337fs	160.0	0.0		155.0	10.0	NM_001004746	B9EGX5|Q6IFC8	Frame_Shift_Del	DEL	ENST00000313264.4	hg19	CCDS31523.1																																																																																			.	.		0.338	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746		-	55999651	T	-	55999651	7	5	282	1	0	1	0	1	0	0	0	0	11191	1606	56	0	67	0	OR5T2	11	55999651	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	864264	55999651	79006865	777	41011										
SMTNL1	219537	hgsc.bcm.edu	37	chr11	57313466	57313466	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cccctgctcggccccgggggCcccgggcacagaaccgcaaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:57313466delC	ENST00000399154.2	+	5	919	c.919delC	c.(919-921)cccfs	p.P307fs	SMTNL1_ENST00000457912.1_Frame_Shift_Del_p.P362fs|SMTNL1_ENST00000527972.1_Frame_Shift_Del_p.P344fs			A8MU46	SMTL1_HUMAN	smoothelin-like 1	307					negative regulation of vasodilation (GO:0045908)|positive regulation of vasoconstriction (GO:0045907)	contractile fiber (GO:0043292)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|large_intestine(1)|lung(4)|ovary(1)	8						GCCCCGGGGGCCCCGGGCACA	0.667																																					p.G343fs		Atlas-INDEL	.											.	SMTNL1	68	.	0			c.1029delG						.						24	29	27					11																	57313466		1852	4093	5945	SO:0001589	frameshift_variant	219537	exon4			.	BX116227		11q12.1	2006-02-02				ENSG00000214872			32394	protein-coding gene	gene with protein product	"calponin homology-associated smooth muscle protein"	613664				15327999	Standard	NM_001105565		Approved	CHASM	uc021qjh.1	A8MU46		ENST00000399154.2:c.919delC	chr11.hg19:g.57313466delC	ENSP00000382108:p.Pro307fs	232.0	0.0		165.0	10.0	NM_001105565		Frame_Shift_Del	DEL	ENST00000399154.2	hg19																																																																																				.	.		0.667	SMTNL1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_166203		-	57313466	C	-	57313466	7	5	282	1	0	1	0	1	0	0	0	0	14830	739	26	0	1102	0	SMTNL1	11	57313466	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1313815	57313466	77693050	778	41012										
UBE2L6	9246	hgsc.bcm.edu	37	chr11	57327822	57327822	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atactcacgggtaggaggagAgcgtgccacaccaggacatt	13	10	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:57327822A>G	ENST00000287156.4	-	2	306	c.111T>C	c.(109-111)gcT>gcC	p.A37A	UBE2L6_ENST00000340573.4_5'UTR	NM_004223.4	NP_004214.1	O14933	UB2L6_HUMAN	ubiquitin-conjugating enzyme E2L 6	37					cellular protein modification process (GO:0006464)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|modification-dependent protein catabolic process (GO:0019941)|negative regulation of type I interferon production (GO:0032480)	cytosol (GO:0005829)	ISG15 ligase activity (GO:0042296)|ubiquitin-protein transferase activity (GO:0004842)			large_intestine(1)|lung(3)|ovary(1)	5						GTAGGAGGAGAGCGTGCCACA	0.567																																					p.A37A		Atlas-SNP	.											.	UBE2L6	20	.	0			c.T111C						.						210	172	185					11																	57327822		2201	4296	6497	SO:0001819	synonymous_variant	9246	exon2			GAGGAGAGCGTGC	AF031141, AK093462, BC032491	CCDS7960.1, CCDS7961.1	11q12.1	2008-02-01			ENSG00000156587	ENSG00000156587		"Ubiquitin-conjugating enzymes E2"	12490	protein-coding gene	gene with protein product		603890				9153201	Standard	NM_004223		Approved	UBCH8	uc001nkn.2	O14933	OTTHUMG00000167047	ENST00000287156.4:c.111T>C	chr11.hg19:g.57327822A>G		171.0	0.0		95.0	6.0	NM_004223	A6NDM6|A8MY53|Q8N5D8|Q9UEZ0	Silent	SNP	ENST00000287156.4	hg19	CCDS7960.1																																																																																			.	.		0.567	UBE2L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392657.1	NM_004223		G	57327822	A	G	57327822	2	3	282	1	0	0	0	0	0	0	0	1	16879	291	11	2		2	UBE2L6	11	57327822	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	14356	57327822	77678694	779	41013										
SERPING1	710	hgsc.bcm.edu	37	chr11	57369544	57369544	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caaaacaaacctggagagcaTcctctcttaccccaaggact	6	14	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:57369544T>C	ENST00000278407.4	+	4	814	c.587T>C	c.(586-588)aTc>aCc	p.I196T	SERPING1_ENST00000378323.4_Missense_Mutation_p.I201T|SERPING1_ENST00000378324.2_Missense_Mutation_p.I144T|SERPING1_ENST00000403558.1_Missense_Mutation_p.I230T|SERPING1_ENST00000340687.6_Missense_Mutation_p.I196T|SERPING1_ENST00000531605.1_3'UTR	NM_000062.2	NP_000053.2	P05155	IC1_HUMAN	serpin peptidase inhibitor, clade G (C1 inhibitor), member 1	196					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|complement activation, classical pathway (GO:0006958)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(11)|pancreas(2)|prostate(1)|urinary_tract(1)	27						CTGGAGAGCATCCTCTCTTAC	0.547																																					p.I196T		Atlas-SNP	.											.	SERPING1	57	.	0			c.T587C						.						116	90	99					11																	57369544		2201	4296	6497	SO:0001583	missense	710	exon3			AGAGCATCCTCTC	X54486	CCDS7962.1	11q12.1	2014-09-17	2008-07-31		ENSG00000149131	ENSG00000149131		"Serine (or cysteine) peptidase inhibitors"	1228	protein-coding gene	gene with protein product	"plasma protease C1 inhibitor", "angioedema, hereditary"	606860	"serine (or cysteine) proteinase inhibitor, clade G (C1 inhibitor), member 1, (angioedema, hereditary)"	C1NH		2026152, 24172014	Standard	NM_000062		Approved	C1IN, C1-INH, HAE1, HAE2	uc001nkp.1	P05155	OTTHUMG00000150304	ENST00000278407.4:c.587T>C	chr11.hg19:g.57369544T>C	ENSP00000278407:p.Ile196Thr	144.0	0.0		137.0	6.0	NM_001032295	A6NMU0|A8KAI9|B2R6L5|B4E1F0|B4E1H2|Q16304|Q547W3|Q59EI5|Q7Z455|Q96FE0|Q9UC49|Q9UCF9	Missense_Mutation	SNP	ENST00000278407.4	hg19	CCDS7962.1	.	.	.	.	.	.	.	.	.	.	T	14.04	2.417116	0.42918	.	.	ENSG00000149131	ENST00000278407;ENST00000340687;ENST00000378323;ENST00000378324;ENST00000403558	D;D;D;D;D	0.84070	-1.8;-1.8;-1.8;-1.8;-1.8	5.76	4.63	0.57726	Serpin domain (3);	0.708670	0.13954	N	0.351283	T	0.78755	0.4333	N	0.04203	-0.255	0.20873	N	0.999832	B;P;B;B	0.36171	0.006;0.541;0.0;0.0	B;P;B;B	0.55161	0.364;0.77;0.017;0.017	T	0.70468	-0.4863	10	0.56958	D	0.05	.	8.6205	0.33857	0.0:0.0868:0.0:0.9132	.	201;230;196;196	B4E1F0;E9PGN7;E9KL26;P05155	.;.;.;IC1_HUMAN	T	196;196;201;144;230	ENSP00000278407:I196T;ENSP00000341861:I196T;ENSP00000367574:I201T;ENSP00000367575:I144T;ENSP00000384420:I230T	ENSP00000278407:I196T	I	+	2	0	SERPING1	57126120	0.963000	0.33076	0.787000	0.31911	0.308000	0.27856	1.717000	0.37991	1.009000	0.39289	0.482000	0.46254	ATC	.	.		0.547	SERPING1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317465.1	NM_000062		C	57369544	T	C	57369544	3	2	282	1	0	0	0	0	1	0	0	0	14131	1435	50	2	597	2	SERPING1	11	57369544	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	41722	57369544	77636972	780	41014										
OR5B2	390190	hgsc.bcm.edu	37	chr11	58190586	58190586	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgggggtgtggagacaagagTccatcaggatcagcaacatc	14	8	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:58190586T>C	ENST00000302581.2	-	1	200	c.149A>G	c.(148-150)gAc>gGc	p.D50G		NM_001005566.2	NP_001005566.1	Q96R09	OR5B2_HUMAN	olfactory receptor, family 5, subfamily B, member 2	50						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|large_intestine(2)|lung(19)|ovary(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				GAGACAAGAGTCCATCAGGAT	0.507																																					p.D50G		Atlas-SNP	.											.	OR5B2	75	.	0			c.A149G						.						106	99	102					11																	58190586		2201	4295	6496	SO:0001583	missense	390190	exon1			CAAGAGTCCATCA	AB065852	CCDS31550.1	11q12.1	2012-08-09			ENSG00000172365	ENSG00000172365		"GPCR / Class A : Olfactory receptors"	8323	protein-coding gene	gene with protein product							Standard	NM_001005566		Approved	OST073	uc010rkg.2	Q96R09	OTTHUMG00000167517	ENST00000302581.2:c.149A>G	chr11.hg19:g.58190586T>C	ENSP00000303076:p.Asp50Gly	201.0	0.0		112.0	6.0	NM_001005566	B2RNJ6|B9EGY7|Q6IEV7|Q8NGF5	Missense_Mutation	SNP	ENST00000302581.2	hg19	CCDS31550.1	.	.	.	.	.	.	.	.	.	.	T	6.378	0.437924	0.12104	.	.	ENSG00000172365	ENST00000302581	T	0.02890	4.12	3.8	2.65	0.31530	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.08223	0.0205	M	0.91561	3.22	0.09310	N	1	B	0.16166	0.016	B	0.23574	0.047	T	0.11275	-1.0594	9	0.66056	D	0.02	-3.1424	8.1655	0.31224	0.0:0.1006:0.0:0.8994	.	50	Q96R09	OR5B2_HUMAN	G	50	ENSP00000303076:D50G	ENSP00000303076:D50G	D	-	2	0	OR5B2	57947162	0.043000	0.20138	0.009000	0.14445	0.011000	0.07611	2.453000	0.44970	0.634000	0.30469	0.524000	0.50904	GAC	.	.		0.507	OR5B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394887.2	NM_001005566		C	58190586	T	C	58190586	3	2	282	1	0	0	0	0	1	0	0	0	11159	1667	58	2	784	2	OR5B2	11	58190586	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	821042	58190586	76815930	781	41015										
PATL1	219988	hgsc.bcm.edu	37	chr11	59419993	59419993	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gggtgataagcttggtgcgcTccttcttagggccatcacct	12	11	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:59419993T>C	ENST00000300146.9	-	11	1454	c.1370A>G	c.(1369-1371)gAg>gGg	p.E457G		NM_152716.2	NP_689929.2	Q86TB9	PATL1_HUMAN	protein associated with topoisomerase II homolog 1 (yeast)	457	Involved in nuclear spleckles localization.|Region C.				cytoplasmic mRNA processing body assembly (GO:0033962)|deadenylation-dependent decapping of nuclear-transcribed mRNA (GO:0000290)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(2)|lung(5)|ovary(1)|prostate(2)	11						CTTGGTGCGCTCCTTCTTAGG	0.428																																					p.E457G		Atlas-SNP	.											.	PATL1	92	.	0			c.A1370G						.						130	121	124					11																	59419993		1903	4107	6010	SO:0001583	missense	219988	exon11			GTGCGCTCCTTCT	AK094193	CCDS44613.1	11q12.1	2012-06-07	2007-10-18		ENSG00000166889	ENSG00000166889			26721	protein-coding gene	gene with protein product		614660				17936923	Standard	NM_152716		Approved	FLJ36874, Pat1b	uc001noe.4	Q86TB9	OTTHUMG00000167423	ENST00000300146.9:c.1370A>G	chr11.hg19:g.59419993T>C	ENSP00000300146:p.Glu457Gly	200.0	0.0		113.0	5.0	NM_152716	B3KXT9|Q2TA86|Q6P166|Q8N9M6|Q8NI63	Missense_Mutation	SNP	ENST00000300146.9	hg19	CCDS44613.1	.	.	.	.	.	.	.	.	.	.	T	28.2	4.897304	0.91962	.	.	ENSG00000166889	ENST00000300146;ENST00000428532	T	0.50813	0.73	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	T	0.63988	0.2558	M	0.61703	1.905	0.80722	D	1	D;D	0.76494	0.99;0.999	P;D	0.81914	0.852;0.995	T	0.60372	-0.7276	10	0.22706	T	0.39	-15.8112	15.0564	0.71917	0.0:0.0:0.0:1.0	.	427;457	Q86TB9-4;Q86TB9	.;PATL1_HUMAN	G	457;427	ENSP00000300146:E457G	ENSP00000300146:E457G	E	-	2	0	PATL1	59176569	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.424000	0.80242	2.037000	0.60232	0.482000	0.46254	GAG	.	.		0.428	PATL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394559.1	NM_152716		C	59419993	T	C	59419993	3	2	282	1	0	0	0	0	1	0	0	0	11484	1551	54	2	978	2	PATL1	11	59419993	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1229407	59419993	75586523	782	41016										
VPS37C	55048	hgsc.bcm.edu	37	chr11	60899827	60899827	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cctgggggactgggcgcaccGggggtggtggacggggtgga					rs199606009		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:60899827delG	ENST00000301765.5	-	5	765	c.533delC	c.(532-534)ccgfs	p.P178fs		NM_017966.4	NP_060436.4	A5D8V6	VP37C_HUMAN	vacuolar protein sorting 37 homolog C (S. cerevisiae)	178	Pro-rich.				endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|membrane organization (GO:0061024)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7						TGGGCGCACCGGGGGTGGTGG	0.682																																					p.P178fs		Atlas-INDEL	.											.	VPS37C	30	.	0			c.534delG						.						12	15	14					11																	60899827		2196	4283	6479	SO:0001589	frameshift_variant	55048	exon5			.	AK097326	CCDS31573.1	11q12.2	2008-02-05	2006-04-04			ENSG00000167987			26097	protein-coding gene	gene with protein product		610038	"vacuolar protein sorting 37C (yeast)"			15509564	Standard	XM_005274077		Approved	FLJ20847	uc001nqv.1	A5D8V6		ENST00000301765.5:c.533delC	chr11.hg19:g.60899827delG	ENSP00000301765:p.Pro178fs	206.0	0.0		196.0	12.0	NM_017966	Q8N3K4	Frame_Shift_Del	DEL	ENST00000301765.5	hg19	CCDS31573.1																																																																																			.	.		0.682	VPS37C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396467.1	NM_017966		-	60899827	G	-	60899827	7	5	282	1	0	1	0	1	0	0	0	0	17222	1116	39	0	538	0	VPS37C	11	60899827	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1479834	60899827	74106689	783	41017										
TMEM216	51259	hgsc.bcm.edu	37	chr11	61165731	61165731	+	Intron	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	attttctttctttctgccatCgtatggacaggatttgaagt	8	7	3	1	rs11382548	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:61165731C>A	ENST00000515837.2	+	5	1376				TMEM216_ENST00000334888.5_Splice_Site|TMEM216_ENST00000398979.3_Intron			Q9P0N5	TM216_HUMAN	transmembrane protein 216						cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)				endometrium(1)|large_intestine(2)|lung(1)|prostate(2)	6						TTTCTGCCATCGTATGGACAG	0.473																																					.		Atlas-SNP	.											.	TMEM216	14	.	0			c.432-2C>A						.						85	82	83					11																	61165731		1945	4154	6099	SO:0001627	intron_variant	51259	exon5			TGCCATCGTATGG		CCDS53640.1	11q13.1	2014-09-17			ENSG00000187049	ENSG00000187049			25018	protein-coding gene	gene with protein product		613277	"cerebello-oculo-renal syndrome 2", "Meckel syndrome, type 2"	CORS2, MKS2		11042152, 20036350, 20512146	Standard	NM_016499		Approved	MGC13379, HSPC244, JBTS2	uc021qkf.1	Q9P0N5		ENST00000515837.2:c.432-11C>A	chr11.hg19:g.61165731C>A		178.0	0.0		107.0	5.0	NM_001173991	A8MZ23|B7Z8N1	Splice_Site	SNP	ENST00000515837.2	hg19	CCDS53640.1	.	.	.	.	.	.	.	.	.	.	C	16.43	3.122110	0.56613	.	.	ENSG00000187049	ENST00000334888	.	.	.	5.75	3.64	0.41730	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.196	0.15239	0.0:0.7087:0.0:0.2913	.	.	.	.	.	-1	.	.	.	+	.	.	TMEM216	60922307	0.985000	0.35326	1.000000	0.80357	0.961000	0.63080	1.261000	0.32980	1.403000	0.46800	0.561000	0.74099	.	.	.		0.473	TMEM216-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398430.1	NM_016499		A	61165731	C	A	61165731	1	1	282	0	1	0	0	0	0	0	0	0	16154	898	31	1		1	TMEM216	11	61165731	Intron	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	265904	61165731	73840785	784	41018										
CPSF7	79869	hgsc.bcm.edu	37	chr11	61196700	61196700	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tatcaatcaagtccactcctTctgacatggctccggaagga	8	12	3	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:61196700T>C	ENST00000394888.4	-	2	180	c.8A>G	c.(7-9)gAa>gGa	p.E3G	RP11-286N22.8_ENST00000543044.1_5'Flank|SDHAF2_ENST00000537782.1_5'Flank|SDHAF2_ENST00000301761.2_5'Flank|CPSF7_ENST00000439958.3_Missense_Mutation_p.E3G|SDHAF2_ENST00000542074.1_5'Flank|SDHAF2_ENST00000543265.1_5'Flank|CPSF7_ENST00000541963.1_Missense_Mutation_p.E3G|CPSF7_ENST00000340437.4_Missense_Mutation_p.E46G|SDHAF2_ENST00000534878.1_5'Flank|CPSF7_ENST00000448745.1_Missense_Mutation_p.E3G	NM_001136040.2	NP_001129512.1	Q8N684	CPSF7_HUMAN	cleavage and polyadenylation specific factor 7, 59kDa	3					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|protein tetramerization (GO:0051262)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)|mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	22						GTCCACTCCTTCTGACATGGC	0.473																																					p.E46G		Atlas-SNP	.											.	CPSF7	46	.	0			c.A137G						.						163	157	159					11																	61196700		2202	4299	6501	SO:0001583	missense	79869	exon2			ACTCCTTCTGACA		CCDS8006.2, CCDS44619.1, CCDS44620.1	11q12.2	2013-06-18			ENSG00000149532	ENSG00000149532		"RNA binding motif (RRM) containing"	30098	protein-coding gene	gene with protein product	"pre mRNA cleavage factor I, 59 kDa subunit", "cleavage factor Im complex 59 kDa subunit"					12477932	Standard	NM_024811		Approved	FLJ12529	uc001nrp.3	Q8N684	OTTHUMG00000168198	ENST00000394888.4:c.8A>G	chr11.hg19:g.61196700T>C	ENSP00000378352:p.Glu3Gly	91.0	0.0		87.0	4.0	NM_024811	B3KU04|C9K0Q4|Q7Z3H9|Q9H025|Q9H9V1	Missense_Mutation	SNP	ENST00000394888.4	hg19	CCDS44619.1	.	.	.	.	.	.	.	.	.	.	T	18.47	3.630367	0.67015	.	.	ENSG00000149532	ENST00000340437;ENST00000394888;ENST00000439958;ENST00000448745;ENST00000477890;ENST00000539952;ENST00000544585;ENST00000413232;ENST00000541963;ENST00000450000;ENST00000449811;ENST00000413184	.	.	.	5.12	5.12	0.69794	.	0.305062	0.31624	N	0.007334	T	0.58963	0.2159	L	0.29908	0.895	0.40142	D	0.976848	D;P;D;P	0.58268	0.982;0.86;0.969;0.914	P;B;P;P	0.55055	0.767;0.354;0.634;0.556	T	0.61936	-0.6960	9	0.46703	T	0.11	.	14.7451	0.69485	0.0:0.0:0.0:1.0	.	3;3;46;3	F5H1W4;Q8N684;Q8N684-3;Q8N684-2	.;CPSF7_HUMAN;.;.	G	46;3;3;3;3;3;3;3;3;3;3;3	.	ENSP00000345412:E46G	E	-	2	0	CPSF7	60953276	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.903000	0.63272	2.150000	0.67090	0.460000	0.39030	GAA	.	.		0.473	CPSF7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347835.2	NM_024811		C	61196700	T	C	61196700	3	2	282	1	0	0	0	0	1	0	0	0	3832	1783	62	2	1439	2	CPSF7	11	61196700	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	30969	61196700	73809816	785	41019										
AHNAK	79026	hgsc.bcm.edu	37	chr11	62288928	62288928	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tggcatgctgaatttgggcaTtttcaccttgggcatcttca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:62288928delT	ENST00000378024.4	-	5	13235	c.12961delA	c.(12961-12963)atgfs	p.M4321fs	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	4321					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				AATTTGGGCATTTTCACCTTG	0.522																																					p.M4321fs		Atlas-INDEL	.											.	AHNAK	532	.	0			c.12962delT						.						174	174	174					11																	62288928		2202	4299	6501	SO:0001589	frameshift_variant	79026	exon5			.	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.12961delA	chr11.hg19:g.62288928delT	ENSP00000367263:p.Met4321fs	255.0	0.0		163.0	10.0	NM_001620	A1A586	Frame_Shift_Del	DEL	ENST00000378024.4	hg19	CCDS31584.1																																																																																			.	.		0.522	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		-	62288928	T	-	62288928	7	5	282	1	0	1	0	1	0	0	0	0	414	1493	52	0	4831	0	AHNAK	11	62288928	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1092228	62288928	72717588	786	41020										
ZBTB3	79842	hgsc.bcm.edu	37	chr11	62520953	62520953	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	attgtgaatacacaccagatCcctcttgtccaattcccgct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:62520953delC	ENST00000394807.3	-	2	459	c.334delG	c.(334-336)gatfs	p.D112fs		NM_024784.3	NP_079060.1	Q9H5J0	ZBTB3_HUMAN	zinc finger and BTB domain containing 3	112	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(9)|ovary(2)|prostate(2)	24						CACACCAGATCCCTCTTGTCC	0.547																																					p.D112fs		Atlas-INDEL	.											.	ZBTB3	47	.	0			c.335delA						.						90	87	88					11																	62520953		2202	4299	6501	SO:0001589	frameshift_variant	79842	exon2			.	AK027045	CCDS8034.1	11q12.3	2013-01-09				ENSG00000185670		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	22918	protein-coding gene	gene with protein product							Standard	NM_024784		Approved	FLJ23392	uc001nuz.3	Q9H5J0		ENST00000394807.3:c.334delG	chr11.hg19:g.62520953delC	ENSP00000378286:p.Asp112fs	239.0	0.0		180.0	11.0	NM_024784		Frame_Shift_Del	DEL	ENST00000394807.3	hg19	CCDS8034.1																																																																																			.	.		0.547	ZBTB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395342.1	NM_024784		-	62520953	C	-	62520953	7	5	282	1	0	1	0	1	0	0	0	0	17549	855	30	0	1394	0	ZBTB3	11	62520953	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	232025	62520953	72485563	787	41021										
OTUB1	55611	hgsc.bcm.edu	37	chr11	63764415	63764415	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgaggatttccacaacacggTgagccctggtgcctgtcttg	12	11	1	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:63764415T>C	ENST00000538426.1	+	5	467		c.e5+2		OTUB1_ENST00000543988.1_Splice_Site|OTUB1_ENST00000541478.1_Intron|OTUB1_ENST00000422031.2_Splice_Site|OTUB1_ENST00000535715.1_Splice_Site|OTUB1_ENST00000543004.1_Splice_Site|OTUB1_ENST00000428192.2_Splice_Site	NM_017670.2	NP_060140.2	Q96FW1	OTUB1_HUMAN	OTU deubiquitinase, ubiquitin aldehyde binding 1						cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|immune system process (GO:0002376)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein K48-linked deubiquitination (GO:0071108)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	NEDD8-specific protease activity (GO:0019784)|omega peptidase activity (GO:0008242)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)	6						CACAACACGGTGAGCCCTGGT	0.597																																					.		Atlas-SNP	.											.	OTUB1	19	.	0			c.423+2T>C						.						82	69	74					11																	63764415		2201	4297	6498	SO:0001630	splice_region_variant	55611	exon5			ACACGGTGAGCCC	AY177200	CCDS8055.1	11q13.1	2014-02-24	2014-02-24			ENSG00000167770		"OTU domain containing"	23077	protein-coding gene	gene with protein product		608337	"OTU domain, ubiquitin aldehyde binding 1"			12704427, 19383985	Standard	NM_017670		Approved	FLJ20113, FLJ40710	uc001nyf.1	Q96FW1		ENST00000538426.1:c.423+2T>C	chr11.hg19:g.63764415T>C		103.0	0.0		70.0	5.0	NM_017670	Q32Q78|Q96II3|Q9NXQ4|Q9P0B8	Splice_Site	SNP	ENST00000538426.1	hg19	CCDS8055.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.005261	0.74932	.	.	ENSG00000167770	ENST00000535715;ENST00000428192;ENST00000422031;ENST00000538426;ENST00000543004;ENST00000543988	.	.	.	3.72	3.72	0.42706	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.6845	0.45835	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	OTUB1	63520991	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	3.989000	0.56958	1.691000	0.51100	0.459000	0.35465	.	.	.		0.597	OTUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396277.1	NM_017670	Intron	C	63764415	T	C	63764415	5	2	282	1	0	0	0	0	0	0	1	0	11320	1710	59	2	443	2	OTUB1	11	63764415	Splice_Site	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1243462	63764415	71242101	788	41022										
KCNK7	10089	hgsc.bcm.edu	37	chr11	65363236	65363236	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atcgggaccagggccttagaCcccccatggcaggccgctgg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:65363236delC	ENST00000340313.4	-	1	231	c.8delG	c.(7-9)ggtfs	p.G3fs	KCNK7_ENST00000342202.4_Frame_Shift_Del_p.G3fs|KCNK7_ENST00000394216.2_Frame_Shift_Del_p.G3fs|KCNK7_ENST00000394217.2_Frame_Shift_Del_p.G3fs	NM_033347.1	NP_203133.1	Q9Y2U2	KCNK7_HUMAN	potassium channel, subfamily K, member 7	3					potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			endometrium(1)|liver(1)|lung(1)	3						GGGCCTTAGACCCCCCATGGC	0.711																																					p.G3fs		Atlas-INDEL	.											.	KCNK7	22	.	0			c.9delT						.						7	9	8					11																	65363236		2147	4242	6389	SO:0001589	frameshift_variant	10089	exon1			.	AF110522	CCDS8106.1, CCDS31608.1, CCDS41673.1	11q13	2012-03-07			ENSG00000173338	ENSG00000173338		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6282	protein-coding gene	gene with protein product		603940				10206991, 11256078, 16382106	Standard	NM_033347		Approved	K2p7.1	uc001oes.3	Q9Y2U2	OTTHUMG00000166528	ENST00000340313.4:c.8delG	chr11.hg19:g.65363236delC	ENSP00000344820:p.Gly3fs	399.0	0.0		275.0	17.0	NM_005714	Q3SYI2|Q9Y2U3|Q9Y2U4	Frame_Shift_Del	DEL	ENST00000340313.4	hg19	CCDS31608.1																																																																																			.	.		0.711	KCNK7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390206.1	NM_005714		-	65363236	C	-	65363236	7	5	282	1	0	1	0	1	0	0	0	0	8080	507	18	0	1028	0	KCNK7	11	65363236	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1598821	65363236	69643280	789	41023										
CTSW	1521	hgsc.bcm.edu	37	chr11	65649694	65649694	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcggagggcagctggaggggTccccagcatgggcagagaaa	18	9	0	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:65649694T>C	ENST00000307886.3	+	4	381	c.335T>C	c.(334-336)gTc>gCc	p.V112A	CTSW_ENST00000528419.1_Missense_Mutation_p.V112A	NM_001335.3	NP_001326	P56202	CATW_HUMAN	cathepsin W	112					immune response (GO:0006955)	membrane (GO:0016020)	cysteine-type peptidase activity (GO:0008234)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(5)	9				READ - Rectum adenocarcinoma(159;0.168)		GCTGGAGGGGTCCCCAGCATG	0.582																																					p.V112A		Atlas-SNP	.											.	CTSW	18	.	0			c.T335C						.						67	72	70					11																	65649694		2201	4296	6497	SO:0001583	missense	1521	exon4			GAGGGGTCCCCAG	AF055903	CCDS8117.1	11q13.1	2008-02-01	2006-12-05		ENSG00000172543	ENSG00000172543		"Cathepsins"	2546	protein-coding gene	gene with protein product		602364	"cathepsin W (lymphopain)"			9108299, 9675123	Standard	NM_001335		Approved		uc001ogc.1	P56202	OTTHUMG00000166663	ENST00000307886.3:c.335T>C	chr11.hg19:g.65649694T>C	ENSP00000311300:p.Val112Ala	194.0	0.0		130.0	6.0	NM_001335	Q86VT4	Missense_Mutation	SNP	ENST00000307886.3	hg19	CCDS8117.1	.	.	.	.	.	.	.	.	.	.	T	0.540	-0.854055	0.02630	.	.	ENSG00000172543	ENST00000307886;ENST00000528419;ENST00000526034	T;T;T	0.28666	1.6;1.6;1.6	4.2	-2.06	0.07298	.	2.672720	0.01187	N	0.007228	T	0.08891	0.0220	N	0.01091	-1.02	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.22941	-1.0202	10	0.07813	T	0.8	.	3.6051	0.08039	0.3113:0.4625:0.0:0.2262	.	112;112	P56202;E9PI30	CATW_HUMAN;.	A	112;112;111	ENSP00000311300:V112A;ENSP00000436568:V112A;ENSP00000434267:V111A	ENSP00000311300:V112A	V	+	2	0	CTSW	65406270	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.467000	0.00993	-0.348000	0.08286	0.533000	0.62120	GTC	.	.		0.582	CTSW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391042.1	NM_001335		C	65649694	T	C	65649694	3	2	282	1	0	0	0	0	1	0	0	0	4044	1667	58	2	349	2	CTSW	11	65649694	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	286458	65649694	69356822	790	41024										
C11orf68	83638	hgsc.bcm.edu	37	chr11	65684997	65684997	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gggcactacccccaagctggAaacggctctcatagagagtg	12	12	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:65684997A>G	ENST00000530188.1	-	1	834	c.689T>C	c.(688-690)tTc>tCc	p.F230S	DRAP1_ENST00000376991.2_5'Flank|DRAP1_ENST00000312515.2_5'Flank|DRAP1_ENST00000527119.1_5'Flank|DRAP1_ENST00000532933.1_5'Flank|C11orf68_ENST00000438576.2_Missense_Mutation_p.F272S|C11orf68_ENST00000449692.3_Missense_Mutation_p.F271S			Q9H3H3	CK068_HUMAN	chromosome 11 open reading frame 68	230							poly(A) RNA binding (GO:0044822)			large_intestine(1)|lung(3)	4				READ - Rectum adenocarcinoma(159;0.166)		CCCAAGCTGGAAACGGCTCTC	0.602																																					p.F272S		Atlas-SNP	.											.	C11orf68	15	.	0			c.T815C						.						68	66	67					11																	65684997		2201	4296	6497	SO:0001583	missense	83638	exon2			AGCTGGAAACGGC	AF073483	CCDS8122.2, CCDS44652.1	11q13.1	2012-08-09			ENSG00000175573	ENSG00000175573			28801	protein-coding gene	gene with protein product	"basophilic leukemia-expressed protein"					16511166	Standard	NM_031450		Approved	P5326, BLES03	uc001ogi.3	Q9H3H3	OTTHUMG00000157153	ENST00000530188.1:c.689T>C	chr11.hg19:g.65684997A>G	ENSP00000433914:p.Phe230Ser	101.0	0.0		91.0	4.0	NM_001135635	J3KQG9|Q9BT13	Missense_Mutation	SNP	ENST00000530188.1	hg19		.	.	.	.	.	.	.	.	.	.	A	20.4	3.985453	0.74589	.	.	ENSG00000175573	ENST00000438576;ENST00000449692;ENST00000530188	T;T;T	0.41400	1.0;1.0;1.0	5.03	3.77	0.43336	Translation Initiation factor eIF- 4e-like  domain (2);	0.119294	0.56097	D	0.000021	T	0.37100	0.0991	N	0.19112	0.55	0.49213	D	0.999766	D;D	0.64830	0.994;0.989	P;P	0.57720	0.826;0.675	T	0.06844	-1.0804	10	0.25106	T	0.35	-11.7888	7.2932	0.26378	0.6722:0.0:0.0:0.3278	.	271;230	Q9H3H3-2;Q9H3H3	.;CK068_HUMAN	S	272;271;230	ENSP00000398350:F272S;ENSP00000409681:F271S;ENSP00000433914:F230S	ENSP00000398350:F272S	F	-	2	0	C11orf68	65441573	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.807000	0.55591	2.023000	0.59567	0.459000	0.35465	TTC	.	.		0.602	C11orf68-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000391173.1	NM_031450		G	65684997	A	G	65684997	3	3	282	1	0	0	0	0	1	0	0	0	1660	246	9	2	70	2	C11orf68	11	65684997	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	35303	65684997	69321519	791	41025										
SART1	9092	hgsc.bcm.edu	37	chr11	65744188	65744188	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cgaatctgacggggaggagaAcatcggctggagcacggtga	17	8	1	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:65744188A>G	ENST00000312397.5	+	14	1900	c.1808A>G	c.(1807-1809)aAc>aGc	p.N603S		NM_005146.4	NP_005137.1	O43290	SNUT1_HUMAN	squamous cell carcinoma antigen recognized by T cells	603					cell cycle arrest (GO:0007050)|intrinsic apoptotic signaling pathway (GO:0097193)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of cytotoxic T cell differentiation (GO:0045585)|spliceosomal snRNP assembly (GO:0000387)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						GGGGAGGAGAACATCGGCTGG	0.662																																					p.N603S		Atlas-SNP	.											.	SART1	41	.	0			c.A1808G						.						29	27	28					11																	65744188		2201	4296	6497	SO:0001583	missense	9092	exon14			AGGAGAACATCGG	AB006198	CCDS31611.1	11q13.1	2009-01-06	2006-12-07		ENSG00000175467	ENSG00000175467			10538	protein-coding gene	gene with protein product	"small nuclear ribonucleoprotein 110kDa (U4/U6.U5)"	605941	"squamous cell carcinoma antigen recognised by T cells"			9449708	Standard	NM_005146		Approved	Ara1, Snu66, SNRNP110	uc001ogl.3	O43290	OTTHUMG00000166771	ENST00000312397.5:c.1808A>G	chr11.hg19:g.65744188A>G	ENSP00000310448:p.Asn603Ser	155.0	0.0		82.0	5.0	NM_005146	A6NDN1|Q53GB5	Missense_Mutation	SNP	ENST00000312397.5	hg19	CCDS31611.1	.	.	.	.	.	.	.	.	.	.	A	14.95	2.687408	0.48097	.	.	ENSG00000175467	ENST00000312397;ENST00000542816	T	0.24538	1.85	4.44	4.44	0.53790	.	0.000000	0.85682	D	0.000000	T	0.30262	0.0759	L	0.36672	1.1	0.47341	D	0.999395	P	0.48503	0.911	P	0.51487	0.671	T	0.05289	-1.0894	10	0.87932	D	0	-26.3971	11.6832	0.51470	1.0:0.0:0.0:0.0	.	603	O43290	SNUT1_HUMAN	S	603;445	ENSP00000310448:N603S	ENSP00000310448:N603S	N	+	2	0	SART1	65500764	1.000000	0.71417	0.999000	0.59377	0.257000	0.26127	4.409000	0.59768	1.869000	0.54173	0.402000	0.26972	AAC	.	.		0.662	SART1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391409.1			G	65744188	A	G	65744188	3	3	282	1	0	0	0	0	1	0	0	0	13861	43	2	2	1862	2	SART1	11	65744188	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	59191	65744188	69262328	792	41026										
RIN1	9610	hgsc.bcm.edu	37	chr11	66103273	66103273	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tagtggctggagacgaaggaGgggccactggcttcaggcaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:66103273delG	ENST00000311320.4	-	3	468	c.342delC	c.(340-342)cccfs	p.P114fs	RIN1_ENST00000424433.2_Frame_Shift_Del_p.P9fs|RIN1_ENST00000530056.1_Frame_Shift_Del_p.P9fs|RIN1_ENST00000524804.1_5'Flank|RP11-867G23.12_ENST00000526655.1_RNA	NM_004292.2	NP_004283.2	Q13671	RIN1_HUMAN	Ras and Rab interactor 1	114	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				associative learning (GO:0008306)|endocytosis (GO:0006897)|memory (GO:0007613)|negative regulation of synaptic plasticity (GO:0031914)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|lung(8)|ovary(1)	14						AGACGAAGGAGGGGCCACTGG	0.647																																					p.S115fs		Atlas-INDEL	.											.	RIN1	64	.	0			c.343delT						.						32	37	35					11																	66103273		2200	4295	6495	SO:0001589	frameshift_variant	9610	exon3			.	L36463	CCDS31614.1	11q13.2	2005-09-18				ENSG00000174791			18749	protein-coding gene	gene with protein product		605965				9144171, 1849280	Standard	NM_004292		Approved		uc001ohn.1	Q13671		ENST00000311320.4:c.342delC	chr11.hg19:g.66103273delG	ENSP00000310406:p.Pro114fs	161.0	0.0		120.0	10.0	NM_004292	O15010|Q00427|Q96CC8	Frame_Shift_Del	DEL	ENST00000311320.4	hg19	CCDS31614.1																																																																																			.	.		0.647	RIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392980.2	NM_004292		-	66103273	G	-	66103273	7	5	282	1	0	1	0	1	0	0	0	0	13386	987	35	0	2041	0	RIN1	11	66103273	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	359085	66103273	68903243	793	41027										
ACTN3	8722	hgsc.bcm.edu	37	chr11	66330266	66330266	+	IGR	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcctggcctctatccctgcaGggggaagtggagtttgctcg					rs374534956		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:66330266delG	ENST00000310325.5	-	0	2035				ACTN3_ENST00000502692.1_RNA|CTD-3074O7.2_ENST00000504911.1_lincRNA|ACTN3_ENST00000513398.1_RNA	NM_003793.3	NP_003784.2	Q9UBX1	CATF_HUMAN	cathepsin F						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|vesicle (GO:0031982)	cysteine-type endopeptidase activity (GO:0004197)			endometrium(1)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	19						TATCCCTGCAGGGGGAAGTGG	0.602																																					.		Atlas-INDEL	.											.	ACTN3	27	.	0			c.2518-2G>-						.						139	153	149					11																	66330266		2194	4292	6486	SO:0001628	intergenic_variant	89	exon20			.	AF071749	CCDS8144.1	11q13.2	2012-02-29			ENSG00000174080	ENSG00000174080		"Cathepsins"	2531	protein-coding gene	gene with protein product		603539				9822672, 10318784	Standard	NM_003793		Approved	CATSF, CLN13	uc001oip.3	Q9UBX1	OTTHUMG00000167090		chr11.hg19:g.66330266delG		316.0	0.0		227.0	15.0	NM_001258371	B2R964|O95240|Q9NSU4|Q9UKQ5	Splice_Site	DEL	ENST00000310325.5	hg19	CCDS8144.1																																																																																			.	.		0.602	CTSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393047.1	NM_003793		-	66330266	G	-	66330266	6	5	282	0	1	1	0	1	0	0	0	0	206	1014	35	0		0	ACTN3	11	66330266	IGR	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	226993	66330266	68676250	794	41028										
SPTBN2	6712	hgsc.bcm.edu	37	chr11	66463797	66463797	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tggtgaggtccttgccgtagTcatccgagtgcagctgggcc	15	11	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:66463797T>C	ENST00000533211.1	-	21	4560	c.4229A>G	c.(4228-4230)gAc>gGc	p.D1410G	SPTBN2_ENST00000529997.1_Missense_Mutation_p.D1410G|SPTBN2_ENST00000309996.2_Missense_Mutation_p.D1410G			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	1410					actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						CTTGCCGTAGTCATCCGAGTG	0.602																																					p.D1410G		Atlas-SNP	.											.	SPTBN2	188	.	0			c.A4229G						.						55	48	50					11																	66463797		2200	4295	6495	SO:0001583	missense	6712	exon20			CCGTAGTCATCCG	AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"Pleckstrin homology (PH) domain containing"	11276	protein-coding gene	gene with protein product		604985	"spinocerebellar ataxia 5"	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.4229A>G	chr11.hg19:g.66463797T>C	ENSP00000432568:p.Asp1410Gly	127.0	0.0		77.0	4.0	NM_006946	O14872|O14873	Missense_Mutation	SNP	ENST00000533211.1	hg19	CCDS8150.1	.	.	.	.	.	.	.	.	.	.	T	25.8	4.679457	0.88542	.	.	ENSG00000173898	ENST00000533211;ENST00000309996;ENST00000529997	T;T;T	0.56611	0.45;0.45;0.45	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	T	0.73938	0.3651	M	0.85630	2.765	0.58432	D	0.999999	D	0.76494	0.999	D	0.70016	0.967	T	0.78919	-0.2014	10	0.72032	D	0.01	.	13.9729	0.64252	0.0:0.0:0.0:1.0	.	1410	O15020	SPTN2_HUMAN	G	1410	ENSP00000432568:D1410G;ENSP00000311489:D1410G;ENSP00000433593:D1410G	ENSP00000311489:D1410G	D	-	2	0	SPTBN2	66220373	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	7.806000	0.86020	2.138000	0.66242	0.455000	0.32223	GAC	.	.		0.602	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946		C	66463797	T	C	66463797	3	2	282	1	0	0	0	0	1	0	0	0	15135	1667	58	2	3015	2	SPTBN2	11	66463797	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	133531	66463797	68542719	795	41029										
LRFN4	78999	hgsc.bcm.edu	37	chr11	66627620	66627620	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gctgctcggggcagggtgccGgggggtaggaggcagcgccg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:66627620delG	ENST00000309602.4	+	2	2105	c.1862delG	c.(1861-1863)cggfs	p.R621fs	LRFN4_ENST00000393952.3_Intron|PC_ENST00000393960.1_Intron|PC_ENST00000393958.2_Intron|PC_ENST00000393955.2_Intron	NM_024036.4	NP_076941.2	Q6PJG9	LRFN4_HUMAN	leucine rich repeat and fibronectin type III domain containing 4	621						integral component of membrane (GO:0016021)				breast(1)|lung(1)|prostate(1)	3						GCAGGGTGCCGGGGGGTAGGA	0.692																																					p.R621fs		Atlas-INDEL	.											.	LRFN4	25	.	0			c.1861delC						.						8	12	11					11																	66627620		1948	3901	5849	SO:0001589	frameshift_variant	78999	exon2			.	BC007718	CCDS8153.1	11q13.1	2013-02-11				ENSG00000173621		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	28456	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 6"	612810				16495444, 16828986	Standard	NM_024036		Approved	MGC3103, SALM3., FIGLER6	uc001ojr.3	Q6PJG9		ENST00000309602.4:c.1862delG	chr11.hg19:g.66627620delG	ENSP00000312535:p.Arg621fs	98.0	0.0		147.0	10.0	NM_024036	Q4VBZ3|Q59GV4|Q8N644|Q9BWJ0	Frame_Shift_Del	DEL	ENST00000309602.4	hg19	CCDS8153.1																																																																																			.	.		0.692	LRFN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393127.1	NM_024036		-	66627620	G	-	66627620	7	5	282	1	0	1	0	1	0	0	0	0	8949	1116	39	0	1868	0	LRFN4	11	66627620	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	163823	66627620	68378896	796	41030										
ALDH3B2	222	hgsc.bcm.edu	37	chr11	67433122	67433122	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggtggcagcagtcatgacaaTcttgcccacacgagggctcc	12	13	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:67433122T>C	ENST00000349015.3	-	7	778	c.340A>G	c.(340-342)Att>Gtt	p.I114V	ALDH3B2_ENST00000531881.1_5'Flank|ALDH3B2_ENST00000530069.1_Missense_Mutation_p.I114V	NM_000695.3	NP_000686	P48448	AL3B2_HUMAN	aldehyde dehydrogenase 3 family, member B2	114					alcohol metabolic process (GO:0006066)|ethanol catabolic process (GO:0006068)|lipid metabolic process (GO:0006629)		3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|prostate(2)|stomach(1)|urinary_tract(1)	18						GTCATGACAATCTTGCCCACA	0.647																																					p.I114V		Atlas-SNP	.											.	ALDH3B2	46	.	0			c.A340G						.						117	126	123					11																	67433122		2200	4294	6494	SO:0001583	missense	222	exon7			TGACAATCTTGCC	U37519	CCDS31622.1	11q13.2	2014-09-04			ENSG00000132746	ENSG00000132746	1.2.1.5	"Aldehyde dehydrogenases"	411	protein-coding gene	gene with protein product	"aldehyde dehydrogenase 8", "acetaldehyde dehydrogenase 8"	601917		ALDH8		8890755, 9161417	Standard	NM_000695		Approved		uc001oms.3	P48448	OTTHUMG00000167284	ENST00000349015.3:c.340A>G	chr11.hg19:g.67433122T>C	ENSP00000255084:p.Ile114Val	138.0	0.0		121.0	6.0	NM_001031615	Q53Y98|Q8NAL5|Q96IB2	Missense_Mutation	SNP	ENST00000349015.3	hg19	CCDS31622.1	.	.	.	.	.	.	.	.	.	.	T	9.294	1.051396	0.19827	.	.	ENSG00000132746	ENST00000530069;ENST00000349015;ENST00000525827	T;T;T	0.75821	-0.97;-0.97;-0.97	4.16	-1.74	0.08056	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.463335	0.21531	N	0.073058	T	0.61739	0.2371	L	0.49699	1.58	0.09310	N	1	B	0.09022	0.002	B	0.17433	0.018	T	0.52764	-0.8532	10	0.56958	D	0.05	.	5.4538	0.16580	0.0:0.1568:0.2723:0.5709	.	114	P48448	AL3B2_HUMAN	V	114	ENSP00000431595:I114V;ENSP00000255084:I114V;ENSP00000433718:I114V	ENSP00000255084:I114V	I	-	1	0	ALDH3B2	67189698	0.128000	0.22383	0.055000	0.19348	0.597000	0.36814	0.373000	0.20484	-0.399000	0.07668	0.379000	0.24179	ATT	.	.		0.647	ALDH3B2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394004.1	NM_000695		C	67433122	T	C	67433122	3	2	282	1	0	0	0	0	1	0	0	0	500	1435	50	2	833	2	ALDH3B2	11	67433122	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	805502	67433122	67573394	797	41031										
SUV420H1	51111	hgsc.bcm.edu	37	chr11	67934514	67934514	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgacagattgactgtctgaaTttttgctgctgtcacctaac							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:67934514delT	ENST00000304363.4	-	10	1462	c.1109delA	c.(1108-1110)aatfs	p.N370fs	SUV420H1_ENST00000405515.1_Frame_Shift_Del_p.N370fs|SUV420H1_ENST00000402789.1_Frame_Shift_Del_p.N370fs|SUV420H1_ENST00000401547.2_Frame_Shift_Del_p.N370fs|SUV420H1_ENST00000402185.2_Frame_Shift_Del_p.N347fs	NM_017635.3	NP_060105	Q4FZB7	SV421_HUMAN	suppressor of variegation 4-20 homolog 1 (Drosophila)	370					histone H4-K20 trimethylation (GO:0034773)|muscle organ development (GO:0007517)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome, centromeric region (GO:0000780)	histone methyltransferase activity (H4-K20 specific) (GO:0042799)|histone-lysine N-methyltransferase activity (GO:0018024)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(15)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46						ACTGTCTGAATTTTTGCTGCT	0.383																																					p.N370fs		Atlas-INDEL	.											.	SUV420H1	125	.	0			c.1110delT						.						161	149	153					11																	67934514		2200	4294	6494	SO:0001589	frameshift_variant	51111	exon10			.	AL512763	CCDS31623.1, CCDS44660.1	11q13.2	2011-07-01			ENSG00000110066	ENSG00000110066		"Chromatin-modifying enzymes / K-methyltransferases"	24283	protein-coding gene	gene with protein product		610881				10810093, 11401438	Standard	NM_016028		Approved	CGI-85, KMT5B	uc001onm.1	Q4FZB7	OTTHUMG00000150484	ENST00000304363.4:c.1109delA	chr11.hg19:g.67934514delT	ENSP00000305899:p.Asn370fs	254.0	0.0		206.0	15.0	NM_017635	B7WNX7|Q3SX56|Q4V775|Q6P150|Q96E44|Q9BUL0|Q9H022|Q9H2K3|Q9NXV3|Q9Y393	Frame_Shift_Del	DEL	ENST00000304363.4	hg19	CCDS31623.1																																																																																			.	.		0.383	SUV420H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318319.1	NM_017635		-	67934514	T	-	67934514	7	5	282	1	0	1	0	1	0	0	0	0	15429	1493	52	0	1564	0	SUV420H1	11	67934514	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	501392	67934514	67072002	798	41032										
SAPS3	55291	hgsc.bcm.edu	37	chr11	68382138	68382138	+	3'UTR	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	actcccaggacagtggagtcAgcagtaagccctgggacagg	14	11	1	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:68382138A>G	ENST00000393800.2	+	0	4429				PPP6R3_ENST00000265637.4_3'UTR|PPP6R3_ENST00000527403.2_3'UTR|PPP6R3_ENST00000265636.5_3'UTR|PPP6R3_ENST00000393799.2_3'UTR|CTD-2007L18.5_ENST00000564469.1_lincRNA|PPP6R3_ENST00000393801.3_3'UTR|PPP6R3_ENST00000529710.1_Missense_Mutation_p.Q790R	NM_001164161.1|NM_001164162.1|NM_001164163.1	NP_001157633.1|NP_001157634.1|NP_001157635.1	Q5H9R7	PP6R3_HUMAN	protein phosphatase 6, regulatory subunit 3						regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)			breast(2)|endometrium(6)|kidney(3)|large_intestine(10)|liver(2)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						CAGTGGAGTCAGCAGTAAGCC	0.502																																					p.Q790R		Atlas-SNP	.											.	PPP6R3	159	.	0			c.A2369G						.						168	160	163					11																	68382138		692	1591	2283	SO:0001624	3_prime_UTR_variant	55291	exon23			GGAGTCAGCAGTA	AF264779	CCDS8182.1, CCDS53671.1, CCDS53672.1, CCDS53673.1, CCDS53674.1, CCDS53675.1	11q13	2012-04-17	2010-06-28	2010-06-28	ENSG00000110075	ENSG00000110075		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"	1173	protein-coding gene	gene with protein product	"sporulation-induced transcript 4-associated protein"	610879	"chromosome 11 open reading frame 23", "SAPS domain family, member 3"	C11orf23, SAPS3		11401438, 16769727	Standard	NM_018312		Approved	SAPLa, DKFZp781E2374, DKFZp781O2362, DKFZp781E17107, SAP190, SAPL, PP6R3, FLJ11058, FLJ43065, KIAA1558, MGC125711, MGC125712	uc001onv.3	Q5H9R7		ENST00000393800.2:c.*1553A>G	chr11.hg19:g.68382138A>G		132.0	0.0		114.0	5.0	NM_001164164	Q3B7I1|Q3I4Y0|Q3KR35|Q68CR3|Q7L4R8|Q8N3B2|Q96MB2|Q9H2K5|Q9H2K6|Q9HCL4|Q9NUY3	Missense_Mutation	SNP	ENST00000393800.2	hg19	CCDS53672.1	.	.	.	.	.	.	.	.	.	.	A	9.825	1.186958	0.21870	.	.	ENSG00000110075	ENST00000529710	T	0.21734	1.99	4.36	-7.93	0.01156	.	.	.	.	.	T	0.08537	0.0212	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30475	-0.9977	8	0.29301	T	0.29	.	1.8042	0.03077	0.3886:0.2247:0.2754:0.1113	.	790	Q5H9R7-3	.	R	790	ENSP00000437329:Q790R	ENSP00000437329:Q790R	Q	+	2	0	PPP6R3	68138714	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.006000	0.01459	-1.328000	0.02261	-0.256000	0.11100	CAG	.	.		0.502	PPP6R3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395275.1	NM_018312		G	68382138	A	G	68382138	1	3	282	0	1	0	0	0	0	0	0	0	13853	188	7	2		2	SAPS3	11	68382138	3'UTR	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	447624	68382138	66624378	799	41033										
TPCN2	219931	hgsc.bcm.edu	37	chr11	68839465	68839465	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaagtcctatcctccatggtGggggagggaggagccttccc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:68839465delG	ENST00000294309.3	+	11	1136	c.1035delG	c.(1033-1035)gtgfs	p.V345fs	TPCN2_ENST00000542467.1_Frame_Shift_Del_p.V345fs|TPCN2_ENST00000442692.2_3'UTR	NM_139075.3	NP_620714.2	Q8NHX9	TPC2_HUMAN	two pore segment channel 2	345					calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|release of sequestered calcium ion into cytosol (GO:0051209)|smooth muscle contraction (GO:0006939)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|protein kinase binding (GO:0019901)|voltage-gated calcium channel activity (GO:0005245)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	32			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			CCTCCATGGTGGGGGAGGGAG	0.627																																					p.V345fs		Atlas-INDEL	.											.	TPCN2	63	.	0			c.1034delT						.						54	58	57					11																	68839465		2200	4294	6494	SO:0001589	frameshift_variant	219931	exon11			.	AK023366	CCDS8189.1	11q13.1	2011-07-05			ENSG00000162341	ENSG00000162341		"Voltage-gated ion channels / Two-pore channels"	20820	protein-coding gene	gene with protein product		612163				16382101	Standard	NM_139075		Approved	TPC2	uc001oos.2	Q8NHX9	OTTHUMG00000167898	ENST00000294309.3:c.1035delG	chr11.hg19:g.68839465delG	ENSP00000294309:p.Val345fs	123.0	0.0		102.0	10.0	NM_139075	Q9NT82	Frame_Shift_Del	DEL	ENST00000294309.3	hg19	CCDS8189.1																																																																																			.	.		0.627	TPCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396878.2	NM_139075		-	68839465	G	-	68839465	7	5	282	1	0	1	0	1	0	0	0	0	16411	1335	47	0	1077	0	TPCN2	11	68839465	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	457327	68839465	66167051	800	41034										
ANO1	55107	hgsc.bcm.edu	37	chr11	70033894	70033894	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gactgggtcatcccggacatCcccaaggacatcagccagca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:70033894delC	ENST00000355303.5	+	26	3050	c.2745delC	c.(2743-2745)atcfs	p.I915fs	ANO1_ENST00000398543.2_Frame_Shift_Del_p.I769fs|ANO1_ENST00000525494.1_3'UTR|ANO1_ENST00000530676.1_Frame_Shift_Del_p.I769fs|ANO1-AS1_ENST00000524987.1_RNA|ANO1_ENST00000538023.1_Frame_Shift_Del_p.I915fs|ANO1_ENST00000531349.1_Frame_Shift_Del_p.I624fs	NM_018043.5	NP_060513.5	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel	915					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of membrane potential (GO:0042391)|trachea development (GO:0060438)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)	p.I915I(2)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(12)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)	29					Crofelemer(DB04941)	TCCCGGACATCCCCAAGGACA	0.582																																					p.I915fs		Atlas-INDEL	.											.	ANO1	156	.	2	Substitution - coding silent(2)	lung(2)	c.2744delT						.						42	48	46					11																	70033894		2117	4239	6356	SO:0001589	frameshift_variant	55107	exon26			.	BC033036	CCDS44663.1	11q13.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000131620	ENSG00000131620		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	21625	protein-coding gene	gene with protein product		610108	"oral cancer overexpressed 2", "transmembrane protein 16A"	ORAOV2, TMEM16A		15067359, 18724360, 24692353	Standard	NM_018043		Approved	TAOS2, FLJ10261, DOG1	uc001opj.3	Q5XXA6	OTTHUMG00000167204	ENST00000355303.5:c.2745delC	chr11.hg19:g.70033894delC	ENSP00000347454:p.Ile915fs	231.0	0.0		180.0	11.0	NM_018043	A8KAM3|Q8IYY8|Q8N7V3	Frame_Shift_Del	DEL	ENST00000355303.5	hg19	CCDS44663.1																																																																																			.	.		0.582	ANO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393685.1	NM_018043		-	70033894	C	-	70033894	7	5	282	1	0	1	0	1	0	0	0	0	695	845	30	0	2847	0	ANO1	11	70033894	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1194429	70033894	64972622	801	41035										
XRRA1	143570	hgsc.bcm.edu	37	chr11	74559430	74559430	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggctctagcatatcctttgaGggagacttggttgtcgtcat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:74559430delG	ENST00000340360.6	-	15	1765	c.1434delC	c.(1432-1434)cccfs	p.P478fs	RN7SL239P_ENST00000490061.2_RNA|XRRA1_ENST00000321448.8_Frame_Shift_Del_p.P203fs|XRRA1_ENST00000527087.1_Frame_Shift_Del_p.P391fs	NM_182969.2	NP_892014.1			X-ray radiation resistance associated 1											breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(3)	20						TATCCTTTGAGGGAGACTTGG	0.542																																					p.S479fs		Atlas-INDEL	.											.	XRRA1	46	.	0			c.1435delT						.						54	60	58					11																	74559430		2080	4189	6269	SO:0001589	frameshift_variant	143570	exon15			.	AK074152	CCDS44680.1, CCDS58159.1, CCDS58160.1	11q13.4	2010-03-19			ENSG00000166435	ENSG00000166435			18868	protein-coding gene	gene with protein product		609788				12908878, 17295261	Standard	NM_182969		Approved	FLJ00225	uc009yub.3	Q6P2D8		ENST00000340360.6:c.1434delC	chr11.hg19:g.74559430delG	ENSP00000339918:p.Pro478fs	210.0	0.0		155.0	12.0	NM_182969		Frame_Shift_Del	DEL	ENST00000340360.6	hg19	CCDS44680.1																																																																																			.	.		0.542	XRRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384715.1	NM_182969		-	74559430	G	-	74559430	7	5	282	1	0	1	0	1	0	0	0	0	17476	987	35	0	964	0	XRRA1	11	74559430	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	4525536	74559430	60447086	802	41036										
XRRA1	143570	hgsc.bcm.edu	37	chr11	74574037	74574037	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agttcctacctctgaggttgAaaatccagggtaagatgaaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:74574037delA	ENST00000340360.6	-	11	1340	c.1009delT	c.(1009-1011)tcafs	p.S337fs	XRRA1_ENST00000321448.8_Frame_Shift_Del_p.S104fs|XRRA1_ENST00000527087.1_Intron	NM_182969.2	NP_892014.1			X-ray radiation resistance associated 1											breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(3)	20						TCTGAGGTTGAAAATCCAGGG	0.378																																					p.S337X		Atlas-INDEL	.											.	XRRA1	46	.	0			c.1010delC						.						49	44	45					11																	74574037		1861	4098	5959	SO:0001589	frameshift_variant	143570	exon11			.	AK074152	CCDS44680.1, CCDS58159.1, CCDS58160.1	11q13.4	2010-03-19			ENSG00000166435	ENSG00000166435			18868	protein-coding gene	gene with protein product		609788				12908878, 17295261	Standard	NM_182969		Approved	FLJ00225	uc009yub.3	Q6P2D8		ENST00000340360.6:c.1009delT	chr11.hg19:g.74574037delA	ENSP00000339918:p.Ser337fs	233.0	0.0		165.0	10.0	NM_182969		Frame_Shift_Del	DEL	ENST00000340360.6	hg19	CCDS44680.1																																																																																			.	.		0.378	XRRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384715.1	NM_182969		-	74574037	A	-	74574037	7	5	282	1	0	1	0	1	0	0	0	0	17476	246	9	0	1405	0	XRRA1	11	74574037	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	14607	74574037	60432479	803	41037										
OR2AT4	341152	hgsc.bcm.edu	37	chr11	74799967	74799967	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aggtcagccctgtaggccacGtaggctatggcaatagatga	13	9	1	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:74799967G>A	ENST00000305159.3	-	1	832	c.792C>T	c.(790-792)taC>taT	p.Y264Y		NM_001005285.1	NP_001005285.1	A6NND4	O2AT4_HUMAN	olfactory receptor, family 2, subfamily AT, member 4	264						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(2)	12						TGTAGGCCACGTAGGCTATGG	0.527																																					p.Y264Y		Atlas-SNP	.											OR2AT4,NS,carcinoma,-2,1	OR2AT4	32	.	0			c.C792T						.						93	85	88					11																	74799967		2200	4293	6493	SO:0001819	synonymous_variant	341152	exon1			GGCCACGTAGGCT	BK004820	CCDS31639.1	11q13.4	2012-08-09			ENSG00000171561	ENSG00000171561		"GPCR / Class A : Olfactory receptors"	19620	protein-coding gene	gene with protein product							Standard	NM_001005285		Approved		uc010rro.2	A6NND4	OTTHUMG00000165370	ENST00000305159.3:c.792C>T	chr11.hg19:g.74799967G>A		235.0	0.0		146.0	69.0	NM_001005285	B9EGZ8	Silent	SNP	ENST00000305159.3	hg19	CCDS31639.1																																																																																			.	.		0.527	OR2AT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383734.1	NM_001005285		A	74799967	G	A	74799967	2	1	282	1	0	0	0	0	0	0	0	1	10996	1140	40	1		1	OR2AT4	11	74799967	Silent	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	225930	74799967	60206549	804	41038										
ODZ4	26011	hgsc.bcm.edu	37	chr11	78433744	78433744	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gatgttggtgacatttccagAggggaagatccttctaatgt	12	6	1	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:78433744A>G	ENST00000278550.7	-	24	4231	c.3769T>C	c.(3769-3771)Tct>Cct	p.S1257P		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	1257					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										ACATTTCCAGAGGGGAAGATC	0.512																																					p.S1257P		Atlas-SNP	.											.	.	.	.	0			c.T3769C						.						116	116	116					11																	78433744		1937	4130	6067	SO:0001583	missense	26011	exon24			TTCCAGAGGGGAA	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"odz, odd Oz/ten-m homolog 4 (Drosophila)"	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.3769T>C	chr11.hg19:g.78433744A>G	ENSP00000278550:p.Ser1257Pro	146.0	0.0		100.0	4.0	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Missense_Mutation	SNP	ENST00000278550.7	hg19	CCDS44688.1	.	.	.	.	.	.	.	.	.	.	A	17.73	3.461786	0.63513	.	.	ENSG00000149256	ENST00000278550	D	0.90676	-2.71	5.64	5.64	0.86602	Six-bladed beta-propeller, TolB-like (1);	0.054825	0.64402	D	0.000001	D	0.90501	0.7024	M	0.79475	2.455	0.50039	D	0.999846	P	0.39391	0.671	B	0.37943	0.261	D	0.90196	0.4253	9	.	.	.	.	16.0238	0.80522	1.0:0.0:0.0:0.0	.	1257	Q6N022	TEN4_HUMAN	P	1257	ENSP00000278550:S1257P	.	S	-	1	0	ODZ4	78111392	1.000000	0.71417	0.997000	0.53966	0.989000	0.77384	6.539000	0.73856	2.367000	0.80283	0.528000	0.53228	TCT	.	.		0.512	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			G	78433744	A	G	78433744	3	3	282	1	0	0	0	0	1	0	0	0	10846	304	11	2	4584	2	ODZ4	11	78433744	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	3633777	78433744	56572772	805	41039										
PRCP	5547	hgsc.bcm.edu	37	chr11	82536121	82536121	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaccagagtgtctgtgatatCcttagttactccacctcctg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:82536121delC	ENST00000313010.3	-	9	1512	c.1318delG	c.(1318-1320)gatfs	p.D440fs	PRCP_ENST00000393399.2_Frame_Shift_Del_p.D461fs|PRCP_ENST00000535099.1_Frame_Shift_Del_p.D335fs|PRCP_ENST00000525772.1_5'UTR	NM_005040.2	NP_005031.1	P42785	PCP_HUMAN	prolylcarboxypeptidase (angiotensinase C)	440					angiogenesis involved in wound healing (GO:0060055)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|energy homeostasis (GO:0097009)|glucose homeostasis (GO:0042593)|negative regulation of systemic arterial blood pressure (GO:0003085)|plasma kallikrein-kinin cascade (GO:0002353)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of thyroid hormone mediated signaling pathway (GO:0002155)	basal part of cell (GO:0045178)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	serine-type carboxypeptidase activity (GO:0004185)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	17						TCTGTGATATCCTTAGTTACT	0.448																																					p.D461fs		Atlas-INDEL	.											.	PRCP	69	.	0			c.1382delA						.						87	80	83					11																	82536121		2203	4300	6503	SO:0001589	frameshift_variant	5547	exon10			.	BC001500, BI827978, L13977	CCDS8262.1, CCDS41695.1	11q14	2005-10-04				ENSG00000137509			9344	protein-coding gene	gene with protein product		176785				8344943	Standard	NM_199418		Approved	PCP, HUMPCP	uc001ozr.3	P42785		ENST00000313010.3:c.1318delG	chr11.hg19:g.82536121delC	ENSP00000317362:p.Asp440fs	244.0	0.0		171.0	11.0	NM_199418	A8MU24|B2R7B7|B3KRK5|B5BU34	Frame_Shift_Del	DEL	ENST00000313010.3	hg19	CCDS8262.1																																																																																			.	.		0.448	PRCP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391792.1	NM_005040		-	82536121	C	-	82536121	7	5	282	1	0	1	0	1	0	0	0	0	12461	855	30	0	176	0	PRCP	11	82536121	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	4102377	82536121	52470395	806	41040										
PCF11	51585	hgsc.bcm.edu	37	chr11	82882908	82882908	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cttttggtcaaggacaacagTttttaccagttcatccacaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:82882908delT	ENST00000298281.4	+	9	4161	c.3709delT	c.(3709-3711)tttfs	p.F1237fs		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	1237					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						AGGACAACAGTTTTTACCAGT	0.328																																					p.Q1236fs		Atlas-INDEL	.											.	PCF11	220	.	0			c.3708delG						.						144	140	141					11																	82882908		1830	4084	5914	SO:0001589	frameshift_variant	51585	exon9			.	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)", "PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.3709delT	chr11.hg19:g.82882908delT	ENSP00000298281:p.Phe1237fs	173.0	0.0		131.0	11.0	NM_015885	A6H8W7|O43671|Q6P0X8	Frame_Shift_Del	DEL	ENST00000298281.4	hg19	CCDS44689.1																																																																																			.	.		0.328	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		-	82882908	T	-	82882908	7	5	282	1	0	1	0	1	0	0	0	0	11582	1725	60	0	3743	0	PCF11	11	82882908	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	346787	82882908	52123608	807	41041										
DLG2	1740	hgsc.bcm.edu	37	chr11	83183770	83183770	+	Splice_Site	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aagcgtgctgggaaacttacTttcctgccttgtaacaggct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:83183770delT	ENST00000532653.1	-	18	2277	c.1975delA	c.(1975-1977)ata>ta	p.I659fs	DLG2_ENST00000376106.3_Splice_Site_p.I141fs|DLG2_ENST00000280241.8_Splice_Site_p.I716fs|DLG2_ENST00000543673.1_Splice_Site_p.I782fs|DLG2_ENST00000418306.2_Splice_Site_p.I556fs|DLG2_ENST00000398309.2_Splice_Site_p.I677fs|DLG2_ENST00000537455.1_Splice_Site_p.I427fs|DLG2_ENST00000404783.3_Splice_Site_p.I155fs|DLG2_ENST00000531015.1_Splice_Site_p.I644fs|DLG2_ENST00000330014.6_Splice_Site_p.I598fs|DLG2_ENST00000426717.2_Splice_Site_p.I141fs|DLG2_ENST00000376104.2_Splice_Site_p.I782fs|DLG2_ENST00000524982.1_Splice_Site_p.I673fs			Q14168	MPP2_HUMAN	discs, large homolog 2 (Drosophila)	371					nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(11)|lung(35)|ovary(3)|pancreas(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	71		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				GGAAACTTACTTTCCTGCCTT	0.428																																					.		Atlas-INDEL	.											.	DLG2	448	.	0			c.2029+1A>-						.						113	111	111					11																	83183770		1908	4100	6008	SO:0001630	splice_region_variant	1740	exon19			.	U32376	CCDS41696.1, CCDS44690.1, CCDS44691.1, CCDS44692.1, CCDS55782.1, CCDS73357.1	11q21	2012-04-17	2008-12-15		ENSG00000150672	ENSG00000150672		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	2901	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 58"	603583	"discs, large homolog 2, chapsyn-110 (Drosophila)"			8755482, 9806853	Standard	NM_001142702		Approved	PSD-93, PSD93, chapsyn-110, PPP1R58	uc001pak.2	Q15700	OTTHUMG00000134309	ENST00000532653.1:c.1975+1A>-	chr11.hg19:g.83183770delT		219.0	0.0		161.0	10.0	NM_001364	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Splice_Site	DEL	ENST00000532653.1	hg19																																																																																				.	.		0.428	DLG2-009	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000259253.2	NM_001364	Frame_Shift_Del	-	83183770	T	-	83183770	8	5	282	1	0	1	0	1	0	0	1	0	4557	1623	56	0	607	0	DLG2	11	83183770	Splice_Site	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	300862	83183770	51822746	808	41042										
TMEM126B	55863	hgsc.bcm.edu	37	chr11	85346800	85346800	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccagttctttggcttttactAaaaatggacgcctggcaacc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:85346800delA	ENST00000358867.6	+	4	510	c.487delA	c.(487-489)aaafs	p.K163fs	TMEM126B_ENST00000534341.1_Frame_Shift_Del_p.K163fs|TMEM126B_ENST00000393375.1_Frame_Shift_Del_p.K133fs	NM_018480.4	NP_060950.3	Q8IUX1	T126B_HUMAN	transmembrane protein 126B	163						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				kidney(1)|large_intestine(2)|lung(3)|prostate(1)	7		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				GGCTTTTACTAAAAATGGACG	0.318																																					p.T162fs		Atlas-INDEL	.											.	TMEM126B	13	.	0			c.486delT						.						117	117	117					11																	85346800		2203	4299	6502	SO:0001589	frameshift_variant	55863	exon4			.		CCDS8267.1, CCDS8267.2, CCDS53686.1	11q14.1	2013-05-24				ENSG00000171204		"Mitochondrial respiratory chain complex assembly factors"	30883	protein-coding gene	gene with protein product		615533				22982022	Standard	NM_018480		Approved	HT007	uc001pap.4	Q8IUX1		ENST00000358867.6:c.487delA	chr11.hg19:g.85346800delA	ENSP00000351737:p.Lys163fs	180.0	0.0		161.0	10.0	NM_018480	A8K535|A8MSS0|Q32Q09|Q8WVU3|Q96EP3|Q9NZ29	Frame_Shift_Del	DEL	ENST00000358867.6	hg19	CCDS8267.2																																																																																			.	.		0.318	TMEM126B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392164.1	NM_018480		-	85346800	A	-	85346800	7	5	282	1	0	1	0	1	0	0	0	0	16054	363	13	0	407	0	TMEM126B	11	85346800	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2163030	85346800	49659716	809	41043										
CCDC89	220388	hgsc.bcm.edu	37	chr11	85397087	85397087	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcctcttcctggttgttcagTttttcattttgcttctctaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:85397087delT	ENST00000316398.3	-	1	233	c.87delA	c.(85-87)aaafs	p.K29fs		NM_152723.1	NP_689936.1	Q8N998	CCD89_HUMAN	coiled-coil domain containing 89	29						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(6)|skin(1)	15		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				GGTTGTTCAGTTTTTCATTTT	0.552																																					p.L30X		Atlas-INDEL	.											.	CCDC89	45	.	0			c.88delC						.						79	76	77					11																	85397087		2203	4299	6502	SO:0001589	frameshift_variant	220388	exon1			.	AK095478	CCDS8270.1	11q14.1	2006-03-16			ENSG00000179071	ENSG00000179071			26762	protein-coding gene	gene with protein product						12477932	Standard	NM_152723		Approved	FLJ38159	uc001pau.1	Q8N998	OTTHUMG00000166976	ENST00000316398.3:c.87delA	chr11.hg19:g.85397087delT	ENSP00000320649:p.Lys29fs	237.0	0.0		176.0	11.0	NM_152723		Frame_Shift_Del	DEL	ENST00000316398.3	hg19	CCDS8270.1																																																																																			.	.		0.552	CCDC89-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392182.1	NM_152723		-	85397087	T	-	85397087	7	5	282	1	0	1	0	1	0	0	0	0	2868	1722	60	0	1041	0	CCDC89	11	85397087	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	50287	85397087	49609429	810	41044										
MTNR1B	4544	hgsc.bcm.edu	37	chr11	92715099	92715099	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccgcaggaaagccaagccagAgagcaggctgtgcctgaagc	14	12	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:92715099A>G	ENST00000257068.2	+	2	716	c.710A>G	c.(709-711)gAg>gGg	p.E237G		NM_005959.3	NP_005950.1	P49286	MTR1B_HUMAN	melatonin receptor 1B	237					G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose homeostasis (GO:0042593)|regulation of insulin secretion (GO:0050796)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|melatonin receptor activity (GO:0008502)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(19)|ovary(1)|prostate(2)|urinary_tract(1)	33		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)			Agomelatine(DB06594)|Melatonin(DB01065)|Ramelteon(DB00980)	GCCAAGCCAGAGAGCAGGCTG	0.567																																					p.E237G		Atlas-SNP	.											.	MTNR1B	75	.	0			c.A710G						.						86	73	77					11																	92715099		2201	4298	6499	SO:0001583	missense	4544	exon2			AGCCAGAGAGCAG	AB033598	CCDS8290.1	11q21-q22	2012-08-08			ENSG00000134640	ENSG00000134640		"GPCR / Class A : Melatonin receptors"	7464	protein-coding gene	gene with protein product		600804					Standard	NM_005959		Approved		uc001pdk.1	P49286	OTTHUMG00000167364	ENST00000257068.2:c.710A>G	chr11.hg19:g.92715099A>G	ENSP00000257068:p.Glu237Gly	156.0	0.0		112.0	5.0	NM_005959		Missense_Mutation	SNP	ENST00000257068.2	hg19	CCDS8290.1	.	.	.	.	.	.	.	.	.	.	A	11.74	1.730245	0.30684	.	.	ENSG00000134640	ENST00000257068	T	0.36878	1.23	4.21	1.63	0.23807	GPCR, rhodopsin-like superfamily (1);	0.264094	0.35495	N	0.003179	T	0.28732	0.0712	L	0.46741	1.465	0.21697	N	0.999583	B	0.12013	0.005	B	0.18561	0.022	T	0.20571	-1.0271	10	0.25106	T	0.35	-3.4918	11.1761	0.48601	0.712:0.288:0.0:0.0	.	237	P49286	MTR1B_HUMAN	G	237	ENSP00000257068:E237G	ENSP00000257068:E237G	E	+	2	0	MTNR1B	92354747	1.000000	0.71417	0.056000	0.19401	0.799000	0.45148	5.305000	0.65750	0.744000	0.32741	0.402000	0.26972	GAG	.	.		0.567	MTNR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394323.1			G	92715099	A	G	92715099	3	3	282	1	0	0	0	0	1	0	0	0	9961	304	11	2	716	2	MTNR1B	11	92715099	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	7318012	92715099	42291417	811	41045										
YAP1	10413	hgsc.bcm.edu	37	chr11	102094405	102094405	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggagcaggatggtgggactcAaaatccagtgtcttctcccg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:102094405delA	ENST00000282441.5	+	7	1473	c.1085delA	c.(1084-1086)caafs	p.Q362fs	YAP1_ENST00000537274.1_Frame_Shift_Del_p.Q350fs|YAP1_ENST00000531439.1_Frame_Shift_Del_p.Q346fs|YAP1_ENST00000526343.1_Frame_Shift_Del_p.Q308fs|YAP1_ENST00000345877.2_Frame_Shift_Del_p.Q312fs|YAP1_ENST00000524575.1_Frame_Shift_Del_p.Q184fs	NM_001130145.2|NM_001282101.1	NP_001123617.1|NP_001269030.1	P46937	YAP1_HUMAN	Yes-associated protein 1	362	Transactivation domain.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|contact inhibition (GO:0060242)|embryonic heart tube morphogenesis (GO:0003143)|gene expression (GO:0010467)|hippo signaling (GO:0035329)|keratinocyte differentiation (GO:0030216)|lateral mesoderm development (GO:0048368)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|notochord development (GO:0030903)|paraxial mesoderm development (GO:0048339)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|positive regulation of organ growth (GO:0046622)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of keratinocyte proliferation (GO:0010837)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of stem cell proliferation (GO:0072091)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)	4	all_cancers(8;0.000575)|all_epithelial(12;0.00564)	Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.00936)	Lung(13;0.245)	BRCA - Breast invasive adenocarcinoma(274;0.0189)		GGTGGGACTCAAAATCCAGTG	0.433																																					p.Q362fs	Colon(50;247 1103 7861 28956)	Atlas-INDEL	.											.	YAP1	45	.	0			c.1084delC						.						105	95	99					11																	102094405		2203	4299	6502	SO:0001589	frameshift_variant	10413	exon7			.		CCDS8314.1, CCDS44716.1, CCDS8314.2, CCDS53699.1, CCDS53700.1, CCDS60944.1, CCDS73373.1, CCDS73374.1	11q13	2010-03-19	2010-03-19		ENSG00000137693	ENSG00000137693			16262	protein-coding gene	gene with protein product		606608	"Yes-associated protein 1, 65kDa"			7782338	Standard	NM_001130145		Approved	YAP65	uc001pgt.3	P46937	OTTHUMG00000167322	ENST00000282441.5:c.1085delA	chr11.hg19:g.102094405delA	ENSP00000282441:p.Gln362fs	247.0	0.0		165.0	11.0	NM_001130145	B4DTY1|B7ZA01|E3WEB5|E3WEB6|E9PRV2|F5H202|K0KQ18|K0KYZ8|K0L195|K0L1G3|Q7Z574|Q8IUY9	Frame_Shift_Del	DEL	ENST00000282441.5	hg19	CCDS44716.1																																																																																			.	.		0.433	YAP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394151.1	NM_006106		-	102094405	A	-	102094405	7	5	282	1	0	1	0	1	0	0	0	0	17481	130	5	0	1123	0	YAP1	11	102094405	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	9379306	102094405	32912111	812	41046										
MMP8	4317	hgsc.bcm.edu	37	chr11	102587087	102587087	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tggtgatagcatcaaatgtcAaactggggtcacagggtttg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:102587087delA	ENST00000236826.3	-	6	946	c.848delT	c.(847-849)ttgfs	p.L283fs		NM_002424.2	NP_002415.1	P22894	MMP8_HUMAN	matrix metallopeptidase 8 (neutrophil collagenase)	283					collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(4)|skin(6)|stomach(1)|urinary_tract(1)	32	all_cancers(8;0.00092)|all_epithelial(12;0.00389)|Lung NSC(15;0.227)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0555)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.189)	BRCA - Breast invasive adenocarcinoma(274;0.0141)	Marimastat(DB00786)	ATCAAATGTCAAACTGGGGTC	0.363																																					p.L283fs		Atlas-INDEL	.											.	MMP8	68	.	0			c.849delG						.						128	133	131					11																	102587087		2203	4299	6502	SO:0001589	frameshift_variant	4317	exon6			.	J05556	CCDS8320.1	11q21-q22	2008-02-05	2005-08-08		ENSG00000118113	ENSG00000118113	3.4.24.34		7175	protein-coding gene	gene with protein product		120355	"matrix metalloproteinase 8 (neutrophil collagenase)"	CLG1			Standard	NM_002424		Approved		uc001phe.2	P22894	OTTHUMG00000167587	ENST00000236826.3:c.848delT	chr11.hg19:g.102587087delA	ENSP00000236826:p.Leu283fs	120.0	0.0		144.0	10.0	NM_002424	Q45F99	Frame_Shift_Del	DEL	ENST00000236826.3	hg19	CCDS8320.1																																																																																			.	.		0.363	MMP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395223.1	NM_002424		-	102587087	A	-	102587087	7	5	282	1	0	1	0	1	0	0	0	0	9677	131	5	0	575	0	MMP8	11	102587087	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	492682	102587087	32419429	813	41047										
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	103090657	103090657	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cttataggatgctagtgagcAaaaaacagaacttgaaagac							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:103090657delA	ENST00000375735.2	+	56	8990	c.8846delA	c.(8845-8847)caafs	p.Q2949fs	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Frame_Shift_Del_p.Q2949fs	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	2949	Stalk. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		GCTAGTGAGCAAAAAACAGAA	0.259																																					p.Q2949fs		Atlas-INDEL	.											.	DYNC2H1	246	.	0			c.8845delC						.						43	41	42					11																	103090657		1788	4046	5834	SO:0001589	frameshift_variant	79659	exon56			.	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.8846delA	chr11.hg19:g.103090657delA	ENSP00000364887:p.Gln2949fs	271.0	0.0		258.0	17.0	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Frame_Shift_Del	DEL	ENST00000375735.2	hg19	CCDS53701.1																																																																																			.	.		0.259	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		-	103090657	A	-	103090657	7	5	282	1	0	1	0	1	0	0	0	0	4848	130	5	0	9068	0	DYNC2H1	11	103090657	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	503570	103090657	31915859	814	41048										
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	103229059	103229059	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtctaatgaactttctcctgTcctcaatctctggaagaaac	6	11	4	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:103229059T>C	ENST00000375735.2	+	83	12272	c.12128T>C	c.(12127-12129)gTc>gCc	p.V4043A	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Missense_Mutation_p.V4050A	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	4043					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		CTTTCTCCTGTCCTCAATCTC	0.388																																					p.V4050A		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.T12149C						.						75	66	68					11																	103229059		1840	4089	5929	SO:0001583	missense	79659	exon84			CTCCTGTCCTCAA	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.12128T>C	chr11.hg19:g.103229059T>C	ENSP00000364887:p.Val4043Ala	139.0	0.0		106.0	5.0	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	hg19	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	T	17.28	3.348564	0.61183	.	.	ENSG00000187240	ENST00000375735;ENST00000398093;ENST00000540621;ENST00000533197	T;T;T	0.52526	2.92;2.92;0.66	5.62	5.62	0.85841	Dynein heavy chain (1);	1.002820	0.08030	N	0.993405	T	0.43523	0.1251	L	0.34521	1.04	0.48511	D	0.999666	B;B	0.26445	0.149;0.123	B;B	0.28553	0.091;0.055	T	0.06534	-1.0821	10	0.32370	T	0.25	.	14.8043	0.69942	0.0:0.0:0.0:1.0	.	4043;4050	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	A	4043;4050;289;30	ENSP00000364887:V4043A;ENSP00000381167:V4050A;ENSP00000436736:V30A	ENSP00000364887:V4043A	V	+	2	0	DYNC2H1	102734269	0.989000	0.36119	0.989000	0.46669	0.998000	0.95712	7.305000	0.78891	2.146000	0.66826	0.459000	0.35465	GTC	.	.		0.388	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		C	103229059	T	C	103229059	3	2	282	1	0	0	0	0	1	0	0	0	4848	1667	58	2	12483	2	DYNC2H1	11	103229059	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	138402	103229059	31777457	815	41049										
RDX	5962	hgsc.bcm.edu	37	chr11	110126047	110126047	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcgattggctttataacaaaTtttttgtcattaaatgaaat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:110126047delT	ENST00000343115.4	-	8	1081	c.762delA	c.(760-762)aaafs	p.K254fs	RDX_ENST00000544551.1_Frame_Shift_Del_p.K118fs|RDX_ENST00000405097.1_Frame_Shift_Del_p.K254fs|RDX_ENST00000528900.1_Intron|RDX_ENST00000530301.1_Intron|RDX_ENST00000528498.1_Frame_Shift_Del_p.K254fs	NM_001260494.1|NM_002906.3	NP_001247423.1|NP_002897.1	P35241	RADI_HUMAN	radixin	254	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin filament capping (GO:0051693)|apical protein localization (GO:0045176)|establishment of endothelial barrier (GO:0061028)|microvillus assembly (GO:0030033)|positive regulation of gene expression (GO:0010628)	apical part of cell (GO:0045177)|cell tip (GO:0051286)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|stereocilium (GO:0032420)|T-tubule (GO:0030315)	poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(2)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	18		all_cancers(61;7.18e-13)|all_epithelial(67;2.61e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.13e-06)|BRCA - Breast invasive adenocarcinoma(274;9.75e-06)|all cancers(92;5.9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0248)		TTATAACAAATTTTTTGTCAT	0.294																																					p.F255fs	Esophageal Squamous(55;25 1062 11040 28755 44273)	Atlas-INDEL	.											.	RDX	59	.	0			c.763delT						.						40	41	40					11																	110126047		2196	4284	6480	SO:0001589	frameshift_variant	5962	exon8			.	BC020751	CCDS8343.1, CCDS58171.1, CCDS58172.1, CCDS58173.1, CCDS58174.1	11q23	2008-03-17				ENSG00000137710			9944	protein-coding gene	gene with protein product		179410	"deafness, autosomal recessive 24"	DFNB24		8486357, 17226784	Standard	NM_001260492		Approved		uc031qdy.1	P35241		ENST00000343115.4:c.762delA	chr11.hg19:g.110126047delT	ENSP00000342830:p.Lys254fs	264.0	0.0		233.0	16.0	NM_001260493	A7YIJ8|A7YIK0|A7YIK3|B7Z9U6|F5H1A7|Q86Y61	Frame_Shift_Del	DEL	ENST00000343115.4	hg19	CCDS8343.1																																																																																			.	.		0.294	RDX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390535.2	NM_002906		-	110126047	T	-	110126047	7	5	282	1	0	1	0	1	0	0	0	0	13213	1490	52	0	1017	0	RDX	11	110126047	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	6896988	110126047	24880469	816	41050										
LAYN	143903	hgsc.bcm.edu	37	chr11	111425961	111425961	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagagctgacaacacctgtaCttccagaagaaacacaggaa	8	11	0	4			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:111425961C>T	ENST00000375615.3	+	6	813	c.628C>T	c.(628-630)Ctt>Ttt	p.L210F	LAYN_ENST00000528924.1_3'UTR|LAYN_ENST00000436913.2_Missense_Mutation_p.L57F|LAYN_ENST00000525126.1_Missense_Mutation_p.L210F|LAYN_ENST00000375614.2_Missense_Mutation_p.L202F|LAYN_ENST00000533265.1_Missense_Mutation_p.L202F	NM_001258390.1	NP_001245319.1	Q6UX15	LAYN_HUMAN	layilin	210						cell surface (GO:0009986)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|ruffle (GO:0001726)	carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(3)|skin(1)	14		all_cancers(61;9.06e-10)|all_epithelial(67;1.34e-05)|Melanoma(852;1.74e-05)|all_hematologic(158;0.000885)|Acute lymphoblastic leukemia(157;0.000966)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Breast(348;0.086)		Epithelial(105;1.5e-06)|BRCA - Breast invasive adenocarcinoma(274;1.63e-06)|all cancers(92;2.45e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0476)	Hyaluronan(DB08818)	AACACCTGTACTTCCAGAAGA	0.408																																					p.L210F	Ovarian(17;551 586 12136 22082 22900)	Atlas-SNP	.											.	LAYN	35	.	0			c.C628T						.						83	78	80					11																	111425961		2201	4297	6498	SO:0001583	missense	143903	exon6			CCTGTACTTCCAG		CCDS31676.1, CCDS58178.1, CCDS58179.1	11q23.1	2006-02-09			ENSG00000204381	ENSG00000204381			29471	protein-coding gene	gene with protein product						15913605	Standard	NM_001258390		Approved	FLJ30977, FLJ31092	uc001plr.2	Q6UX15	OTTHUMG00000166721	ENST00000375615.3:c.628C>T	chr11.hg19:g.111425961C>T	ENSP00000364765:p.Leu210Phe	185.0	0.0		136.0	6.0	NM_001258390	A6NJB0|B4DJU0|Q8TAY8|Q96NC5|Q96NF3	Missense_Mutation	SNP	ENST00000375615.3	hg19	CCDS58178.1	.	.	.	.	.	.	.	.	.	.	C	11.95	1.791993	0.31685	.	.	ENSG00000204381	ENST00000375614;ENST00000375615;ENST00000525126;ENST00000436913;ENST00000533265;ENST00000541011;ENST00000530962	T;T;T;T	0.06449	3.79;3.39;3.3;3.99	4.99	-3.16	0.05217	.	1.775820	0.02629	N	0.104077	T	0.16854	0.0405	M	0.63428	1.95	0.09310	N	0.999998	D;P;P;P;P	0.76494	0.999;0.802;0.883;0.536;0.928	D;B;B;B;P	0.83275	0.996;0.312;0.391;0.154;0.494	T	0.35599	-0.9782	9	.	.	.	0.1172	0.4986	0.00576	0.2968:0.2051:0.1255:0.3726	.	57;202;210;210;202	B4DJU0;E9PMI0;Q6UX15;E9PQU7;Q6UX15-2	.;.;LAYN_HUMAN;.;.	F	202;210;210;57;202;165;58	ENSP00000364764:L202F;ENSP00000364765:L210F;ENSP00000434328:L210F;ENSP00000434972:L202F	.	L	+	1	0	LAYN	110931171	0.014000	0.17966	0.014000	0.15608	0.210000	0.24377	-0.043000	0.12043	-0.429000	0.07329	-0.165000	0.13383	CTT	.	.		0.408	LAYN-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000391187.1	NM_178834		T	111425961	C	T	111425961	3	4	282	1	0	0	0	0	1	0	0	0	8658	565	20	3	622	3	LAYN	11	111425961	Missense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1299914	111425961	23580555	817	41051										
CEP164	22897	hgsc.bcm.edu	37	chr11	117222658	117222658	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	taagaagaagaaaaaaaaaaAggaaaagaaagacaagaagg	10	1	0	6			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:117222658A>G	ENST00000278935.3	+	5	494	c.347A>G	c.(346-348)aAg>aGg	p.K116R		NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	116	Interaction with ATRIP.|Lys-rich.				cilium assembly (GO:0042384)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(7)|large_intestine(12)|lung(18)|ovary(3)|prostate(3)	47	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		aaaaaaaaaaaggaaaagaaa	0.502																																					p.K116R		Atlas-SNP	.											CEP164,caecum,carcinoma,0,1	CEP164	121	.	0			c.A347G						.						33	34	34					11																	117222658		2201	4296	6497	SO:0001583	missense	22897	exon4			AAAAAAAGGAAAA	AB028975	CCDS31683.1	11q23.3	2014-02-20			ENSG00000110274	ENSG00000110274			29182	protein-coding gene	gene with protein product		614848				10470851, 14654843	Standard	NM_014956		Approved	KIAA1052, NPHP15	uc001prc.3	Q9UPV0	OTTHUMG00000167070	ENST00000278935.3:c.347A>G	chr11.hg19:g.117222658A>G	ENSP00000278935:p.Lys116Arg	57.0	0.0		62.0	3.0	NM_001271933	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	Missense_Mutation	SNP	ENST00000278935.3	hg19	CCDS31683.1	.	.	.	.	.	.	.	.	.	.	A	15.14	2.744661	0.49151	.	.	ENSG00000110274	ENST00000533153;ENST00000278935;ENST00000525416;ENST00000545330;ENST00000533570;ENST00000529538	T;T;T;T	0.76060	-0.34;-0.03;-0.29;-0.99	5.95	4.82	0.62117	.	0.243999	0.29172	N	0.012934	T	0.80221	0.4583	M	0.62723	1.935	0.34770	D	0.733632	D;P;B;D	0.56521	0.959;0.482;0.023;0.976	P;B;B;P	0.56960	0.65;0.11;0.01;0.81	D	0.85776	0.1358	10	0.62326	D	0.03	-27.2573	11.2799	0.49188	0.9276:0.0:0.0724:0.0	.	116;70;116;116	E9PI34;B7Z884;Q9UPV0;Q9UPV0-2	.;.;CE164_HUMAN;.	R	70;116;70;70;116;116	ENSP00000436034:K70R;ENSP00000278935:K116R;ENSP00000435759:K70R;ENSP00000431302:K116R	ENSP00000278935:K116R	K	+	2	0	CEP164	116727868	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	8.713000	0.91408	1.068000	0.40764	0.533000	0.62120	AAG	.	.		0.502	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1	NM_014956		G	117222658	A	G	117222658	3	3	282	1	0	0	0	0	1	0	0	0	3251	72	3	2	357	2	CEP164	11	117222658	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	5796697	117222658	17783858	818	41052										
CD3G	917	hgsc.bcm.edu	37	chr11	118220461	118220461	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggcttttctcatttcaggaaAccacttggttaaggtgtatg	10	7	2	0	rs483352927		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:118220461A>G	ENST00000532917.1	+	3	151	c.83A>G	c.(82-84)aAc>aGc	p.N28S	CD3G_ENST00000532903.1_3'UTR|CD3G_ENST00000392883.2_5'UTR	NM_000073.2	NP_000064.1	P09693	CD3G_HUMAN	CD3g molecule, gamma (CD3-TCR complex)	28					cell surface receptor signaling pathway (GO:0007166)|establishment or maintenance of cell polarity (GO:0007163)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)|protein transport (GO:0015031)|regulation of immune response (GO:0050776)|regulation of lymphocyte apoptotic process (GO:0070228)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	alpha-beta T cell receptor complex (GO:0042105)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	protein heterodimerization activity (GO:0046982)|receptor signaling complex scaffold activity (GO:0030159)|T cell receptor binding (GO:0042608)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|kidney(1)|large_intestine(2)|skin(1)	6	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.04e-05)	Muromonab(DB00075)	ATTTCAGGAAACCACTTGGTT	0.403																																					p.N28S		Atlas-SNP	.											.	CD3G	31	.	0			c.A83G						.						77	74	75					11																	118220461		2200	4296	6496	SO:0001583	missense	917	exon3			CAGGAAACCACTT	X60491	CCDS8395.1	11q23	2014-09-17	2006-03-28		ENSG00000160654	ENSG00000160654		"CD molecules"	1675	protein-coding gene	gene with protein product		186740	"CD3g antigen, gamma polypeptide (TiT3 complex)"				Standard	NM_000073		Approved		uc001psu.2	P09693	OTTHUMG00000166971	ENST00000532917.1:c.83A>G	chr11.hg19:g.118220461A>G	ENSP00000431445:p.Asn28Ser	123.0	0.0		116.0	5.0	NM_000073	Q2HIZ6	Missense_Mutation	SNP	ENST00000532917.1	hg19	CCDS8395.1	.	.	.	.	.	.	.	.	.	.	A	3.587	-0.084497	0.07097	.	.	ENSG00000160654	ENST00000532917	T	0.53857	0.6	5.73	-0.901	0.10540	Immunoglobulin-like fold (1);	2.039550	0.01799	N	0.032805	T	0.36936	0.0985	L	0.40543	1.245	0.22562	N	0.998981	B	0.09022	0.002	B	0.06405	0.002	T	0.03403	-1.1040	10	0.09843	T	0.71	.	1.1051	0.01692	0.4722:0.1384:0.243:0.1464	.	28	P09693	CD3G_HUMAN	S	28	ENSP00000431445:N28S	ENSP00000431445:N28S	N	+	2	0	CD3G	117725671	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.061000	0.11693	-0.127000	0.11661	0.455000	0.32223	AAC	.	.		0.403	CD3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392135.1	NM_000073		G	118220461	A	G	118220461	3	3	282	1	0	0	0	0	1	0	0	0	3015	43	2	2	93	2	CD3G	11	118220461	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	997803	118220461	16786055	819	41053										
MLL	4297	hgsc.bcm.edu	37	chr11	118342966	118342966	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gttaggattattccttcttcAaaaaggacagatgcaaccat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:118342966delA	ENST00000389506.5	+	3	1092	c.1092delA	c.(1090-1092)tcafs	p.S364fs	KMT2A_ENST00000354520.4_Frame_Shift_Del_p.S364fs|KMT2A_ENST00000534358.1_Frame_Shift_Del_p.S364fs			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	364					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										TTCCTTCTTCAAAAAGGACAG	0.423																																					p.S364X		Atlas-INDEL	.											.	MLL	548	.	0			c.1091delC						.						65	67	66					11																	118342966		2200	4296	6496	SO:0001589	frameshift_variant	4297	exon3			.	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.1092delA	chr11.hg19:g.118342966delA	ENSP00000374157:p.Ser364fs	346.0	0.0		249.0	15.0	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Frame_Shift_Del	DEL	ENST00000389506.5	hg19	CCDS31686.1																																																																																			.	.		0.423	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		-	118342966	A	-	118342966	7	5	282	1	0	1	0	1	0	0	0	0	9629	117	5	0	1102	0	MLL	11	118342966	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	122505	118342966	16663550	820	41054										
MLL	4297	hgsc.bcm.edu	37	chr11	118377153	118377153	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aagccagccccacctctcctGggggttctccatcctctcca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:118377153delG	ENST00000389506.5	+	27	10537	c.10537delG	c.(10537-10539)gggfs	p.G3514fs	KMT2A_ENST00000354520.4_Frame_Shift_Del_p.G3476fs|KMT2A_ENST00000534358.1_Frame_Shift_Del_p.G3517fs			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	3514					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										CACCTCTCCTGGGGGTTCTCC	0.552																																					p.P3515fs		Atlas-INDEL	.											.	MLL	548	.	0			c.10545delT						.						70	70	70					11																	118377153		2200	4295	6495	SO:0001589	frameshift_variant	4297	exon27			.	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.10537delG	chr11.hg19:g.118377153delG	ENSP00000374157:p.Gly3514fs	131.0	0.0		106.0	10.0	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Frame_Shift_Del	DEL	ENST00000389506.5	hg19	CCDS31686.1																																																																																			.	.		0.552	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		-	118377153	G	-	118377153	7	5	282	1	0	1	0	1	0	0	0	0	9629	1348	47	0	10643	0	MLL	11	118377153	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	34187	118377153	16629363	821	41055										
ARCN1	372	hgsc.bcm.edu	37	chr11	118452086	118452086	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccaaagctcatgaacactggAaaacaacatacgtttgttga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:118452086delA	ENST00000264028.4	+	2	224	c.129delA	c.(127-129)ggafs	p.G43fs	ARCN1_ENST00000392859.3_Intron|ARCN1_ENST00000359415.4_Frame_Shift_Del_p.G84fs|ARCN1_ENST00000534182.2_Frame_Shift_Del_p.G43fs	NM_001655.4	NP_001646.2	P48444	COPD_HUMAN	archain 1	43					adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer maturation (GO:0021691)|COPI coating of Golgi vesicle (GO:0048205)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|pigmentation (GO:0043473)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	clathrin adaptor complex (GO:0030131)|COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(3)|lung(4)|ovary(2)|urinary_tract(1)	13	all_hematologic(175;0.0349)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)		TGAACACTGGAAAACAACATA	0.403																																					p.G43fs		Atlas-INDEL	.											.	ARCN1	33	.	0			c.128delG						.						110	103	106					11																	118452086		2200	4295	6495	SO:0001589	frameshift_variant	372	exon2			.	X81197	CCDS8400.1, CCDS44749.1	11q23.3	2010-04-21	2003-01-29		ENSG00000095139	ENSG00000095139			649	protein-coding gene	gene with protein product		600820	"coatomer protein complex, subunit delta"	COPD		7782067, 8854871	Standard	NM_001655		Approved		uc001ptq.3	P48444	OTTHUMG00000166340	ENST00000264028.4:c.129delA	chr11.hg19:g.118452086delA	ENSP00000264028:p.Gly43fs	260.0	0.0		151.0	10.0	NM_001655	B4E1X2|E9PEU4|Q52M80	Frame_Shift_Del	DEL	ENST00000264028.4	hg19	CCDS8400.1																																																																																			.	.		0.403	ARCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389278.1			-	118452086	A	-	118452086	7	5	282	1	0	1	0	1	0	0	0	0	842	233	9	0	135	0	ARCN1	11	118452086	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	74933	118452086	16554430	822	41056										
PHLDB1	23187	hgsc.bcm.edu	37	chr11	118526376	118526376	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gccattgaggaagtgtactaCgaccacctgcgcagtgcagc	12	12	0	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:118526376C>T	ENST00000361417.2	+	22	4347	c.3936C>T	c.(3934-3936)taC>taT	p.Y1312Y	PHLDB1_ENST00000527898.1_Silent_p.Y363Y|PHLDB1_ENST00000356063.5_Silent_p.Y1265Y|PHLDB1_ENST00000534672.1_3'UTR|PHLDB1_ENST00000524713.1_Silent_p.Y455Y	NM_015157.3	NP_055972.1	Q86UU1	PHLB1_HUMAN	pleckstrin homology-like domain, family B, member 1	1312	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.									breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(10)|liver(3)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(1)	46	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.0735)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)		AAGTGTACTACGACCACCTGC	0.607																																					p.Y1312Y		Atlas-SNP	.											.	PHLDB1	103	.	0			c.C3936T						.						110	93	99					11																	118526376		2200	4295	6495	SO:0001819	synonymous_variant	23187	exon21			GTACTACGACCAC		CCDS8401.1, CCDS44750.1	11q23.3	2013-01-10			ENSG00000019144	ENSG00000019144		"Pleckstrin homology (PH) domain containing"	23697	protein-coding gene	gene with protein product		612834				14532993	Standard	NM_015157		Approved	FLJ00141, LL5a, KIAA0638	uc001pts.3	Q86UU1	OTTHUMG00000166341	ENST00000361417.2:c.3936C>T	chr11.hg19:g.118526376C>T		88.0	0.0		64.0	27.0	NM_001144758	B0YJ63|B0YJ64|O75133|Q4KMF8|Q8TEQ2	Silent	SNP	ENST00000361417.2	hg19	CCDS8401.1																																																																																			.	.		0.607	PHLDB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389279.1	NM_015157		T	118526376	C	T	118526376	2	4	282	1	0	0	0	0	0	0	0	1	11860	547	19	1		1	PHLDB1	11	118526376	Silent	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	74290	118526376	16480140	823	41057										
BCL9L	283149	hgsc.bcm.edu	37	chr11	118779099	118779099	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaaagggggcacccctgcctGggggttcttcagacttgagt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:118779099delG	ENST00000334801.3	-	2	1256	c.292delC	c.(292-294)cagfs	p.Q98fs	BCL9L_ENST00000526143.1_5'UTR|MIR4492_ENST00000581627.1_RNA	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	98					canonical Wnt signaling pathway (GO:0060070)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell morphogenesis (GO:0022604)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|transcription coactivator activity (GO:0003713)			NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		ACCCCTGCCTGGGGGTTCTTC	0.642																																					p.Q98fs		Atlas-INDEL	.											.	BCL9L	254	.	0			c.293delA						.						75	72	73					11																	118779099		2200	4295	6495	SO:0001589	frameshift_variant	283149	exon2			.	AB094091	CCDS8403.1	11q23.3	2012-06-06				ENSG00000186174			23688	protein-coding gene	gene with protein product		609004				12964048	Standard	NM_182557		Approved	DLNB11	uc001pug.3	Q86UU0		ENST00000334801.3:c.292delC	chr11.hg19:g.118779099delG	ENSP00000335320:p.Gln98fs	276.0	0.0		172.0	11.0	NM_182557	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Frame_Shift_Del	DEL	ENST00000334801.3	hg19	CCDS8403.1																																																																																			.	.		0.642	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557		-	118779099	G	-	118779099	7	5	282	1	0	1	0	1	0	0	0	0	1382	1357	47	0	4235	0	BCL9L	11	118779099	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	252723	118779099	16227417	824	41058										
TRAPPC4	51399	hgsc.bcm.edu	37	chr11	118889616	118889616	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	actttcagttatccgctggaTctgctgctcaagctacacga	8	12	3	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:118889616T>C	ENST00000533632.1	+	1	475	c.111T>C	c.(109-111)gaT>gaC	p.D37D	TRAPPC4_ENST00000528230.1_Silent_p.D37D|TRAPPC4_ENST00000434101.2_Silent_p.D37D|RPS25_ENST00000528547.1_5'Flank|MIR3656_ENST00000577421.1_RNA|TRAPPC4_ENST00000525303.1_Silent_p.D37D|RPS25_ENST00000527673.1_5'Flank|TRAPPC4_ENST00000533058.1_Silent_p.D37D|TRAPPC4_ENST00000359005.4_Silent_p.D37D	NM_016146.4	NP_057230.1	Q9Y296	TPPC4_HUMAN	trafficking protein particle complex 4	37					dendrite development (GO:0016358)|ER to Golgi vesicle-mediated transport (GO:0006888)|extracellular matrix organization (GO:0030198)	cis-Golgi network (GO:0005801)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi stack (GO:0005795)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)|TRAPP complex (GO:0030008)				NS(1)|endometrium(1)|large_intestine(2)|lung(1)	5	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_neural(223;0.224)|all_hematologic(192;0.243)		BRCA - Breast invasive adenocarcinoma(274;7.58e-05)		ATCCGCTGGATCTGCTGCTCA	0.592																																					p.D37D		Atlas-SNP	.											.	TRAPPC4	8	.	0			c.T111C						.						100	95	97					11																	118889616		2200	4295	6495	SO:0001819	synonymous_variant	51399	exon1			GCTGGATCTGCTG	AF078862	CCDS8407.1	11q23.3	2011-10-10				ENSG00000196655		"Trafficking protein particle complex"	19943	protein-coding gene	gene with protein product		610971				10810093	Standard	NM_016146		Approved	TRS23, SBDN, PTD009	uc010ryo.2	Q9Y296		ENST00000533632.1:c.111T>C	chr11.hg19:g.118889616T>C		119.0	0.0		74.0	4.0	NM_016146	A8K3A5|B4DME1	Silent	SNP	ENST00000533632.1	hg19	CCDS8407.1																																																																																			.	.		0.592	TRAPPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389332.1	NM_016146		C	118889616	T	C	118889616	2	2	282	1	0	0	0	0	0	0	0	1	16476	1432	50	2		2	TRAPPC4	11	118889616	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	110517	118889616	16116900	825	41059										
OR10S1	219873	hgsc.bcm.edu	37	chr11	123847962	123847962	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttctgttcatggccactgggTagtgcaggggttgacagata	14	7	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:123847962T>C	ENST00000531945.1	-	1	526	c.437A>G	c.(436-438)tAc>tGc	p.Y146C		NM_001004474.1	NP_001004474.1	Q8NGN2	O10S1_HUMAN	olfactory receptor, family 10, subfamily S, member 1	146						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	36		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		GGCCACTGGGTAGTGCAGGGG	0.547																																					p.Y146C		Atlas-SNP	.											.	OR10S1	78	.	0			c.A437G						.						98	86	90					11																	123847962		2202	4299	6501	SO:0001583	missense	219873	exon1			ACTGGGTAGTGCA	BK004509	CCDS31701.1	11q24.1	2012-08-09			ENSG00000196248	ENSG00000196248		"GPCR / Class A : Olfactory receptors"	14807	protein-coding gene	gene with protein product							Standard	NM_001004474		Approved		uc001pzm.1	Q8NGN2	OTTHUMG00000165963	ENST00000531945.1:c.437A>G	chr11.hg19:g.123847962T>C	ENSP00000431914:p.Tyr146Cys	147.0	0.0		90.0	4.0	NM_001004474	B9EH43|Q6IEV3|Q96R78	Missense_Mutation	SNP	ENST00000531945.1	hg19	CCDS31701.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.956951	0.73902	.	.	ENSG00000196248	ENST00000531945	T	0.33865	1.39	4.74	4.74	0.60224	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38005	U	0.001846	T	0.69133	0.3077	H	0.94542	3.55	0.42479	D	0.992853	D	0.89917	1.0	D	0.72625	0.978	T	0.79652	-0.1714	10	0.87932	D	0	-10.7432	14.1974	0.65679	0.0:0.0:0.0:1.0	.	146	Q8NGN2	O10S1_HUMAN	C	146	ENSP00000431914:Y146C	ENSP00000431914:Y146C	Y	-	2	0	OR10S1	123353172	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	7.513000	0.81739	2.019000	0.59389	0.467000	0.42956	TAC	.	.		0.547	OR10S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387265.2	NM_001004474		C	123847962	T	C	123847962	3	2	282	1	0	0	0	0	1	0	0	0	10927	1638	57	2	562	2	OR10S1	11	123847962	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	4958346	123847962	11158554	826	41060										
OR10G9	219870	hgsc.bcm.edu	37	chr11	123894415	123894415	+	Silent	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cggatccacacctcagagggGaggcacagagcctttcagac	12	13	2	3	rs150463109	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:123894415G>C	ENST00000375024.1	+	1	696	c.696G>C	c.(694-696)ggG>ggC	p.G232G		NM_001001953.1	NP_001001953.1	Q8NGN4	O10G9_HUMAN	olfactory receptor, family 10, subfamily G, member 9	232						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(33)|prostate(2)|skin(4)|stomach(8)|urinary_tract(1)	61		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		CCTCAGAGGGGAGGCACAGAG	0.542																																					p.G232G		Atlas-SNP	.											.	OR10G9	80	.	0			c.G696C						.						166	144	152					11																	123894415		2201	4299	6500	SO:0001819	synonymous_variant	219870	exon1			AGAGGGGAGGCAC	AB065756	CCDS31703.1	11q24.1	2012-08-09			ENSG00000236981	ENSG00000236981		"GPCR / Class A : Olfactory receptors"	15129	protein-coding gene	gene with protein product				OR10G10P			Standard	NM_001001953		Approved		uc010sad.2	Q8NGN4	OTTHUMG00000165967	ENST00000375024.1:c.696G>C	chr11.hg19:g.123894415G>C		441.0	0.0		376.0	173.0	NM_001001953		Silent	SNP	ENST00000375024.1	hg19	CCDS31703.1																																																																																			.	G|0.997;T|0.003		0.542	OR10G9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387269.1	NM_001001953		C	123894415	G	C	123894415	2	2	282	1	0	0	0	0	0	0	0	1	10913	1161	41	4		4	OR10G9	11	123894415	Silent	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	46453	123894415	11112101	827	41061										
HYLS1	219844	hgsc.bcm.edu	37	chr11	125769979	125769979	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcatagaaaggaattacgctGgggtgtccgagagcagatgc					rs372527418		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:125769979delG	ENST00000425380.2	+	3	1497	c.716delG	c.(715-717)tggfs	p.W239fs	PUS3_ENST00000227474.3_Intron|HYLS1_ENST00000526028.1_Frame_Shift_Del_p.W239fs|HYLS1_ENST00000356438.3_Frame_Shift_Del_p.W239fs	NM_001134793.1	NP_001128265.1	Q96M11	HYLS1_HUMAN	hydrolethalus syndrome 1	239						centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|large_intestine(3)|skin(3)|upper_aerodigestive_tract(1)	9	all_hematologic(175;0.177)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.131)|all_lung(97;0.139)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0446)		GAATTACGCTGGGGTGTCCGA	0.473																																					p.W239fs	Esophageal Squamous(172;2590 2636 8884 10471)	Atlas-INDEL	.											.	HYLS1	25	.	0			c.715delT						.						84	76	78					11																	125769979		2201	4299	6500	SO:0001589	frameshift_variant	219844	exon3			.	AK057477	CCDS8467.1	11q24	2014-06-18				ENSG00000198331			26558	protein-coding gene	gene with protein product		610693				15843405	Standard	NM_145014		Approved	FLJ32915	uc009zbv.3	Q96M11		ENST00000425380.2:c.716delG	chr11.hg19:g.125769979delG	ENSP00000414884:p.Trp239fs	181.0	0.0		128.0	10.0	NM_001134793	B3KXI8|Q96BX9	Frame_Shift_Del	DEL	ENST00000425380.2	hg19	CCDS8467.1																																																																																			.	.		0.473	HYLS1-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386733.1	NM_145014		-	125769979	G	-	125769979	7	5	282	1	0	1	0	1	0	0	0	0	7478	1357	47	0	718	0	HYLS1	11	125769979	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1875564	125769979	9236537	828	41062										
FAM118B	79607	hgsc.bcm.edu	37	chr11	126120425	126120425	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccagtaatgttcgatccacaTttttcaaggactgtttatat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:126120425delT	ENST00000533050.1	+	5	857	c.364delT	c.(364-366)tttfs	p.F123fs	FAM118B_ENST00000525728.1_3'UTR|FAM118B_ENST00000360194.4_Frame_Shift_Del_p.F123fs|FAM118B_ENST00000529731.1_Intron	NM_024556.3	NP_078832.1	Q9BPY3	F118B_HUMAN	family with sequence similarity 118, member B	123										breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(1)	13	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00948)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0784)		TCGATCCACATTTTTCAAGGA	0.378																																					p.T121fs		Atlas-INDEL	.											.	FAM118B	29	.	0			c.363delA						.						90	90	90					11																	126120425		2201	4299	6500	SO:0001589	frameshift_variant	79607	exon5			.	BC001340	CCDS8470.1	11q24.2	2014-03-13				ENSG00000197798			26110	protein-coding gene	gene with protein product						24569877	Standard	NM_024556		Approved	FLJ21103	uc001qdf.3	Q9BPY3		ENST00000533050.1:c.364delT	chr11.hg19:g.126120425delT	ENSP00000433343:p.Phe123fs	220.0	0.0		160.0	10.0	NM_024556	Q9H7B0	Frame_Shift_Del	DEL	ENST00000533050.1	hg19	CCDS8470.1																																																																																			.	.		0.378	FAM118B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386346.1	NM_024556		-	126120425	T	-	126120425	7	5	282	1	0	1	0	1	0	0	0	0	5417	1493	52	0	374	0	FAM118B	11	126120425	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	350446	126120425	8886091	829	41063										
WNK1	65125	hgsc.bcm.edu	37	chr12	987482	987482	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	actgcacagccagtgagtcaGcctcaagctccacaagtctt					rs1012729	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:987482delG	ENST00000315939.6	+	10	2971	c.2328delG	c.(2326-2328)cagfs	p.Q776fs	WNK1_ENST00000537687.1_Frame_Shift_Del_p.Q1189fs|WNK1_ENST00000535572.1_Frame_Shift_Del_p.Q775fs|WNK1_ENST00000530271.2_Frame_Shift_Del_p.Q1274fs|WNK1_ENST00000340908.4_Frame_Shift_Del_p.Q369fs	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	776					intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			CAGTGAGTCAGCCTCAAGCTC	0.443																																					p.Q1274fs	Colon(19;451 567 6672 12618 28860)	Atlas-INDEL	.											.	WNK1	403	.	0			c.3821delA						.						95	86	89					12																	987482		2203	4300	6503	SO:0001589	frameshift_variant	65125	exon12			.	AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 167"	605232	"protein kinase, lysine deficient 1", "hereditary sensory neuropathy, type II"	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.2328delG	chr12.hg19:g.987482delG	ENSP00000313059:p.Gln776fs	256.0	0.0		216.0	13.0	NM_213655	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Frame_Shift_Del	DEL	ENST00000315939.6	hg19	CCDS8506.1																																																																																			.	.		0.443	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979		-	987482	G	-	987482	7	5	282	1	0	1	0	1	0	0	0	0	17392	962	34	0	3868	0	WNK1	12	987482	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10		987482	132864413	830	41064										
WNK1	65125	hgsc.bcm.edu	37	chr12	989892	989892	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcatttctgtcacagggcttCccacctcgactgccaccaca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:989892delC	ENST00000315939.6	+	12	3481	c.2838delC	c.(2836-2838)ttcfs	p.F946fs	WNK1_ENST00000537687.1_Frame_Shift_Del_p.F1206fs|WNK1_ENST00000535572.1_Intron|WNK1_ENST00000530271.2_Frame_Shift_Del_p.F1444fs|WNK1_ENST00000340908.4_Frame_Shift_Del_p.F539fs	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	946					intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			CACAGGGCTTCCCACCTCGAC	0.463																																					p.F1206fs	Colon(19;451 567 6672 12618 28860)	Atlas-INDEL	.											.	WNK1	403	.	0			c.3617delT						.						297	317	310					12																	989892		2203	4300	6503	SO:0001589	frameshift_variant	65125	exon12			.	AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 167"	605232	"protein kinase, lysine deficient 1", "hereditary sensory neuropathy, type II"	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.2838delC	chr12.hg19:g.989892delC	ENSP00000313059:p.Phe946fs	317.0	0.0		220.0	14.0	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Frame_Shift_Del	DEL	ENST00000315939.6	hg19	CCDS8506.1																																																																																			.	.		0.463	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979		-	989892	C	-	989892	7	5	282	1	0	1	0	1	0	0	0	0	17392	854	30	0	4386	0	WNK1	12	989892	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	2410	989892	132862003	831	41065										
FKBP4	2288	hgsc.bcm.edu	37	chr12	2907011	2907011	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caggcagtcctccaaagattCcccccaatgccacgcttgta							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:2907011delC	ENST00000001008.4	+	3	554	c.367delC	c.(367-369)cccfs	p.P124fs	RP4-816N1.7_ENST00000547042.1_RNA|RP4-816N1.6_ENST00000547834.1_RNA	NM_002014.3	NP_002005.1	Q02790	FKBP4_HUMAN	FK506 binding protein 4, 59kDa	124	PPIase FKBP-type 1. {ECO:0000255|PROSITE- ProRule:PRU00277}.				androgen receptor signaling pathway (GO:0030521)|chaperone-mediated protein folding (GO:0061077)|copper ion transport (GO:0006825)|embryo implantation (GO:0007566)|male sex differentiation (GO:0046661)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)|negative regulation of neuron projection development (GO:0010977)|prostate gland development (GO:0030850)|protein complex localization (GO:0031503)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)|steroid hormone receptor complex assembly (GO:0006463)	axonal growth cone (GO:0044295)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|FK506 binding (GO:0005528)|GTP binding (GO:0005525)|heat shock protein binding (GO:0031072)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(1)	14			OV - Ovarian serous cystadenocarcinoma(31;0.00105)			TCCAAAGATTCCCCCCAATGC	0.552																																					p.I122fs		Atlas-INDEL	.											.	FKBP4	29	.	0			c.366delT						.						161	136	145					12																	2907011		2203	4300	6503	SO:0001589	frameshift_variant	2288	exon3			.	M88279	CCDS8512.1	12p13.33	2013-01-10	2002-08-29		ENSG00000004478	ENSG00000004478		"Tetratricopeptide (TTC) repeat domain containing"	3720	protein-coding gene	gene with protein product		600611	"FK506-binding protein 4 (59kD)"			1279700	Standard	NM_002014		Approved	FKBP59, FKBP52	uc001qkz.3	Q02790	OTTHUMG00000090429	ENST00000001008.4:c.367delC	chr12.hg19:g.2907011delC	ENSP00000001008:p.Pro124fs	213.0	0.0		187.0	13.0	NM_002014	D3DUQ1|Q9UCP1|Q9UCV7	Frame_Shift_Del	DEL	ENST00000001008.4	hg19	CCDS8512.1																																																																																			.	.		0.552	FKBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206861.1			-	2907011	C	-	2907011	7	5	282	1	0	1	0	1	0	0	0	0	5918	855	30	0	377	0	FKBP4	12	2907011	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1917119	2907011	130944884	832	41066										
TEAD4	7004	hgsc.bcm.edu	37	chr12	3126664	3126664	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagtagcatggccctcgcccGgggccccggccgcccagcag	14	19	0	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:3126664G>A	ENST00000397122.2	+	4	353	c.68G>A	c.(67-69)cGg>cAg	p.R23Q	TEAD4_ENST00000358409.2_Intron|TEAD4_ENST00000359864.2_Missense_Mutation_p.R152Q	NM_201443.2	NP_958851.1	Q15561	TEAD4_HUMAN	TEA domain family member 4	152					gene expression (GO:0010467)|hippo signaling (GO:0035329)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10	Ovarian(42;0.211)		OV - Ovarian serous cystadenocarcinoma(31;0.000563)|COAD - Colon adenocarcinoma(12;0.0831)			GCCCTcgcccggggccccggc	0.667																																					p.R152Q		Atlas-SNP	.											.	TEAD4	45	.	0			c.G455A						.						30	29	30					12																	3126664		2203	4300	6503	SO:0001583	missense	7004	exon6			TCGCCCGGGGCCC	X94438	CCDS31729.1, CCDS31730.1, CCDS41737.1	12p13.3-p13.2	2008-05-14				ENSG00000197905			11717	protein-coding gene	gene with protein product		601714		TCF13L1		9889009, 8921372	Standard	NM_003213		Approved	TEF-3, TEFR-1, EFTR-2, RTEF-1	uc010sej.2	Q15561		ENST00000397122.2:c.68G>A	chr12.hg19:g.3126664G>A	ENSP00000380311:p.Arg23Gln	304.0	0.0		197.0	78.0	NM_003213	H0Y308|Q6MZR9|Q8NEV5|Q92883|Q96BK2	Missense_Mutation	SNP	ENST00000397122.2	hg19	CCDS41737.1	.	.	.	.	.	.	.	.	.	.	G	14.17	2.455934	0.43634	.	.	ENSG00000197905	ENST00000359864;ENST00000543035;ENST00000397122	T;T;T	0.54479	0.57;1.61;0.58	5.95	3.18	0.36537	.	0.133068	0.49305	N	0.000157	T	0.34542	0.0901	N	0.19112	0.55	0.23101	N	0.998292	.	.	.	.	.	.	T	0.20438	-1.0275	8	0.16420	T	0.52	-17.3336	8.9551	0.35812	0.2792:0.0:0.7208:0.0	.	.	.	.	Q	152;152;23	ENSP00000352926:R152Q;ENSP00000444528:R152Q;ENSP00000380311:R23Q	ENSP00000352926:R152Q	R	+	2	0	TEAD4	2996925	1.000000	0.71417	1.000000	0.80357	0.208000	0.24298	1.921000	0.40035	0.433000	0.26313	-0.793000	0.03317	CGG	.	.		0.667	TEAD4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398477.1	NM_003213		A	3126664	G	A	3126664	3	1	282	1	0	0	0	0	1	0	0	0	15756	1116	39	1	469	1	TEAD4	12	3126664	Missense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	219653	3126664	130725231	833	41067										
C12orf5	57103	hgsc.bcm.edu	37	chr12	4459033	4459033	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aattttgcaaagatatgacgGtaaagtatgactcaagactt	8	5	1	4			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:4459033G>A	ENST00000179259.4	+	4	308	c.241G>A	c.(241-243)Gta>Ata	p.V81I	C12orf5_ENST00000537251.1_3'UTR	NM_020375.2	NP_065108.1	Q9NQ88	TIGAR_HUMAN	chromosome 12 open reading frame 5	81					intestinal epithelial cell development (GO:0060576)|negative regulation of macromitophagy (GO:1901525)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|response to gamma radiation (GO:0010332)|response to xenobiotic stimulus (GO:0009410)	intracellular (GO:0005622)	fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)			endometrium(1)|large_intestine(1)|lung(5)|skin(3)	10			all cancers(3;1.15e-07)|Colorectal(7;0.00165)|OV - Ovarian serous cystadenocarcinoma(31;0.00596)|COAD - Colon adenocarcinoma(12;0.0229)|GBM - Glioblastoma multiforme(3;0.0266)|STAD - Stomach adenocarcinoma(119;0.206)			AGATATGACGGTAAAGTATGA	0.353																																					p.V81I	Colon(1;100 192 35375 49454 52532)	Atlas-SNP	.											C12orf5,NS,adenoma,0,1	C12orf5	28	.	0			c.G241A						.						97	100	99					12																	4459033		2203	4300	6503	SO:0001583	missense	57103	exon4			ATGACGGTAAAGT	AJ272206	CCDS8525.1	12p13.32	2014-05-29	2009-11-24	2009-11-24	ENSG00000078237	ENSG00000078237	3.1.3.46		1185	protein-coding gene	gene with protein product	"TP53-induced glycolysis and apoptosis regulator"	610775				16140933, 16839880, 18945750, 19713938	Standard	NM_020375		Approved	TIGAR	uc001qmp.3	Q9NQ88		ENST00000179259.4:c.241G>A	chr12.hg19:g.4459033G>A	ENSP00000179259:p.Val81Ile	199.0	0.0		159.0	0.0	NM_020375	B2R840	Missense_Mutation	SNP	ENST00000179259.4	hg19	CCDS8525.1	.	.	.	.	.	.	.	.	.	.	G	2.436	-0.329820	0.05314	.	.	ENSG00000078237	ENST00000179259	T	0.71103	-0.54	4.58	4.58	0.56647	Histidine phosphatase superfamily, clade-1 (2);	0.167136	0.51477	D	0.000092	T	0.47284	0.1437	N	0.10645	0.015	0.09310	N	0.999994	B	0.21520	0.057	B	0.23275	0.045	T	0.27020	-1.0086	10	0.30078	T	0.28	-22.6516	8.4664	0.32958	0.1791:0.0:0.8209:0.0	.	81	Q9NQ88	TIGAR_HUMAN	I	81	ENSP00000179259:V81I	ENSP00000179259:V81I	V	+	1	0	C12orf5	4329294	1.000000	0.71417	0.857000	0.33713	0.340000	0.28889	2.645000	0.46621	2.536000	0.85505	0.655000	0.94253	GTA	.	.		0.353	C12orf5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398290.1	NM_020375		A	4459033	G	A	4459033	3	1	282	1	0	0	0	0	1	0	0	0	1696	1261	44	3	255	3	C12orf5	12	4459033	Missense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1332369	4459033	129392862	834	41068										
KCNA5	3741	hgsc.bcm.edu	37	chr12	5154463	5154463	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagagcagcagccagggggtGgaggaggcggccagaatggg	21	8	0	2	rs76708779	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:5154463G>C	ENST00000252321.3	+	1	1379	c.1150G>C	c.(1150-1152)Gga>Cga	p.G384R		NM_002234.3	NP_002225.2	P22460	KCNA5_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 5	384	Poly-Gly.				atrial cardiac muscle cell action potential (GO:0086014)|membrane hyperpolarization (GO:0060081)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of potassium ion transport (GO:0043267)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of myoblast proliferation (GO:2000288)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transport (GO:0043266)|regulation of vasoconstriction (GO:0019229)|response to hypoxia (GO:0001666)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|intracellular canaliculus (GO:0046691)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|potassium channel inhibitor activity (GO:0019870)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization (GO:0086089)			NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(21)|ovary(5)|prostate(2)|upper_aerodigestive_tract(2)	52					Dalfampridine(DB06637)	GCCAGGGGGTGGAGGAGGCGG	0.622																																					p.G384R		Atlas-SNP	.											KCNA5,NS,carcinoma,0,1	KCNA5	138	.	0			c.G1150C						.						56	52	53					12																	5154463		2203	4300	6503	SO:0001583	missense	3741	exon1			GGGGGTGGAGGAG	M83254	CCDS8536.1	12p13	2012-07-05				ENSG00000130037		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6224	protein-coding gene	gene with protein product		176267				16382104	Standard	NM_002234		Approved	Kv1.5, HK2, HPCN1	uc001qni.4	P22460		ENST00000252321.3:c.1150G>C	chr12.hg19:g.5154463G>C	ENSP00000252321:p.Gly384Arg	273.0	1.0		222.0	0.0	NM_002234	Q4KKT8|Q4VAJ1|Q4VAJ2|Q9UDA4	Missense_Mutation	SNP	ENST00000252321.3	hg19	CCDS8536.1	.	.	.	.	.	.	.	.	.	.	G	9.013	0.982930	0.18889	.	.	ENSG00000130037	ENST00000252321	D	0.97710	-4.5	4.62	4.62	0.57501	Ion transport (1);	2.171590	0.03002	U	0.148348	D	0.96156	0.8747	N	0.05050	-0.12	0.09310	N	0.999996	D	0.54964	0.969	P	0.59288	0.855	D	0.91348	0.5102	10	0.45353	T	0.12	.	8.6668	0.34125	0.1726:0.0:0.8274:0.0	.	384	P22460	KCNA5_HUMAN	R	384	ENSP00000252321:G384R	ENSP00000252321:G384R	G	+	1	0	KCNA5	5024724	0.030000	0.19436	0.120000	0.21714	0.199000	0.23934	1.527000	0.35975	2.390000	0.81377	0.561000	0.74099	GGA	.	G|0.995;A|0.005		0.622	KCNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398925.2	NM_002234		C	5154463	G	C	5154463	3	2	282	1	0	0	0	0	1	0	0	0	8015	1349	47	4	1152	4	KCNA5	12	5154463	Missense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	695430	5154463	128697432	835	41069										
GPR162	27239	hgsc.bcm.edu	37	chr12	6936291	6936291	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gggagacgctgctccctgacGgggggtgaagaaagtgcaag					rs139203738	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:6936291delG	ENST00000311268.3	+	5	2476	c.1689delG	c.(1687-1689)acgfs	p.T563fs	LEPREL2_ENST00000251761.8_RNA|LEPREL2_ENST00000606935.1_RNA|GPR162_ENST00000382315.3_Frame_Shift_Del_p.T259fs|GPR162_ENST00000428545.2_Frame_Shift_Del_p.T279fs|LEPREL2_ENST00000396725.2_RNA	NM_019858.1	NP_062832.1	Q16538	GP162_HUMAN	G protein-coupled receptor 162	563						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(2)|skin(1)	18						GCTCCCTGACGGGGGGTGAAG	0.642																																					p.T563fs		Atlas-INDEL	.											.	GPR162	55	.	0			c.1688delC						.						31	38	35					12																	6936291		2163	4204	6367	SO:0001589	frameshift_variant	27239	exon5			.	U47928, U47929, U47924, U47925	CCDS8563.1, CCDS44819.1	12p13	2012-08-21						"GPCR / Class A : Orphans"	16693	protein-coding gene	gene with protein product						15777626	Standard	NM_014449		Approved	A-2, GRCA	uc001qqw.1	Q16538		ENST00000311268.3:c.1689delG	chr12.hg19:g.6936291delG	ENSP00000311528:p.Thr563fs	146.0	0.0		153.0	10.0	NM_019858	Q16664|Q59EH5|Q66K56	Frame_Shift_Del	DEL	ENST00000311268.3	hg19	CCDS8563.1																																																																																			.	.		0.642	GPR162-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399478.1	NM_019858		-	6936291	G	-	6936291	7	5	282	1	0	1	0	1	0	0	0	0	6674	1103	39	0	1722	0	GPR162	12	6936291	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1781828	6936291	126915604	836	41070										
CLSTN3	9746	hgsc.bcm.edu	37	chr12	7301639	7301639	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggtcgtccttcagcctgacgCcccccagatcctgctgagtg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:7301639delC	ENST00000266546.6	+	13	2369	c.1919delC	c.(1918-1920)gccfs	p.A640fs	CLSTN3_ENST00000537408.1_Frame_Shift_Del_p.A652fs	NM_014718.3	NP_055533.2	Q9BQT9	CSTN3_HUMAN	calsyntenin 3	640					homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(7)|prostate(1)|skin(1)	33						CAGCCTGACGCCCCCCAGATC	0.567																																					p.A640fs		Atlas-INDEL	.											CLSTN3,NS,adenocarcinoma,0,1	CLSTN3	84	.	0			c.1918delG						.						89	70	76					12																	7301639		2203	4300	6503	SO:0001589	frameshift_variant	9746	exon13			.	AB018269	CCDS8575.1	12p13.31	2011-07-01			ENSG00000139182	ENSG00000139182		"Cadherins / Cadherin-related"	18371	protein-coding gene	gene with protein product	"cadherin-related family member 14"	611324				12498782	Standard	NM_014718		Approved	CSTN3, KIAA0726, CDHR14	uc001qsr.3	Q9BQT9	OTTHUMG00000168167	ENST00000266546.6:c.1919delC	chr12.hg19:g.7301639delC	ENSP00000266546:p.Ala640fs	163.0	0.0		141.0	11.0	NM_014718	D3DUT6|O94831|Q2T9J5|Q5UE57	Frame_Shift_Del	DEL	ENST00000266546.6	hg19	CCDS8575.1																																																																																			.	.		0.567	CLSTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398560.2	NM_014718		-	7301639	C	-	7301639	7	5	282	1	0	1	0	1	0	0	0	0	3565	739	26	0	1969	0	CLSTN3	12	7301639	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	365348	7301639	126550256	837	41071										
DPPA3	359787	hgsc.bcm.edu	37	chr12	7864219	7864219	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cccagggtctccacaaatgcTcaccgaagaaaattcccggg	9	14	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:7864219T>C	ENST00000345088.2	+	1	170	c.53T>C	c.(52-54)cTc>cCc	p.L18P		NM_199286.2	NP_954980.1	Q6W0C5	DPPA3_HUMAN	developmental pluripotency associated 3	18					chromatin modification (GO:0016568)|embryonic cleavage (GO:0040016)|negative regulation of DNA demethylation (GO:1901536)|protection of DNA demethylation of female pronucleus (GO:0044726)|regulation of genetic imprinting (GO:2000653)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|nucleus (GO:0005634)	methylated histone binding (GO:0035064)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(2)	8				Kidney(36;0.0887)		CCACAAATGCTCACCGAAGAA	0.493																																					p.L18P		Atlas-SNP	.											.	DPPA3	26	.	0			c.T53C						.						66	57	60					12																	7864219		2203	4300	6503	SO:0001583	missense	359787	exon1			AAATGCTCACCGA	AY317075	CCDS8582.1	12p13.31	2012-10-02			ENSG00000187569	ENSG00000187569			19199	protein-coding gene	gene with protein product		608408					Standard	NM_199286		Approved	Stella	uc001qtf.3	Q6W0C5	OTTHUMG00000168434	ENST00000345088.2:c.53T>C	chr12.hg19:g.7864219T>C	ENSP00000339250:p.Leu18Pro	122.0	0.0		107.0	5.0	NM_199286	Q0P5U3|Q6JZS6	Missense_Mutation	SNP	ENST00000345088.2	hg19	CCDS8582.1	.	.	.	.	.	.	.	.	.	.	T	8.395	0.840553	0.16891	.	.	ENSG00000187569	ENST00000345088	T	0.42900	0.96	2.82	0.816	0.18768	.	.	.	.	.	T	0.21801	0.0525	N	0.14661	0.345	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.17623	-1.0363	9	0.36615	T	0.2	1.5698	4.1081	0.10047	0.0:0.5724:0.0:0.4276	.	18	Q6W0C5	DPPA3_HUMAN	P	18	ENSP00000339250:L18P	ENSP00000339250:L18P	L	+	2	0	DPPA3	7755486	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.148000	0.10219	0.201000	0.20466	0.533000	0.62120	CTC	.	.		0.493	DPPA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399718.1	NM_199286		C	7864219	T	C	7864219	3	2	282	1	0	0	0	0	1	0	0	0	4737	1551	54	2	55	2	DPPA3	12	7864219	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	562580	7864219	125987676	838	41072										
CLEC4A	50856	hgsc.bcm.edu	37	chr12	8289428	8289428	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaagaatctgcttattttgtGgggctctcagatccagaagg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:8289428delG	ENST00000229332.5	+	5	742	c.495delG	c.(493-495)gtgfs	p.V165fs	CLEC4A_ENST00000345999.3_Frame_Shift_Del_p.V93fs|CLEC4A_ENST00000360500.3_Frame_Shift_Del_p.V126fs|CLEC4A_ENST00000352620.3_Frame_Shift_Del_p.V132fs	NM_016184.3|NM_194447.2|NM_194450.2	NP_057268.1|NP_919429.2|NP_919432.1	Q9UMR7	CLC4A_HUMAN	C-type lectin domain family 4, member A	165	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(3)|large_intestine(2)|lung(4)|prostate(1)	11				Kidney(36;0.0915)		CTTATTTTGTGGGGCTCTCAG	0.413																																					p.V165fs		Atlas-INDEL	.											.	CLEC4A	28	.	0			c.494delT						.						97	102	100					12																	8289428		2203	4300	6503	SO:0001589	frameshift_variant	50856	exon5			.	AJ133532	CCDS8590.1, CCDS8591.1, CCDS8592.1, CCDS41745.1	12p13	2005-02-09	2005-02-09	2005-02-09	ENSG00000111729	ENSG00000111729		"C-type lectin domain containing"	13257	protein-coding gene	gene with protein product		605306	"C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 6"	CLECSF6		10438934	Standard	NM_016184		Approved	DCIR, DDB27	uc001qtz.1	Q9UMR7	OTTHUMG00000168571	ENST00000229332.5:c.495delG	chr12.hg19:g.8289428delG	ENSP00000229332:p.Val165fs	274.0	0.0		176.0	11.0	NM_016184	Q17R69|Q8WXW9|Q9H2Z9|Q9NS33|Q9UI34	Frame_Shift_Del	DEL	ENST00000229332.5	hg19	CCDS8590.1																																																																																			.	.		0.413	CLEC4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400257.1	NM_194450		-	8289428	G	-	8289428	7	5	282	1	0	1	0	1	0	0	0	0	3514	1335	47	0	513	0	CLEC4A	12	8289428	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	425209	8289428	125562467	839	41073										
ZNF705A	440077	hgsc.bcm.edu	37	chr12	8330032	8330032	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	catgagagaactcaccttggAaaaaagtgttatgaatgtga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:8330032delA	ENST00000359286.4	+	5	845	c.756delA	c.(754-756)ggafs	p.G252fs	FAM66C_ENST00000541558.1_RNA|FAM66C_ENST00000454799.2_RNA|FAM66C_ENST00000544214.1_RNA|FAM66C_ENST00000456135.2_RNA	NM_001004328.2|NM_001278713.1	NP_001004328.1|NP_001265642.1	Q6ZN79	Z705A_HUMAN	zinc finger protein 705A	252					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|skin(3)|stomach(4)	18				Kidney(36;0.0877)		CTCACCTTGGAAAAAAGTGTT	0.388																																					p.G252fs		Atlas-INDEL	.											.	ZNF705A	32	.	0			c.755delG						.						38	42	41					12																	8330032		2194	4289	6483	SO:0001589	frameshift_variant	440077	exon5			.	AK131339	CCDS31737.1	12p13.31	2014-02-12	2005-09-22		ENSG00000196946	ENSG00000196946		"Zinc fingers, C2H2-type", "-"	32281	protein-coding gene	gene with protein product							Standard	NM_001004328		Approved	FLJ16353	uc001qud.1	Q6ZN79	OTTHUMG00000168635	ENST00000359286.4:c.756delA	chr12.hg19:g.8330032delA	ENSP00000352233:p.Gly252fs	396.0	0.0		275.0	17.0	NM_001004328		Frame_Shift_Del	DEL	ENST00000359286.4	hg19	CCDS31737.1																																																																																			.	.		0.388	ZNF705A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400449.1	NM_001004328		-	8330032	A	-	8330032	7	5	282	1	0	1	0	1	0	0	0	0	18123	233	9	0	774	0	ZNF705A	12	8330032	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	40604	8330032	125521863	840	41074										
TAS2R10	50839	hgsc.bcm.edu	37	chr12	10978230	10978230	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tctgtgttggagtctctcaaTcctgtcacattcgattgcat	8	10	4	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:10978230T>C	ENST00000240619.2	-	1	727	c.639A>G	c.(637-639)ggA>ggG	p.G213G		NM_023921.1	NP_076410.1	Q9NYW0	T2R10_HUMAN	taste receptor, type 2, member 10	213					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			breast(1)|central_nervous_system(1)|large_intestine(7)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17						AGTCTCTCAATCCTGTCACAT	0.363																																					p.G213G		Atlas-SNP	.											.	TAS2R10	44	.	0			c.A639G						.						107	105	106					12																	10978230		2203	4300	6503	SO:0001819	synonymous_variant	50839	exon1			TCTCAATCCTGTC	AF227136	CCDS8634.1	12p13	2012-08-22			ENSG00000121318	ENSG00000121318		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14918	protein-coding gene	gene with protein product		604791				10761934, 10766242	Standard	NM_023921		Approved	T2R10, TRB2	uc001qyy.1	Q9NYW0	OTTHUMG00000168508	ENST00000240619.2:c.639A>G	chr12.hg19:g.10978230T>C		131.0	0.0		114.0	5.0	NM_023921	Q3MIM9|Q6NTD9	Silent	SNP	ENST00000240619.2	hg19	CCDS8634.1																																																																																			.	.		0.363	TAS2R10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399934.1			C	10978230	T	C	10978230	2	2	282	1	0	0	0	0	0	0	0	1	15581	1422	50	2		2	TAS2R10	12	10978230	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2648198	10978230	122873665	841	41075										
GSG1	57613	hgsc.bcm.edu	37	chr12	13237891	13237891	+	IGR	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttctttcagctcctggctggCccctctttgaaatcccttgt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:13237891delC	ENST00000197268.8	+	0	4808				GSG1_ENST00000537302.1_Frame_Shift_Del_p.A281fs|GSG1_ENST00000432710.2_Frame_Shift_Del_p.A322fs|GSG1_ENST00000396310.2_Frame_Shift_Del_p.A278fs|GSG1_ENST00000351606.6_3'UTR|GSG1_ENST00000396302.3_3'UTR|GSG1_ENST00000324458.8_Frame_Shift_Del_p.A345fs|GSG1_ENST00000337630.6_Frame_Shift_Del_p.A309fs|GSG1_ENST00000457134.2_Frame_Shift_Del_p.A258fs	NM_020853.1	NP_065904.1	A2RU67	K1467_HUMAN	KIAA1467							integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|prostate(1)|skin(4)	36		Prostate(47;0.184)		BRCA - Breast invasive adenocarcinoma(232;0.157)		TCCTGGCTGGCCCCTCTTTGA	0.517																																					p.A345fs		Atlas-INDEL	.											.	GSG1	62	.	0			c.1034delC						.						95	104	101					12																	13237891		1280	2295	3575	SO:0001628	intergenic_variant	83445	exon7			.	AB040900	CCDS31750.1	12p13.1	2006-01-23				ENSG00000084444			29288	protein-coding gene	gene with protein product						10819331	Standard	XM_005253450		Approved		uc001rbi.3	A2RU67			chr12.hg19:g.13237891delC		342.0	0.0		209.0	13.0	NM_001080555	Q49AF2|Q5CZ81|Q6ZUV7|Q9P261	Frame_Shift_Del	DEL	ENST00000197268.8	hg19	CCDS31750.1																																																																																			.	.		0.517	KIAA1467-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401007.1	NM_020853		-	13237891	C	-	13237891	6	5	282	0	1	1	0	1	0	0	0	0	6829	739	26	0		0	GSG1	12	13237891	IGR	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	2259661	13237891	120614004	842	41076										
PLBD1	79887	hgsc.bcm.edu	37	chr12	14693810	14693810	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagtcttgtattctttgataTttttccgggtccacttatct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:14693810delT	ENST00000240617.5	-	4	1098	c.446delA	c.(445-447)aatfs	p.N149fs		NM_024829.5	NP_079105.4	Q6P4A8	PLBL1_HUMAN	phospholipase B domain containing 1	149					glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)	hydrolase activity (GO:0016787)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	16						TTCTTTGATATTTTTCCGGGT	0.393																																					p.N149fs		Atlas-INDEL	.											.	PLBD1	36	.	0			c.447delT						.						166	162	163					12																	14693810		2203	4300	6503	SO:0001589	frameshift_variant	79887	exon4			.	BC000909	CCDS31751.1	12p13.1	2013-10-11			ENSG00000121316	ENSG00000121316			26215	protein-coding gene	gene with protein product	"PLB homolog 1 (Dictyostelium)"					15193148, 19019078	Standard	NM_024829		Approved	FLJ22662	uc001rcc.1	Q6P4A8	OTTHUMG00000168821	ENST00000240617.5:c.446delA	chr12.hg19:g.14693810delT	ENSP00000240617:p.Asn149fs	209.0	0.0		165.0	12.0	NM_024829	A8K4E9|Q9BVV3|Q9H625	Frame_Shift_Del	DEL	ENST00000240617.5	hg19	CCDS31751.1																																																																																			.	.		0.393	PLBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401203.1	NM_024829		-	14693810	T	-	14693810	7	5	282	1	0	1	0	1	0	0	0	0	12034	1493	52	0	1247	0	PLBD1	12	14693810	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1455919	14693810	119158085	843	41077										
GUCY2C	2984	hgsc.bcm.edu	37	chr12	14825857	14825857	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caccatggtactgtcaacatCcccccagtcatccaaggtca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:14825857delC	ENST00000261170.3	-	9	1256	c.1120delG	c.(1120-1122)gatfs	p.D374fs	RP11-174G6.1_ENST00000501178.2_RNA	NM_004963.3	NP_004954.2	P25092	GUC2C_HUMAN	guanylate cyclase 2C (heat stable enterotoxin receptor)	374					intracellular signal transduction (GO:0035556)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of cell proliferation (GO:0042127)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|toxic substance binding (GO:0015643)			breast(3)|endometrium(7)|kidney(3)|large_intestine(9)|lung(17)|ovary(4)|skin(7)|urinary_tract(1)	51					Linaclotide(DB08890)	CTGTCAACATCCCCCCAGTCA	0.473																																					p.D374fs		Atlas-INDEL	.											.	GUCY2C	126	.	0			c.1121delA						.						195	163	174					12																	14825857		2203	4300	6503	SO:0001589	frameshift_variant	2984	exon9			.		CCDS8664.1	12p12	2008-08-18			ENSG00000070019	ENSG00000070019			4688	protein-coding gene	gene with protein product		601330		GUC2C		8661067	Standard	NM_004963		Approved	STAR	uc001rcd.3	P25092	OTTHUMG00000168732	ENST00000261170.3:c.1120delG	chr12.hg19:g.14825857delC	ENSP00000261170:p.Asp374fs	246.0	0.0		177.0	11.0	NM_004963	B2RMY6	Frame_Shift_Del	DEL	ENST00000261170.3	hg19	CCDS8664.1																																																																																			.	.		0.473	GUCY2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400835.1			-	14825857	C	-	14825857	7	5	282	1	0	1	0	1	0	0	0	0	6905	855	30	0	2177	0	GUCY2C	12	14825857	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	132047	14825857	119026038	844	41078										
WBP11	51729	hgsc.bcm.edu	37	chr12	14941929	14941929	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttggtgggggtccacgaggaGggggaccaggaggcagacct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:14941929delG	ENST00000261167.2	-	11	1681	c.1448delC	c.(1447-1449)cctfs	p.P484fs		NM_016312.2	NP_057396.1	Q9Y2W2	WBP11_HUMAN	WW domain binding protein 11	484	Pro-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein phosphatase type 1 regulator activity (GO:0008599)|single-stranded DNA binding (GO:0003697)|WW domain binding (GO:0050699)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)	30						TCCACGAGGAGGGGGACCAGG	0.582																																					p.P483fs		Atlas-INDEL	.											.	WBP11	66	.	0			c.1449delT						.						17	20	19					12																	14941929		2203	4299	6502	SO:0001589	frameshift_variant	51729	exon11			.	AB029309	CCDS8666.1	12p12.3	2014-06-13			ENSG00000084463	ENSG00000084463			16461	protein-coding gene	gene with protein product	"splicing factor, PQBP1 and PP1 interacting", "protein phosphatase 1, regulatory subunit 165"					10593949	Standard	NM_016312		Approved	NPWBP, SIPP1, PPP1R165	uc001rci.3	Q9Y2W2	OTTHUMG00000168737	ENST00000261167.2:c.1448delC	chr12.hg19:g.14941929delG	ENSP00000261167:p.Pro484fs	181.0	0.0		151.0	10.0	NM_016312	Q96AY8	Frame_Shift_Del	DEL	ENST00000261167.2	hg19	CCDS8666.1																																																																																			.	.		0.582	WBP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400850.1	NM_016312		-	14941929	G	-	14941929	7	5	282	1	0	1	0	1	0	0	0	0	17273	1000	35	0	485	0	WBP11	12	14941929	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	116072	14941929	118909966	845	41079										
WBP11	51729	hgsc.bcm.edu	37	chr12	14943574	14943574	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccatcagaatgggattcctcTttatgctgcttttgtgattg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:14943574delT	ENST00000261167.2	-	10	1358	c.1125delA	c.(1123-1125)aaafs	p.K375fs		NM_016312.2	NP_057396.1	Q9Y2W2	WBP11_HUMAN	WW domain binding protein 11	375					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein phosphatase type 1 regulator activity (GO:0008599)|single-stranded DNA binding (GO:0003697)|WW domain binding (GO:0050699)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)	30						GGGATTCCTCTTTATGCTGCT	0.498																																					p.E376fs		Atlas-INDEL	.											.	WBP11	66	.	0			c.1126delG						.						172	156	161					12																	14943574		2203	4300	6503	SO:0001589	frameshift_variant	51729	exon10			.	AB029309	CCDS8666.1	12p12.3	2014-06-13			ENSG00000084463	ENSG00000084463			16461	protein-coding gene	gene with protein product	"splicing factor, PQBP1 and PP1 interacting", "protein phosphatase 1, regulatory subunit 165"					10593949	Standard	NM_016312		Approved	NPWBP, SIPP1, PPP1R165	uc001rci.3	Q9Y2W2	OTTHUMG00000168737	ENST00000261167.2:c.1125delA	chr12.hg19:g.14943574delT	ENSP00000261167:p.Lys375fs	246.0	0.0		163.0	10.0	NM_016312	Q96AY8	Frame_Shift_Del	DEL	ENST00000261167.2	hg19	CCDS8666.1																																																																																			.	.		0.498	WBP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400850.1	NM_016312		-	14943574	T	-	14943574	7	5	282	1	0	1	0	1	0	0	0	0	17273	1606	56	0	812	0	WBP11	12	14943574	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1645	14943574	118908321	846	41080										
STRAP	11171	hgsc.bcm.edu	37	chr12	16047053	16047053	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagtgaggataaacagattcTttctgctgatgacaaaactg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:16047053delT	ENST00000419869.2	+	5	789	c.476delT	c.(475-477)cttfs	p.L159fs	STRAP_ENST00000538352.1_Frame_Shift_Del_p.L65fs|STRAP_ENST00000025399.6_Frame_Shift_Del_p.L172fs	NM_007178.3	NP_009109.3	Q9Y3F4	STRAP_HUMAN	serine/threonine kinase receptor associated protein	159					maintenance of gastrointestinal epithelium (GO:0030277)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|spliceosomal snRNP assembly (GO:0000387)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(6)|skin(1)	15		Hepatocellular(102;0.121)				AAACAGATTCTTTCTGCTGAT	0.358																																					p.L159fs		Atlas-INDEL	.											.	STRAP	33	.	0			c.475delC						.						107	118	115					12																	16047053		2203	4300	6503	SO:0001589	frameshift_variant	11171	exon5			.	AB024327	CCDS8676.1	12p13.1	2013-01-10			ENSG00000023734	ENSG00000023734		"WD repeat domain containing"	30796	protein-coding gene	gene with protein product	"Unr-interacting protein"	605986					Standard	NM_007178		Approved	UNRIP, pt-wd, MAWD	uc001rdc.4	Q9Y3F4	OTTHUMG00000168791	ENST00000419869.2:c.476delT	chr12.hg19:g.16047053delT	ENSP00000392270:p.Leu159fs	256.0	0.0		171.0	14.0	NM_007178	B2R5S5|B4DNJ6|Q5TZT4|Q9NTK0|Q9UQC8	Frame_Shift_Del	DEL	ENST00000419869.2	hg19	CCDS8676.1																																																																																			.	.		0.358	STRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401114.1	NM_007178		-	16047053	T	-	16047053	7	5	282	1	0	1	0	1	0	0	0	0	15341	1609	56	0	494	0	STRAP	12	16047053	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1103479	16047053	117804842	847	41081										
PIK3C2G	5288	hgsc.bcm.edu	37	chr12	18552597	18552597	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caatctggtttttcagactcTctgaagaaaagaaaagatat	7	6	3	5			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:18552597T>C	ENST00000266497.5	+	14	2046	c.2008T>C	c.(2008-2010)Tct>Cct	p.S670P	PIK3C2G_ENST00000433979.1_Missense_Mutation_p.S670P|PIK3C2G_ENST00000538779.1_Missense_Mutation_p.S711P			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	670	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)			breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				TTTCAGACTCTCTGAAGAAAA	0.373																																					p.S670P		Atlas-SNP	.											.	PIK3C2G	315	.	0			c.T2008C						.						64	65	64					12																	18552597		1810	4075	5885	SO:0001583	missense	5288	exon15			AGACTCTCTGAAG	AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"phosphoinositide-3-kinase, class 2, gamma polypeptide"			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.2008T>C	chr12.hg19:g.18552597T>C	ENSP00000266497:p.Ser670Pro	113.0	0.0		104.0	6.0	NM_004570	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	hg19	CCDS44839.1	.	.	.	.	.	.	.	.	.	.	T	17.77	3.470345	0.63625	.	.	ENSG00000139144	ENST00000433979;ENST00000266497;ENST00000538779	T;T;T	0.65549	-0.16;-0.16;-0.16	5.03	3.86	0.44501	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.084055	0.50627	D	0.000117	T	0.73148	0.3550	L	0.61218	1.895	0.39200	D	0.963122	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77004	0.989;0.981;0.989	T	0.72991	-0.4123	10	0.39692	T	0.17	-17.1781	10.5523	0.45097	0.1446:0.0:0.0:0.8554	.	710;711;670	B7ZLY6;F5H369;O75747	.;.;P3C2G_HUMAN	P	670;670;711	ENSP00000404845:S670P;ENSP00000266497:S670P;ENSP00000445381:S711P	ENSP00000266497:S670P	S	+	1	0	PIK3C2G	18443864	1.000000	0.71417	0.998000	0.56505	0.981000	0.71138	3.446000	0.52928	0.913000	0.36797	0.477000	0.44152	TCT	.	.		0.373	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570		C	18552597	T	C	18552597	3	2	282	1	0	0	0	0	1	0	0	0	11920	1551	54	2	2062	2	PIK3C2G	12	18552597	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2505544	18552597	115299298	848	41082										
PIK3C2G	5288	hgsc.bcm.edu	37	chr12	18716360	18716360	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caacgaaacaagcctgacagAaaaatcatttgagcagtttt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:18716360delA	ENST00000266497.5	+	26	3745	c.3707delA	c.(3706-3708)gaafs	p.E1236fs	PIK3C2G_ENST00000433979.1_Frame_Shift_Del_p.E1236fs|PIK3C2G_ENST00000538779.1_Frame_Shift_Del_p.E1277fs			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	1236	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)			breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				AGCCTGACAGAAAAATCATTT	0.403																																					p.E1236fs		Atlas-INDEL	.											.	PIK3C2G	315	.	0			c.3706delG						.						69	64	66					12																	18716360		1860	4113	5973	SO:0001589	frameshift_variant	5288	exon27			.	AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"phosphoinositide-3-kinase, class 2, gamma polypeptide"			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.3707delA	chr12.hg19:g.18716360delA	ENSP00000266497:p.Glu1236fs	162.0	0.0		131.0	10.0	NM_004570	A1L3U0	Frame_Shift_Del	DEL	ENST00000266497.5	hg19	CCDS44839.1																																																																																			.	.		0.403	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570		-	18716360	A	-	18716360	7	5	282	1	0	1	0	1	0	0	0	0	11920	246	9	0	3809	0	PIK3C2G	12	18716360	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	163763	18716360	115135535	849	41083										
SLCO1C1	53919	hgsc.bcm.edu	37	chr12	20885884	20885884	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tggcccttggaatattctctGgggggatagttatgaaaaaa					rs368038819		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:20885884delG	ENST00000266509.2	+	10	1596	c.1228delG	c.(1228-1230)gggfs	p.G411fs	SLCO1C1_ENST00000545604.1_Frame_Shift_Del_p.G411fs|SLCO1C1_ENST00000540354.1_Frame_Shift_Del_p.G362fs|SLCO1C1_ENST00000545102.1_Frame_Shift_Del_p.G293fs|SLCO1C1_ENST00000381552.1_Frame_Shift_Del_p.G411fs	NM_017435.4	NP_059131.1	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family, member 1C1	411					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			NS(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	60	Esophageal squamous(101;0.149)				Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Meclofenamic acid(DB00939)|Methotrexate(DB00563)|Ouabain(DB01092)|Phenytoin(DB00252)|Probenecid(DB01032)	AATATTCTCTGGGGGGATAGT	0.383																																					p.S409fs		Atlas-INDEL	.											.	SLCO1C1	216	.	0			c.1227delT						.						104	101	102					12																	20885884		2203	4300	6503	SO:0001589	frameshift_variant	53919	exon10			.	AF260704	CCDS8683.1, CCDS53757.1, CCDS53758.1, CCDS53759.1	12p12.2	2013-05-22	2003-11-25	2003-11-26	ENSG00000139155	ENSG00000139155		"Solute carriers"	13819	protein-coding gene	gene with protein product		613389	"solute carrier family 21 (organic anion transporter), member 14"	SLC21A14			Standard	NM_017435		Approved	OATP-F, OATP1C1, OATP1	uc010sii.2	Q9NYB5	OTTHUMG00000168966	ENST00000266509.2:c.1228delG	chr12.hg19:g.20885884delG	ENSP00000266509:p.Gly411fs	201.0	0.0		151.0	11.0	NM_017435	B7Z251|B7Z3Q3|B7Z8P1|F5GZD6|Q5JPA4	Frame_Shift_Del	DEL	ENST00000266509.2	hg19	CCDS8683.1																																																																																			.	.		0.383	SLCO1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401765.1	NM_017435		-	20885884	G	-	20885884	7	5	282	1	0	1	0	1	0	0	0	0	14740	1348	47	0	1262	0	SLCO1C1	12	20885884	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	2169524	20885884	112966011	850	41084										
SLCO1B3	28234	hgsc.bcm.edu	37	chr12	21054325	21054325	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	attttggggctctgattgatAaaacatgtatgaagtggtcc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:21054325delA	ENST00000381545.3	+	15	2008	c.1789delA	c.(1789-1791)aaafs	p.K597fs	SLCO1B3_ENST00000261196.2_Frame_Shift_Del_p.K597fs|SLCO1B7_ENST00000554957.1_Intron|SLCO1B3_ENST00000553473.1_Frame_Shift_Del_p.K597fs|LST3_ENST00000540229.1_Frame_Shift_Del_p.K597fs|LST3_ENST00000381541.3_Intron	NM_019844.3	NP_062818.1	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family, member 1B3	597					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	organic anion transmembrane transporter activity (GO:0008514)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(23)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(2)	63	Esophageal squamous(101;0.149)				Atorvastatin(DB01076)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Dabrafenib(DB08912)|Digoxin(DB00390)|Docetaxel(DB01248)|Estradiol(DB00783)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Olmesartan(DB00275)|Ouabain(DB01092)|Paclitaxel(DB01229)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Rosuvastatin(DB01098)|Valsartan(DB00177)	TCTGATTGATAAAACATGTAT	0.383																																					p.D596fs		Atlas-INDEL	.											.	SLCO1B3	151	.	0			c.1788delT						.						185	178	180					12																	21054325		2203	4300	6503	SO:0001589	frameshift_variant	28234	exon15			.		CCDS8684.1	12p12	2013-05-22	2003-11-25	2003-11-26		ENSG00000111700		"Solute carriers"	10961	protein-coding gene	gene with protein product		605495	"solute carrier family 21 (organic anion transporter), member 8"	SLC21A8			Standard	NM_019844		Approved	OATP8, OATP1B3	uc001rel.4	Q9NPD5	OTTHUMG00000169011	ENST00000381545.3:c.1789delA	chr12.hg19:g.21054325delA	ENSP00000370956:p.Lys597fs	244.0	0.0		200.0	14.0	NM_019844	E7EMT8|Q5JAR4	Frame_Shift_Del	DEL	ENST00000381545.3	hg19	CCDS8684.1																																																																																			.	.		0.383	SLCO1B3-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401936.1	NM_019844		-	21054325	A	-	21054325	7	5	282	1	0	1	0	1	0	0	0	0	14739	363	13	0	1839	0	SLCO1B3	12	21054325	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	168441	21054325	112797570	851	41085										
SLCO1B1	10599	hgsc.bcm.edu	37	chr12	21375253	21375253	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaattgttcaacctgaattgAaatcacttgcactgggtttc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:21375253delA	ENST00000256958.2	+	13	1798	c.1702delA	c.(1702-1704)aaafs	p.K568fs		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	568					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	70					Acetylcysteine(DB06151)|Aminohippurate(DB00345)|Atorvastatin(DB01076)|Axitinib(DB06626)|Benzylpenicillin(DB01053)|Bezafibrate(DB01393)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Eltrombopag(DB06210)|Estradiol(DB00783)|Estrone(DB00655)|Ezetimibe(DB00973)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Gemfibrozil(DB01241)|Indinavir(DB00224)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Olmesartan(DB00275)|Ouabain(DB01092)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Penicillamine(DB00859)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Quinidine(DB00908)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sumatriptan(DB00669)|Valsartan(DB00177)|Verapamil(DB00661)	ACCTGAATTGAAATCACTTGC	0.264																																					p.L567fs		Atlas-INDEL	.											.	SLCO1B1	151	.	0			c.1701delG						.						110	106	107					12																	21375253		2203	4300	6503	SO:0001589	frameshift_variant	10599	exon13			.		CCDS8685.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000134538	ENSG00000134538		"Solute carriers"	10959	protein-coding gene	gene with protein product		604843	"solute carrier family 21 (organic anion transporter), member 6"	SLC21A6		10358072	Standard	NM_006446		Approved	OATP-C, LST-1, OATP1B1	uc001req.4	Q9Y6L6	OTTHUMG00000169047	ENST00000256958.2:c.1702delA	chr12.hg19:g.21375253delA	ENSP00000256958:p.Lys568fs	252.0	0.0		182.0	13.0	NM_006446	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Frame_Shift_Del	DEL	ENST00000256958.2	hg19	CCDS8685.1																																																																																			.	.		0.264	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446		-	21375253	A	-	21375253	7	5	282	1	0	1	0	1	0	0	0	0	14738	247	9	0	1748	0	SLCO1B1	12	21375253	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	320928	21375253	112476642	852	41086										
C12orf39	80763	hgsc.bcm.edu	37	chr12	21684114	21684114	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	accagattcctggaagacagTctgcttaactggtgaaaata	9	8	1	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:21684114T>C	ENST00000256969.2	+	6	502	c.336T>C	c.(334-336)agT>agC	p.S112S	C12orf39_ENST00000543800.1_3'UTR	NM_030572.2	NP_085049.1	Q9BT56	SPXN_HUMAN		112					long-chain fatty acid import (GO:0044539)|negative regulation of appetite (GO:0032099)|negative regulation of heart rate (GO:0010459)|negative regulation of renal sodium excretion (GO:0035814)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of sensory perception of pain (GO:0051930)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)	neuropeptide hormone activity (GO:0005184)|type 2 galanin receptor binding (GO:0031765)|type 3 galanin receptor binding (GO:0031766)			endometrium(3)|large_intestine(1)|lung(2)|urinary_tract(1)	7						TGGAAGACAGTCTGCTTAACT	0.294																																					p.S112S		Atlas-SNP	.											.	C12orf39	18	.	0			c.T336C						.						80	79	79					12																	21684114		2202	4299	6501	SO:0001819	synonymous_variant	80763	exon6			AGACAGTCTGCTT																												ENST00000256969.2:c.336T>C	chr12.hg19:g.21684114T>C		236.0	0.0		148.0	6.0	NM_030572	B3KND6	Silent	SNP	ENST00000256969.2	hg19	CCDS31757.1																																																																																			.	.		0.294	C12orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402389.1			C	21684114	T	C	21684114	2	2	282	1	0	0	0	0	0	0	0	1	1686	1664	58	2		2	C12orf39	12	21684114	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	308861	21684114	112167781	853	41087										
KIAA0528	9847	hgsc.bcm.edu	37	chr12	22666279	22666279	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cttaaaagagctttaaagggCcccccttcttttccagcact							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:22666279delC	ENST00000333957.4	-	9	1242	c.987delG	c.(985-987)gggfs	p.G329fs	C2CD5_ENST00000396028.2_Frame_Shift_Del_p.G320fs|C2CD5_ENST00000545552.1_Frame_Shift_Del_p.G320fs|C2CD5_ENST00000536386.1_Frame_Shift_Del_p.G320fs|C2CD5_ENST00000542676.1_Frame_Shift_Del_p.G329fs|C2CD5_ENST00000446597.1_Frame_Shift_Del_p.G329fs|C2CD5_ENST00000544930.1_Frame_Shift_Del_p.G122fs	NM_014802.1	NP_055617.1	Q86YS7	C2CD5_HUMAN	C2 calcium-dependent domain containing 5	329					cellular response to insulin stimulus (GO:0032869)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|intracellular protein transmembrane transport (GO:0065002)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)										CTTTAAAGGGCCCCCCTTCTT	0.363																																					p.P330fs		Atlas-INDEL	.											.	.	.	.	0			c.988delC						.						144	133	137					12																	22666279		2203	4300	6503	SO:0001589	frameshift_variant	9847	exon9			.	AB011100	CCDS31758.1, CCDS66337.1, CCDS66338.1, CCDS66339.1, CCDS66340.1	12p12.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000111731	ENSG00000111731			29062	protein-coding gene	gene with protein product	"138 kDa C2 domain-containing phosphoprotein"		"KIAA0528"	KIAA0528		21907143	Standard	XM_005253538		Approved	CDP138	uc001rfq.3	Q86YS7	OTTHUMG00000169100	ENST00000333957.4:c.987delG	chr12.hg19:g.22666279delC	ENSP00000334229:p.Gly329fs	180.0	0.0		163.0	11.0	NM_014802	B4DJ03|B4DRN7|B7ZLL0|F5H2A1|F5H5R1|O60280|Q17RY7|Q7Z619|Q86SU3	Frame_Shift_Del	DEL	ENST00000333957.4	hg19	CCDS31758.1																																																																																			.	.		0.363	C2CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402257.1	NM_014802		-	22666279	C	-	22666279	7	5	282	1	0	1	0	1	0	0	0	0	8191	726	26	0	2083	0	KIAA0528	12	22666279	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	982165	22666279	111185616	854	41088										
KIAA0528	9847	hgsc.bcm.edu	37	chr12	22671015	22671015	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aataagtttggtttttcagaGgggttgagggtcctgatgag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:22671015delG	ENST00000333957.4	-	8	1112	c.857delC	c.(856-858)cctfs	p.P286fs	C2CD5_ENST00000396028.2_Intron|C2CD5_ENST00000545552.1_Intron|C2CD5_ENST00000536386.1_Intron|C2CD5_ENST00000542676.1_Frame_Shift_Del_p.P286fs|C2CD5_ENST00000446597.1_Frame_Shift_Del_p.P286fs|C2CD5_ENST00000540703.1_5'Flank|C2CD5_ENST00000544930.1_Intron	NM_014802.1	NP_055617.1	Q86YS7	C2CD5_HUMAN	C2 calcium-dependent domain containing 5	286					cellular response to insulin stimulus (GO:0032869)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|intracellular protein transmembrane transport (GO:0065002)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)										GTTTTTCAGAGGGGTTGAGGG	0.428																																					p.P286fs		Atlas-INDEL	.											.	.	.	.	0			c.858delT						.						240	229	233					12																	22671015		2203	4300	6503	SO:0001589	frameshift_variant	9847	exon8			.	AB011100	CCDS31758.1, CCDS66337.1, CCDS66338.1, CCDS66339.1, CCDS66340.1	12p12.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000111731	ENSG00000111731			29062	protein-coding gene	gene with protein product	"138 kDa C2 domain-containing phosphoprotein"		"KIAA0528"	KIAA0528		21907143	Standard	XM_005253538		Approved	CDP138	uc001rfq.3	Q86YS7	OTTHUMG00000169100	ENST00000333957.4:c.857delC	chr12.hg19:g.22671015delG	ENSP00000334229:p.Pro286fs	220.0	0.0		162.0	10.0	NM_014802	B4DJ03|B4DRN7|B7ZLL0|F5H2A1|F5H5R1|O60280|Q17RY7|Q7Z619|Q86SU3	Frame_Shift_Del	DEL	ENST00000333957.4	hg19	CCDS31758.1																																																																																			.	.		0.428	C2CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402257.1	NM_014802		-	22671015	G	-	22671015	7	5	282	1	0	1	0	1	0	0	0	0	8191	1000	35	0	2217	0	KIAA0528	12	22671015	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	4736	22671015	111180880	855	41089										
CASC1	55259	hgsc.bcm.edu	37	chr12	25308338	25308338	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcaagttcttcatttctcctTtctagatcctgttgcacaag	5	11	5	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:25308338T>C	ENST00000320267.9	-	4	270	c.189A>G	c.(187-189)gaA>gaG	p.E63E	CASC1_ENST00000557684.1_5'UTR|CASC1_ENST00000395987.3_Silent_p.E69E|CASC1_ENST00000354189.5_Silent_p.E127E|CASC1_ENST00000537577.1_5'UTR|CASC1_ENST00000395990.2_Silent_p.E23E|CASC1_ENST00000545133.1_Silent_p.E4E	NM_001082973.1	NP_001076442	Q6TDU7	CASC1_HUMAN	cancer susceptibility candidate 1	63	Glu-rich.									breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(3)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Melanoma(3;0.0301)|Colorectal(261;0.11)		OV - Ovarian serous cystadenocarcinoma(3;7.42e-20)|Epithelial(3;7.58e-16)|all cancers(3;1.07e-13)			CATTTCTCCTTTCTAGATCCT	0.338																																					p.E127E		Atlas-SNP	.											.	CASC1	146	.	0			c.A381G						.						91	93	93					12																	25308338		2203	4297	6500	SO:0001819	synonymous_variant	55259	exon5			TCTCCTTTCTAGA	AK093102	CCDS31759.2, CCDS41762.1, CCDS41763.1, CCDS55810.1, CCDS55811.1	12p12.1	2012-04-17			ENSG00000118307	ENSG00000118307		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	29599	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 54"					14583591	Standard	NM_018272		Approved	LAS1, FLJ10921, PPP1R54	uc001rgk.3	Q6TDU7	OTTHUMG00000150195	ENST00000320267.9:c.189A>G	chr12.hg19:g.25308338T>C		96.0	0.0		88.0	4.0	NM_001082972	B4DNP2|F5H6T6|Q17RL2|Q4G171|Q5U5K5|Q9NV50	Silent	SNP	ENST00000320267.9	hg19	CCDS41762.1	.	.	.	.	.	.	.	.	.	.	T	10.39	1.337184	0.24253	.	.	ENSG00000118307	ENST00000556006	.	.	.	4.71	0.895	0.19247	.	.	.	.	.	T	0.21962	0.0529	.	.	.	0.22050	N	0.999399	.	.	.	.	.	.	T	0.21895	-1.0232	4	.	.	.	-7.6911	2.6752	0.05079	0.1935:0.2087:0.0:0.5979	.	.	.	.	E	39	.	.	K	-	1	0	CASC1	25199605	0.979000	0.34478	0.847000	0.33407	0.959000	0.62525	0.766000	0.26560	0.418000	0.25898	0.523000	0.50628	AAG	.	.		0.338	CASC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316761.1	NM_018272		C	25308338	T	C	25308338	2	2	282	1	0	0	0	0	0	0	0	1	2662	1838	64	2		2	CASC1	12	25308338	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2637323	25308338	108543557	856	41090										
ITPR2	3709	hgsc.bcm.edu	37	chr12	26839461	26839461	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agagttgtggcatctagttcAaaaagggatgcaatgtcatt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:26839461delA	ENST00000381340.3	-	11	1517	c.1101delT	c.(1099-1101)tttfs	p.F367fs		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	367	MIR 4. {ECO:0000255|PROSITE- ProRule:PRU00131}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	CATCTAGTTCAAAAAGGGATG	0.408																																					p.E368fs		Atlas-INDEL	.											ITPR2,NS,carcinoma,0,1	ITPR2	270	.	0			c.1102delG						.						140	132	134					12																	26839461		1894	4119	6013	SO:0001589	frameshift_variant	3709	exon11			.	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"Ion channels / Inositol triphosphate receptors"	6181	protein-coding gene	gene with protein product	"cilia and flagella associated protein 48"	600144	"inositol 1,4,5-triphosphate receptor, type 2"			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.1101delT	chr12.hg19:g.26839461delA	ENSP00000370744:p.Phe367fs	200.0	0.0		142.0	14.0	NM_002223	O94773	Frame_Shift_Del	DEL	ENST00000381340.3	hg19	CCDS41764.1																																																																																			.	.		0.408	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		-	26839461	A	-	26839461	7	5	282	1	0	1	0	1	0	0	0	0	7930	127	5	0	7192	0	ITPR2	12	26839461	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1531123	26839461	107012434	857	41091										
PPFIBP1	8496	hgsc.bcm.edu	37	chr12	27800732	27800732	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tttggagttttgtcttgaagAgcacagagagaaggtgaatg	14	3	1	5			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:27800732A>G	ENST00000318304.8	+	6	711	c.428A>G	c.(427-429)gAg>gGg	p.E143G	PPFIBP1_ENST00000542629.1_Missense_Mutation_p.E143G|PPFIBP1_ENST00000228425.6_Missense_Mutation_p.E143G|PPFIBP1_ENST00000537927.1_5'UTR|PPFIBP1_ENST00000535047.1_Missense_Mutation_p.E143G	NM_001198916.1|NM_177444.2	NP_001185845.1|NP_803193	Q86W92	LIPB1_HUMAN	PTPRF interacting protein, binding protein 1 (liprin beta 1)	143					cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)			PPFIBP1/ALK(3)	central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(13)|prostate(2)|skin(1)	32	Lung SC(9;0.0873)					TGTCTTGAAGAGCACAGAGAG	0.453																																					p.E143G		Atlas-SNP	.											.	PPFIBP1	153	.	0			c.A428G						.						172	170	170					12																	27800732		2203	4300	6503	SO:0001583	missense	8496	exon6			TTGAAGAGCACAG	AF034802	CCDS8713.1, CCDS55812.1, CCDS55813.1, CCDS55814.1	12p12.1	2013-01-10						"Sterile alpha motif (SAM) domain containing"	9249	protein-coding gene	gene with protein product		603141				9624153, 11836260	Standard	NM_003622		Approved	L2, hSGT2, hSgt2p, SGT2	uc001ric.2	Q86W92		ENST00000318304.8:c.428A>G	chr12.hg19:g.27800732A>G	ENSP00000314724:p.Glu143Gly	193.0	0.0		131.0	7.0	NM_003622	O75336|Q86X70|Q9NY03|Q9ULJ0	Missense_Mutation	SNP	ENST00000318304.8	hg19	CCDS55812.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.981728	0.74474	.	.	ENSG00000110841	ENST00000543820;ENST00000545381;ENST00000318304;ENST00000535047;ENST00000542629;ENST00000228425	T;T;T;T;T	0.18016	2.24;2.24;2.24;2.24;2.24	5.26	5.26	0.73747	.	0.000000	0.34338	U	0.004054	T	0.33030	0.0849	L	0.43923	1.385	0.80722	D	1	P;D;D;P	0.89917	0.573;1.0;0.986;0.902	B;D;D;B	0.85130	0.227;0.997;0.939;0.415	T	0.02093	-1.1215	10	0.29301	T	0.29	-28.2831	14.8457	0.70259	1.0:0.0:0.0:0.0	.	143;143;143;143	Q86W92;Q86W92-2;Q86W92-4;Q86W92-5	LIPB1_HUMAN;.;.;.	G	145;143;143;143;143;143	ENSP00000445822:E143G;ENSP00000314724:E143G;ENSP00000444046:E143G;ENSP00000443442:E143G;ENSP00000228425:E143G	ENSP00000228425:E143G	E	+	2	0	PPFIBP1	27691999	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.280000	0.95786	1.975000	0.57531	0.528000	0.53228	GAG	.	.		0.453	PPFIBP1-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402877.1	NM_003622		G	27800732	A	G	27800732	3	3	282	1	0	0	0	0	1	0	0	0	12322	304	11	2	442	2	PPFIBP1	12	27800732	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	961271	27800732	106051163	858	41092										
TMTC1	83857	hgsc.bcm.edu	37	chr12	29667503	29667503	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgacttttgggtcctttggtTtcagctggagagccttgtct	12	8	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:29667503T>C	ENST00000539277.1	-	16	2400	c.2342A>G	c.(2341-2343)aAa>aGa	p.K781R	TMTC1_ENST00000319685.8_5'UTR|TMTC1_ENST00000551659.1_Missense_Mutation_p.K843R|TMTC1_ENST00000256062.5_Missense_Mutation_p.K673R|TMTC1_ENST00000552618.1_Missense_Mutation_p.K805R	NM_001193451.1	NP_001180380.1	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat containing 1	781						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(1)|endometrium(4)|kidney(3)|large_intestine(17)|lung(45)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					GTCCTTTGGTTTCAGCTGGAG	0.363																																					p.K781R		Atlas-SNP	.											.	TMTC1	147	.	0			c.A2342G						.						94	94	94					12																	29667503		2203	4300	6503	SO:0001583	missense	83857	exon16			TTTGGTTTCAGCT		CCDS8718.1, CCDS53772.1	12p11.22	2014-06-09	2006-01-06			ENSG00000133687		"Tetratricopeptide (TTC) repeat domain containing"	24099	protein-coding gene	gene with protein product		615855				24764305	Standard	NM_001193451		Approved	ARG99, OLF, FLJ31400, FLJ41625	uc021qwi.1	Q8IUR5	OTTHUMG00000169324	ENST00000539277.1:c.2342A>G	chr12.hg19:g.29667503T>C	ENSP00000442046:p.Lys781Arg	117.0	0.0		99.0	4.0	NM_001193451	D0EP37|F5H8B5|Q6PIU4|Q6ZSM5|Q96N52|Q9BXM2	Missense_Mutation	SNP	ENST00000539277.1	hg19	CCDS53772.1	.	.	.	.	.	.	.	.	.	.	T	16.53	3.149075	0.57151	.	.	ENSG00000133687	ENST00000540901;ENST00000256062;ENST00000551659;ENST00000552618;ENST00000539277	T;T;T;T	0.62788	-0.0;-0.0;-0.0;-0.0	5.09	5.09	0.68999	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.149585	0.64402	D	0.000020	T	0.66925	0.2839	L	0.45744	1.44	0.80722	D	1	P;D;P	0.57571	0.872;0.98;0.763	B;P;B	0.56960	0.301;0.81;0.229	T	0.65389	-0.6180	10	0.34782	T	0.22	-19.3133	12.5219	0.56065	0.0:0.0:0.0:1.0	.	781;843;126	Q8IUR5;F8VTQ9;Q8IUR5-4	TMTC1_HUMAN;.;.	R	544;673;843;805;781	ENSP00000256062:K673R;ENSP00000448112:K843R;ENSP00000449043:K805R;ENSP00000442046:K781R	ENSP00000256062:K673R	K	-	2	0	TMTC1	29558770	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.362000	0.66098	2.027000	0.59764	0.533000	0.62120	AAA	.	.		0.363	TMTC1-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403509.1	NM_031920		C	29667503	T	C	29667503	3	2	282	1	0	0	0	0	1	0	0	0	16275	1841	64	2	318	2	TMTC1	12	29667503	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1866771	29667503	104184392	859	41093										
IPO8	10526	hgsc.bcm.edu	37	chr12	30818240	30818240	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	catttggtccttgaataaacTcttctattaggaaacaaatt	5	7	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:30818240T>C	ENST00000256079.4	-	13	1680	c.1342A>G	c.(1342-1344)Agt>Ggt	p.S448G	IPO8_ENST00000544829.1_Missense_Mutation_p.S243G	NM_006390.3	NP_006381.2	O15397	IPO8_HUMAN	importin 8	448					intracellular protein transport (GO:0006886)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	Ran GTPase binding (GO:0008536)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(16)|liver(1)|lung(22)|prostate(2)|skin(2)|urinary_tract(2)	52	all_lung(12;6.66e-10)|Lung NSC(12;4.84e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					TTGAATAAACTCTTCTATTAG	0.299																																					p.S448G		Atlas-SNP	.											.	IPO8	105	.	0			c.A1342G						.						71	76	74					12																	30818240		2201	4293	6494	SO:0001583	missense	10526	exon13			ATAAACTCTTCTA	U77494	CCDS8719.1, CCDS53773.1	12p11.21	2011-05-23	2003-03-11	2003-03-14	ENSG00000133704	ENSG00000133704		"Importins"	9853	protein-coding gene	gene with protein product		605600	"RAN binding protein 8"	RANBP8		9214382	Standard	NM_006390		Approved	IMP8	uc001rjd.3	O15397	OTTHUMG00000169172	ENST00000256079.4:c.1342A>G	chr12.hg19:g.30818240T>C	ENSP00000256079:p.Ser448Gly	174.0	0.0		150.0	6.0	NM_006390	B7Z7M3	Missense_Mutation	SNP	ENST00000256079.4	hg19	CCDS8719.1	.	.	.	.	.	.	.	.	.	.	T	14.54	2.564746	0.45694	.	.	ENSG00000133704	ENST00000256079;ENST00000544829	T;T	0.61627	0.09;0.09	5.02	5.02	0.67125	Armadillo-like helical (1);Armadillo-type fold (1);	0.189360	0.56097	D	0.000024	T	0.55862	0.1947	L	0.42245	1.32	0.34625	D	0.719025	B;P	0.36183	0.232;0.542	B;P	0.44921	0.193;0.464	T	0.68262	-0.5455	10	0.48119	T	0.1	-9.8359	10.3089	0.43697	0.147:0.0:0.0:0.853	.	243;448	B7Z7M3;O15397	.;IPO8_HUMAN	G	448;243	ENSP00000256079:S448G;ENSP00000444520:S243G	ENSP00000256079:S448G	S	-	1	0	IPO8	30709507	1.000000	0.71417	1.000000	0.80357	0.809000	0.45718	2.830000	0.48136	2.005000	0.58758	0.528000	0.53228	AGT	.	.		0.299	IPO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402700.2	NM_006390		C	30818240	T	C	30818240	3	2	282	1	0	0	0	0	1	0	0	0	7807	1551	54	2	1823	2	IPO8	12	30818240	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1150737	30818240	103033655	860	41094										
PKP2	5318	hgsc.bcm.edu	37	chr12	33031092	33031092	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tccctggcctggggtacgtgAgcagggccgggttggcaggg	20	10	0	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:33031092A>G	ENST00000070846.6	-	3	746	c.722T>C	c.(721-723)cTc>cCc	p.L241P	PKP2_ENST00000340811.4_Missense_Mutation_p.L241P	NM_004572.3	NP_004563.2	Q99959	PKP2_HUMAN	plakophilin 2	241					adherens junction maintenance (GO:0034334)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential (GO:0086001)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cell-cell signaling involved in cardiac conduction (GO:0086019)|desmosome assembly (GO:0002159)|gap junction assembly (GO:0016264)|heart development (GO:0007507)|intermediate filament bundle assembly (GO:0045110)|lipid homeostasis (GO:0055088)|maintenance of organ identity (GO:0048496)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of tight junction assembly (GO:2000810)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	adherens junction (GO:0005912)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|protein kinase C binding (GO:0005080)|sodium channel regulator activity (GO:0017080)	p.L241R(1)		NS(1)|breast(2)|endometrium(1)|kidney(9)|large_intestine(8)|lung(21)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	50	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					GGGGTACGTGAGCAGGGCCGG	0.612																																					p.L241P		Atlas-SNP	.											PKP2,caecum,carcinoma,0,1	PKP2	110	.	1	Substitution - Missense(1)	large_intestine(1)	c.T722C						.						72	64	67					12																	33031092		2203	4298	6501	SO:0001583	missense	5318	exon3			TACGTGAGCAGGG	X97675	CCDS8731.1, CCDS31771.1	12p11	2014-09-17				ENSG00000057294		"Armadillo repeat containing"	9024	protein-coding gene	gene with protein product		602861				8922383	Standard	NM_001005242		Approved		uc001rlj.4	Q99959	OTTHUMG00000169500	ENST00000070846.6:c.722T>C	chr12.hg19:g.33031092A>G	ENSP00000070846:p.Leu241Pro	249.0	2.0		175.0	7.0	NM_004572	A0AV37|B8QFA1|B8QGS6|B8QGS7|D3DUW9|Q4VC01|Q99960	Missense_Mutation	SNP	ENST00000070846.6	hg19	CCDS8731.1	.	.	.	.	.	.	.	.	.	.	A	9.274	1.046450	0.19748	.	.	ENSG00000057294	ENST00000340811;ENST00000070846;ENST00000537278	T;T	0.80393	-1.37;-1.35	5.29	4.12	0.48240	.	4.458510	0.00550	N	0.000248	T	0.69006	0.3063	N	0.16743	0.435	0.09310	N	0.999999	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.54833	-0.8234	10	0.35671	T	0.21	-6.4718	4.6101	0.12399	0.6874:0.1868:0.1258:0.0	.	241;241;241	Q99959-2;A0AV37;Q99959	.;.;PKP2_HUMAN	P	241	ENSP00000342800:L241P;ENSP00000070846:L241P	ENSP00000070846:L241P	L	-	2	0	PKP2	32922359	0.000000	0.05858	0.058000	0.19502	0.668000	0.39293	0.310000	0.19356	0.827000	0.34685	0.529000	0.55759	CTC	.	.		0.612	PKP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404449.1	NM_004572		G	33031092	A	G	33031092	3	3	282	1	0	0	0	0	1	0	0	0	11994	304	11	2	1971	2	PKP2	12	33031092	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2212852	33031092	100820803	861	41095										
C12orf40	283461	hgsc.bcm.edu	37	chr12	40041671	40041671	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgcagtttcactccatcatcTttttcagtggagttaccttc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:40041671delT	ENST00000324616.5	+	6	616	c.462delT	c.(460-462)tctfs	p.S154fs	C12orf40_ENST00000405531.3_Frame_Shift_Del_p.S154fs|C12orf40_ENST00000398716.1_Frame_Shift_Del_p.S77fs	NM_001031748.2	NP_001026918.2	Q86WS4	CL040_HUMAN	chromosome 12 open reading frame 40	154										breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(6)|prostate(1)|skin(2)	38						CTCCATCATCTTTTTCAGTGG	0.363																																					p.S154fs		Atlas-INDEL	.											.	C12orf40	118	.	0			c.461delC						.						90	86	88					12																	40041671		1836	4093	5929	SO:0001589	frameshift_variant	283461	exon6			.	AK097445	CCDS41770.1	12q12	2008-08-04			ENSG00000180116	ENSG00000180116			26846	protein-coding gene	gene with protein product						12477932	Standard	XM_005268806		Approved	FLJ40126	uc001rmc.3	Q86WS4	OTTHUMG00000133567	ENST00000324616.5:c.462delT	chr12.hg19:g.40041671delT	ENSP00000317671:p.Ser154fs	310.0	0.0		221.0	15.0	NM_001031748	B7WNU1|Q8IXY6|Q8N818|V9HW02	Frame_Shift_Del	DEL	ENST00000324616.5	hg19	CCDS41770.1																																																																																			.	.		0.363	C12orf40-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257664.2	NM_173599		-	40041671	T	-	40041671	7	5	282	1	0	1	0	1	0	0	0	0	1688	1596	56	0	484	0	C12orf40	12	40041671	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	7010579	40041671	93810224	862	41096										
PRICKLE1	144165	hgsc.bcm.edu	37	chr12	42858256	42858256	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaacactttgctctggtttcAggtctgacagacactccagg	10	11	3	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:42858256A>G	ENST00000455697.1	-	7	1865	c.1580T>C	c.(1579-1581)cTg>cCg	p.L527P	PRICKLE1_ENST00000548696.1_Missense_Mutation_p.L527P|PRICKLE1_ENST00000345127.3_Missense_Mutation_p.L527P|RP11-328C8.4_ENST00000547824.1_RNA|PRICKLE1_ENST00000552240.1_Missense_Mutation_p.L527P|PRICKLE1_ENST00000445766.2_Missense_Mutation_p.L527P	NM_001144882.1|NM_001144883.1	NP_001138354.1|NP_001138355.1	Q96MT3	PRIC1_HUMAN	prickle homolog 1 (Drosophila)	527					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell myoblast differentiation (GO:2000691)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(13)|ovary(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	47	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)		CTCTGGTTTCAGGTCTGACAG	0.443																																					p.L527P		Atlas-SNP	.											.	PRICKLE1	105	.	0			c.T1580C						.						140	137	138					12																	42858256		2203	4300	6503	SO:0001583	missense	144165	exon7			GGTTTCAGGTCTG	AK056499	CCDS8742.1	12p11-q12	2010-08-13	2006-09-12			ENSG00000139174			17019	protein-coding gene	gene with protein product		608500	"prickle-like 1 (Drosophila)"			12525887, 18976727	Standard	NM_153026		Approved	FLJ31937, EPM1B	uc010skv.2	Q96MT3		ENST00000455697.1:c.1580T>C	chr12.hg19:g.42858256A>G	ENSP00000401060:p.Leu527Pro	328.0	0.0		264.0	98.0	NM_001144882	Q14C83|Q71QF8|Q96N00	Missense_Mutation	SNP	ENST00000455697.1	hg19	CCDS8742.1	.	.	.	.	.	.	.	.	.	.	A	17.45	3.391579	0.62066	.	.	ENSG00000139174	ENST00000455697;ENST00000445766;ENST00000548696;ENST00000345127;ENST00000552240	T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;-0.2	5.55	5.55	0.83447	.	0.079095	0.56097	D	0.000038	T	0.77301	0.4110	M	0.72894	2.215	0.80722	D	1	D	0.89917	1.0	D	0.66351	0.943	T	0.79999	-0.1566	10	0.72032	D	0.01	-10.8538	15.993	0.80220	1.0:0.0:0.0:0.0	.	527	Q96MT3	PRIC1_HUMAN	P	527	ENSP00000401060:L527P;ENSP00000398947:L527P;ENSP00000448359:L527P;ENSP00000345064:L527P;ENSP00000449819:L527P	ENSP00000345064:L527P	L	-	2	0	PRICKLE1	41144523	1.000000	0.71417	0.995000	0.50966	0.983000	0.72400	8.910000	0.92685	2.236000	0.73375	0.528000	0.53228	CTG	.	.		0.443	PRICKLE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404069.1			G	42858256	A	G	42858256	3	3	282	1	0	0	0	0	1	0	0	0	12498	188	7	2	923	2	PRICKLE1	12	42858256	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2816585	42858256	90993639	863	41097										
PUS7L	83448	hgsc.bcm.edu	37	chr12	44139933	44139933	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tttaaatttctaatgacaatAtcaaagtgatttcctttgag	5	5	2	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:44139933A>G	ENST00000416848.2	-	4	1667	c.1179T>C	c.(1177-1179)gaT>gaC	p.D393D	PUS7L_ENST00000431332.3_Silent_p.D80D|PUS7L_ENST00000344862.5_Silent_p.D393D|PUS7L_ENST00000551923.1_Silent_p.D393D	NM_001098615.1|NM_001271826.1	NP_001092085.1|NP_001258755.1	Q9H0K6	PUS7L_HUMAN	pseudouridylate synthase 7 homolog (S. cerevisiae)-like	393					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(15)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	all_cancers(12;0.00027)	Lung NSC(34;0.114)|all_lung(34;0.24)		GBM - Glioblastoma multiforme(48;0.0402)		TAATGACAATATCAAAGTGAT	0.289																																					p.D393D		Atlas-SNP	.											.	PUS7L	73	.	0			c.T1179C						.						43	41	42					12																	44139933		2202	4296	6498	SO:0001819	synonymous_variant	83448	exon4			GACAATATCAAAG	BX647494	CCDS8743.1, CCDS61104.1	12q12	2006-02-07				ENSG00000129317			25276	protein-coding gene	gene with protein product						11230166	Standard	NM_001098615		Approved	DKFZP434G1415	uc001rnr.5	Q9H0K6	OTTHUMG00000169423	ENST00000416848.2:c.1179T>C	chr12.hg19:g.44139933A>G		111.0	0.0		89.0	4.0	NM_001098614	B3KUJ1|Q05CU0|Q6AHZ3|Q6NUP2	Silent	SNP	ENST00000416848.2	hg19	CCDS8743.1																																																																																			.	.		0.289	PUS7L-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403931.1	NM_031292		G	44139933	A	G	44139933	2	3	282	1	0	0	0	0	0	0	0	1	12849	446	16	2		2	PUS7L	12	44139933	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1281677	44139933	89711962	864	41098										
COL2A1	1280	hgsc.bcm.edu	37	chr12	48387630	48387630	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cgcctctcccttagcaccgtCcaggcctggataaccctagg	9	17	1	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:48387630C>T	ENST00000380518.3	-	14	1050	c.886G>A	c.(886-888)Gac>Aac	p.D296N	COL2A1_ENST00000337299.6_Missense_Mutation_p.D227N	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	296	Triple-helical region.				axon guidance (GO:0007411)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to BMP stimulus (GO:0071773)|central nervous system development (GO:0007417)|chondrocyte differentiation (GO:0002062)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal joint morphogenesis (GO:0060272)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|limb bud formation (GO:0060174)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|notochord development (GO:0030903)|otic vesicle development (GO:0071599)|palate development (GO:0060021)|proteoglycan metabolic process (GO:0006029)|regulation of gene expression (GO:0010468)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|tissue homeostasis (GO:0001894)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen type II trimer (GO:0005585)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(3)	64		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	TTAGCACCGTCCAGGCCTGGA	0.532																																					p.D296N		Atlas-SNP	.											.	COL2A1	368	.	0			c.G886A						.						79	76	77					12																	48387630		2203	4300	6503	SO:0001583	missense	1280	exon14			CACCGTCCAGGCC	X16468	CCDS8759.1, CCDS41778.1	12q12-q13.2	2013-11-14	2008-02-04		ENSG00000139219	ENSG00000139219		"Collagens"	2200	protein-coding gene	gene with protein product		120140	"collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital)", "arthroophthalmopathy, progressive (Stickler syndrome)"	SEDC, AOM		1677770	Standard	NM_033150		Approved	STL1	uc001rqu.3	P02458	OTTHUMG00000149896	ENST00000380518.3:c.886G>A	chr12.hg19:g.48387630C>T	ENSP00000369889:p.Asp296Asn	253.0	0.0		169.0	71.0	NM_001844	A6NGA0|Q12985|Q14009|Q14044|Q14045|Q14046|Q14047|Q14056|Q14058|Q16672|Q1JQ82|Q2V4X7|Q6LBY1|Q6LBY2|Q6LBY3|Q96IT5|Q99227|Q9UE38|Q9UE39|Q9UE40|Q9UE41|Q9UE42|Q9UE43	Missense_Mutation	SNP	ENST00000380518.3	hg19	CCDS41778.1	.	.	.	.	.	.	.	.	.	.	C	15.74	2.921489	0.52653	.	.	ENSG00000139219	ENST00000380518;ENST00000395281;ENST00000337299	D;D	0.92699	-3.09;-3.09	5.12	4.22	0.49857	.	0.000000	0.85682	D	0.000000	D	0.86485	0.5944	N	0.26092	0.79	0.53688	D	0.999973	B;B	0.11235	0.003;0.004	B;B	0.15484	0.005;0.013	T	0.83200	-0.0079	10	0.72032	D	0.01	.	12.5558	0.56252	0.0:0.9185:0.0:0.0815	.	227;296	P02458-1;P02458	.;CO2A1_HUMAN	N	296;227;227	ENSP00000369889:D296N;ENSP00000338213:D227N	ENSP00000338213:D227N	D	-	1	0	COL2A1	46673897	1.000000	0.71417	0.819000	0.32651	0.778000	0.44026	5.679000	0.68160	1.384000	0.46424	0.655000	0.94253	GAC	.	.		0.532	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844		T	48387630	C	T	48387630	3	4	282	1	0	0	0	0	1	0	0	0	3689	855	30	3	3741	3	COL2A1	12	48387630	Missense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	4247697	48387630	85464265	865	41099										
MLL2	8085	hgsc.bcm.edu	37	chr12	49420553	49420554	+	Frame_Shift_Del	DEL	AC	AC	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggtctcatacacctccgtggAccaaagggcacagttgaggt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:49420553_49420554delAC	ENST00000301067.7	-	48	15194_15195	c.15195_15196delGT	c.(15193-15198)tggtccfs	p.WS5065fs		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	5065					chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										ACCTCCGTGGACCAAAGGGCAC	0.619																																					p.5066_5066del		Atlas-Indel,Pindel	.											.	MLL2	1173	.	0			c.15196_15197del						.																																			SO:0001589	frameshift_variant	8085	exon48			.	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.15195_15196delGT	chr12.hg19:g.49420553_49420554delAC	ENSP00000301067:p.Trp5065fs	108.0	0.0		87.0	31.0	NM_003482	O14687	Frame_Shift_Del	DEL	ENST00000301067.7	hg19	CCDS44873.1																																																																																			.	.		0.619	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			-	49420554	AC	-	49420553	7	5	282	1	0	1	0	1	0	0	0	0	9630	275	10	0	1445	0	MLL2	12	49420553	Frame_Shift_Del	DEL	AC	TCGA-G3-A3CJ-01A-11D-A20W-10	1032923	49420553	84431342	866	41100										
MLL2	8085	hgsc.bcm.edu	37	chr12	49444268	49444268	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctgggaaggaggggagttttGgggaaccagggaatgctgaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:49444268delG	ENST00000301067.7	-	11	3102	c.3103delC	c.(3103-3105)caafs	p.Q1035fs		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	1035	Pro-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										GGGGAGTTTTGGGGAACCAGG	0.622																																					p.Q1035fs		Atlas-INDEL	.											.	MLL2	1173	.	0			c.3104delA						.						68	77	74					12																	49444268		2085	4223	6308	SO:0001589	frameshift_variant	8085	exon11			.	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.3103delC	chr12.hg19:g.49444268delG	ENSP00000301067:p.Gln1035fs	310.0	0.0		223.0	15.0	NM_003482	O14687	Frame_Shift_Del	DEL	ENST00000301067.7	hg19	CCDS44873.1																																																																																			.	.		0.622	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			-	49444268	G	-	49444268	7	5	282	1	0	1	0	1	0	0	0	0	9630	1357	47	0	13686	0	MLL2	12	49444268	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	23715	49444268	84407627	867	41101										
FAM186B	84070	hgsc.bcm.edu	37	chr12	49993487	49993487	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tatctgcaaagagggccaggTcagccttcggatggatgtcc	13	10	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:49993487T>C	ENST00000257894.2	-	4	2097	c.1936A>G	c.(1936-1938)Acc>Gcc	p.T646A	FAM186B_ENST00000551047.1_Intron|FAM186B_ENST00000544141.1_Missense_Mutation_p.T556A	NM_032130.2	NP_115506.1	Q8IYM0	F186B_HUMAN	family with sequence similarity 186, member B	646						protein complex (GO:0043234)				breast(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GAGGGCCAGGTCAGCCTTCGG	0.532																																					p.T646A		Atlas-SNP	.											.	FAM186B	72	.	0			c.A1936G						.						78	71	74					12																	49993487		2203	4300	6503	SO:0001583	missense	84070	exon4			GCCAGGTCAGCCT	AL136748	CCDS8788.1	12q13.12	2008-09-17	2008-09-17	2008-09-17	ENSG00000135436	ENSG00000135436			25296	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 25"	C12orf25		11230166	Standard	NM_032130		Approved	DKFZP434J0113	uc001ruo.3	Q8IYM0	OTTHUMG00000167427	ENST00000257894.2:c.1936A>G	chr12.hg19:g.49993487T>C	ENSP00000257894:p.Thr646Ala	119.0	0.0		86.0	4.0	NM_032130	B4DZ15|Q8TCP7|Q9H0L3	Missense_Mutation	SNP	ENST00000257894.2	hg19	CCDS8788.1	.	.	.	.	.	.	.	.	.	.	T	7.969	0.748676	0.15710	.	.	ENSG00000135436	ENST00000544141;ENST00000532262;ENST00000257894	T;T;T	0.12147	2.71;2.71;2.92	4.72	-9.44	0.00603	.	1.359190	0.04820	N	0.436840	T	0.06600	0.0169	L	0.31294	0.92	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.28170	-1.0052	9	.	.	.	-0.6912	0.9145	0.01301	0.4187:0.2184:0.2004:0.1626	.	556;646	B4DZ15;Q8IYM0	.;F186B_HUMAN	A	556;259;646	ENSP00000438569:T556A;ENSP00000436995:T259A;ENSP00000257894:T646A	.	T	-	1	0	FAM186B	48279754	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.023000	0.00641	-2.805000	0.00350	-0.280000	0.10049	ACC	.	.		0.532	FAM186B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394583.2	NM_032130		C	49993487	T	C	49993487	3	2	282	1	0	0	0	0	1	0	0	0	5517	1667	58	2	761	2	FAM186B	12	49993487	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	549219	49993487	83858408	868	41102										
FMNL3	91010	hgsc.bcm.edu	37	chr12	50100871	50100871	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aacctttcctccagctcacaGggctcaggcatcggcatctt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:50100871delG	ENST00000293590.5	-	1	326	c.93delC	c.(91-93)cccfs	p.P31fs	FMNL3_ENST00000335154.5_Frame_Shift_Del_p.P31fs|FMNL3_ENST00000352151.5_Frame_Shift_Del_p.P31fs|FMNL3_ENST00000550488.1_Frame_Shift_Del_p.P31fs			Q8IVF7	FMNL3_HUMAN	formin-like 3	31	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin cytoskeleton organization (GO:0030036)|cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)	GTPase activating protein binding (GO:0032794)			breast(4)|endometrium(7)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(2)|stomach(1)	39						CCAGCTCACAGGGCTCAGGCA	0.716																																					p.C32fs		Atlas-INDEL	.											.	FMNL3	137	.	0			c.94delT						.						14	22	19					12																	50100871		2011	4175	6186	SO:0001589	frameshift_variant	91010	exon1			.	AK128195	CCDS41780.1, CCDS44874.1	12q13.12	2006-04-10							23698	protein-coding gene	gene with protein product						12684686	Standard	NM_198900		Approved	DKFZp762B245, MGC45819, WBP3	uc001ruv.1	Q8IVF7	OTTHUMG00000169651	ENST00000293590.5:c.93delC	chr12.hg19:g.50100871delG	ENSP00000293590:p.Pro31fs	321.0	0.0		228.0	14.0	NM_175736	B0JZA7|Q6ZRJ1	Frame_Shift_Del	DEL	ENST00000293590.5	hg19																																																																																				.	.		0.716	FMNL3-201	KNOWN	basic	protein_coding	protein_coding		NM_175736		-	50100871	G	-	50100871	7	5	282	1	0	1	0	1	0	0	0	0	5961	987	35	0	3094	0	FMNL3	12	50100871	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	107384	50100871	83751024	869	41103										
NCKAP5L	57701	hgsc.bcm.edu	37	chr12	50186232	50186232	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tctgctgcaattctcaccatGggggtcctgggcagcccctc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:50186232delG	ENST00000335999.6	-	12	3990	c.3789delC	c.(3787-3789)cccfs	p.P1263fs		NM_001037806.3	NP_001032895.2	Q9HCH0	NCK5L_HUMAN	NCK-associated protein 5-like	1259	Pro-rich.									central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(8)|prostate(2)	18						TTCTCACCATGGGGGTCCTGG	0.612																																					p.M1264fs		Atlas-INDEL	.											.	NCKAP5L	142	.	0			c.3790delA						.						27	31	29					12																	50186232		1950	4137	6087	SO:0001589	frameshift_variant	57701	exon12			.	AB046822	CCDS41781.2	12q13.12	2009-08-14	2009-08-14	2009-08-14	ENSG00000167566	ENSG00000167566			29321	protein-coding gene	gene with protein product		615104	"KIAA1602"	KIAA1602			Standard	NM_001037806		Approved		uc009zlk.2	Q9HCH0	OTTHUMG00000156969	ENST00000335999.6:c.3789delC	chr12.hg19:g.50186232delG	ENSP00000337998:p.Pro1263fs	165.0	0.0		149.0	13.0	NM_001037806	Q2TB26|Q71RH1|Q8N4W1|Q96HX2	Frame_Shift_Del	DEL	ENST00000335999.6	hg19	CCDS41781.2																																																																																			.	.		0.612	NCKAP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346884.2	XM_035497		-	50186232	G	-	50186232	7	5	282	1	0	1	0	1	0	0	0	0	10233	1335	47	0	223	0	NCKAP5L	12	50186232	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	85361	50186232	83665663	870	41104										
KRT72	140807	hgsc.bcm.edu	37	chr12	52981443	52981443	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctcgctctccagcagcttgcGgtaggtggcgatctccatat	11	13	2	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:52981443G>A	ENST00000537672.2	-	7	1292	c.1282C>T	c.(1282-1284)Cgc>Tgc	p.R428C	KRT72_ENST00000354310.4_Missense_Mutation_p.R386C|KRT72_ENST00000293745.2_Missense_Mutation_p.R428C|KRT72_ENST00000398066.3_Missense_Mutation_p.R240C	NM_001146225.1	NP_001139697.1	Q14CN4	K2C72_HUMAN	keratin 72	428	Coil 2.|Rod.		R -> L (in dbSNP:rs11170183). {ECO:0000269|PubMed:14702039}.			extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(357;0.195)		AGCAGCTTGCGGTAGGTGGCG	0.612																																					p.R428C		Atlas-SNP	.											KRT72,caecum,carcinoma,+1,1	KRT72	70	.	0			c.C1282T						.						107	98	101					12																	52981443		2203	4300	6503	SO:0001583	missense	140807	exon7			GCTTGCGGTAGGT	AY033495	CCDS8833.1, CCDS53795.1	12q13.13	2013-06-25			ENSG00000170486	ENSG00000170486		"-", "Intermediate filaments type II, keratins (basic)"	28932	protein-coding gene	gene with protein product		608246				12648212, 11703281, 16831889	Standard	NM_080747		Approved	K6IRS2, KRT6IRS2, KRT6, K6irs	uc001saq.2	Q14CN4	OTTHUMG00000169744	ENST00000537672.2:c.1282C>T	chr12.hg19:g.52981443G>A	ENSP00000441160:p.Arg428Cys	267.0	0.0		161.0	0.0	NM_001146225	B4DEI8|H9KV51|Q8NA87|Q8WWY9|Q8WWZ0	Missense_Mutation	SNP	ENST00000537672.2	hg19	CCDS8833.1	.	.	.	.	.	.	.	.	.	.	G	17.89	3.499073	0.64298	.	.	ENSG00000170486	ENST00000537672;ENST00000293745;ENST00000354310;ENST00000398066	D;D;D;D	0.94828	-3.53;-3.53;-3.53;-3.53	4.92	1.52	0.23074	Filament (1);Intermediate filament protein, conserved site (1);	0.000000	0.44483	D	0.000445	D	0.97688	0.9242	H	0.95004	3.61	0.44409	D	0.997323	D	0.76494	0.999	D	0.66716	0.946	D	0.98190	1.0462	10	0.72032	D	0.01	.	15.7025	0.77552	0.0:0.0:0.2567:0.7433	.	428	Q14CN4	K2C72_HUMAN	C	428;428;386;240	ENSP00000441160:R428C;ENSP00000293745:R428C;ENSP00000346269:R386C;ENSP00000446151:R240C	ENSP00000293745:R428C	R	-	1	0	KRT72	51267710	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	0.987000	0.29603	0.133000	0.18654	-0.284000	0.09977	CGC	.	.		0.612	KRT72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405693.1	NM_080747		A	52981443	G	A	52981443	3	1	282	1	0	0	0	0	1	0	0	0	8494	1116	39	1	265	1	KRT72	12	52981443	Missense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	2795211	52981443	80870452	871	41105										
KIAA0748	9840	hgsc.bcm.edu	37	chr12	55356761	55356761	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tggtccaaactgttccttttGggggtgttgtggggtggtgg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:55356761delG	ENST00000449076.1	-	9	1053	c.921delC	c.(919-921)cccfs	p.P307fs	TESPA1_ENST00000531122.1_Frame_Shift_Del_p.P169fs|TESPA1_ENST00000532804.1_Frame_Shift_Del_p.P169fs|TESPA1_ENST00000524959.1_5'Flank|TESPA1_ENST00000524622.1_Frame_Shift_Del_p.P169fs|TESPA1_ENST00000316577.8_Frame_Shift_Del_p.P307fs	NM_001136030.2	NP_001129502.1	A2RU30	TESP1_HUMAN	thymocyte expressed, positive selection associated 1	307					COP9 signalosome assembly (GO:0010387)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of T cell receptor signaling pathway (GO:0050862)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)											TGTTCCTTTTGGGGGTGTTGT	0.532																																					p.K308fs		Atlas-INDEL	.											.	.	.	.	0			c.922delA						.						62	63	63					12																	55356761		1914	4111	6025	SO:0001589	frameshift_variant	9840	exon9			.	AB018291	CCDS44913.1, CCDS58240.1	12q13.2	2012-03-21	2012-03-21	2012-03-21	ENSG00000135426	ENSG00000135426			29109	protein-coding gene	gene with protein product		615664	"KIAA0748"	KIAA0748		9872452	Standard	NM_001136030		Approved		uc001sgn.4	A2RU30	OTTHUMG00000165407	ENST00000449076.1:c.921delC	chr12.hg19:g.55356761delG	ENSP00000400892:p.Pro307fs	169.0	0.0		153.0	12.0	NM_001098815	B4DPM3|B4E048|B7Z9K7|O94849|Q4G0P2|Q9P0C4	Frame_Shift_Del	DEL	ENST00000449076.1	hg19	CCDS44913.1																																																																																			.	.		0.532	TESPA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383822.1	NM_001098815		-	55356761	G	-	55356761	7	5	282	1	0	1	0	1	0	0	0	0	8199	1335	47	0	652	0	KIAA0748	12	55356761	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	2375318	55356761	78495134	872	41106										
SARNP	84324	hgsc.bcm.edu	37	chr12	56154345	56154345	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atatttttacctctgtatccTctgtggttccagttccagct	6	11	2	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:56154345T>C	ENST00000336133.3	-	10	635	c.581A>G	c.(580-582)gAg>gGg	p.E194G	RP11-762I7.4_ENST00000547009.1_RNA|SARNP_ENST00000444631.2_Missense_Mutation_p.E134G|SARNP_ENST00000552080.1_Missense_Mutation_p.E194G|RP11-762I7.5_ENST00000546837.1_Silent_p.R506R	NM_033082.3	NP_149073.1	P82979	SARNP_HUMAN	SAP domain containing ribonucleoprotein	194					mRNA export from nucleus (GO:0006406)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|transcription, DNA-templated (GO:0006351)	intracellular membrane-bounded organelle (GO:0043231)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|transcription export complex (GO:0000346)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	6						CTCTGTATCCTCTGTGGTTCC	0.398																																					p.E194G		Atlas-SNP	.											.	SARNP	19	.	0			c.A581G						.						140	131	134					12																	56154345		2203	4300	6503	SO:0001583	missense	84324	exon10			GTATCCTCTGTGG	AJ409089	CCDS8892.1	12q13.2	2009-07-09				ENSG00000205323			24432	protein-coding gene	gene with protein product	"hepatocellular carcinoma 1", "cytokine induced protein 29 kDa"	610049				11356193, 11922608	Standard	NM_033082		Approved	THO1, Hcc-1, CIP29		P82979	OTTHUMG00000170441	ENST00000336133.3:c.581A>G	chr12.hg19:g.56154345T>C	ENSP00000337632:p.Glu194Gly	124.0	0.0		98.0	4.0	NM_033082	A8K393|Q9P066	Missense_Mutation	SNP	ENST00000336133.3	hg19	CCDS8892.1	.	.	.	.	.	.	.	.	.	.	T	27.1	4.801171	0.90538	.	.	ENSG00000205323	ENST00000444631;ENST00000336133;ENST00000552080	.	.	.	5.72	5.72	0.89469	.	0.183998	0.49305	D	0.000146	T	0.45034	0.1322	L	0.49778	1.585	0.51482	D	0.999922	P	0.40970	0.734	B	0.31751	0.135	T	0.52434	-0.8576	9	0.66056	D	0.02	-13.3564	14.2653	0.66113	0.0:0.0:0.0:1.0	.	194	P82979	SARNP_HUMAN	G	134;194;194	.	ENSP00000337632:E194G	E	-	2	0	SARNP	54440612	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.989000	0.56958	2.320000	0.78422	0.528000	0.53228	GAG	.	.		0.398	SARNP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409159.2	NM_033082		C	56154345	T	C	56154345	3	2	282	1	0	0	0	0	1	0	0	0	13858	1551	54	2	59	2	SARNP	12	56154345	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	797584	56154345	77697550	873	41107										
PAN2	9924	hgsc.bcm.edu	37	chr12	56716892	56716892	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgcaaacatccagccctttgTttttggtcatcttcatgcga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:56716892delT	ENST00000425394.2	-	17	2835	c.2459delA	c.(2458-2460)aacfs	p.N820fs	PAN2_ENST00000548043.1_Frame_Shift_Del_p.N820fs|PAN2_ENST00000257931.5_Frame_Shift_Del_p.N819fs|PAN2_ENST00000440411.3_Frame_Shift_Del_p.N816fs	NM_001127460.2	NP_001120932	Q9HBH5	RDH14_HUMAN	PAN2 poly(A) specific ribonuclease subunit	142					osteoblast differentiation (GO:0001649)	endoplasmic reticulum (GO:0005783)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	41					Vitamin A(DB00162)	CAGCCCTTTGTTTTTGGTCAT	0.498																																					p.N820fs		Atlas-INDEL	.											.	PAN2	107	.	0			c.2460delC						.						162	160	161					12																	56716892		2203	4300	6503	SO:0001589	frameshift_variant	9924	exon17			.	AB014610	CCDS8915.1, CCDS44922.1, CCDS53802.1	12q13.2	2014-03-27	2014-03-27	2008-01-08		ENSG00000135473		"Ubiquitin-specific peptidases"	20074	protein-coding gene	gene with protein product	"PAN2 homolog, PABP1 dependent poly A specific ribonuclease subunit (S. cerevisiae)"		"ubiquitin specific protease 52", "ubiquitin specific peptidase 52", "PAN2 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)"	USP52		12838346, 14583602	Standard	NM_014871		Approved	KIAA0710, hPAN2	uc001skx.3	Q504Q3	OTTHUMG00000170412	ENST00000425394.2:c.2459delA	chr12.hg19:g.56716892delT	ENSP00000401721:p.Asn820fs	188.0	0.0		150.0	10.0	NM_001127460		Frame_Shift_Del	DEL	ENST00000425394.2	hg19	CCDS44922.1																																																																																			.	.		0.498	PAN2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409024.1	NM_014871		-	56716892	T	-	56716892	7	5	282	1	0	1	0	1	0	0	0	0	11423	1725	60	0	1189	0	PAN2	12	56716892	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	562547	56716892	77135003	874	41108										
APOF	319	hgsc.bcm.edu	37	chr12	56755066	56755066	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tagctcttgattatggcccaCccccagtagggagctgaact							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:56755066delC	ENST00000398189.3	-	2	1001	c.924delG	c.(922-924)gggfs	p.G308fs	APOF_ENST00000541105.1_Frame_Shift_Del_p.G290fs|STAT2_ENST00000418572.2_5'Flank|STAT2_ENST00000314128.4_5'Flank|STAT2_ENST00000557235.1_5'Flank	NM_001638.2	NP_001629.1	Q13790	APOF_HUMAN	apolipoprotein F	308					cholesterol efflux (GO:0033344)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	extracellular region (GO:0005576)|high-density lipoprotein particle (GO:0034364)|low-density lipoprotein particle (GO:0034362)	cholesterol binding (GO:0015485)|lipid transporter activity (GO:0005319)|receptor binding (GO:0005102)			breast(1)|lung(3)|prostate(1)|stomach(1)	6						TTATGGCCCACCCCCAGTAGG	0.448																																					p.W309fs		Atlas-INDEL	.											.	APOF	13	.	0			c.925delT						.						63	63	63					12																	56755066		1869	4084	5953	SO:0001589	frameshift_variant	319	exon2			.	L27050	CCDS44923.1	12q13	2013-01-24				ENSG00000175336		"Apolipoproteins"	615	protein-coding gene	gene with protein product		107760				8093033	Standard	NM_001638		Approved		uc001sle.1	Q13790		ENST00000398189.3:c.924delG	chr12.hg19:g.56755066delC	ENSP00000381250:p.Gly308fs	251.0	0.0		192.0	12.0	NM_001638	Q8TC13	Frame_Shift_Del	DEL	ENST00000398189.3	hg19	CCDS44923.1																																																																																			.	.		0.448	APOF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410076.1			-	56755066	C	-	56755066	7	5	282	1	0	1	0	1	0	0	0	0	803	494	18	0	60	0	APOF	12	56755066	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	38174	56755066	77096829	875	41109										
MIP	4284	hgsc.bcm.edu	37	chr12	56848277	56848277	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgccatagccacctgcagaaCatgcaggggtccaggagccc	12	14	0	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:56848277C>A	ENST00000257979.4	-	1	149	c.121G>T	c.(121-123)Gtt>Ttt	p.V41F	MIP_ENST00000555551.1_Intron	NM_012064.3	NP_036196.1	P30301	MIP_HUMAN	major intrinsic protein of lens fiber	41					canalicular bile acid transport (GO:0015722)|lens development in camera-type eye (GO:0002088)|response to stimulus (GO:0050896)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)|water transport (GO:0006833)	gap junction (GO:0005921)|integral component of plasma membrane (GO:0005887)|intracellular canaliculus (GO:0046691)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|structural constituent of eye lens (GO:0005212)|transporter activity (GO:0005215)|water channel activity (GO:0015250)			kidney(1)|large_intestine(2)|lung(8)|prostate(1)|skin(3)|urinary_tract(1)	16						ACCTGCAGAACATGCAGGGGT	0.572																																					p.V41F		Atlas-SNP	.											.	MIP	39	.	0			c.G121T						.						84	80	81					12																	56848277		2203	4300	6503	SO:0001583	missense	4284	exon1			GCAGAACATGCAG		CCDS8919.1	12q13	2012-10-02				ENSG00000135517		"Ion channels / Aquaporins"	7103	protein-coding gene	gene with protein product	aquaporin 0	154050				1840563, 7536742	Standard	NM_012064		Approved	MP26, LIM1, AQP0	uc001slh.3	P30301		ENST00000257979.4:c.121G>T	chr12.hg19:g.56848277C>A	ENSP00000257979:p.Val41Phe	439.0	0.0		334.0	133.0	NM_012064	Q17R41	Missense_Mutation	SNP	ENST00000257979.4	hg19	CCDS8919.1	.	.	.	.	.	.	.	.	.	.	C	18.63	3.665011	0.67700	.	.	ENSG00000135517	ENST00000257979	D	0.85171	-1.95	5.31	3.49	0.39957	Aquaporin-like (2);	0.058543	0.64402	D	0.000002	T	0.79896	0.4525	N	0.16368	0.405	0.58432	D	0.999999	P	0.39376	0.67	P	0.48770	0.589	T	0.78575	-0.2151	10	0.59425	D	0.04	-20.4468	9.2039	0.37278	0.0:0.7625:0.0:0.2375	.	41	P30301	MIP_HUMAN	F	41	ENSP00000257979:V41F	ENSP00000257979:V41F	V	-	1	0	MIP	55134544	0.767000	0.28508	0.978000	0.43139	0.901000	0.52897	0.272000	0.18644	0.749000	0.32854	0.655000	0.94253	GTT	.	.		0.572	MIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409620.1	NM_012064		A	56848277	C	A	56848277	3	1	282	1	0	0	0	0	1	0	0	0	9600	478	17	3	686	3	MIP	12	56848277	Missense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	93211	56848277	77003618	876	41110										
BAZ2A	11176	hgsc.bcm.edu	37	chr12	56994135	56994135	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gccgcatcacagccaggtccAaagggttggtagttttacgc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:56994135delA	ENST00000551812.1	-	24	4941	c.4748delT	c.(4747-4749)ttgfs	p.L1583fs	BAZ2A_ENST00000179765.5_Frame_Shift_Del_p.L1551fs|BAZ2A_ENST00000549884.1_Frame_Shift_Del_p.L1581fs|BAZ2A_ENST00000553222.1_5'Flank|BAZ2A_ENST00000379441.3_Frame_Shift_Del_p.L1553fs	NM_013449.3	NP_038477.2	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	1583					chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA methylation (GO:0006306)|heterochromatin assembly involved in chromatin silencing (GO:0070869)|histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|histone H4 deacetylation (GO:0070933)|histone H4-K20 methylation (GO:0034770)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|nucleolus (GO:0005730)|rDNA heterochromatin (GO:0033553)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|lysine-acetylated histone binding (GO:0070577)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(15)|urinary_tract(1)	31						AGCCAGGTCCAAAGGGTTGGT	0.607																																					p.L1583fs		Atlas-INDEL	.											.	BAZ2A	263	.	0			c.4749delG						.						50	57	55					12																	56994135		2082	4201	6283	SO:0001589	frameshift_variant	11176	exon24			.	AB032254	CCDS44924.1, CCDS73483.1	12q13.3	2013-01-28				ENSG00000076108		"Zinc fingers, PHD-type"	962	protein-coding gene	gene with protein product	"TTF-I interacting peptide 5"	605682				10662543, 11532953	Standard	XM_005268596		Approved	KIAA0314, TIP5, WALp3	uc001slq.1	Q9UIF9	OTTHUMG00000170332	ENST00000551812.1:c.4748delT	chr12.hg19:g.56994135delA	ENSP00000446880:p.Leu1583fs	169.0	0.0		129.0	10.0	NM_013449	B3KN66|O00536|O15030|Q68DI8|Q96H26	Frame_Shift_Del	DEL	ENST00000551812.1	hg19	CCDS44924.1																																																																																			.	.		0.607	BAZ2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408561.1	NM_013449		-	56994135	A	-	56994135	7	5	282	1	0	1	0	1	0	0	0	0	1331	131	5	0	993	0	BAZ2A	12	56994135	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	145858	56994135	76857760	877	41111										
LRP1	4035	hgsc.bcm.edu	37	chr12	57550002	57550002	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tttaacagcaccgagtaccaGgttgtcacccgggtggacaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:57550002delG	ENST00000243077.3	+	9	1819	c.1353delG	c.(1351-1353)cagfs	p.Q451fs		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	451					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	CCGAGTACCAGGTTGTCACCC	0.572																																					p.Q451fs		Atlas-INDEL	.											.	LRP1	428	.	0			c.1352delA						.						146	113	124					12																	57550002		2203	4300	6503	SO:0001589	frameshift_variant	4035	exon9			.	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"CD molecules", "Low density lipoprotein receptors"	6692	protein-coding gene	gene with protein product		107770	"alpha-2-macroglobulin receptor"	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.1353delG	chr12.hg19:g.57550002delG	ENSP00000243077:p.Gln451fs	225.0	0.0		177.0	11.0	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Frame_Shift_Del	DEL	ENST00000243077.3	hg19	CCDS8932.1																																																																																			.	.		0.572	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		-	57550002	G	-	57550002	7	5	282	1	0	1	0	1	0	0	0	0	8960	991	35	0	1387	0	LRP1	12	57550002	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	555867	57550002	76301893	878	41112										
LRP1	4035	hgsc.bcm.edu	37	chr12	57556256	57556256	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cccttctgcgcagtgagcggCcccccatctttgagatccga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:57556256delC	ENST00000243077.3	+	14	2825	c.2359delC	c.(2359-2361)cccfs	p.P788fs		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	788					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	CAGTGAGCGGCCCCCCATCTT	0.617																																					p.R786fs		Atlas-INDEL	.											.	LRP1	428	.	0			c.2358delG						.						90	80	83					12																	57556256		2203	4300	6503	SO:0001589	frameshift_variant	4035	exon14			.	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"CD molecules", "Low density lipoprotein receptors"	6692	protein-coding gene	gene with protein product		107770	"alpha-2-macroglobulin receptor"	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.2359delC	chr12.hg19:g.57556256delC	ENSP00000243077:p.Pro788fs	185.0	0.0		118.0	10.0	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Frame_Shift_Del	DEL	ENST00000243077.3	hg19	CCDS8932.1																																																																																			.	.		0.617	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		-	57556256	C	-	57556256	7	5	282	1	0	1	0	1	0	0	0	0	8960	739	26	0	2413	0	LRP1	12	57556256	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	6254	57556256	76295639	879	41113										
DCTN2	10540	hgsc.bcm.edu	37	chr12	57928844	57928844	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agagtttgtagttaccttgaTtttttcaacttcagttgtca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:57928844delT	ENST00000548249.1	-	5	625	c.358delA	c.(358-360)atcfs	p.I120fs	DCTN2_ENST00000551400.1_5'UTR|DCTN2_ENST00000543672.1_Frame_Shift_Del_p.I125fs|DCTN2_ENST00000537439.1_Frame_Shift_Del_p.I97fs|DCTN2_ENST00000434715.3_Frame_Shift_Del_p.I125fs	NM_001261412.1|NM_001261413.1	NP_001248341.1|NP_001248342.1	Q13561	DCTN2_HUMAN	dynactin 2 (p50)	120					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|melanosome transport (GO:0032402)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|vesicle (GO:0031982)	motor activity (GO:0003774)|spectrin binding (GO:0030507)			endometrium(1)|large_intestine(4)|lung(2)|ovary(2)|upper_aerodigestive_tract(2)	11						GTTACCTTGATTTTTTCAACT	0.493																																					p.I122fs		Atlas-INDEL	.											.	DCTN2	51	.	0			c.365delT						.						149	143	145					12																	57928844		1942	4133	6075	SO:0001589	frameshift_variant	10540	exon5			.	U50733	CCDS44930.1, CCDS58245.1, CCDS73489.1	12q13.3	2008-05-14				ENSG00000175203			2712	protein-coding gene	gene with protein product		607376				8647893	Standard	NM_001261412		Approved	RBP50, DCTN-50	uc001som.2	Q13561	OTTHUMG00000170124	ENST00000548249.1:c.358delA	chr12.hg19:g.57928844delT	ENSP00000447824:p.Ile120fs	289.0	0.0		209.0	13.0	NM_001261412	B2RBK5|Q86YN2|Q9BW17	Frame_Shift_Del	DEL	ENST00000548249.1	hg19	CCDS58245.1																																																																																			.	.		0.493	DCTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407393.2	NM_006400		-	57928844	T	-	57928844	7	5	282	1	0	1	0	1	0	0	0	0	4309	1493	52	0	887	0	DCTN2	12	57928844	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	372588	57928844	75923051	880	41114										
TSPAN31	6302	hgsc.bcm.edu	37	chr12	58140374	58140374	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tctacccatatctttcagacAgatgtcatcaatgcttcttg	5	11	6	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:58140374A>G	ENST00000257910.3	+	4	589	c.315A>G	c.(313-315)acA>acG	p.T105T	CDK4_ENST00000551888.1_5'Flank|TSPAN31_ENST00000553221.1_3'UTR|TSPAN31_ENST00000547472.1_Silent_p.T22T|TSPAN31_ENST00000547992.1_Intron	NM_005981.3	NP_005972.1	Q12999	TSN31_HUMAN	tetraspanin 31	105					positive regulation of cell proliferation (GO:0008284)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				endometrium(1)|kidney(1)|lung(5)	7	all_cancers(7;4.96e-69)|Lung NSC(6;5.5e-25)|all_lung(6;3.87e-23)|all_epithelial(6;1.66e-15)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)		GBM - Glioblastoma multiforme(5;4.21e-120)|all cancers(5;3.75e-83)|BRCA - Breast invasive adenocarcinoma(9;0.0294)			TCTTTCAGACAGATGTCATCA	0.433																																					p.T105T		Atlas-SNP	.											.	TSPAN31	20	.	0			c.A315G						.						142	126	132					12																	58140374		2203	4300	6503	SO:0001819	synonymous_variant	6302	exon4			TCAGACAGATGTC		CCDS8952.1	12q13-q14	2013-02-14	2005-08-16	2005-08-16		ENSG00000135452		"Tetraspanins"	10539	protein-coding gene	gene with protein product		181035	"sarcoma amplified sequence"	SAS			Standard	NM_005981		Approved		uc001spt.3	Q12999		ENST00000257910.3:c.315A>G	chr12.hg19:g.58140374A>G		208.0	0.0		122.0	5.0	NM_005981	O00577|Q53X76	Silent	SNP	ENST00000257910.3	hg19	CCDS8952.1																																																																																			.	.		0.433	TSPAN31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408778.1			G	58140374	A	G	58140374	2	3	282	1	0	0	0	0	0	0	0	1	16661	175	7	2		2	TSPAN31	12	58140374	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	211530	58140374	75711521	881	41115										
USP15	9958	hgsc.bcm.edu	37	chr12	62785098	62785098	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaggtcaactcacgggacacAaaaaacgattgtttacattc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:62785098delA	ENST00000280377.5	+	16	2180	c.2122delA	c.(2122-2124)aaafs	p.K709fs	USP15_ENST00000393654.3_Frame_Shift_Del_p.K684fs|USP15_ENST00000353364.3_Frame_Shift_Del_p.K680fs	NM_001252078.1	NP_001239007.1	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15	709	USP.				BMP signaling pathway (GO:0030509)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|protein deubiquitination (GO:0016579)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|identical protein binding (GO:0042802)|SMAD binding (GO:0046332)|transforming growth factor beta receptor binding (GO:0005160)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(15)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	37			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)		CACGGGACACAAAAAACGATT	0.368																																					p.H707fs	Melanoma(181;615 2041 39364 49691 50001)	Atlas-INDEL	.											.	USP15	105	.	0			c.2121delC						.						116	114	115					12																	62785098		2203	4300	6503	SO:0001589	frameshift_variant	9958	exon16			.	AB011101	CCDS8963.1, CCDS58250.1, CCDS58251.1	12q14	2006-07-18	2005-08-08					"Ubiquitin-specific peptidases"	12613	protein-coding gene	gene with protein product		604731	"ubiquitin specific protease 15"			12838346	Standard	NM_001252078		Approved	KIAA0529, UNPH4	uc001src.2	Q9Y4E8	OTTHUMG00000170186	ENST00000280377.5:c.2122delA	chr12.hg19:g.62785098delA	ENSP00000280377:p.Lys709fs	213.0	0.0		164.0	11.0	NM_001252078	Q08AL5|Q9H8G9|Q9HCA6|Q9UNP0|Q9Y5B5	Frame_Shift_Del	DEL	ENST00000280377.5	hg19	CCDS58251.1																																																																																			.	.		0.368	USP15-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407831.2	NM_006313		-	62785098	A	-	62785098	7	5	282	1	0	1	0	1	0	0	0	0	17061	131	5	0	2093	0	USP15	12	62785098	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	4644724	62785098	71066797	882	41116										
CNOT2	4848	hgsc.bcm.edu	37	chr12	70747643	70747643	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atatgacaaattagaagaacGgcctcacctgccatccacct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:70747643delG	ENST00000418359.3	+	17	2022	c.1571delG	c.(1570-1572)cggfs	p.R524fs	CNOT2_ENST00000229195.3_Frame_Shift_Del_p.R524fs|CNOT2_ENST00000551483.1_Frame_Shift_Del_p.R175fs	NM_001199302.1	NP_001186231.1	Q9NZN8	CNOT2_HUMAN	CCR4-NOT transcription complex, subunit 2	524	Repressor domain.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription from RNA polymerase II promoter (GO:0006366)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription corepressor binding (GO:0001226)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|pancreas(2)|urinary_tract(1)	20	Renal(347;0.236)		GBM - Glioblastoma multiforme(1;4.77e-09)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00243)|STAD - Stomach adenocarcinoma(21;0.0118)			TTAGAAGAACGGCCTCACCTG	0.343																																					p.R524fs		Atlas-INDEL	.											CNOT2,NS,carcinoma,0,1	CNOT2	53	.	0			c.1570delC						.						79	87	84					12																	70747643		2203	4300	6503	SO:0001589	frameshift_variant	4848	exon17			.	AF180473	CCDS31857.1	12q15	2008-05-14				ENSG00000111596			7878	protein-coding gene	gene with protein product		604909		NOT2		10637334	Standard	NM_014515		Approved	CDC36, NOT2H	uc001svv.3	Q9NZN8		ENST00000418359.3:c.1571delG	chr12.hg19:g.70747643delG	ENSP00000412091:p.Arg524fs	261.0	0.0		175.0	11.0	NM_001199302	Q9H3E0|Q9NSX5|Q9NWR6|Q9P028	Frame_Shift_Del	DEL	ENST00000418359.3	hg19	CCDS31857.1																																																																																			.	.		0.343	CNOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404260.1			-	70747643	G	-	70747643	7	5	282	1	0	1	0	1	0	0	0	0	3621	1116	39	0	1629	0	CNOT2	12	70747643	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	7962545	70747643	63104252	883	41117										
PTPRB	5787	hgsc.bcm.edu	37	chr12	70928316	70928316	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccgggcttctgttgatgtagTccctgacagttctcacaaac	9	12	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:70928316T>C	ENST00000261266.5	-	29	5695	c.5666A>G	c.(5665-5667)gAc>gGc	p.D1889G	RP11-588H23.3_ENST00000548687.1_RNA|PTPRB_ENST00000550857.1_Missense_Mutation_p.D1799G|RP11-588H23.3_ENST00000549460.1_RNA|PTPRB_ENST00000550358.1_Missense_Mutation_p.D2019G|RP11-588H23.3_ENST00000551438.1_RNA|PTPRB_ENST00000538708.1_Missense_Mutation_p.D1799G|RP11-588H23.3_ENST00000546836.1_RNA|PTPRB_ENST00000451516.2_Missense_Mutation_p.D1799G|RP11-588H23.3_ENST00000547656.1_RNA|PTPRB_ENST00000334414.6_Missense_Mutation_p.D2107G	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	1889	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			GTTGATGTAGTCCCTGACAGT	0.547																																					p.D2107G		Atlas-SNP	.											.	PTPRB	676	.	0			c.A6320G						.						44	43	44					12																	70928316		1903	4128	6031	SO:0001583	missense	5787	exon31			ATGTAGTCCCTGA	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.5666A>G	chr12.hg19:g.70928316T>C	ENSP00000261266:p.Asp1889Gly	235.0	0.0		142.0	6.0	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Missense_Mutation	SNP	ENST00000261266.5	hg19	CCDS44944.1	.	.	.	.	.	.	.	.	.	.	T	17.62	3.434254	0.62955	.	.	ENSG00000127329	ENST00000334414;ENST00000451516;ENST00000550358;ENST00000538708;ENST00000550857;ENST00000261266	D;D;D;D;D;D	0.83506	-1.73;-1.73;-1.73;-1.73;-1.73;-1.73	5.67	5.67	0.87782	Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.85682	D	0.000000	D	0.87767	0.6260	L	0.39898	1.24	0.80722	D	1	P;P;D;P;B	0.89917	0.697;0.936;1.0;0.888;0.414	P;P;D;P;P	0.91635	0.612;0.897;0.999;0.815;0.457	D	0.89075	0.3472	10	0.87932	D	0	.	15.9212	0.79575	0.0:0.0:0.0:1.0	.	1799;1799;2107;1889;2019	P23467-2;F5H3G6;P23467-3;P23467;F8VU56	.;.;.;PTPRB_HUMAN;.	G	2107;1799;2019;1799;1799;1889	ENSP00000334928:D2107G;ENSP00000393028:D1799G;ENSP00000448058:D2019G;ENSP00000438927:D1799G;ENSP00000447302:D1799G;ENSP00000261266:D1889G	ENSP00000261266:D1889G	D	-	2	0	PTPRB	69214583	1.000000	0.71417	1.000000	0.80357	0.833000	0.47200	6.186000	0.72026	2.155000	0.67459	0.460000	0.39030	GAC	.	.		0.547	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1			C	70928316	T	C	70928316	3	2	282	1	0	0	0	0	1	0	0	0	12811	1667	58	2	343	2	PTPRB	12	70928316	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	180673	70928316	62923579	884	41118										
CAPS2	84698	hgsc.bcm.edu	37	chr12	75692472	75692472	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acacacaccacttacaacatAaaaatcaccaagtcggtatt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:75692472delA	ENST00000409445.3	-	12	1292	c.1096delT	c.(1096-1098)tatfs	p.Y366fs	CAPS2_ENST00000409799.1_Frame_Shift_Del_p.Y284fs|CAPS2_ENST00000393284.3_Frame_Shift_Del_p.Y134fs|CAPS2_ENST00000409004.1_5'UTR|CAPS2_ENST00000442339.2_Intron|RP11-560G2.1_ENST00000534648.2_RNA	NM_032606.3	NP_115995.2	Q9BXY5	CAYP2_HUMAN	calcyphosine 2	366							calcium ion binding (GO:0005509)			endometrium(2)|large_intestine(1)|lung(4)|ovary(2)|skin(1)	10						CTTACAACATAAAAATCACCA	0.383																																					p.Y366fs		Atlas-INDEL	.											.	CAPS2	96	.	0			c.1097delA						.						137	134	135					12																	75692472		2203	4299	6502	SO:0001589	frameshift_variant	84698	exon12			.	AF251056	CCDS9008.2, CCDS66424.1, CCDS73497.1	12q14.1	2013-01-10	2005-05-09		ENSG00000180881	ENSG00000180881		"EF-hand domain containing"	16471	protein-coding gene	gene with protein product		607724	"calcyphosphine 2"			11846421	Standard	NM_032606		Approved		uc001sxk.4	Q9BXY5	OTTHUMG00000152787	ENST00000409445.3:c.1096delT	chr12.hg19:g.75692472delA	ENSP00000386959:p.Tyr366fs	234.0	0.0		173.0	11.0	NM_032606	Q6PH84|Q8N242|Q8NAY5	Frame_Shift_Del	DEL	ENST00000409445.3	hg19	CCDS9008.2																																																																																			.	.		0.383	CAPS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000327880.2			-	75692472	A	-	75692472	7	5	282	1	0	1	0	1	0	0	0	0	2640	362	13	0	605	0	CAPS2	12	75692472	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	4764156	75692472	58159423	885	41119										
NAP1L1	4673	hgsc.bcm.edu	37	chr12	76449901	76449901	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggtcttctttttcttcatctTttttctcatcttcaatcttg	3	10	9	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:76449901T>C	ENST00000261182.8	-	7	956	c.470A>G	c.(469-471)aAa>aGa	p.K157R	NAP1L1_ENST00000535020.2_Missense_Mutation_p.K157R|NAP1L1_ENST00000542344.1_Missense_Mutation_p.K115R|NAP1L1_ENST00000548044.1_Missense_Mutation_p.K116R|NAP1L1_ENST00000431879.3_Missense_Mutation_p.K89R|NAP1L1_ENST00000552342.1_Missense_Mutation_p.K168R|NAP1L1_ENST00000547773.1_Missense_Mutation_p.K94R|NAP1L1_ENST00000544816.1_5'UTR|NAP1L1_ENST00000393263.3_Missense_Mutation_p.K157R|NAP1L1_ENST00000547993.1_5'UTR|NAP1L1_ENST00000549596.1_Missense_Mutation_p.K157R	NM_004537.4|NM_139207.2	NP_004528.1|NP_631946.1	P55209	NP1L1_HUMAN	nucleosome assembly protein 1-like 1	157					DNA replication (GO:0006260)|nucleosome assembly (GO:0006334)|positive regulation of cell proliferation (GO:0008284)	membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|skin(1)	9		Colorectal(145;0.09)				TTCTTCATCTTTTTTCTCATC	0.323																																					p.K157R		Atlas-SNP	.											NAP1L1,NS,carcinoma,0,1	NAP1L1	33	.	0			c.A470G						.						66	62	63					12																	76449901		2202	4299	6501	SO:0001583	missense	4673	exon7			TCATCTTTTTTCT		CCDS9013.1	12q21.1	2010-03-17			ENSG00000187109	ENSG00000187109			7637	protein-coding gene	gene with protein product		164060				8297347	Standard	NM_004537		Approved	NRP, NAP1, NAP1L, MGC8688, MGC23410	uc001sxx.2	P55209		ENST00000261182.8:c.470A>G	chr12.hg19:g.76449901T>C	ENSP00000261182:p.Lys157Arg	565.0	2.0		428.0	0.0	NM_004537	B3KNT8	Missense_Mutation	SNP	ENST00000261182.8	hg19	CCDS9013.1	.	.	.	.	.	.	.	.	.	.	T	18.36	3.606596	0.66445	.	.	ENSG00000187109	ENST00000261182;ENST00000552056;ENST00000393263;ENST00000431879;ENST00000547773;ENST00000542344;ENST00000535020;ENST00000549596;ENST00000552342;ENST00000548044;ENST00000550934;ENST00000551992;ENST00000548273;ENST00000551600;ENST00000547704	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.26067	1.76;1.76;1.76;1.76;1.76;1.76;1.76;1.76;1.76;1.76;1.76;1.76;1.76;1.76;1.76	6.05	4.91	0.64330	.	0.041854	0.85682	D	0.000000	T	0.35008	0.0917	M	0.66939	2.045	0.54753	D	0.999985	P;P;P;P;B;B;B	0.41188	0.696;0.741;0.523;0.578;0.221;0.066;0.061	B;P;B;P;B;B;B	0.48334	0.438;0.574;0.358;0.574;0.091;0.033;0.063	T	0.07177	-1.0786	10	0.18710	T	0.47	.	11.8846	0.52594	0.0:0.0684:0.0:0.9316	.	157;115;168;157;89;94;157	F5H4R6;B7Z9C2;F8W0J6;B3KNT8;B3KV44;F8W543;P55209	.;.;.;.;.;.;NP1L1_HUMAN	R	157;151;157;89;94;115;157;157;168;116;130;157;116;163;164	ENSP00000261182:K157R;ENSP00000450236:K151R;ENSP00000376947:K157R;ENSP00000409795:K89R;ENSP00000448167:K94R;ENSP00000444759:K115R;ENSP00000445008:K157R;ENSP00000447793:K157R;ENSP00000447196:K168R;ENSP00000449649:K116R;ENSP00000448133:K130R;ENSP00000448764:K157R;ENSP00000446787:K116R;ENSP00000448836:K163R;ENSP00000446756:K164R	ENSP00000261182:K157R	K	-	2	0	NAP1L1	74736168	1.000000	0.71417	0.988000	0.46212	0.944000	0.59088	8.036000	0.88901	1.107000	0.41642	-0.263000	0.10527	AAA	.	.		0.323	NAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405850.3	NM_139207		C	76449901	T	C	76449901	3	2	282	1	0	0	0	0	1	0	0	0	10165	1841	64	2	741	2	NAP1L1	12	76449901	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	757429	76449901	57401994	886	41120										
NAV3	89795	hgsc.bcm.edu	37	chr12	78443808	78443808	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caagaagaatgagaacagttAaaaacatagcagacttgagg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:78443808delA	ENST00000397909.2	+	10	2232	c.2059delA	c.(2059-2061)aaafs	p.K687fs	NAV3_ENST00000266692.7_Frame_Shift_Del_p.K687fs|NAV3_ENST00000228327.6_Frame_Shift_Del_p.K687fs|RP11-136F16.1_ENST00000549103.1_RNA|NAV3_ENST00000536525.2_Frame_Shift_Del_p.K687fs			Q8IVL0	NAV3_HUMAN	neuron navigator 3	687						membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						GAGAACAGTTAAAAACATAGC	0.343										HNSCC(70;0.22)																											p.V686fs		Atlas-INDEL	.											.	NAV3	506	.	0			c.2058delT						.						85	84	85					12																	78443808		1843	4084	5927	SO:0001589	frameshift_variant	89795	exon10			.	AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.2059delA	chr12.hg19:g.78443808delA	ENSP00000381007:p.Lys687fs	177.0	0.0		153.0	13.0	NM_014903	Q8NFW7|Q9Y2E7	Frame_Shift_Del	DEL	ENST00000397909.2	hg19																																																																																				.	.		0.343	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		-	78443808	A	-	78443808	7	5	282	1	0	1	0	1	0	0	0	0	10194	363	13	0	2097	0	NAV3	12	78443808	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1993907	78443808	55408087	887	41121										
PPFIA2	8499	hgsc.bcm.edu	37	chr12	81851632	81851632	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aggcatttaattcttttgtcAgtgcagcaaattcctggaaa	8	7	2	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:81851632A>G	ENST00000549396.1	-	5	477	c.317T>C	c.(316-318)cTg>cCg	p.L106P	PPFIA2_ENST00000552948.1_Missense_Mutation_p.L106P|PPFIA2_ENST00000443686.3_Missense_Mutation_p.L32P|PPFIA2_ENST00000550584.2_Missense_Mutation_p.L106P|PPFIA2_ENST00000545296.2_5'UTR|PPFIA2_ENST00000549325.1_Missense_Mutation_p.L88P|PPFIA2_ENST00000407050.4_Missense_Mutation_p.L32P|PPFIA2_ENST00000550359.2_5'UTR|RP11-315E17.1_ENST00000550272.1_RNA|PPFIA2_ENST00000548586.1_Missense_Mutation_p.L106P|PPFIA2_ENST00000333447.7_Missense_Mutation_p.L88P	NM_001220476.1|NM_001282536.1|NM_003625.3	NP_001207405.1|NP_001269465.1|NP_003616.2	O75334	LIPA2_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2	106					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|presynaptic active zone (GO:0048786)				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(37)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)	85						TTCTTTTGTCAGTGCAGCAAA	0.284																																					p.L106P		Atlas-SNP	.											.	PPFIA2	207	.	0			c.T317C						.						88	74	78					12																	81851632		1785	4055	5840	SO:0001583	missense	8499	exon4			TTTGTCAGTGCAG	AF034799	CCDS55850.1, CCDS55851.1, CCDS55852.1, CCDS55853.1, CCDS55854.1, CCDS55855.1, CCDS55856.1, CCDS55857.1, CCDS59236.1, CCDS73503.1	12q21.31	2013-01-10						"Sterile alpha motif (SAM) domain containing"	9246	protein-coding gene	gene with protein product	"Liprin-alpha2"	603143				9624153	Standard	NM_003625		Approved		uc031qis.1	O75334		ENST00000549396.1:c.317T>C	chr12.hg19:g.81851632A>G	ENSP00000450337:p.Leu106Pro	118.0	0.0		95.0	4.0	NM_001220476	B3KVT5|B3KXA0|B7Z2A6|B7Z3U9|B7Z663|B7ZKZ5|E7ERB8|E7ETG6|F8VP68|Q2M3G8	Missense_Mutation	SNP	ENST00000549396.1	hg19	CCDS55857.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.362692	0.82353	.	.	ENSG00000139220	ENST00000549396;ENST00000549325;ENST00000407050;ENST00000541501;ENST00000333447;ENST00000548586;ENST00000443686;ENST00000552948;ENST00000551442;ENST00000547623	T;T;T;T;T;T;T;T;T	0.53640	1.12;1.12;1.12;1.12;1.12;1.12;1.12;1.12;0.61	5.66	5.66	0.87406	.	0.000000	0.64402	D	0.000003	T	0.64011	0.2560	L	0.52759	1.655	0.80722	D	1	D;D	0.69078	0.997;0.995	D;D	0.80764	0.994;0.986	T	0.66744	-0.5846	10	0.87932	D	0	-9.0674	15.8839	0.79226	1.0:0.0:0.0:0.0	.	6;106	B7Z4H8;O75334	.;LIPA2_HUMAN	P	106;88;32;117;88;106;32;106;88;106	ENSP00000450337:L106P;ENSP00000450298:L88P;ENSP00000385093:L32P;ENSP00000327416:L88P;ENSP00000449338:L106P;ENSP00000388373:L32P;ENSP00000447868:L106P;ENSP00000449469:L88P;ENSP00000447918:L106P	ENSP00000327416:L88P	L	-	2	0	PPFIA2	80375763	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.828000	0.92047	2.158000	0.67659	0.533000	0.62120	CTG	.	.		0.284	PPFIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408030.1			G	81851632	A	G	81851632	3	3	282	1	0	0	0	0	1	0	0	0	12319	188	7	2	3568	2	PPFIA2	12	81851632	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	3407824	81851632	52000263	888	41122										
TSPAN19	144448	hgsc.bcm.edu	37	chr12	85421730	85421730	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcctatataacccaatagacAaaaaagaacagtagaagatc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:85421730delA	ENST00000532498.2	-	4	291	c.211delT	c.(211-213)tgtfs	p.C71fs	TSPAN19_ENST00000547403.2_Intron	NM_001100917.1	NP_001094387.1	P0C672	TSN19_HUMAN	tetraspanin 19	71						integral component of membrane (GO:0016021)				ovary(1)	1						CCCAATAGACAAAAAAGAACA	0.289																																					p.C71fs		Atlas-INDEL	.											.	TSPAN19	23	.	0			c.212delG						.						60	56	57					12																	85421730		1810	4063	5873	SO:0001589	frameshift_variant	144448	exon4			.		CCDS44949.1	12q21.31	2013-02-14			ENSG00000231738	ENSG00000231738		"Tetraspanins"	31886	protein-coding gene	gene with protein product							Standard	NM_001100917		Approved		uc009zsj.3	P0C672	OTTHUMG00000166181	ENST00000532498.2:c.211delT	chr12.hg19:g.85421730delA	ENSP00000433816:p.Cys71fs	206.0	0.0		171.0	14.0	NM_001100917		Frame_Shift_Del	DEL	ENST00000532498.2	hg19	CCDS44949.1																																																																																			.	.		0.289	TSPAN19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388240.2	NM_001100917		-	85421730	A	-	85421730	7	5	282	1	0	1	0	1	0	0	0	0	16658	130	5	0	559	0	TSPAN19	12	85421730	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	3570098	85421730	48430165	889	41123										
GALNT4	8693	hgsc.bcm.edu	37	chr12	89917665	89917665	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aatccaggaaagtgaggacgTccccagtggcgaaagtggcc	14	10	0	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:89917665T>C	ENST00000529983.2	-	1	918	c.662A>G	c.(661-663)gAc>gGc	p.D221G	POC1B_ENST00000549035.1_Intron|POC1B_ENST00000313546.3_Intron|POC1B_ENST00000541909.1_Intron|POC1B-GALNT4_ENST00000547474.1_Intron|POC1B_ENST00000393179.4_Intron|POC1B_ENST00000549504.1_Intron|GALNT4_ENST00000413530.1_Intron|RP11-734K2.4_ENST00000605233.1_RNA|POC1B-GALNT4_ENST00000548729.1_Missense_Mutation_p.D218G	NM_003774.4	NP_003765.2	Q8N4A0	GALT4_HUMAN	polypeptide N-acetylgalactosaminyltransferase 4	221	Catalytic subdomain A.				carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			endometrium(4)|kidney(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)	14						AGTGAGGACGTCCCCAGTGGC	0.507											OREG0022018	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D221G		Atlas-SNP	.											.	GALNT4	38	.	0			c.A662G						.						81	82	82					12																	89917665		1946	4139	6085	SO:0001583	missense	8693	exon1			AGGACGTCCCCAG	Y08564	CCDS53817.1	12q21.33	2014-03-13	2014-03-13		ENSG00000257594	ENSG00000257594	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4126	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 4"	603565	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 4 (GalNAc-T4)"			9804815	Standard	NM_003774		Approved	GalNAc-T4	uc001tbd.3	Q8N4A0	OTTHUMG00000166292	ENST00000529983.2:c.662A>G	chr12.hg19:g.89917665T>C	ENSP00000436604:p.Asp221Gly	136.0	0.0	1271	85.0	4.0	NM_003774	B2R775|B4DMX6|O00208	Missense_Mutation	SNP	ENST00000529983.2	hg19	CCDS53817.1	.	.	.	.	.	.	.	.	.	.	T	19.79	3.893521	0.72639	.	.	ENSG00000259075;ENSG00000257594	ENST00000548729;ENST00000529983	T;T	0.66815	-0.23;-0.23	5.88	5.88	0.94601	Glycosyl transferase, family 2 (1);	.	.	.	.	T	0.76343	0.3974	M	0.79805	2.47	0.36632	D	0.876357	P;P	0.38473	0.58;0.633	B;P	0.46208	0.373;0.507	T	0.83223	-0.0067	9	0.87932	D	0	.	15.4562	0.75314	0.0:0.0:0.0:1.0	.	218;221	F8VUJ3;Q8N4A0	.;GALT4_HUMAN	G	218;221	ENSP00000447852:D218G;ENSP00000436604:D221G	ENSP00000436604:D221G	D	-	2	0	GALNT4;RP11-1109F11.4	88441796	1.000000	0.71417	0.990000	0.47175	0.997000	0.91878	6.167000	0.71902	2.246000	0.74042	0.533000	0.62120	GAC	.	.		0.507	GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388973.2	NM_003774		C	89917665	T	C	89917665	3	2	282	1	0	0	0	0	1	0	0	0	6223	1667	58	2	1078	2	GALNT4	12	89917665	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	4495935	89917665	43934230	890	41124										
PLXNC1	10154	hgsc.bcm.edu	37	chr12	94692568	94692568	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cgtacatatttggaaaacaaAcaggtgggaatgtaggtgat	12	4	0	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:94692568A>G	ENST00000258526.4	+	27	4484	c.4235A>G	c.(4234-4236)aAc>aGc	p.N1412S	PLXNC1_ENST00000547057.1_Missense_Mutation_p.N459S|PLXNC1_ENST00000545312.1_Missense_Mutation_p.N151S	NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	1412					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(12)|lung(30)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						TGGAAAACAAACAGGTGGGAA	0.343																																					p.N1412S		Atlas-SNP	.											.	PLXNC1	135	.	0			c.A4235G						.						56	59	58					12																	94692568		2203	4300	6503	SO:0001583	missense	10154	exon27			AAACAAACAGGTG	AF030339	CCDS9049.1	12q23	2009-04-17				ENSG00000136040		"CD molecules", "Plexins"	9106	protein-coding gene	gene with protein product		604259					Standard	NR_037687		Approved	VESPR, CD232	uc001tdc.3	O60486	OTTHUMG00000170235	ENST00000258526.4:c.4235A>G	chr12.hg19:g.94692568A>G	ENSP00000258526:p.Asn1412Ser	56.0	0.0		63.0	4.0	NM_005761	Q59H25	Missense_Mutation	SNP	ENST00000258526.4	hg19	CCDS9049.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.456106	0.84209	.	.	ENSG00000136040	ENST00000258526;ENST00000547057;ENST00000545312	T;T;T	0.22336	1.96;1.96;1.96	5.95	5.95	0.96441	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.48768	0.1518	M	0.75150	2.29	0.80722	D	1	D;D	0.89917	0.997;1.0	D;D	0.87578	0.994;0.998	T	0.50634	-0.8805	10	0.87932	D	0	.	16.4237	0.83790	1.0:0.0:0.0:0.0	.	459;1412	B4DHQ7;O60486	.;PLXC1_HUMAN	S	1412;459;151	ENSP00000258526:N1412S;ENSP00000446720:N459S;ENSP00000439225:N151S	ENSP00000258526:N1412S	N	+	2	0	PLXNC1	93216699	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.339000	0.96797	2.279000	0.76181	0.533000	0.62120	AAC	.	.		0.343	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2			G	94692568	A	G	94692568	3	3	282	1	0	0	0	0	1	0	0	0	12135	43	2	2	4341	2	PLXNC1	12	94692568	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	4774903	94692568	39159327	891	41125										
CCDC38	120935	hgsc.bcm.edu	37	chr12	96275288	96275288	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caacgtccatttcatcatctAaaaggaattccaaactgtct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:96275288delA	ENST00000344280.3	-	11	1522	c.965delT	c.(964-966)ttafs	p.L322fs	SNRPF_ENST00000552085.1_Intron	NM_182496.2	NP_872302.2	Q502W7	CCD38_HUMAN	coiled-coil domain containing 38	322										breast(1)|endometrium(2)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TTCATCATCTAAAAGGAATTC	0.318																																					p.L322fs		Atlas-INDEL	.											.	CCDC38	45	.	0			c.966delA						.						80	76	77					12																	96275288		2203	4300	6503	SO:0001589	frameshift_variant	120935	exon11			.	AK097408	CCDS9056.1	12q23.1	2005-11-02				ENSG00000165972			26843	protein-coding gene	gene with protein product							Standard	NM_182496		Approved	FLJ40089	uc001tek.2	Q502W7	OTTHUMG00000170352	ENST00000344280.3:c.965delT	chr12.hg19:g.96275288delA	ENSP00000345470:p.Leu322fs	244.0	0.0		194.0	12.0	NM_182496	Q8N835	Frame_Shift_Del	DEL	ENST00000344280.3	hg19	CCDS9056.1																																																																																			.	.		0.318	CCDC38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408634.1	NM_182496		-	96275288	A	-	96275288	7	5	282	1	0	1	0	1	0	0	0	0	2812	372	13	0	750	0	CCDC38	12	96275288	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1582720	96275288	37576607	892	41126										
NR1H4	9971	hgsc.bcm.edu	37	chr12	100904639	100904639	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aatacagcaatgttcagtttCcccaagttcaaccacagatt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:100904639delC	ENST00000551379.1	+	2	221	c.193delC	c.(193-195)cccfs	p.P65fs	NR1H4_ENST00000549996.1_Frame_Shift_Del_p.P55fs|NR1H4_ENST00000392986.3_Frame_Shift_Del_p.P55fs|NR1H4_ENST00000188403.7_Frame_Shift_Del_p.P65fs|NR1H4_ENST00000548884.1_Frame_Shift_Del_p.P55fs			Q96RI1	NR1H4_HUMAN	nuclear receptor subfamily 1, group H, member 4	65					bile acid metabolic process (GO:0008206)|cellular response to acid chemical (GO:0071229)|cellular response to organonitrogen compound (GO:0071417)|digestive tract development (GO:0048565)|gene expression (GO:0010467)|intracellular bile acid receptor signaling pathway (GO:0038185)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of bile acid biosynthetic process (GO:0070858)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nitrogen catabolite activation of transcription from RNA polymerase II promoter (GO:0001080)|positive regulation of ammonia assimilation cycle (GO:2001250)|positive regulation of glutamate metabolic process (GO:2000213)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of carbohydrate metabolic process (GO:0006109)|regulation of cholesterol metabolic process (GO:0090181)|regulation of urea metabolic process (GO:0034255)|response to glucose (GO:0009749)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)	bile acid binding (GO:0032052)|bile acid receptor activity (GO:0038181)|chenodeoxycholic acid binding (GO:1902122)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|ligand-dependent nuclear receptor binding (GO:0016922)|peptide binding (GO:0042277)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|thyroid hormone receptor activity (GO:0004887)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	44					Chenodeoxycholic acid(DB06777)	TGTTCAGTTTCCCCAAGTTCA	0.458																																					p.F64fs		Atlas-INDEL	.											.	NR1H4	145	.	0			c.192delT						.						94	84	87					12																	100904639		2203	4300	6503	SO:0001589	frameshift_variant	9971	exon2			.	U68233	CCDS9078.1, CCDS55873.1, CCDS55874.1, CCDS55875.1, CCDS55876.1	12q23.1	2013-01-16				ENSG00000012504		"Nuclear hormone receptors"	7967	protein-coding gene	gene with protein product		603826				7774010, 9223286	Standard	NM_001206977		Approved	FXR, RIP14, HRR1, HRR-1	uc001tht.2	Q96RI1	OTTHUMG00000170359	ENST00000551379.1:c.193delC	chr12.hg19:g.100904639delC	ENSP00000447149:p.Pro65fs	403.0	0.0		258.0	17.0	NM_001206992	A1L4K5|B7Z412|B7ZM06|F8VYG8|Q8NFP5|Q8NFP6|Q92943	Frame_Shift_Del	DEL	ENST00000551379.1	hg19	CCDS55876.1																																																																																			.	.		0.458	NR1H4-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409140.1	NM_005123		-	100904639	C	-	100904639	7	5	282	1	0	1	0	1	0	0	0	0	10628	855	30	0	169	0	NR1H4	12	100904639	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	4629351	100904639	32947256	893	41127										
GAS2L3	283431	hgsc.bcm.edu	37	chr12	101018209	101018209	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagtctcaaccatccgatggAgccccacaagcaaagccagt	8	15	1	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:101018209A>G	ENST00000539410.1	+	9	2012	c.1626A>G	c.(1624-1626)ggA>ggG	p.G542G	GAS2L3_ENST00000547754.1_Silent_p.G542G|GAS2L3_ENST00000537247.1_Silent_p.G438G|GAS2L3_ENST00000266754.5_Silent_p.G542G			Q86XJ1	GA2L3_HUMAN	growth arrest-specific 2 like 3	542					actin cytoskeleton organization (GO:0030036)|cell cycle arrest (GO:0007050)|microtubule cytoskeleton organization (GO:0000226)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	actin binding (GO:0003779)|microtubule binding (GO:0008017)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(15)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35						CATCCGATGGAGCCCCACAAG	0.458																																					p.G542G		Atlas-SNP	.											.	GAS2L3	76	.	0			c.A1626G						.						48	47	48					12																	101018209		2203	4300	6503	SO:0001819	synonymous_variant	283431	exon10			CGATGGAGCCCCA	AK095594	CCDS9079.1	12q23.1	2014-09-11			ENSG00000139354	ENSG00000139354			27475	protein-coding gene	gene with protein product							Standard	NM_174942		Approved		uc001thu.3	Q86XJ1	OTTHUMG00000170439	ENST00000539410.1:c.1626A>G	chr12.hg19:g.101018209A>G		85.0	0.0		62.0	4.0	NM_174942	B2RCN2	Silent	SNP	ENST00000539410.1	hg19	CCDS9079.1																																																																																			.	.		0.458	GAS2L3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409143.1	NM_174942		G	101018209	A	G	101018209	2	3	282	1	0	0	0	0	0	0	0	1	6256	291	11	2		2	GAS2L3	12	101018209	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	113570	101018209	32833686	894	41128										
GNPTAB	79158	hgsc.bcm.edu	37	chr12	102158140	102158140	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tctctttttctttccctgtgAttttcttttcttttgtcatc	3	10	5	1	rs281864996		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:102158140A>G	ENST00000299314.7	-	13	2817	c.2555T>C	c.(2554-2556)aTc>aCc	p.I852T	RNU6-101P_ENST00000410323.1_RNA	NM_024312.4	NP_077288.2	Q3T906	GNPTA_HUMAN	N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits	852					carbohydrate phosphorylation (GO:0046835)|cell differentiation (GO:0030154)|lysosome organization (GO:0007040)|protein secretion (GO:0009306)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity (GO:0003976)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(8)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	37						TTTCCCTGTGATTTTCTTTTC	0.403																																					p.I852T		Atlas-SNP	.											.	GNPTAB	120	.	0			c.T2555C						.						258	255	256					12																	102158140		2203	4300	6503	SO:0001583	missense	79158	exon13			CCTGTGATTTTCT	AY687932	CCDS9088.1	12q23.3	2013-01-10				ENSG00000111670		"EF-hand domain containing"	29670	protein-coding gene	gene with protein product		607840		GNPTA		10574462, 16116615	Standard	NM_024312		Approved	KIAA1208, MGC4170	uc001tit.3	Q3T906	OTTHUMG00000170444	ENST00000299314.7:c.2555T>C	chr12.hg19:g.102158140A>G	ENSP00000299314:p.Ile852Thr	141.0	0.0		124.0	5.0	NM_024312	A2RRQ9|Q3ZQK2|Q6IPW5|Q86TQ2|Q96N13|Q9ULL2	Missense_Mutation	SNP	ENST00000299314.7	hg19	CCDS9088.1	.	.	.	.	.	.	.	.	.	.	A	6.778	0.512407	0.12944	.	.	ENSG00000111670	ENST00000299314	D	0.95980	-3.87	4.66	-6.51	0.01878	.	1.082130	0.07043	N	0.830477	D	0.86834	0.6028	N	0.22421	0.69	0.09310	N	1	B	0.15473	0.013	B	0.11329	0.006	T	0.78198	-0.2297	10	0.02654	T	1	-1.1474	8.6838	0.34225	0.3297:0.3919:0.2784:0.0	.	852	Q3T906	GNPTA_HUMAN	T	852	ENSP00000299314:I852T	ENSP00000299314:I852T	I	-	2	0	GNPTAB	100682271	0.000000	0.05858	0.000000	0.03702	0.382000	0.30200	-0.563000	0.05943	-0.804000	0.04410	0.533000	0.62120	ATC	.	.		0.403	GNPTAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409182.1			G	102158140	A	G	102158140	3	3	282	1	0	0	0	0	1	0	0	0	6553	333	12	2	1251	2	GNPTAB	12	102158140	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1139931	102158140	31693755	895	41129										
CCDC53	51019	hgsc.bcm.edu	37	chr12	102455700	102455700	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttttacaaaccttggtcaggTctatgcctgaccccatgaga	8	11	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:102455700T>C	ENST00000240079.6	-	1	202	c.41A>G	c.(40-42)gAc>gGc	p.D14G	RP11-554E23.4_ENST00000552707.1_RNA|CCDC53_ENST00000539515.1_Intron|CCDC53_ENST00000545679.1_Missense_Mutation_p.D14G	NM_016053.2	NP_057137.1	Q9Y3C0	CCD53_HUMAN	coiled-coil domain containing 53	14						actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|WASH complex (GO:0071203)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4						CTTGGTCAGGTCTATGCCTGA	0.632																																					p.D14G		Atlas-SNP	.											.	CCDC53	14	.	0			c.A41G						.						27	31	30					12																	102455700		1925	4125	6050	SO:0001583	missense	51019	exon1			GTCAGGTCTATGC	AF151874	CCDS44959.1, CCDS73512.1	12q23.3	2014-05-09			ENSG00000120860	ENSG00000120860			24256	protein-coding gene	gene with protein product						10810093, 20498093	Standard	XM_005268939		Approved	CGI-116	uc010svw.2	Q9Y3C0	OTTHUMG00000168187	ENST00000240079.6:c.41A>G	chr12.hg19:g.102455700T>C	ENSP00000240079:p.Asp14Gly	84.0	0.0		74.0	4.0	NM_016053	B2RC74|Q53FF0|Q6IAI4|Q96QK0	Missense_Mutation	SNP	ENST00000240079.6	hg19	CCDS44959.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.344310	0.82022	.	.	ENSG00000120860	ENST00000240079;ENST00000545679	.	.	.	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.71728	0.3374	M	0.81497	2.545	0.80722	D	1	B;B	0.29232	0.238;0.153	B;B	0.33846	0.171;0.083	T	0.74231	-0.3732	9	0.72032	D	0.01	.	15.6229	0.76820	0.0:0.0:0.0:1.0	.	14;14	F5GZ97;Q9Y3C0	.;CCD53_HUMAN	G	14	.	ENSP00000240079:D14G	D	-	2	0	CCDC53	100979830	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.734000	0.74801	2.279000	0.76181	0.402000	0.26972	GAC	.	.		0.632	CCDC53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398685.1	NM_016053		C	102455700	T	C	102455700	3	2	282	1	0	0	0	0	1	0	0	0	2825	1667	58	2	502	2	CCDC53	12	102455700	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	297560	102455700	31396195	896	41130										
UNG	7374	hgsc.bcm.edu	37	chr12	109541376	109541376	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tggccttgttttcttgctctGgggctcttatgctcagaaga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:109541376delG	ENST00000242576.2	+	6	867	c.761delG	c.(760-762)tggfs	p.W254fs	UNG_ENST00000336865.2_Frame_Shift_Del_p.W245fs	NM_080911.2	NP_550433.1			uracil-DNA glycosylase											central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(4)|ovary(1)	9						TTCTTGCTCTGGGGCTCTTAT	0.403								Base excision repair (BER), DNA glycosylases	Immune Deficiency with Hyper-IgM																												p.W254fs		Atlas-INDEL	.											.	UNG	30	.	0			c.760delT						.						79	62	68					12																	109541376		2203	4300	6503	SO:0001589	frameshift_variant	7374	exon6	Familial Cancer Database	Hypogammaglobulinemia with Hyper-IgM, HIGM type I-V, XLHIGM	.	A64377	CCDS9124.1, CCDS9125.1	12q23-q24.1	2014-09-17			ENSG00000076248	ENSG00000076248	3.2.2.27		12572	protein-coding gene	gene with protein product	"uracil-DNA glycosylase 1, uracil-DNA glycosylase 2"	191525		DGU		1923798, 17101234	Standard	NM_080911		Approved	UDG, UNG1, UNG2, HIGM4	uc001tnz.2	P13051	OTTHUMG00000169247	ENST00000242576.2:c.761delG	chr12.hg19:g.109541376delG	ENSP00000242576:p.Trp254fs	227.0	0.0		147.0	11.0	NM_080911		Frame_Shift_Del	DEL	ENST00000242576.2	hg19	CCDS9124.1																																																																																			.	.		0.403	UNG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403067.1	NM_080911		-	109541376	G	-	109541376	7	5	282	1	0	1	0	1	0	0	0	0	17014	1357	47	0	888	0	UNG	12	109541376	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	7085676	109541376	24310519	897	41131										
UBE3B	89910	hgsc.bcm.edu	37	chr12	109921448	109921448	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgtgcagaaggaacgggagcGggcagctgttgtgatccagg					rs139172208		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:109921448delG	ENST00000342494.3	+	3	687	c.92delG	c.(91-93)cggfs	p.R31fs	UBE3B_ENST00000434735.2_Frame_Shift_Del_p.R31fs|UBE3B_ENST00000536398.1_Frame_Shift_Del_p.R31fs|UBE3B_ENST00000537063.1_Frame_Shift_Del_p.R31fs|UBE3B_ENST00000280774.5_Frame_Shift_Del_p.R31fs|UBE3B_ENST00000540230.1_Frame_Shift_Del_p.R31fs|UBE3B_ENST00000340074.5_Frame_Shift_Del_p.R31fs	NM_130466.3	NP_569733.2	Q7Z3V4	UBE3B_HUMAN	ubiquitin protein ligase E3B	31	IQ. {ECO:0000255|PROSITE- ProRule:PRU00116}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.R31Q(1)		NS(1)|breast(3)|endometrium(6)|kidney(4)|large_intestine(7)|lung(20)|ovary(2)|urinary_tract(2)	45						GAACGGGAGCGGGCAGCTGTT	0.532																																					p.R31fs		Atlas-INDEL	.											.	UBE3B	116	.	1	Substitution - Missense(1)	endometrium(1)	c.91delC						.						161	151	155					12																	109921448		2203	4300	6503	SO:0001589	frameshift_variant	89910	exon3			.	BC032301	CCDS9129.1, CCDS58277.1	12q24.12	2004-03-02			ENSG00000151148	ENSG00000151148			13478	protein-coding gene	gene with protein product		608047					Standard	NM_130466		Approved		uc001toq.4	Q7Z3V4	OTTHUMG00000169254	ENST00000342494.3:c.92delG	chr12.hg19:g.109921448delG	ENSP00000340596:p.Arg31fs	191.0	0.0		208.0	13.0	NM_001270451	A5D8Z3|Q05BX9|Q659F7|Q7Z7Q1|Q9BXZ4	Frame_Shift_Del	DEL	ENST00000342494.3	hg19	CCDS9129.1																																																																																			.	.		0.532	UBE3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403119.1	NM_183415		-	109921448	G	-	109921448	7	5	282	1	0	1	0	1	0	0	0	0	16895	1116	39	0	94	0	UBE3B	12	109921448	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	380072	109921448	23930447	898	41132										
TCTN1	79600	hgsc.bcm.edu	37	chr12	111078953	111078953	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtttgaaattcattttcttcAggtaaggttgatcaatttgg	9	4	4	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:111078953A>G	ENST00000551590.1	+	9	1259	c.1103A>G	c.(1102-1104)cAg>cGg	p.Q368R	TCTN1_ENST00000397655.3_Splice_Site_p.Q354R|TCTN1_ENST00000377654.3_Splice_Site_p.Q190R|TCTN1_ENST00000397659.4_Splice_Site_p.Q368R|HVCN1_ENST00000548312.1_Intron			Q2MV58	TECT1_HUMAN	tectonic family member 1	368					central nervous system interneuron axonogenesis (GO:0021956)|cilium morphogenesis (GO:0060271)|dorsal/ventral neural tube patterning (GO:0021904)|in utero embryonic development (GO:0001701)|neural tube formation (GO:0001841)|regulation of smoothened signaling pathway (GO:0008589)|somatic motor neuron differentiation (GO:0021523)|telencephalon development (GO:0021537)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|membrane (GO:0016020)|TCTN-B9D complex (GO:0036038)				NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(9)|urinary_tract(1)	15						CATTTTCTTCAGGTAAGGTTG	0.373																																					p.Q368R		Atlas-SNP	.											.	TCTN1	37	.	0			c.A1103G						.						132	121	125					12																	111078953		1870	4093	5963	SO:0001630	splice_region_variant	79600	exon9			TTCTTCAGGTAAG	AK055891	CCDS41833.1, CCDS41834.1, CCDS41835.1	12q24.11	2011-09-07			ENSG00000204852	ENSG00000204852		"Tectonic proteins"	26113	protein-coding gene	gene with protein product		609863				16357211	Standard	NM_001082537		Approved	FLJ21127, TECT1, JBTS13	uc001trn.4	Q2MV58	OTTHUMG00000150051	ENST00000551590.1:c.1104+1A>G	chr12.hg19:g.111078953A>G		140.0	0.0		82.0	4.0	NM_001082537	A8MX11|Q49A60|Q6P5X1|Q6UXW2|Q8NAE9|Q96N72|Q9H798	Missense_Mutation	SNP	ENST00000551590.1	hg19	CCDS41835.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.110449	0.77210	.	.	ENSG00000204852	ENST00000397650;ENST00000551590;ENST00000397655;ENST00000377654;ENST00000397657;ENST00000397659;ENST00000397652	D;D;D;D	0.82803	-1.65;-1.65;-1.65;-1.65	5.87	4.73	0.59995	Domain of unknown function DUF1619 (1);	0.108690	0.64402	N	0.000004	D	0.91047	0.7183	M	0.85710	2.77	0.47476	D	0.999434	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.998;0.998;0.998;0.993;0.999	D	0.91301	0.5067	10	0.62326	D	0.03	-13.764	11.8497	0.52405	0.9317:0.0:0.0683:0.0	.	368;354;368;308;312	Q2MV58;Q2MV58-3;Q2MV58-2;C9J1H5;C9J1H4	TECT1_HUMAN;.;.;.;.	R	308;368;354;190;190;368;312	ENSP00000448735:Q368R;ENSP00000380775:Q354R;ENSP00000366882:Q190R;ENSP00000380779:Q368R	ENSP00000366882:Q190R	Q	+	2	0	TCTN1	109563336	1.000000	0.71417	0.995000	0.50966	0.835000	0.47333	5.088000	0.64486	1.049000	0.40321	0.533000	0.62120	CAG	.	.		0.373	TCTN1-001	KNOWN	non_canonical_TEC|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316016.2	NM_024549	Missense_Mutation	G	111078953	A	G	111078953	5	3	282	1	0	0	0	0	0	0	1	0	15737	202	7	2	1309	2	TCTN1	12	111078953	Splice_Site	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1157505	111078953	22772942	899	41133										
CUX2	23316	hgsc.bcm.edu	37	chr12	111785948	111785948	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctccccatccccacctggcgCcccccctgccaaagtgccga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:111785948delC	ENST00000261726.6	+	22	4434	c.4280delC	c.(4279-4281)gccfs	p.A1427fs		NM_015267.3	NP_056082.2	O14529	CUX2_HUMAN	cut-like homeobox 2	1427	Pro-rich.				cellular response to organic substance (GO:0071310)|cognition (GO:0050890)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of synapse assembly (GO:0051965)|short-term memory (GO:0007614)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(24)|ovary(5)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	55						CCACCTGGCGCCCCCCCTGCC	0.657																																					p.A1427fs		Atlas-INDEL	.											CUX2,NS,carcinoma,0,1	CUX2	145	.	0			c.4279delG						.						45	53	50					12																	111785948		2032	4169	6201	SO:0001589	frameshift_variant	23316	exon22			.	AB006631	CCDS41837.1	12q24.12	2011-06-20	2007-11-07	2007-11-07	ENSG00000111249	ENSG00000111249		"Homeoboxes / CUT class"	19347	protein-coding gene	gene with protein product		610648	"cut-like 2 (Drosophila)"	CUTL2			Standard	NM_015267		Approved	KIAA0293, CDP2	uc001tsa.2	O14529	OTTHUMG00000169546	ENST00000261726.6:c.4280delC	chr12.hg19:g.111785948delC	ENSP00000261726:p.Ala1427fs	223.0	0.0		166.0	10.0	NM_015267	A7E2Y4	Frame_Shift_Del	DEL	ENST00000261726.6	hg19	CCDS41837.1																																																																																			.	.		0.657	CUX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404765.1	NM_015267		-	111785948	C	-	111785948	7	5	282	1	0	1	0	1	0	0	0	0	4067	739	26	0	4366	0	CUX2	12	111785948	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	706995	111785948	22065947	900	41134										
ATXN2	6311	hgsc.bcm.edu	37	chr12	111926535	111926535	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttgatttttctccctctctaTttttgtttagtagttgatcc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:111926535delT	ENST00000377617.3	-	15	2626	c.2465delA	c.(2464-2466)aatfs	p.N822fs	AC002395.1_ENST00000581907.1_RNA|ATXN2_ENST00000535949.1_Frame_Shift_Del_p.N533fs|ATXN2_ENST00000389153.4_Frame_Shift_Del_p.N557fs|ATXN2_ENST00000542287.2_Frame_Shift_Del_p.N557fs|ATXN2_ENST00000608853.1_Frame_Shift_Del_p.N662fs|ATXN2_ENST00000550104.1_Frame_Shift_Del_p.N822fs	NM_002973.3	NP_002964.3	Q99700	ATX2_HUMAN	ataxin 2	822					cell death (GO:0008219)|cerebellar Purkinje cell differentiation (GO:0021702)|cytoplasmic mRNA processing body assembly (GO:0033962)|homeostasis of number of cells (GO:0048872)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of receptor internalization (GO:0002091)|neuromuscular process (GO:0050905)|neuron projection morphogenesis (GO:0048812)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA transport (GO:0050658)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|trans-Golgi network (GO:0005802)	epidermal growth factor receptor binding (GO:0005154)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37						TCCCTCTCTATTTTTGTTTAG	0.308																																					p.N822fs		Atlas-INDEL	.											.	ATXN2	99	.	0			c.2466delT						.						43	42	42					12																	111926535		2203	4300	6503	SO:0001589	frameshift_variant	6311	exon15			.	U80749	CCDS31902.1	12q23-q24.1	2014-09-17	2004-08-12	2004-08-13	ENSG00000204842	ENSG00000204842		"Ataxins"	10555	protein-coding gene	gene with protein product	"trinucleotide repeat containing 13"	601517	"spinocerebellar ataxia 2 (olivopontocerebellar ataxia 2, autosomal dominant, ataxin 2)"	SCA2, TNRC13		8358438, 9225980	Standard	NM_002973		Approved	ATX2	uc001tsj.3	Q99700	OTTHUMG00000133475	ENST00000377617.3:c.2465delA	chr12.hg19:g.111926535delT	ENSP00000366843:p.Asn822fs	172.0	0.0		162.0	10.0	NM_002973	A6NLD4|Q6ZQZ7|Q99493	Frame_Shift_Del	DEL	ENST00000377617.3	hg19	CCDS31902.1																																																																																			.	.		0.308	ATXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257351.3	NM_002973		-	111926535	T	-	111926535	7	5	282	1	0	1	0	1	0	0	0	0	1211	1493	52	0	1520	0	ATXN2	12	111926535	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	140587	111926535	21925360	901	41135										
BRAP	8315	hgsc.bcm.edu	37	chr12	112082345	112082345	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcgttggtgagtttggccacTtttgtgtttagctgagtgca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:112082345delT	ENST00000327551.6	-	12	1487	c.1347delA	c.(1345-1347)aaafs	p.K449fs	BRAP_ENST00000539060.1_Frame_Shift_Del_p.K300fs|BRAP_ENST00000419234.4_Frame_Shift_Del_p.K479fs			Q6UWU4	CF089_HUMAN	BRCA1 associated protein	0					epithelial cell proliferation (GO:0050673)|positive regulation of cell cycle (GO:0045787)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	20						GTTTGGCCACTTTTGTGTTTA	0.448																																					p.V480fs	Pancreas(146;846 1904 7830 25130 26065)	Atlas-INDEL	.											.	BRAP	42	.	0			c.1438delG						.						103	97	99					12																	112082345		2203	4300	6503	SO:0001589	frameshift_variant	8315	exon12			.	AF035620	CCDS9154.1	12q24.12	2014-09-11			ENSG00000089234	ENSG00000089234		"RING-type (C3HC4) zinc fingers"	1099	protein-coding gene	gene with protein product	"impedes mitogenic signal propagation", "galectin-2-binding protein"	604986				9497340, 19198608	Standard	XM_005253944		Approved	BRAP2, RNF52, IMP	uc001tsn.4	Q7Z569	OTTHUMG00000169600	ENST00000327551.6:c.1347delA	chr12.hg19:g.112082345delT	ENSP00000330813:p.Lys449fs	236.0	0.0		186.0	13.0	NM_006768	B4DTT1|F4NAR0|F4NAR1|Q6ZMG5|Q7Z356|Q8IZ35	Frame_Shift_Del	DEL	ENST00000327551.6	hg19																																																																																				.	.		0.448	BRAP-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404994.2			-	112082345	T	-	112082345	7	5	282	1	0	1	0	1	0	0	0	0	1499	1606	56	0	345	0	BRAP	12	112082345	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	155810	112082345	21769550	902	41136										
MAPKAPK5	8550	hgsc.bcm.edu	37	chr12	112330837	112330837	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgtgaagcaggtgatagaagAgcaaaccacgtcccacgaat	11	9	0	4			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:112330837A>T	ENST00000551404.2	+	14	1502	c.1394A>T	c.(1393-1395)gAg>gTg	p.E465V	MAPKAPK5_ENST00000550735.2_Missense_Mutation_p.E463V			Q8IW41	MAPK5_HUMAN	mitogen-activated protein kinase-activated protein kinase 5	465					activation of MAPK activity (GO:0000187)|MAPK cascade (GO:0000165)|negative regulation of TOR signaling (GO:0032007)|protein autophosphorylation (GO:0046777)|Ras protein signal transduction (GO:0007265)|regulation of translation (GO:0006417)|signal transduction (GO:0007165)|stress-induced premature senescence (GO:0090400)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|lung(11)|ovary(1)	13						GTGATAGAAGAGCAAACCACG	0.338																																					p.E465V		Atlas-SNP	.											.	MAPKAPK5	56	.	0			c.A1394T						.						79	79	79					12																	112330837		1888	4122	6010	SO:0001583	missense	8550	exon14			TAGAAGAGCAAAC	AF032437	CCDS44975.1, CCDS44976.1	12q24.13	2012-05-30			ENSG00000089022	ENSG00000089022			6889	protein-coding gene	gene with protein product		606723				9628874	Standard	NM_003668		Approved	PRAK	uc001tta.4	Q8IW41	OTTHUMG00000169605	ENST00000551404.2:c.1394A>T	chr12.hg19:g.112330837A>T	ENSP00000449381:p.Glu465Val	143.0	0.0		95.0	40.0	NM_139078	B3KVA5|O60491|Q86X46|Q9BVX9|Q9UG86	Missense_Mutation	SNP	ENST00000551404.2	hg19	CCDS44975.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.262163	0.80358	.	.	ENSG00000089022	ENST00000550735;ENST00000202788;ENST00000428907;ENST00000551404;ENST00000547067	T;T	0.57595	0.4;0.39	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.59676	0.2211	N	0.19112	0.55	0.80722	D	1	D;D;D	0.61080	0.981;0.981;0.989	D;D;D	0.72625	0.95;0.95;0.978	T	0.65512	-0.6150	10	0.87932	D	0	.	16.0382	0.80645	1.0:0.0:0.0:0.0	.	459;465;463	C9J458;Q8IW41;Q8IW41-2	.;MAPK5_HUMAN;.	V	463;465;463;465;126	ENSP00000449667:E463V;ENSP00000449381:E465V	ENSP00000202788:E465V	E	+	2	0	MAPKAPK5	110815220	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.613000	0.90913	2.194000	0.70268	0.533000	0.62120	GAG	.	.		0.338	MAPKAPK5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405019.2	NM_139078		T	112330837	A	T	112330837	3	4	282	1	0	0	0	0	1	0	0	0	9300	304	11	4	1448	4	MAPKAPK5	12	112330837	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	248492	112330837	21521058	903	41137										
C12orf51	283450	hgsc.bcm.edu	37	chr12	112685271	112685271	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	attaatacgactaacctcagTgataggaccatgttttcaag	7	8	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:112685271T>C	ENST00000430131.2	-	27	4211	c.3066A>G	c.(3064-3066)tcA>tcG	p.S1022S	HECTD4_ENST00000550722.1_Silent_p.S1298S|HECTD4_ENST00000377560.5_Silent_p.S1272S			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	1022					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										CTAACCTCAGTGATAGGACCA	0.303																																					p.S1310S		Atlas-SNP	.											.	.	.	.	0			c.A3930G						.						57	54	55					12																	112685271		1840	4069	5909	SO:0001819	synonymous_variant	283450	exon28			CCTCAGTGATAGG	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 51"	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.3066A>G	chr12.hg19:g.112685271T>C		188.0	0.0		121.0	5.0	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Silent	SNP	ENST00000430131.2	hg19																																																																																				.	.		0.303	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		C	112685271	T	C	112685271	2	2	282	1	0	0	0	0	0	0	0	1	1698	1683	59	2		2	C12orf51	12	112685271	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	354434	112685271	21166624	904	41138										
TBX3	6926	hgsc.bcm.edu	37	chr12	115118903	115118903	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atcaataaaatgtatttggcTtttttatccagcccagaaca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:115118903delT	ENST00000257566.3	-	2	827	c.438delA	c.(436-438)aaafs	p.K146fs	TBX3_ENST00000349155.2_Frame_Shift_Del_p.K146fs	NM_016569.3	NP_057653.3	O15119	TBX3_HUMAN	T-box 3	146					anterior/posterior axis specification, embryo (GO:0008595)|atrioventricular bundle cell differentiation (GO:0003167)|blood vessel development (GO:0001568)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cardiac muscle cell fate commitment (GO:0060923)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|female genitalia development (GO:0030540)|follicle-stimulating hormone secretion (GO:0046884)|forelimb morphogenesis (GO:0035136)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|limbic system development (GO:0021761)|luteinizing hormone secretion (GO:0032275)|male genitalia development (GO:0030539)|mammary gland development (GO:0030879)|mammary placode formation (GO:0060596)|mesoderm morphogenesis (GO:0048332)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sinoatrial node cell development (GO:0060931)|skeletal system development (GO:0001501)|specification of organ position (GO:0010159)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum morphogenesis (GO:0060412)	nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			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)		TGTATTTGGCTTTTTTATCCA	0.383																																					p.A147fs		Atlas-INDEL	.											.,2	TBX3	106	.	0			c.439delG						.						131	139	136					12																	115118903		2203	4300	6503	SO:0001589	frameshift_variant	6926	exon2			.	BC025258	CCDS9175.1, CCDS9176.1	12q24.21	2013-09-05	2008-07-31		ENSG00000135111	ENSG00000135111		"T-boxes"	11602	protein-coding gene	gene with protein product		601621	"ulnar mammary syndrome"	UMS		8988164	Standard	NM_005996		Approved	TBX3-ISO, XHL	uc001tvt.1	O15119	OTTHUMG00000169586	ENST00000257566.3:c.438delA	chr12.hg19:g.115118903delT	ENSP00000257566:p.Lys146fs	244.0	0.0		182.0	11.0	NM_005996	Q8TB20|Q9UKF8	Frame_Shift_Del	DEL	ENST00000257566.3	hg19	CCDS9176.1																																																																																			.	.		0.383	TBX3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404947.2	NM_016569, NM_005996		-	115118903	T	-	115118903	7	5	282	1	0	1	0	1	0	0	0	0	15674	1606	56	0	1821	0	TBX3	12	115118903	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2433632	115118903	18732992	905	41139										
MED13L	23389	hgsc.bcm.edu	37	chr12	116428868	116428868	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acagtggcacttctcaccagAgcttcgtccacttttccacc	6	16	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:116428868A>G	ENST00000281928.3	-	17	4097	c.3891T>C	c.(3889-3891)gcT>gcC	p.A1297A		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	1297						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		TTCTCACCAGAGCTTCGTCCA	0.468																																					p.A1297A		Atlas-SNP	.											.	MED13L	193	.	0			c.T3891C						.						101	96	98					12																	116428868		2203	4300	6503	SO:0001819	synonymous_variant	23389	exon17			CACCAGAGCTTCG	AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"thyroid hormone receptor associated protein 2"	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.3891T>C	chr12.hg19:g.116428868A>G		106.0	0.0		94.0	4.0	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Silent	SNP	ENST00000281928.3	hg19	CCDS9177.1																																																																																			.	.		0.468	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3			G	116428868	A	G	116428868	2	3	282	1	0	0	0	0	0	0	0	1	9440	291	11	2		2	MED13L	12	116428868	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1309965	116428868	17423027	906	41140										
RFC5	5985	hgsc.bcm.edu	37	chr12	118464801	118464801	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctggactggatgttgaatcaAgatttcaccacagcctacag	9	10	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:118464801A>C	ENST00000454402.2	+	8	889	c.771A>C	c.(769-771)caA>caC	p.Q257H	RFC5_ENST00000392542.2_Missense_Mutation_p.Q236H|RFC5_ENST00000229043.3_Missense_Mutation_p.Q172H|RFC5_ENST00000543153.1_3'UTR	NM_001206801.1|NM_007370.5	NP_001193730.1|NP_031396.1	P40937	RFC5_HUMAN	replication factor C (activator 1) 5, 36.5kDa	257					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor C complex (GO:0005663)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			NS(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(3)	9	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TGTTGAATCAAGATTTCACCA	0.547																																					p.Q257H		Atlas-SNP	.											.	RFC5	35	.	0			c.A771C						.						141	139	140					12																	118464801		2203	4300	6503	SO:0001583	missense	5985	exon8			GAATCAAGATTTC		CCDS9185.1, CCDS41843.2	12q24.3	2010-04-21	2002-08-29		ENSG00000111445	ENSG00000111445		"ATPases / AAA-type"	9973	protein-coding gene	gene with protein product		600407	"replication factor C (activator 1) 5 (36.5kD)"			7774928	Standard	NM_007370		Approved	RFC36	uc001twq.3	P40937	OTTHUMG00000156438	ENST00000454402.2:c.771A>C	chr12.hg19:g.118464801A>C	ENSP00000408295:p.Gln257His	123.0	0.0		72.0	30.0	NM_007370	A8MZ62|B3KSX8	Missense_Mutation	SNP	ENST00000454402.2	hg19	CCDS9185.1	.	.	.	.	.	.	.	.	.	.	A	14.60	2.582831	0.46006	.	.	ENSG00000111445	ENST00000229043;ENST00000454402;ENST00000392542	T;T;T	0.43688	0.94;0.94;0.94	5.75	-2.69	0.06022	Replication factor C (1);DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal (1);	0.387817	0.30483	N	0.009530	T	0.20780	0.0500	N	0.14661	0.345	0.33998	D	0.649963	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.12837	0.005;0.008;0.008	T	0.03249	-1.1056	10	0.52906	T	0.07	-8.3921	7.9384	0.29944	0.3877:0.1176:0.4947:0.0	.	236;271;257	A8MZ62;Q59GW7;P40937	.;.;RFC5_HUMAN	H	172;257;236	ENSP00000229043:Q172H;ENSP00000408295:Q257H;ENSP00000376325:Q236H	ENSP00000229043:Q172H	Q	+	3	2	RFC5	116949184	0.971000	0.33674	0.938000	0.37757	0.930000	0.56654	0.192000	0.17096	-0.374000	0.07967	-0.316000	0.08728	CAA	.	.		0.547	RFC5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344196.2	NM_007370		C	118464801	A	C	118464801	3	2	282	1	0	0	0	0	1	0	0	0	13263	69	3	5	807	5	RFC5	12	118464801	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2035933	118464801	15387094	907	41141										
RFC5	5985	hgsc.bcm.edu	37	chr12	118464813	118464813	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttgaatcaagatttcaccacAgcctacagaagtatcctttc	5	11	2	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:118464813A>G	ENST00000454402.2	+	8	901	c.783A>G	c.(781-783)acA>acG	p.T261T	RFC5_ENST00000392542.2_Silent_p.T240T|RFC5_ENST00000229043.3_Silent_p.T176T|RFC5_ENST00000543153.1_3'UTR	NM_001206801.1|NM_007370.5	NP_001193730.1|NP_031396.1	P40937	RFC5_HUMAN	replication factor C (activator 1) 5, 36.5kDa	261					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor C complex (GO:0005663)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			NS(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(3)	9	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					ATTTCACCACAGCCTACAGAA	0.552																																					p.T261T		Atlas-SNP	.											.	RFC5	35	.	0			c.A783G						.						135	135	135					12																	118464813		2203	4300	6503	SO:0001819	synonymous_variant	5985	exon8			CACCACAGCCTAC		CCDS9185.1, CCDS41843.2	12q24.3	2010-04-21	2002-08-29		ENSG00000111445	ENSG00000111445		"ATPases / AAA-type"	9973	protein-coding gene	gene with protein product		600407	"replication factor C (activator 1) 5 (36.5kD)"			7774928	Standard	NM_007370		Approved	RFC36	uc001twq.3	P40937	OTTHUMG00000156438	ENST00000454402.2:c.783A>G	chr12.hg19:g.118464813A>G		116.0	0.0		68.0	26.0	NM_007370	A8MZ62|B3KSX8	Silent	SNP	ENST00000454402.2	hg19	CCDS9185.1																																																																																			.	.		0.552	RFC5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344196.2	NM_007370		G	118464813	A	G	118464813	2	3	282	1	0	0	0	0	0	0	0	1	13263	175	7	2		2	RFC5	12	118464813	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	12	118464813	15387082	908	41142										
GCN1L1	10985	hgsc.bcm.edu	37	chr12	120580649	120580649	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttgttggactgggcagttccAaagttatcatcctcagaggc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:120580649delA	ENST00000300648.6	-	43	5604	c.5592delT	c.(5590-5592)tttfs	p.F1864fs		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	1864					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GGGCAGTTCCAAAGTTATCAT	0.537																																					p.G1865fs		Atlas-INDEL	.											.	GCN1L1	207	.	0			c.5593delG						.						155	156	156					12																	120580649		2049	4196	6245	SO:0001589	frameshift_variant	10985	exon43			.	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.5592delT	chr12.hg19:g.120580649delA	ENSP00000300648:p.Phe1864fs	290.0	0.0		195.0	12.0	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Frame_Shift_Del	DEL	ENST00000300648.6	hg19	CCDS41847.1																																																																																			.	.		0.537	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1			-	120580649	A	-	120580649	7	5	282	1	0	1	0	1	0	0	0	0	6307	127	5	0	2487	0	GCN1L1	12	120580649	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2115836	120580649	13271246	909	41143										
GCN1L1	10985	hgsc.bcm.edu	37	chr12	120582745	120582745	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	accctgtgcagcgcctgagcGatccacagagctctgctcat	10	15	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:120582745G>T	ENST00000300648.6	-	40	5149	c.5137C>A	c.(5137-5139)Cgc>Agc	p.R1713S		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	1713					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GCGCCTGAGCGATCCACAGAG	0.602																																					p.R1713S		Atlas-SNP	.											.	GCN1L1	207	.	0			c.C5137A						.						73	78	76					12																	120582745		2129	4250	6379	SO:0001583	missense	10985	exon40			CTGAGCGATCCAC	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.5137C>A	chr12.hg19:g.120582745G>T	ENSP00000300648:p.Arg1713Ser	129.0	0.0		87.0	34.0	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Missense_Mutation	SNP	ENST00000300648.6	hg19	CCDS41847.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.004690	0.93287	.	.	ENSG00000089154	ENST00000300648	T	0.67523	-0.27	5.5	5.5	0.81552	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.87253	0.6131	M	0.93375	3.41	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89906	0.4048	10	0.87932	D	0	-16.5971	19.7578	0.96301	0.0:0.0:1.0:0.0	.	1713	Q92616	GCN1L_HUMAN	S	1713	ENSP00000300648:R1713S	ENSP00000300648:R1713S	R	-	1	0	GCN1L1	119067128	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.554000	0.98121	2.748000	0.94277	0.655000	0.94253	CGC	.	.		0.602	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1			T	120582745	G	T	120582745	3	4	282	1	0	0	0	0	1	0	0	0	6307	1058	37	1	2954	1	GCN1L1	12	120582745	Missense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	2096	120582745	13269150	910	41144										
SIRT4	23409	hgsc.bcm.edu	37	chr12	120750552	120750552	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggtggtgggatcatccttgcAggtatctgacttggcaagag	15	7	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:120750552A>G	ENST00000202967.4	+	3	850	c.791A>G	c.(790-792)cAg>cGg	p.Q264R	RNU6-1088P_ENST00000516850.1_RNA|SIRT4_ENST00000537892.1_3'UTR	NM_012240.2	NP_036372.1			sirtuin 4											haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)	9	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TCATCCTTGCAGGTATCTGAC	0.498																																					p.Q264R		Atlas-SNP	.											.	SIRT4	29	.	0			c.A791G						.						59	56	57					12																	120750552		2203	4300	6503	SO:0001630	splice_region_variant	23409	exon3			CCTTGCAGGTATC	AF083109	CCDS9194.1	12q24.31	2010-06-25	2010-06-25		ENSG00000089163	ENSG00000089163			14932	protein-coding gene	gene with protein product		604482	"sirtuin (silent mating type information regulation 2, S. cerevisiae, homolog) 4", "sirtuin (silent mating type information regulation 2 homolog) 4 (S. cerevisiae)"			10381378	Standard	NM_012240		Approved	SIR2L4	uc001tyc.3	Q9Y6E7	OTTHUMG00000169028	ENST00000202967.4:c.792+1A>G	chr12.hg19:g.120750552A>G		131.0	0.0		123.0	6.0	NM_012240		Missense_Mutation	SNP	ENST00000202967.4	hg19	CCDS9194.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.972673	0.74246	.	.	ENSG00000089163	ENST00000202967	T	0.17691	2.26	4.59	4.59	0.56863	.	0.000000	0.85682	D	0.000000	T	0.36963	0.0986	M	0.83384	2.64	0.80722	D	1	P	0.51240	0.943	P	0.55965	0.788	T	0.26430	-1.0103	10	0.21014	T	0.42	-24.562	14.7214	0.69308	1.0:0.0:0.0:0.0	.	264	Q9Y6E7	SIRT4_HUMAN	R	264	ENSP00000202967:Q264R	ENSP00000202967:Q264R	Q	+	2	0	SIRT4	119234935	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	8.964000	0.93389	2.014000	0.59158	0.529000	0.55759	CAG	.	.		0.498	SIRT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402003.1	NM_012240	Missense_Mutation	G	120750552	A	G	120750552	5	3	282	1	0	0	0	0	0	0	1	0	14355	202	7	2	797	2	SIRT4	12	120750552	Splice_Site	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	167807	120750552	13101343	911	41145										
KDM2B	84678	hgsc.bcm.edu	37	chr12	121880092	121880092	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccaggggtagcgagtcaggcGgggggctgatggggggtggc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:121880092delG	ENST00000377071.4	-	19	3224	c.3152delC	c.(3151-3153)ccgfs	p.P1052fs	KDM2B_ENST00000536437.1_Intron|KDM2B_ENST00000542973.1_Frame_Shift_Del_p.P420fs|KDM2B_ENST00000377069.4_Frame_Shift_Del_p.P983fs	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	1052	Pro-rich.				embryonic camera-type eye morphogenesis (GO:0048596)|forebrain development (GO:0030900)|fourth ventricle development (GO:0021592)|hindbrain development (GO:0030902)|histone demethylation (GO:0016577)|histone H2A monoubiquitination (GO:0035518)|initiation of neural tube closure (GO:0021993)|lateral ventricle development (GO:0021670)|midbrain development (GO:0030901)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K36 specific) (GO:0051864)|rRNA binding (GO:0019843)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	19						CGAGTCAGGCGGGGGGCTGAT	0.672																																					p.P1051fs		Atlas-INDEL	.											.	KDM2B	218	.	0			c.3153delG						.						14	16	16					12																	121880092		1912	4085	5997	SO:0001589	frameshift_variant	84678	exon19			.	AJ459424	CCDS41849.1, CCDS41850.1	12q24.31	2014-02-18	2009-04-06	2009-04-06	ENSG00000089094	ENSG00000089094		"F-boxes / Leucine-rich repeats", "Chromatin-modifying enzymes / K-demethylases"	13610	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 1B"	609078	"F-box and leucine-rich repeat protein 10"	FBXL10		10799292	Standard	NM_032590		Approved	PCCX2, CXXC2, Fbl10, JHDM1B	uc001uat.3	Q8NHM5	OTTHUMG00000169071	ENST00000377071.4:c.3152delC	chr12.hg19:g.121880092delG	ENSP00000366271:p.Pro1052fs	171.0	0.0		178.0	13.0	NM_032590	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Frame_Shift_Del	DEL	ENST00000377071.4	hg19	CCDS41850.1																																																																																			.	.		0.672	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590		-	121880092	G	-	121880092	7	5	282	1	0	1	0	1	0	0	0	0	8134	1116	39	0	930	0	KDM2B	12	121880092	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1129540	121880092	11971803	912	41146										
MLXIP	22877	hgsc.bcm.edu	37	chr12	122614541	122614541	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gatggatggaagacccccgtCcccatggaggaggatcccct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:122614541delC	ENST00000319080.7	+	6	924	c.792delC	c.(790-792)gtcfs	p.V264fs	MLXIP_ENST00000538698.1_5'Flank					MLX interacting protein											NS(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)	20	all_neural(191;0.0837)|Medulloblastoma(191;0.163)	Lung NSC(355;0.0659)		OV - Ovarian serous cystadenocarcinoma(86;0.000599)|Epithelial(86;0.00102)|BRCA - Breast invasive adenocarcinoma(302;0.233)		AGACCCCCGTCCCCATGGAGG	0.557																																					p.V264fs	Esophageal Squamous(105;787 1493 16200 18566 52466)	Atlas-INDEL	.											.	MLXIP	46	.	0			c.791delT						.						65	69	67					12																	122614541		2082	4219	6301	SO:0001589	frameshift_variant	22877	exon6			.	AB020674	CCDS73540.1	12q21.31	2013-05-21				ENSG00000175727		"Basic helix-loop-helix proteins"	17055	protein-coding gene	gene with protein product		608090				10048485, 11073985	Standard	XM_006719290		Approved	MONDOA, KIAA0867, MIR, bHLHe36	uc001ubq.3	Q9HAP2		ENST00000319080.7:c.792delC	chr12.hg19:g.122614541delC	ENSP00000312834:p.Val264fs	216.0	0.0		157.0	10.0	NM_014938		Frame_Shift_Del	DEL	ENST00000319080.7	hg19																																																																																				.	.		0.557	MLXIP-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401718.2	NM_014938		-	122614541	C	-	122614541	7	5	282	1	0	1	0	1	0	0	0	0	9645	842	30	0	814	0	MLXIP	12	122614541	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	734449	122614541	11237354	913	41147										
B3GNT4	79369	hgsc.bcm.edu	37	chr12	122691000	122691000	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cccaccagcctttctgggctCccccaacaccccgtcacagc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:122691000delC	ENST00000324189.4	+	3	558	c.202delC	c.(202-204)cccfs	p.P69fs	B3GNT4_ENST00000545141.1_Intron|B3GNT4_ENST00000546192.1_Frame_Shift_Del_p.P44fs|B3GNT4_ENST00000535274.1_Frame_Shift_Del_p.P44fs	NM_030765.2	NP_110392.1	Q9C0J1	B3GN4_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 4	69					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	13	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000297)|Epithelial(86;0.000497)|BRCA - Breast invasive adenocarcinoma(302;0.222)		TTTCTGGGCTCCCCCAACACC	0.637																																					p.A67fs		Atlas-INDEL	.											.	B3GNT4	35	.	0			c.201delT						.						130	136	134					12																	122691000		2203	4300	6503	SO:0001589	frameshift_variant	79369	exon3			.	AB049586	CCDS9227.1	12q24	2013-02-19						"Beta 3-glycosyltransferases"	15683	protein-coding gene	gene with protein product		605864				11042166	Standard	NM_030765		Approved	B3GN-T4, beta3Gn-T4	uc001ubx.3	Q9C0J1		ENST00000324189.4:c.202delC	chr12.hg19:g.122691000delC	ENSP00000319636:p.Pro69fs	227.0	0.0		138.0	10.0	NM_030765	Q8N5W4|Q8N934|Q8ND21|Q8WWR5|Q8WY02|Q96QH5	Frame_Shift_Del	DEL	ENST00000324189.4	hg19	CCDS9227.1																																																																																			.	.		0.637	B3GNT4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000401595.1	NM_030765		-	122691000	C	-	122691000	7	5	282	1	0	1	0	1	0	0	0	0	1259	855	30	0	208	0	B3GNT4	12	122691000	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	76459	122691000	11160895	914	41148										
RILPL2	196383	hgsc.bcm.edu	37	chr12	123907659	123907659	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcactagtaaccacagcatcTttttctcttcttcctcctgg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:123907659delT	ENST00000280571.8	-	3	833	c.537delA	c.(535-537)aaafs	p.K179fs		NM_145058.1	NP_659495.1	Q969X0	RIPL2_HUMAN	Rab interacting lysosomal protein-like 2	179					epithelial cell morphogenesis (GO:0003382)|intracellular protein transport (GO:0006886)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|primary cilium (GO:0072372)	identical protein binding (GO:0042802)			endometrium(1)|large_intestine(2)|lung(2)|skin(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000546)|Epithelial(86;0.00179)|all cancers(50;0.0168)		CCACAGCATCTTTTTCTCTTC	0.443																																					p.D180fs		Atlas-INDEL	.											.	RILPL2	10	.	0			c.538delG						.						172	159	163					12																	123907659		2203	4300	6503	SO:0001589	frameshift_variant	196383	exon3			.	AB085763	CCDS9248.1	12q24.31	2007-11-27				ENSG00000150977			28787	protein-coding gene	gene with protein product		614093				14668488	Standard	NM_145058		Approved	MGC7036, FLJ30380, FLJ32372	uc001uey.1	Q969X0		ENST00000280571.8:c.537delA	chr12.hg19:g.123907659delT	ENSP00000280571:p.Lys179fs	321.0	0.0		255.0	16.0	NM_145058		Frame_Shift_Del	DEL	ENST00000280571.8	hg19	CCDS9248.1																																																																																			.	.		0.443	RILPL2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_145058		-	123907659	T	-	123907659	7	5	282	1	0	1	0	1	0	0	0	0	13377	1606	56	0	106	0	RILPL2	12	123907659	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1216659	123907659	9944236	915	41149										
TPTE2	93492	hgsc.bcm.edu	37	chr13	20039443	20039443	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tccatcccttgtgtatcgccTtttgttttctgaaacctgag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:20039443delT	ENST00000400230.2	-	9	672	c.628delA	c.(628-630)aggfs	p.R211fs	TPTE2_ENST00000400103.2_Frame_Shift_Del_p.R100fs|TPTE2_ENST00000457266.2_Frame_Shift_Del_p.R100fs|TPTE2_ENST00000255310.6_Frame_Shift_Del_p.R134fs|TPTE2_ENST00000382975.4_Frame_Shift_Del_p.R171fs|TPTE2_ENST00000390680.2_Frame_Shift_Del_p.R134fs|TPTE2_ENST00000382977.4_Frame_Shift_Del_p.R211fs|TPTE2_ENST00000382978.1_Frame_Shift_Del_p.R171fs			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	211	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		GTGTATCGCCTTTTGTTTTCT	0.313																																					p.R210fs		Atlas-INDEL	.											.	TPTE2	225	.	0			c.629delG						.						182	168	173					13																	20039443		2203	4300	6503	SO:0001589	frameshift_variant	93492	exon10			.	AJ421032	CCDS9285.1, CCDS45013.1, CCDS45014.1	13q12.11	2012-12-10			ENSG00000132958	ENSG00000132958		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	17299	protein-coding gene	gene with protein product		606791				11716755, 12717346, 15057823	Standard	NM_130785		Approved	TPIP	uc001umd.3	Q6XPS3	OTTHUMG00000016493	ENST00000400230.2:c.628delA	chr13.hg19:g.20039443delT	ENSP00000383089:p.Arg211fs	253.0	0.0		191.0	12.0	NM_199254	A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	Frame_Shift_Del	DEL	ENST00000400230.2	hg19	CCDS45014.1																																																																																			.	.		0.313	TPTE2-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_199254		-	20039443	T	-	20039443	7	5	282	1	0	1	0	1	0	0	0	0	16446	1608	56	0	988	0	TPTE2	13	20039443	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10		20039443	95130435	916	41150										
FGF9	2254	hgsc.bcm.edu	37	chr13	22246178	22246178	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acctgggtcagtccgaagcaGgggggctccccaggggaccc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:22246178delG	ENST00000382353.5	+	1	657	c.127delG	c.(127-129)gggfs	p.G44fs		NM_002010.2	NP_002001.1	P31371	FGF9_HUMAN	fibroblast growth factor 9	44					angiogenesis (GO:0001525)|cell-cell signaling (GO:0007267)|chondrocyte differentiation (GO:0002062)|embryonic digestive tract development (GO:0048566)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system development (GO:0048706)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lung-associated mesenchyme development (GO:0060484)|male gonad development (GO:0008584)|male sex determination (GO:0030238)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|neurotrophin TRK receptor signaling pathway (GO:0048011)|osteoblast differentiation (GO:0001649)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein import into nucleus (GO:0006606)|regulation of timing of cell differentiation (GO:0048505)|signal transduction (GO:0007165)|substantia nigra development (GO:0021762)	basement membrane (GO:0005604)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|skin(2)	9		all_cancers(29;1.23e-20)|all_epithelial(30;9.83e-19)|all_lung(29;9.64e-17)|Lung SC(185;0.0262)|Breast(139;0.106)		all cancers(112;3.92e-05)|Epithelial(112;0.000166)|OV - Ovarian serous cystadenocarcinoma(117;0.00314)|Lung(94;0.163)		GTCCGAAGCAGGGGGGCTCCC	0.562																																					p.A42fs	Melanoma(195;1939 2127 12623 13963 52730)	Atlas-INDEL	.											.	FGF9	25	.	0			c.126delA						.						68	74	72					13																	22246178		2203	4300	6503	SO:0001589	frameshift_variant	2254	exon1			.	D14838	CCDS9298.1	13q11-q12	2014-01-30	2013-06-18		ENSG00000102678	ENSG00000102678		"Endogenous ligands"	3687	protein-coding gene	gene with protein product	"glia-activating factor"	600921	"fibroblast growth factor 9 (glia-activating factor)"			8321227	Standard	NM_002010		Approved		uc001uog.2	P31371	OTTHUMG00000017412	ENST00000382353.5:c.127delG	chr13.hg19:g.22246178delG	ENSP00000371790:p.Gly44fs	227.0	0.0		175.0	12.0	NM_002010	A8K427|Q3SY32	Frame_Shift_Del	DEL	ENST00000382353.5	hg19	CCDS9298.1																																																																																			.	.		0.562	FGF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046002.2			-	22246178	G	-	22246178	7	5	282	1	0	1	0	1	0	0	0	0	5867	1000	35	0	129	0	FGF9	13	22246178	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	2206735	22246178	92923700	917	41151										
SACS	26278	hgsc.bcm.edu	37	chr13	23929049	23929049	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctgctccaacctgacccagtCacagctaattgaataaatca	5	13	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:23929049C>A	ENST00000382292.3	-	7	1975	c.1702G>T	c.(1702-1704)Gac>Tac	p.D568Y	SACS_ENST00000382298.3_Missense_Mutation_p.D568Y|SACS_ENST00000476776.1_5'Flank|SACS_ENST00000402364.1_5'UTR			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	568					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		CTGACCCAGTCACAGCTAATT	0.473																																					p.D568Y		Atlas-SNP	.											.	SACS	871	.	0			c.G1702T						.						102	97	98					13																	23929049		2203	4300	6503	SO:0001583	missense	26278	exon8			CCCAGTCACAGCT	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.1702G>T	chr13.hg19:g.23929049C>A	ENSP00000371729:p.Asp568Tyr	180.0	0.0		142.0	48.0	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	hg19	CCDS9300.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	3.352|3.352	-0.132318|-0.132318	0.06753|0.06753	.|.	.|.	ENSG00000151835|ENSG00000151835	ENST00000382292;ENST00000382298;ENST00000423156|ENST00000455470	T;T;T|.	0.17054|.	2.3;2.3;2.3|.	5.74|5.74	3.05|3.05	0.35203|0.35203	.|.	0.784986|.	0.13011|.	N|.	0.420898|.	T|.	0.23289|.	0.0563|.	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	N|N	1|1	B;B;B|.	0.31290|.	0.318;0.098;0.0|.	B;B;B|.	0.32624|.	0.149;0.123;0.004|.	T|.	0.22068|.	-1.0227|.	10|.	0.48119|.	T|.	0.1|.	.|.	6.9614|6.9614	0.24599|0.24599	0.0788:0.5348:0.2873:0.0991|0.0788:0.5348:0.2873:0.0991	.|.	467;355;568|.	B2REB1;E9PAL4;Q9NZJ4|.	.;.;SACS_HUMAN|.	Y|L	568;568;192|467	ENSP00000371729:D568Y;ENSP00000371735:D568Y;ENSP00000390925:D192Y|.	ENSP00000371729:D568Y|.	D|X	-|-	1|2	0|2	SACS|SACS	22827049|22827049	0.483000|0.483000	0.25956|0.25956	0.000000|0.000000	0.03702|0.03702	0.017000|0.017000	0.09413|0.09413	2.444000|2.444000	0.44890|0.44890	0.426000|0.426000	0.26116|0.26116	0.561000|0.561000	0.74099|0.74099	GAC|TGA	.	.		0.473	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		A	23929049	C	A	23929049	3	1	282	1	0	0	0	0	1	0	0	0	13819	826	29	3	12049	3	SACS	13	23929049	Missense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1682871	23929049	91240829	918	41152										
SHISA2	387914	hgsc.bcm.edu	37	chr13	26620702	26620702	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcactgttggtgtgagggaaGggggactgaatctgcctgta							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:26620702delG	ENST00000319420.3	-	2	892	c.837delC	c.(835-837)cccfs	p.P279fs		NM_001007538.1	NP_001007539.1	Q6UWI4	SHSA2_HUMAN	shisa family member 2	279					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(2)|skin(1)	17						TGTGAGGGAAGGGGGACTGAA	0.572																																					p.F280fs		Atlas-Indel,Pindel	.											.	SHISA2	43	.	0			c.838delT						.						103	91	95					13																	26620702		2203	4300	6503	SO:0001589	frameshift_variant	387914	exon2			.		CCDS31951.1	13q12.13	2013-07-31	2013-07-31	2008-04-01	ENSG00000180730	ENSG00000180730		"Shisa homologs"	20366	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 13", "transmembrane protein 46", "shisa homolog 2 (Xenopus laevis)"	C13orf13, TMEM46			Standard	NM_001007538		Approved	bA398O19.2, PRO28631, WGAR9166, hShisa	uc001uqm.1	Q6UWI4	OTTHUMG00000016612	ENST00000319420.3:c.837delC	chr13.hg19:g.26620702delG	ENSP00000313079:p.Pro279fs	95.0	0.0		90.0	27.0	NM_001007538	B9EH70|Q5W0G8	Frame_Shift_Del	DEL	ENST00000319420.3	hg19	CCDS31951.1																																																																																			.	.		0.572	SHISA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044239.2	NM_001007538		-	26620702	G	-	26620702	7	5	282	1	0	1	0	1	0	0	0	0	14295	987	35	0	54	0	SHISA2	13	26620702	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	2691653	26620702	88549176	919	41153										
CDK8	1024	hgsc.bcm.edu	37	chr13	26923240	26923240	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcttaagcatccaaacgtcaTttctcttcaaaaggtgtttc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:26923240delT	ENST00000381527.3	+	3	739	c.236delT	c.(235-237)attfs	p.I79fs	CDK8_ENST00000536792.1_Frame_Shift_Del_p.I79fs	NM_001260.1	NP_001251.1	P49336	CDK8_HUMAN	cyclin-dependent kinase 8	79	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	25	Colorectal(5;0.000442)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0384)|Epithelial(112;0.142)|OV - Ovarian serous cystadenocarcinoma(117;0.188)		CCAAACGTCATTTCTCTTCAA	0.403																																					p.I79fs		Atlas-INDEL	.											.	CDK8	61	.	0			c.235delA						.						236	215	222					13																	26923240		2203	4300	6503	SO:0001589	frameshift_variant	1024	exon3			.	X85753	CCDS9317.1	13q12	2011-11-08			ENSG00000132964	ENSG00000132964		"Cyclin-dependent kinases"	1779	protein-coding gene	gene with protein product		603184				7568034	Standard	NM_001260		Approved	K35	uc001uqr.1	P49336	OTTHUMG00000016617	ENST00000381527.3:c.236delT	chr13.hg19:g.26923240delT	ENSP00000370938:p.Ile79fs	251.0	0.0		182.0	11.0	NM_001260	Q5VUF3|Q6ISB5	Frame_Shift_Del	DEL	ENST00000381527.3	hg19	CCDS9317.1																																																																																			.	.		0.403	CDK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044250.1			-	26923240	T	-	26923240	7	5	282	1	0	1	0	1	0	0	0	0	3152	1493	52	0	246	0	CDK8	13	26923240	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	302538	26923240	88246638	920	41154										
FLT3	2322	hgsc.bcm.edu	37	chr13	28626770	28626770	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagggcgtcctggttttccaTttttctaaagtaaggtcttc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:28626770delT	ENST00000241453.7	-	5	607	c.526delA	c.(526-528)atgfs	p.M176fs	FLT3_ENST00000380982.4_Frame_Shift_Del_p.M176fs|FLT3_ENST00000537084.1_Frame_Shift_Del_p.M176fs	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	176					B cell differentiation (GO:0030183)|cellular response to cytokine stimulus (GO:0071345)|common myeloid progenitor cell proliferation (GO:0035726)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell differentiation (GO:0097028)|hemopoiesis (GO:0030097)|leukocyte homeostasis (GO:0001776)|lymphocyte proliferation (GO:0046651)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|pro-B cell differentiation (GO:0002328)|pro-T cell differentiation (GO:0002572)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor signaling pathway (GO:0038084)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|cytokine receptor activity (GO:0004896)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.M176V(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(12329)|kidney(2)|large_intestine(8)|lung(30)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12390	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Ponatinib(DB08901)|Sorafenib(DB00398)|Sunitinib(DB01268)	TGGTTTTCCATTTTTCTAAAG	0.408			"Mis, O"		"AML, ALL"																																p.M176fs		Atlas-INDEL	.		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	.	FLT3	15525	.	1	Substitution - Missense(1)	lung(1)	c.527delT						.						109	107	108					13																	28626770		2203	4300	6503	SO:0001589	frameshift_variant	2322	exon5			.	U02687	CCDS31953.1	13q12	2014-09-17			ENSG00000122025	ENSG00000122025	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3765	protein-coding gene	gene with protein product		136351				8394751	Standard	NM_004119		Approved	STK1, FLK2, CD135	uc001urw.3	P36888	OTTHUMG00000016646	ENST00000241453.7:c.526delA	chr13.hg19:g.28626770delT	ENSP00000241453:p.Met176fs	174.0	0.0		152.0	10.0	NM_004119	A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	Frame_Shift_Del	DEL	ENST00000241453.7	hg19	CCDS31953.1																																																																																			.	.		0.408	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044319.2			-	28626770	T	-	28626770	7	5	282	1	0	1	0	1	0	0	0	0	5950	1493	52	0	2535	0	FLT3	13	28626770	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1703530	28626770	86543108	921	41155										
PAN3	255967	hgsc.bcm.edu	37	chr13	28748431	28748431	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccaggaatggatggaggtgcTttaactgatacaagtctcac							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:28748431delT	ENST00000380958.3	+	2	605	c.453delT	c.(451-453)gctfs	p.A151fs	PAN3_ENST00000399613.1_Frame_Shift_Del_p.A5fs	NM_175854.7	NP_787050.6			PAN3 poly(A) specific ribonuclease subunit											endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)	Colorectal(13;0.000334)	all cancers(112;0.0102)|Epithelial(112;0.0803)|GBM - Glioblastoma multiforme(144;0.121)|OV - Ovarian serous cystadenocarcinoma(117;0.13)|Lung(94;0.174)		ATGGAGGTGCTTTAACTGATA	0.368																																					p.A151fs		Atlas-INDEL	.											.	PAN3	123	.	0			c.452delC						.						100	97	98					13																	28748431		2203	4300	6503	SO:0001589	frameshift_variant	255967	exon2			.	AK091307	CCDS9329.1, CCDS9329.2	13q12.2	2014-03-27	2014-03-27		ENSG00000152520	ENSG00000152520			29991	protein-coding gene	gene with protein product			"PAN3 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)"			14583602	Standard	NM_175854		Approved		uc001urz.3	Q58A45	OTTHUMG00000016645	ENST00000380958.3:c.453delT	chr13.hg19:g.28748431delT	ENSP00000370345:p.Ala151fs	187.0	0.0		149.0	10.0	NM_175854		Frame_Shift_Del	DEL	ENST00000380958.3	hg19	CCDS9329.2																																																																																			.	.		0.368	PAN3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044318.4	NM_175854		-	28748431	T	-	28748431	7	5	282	1	0	1	0	1	0	0	0	0	11424	1596	56	0	459	0	PAN3	13	28748431	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	121661	28748431	86421447	922	41156										
SLC46A3	283537	hgsc.bcm.edu	37	chr13	29286951	29286951	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atattcctaggaaactagtcAaaaaagaggcactacccaaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:29286951delA	ENST00000266943.6	-	3	1295	c.926delT	c.(925-927)ttgfs	p.L309fs	SLC46A3_ENST00000380814.4_Frame_Shift_Del_p.L309fs	NM_001135919.1|NM_181785.3	NP_001129391.1|NP_861450.1	Q7Z3Q1	S46A3_HUMAN	solute carrier family 46, member 3	309					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(2)|prostate(1)|skin(1)	15		Lung SC(185;0.0367)		all cancers(112;0.159)		GAAACTAGTCAAAAAAGAGGC	0.383																																					p.L309fs		Atlas-INDEL	.											.	SLC46A3	86	.	0			c.927delG						.						94	93	94					13																	29286951		2203	4300	6503	SO:0001589	frameshift_variant	283537	exon3			.		CCDS9332.1, CCDS45021.1	13q12.3	2013-05-22	2007-03-29		ENSG00000139508	ENSG00000139508		"Solute carriers"	27501	protein-coding gene	gene with protein product							Standard	NM_001135919		Approved	DKFZp686A1775, FLJ42613	uc001usj.3	Q7Z3Q1	OTTHUMG00000016650	ENST00000266943.6:c.926delT	chr13.hg19:g.29286951delA	ENSP00000266943:p.Leu309fs	204.0	0.0		147.0	10.0	NM_181785	Q3ZCV8|Q6NUK5|Q6P9B3|Q6ZVG5|Q96QA1	Frame_Shift_Del	DEL	ENST00000266943.6	hg19	CCDS9332.1																																																																																			.	.		0.383	SLC46A3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276111.1	NM_181785		-	29286951	A	-	29286951	7	5	282	1	0	1	0	1	0	0	0	0	14661	131	5	0	489	0	SLC46A3	13	29286951	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	538520	29286951	85882927	923	41157										
MTUS2	23281	hgsc.bcm.edu	37	chr13	29600946	29600946	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaaattcaagccagacctgcAgaagccaagggtcttcagtt	10	10	3	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:29600946A>G	ENST00000431530.3	+	1	2199	c.2141A>G	c.(2140-2142)cAg>cGg	p.Q714R		NM_001033602.2	NP_001028774.2	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	704	Mediates interaction with MAPRE1.					cytoplasm (GO:0005737)|microtubule (GO:0005874)	microtubule binding (GO:0008017)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	20						CCAGACCTGCAGAAGCCAAGG	0.517																																					p.Q714R		Atlas-SNP	.											MTUS2_ENST00000431530,right_upper_lobe,carcinoma,0,1	MTUS2	279	.	0			c.A2141G						.						59	61	61					13																	29600946		1899	4110	6009	SO:0001583	missense	23281	exon1			ACCTGCAGAAGCC	AB018317	CCDS41874.1, CCDS45022.1	13q12.3	2013-01-17	2009-10-20	2009-10-20	ENSG00000132938	ENSG00000132938			20595	protein-coding gene	gene with protein product	"+TIP of 150 kDa", "cardiac zipper protein"		"KIAA0774"	KIAA0774		19543227	Standard	NM_001033602		Approved	TIP150, CAZIP, ICIS	uc001usl.4	Q5JR59	OTTHUMG00000016657	ENST00000431530.3:c.2141A>G	chr13.hg19:g.29600946A>G	ENSP00000392057:p.Gln714Arg	26.0	0.0		34.0	2.0	NM_001033602	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Missense_Mutation	SNP	ENST00000431530.3	hg19	CCDS45022.1	.	.	.	.	.	.	.	.	.	.	a	23.4	4.410080	0.83340	.	.	ENSG00000132938	ENST00000431530	T	0.36699	1.24	6.17	6.17	0.99709	.	0.000000	0.56097	D	0.000034	T	0.59293	0.2183	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.57969	-0.7719	9	.	.	.	.	16.0034	0.80327	1.0:0.0:0.0:0.0	.	704	Q5JR59	MTUS2_HUMAN	R	714	ENSP00000392057:Q714R	.	Q	+	2	0	MTUS2	28498946	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.857000	0.55972	2.371000	0.80710	0.533000	0.62120	CAG	.	.		0.517	MTUS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044336.3	XM_166270		G	29600946	A	G	29600946	3	3	282	1	0	0	0	0	1	0	0	0	9975	188	7	2	2143	2	MTUS2	13	29600946	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	313995	29600946	85568932	924	41158										
KATNAL1	84056	hgsc.bcm.edu	37	chr13	30814622	30814622	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atggccttctaatccctttgAaaaagtcaggcatccacatt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:30814622delA	ENST00000380615.3	-	6	868	c.701delT	c.(700-702)ttcfs	p.F234fs	KATNAL1_ENST00000380617.3_Frame_Shift_Del_p.F234fs	NM_032116.4	NP_115492.1			katanin p60 subunit A-like 1											autonomic_ganglia(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|skin(1)|urinary_tract(3)	19		Lung SC(185;0.0257)		all cancers(112;0.114)|OV - Ovarian serous cystadenocarcinoma(117;0.213)		AATCCCTTTGAAAAAGTCAGG	0.398																																					p.F234fs		Atlas-INDEL	.											.	KATNAL1	53	.	0			c.702delC						.						114	106	109					13																	30814622		2203	4300	6503	SO:0001589	frameshift_variant	84056	exon6			.	AK097423	CCDS31956.1	13q12.3	2010-04-21			ENSG00000102781	ENSG00000102781		"ATPases / AAA-type"	28361	protein-coding gene	gene with protein product		614764				12477932	Standard	NM_001014380		Approved	MGC2599	uc001uss.4	Q9BW62	OTTHUMG00000016665	ENST00000380615.3:c.701delT	chr13.hg19:g.30814622delA	ENSP00000369989:p.Phe234fs	139.0	0.0		147.0	10.0	NM_001014380		Frame_Shift_Del	DEL	ENST00000380615.3	hg19	CCDS31956.1																																																																																			.	.		0.398	KATNAL1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044346.2	NM_032116		-	30814622	A	-	30814622	7	5	282	1	0	1	0	1	0	0	0	0	7994	246	9	0	795	0	KATNAL1	13	30814622	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1213676	30814622	84355256	925	41159										
B3GALTL	145173	hgsc.bcm.edu	37	chr13	31821164	31821164	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atcattgttttctcaggagcTccccagtgtcctcctccttc	6	15	2	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:31821164T>C	ENST00000343307.4	+	5	424	c.275T>C	c.(274-276)cTc>cCc	p.L92P		NM_194318.3	NP_919299.3	Q6Y288	B3GLT_HUMAN	beta 1,3-galactosyltransferase-like	92					fucose metabolic process (GO:0006004)|protein glycosylation (GO:0006486)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19		Lung SC(185;0.0257)		all cancers(112;0.00436)|Epithelial(112;0.0285)|OV - Ovarian serous cystadenocarcinoma(117;0.0512)|GBM - Glioblastoma multiforme(144;0.184)		TCTCAGGAGCTCCCCAGTGTC	0.363																																					p.L92P		Atlas-SNP	.											.	B3GALTL	48	.	0			c.T275C						.						132	113	119					13																	31821164		2203	4300	6503	SO:0001583	missense	145173	exon5			AGGAGCTCCCCAG	AB101481	CCDS9341.1	13q12.3	2014-03-24			ENSG00000187676	ENSG00000187676		"Beta 3-glycosyltransferases"	20207	protein-coding gene	gene with protein product		610308				12943678, 16899492, 17032646	Standard	NM_194318		Approved	B3GTL, B3Glc-T	uc010aaz.3	Q6Y288	OTTHUMG00000016688	ENST00000343307.4:c.275T>C	chr13.hg19:g.31821164T>C	ENSP00000343002:p.Leu92Pro	194.0	0.0		150.0	6.0	NM_194318	A8K5F8|Q5W0H2|Q6NUI3	Missense_Mutation	SNP	ENST00000343307.4	hg19	CCDS9341.1	.	.	.	.	.	.	.	.	.	.	T	2.161	-0.392174	0.04932	.	.	ENSG00000187676	ENST00000343307	T	0.72942	-0.7	5.61	-2.01	0.07410	.	0.459579	0.23293	N	0.049772	T	0.47985	0.1475	L	0.27053	0.805	0.25348	N	0.988896	B	0.11235	0.004	B	0.08055	0.003	T	0.20240	-1.0281	10	0.41790	T	0.15	-0.0451	3.9961	0.09559	0.1231:0.0693:0.3836:0.424	.	92	Q6Y288	B3GLT_HUMAN	P	92	ENSP00000343002:L92P	ENSP00000343002:L92P	L	+	2	0	B3GALTL	30719164	0.001000	0.12720	0.037000	0.18230	0.141000	0.21300	0.309000	0.19332	-0.541000	0.06257	0.377000	0.23210	CTC	.	.		0.363	B3GALTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044396.3	NM_194318		C	31821164	T	C	31821164	3	2	282	1	0	0	0	0	1	0	0	0	1252	1551	54	2	293	2	B3GALTL	13	31821164	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1006542	31821164	83348714	926	41160										
FRY	10129	hgsc.bcm.edu	37	chr13	32722055	32722055	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gggacatgcctctgaacatcTttgtgaaaatcatccagttc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:32722055delT	ENST00000380250.3	+	13	1859	c.1363delT	c.(1363-1365)tttfs	p.F455fs		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	455						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		TCTGAACATCTTTGTGAAAAT	0.473																																					p.I454fs		Atlas-INDEL	.											.	FRY	312	.	0			c.1362delC						.						124	119	121					13																	32722055		1853	4096	5949	SO:0001589	frameshift_variant	10129	exon13			.	AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"chromosome 13 open reading frame 14"	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.1363delT	chr13.hg19:g.32722055delT	ENSP00000369600:p.Phe455fs	225.0	0.0		174.0	12.0	NM_023037	Q9Y3N6	Frame_Shift_Del	DEL	ENST00000380250.3	hg19	CCDS41875.1																																																																																			.	.		0.473	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037		-	32722055	T	-	32722055	7	5	282	1	0	1	0	1	0	0	0	0	6071	1609	56	0	1413	0	FRY	13	32722055	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	900891	32722055	82447823	927	41161										
FRY	10129	hgsc.bcm.edu	37	chr13	32776158	32776158	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caacagagagatttatgaaaTctccatgcagctcatgcagg	9	9	2	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:32776158T>C	ENST00000380250.3	+	30	4323	c.3827T>C	c.(3826-3828)aTc>aCc	p.I1276T		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	1276						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		ATTTATGAAATCTCCATGCAG	0.378																																					p.I1276T		Atlas-SNP	.											.	FRY	312	.	0			c.T3827C						.						136	121	126					13																	32776158		1893	4115	6008	SO:0001583	missense	10129	exon30			ATGAAATCTCCAT	AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"chromosome 13 open reading frame 14"	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.3827T>C	chr13.hg19:g.32776158T>C	ENSP00000369600:p.Ile1276Thr	142.0	0.0		112.0	5.0	NM_023037	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	hg19	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	T	12.99	2.103089	0.37145	.	.	ENSG00000073910	ENST00000380250;ENST00000380257	T	0.62941	-0.01	5.77	5.77	0.91146	.	0.051843	0.85682	D	0.000000	T	0.57902	0.2085	N	0.25144	0.715	0.80722	D	1	B	0.23490	0.086	B	0.40410	0.328	T	0.54016	-0.8356	10	0.22109	T	0.4	.	16.0977	0.81139	0.0:0.0:0.0:1.0	.	1276	Q5TBA9	FRY_HUMAN	T	1276;115	ENSP00000369600:I1276T	ENSP00000369600:I1276T	I	+	2	0	FRY	31674158	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.954000	0.87848	2.216000	0.71823	0.528000	0.53228	ATC	.	.		0.378	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037		C	32776158	T	C	32776158	3	2	282	1	0	0	0	0	1	0	0	0	6071	1435	50	2	3945	2	FRY	13	32776158	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	54103	32776158	82393720	928	41162										
BRCA2	675	hgsc.bcm.edu	37	chr13	32911166	32911166	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acaatgagaataattttgtcTtccaagtagctaatgaaagg	8	5	1	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:32911166T>C	ENST00000380152.3	+	11	2907	c.2674T>C	c.(2674-2676)Ttc>Ctc	p.F892L	BRCA2_ENST00000544455.1_Missense_Mutation_p.F892L			P51587	BRCA2_HUMAN	breast cancer 2, early onset	892	Interaction with NPM1.				brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TAATTTTGTCTTCCAAGTAGC	0.318			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											p.F892L	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	.	BRCA2	812	.	0			c.T2674C						.						53	57	55					13																	32911166		2203	4297	6500	SO:0001583	missense	675	exon11	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	TTTGTCTTCCAAG	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.2674T>C	chr13.hg19:g.32911166T>C	ENSP00000369497:p.Phe892Leu	160.0	0.0		148.0	6.0	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	hg19	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	T	15.01	2.705580	0.48412	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.59638	0.25;0.25	5.77	3.32	0.38043	.	0.610727	0.16404	N	0.215917	T	0.38241	0.1033	L	0.31578	0.945	0.09310	N	1	B	0.18461	0.028	B	0.13407	0.009	T	0.21930	-1.0231	10	0.15066	T	0.55	.	5.2141	0.15332	0.1567:0.0841:0.0:0.7592	.	892	P51587	BRCA2_HUMAN	L	892	ENSP00000369497:F892L;ENSP00000439902:F892L	ENSP00000369497:F892L	F	+	1	0	BRCA2	31809166	0.001000	0.12720	0.003000	0.11579	0.568000	0.35870	0.720000	0.25896	0.442000	0.26555	0.482000	0.46254	TTC	.	.		0.318	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		C	32911166	T	C	32911166	3	2	282	1	0	0	0	0	1	0	0	0	1501	1609	56	2	2712	2	BRCA2	13	32911166	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	135008	32911166	82258712	929	41163										
PDS5B	23047	hgsc.bcm.edu	37	chr13	33332689	33332689	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagaaactgtacactgtgtgTgatgttgccatgaatatcat	9	7	1	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:33332689T>C	ENST00000315596.10	+	28	3393	c.3207T>C	c.(3205-3207)tgT>tgC	p.C1069C		NM_015032.3	NP_055847.1	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae)	1069					cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of cell proliferation (GO:0008285)|regulation of cell proliferation (GO:0042127)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|lung(14)|ovary(5)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	62		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)		ACACTGTGTGTGATGTTGCCA	0.368																																					p.C1069C		Atlas-SNP	.											.	PDS5B	141	.	0			c.T3207C						.						121	114	116					13																	33332689		1841	4091	5932	SO:0001819	synonymous_variant	23047	exon28			TGTGTGTGATGTT	AB023196	CCDS41878.1	13q12.3	2008-02-05	2007-07-18	2007-07-18	ENSG00000083642	ENSG00000083642			20418	protein-coding gene	gene with protein product		605333	"androgen-induced proliferation inhibitor"	APRIN		8812419, 10215036	Standard	NM_015032		Approved	AS3, KIAA0979, FLJ23236, CG008	uc010abf.3	Q9NTI5	OTTHUMG00000016704	ENST00000315596.10:c.3207T>C	chr13.hg19:g.33332689T>C		106.0	0.0		79.0	5.0	NM_015032	Q5R3S3|Q5W0K8|Q6NSC3|Q8IXT6|Q9H5N8|Q9Y2I5|Q9Y451	Silent	SNP	ENST00000315596.10	hg19	CCDS41878.1																																																																																			.	.		0.368	PDS5B-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044428.3	NM_015032		C	33332689	T	C	33332689	2	2	282	1	0	0	0	0	0	0	0	1	11701	1702	59	2		2	PDS5B	13	33332689	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	421523	33332689	81837189	930	41164										
SOHLH2	54937	hgsc.bcm.edu	37	chr13	36764122	36764122	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttgaatgaagaagagagatcTttttgtttttctcgaactct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:36764122delT	ENST00000379881.3	-	6	690	c.602delA	c.(601-603)aagfs	p.K201fs	SOHLH2_ENST00000554962.1_Frame_Shift_Del_p.K278fs|SOHLH2_ENST00000317764.6_Frame_Shift_Del_p.K201fs|CCDC169-SOHLH2_ENST00000511166.1_Frame_Shift_Del_p.K278fs	NM_017826.2	NP_060296.2	Q9NX45	SOLH2_HUMAN	spermatogenesis and oogenesis specific basic helix-loop-helix 2	201	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;4.63e-08)|Epithelial(112;2.67e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00272)|BRCA - Breast invasive adenocarcinoma(63;0.00685)|GBM - Glioblastoma multiforme(144;0.0273)		AAGAGAGATCTTTTTGTTTTT	0.318																																					p.K278fs		Atlas-INDEL	.											.	.	.	.	0			c.834delG						.						107	107	107					13																	36764122		2203	4300	6503	SO:0001589	frameshift_variant	100526761	exon11			.	AK000456	CCDS9355.1, CCDS61309.1	13q13.3	2013-05-21			ENSG00000120669	ENSG00000120669		"Basic helix-loop-helix proteins"	26026	protein-coding gene	gene with protein product	"spermatogenesis associated 28"					12477932	Standard	NM_017826		Approved	FLJ20449, TEB1, bHLHe81, SPATA28		Q9NX45	OTTHUMG00000016728	ENST00000379881.3:c.602delA	chr13.hg19:g.36764122delT	ENSP00000369210:p.Lys201fs	216.0	0.0		171.0	11.0	NM_001198910	B4DX90|Q5EGC3|Q8TC74|Q96QX4	Frame_Shift_Del	DEL	ENST00000379881.3	hg19	CCDS9355.1																																																																																			.	.		0.318	SOHLH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044477.2	NM_017826		-	36764122	T	-	36764122	7	5	282	1	0	1	0	1	0	0	0	0	14939	1609	56	0	699	0	SOHLH2	13	36764122	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3431433	36764122	78405756	931	41165										
COG6	57511	hgsc.bcm.edu	37	chr13	40251685	40251685	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttctgatgaaatgagtcttcTccgaggtacaagagaaggac	11	7	3	4			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:40251685T>C	ENST00000455146.3	+	5	559	c.509T>C	c.(508-510)cTc>cCc	p.L170P	COG6_ENST00000416691.1_Missense_Mutation_p.L170P	NM_020751.2	NP_065802.1	Q9Y2V7	COG6_HUMAN	component of oligomeric golgi complex 6	170					glycosylation (GO:0070085)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				NS(1)|kidney(2)|large_intestine(5)|lung(4)|skin(1)	13		Lung NSC(96;0.000124)|Breast(139;0.0199)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.03e-09)|Epithelial(112;7e-07)|OV - Ovarian serous cystadenocarcinoma(117;0.00015)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.0168)		ATGAGTCTTCTCCGAGGTACA	0.358																																					p.L170P		Atlas-SNP	.											.	COG6	49	.	0			c.T509C						.						84	79	81					13																	40251685		2203	4300	6503	SO:0001583	missense	57511	exon5			GTCTTCTCCGAGG	AK026638	CCDS9370.1, CCDS45042.1	13q13.2	2011-08-01			ENSG00000133103	ENSG00000133103		"Components of oligomeric golgi complex"	18621	protein-coding gene	gene with protein product		606977				11980916	Standard	NM_020751		Approved	COD2, KIAA1134	uc001uxh.2	Q9Y2V7	OTTHUMG00000016768	ENST00000455146.3:c.509T>C	chr13.hg19:g.40251685T>C	ENSP00000397441:p.Leu170Pro	112.0	0.0		91.0	4.0	NM_001145079	Q5T0U1|Q6AI19|Q86V49|Q9ULT5	Missense_Mutation	SNP	ENST00000455146.3	hg19	CCDS9370.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.103478	0.76983	.	.	ENSG00000133103	ENST00000416691;ENST00000255468;ENST00000422759;ENST00000455146	T;T;T	0.77489	-1.1;-1.1;-1.1	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	D	0.89989	0.6875	M	0.89785	3.06	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	D	0.92007	0.5615	10	0.87932	D	0	-0.936	15.0173	0.71597	0.0:0.0:0.0:1.0	.	191;170	Q5T0U2;Q9Y2V7	.;COG6_HUMAN	P	170;201;170;170	ENSP00000403733:L170P;ENSP00000412877:L170P;ENSP00000397441:L170P	ENSP00000255468:L201P	L	+	2	0	COG6	39149685	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	6.973000	0.76116	2.131000	0.65755	0.477000	0.44152	CTC	.	.		0.358	COG6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044622.3			C	40251685	T	C	40251685	3	2	282	1	0	0	0	0	1	0	0	0	3664	1551	54	2	527	2	COG6	13	40251685	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3487563	40251685	74918193	932	41166										
TNFSF11	8600	hgsc.bcm.edu	37	chr13	43180938	43180938	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	attccataaacgttggtggaTtttttaagttacggtctgga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:43180938delT	ENST00000239849.6	+	5	989	c.838delT	c.(838-840)tttfs	p.F281fs	TNFSF11_ENST00000405262.2_Frame_Shift_Del_p.F208fs|TNFSF11_ENST00000398795.2_Frame_Shift_Del_p.F208fs|TNFSF11_ENST00000544862.1_Frame_Shift_Del_p.F208fs|TNFSF11_ENST00000358545.2_Frame_Shift_Del_p.F208fs			O14788	TNF11_HUMAN	tumor necrosis factor (ligand) superfamily, member 11	281					activation of JUN kinase activity (GO:0007257)|bone resorption (GO:0045453)|calcium ion homeostasis (GO:0055074)|cytokine-mediated signaling pathway (GO:0019221)|ERK1 and ERK2 cascade (GO:0070371)|immune response (GO:0006955)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|monocyte chemotaxis (GO:0002548)|organ morphogenesis (GO:0009887)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|osteoclast proliferation (GO:0002158)|positive regulation of bone resorption (GO:0045780)|positive regulation of corticotropin-releasing hormone secretion (GO:0051466)|positive regulation of ERK1 and ERK2 cascade via TNFSF11-mediated signaling (GO:0071848)|positive regulation of fever generation by positive regulation of prostaglandin secretion (GO:0071812)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoclast development (GO:2001206)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell activation (GO:0050870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homooligomerization (GO:0051260)|TNFSF11-mediated signaling pathway (GO:0071847)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	cytokine activity (GO:0005125)|tumor necrosis factor receptor binding (GO:0005164)|tumor necrosis factor receptor superfamily binding (GO:0032813)			kidney(1)|large_intestine(4)|lung(3)|prostate(1)|urinary_tract(1)	10		Lung NSC(96;1.11e-05)|Breast(139;0.00868)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000249)|GBM - Glioblastoma multiforme(144;0.00119)|BRCA - Breast invasive adenocarcinoma(63;0.073)	Denosumab(DB06643)|Lenalidomide(DB00480)	CGTTGGTGGATTTTTTAAGTT	0.428																																					p.G279fs		Atlas-INDEL	.											.	TNFSF11	43	.	0			c.837delA						.						91	91	91					13																	43180938		2203	4300	6503	SO:0001589	frameshift_variant	8600	exon5			.	AF013171	CCDS9384.1, CCDS9385.1	13q14	2008-02-05			ENSG00000120659	ENSG00000120659		"Tumor necrosis factor (ligand) superfamily", "CD molecules"	11926	protein-coding gene	gene with protein product		602642				9312132, 9367155	Standard	NM_003701		Approved	TRANCE, RANKL, OPGL, ODF, CD254	uc001uyu.2	O14788	OTTHUMG00000016807	ENST00000239849.6:c.838delT	chr13.hg19:g.43180938delT	ENSP00000239849:p.Phe281fs	303.0	0.0		194.0	13.0	NM_003701	O14723|Q96Q17|Q9P2Q3	Frame_Shift_Del	DEL	ENST00000239849.6	hg19	CCDS9384.1																																																																																			.	.		0.428	TNFSF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044702.2			-	43180938	T	-	43180938	7	5	282	1	0	1	0	1	0	0	0	0	16317	1493	52	0	856	0	TNFSF11	13	43180938	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2929253	43180938	71988940	933	41167										
EPSTI1	94240	hgsc.bcm.edu	37	chr13	43543237	43543237	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgtgcttgcttacctagccgTctgggcaccaggtgaaccgg	13	12	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:43543237T>C	ENST00000398762.3	-	3	323	c.324A>G	c.(322-324)agA>agG	p.R108R	EPSTI1_ENST00000313624.7_Silent_p.R108R|EPSTI1_ENST00000313640.7_Silent_p.R108R|EPSTI1_ENST00000476830.2_5'UTR			Q96J88	ESIP1_HUMAN	epithelial stromal interaction 1 (breast)	108										endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|skin(1)	17		Lung NSC(96;3.6e-06)|Breast(139;0.00869)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		GBM - Glioblastoma multiforme(144;0.000528)|BRCA - Breast invasive adenocarcinoma(63;0.0858)		TACCTAGCCGTCTGGGCACCA	0.557																																					p.R108R		Atlas-SNP	.											.	EPSTI1	47	.	0			c.A324G						.						94	74	81					13																	43543237		2203	4300	6503	SO:0001819	synonymous_variant	94240	exon3			TAGCCGTCTGGGC	AF396928	CCDS9387.1, CCDS31964.1	13q13.3	2011-06-27			ENSG00000133106	ENSG00000133106			16465	protein-coding gene	gene with protein product	"epithelial stromal interaction protein 1"	607441				11991720	Standard	NM_033255		Approved	BRESI1, MGC29634	uc001uyw.2	Q96J88	OTTHUMG00000016814	ENST00000398762.3:c.324A>G	chr13.hg19:g.43543237T>C		141.0	0.0		112.0	6.0	NM_001002264	Q8IVC7|Q8NDQ7	Silent	SNP	ENST00000398762.3	hg19	CCDS9387.1																																																																																			.	.		0.557	EPSTI1-010	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400321.1	NM_001002264		C	43543237	T	C	43543237	2	2	282	1	0	0	0	0	0	0	0	1	5200	1664	58	2		2	EPSTI1	13	43543237	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	362299	43543237	71626641	934	41168										
RNASEH2B	79621	hgsc.bcm.edu	37	chr13	51523618	51523618	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggcttccagaaccttcagccTcattgccaaatcctccatca	5	16	3	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:51523618T>C	ENST00000336617.3	+	9	1117	c.718T>C	c.(718-720)Tca>Cca	p.S240P	RNASEH2B_ENST00000495244.2_3'UTR|RNASEH2B_ENST00000422660.1_Missense_Mutation_p.S240P	NM_024570.3	NP_078846.2	Q5TBB1	RNH2B_HUMAN	ribonuclease H2, subunit B	240					in utero embryonic development (GO:0001701)|negative regulation of gene expression (GO:0010629)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of DNA damage checkpoint (GO:2000001)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|ribonucleotide metabolic process (GO:0009259)|RNA catabolic process (GO:0006401)	nucleus (GO:0005634)|ribonuclease H2 complex (GO:0032299)	RNA-DNA hybrid ribonuclease activity (GO:0004523)			endometrium(2)|liver(1)|lung(1)|upper_aerodigestive_tract(1)	5		Acute lymphoblastic leukemia(7;1.03e-07)|Breast(56;0.00122)|Lung NSC(96;0.00143)|Prostate(109;0.0047)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;9e-08)		ACCTTCAGCCTCATTGCCAAA	0.368																																					p.S240P		Atlas-SNP	.											.	RNASEH2B	26	.	0			c.T718C						.						106	102	104					13																	51523618		2203	4300	6503	SO:0001583	missense	79621	exon9			TCAGCCTCATTGC	AK021774	CCDS9425.1, CCDS45047.1	13q14.3	2014-09-17	2006-08-17	2006-08-17	ENSG00000136104	ENSG00000136104			25671	protein-coding gene	gene with protein product		610326	"deleted in lymphocytic leukemia 8", "Aicardi-Goutieres syndrome 2"	DLEU8, AGS2		16845400	Standard	NM_001142279		Approved	FLJ11712	uc001vfa.4	Q5TBB1	OTTHUMG00000016937	ENST00000336617.3:c.718T>C	chr13.hg19:g.51523618T>C	ENSP00000337623:p.Ser240Pro	172.0	0.0		173.0	7.0	NM_024570	G3XAJ1|Q05DR2|Q6PK48|Q9HAF7	Missense_Mutation	SNP	ENST00000336617.3	hg19	CCDS9425.1	.	.	.	.	.	.	.	.	.	.	T	8.785	0.929084	0.18131	.	.	ENSG00000136104	ENST00000336617;ENST00000539292;ENST00000422660	D;D	0.96334	-3.94;-3.98	5.96	-4.27	0.03744	.	0.385674	0.31847	N	0.006980	D	0.84224	0.5425	N	0.01438	-0.865	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.12156	0.003;0.007	T	0.76621	-0.2892	10	0.32370	T	0.25	1.846	10.1642	0.42871	0.0:0.6098:0.1214:0.2687	.	240;240	G3XAJ1;Q5TBB1	.;RNH2B_HUMAN	P	240	ENSP00000337623:S240P;ENSP00000389877:S240P	ENSP00000337623:S240P	S	+	1	0	RNASEH2B	50421619	0.000000	0.05858	0.005000	0.12908	0.897000	0.52465	-0.060000	0.11712	-0.500000	0.06614	0.533000	0.62120	TCA	.	.		0.368	RNASEH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045006.3	NM_024570		C	51523618	T	C	51523618	3	2	282	1	0	0	0	0	1	0	0	0	13428	1551	54	2	752	2	RNASEH2B	13	51523618	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	7980381	51523618	63646260	935	41169										
NEK5	341676	hgsc.bcm.edu	37	chr13	52650224	52650224	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctttatatttctgttctggaTttttactttcctttgtgttc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:52650224delT	ENST00000355568.4	-	19	1842	c.1703delA	c.(1702-1704)aatfs	p.N568fs		NM_199289.1	NP_954983.1	Q6P3R8	NEK5_HUMAN	NIMA-related kinase 5	568					positive regulation of cysteine-type endopeptidase activity (GO:2001056)|positive regulation of striated muscle cell differentiation (GO:0051155)		ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(11)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	39		Breast(56;0.00173)|Lung NSC(96;0.0168)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;3.7e-08)		CTGTTCTGGATTTTTACTTTC	0.358																																					p.N568fs		Atlas-INDEL	.											.	NEK5	189	.	0			c.1704delT						.						141	137	139					13																	52650224		2203	4299	6502	SO:0001589	frameshift_variant	341676	exon19			.	BC063885	CCDS31979.1	13q14.2	2012-11-15	2012-11-15		ENSG00000197168	ENSG00000197168			7748	protein-coding gene	gene with protein product			"NIMA (never in mitosis gene a)-related kinase 5"			9552363	Standard	XM_006719807		Approved		uc001vge.3	Q6P3R8	OTTHUMG00000016957	ENST00000355568.4:c.1703delA	chr13.hg19:g.52650224delT	ENSP00000347767:p.Asn568fs	162.0	0.0		171.0	11.0	NM_199289	Q5TAP5	Frame_Shift_Del	DEL	ENST00000355568.4	hg19	CCDS31979.1																																																																																			.	.		0.358	NEK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045045.3	NM_199289		-	52650224	T	-	52650224	7	5	282	1	0	1	0	1	0	0	0	0	10336	1493	52	0	439	0	NEK5	13	52650224	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1126606	52650224	62519654	936	41170										
DACH1	1602	hgsc.bcm.edu	37	chr13	72147000	72147000	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctgatgtctcaactctggatGggggactctgaacttgtgct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:72147000delG	ENST00000359684.2	-	5	1432	c.1433delC	c.(1432-1434)ccafs	p.P478fs	DACH1_ENST00000313174.7_Intron|DACH1_ENST00000354591.4_Intron|DACH1_ENST00000305425.4_Frame_Shift_Del_p.P426fs			Q9UI36	DACH1_HUMAN	dachshund family transcription factor 1	478					cell proliferation (GO:0008283)|development of primary female sexual characteristics (GO:0046545)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of transcription by competitive promoter binding (GO:0010944)|respiratory gaseous exchange (GO:0007585)|suckling behavior (GO:0001967)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity involved in preinitiation complex assembly (GO:0001075)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(23)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198)		GBM - Glioblastoma multiforme(99;0.00032)		AACTCTGGATGGGGGACTCTG	0.423																																					p.P426fs		Atlas-INDEL	.											.	DACH1	123	.	0			c.1278delA						.						96	97	97					13																	72147000		2027	4202	6229	SO:0001589	frameshift_variant	1602	exon4			.	AJ005670	CCDS41899.1, CCDS53874.1, CCDS53873.1	13q22	2014-02-03	2014-02-03	2004-04-02	ENSG00000165659	ENSG00000276644			2663	protein-coding gene	gene with protein product		603803	"dachshund homolog (Drosophila)", "dachshund homolog 1 (Drosophila)"	DACH		9933575, 10395809, 15057823	Standard	NM_004392		Approved		uc021rkj.1	Q9UI36	OTTHUMG00000017063	ENST00000359684.2:c.1433delC	chr13.hg19:g.72147000delG	ENSP00000352712:p.Pro478fs	208.0	0.0		150.0	10.0	NM_080759	D0FY35|D0FY36|O75523|O75687|Q5VYY3|Q5VYY4|Q96SG3|Q96SG4|Q9H524|Q9UMH4	Frame_Shift_Del	DEL	ENST00000359684.2	hg19																																																																																				.	.		0.423	DACH1-002	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000045240.1	NM_004392		-	72147000	G	-	72147000	7	5	282	1	0	1	0	1	0	0	0	0	4222	1348	47	0	881	0	DACH1	13	72147000	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	19496776	72147000	43022878	937	41171										
UCHL3	7347	hgsc.bcm.edu	37	chr13	76143594	76143594	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aatacctttattcttattacAggccatccgagttactcatg	5	10	2	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:76143594A>G	ENST00000377595.3	+	6	456		c.e6-1		RP11-29G8.3_ENST00000563635.1_RNA|UCHL3_ENST00000606347.1_3'UTR	NM_001270952.1|NM_006002.4	NP_001257881.1|NP_005993.1	P15374	UCHL3_HUMAN	ubiquitin carboxyl-terminal esterase L3 (ubiquitin thiolesterase)						protein catabolic process (GO:0030163)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			kidney(1)|large_intestine(2)|lung(3)|skin(1)	7				GBM - Glioblastoma multiforme(99;0.0125)		TTCTTATTACAGGCCATCCGA	0.308																																					.		Atlas-SNP	.											.	UCHL3	9	.	0			c.319-2A>G						.						84	86	85					13																	76143594		2203	4300	6503	SO:0001630	splice_region_variant	7347	exon6			TATTACAGGCCAT	M30496	CCDS9453.1, CCDS73586.1	13q21.33	2008-02-05			ENSG00000118939	ENSG00000118939	3.2.1.15		12515	protein-coding gene	gene with protein product		603090				2530630	Standard	NM_001270952		Approved		uc001vjq.4	P15374	OTTHUMG00000017090	ENST00000377595.3:c.427-1A>G	chr13.hg19:g.76143594A>G		95.0	0.0		78.0	4.0	NM_001270952	B2R970|Q5TBK8|Q6IBE9	Splice_Site	SNP	ENST00000377595.3	hg19	CCDS9453.1	.	.	.	.	.	.	.	.	.	.	A	19.04	3.749064	0.69533	.	.	ENSG00000118939	ENST00000377595;ENST00000377589;ENST00000419068	.	.	.	5.03	5.03	0.67393	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7714	0.69681	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	UCHL3	75041595	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.130000	0.89598	1.872000	0.54250	0.533000	0.62120	.	.	.		0.308	UCHL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045292.2	NM_006002	Intron	G	76143594	A	G	76143594	5	3	282	1	0	0	0	0	0	0	1	0	16936	202	7	2	447	2	UCHL3	13	76143594	Splice_Site	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	3996594	76143594	39026284	938	41172										
MYCBP2	23077	hgsc.bcm.edu	37	chr13	77636737	77636737	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aattctgatcttaccatttgTttttgttgtccatcctttcc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:77636737delT	ENST00000544440.2	-	74	12671	c.12654delA	c.(12652-12654)aaafs	p.K4218fs	MYCBP2_ENST00000407578.2_Frame_Shift_Del_p.K4256fs|MYCBP2_ENST00000357337.6_Frame_Shift_Del_p.K4218fs					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		TTACCATTTGTTTTTGTTGTC	0.393																																					p.Q4257fs		Atlas-INDEL	.											MYCBP2_ENST00000407578,NS,carcinoma,0,2	MYCBP2	1029	.	0			c.12769delC						.						198	170	179					13																	77636737		2203	4300	6503	SO:0001589	frameshift_variant	23077	exon74			.	AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"MYC binding protein 2"			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.12654delA	chr13.hg19:g.77636737delT	ENSP00000444596:p.Lys4218fs	217.0	0.0		173.0	13.0	NM_015057		Frame_Shift_Del	DEL	ENST00000544440.2	hg19																																																																																				.	.		0.393	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057		-	77636737	T	-	77636737	7	5	282	1	0	1	0	1	0	0	0	0	10027	1722	60	0	1308	0	MYCBP2	13	77636737	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1493143	77636737	37533141	939	41173										
SCEL	8796	hgsc.bcm.edu	37	chr13	78188077	78188077	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atgtcagccccaaagctgtcAaaaacactgatgggtaagag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:78188077delA	ENST00000349847.3	+	24	1522	c.1438delA	c.(1438-1440)aaafs	p.K480fs	SCEL_ENST00000377246.3_Frame_Shift_Del_p.K460fs|SCEL_ENST00000469982.1_3'UTR|SCEL_ENST00000535157.1_Frame_Shift_Del_p.K438fs	NM_144777.2	NP_659001.2	O95171	SCEL_HUMAN	sciellin	480	16 X approximate tandem repeats.		K -> R (in dbSNP:rs8002725).		embryo development (GO:0009790)|epidermis development (GO:0008544)|keratinocyte differentiation (GO:0030216)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(18)|ovary(5)|prostate(1)|stomach(1)|urinary_tract(1)	40		Acute lymphoblastic leukemia(28;0.0282)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0233)		CAAAGCTGTCAAAAACACTGA	0.328																																					p.V479fs		Atlas-INDEL	.											.	SCEL	85	.	0			c.1437delC						.						181	173	176					13																	78188077		2203	4300	6503	SO:0001589	frameshift_variant	8796	exon24			.	AF045941	CCDS9458.1, CCDS9459.1, CCDS53877.1	13q22	2008-07-18			ENSG00000136155	ENSG00000136155			10573	protein-coding gene	gene with protein product		604112				9813070	Standard	NM_003843		Approved	FLJ21667, MGC22531	uc001vki.3	O95171	OTTHUMG00000017107	ENST00000349847.3:c.1438delA	chr13.hg19:g.78188077delA	ENSP00000302579:p.Lys480fs	300.0	0.0		204.0	15.0	NM_144777	B7Z797|F5H651|Q53H61|Q5W0S8|Q5W0S9|Q86X00	Frame_Shift_Del	DEL	ENST00000349847.3	hg19	CCDS9459.1																																																																																			.	.		0.328	SCEL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045339.2	NM_144777		-	78188077	A	-	78188077	7	5	282	1	0	1	0	1	0	0	0	0	13903	131	5	0	1528	0	SCEL	13	78188077	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	551340	78188077	36981801	940	41174										
SCEL	8796	hgsc.bcm.edu	37	chr13	78216918	78216918	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tatagacagacaatacactgTgaaccttgctactctaaaat	5	9	1	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:78216918T>C	ENST00000349847.3	+	32	2109	c.2025T>C	c.(2023-2025)tgT>tgC	p.C675C	SCEL_ENST00000377246.3_Silent_p.C655C|SCEL_ENST00000535157.1_Silent_p.C633C	NM_144777.2	NP_659001.2	O95171	SCEL_HUMAN	sciellin	675	LIM zinc-binding. {ECO:0000255|PROSITE- ProRule:PRU00125}.				embryo development (GO:0009790)|epidermis development (GO:0008544)|keratinocyte differentiation (GO:0030216)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(18)|ovary(5)|prostate(1)|stomach(1)|urinary_tract(1)	40		Acute lymphoblastic leukemia(28;0.0282)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0233)		CAATACACTGTGAACCTTGCT	0.313																																					p.C675C		Atlas-SNP	.											.	SCEL	85	.	0			c.T2025C						.						106	106	106					13																	78216918		2203	4298	6501	SO:0001819	synonymous_variant	8796	exon32			ACACTGTGAACCT	AF045941	CCDS9458.1, CCDS9459.1, CCDS53877.1	13q22	2008-07-18			ENSG00000136155	ENSG00000136155			10573	protein-coding gene	gene with protein product		604112				9813070	Standard	NM_003843		Approved	FLJ21667, MGC22531	uc001vki.3	O95171	OTTHUMG00000017107	ENST00000349847.3:c.2025T>C	chr13.hg19:g.78216918T>C		171.0	0.0		118.0	5.0	NM_144777	B7Z797|F5H651|Q53H61|Q5W0S8|Q5W0S9|Q86X00	Silent	SNP	ENST00000349847.3	hg19	CCDS9459.1																																																																																			.	.		0.313	SCEL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045339.2	NM_144777		C	78216918	T	C	78216918	2	2	282	1	0	0	0	0	0	0	0	1	13903	1702	59	2		2	SCEL	13	78216918	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	28841	78216918	36952960	941	41175										
DCT	1638	hgsc.bcm.edu	37	chr13	95118899	95118899	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gagaaatctatggccctgtaGgggcgtcctggtcctgaaac					rs12876972		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:95118899delG	ENST00000377028.5	-	3	1022	c.609delC	c.(607-609)cccfs	p.P203fs	DCT_ENST00000446125.1_Frame_Shift_Del_p.P203fs|DCT_ENST00000490854.1_5'UTR|AL139318.1_ENST00000390768.1_RNA	NM_001922.3	NP_001913.2	P40126	TYRP2_HUMAN	dopachrome tautomerase	203					cell development (GO:0048468)|developmental pigmentation (GO:0048066)|epidermis development (GO:0008544)|melanin biosynthetic process from tyrosine (GO:0006583)|positive regulation of neuroblast proliferation (GO:0002052)|ventricular zone neuroblast division (GO:0021847)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)	copper ion binding (GO:0005507)|dopachrome isomerase activity (GO:0004167)|oxidoreductase activity (GO:0016491)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	50	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;3.71e-42)|all_epithelial(2;3.76e-31)|all_lung(2;5.16e-14)|Lung NSC(4;1.33e-13)|Breast(118;0.0013)|Hepatocellular(115;0.00886)|Renal(2;0.00988)		COAD - Colon adenocarcinoma(199;7.07e-05)|GBM - Glioblastoma multiforme(99;0.000472)		TGGCCCTGTAGGGGCGTCCTG	0.418																																					p.Y204fs		Atlas-INDEL	.											.	DCT	186	.	0			c.610delT						.						56	58	57					13																	95118899		2203	4300	6503	SO:0001589	frameshift_variant	1638	exon3			.	D17547	CCDS9470.1, CCDS45060.1	13q32	2012-09-28	2012-09-28		ENSG00000080166	ENSG00000080166	5.3.3.12		2709	protein-coding gene	gene with protein product	"dopachrome delta-isomerase"	191275	"tyrosine-related protein 2"	TYRP2		8306979	Standard	NM_001922		Approved		uc010afh.3	P40126	OTTHUMG00000017206	ENST00000377028.5:c.609delC	chr13.hg19:g.95118899delG	ENSP00000366227:p.Pro203fs	293.0	0.0		199.0	12.0	NM_001129889	Q09GT4	Frame_Shift_Del	DEL	ENST00000377028.5	hg19	CCDS9470.1																																																																																			.	.		0.418	DCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045461.3			-	95118899	G	-	95118899	7	5	282	1	0	1	0	1	0	0	0	0	4306	987	35	0	1081	0	DCT	13	95118899	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	16901981	95118899	20050979	942	41176										
DCT	1638	hgsc.bcm.edu	37	chr13	95121142	95121142	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atcacgtagtcggggtgtacTctcttcttcgcgagatctaa	10	10	4	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:95121142T>C	ENST00000377028.5	-	2	866	c.453A>G	c.(451-453)agA>agG	p.R151R	DCT_ENST00000446125.1_Silent_p.R151R|DCT_ENST00000490854.1_5'Flank	NM_001922.3	NP_001913.2	P40126	TYRP2_HUMAN	dopachrome tautomerase	151					cell development (GO:0048468)|developmental pigmentation (GO:0048066)|epidermis development (GO:0008544)|melanin biosynthetic process from tyrosine (GO:0006583)|positive regulation of neuroblast proliferation (GO:0002052)|ventricular zone neuroblast division (GO:0021847)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)	copper ion binding (GO:0005507)|dopachrome isomerase activity (GO:0004167)|oxidoreductase activity (GO:0016491)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	50	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;3.71e-42)|all_epithelial(2;3.76e-31)|all_lung(2;5.16e-14)|Lung NSC(4;1.33e-13)|Breast(118;0.0013)|Hepatocellular(115;0.00886)|Renal(2;0.00988)		COAD - Colon adenocarcinoma(199;7.07e-05)|GBM - Glioblastoma multiforme(99;0.000472)		CGGGGTGTACTCTCTTCTTCG	0.532																																					p.R151R		Atlas-SNP	.											.	DCT	186	.	0			c.A453G						.						233	229	230					13																	95121142		2203	4300	6503	SO:0001819	synonymous_variant	1638	exon2			GTGTACTCTCTTC	D17547	CCDS9470.1, CCDS45060.1	13q32	2012-09-28	2012-09-28		ENSG00000080166	ENSG00000080166	5.3.3.12		2709	protein-coding gene	gene with protein product	"dopachrome delta-isomerase"	191275	"tyrosine-related protein 2"	TYRP2		8306979	Standard	NM_001922		Approved		uc010afh.3	P40126	OTTHUMG00000017206	ENST00000377028.5:c.453A>G	chr13.hg19:g.95121142T>C		180.0	0.0		131.0	6.0	NM_001129889	Q09GT4	Silent	SNP	ENST00000377028.5	hg19	CCDS9470.1																																																																																			.	.		0.532	DCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045461.3			C	95121142	T	C	95121142	2	2	282	1	0	0	0	0	0	0	0	1	4306	1548	54	2		2	DCT	13	95121142	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2243	95121142	20048736	943	41177										
FARP1	10160	hgsc.bcm.edu	37	chr13	99092237	99092237	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgaggagagcgaagacgagtGgggggtgccccactgcctga					rs201529177		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:99092237delG	ENST00000319562.6	+	22	2721	c.2456delG	c.(2455-2457)tggfs	p.W819fs	FARP1_ENST00000595437.1_Frame_Shift_Del_p.W850fs|FARP1_ENST00000376586.2_Frame_Shift_Del_p.W850fs	NM_005766.2	NP_005757.1	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)	819	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				dendrite morphogenesis (GO:0048813)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|synapse assembly (GO:0007416)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|synapse (GO:0045202)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|endometrium(6)|kidney(6)|large_intestine(13)|lung(16)|ovary(1)|skin(3)|urinary_tract(1)	49	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			GAAGACGAGTGGGGGGTGCCC	0.617																																					p.W819fs		Atlas-INDEL	.											.	FARP1	207	.	0			c.2455delT						.						142	158	153					13																	99092237		2203	4300	6503	SO:0001589	frameshift_variant	10160	exon22			.	AB008430	CCDS9487.1, CCDS32000.1, CCDS66572.1	13q32.2	2013-01-10			ENSG00000152767	ENSG00000152767		"Rho guanine nucleotide exchange factors", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Pleckstrin homology (PH) domain containing"	3591	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 75"	602654				9425278	Standard	NM_005766		Approved	CDEP, PLEKHC2, MGC87400, PPP1R75	uc001vnj.3	Q9Y4F1	OTTHUMG00000017248	ENST00000319562.6:c.2456delG	chr13.hg19:g.99092237delG	ENSP00000322926:p.Trp819fs	143.0	0.0		122.0	10.0	NM_005766	Q5JVI9|Q6IQ29	Frame_Shift_Del	DEL	ENST00000319562.6	hg19	CCDS9487.1																																																																																			.	.		0.617	FARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045541.3	NM_005766		-	99092237	G	-	99092237	7	5	282	1	0	1	0	1	0	0	0	0	5684	1357	47	0	2761	0	FARP1	13	99092237	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	3971095	99092237	16077641	944	41178										
STK24	8428	hgsc.bcm.edu	37	chr13	99109511	99109511	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tagatggcccctcgcagctcTtcaatggaccccaagttccc	8	16	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:99109511T>C	ENST00000376547.3	-	10	1351	c.1206A>G	c.(1204-1206)gaA>gaG	p.E402E	STK24_ENST00000539966.1_Silent_p.E371E|STK24_ENST00000397517.2_Silent_p.E390E	NM_003576.3	NP_003567.2	Q9Y6E0	STK24_HUMAN	serine/threonine kinase 24	402					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|execution phase of apoptosis (GO:0097194)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of cell migration (GO:0030336)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of axon regeneration (GO:0048679)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	17	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			CTCGCAGCTCTTCAATGGACC	0.587																																					p.E402E		Atlas-SNP	.											.	STK24	40	.	0			c.A1206G						.						59	54	56					13																	99109511		2203	4300	6503	SO:0001819	synonymous_variant	8428	exon10			CAGCTCTTCAATG	AF024636	CCDS9488.1, CCDS32001.1, CCDS66573.1	13q31.2-q32.3	2010-06-25	2010-06-25		ENSG00000102572	ENSG00000102572			11403	protein-coding gene	gene with protein product	"STE20-like kinase 3", "sterile 20-like kinase 3"	604984	"serine/threonine kinase 24 (Ste20, yeast homolog)"			9353338, 10644707	Standard	NM_003576		Approved	MST-3, MST3, MST3B, STK3, STE20	uc001vnn.1	Q9Y6E0	OTTHUMG00000017250	ENST00000376547.3:c.1206A>G	chr13.hg19:g.99109511T>C		87.0	0.0		65.0	4.0	NM_003576	O14840|Q5JV92	Silent	SNP	ENST00000376547.3	hg19	CCDS9488.1	.	.	.	.	.	.	.	.	.	.	T	6.789	0.514626	0.12944	.	.	ENSG00000102572	ENST00000444574	.	.	.	5.26	-8.27	0.01017	.	.	.	.	.	T	0.49847	0.1581	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57254	-0.7843	4	.	.	.	.	9.798	0.40746	0.2148:0.5515:0.0:0.2337	.	.	.	.	G	308	.	.	R	-	1	2	STK24	97907512	0.000000	0.05858	0.802000	0.32245	0.536000	0.34869	-1.618000	0.02049	-1.416000	0.02019	0.533000	0.62120	AGA	.	.		0.587	STK24-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045549.2	NM_003576		C	99109511	T	C	99109511	2	2	282	1	0	0	0	0	0	0	0	1	15308	1606	56	2		2	STK24	13	99109511	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	17274	99109511	16060367	945	41179										
STK24	8428	hgsc.bcm.edu	37	chr13	99114125	99114125	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tccagtccccagaatcactgCcccccgaggcttggccatct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:99114125delC	ENST00000376547.3	-	8	1137	c.992delG	c.(991-993)ggcfs	p.G331fs	STK24_ENST00000539966.1_Frame_Shift_Del_p.G300fs|STK24_ENST00000397517.2_Frame_Shift_Del_p.G319fs	NM_003576.3	NP_003567.2	Q9Y6E0	STK24_HUMAN	serine/threonine kinase 24	331					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|execution phase of apoptosis (GO:0097194)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of cell migration (GO:0030336)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of axon regeneration (GO:0048679)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	17	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			AGAATCACTGCCCCCCGAGGC	0.532																																					p.G331fs		Atlas-INDEL	.											.,1	STK24	40	.	0			c.993delC						.						108	105	106					13																	99114125		2203	4300	6503	SO:0001589	frameshift_variant	8428	exon8			.	AF024636	CCDS9488.1, CCDS32001.1, CCDS66573.1	13q31.2-q32.3	2010-06-25	2010-06-25		ENSG00000102572	ENSG00000102572			11403	protein-coding gene	gene with protein product	"STE20-like kinase 3", "sterile 20-like kinase 3"	604984	"serine/threonine kinase 24 (Ste20, yeast homolog)"			9353338, 10644707	Standard	NM_003576		Approved	MST-3, MST3, MST3B, STK3, STE20	uc001vnn.1	Q9Y6E0	OTTHUMG00000017250	ENST00000376547.3:c.992delG	chr13.hg19:g.99114125delC	ENSP00000365730:p.Gly331fs	289.0	0.0		178.0	11.0	NM_003576	O14840|Q5JV92	Frame_Shift_Del	DEL	ENST00000376547.3	hg19	CCDS9488.1																																																																																			.	.		0.532	STK24-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045549.2	NM_003576		-	99114125	C	-	99114125	7	5	282	1	0	1	0	1	0	0	0	0	15308	739	26	0	355	0	STK24	13	99114125	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	4614	99114125	16055753	946	41180										
UBAC2	337867	hgsc.bcm.edu	37	chr13	99896772	99896772	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gctgttttattttgtagtccTttttgctgggttcctgggtt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:99896772delT	ENST00000403766.3	+	4	418	c.283delT	c.(283-285)tttfs	p.F95fs	UBAC2_ENST00000376440.2_Intron	NM_001144072.1	NP_001137544.1	Q8NBM4	UBAC2_HUMAN	UBA domain containing 2	95					protein localization to endoplasmic reticulum (GO:0070972)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)	10	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					TTTGTAGTCCTTTTTGCTGGG	0.368																																					p.S94fs		Atlas-INDEL	.											.	UBAC2	23	.	0			c.282delC						.						152	122	131					13																	99896772		1566	3582	5148	SO:0001589	frameshift_variant	337867	exon4			.	AK055110	CCDS9490.1, CCDS45064.1	13q32.3	2012-02-01	2007-04-20	2007-04-20	ENSG00000134882	ENSG00000134882			20486	protein-coding gene	gene with protein product			"phosphoglycerate dehydrogenase like 1"	PHGDHL1			Standard	NM_177967		Approved	FLJ30548, RP11-178C10.1	uc001voa.4	Q8NBM4	OTTHUMG00000017267	ENST00000403766.3:c.283delT	chr13.hg19:g.99896772delT	ENSP00000383911:p.Phe95fs	196.0	0.0		145.0	10.0	NM_001144072	B3KNV7|Q0VAB5|Q5W0W6|Q5W0W9|Q6GQR2|Q6P4B0|Q8N2E8|Q96NW2	Frame_Shift_Del	DEL	ENST00000403766.3	hg19	CCDS45064.1																																																																																			.	.		0.368	UBAC2-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045588.1	NM_177967		-	99896772	T	-	99896772	7	5	282	1	0	1	0	1	0	0	0	0	16850	1609	56	0	457	0	UBAC2	13	99896772	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	782647	99896772	15273106	947	41181										
ERCC5	2073	hgsc.bcm.edu	37	chr13	103508419	103508419	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagttcagaagaggaagatgAaaaagaatggcaagaaagaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:103508419delA	ENST00000355739.4	+	5	1908	c.485delA	c.(484-486)gaafs	p.E162fs	BIVM-ERCC5_ENST00000602836.1_Frame_Shift_Del_p.*587fs|ERCC5_ENST00000535557.1_Frame_Shift_Del_p.E162fs	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	162					DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|response to UV (GO:0009411)|response to UV-C (GO:0010225)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|double-stranded DNA binding (GO:0003690)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	51	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					GAGGAAGATGAAAAAGAATGG	0.313			"Mis, N, F"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.E616fs		Atlas-INDEL	.	yes	Rec		Xeroderma pigmentosum (G)	13	13q33	2073	"excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))"		E	.	.	.	.	0			c.1846delG						.						119	120	119					13																	103508419		2203	4300	6503	SO:0001589	frameshift_variant	0	exon13	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	.	X71342	CCDS32004.1	13q22-q34	2014-09-17	2014-03-07		ENSG00000134899	ENSG00000134899			3437	protein-coding gene	gene with protein product	"Cockayne syndrome"	133530	"xeroderma pigmentosum, complementation group G", "excision repair cross-complementing rodent repair deficiency, complementation group 5"	ERCM2, XPGC		8088806	Standard	NM_000123		Approved			P28715	OTTHUMG00000017310	ENST00000355739.4:c.485delA	chr13.hg19:g.103508419delA	ENSP00000347978:p.Glu162fs	552.0	0.0		333.0	21.0	NM_001204425	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Frame_Shift_Del	DEL	ENST00000355739.4	hg19	CCDS32004.1																																																																																			.	.		0.313	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1			-	103508419	A	-	103508419	7	5	282	1	0	1	0	1	0	0	0	0	5218	246	9	0	503	0	ERCC5	13	103508419	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	3611647	103508419	11661459	948	41182										
ARGLU1	55082	hgsc.bcm.edu	37	chr13	107219922	107219922	+	Splice_Site	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tccccgcgcgggcactcacaTttttcgctgccgctcgaact							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:107219922delT	ENST00000400198.3	-	1	590	c.346delA	c.(346-348)att>tt	p.I116fs		NM_018011.3	NP_060481.3	Q9NWB6	ARGL1_HUMAN	arginine and glutamate rich 1	116	Glu-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)				large_intestine(1)|lung(5)|pancreas(1)	7	Lung NSC(43;0.015)|all_neural(89;0.0741)|Lung SC(71;0.14)|Medulloblastoma(90;0.169)					GGCACTCACATTTTTCGCTGC	0.711																																					p.I116fs		Atlas-INDEL	.											.	ARGLU1	17	.	0			c.347delT						.						40	41	41					13																	107219922		1985	4159	6144	SO:0001630	splice_region_variant	55082	exon1			.	BC071587	CCDS41906.1	13q33.3	2011-10-03	2007-11-28		ENSG00000134884	ENSG00000134884			25482	protein-coding gene	gene with protein product		614046				21454576	Standard	NM_018011		Approved	FLJ10154	uc001vqk.4	Q9NWB6	OTTHUMG00000017321	ENST00000400198.3:c.347+1A>-	chr13.hg19:g.107219922delT		201.0	0.0		140.0	10.0	NM_018011	B4E0Y3|Q5T257|Q6IQ34	Frame_Shift_Del	DEL	ENST00000400198.3	hg19	CCDS41906.1																																																																																			.	.		0.711	ARGLU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045727.1	NM_018011	Frame_Shift_Del	-	107219922	T	-	107219922	8	5	282	1	0	1	0	1	0	0	1	0	860	1507	52	0	491	0	ARGLU1	13	107219922	Splice_Site	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3711503	107219922	7949956	949	41183										
LIG4	3981	hgsc.bcm.edu	37	chr13	108862228	108862228	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tatcctccaacaattaaaatGtccaattcatccattagtcc	2	12	1	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:108862228G>T	ENST00000356922.4	-	2	1661	c.1389C>A	c.(1387-1389)gaC>gaA	p.D463E	LIG4_ENST00000442234.1_Missense_Mutation_p.D463E|LIG4_ENST00000405925.1_Missense_Mutation_p.D463E	NM_002312.3|NM_206937.1	NP_002303.2|NP_996820.1	P49917	DNLI4_HUMAN	ligase IV, DNA, ATP-dependent	463					cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|chromosome organization (GO:0051276)|DNA biosynthetic process (GO:0071897)|DNA ligation (GO:0006266)|DNA ligation involved in DNA recombination (GO:0051102)|DNA ligation involved in DNA repair (GO:0051103)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|in utero embryonic development (GO:0001701)|isotype switching (GO:0045190)|lagging strand elongation (GO:0006273)|negative regulation of neuron apoptotic process (GO:0043524)|neuron apoptotic process (GO:0051402)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of neurogenesis (GO:0050769)|pro-B cell differentiation (GO:0002328)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|single strand break repair (GO:0000012)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA ligase IV complex (GO:0032807)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|focal adhesion (GO:0005925)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	42	all_lung(23;0.000238)|all_neural(89;0.00256)|Lung NSC(43;0.0056)|Medulloblastoma(90;0.00596)|Lung SC(71;0.104)					CAATTAAAATGTCCAATTCAT	0.433								Non-homologous end-joining																													p.D463E		Atlas-SNP	.											.	LIG4	91	.	0			c.C1389A						.						225	230	228					13																	108862228		2203	4300	6503	SO:0001583	missense	3981	exon3			TAAAATGTCCAAT	X83441	CCDS9508.1	13q33-q34	2014-09-17			ENSG00000174405	ENSG00000174405	6.5.1.1		6601	protein-coding gene	gene with protein product	"polydeoxyribonucleotide synthase [ATP] 4", "polynucleotide ligase", "sealase", "DNA repair enzyme", "DNA joinase"	601837				7760816	Standard	NM_001098268		Approved		uc001vqo.3	P49917	OTTHUMG00000017328	ENST00000356922.4:c.1389C>A	chr13.hg19:g.108862228G>T	ENSP00000349393:p.Asp463Glu	136.0	0.0		92.0	4.0	NM_206937	Q8IY66|Q8TEU5	Missense_Mutation	SNP	ENST00000356922.4	hg19	CCDS9508.1	.	.	.	.	.	.	.	.	.	.	G	15.81	2.944046	0.53079	.	.	ENSG00000174405	ENST00000405925;ENST00000442234;ENST00000356922	T;T;T	0.71817	-0.6;-0.6;-0.6	5.06	3.3	0.37823	Nucleic acid-binding, OB-fold-like (1);DNA ligase, ATP-dependent, central (1);Nucleic acid-binding, OB-fold (1);	0.000000	0.85682	D	0.000000	T	0.81607	0.4858	M	0.75085	2.285	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	T	0.82812	-0.0272	10	0.66056	D	0.02	.	10.9529	0.47341	0.2205:0.0:0.7795:0.0	.	463	P49917	DNLI4_HUMAN	E	463	ENSP00000385955:D463E;ENSP00000402030:D463E;ENSP00000349393:D463E	ENSP00000349393:D463E	D	-	3	2	LIG4	107660229	1.000000	0.71417	0.996000	0.52242	0.982000	0.71751	2.785000	0.47782	1.260000	0.44134	0.551000	0.68910	GAC	.	.		0.433	LIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045738.4	NM_002312		T	108862228	G	T	108862228	3	4	282	1	0	0	0	0	1	0	0	0	8792	1368	48	3	1350	3	LIG4	13	108862228	Missense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1642306	108862228	6307650	950	41184										
TFDP1	7027	hgsc.bcm.edu	37	chr13	114240158	114240158	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cccggatctggtaacatggcAaaagatgtaagtatgtttgc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:114240158delA	ENST00000375370.5	+	2	218	c.6delA	c.(4-6)gcafs	p.A2fs	TFDP1_ENST00000544902.1_5'UTR|TFDP1_ENST00000538138.1_5'UTR|TFDP1_ENST00000465174.1_3'UTR	NM_007111.4	NP_009042.1	Q14186	TFDP1_HUMAN	transcription factor Dp-1	2					anoikis (GO:0043276)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|epidermis development (GO:0008544)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic cell cycle (GO:0000278)|Notch signaling pathway (GO:0007219)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA biosynthetic process (GO:2000278)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(10)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	26	Lung NSC(43;0.0113)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.132)|all_epithelial(44;0.0731)|all_lung(25;0.149)|Breast(118;0.153)	all cancers(43;0.0576)			GTAACATGGCAAAAGATGTAA	0.348										TSP Lung(29;0.18)																											p.A2fs		Atlas-INDEL	.											.	TFDP1	70	.	0			c.5delC						.						137	122	127					13																	114240158		2203	4300	6503	SO:0001589	frameshift_variant	7027	exon2			.	BC011685	CCDS9538.1	13q34	2008-07-18			ENSG00000198176	ENSG00000198176			11749	protein-coding gene	gene with protein product		189902				8413592, 9027491	Standard	NM_007111		Approved	Dp-1, DRTF1, DP1	uc001vtw.3	Q14186	OTTHUMG00000017388	ENST00000375370.5:c.6delA	chr13.hg19:g.114240158delA	ENSP00000364519:p.Ala2fs	167.0	0.0		123.0	12.0	NM_007111	B4DLQ9|Q5JSB4|Q8IZL5	Frame_Shift_Del	DEL	ENST00000375370.5	hg19	CCDS9538.1																																																																																			.	.		0.348	TFDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045918.3	NM_007111		-	114240158	A	-	114240158	7	5	282	1	0	1	0	1	0	0	0	0	15812	117	5	0	8	0	TFDP1	13	114240158	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	5377930	114240158	929720	951	41185										
RNASE12	493901	hgsc.bcm.edu	37	chr14	21058692	21058692	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	catggatgaagacatgctccTttttacaagtgtggtcaggt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:21058692delT	ENST00000556526.1	-	1	290	c.191delA	c.(190-192)aagfs	p.K64fs	RNASE11_ENST00000553849.1_5'Flank|RNASE11_ENST00000398008.2_5'Flank|RP11-14J7.6_ENST00000556487.1_RNA|RP11-14J7.6_ENST00000554529.1_RNA|RNASE11_ENST00000398009.2_5'Flank|RP11-14J7.6_ENST00000553604.1_RNA|RNASE11_ENST00000432835.2_5'Flank|RNASE11_ENST00000555283.1_Intron|RP11-14J7.6_ENST00000554993.1_RNA|RP11-14J7.6_ENST00000554006.1_RNA|RNASE11_ENST00000555841.1_5'Flank|RNASE11_ENST00000610205.1_5'Flank	NM_001024822.2	NP_001019993.1	Q5GAN4	RNS12_HUMAN	ribonuclease, RNase A family, 12 (non-active)	64						extracellular region (GO:0005576)	nucleic acid binding (GO:0003676)			kidney(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	8	all_cancers(95;0.00238)		Epithelial(56;1.85e-06)|all cancers(55;1.46e-05)	GBM - Glioblastoma multiforme(265;0.013)		GACATGCTCCTTTTTACAAGT	0.448																																					p.K64fs		Atlas-INDEL	.											.	RNASE12	19	.	0			c.192delG						.						146	123	131					14																	21058692		2203	4300	6503	SO:0001589	frameshift_variant	493901	exon1			.		CCDS32037.1	14q11.1	2012-10-05			ENSG00000258436	ENSG00000258436		"Ribonucleases, RNase A"	24211	protein-coding gene	gene with protein product							Standard	NM_001024822		Approved		uc001vxt.3	Q5GAN4	OTTHUMG00000170991	ENST00000556526.1:c.191delA	chr14.hg19:g.21058692delT	ENSP00000450580:p.Lys64fs	192.0	0.0		165.0	11.0	NM_001024822		Frame_Shift_Del	DEL	ENST00000556526.1	hg19	CCDS32037.1																																																																																			.	.		0.448	RNASE12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411107.1			-	21058692	T	-	21058692	7	5	282	1	0	1	0	1	0	0	0	0	13417	1609	56	0	256	0	RNASE12	14	21058692	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10		21058692	86290848	952	41186										
CHD8	57680	hgsc.bcm.edu	37	chr14	21865984	21865984	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acaaatactaatgcttacccTtctactatgtcagagaagtt	5	9	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:21865984T>C	ENST00000557364.1	-	27	5312	c.5049A>G	c.(5047-5049)gaA>gaG	p.E1683E	CHD8_ENST00000555962.1_5'UTR|SNORD8_ENST00000363915.1_RNA|CHD8_ENST00000430710.3_Silent_p.E1404E|CHD8_ENST00000399982.2_Silent_p.E1683E			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	1683					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|canonical Wnt signaling pathway (GO:0060070)|DNA duplex unwinding (GO:0032508)|in utero embryonic development (GO:0001701)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(33)|ovary(6)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	85	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		ATGCTTACCCTTCTACTATGT	0.398																																					p.E1683E		Atlas-SNP	.											.	CHD8	339	.	0			c.A5049G						.						84	78	80					14																	21865984		1890	4123	6013	SO:0001819	synonymous_variant	57680	exon26			TTACCCTTCTACT	AB046784	CCDS45081.1, CCDS53885.1	14q11.2	2008-02-05	2004-06-22	2004-06-23		ENSG00000100888			20153	protein-coding gene	gene with protein product		610528	"helicase with SNF2 domain 1"	HELSNF1		10997877	Standard	NM_020920		Approved	KIAA1564, DUPLIN	uc001war.2	Q9HCK8		ENST00000557364.1:c.5049A>G	chr14.hg19:g.21865984T>C		153.0	0.0		95.0	4.0	NM_001170629	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Silent	SNP	ENST00000557364.1	hg19	CCDS53885.1																																																																																			.	.		0.398	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920		C	21865984	T	C	21865984	2	2	282	1	0	0	0	0	0	0	0	1	3333	1606	56	2		2	CHD8	14	21865984	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	807292	21865984	85483556	953	41187										
MRPL52	122704	hgsc.bcm.edu	37	chr14	23302670	23302670	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaaggccagcttcgaagaaaAgctgaaagggagacgtttgc	13	7	0	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:23302670A>G	ENST00000355151.5	+	4	231	c.201A>G	c.(199-201)aaA>aaG	p.K67K	MRPL52_ENST00000556840.1_Silent_p.K8K|MRPL52_ENST00000555345.1_Silent_p.K8K|MRPL52_ENST00000397496.3_Silent_p.K66K|MRPL52_ENST00000432849.3_Silent_p.K66K|MRPL52_ENST00000311892.6_Intron|MRPL52_ENST00000397505.2_Intron|MRPL52_ENST00000557221.1_Intron|MRPL52_ENST00000461594.1_3'UTR|MRPL52_ENST00000553711.1_Silent_p.K8K|MRPL52_ENST00000555536.1_Silent_p.K8K	NM_178336.2|NM_180982.2|NM_181306.2	NP_848026.1|NP_851313.1|NP_851823.1	Q86TS9	RM52_HUMAN	mitochondrial ribosomal protein L52	67					translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)	structural constituent of ribosome (GO:0003735)					all_cancers(95;9.47e-05)			GBM - Glioblastoma multiforme(265;0.00551)		TTCGAAGAAAAGCTGAAAGGG	0.478																																					p.K67K		Atlas-SNP	.											.	MRPL52	7	.	0			c.A201G						.						108	90	96					14																	23302670		2203	4300	6503	SO:0001819	synonymous_variant	122704	exon4			AAGAAAAGCTGAA	AK000450	CCDS9575.1, CCDS9576.1, CCDS41917.1, CCDS41918.1	14q11.2	2012-09-13			ENSG00000172590	ENSG00000172590		"Mitochondrial ribosomal proteins / large subunits"	16655	protein-coding gene	gene with protein product		611856				11551941, 11943462	Standard	NM_178336		Approved		uc001wgw.4	Q86TS9	OTTHUMG00000028703	ENST00000355151.5:c.201A>G	chr14.hg19:g.23302670A>G		134.0	0.0		83.0	4.0	NM_178336	A6NMQ8|A8MXK5|A8MYI6|G3XCN9|Q6NVH8	Silent	SNP	ENST00000355151.5	hg19	CCDS41917.1																																																																																			.	.		0.478	MRPL52-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071657.4	NM_180982		G	23302670	A	G	23302670	2	3	282	1	0	0	0	0	0	0	0	1	9825	69	3	2		2	MRPL52	14	23302670	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1436686	23302670	84046870	954	41188										
PRMT5	10419	hgsc.bcm.edu	37	chr14	23391406	23391406	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttaatagggaagaggatgggAaaccatgagaacatcccagg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:23391406delA	ENST00000324366.8	-	16	1963	c.1740delT	c.(1738-1740)tttfs	p.F580fs	PRMT5_ENST00000553897.1_Frame_Shift_Del_p.F536fs|PRMT5-AS1_ENST00000599580.2_RNA|PRMT5-AS1_ENST00000590290.1_RNA|PRMT5_ENST00000538452.1_Frame_Shift_Del_p.F474fs|PRMT5-AS1_ENST00000457443.2_RNA|PRMT5_ENST00000397440.4_Frame_Shift_Del_p.F409fs|PRMT5-AS1_ENST00000595662.1_RNA|PRMT5_ENST00000216350.8_Frame_Shift_Del_p.F519fs|PRMT5_ENST00000397441.2_Frame_Shift_Del_p.F563fs|PRMT5-AS1_ENST00000587245.2_RNA|PRMT5-AS1_ENST00000609885.1_RNA|PRMT5-AS1_ENST00000424245.2_RNA	NM_006109.3	NP_006100.2	O14744	ANM5_HUMAN	protein arginine methyltransferase 5	580	Beta barrel. {ECO:0000269|PubMed:23071334}.|SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				cell proliferation (GO:0008283)|circadian regulation of gene expression (GO:0032922)|endothelial cell activation (GO:0042118)|gene expression (GO:0010467)|histone H4-R3 methylation (GO:0043985)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to symmetrical-dimethyl arginine (GO:0019918)|peptidyl-arginine N-methylation (GO:0035246)|regulation of mitosis (GO:0007088)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|methylosome (GO:0034709)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|histone-arginine N-methyltransferase activity (GO:0008469)|methyltransferase activity (GO:0008168)|protein-arginine omega-N symmetric methyltransferase activity (GO:0035243)|ribonucleoprotein complex binding (GO:0043021)|transcription corepressor activity (GO:0003714)			endometrium(4)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	25	all_cancers(95;2.76e-05)			GBM - Glioblastoma multiforme(265;0.0126)		AGAGGATGGGAAACCATGAGA	0.443																																					p.P581fs		Atlas-INDEL	.											.	PRMT5	101	.	0			c.1741delC						.						176	172	173					14																	23391406		2203	4300	6503	SO:0001589	frameshift_variant	10419	exon16			.	AF015913	CCDS9579.1, CCDS41922.1, CCDS61394.1, CCDS61395.1, CCDS61396.1	14q11.2	2014-06-12	2006-02-16	2006-02-16	ENSG00000100462	ENSG00000100462	2.1.1.125	"Protein arginine methyltransferases"	10894	protein-coding gene	gene with protein product		604045	"skb1 (S. pombe) homolog", "SKB1 homolog (S. pombe)"	HRMT1L5, SKB1		9843966	Standard	NM_001282955		Approved	SKB1Hs	uc001whm.1	O14744	OTTHUMG00000028709	ENST00000324366.8:c.1740delT	chr14.hg19:g.23391406delA	ENSP00000319169:p.Phe580fs	193.0	0.0		135.0	12.0	NM_006109	A8MTP3|A8MZ91|B4DX49|B4DY30|B5BU10|D3DS33|E2QRE7|Q6IBR1|Q9UKH1	Frame_Shift_Del	DEL	ENST00000324366.8	hg19	CCDS9579.1																																																																																			.	.		0.443	PRMT5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071674.3			-	23391406	A	-	23391406	7	5	282	1	0	1	0	1	0	0	0	0	12551	243	9	0	181	0	PRMT5	14	23391406	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	88736	23391406	83958134	955	41189										
PRMT5	10419	hgsc.bcm.edu	37	chr14	23398414	23398414	+	Intron	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	actagtctgcccttctccgtCcccgagttcggaccccgcat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:23398414delC	ENST00000324366.8	-	1	334				RP11-298I3.1_ENST00000548819.1_RNA|PRMT5_ENST00000553897.1_Intron|PRMT5-AS1_ENST00000599580.2_RNA|RP11-298I3.1_ENST00000548322.1_RNA|PRMT5-AS1_ENST00000590290.1_RNA|PRMT5_ENST00000538452.1_5'UTR|PRMT5_ENST00000397440.4_Frame_Shift_Del_p.G7fs|PRMT5-AS1_ENST00000595662.1_RNA|PRMT5_ENST00000216350.8_Frame_Shift_Del_p.G7fs|PRMT5_ENST00000397441.2_Frame_Shift_Del_p.G7fs|PRMT5-AS1_ENST00000587245.2_RNA|PRMT5_ENST00000553641.1_Intron	NM_006109.3	NP_006100.2	O14744	ANM5_HUMAN	protein arginine methyltransferase 5						cell proliferation (GO:0008283)|circadian regulation of gene expression (GO:0032922)|endothelial cell activation (GO:0042118)|gene expression (GO:0010467)|histone H4-R3 methylation (GO:0043985)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to symmetrical-dimethyl arginine (GO:0019918)|peptidyl-arginine N-methylation (GO:0035246)|regulation of mitosis (GO:0007088)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|methylosome (GO:0034709)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|histone-arginine N-methyltransferase activity (GO:0008469)|methyltransferase activity (GO:0008168)|protein-arginine omega-N symmetric methyltransferase activity (GO:0035243)|ribonucleoprotein complex binding (GO:0043021)|transcription corepressor activity (GO:0003714)			endometrium(4)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	25	all_cancers(95;2.76e-05)			GBM - Glioblastoma multiforme(265;0.0126)		CCTTCTCCGTCCCCGAGTTCG	0.627																																					p.T8fs		Atlas-INDEL	.											.	PRMT5	101	.	0			c.22delA						.						67	72	71					14																	23398414		2203	4300	6503	SO:0001627	intron_variant	10419	exon1			.	AF015913	CCDS9579.1, CCDS41922.1, CCDS61394.1, CCDS61395.1, CCDS61396.1	14q11.2	2014-06-12	2006-02-16	2006-02-16	ENSG00000100462	ENSG00000100462	2.1.1.125	"Protein arginine methyltransferases"	10894	protein-coding gene	gene with protein product		604045	"skb1 (S. pombe) homolog", "SKB1 homolog (S. pombe)"	HRMT1L5, SKB1		9843966	Standard	NM_001282955		Approved	SKB1Hs	uc001whm.1	O14744	OTTHUMG00000028709	ENST00000324366.8:c.110+46G>-	chr14.hg19:g.23398414delC		188.0	0.0		180.0	12.0	NM_001039619	A8MTP3|A8MZ91|B4DX49|B4DY30|B5BU10|D3DS33|E2QRE7|Q6IBR1|Q9UKH1	Frame_Shift_Del	DEL	ENST00000324366.8	hg19	CCDS9579.1																																																																																			.	.		0.627	PRMT5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071674.3			-	23398414	C	-	23398414	6	5	282	0	1	1	0	1	0	0	0	0	12551	842	30	0		0	PRMT5	14	23398414	Intron	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	7008	23398414	83951126	956	41190										
RIPK3	11035	hgsc.bcm.edu	37	chr14	24808407	24808407	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaggagccgttctccatgaaTttagtcaccagagccggctt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:24808407delT	ENST00000216274.5	-	3	503	c.285delA	c.(283-285)aaafs	p.K95fs	RP11-934B9.3_ENST00000555591.1_5'Flank|RIPK3_ENST00000554338.1_5'UTR	NM_006871.3	NP_006862.2	Q9Y572	RIPK3_HUMAN	receptor-interacting serine-threonine kinase 3	95	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|amyloid fibril formation (GO:1990000)|apoptotic signaling pathway (GO:0097190)|cellular protein modification process (GO:0006464)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|lymph node development (GO:0048535)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of ligase activity (GO:0051351)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phosphatase activity (GO:0010922)|positive regulation of protein deacetylation (GO:0090312)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of type I interferon production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of activated T cell proliferation (GO:0046006)|regulation of activation-induced cell death of T cells (GO:0070235)|regulation of adaptive immune response (GO:0002819)|regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation (GO:2000452)|regulation of interferon-gamma production (GO:0032649)|regulation of T cell mediated cytotoxicity (GO:0001914)|signal transduction (GO:0007165)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|NF-kappaB-inducing kinase activity (GO:0004704)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				GBM - Glioblastoma multiforme(265;0.0181)		TCTCCATGAATTTAGTCACCA	0.582																																					p.F96fs	Pancreas(58;918 1191 4668 13304 15331)	Atlas-INDEL	.											.	RIPK3	43	.	0			c.286delT						.						83	75	78					14																	24808407		2203	4300	6503	SO:0001589	frameshift_variant	11035	exon3			.	AF156884	CCDS9628.1	14q12	2006-05-15			ENSG00000129465	ENSG00000129465			10021	protein-coding gene	gene with protein product		605817				10339433, 10358032	Standard	NM_006871		Approved	RIP3	uc001wpb.3	Q9Y572	OTTHUMG00000029349	ENST00000216274.5:c.285delA	chr14.hg19:g.24808407delT	ENSP00000216274:p.Lys95fs	195.0	0.0		162.0	10.0	NM_006871	B4DJL9|C4AM87|Q5J795|Q5J796|Q6P5Y1	Frame_Shift_Del	DEL	ENST00000216274.5	hg19	CCDS9628.1																																																																																			.	.		0.582	RIPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073203.4	NM_006871		-	24808407	T	-	24808407	7	5	282	1	0	1	0	1	0	0	0	0	13397	1490	52	0	1303	0	RIPK3	14	24808407	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1409993	24808407	82541133	957	41191										
ARHGAP5	394	hgsc.bcm.edu	37	chr14	32560705	32560705	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cacagcaacagataagtttgAaaaacttgtgcagactgtga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:32560705delA	ENST00000345122.3	+	2	1145	c.830delA	c.(829-831)gaafs	p.E277fs	ARHGAP5_ENST00000396582.2_Intron|ARHGAP5_ENST00000432921.1_Frame_Shift_Del_p.E277fs|ARHGAP5_ENST00000433497.1_Intron|ARHGAP5_ENST00000539826.2_Frame_Shift_Del_p.E277fs|ARHGAP5_ENST00000556611.1_Frame_Shift_Del_p.E277fs	NM_001030055.1	NP_001025226.1	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5	277	FF 1.				cell adhesion (GO:0007155)|GTP catabolic process (GO:0006184)|mammary gland development (GO:0030879)|positive regulation of cell migration (GO:0030335)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell size (GO:0008361)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(10)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(12)|ovary(4)|skin(1)|stomach(1)|urinary_tract(4)	55	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)		GATAAGTTTGAAAAACTTGTG	0.323																																					p.E277fs	NSCLC(9;77 350 3443 29227 41353)	Atlas-INDEL	.											.	ARHGAP5	166	.	0			c.829delG						.						114	131	125					14																	32560705		2202	4298	6500	SO:0001589	frameshift_variant	394	exon2			.	U17032	CCDS32062.1, CCDS45095.1	14q12	2010-02-05						"Rho GTPase activating proteins"	675	protein-coding gene	gene with protein product		602680	"growth factor independent 2"	GFI2		8537347	Standard	XM_005267635		Approved	RhoGAP5, p190-B, p190BRhoGAP	uc001wrn.3	Q13017		ENST00000345122.3:c.830delA	chr14.hg19:g.32560705delA	ENSP00000371897:p.Glu277fs	215.0	0.0		169.0	13.0	NM_001173	A1L375|A1L376|A8KAA1|D3DS89|D3DS90|Q05BE8|Q05BU8|Q59ER0|Q6DHZ3	Frame_Shift_Del	DEL	ENST00000345122.3	hg19	CCDS32062.1																																																																																			.	.		0.323	ARHGAP5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409735.1	NM_001030055		-	32560705	A	-	32560705	7	5	282	1	0	1	0	1	0	0	0	0	886	246	9	0	832	0	ARHGAP5	14	32560705	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	7752298	32560705	74788835	958	41192										
SRP54	6729	hgsc.bcm.edu	37	chr14	35497334	35497334	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtgagccagtcacagatggcAaaattgaaccaacaaatggc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:35497334delA	ENST00000556994.1	+	16	1765	c.1368delA	c.(1366-1368)gcafs	p.A456fs	SRP54_ENST00000216774.6_Frame_Shift_Del_p.A456fs|SRP54_ENST00000546080.1_Frame_Shift_Del_p.A407fs|SRP54_ENST00000555557.1_Frame_Shift_Del_p.A392fs			P61011	SRP54_HUMAN	signal recognition particle 54kDa	456	M-domain.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|protein targeting to ER (GO:0045047)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition (GO:0006617)|SRP-dependent cotranslational protein targeting to membrane, translocation (GO:0006616)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|drug binding (GO:0008144)|endoplasmic reticulum signal peptide binding (GO:0030942)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|ribonucleoprotein complex binding (GO:0043021)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	14	Breast(36;0.0545)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;2.48e-05)|Lung(238;3.13e-05)|Epithelial(34;0.0314)|all cancers(34;0.0797)|BRCA - Breast invasive adenocarcinoma(188;0.243)	GBM - Glioblastoma multiforme(112;0.0396)		CACAGATGGCAAAATTGAACC	0.383																																					p.A456fs		Atlas-INDEL	.											.	SRP54	38	.	0			c.1367delC						.						134	115	122					14																	35497334		2203	4300	6503	SO:0001589	frameshift_variant	6729	exon15			.	X86373	CCDS9652.1, CCDS53893.1	14q13.2	2014-06-02	2002-08-29		ENSG00000100883	ENSG00000100883			11301	protein-coding gene	gene with protein product		604857	"signal recognition particle 54kD"			8722571	Standard	NM_003136		Approved		uc001wso.3	P61011	OTTHUMG00000140214	ENST00000556994.1:c.1368delA	chr14.hg19:g.35497334delA	ENSP00000451818:p.Ala456fs	161.0	0.0		158.0	11.0	NM_003136	B2R759|B4DUW6|P13624	Frame_Shift_Del	DEL	ENST00000556994.1	hg19	CCDS9652.1																																																																																			.	.		0.383	SRP54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276643.2	NM_003136		-	35497334	A	-	35497334	7	5	282	1	0	1	0	1	0	0	0	0	15170	117	5	0	1422	0	SRP54	14	35497334	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2936629	35497334	71852206	959	41193										
FOXA1	3169	hgsc.bcm.edu	37	chr14	38061910	38061910	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gttgctgaccgggacggaggAgtaggcctggagtggagaca	19	7	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:38061910A>G	ENST00000250448.2	-	2	140	c.79T>C	c.(79-81)Tcc>Ccc	p.S27P	FOXA1_ENST00000540786.1_5'UTR|FOXA1_ENST00000545425.2_5'UTR	NM_004496.3	NP_004487.2	P55317	FOXA1_HUMAN	forkhead box A1	27					anatomical structure formation involved in morphogenesis (GO:0048646)|chromatin remodeling (GO:0006338)|dorsal/ventral neural tube patterning (GO:0021904)|epithelial cell maturation involved in prostate gland development (GO:0060743)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|epithelial-mesenchymal signaling involved in prostate gland development (GO:0060738)|glucose homeostasis (GO:0042593)|hormone metabolic process (GO:0042445)|lung epithelial cell differentiation (GO:0060487)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron fate specification (GO:0048665)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland epithelium morphogenesis (GO:0060740)|prostate gland stromal morphogenesis (GO:0060741)|response to estradiol (GO:0032355)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)	microvillus (GO:0005902)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(1)|large_intestine(2)|lung(3)|prostate(12)	19	Breast(36;0.0954)|Esophageal squamous(585;0.164)|Hepatocellular(127;0.213)		Lung(238;5.41e-07)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.0454)|LUSC - Lung squamous cell carcinoma(13;0.0917)|all cancers(34;0.0925)|BRCA - Breast invasive adenocarcinoma(188;0.239)	GBM - Glioblastoma multiforme(112;0.0222)		GGGACGGAGGAGTAGGCCTGG	0.617																																					p.S27P		Atlas-SNP	.											.	FOXA1	56	.	0			c.T79C						.						123	107	112					14																	38061910		2203	4300	6503	SO:0001583	missense	3169	exon2			CGGAGGAGTAGGC	U39840	CCDS9665.1	14q12-q13	2008-04-10		2002-09-20	ENSG00000129514	ENSG00000129514		"Forkhead boxes"	5021	protein-coding gene	gene with protein product		602294	"hepatocyte nuclear factor 3, alpha"	HNF3A		9119385, 8652662	Standard	NM_004496		Approved		uc001wuf.4	P55317	OTTHUMG00000140253	ENST00000250448.2:c.79T>C	chr14.hg19:g.38061910A>G	ENSP00000250448:p.Ser27Pro	98.0	0.0		75.0	5.0	NM_004496	B2R9H6|B7ZAP5|Q9H2A0	Missense_Mutation	SNP	ENST00000250448.2	hg19	CCDS9665.1	.	.	.	.	.	.	.	.	.	.	A	15.23	2.771320	0.49680	.	.	ENSG00000129514	ENST00000250448	T	0.27890	1.64	4.15	2.99	0.34606	Fork-head N-terminal (1);	0.892392	0.09670	N	0.771264	T	0.33323	0.0859	M	0.64404	1.975	0.80722	D	1	B	0.10296	0.003	B	0.17722	0.019	T	0.09997	-1.0649	10	0.59425	D	0.04	.	9.747	0.40453	0.8453:0.0:0.0:0.1547	.	27	P55317	FOXA1_HUMAN	P	27	ENSP00000250448:S27P	ENSP00000250448:S27P	S	-	1	0	FOXA1	37131661	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.417000	0.52714	0.626000	0.30322	0.454000	0.30748	TCC	.	.		0.617	FOXA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276735.1			G	38061910	A	G	38061910	3	3	282	1	0	0	0	0	1	0	0	0	5997	304	11	2	1343	2	FOXA1	14	38061910	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2564576	38061910	69287630	960	41194										
POLE2	5427	hgsc.bcm.edu	37	chr14	50141076	50141076	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgacatacttacggaagaaaTttttttctttctgaattgta							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:50141076delT	ENST00000216367.5	-	4	414	c.315delA	c.(313-315)aaafs	p.K105fs	POLE2_ENST00000554396.1_Frame_Shift_Del_p.K105fs|POLE2_ENST00000556584.1_Intron|POLE2_ENST00000539565.2_Intron	NM_002692.3	NP_002683.2	P56282	DPOE2_HUMAN	polymerase (DNA directed), epsilon 2, accessory subunit	105					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	epsilon DNA polymerase complex (GO:0008622)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)			kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	10	all_epithelial(31;0.0021)|Breast(41;0.0124)				Cladribine(DB00242)	ACGGAAGAAATTTTTTTCTTT	0.328																																					p.F106fs		Atlas-INDEL	.											.	POLE2	36	.	0			c.316delT						.						73	75	74					14																	50141076		2203	4300	6503	SO:0001589	frameshift_variant	5427	exon4			.	AF025840	CCDS32073.1, CCDS55914.1, CCDS55915.1	14q21-q22	2012-05-18	2012-05-18		ENSG00000100479	ENSG00000100479		"DNA polymerases"	9178	protein-coding gene	gene with protein product	"DNA polymerase epsilon subunit B"	602670	"polymerase (DNA directed), epsilon 2 (p59 subunit)"			9405441, 9443964	Standard	NM_002692		Approved	DPE2	uc001wwu.3	P56282	OTTHUMG00000170813	ENST00000216367.5:c.315delA	chr14.hg19:g.50141076delT	ENSP00000216367:p.Lys105fs	236.0	0.0		163.0	10.0	NM_001197331	A0AV55|A4FU92|A4LBB7|A6NH58|B4DDE6|O43560	Frame_Shift_Del	DEL	ENST00000216367.5	hg19	CCDS32073.1																																																																																			.	.		0.328	POLE2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410512.1	NM_002692		-	50141076	T	-	50141076	7	5	282	1	0	1	0	1	0	0	0	0	12206	1490	52	0	1332	0	POLE2	14	50141076	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	12079166	50141076	57208464	961	41195										
KLHDC1	122773	hgsc.bcm.edu	37	chr14	50190646	50190646	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cacagtgaactccaagactgTtttgatgttcatgatgcatc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:50190646delT	ENST00000359332.2	+	5	549	c.459delT	c.(457-459)tgtfs	p.C153fs		NM_172193.2	NP_751943.1	Q8N7A1	KLDC1_HUMAN	kelch domain containing 1	153						cytoplasm (GO:0005737)				kidney(1)|large_intestine(1)|liver(2)|lung(5)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	12	all_epithelial(31;0.00244)|Breast(41;0.00964)					TCCAAGACTGTTTTGATGTTC	0.353																																					p.C153fs		Atlas-INDEL	.											.	KLHDC1	24	.	0			c.458delG						.						206	182	190					14																	50190646		2203	4300	6503	SO:0001589	frameshift_variant	122773	exon5			.	AF111806	CCDS9692.1	14q21.3	2007-08-01			ENSG00000197776	ENSG00000197776			19836	protein-coding gene	gene with protein product		611281					Standard	NM_172193		Approved	MST025	uc001www.3	Q8N7A1	OTTHUMG00000140295	ENST00000359332.2:c.459delT	chr14.hg19:g.50190646delT	ENSP00000352282:p.Cys153fs	178.0	0.0		143.0	10.0	NM_172193	B3KXD9|Q8WYI1	Frame_Shift_Del	DEL	ENST00000359332.2	hg19	CCDS9692.1																																																																																			.	.		0.353	KLHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276882.2	NM_172193		-	50190646	T	-	50190646	7	5	282	1	0	1	0	1	0	0	0	0	8363	1731	60	0	477	0	KLHDC1	14	50190646	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	49570	50190646	57158894	962	41196										
SDCCAG1	9147	hgsc.bcm.edu	37	chr14	50267183	50267183	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caatggtagtatcaggataaTttaatgtctcttccccttca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:50267183delT	ENST00000298310.5	-	23	2776	c.2327delA	c.(2326-2328)aatfs	p.N776fs	NEMF_ENST00000546046.1_Frame_Shift_Del_p.N755fs|NEMF_ENST00000545773.1_Frame_Shift_Del_p.N734fs|NEMF_ENST00000556925.1_5'UTR			O60524	NEMF_HUMAN	nuclear export mediator factor	776					nuclear export (GO:0051168)	nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(13)|liver(1)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	36						ATCAGGATAATTTAATGTCTC	0.348																																					p.N776fs		Atlas-INDEL	.											.	NEMF	79	.	0			c.2328delT						.						133	117	123					14																	50267183		2203	4300	6503	SO:0001589	frameshift_variant	9147	exon23			.	AF039687	CCDS9694.1	14q21.3	2012-11-19	2011-01-31	2011-01-31	ENSG00000165525	ENSG00000165525			10663	protein-coding gene	gene with protein product		608378	"serologically defined colon cancer antigen 1"	SDCCAG1		9610721, 10575219	Standard	XR_429334		Approved	NY-CO-1, FLJ10051	uc001wxc.3	O60524	OTTHUMG00000170857	ENST00000298310.5:c.2327delA	chr14.hg19:g.50267183delT	ENSP00000298310:p.Asn776fs	273.0	0.0		204.0	14.0	NM_004713	A0JLQ3|B3KSK1|B4DDL3|B4DHA9|B4E3F3|Q32Q66|Q8WW70|Q9NWG1	Frame_Shift_Del	DEL	ENST00000298310.5	hg19	CCDS9694.1																																																																																			.	.		0.348	NEMF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410798.1	NM_004713		-	50267183	T	-	50267183	7	5	282	1	0	1	0	1	0	0	0	0	13972	1493	52	0	947	0	SDCCAG1	14	50267183	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	76537	50267183	57082357	963	41197										
ATL1	51062	hgsc.bcm.edu	37	chr14	51094799	51094799	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccaaatgacttgcagaccaaAcacctgcaacttaaggaaga	7	11	0	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:51094799A>G	ENST00000358385.6	+	12	1411	c.1170A>G	c.(1168-1170)aaA>aaG	p.K390K	ATL1_ENST00000357032.3_Silent_p.K390K|ATL1_ENST00000441560.2_Silent_p.K390K|ATL1_ENST00000354525.4_Silent_p.K390K	NM_015915.4	NP_056999.2	Q8WXF7	ATLA1_HUMAN	atlastin GTPase 1	390					axonogenesis (GO:0007409)|cell death (GO:0008219)|endoplasmic reticulum organization (GO:0007029)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi cis cisterna (GO:0000137)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			central_nervous_system(1)|cervix(2)|large_intestine(4)|liver(1)|lung(6)|ovary(1)|skin(3)	18						TGCAGACCAAACACCTGCAAC	0.453																																					p.K390K		Atlas-SNP	.											.	ATL1	46	.	0			c.A1170G						.						67	69	68					14																	51094799		2203	4300	6503	SO:0001819	synonymous_variant	51062	exon12			GACCAAACACCTG	AF131801	CCDS9700.1, CCDS32077.1	14q21.3	2014-09-17	2008-09-17	2008-09-17	ENSG00000198513	ENSG00000198513			11231	protein-coding gene	gene with protein product	"atlastin"	606439	"spastic paraplegia 3A (autosomal dominant)"	SPG3, SPG3A		8252041, 7825576	Standard	NM_015915		Approved	FSP1, AD-FSP	uc001wyd.4	Q8WXF7	OTTHUMG00000140297	ENST00000358385.6:c.1170A>G	chr14.hg19:g.51094799A>G		107.0	0.0		92.0	4.0	NM_015915	A6NND5|A8K2C0|G5E9T1|O95890|Q69YH7|Q96FK0	Silent	SNP	ENST00000358385.6	hg19	CCDS9700.1																																																																																			.	.		0.453	ATL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276884.2			G	51094799	A	G	51094799	2	3	282	1	0	0	0	0	0	0	0	1	1106	40	2	2		2	ATL1	14	51094799	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	827616	51094799	56254741	964	41198										
NIN	51199	hgsc.bcm.edu	37	chr14	51233604	51233604	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gctcattttccagacgactgTtttcctgaacaagtatgggg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:51233604delT	ENST00000382041.3	-	13	1629	c.1439delA	c.(1438-1440)aacfs	p.N480fs	NIN_ENST00000389868.3_Frame_Shift_Del_p.N480fs|NIN_ENST00000530997.2_Frame_Shift_Del_p.N480fs|NIN_ENST00000382043.4_Frame_Shift_Del_p.N480fs|NIN_ENST00000324330.9_Frame_Shift_Del_p.N480fs|NIN_ENST00000453196.1_Frame_Shift_Del_p.N480fs|NIN_ENST00000245441.5_Frame_Shift_Del_p.N480fs	NM_016350.4|NM_182946.1	NP_057434.4|NP_891991	Q8N4C6	NIN_HUMAN	ninein (GSK3B interacting protein)	480					centrosome localization (GO:0051642)|centrosome-templated microtubule nucleation (GO:0090222)|microtubule anchoring at centrosome (GO:0034454)	centriole (GO:0005814)|centrosome (GO:0005813)|microtubule (GO:0005874)|nucleolus (GO:0005730)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(13)|lung(16)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	71	all_epithelial(31;0.00244)|Breast(41;0.127)					CAGACGACTGTTTTCCTGAAC	0.338			T	PDGFRB	MPD																																p.N480fs		Atlas-INDEL	.		Dom	yes		14	14q24	51199	ninein (GSK3B interacting protein)		L	.	NIN	475	.	0			c.1440delC						.						120	116	117					14																	51233604		2203	4298	6501	SO:0001589	frameshift_variant	51199	exon13			.	AF212162	CCDS32078.1, CCDS32079.1, CCDS32078.2	14q21-q22	2013-01-10			ENSG00000100503	ENSG00000100503		"EF-hand domain containing"	14906	protein-coding gene	gene with protein product		608684				11004522, 11162463	Standard	NM_020921		Approved		uc001wyi.3	Q8N4C6	OTTHUMG00000029569	ENST00000382041.3:c.1439delA	chr14.hg19:g.51233604delT	ENSP00000371472:p.Asn480fs	168.0	0.0		113.0	10.0	NM_020921	A6NDB8|B7WPA3|C9JSB6|C9JSG2|C9JXL2|Q5BKU3|Q6P0P6|Q9BWU6|Q9C012|Q9C013|Q9C014|Q9H5I6|Q9HAT7|Q9HBY5|Q9HCK7|Q9UH61	Frame_Shift_Del	DEL	ENST00000382041.3	hg19	CCDS32079.1																																																																																			.	.		0.338	NIN-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395207.2	NM_182946		-	51233604	T	-	51233604	7	5	282	1	0	1	0	1	0	0	0	0	10426	1725	60	0	5186	0	NIN	14	51233604	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	138805	51233604	56115936	965	41199										
DLGAP5	9787	hgsc.bcm.edu	37	chr14	55647496	55647496	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgggcattacaggctgcacaActgtgggaaaaaaaaataac	10	7	0	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:55647496A>G	ENST00000247191.2	-	6	797	c.581T>C	c.(580-582)gTt>gCt	p.V194A	DLGAP5_ENST00000395425.2_Splice_Site_p.V194A	NM_014750.4	NP_055565.3	Q15398	DLGP5_HUMAN	discs, large (Drosophila) homolog-associated protein 5	194					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|dephosphorylation (GO:0016311)|mitotic chromosome movement towards spindle pole (GO:0007079)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|spindle pole centrosome (GO:0031616)	phosphoprotein phosphatase activity (GO:0004721)			biliary_tract(1)|breast(2)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	44						AGGCTGCACAACTGTGGGAAA	0.453																																					p.V194A		Atlas-SNP	.											.	DLGAP5	84	.	0			c.T581C						.						132	121	124					14																	55647496		2203	4300	6503	SO:0001630	splice_region_variant	9787	exon6			TGCACAACTGTGG	D13633	CCDS9723.1, CCDS53897.1	14q22.3	2008-05-30	2008-05-30	2008-05-30	ENSG00000126787	ENSG00000126787			16864	protein-coding gene	gene with protein product			"discs, large homolog 7 (Drosophila)"	DLG7		7584026, 7584028	Standard	NM_014750		Approved	KIAA0008, DLG1, HURP	uc001xbs.3	Q15398	OTTHUMG00000140310	ENST00000247191.2:c.581-1T>C	chr14.hg19:g.55647496A>G		172.0	0.0		124.0	49.0	NM_014750	A8MTM6|B4DRM8|Q86T11|Q8NG58	Missense_Mutation	SNP	ENST00000247191.2	hg19	CCDS9723.1	.	.	.	.	.	.	.	.	.	.	A	2.792	-0.251016	0.05867	.	.	ENSG00000126787	ENST00000395425;ENST00000247191;ENST00000557645	T;T;T	0.19806	2.12;2.12;2.12	5.03	1.91	0.25777	.	1.660750	0.03176	N	0.171367	T	0.12092	0.0294	N	0.17082	0.46	0.23966	N	0.996324	B;B	0.19200	0.007;0.034	B;B	0.15052	0.006;0.012	T	0.24261	-1.0165	10	0.07325	T	0.83	.	5.2921	0.15733	0.6005:0.0:0.3994:0.0	.	194;194	A8MTM6;Q15398	.;DLGP5_HUMAN	A	194	ENSP00000378815:V194A;ENSP00000247191:V194A;ENSP00000451747:V194A	ENSP00000247191:V194A	V	-	2	0	DLGAP5	54717249	0.004000	0.15560	0.083000	0.20561	0.004000	0.04260	-0.405000	0.07196	0.139000	0.18822	0.533000	0.62120	GTT	.	.		0.453	DLGAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276908.2	NM_014750	Missense_Mutation	G	55647496	A	G	55647496	5	3	282	1	0	0	0	0	0	0	1	0	4565	57	2	2	2110	2	DLGAP5	14	55647496	Splice_Site	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	4413892	55647496	51702044	966	41200										
ARID4A	5926	hgsc.bcm.edu	37	chr14	58796746	58796746	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagaaagcaagcatcttcttAaaaactagagttgttcctga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:58796746delA	ENST00000355431.3	+	11	1138	c.765delA	c.(763-765)ttafs	p.L255fs	ARID4A_ENST00000348476.3_Frame_Shift_Del_p.L255fs|ARID4A_ENST00000395168.3_Frame_Shift_Del_p.L255fs|ARID4A_ENST00000431317.2_Frame_Shift_Del_p.L255fs	NM_002892.3	NP_002883.3	P29374	ARI4A_HUMAN	AT rich interactive domain 4A (RBP1-like)	255					erythrocyte development (GO:0048821)|histone H3-K4 trimethylation (GO:0080182)|histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|central_nervous_system(1)|cervix(4)|endometrium(8)|kidney(2)|large_intestine(14)|lung(19)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						GCATCTTCTTAAAAACTAGAG	0.388																																					p.L255X		Atlas-INDEL	.											.	ARID4A	222	.	0			c.764delT						.						94	101	98					14																	58796746		2203	4300	6503	SO:0001589	frameshift_variant	5926	exon11			.	S57153	CCDS9732.1, CCDS9733.1, CCDS45114.1	14q22.3	2013-02-07	2004-01-28	2004-01-28	ENSG00000032219	ENSG00000032219		"-"	9885	protein-coding gene	gene with protein product		180201	"retinoblastoma-binding protein 1"	RBBP1		1857421, 8455946	Standard	NM_023000		Approved	RBP1, RBP-1	uc001xdp.3	P29374	OTTHUMG00000140320	ENST00000355431.3:c.765delA	chr14.hg19:g.58796746delA	ENSP00000347602:p.Leu255fs	195.0	0.0		167.0	11.0	NM_002892	Q15991|Q15992|Q15993	Frame_Shift_Del	DEL	ENST00000355431.3	hg19	CCDS9732.1																																																																																			.	.		0.388	ARID4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276927.2	NM_023001		-	58796746	A	-	58796746	7	5	282	1	0	1	0	1	0	0	0	0	919	359	13	0	803	0	ARID4A	14	58796746	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	3149250	58796746	48552794	967	41201										
C14orf135	64430	hgsc.bcm.edu	37	chr14	60581571	60581571	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gttttagagttcggccttggAggctcatctatgtcaaccca	10	10	3	1	rs369124921		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:60581571A>G	ENST00000406854.1	+	3	1397	c.843A>G	c.(841-843)ggA>ggG	p.G281G	PCNXL4_ENST00000406949.1_Silent_p.G47G|PCNXL4_ENST00000404681.2_Silent_p.G281G|PCNXL4_ENST00000317623.4_Silent_p.G47G			Q63HM2	PCX4_HUMAN	pecanex-like 4 (Drosophila)	281						integral component of membrane (GO:0016021)											TCGGCCTTGGAGGCTCATCTA	0.368																																					p.G47G		Atlas-SNP	.											.	.	.	.	0			c.A141G						.	A		1,3657		0,1,1828	142	136	138		141	2.7	1	14		138	0,8148		0,0,4074	no	coding-synonymous	C14orf135	NM_022495.5		0,1,5902	GG,GA,AA		0.0,0.0273,0.0085		47/939	60581571	1,11805	1829	4074	5903	SO:0001819	synonymous_variant	64430	exon2			CCTTGGAGGCTCA	AK022861		14q23.1	2012-07-18	2012-07-18	2012-07-18	ENSG00000126773	ENSG00000126773			20349	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 135"	C14orf135			Standard	NM_022495		Approved		uc001xer.4	Q63HM2	OTTHUMG00000150361	ENST00000406854.1:c.843A>G	chr14.hg19:g.60581571A>G		112.0	0.0		95.0	5.0	NM_022495	A8MXM2|Q9BQG8|Q9H9F2	Silent	SNP	ENST00000406854.1	hg19																																																																																				.	.		0.368	PCNXL4-005	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000317847.1	NM_022495		G	60581571	A	G	60581571	2	3	282	1	0	0	0	0	0	0	0	1	1747	291	11	2		2	C14orf135	14	60581571	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1784825	60581571	46767969	968	41202										
C14orf135	64430	hgsc.bcm.edu	37	chr14	60587948	60587948	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggatctcattacttgggccgTtttcaggatcgtttaatgtg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:60587948delT	ENST00000406854.1	+	8	2531	c.1977delT	c.(1975-1977)cgtfs	p.R659fs	PCNXL4_ENST00000535349.1_5'UTR|PCNXL4_ENST00000406949.1_Frame_Shift_Del_p.R425fs|PCNXL4_ENST00000404681.2_Frame_Shift_Del_p.R659fs|PCNXL4_ENST00000317623.4_Frame_Shift_Del_p.R425fs			Q63HM2	PCX4_HUMAN	pecanex-like 4 (Drosophila)	659						integral component of membrane (GO:0016021)											ACTTGGGCCGTTTTCAGGATC	0.318																																					p.R425fs		Atlas-INDEL	.											.	.	.	.	0			c.1274delG						.						183	169	174					14																	60587948		2203	4300	6503	SO:0001589	frameshift_variant	64430	exon7			.	AK022861		14q23.1	2012-07-18	2012-07-18	2012-07-18	ENSG00000126773	ENSG00000126773			20349	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 135"	C14orf135			Standard	NM_022495		Approved		uc001xer.4	Q63HM2	OTTHUMG00000150361	ENST00000406854.1:c.1977delT	chr14.hg19:g.60587948delT	ENSP00000384801:p.Arg659fs	233.0	0.0		180.0	12.0	NM_022495	A8MXM2|Q9BQG8|Q9H9F2	Frame_Shift_Del	DEL	ENST00000406854.1	hg19																																																																																				.	.		0.318	PCNXL4-005	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000317847.1	NM_022495		-	60587948	T	-	60587948	7	5	282	1	0	1	0	1	0	0	0	0	1747	1712	60	0	1297	0	C14orf135	14	60587948	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	6377	60587948	46761592	969	41203										
TMEM229B	161145	hgsc.bcm.edu	37	chr14	67940172	67940172	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atggccgttggccagggctaGggcgccgctgggctccccgg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:67940172delG	ENST00000557006.1	-	4	751	c.469delC	c.(469-471)ctafs	p.L157fs	TMEM229B_ENST00000357461.2_Frame_Shift_Del_p.L157fs			Q8NBD8	T229B_HUMAN	transmembrane protein 229B	157						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	5						GCCAGGGCTAGGGCGCCGCTG	0.637																																					p.L157fs		Atlas-INDEL	.											.	TMEM229B	20	.	0			c.470delT						.						45	50	48					14																	67940172		2203	4300	6503	SO:0001589	frameshift_variant	161145	exon3			.	AK090706	CCDS9783.1	14q23.3-q24.1	2009-09-22	2009-09-22	2009-09-22	ENSG00000198133	ENSG00000198133			20130	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 83"	C14orf83			Standard	NM_182526		Approved	FLJ33387	uc001xjk.3	Q8NBD8		ENST00000557006.1:c.469delC	chr14.hg19:g.67940172delG	ENSP00000451774:p.Leu157fs	209.0	0.0		153.0	10.0	NM_182526		Frame_Shift_Del	DEL	ENST00000557006.1	hg19	CCDS9783.1																																																																																			.	.		0.637	TMEM229B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412718.2	NM_182526		-	67940172	G	-	67940172	7	5	282	1	0	1	0	1	0	0	0	0	16163	991	35	0	38	0	TMEM229B	14	67940172	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	7352224	67940172	39409368	970	41204										
PCNX	22990	hgsc.bcm.edu	37	chr14	71500186	71500186	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tattccagtacttttctccaTtttttgtggtttattagtgg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:71500186delT	ENST00000304743.2	+	17	4045	c.3599delT	c.(3598-3600)attfs	p.I1200fs	PCNX_ENST00000439984.3_Frame_Shift_Del_p.I1089fs|PCNX_ENST00000238570.5_Frame_Shift_Del_p.I1200fs	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	1200						integral component of membrane (GO:0016021)				NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		CTTTTCTCCATTTTTTGTGGT	0.338																																					p.I1200fs		Atlas-INDEL	.											.	PCNX	198	.	0			c.3598delA						.						168	150	156					14																	71500186		2203	4300	6503	SO:0001589	frameshift_variant	22990	exon17			.	AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"pecanex-like 1 (Drosophila)"	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.3599delT	chr14.hg19:g.71500186delT	ENSP00000304192:p.Ile1200fs	212.0	0.0		163.0	11.0	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Frame_Shift_Del	DEL	ENST00000304743.2	hg19	CCDS9806.1																																																																																			.	.		0.338	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982		-	71500186	T	-	71500186	7	5	282	1	0	1	0	1	0	0	0	0	11600	1493	52	0	3665	0	PCNX	14	71500186	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3560014	71500186	35849354	971	41205										
NUMB	8650	hgsc.bcm.edu	37	chr14	73822379	73822379	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtgcgaacgccttcttcatcTgtctgccactgatgtggacg	11	12	4	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:73822379T>C	ENST00000355058.3	-	4	359	c.81A>G	c.(79-81)acA>acG	p.T27T	NUMB_ENST00000555238.1_Silent_p.T27T|NUMB_ENST00000544991.3_Silent_p.T27T|NUMB_ENST00000557597.1_Silent_p.T27T|NUMB_ENST00000554546.1_Silent_p.T27T|NUMB_ENST00000359560.3_Silent_p.T27T|NUMB_ENST00000555738.2_Silent_p.T27T|NUMB_ENST00000559312.1_Silent_p.T27T|NUMB_ENST00000560335.1_Silent_p.T27T|NUMB_ENST00000535282.1_Silent_p.T27T|NUMB_ENST00000454166.4_Silent_p.T27T|NUMB_ENST00000356296.4_Silent_p.T27T|NUMB_ENST00000555394.1_Silent_p.T27T|NUMB_ENST00000554521.2_Silent_p.T27T			P49757	NUMB_HUMAN	numb homolog (Drosophila)	27					adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|lateral ventricle development (GO:0021670)|lung epithelial cell differentiation (GO:0060487)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of protein localization to plasma membrane (GO:1903077)|neuroblast division in subventricular zone (GO:0021849)|Notch signaling pathway (GO:0007219)|positive regulation of cell migration (GO:0030335)|positive regulation of neurogenesis (GO:0050769)|positive regulation of polarized epithelial cell differentiation (GO:0030862)	apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|clathrin-coated vesicle (GO:0030136)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00471)|OV - Ovarian serous cystadenocarcinoma(108;0.161)		CTTCTTCATCTGTCTGCCACT	0.413																																					p.T27T		Atlas-SNP	.											.	NUMB	56	.	0			c.A81G						.						112	106	108					14																	73822379		2203	4300	6503	SO:0001819	synonymous_variant	8650	exon4			TTCATCTGTCTGC	L40393	CCDS9814.1, CCDS32115.1, CCDS32116.1, CCDS55927.1	14q24.3	2011-11-25	2001-11-28			ENSG00000133961			8060	protein-coding gene	gene with protein product		603728	"numb (Drosophila) homolog", "chromosome 14 open reading frame 41"	C14orf41			Standard	NM_003744		Approved		uc001xny.1	P49757		ENST00000355058.3:c.81A>G	chr14.hg19:g.73822379T>C		128.0	0.0		99.0	4.0	NM_003744	B1P2N5|B1P2N6|B1P2N7|B1P2N8|B1P2N9|B4E2B1|Q6NUQ7|Q86SY1|Q8WW73|Q9UBG1|Q9UEQ4|Q9UKE8|Q9UKE9|Q9UKF0|Q9UQJ4	Silent	SNP	ENST00000355058.3	hg19	CCDS32116.1																																																																																			.	.		0.413	NUMB-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414416.1			C	73822379	T	C	73822379	2	2	282	1	0	0	0	0	0	0	0	1	10760	1567	55	2		2	NUMB	14	73822379	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2322193	73822379	33527161	972	41206										
ACOT4	122970	hgsc.bcm.edu	37	chr14	74058947	74058947	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcctttttggcgcttcctgaAgcgggacgtacagattcctt	11	11	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:74058947A>G	ENST00000326303.4	+	1	538	c.284A>G	c.(283-285)aAg>aGg	p.K95R		NM_152331.3	NP_689544.3	Q8N9L9	ACOT4_HUMAN	acyl-CoA thioesterase 4	95					acyl-CoA metabolic process (GO:0006637)|dicarboxylic acid catabolic process (GO:0043649)|dicarboxylic acid metabolic process (GO:0043648)|long-chain fatty acid metabolic process (GO:0001676)|saturated monocarboxylic acid metabolic process (GO:0032788)|short-chain fatty acid metabolic process (GO:0046459)|succinyl-CoA metabolic process (GO:0006104)|unsaturated monocarboxylic acid metabolic process (GO:0032789)|very long-chain fatty acid metabolic process (GO:0000038)	peroxisome (GO:0005777)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)|succinyl-CoA hydrolase activity (GO:0004778)			endometrium(1)|large_intestine(3)|lung(4)	8				BRCA - Breast invasive adenocarcinoma(234;0.00331)		CGCTTCCTGAAGCGGGACGTA	0.682																																					p.K95R		Atlas-SNP	.											.	ACOT4	25	.	0			c.A284G						.						26	27	27					14																	74058947		2155	4145	6300	SO:0001583	missense	122970	exon1			TCCTGAAGCGGGA	BC031799	CCDS9817.1	14q24.1	2011-02-16			ENSG00000177465	ENSG00000177465		"Acyl CoA thioesterases"	19748	protein-coding gene	gene with protein product		614314				16103133, 16940157	Standard	NM_152331		Approved	FLJ31235, PTE-Ib, PTE2B	uc001xoo.3	Q8N9L9	OTTHUMG00000169485	ENST00000326303.4:c.284A>G	chr14.hg19:g.74058947A>G	ENSP00000323071:p.Lys95Arg	143.0	0.0		85.0	4.0	NM_152331	Q17RF4|Q5BKT6|Q86TX0|Q86TX1|Q96N88	Missense_Mutation	SNP	ENST00000326303.4	hg19	CCDS9817.1	.	.	.	.	.	.	.	.	.	.	A	17.83	3.486010	0.63962	.	.	ENSG00000177465	ENST00000326303	T	0.42513	0.97	4.93	4.93	0.64822	Acyl-CoA thioester hydrolase/bile acid-CoA amino acid N-acetyltransferase (1);	0.182827	0.48286	D	0.000196	T	0.67515	0.2901	M	0.88450	2.955	0.37348	D	0.910666	D	0.67145	0.996	D	0.72625	0.978	T	0.76913	-0.2783	10	0.56958	D	0.05	-7.8835	12.0859	0.53698	0.8568:0.1432:0.0:0.0	.	95	Q8N9L9	ACOT4_HUMAN	R	95	ENSP00000323071:K95R	ENSP00000323071:K95R	K	+	2	0	ACOT4	73128700	1.000000	0.71417	0.998000	0.56505	0.510000	0.34073	4.494000	0.60347	1.974000	0.57490	0.379000	0.24179	AAG	.	.		0.682	ACOT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404298.2	NM_152331		G	74058947	A	G	74058947	3	3	282	1	0	0	0	0	1	0	0	0	153	72	3	2	286	2	ACOT4	14	74058947	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	236568	74058947	33290593	973	41207										
DNAL1	83544	hgsc.bcm.edu	37	chr14	74156191	74156191	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggattgaagaagcaaccaagAgagtgcccaaactgaaaaag	11	7	0	4			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:74156191A>G	ENST00000553645.2	+	7	546	c.505A>G	c.(505-507)Aga>Gga	p.R169G	DNAL1_ENST00000554871.1_Missense_Mutation_p.R130G|DNAL1_ENST00000554339.1_Missense_Mutation_p.R82G|DNAL1_ENST00000311089.3_Missense_Mutation_p.R56G|DNAL1_ENST00000540526.1_Missense_Mutation_p.R130G	NM_031427.3	NP_113615.2	Q4LDG9	DNAL1_HUMAN	dynein, axonemal, light chain 1	169	LRRCT.									kidney(1)|lung(2)	3				BRCA - Breast invasive adenocarcinoma(234;0.00384)|KIRC - Kidney renal clear cell carcinoma(182;0.095)		AGCAACCAAGAGAGTGCCCAA	0.448																																					p.R169G		Atlas-SNP	.											.	DNAL1	16	.	0			c.A505G						.						88	88	88					14																	74156191		1916	4123	6039	SO:0001583	missense	83544	exon7			ACCAAGAGAGTGC	BC005343	CCDS45134.1, CCDS55928.1	14q24.3	2012-05-03	2006-09-04	2006-09-04	ENSG00000119661	ENSG00000119661			23247	protein-coding gene	gene with protein product		610062	"chromosome 14 open reading frame 168"	C14orf168		15845866	Standard	NM_031427		Approved	MGC12435, 1700010H15RiK, CILD16	uc001xoq.4	Q4LDG9		ENST00000553645.2:c.505A>G	chr14.hg19:g.74156191A>G	ENSP00000452037:p.Arg169Gly	235.0	0.0		142.0	6.0	NM_031427	B2RD38|Q5JPB7|Q9BS43	Missense_Mutation	SNP	ENST00000553645.2	hg19	CCDS45134.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.573670	0.86542	.	.	ENSG00000119661	ENST00000554113;ENST00000555631;ENST00000553645;ENST00000311089;ENST00000554339;ENST00000554871;ENST00000540526	T;T;T;T;T;T	0.79033	-1.23;1.81;1.81;1.81;1.81;1.81	5.68	4.58	0.56647	.	0.000000	0.85682	D	0.000000	T	0.82235	0.4993	M	0.86343	2.81	0.80722	D	1	P	0.42123	0.771	P	0.45829	0.494	D	0.84042	0.0365	10	0.49607	T	0.09	-21.5477	10.8526	0.46780	0.6015:0.3985:0.0:0.0	.	169	Q4LDG9	DNAL1_HUMAN	G	56;56;169;56;82;130;130	ENSP00000452368:R56G;ENSP00000452037:R169G;ENSP00000310360:R56G;ENSP00000450744:R82G;ENSP00000451834:R130G;ENSP00000439695:R130G	ENSP00000310360:R169G	R	+	1	2	DNAL1	73225944	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.491000	0.66887	2.155000	0.67459	0.460000	0.39030	AGA	.	.		0.448	DNAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414565.2	NM_031427		G	74156191	A	G	74156191	3	3	282	1	0	0	0	0	1	0	0	0	4659	296	11	2	531	2	DNAL1	14	74156191	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	97244	74156191	33193349	974	41208										
COQ6	51004	hgsc.bcm.edu	37	chr14	74422603	74422603	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aatgatgtcatcatgcatgcTctcactaagcagttggaggc	10	9	3	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:74422603T>C	ENST00000334571.2	+	4	493	c.453T>C	c.(451-453)gcT>gcC	p.A151A	COQ6_ENST00000554920.1_Silent_p.A151A|COQ6_ENST00000238709.4_Silent_p.A76A|COQ6_ENST00000394026.4_Silent_p.A126A|COQ6_ENST00000555552.1_3'UTR	NM_182476.2	NP_872282.1	Q9Y2Z9	COQ6_HUMAN	coenzyme Q6 monooxygenase	151					small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	cell projection (GO:0042995)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)			breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	16				BRCA - Breast invasive adenocarcinoma(234;0.00337)		TCATGCATGCTCTCACTAAGC	0.478																																					p.A151A		Atlas-SNP	.											.	COQ6	27	.	0			c.T453C						.						169	158	161					14																	74422603		2203	4300	6503	SO:0001819	synonymous_variant	51004	exon4			GCATGCTCTCACT	AF132944	CCDS9823.1, CCDS9824.1, CCDS9824.2	14q24.1	2013-05-01	2013-05-01		ENSG00000119723	ENSG00000119723			20233	protein-coding gene	gene with protein product		614647	"coenzyme Q6 homolog (yeast)", "coenzyme Q6 homolog, monooxygenase (yeast)", "coenzyme Q6 homolog, monooxygenase (S. cerevisiae)"			21540551	Standard	NM_182476		Approved	CGI-10	uc001xph.3	Q9Y2Z9	OTTHUMG00000171260	ENST00000334571.2:c.453T>C	chr14.hg19:g.74422603T>C		166.0	0.0		118.0	5.0	NM_182476	B7Z3K8|Q53GG6|Q86U30|Q96CA1|Q96CK2	Silent	SNP	ENST00000334571.2	hg19	CCDS9823.1																																																																																			.	.		0.478	COQ6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412616.1			C	74422603	T	C	74422603	2	2	282	1	0	0	0	0	0	0	0	1	3751	1538	54	2		2	COQ6	14	74422603	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	266412	74422603	32926937	975	41209										
C14orf174	161394	hgsc.bcm.edu	37	chr14	77845359	77845359	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agatgacgaaacccagccagAaaaagggactgagttacaat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:77845359delA	ENST00000216471.4	+	1	1884	c.1598delA	c.(1597-1599)gaafs	p.E533fs	TMED8_ENST00000216468.7_5'Flank|SAMD15_ENST00000533095.2_Intron	NM_001010860.1	NP_001010860.1	Q9P1V8	SAM15_HUMAN	sterile alpha motif domain containing 15	533										breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						ACCCAGCCAGAAAAAGGGACT	0.428																																					p.E533fs		Atlas-INDEL	.											.	SAMD15	60	.	0			c.1597delG						.						76	73	74					14																	77845359		2203	4300	6503	SO:0001589	frameshift_variant	161394	exon1			.	AK093282	CCDS32126.1	14q24.3	2013-01-10	2010-10-20	2010-10-20	ENSG00000100583	ENSG00000100583		"Sterile alpha motif (SAM) domain containing"	18631	protein-coding gene	gene with protein product			"family with sequence similarity 15, member A", "chromosome 14 open reading frame 174"	FAM15A, C14orf174			Standard	XM_006720069		Approved	FLJ35963	uc001xtq.1	Q9P1V8		ENST00000216471.4:c.1598delA	chr14.hg19:g.77845359delA	ENSP00000216471:p.Glu533fs	278.0	0.0		191.0	12.0	NM_001010860	Q2M3P3	Frame_Shift_Del	DEL	ENST00000216471.4	hg19	CCDS32126.1																																																																																			.	.		0.428	SAMD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394587.2	NM_001010860		-	77845359	A	-	77845359	7	5	282	1	0	1	0	1	0	0	0	0	1761	246	9	0	1600	0	C14orf174	14	77845359	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	3422756	77845359	29504181	976	41210										
AHSA1	10598	hgsc.bcm.edu	37	chr14	77935521	77935521	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctcctgaggaagagcggacgCgacagggctggcagcggtac	17	11	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:77935521C>A	ENST00000216479.3	+	9	1106	c.946C>A	c.(946-948)Cga>Aga	p.R316R	AHSA1_ENST00000555457.1_3'UTR|SNORA46_ENST00000391069.1_RNA	NM_012111.2	NP_036243.1	O95433	AHSA1_HUMAN	AHA1, activator of heat shock 90kDa protein ATPase homolog 1 (yeast)	316					positive regulation of ATPase activity (GO:0032781)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	ATPase activator activity (GO:0001671)|chaperone binding (GO:0051087)			endometrium(1)|kidney(3)|large_intestine(1)|prostate(1)|skin(1)|stomach(1)	8			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)		AGAGCGGACGCGACAGGGCTG	0.572																																					p.R316R		Atlas-SNP	.											AHSA1,NS,carcinoma,0,1	AHSA1	24	.	0			c.C946A						.						170	159	162					14																	77935521		2203	4300	6503	SO:0001819	synonymous_variant	10598	exon9			CGGACGCGACAGG	AJ243310	CCDS9863.1	14q	2008-02-05	2003-04-04	2003-04-11		ENSG00000100591			1189	protein-coding gene	gene with protein product		608466	"chromosome 14 open reading frame 3"	C14orf3			Standard	NM_012111		Approved	p38	uc001xtw.3	O95433		ENST00000216479.3:c.946C>A	chr14.hg19:g.77935521C>A		292.0	0.0		159.0	0.0	NM_012111	B2R9L2|B4DUR9|Q96IL6|Q9P060	Silent	SNP	ENST00000216479.3	hg19	CCDS9863.1	.	.	.	.	.	.	.	.	.	.	C	6.398	0.441552	0.12164	.	.	ENSG00000100591	ENST00000555729	.	.	.	5.46	2.44	0.29823	.	.	.	.	.	T	0.33059	0.0850	.	.	.	0.09310	N	0.999992	.	.	.	.	.	.	T	0.19679	-1.0298	4	.	.	.	-4.2088	7.4374	0.27164	0.5001:0.4161:0.0:0.0837	.	.	.	.	E	110	.	.	A	+	2	0	AHSA1	77005274	0.801000	0.28930	0.972000	0.41901	0.782000	0.44232	1.616000	0.36933	0.865000	0.35603	-0.229000	0.12294	GCG	.	.		0.572	AHSA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414017.1	NM_012111		A	77935521	C	A	77935521	2	1	282	1	0	0	0	0	0	0	0	1	418	760	27	1		1	AHSA1	14	77935521	Silent	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	90162	77935521	29414019	977	41211										
ISM2	145501	hgsc.bcm.edu	37	chr14	77942048	77942048	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agcgtggaggcggctccagtCccccttgcacaggatccagg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:77942048delC	ENST00000342219.4	-	7	1662	c.1606delG	c.(1606-1608)gacfs	p.D536fs	ISM2_ENST00000412904.1_Frame_Shift_Del_p.D455fs|ISM2_ENST00000493585.1_3'UTR|ISM2_ENST00000393684.3_Frame_Shift_Del_p.D448fs|ISM2_ENST00000429906.1_Frame_Shift_Del_p.D455fs	NM_199296.2	NP_954993.1	Q6H9L7	ISM2_HUMAN	isthmin 2	536	AMOP. {ECO:0000255|PROSITE- ProRule:PRU00347}.					extracellular region (GO:0005576)				endometrium(3)|large_intestine(4)|lung(11)|prostate(1)|skin(1)|urinary_tract(1)	21						CGGCTCCAGTCCCCCTTGCAC	0.637																																					p.D536fs		Atlas-INDEL	.											.	ISM2	68	.	0			c.1607delA						.						89	84	86					14																	77942048		2203	4300	6503	SO:0001589	frameshift_variant	145501	exon7			.	AK056709	CCDS9864.1, CCDS45143.1	14q24.3	2013-05-15	2013-05-15	2008-12-23	ENSG00000100593	ENSG00000100593			23176	protein-coding gene	gene with protein product	"thrombospondin and AMOP containing isthmin-like 1"	612684	"thrombospondin, type I domain-containing 3", "thrombospondin, type I, domain containing 3", "isthmin 2 homolog (zebrafish)"	THSD3		15194193	Standard	NM_199296		Approved	FLJ32147, TAIL1	uc001xtz.3	Q6H9L7	OTTHUMG00000158563	ENST00000342219.4:c.1606delG	chr14.hg19:g.77942048delC	ENSP00000341490:p.Asp536fs	230.0	0.0		166.0	10.0	NM_199296	A8K6D5|O95432|Q495U5|Q68CN3|Q86TQ7|Q86TW3|Q86TW4|Q8N501|Q8NBL0	Frame_Shift_Del	DEL	ENST00000342219.4	hg19	CCDS9864.1																																																																																			.	.		0.637	ISM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351309.1	NM_182509		-	77942048	C	-	77942048	7	5	282	1	0	1	0	1	0	0	0	0	7870	855	30	0	113	0	ISM2	14	77942048	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	6527	77942048	29407492	978	41212										
C14orf145	145508	hgsc.bcm.edu	37	chr14	81227952	81227952	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcctcttcaatgcttatatgTttttcctaaggcattgaaag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:81227952delT	ENST00000555265.1	-	17	2757	c.2382delA	c.(2380-2382)aaafs	p.K794fs	CEP128_ENST00000281129.3_Frame_Shift_Del_p.K794fs			Q6ZU80	CE128_HUMAN	centrosomal protein 128kDa	794						centriole (GO:0005814)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	51						TGCTTATATGTTTTTCCTAAG	0.383																																					p.H795fs		Atlas-INDEL	.											.	CEP128	146	.	0			c.2383delC						.						94	82	86					14																	81227952		2203	4300	6503	SO:0001589	frameshift_variant	145508	exon16			.	AK056756	CCDS32130.1	14q31.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000100629	ENSG00000100629			20359	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 61", "chromosome 14 open reading frame 145"	C14orf61, C14orf145		21399614	Standard	NM_152446		Approved		uc001xux.2	Q6ZU80		ENST00000555265.1:c.2382delA	chr14.hg19:g.81227952delT	ENSP00000451162:p.Lys794fs	234.0	0.0		173.0	12.0	NM_152446	B9EK52|Q86X97|Q96ML4	Frame_Shift_Del	DEL	ENST00000555265.1	hg19	CCDS32130.1																																																																																			.	.		0.383	CEP128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413415.1	NM_152446		-	81227952	T	-	81227952	7	5	282	1	0	1	0	1	0	0	0	0	1751	1722	60	0	938	0	C14orf145	14	81227952	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3285904	81227952	26121588	979	41213										
C14orf145	145508	hgsc.bcm.edu	37	chr14	81307070	81307070	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcttagcttattttttattgCcccctcatgctcatctgctt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:81307070delC	ENST00000555265.1	-	10	1180	c.805delG	c.(805-807)gcafs	p.A269fs	CEP128_ENST00000281129.3_Frame_Shift_Del_p.A269fs|CEP128_ENST00000216517.6_Frame_Shift_Del_p.A269fs			Q6ZU80	CE128_HUMAN	centrosomal protein 128kDa	269						centriole (GO:0005814)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	51						TTTTTTATTGCCCCCTCATGC	0.338																																					p.A269fs		Atlas-INDEL	.											.	CEP128	146	.	0			c.806delC						.						233	222	226					14																	81307070		2202	4299	6501	SO:0001589	frameshift_variant	145508	exon9			.	AK056756	CCDS32130.1	14q31.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000100629	ENSG00000100629			20359	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 61", "chromosome 14 open reading frame 145"	C14orf61, C14orf145		21399614	Standard	NM_152446		Approved		uc001xux.2	Q6ZU80		ENST00000555265.1:c.805delG	chr14.hg19:g.81307070delC	ENSP00000451162:p.Ala269fs	209.0	0.0		180.0	11.0	NM_152446	B9EK52|Q86X97|Q96ML4	Frame_Shift_Del	DEL	ENST00000555265.1	hg19	CCDS32130.1																																																																																			.	.		0.338	CEP128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413415.1	NM_152446		-	81307070	C	-	81307070	7	5	282	1	0	1	0	1	0	0	0	0	1751	739	26	0	2543	0	C14orf145	14	81307070	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	79118	81307070	26042470	980	41214										
KCNK10	54207	hgsc.bcm.edu	37	chr14	88693828	88693828	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaattccaaagatggcatatAaaatacaaaagattttgcct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:88693828delA	ENST00000340700.5	-	4	1008	c.557delT	c.(556-558)ttafs	p.L186fs	KCNK10_ENST00000312350.5_Frame_Shift_Del_p.L191fs|KCNK10_ENST00000319231.5_Frame_Shift_Del_p.L191fs	NM_021161.4	NP_066984.1	P57789	KCNKA_HUMAN	potassium channel, subfamily K, member 10	186					signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	47						GATGGCATATAAAATACAAAA	0.413																																					p.L191fs		Atlas-Indel,Pindel	.											.	KCNK10	273	.	0			c.573delA						.						117	122	120					14																	88693828		2203	4300	6503	SO:0001589	frameshift_variant	54207	exon4			.	AF279890	CCDS9880.1, CCDS9881.1, CCDS9882.1	14q31	2014-06-12						"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6273	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 97"	605873				10880510, 16382106	Standard	NM_021161		Approved	K2p10.1, TREK-2, TREK2, PPP1R97	uc001xwn.3	P57789		ENST00000340700.5:c.557delT	chr14.hg19:g.88693828delA	ENSP00000343104:p.Leu186fs	80.0	0.0		96.0	37.0	NM_138318	B2R8T4|B2RCT3|B5TJL4|Q6B014|Q8TDK7|Q8TDK8|Q9HB59	Frame_Shift_Del	DEL	ENST00000340700.5	hg19	CCDS9880.1																																																																																			.	.		0.413	KCNK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410167.1	NM_021161		-	88693828	A	-	88693828	7	5	282	1	0	1	0	1	0	0	0	0	8068	372	13	0	1075	0	KCNK10	14	88693828	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	7386758	88693828	18655712	981	41215										
TDP1	55775	hgsc.bcm.edu	37	chr14	90499504	90499504	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcgctggcagccaggagccaAtggccacctttcctgtgcca	11	15	0	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:90499504A>G	ENST00000335725.4	+	16	1949	c.1699A>G	c.(1699-1701)Atg>Gtg	p.M567V	TDP1_ENST00000393452.3_Missense_Mutation_p.N582S|TDP1_ENST00000357382.3_Missense_Mutation_p.M328V|TDP1_ENST00000393454.2_Missense_Mutation_p.M567V|TDP1_ENST00000555880.1_Intron	NM_018319.3	NP_060789.2	Q9NUW8	TYDP1_HUMAN	tyrosyl-DNA phosphodiesterase 1	567					cell death (GO:0008219)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	3'-tyrosyl-DNA phosphodiesterase activity (GO:0017005)|double-stranded DNA binding (GO:0003690)|exonuclease activity (GO:0004527)|single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|urinary_tract(1)	25		all_cancers(154;0.185)		COAD - Colon adenocarcinoma(157;0.23)		CCAGGAGCCAATGGCCACCTT	0.463								Repair of DNA-protein crosslinks																													p.M567V		Atlas-SNP	.											.	TDP1	47	.	0			c.A1699G						.						60	57	58					14																	90499504		2203	4300	6503	SO:0001583	missense	55775	exon16			GAGCCAATGGCCA	AF182002	CCDS9888.1	14q32.11	2008-08-11				ENSG00000042088			18884	protein-coding gene	gene with protein product		607198				11839309, 12244316	Standard	XM_005267847		Approved	FLJ11090, SCAN1	uc001xxz.3	Q9NUW8		ENST00000335725.4:c.1699A>G	chr14.hg19:g.90499504A>G	ENSP00000337353:p.Met567Val	163.0	0.0		94.0	5.0	NM_018319	Q2HXX4|Q86TV8|Q96BK7|Q9NZM7|Q9NZM8	Missense_Mutation	SNP	ENST00000335725.4	hg19	CCDS9888.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	0.010|0.010	-1.793611|-1.793611	0.00623|0.00623	.|.	.|.	ENSG00000042088|ENSG00000042088	ENST00000393454;ENST00000335725;ENST00000357382|ENST00000393452;ENST00000556063	T;T;T|T	0.39787|0.29917	1.06;1.06;1.06|1.55	5.68|5.68	-4.14|-4.14	0.03892|0.03892	.|.	1.929260|.	0.01799|.	N|.	0.032794|.	T|T	0.08935|0.08935	0.0221|0.0221	N|N	0.00677|0.00677	-1.265|-1.265	0.09310|0.09310	N|N	1|1	B;B;B|B	0.02656|0.02656	0.0;0.0;0.0|0.0	B;B;B|B	0.01281|0.01281	0.0;0.0;0.0|0.0	T|T	0.35400|0.35400	-0.9790|-0.9790	10|9	0.18710|0.54805	T|T	0.47|0.06	-34.4799|-34.4799	9.2837|9.2837	0.37744|0.37744	0.205:0.1235:0.6715:0.0|0.205:0.1235:0.6715:0.0	.|.	567;328;567|582	B2RDI0;Q86TV8;Q9NUW8|E7EPD8	.;.;TYDP1_HUMAN|.	V|S	567;567;328|582;207	ENSP00000377099:M567V;ENSP00000337353:M567V;ENSP00000349952:M328V|ENSP00000377098:N582S	ENSP00000337353:M567V|ENSP00000377098:N582S	M|N	+|+	1|2	0|0	TDP1|TDP1	89569257|89569257	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.122000|0.122000	0.20287|0.20287	-0.699000|-0.699000	0.05087|0.05087	-1.222000|-1.222000	0.02587|0.02587	0.477000|0.477000	0.44152|0.44152	ATG|AAT	.	.		0.463	TDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411239.1	NM_018319		G	90499504	A	G	90499504	3	3	282	1	0	0	0	0	1	0	0	0	15743	101	4	2	1753	2	TDP1	14	90499504	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1805676	90499504	16850036	982	41216										
CPSF2	53981	hgsc.bcm.edu	37	chr14	92604666	92604666	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acatatgtacagcctagaagAaaacagagagatgagcagct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:92604666delA	ENST00000298875.4	+	7	921	c.636delA	c.(634-636)agafs	p.R212fs		NM_017437.2	NP_059133.1	Q9P2I0	CPSF2_HUMAN	cleavage and polyadenylation specific factor 2, 100kDa	212					gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)|mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	RNA binding (GO:0003723)			breast(2)|cervix(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	24		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.222)		AGCCTAGAAGAAAACAGAGAG	0.333																																					p.R212fs	Ovarian(78;28 1788 18702 44111)	Atlas-INDEL	.											.	CPSF2	63	.	0			c.635delG						.						112	112	112					14																	92604666		2203	4300	6503	SO:0001589	frameshift_variant	53981	exon7			.	AB037788	CCDS9902.1	14q31.1	2008-07-28	2002-08-29			ENSG00000165934			2325	protein-coding gene	gene with protein product		606028	"cleavage and polyadenylation specific factor 2, 100kD subunit"			7969155, 11124543	Standard	NM_017437		Approved	KIAA1367	uc001yah.2	Q9P2I0		ENST00000298875.4:c.636delA	chr14.hg19:g.92604666delA	ENSP00000298875:p.Arg212fs	437.0	0.0		347.0	23.0	NM_017437	B3KME1|Q6NSJ1|Q9H3W7	Frame_Shift_Del	DEL	ENST00000298875.4	hg19	CCDS9902.1																																																																																			.	.		0.333	CPSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412123.1			-	92604666	A	-	92604666	7	5	282	1	0	1	0	1	0	0	0	0	3827	243	9	0	654	0	CPSF2	14	92604666	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2105162	92604666	14744874	983	41217										
IFI27L1	122509	hgsc.bcm.edu	37	chr14	94568273	94568273	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctacagcagccattgccaacGggggcggagttgctgctggc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:94568273delG	ENST00000555523.1	+	4	394	c.175delG	c.(175-177)gggfs	p.G61fs	IFI27L1_ENST00000554562.1_Frame_Shift_Del_p.G61fs|IFI27L1_ENST00000554544.1_Intron|IFI27L1_ENST00000557066.1_Intron|IFI27L1_ENST00000556381.1_Frame_Shift_Del_p.G60fs|IFI27L1_ENST00000553664.1_Frame_Shift_Del_p.R81fs|IFI27L1_ENST00000557218.1_Intron|IFI27L1_ENST00000553350.1_Intron|IFI27L1_ENST00000393115.3_Frame_Shift_Del_p.G61fs	NM_206949.2	NP_996832.1	Q96BM0	I27L1_HUMAN	interferon, alpha-inducible protein 27-like 1	61						integral component of membrane (GO:0016021)				lung(2)	2						CATTGCCAACGGGGGCGGAGT	0.592																																					p.N58fs		Atlas-INDEL	.											.	IFI27L1	11	.	0			c.174delC						.						114	95	101					14																	94568273		2203	4300	6503	SO:0001589	frameshift_variant	122509	exon4			.	BC015423	CCDS9919.1	14q32.13	2008-10-08	2008-10-08	2008-10-08		ENSG00000165948			19754	protein-coding gene	gene with protein product		611320	"family with sequence similarity 14, member B"	FAM14B			Standard	NM_145249		Approved		uc001yck.3	Q96BM0		ENST00000555523.1:c.175delG	chr14.hg19:g.94568273delG	ENSP00000451851:p.Gly61fs	319.0	0.0		265.0	16.0	NM_145249		Frame_Shift_Del	DEL	ENST00000555523.1	hg19	CCDS9919.1																																																																																			.	.		0.592	IFI27L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412868.1	NM_206949		-	94568273	G	-	94568273	7	5	282	1	0	1	0	1	0	0	0	0	7522	1116	39	0	185	0	IFI27L1	14	94568273	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1963607	94568273	12781267	984	41218										
SERPINA3	12	hgsc.bcm.edu	37	chr14	95081176	95081176	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caatcagtccagcgatgagcTgcagctgagtatgggaaatg	13	8	1	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:95081176T>C	ENST00000467132.1	+	2	1546	c.398T>C	c.(397-399)cTg>cCg	p.L133P	RP11-986E7.7_ENST00000553947.1_3'UTR|SERPINA3_ENST00000393080.4_Missense_Mutation_p.L133P|SERPINA3_ENST00000482740.1_5'Flank|SERPINA3_ENST00000393078.3_Missense_Mutation_p.L133P			P01011	AACT_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3	133					acute-phase response (GO:0006953)|inflammatory response (GO:0006954)|maintenance of gastrointestinal epithelium (GO:0030277)|negative regulation of endopeptidase activity (GO:0010951)|regulation of lipid metabolic process (GO:0019216)|regulation of proteolysis (GO:0030162)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	DNA binding (GO:0003677)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(17)|ovary(2)|pancreas(1)|skin(3)|stomach(1)	40		all_cancers(154;0.0525)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.212)|Epithelial(152;0.228)		AGCGATGAGCTGCAGCTGAGT	0.537																																					p.L133P		Atlas-SNP	.											.	SERPINA3	78	.	0			c.T398C						.						64	59	61					14																	95081176		2203	4300	6503	SO:0001583	missense	12	exon2			ATGAGCTGCAGCT	K01500	CCDS32150.1	14q32.1	2014-06-03	2005-08-18		ENSG00000196136	ENSG00000196136		"Serine (or cysteine) peptidase inhibitors"	16	protein-coding gene	gene with protein product		107280	"alpha-1-antichymotrypsin", "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3"	AACT		3260956, 24172014	Standard	NM_001085		Approved	ACT, alpha-1-antichymotrypsin	uc001ydp.3	P01011	OTTHUMG00000029851	ENST00000467132.1:c.398T>C	chr14.hg19:g.95081176T>C	ENSP00000450540:p.Leu133Pro	159.0	0.0		96.0	4.0	NM_001085	B3KVQ7|Q13703|Q2TU87|Q2TU88|Q59GP9|Q6LBY8|Q6LDT7|Q6NSC9|Q8N177|Q96DW8|Q9UC47|Q9UNU9	Missense_Mutation	SNP	ENST00000467132.1	hg19	CCDS32150.1	.	.	.	.	.	.	.	.	.	.	T	12.51	1.960668	0.34565	.	.	ENSG00000196136	ENST00000553947;ENST00000393078;ENST00000393080;ENST00000555820;ENST00000467132	D;D;D;D	0.88354	-2.37;-2.37;-2.37;-2.37	5.13	3.97	0.46021	Serpin domain (3);	0.704300	0.12614	N	0.453649	D	0.91536	0.7327	L	0.58510	1.815	0.36505	D	0.86921	P;P	0.49862	0.929;0.683	P;B	0.58210	0.835;0.244	D	0.90756	0.4661	10	0.66056	D	0.02	.	10.8196	0.46597	0.1418:0.0:0.0:0.8582	.	133;158	P01011;G3V5I3	AACT_HUMAN;.	P	158;133;133;133;133	ENSP00000452367:L158P;ENSP00000376793:L133P;ENSP00000376795:L133P;ENSP00000450540:L133P	ENSP00000376793:L133P	L	+	2	0	SERPINA3	94150929	0.017000	0.18338	0.090000	0.20809	0.008000	0.06430	2.137000	0.42130	0.868000	0.35678	0.459000	0.35465	CTG	.	.		0.537	SERPINA3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268080.3	NM_001085		C	95081176	T	C	95081176	3	2	282	1	0	0	0	0	1	0	0	0	14105	1580	55	2	400	2	SERPINA3	14	95081176	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	512903	95081176	12268364	985	41219										
AK7	122481	hgsc.bcm.edu	37	chr14	96944888	96944888	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcatcgtggcggggacccacTacagccaagaccgattcctc	11	15	0	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:96944888T>C	ENST00000267584.4	+	15	1686	c.1642T>C	c.(1642-1644)Tac>Cac	p.Y548H		NM_152327.3	NP_689540.2	Q96M32	KAD7_HUMAN	adenylate kinase 7	548	Adenylate kinase.				axoneme assembly (GO:0035082)|brain development (GO:0007420)|epithelial cilium movement (GO:0003351)|inflammatory response to antigenic stimulus (GO:0002437)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)			breast(2)|cervix(2)|endometrium(3)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)		GGGGACCCACTACAGCCAAGA	0.502																																					p.Y548H		Atlas-SNP	.											.	AK7	69	.	0			c.T1642C						.						105	96	99					14																	96944888		2203	4300	6503	SO:0001583	missense	122481	exon15			ACCCACTACAGCC	AK057426	CCDS9945.1	14q32.31	2012-08-15			ENSG00000140057	ENSG00000140057		"Adenylate kinases"	20091	protein-coding gene	gene with protein product		615364					Standard	NM_152327		Approved	FLJ32864	uc001yfn.3	Q96M32	OTTHUMG00000171421	ENST00000267584.4:c.1642T>C	chr14.hg19:g.96944888T>C	ENSP00000267584:p.Tyr548His	227.0	0.0		148.0	6.0	NM_152327	Q8IYP6	Missense_Mutation	SNP	ENST00000267584.4	hg19	CCDS9945.1	.	.	.	.	.	.	.	.	.	.	T	17.18	3.324697	0.60634	.	.	ENSG00000140057	ENST00000267584	D	0.94687	-3.49	5.05	5.05	0.67936	.	0.112267	0.64402	D	0.000006	D	0.96962	0.9008	M	0.83384	2.64	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.96289	0.9212	10	0.25751	T	0.34	-21.7565	14.7748	0.69724	0.0:0.0:0.0:1.0	.	548	Q96M32	KAD7_HUMAN	H	548	ENSP00000267584:Y548H	ENSP00000267584:Y548H	Y	+	1	0	AK7	96014641	1.000000	0.71417	1.000000	0.80357	0.337000	0.28794	7.714000	0.84703	1.896000	0.54893	0.402000	0.26972	TAC	.	.		0.502	AK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413340.1			C	96944888	T	C	96944888	3	2	282	1	0	0	0	0	1	0	0	0	444	1522	53	2	1700	2	AK7	14	96944888	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1863712	96944888	10404652	986	41220										
PAPOLA	10914	hgsc.bcm.edu	37	chr14	97022557	97022557	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aactgccacacaaccagccaTttctccaccaccaaagccta							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:97022557delT	ENST00000216277.8	+	19	2031	c.1811delT	c.(1810-1812)attfs	p.I604fs	PAPOLA_ENST00000392990.2_Frame_Shift_Del_p.I604fs	NM_032632.4	NP_116021.2	P51003	PAPOA_HUMAN	poly(A) polymerase alpha	604	Ser/Thr-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|RNA polyadenylation (GO:0043631)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)			breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(6)|skin(1)|urinary_tract(1)	21		all_cancers(154;0.0555)|all_epithelial(191;0.149)|Melanoma(154;0.155)		COAD - Colon adenocarcinoma(157;0.213)		CAACCAGCCATTTCTCCACCA	0.413																																					p.I604fs	NSCLC(19;254 734 11908 35501 39234)	Atlas-INDEL	.											.	PAPOLA	58	.	0			c.1810delA						.						160	145	150					14																	97022557		2203	4300	6503	SO:0001589	frameshift_variant	10914	exon19			.	X76770	CCDS9946.1, CCDS58334.1, CCDS58335.1	14q32.1-q32.2	2008-02-08				ENSG00000090060	2.7.7.19		14981	protein-coding gene	gene with protein product		605553				8302877, 10429366	Standard	NM_032632		Approved	PAP	uc001yfq.3	P51003		ENST00000216277.8:c.1811delT	chr14.hg19:g.97022557delT	ENSP00000216277:p.Ile604fs	209.0	0.0		169.0	13.0	NM_032632	Q86SX4|Q86TV0|Q8IYF5|Q9BVU2	Frame_Shift_Del	DEL	ENST00000216277.8	hg19	CCDS9946.1																																																																																			.	.		0.413	PAPOLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413411.2			-	97022557	T	-	97022557	7	5	282	1	0	1	0	1	0	0	0	0	11438	1493	52	0	1885	0	PAPOLA	14	97022557	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	77669	97022557	10326983	987	41221										
EML1	2009	hgsc.bcm.edu	37	chr14	100375708	100375708	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aatgaagctgtgtttgctgcGgatttccaccccacggacac	10	12	0	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:100375708G>T	ENST00000262233.6	+	11	1270	c.1131G>T	c.(1129-1131)gcG>gcT	p.A377A	EML1_ENST00000334192.4_Silent_p.A396A|EML1_ENST00000327921.9_Silent_p.A365A	NM_004434.2	NP_004425.2	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1	377	Tandem atypical propeller in EMLs.		A -> V (in dbSNP:rs34198557).		brain development (GO:0007420)|hematopoietic progenitor cell differentiation (GO:0002244)|microtubule cytoskeleton organization (GO:0000226)|mitotic spindle organization (GO:0007052)|neuroblast proliferation (GO:0007405)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	calcium ion binding (GO:0005509)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)	p.A396A(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Melanoma(154;0.0879)|all_epithelial(191;0.216)				TGTTTGCTGCGGATTTCCACC	0.428																																					p.A396A		Atlas-SNP	.											EML1,colon,carcinoma,+1,1	EML1	97	.	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.G1188T						.						177	174	175					14																	100375708		2203	4300	6503	SO:0001819	synonymous_variant	2009	exon12			TGCTGCGGATTTC	AK023861	CCDS32154.1, CCDS32155.1	14q32	2013-01-10		2002-02-15		ENSG00000066629		"WD repeat domain containing"	3330	protein-coding gene	gene with protein product		602033		EMAPL		9226380, 10521658	Standard	XM_005267397		Approved	EMAP, HuEMAP, ELP79	uc001ygr.3	O00423		ENST00000262233.6:c.1131G>T	chr14.hg19:g.100375708G>T		335.0	0.0		214.0	0.0	NM_001008707	Q86U15|Q8N536|Q8N5C4|Q8WWL6	Silent	SNP	ENST00000262233.6	hg19	CCDS32155.1	.	.	.	.	.	.	.	.	.	.	G	10.27	1.302596	0.23736	.	.	ENSG00000066629	ENST00000554386	.	.	.	5.18	-0.833	0.10782	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-11.5461	2.25	0.04041	0.2513:0.4057:0.1964:0.1466	.	.	.	.	X	70	.	.	G	+	1	0	EML1	99445461	0.462000	0.25791	0.763000	0.31416	0.916000	0.54674	-0.278000	0.08490	-0.044000	0.13491	-0.136000	0.14681	GGA	.	.		0.428	EML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413943.1	NM_001008707		T	100375708	G	T	100375708	2	4	282	1	0	0	0	0	0	0	0	1	5098	1103	39	1		1	EML1	14	100375708	Silent	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	3353151	100375708	6973832	988	41222										
EML1	2009	hgsc.bcm.edu	37	chr14	100376661	100376661	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tggagattcaagtggcaacaTcttagtatggggaaaaggta	13	4	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:100376661T>C	ENST00000262233.6	+	12	1461	c.1322T>C	c.(1321-1323)aTc>aCc	p.I441T	EML1_ENST00000334192.4_Missense_Mutation_p.I460T|EML1_ENST00000327921.9_Missense_Mutation_p.I429T	NM_004434.2	NP_004425.2	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1	441	Tandem atypical propeller in EMLs.				brain development (GO:0007420)|hematopoietic progenitor cell differentiation (GO:0002244)|microtubule cytoskeleton organization (GO:0000226)|mitotic spindle organization (GO:0007052)|neuroblast proliferation (GO:0007405)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	calcium ion binding (GO:0005509)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Melanoma(154;0.0879)|all_epithelial(191;0.216)				AGTGGCAACATCTTAGTATGG	0.358																																					p.I460T		Atlas-SNP	.											.	EML1	97	.	0			c.T1379C						.						93	90	91					14																	100376661		2203	4300	6503	SO:0001583	missense	2009	exon13			GCAACATCTTAGT	AK023861	CCDS32154.1, CCDS32155.1	14q32	2013-01-10		2002-02-15		ENSG00000066629		"WD repeat domain containing"	3330	protein-coding gene	gene with protein product		602033		EMAPL		9226380, 10521658	Standard	XM_005267397		Approved	EMAP, HuEMAP, ELP79	uc001ygr.3	O00423		ENST00000262233.6:c.1322T>C	chr14.hg19:g.100376661T>C	ENSP00000262233:p.Ile441Thr	121.0	0.0		74.0	4.0	NM_001008707	Q86U15|Q8N536|Q8N5C4|Q8WWL6	Missense_Mutation	SNP	ENST00000262233.6	hg19	CCDS32155.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.554824	0.86231	.	.	ENSG00000066629	ENST00000327921;ENST00000262233;ENST00000334192;ENST00000542138	T;T;T	0.52754	0.65;0.65;0.65	5.24	5.24	0.73138	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);	0.047715	0.85682	D	0.000000	T	0.70762	0.3261	M	0.89601	3.045	0.80722	D	1	P;P;D;P	0.55800	0.852;0.922;0.973;0.77	P;P;P;B	0.58660	0.635;0.824;0.843;0.432	T	0.78630	-0.2129	10	0.87932	D	0	-29.9624	15.149	0.72681	0.0:0.0:0.0:1.0	.	429;441;460;460	F8W717;O00423;O00423-3;B3KXA3	.;EMAL1_HUMAN;.;.	T	429;441;460;460	ENSP00000327384:I429T;ENSP00000262233:I441T;ENSP00000334314:I460T	ENSP00000262233:I441T	I	+	2	0	EML1	99446414	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.868000	0.87116	1.979000	0.57680	0.533000	0.62120	ATC	.	.		0.358	EML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413943.1	NM_001008707		C	100376661	T	C	100376661	3	2	282	1	0	0	0	0	1	0	0	0	5098	1435	50	2	1429	2	EML1	14	100376661	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	953	100376661	6972879	989	41223										
DYNC1H1	1778	hgsc.bcm.edu	37	chr14	102514166	102514166	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tggcccaggtgtggacatgaTcagtaaaatgctgaagatgc	13	7	1	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:102514166T>C	ENST00000360184.4	+	73	13183	c.13019T>C	c.(13018-13020)aTc>aCc	p.I4340T	RP11-1017G21.4_ENST00000553701.1_RNA|RP11-1017G21.4_ENST00000557242.1_RNA	NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	4340					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						GTGGACATGATCAGTAAAATG	0.567																																					p.I4340T		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.T13019C						.						124	95	105					14																	102514166		2203	4300	6503	SO:0001583	missense	1778	exon73			ACATGATCAGTAA	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"Cytoplasmic dyneins"	2961	protein-coding gene	gene with protein product		600112	"dynein, cytoplasmic, heavy polypeptide 1"	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.13019T>C	chr14.hg19:g.102514166T>C	ENSP00000348965:p.Ile4340Thr	89.0	0.0		66.0	4.0	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	hg19	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	T	16.44	3.124716	0.56613	.	.	ENSG00000197102	ENST00000360184	T	0.10288	2.89	5.37	5.37	0.77165	Dynein heavy chain (1);	0.097569	0.64402	D	0.000001	T	0.18215	0.0437	M	0.78049	2.395	0.58432	D	0.999999	B	0.14438	0.01	B	0.14023	0.01	T	0.01512	-1.1336	10	0.54805	T	0.06	.	15.3709	0.74564	0.0:0.0:0.0:1.0	.	4340	Q14204	DYHC1_HUMAN	T	4340	ENSP00000348965:I4340T	ENSP00000348965:I4340T	I	+	2	0	DYNC1H1	101583919	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	7.968000	0.87980	2.031000	0.59945	0.533000	0.62120	ATC	.	.		0.567	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		C	102514166	T	C	102514166	3	2	282	1	0	0	0	0	1	0	0	0	4843	1435	50	2	13309	2	DYNC1H1	14	102514166	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2137505	102514166	4835374	990	41224										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105407396	105407396	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caaggcagctctgggaacagTcacctggtattttgtaagtg	12	8	2	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:105407396T>C	ENST00000333244.5	-	7	14511	c.14392A>G	c.(14392-14394)Act>Gct	p.T4798A	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4798						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				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)			CTGGGAACAGTCACCTGGTAT	0.502																																					p.T4798A		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A14392G						.						84	87	86					14																	105407396		1943	4139	6082	SO:0001583	missense	113146	exon7			GAACAGTCACCTG	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.14392A>G	chr14.hg19:g.105407396T>C	ENSP00000353114:p.Thr4798Ala	171.0	0.0		112.0	5.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	hg19	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	T	3.473	-0.107529	0.06924	.	.	ENSG00000185567	ENST00000333244	T	0.04917	3.53	3.95	-0.848	0.10727	.	.	.	.	.	T	0.03695	0.0105	L	0.29908	0.895	0.09310	N	1	B	0.25312	0.123	B	0.22152	0.038	T	0.48019	-0.9071	9	0.09843	T	0.71	.	4.5371	0.12038	0.0:0.1387:0.358:0.5032	.	4798	Q8IVF2	AHNK2_HUMAN	A	4798	ENSP00000353114:T4798A	ENSP00000353114:T4798A	T	-	1	0	AHNAK2	104478441	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-1.085000	0.03390	-0.394000	0.07727	0.383000	0.25322	ACT	.	.		0.502	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		C	105407396	T	C	105407396	3	2	282	1	0	0	0	0	1	0	0	0	415	1667	58	2	2999	2	AHNAK2	14	105407396	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2893230	105407396	1942144	991	41225										
MKRN3	7681	hgsc.bcm.edu	37	chr15	23811295	23811295	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cgctattcgcacgacctttcTggtcggaagatggccactga	11	12	1	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:23811295T>C	ENST00000314520.3	+	1	842	c.366T>C	c.(364-366)tcT>tcC	p.S122S	MKRN3_ENST00000564592.1_Intron|RP11-73C9.1_ENST00000563044.1_RNA|MKRN3_ENST00000568252.1_Intron	NM_005664.3	NP_005655.1	Q13064	MKRN3_HUMAN	makorin ring finger protein 3	122					protein ubiquitination (GO:0016567)	ribonucleoprotein complex (GO:0030529)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(33)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		all_cancers(20;8.44e-25)|all_epithelial(15;3.69e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000353)|Colorectal(260;0.14)		all cancers(64;3.02e-06)|Epithelial(43;1.94e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0012)		ACGACCTTTCTGGTCGGAAGA	0.602																																					p.S122S		Atlas-SNP	.											.	MKRN3	155	.	0			c.T366C						.						55	57	56					15																	23811295		2203	4300	6503	SO:0001819	synonymous_variant	7681	exon1			CCTTTCTGGTCGG	U19107	CCDS10013.1	15q11-q13	2013-01-09	2008-08-13		ENSG00000179455	ENSG00000179455		"RING-type (C3HC4) zinc fingers"	7114	protein-coding gene	gene with protein product	"zinc finger protein 127"	603856		ZNF127, D15S9		10196367	Standard	NM_005664		Approved	RNF63, ZFP127, MGC88288	uc001ywh.4	Q13064	OTTHUMG00000129160	ENST00000314520.3:c.366T>C	chr15.hg19:g.23811295T>C		151.0	0.0		100.0	4.0	NM_005664		Silent	SNP	ENST00000314520.3	hg19	CCDS10013.1																																																																																			.	.		0.602	MKRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251225.1	NM_005664		C	23811295	T	C	23811295	2	2	282	1	0	0	0	0	0	0	0	1	9617	1567	55	2		2	MKRN3	15	23811295	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10		23811295	78720097	992	41226										
HERC2	8924	hgsc.bcm.edu	37	chr15	28421641	28421641	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tccacactcaatctggcacaCcccctgtccatttagtctct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:28421641delC	ENST00000261609.7	-	63	9727	c.9619delG	c.(9619-9621)gtgfs	p.V3207fs		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		ATCTGGCACACCCCCTGTCCA	0.537																																					p.V3207fs		Atlas-INDEL	.											.	HERC2	501	.	0			c.9620delT						.						82	82	82					15																	28421641		2203	4300	6503	SO:0001589	frameshift_variant	8924	exon63			.	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.9619delG	chr15.hg19:g.28421641delC	ENSP00000261609:p.Val3207fs	283.0	0.0		231.0	15.0	NM_004667		Frame_Shift_Del	DEL	ENST00000261609.7	hg19	CCDS10021.1																																																																																			.	.		0.537	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		-	28421641	C	-	28421641	7	5	282	1	0	1	0	1	0	0	0	0	7067	507	18	0	5009	0	HERC2	15	28421641	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	4610346	28421641	74109751	993	41227										
APBA2	321	hgsc.bcm.edu	37	chr15	29393815	29393815	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccgacaggaaaccatgatggAccacgccttgcgtaccatct	9	14	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:29393815A>G	ENST00000558402.1	+	11	1951	c.1352A>G	c.(1351-1353)gAc>gGc	p.D451G	APBA2_ENST00000561069.1_Missense_Mutation_p.D451G|APBA2_ENST00000411764.1_Missense_Mutation_p.D439G|APBA2_ENST00000558330.1_Missense_Mutation_p.D439G|APBA2_ENST00000558259.1_Missense_Mutation_p.D451G			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	451	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				in utero embryonic development (GO:0001701)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|liver(2)|lung(33)|stomach(1)|urinary_tract(1)	59		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		ACCATGATGGACCACGCCTTG	0.572																																					p.D451G		Atlas-SNP	.											.	APBA2	132	.	0			c.A1352G						.						97	67	77					15																	29393815		2203	4300	6503	SO:0001583	missense	321	exon9			TGATGGACCACGC	AB014719	CCDS10022.1, CCDS45197.1	15q11-q12	2008-07-18	2008-07-18		ENSG00000034053	ENSG00000034053			579	protein-coding gene	gene with protein product		602712	"X11-like", "amyloid beta (A4) precursor protein-binding, family A, member 2 (X11-like)"	X11L, MINT2		8955346	Standard	NM_005503		Approved	D15S1518E, LIN-10, MGC:14091, HsT16821	uc001zck.3	Q99767	OTTHUMG00000129255	ENST00000558402.1:c.1352A>G	chr15.hg19:g.29393815A>G	ENSP00000453293:p.Asp451Gly	182.0	0.0		130.0	6.0	NM_005503	E9PGI4|O60571|Q5XKC0	Missense_Mutation	SNP	ENST00000558402.1	hg19	CCDS10022.1	.	.	.	.	.	.	.	.	.	.	A	23.6	4.437972	0.83885	.	.	ENSG00000034053	ENST00000411764;ENST00000219865;ENST00000382938	T	0.56776	0.44	4.27	4.27	0.50696	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.054268	0.64402	D	0.000001	T	0.73048	0.3537	M	0.83483	2.645	0.80722	D	1	D;D;D;D	0.89917	0.998;0.998;1.0;0.973	D;D;D;D	0.97110	0.978;0.988;1.0;0.95	T	0.78097	-0.2337	10	0.87932	D	0	.	13.0159	0.58757	1.0:0.0:0.0:0.0	.	439;143;439;451	Q5XKC0;Q6ZVB1;E9PGI4;Q99767	.;.;.;APBA2_HUMAN	G	439;451;143	ENSP00000409312:D439G	ENSP00000219865:D451G	D	+	2	0	APBA2	27181107	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.853000	0.92222	1.916000	0.55485	0.533000	0.62120	GAC	.	.		0.572	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503		G	29393815	A	G	29393815	3	3	282	1	0	0	0	0	1	0	0	0	757	275	10	2	1378	2	APBA2	15	29393815	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	972174	29393815	73137577	994	41228										
GREM1	26585	hgsc.bcm.edu	37	chr15	33022990	33022990	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaagggtcccaaggtgccatCcccccgccagacaaggccca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:33022990delC	ENST00000300177.4	+	2	288	c.99delC	c.(97-99)atcfs	p.I33fs	GREM1_ENST00000560677.1_Frame_Shift_Del_p.I33fs|GREM1_ENST00000560830.1_Frame_Shift_Del_p.I33fs|GREM1_ENST00000322805.4_Frame_Shift_Del_p.I33fs	NM_001191322.1|NM_001191323.1|NM_013372.6	NP_001178251.1|NP_001178252.1|NP_037504.1	O60565	GREM1_HUMAN	gremlin 1, DAN family BMP antagonist	33					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell morphogenesis (GO:0000902)|collagen fibril organization (GO:0030199)|determination of dorsal identity (GO:0048263)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of bone mineralization (GO:0030502)|negative regulation of bone mineralization involved in bone maturation (GO:1900158)|negative regulation of bone remodeling (GO:0046851)|negative regulation of bone trabecula formation (GO:1900155)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of osteoclast proliferation (GO:0090291)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cell proliferation (GO:0008284)|positive regulation of peptidyl-tyrosine autophosphorylation (GO:1900086)|positive regulation of receptor activity (GO:2000273)|positive regulation of receptor internalization (GO:0002092)|positive regulation of telomerase activity (GO:0051973)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|regulation of epithelial to mesenchymal transition (GO:0010717)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	BMP binding (GO:0036122)|morphogen activity (GO:0016015)|receptor agonist activity (GO:0048018)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(1)|endometrium(1)|large_intestine(1)|lung(6)|prostate(1)	10		all_lung(180;1.49e-09)		all cancers(64;2.97e-18)|Epithelial(43;3.15e-12)|GBM - Glioblastoma multiforme(186;2.32e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0107)		AAGGTGCCATCCCCCCGCCAG	0.662																																					p.I33fs		Atlas-INDEL	.											.	GREM1	18	.	0			c.98delT						.						27	31	30					15																	33022990		2199	4296	6495	SO:0001589	frameshift_variant	26585	exon2			.		CCDS10029.1, CCDS53927.1	15q13.3	2014-02-07	2013-02-26	2004-05-07	ENSG00000166923	ENSG00000166923			2001	protein-coding gene	gene with protein product		603054	"cysteine knot superfamily 1, BMP antagonist 1", "gremlin 1, cysteine knot superfamily, homolog (Xenopus laevis)", "gremlin 1", "colorectal adenoma and carcinoma 1"	CKTSF1B1, CRAC1		9660951, 10026205, 22561515	Standard	NM_013372		Approved	DRM, gremlin, DAND2, HMPS	uc001zhe.2	O60565	OTTHUMG00000129319	ENST00000300177.4:c.99delC	chr15.hg19:g.33022990delC	ENSP00000300177:p.Ile33fs	143.0	0.0		114.0	11.0	NM_013372	Q52LV3|Q8N914|Q8N936	Frame_Shift_Del	DEL	ENST00000300177.4	hg19	CCDS10029.1																																																																																			.	.		0.662	GREM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251455.2	NM_013372		-	33022990	C	-	33022990	7	5	282	1	0	1	0	1	0	0	0	0	6770	845	30	0	101	0	GREM1	15	33022990	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	3629175	33022990	69508402	995	41229										
CASC5	57082	hgsc.bcm.edu	37	chr15	40913467	40913467	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atcttacctgcaacaggtaaTttttctgaaatagaaaatca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:40913467delT	ENST00000346991.5	+	11	1473	c.1083delT	c.(1081-1083)aatfs	p.N361fs	CASC5_ENST00000527044.1_3'UTR|CASC5_ENST00000399668.2_Frame_Shift_Del_p.N335fs			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	361	Interaction with BUB1 and BUB1B.				acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		CAACAGGTAATTTTTCTGAAA	0.328																																					p.N361fs		Atlas-INDEL	.											CASC5_ENST00000346991,colon,carcinoma,0,2	CASC5	269	.	0			c.1082delA						.						59	56	57					15																	40913467		1823	4082	5905	SO:0001589	frameshift_variant	57082	exon11			.	AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	24054	protein-coding gene	gene with protein product	"cancer/testis antigen 29", "kinetochore null 1 homolog (C. elegans)", "blinkin, bub-linking kinetochore protein", "protein phosphatase 1, regulatory subunit 55"	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.1083delT	chr15.hg19:g.40913467delT	ENSP00000335463:p.Asn361fs	175.0	0.0		137.0	10.0	NM_170589	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Frame_Shift_Del	DEL	ENST00000346991.5	hg19	CCDS42023.1																																																																																			.	.		0.328	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508		-	40913467	T	-	40913467	7	5	282	1	0	1	0	1	0	0	0	0	2665	1490	52	0	1121	0	CASC5	15	40913467	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	7890477	40913467	61617925	996	41230										
CASC5	57082	hgsc.bcm.edu	37	chr15	40920324	40920324	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agtgctaacagtgtattgatAaaaaacctgagcaggacccc					rs200029926	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:40920324delA	ENST00000346991.5	+	12	5901	c.5511delA	c.(5509-5511)atafs	p.I1837fs	CASC5_ENST00000399668.2_Frame_Shift_Del_p.I1811fs			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	1837	Necessary for kinetochore localization and for interaction with NSL1 and DSN1.				acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		GTGTATTGATAAAAAACCTGA	0.388																																					p.I1837fs		Atlas-INDEL	.											.	CASC5	269	.	0			c.5510delT						.						88	90	90					15																	40920324		1833	4084	5917	SO:0001589	frameshift_variant	57082	exon12			.	AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	24054	protein-coding gene	gene with protein product	"cancer/testis antigen 29", "kinetochore null 1 homolog (C. elegans)", "blinkin, bub-linking kinetochore protein", "protein phosphatase 1, regulatory subunit 55"	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.5511delA	chr15.hg19:g.40920324delA	ENSP00000335463:p.Ile1837fs	272.0	0.0		172.0	11.0	NM_170589	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Frame_Shift_Del	DEL	ENST00000346991.5	hg19	CCDS42023.1																																																																																			.	.		0.388	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508		-	40920324	A	-	40920324	7	5	282	1	0	1	0	1	0	0	0	0	2665	352	13	0	5553	0	CASC5	15	40920324	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	6857	40920324	61611068	997	41231										
LTK	4058	hgsc.bcm.edu	37	chr15	41805238	41805238	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggcgctgactttcgggtcccGggggctgggacttgccagcg	18	12	0	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:41805238G>T	ENST00000263800.6	-	2	220	c.124C>A	c.(124-126)Cgg>Agg	p.R42R	LTK_ENST00000453182.2_Silent_p.R42R|LTK_ENST00000355166.5_Silent_p.R42R|LTK_ENST00000561619.1_Intron	NM_002344.5	NP_002335.2	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase	42			R -> Q (in dbSNP:rs2305030). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:7685902}.		cell proliferation (GO:0008283)|cellular response to retinoic acid (GO:0071300)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of neuron projection development (GO:0010976)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(16)|skin(3)|urinary_tract(1)	26		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		TTCGGGTCCCGGGGGCTGGGA	0.632										TSP Lung(18;0.14)																											p.R42R		Atlas-SNP	.											.	LTK	117	.	0			c.C124A						.						19	24	22					15																	41805238		2197	4292	6489	SO:0001819	synonymous_variant	4058	exon2			GGTCCCGGGGGCT	D16105	CCDS10077.1, CCDS10078.1, CCDS45237.1	15q15.1-q21.1	2009-07-10	2008-01-23		ENSG00000062524	ENSG00000062524	2.7.10.1		6721	protein-coding gene	gene with protein product		151520	"leukocyte tyrosine kinase"			2320375	Standard	NM_206961		Approved	TYK1	uc001zoa.3	P29376	OTTHUMG00000130339	ENST00000263800.6:c.124C>A	chr15.hg19:g.41805238G>T		64.0	0.0		70.0	4.0	NM_001135685	A6NNJ8|B4DL89|E9PFX4	Silent	SNP	ENST00000263800.6	hg19	CCDS10077.1																																																																																			.	.		0.632	LTK-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252690.2			T	41805238	G	T	41805238	2	4	282	1	0	0	0	0	0	0	0	1	9089	1115	39	1		1	LTK	15	41805238	Silent	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	884914	41805238	60726154	998	41232										
RPAP1	26015	hgsc.bcm.edu	37	chr15	41819194	41819194	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tagactaggggtaggccctgCccccacaggagaccaactgg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:41819194delC	ENST00000304330.4	-	14	1935	c.1819delG	c.(1819-1821)gcafs	p.A607fs	RPAP1_ENST00000561603.1_Frame_Shift_Del_p.A607fs|RPAP1_ENST00000568413.1_5'Flank	NM_015540.2	NP_056355.2	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	607						nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	45		all_cancers(109;6.59e-20)|all_epithelial(112;7.67e-17)|Lung NSC(122;5.34e-11)|all_lung(180;4.17e-10)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		OV - Ovarian serous cystadenocarcinoma(18;2.84e-17)|GBM - Glioblastoma multiforme(113;1.68e-06)|Colorectal(105;0.0163)|BRCA - Breast invasive adenocarcinoma(123;0.117)		GTAGGCCCTGCCCCCACAGGA	0.557																																					p.A607fs		Atlas-INDEL	.											.	RPAP1	111	.	0			c.1820delC						.						89	90	89					15																	41819194		2203	4300	6503	SO:0001589	frameshift_variant	26015	exon14			.	BC000246	CCDS10079.1	15q14	2004-03-16			ENSG00000103932	ENSG00000103932			24567	protein-coding gene	gene with protein product		611475				10718198	Standard	XM_005254297		Approved	DKFZP727M111, KIAA1403, MGC858, FLJ12732	uc001zod.3	Q9BWH6	OTTHUMG00000130342	ENST00000304330.4:c.1819delG	chr15.hg19:g.41819194delC	ENSP00000306123:p.Ala607fs	180.0	0.0		151.0	10.0	NM_015540	Q9H9I2|Q9NSQ5|Q9P2E4|Q9UFS7	Frame_Shift_Del	DEL	ENST00000304330.4	hg19	CCDS10079.1																																																																																			.	.		0.557	RPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252694.2	NM_015540		-	41819194	C	-	41819194	7	5	282	1	0	1	0	1	0	0	0	0	13556	739	26	0	2410	0	RPAP1	15	41819194	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	13956	41819194	60712198	999	41233										
MGA	23269	hgsc.bcm.edu	37	chr15	41988795	41988795	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggcaaggaatcagaaaatggTcttagaaaacattcaccaga	9	7	3	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:41988795T>C	ENST00000570161.1	+	2	1587	c.1587T>C	c.(1585-1587)ggT>ggC	p.G529G	MGA_ENST00000219905.7_Silent_p.G529G|MGA_ENST00000389936.4_Silent_p.G529G|MGA_ENST00000545763.1_Silent_p.G529G|MGA_ENST00000566586.1_Silent_p.G529G			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	Maltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	CAGAAAATGGTCTTAGAAAAC	0.378																																					p.G529G		Atlas-SNP	.											.	MGA	264	.	0			c.T1587C						.						73	65	67					15																	41988795		1843	4090	5933	SO:0001819	synonymous_variant	23269	exon3			AAATGGTCTTAGA	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.1587T>C	chr15.hg19:g.41988795T>C		131.0	0.0		84.0	4.0	NM_001080541	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000570161.1	hg19	CCDS55959.1																																																																																			.	.		0.378	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		C	41988795	T	C	41988795	2	2	282	1	0	0	0	0	0	0	0	1	9549	1654	58	2		2	MGA	15	41988795	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	169601	41988795	60542597	1000	41234										
MGA	23269	hgsc.bcm.edu	37	chr15	42035016	42035016	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cacctatgactgctatttctGacgtggaaactaaagaaact	7	9	1	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:42035016G>A	ENST00000570161.1	+	14	4858	c.4858G>A	c.(4858-4860)Gac>Aac	p.D1620N	MGA_ENST00000219905.7_Missense_Mutation_p.D1620N|MGA_ENST00000389936.4_Missense_Mutation_p.D1620N|MGA_ENST00000545763.1_Intron|MGA_ENST00000566586.1_Intron			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	Glucoamylase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TGCTATTTCTGACGTGGAAAC	0.453																																					p.D1620N		Atlas-SNP	.											.	MGA	264	.	0			c.G4858A						.						88	84	85					15																	42035016		1891	4122	6013	SO:0001583	missense	23269	exon15			ATTTCTGACGTGG	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.4858G>A	chr15.hg19:g.42035016G>A	ENSP00000457035:p.Asp1620Asn	70.0	0.0		48.0	20.0	NM_001164273	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	hg19	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	G	13.82	2.352171	0.41700	.	.	ENSG00000174197	ENST00000219905;ENST00000389936	D;D	0.84800	-1.9;-1.81	4.96	3.97	0.46021	.	1.710450	0.03356	N	0.196836	T	0.71693	0.3370	N	0.14661	0.345	0.80722	D	1	B;B	0.33694	0.421;0.421	B;B	0.27500	0.08;0.058	T	0.67833	-0.5568	10	0.25106	T	0.35	.	4.8545	0.13552	0.187:0.271:0.542:0.0	.	236;1620	B4DVS1;E7ENI0	.;.	N	1620	ENSP00000219905:D1620N;ENSP00000374586:D1620N	ENSP00000219905:D1620N	D	+	1	0	MGA	39822308	0.998000	0.40836	1.000000	0.80357	0.995000	0.86356	2.443000	0.44881	2.577000	0.86979	0.563000	0.77884	GAC	.	.		0.453	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		A	42035016	G	A	42035016	3	1	282	1	0	0	0	0	1	0	0	0	9549	1290	45	3	4912	3	MGA	15	42035016	Missense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	46221	42035016	60496376	1001	41235										
MGA	23269	hgsc.bcm.edu	37	chr15	42035364	42035364	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggagtccaccagtgagccagAgaccaggtaaggcctagatg	14	10	0	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:42035364A>G	ENST00000570161.1	+	14	5206	c.5206A>G	c.(5206-5208)Aga>Gga	p.R1736G	MGA_ENST00000219905.7_Missense_Mutation_p.R1736G|MGA_ENST00000389936.4_Missense_Mutation_p.R1736G|MGA_ENST00000545763.1_Intron|MGA_ENST00000566586.1_Intron			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	Glucoamylase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	AGTGAGCCAGAGACCAGGTAA	0.418																																					p.R1736G		Atlas-SNP	.											.	MGA	264	.	0			c.A5206G						.						58	56	56					15																	42035364		1917	4146	6063	SO:0001583	missense	23269	exon15			AGCCAGAGACCAG	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.5206A>G	chr15.hg19:g.42035364A>G	ENSP00000457035:p.Arg1736Gly	176.0	0.0		149.0	6.0	NM_001164273	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	hg19	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	A	17.47	3.398223	0.62177	.	.	ENSG00000174197	ENST00000219905;ENST00000389936	D;D	0.87179	-2.0;-2.22	4.9	4.9	0.64082	.	0.416111	0.20973	N	0.082347	D	0.83580	0.5285	N	0.19112	0.55	0.80722	D	1	P;P	0.52842	0.948;0.956	P;P	0.49528	0.614;0.468	D	0.86210	0.1624	10	0.72032	D	0.01	.	14.6863	0.69052	1.0:0.0:0.0:0.0	.	352;1736	B4DVS1;E7ENI0	.;.	G	1736	ENSP00000219905:R1736G;ENSP00000374586:R1736G	ENSP00000219905:R1736G	R	+	1	2	MGA	39822656	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.921000	0.70028	2.056000	0.61249	0.460000	0.39030	AGA	.	.		0.418	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		G	42035364	A	G	42035364	3	3	282	1	0	0	0	0	1	0	0	0	9549	296	11	2	5260	2	MGA	15	42035364	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	348	42035364	60496028	1002	41236										
MGA	23269	hgsc.bcm.edu	37	chr15	42054541	42054541	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaacctttgattctttccagAaaaaaagaccaggccacagg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:42054541delA	ENST00000570161.1	+	21	7725	c.7725delA	c.(7723-7725)agafs	p.R2575fs	MGA_ENST00000219905.7_Frame_Shift_Del_p.R2575fs|MGA_ENST00000389936.4_Frame_Shift_Del_p.R2536fs|MGA_ENST00000545763.1_Frame_Shift_Del_p.R2366fs|MGA_ENST00000566586.1_Frame_Shift_Del_p.R2366fs			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TTCTTTCCAGAAAAAAAGACC	0.423																																					p.R2575fs		Atlas-INDEL	.											.,1	MGA	264	.	0			c.7724delG						.						72	73	73					15																	42054541		1839	4074	5913	SO:0001589	frameshift_variant	23269	exon22			.	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.7725delA	chr15.hg19:g.42054541delA	ENSP00000457035:p.Arg2575fs	248.0	0.0		155.0	10.0	NM_001164273	Q0VAX6|Q75ME7|Q86UM5	Frame_Shift_Del	DEL	ENST00000570161.1	hg19	CCDS55959.1																																																																																			.	.		0.423	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		-	42054541	A	-	42054541	7	5	282	1	0	1	0	1	0	0	0	0	9549	243	9	0	7807	0	MGA	15	42054541	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	19177	42054541	60476851	1003	41237										
MAPKBP1	23005	hgsc.bcm.edu	37	chr15	42092080	42092080	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggcagaggacttgcctgtgaCccccgatcaggtttagttgc					rs367612663		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:42092080delC	ENST00000456763.2	+	3	370	c.174delC	c.(172-174)gacfs	p.D58fs	MAPKBP1_ENST00000507762.1_3'UTR|MAPKBP1_ENST00000457542.2_Frame_Shift_Del_p.D58fs|MAPKBP1_ENST00000221214.6_Frame_Shift_Del_p.D58fs|MAPKBP1_ENST00000514566.1_Frame_Shift_Del_p.D58fs|MAPKBP1_ENST00000260357.7_Intron	NM_001128608.1	NP_001122080.1	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein 1	58										breast(6)|central_nervous_system(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)		TTGCCTGTGACCCCCGATCAG	0.502																																					p.D58fs		Atlas-INDEL	.											.	MAPKBP1	120	.	0			c.173delA						.						169	146	154					15																	42092080		2203	4300	6503	SO:0001589	frameshift_variant	23005	exon3			.	AB011168	CCDS32201.1, CCDS45239.1, CCDS58359.1	15q15.1	2013-01-10	2008-01-30		ENSG00000137802	ENSG00000137802		"WD repeat domain containing"	29536	protein-coding gene	gene with protein product			"mitogen activated protein kinase binding protein 1"			9628581, 10471813	Standard	NM_014994		Approved	KIAA0596	uc001zok.4	O60336	OTTHUMG00000160227	ENST00000456763.2:c.174delC	chr15.hg19:g.42092080delC	ENSP00000393099:p.Asp58fs	254.0	0.0		158.0	14.0	NM_001128608	A6NM93|A8K8P9|Q14CB5|Q14CD8|Q49AJ8|Q5W9G9	Frame_Shift_Del	DEL	ENST00000456763.2	hg19	CCDS45239.1																																																																																			.	.		0.502	MAPKBP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359745.1	NM_014994		-	42092080	C	-	42092080	7	5	282	1	0	1	0	1	0	0	0	0	9301	506	18	0	180	0	MAPKBP1	15	42092080	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	37539	42092080	60439312	1004	41238										
SPTBN5	51332	hgsc.bcm.edu	37	chr15	42145939	42145939	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gctggcccagtcggcaggccTccgtctgtagccgtgccacc	13	17	1	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:42145939T>C	ENST00000320955.6	-	58	10048	c.9821A>G	c.(9820-9822)gAg>gGg	p.E3274G	RNA5SP393_ENST00000363423.1_RNA	NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	3274					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		TCGGCAGGCCTCCGTCTGTAG	0.672																																					p.E3239G		Atlas-SNP	.											.	SPTBN5	171	.	0			c.A9716G						.						25	30	28					15																	42145939		2013	4150	6163	SO:0001583	missense	51332	exon58			CAGGCCTCCGTCT	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"beta V spectrin"	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.9821A>G	chr15.hg19:g.42145939T>C	ENSP00000317790:p.Glu3274Gly	92.0	0.0		64.0	5.0	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	hg19		.	.	.	.	.	.	.	.	.	.	.	18.32	3.597766	0.66332	.	.	ENSG00000137877	ENST00000320955	T	0.51325	0.71	4.74	4.74	0.60224	.	0.086227	0.44285	D	0.000465	T	0.70937	0.3281	M	0.87547	2.89	0.37850	D	0.929361	D	0.89917	1.0	D	0.75484	0.986	T	0.78595	-0.2143	10	0.54805	T	0.06	.	13.1133	0.59285	0.0:0.0:0.0:1.0	.	3274	Q9NRC6	SPTN5_HUMAN	G	3274	ENSP00000317790:E3274G	ENSP00000317790:E3274G	E	-	2	0	SPTBN5	39933231	0.998000	0.40836	0.208000	0.23602	0.027000	0.11550	3.165000	0.50778	1.900000	0.55004	0.260000	0.18958	GAG	.	.		0.672	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642		C	42145939	T	C	42145939	3	2	282	1	0	0	0	0	1	0	0	0	15137	1551	54	2	1247	2	SPTBN5	15	42145939	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	53859	42145939	60385453	1005	41239										
PLA2G4D	283748	hgsc.bcm.edu	37	chr15	42377319	42377319	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgactttgttggtgatgaggTtttctgggcgatctgacctg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:42377319delT	ENST00000290472.3	-	6	540	c.446delA	c.(445-447)aacfs	p.N149fs		NM_178034.3	NP_828848.3	Q86XP0	PA24D_HUMAN	phospholipase A2, group IVD (cytosolic)	149					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(7)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(109;6.37e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.019)|Ovarian(310;0.143)|Colorectal(260;0.245)		OV - Ovarian serous cystadenocarcinoma(18;4.9e-17)|GBM - Glioblastoma multiforme(94;1.02e-06)		GGTGATGAGGTTTTCTGGGCG	0.592																																					p.N149fs		Atlas-INDEL	.											.	PLA2G4D	72	.	0			c.447delC						.						132	120	124					15																	42377319		2203	4299	6502	SO:0001589	frameshift_variant	283748	exon6			.	AB090876	CCDS32203.1	15q14	2008-09-19				ENSG00000159337	3.1.1.4		30038	protein-coding gene	gene with protein product		612864				14709560	Standard	NM_178034		Approved	cPLA2delta	uc001zox.3	Q86XP0		ENST00000290472.3:c.446delA	chr15.hg19:g.42377319delT	ENSP00000290472:p.Asn149fs	137.0	0.0		116.0	12.0	NM_178034	Q8N176	Frame_Shift_Del	DEL	ENST00000290472.3	hg19	CCDS32203.1																																																																																			.	.		0.592	PLA2G4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419317.1	NM_178034		-	42377319	T	-	42377319	7	5	282	1	0	1	0	1	0	0	0	0	12013	1725	60	0	2070	0	PLA2G4D	15	42377319	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	231380	42377319	60154073	1006	41240										
VPS39	23339	hgsc.bcm.edu	37	chr15	42480005	42480005	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agaaatagagctgcagcttcTtttttactgccacacacatc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:42480005delT	ENST00000348544.4	-	7	424	c.425delA	c.(424-426)aagfs	p.K143fs	VPS39_ENST00000318006.5_Frame_Shift_Del_p.K132fs			Q96JC1	VPS39_HUMAN	vacuolar protein sorting 39 homolog (S. cerevisiae)	143	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	endosome (GO:0005768)|HOPS complex (GO:0030897)|lysosomal membrane (GO:0005765)	small GTPase regulator activity (GO:0005083)			breast(2)|kidney(5)|large_intestine(4)|lung(8)|ovary(1)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		all_cancers(109;6.78e-16)|all_epithelial(112;1.81e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;3.05e-06)		CTGCAGCTTCTTTTTTACTGC	0.493																																					p.K131fs		Atlas-INDEL	.											.	VPS39	53	.	0			c.393delG						.						214	213	213					15																	42480005		2203	4299	6502	SO:0001589	frameshift_variant	23339	exon6			.	AF280814	CCDS10083.1, CCDS73710.1	15q14	2008-02-05	2006-12-19		ENSG00000166887	ENSG00000166887			20593	protein-coding gene	gene with protein product		612188	"vacuolar protein sorting 39 (yeast)"			11448994	Standard	XM_005254259		Approved	KIAA0770, VAM6	uc001zpc.3	Q96JC1	OTTHUMG00000130467	ENST00000348544.4:c.425delA	chr15.hg19:g.42480005delT	ENSP00000335193:p.Lys143fs	239.0	0.0		162.0	11.0	NM_015289	O94869|Q71SQ6|Q7Z3V3|Q96B93|Q96RM0	Frame_Shift_Del	DEL	ENST00000348544.4	hg19	CCDS10083.1																																																																																			.	.		0.493	VPS39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000420472.1	NM_015289		-	42480005	T	-	42480005	7	5	282	1	0	1	0	1	0	0	0	0	17224	1609	56	0	2315	0	VPS39	15	42480005	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	102686	42480005	60051387	1007	41241										
UBR1	197131	hgsc.bcm.edu	37	chr15	43363019	43363019	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tggagttcaggaggcagttcTttttcctcttcccatatagt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:43363019delT	ENST00000290650.4	-	5	711	c.633delA	c.(631-633)aaafs	p.K211fs	UBR1_ENST00000382177.2_Frame_Shift_Del_p.K211fs	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	211					cellular response to leucine (GO:0071233)|negative regulation of TOR signaling (GO:0032007)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|proteasome complex (GO:0000502)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		GAGGCAGTTCTTTTTCCTCTT	0.378																																					p.E212fs		Atlas-INDEL	.											UBR1,NS,carcinoma,0,1	UBR1	124	.	0			c.634delG						.						180	171	174					15																	43363019		2203	4299	6502	SO:0001589	frameshift_variant	197131	exon5			.		CCDS10091.1	15q13	2008-06-23			ENSG00000159459	ENSG00000159459		"Ubiquitin protein ligase E3 component n-recognins"	16808	protein-coding gene	gene with protein product		605981				9653112	Standard	NM_174916		Approved		uc001zqq.3	Q8IWV7	OTTHUMG00000130702	ENST00000290650.4:c.633delA	chr15.hg19:g.43363019delT	ENSP00000290650:p.Lys211fs	121.0	0.0		130.0	10.0	NM_174916	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Frame_Shift_Del	DEL	ENST00000290650.4	hg19	CCDS10091.1																																																																																			.	.		0.378	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916		-	43363019	T	-	43363019	7	5	282	1	0	1	0	1	0	0	0	0	16916	1606	56	0	4788	0	UBR1	15	43363019	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	883014	43363019	59168373	1008	41242										
TMEM62	80021	hgsc.bcm.edu	37	chr15	43461843	43461843	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccagctcaccattctcattaTttttagatatcgaggatacc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:43461843delT	ENST00000260403.2	+	11	1628	c.1349delT	c.(1348-1350)attfs	p.I450fs	TMEM62_ENST00000569369.1_3'UTR	NM_024956.3	NP_079232.3	Q0P6H9	TMM62_HUMAN	transmembrane protein 62	450						integral component of membrane (GO:0016021)				breast(1)|cervix(1)|endometrium(3)|large_intestine(3)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	18		all_cancers(109;1.16e-10)|all_epithelial(112;2.01e-09)|Lung NSC(122;8.91e-07)|all_lung(180;8.8e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;4.23e-07)		ATTCTCATTATTTTTAGATAT	0.388																																					p.I450fs		Atlas-INDEL	.											.	TMEM62	47	.	0			c.1348delA						.						127	125	126					15																	43461843		2203	4299	6502	SO:0001589	frameshift_variant	80021	exon11			.	BC009981	CCDS32210.1	15q15.2	2014-09-11			ENSG00000137842	ENSG00000137842			26269	protein-coding gene	gene with protein product							Standard	NM_024956		Approved	FLJ23375	uc001zqr.3	Q0P6H9	OTTHUMG00000176485	ENST00000260403.2:c.1349delT	chr15.hg19:g.43461843delT	ENSP00000260403:p.Ile450fs	186.0	0.0		163.0	12.0	NM_024956	Q6I9Y5|Q9H5J6	Frame_Shift_Del	DEL	ENST00000260403.2	hg19	CCDS32210.1																																																																																			.	.		0.388	TMEM62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432227.1	NM_024956		-	43461843	T	-	43461843	7	5	282	1	0	1	0	1	0	0	0	0	16204	1493	52	0	1391	0	TMEM62	15	43461843	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	98824	43461843	59069549	1009	41243										
TUBGCP4	27229	hgsc.bcm.edu	37	chr15	43668306	43668306	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cttcctgcaggtatcgcaggActtccctttcctccacccca	6	18	0	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:43668306A>G	ENST00000260383.7	+	2	343	c.89A>G	c.(88-90)gAc>gGc	p.D30G	TUBGCP4_ENST00000570081.1_3'UTR|TUBGCP4_ENST00000399460.3_5'Flank|TUBGCP4_ENST00000564079.1_Missense_Mutation_p.D30G			Q9UGJ1	GCP4_HUMAN	tubulin, gamma complex associated protein 4	30					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|protein complex assembly (GO:0006461)	centrosome (GO:0005813)|cytosol (GO:0005829)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|spindle pole (GO:0000922)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(4)|prostate(2)|upper_aerodigestive_tract(2)	21		all_cancers(109;1.27e-10)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.72e-06)|all_lung(180;1.59e-05)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;3.53e-07)		GTATCGCAGGACTTCCCTTTC	0.517											OREG0023088	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D30G		Atlas-SNP	.											.	TUBGCP4	48	.	0			c.A89G						.						148	156	153					15																	43668306		2026	4179	6205	SO:0001583	missense	27229	exon2			CGCAGGACTTCCC	AJ249677	CCDS42030.1, CCDS66745.1	15q15.3	2014-08-12			ENSG00000137822	ENSG00000137822			16691	protein-coding gene	gene with protein product		609610				10562286	Standard	NM_001286414		Approved	76P, FLJ14797	uc001zrn.3	Q9UGJ1	OTTHUMG00000176647	ENST00000260383.7:c.89A>G	chr15.hg19:g.43668306A>G	ENSP00000260383:p.Asp30Gly	142.0	0.0	918	97.0	4.0	NM_014444	B3KNK6|Q969X3|Q9NVF0	Missense_Mutation	SNP	ENST00000260383.7	hg19		.	.	.	.	.	.	.	.	.	.	A	17.57	3.421859	0.62622	.	.	ENSG00000137822	ENST00000260383	T	0.07688	3.17	5.64	5.64	0.86602	.	0.087261	0.85682	D	0.000000	T	0.11024	0.0269	L	0.59436	1.845	0.80722	D	1	B;B	0.14805	0.011;0.008	B;B	0.16289	0.015;0.009	T	0.11108	-1.0601	10	0.17832	T	0.49	-20.0	15.3291	0.74193	1.0:0.0:0.0:0.0	.	30;30	Q9UGJ1;Q9UGJ1-2	GCP4_HUMAN;.	G	30	ENSP00000260383:D30G	ENSP00000260383:D30G	D	+	2	0	TUBGCP4	41455598	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	8.237000	0.89807	2.265000	0.75225	0.482000	0.46254	GAC	.	.		0.517	TUBGCP4-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000432970.1	NM_014444		G	43668306	A	G	43668306	3	3	282	1	0	0	0	0	1	0	0	0	16783	275	10	2	95	2	TUBGCP4	15	43668306	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	206463	43668306	58863086	1010	41244										
MFAP1	4236	hgsc.bcm.edu	37	chr15	44109627	44109627	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acataacgctttaccttcacTttttccattgaaatctcacc					rs373137037		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:44109627delT	ENST00000267812.3	-	2	331	c.99delA	c.(97-99)aaafs	p.K33fs		NM_005926.2	NP_005917.2	P55081	MFAP1_HUMAN	microfibrillar-associated protein 1	33					extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|microfibril (GO:0001527)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|kidney(1)|lung(6)|skin(2)|upper_aerodigestive_tract(3)	15		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.33e-07)		TTACCTTCACTTTTTCCATTG	0.443																																					p.V34X		Atlas-INDEL	.											.	MFAP1	36	.	0			c.100delG						.						92	87	89					15																	44109627		2198	4298	6496	SO:0001589	frameshift_variant	4236	exon2			.		CCDS10105.1	15q15-q21	2014-05-20			ENSG00000140259	ENSG00000140259			7032	protein-coding gene	gene with protein product		600215				7835894	Standard	NM_005926		Approved		uc001zth.1	P55081	OTTHUMG00000060145	ENST00000267812.3:c.99delA	chr15.hg19:g.44109627delT	ENSP00000267812:p.Lys33fs	482.0	0.0		378.0	23.0	NM_005926	Q86TG6	Frame_Shift_Del	DEL	ENST00000267812.3	hg19	CCDS10105.1																																																																																			.	.		0.443	MFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133491.2	NM_005926		-	44109627	T	-	44109627	7	5	282	1	0	1	0	1	0	0	0	0	9522	1606	56	0	1252	0	MFAP1	15	44109627	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	441321	44109627	58421765	1011	41245										
DUOX1	53905	hgsc.bcm.edu	37	chr15	45446158	45446158	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cttccacacaggtctgagctCccccagaagtattactggtg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:45446158delC	ENST00000321429.4	+	28	3941	c.3534delC	c.(3532-3534)ctcfs	p.L1178fs	DUOX1_ENST00000389037.3_Frame_Shift_Del_p.L1178fs|CTD-2651B20.1_ENST00000558039.1_lincRNA|DUOX1_ENST00000561166.1_Frame_Shift_Del_p.L824fs|DUOX1_ENST00000559221.1_3'UTR	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	1178	Ferric oxidoreductase.|Interaction with TXNDC11. {ECO:0000250}.		L -> F (in dbSNP:rs2458236). {ECO:0000269|PubMed:11514595}.		cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide biosynthetic process (GO:0050665)|hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|superoxide anion generation (GO:0042554)|thyroid hormone generation (GO:0006590)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|NADP binding (GO:0050661)|peroxidase activity (GO:0004601)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|lung(16)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)	57		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		GGTCTGAGCTCCCCCAGAAGT	0.493																																					p.L1178fs		Atlas-INDEL	.											.	DUOX1	125	.	0			c.3533delT						.						97	88	91					15																	45446158		2198	4298	6496	SO:0001589	frameshift_variant	53905	exon28			.	AF213465	CCDS32221.1	15q21	2013-01-10				ENSG00000137857		"EF-hand domain containing"	3062	protein-coding gene	gene with protein product	"NADPH thyroid oxidase 1", "flavoprotein NADPH oxidase", "nicotinamide adenine dinucleotide phosphate oxidase"	606758				10806195	Standard	XM_005254463		Approved	NOXEF1, THOX1, LNOX1	uc001zut.1	Q9NRD9		ENST00000321429.4:c.3534delC	chr15.hg19:g.45446158delC	ENSP00000317997:p.Leu1178fs	182.0	0.0		152.0	11.0	NM_017434	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Frame_Shift_Del	DEL	ENST00000321429.4	hg19	CCDS32221.1																																																																																			.	.		0.493	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434		-	45446158	C	-	45446158	7	5	282	1	0	1	0	1	0	0	0	0	4802	842	30	0	3636	0	DUOX1	15	45446158	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1336531	45446158	57085234	1012	41246										
SEMA6D	80031	hgsc.bcm.edu	37	chr15	48056088	48056088	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cgcatatgtaaaaacgacatGggtggttcccagcgggtcct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:48056088delG	ENST00000316364.5	+	10	1228	c.789delG	c.(787-789)atgfs	p.M263fs	SEMA6D_ENST00000389428.3_Frame_Shift_Del_p.M263fs|SEMA6D_ENST00000558014.1_Frame_Shift_Del_p.M263fs|SEMA6D_ENST00000558816.1_Frame_Shift_Del_p.M263fs|SEMA6D_ENST00000358066.4_Frame_Shift_Del_p.M263fs|SEMA6D_ENST00000389425.3_Frame_Shift_Del_p.M263fs|SEMA6D_ENST00000355997.3_Frame_Shift_Del_p.M263fs|SEMA6D_ENST00000389433.2_Frame_Shift_Del_p.M263fs|SEMA6D_ENST00000389432.2_Frame_Shift_Del_p.M263fs|SEMA6D_ENST00000537942.1_Frame_Shift_Del_p.M263fs|SEMA6D_ENST00000536845.2_Frame_Shift_Del_p.M263fs|SEMA6D_ENST00000354744.4_Frame_Shift_Del_p.M263fs	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	263	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		AAAACGACATGGGTGGTTCCC	0.488																																					p.M263fs		Atlas-INDEL	.											.	SEMA6D	322	.	0			c.788delT						.						152	145	148					15																	48056088		2198	4297	6495	SO:0001589	frameshift_variant	80031	exon10			.	AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"Semaphorins"	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.789delG	chr15.hg19:g.48056088delG	ENSP00000324857:p.Met263fs	301.0	0.0		193.0	12.0	NM_153617	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Frame_Shift_Del	DEL	ENST00000316364.5	hg19	CCDS32225.1																																																																																			.	.		0.488	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966		-	48056088	G	-	48056088	7	5	282	1	0	1	0	1	0	0	0	0	14057	1348	47	0	823	0	SEMA6D	15	48056088	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	2609930	48056088	54475304	1013	41247										
FBN1	2200	hgsc.bcm.edu	37	chr15	48748935	48748935	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctccattttcacagacccctGggatctcccggcactcatca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:48748935delG	ENST00000316623.5	-	44	5776	c.5321delC	c.(5320-5322)ccafs	p.P1774fs		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	1774	EGF-like 29; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		ACAGACCCCTGGGATCTCCCG	0.458																																					p.P1774fs		Atlas-INDEL	.											.	FBN1	310	.	0			c.5322delA						.						113	100	105					15																	48748935		2198	4296	6494	SO:0001589	frameshift_variant	2200	exon44			.	X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.5321delC	chr15.hg19:g.48748935delG	ENSP00000325527:p.Pro1774fs	205.0	0.0		157.0	11.0	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Frame_Shift_Del	DEL	ENST00000316623.5	hg19	CCDS32232.1																																																																																			.	.		0.458	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			-	48748935	G	-	48748935	7	5	282	1	0	1	0	1	0	0	0	0	5710	1348	47	0	3386	0	FBN1	15	48748935	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	692847	48748935	53782457	1014	41248										
CEP152	22995	hgsc.bcm.edu	37	chr15	49061255	49061255	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggccataattgattctttggTttttctgaggtatctgtttt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:49061255delT	ENST00000380950.2	-	14	1993	c.1806delA	c.(1804-1806)aaafs	p.K602fs	CEP152_ENST00000399334.3_Frame_Shift_Del_p.K602fs|CEP152_ENST00000325747.5_Frame_Shift_Del_p.K509fs|CEP152_ENST00000559398.1_5'UTR	NM_001194998.1|NM_014985.3	NP_001181927.1|NP_055800.2	O94986	CE152_HUMAN	centrosomal protein 152kDa	602					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)			breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		GATTCTTTGGTTTTTCTGAGG	0.284																																					p.P603fs		Atlas-INDEL	.											CEP152,caecum,carcinoma,0,1	CEP152	145	.	0			c.1807delC						.						92	87	89					15																	49061255		1787	4051	5838	SO:0001589	frameshift_variant	22995	exon14			.	AB020719	CCDS42033.1, CCDS58361.1	15q21.1	2014-02-20							29298	protein-coding gene	gene with protein product	"asterless"	613529	"microcephaly, primary autosomal recessive 4"	MCPH4		14654843, 21131973	Standard	NM_014985		Approved	KIAA0912, SCKL5	uc001zwz.3	O94986		ENST00000380950.2:c.1806delA	chr15.hg19:g.49061255delT	ENSP00000370337:p.Lys602fs	144.0	0.0		148.0	10.0	NM_014985	E7ER66|Q17RV1|Q6NTA0	Frame_Shift_Del	DEL	ENST00000380950.2	hg19	CCDS58361.1																																																																																			.	.		0.284	CEP152-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417365.1	NM_014985		-	49061255	T	-	49061255	7	5	282	1	0	1	0	1	0	0	0	0	3250	1722	60	0	3210	0	CEP152	15	49061255	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	312320	49061255	53470137	1015	41249										
SECISBP2L	9728	hgsc.bcm.edu	37	chr15	49304846	49304846	+	Splice_Site	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccaccagattttggtttaccTttttaagtgctgtgggtcgt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:49304846delT	ENST00000559471.1	-	12	1993	c.1730delA	c.(1729-1731)aag>ag	p.K577fs	SECISBP2L_ENST00000261847.3_Splice_Site_p.K532fs	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	577							poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(8)|large_intestine(12)|lung(11)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	46						TTGGTTTACCTTTTTAAGTGC	0.328																																					p.K577fs		Atlas-INDEL	.											.	SECISBP2L	118	.	0			c.1731delG						.						94	97	96					15																	49304846		2197	4295	6492	SO:0001630	splice_region_variant	9728	exon12			.	BC033001	CCDS32234.1, CCDS53942.1	15q21.1	2014-02-12				ENSG00000138593			28997	protein-coding gene	gene with protein product		615756					Standard	NM_001193489		Approved	KIAA0256	uc001zxe.2	Q93073		ENST00000559471.1:c.1731+1A>-	chr15.hg19:g.49304846delT		165.0	0.0		141.0	10.0	NM_001193489	Q8N767	Frame_Shift_Del	DEL	ENST00000559471.1	hg19	CCDS53942.1																																																																																			.	.		0.328	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417277.1	NM_014701	Frame_Shift_Del	-	49304846	T	-	49304846	8	5	282	1	0	1	0	1	0	0	1	0	14022	1623	56	0	1603	0	SECISBP2L	15	49304846	Splice_Site	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	243591	49304846	53226546	1016	41250										
SECISBP2L	9728	hgsc.bcm.edu	37	chr15	49319614	49319614	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cacctctagaaaatgtctgaTttttttccatccaaggtttt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:49319614delT	ENST00000559471.1	-	7	1246	c.983delA	c.(982-984)aatfs	p.N328fs	SECISBP2L_ENST00000261847.3_Frame_Shift_Del_p.N328fs	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	328							poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(8)|large_intestine(12)|lung(11)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	46						AAATGTCTGATTTTTTTCCAT	0.318																																					p.N328fs		Atlas-INDEL	.											.	SECISBP2L	118	.	0			c.984delT						.						113	113	113					15																	49319614		2197	4295	6492	SO:0001589	frameshift_variant	9728	exon7			.	BC033001	CCDS32234.1, CCDS53942.1	15q21.1	2014-02-12				ENSG00000138593			28997	protein-coding gene	gene with protein product		615756					Standard	NM_001193489		Approved	KIAA0256	uc001zxe.2	Q93073		ENST00000559471.1:c.983delA	chr15.hg19:g.49319614delT	ENSP00000453854:p.Asn328fs	229.0	0.0		184.0	12.0	NM_001193489	Q8N767	Frame_Shift_Del	DEL	ENST00000559471.1	hg19	CCDS53942.1																																																																																			.	.		0.318	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417277.1	NM_014701		-	49319614	T	-	49319614	7	5	282	1	0	1	0	1	0	0	0	0	14022	1493	52	0	2231	0	SECISBP2L	15	49319614	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	14768	49319614	53211778	1017	41251										
COPS2	9318	hgsc.bcm.edu	37	chr15	49436467	49436467	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tttgtttcagtgctttaaatCcccattctcctttttcacct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:49436467delC	ENST00000388901.5	-	3	276	c.203delG	c.(202-204)ggafs	p.G68fs	COPS2_ENST00000542928.1_Intron|COPS2_ENST00000299259.6_Frame_Shift_Del_p.G68fs	NM_001143887.1|NM_004236.3	NP_001137359.1|NP_004227.1	P61201	CSN2_HUMAN	COP9 signalosome subunit 2	68					cell proliferation (GO:0008283)|cullin deneddylation (GO:0010388)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|prostate(1)|skin(2)	18		all_lung(180;0.0428)		all cancers(107;1.34e-07)|GBM - Glioblastoma multiforme(94;3.02e-05)		TGCTTTAAATCCCCATTCTCC	0.284																																					p.G68fs	NSCLC(36;322 1063 10349 30082 48062)|Esophageal Squamous(122;685 1633 15569 21293 52803)	Atlas-INDEL	.											.	COPS2	41	.	0			c.204delA						.						71	71	71					15																	49436467		2194	4277	6471	SO:0001589	frameshift_variant	9318	exon3			.	AF212227	CCDS32235.1, CCDS45257.1	15q21.2	2013-03-14	2013-03-14						30747	protein-coding gene	gene with protein product		604508	"COP9 constitutive photomorphogenic homolog subunit 2 (Arabidopsis)"			7776974, 9535219	Standard	NM_004236		Approved	TRIP15, ALIEN, CSN2	uc001zxh.3	P61201		ENST00000388901.5:c.203delG	chr15.hg19:g.49436467delC	ENSP00000373553:p.Gly68fs	238.0	0.0		149.0	12.0	NM_004236	O88950|Q15647|Q6FGP4|Q9BY54|Q9R249|Q9UNI2|Q9UNQ5	Frame_Shift_Del	DEL	ENST00000388901.5	hg19	CCDS32235.1																																																																																			.	.		0.284	COPS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417840.1	NM_004236		-	49436467	C	-	49436467	7	5	282	1	0	1	0	1	0	0	0	0	3735	855	30	0	1193	0	COPS2	15	49436467	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	116853	49436467	53094925	1018	41252										
LYSMD2	256586	hgsc.bcm.edu	37	chr15	52017185	52017185	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aactgttatcagcagtttcaTtttctggagaatcaatggag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:52017185delT	ENST00000267838.3	-	2	921	c.407delA	c.(406-408)aatfs	p.N136fs	LYSMD2_ENST00000558126.1_Frame_Shift_Del_p.N29fs|LYSMD2_ENST00000560491.1_Frame_Shift_Del_p.N45fs|LYSMD2_ENST00000454181.2_Frame_Shift_Del_p.N45fs	NM_153374.2	NP_699205.1	Q8IV50	LYSM2_HUMAN	LysM, putative peptidoglycan-binding, domain containing 2	136										lung(2)|upper_aerodigestive_tract(1)	3				all cancers(107;0.00258)		AGCAGTTTCATTTTCTGGAGA	0.428																																					p.N136fs		Atlas-INDEL	.											.	LYSMD2	8	.	0			c.408delT						.						93	102	99					15																	52017185		2195	4293	6488	SO:0001589	frameshift_variant	256586	exon2			.	AY125955	CCDS10143.1, CCDS45259.1	15q21.2	2005-08-09			ENSG00000140280	ENSG00000140280			28571	protein-coding gene	gene with protein product						12477932	Standard	NM_153374		Approved	MGC35274	uc002abi.3	Q8IV50	OTTHUMG00000131804	ENST00000267838.3:c.407delA	chr15.hg19:g.52017185delT	ENSP00000267838:p.Asn136fs	234.0	0.0		179.0	11.0	NM_153374	Q5CZ88|Q8WTV3	Frame_Shift_Del	DEL	ENST00000267838.3	hg19	CCDS10143.1																																																																																			.	.		0.428	LYSMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254741.1	NM_153374		-	52017185	T	-	52017185	7	5	282	1	0	1	0	1	0	0	0	0	9134	1493	52	0	248	0	LYSMD2	15	52017185	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2580718	52017185	50514207	1019	41253										
MYO5A	4644	hgsc.bcm.edu	37	chr15	52688534	52688534	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atattgaattgttgctgtagTttttcatttgcataatttat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:52688534delT	ENST00000399231.3	-	11	1623	c.1380delA	c.(1378-1380)aaafs	p.K460fs	MYO5A_ENST00000399233.2_Frame_Shift_Del_p.K460fs|MYO5A_ENST00000358212.6_Frame_Shift_Del_p.K460fs|MYO5A_ENST00000553916.1_Frame_Shift_Del_p.K460fs|MYO5A_ENST00000356338.6_Frame_Shift_Del_p.K460fs	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	460	Myosin motor.				actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		GTTGCTGTAGTTTTTCATTTG	0.279																																					p.L461fs		Atlas-INDEL	.											.	MYO5A	145	.	0			c.1381delC						.						63	59	60					15																	52688534		1767	4049	5816	SO:0001589	frameshift_variant	4644	exon11			.		CCDS42037.1, CCDS45262.1	15q21	2014-09-17	2006-09-29		ENSG00000197535	ENSG00000197535		"Myosins / Myosin superfamily : Class V"	7602	protein-coding gene	gene with protein product	"myosin, heavy polypeptide kinase", "myosin heavy chain 12", "myoxin", "myosin V"	160777	"myosin VA (heavy polypeptide 12, myoxin)"	MYH12		8188282, 8022818	Standard	NM_000259		Approved	MYO5, GS1, MYR12	uc002aby.2	Q9Y4I1	OTTHUMG00000137383	ENST00000399231.3:c.1380delA	chr15.hg19:g.52688534delT	ENSP00000382177:p.Lys460fs	260.0	0.0		179.0	12.0	NM_000259	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Frame_Shift_Del	DEL	ENST00000399231.3	hg19	CCDS42037.1																																																																																			.	.		0.279	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259		-	52688534	T	-	52688534	7	5	282	1	0	1	0	1	0	0	0	0	10087	1722	60	0	4311	0	MYO5A	15	52688534	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	671349	52688534	49842858	1020	41254										
MYO5A	4644	hgsc.bcm.edu	37	chr15	52720687	52720687	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gatagctgagggctgtgaggTcattttcaccaacaagtatg	12	7	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:52720687T>C	ENST00000399231.3	-	3	461	c.218A>G	c.(217-219)gAc>gGc	p.D73G	MYO5A_ENST00000399233.2_Missense_Mutation_p.D73G|MYO5A_ENST00000358212.6_Missense_Mutation_p.D73G|MYO5A_ENST00000553916.1_Missense_Mutation_p.D73G|MYO5A_ENST00000356338.6_Missense_Mutation_p.D73G	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	73	Myosin motor.				actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)	p.D73V(1)		breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		GGCTGTGAGGTCATTTTCACC	0.423																																					p.D73G		Atlas-SNP	.											MYO5A,right_upper_lobe,carcinoma,0,2	MYO5A	145	.	1	Substitution - Missense(1)	lung(1)	c.A218G						.						177	165	169					15																	52720687		1988	4170	6158	SO:0001583	missense	4644	exon3			GTGAGGTCATTTT		CCDS42037.1, CCDS45262.1	15q21	2014-09-17	2006-09-29		ENSG00000197535	ENSG00000197535		"Myosins / Myosin superfamily : Class V"	7602	protein-coding gene	gene with protein product	"myosin, heavy polypeptide kinase", "myosin heavy chain 12", "myoxin", "myosin V"	160777	"myosin VA (heavy polypeptide 12, myoxin)"	MYH12		8188282, 8022818	Standard	NM_000259		Approved	MYO5, GS1, MYR12	uc002aby.2	Q9Y4I1	OTTHUMG00000137383	ENST00000399231.3:c.218A>G	chr15.hg19:g.52720687T>C	ENSP00000382177:p.Asp73Gly	401.0	2.0		248.0	10.0	NM_000259	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Missense_Mutation	SNP	ENST00000399231.3	hg19	CCDS42037.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.828635	0.90955	.	.	ENSG00000197535	ENST00000399231;ENST00000399233;ENST00000356338;ENST00000358212;ENST00000553916	D;D;D;D;D	0.98493	-4.96;-4.96;-4.96;-4.96;-4.96	5.76	5.76	0.90799	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.99450	0.9805	H	0.98738	4.315	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.98117	1.0423	10	0.72032	D	0.01	.	16.0637	0.80856	0.0:0.0:0.0:1.0	.	73;73	Q9Y4I1;Q9Y4I1-2	MYO5A_HUMAN;.	G	73	ENSP00000382177:D73G;ENSP00000382179:D73G;ENSP00000348693:D73G;ENSP00000350945:D73G;ENSP00000451109:D73G	ENSP00000348693:D73G	D	-	2	0	MYO5A	50507979	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	8.040000	0.89188	2.197000	0.70478	0.533000	0.62120	GAC	.	.		0.423	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259		C	52720687	T	C	52720687	3	2	282	1	0	0	0	0	1	0	0	0	10087	1667	58	2	5505	2	MYO5A	15	52720687	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	32153	52720687	49810705	1021	41255										
TCF12	6938	hgsc.bcm.edu	37	chr15	57484418	57484418	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagctatcttcttcaggaaaAcctgggacagcatactattc	7	11	3	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:57484418A>G	ENST00000267811.5	+	7	757	c.453A>G	c.(451-453)aaA>aaG	p.K151K	TCF12_ENST00000452095.2_Silent_p.K147K|TCF12_ENST00000557843.1_Silent_p.K151K|TCF12_ENST00000333725.5_Silent_p.K151K|TCF12_ENST00000438423.2_Silent_p.K151K	NM_003205.3|NM_207038.1	NP_003196.1|NP_996921.1	Q99081	HTF4_HUMAN	transcription factor 12	151					immune response (GO:0006955)|muscle organ development (GO:0007517)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription factor binding (GO:0008134)		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)		CTTCAGGAAAACCTGGGACAG	0.468			T	TEC	extraskeletal myxoid chondrosarcoma																																p.K151K		Atlas-SNP	.		Dom	yes		15	15q21	6938	"transcription factor 12 (HTF4, helix-loop-helix transcription factors 4)"		M	.	TCF12	242	.	0			c.A453G						.						94	95	95					15																	57484418		2192	4292	6484	SO:0001819	synonymous_variant	6938	exon7			AGGAAAACCTGGG	BC050556	CCDS10159.1, CCDS10160.1, CCDS42042.1	15q21	2013-05-21	2008-07-31		ENSG00000140262	ENSG00000140262		"Basic helix-loop-helix proteins"	11623	protein-coding gene	gene with protein product	"helix-loop-helix transcription factor 4"	600480				1886779	Standard	NM_003205		Approved	HEB, HTF4, HsT17266, bHLHb20	uc002aeb.3	Q99081	OTTHUMG00000132047	ENST00000267811.5:c.453A>G	chr15.hg19:g.57484418A>G		160.0	0.0		96.0	5.0	NM_207036	Q7Z3D9|Q86TC1|Q86VM2	Silent	SNP	ENST00000267811.5	hg19	CCDS10159.1																																																																																			.	.		0.468	TCF12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255069.3	NM_003205		G	57484418	A	G	57484418	2	3	282	1	0	0	0	0	0	0	0	1	15702	40	2	2		2	TCF12	15	57484418	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	4763731	57484418	45046974	1022	41256										
ADAM10	102	hgsc.bcm.edu	37	chr15	58957384	58957384	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agcccccctgaggaccgtatTtatggggatagtctaaaata	10	9	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:58957384T>C	ENST00000260408.3	-	5	940	c.497A>G	c.(496-498)aAa>aGa	p.K166R	ADAM10_ENST00000402627.1_Intron|ADAM10_ENST00000396140.2_Intron|ADAM10_ENST00000561288.1_Intron|ADAM10_ENST00000558733.1_5'UTR	NM_001110.2	NP_001101.1	O14672	ADA10_HUMAN	ADAM metallopeptidase domain 10	166					cell death (GO:0008219)|cell-cell signaling (GO:0007267)|collagen catabolic process (GO:0030574)|constitutive protein ectodomain proteolysis (GO:0051089)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte activation (GO:0042117)|negative regulation of cell adhesion (GO:0007162)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of T cell chemotaxis (GO:0010820)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|tetraspanin-enriched microdomain (GO:0097197)	endopeptidase activity (GO:0004175)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(5)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)|skin(3)	27				GBM - Glioblastoma multiforme(80;0.202)		AGGACCGTATTTATGGGGATA	0.348																																					p.K166R		Atlas-SNP	.											.	ADAM10	59	.	0			c.A497G						.						117	115	115					15																	58957384		2192	4292	6484	SO:0001583	missense	102	exon5			CCGTATTTATGGG	AF009615	CCDS10167.1	15q2	2006-09-25	2005-08-18		ENSG00000137845	ENSG00000137845		"ADAM metallopeptidase domain containing", "CD molecules"	188	protein-coding gene	gene with protein product		602192	"a disintegrin and metalloproteinase domain 10"			9344679, 9441766	Standard	XM_005254117		Approved	kuz, MADM, HsT18717, CD156c	uc002afd.1	O14672	OTTHUMG00000132633	ENST00000260408.3:c.497A>G	chr15.hg19:g.58957384T>C	ENSP00000260408:p.Lys166Arg	134.0	0.0		97.0	4.0	NM_001110	B4DU28|Q10742|Q92650	Missense_Mutation	SNP	ENST00000260408.3	hg19	CCDS10167.1	.	.	.	.	.	.	.	.	.	.	T	27.8	4.864689	0.91511	.	.	ENSG00000137845	ENST00000260408;ENST00000439637	T;T	0.80824	1.84;-1.42	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.75503	0.3858	M	0.64997	1.995	0.80722	D	1	B;B	0.26445	0.149;0.149	B;B	0.24394	0.032;0.053	T	0.70346	-0.4897	10	0.09590	T	0.72	-33.2421	13.9508	0.64116	0.0:0.0:0.0:1.0	.	166;166	A0AV88;O14672	.;ADA10_HUMAN	R	166;113	ENSP00000260408:K166R;ENSP00000391930:K113R	ENSP00000260408:K166R	K	-	2	0	ADAM10	56744676	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.061000	0.64319	2.174000	0.68829	0.528000	0.53228	AAA	.	.		0.348	ADAM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255880.2	NM_001110		C	58957384	T	C	58957384	3	2	282	1	0	0	0	0	1	0	0	0	234	1841	64	2	1797	2	ADAM10	15	58957384	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1472966	58957384	43574008	1023	41257										
SLTM	79811	hgsc.bcm.edu	37	chr15	59204795	59204795	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaggtatcatcttcaccttcTtgagcttcaatttcctaagt	5	10	5	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:59204795T>C	ENST00000380516.2	-	5	615	c.528A>G	c.(526-528)caA>caG	p.Q176Q	SLTM_ENST00000557950.1_5'UTR|SLTM_ENST00000536328.1_5'UTR	NM_001013843.1|NM_024755.2	NP_001013865.1|NP_079031.2	Q9NWH9	SLTM_HUMAN	SAFB-like, transcription modulator	176	Glu-rich.				apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						cttcaccttcttgagcttcaa	0.358																																					p.Q176Q		Atlas-SNP	.											.	SLTM	90	.	0			c.A528G						.						97	87	90					15																	59204795		2192	4292	6484	SO:0001819	synonymous_variant	79811	exon5			ACCTTCTTGAGCT	BC046119	CCDS10168.2	15q21.3	2013-02-12			ENSG00000137776	ENSG00000137776		"RNA binding motif (RRM) containing"	20709	protein-coding gene	gene with protein product							Standard	XR_243128		Approved	Met, FLJ13213	uc002afp.3	Q9NWH9	OTTHUMG00000074033	ENST00000380516.2:c.528A>G	chr15.hg19:g.59204795T>C		113.0	0.0		97.0	4.0	NM_001013843	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000380516.2	hg19	CCDS10168.2																																																																																			.	.		0.358	SLTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157124.1	NM_024755		C	59204795	T	C	59204795	2	2	282	1	0	0	0	0	0	0	0	1	14769	1606	56	2		2	SLTM	15	59204795	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	247411	59204795	43326597	1024	41258										
RNF111	54778	hgsc.bcm.edu	37	chr15	59383348	59383348	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtacatatccacataaatacAaaaaggtaagaatttattct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:59383348delA	ENST00000557998.1	+	12	3021	c.2734delA	c.(2734-2736)aaafs	p.K913fs	RNF111_ENST00000434298.1_Frame_Shift_Del_p.K922fs|RNF111_ENST00000348370.4_Frame_Shift_Del_p.K913fs|RNF111_ENST00000559209.1_Frame_Shift_Del_p.K922fs|RNF111_ENST00000561186.1_Frame_Shift_Del_p.K922fs	NM_001270530.1	NP_001257459.1	Q6ZNA4	RN111_HUMAN	ring finger protein 111	913					gene expression (GO:0010467)|pattern specification process (GO:0007389)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein polyubiquitination (GO:0000209)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|SUMO polymer binding (GO:0032184)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35				all cancers(107;0.194)		ACATAAATACAAAAAGGTAAG	0.333																																					p.Y920X	NSCLC(72;983 1365 10746 34387 47081)	Atlas-INDEL	.											.	RNF111	179	.	0			c.2760delC						.						88	93	91					15																	59383348		2192	4291	6483	SO:0001589	frameshift_variant	54778	exon12			.	AL157474	CCDS10169.1, CCDS58365.1, CCDS58366.1	15q21	2013-01-09			ENSG00000157450	ENSG00000157450		"RING-type (C3HC4) zinc fingers"	17384	protein-coding gene	gene with protein product		605840				11298452	Standard	NM_017610		Approved	ARK, Arkadia, FLJ38008, DKFZP761D081	uc002aft.4	Q6ZNA4	OTTHUMG00000132716	ENST00000557998.1:c.2734delA	chr15.hg19:g.59383348delA	ENSP00000452732:p.Lys913fs	248.0	0.0		204.0	13.0	NM_001270528	C9JUS4|H0YN55|Q6P9A4|Q6ZMU2|Q7L428|Q7Z346|Q8N1P9|Q8WUA3|Q9NSR1	Frame_Shift_Del	DEL	ENST00000557998.1	hg19	CCDS58366.1																																																																																			.	.		0.333	RNF111-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000416012.1	NM_017610		-	59383348	A	-	59383348	7	5	282	1	0	1	0	1	0	0	0	0	13440	131	5	0	2776	0	RNF111	15	59383348	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	178553	59383348	43148044	1025	41259										
BNIP2	663	hgsc.bcm.edu	37	chr15	59970126	59970126	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttacccccatggctgataacTtttttatagggttcaattgc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:59970126delT	ENST00000607373.1	-	5	658	c.456delA	c.(454-456)aaafs	p.K152fs	BNIP2_ENST00000415213.2_Frame_Shift_Del_p.K214fs|BNIP2_ENST00000267859.3_Frame_Shift_Del_p.K273fs	NM_004330.2	NP_004321.2	Q12982	BNIP2_HUMAN	BCL2/adenovirus E1B 19kDa interacting protein 2	152	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				apoptotic process (GO:0006915)|muscle cell differentiation (GO:0042692)|negative regulation of apoptotic process (GO:0043066)|positive regulation of GTPase activity (GO:0043547)|positive regulation of muscle cell differentiation (GO:0051149)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)	calcium ion binding (GO:0005509)|GTPase activator activity (GO:0005096)|identical protein binding (GO:0042802)			NS(1)|large_intestine(2)|lung(5)|ovary(1)	9						GGCTGATAACTTTTTTATAGG	0.388																																					p.V274fs	Ovarian(174;1936 1978 6671 8240 38212)	Atlas-INDEL	.											.	BNIP2	27	.	0			c.820delG						.						130	130	130					15																	59970126		2190	4290	6480	SO:0001589	frameshift_variant	663	exon5			.	U15173	CCDS10174.2	15q21.3	2008-07-18	2002-08-29		ENSG00000140299	ENSG00000140299			1083	protein-coding gene	gene with protein product		603292	"BCL2/adenovirus E1B 19kD-interacting protein 2"			7954800	Standard	NM_004330		Approved	Nip2, BNIP-2	uc010uhc.2	Q12982	OTTHUMG00000132727	ENST00000607373.1:c.456delA	chr15.hg19:g.59970126delT	ENSP00000475320:p.Lys152fs	259.0	0.0		204.0	13.0	NM_004330	B4DS94	Frame_Shift_Del	DEL	ENST00000607373.1	hg19																																																																																				.	.		0.388	BNIP2-012	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470740.1	NM_004330		-	59970126	T	-	59970126	7	5	282	1	0	1	0	1	0	0	0	0	1477	1606	56	0	512	0	BNIP2	15	59970126	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	586778	59970126	42561266	1026	41260										
HERC1	8925	hgsc.bcm.edu	37	chr15	63999002	63999002	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tctttctgtgagatgctgccAaatccaaatcaacatttcgt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:63999002delA	ENST00000443617.2	-	25	4700	c.4613delT	c.(4612-4614)ttgfs	p.L1538fs	RP11-317G6.1_ENST00000559303.2_RNA	NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	1538					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						AGATGCTGCCAAATCCAAATC	0.274																																					p.L1538fs		Atlas-INDEL	.											.	HERC1	624	.	0			c.4614delG						.						33	30	31					15																	63999002		1775	3950	5725	SO:0001589	frameshift_variant	8925	exon25			.	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.4613delT	chr15.hg19:g.63999002delA	ENSP00000390158:p.Leu1538fs	189.0	0.0		198.0	12.0	NM_003922	Q8IW65	Frame_Shift_Del	DEL	ENST00000443617.2	hg19	CCDS45277.1																																																																																			.	.		0.274	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		-	63999002	A	-	63999002	7	5	282	1	0	1	0	1	0	0	0	0	7066	131	5	0	10188	0	HERC1	15	63999002	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	4028876	63999002	38532390	1027	41261										
SPG21	51324	hgsc.bcm.edu	37	chr15	65273320	65273320	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgatacttcgggggcccgcgTcatagagcgaccatatctta	11	11	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:65273320T>C	ENST00000204566.2	-	3	402	c.107A>G	c.(106-108)gAc>gGc	p.D36G	SPG21_ENST00000416889.2_Missense_Mutation_p.D36G|SPG21_ENST00000559199.1_5'UTR|SPG21_ENST00000560564.1_5'UTR|SPG21_ENST00000433215.2_Missense_Mutation_p.D36G	NM_016630.3	NP_057714.1	Q9NZD8	SPG21_HUMAN	spastic paraplegia 21 (autosomal recessive, Mast syndrome)	36					antigen receptor-mediated signaling pathway (GO:0050851)|cell death (GO:0008219)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network transport vesicle (GO:0030140)	CD4 receptor binding (GO:0042609)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|urinary_tract(1)	10						GGGGCCCGCGTCATAGAGCGA	0.443																																					p.D36G		Atlas-SNP	.											.	SPG21	29	.	0			c.A107G						.						83	78	80					15																	65273320		2202	4299	6501	SO:0001583	missense	51324	exon3			CCCGCGTCATAGA	AF208861	CCDS10198.1, CCDS45279.1	15q21-q22	2008-02-05	2007-04-23		ENSG00000090487	ENSG00000090487			20373	protein-coding gene	gene with protein product	"maspardin"	608181				11113139, 14564668	Standard	XM_006720564		Approved	ACP33, GL010, BM-019, MAST	uc002aoe.3	Q9NZD8	OTTHUMG00000133098	ENST00000204566.2:c.107A>G	chr15.hg19:g.65273320T>C	ENSP00000204566:p.Asp36Gly	118.0	0.0		97.0	6.0	NM_001127889	B4DW44|Q6ZMB6	Missense_Mutation	SNP	ENST00000204566.2	hg19	CCDS10198.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.450266	0.84101	.	.	ENSG00000090487	ENST00000204566;ENST00000416889;ENST00000433215	T;T	0.32023	1.47;1.47	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.58409	0.2120	M	0.80616	2.505	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.995	T	0.62599	-0.6820	10	0.56958	D	0.05	-16.817	15.1312	0.72527	0.0:0.0:0.0:1.0	.	36;36	Q9NZD8-2;Q9NZD8	.;SPG21_HUMAN	G	36	ENSP00000204566:D36G;ENSP00000404111:D36G	ENSP00000204566:D36G	D	-	2	0	SPG21	63060373	1.000000	0.71417	0.867000	0.34043	0.640000	0.38277	7.959000	0.87885	2.167000	0.68274	0.528000	0.53228	GAC	.	.		0.443	SPG21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256758.3	NM_016630		C	65273320	T	C	65273320	3	2	282	1	0	0	0	0	1	0	0	0	15058	1667	58	2	847	2	SPG21	15	65273320	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1274318	65273320	37258072	1028	41262										
CLPX	10845	hgsc.bcm.edu	37	chr15	65449246	65449246	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctggcacactgccaatcttaTctacttcatccagaaagaca	5	13	3	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:65449246T>C	ENST00000300107.3	-	9	1270	c.1082A>G	c.(1081-1083)gAt>gGt	p.D361G		NM_006660.3	NP_006651.2	O76031	CLPX_HUMAN	caseinolytic mitochondrial matrix peptidase chaperone subunit	361					ATP catabolic process (GO:0006200)|positive regulation of peptidase activity (GO:0010952)|protein folding (GO:0006457)|proteolysis involved in cellular protein catabolic process (GO:0051603)	endopeptidase Clp complex (GO:0009368)|mitochondrial endopeptidase Clp complex (GO:0009841)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|metal ion binding (GO:0046872)|peptidase activator activity (GO:0016504)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(4)|prostate(1)|skin(2)	16						GCCAATCTTATCTACTTCATC	0.368																																					p.D361G		Atlas-SNP	.											.	CLPX	49	.	0			c.A1082G						.						137	120	126					15																	65449246		2202	4299	6501	SO:0001583	missense	10845	exon9			ATCTTATCTACTT	AJ006267	CCDS10202.1	15q22.31	2013-09-12	2013-09-12		ENSG00000166855	ENSG00000166855		"ATPases / AAA-type"	2088	protein-coding gene	gene with protein product		615611	"ClpX (caseinolytic protease X, E. coli) homolog", "ClpX caseinolytic protease X homolog (E. coli)", "ClpX caseinolytic peptidase X homolog (E. coli)"			22841477	Standard	NM_006660		Approved		uc002aom.3	O76031	OTTHUMG00000133139	ENST00000300107.3:c.1082A>G	chr15.hg19:g.65449246T>C	ENSP00000300107:p.Asp361Gly	153.0	0.0		90.0	5.0	NM_006660	A1L428|A8K8F1|B9EGI8|Q9H4D9	Missense_Mutation	SNP	ENST00000300107.3	hg19	CCDS10202.1	.	.	.	.	.	.	.	.	.	.	T	29.8	5.033794	0.93575	.	.	ENSG00000166855	ENST00000300107;ENST00000546194	T	0.59502	0.26	5.94	5.94	0.96194	ATPase, AAA-2 (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.87051	0.6081	H	0.99391	4.545	0.80722	D	1	D;D	0.89917	0.994;1.0	P;D	0.91635	0.9;0.999	D	0.92711	0.6183	10	0.87932	D	0	.	16.3908	0.83537	0.0:0.0:0.0:1.0	.	361;361	Q9H072;O76031	.;CLPX_HUMAN	G	361	ENSP00000300107:D361G	ENSP00000300107:D361G	D	-	2	0	CLPX	63236299	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.269000	0.75478	0.455000	0.32223	GAT	.	.		0.368	CLPX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256828.2	NM_006660		C	65449246	T	C	65449246	3	2	282	1	0	0	0	0	1	0	0	0	3558	1435	50	2	843	2	CLPX	15	65449246	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	175926	65449246	37082146	1029	41263										
DENND4A	10260	hgsc.bcm.edu	37	chr15	65993392	65993392	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acacatacatcccttacctgAgagagttgtttgtgataagt	8	8	0	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:65993392A>G	ENST00000431932.2	-	19	2906	c.2698T>C	c.(2698-2700)Tca>Cca	p.S900P	DENND4A_ENST00000443035.3_Missense_Mutation_p.S900P	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	900					positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						CCCTTACCTGAGAGAGTTGTT	0.284																																					p.S900P		Atlas-SNP	.											.	DENND4A	217	.	0			c.T2698C						.						164	153	156					15																	65993392		1834	4086	5920	SO:0001583	missense	10260	exon19			TACCTGAGAGAGT	AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27				"DENN/MADD domain containing"	24321	protein-coding gene	gene with protein product		600382	"c-myc promoter binding protein"	MYCPBP		8056341, 12906859	Standard	NM_005848		Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.2698T>C	chr15.hg19:g.65993392A>G	ENSP00000396830:p.Ser900Pro	141.0	0.0		133.0	7.0	NM_001144823	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Missense_Mutation	SNP	ENST00000431932.2	hg19	CCDS45285.1	.	.	.	.	.	.	.	.	.	.	A	14.69	2.610352	0.46527	.	.	ENSG00000174485	ENST00000443035;ENST00000431932	T;T	0.05996	3.41;3.36	5.98	5.98	0.97165	.	0.480266	0.14514	U	0.314903	T	0.07007	0.0178	L	0.38953	1.18	0.45005	D	0.998021	B;P	0.49961	0.009;0.93	B;B	0.41571	0.004;0.36	T	0.41034	-0.9531	10	0.35671	T	0.21	.	11.0498	0.47880	0.9227:0.0:0.0773:0.0	.	900;900	E7EPL3;Q7Z401	.;MYCPP_HUMAN	P	900	ENSP00000391167:S900P;ENSP00000396830:S900P	ENSP00000396830:S900P	S	-	1	0	DENND4A	63780446	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.880000	0.75578	2.289000	0.77006	0.482000	0.46254	TCA	.	.		0.284	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848		G	65993392	A	G	65993392	3	3	282	1	0	0	0	0	1	0	0	0	4435	304	11	2	3082	2	DENND4A	15	65993392	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	544146	65993392	36538000	1030	41264										
ZWILCH	55055	hgsc.bcm.edu	37	chr15	66806411	66806411	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaatgacatagtattcatagTggaaaaagtggtaagtactg	10	3	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:66806411T>C	ENST00000307897.5	+	3	571	c.191T>C	c.(190-192)gTg>gCg	p.V64A	ZWILCH_ENST00000446801.2_5'UTR|RPL4_ENST00000564517.1_Intron|ZWILCH_ENST00000535141.2_5'UTR|RPL4_ENST00000568588.1_Intron|ZWILCH_ENST00000565627.1_Intron|ZWILCH_ENST00000565960.1_3'UTR	NM_017975.3	NP_060445.3	Q9H900	ZWILC_HUMAN	zwilch kinetochore protein	64					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)	cytosol (GO:0005829)|kinetochore (GO:0000776)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|liver(1)|lung(6)|ovary(1)	18						GTATTCATAGTGGAAAAAGTG	0.343																																					p.V64A		Atlas-SNP	.											.	ZWILCH	46	.	0			c.T191C						.						58	58	58					15																	66806411		2201	4299	6500	SO:0001583	missense	55055	exon3			TCATAGTGGAAAA	AK023175	CCDS10219.1, CCDS73746.1	15q22.31	2013-01-17	2012-12-13		ENSG00000174442	ENSG00000174442			25468	protein-coding gene	gene with protein product		609984	"Zwilch, kinetochore associated, homolog (Drosophila)"			12686595	Standard	NM_017975		Approved	FLJ10036, KNTC1AP	uc002aqb.3	Q9H900	OTTHUMG00000133194	ENST00000307897.5:c.191T>C	chr15.hg19:g.66806411T>C	ENSP00000311429:p.Val64Ala	109.0	0.0		72.0	4.0	NM_017975	B3KVB8|Q6N049|Q8N404|Q96SY7|Q9NWG7	Missense_Mutation	SNP	ENST00000307897.5	hg19	CCDS10219.1	.	.	.	.	.	.	.	.	.	.	T	10.69	1.420712	0.25639	.	.	ENSG00000174442	ENST00000307897	T	0.49720	0.77	6.16	2.66	0.31614	.	0.773508	0.12966	N	0.424599	T	0.42040	0.1185	L	0.54323	1.7	0.30310	N	0.788609	B	0.28128	0.201	B	0.28385	0.089	T	0.40308	-0.9570	10	0.48119	T	0.1	-0.8818	8.4821	0.33049	0.0:0.2232:0.0:0.7768	.	64	Q9H900	ZWILC_HUMAN	A	64	ENSP00000311429:V64A	ENSP00000311429:V64A	V	+	2	0	ZWILCH	64593465	0.867000	0.29959	0.202000	0.23494	0.800000	0.45204	1.082000	0.30803	0.218000	0.20820	-0.263000	0.10527	GTG	.	.		0.343	ZWILCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256904.4	NM_017975		C	66806411	T	C	66806411	3	2	282	1	0	0	0	0	1	0	0	0	18263	1696	59	2	201	2	ZWILCH	15	66806411	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	813019	66806411	35724981	1031	41265										
FEM1B	10116	hgsc.bcm.edu	37	chr15	68582064	68582064	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	taccacagtaactaattcaaCccccctgcgggcagcatgct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:68582064delC	ENST00000306917.4	+	2	983	c.368delC	c.(367-369)accfs	p.T123fs		NM_015322.4	NP_056137.1	Q9UK73	FEM1B_HUMAN	fem-1 homolog b (C. elegans)	123					apoptotic process (GO:0006915)|branching involved in prostate gland morphogenesis (GO:0060442)|epithelial cell maturation involved in prostate gland development (GO:0060743)|regulation of DNA damage checkpoint (GO:2000001)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|regulation of ubiquitin-protein transferase activity (GO:0051438)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	death receptor binding (GO:0005123)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(1)	9						ACTAATTCAACCCCCCTGCGG	0.453																																					p.T123fs		Atlas-INDEL	.											.	FEM1B	38	.	0			c.367delA						.						91	77	82					15																	68582064		2200	4298	6498	SO:0001589	frameshift_variant	10116	exon2			.		CCDS10228.1	15q22	2013-02-19	2001-11-28		ENSG00000169018	ENSG00000169018		"Ankyrin repeat domain containing"	3649	protein-coding gene	gene with protein product		613539	"FEM-1 (C. elegans) homolog b"			10623617	Standard	NM_015322		Approved		uc002arg.3	Q9UK73	OTTHUMG00000133285	ENST00000306917.4:c.368delC	chr15.hg19:g.68582064delC	ENSP00000307298:p.Thr123fs	260.0	0.0		161.0	11.0	NM_015322	O43146	Frame_Shift_Del	DEL	ENST00000306917.4	hg19	CCDS10228.1																																																																																			.	.		0.453	FEM1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257065.1			-	68582064	C	-	68582064	7	5	282	1	0	1	0	1	0	0	0	0	5818	507	18	0	374	0	FEM1B	15	68582064	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1775653	68582064	33949328	1032	41266										
ITGA11	22801	hgsc.bcm.edu	37	chr15	68624271	68624271	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcctgcgtggttgtcctccaGgggggctcccaccaccacgt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:68624271delG	ENST00000315757.7	-	14	1782	c.1696delC	c.(1696-1698)ctgfs	p.L566fs	ITGA11_ENST00000423218.2_Frame_Shift_Del_p.L566fs	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	566					cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|collagen-activated signaling pathway (GO:0038065)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|osteoblast differentiation (GO:0001649)|substrate-dependent cell migration (GO:0006929)	focal adhesion (GO:0005925)|integrin alpha11-beta1 complex (GO:0034681)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(6)|lung(22)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	52						TTGTCCTCCAGGGGGGCTCCC	0.572																																					p.L566fs		Atlas-INDEL	.											.	ITGA11	110	.	0			c.1697delT						.						57	56	56					15																	68624271		1979	4149	6128	SO:0001589	frameshift_variant	22801	exon14			.	AF109681	CCDS45291.1	15q22.3-q23	2010-03-23				ENSG00000137809		"Integrins"	6136	protein-coding gene	gene with protein product		604789				10486209	Standard	NM_001004439		Approved	HsT18964	uc002ari.3	Q9UKX5		ENST00000315757.7:c.1696delC	chr15.hg19:g.68624271delG	ENSP00000327290:p.Leu566fs	249.0	0.0		164.0	10.0	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Frame_Shift_Del	DEL	ENST00000315757.7	hg19	CCDS45291.1																																																																																			.	.		0.572	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211		-	68624271	G	-	68624271	7	5	282	1	0	1	0	1	0	0	0	0	7883	991	35	0	1938	0	ITGA11	15	68624271	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	42207	68624271	33907121	1033	41267										
MYO9A	4649	hgsc.bcm.edu	37	chr15	72244126	72244126	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttgtagccttactgtacttcTcttccttgcatctctgcaga	6	12	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:72244126T>C	ENST00000356056.5	-	15	2766	c.2294A>G	c.(2293-2295)gAg>gGg	p.E765G	MYO9A_ENST00000444904.1_Missense_Mutation_p.E746G|MYO9A_ENST00000564571.1_Missense_Mutation_p.E765G|MYO9A_ENST00000424560.1_Missense_Mutation_p.E765G|MYO9A_ENST00000566885.1_Missense_Mutation_p.E360G|MYO9A_ENST00000563542.1_5'UTR	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	765	Myosin motor.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)			NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						ACTGTACTTCTCTTCCTTGCA	0.423																																					p.E765G		Atlas-SNP	.											.	MYO9A	203	.	0			c.A2294G						.						211	195	200					15																	72244126		2199	4297	6496	SO:0001583	missense	4649	exon15			TACTTCTCTTCCT	AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"Myosins / Myosin superfamily : Class IX"	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.2294A>G	chr15.hg19:g.72244126T>C	ENSP00000348349:p.Glu765Gly	215.0	0.0		146.0	6.0	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	hg19	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.850458	0.91277	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904;ENST00000261864	D;D;D	0.86366	-2.11;-2.1;-2.11	5.35	5.35	0.76521	Myosin head, motor domain (1);	.	.	.	.	D	0.85635	0.5742	N	0.14661	0.345	0.80722	D	1	D;B;P	0.67145	0.996;0.129;0.933	P;B;P	0.59424	0.857;0.138;0.739	D	0.85851	0.1404	9	0.33940	T	0.23	.	15.6409	0.77001	0.0:0.0:0.0:1.0	.	746;746;765	B2RTY4-2;B7WP69;B2RTY4	.;.;MYO9A_HUMAN	G	765;765;746;746	ENSP00000348349:E765G;ENSP00000399162:E765G;ENSP00000398250:E746G	ENSP00000261864:E746G	E	-	2	0	MYO9A	70031180	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.921000	0.87530	2.151000	0.67156	0.460000	0.39030	GAG	.	.		0.423	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901		C	72244126	T	C	72244126	3	2	282	1	0	0	0	0	1	0	0	0	10093	1551	54	2	5464	2	MYO9A	15	72244126	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3619855	72244126	30287266	1034	41268										
STOML1	9399	hgsc.bcm.edu	37	chr15	74281130	74281130	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccacggacagcacagccccgTccttagaggccagctgttgg	12	15	0	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:74281130T>C	ENST00000316900.5	-	4	528	c.404A>G	c.(403-405)gAc>gGc	p.D135G	STOML1_ENST00000541638.1_Missense_Mutation_p.D93G|STOML1_ENST00000316911.6_Missense_Mutation_p.D85G|STOML1_ENST00000561656.1_Missense_Mutation_p.D48G|STOML1_ENST00000359750.4_Missense_Mutation_p.D135G|STOML1_ENST00000564777.1_Missense_Mutation_p.D85G	NM_001256672.1|NM_001256675.1|NM_001256677.1|NM_004809.4	NP_001243601.1|NP_001243604.1|NP_001243606.1|NP_004800.2	Q9UBI4	STML1_HUMAN	stomatin (EPB72)-like 1	135						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	8						CACAGCCCCGTCCTTAGAGGC	0.627																																					p.D135G		Atlas-SNP	.											.	STOML1	22	.	0			c.A404G						.						73	70	71					15																	74281130		2198	4297	6495	SO:0001583	missense	9399	exon4			GCCCCGTCCTTAG	Y16522	CCDS10254.1, CCDS58381.1, CCDS58382.1, CCDS58383.1, CCDS58384.1, CCDS58385.1	15q24-q25	2008-07-18			ENSG00000067221	ENSG00000067221			14560	protein-coding gene	gene with protein product	"stomatin-like 1", "stomatin (EBP72)-like 1"	608326				9931417	Standard	NM_004809		Approved	hUNC-24, SLP-1, STORP, FLJ36370	uc002awe.4	Q9UBI4	OTTHUMG00000137608	ENST00000316900.5:c.404A>G	chr15.hg19:g.74281130T>C	ENSP00000319323:p.Asp135Gly	111.0	0.0		91.0	6.0	NM_001256672	B3KQN0|B4DUU5|B4DXM9|E7ESC0|H3BRP3|O95675|Q4PNR4|Q6FGL8|Q8WYI7|Q9UMB9|Q9UMC0|Q9Y6H9	Missense_Mutation	SNP	ENST00000316900.5	hg19	CCDS10254.1	.	.	.	.	.	.	.	.	.	.	T	17.88	3.498238	0.64186	.	.	ENSG00000067221	ENST00000316900;ENST00000316911;ENST00000541638;ENST00000359750	D;D;D;D	0.97791	-4.54;-4.54;-4.54;-4.54	4.34	4.34	0.51931	.	0.046263	0.85682	D	0.000000	D	0.98836	0.9607	H	0.94542	3.55	0.80722	D	1	D;D;D;D;D;D	0.69078	0.982;0.997;0.977;0.997;0.964;0.982	P;D;P;D;P;P	0.64321	0.779;0.924;0.78;0.924;0.779;0.762	D	0.99399	1.0927	10	0.72032	D	0.01	-17.3175	12.5167	0.56036	0.0:0.0:0.0:1.0	.	93;135;85;135;135;135	B4DUU5;E7ESC0;Q9UBI4-2;Q4PNR4;Q53HB6;Q9UBI4	.;.;.;.;.;STML1_HUMAN	G	135;85;93;135	ENSP00000319323:D135G;ENSP00000319384:D85G;ENSP00000442478:D93G;ENSP00000352788:D135G	ENSP00000319323:D135G	D	-	2	0	STOML1	72068183	1.000000	0.71417	0.998000	0.56505	0.457000	0.32468	6.904000	0.75708	1.827000	0.53221	0.533000	0.62120	GAC	.	.		0.627	STOML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269022.1	NM_004809		C	74281130	T	C	74281130	3	2	282	1	0	0	0	0	1	0	0	0	15328	1667	58	2	808	2	STOML1	15	74281130	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2037004	74281130	28250262	1035	41269										
NRG4	145957	hgsc.bcm.edu	37	chr15	76301620	76301620	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cgacttgtgactgggaccacAgggctcttcgtgatctagaa	12	10	2	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:76301620A>G	ENST00000394907.3	-	3	206	c.25T>C	c.(25-27)Tgt>Cgt	p.C9R	NRG4_ENST00000305435.10_Missense_Mutation_p.C9R|NRG4_ENST00000535975.1_Missense_Mutation_p.C9R	NM_138573.3	NP_612640.1	Q8WWG1	NRG4_HUMAN	neuregulin 4	9	EGF-like. {ECO:0000255|PROSITE- ProRule:PRU00076}.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	5						CTGGGACCACAGGGCTCTTCG	0.398																																					p.C9R		Atlas-SNP	.											.	NRG4	9	.	0			c.T25C						.						79	80	80					15																	76301620		2197	4294	6491	SO:0001583	missense	145957	exon3			GACCACAGGGCTC	BC017568	CCDS10288.1	15q23	2005-10-30			ENSG00000169752	ENSG00000169752			29862	protein-coding gene	gene with protein product		610894				12477932	Standard	NM_138573		Approved	HRG4	uc002bbo.3	Q8WWG1	OTTHUMG00000142917	ENST00000394907.3:c.25T>C	chr15.hg19:g.76301620A>G	ENSP00000378367:p.Cys9Arg	73.0	0.0		49.0	4.0	NM_138573	A6NIE8	Missense_Mutation	SNP	ENST00000394907.3	hg19	CCDS10288.1	.	.	.	.	.	.	.	.	.	.	A	18.68	3.676083	0.67928	.	.	ENSG00000169752	ENST00000394907;ENST00000535975;ENST00000305435	T;T	0.53640	0.61;0.61	5.37	5.37	0.77165	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.799345	0.09908	U	0.740151	T	0.77745	0.4176	M	0.93854	3.465	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.77427	-0.2592	10	0.87932	D	0	-10.6545	13.3384	0.60530	1.0:0.0:0.0:0.0	.	9	Q8WWG1	NRG4_HUMAN	R	9	ENSP00000378367:C9R;ENSP00000441129:C9R	ENSP00000303071:C9R	C	-	1	0	NRG4	74088675	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.094000	0.64523	2.019000	0.59389	0.528000	0.53228	TGT	.	.		0.398	NRG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286632.1	NM_138573		G	76301620	A	G	76301620	3	3	282	1	0	0	0	0	1	0	0	0	10659	188	7	2	338	2	NRG4	15	76301620	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2020490	76301620	26229772	1036	41270										
EFTUD1	79631	hgsc.bcm.edu	37	chr15	82512000	82512000	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tttcaattcttacccttcgtAaaaactcaagaggactgtat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:82512000delA	ENST00000268206.7	-	14	1772	c.1604delT	c.(1603-1605)ttafs	p.L535fs	EFTUD1_ENST00000359445.3_Frame_Shift_Del_p.L484fs	NM_024580.5	NP_078856.4	Q7Z2Z2	ETUD1_HUMAN	elongation factor Tu GTP binding domain containing 1	535					GTP catabolic process (GO:0006184)|mature ribosome assembly (GO:0042256)		GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ribosome binding (GO:0043022)|translation elongation factor activity (GO:0003746)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(14)|ovary(1)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32						TACCCTTCGTAAAAACTCAAG	0.378																																					p.L535fs		Atlas-INDEL	.											.	EFTUD1	74	.	0			c.1605delA						.						20	20	20					15																	82512000		1777	4045	5822	SO:0001589	frameshift_variant	79631	exon14			.	AK056656	CCDS42070.1, CCDS42071.1	15q25.2	2012-07-04			ENSG00000140598	ENSG00000140598			25789	protein-coding gene	gene with protein product	"ribosome assembly 1 homolog (yeast)"					14702039	Standard	NM_024580		Approved	FLJ13119, FAM42A, HsT19294, RIA1	uc002bgt.1	Q7Z2Z2	OTTHUMG00000172573	ENST00000268206.7:c.1604delT	chr15.hg19:g.82512000delA	ENSP00000268206:p.Leu535fs	253.0	0.0		244.0	19.0	NM_024580	A6NKY5|B7Z6I0|Q9H8Z6	Frame_Shift_Del	DEL	ENST00000268206.7	hg19	CCDS42071.1																																																																																			.	.		0.378	EFTUD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419252.1	NM_024580		-	82512000	A	-	82512000	7	5	282	1	0	1	0	1	0	0	0	0	4962	372	13	0	1786	0	EFTUD1	15	82512000	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	6210380	82512000	20019392	1037	41271										
HOMER2	9455	hgsc.bcm.edu	37	chr15	83523520	83523520	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgctctcccgaagggtctgcAgctcgatctcccacttcttc	8	16	4	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:83523520A>G	ENST00000304231.8	-	6	752	c.560T>C	c.(559-561)cTg>cCg	p.L187P	HOMER2_ENST00000426485.1_Intron|HOMER2_ENST00000450735.2_Missense_Mutation_p.L176P|HOMER2_ENST00000399166.2_Intron	NM_199330.2	NP_955362.1	Q9NSB8	HOME2_HUMAN	homer homolog 2 (Drosophila)	187					behavioral response to cocaine (GO:0048148)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|chemical homeostasis within a tissue (GO:0048875)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)				cervix(1)|endometrium(2)|lung(6)	9						AAGGGTCTGCAGCTCGATCTC	0.652																																					p.L187P		Atlas-SNP	.											.	HOMER2	63	.	0			c.T560C						.						58	63	61					15																	83523520		2161	4257	6418	SO:0001583	missense	9455	exon6			GTCTGCAGCTCGA	AF093264	CCDS45334.1, CCDS45336.1	15q24.3	2008-02-05				ENSG00000103942			17513	protein-coding gene	gene with protein product		604799				9808459, 9808458	Standard	NM_199330		Approved	CPD, Cupidin, Vesl-2, HOMER-2B, HOMER-2, HOMER-2A	uc002bjg.3	Q9NSB8		ENST00000304231.8:c.560T>C	chr15.hg19:g.83523520A>G	ENSP00000305632:p.Leu187Pro	142.0	0.0		91.0	4.0	NM_199330	O95269|O95349|Q9NSB6|Q9NSB7|Q9UNT7	Missense_Mutation	SNP	ENST00000304231.8	hg19	CCDS45334.1	.	.	.	.	.	.	.	.	.	.	A	26.4	4.738742	0.89573	.	.	ENSG00000103942	ENST00000304231;ENST00000450735	T;D	0.83591	1.53;-1.74	5.47	5.47	0.80525	.	0.000000	0.64402	D	0.000001	D	0.91603	0.7347	M	0.86028	2.79	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.92651	0.6133	10	0.62326	D	0.03	.	14.7216	0.69311	1.0:0.0:0.0:0.0	.	176;187	Q9NSB8-2;Q9NSB8	.;HOME2_HUMAN	P	187;176	ENSP00000305632:L187P;ENSP00000407634:L176P	ENSP00000305632:L187P	L	-	2	0	HOMER2	81320574	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.833000	0.92089	2.088000	0.63022	0.533000	0.62120	CTG	.	.		0.652	HOMER2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418689.1			G	83523520	A	G	83523520	3	3	282	1	0	0	0	0	1	0	0	0	7288	188	7	2	520	2	HOMER2	15	83523520	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1011520	83523520	19007872	1038	41272										
ALPK3	57538	hgsc.bcm.edu	37	chr15	85406007	85406007	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtgtggccttcggaaggcctCccaggccaaggtcatctacg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:85406007delC	ENST00000258888.5	+	10	5044	c.4877delC	c.(4876-4878)tccfs	p.S1626fs		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1626	Alpha-type protein kinase. {ECO:0000255|PROSITE-ProRule:PRU00501}.				heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			CGGAAGGCCTCCCAGGCCAAG	0.627																																					p.S1626fs		Atlas-INDEL	.											.	ALPK3	289	.	0			c.4876delT						.						88	85	86					15																	85406007		2203	4299	6502	SO:0001589	frameshift_variant	57538	exon10			.	AY044449	CCDS10333.1	15q25.2	2013-01-29			ENSG00000136383	ENSG00000136383		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17574	protein-coding gene	gene with protein product	"myocyte induction differentiation originator", "muscle alpha-kinase"					10021370	Standard	NM_020778		Approved	MAK, KIAA1330, Midori	uc002ble.3	Q96L96	OTTHUMG00000148667	ENST00000258888.5:c.4877delC	chr15.hg19:g.85406007delC	ENSP00000258888:p.Ser1626fs	227.0	0.0		176.0	11.0	NM_020778	Q9P2L6	Frame_Shift_Del	DEL	ENST00000258888.5	hg19	CCDS10333.1																																																																																			.	.		0.627	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778		-	85406007	C	-	85406007	7	5	282	1	0	1	0	1	0	0	0	0	546	855	30	0	4915	0	ALPK3	15	85406007	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1882487	85406007	17125385	1039	41273										
SLC28A1	9154	hgsc.bcm.edu	37	chr15	85431063	85431063	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gccaagggtctggagaacatGggggctgatttcttggaaag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:85431063delG	ENST00000286749.3	+	2	162	c.72delG	c.(70-72)atgfs	p.M24fs	SLC28A1_ENST00000537624.1_Frame_Shift_Del_p.M24fs|SLC28A1_ENST00000338602.2_Frame_Shift_Del_p.M24fs|SLC28A1_ENST00000538177.1_Frame_Shift_Del_p.M24fs|SLC28A1_ENST00000537703.1_5'UTR|SLC28A1_ENST00000537216.1_Frame_Shift_Del_p.M24fs|SLC28A1_ENST00000394573.1_Frame_Shift_Del_p.M24fs			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	24					nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside transmembrane transporter activity (GO:0005337)|nucleoside:sodium symporter activity (GO:0005415)			breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	41			BRCA - Breast invasive adenocarcinoma(143;0.0587)		Gemcitabine(DB00441)|Stavudine(DB00649)|Zidovudine(DB00495)	TGGAGAACATGGGGGCTGATT	0.567																																					p.M24fs		Atlas-INDEL	.											.	SLC28A1	118	.	0			c.71delT						.						172	155	161					15																	85431063		2203	4299	6502	SO:0001589	frameshift_variant	9154	exon3			.	U62967	CCDS10334.1, CCDS10335.1, CCDS73777.1	15q25.3	2013-07-17	2013-07-17		ENSG00000156222	ENSG00000156222		"Solute carriers"	11001	protein-coding gene	gene with protein product		606207	"solute carrier family 28 (sodium-coupled nucleoside transporter), member 1"			9124315	Standard	NM_004213		Approved	CNT1	uc002blg.3	O00337	OTTHUMG00000148668	ENST00000286749.3:c.72delG	chr15.hg19:g.85431063delG	ENSP00000286749:p.Met24fs	231.0	0.0		156.0	11.0	NM_201651	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Frame_Shift_Del	DEL	ENST00000286749.3	hg19	CCDS10334.1																																																																																			.	.		0.567	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2			-	85431063	G	-	85431063	7	5	282	1	0	1	0	1	0	0	0	0	14546	1348	47	0	74	0	SLC28A1	15	85431063	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	25056	85431063	17100329	1040	41274										
AKAP13	11214	hgsc.bcm.edu	37	chr15	86122651	86122651	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgtgcttcagagagacttggTcatggagccaggcacagccc	13	11	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:86122651T>C	ENST00000394518.2	+	7	1447	c.1352T>C	c.(1351-1353)gTc>gCc	p.V451A	RP11-815J21.2_ENST00000561409.1_RNA|AKAP13_ENST00000361243.2_Missense_Mutation_p.V451A	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	451					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						AGAGACTTGGTCATGGAGCCA	0.498																																					p.V451A	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.T1352C						.						63	67	66					15																	86122651		2202	4299	6501	SO:0001583	missense	11214	exon7			ACTTGGTCATGGA	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"A-kinase anchor proteins", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	371	protein-coding gene	gene with protein product		604686	"lymphoid blast crisis oncogene"	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.1352T>C	chr15.hg19:g.86122651T>C	ENSP00000378026:p.Val451Ala	248.0	0.0		214.0	9.0	NM_007200	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	hg19	CCDS32319.1	.	.	.	.	.	.	.	.	.	.	T	11.43	1.636992	0.29157	.	.	ENSG00000170776	ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540	T;T	0.12774	2.69;2.65	4.55	-4.25	0.03766	.	.	.	.	.	T	0.05777	0.0151	N	0.24115	0.695	0.09310	N	1	B;B	0.09022	0.001;0.002	B;B	0.06405	0.001;0.002	T	0.44329	-0.9335	9	0.02654	T	1	.	5.5114	0.16882	0.0:0.374:0.2986:0.3274	.	451;451	Q12802;Q12802-2	AKP13_HUMAN;.	A	451;451;450;450	ENSP00000354718:V451A;ENSP00000378026:V451A	ENSP00000354718:V451A	V	+	2	0	AKAP13	83923655	0.000000	0.05858	0.000000	0.03702	0.073000	0.16967	-0.902000	0.04088	-0.908000	0.03857	0.460000	0.39030	GTC	.	.		0.498	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200		C	86122651	T	C	86122651	3	2	282	1	0	0	0	0	1	0	0	0	449	1667	58	2	1374	2	AKAP13	15	86122651	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	691588	86122651	16408741	1041	41275										
C15orf42	90381	hgsc.bcm.edu	37	chr15	90138760	90138760	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccggatgtggctggggagaaAggaatccaaaagatacctag	14	7	0	2	rs545887163		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:90138760A>G	ENST00000268138.7	+	7	1923	c.1818A>G	c.(1816-1818)aaA>aaG	p.K606K	TICRR_ENST00000560985.1_Silent_p.K605K			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	606					cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|formation of translation preinitiation complex (GO:0001731)|mitotic DNA replication checkpoint (GO:0033314)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)	chromatin binding (GO:0003682)										CTGGGGAGAAAGGAATCCAAA	0.438													A|||	1	0.000199681	0	0	5008	,	,		17318	0.001		0	False		,,,				2504	0				p.K606K		Atlas-SNP	.											.	.	.	.	0			c.A1818G						.						101	97	98					15																	90138760		1871	4106	5977	SO:0001819	synonymous_variant	90381	exon7			GGAGAAAGGAATC	AK123612	CCDS10352.2	15q26.1	2012-07-11	2012-07-11	2012-07-11	ENSG00000140534	ENSG00000140534			28704	protein-coding gene	gene with protein product	"TOPBP1-interacting replication-stimulating protein", "SLD3 homolog (S. cerevisiae)"	613298	"chromosome 15 open reading frame 42"	C15orf42		20116089, 20080954	Standard	NM_152259		Approved	MGC45866, FLJ41618, Treslin, SLD3	uc002boe.3	Q7Z2Z1	OTTHUMG00000149648	ENST00000268138.7:c.1818A>G	chr15.hg19:g.90138760A>G		181.0	0.0		126.0	6.0	NM_152259	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Silent	SNP	ENST00000268138.7	hg19	CCDS10352.2																																																																																			.	.		0.438	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259		G	90138760	A	G	90138760	2	3	282	1	0	0	0	0	0	0	0	1	1798	69	3	2		2	C15orf42	15	90138760	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	4016109	90138760	12392632	1042	41276										
WDR93	56964	hgsc.bcm.edu	37	chr15	90278766	90278766	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atctgtgccgtggccccagtCccagccttacctggcatggt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:90278766delC	ENST00000268130.7	+	14	1691	c.1590delC	c.(1588-1590)gtcfs	p.V530fs	WDR93_ENST00000444934.2_Frame_Shift_Del_p.V247fs|WDR93_ENST00000560294.1_Frame_Shift_Del_p.V502fs	NM_020212.1	NP_064597.1	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	530					electron transport chain (GO:0022900)		oxidoreductase activity, acting on NAD(P)H (GO:0016651)			NS(1)|breast(3)|endometrium(2)|kidney(4)|large_intestine(5)|liver(2)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	33	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)			TGGCCCCAGTCCCAGCCTTAC	0.443																																					p.V530fs		Atlas-INDEL	.											.	WDR93	63	.	0			c.1589delT						.						125	117	120					15																	90278766		2200	4299	6499	SO:0001589	frameshift_variant	56964	exon14			.		CCDS32326.1, CCDS66862.1, CCDS73779.1	15q26.1	2012-11-02						"WD repeat domain containing"	26924	protein-coding gene	gene with protein product							Standard	NM_020212		Approved		uc002boj.3	Q6P2C0		ENST00000268130.7:c.1590delC	chr15.hg19:g.90278766delC	ENSP00000268130:p.Val530fs	156.0	0.0		137.0	10.0	NM_020212	Q8N7Y8|Q9NP89	Frame_Shift_Del	DEL	ENST00000268130.7	hg19	CCDS32326.1																																																																																			.	.		0.443	WDR93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416369.1	NM_020212		-	90278766	C	-	90278766	7	5	282	1	0	1	0	1	0	0	0	0	17355	842	30	0	1640	0	WDR93	15	90278766	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	140006	90278766	12252626	1043	41277										
SV2B	9899	hgsc.bcm.edu	37	chr15	91811750	91811750	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acaagtctaaaatgaaggtgTtttttggtgagcatgtgtac							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:91811750delT	ENST00000394232.1	+	9	1758	c.1288delT	c.(1288-1290)tttfs	p.F431fs	SV2B_ENST00000330276.4_Frame_Shift_Del_p.F431fs|SV2B_ENST00000545111.2_Frame_Shift_Del_p.F280fs	NM_014848.4	NP_055663.1	Q7L1I2	SV2B_HUMAN	synaptic vesicle glycoprotein 2B	431					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)			NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(17)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)			AATGAAGGTGTTTTTTGGTGA	0.408																																					p.V429fs		Atlas-INDEL	.											.	SV2B	98	.	0			c.1287delG						.						170	162	165					15																	91811750		2198	4298	6496	SO:0001589	frameshift_variant	9899	exon10			.	AB018278	CCDS10370.1, CCDS53972.1	15q26.1	2005-01-10			ENSG00000185518	ENSG00000185518			16874	protein-coding gene	gene with protein product		185861				9872452, 7681585	Standard	NM_014848		Approved	KIAA0735, HsT19680	uc002bqv.3	Q7L1I2	OTTHUMG00000149833	ENST00000394232.1:c.1288delT	chr15.hg19:g.91811750delT	ENSP00000377779:p.Phe431fs	262.0	0.0		166.0	11.0	NM_014848	B4DH30|C6G489|O94840|Q6IAR8	Frame_Shift_Del	DEL	ENST00000394232.1	hg19	CCDS10370.1																																																																																			.	.		0.408	SV2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313494.3	NM_014848		-	91811750	T	-	91811750	7	5	282	1	0	1	0	1	0	0	0	0	15433	1725	60	0	1318	0	SV2B	15	91811750	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1532984	91811750	10719642	1044	41278										
SLCO3A1	28232	hgsc.bcm.edu	37	chr15	92706012	92706012	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tccctccacccctcatcttcGgggctggcatcgactccacc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:92706012delG	ENST00000318445.6	+	10	1994	c.1780delG	c.(1780-1782)gggfs	p.G594fs	RP11-152L20.3_ENST00000561674.1_RNA|SLCO3A1_ENST00000424469.2_Frame_Shift_Del_p.G594fs|SLCO3A1_ENST00000555549.1_3'UTR|RP11-24J19.1_ENST00000557683.1_RNA	NM_013272.3	NP_037404.2	Q9UIG8	SO3A1_HUMAN	solute carrier organic anion transporter family, member 3A1	594					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)|skin(2)	25	Lung NSC(78;0.0158)|all_lung(78;0.0255)		BRCA - Breast invasive adenocarcinoma(143;0.0841)		Alprostadil(DB00770)|Aminohippurate(DB00345)|Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Iloprost(DB01088)|Methotrexate(DB00563)	CCTCATCTTCGGGGCTGGCAT	0.567																																					p.F593fs		Atlas-INDEL	.											.	SLCO3A1	84	.	0			c.1779delC						.						54	49	51					15																	92706012		2198	4298	6496	SO:0001589	frameshift_variant	28232	exon10			.	AB031050	CCDS10371.1, CCDS45354.1	15q26	2013-05-22	2003-11-25	2003-11-26	ENSG00000176463	ENSG00000176463		"Solute carriers"	10952	protein-coding gene	gene with protein product		612435	"solute carrier family 21 (organic anion transporter), member 11"	SLC21A11			Standard	NM_001145044		Approved	OATP-D, OATP3A1	uc002bqx.2	Q9UIG8	OTTHUMG00000149846	ENST00000318445.6:c.1780delG	chr15.hg19:g.92706012delG	ENSP00000320634:p.Gly594fs	329.0	0.0		211.0	13.0	NM_013272	A8K4A7|B3KPY5|B3KUR7|C6G486|Q9BW73|Q9GZV2	Frame_Shift_Del	DEL	ENST00000318445.6	hg19	CCDS10371.1																																																																																			.	.		0.567	SLCO3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313529.1	NM_013272		-	92706012	G	-	92706012	7	5	282	1	0	1	0	1	0	0	0	0	14743	1116	39	0	1818	0	SLCO3A1	15	92706012	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	894262	92706012	9825380	1045	41279										
IGF1R	3480	hgsc.bcm.edu	37	chr15	99440006	99440006	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	catgtactgcatcccttgtgAaggtccttgcccgaaggtct	10	12	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:99440006A>G	ENST00000268035.6	+	4	1585	c.974A>G	c.(973-975)gAa>gGa	p.E325G	IGF1R_ENST00000560432.1_3'UTR|IGF1R_ENST00000558762.1_Missense_Mutation_p.E325G	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	325					axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"	ATCCCTTGTGAAGGTCCTTGC	0.398																																					p.E325G		Atlas-SNP	.											.	IGF1R	147	.	0			c.A974G						.						93	84	87					15																	99440006		2197	4297	6494	SO:0001583	missense	3480	exon4			CTTGTGAAGGTCC	M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"CD molecules", "Fibronectin type III domain containing"	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.974A>G	chr15.hg19:g.99440006A>G	ENSP00000268035:p.Glu325Gly	94.0	0.0		89.0	4.0	NM_000875	B1B5Y2|Q14CV2|Q9UCC0	Missense_Mutation	SNP	ENST00000268035.6	hg19	CCDS10378.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.017997	0.75275	.	.	ENSG00000140443	ENST00000268035	D	0.97404	-4.37	5.79	5.79	0.91817	Growth factor, receptor (1);Furin-like cysteine-rich domain (1);	0.000000	0.64402	D	0.000016	D	0.95465	0.8527	L	0.53729	1.69	0.58432	D	0.999999	P;P	0.45986	0.87;0.499	B;B	0.40741	0.339;0.217	D	0.95081	0.8213	10	0.41790	T	0.15	.	16.1354	0.81481	1.0:0.0:0.0:0.0	.	325;325	C9J5X1;P08069	.;IGF1R_HUMAN	G	325	ENSP00000268035:E325G	ENSP00000268035:E325G	E	+	2	0	IGF1R	97257529	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	7.497000	0.81536	2.207000	0.71202	0.533000	0.62120	GAA	.	.		0.398	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875		G	99440006	A	G	99440006	3	3	282	1	0	0	0	0	1	0	0	0	7580	246	9	2	988	2	IGF1R	15	99440006	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	6733994	99440006	3091386	1046	41280										
IGF1R	3480	hgsc.bcm.edu	37	chr15	99459962	99459962	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	attgaggaggtcacagagaaCcccaagactgaggtgtgtgg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:99459962delC	ENST00000268035.6	+	10	2669	c.2058delC	c.(2056-2058)aacfs	p.N686fs	IGF1R_ENST00000558762.1_Frame_Shift_Del_p.N686fs	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	686	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"	TCACAGAGAACCCCAAGACTG	0.542																																					p.N686fs		Atlas-INDEL	.											.	IGF1R	147	.	0			c.2057delA						.						79	80	80					15																	99459962		2197	4297	6494	SO:0001589	frameshift_variant	3480	exon10			.	M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"CD molecules", "Fibronectin type III domain containing"	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.2058delC	chr15.hg19:g.99459962delC	ENSP00000268035:p.Asn686fs	220.0	0.0		165.0	10.0	NM_000875	B1B5Y2|Q14CV2|Q9UCC0	Frame_Shift_Del	DEL	ENST00000268035.6	hg19	CCDS10378.1																																																																																			.	.		0.542	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875		-	99459962	C	-	99459962	7	5	282	1	0	1	0	1	0	0	0	0	7580	506	18	0	2096	0	IGF1R	15	99459962	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	19956	99459962	3071430	1047	41281										
AXIN1	8312	hgsc.bcm.edu	37	chr16	341208	341208	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	actctgtctcggagagctccAtgtccgacacggctggtacc	11	14	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:341208A>G	ENST00000262320.3	-	9	2647	c.2276T>C	c.(2275-2277)aTg>aCg	p.M759T	AXIN1_ENST00000354866.3_Intron	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	759	Interaction with PPP2CA.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				GGAGAGCTCCATGTCCGACAC	0.677																																					p.M759T		Atlas-SNP	.											.	AXIN1	290	.	0			c.T2276C						.						58	41	47					16																	341208		2183	4285	6468	SO:0001583	missense	8312	exon9			AGCTCCATGTCCG	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.2276T>C	chr16.hg19:g.341208A>G	ENSP00000262320:p.Met759Thr	121.0	0.0		95.0	4.0	NM_003502	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Missense_Mutation	SNP	ENST00000262320.3	hg19	CCDS10405.1	.	.	.	.	.	.	.	.	.	.	A	1.208	-0.630629	0.03584	.	.	ENSG00000103126	ENST00000262320	T	0.59224	0.28	3.57	2.46	0.29980	.	0.590702	0.15688	N	0.249550	T	0.37919	0.1021	N	0.25647	0.755	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.07908	-1.0748	10	0.12430	T	0.62	-0.7091	7.74	0.28835	0.8929:0.0:0.1071:0.0	.	759	O15169	AXIN1_HUMAN	T	759	ENSP00000262320:M759T	ENSP00000262320:M759T	M	-	2	0	AXIN1	281209	0.996000	0.38824	0.990000	0.47175	0.992000	0.81027	1.118000	0.31246	0.458000	0.26988	0.402000	0.26972	ATG	.	.		0.677	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3			G	341208	A	G	341208	3	3	282	1	0	0	0	0	1	0	0	0	1236	217	8	2	324	2	AXIN1	16	341208	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10		341208	90013545	1048	41282										
CACNA1H	8912	hgsc.bcm.edu	37	chr16	1245064	1245064	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggacgttgagtgcggctccgAgcgctgcaacatcctggagg	16	11	0	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:1245064A>G	ENST00000348261.5	+	3	640	c.392A>G	c.(391-393)gAg>gGg	p.E131G	CACNA1H_ENST00000358590.4_Missense_Mutation_p.E131G|CACNA1H_ENST00000565831.1_Missense_Mutation_p.E131G	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	131					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	TGCGGCTCCGAGCGCTGCAAC	0.647											OREG0023543	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E131G		Atlas-SNP	.											.	CACNA1H	317	.	0			c.A392G						.						77	83	81					16																	1245064		2073	4192	6265	SO:0001583	missense	8912	exon3			GCTCCGAGCGCTG	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.392A>G	chr16.hg19:g.1245064A>G	ENSP00000334198:p.Glu131Gly	130.0	0.0	594	94.0	4.0	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	hg19	CCDS45375.1	.	.	.	.	.	.	.	.	.	.	A	16.77	3.214953	0.58452	.	.	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.97279	-4.32;-4.32	4.48	4.48	0.54585	.	0.793515	0.11701	N	0.537916	D	0.97779	0.9271	L	0.54323	1.7	0.35120	D	0.766995	D;D	0.89917	1.0;0.97	D;P	0.85130	0.997;0.683	D	0.98220	1.0477	10	0.62326	D	0.03	.	13.2699	0.60155	1.0:0.0:0.0:0.0	.	131;131	O95180-2;O95180	.;CAC1H_HUMAN	G	131	ENSP00000334198:E131G;ENSP00000351401:E131G	ENSP00000334198:E131G	E	+	2	0	CACNA1H	1185065	1.000000	0.71417	0.996000	0.52242	0.081000	0.17604	4.657000	0.61490	1.797000	0.52628	0.392000	0.25879	GAG	.	.		0.647	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407		G	1245064	A	G	1245064	3	3	282	1	0	0	0	0	1	0	0	0	2547	304	11	2	398	2	CACNA1H	16	1245064	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	903856	1245064	89109689	1049	41283										
CACNA1H	8912	hgsc.bcm.edu	37	chr16	1252154	1252154	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccaggccgcggaccccccgaCgcagagtctgtgcacagcat	12	17	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:1252154C>T	ENST00000348261.5	+	9	1952	c.1704C>T	c.(1702-1704)gaC>gaT	p.D568D	CACNA1H_ENST00000358590.4_Silent_p.D568D|CACNA1H_ENST00000565831.1_Silent_p.D568D	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	568					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	GACCCCCCGACGCAGAGTCTG	0.751																																					p.D568D		Atlas-SNP	.											CACNA1H_ENST00000358590,colon,carcinoma,0,2	CACNA1H	317	.	0			c.C1704T						.						2	3	3					16																	1252154		1441	3415	4856	SO:0001819	synonymous_variant	8912	exon9			CCCCGACGCAGAG	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.1704C>T	chr16.hg19:g.1252154C>T		72.0	1.0		47.0	3.0	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Silent	SNP	ENST00000348261.5	hg19	CCDS45375.1																																																																																			.	.		0.751	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407		T	1252154	C	T	1252154	2	4	282	1	0	0	0	0	0	0	0	1	2547	535	19	1		1	CACNA1H	16	1252154	Silent	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	7090	1252154	89102599	1050	41284										
HAGH	3029	hgsc.bcm.edu	37	chr16	1866951	1866951	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccgggctccacgtggcgtgcAaacttgaggttgttgatggt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:1866951delA	ENST00000397356.3	-	7	1096	c.690delT	c.(688-690)tttfs	p.F230fs	HAGH_ENST00000566709.1_Frame_Shift_Del_p.F182fs|HAGH_ENST00000397353.2_Frame_Shift_Del_p.F182fs|HAGH_ENST00000455446.2_Frame_Shift_Del_p.L194fs	NM_005326.4	NP_005317.2	Q16775	GLO2_HUMAN	hydroxyacylglutathione hydrolase	230					glutathione biosynthetic process (GO:0006750)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	hydroxyacylglutathione hydrolase activity (GO:0004416)|zinc ion binding (GO:0008270)			kidney(2)|lung(1)|ovary(1)|skin(1)	5		Hepatocellular(780;0.00335)			Glutathione(DB00143)	CGTGGCGTGCAAACTTGAGGT	0.607																																					p.A231fs	Pancreas(55;1048 1176 25227 40124 41333)	Atlas-INDEL	.											.	HAGH	20	.	0			c.691delG						.						122	100	108					16																	1866951		2199	4300	6499	SO:0001589	frameshift_variant	3029	exon7			.	X90999	CCDS32366.1, CCDS10447.2, CCDS66900.1	16p13.3	2012-10-02	2003-11-04		ENSG00000063854	ENSG00000063854	3.1.2.6		4805	protein-coding gene	gene with protein product		138760	"hydroxyacyl glutathione hydrolase"			3025077, 7327557	Standard	NM_001286249		Approved	GLO2, GLXII, HAGH1	uc002cna.3	Q16775	OTTHUMG00000128662	ENST00000397356.3:c.690delT	chr16.hg19:g.1866951delA	ENSP00000380514:p.Phe230fs	188.0	0.0		165.0	10.0	NM_005326	A8K290|B4DP33|B4DRA7|E7EN93	Frame_Shift_Del	DEL	ENST00000397356.3	hg19	CCDS10447.2																																																																																			.	.		0.607	HAGH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250548.2	NM_005326		-	1866951	A	-	1866951	7	5	282	1	0	1	0	1	0	0	0	0	6954	127	5	0	248	0	HAGH	16	1866951	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	614797	1866951	88487802	1051	41285										
PDPK1	5170	hgsc.bcm.edu	37	chr16	2607955	2607955	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaaatccttggggaaggctcTttttccacggtgagtatttg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:2607955delT	ENST00000342085.4	+	2	425	c.276delT	c.(274-276)tctfs	p.S92fs	PDPK1_ENST00000354836.5_Frame_Shift_Del_p.S92fs|PDPK1_ENST00000441549.3_Frame_Shift_Del_p.S92fs|PDPK1_ENST00000389224.3_Frame_Shift_Del_p.S65fs|PDPK1_ENST00000268673.7_Frame_Shift_Del_p.S92fs|RP11-20I23.13_ENST00000563449.2_RNA|RP11-20I23.11_ENST00000569220.1_RNA	NM_002613.4	NP_002604.1	O15530	PDPK1_HUMAN	3-phosphoinositide dependent protein kinase 1	92	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|activation of protein kinase B activity (GO:0032148)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|cell migration (GO:0016477)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway (GO:0097191)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|focal adhesion assembly (GO:0048041)|hyperosmotic response (GO:0006972)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of endothelial cell migration (GO:0010594)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of mast cell degranulation (GO:0043304)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell development (GO:0003323)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	3-phosphoinositide-dependent protein kinase activity (GO:0004676)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)	7		Ovarian(90;0.17)			Celecoxib(DB00482)	GGGAAGGCTCTTTTTCCACGG	0.607																																					p.S92fs		Atlas-INDEL	.											.	PDPK1	37	.	0			c.275delC						.						49	56	54					16																	2607955		2103	4138	6241	SO:0001589	frameshift_variant	5170	exon2			.	AF017995	CCDS10472.1, CCDS10473.1, CCDS58411.1	16p13.3	2014-03-20	2014-03-20		ENSG00000140992	ENSG00000140992			8816	protein-coding gene	gene with protein product	"PkB kinase"	605213				9094314, 9445477	Standard	NM_002613		Approved	PDK1	uc002cqs.4	O15530	OTTHUMG00000128874	ENST00000342085.4:c.276delT	chr16.hg19:g.2607955delT	ENSP00000344220:p.Ser92fs	339.0	0.0		208.0	16.0	NM_001261816	H0Y4Z0|Q59EH6|Q6FI20|Q8IV52|Q9BRD5	Frame_Shift_Del	DEL	ENST00000342085.4	hg19	CCDS10472.1																																																																																			.	.		0.607	PDPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250831.3			-	2607955	T	-	2607955	7	5	282	1	0	1	0	1	0	0	0	0	11696	1596	56	0	282	0	PDPK1	16	2607955	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	741004	2607955	87746798	1052	41286										
ZNF200	7752	hgsc.bcm.edu	37	chr16	3273915	3273915	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cttctgctttcgggtcttacAggctgagtgggttttctcat	11	9	3	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:3273915A>G	ENST00000431561.3	-	5	1777	c.1165T>C	c.(1165-1167)Tgt>Cgt	p.C389R	ZNF200_ENST00000414144.2_Missense_Mutation_p.C389R|ZNF200_ENST00000396868.3_Missense_Mutation_p.C388R|ZNF200_ENST00000575948.1_Missense_Mutation_p.C388R|ZNF200_ENST00000396870.4_Missense_Mutation_p.C388R|ZNF200_ENST00000396871.4_Missense_Mutation_p.C388R|AJ003147.9_ENST00000576468.1_RNA	NM_001145447.1|NM_003454.3	NP_001138919.1|NP_003445.2	P98182	ZN200_HUMAN	zinc finger protein 200	389					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(2)|kidney(2)|large_intestine(4)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	17						CGGGTCTTACAGGCTGAGTGG	0.483																																					p.C389R		Atlas-SNP	.											.	ZNF200	36	.	0			c.T1165C						.						195	207	203					16																	3273915		2197	4300	6497	SO:0001583	missense	7752	exon5			TCTTACAGGCTGA	AF060866	CCDS10497.1, CCDS42112.1, CCDS45395.1	16p13.3	2013-01-08			ENSG00000010539	ENSG00000010539		"Zinc fingers, C2H2-type"	12993	protein-coding gene	gene with protein product		603231				9288094, 9787081	Standard	NM_003454		Approved		uc002cuk.2	P98182	OTTHUMG00000129317	ENST00000431561.3:c.1165T>C	chr16.hg19:g.3273915A>G	ENSP00000395723:p.Cys389Arg	141.0	0.0		108.0	5.0	NM_003454	D3DUB7|D3DUB8|O15361|Q5XKM5|Q7Z5V1	Missense_Mutation	SNP	ENST00000431561.3	hg19	CCDS10497.1	.	.	.	.	.	.	.	.	.	.	A	3.233	-0.157040	0.06544	.	.	ENSG00000010539	ENST00000396870;ENST00000396868;ENST00000396871;ENST00000414144;ENST00000431561	T;T;T	0.05786	3.4;3.39;3.44	5.42	3.06	0.35304	Zinc finger, C2H2 (1);	0.536582	0.15812	N	0.243428	T	0.02455	0.0075	N	0.04746	-0.17	0.09310	N	1	P;P;P	0.37636	0.468;0.468;0.603	B;B;B	0.31812	0.064;0.064;0.136	T	0.40496	-0.9560	10	0.33940	T	0.23	-26.442	3.4599	0.07529	0.6953:0.0:0.1061:0.1986	.	388;389;388	D3DUB7;P98182;P98182-2	.;ZN200_HUMAN;.	R	389;388;388;388;389	ENSP00000380077:C388R;ENSP00000380080:C388R;ENSP00000395723:C389R	ENSP00000380077:C388R	C	-	1	0	ZNF200	3213916	0.003000	0.15002	0.284000	0.24805	0.894000	0.52154	1.828000	0.39111	1.019000	0.39547	0.455000	0.32223	TGT	.	.		0.483	ZNF200-005	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000437545.1			G	3273915	A	G	3273915	3	3	282	1	0	0	0	0	1	0	0	0	17777	188	7	2	26	2	ZNF200	16	3273915	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	665960	3273915	87080838	1053	41287										
ZNF200	7752	hgsc.bcm.edu	37	chr16	3274133	3274133	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gatgagaattctgacggaagTtttttccacactgagaacag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:3274133delT	ENST00000431561.3	-	5	1559	c.947delA	c.(946-948)aacfs	p.N316fs	ZNF200_ENST00000414144.2_Frame_Shift_Del_p.N316fs|ZNF200_ENST00000396868.3_Frame_Shift_Del_p.N315fs|ZNF200_ENST00000575948.1_Frame_Shift_Del_p.N315fs|ZNF200_ENST00000396870.4_Frame_Shift_Del_p.N315fs|ZNF200_ENST00000396871.4_Frame_Shift_Del_p.N315fs|AJ003147.9_ENST00000576468.1_RNA	NM_001145447.1|NM_003454.3	NP_001138919.1|NP_003445.2	P98182	ZN200_HUMAN	zinc finger protein 200	316					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(2)|kidney(2)|large_intestine(4)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	17						CTGACGGAAGTTTTTTCCACA	0.388																																					p.N316fs		Atlas-INDEL	.											.	ZNF200	36	.	0			c.948delC						.						112	111	111					16																	3274133		2197	4300	6497	SO:0001589	frameshift_variant	7752	exon5			.	AF060866	CCDS10497.1, CCDS42112.1, CCDS45395.1	16p13.3	2013-01-08			ENSG00000010539	ENSG00000010539		"Zinc fingers, C2H2-type"	12993	protein-coding gene	gene with protein product		603231				9288094, 9787081	Standard	NM_003454		Approved		uc002cuk.2	P98182	OTTHUMG00000129317	ENST00000431561.3:c.947delA	chr16.hg19:g.3274133delT	ENSP00000395723:p.Asn316fs	221.0	0.0		175.0	11.0	NM_003454	D3DUB7|D3DUB8|O15361|Q5XKM5|Q7Z5V1	Frame_Shift_Del	DEL	ENST00000431561.3	hg19	CCDS10497.1																																																																																			.	.		0.388	ZNF200-005	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000437545.1			-	3274133	T	-	3274133	7	5	282	1	0	1	0	1	0	0	0	0	17777	1725	60	0	244	0	ZNF200	16	3274133	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	218	3274133	87080620	1054	41288										
ZNF200	7752	hgsc.bcm.edu	37	chr16	3283724	3283724	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	taaaggactgctttggctttGggggcataggaaccactttt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:3283724delG	ENST00000431561.3	-	2	644	c.32delC	c.(31-33)ccafs	p.P11fs	ZNF200_ENST00000414144.2_Frame_Shift_Del_p.P11fs|ZNF200_ENST00000396868.3_Frame_Shift_Del_p.P11fs|ZNF200_ENST00000575948.1_Frame_Shift_Del_p.P11fs|ZNF200_ENST00000396870.4_Frame_Shift_Del_p.P11fs|ZNF200_ENST00000396871.4_Frame_Shift_Del_p.P11fs	NM_001145447.1|NM_003454.3	NP_001138919.1|NP_003445.2	P98182	ZN200_HUMAN	zinc finger protein 200	11					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(2)|kidney(2)|large_intestine(4)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	17						CTTTGGCTTTGGGGGCATAGG	0.552																																					p.P11fs		Atlas-INDEL	.											.	ZNF200	36	.	0			c.33delA						.						140	133	136					16																	3283724		2197	4300	6497	SO:0001589	frameshift_variant	7752	exon2			.	AF060866	CCDS10497.1, CCDS42112.1, CCDS45395.1	16p13.3	2013-01-08			ENSG00000010539	ENSG00000010539		"Zinc fingers, C2H2-type"	12993	protein-coding gene	gene with protein product		603231				9288094, 9787081	Standard	NM_003454		Approved		uc002cuk.2	P98182	OTTHUMG00000129317	ENST00000431561.3:c.32delC	chr16.hg19:g.3283724delG	ENSP00000395723:p.Pro11fs	234.0	0.0		156.0	12.0	NM_003454	D3DUB7|D3DUB8|O15361|Q5XKM5|Q7Z5V1	Frame_Shift_Del	DEL	ENST00000431561.3	hg19	CCDS10497.1																																																																																			.	.		0.552	ZNF200-005	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000437545.1			-	3283724	G	-	3283724	7	5	282	1	0	1	0	1	0	0	0	0	17777	1348	47	0	1171	0	ZNF200	16	3283724	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	9591	3283724	87071029	1055	41289										
ADCY9	115	hgsc.bcm.edu	37	chr16	4027526	4027526	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gagcaggagcagcggcccggCccccacgacggtggcgaggg					rs144319192		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:4027526delC	ENST00000294016.3	-	9	3323	c.2785delG	c.(2785-2787)gccfs	p.A929fs		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	929					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						AGCGGCCCGGCCCCCACGACG	0.667																																					p.A929fs		Atlas-INDEL	.											.	ADCY9	151	.	0			c.2786delC						.						33	26	28					16																	4027526		2182	4295	6477	SO:0001589	frameshift_variant	115	exon9			.	AF036927	CCDS32382.1	16p13.3	2013-02-04				ENSG00000162104	4.6.1.1	"Adenylate cyclases"	240	protein-coding gene	gene with protein product		603302				9628827	Standard	NM_001116		Approved	AC9	uc002cvx.3	O60503		ENST00000294016.3:c.2785delG	chr16.hg19:g.4027526delC	ENSP00000294016:p.Ala929fs	306.0	0.0		203.0	13.0	NM_001116	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Frame_Shift_Del	DEL	ENST00000294016.3	hg19	CCDS32382.1																																																																																			.	.		0.667	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1			-	4027526	C	-	4027526	7	5	282	1	0	1	0	1	0	0	0	0	301	739	26	0	1288	0	ADCY9	16	4027526	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	743802	4027526	86327227	1056	41290										
CORO7	79585	hgsc.bcm.edu	37	chr16	4410485	4410485	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tccggggcctgtagacccgcAcacgcccatccttgcagaca	10	17	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:4410485A>G	ENST00000251166.4	-	20	2127	c.1982T>C	c.(1981-1983)gTg>gCg	p.V661A	CORO7-PAM16_ENST00000572467.1_Missense_Mutation_p.V661A|CORO7_ENST00000539968.1_Missense_Mutation_p.V441A|CORO7_ENST00000537233.2_Missense_Mutation_p.V643A|CORO7-PAM16_ENST00000572274.1_5'Flank|CORO7_ENST00000423908.2_3'UTR|CORO7_ENST00000574025.1_Missense_Mutation_p.V576A	NM_024535.4	NP_078811.3	P57737	CORO7_HUMAN	coronin 7	661					actin filament polymerization (GO:0030041)|Golgi to endosome transport (GO:0006895)|protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)			breast(3)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(8)|prostate(2)|skin(2)|urinary_tract(2)	23						GTAGACCCGCACACGCCCATC	0.652																																					p.V661A		Atlas-SNP	.											.	CORO7	73	.	0			c.T1982C						.						36	40	38					16																	4410485		2193	4297	6490	SO:0001583	missense	79585	exon20			ACCCGCACACGCC	AK097238	CCDS10513.1, CCDS55982.1, CCDS58417.1	16p13.3	2013-01-10			ENSG00000262246	ENSG00000262246		"Coronins", "WD repeat domain containing"	26161	protein-coding gene	gene with protein product		611668				15327992	Standard	NM_024535		Approved	FLJ22021		P57737	OTTHUMG00000129465	ENST00000251166.4:c.1982T>C	chr16.hg19:g.4410485A>G	ENSP00000251166:p.Val661Ala	155.0	0.0		131.0	7.0	NM_024535	B4DFD6|B4DL18|I3L416|Q17RK4	Missense_Mutation	SNP	ENST00000251166.4	hg19	CCDS10513.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.230187	0.79688	.	.	ENSG00000103426	ENST00000251166;ENST00000537233;ENST00000539968	T;T	0.66460	-0.21;-0.21	5.18	5.18	0.71444	WD40/YVTN repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.599767	0.16100	N	0.229640	T	0.66992	0.2846	L	0.58583	1.82	0.80722	D	1	B;B;B;P;P	0.40578	0.234;0.201;0.406;0.722;0.67	B;B;B;B;B	0.41440	0.297;0.13;0.32;0.205;0.357	T	0.69510	-0.5126	10	0.54805	T	0.06	-4.6904	14.6767	0.68986	1.0:0.0:0.0:0.0	.	576;643;441;661;642	P57737-2;B4DFD6;B3KUH7;P57737;B4DKU9	.;.;.;CORO7_HUMAN;.	A	661;576;441	ENSP00000251166:V661A;ENSP00000446221:V441A	ENSP00000251166:V661A	V	-	2	0	CORO7	4350486	0.922000	0.31269	0.894000	0.35097	0.654000	0.38779	8.317000	0.89987	1.952000	0.56665	0.379000	0.24179	GTG	.	.		0.652	CORO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251628.2	NM_024535		G	4410485	A	G	4410485	3	3	282	1	0	0	0	0	1	0	0	0	3761	159	6	2	831	2	CORO7	16	4410485	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	382959	4410485	85944268	1057	41291										
C16orf71	146562	hgsc.bcm.edu	37	chr16	4797357	4797357	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtcacaggacctgtaccgggAaaagccagcttctccagcag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:4797357delA	ENST00000299320.5	+	9	1772	c.1294delA	c.(1294-1296)aaafs	p.K432fs	C16orf71_ENST00000590191.1_Frame_Shift_Del_p.K449fs|RP11-127I20.7_ENST00000588099.1_RNA	NM_139170.2	NP_631909.2	Q8IYS4	CP071_HUMAN	chromosome 16 open reading frame 71	432										breast(1)|central_nervous_system(1)|large_intestine(4)|lung(4)|ovary(1)	11						CTGTACCGGGAAAAGCCAGCT	0.632																																					p.G431fs		Atlas-INDEL	.											.	C16orf71	46	.	0			c.1293delG						.						55	64	61					16																	4797357		2187	4280	6467	SO:0001589	frameshift_variant	146562	exon9			.	AF447587	CCDS10521.1	16p13.3	2008-02-05			ENSG00000166246	ENSG00000166246			25081	protein-coding gene	gene with protein product						12477932	Standard	XM_005255144		Approved	FLJ43261, DKFZp686H2240	uc002cxn.3	Q8IYS4	OTTHUMG00000129480	ENST00000299320.5:c.1294delA	chr16.hg19:g.4797357delA	ENSP00000299320:p.Lys432fs	296.0	0.0		191.0	12.0	NM_139170	Q8NCV0	Frame_Shift_Del	DEL	ENST00000299320.5	hg19	CCDS10521.1																																																																																			.	.		0.632	C16orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251644.1	NM_139170		-	4797357	A	-	4797357	7	5	282	1	0	1	0	1	0	0	0	0	1832	247	9	0	1324	0	C16orf71	16	4797357	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	386872	4797357	85557396	1058	41292										
A2BP1	54715	hgsc.bcm.edu	37	chr16	7568215	7568215	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acgcttcggcccagtttgctCccccgcagaacggtatcccc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:7568215delC	ENST00000550418.1	+	5	1082	c.94delC	c.(94-96)cccfs	p.P33fs	RBFOX1_ENST00000311745.5_Frame_Shift_Del_p.P53fs|RBFOX1_ENST00000422070.4_Frame_Shift_Del_p.P76fs|RBFOX1_ENST00000436368.2_Frame_Shift_Del_p.P53fs|RBFOX1_ENST00000355637.4_Frame_Shift_Del_p.P53fs|RBFOX1_ENST00000535565.2_Frame_Shift_Del_p.P69fs|RBFOX1_ENST00000340209.4_Frame_Shift_Del_p.P38fs|RBFOX1_ENST00000547372.1_Frame_Shift_Del_p.P76fs|RBFOX1_ENST00000553186.1_Frame_Shift_Del_p.P33fs|RBFOX1_ENST00000552089.1_Frame_Shift_Del_p.P69fs|RBFOX1_ENST00000547338.1_Frame_Shift_Del_p.P33fs	NM_018723.3	NP_061193.2	Q9NWB1	RFOX1_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 1	33					mRNA processing (GO:0006397)|neuromuscular process controlling balance (GO:0050885)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|RNA transport (GO:0050658)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	nucleotide binding (GO:0000166)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|lung(17)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)	55						CCAGTTTGCTCCCCCGCAGAA	0.587																																					p.A51fs	Ovarian(157;934 2567 15163 39509)	Atlas-INDEL	.											.	RBFOX1	341	.	0			c.153delT						.						130	130	130					16																	7568215		2197	4300	6497	SO:0001589	frameshift_variant	54715	exon2			.	AF107203	CCDS10531.1, CCDS10532.1, CCDS45405.1, CCDS55983.1, CCDS55984.1	16p13.3	2013-02-12			ENSG00000078328	ENSG00000078328		"RNA binding motif (RRM) containing"	18222	protein-coding gene	gene with protein product	"ataxin 2-binding protein 1", "hexaribonucleotide binding protein 1"	605104				10814712, 16260614	Standard	NM_018723		Approved	A2BP1, FOX-1, HRNBP1	uc002cyy.2	Q9NWB1	OTTHUMG00000129551	ENST00000550418.1:c.94delC	chr16.hg19:g.7568215delC	ENSP00000450031:p.Pro33fs	194.0	0.0		160.0	11.0	NM_145891	Q7Z7I7|Q8TAE3|Q8TAF2|Q8WYB2|Q9NS20	Frame_Shift_Del	DEL	ENST00000550418.1	hg19	CCDS55983.1																																																																																			.	.		0.587	RBFOX1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409492.2	NM_145891		-	7568215	C	-	7568215	7	5	282	1	0	1	0	1	0	0	0	0	3	855	30	0	191	0	A2BP1	16	7568215	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	2770858	7568215	82786538	1059	41293										
TMEM186	25880	hgsc.bcm.edu	37	chr16	8890335	8890335	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccttcgagatgggtgaactgCtgcccacccacctcttagga	10	14	1	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:8890335C>T	ENST00000333050.6	-	2	149	c.116G>A	c.(115-117)aGc>aAc	p.S39N	TMEM186_ENST00000564869.1_Intron|PMM2_ENST00000569958.1_5'Flank|PMM2_ENST00000566983.1_Intron|PMM2_ENST00000268261.4_5'Flank|PMM2_ENST00000537352.1_5'Flank|PMM2_ENST00000539622.1_5'Flank	NM_015421.3	NP_056236.2	Q96B77	TM186_HUMAN	transmembrane protein 186	39						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				NS(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	9						GGGTGAACTGCTGCCCACCCA	0.537																																					p.S39N		Atlas-SNP	.											.	TMEM186	21	.	0			c.G116A						.						116	121	120					16																	8890335		2197	4300	6497	SO:0001583	missense	25880	exon2			GAACTGCTGCCCA	BC015912	CCDS10535.1	16p13.2	2008-02-05	2007-02-08	2007-02-08	ENSG00000184857	ENSG00000184857			24530	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 51"	C16orf51		11230166	Standard	NM_015421		Approved	DKFZP564K2062	uc002cze.3	Q96B77	OTTHUMG00000129696	ENST00000333050.6:c.116G>A	chr16.hg19:g.8890335C>T	ENSP00000331640:p.Ser39Asn	204.0	0.0		139.0	6.0	NM_015421	B2RAY0|Q9Y4T4	Missense_Mutation	SNP	ENST00000333050.6	hg19	CCDS10535.1	.	.	.	.	.	.	.	.	.	.	C	12.58	1.980444	0.34942	.	.	ENSG00000184857	ENST00000333050	.	.	.	5.31	2.28	0.28536	.	0.394396	0.21823	N	0.068584	T	0.41050	0.1142	M	0.63428	1.95	0.09310	N	0.999997	B	0.14012	0.009	B	0.16289	0.015	T	0.36866	-0.9730	9	0.51188	T	0.08	-12.7793	6.6541	0.22979	0.0:0.6926:0.1563:0.1511	.	39	Q96B77	TM186_HUMAN	N	39	.	ENSP00000331640:S39N	S	-	2	0	TMEM186	8797836	0.041000	0.20044	0.025000	0.17156	0.008000	0.06430	0.638000	0.24674	0.324000	0.23333	0.655000	0.94253	AGC	.	.		0.537	TMEM186-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251903.1	NM_015421		T	8890335	C	T	8890335	3	4	282	1	0	0	0	0	1	0	0	0	16123	797	28	3	529	3	TMEM186	16	8890335	Missense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1322120	8890335	81464418	1060	41294										
ATF7IP2	80063	hgsc.bcm.edu	37	chr16	10525288	10525288	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtgcagactcaacatggcagTcatcacttgacactaataac	7	11	3	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:10525288T>C	ENST00000396560.2	+	3	1038	c.811T>C	c.(811-813)Tca>Cca	p.S271P	ATF7IP2_ENST00000543967.1_Intron|ATF7IP2_ENST00000396559.1_Missense_Mutation_p.S271P|ATF7IP2_ENST00000324570.5_Missense_Mutation_p.S271P|ATF7IP2_ENST00000356427.2_Missense_Mutation_p.S271P	NM_024997.3	NP_079273.2	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting protein 2	271					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				large_intestine(3)	3						AACATGGCAGTCATCACTTGA	0.318																																					p.S271P		Atlas-SNP	.											.	ATF7IP2	40	.	0			c.T811C						.						51	52	51					16																	10525288		2191	4296	6487	SO:0001583	missense	80063	exon3			TGGCAGTCATCAC	AK022730	CCDS10540.1, CCDS58422.1	16p13.2	2008-02-05			ENSG00000166669	ENSG00000166669			20397	protein-coding gene	gene with protein product		613645					Standard	NM_001256160		Approved	FLJ12668	uc002czu.3	Q5U623	OTTHUMG00000129749	ENST00000396560.2:c.811T>C	chr16.hg19:g.10525288T>C	ENSP00000379808:p.Ser271Pro	235.0	0.0		156.0	7.0	NM_024997	B2RNR2|Q53EZ7|Q658U2|Q6IS97|Q8N9X8|Q9H9L6	Missense_Mutation	SNP	ENST00000396560.2	hg19	CCDS10540.1	.	.	.	.	.	.	.	.	.	.	T	5.177	0.218143	0.09810	.	.	ENSG00000166669	ENST00000396559;ENST00000396560;ENST00000535850;ENST00000356427;ENST00000324570	T;T;T;T;T	0.45668	0.89;0.89;0.89;0.89;0.89	5.61	3.35	0.38373	.	0.427317	0.17377	N	0.176434	T	0.31199	0.0789	L	0.40543	1.245	0.09310	N	1	B;B	0.21606	0.058;0.033	B;B	0.21546	0.035;0.035	T	0.23619	-1.0183	10	0.45353	T	0.12	-0.6523	5.7072	0.17915	0.0:0.087:0.1709:0.7421	.	271;271	Q5U623-2;Q5U623	.;MCAF2_HUMAN	P	271	ENSP00000379807:S271P;ENSP00000379808:S271P;ENSP00000440791:S271P;ENSP00000348799:S271P;ENSP00000322811:S271P	ENSP00000322811:S271P	S	+	1	0	ATF7IP2	10432789	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	0.113000	0.15499	0.409000	0.25649	0.459000	0.35465	TCA	.	.		0.318	ATF7IP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251961.1	NM_024997		C	10525288	T	C	10525288	3	2	282	1	0	0	0	0	1	0	0	0	1088	1667	58	2	813	2	ATF7IP2	16	10525288	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1634953	10525288	79829465	1061	41295										
ATF7IP2	80063	hgsc.bcm.edu	37	chr16	10551340	10551340	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acccttccgaaaaaggaagtAaaaaaattaatttgtcatca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:10551340delA	ENST00000396560.2	+	7	1533	c.1306delA	c.(1306-1308)aaafs	p.K437fs	ATF7IP2_ENST00000543967.1_Intron|ATF7IP2_ENST00000396559.1_Frame_Shift_Del_p.K437fs|ATF7IP2_ENST00000324570.5_Frame_Shift_Del_p.K437fs|ATF7IP2_ENST00000356427.2_Frame_Shift_Del_p.K437fs	NM_024997.3	NP_079273.2	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting protein 2	437					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				large_intestine(3)	3						AAAAGGAAGTAAAAAAATTAA	0.294																																					p.S435fs		Atlas-INDEL	.											.	ATF7IP2	40	.	0			c.1305delT						.						93	105	101					16																	10551340		2196	4295	6491	SO:0001589	frameshift_variant	80063	exon7			.	AK022730	CCDS10540.1, CCDS58422.1	16p13.2	2008-02-05			ENSG00000166669	ENSG00000166669			20397	protein-coding gene	gene with protein product		613645					Standard	NM_001256160		Approved	FLJ12668	uc002czu.3	Q5U623	OTTHUMG00000129749	ENST00000396560.2:c.1306delA	chr16.hg19:g.10551340delA	ENSP00000379808:p.Lys437fs	212.0	0.0		186.0	13.0	NM_024997	B2RNR2|Q53EZ7|Q658U2|Q6IS97|Q8N9X8|Q9H9L6	Frame_Shift_Del	DEL	ENST00000396560.2	hg19	CCDS10540.1																																																																																			.	.		0.294	ATF7IP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251961.1	NM_024997		-	10551340	A	-	10551340	7	5	282	1	0	1	0	1	0	0	0	0	1088	363	13	0	1324	0	ATF7IP2	16	10551340	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	26052	10551340	79803413	1062	41296										
MKL2	57496	hgsc.bcm.edu	37	chr16	14352004	14352004	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggatgacctctttgatatccTcattaagagtggaggtaagt	11	6	2	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:14352004T>C	ENST00000341243.5	+	14	2717	c.2717T>C	c.(2716-2718)cTc>cCc	p.L906P	MKL2_ENST00000318282.5_Missense_Mutation_p.L867P|MKL2_ENST00000574045.1_Missense_Mutation_p.L867P|MKL2_ENST00000571589.1_Missense_Mutation_p.L917P			Q9ULH7	MKL2_HUMAN	MKL/myocardin-like 2	906					blood vessel morphogenesis (GO:0048514)|cardiac muscle tissue development (GO:0048738)|embryonic organ development (GO:0048568)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|muscle organ development (GO:0007517)|positive regulation of striated muscle tissue development (GO:0045844)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(6)|liver(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						TTTGATATCCTCATTAAGAGT	0.393																																					p.L867P		Atlas-SNP	.											.	MKL2	103	.	0			c.T2600C						.						102	86	92					16																	14352004		2197	4300	6497	SO:0001583	missense	57496	exon16			ATATCCTCATTAA	AB033069	CCDS32391.1	16p13.12	2012-11-29			ENSG00000186260	ENSG00000186260			29819	protein-coding gene	gene with protein product		609463				10574462	Standard	NM_014048		Approved	MRTF-B, FLJ31823	uc002dcg.3	Q9ULH7	OTTHUMG00000177379	ENST00000341243.5:c.2717T>C	chr16.hg19:g.14352004T>C	ENSP00000345841:p.Leu906Pro	151.0	0.0		124.0	5.0	NM_014048	A6ND53|B4DGT8|Q68CT1|Q6UB16|Q86WW2|Q8N226	Missense_Mutation	SNP	ENST00000341243.5	hg19		.	.	.	.	.	.	.	.	.	.	T	22.5	4.295194	0.81025	.	.	ENSG00000186260	ENST00000318282;ENST00000341243	.	.	.	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.79975	0.4539	M	0.81497	2.545	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.83039	-0.0158	9	0.87932	D	0	-21.2488	14.7871	0.69810	0.0:0.0:0.0:1.0	.	917;867	B4DGT8;Q9ULH7-4	.;.	P	867;906	.	ENSP00000339086:L867P	L	+	2	0	MKL2	14259505	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.577000	0.82486	2.098000	0.63641	0.460000	0.39030	CTC	.	.		0.393	MKL2-202	KNOWN	basic	protein_coding	protein_coding		NM_014048		C	14352004	T	C	14352004	3	2	282	1	0	0	0	0	1	0	0	0	9611	1551	54	2	2654	2	MKL2	16	14352004	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3800664	14352004	76002749	1063	41297										
PARN	5073	hgsc.bcm.edu	37	chr16	14576541	14576541	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagggtgtagggtatgcactGggggtttaaccgtttgctgt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:14576541delG	ENST00000437198.2	-	22	1765	c.1624delC	c.(1624-1626)cagfs	p.Q542fs	PARN_ENST00000420015.2_Frame_Shift_Del_p.Q496fs|PARN_ENST00000341484.7_Frame_Shift_Del_p.Q481fs|PARN_ENST00000539279.1_Frame_Shift_Del_p.Q367fs	NM_001134477.2|NM_002582.3	NP_001127949.1|NP_002573.1	O95453	PARN_HUMAN	poly(A)-specific ribonuclease	542					female gamete generation (GO:0007292)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA metabolic process (GO:0016070)|RNA modification (GO:0009451)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|mRNA 3'-UTR binding (GO:0003730)|nuclease activity (GO:0004518)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(A)-specific ribonuclease activity (GO:0004535)|protein kinase binding (GO:0019901)			cervix(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|urinary_tract(1)	21						GGTATGCACTGGGGGTTTAAC	0.443																																					p.Q542fs		Atlas-INDEL	.											.	PARN	72	.	0			c.1625delA						.						213	194	200					16																	14576541		1889	4130	6019	SO:0001589	frameshift_variant	5073	exon22			.	AJ005698	CCDS45419.1, CCDS45420.1, CCDS58425.1	16p13	2014-08-08	2011-07-07		ENSG00000140694	ENSG00000140694	3.1.13.4		8609	protein-coding gene	gene with protein product	"deadenylation nuclease"	604212	"poly(A)-specific ribonuclease (deadenylation nuclease)"			10640832	Standard	NM_002582		Approved	DAN	uc010uzd.2	O95453	OTTHUMG00000173199	ENST00000437198.2:c.1624delC	chr16.hg19:g.14576541delG	ENSP00000387911:p.Gln542fs	317.0	0.0		200.0	15.0	NM_002582	B2RCB3|B4DDG8|B4DWR4|B4E1H6	Frame_Shift_Del	DEL	ENST00000437198.2	hg19	CCDS45419.1																																																																																			.	.		0.443	PARN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422383.1	NM_002582		-	14576541	G	-	14576541	7	5	282	1	0	1	0	1	0	0	0	0	11462	1357	47	0	307	0	PARN	16	14576541	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	224537	14576541	75778212	1064	41298										
ABCC1	4363	hgsc.bcm.edu	37	chr16	16235094	16235094	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	catcggacctcctgcagcagAgaggtcttttctacagcatg	10	12	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:16235094A>G	ENST00000399410.3	+	31	4727	c.4552A>G	c.(4552-4554)Aga>Gga	p.R1518G	ABCC1_ENST00000345148.5_Missense_Mutation_p.R1453G|ABCC1_ENST00000351154.5_Missense_Mutation_p.R1459G|ABCC1_ENST00000349029.5_Missense_Mutation_p.R1403G|ABCC1_ENST00000399408.2_Missense_Mutation_p.R1528G|ABCC1_ENST00000346370.5_Missense_Mutation_p.R1462G	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	1518	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				arachidonic acid metabolic process (GO:0019369)|ATP catabolic process (GO:0006200)|cobalamin metabolic process (GO:0009235)|leukotriene metabolic process (GO:0006691)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(5)|prostate(1)|skin(3)	56					Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	CCTGCAGCAGAGAGGTCTTTT	0.592																																					p.R1518G		Atlas-SNP	.											.	ABCC1	156	.	0			c.A4552G						.						118	122	121					16																	16235094		1921	4115	6036	SO:0001583	missense	4363	exon31			CAGCAGAGAGGTC	L05628	CCDS42122.1	16p13.1	2012-03-14			ENSG00000103222	ENSG00000103222		"ATP binding cassette transporters / subfamily C"	51	protein-coding gene	gene with protein product		158343	"multidrug resistance associated protein 1"	MRP, MRP1		8098549, 1360704	Standard	NM_004996		Approved	GS-X	uc010bvi.3	P33527	OTTHUMG00000048267	ENST00000399410.3:c.4552A>G	chr16.hg19:g.16235094A>G	ENSP00000382342:p.Arg1518Gly	106.0	0.0		117.0	5.0	NM_004996	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Missense_Mutation	SNP	ENST00000399410.3	hg19	CCDS42122.1	.	.	.	.	.	.	.	.	.	.	A	15.86	2.957170	0.53293	.	.	ENSG00000103222	ENST00000399410;ENST00000399408;ENST00000346370;ENST00000351154;ENST00000345148;ENST00000349029;ENST00000536381	T;T;T;T;T;T	0.68181	-0.31;-0.31;-0.31;-0.31;0.1;-0.31	5.26	4.16	0.48862	ABC transporter-like (1);	0.395203	0.29783	N	0.011204	T	0.42877	0.1222	N	0.01771	-0.73	0.27345	N	0.9564	B;P;B;P;B;B	0.44521	0.011;0.837;0.246;0.554;0.159;0.246	B;P;B;B;B;B	0.44673	0.016;0.457;0.197;0.155;0.097;0.197	T	0.36163	-0.9759	10	0.36615	T	0.2	-5.7442	10.6785	0.45799	0.6928:0.3072:0.0:0.0	.	1403;1453;1462;1459;1518;1528	P33527-5;P33527-4;P33527-3;P33527-2;P33527;P33527-9	.;.;.;.;MRP1_HUMAN;.	G	1518;1528;1462;1459;1453;1403;1202	ENSP00000382342:R1518G;ENSP00000382340:R1528G;ENSP00000263019:R1462G;ENSP00000263017:R1459G;ENSP00000263014:R1453G;ENSP00000263016:R1403G	ENSP00000263014:R1453G	R	+	1	2	ABCC1	16142595	0.995000	0.38212	0.853000	0.33588	0.698000	0.40448	3.563000	0.53784	0.815000	0.34398	0.533000	0.62120	AGA	.	.		0.592	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996		G	16235094	A	G	16235094	3	3	282	1	0	0	0	0	1	0	0	0	49	296	11	2	4674	2	ABCC1	16	16235094	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1658553	16235094	74119659	1065	41299										
PDILT	204474	hgsc.bcm.edu	37	chr16	20387460	20387460	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cctgctcgctgctgttgaacAaaaatgctttctggctaatt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:20387460delA	ENST00000302451.4	-	4	721	c.473delT	c.(472-474)ttgfs	p.L158fs		NM_174924.1	NP_777584.1	Q8N807	PDILT_HUMAN	protein disulfide isomerase-like, testis expressed	158					cell migration (GO:0016477)|cell redox homeostasis (GO:0045454)|multicellular organismal development (GO:0007275)|protein folding (GO:0006457)|spermatid development (GO:0007286)	endoplasmic reticulum (GO:0005783)	protein disulfide isomerase activity (GO:0003756)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(33)|prostate(3)|skin(1)|urinary_tract(1)	61						GCTGTTGAACAAAAATGCTTT	0.488																																					p.L158fs		Atlas-INDEL	.											.	PDILT	120	.	0			c.474delG						.						132	101	111					16																	20387460		2203	4300	6503	SO:0001589	frameshift_variant	204474	exon4			.		CCDS10584.1	16p12.3	2011-11-10	2009-02-23		ENSG00000169340	ENSG00000169340		"Protein disulfide isomerases"	27338	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 7", "protein disulfide isomerase-like protein of the testis"					15475357	Standard	NM_174924		Approved	PDIA7	uc002dhc.1	Q8N807	OTTHUMG00000131487	ENST00000302451.4:c.473delT	chr16.hg19:g.20387460delA	ENSP00000305465:p.Leu158fs	221.0	0.0		132.0	10.0	NM_174924	Q8IVQ5	Frame_Shift_Del	DEL	ENST00000302451.4	hg19	CCDS10584.1																																																																																			.	.		0.488	PDILT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254332.1	NM_174924		-	20387460	A	-	20387460	7	5	282	1	0	1	0	1	0	0	0	0	11683	131	5	0	1317	0	PDILT	16	20387460	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	4152366	20387460	69967293	1066	41300										
THUMPD1	55623	hgsc.bcm.edu	37	chr16	20749224	20749224	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcaaaataactcgagtcttcTttttcttggttttgtacata							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:20749224delT	ENST00000381337.2	-	3	805	c.461delA	c.(460-462)aagfs	p.K155fs	THUMPD1_ENST00000396083.2_Frame_Shift_Del_p.K155fs|THUMPD1_ENST00000431224.2_Frame_Shift_Del_p.K241fs	NM_017736.3	NP_060206.2	Q9NXG2	THUM1_HUMAN	THUMP domain containing 1	155	THUMP. {ECO:0000255|PROSITE- ProRule:PRU00529}.						poly(A) RNA binding (GO:0044822)			NS(2)|large_intestine(2)|lung(6)|pancreas(1)|urinary_tract(1)	12						TCGAGTCTTCTTTTTCTTGGT	0.338																																					p.K154fs		Atlas-INDEL	.											.	THUMPD1	33	.	0			c.462delG						.						109	120	116					16																	20749224		2201	4300	6501	SO:0001589	frameshift_variant	55623	exon3			.	BC000448	CCDS10588.1	16p13.11	2010-06-17			ENSG00000066654	ENSG00000066654			23807	protein-coding gene	gene with protein product							Standard	XM_005255422		Approved	FLJ20274	uc002dho.3	Q9NXG2	OTTHUMG00000131558	ENST00000381337.2:c.461delA	chr16.hg19:g.20749224delT	ENSP00000370741:p.Lys155fs	240.0	0.0		193.0	14.0	NM_017736	Q9BWC3	Frame_Shift_Del	DEL	ENST00000381337.2	hg19	CCDS10588.1																																																																																			.	.		0.338	THUMPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254420.1	NM_017736		-	20749224	T	-	20749224	7	5	282	1	0	1	0	1	0	0	0	0	15897	1609	56	0	608	0	THUMPD1	16	20749224	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	361764	20749224	69605529	1067	41301										
USP31	57478	hgsc.bcm.edu	37	chr16	23093870	23093870	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gggcaacgccaggcatcatcGggggcaagctgaaaacagaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:23093870delG	ENST00000219689.7	-	12	1838	c.1839delC	c.(1837-1839)cccfs	p.P613fs		NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	264	DUSP 2. {ECO:0000255|PROSITE- ProRule:PRU00613}.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	57				GBM - Glioblastoma multiforme(48;0.0187)		AGGCATCATCGGGGGCAAGCT	0.498																																					p.D614fs		Atlas-INDEL	.											USP31,right_lower_lobe,carcinoma,0,1	USP31	122	.	0			c.1840delG						.						76	65	68					16																	23093870		2197	4300	6497	SO:0001589	frameshift_variant	57478	exon12			.	AB033029	CCDS10607.1	16p12.3	2008-02-05	2005-08-08		ENSG00000103404	ENSG00000103404		"Ubiquitin-specific peptidases"	20060	protein-coding gene	gene with protein product			"ubiquitin specific protease 31"			12838346	Standard	NM_020718		Approved	KIAA1203	uc002dll.3	Q70CQ4	OTTHUMG00000094793	ENST00000219689.7:c.1839delC	chr16.hg19:g.23093870delG	ENSP00000219689:p.Pro613fs	253.0	0.0		147.0	10.0	NM_020718	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Frame_Shift_Del	DEL	ENST00000219689.7	hg19	CCDS10607.1																																																																																			.	.		0.498	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718		-	23093870	G	-	23093870	7	5	282	1	0	1	0	1	0	0	0	0	17077	1103	39	0	2239	0	USP31	16	23093870	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	2344646	23093870	67260883	1068	41302										
ERN2	10595	hgsc.bcm.edu	37	chr16	23717673	23717673	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttcccaggtgagccatccatGgggggcgctgagtagcggcg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:23717673delG	ENST00000457008.2	-	7	605	c.567delC	c.(565-567)cccfs	p.P189fs	ERN2_ENST00000256797.4_Frame_Shift_Del_p.P237fs					endoplasmic reticulum to nucleus signaling 2											large_intestine(2)|lung(2)|ovary(2)	6				GBM - Glioblastoma multiforme(48;0.0156)		AGCCATCCATGGGGGGCGCTG	0.587																																					p.M238fs		Atlas-INDEL	.											.	ERN2	131	.	0			c.712delA						.						39	34	36					16																	23717673		2196	4298	6494	SO:0001589	frameshift_variant	10595	exon7			.	AA527544	CCDS32407.1	16p12.2	2008-02-05	2007-08-14			ENSG00000134398			16942	protein-coding gene	gene with protein product		604034	"ER to nucleus signalling 2"			9755171, 11175748	Standard	NM_033266		Approved	IRE1b	uc002dma.4	Q76MJ5		ENST00000457008.2:c.567delC	chr16.hg19:g.23717673delG	ENSP00000413812:p.Pro189fs	210.0	0.0		166.0	12.0	NM_033266		Frame_Shift_Del	DEL	ENST00000457008.2	hg19																																																																																				.	.		0.587	ERN2-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000434886.1			-	23717673	G	-	23717673	7	5	282	1	0	1	0	1	0	0	0	0	5240	1335	47	0	2277	0	ERN2	16	23717673	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	623803	23717673	66637080	1069	41303										
CACNG3	10368	hgsc.bcm.edu	37	chr16	24358078	24358078	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctttccgaggcgtgtgcaagAaaatcgatcacttccctgaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:24358078delA	ENST00000005284.3	+	2	1437	c.235delA	c.(235-237)aaafs	p.K79fs		NM_006539.3	NP_006530.1	O60359	CCG3_HUMAN	calcium channel, voltage-dependent, gamma subunit 3	79					calcium ion transport (GO:0006816)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|prostate(4)|skin(2)	40				GBM - Glioblastoma multiforme(48;0.0809)		CGTGTGCAAGAAAATCGATCA	0.577																																					p.K78fs		Atlas-INDEL	.											CACNG3,NS,carcinoma,0,1	CACNG3	112	.	0			c.234delG						.						81	76	78					16																	24358078		2197	4300	6497	SO:0001589	frameshift_variant	10368	exon2			.	AF131911	CCDS10620.1	16p12.1	2008-05-14			ENSG00000006116	ENSG00000006116		"Calcium channel subunits"	1407	protein-coding gene	gene with protein product		606403				10221464, 10493829	Standard	NM_006539		Approved		uc002dmf.3	O60359	OTTHUMG00000131651	ENST00000005284.3:c.235delA	chr16.hg19:g.24358078delA	ENSP00000005284:p.Lys79fs	174.0	0.0		112.0	11.0	NM_006539		Frame_Shift_Del	DEL	ENST00000005284.3	hg19	CCDS10620.1																																																																																			.	.		0.577	CACNG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254548.1	NM_006539		-	24358078	A	-	24358078	7	5	282	1	0	1	0	1	0	0	0	0	2560	247	9	0	241	0	CACNG3	16	24358078	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	640405	24358078	65996675	1070	41304										
TNRC6A	27327	hgsc.bcm.edu	37	chr16	24802560	24802560	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aacttcaaggaataaccattGgggtgaggccaataagaaat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:24802560delG	ENST00000395799.3	+	6	2726	c.2597delG	c.(2596-2598)tggfs	p.W866fs	TNRC6A_ENST00000315183.7_Frame_Shift_Del_p.W866fs	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	866	Interaction with argonaute family proteins.|Sufficient for interaction with AGO1 and AGO4.				cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.W866L(1)		breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		AATAACCATTGGGGTGAGGCC	0.463																																					p.W866fs		Atlas-INDEL	.											.	TNRC6A	171	.	1	Substitution - Missense(1)	lung(1)	c.2596delT						.						83	80	81					16																	24802560		2197	4300	6497	SO:0001589	frameshift_variant	27327	exon6			.	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"Trinucleotide (CAG) repeat containing"	11969	protein-coding gene	gene with protein product		610739	"trinucleotide repeat containing 6"	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.2597delG	chr16.hg19:g.24802560delG	ENSP00000379144:p.Trp866fs	306.0	0.0		227.0	15.0	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Frame_Shift_Del	DEL	ENST00000395799.3	hg19	CCDS10624.2																																																																																			.	.		0.463	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		-	24802560	G	-	24802560	7	5	282	1	0	1	0	1	0	0	0	0	16355	1357	47	0	2619	0	TNRC6A	16	24802560	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	444482	24802560	65552193	1071	41305										
ARHGAP17	55114	hgsc.bcm.edu	37	chr16	24964264	24964264	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcgctcacctgctacagcatGggggtctgaatagaactcat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:24964264delG	ENST00000289968.6	-	11	1021	c.952delC	c.(952-954)catfs	p.H318fs	ARHGAP17_ENST00000441763.2_3'UTR|ARHGAP17_ENST00000575975.1_5'Flank|ARHGAP17_ENST00000303665.5_Frame_Shift_Del_p.H318fs	NM_001006634.1	NP_001006635.1	Q68EM7	RHG17_HUMAN	Rho GTPase activating protein 17	318	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	GTPase activator activity (GO:0005096)			breast(2)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|urinary_tract(2)	30				GBM - Glioblastoma multiforme(48;0.0407)		GCTACAGCATGGGGGTCTGAA	0.507																																					p.H318fs		Atlas-INDEL	.											.	ARHGAP17	138	.	0			c.953delA						.						92	91	91					16																	24964264		2197	4300	6497	SO:0001589	frameshift_variant	55114	exon11			.	AJ306731	CCDS32408.1, CCDS32409.1	16p12.2-p12.1	2011-06-29				ENSG00000140750		"Rho GTPase activating proteins"	18239	protein-coding gene	gene with protein product		608293				10967100, 11431473	Standard	XM_005255413		Approved	RICH1, FLJ10308, NADRIN, FLJ13219, WBP15	uc002dnb.3	Q68EM7		ENST00000289968.6:c.952delC	chr16.hg19:g.24964264delG	ENSP00000289968:p.His318fs	236.0	0.0		160.0	10.0	NM_001006634	A8K6M6|Q6ZUS4|Q7Z2F2|Q8NDG2|Q96KS2|Q96KS3|Q96SS8|Q9BVF6|Q9H8U5|Q9NW54	Frame_Shift_Del	DEL	ENST00000289968.6	hg19	CCDS32409.1																																																																																			.	.		0.507	ARHGAP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436548.3	NM_018054		-	24964264	G	-	24964264	7	5	282	1	0	1	0	1	0	0	0	0	867	1348	47	0	1733	0	ARHGAP17	16	24964264	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	161704	24964264	65390489	1072	41306										
SEZ6L2	26470	hgsc.bcm.edu	37	chr16	29899871	29899871	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggagactcacccatgcagctGggggtttcaccgttccagga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:29899871delG	ENST00000308713.5	-	6	1556	c.1029delC	c.(1027-1029)cccfs	p.P343fs	SEZ6L2_ENST00000350527.3_Frame_Shift_Del_p.P273fs|SEZ6L2_ENST00000562159.1_5'UTR|SEZ6L2_ENST00000537485.1_Frame_Shift_Del_p.P299fs|SEZ6L2_ENST00000346932.5_Frame_Shift_Del_p.P229fs	NM_001114099.2|NM_201575.3	NP_001107571.1|NP_963869.2	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2	343	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CCATGCAGCTGGGGGTTTCAC	0.612																																					p.S344fs		Atlas-INDEL	.											.	SEZ6L2	137	.	0			c.1030delA						.						75	63	67					16																	29899871		2197	4300	6497	SO:0001589	frameshift_variant	26470	exon6			.	AY358404	CCDS10658.1, CCDS10659.1, CCDS45458.1, CCDS58447.1, CCDS73865.1	16p12.1	2008-02-05			ENSG00000174938	ENSG00000174938			30844	protein-coding gene	gene with protein product	"type I transmembrane receptor (seizure related protein)"					12975309	Standard	NM_012410		Approved	PSK-1, FLJ90517	uc010vec.2	Q6UXD5	OTTHUMG00000132112	ENST00000308713.5:c.1029delC	chr16.hg19:g.29899871delG	ENSP00000312550:p.Pro343fs	133.0	0.0		147.0	10.0	NM_001243332	B7Z1N0|F5H293|H7BXQ6|Q9BW82|Q9UJ45|Q9UJ46|Q9UJ47	Frame_Shift_Del	DEL	ENST00000308713.5	hg19	CCDS10659.1																																																																																			.	.		0.612	SEZ6L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255154.2	NM_012410		-	29899871	G	-	29899871	7	5	282	1	0	1	0	1	0	0	0	0	14159	1335	47	0	1794	0	SEZ6L2	16	29899871	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	4935607	29899871	60454882	1073	41307										
TBC1D10B	26000	hgsc.bcm.edu	37	chr16	30369601	30369601	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gatggatgcagtccctcagcAgtgaccacaggccctggggc	14	13	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:30369601A>G	ENST00000409939.3	-	9	2171	c.2091T>C	c.(2089-2091)acT>acC	p.T697T	CD2BP2_ENST00000305596.3_5'Flank|RP11-347C12.10_ENST00000563252.1_lincRNA	NM_015527.3	NP_056342.3	Q4KMP7	TB10B_HUMAN	TBC1 domain family, member 10B	697					positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab GTPase activity (GO:0032313)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)			endometrium(2)|kidney(1)|lung(2)|urinary_tract(1)	6			Colorectal(24;0.193)			GTCCCTCAGCAGTGACCACAG	0.692																																					p.T697T		Atlas-SNP	.											.	TBC1D10B	32	.	0			c.T2091C						.						29	24	26					16																	30369601		2192	4291	6483	SO:0001819	synonymous_variant	26000	exon9			CTCAGCAGTGACC	BC063112	CCDS10676.2	16p11.2	2013-07-09			ENSG00000169221	ENSG00000169221			24510	protein-coding gene	gene with protein product		613620				20404108	Standard	NM_015527		Approved	DKFZP434P1750, Rab27A-GAPbeta, FLJ13130, EPI64B	uc002dxt.3	Q4KMP7	OTTHUMG00000132396	ENST00000409939.3:c.2091T>C	chr16.hg19:g.30369601A>G		131.0	0.0		73.0	6.0	NM_015527	B9A6L0|Q6IN54|Q6P530|Q71RG7|Q86VC5|Q9H8Z2|Q9NUN6|Q9UFP2	Silent	SNP	ENST00000409939.3	hg19	CCDS10676.2																																																																																			.	.		0.692	TBC1D10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255527.3	NM_015527		G	30369601	A	G	30369601	2	3	282	1	0	0	0	0	0	0	0	1	15614	175	7	2		2	TBC1D10B	16	30369601	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	469730	30369601	59985152	1074	41308										
ITGAL	3683	hgsc.bcm.edu	37	chr16	30521788	30521788	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcccatcttcaaagcaggccActcggtgagtgcttcaagtc	9	13	3	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:30521788A>G	ENST00000356798.6	+	22	2795	c.2615A>G	c.(2614-2616)cAc>cGc	p.H872R	ITGAL_ENST00000358164.5_Missense_Mutation_p.H788R|ITGAL_ENST00000433423.2_Intron	NM_002209.2	NP_002200.2	P20701	ITAL_HUMAN	integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)	872					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell proliferation (GO:0042102)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(10)|kidney(4)|large_intestine(12)|lung(32)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	76					Antithymocyte globulin(DB00098)|Efalizumab(DB00095)|Lovastatin(DB00227)	AAAGCAGGCCACTCGGTGAGT	0.577																																					p.H872R	NSCLC(110;1462 1641 3311 33990 49495)	Atlas-SNP	.											.	ITGAL	149	.	0			c.A2615G						.						83	75	78					16																	30521788		2197	4300	6497	SO:0001583	missense	3683	exon22			CAGGCCACTCGGT		CCDS32433.1, CCDS45461.1	16p13.1-p11	2010-03-23				ENSG00000005844		"CD molecules", "Integrins"	6148	protein-coding gene	gene with protein product		153370		CD11A		3284962	Standard	NM_002209		Approved	LFA-1	uc002dyi.4	P20701		ENST00000356798.6:c.2615A>G	chr16.hg19:g.30521788A>G	ENSP00000349252:p.His872Arg	176.0	0.0		123.0	6.0	NM_002209	O43746|Q45H73|Q96HB1|Q9UBC8	Missense_Mutation	SNP	ENST00000356798.6	hg19	CCDS32433.1	.	.	.	.	.	.	.	.	.	.	a	11.65	1.701628	0.30142	.	.	ENSG00000005844	ENST00000356798;ENST00000358164	T;T	0.43688	0.94;0.94	4.36	-2.08	0.07254	Integrin alpha-2 (1);	1.623940	0.03218	N	0.177136	T	0.15998	0.0385	N	0.02011	-0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.13282	-1.0515	10	0.45353	T	0.12	.	1.122	0.01727	0.215:0.329:0.2888:0.1672	.	788;872	Q96HB1;P20701	.;ITAL_HUMAN	R	872;788	ENSP00000349252:H872R;ENSP00000350886:H788R	ENSP00000349252:H872R	H	+	2	0	ITGAL	30429289	0.000000	0.05858	0.003000	0.11579	0.406000	0.30931	-0.176000	0.09811	-0.082000	0.12640	0.158000	0.16466	CAC	.	.		0.577	ITGAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434508.2			G	30521788	A	G	30521788	3	3	282	1	0	0	0	0	1	0	0	0	7895	159	6	2	2701	2	ITGAL	16	30521788	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	152187	30521788	59832965	1075	41309										
ITGAL	3683	hgsc.bcm.edu	37	chr16	30529197	30529197	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccaagtgatcgggactctggAgctggtgggagagatcgagg	18	7	1	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:30529197A>G	ENST00000356798.6	+	28	3293	c.3113A>G	c.(3112-3114)gAg>gGg	p.E1038G	ITGAL_ENST00000358164.5_Missense_Mutation_p.E954G|ITGAL_ENST00000433423.2_Missense_Mutation_p.E272G	NM_002209.2	NP_002200.2	P20701	ITAL_HUMAN	integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)	1038					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell proliferation (GO:0042102)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(10)|kidney(4)|large_intestine(12)|lung(32)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	76					Antithymocyte globulin(DB00098)|Efalizumab(DB00095)|Lovastatin(DB00227)	GGGACTCTGGAGCTGGTGGGA	0.622																																					p.E1038G	NSCLC(110;1462 1641 3311 33990 49495)	Atlas-SNP	.											.	ITGAL	149	.	0			c.A3113G						.						80	74	76					16																	30529197		2197	4300	6497	SO:0001583	missense	3683	exon28			CTCTGGAGCTGGT		CCDS32433.1, CCDS45461.1	16p13.1-p11	2010-03-23				ENSG00000005844		"CD molecules", "Integrins"	6148	protein-coding gene	gene with protein product		153370		CD11A		3284962	Standard	NM_002209		Approved	LFA-1	uc002dyi.4	P20701		ENST00000356798.6:c.3113A>G	chr16.hg19:g.30529197A>G	ENSP00000349252:p.Glu1038Gly	95.0	0.0		81.0	4.0	NM_002209	O43746|Q45H73|Q96HB1|Q9UBC8	Missense_Mutation	SNP	ENST00000356798.6	hg19	CCDS32433.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.560669	0.86335	.	.	ENSG00000005844	ENST00000356798;ENST00000358164;ENST00000433423	T;T;T	0.58940	0.3;0.65;1.79	4.99	4.99	0.66335	.	0.000000	0.52532	D	0.000075	T	0.72732	0.3497	M	0.72479	2.2	0.31854	N	0.621817	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.997;0.998;0.998	T	0.78270	-0.2269	10	0.72032	D	0.01	.	10.9958	0.47575	1.0:0.0:0.0:0.0	.	272;954;1038	B4E021;Q96HB1;P20701	.;.;ITAL_HUMAN	G	1038;954;272	ENSP00000349252:E1038G;ENSP00000350886:E954G;ENSP00000409377:E272G	ENSP00000349252:E1038G	E	+	2	0	ITGAL	30436698	1.000000	0.71417	0.724000	0.30704	0.840000	0.47671	2.348000	0.44045	2.078000	0.62432	0.460000	0.39030	GAG	.	.		0.622	ITGAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434508.2			G	30529197	A	G	30529197	3	3	282	1	0	0	0	0	1	0	0	0	7895	304	11	2	3223	2	ITGAL	16	30529197	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	7409	30529197	59825556	1076	41310										
ZNF689	115509	hgsc.bcm.edu	37	chr16	30616564	30616564	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agtctgggcaagggtaaggcTtttttagattctgggcgcac							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:30616564delT	ENST00000287461.3	-	3	861	c.524delA	c.(523-525)aagfs	p.K175fs	ZNF689_ENST00000566673.1_5'UTR|RP11-146F11.5_ENST00000563540.1_RNA	NM_138447.1	NP_612456.1	Q96CS4	ZN689_HUMAN	zinc finger protein 689	175					regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(1)	14			Colorectal(24;0.198)			AGGGTAAGGCTTTTTTAGATT	0.617																																					p.K175fs		Atlas-INDEL	.											.	ZNF689	48	.	0			c.525delG						.						73	79	77					16																	30616564		2197	4300	6497	SO:0001589	frameshift_variant	115509	exon3			.	BC014000	CCDS10686.1	16p11.2	2013-01-08			ENSG00000156853	ENSG00000156853		"Zinc fingers, C2H2-type", "-"	25173	protein-coding gene	gene with protein product							Standard	NM_138447		Approved	FLJ90415	uc031qvq.1	Q96CS4	OTTHUMG00000132415	ENST00000287461.3:c.524delA	chr16.hg19:g.30616564delT	ENSP00000287461:p.Lys175fs	235.0	0.0		166.0	11.0	NM_138447	Q658J5	Frame_Shift_Del	DEL	ENST00000287461.3	hg19	CCDS10686.1																																																																																			.	.		0.617	ZNF689-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255552.1	NM_138447		-	30616564	T	-	30616564	7	5	282	1	0	1	0	1	0	0	0	0	18109	1609	56	0	982	0	ZNF689	16	30616564	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	87367	30616564	59738189	1077	41311										
SRCAP	10847	hgsc.bcm.edu	37	chr16	30745026	30745026	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gacaggagcagacactgttgTtttttatgacagcgactgga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:30745026delT	ENST00000262518.4	+	29	6786	c.6401delT	c.(6400-6402)gttfs	p.V2134fs	SRCAP_ENST00000395059.2_Frame_Shift_Del_p.V2072fs|SRCAP_ENST00000344771.4_Frame_Shift_Del_p.V1976fs	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	2134	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			GACACTGTTGTTTTTTATGAC	0.517																																					p.V2134fs		Atlas-INDEL	.											.	SRCAP	298	.	0			c.6400delG						.						115	115	115					16																	30745026		2197	4300	6497	SO:0001589	frameshift_variant	10847	exon29			.	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.6401delT	chr16.hg19:g.30745026delT	ENSP00000262518:p.Val2134fs	155.0	0.0		171.0	13.0	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Frame_Shift_Del	DEL	ENST00000262518.4	hg19	CCDS10689.2																																																																																			.	.		0.517	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		-	30745026	T	-	30745026	7	5	282	1	0	1	0	1	0	0	0	0	15150	1725	60	0	6507	0	SRCAP	16	30745026	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	128462	30745026	59609727	1078	41312										
ZNF646	9726	hgsc.bcm.edu	37	chr16	31092588	31092588	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccaggaggccccatcagaaaCccccagaggcccaggagaga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:31092588delC	ENST00000394979.2	+	1	5366	c.4943delC	c.(4942-4944)accfs	p.T1648fs	ZNF646_ENST00000300850.5_Frame_Shift_Del_p.T1648fs			O15015	ZN646_HUMAN	zinc finger protein 646	1648					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(1)|lung(21)|ovary(1)|prostate(4)|skin(3)	49						CCATCAGAAACCCCCAGAGGC	0.657																																					p.T1648fs		Atlas-INDEL	.											.	ZNF646	133	.	0			c.4942delA						.						43	53	50					16																	31092588		2196	4299	6495	SO:0001589	frameshift_variant	9726	exon2			.	AB002294	CCDS10702.1	16p11.2	2013-01-08			ENSG00000167395	ENSG00000167395		"Zinc fingers, C2H2-type"	29004	protein-coding gene	gene with protein product							Standard	NM_014699		Approved	KIAA0296	uc002eap.3	O15015	OTTHUMG00000047355	ENST00000394979.2:c.4943delC	chr16.hg19:g.31092588delC	ENSP00000378429:p.Thr1648fs	230.0	0.0		165.0	10.0	NM_014699	Q8IVD8	Frame_Shift_Del	DEL	ENST00000394979.2	hg19																																																																																				.	.		0.657	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699		-	31092588	C	-	31092588	7	5	282	1	0	1	0	1	0	0	0	0	18077	507	18	0	4945	0	ZNF646	16	31092588	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	347562	31092588	59262165	1079	41313										
ITGAX	3687	hgsc.bcm.edu	37	chr16	31382664	31382664	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tctgcccgcaggaccagaccTgtgctctgggtgggggtgag	17	11	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:31382664T>C	ENST00000268296.4	+	16	1972	c.1851T>C	c.(1849-1851)ccT>ccC	p.P617P	ITGAX_ENST00000562522.1_Silent_p.P617P	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	617					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						GGACCAGACCTGTGCTCTGGG	0.647																																					p.P617P		Atlas-SNP	.											.	ITGAX	198	.	0			c.T1851C						.						47	40	42					16																	31382664		2197	4300	6497	SO:0001819	synonymous_variant	3687	exon16			CAGACCTGTGCTC	BC038237	CCDS10711.1, CCDS67014.1	16p11.2	2010-03-23	2006-02-10		ENSG00000140678	ENSG00000140678		"CD molecules", "Complement system", "Integrins"	6152	protein-coding gene	gene with protein product		151510	"integrin, alpha X (antigen CD11C (p150), alpha polypeptide)"	CD11C		3284962, 2303426	Standard	NM_001286375		Approved	CD11c	uc002ebu.1	P20702	OTTHUMG00000132465	ENST00000268296.4:c.1851T>C	chr16.hg19:g.31382664T>C		110.0	0.0		94.0	4.0	NM_000887	Q8IVA6	Silent	SNP	ENST00000268296.4	hg19	CCDS10711.1																																																																																			.	.		0.647	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887		C	31382664	T	C	31382664	2	2	282	1	0	0	0	0	0	0	0	1	7898	1567	55	2		2	ITGAX	16	31382664	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	290076	31382664	58972089	1080	41314										
ITGAD	3681	hgsc.bcm.edu	37	chr16	31405596	31405596	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	attcaacctggatgtggaggAgcctacgatcttccaggagg	13	9	2	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:31405596A>G	ENST00000389202.2	+	2	120	c.71A>G	c.(70-72)gAg>gGg	p.E24G		NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	24					activated T cell proliferation (GO:0050798)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)	cell surface (GO:0009986)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(43)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						GATGTGGAGGAGCCTACGATC	0.577																																					p.E24G		Atlas-SNP	.											.	ITGAD	154	.	0			c.A71G						.						95	82	86					16																	31405596		2197	4300	6497	SO:0001583	missense	3681	exon2			TGGAGGAGCCTAC	U40274	CCDS32438.1	16p13.1-p11	2010-03-23				ENSG00000156886		"CD molecules", "Integrins"	6146	protein-coding gene	gene with protein product		602453				8666289, 9598326	Standard	NM_005353		Approved	CD11d, ADB2	uc002ebv.1	Q13349		ENST00000389202.2:c.71A>G	chr16.hg19:g.31405596A>G	ENSP00000373854:p.Glu24Gly	170.0	0.0		114.0	5.0	NM_005353	Q15575|Q15576	Missense_Mutation	SNP	ENST00000389202.2	hg19	CCDS32438.1	.	.	.	.	.	.	.	.	.	.	A	11.36	1.616205	0.28801	.	.	ENSG00000156886	ENST00000444228;ENST00000389202	T	0.71698	-0.59	4.54	3.41	0.39046	.	.	.	.	.	T	0.53690	0.1812	L	0.28274	0.84	0.09310	N	1	B;B;B	0.20164	0.01;0.042;0.042	B;B;B	0.14023	0.005;0.01;0.01	T	0.35549	-0.9784	9	0.20519	T	0.43	.	8.0133	0.30365	0.7928:0.2072:0.0:0.0	.	24;40;24	B7Z6V7;Q59H14;Q13349	.;.;ITAD_HUMAN	G	40;24	ENSP00000373854:E24G	ENSP00000373854:E24G	E	+	2	0	ITGAD	31313097	0.008000	0.16893	0.215000	0.23724	0.882000	0.50991	2.169000	0.42434	0.551000	0.29008	0.459000	0.35465	GAG	.	.		0.577	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353		G	31405596	A	G	31405596	3	3	282	1	0	0	0	0	1	0	0	0	7893	304	11	2	77	2	ITGAD	16	31405596	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	22932	31405596	58949157	1081	41315										
VPS35	55737	hgsc.bcm.edu	37	chr16	46696258	46696258	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttagaagtttggatgcagcaAgggcacactgagtcctcaga	12	8	1	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:46696258A>C	ENST00000299138.7	-	15	2022	c.1964T>G	c.(1963-1965)cTt>cGt	p.L655R	RP11-93O14.2_ENST00000569353.1_RNA	NM_018206.4	NP_060676.2	Q96QK1	VPS35_HUMAN	vacuolar protein sorting 35 homolog (S. cerevisiae)	655					cell death (GO:0008219)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|retromer complex (GO:0030904)				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(11)|pancreas(1)|prostate(1)|urinary_tract(1)	23		all_cancers(37;7.65e-05)|all_epithelial(9;0.000154)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				GGATGCAGCAAGGGCACACTG	0.493																																					p.L655R		Atlas-SNP	.											.	VPS35	49	.	0			c.T1964G						.						99	87	91					16																	46696258		2203	4300	6503	SO:0001583	missense	55737	exon15			GCAGCAAGGGCAC	AF175265	CCDS10721.1	16q12	2012-06-27	2006-12-19		ENSG00000069329	ENSG00000069329		"Parkinson disease"	13487	protein-coding gene	gene with protein product		601501	"vacuolar protein sorting 35 (yeast homolog)", "vacuolar protein sorting 35 (yeast)"			11112353, 21763482	Standard	NM_018206		Approved	FLJ10752, MEM3, PARK17	uc002eef.4	Q96QK1	OTTHUMG00000132542	ENST00000299138.7:c.1964T>G	chr16.hg19:g.46696258A>C	ENSP00000299138:p.Leu655Arg	211.0	0.0		141.0	52.0	NM_018206	Q561W2|Q9H016|Q9H096|Q9H4P3|Q9H8J0|Q9NRS7|Q9NVG2|Q9NX80|Q9NZK2	Missense_Mutation	SNP	ENST00000299138.7	hg19	CCDS10721.1	.	.	.	.	.	.	.	.	.	.	.	23.7	4.444215	0.83993	.	.	ENSG00000069329	ENST00000299138;ENST00000541330	T	0.64260	-0.09	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.78528	0.4297	M	0.86502	2.82	0.80722	D	1	D;D	0.76494	0.999;0.981	D;P	0.70227	0.968;0.557	T	0.78125	-0.2326	10	0.07482	T	0.82	-16.6205	15.624	0.76833	1.0:0.0:0.0:0.0	.	655;520	Q96QK1;F5GYF5	VPS35_HUMAN;.	R	655;520	ENSP00000299138:L655R	ENSP00000299138:L655R	L	-	2	0	VPS35	45253759	1.000000	0.71417	0.993000	0.49108	0.994000	0.84299	9.339000	0.96797	2.090000	0.63153	0.459000	0.35465	CTT	.	.		0.493	VPS35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255742.3			C	46696258	A	C	46696258	3	2	282	1	0	0	0	0	1	0	0	0	17218	72	3	5	438	5	VPS35	16	46696258	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	15290662	46696258	43658495	1082	41316										
MYLK3	91807	hgsc.bcm.edu	37	chr16	46781803	46781803	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccgtgctgggccgcatcctgCtgcatggccctcaccagctc	11	18	1	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:46781803C>T	ENST00000394809.4	-	1	418	c.303G>A	c.(301-303)caG>caA	p.Q101Q	MYLK3_ENST00000536476.1_Intron	NM_182493.2	NP_872299.2	Q32MK0	MYLK3_HUMAN	myosin light chain kinase 3	101					cardiac myofibril assembly (GO:0055003)|cellular response to interleukin-1 (GO:0071347)|positive regulation of sarcomere organization (GO:0060298)|protein phosphorylation (GO:0006468)|regulation of vascular permeability involved in acute inflammatory response (GO:0002528)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|myosin light chain kinase activity (GO:0004687)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(5)|stomach(3)	37		all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				CCGCATCCTGCTGCATGGCCC	0.697																																					p.Q101Q		Atlas-SNP	.											.	MYLK3	82	.	0			c.G303A						.						34	31	32					16																	46781803		2203	4299	6502	SO:0001819	synonymous_variant	91807	exon1			ATCCTGCTGCATG	AJ247087	CCDS10723.2	16q11.2	2008-10-23			ENSG00000140795	ENSG00000140795			29826	protein-coding gene	gene with protein product	"MLC kinase"	612147				17885681	Standard	NM_182493		Approved	caMLCK, MLCK	uc002eei.4	Q32MK0	OTTHUMG00000132543	ENST00000394809.4:c.303G>A	chr16.hg19:g.46781803C>T		150.0	0.0		122.0	5.0	NM_182493	B5BUL9|B7Z5U8|Q32MK1|Q96DV1	Silent	SNP	ENST00000394809.4	hg19	CCDS10723.2																																																																																			.	.		0.697	MYLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255743.2	NM_182493		T	46781803	C	T	46781803	2	4	282	1	0	0	0	0	0	0	0	1	10067	796	28	3		3	MYLK3	16	46781803	Silent	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	85545	46781803	43572950	1083	41317										
PHKB	5257	hgsc.bcm.edu	37	chr16	47630338	47630338	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agctgactttgtagaatatgAaaaaaataaccctggtagtc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:47630338delA	ENST00000323584.5	+	13	1283	c.1259delA	c.(1258-1260)gaafs	p.E420fs	PHKB_ENST00000455779.1_Frame_Shift_Del_p.E413fs|PHKB_ENST00000566044.1_Frame_Shift_Del_p.E413fs|PHKB_ENST00000299167.8_Frame_Shift_Del_p.E420fs	NM_000293.2	NP_000284.1	Q93100	KPBB_HUMAN	phosphorylase kinase, beta	420					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|liver(1)|lung(18)|ovary(1)|skin(1)	41		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				GTAGAATATGAAAAAAATAAC	0.338																																					p.E420fs		Atlas-INDEL	.											.	PHKB	298	.	0			c.1258delG						.						89	95	93					16																	47630338		2201	4300	6501	SO:0001589	frameshift_variant	5257	exon13			.		CCDS10729.1, CCDS42161.1	16q12-q13	2009-07-10			ENSG00000102893	ENSG00000102893	2.7.11.19		8927	protein-coding gene	gene with protein product		172490					Standard	NM_000293		Approved		uc002eev.4	Q93100	OTTHUMG00000133102	ENST00000323584.5:c.1259delA	chr16.hg19:g.47630338delA	ENSP00000313504:p.Glu420fs	114.0	0.0		131.0	11.0	NM_000293	Q8N4T5	Frame_Shift_Del	DEL	ENST00000323584.5	hg19	CCDS10729.1																																																																																			.	.		0.338	PHKB-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000430413.1			-	47630338	A	-	47630338	7	5	282	1	0	1	0	1	0	0	0	0	11854	246	9	0	1368	0	PHKB	16	47630338	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	848535	47630338	42724415	1084	41318										
CYLD	1540	hgsc.bcm.edu	37	chr16	50811827	50811827	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcacaaccacaatccaaatcAaaaaatacatggtacattga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:50811827delA	ENST00000427738.3	+	7	1318	c.1113delA	c.(1111-1113)tcafs	p.S371fs	CYLD_ENST00000566206.1_Frame_Shift_Del_p.S368fs|CYLD_ENST00000569418.1_Frame_Shift_Del_p.S368fs|CYLD_ENST00000568704.2_Frame_Shift_Del_p.S368fs|CYLD_ENST00000540145.1_Frame_Shift_Del_p.S371fs|CYLD_ENST00000311559.9_Frame_Shift_Del_p.S371fs|CYLD_ENST00000564326.1_Frame_Shift_Del_p.S368fs|CYLD_ENST00000398568.2_Frame_Shift_Del_p.S368fs			Q9NQC7	CYLD_HUMAN	cylindromatosis (turban tumor syndrome)	371	Interaction with TRIP.				cell cycle (GO:0007049)|innate immune response (GO:0045087)|necroptotic process (GO:0070266)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|protein K63-linked deubiquitination (GO:0070536)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of mitotic cell cycle (GO:0007346)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|microtubule (GO:0005874)|nucleus (GO:0005634)	Lys63-specific deubiquitinase activity (GO:0061578)|proline-rich region binding (GO:0070064)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(9)|lung(17)|pancreas(1)|skin(22)|upper_aerodigestive_tract(1)	62		all_cancers(37;0.0156)				AATCCAAATCAAAAAATACAT	0.313			"Mis, N, F, S"		cylindroma	cylindroma			Multiple Trichoepithelioma, Familial;Familial Cylindromatosis																												p.S371X		Atlas-INDEL	.	yes	Rec	yes	Familial cylindromatosis	16	16q12-q13	1540	familial cylindromatosis gene		E	CYLD,colon,carcinoma,-1,1	CYLD	150	.	0			c.1112delC						.						86	80	81					16																	50811827		1813	4063	5876	SO:0001589	frameshift_variant	1540	exon9	Familial Cancer Database	;FADC, Turban Tumor syndrome, Epithelioma Adenoides Cysticum of Brooke, Hereditary Multiple Benign Cystic Epithelioma, Dermal Eccrine Cylindromatosis, Brooke-Spiegler s.	.	AB020656	CCDS42164.1, CCDS45482.1	16q12-q13	2014-09-17							2584	protein-coding gene	gene with protein product	"ubiquitin specific peptidase like 2"	605018		CYLD1		7493027	Standard	NM_015247		Approved	KIAA0849, USPL2	uc002egq.1	Q9NQC7		ENST00000427738.3:c.1113delA	chr16.hg19:g.50811827delA	ENSP00000392025:p.Ser371fs	165.0	0.0		152.0	10.0	NM_015247	O94934|Q7L3N6|Q96EH0|Q9NZX9	Frame_Shift_Del	DEL	ENST00000427738.3	hg19	CCDS45482.1																																																																																			.	.		0.313	CYLD-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422998.2			-	50811827	A	-	50811827	7	5	282	1	0	1	0	1	0	0	0	0	4145	117	5	0	1135	0	CYLD	16	50811827	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	3181489	50811827	39542926	1085	41319										
SETD6	79918	hgsc.bcm.edu	37	chr16	58550759	58550759	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggatgaaaaggagcccaactCccccgtgatggtgcctgctg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:58550759delC	ENST00000219315.4	+	5	769	c.719delC	c.(718-720)tccfs	p.S240fs	SETD6_ENST00000394266.4_Frame_Shift_Del_p.S171fs|SETD6_ENST00000310682.2_Frame_Shift_Del_p.S216fs|SETD6_ENST00000418480.1_3'UTR			Q8TBK2	SETD6_HUMAN	SET domain containing 6	240	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				negative regulation of NF-kappaB transcription factor activity (GO:0032088)|peptidyl-lysine monomethylation (GO:0018026)|regulation of inflammatory response (GO:0050727)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	NF-kappaB binding (GO:0051059)|protein-lysine N-methyltransferase activity (GO:0016279)	p.S216C(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	7						GAGCCCAACTCCCCCGTGATG	0.532																																					p.S240fs		Atlas-INDEL	.											.	SETD6	27	.	1	Substitution - Missense(1)	kidney(1)	c.718delT						.						192	192	192					16																	58550759		2198	4300	6498	SO:0001589	frameshift_variant	79918	exon5			.	AK024801	CCDS10798.1, CCDS54013.1	16q21	2008-02-05			ENSG00000103037	ENSG00000103037			26116	protein-coding gene	gene with protein product						12477932	Standard	NM_024860		Approved	FLJ21148	uc002ens.3	Q8TBK2	OTTHUMG00000150276	ENST00000219315.4:c.719delC	chr16.hg19:g.58550759delC	ENSP00000219315:p.Ser240fs	197.0	0.0		164.0	10.0	NM_001160305	A8K380|B5ME38|Q9H787	Frame_Shift_Del	DEL	ENST00000219315.4	hg19	CCDS54013.1																																																																																			.	.		0.532	SETD6-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317274.2	NM_024860		-	58550759	C	-	58550759	7	5	282	1	0	1	0	1	0	0	0	0	14150	855	30	0	737	0	SETD6	16	58550759	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	7738932	58550759	31803994	1086	41320										
CNOT1	23019	hgsc.bcm.edu	37	chr16	58621151	58621151	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaattcaacagggcaaggccAaaaattacctgaaacaagaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:58621151delA	ENST00000317147.5	-	6	719	c.387delT	c.(385-387)tttfs	p.F129fs	CNOT1_ENST00000441024.2_Frame_Shift_Del_p.F129fs|CNOT1_ENST00000569240.1_Frame_Shift_Del_p.F129fs	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	129					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		GGGCAAGGCCAAAAATTACCT	0.358																																					p.G130fs		Atlas-INDEL	.											.	CNOT1	359	.	0			c.388delG						.						104	107	106					16																	58621151		2198	4300	6498	SO:0001589	frameshift_variant	23019	exon6			.	AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.387delT	chr16.hg19:g.58621151delA	ENSP00000320949:p.Phe129fs	125.0	0.0		122.0	12.0	NM_206999	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Frame_Shift_Del	DEL	ENST00000317147.5	hg19	CCDS10799.1																																																																																			.	.		0.358	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284		-	58621151	A	-	58621151	7	5	282	1	0	1	0	1	0	0	0	0	3619	127	5	0	7141	0	CNOT1	16	58621151	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	70392	58621151	31733602	1087	41321										
EDC4	23644	hgsc.bcm.edu	37	chr16	67917535	67917535	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aactgtggacccagcccaggTttttgggcagccaccctgcc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:67917535delT	ENST00000358933.5	+	28	4153	c.3914delT	c.(3913-3915)gttfs	p.V1305fs	NRN1L_ENST00000576147.1_5'Flank|NRN1L_ENST00000339176.3_5'Flank|CTC-479C5.10_ENST00000572067.1_lincRNA	NM_014329.4	NP_055144.3	Q6P2E9	EDC4_HUMAN	enhancer of mRNA decapping 4	1305					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	41		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)		CCAGCCCAGGTTTTTGGGCAG	0.562											OREG0023890	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V1305fs		Atlas-INDEL	.											.	EDC4	101	.	0			c.3913delG						.						150	157	154					16																	67917535		2198	4300	6498	SO:0001589	frameshift_variant	23644	exon28			.	U17474	CCDS10849.1	16q22.1	2008-02-05			ENSG00000038358	ENSG00000038358			17157	protein-coding gene	gene with protein product		606030				9067524	Standard	NM_014329		Approved	RCD-8, Ge-1, HEDLS	uc002eur.3	Q6P2E9	OTTHUMG00000137543	ENST00000358933.5:c.3914delT	chr16.hg19:g.67917535delT	ENSP00000351811:p.Val1305fs	172.0	0.0	1103	147.0	11.0	NM_014329	A6NGM1|A8K4T4|Q13025|Q13826|Q6ZR12|Q7Z6H7	Frame_Shift_Del	DEL	ENST00000358933.5	hg19	CCDS10849.1																																																																																			.	.		0.562	EDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268874.2	NM_014329		-	67917535	T	-	67917535	7	5	282	1	0	1	0	1	0	0	0	0	4910	1725	60	0	4024	0	EDC4	16	67917535	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	9296384	67917535	22437218	1088	41322										
AARS	16	hgsc.bcm.edu	37	chr16	70302272	70302272	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agctcggcggagaatccgtcTcaacacatatctgtaagagg	11	10	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:70302272T>C	ENST00000261772.8	-	8	1116	c.973A>G	c.(973-975)Aga>Gga	p.R325G		NM_001605.2	NP_001596.2			alanyl-tRNA synthetase											breast(3)|cervix(2)|endometrium(5)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)	27		Ovarian(137;0.0365)		BRCA - Breast invasive adenocarcinoma(221;0.161)		AGAATCCGTCTCAACACATAT	0.512																																					p.R325G		Atlas-SNP	.											.	AARS	62	.	0			c.A973G						.						83	74	77					16																	70302272		2198	4300	6498	SO:0001583	missense	16	exon8			TCCGTCTCAACAC	D32050	CCDS32474.1	16q22.1	2014-09-17			ENSG00000090861	ENSG00000090861	6.1.1.7	"Aminoacyl tRNA synthetases / Class II"	20	protein-coding gene	gene with protein product	"alanine tRNA ligase 1, cytoplasmic"	601065				8595897	Standard	NM_001605		Approved		uc002eyn.1	P49588	OTTHUMG00000177042	ENST00000261772.8:c.973A>G	chr16.hg19:g.70302272T>C	ENSP00000261772:p.Arg325Gly	100.0	0.0		69.0	5.0	NM_001605		Missense_Mutation	SNP	ENST00000261772.8	hg19	CCDS32474.1	.	.	.	.	.	.	.	.	.	.	T	19.00	3.742391	0.69418	.	.	ENSG00000090861	ENST00000261772	D	0.87887	-2.31	5.66	1.9	0.25705	Alanyl-tRNA synthetase, class IIc, anti-codon-binding domain (1);Alanyl-tRNA synthetase, class IIc, core domain (1);Alanyl-tRNA synthetase, class IIc, N-terminal (1);	0.044018	0.85682	D	0.000000	D	0.96175	0.8753	H	0.99573	4.635	0.58432	D	0.999999	D;D	0.89917	0.975;1.0	D;D	0.97110	0.949;1.0	D	0.95711	0.8758	10	0.87932	D	0	-6.9159	13.0037	0.58692	0.0:0.0:0.5199:0.4801	.	333;325	E7ETK8;P49588	.;SYAC_HUMAN	G	325	ENSP00000261772:R325G	ENSP00000261772:R325G	R	-	1	2	AARS	68859773	1.000000	0.71417	0.610000	0.28997	0.979000	0.70002	1.724000	0.38064	0.043000	0.15746	0.529000	0.55759	AGA	.	.		0.512	AARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435021.2	NM_001605		C	70302272	T	C	70302272	3	2	282	1	0	0	0	0	1	0	0	0	19	1559	54	2	1989	2	AARS	16	70302272	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2384737	70302272	20052481	1089	41323										
HYDIN	54768	hgsc.bcm.edu	37	chr16	70843883	70843883	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaaggtttctccagctttcaGgggctgaaattcaaatgaga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:70843883delG	ENST00000393567.2	-	85	14836	c.14686delC	c.(14686-14688)ctgfs	p.L4896fs		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	4896					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.L4895M(1)|p.L4847M(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				CCAGCTTTCAGGGGCTGAAAT	0.483																																					p.L4896fs		Atlas-INDEL	.											.	HYDIN	788	.	2	Substitution - Missense(2)	lung(2)	c.14687delT						.						220	227	225					16																	70843883		1940	4133	6073	SO:0001589	frameshift_variant	54768	exon85			.	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.14686delC	chr16.hg19:g.70843883delG	ENSP00000377197:p.Leu4896fs	241.0	0.0		145.0	10.0	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Frame_Shift_Del	DEL	ENST00000393567.2	hg19	CCDS59269.1																																																																																			.	.		0.483	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			-	70843883	G	-	70843883	7	5	282	1	0	1	0	1	0	0	0	0	7476	991	35	0	687	0	HYDIN	16	70843883	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	541611	70843883	19510870	1090	41324										
PHLPP2	23035	hgsc.bcm.edu	37	chr16	71724608	71724608	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaacgatccatgtggcatggTttttctgaaaaggaaataat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:71724608delT	ENST00000568954.1	-	4	801	c.423delA	c.(421-423)aaafs	p.K141fs	PHLPP2_ENST00000393524.2_Frame_Shift_Del_p.K141fs|PHLPP2_ENST00000360429.3_Frame_Shift_Del_p.K141fs|PHLPP2_ENST00000356272.3_Frame_Shift_Del_p.K141fs|PHLPP2_ENST00000567016.1_Frame_Shift_Del_p.K176fs			Q6ZVD8	PHLP2_HUMAN	PH domain and leucine rich repeat protein phosphatase 2	141					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment membrane (GO:0042622)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(7)|lung(15)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37						TGTGGCATGGTTTTTCTGAAA	0.403																																					p.P142fs		Atlas-INDEL	.											.	PHLPP2	96	.	0			c.424delC						.						66	58	60					16																	71724608		2198	4300	6498	SO:0001589	frameshift_variant	23035	exon3			.	BX647823	CCDS32479.1, CCDS73910.1	16q22.2	2013-01-11	2009-05-26	2009-05-26	ENSG00000040199	ENSG00000040199		"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent", "Pleckstrin homology (PH) domain containing"	29149	protein-coding gene	gene with protein product		611066	"PH domain and leucine rich repeat protein phosphatase-like"	PHLPPL		17386267	Standard	NM_001289003		Approved	KIAA0931	uc002fax.3	Q6ZVD8		ENST00000568954.1:c.423delA	chr16.hg19:g.71724608delT	ENSP00000457991:p.Lys141fs	181.0	0.0		144.0	10.0	NM_015020	A1L374|Q9NV17|Q9Y2E3	Frame_Shift_Del	DEL	ENST00000568954.1	hg19	CCDS32479.1																																																																																			.	.		0.403	PHLPP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000434139.1	NM_015020		-	71724608	T	-	71724608	7	5	282	1	0	1	0	1	0	0	0	0	11864	1722	60	0	3612	0	PHLPP2	16	71724608	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	880725	71724608	18630145	1091	41325										
ZFHX3	463	hgsc.bcm.edu	37	chr16	72829729	72829729	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgaaaccacaccactatcacTcgggttggaaggttcagtaa	9	10	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:72829729T>C	ENST00000268489.5	-	9	7524	c.6852A>G	c.(6850-6852)cgA>cgG	p.R2284R	ZFHX3_ENST00000397992.5_Silent_p.R1370R	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	2284					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				CCACTATCACTCGGGTTGGAA	0.473																																					p.R2284R		Atlas-SNP	.											.	ZFHX3	404	.	0			c.A6852G						.						159	159	159					16																	72829729		2198	4300	6498	SO:0001819	synonymous_variant	463	exon9			TATCACTCGGGTT	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	777	protein-coding gene	gene with protein product		104155	"AT-binding transcription factor 1"	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.6852A>G	chr16.hg19:g.72829729T>C		183.0	0.0		121.0	5.0	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	hg19	CCDS10908.1																																																																																			.	.		0.473	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		C	72829729	T	C	72829729	2	2	282	1	0	0	0	0	0	0	0	1	17649	1538	54	2		2	ZFHX3	16	72829729	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1105121	72829729	17525024	1092	41326										
MLKL	197259	hgsc.bcm.edu	37	chr16	74725195	74725195	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcaatgctgccagcctggagTtttttgaatacttttatggc					rs56247416	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:74725195delT	ENST00000308807.7	-	4	1165	c.702delA	c.(700-702)aaafs	p.K234fs	MLKL_ENST00000306247.7_Intron	NM_152649.2	NP_689862.1			mixed lineage kinase domain-like											breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(6)|skin(1)|stomach(2)	19						CAGCCTGGAGTTTTTTGAATA	0.438																																					p.L235fs		Atlas-INDEL	.											.	MLKL	51	.	0			c.703delC						.						255	264	261					16																	74725195		2198	4300	6498	SO:0001589	frameshift_variant	197259	exon4			.	AK091708	CCDS32487.1, CCDS45528.1	16q22.3	2008-02-05				ENSG00000168404			26617	protein-coding gene	gene with protein product		615153				12477932	Standard	NM_152649		Approved	FLJ34389	uc002fdb.2	Q8NB16		ENST00000308807.7:c.702delA	chr16.hg19:g.74725195delT	ENSP00000308351:p.Lys234fs	195.0	0.0		140.0	10.0	NM_152649		Frame_Shift_Del	DEL	ENST00000308807.7	hg19	CCDS32487.1																																																																																			.	.		0.438	MLKL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436403.3	NM_152649		-	74725195	T	-	74725195	7	5	282	1	0	1	0	1	0	0	0	0	9628	1722	60	0	776	0	MLKL	16	74725195	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1895466	74725195	15629558	1093	41327										
CFDP1	10428	hgsc.bcm.edu	37	chr16	75339067	75339067	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caaaaggctgctcatgccacTtgatctttttaacctaagga	7	10	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:75339067T>C	ENST00000283882.3	-	6	796	c.664A>G	c.(664-666)Agt>Ggt	p.S222G		NM_006324.2	NP_006315.1	Q9UEE9	CFDP1_HUMAN	craniofacial development protein 1	222	BCNT-C. {ECO:0000255|PROSITE- ProRule:PRU00610}.				cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|negative regulation of fibroblast apoptotic process (GO:2000270)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)					endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	5						CTCATGCCACTTGATCTTTTT	0.408																																					p.S222G		Atlas-SNP	.											.	CFDP1	17	.	0			c.A664G						.						85	87	86					16																	75339067		2198	4300	6498	SO:0001583	missense	10428	exon6			TGCCACTTGATCT	AB009285	CCDS10916.1	16q22.2-q22.3	2011-08-12			ENSG00000153774	ENSG00000153774			1873	protein-coding gene	gene with protein product	"Bucentaur", "centromere protein 29"	608108				9602175, 9006920, 11992732	Standard	NM_006324		Approved	BCNT, p97, CP27, SWC5, Yeti, CENP-29	uc002fdy.3	Q9UEE9	OTTHUMG00000137615	ENST00000283882.3:c.664A>G	chr16.hg19:g.75339067T>C	ENSP00000283882:p.Ser222Gly	107.0	0.0		96.0	4.0	NM_006324	O00393|O00404|Q9UEF0|Q9UEF1|Q9UEF8	Missense_Mutation	SNP	ENST00000283882.3	hg19	CCDS10916.1	.	.	.	.	.	.	.	.	.	.	T	8.252	0.809285	0.16537	.	.	ENSG00000153774	ENST00000283882	T	0.45276	0.9	5.45	5.45	0.79879	.	0.249302	0.40469	N	0.001087	T	0.20981	0.0505	N	0.05574	-0.02	0.43965	D	0.996643	B;B	0.12013	0.005;0.005	B;B	0.14023	0.01;0.01	T	0.13019	-1.0525	10	0.16896	T	0.51	-4.2101	8.9547	0.35809	0.0:0.0833:0.0:0.9167	.	222;222	B2R9W9;Q9UEE9	.;CFDP1_HUMAN	G	222	ENSP00000283882:S222G	ENSP00000283882:S222G	S	-	1	0	CFDP1	73896568	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.906000	0.48735	2.060000	0.61445	0.528000	0.53228	AGT	.	.		0.408	CFDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269031.2	NM_006324		C	75339067	T	C	75339067	3	2	282	1	0	0	0	0	1	0	0	0	3284	1609	56	2	243	2	CFDP1	16	75339067	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	613872	75339067	15015686	1094	41328										
CFDP1	10428	hgsc.bcm.edu	37	chr16	75445767	75445767	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aacaccttggtgattttaacTttttctgtttctttaggttt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:75445767delT	ENST00000283882.3	-	4	618	c.486delA	c.(484-486)aaafs	p.K162fs	RP11-77K12.1_ENST00000561887.1_5'Flank|SNORA76_ENST00000516313.1_RNA|CFDP1_ENST00000564286.1_5'UTR	NM_006324.2	NP_006315.1	Q9UEE9	CFDP1_HUMAN	craniofacial development protein 1	162					cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|negative regulation of fibroblast apoptotic process (GO:2000270)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)					endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	5						TGATTTTAACTTTTTCTGTTT	0.338																																					p.V163fs		Atlas-INDEL	.											.	CFDP1	17	.	0			c.487delG						.						123	110	115					16																	75445767		2198	4299	6497	SO:0001589	frameshift_variant	10428	exon4			.	AB009285	CCDS10916.1	16q22.2-q22.3	2011-08-12			ENSG00000153774	ENSG00000153774			1873	protein-coding gene	gene with protein product	"Bucentaur", "centromere protein 29"	608108				9602175, 9006920, 11992732	Standard	NM_006324		Approved	BCNT, p97, CP27, SWC5, Yeti, CENP-29	uc002fdy.3	Q9UEE9	OTTHUMG00000137615	ENST00000283882.3:c.486delA	chr16.hg19:g.75445767delT	ENSP00000283882:p.Lys162fs	205.0	0.0		140.0	10.0	NM_006324	O00393|O00404|Q9UEF0|Q9UEF1|Q9UEF8	Frame_Shift_Del	DEL	ENST00000283882.3	hg19	CCDS10916.1																																																																																			.	.		0.338	CFDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269031.2	NM_006324		-	75445767	T	-	75445767	7	5	282	1	0	1	0	1	0	0	0	0	3284	1606	56	0	429	0	CFDP1	16	75445767	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	106700	75445767	14908986	1095	41329										
PKD1L2	114780	hgsc.bcm.edu	37	chr16	81241219	81241219	+	RNA	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgtcaaagatgaaactctcaCtggacaccatcagctgcagg	9	11	3	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:81241219C>T	ENST00000525539.1	-	0	781				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)	p.S261I(2)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						GAAACTCTCACTGGACACCAT	0.448																																					p.S261N		Atlas-SNP	.											PKD1L2_ENST00000525539,NS,carcinoma,0,2	PKD1L2	361	.	2	Substitution - Missense(2)	kidney(2)	c.G782A						.						118	118	118					16																	81241219		1982	4163	6145			114780	exon5			CTCTCACTGGACA	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		chr16.hg19:g.81241219C>T		81.0	0.0		47.0	4.0	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	hg19		.	.	.	.	.	.	.	.	.	.	C	0.014	-1.572444	0.00887	.	.	ENSG00000166473	ENST00000337114	T	0.01258	5.09	5.47	0.0931	0.14475	.	0.645577	0.16079	N	0.230614	T	0.00936	0.0031	.	.	.	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.48375	-0.9041	9	0.21014	T	0.42	0.3378	5.6149	0.17426	0.0:0.1572:0.262:0.5809	.	261;261	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	N	261	ENSP00000337397:S261N	ENSP00000337397:S261N	S	-	2	0	PKD1L2	79798720	0.057000	0.20700	0.000000	0.03702	0.003000	0.03518	1.679000	0.37597	-0.265000	0.09352	-0.253000	0.11424	AGT	.	.		0.448	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2			T	81241219	C	T	81241219	1	4	282	0	1	0	0	0	0	0	0	0	11974	565	20	3		3	PKD1L2	16	81241219	RNA	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	5795452	81241219	9113534	1096	41330										
PKD1L2	114780	hgsc.bcm.edu	37	chr16	81242150	81242150	+	RNA	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gccctgagtcggacacaggtTtccaaagtaggtctcatctg	11	11	2	1	rs55980345|rs532218091|rs548490632|rs386792900	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:81242150T>C	ENST00000525539.1	-	0	705				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)	p.N236fs*26(6)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						GGACACAGGTTTCCAAAGTAG	0.557																																					p.N236D		Atlas-SNP	.											.,52	PKD1L2	361	.	6	Deletion - Frameshift(6)	breast(4)|lung(2)	c.A706G						.						77	61	66					16																	81242150		2025	3850	5875			114780	exon4			ACAGGTTTCCAAA	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		chr16.hg19:g.81242150T>C		4.0	1.0		4.0	3.0	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	hg19		.	.	.	.	.	.	.	.	.	.	T	1.316	-0.600871	0.03744	.	.	ENSG00000166473	ENST00000337114	T	0.10668	2.85	4.29	2.17	0.27698	D-galactoside/L-rhamnose binding SUEL lectin domain (2);	0.205291	0.40469	N	0.001088	T	0.03739	0.0106	.	.	.	0.21184	N	0.999765	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46048	-0.9219	9	0.02654	T	1	-7.787	7.6885	0.28554	0.0:0.7269:0.0:0.2731	.	236;236	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	D	236	ENSP00000337397:N236D	ENSP00000337397:N236D	N	-	1	0	PKD1L2	79799651	1.000000	0.71417	1.000000	0.80357	0.842000	0.47809	1.014000	0.29950	0.269000	0.21961	-0.624000	0.04008	AAC	.	.		0.557	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2			C	81242150	T	C	81242150	1	2	282	0	1	0	0	0	0	0	0	0	11974	1841	64	2		2	PKD1L2	16	81242150	RNA	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	931	81242150	9112603	1097	41331										
MBTPS1	8720	hgsc.bcm.edu	37	chr16	84118656	84118656	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtccctgagagggcccggcaCccccctttcacgccagaacc					rs145922793		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:84118656delC	ENST00000343411.3	-	10	1713	c.1218delG	c.(1216-1218)gggfs	p.G406fs	MBTPS1_ENST00000569770.1_5'UTR	NM_003791.2	NP_003782.1	Q14703	MBTP1_HUMAN	membrane-bound transcription factor peptidase, site 1	406	Peptidase S8.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cholesterol metabolic process (GO:0008203)|endoplasmic reticulum unfolded protein response (GO:0030968)|lipid metabolic process (GO:0006629)|lysosome organization (GO:0007040)|proteolysis (GO:0006508)|regulation of transcription factor import into nucleus (GO:0042990)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(10)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						GGGCCCGGCACCCCCCTTTCA	0.582											OREG0023982	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C407fs		Atlas-INDEL	.											.	MBTPS1	85	.	0			c.1219delT						.						82	71	75					16																	84118656		2200	4300	6500	SO:0001589	frameshift_variant	8720	exon10			.	D42053	CCDS10941.1	16q24	2008-08-04	2005-08-17		ENSG00000140943	ENSG00000140943			15456	protein-coding gene	gene with protein product		603355	"membrane-bound transcription factor protease, site 1"			9809072, 10944850	Standard	NM_003791		Approved	S1P, KIAA0091, SKI-1, PCSK8	uc002fhi.3	Q14703	OTTHUMG00000137639	ENST00000343411.3:c.1218delG	chr16.hg19:g.84118656delC	ENSP00000344223:p.Gly406fs	301.0	0.0	1226	212.0	13.0	NM_003791	A8K6V8|Q24JQ2|Q9UF67	Frame_Shift_Del	DEL	ENST00000343411.3	hg19	CCDS10941.1																																																																																			.	.		0.582	MBTPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269080.2	NM_003791		-	84118656	C	-	84118656	7	5	282	1	0	1	0	1	0	0	0	0	9370	494	18	0	1996	0	MBTPS1	16	84118656	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	2876506	84118656	6236097	1098	41332										
ADAD2	161931	hgsc.bcm.edu	37	chr16	84230305	84230305	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aggcctcctttctccgggccTttcaccaggcggccagggct	12	16	2	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:84230305T>C	ENST00000315906.5	+	9	1631	c.1579T>C	c.(1579-1581)Ttt>Ctt	p.F527L	RP11-486L19.2_ENST00000561900.1_RNA|ADAD2_ENST00000268624.3_Missense_Mutation_p.F609L|RP11-486L19.2_ENST00000536986.1_RNA|RP11-486L19.2_ENST00000569834.1_RNA|RP11-486L19.2_ENST00000565643.1_RNA	NM_001145400.1	NP_001138872.1	Q8NCV1	ADAD2_HUMAN	adenosine deaminase domain containing 2	527	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				RNA processing (GO:0006396)		adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(1)	13						TCTCCGGGCCTTTCACCAGGC	0.642																																					p.F609L		Atlas-SNP	.											.	ADAD2	46	.	0			c.T1825C						.						71	75	74					16																	84230305		2200	4300	6500	SO:0001583	missense	161931	exon10			CGGGCCTTTCACC	AF447586	CCDS10944.1, CCDS45536.1	16q24.1	2007-05-31			ENSG00000140955	ENSG00000140955			30714	protein-coding gene	gene with protein product							Standard	NM_139174		Approved	TENRL, FLJ00337	uc002fhr.2	Q8NCV1	OTTHUMG00000137637	ENST00000315906.5:c.1579T>C	chr16.hg19:g.84230305T>C	ENSP00000325153:p.Phe527Leu	92.0	0.0		100.0	4.0	NM_139174	B2RCL6|Q8NA94	Missense_Mutation	SNP	ENST00000315906.5	hg19	CCDS45536.1	.	.	.	.	.	.	.	.	.	.	T	15.96	2.985827	0.53934	.	.	ENSG00000140955	ENST00000315906;ENST00000268624	D;D	0.94931	-3.56;-3.56	5.27	4.18	0.49190	Adenosine deaminase/editase (2);	0.065249	0.64402	N	0.000010	D	0.96583	0.8885	M	0.85462	2.755	0.39372	D	0.966105	D;D	0.76494	0.998;0.999	D;D	0.72338	0.977;0.973	D	0.96633	0.9468	10	0.87932	D	0	-34.6595	7.0084	0.24849	0.0:0.1003:0.0:0.8997	.	527;609	Q8NCV1;Q8NCV1-2	ADAD2_HUMAN;.	L	527;609	ENSP00000325153:F527L;ENSP00000268624:F609L	ENSP00000268624:F609L	F	+	1	0	ADAD2	82787806	1.000000	0.71417	1.000000	0.80357	0.033000	0.12548	2.896000	0.48656	1.975000	0.57531	0.477000	0.44152	TTT	.	.		0.642	ADAD2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433385.1	NM_139174		C	84230305	T	C	84230305	3	2	282	1	0	0	0	0	1	0	0	0	232	1609	56	2	1863	2	ADAD2	16	84230305	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	111649	84230305	6124448	1099	41333										
KIAA1609	57707	hgsc.bcm.edu	37	chr16	84520325	84520325	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcgaggacagccacacagggTccccggtgagtgatgtggcc					rs431389	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:84520325delT	ENST00000343629.6	-	5	1052	c.870delA	c.(868-870)ggafs	p.G290fs	TLDC1_ENST00000535580.1_Frame_Shift_Del_p.G263fs|TLDC1_ENST00000561807.1_5'Flank	NM_020947.3	NP_065998.3	Q6P9B6	TLDC1_HUMAN	TBC/LysM-associated domain containing 1	290	TLD.					lysosomal membrane (GO:0005765)											CCACACAGGGTCCCCGGTGAG	0.587																																					p.P291fs		Atlas-INDEL	.											.	KIAA1609	39	.	0			c.871delC						.						77	69	72					16																	84520325		2200	4300	6500	SO:0001589	frameshift_variant	57707	exon5			.	AB046829	CCDS32498.1	16q24.1	2013-03-14	2013-03-14	2013-03-14	ENSG00000140950	ENSG00000140950			29325	protein-coding gene	gene with protein product	"TLD domain containing 1"		"KIAA1609"	KIAA1609		10997877	Standard	NM_020947		Approved		uc002fib.3	Q6P9B6	OTTHUMG00000176739	ENST00000343629.6:c.870delA	chr16.hg19:g.84520325delT	ENSP00000343635:p.Gly290fs	244.0	0.0		138.0	10.0	NM_020947	Q8IZ64|Q9HCG3|Q9NTE8	Frame_Shift_Del	DEL	ENST00000343629.6	hg19	CCDS32498.1																																																																																			.	.		0.587	TLDC1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433421.1	NM_020947		-	84520325	T	-	84520325	7	5	282	1	0	1	0	1	0	0	0	0	8256	1654	58	0	516	0	KIAA1609	16	84520325	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	290020	84520325	5834428	1100	41334										
ZCCHC14	23174	hgsc.bcm.edu	37	chr16	87445899	87445899	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggctgtgtacagagcagtccGggggtttattattgcagggg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:87445899delG	ENST00000268616.4	-	12	2234	c.2017delC	c.(2017-2019)cggfs	p.R673fs		NM_015144.2	NP_055959.1	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14	673							nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)	p.R673R(1)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	36				BRCA - Breast invasive adenocarcinoma(80;0.0285)		AGAGCAGTCCGGGGGTTTATT	0.512																																					p.R673fs		Atlas-INDEL	.											.	ZCCHC14	87	.	1	Substitution - coding silent(1)	lung(1)	c.2018delG						.						77	94	88					16																	87445899		2197	4290	6487	SO:0001589	frameshift_variant	23174	exon12			.	AB011151	CCDS10961.1	16q24.2	2013-01-10			ENSG00000140948	ENSG00000140948		"Zinc fingers, CCHC domain containing", "Sterile alpha motif (SAM) domain containing"	24134	protein-coding gene	gene with protein product						9628581	Standard	XM_005255858		Approved	BDG29, MGC14139	uc002fjz.1	Q8WYQ9	OTTHUMG00000137655	ENST00000268616.4:c.2017delC	chr16.hg19:g.87445899delG	ENSP00000268616:p.Arg673fs	243.0	0.0		229.0	15.0	NM_015144	D3DUN1|O60324|Q3MJD8|Q9UFP0	Frame_Shift_Del	DEL	ENST00000268616.4	hg19	CCDS10961.1																																																																																			.	.		0.512	ZCCHC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269107.1	NM_015144		-	87445899	G	-	87445899	7	5	282	1	0	1	0	1	0	0	0	0	17598	1115	39	0	840	0	ZCCHC14	16	87445899	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	2925574	87445899	2908854	1101	41335										
PRPF8	10594	hgsc.bcm.edu	37	chr17	1554134	1554134	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccgatccgcagagtaaacctCcccctcctgcaggagagcaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:1554134delC	ENST00000572621.1	-	42	7235	c.6970delG	c.(6970-6972)gagfs	p.E2324fs	PRPF8_ENST00000304992.6_Frame_Shift_Del_p.E2324fs|RILP_ENST00000301336.6_5'Flank|PRPF8_ENST00000575116.1_5'Flank			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	2324	Required for interaction with EFTUD2 and SNRNP200.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		GAGTAAACCTCCCCCTCCTGC	0.592																																					p.E2324fs		Atlas-INDEL	.											.	PRPF8	169	.	0			c.6971delA						.						137	111	120					17																	1554134		2203	4300	6503	SO:0001589	frameshift_variant	10594	exon43			.	AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231			17340	protein-coding gene	gene with protein product		607300	"PRP8 pre-mRNA processing factor 8 homolog (yeast)", "PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)"	RP13		11468273, 10411133	Standard	NM_006445		Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.6970delG	chr17.hg19:g.1554134delC	ENSP00000460348:p.Glu2324fs	131.0	0.0		126.0	11.0	NM_006445	O14547|O75965	Frame_Shift_Del	DEL	ENST00000572621.1	hg19	CCDS11010.1																																																																																			.	.		0.592	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2			-	1554134	C	-	1554134	7	5	282	1	0	1	0	1	0	0	0	0	12587	864	30	0	41	0	PRPF8	17	1554134	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10		1554134	79641076	1102	41336										
TRPV1	7442	hgsc.bcm.edu	37	chr17	3495572	3495572	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggagttagggtctccatccaGggggtctgggcaggtgtcct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:3495572delG	ENST00000571088.1	-	2	286	c.73delC	c.(73-75)ctgfs	p.L25fs	TRPV1_ENST00000576351.1_Frame_Shift_Del_p.L25fs|TRPV1_ENST00000310522.5_Frame_Shift_Del_p.L25fs|SHPK_ENST00000572705.1_Frame_Shift_Del_p.L25fs|TRPV1_ENST00000399759.3_Frame_Shift_Del_p.L25fs|TRPV1_ENST00000399756.4_Frame_Shift_Del_p.L25fs|TRPV1_ENST00000425167.2_Frame_Shift_Del_p.L25fs|TRPV1_ENST00000174621.6_5'UTR	NM_018727.5	NP_061197.4	Q8NER1	TRPV1_HUMAN	transient receptor potential cation channel, subfamily V, member 1	25					calcium ion transmembrane transport (GO:0070588)|cell surface receptor signaling pathway (GO:0007166)|cellular response to alkaloid (GO:0071312)|cellular response to ATP (GO:0071318)|chemosensory behavior (GO:0007635)|ion transmembrane transport (GO:0034220)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|calcium-release channel activity (GO:0015278)|excitatory extracellular ligand-gated ion channel activity (GO:0005231)|phosphoprotein binding (GO:0051219)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	17				Lung(1;0.055)|COAD - Colon adenocarcinoma(5;0.0896)|LUAD - Lung adenocarcinoma(1115;0.131)	Alpha-Linolenic Acid(DB00132)|Aspartame(DB00168)|Icosapent(DB00159)	TCTCCATCCAGGGGGTCTGGG	0.632																																					p.L25fs	Melanoma(38;962 1762 15789)	Atlas-INDEL	.											.	TRPV1	99	.	0			c.74delT						.						44	49	48					17																	3495572		2027	4179	6206	SO:0001589	frameshift_variant	7442	exon2			.	AJ272063	CCDS45576.1	17p13.2	2014-08-12	2002-01-29	2002-02-01	ENSG00000196689	ENSG00000262304		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	12716	protein-coding gene	gene with protein product		602076	"vanilloid receptor subtype 1"	VR1		9349813, 11549313, 16382100	Standard	NM_018727		Approved		uc010vrt.2	Q8NER1	OTTHUMG00000177649	ENST00000571088.1:c.73delC	chr17.hg19:g.3495572delG	ENSP00000461007:p.Leu25fs	159.0	0.0		132.0	11.0	NM_018727	A2RUA9|Q3LU47|Q9H0G9|Q9H303|Q9H304|Q9NQ74|Q9NY22	Frame_Shift_Del	DEL	ENST00000571088.1	hg19	CCDS45576.1																																																																																			.	.		0.632	TRPV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438254.1	NM_018727		-	3495572	G	-	3495572	7	5	282	1	0	1	0	1	0	0	0	0	16610	991	35	0	2179	0	TRPV1	17	3495572	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1941438	3495572	77699638	1103	41337										
PELP1	27043	hgsc.bcm.edu	37	chr17	4576386	4576386	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gggctgcaggggaggaacccGggggtgggtcagagcagcac							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:4576386delG	ENST00000574876.1	-	16	1917	c.1900delC	c.(1900-1902)cggfs	p.R634fs	PELP1_ENST00000269230.7_Frame_Shift_Del_p.R546fs|PELP1_ENST00000572293.1_Frame_Shift_Del_p.R684fs|PELP1_ENST00000436683.2_Frame_Shift_Del_p.R487fs|AC091153.4_ENST00000441700.2_RNA|PELP1_ENST00000301396.4_Frame_Shift_Del_p.R778fs			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	634	Pro-rich.				cellular response to estrogen stimulus (GO:0071391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	15						GGAGGAACCCGGGGGTGGGTC	0.627																																					p.R634fs		Atlas-INDEL	.											.	PELP1	102	.	0			c.1901delG						.						19	22	21					17																	4576386		1945	4080	6025	SO:0001589	frameshift_variant	27043	exon16			.		CCDS58503.1, CCDS58503.2, CCDS62038.1	17p13.2	2012-05-02	2008-02-21			ENSG00000141456			30134	protein-coding gene	gene with protein product		609455	"proline, glutamic acid and leucine rich protein 1"			11481323, 12682072	Standard	NM_014389		Approved	MNAR	uc002fyi.4	Q8IZL8		ENST00000574876.1:c.1900delC	chr17.hg19:g.4576386delG	ENSP00000461625:p.Arg634fs	178.0	0.0		166.0	11.0	NM_014389	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	Frame_Shift_Del	DEL	ENST00000574876.1	hg19	CCDS58503.1																																																																																			.	.		0.627	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389		-	4576386	G	-	4576386	7	5	282	1	0	1	0	1	0	0	0	0	11734	1115	39	0	1500	0	PELP1	17	4576386	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1080814	4576386	76618824	1104	41338										
PLD2	5338	hgsc.bcm.edu	37	chr17	4719139	4719139	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaccaagtggtagcattcctGgggggactggaccttgccta					rs368018438		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:4719139delG	ENST00000263088.6	+	14	1496	c.1365delG	c.(1363-1365)ctgfs	p.L455fs	PLD2_ENST00000572940.1_Frame_Shift_Del_p.L455fs	NM_001243108.1|NM_002663.4	NP_001230037.1|NP_002654.3	O14939	PLD2_HUMAN	phospholipase D2	455	Catalytic.|PLD phosphodiesterase 1. {ECO:0000255|PROSITE-ProRule:PRU00153}.				cytoskeleton organization (GO:0007010)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G-protein coupled receptor internalization (GO:0002031)|glycerophospholipid biosynthetic process (GO:0046474)|innate immune response (GO:0045087)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	brush border membrane (GO:0031526)|endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)			autonomic_ganglia(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)	31					Choline(DB00122)	TAGCATTCCTGGGGGGACTGG	0.597											OREG0024105	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L455fs		Atlas-INDEL	.											.	PLD2	138	.	0			c.1364delT						.						168	134	146					17																	4719139		2203	4300	6503	SO:0001589	frameshift_variant	5338	exon14			.	AF035483	CCDS11057.1, CCDS58507.1	17p13.3	2008-04-14			ENSG00000129219	ENSG00000129219	3.1.4.4		9068	protein-coding gene	gene with protein product	"choline phosphatase 2"	602384				9858823, 9582313	Standard	NM_002663		Approved		uc002fzc.3	O14939	OTTHUMG00000090779	ENST00000263088.6:c.1365delG	chr17.hg19:g.4719139delG	ENSP00000263088:p.Leu455fs	376.0	0.0	621	228.0	14.0	NM_001243108	I3L2C9|O43540|O43579|O43580|Q6PGR0|Q96BY3	Frame_Shift_Del	DEL	ENST00000263088.6	hg19	CCDS11057.1																																																																																			.	.		0.597	PLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207561.3	NM_002663		-	4719139	G	-	4719139	7	5	282	1	0	1	0	1	0	0	0	0	12055	1335	47	0	1415	0	PLD2	17	4719139	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	142753	4719139	76476071	1105	41339										
USP6	9098	hgsc.bcm.edu	37	chr17	5073793	5073793	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggttctccttcttcatcaagAaaaagtggaaccagctgtcc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:5073793delA	ENST00000574788.1	+	36	5767	c.3537delA	c.(3535-3537)agafs	p.R1179fs	USP6_ENST00000332776.4_3'UTR|USP6_ENST00000304328.5_Frame_Shift_Del_p.R862fs|USP6_ENST00000250066.6_Frame_Shift_Del_p.R1179fs			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	1179	USP.				cellular protein modification process (GO:0006464)|protein deubiquitination (GO:0016579)|regulation of vesicle-mediated transport (GO:0060627)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	calmodulin binding (GO:0005516)|cysteine-type endopeptidase activity (GO:0004197)|nucleic acid binding (GO:0003676)|Rab GTPase activator activity (GO:0005097)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						CTTCATCAAGAAAAAGTGGAA	0.507			T	"COL1A1, CDH11, ZNF9, OMD"	aneurysmal bone cysts																																p.R1179fs		Atlas-INDEL	.		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	.	USP6	213	.	0			c.3536delG						.						16	18	17					17																	5073793		2044	4157	6201	SO:0001589	frameshift_variant	9098	exon28			.	X63547	CCDS11069.2	17p13	2014-06-12	2014-06-12		ENSG00000129204	ENSG00000129204	3.4.19.12	"Ubiquitin-specific peptidases"	12629	protein-coding gene	gene with protein product	"ubiquitin carboxyl-terminal hydrolase 6", "TBC1D3 and USP32 fusion", "Tre-2 oncogene"	604334	"ubiquitin specific protease 6 (Tre-2 oncogene)", "TRE oncogene, Smith Magenis syndrome chromosome region", "ubiquitin specific peptidase 6 (Tre-2 oncogene)"	HRP1, TRESMCR		12838346, 1349106	Standard	NM_004505		Approved	Tre-2, TRE17, Tre2	uc002gav.1	P35125	OTTHUMG00000099449	ENST00000574788.1:c.3537delA	chr17.hg19:g.5073793delA	ENSP00000460380:p.Arg1179fs	155.0	0.0		160.0	10.0	NM_004505	Q15634|Q86WP6|Q8IWT4	Frame_Shift_Del	DEL	ENST00000574788.1	hg19	CCDS11069.2																																																																																			.	.		0.507	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505		-	5073793	A	-	5073793	7	5	282	1	0	1	0	1	0	0	0	0	17101	243	9	0	3643	0	USP6	17	5073793	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	354654	5073793	76121417	1106	41340										
RABEP1	9135	hgsc.bcm.edu	37	chr17	5250197	5250197	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tctacaggaagatgctgagaAactgcggaaagaattgcatg	12	6	1	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:5250197A>G	ENST00000546142.2	+	6	948	c.761A>G	c.(760-762)aAa>aGa	p.K254R	RABEP1_ENST00000262477.6_Missense_Mutation_p.K254R|RABEP1_ENST00000408982.2_Missense_Mutation_p.K254R|RABEP1_ENST00000537505.1_Missense_Mutation_p.K211R|RABEP1_ENST00000341923.6_Missense_Mutation_p.K254R			Q15276	RABE1_HUMAN	rabaptin, RAB GTPase binding effector protein 1	254					apoptotic process (GO:0006915)|endocytosis (GO:0006897)|membrane fusion (GO:0061025)|protein transport (GO:0015031)	early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)|protein homodimerization activity (GO:0042803)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	8						GATGCTGAGAAACTGCGGAAA	0.328																																					p.K254R		Atlas-SNP	.											.	RABEP1	59	.	0			c.A761G						.						75	71	72					17																	5250197		1832	4085	5917	SO:0001583	missense	9135	exon6			CTGAGAAACTGCG	AF098638	CCDS42243.1, CCDS45592.1	17p13.2	2008-02-05				ENSG00000029725			17677	protein-coding gene	gene with protein product		603616				8521472	Standard	NM_001291582		Approved	neurocrescin, RAB5EP, RABPT5, rabaptin-5	uc002gbm.4	Q15276		ENST00000546142.2:c.761A>G	chr17.hg19:g.5250197A>G	ENSP00000437701:p.Lys254Arg	71.0	0.0		53.0	4.0	NM_004703	B2RAG7|O95369|Q8IVX3	Missense_Mutation	SNP	ENST00000546142.2	hg19	CCDS45592.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.639999	0.87760	.	.	ENSG00000029725	ENST00000262477;ENST00000408982;ENST00000539669;ENST00000546142;ENST00000341923;ENST00000537505	T;T;T;T;T	0.47869	0.83;0.84;0.83;0.84;0.83	5.26	5.26	0.73747	.	0.098208	0.64402	D	0.000001	T	0.50599	0.1625	N	0.14661	0.345	0.53688	D	0.99997	D;D;D;D;D	0.71674	0.993;0.988;0.997;0.996;0.998	P;P;D;P;D	0.78314	0.84;0.696;0.98;0.883;0.991	T	0.51301	-0.8723	10	0.31617	T	0.26	-25.6589	14.7166	0.69275	1.0:0.0:0.0:0.0	.	211;211;254;254;254	F5H355;B4DMM4;Q05BX6;Q15276;Q15276-2	.;.;.;RABE1_HUMAN;.	R	254;254;254;254;254;211	ENSP00000262477:K254R;ENSP00000386150:K254R;ENSP00000437701:K254R;ENSP00000339569:K254R;ENSP00000445408:K211R	ENSP00000262477:K254R	K	+	2	0	RABEP1	5190921	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.857000	0.92250	2.141000	0.66446	0.451000	0.29950	AAA	.	.		0.328	RABEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439349.1	NM_004703		G	5250197	A	G	5250197	3	3	282	1	0	0	0	0	1	0	0	0	12976	14	1	2	783	2	RABEP1	17	5250197	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	176404	5250197	75945013	1107	41341										
RABEP1	9135	hgsc.bcm.edu	37	chr17	5268420	5268420	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cttttaaaatgatacaggtgAaaaaactacagctgatgcta							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:5268420delA	ENST00000546142.2	+	11	1859	c.1672delA	c.(1672-1674)aaafs	p.K559fs	RP11-420A6.2_ENST00000572792.1_RNA|RABEP1_ENST00000262477.6_Frame_Shift_Del_p.K559fs|RABEP1_ENST00000408982.2_Frame_Shift_Del_p.K559fs|RABEP1_ENST00000537505.1_Frame_Shift_Del_p.K516fs|RABEP1_ENST00000341923.6_Frame_Shift_Del_p.K559fs|NUP88_ENST00000573169.1_Intron			Q15276	RABE1_HUMAN	rabaptin, RAB GTPase binding effector protein 1	559					apoptotic process (GO:0006915)|endocytosis (GO:0006897)|membrane fusion (GO:0061025)|protein transport (GO:0015031)	early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)|protein homodimerization activity (GO:0042803)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	8						GATACAGGTGAAAAAACTACA	0.303																																					p.V557fs		Atlas-INDEL	.											.	RABEP1	59	.	0			c.1671delG						.						87	78	81					17																	5268420		1823	4082	5905	SO:0001589	frameshift_variant	9135	exon11			.	AF098638	CCDS42243.1, CCDS45592.1	17p13.2	2008-02-05				ENSG00000029725			17677	protein-coding gene	gene with protein product		603616				8521472	Standard	NM_001291582		Approved	neurocrescin, RAB5EP, RABPT5, rabaptin-5	uc002gbm.4	Q15276		ENST00000546142.2:c.1672delA	chr17.hg19:g.5268420delA	ENSP00000437701:p.Lys559fs	208.0	0.0		191.0	16.0	NM_004703	B2RAG7|O95369|Q8IVX3	Frame_Shift_Del	DEL	ENST00000546142.2	hg19	CCDS45592.1																																																																																			.	.		0.303	RABEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439349.1	NM_004703		-	5268420	A	-	5268420	7	5	282	1	0	1	0	1	0	0	0	0	12976	247	9	0	1714	0	RABEP1	17	5268420	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	18223	5268420	75926790	1108	41342										
NUP88	4927	hgsc.bcm.edu	37	chr17	5291154	5291154	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gagaatgtactgctctctgaAcacctgggtggctctgctga	12	10	2	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:5291154A>G	ENST00000573584.1	-	12	2223	c.1714T>C	c.(1714-1716)Ttc>Ctc	p.F572L	NUP88_ENST00000573169.1_5'Flank	NM_002532.4	NP_002523.2	Q99567	NUP88_HUMAN	nucleoporin 88kDa	572					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	transporter activity (GO:0005215)			endometrium(4)|kidney(4)|large_intestine(4)|lung(3)	15						TGCTCTCTGAACACCTGGGTG	0.478																																					p.F572L		Atlas-SNP	.											.	NUP88	47	.	0			c.T1714C						.						87	87	87					17																	5291154		2203	4300	6503	SO:0001583	missense	4927	exon12			CTCTGAACACCTG	Y08612	CCDS11070.1	17p13	2004-02-18	2002-08-29		ENSG00000108559	ENSG00000108559			8067	protein-coding gene	gene with protein product		602552	"nucleoporin 88kD"			9049309	Standard	NM_002532		Approved	MGC8530	uc002gbo.2	Q99567	OTTHUMG00000099453	ENST00000573584.1:c.1714T>C	chr17.hg19:g.5291154A>G	ENSP00000458954:p.Phe572Leu	158.0	0.0		89.0	4.0	NM_002532	D3DTM2|Q9BWE5	Missense_Mutation	SNP	ENST00000573584.1	hg19	CCDS11070.1	.	.	.	.	.	.	.	.	.	.	A	16.15	3.042942	0.55003	.	.	ENSG00000108559	ENST00000225696;ENST00000543132	.	.	.	4.76	4.76	0.60689	.	0.000000	0.85682	D	0.000000	T	0.41673	0.1169	L	0.33792	1.035	0.58432	D	0.999995	B;P	0.46859	0.042;0.885	B;P	0.45538	0.047;0.484	T	0.37197	-0.9716	9	0.02654	T	1	-17.8569	13.9189	0.63919	1.0:0.0:0.0:0.0	.	457;572	B4DP20;Q99567	.;NUP88_HUMAN	L	572;457	.	ENSP00000225696:F572L	F	-	1	0	NUP88	5231878	1.000000	0.71417	0.999000	0.59377	0.983000	0.72400	8.167000	0.89668	2.137000	0.66172	0.454000	0.30748	TTC	.	.		0.478	NUP88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216918.3	NM_002532		G	5291154	A	G	5291154	3	3	282	1	0	0	0	0	1	0	0	0	10780	43	2	2	535	2	NUP88	17	5291154	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	22734	5291154	75904056	1109	41343										
TMEM102	284114	hgsc.bcm.edu	37	chr17	7340045	7340045	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gccgtcgaaagcccagtcccAaagccgtcggaggctcggga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:7340045delA	ENST00000323206.1	+	3	1020	c.747delA	c.(745-747)ccafs	p.P249fs	RP11-104H15.9_ENST00000570444.1_RNA|FGF11_ENST00000575235.1_5'Flank|RP11-104H15.7_ENST00000575310.1_RNA|TMEM102_ENST00000396568.1_Frame_Shift_Del_p.P249fs|RP11-104H15.8_ENST00000576615.1_RNA|RP11-104H15.10_ENST00000575331.1_RNA|FGF11_ENST00000293829.4_5'Flank	NM_178518.2	NP_848613.1	Q8N9M5	TM102_HUMAN	transmembrane protein 102	249					apoptotic process (GO:0006915)|positive regulation of cell adhesion (GO:0045785)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of T cell migration (GO:2000406)|regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901028)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to cytokine (GO:0034097)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|protein complex (GO:0043234)				kidney(1)|lung(3)|skin(1)	5		Prostate(122;0.173)				GCCCAGTCCCAAAGCCGTCGG	0.612																																					p.P249fs		Atlas-INDEL	.											.	TMEM102	11	.	0			c.746delC						.						77	80	79					17																	7340045		2203	4300	6503	SO:0001589	frameshift_variant	284114	exon3			.	AK094197	CCDS11104.1	17p13.1	2008-04-21			ENSG00000181284	ENSG00000181284			26722	protein-coding gene	gene with protein product		613936				12477932	Standard	NM_178518		Approved	FLJ36878	uc002ggx.1	Q8N9M5	OTTHUMG00000132901	ENST00000323206.1:c.747delA	chr17.hg19:g.7340045delA	ENSP00000315387:p.Pro249fs	212.0	0.0		161.0	10.0	NM_178518	D3DTP8	Frame_Shift_Del	DEL	ENST00000323206.1	hg19	CCDS11104.1																																																																																			.	.		0.612	TMEM102-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256405.1	NM_178518		-	7340045	A	-	7340045	7	5	282	1	0	1	0	1	0	0	0	0	16032	117	5	0	753	0	TMEM102	17	7340045	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	2048891	7340045	73855165	1110	41344										
TP53	7157	hgsc.bcm.edu	37	chr17	7578503	7578503	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggaatcaacccacagctgcaCagggcaggtcttggccagtt	12	12	2	0	rs587782620		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:7578503C>T	ENST00000269305.4	-	5	616	c.427G>A	c.(427-429)Gtg>Atg	p.V143M	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Missense_Mutation_p.V143M|TP53_ENST00000420246.2_Missense_Mutation_p.V143M|TP53_ENST00000359597.4_Missense_Mutation_p.V143M|TP53_ENST00000455263.2_Missense_Mutation_p.V143M|TP53_ENST00000445888.2_Missense_Mutation_p.V143M	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	143	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		V -> A (in sporadic cancers; somatic mutation; strong DNA binding ability at 32.5 degrees Celsius; strong reduction of transcriptional activity at 37.5 degrees Celsius; severely represses interaction with ZNF385A).|V -> E (in sporadic cancers; somatic mutation).|V -> G (in sporadic cancers; somatic mutation).|V -> L (in sporadic cancers; somatic mutation).|V -> M (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.V143M(19)|p.0?(8)|p.V143L(4)|p.V143fs*27(2)|p.V11M(1)|p.L137_W146del10(1)|p.V143fs*29(1)|p.P142_Q144delPVQ(1)|p.K139fs*4(1)|p.A138_V143delAKTCPV(1)|p.V50M(1)|p.V143_S149del(1)|p.C141fs*5(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CACAGCTGCACAGGGCAGGTC	0.587		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.V143M	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,carcinoma,0,5	TP53	33396	.	42	Substitution - Missense(25)|Whole gene deletion(8)|Deletion - In frame(4)|Deletion - Frameshift(4)|Insertion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(8)|breast(6)|bone(4)|upper_aerodigestive_tract(3)|central_nervous_system(3)|urinary_tract(3)|lung(3)|ovary(3)|salivary_gland(2)|large_intestine(2)|oesophagus(2)|cervix(1)|stomach(1)|prostate(1)	c.G427A						.						56	56	56					17																	7578503		2203	4300	6503	SO:0001583	missense	7157	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GCTGCACAGGGCA	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.427G>A	chr17.hg19:g.7578503C>T	ENSP00000269305:p.Val143Met	167.0	0.0		124.0	52.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	13.43	2.235817	0.39498	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793	D;D;D;D;D;D;D;D;D	0.99837	-7.06;-7.06;-7.06;-7.06;-7.06;-7.06;-7.06;-7.06;-7.06	5.48	4.51	0.55191	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.343688	0.28219	N	0.016151	D	0.99684	0.9881	M	0.76328	2.33	0.43018	D	0.994566	D;D;D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.87578	0.995;0.994;0.985;0.994;0.998;0.998;0.995	D	0.98175	1.0454	10	0.87932	D	0	-32.0412	7.6505	0.28346	0.1615:0.7548:0.0:0.0837	.	104;143;143;50;143;143;143	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	M	143;143;143;143;143;143;132;50;11;50;11;143	ENSP00000410739:V143M;ENSP00000352610:V143M;ENSP00000269305:V143M;ENSP00000398846:V143M;ENSP00000391127:V143M;ENSP00000391478:V143M;ENSP00000425104:V11M;ENSP00000423862:V50M;ENSP00000424104:V143M	ENSP00000269305:V143M	V	-	1	0	TP53	7519228	0.854000	0.29725	0.596000	0.28811	0.011000	0.07611	1.561000	0.36342	1.448000	0.47680	0.655000	0.94253	GTG	.	.		0.587	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7578503	C	T	7578503	3	4	282	1	0	0	0	0	1	0	0	0	16396	478	17	3	871	3	TP53	17	7578503	Missense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	238458	7578503	73616707	1111	41345										
CHD3	1107	hgsc.bcm.edu	37	chr17	7793914	7793914	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgaggaggaatttggttctgAgcgagatgagtaccgggaga	17	4	1	5			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:7793914A>G	ENST00000330494.7	+	3	389	c.239A>G	c.(238-240)gAg>gGg	p.E80G	CHD3_ENST00000570758.1_3'UTR|CHD3_ENST00000380358.4_Missense_Mutation_p.E139G|CHD3_ENST00000358181.4_Missense_Mutation_p.E80G	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	80					centrosome organization (GO:0051297)|chromatin assembly or disassembly (GO:0006333)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|spindle organization (GO:0007051)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(11)|kidney(6)|large_intestine(13)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	65		Prostate(122;0.202)				TTTGGTTCTGAGCGAGATGAG	0.453																																					p.E139G		Atlas-SNP	.											.	CHD3	169	.	0			c.A416G						.						40	43	42					17																	7793914		2203	4300	6503	SO:0001583	missense	1107	exon3			GTTCTGAGCGAGA	U08379	CCDS32553.2, CCDS32554.1, CCDS32555.1	17p13	2013-01-28			ENSG00000170004	ENSG00000170004		"Zinc fingers, PHD-type"	1918	protein-coding gene	gene with protein product		602120				9326634, 7560064	Standard	NM_001005271		Approved	Mi-2a, ZFH, Mi2-ALPHA	uc002gjd.2	Q12873	OTTHUMG00000150427	ENST00000330494.7:c.239A>G	chr17.hg19:g.7793914A>G	ENSP00000332628:p.Glu80Gly	136.0	0.0		113.0	5.0	NM_001005271	D3DTQ9|E9PG89|Q9Y4I0	Missense_Mutation	SNP	ENST00000330494.7	hg19	CCDS32554.1	.	.	.	.	.	.	.	.	.	.	A	14.10	2.435216	0.43224	.	.	ENSG00000170004	ENST00000380358;ENST00000358181;ENST00000330494	T;D;D	0.90563	1.47;-2.68;-2.69	4.61	4.61	0.57282	.	0.000000	0.40302	N	0.001136	D	0.85204	0.5643	L	0.43152	1.355	0.54753	D	0.999983	B;P;P	0.34522	0.447;0.455;0.455	B;B;B	0.30646	0.118;0.055;0.081	T	0.82645	-0.0355	10	0.20046	T	0.44	-22.9644	14.006	0.64463	1.0:0.0:0.0:0.0	.	80;80;139	Q12873-2;Q12873;E9PG89	.;CHD3_HUMAN;.	G	139;80;80	ENSP00000369716:E139G;ENSP00000350907:E80G;ENSP00000332628:E80G	ENSP00000332628:E80G	E	+	2	0	CHD3	7734639	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	5.159000	0.64923	1.691000	0.51100	0.383000	0.25322	GAG	.	.		0.453	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1	NM_001005273		G	7793914	A	G	7793914	3	3	282	1	0	0	0	0	1	0	0	0	3328	304	11	2	530	2	CHD3	17	7793914	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	215411	7793914	73401296	1112	41346										
WDR16	146845	hgsc.bcm.edu	37	chr17	9489226	9489226	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	catggcaacaacgtctcctgCttggccatctccaggtctgg	10	14	3	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:9489226C>T	ENST00000576499.1	+	2	221	c.207C>T	c.(205-207)tgC>tgT	p.C69C	WDR16_ENST00000352665.5_Silent_p.C69C|WDR16_ENST00000299764.5_Silent_p.C79C|WDR16_ENST00000396219.3_Intron					WD repeat domain 16											NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	31						ACGTCTCCTGCTTGGCCATCT	0.453																																					p.C69C		Atlas-SNP	.											.	WDR16	67	.	0			c.C207T						.						186	165	172					17																	9489226		2203	4300	6503	SO:0001819	synonymous_variant	146845	exon2			CTCCTGCTTGGCC	AB065281	CCDS11149.2, CCDS42262.1	17p13.1	2014-08-01			ENSG00000166596	ENSG00000166596		"WD repeat domain containing"	16053	protein-coding gene	gene with protein product	"WD40-repeat protein upregulated in HCC"	609804				15967112	Standard	NM_001080556		Approved	WDRPUH, FLJ37528	uc002gly.3	Q8N1V2	OTTHUMG00000150149	ENST00000576499.1:c.207C>T	chr17.hg19:g.9489226C>T		139.0	0.0		93.0	4.0	NM_145054		Silent	SNP	ENST00000576499.1	hg19																																																																																				.	.		0.453	WDR16-009	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000439850.2	NM_145054		T	9489226	C	T	9489226	2	4	282	1	0	0	0	0	0	0	0	1	17291	805	28	3		3	WDR16	17	9489226	Silent	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1695312	9489226	71705984	1113	41347										
USP43	124739	hgsc.bcm.edu	37	chr17	9586141	9586141	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtcattctctcccttctagcTcatccactgggtctgtcggc	8	15	5	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:9586141T>C	ENST00000285199.7	+	7	1203	c.1107T>C	c.(1105-1107)gcT>gcC	p.A369A	USP43_ENST00000570475.1_Splice_Site_p.A369A|USP43_ENST00000570827.2_3'UTR	NM_001267576.1|NM_153210.4	NP_001254505.1|NP_694942.3	Q70EL4	UBP43_HUMAN	ubiquitin specific peptidase 43	369	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	26						CCCTTCTAGCTCATCCACTGG	0.532																																					p.A369A		Atlas-SNP	.											.	USP43	65	.	0			c.T1107C						.						70	72	72					17																	9586141		1959	4145	6104	SO:0001630	splice_region_variant	124739	exon7			TCTAGCTCATCCA	AK055188	CCDS45610.1, CCDS58516.1	17p12	2005-08-08	2005-08-08			ENSG00000154914		"Ubiquitin-specific peptidases"	20072	protein-coding gene	gene with protein product			"ubiquitin specific protease 43"			12838346	Standard	NM_153210		Approved	FLJ30626	uc010cod.4	Q70EL4		ENST00000285199.7:c.1106-1T>C	chr17.hg19:g.9586141T>C		122.0	0.0		114.0	5.0	NM_001267576	A6NDT9|B7ZLT9|B7ZVX5|Q8N2C5|Q96DQ6	Silent	SNP	ENST00000285199.7	hg19	CCDS45610.1																																																																																			.	.		0.532	USP43-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439855.3	NM_153210	Silent	C	9586141	T	C	9586141	5	2	282	1	0	0	0	0	0	0	1	0	17089	1565	54	2	1133	2	USP43	17	9586141	Splice_Site	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	96915	9586141	71609069	1114	41348										
USP43	124739	hgsc.bcm.edu	37	chr17	9604952	9604952	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcccaccagttacccgctggActtcctgtacgacctgtatg	9	15	0	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:9604952A>G	ENST00000285199.7	+	12	2042	c.1946A>G	c.(1945-1947)gAc>gGc	p.D649G	USP43_ENST00000570475.1_Missense_Mutation_p.D649G|USP43_ENST00000570827.2_3'UTR	NM_001267576.1|NM_153210.4	NP_001254505.1|NP_694942.3	Q70EL4	UBP43_HUMAN	ubiquitin specific peptidase 43	649	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	26						TACCCGCTGGACTTCCTGTAC	0.617																																					p.D649G		Atlas-SNP	.											.	USP43	65	.	0			c.A1946G						.						26	27	26					17																	9604952		2098	4225	6323	SO:0001583	missense	124739	exon12			CGCTGGACTTCCT	AK055188	CCDS45610.1, CCDS58516.1	17p12	2005-08-08	2005-08-08			ENSG00000154914		"Ubiquitin-specific peptidases"	20072	protein-coding gene	gene with protein product			"ubiquitin specific protease 43"			12838346	Standard	NM_153210		Approved	FLJ30626	uc010cod.4	Q70EL4		ENST00000285199.7:c.1946A>G	chr17.hg19:g.9604952A>G	ENSP00000285199:p.Asp649Gly	100.0	0.0		89.0	5.0	NM_001267576	A6NDT9|B7ZLT9|B7ZVX5|Q8N2C5|Q96DQ6	Missense_Mutation	SNP	ENST00000285199.7	hg19	CCDS45610.1	.	.	.	.	.	.	.	.	.	.	A	18.15	3.559789	0.65538	.	.	ENSG00000154914	ENST00000285199	T	0.02916	4.11	4.71	4.71	0.59529	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	2.618330	0.03151	U	0.167957	T	0.13372	0.0324	L	0.45470	1.425	0.80722	D	1	D;D;P;D	0.76494	0.999;0.98;0.745;0.999	D;P;P;D	0.76071	0.981;0.791;0.657;0.987	T	0.00118	-1.2033	10	0.49607	T	0.09	-29.4872	12.4203	0.55516	1.0:0.0:0.0:0.0	.	649;338;649;161	B7ZVX5;Q70EL4-3;Q70EL4;Q70EL4-2	.;.;UBP43_HUMAN;.	G	649	ENSP00000285199:D649G	ENSP00000285199:D649G	D	+	2	0	USP43	9545677	1.000000	0.71417	0.998000	0.56505	0.543000	0.35085	8.714000	0.91412	1.874000	0.54306	0.460000	0.39030	GAC	.	.		0.617	USP43-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439855.3	NM_153210		G	9604952	A	G	9604952	3	3	282	1	0	0	0	0	1	0	0	0	17089	275	10	2	1992	2	USP43	17	9604952	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	18811	9604952	71590258	1115	41349										
MYH4	4622	hgsc.bcm.edu	37	chr17	10369889	10369889	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcggtcttggctgtcaccttCcccccttccctgctctgcac					rs143441825	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:10369889delC	ENST00000255381.2	-	3	284	c.174delG	c.(172-174)gggfs	p.G58fs	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	58					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						CTGTCACCTTCCCCCCTTCCC	0.458																																					p.K59fs		Atlas-INDEL	.											.	MYH4	349	.	0			c.175delA						.						209	194	199					17																	10369889		2203	4300	6503	SO:0001589	frameshift_variant	4622	exon3			.		CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"Myosins / Myosin superfamily : Class II"	7574	protein-coding gene	gene with protein product		160742	"myosin, heavy polypeptide 4, skeletal muscle"			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.174delG	chr17.hg19:g.10369889delC	ENSP00000255381:p.Gly58fs	357.0	0.0		261.0	17.0	NM_017533		Frame_Shift_Del	DEL	ENST00000255381.2	hg19	CCDS11154.1																																																																																			.	.		0.458	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533		-	10369889	C	-	10369889	7	5	282	1	0	1	0	1	0	0	0	0	10046	842	30	0	5797	0	MYH4	17	10369889	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	764937	10369889	70825321	1116	41350										
CCDC144A	9720	hgsc.bcm.edu	37	chr17	16638176	16638176	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agaaaagaatgataaccttcAaaaaattataaaactaaatg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:16638176delA	ENST00000360524.8	+	12	2667	c.2591delA	c.(2590-2592)caafs	p.Q864fs	CCDC144A_ENST00000399273.1_Frame_Shift_Del_p.Q864fs|RP11-219A15.1_ENST00000448331.3_Frame_Shift_Del_p.Q864fs|CCDC144A_ENST00000443444.2_Frame_Shift_Del_p.Q864fs|CCDC144A_ENST00000456009.1_Frame_Shift_Del_p.Q584fs	NM_014695.1	NP_055510.1	A2RUR9	C144A_HUMAN	coiled-coil domain containing 144A	864																	GATAACCTTCAAAAAATTATA	0.318																																					p.Q864fs		Atlas-INDEL	.											.	CCDC144A	53	.	0			c.2590delC						.						4	4	4					17																	16638176		1599	3602	5201	SO:0001589	frameshift_variant	9720	exon12			.	BC133019	CCDS45621.1	17p11.2	2008-10-23			ENSG00000170160	ENSG00000170160			29072	protein-coding gene	gene with protein product						9628581, 11997339	Standard	NM_014695		Approved	KIAA0565, FLJ43983	uc002gqk.1	A2RUR9	OTTHUMG00000059178	ENST00000360524.8:c.2591delA	chr17.hg19:g.16638176delA	ENSP00000353717:p.Gln864fs	183.0	0.0		169.0	12.0	NM_014695	O60311|Q6ZU57	Frame_Shift_Del	DEL	ENST00000360524.8	hg19	CCDS45621.1																																																																																			.	.		0.318	CCDC144A-013	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000444093.1			-	16638176	A	-	16638176	7	5	282	1	0	1	0	1	0	0	0	0	2779	130	5	0	2637	0	CCDC144A	17	16638176	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	6268287	16638176	64557034	1117	41351										
MPRIP	23164	hgsc.bcm.edu	37	chr17	17061760	17061760	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccacagctcgttgccagaggAaaaaaacaagagcagctgct					rs551557602		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:17061760delA	ENST00000341712.4	+	14	1490	c.1490delA	c.(1489-1491)gaafs	p.E497fs	MPRIP_ENST00000395804.3_Frame_Shift_Del_p.E497fs|MPRIP_ENST00000395811.5_Frame_Shift_Del_p.E497fs|MPRIP_ENST00000444976.1_Frame_Shift_Del_p.E459fs			Q6WCQ1	MPRIP_HUMAN	myosin phosphatase Rho interacting protein	497						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						TTGCCAGAGGAAAAAAACAAG	0.612																																					p.E497fs		Pindel	.											.	MPRIP	87	.	0			c.1489delG						.						18	22	21					17																	17061760		2201	4289	6490	SO:0001589	frameshift_variant	23164	exon14			.	BC014102	CCDS32578.1, CCDS42268.1	17p11.2	2013-01-10			ENSG00000133030	ENSG00000133030		"Pleckstrin homology (PH) domain containing"	30321	protein-coding gene	gene with protein product	"Rho interacting protein 3"	612935				10048485	Standard	NM_201274		Approved	RHOIP3, M-RIP, p116Rip	uc002gqy.2	Q6WCQ1	OTTHUMG00000059276	ENST00000341712.4:c.1490delA	chr17.hg19:g.17061760delA	ENSP00000342379:p.Glu497fs	432.0	0.0		273.0	12.0	NM_015134	Q3KQZ5|Q5FB94|Q6DHW2|Q7Z5Y2|Q8N390|Q96G40	Frame_Shift_Del	DEL	ENST00000341712.4	hg19	CCDS32578.1																																																																																			.	.		0.612	MPRIP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131587.1	NM_015134		-	17061760	A	-	17061760	7	5	282	1	0	1	0	1	0	0	0	0	9752	246	9	0	1544	0	MPRIP	17	17061760	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	423584	17061760	64133450	1118	41352										
CYTSB	92521	hgsc.bcm.edu	37	chr17	20109062	20109062	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgagaagcagaaagccacagAggccagtgctgtggagcaga	15	8	0	4			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:20109062A>G	ENST00000261503.5	+	4	1751	c.1700A>G	c.(1699-1701)gAg>gGg	p.E567G	SPECC1_ENST00000472876.1_Intron|SPECC1_ENST00000395522.2_Missense_Mutation_p.E486G|SPECC1_ENST00000395525.3_Missense_Mutation_p.E486G|SPECC1_ENST00000395527.4_Missense_Mutation_p.E567G|SPECC1_ENST00000536879.1_Intron|SPECC1_ENST00000395530.2_Missense_Mutation_p.E486G|AC004702.2_ENST00000580225.1_lincRNA|SPECC1_ENST00000395529.3_Missense_Mutation_p.E567G|SPECC1_ENST00000584527.1_5'Flank	NM_001033553.2	NP_001028725.1	Q5M775	CYTSB_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1	567					cell adhesion (GO:0007155)	nucleus (GO:0005634)				breast(1)|large_intestine(3)|ovary(4)	8				KIRC - Kidney renal clear cell carcinoma(2;0.166)|Kidney(2;0.196)		AAAGCCACAGAGGCCAGTGCT	0.473																																					p.E567G		Atlas-SNP	.											.	SPECC1	100	.	0			c.A1700G						.						69	71	70					17																	20109062		2203	4300	6503	SO:0001583	missense	92521	exon4			CCACAGAGGCCAG	AY816329, AB041533	CCDS32590.1, CCDS42280.1, CCDS42281.1, CCDS45628.1, CCDS58531.1	17p11.2	2012-11-19	2010-09-17	2010-09-17	ENSG00000128487	ENSG00000128487			30615	protein-coding gene	gene with protein product	"sperm antigen HCMOGT 1", "cytokinesis and spindle organization B", "cytospin B"	608793				15602574, 18763323, 15087372	Standard	NM_001033553		Approved	HCMOGT-1, FLJ36955, NSP, CYTSB	uc002gwq.3	Q5M775	OTTHUMG00000179808	ENST00000261503.5:c.1700A>G	chr17.hg19:g.20109062A>G	ENSP00000261503:p.Glu567Gly	153.0	0.0		85.0	4.0	NM_001033553	B4DHH0|B7WNS8|Q5IBP1|Q5IBP2|Q5IBP3|Q5IBP4|Q5M772|Q5M773|Q5M774|Q86XT8|Q8N4U4|Q8WU84|Q9HCQ3	Missense_Mutation	SNP	ENST00000261503.5	hg19	CCDS32590.1	.	.	.	.	.	.	.	.	.	.	A	6.165	0.398668	0.11696	.	.	ENSG00000128487	ENST00000395530;ENST00000261503;ENST00000395529;ENST00000395522;ENST00000395527;ENST00000395525	T;T;T;T	0.75050	-0.9;2.12;2.17;2.16	5.37	-1.03	0.10102	.	0.254962	0.45126	N	0.000384	T	0.60612	0.2282	L	0.53780	1.695	0.80722	D	1	B;B;B;B;B	0.22080	0.024;0.018;0.018;0.018;0.064	B;B;B;B;B	0.23716	0.03;0.014;0.023;0.023;0.048	T	0.48043	-0.9069	10	0.66056	D	0.02	-6.7994	0.7713	0.01024	0.4611:0.1322:0.1513:0.2554	.	567;486;486;567;567	A8MV89;Q5M775-4;Q5M775-3;Q5M775-2;Q5M775	.;.;.;.;CYTSB_HUMAN	G	567;567;567;486;486;486	ENSP00000261503:E567G;ENSP00000378900:E567G;ENSP00000378893:E486G;ENSP00000378896:E486G	ENSP00000261503:E567G	E	+	2	0	SPECC1	20049654	1.000000	0.71417	0.000000	0.03702	0.006000	0.05464	2.892000	0.48625	-0.423000	0.07394	0.533000	0.62120	GAG	.	.		0.473	SPECC1-018	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441206.1	NM_152904		G	20109062	A	G	20109062	3	3	282	1	0	0	0	0	1	0	0	0	4212	304	11	2	1754	2	CYTSB	17	20109062	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	3047302	20109062	61086148	1119	41353										
KSR1	8844	hgsc.bcm.edu	37	chr17	25930890	25930890	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctttgcacacgcagccccgcTccctgaagctgccgacggta	10	17	0	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:25930890T>C	ENST00000319524.6	+	13	1607	c.1607T>C	c.(1606-1608)cTc>cCc	p.L536P	KSR1_ENST00000581975.1_3'UTR|KSR1_ENST00000268763.6_Missense_Mutation_p.L399P|KSR1_ENST00000509603.2_Missense_Mutation_p.L514P|KSR1_ENST00000398988.3_Missense_Mutation_p.L399P			Q8IVT5	KSR1_HUMAN	kinase suppressor of ras 1	536					Ras protein signal transduction (GO:0007265)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(12)|prostate(2)|urinary_tract(1)	28	Lung NSC(42;0.00836)		BRCA - Breast invasive adenocarcinoma(3;0.00122)	UCEC - Uterine corpus endometrioid carcinoma (53;0.168)		GCAGCCCCGCTCCCTGAAGCT	0.537											OREG0024261	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L399P	Esophageal Squamous(88;1120 1336 6324 10502 16832)	Atlas-SNP	.											.	KSR1	151	.	0			c.T1196C						.						65	75	72					17																	25930890		1989	4163	6152	SO:0001583	missense	8844	exon13			CCCCGCTCCCTGA	U43586	CCDS58532.1	17q11.2	2012-05-23	2005-12-14	2005-12-14	ENSG00000141068	ENSG00000141068			6465	protein-coding gene	gene with protein product		601132	"kinase suppressor of ras"	KSR		8521512	Standard	XM_006722151		Approved	RSU2	uc031qzj.1	Q8IVT5	OTTHUMG00000132051	ENST00000319524.6:c.1607T>C	chr17.hg19:g.25930890T>C	ENSP00000323178:p.Leu536Pro	153.0	0.0	782	104.0	5.0	NM_014238	F8WEA9|H7BYU0|Q13476	Missense_Mutation	SNP	ENST00000319524.6	hg19		.	.	.	.	.	.	.	.	.	.	T	11.01	1.513503	0.27123	.	.	ENSG00000141068	ENST00000319524;ENST00000509603;ENST00000268763;ENST00000398982	T;T;T	0.80033	-1.33;-1.33;-1.32	5.76	-5.87	0.02297	.	1.468070	0.03281	N	0.186136	T	0.59252	0.2180	N	0.11560	0.145	0.20307	N	0.999917	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46005	-0.9222	10	0.35671	T	0.21	.	4.3566	0.11181	0.1192:0.5168:0.1213:0.2428	.	534;514	Q8IVT5;F5H0K8	KSR1_HUMAN;.	P	536;514;399;399	ENSP00000323178:L536P;ENSP00000438795:L514P;ENSP00000268763:L399P	ENSP00000268763:L399P	L	+	2	0	KSR1	22955017	0.000000	0.05858	0.000000	0.03702	0.102000	0.19082	-0.631000	0.05496	-0.939000	0.03709	0.533000	0.62120	CTC	.	.		0.537	KSR1-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_014238		C	25930890	T	C	25930890	3	2	282	1	0	0	0	0	1	0	0	0	8590	1551	54	2	1234	2	KSR1	17	25930890	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	5821828	25930890	55264320	1120	41354										
NOS2	4843	hgsc.bcm.edu	37	chr17	26092677	26092677	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctgggcaaaccccaaggtgcTcccccggcaggtagttcagg	13	14	1	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:26092677T>C	ENST00000313735.6	-	20	2545	c.2312A>G	c.(2311-2313)gAg>gGg	p.E771G		NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN	nitric oxide synthase 2, inducible	771	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				arginine catabolic process (GO:0006527)|blood coagulation (GO:0007596)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|circadian rhythm (GO:0007623)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide mediated signal transduction (GO:0007263)|peptidyl-cysteine S-nitrosylation (GO:0018119)|phagosome maturation (GO:0090382)|positive regulation of guanylate cyclase activity (GO:0031284)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of leukocyte mediated cytotoxicity (GO:0001912)|positive regulation of vasodilation (GO:0045909)|regulation of cell proliferation (GO:0042127)|regulation of cellular respiration (GO:0043457)|regulation of insulin secretion (GO:0050796)|response to bacterium (GO:0009617)|response to hypoxia (GO:0001666)|superoxide metabolic process (GO:0006801)	cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	arginine binding (GO:0034618)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric-oxide synthase activity (GO:0004517)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|tetrahydrobiopterin binding (GO:0034617)			autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(28)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	56					Dexamethasone(DB01234)|Doxorubicin(DB00997)|L-Arginine(DB00125)|L-Citrulline(DB00155)|Miconazole(DB01110)|Triflusal(DB08814)	CCCAAGGTGCTCCCCCGGCAG	0.632																																					p.E771G		Atlas-SNP	.											.	NOS2	113	.	0			c.A2312G						.						32	36	34					17																	26092677		2203	4300	6503	SO:0001583	missense	4843	exon20			AGGTGCTCCCCCG	U20141	CCDS11223.1	17q11.2	2014-06-12	2008-09-16	2008-09-16	ENSG00000007171	ENSG00000007171	1.14.13.39		7873	protein-coding gene	gene with protein product		163730	"nitric oxide synthase 2A (inducible, hepatocytes)"	NOS2A		7682706	Standard	NM_000625		Approved	iNOS, NOS, HEP-NOS	uc002gzu.3	P35228	OTTHUMG00000132445	ENST00000313735.6:c.2312A>G	chr17.hg19:g.26092677T>C	ENSP00000327251:p.Glu771Gly	186.0	0.0		158.0	7.0	NM_000625	A1L3U5|B7ZLY2|O60757|O94994|Q16263|Q16692|Q4TTS5|Q9UD42	Missense_Mutation	SNP	ENST00000313735.6	hg19	CCDS11223.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.410709	0.83340	.	.	ENSG00000007171	ENST00000313735;ENST00000379105	T	0.33654	1.4	5.19	5.19	0.71726	Riboflavin synthase-like beta-barrel (1);FAD-binding, type 1 (1);NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain-3 (1);Ferredoxin reductase-type FAD-binding domain (1);Flavoprotein pyridine nucleotide cytochrome reductase (1);	0.192304	0.43416	D	0.000561	T	0.59891	0.2227	M	0.84326	2.69	0.58432	D	0.999999	P	0.49862	0.929	P	0.59546	0.859	T	0.66622	-0.5877	10	0.87932	D	0	.	14.2942	0.66300	0.0:0.0:0.0:1.0	.	771	P35228	NOS2_HUMAN	G	771;732	ENSP00000327251:E771G	ENSP00000327251:E771G	E	-	2	0	NOS2	23116804	1.000000	0.71417	0.981000	0.43875	0.514000	0.34195	5.742000	0.68646	1.979000	0.57680	0.374000	0.22700	GAG	.	.		0.632	NOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255597.1	NM_000625		C	26092677	T	C	26092677	3	2	282	1	0	0	0	0	1	0	0	0	10552	1551	54	2	1181	2	NOS2	17	26092677	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	161787	26092677	55102533	1121	41355										
SLC13A2	9058	hgsc.bcm.edu	37	chr17	26817514	26817514	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	actccaacctcctgttcttcGgggggctgctggtggccatc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:26817514delG	ENST00000314669.5	+	3	694	c.274delG	c.(274-276)gggfs	p.G93fs	SLC13A2_ENST00000545060.1_Frame_Shift_Del_p.G50fs|SLC13A2_ENST00000537681.1_Frame_Shift_Del_p.G22fs|SLC13A2_ENST00000444914.3_Frame_Shift_Del_p.G142fs	NM_003984.3	NP_003975.1	Q13183	S13A2_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2	93					dicarboxylic acid transport (GO:0006835)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	low-affinity sodium:dicarboxylate symporter activity (GO:0015361)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	all_lung(13;0.000871)|Lung NSC(42;0.0027)			UCEC - Uterine corpus endometrioid carcinoma (53;0.154)	Succinic acid(DB00139)	CCTGTTCTTCGGGGGGCTGCT	0.637																																					p.F140fs		Atlas-INDEL	.											.	SLC13A2	125	.	0			c.420delC						.						124	110	115					17																	26817514		2203	4300	6503	SO:0001589	frameshift_variant	9058	exon3			.	U26209	CCDS11231.1, CCDS54098.1	17p13.2	2013-05-22			ENSG00000007216	ENSG00000007216		"Solute carriers"	10917	protein-coding gene	gene with protein product		604148				8967342, 10343111	Standard	NM_001145975		Approved	NaDC-1	uc010wan.2	Q13183	OTTHUMG00000132523	ENST00000314669.5:c.274delG	chr17.hg19:g.26817514delG	ENSP00000316202:p.Gly93fs	223.0	0.0		148.0	11.0	NM_001145975	B2RBI9|B4DPL1|E7ETH5|Q4VAR7	Frame_Shift_Del	DEL	ENST00000314669.5	hg19	CCDS11231.1																																																																																			.	.		0.637	SLC13A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255722.1	NM_003984		-	26817514	G	-	26817514	7	5	282	1	0	1	0	1	0	0	0	0	14407	1116	39	0	431	0	SLC13A2	17	26817514	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	724837	26817514	54377696	1122	41356										
PROCA1	6830	hgsc.bcm.edu	37	chr17	27030897	27030897	+	IGR	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtcaactggcctttcttggcTtttttcttcagctttgcctt					rs151135532		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:27030897delT	ENST00000314616.6	+	0	6518				PROCA1_ENST00000579650.1_5'Flank|PROCA1_ENST00000301039.2_Frame_Shift_Del_p.K230fs|PROCA1_ENST00000581289.1_3'UTR|PROCA1_ENST00000439862.3_Frame_Shift_Del_p.K232fs	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)						chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					CTTTCTTGGcttttttcttca	0.483																																					p.A231fs		Atlas-INDEL	.											.	PROCA1	28	.	0			c.691delG						.						91	95	94					17																	27030897		2202	4300	6502	SO:0001628	intergenic_variant	147011	exon4			.	U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"SH2 domain containing"	11470	protein-coding gene	gene with protein product		601333	"suppressor of Ty (S.cerevisiae) 6 homolog"			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85			chr17.hg19:g.27030897delT		311.0	0.0		237.0	15.0	NM_152465	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Frame_Shift_Del	DEL	ENST00000314616.6	hg19	CCDS32596.1																																																																																			.	.		0.483	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170		-	27030897	T	-	27030897	6	5	282	0	1	1	0	1	0	0	0	0	12558	1606	56	0		0	PROCA1	17	27030897	IGR	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	213383	27030897	54164313	1123	41357										
ERAL1	26284	hgsc.bcm.edu	37	chr17	27182148	27182148	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcgagggagcgggtgatcccTttttcctcactcttaggctt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:27182148delT	ENST00000254928.5	+	1	193	c.96delT	c.(94-96)cctfs	p.P32fs	FAM222B_ENST00000583953.1_5'Flank|ERAL1_ENST00000578001.1_3'UTR	NM_005702.2	NP_005693.1	O75616	ERAL1_HUMAN	Era-like 12S mitochondrial rRNA chaperone 1	32					ribosomal small subunit assembly (GO:0000028)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|rRNA binding (GO:0019843)			endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(2)	11	all_cancers(5;2.12e-15)|all_epithelial(6;3.44e-19)|Lung NSC(42;0.01)		Epithelial(11;1.12e-05)|all cancers(11;5.32e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000272)|OV - Ovarian serous cystadenocarcinoma(11;0.105)			GGGTGATCCCTTTTTCCTCAC	0.627																																					p.P32fs		Atlas-INDEL	.											ERAL1,NS,carcinoma,0,1	ERAL1	28	.	0			c.95delC						.						89	77	81					17																	27182148		2203	4300	6503	SO:0001589	frameshift_variant	26284	exon1			.	AF082657	CCDS11244.1	17q11.2	2013-05-22	2013-05-22		ENSG00000132591	ENSG00000132591			3424	protein-coding gene	gene with protein product		607435	"Era (E. coli G-protein homolog)-like 1", "Era G-protein-like 1 (E. coli)"			10945472, 20604745	Standard	NM_005702		Approved	HERA-B	uc002hcy.1	O75616	OTTHUMG00000132675	ENST00000254928.5:c.96delT	chr17.hg19:g.27182148delT	ENSP00000254928:p.Pro32fs	214.0	0.0		175.0	13.0	NM_005702	B3KN21|C9JEC6|O75617|Q8WUY4|Q96LE2|Q96TC0	Frame_Shift_Del	DEL	ENST00000254928.5	hg19	CCDS11244.1																																																																																			.	.		0.627	ERAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255937.2			-	27182148	T	-	27182148	7	5	282	1	0	1	0	1	0	0	0	0	5204	1596	56	0	98	0	ERAL1	17	27182148	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	151251	27182148	54013062	1124	41358										
SEZ6	124925	hgsc.bcm.edu	37	chr17	27284100	27284100	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggggggtcactccaatgcgaGgggtgcccaggcacacactt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:27284100delG	ENST00000317338.12	-	13	3083	c.2655delC	c.(2653-2655)cccfs	p.P885fs	SEZ6_ENST00000442608.3_Frame_Shift_Del_p.P885fs|SEZ6_ENST00000360295.9_Frame_Shift_Del_p.P885fs|PIPOX_ENST00000583215.1_Intron|SEZ6_ENST00000335960.6_Intron			Q53EL9	SEZ6_HUMAN	seizure related 6 homolog (mouse)	885	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|negative regulation of dendrite development (GO:2000171)|positive regulation of dendrite development (GO:1900006)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	apical dendrite (GO:0097440)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(4)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	29	Lung NSC(42;0.0137)		Epithelial(11;4.73e-06)|all cancers(11;2.91e-05)|BRCA - Breast invasive adenocarcinoma(11;8.06e-05)|OV - Ovarian serous cystadenocarcinoma(11;0.111)			TCCAATGCGAGGGGTGCCCAG	0.617																																					p.S886fs		Atlas-INDEL	.											.	SEZ6	61	.	0			c.2656delT						.						22	24	23					17																	27284100		2050	4181	6231	SO:0001589	frameshift_variant	124925	exon13			.	AY038048	CCDS45638.1, CCDS45639.1	17q11.2	2008-03-06	2001-11-28		ENSG00000063015	ENSG00000063015			15955	protein-coding gene	gene with protein product			"seizure related gene 6 (mouse) homolog"			17086543	Standard	NM_178860		Approved		uc002hdp.2	Q53EL9	OTTHUMG00000168010	ENST00000317338.12:c.2655delC	chr17.hg19:g.27284100delG	ENSP00000312942:p.Pro885fs	196.0	0.0		156.0	10.0	NM_001098635	B6ZDN1|Q8N701|Q8NB57|Q8ND50|Q8TD25|Q96NI5|Q96NQ3	Frame_Shift_Del	DEL	ENST00000317338.12	hg19	CCDS45639.1																																																																																			.	.		0.617	SEZ6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397475.3			-	27284100	G	-	27284100	7	5	282	1	0	1	0	1	0	0	0	0	14157	987	35	0	362	0	SEZ6	17	27284100	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	101952	27284100	53911110	1125	41359										
TP53I13	90313	hgsc.bcm.edu	37	chr17	27899664	27899664	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgcacagaaacttccgacgcGgggagagcatctactggggg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:27899664delG	ENST00000301057.7	+	6	1133	c.1018delG	c.(1018-1020)gggfs	p.G340fs	RP11-68I3.4_ENST00000579050.1_RNA|RP11-68I3.2_ENST00000581474.1_RNA	NM_138349.2	NP_612358.3	Q8NBR0	P5I13_HUMAN	tumor protein p53 inducible protein 13	340						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|kidney(1)|lung(1)|urinary_tract(1)	4				READ - Rectum adenocarcinoma(3;0.236)		CTTCCGACGCGGGGAGAGCAT	0.682																																					p.R339fs		Atlas-INDEL	.											.	TP53I13	17	.	0			c.1017delC						.						7	8	7					17																	27899664		2092	4184	6276	SO:0001589	frameshift_variant	90313	exon6			.	AK075341	CCDS42289.1	17q11.2	2006-01-16				ENSG00000167543			25102	protein-coding gene	gene with protein product						14767535	Standard	NM_138349		Approved	DSCP1	uc002hee.3	Q8NBR0		ENST00000301057.7:c.1018delG	chr17.hg19:g.27899664delG	ENSP00000301057:p.Gly340fs	204.0	0.0		155.0	11.0	NM_138349	Q7L5U3	Frame_Shift_Del	DEL	ENST00000301057.7	hg19	CCDS42289.1																																																																																			.	.		0.682	TP53I13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447804.2	NM_138349		-	27899664	G	-	27899664	7	5	282	1	0	1	0	1	0	0	0	0	16401	1116	39	0	1040	0	TP53I13	17	27899664	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	615564	27899664	53295546	1126	41360										
SLC6A4	6532	hgsc.bcm.edu	37	chr17	28544272	28544272	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gggccagctgccagctgatgCcccccaggtcctggagcccc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:28544272delC	ENST00000401766.2	-	5	1261	c.749delG	c.(748-750)ggcfs	p.G250fs	SLC6A4_ENST00000261707.3_Frame_Shift_Del_p.G250fs			P31645	SC6A4_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 4	250					brain morphogenesis (GO:0048854)|cellular response to cGMP (GO:0071321)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|memory (GO:0007613)|monoamine transport (GO:0015844)|negative regulation of cerebellar granule cell precursor proliferation (GO:0021941)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of organ growth (GO:0046621)|negative regulation of synaptic transmission, dopaminergic (GO:0032227)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein homooligomerization (GO:0051260)|protein oligomerization (GO:0051259)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|response to toxic substance (GO:0009636)|serotonin transport (GO:0006837)|serotonin uptake (GO:0051610)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|thalamus development (GO:0021794)|vasoconstriction (GO:0042310)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|cocaine binding (GO:0019811)|monoamine transmembrane transporter activity (GO:0008504)|Rab GTPase binding (GO:0017137)|serotonin transmembrane transporter activity (GO:0015222)|serotonin:sodium symporter activity (GO:0005335)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(4)	25					Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexfenfluramine(DB01191)|Dexmethylphenidate(DB06701)|Dextromethorphan(DB00514)|Dopamine(DB00988)|Doxepin(DB01142)|Duloxetine(DB00476)|Ephedra(DB01363)|Escitalopram(DB01175)|Fluoxetine(DB00472)|Fluvoxamine(DB00176)|Imipramine(DB00458)|Levomilnacipran(DB08918)|Loxapine(DB00408)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Milnacipran(DB04896)|Minaprine(DB00805)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Paroxetine(DB00715)|Pethidine(DB00454)|Phentermine(DB00191)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Sertraline(DB01104)|Sibutramine(DB01105)|Tapentadol(DB06204)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)	CCAGCTGATGCCCCCCAGGTC	0.582																																					p.G250fs		Atlas-INDEL	.											SLC6A4,NS,carcinoma,0,1	SLC6A4	60	.	0			c.750delC						.						79	80	79					17																	28544272		2203	4300	6503	SO:0001589	frameshift_variant	6532	exon6			.	L05568	CCDS11256.1	17q11.2	2014-01-30	2013-07-19		ENSG00000108576	ENSG00000108576		"Solute carriers"	11050	protein-coding gene	gene with protein product	"serotonin transporter 1"	182138	"solute carrier family 6 (neurotransmitter transporter, serotonin), member 4", "5-hydroxytryptamine (serotonin) transporter", "obsessive-compulsive disorder 1"	HTT, OCD1		7681602, 19806148	Standard	NM_001045		Approved	5-HTT, SERT1	uc002hey.5	P31645	OTTHUMG00000132751	ENST00000401766.2:c.749delG	chr17.hg19:g.28544272delC	ENSP00000385822:p.Gly250fs	212.0	0.0		169.0	12.0	NM_001045	Q5EE02	Frame_Shift_Del	DEL	ENST00000401766.2	hg19	CCDS11256.1																																																																																			.	.		0.582	SLC6A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256115.3	NM_001045		-	28544272	C	-	28544272	7	5	282	1	0	1	0	1	0	0	0	0	14701	739	26	0	1183	0	SLC6A4	17	28544272	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	644608	28544272	52650938	1127	41361										
C17orf42	79736	hgsc.bcm.edu	37	chr17	29231265	29231265	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aattctgaaatggcccaaagTtttctctgtgctctacgata							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:29231265delT	ENST00000581216.1	-	2	935	c.314delA	c.(313-315)aacfs	p.N105fs	TEFM_ENST00000580840.1_Frame_Shift_Del_p.N105fs	NM_024683.3	NP_078959.3	Q96QE5	TEFM_HUMAN	transcription elongation factor, mitochondrial	105					DNA metabolic process (GO:0006259)|oxidative phosphorylation (GO:0006119)|regulation of transcription, DNA-templated (GO:0006355)|transcription from mitochondrial promoter (GO:0006390)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|ribonucleoprotein complex (GO:0030529)	DNA polymerase processivity factor activity (GO:0030337)|poly(A) RNA binding (GO:0044822)										TGGCCCAAAGTTTTCTCTGTG	0.373																																					p.N105fs		Atlas-INDEL	.											.	.	.	.	0			c.315delC						.						100	92	94					17																	29231265		1842	4080	5922	SO:0001589	frameshift_variant	79736	exon2			.		CCDS42291.1	17q11.2	2011-12-12	2011-12-12	2011-12-12	ENSG00000172171	ENSG00000172171			26223	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 42"	C17orf42		11468690, 10843809, 21278163	Standard	NM_024683		Approved	FLJ22729	uc002hfu.2	Q96QE5		ENST00000581216.1:c.314delA	chr17.hg19:g.29231265delT	ENSP00000462963:p.Asn105fs	246.0	0.0		164.0	10.0	NM_024683	E1P655|Q6GPG5|Q6PJ19|Q96H04|Q9H5Z9	Frame_Shift_Del	DEL	ENST00000581216.1	hg19	CCDS42291.1																																																																																			.	.		0.373	TEFM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444498.1	NM_024683		-	29231265	T	-	29231265	7	5	282	1	0	1	0	1	0	0	0	0	1858	1725	60	0	780	0	C17orf42	17	29231265	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	686993	29231265	51963945	1128	41362										
SUZ12	23512	hgsc.bcm.edu	37	chr17	30315475	30315475	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaattcagagagtctccatcAggaaaacaagcctggttcag	9	9	4	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:30315475A>G	ENST00000322652.5	+	10	1389	c.1160A>G	c.(1159-1161)cAg>cGg	p.Q387R	SUZ12_ENST00000580398.1_Missense_Mutation_p.Q364R	NM_015355.2	NP_056170.2	Q15022	SUZ12_HUMAN	SUZ12 polycomb repressive complex 2 subunit	387					histone ubiquitination (GO:0016574)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|histone methyltransferase activity (GO:0042054)|metal ion binding (GO:0046872)|methylated histone binding (GO:0035064)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)		SSH2/SUZ12(2)|JAZF1/SUZ12(133)	breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|lung(5)|skin(1)	21		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.041)|Ovarian(249;0.182)|Breast(31;0.231)				AGTCTCCATCAGGAAAACAAG	0.398			T	JAZF1	endometrial stromal tumours																																p.Q387R		Atlas-SNP	.		Dom	yes		17	17q11.2	23512	suppressor of zeste 12 homolog (Drosophila)		M	.	SUZ12	61	.	0			c.A1160G						.						75	75	75					17																	30315475		2203	4300	6503	SO:0001583	missense	23512	exon10			TCCATCAGGAAAA	D63881	CCDS11270.1	17q21	2013-06-05	2013-06-05		ENSG00000178691	ENSG00000178691		"Zinc fingers, C2H2-type"	17101	protein-coding gene	gene with protein product		606245	"suppressor of zeste 12 homolog (Drosophila)"			8590280, 11371647, 18784248	Standard	NM_015355		Approved	JJAZ1, KIAA0160, CHET9	uc002hgs.2	Q15022	OTTHUMG00000132813	ENST00000322652.5:c.1160A>G	chr17.hg19:g.30315475A>G	ENSP00000316578:p.Gln387Arg	217.0	0.0		183.0	9.0	NM_015355	Q96BD9	Missense_Mutation	SNP	ENST00000322652.5	hg19	CCDS11270.1	.	.	.	.	.	.	.	.	.	.	a	13.26	2.183387	0.38511	.	.	ENSG00000178691	ENST00000322652	T	0.44881	0.91	5.53	4.44	0.53790	.	0.155378	0.64402	D	0.000014	T	0.31888	0.0811	L	0.36672	1.1	0.46396	D	0.999025	B;B	0.23650	0.012;0.089	B;B	0.19391	0.004;0.025	T	0.05468	-1.0883	10	0.23302	T	0.38	-11.5643	11.953	0.52966	0.8698:0.0:0.0:0.1302	.	387;387	A8K1U9;Q15022	.;SUZ12_HUMAN	R	387	ENSP00000316578:Q387R	ENSP00000316578:Q387R	Q	+	2	0	SUZ12	27339588	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.095000	0.76952	0.900000	0.36469	0.528000	0.53228	CAG	.	.		0.398	SUZ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256260.2	NM_015355		G	30315475	A	G	30315475	3	3	282	1	0	0	0	0	1	0	0	0	15431	188	7	2	1198	2	SUZ12	17	30315475	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1084210	30315475	50879735	1129	41363										
C17orf75	64149	hgsc.bcm.edu	37	chr17	30660500	30660500	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tacctcctttggcaccatttAaaaaagcttgcatccaatcc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:30660500delA	ENST00000577809.1	-	9	960	c.911delT	c.(910-912)ttafs	p.L304fs	C17orf75_ENST00000225805.4_Frame_Shift_Del_p.L304fs|RP11-227G15.3_ENST00000581915.1_RNA	NM_022344.3	NP_071739.2	Q9HAS0	NJMU_HUMAN	chromosome 17 open reading frame 75	304										ovary(1)	1		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)			GGCACCATTTAAAAAAGCTTG	0.338																																					p.L304fs		Atlas-INDEL	.											.	C17orf75	23	.	0			c.912delA						.						141	139	140					17																	30660500		1816	4073	5889	SO:0001589	frameshift_variant	64149	exon9			.	AB062437	CCDS58537.1	17q11.2	2013-01-21			ENSG00000108666	ENSG00000108666			30173	protein-coding gene	gene with protein product							Standard	NM_022344		Approved	NJMU-R1	uc002hhg.3	Q9HAS0		ENST00000577809.1:c.911delT	chr17.hg19:g.30660500delA	ENSP00000464275:p.Leu304fs	234.0	0.0		224.0	16.0	NM_022344	Q7Z2H4	Frame_Shift_Del	DEL	ENST00000577809.1	hg19	CCDS58537.1																																																																																			.	.		0.338	C17orf75-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447204.1	NM_022344		-	30660500	A	-	30660500	7	5	282	1	0	1	0	1	0	0	0	0	1882	372	13	0	287	0	C17orf75	17	30660500	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	345025	30660500	50534710	1130	41364										
SLFN5	162394	hgsc.bcm.edu	37	chr17	33586258	33586258	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gatagaaagcggcttcagtaTctggaaaaactcaaccttcc	8	10	3	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:33586258T>C	ENST00000299977.4	+	2	697	c.549T>C	c.(547-549)taT>taC	p.Y183Y	SLFN5_ENST00000542451.1_Silent_p.Y183Y|SLFN5_ENST00000592325.1_Silent_p.Y183Y	NM_144975.3	NP_659412.3	Q08AF3	SLFN5_HUMAN	schlafen family member 5	183				Y -> H (in Ref. 1; AAI25202). {ECO:0000305}.	cell differentiation (GO:0030154)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(8)|liver(2)|lung(6)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	34		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0191)		GGCTTCAGTATCTGGAAAAAC	0.418																																					p.Y183Y		Atlas-SNP	.											.	SLFN5	92	.	0			c.T549C						.						135	130	132					17																	33586258		2203	4300	6503	SO:0001819	synonymous_variant	162394	exon2			TCAGTATCTGGAA	BX647942	CCDS32619.1	17q12	2006-04-05				ENSG00000166750			28286	protein-coding gene	gene with protein product		614952				9846487	Standard	NM_144975		Approved	MGC19764	uc002hjf.4	Q08AF3		ENST00000299977.4:c.549T>C	chr17.hg19:g.33586258T>C		197.0	0.0		161.0	9.0	NM_144975	Q08AF2|Q8WU54|Q96A82	Silent	SNP	ENST00000299977.4	hg19	CCDS32619.1																																																																																			.	.		0.418	SLFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448649.2	NM_144975		C	33586258	T	C	33586258	2	2	282	1	0	0	0	0	0	0	0	1	14752	1442	50	2		2	SLFN5	17	33586258	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2925758	33586258	47608952	1131	41365										
C17orf66	256957	hgsc.bcm.edu	37	chr17	34195732	34195732	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acatcagagatatcagttgaTttttcataggccatcttctt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:34195732delT	ENST00000311880.2	-	1	163	c.15delA	c.(13-15)aaafs	p.K5fs	C17orf66_ENST00000592980.1_Frame_Shift_Del_p.K5fs|AC015849.2_ENST00000413928.1_RNA|C17orf66_ENST00000587585.1_5'UTR	NM_152781.2	NP_689994.2	A2RTY3	HEAT9_HUMAN		5					hematopoietic progenitor cell differentiation (GO:0002244)					breast(3)|central_nervous_system(1)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(6)|lung(11)|skin(2)|stomach(4)	38		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0184)		TATCAGTTGATTTTTCATAGG	0.527																																					p.S6fs		Atlas-INDEL	.											.	C17orf66	57	.	0			c.16delT						.						120	98	106					17																	34195732		2203	4300	6503	SO:0001589	frameshift_variant	256957	exon1			.																												ENST00000311880.2:c.15delA	chr17.hg19:g.34195732delT	ENSP00000309560:p.Lys5fs	157.0	0.0		112.0	10.0	NM_152781	B4DX21|B4DXA4|B4DXF0|Q8N4R4|Q96M46	Frame_Shift_Del	DEL	ENST00000311880.2	hg19	CCDS11299.1																																																																																			.	.		0.527	C17orf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256487.1			-	34195732	T	-	34195732	7	5	282	1	0	1	0	1	0	0	0	0	1876	1490	52	0	1757	0	C17orf66	17	34195732	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	609474	34195732	46999478	1132	41366										
PIGW	284098	hgsc.bcm.edu	37	chr17	34893402	34893402	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tttggctgtggacttcccacTttttcccagaagatttgcca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:34893402delT	ENST00000592983.1	+	2	1032	c.452delT	c.(451-453)cttfs	p.L151fs	MYO19_ENST00000431794.3_5'Flank|MYO19_ENST00000544606.1_5'Flank|PIGW_ENST00000328396.2_Frame_Shift_Del_p.L151fs|MYO19_ENST00000590081.1_Intron|MYO19_ENST00000268852.9_5'Flank|MYO19_ENST00000586007.1_5'Flank			Q7Z7B1	PIGW_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class W	151					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transferase activity, transferring acyl groups (GO:0016746)			breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		GACTTCCCACTTTTTCCCAGA	0.433																																					p.L151fs		Atlas-INDEL	.											.	PIGW	50	.	0			c.451delC						.						228	226	227					17																	34893402		2203	4300	6503	SO:0001589	frameshift_variant	284098	exon2			.	AB097818	CCDS11313.1	17q21.1	2014-05-06	2006-06-28		ENSG00000184886	ENSG00000277161		"Phosphatidylinositol glycan anchor biosynthesis"	23213	protein-coding gene	gene with protein product		610275	"phosphatidylinositol glycan, class W"			14517336, 12714589	Standard	XM_005257238		Approved	Gwt1, FLJ37433	uc002hmz.1	Q7Z7B1	OTTHUMG00000188438	ENST00000592983.1:c.452delT	chr17.hg19:g.34893402delT	ENSP00000468778:p.Leu151fs	311.0	0.0		246.0	15.0	NM_178517	Q8N9G3	Frame_Shift_Del	DEL	ENST00000592983.1	hg19	CCDS11313.1																																																																																			.	.		0.433	PIGW-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451318.1	NM_178517		-	34893402	T	-	34893402	7	5	282	1	0	1	0	1	0	0	0	0	11911	1609	56	0	454	0	PIGW	17	34893402	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	697670	34893402	46301808	1133	41367										
SRCIN1	80725	hgsc.bcm.edu	37	chr17	36689629	36689629	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctgagactgggctcgaggtcTcattcgacccgctcatctct	10	14	3	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:36689629T>C	ENST00000264659.7	-	19	3679	c.3455A>G	c.(3454-3456)gAg>gGg	p.E1152G	SRCIN1_ENST00000578925.1_Missense_Mutation_p.E1186G	NM_025248.2	NP_079524.2	Q9C0H9	SRCN1_HUMAN	SRC kinase signaling inhibitor 1	1024					exocytosis (GO:0006887)|negative regulation of protein tyrosine kinase activity (GO:0061099)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell migration (GO:0030334)|regulation of dendritic spine morphogenesis (GO:0061001)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	protein kinase binding (GO:0019901)			endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)	19						GCTCGAGGTCTCATTCGACCC	0.542																																					p.E1152G		Atlas-SNP	.											.	SRCIN1	66	.	0			c.A3455G						.						60	62	61					17																	36689629		1864	4094	5958	SO:0001583	missense	80725	exon19			GAGGTCTCATTCG		CCDS45660.1	17q12	2009-12-14			ENSG00000017373	ENSG00000277363			29506	protein-coding gene	gene with protein product	"p130Cas-associated protein", "SNAP-25-interacting protein"	610786				11214970	Standard	NM_025248		Approved	SNIP, p140Cap, KIAA1684	uc002hqd.3	Q9C0H9		ENST00000264659.7:c.3455A>G	chr17.hg19:g.36689629T>C	ENSP00000264659:p.Glu1152Gly	157.0	0.0		93.0	4.0	NM_025248	Q75T46|Q8N4W8	Missense_Mutation	SNP	ENST00000264659.7	hg19	CCDS45660.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.793798	0.90453	.	.	ENSG00000017373	ENST00000264659	T	0.50001	0.76	5.27	5.27	0.74061	.	0.196420	0.34906	N	0.003584	T	0.57695	0.2071	L	0.36672	1.1	0.39645	D	0.970379	D	0.76494	0.999	D	0.75484	0.986	T	0.57087	-0.7871	10	0.33940	T	0.23	-33.2504	14.4655	0.67480	0.0:0.0:0.0:1.0	.	1152	Q9C0H9-5	.	G	1152	ENSP00000264659:E1152G	ENSP00000264659:E1152G	E	-	2	0	SRCIN1	33943155	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.007000	0.63984	2.109000	0.64355	0.460000	0.39030	GAG	.	.		0.542	SRCIN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441878.4	NM_025248		C	36689629	T	C	36689629	3	2	282	1	0	0	0	0	1	0	0	0	15151	1551	54	2	100	2	SRCIN1	17	36689629	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1796227	36689629	44505581	1134	41368										
SRCIN1	80725	hgsc.bcm.edu	37	chr17	36704821	36704821	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctgcgatgatgcgatcctcgTcatcctcgtccttgatggcc	10	14	1	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:36704821T>C	ENST00000264659.7	-	17	3466	c.3242A>G	c.(3241-3243)gAc>gGc	p.D1081G	SRCIN1_ENST00000578925.1_Missense_Mutation_p.D1115G|SRCIN1_ENST00000398579.4_5'UTR	NM_025248.2	NP_079524.2	Q9C0H9	SRCN1_HUMAN	SRC kinase signaling inhibitor 1	953					exocytosis (GO:0006887)|negative regulation of protein tyrosine kinase activity (GO:0061099)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell migration (GO:0030334)|regulation of dendritic spine morphogenesis (GO:0061001)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	protein kinase binding (GO:0019901)			endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)	19						GCGATCCTCGTCATCCTCGTC	0.672																																					p.D1081G		Atlas-SNP	.											.	SRCIN1	66	.	0			c.A3242G						.						87	91	89					17																	36704821		2102	4200	6302	SO:0001583	missense	80725	exon17			TCCTCGTCATCCT		CCDS45660.1	17q12	2009-12-14			ENSG00000017373	ENSG00000277363			29506	protein-coding gene	gene with protein product	"p130Cas-associated protein", "SNAP-25-interacting protein"	610786				11214970	Standard	NM_025248		Approved	SNIP, p140Cap, KIAA1684	uc002hqd.3	Q9C0H9		ENST00000264659.7:c.3242A>G	chr17.hg19:g.36704821T>C	ENSP00000264659:p.Asp1081Gly	123.0	0.0		95.0	4.0	NM_025248	Q75T46|Q8N4W8	Missense_Mutation	SNP	ENST00000264659.7	hg19	CCDS45660.1	.	.	.	.	.	.	.	.	.	.	T	17.38	3.375721	0.61735	.	.	ENSG00000017373	ENST00000264659;ENST00000542707;ENST00000398579	T	0.44083	0.93	4.53	4.53	0.55603	.	0.180161	0.46758	D	0.000266	T	0.42131	0.1189	L	0.50333	1.59	0.58432	D	0.999996	P;P;B	0.39480	0.675;0.675;0.449	B;B;B	0.41813	0.367;0.367;0.205	T	0.46331	-0.9199	10	0.72032	D	0.01	-8.7264	12.9793	0.58554	0.0:0.0:0.0:1.0	.	953;953;1081	Q9C0H9-2;Q9C0H9;Q9C0H9-5	.;SRCN1_HUMAN;.	G	1081;862;935	ENSP00000264659:D1081G	ENSP00000264659:D1081G	D	-	2	0	SRCIN1	33958347	1.000000	0.71417	0.606000	0.28943	0.911000	0.54048	7.327000	0.79147	1.904000	0.55121	0.379000	0.24179	GAC	.	.		0.672	SRCIN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441878.4	NM_025248		C	36704821	T	C	36704821	3	2	282	1	0	0	0	0	1	0	0	0	15151	1667	58	2	321	2	SRCIN1	17	36704821	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	15192	36704821	44490389	1135	41369										
MLLT6	4302	hgsc.bcm.edu	37	chr17	36861960	36861960	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gagaacccgctggtctactgCgatgggcacgcgtgcagcgt	15	12	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:36861960C>T	ENST00000325718.7	+	1	166	c.75C>T	c.(73-75)tgC>tgT	p.C25C	MLLT6_ENST00000378137.5_Silent_p.C25C|CTB-58E17.3_ENST00000583409.1_RNA|CTB-58E17.1_ENST00000563897.1_lincRNA	NM_005937.3	NP_005928	P55198	AF17_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6	25					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(3)|lung(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8	Breast(7;4.43e-21)					TGGTCTACTGCGATGGGCACG	0.736			T	MLL	AL																																p.C25C		Atlas-SNP	.		Dom	yes		17	17q21	4302	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6 (AF17)"		L	.	MLLT6	80	.	0			c.C75T						.						53	46	48					17																	36861960		2203	4300	6503	SO:0001819	synonymous_variant	4302	exon1			CTACTGCGATGGG		CCDS11327.1	17q21	2014-04-10	2001-11-28		ENSG00000108292	ENSG00000275023		"Zinc fingers, PHD-type"	7138	protein-coding gene	gene with protein product	"Myeloid/lymphoid or mixed-lineage leukemia, translocated to, 6", "trithorax homolog"	600328	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 6"			8058765	Standard	NM_005937		Approved	AF17, FLJ23480	uc002hqi.4	P55198	OTTHUMG00000188498	ENST00000325718.7:c.75C>T	chr17.hg19:g.36861960C>T		166.0	0.0		88.0	29.0	NM_005937	Q59F28|Q96IU3|Q9H5F6|Q9UF49	Silent	SNP	ENST00000325718.7	hg19	CCDS11327.1																																																																																			.	.		0.736	MLLT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256799.1	NM_005937		T	36861960	C	T	36861960	2	4	282	1	0	0	0	0	0	0	0	1	9639	776	27	1		1	MLLT6	17	36861960	Silent	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	157139	36861960	44333250	1136	41370										
PCGF2	7703	hgsc.bcm.edu	37	chr17	36891838	36891838	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tggctggacacggtacttgaGggggagaggcccgttctgcg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:36891838delG	ENST00000580830.1	-	12	1374	c.673delC	c.(673-675)ctcfs	p.L225fs	PCGF2_ENST00000581345.1_Frame_Shift_Del_p.L225fs|PCGF2_ENST00000360797.2_Frame_Shift_Del_p.L225fs|PCGF2_ENST00000585100.1_Frame_Shift_Del_p.P226fs|PCGF2_ENST00000578109.1_Frame_Shift_Del_p.P172fs|PCGF2_ENST00000579882.1_Frame_Shift_Del_p.P226fs			P35227	PCGF2_HUMAN	polycomb group ring finger 2	225					anterior/posterior pattern specification (GO:0009952)|cellular response to hydrogen peroxide (GO:0070301)|embryonic skeletal system morphogenesis (GO:0048704)|histone acetylation (GO:0016573)|in utero embryonic development (GO:0001701)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	10	Breast(7;9.07e-22)					CGGTACTTGAGGGGGAGAGGC	0.652											OREG0024367	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L225fs		Atlas-INDEL	.											.	PCGF2	24	.	0			c.674delT						.						6	7	7					17																	36891838		2160	4243	6403	SO:0001589	frameshift_variant	7703	exon11			.	D13969	CCDS32638.1	17q12	2013-01-09	2005-01-17	2005-01-19		ENSG00000277258		"RING-type (C3HC4) zinc fingers", "Polycomb group ring fingers"	12929	protein-coding gene	gene with protein product		600346	"ring finger protein 110"	ZNF144, RNF110		8325509	Standard	NM_007144		Approved	MEL-18	uc002hqp.1	P35227		ENST00000580830.1:c.673delC	chr17.hg19:g.36891838delG	ENSP00000461961:p.Leu225fs	124.0	0.0	866	133.0	10.0	NM_007144	A6NGD8	Frame_Shift_Del	DEL	ENST00000580830.1	hg19	CCDS32638.1																																																																																			.	.		0.652	PCGF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442246.2	NM_007144		-	36891838	G	-	36891838	7	5	282	1	0	1	0	1	0	0	0	0	11584	1000	35	0	365	0	PCGF2	17	36891838	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	29878	36891838	44303372	1137	41371										
RPL23	9349	hgsc.bcm.edu	37	chr17	37008859	37008859	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggctcagtgtttactcacccTtttttctgagctctggtttg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:37008859delT	ENST00000479035.2	-	3	356	c.224delA	c.(223-225)aagfs	p.K75fs	RPL23_ENST00000394333.1_Frame_Shift_Del_p.K75fs|RPL23_ENST00000245857.5_Frame_Shift_Del_p.K16fs|SNORA21_ENST00000362423.1_RNA|RPL23_ENST00000577407.1_Frame_Shift_Del_p.K75fs|RPL23_ENST00000394332.1_Frame_Shift_Del_p.K75fs|SNORA21_ENST00000516890.1_RNA	NM_000978.3	NP_000969.1	P62829	RL23_HUMAN	ribosomal protein L23	75					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosomal protein import into nucleus (GO:0006610)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(2)|large_intestine(1)	3						TTACTCACCCTTTTTTCTGAG	0.488																																					p.K75fs		Atlas-INDEL	.											.	RPL23	7	.	0			c.225delG						.						138	111	120					17																	37008859		2203	4300	6503	SO:0001589	frameshift_variant	9349	exon3			.	X52839	CCDS11330.1	17q12	2011-04-06			ENSG00000125691	ENSG00000125691		"L ribosomal proteins"	10316	protein-coding gene	gene with protein product		603662				1861993	Standard	NM_000978		Approved	rpL17, L23	uc002hqx.1	P62829	OTTHUMG00000133118	ENST00000479035.2:c.224delA	chr17.hg19:g.37008859delT	ENSP00000420311:p.Lys75fs	292.0	0.0		211.0	14.0	NM_000978	P23131|P24048|Q29246|Q3SWV7|Q6P5S1	Frame_Shift_Del	DEL	ENST00000479035.2	hg19	CCDS11330.1																																																																																			.	.		0.488	RPL23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256785.3	NM_000978		-	37008859	T	-	37008859	7	5	282	1	0	1	0	1	0	0	0	0	13585	1609	56	0	210	0	RPL23	17	37008859	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	117021	37008859	44186351	1138	41372										
CDK12	51755	hgsc.bcm.edu	37	chr17	37681026	37681026	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gagccacctccatccaaaacTtctcgaaaagaaactacctc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:37681026delT	ENST00000447079.4	+	12	3228	c.3195delT	c.(3193-3195)actfs	p.T1065fs	CDK12_ENST00000430627.2_Frame_Shift_Del_p.T1065fs	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	1065					mRNA processing (GO:0006397)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|protein autophosphorylation (GO:0046777)|regulation of MAP kinase activity (GO:0043405)|RNA splicing (GO:0008380)	cyclin K-CDK12 complex (GO:0002944)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(4)|breast(3)|endometrium(5)|kidney(4)|large_intestine(11)|lung(23)|ovary(11)|prostate(4)|skin(2)|urinary_tract(3)	70						CATCCAAAACTTCTCGAAAAG	0.557			"Mis, N, F"		serous ovarian					TCGA Ovarian(9;0.13)																											p.T1065fs		Atlas-INDEL	.		Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	.	CDK12	161	.	0			c.3194delC						.						118	118	118					17																	37681026		2203	4300	6503	SO:0001589	frameshift_variant	51755	exon12			.	AF227198	CCDS11337.1, CCDS45666.1	17q12	2011-10-25	2009-12-16	2009-12-16	ENSG00000167258	ENSG00000167258		"Cyclin-dependent kinases"	24224	protein-coding gene	gene with protein product	"CDC2 related protein kinase 7"	615514	"Cdc2-related kinase, arginine/serine-rich"	CRKRS		10048485, 11683387, 19884882	Standard	XM_005257456		Approved	CRK7, CRKR, KIAA0904	uc010cvv.3	Q9NYV4	OTTHUMG00000133214	ENST00000447079.4:c.3195delT	chr17.hg19:g.37681026delT	ENSP00000398880:p.Thr1065fs	226.0	0.0		156.0	10.0	NM_016507	A7E2B2|B4DYX4|B9EIQ6|O94978	Frame_Shift_Del	DEL	ENST00000447079.4	hg19	CCDS11337.1																																																																																			.	.		0.557	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256941.4	NM_016507		-	37681026	T	-	37681026	7	5	282	1	0	1	0	1	0	0	0	0	3130	1596	56	0	3241	0	CDK12	17	37681026	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	672167	37681026	43514184	1139	41373										
GSDMA	284110	hgsc.bcm.edu	37	chr17	38132221	38132221	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgctggtgaaatccatggagAaaaagatcctacccgtgcag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:38132221delA	ENST00000301659.4	+	11	1184	c.1066delA	c.(1066-1068)aaafs	p.K357fs		NM_178171.4	NP_835465.2	Q96QA5	GSDMA_HUMAN	gasdermin A	357					apoptotic process (GO:0006915)	perinuclear region of cytoplasm (GO:0048471)				NS(1)|endometrium(2)|large_intestine(3)|lung(1)	7						ATCCATGGAGAAAAAGATCCT	0.517																																					p.E355fs		Atlas-INDEL	.											.	GSDMA	26	.	0			c.1065delG						.						53	54	54					17																	38132221		1900	4143	6043	SO:0001589	frameshift_variant	284110	exon11			.	AB093591	CCDS45669.1	17q21.2	2008-07-31	2008-07-31	2008-07-31		ENSG00000167914			13311	protein-coding gene	gene with protein product		611218	"gasdermin", "gasdermin 1"	GSDM, GSDM1		12883658, 15010812, 17350798	Standard	NM_178171		Approved	FLJ39120	uc002htl.1	Q96QA5		ENST00000301659.4:c.1066delA	chr17.hg19:g.38132221delA	ENSP00000301659:p.Lys357fs	325.0	0.0		217.0	15.0	NM_178171	Q32MC5|Q86VE7|Q8N1M6	Frame_Shift_Del	DEL	ENST00000301659.4	hg19	CCDS45669.1																																																																																			.	.		0.517	GSDMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446847.1	NM_178171		-	38132221	A	-	38132221	7	5	282	1	0	1	0	1	0	0	0	0	6825	247	9	0	1104	0	GSDMA	17	38132221	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	451195	38132221	43062989	1140	41374										
TOP2A	7153	hgsc.bcm.edu	37	chr17	38552661	38552661	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtttttttccccttggccttCccccctttcccaggaagtcc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:38552661delC	ENST00000423485.1	-	28	3752	c.3594delG	c.(3592-3594)gggfs	p.G1198fs		NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	1198					apoptotic chromosome condensation (GO:0030263)|ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA ligation (GO:0006266)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|embryonic cleavage (GO:0040016)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|positive regulation of apoptotic process (GO:0043065)|positive regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral genome replication (GO:0045070)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|DNA-dependent ATPase activity (GO:0008094)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(9)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	39		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	CCTTGGCCTTCCCCCCTTTCC	0.428																																					p.K1199fs		Atlas-INDEL	.											.	TOP2A	124	.	0			c.3595delA						.						118	110	112					17																	38552661		1841	4091	5932	SO:0001589	frameshift_variant	7153	exon28			.		CCDS45672.1	17q21-q22	2008-08-06	2002-08-29		ENSG00000131747	ENSG00000131747	5.99.1.2		11989	protein-coding gene	gene with protein product		126430	"topoisomerase (DNA) II alpha (170kD)"	TOP2			Standard	NM_001067		Approved		uc002huq.3	P11388	OTTHUMG00000155008	ENST00000423485.1:c.3594delG	chr17.hg19:g.38552661delC	ENSP00000411532:p.Gly1198fs	205.0	0.0		120.0	10.0	NM_001067	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Frame_Shift_Del	DEL	ENST00000423485.1	hg19	CCDS45672.1																																																																																			.	.		0.428	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1			-	38552661	C	-	38552661	7	5	282	1	0	1	0	1	0	0	0	0	16380	842	30	0	1033	0	TOP2A	17	38552661	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	420440	38552661	42642549	1141	41375										
KRT24	192666	hgsc.bcm.edu	37	chr17	38856499	38856499	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgttgaaccgctcctcagccTctcggcggttttgctcagcc	10	15	3	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:38856499T>C	ENST00000264651.2	-	4	1048	c.992A>G	c.(991-993)gAg>gGg	p.E331G		NM_019016.2	NP_061889.2	Q2M2I5	K1C24_HUMAN	keratin 24	331	Coil 2.|Rod.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Breast(137;0.00526)				CTCCTCAGCCTCTCGGCGGTT	0.552																																					p.E331G	GBM(61;380 1051 14702 23642 31441)	Atlas-SNP	.											.	KRT24	60	.	0			c.A992G						.						147	144	145					17																	38856499		2203	4300	6503	SO:0001583	missense	192666	exon4			TCAGCCTCTCGGC		CCDS11372.1	17q21.2	2013-06-25			ENSG00000167916	ENSG00000167916		"-", "Intermediate filaments type I, keratins (acidic)"	18527	protein-coding gene	gene with protein product		607742				16831889	Standard	NM_019016		Approved	FLJ20261, MGC138169, MGC138173	uc002hvd.3	Q2M2I5	OTTHUMG00000133372	ENST00000264651.2:c.992A>G	chr17.hg19:g.38856499T>C	ENSP00000264651:p.Glu331Gly	203.0	0.0		144.0	6.0	NM_019016	Q9NXG7	Missense_Mutation	SNP	ENST00000264651.2	hg19	CCDS11372.1	.	.	.	.	.	.	.	.	.	.	T	28.5	4.927192	0.92389	.	.	ENSG00000167916	ENST00000264651	D	0.81739	-1.53	5.86	5.86	0.93980	Prefoldin (1);Filament (1);	.	.	.	.	D	0.91713	0.7380	M	0.92268	3.29	0.58432	D	0.999999	D	0.71674	0.998	D	0.66847	0.947	D	0.93580	0.6912	9	0.87932	D	0	.	16.2605	0.82541	0.0:0.0:0.0:1.0	.	331	Q2M2I5	K1C24_HUMAN	G	331	ENSP00000264651:E331G	ENSP00000264651:E331G	E	-	2	0	KRT24	36110025	1.000000	0.71417	0.853000	0.33588	0.825000	0.46686	6.172000	0.71932	2.237000	0.73441	0.460000	0.39030	GAG	.	.		0.552	KRT24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257217.1	NM_019016		C	38856499	T	C	38856499	3	2	282	1	0	0	0	0	1	0	0	0	8470	1551	54	2	605	2	KRT24	17	38856499	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	303838	38856499	42338711	1142	41376										
JUP	3728	hgsc.bcm.edu	37	chr17	39919572	39919572	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcagcacactctccaggcccTcctggagggcaaggaaggga	13	13	2	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:39919572T>C	ENST00000393931.3	-	8	1278	c.1160A>G	c.(1159-1161)gAg>gGg	p.E387G	JUP_ENST00000310706.5_Splice_Site_p.E387G|JUP_ENST00000540235.1_Intron|JUP_ENST00000393930.1_Splice_Site_p.E387G	NM_002230.2	NP_002221.1	P14923	PLAK_HUMAN	junction plakoglobin	387					adherens junction organization (GO:0034332)|atrioventricular valve morphogenesis (GO:0003181)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell-cell junction organization (GO:0045216)|cellular response to indole-3-methanol (GO:0071681)|cytoskeletal anchoring at plasma membrane (GO:0007016)|desmosome assembly (GO:0002159)|detection of mechanical stimulus (GO:0050982)|ectoderm development (GO:0007398)|endothelial cell-cell adhesion (GO:0071603)|establishment of protein localization to plasma membrane (GO:0090002)|gastrulation (GO:0007369)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of Wnt signaling pathway involved in heart development (GO:0003308)|nervous system development (GO:0007399)|oocyte development (GO:0048599)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein heterooligomerization (GO:0051291)|regulation of cell proliferation (GO:0042127)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|skin development (GO:0043588)|ventricular cardiac muscle cell action potential (GO:0086005)	actin cytoskeleton (GO:0015629)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|gamma-catenin-TCF7L2 complex (GO:0071665)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|cadherin binding (GO:0045296)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|structural constituent of cell wall (GO:0005199)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)	23		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)		CTCCAGGCCCTCCTGGAGGGC	0.587																																					p.E387G	Colon(16;42 520 6044 17852 28530)	Atlas-SNP	.											.	JUP	64	.	0			c.A1160G						.						53	49	51					17																	39919572		2203	4300	6503	SO:0001630	splice_region_variant	3728	exon8			AGGCCCTCCTGGA	AF233882	CCDS11407.1	17q21	2014-09-17	2004-08-09		ENSG00000173801	ENSG00000173801		"Armadillo repeat containing"	6207	protein-coding gene	gene with protein product		173325	"catenin (cadherin-associated protein), gamma 80kDa"	CTNNG		1889810, 7604000	Standard	NM_021991		Approved	DP3, PDGB, PKGB, DPIII	uc002hxs.2	P14923	OTTHUMG00000133494	ENST00000393931.3:c.1159-1A>G	chr17.hg19:g.39919572T>C		133.0	0.0		85.0	4.0	NM_021991	Q15093|Q15151|Q7L3S5|Q86W21|Q9BWC4|Q9HCX9	Missense_Mutation	SNP	ENST00000393931.3	hg19	CCDS11407.1	.	.	.	.	.	.	.	.	.	.	T	16.11	3.029133	0.54790	.	.	ENSG00000173801	ENST00000393930;ENST00000310706;ENST00000393931	T;T;T	0.66815	-0.23;-0.23;-0.23	4.9	4.9	0.64082	Armadillo-like helical (1);Armadillo-type fold (1);	0.096735	0.64402	D	0.000001	T	0.62684	0.2448	M	0.67397	2.05	0.80722	D	1	P	0.37612	0.602	B	0.31390	0.129	T	0.69716	-0.5070	10	0.87932	D	0	-41.7617	13.8482	0.63481	0.0:0.0:0.0:1.0	.	387	P14923	PLAK_HUMAN	G	387	ENSP00000377507:E387G;ENSP00000311113:E387G;ENSP00000377508:E387G	ENSP00000311113:E387G	E	-	2	0	JUP	37173098	1.000000	0.71417	1.000000	0.80357	0.642000	0.38348	7.760000	0.85248	2.059000	0.61396	0.397000	0.26171	GAG	.	.		0.587	JUP-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257406.1		Missense_Mutation	C	39919572	T	C	39919572	5	2	282	1	0	0	0	0	0	0	1	0	7981	1565	54	2	1105	2	JUP	17	39919572	Splice_Site	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1063073	39919572	41275638	1143	41377										
CNP	1267	hgsc.bcm.edu	37	chr17	40123969	40123969	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcacctactttggaaagagaCccccaggcgtgctgcattgc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:40123969delC	ENST00000393892.3	+	3	880	c.736delC	c.(736-738)cccfs	p.P247fs	CNP_ENST00000591072.1_Frame_Shift_Del_p.P12fs|CNP_ENST00000393888.1_Frame_Shift_Del_p.P227fs|CNP_ENST00000472031.1_Frame_Shift_Del_p.D21fs	NM_033133.4	NP_149124.3	P09543	CN37_HUMAN	2',3'-cyclic nucleotide 3' phosphodiesterase	247					adult locomotory behavior (GO:0008344)|aging (GO:0007568)|axonogenesis (GO:0007409)|cyclic nucleotide catabolic process (GO:0009214)|microtubule cytoskeleton organization (GO:0000226)|oligodendrocyte differentiation (GO:0048709)|regulation of mitochondrial membrane permeability (GO:0046902)|response to lipopolysaccharide (GO:0032496)|response to toxic substance (GO:0009636)|substantia nigra development (GO:0021762)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule (GO:0005874)|microvillus (GO:0005902)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|myelin sheath abaxonal region (GO:0035748)|myelin sheath adaxonal region (GO:0035749)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	2',3'-cyclic-nucleotide 3'-phosphodiesterase activity (GO:0004113)|cyclic nucleotide binding (GO:0030551)|RNA binding (GO:0003723)			breast(1)|kidney(2)|large_intestine(1)|lung(4)|upper_aerodigestive_tract(1)	9		all_cancers(22;2.38e-06)|all_epithelial(22;6.79e-05)|Breast(137;0.000143)		UCEC - Uterine corpus endometrioid carcinoma (308;0.171)		TGGAAAGAGACCCCCAGGCGT	0.592																																					p.R245fs		Atlas-INDEL	.											.	CNP	58	.	0			c.735delA						.						56	58	57					17																	40123969		1986	4151	6137	SO:0001589	frameshift_variant	1267	exon3			.		CCDS11414.2	17q21	2008-02-05			ENSG00000173786	ENSG00000173786	3.1.4.37		2158	protein-coding gene	gene with protein product		123830				1322358	Standard	XM_006721701		Approved		uc002hyl.1	P09543	OTTHUMG00000133502	ENST00000393892.3:c.736delC	chr17.hg19:g.40123969delC	ENSP00000377470:p.Pro247fs	324.0	0.0		193.0	12.0	NM_033133		Frame_Shift_Del	DEL	ENST00000393892.3	hg19	CCDS11414.2																																																																																			.	.		0.592	CNP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257443.2			-	40123969	C	-	40123969	7	5	282	1	0	1	0	1	0	0	0	0	3628	507	18	0	746	0	CNP	17	40123969	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	204397	40123969	41071241	1144	41378										
DNAJC7	7266	hgsc.bcm.edu	37	chr17	40141477	40141477	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccatcctgagagcctgtacgAaaaactgaactgccttctca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:40141477delA	ENST00000457167.4	-	7	934	c.698delT	c.(697-699)ttcfs	p.F233fs	DNAJC7_ENST00000426588.3_Frame_Shift_Del_p.F177fs|DNAJC7_ENST00000316603.7_Frame_Shift_Del_p.F177fs	NM_003315.3	NP_003306.3	Q99615	DNJC7_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 7	233					chaperone cofactor-dependent protein refolding (GO:0070389)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	heat shock protein binding (GO:0031072)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)	9		all_cancers(22;0.00273)|Breast(137;0.00104)|all_epithelial(22;0.0305)				AGCCTGTACGAAAAACTGAAC	0.463																																					p.F233fs	Colon(63;618 1117 8600 10857 19751)	Atlas-INDEL	.											.	DNAJC7	51	.	0			c.699delC						.						151	142	145					17																	40141477		1909	4128	6037	SO:0001589	frameshift_variant	7266	exon7			.	U46571	CCDS45677.1, CCDS45678.1	17q11.2	2013-01-10				ENSG00000168259		"Heat shock proteins / DNAJ (HSP40)", "Tetratricopeptide (TTC) repeat domain containing"	12392	protein-coding gene	gene with protein product		601964		TTC2		8836031, 11147971	Standard	NR_029431		Approved	TPR2	uc002hyo.3	Q99615		ENST00000457167.4:c.698delT	chr17.hg19:g.40141477delA	ENSP00000406463:p.Phe233fs	240.0	0.0		170.0	11.0	NM_003315	Q7Z784	Frame_Shift_Del	DEL	ENST00000457167.4	hg19	CCDS45677.1																																																																																			.	.		0.463	DNAJC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453366.2			-	40141477	A	-	40141477	7	5	282	1	0	1	0	1	0	0	0	0	4656	246	9	0	818	0	DNAJC7	17	40141477	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	17508	40141477	41053733	1145	41379										
PLEKHH3	79990	hgsc.bcm.edu	37	chr17	40823012	40823012	+	Splice_Site	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggctggggctggacatttacTtctcaaacctggtgagcacg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:40823012delT	ENST00000591022.1	-	9	1808	c.1421delA	c.(1420-1422)aac>ac	p.N474fs	PLEKHH3_ENST00000412503.1_Intron|PLEKHH3_ENST00000293349.6_Intron|PLEKHH3_ENST00000456950.2_Intron	NM_024927.4	NP_079203	Q7Z736	PKHH3_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 3	474	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				signal transduction (GO:0007165)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)				endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)|skin(2)	13		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.14)		GGACATTTACTTCTCAAACCT	0.632																																					.		Atlas-INDEL	.											.	PLEKHH3	49	.	0			c.1421+1A>-						.						56	64	61					17																	40823012		2125	4233	6358	SO:0001630	splice_region_variant	79990	exon10			.	BC052978	CCDS11434.1	17q21.2	2013-01-11				ENSG00000068137		"Pleckstrin homology (PH) domain containing"	26105	protein-coding gene	gene with protein product						12477932	Standard	NM_024927		Approved	FLJ21019	uc002iau.3	Q7Z736		ENST00000591022.1:c.1421+1A>-	chr17.hg19:g.40823012delT		193.0	0.0		159.0	10.0	NM_024927	C9JQ76|Q59H20|Q96B28|Q9H7D6|Q9NT18	Splice_Site	DEL	ENST00000591022.1	hg19	CCDS11434.1																																																																																			.	.		0.632	PLEKHH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452332.1	NM_024927	Frame_Shift_Del	-	40823012	T	-	40823012	8	5	282	1	0	1	0	1	0	0	1	0	12087	1623	56	0	980	0	PLEKHH3	17	40823012	Splice_Site	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	681535	40823012	40372198	1146	41380										
PLEKHH3	79990	hgsc.bcm.edu	37	chr17	40823047	40823047	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agcacgtcggccacgagggtCcccccagccagggctcgctc					rs538834328		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:40823047delC	ENST00000591022.1	-	9	1773	c.1386delG	c.(1384-1386)gggfs	p.G462fs	PLEKHH3_ENST00000412503.1_Frame_Shift_Del_p.G462fs|PLEKHH3_ENST00000293349.6_Frame_Shift_Del_p.G462fs|PLEKHH3_ENST00000456950.2_5'UTR	NM_024927.4	NP_079203	Q7Z736	PKHH3_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 3	462	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				signal transduction (GO:0007165)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)				endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)|skin(2)	13		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.14)		CCACGAGGGTCCCCCCAGCCA	0.652																																					p.T463fs		Atlas-INDEL	.											.	PLEKHH3	49	.	0			c.1387delA						.						40	48	45					17																	40823047		2141	4246	6387	SO:0001589	frameshift_variant	79990	exon9			.	BC052978	CCDS11434.1	17q21.2	2013-01-11				ENSG00000068137		"Pleckstrin homology (PH) domain containing"	26105	protein-coding gene	gene with protein product						12477932	Standard	NM_024927		Approved	FLJ21019	uc002iau.3	Q7Z736		ENST00000591022.1:c.1386delG	chr17.hg19:g.40823047delC	ENSP00000468678:p.Gly462fs	132.0	0.0		116.0	10.0	NM_024927	C9JQ76|Q59H20|Q96B28|Q9H7D6|Q9NT18	Frame_Shift_Del	DEL	ENST00000591022.1	hg19	CCDS11434.1																																																																																			.	.		0.652	PLEKHH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452332.1	NM_024927		-	40823047	C	-	40823047	7	5	282	1	0	1	0	1	0	0	0	0	12087	842	30	0	1015	0	PLEKHH3	17	40823047	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	35	40823047	40372163	1147	41381										
IFI35	3430	hgsc.bcm.edu	37	chr17	41164212	41164212	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acaggccctccacgcccttcAggaggagcaggccagactca	11	16	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:41164212A>G	ENST00000415816.2	+	2	261	c.38A>G	c.(37-39)cAg>cGg	p.Q13R	IFI35_ENST00000536969.1_3'UTR|IFI35_ENST00000438323.2_Missense_Mutation_p.Q13R	NM_005533.4	NP_005524.2	P80217	IN35_HUMAN	interferon-induced protein 35	13	Leucine-zipper.				cytokine-mediated signaling pathway (GO:0019221)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)	8		Breast(137;0.00499)		BRCA - Breast invasive adenocarcinoma(366;0.157)		CACGCCCTTCAGGAGGAGCAG	0.587																																					p.Q13R		Atlas-SNP	.											.	IFI35	23	.	0			c.A38G						.						29	29	29					17																	41164212		2191	4285	6476	SO:0001583	missense	3430	exon2			CCCTTCAGGAGGA	BC001356	CCDS11450.1	17q21	2006-04-05			ENSG00000068079	ENSG00000068079			5399	protein-coding gene	gene with protein product		600735					Standard	NM_005533		Approved	IFP35	uc021txx.1	P80217	OTTHUMG00000167720	ENST00000415816.2:c.38A>G	chr17.hg19:g.41164212A>G	ENSP00000394579:p.Gln13Arg	106.0	0.0		94.0	5.0	NM_005533	C9JGX1|Q92984|Q99537|Q9BV98	Missense_Mutation	SNP	ENST00000415816.2	hg19		.	.	.	.	.	.	.	.	.	.	A	6.756	0.508395	0.12883	.	.	ENSG00000068079	ENST00000415816;ENST00000438323	T;T	0.45276	0.9;0.9	4.9	-2.44	0.06502	Interferon induced 35kDa, N-terminal (1);	0.753193	0.12202	N	0.490143	T	0.21427	0.0516	N	0.21448	0.665	0.18873	N	0.999989	B	0.02656	0.0	B	0.08055	0.003	T	0.14282	-1.0478	10	0.29301	T	0.29	.	3.6023	0.08030	0.2968:0.0:0.2224:0.4808	.	13	P80217	IN35_HUMAN	R	13	ENSP00000394579:Q13R;ENSP00000395590:Q13R	ENSP00000394579:Q13R	Q	+	2	0	IFI35	38417738	0.598000	0.26882	0.438000	0.26821	0.034000	0.12701	-0.198000	0.09505	-0.552000	0.06167	-0.301000	0.09380	CAG	.	.		0.587	IFI35-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000395851.1	NM_005533		G	41164212	A	G	41164212	3	3	282	1	0	0	0	0	1	0	0	0	7525	188	7	2	44	2	IFI35	17	41164212	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	341165	41164212	40030998	1148	41382										
BRCA1	672	hgsc.bcm.edu	37	chr17	41219686	41219686	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttagttaaagtgatgtggtgTtttctggcaaacttgtacac							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:41219686delT	ENST00000357654.3	-	16	5131	c.5013delA	c.(5011-5013)aaafs	p.K1671fs	BRCA1_ENST00000493795.1_Frame_Shift_Del_p.K1624fs|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000471181.2_Frame_Shift_Del_p.K1692fs|BRCA1_ENST00000346315.3_Intron|BRCA1_ENST00000351666.3_Frame_Shift_Del_p.K488fs|BRCA1_ENST00000468300.1_Frame_Shift_Del_p.K567fs|BRCA1_ENST00000352993.3_Frame_Shift_Del_p.K529fs|BRCA1_ENST00000591534.1_Frame_Shift_Del_p.K162fs|BRCA1_ENST00000309486.4_Frame_Shift_Del_p.K1375fs|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000491747.2_Frame_Shift_Del_p.K567fs|BRCA1_ENST00000354071.3_Intron	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	1671	BRCT 1. {ECO:0000255|PROSITE- ProRule:PRU00033}.				androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		TGATGTGGTGTTTTCTGGCAA	0.358			"D, Mis, N, F, S"		ovarian	"breast, ovarian"		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																											p.H1693fs		Atlas-INDEL	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	.	BRCA1	304	.	0			c.5077delC						.						131	127	128					17																	41219686		2202	4300	6502	SO:0001589	frameshift_variant	672	exon17	Familial Cancer Database		.	U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1100	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 1", "protein phosphatase 1, regulatory subunit 53"	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.5013delA	chr17.hg19:g.41219686delT	ENSP00000350283:p.Lys1671fs	145.0	0.0		116.0	10.0	NM_007300	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Frame_Shift_Del	DEL	ENST00000357654.3	hg19	CCDS11453.1																																																																																			.	.		0.358	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294		-	41219686	T	-	41219686	7	5	282	1	0	1	0	1	0	0	0	0	1500	1722	60	0	610	0	BRCA1	17	41219686	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	55474	41219686	39975524	1149	41383										
BRCA1	672	hgsc.bcm.edu	37	chr17	41251836	41251836	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tttgaggttgtatccgctgcTttgtcctcagagttctcaca					rs273901743		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:41251836delT	ENST00000357654.3	-	7	621	c.503delA	c.(502-504)aagfs	p.K168fs	BRCA1_ENST00000493795.1_Frame_Shift_Del_p.K121fs|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000471181.2_Frame_Shift_Del_p.K168fs|BRCA1_ENST00000346315.3_Frame_Shift_Del_p.K168fs|BRCA1_ENST00000351666.3_Frame_Shift_Del_p.K168fs|BRCA1_ENST00000468300.1_Frame_Shift_Del_p.K168fs|BRCA1_ENST00000352993.3_Frame_Shift_Del_p.K168fs|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000309486.4_5'UTR|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000491747.2_Frame_Shift_Del_p.K168fs|BRCA1_ENST00000354071.3_Frame_Shift_Del_p.K168fs	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	168					androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		TATCCGCTGCTTTGTCCTCAG	0.398			"D, Mis, N, F, S"		ovarian	"breast, ovarian"		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																											p.K168fs		Atlas-INDEL	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	.	BRCA1	304	.	0			c.504delG						.						178	170	173					17																	41251836		2203	4300	6503	SO:0001589	frameshift_variant	672	exon6	Familial Cancer Database		.	U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1100	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 1", "protein phosphatase 1, regulatory subunit 53"	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.503delA	chr17.hg19:g.41251836delT	ENSP00000350283:p.Lys168fs	236.0	0.0		158.0	11.0	NM_007298	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Frame_Shift_Del	DEL	ENST00000357654.3	hg19	CCDS11453.1																																																																																			.	.		0.398	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294		-	41251836	T	-	41251836	7	5	282	1	0	1	0	1	0	0	0	0	1500	1609	56	0	5226	0	BRCA1	17	41251836	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	32150	41251836	39943374	1150	41384										
ETV4	2118	hgsc.bcm.edu	37	chr17	41605953	41605953	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gccagctctgggaggtaggcGgggctctcatccaagtggga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:41605953delG	ENST00000319349.5	-	13	1687	c.1389delC	c.(1387-1389)cccfs	p.P463fs	ETV4_ENST00000545089.1_Frame_Shift_Del_p.P409fs|ETV4_ENST00000393664.2_Frame_Shift_Del_p.P463fs|ETV4_ENST00000545954.1_Frame_Shift_Del_p.P424fs|ETV4_ENST00000586826.1_Frame_Shift_Del_p.P186fs|ETV4_ENST00000591713.1_Frame_Shift_Del_p.P463fs|ETV4_ENST00000538265.1_Frame_Shift_Del_p.P424fs	NM_001079675.2	NP_001073143.1	P43268	ETV4_HUMAN	ets variant 4	463					branching involved in mammary gland duct morphogenesis (GO:0060444)|cell differentiation (GO:0030154)|motor neuron axon guidance (GO:0008045)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)	nucleolus (GO:0005730)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)		EWSR1/ETV4(6)|CANT1/ETV4(3)|TMPRSS2/ETV4(13)|DDX5_ENST00000540698/ETV4(2)|KLK2/ETV4(2)	ovary(2)|upper_aerodigestive_tract(1)	3		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.0798)		GGAGGTAGGCGGGGCTCTCAT	0.642			T	"EWSR1, TMPRSS2, DDX5, KLK2, CANT1"	"Ewing sarcoma, Prostate carcinoma"																																p.A464fs	Esophageal Squamous(116;1540 1611 12927 31103 34118)	Atlas-INDEL	.		Dom	yes		17	17q21	2118	"ets variant gene 4 (E1A enhancer binding protein, E1AF)"		"M, E"	.	ETV4	36	.	0			c.1390delG						.						39	37	38					17																	41605953		2203	4300	6503	SO:0001589	frameshift_variant	2118	exon13			.	U18018	CCDS11465.1, CCDS58553.1, CCDS59292.1	17q21	2014-04-30	2008-09-12			ENSG00000175832			3493	protein-coding gene	gene with protein product	"E1A enhancer binding protein"	600711	"ets variant gene 4 (E1A enhancer-binding protein, E1AF)"			8530053, 1547944	Standard	NM_001986		Approved	E1A-F, E1AF, PEA3	uc002idw.3	P43268		ENST00000319349.5:c.1389delC	chr17.hg19:g.41605953delG	ENSP00000321835:p.Pro463fs	221.0	0.0		176.0	11.0	NM_001986	A8K314|B7Z5J3|B7Z9J6|Q96AW9	Frame_Shift_Del	DEL	ENST00000319349.5	hg19	CCDS11465.1																																																																																			.	.		0.642	ETV4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453489.1	NM_001986		-	41605953	G	-	41605953	7	5	282	1	0	1	0	1	0	0	0	0	5283	1103	39	0	69	0	ETV4	17	41605953	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	354117	41605953	39589257	1151	41385										
NAGS	162417	hgsc.bcm.edu	37	chr17	42084998	42084998	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctgaccatggagcccgtcctGgggggcaccccgtacctgga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:42084998delG	ENST00000293404.3	+	6	1426	c.1308delG	c.(1306-1308)ctgfs	p.L436fs		NM_153006.2	NP_694551.1	Q8N159	NAGS_HUMAN	N-acetylglutamate synthase	436	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				arginine biosynthetic process (GO:0006526)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	mitochondrial matrix (GO:0005759)	acetyl-CoA:L-glutamate N-acetyltransferase activity (GO:0004042)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8		Breast(137;0.00536)|Prostate(33;0.0724)		BRCA - Breast invasive adenocarcinoma(366;0.113)		AGCCCGTCCTGGGGGGCACCC	0.682											OREG0024449	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L436fs		Atlas-INDEL	.											.	NAGS	25	.	0			c.1307delT						.						15	18	17					17																	42084998		2197	4293	6490	SO:0001589	frameshift_variant	162417	exon6			.	AY116537	CCDS11473.1	17q21.31	2008-02-05				ENSG00000161653			17996	protein-coding gene	gene with protein product		608300				15050968, 12459178	Standard	NM_153006		Approved	AGAS, ARGA, NAT7	uc002ies.3	Q8N159		ENST00000293404.3:c.1308delG	chr17.hg19:g.42084998delG	ENSP00000293404:p.Leu436fs	254.0	0.0	906	153.0	11.0	NM_153006	B2RAZ9|Q8IWR4	Frame_Shift_Del	DEL	ENST00000293404.3	hg19	CCDS11473.1																																																																																			.	.		0.682	NAGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457660.1	NM_153006		-	42084998	G	-	42084998	7	5	282	1	0	1	0	1	0	0	0	0	10154	1335	47	0	1330	0	NAGS	17	42084998	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	479045	42084998	39110212	1152	41386										
MAPT	4137	hgsc.bcm.edu	37	chr17	44039763	44039763	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cacgctgggacgtacgggttGggggacaggaaagatcaggg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:44039763delG	ENST00000571987.1	+	1	60	c.60delG	c.(58-60)ttgfs	p.L20fs	MAPT_ENST00000446361.3_Frame_Shift_Del_p.L20fs|MAPT_ENST00000334239.8_Frame_Shift_Del_p.L20fs|MAPT_ENST00000262410.5_Frame_Shift_Del_p.L20fs|MAPT_ENST00000347967.5_5'UTR|MAPT_ENST00000351559.5_Frame_Shift_Del_p.L20fs|MAPT_ENST00000535772.1_Frame_Shift_Del_p.L20fs|MAPT_ENST00000431008.3_Frame_Shift_Del_p.L20fs|MAPT_ENST00000420682.2_Frame_Shift_Del_p.L20fs|MAPT_ENST00000340799.5_Frame_Shift_Del_p.L20fs|MAPT_ENST00000574436.1_Frame_Shift_Del_p.L20fs|MAPT_ENST00000415613.2_Frame_Shift_Del_p.L20fs|MAPT_ENST00000344290.5_Frame_Shift_Del_p.L20fs|MAPT_ENST00000570299.1_3'UTR			P10636	TAU_HUMAN	microtubule-associated protein tau	20					adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	CGTACGGGTTGGGGGACAGGA	0.577																																					p.L20fs		Atlas-INDEL	.											.	MAPT	135	.	0			c.59delT						.						54	43	47					17																	44039763		2203	4300	6503	SO:0001589	frameshift_variant	4137	exon2			.	J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"G protein beta1/gamma2 subunit-interacting factor 1", "microtubule-associated protein tau, isoform 4", "protein phosphatase 1, regulatory subunit 103"	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.60delG	chr17.hg19:g.44039763delG	ENSP00000458742:p.Leu20fs	151.0	0.0		151.0	10.0	NM_005910	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Frame_Shift_Del	DEL	ENST00000571987.1	hg19	CCDS11501.1																																																																																			.	.		0.577	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835		-	44039763	G	-	44039763	7	5	282	1	0	1	0	1	0	0	0	0	9306	1339	47	0	62	0	MAPT	17	44039763	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1954765	44039763	37155447	1153	41387										
STH	246744	hgsc.bcm.edu	37	chr17	44076686	44076686	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agtctcatgcatttttgcagCccccacaagactgtgcaggt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:44076686delC	ENST00000537309.1	+	1	71	c.41delC	c.(40-42)gccfs	p.A14fs	MAPT_ENST00000446361.3_Intron|MAPT_ENST00000576518.1_Intron|MAPT_ENST00000262410.5_Intron|MAPT_ENST00000347967.5_Intron|MAPT_ENST00000351559.5_Intron|MAPT_ENST00000535772.1_Intron|MAPT_ENST00000431008.3_Intron|MAPT_ENST00000571987.1_Intron|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000334239.8_Intron|MAPT_ENST00000574436.1_Intron|MAPT_ENST00000415613.2_Intron|MAPT_ENST00000344290.5_Intron|MAPT_ENST00000570299.1_Intron	NM_001007532.2	NP_001007533.1	Q8IWL8	STH_HUMAN	saitohin	14						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	7						atttttgcagcccccacaaga	0.537																																					p.A14fs		Atlas-INDEL	.											.	STH	14	.	0			c.40delG						.						55	54	54					17																	44076686		1962	4160	6122	SO:0001589	frameshift_variant	246744	exon1			.	AA325304	CCDS54136.1	17q21.1	2008-01-22				ENSG00000256762			18839	protein-coding gene	gene with protein product	"microtubule-associated protein tau (MAPT) intronic transcript"	607067				12032355, 16186110	Standard	NM_001007532		Approved	MAPTIT	uc002ijy.2	Q8IWL8		ENST00000537309.1:c.41delC	chr17.hg19:g.44076686delC	ENSP00000443168:p.Ala14fs	288.0	0.0		205.0	13.0	NM_001007532	A1L3X7	Frame_Shift_Del	DEL	ENST00000537309.1	hg19	CCDS54136.1																																																																																			.	.		0.537	STH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400444.1			-	44076686	C	-	44076686	7	5	282	1	0	1	0	1	0	0	0	0	15296	739	26	0	43	0	STH	17	44076686	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	36923	44076686	37118524	1154	41388										
CDC27	996	hgsc.bcm.edu	37	chr17	45209674	45209674	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgagggttgatatcaagcgcTttttggaaatgcatttctgc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:45209674delT	ENST00000066544.3	-	15	2073	c.1980delA	c.(1978-1980)aaafs	p.K660fs	CDC27_ENST00000446365.2_Frame_Shift_Del_p.K599fs|CDC27_ENST00000527547.1_Frame_Shift_Del_p.K659fs|CDC27_ENST00000531206.1_Frame_Shift_Del_p.K666fs	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	660					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TATCAAGCGCTTTTTGGAAAT	0.299																																					p.A667fs		Atlas-INDEL	.											.	CDC27	337	.	0			c.1999delG						.						84	85	84					17																	45209674		2203	4300	6503	SO:0001589	frameshift_variant	996	exon15			.	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1728	protein-coding gene	gene with protein product	"anaphase promoting complex subunit 3"	116946	"cell division cycle 27", "cell division cycle 27 homolog (S. cerevisiae)"	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.1980delA	chr17.hg19:g.45209674delT	ENSP00000066544:p.Lys660fs	118.0	0.0		115.0	10.0	NM_001114091	G3V1C4|Q16349|Q96F35	Frame_Shift_Del	DEL	ENST00000066544.3	hg19	CCDS11509.1																																																																																			.	.		0.299	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2			-	45209674	T	-	45209674	7	5	282	1	0	1	0	1	0	0	0	0	3068	1606	56	0	514	0	CDC27	17	45209674	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1132988	45209674	35985536	1155	41389										
TTLL6	284076	hgsc.bcm.edu	37	chr17	46846369	46846369	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acctagctcctctcacatccTttttggccagagatcaggca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:46846369delT	ENST00000393382.3	-	15	2799	c.2658delA	c.(2656-2658)aaafs	p.K886fs	TTLL6_ENST00000433608.2_Frame_Shift_Del_p.K579fs	NM_001130918.1	NP_001124390.1			tubulin tyrosine ligase-like family, member 6											endometrium(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)	18						TCTCACATCCTTTTTGGCCAG	0.493																																					p.G887fs		Atlas-INDEL	.											.	TTLL6	113	.	0			c.2659delG						.						175	146	156					17																	46846369		2203	4300	6503	SO:0001589	frameshift_variant	284076	exon15			.	AK093127	CCDS11537.2, CCDS45724.1	17q21.32	2013-02-14			ENSG00000170703	ENSG00000170703		"Tubulin tyrosine ligase-like family"	26664	protein-coding gene	gene with protein product		610849				15890843	Standard	NM_173623		Approved	FLJ35808	uc021tzm.1	Q8N841	OTTHUMG00000156978	ENST00000393382.3:c.2658delA	chr17.hg19:g.46846369delT	ENSP00000377043:p.Lys886fs	246.0	0.0		204.0	13.0	NM_001130918		Frame_Shift_Del	DEL	ENST00000393382.3	hg19	CCDS45724.1																																																																																			.	.		0.493	TTLL6-003	KNOWN	downstream_ATG|non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346939.3	NM_173623		-	46846369	T	-	46846369	7	5	282	1	0	1	0	1	0	0	0	0	16746	1606	56	0	21	0	TTLL6	17	46846369	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1636695	46846369	34348841	1156	41390										
SGCA	6442	hgsc.bcm.edu	37	chr17	48245832	48245832	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agccgcttcctctcagccttGgggggactctgggagcccgg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:48245832delG	ENST00000262018.3	+	5	519	c.483delG	c.(481-483)ttgfs	p.L161fs	SGCA_ENST00000451235.2_Frame_Shift_Del_p.L59fs|SGCA_ENST00000543315.1_Frame_Shift_Del_p.L161fs|HILS1_ENST00000504307.1_RNA|SGCA_ENST00000513942.1_3'UTR|SGCA_ENST00000344627.6_Frame_Shift_Del_p.L161fs	NM_000023.2	NP_000014.1	Q16586	SGCA_HUMAN	sarcoglycan, alpha (50kDa dystrophin-associated glycoprotein)	161					muscle contraction (GO:0006936)|muscle organ development (GO:0007517)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(7)|ovary(2)|skin(1)	14						TCTCAGCCTTGGGGGGACTCT	0.657																																					p.L161fs		Atlas-INDEL	.											.	SGCA	35	.	0			c.482delT						.						18	19	19					17																	48245832		2200	4297	6497	SO:0001589	frameshift_variant	6442	exon5			.	L34355	CCDS32679.1, CCDS45729.1	17q21	2014-09-17	2002-08-29		ENSG00000108823	ENSG00000108823			10805	protein-coding gene	gene with protein product	"50kD DAG", "Sarcoglycan, alpha (50kD dystrophin-associated glycoprotein; adhalin)", "adhalin (limb girdle muscular dystrophy 2D)"	600119	"sarcoglycan, alpha (50kD dystrophin-associated glycoprotein)"	ADL		7937874	Standard	NM_000023		Approved	SCARMD1, LGMD2D, adhalin, DMDA2, A2	uc002iqi.3	Q16586	OTTHUMG00000162024	ENST00000262018.3:c.483delG	chr17.hg19:g.48245832delG	ENSP00000262018:p.Leu161fs	232.0	0.0		163.0	12.0	NM_001135697	A6NEB8|A8K3K7|Q13710|Q13712	Frame_Shift_Del	DEL	ENST00000262018.3	hg19	CCDS32679.1																																																																																			.	.		0.657	SGCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366841.1	NM_000023		-	48245832	G	-	48245832	7	5	282	1	0	1	0	1	0	0	0	0	14214	1339	47	0	501	0	SGCA	17	48245832	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1399463	48245832	32949378	1157	41391										
EME1	146956	hgsc.bcm.edu	37	chr17	48452975	48452975	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaggtgcatcatgtgactggAaaaagccctttccaaagatc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:48452975delA	ENST00000338165.4	+	2	488	c.406delA	c.(406-408)aaafs	p.K137fs	MRPL27_ENST00000225969.4_5'Flank|MRPL27_ENST00000503633.1_5'Flank|MRPL27_ENST00000507088.1_5'Flank|EME1_ENST00000393271.2_Frame_Shift_Del_p.K137fs|MRPL27_ENST00000442592.3_5'Flank|EME1_ENST00000511648.2_Frame_Shift_Del_p.K137fs	NM_152463.2	NP_689676.2	Q96AY2	EME1_HUMAN	essential meiotic structure-specific endonuclease 1	137					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cytoplasm (GO:0005737)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(4)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	19	Breast(11;5.62e-19)		BRCA - Breast invasive adenocarcinoma(22;2.43e-08)			ATGTGACTGGAAAAAGCCCTT	0.463								Direct reversal of damage;Homologous recombination																													p.W135X		Atlas-INDEL	.											.	EME1	39	.	0			c.405delG						.						77	81	79					17																	48452975		2203	4300	6503	SO:0001589	frameshift_variant	146956	exon2			.	BC016470	CCDS11565.1, CCDS54141.1	17q21.33	2013-07-03	2013-07-03			ENSG00000154920			24965	protein-coding gene	gene with protein product	"SLX2 structure-specific endonuclease subunit homolog A (S. cerevisiae)"	610885	"essential meiotic endonuclease 1 homolog 1 (S. pombe)"			12721304	Standard	NM_001166131		Approved	FLJ31364, MMS4L, SLX2A	uc010dbp.2	Q96AY2		ENST00000338165.4:c.406delA	chr17.hg19:g.48452975delA	ENSP00000339897:p.Lys137fs	257.0	0.0		173.0	11.0	NM_152463	Q96N62	Frame_Shift_Del	DEL	ENST00000338165.4	hg19	CCDS11565.1																																																																																			.	.		0.463	EME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367118.3	NM_152463		-	48452975	A	-	48452975	7	5	282	1	0	1	0	1	0	0	0	0	5090	247	9	0	408	0	EME1	17	48452975	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	207143	48452975	32742235	1158	41392										
LUC7L3	51747	hgsc.bcm.edu	37	chr17	48814327	48814327	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tttttctttactaggtttgtAaatattatctctgtggtttt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:48814327delA	ENST00000505658.1	+	2	295	c.106delA	c.(106-108)aaafs	p.K36fs	LUC7L3_ENST00000240304.1_Frame_Shift_Del_p.K36fs|LUC7L3_ENST00000393227.2_Frame_Shift_Del_p.K36fs|LUC7L3_ENST00000544170.1_Intron|LUC7L3_ENST00000311571.3_Frame_Shift_Del_p.K36fs			O95232	LC7L3_HUMAN	LUC7-like 3 (S. cerevisiae)	36					mRNA splice site selection (GO:0006376)|RNA splicing (GO:0008380)	focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|U1 snRNP (GO:0005685)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)	12						CTAGGTTTGTAAATATTATCT	0.299																																					p.C35X		Atlas-INDEL	.											.	LUC7L3	32	.	0			c.105delT						.						108	102	104					17																	48814327		2203	4297	6500	SO:0001589	frameshift_variant	51747	exon2			.		CCDS11573.1	17q21.33	2010-02-17			ENSG00000108848	ENSG00000108848			24309	protein-coding gene	gene with protein product	"cisplatin resistance associated overexpressed protein", "CRE-associated protein"	609434				10631324, 12565863	Standard	NM_016424		Approved	LUC7A, CROP, OA48-18, CREAP-1, FLJ11063, CRA, hLuc7A	uc002iss.3	O95232	OTTHUMG00000162257	ENST00000505658.1:c.106delA	chr17.hg19:g.48814327delA	ENSP00000425092:p.Lys36fs	209.0	0.0		165.0	11.0	NM_006107	B3KN54|D3DTY1|Q6PHR9|Q9NUY0|Q9P2S7	Frame_Shift_Del	DEL	ENST00000505658.1	hg19	CCDS11573.1																																																																																			.	.		0.299	LUC7L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368205.2	NM_016424		-	48814327	A	-	48814327	7	5	282	1	0	1	0	1	0	0	0	0	9093	363	13	0	112	0	LUC7L3	17	48814327	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	361352	48814327	32380883	1159	41393										
SPAG9	9043	hgsc.bcm.edu	37	chr17	49071274	49071274	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gactggataattcttcttgaTtttttaactccttctgctgt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:49071274delT	ENST00000262013.7	-	19	2457	c.2249delA	c.(2248-2250)aatfs	p.N750fs	SPAG9_ENST00000510283.1_Frame_Shift_Del_p.N593fs|SPAG9_ENST00000505279.1_Frame_Shift_Del_p.N740fs|SPAG9_ENST00000357122.4_Frame_Shift_Del_p.N736fs	NM_001130528.2	NP_001124000.1	O60271	JIP4_HUMAN	sperm associated antigen 9	750					activation of JUN kinase activity (GO:0007257)|muscle cell differentiation (GO:0042692)|negative regulation of protein homodimerization activity (GO:0090074)|positive regulation of cell migration (GO:0030335)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron differentiation (GO:0045666)|protein homooligomerization (GO:0051260)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|striated muscle cell differentiation (GO:0051146)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)				NS(1)|breast(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			TTCTTCTTGATTTTTTAACTC	0.358																																					p.N750fs		Atlas-Indel,Pindel	.											.	SPAG9	151	.	0			c.2250delT						.						100	91	94					17																	49071274		2203	4300	6503	SO:0001589	frameshift_variant	9043	exon19			.	AB011088	CCDS11577.1, CCDS45740.1, CCDS58577.1, CCDS58578.1	17q21.33	2013-09-23			ENSG00000008294	ENSG00000008294			14524	protein-coding gene	gene with protein product	"sperm surface protein", "JNK/SAPK-associated protein", "JNK interacting protein", "sperm specific protein", "c-Jun NH2-terminal kinase-associated leucine zipper protein", "Max-binding protein", "JNK-associated leucine-zipper protein", "HLC-4 protein", "lung cancer oncogene 4", "proliferation-inducing gene 6", "cancer/testis antigen 89"	605430				9480848, 11106729	Standard	NM_003971		Approved	HSS, SYD1, KIAA0516, MGC14967, MGC74461, MGC117291, JLP, PHET, HLC4, PIG6, FLJ13450, FLJ14006, FLJ26141, FLJ34602, CT89	uc002itc.3	O60271	OTTHUMG00000162316	ENST00000262013.7:c.2249delA	chr17.hg19:g.49071274delT	ENSP00000262013:p.Asn750fs	313.0	0.0		192.0	15.0	NM_001130528	A6H8U5|A8MSX0|B4DHH2|O60905|Q3KQU8|Q3MKM7|Q86WC7|Q86WC8|Q8IZX7|Q96II0|Q9H811	Frame_Shift_Del	DEL	ENST00000262013.7	hg19	CCDS45740.1																																																																																			.	.		0.358	SPAG9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368543.2	NM_003971		-	49071274	T	-	49071274	7	5	282	1	0	1	0	1	0	0	0	0	15000	1493	52	0	1764	0	SPAG9	17	49071274	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	256947	49071274	32123936	1160	41394										
TOM1L1	10040	hgsc.bcm.edu	37	chr17	53027460	53027460	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctacgaggtaatggagtttgAtcccttagctcctgctgtca	10	10	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:53027460A>G	ENST00000575882.1	+	14	1696	c.1343A>G	c.(1342-1344)gAt>gGt	p.D448G	TOM1L1_ENST00000540336.1_Missense_Mutation_p.D336G|TOM1L1_ENST00000536554.1_Missense_Mutation_p.D371G|TOM1L1_ENST00000572158.1_Missense_Mutation_p.D441G|TOM1L1_ENST00000348161.4_Missense_Mutation_p.D371G|COX11_ENST00000573912.1_5'Flank|TOM1L1_ENST00000445275.2_Missense_Mutation_p.D437G	NM_005486.2	NP_005477.2	O75674	TM1L1_HUMAN	target of myb1 (chicken)-like 1	448					activation of protein kinase activity (GO:0032147)|intracellular protein transport (GO:0006886)|negative regulation of mitosis (GO:0045839)|positive regulation of protein autophosphorylation (GO:0031954)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)	clathrin binding (GO:0030276)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|ubiquitin binding (GO:0043130)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	15						ATGGAGTTTGATCCCTTAGCT	0.393																																					p.D448G		Atlas-SNP	.											.	TOM1L1	33	.	0			c.A1343G						.						103	98	100					17																	53027460		2203	4300	6503	SO:0001583	missense	10040	exon14			AGTTTGATCCCTT	AJ010071	CCDS11582.1	17q23.2	2008-01-03	2007-01-12			ENSG00000141198			11983	protein-coding gene	gene with protein product		604701	"target of myb1 (chicken) homolog-like 1"			10329004, 15611048, 17977829	Standard	NM_005486		Approved	SRCASM	uc002iud.2	O75674		ENST00000575882.1:c.1343A>G	chr17.hg19:g.53027460A>G	ENSP00000460823:p.Asp448Gly	147.0	0.0		99.0	4.0	NM_005486	Q53G06|Q8N749	Missense_Mutation	SNP	ENST00000575882.1	hg19	CCDS11582.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.160106	0.78226	.	.	ENSG00000141198	ENST00000445275;ENST00000540336;ENST00000348161;ENST00000536554	T;T;T	0.34275	1.37;1.52;1.52	5.51	5.51	0.81932	.	0.000000	0.64402	D	0.000001	T	0.57110	0.2031	M	0.66939	2.045	0.51767	D	0.999936	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.998;0.998;0.998	T	0.57300	-0.7835	10	0.48119	T	0.1	-25.0899	13.1152	0.59295	1.0:0.0:0.0:0.0	.	336;441;371;448	B4DUW5;B4E1N0;B7Z9E2;O75674	.;.;.;TM1L1_HUMAN	G	448;336;371;371	ENSP00000441242:D336G;ENSP00000343901:D371G;ENSP00000443099:D371G	ENSP00000343901:D371G	D	+	2	0	TOM1L1	50382459	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.280000	0.58959	2.317000	0.78254	0.459000	0.35465	GAT	.	.		0.393	TOM1L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439029.2	NM_005486		G	53027460	A	G	53027460	3	3	282	1	0	0	0	0	1	0	0	0	16367	333	12	2	1397	2	TOM1L1	17	53027460	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	3956186	53027460	28167750	1161	41395										
EPX	8288	hgsc.bcm.edu	37	chr17	56274371	56274371	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttccgctcggcaccctcatgCccccaaaacaagaacagagt					rs186927462		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:56274371delC	ENST00000225371.5	+	7	983	c.873delC	c.(871-873)tgcfs	p.C291fs		NM_000502.4	NP_000493.1	P11678	PERE_HUMAN	eosinophil peroxidase	291					defense response to nematode (GO:0002215)|eosinophil migration (GO:0072677)|hydrogen peroxide catabolic process (GO:0042744)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-5 production (GO:0032714)|positive regulation of interleukin-4 production (GO:0032753)	extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(2)|endometrium(9)|kidney(1)|large_intestine(9)|liver(2)|lung(20)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	48					Melatonin(DB01065)	CACCCTCATGCCCCCAAAACA	0.582																																					p.C291fs		Atlas-INDEL	.											.	EPX	95	.	0			c.872delG						.						177	160	166					17																	56274371		2203	4300	6503	SO:0001589	frameshift_variant	8288	exon7			.	M26515	CCDS11602.1	17q23.1	2006-09-25				ENSG00000121053	1.11.1.7		3423	protein-coding gene	gene with protein product		131399				2550461, 2541222	Standard	NM_000502		Approved	EPO, EPP, EPX-PEN	uc002ivq.3	P11678		ENST00000225371.5:c.873delC	chr17.hg19:g.56274371delC	ENSP00000225371:p.Cys291fs	177.0	0.0		189.0	12.0	NM_000502	Q4TVP3	Frame_Shift_Del	DEL	ENST00000225371.5	hg19	CCDS11602.1																																																																																			.	.		0.582	EPX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443367.1	NM_000502		-	56274371	C	-	56274371	7	5	282	1	0	1	0	1	0	0	0	0	5202	747	26	0	899	0	EPX	17	56274371	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	3246911	56274371	24920839	1162	41396										
SCN4A	6329	hgsc.bcm.edu	37	chr17	62026109	62026109	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atgtccacgtagaggcagggCcagcgctgcacgcaggctga	15	12	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:62026109C>T	ENST00000435607.1	-	16	3082	c.3006G>A	c.(3004-3006)tgG>tgA	p.W1002*	SCN4A_ENST00000578147.1_Nonsense_Mutation_p.W1002*	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	1002					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AGAGGCAGGGCCAGCGCTGCA	0.642																																					p.W1002X		Atlas-SNP	.											.	SCN4A	205	.	0			c.G3006A						.						32	35	34					17																	62026109		2177	4275	6452	SO:0001587	stop_gained	6329	exon16			GCAGGGCCAGCGC	U24693		17q23.3	2012-02-26	2007-01-23					"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.3006G>A	chr17.hg19:g.62026109C>T	ENSP00000396320:p.Trp1002*	80.0	0.0		90.0	4.0	NM_000334	Q15478|Q16447|Q7Z6B1	Nonsense_Mutation	SNP	ENST00000435607.1	hg19	CCDS45761.1	.	.	.	.	.	.	.	.	.	.	C	38	6.848558	0.97885	.	.	ENSG00000007314	ENST00000435607	.	.	.	4.16	-4.15	0.03881	.	0.621771	0.18186	N	0.148995	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	.	6.7542	0.23503	0.5586:0.2624:0.1791:0.0	.	.	.	.	X	1002	.	ENSP00000396320:W1002X	W	-	3	0	SCN4A	59379841	0.110000	0.22057	0.357000	0.25798	0.788000	0.44548	0.120000	0.15647	-0.871000	0.04042	0.313000	0.20887	TGG	.	.		0.642	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334		T	62026109	C	T	62026109	4	4	282	1	0	0	0	0	0	1	0	0	13935	740	26	3	2540	3	SCN4A	17	62026109	Nonsense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	5751738	62026109	19169101	1163	41397										
APOH	350	hgsc.bcm.edu	37	chr17	64212962	64212962	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tggtacattctatttcttccGggccatccagagaatatcca					rs142113711		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:64212962delG	ENST00000205948.6	-	6	765	c.728delC	c.(727-729)ccgfs	p.P243fs		NM_000042.2	NP_000033.2	P02749	APOH_HUMAN	apolipoprotein H (beta-2-glycoprotein I)	243	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation, intrinsic pathway (GO:0007597)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood coagulation (GO:0030195)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of myeloid cell apoptotic process (GO:0033033)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|plasminogen activation (GO:0031639)|positive regulation of blood coagulation (GO:0030194)|positive regulation of lipoprotein lipase activity (GO:0051006)|regulation of fibrinolysis (GO:0051917)|triglyceride metabolic process (GO:0006641)|triglyceride transport (GO:0034197)	cell surface (GO:0009986)|chylomicron (GO:0042627)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipid binding (GO:0005543)			central_nervous_system(1)|kidney(3)|large_intestine(5)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(6;9.74e-08)			TATTTCTTCCGGGCCATCCAG	0.418																																					p.P243fs	Melanoma(155;624 1882 16869 48804 51309)	Atlas-INDEL	.											.	APOH	45	.	0			c.729delG						.						156	152	153					17																	64212962		2203	4300	6503	SO:0001589	frameshift_variant	350	exon6			.		CCDS11663.1	17q24.2	2013-01-24				ENSG00000091583		"Apolipoproteins"	616	protein-coding gene	gene with protein product	"beta-2-glycoprotein I"	138700		B2G1		1582254	Standard	NM_000042		Approved	BG	uc002jfn.4	P02749		ENST00000205948.6:c.728delC	chr17.hg19:g.64212962delG	ENSP00000205948:p.Pro243fs	196.0	0.0		199.0	12.0	NM_000042	B2R9M3|Q9UCN7	Frame_Shift_Del	DEL	ENST00000205948.6	hg19	CCDS11663.1																																																																																			.	.		0.418	APOH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446926.1	NM_000042		-	64212962	G	-	64212962	7	5	282	1	0	1	0	1	0	0	0	0	804	1116	39	0	321	0	APOH	17	64212962	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	2186853	64212962	16982248	1164	41398										
PSMD12	5718	hgsc.bcm.edu	37	chr17	65346351	65346351	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aacagaaaatttaccttgccTtcggtaaccattcgtagagt	7	9	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:65346351T>C	ENST00000356126.3	-	4	506	c.399A>G	c.(397-399)gaA>gaG	p.E133E	PSMD12_ENST00000357146.4_Silent_p.E113E|PSMD12_ENST00000581618.1_5'Flank	NM_002816.3	NP_002807.1	O00232	PSD12_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 12	133					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				breast(1)|large_intestine(4)|lung(6)|pancreas(1)|urinary_tract(1)	13	all_cancers(12;2.38e-11)|all_epithelial(3;8.27e-13)					TTACCTTGCCTTCGGTAACCA	0.318																																					p.E133E		Atlas-SNP	.											.	PSMD12	32	.	0			c.A399G						.						76	70	72					17																	65346351		2203	4300	6503	SO:0001819	synonymous_variant	5718	exon4			CTTGCCTTCGGTA	AB003103	CCDS11669.1, CCDS11670.1	17q24.3	2008-05-22			ENSG00000197170	ENSG00000197170		"Proteasome (prosome, macropain) subunits"	9557	protein-coding gene	gene with protein product		604450				9426256	Standard	NM_002816		Approved	p55, Rpn5	uc002jfy.3	O00232	OTTHUMG00000140376	ENST00000356126.3:c.399A>G	chr17.hg19:g.65346351T>C		137.0	0.0		154.0	47.0	NM_002816	A6NP15|Q53HA2|Q6P053	Silent	SNP	ENST00000356126.3	hg19	CCDS11669.1																																																																																			.	.		0.318	PSMD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277103.1	NM_002816, NM_174871		C	65346351	T	C	65346351	2	2	282	1	0	0	0	0	0	0	0	1	12707	1606	56	2		2	PSMD12	17	65346351	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1133389	65346351	15848859	1165	41399										
ARSG	22901	hgsc.bcm.edu	37	chr17	66391287	66391287	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaggacggcgctttgatggtGtggacgtctccgaggtgctc	16	9	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:66391287G>T	ENST00000448504.2	+	10	1961	c.1165G>T	c.(1165-1167)Gtg>Ttg	p.V389L	ARSG_ENST00000582154.1_3'UTR|ARSG_ENST00000452479.2_Missense_Mutation_p.V225L	NM_014960.4	NP_055775.2	Q96EG1	ARSG_HUMAN	arylsulfatase G	389					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sulfur compound metabolic process (GO:0006790)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular space (GO:0005615)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			NS(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	26			BRCA - Breast invasive adenocarcinoma(8;5.34e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)			CTTTGATGGTGTGGACGTCTC	0.572																																					p.V389L		Atlas-SNP	.											.	ARSG	55	.	0			c.G1165T						.						161	125	137					17																	66391287		2203	4300	6503	SO:0001583	missense	22901	exon10			GATGGTGTGGACG	AB023218	CCDS11676.1	17q24.2	2013-07-15	2006-02-15		ENSG00000141337	ENSG00000141337		"Arylsulfatase family"	24102	protein-coding gene	gene with protein product		610008				12461688, 16174644	Standard	NM_014960		Approved	KIAA1001	uc002jhc.2	Q96EG1	OTTHUMG00000179810	ENST00000448504.2:c.1165G>T	chr17.hg19:g.66391287G>T	ENSP00000407193:p.Val389Leu	289.0	0.0		281.0	24.0	NM_001267727	Q6UXF2|Q9Y2K4	Missense_Mutation	SNP	ENST00000448504.2	hg19	CCDS11676.1	.	.	.	.	.	.	.	.	.	.	G	7.084	0.570898	0.13623	.	.	ENSG00000141337	ENST00000452479;ENST00000448504	.	.	.	5.25	-0.499	0.12015	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.892392	0.09618	N	0.777970	T	0.14485	0.0350	N	0.05280	-0.08	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.31833	-0.9929	9	0.14656	T	0.56	.	5.2398	0.15465	0.0:0.3568:0.3588:0.2844	.	389	Q96EG1	ARSG_HUMAN	L	389;288	.	ENSP00000407193:V288L	V	+	1	0	ARSG	63902882	0.003000	0.15002	0.033000	0.17914	0.907000	0.53573	-0.117000	0.10708	-0.169000	0.10834	0.555000	0.69702	GTG	.	.		0.572	ARSG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448369.1	NM_014960		T	66391287	G	T	66391287	3	4	282	1	0	0	0	0	1	0	0	0	992	1377	48	3	1199	3	ARSG	17	66391287	Missense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1044936	66391287	14803923	1166	41400										
ABCA5	23461	hgsc.bcm.edu	37	chr17	67285378	67285378	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cttttttgaccaccacttaaTtttttagcttggttatcttt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:67285378delT	ENST00000392676.3	-	14	1906	c.1842delA	c.(1840-1842)aaafs	p.K614fs	ABCA5_ENST00000588877.1_Frame_Shift_Del_p.K614fs|ABCA5_ENST00000392677.2_Frame_Shift_Del_p.K614fs			Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 5	614	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cholesterol efflux (GO:0033344)|high-density lipoprotein particle remodeling (GO:0034375)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|reverse cholesterol transport (GO:0043691)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(18)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	54	Breast(10;3.72e-11)				Tacrolimus(DB00864)	CACCACTTAATTTTTTAGCTT	0.303																																					p.L615X		Atlas-INDEL	.											ABCA5,NS,carcinoma,0,1	ABCA5	162	.	0			c.1843delT						.						93	91	92					17																	67285378		2203	4297	6500	SO:0001589	frameshift_variant	23461	exon13			.	U66672	CCDS11685.1	17q24.3	2012-03-14			ENSG00000154265	ENSG00000154265		"ATP binding cassette transporters / subfamily A"	35	protein-coding gene	gene with protein product		612503				8894702	Standard	NM_172232		Approved	EST90625	uc002jig.2	Q8WWZ7		ENST00000392676.3:c.1842delA	chr17.hg19:g.67285378delT	ENSP00000376443:p.Lys614fs	217.0	0.0		199.0	12.0	NM_018672	Q8IVJ2|Q96LJ1|Q96MS4|Q96PZ9|Q9NY14	Frame_Shift_Del	DEL	ENST00000392676.3	hg19	CCDS11685.1																																																																																			.	.		0.303	ABCA5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450654.1	NM_018672		-	67285378	T	-	67285378	7	5	282	1	0	1	0	1	0	0	0	0	35	1490	52	0	3190	0	ABCA5	17	67285378	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	894091	67285378	13909832	1167	41401										
GRIN2C	2905	hgsc.bcm.edu	37	chr17	72838789	72838789	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tggaaggtgaggacagacagCcccccagcaaaatggcaggt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:72838789delC	ENST00000293190.5	-	13	3633	c.3487delG	c.(3487-3489)gctfs	p.A1163fs		NM_000835.3	NP_000826.2	Q14957	NMDE3_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2C	1163					directional locomotion (GO:0033058)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of protein catabolic process (GO:0042177)|neuromuscular process controlling balance (GO:0050885)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|response to wounding (GO:0009611)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	33	all_lung(278;0.172)|Lung NSC(278;0.207)				Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GGACAGACAGCCCCCCAGCAA	0.726																																					p.A1163fs		Atlas-INDEL	.											.	GRIN2C	144	.	0			c.3488delC						.						10	15	13					17																	72838789		2152	4233	6385	SO:0001589	frameshift_variant	2905	exon13			.		CCDS32724.1, CCDS62330.1	17q25.1	2012-08-29			ENSG00000161509	ENSG00000161509		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4587	protein-coding gene	gene with protein product		138254		NMDAR2C		9480759	Standard	NM_001278553		Approved	GluN2C	uc002jlt.1	Q14957	OTTHUMG00000044524	ENST00000293190.5:c.3487delG	chr17.hg19:g.72838789delC	ENSP00000293190:p.Ala1163fs	160.0	0.0		165.0	10.0	NM_000835	B2RTT1	Frame_Shift_Del	DEL	ENST00000293190.5	hg19	CCDS32724.1																																																																																			.	.		0.726	GRIN2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103824.1			-	72838789	C	-	72838789	7	5	282	1	0	1	0	1	0	0	0	0	6790	739	26	0	218	0	GRIN2C	17	72838789	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	5553411	72838789	8356421	1168	41402										
LLGL2	3993	hgsc.bcm.edu	37	chr17	73560534	73560534	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gccagcagacggccttcgacTtcacctcccgtgtcatcggc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:73560534delT	ENST00000392550.3	+	10	1099	c.982delT	c.(982-984)ttcfs	p.F328fs	LLGL2_ENST00000167462.5_Frame_Shift_Del_p.F328fs|LLGL2_ENST00000375227.4_Frame_Shift_Del_p.F328fs|LLGL2_ENST00000578363.1_Frame_Shift_Del_p.F328fs|LLGL2_ENST00000577200.1_Frame_Shift_Del_p.F328fs	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	328					cell cycle (GO:0007049)|cell division (GO:0051301)|exocytosis (GO:0006887)|regulation of establishment or maintenance of cell polarity (GO:0032878)	cytoplasm (GO:0005737)	PDZ domain binding (GO:0030165)			NS(1)|breast(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)			GGCCTTCGACTTCACCTCCCG	0.632																																					p.D327fs		Atlas-INDEL	.											.	LLGL2	155	.	0			c.981delC						.						66	62	63					17																	73560534		2203	4300	6503	SO:0001589	frameshift_variant	3993	exon10			.	X87342	CCDS11725.1, CCDS32733.1, CCDS45776.1	17q25.1	2013-01-10	2001-11-28			ENSG00000073350		"WD repeat domain containing"	6629	protein-coding gene	gene with protein product			"lethal giant larvae (Drosophila) homolog 2"				Standard	XR_243659		Approved	HGL	uc002joh.3	Q6P1M3		ENST00000392550.3:c.982delT	chr17.hg19:g.73560534delT	ENSP00000376333:p.Phe328fs	180.0	0.0		182.0	11.0	NM_001015002	Q14521|Q9BR62	Frame_Shift_Del	DEL	ENST00000392550.3	hg19	CCDS32733.1																																																																																			.	.		0.632	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524		-	73560534	T	-	73560534	7	5	282	1	0	1	0	1	0	0	0	0	8843	1609	56	0	1016	0	LLGL2	17	73560534	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	721745	73560534	7634676	1169	41403										
UNC13D	201294	hgsc.bcm.edu	37	chr17	73836368	73836368	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtctgggtaggtctcagtgcGgggttccagggggtaccact							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:73836368delG	ENST00000207549.4	-	10	1175	c.796delC	c.(796-798)cgcfs	p.R266fs	UNC13D_ENST00000412096.2_Frame_Shift_Del_p.R266fs|UNC13D_ENST00000587504.1_5'UTR	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	unc-13 homolog D (C. elegans)	266	Interaction with RAB27A.				defense response to virus (GO:0051607)|germinal center formation (GO:0002467)|granuloma formation (GO:0002432)|natural killer cell degranulation (GO:0043320)|phagocytosis (GO:0006909)|positive regulation of exocytosis (GO:0045921)|regulation of mast cell degranulation (GO:0043304)	endosome (GO:0005768)|exocytic vesicle (GO:0070382)|lysosome (GO:0005764)|membrane (GO:0016020)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)			GTCTCAGTGCGGGGTTCCAGG	0.652									Familial Hemophagocytic Lymphohistiocytosis																												p.R266fs		Atlas-INDEL	.											.	UNC13D	68	.	0			c.797delG						.						51	47	48					17																	73836368		2203	4300	6503	SO:0001589	frameshift_variant	201294	exon10	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	.	AK024474	CCDS11730.1	17q25.3	2014-09-17				ENSG00000092929			23147	protein-coding gene	gene with protein product		608897					Standard	NM_199242		Approved	Munc13-4	uc002jpp.3	Q70J99		ENST00000207549.4:c.796delC	chr17.hg19:g.73836368delG	ENSP00000207549:p.Arg266fs	196.0	0.0		155.0	10.0	NM_199242	B4DWG9|Q9H7K5	Frame_Shift_Del	DEL	ENST00000207549.4	hg19	CCDS11730.1																																																																																			.	.		0.652	UNC13D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448847.2	XM_113950		-	73836368	G	-	73836368	7	5	282	1	0	1	0	1	0	0	0	0	17002	1116	39	0	2568	0	UNC13D	17	73836368	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	275834	73836368	7358842	1170	41404										
TRIM65	201292	hgsc.bcm.edu	37	chr17	73887372	73887372	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cttcacctgctggtcctggcGcgacagatagaagtgacggt	13	11	1	3	rs144407004		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:73887372G>A	ENST00000269383.3	-	6	1107	c.1042C>T	c.(1042-1044)Cgc>Tgc	p.R348C		NM_001256124.1|NM_173547.3	NP_001243053.1|NP_775818.2	Q6PJ69	TRI65_HUMAN	tripartite motif containing 65	348	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|lung(5)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	12			Epithelial(20;7.53e-06)|all cancers(21;9.11e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00092)|LUSC - Lung squamous cell carcinoma(166;0.154)			TGGTCCTGGCGCGACAGATAG	0.612																																					p.R348C		Atlas-SNP	.											.	TRIM65	23	.	0			c.C1042T						.	G	CYS/ARG	1,4387		0,1,2193	25	28	27		1042	-0.2	0	17	dbSNP_134	27	1,8535		0,1,4267	no	missense	TRIM65	NM_173547.2	180	0,2,6460	AA,AG,GG		0.0117,0.0228,0.0155	benign	348/518	73887372	2,12922	2194	4268	6462	SO:0001583	missense	201292	exon6			CCTGGCGCGACAG	BC006138	CCDS11732.1	17q25.1	2013-01-09	2011-01-25		ENSG00000141569	ENSG00000141569		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	27316	protein-coding gene	gene with protein product			"tripartite motif-containing 65"			12477932	Standard	NM_173547		Approved		uc002jpx.4	Q6PJ69	OTTHUMG00000132127	ENST00000269383.3:c.1042C>T	chr17.hg19:g.73887372G>A	ENSP00000269383:p.Arg348Cys	131.0	0.0		115.0	35.0	NM_173547	Q4G0F0|Q6DKJ6|Q9BRP6	Missense_Mutation	SNP	ENST00000269383.3	hg19	CCDS11732.1	.	.	.	.	.	.	.	.	.	.	G	2.643	-0.283636	0.05642	2.28E-4	1.17E-4	ENSG00000141569	ENST00000269383	T	0.73789	-0.78	5.2	-0.155	0.13395	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);	1.244230	0.05581	N	0.572948	T	0.61578	0.2358	L	0.35723	1.085	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.49995	-0.8879	10	0.54805	T	0.06	.	2.7844	0.05370	0.3849:0.1102:0.3925:0.1124	.	348	Q6PJ69	TRI65_HUMAN	C	348	ENSP00000269383:R348C	ENSP00000269383:R348C	R	-	1	0	TRIM65	71398967	0.000000	0.05858	0.025000	0.17156	0.016000	0.09150	-0.389000	0.07342	0.241000	0.21283	-0.986000	0.02555	CGC	.	G|1.000;A|0.000		0.612	TRIM65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255170.2	NM_173547		A	73887372	G	A	73887372	3	1	282	1	0	0	0	0	1	0	0	0	16554	1087	38	1	515	1	TRIM65	17	73887372	Missense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	51004	73887372	7307838	1171	41405										
EVPL	2125	hgsc.bcm.edu	37	chr17	74004439	74004439	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tctggctgagcagcttcgacTcctcctgcagctgcagtgtc	11	14	1	1	rs372600391		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:74004439T>C	ENST00000301607.3	-	22	5100	c.4847A>G	c.(4846-4848)gAg>gGg	p.E1616G	EVPL_ENST00000586740.1_Missense_Mutation_p.E1638G|TEN1-CDK3_ENST00000567351.1_RNA	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	1616	Central fibrous rod domain.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						CAGCTTCGACTCCTCCTGCAG	0.697																																					p.E1616G		Atlas-SNP	.											.	EVPL	155	.	0			c.A4847G						.						12	12	12					17																	74004439		2195	4275	6470	SO:0001583	missense	2125	exon22			TTCGACTCCTCCT	U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.4847A>G	chr17.hg19:g.74004439T>C	ENSP00000301607:p.Glu1616Gly	88.0	0.0		89.0	4.0	NM_001988	A0AUV5	Missense_Mutation	SNP	ENST00000301607.3	hg19	CCDS11737.1	.	.	.	.	.	.	.	.	.	.	T	13.33	2.203599	0.38905	.	.	ENSG00000167880	ENST00000301607	T	0.69040	-0.37	5.05	3.97	0.46021	.	0.271401	0.36444	N	0.002591	T	0.63105	0.2483	M	0.62723	1.935	0.40318	D	0.978794	B;B	0.25351	0.124;0.061	B;B	0.23275	0.045;0.045	T	0.62937	-0.6748	10	0.72032	D	0.01	-42.4383	12.1255	0.53915	0.0:0.0:0.1437:0.8563	.	1638;1616	B7ZLH8;Q92817	.;EVPL_HUMAN	G	1616	ENSP00000301607:E1616G	ENSP00000301607:E1616G	E	-	2	0	EVPL	71516034	1.000000	0.71417	0.836000	0.33094	0.912000	0.54170	4.769000	0.62300	0.769000	0.33313	-0.375000	0.07067	GAG	.	.		0.697	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988		C	74004439	T	C	74004439	3	2	282	1	0	0	0	0	1	0	0	0	5294	1551	54	2	1258	2	EVPL	17	74004439	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	117067	74004439	7190771	1172	41406										
EVPL	2125	hgsc.bcm.edu	37	chr17	74018287	74018287	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caccagtaggtctcggtattGgctccggatggtggctgcat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:74018287delG	ENST00000301607.3	-	6	881	c.628delC	c.(628-630)caafs	p.Q210fs	EVPL_ENST00000586740.1_Frame_Shift_Del_p.Q210fs	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	210	Globular 1.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						TCTCGGTATTGGCTCCGGATG	0.687																																					p.Q210fs		Atlas-INDEL	.											.	EVPL	155	.	0			c.629delA						.						27	31	29					17																	74018287		2203	4299	6502	SO:0001589	frameshift_variant	2125	exon6			.	U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.628delC	chr17.hg19:g.74018287delG	ENSP00000301607:p.Gln210fs	130.0	0.0		164.0	10.0	NM_001988	A0AUV5	Frame_Shift_Del	DEL	ENST00000301607.3	hg19	CCDS11737.1																																																																																			.	.		0.687	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988		-	74018287	G	-	74018287	7	5	282	1	0	1	0	1	0	0	0	0	5294	1357	47	0	5541	0	EVPL	17	74018287	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	13848	74018287	7176923	1173	41407										
SPHK1	8877	hgsc.bcm.edu	37	chr17	74381231	74381231	+	Intron	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttacgcagctggactcccctCcccctggcagccccgagggg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:74381231delC	ENST00000545180.1	+	4	615				SPHK1_ENST00000592299.1_Intron|SPHK1_ENST00000323374.4_Frame_Shift_Del_p.L15fs|SPHK1_ENST00000590959.1_Intron|SPHK1_ENST00000392496.3_5'Flank			Q9NYA1	SPHK1_HUMAN	sphingosine kinase 1						'de novo' posttranslational protein folding (GO:0051084)|blood vessel development (GO:0001568)|brain development (GO:0007420)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|female pregnancy (GO:0007565)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|lipid phosphorylation (GO:0046834)|negative regulation of apoptotic process (GO:0043066)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neurotransmitter secretion (GO:0001956)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of smooth muscle contraction (GO:0045987)|protein folding (GO:0006457)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of interleukin-1 beta production (GO:0032651)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|response to amine (GO:0014075)|response to ATP (GO:0033198)|response to interleukin-1 (GO:0070555)|response to magnesium ion (GO:0032026)|response to progesterone (GO:0032570)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingoid catabolic process (GO:0046521)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|D-erythro-sphingosine kinase activity (GO:0017050)|diacylglycerol kinase activity (GO:0004143)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|NAD+ kinase activity (GO:0003951)|protein phosphatase 2A binding (GO:0051721)|sphinganine kinase activity (GO:0008481)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)	11					Fingolimod(DB08868)	GGACTCCCCTCCCCCTGGCAG	0.657																																					p.L15fs	GBM(90;966 1307 27369 33775 44498)	Atlas-INDEL	.											.	SPHK1	24	.	0			c.44delT						.						34	27	29					17																	74381231		2193	4292	6485	SO:0001627	intron_variant	8877	exon1			.	BC030553	CCDS11744.1, CCDS45785.1, CCDS59297.1	17q25.2	2004-02-18				ENSG00000176170			11240	protein-coding gene	gene with protein product		603730				9726979	Standard	NM_182965		Approved	SPHK	uc002jrj.2	Q9NYA1		ENST00000545180.1:c.-194-301C>-	chr17.hg19:g.74381231delC		212.0	0.0		222.0	14.0	NM_182965	Q8N632|Q96GK1|Q9HD92|Q9NY70|Q9NYL3	Frame_Shift_Del	DEL	ENST00000545180.1	hg19	CCDS45785.1																																																																																			.	.		0.657	SPHK1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450113.1	NM_182965, NM_021972		-	74381231	C	-	74381231	6	5	282	0	1	1	0	1	0	0	0	0	15061	842	30	0		0	SPHK1	17	74381231	Intron	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	362944	74381231	6813979	1174	41408										
SPHK1	8877	hgsc.bcm.edu	37	chr17	74383417	74383417	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcgtgccatgctgctgcgccTcttcctggccatggagaagg	13	13	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:74383417T>C	ENST00000545180.1	+	8	1714	c.905T>C	c.(904-906)cTc>cCc	p.L302P	SPHK1_ENST00000592299.1_Missense_Mutation_p.L302P|SPHK1_ENST00000323374.4_Missense_Mutation_p.L388P|SPHK1_ENST00000590959.1_Missense_Mutation_p.L316P|SPHK1_ENST00000392496.3_Missense_Mutation_p.L302P			Q9NYA1	SPHK1_HUMAN	sphingosine kinase 1	302				L -> F (in Ref. 2; AAF73423). {ECO:0000305}.	'de novo' posttranslational protein folding (GO:0051084)|blood vessel development (GO:0001568)|brain development (GO:0007420)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|female pregnancy (GO:0007565)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|lipid phosphorylation (GO:0046834)|negative regulation of apoptotic process (GO:0043066)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neurotransmitter secretion (GO:0001956)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of smooth muscle contraction (GO:0045987)|protein folding (GO:0006457)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of interleukin-1 beta production (GO:0032651)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|response to amine (GO:0014075)|response to ATP (GO:0033198)|response to interleukin-1 (GO:0070555)|response to magnesium ion (GO:0032026)|response to progesterone (GO:0032570)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingoid catabolic process (GO:0046521)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|D-erythro-sphingosine kinase activity (GO:0017050)|diacylglycerol kinase activity (GO:0004143)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|NAD+ kinase activity (GO:0003951)|protein phosphatase 2A binding (GO:0051721)|sphinganine kinase activity (GO:0008481)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)	11					Fingolimod(DB08868)	CTGCTGCGCCTCTTCCTGGCC	0.597																																					p.L388P	GBM(90;966 1307 27369 33775 44498)	Atlas-SNP	.											.	SPHK1	24	.	0			c.T1163C						.						83	68	73					17																	74383417		2203	4300	6503	SO:0001583	missense	8877	exon6			TGCGCCTCTTCCT	BC030553	CCDS11744.1, CCDS45785.1, CCDS59297.1	17q25.2	2004-02-18				ENSG00000176170			11240	protein-coding gene	gene with protein product		603730				9726979	Standard	NM_182965		Approved	SPHK	uc002jrj.2	Q9NYA1		ENST00000545180.1:c.905T>C	chr17.hg19:g.74383417T>C	ENSP00000440970:p.Leu302Pro	169.0	0.0		169.0	9.0	NM_182965	Q8N632|Q96GK1|Q9HD92|Q9NY70|Q9NYL3	Missense_Mutation	SNP	ENST00000545180.1	hg19	CCDS45785.1	.	.	.	.	.	.	.	.	.	.	T	25.8	4.676522	0.88445	.	.	ENSG00000176170	ENST00000545180;ENST00000323374;ENST00000392496;ENST00000543830	T;T;T	0.17528	2.27;2.27;2.27	5.08	5.08	0.68730	.	0.129908	0.52532	D	0.000065	T	0.40956	0.1138	M	0.79011	2.435	0.80722	D	1	P;D;D	0.60160	0.721;0.985;0.987	B;P;P	0.61940	0.349;0.781;0.896	T	0.41610	-0.9499	10	0.87932	D	0	-7.6684	14.8579	0.70355	0.0:0.0:0.0:1.0	.	388;316;302	Q9NYA1-2;Q96GK1;Q9NYA1	.;.;SPHK1_HUMAN	P	302;388;302;301	ENSP00000440970:L302P;ENSP00000313681:L388P;ENSP00000376285:L302P	ENSP00000313681:L388P	L	+	2	0	SPHK1	71895012	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.515000	0.81761	1.901000	0.55032	0.460000	0.39030	CTC	.	.		0.597	SPHK1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450113.1	NM_182965, NM_021972		C	74383417	T	C	74383417	3	2	282	1	0	0	0	0	1	0	0	0	15061	1551	54	2	1227	2	SPHK1	17	74383417	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2186	74383417	6811793	1175	41409										
UBE2O	63893	hgsc.bcm.edu	37	chr17	74388089	74388089	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttgggagaggtagcagaagtGggggggcacggctgggtaga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:74388089delG	ENST00000319380.7	-	16	3116	c.3052delC	c.(3052-3054)cacfs	p.H1018fs		NM_022066.3	NP_071349.3	Q9C0C9	UBE2O_HUMAN	ubiquitin-conjugating enzyme E2O	1018					positive regulation of BMP signaling pathway (GO:0030513)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	36						TAGCAGAAGTGGGGGGGCACG	0.582																																					p.H1018fs		Atlas-INDEL	.											.	UBE2O	207	.	0			c.3053delA						.						29	29	29					17																	74388089		2203	4300	6503	SO:0001589	frameshift_variant	63893	exon16			.	AB051521	CCDS32742.1	17q25.1	2013-10-09			ENSG00000175931	ENSG00000175931			29554	protein-coding gene	gene with protein product						11311559, 11214970	Standard	NM_022066		Approved	E2-230K	uc002jrm.4	Q9C0C9	OTTHUMG00000180178	ENST00000319380.7:c.3052delC	chr17.hg19:g.74388089delG	ENSP00000323687:p.His1018fs	126.0	0.0		178.0	13.0	NM_022066	A6NDU5|Q69YP4|Q6PIZ2|Q86UA4|Q8N425|Q8TBN1|Q9BSW1|Q9H6E6|Q9H7E4|Q9H9B2	Frame_Shift_Del	DEL	ENST00000319380.7	hg19	CCDS32742.1																																																																																			.	.		0.582	UBE2O-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450123.1	NM_022066		-	74388089	G	-	74388089	7	5	282	1	0	1	0	1	0	0	0	0	16883	1348	47	0	838	0	UBE2O	17	74388089	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	4672	74388089	6807121	1176	41410										
ST6GALNAC2	10610	hgsc.bcm.edu	37	chr17	74581809	74581809	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtaccgctgcaccgccgagaAgtacagggcaaagaggagcc	14	12	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:74581809A>G	ENST00000225276.5	-	1	401	c.82T>C	c.(82-84)Ttc>Ctc	p.F28L	ST6GALNAC2_ENST00000586520.1_5'UTR	NM_006456.2	NP_006447.2	Q9UJ37	SIA7B_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2	28					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	sialyltransferase activity (GO:0008373)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	11						ACCGCCGAGAAGTACAGGGCA	0.751																																					p.F28L		Atlas-SNP	.											.	ST6GALNAC2	29	.	0			c.T82C						.						8	10	9					17																	74581809		2072	4044	6116	SO:0001583	missense	10610	exon1			CCGAGAAGTACAG	U14550	CCDS11747.1	17q25.1	2013-03-01	2003-12-05	2005-02-07	ENSG00000070731	ENSG00000070731	2.4.99.7	"Sialyltransferases"	10867	protein-coding gene	gene with protein product		610137	"sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase)", "sialyltransferase-like 1"	SIAT7, SIAT7B, SIATL1		11984005	Standard	NM_006456		Approved	ST6GalNAII, STHM	uc002jsg.4	Q9UJ37	OTTHUMG00000180301	ENST00000225276.5:c.82T>C	chr17.hg19:g.74581809A>G	ENSP00000225276:p.Phe28Leu	76.0	0.0		51.0	4.0	NM_006456	Q12971	Missense_Mutation	SNP	ENST00000225276.5	hg19	CCDS11747.1	.	.	.	.	.	.	.	.	.	.	a	7.295	0.611809	0.14066	.	.	ENSG00000070731	ENST00000225276	T	0.28454	1.61	3.27	1.03	0.20045	.	1.130430	0.06718	U	0.774375	T	0.17152	0.0412	N	0.22421	0.69	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.30937	-0.9961	10	0.11182	T	0.66	-2.9009	4.2764	0.10811	0.6821:0.0:0.3179:0.0	.	28	Q9UJ37	SIA7B_HUMAN	L	28	ENSP00000225276:F28L	ENSP00000225276:F28L	F	-	1	0	ST6GALNAC2	72093404	0.050000	0.20438	0.031000	0.17742	0.115000	0.19883	0.090000	0.15025	0.432000	0.26286	0.255000	0.18592	TTC	.	.		0.751	ST6GALNAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450650.1	NM_006456		G	74581809	A	G	74581809	3	3	282	1	0	0	0	0	1	0	0	0	15239	72	3	2	1078	2	ST6GALNAC2	17	74581809	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	193720	74581809	6613401	1177	41411										
LGALS3BP	3959	hgsc.bcm.edu	37	chr17	76968422	76968422	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctcctcatgggaggcacgctCcccccagctccaggtgtcca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:76968422delC	ENST00000262776.3	-	6	1302	c.994delG	c.(994-996)gagfs	p.E332fs	LGALS3BP_ENST00000591778.1_3'UTR	NM_005567.3	NP_005558.1	Q08380	LG3BP_HUMAN	lectin, galactoside-binding, soluble, 3 binding protein	332	BACK.				cell adhesion (GO:0007155)|cellular defense response (GO:0006968)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|central_nervous_system(5)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(99;0.0677)|OV - Ovarian serous cystadenocarcinoma(97;0.139)			GAGGCACGCTCCCCCCAGCTC	0.642																																					p.E332fs	GBM(89;1105 1755 18102 21513)	Atlas-INDEL	.											.	LGALS3BP	47	.	0			c.995delA						.						46	48	47					17																	76968422		2203	4300	6503	SO:0001589	frameshift_variant	3959	exon6			.	L13210	CCDS11759.1	17q25	2014-07-09				ENSG00000108679		"BTB/POZ domain containing", "Endogenous ligands"	6564	protein-coding gene	gene with protein product	"L3 antigen", "Mac-2-binding protein", "serum protein 90K", "transport and golgi organization 10 homolog B (Drosophila)"	600626				7698018, 8034587, 8390986	Standard	NM_005567		Approved	MAC-2-BP, 90K, BTBD17B, TANGO10B, M2BP, gp90, CyCAP	uc002jwh.3	Q08380		ENST00000262776.3:c.994delG	chr17.hg19:g.76968422delC	ENSP00000262776:p.Glu332fs	101.0	0.0		143.0	11.0	NM_005567	Q7M4S0|Q9UCH8|Q9UCH9|Q9UCI0	Frame_Shift_Del	DEL	ENST00000262776.3	hg19	CCDS11759.1																																																																																			.	.		0.642	LGALS3BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437785.3	NM_005567		-	76968422	C	-	76968422	7	5	282	1	0	1	0	1	0	0	0	0	8753	864	30	0	767	0	LGALS3BP	17	76968422	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	2386613	76968422	4226788	1178	41412										
ENGASE	64772	hgsc.bcm.edu	37	chr17	77075666	77075666	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagccaccacaccgtcaccaTtcccccagtgggctggacca					rs113488517		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:77075666delT	ENST00000579016.1	+	4	512	c.512delT	c.(511-513)attfs	p.I171fs	ENGASE_ENST00000539857.2_Intron	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	171						cytoplasm (GO:0005737)	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925)			breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						ACCGTCACCATTCCCCCAGTG	0.587																																					p.I171fs		Atlas-INDEL	.											.	ENGASE	55	.	0			c.511delA						.						105	129	121					17																	77075666		2116	4222	6338	SO:0001589	frameshift_variant	64772	exon4			.	AF512564	CCDS42394.1	17q25.3	2009-03-03			ENSG00000167280	ENSG00000167280	3.2.1.96		24622	protein-coding gene	gene with protein product	"Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase", "Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase"	611898				12114544, 18586680	Standard	NM_001042573		Approved	FLJ21865	uc002jwv.4	Q8NFI3	OTTHUMG00000167714	ENST00000579016.1:c.512delT	chr17.hg19:g.77075666delT	ENSP00000462333:p.Ile171fs	156.0	0.0		156.0	10.0	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Frame_Shift_Del	DEL	ENST00000579016.1	hg19	CCDS42394.1																																																																																			.	.		0.587	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759		-	77075666	T	-	77075666	7	5	282	1	0	1	0	1	0	0	0	0	5120	1493	52	0	526	0	ENGASE	17	77075666	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	107244	77075666	4119544	1179	41413	206	2								
ENGASE	64772	hgsc.bcm.edu	37	chr17	77075671	77075671	+	Missense_Mutation	SNP	C	C	T													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	accacaccgtcaccattcccCcagtgggctggaccaacact							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:77075671C>T	ENST00000579016.1	+	4	517	c.517C>T	c.(517-519)Cca>Tca	p.P173S	ENGASE_ENST00000539857.2_Intron	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	173						cytoplasm (GO:0005737)	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925)			breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						CACCATTCCCCCAGTGGGCTG	0.587																																					p.P173S		Atlas-SNP	.											.	ENGASE	55	.	0			c.C517T						.						97	123	115					17																	77075671		2111	4218	6329	SO:0001583	missense	64772	exon4			ATTCCCCCAGTGG	AF512564	CCDS42394.1	17q25.3	2009-03-03			ENSG00000167280	ENSG00000167280	3.2.1.96		24622	protein-coding gene	gene with protein product	"Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase", "Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase"	611898				12114544, 18586680	Standard	NM_001042573		Approved	FLJ21865	uc002jwv.4	Q8NFI3	OTTHUMG00000167714	ENST00000579016.1:c.517C>T	chr17.hg19:g.77075671C>T	ENSP00000462333:p.Pro173Ser	152.0	0.0		151.0	9.0	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Missense_Mutation	SNP	ENST00000579016.1	hg19	CCDS42394.1	.	.	.	.	.	.	.	.	.	.	C	19.31	3.802634	0.70682	.	.	ENSG00000167280	ENST00000311595;ENST00000545583	.	.	.	5.22	5.22	0.72569	Glycoside hydrolase, family 85 (1);	0.049431	0.85682	D	0.000000	T	0.75012	0.3792	M	0.72118	2.19	0.80722	D	1	D;P	0.55800	0.973;0.939	P;P	0.57152	0.758;0.814	T	0.78076	-0.2345	9	0.72032	D	0.01	-18.8426	17.3151	0.87221	0.0:1.0:0.0:0.0	.	173;173	Q8NFI3;Q8NFI3-3	ENASE_HUMAN;.	S	173	.	ENSP00000308158:P173S	P	+	1	0	ENGASE	74587266	1.000000	0.71417	0.995000	0.50966	0.271000	0.26615	5.412000	0.66392	2.587000	0.87381	0.655000	0.94253	CCA	.	.		0.587	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759		T	77075671	C	T	77075671	3	4	282	1	0	0	0	0	1	0	0	0	5120	623	22	3	531	3	ENGASE	17	77075671	Missense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	5	77075671	4119539	1180	41414	206	2								
METTL4	64863	hgsc.bcm.edu	37	chr18	2544668	2544668	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctacctcaatggtagagcagTtttttcttgaaccctcccca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:2544668delT	ENST00000574538.1	-	7	1940	c.1165delA	c.(1165-1167)actfs	p.T389fs	METTL4_ENST00000319888.6_Frame_Shift_Del_p.T389fs	NM_022840.3	NP_073751.3	Q8N3J2	METL4_HUMAN	methyltransferase like 4	389					nucleobase-containing compound metabolic process (GO:0006139)		methyltransferase activity (GO:0008168)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	17						GGTAGAGCAGTTTTTTCTTGA	0.328																																					p.T389fs		Atlas-INDEL	.											.	METTL4	40	.	0			c.1166delC						.						104	100	102					18																	2544668		2203	4300	6503	SO:0001589	frameshift_variant	64863	exon7			.		CCDS11826.1	18p11.31	2008-02-05			ENSG00000101574	ENSG00000101574			24726	protein-coding gene	gene with protein product						12477932	Standard	NM_022840		Approved	FLJ23017, HsT661	uc002klh.4	Q8N3J2	OTTHUMG00000131482	ENST00000574538.1:c.1165delA	chr18.hg19:g.2544668delT	ENSP00000458290:p.Thr389fs	257.0	0.0		165.0	12.0	NM_022840	B2RNA1|Q2TAA7|Q9H5U9	Frame_Shift_Del	DEL	ENST00000574538.1	hg19	CCDS11826.1																																																																																			.	.		0.328	METTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254326.3	NM_022840		-	2544668	T	-	2544668	7	5	282	1	0	1	0	1	0	0	0	0	9511	1725	60	0	265	0	METTL4	18	2544668	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10		2544668	75532580	1181	41415										
LAMA1	284217	hgsc.bcm.edu	37	chr18	7017287	7017287	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgcatcttaccaagcactggTcacactgctgtccagtcacg	8	14	3	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:7017287T>C	ENST00000389658.3	-	20	2891	c.2798A>G	c.(2797-2799)gAc>gGc	p.D933G		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	933	Laminin EGF-like 9. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				CAAGCACTGGTCACACTGCTG	0.498																																					p.D933G		Atlas-SNP	.											.	LAMA1	458	.	0			c.A2798G						.						170	123	139					18																	7017287		2203	4300	6503	SO:0001583	missense	284217	exon20			CACTGGTCACACT	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.2798A>G	chr18.hg19:g.7017287T>C	ENSP00000374309:p.Asp933Gly	183.0	0.0		92.0	5.0	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	hg19	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.372282	0.82573	.	.	ENSG00000101680	ENST00000389658	T	0.65916	-0.18	5.44	5.44	0.79542	EGF-like, laminin (4);	0.122628	0.52532	D	0.000078	T	0.79822	0.4512	M	0.82132	2.575	0.58432	D	0.999999	D	0.89917	1.0	D	0.77557	0.99	T	0.82028	-0.0660	10	0.54805	T	0.06	.	15.486	0.75569	0.0:0.0:0.0:1.0	.	933	P25391	LAMA1_HUMAN	G	933	ENSP00000374309:D933G	ENSP00000374309:D933G	D	-	2	0	LAMA1	7007287	1.000000	0.71417	1.000000	0.80357	0.776000	0.43924	7.658000	0.83755	2.068000	0.61886	0.519000	0.50382	GAC	.	.		0.498	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		C	7017287	T	C	7017287	3	2	282	1	0	0	0	0	1	0	0	0	8614	1667	58	2	6605	2	LAMA1	18	7017287	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	4472619	7017287	71059961	1182	41416										
KIAA0802	23255	hgsc.bcm.edu	37	chr18	8783591	8783591	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aggaagccttcctgatgcgcAaaaagatggccaagctagga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:8783591delA	ENST00000306329.11	+	5	1561	c.1561delA	c.(1561-1563)aaafs	p.K522fs	SOGA2_ENST00000517570.1_Frame_Shift_Del_p.K162fs|SOGA2_ENST00000359865.3_Frame_Shift_Del_p.K162fs|SOGA2_ENST00000306285.7_5'UTR|SOGA2_ENST00000400050.3_Frame_Shift_Del_p.K162fs																							CCTGATGCGCAAAAAGATGGC	0.567																																					p.R160fs		Atlas-INDEL	.											.	.	.	.	0			c.480delC						.						39	41	40					18																	8783591		2203	4300	6503	SO:0001589	frameshift_variant	23255	exon6			.																												ENST00000306329.11:c.1561delA	chr18.hg19:g.8783591delA	ENSP00000305027:p.Lys522fs	253.0	0.0		187.0	13.0	NM_015210		Frame_Shift_Del	DEL	ENST00000306329.11	hg19																																																																																				.	.		0.567	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1			-	8783591	A	-	8783591	7	5	282	1	0	1	0	1	0	0	0	0	8203	131	5	0	495	0	KIAA0802	18	8783591	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1766304	8783591	69293657	1183	41417										
ANKRD12	23253	hgsc.bcm.edu	37	chr18	9257082	9257082	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tggctgacttgccggagcggAttaaaccaccatatgcaaac	10	11	0	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:9257082A>G	ENST00000262126.4	+	9	4057	c.3817A>G	c.(3817-3819)Att>Gtt	p.I1273V	ANKRD12_ENST00000383440.2_Missense_Mutation_p.I1250V|ANKRD12_ENST00000400020.3_Missense_Mutation_p.I1250V|RP11-888D10.4_ENST00000609701.1_RNA	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	1273						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						GCCGGAGCGGATTAAACCACC	0.433																																					p.I1273V		Atlas-SNP	.											.	ANKRD12	167	.	0			c.A3817G						.						77	75	75					18																	9257082		2203	4300	6503	SO:0001583	missense	23253	exon9			GAGCGGATTAAAC	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.3817A>G	chr18.hg19:g.9257082A>G	ENSP00000262126:p.Ile1273Val	309.0	1.0		235.0	86.0	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Missense_Mutation	SNP	ENST00000262126.4	hg19	CCDS11843.1	.	.	.	.	.	.	.	.	.	.	A	3.217	-0.160324	0.06502	.	.	ENSG00000101745	ENST00000383440;ENST00000262126	T;T	0.63913	-0.07;-0.07	5.89	3.49	0.39957	.	0.298503	0.36338	N	0.002644	T	0.39784	0.1091	N	0.16478	0.41	0.22675	N	0.998865	B;B	0.11235	0.004;0.003	B;B	0.10450	0.005;0.002	T	0.18053	-1.0349	10	0.21540	T	0.41	-30.3326	6.0617	0.19842	0.7172:0.1433:0.1395:0.0	.	1250;1273	Q6UB98-2;Q6UB98	.;ANR12_HUMAN	V	1250;1273	ENSP00000372932:I1250V;ENSP00000262126:I1273V	ENSP00000262126:I1273V	I	+	1	0	ANKRD12	9247082	0.384000	0.25164	0.983000	0.44433	0.746000	0.42486	0.790000	0.26900	0.478000	0.27488	0.533000	0.62120	ATT	.	.		0.433	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		G	9257082	A	G	9257082	3	3	282	1	0	0	0	0	1	0	0	0	640	333	12	2	3847	2	ANKRD12	18	9257082	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	473491	9257082	68820166	1184	41418										
ROCK1	6093	hgsc.bcm.edu	37	chr18	18690859	18690859	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaatcgagtctcaaaactgtCcccagtcgacatgttgctgc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:18690859delC	ENST00000399799.2	-	1	953	c.13delG	c.(13-15)gacfs	p.D5fs		NM_005406.2	NP_005397.1	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein kinase 1	5					actin cytoskeleton organization (GO:0030036)|apical constriction (GO:0003383)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|bleb assembly (GO:0032060)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of focal adhesion assembly (GO:0051894)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(4)|central_nervous_system(1)|large_intestine(8)|lung(2)	16	Melanoma(1;0.165)					TCAAAACTGTCCCCAGTCGAC	0.517																																					p.D5fs		Atlas-INDEL	.											.	ROCK1	162	.	0			c.14delA						.						164	147	152					18																	18690859		2203	4300	6503	SO:0001589	frameshift_variant	6093	exon1			.		CCDS11870.2	18q11.2	2013-01-10			ENSG00000067900	ENSG00000067900	2.7.11.1	"Pleckstrin homology (PH) domain containing"	10251	protein-coding gene	gene with protein product		601702				8617235	Standard	NM_005406		Approved	p160ROCK	uc002kte.3	Q13464	OTTHUMG00000131723	ENST00000399799.2:c.13delG	chr18.hg19:g.18690859delC	ENSP00000382697:p.Asp5fs	174.0	0.0		143.0	10.0	NM_005406	B0YJ91|Q2KHM4|Q59GZ4	Frame_Shift_Del	DEL	ENST00000399799.2	hg19	CCDS11870.2																																																																																			.	.		0.517	ROCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254641.2	NM_005406		-	18690859	C	-	18690859	7	5	282	1	0	1	0	1	0	0	0	0	13532	855	30	0	4183	0	ROCK1	18	18690859	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	9433777	18690859	59386389	1185	41419										
ABHD3	171586	hgsc.bcm.edu	37	chr18	19231648	19231648	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cttggccagattccctccagAaaaccaatatggcctccata							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:19231648delA	ENST00000289119.2	-	9	1273	c.1134delT	c.(1132-1134)tttfs	p.F378fs	ABHD3_ENST00000580981.1_Frame_Shift_Del_p.F325fs|ABHD3_ENST00000578270.1_Frame_Shift_Del_p.F183fs	NM_138340.4	NP_612213.2	Q8WU67	ABHD3_HUMAN	abhydrolase domain containing 3	378						integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|prostate(2)	10						TTCCCTCCAGAAAACCAATAT	0.418																																					p.L379fs		Atlas-INDEL	.											.	ABHD3	32	.	0			c.1135delC						.						117	102	107					18																	19231648		2203	4300	6503	SO:0001589	frameshift_variant	171586	exon9			.	AK024880	CCDS32802.1	18q11.1	2011-02-16			ENSG00000158201	ENSG00000158201		"Abhydrolase domain containing"	18718	protein-coding gene	gene with protein product		612197					Standard	NM_138340		Approved	LABH3	uc002ktl.2	Q8WU67		ENST00000289119.2:c.1134delT	chr18.hg19:g.19231648delA	ENSP00000289119:p.Phe378fs	228.0	0.0		139.0	12.0	NM_138340	B0YIV0|B7Z5C2|O43411	Frame_Shift_Del	DEL	ENST00000289119.2	hg19	CCDS32802.1																																																																																			.	.		0.418	ABHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444757.1			-	19231648	A	-	19231648	7	5	282	1	0	1	0	1	0	0	0	0	83	243	9	0	99	0	ABHD3	18	19231648	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	540789	19231648	58845600	1186	41420										
NPC1	4864	hgsc.bcm.edu	37	chr18	21141327	21141327	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggaatctttatacctacctgAaaacacaggagtgatggtaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:21141327delA	ENST00000269228.5	-	5	1182	c.628delT	c.(628-630)tcafs	p.S210fs	NPC1_ENST00000412552.2_5'Flank|NPC1_ENST00000540608.1_5'UTR	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	210					adult walking behavior (GO:0007628)|autophagy (GO:0006914)|bile acid metabolic process (GO:0008206)|cellular response to low-density lipoprotein particle stimulus (GO:0071404)|cellular response to steroid hormone stimulus (GO:0071383)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|establishment of protein localization to membrane (GO:0090150)|lysosomal transport (GO:0007041)|membrane raft organization (GO:0031579)|negative regulation of cell death (GO:0060548)|negative regulation of macroautophagy (GO:0016242)|protein glycosylation (GO:0006486)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|hedgehog receptor activity (GO:0008158)|receptor activity (GO:0004872)|sterol transporter activity (GO:0015248)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(10)|lung(13)|ovary(2)|stomach(1)	38	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)					TACCTACCTGAAAACACAGGA	0.463																																					p.S210X		Atlas-INDEL	.											.	NPC1	114	.	0			c.629delC						.						169	153	158					18																	21141327		2203	4300	6503	SO:0001589	frameshift_variant	4864	exon5			.	AF002020	CCDS11878.1	18q11.2	2014-06-17			ENSG00000141458	ENSG00000141458			7897	protein-coding gene	gene with protein product		607623				8446622	Standard	NM_000271		Approved		uc002kum.4	O15118	OTTHUMG00000131873	ENST00000269228.5:c.628delT	chr18.hg19:g.21141327delA	ENSP00000269228:p.Ser210fs	180.0	0.0		127.0	10.0	NM_000271	B4DET3|Q9P130	Frame_Shift_Del	DEL	ENST00000269228.5	hg19	CCDS11878.1																																																																																			.	.		0.463	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271		-	21141327	A	-	21141327	7	5	282	1	0	1	0	1	0	0	0	0	10579	246	9	0	3292	0	NPC1	18	21141327	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1909679	21141327	56935921	1187	41421										
CABYR	26256	hgsc.bcm.edu	37	chr18	21723346	21723346	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aatactactatggatataaaAgatctggttaaacaatttca	5	5	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:21723346A>G	ENST00000399496.3	+	3	333	c.168A>G	c.(166-168)aaA>aaG	p.K56K	CABYR_ENST00000399481.2_Intron|CABYR_ENST00000399499.1_Silent_p.K56K|CABYR_ENST00000581397.1_Silent_p.K56K|CABYR_ENST00000327201.6_Intron|CABYR_ENST00000415309.2_Silent_p.K56K	NM_012189.2|NM_153769.1	NP_036321.2|NP_722453.1	O75952	CABYR_HUMAN	calcium binding tyrosine-(Y)-phosphorylation regulated	56					epithelial cilium movement (GO:0003351)|sperm capacitation (GO:0048240)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|motile cilium (GO:0031514)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)|protein heterodimerization activity (GO:0046982)|SH3 domain binding (GO:0017124)	p.K56K(2)		breast(1)|endometrium(2)|large_intestine(4)|lung(4)	11	all_cancers(21;9.13e-05)|all_epithelial(16;5.49e-07)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0305)|Ovarian(20;0.17)					TGGATATAAAAGATCTGGTTA	0.274																																					p.K56K		Atlas-SNP	.											CABYR,NS,carcinoma,0,1	CABYR	51	.	2	Substitution - coding silent(2)	lung(2)	c.A168G						.						39	42	41					18																	21723346		2191	4288	6479	SO:0001819	synonymous_variant	26256	exon3			TATAAAAGATCTG	AF088868	CCDS11881.1, CCDS11882.1, CCDS11883.1, CCDS42420.1, CCDS45840.1	18q11.2	2009-08-06	2007-11-22		ENSG00000154040	ENSG00000154040			15569	protein-coding gene	gene with protein product	"fibrousheathin 2", "cancer/testis antigen 88"	612135				11820818, 17317841, 16139264	Standard	NM_012189		Approved	FSP-2, CBP86, CT88	uc002kux.3	O75952	OTTHUMG00000037365	ENST00000399496.3:c.168A>G	chr18.hg19:g.21723346A>G		57.0	0.0		72.0	4.0	NM_153769	B2R857|Q8WXW5|Q9HAY3|Q9HAY4|Q9HAY5|Q9HCY9	Silent	SNP	ENST00000399496.3	hg19	CCDS42420.1																																																																																			.	.		0.274	CABYR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090926.2	NM_153770		G	21723346	A	G	21723346	2	3	282	1	0	0	0	0	0	0	0	1	2538	69	3	2		2	CABYR	18	21723346	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	582019	21723346	56353902	1188	41422										
DSG3	1830	hgsc.bcm.edu	37	chr18	29037066	29037066	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agagaaggagaagataactcAaaaagaaacccaattgccaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:29037066delA	ENST00000257189.4	+	3	278	c.195delA	c.(193-195)tcafs	p.S65fs		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	65	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(28)|ovary(4)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			AAGATAACTCAAAAAGAAACC	0.343																																					p.S65X		Atlas-INDEL	.											.	DSG3	172	.	0			c.194delC						.						108	102	104					18																	29037066		2203	4300	6503	SO:0001589	frameshift_variant	1830	exon3			.	M76482	CCDS11898.1	18q12.1	2010-06-24	2010-06-24		ENSG00000134757	ENSG00000134757		"Cadherins / Major cadherins"	3050	protein-coding gene	gene with protein product	"pemphigus vulgaris antigen"	169615	"desmoglein 3 (pemphigus vulgaris antigen)"			1601426	Standard	NM_001944		Approved	CDHF6	uc002kws.3	P32926	OTTHUMG00000131985	ENST00000257189.4:c.195delA	chr18.hg19:g.29037066delA	ENSP00000257189:p.Ser65fs	157.0	0.0		126.0	11.0	NM_001944	A8K2V2	Frame_Shift_Del	DEL	ENST00000257189.4	hg19	CCDS11898.1																																																																																			.	.		0.343	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944		-	29037066	A	-	29037066	7	5	282	1	0	1	0	1	0	0	0	0	4780	117	5	0	205	0	DSG3	18	29037066	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	7313720	29037066	49040182	1189	41423										
C18orf34	374864	hgsc.bcm.edu	37	chr18	30846924	30846924	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttgttaatatcaatctcaagTtttttattgtcttccgtcag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:30846924delT	ENST00000383096.3	-	14	1547	c.1365delA	c.(1363-1365)aaafs	p.K455fs	CCDC178_ENST00000583930.1_Frame_Shift_Del_p.K455fs|CCDC178_ENST00000579947.1_Frame_Shift_Del_p.K455fs|CCDC178_ENST00000579916.1_Intron|CCDC178_ENST00000406524.2_Frame_Shift_Del_p.K455fs|CCDC178_ENST00000402325.1_Frame_Shift_Del_p.K455fs|CCDC178_ENST00000300227.8_Frame_Shift_Del_p.K455fs|CCDC178_ENST00000403303.1_Frame_Shift_Del_p.K455fs			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178	455																	CAATCTCAAGTTTTTTATTGT	0.269																																					p.L456fs		Atlas-INDEL	.											.	.	.	.	0			c.1366delC						.						50	48	49					18																	30846924		2201	4285	6486	SO:0001589	frameshift_variant	374864	exon13			.	AK126038	CCDS11906.1, CCDS42424.1	18q12.1	2012-10-15	2012-10-15	2012-10-15	ENSG00000166960	ENSG00000166960			29588	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 34"	C18orf34			Standard	NM_198995		Approved	FLJ44050	uc002kxn.2	Q5BJE1	OTTHUMG00000132279	ENST00000383096.3:c.1365delA	chr18.hg19:g.30846924delT	ENSP00000372576:p.Lys455fs	278.0	0.0		225.0	17.0	NM_001105528	A6NDC6|J3KS92|Q6ZP67|Q6ZU20	Frame_Shift_Del	DEL	ENST00000383096.3	hg19	CCDS42424.1																																																																																			.	.		0.269	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255373.2	NM_198995		-	30846924	T	-	30846924	7	5	282	1	0	1	0	1	0	0	0	0	1904	1722	60	0	1278	0	C18orf34	18	30846924	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1809858	30846924	47230324	1190	41424										
MOCOS	55034	hgsc.bcm.edu	37	chr18	33785127	33785127	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tctccagtaccccaatggagCccctgtggtgcggatttaca					rs533721204		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:33785127delC	ENST00000261326.5	+	6	1127	c.1106delC	c.(1105-1107)gccfs	p.A369fs		NM_017947.2	NP_060417.2			molybdenum cofactor sulfurase											breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|liver(1)|lung(15)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						CCCAATGGAGCCCCTGTGGTG	0.488																																					p.A369fs		Atlas-INDEL	.											.	MOCOS	84	.	0			c.1105delG						.						115	107	110					18																	33785127		2203	4300	6503	SO:0001589	frameshift_variant	55034	exon6			.	AK000740	CCDS11919.1	18q12	2003-12-18			ENSG00000075643	ENSG00000075643			18234	protein-coding gene	gene with protein product		613274				11302742	Standard	NM_017947		Approved	HMCS, FLJ20733, MOS	uc002kzq.4	Q96EN8	OTTHUMG00000132590	ENST00000261326.5:c.1106delC	chr18.hg19:g.33785127delC	ENSP00000261326:p.Ala369fs	260.0	0.0		199.0	12.0	NM_017947		Frame_Shift_Del	DEL	ENST00000261326.5	hg19	CCDS11919.1																																																																																			.	.		0.488	MOCOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255801.1			-	33785127	C	-	33785127	7	5	282	1	0	1	0	1	0	0	0	0	9698	739	26	0	1128	0	MOCOS	18	33785127	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	2938203	33785127	44292121	1191	41425										
FHOD3	80206	hgsc.bcm.edu	37	chr18	34320658	34320658	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccaccgatgaggagaagcagAaaatccaggaagctcagctg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:34320658delA	ENST00000359247.4	+	17	3040	c.3040delA	c.(3040-3042)aaafs	p.K1014fs	FHOD3_ENST00000257209.4_Frame_Shift_Del_p.K1031fs|FHOD3_ENST00000590592.1_Frame_Shift_Del_p.K1206fs|FHOD3_ENST00000591635.1_Frame_Shift_Del_p.K227fs|FHOD3_ENST00000592128.1_Frame_Shift_Del_p.K10fs|FHOD3_ENST00000445677.1_Frame_Shift_Del_p.K993fs	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	1014	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)				NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				GGAGAAGCAGAAAATCCAGGA	0.507																																					p.Q1030fs		Atlas-INDEL	.											.	FHOD3	210	.	0			c.3090delG						.						69	62	65					18																	34320658		2203	4300	6503	SO:0001589	frameshift_variant	80206	exon18			.	AK091899	CCDS32816.1, CCDS62418.1, CCDS62419.1	18q12	2007-08-02				ENSG00000134775			26178	protein-coding gene	gene with protein product		609691				11214970	Standard	NM_025135		Approved	FHOS2, KIAA1695, FLJ22297, FLJ22717	uc021uiv.1	Q2V2M9		ENST00000359247.4:c.3040delA	chr18.hg19:g.34320658delA	ENSP00000352186:p.Lys1014fs	239.0	0.0		190.0	12.0	NM_025135	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Frame_Shift_Del	DEL	ENST00000359247.4	hg19																																																																																				.	.		0.507	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114		-	34320658	A	-	34320658	7	5	282	1	0	1	0	1	0	0	0	0	5891	247	9	0	3161	0	FHOD3	18	34320658	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	535531	34320658	43756590	1192	41426										
TCEB3B	51224	hgsc.bcm.edu	37	chr18	44560926	44560926	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gccaatctccctgggcacacAaggggcgtttttcctggcga	12	13	1	0	rs373872961		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:44560926A>T	ENST00000332567.4	-	1	1062	c.710T>A	c.(709-711)tTg>tAg	p.L237*	KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000592005.1_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	237					regulation of DNA-templated transcription, elongation (GO:0032784)|transcription from RNA polymerase II promoter (GO:0006366)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|lung(24)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						CTGGGCACACAAGGGGCGTTT	0.602																																					p.L237X		Atlas-SNP	.											.	TCEB3B	141	.	0			c.T710A						.						40	42	41					18																	44560926		2203	4300	6503	SO:0001587	stop_gained	51224	exon1			GCACACAAGGGGC	BC036022	CCDS11932.1	18q21.1	2009-08-04			ENSG00000206181	ENSG00000206181			30771	protein-coding gene	gene with protein product	"transcription elongation factor (SIII) elongin A2", "elongin A2"	609522				7660129, 8244996	Standard	NM_016427		Approved	HsT832, TCEB3L	uc002lcr.1	Q8IYF1	OTTHUMG00000132649	ENST00000332567.4:c.710T>A	chr18.hg19:g.44560926A>T	ENSP00000331302:p.Leu237*	255.0	1.0		224.0	100.0	NM_016427	Q9P2V9	Nonsense_Mutation	SNP	ENST00000332567.4	hg19	CCDS11932.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.334294	0.81801	.	.	ENSG00000206181	ENST00000332567	.	.	.	1.37	0.185	0.15096	.	2.229110	0.03378	U	0.200007	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	3.1294	0.06418	0.7396:0.0:0.2604:0.0	.	.	.	.	X	237	.	ENSP00000331302:L237X	L	-	2	0	TCEB3B	42814924	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	1.249000	0.32839	0.044000	0.15775	0.379000	0.24179	TTG	.	.		0.602	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427		T	44560926	A	T	44560926	4	4	282	1	0	0	0	0	0	1	0	0	15697	131	5	4	1555	4	TCEB3B	18	44560926	Nonsense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	10240268	44560926	33516322	1193	41427										
ONECUT2	9480	hgsc.bcm.edu	37	chr18	55102980	55102980	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctacaccgcctatcgatgccTcaccaaagacctagaaggct	7	15	1	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:55102980T>C	ENST00000491143.2	+	1	64	c.32T>C	c.(31-33)cTc>cCc	p.L11P	AC090340.1_ENST00000581316.1_RNA	NM_004852.2	NP_004843.2	O95948	ONEC2_HUMAN	one cut homeobox 2	11					cell fate commitment (GO:0045165)|cilium assembly (GO:0042384)|endocrine pancreas development (GO:0031018)|epithelial cell development (GO:0002064)|liver development (GO:0001889)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ morphogenesis (GO:0009887)|peripheral nervous system neuron development (GO:0048935)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell-matrix adhesion (GO:0001952)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|lung(4)|ovary(2)|skin(1)	15		Colorectal(73;0.234)		READ - Rectum adenocarcinoma(59;0.227)|Colorectal(16;0.245)		TATCGATGCCTCACCAAAGAC	0.726																																					p.L11P		Atlas-SNP	.											.	ONECUT2	42	.	0			c.T32C						.						13	14	14					18																	55102980		1718	3861	5579	SO:0001583	missense	9480	exon1			GATGCCTCACCAA	Y18198	CCDS42440.1	18q21.31	2012-03-09	2007-07-16		ENSG00000119547	ENSG00000119547		"Homeoboxes / CUT class"	8139	protein-coding gene	gene with protein product		604894	"one cut domain, family member 2"			9915796	Standard	NM_004852		Approved	OC-2	uc002lgo.3	O95948	OTTHUMG00000159776	ENST00000491143.2:c.32T>C	chr18.hg19:g.55102980T>C	ENSP00000419185:p.Leu11Pro	197.0	0.0		100.0	4.0	NM_004852		Missense_Mutation	SNP	ENST00000491143.2	hg19	CCDS42440.1	.	.	.	.	.	.	.	.	.	.	t	13.84	2.358105	0.41801	.	.	ENSG00000119547	ENST00000262095	.	.	.	1.93	1.93	0.25924	.	.	.	.	.	T	0.45115	0.1326	N	0.08118	0	0.58432	D	0.999996	D	0.63046	0.992	P	0.60789	0.879	T	0.48305	-0.9047	8	0.87932	D	0	.	8.3564	0.32333	0.0:0.0:0.0:1.0	.	11	O95948	ONEC2_HUMAN	P	11	.	ENSP00000262095:L11P	L	+	2	0	ONECUT2	53253978	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	1.094000	0.30951	0.753000	0.32945	0.242000	0.17961	CTC	.	.		0.726	ONECUT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357264.3			C	55102980	T	C	55102980	3	2	282	1	0	0	0	0	1	0	0	0	10878	1551	54	2	34	2	ONECUT2	18	55102980	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	10542054	55102980	22974268	1194	41428										
CDH20	28316	hgsc.bcm.edu	37	chr18	59221661	59221661	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agcctctcccgctacgtgccTcagacgtgcgcagtgaacag	11	15	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:59221661T>C	ENST00000262717.4	+	12	2537	c.2139T>C	c.(2137-2139)ccT>ccC	p.P713P	CDH20_ENST00000536675.2_Silent_p.P713P|CDH20_ENST00000538374.1_Silent_p.P713P			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2	713					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|skin(3)	61		Colorectal(73;0.186)				GCTACGTGCCTCAGACGTGCG	0.682																																					p.P713P		Atlas-SNP	.											.	CDH20	117	.	0			c.T2139C						.						42	38	39					18																	59221661		2203	4300	6503	SO:0001819	synonymous_variant	28316	exon11			CGTGCCTCAGACG	AF217289	CCDS11977.1	18q21.33	2010-01-26			ENSG00000101542	ENSG00000101542		"Cadherins / Major cadherins"	1760	protein-coding gene	gene with protein product		605807				10995570	Standard	NM_031891		Approved	CDH7L3, Cdh7	uc010dps.1	Q9HBT6	OTTHUMG00000132768	ENST00000262717.4:c.2139T>C	chr18.hg19:g.59221661T>C		119.0	0.0		84.0	4.0	NM_031891	Q495S3	Silent	SNP	ENST00000262717.4	hg19	CCDS11977.1																																																																																			.	.		0.682	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256141.2	NM_031891		C	59221661	T	C	59221661	2	2	282	1	0	0	0	0	0	0	0	1	3108	1538	54	2		2	CDH20	18	59221661	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	4118681	59221661	18855587	1195	41429										
KIAA1468	57614	hgsc.bcm.edu	37	chr18	59895676	59895676	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtaaatagttcagacaagggAaaaaacacagacatccatct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:59895676delA	ENST00000398130.2	+	8	1525	c.1293delA	c.(1291-1293)ggafs	p.G431fs	KIAA1468_ENST00000256858.6_Frame_Shift_Del_p.G431fs|KIAA1468_ENST00000592479.1_3'UTR	NM_020854.3	NP_065905.2	Q9P260	K1468_HUMAN	KIAA1468	431										autonomic_ganglia(1)|breast(4)|endometrium(4)|kidney(4)|large_intestine(7)|lung(20)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47		Colorectal(73;0.186)				CAGACAAGGGAAAAAACACAG	0.433																																					p.G431fs		Atlas-INDEL	.											.	KIAA1468	93	.	0			c.1292delG						.						111	99	103					18																	59895676		2203	4300	6503	SO:0001589	frameshift_variant	57614	exon8			.	BC011992	CCDS11979.2	18q21.33	2005-11-03			ENSG00000134444	ENSG00000134444			29289	protein-coding gene	gene with protein product						11973628	Standard	NM_020854		Approved	HsT885, HsT3308, FLJ33841	uc002lil.3	Q9P260	OTTHUMG00000132780	ENST00000398130.2:c.1293delA	chr18.hg19:g.59895676delA	ENSP00000381198:p.Gly431fs	215.0	0.0		137.0	14.0	NM_020854		Frame_Shift_Del	DEL	ENST00000398130.2	hg19	CCDS11979.2																																																																																			.	.		0.433	KIAA1468-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256187.1	NM_020854		-	59895676	A	-	59895676	7	5	282	1	0	1	0	1	0	0	0	0	8245	233	9	0	1323	0	KIAA1468	18	59895676	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	674015	59895676	18181572	1196	41430										
TMX3	54495	hgsc.bcm.edu	37	chr18	66348255	66348255	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaatgttattaataaactggAccatgtcttcaacattctta	4	7	3	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:66348255A>G	ENST00000299608.2	-	14	1314	c.998T>C	c.(997-999)gTc>gCc	p.V333A		NM_019022.3	NP_061895.3	Q96JJ7	TMX3_HUMAN	thioredoxin-related transmembrane protein 3	333					cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein disulfide isomerase activity (GO:0003756)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	17						AATAAACTGGACCATGTCTTC	0.363																																					p.V333A		Atlas-SNP	.											.	TMX3	44	.	0			c.T998C						.						145	140	142					18																	66348255		2203	4300	6503	SO:0001583	missense	54495	exon14			AACTGGACCATGT	BX647846	CCDS32840.1	18q22	2011-10-19	2009-02-23	2009-02-23		ENSG00000166479		"Protein disulfide isomerases"	24718	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 13"		"thioredoxin domain containing 10"	TXNDC10		15623505	Standard	NM_019022		Approved	FLJ20793, KIAA1830, PDIA13	uc002lkf.3	Q96JJ7		ENST00000299608.2:c.998T>C	chr18.hg19:g.66348255A>G	ENSP00000299608:p.Val333Ala	140.0	0.0		99.0	4.0	NM_019022	B3KV75|Q52LT7|Q8N5J0|Q9NWJ9	Missense_Mutation	SNP	ENST00000299608.2	hg19	CCDS32840.1	.	.	.	.	.	.	.	.	.	.	A	16.75	3.209804	0.58343	.	.	ENSG00000166479	ENST00000299608;ENST00000544714	T	0.29917	1.55	5.81	4.65	0.58169	.	0.412804	0.27214	N	0.020382	T	0.23133	0.0559	L	0.44542	1.39	0.80722	D	1	P	0.39576	0.679	B	0.37387	0.248	T	0.02581	-1.1138	10	0.09338	T	0.73	.	11.1721	0.48577	0.9278:0.0:0.0722:0.0	.	333	Q96JJ7	TMX3_HUMAN	A	333	ENSP00000299608:V333A	ENSP00000299608:V333A	V	-	2	0	TMX3	64499235	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	6.594000	0.74104	1.022000	0.39626	0.533000	0.62120	GTC	.	.		0.363	TMX3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420155.1	NM_019022		G	66348255	A	G	66348255	3	3	282	1	0	0	0	0	1	0	0	0	16283	275	10	2	378	2	TMX3	18	66348255	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	6452579	66348255	11728993	1197	41431										
FBXO15	201456	hgsc.bcm.edu	37	chr18	71749166	71749166	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acggttctgtttttacctttAtacagccatcaaaaatatca	4	9	3	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:71749166A>T	ENST00000419743.2	-	9	1338	c.1259T>A	c.(1258-1260)aTa>aAa	p.I420K	FBXO15_ENST00000580806.1_5'UTR|FBXO15_ENST00000269500.5_Missense_Mutation_p.I344K	NM_001142958.1	NP_001136430.1	Q8NCQ5	FBX15_HUMAN	F-box protein 15	420						SCF ubiquitin ligase complex (GO:0019005)				autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)	27		Esophageal squamous(42;0.103)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.143)		TTTTACCTTTATACAGCCATC	0.279																																					p.I420K		Atlas-SNP	.											.	FBXO15	97	.	0			c.T1259A						.						71	67	68					18																	71749166		2202	4298	6500	SO:0001583	missense	201456	exon9			ACCTTTATACAGC	AK094215	CCDS45884.1	18q22.3	2006-03-09	2004-06-15		ENSG00000141665	ENSG00000141665		"F-boxes /  "other""	13617	protein-coding gene	gene with protein product		609093	"F-box only protein 15"			12665572	Standard	NM_152676		Approved	MGC39671, FBX15	uc002llf.2	Q8NCQ5	OTTHUMG00000132842	ENST00000419743.2:c.1259T>A	chr18.hg19:g.71749166A>T	ENSP00000393154:p.Ile420Lys	125.0	0.0		106.0	5.0	NM_001142958	B3KST3	Missense_Mutation	SNP	ENST00000419743.2	hg19	CCDS45884.1	.	.	.	.	.	.	.	.	.	.	A	16.41	3.115189	0.56505	.	.	ENSG00000141665	ENST00000269500;ENST00000419743	T;T	0.46063	0.88;0.88	4.78	4.78	0.61160	.	0.313569	0.34603	N	0.003821	T	0.45155	0.1328	M	0.67953	2.075	0.58432	D	0.999998	P;P	0.50272	0.933;0.933	B;B	0.42386	0.386;0.231	T	0.55042	-0.8202	10	0.87932	D	0	-8.4474	14.6301	0.68650	1.0:0.0:0.0:0.0	.	420;344	B3KST3;Q8NCQ5	.;FBX15_HUMAN	K	344;420	ENSP00000269500:I344K;ENSP00000393154:I420K	ENSP00000269500:I344K	I	-	2	0	FBXO15	69900146	0.710000	0.27896	0.988000	0.46212	0.890000	0.51754	6.256000	0.72473	1.907000	0.55213	0.533000	0.62120	ATA	.	.		0.279	FBXO15-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000444223.1	NM_152676		T	71749166	A	T	71749166	3	4	282	1	0	0	0	0	1	0	0	0	5736	449	16	4	281	4	FBXO15	18	71749166	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	5400911	71749166	6328082	1198	41432										
FAM69C	125704	hgsc.bcm.edu	37	chr18	72113977	72113977	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgatggccttggcctggccaCccccaggggcacctggggcc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:72113977delC	ENST00000343998.6	-	2	748	c.740delG	c.(739-741)ggtfs	p.G248fs	FAM69C_ENST00000400291.2_Intron	NM_001044369.2	NP_001037834.2	Q0P6D2	FA69C_HUMAN	family with sequence similarity 69, member C	248						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	transferase activity, transferring phosphorus-containing groups (GO:0016772)			breast(1)|large_intestine(2)|ovary(2)	5						GGCCTGGCCACCCCCAGGGGC	0.647																																					p.G247fs		Atlas-INDEL	.											.	FAM69C	45	.	0			c.741delT						.						92	88	90					18																	72113977		692	1591	2283	SO:0001589	frameshift_variant	125704	exon2			.	BC019628	CCDS42445.2	18q22.3	2012-08-03	2009-07-23	2009-07-23	ENSG00000187773	ENSG00000187773			31729	protein-coding gene	gene with protein product		614544	"chromosome 18 open reading frame 51"	C18orf51		21334309	Standard	NM_001044369		Approved		uc002llk.3	Q0P6D2	OTTHUMG00000156984	ENST00000343998.6:c.740delG	chr18.hg19:g.72113977delC	ENSP00000344331:p.Gly248fs	223.0	0.0		131.0	10.0	NM_001044369		Frame_Shift_Del	DEL	ENST00000343998.6	hg19	CCDS42445.2																																																																																			.	.		0.647	FAM69C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346971.2	XM_058931		-	72113977	C	-	72113977	7	5	282	1	0	1	0	1	0	0	0	0	5612	507	18	0	531	0	FAM69C	18	72113977	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	364811	72113977	5963271	1199	41433										
ZNF77	58492	hgsc.bcm.edu	37	chr19	2934192	2934192	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgcgtcctcacgtgatctctAaaggaggagtaacagctgaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:2934192delA	ENST00000314531.4	-	4	1025	c.933delT	c.(931-933)tttfs	p.F311fs		NM_021217.2	NP_067040.1	Q15935	ZNF77_HUMAN	zinc finger protein 77	311					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(5)|ovary(1)	17				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|GBM - Glioblastoma multiforme(1328;2.11e-07)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.174)|STAD - Stomach adenocarcinoma(1328;0.18)		CGTGATCTCTAAAGGAGGAGT	0.453																																					p.R312fs		Atlas-INDEL	.											.	ZNF77	47	.	0			c.934delA						.						177	159	166					19																	2934192		2203	4300	6503	SO:0001589	frameshift_variant	58492	exon4			.	X65230	CCDS12099.1	19p13.3	2013-01-08	2006-05-12					"Zinc fingers, C2H2-type", "-"	13150	protein-coding gene	gene with protein product		194551	"zinc finger protein 77 (pT1)"			8478004	Standard	NM_021217		Approved	pT1	uc002lws.4	Q15935		ENST00000314531.4:c.933delT	chr19.hg19:g.2934192delA	ENSP00000319053:p.Phe311fs	258.0	0.0		180.0	12.0	NM_021217	Q86XJ3|Q9NPP0	Frame_Shift_Del	DEL	ENST00000314531.4	hg19	CCDS12099.1																																																																																			.	.		0.453	ZNF77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451924.1	NM_021217		-	2934192	A	-	2934192	7	5	282	1	0	1	0	1	0	0	0	0	18157	359	13	0	708	0	ZNF77	19	2934192	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10		2934192	56194791	1200	41434										
ANKRD24	170961	hgsc.bcm.edu	37	chr19	4216608	4216608	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggaagctttggcagaggtcaTccctcttgccctctatgact	10	12	3	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:4216608T>C	ENST00000600132.1	+	18	1727	c.1451T>C	c.(1450-1452)aTc>aCc	p.I484T	ANKRD24_ENST00000262970.5_Missense_Mutation_p.I574T|ANKRD24_ENST00000318934.4_Missense_Mutation_p.I484T	NM_133475.1	NP_597732.1	Q8TF21	ANR24_HUMAN	ankyrin repeat domain 24	484										endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)	21				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0233)|STAD - Stomach adenocarcinoma(1328;0.181)		GCAGAGGTCATCCCTCTTGCC	0.602																																					p.I484T		Atlas-SNP	.											.	ANKRD24	180	.	0			c.T1451C						.						31	32	32					19																	4216608		2036	4182	6218	SO:0001583	missense	170961	exon18			AGGTCATCCCTCT	AB075861	CCDS45925.1	19p13.3	2013-01-10				ENSG00000089847		"Ankyrin repeat domain containing"	29424	protein-coding gene	gene with protein product						11853319	Standard	NM_133475		Approved	KIAA1981	uc010dtt.1	Q8TF21		ENST00000600132.1:c.1451T>C	chr19.hg19:g.4216608T>C	ENSP00000471252:p.Ile484Thr	143.0	0.0		114.0	5.0	NM_133475	O75268|O95781	Missense_Mutation	SNP	ENST00000600132.1	hg19	CCDS45925.1	.	.	.	.	.	.	.	.	.	.	t	14.32	2.500512	0.44455	.	.	ENSG00000089847	ENST00000318934;ENST00000262970	T;T	0.37584	1.25;1.19	4.6	4.6	0.57074	.	0.667324	0.11739	N	0.534234	T	0.26085	0.0636	N	0.19112	0.55	0.30152	N	0.802933	B;P	0.40731	0.421;0.728	B;B	0.39339	0.118;0.297	T	0.07028	-1.0794	10	0.33141	T	0.24	-13.4777	11.6628	0.51356	0.0:0.0:0.0:1.0	.	484;574	Q8TF21;Q8TF21-2	ANR24_HUMAN;.	T	484;574	ENSP00000321731:I484T;ENSP00000262970:I574T	ENSP00000262970:I574T	I	+	2	0	ANKRD24	4167608	1.000000	0.71417	0.991000	0.47740	0.403000	0.30841	3.567000	0.53813	1.854000	0.53819	0.260000	0.18958	ATC	.	.		0.602	ANKRD24-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458188.1	XM_114000		C	4216608	T	C	4216608	3	2	282	1	0	0	0	0	1	0	0	0	653	1435	50	2	1517	2	ANKRD24	19	4216608	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1282416	4216608	54912375	1201	41435										
SH3GL1	6455	hgsc.bcm.edu	37	chr19	4364123	4364123	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tttctcgcacaggttctggaGggggtcaatgaagttctgct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:4364123delG	ENST00000269886.3	-	5	605	c.427delC	c.(427-429)ctcfs	p.L143fs	AC007292.6_ENST00000594444.1_RNA|SH3GL1_ENST00000417295.2_Frame_Shift_Del_p.L95fs|SH3GL1_ENST00000598564.1_Intron	NM_003025.3	NP_003016.1	Q99961	SH3G1_HUMAN	SH3-domain GRB2-like 1	143	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				central nervous system development (GO:0007417)|endocytosis (GO:0006897)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|endosome (GO:0005768)|membrane (GO:0016020)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)			NS(1)|endometrium(2)|kidney(16)|large_intestine(3)|lung(2)|ovary(2)	26				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0152)|STAD - Stomach adenocarcinoma(1328;0.182)		AGGTTCTGGAGGGGGTCAATG	0.622			T	MLL	AL																																p.L143fs	NSCLC(94;1152 2133 30346 33362)	Atlas-INDEL	.		Dom	yes		19	19p13.3	6455	SH3-domain GRB2-like 1 (EEN)		L	.	SH3GL1	52	.	0			c.428delT						.						45	40	42					19																	4364123		2203	4300	6503	SO:0001589	frameshift_variant	6455	exon5			.		CCDS32874.1, CCDS56076.1, CCDS59335.1	19p13.3	2008-07-22							10830	protein-coding gene	gene with protein product	"extra 11-19 leukemia fusion", "fusion partner of MLL", "SH3-containing Grb-2-like 1 protein", "SH3-containing protein EEN", "SH3 domain GRB2-like 1"	601768				9169142	Standard	NM_003025		Approved	SH3P8, SH3D2B, CNSA1, EEN, MGC111371	uc002maj.3	Q99961		ENST00000269886.3:c.427delC	chr19.hg19:g.4364123delG	ENSP00000269886:p.Leu143fs	299.0	0.0		206.0	14.0	NM_003025	B4DRA1|E7EVZ4|M0QZV5|Q99668	Frame_Shift_Del	DEL	ENST00000269886.3	hg19	CCDS32874.1																																																																																			.	.		0.622	SH3GL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458302.1	NM_003025		-	4364123	G	-	4364123	7	5	282	1	0	1	0	1	0	0	0	0	14265	1000	35	0	703	0	SH3GL1	19	4364123	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	147515	4364123	54764860	1202	41436										
PLIN4	729359	hgsc.bcm.edu	37	chr19	4512723	4512723	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gttcagcccagtttgcatggCccccttggccacattcgctg					rs560523069	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:4512723delC	ENST00000301286.3	-	3	1206	c.1207delG	c.(1207-1209)gccfs	p.A403fs		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	403	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						GTTTGCATGGCCCCCTTGGCC	0.567																																					p.A403fs		Atlas-INDEL	.											.	PLIN4	191	.	0			c.1208delC						.						74	104	95					19																	4512723		1570	4153	5723	SO:0001589	frameshift_variant	729359	exon3			.	AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"Perilipins"	29393	protein-coding gene	gene with protein product		613247	"KIAA1881"	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.1207delG	chr19.hg19:g.4512723delC	ENSP00000301286:p.Ala403fs	334.0	0.0		228.0	14.0	NM_001080400	A6NEI2	Frame_Shift_Del	DEL	ENST00000301286.3	hg19	CCDS45927.1																																																																																			.	.		0.567	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901		-	4512723	C	-	4512723	7	5	282	1	0	1	0	1	0	0	0	0	12101	739	26	0	2882	0	PLIN4	19	4512723	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	148600	4512723	54616260	1203	41437										
PLIN3	10226	hgsc.bcm.edu	37	chr19	4839252	4839252	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtgattccaggggcaaagggTcccacgagccacgtgacagg	15	11	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:4839252T>C	ENST00000221957.4	-	8	1433	c.1257A>G	c.(1255-1257)ggA>ggG	p.G419G	PLIN3_ENST00000585479.1_Silent_p.G418G|PLIN3_ENST00000592528.1_Silent_p.G407G|CTC-518P12.6_ENST00000591657.1_RNA	NM_001164189.1|NM_001164194.1|NM_005817.4	NP_001157661.1|NP_001157666.1|NP_005808.3	O60664	PLIN3_HUMAN	perilipin 3	419					vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|membrane (GO:0016020)				cervix(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	9					Galsulfase(DB01279)|Idursulfase(DB01271)	GGGCAAAGGGTCCCACGAGCC	0.622																																					p.G419G		Atlas-SNP	.											.	PLIN3	36	.	0			c.A1257G						.						66	72	69					19																	4839252		2203	4300	6503	SO:0001819	synonymous_variant	10226	exon8			AAAGGGTCCCACG	AF051314	CCDS12137.1, CCDS59337.1, CCDS59338.1	19p13.3	2009-08-12	2009-08-12	2009-08-12		ENSG00000105355		"Perilipins"	16893	protein-coding gene	gene with protein product	"cargo selection protein (mannose 6 phosphate receptor binding protein)", "placental protein 17", "MPR-BINDING PROTEIN, 47-KD"	602702	"mannose-6-phosphate receptor binding protein 1"	M6PRBP1		9590177, 6856484, 19638644	Standard	NM_005817		Approved	TIP47, PP17	uc002mbj.2	O60664		ENST00000221957.4:c.1257A>G	chr19.hg19:g.4839252T>C		206.0	0.0		115.0	7.0	NM_005817	A8K4Y9|K7EQF4|Q53G77|Q9BS03|Q9UBD7|Q9UP92	Silent	SNP	ENST00000221957.4	hg19	CCDS12137.1																																																																																			.	.		0.622	PLIN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450436.1	NM_005817		C	4839252	T	C	4839252	2	2	282	1	0	0	0	0	0	0	0	1	12100	1654	58	2		2	PLIN3	19	4839252	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	326529	4839252	54289731	1204	41438										
PRR22	163154	hgsc.bcm.edu	37	chr19	5783634	5783634	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tggaggtggctgtaggcgtcTgggggcagtgtgggctctgc					rs2446210	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:5783634delT	ENST00000419421.2	-	3	728	c.624delA	c.(622-624)ccafs	p.P208fs		NM_001134316.1	NP_001127788.1	Q8IZ63	PRR22_HUMAN	proline rich 22	208	Pro-rich.									endometrium(2)|large_intestine(1)|prostate(1)|urinary_tract(1)	5						TGTAGGCGTCTGGGGGCAGTG	0.706																																					p.D209fs		Atlas-INDEL	.											.	PRR22	25	.	0			c.625delG						.						13	16	15					19																	5783634		2189	4293	6482	SO:0001589	frameshift_variant	163154	exon3			.	BC023278	CCDS45933.1	19p13.3	2012-12-20			ENSG00000212123	ENSG00000212123			28354	protein-coding gene	gene with protein product						12477932	Standard	NM_001134316		Approved	MGC24975	uc010xiv.1	Q8IZ63	OTTHUMG00000180553	ENST00000419421.2:c.624delA	chr19.hg19:g.5783634delT	ENSP00000407653:p.Pro208fs	263.0	0.0		182.0	11.0	NM_001134316	E9PB31	Frame_Shift_Del	DEL	ENST00000419421.2	hg19	CCDS45933.1																																																																																			.	.		0.706	PRR22-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368523.1	NM_153359		-	5783634	T	-	5783634	7	5	282	1	0	1	0	1	0	0	0	0	12605	1567	55	0	648	0	PRR22	19	5783634	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	944382	5783634	53345349	1205	41439										
SLC25A23	79085	hgsc.bcm.edu	37	chr19	6454721	6454721	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctgtcaggcactcgccaatgTccaggacctaaagatacagg	10	12	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:6454721T>C	ENST00000301454.4	-	5	597	c.491A>G	c.(490-492)gAc>gGc	p.D164G	SLC25A23_ENST00000334510.5_Missense_Mutation_p.D164G|SLC25A23_ENST00000414491.2_5'Flank	NM_024103.2	NP_077008.2	Q9BV35	SCMC3_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 23	164					adenine nucleotide transport (GO:0051503)|cellular response to calcium ion (GO:0071277)|regulation of cellular respiration (GO:0043457)|regulation of oxidative phosphorylation (GO:0002082)|regulation of sequestering of calcium ion (GO:0051282)|transmembrane transport (GO:0055085)|urea homeostasis (GO:0097274)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)			endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|pancreas(1)|skin(1)	17						CTCGCCAATGTCCAGGACCTA	0.567																																					p.D164G		Atlas-SNP	.											.	SLC25A23	43	.	0			c.A491G						.						49	44	46					19																	6454721		2203	4300	6503	SO:0001583	missense	79085	exon5			CCAATGTCCAGGA	AJ619962	CCDS32882.1	19p13.1	2014-02-06			ENSG00000125648	ENSG00000125648		"Solute carriers", "EF-hand domain containing"	19375	protein-coding gene	gene with protein product		608746				15123600	Standard	NM_024103		Approved	FLJ30339, MGC2615, APC2	uc002mex.1	Q9BV35	OTTHUMG00000180852	ENST00000301454.4:c.491A>G	chr19.hg19:g.6454721T>C	ENSP00000301454:p.Asp164Gly	109.0	0.0		80.0	4.0	NM_024103	B4DGB6|Q4LBC2|Q705K3|Q86Y43|Q8N2N4|Q96NQ4	Missense_Mutation	SNP	ENST00000301454.4	hg19	CCDS32882.1	.	.	.	.	.	.	.	.	.	.	T	19.87	3.908212	0.72868	.	.	ENSG00000125648	ENST00000264088;ENST00000301454;ENST00000334510	T;T;T	0.81330	-1.48;-1.34;-1.21	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	D	0.90988	0.7166	M	0.88906	2.99	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.92586	0.6079	10	0.87932	D	0	-44.7766	15.1042	0.72306	0.0:0.0:0.0:1.0	.	164	Q9BV35	SCMC3_HUMAN	G	211;164;164	ENSP00000264088:D211G;ENSP00000301454:D164G;ENSP00000334537:D164G	ENSP00000264088:D211G	D	-	2	0	SLC25A23	6405721	1.000000	0.71417	1.000000	0.80357	0.458000	0.32498	7.671000	0.83941	2.217000	0.71921	0.533000	0.62120	GAC	.	.		0.567	SLC25A23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453325.1	NM_024103		C	6454721	T	C	6454721	3	2	282	1	0	0	0	0	1	0	0	0	14501	1667	58	2	939	2	SLC25A23	19	6454721	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	671087	6454721	52674262	1206	41440										
SLC25A23	79085	hgsc.bcm.edu	37	chr19	6456486	6456486	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cattttccagcgaatgcaacAggaagtggtcgcgccattct	10	11	1	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:6456486A>G	ENST00000301454.4	-	4	534	c.428T>C	c.(427-429)cTg>cCg	p.L143P	SLC25A23_ENST00000334510.5_Missense_Mutation_p.L143P|SLC25A23_ENST00000414491.2_5'Flank	NM_024103.2	NP_077008.2	Q9BV35	SCMC3_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 23	143	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				adenine nucleotide transport (GO:0051503)|cellular response to calcium ion (GO:0071277)|regulation of cellular respiration (GO:0043457)|regulation of oxidative phosphorylation (GO:0002082)|regulation of sequestering of calcium ion (GO:0051282)|transmembrane transport (GO:0055085)|urea homeostasis (GO:0097274)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)			endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|pancreas(1)|skin(1)	17						CGAATGCAACAGGAAGTGGTC	0.577																																					p.L143P		Atlas-SNP	.											.	SLC25A23	43	.	0			c.T428C						.						168	126	140					19																	6456486		2203	4300	6503	SO:0001583	missense	79085	exon4			TGCAACAGGAAGT	AJ619962	CCDS32882.1	19p13.1	2014-02-06			ENSG00000125648	ENSG00000125648		"Solute carriers", "EF-hand domain containing"	19375	protein-coding gene	gene with protein product		608746				15123600	Standard	NM_024103		Approved	FLJ30339, MGC2615, APC2	uc002mex.1	Q9BV35	OTTHUMG00000180852	ENST00000301454.4:c.428T>C	chr19.hg19:g.6456486A>G	ENSP00000301454:p.Leu143Pro	136.0	0.0		122.0	5.0	NM_024103	B4DGB6|Q4LBC2|Q705K3|Q86Y43|Q8N2N4|Q96NQ4	Missense_Mutation	SNP	ENST00000301454.4	hg19	CCDS32882.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.349068	0.82132	.	.	ENSG00000125648	ENST00000264088;ENST00000301454;ENST00000334510	T;T;T	0.41400	1.0;1.0;1.0	4.86	4.86	0.63082	EF-hand-like domain (1);	0.000000	0.64402	D	0.000002	T	0.65698	0.2716	M	0.84082	2.675	0.80722	D	1	D	0.89917	1.0	D	0.70935	0.971	T	0.71938	-0.4441	10	0.87932	D	0	-14.342	13.4103	0.60938	1.0:0.0:0.0:0.0	.	143	Q9BV35	SCMC3_HUMAN	P	143	ENSP00000264088:L143P;ENSP00000301454:L143P;ENSP00000334537:L143P	ENSP00000264088:L143P	L	-	2	0	SLC25A23	6407486	1.000000	0.71417	0.995000	0.50966	0.988000	0.76386	8.812000	0.91959	1.824000	0.53156	0.402000	0.26972	CTG	.	.		0.577	SLC25A23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453325.1	NM_024103		G	6456486	A	G	6456486	3	3	282	1	0	0	0	0	1	0	0	0	14501	188	7	2	1006	2	SLC25A23	19	6456486	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1765	6456486	52672497	1207	41441										
TIMM44	10469	hgsc.bcm.edu	37	chr19	8002975	8002975	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cttctggcctcgtcacggaaTttttttatactttctttcat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:8002975delT	ENST00000270538.3	-	3	517	c.249delA	c.(247-249)aaafs	p.K83fs		NM_006351.3	NP_006342.2	O43615	TIM44_HUMAN	translocase of inner mitochondrial membrane 44 homolog (yeast)	83					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|P-P-bond-hydrolysis-driven protein transmembrane transporter activity (GO:0015450)			NS(1)|endometrium(3)|kidney(3)|large_intestine(2)|liver(2)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	17						CGTCACGGAATTTTTTTATAC	0.413																																					p.F84fs		Atlas-INDEL	.											.	TIMM44	47	.	0			c.250delT						.						243	241	242					19																	8002975		2203	4300	6503	SO:0001589	frameshift_variant	10469	exon3			.	AF026030	CCDS12192.1	19p13.3-p13.2	2008-07-04				ENSG00000104980			17316	protein-coding gene	gene with protein product		605058				10848612, 10339406	Standard	NM_006351		Approved	TIM44	uc002miz.3	O43615		ENST00000270538.3:c.249delA	chr19.hg19:g.8002975delT	ENSP00000270538:p.Lys83fs	204.0	0.0		191.0	13.0	NM_006351	A8K0R9|D6W664|Q8N193	Frame_Shift_Del	DEL	ENST00000270538.3	hg19	CCDS12192.1																																																																																			.	.		0.413	TIMM44-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461596.3			-	8002975	T	-	8002975	7	5	282	1	0	1	0	1	0	0	0	0	15927	1490	52	0	1153	0	TIMM44	19	8002975	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1546489	8002975	51126008	1208	41442										
HNRNPM	4670	hgsc.bcm.edu	37	chr19	8533662	8533662	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tttctttctctttcaggatgAgagggccttaccaaaaggag	10	8	3	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:8533662A>G	ENST00000325495.4	+	9	880	c.839A>G	c.(838-840)gAg>gGg	p.E280G	HNRNPM_ENST00000348943.3_Missense_Mutation_p.E241G	NM_005968.4	NP_005959.2	P52272	HNRPM_HUMAN	heterogeneous nuclear ribonucleoprotein M	280	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|RNA binding (GO:0003723)			endometrium(5)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)	25						TTTCAGGATGAGAGGGCCTTA	0.458																																					p.E280G		Atlas-SNP	.											.	HNRNPM	61	.	0			c.A839G						.						79	69	72					19																	8533662		2203	4300	6503	SO:0001583	missense	4670	exon9			AGGATGAGAGGGC	L03532	CCDS12203.1, CCDS12204.1	19p13.2	2013-06-12		2008-04-18	ENSG00000099783	ENSG00000099783		"RNA binding motif (RRM) containing"	5046	protein-coding gene	gene with protein product	"CEA receptor"	160994		NAGR1, HNRPM		8441656, 7558047	Standard	NM_005968		Approved	HTGR1, HNRNPM4, HNRPM4, CEAR	uc010dwe.3	P52272	OTTHUMG00000182383	ENST00000325495.4:c.839A>G	chr19.hg19:g.8533662A>G	ENSP00000325376:p.Glu280Gly	49.0	0.0		48.0	4.0	NM_005968	Q15584|Q8WZ44|Q96H56|Q9BWL9|Q9Y492	Missense_Mutation	SNP	ENST00000325495.4	hg19	CCDS12203.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.121480	0.77436	.	.	ENSG00000099783	ENST00000325495;ENST00000348943;ENST00000544159	T;T	0.36157	1.27;2.71	5.61	5.61	0.85477	RNA recognition motif domain (1);	0.095738	0.64402	D	0.000001	T	0.42877	0.1222	L	0.42245	1.32	0.80722	D	1	B;B;P;B;B	0.48911	0.139;0.047;0.917;0.32;0.067	B;B;P;B;B	0.50405	0.171;0.046;0.64;0.086;0.119	T	0.37663	-0.9696	10	0.72032	D	0.01	.	14.676	0.68981	1.0:0.0:0.0:0.0	.	120;280;241;241;180	Q7KYM9;P52272;P52272-2;B4DEG4;Q59ES8	.;HNRPM_HUMAN;.;.;.	G	280;241;180	ENSP00000325376:E280G;ENSP00000325732:E241G	ENSP00000325376:E280G	E	+	2	0	HNRNPM	8439662	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	8.429000	0.90280	2.144000	0.66660	0.529000	0.55759	GAG	.	.		0.458	HNRNPM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460894.1			G	8533662	A	G	8533662	3	3	282	1	0	0	0	0	1	0	0	0	7280	304	11	2	873	2	HNRNPM	19	8533662	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	530687	8533662	50595321	1209	41443										
PRAM1	84106	hgsc.bcm.edu	37	chr19	8564429	8564429	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcttcttggggaggtcagtgAcctcaggcggcgggggcttc	18	10	3	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:8564429A>G	ENST00000423345.4	-	2	783	c.263T>C	c.(262-264)gTc>gCc	p.V88A	PRAM1_ENST00000255612.3_Missense_Mutation_p.V88A			Q96QH2	PRAM_HUMAN	PML-RARA regulated adaptor molecule 1	136	8 X 12 AA repeats of K-P-P-[PQ]-P-[EQ]- [VAF]-T-D-L-P-K.|Pro-rich.				integrin-mediated signaling pathway (GO:0007229)|regulation of neutrophil degranulation (GO:0043313)		lipid binding (GO:0008289)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(1)	19						GAGGTCAGTGACCTCAGGCGG	0.667																																					p.V88A		Atlas-SNP	.											.	PRAM1	53	.	0			c.T263C						.						14	17	16					19																	8564429		1151	2895	4046	SO:0001583	missense	84106	exon2			TCAGTGACCTCAG	BC028012	CCDS45954.1, CCDS45954.2	19p13.2	2009-01-21				ENSG00000133246			30091	protein-coding gene	gene with protein product		606466				11301322, 15572693	Standard	NM_032152		Approved	PML-RAR	uc002mkd.3	Q96QH2		ENST00000423345.4:c.263T>C	chr19.hg19:g.8564429A>G	ENSP00000408342:p.Val88Ala	67.0	0.0		57.0	6.0	NM_032152	Q8N6W7	Missense_Mutation	SNP	ENST00000423345.4	hg19	CCDS45954.2	.	.	.	.	.	.	.	.	.	.	A	0.892	-0.725077	0.03158	.	.	ENSG00000133246	ENST00000255612;ENST00000423345	T;T	0.16196	2.36;2.36	3.38	2.36	0.29203	.	0.680970	0.12143	N	0.495622	T	0.08891	0.0220	N	0.14661	0.345	0.09310	N	1	B;B	0.12013	0.005;0.004	B;B	0.12156	0.005;0.007	T	0.39663	-0.9603	10	0.18276	T	0.48	.	6.9376	0.24474	0.8825:0.0:0.1175:0.0	.	88;136	Q96QH2-2;Q96QH2	.;PRAM_HUMAN	A	88	ENSP00000255612:V88A;ENSP00000408342:V88A	ENSP00000255612:V88A	V	-	2	0	PRAM1	8470429	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	0.198000	0.17217	0.673000	0.31224	0.478000	0.44815	GTC	.	.		0.667	PRAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397040.3	NM_032152		G	8564429	A	G	8564429	3	3	282	1	0	0	0	0	1	0	0	0	12435	275	10	2	1782	2	PRAM1	19	8564429	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	30767	8564429	50564554	1210	41444										
MBD3L1	85509	hgsc.bcm.edu	37	chr19	8953814	8953814	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttctggttactgaggaagatAtcaggaaacaggaagggaaa	13	4	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:8953814A>G	ENST00000595891.1	+	3	691	c.460A>G	c.(460-462)Atc>Gtc	p.I154V	MBD3L1_ENST00000305625.2_Missense_Mutation_p.I154V			Q8WWY6	MB3L1_HUMAN	methyl-CpG binding domain protein 3-like 1	154					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|large_intestine(5)|liver(1)|lung(2)|skin(2)	12						TGAGGAAGATATCAGGAAACA	0.498																																					p.I154V		Atlas-SNP	.											.	MBD3L1	24	.	0			c.A460G						.						42	38	39					19																	8953814		2203	4300	6503	SO:0001583	missense	85509	exon1			GAAGATATCAGGA	AY038022	CCDS12209.1	19p13.2	2011-01-31	2003-03-19	2003-03-21	ENSG00000170948	ENSG00000170948			15774	protein-coding gene	gene with protein product		607963	"methyl-CpG binding domain protein 3-like"	MBD3L		12504854	Standard	NM_145208		Approved		uc002mko.2	Q8WWY6		ENST00000595891.1:c.460A>G	chr19.hg19:g.8953814A>G	ENSP00000471575:p.Ile154Val	132.0	0.0		93.0	4.0	NM_145208	B5BUM6|Q2M291	Missense_Mutation	SNP	ENST00000595891.1	hg19	CCDS12209.1	.	.	.	.	.	.	.	.	.	.	A	13.89	2.371245	0.42003	.	.	ENSG00000170948	ENST00000305625	T	0.62232	0.04	3.92	2.9	0.33743	.	0.139066	0.29369	N	0.012359	T	0.61451	0.2348	M	0.83384	2.64	0.47994	D	0.999562	P	0.42735	0.788	B	0.41202	0.35	T	0.61686	-0.7012	10	0.49607	T	0.09	-5.6283	6.1829	0.20482	0.8854:0.0:0.1146:0.0	.	154	Q8WWY6	MB3L1_HUMAN	V	154	ENSP00000304198:I154V	ENSP00000304198:I154V	I	+	1	0	MBD3L1	8814814	1.000000	0.71417	0.950000	0.38849	0.533000	0.34776	3.640000	0.54350	0.840000	0.34995	0.533000	0.62120	ATC	.	.		0.498	MBD3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459973.1	NM_145208		G	8953814	A	G	8953814	3	3	282	1	0	0	0	0	1	0	0	0	9354	449	16	2	462	2	MBD3L1	19	8953814	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	389385	8953814	50175169	1211	41445										
MUC16	94025	hgsc.bcm.edu	37	chr19	9024995	9024995	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtggctgccccatctttctcGggcctggggagggtcagtgg	17	11	3	0	rs375977247		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:9024995G>T	ENST00000397910.4	-	16	37070	c.36867C>A	c.(36865-36867)ccC>ccA	p.P12289P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12291	SEA 2. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.P12289P(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CATCTTTCTCGGGCCTGGGGA	0.542																																					p.P12289P		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,0,1	MUC16	4315	.	1	Substitution - coding silent(1)	lung(1)	c.C36867A						.						56	53	54					19																	9024995		1856	4101	5957	SO:0001819	synonymous_variant	94025	exon16			TTTCTCGGGCCTG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.36867C>A	chr19.hg19:g.9024995G>T		173.0	2.0		138.0	0.0	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.542	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9024995	G	T	9024995	2	4	282	1	0	0	0	0	0	0	0	1	9982	1103	39	1		1	MUC16	19	9024995	Silent	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	71181	9024995	50103988	1212	41446										
ILF3	3609	hgsc.bcm.edu	37	chr19	10798146	10798146	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tacaactcaccggtgcccccAaaacacgctgggaagaagca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:10798146delA	ENST00000590261.1	+	17	2184	c.2184delA	c.(2182-2184)ccafs	p.P728fs	ILF3_ENST00000449870.1_Frame_Shift_Del_p.P732fs|ILF3_ENST00000318511.3_Frame_Shift_Del_p.P728fs|ILF3_ENST00000588657.1_Frame_Shift_Del_p.P732fs			Q12906	ILF3_HUMAN	interleukin enhancer binding factor 3, 90kDa	728	Interaction with PRMT1.				defense response to virus (GO:0051607)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|negative regulation of viral genome replication (GO:0045071)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31			Epithelial(33;6.86e-06)|all cancers(31;1.65e-05)			CGGTGCCCCCAAAACACGCTG	0.647																																					p.P732fs		Atlas-INDEL	.											.	ILF3	99	.	0			c.2195delC						.						32	31	32					19																	10798146		2203	4299	6502	SO:0001589	frameshift_variant	3609	exon18			.	U10324	CCDS12246.1, CCDS12247.1, CCDS45965.1, CCDS45966.1, CCDS45967.1	19p13.2	2012-08-10	2002-08-29		ENSG00000129351	ENSG00000129351			6038	protein-coding gene	gene with protein product	"M-phase phosphoprotein 4"	603182	"interleukin enhancer binding factor 3, 90kD"			7519613, 8885239	Standard	NM_012218		Approved	NF90, MPHOSPH4, MPP4, DRBP76, NFAR-1	uc002mpo.3	Q12906		ENST00000590261.1:c.2184delA	chr19.hg19:g.10798146delA	ENSP00000468156:p.Pro728fs	182.0	0.0		146.0	11.0	NM_017620	A8K6F2|G5E9M5|O43409|Q6P1X1|Q86XY7|Q99544|Q99545|Q9BZH4|Q9BZH5|Q9NQ95|Q9NQ96|Q9NQ97|Q9NQ98|Q9NQ99|Q9NQA0|Q9NQA1|Q9NQA2|Q9NRN2|Q9NRN3|Q9NRN4|Q9UMZ9|Q9UN00|Q9UN84|Q9UNA2	Frame_Shift_Del	DEL	ENST00000590261.1	hg19	CCDS12246.1																																																																																			.	.		0.647	ILF3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452074.1			-	10798146	A	-	10798146	7	5	282	1	0	1	0	1	0	0	0	0	7721	117	5	0	2334	0	ILF3	19	10798146	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1773151	10798146	48330837	1213	41447										
DOCK6	57572	hgsc.bcm.edu	37	chr19	11363499	11363499	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctccgtggtccggcattcccGgggctgcagcagcagctcca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:11363499delG	ENST00000294618.7	-	3	279	c.268delC	c.(268-270)cggfs	p.R90fs		NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	90					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(8)|liver(2)|lung(9)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	39						CGGCATTCCCGGGGCTGCAGC	0.632																																					p.R90fs		Atlas-INDEL	.											.	DOCK6	104	.	0			c.269delG						.						24	27	26					19																	11363499		1891	4110	6001	SO:0001589	frameshift_variant	57572	exon3			.		CCDS45975.1	19p13.2	2011-08-04			ENSG00000130158	ENSG00000130158			19189	protein-coding gene	gene with protein product		614194				12432077	Standard	NM_020812		Approved	KIAA1395, ZIR1	uc002mqs.5	Q96HP0		ENST00000294618.7:c.268delC	chr19.hg19:g.11363499delG	ENSP00000294618:p.Arg90fs	231.0	0.0		165.0	11.0	NM_020812	A6H8X5|Q7Z7P4|Q9P2F2	Frame_Shift_Del	DEL	ENST00000294618.7	hg19	CCDS45975.1																																																																																			.	.		0.632	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812		-	11363499	G	-	11363499	7	5	282	1	0	1	0	1	0	0	0	0	4693	1115	39	0	6059	0	DOCK6	19	11363499	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	565353	11363499	47765484	1214	41448										
LPPR2	64748	hgsc.bcm.edu	37	chr19	11470601	11470601	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggggcctgctgccgcttcagCcccccagtgcggaggctggt					rs201978882		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:11470601delC	ENST00000251473.5	+	5	736	c.360delC	c.(358-360)agcfs	p.S120fs	DKFZP761J1410_ENST00000591608.1_Frame_Shift_Del_p.S95fs	NM_001170635.1|NM_022737.2	NP_001164106.1|NP_073574.2																					GCCGCTTCAGCCCCCCAGTGC	0.627																																					p.S120fs		Atlas-INDEL	.											.	LPPR2	21	.	0			c.359delG						.						34	35	35					19																	11470601		2203	4300	6503	SO:0001589	frameshift_variant	0	exon5			.																												ENST00000251473.5:c.360delC	chr19.hg19:g.11470601delC	ENSP00000251473:p.Ser120fs	173.0	0.0		123.0	10.0	NM_022737		Frame_Shift_Del	DEL	ENST00000251473.5	hg19	CCDS12258.1																																																																																			.	.		0.627	DKFZP761J1410-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458779.1			-	11470601	C	-	11470601	7	5	282	1	0	1	0	1	0	0	0	0	8934	738	26	0	370	0	LPPR2	19	11470601	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	107102	11470601	47658382	1215	41449										
ZNF439	90594	hgsc.bcm.edu	37	chr19	11977010	11977010	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atcctcctctacacatgtgaGatgtttcaggacccagtggc	9	12	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:11977010G>A	ENST00000304030.2	+	1	239	c.39G>A	c.(37-39)gaG>gaA	p.E13E	ZNF439_ENST00000592534.1_Intron|ZNF439_ENST00000455282.1_Intron	NM_152262.2	NP_689475.1	Q8NDP4	ZN439_HUMAN	zinc finger protein 439	13					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(7)|pancreas(1)|skin(2)	27						ACACATGTGAGATGTTTCAGG	0.493																																					p.E13E		Atlas-SNP	.											.	ZNF439	67	.	0			c.G39A						.						133	132	132					19																	11977010		2203	4300	6503	SO:0001819	synonymous_variant	90594	exon1			ATGTGAGATGTTT	AL833935	CCDS12268.1	19p13.13	2013-01-08			ENSG00000171291	ENSG00000171291		"Zinc fingers, C2H2-type", "-"	20873	protein-coding gene	gene with protein product							Standard	NM_152262		Approved	DKFZp571K0837	uc002mss.3	Q8NDP4	OTTHUMG00000156527	ENST00000304030.2:c.39G>A	chr19.hg19:g.11977010G>A		133.0	0.0		87.0	5.0	NM_152262	Q8IYZ7|Q96SU1	Silent	SNP	ENST00000304030.2	hg19	CCDS12268.1																																																																																			.	.		0.493	ZNF439-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344513.1			A	11977010	G	A	11977010	2	1	282	1	0	0	0	0	0	0	0	1	17926	933	33	3		3	ZNF439	19	11977010	Silent	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	506409	11977010	47151973	1216	41450										
CC2D1A	54862	hgsc.bcm.edu	37	chr19	14024365	14024365	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggcccctagaatcgcgtcagCcccagagcccagggtcaccc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:14024365delC	ENST00000318003.7	+	6	903	c.662delC	c.(661-663)gccfs	p.A221fs	CC2D1A_ENST00000589606.1_Frame_Shift_Del_p.A221fs	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	221	Pro-rich.				positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	27			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)			ATCGCGTCAGCCCCAGAGCCC	0.677																																					p.A221fs		Atlas-INDEL	.											.	CC2D1A	67	.	0			c.661delG						.						30	38	35					19																	14024365		1964	4121	6085	SO:0001589	frameshift_variant	54862	exon6			.	AF536205	CCDS42512.1	19p13.12	2007-01-08				ENSG00000132024			30237	protein-coding gene	gene with protein product	"mental retardation, nonsyndromic, autosomal recessive, 3"	610055				12761501, 16033914	Standard	NM_017721		Approved	FLJ20241, MRT3	uc002mxo.2	Q6P1N0		ENST00000318003.7:c.662delC	chr19.hg19:g.14024365delC	ENSP00000313601:p.Ala221fs	217.0	0.0		155.0	10.0	NM_017721	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Frame_Shift_Del	DEL	ENST00000318003.7	hg19	CCDS42512.1																																																																																			.	.		0.677	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721		-	14024365	C	-	14024365	7	5	282	1	0	1	0	1	0	0	0	0	2728	739	26	0	684	0	CC2D1A	19	14024365	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	2047355	14024365	45104618	1217	41451										
CC2D1A	54862	hgsc.bcm.edu	37	chr19	14031457	14031457	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagccccaacagccaaagcgCcccccaaagccacatccacc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:14031457delC	ENST00000318003.7	+	13	1685	c.1444delC	c.(1444-1446)cccfs	p.P483fs	CC2D1A_ENST00000589606.1_Frame_Shift_Del_p.P483fs	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	483					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	27			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)			AGCCAAAGCGCCCCCCAAAGC	0.647																																					p.A481fs		Atlas-INDEL	.											CC2D1A,colon,carcinoma,0,1	CC2D1A	67	.	0			c.1443delG						.						41	55	50					19																	14031457		1912	4119	6031	SO:0001589	frameshift_variant	54862	exon13			.	AF536205	CCDS42512.1	19p13.12	2007-01-08				ENSG00000132024			30237	protein-coding gene	gene with protein product	"mental retardation, nonsyndromic, autosomal recessive, 3"	610055				12761501, 16033914	Standard	NM_017721		Approved	FLJ20241, MRT3	uc002mxo.2	Q6P1N0		ENST00000318003.7:c.1444delC	chr19.hg19:g.14031457delC	ENSP00000313601:p.Pro483fs	209.0	0.0		182.0	11.0	NM_017721	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Frame_Shift_Del	DEL	ENST00000318003.7	hg19	CCDS42512.1																																																																																			.	.		0.647	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721		-	14031457	C	-	14031457	7	5	282	1	0	1	0	1	0	0	0	0	2728	739	26	0	1494	0	CC2D1A	19	14031457	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	7092	14031457	45097526	1218	41452										
IL27RA	9466	hgsc.bcm.edu	37	chr19	14150617	14150617	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtggacttttccgaggatgaCcccctggaggccactgtcca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:14150617delC	ENST00000263379.2	+	4	554	c.429delC	c.(427-429)gacfs	p.D143fs		NM_004843.3	NP_004834.1	Q6UWB1	I27RA_HUMAN	interleukin 27 receptor, alpha	143	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T-helper 1 type immune response (GO:0002827)|regulation of isotype switching to IgG isotypes (GO:0048302)	integral component of plasma membrane (GO:0005887)	interleukin-27 receptor activity (GO:0045509)|transmembrane signaling receptor activity (GO:0004888)			breast(3)|endometrium(3)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	26						CCGAGGATGACCCCCTGGAGG	0.602																																					p.D143fs	Colon(164;1849 1896 4443 37792 47834)	Atlas-INDEL	.											.	IL27RA	56	.	0			c.428delA						.						66	68	67					19																	14150617		2203	4300	6503	SO:0001589	frameshift_variant	9466	exon4			.	AF053004	CCDS12303.1	19p13.11	2013-02-11				ENSG00000104998		"Interleukins and interleukin receptors", "Fibronectin type III domain containing"	17290	protein-coding gene	gene with protein product	"T-cell cytokine receptor type 1"	605350				9600072, 11057672	Standard	NM_004843		Approved	WSX-1, TCCR, CRL1, WSX1, zcytor1, IL-27R	uc002mxx.4	Q6UWB1		ENST00000263379.2:c.429delC	chr19.hg19:g.14150617delC	ENSP00000263379:p.Asp143fs	221.0	0.0		152.0	10.0	NM_004843	A0N0L1|O60624	Frame_Shift_Del	DEL	ENST00000263379.2	hg19	CCDS12303.1																																																																																			.	.		0.602	IL27RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458539.1	NM_004843		-	14150617	C	-	14150617	7	5	282	1	0	1	0	1	0	0	0	0	7690	506	18	0	443	0	IL27RA	19	14150617	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	119160	14150617	44978366	1219	41453										
CD97	976	hgsc.bcm.edu	37	chr19	14508727	14508727	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctttctccacctggaccccgCcccctggagtccacagccag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:14508727delC	ENST00000242786.5	+	8	879	c.799delC	c.(799-801)cccfs	p.P268fs	CD97_ENST00000358600.3_Frame_Shift_Del_p.P175fs|CD97_ENST00000357355.3_Frame_Shift_Del_p.P219fs	NM_078481.3	NP_510966.1	P48960	CD97_HUMAN	CD97 molecule	268					cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						CTGGACCCCGCCCCCTGGAGT	0.607																																					p.P266fs		Atlas-INDEL	.											.	CD97	86	.	0			c.798delG						.						6	9	8					19																	14508727		1874	3927	5801	SO:0001589	frameshift_variant	976	exon8			.		CCDS32929.1, CCDS32930.1, CCDS32931.1	19p13	2014-08-08	2006-03-28			ENSG00000123146		"CD molecules", "-", "GPCR / Class B : Orphans"	1711	protein-coding gene	gene with protein product	"leukocyte antigen CD97", "seven-span transmembrane protein", "seven-transmembrane, heterodimeric receptor associated with inflammation", "seven transmembrane helix receptor"	601211	"CD97 antigen"			7636245, 8786105	Standard	NM_078481		Approved	TM7LN1	uc002myl.3	P48960		ENST00000242786.5:c.799delC	chr19.hg19:g.14508727delC	ENSP00000242786:p.Pro268fs	183.0	0.0		170.0	12.0	NM_078481	A8K7Z4|B2RBJ9|O00718|O76101|Q8NG72|Q8TBQ7	Frame_Shift_Del	DEL	ENST00000242786.5	hg19	CCDS32929.1																																																																																			.	.		0.607	CD97-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459821.2	NM_078481		-	14508727	C	-	14508727	7	5	282	1	0	1	0	1	0	0	0	0	3051	739	26	0	829	0	CD97	19	14508727	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	358110	14508727	44620256	1220	41454										
BRD4	23476	hgsc.bcm.edu	37	chr19	15349696	15349696	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gctgttgctgctgctgctgtTgctcctggcgctgctgctgc	14	13	0	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:15349696T>C	ENST00000263377.2	-	19	4099	c.3878A>G	c.(3877-3879)cAa>cGa	p.Q1293R	AC004257.3_ENST00000602793.1_lincRNA	NM_058243.2	NP_490597.1	O60885	BRD4_HUMAN	bromodomain containing 4	1293	C-terminal (CTD) region.|Poly-Gln.				cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|chromosome segregation (GO:0007059)|histone H3-K14 acetylation (GO:0044154)|histone H4-K12 acetylation (GO:0043983)|inner cell mass cell proliferation (GO:0001833)|negative regulation of DNA damage checkpoint (GO:2000002)|positive regulation of DNA binding (GO:0043388)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of phosphorylation of RNA polymerase II C-terminal domain (GO:1901407)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18)			ctgctgctgttgctcctggcg	0.711			T	C15orf55	lethal midline carcinoma of young people																																p.Q1293R		Atlas-SNP	.		Dom	yes		19	19p13.1	23476	bromodomain containing 4		E	.	BRD4	172	.	0			c.A3878G						.						8	9	9					19																	15349696		2154	4226	6380	SO:0001583	missense	23476	exon19			TGCTGTTGCTCCT	Y12059	CCDS12328.1, CCDS46004.1	19p13.12	2013-09-20	2002-01-14		ENSG00000141867	ENSG00000141867			13575	protein-coding gene	gene with protein product	"chromosome-associated protein"	608749	"bromodomain-containing 4"			10938129	Standard	NM_058243		Approved	HUNKI, MCAP, CAP, HUNK1	uc002nar.3	O60885	OTTHUMG00000183252	ENST00000263377.2:c.3878A>G	chr19.hg19:g.15349696T>C	ENSP00000263377:p.Gln1293Arg	107.0	0.0		77.0	5.0	NM_058243	O60433|Q4G0X8|Q86YS8|Q96PD3	Missense_Mutation	SNP	ENST00000263377.2	hg19	CCDS12328.1	.	.	.	.	.	.	.	.	.	.	t	13.20	2.166187	0.38217	.	.	ENSG00000141867	ENST00000263377	T	0.16897	2.31	5.1	4.0	0.46444	.	0.662303	0.12533	N	0.460603	T	0.11537	0.0281	N	0.14661	0.345	0.80722	D	1	B	0.27498	0.18	B	0.26969	0.075	T	0.12218	-1.0556	10	0.87932	D	0	.	10.9916	0.47553	0.0:0.0:0.156:0.844	.	1293	O60885	BRD4_HUMAN	R	1293	ENSP00000263377:Q1293R	ENSP00000263377:Q1293R	Q	-	2	0	BRD4	15210696	1.000000	0.71417	0.931000	0.37212	0.871000	0.50021	3.762000	0.55250	2.033000	0.60031	0.524000	0.50904	CAA	.	.		0.711	BRD4-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465800.3	NM_058243		C	15349696	T	C	15349696	3	2	282	1	0	0	0	0	1	0	0	0	1506	1812	63	2	218	2	BRD4	19	15349696	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	840969	15349696	43779287	1221	41455										
OR10H2	26538	hgsc.bcm.edu	37	chr19	15838973	15838973	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atgtacctgttcacgctgctGggcaacctgctcatcatggc	10	13	3	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:15838973G>A	ENST00000305899.3	+	1	140	c.120G>A	c.(118-120)ctG>ctA	p.L40L		NM_013939.2	NP_039227.1	O60403	O10H2_HUMAN	olfactory receptor, family 10, subfamily H, member 2	40			L -> Q (in dbSNP:rs4569397).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L40L(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(1)	27	all_hematologic(1;0.0517)|Acute lymphoblastic leukemia(2;0.074)					TCACGCTGCTGGGCAACCTGC	0.582																																					p.L40L		Atlas-SNP	.											OR10H2,NS,carcinoma,0,1	OR10H2	59	.	1	Substitution - coding silent(1)	lung(1)	c.G120A						.						227	188	201					19																	15838973		2203	4298	6501	SO:0001819	synonymous_variant	26538	exon1			GCTGCTGGGCAAC	AC004597	CCDS12333.1	19p13.1	2012-08-09				ENSG00000171942		"GPCR / Class A : Olfactory receptors"	8173	protein-coding gene	gene with protein product							Standard	NM_013939		Approved		uc002nbm.2	O60403		ENST00000305899.3:c.120G>A	chr19.hg19:g.15838973G>A		391.0	1.0		307.0	0.0	NM_013939	Q6IFQ1|Q96R58	Silent	SNP	ENST00000305899.3	hg19	CCDS12333.1																																																																																			.	.		0.582	OR10H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460917.1			A	15838973	G	A	15838973	2	1	282	1	0	0	0	0	0	0	0	1	10915	1335	47	3		3	OR10H2	19	15838973	Silent	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	489277	15838973	43290010	1222	41456										
OR10H1	26539	hgsc.bcm.edu	37	chr19	15917904	15917904	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atttctcctacatcattacaTttttttctgggtagagttta							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:15917904delT	ENST00000334920.2	-	1	1032	c.944delA	c.(943-945)aatfs	p.N315fs		NM_013940.2	NP_039228.1	Q9Y4A9	O10H1_HUMAN	olfactory receptor, family 10, subfamily H, member 1	315						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|skin(2)|urinary_tract(1)	29						CATCATTACATTTTTTTCTGG	0.438																																					p.N315fs		Atlas-INDEL	.											.	OR10H1	59	.	0			c.945delT						.						87	86	86					19																	15917904		2203	4300	6503	SO:0001589	frameshift_variant	26539	exon1			.	AC004510	CCDS12335.1	19p13.1	2012-08-09				ENSG00000186723		"GPCR / Class A : Olfactory receptors"	8172	protein-coding gene	gene with protein product							Standard	NM_013940		Approved		uc002nbq.2	Q9Y4A9		ENST00000334920.2:c.944delA	chr19.hg19:g.15917904delT	ENSP00000335596:p.Asn315fs	250.0	0.0		178.0	11.0	NM_013940	Q6IFQ2|Q96R59	Frame_Shift_Del	DEL	ENST00000334920.2	hg19	CCDS12335.1																																																																																			.	.		0.438	OR10H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460364.1			-	15917904	T	-	15917904	7	5	282	1	0	1	0	1	0	0	0	0	10914	1493	52	0	16	0	OR10H1	19	15917904	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	78931	15917904	43211079	1223	41457										
CIB3	117286	hgsc.bcm.edu	37	chr19	16275654	16275654	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctcacctcctcggcactcagCcccccccgcgtcagtttggt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:16275654delC	ENST00000269878.4	-	5	466	c.417delG	c.(415-417)gggfs	p.G139fs	CIB3_ENST00000379859.3_Frame_Shift_Del_p.G90fs|CIB3_ENST00000541493.1_5'UTR	NM_054113.2	NP_473454.1	Q96Q77	CIB3_HUMAN	calcium and integrin binding family member 3	139			G -> E (in dbSNP:rs6512087). {ECO:0000269|PubMed:15489334}.				calcium ion binding (GO:0005509)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|skin(2)	16						CGGCACTCAGCCCCCCCCGCG	0.567																																					p.L140X		Atlas-INDEL	.											CIB3,NS,carcinoma,0,3	CIB3	35	.	0			c.418delC						.						131	118	122					19																	16275654		2203	4300	6503	SO:0001589	frameshift_variant	117286	exon5			.	AB050868	CCDS12340.1, CCDS74305.1	19p13.12	2013-01-10						"EF-hand domain containing"	24580	protein-coding gene	gene with protein product		610645					Standard	XM_005259728		Approved	KIP3	uc002nds.3	Q96Q77		ENST00000269878.4:c.417delG	chr19.hg19:g.16275654delC	ENSP00000269878:p.Gly139fs	243.0	0.0		226.0	16.0	NM_054113	E7EUX1|Q2M1W0|Q6ISP1	Frame_Shift_Del	DEL	ENST00000269878.4	hg19	CCDS12340.1																																																																																			.	.		0.567	CIB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460351.1	NM_054113		-	16275654	C	-	16275654	7	5	282	1	0	1	0	1	0	0	0	0	3424	726	26	0	154	0	CIB3	19	16275654	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	357750	16275654	42853329	1224	41458										
NWD1	284434	hgsc.bcm.edu	37	chr19	16860649	16860649	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggtgtgcctggcctatgggcTgcccttgccccctgcccagg	14	16	0	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:16860649T>C	ENST00000552788.1	+	4	1196	c.1196T>C	c.(1195-1197)cTg>cCg	p.L399P	NWD1_ENST00000523826.1_Missense_Mutation_p.L193P|NWD1_ENST00000549814.1_Missense_Mutation_p.L399P|NWD1_ENST00000339803.6_Missense_Mutation_p.L264P|NWD1_ENST00000379808.3_Missense_Mutation_p.L399P|NWD1_ENST00000524140.2_Missense_Mutation_p.L399P			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	399	NACHT.						ATP binding (GO:0005524)			NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						GCCTATGGGCTGCCCTTGCCC	0.602																																					p.L399P		Atlas-SNP	.											.	NWD1	303	.	0			c.T1196C						.						41	43	42					19																	16860649		2203	4300	6503	SO:0001583	missense	284434	exon6			ATGGGCTGCCCTT	BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"WD repeat domain containing"	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.1196T>C	chr19.hg19:g.16860649T>C	ENSP00000447224:p.Leu399Pro	100.0	0.0		69.0	4.0	NM_001007525	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	hg19		.	.	.	.	.	.	.	.	.	.	t	18.69	3.677099	0.68042	.	.	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803	T;T;T;T;T;T	0.77489	-1.1;-1.1;-1.1;-1.1;-1.1;-1.1	4.53	4.53	0.55603	.	0.000000	0.64402	D	0.000006	D	0.86661	0.5986	M	0.79475	2.455	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.996;0.999;1.0	D	0.86910	0.2060	10	0.46703	T	0.11	-17.5849	12.067	0.53594	0.0:0.0:0.0:1.0	.	399;399;264	Q149M9;Q149M9-3;C9J2Y8	NWD1_HUMAN;.;.	P	264;399;399;399;193;399;264	ENSP00000428579:L399P;ENSP00000447548:L399P;ENSP00000369136:L399P;ENSP00000428955:L193P;ENSP00000447224:L399P;ENSP00000340159:L264P	ENSP00000340159:L264P	L	+	2	0	NWD1	16721649	1.000000	0.71417	0.998000	0.56505	0.890000	0.51754	6.076000	0.71267	1.808000	0.52836	0.520000	0.50463	CTG	.	.		0.602	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525		C	16860649	T	C	16860649	3	2	282	1	0	0	0	0	1	0	0	0	10790	1580	55	2	797	2	NWD1	19	16860649	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	584995	16860649	42268334	1225	41459										
BST2	684	hgsc.bcm.edu	37	chr19	17516225	17516225	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cactgcccgaaggccgtcccGgcaggcctcgctgttggcct					rs200950817	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:17516225delG	ENST00000252593.6	-	1	232	c.160delC	c.(160-162)cggfs	p.R54fs	CTD-2521M24.9_ENST00000500836.2_lincRNA|BST2_ENST00000527220.1_5'UTR	NM_004335.2	NP_004326.1	Q10589	BST2_HUMAN	bone marrow stromal cell antigen 2	54					B cell activation (GO:0042113)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of intracellular transport of viral material (GO:1901253)|negative regulation of plasmacytoid dendritic cell cytokine production (GO:0002737)|negative regulation of viral genome replication (GO:0045071)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of actin cytoskeleton organization (GO:0032956)|response to interferon-alpha (GO:0035455)|response to interferon-beta (GO:0035456)|response to interferon-gamma (GO:0034341)|response to virus (GO:0009615)|signal transduction (GO:0007165)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metalloendopeptidase inhibitor activity (GO:0008191)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			endometrium(1)|large_intestine(2)|lung(1)|ovary(3)|prostate(2)	9						AGGCCGTCCCGGCAGGCCTCG	0.572																																					p.R54fs		Atlas-INDEL	.											.	BST2	28	.	0			c.161delG						.						92	77	82					19																	17516225		2203	4300	6503	SO:0001589	frameshift_variant	684	exon1			.		CCDS12358.1	19p13.2	2009-10-30				ENSG00000130303		"CD molecules"	1119	protein-coding gene	gene with protein product		600534				7607676	Standard	NM_004335		Approved	CD317, tetherin	uc002ngl.3	Q10589		ENST00000252593.6:c.160delC	chr19.hg19:g.17516225delG	ENSP00000252593:p.Arg54fs	203.0	0.0		173.0	11.0	NM_004335	A8K4Y4|Q53G07	Frame_Shift_Del	DEL	ENST00000252593.6	hg19	CCDS12358.1																																																																																			.	.		0.572	BST2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387346.1	NM_004335		-	17516225	G	-	17516225	7	5	282	1	0	1	0	1	0	0	0	0	1536	1115	39	0	398	0	BST2	19	17516225	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	655576	17516225	41612758	1226	41460										
JAK3	3718	hgsc.bcm.edu	37	chr19	17948866	17948866	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaaggacccatggcccaggtTctcatgctgaatggtgaggg	15	9	1	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:17948866T>C	ENST00000527670.1	-	11	1605	c.1576A>G	c.(1576-1578)Aac>Gac	p.N526D	JAK3_ENST00000534444.1_Missense_Mutation_p.N526D|JAK3_ENST00000458235.1_Missense_Mutation_p.N526D|JAK3_ENST00000526008.1_5'Flank			P52333	JAK3_HUMAN	Janus kinase 3	526	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell differentiation (GO:0030183)|enzyme linked receptor protein signaling pathway (GO:0007167)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of dendritic cell cytokine production (GO:0002731)|negative regulation of FasL biosynthetic process (GO:0045221)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of T cell activation (GO:0050868)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|negative regulation of thymocyte apoptotic process (GO:0070244)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of T cell apoptotic process (GO:0070232)|response to interleukin-15 (GO:0070672)|response to interleukin-2 (GO:0070669)|response to interleukin-4 (GO:0070670)|response to interleukin-9 (GO:0071104)|STAT protein import into nucleus (GO:0007262)|T cell homeostasis (GO:0043029)|tyrosine phosphorylation of STAT protein (GO:0007260)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(85)|kidney(4)|large_intestine(11)|lung(22)|ovary(3)|prostate(5)|skin(1)|stomach(2)|upper_aerodigestive_tract(5)	147					Tofacitinib(DB08895)	TGGCCCAGGTTCTCATGCTGA	0.587		2	Mis		"acute megakaryocytic leukemia, ETP ALL"																																p.N526D		Atlas-SNP	.		Dom	yes		19	19p13.1	3718	Janus kinase 3		L	JAK3_ENST00000458235,bladder,carcinoma,0,2	JAK3	341	.	0			c.A1576G						.						88	84	85					19																	17948866		2203	4300	6503	SO:0001583	missense	3718	exon12			CCAGGTTCTCATG	U31601	CCDS12366.1	19p13-p12	2014-09-17	2009-04-23		ENSG00000105639	ENSG00000105639	2.7.10.1		6193	protein-coding gene	gene with protein product	"tyrosine-protein kinase JAK3", "leukocyte Janus kinase"	600173				8921370, 9226382	Standard	NM_000215		Approved	L-JAK, JAKL, LJAK, JAK3_HUMAN, JAK-3	uc002nhn.4	P52333	OTTHUMG00000165648	ENST00000527670.1:c.1576A>G	chr19.hg19:g.17948866T>C	ENSP00000432511:p.Asn526Asp	159.0	0.0		115.0	5.0	NM_000215	Q13259|Q13260|Q13611|Q8N1E8|Q99699|Q9Y6S2	Missense_Mutation	SNP	ENST00000527670.1	hg19	CCDS12366.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.205384	0.79127	.	.	ENSG00000105639	ENST00000458235;ENST00000428406;ENST00000527670;ENST00000534444	T;T;T	0.24538	1.85;1.85;1.85	4.93	4.93	0.64822	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.105140	0.64402	D	0.000005	T	0.27967	0.0689	L	0.43152	1.355	0.37246	D	0.906344	P;P	0.50528	0.936;0.889	P;P	0.50192	0.57;0.634	T	0.10520	-1.0626	10	0.11794	T	0.64	-40.616	12.5164	0.56034	0.0:0.0:0.0:1.0	.	526;526	P52333-2;P52333	.;JAK3_HUMAN	D	526	ENSP00000391676:N526D;ENSP00000432511:N526D;ENSP00000436421:N526D	ENSP00000413248:N526D	N	-	1	0	JAK3	17809866	1.000000	0.71417	1.000000	0.80357	0.814000	0.46013	7.299000	0.78831	1.852000	0.53769	0.260000	0.18958	AAC	.	.		0.587	JAK3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385549.1	NM_000215		C	17948866	T	C	17948866	3	2	282	1	0	0	0	0	1	0	0	0	7948	1783	62	2	1850	2	JAK3	19	17948866	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	432641	17948866	41180117	1227	41461										
MPV17L2	84769	hgsc.bcm.edu	37	chr19	18305819	18305819	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcgtgaacttcctcttcgtgCccccccaatttcgagtcacc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:18305819delC	ENST00000599612.2	+	4	587	c.487delC	c.(487-489)cccfs	p.P164fs		NM_032683.2	NP_116072.2	Q567V2	M17L2_HUMAN	MPV17 mitochondrial membrane protein-like 2	164						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				large_intestine(1)|lung(2)|urinary_tract(1)	4						CCTCTTCGTGCCCCCCCAATT	0.652																																					p.V162fs		Atlas-INDEL	.											.	MPV17L2	12	.	0			c.486delG						.						114	114	114					19																	18305819		2081	4206	6287	SO:0001589	frameshift_variant	84769	exon4			.	AK094091	CCDS42522.1	19p13.11	2011-05-26			ENSG00000254858	ENSG00000254858			28177	protein-coding gene	gene with protein product						12477932	Standard	NM_032683		Approved	FKSG24, MGC12972	uc002nid.3	Q567V2	OTTHUMG00000165628	ENST00000599612.2:c.487delC	chr19.hg19:g.18305819delC	ENSP00000469836:p.Pro164fs	190.0	0.0		137.0	10.0	NM_032683	Q96P34|Q96QA0|Q9BSG4	Frame_Shift_Del	DEL	ENST00000599612.2	hg19	CCDS42522.1																																																																																			.	.		0.652	MPV17L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466294.2	NM_032683		-	18305819	C	-	18305819	7	5	282	1	0	1	0	1	0	0	0	0	9756	739	26	0	501	0	MPV17L2	19	18305819	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	356953	18305819	40823164	1228	41462										
PDE4C	5143	hgsc.bcm.edu	37	chr19	18331057	18331057	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caggaaggtccgggagatgtActcggacacctggttcccgg	15	11	0	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:18331057A>G	ENST00000355502.3	-	11	1652	c.781T>C	c.(781-783)Tac>Cac	p.Y261H	PDE4C_ENST00000598111.2_Missense_Mutation_p.Y31H|PDE4C_ENST00000594617.3_Missense_Mutation_p.Y261H|PDE4C_ENST00000447275.3_Missense_Mutation_p.Y155H|PDE4C_ENST00000539010.1_Missense_Mutation_p.Y30H|PDE4C_ENST00000597297.1_Missense_Mutation_p.Y31H|PDE4C_ENST00000262805.12_Missense_Mutation_p.Y229H|AC068499.10_ENST00000594805.3_RNA|PDE4C_ENST00000594465.3_Missense_Mutation_p.Y261H			Q08493	PDE4C_HUMAN	phosphodiesterase 4C, cAMP-specific	261					cAMP catabolic process (GO:0006198)|signal transduction (GO:0007165)	cytosol (GO:0005829)|extracellular space (GO:0005615)|primary cilium (GO:0072372)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	33					Caffeine(DB00201)|Dyphylline(DB00651)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Roflumilast(DB01656)	CGGGAGATGTACTCGGACACC	0.537																																					p.Y261H		Atlas-SNP	.											.	PDE4C	80	.	0			c.T781C						.						116	123	121					19																	18331057		2203	4300	6503	SO:0001583	missense	5143	exon8			AGATGTACTCGGA		CCDS12373.1, CCDS42523.1, CCDS46016.1	19p13.11	2010-06-24	2010-06-24			ENSG00000105650	3.1.4.17	"Phosphodiesterases"	8782	protein-coding gene	gene with protein product	"phosphodiesterase E1 dunce homolog (Drosophila)"	600128	"phosphodiesterase 4C, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E1)"	DPDE1			Standard	NM_001098818		Approved		uc002nik.4	Q08493		ENST00000355502.3:c.781T>C	chr19.hg19:g.18331057A>G	ENSP00000347689:p.Tyr261His	156.0	0.0		129.0	7.0	NM_000923	B3KTC4|Q9UN44|Q9UN45|Q9UN46|Q9UPJ6	Missense_Mutation	SNP	ENST00000355502.3	hg19	CCDS12373.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.208577	0.79240	.	.	ENSG00000105650	ENST00000536045;ENST00000355502;ENST00000536507;ENST00000262805;ENST00000447275;ENST00000545961;ENST00000336173;ENST00000539010;ENST00000543547	T;T;T;T	0.75938	-0.98;-0.94;-0.86;-0.41	4.83	4.83	0.62350	.	0.371406	0.28635	N	0.014647	D	0.87257	0.6132	M	0.89715	3.055	0.35605	D	0.808203	D;D;D;D	0.76494	0.999;0.991;0.969;0.985	D;D;P;P	0.69142	0.962;0.917;0.781;0.845	D	0.92425	0.5949	10	0.87932	D	0	.	12.3551	0.55171	1.0:0.0:0.0:0.0	.	261;229;67;31	Q08493;Q08493-3;O43850;O76104	PDE4C_HUMAN;.;.;.	H	340;261;249;229;155;67;30;30;370	ENSP00000347689:Y261H;ENSP00000262805:Y229H;ENSP00000402091:Y155H;ENSP00000439470:Y30H	ENSP00000262805:Y229H	Y	-	1	0	PDE4C	18192057	1.000000	0.71417	0.982000	0.44146	0.772000	0.43724	8.815000	0.91973	1.823000	0.53134	0.398000	0.26397	TAC	.	.		0.537	PDE4C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466295.1			G	18331057	A	G	18331057	3	3	282	1	0	0	0	0	1	0	0	0	11650	391	14	2	1393	2	PDE4C	19	18331057	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	25238	18331057	40797926	1229	41463										
UPF1	5976	hgsc.bcm.edu	37	chr19	18971165	18971165	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agggatttgacttccagtggCcccaacccgataaaccgatg					rs1062846		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:18971165delC	ENST00000599848.1	+	16	2460	c.2251delC	c.(2251-2253)cccfs	p.P751fs	UPF1_ENST00000262803.5_Frame_Shift_Del_p.P740fs			Q92900	RENT1_HUMAN	UPF1 regulator of nonsense transcripts homolog (yeast)	751					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|dosage compensation by inactivation of X chromosome (GO:0009048)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translational termination (GO:0006449)|RNA metabolic process (GO:0016070)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	40						CTTCCAGTGGCCCCAACCCGA	0.557																																					p.W739fs		Atlas-INDEL	.											.	UPF1	88	.	0			c.2217delG						.						171	153	159					19																	18971165		2203	4300	6503	SO:0001589	frameshift_variant	5976	exon16			.	AF074016	CCDS12386.1, CCDS74315.1	19p13.2-p13.11	2012-02-29	2006-02-07	2006-02-07	ENSG00000005007	ENSG00000005007			9962	protein-coding gene	gene with protein product	"UP Frameshift 1", "smg-2 homolog, nonsense mediated mRNA decay factor (C. elegans)"	601430	"regulator of nonsense transcripts 1"	RENT1		8855285, 9064659	Standard	XM_005260015		Approved	HUPF1, KIAA0221, NORF1, pNORF1, smg-2	uc002nkf.3	Q92900		ENST00000599848.1:c.2251delC	chr19.hg19:g.18971165delC	ENSP00000470142:p.Pro751fs	269.0	0.0		175.0	11.0	NM_002911	O00239|O43343|Q86Z25|Q92842	Frame_Shift_Del	DEL	ENST00000599848.1	hg19																																																																																				.	.		0.557	UPF1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000464684.1	NM_002911		-	18971165	C	-	18971165	7	5	282	1	0	1	0	1	0	0	0	0	17018	739	26	0	2280	0	UPF1	19	18971165	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	640108	18971165	40157818	1230	41464										
COPE	11316	hgsc.bcm.edu	37	chr19	19021789	19021789	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tggggcctcacctccgactcTcgtgggcgaggtagtcagca	14	13	3	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:19021789T>C	ENST00000262812.4	-	3	329	c.281A>G	c.(280-282)gAg>gGg	p.E94G	COPE_ENST00000349893.4_Missense_Mutation_p.E94G|COPE_ENST00000351079.4_Missense_Mutation_p.E94G|COPE_ENST00000600932.1_Missense_Mutation_p.E94G|COPE_ENST00000598969.1_5'UTR|AC002985.3_ENST00000596918.1_3'UTR	NM_007263.3	NP_009194.2	O14579	COPE_HUMAN	coatomer protein complex, subunit epsilon	94					COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|membrane organization (GO:0061024)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	11						CCTCCGACTCTCGTGGGCGAG	0.632																																					p.E94G		Atlas-SNP	.											.	COPE	26	.	0			c.A281G						.						93	80	84					19																	19021789		2203	4300	6503	SO:0001583	missense	11316	exon3			CGACTCTCGTGGG	AJ131182	CCDS12387.1, CCDS12388.1, CCDS12389.1	19p13.11	2008-02-05				ENSG00000105669			2234	protein-coding gene	gene with protein product		606942				10469566	Standard	NM_007263		Approved	epsilon-COP	uc002nkk.3	O14579		ENST00000262812.4:c.281A>G	chr19.hg19:g.19021789T>C	ENSP00000262812:p.Glu94Gly	157.0	0.0		123.0	6.0	NM_007263	A6NE29|A6NKA3|O76097|Q6IBB8|Q9UGP6	Missense_Mutation	SNP	ENST00000262812.4	hg19	CCDS12387.1	.	.	.	.	.	.	.	.	.	.	T	11.29	1.594281	0.28445	.	.	ENSG00000105669	ENST00000262812;ENST00000351079;ENST00000349893;ENST00000538245	T;T;T	0.44083	0.93;0.93;0.93	4.8	4.8	0.61643	.	0.184840	0.48767	D	0.000178	T	0.35828	0.0945	L	0.41236	1.265	0.80722	D	1	B;B;B;B	0.22851	0.0;0.076;0.0;0.0	B;B;B;B	0.29440	0.005;0.102;0.005;0.002	T	0.12889	-1.0530	10	0.23891	T	0.37	-28.9307	13.1643	0.59562	0.0:0.0:0.0:1.0	.	94;94;94;94	Q53HJ6;A6NE29;A6NKA3;O14579	.;.;.;COPE_HUMAN	G	94;94;94;93	ENSP00000262812:E94G;ENSP00000345674:E94G;ENSP00000343134:E94G	ENSP00000262812:E94G	E	-	2	0	COPE	18882789	1.000000	0.71417	0.624000	0.29186	0.200000	0.23975	7.306000	0.78905	1.797000	0.52628	0.421000	0.28195	GAG	.	.		0.632	COPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464801.1	NM_007263		C	19021789	T	C	19021789	3	2	282	1	0	0	0	0	1	0	0	0	3732	1551	54	2	677	2	COPE	19	19021789	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	50624	19021789	40107194	1231	41465										
KIAA0892	23383	hgsc.bcm.edu	37	chr19	19455688	19455688	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tctgccagctgtgccagcagTccccccggctcttctccaac	8	19	3	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:19455688T>C	ENST00000392313.6	+	11	1287	c.1108T>C	c.(1108-1110)Tcc>Ccc	p.S370P	MAU2_ENST00000262815.8_Missense_Mutation_p.S370P	NM_015329.3	NP_056144.3	Q9Y6X3	SCC4_HUMAN	MAU2 sister chromatid cohesion factor	370					maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	protein N-terminus binding (GO:0047485)			NS(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	18						GTGCCAGCAGTCCCCCCGGCT	0.577																																					p.S370P		Atlas-SNP	.											.	MAU2	38	.	0			c.T1108C						.						31	33	32					19																	19455688		2001	4172	6173	SO:0001583	missense	23383	exon11			CAGCAGTCCCCCC	AB020699	CCDS32969.2	19p13.11	2013-08-28	2013-08-28	2013-08-28	ENSG00000129933	ENSG00000129933			29140	protein-coding gene	gene with protein product	"sister chromatid cohesion 4"	614560	"KIAA0892", "MAU2 chromatid cohesion factor homolog (C. elegans)"	KIAA0892		10048485	Standard	NM_015329		Approved	MGC75361, mau-2, MAU2L, SCC4	uc002nmk.4	Q9Y6X3	OTTHUMG00000150188	ENST00000392313.6:c.1108T>C	chr19.hg19:g.19455688T>C	ENSP00000376127:p.Ser370Pro	126.0	0.0		104.0	6.0	NM_015329	Q66PT1|Q6P3S7|Q6ZTT2|Q9UFX8	Missense_Mutation	SNP	ENST00000392313.6	hg19	CCDS32969.2	.	.	.	.	.	.	.	.	.	.	T	18.28	3.589970	0.66105	.	.	ENSG00000129933	ENST00000392313;ENST00000262815	.	.	.	5.38	5.38	0.77491	Tetratricopeptide-like helical (1);	0.000000	0.85682	U	0.000000	T	0.42517	0.1206	N	0.17082	0.46	0.80722	D	1	B	0.14012	0.009	B	0.12837	0.008	T	0.27262	-1.0079	9	0.35671	T	0.21	.	14.2523	0.66028	0.0:0.0:0.0:1.0	.	370	Q9Y6X3	SCC4_HUMAN	P	370	.	ENSP00000262815:S370P	S	+	1	0	MAU2	19316688	1.000000	0.71417	0.996000	0.52242	0.989000	0.77384	7.725000	0.84808	2.054000	0.61138	0.454000	0.30748	TCC	.	.		0.577	MAU2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000316748.6	NM_015329		C	19455688	T	C	19455688	3	2	282	1	0	0	0	0	1	0	0	0	8205	1667	58	2	1150	2	KIAA0892	19	19455688	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	433899	19455688	39673295	1232	41466										
PBX4	80714	hgsc.bcm.edu	37	chr19	19681606	19681606	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcctcaggagctgggcgtcaGggggatcttcgtcttgaatg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:19681606delG	ENST00000251203.9	-	3	516	c.230delC	c.(229-231)cctfs	p.P77fs		NM_025245.2	NP_079521.1	Q9BYU1	PBX4_HUMAN	pre-B-cell leukemia homeobox 4	77					positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|XY body (GO:0001741)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(1)|lung(4)|ovary(1)|prostate(3)	9						CTGGGCGTCAGGGGGATCTTC	0.552																																					p.P77fs		Atlas-INDEL	.											.	PBX4	34	.	0			c.231delT						.						67	69	69					19																	19681606		2203	4300	6503	SO:0001589	frameshift_variant	80714	exon3			.	AJ300182	CCDS12406.1	19p13.11	2014-09-11	2007-01-30		ENSG00000105717			"Homeoboxes / TALE class"	13403	protein-coding gene	gene with protein product		608127	"pre-B-cell leukemia transcription factor 4"				Standard	NM_025245		Approved		uc002nmy.3	Q9BYU1	OTTHUMG00000172310	ENST00000251203.9:c.230delC	chr19.hg19:g.19681606delG	ENSP00000251203:p.Pro77fs	198.0	0.0		136.0	11.0	NM_025245	A5D8Y0|B3KUK9	Frame_Shift_Del	DEL	ENST00000251203.9	hg19	CCDS12406.1																																																																																			.	.		0.552	PBX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417784.6			-	19681606	G	-	19681606	7	5	282	1	0	1	0	1	0	0	0	0	11504	1000	35	0	918	0	PBX4	19	19681606	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	225918	19681606	39447377	1233	41467										
ZNF429	353088	hgsc.bcm.edu	37	chr19	21719985	21719985	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atgtgaagaatgtggcaaagCttttaaccagtcttcaagac	9	7	2	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:21719985C>A	ENST00000358491.4	+	4	1338	c.1130C>A	c.(1129-1131)gCt>gAt	p.A377D	ZNF429_ENST00000597078.1_Intron	NM_001001415.2	NP_001001415.2	Q86V71	ZN429_HUMAN	zinc finger protein 429	377					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(13)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	34						TGTGGCAAAGCTTTTAACCAG	0.373																																					p.A377D		Atlas-SNP	.											.	ZNF429	338	.	0			c.C1130A						.						41	47	45					19																	21719985		2099	4257	6356	SO:0001583	missense	353088	exon4			GCAAAGCTTTTAA	AY269786	CCDS42537.1	19p12	2014-02-14			ENSG00000197013	ENSG00000197013		"Zinc fingers, C2H2-type", "-"	20817	protein-coding gene	gene with protein product							Standard	NM_001001415		Approved		uc002nqd.1	Q86V71	OTTHUMG00000182848	ENST00000358491.4:c.1130C>A	chr19.hg19:g.21719985C>A	ENSP00000351280:p.Ala377Asp	33.0	0.0		28.0	9.0	NM_001001415	A6NLV7|Q9BZE6	Missense_Mutation	SNP	ENST00000358491.4	hg19	CCDS42537.1	.	.	.	.	.	.	.	.	.	.	.	7.998	0.754724	0.15778	.	.	ENSG00000197013	ENST00000358491	T	0.14266	2.52	0.876	0.876	0.19138	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12433	0.0302	L	0.48877	1.53	0.09310	N	1	B	0.22541	0.071	B	0.23574	0.047	T	0.28839	-1.0031	9	0.87932	D	0	.	6.2723	0.20961	0.0:0.4389:0.5611:0.0	.	377	Q86V71	ZN429_HUMAN	D	377	ENSP00000351280:A377D	ENSP00000351280:A377D	A	+	2	0	ZNF429	21511825	0.000000	0.05858	0.467000	0.27180	0.469000	0.32828	0.344000	0.19962	0.293000	0.22520	0.298000	0.19748	GCT	.	.		0.373	ZNF429-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463981.1	NM_001001415		A	21719985	C	A	21719985	3	1	282	1	0	0	0	0	1	0	0	0	17917	797	28	3	1144	3	ZNF429	19	21719985	Missense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	2038379	21719985	37408998	1234	41468										
ZNF208	7757	hgsc.bcm.edu	37	chr19	22155940	22155940	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	catttgtagggcttctctccAgcatgaattgccttatgtgt	9	9	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:22155940A>G	ENST00000397126.4	-	4	2044	c.1896T>C	c.(1894-1896)gcT>gcC	p.A632A	ZNF208_ENST00000601773.1_Intron|ZNF208_ENST00000599916.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	632					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				GCTTCTCTCCAGCATGAATTG	0.398																																					p.A632A		Atlas-SNP	.											.	ZNF208	817	.	0			c.T1896C						.						78	86	83					19																	22155940		2120	4248	6368	SO:0001819	synonymous_variant	7757	exon4			CTCTCCAGCATGA	BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"Zinc fingers, C2H2-type", "-"	12999	protein-coding gene	gene with protein product	"zinc finger protein 95"	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.1896T>C	chr19.hg19:g.22155940A>G		69.0	0.0		83.0	30.0	NM_007153		Silent	SNP	ENST00000397126.4	hg19	CCDS54240.1																																																																																			.	.		0.398	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		G	22155940	A	G	22155940	2	3	282	1	0	0	0	0	0	0	0	1	17781	175	7	2		2	ZNF208	19	22155940	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	435955	22155940	36973043	1235	41469										
ZNF676	163223	hgsc.bcm.edu	37	chr19	22363757	22363757	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cctttgccacattcttcacaTttgtagggtttctctccagt	6	12	3	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:22363757T>C	ENST00000397121.2	-	3	1079	c.762A>G	c.(760-762)aaA>aaG	p.K254K		NM_001001411.2	NP_001001411.2	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	254					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K254K(1)		NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(49)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	67		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				ATTCTTCACATTTGTAGGGTT	0.383																																					p.K254K		Atlas-SNP	.											ZNF676,NS,carcinoma,0,1	ZNF676	146	.	1	Substitution - coding silent(1)	lung(1)	c.A762G						.						80	87	85					19																	22363757		2162	4277	6439	SO:0001819	synonymous_variant	163223	exon3			TTCACATTTGTAG	AK097798	CCDS42539.1	19p12	2013-01-08				ENSG00000196109		"Zinc fingers, C2H2-type"	20429	protein-coding gene	gene with protein product							Standard	NM_001001411		Approved		uc002nqs.1	Q8N7Q3		ENST00000397121.2:c.762A>G	chr19.hg19:g.22363757T>C		68.0	0.0		50.0	2.0	NM_001001411	A8MVX5	Silent	SNP	ENST00000397121.2	hg19	CCDS42539.1																																																																																			.	.		0.383	ZNF676-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464392.1	NM_001001411		C	22363757	T	C	22363757	2	2	282	1	0	0	0	0	0	0	0	1	18098	1490	52	2		2	ZNF676	19	22363757	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	207817	22363757	36765226	1236	41470										
ZNF536	9745	hgsc.bcm.edu	37	chr19	30935925	30935925	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcgtcccggagggggacaagCactccctcctgggatgcctc	14	15	0	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:30935925C>A	ENST00000355537.3	+	2	1603	c.1456C>A	c.(1456-1458)Cac>Aac	p.H486N		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	486					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					GGGGGACAAGCACTCCCTCCT	0.652																																					p.H486N		Atlas-SNP	.											.	ZNF536	424	.	0			c.C1456A						.						35	39	37					19																	30935925		2203	4299	6502	SO:0001583	missense	9745	exon2			GACAAGCACTCCC		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"Zinc fingers, C2H2-type"	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.1456C>A	chr19.hg19:g.30935925C>A	ENSP00000347730:p.His486Asn	75.0	0.0		59.0	19.0	NM_014717	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	hg19	CCDS32984.1	.	.	.	.	.	.	.	.	.	.	C	10.58	1.390145	0.25118	.	.	ENSG00000198597	ENST00000355537	T	0.07908	3.15	5.53	5.53	0.82687	.	0.048823	0.85682	D	0.000000	T	0.11580	0.0282	L	0.40543	1.245	0.51482	D	0.999923	D;D	0.53151	0.958;0.958	P;P	0.45276	0.475;0.475	T	0.13710	-1.0499	10	0.24483	T	0.36	-36.3673	19.4573	0.94900	0.0:1.0:0.0:0.0	.	486;486	A7E228;O15090	.;ZN536_HUMAN	N	486	ENSP00000347730:H486N	ENSP00000347730:H486N	H	+	1	0	ZNF536	35627765	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.788000	0.85771	2.582000	0.87167	0.655000	0.94253	CAC	.	.		0.652	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		A	30935925	C	A	30935925	3	1	282	1	0	0	0	0	1	0	0	0	17989	710	25	3	1458	3	ZNF536	19	30935925	Missense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	8572168	30935925	28193058	1237	41471										
ZNF507	22847	hgsc.bcm.edu	37	chr19	32873700	32873700	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcccgtcactggaagttcagAaaatgcagtgtcatcttcag	9	10	5	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:32873700A>G	ENST00000311921.4	+	6	2765	c.2573A>G	c.(2572-2574)gAa>gGa	p.E858G	ZNF507_ENST00000355898.5_Missense_Mutation_p.E858G|ZNF507_ENST00000544431.1_Missense_Mutation_p.E862G	NM_001136156.1|NM_014910.4	NP_001129628.1|NP_055725.2	Q8TCN5	ZN507_HUMAN	zinc finger protein 507	858					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	31	Esophageal squamous(110;0.162)					GGAAGTTCAGAAAATGCAGTG	0.438																																					p.E858G		Atlas-SNP	.											.	ZNF507	92	.	0			c.A2573G						.						55	52	53					19																	32873700		2203	4300	6503	SO:0001583	missense	22847	exon7			GTTCAGAAAATGC	AB029007	CCDS32985.1	19q13.12	2008-02-05				ENSG00000168813		"Zinc fingers, C2H2-type"	23783	protein-coding gene	gene with protein product							Standard	NM_014910		Approved	KIAA1084	uc002ntd.3	Q8TCN5		ENST00000311921.4:c.2573A>G	chr19.hg19:g.32873700A>G	ENSP00000312277:p.Glu858Gly	128.0	0.0		81.0	6.0	NM_001136156	A8K911|Q2TBF1|Q6MZU0|Q9UPR8	Missense_Mutation	SNP	ENST00000311921.4	hg19	CCDS32985.1	.	.	.	.	.	.	.	.	.	.	A	13.63	2.294810	0.40594	.	.	ENSG00000168813	ENST00000355898;ENST00000311921;ENST00000544431	T;T;T	0.07688	3.49;3.49;3.17	5.87	5.87	0.94306	.	0.330421	0.37012	N	0.002298	T	0.13030	0.0316	M	0.66939	2.045	0.39673	D	0.970786	B	0.15141	0.012	B	0.09377	0.004	T	0.01767	-1.1278	10	0.48119	T	0.1	.	14.8516	0.70300	1.0:0.0:0.0:0.0	.	858	Q8TCN5	ZN507_HUMAN	G	858;858;862	ENSP00000348162:E858G;ENSP00000312277:E858G;ENSP00000441549:E862G	ENSP00000312277:E858G	E	+	2	0	ZNF507	37565540	1.000000	0.71417	0.746000	0.31095	0.038000	0.13279	4.769000	0.62300	2.248000	0.74166	0.533000	0.62120	GAA	.	.		0.438	ZNF507-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450301.3	NM_014910		G	32873700	A	G	32873700	3	3	282	1	0	0	0	0	1	0	0	0	17968	246	9	2	2591	2	ZNF507	19	32873700	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1937775	32873700	26255283	1238	41472										
FAM187B	148109	hgsc.bcm.edu	37	chr19	35715757	35715757	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caccagcacctgtgtgcttcTcctgcccggggaagggtgga	14	13	1	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:35715757T>C	ENST00000324675.3	-	2	1129	c.1081A>G	c.(1081-1083)Aga>Gga	p.R361G		NM_152481.1	NP_689694.1	Q17R55	F187B_HUMAN	family with sequence similarity 187, member B	361						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	9						TGTGTGCTTCTCCTGCCCGGG	0.652																																					p.R361G		Atlas-SNP	.											.	FAM187B	28	.	0			c.A1081G						.						25	27	26					19																	35715757		2202	4294	6496	SO:0001583	missense	148109	exon2			TGCTTCTCCTGCC	AK098526	CCDS12448.1	19q13.12	2008-10-16	2008-10-16	2008-10-16	ENSG00000177558	ENSG00000177558			26366	protein-coding gene	gene with protein product			"transmembrane protein 162"	TMEM162			Standard	NM_152481		Approved	FLJ25660	uc002nyk.1	Q17R55	OTTHUMG00000164450	ENST00000324675.3:c.1081A>G	chr19.hg19:g.35715757T>C	ENSP00000323355:p.Arg361Gly	157.0	0.0		125.0	5.0	NM_152481	Q8N7G6	Missense_Mutation	SNP	ENST00000324675.3	hg19	CCDS12448.1	.	.	.	.	.	.	.	.	.	.	T	12.48	1.949923	0.34377	.	.	ENSG00000177558	ENST00000324675	T	0.27557	1.66	4.38	0.756	0.18421	.	1.038280	0.07644	N	0.930799	T	0.22205	0.0535	L	0.27053	0.805	0.09310	N	1	B	0.26195	0.144	B	0.30782	0.12	T	0.37957	-0.9683	10	0.72032	D	0.01	-8.487	4.8902	0.13722	0.1834:0.0:0.3782:0.4384	.	361	Q17R55	F187B_HUMAN	G	361	ENSP00000323355:R361G	ENSP00000323355:R361G	R	-	1	2	FAM187B	40407597	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.581000	0.05820	0.288000	0.22398	0.460000	0.39030	AGA	.	.		0.652	FAM187B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378854.1	NM_152481		C	35715757	T	C	35715757	3	2	282	1	0	0	0	0	1	0	0	0	5518	1559	54	2	32	2	FAM187B	19	35715757	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2842057	35715757	23413226	1239	41473										
HAMP	57817	hgsc.bcm.edu	37	chr19	35775716	35775716	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gacaacttgcagagctgcaaCcccaggacagagctggagcc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:35775716delC	ENST00000598398.1	+	3	411	c.115delC	c.(115-117)cccfs	p.P39fs	HAMP_ENST00000222304.3_Frame_Shift_Del_p.P39fs	NM_021175.2	NP_066998.1	P81172	HEPC_HUMAN	hepcidin antimicrobial peptide	39					cellular iron ion homeostasis (GO:0006879)|defense response to bacterium (GO:0042742)|defense response to fungus (GO:0050832)|immune response (GO:0006955)|killing of cells of other organism (GO:0031640)	apical cortex (GO:0045179)|extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|large_intestine(1)|lung(1)	4	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)		Epithelial(14;7.4e-20)|OV - Ovarian serous cystadenocarcinoma(14;6.47e-19)|all cancers(14;4.17e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			AGAGCTGCAACCCCAGGACAG	0.637																																					p.Q38fs		Atlas-INDEL	.											.	HAMP	14	.	0			c.114delA						.						87	85	85					19																	35775716		2203	4300	6503	SO:0001589	frameshift_variant	57817	exon2			.	AF309489	CCDS12454.1	19q13.1	2014-09-17				ENSG00000105697			15598	protein-coding gene	gene with protein product		606464				11034317, 11113132	Standard	NM_021175		Approved	LEAP-1, HEPC, HFE2B, LEAP1	uc002nyw.3	P81172		ENST00000598398.1:c.115delC	chr19.hg19:g.35775716delC	ENSP00000471894:p.Pro39fs	205.0	0.0		156.0	14.0	NM_021175	Q1HE14|Q9BY68	Frame_Shift_Del	DEL	ENST00000598398.1	hg19	CCDS12454.1																																																																																			.	.		0.637	HAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466067.1	NM_021175		-	35775716	C	-	35775716	7	5	282	1	0	1	0	1	0	0	0	0	6957	507	18	0	121	0	HAMP	19	35775716	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	59959	35775716	23353267	1240	41474										
MLL4	9757	hgsc.bcm.edu	37	chr19	36212560	36212560	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cgtcaccacagcagatgcctCccctggaaaaagcccggatt					rs531978572	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:36212560delC	ENST00000222270.7	+	3	2311	c.2311delC	c.(2311-2313)cccfs	p.P771fs	KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000420124.1_Frame_Shift_Del_p.P771fs	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	771	Pro-rich.				chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										GCAGATGCCTCCCCTGGAAAA	0.622																																					p.P770fs		Atlas-INDEL	.											.	MLL4	229	.	0			c.2310delT						.						26	35	32					19																	36212560		2102	4245	6347	SO:0001589	frameshift_variant	8085	exon3			.	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"Chromatin-modifying enzymes / K-methyltransferases"	15840	protein-coding gene	gene with protein product	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.2311delC	chr19.hg19:g.36212560delC	ENSP00000222270:p.Pro771fs	135.0	0.0		103.0	10.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Frame_Shift_Del	DEL	ENST00000222270.7	hg19	CCDS46055.1																																																																																			.	.		0.622	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727		-	36212560	C	-	36212560	7	5	282	1	0	1	0	1	0	0	0	0	9632	855	30	0	2321	0	MLL4	19	36212560	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	436844	36212560	22916423	1241	41475										
CLIP3	25999	hgsc.bcm.edu	37	chr19	36523228	36523228	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cctcctctcctcggggtggcGgggccatcggggcaggatct					rs200629687		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:36523228delG	ENST00000360535.4	-	2	259	c.32delC	c.(31-33)ccgfs	p.P13fs	CLIP3_ENST00000593074.1_Frame_Shift_Del_p.P13fs|AC002116.7_ENST00000586962.1_RNA	NM_015526.2	NP_056341.1	Q96DZ5	CLIP3_HUMAN	CAP-GLY domain containing linker protein 3	13					chaperone-mediated protein transport (GO:0072321)|fat cell differentiation (GO:0045444)|membrane biogenesis (GO:0044091)|negative regulation of microtubule polymerization (GO:0031115)|peptidyl-L-cysteine S-palmitoylation (GO:0018230)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endocytosis (GO:0045807)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein phosphorylation (GO:0001934)	early endosome membrane (GO:0031901)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)|trans-Golgi network (GO:0005802)|trans-Golgi network membrane (GO:0032588)	ganglioside binding (GO:0035594)|microtubule binding (GO:0008017)			cervix(1)|endometrium(6)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	23	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			tcGGGGTGGCGGGGCCATCGG	0.677																																					p.P11fs		Atlas-INDEL	.											.	CLIP3	53	.	0			c.33delG						.						3	4	4					19																	36523228		1968	3910	5878	SO:0001589	frameshift_variant	25999	exon1			.	AJ427922	CCDS12486.1	19q13.12	2014-08-12			ENSG00000105270	ENSG00000105270		"Ankyrin repeat domain containing"	24314	protein-coding gene	gene with protein product	"CLIP-170-related", "restin-like 1"	607382				11854307	Standard	NM_015526		Approved	CLIPR-59, RSNL1	uc002ocz.2	Q96DZ5	OTTHUMG00000181747	ENST00000360535.4:c.32delC	chr19.hg19:g.36523228delG	ENSP00000353732:p.Pro13fs	153.0	0.0		149.0	11.0	NM_001199570	A8K0E4|Q8WWL1|Q96C99|Q9UFT7	Frame_Shift_Del	DEL	ENST00000360535.4	hg19	CCDS12486.1																																																																																			.	.		0.677	CLIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457426.1	NM_015526		-	36523228	G	-	36523228	7	5	282	1	0	1	0	1	0	0	0	0	3536	1116	39	0	1663	0	CLIP3	19	36523228	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	310668	36523228	22605755	1242	41476										
ZNF829	374899	hgsc.bcm.edu	37	chr19	37398844	37398844	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tacttacctgaacacaggccTctagtcagctctctatcaac	5	14	4	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:37398844T>C	ENST00000391711.3	-	5	670	c.306A>G	c.(304-306)agA>agG	p.R102R	ZNF829_ENST00000520965.1_Silent_p.R183R|ZNF345_ENST00000432005.2_Intron	NM_001037232.3	NP_001032309.2	Q3KNS6	ZN829_HUMAN	zinc finger protein 829	102	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|large_intestine(11)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AACACAGGCCTCTAGTCAGCT	0.443																																					p.R183R		Atlas-SNP	.											.	ZNF829	70	.	0			c.A549G						.						105	105	105					19																	37398844		2181	4290	6471	SO:0001819	synonymous_variant	374899	exon5			CAGGCCTCTAGTC	BC107131	CCDS42557.1, CCDS59380.1	19q13.12	2013-01-08			ENSG00000185869	ENSG00000185869		"Zinc fingers, C2H2-type", "-"	34032	protein-coding gene	gene with protein product							Standard	NM_001037232		Approved	DKFZp779O175	uc021utr.1	Q3KNS6	OTTHUMG00000048161	ENST00000391711.3:c.306A>G	chr19.hg19:g.37398844T>C		157.0	0.0		113.0	5.0	NM_001171979	Q3KNS7|Q6ZNN0|Q7Z657	Silent	SNP	ENST00000391711.3	hg19	CCDS42557.1																																																																																			.	.		0.443	ZNF829-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109575.3	NM_001037232		C	37398844	T	C	37398844	2	2	282	1	0	0	0	0	0	0	0	1	18197	1548	54	2		2	ZNF829	19	37398844	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	875616	37398844	21730139	1243	41477										
ZNF585B	92285	hgsc.bcm.edu	37	chr19	37678072	37678072	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggatttttccccagaataaaTtttttgatcttgagaggaag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:37678072delT	ENST00000532828.2	-	5	618	c.367delA	c.(367-369)attfs	p.I123fs	ZNF585B_ENST00000531805.1_Frame_Shift_Del_p.I68fs|ZNF585B_ENST00000527838.1_Frame_Shift_Del_p.I123fs|ZNF585B_ENST00000312908.5_5'Flank|CTC-454I21.3_ENST00000585860.2_Intron	NM_152279.3	NP_689492.3	Q52M93	Z585B_HUMAN	zinc finger protein 585B	123					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|endometrium(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CCAGAATAAATTTTTTGATCT	0.373																																					p.I123fs	Melanoma(93;882 1454 18863 28917 48427)	Atlas-INDEL	.											.	ZNF585B	91	.	0			c.368delT						.						59	64	62					19																	37678072		2202	4299	6501	SO:0001589	frameshift_variant	92285	exon5			.	AK027834	CCDS12500.1	19q13.13	2013-01-08				ENSG00000245680		"Zinc fingers, C2H2-type", "-"	30948	protein-coding gene	gene with protein product						12477932	Standard	NM_152279		Approved	FLJ14928, SZFP41	uc002ofq.3	Q52M93		ENST00000532828.2:c.367delA	chr19.hg19:g.37678072delT	ENSP00000433773:p.Ile123fs	206.0	0.0		191.0	16.0	NM_152279	Q8IZD3|Q96JW6	Frame_Shift_Del	DEL	ENST00000532828.2	hg19	CCDS12500.1																																																																																			.	.		0.373	ZNF585B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388272.2	NM_152279		-	37678072	T	-	37678072	7	5	282	1	0	1	0	1	0	0	0	0	18033	1493	52	0	1946	0	ZNF585B	19	37678072	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	279228	37678072	21450911	1244	41478										
PLEKHG2	64857	hgsc.bcm.edu	37	chr19	39906055	39906055	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gggcacgctgtttgccaacaTtgaggacatctacgagttca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:39906055delT	ENST00000409794.3	+	4	1305	c.455delT	c.(454-456)attfs	p.I152fs	PLEKHG2_ENST00000409797.2_Frame_Shift_Del_p.I152fs|PLEKHG2_ENST00000378550.1_Frame_Shift_Del_p.I152fs|PLEKHG2_ENST00000425673.1_Frame_Shift_Del_p.I152fs|PLEKHG2_ENST00000458508.2_Frame_Shift_Del_p.I93fs	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	152	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|pancreas(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			TTTGCCAACATTGAGGACATC	0.602																																					p.I152fs		Atlas-INDEL	.											.	PLEKHG2	329	.	0			c.454delA						.						41	39	40					19																	39906055		2203	4300	6503	SO:0001589	frameshift_variant	64857	exon4			.	AK024429	CCDS33022.2	19q13.2	2013-01-11			ENSG00000090924	ENSG00000090924		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	29515	protein-coding gene	gene with protein product		611893				11839748, 18045877	Standard	NM_022835		Approved	CLG, FLJ00018, ARHGEF42	uc010xuz.2	Q9H7P9	OTTHUMG00000152570	ENST00000409794.3:c.455delT	chr19.hg19:g.39906055delT	ENSP00000386733:p.Ile152fs	218.0	0.0		205.0	13.0	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Frame_Shift_Del	DEL	ENST00000409794.3	hg19	CCDS33022.2																																																																																			.	.		0.602	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835		-	39906055	T	-	39906055	7	5	282	1	0	1	0	1	0	0	0	0	12078	1493	52	0	465	0	PLEKHG2	19	39906055	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2227983	39906055	19222928	1245	41479										
SUPT5H	6829	hgsc.bcm.edu	37	chr19	39959402	39959402	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccatcaaattccaggtccctGgggggtgatgttgcctctga					rs140361350	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:39959402delG	ENST00000599117.1	+	15	1411	c.1044delG	c.(1042-1044)ctgfs	p.L348fs	SUPT5H_ENST00000432763.2_Frame_Shift_Del_p.L348fs|SUPT5H_ENST00000402194.2_Frame_Shift_Del_p.L344fs|SUPT5H_ENST00000359191.6_Frame_Shift_Del_p.L344fs|SUPT5H_ENST00000598725.1_Frame_Shift_Del_p.L348fs			O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog (S. cerevisiae)	348	Interaction with RNA polymerase II.				7-methylguanosine mRNA capping (GO:0006370)|cell cycle (GO:0007049)|chromatin remodeling (GO:0006338)|DNA-templated transcription, elongation (GO:0006354)|gene expression (GO:0010467)|negative regulation of DNA-templated transcription, elongation (GO:0032785)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to organic substance (GO:0010033)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	DSIF complex (GO:0032044)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)			breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(13)|lung(12)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	51	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			CCAGGTCCCTGGGGGGTGATG	0.517																																					p.L348fs		Atlas-INDEL	.											.	SUPT5H	119	.	0			c.1043delT						.						61	60	60					19																	39959402		2203	4300	6503	SO:0001589	frameshift_variant	6829	exon13			.	U56402	CCDS12536.1, CCDS46072.1	19q13	2008-07-22	2001-11-28			ENSG00000196235			11469	protein-coding gene	gene with protein product		602102	"suppressor of Ty (S.cerevisiae) 5 homolog"			8975720	Standard	NM_003169		Approved	SPT5H, SPT5, FLJ34157	uc002olp.4	O00267		ENST00000599117.1:c.1044delG	chr19.hg19:g.39959402delG	ENSP00000470252:p.Leu348fs	167.0	0.0		121.0	10.0	NM_003169	O43279|Q59G52|Q99639	Frame_Shift_Del	DEL	ENST00000599117.1	hg19	CCDS12536.1																																																																																			.	.		0.517	SUPT5H-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464918.1	NM_003169		-	39959402	G	-	39959402	7	5	282	1	0	1	0	1	0	0	0	0	15414	1335	47	0	1094	0	SUPT5H	19	39959402	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	53347	39959402	19169581	1246	41480										
SERTAD1	29950	hgsc.bcm.edu	37	chr19	40929172	40929172	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcagccacactgggggctgcAggtgggctaggcacaggtgg	18	10	1	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:40929172A>G	ENST00000357949.4	-	2	440	c.282T>C	c.(280-282)ccT>ccC	p.P94P		NM_013376.3	NP_037508.2	Q9UHV2	SRTD1_HUMAN	SERTA domain containing 1	94					positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription, DNA-templated (GO:0006351)					endometrium(2)|lung(1)|prostate(1)|skin(1)	5			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)			TGGGGGCTGCAGGTGGGCTAG	0.672																																					p.P94P		Atlas-SNP	.											.	SERTAD1	18	.	0			c.T282C						.						15	16	16					19																	40929172		2199	4297	6496	SO:0001819	synonymous_variant	29950	exon2			GGCTGCAGGTGGG	AF117959	CCDS12557.1	19q13.1-q13.2	2008-02-05				ENSG00000197019			17932	protein-coding gene	gene with protein product	"CDK4-binding protein p34SEI", "transcriptional regulator interacting with the PHD-bromodomain 1"					6434876, 10580009	Standard	NM_013376		Approved	SEI1, TRIP-Br1	uc002ont.4	Q9UHV2		ENST00000357949.4:c.282T>C	chr19.hg19:g.40929172A>G		182.0	0.0		148.0	6.0	NM_013376	Q9BUE7	Silent	SNP	ENST00000357949.4	hg19	CCDS12557.1																																																																																			.	.		0.672	SERTAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462571.1	NM_013376		G	40929172	A	G	40929172	2	3	282	1	0	0	0	0	0	0	0	1	14135	175	7	2		2	SERTAD1	19	40929172	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	969770	40929172	18199811	1247	41481										
SPTBN4	57731	hgsc.bcm.edu	37	chr19	41009859	41009859	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcggagctggcccaggcattGgcagccgaaggctactacga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:41009859delG	ENST00000352632.3	+	12	1571	c.1485delG	c.(1483-1485)ttgfs	p.L495fs	SPTBN4_ENST00000595535.1_Frame_Shift_Del_p.L495fs|SPTBN4_ENST00000344104.3_Frame_Shift_Del_p.L495fs|SPTBN4_ENST00000338932.3_Frame_Shift_Del_p.L495fs|SPTBN4_ENST00000598249.1_Frame_Shift_Del_p.L495fs			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	495					actin filament capping (GO:0051693)|adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cardiac conduction (GO:0061337)|central nervous system projection neuron axonogenesis (GO:0021952)|clustering of voltage-gated sodium channels (GO:0045162)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization to plasma membrane (GO:0090002)|fertilization (GO:0009566)|negative regulation of heart rate (GO:0010459)|positive regulation of multicellular organism growth (GO:0040018)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of sodium ion transport (GO:0002028)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|axon hillock (GO:0043203)|axon initial segment (GO:0043194)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|nuclear matrix (GO:0016363)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|PML body (GO:0016605)|spectrin (GO:0008091)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phosphatase binding (GO:0019902)|phospholipid binding (GO:0005543)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			breast(4)|central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	73			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			CCCAGGCATTGGCAGCCGAAG	0.667																																					p.L495fs		Atlas-INDEL	.											.	SPTBN4	213	.	0			c.1484delT						.						36	38	37					19																	41009859		2203	4300	6503	SO:0001589	frameshift_variant	57731	exon12			.	AF082075	CCDS12559.1, CCDS42569.1	19q13.13	2013-01-10				ENSG00000160460		"Pleckstrin homology (PH) domain containing"	14896	protein-coding gene	gene with protein product		606214				11086001	Standard	NM_020971		Approved	SPTBN3, KIAA1642	uc002onz.3	Q9H254		ENST00000352632.3:c.1485delG	chr19.hg19:g.41009859delG	ENSP00000263373:p.Leu495fs	213.0	0.0		148.0	10.0	NM_020971	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Frame_Shift_Del	DEL	ENST00000352632.3	hg19	CCDS12559.1																																																																																			.	.		0.667	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2			-	41009859	G	-	41009859	7	5	282	1	0	1	0	1	0	0	0	0	15136	1339	47	0	1527	0	SPTBN4	19	41009859	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	80687	41009859	18119124	1248	41482										
NUMBL	9253	hgsc.bcm.edu	37	chr19	41174028	41174028	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagggggcacggagggctcaCcccaggcagaagtccctgga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:41174028delC	ENST00000252891.4	-	10	1342	c.1175delG	c.(1174-1176)ggtfs	p.G392fs	NUMBL_ENST00000598779.1_Frame_Shift_Del_p.G351fs|NUMBL_ENST00000540131.1_Frame_Shift_Del_p.G351fs	NM_004756.3	NP_004747.1	Q9Y6R0	NUMBL_HUMAN	numb homolog (Drosophila)-like	392					adherens junction organization (GO:0034332)|axonogenesis (GO:0007409)|cytokine-mediated signaling pathway (GO:0019221)|lateral ventricle development (GO:0021670)|nervous system development (GO:0007399)|neuroblast division in subventricular zone (GO:0021849)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of neurogenesis (GO:0050769)|protein metabolic process (GO:0019538)	cytoplasm (GO:0005737)				NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(6)|ovary(2)	16			Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105)			GGAGGGCTCACCCCAGGCAGA	0.652																																					p.G392fs		Atlas-INDEL	.											.	NUMBL	49	.	0			c.1176delT						.						10	12	11					19																	41174028		2192	4279	6471	SO:0001589	frameshift_variant	9253	exon10			.	AF015401	CCDS12561.1	19q13.13-q13.2	2008-07-17	2001-11-28			ENSG00000105245			8061	protein-coding gene	gene with protein product		604018	"numb (Drosophila) homolog-like"			9225980, 9303539	Standard	XM_006723471		Approved	NUMB-R, CTG3a, CAG3A, TNRC23, NUMBR, NUMBLIKE	uc002oon.3	Q9Y6R0		ENST00000252891.4:c.1175delG	chr19.hg19:g.41174028delC	ENSP00000252891:p.Gly392fs	148.0	0.0		142.0	11.0	NM_004756	Q7Z4J9	Frame_Shift_Del	DEL	ENST00000252891.4	hg19	CCDS12561.1																																																																																			.	.		0.652	NUMBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462749.2	NM_004756		-	41174028	C	-	41174028	7	5	282	1	0	1	0	1	0	0	0	0	10761	507	18	0	658	0	NUMBL	19	41174028	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	164169	41174028	17954955	1249	41483										
CYP2S1	29785	hgsc.bcm.edu	37	chr19	41700601	41700601	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtagcgatgctggaagggacTtttgatggccatggtaagtc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:41700601delT	ENST00000310054.4	+	2	546	c.330delT	c.(328-330)actfs	p.T110fs	CYP2S1_ENST00000542619.1_5'UTR	NM_030622.6	NP_085125.1	Q96SQ9	CP2S1_HUMAN	cytochrome P450, family 2, subfamily S, polypeptide 1	110					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(1)|endometrium(3)|large_intestine(3)|lung(5)|skin(2)	14						TGGAAGGGACTTTTGATGGCC	0.612																																					p.T110fs		Atlas-INDEL	.											.	CYP2S1	47	.	0			c.329delC						.						135	103	114					19																	41700601		2203	4300	6503	SO:0001589	frameshift_variant	29785	exon2			.	AA301039	CCDS12573.1	19q13.2	2013-11-11	2003-01-14		ENSG00000167600	ENSG00000167600		"Cytochrome P450s"	15654	protein-coding gene	gene with protein product		611529	"cytochrome P450, subfamily IIS, polypeptide 1"			11181079	Standard	NM_030622		Approved		uc002opw.3	Q96SQ9	OTTHUMG00000182721	ENST00000310054.4:c.330delT	chr19.hg19:g.41700601delT	ENSP00000308032:p.Thr110fs	328.0	0.0		229.0	14.0	NM_030622	Q9BZ66	Frame_Shift_Del	DEL	ENST00000310054.4	hg19	CCDS12573.1																																																																																			.	.		0.612	CYP2S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463287.1			-	41700601	T	-	41700601	7	5	282	1	0	1	0	1	0	0	0	0	4176	1596	56	0	336	0	CYP2S1	19	41700601	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	526573	41700601	17428382	1250	41484										
ATP1A3	478	hgsc.bcm.edu	37	chr19	42479905	42479905	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atgtcggccttcttcagagcGggggagtcgttcacaccatc					rs141362710		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:42479905delG	ENST00000302102.5	-	16	2289	c.2139delC	c.(2137-2139)cccfs	p.P713fs	ATP1A3_ENST00000543770.1_Frame_Shift_Del_p.P724fs|ATP1A3_ENST00000545399.1_Frame_Shift_Del_p.P726fs|ATP1A3_ENST00000602133.1_Frame_Shift_Del_p.P683fs	NM_152296.4	NP_689509.1	P13637	AT1A3_HUMAN	ATPase, Na+/K+ transporting, alpha 3 polypeptide	713					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|memory (GO:0007613)|potassium ion import (GO:0010107)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	axon (GO:0030424)|dendritic spine head (GO:0044327)|dendritic spine neck (GO:0044326)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(19)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	52						TCTTCAGAGCGGGGGAGTCGT	0.612																																					p.A727fs		Atlas-INDEL	.											.	ATP1A3	117	.	0			c.2179delG						.						131	112	118					19																	42479905		2203	4300	6503	SO:0001589	frameshift_variant	478	exon16			.		CCDS12594.1, CCDS58663.1, CCDS58664.1	19q13.2	2012-10-22			ENSG00000105409	ENSG00000105409	3.6.3.9	"ATPases / P-type"	801	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-3", "sodium pump subunit alpha-3", "sodium-potassium ATPase catalytic subunit alpha-3"	182350	"dystonia 12"	DYT12		17282997	Standard	NM_152296		Approved		uc002osh.4	P13637	OTTHUMG00000137384	ENST00000302102.5:c.2139delC	chr19.hg19:g.42479905delG	ENSP00000302397:p.Pro713fs	215.0	0.0		165.0	12.0	NM_001256214	B7Z2T0|B7Z401|F5H6J6|Q16732|Q16735|Q969K5	Frame_Shift_Del	DEL	ENST00000302102.5	hg19	CCDS12594.1																																																																																			.	.		0.612	ATP1A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268107.1	NM_152296		-	42479905	G	-	42479905	7	5	282	1	0	1	0	1	0	0	0	0	1130	1103	39	0	934	0	ATP1A3	19	42479905	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	779304	42479905	16649078	1251	41485										
GSK3A	2931	hgsc.bcm.edu	37	chr19	42736820	42736820	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcgatggcctctggcggcgtTcgagatttgaacacctgagg	15	10	1	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:42736820T>G	ENST00000222330.3	-	9	1240	c.1113A>C	c.(1111-1113)cgA>cgC	p.R371R	GSK3A_ENST00000398249.4_Silent_p.R289R	NM_019884.2	NP_063937.2	P49840	GSK3A_HUMAN	glycogen synthase kinase 3 alpha	371	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cardiac left ventricle morphogenesis (GO:0003214)|cell migration (GO:0016477)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|cellular response to interleukin-3 (GO:0036016)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|endoplasmic reticulum unfolded protein response (GO:0030968)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glycogen metabolic process (GO:0005977)|hypermethylation of CpG island (GO:0044027)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell growth involved in cardiac muscle cell development (GO:0061052)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transferase activity (GO:0051348)|negative regulation of type B pancreatic cell development (GO:2000077)|negative regulation of UDP-glucose catabolic process (GO:0010905)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of adrenergic receptor signaling pathway (GO:0071879)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of heart contraction (GO:0045823)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein phosphorylation (GO:0006468)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of systemic arterial blood pressure (GO:0003073)|Wnt signaling pathway (GO:0016055)	beta-catenin destruction complex (GO:0030877)|cytosol (GO:0005829)	ATP binding (GO:0005524)|protein kinase A catalytic subunit binding (GO:0034236)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			endometrium(3)|large_intestine(3)|lung(6)|ovary(3)|prostate(2)|skin(1)|urinary_tract(1)	19		Prostate(69;0.00682)				CTGGCGGCGTTCGAGATTTGA	0.597																																					p.R371R		Atlas-SNP	.											.	GSK3A	45	.	0			c.A1113C						.						50	51	51					19																	42736820		2203	4300	6503	SO:0001819	synonymous_variant	2931	exon9			CGGCGTTCGAGAT		CCDS12599.1	19q13	2008-02-15			ENSG00000105723	ENSG00000105723			4616	protein-coding gene	gene with protein product		606784				9809441	Standard	NM_019884		Approved		uc002otb.1	P49840	OTTHUMG00000150722	ENST00000222330.3:c.1113A>C	chr19.hg19:g.42736820T>G		126.0	0.0		128.0	59.0	NM_019884	O14959	Silent	SNP	ENST00000222330.3	hg19	CCDS12599.1																																																																																			.	.		0.597	GSK3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319782.1			G	42736820	T	G	42736820	2	3	282	1	0	0	0	0	0	0	0	1	6832	1770	62	5		5	GSK3A	19	42736820	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	256915	42736820	16392163	1252	41486										
ERF	2077	hgsc.bcm.edu	37	chr19	42753385	42753385	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cctccccctgagccgctgggCcccccgccaccactggggta					rs201956380		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:42753385delC	ENST00000222329.4	-	4	1036	c.879delG	c.(877-879)gggfs	p.G293fs	ERF_ENST00000595941.1_5'Flank|AC006486.9_ENST00000594664.1_Intron|ERF_ENST00000440177.2_Frame_Shift_Del_p.G218fs	NM_006494.2	NP_006485.2	P50548	ERF_HUMAN	Ets2 repressor factor	293	Poly-Gly.				cell cycle (GO:0007049)|cell differentiation (GO:0030154)|chorio-allantoic fusion (GO:0060710)|ectodermal cell differentiation (GO:0010668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)|trophoblast giant cell differentiation (GO:0060707)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(1)	17		Prostate(69;0.00682)				AGCCGCTGGGCCCCCCGCCAC	0.667																																					p.P294fs		Atlas-INDEL	.											.	ERF	47	.	0			c.880delC						.						26	30	29					19																	42753385		2197	4288	6485	SO:0001589	frameshift_variant	2077	exon4			.	U58535	CCDS12600.1	19q13	2008-07-16				ENSG00000105722			3444	protein-coding gene	gene with protein product	"Ets2 repressor factor"	611888				7588608, 9192842	Standard	XM_005258644		Approved	PE-2, PE2	uc002ote.4	P50548		ENST00000222329.4:c.879delG	chr19.hg19:g.42753385delC	ENSP00000222329:p.Gly293fs	187.0	0.0		163.0	11.0	NM_006494	B2RAP1|B7Z4R0|Q59G38|Q9UPI7	Frame_Shift_Del	DEL	ENST00000222329.4	hg19	CCDS12600.1																																																																																			.	.		0.667	ERF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463684.1	NM_006494		-	42753385	C	-	42753385	7	5	282	1	0	1	0	1	0	0	0	0	5223	726	26	0	771	0	ERF	19	42753385	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	16565	42753385	16375598	1253	41487										
CIC	23152	hgsc.bcm.edu	37	chr19	42794469	42794469	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tggaccctgagcccccagggCccccggatcctcctgtagcc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:42794469delC	ENST00000575354.2	+	10	1589	c.1549delC	c.(1549-1551)cccfs	p.P518fs	CIC_ENST00000160740.3_Frame_Shift_Del_p.P518fs|CIC_ENST00000572681.2_Frame_Shift_Del_p.P1427fs	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	518	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.P518fs*5(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				GCCCCCAGGGCCCCCGGATCC	0.627			"Mis, F, S"		oligodendroglioma																																p.G516fs		Atlas-INDEL	.		Rec	yes		19	19q13.2	23152	capicua homolog		O	.	CIC	249	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1548delG						.						64	64	64					19																	42794469		2203	4300	6503	SO:0001589	frameshift_variant	23152	exon10			.	AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"capicua (Drosophila) homolog", "capicua homolog (Drosophila)"			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.1549delC	chr19.hg19:g.42794469delC	ENSP00000458663:p.Pro518fs	270.0	0.0		222.0	14.0	NM_015125	Q7LGI1|Q9UEG5|Q9Y6T1	Frame_Shift_Del	DEL	ENST00000575354.2	hg19	CCDS12601.1																																																																																			.	.		0.627	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			-	42794469	C	-	42794469	7	5	282	1	0	1	0	1	0	0	0	0	3426	739	26	0	1587	0	CIC	19	42794469	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	41084	42794469	16334514	1254	41488										
ZNF221	7638	hgsc.bcm.edu	37	chr19	44471324	44471324	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	catgcaccagagggtccacgGgggagagcgaccctataatt	13	11	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:44471324G>A	ENST00000251269.5	+	6	1998	c.1670G>A	c.(1669-1671)gGg>gAg	p.G557E	ZNF221_ENST00000587682.1_Missense_Mutation_p.G557E|ZNF221_ENST00000592350.1_Missense_Mutation_p.G557E	NM_013359.2	NP_037491	Q9UK13	ZN221_HUMAN	zinc finger protein 221	557			G -> R (in dbSNP:rs366111). {ECO:0000269|PubMed:12743021, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.5}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G557V(1)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(11)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	30		Prostate(69;0.0352)				AGGGTCCACGGGGGAGAGCGA	0.453																																					p.G557E		Atlas-SNP	.											.,1	ZNF221	59	.	1	Substitution - Missense(1)	lung(1)	c.G1670A						.						86	84	85					19																	44471324		2203	4300	6503	SO:0001583	missense	7638	exon6			TCCACGGGGGAGA	AF187987	CCDS12633.1	19q13.31	2013-01-08				ENSG00000159905		"Zinc fingers, C2H2-type", "-"	13014	protein-coding gene	gene with protein product							Standard	NM_013359		Approved		uc002oxx.2	Q9UK13		ENST00000251269.5:c.1670G>A	chr19.hg19:g.44471324G>A	ENSP00000251269:p.Gly557Glu	115.0	0.0		87.0	0.0	NM_013359	B2RAI6|Q2M2H2|Q9P1U8	Missense_Mutation	SNP	ENST00000251269.5	hg19	CCDS12633.1	.	.	.	.	.	.	.	.	.	.	g	15.07	2.725374	0.48833	.	.	ENSG00000159905	ENST00000251269	T	0.17054	2.3	2.77	0.498	0.16908	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07593	0.0191	N	0.04508	-0.205	0.09310	N	0.999994	B	0.02656	0.0	B	0.04013	0.001	T	0.31916	-0.9926	9	0.87932	D	0	.	6.751	0.23487	0.0:0.6588:0.2182:0.123	.	557	Q9UK13	ZN221_HUMAN	E	557	ENSP00000251269:G557E	ENSP00000251269:G557E	G	+	2	0	ZNF221	49163164	0.011000	0.17503	0.260000	0.24451	0.883000	0.51084	0.266000	0.18534	0.463000	0.27118	0.456000	0.33151	GGG	.	.		0.453	ZNF221-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460068.1			A	44471324	G	A	44471324	3	1	282	1	0	0	0	0	1	0	0	0	17790	1232	43	3	1684	3	ZNF221	19	44471324	Missense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1676855	44471324	14657659	1255	41489										
ZNF234	10780	hgsc.bcm.edu	37	chr19	44660629	44660629	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tttaccaatgtgatgagtacAaaaaatccttcactgatgtc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:44660629delA	ENST00000426739.2	+	6	718	c.460delA	c.(460-462)aaafs	p.K155fs	ZNF234_ENST00000592437.1_Frame_Shift_Del_p.K155fs	NM_006630.2	NP_006621.1	Q14588	ZN234_HUMAN	zinc finger protein 234	155					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)	23		Prostate(69;0.0435)				TGATGAGTACAAAAAATCCTT	0.403																																					p.Y153X		Atlas-INDEL	.											.	ZNF234	132	.	0			c.459delC						.						63	68	66					19																	44660629		2193	4295	6488	SO:0001589	frameshift_variant	10780	exon6			.	X78927	CCDS46101.1	19q13	2013-01-08				ENSG00000263002		"Zinc fingers, C2H2-type", "-"	13027	protein-coding gene	gene with protein product		604750		ZNF269		7865130	Standard	NM_006630		Approved	HZF4	uc002oyl.4	Q14588		ENST00000426739.2:c.460delA	chr19.hg19:g.44660629delA	ENSP00000400878:p.Lys155fs	300.0	0.0		169.0	11.0	NM_006630	A8K1C8|Q96IR4|Q9NS45|Q9NYT7	Frame_Shift_Del	DEL	ENST00000426739.2	hg19	CCDS46101.1																																																																																			.	.		0.403	ZNF234-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460586.2			-	44660629	A	-	44660629	7	5	282	1	0	1	0	1	0	0	0	0	17802	131	5	0	474	0	ZNF234	19	44660629	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	189305	44660629	14468354	1256	41490										
EXOC3L2	90332	hgsc.bcm.edu	37	chr19	45731493	45731493	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agtgctcttcgtcctcctgcAgcacacggagaagggcagcc	12	14	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:45731493A>G	ENST00000252482.3	-	2	149	c.122T>C	c.(121-123)cTg>cCg	p.L41P	EXOC3L2_ENST00000413988.1_Missense_Mutation_p.L41P			Q2M3D2	EX3L2_HUMAN	exocyst complex component 3-like 2	41					exocytosis (GO:0006887)	exocyst (GO:0000145)				endometrium(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00883)		GTCCTCCTGCAGCACACGGAG	0.632																																					p.L41P		Atlas-SNP	.											.	EXOC3L2	30	.	0			c.T122C						.						73	77	76					19																	45731493		2203	4300	6503	SO:0001583	missense	90332	exon3			TCCTGCAGCACAC	AK093466	CCDS12657.1	19q13.32	2011-07-07			ENSG00000130201	ENSG00000130201			30162	protein-coding gene	gene with protein product						21566143	Standard	NM_138568		Approved	FLJ36147, XTP7	uc002pay.1	Q2M3D2	OTTHUMG00000155018	ENST00000252482.3:c.122T>C	chr19.hg19:g.45731493A>G	ENSP00000252482:p.Leu41Pro	129.0	0.0		110.0	5.0	NM_138568	Q8N9W2|Q96GV2	Missense_Mutation	SNP	ENST00000252482.3	hg19	CCDS12657.1	.	.	.	.	.	.	.	.	.	.	A	14.41	2.526296	0.44969	.	.	ENSG00000130201	ENST00000252482;ENST00000413988	T;T	0.09073	3.02;3.02	4.89	4.89	0.63831	.	0.000000	0.50627	D	0.000102	T	0.26085	0.0636	M	0.72894	2.215	0.53688	D	0.99997	D	0.89917	1.0	D	0.97110	1.0	T	0.00912	-1.1517	10	0.87932	D	0	.	10.8643	0.46844	1.0:0.0:0.0:0.0	.	41	Q2M3D2	EX3L2_HUMAN	P	41	ENSP00000252482:L41P;ENSP00000400713:L41P	ENSP00000252482:L41P	L	-	2	0	EXOC3L2	50423333	0.966000	0.33281	0.666000	0.29783	0.136000	0.21042	4.999000	0.63934	1.836000	0.53414	0.254000	0.18369	CTG	.	.		0.632	EXOC3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338073.1	NM_138568		G	45731493	A	G	45731493	3	3	282	1	0	0	0	0	1	0	0	0	5307	188	7	2	1139	2	EXOC3L2	19	45731493	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1070864	45731493	13397490	1257	41491										
PRKD2	25865	hgsc.bcm.edu	37	chr19	47219519	47219519	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggaacccggggccgggatctGgggcagtagcggtggcggcg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:47219519delG	ENST00000291281.4	-	1	334	c.109delC	c.(109-111)cagfs	p.Q37fs	PRKD2_ENST00000600194.1_5'Flank|PRKD2_ENST00000433867.1_Frame_Shift_Del_p.Q37fs|PRKD2_ENST00000601806.1_Intron|PRKD2_ENST00000595515.1_Frame_Shift_Del_p.Q37fs			Q9BZL6	KPCD2_HUMAN	protein kinase D2	37					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial tube morphogenesis (GO:0061154)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(13)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	41		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000189)|all cancers(93;0.000545)|Epithelial(262;0.0219)|GBM - Glioblastoma multiforme(486;0.0353)		GCCGGGATCTGGGGCAGTAGC	0.721																																					p.Q37fs		Atlas-INDEL	.											.	PRKD2	94	.	0			c.110delA						.						18	24	22					19																	47219519		2185	4261	6446	SO:0001589	frameshift_variant	25865	exon1			.	AF151021	CCDS12689.1, CCDS59401.1	19q13.2	2013-01-10				ENSG00000105287		"Pleckstrin homology (PH) domain containing"	17293	protein-coding gene	gene with protein product		607074				11042152, 11062248	Standard	NM_001079880		Approved	PKD2, HSPC187, DKFZP586E0820	uc002pfj.3	Q9BZL6		ENST00000291281.4:c.109delC	chr19.hg19:g.47219519delG	ENSP00000291281:p.Gln37fs	218.0	0.0		180.0	11.0	NM_016457	Q8TB08|Q9P0T6|Q9Y3X8	Frame_Shift_Del	DEL	ENST00000291281.4	hg19	CCDS12689.1																																																																																			.	.		0.721	PRKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466591.1	NM_016457		-	47219519	G	-	47219519	7	5	282	1	0	1	0	1	0	0	0	0	12531	1357	47	0	2599	0	PRKD2	19	47219519	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1488026	47219519	11909464	1258	41492										
DHX34	9704	hgsc.bcm.edu	37	chr19	47880440	47880440	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acaagccgtacctggtgaacTgcgtccgcatccctgccctc	9	17	0	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:47880440T>A	ENST00000328771.4	+	13	3032	c.2683T>A	c.(2683-2685)Tgc>Agc	p.C895S		NM_014681.5	NP_055496.2	Q14147	DHX34_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 34	895					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	membrane (GO:0016020)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(5)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;7.16e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000489)|GBM - Glioblastoma multiforme(486;0.00413)|Epithelial(262;0.0132)		CCTGGTGAACTGCGTCCGCAT	0.637																																					p.C895S		Atlas-SNP	.											.	DHX34	98	.	0			c.T2683A						.						72	60	64					19																	47880440		2203	4300	6503	SO:0001583	missense	9704	exon13			GTGAACTGCGTCC	D50924	CCDS12700.1	19q13.3	2003-06-13	2003-06-13	2003-06-13	ENSG00000134815	ENSG00000134815		"DEAH-boxes"	16719	protein-coding gene	gene with protein product		615475	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 34"	DDX34		10708517, 8590280	Standard	NM_014681		Approved	KIAA0134	uc010xyn.2	Q14147	OTTHUMG00000149959	ENST00000328771.4:c.2683T>A	chr19.hg19:g.47880440T>A	ENSP00000331907:p.Cys895Ser	134.0	0.0		76.0	30.0	NM_014681	B4DMY8	Missense_Mutation	SNP	ENST00000328771.4	hg19	CCDS12700.1	.	.	.	.	.	.	.	.	.	.	T	16.64	3.179885	0.57800	.	.	ENSG00000134815	ENST00000328771	T	0.02579	4.24	3.43	3.43	0.39272	Domain of unknown function DUF1605 (1);	0.229124	0.29767	N	0.011260	T	0.03783	0.0107	L	0.58669	1.825	0.51482	D	0.999926	P	0.36086	0.536	B	0.31686	0.134	T	0.50056	-0.8872	10	0.40728	T	0.16	-23.6463	11.2761	0.49168	0.0:0.0:0.0:1.0	.	895	Q14147	DHX34_HUMAN	S	895	ENSP00000331907:C895S	ENSP00000331907:C895S	C	+	1	0	DHX34	52572238	1.000000	0.71417	0.999000	0.59377	0.986000	0.74619	5.151000	0.64875	1.561000	0.49584	0.459000	0.35465	TGC	.	.		0.637	DHX34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314313.3	NM_014681		A	47880440	T	A	47880440	3	1	282	1	0	0	0	0	1	0	0	0	4509	1580	55	4	2729	4	DHX34	19	47880440	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	660921	47880440	11248543	1259	41493										
KPTN	11133	hgsc.bcm.edu	37	chr19	47983122	47983122	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctcaaacccagagctcacccTtggcggccgagaggctgaac	11	15	2	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:47983122T>C	ENST00000338134.3	-	8	892	c.785A>G	c.(784-786)aAg>aGg	p.K262R	KPTN_ENST00000595484.1_5'Flank|KPTN_ENST00000536339.1_Missense_Mutation_p.K22R	NM_007059.2	NP_008990.2	Q9Y664	KPTN_HUMAN	kaptin (actin binding protein)	262					actin filament organization (GO:0007015)|cellular component movement (GO:0006928)|sensory perception of sound (GO:0007605)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	actin binding (GO:0003779)			breast(1)|lung(3)|ovary(2)|pancreas(2)	8		all_cancers(25;1.55e-10)|all_epithelial(76;3.4e-08)|all_lung(116;1.73e-07)|Lung NSC(112;3.95e-07)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		OV - Ovarian serous cystadenocarcinoma(262;0.000428)|all cancers(93;0.000631)|Epithelial(262;0.0153)|GBM - Glioblastoma multiforme(486;0.0694)		GAGCTCACCCTTGGCGGCCGA	0.602																																					p.K262R		Atlas-SNP	.											.	KPTN	34	.	0			c.A785G						.						36	41	39					19																	47983122		1985	4150	6135	SO:0001583	missense	11133	exon8			TCACCCTTGGCGG	AF105369	CCDS42583.1	19q13.32	2014-08-13	2001-11-28		ENSG00000118162	ENSG00000118162			6404	protein-coding gene	gene with protein product		615620	"kaptin (actin-binding protein)"			10099934	Standard	XM_005258467		Approved	2E4	uc002pgy.3	Q9Y664	OTTHUMG00000183443	ENST00000338134.3:c.785A>G	chr19.hg19:g.47983122T>C	ENSP00000337850:p.Lys262Arg	100.0	0.0		88.0	4.0	NM_007059	B3KN86|B4DQ76|Q96GT1	Missense_Mutation	SNP	ENST00000338134.3	hg19	CCDS42583.1	.	.	.	.	.	.	.	.	.	.	T	12.81	2.048138	0.36181	.	.	ENSG00000118162	ENST00000338134;ENST00000536339	.	.	.	3.31	0.887	0.19200	.	0.703686	0.13491	N	0.383969	T	0.15696	0.0378	N	0.08118	0	0.09310	N	1	B	0.12630	0.006	B	0.15870	0.014	T	0.28996	-1.0026	9	0.16896	T	0.51	-11.0182	7.0573	0.25106	0.0:0.0:0.4742:0.5258	.	262	Q9Y664	KPTN_HUMAN	R	262;22	.	ENSP00000337850:K262R	K	-	2	0	KPTN	52674934	0.003000	0.15002	0.747000	0.31113	0.846000	0.48090	1.123000	0.31308	0.451000	0.26802	0.255000	0.18592	AAG	.	.		0.602	KPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466672.2			C	47983122	T	C	47983122	3	2	282	1	0	0	0	0	1	0	0	0	8446	1609	56	2	545	2	KPTN	19	47983122	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	102682	47983122	11145861	1260	41494										
EHD2	30846	hgsc.bcm.edu	37	chr19	48229399	48229399	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cgagctggaggagcaggaccTcttccgcgacatccagggcc	14	14	1	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:48229399T>C	ENST00000263277.3	+	4	1084	c.833T>C	c.(832-834)cTc>cCc	p.L278P	EHD2_ENST00000538399.1_Missense_Mutation_p.L142P|CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_014601.3	NP_055416.2	Q9NZN4	EHD2_HUMAN	EH-domain containing 2	278	Dynamin-type G.				blood coagulation (GO:0007596)|cortical actin cytoskeleton organization (GO:0030866)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of myoblast fusion (GO:1901741)|protein localization to plasma membrane (GO:0072659)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|nucleic acid binding (GO:0003676)			endometrium(3)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	19		all_cancers(25;6.74e-07)|all_lung(116;2.02e-05)|Lung NSC(112;3.77e-05)|all_epithelial(76;4.89e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		OV - Ovarian serous cystadenocarcinoma(262;0.000336)|all cancers(93;0.000415)|Epithelial(262;0.0132)|GBM - Glioblastoma multiforme(486;0.0537)		GAGCAGGACCTCTTCCGCGAC	0.687																																					p.L278P		Atlas-SNP	.											.	EHD2	59	.	0			c.T833C						.						18	18	18					19																	48229399		2201	4296	6497	SO:0001583	missense	30846	exon4			AGGACCTCTTCCG	AF181263	CCDS12704.1	19q13.3	2014-08-12			ENSG00000024422	ENSG00000024422		"EF-hand domain containing"	3243	protein-coding gene	gene with protein product		605890		PAST2		10673336	Standard	NM_014601		Approved		uc002phj.4	Q9NZN4	OTTHUMG00000183266	ENST00000263277.3:c.833T>C	chr19.hg19:g.48229399T>C	ENSP00000263277:p.Leu278Pro	65.0	0.0		48.0	4.0	NM_014601	B2RDH9|B4DNU6|Q96CB6	Missense_Mutation	SNP	ENST00000263277.3	hg19	CCDS12704.1	.	.	.	.	.	.	.	.	.	.	T	19.76	3.887744	0.72410	.	.	ENSG00000024422	ENST00000263277;ENST00000539439;ENST00000540364;ENST00000538399	D;D	0.96587	-4.06;-4.06	3.66	3.66	0.41972	.	0.186089	0.34879	N	0.003613	D	0.98049	0.9357	M	0.89840	3.065	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	D	0.98385	1.0560	10	0.87932	D	0	-23.6188	10.6051	0.45390	0.0:0.0:0.0:1.0	.	278	Q9NZN4	EHD2_HUMAN	P	278;278;268;142	ENSP00000263277:L278P;ENSP00000439036:L142P	ENSP00000263277:L278P	L	+	2	0	EHD2	52921211	0.999000	0.42202	0.998000	0.56505	0.992000	0.81027	7.828000	0.86729	1.463000	0.47967	0.374000	0.22700	CTC	.	.		0.687	EHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465851.1			C	48229399	T	C	48229399	3	2	282	1	0	0	0	0	1	0	0	0	4980	1551	54	2	843	2	EHD2	19	48229399	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	246277	48229399	10899584	1261	41495										
PLA2G4C	8605	hgsc.bcm.edu	37	chr19	48558214	48558214	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttcaggatgtagcagctggcGggggccttggaccacaaatc					rs557617265	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:48558214delG	ENST00000599921.1	-	15	1707	c.1350delC	c.(1348-1350)cccfs	p.P450fs	PLA2G4C_ENST00000596510.1_5'UTR|PLA2G4C_ENST00000354276.3_Frame_Shift_Del_p.P450fs|PLA2G4C_ENST00000599111.1_Frame_Shift_Del_p.P460fs|PLA2G4C_ENST00000413144.2_Frame_Shift_Del_p.P450fs			Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC (cytosolic, calcium-independent)	450	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid metabolic process (GO:0019369)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|parturition (GO:0007567)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(12)|lung(13)|ovary(2)|prostate(1)|skin(3)	38		all_cancers(25;2.84e-05)|all_lung(116;4.62e-05)|Lung NSC(112;7.61e-05)|all_epithelial(76;0.000192)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;8.09e-05)|all cancers(93;0.000517)|Epithelial(262;0.0135)|GBM - Glioblastoma multiforme(486;0.0717)		AGCAGCTGGCGGGGGCCTTGG	0.567																																					p.A461fs		Atlas-INDEL	.											PLA2G4C,NS,carcinoma,0,2	PLA2G4C	76	.	0			c.1381delG						.						99	98	98					19																	48558214		2203	4300	6503	SO:0001589	frameshift_variant	8605	exon15			.	AF065214	CCDS12710.1, CCDS54286.1, CCDS59403.1	19q13.3	2008-09-19					3.1.1.4		9037	protein-coding gene	gene with protein product		603602				9705332	Standard	NM_003706		Approved	cPLA2-gamma	uc002phx.3	Q9UP65		ENST00000599921.1:c.1350delC	chr19.hg19:g.48558214delG	ENSP00000469473:p.Pro450fs	180.0	0.0		171.0	11.0	NM_001159322	B2RB71|B4DI40|O75457|Q6IBI8|Q9UG68	Frame_Shift_Del	DEL	ENST00000599921.1	hg19	CCDS12710.1																																																																																			.	.		0.567	PLA2G4C-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465551.1			-	48558214	G	-	48558214	7	5	282	1	0	1	0	1	0	0	0	0	12012	1103	39	0	291	0	PLA2G4C	19	48558214	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	328815	48558214	10570769	1262	41496										
GRIN2D	2906	hgsc.bcm.edu	37	chr19	48918135	48918135	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccgcagccctccaccggatgCcccccgcccggaaaagcgct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:48918135delC	ENST00000263269.3	+	6	1515	c.1427delC	c.(1426-1428)gccfs	p.A476fs		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	476					adult locomotory behavior (GO:0008344)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|regulation of sensory perception of pain (GO:0051930)|signal transduction (GO:0007165)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)			autonomic_ganglia(1)|breast(6)|endometrium(2)|large_intestine(9)|lung(12)|ovary(5)|pancreas(1)|prostate(1)	37		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CCACCGGATGCCCCCCGCCCG	0.607																																					p.A476fs		Atlas-INDEL	.											.	GRIN2D	76	.	0			c.1426delG						.						43	49	47					19																	48918135		2203	4300	6503	SO:0001589	frameshift_variant	2906	exon6			.	U77783	CCDS12719.1	19q13.33	2012-08-29			ENSG00000105464	ENSG00000105464		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4588	protein-coding gene	gene with protein product	"N-methyl-d-aspartate receptor subunit 2D"	602717		NMDAR2D		9480759, 9418891	Standard	NM_000836		Approved	GluN2D, EB11, NR2D	uc002pjc.4	O15399		ENST00000263269.3:c.1427delC	chr19.hg19:g.48918135delC	ENSP00000263269:p.Ala476fs	244.0	0.0		162.0	11.0	NM_000836		Frame_Shift_Del	DEL	ENST00000263269.3	hg19	CCDS12719.1																																																																																			.	.		0.607	GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466121.1			-	48918135	C	-	48918135	7	5	282	1	0	1	0	1	0	0	0	0	6791	739	26	0	1445	0	GRIN2D	19	48918135	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	359921	48918135	10210848	1263	41497										
SPHK2	56848	hgsc.bcm.edu	37	chr19	49132347	49132347	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctgacctgcctcttcccctgCcccagcctgccctggcctct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:49132347delC	ENST00000245222.4	+	7	1648	c.1282delC	c.(1282-1284)cccfs	p.P428fs	SPHK2_ENST00000340932.3_Frame_Shift_Del_p.P390fs|SPHK2_ENST00000600537.1_Frame_Shift_Del_p.P369fs|SPHK2_ENST00000599029.1_Frame_Shift_Del_p.P392fs|SPHK2_ENST00000598088.1_Frame_Shift_Del_p.P428fs|SPHK2_ENST00000443164.1_Frame_Shift_Del_p.P490fs|SPHK2_ENST00000599748.1_Frame_Shift_Del_p.P392fs	NM_001204158.2|NM_001243876.1|NM_020126.4	NP_001191087.1|NP_001230805.1|NP_064511.2	Q9NRA0	SPHK2_HUMAN	sphingosine kinase 2	428					blood vessel development (GO:0001568)|brain development (GO:0007420)|cell proliferation (GO:0008283)|lipid phosphorylation (GO:0046834)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|small molecule metabolic process (GO:0044281)|sphinganine-1-phosphate biosynthetic process (GO:0006669)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	ATP binding (GO:0005524)|D-erythro-sphingosine kinase activity (GO:0017050)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)|Ras GTPase binding (GO:0017016)|sphinganine kinase activity (GO:0008481)			NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	19		all_lung(116;0.000125)|Lung NSC(112;0.000202)|all_epithelial(76;0.000283)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)		tcttcccctgccccagcctgc	0.697																																					p.L427fs		Atlas-INDEL	.											.	SPHK2	62	.	0			c.1281delG						.						22	24	23					19																	49132347		2201	4293	6494	SO:0001589	frameshift_variant	56848	exon7			.	AF245447	CCDS12727.1, CCDS59404.1, CCDS59405.1, CCDS74414.1	19q13.33	2013-09-20			ENSG00000063176	ENSG00000063176			18859	protein-coding gene	gene with protein product		607092				10751414, 17895250	Standard	NM_020126		Approved		uc002pjs.3	Q9NRA0	OTTHUMG00000183318	ENST00000245222.4:c.1282delC	chr19.hg19:g.49132347delC	ENSP00000245222:p.Pro428fs	235.0	0.0		177.0	11.0	NM_020126	A0T4C8|B4DU87|Q9BRN1|Q9H0Q2|Q9NWU7	Frame_Shift_Del	DEL	ENST00000245222.4	hg19	CCDS12727.1																																																																																			.	.		0.697	SPHK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466153.1			-	49132347	C	-	49132347	7	5	282	1	0	1	0	1	0	0	0	0	15062	739	26	0	1304	0	SPHK2	19	49132347	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	214212	49132347	9996636	1264	41498										
PLEKHA4	57664	hgsc.bcm.edu	37	chr19	49342505	49342505	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gagccatttctgggctcccgAgtgtcctacgacaggctgga	13	12	1	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:49342505A>G	ENST00000263265.6	-	18	2476	c.1921T>C	c.(1921-1923)Tcg>Ccg	p.S641P	PLEKHA4_ENST00000355496.5_Intron|HSD17B14_ENST00000599157.1_5'Flank|HSD17B14_ENST00000263278.4_5'Flank	NM_020904.2	NP_065955.2	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4	641						cytoplasm (GO:0005737)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	30		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;0.000108)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.00027)|all cancers(93;0.00084)|GBM - Glioblastoma multiforme(486;0.0244)|Epithelial(262;0.0364)		TGGGCTCCCGAGTGTCCTACG	0.512																																					p.S641P		Atlas-SNP	.											.	PLEKHA4	70	.	0			c.T1921C						.						56	51	53					19																	49342505		2203	4300	6503	SO:0001583	missense	57664	exon18			CTCCCGAGTGTCC	AY007233	CCDS12737.1, CCDS54291.1	19q13.33	2013-01-10	2002-01-14			ENSG00000105559		"Pleckstrin homology (PH) domain containing"	14339	protein-coding gene	gene with protein product		607769	"pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 4"			11001876	Standard	NM_020904		Approved	PEPP1	uc002pkx.3	Q9H4M7		ENST00000263265.6:c.1921T>C	chr19.hg19:g.49342505A>G	ENSP00000263265:p.Ser641Pro	176.0	0.0		116.0	5.0	NM_020904	Q8N4M8|Q8N658	Missense_Mutation	SNP	ENST00000263265.6	hg19	CCDS12737.1	.	.	.	.	.	.	.	.	.	.	a	9.464	1.093886	0.20471	.	.	ENSG00000105559	ENST00000263265	T	0.25250	1.81	2.96	-1.13	0.09775	.	3.198660	0.01273	N	0.009506	T	0.17704	0.0425	N	0.24115	0.695	0.27321	N	0.957047	B	0.22604	0.072	B	0.22601	0.04	T	0.29731	-1.0002	10	0.72032	D	0.01	.	3.3348	0.07097	0.34:0.1992:0.0:0.4608	.	641	Q9H4M7	PKHA4_HUMAN	P	641	ENSP00000263265:S641P	ENSP00000263265:S641P	S	-	1	0	PLEKHA4	54034317	0.795000	0.28851	0.565000	0.28409	0.687000	0.40016	0.083000	0.14871	-0.037000	0.13646	0.364000	0.22116	TCG	.	.		0.512	PLEKHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466216.1			G	49342505	A	G	49342505	3	3	282	1	0	0	0	0	1	0	0	0	12067	304	11	2	430	2	PLEKHA4	19	49342505	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	210158	49342505	9786478	1265	41499										
DHDH	27294	hgsc.bcm.edu	37	chr19	49442857	49442857	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccgggcccaggctgggggggCcctgctggacatcggcatct	17	14	1	0	rs543413361		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:49442857C>G	ENST00000221403.2	+	4	558	c.518C>G	c.(517-519)gCc>gGc	p.A173G	DHDH_ENST00000522614.1_Missense_Mutation_p.A173G|DHDH_ENST00000523250.1_Intron	NM_014475.3	NP_055290.1	Q9UQ10	DHDH_HUMAN	dihydrodiol dehydrogenase (dimeric)	173					carbohydrate metabolic process (GO:0005975)|D-xylose catabolic process (GO:0042843)		D-xylose 1-dehydrogenase (NADP+) activity (GO:0047837)|electron carrier activity (GO:0009055)|NAD(P)+ transhydrogenase activity (GO:0008746)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			central_nervous_system(1)|large_intestine(3)|lung(3)|ovary(1)|soft_tissue(1)	9		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000158)|all cancers(93;0.000258)|Epithelial(262;0.0173)|GBM - Glioblastoma multiforme(486;0.0179)		GCTGGGGGGGCCCTGCTGGAC	0.602													C|||	1	0.000199681	8e-04	0	5008	,	,		17572	0		0	False		,,,				2504	0				p.A173G		Atlas-SNP	.											DHDH,colon,carcinoma,0,1	DHDH	35	.	0			c.C518G						.						53	56	55					19																	49442857		2203	4300	6503	SO:0001583	missense	27294	exon4			GGGGGGCCCTGCT	AB021933	CCDS12741.1	19q13.3	2008-02-05			ENSG00000104808	ENSG00000104808	1.3.1.20		17887	protein-coding gene	gene with protein product		606377				10477285	Standard	NM_014475		Approved	HUM2DD	uc002ple.1	Q9UQ10	OTTHUMG00000165029	ENST00000221403.2:c.518C>G	chr19.hg19:g.49442857C>G	ENSP00000221403:p.Ala173Gly	105.0	1.0		80.0	5.0	NM_014475		Missense_Mutation	SNP	ENST00000221403.2	hg19	CCDS12741.1	.	.	.	.	.	.	.	.	.	.	C	1.710	-0.499278	0.04291	.	.	ENSG00000104808	ENST00000221403;ENST00000522614	T;T	0.38560	1.13;1.13	5.12	0.225	0.15325	.	0.219759	0.45606	N	0.000342	T	0.35653	0.0939	L	0.45228	1.405	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.36138	-0.9760	10	0.42905	T	0.14	-7.1401	17.2381	0.87005	0.0:0.6748:0.3252:0.0	rs58913518	173	Q9UQ10	DHDH_HUMAN	G	173	ENSP00000221403:A173G;ENSP00000428672:A173G	ENSP00000221403:A173G	A	+	2	0	DHDH	54134669	0.094000	0.21725	0.003000	0.11579	0.006000	0.05464	0.971000	0.29396	0.096000	0.17463	-0.270000	0.10280	GCC	.	.		0.602	DHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381477.1	NM_014475		G	49442857	C	G	49442857	3	3	282	1	0	0	0	0	1	0	0	0	4481	739	26	4	532	4	DHDH	19	49442857	Missense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	100352	49442857	9686126	1266	41500										
PRR12	57479	hgsc.bcm.edu	37	chr19	50123635	50123635	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagtacctgggcgtctgctcAaaaccagggcgatgcgggag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:50123635delA	ENST00000418929.2	+	10	5536	c.5524delA	c.(5524-5526)aaafs	p.K1842fs		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	1021							DNA binding (GO:0003677)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)|prostate(2)	11		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		GCGTCTGCTCAAAACCAGGGC	0.577																																					p.L1841fs		Atlas-INDEL	.											.	PRR12	157	.	0			c.5523delC						.						45	49	48					19																	50123635		2114	4233	6347	SO:0001589	frameshift_variant	57479	exon10			.	AB033031	CCDS46143.1	19q13.33	2008-07-02	2006-02-06	2006-02-06		ENSG00000126464			29217	protein-coding gene	gene with protein product			"KIAA1205"	KIAA1205		10574462	Standard	NM_020719		Approved		uc002poo.4	Q9ULL5		ENST00000418929.2:c.5524delA	chr19.hg19:g.50123635delA	ENSP00000394510:p.Lys1842fs	218.0	0.0		185.0	12.0	NM_020719	E9PB06|Q8N4J6	Frame_Shift_Del	DEL	ENST00000418929.2	hg19	CCDS46143.1																																																																																			.	.		0.577	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719		-	50123635	A	-	50123635	7	5	282	1	0	1	0	1	0	0	0	0	12596	131	5	0	5562	0	PRR12	19	50123635	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	680778	50123635	9005348	1267	41501										
MED25	81857	hgsc.bcm.edu	37	chr19	50339074	50339074	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agccccaaggtactgcccagCccccgccaggtgcccctcaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:50339074delC	ENST00000312865.6	+	16	1890	c.1837delC	c.(1837-1839)cccfs	p.P615fs	PTOV1-AS1_ENST00000596521.1_RNA|MED25_ENST00000538643.1_Frame_Shift_Del_p.P402fs	NM_030973.3	NP_112235.2	Q71SY5	MED25_HUMAN	mediator complex subunit 25	615	Interaction with RARA.|Pro-rich.				cell death (GO:0008219)|gene expression (GO:0010467)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of chromatin binding (GO:0035563)|positive regulation of mediator complex assembly (GO:2001178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|transcription factor binding (GO:0008134)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)|stomach(1)|urinary_tract(1)	17		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00822)|GBM - Glioblastoma multiforme(134;0.0122)		TACTGCCCAGCCCCCGCCAGG	0.721																																					p.Q612fs	GBM(51;894 1657 37868)	Atlas-INDEL	.											.	MED25	98	.	0			c.1836delG						.																																			SO:0001589	frameshift_variant	81857	exon16			.	AL136746	CCDS33075.1	19q13.3	2014-09-17	2007-07-30			ENSG00000104973			28845	protein-coding gene	gene with protein product		610197	"mediator of RNA polymerase II transcription, subunit 25 homolog (S. cerevisiae)"			9110174, 11230166	Standard	NM_030973		Approved	ARC92, ACID1, TCBAP0758, DKFZp434K0512	uc002ppw.2	Q71SY5		ENST00000312865.6:c.1837delC	chr19.hg19:g.50339074delC	ENSP00000326767:p.Pro615fs	187.0	0.0		147.0	11.0	NM_030973	A8K095|B9TX30|O95783|Q6P143|Q6QMH5|Q707U4|Q8TB55|Q9H0L5|Q9HB34	Frame_Shift_Del	DEL	ENST00000312865.6	hg19	CCDS33075.1																																																																																			.	.		0.721	MED25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465316.1	NM_030973		-	50339074	C	-	50339074	7	5	282	1	0	1	0	1	0	0	0	0	9452	739	26	0	1899	0	MED25	19	50339074	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	215439	50339074	8789909	1268	41502										
MYH14	79784	hgsc.bcm.edu	37	chr19	50771494	50771494	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgcagaggccgaggagacgcGggggaggctggcagcccgca					rs561594120		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:50771494delG	ENST00000596571.1	+	21	2780	c.2780delG	c.(2779-2781)cggfs	p.R927fs	MYH14_ENST00000262269.8_Frame_Shift_Del_p.R968fs|MYH14_ENST00000440075.2_Frame_Shift_Del_p.R968fs|MYH14_ENST00000598205.1_Frame_Shift_Del_p.R935fs|MYH14_ENST00000425460.1_Frame_Shift_Del_p.R935fs|MYH14_ENST00000376970.2_Frame_Shift_Del_p.R960fs|MYH14_ENST00000601313.1_Frame_Shift_Del_p.R968fs			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	927					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		GAGGAGACGCGGGGGAGGCTG	0.657																																					p.R968fs		Atlas-INDEL	.											.	MYH14	261	.	0			c.2902delC						.																																			SO:0001589	frameshift_variant	79784	exon24			.	AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"Myosins / Myosin superfamily : Class II"	23212	protein-coding gene	gene with protein product		608568	"myosin, heavy polypeptide 14", "myosin, heavy chain 14"	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.2780delG	chr19.hg19:g.50771494delG	ENSP00000472819:p.Arg927fs	219.0	0.0		161.0	10.0	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Frame_Shift_Del	DEL	ENST00000596571.1	hg19	CCDS59411.1																																																																																			.	.		0.657	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729		-	50771494	G	-	50771494	7	5	282	1	0	1	0	1	0	0	0	0	10042	1116	39	0	2993	0	MYH14	19	50771494	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	432420	50771494	8357489	1269	41503										
C19orf63	284361	hgsc.bcm.edu	37	chr19	50983927	50983927	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggcgtgtcggtggtgacgcaCcccgggggctgccggggcca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:50983927delC	ENST00000334976.6	+	5	538	c.492delC	c.(490-492)cacfs	p.H164fs	EMC10_ENST00000598585.1_Frame_Shift_Del_p.H164fs|EMC10_ENST00000376918.3_Frame_Shift_Del_p.H164fs|CTD-2545M3.2_ENST00000598194.1_RNA	NM_206538.2	NP_996261.1	Q5UCC4	EMC10_HUMAN	ER membrane protein complex subunit 10	164						ER membrane protein complex (GO:0072546)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)											TGGTGACGCACCCCGGGGGCT	0.697																																					p.H164fs		Atlas-INDEL	.											.	.	.	.	0			c.491delA						.						24	25	25					19																	50983927		2189	4291	6480	SO:0001589	frameshift_variant	284361	exon5			.	BC062607	CCDS12796.1, CCDS42594.1	19q13.33	2012-05-30	2012-05-30	2012-05-30	ENSG00000161671	ENSG00000161671			27609	protein-coding gene	gene with protein product	"hematopoietic signal peptide-containing secreted 1", "hematopoietic signal peptide-containing membrane domain-containing 1"	614545	"chromosome 19 open reading frame 63"	C19orf63		12975309, 22119785	Standard	NM_175063		Approved	INM02, HSS1, HSM1	uc002psl.3	Q5UCC4		ENST00000334976.6:c.492delC	chr19.hg19:g.50983927delC	ENSP00000334037:p.His164fs	94.0	0.0		77.0	10.0	NM_175063	Q5UCC6|Q69YT5|Q6UWP3|Q86YL4|Q8N541	Frame_Shift_Del	DEL	ENST00000334976.6	hg19	CCDS12796.1																																																																																			.	.		0.697	EMC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464760.2	NM_175063		-	50983927	C	-	50983927	7	5	282	1	0	1	0	1	0	0	0	0	1947	506	18	0	510	0	C19orf63	19	50983927	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	212433	50983927	8145056	1270	41504	207	2								
C19orf63	284361	hgsc.bcm.edu	37	chr19	50983931	50983931	+	Missense_Mutation	SNP	G	G	T													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgtcggtggtgacgcaccccGggggctgccggggccatgag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:50983931G>T	ENST00000334976.6	+	5	542	c.496G>T	c.(496-498)Ggg>Tgg	p.G166W	EMC10_ENST00000598585.1_Missense_Mutation_p.G166W|EMC10_ENST00000376918.3_Missense_Mutation_p.G166W|CTD-2545M3.2_ENST00000598194.1_RNA	NM_206538.2	NP_996261.1	Q5UCC4	EMC10_HUMAN	ER membrane protein complex subunit 10	166						ER membrane protein complex (GO:0072546)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)											GACGCACCCCGGGGGCTGCCG	0.697																																					p.G166W		Atlas-SNP	.											.	.	.	.	0			c.G496T						.						24	25	24					19																	50983931		2192	4294	6486	SO:0001583	missense	284361	exon5			CACCCCGGGGGCT	BC062607	CCDS12796.1, CCDS42594.1	19q13.33	2012-05-30	2012-05-30	2012-05-30	ENSG00000161671	ENSG00000161671			27609	protein-coding gene	gene with protein product	"hematopoietic signal peptide-containing secreted 1", "hematopoietic signal peptide-containing membrane domain-containing 1"	614545	"chromosome 19 open reading frame 63"	C19orf63		12975309, 22119785	Standard	NM_175063		Approved	INM02, HSS1, HSM1	uc002psl.3	Q5UCC4		ENST00000334976.6:c.496G>T	chr19.hg19:g.50983931G>T	ENSP00000334037:p.Gly166Trp	93.0	0.0		73.0	5.0	NM_175063	Q5UCC6|Q69YT5|Q6UWP3|Q86YL4|Q8N541	Missense_Mutation	SNP	ENST00000334976.6	hg19	CCDS12796.1	.	.	.	.	.	.	.	.	.	.	G	17.72	3.459701	0.63401	.	.	ENSG00000161671	ENST00000334976;ENST00000376918;ENST00000376920	.	.	.	4.26	4.26	0.50523	.	0.000000	0.85682	D	0.000000	T	0.79311	0.4424	M	0.78637	2.42	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	T	0.82959	-0.0198	9	0.87932	D	0	-3.8968	16.2935	0.82761	0.0:0.0:1.0:0.0	.	166;166;166	Q5UCC4;Q5UCC4-2;Q5UCC4-3	INM02_HUMAN;.;.	W	166	.	ENSP00000334037:G166W	G	+	1	0	C19orf63	55675743	1.000000	0.71417	0.969000	0.41365	0.089000	0.18198	8.578000	0.90777	2.299000	0.77371	0.491000	0.48974	GGG	.	.		0.697	EMC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464760.2	NM_175063		T	50983931	G	T	50983931	3	4	282	1	0	0	0	0	1	0	0	0	1947	1116	39	1	514	1	C19orf63	19	50983931	Missense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	4	50983931	8145052	1271	41505	207	2								
ZNF615	284370	hgsc.bcm.edu	37	chr19	52497175	52497175	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gctgatgtgtgataagactgTtcttcaaggtgaagcctttc	11	7	2	4			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:52497175T>C	ENST00000602063.1	-	6	1503	c.1154A>G	c.(1153-1155)aAc>aGc	p.N385S	ZNF615_ENST00000391795.3_Missense_Mutation_p.N390S|ZNF615_ENST00000594083.1_Missense_Mutation_p.N396S|ZNF615_ENST00000376716.5_Missense_Mutation_p.N385S|ZNF615_ENST00000598071.1_Missense_Mutation_p.N396S			Q8N8J6	ZN615_HUMAN	zinc finger protein 615	385					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(5)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	42		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00142)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		GATAAGACTGTTCTTCAAGGT	0.398																																					p.N396S		Atlas-SNP	.											.	ZNF615	111	.	0			c.A1187G						.						96	91	93					19																	52497175		2203	4300	6503	SO:0001583	missense	284370	exon7			AGACTGTTCTTCA	AK096691	CCDS12846.1, CCDS59418.1	19q13.41	2013-01-08						"Zinc fingers, C2H2-type", "-"	24740	protein-coding gene	gene with protein product						12477932	Standard	NM_001199324		Approved	FLJ33710	uc002pyf.2	Q8N8J6		ENST00000602063.1:c.1154A>G	chr19.hg19:g.52497175T>C	ENSP00000473089:p.Asn385Ser	132.0	0.0		113.0	7.0	NM_001199324	B7ZKW9|Q2M2Y6|Q5CZB0|Q6ZMT7|Q6ZRB3	Missense_Mutation	SNP	ENST00000602063.1	hg19	CCDS12846.1	.	.	.	.	.	.	.	.	.	.	T	0.006	-2.083355	0.00371	.	.	ENSG00000197619	ENST00000376716;ENST00000354939;ENST00000391795;ENST00000391793	T;T	0.48522	0.81;0.81	3.26	0.971	0.19698	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12603	0.0306	N	0.01405	-0.89	0.09310	N	1	B;B;B;B	0.14012	0.005;0.009;0.009;0.005	B;B;B;B	0.09377	0.002;0.004;0.004;0.002	T	0.31308	-0.9948	9	0.02654	T	1	.	1.0254	0.01526	0.2216:0.1139:0.1672:0.4972	.	390;392;396;385	B4DH87;Q8N8J6-3;Q8N8J6-2;Q8N8J6	.;.;.;ZN615_HUMAN	S	385;395;390;395	ENSP00000365906:N385S;ENSP00000375672:N390S	ENSP00000347019:N395S	N	-	2	0	ZNF615	57188987	0.000000	0.05858	0.082000	0.20525	0.797000	0.45037	-0.942000	0.03921	0.341000	0.23771	0.528000	0.53228	AAC	.	.		0.398	ZNF615-009	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462391.1	NM_198480		C	52497175	T	C	52497175	3	2	282	1	0	0	0	0	1	0	0	0	18055	1725	60	2	1045	2	ZNF615	19	52497175	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1513244	52497175	6631808	1272	41506										
ZNF480	147657	hgsc.bcm.edu	37	chr19	52803707	52803707	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagaagagaaggaagaggaaAgcaaaggagtcagggatggc	17	4	1	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:52803707A>G	ENST00000595962.1	+	2	108	c.42A>G	c.(40-42)aaA>aaG	p.K14K	CTD-2525I3.5_ENST00000594865.1_RNA|ZNF480_ENST00000335090.6_5'UTR|ZNF480_ENST00000334564.7_Silent_p.K14K|CTD-2525I3.6_ENST00000594379.1_RNA|ZNF480_ENST00000490272.1_Silent_p.K14K	NM_144684.2	NP_653285.2	Q8WV37	ZN480_HUMAN	zinc finger protein 480	14					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	12				GBM - Glioblastoma multiforme(134;0.00212)|OV - Ovarian serous cystadenocarcinoma(262;0.00369)		GGAAGAGGAAAGCAAAGGAGT	0.443																																					p.K14K		Atlas-SNP	.											.	ZNF480	123	.	0			c.A42G						.						177	141	153					19																	52803707		2203	4300	6503	SO:0001819	synonymous_variant	147657	exon2			GAGGAAAGCAAAG	AY512662	CCDS12850.2, CCDS74437.1	19q13.41	2013-01-08			ENSG00000198464	ENSG00000198464		"Zinc fingers, C2H2-type", "-"	23305	protein-coding gene	gene with protein product		613910				15219843	Standard	XM_005258525		Approved	MGC32104	uc010ydl.2	Q8WV37	OTTHUMG00000157507	ENST00000595962.1:c.42A>G	chr19.hg19:g.52803707A>G		114.0	0.0		80.0	4.0	NM_144684	Q5JPG9|Q6P0Q4|Q8N1M5	Silent	SNP	ENST00000595962.1	hg19	CCDS12850.2																																																																																			.	.		0.443	ZNF480-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349001.3	NM_144684		G	52803707	A	G	52803707	2	3	282	1	0	0	0	0	0	0	0	1	17950	69	3	2		2	ZNF480	19	52803707	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	306532	52803707	6325276	1273	41507										
ZNF480	147657	hgsc.bcm.edu	37	chr19	52824876	52824876	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atgcagaagacaaaccaattAaaaaacaacttggagtatcc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:52824876delA	ENST00000595962.1	+	5	439	c.373delA	c.(373-375)aaafs	p.K126fs	ZNF480_ENST00000335090.6_Frame_Shift_Del_p.K49fs|ZNF480_ENST00000334564.7_Frame_Shift_Del_p.K83fs|CTD-2525I3.6_ENST00000594379.1_RNA|ZNF480_ENST00000490272.1_Frame_Shift_Del_p.L39fs	NM_144684.2	NP_653285.2	Q8WV37	ZN480_HUMAN	zinc finger protein 480	126					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	12				GBM - Glioblastoma multiforme(134;0.00212)|OV - Ovarian serous cystadenocarcinoma(262;0.00369)		CAAACCAATTAAAAAACAACT	0.363																																					p.I124fs		Atlas-INDEL	.											.	ZNF480	123	.	0			c.372delT						.						73	69	70					19																	52824876		2203	4300	6503	SO:0001589	frameshift_variant	147657	exon5			.	AY512662	CCDS12850.2, CCDS74437.1	19q13.41	2013-01-08			ENSG00000198464	ENSG00000198464		"Zinc fingers, C2H2-type", "-"	23305	protein-coding gene	gene with protein product		613910				15219843	Standard	XM_005258525		Approved	MGC32104	uc010ydl.2	Q8WV37	OTTHUMG00000157507	ENST00000595962.1:c.373delA	chr19.hg19:g.52824876delA	ENSP00000471754:p.Lys126fs	127.0	0.0		104.0	12.0	NM_144684	Q5JPG9|Q6P0Q4|Q8N1M5	Frame_Shift_Del	DEL	ENST00000595962.1	hg19	CCDS12850.2																																																																																			.	.		0.363	ZNF480-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349001.3	NM_144684		-	52824876	A	-	52824876	7	5	282	1	0	1	0	1	0	0	0	0	17950	363	13	0	387	0	ZNF480	19	52824876	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	21169	52824876	6304107	1274	41508										
ZNF528	84436	hgsc.bcm.edu	37	chr19	52918902	52918902	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcaaagaattcatactggagAgaagccttacaaatgtcatg	8	7	3	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:52918902A>G	ENST00000360465.3	+	7	1223	c.797A>G	c.(796-798)gAg>gGg	p.E266G	ZNF528_ENST00000391788.2_3'UTR	NM_032423.2	NP_115799.2	Q3MIS6	ZN528_HUMAN	zinc finger protein 528	266					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(6)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	39				GBM - Glioblastoma multiforme(134;0.00249)|OV - Ovarian serous cystadenocarcinoma(262;0.00817)		CATACTGGAGAGAAGCCTTAC	0.388																																					p.E266G		Atlas-SNP	.											.	ZNF528	95	.	0			c.A797G						.						80	85	83					19																	52918902		2203	4300	6503	SO:0001583	missense	84436	exon7			CTGGAGAGAAGCC	AB058730	CCDS33091.1	19q13	2013-01-08			ENSG00000167555	ENSG00000167555		"Zinc fingers, C2H2-type", "-"	29384	protein-coding gene	gene with protein product		615580				11347906	Standard	NM_032423		Approved	KIAA1827	uc002pzh.3	Q3MIS6	OTTHUMG00000156494	ENST00000360465.3:c.797A>G	chr19.hg19:g.52918902A>G	ENSP00000353652:p.Glu266Gly	112.0	0.0		91.0	6.0	NM_032423	B3KPN4|Q86T88|Q96JK0	Missense_Mutation	SNP	ENST00000360465.3	hg19	CCDS33091.1	.	.	.	.	.	.	.	.	.	.	A	13.95	2.391392	0.42410	.	.	ENSG00000167555	ENST00000360465	T	0.27557	1.66	1.69	0.527	0.17084	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.42381	0.1200	L	0.56199	1.76	0.23227	N	0.998081	D	0.76494	0.999	D	0.72075	0.976	T	0.23226	-1.0194	9	0.87932	D	0	.	3.1613	0.06521	0.5227:0.2412:0.0:0.2361	.	266	Q3MIS6	ZN528_HUMAN	G	266	ENSP00000353652:E266G	ENSP00000353652:E266G	E	+	2	0	ZNF528	57610714	0.998000	0.40836	0.126000	0.21872	0.084000	0.17831	2.076000	0.41548	-0.079000	0.12707	0.260000	0.18958	GAG	.	.		0.388	ZNF528-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344336.1	NM_032423		G	52918902	A	G	52918902	3	3	282	1	0	0	0	0	1	0	0	0	17984	304	11	2	811	2	ZNF528	19	52918902	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	94026	52918902	6210081	1275	41509										
ZNF160	90338	hgsc.bcm.edu	37	chr19	53578336	53578336	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaacaaggttccagtagttcTccaacatcacgtccctgtat	6	12	2	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:53578336T>C	ENST00000429604.1	-	5	531	c.116A>G	c.(115-117)gAg>gGg	p.E39G	ZNF160_ENST00000599056.1_Missense_Mutation_p.E39G|ZNF160_ENST00000418871.1_Missense_Mutation_p.E39G|ZNF160_ENST00000599729.1_5'Flank|ZNF160_ENST00000601421.1_Missense_Mutation_p.E3G|ZNF160_ENST00000355147.5_Missense_Mutation_p.E39G	NM_001102603.1|NM_198893.2	NP_001096073.1|NP_942596.1	Q9HCG1	ZN160_HUMAN	zinc finger protein 160	39	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				hemopoiesis (GO:0030097)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(8)|lung(10)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	35				GBM - Glioblastoma multiforme(134;0.02)		CCAGTAGTTCTCCAACATCAC	0.468																																					p.E39G		Atlas-SNP	.											.	ZNF160	75	.	0			c.A116G						.						149	131	137					19																	53578336		2203	4300	6503	SO:0001583	missense	90338	exon5			TAGTTCTCCAACA	X78928	CCDS12859.1	19q13.42	2013-01-08				ENSG00000170949		"Zinc fingers, C2H2-type", "-"	12948	protein-coding gene	gene with protein product		600398				7774943, 7865130	Standard	NM_198893		Approved	HZF5, F11, KR18, HKr18, FLJ00032, KIAA1611	uc002qar.4	Q9HCG1		ENST00000429604.1:c.116A>G	chr19.hg19:g.53578336T>C	ENSP00000406201:p.Glu39Gly	129.0	0.0		91.0	4.0	NM_001102603	Q14589|Q504Q8|Q96JC5|Q9BVY9|Q9H7N6	Missense_Mutation	SNP	ENST00000429604.1	hg19	CCDS12859.1	.	.	.	.	.	.	.	.	.	.	T	16.89	3.248370	0.59103	.	.	ENSG00000170949	ENST00000429604;ENST00000418871;ENST00000355147	T;T;T	0.04406	3.63;3.63;3.63	2.46	2.46	0.29980	Krueppel-associated box (4);	.	.	.	.	T	0.31638	0.0803	H	0.97962	4.115	0.26898	N	0.967164	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.995	T	0.18209	-1.0344	9	0.87932	D	0	.	8.0455	0.30547	0.0:0.0:0.0:1.0	.	39;39	Q9BVY9;Q9HCG1	.;ZN160_HUMAN	G	39	ENSP00000406201:E39G;ENSP00000409597:E39G;ENSP00000347273:E39G	ENSP00000347273:E39G	E	-	2	0	ZNF160	58270148	0.979000	0.34478	0.999000	0.59377	0.842000	0.47809	2.557000	0.45871	1.116000	0.41820	0.379000	0.24179	GAG	.	.		0.468	ZNF160-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463994.2	NM_033288		C	53578336	T	C	53578336	3	2	282	1	0	0	0	0	1	0	0	0	17754	1551	54	2	2352	2	ZNF160	19	53578336	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	659434	53578336	5550647	1276	41510										
ZNF331	55422	hgsc.bcm.edu	37	chr19	54079990	54079990	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaataagagtttacctacagAaaaaaacattcatgaaataa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:54079990delA	ENST00000253144.9	+	7	1509	c.176delA	c.(175-177)gaafs	p.E59fs	ZNF331_ENST00000449416.1_Frame_Shift_Del_p.E59fs|ZNF331_ENST00000511154.1_Frame_Shift_Del_p.E59fs|ZNF331_ENST00000513265.1_Frame_Shift_Del_p.E59fs|ZNF331_ENST00000513999.1_Frame_Shift_Del_p.E59fs|ZNF331_ENST00000512387.1_Frame_Shift_Del_p.E59fs|ZNF331_ENST00000511593.2_Frame_Shift_Del_p.E59fs|ZNF331_ENST00000411977.2_Frame_Shift_Del_p.E59fs	NM_001253801.1|NM_018555.5	NP_001240730.1|NP_061025.5	Q9NQX6	ZN331_HUMAN	zinc finger protein 331	59	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.			E -> K (in Ref. 3; AAH09433). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(1)|lung(1)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	10				GBM - Glioblastoma multiforme(134;0.00555)		TTACCTACAGAAAAAAACATT	0.368			T	?	follicular thyroid adenoma																																p.E59fs		Atlas-INDEL	.		Dom	yes		19	19q13.3-q13.4	55422	zinc finger protein 331		E	.	ZNF331	66	.	0			c.175delG						.						42	45	44					19																	54079990		2203	4300	6503	SO:0001589	frameshift_variant	55422	exon5			.	AF251515	CCDS33102.1	19q13	2013-12-10				ENSG00000130844		"Zinc fingers, C2H2-type", "-"	15489	protein-coding gene	gene with protein product	"rearranged in thyroid adenomas"	606043					Standard	NM_001079906		Approved	RITA, ZNF463, ZNF361	uc021uzh.1	Q9NQX6		ENST00000253144.9:c.176delA	chr19.hg19:g.54079990delA	ENSP00000253144:p.Glu59fs	221.0	0.0		180.0	13.0	NM_001253801	Q96GJ4	Frame_Shift_Del	DEL	ENST00000253144.9	hg19	CCDS33102.1																																																																																			.	.		0.368	ZNF331-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371366.1	NM_018555		-	54079990	A	-	54079990	7	5	282	1	0	1	0	1	0	0	0	0	17864	246	9	0	186	0	ZNF331	19	54079990	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	501654	54079990	5048993	1277	41511										
LILRA1	11024	hgsc.bcm.edu	37	chr19	55105714	55105714	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agtgggaggagacgctatgaCccccatcgtcacagtcctga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:55105714delC	ENST00000251372.3	+	2	187	c.5delC	c.(4-6)accfs	p.T2fs	LILRB1_ENST00000418536.2_Intron|LILRA1_ENST00000473156.1_Intron|LILRA1_ENST00000453777.1_Frame_Shift_Del_p.T2fs|LILRB1_ENST00000448689.1_Intron|LILRB1_ENST00000396321.2_Intron	NM_006863.2	NP_006854.1	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1	2					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	47				GBM - Glioblastoma multiforme(193;0.0348)		GACGCTATGACCCCCATCGTC	0.587																																					p.T2fs		Atlas-INDEL	.											.	LILRA1	105	.	0			c.4delA						.						93	108	103					19																	55105714		2203	4300	6503	SO:0001589	frameshift_variant	11024	exon2			.	AF025530	CCDS12901.1, CCDS62802.1	19q13.4	2013-01-11			ENSG00000104974	ENSG00000104974		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6602	protein-coding gene	gene with protein product		604810				9548455	Standard	NM_006863		Approved	LIR-6, CD85i, LIR6	uc002qgh.2	O75019	OTTHUMG00000065701	ENST00000251372.3:c.5delC	chr19.hg19:g.55105714delC	ENSP00000251372:p.Thr2fs	254.0	0.0		216.0	15.0	NM_006863	O75018|Q3MJA6	Frame_Shift_Del	DEL	ENST00000251372.3	hg19	CCDS12901.1																																																																																			.	.		0.587	LILRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140807.2	NM_006863		-	55105714	C	-	55105714	7	5	282	1	0	1	0	1	0	0	0	0	8793	507	18	0	7	0	LILRA1	19	55105714	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1025724	55105714	4023269	1278	41512										
ZNF71	58491	hgsc.bcm.edu	37	chr19	57133366	57133366	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagcacgagcggatccacacGggggagaagccctacgcgtg					rs373155014		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:57133366delG	ENST00000328070.6	+	3	945	c.711delG	c.(709-711)acgfs	p.T237fs		NM_021216.4	NP_067039.1	Q9NQZ8	ZNF71_HUMAN	zinc finger protein 71	237					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			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)		GGATCCACACGGGGGAGAAGC	0.652																																					p.T237fs		Atlas-INDEL	.											.	ZNF71	69	.	0			c.710delC						.						50	47	48					19																	57133366		2203	4300	6503	SO:0001589	frameshift_variant	58491	exon3			.	X60074	CCDS12947.1	19q13.4	2013-01-08	2006-05-12			ENSG00000197951		"Zinc fingers, C2H2-type"	13141	protein-coding gene	gene with protein product		194545	"zinc finger protein 71 (Cos26)"			1639391	Standard	NM_021216		Approved	Cos26, EZFIT	uc002qnm.4	Q9NQZ8		ENST00000328070.6:c.711delG	chr19.hg19:g.57133366delG	ENSP00000328245:p.Thr237fs	239.0	0.0		163.0	10.0	NM_021216	Q15919|Q9UC09|Q9UQD3	Frame_Shift_Del	DEL	ENST00000328070.6	hg19	CCDS12947.1																																																																																			.	.		0.652	ZNF71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459798.2	NM_021216		-	57133366	G	-	57133366	7	5	282	1	0	1	0	1	0	0	0	0	18129	1103	39	0	713	0	ZNF71	19	57133366	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	2027652	57133366	1995617	1279	41513										
ZSCAN4	201516	hgsc.bcm.edu	37	chr19	58189897	58189897	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaaaggatcccatggagtccAaaaatcatacaaatgtgaag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:58189897delA	ENST00000318203.5	+	5	1623	c.926delA	c.(925-927)caafs	p.Q309fs		NM_152677.2	NP_689890.1	Q8NAM6	ZSCA4_HUMAN	zinc finger and SCAN domain containing 4	309					telomere maintenance via telomere lengthening (GO:0010833)|transcription, DNA-templated (GO:0006351)	nuclear chromosome, telomeric region (GO:0000784)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|large_intestine(5)|liver(2)|lung(17)|ovary(1)|skin(1)|stomach(1)	30		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		CATGGAGTCCAAAAATCATAC	0.458																																					p.Q309fs		Atlas-INDEL	.											.	ZSCAN4	72	.	0			c.925delC						.						106	98	101					19																	58189897		2203	4300	6503	SO:0001589	frameshift_variant	201516	exon5			.	AK092424	CCDS12958.1	19q13.43	2013-01-08	2004-11-01	2004-11-02		ENSG00000180532		"-", "Zinc fingers, C2H2-type"	23709	protein-coding gene	gene with protein product		613419	"zinc finger protein 494"	ZNF494			Standard	NM_152677		Approved	FLJ35105	uc002qpu.3	Q8NAM6		ENST00000318203.5:c.926delA	chr19.hg19:g.58189897delA	ENSP00000321963:p.Gln309fs	213.0	0.0		143.0	11.0	NM_152677	Q3MIQ2	Frame_Shift_Del	DEL	ENST00000318203.5	hg19	CCDS12958.1																																																																																			.	.		0.458	ZSCAN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466812.1	NM_152677		-	58189897	A	-	58189897	7	5	282	1	0	1	0	1	0	0	0	0	18252	130	5	0	936	0	ZSCAN4	19	58189897	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1056531	58189897	939086	1280	41514										
ZNF324	25799	hgsc.bcm.edu	37	chr19	58983203	58983203	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagcaccagctcctgcacacGggcgagcggcccttccgctg					rs536947978	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:58983203delG	ENST00000536459.2	+	4	2053	c.1344delG	c.(1342-1344)acgfs	p.T448fs	ZNF324_ENST00000196482.3_Frame_Shift_Del_p.T448fs|ZNF324_ENST00000535298.1_Frame_Shift_Del_p.T225fs|ZNF446_ENST00000596341.1_5'Flank			O75467	Z324A_HUMAN	zinc finger protein 324	448					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(2)|prostate(2)|urinary_tract(2)	16		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)		TCCTGCACACGGGCGAGCGGC	0.692																																					p.T448fs		Atlas-INDEL	.											.	ZNF324	46	.	0			c.1343delC						.						44	47	46					19																	58983203		2203	4298	6501	SO:0001589	frameshift_variant	25799	exon4			.	AF060503	CCDS12981.1	19q13.43	2013-01-08				ENSG00000083812		"Zinc fingers, C2H2-type", "-"	14096	protein-coding gene	gene with protein product							Standard	NM_014347		Approved	ZF5128, ZNF324A	uc002qsw.2	O75467		ENST00000536459.2:c.1344delG	chr19.hg19:g.58983203delG	ENSP00000444812:p.Thr448fs	219.0	0.0		153.0	11.0	NM_014347	B3KRX1	Frame_Shift_Del	DEL	ENST00000536459.2	hg19	CCDS12981.1																																																																																			.	.		0.692	ZNF324-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467044.1	NM_014347		-	58983203	G	-	58983203	7	5	282	1	0	1	0	1	0	0	0	0	17859	1103	39	0	1354	0	ZNF324	19	58983203	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	793306	58983203	145780	1281	41515										
SLC27A5	10998	hgsc.bcm.edu	37	chr19	59010549	59010549	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agtccacctgcgacaacacgCcctccacctcgtgcgtggac							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:59010549delC	ENST00000263093.2	-	8	1815	c.1706delG	c.(1705-1707)ggcfs	p.G569fs	SLC27A5_ENST00000594786.1_5'UTR|SLC27A5_ENST00000601355.1_Frame_Shift_Del_p.G485fs|SLC27A5_ENST00000599700.1_5'UTR	NM_012254.2	NP_036386.1	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid transporter), member 5	569					bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|ketone body biosynthetic process (GO:0046951)|plasma membrane long-chain fatty acid transport (GO:0015911)|small molecule metabolic process (GO:0044281)|triglyceride mobilization (GO:0006642)|very long-chain fatty acid metabolic process (GO:0000038)	basal plasma membrane (GO:0009925)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|protein complex (GO:0043234)	ATP binding (GO:0005524)|cholate-CoA ligase activity (GO:0047747)|fatty acid transporter activity (GO:0015245)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.181)		CGACAACACGCCCTCCACCTC	0.607																																					p.G569fs		Atlas-INDEL	.											.	SLC27A5	58	.	0			c.1707delC						.						90	81	84					19																	59010549		2203	4300	6503	SO:0001589	frameshift_variant	10998	exon8			.	AF064255	CCDS12983.1	19q13.43	2013-07-15			ENSG00000083807	ENSG00000083807		"Acyl-CoA synthetase family", "Solute carriers"	10999	protein-coding gene	gene with protein product	"fatty-acid-Coenzyme A ligase, very long-chain 3"	603314				10479480, 10749848	Standard	NM_012254		Approved	FATP5, VLACSR, VLCS-H2, VLCSH2, FACVL3, FLJ22987, ACSVL6, ACSB	uc002qtc.2	Q9Y2P5	OTTHUMG00000183543	ENST00000263093.2:c.1706delG	chr19.hg19:g.59010549delC	ENSP00000263093:p.Gly569fs	249.0	0.0		168.0	11.0	NM_012254	B3KVP6|B4DPQ1	Frame_Shift_Del	DEL	ENST00000263093.2	hg19	CCDS12983.1																																																																																			.	.		0.607	SLC27A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467060.1	NM_012254		-	59010549	C	-	59010549	7	5	282	1	0	1	0	1	0	0	0	0	14544	739	26	0	378	0	SLC27A5	19	59010549	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	27346	59010549	118434	1282	41516										
TBC1D20	128637	hgsc.bcm.edu	37	chr20	421020	421020	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccagctgagggcaaagatggTccctacctcagcactagaaa	10	12	1	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:421020T>C	ENST00000354200.4	-	6	787	c.640A>G	c.(640-642)Acc>Gcc	p.T214A	TBC1D20_ENST00000461188.1_5'UTR	NM_144628.2	NP_653229.1	Q96BZ9	TBC20_HUMAN	TBC1 domain family, member 20	214	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				acrosome assembly (GO:0001675)|cargo loading into COPII-coated vesicle (GO:0090110)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|lens fiber cell morphogenesis (GO:0070309)|lipid particle organization (GO:0034389)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|seminiferous tubule development (GO:0072520)|virion assembly (GO:0019068)	endoplasmic reticulum membrane (GO:0005789)|integral component of Golgi membrane (GO:0030173)|nuclear membrane (GO:0031965)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	12		all_epithelial(17;0.228)|Breast(17;0.231)				GCAAAGATGGTCCCTACCTCA	0.562																																					p.T214A		Atlas-SNP	.											.	TBC1D20	34	.	0			c.A640G						.						101	86	91					20																	421020		2203	4300	6503	SO:0001583	missense	128637	exon6			AGATGGTCCCTAC	AK055573	CCDS13002.1	20p13	2013-07-10	2005-01-05	2005-01-05	ENSG00000125875	ENSG00000125875			16133	protein-coding gene	gene with protein product		611663	"chromosome 20 open reading frame 140"	C20orf140		17901050	Standard	XM_005260661		Approved	dJ852M4.2	uc002wds.3	Q96BZ9	OTTHUMG00000031637	ENST00000354200.4:c.640A>G	chr20.hg19:g.421020T>C	ENSP00000346139:p.Thr214Ala	154.0	0.0		82.0	5.0	NM_144628	A8K6I3|B9A6M1|Q5JWQ7|Q6ZSY8|Q96NE1|Q9BYM7|Q9H140	Missense_Mutation	SNP	ENST00000354200.4	hg19	CCDS13002.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.358342	0.82243	.	.	ENSG00000125875	ENST00000354200;ENST00000246077	T	0.22539	1.95	5.82	4.66	0.58398	Rab-GAP/TBC domain (4);	0.000000	0.85682	D	0.000000	T	0.42108	0.1188	M	0.71036	2.16	0.80722	D	1	D	0.63880	0.993	D	0.67382	0.951	T	0.24764	-1.0151	10	0.48119	T	0.1	-27.7933	12.0041	0.53248	0.0:0.0:0.1443:0.8557	.	214	Q96BZ9	TBC20_HUMAN	A	214;239	ENSP00000346139:T214A	ENSP00000246077:T239A	T	-	1	0	TBC1D20	369020	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.918000	0.69996	2.225000	0.72522	0.460000	0.39030	ACC	.	.		0.562	TBC1D20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251397.2	NM_144628		C	421020	T	C	421020	3	2	282	1	0	0	0	0	1	0	0	0	15624	1667	58	2	583	2	TBC1D20	20	421020	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10		421020	62604500	1283	41517										
PANK2	80025	hgsc.bcm.edu	37	chr20	3899427	3899427	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caaggggcagttgaaagcacTtttttcggaacacgaggtaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:3899427delT	ENST00000316562.4	+	6	1652	c.1646delT	c.(1645-1647)cttfs	p.L549fs	MIR103A2_ENST00000362154.1_RNA|PANK2_ENST00000497424.1_Frame_Shift_Del_p.L258fs|PANK2_ENST00000610179.1_Frame_Shift_Del_p.L426fs	NM_153638.2	NP_705902.2	Q9BZ23	PANK2_HUMAN	pantothenate kinase 2	549					aerobic respiration (GO:0009060)|cell death (GO:0008219)|coenzyme A biosynthetic process (GO:0015937)|coenzyme biosynthetic process (GO:0009108)|mitochondrion morphogenesis (GO:0070584)|pantothenate metabolic process (GO:0015939)|regulation of mitochondrial membrane potential (GO:0051881)|small molecule metabolic process (GO:0044281)|spermatid development (GO:0007286)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial intermembrane space (GO:0005758)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						TTGAAAGCACTTTTTTCGGAA	0.448																																					p.L549fs		Atlas-INDEL	.											.	PANK2	37	.	0			c.1645delC						.						238	234	235					20																	3899427		2203	4300	6503	SO:0001589	frameshift_variant	80025	exon6			.	AK021791	CCDS13071.2, CCDS13072.1	20p13	2008-07-31	2008-07-31	2002-09-06	ENSG00000125779	ENSG00000125779	2.7.1.33		15894	protein-coding gene	gene with protein product	"Hallervorden-Spatz syndrome"	606157	"neurodegeneration with brain iron accumulation 1 (Hallervorden-Spatz syndrome)"	C20orf48, NBIA1		8944032, 11479594	Standard	XM_005260835		Approved	HSS, FLJ11729, PKAN, HARP	uc002wkc.3	Q9BZ23	OTTHUMG00000031768	ENST00000316562.4:c.1646delT	chr20.hg19:g.3899427delT	ENSP00000313377:p.Leu549fs	385.0	0.0		250.0	15.0	NM_153638	B1AK33|B2Z3X0|D3DVZ0|Q5T7I2|Q5T7I4|Q7RTX5|Q8N7Q4|Q8TCR5|Q9BYW5|Q9HAF2	Frame_Shift_Del	DEL	ENST00000316562.4	hg19	CCDS13071.2																																																																																			.	.		0.448	PANK2-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077793.2	NM_024960		-	3899427	T	-	3899427	7	5	282	1	0	1	0	1	0	0	0	0	11426	1609	56	0	1668	0	PANK2	20	3899427	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3478407	3899427	59126093	1284	41518										
CHGB	1114	hgsc.bcm.edu	37	chr20	5903325	5903325	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	actatcaaaaaggggagcgaGgggaagatagcagtgaagag	16	4	1	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:5903325G>A	ENST00000378961.4	+	4	739	c.535G>A	c.(535-537)Ggg>Agg	p.G179R		NM_001819.2	NP_001810.2	P05060	SCG1_HUMAN	chromogranin B (secretogranin 1)	179						extracellular region (GO:0005576)|secretory granule (GO:0030141)	hormone activity (GO:0005179)			breast(7)|kidney(2)|large_intestine(8)|lung(19)|ovary(1)|pancreas(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	47						AGGGGAGCGAGGGGAAGATAG	0.473																																					p.G179R		Atlas-SNP	.											.	CHGB	112	.	0			c.G535A						.						90	92	91					20																	5903325		2203	4300	6503	SO:0001583	missense	1114	exon4			GAGCGAGGGGAAG		CCDS13092.1	20p12.3	2013-09-19			ENSG00000089199	ENSG00000089199			1930	protein-coding gene	gene with protein product	"secretogranin B"	118920		SCG1		3608978	Standard	NM_001819		Approved		uc002wmg.3	P05060	OTTHUMG00000031821	ENST00000378961.4:c.535G>A	chr20.hg19:g.5903325G>A	ENSP00000368244:p.Gly179Arg	126.0	0.0		99.0	4.0	NM_001819	A8K021|Q59EU9|Q6IBS6|Q9BQV6|Q9UC25|Q9UJA6	Missense_Mutation	SNP	ENST00000378961.4	hg19	CCDS13092.1	.	.	.	.	.	.	.	.	.	.	G	13.94	2.386011	0.42308	.	.	ENSG00000089199	ENST00000378961;ENST00000455042	T;T	0.01665	4.7;4.7	5.57	-0.627	0.11541	.	0.771709	0.11798	N	0.528494	T	0.01800	0.0057	L	0.43923	1.385	0.09310	N	1	B	0.12630	0.006	B	0.17433	0.018	T	0.43814	-0.9368	10	0.36615	T	0.2	-3.5937	5.0458	0.14483	0.593:0.177:0.23:0.0	.	179	P05060	SCG1_HUMAN	R	179;159	ENSP00000368244:G179R;ENSP00000416643:G159R	ENSP00000368244:G179R	G	+	1	0	CHGB	5851325	0.024000	0.19004	0.000000	0.03702	0.004000	0.04260	1.754000	0.38369	0.015000	0.14971	-0.251000	0.11542	GGG	.	.		0.473	CHGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077897.2	NM_001819		A	5903325	G	A	5903325	3	1	282	1	0	0	0	0	1	0	0	0	3341	1000	35	3	549	3	CHGB	20	5903325	Missense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	2003898	5903325	57122195	1285	41519										
SNRPB2	6629	hgsc.bcm.edu	37	chr20	16721542	16721542	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccagggaggcatgacattgcTtttgttgaatttgaaaatga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:16721542delT	ENST00000246071.6	+	7	786	c.570delT	c.(568-570)gctfs	p.A190fs	SNRPB2_ENST00000377943.5_Frame_Shift_Del_p.A190fs	NM_003092.4	NP_003083.1	P08579	RU2B_HUMAN	small nuclear ribonucleoprotein polypeptide B	190	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U2 snRNP (GO:0005686)	nucleotide binding (GO:0000166)|snRNA binding (GO:0017069)			large_intestine(2)|lung(2)|urinary_tract(1)	5						ATGACATTGCTTTTGTTGAAT	0.428																																					p.A190fs		Atlas-INDEL	.											.	SNRPB2	12	.	0			c.569delC						.						108	98	101					20																	16721542		2203	4300	6503	SO:0001589	frameshift_variant	6629	exon7			.		CCDS13123.1	20p12.1	2013-02-12	2010-07-07		ENSG00000125870	ENSG00000125870		"RNA binding motif (RRM) containing"	11155	protein-coding gene	gene with protein product		603520	"small nuclear ribonucleoprotein polypeptide B2", "small nuclear ribonucleoprotein polypeptide B''"			2951739	Standard	NM_198220		Approved	Msl1	uc002wpi.2	P08579	OTTHUMG00000031933	ENST00000246071.6:c.570delT	chr20.hg19:g.16721542delT	ENSP00000246071:p.Ala190fs	193.0	0.0		152.0	10.0	NM_003092	B2R7J3|D3DW21|Q9UJD4	Frame_Shift_Del	DEL	ENST00000246071.6	hg19	CCDS13123.1																																																																																			.	.		0.428	SNRPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078110.1	NM_003092		-	16721542	T	-	16721542	7	5	282	1	0	1	0	1	0	0	0	0	14877	1596	56	0	592	0	SNRPB2	20	16721542	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	10818217	16721542	46303978	1286	41520										
OVOL2	58495	hgsc.bcm.edu	37	chr20	18022253	18022253	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcagaaggtgcacaggtgtcTtttcacctggttgtggcact							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:18022253delT	ENST00000278780.6	-	3	678	c.436delA	c.(436-438)agafs	p.R146fs	OVOL2_ENST00000483661.1_5'UTR	NM_021220.2	NP_067043.2	Q9BRP0	OVOL2_HUMAN	ovo-like zinc finger 2	146					angiogenesis (GO:0001525)|dorsal/ventral pattern formation (GO:0009953)|embryonic digestive tract morphogenesis (GO:0048557)|endocardium formation (GO:0060214)|heart looping (GO:0001947)|heart trabecula formation (GO:0060347)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell migration (GO:0001755)|neural fold formation (GO:0001842)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle (GO:0051726)|regulation of keratinocyte proliferation (GO:0010837)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(3)	6						CACAGGTGTCTTTTCACCTGG	0.592																																					p.R146fs		Atlas-INDEL	.											.	OVOL2	18	.	0			c.437delG						.						148	93	112					20																	18022253		2203	4300	6503	SO:0001589	frameshift_variant	58495	exon3			.	AK022284	CCDS13132.1	20p11.23	2013-10-17	2013-10-17	2005-05-31	ENSG00000125850	ENSG00000125850		"Zinc fingers, C2H2-type"	15804	protein-coding gene	gene with protein product			"zinc finger protein 339", "ovo-like 2 (Drosophila)"	ZNF339			Standard	NM_021220		Approved	bA504H3.3, HOVO2	uc002wqi.1	Q9BRP0	OTTHUMG00000031960	ENST00000278780.6:c.436delA	chr20.hg19:g.18022253delT	ENSP00000278780:p.Arg146fs	189.0	0.0		145.0	10.0	NM_021220	Q5T8B4|Q9BX22|Q9HA54|Q9Y4M0	Frame_Shift_Del	DEL	ENST00000278780.6	hg19	CCDS13132.1																																																																																			.	.		0.592	OVOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078148.5	NM_021220		-	18022253	T	-	18022253	7	5	282	1	0	1	0	1	0	0	0	0	11336	1617	56	0	399	0	OVOL2	20	18022253	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1300711	18022253	45003267	1287	41521										
CRNKL1	51340	hgsc.bcm.edu	37	chr20	20018161	20018161	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ataaatttgtctgcatttagTcaaacttccttcttttcctg	4	9	3	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:20018161T>C	ENST00000377340.2	-	14	2216	c.2185A>G	c.(2185-2187)Act>Gct	p.T729A	CRNKL1_ENST00000377327.4_Missense_Mutation_p.T717A|CRNKL1_ENST00000521379.1_5'UTR|CRNKL1_ENST00000536226.1_Missense_Mutation_p.T568A	NM_001278628.1|NM_016652.4	NP_001265557.1|NP_057736.4	Q9BZJ0	CRNL1_HUMAN	crooked neck pre-mRNA splicing factor 1	729					mRNA splicing, via spliceosome (GO:0000398)|spliceosomal complex assembly (GO:0000245)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|cervix(2)|endometrium(7)|large_intestine(11)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(6)	45						CTGCATTTAGTCAAACTTCCT	0.353																																					p.T729A		Atlas-SNP	.											.	CRNKL1	101	.	0			c.A2185G						.						125	123	124					20																	20018161		2203	4300	6503	SO:0001583	missense	51340	exon14			ATTTAGTCAAACT	AF255443	CCDS33446.1, CCDS63238.1, CCDS63239.1	20p11.2	2013-10-03	2013-10-03		ENSG00000101343	ENSG00000101343			15762	protein-coding gene	gene with protein product	"SYF3 pre-mRNA-splicing factor"	610952	"crooked neck (Drosophila Crn homolog)-like 1", "Crn, crooked neck-like 1 (Drosophila)", "crooked neck pre-mRNA splicing factor-like 1 (Drosophila)"				Standard	NM_016652		Approved	CRN, CLF, SYF3, Clf1	uc002wrs.3	Q9BZJ0	OTTHUMG00000032000	ENST00000377340.2:c.2185A>G	chr20.hg19:g.20018161T>C	ENSP00000366557:p.Thr729Ala	185.0	0.0		149.0	7.0	NM_016652	A8K9T4|Q5JY64|Q8WYI5|Q9BZI9|Q9BZJ1|Q9BZJ2|Q9GZW7|Q9H8F8|Q9NQH5|Q9NYD8	Missense_Mutation	SNP	ENST00000377340.2	hg19	CCDS33446.1	.	.	.	.	.	.	.	.	.	.	T	2.462	-0.323813	0.05350	.	.	ENSG00000101343	ENST00000377327;ENST00000377340;ENST00000536226	T;T;T	0.41065	1.52;1.52;1.01	5.02	0.433	0.16534	.	0.712402	0.14703	N	0.303457	T	0.09862	0.0242	N	0.01003	-1.06	0.09310	N	0.999991	B	0.02656	0.0	B	0.04013	0.001	T	0.25710	-1.0124	10	0.07813	T	0.8	-2.1383	0.7921	0.01059	0.2464:0.332:0.1213:0.3003	.	729	Q9BZJ0	CRNL1_HUMAN	A	717;729;568	ENSP00000366544:T717A;ENSP00000366557:T729A;ENSP00000440733:T568A	ENSP00000366544:T717A	T	-	1	0	CRNKL1	19966161	0.150000	0.22732	1.000000	0.80357	0.989000	0.77384	-0.394000	0.07296	0.245000	0.21373	-0.354000	0.07668	ACT	.	.		0.353	CRNKL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000127787.1			C	20018161	T	C	20018161	3	2	282	1	0	0	0	0	1	0	0	0	3893	1667	58	2	369	2	CRNKL1	20	20018161	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1995908	20018161	43007359	1288	41522										
C20orf26	26074	hgsc.bcm.edu	37	chr20	20226815	20226815	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcaactcatggactcccaggAaaaaaacttctggacactga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:20226815delA	ENST00000245957.5	+	19	2191	c.2115delA	c.(2113-2115)ggafs	p.G705fs	C20orf26_ENST00000389656.3_Frame_Shift_Del_p.G61fs|C20orf26_ENST00000377309.2_Frame_Shift_Del_p.G61fs|C20orf26_ENST00000377293.1_Frame_Shift_Del_p.G61fs	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN		705										NS(2)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(42)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	77				READ - Rectum adenocarcinoma(2;0.171)		GACTCCCAGGAAAAAAACTTC	0.353																																					p.G705fs		Pindel	.											.	C20orf26	188	.	0			c.2114delG						.						77	86	83					20																	20226815		2203	4300	6503	SO:0001589	frameshift_variant	26074	exon19			.																												ENST00000245957.5:c.2115delA	chr20.hg19:g.20226815delA	ENSP00000245957:p.Gly705fs	237.0	0.0		217.0	10.0	NM_015585	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Frame_Shift_Del	DEL	ENST00000245957.5	hg19	CCDS33447.1																																																																																			.	.		0.353	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3			-	20226815	A	-	20226815	7	5	282	1	0	1	0	1	0	0	0	0	2108	233	9	0	2217	0	C20orf26	20	20226815	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	208654	20226815	42798705	1289	41523										
ENTPD6	955	hgsc.bcm.edu	37	chr20	25203522	25203522	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cagagtgtcagaggtccttcAaaacagagtgcacaggacgg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:25203522delA	ENST00000376652.4	+	12	1257	c.1094delA	c.(1093-1095)caafs	p.Q365fs	ENTPD6_ENST00000360031.2_Frame_Shift_Del_p.Q364fs|ENTPD6_ENST00000485936.1_3'UTR|ENTPD6_ENST00000433259.2_Frame_Shift_Del_p.Q331fs|ENTPD6_ENST00000354989.5_Frame_Shift_Del_p.Q348fs			O75354	ENTP6_HUMAN	ectonucleoside triphosphate diphosphohydrolase 6 (putative)	365					response to calcium ion (GO:0051592)|response to magnesium ion (GO:0032026)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	guanosine-5'-triphosphate,3'-diphosphate diphosphatase activity (GO:0008894)|nucleoside-triphosphatase activity (GO:0017111)|uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|prostate(1)|skin(1)	27						GAGGTCCTTCAAAACAGAGTG	0.577																																					p.Q365fs		Atlas-INDEL	.											.	ENTPD6	57	.	0			c.1093delC						.						176	145	156					20																	25203522		2203	4300	6503	SO:0001589	frameshift_variant	955	exon12			.	AF039916	CCDS13170.1, CCDS46586.1	20p11.21	2010-06-24	2010-06-24		ENSG00000197586	ENSG00000197586			3368	protein-coding gene	gene with protein product		603160	"interleukin 6 signal transducer-2"	CD39L2, IL6ST2		9676430	Standard	NM_001247		Approved	NTPDase-6, dJ738P15.3	uc002wuj.2	O75354	OTTHUMG00000032116	ENST00000376652.4:c.1094delA	chr20.hg19:g.25203522delA	ENSP00000365840:p.Gln365fs	227.0	0.0		151.0	10.0	NM_001247	A6NCX6|D3DW49|Q5QPJ2|Q5QPJ5|Q7Z5B5|Q8N3H3|Q8TAS7|Q9UJD1	Frame_Shift_Del	DEL	ENST00000376652.4	hg19	CCDS13170.1																																																																																			.	.		0.577	ENTPD6-020	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078414.2			-	25203522	A	-	25203522	7	5	282	1	0	1	0	1	0	0	0	0	5145	130	5	0	1143	0	ENTPD6	20	25203522	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	4976707	25203522	37821998	1290	41524										
PYGB	5834	hgsc.bcm.edu	37	chr20	25273090	25273090	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gatctccactgcaggcaccgAggcctcaggcacaggcaaca	11	15	2	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:25273090A>G	ENST00000216962.4	+	17	2128	c.2018A>G	c.(2017-2019)gAg>gGg	p.E673G		NM_002862.3	NP_002853.2	P11216	PYGB_HUMAN	phosphorylase, glycogen; brain	673					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	glycogen phosphorylase activity (GO:0008184)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	31						GCAGGCACCGAGGCCTCAGGC	0.652																																					p.E673G		Atlas-SNP	.											.	PYGB	84	.	0			c.A2018G						.						93	86	88					20																	25273090		2203	4300	6503	SO:0001583	missense	5834	exon17			GCACCGAGGCCTC		CCDS13171.1	20p11.21	2013-03-01			ENSG00000100994	ENSG00000100994	2.4.1.1	"Glycogen phosphorylases"	9723	protein-coding gene	gene with protein product	"glycogen phosphorylase, brain form"	138550					Standard	NM_002862		Approved		uc002wup.3	P11216	OTTHUMG00000032117	ENST00000216962.4:c.2018A>G	chr20.hg19:g.25273090A>G	ENSP00000216962:p.Glu673Gly	147.0	0.0		79.0	4.0	NM_002862	Q96AK1|Q9NPX8	Missense_Mutation	SNP	ENST00000216962.4	hg19	CCDS13171.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	26.1|26.1	4.704543|4.704543	0.88924|0.88924	.|.	.|.	ENSG00000100994|ENSG00000100994	ENST00000216962|ENST00000428458	D|.	0.99458|.	-5.93|.	4.28|4.28	4.28|4.28	0.50868|0.50868	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.88930|0.88930	0.6571|0.6571	H|H	0.99117|0.99117	4.435|4.435	0.80722|0.80722	D|D	1|1	D|.	0.67145|.	0.996|.	D|.	0.76071|.	0.987|.	D|D	0.93026|0.93026	0.6444|0.6444	10|5	0.87932|.	D|.	0|.	-46.7873|-46.7873	13.5385|13.5385	0.61659|0.61659	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	673|.	P11216|.	PYGB_HUMAN|.	G|G	673|92	ENSP00000216962:E673G|.	ENSP00000216962:E673G|.	E|R	+|+	2|1	0|2	PYGB|PYGB	25221090|25221090	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.965000|0.965000	0.64279|0.64279	8.975000|8.975000	0.93437|0.93437	1.933000|1.933000	0.56026|0.56026	0.379000|0.379000	0.24179|0.24179	GAG|AGG	.	.		0.652	PYGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078415.2	NM_002862		G	25273090	A	G	25273090	3	3	282	1	0	0	0	0	1	0	0	0	12875	304	11	2	2084	2	PYGB	20	25273090	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	69568	25273090	37752430	1291	41525										
HCK	3055	hgsc.bcm.edu	37	chr20	30640230	30640230	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acctcaggggctgccgagctGggggggcgctcaagctgcga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:30640230delG	ENST00000375852.2	+	1	167	c.3delG	c.(1-3)ctgfs	p.L1fs	HCK_ENST00000538448.1_5'UTR|HCK_ENST00000518730.1_5'UTR|RNA5SP482_ENST00000391269.1_RNA|HCK_ENST00000375862.2_Frame_Shift_Del_p.L1fs|HCK_ENST00000534862.1_5'UTR|HCK_ENST00000520553.1_5'UTR			P08631	HCK_HUMAN	HCK proto-oncogene, Src family tyrosine kinase	1					cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|innate immune response-activating signal transduction (GO:0002758)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte degranulation (GO:0043299)|leukocyte migration involved in immune response (GO:0002522)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|mesoderm development (GO:0007498)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell proliferation (GO:0008284)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of defense response to virus by virus (GO:0050690)|regulation of inflammatory response (GO:0050727)|regulation of phagocytosis (GO:0050764)|regulation of podosome assembly (GO:0071801)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|respiratory burst after phagocytosis (GO:0045728)|viral process (GO:0016032)	caveola (GO:0005901)|cell projection (GO:0042995)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|nucleus (GO:0005634)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)	p.R4fs*38(1)		NS(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(18)|ovary(2)|pancreas(1)|prostate(2)|skin(4)	36			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)		Bosutinib(DB06616)	CTGCCGAGCTGGGGGGGCGCT	0.721																																					p.L1fs		Atlas-INDEL	.											.,1	HCK	181	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.2delT						.		,,,,,	10,1862		2,6,928	1	2	2		,,,,,	3	1	20		2	30,4280		11,8,2136	no	frameshift,utr-5,utr-5,utr-5,frameshift,utr-5	HCK	NM_002110.3,NM_001172133.1,NM_001172132.1,NM_001172131.1,NM_001172130.1,NM_001172129.1	,,,,,	13,14,3064	A1A1,A1R,RR		0.6961,0.5342,0.647	,,,,,	,,,,,	30640230	40,6142	1158	2568	3726	SO:0001589	frameshift_variant	3055	exon1			.	AK026432	CCDS33460.1, CCDS54453.1, CCDS54455.1, CCDS54456.1	20q11-q12	2014-06-25	2014-06-25		ENSG00000101336	ENSG00000101336		"SH2 domain containing"	4840	protein-coding gene	gene with protein product		142370	"hemopoietic cell kinase"			3496523	Standard	NM_002110		Approved	JTK9	uc002wxh.3	P08631	OTTHUMG00000032204	ENST00000375852.2:c.3delG	chr20.hg19:g.30640230delG	ENSP00000365012:p.Leu1fs	299.0	0.0		197.0	13.0	NM_001172130	A8K1I1|B4DQB6|E1P5M2|Q29RX1|Q2VPE2|Q504R5|Q5T7K1|Q5T7K2|Q96CC0|Q9H5Y5|Q9NUA4|Q9UMJ5	Frame_Shift_Del	DEL	ENST00000375852.2	hg19	CCDS33460.1																																																																																			.	.		0.721	HCK-001	KNOWN	NAGNAG_splice_site|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078603.4			-	30640230	G	-	30640230	7	5	282	1	0	1	0	1	0	0	0	0	7003	1335	47	0	5	0	HCK	20	30640230	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	5367140	30640230	32385290	1292	41526										
GDF5	8200	hgsc.bcm.edu	37	chr20	34022065	34022065	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgccctggcgagtggccagtGgggcccgccgttttcgccgc					rs149633982	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:34022065delG	ENST00000374372.1	-	4	1651	c.1148delC	c.(1147-1149)ccafs	p.P383fs	GDF5OS_ENST00000374375.1_Frame_Shift_Del_p.G37fs|GDF5_ENST00000374369.3_Frame_Shift_Del_p.P383fs			P43026	GDF5_HUMAN	growth differentiation factor 5	383					cell-cell signaling (GO:0007267)|chondrocyte differentiation (GO:0002062)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix organization (GO:0030198)|forelimb morphogenesis (GO:0035136)|growth (GO:0040007)|hindlimb morphogenesis (GO:0035137)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuron differentiation (GO:0045666)|regulation of multicellular organism growth (GO:0040014)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	growth factor activity (GO:0008083)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(9)|skin(3)	26	Lung NSC(9;0.00642)|all_lung(11;0.0094)		BRCA - Breast invasive adenocarcinoma(18;0.00663)			AGTGGCCAGTGGGGCCCGCCG	0.582																																					p.P383fs		Atlas-INDEL	.											.	GDF5	66	.	0			c.1149delA						.						75	79	78					20																	34022065		2203	4300	6503	SO:0001589	frameshift_variant	8200	exon2			.	X80915	CCDS13254.1	20q11.2	2008-05-22	2007-04-12		ENSG00000125965	ENSG00000125965			4220	protein-coding gene	gene with protein product	"cartilage-derived morphogenetic protein-1"	601146				9288091, 9288098	Standard	NM_000557		Approved	CDMP1, BMP14	uc002xck.1	P43026	OTTHUMG00000032341	ENST00000374372.1:c.1148delC	chr20.hg19:g.34022065delG	ENSP00000363492:p.Pro383fs	195.0	0.0		154.0	11.0	NM_000557	E1P5Q2|Q96SB1	Frame_Shift_Del	DEL	ENST00000374372.1	hg19	CCDS13254.1																																																																																			.	.		0.582	GDF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078875.2			-	34022065	G	-	34022065	7	5	282	1	0	1	0	1	0	0	0	0	6324	1348	47	0	361	0	GDF5	20	34022065	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	3381835	34022065	29003455	1293	41527										
GDF5	8200	hgsc.bcm.edu	37	chr20	34025211	34025211	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atgtactcgtggggtgtgatGgggggtgggcgaaacggctc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:34025211delG	ENST00000374372.1	-	3	1001	c.498delC	c.(496-498)cccfs	p.P166fs	GDF5_ENST00000374369.3_Frame_Shift_Del_p.P166fs			P43026	GDF5_HUMAN	growth differentiation factor 5	166					cell-cell signaling (GO:0007267)|chondrocyte differentiation (GO:0002062)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix organization (GO:0030198)|forelimb morphogenesis (GO:0035136)|growth (GO:0040007)|hindlimb morphogenesis (GO:0035137)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuron differentiation (GO:0045666)|regulation of multicellular organism growth (GO:0040014)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	growth factor activity (GO:0008083)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(9)|skin(3)	26	Lung NSC(9;0.00642)|all_lung(11;0.0094)		BRCA - Breast invasive adenocarcinoma(18;0.00663)			GGGGTGTGATGGGGGGTGGGC	0.637																																					p.I167fs		Atlas-INDEL	.											.	GDF5	66	.	0			c.499delA						.						64	63	63					20																	34025211		2203	4300	6503	SO:0001589	frameshift_variant	8200	exon1			.	X80915	CCDS13254.1	20q11.2	2008-05-22	2007-04-12		ENSG00000125965	ENSG00000125965			4220	protein-coding gene	gene with protein product	"cartilage-derived morphogenetic protein-1"	601146				9288091, 9288098	Standard	NM_000557		Approved	CDMP1, BMP14	uc002xck.1	P43026	OTTHUMG00000032341	ENST00000374372.1:c.498delC	chr20.hg19:g.34025211delG	ENSP00000363492:p.Pro166fs	154.0	0.0		146.0	11.0	NM_000557	E1P5Q2|Q96SB1	Frame_Shift_Del	DEL	ENST00000374372.1	hg19	CCDS13254.1																																																																																			.	.		0.637	GDF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078875.2			-	34025211	G	-	34025211	7	5	282	1	0	1	0	1	0	0	0	0	6324	1335	47	0	1015	0	GDF5	20	34025211	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	3146	34025211	29000309	1294	41528										
SRC	6714	hgsc.bcm.edu	37	chr20	36022608	36022608	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcaagatcaccagacgggagTcagagcggttactgctcaat	12	10	3	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:36022608T>C	ENST00000373578.2	+	7	830	c.481T>C	c.(481-483)Tca>Cca	p.S161P	SRC_ENST00000358208.4_Missense_Mutation_p.S161P|SRC_ENST00000373567.2_Missense_Mutation_p.S161P|SRC_ENST00000360723.4_Missense_Mutation_p.S167P|SRC_ENST00000373558.2_Missense_Mutation_p.S167P|SRC_ENST00000445403.1_Missense_Mutation_p.S161P	NM_198291.1	NP_938033.1	P12931	SRC_HUMAN	SRC proto-oncogene, non-receptor tyrosine kinase	161	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|bone resorption (GO:0045453)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cellular response to progesterone stimulus (GO:0071393)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|membrane organization (GO:0061024)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of mitochondrial depolarization (GO:0051902)|negative regulation of protein homooligomerization (GO:0032463)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oogenesis (GO:0048477)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of integrin activation (GO:0033625)|positive regulation of podosome assembly (GO:0071803)|positive regulation of protein kinase B signaling (GO:0051897)|progesterone receptor signaling pathway (GO:0050847)|protein autophosphorylation (GO:0046777)|Ras protein signal transduction (GO:0007265)|regulation of bone resorption (GO:0045124)|regulation of caveolin-mediated endocytosis (GO:2001286)|regulation of cell-cell adhesion (GO:0022407)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of epithelial cell migration (GO:0010632)|regulation of intracellular estrogen receptor signaling pathway (GO:0033146)|regulation of protein binding (GO:0043393)|regulation of vascular permeability (GO:0043114)|response to interleukin-1 (GO:0070555)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|stress fiber assembly (GO:0043149)|T cell costimulation (GO:0031295)|transforming growth factor beta receptor signaling pathway (GO:0007179)|uterus development (GO:0060065)|viral process (GO:0016032)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|ephrin receptor binding (GO:0046875)|growth factor receptor binding (GO:0070851)|heme binding (GO:0020037)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphoprotein binding (GO:0051219)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(16)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	30		Myeloproliferative disorder(115;0.00878)			Bosutinib(DB06616)|Dasatinib(DB01254)|Ponatinib(DB08901)	CAGACGGGAGTCAGAGCGGTT	0.582																																					p.S161P		Atlas-SNP	.											.	SRC	52	.	0			c.T481C						.						105	102	103					20																	36022608		2203	4300	6503	SO:0001583	missense	6714	exon7			CGGGAGTCAGAGC	AF077754	CCDS13294.1	20q12-q13	2014-06-25	2014-06-25		ENSG00000197122	ENSG00000197122		"SH2 domain containing"	11283	protein-coding gene	gene with protein product		190090	"v-src avian sarcoma (Schmidt-Ruppin A-2) viral oncogene homolog"	SRC1		2582238	Standard	NM_005417		Approved	ASV, c-src	uc002xgy.3	P12931	OTTHUMG00000032417	ENST00000373578.2:c.481T>C	chr20.hg19:g.36022608T>C	ENSP00000362680:p.Ser161Pro	70.0	0.0		49.0	4.0	NM_005417	E1P5V4|Q76P87|Q86VB9|Q9H5A8	Missense_Mutation	SNP	ENST00000373578.2	hg19	CCDS13294.1	.	.	.	.	.	.	.	.	.	.	T	19.95	3.922004	0.73213	.	.	ENSG00000197122	ENST00000445403;ENST00000373578;ENST00000360723;ENST00000358208;ENST00000373567;ENST00000373558	T;T;T;T;T;T	0.27402	1.67;1.67;1.67;1.67;1.67;1.67	4.88	3.76	0.43208	SH2 motif (5);	0.126165	0.56097	D	0.000035	T	0.49795	0.1578	M	0.88704	2.975	0.80722	D	1	D	0.54601	0.967	P	0.53185	0.72	T	0.56232	-0.8013	10	0.87932	D	0	.	9.1069	0.36703	0.0:0.0:0.3627:0.6373	.	161	P12931	SRC_HUMAN	P	161;161;167;161;161;167	ENSP00000408503:S161P;ENSP00000362680:S161P;ENSP00000353950:S167P;ENSP00000350941:S161P;ENSP00000362668:S161P;ENSP00000362659:S167P	ENSP00000350941:S161P	S	+	1	0	SRC	35456022	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	3.174000	0.50847	0.865000	0.35603	0.459000	0.35465	TCA	.	.		0.582	SRC-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268142.1	NM_005417		C	36022608	T	C	36022608	3	2	282	1	0	0	0	0	1	0	0	0	15149	1667	58	2	495	2	SRC	20	36022608	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1997397	36022608	27002912	1295	41529										
VSTM2L	128434	hgsc.bcm.edu	37	chr20	36560082	36560082	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	catgacagcacggacgggcgAggacgtggagatggcctgct	17	10	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:36560082A>G	ENST00000373461.4	+	2	414	c.167A>G	c.(166-168)gAg>gGg	p.E56G	VSTM2L_ENST00000373459.4_Intron|VSTM2L_ENST00000373458.3_Missense_Mutation_p.E56G	NM_080607.2	NP_542174.1	Q96N03	VTM2L_HUMAN	V-set and transmembrane domain containing 2 like	56	Ig-like.									central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(4)|ovary(1)|skin(1)	8		Myeloproliferative disorder(115;0.00878)				CGGACGGGCGAGGACGTGGAG	0.637																																					p.E56G		Atlas-SNP	.											.	VSTM2L	20	.	0			c.A167G						.						151	137	142					20																	36560082		2203	4300	6503	SO:0001583	missense	128434	exon2			CGGGCGAGGACGT	AL109964	CCDS13299.1	20q11.23	2013-01-11	2007-08-10	2007-08-10	ENSG00000132821	ENSG00000132821		"Immunoglobulin superfamily / V-set domain containing"	16096	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 102"	C20orf102			Standard	NM_080607		Approved	dJ1118M15.2	uc002xhk.4	Q96N03	OTTHUMG00000032430	ENST00000373461.4:c.167A>G	chr20.hg19:g.36560082A>G	ENSP00000362560:p.Glu56Gly	95.0	0.0		71.0	4.0	NM_080607	E1P5V7|Q5JWZ4|Q5JWZ5|Q8ND45|Q9BR37	Missense_Mutation	SNP	ENST00000373461.4	hg19	CCDS13299.1	.	.	.	.	.	.	.	.	.	.	A	27.9	4.871050	0.91587	.	.	ENSG00000132821	ENST00000373458;ENST00000373461;ENST00000448944	T;T;T	0.29655	1.56;1.56;1.56	4.66	4.66	0.58398	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.107942	0.64402	D	0.000008	T	0.40094	0.1103	L	0.46614	1.455	0.58432	D	0.999999	D	0.56287	0.975	P	0.54372	0.75	T	0.17289	-1.0374	10	0.44086	T	0.13	-23.935	13.5528	0.61743	1.0:0.0:0.0:0.0	.	56	Q96N03	VTM2L_HUMAN	G	56	ENSP00000362557:E56G;ENSP00000362560:E56G;ENSP00000406537:E56G	ENSP00000362557:E56G	E	+	2	0	VSTM2L	35993496	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	9.127000	0.94417	1.859000	0.53934	0.397000	0.26171	GAG	.	.		0.637	VSTM2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079133.1			G	36560082	A	G	36560082	3	3	282	1	0	0	0	0	1	0	0	0	17245	304	11	2	173	2	VSTM2L	20	36560082	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	537474	36560082	26465438	1296	41530										
CHD6	84181	hgsc.bcm.edu	37	chr20	40033271	40033271	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggagtctttgagtgccccctCcccagcctgtgccccatgtt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:40033271delC	ENST00000373233.3	-	37	8287	c.8110delG	c.(8110-8112)gagfs	p.E2704fs	CHD6_ENST00000480022.1_5'UTR	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	2704					ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				AGTGCCCCCTCCCCAGCCTGT	0.493																																					p.E2704fs		Atlas-INDEL	.											.	CHD6	312	.	0			c.8111delA						.						109	119	116					20																	40033271		2203	4300	6503	SO:0001589	frameshift_variant	84181	exon37			.	AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.8110delG	chr20.hg19:g.40033271delC	ENSP00000362330:p.Glu2704fs	194.0	0.0		152.0	10.0	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Frame_Shift_Del	DEL	ENST00000373233.3	hg19	CCDS13317.1																																																																																			.	.		0.493	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			-	40033271	C	-	40033271	7	5	282	1	0	1	0	1	0	0	0	0	3331	864	30	0	41	0	CHD6	20	40033271	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	3473189	40033271	22992249	1297	41531										
CHD6	84181	hgsc.bcm.edu	37	chr20	40084446	40084446	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agaaggccctgtaccttggcAaaagtggaccctttcccctc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:40084446delA	ENST00000373233.3	-	19	3180	c.3003delT	c.(3001-3003)tttfs	p.F1001fs	CHD6_ENST00000309279.7_Intron	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1001					ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				GTACCTTGGCAAAAGTGGACC	0.483																																					p.A1002fs		Atlas-INDEL	.											.	CHD6	312	.	0			c.3004delG						.						221	209	213					20																	40084446		2203	4300	6503	SO:0001589	frameshift_variant	84181	exon19			.	AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.3003delT	chr20.hg19:g.40084446delA	ENSP00000362330:p.Phe1001fs	274.0	0.0		202.0	13.0	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Frame_Shift_Del	DEL	ENST00000373233.3	hg19	CCDS13317.1																																																																																			.	.		0.483	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			-	40084446	A	-	40084446	7	5	282	1	0	1	0	1	0	0	0	0	3331	127	5	0	5220	0	CHD6	20	40084446	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	51175	40084446	22941074	1298	41532										
PTPRT	11122	hgsc.bcm.edu	37	chr20	40944372	40944372	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gccatacttactccattggcTttgctgagtgcctggaagta							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:40944372delT	ENST00000373187.1	-	12	2129	c.2130delA	c.(2128-2130)aaafs	p.K710fs	PTPRT_ENST00000373184.1_Frame_Shift_Del_p.K710fs|PTPRT_ENST00000356100.2_Frame_Shift_Del_p.K710fs|PTPRT_ENST00000373190.1_Frame_Shift_Del_p.K710fs|PTPRT_ENST00000373198.4_Frame_Shift_Del_p.K710fs|PTPRT_ENST00000373201.1_Frame_Shift_Del_p.K710fs|PTPRT_ENST00000373193.3_Frame_Shift_Del_p.K710fs			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	710	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)			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)				CTCCATTGGCTTTGCTGAGTG	0.468																																					p.A711fs		Atlas-INDEL	.											.	PTPRT	372	.	0			c.2131delG						.						74	71	72					20																	40944372		1948	4140	6088	SO:0001589	frameshift_variant	11122	exon12			.	AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.2130delA	chr20.hg19:g.40944372delT	ENSP00000362283:p.Lys710fs	245.0	0.0		198.0	12.0	NM_007050	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Frame_Shift_Del	DEL	ENST00000373187.1	hg19	CCDS42874.1																																																																																			.	.		0.468	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			-	40944372	T	-	40944372	7	5	282	1	0	1	0	1	0	0	0	0	12827	1606	56	0	2336	0	PTPRT	20	40944372	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	859926	40944372	22081148	1299	41533										
IFT52	51098	hgsc.bcm.edu	37	chr20	42249541	42249541	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acaggagacatccacctaaaCcagattgatgctgaggaccc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:42249541delC	ENST00000373030.3	+	9	874	c.744delC	c.(742-744)aacfs	p.N248fs	IFT52_ENST00000373039.4_Frame_Shift_Del_p.N248fs	NM_016004.2	NP_057088.2	Q9Y366	IFT52_HUMAN	intraflagellar transport 52	248					cilium morphogenesis (GO:0060271)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|intraciliary transport (GO:0042073)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube formation (GO:0001841)|regulation of protein processing (GO:0070613)|smoothened signaling pathway (GO:0007224)	centriole (GO:0005814)|ciliary base (GO:0097546)|ciliary tip (GO:0097542)|cilium (GO:0005929)|dendrite terminus (GO:0044292)|intraciliary transport particle B (GO:0030992)|motile cilium (GO:0031514)|photoreceptor connecting cilium (GO:0032391)	protein C-terminus binding (GO:0008022)			endometrium(5)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)|urinary_tract(1)	21		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			TCCACCTAAACCAGATTGATG	0.368																																					p.N248fs		Atlas-INDEL	.											.	IFT52	40	.	0			c.743delA						.						96	101	99					20																	42249541		2203	4300	6503	SO:0001589	frameshift_variant	51098	exon9			.	AF151811	CCDS33470.1	20q12-q13.1	2014-07-03	2014-07-03	2005-11-02	ENSG00000101052	ENSG00000101052		"Intraflagellar transport homologs"	15901	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 9", "intraflagellar transport 52 homolog (Chlamydomonas)"	C20orf9		10810093	Standard	NM_016004		Approved	CGI-53, NGD5, dJ1028D15.1, NGD2	uc002xkw.3	Q9Y366	OTTHUMG00000032513	ENST00000373030.3:c.744delC	chr20.hg19:g.42249541delC	ENSP00000362121:p.Asn248fs	259.0	0.0		208.0	13.0	NM_016004	B3KMA1|E1P5W9|Q5H8Z0|Q9H1G3|Q9H1G4|Q9H1H2	Frame_Shift_Del	DEL	ENST00000373030.3	hg19	CCDS33470.1																																																																																			.	.		0.368	IFT52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079317.1	NM_016004		-	42249541	C	-	42249541	7	5	282	1	0	1	0	1	0	0	0	0	7570	506	18	0	774	0	IFT52	20	42249541	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1305169	42249541	20775979	1300	41534										
TOX2	84969	hgsc.bcm.edu	37	chr20	42694668	42694668	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acctgttagcatgtccccagCcccccagccccctgtcctgc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:42694668delC	ENST00000358131.5	+	6	1431	c.1223delC	c.(1222-1224)gccfs	p.A408fs	TOX2_ENST00000435864.2_3'UTR|TOX2_ENST00000341197.4_Frame_Shift_Del_p.A426fs|TOX2_ENST00000372999.1_Frame_Shift_Del_p.A384fs|TOX2_ENST00000423191.2_Frame_Shift_Del_p.A384fs	NM_001098798.1	NP_001092268.1	Q96NM4	TOX2_HUMAN	TOX high mobility group box family member 2	408	Pro-rich.				female gonad development (GO:0008585)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to gonadotropin (GO:0034698)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|skin(2)	26		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.00189)			ATGTCCCCAGCCCCCCAGCCC	0.682																																					p.A426fs		Atlas-INDEL	.											.	TOX2	158	.	0			c.1276delG						.						16	18	17					20																	42694668		2199	4290	6489	SO:0001589	frameshift_variant	84969	exon7			.	BC007636	CCDS13324.1, CCDS42875.1, CCDS46603.1	20q13.12	2007-03-20	2007-03-20	2007-03-20					16095	protein-coding gene	gene with protein product	"granulosa cell HMG box 1"	611163	"chromosome 20 open reading frame 100"	C20orf100		14764631	Standard	NM_001098796		Approved	dJ1108D11.2, GCX-1	uc010ggo.3	Q96NM4		ENST00000358131.5:c.1223delC	chr20.hg19:g.42694668delC	ENSP00000350849:p.Ala408fs	276.0	0.0		213.0	16.0	NM_001098797	A8K1J1|E1P5X0|G3XAC7|Q5TE33|Q5TE34|Q5TE35|Q96IC9|Q9BQN5	Frame_Shift_Del	DEL	ENST00000358131.5	hg19	CCDS42875.1																																																																																			.	.		0.682	TOX2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079329.2			-	42694668	C	-	42694668	7	5	282	1	0	1	0	1	0	0	0	0	16393	739	26	0	1433	0	TOX2	20	42694668	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	445127	42694668	20330852	1301	41535										
PABPC1L	80336	hgsc.bcm.edu	37	chr20	43541304	43541304	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctcttccttctgtccagcggAgcgggcactggacacaatga	11	13	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:43541304A>G	ENST00000217073.2	+	2	197	c.197A>G	c.(196-198)gAg>gGg	p.E66G	PABPC1L_ENST00000255136.3_Missense_Mutation_p.E66G|PABPC1L_ENST00000217074.4_Missense_Mutation_p.E66G|PABPC1L_ENST00000537323.1_Missense_Mutation_p.E66G			Q4VXU2	PAP1L_HUMAN	poly(A) binding protein, cytoplasmic 1-like	66	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA polyadenylation (GO:0006378)|oocyte maturation (GO:0001556)	extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	20						TGTCCAGCGGAGCGGGCACTG	0.517																																					p.E66G		Atlas-SNP	.											.	PABPC1L	59	.	0			c.A197G						.						58	54	56					20																	43541304		1568	3582	5150	SO:0001583	missense	80336	exon2			CAGCGGAGCGGGC	AK026760	CCDS42878.1	20q12-q13.1	2013-02-12	2007-11-21	2007-11-21	ENSG00000101104	ENSG00000101104		"RNA binding motif (RRM) containing"	15797	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 119"	C20orf119		11549316	Standard	NM_001124756		Approved	dJ1069P2.3, PABPC1L1, ePAB	uc010ggv.1	Q4VXU2	OTTHUMG00000032553	ENST00000217073.2:c.197A>G	chr20.hg19:g.43541304A>G	ENSP00000217073:p.Glu66Gly	132.0	0.0		122.0	5.0	NM_001124756	Q4VY17	Missense_Mutation	SNP	ENST00000217073.2	hg19	CCDS42878.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.748989	0.89753	.	.	ENSG00000101104	ENST00000217074;ENST00000255136;ENST00000537323;ENST00000217073	T;T;T;T	0.19250	2.16;2.16;2.16;2.16	5.79	5.79	0.91817	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.098515	0.64402	D	0.000001	T	0.37156	0.0993	L	0.35644	1.08	0.80722	D	1	D	0.76494	0.999	D	0.69307	0.963	T	0.11717	-1.0576	10	0.87932	D	0	.	16.1175	0.81319	1.0:0.0:0.0:0.0	.	66	Q4VXU2	PAP1L_HUMAN	G	66	ENSP00000217074:E66G;ENSP00000255136:E66G;ENSP00000445661:E66G;ENSP00000217073:E66G	ENSP00000217073:E66G	E	+	2	0	PABPC1L	42974718	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.253000	0.95501	2.211000	0.71520	0.460000	0.39030	GAG	.	.		0.517	PABPC1L-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127816.2			G	43541304	A	G	43541304	3	3	282	1	0	0	0	0	1	0	0	0	11373	304	11	2	203	2	PABPC1L	20	43541304	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	846636	43541304	19484216	1302	41536										
SNX21	90203	hgsc.bcm.edu	37	chr20	44463730	44463730	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agtgaccagcgctaacgttgTcaaggacccgccctccaagt	10	14	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:44463730T>C	ENST00000491381.1	+	3	490	c.422T>C	c.(421-423)gTc>gCc	p.V141A	SNX21_ENST00000462307.1_Missense_Mutation_p.V141A|SNX21_ENST00000372541.1_Missense_Mutation_p.V132A|SNX21_ENST00000342644.5_Missense_Mutation_p.V141A|SNX21_ENST00000372542.1_Missense_Mutation_p.V132A|TNNC2_ENST00000372557.1_5'Flank|SNX21_ENST00000344780.4_3'UTR			Q969T3	SNX21_HUMAN	sorting nexin family member 21	141	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|pancreas(1)	7		Myeloproliferative disorder(115;0.0122)				GCTAACGTTGTCAAGGACCCG	0.587																																					p.V141A		Atlas-SNP	.											.	SNX21	23	.	0			c.T422C						.						51	48	49					20																	44463730		2203	4300	6503	SO:0001583	missense	90203	exon3			ACGTTGTCAAGGA	AK095851	CCDS13376.1, CCDS13377.1, CCDS42883.1	20q13.12	2013-01-10	2006-07-24	2006-07-24	ENSG00000124104	ENSG00000124104		"Sorting nexins", "Tetratricopeptide (TTC) repeat domain containing"	16154	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 161"	C20orf161		12461558, 12459172	Standard	NM_152897		Approved	dJ337O18.4, SNX-L	uc002xpv.1	Q969T3	OTTHUMG00000032624	ENST00000491381.1:c.422T>C	chr20.hg19:g.44463730T>C	ENSP00000418593:p.Val141Ala	137.0	0.0		105.0	7.0	NM_033421	Q5JZH5|Q5JZH6|Q5JZH7|Q8WUR6|Q9BR16	Missense_Mutation	SNP	ENST00000491381.1	hg19	CCDS13377.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.594696	0.86953	.	.	ENSG00000124104	ENST00000462307;ENST00000491381;ENST00000342644;ENST00000372542;ENST00000372541;ENST00000372545	T;T;T	0.31769	1.48;1.48;1.48	5.25	5.25	0.73442	Phox homologous domain (4);	0.131248	0.50627	D	0.000107	T	0.44664	0.1304	L	0.40543	1.245	0.38052	D	0.935818	P;D;D;P;D;D	0.60160	0.873;0.977;0.977;0.925;0.982;0.987	B;P;P;P;D;P	0.70227	0.291;0.766;0.766;0.513;0.968;0.856	T	0.43376	-0.9395	10	0.45353	T	0.12	-20.9992	13.0413	0.58901	0.0:0.0:0.0:1.0	.	132;132;141;141;141;141	Q5JZH4;Q5JZH3;Q969T3;Q5JZH7;Q05DJ0;Q5JZH5	.;.;SNX21_HUMAN;.;.;.	A	141;141;141;132;132;132	ENSP00000418593:V141A;ENSP00000344586:V141A;ENSP00000361620:V132A	ENSP00000344586:V141A	V	+	2	0	SNX21	43897137	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	6.269000	0.72558	2.200000	0.70718	0.460000	0.39030	GTC	.	.		0.587	SNX21-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079534.1	NM_033421		C	44463730	T	C	44463730	3	2	282	1	0	0	0	0	1	0	0	0	14908	1667	58	2	432	2	SNX21	20	44463730	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	922426	44463730	18561790	1303	41537										
ACOT8	10005	hgsc.bcm.edu	37	chr20	44477311	44477311	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acagtactggcagcttcgggTcccctgcagtgggcacaagg	14	12	0	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:44477311T>C	ENST00000217455.4	-	3	356	c.266A>G	c.(265-267)gAc>gGc	p.D89G		NM_005469.3	NP_005460.2	O14734	ACOT8_HUMAN	acyl-CoA thioesterase 8	89					acyl-CoA metabolic process (GO:0006637)|alpha-linolenic acid metabolic process (GO:0036109)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|dicarboxylic acid catabolic process (GO:0043649)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|peroxisome fission (GO:0016559)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|viral process (GO:0016032)	mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|choloyl-CoA hydrolase activity (GO:0033882)|medium-chain acyl-CoA hydrolase activity (GO:0052815)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)			kidney(2)|large_intestine(3)|lung(4)|skin(1)	10		Myeloproliferative disorder(115;0.0122)				CAGCTTCGGGTCCCCTGCAGT	0.567																																					p.D89G		Atlas-SNP	.											.	ACOT8	29	.	0			c.A266G						.						59	55	56					20																	44477311		2203	4300	6503	SO:0001583	missense	10005	exon3			TTCGGGTCCCCTG	AF014404	CCDS13378.1	20q13.12	2012-05-16	2005-09-19	2005-09-19	ENSG00000101473	ENSG00000101473	3.1.2.27	"Acyl CoA thioesterases"	15919	protein-coding gene	gene with protein product	"choloyl-CoA hydrolase"	608123	"peroxisomal acyl-CoA thioesterase", "peroxisomal acyl-CoA thioesterase 1"	PTE1		10092594, 9153233, 16103133, 16940157	Standard	NM_005469		Approved	hACTE-III, hTE, PTE-2	uc002xqa.2	O14734	OTTHUMG00000033045	ENST00000217455.4:c.266A>G	chr20.hg19:g.44477311T>C	ENSP00000217455:p.Asp89Gly	74.0	0.0		56.0	5.0	NM_005469	O15261|Q17RX4	Missense_Mutation	SNP	ENST00000217455.4	hg19	CCDS13378.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.54|14.54	2.566117|2.566117	0.45694|0.45694	.|.	.|.	ENSG00000101473|ENSG00000101473	ENST00000217455|ENST00000487205	.|.	.|.	.|.	5.38|5.38	5.38|5.38	0.77491|0.77491	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.88577|0.88577	0.6474|0.6474	H|H	0.98218|0.98218	4.175|4.175	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;0.999|.	D;D;D|.	0.91635|.	0.99;0.999;0.99|.	D|D	0.92746|0.92746	0.6212|0.6212	9|6	0.87932|0.87932	D|D	0|0	.|.	15.566|15.566	0.76294|0.76294	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	89;36;89|.	B4DLF4;A8K8X9;O14734|.	.;.;ACOT8_HUMAN|.	G|A	89|44	.|.	ENSP00000217455:D89G|ENSP00000433923:T110A	D|T	-|-	2|1	0|0	ACOT8|ACOT8	43910718|43910718	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.955000|0.955000	0.61496|0.61496	7.326000|7.326000	0.79133|0.79133	2.254000|2.254000	0.74563|0.74563	0.533000|0.533000	0.62120|0.62120	GAC|ACC	.	.		0.567	ACOT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080338.2	NM_183386		C	44477311	T	C	44477311	3	2	282	1	0	0	0	0	1	0	0	0	156	1667	58	2	709	2	ACOT8	20	44477311	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	13581	44477311	18548209	1304	41538										
CD40	958	hgsc.bcm.edu	37	chr20	44747014	44747014	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcctctgcagtgcgtcctctGgggctgcttgctgaccgctg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:44747014delG	ENST00000372285.3	+	1	104	c.32delG	c.(31-33)tggfs	p.W11fs	CD40_ENST00000372276.3_Frame_Shift_Del_p.W11fs|CD40_ENST00000489304.1_3'UTR	NM_001250.4	NP_001241.1	P25942	TNR5_HUMAN	CD40 molecule, TNF receptor superfamily member 5	11					B cell proliferation (GO:0042100)|cellular calcium ion homeostasis (GO:0006874)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|immune response-regulating cell surface receptor signaling pathway (GO:0002768)|inflammatory response (GO:0006954)|platelet activation (GO:0030168)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|protein complex assembly (GO:0006461)|regulation of immune response (GO:0050776)|regulation of immunoglobulin secretion (GO:0051023)	CD40 receptor complex (GO:0035631)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|enzyme binding (GO:0019899)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10		Myeloproliferative disorder(115;0.0122)				TGCGTCCTCTGGGGCTGCTTG	0.632									Immune Deficiency with Hyper-IgM																												p.W11fs		Atlas-INDEL	.											.	CD40	33	.	0			c.31delT						.						70	59	62					20																	44747014		2203	4300	6503	SO:0001589	frameshift_variant	958	exon1	Familial Cancer Database	Hypogammaglobulinemia with Hyper-IgM, HIGM type I-V, XLHIGM	.	X60592	CCDS13393.1, CCDS13394.1	20q12-q13.2	2014-09-17	2006-03-28	2005-01-14	ENSG00000101017	ENSG00000101017		"Tumor necrosis factor receptor superfamily", "CD molecules"	11919	protein-coding gene	gene with protein product		109535	"tumor necrosis factor receptor superfamily, member 5"	TNFRSF5		7687385, 2998589	Standard	XM_005260617		Approved	p50, Bp50	uc002xrg.1	P25942	OTTHUMG00000033053	ENST00000372285.3:c.32delG	chr20.hg19:g.44747014delG	ENSP00000361359:p.Trp11fs	244.0	0.0		171.0	11.0	NM_152854	E1P5S9|Q53GN5|Q5JY15|Q5U007|Q7M4Q8|Q86YK5|Q9BYU0	Frame_Shift_Del	DEL	ENST00000372285.3	hg19	CCDS13393.1																																																																																			.	.		0.632	CD40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080376.1	NM_001250		-	44747014	G	-	44747014	7	5	282	1	0	1	0	1	0	0	0	0	3017	1357	47	0	34	0	CD40	20	44747014	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	269703	44747014	18278506	1305	41539										
NCOA3	8202	hgsc.bcm.edu	37	chr20	46252672	46252672	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tagtcttacctgcagtggtgAaaaacggagacgggagcagg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:46252672delA	ENST00000371998.3	+	4	292	c.101delA	c.(100-102)gaafs	p.E34fs	NCOA3_ENST00000371997.3_Frame_Shift_Del_p.E34fs|NCOA3_ENST00000341724.6_Frame_Shift_Del_p.E34fs|NCOA3_ENST00000372004.3_Frame_Shift_Del_p.E34fs			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	34	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			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						TGCAGTGGTGAAAAACGGAGA	0.398																																					p.E34fs		Atlas-INDEL	.											.	NCOA3	156	.	0			c.100delG						.						64	68	67					20																	46252672		2203	4300	6503	SO:0001589	frameshift_variant	8202	exon4			.	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7670	protein-coding gene	gene with protein product	"receptor-associated coactivator 3", "thyroid hormone receptor activator molecule 1"	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.101delA	chr20.hg19:g.46252672delA	ENSP00000361066:p.Glu34fs	225.0	0.0		180.0	11.0	NM_181659	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Frame_Shift_Del	DEL	ENST00000371998.3	hg19	CCDS13407.1																																																																																			.	.		0.398	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534		-	46252672	A	-	46252672	7	5	282	1	0	1	0	1	0	0	0	0	10239	246	9	0	107	0	NCOA3	20	46252672	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1505658	46252672	16772848	1306	41540										
ZNF217	7764	hgsc.bcm.edu	37	chr20	52193620	52193620	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtaacatctttggcaccatcAaaaaatcttttcaaattttt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:52193620delA	ENST00000371471.2	-	4	2108	c.1683delT	c.(1681-1683)tttfs	p.F561fs	ZNF217_ENST00000302342.3_Frame_Shift_Del_p.F561fs|RP4-724E16.2_ENST00000424252.1_RNA			O75362	ZN217_HUMAN	zinc finger protein 217	561					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			TGGCACCATCAAAAAATCTTT	0.443																																					p.D562fs		Atlas-INDEL	.											.	ZNF217	227	.	0			c.1684delG						.						129	125	126					20																	52193620		2203	4300	6503	SO:0001589	frameshift_variant	7764	exon3			.	AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"Zinc fingers, C2H2-type"	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.1683delT	chr20.hg19:g.52193620delA	ENSP00000360526:p.Phe561fs	178.0	0.0		139.0	12.0	NM_006526	E1P5Y6|Q14DB8	Frame_Shift_Del	DEL	ENST00000371471.2	hg19	CCDS13443.1																																																																																			.	.		0.443	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526		-	52193620	A	-	52193620	7	5	282	1	0	1	0	1	0	0	0	0	17787	127	5	0	1471	0	ZNF217	20	52193620	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	5940948	52193620	10831900	1307	41541										
LAMA5	3911	hgsc.bcm.edu	37	chr20	60894843	60894843	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tggctcgcctggtctcgggtCcccacggcctgtggaggaag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:60894843delC	ENST00000252999.3	-	51	6834	c.6768delG	c.(6766-6768)gggfs	p.G2256fs		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2256	Domain II and I.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			GGTCTCGGGTCCCCACGGCCT	0.711																																					p.T2257fs		Atlas-INDEL	.											.	LAMA5	268	.	0			c.6769delA						.						11	11	11					20																	60894843		2063	4088	6151	SO:0001589	frameshift_variant	3911	exon51			.	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"Laminins"	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.6768delG	chr20.hg19:g.60894843delC	ENSP00000252999:p.Gly2256fs	124.0	0.0		104.0	10.0	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Frame_Shift_Del	DEL	ENST00000252999.3	hg19	CCDS33502.1																																																																																			.	.		0.711	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		-	60894843	C	-	60894843	7	5	282	1	0	1	0	1	0	0	0	0	8618	842	30	0	4439	0	LAMA5	20	60894843	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	8701223	60894843	2130677	1308	41542										
SLC2A4RG	56731	hgsc.bcm.edu	37	chr20	62373698	62373698	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtctcccgcaggaggcaggcAgagcctgagcagagtgatgg	17	10	1	4			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:62373698A>G	ENST00000266077.2	+	6	742	c.690A>G	c.(688-690)gcA>gcG	p.A230A	RP4-583P15.10_ENST00000447343.2_RNA|SLC2A4RG_ENST00000493772.1_3'UTR	NM_020062.3	NP_064446.2	Q9NR83	S2A4R_HUMAN	SLC2A4 regulator	230					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|kidney(1)|lung(2)|prostate(2)|skin(1)	7	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					GGAGGCAGGCAGAGCCTGAGC	0.662																																					p.A230A		Atlas-SNP	.											.	SLC2A4RG	20	.	0			c.A690G						.						45	31	36					20																	62373698		2199	4300	6499	SO:0001819	synonymous_variant	56731	exon6			GCAGGCAGAGCCT	AF249267	CCDS13537.1	20q13.33	2010-03-11			ENSG00000125520	ENSG00000125520			15930	protein-coding gene	gene with protein product	"GLUT4 enhancer factor", "Huntington's disease gene regulatory region-binding protein 1"	609493				10825161	Standard	NM_020062		Approved	GEF, HDBP1, Si-1-2, Si-1-2-19	uc002ygq.3	Q9NR83	OTTHUMG00000032997	ENST00000266077.2:c.690A>G	chr20.hg19:g.62373698A>G		189.0	0.0		140.0	6.0	NM_020062	Q2PHL5|Q6F6I6|Q6F6I7|Q6GTK5|Q8TAH5|Q8WVW7|Q96QD3|Q9BV85	Silent	SNP	ENST00000266077.2	hg19	CCDS13537.1																																																																																			.	.		0.662	SLC2A4RG-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080202.1	NM_020062		G	62373698	A	G	62373698	2	3	282	1	0	0	0	0	0	0	0	1	14562	175	7	2		2	SLC2A4RG	20	62373698	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1478855	62373698	651822	1309	41543										
MYT1	4661	hgsc.bcm.edu	37	chr20	62851088	62851088	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgtggatatcgaggtagacgAaaatggaaccctggacttga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:62851088delA	ENST00000328439.1	+	13	2358	c.1994delA	c.(1993-1995)gaafs	p.E665fs	MYT1_ENST00000536311.1_Frame_Shift_Del_p.E692fs|MYT1_ENST00000360149.4_Frame_Shift_Del_p.E367fs	NM_004535.2	NP_004526.1	Q99640	PMYT1_HUMAN	myelin transcription factor 1	0					G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(12)|liver(1)|lung(17)|ovary(5)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					GAGGTAGACGAAAATGGAACC	0.517																																					p.E665fs	GBM(59;481 1041 20555 21139 33705)	Atlas-INDEL	.											MYT1,caecum,carcinoma,0,2	MYT1	152	.	0			c.1993delG						.						108	100	103					20																	62851088		2203	4300	6503	SO:0001589	frameshift_variant	4661	exon13			.	M96980	CCDS13558.1	20q13.33	2014-03-24			ENSG00000196132	ENSG00000196132		"Zinc fingers, C2HC-type containing"	7622	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 2"	600379		PLPB1		1280325, 9268380	Standard	NM_004535		Approved	MTF1, MYTI, ZC2HC4A, NZF2	uc002yii.3	Q01538	OTTHUMG00000149988	ENST00000328439.1:c.1994delA	chr20.hg19:g.62851088delA	ENSP00000327465:p.Glu665fs	334.0	0.0		196.0	15.0	NM_004535	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Frame_Shift_Del	DEL	ENST00000328439.1	hg19	CCDS13558.1																																																																																			.	.		0.517	MYT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080297.1	NM_004535		-	62851088	A	-	62851088	7	5	282	1	0	1	0	1	0	0	0	0	10115	246	9	0	2036	0	MYT1	20	62851088	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	477390	62851088	174432	1310	41544										
NRIP1	8204	hgsc.bcm.edu	37	chr21	16339766	16339766	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgaggtggcaggactagcccTtttttccaccatgcttgcaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr21:16339766delT	ENST00000400202.1	-	3	1460	c.748delA	c.(748-750)aggfs	p.R250fs	NRIP1_ENST00000318948.4_Frame_Shift_Del_p.R250fs|NRIP1_ENST00000400199.1_Frame_Shift_Del_p.R250fs			P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	250	Interaction with ZNF366.|Repression domain 1.				androgen receptor signaling pathway (GO:0030521)|lipid storage (GO:0019915)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|ovarian follicle rupture (GO:0001543)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|estrogen receptor binding (GO:0030331)|glucocorticoid receptor binding (GO:0035259)|nuclear hormone receptor binding (GO:0035257)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			cervix(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(13)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	39				Epithelial(23;1.19e-05)|all cancers(11;4.64e-05)|COAD - Colon adenocarcinoma(22;0.000232)|Colorectal(24;0.0006)|OV - Ovarian serous cystadenocarcinoma(11;0.00418)|Lung(58;0.199)|LUSC - Lung squamous cell carcinoma(23;0.24)		GGACTAGCCCTTTTTTCCACC	0.468																																					p.R250fs		Atlas-INDEL	.											.	NRIP1	103	.	0			c.749delG						.						187	164	172					21																	16339766		2203	4300	6503	SO:0001589	frameshift_variant	8204	exon4			.	X84373	CCDS13568.1	21q11.2	2008-07-31			ENSG00000180530	ENSG00000180530			8001	protein-coding gene	gene with protein product	"receptor interacting protein 140", "nuclear factor RIP140"	602490				7641693, 9521594	Standard	NM_003489		Approved	RIP140	uc002yjx.2	P48552	OTTHUMG00000074323	ENST00000400202.1:c.748delA	chr21.hg19:g.16339766delT	ENSP00000383063:p.Arg250fs	177.0	0.0		144.0	12.0	NM_003489	Q8IWE8	Frame_Shift_Del	DEL	ENST00000400202.1	hg19	CCDS13568.1																																																																																			.	.		0.468	NRIP1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157926.1	NM_003489		-	16339766	T	-	16339766	7	5	282	1	0	1	0	1	0	0	0	0	10661	1608	56	0	2732	0	NRIP1	21	16339766	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10		16339766	31790129	1311	41545										
BTG3	10950	hgsc.bcm.edu	37	chr21	18981340	18981340	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggataccagtgatttttataTttttcttgaagtattagggt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr21:18981340delT	ENST00000348354.6	-	2	379	c.123delA	c.(121-123)aaafs	p.K41fs	BTG3_ENST00000464058.1_5'UTR|BTG3_ENST00000339775.6_Frame_Shift_Del_p.K41fs	NM_006806.4	NP_006797.3	Q14201	BTG3_HUMAN	BTG family, member 3	41					negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)	cytoplasm (GO:0005737)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)	8				Epithelial(23;0.000283)|all cancers(11;0.0012)|Lung(58;0.0191)|OV - Ovarian serous cystadenocarcinoma(11;0.0206)|COAD - Colon adenocarcinoma(22;0.0315)|LUSC - Lung squamous cell carcinoma(23;0.0703)|Colorectal(24;0.0971)		GATTTTTATATTTTTCTTGAA	0.393																																					p.Y42fs		Atlas-INDEL	.											.	BTG3	27	.	0			c.124delT						.						140	134	136					21																	18981340		2203	4300	6503	SO:0001589	frameshift_variant	10950	exon2			.	D64110	CCDS13569.1, CCDS46636.1	21q21.1	2006-12-16			ENSG00000154640	ENSG00000154640			1132	protein-coding gene	gene with protein product		605674				9632145	Standard	NM_006806		Approved	ANA, tob55	uc002ykk.3	Q14201	OTTHUMG00000074501	ENST00000348354.6:c.123delA	chr21.hg19:g.18981340delT	ENSP00000284879:p.Lys41fs	153.0	0.0		166.0	11.0	NM_006806	D3DSC4|Q53XV1|Q96ET7	Frame_Shift_Del	DEL	ENST00000348354.6	hg19	CCDS13569.1																																																																																			.	.		0.393	BTG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158196.1	NM_006806		-	18981340	T	-	18981340	7	5	282	1	0	1	0	1	0	0	0	0	1557	1490	52	0	787	0	BTG3	21	18981340	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2641574	18981340	29148555	1312	41546										
USP16	10600	hgsc.bcm.edu	37	chr21	30409650	30409650	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ataaaaaattagaaaaagagAgtaagaatgaacaagagaga	9	1	0	6			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr21:30409650A>G	ENST00000334352.4	+	7	733	c.502A>G	c.(502-504)Agt>Ggt	p.S168G	USP16_ENST00000399976.2_Missense_Mutation_p.S168G|USP16_ENST00000535828.1_Intron|USP16_ENST00000399975.3_Missense_Mutation_p.S167G	NM_001032410.1	NP_001027582.1			ubiquitin specific peptidase 16											breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(2)	34						AGAAAAAGAGAGTAAGAATGA	0.303																																					p.S168G	Melanoma(92;625 1444 27493 34101 44971)	Atlas-SNP	.											.	USP16	65	.	0			c.A502G						.						72	79	77					21																	30409650		2203	4300	6503	SO:0001583	missense	10600	exon6			AAAGAGAGTAAGA	AF126736	CCDS13583.1, CCDS42912.1	21q21	2008-04-11	2005-08-08		ENSG00000156256	ENSG00000156256		"Ubiquitin-specific peptidases"	12614	protein-coding gene	gene with protein product		604735	"ubiquitin specific protease 16"			12838346	Standard	NM_006447		Approved	Ubp-M	uc002ymy.3	Q9Y5T5	OTTHUMG00000078802	ENST00000334352.4:c.502A>G	chr21.hg19:g.30409650A>G	ENSP00000334808:p.Ser168Gly	98.0	0.0		75.0	5.0	NM_006447		Missense_Mutation	SNP	ENST00000334352.4	hg19	CCDS13583.1	.	.	.	.	.	.	.	.	.	.	A	11.94	1.787301	0.31593	.	.	ENSG00000156256	ENST00000399975;ENST00000399976;ENST00000334352	T;T;T	0.06849	3.25;3.26;3.26	5.9	5.9	0.94986	.	0.495710	0.27176	N	0.020565	T	0.06508	0.0167	L	0.27053	0.805	0.80722	D	1	B;B;B	0.31548	0.328;0.163;0.102	B;B;B	0.26310	0.045;0.068;0.031	T	0.46133	-0.9213	10	0.22706	T	0.39	.	12.7923	0.57541	0.8636:0.1364:0.0:0.0	.	153;167;168	Q9Y5T5-3;Q9Y5T5-2;Q9Y5T5	.;.;UBP16_HUMAN	G	167;168;168	ENSP00000382857:S167G;ENSP00000382858:S168G;ENSP00000334808:S168G	ENSP00000334808:S168G	S	+	1	0	USP16	29331521	0.997000	0.39634	1.000000	0.80357	0.992000	0.81027	4.180000	0.58296	2.251000	0.74343	0.528000	0.53228	AGT	.	.		0.303	USP16-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171847.1			G	30409650	A	G	30409650	3	3	282	1	0	0	0	0	1	0	0	0	17062	304	11	2	520	2	USP16	21	30409650	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	11428310	30409650	17720245	1313	41547										
CCT8	10694	hgsc.bcm.edu	37	chr21	30439316	30439316	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cttcatcaatatctcgaaggTtttttgcagaacaacatacc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr21:30439316delT	ENST00000286788.4	-	5	664	c.458delA	c.(457-459)aacfs	p.N153fs	CCT8_ENST00000540844.1_Frame_Shift_Del_p.N80fs|CCT8_ENST00000470450.1_5'UTR|CCT8_ENST00000542732.1_Frame_Shift_Del_p.N134fs	NM_006585.2	NP_006576.2	P50990	TCPQ_HUMAN	chaperonin containing TCP1, subunit 8 (theta)	153					'de novo' posttranslational protein folding (GO:0051084)|ATP catabolic process (GO:0006200)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	aggresome (GO:0016235)|cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|microtubule (GO:0005874)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(1)|prostate(3)	14						ATCTCGAAGGTTTTTTGCAGA	0.358																																					p.N153fs		Atlas-INDEL	.											CCT8,NS,carcinoma,0,1	CCT8	38	.	0			c.459delC						.						88	83	84					21																	30439316		2203	4300	6503	SO:0001589	frameshift_variant	10694	exon5			.	Z37163	CCDS33528.1, CCDS68180.1	21q21.3	2011-09-02			ENSG00000156261	ENSG00000156261		"Heat Shock Proteins / Chaperonins"	1623	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 112"	C21orf112		7890169	Standard	NM_006585		Approved	Cctq, PRED71	uc002ynb.3	P50990	OTTHUMG00000044595	ENST00000286788.4:c.458delA	chr21.hg19:g.30439316delT	ENSP00000286788:p.Asn153fs	317.0	0.0		257.0	16.0	NM_006585	A6NN54|B4DEM7|B4DQH4|Q4VBP8	Frame_Shift_Del	DEL	ENST00000286788.4	hg19	CCDS33528.1																																																																																			.	.		0.358	CCT8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171822.1			-	30439316	T	-	30439316	7	5	282	1	0	1	0	1	0	0	0	0	2962	1725	60	0	1232	0	CCT8	21	30439316	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	29666	30439316	17690579	1314	41548										
BACH1	571	hgsc.bcm.edu	37	chr21	30701858	30701858	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atttcactgtctcgaaatgaTtttcagtccttgttgaaaat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr21:30701858delT	ENST00000399921.1	+	4	1863	c.1620delT	c.(1618-1620)gatfs	p.D540fs	BACH1_ENST00000286800.3_Frame_Shift_Del_p.D540fs	NM_206866.1	NP_996749.1	Q9BX63	FANCJ_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 1	0			Q -> L (in dbSNP:rs4988349). {ECO:0000269|PubMed:12872252}.		DNA damage checkpoint (GO:0000077)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|urinary_tract(2)	27						CTCGAAATGATTTTCAGTCCT	0.328																																					p.D540fs		Atlas-INDEL	.											.	BACH1	66	.	0			c.1619delA						.						74	71	72					21																	30701858		2203	4300	6503	SO:0001589	frameshift_variant	571	exon4			.	AF026200	CCDS13585.1	21q22.1	2013-01-10			ENSG00000156273	ENSG00000156273		"BTB/POZ domain containing", "basic leucine zipper proteins"	935	protein-coding gene	gene with protein product		602751				9544839, 9479503	Standard	NR_027655		Approved	BACH-1, BTBD24	uc002ynj.3	O14867	OTTHUMG00000078878	ENST00000399921.1:c.1620delT	chr21.hg19:g.30701858delT	ENSP00000382805:p.Asp540fs	301.0	0.0		181.0	12.0	NM_206866	Q3MJE2|Q8NCI5	Frame_Shift_Del	DEL	ENST00000399921.1	hg19	CCDS13585.1																																																																																			.	.		0.328	BACH1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171974.1	NM_206866		-	30701858	T	-	30701858	7	5	282	1	0	1	0	1	0	0	0	0	1283	1490	52	0	1630	0	BACH1	21	30701858	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	262542	30701858	17428037	1315	41549										
MRPS6	64968	hgsc.bcm.edu	37	chr21	35497667	35497667	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	actgctgctactttgaaacgTacgatagaggccctgatgga	11	9	0	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr21:35497667T>C	ENST00000399312.2	+	2	250	c.72T>C	c.(70-72)cgT>cgC	p.R24R	MRPS6_ENST00000482679.1_3'UTR|AP000320.7_ENST00000362077.4_RNA	NM_032476.3	NP_115865.1	P82932	RT06_HUMAN	mitochondrial ribosomal protein S6	24					translation (GO:0006412)	mitochondrion (GO:0005739)|small ribosomal subunit (GO:0015935)	rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|pancreas(1)|skin(1)	6						CTTTGAAACGTACGATAGAGG	0.423																																					p.R24R		Atlas-SNP	.											.	MRPS6	18	.	0			c.T72C						.						140	147	144					21																	35497667		2203	4300	6503	SO:0001819	synonymous_variant	64968	exon2			GAAACGTACGATA	AB051347	CCDS33548.1	21q22.11	2012-09-13	2002-06-20		ENSG00000243927	ENSG00000243927		"Mitochondrial ribosomal proteins / small subunits"	14051	protein-coding gene	gene with protein product		611973	"chromosome 21 open reading frame 101"	C21orf101			Standard	NM_032476		Approved	MRP-S6, RPMS6	uc002ytp.2	P82932	OTTHUMG00000065820	ENST00000399312.2:c.72T>C	chr21.hg19:g.35497667T>C		103.0	0.0		87.0	4.0	NM_032476	B2R573|Q96Q64|Q9BSK8|Q9BW89	Silent	SNP	ENST00000399312.2	hg19	CCDS33548.1																																																																																			.	.		0.423	MRPS6-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000141033.1	NM_032476		C	35497667	T	C	35497667	2	2	282	1	0	0	0	0	0	0	0	1	9856	1625	57	2		2	MRPS6	21	35497667	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	4795809	35497667	12632228	1316	41550										
SETD4	54093	hgsc.bcm.edu	37	chr21	37418076	37418076	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	acagaggctgcagagaagagAaaaagtctctggaggaagca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr21:37418076delA	ENST00000399215.1	-	5	1902	c.530delT	c.(529-531)ttcfs	p.F177fs	SETD4_ENST00000399207.1_Frame_Shift_Del_p.F177fs|SETD4_ENST00000399205.1_Frame_Shift_Del_p.F153fs|SETD4_ENST00000332131.4_Frame_Shift_Del_p.F177fs|SETD4_ENST00000399212.1_Frame_Shift_Del_p.F153fs|SETD4_ENST00000399201.1_Frame_Shift_Del_p.F153fs|SETD4_ENST00000399208.2_Frame_Shift_Del_p.F177fs|SETD4_ENST00000481477.1_5'UTR			Q9NVD3	SETD4_HUMAN	SET domain containing 4	177	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.						methyltransferase activity (GO:0008168)			autonomic_ganglia(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)	15						CAGAGAAGAGAAAAAGTCTCT	0.532																																					p.F177fs		Atlas-INDEL	.											.	SETD4	37	.	0			c.531delC						.						79	89	86					21																	37418076		2203	4300	6503	SO:0001589	frameshift_variant	54093	exon6			.	AK001660	CCDS13640.1, CCDS42923.1, CCDS74791.1, CCDS74792.1	21q22.13	2006-02-15	2006-02-15	2006-02-15	ENSG00000185917	ENSG00000185917			1258	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 27", "chromosome 21 open reading frame 18"	C21orf27, C21orf18			Standard	XM_005261000		Approved		uc021wiy.1	Q9NVD3	OTTHUMG00000086483	ENST00000399215.1:c.530delT	chr21.hg19:g.37418076delA	ENSP00000382163:p.Phe177fs	215.0	0.0		160.0	10.0	NM_001007259	B4DT14|D3DSG2|D3DSG4|Q8NE19|Q9BU46	Frame_Shift_Del	DEL	ENST00000399215.1	hg19	CCDS13640.1																																																																																			.	.		0.532	SETD4-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194456.1	NM_017438		-	37418076	A	-	37418076	7	5	282	1	0	1	0	1	0	0	0	0	14148	246	9	0	839	0	SETD4	21	37418076	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1920409	37418076	10711819	1317	41551										
DOPEY2	9980	hgsc.bcm.edu	37	chr21	37603030	37603030	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttggagtacagctgacagcgTcaggagaagaaagcaagtcc	13	8	1	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr21:37603030T>C	ENST00000399151.3	+	14	2033	c.1948T>C	c.(1948-1950)Tca>Cca	p.S650P		NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	650					cognition (GO:0050890)|endoplasmic reticulum organization (GO:0007029)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(6)|lung(25)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						GCTGACAGCGTCAGGAGAAGA	0.537																																					p.S650P		Atlas-SNP	.											.	DOPEY2	184	.	0			c.T1948C						.						58	59	59					21																	37603030		2203	4300	6503	SO:0001583	missense	9980	exon14			ACAGCGTCAGGAG	AJ237839	CCDS13643.1	21q22.2	2013-03-05	2006-02-02	2006-02-02	ENSG00000142197	ENSG00000142197			1291	protein-coding gene	gene with protein product		604803	"chromosome 21 open reading frame 5"	C21orf5		16301316, 16303751, 10931277	Standard	NM_005128		Approved	KIAA0933	uc002yvg.3	Q9Y3R5	OTTHUMG00000086619	ENST00000399151.3:c.1948T>C	chr21.hg19:g.37603030T>C	ENSP00000382104:p.Ser650Pro	162.0	0.0		137.0	6.0	NM_005128	D3DSG5|Q6PJQ7|Q9UEZ3	Missense_Mutation	SNP	ENST00000399151.3	hg19	CCDS13643.1	.	.	.	.	.	.	.	.	.	.	T	3.739	-0.053918	0.07362	.	.	ENSG00000142197	ENST00000399151	T	0.12039	2.72	5.43	-0.204	0.13200	.	0.807665	0.11689	N	0.539140	T	0.08044	0.0201	L	0.35414	1.06	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.11329	0.006;0.003	T	0.37430	-0.9706	10	0.30078	T	0.28	.	1.4164	0.02302	0.1209:0.2628:0.2478:0.3685	.	650;650	Q9Y3R5-2;Q9Y3R5	.;DOP2_HUMAN	P	650	ENSP00000382104:S650P	ENSP00000382104:S650P	S	+	1	0	DOPEY2	36524900	0.000000	0.05858	0.002000	0.10522	0.113000	0.19764	0.027000	0.13621	0.095000	0.17434	0.402000	0.26972	TCA	.	.		0.537	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	NM_005128		C	37603030	T	C	37603030	3	2	282	1	0	0	0	0	1	0	0	0	4710	1667	58	2	1998	2	DOPEY2	21	37603030	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	184954	37603030	10526865	1318	41552										
LCA5L	150082	hgsc.bcm.edu	37	chr21	40782217	40782217	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtcaaaggtggaacatctgaTttttgggttccctggtgtct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr21:40782217delT	ENST00000358268.2	-	8	1665	c.1137delA	c.(1135-1137)aaafs	p.K379fs	LCA5L_ENST00000380671.2_Frame_Shift_Del_p.K379fs|WRB_ENST00000541890.1_Intron|LCA5L_ENST00000495240.1_5'UTR|LCA5L_ENST00000288350.3_Frame_Shift_Del_p.K379fs			O95447	LCA5L_HUMAN	Leber congenital amaurosis 5-like	379										breast(1)|cervix(1)|endometrium(3)|large_intestine(8)|lung(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	24		Prostate(19;1.2e-06)				GAACATCTGATTTTTGGGTTC	0.368																																					p.S380fs		Atlas-INDEL	.											.	LCA5L	57	.	0			c.1138delT						.						232	223	227					21																	40782217		2203	4300	6503	SO:0001589	frameshift_variant	150082	exon8			.	AF121781	CCDS13665.1	21q22.2	2007-12-18	2007-12-18	2007-12-18	ENSG00000157578	ENSG00000157578			1255	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 13"	C21orf13			Standard	XM_005260926		Approved	MGC33295	uc002yxu.3	O95447	OTTHUMG00000066280	ENST00000358268.2:c.1137delA	chr21.hg19:g.40782217delT	ENSP00000351008:p.Lys379fs	223.0	0.0		152.0	10.0	NM_152505	D3DSI0|Q3ZCT0	Frame_Shift_Del	DEL	ENST00000358268.2	hg19	CCDS13665.1																																																																																			.	.		0.368	LCA5L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141807.2	NM_152505		-	40782217	T	-	40782217	7	5	282	1	0	1	0	1	0	0	0	0	8666	1490	52	0	887	0	LCA5L	21	40782217	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3179187	40782217	7347678	1319	41553										
PCP4	5121	hgsc.bcm.edu	37	chr21	41300935	41300935	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agaagaaagttcaagaagaaTttgacattgacatggatgca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr21:41300935delT	ENST00000328619.5	+	3	273	c.88delT	c.(88-90)tttfs	p.F30fs	PCP4_ENST00000468717.1_3'UTR	NM_006198.2	NP_006189.2	P48539	PCP4_HUMAN	Purkinje cell protein 4	30					central nervous system development (GO:0007417)	cytosol (GO:0005829)|nucleus (GO:0005634)				large_intestine(2)|lung(1)|skin(1)	4		Prostate(19;2.65e-06)|all_epithelial(19;0.138)				TCAAGAAGAATTTGACATTGA	0.448																																					p.E29fs		Atlas-INDEL	.											.	PCP4	11	.	0			c.87delA						.						117	107	110					21																	41300935		2203	4300	6503	SO:0001589	frameshift_variant	5121	exon3			.	X93349, U53709	CCDS33563.1	21q22.2	2006-12-01			ENSG00000183036	ENSG00000183036			8742	protein-coding gene	gene with protein product		601629				8931698, 8914602	Standard	NM_006198		Approved	PEP-19	uc002yyp.3	P48539	OTTHUMG00000086731	ENST00000328619.5:c.88delT	chr21.hg19:g.41300935delT	ENSP00000329403:p.Phe30fs	239.0	0.0		188.0	12.0	NM_006198	A6NDJ9|Q6ICS4|Q93059	Frame_Shift_Del	DEL	ENST00000328619.5	hg19	CCDS33563.1																																																																																			.	.		0.448	PCP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195025.1	NM_006198		-	41300935	T	-	41300935	7	5	282	1	0	1	0	1	0	0	0	0	11607	1493	52	0	98	0	PCP4	21	41300935	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	518718	41300935	6828960	1320	41554										
RSPH1	89765	hgsc.bcm.edu	37	chr21	43905780	43905780	+	Splice_Site	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcacttcccatggacttacaTttttgttcaagaacttgccc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr21:43905780delT	ENST00000291536.3	-	5	667	c.500delA	c.(499-501)aat>at	p.N167fs	RSPH1_ENST00000398352.3_Splice_Site_p.N129fs	NM_080860.2	NP_543136.1	Q8WYR4	RSPH1_HUMAN	radial spoke head 1 homolog (Chlamydomonas)	167					axoneme assembly (GO:0035082)|meiotic nuclear division (GO:0007126)	cytosol (GO:0005829)|motile cilium (GO:0031514)|nucleus (GO:0005634)				large_intestine(7)|lung(2)|ovary(1)|prostate(1)|stomach(1)	12						TGGACTTACATTTTTGTTCAA	0.493																																					p.N167fs	Esophageal Squamous(23;63 706 6286 10288 12913)	Atlas-INDEL	.											.	RSPH1	36	.	0			c.501delT						.						130	115	120					21																	43905780		2203	4300	6503	SO:0001630	splice_region_variant	89765	exon5			.	AB006536	CCDS13688.1, CCDS68210.1	21q22.3	2014-02-03	2007-06-25	2007-06-25	ENSG00000160188	ENSG00000160188			12371	protein-coding gene	gene with protein product	"meichroacidin"	609314	"testis specific A2 homolog (mouse)"	TSGA2		9403069, 9578619, 17451891	Standard	XM_005261208		Approved	FLJ32753, RSP44, RSPH10A, CILD24	uc002zbg.3	Q8WYR4	OTTHUMG00000086804	ENST00000291536.3:c.501+1A>-	chr21.hg19:g.43905780delT		267.0	0.0		199.0	12.0	NM_080860	A8MWV0|B2RBN9|Q3MJA1	Frame_Shift_Del	DEL	ENST00000291536.3	hg19	CCDS13688.1																																																																																			.	.		0.493	RSPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195379.1		Frame_Shift_Del	-	43905780	T	-	43905780	8	5	282	1	0	1	0	1	0	0	1	0	13717	1507	52	0	449	0	RSPH1	21	43905780	Splice_Site	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2604845	43905780	4224115	1321	41555										
SLC37A1	54020	hgsc.bcm.edu	37	chr21	43999901	43999901	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cccagggtcagctacgggggAccaagttccgtaagtcccac	12	14	1	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr21:43999901A>G	ENST00000352133.2	+	19	2559	c.1577A>G	c.(1576-1578)gAc>gGc	p.D526G	SLC37A1_ENST00000398341.3_Missense_Mutation_p.D526G			P57057	GLPT_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 1	526					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	transporter activity (GO:0005215)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|liver(2)|lung(3)	15						GCTACGGGGGACCAAGTTCCG	0.582																																					p.D526G		Atlas-SNP	.											.	SLC37A1	48	.	0			c.A1577G						.						67	54	59					21																	43999901		2203	4300	6503	SO:0001583	missense	54020	exon20			CGGGGGACCAAGT	AJ269529	CCDS13689.1	21q22.3	2013-07-17	2013-07-17		ENSG00000160190	ENSG00000160190		"Solute carriers"	11024	protein-coding gene	gene with protein product		608094	"solute carrier family 37 (glycerol-3-phosphate transporter), member 1"			11112347	Standard	NM_018964		Approved		uc002zbi.3	P57057	OTTHUMG00000086803	ENST00000352133.2:c.1577A>G	chr21.hg19:g.43999901A>G	ENSP00000344648:p.Asp526Gly	100.0	0.0		60.0	4.0	NM_018964	D3DSJ7|Q9HAQ1	Missense_Mutation	SNP	ENST00000352133.2	hg19	CCDS13689.1	.	.	.	.	.	.	.	.	.	.	A	13.26	2.183825	0.38609	.	.	ENSG00000160190	ENST00000398341;ENST00000352133	T;T	0.22743	1.94;1.94	4.86	-0.408	0.12381	.	1.249670	0.05359	N	0.533344	T	0.13884	0.0336	L	0.29908	0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30475	-0.9977	10	0.30078	T	0.28	-9.898	3.5469	0.07832	0.5668:0.0:0.266:0.1672	.	526	P57057	GLPT_HUMAN	G	526	ENSP00000381383:D526G;ENSP00000344648:D526G	ENSP00000344648:D526G	D	+	2	0	SLC37A1	42872970	0.494000	0.26043	0.026000	0.17262	0.470000	0.32858	0.519000	0.22862	-0.240000	0.09696	0.379000	0.24179	GAC	.	.		0.582	SLC37A1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195377.1			G	43999901	A	G	43999901	3	3	282	1	0	0	0	0	1	0	0	0	14612	275	10	2	1647	2	SLC37A1	21	43999901	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	94121	43999901	4129994	1322	41556										
CBS	875	hgsc.bcm.edu	37	chr21	44479032	44479032	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggtgatggtcgggagcacggTcagcggggctgacaggccca	19	10	1	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr21:44479032T>C	ENST00000398165.3	-	14	1529	c.1270A>G	c.(1270-1272)Acc>Gcc	p.T424A	CBS_ENST00000398158.1_Missense_Mutation_p.T424A|CBS_ENST00000544202.1_Missense_Mutation_p.T336A|CBS_ENST00000398168.1_Missense_Mutation_p.T424A|CBS_ENST00000359624.3_Missense_Mutation_p.T424A|CBS_ENST00000352178.5_Missense_Mutation_p.T424A	NM_000071.2	NP_000062.1	P35520	CBS_HUMAN	cystathionine-beta-synthase	424	CBS. {ECO:0000255|PROSITE- ProRule:PRU00703}.				cellular nitrogen compound metabolic process (GO:0034641)|cysteine biosynthetic process from serine (GO:0006535)|cysteine biosynthetic process via cystathionine (GO:0019343)|homocysteine catabolic process (GO:0043418)|homocysteine metabolic process (GO:0050667)|hydrogen sulfide biosynthetic process (GO:0070814)|L-cysteine catabolic process (GO:0019448)|L-serine catabolic process (GO:0006565)|L-serine metabolic process (GO:0006563)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|transsulfuration (GO:0019346)	cytosol (GO:0005829)|nucleus (GO:0005634)	adenyl nucleotide binding (GO:0030554)|cystathionine beta-synthase activity (GO:0004122)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|modified amino acid binding (GO:0072341)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|ubiquitin protein ligase binding (GO:0031625)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(8)	17					L-Cysteine(DB00151)|L-Serine(DB00133)|S-Adenosylmethionine(DB00118)	GGGAGCACGGTCAGCGGGGCT	0.657																																					p.T424A		Atlas-SNP	.											.	CBS	85	.	0			c.A1270G						.						36	31	32					21																	44479032		2177	4291	6468	SO:0001583	missense	875	exon14			GCACGGTCAGCGG	L14577	CCDS13693.1	21q22.3	2014-09-17			ENSG00000160200	ENSG00000160200	4.2.1.22		1550	protein-coding gene	gene with protein product		613381				9790750	Standard	NM_000071		Approved	HIP4	uc002zcv.2	P35520	OTTHUMG00000086834	ENST00000398165.3:c.1270A>G	chr21.hg19:g.44479032T>C	ENSP00000381231:p.Thr424Ala	105.0	0.0		88.0	5.0	NM_000071	B2R993|D3DSK4|Q99425|Q9BWC5	Missense_Mutation	SNP	ENST00000398165.3	hg19	CCDS13693.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	15.44|15.44|15.44	2.835561|2.835561|2.835561	0.50951|0.50951|0.50951	.|.|.	.|.|.	ENSG00000160200|ENSG00000160200|ENSG00000160200	ENST00000451248|ENST00000398158;ENST00000398165;ENST00000359624;ENST00000352178;ENST00000398168;ENST00000539520;ENST00000544202|ENST00000458223;ENST00000430013	.|D;D;D;D;D;D|.	.|0.95001|.	.|-3.58;-3.58;-3.58;-3.58;-3.58;-3.58|.	4.71|4.71|4.71	4.71|4.71|4.71	0.59529|0.59529|0.59529	.|Cystathionine beta-synthase, core (3);|.	.|0.165190|.	.|0.53938|.	.|D|.	.|0.000055|.	T|T|.	0.77665|0.77665|.	0.4164|0.4164|.	M|M|M	0.85462|0.85462|0.85462	2.755|2.755|2.755	0.54753|0.54753|0.54753	D|D|D	0.99998|0.99998|0.99998	.|B;B;B|.	.|0.28552|.	.|0.215;0.037;0.167|.	.|B;B;B|.	.|0.38327|.	.|0.202;0.088;0.271|.	T|T|.	0.80694|0.80694|.	-0.1268|-0.1268|.	5|10|.	.|0.38643|.	.|T|.	.|0.18|.	-22.9848|-22.9848|-22.9848	13.9291|13.9291|13.9291	0.63983|0.63983|0.63983	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.|.	.|424;424;381|.	.|P35520-2;P35520;B7Z2D6|.	.|.;CBS_HUMAN;.|.	G|A|W	7|424;424;424;424;424;381;336|11;77	.|ENSP00000381225:T424A;ENSP00000381231:T424A;ENSP00000352643:T424A;ENSP00000344460:T424A;ENSP00000381234:T424A;ENSP00000439332:T336A|.	.|ENSP00000344460:T424A|.	D|T|X	-|-|-	2|1|3	0|0|0	CBS|CBS|CBS	43352101|43352101|43352101	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.955000|0.955000|0.955000	0.39395|0.39395|0.39395	0.025000|0.025000|0.025000	0.11179|0.11179|0.11179	5.792000|5.792000|5.792000	0.69052|0.69052|0.69052	1.781000|1.781000|1.781000	0.52344|0.52344|0.52344	0.456000|0.456000|0.456000	0.33151|0.33151|0.33151	GAC|ACC|TGA	.	.		0.657	CBS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195525.1	NM_000071		C	44479032	T	C	44479032	3	2	282	1	0	0	0	0	1	0	0	0	2713	1667	58	2	401	2	CBS	21	44479032	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	479131	44479032	3650863	1323	41557										
C21orf33	8209	hgsc.bcm.edu	37	chr21	45556049	45556049	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggggcagccgtccgaaggcgAgagcaggtgtgggggtggga	23	7	0	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr21:45556049A>G	ENST00000291577.6	+	3	395	c.302A>G	c.(301-303)gAg>gGg	p.E101G	C21orf33_ENST00000493883.1_3'UTR|C21orf33_ENST00000427803.2_Missense_Mutation_p.E101G|C21orf33_ENST00000348499.5_Missense_Mutation_p.E101G	NM_004649.6	NP_004640	P30042	ES1_HUMAN	chromosome 21 open reading frame 33	101						mitochondrion (GO:0005739)				NS(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	8				STAD - Stomach adenocarcinoma(101;0.168)|Colorectal(79;0.191)		TCCGAAGGCGAGAGCAGGTGT	0.557																																					p.E101G		Atlas-SNP	.											.	C21orf33	23	.	0			c.A302G						.						71	64	66					21																	45556049		2203	4300	6503	SO:0001583	missense	8209	exon3			AAGGCGAGAGCAG	Y07572	CCDS33580.1, CCDS33581.1	21q22.3	2008-07-29			ENSG00000160221	ENSG00000160221			1273	protein-coding gene	gene with protein product		601659				9150728, 8975701	Standard	NM_004649		Approved	KNP-Ia, GT335, ES1, HES1, D21S2048E, KNPI, KNPH, KNP-I	uc002zec.4	P30042	OTTHUMG00000086916	ENST00000291577.6:c.302A>G	chr21.hg19:g.45556049A>G	ENSP00000291577:p.Glu101Gly	190.0	0.0		133.0	6.0	NM_198155	A6NFJ6|A6NJY7|O00650|O00660|O15011|O15012|P55346|P78474|Q92505|Q92507	Missense_Mutation	SNP	ENST00000291577.6	hg19	CCDS33580.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.7|21.7	4.186014|4.186014	0.78789|0.78789	.|.	.|.	ENSG00000248354;ENSG00000160221;ENSG00000160221;ENSG00000160221;ENSG00000160221|ENSG00000160221	ENST00000433711;ENST00000291577;ENST00000427803;ENST00000348499;ENST00000389690|ENST00000419699	T;T;T;T|.	0.81247|.	-1.47;-1.47;1.36;-1.47|.	4.93|4.93	3.78|3.78	0.43462|0.43462	ThiJ/PfpI (1);|.	0.052417|.	0.64402|.	D|.	0.000001|.	T|T	0.80808|0.80808	0.4694|0.4694	M|M	0.93150|0.93150	3.385|3.385	0.80722|0.80722	D|D	1|1	D;D|.	0.59767|.	0.986;0.979|.	P;P|.	0.62298|.	0.839;0.9|.	D|D	0.83439|0.83439	0.0042|0.0042	10|5	0.87932|.	D|.	0|.	-21.7287|-21.7287	10.689|10.689	0.45860|0.45860	0.9243:0.0:0.0757:0.0|0.9243:0.0:0.0757:0.0	.|.	101;101|.	P30042-2;P30042|.	.;ES1_HUMAN|.	G|G	80;101;101;101;74|17	ENSP00000291577:E101G;ENSP00000396655:E101G;ENSP00000344901:E101G;ENSP00000374340:E74G|.	ENSP00000415634:E80G|.	E|R	+|+	2|1	0|2	C21orf33;AP001055.7|C21orf33	44380477|44380477	1.000000|1.000000	0.71417|0.71417	0.012000|0.012000	0.15200|0.15200	0.034000|0.034000	0.12701|0.12701	4.610000|4.610000	0.61155|0.61155	0.841000|0.841000	0.35020|0.35020	0.533000|0.533000	0.62120|0.62120	GAG|AGA	.	.		0.557	C21orf33-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195824.1	NM_004649		G	45556049	A	G	45556049	3	3	282	1	0	0	0	0	1	0	0	0	2127	304	11	2	312	2	C21orf33	21	45556049	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1077017	45556049	2573846	1324	41558										
MCM3AP	8888	hgsc.bcm.edu	37	chr21	47674393	47674393	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gctcctgcctcccagggaggTgctcagccacgagggatggc	15	14	1	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr21:47674393T>C	ENST00000397708.1	-	20	4303	c.4049A>G	c.(4048-4050)cAc>cGc	p.H1350R	MCM3AP-AS1_ENST00000455567.1_RNA|AP001469.9_ENST00000447037.1_RNA|MCM3AP_ENST00000291688.1_Missense_Mutation_p.H1350R|MCM3AP_ENST00000467026.1_5'UTR|AP001469.9_ENST00000430259.1_RNA|MCM3AP-AS1_ENST00000590829.1_RNA|MCM3AP-AS1_ENST00000414659.1_RNA			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	1350					DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					CCCAGGGAGGTGCTCAGCCAC	0.597																																					p.H1350R		Atlas-SNP	.											.	MCM3AP	146	.	0			c.A4049G						.						78	65	69					21																	47674393		2203	4300	6503	SO:0001583	missense	8888	exon19			GGGAGGTGCTCAG	AB005543	CCDS13734.1	21q22.3	2012-12-19	2007-04-04		ENSG00000160294	ENSG00000160294			6946	protein-coding gene	gene with protein product	"germinal-centre associated nuclear protein"	603294	"minichromosome maintenance deficient (S. cerevisiae) 3-associated protein", "MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein"			9712829, 16914116, 21195085	Standard	XM_005261205		Approved	Map80, KIAA0572, GANP, SAC3	uc002zir.1	O60318	OTTHUMG00000090630	ENST00000397708.1:c.4049A>G	chr21.hg19:g.47674393T>C	ENSP00000380820:p.His1350Arg	91.0	0.0		100.0	4.0	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Missense_Mutation	SNP	ENST00000397708.1	hg19	CCDS13734.1	.	.	.	.	.	.	.	.	.	.	T	14.27	2.484361	0.44147	.	.	ENSG00000160294	ENST00000397708;ENST00000291688	T;T	0.51817	0.69;0.69	5.22	5.22	0.72569	.	0.148969	0.64402	D	0.000014	T	0.49541	0.1563	M	0.68317	2.08	0.35939	D	0.833051	P	0.49961	0.93	B	0.42319	0.383	T	0.66368	-0.5941	10	0.59425	D	0.04	-16.395	15.1243	0.72469	0.0:0.0:0.0:1.0	.	1350	O60318	MCM3A_HUMAN	R	1350	ENSP00000380820:H1350R;ENSP00000291688:H1350R	ENSP00000291688:H1350R	H	-	2	0	MCM3AP	46498821	1.000000	0.71417	0.970000	0.41538	0.216000	0.24613	3.476000	0.53143	1.974000	0.57490	0.533000	0.62120	CAC	.	.		0.597	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906		C	47674393	T	C	47674393	3	2	282	1	0	0	0	0	1	0	0	0	9397	1696	59	2	1933	2	MCM3AP	21	47674393	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2118344	47674393	455502	1325	41559										
MICAL3	57553	hgsc.bcm.edu	37	chr22	18364031	18364031	+	Intron	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggaggagacagggtgatcacTtttttggggcaggtccgaga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:18364031delT	ENST00000441493.2	-	16	2594				MICAL3_ENST00000207726.7_Intron|MICAL3_ENST00000383094.3_Intron|MICAL3_ENST00000414725.2_Intron|MICAL3_ENST00000585038.1_Frame_Shift_Del_p.K760fs|MICAL3_ENST00000400561.2_Intron|MICAL3_ENST00000444520.1_Intron|MICAL3_ENST00000429452.1_Frame_Shift_Del_p.K760fs	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3						actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		GGGTGATCACTTTTTTGGGGC	0.537																																					p.V761X		Atlas-INDEL	.											.	MICAL3	53	.	0			c.2281delG						.						158	155	156					22																	18364031		1568	3582	5150	SO:0001627	intron_variant	57553	exon17			.	AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156			24694	protein-coding gene	gene with protein product		608882				12110185	Standard	NM_015241		Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.2241+4612A>-	chr22.hg19:g.18364031delT		258.0	0.0		222.0	14.0	NM_001136004	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Frame_Shift_Del	DEL	ENST00000441493.2	hg19	CCDS46659.1																																																																																			.	.		0.537	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1			-	18364031	T	-	18364031	6	5	282	0	1	1	0	1	0	0	0	0	9580	1606	56	0		0	MICAL3	22	18364031	Intron	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10		18364031	32940535	1326	41560										
HIRA	7290	hgsc.bcm.edu	37	chr22	19346949	19346949	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcaggcggctcagcttcacgCcccccaccactgtcacttca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:19346949delC	ENST00000263208.5	-	18	2400	c.2144delG	c.(2143-2145)ggcfs	p.G715fs	HIRA_ENST00000541063.1_Frame_Shift_Del_p.G671fs|HIRA_ENST00000340170.4_Intron|HIRA_ENST00000546308.1_Frame_Shift_Del_p.G671fs	NM_003325.3	NP_003316.3	P54198	HIRA_HUMAN	histone cell cycle regulator	715	Interaction with CCNA1.|Interaction with PAX3. {ECO:0000250}.|Interaction with histone H2B.				anatomical structure morphogenesis (GO:0009653)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|gastrulation (GO:0007369)|muscle cell differentiation (GO:0042692)|osteoblast differentiation (GO:0001649)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(2)|prostate(1)|skin(1)	37	Colorectal(54;0.0993)					CAGCTTCACGCCCCCCACCAC	0.597																																					p.G715fs		Atlas-INDEL	.											.	HIRA	100	.	0			c.2145delC						.						146	121	129					22																	19346949		2203	4300	6503	SO:0001589	frameshift_variant	7290	exon18			.	X75296	CCDS13759.1	22q11.2	2013-05-03	2013-05-03		ENSG00000100084	ENSG00000100084		"WD repeat domain containing"	4916	protein-coding gene	gene with protein product	"DiGeorge critical region gene 1"	600237	"HIR (histone cell cycle regulation defective) homolog A (S. cerevisiae)", "HIR histone cell cycle regulation defective homolog A (S. cerevisiae)"	TUPLE1		8111380, 7633437, 9731536	Standard	NM_003325		Approved	DGCR1, TUP1	uc002zpf.1	P54198	OTTHUMG00000150134	ENST00000263208.5:c.2144delG	chr22.hg19:g.19346949delC	ENSP00000263208:p.Gly715fs	182.0	0.0		147.0	10.0	NM_003325	Q05BU9|Q8IXN2	Frame_Shift_Del	DEL	ENST00000263208.5	hg19	CCDS13759.1																																																																																			.	.		0.597	HIRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316488.2	NM_003325		-	19346949	C	-	19346949	7	5	282	1	0	1	0	1	0	0	0	0	7129	739	26	0	941	0	HIRA	22	19346949	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	982918	19346949	31957617	1327	41561										
ZNF280B	140883	hgsc.bcm.edu	37	chr22	22842771	22842771	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cgtgattcataaacttaacaTtttttagaactttcacgcag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:22842771delT	ENST00000406426.1	-	4	1695	c.953delA	c.(952-954)aatfs	p.N318fs	ZNF280B_ENST00000360412.2_Frame_Shift_Del_p.N318fs			Q86YH2	Z280B_HUMAN	zinc finger protein 280B	318					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(2)	22	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)		AAACTTAACATTTTTTAGAAC	0.463																																					p.N318fs		Atlas-INDEL	.											.	ZNF280B	67	.	0			c.954delT						.						139	130	133					22																	22842771		2203	4300	6503	SO:0001589	frameshift_variant	140883	exon4			.	AK097608	CCDS13799.1	22q11.2	2007-09-20	2007-09-20	2007-09-20	ENSG00000198477	ENSG00000275004			23022	protein-coding gene	gene with protein product			"zinc finger protein 279", "suppressor of hairy wing homolog 2 (Drosophila)"	ZNF279, SUHW2		9074928	Standard	NM_080764		Approved	5'OY11.1, ZNF632	uc002zwc.1	Q86YH2	OTTHUMG00000151066	ENST00000406426.1:c.953delA	chr22.hg19:g.22842771delT	ENSP00000385998:p.Asn318fs	204.0	0.0		166.0	12.0	NM_080764		Frame_Shift_Del	DEL	ENST00000406426.1	hg19	CCDS13799.1																																																																																			.	.		0.463	ZNF280B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321170.2	NM_080764		-	22842771	T	-	22842771	7	5	282	1	0	1	0	1	0	0	0	0	17830	1493	52	0	682	0	ZNF280B	22	22842771	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3495822	22842771	28461795	1328	41562										
PIWIL3	440822	hgsc.bcm.edu	37	chr22	25153878	25153878	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gttctagaccaacatacctgTttttgagtctttaacatgct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:25153878delT	ENST00000332271.5	-	4	768	c.352delA	c.(352-354)acafs	p.T118fs	PIWIL3_ENST00000532537.2_5'UTR|PIWIL3_ENST00000533313.1_Frame_Shift_Del_p.T9fs|PIWIL3_ENST00000527701.1_Frame_Shift_Del_p.T9fs	NM_001008496.3|NM_001255975.1	NP_001008496.2|NP_001242904.1	Q7Z3Z3	PIWL3_HUMAN	piwi-like RNA-mediated gene silencing 3	118					cell differentiation (GO:0030154)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	RNA binding (GO:0003723)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(15)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50						AACATACCTGTTTTTGAGTCT	0.418																																					p.T118fs		Atlas-INDEL	.											.	PIWIL3	115	.	0			c.353delC						.			4,4260		1,2,2129	163	162	162			-0.9	0	22		161	11,8243		2,7,4118	no	frameshift	PIWIL3	NM_001008496.2		3,9,6247	A1A1,A1R,RR		0.1333,0.0938,0.1198			25153878	15,12503	2203	4300	6503	SO:0001589	frameshift_variant	440822	exon4			.	AB079368	CCDS33623.1	22q11.23	2013-02-15	2013-02-15		ENSG00000184571	ENSG00000184571		"Argonaute/PIWI family"	18443	protein-coding gene	gene with protein product		610314	"piwi-like 3 (Drosophila)"			12906857	Standard	NM_001008496		Approved	HIWI3	uc003abd.2	Q7Z3Z3	OTTHUMG00000150788	ENST00000332271.5:c.352delA	chr22.hg19:g.25153878delT	ENSP00000330031:p.Thr118fs	176.0	0.0		137.0	12.0	NM_001008496		Frame_Shift_Del	DEL	ENST00000332271.5	hg19	CCDS33623.1																																																																																			.	.		0.418	PIWIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320084.2	NM_001008496		-	25153878	T	-	25153878	7	5	282	1	0	1	0	1	0	0	0	0	11968	1725	60	0	2368	0	PIWIL3	22	25153878	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2311107	25153878	26150688	1329	41563										
CRYBB3	1417	hgsc.bcm.edu	37	chr22	25603032	25603032	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aggtgggttggctatgagttCcccggctaccgtgggcgcca							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:25603032delC	ENST00000215855.2	+	6	569	c.489delC	c.(487-489)ttcfs	p.F163fs	CRYBB3_ENST00000404334.1_3'UTR	NM_004076.3	NP_004067.1	P26998	CRBB3_HUMAN	crystallin, beta B3	163	Beta/gamma crystallin 'Greek key' 4. {ECO:0000255|PROSITE-ProRule:PRU00028}.				visual perception (GO:0007601)		structural constituent of eye lens (GO:0005212)			large_intestine(2)|lung(2)|prostate(1)	5						GCTATGAGTTCCCCGGCTACC	0.642																																					p.L163fs		Atlas-INDEL	.											.	CRYBB3	13	.	0			c.488delT						.						69	60	63					22																	25603032		2203	4298	6501	SO:0001589	frameshift_variant	1417	exon6			.		CCDS13830.1	22q11.23	2008-06-10			ENSG00000100053	ENSG00000100053			2400	protein-coding gene	gene with protein product		123630		CRYB3		8999933	Standard	NM_004076		Approved		uc003abo.2	P26998	OTTHUMG00000150869	ENST00000215855.2:c.489delC	chr22.hg19:g.25603032delC	ENSP00000215855:p.Phe163fs	212.0	0.0		139.0	10.0	NM_004076	Q3B7S9|Q3T1B7|Q6ISK6|Q92965|Q9UH09	Frame_Shift_Del	DEL	ENST00000215855.2	hg19	CCDS13830.1																																																																																			.	.		0.642	CRYBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320352.1	NM_004076		-	25603032	C	-	25603032	7	5	282	1	0	1	0	1	0	0	0	0	3914	854	30	0	507	0	CRYBB3	22	25603032	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	449154	25603032	25701534	1330	41564										
MYO18B	84700	hgsc.bcm.edu	37	chr22	26176036	26176036	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccaacagtggagaagatccgAgccaccttcactgtcctccg	9	15	1	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:26176036A>G	ENST00000407587.2	+	9	2251	c.2082A>G	c.(2080-2082)cgA>cgG	p.R694R	MYO18B_ENST00000536101.1_Silent_p.R694R|MYO18B_ENST00000335473.7_Silent_p.R694R			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	694	Myosin motor.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						AGAAGATCCGAGCCACCTTCA	0.627																																					p.R694R		Atlas-SNP	.											.	MYO18B	322	.	0			c.A2082G						.						19	24	22					22																	26176036		2080	4194	6274	SO:0001819	synonymous_variant	84700	exon9			GATCCGAGCCACC	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.2082A>G	chr22.hg19:g.26176036A>G		88.0	0.0		60.0	4.0	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	hg19																																																																																				.	.		0.627	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		G	26176036	A	G	26176036	2	3	282	1	0	0	0	0	0	0	0	1	10075	291	11	2		2	MYO18B	22	26176036	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	573004	26176036	25128530	1331	41565										
DRG1	4733	hgsc.bcm.edu	37	chr22	31796695	31796695	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cttcgtcgagaactcattacTccaaagggtggtggtggtgg	14	8	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:31796695T>C	ENST00000331457.4	+	2	293	c.132T>C	c.(130-132)acT>acC	p.T44T	DRG1_ENST00000433341.1_3'UTR	NM_004147.3	NP_004138.1	Q9Y295	DRG1_HUMAN	developmentally regulated GTP binding protein 1	44					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|polysome (GO:0005844)	GTP binding (GO:0005525)|identical protein binding (GO:0042802)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|urinary_tract(1)	11						AACTCATTACTCCAAAGGGTG	0.428																																					p.T44T		Atlas-SNP	.											.	DRG1	28	.	0			c.T132C						.						83	77	79					22																	31796695		2203	4300	6503	SO:0001819	synonymous_variant	4733	exon2			CATTACTCCAAAG	AJ005940	CCDS13897.1	22q12.2	2010-02-26	2001-11-28		ENSG00000185721	ENSG00000185721			3029	protein-coding gene	gene with protein product		603952	"developmentally regulated GTP-binding protein 1"	NEDD3		7929244, 1449490	Standard	NM_004147		Approved		uc003aku.3	Q9Y295	OTTHUMG00000030792	ENST00000331457.4:c.132T>C	chr22.hg19:g.31796695T>C		113.0	0.0		87.0	4.0	NM_004147	B2RDS8|Q6FGP8|Q8WW69|Q9UGF2	Silent	SNP	ENST00000331457.4	hg19	CCDS13897.1																																																																																			.	.		0.428	DRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075680.5	NM_004147		C	31796695	T	C	31796695	2	2	282	1	0	0	0	0	0	0	0	1	4763	1538	54	2		2	DRG1	22	31796695	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	5620659	31796695	19507871	1332	41566										
FBXO7	25793	hgsc.bcm.edu	37	chr22	32871071	32871071	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cgacgctggggcatttgcgcTcgcacctgaggcagtccctg	14	14	0	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:32871071T>C	ENST00000266087.7	+	1	409	c.82T>C	c.(82-84)Tcg>Ccg	p.S28P	FBXO7_ENST00000397426.1_5'Flank|FBXO7_ENST00000382058.3_5'Flank	NM_012179.3	NP_036311.3	Q9Y3I1	FBX7_HUMAN	F-box protein 7	28	Ubiquitin-like.				cell death (GO:0008219)|mitochondrion degradation (GO:0000422)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of lymphocyte differentiation (GO:0045620)|protein targeting to mitochondrion (GO:0006626)|protein ubiquitination (GO:0016567)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GCATTTGCGCTCGCACCTGAG	0.736																																					p.S28P		Atlas-SNP	.											.	FBXO7	131	.	0			c.T82C						.						7	9	8					22																	32871071		1905	3746	5651	SO:0001583	missense	25793	exon1			TTGCGCTCGCACC	AF129537	CCDS13907.1, CCDS58806.1	22q12.3	2013-09-19	2004-06-15		ENSG00000100225	ENSG00000100225		"F-boxes /  "other"", "Parkinson disease"	13586	protein-coding gene	gene with protein product		605648	"F-box only protein 7"			10531035, 10531037, 19038853	Standard	NM_001257990		Approved	FBX7, Fbx, PARK15	uc003amq.3	Q9Y3I1	OTTHUMG00000030674	ENST00000266087.7:c.82T>C	chr22.hg19:g.32871071T>C	ENSP00000266087:p.Ser28Pro	178.0	0.0		97.0	4.0	NM_012179	B4DNB3|B4DWX5|Q5TGC4|Q5TI86|Q96HM6|Q9UF21|Q9UKT2	Missense_Mutation	SNP	ENST00000266087.7	hg19	CCDS13907.1	.	.	.	.	.	.	.	.	.	.	T	10.91	1.484048	0.26598	.	.	ENSG00000100225	ENST00000266087	T	0.39787	1.06	4.14	-0.609	0.11608	.	.	.	.	.	T	0.18676	0.0448	N	0.08118	0	0.80722	D	1	B	0.20550	0.046	B	0.17722	0.019	T	0.03993	-1.0986	9	0.44086	T	0.13	0.6075	4.7956	0.13270	0.1653:0.0:0.5365:0.2983	.	28	Q9Y3I1	FBX7_HUMAN	P	28	ENSP00000266087:S28P	ENSP00000266087:S28P	S	+	1	0	FBXO7	31201071	0.974000	0.33945	0.775000	0.31657	0.022000	0.10575	1.334000	0.33827	-0.097000	0.12307	-1.585000	0.00851	TCG	.	.		0.736	FBXO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129001.1			C	32871071	T	C	32871071	3	2	282	1	0	0	0	0	1	0	0	0	5768	1551	54	2	84	2	FBXO7	22	32871071	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1074376	32871071	18433495	1333	41567										
FBXO7	25793	hgsc.bcm.edu	37	chr22	32887083	32887083	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aatattctaggggaaaatgtAgccaacatatacaaagatct	7	6	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:32887083A>G	ENST00000266087.7	+	6	1209	c.882A>G	c.(880-882)gtA>gtG	p.V294V	FBXO7_ENST00000397426.1_Silent_p.V180V|FBXO7_ENST00000382058.3_Silent_p.V215V	NM_012179.3	NP_036311.3	Q9Y3I1	FBX7_HUMAN	F-box protein 7	294	Important for dimerization and interaction with PSMF1.				cell death (GO:0008219)|mitochondrion degradation (GO:0000422)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of lymphocyte differentiation (GO:0045620)|protein targeting to mitochondrion (GO:0006626)|protein ubiquitination (GO:0016567)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GGGAAAATGTAGCCAACATAT	0.363																																					p.V294V		Atlas-SNP	.											.	FBXO7	131	.	0			c.A882G						.						73	78	77					22																	32887083		2203	4300	6503	SO:0001819	synonymous_variant	25793	exon6			AAATGTAGCCAAC	AF129537	CCDS13907.1, CCDS58806.1	22q12.3	2013-09-19	2004-06-15		ENSG00000100225	ENSG00000100225		"F-boxes /  "other"", "Parkinson disease"	13586	protein-coding gene	gene with protein product		605648	"F-box only protein 7"			10531035, 10531037, 19038853	Standard	NM_001257990		Approved	FBX7, Fbx, PARK15	uc003amq.3	Q9Y3I1	OTTHUMG00000030674	ENST00000266087.7:c.882A>G	chr22.hg19:g.32887083A>G		104.0	0.0		79.0	5.0	NM_012179	B4DNB3|B4DWX5|Q5TGC4|Q5TI86|Q96HM6|Q9UF21|Q9UKT2	Silent	SNP	ENST00000266087.7	hg19	CCDS13907.1																																																																																			.	.		0.363	FBXO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129001.1			G	32887083	A	G	32887083	2	3	282	1	0	0	0	0	0	0	0	1	5768	407	15	2		2	FBXO7	22	32887083	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	16012	32887083	18417483	1334	41568										
RBM9	23543	hgsc.bcm.edu	37	chr22	36161472	36161472	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aagattataatttcttaccaTttgcatatggtgtgaccatc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:36161472delT	ENST00000438146.2	-	7	814	c.815delA	c.(814-816)aatfs	p.N272fs	RBFOX2_ENST00000449924.2_Frame_Shift_Del_p.N201fs|RBFOX2_ENST00000414461.2_Frame_Shift_Del_p.N201fs|RBFOX2_ENST00000416721.2_Frame_Shift_Del_p.N201fs|RBFOX2_ENST00000397303.2_Frame_Shift_Del_p.N182fs|RBFOX2_ENST00000359369.4_Frame_Shift_Del_p.N181fs|RBFOX2_ENST00000405409.2_Frame_Shift_Del_p.N202fs|RBFOX2_ENST00000262829.7_Frame_Shift_Del_p.N183fs	NM_001082578.1|NM_001082579.1	NP_001076047|NP_001076048.1	O43251	RFOX2_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 2	211					dendrite morphogenesis (GO:0048813)|intracellular estrogen receptor signaling pathway (GO:0030520)|mRNA processing (GO:0006397)|negative regulation of transcription, DNA-templated (GO:0045892)|neuromuscular process controlling balance (GO:0050885)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of cell proliferation (GO:0042127)|regulation of definitive erythrocyte differentiation (GO:0010724)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			endometrium(4)|large_intestine(7)|lung(7)	18						TTTCTTACCATTTGCATATGG	0.328																																					p.N272fs		Atlas-INDEL	.											.	RBFOX2	62	.	0			c.816delT						.						79	70	73					22																	36161472		2203	4298	6501	SO:0001589	frameshift_variant	23543	exon7			.	AL009266	CCDS13921.1, CCDS43013.1, CCDS46699.1, CCDS46700.1, CCDS46701.1	22q12-q13	2013-02-12	2010-09-10	2010-09-10	ENSG00000100320	ENSG00000100320		"RNA binding motif (RRM) containing"	9906	protein-coding gene	gene with protein product	"hexaribonucleotide binding protein 2"	612149	"RNA binding motif protein 9"	RBM9			Standard	NM_014309		Approved	HNRBP2, FOX-2, HRNBP2	uc003aon.4	O43251	OTTHUMG00000150585	ENST00000438146.2:c.815delA	chr22.hg19:g.36161472delT	ENSP00000413035:p.Asn272fs	243.0	0.0		183.0	11.0	NM_001082578	A4F5G8|A8K5Z5|B0QYY8|B0QYY9|Q0PRL5|Q0VH35|Q5TF71|Q6IC09|Q8TD00|Q8WYB1|Q96DZ6|Q96NL7|Q9UGW4|Q9UH33	Frame_Shift_Del	DEL	ENST00000438146.2	hg19	CCDS43013.1																																																																																			.	.		0.328	RBFOX2-005	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319299.3			-	36161472	T	-	36161472	7	5	282	1	0	1	0	1	0	0	0	0	13162	1493	52	0	582	0	RBM9	22	36161472	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3274389	36161472	15143094	1335	41569										
APOL2	23780	hgsc.bcm.edu	37	chr22	36623560	36623560	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctcagctgactctgactttgCcccctcaagcaagtgctttg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:36623560delC	ENST00000249066.6	-	6	1380	c.904delG	c.(904-906)gcafs	p.A302fs	APOL2_ENST00000358502.5_Frame_Shift_Del_p.A302fs|APOL2_ENST00000451256.2_Frame_Shift_Del_p.A414fs	NM_145637.1	NP_663612.1	Q9BQE5	APOL2_HUMAN	apolipoprotein L, 2	302					acute-phase response (GO:0006953)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|maternal process involved in female pregnancy (GO:0060135)|multicellular organismal development (GO:0007275)	endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|membrane (GO:0016020)	high-density lipoprotein particle binding (GO:0008035)|lipid binding (GO:0008289)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)|skin(1)|urinary_tract(2)	9						TCTGACTTTGCCCCCTCAAGC	0.557																																					p.A302fs		Atlas-INDEL	.											.	APOL2	20	.	0			c.905delC						.						98	104	102					22																	36623560		2203	4300	6503	SO:0001589	frameshift_variant	23780	exon5			.	AF324224	CCDS43014.1	22q12.3	2013-09-20			ENSG00000128335	ENSG00000128335		"Apolipoproteins"	619	protein-coding gene	gene with protein product	"apolipoprotein L-II"	607252				10591208, 11374903	Standard	NM_145637		Approved	APOL-II	uc003apa.3	Q9BQE5	OTTHUMG00000150634	ENST00000249066.6:c.904delG	chr22.hg19:g.36623560delC	ENSP00000249066:p.Ala302fs	266.0	0.0		166.0	10.0	NM_030882	B0QYK7|O95915|Q59GW9|Q5TH96|Q969T6|Q9BT28|Q9UGT1|Q9UH10	Frame_Shift_Del	DEL	ENST00000249066.6	hg19	CCDS43014.1																																																																																			.	.		0.557	APOL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000319279.1	NM_145637		-	36623560	C	-	36623560	7	5	282	1	0	1	0	1	0	0	0	0	806	739	26	0	113	0	APOL2	22	36623560	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	462088	36623560	14681006	1336	41570										
TMPRSS6	164656	hgsc.bcm.edu	37	chr22	37480793	37480793	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtgccaggagcagtgggtttGgggcgagtagtagctgggga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:37480793delG	ENST00000346753.3	-	9	1203	c.1087delC	c.(1087-1089)caafs	p.Q363fs	TMPRSS6_ENST00000406725.1_Frame_Shift_Del_p.Q354fs|RP5-1170K4.7_ENST00000414203.2_RNA|TMPRSS6_ENST00000381792.2_Frame_Shift_Del_p.Q354fs|TMPRSS6_ENST00000442782.2_Frame_Shift_Del_p.Q363fs|TMPRSS6_ENST00000406856.1_Frame_Shift_Del_p.Q354fs	NM_153609.2	NP_705837.1	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6	363	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				angiogenesis (GO:0001525)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|intracellular signal transduction (GO:0035556)|iron ion homeostasis (GO:0055072)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			breast(5)|central_nervous_system(4)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)	40						CAGTGGGTTTGGGGCGAGTAG	0.647																																					p.Q363fs		Atlas-INDEL	.											.	TMPRSS6	99	.	0			c.1088delA						.						83	70	75					22																	37480793		2199	4292	6491	SO:0001589	frameshift_variant	164656	exon9			.	AY055383	CCDS13941.1, CCDS74856.1, CCDS74857.1	22q13.1	2010-04-13			ENSG00000187045	ENSG00000187045		"Serine peptidases / Transmembrane"	16517	protein-coding gene	gene with protein product		609862					Standard	NM_001289000		Approved	FLJ30744	uc003aqs.1	Q8IU80	OTTHUMG00000150541	ENST00000346753.3:c.1087delC	chr22.hg19:g.37480793delG	ENSP00000334962:p.Gln363fs	144.0	0.0		147.0	10.0	NM_153609	B0QYB4|B0QYB7|B0QYB8|Q5TI06|Q6ICC2|Q6UXD8|Q8IUE2|Q8IXV8	Frame_Shift_Del	DEL	ENST00000346753.3	hg19	CCDS13941.1																																																																																			.	.		0.647	TMPRSS6-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318822.1	NM_153609		-	37480793	G	-	37480793	7	5	282	1	0	1	0	1	0	0	0	0	16266	1357	47	0	1388	0	TMPRSS6	22	37480793	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	857233	37480793	13823773	1337	41571										
SH3BP1	23616	hgsc.bcm.edu	37	chr22	38035826	38035826	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcagctgcaccgcatgcggcAgctggcccagacgggcagct	15	15	0	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:38035826A>G	ENST00000357436.4	+	1	345	c.32A>G	c.(31-33)cAg>cGg	p.Q11R	SH3BP1_ENST00000336738.5_Missense_Mutation_p.Q11R|SH3BP1_ENST00000599616.1_5'Flank|Z83844.1_ENST00000456099.1_RNA|SH3BP1_ENST00000442465.2_Missense_Mutation_p.Q11R	NM_018957.3	NP_061830.3	Q9Y3L3	3BP1_HUMAN	SH3-domain binding protein 1	11					signal transduction (GO:0007165)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	Melanoma(58;0.0574)					CGCATGCGGCAGCTGGCCCAG	0.711																																					p.Q11R		Atlas-SNP	.											.	SH3BP1	41	.	0			c.A32G						.						5	7	7					22																	38035826		1942	3910	5852	SO:0001583	missense	23616	exon1			TGCGGCAGCTGGC		CCDS13952.2	22q13.1	2011-07-04			ENSG00000100092	ENSG00000100092		"Rho GTPase activating proteins"	10824	protein-coding gene	gene with protein product						10591208, 12029088	Standard	NM_018957		Approved	ARHGAP43	uc003ati.3	Q9Y3L3	OTTHUMG00000030996	ENST00000357436.4:c.32A>G	chr22.hg19:g.38035826A>G	ENSP00000350018:p.Gln11Arg	203.0	0.0		114.0	5.0	NM_018957	Q5R3N0|Q6IBZ2|Q6ZVL9|Q96HQ5|Q9NSQ9	Missense_Mutation	SNP	ENST00000357436.4	hg19	CCDS13952.2	.	.	.	.	.	.	.	.	.	.	A	25.7	4.668614	0.88348	.	.	ENSG00000100092	ENST00000357436;ENST00000336738;ENST00000442465	T;T;T	0.70869	-0.52;-0.52;-0.52	3.95	3.95	0.45737	BAR (1);	0.000000	0.44097	D	0.000487	T	0.74673	0.3747	L	0.56199	1.76	0.38041	D	0.93545	D;D	0.63880	0.98;0.993	P;P	0.57620	0.759;0.824	T	0.76121	-0.3075	10	0.36615	T	0.2	.	11.4711	0.50268	1.0:0.0:0.0:0.0	.	11;11	F5GZA8;Q9Y3L3	.;3BP1_HUMAN	R	11	ENSP00000350018:Q11R;ENSP00000337213:Q11R;ENSP00000395126:Q11R	ENSP00000337213:Q11R	Q	+	2	0	SH3BP1	36365772	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.948000	0.70249	1.774000	0.52232	0.496000	0.49642	CAG	.	.		0.711	SH3BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075884.4	NM_018957		G	38035826	A	G	38035826	3	3	282	1	0	0	0	0	1	0	0	0	14259	188	7	2	34	2	SH3BP1	22	38035826	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	555033	38035826	13268740	1338	41572										
RPL3	6122	hgsc.bcm.edu	37	chr22	39711388	39711388	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gctcacctttgtagcctttgCccttggtcaccccgatgacg	9	15	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:39711388C>T	ENST00000216146.4	-	5	847	c.674G>A	c.(673-675)gGc>gAc	p.G225D	RPL3_ENST00000401609.1_Missense_Mutation_p.G173D|SNORD83A_ENST00000386747.1_RNA|SNORD83B_ENST00000386745.1_RNA|RPL3_ENST00000465618.1_5'UTR	NM_000967.3|NM_001033853.1	NP_000958.1|NP_001029025.1	P39023	RL3_HUMAN	ribosomal protein L3	225					cellular protein metabolic process (GO:0044267)|cellular response to interleukin-4 (GO:0071353)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			breast(1)|kidney(4)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	Melanoma(58;0.04)				Homoharringtonine(DB04865)	GTAGCCTTTGCCCTTGGTCAC	0.567																																					p.G225D		Atlas-SNP	.											.	RPL3	29	.	0			c.G674A						.						124	111	115					22																	39711388		2203	4300	6503	SO:0001583	missense	6122	exon5			CCTTTGCCCTTGG	AB007166	CCDS13988.1	22q13	2011-04-06			ENSG00000100316	ENSG00000100316		"L ribosomal proteins"	10332	protein-coding gene	gene with protein product		604163				2891103, 9582194	Standard	NM_000967		Approved	L3	uc003axi.3	P39023	OTTHUMG00000151079	ENST00000216146.4:c.674G>A	chr22.hg19:g.39711388C>T	ENSP00000346001:p.Gly225Asp	271.0	0.0		148.0	6.0	NM_000967	B2RDV9|Q15548|Q5I0G0	Missense_Mutation	SNP	ENST00000216146.4	hg19	CCDS13988.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.173817	0.78452	.	.	ENSG00000100316	ENST00000401609;ENST00000216146;ENST00000402527;ENST00000453303	D;D;D;D	0.81739	-1.53;-1.53;-1.53;-1.53	5.09	5.09	0.68999	Ribosomal protein L3, conserved site (1);Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	0.000000	0.85682	D	0.000000	D	0.92169	0.7517	M	0.93898	3.47	0.80722	D	1	B;P;B;P	0.39131	0.356;0.607;0.049;0.661	B;P;B;P	0.57548	0.432;0.71;0.226;0.823	D	0.93593	0.6923	10	0.87932	D	0	.	18.4787	0.90802	0.0:1.0:0.0:0.0	.	196;173;225;176	Q8TBW1;G5E9G0;P39023;B3KS36	.;.;RL3_HUMAN;.	D	173;225;173;252	ENSP00000386101:G173D;ENSP00000346001:G225D;ENSP00000385762:G173D;ENSP00000415198:G252D	ENSP00000346001:G225D	G	-	2	0	RPL3	38041334	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.726000	0.84824	2.384000	0.81235	0.462000	0.41574	GGC	.	.		0.567	RPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321196.1	NM_000967		T	39711388	C	T	39711388	3	4	282	1	0	0	0	0	1	0	0	0	13594	739	26	3	561	3	RPL3	22	39711388	Missense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1675562	39711388	11593178	1339	41573										
ATF4	468	hgsc.bcm.edu	37	chr22	39917489	39917489	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctgagcagcgaggtgttggtGggggacttgatgtccccctt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:39917489delG	ENST00000337304.2	+	1	921	c.39delG	c.(37-39)gtgfs	p.V13fs	ATF4_ENST00000396680.1_Frame_Shift_Del_p.V13fs|ATF4_ENST00000404241.2_Frame_Shift_Del_p.V13fs	NM_001675.2	NP_001666.2	P18848	ATF4_HUMAN	activating transcription factor 4	13					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular amino acid metabolic process (GO:0006520)|cellular protein metabolic process (GO:0044267)|circadian regulation of gene expression (GO:0032922)|endoplasmic reticulum unfolded protein response (GO:0030968)|gamma-aminobutyric acid signaling pathway (GO:0007214)|gluconeogenesis (GO:0006094)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of oxidative stress-induced neuron death (GO:1903204)|negative regulation of potassium ion transport (GO:0043267)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress (GO:1990440)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to endoplasmic reticulum stress (GO:0034976)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite membrane (GO:0032590)|Lewy body core (GO:1990037)|neuron projection (GO:0043005)|nuclear periphery (GO:0034399)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	11	Melanoma(58;0.04)				Pseudoephedrine(DB00852)	AGGTGTTGGTGGGGGACTTGA	0.522																																					p.V13fs		Atlas-INDEL	.											.	ATF4	27	.	0			c.38delT						.						70	69	69					22																	39917489		2203	4300	6503	SO:0001589	frameshift_variant	468	exon1			.	D90209	CCDS13996.1	22q13.1	2013-05-23	2013-05-23		ENSG00000128272	ENSG00000128272		"basic leucine zipper proteins"	786	protein-coding gene	gene with protein product	"tax-responsive enhancer element B67"	604064	"activating transcription factor 4 (tax-responsive enhancer element B67)"	TXREB		1847461, 1534408	Standard	NM_182810		Approved	TAXREB67, CREB-2	uc003axz.3	P18848	OTTHUMG00000151099	ENST00000337304.2:c.39delG	chr22.hg19:g.39917489delG	ENSP00000336790:p.Val13fs	215.0	0.0		181.0	11.0	NM_001675	Q9UH31	Frame_Shift_Del	DEL	ENST00000337304.2	hg19	CCDS13996.1																																																																																			.	.		0.522	ATF4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321305.1	NM_001675		-	39917489	G	-	39917489	7	5	282	1	0	1	0	1	0	0	0	0	1082	1335	47	0	41	0	ATF4	22	39917489	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	206101	39917489	11387077	1340	41574										
TNRC6B	23112	hgsc.bcm.edu	37	chr22	40657900	40657900	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agcccaattggcagctctccAtcgccaccagtcaatggtgg	10	14	2	0	rs376736908		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:40657900A>G	ENST00000454349.2	+	4	391	c.180A>G	c.(178-180)ccA>ccG	p.P60P	TNRC6B_ENST00000335727.9_Silent_p.P60P|TNRC6B_ENST00000402203.1_Silent_p.P96P|TNRC6B_ENST00000301923.9_Silent_p.P96P	NM_001162501.1	NP_001155973.1	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B	60	Interaction with argonaute proteins.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)	1						GCAGCTCTCCATCGCCACCAG	0.582																																					p.P96P		Atlas-SNP	.											.	TNRC6B	195	.	0			c.A288G						.	A	,,	2,3814		0,2,1906	22	26	25		288,180,180	5.9	1	22		25	0,8162		0,0,4081	no	coding-synonymous,coding-synonymous,coding-synonymous	TNRC6B	NM_001024843.1,NM_001162501.1,NM_015088.2	,,	0,2,5987	GG,GA,AA		0.0,0.0524,0.0167	,,	96/1030,60/1834,60/1724	40657900	2,11976	1908	4081	5989	SO:0001819	synonymous_variant	23112	exon7			CTCTCCATCGCCA	AB029016	CCDS46712.1, CCDS46713.1, CCDS54533.1	22q13	2006-08-22			ENSG00000100354	ENSG00000100354		"Trinucleotide (CAG) repeat containing"	29190	protein-coding gene	gene with protein product		610740					Standard	NM_015088		Approved	KIAA1093	uc011aor.2	Q9UPQ9	OTTHUMG00000151114	ENST00000454349.2:c.180A>G	chr22.hg19:g.40657900A>G		248.0	0.0		181.0	69.0	NM_001024843	B0QY73|B0QY78|B4DGC0|Q5TH52|Q8TBX2	Silent	SNP	ENST00000454349.2	hg19	CCDS54533.1																																																																																			.	.		0.582	TNRC6B-202	KNOWN	basic|CCDS	protein_coding	protein_coding				G	40657900	A	G	40657900	2	3	282	1	0	0	0	0	0	0	0	1	16356	204	8	2		2	TNRC6B	22	40657900	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	740411	40657900	10646666	1341	41575										
XRCC6	2547	hgsc.bcm.edu	37	chr22	42033647	42033647	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgatgcacctgaagaaacctGggggctttgacatatccttg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:42033647delG	ENST00000359308.4	+	5	1280	c.625delG	c.(625-627)gggfs	p.G210fs	XRCC6_ENST00000405878.1_Frame_Shift_Del_p.G210fs|XRCC6_ENST00000405506.1_Frame_Shift_Del_p.G160fs|XRCC6_ENST00000402580.3_Frame_Shift_Del_p.G169fs|XRCC6_ENST00000360079.3_Frame_Shift_Del_p.G210fs|XRCC6_ENST00000428575.2_Frame_Shift_Del_p.G77fs			P12956	XRCC6_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 6	210					brain development (GO:0007420)|cellular hyperosmotic salinity response (GO:0071475)|cellular response to X-ray (GO:0071481)|DNA duplex unwinding (GO:0032508)|DNA ligation (GO:0006266)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|telomere maintenance (GO:0000723)|transcription, DNA-templated (GO:0006351)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	cytosol (GO:0005829)|Ku70:Ku80 complex (GO:0043564)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nuclear telomere cap complex (GO:0000783)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	5'-deoxyribose-5-phosphate lyase activity (GO:0051575)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|telomeric DNA binding (GO:0042162)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|liver(2)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	31						GAAGAAACCTGGGGGCTTTGA	0.443								Non-homologous end-joining																													p.P208fs		Atlas-INDEL	.											.	XRCC6	64	.	0			c.624delT						.						32	28	29					22																	42033647		2203	4300	6503	SO:0001589	frameshift_variant	2547	exon6			.	J04607	CCDS14021.1, CCDS74870.1, CCDS74871.1	22q13.2	2011-09-12	2008-07-31	2005-05-06	ENSG00000196419	ENSG00000196419			4055	protein-coding gene	gene with protein product	"Ku autoantigen, 70kDa"	152690	"thyroid autoantigen 70kD (Ku antigen)", "thyroid autoantigen 70kDa (Ku antigen)"	G22P1		9200330, 9223317	Standard	NM_001469		Approved	D22S731, D22S671, KU70, ML8	uc003bao.1	P12956	OTTHUMG00000151190	ENST00000359308.4:c.625delG	chr22.hg19:g.42033647delG	ENSP00000352257:p.Gly210fs	301.0	0.0		249.0	15.0	NM_001469	B1AHC8|Q6FG89|Q9UCQ2|Q9UCQ3	Frame_Shift_Del	DEL	ENST00000359308.4	hg19	CCDS14021.1																																																																																			.	.		0.443	XRCC6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321688.1	NM_001469		-	42033647	G	-	42033647	7	5	282	1	0	1	0	1	0	0	0	0	17472	1348	47	0	643	0	XRCC6	22	42033647	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1375747	42033647	9270919	1342	41576										
RRP7A	27341	hgsc.bcm.edu	37	chr22	42911202	42911202	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gctctctgtggacaccagcaGggggcccttcagggccaagg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:42911202delG	ENST00000323013.6	-	4	430	c.415delC	c.(415-417)ctgfs	p.L140fs	SERHL_ENST00000359906.2_RNA	NM_015703.4	NP_056518.2	Q9Y3A4	RRP7A_HUMAN	ribosomal RNA processing 7 homolog A (S. cerevisiae)	140							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|liver(2)|lung(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	10						GACACCAGCAGGGGGCCCTTC	0.602																																					p.L139fs		Atlas-INDEL	.											.	RRP7A	25	.	0			c.416delT						.						4	8	7					22																	42911202		1658	3948	5606	SO:0001589	frameshift_variant	27341	exon4			.	BC035992	CCDS14036.1	22q13.2	2008-08-08			ENSG00000189306	ENSG00000189306			24286	protein-coding gene	gene with protein product						10810093, 12087473	Standard	NM_015703		Approved	CGI-96	uc003bcq.3	Q9Y3A4	OTTHUMG00000150891	ENST00000323013.6:c.415delC	chr22.hg19:g.42911202delG	ENSP00000321449:p.Leu140fs	225.0	0.0		168.0	12.0	NM_015703	A4FTX2|B2RBG4|Q0VAD0|Q5JZ94|Q6P4B5|Q8IVR9|Q8IVY0|Q8N5Q3|Q8NEY6|Q9Y3H5	Frame_Shift_Del	DEL	ENST00000323013.6	hg19	CCDS14036.1																																																																																			.	.		0.602	RRP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320451.1	NM_015703		-	42911202	G	-	42911202	7	5	282	1	0	1	0	1	0	0	0	0	13704	991	35	0	443	0	RRP7A	22	42911202	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	877555	42911202	8393364	1343	41577										
SERHL2	253190	hgsc.bcm.edu	37	chr22	42951001	42951001	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccacatcgcagccaaagcctGgggctccctgcagggccctc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:42951001delG	ENST00000327678.5	+	2	182	c.80delG	c.(79-81)tggfs	p.W27fs	SERHL2_ENST00000340239.4_Frame_Shift_Del_p.W27fs|SERHL2_ENST00000335879.5_Intron|Z93241.1_ENST00000580472.1_RNA|SERHL2_ENST00000407614.4_Intron|RRP7B_ENST00000357802.2_RNA	NM_014509.3	NP_055324.2	Q9NQF3	SERHL_HUMAN	serine hydrolase-like 2	27							hydrolase activity (GO:0016787)			breast(1)|endometrium(2)|lung(3)|skin(1)|stomach(1)	8						GCCAAAGCCTGGGGCTCCCTG	0.597																																					p.W27fs		Atlas-INDEL	.											.	SERHL2	23	.	0			c.79delT						.						5	5	5					22																	42951001		1769	3734	5503	SO:0001589	frameshift_variant	253190	exon2			.		CCDS14037.1, CCDS63498.1	22q13	2005-08-09			ENSG00000183569	ENSG00000183569			29446	protein-coding gene	gene with protein product							Standard	NM_014509		Approved		uc003bcr.3	Q9H4I8	OTTHUMG00000150892	ENST00000327678.5:c.80delG	chr22.hg19:g.42951001delG	ENSP00000331376:p.Trp27fs	225.0	0.0		165.0	10.0	NM_014509	Q5JZ95|Q9UH21	Frame_Shift_Del	DEL	ENST00000327678.5	hg19	CCDS14037.1																																																																																			.	.		0.597	SERHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320454.1	NM_014509		-	42951001	G	-	42951001	7	5	282	1	0	1	0	1	0	0	0	0	14093	1357	47	0	86	0	SERHL2	22	42951001	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	39799	42951001	8353565	1344	41578										
SAMM50	25813	hgsc.bcm.edu	37	chr22	44368791	44368791	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	taatcttcttggtcgtgcagAaaaggtgacctttcagtttt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:44368791delA	ENST00000350028.4	+	6	627	c.470delA	c.(469-471)gaafs	p.E157fs	SAMM50_ENST00000493161.1_3'UTR|SAMM50_ENST00000396202.3_Intron	NM_015380.4	NP_056195.3	Q9Y512	SAM50_HUMAN	SAMM50 sorting and assembly machinery component	157					cellular protein metabolic process (GO:0044267)|protein import into mitochondrial outer membrane (GO:0045040)|protein targeting to mitochondrion (GO:0006626)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrial sorting and assembly machinery complex (GO:0001401)|mitochondrion (GO:0005739)				endometrium(3)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				GGTCGTGCAGAAAAGGTGACC	0.433																																					p.E157fs		Atlas-INDEL	.											.	SAMM50	30	.	0			c.469delG						.						126	131	129					22																	44368791		2203	4300	6503	SO:0001589	frameshift_variant	25813	exon6			.	AK001087	CCDS14055.1	22q13.31	2013-08-21	2013-08-21	2005-11-20	ENSG00000100347	ENSG00000100347			24276	protein-coding gene	gene with protein product		612058	"sorting and assembly machinery component 50 homolog (S. cerevisiae)"			15644312	Standard	NM_015380		Approved	CGI-51, TRG-3, YNL026W, OMP85, TOB55	uc003bej.3	Q9Y512	OTTHUMG00000150557	ENST00000350028.4:c.470delA	chr22.hg19:g.44368791delA	ENSP00000345445:p.Glu157fs	208.0	0.0		142.0	11.0	NM_015380	Q53HC4|Q56VW7|Q969Y9|Q96I46|Q9NW85|Q9UQM9	Frame_Shift_Del	DEL	ENST00000350028.4	hg19	CCDS14055.1																																																																																			.	.		0.433	SAMM50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318898.2	NM_015380		-	44368791	A	-	44368791	7	5	282	1	0	1	0	1	0	0	0	0	13844	246	9	0	492	0	SAMM50	22	44368791	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1417790	44368791	6935775	1345	41579										
SMC1B	27127	hgsc.bcm.edu	37	chr22	45767392	45767392	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttctttaattcttcgttgtcGttccttgattccttcactca	4	11	4	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:45767392G>T	ENST00000357450.4	-	14	2271	c.2272C>A	c.(2272-2274)Cga>Aga	p.R758R	SMC1B_ENST00000404354.3_Silent_p.R758R	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	758			R -> Q (in dbSNP:rs9614653).		meiotic nuclear division (GO:0007126)|sister chromatid cohesion (GO:0007062)	chromosome, centromeric region (GO:0000775)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		CTTCGTTGTCGTTCCTTGATT	0.284																																					p.R758R		Atlas-SNP	.											SMC1B_ENST00000357450,rectum,carcinoma,0,2	SMC1B	215	.	0			c.C2272A						.						102	92	95					22																	45767392		1814	4070	5884	SO:0001819	synonymous_variant	27127	exon14			GTTGTCGTTCCTT	AJ504806	CCDS43027.1, CCDS74876.1	22q13	2006-07-06	2006-07-06	2006-07-06	ENSG00000077935	ENSG00000077935		"Structural maintenance of chromosomes proteins"	11112	protein-coding gene	gene with protein product		608685	"SMC1 (structural maintenance of chromosomes 1, yeast)-like 1", "SMC1 structural maintenance of chromosomes 1-like 2 (yeast)"	SMC1L2		10591208, 11564881	Standard	XM_005261566		Approved	bK268H5	uc003bgc.3	Q8NDV3	OTTHUMG00000151334	ENST00000357450.4:c.2272C>A	chr22.hg19:g.45767392G>T		272.0	0.0		126.0	0.0	NM_148674	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Silent	SNP	ENST00000357450.4	hg19	CCDS43027.1																																																																																			.	.		0.284	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674		T	45767392	G	T	45767392	2	4	282	1	0	0	0	0	0	0	0	1	14797	1153	40	1		1	SMC1B	22	45767392	Silent	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	1398601	45767392	5537174	1346	41580										
SAPS2	9701	hgsc.bcm.edu	37	chr22	50876270	50876270	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gccatcccccttgctcttgcAgtgccccgtttgacaggatc	9	16	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:50876270A>G	ENST00000216061.5	+	18	2151		c.e18-1		PPP6R2_ENST00000359139.3_Splice_Site|PPP6R2_ENST00000395744.3_Splice_Site|PPP6R2_ENST00000395741.3_Splice_Site			O75170	PP6R2_HUMAN	protein phosphatase 6, regulatory subunit 2							cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	22						TTGCTCTTGCAGTGCCCCGTT	0.632																																					.		Atlas-SNP	.											.	PPP6R2	71	.	0			c.1704-2A>G						.						62	44	50					22																	50876270		2161	4209	6370	SO:0001630	splice_region_variant	9701	exon16			TCTTGCAGTGCCC	AB014585	CCDS33681.1, CCDS56235.1, CCDS56236.1, CCDS74881.1	22q13.33	2012-04-17	2010-06-28	2010-06-28	ENSG00000100239	ENSG00000100239		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"	19253	protein-coding gene	gene with protein product		610877	"KIAA0685", "SAPS domain family, member 2"	KIAA0685, SAPS2		16769727	Standard	NM_014678		Approved	dJ579N16.1, SAP190	uc003blc.3	O75170	OTTHUMG00000150199	ENST00000216061.5:c.1782-1A>G	chr22.hg19:g.50876270A>G		208.0	0.0		69.0	4.0	NM_001242899	A6PVG3|B7Z7T3|Q5U5P3|Q7Z2L2|Q7Z5G5|Q7Z731|Q9UGB9	Splice_Site	SNP	ENST00000216061.5	hg19		.	.	.	.	.	.	.	.	.	.	A	18.73	3.686966	0.68157	.	.	ENSG00000100239	ENST00000359139;ENST00000395741;ENST00000395744;ENST00000216061	.	.	.	5.58	5.58	0.84498	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7234	0.69326	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PPP6R2	49223136	1.000000	0.71417	0.566000	0.28421	0.207000	0.24258	8.374000	0.90133	2.129000	0.65627	0.260000	0.18958	.	.	.		0.632	PPP6R2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316809.1	NM_014678	Intron	G	50876270	A	G	50876270	5	3	282	1	0	0	0	0	0	0	1	0	13852	202	7	2	1753	2	SAPS2	22	50876270	Splice_Site	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	5108878	50876270	428296	1347	41581										
SBF1	6305	hgsc.bcm.edu	37	chr22	50893474	50893474	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgcgctcatagtcagagtcgAgcaggaaggtccggaaacgg	15	9	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:50893474A>G	ENST00000390679.3	-	33	4758	c.4574T>C	c.(4573-4575)cTc>cCc	p.L1525P	SBF1_ENST00000348911.6_Missense_Mutation_p.L1526P|SBF1_ENST00000380817.3_Missense_Mutation_p.L1551P|SBF1_ENST00000476293.1_5'Flank			O95248	MTMR5_HUMAN	SET binding factor 1	1525	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				cell death (GO:0008219)|positive regulation of Rab GTPase activity (GO:0032851)|protein dephosphorylation (GO:0006470)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(8)|large_intestine(3)|lung(18)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	43		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)		GTCAGAGTCGAGCAGGAAGGT	0.612																																					p.L1551P		Atlas-SNP	.											.	SBF1	211	.	0			c.T4652C						.						45	51	49					22																	50893474		2091	4216	6307	SO:0001583	missense	6305	exon34			GAGTCGAGCAGGA	U93181	CCDS14091.1, CCDS14091.2	22q13.33	2013-01-10			ENSG00000100241	ENSG00000100241		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins", "DENN/MADD domain containing", "Pleckstrin homology (PH) domain containing"	10542	protein-coding gene	gene with protein product	"myotubularin related 5", "DENN/MADD domain containing 7A"	603560				9537414, 9736772	Standard	NM_002972		Approved	MTMR5, DENND7A	uc003blh.3	O95248	OTTHUMG00000150204	ENST00000390679.3:c.4574T>C	chr22.hg19:g.50893474A>G	ENSP00000375097:p.Leu1525Pro	191.0	0.0		79.0	4.0	NM_002972	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Missense_Mutation	SNP	ENST00000390679.3	hg19		.	.	.	.	.	.	.	.	.	.	A	21.2	4.109351	0.77096	.	.	ENSG00000100241	ENST00000380817;ENST00000348911;ENST00000337034;ENST00000390679	D;D;D	0.90732	-2.72;-2.72;-2.72	3.74	3.74	0.42951	Myotubularin phosphatase domain (1);	0.170909	0.37219	N	0.002200	D	0.93903	0.8049	M	0.66939	2.045	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.91635	0.998;0.997;0.999	D	0.94240	0.7484	10	0.72032	D	0.01	.	12.5669	0.56314	1.0:0.0:0.0:0.0	.	1525;1551;84	O95248;O95248-4;A6PVG7	MTMR5_HUMAN;.;.	P	1551;1526;1561;1525	ENSP00000370196:L1551P;ENSP00000252027:L1526P;ENSP00000375097:L1525P	ENSP00000336522:L1561P	L	-	2	0	SBF1	49240340	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	8.702000	0.91338	1.701000	0.51217	0.379000	0.24179	CTC	.	.		0.612	SBF1-201	KNOWN	basic	protein_coding	protein_coding				G	50893474	A	G	50893474	3	3	282	1	0	0	0	0	1	0	0	0	13873	304	11	2	1061	2	SBF1	22	50893474	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	17204	50893474	411092	1348	41582										
ARSE	415	hgsc.bcm.edu	37	chrX	2861192	2861192	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gatccgacgtaaaataaatgAgggtgctgttgctcaaaccc	10	9	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:2861192A>G	ENST00000381134.3	-	8	1106	c.1040T>C	c.(1039-1041)cTc>cCc	p.L347P	ARSE_ENST00000540563.1_Missense_Mutation_p.L302P|ARSE_ENST00000545496.1_Missense_Mutation_p.L372P	NM_000047.2	NP_000038.2	P51690	ARSE_HUMAN	arylsulfatase E (chondrodysplasia punctata 1)	347					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				AAAATAAATGAGGGTGCTGTT	0.448																																					p.L347P		Atlas-SNP	.											.	ARSE	43	.	0			c.T1040C						.						84	74	77					X																	2861192		2203	4300	6503	SO:0001583	missense	415	exon8			TAAATGAGGGTGC	X83573	CCDS14122.1, CCDS75948.1, CCDS75949.1	Xp22.33	2013-02-14			ENSG00000157399	ENSG00000157399		"Arylsulfatase family"	719	protein-coding gene	gene with protein product		300180		CDPX, CDPX1		7720070	Standard	NM_000047		Approved		uc004crc.4	P51690	OTTHUMG00000137358	ENST00000381134.3:c.1040T>C	chrX.hg19:g.2861192A>G	ENSP00000370526:p.Leu347Pro	107.0	0.0		80.0	4.0	NM_000047	Q53FT2|Q53FU8	Missense_Mutation	SNP	ENST00000381134.3	hg19	CCDS14122.1	.	.	.	.	.	.	.	.	.	.	A	12.74	2.028353	0.35797	.	.	ENSG00000157399	ENST00000540563;ENST00000545496;ENST00000381134	D;D;D	0.95342	-3.68;-3.68;-3.68	3.66	3.66	0.41972	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.070336	0.64402	D	0.000020	D	0.98327	0.9445	H	0.99197	4.465	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.98109	1.0419	10	0.87932	D	0	.	11.073	0.48014	1.0:0.0:0.0:0.0	.	302;372;347	F5H324;F5GYY5;P51690	.;.;ARSE_HUMAN	P	302;372;347	ENSP00000438198:L302P;ENSP00000441417:L372P;ENSP00000370526:L347P	ENSP00000370526:L347P	L	-	2	0	ARSE	2871192	0.921000	0.31238	0.024000	0.17045	0.007000	0.05969	7.154000	0.77437	1.301000	0.44836	0.486000	0.48141	CTC	.	.		0.448	ARSE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055643.1	NM_000047		G	2861192	A	G	2861192	3	3	282	1	0	0	0	0	1	0	0	0	990	304	11	2	745	2	ARSE	23	2861192	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10		2861192	152409368	1349	41583										
AMELX	265	hgsc.bcm.edu	37	chrX	11316394	11316394	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tggtaccagagcataaggccAccggtatgtagacattttgt	11	8	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:11316394A>G	ENST00000380714.3	+	4	209	c.141A>G	c.(139-141)ccA>ccG	p.P47P	ARHGAP6_ENST00000380736.1_Intron|ARHGAP6_ENST00000380718.1_Intron|ARHGAP6_ENST00000337414.4_Intron|ARHGAP6_ENST00000380732.3_Intron|AMELX_ENST00000380712.3_Silent_p.P61P|AMELX_ENST00000348912.4_Silent_p.P31P|ARHGAP6_ENST00000413512.3_Intron	NM_001142.2	NP_001133.1	Q99217	AMELX_HUMAN	amelogenin, X-linked	47					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|chondrocyte differentiation (GO:0002062)|enamel mineralization (GO:0070166)|epithelial to mesenchymal transition (GO:0001837)|ion homeostasis (GO:0050801)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of tooth mineralization (GO:0070172)|signal transduction (GO:0007165)|tooth mineralization (GO:0034505)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	growth factor activity (GO:0008083)|hydroxyapatite binding (GO:0046848)|identical protein binding (GO:0042802)|structural constituent of tooth enamel (GO:0030345)			endometrium(3)|kidney(2)|large_intestine(1)|lung(9)	15						GCATAAGGCCACCGGTATGTA	0.348																																					p.P61P		Atlas-SNP	.											.	AMELX	31	.	0			c.A183G						.						191	191	191					X																	11316394		2203	4300	6503	SO:0001819	synonymous_variant	265	exon5			AAGGCCACCGGTA		CCDS14144.1, CCDS14145.1, CCDS14146.1	Xp22.31-p22.1	2010-04-20	2010-04-20		ENSG00000125363	ENSG00000125363			461	protein-coding gene	gene with protein product	"amelogenesis imperfecta 1"	300391	"amelogenin (X chromosome, amelogenesis imperfecta 1)"	AMG, AIH1		1734713	Standard	NM_182680		Approved		uc004cus.3	Q99217	OTTHUMG00000021130	ENST00000380714.3:c.141A>G	chrX.hg19:g.11316394A>G		69.0	0.0		71.0	4.0	NM_182680	Q96NW6|Q9UCA7	Silent	SNP	ENST00000380714.3	hg19	CCDS14144.1																																																																																			.	.		0.348	AMELX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055746.1	NM_001142		G	11316394	A	G	11316394	2	3	282	1	0	0	0	0	0	0	0	1	569	146	6	2		2	AMELX	23	11316394	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	8455202	11316394	143954166	1350	41584										
FIGF	2277	hgsc.bcm.edu	37	chrX	15365316	15365316	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ctgggtgaaatagcttgtgcTtctggcagcaggtctccaga	13	9	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:15365316T>C	ENST00000297904.3	-	6	1337	c.908A>G	c.(907-909)aAg>aGg	p.K303R	FIGF_ENST00000488351.1_5'UTR	NM_004469.4	NP_004460.1	O43915	VEGFD_HUMAN	c-fos induced growth factor (vascular endothelial growth factor D)	303	4 X 16 AA repeats of C-X(10)-C-X-C- X(1,3)-C.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|induction of positive chemotaxis (GO:0050930)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of mast cell chemotaxis (GO:0060754)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	chemoattractant activity (GO:0042056)|platelet-derived growth factor receptor binding (GO:0005161)|vascular endothelial growth factor receptor binding (GO:0005172)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	17	Hepatocellular(33;0.183)					TAGCTTGTGCTTCTGGCAGCA	0.443																																					p.K303R		Atlas-SNP	.											.	FIGF	39	.	0			c.A908G						.						160	149	152					X																	15365316		2203	4300	6503	SO:0001583	missense	2277	exon6			TTGTGCTTCTGGC	AJ000185	CCDS14166.1	Xp22.31	2008-02-05			ENSG00000165197	ENSG00000165197			3708	protein-coding gene	gene with protein product		300091		VEGFD		9479493	Standard	NM_004469		Approved	VEGF-D	uc004cwt.2	O43915	OTTHUMG00000021175	ENST00000297904.3:c.908A>G	chrX.hg19:g.15365316T>C	ENSP00000297904:p.Lys303Arg	115.0	0.0		83.0	4.0	NM_004469	B2R7Z3	Missense_Mutation	SNP	ENST00000297904.3	hg19	CCDS14166.1	.	.	.	.	.	.	.	.	.	.	T	15.20	2.763705	0.49574	.	.	ENSG00000165197	ENST00000297904	.	.	.	5.16	5.16	0.70880	.	0.446510	0.24713	N	0.036220	T	0.45895	0.1365	M	0.64997	1.995	0.34381	D	0.693098	P	0.38597	0.639	B	0.27380	0.079	T	0.63413	-0.6643	9	0.44086	T	0.13	-20.9609	13.3791	0.60757	0.0:0.0:0.0:1.0	.	303	O43915	VEGFD_HUMAN	R	303	.	ENSP00000297904:K303R	K	-	2	0	FIGF	15275237	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	5.461000	0.66699	1.822000	0.53115	0.486000	0.48141	AAG	.	.		0.443	FIGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055859.1	NM_004469		C	15365316	T	C	15365316	3	2	282	1	0	0	0	0	1	0	0	0	5897	1609	56	2	164	2	FIGF	23	15365316	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	4048922	15365316	139905244	1351	41585										
REPS2	9185	hgsc.bcm.edu	37	chrX	17024379	17024379	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggtgcaaagcgggttggttaTtttggtccaacacagtttta							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:17024379delT	ENST00000357277.3	+	2	480	c.309delT	c.(307-309)tatfs	p.Y103fs	REPS2_ENST00000303843.7_Frame_Shift_Del_p.Y103fs|REPS2_ENST00000380064.4_5'UTR	NM_001080975.1|NM_004726.2	NP_001074444.1|NP_004717.2	Q8NFH8	REPS2_HUMAN	RALBP1 associated Eps domain containing 2	103	EH 1. {ECO:0000255|PROSITE- ProRule:PRU00077}.				epidermal growth factor receptor signaling pathway (GO:0007173)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|ovary(2)|skin(3)|urinary_tract(1)	17	Hepatocellular(33;0.183)					GGGTTGGTTATTTTGGTCCAA	0.423																																					p.Y103fs		Atlas-INDEL	.											.	REPS2	76	.	0			c.308delA						.						242	206	217					X																	17024379		1902	4115	6017	SO:0001589	frameshift_variant	9185	exon2			.	AF010233	CCDS14180.2, CCDS43919.1	Xp22.2	2013-01-10			ENSG00000169891	ENSG00000169891		"EF-hand domain containing"	9963	protein-coding gene	gene with protein product		300317				9422736, 9928989	Standard	NM_001080975		Approved	POB1	uc004cxv.1	Q8NFH8	OTTHUMG00000021199	ENST00000357277.3:c.309delT	chrX.hg19:g.17024379delT	ENSP00000349824:p.Tyr103fs	167.0	0.0		153.0	10.0	NM_001080975	A6PWZ6|O43428|Q5JNZ8|Q8NFI5	Frame_Shift_Del	DEL	ENST00000357277.3	hg19	CCDS14180.2																																																																																			.	.		0.423	REPS2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000316778.1	NM_004726		-	17024379	T	-	17024379	7	5	282	1	0	1	0	1	0	0	0	0	13244	1500	52	0	315	0	REPS2	23	17024379	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1659063	17024379	138246181	1352	41586										
MAP7D2	256714	hgsc.bcm.edu	37	chrX	20031688	20031688	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tggtcatttgaattcctaccTtcacttgtggagacacatca	7	10	3	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:20031688T>C	ENST00000379651.3	-	12	1700	c.1682A>G	c.(1681-1683)aAg>aGg	p.K561R	MAP7D2_ENST00000379643.5_Splice_Site_p.K602R|MAP7D2_ENST00000543767.1_Splice_Site_p.K446R|MAP7D2_ENST00000443379.3_Splice_Site_p.K516R|MAP7D2_ENST00000452324.3_Splice_Site_p.K509R	NM_152780.3	NP_689993.2	Q96T17	MA7D2_HUMAN	MAP7 domain containing 2	561					microtubule cytoskeleton organization (GO:0000226)	microtubule (GO:0005874)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(13)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	37						AATTCCTACCTTCACTTGTGG	0.328																																					p.K602R		Atlas-SNP	.											.	MAP7D2	165	.	0			c.A1805G						.						208	171	183					X																	20031688		2203	4299	6502	SO:0001630	splice_region_variant	256714	exon13			CCTACCTTCACTT	BC089400	CCDS14195.1, CCDS55384.1, CCDS55385.1, CCDS55386.1	Xp22.12	2008-02-05			ENSG00000184368	ENSG00000184368			25899	protein-coding gene	gene with protein product						12477932	Standard	NM_152780		Approved	FLJ14503	uc010nfo.2	Q96T17	OTTHUMG00000021228	ENST00000379651.3:c.1683+1A>G	chrX.hg19:g.20031688T>C		152.0	0.0		100.0	4.0	NM_001168465	B7Z2J8|B7Z3S7|B9EGC7|C9JMA4|C9JYW0|Q5EBN1|Q5JPS7|Q6PIC7|Q8N792	Missense_Mutation	SNP	ENST00000379651.3	hg19	CCDS14195.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.516929	0.85495	.	.	ENSG00000184368	ENST00000379651;ENST00000379643;ENST00000543767;ENST00000443379;ENST00000544957;ENST00000452324	T;T;T;T;T	0.26810	1.71;1.71;1.71;1.71;1.71	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.53270	0.1786	M	0.81497	2.545	0.49915	D	0.99983	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.997	D;D;D;D;D	0.87578	0.997;0.995;0.995;0.998;0.981	T	0.56571	-0.7957	10	0.49607	T	0.09	-24.7971	14.2709	0.66152	0.0:0.0:0.0:1.0	.	516;509;602;561;446	B7Z3S7;C9JYW0;Q96T17-2;Q96T17;F5GYC2	.;.;.;MA7D2_HUMAN;.	R	561;602;446;516;244;509	ENSP00000368972:K561R;ENSP00000368964:K602R;ENSP00000440691:K446R;ENSP00000388239:K516R;ENSP00000413301:K509R	ENSP00000368964:K602R	K	-	2	0	MAP7D2	19941609	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.067000	0.71193	1.968000	0.57251	0.483000	0.47432	AAG	.	.		0.328	MAP7D2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056001.1	NM_152780	Missense_Mutation	C	20031688	T	C	20031688	5	2	282	1	0	0	0	0	0	0	1	0	9277	1623	56	2	532	2	MAP7D2	23	20031688	Splice_Site	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3007309	20031688	135238872	1353	41587										
PCYT1B	9468	hgsc.bcm.edu	37	chrX	24605386	24605386	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tttatgtgcttgtaaacatcAtcagagccagcagaggaata	9	7	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:24605386A>G	ENST00000379144.2	-	5	667	c.537T>C	c.(535-537)gaT>gaC	p.D179D	PCYT1B_ENST00000379145.1_Silent_p.D161D|PCYT1B_ENST00000356768.4_Silent_p.D179D	NM_004845.4	NP_004836.2	Q9Y5K3	PCY1B_HUMAN	phosphate cytidylyltransferase 1, choline, beta	179					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|ovarian follicle development (GO:0001541)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)	choline-phosphate cytidylyltransferase activity (GO:0004105)			breast(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)	17					Choline(DB00122)	TGTAAACATCATCAGAGCCAG	0.463																																					p.D179D		Atlas-SNP	.											.	PCYT1B	88	.	0			c.T537C						.						165	110	129					X																	24605386		2203	4300	6503	SO:0001819	synonymous_variant	9468	exon5			AACATCATCAGAG	AF052510	CCDS14213.1, CCDS55391.1, CCDS55392.1	Xp22	2008-02-05	2005-09-05		ENSG00000102230	ENSG00000102230	2.7.7.15		8755	protein-coding gene	gene with protein product		604926	"phosphate cytidylyltransferase 1, choline, beta isoform"			9593753	Standard	NM_004845		Approved	CCT-beta, CTB	uc004dbi.3	Q9Y5K3	OTTHUMG00000021270	ENST00000379144.2:c.537T>C	chrX.hg19:g.24605386A>G		69.0	0.0		59.0	4.0	NM_004845	A8IX00|B2RCX8|B4DK10|E9PD84|O60621|Q86XC9	Silent	SNP	ENST00000379144.2	hg19	CCDS14213.1																																																																																			.	.		0.463	PCYT1B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056103.1	NM_004845		G	24605386	A	G	24605386	2	3	282	1	0	0	0	0	0	0	0	1	11620	214	8	2		2	PCYT1B	23	24605386	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	4573698	24605386	130665174	1354	41588										
DMD	1756	hgsc.bcm.edu	37	chrX	31198546	31198546	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gccttttgcaactcgaccagAaaaaaagcagctttggcaga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:31198546delA	ENST00000357033.4	-	69	10233	c.10027delT	c.(10027-10029)tctfs	p.S3343fs	DMD_ENST00000474231.1_Frame_Shift_Del_p.S883fs|DMD_ENST00000378677.2_Frame_Shift_Del_p.S3339fs|DMD_ENST00000541735.1_Frame_Shift_Del_p.S883fs|DMD_ENST00000343523.2_Frame_Shift_Del_p.S883fs|DMD_ENST00000359836.1_Frame_Shift_Del_p.S883fs|DMD_ENST00000378680.2_Frame_Shift_Del_p.S275fs|DMD_ENST00000378707.3_Frame_Shift_Del_p.S883fs|DMD_ENST00000361471.4_Frame_Shift_Del_p.S275fs|DMD_ENST00000378702.4_Frame_Shift_Del_p.S275fs|DMD_ENST00000378723.3_Frame_Shift_Del_p.S275fs	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	3343	Interaction with SYNM. {ECO:0000250}.				cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				ACTCGACCAGAAAAAAAGCAG	0.408																																					p.S3343fs		Atlas-INDEL	.											.	DMD	2127	.	0			c.10028delC						.						121	104	110					X																	31198546		2202	4300	6502	SO:0001589	frameshift_variant	1756	exon69			.	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.10027delT	chrX.hg19:g.31198546delA	ENSP00000354923:p.Ser3343fs	261.0	0.0		221.0	14.0	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Frame_Shift_Del	DEL	ENST00000357033.4	hg19	CCDS14233.1																																																																																			.	.		0.408	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		-	31198546	A	-	31198546	7	5	282	1	0	1	0	1	0	0	0	0	4582	246	9	0	1164	0	DMD	23	31198546	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	6593160	31198546	124072014	1355	41589										
FAM47B	170062	hgsc.bcm.edu	37	chrX	34961258	34961258	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgctcaagaaagcggccctaTtttccgagctctcgccagta							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:34961258delT	ENST00000329357.5	+	1	346	c.310delT	c.(310-312)tttfs	p.F104fs		NM_152631.2	NP_689844.2	Q8NA70	FA47B_HUMAN	family with sequence similarity 47, member B	104										breast(3)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	71						AGCGGCCCTATTTTCCGAGCT	0.532																																					p.L103fs		Atlas-INDEL	.											.	FAM47B	209	.	0			c.309delA						.						89	82	84					X																	34961258		2202	4300	6502	SO:0001589	frameshift_variant	170062	exon1			.	BC035026	CCDS14236.1	Xp21.1	2004-08-09			ENSG00000189132	ENSG00000189132			26659	protein-coding gene	gene with protein product						14702039	Standard	NM_152631		Approved	FLJ35782	uc004ddi.2	Q8NA70	OTTHUMG00000021345	ENST00000329357.5:c.310delT	chrX.hg19:g.34961258delT	ENSP00000328307:p.Phe104fs	183.0	0.0		165.0	12.0	NM_152631	Q5JQN5|Q6PIG3	Frame_Shift_Del	DEL	ENST00000329357.5	hg19	CCDS14236.1																																																																																			.	.		0.532	FAM47B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056211.1	NM_152631		-	34961258	T	-	34961258	7	5	282	1	0	1	0	1	0	0	0	0	5578	1493	52	0	312	0	FAM47B	23	34961258	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3762712	34961258	120309302	1356	41590										
USP9X	8239	hgsc.bcm.edu	37	chrX	41043827	41043827	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtgcctacctcaatgctcttAaaatagccaagcttttgcta							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:41043827delA	ENST00000324545.8	+	23	4090	c.3457delA	c.(3457-3459)aaafs	p.K1153fs	USP9X_ENST00000378308.2_Frame_Shift_Del_p.K1153fs	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	1153					axon extension (GO:0048675)|BMP signaling pathway (GO:0030509)|cerebellar cortex structural organization (GO:0021698)|chromosome segregation (GO:0007059)|female gamete generation (GO:0007292)|gene expression (GO:0010467)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|protein deubiquitination (GO:0016579)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)	co-SMAD binding (GO:0070410)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						CAATGCTCTTAAAATAGCCAA	0.473																																					p.L1152fs	Ovarian(172;1807 2695 35459 49286)	Atlas-INDEL	.											.	USP9X	385	.	0			c.3456delT						.						94	86	89					X																	41043827		2172	4280	6452	SO:0001589	frameshift_variant	8239	exon23			.	X98296	CCDS43930.1, CCDS55403.1	Xp11.4	2010-08-03	2006-02-14		ENSG00000124486	ENSG00000124486		"Ubiquitin-specific peptidases"	12632	protein-coding gene	gene with protein product		300072	"ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila)", "ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila)", "ubiquitin specific peptidase 9, X-linked (fat facets-like, Drosophila)"			8922996	Standard	NM_001039590		Approved	DFFRX, FAF	uc004dfb.3	Q93008	OTTHUMG00000021367	ENST00000324545.8:c.3457delA	chrX.hg19:g.41043827delA	ENSP00000316357:p.Lys1153fs	160.0	0.0		143.0	10.0	NM_001039591	O75550|Q8WWT3|Q8WX12	Frame_Shift_Del	DEL	ENST00000324545.8	hg19	CCDS43930.1																																																																																			.	.		0.473	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652		-	41043827	A	-	41043827	7	5	282	1	0	1	0	1	0	0	0	0	17105	363	13	0	3543	0	USP9X	23	41043827	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	6082569	41043827	114226733	1357	41591										
CASK	8573	hgsc.bcm.edu	37	chrX	41495868	41495868	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cattgaatttcctcagctgcTctactgtttctggaagatga	8	9	3	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:41495868T>C	ENST00000378163.1	-	9	1352	c.878A>G	c.(877-879)gAg>gGg	p.E293G	CASK_ENST00000378166.4_Missense_Mutation_p.E293G|CASK_ENST00000442742.2_Missense_Mutation_p.E293G|CASK_ENST00000378158.1_Missense_Mutation_p.E293G|CASK_ENST00000421587.2_Missense_Mutation_p.E293G|RN7SL406P_ENST00000582021.1_RNA|CASK_ENST00000318588.9_Missense_Mutation_p.E293G|CASK_ENST00000378154.1_Missense_Mutation_p.E293G|CASK_ENST00000361962.4_Missense_Mutation_p.E293G			O14936	CSKP_HUMAN	calcium/calmodulin-dependent serine protein kinase (MAGUK family)	293					calcium ion import (GO:0070509)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of wound healing (GO:0061045)|nucleotide phosphorylation (GO:0046939)|positive regulation of calcium ion import (GO:0090280)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	actin cytoskeleton (GO:0015629)|basement membrane (GO:0005604)|basolateral plasma membrane (GO:0016323)|cell-cell junction (GO:0005911)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nuclear lamina (GO:0005652)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	ATP binding (GO:0005524)|guanylate kinase activity (GO:0004385)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(5)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|ovary(3)|prostate(1)|stomach(1)	32						CCTCAGCTGCTCTACTGTTTC	0.338																																					p.E293G	NSCLC(42;104 1086 3090 27189 35040)	Atlas-SNP	.											.	CASK	93	.	0			c.A878G						.						192	163	173					X																	41495868		2203	4300	6503	SO:0001583	missense	8573	exon9			AGCTGCTCTACTG	AF035582	CCDS14257.1, CCDS48094.1, CCDS48095.1	Xp11.4	2010-02-09			ENSG00000147044	ENSG00000147044			1497	protein-coding gene	gene with protein product		300172	"trinucleotide repeat containing 8"	TNRC8		9722958	Standard	NM_003688		Approved	LIN2, CAGH39, FGS4	uc004dfl.4	O14936	OTTHUMG00000021378	ENST00000378163.1:c.878A>G	chrX.hg19:g.41495868T>C	ENSP00000367405:p.Glu293Gly	136.0	0.0		116.0	5.0	NM_001126054	A6NES1|B7ZKY0|O43215|Q17RI4|Q59HA0|Q5VT16|Q5VT17|Q5VT18|Q5VT19|Q66T42|Q9BYH6|Q9NYB2|Q9NYB3	Missense_Mutation	SNP	ENST00000378163.1	hg19		.	.	.	.	.	.	.	.	.	.	T	27.1	4.798453	0.90538	.	.	ENSG00000147044	ENST00000421587;ENST00000318588;ENST00000361962;ENST00000378163;ENST00000378158;ENST00000378166;ENST00000442742;ENST00000378154	T;T;T;T;T;T;T;T	0.70631	-0.48;-0.48;-0.48;-0.48;-0.48;-0.48;-0.47;-0.5	5.78	5.78	0.91487	Protein kinase-like domain (1);	0.000000	0.64402	D	0.000015	T	0.82029	0.4948	M	0.64997	1.995	0.80722	D	1	D;D;D;D	0.89917	1.0;0.964;0.993;0.993	D;P;P;P	0.81914	0.995;0.902;0.791;0.812	D	0.83803	0.0237	10	0.72032	D	0.01	.	14.9334	0.70935	0.0:0.0:0.0:1.0	.	293;293;293;293	O14936-3;O14936-4;O14936-2;O14936	.;.;.;CSKP_HUMAN	G	293	ENSP00000400526:E293G;ENSP00000322727:E293G;ENSP00000354641:E293G;ENSP00000367405:E293G;ENSP00000367400:E293G;ENSP00000367408:E293G;ENSP00000398007:E293G;ENSP00000367396:E293G	ENSP00000322727:E293G	E	-	2	0	CASK	41380812	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.294000	0.78760	2.056000	0.61249	0.441000	0.28932	GAG	.	.		0.338	CASK-007	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000056285.1	NM_003688		C	41495868	T	C	41495868	3	2	282	1	0	0	0	0	1	0	0	0	2667	1551	54	2	1978	2	CASK	23	41495868	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	452041	41495868	113774692	1358	41592										
MAOB	4129	hgsc.bcm.edu	37	chrX	43637948	43637948	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cctccagagcttctagggaaCccagaaccttggcatagagt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:43637948delC	ENST00000378069.4	-	11	1265	c.1118delG	c.(1117-1119)ggtfs	p.G373fs	MAOB_ENST00000538942.1_Frame_Shift_Del_p.G357fs|MAOB_ENST00000536181.1_Frame_Shift_Del_p.G357fs	NM_000898.4	NP_000889.3	P27338	AOFB_HUMAN	monoamine oxidase B	373					negative regulation of serotonin secretion (GO:0014063)|positive regulation of dopamine metabolic process (GO:0045964)|response to aluminum ion (GO:0010044)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|primary amine oxidase activity (GO:0008131)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(2)|skin(5)	21					Amantadine(DB00915)|Amphetamine(DB00182)|Dopamine(DB00988)|Ephedra(DB01363)|Flavin adenine dinucleotide(DB03147)|Furazolidone(DB00614)|Isocarboxazid(DB01247)|Linezolid(DB00601)|Methamphetamine(DB01577)|Moclobemide(DB01171)|Nandrolone decanoate(DB08804)|Nicotine(DB00184)|Pargyline(DB01626)|Phenelzine(DB00780)|Phentermine(DB00191)|Procaine(DB00721)|Rasagiline(DB01367)|Selegiline(DB01037)|Sertraline(DB01104)|Tranylcypromine(DB00752)|Zonisamide(DB00909)	TTCTAGGGAACCCAGAACCTT	0.443																																					p.G373fs		Atlas-INDEL	.											.	MAOB	52	.	0			c.1119delT						.						71	58	63					X																	43637948		2203	4300	6503	SO:0001589	frameshift_variant	4129	exon11			.		CCDS14261.1	Xp11.4-p11.3	2008-02-05			ENSG00000069535	ENSG00000069535	1.4.3.4		6834	protein-coding gene	gene with protein product		309860					Standard	NM_000898		Approved		uc004dfz.4	P27338	OTTHUMG00000021388	ENST00000378069.4:c.1118delG	chrX.hg19:g.43637948delC	ENSP00000367309:p.Gly373fs	257.0	0.0		175.0	12.0	NM_000898	B2R6R3|B7Z5H3|D3DWC3|Q7Z6S2	Frame_Shift_Del	DEL	ENST00000378069.4	hg19	CCDS14261.1																																																																																			.	.		0.443	MAOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056303.1	NM_000898		-	43637948	C	-	43637948	7	5	282	1	0	1	0	1	0	0	0	0	9235	507	18	0	464	0	MAOB	23	43637948	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	2142080	43637948	111632612	1359	41593										
CXorf36	79742	hgsc.bcm.edu	37	chrX	45051113	45051113	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gatgcagaggcacagattctCctgtctgagatctcgttttg	11	9	3	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:45051113C>T	ENST00000398000.2	-	2	455	c.381G>A	c.(379-381)agG>agA	p.R127R	RP11-342D14.1_ENST00000438181.1_RNA|RP11-342D14.1_ENST00000450527.1_RNA|CXorf36_ENST00000477281.1_5'UTR|CXorf36_ENST00000377934.4_Silent_p.R127R	NM_176819.3	NP_789789.2	Q9H7Y0	DIA1R_HUMAN	chromosome X open reading frame 36	127						extracellular region (GO:0005576)				endometrium(1)|large_intestine(2)|lung(4)	7						CACAGATTCTCCTGTCTGAGA	0.493																																					p.R127R		Atlas-SNP	.											.	CXorf36	53	.	0			c.G381A						.						89	84	86					X																	45051113		2203	4300	6503	SO:0001819	synonymous_variant	79742	exon2			GATTCTCCTGTCT	AF289581	CCDS14266.1, CCDS48096.1	Xp11.3-p11.23	2012-08-03			ENSG00000147113	ENSG00000147113			25866	protein-coding gene	gene with protein product						11944989, 21283809	Standard	NM_176819		Approved	FLJ14103, DIA1R	uc004dgg.2	Q9H7Y0	OTTHUMG00000021403	ENST00000398000.2:c.381G>A	chrX.hg19:g.45051113C>T		121.0	0.0		84.0	4.0	NM_176819	A8MUU5|B2RPN7|Q6UWJ5	Silent	SNP	ENST00000398000.2	hg19	CCDS48096.1																																																																																			.	.		0.493	CXorf36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056333.2	NM_024689		T	45051113	C	T	45051113	2	4	282	1	0	0	0	0	0	0	0	1	4108	854	30	3		3	CXorf36	23	45051113	Silent	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1413165	45051113	110219447	1360	41594										
PHF16	9767	hgsc.bcm.edu	37	chrX	46884293	46884293	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	catcttctggcttcaggaacTcaatgaagaccttgcagaaa	8	10	4	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:46884293T>C	ENST00000218343.4	+	5	750	c.452T>C	c.(451-453)cTc>cCc	p.L151P	PHF16_ENST00000397189.1_Missense_Mutation_p.L151P	NM_014735.3	NP_055550.1														NS(2)|endometrium(8)|kidney(4)|large_intestine(5)|lung(12)|upper_aerodigestive_tract(2)	33						CTTCAGGAACTCAATGAAGAC	0.413																																					p.L151P		Atlas-SNP	.											.	PHF16	72	.	0			c.T452C						.						125	101	109					X																	46884293		2203	4300	6503	SO:0001583	missense	9767	exon5			AGGAACTCAATGA																												ENST00000218343.4:c.452T>C	chrX.hg19:g.46884293T>C	ENSP00000218343:p.Leu151Pro	92.0	0.0		67.0	4.0	NM_001077445		Missense_Mutation	SNP	ENST00000218343.4	hg19	CCDS14271.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.977923	0.74360	.	.	ENSG00000102221	ENST00000424392;ENST00000397189;ENST00000218343	T;T;T	0.49139	0.79;0.79;0.79	5.99	5.99	0.97316	Enhancer of polycomb-like, N-terminal (1);	0.341890	0.31156	N	0.008142	T	0.61689	0.2367	M	0.71581	2.175	0.80722	D	1	P	0.47762	0.9	P	0.56163	0.793	T	0.65697	-0.6105	10	0.72032	D	0.01	.	11.3736	0.49715	0.0:0.0:0.149:0.851	.	151	Q92613	JADE3_HUMAN	P	151	ENSP00000391009:L151P;ENSP00000380373:L151P;ENSP00000218343:L151P	ENSP00000218343:L151P	L	+	2	0	PHF16	46769237	1.000000	0.71417	0.995000	0.50966	0.988000	0.76386	3.809000	0.55606	2.014000	0.59158	0.486000	0.48141	CTC	.	.		0.413	PHF16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056376.1			C	46884293	T	C	46884293	3	2	282	1	0	0	0	0	1	0	0	0	11836	1551	54	2	466	2	PHF16	23	46884293	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1833180	46884293	108386267	1361	41595										
ZNF157	7712	hgsc.bcm.edu	37	chrX	47271956	47271956	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cacccagaggagataaaaacTttgaatgtcatgaatgtggg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:47271956delT	ENST00000377073.3	+	4	570	c.484delT	c.(484-486)tttfs	p.F162fs		NM_003446.3	NP_003437.2	P51786	ZN157_HUMAN	zinc finger protein 157	162					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	11						AGATAAAAACTTTGAATGTCA	0.393																																					p.N161fs		Atlas-INDEL	.											.	ZNF157	46	.	0			c.483delC						.						71	60	64					X																	47271956		2203	4300	6503	SO:0001589	frameshift_variant	7712	exon4			.	U28687	CCDS14278.1	Xp11.2	2013-01-08	2006-08-22		ENSG00000147117	ENSG00000147117		"Zinc fingers, C2H2-type", "-"	12942	protein-coding gene	gene with protein product		300024	"zinc finger protein 157 (HZF22)"			8586441	Standard	NM_003446		Approved	HZF22	uc004dhr.1	P51786	OTTHUMG00000021443	ENST00000377073.3:c.484delT	chrX.hg19:g.47271956delT	ENSP00000366273:p.Phe162fs	182.0	0.0		162.0	10.0	NM_003446	Q96LE9	Frame_Shift_Del	DEL	ENST00000377073.3	hg19	CCDS14278.1																																																																																			.	.		0.393	ZNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056415.1	NM_003446		-	47271956	T	-	47271956	7	5	282	1	0	1	0	1	0	0	0	0	17752	1609	56	0	498	0	ZNF157	23	47271956	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	387663	47271956	107998604	1362	41596										
ARAF	369	hgsc.bcm.edu	37	chrX	47426094	47426094	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cttccctgccccagccaatgCccccctacagcgcatccgct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:47426094delC	ENST00000377045.4	+	7	808	c.614delC	c.(613-615)gccfs	p.A205fs	ARAF_ENST00000290277.6_Intron	NM_001256196.1|NM_001654.4	NP_001243125.1|NP_001645.1	P10398	ARAF_HUMAN	A-Raf proto-oncogene, serine/threonine kinase	205					cellular protein modification process (GO:0006464)|negative regulation of apoptotic process (GO:0043066)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|regulation of TOR signaling (GO:0032006)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)	p.L207fs*85(1)		biliary_tract(1)|endometrium(4)|large_intestine(7)|liver(2)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	29					Adenosine triphosphate(DB00171)	CCAGCCAATGCCCCCCTACAG	0.632																																					p.A208fs		Atlas-INDEL	.											.	ARAF	67	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.622delG						.						49	39	43					X																	47426094		2203	4300	6503	SO:0001589	frameshift_variant	369	exon7			.	X04790	CCDS35232.1, CCDS59164.1, CCDS75970.1	Xp11.3-p11.23	2014-06-26	2014-06-26	2005-01-19	ENSG00000078061	ENSG00000078061			646	protein-coding gene	gene with protein product		311010	"v-raf murine sarcoma 3611 viral oncogene homolog 1"	ARAF1			Standard	NM_001654		Approved		uc004dic.2	P10398	OTTHUMG00000021446	ENST00000377045.4:c.614delC	chrX.hg19:g.47426094delC	ENSP00000366244:p.Ala205fs	383.0	0.0		263.0	17.0	NM_001256196	P07557|Q5H9B2|Q5H9B3	Frame_Shift_Del	DEL	ENST00000377045.4	hg19	CCDS35232.1																																																																																			.	.		0.632	ARAF-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056418.1			-	47426094	C	-	47426094	7	5	282	1	0	1	0	1	0	0	0	0	837	739	26	0	636	0	ARAF	23	47426094	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	154138	47426094	107844466	1363	41597										
SYN1	6853	hgsc.bcm.edu	37	chrX	47466556	47466556	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttacctgttctactttaatgTcaatttctccatggatcttt	4	9	4	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:47466556T>C	ENST00000295987.7	-	2	543	c.419A>G	c.(418-420)gAc>gGc	p.D140G	SYN1_ENST00000340666.4_Missense_Mutation_p.D140G	NM_006950.3	NP_008881.2	P17600	SYN1_HUMAN	synapsin I	140	C; actin-binding and synaptic-vesicle binding.				neurotransmitter secretion (GO:0007269)|regulation of neurotransmitter secretion (GO:0046928)|regulation of synaptic vesicle exocytosis (GO:2000300)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|protein kinase binding (GO:0019901)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(6)|lung(6)|ovary(1)	21						TACTTTAATGTCAATTTCTCC	0.413																																					p.D140G		Atlas-SNP	.											.	SYN1	84	.	0			c.A419G						.						228	189	202					X																	47466556		2203	4300	6503	SO:0001583	missense	6853	exon2			TTAATGTCAATTT		CCDS14280.1, CCDS35233.1	Xp11.2	2012-10-02			ENSG00000008056	ENSG00000008056			11494	protein-coding gene	gene with protein product		313440					Standard	NM_133499		Approved		uc004die.3	P17600	OTTHUMG00000021454	ENST00000295987.7:c.419A>G	chrX.hg19:g.47466556T>C	ENSP00000295987:p.Asp140Gly	106.0	0.0		99.0	5.0	NM_006950	B1AJQ1|O75825|Q5H9A9	Missense_Mutation	SNP	ENST00000295987.7	hg19	CCDS14280.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.298744	0.81025	.	.	ENSG00000008056	ENST00000295987;ENST00000340666	T;T	0.36340	1.71;1.26	5.96	5.96	0.96718	Pre-ATP-grasp fold (1);PreATP-grasp-like fold (1);Synapsin, pre-ATP-grasp domain (1);	0.000000	0.85682	D	0.000000	T	0.57902	0.2085	M	0.69248	2.105	0.80722	D	1	D;D	0.76494	0.984;0.999	P;D	0.79108	0.866;0.992	T	0.61662	-0.7017	10	0.87932	D	0	-19.8199	13.1508	0.59488	0.0:0.0:0.0:1.0	.	140;140	P17600;P17600-2	SYN1_HUMAN;.	G	140	ENSP00000295987:D140G;ENSP00000343206:D140G	ENSP00000295987:D140G	D	-	2	0	SYN1	47351500	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.319000	0.65835	2.014000	0.59158	0.481000	0.45027	GAC	.	.		0.413	SYN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056445.1	NM_006950		C	47466556	T	C	47466556	3	2	282	1	0	0	0	0	1	0	0	0	15455	1667	58	2	1746	2	SYN1	23	47466556	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	40462	47466556	107804004	1364	41598										
GATA1	2623	hgsc.bcm.edu	37	chrX	48652397	48652397	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcttcaggcctgacactgggCcccccaggtactgcccatct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:48652397delC	ENST00000376670.3	+	6	1179	c.1068delC	c.(1066-1068)ggcfs	p.G356fs	GATA1_ENST00000376665.3_Intron	NM_002049.3	NP_002040.1	P15976	GATA1_HUMAN	GATA binding protein 1 (globin transcription factor 1)	356					basophil differentiation (GO:0030221)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cellular response to thyroid hormone stimulus (GO:0097067)|dendritic cell differentiation (GO:0097028)|embryonic hemopoiesis (GO:0035162)|eosinophil differentiation (GO:0030222)|eosinophil fate commitment (GO:0035854)|erythrocyte development (GO:0048821)|erythrocyte differentiation (GO:0030218)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|megakaryocyte differentiation (GO:0030219)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of definitive erythrocyte differentiation (GO:0010724)|regulation of glycoprotein biosynthetic process (GO:0010559)|transcription from RNA polymerase II promoter (GO:0006366)|transcriptional activation by promoter-enhancer looping (GO:0071733)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	C2H2 zinc finger domain binding (GO:0070742)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|enhancer sequence-specific DNA binding (GO:0001158)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(259)|large_intestine(8)|lung(9)|prostate(1)	283						TGACACTGGGCCCCCCAGGTA	0.647			"Mis, F"		megakaryoblastic leukemia of Downs Syndrome																																p.G356fs	Pancreas(9;429 505 11287 29617)	Atlas-INDEL	.		Dom	yes		X	Xp11.23	2623	GATA binding protein 1 (globin transcription factor 1)		L	.	GATA1	342	.	0			c.1067delG						.						36	33	34					X																	48652397		2203	4299	6502	SO:0001589	frameshift_variant	2623	exon6			.	X17254	CCDS14305.1	Xp11.23	2014-09-17	2001-11-28		ENSG00000102145	ENSG00000102145		"GATA zinc finger domain containing"	4170	protein-coding gene	gene with protein product	"nuclear factor, erythroid 1"	305371	"GATA-binding protein 1 (globin transcription factor 1)"	GF1		1999341	Standard	NM_002049		Approved	ERYF1, NFE1, GATA-1, NF-E1	uc004dkq.4	P15976	OTTHUMG00000021504	ENST00000376670.3:c.1068delC	chrX.hg19:g.48652397delC	ENSP00000365858:p.Gly356fs	179.0	0.0		159.0	10.0	NM_002049	Q96GB8	Frame_Shift_Del	DEL	ENST00000376670.3	hg19	CCDS14305.1																																																																																			.	.		0.647	GATA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056517.1	NM_002049		-	48652397	C	-	48652397	7	5	282	1	0	1	0	1	0	0	0	0	6261	726	26	0	1086	0	GATA1	23	48652397	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1185841	48652397	106618163	1365	41599										
HDAC6	10013	hgsc.bcm.edu	37	chrX	48672876	48672876	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tttctccatccaccgctacgAgcagggtaggttctggcccc	10	15	2	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:48672876A>G	ENST00000334136.5	+	11	1014	c.836A>G	c.(835-837)gAg>gGg	p.E279G	HDAC6_ENST00000444343.2_Missense_Mutation_p.E293G|HDAC6_ENST00000413163.2_Missense_Mutation_p.E224G|HDAC6_ENST00000376619.2_Missense_Mutation_p.E279G			Q9UBN7	HDAC6_HUMAN	histone deacetylase 6	279	Histone deacetylase 1.				aggresome assembly (GO:0070842)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to misfolded protein (GO:0071218)|cellular response to topologically incorrect protein (GO:0035967)|histone deacetylation (GO:0016575)|Hsp90 deacetylation (GO:0070846)|intracellular protein transport (GO:0006886)|lysosome localization (GO:0032418)|macroautophagy (GO:0016236)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of oxidoreductase activity (GO:0051354)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of proteolysis (GO:0045861)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of chaperone-mediated protein complex assembly (GO:0090035)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of hydrogen peroxide-mediated programmed cell death (GO:1901300)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of signal transduction (GO:0009967)|protein complex disassembly (GO:0043241)|protein deacetylation (GO:0006476)|protein polyubiquitination (GO:0000209)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of establishment of protein localization (GO:0070201)|regulation of gene expression, epigenetic (GO:0040029)|regulation of microtubule-based movement (GO:0060632)|regulation of receptor activity (GO:0010469)|response to growth factor (GO:0070848)|response to misfolded protein (GO:0051788)|response to organic substance (GO:0010033)|response to toxic substance (GO:0009636)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	aggresome (GO:0016235)|axon (GO:0030424)|caveola (GO:0005901)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|dendrite (GO:0030425)|histone deacetylase complex (GO:0000118)|inclusion body (GO:0016234)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)	alpha-tubulin binding (GO:0043014)|beta-catenin binding (GO:0008013)|core promoter binding (GO:0001047)|dynein complex binding (GO:0070840)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|Hsp90 protein binding (GO:0051879)|microtubule binding (GO:0008017)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|polyubiquitin binding (GO:0031593)|tau protein binding (GO:0048156)|tubulin deacetylase activity (GO:0042903)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|kidney(5)|large_intestine(8)|lung(9)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	40					Vorinostat(DB02546)	CACCGCTACGAGCAGGGTAGG	0.537																																					p.E279G	Pancreas(112;205 1675 2305 8976 15959)	Atlas-SNP	.											.	HDAC6	111	.	0			c.A836G						.						115	104	107					X																	48672876		2203	4300	6503	SO:0001583	missense	10013	exon11			GCTACGAGCAGGG	AF132609	CCDS14306.1	Xp11.23	2014-06-12			ENSG00000094631	ENSG00000094631			14064	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 90"	300272				10220385, 10048485	Standard	NM_006044		Approved	KIAA0901, JM21, HD6, FLJ16239, PPP1R90	uc004dks.1	Q9UBN7	OTTHUMG00000034496	ENST00000334136.5:c.836A>G	chrX.hg19:g.48672876A>G	ENSP00000334061:p.Glu279Gly	64.0	0.0		55.0	4.0	NM_006044	O94975|Q6NT75|Q7L3E5|Q96CY0	Missense_Mutation	SNP	ENST00000334136.5	hg19	CCDS14306.1	.	.	.	.	.	.	.	.	.	.	A	17.65	3.441641	0.63067	.	.	ENSG00000094631	ENST00000444343;ENST00000334136;ENST00000376619;ENST00000436813;ENST00000413163	T;T;T;T	0.65364	-0.02;-0.01;-0.01;-0.15	5.05	5.05	0.67936	Histone deacetylase domain (2);	0.136762	0.46442	D	0.000293	T	0.75708	0.3886	M	0.66297	2.02	0.58432	D	0.999998	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.81914	0.99;0.995;0.99	T	0.78355	-0.2236	10	0.87932	D	0	-18.4327	11.7749	0.51981	1.0:0.0:0.0:0.0	.	269;224;279	B4DZN1;E7EUZ1;Q9UBN7	.;.;HDAC6_HUMAN	G	293;279;279;279;224	ENSP00000398566:E293G;ENSP00000334061:E279G;ENSP00000365804:E279G;ENSP00000398801:E224G	ENSP00000334061:E279G	E	+	2	0	HDAC6	48557820	1.000000	0.71417	0.978000	0.43139	0.282000	0.26991	5.552000	0.67281	1.682000	0.51000	0.430000	0.28490	GAG	.	.		0.537	HDAC6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083394.2	NM_006044		G	48672876	A	G	48672876	3	3	282	1	0	0	0	0	1	0	0	0	7020	304	11	2	874	2	HDAC6	23	48672876	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	20479	48672876	106597684	1366	41600										
HDAC6	10013	hgsc.bcm.edu	37	chrX	48675759	48675759	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aatggtgctgctgtggtgcgTcccccaggacaccacgcaga	13	13	0	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:48675759T>C	ENST00000334136.5	+	20	1996	c.1818T>C	c.(1816-1818)cgT>cgC	p.R606R	HDAC6_ENST00000444343.2_Silent_p.R620R|HDAC6_ENST00000376619.2_Silent_p.R606R			Q9UBN7	HDAC6_HUMAN	histone deacetylase 6	606	Histone deacetylase 2.				aggresome assembly (GO:0070842)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to misfolded protein (GO:0071218)|cellular response to topologically incorrect protein (GO:0035967)|histone deacetylation (GO:0016575)|Hsp90 deacetylation (GO:0070846)|intracellular protein transport (GO:0006886)|lysosome localization (GO:0032418)|macroautophagy (GO:0016236)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of oxidoreductase activity (GO:0051354)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of proteolysis (GO:0045861)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of chaperone-mediated protein complex assembly (GO:0090035)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of hydrogen peroxide-mediated programmed cell death (GO:1901300)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of signal transduction (GO:0009967)|protein complex disassembly (GO:0043241)|protein deacetylation (GO:0006476)|protein polyubiquitination (GO:0000209)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of establishment of protein localization (GO:0070201)|regulation of gene expression, epigenetic (GO:0040029)|regulation of microtubule-based movement (GO:0060632)|regulation of receptor activity (GO:0010469)|response to growth factor (GO:0070848)|response to misfolded protein (GO:0051788)|response to organic substance (GO:0010033)|response to toxic substance (GO:0009636)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	aggresome (GO:0016235)|axon (GO:0030424)|caveola (GO:0005901)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|dendrite (GO:0030425)|histone deacetylase complex (GO:0000118)|inclusion body (GO:0016234)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)	alpha-tubulin binding (GO:0043014)|beta-catenin binding (GO:0008013)|core promoter binding (GO:0001047)|dynein complex binding (GO:0070840)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|Hsp90 protein binding (GO:0051879)|microtubule binding (GO:0008017)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|polyubiquitin binding (GO:0031593)|tau protein binding (GO:0048156)|tubulin deacetylase activity (GO:0042903)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|kidney(5)|large_intestine(8)|lung(9)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	40					Vorinostat(DB02546)	CTGTGGTGCGTCCCCCAGGAC	0.527																																					p.R606R	Pancreas(112;205 1675 2305 8976 15959)	Atlas-SNP	.											.	HDAC6	111	.	0			c.T1818C						.						81	61	67					X																	48675759		2203	4300	6503	SO:0001819	synonymous_variant	10013	exon20			GGTGCGTCCCCCA	AF132609	CCDS14306.1	Xp11.23	2014-06-12			ENSG00000094631	ENSG00000094631			14064	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 90"	300272				10220385, 10048485	Standard	NM_006044		Approved	KIAA0901, JM21, HD6, FLJ16239, PPP1R90	uc004dks.1	Q9UBN7	OTTHUMG00000034496	ENST00000334136.5:c.1818T>C	chrX.hg19:g.48675759T>C		108.0	0.0		103.0	5.0	NM_006044	O94975|Q6NT75|Q7L3E5|Q96CY0	Silent	SNP	ENST00000334136.5	hg19	CCDS14306.1																																																																																			.	.		0.527	HDAC6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083394.2	NM_006044		C	48675759	T	C	48675759	2	2	282	1	0	0	0	0	0	0	0	1	7020	1654	58	2		2	HDAC6	23	48675759	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2883	48675759	106594801	1367	41601										
PPP1R3F	89801	hgsc.bcm.edu	37	chrX	49138448	49138448	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tttctcttccctctagcagaGcatcctgatgtccaggagtc	8	13	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:49138448G>A	ENST00000055335.6	+	3	1081	c.1065G>A	c.(1063-1065)gaG>gaA	p.E355E	PPP1R3F_ENST00000376188.1_Splice_Site_p.E9E|PPP1R3F_ENST00000438316.1_Splice_Site_p.E26E|PPP1R3F_ENST00000495799.1_Splice_Site_p.E9E|PPP1R3F_ENST00000466508.1_Splice_Site_p.E9E	NM_033215.4	NP_149992.3	Q6ZSY5	PPR3F_HUMAN	protein phosphatase 1, regulatory subunit 3F	355					regulation of glycogen (starch) synthase activity (GO:2000465)|regulation of glycogen biosynthetic process (GO:0005979)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycogen binding (GO:2001069)|protein phosphatase binding (GO:0019903)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(4)	27	Ovarian(276;0.236)					CTCTAGCAGAGCATCCTGATG	0.527																																					p.E355E		Atlas-SNP	.											.	PPP1R3F	56	.	0			c.G1065A						.						136	96	109					X																	49138448		2203	4300	6503	SO:0001819	synonymous_variant	89801	exon3			AGCAGAGCATCCT		CCDS35254.1, CCDS55415.1	Xp11.23	2012-04-17	2011-10-04		ENSG00000049769	ENSG00000049769		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14944	protein-coding gene	gene with protein product			"protein phosphatase 1, regulatory (inhibitor) subunit 3F"			11948623	Standard	NM_033215		Approved	Hb2E	uc004dnh.2	Q6ZSY5	OTTHUMG00000024139	ENST00000055335.6:c.1065G>A	chrX.hg19:g.49138448G>A		93.0	0.0		71.0	4.0	NM_033215	A2VDJ8|B3KPW2|E9PCM3	Silent	SNP	ENST00000055335.6	hg19	CCDS35254.1	.	.	.	.	.	.	.	.	.	.	G	2.675	-0.276732	0.05679	.	.	ENSG00000049769	ENST00000471261	.	.	.	3.81	-5.82	0.02333	.	.	.	.	.	T	0.19604	0.0471	.	.	.	0.21553	N	0.999645	.	.	.	.	.	.	T	0.17992	-1.0351	4	.	.	.	-0.0275	4.3718	0.11251	0.3969:0.0:0.2789:0.3242	.	.	.	.	N	105	.	.	S	+	2	0	PPP1R3F	49025392	0.000000	0.05858	0.000000	0.03702	0.241000	0.25554	-1.873000	0.01637	-2.363000	0.00608	-1.225000	0.01585	AGC	.	.		0.527	PPP1R3F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060819.2	NM_033215		A	49138448	G	A	49138448	2	1	282	1	0	0	0	0	0	0	0	1	12387	985	34	3		3	PPP1R3F	23	49138448	Silent	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	462689	49138448	106132112	1368	41602										
MAGED1	9500	hgsc.bcm.edu	37	chrX	51637805	51637806	+	Intron	DEL	TG	TG	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tctttctgcattccccactcTgtgcgaccccccttattctc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:51637805_51637806delTG	ENST00000375722.1	+	3	297				MAGED1_ENST00000375772.3_Intron|MAGED1_ENST00000326587.7_Intron|MAGED1_ENST00000375695.2_Frame_Shift_Del_p.L43fs|MAGED1_ENST00000494718.1_Intron			Q9Y5V3	MAGD1_HUMAN	melanoma antigen family D, 1						apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|circadian regulation of gene expression (GO:0032922)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of circadian rhythm (GO:0042752)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	transcription coactivator activity (GO:0003713)			breast(1)|endometrium(4)|large_intestine(10)|lung(13)|ovary(3)|upper_aerodigestive_tract(1)	32	Ovarian(276;0.236)					TTCCCCACTCTGTGCGACCCCC	0.584										Multiple Myeloma(10;0.10)																											p.43_43del		Atlas-Indel,Pindel	.											.	MAGED1	84	.	0			c.127_128del						.																																			SO:0001627	intron_variant	9500	exon3			.	AF124440	CCDS14337.1, CCDS35279.1	Xp11.23	2008-08-01			ENSG00000179222	ENSG00000179222			6813	protein-coding gene	gene with protein product		300224				10409427	Standard	NM_006986		Approved	NRAGE, DLXIN-1	uc004dpn.3	Q9Y5V3	OTTHUMG00000021540	ENST00000375722.1:c.46-343TG>-	chrX.hg19:g.51637807_51637808delTG		223.0	0.0		130.0	85.0	NM_001005333	Q5VSH6|Q8IZ84|Q8WY92|Q9H352|Q9HBT4|Q9UF36	Frame_Shift_Del	DEL	ENST00000375722.1	hg19	CCDS14337.1																																																																																			.	.		0.584	MAGED1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056593.1	NM_001005332		-	51637806	TG	-	51637805	6	5	282	0	1	1	0	1	0	0	0	0	9192	1580	55	0		0	MAGED1	23	51637805	Intron	DEL	TG	TCGA-G3-A3CJ-01A-11D-A20W-10	2499357	51637805	103632755	1369	41603										
TSPYL2	64061	hgsc.bcm.edu	37	chrX	53113779	53113779	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caaccgacgtgatgaagacaTtttccgctacttgaccaatc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:53113779delT	ENST00000375442.4	+	2	992	c.860delT	c.(859-861)attfs	p.I287fs		NM_022117.3	NP_071400.1	Q9H2G4	TSYL2_HUMAN	TSPY-like 2	287					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell cycle (GO:0007049)|cellular protein metabolic process (GO:0044267)|chromatin modification (GO:0016568)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA replication (GO:0008156)|nucleosome assembly (GO:0006334)|regulation of protein kinase activity (GO:0045859)|regulation of signal transduction (GO:0009966)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	rDNA binding (GO:0000182)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(1)	19						GATGAAGACATTTTCCGCTAC	0.483																																					p.I287fs		Atlas-INDEL	.											.	TSPYL2	53	.	0			c.859delA						.						145	125	131					X																	53113779		2203	4300	6503	SO:0001589	frameshift_variant	64061	exon2			.	AF273046	CCDS14350.1	Xp11	2014-06-09			ENSG00000184205	ENSG00000184205			24358	protein-coding gene	gene with protein product		300564				11318608, 11395479	Standard	NM_022117		Approved	SE20-4, HRIHFB2216, CTCL, DENTT, CDA1, CINAP, TSPX	uc004drw.3	Q9H2G4	OTTHUMG00000021597	ENST00000375442.4:c.860delT	chrX.hg19:g.53113779delT	ENSP00000364591:p.Ile287fs	201.0	0.0		118.0	10.0	NM_022117	O94799|Q96DG7|Q9BZW6	Frame_Shift_Del	DEL	ENST00000375442.4	hg19	CCDS14350.1																																																																																			.	.		0.483	TSPYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056718.1	NM_022117		-	53113779	T	-	53113779	7	5	282	1	0	1	0	1	0	0	0	0	16675	1493	52	0	866	0	TSPYL2	23	53113779	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	1475974	53113779	102156781	1370	41604										
HUWE1	10075	hgsc.bcm.edu	37	chrX	53630379	53630379	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtgctttcccacaccagggaAcagtataactggctcagctt	9	12	1	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:53630379A>G	ENST00000342160.3	-	26	3283	c.2826T>C	c.(2824-2826)tgT>tgC	p.C942C	HUWE1_ENST00000218328.8_Silent_p.C942C|HUWE1_ENST00000262854.6_Silent_p.C942C			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	942					base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						ACACCAGGGAACAGTATAACT	0.458																																					p.C942C		Atlas-SNP	.											.	HUWE1	724	.	0			c.T2826C						.						106	82	90					X																	53630379		2203	4300	6503	SO:0001819	synonymous_variant	10075	exon27			CAGGGAACAGTAT	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"HECT, UBA and WWE domain containing 1"			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.2826T>C	chrX.hg19:g.53630379A>G		125.0	0.0		94.0	4.0	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Silent	SNP	ENST00000342160.3	hg19	CCDS35301.1																																																																																			.	.		0.458	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		G	53630379	A	G	53630379	2	3	282	1	0	0	0	0	0	0	0	1	7470	41	2	2		2	HUWE1	23	53630379	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	516600	53630379	101640181	1371	41605										
SPIN2B	474343	hgsc.bcm.edu	37	chrX	57146927	57146927	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gcagcccacgatgttcctgcGgggctgggatgaaggtcggc					rs201872206		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:57146927delG	ENST00000333933.3	-	2	446	c.136delC	c.(136-138)cgcfs	p.R47fs	SPIN2B_ENST00000460948.1_5'UTR|RP3-323P24.3_ENST00000439622.1_RNA|SPIN2B_ENST00000374912.5_Frame_Shift_Del_p.R47fs|SPIN2B_ENST00000374910.3_Frame_Shift_Del_p.R47fs|SPIN2B_ENST00000275988.5_Frame_Shift_Del_p.R47fs	NM_001006681.1	NP_001006682.1	Q9BPZ2	SPI2B_HUMAN	spindlin family, member 2B	47					apoptotic process (GO:0006915)|cell cycle (GO:0007049)|gamete generation (GO:0007276)|regulation of cell cycle (GO:0051726)	nucleus (GO:0005634)				endometrium(3)|large_intestine(1)|skin(1)	5						ATGTTCCTGCGGGGCTGGGAT	0.532																																					p.R46fs		Atlas-INDEL	.											.	SPIN2B	11	.	0			c.137delG						.																																			SO:0001589	frameshift_variant	474343	exon2			.	AF356353	CCDS35311.1, CCDS65274.1	Xp11.1	2014-02-12	2006-12-05		ENSG00000186787	ENSG00000186787			33147	protein-coding gene	gene with protein product		300517				12145692	Standard	XM_005262010		Approved	SPIN-2	uc004dva.3	Q9BPZ2	OTTHUMG00000021680	ENST00000333933.3:c.136delC	chrX.hg19:g.57146927delG	ENSP00000335008:p.Arg47fs	279.0	0.0		157.0	10.0	NM_001006683	Q7Z2M0	Frame_Shift_Del	DEL	ENST00000333933.3	hg19	CCDS35311.1																																																																																			.	.		0.532	SPIN2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056912.1	NM_001006681		-	57146927	G	-	57146927	7	5	282	1	0	1	0	1	0	0	0	0	15069	1116	39	0	644	0	SPIN2B	23	57146927	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	3516548	57146927	98123633	1372	41606										
DGAT2L6	347516	hgsc.bcm.edu	37	chrX	69424364	69424364	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caatcggcccattaccactgTtggtgagctttcccttatct	7	13	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:69424364T>C	ENST00000333026.3	+	6	957	c.857T>C	c.(856-858)gTt>gCt	p.V286A		NM_198512.1	NP_940914.1	Q6ZPD8	DG2L6_HUMAN	diacylglycerol O-acyltransferase 2-like 6	286					lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	transferase activity, transferring acyl groups other than amino-acyl groups (GO:0016747)			breast(1)|endometrium(2)|large_intestine(3)|lung(5)|ovary(1)	12						ATTACCACTGTTGGTGAGCTT	0.502																																					p.V286A		Atlas-SNP	.											.	DGAT2L6	40	.	0			c.T857C						.						68	63	65					X																	69424364		2203	4300	6503	SO:0001583	missense	347516	exon6			CCACTGTTGGTGA	AK129500	CCDS14397.1	Xq13.1	2008-02-05			ENSG00000184210	ENSG00000184210			23250	protein-coding gene	gene with protein product		300926				15671038	Standard	NM_198512		Approved	DC3, FLJ25989	uc004dxx.1	Q6ZPD8	OTTHUMG00000021774	ENST00000333026.3:c.857T>C	chrX.hg19:g.69424364T>C	ENSP00000328036:p.Val286Ala	134.0	0.0		83.0	4.0	NM_198512	Q6IEE2	Missense_Mutation	SNP	ENST00000333026.3	hg19	CCDS14397.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.580714	0.86748	.	.	ENSG00000184210	ENST00000333026	T	0.25579	1.79	4.98	4.98	0.66077	.	0.000000	0.64402	D	0.000009	T	0.53997	0.1831	M	0.88842	2.985	0.58432	D	0.999992	D	0.71674	0.998	D	0.67382	0.951	T	0.62877	-0.6761	10	0.87932	D	0	-7.6613	11.5384	0.50653	0.0:0.0:0.0:1.0	.	286	Q6ZPD8	DG2L6_HUMAN	A	286	ENSP00000328036:V286A	ENSP00000328036:V286A	V	+	2	0	DGAT2L6	69341089	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.102000	0.77005	1.852000	0.53769	0.486000	0.48141	GTT	.	.		0.502	DGAT2L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057067.1	NM_198512		C	69424364	T	C	69424364	3	2	282	1	0	0	0	0	1	0	0	0	4461	1725	60	2	879	2	DGAT2L6	23	69424364	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	12277437	69424364	85846196	1373	41607										
TEX11	56159	hgsc.bcm.edu	37	chrX	70072999	70072999	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atttgacgtataattgctccAgactctggaaaataaaccca	6	9	1	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:70072999A>G	ENST00000395889.2	-	8	610	c.455T>C	c.(454-456)cTg>cCg	p.L152P	TEX11_ENST00000374333.2_Missense_Mutation_p.L137P|TEX11_ENST00000344304.3_Missense_Mutation_p.L152P	NM_001003811.1	NP_001003811.1	Q8IYF3	TEX11_HUMAN	testis expressed 11	152					chiasma assembly (GO:0051026)|fertilization (GO:0009566)|male gonad development (GO:0008584)|male meiosis chromosome segregation (GO:0007060)|meiotic gene conversion (GO:0006311)|negative regulation of apoptotic process (GO:0043066)|reciprocal meiotic recombination (GO:0007131)|resolution of meiotic recombination intermediates (GO:0000712)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)				breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(13)|ovary(3)|prostate(3)|skin(3)	48	Renal(35;0.156)					TAATTGCTCCAGACTCTGGAA	0.398																																					p.L152P		Atlas-SNP	.											.	TEX11	132	.	0			c.T455C						.						72	60	64					X																	70072999		2203	4300	6503	SO:0001583	missense	56159	exon8			TGCTCCAGACTCT	AF285594	CCDS35323.1, CCDS43968.1	Xp11	2008-02-05	2007-03-13		ENSG00000120498	ENSG00000120498			11733	protein-coding gene	gene with protein product		300311	"testis expressed sequence 11"			11279525	Standard	NM_001003811		Approved	TSGA3, TGC1	uc004dyl.3	Q8IYF3	OTTHUMG00000021782	ENST00000395889.2:c.455T>C	chrX.hg19:g.70072999A>G	ENSP00000379226:p.Leu152Pro	98.0	0.0		62.0	4.0	NM_001003811	A8K8V6|Q5JQQ8|Q96LZ4|Q96M47|Q9BXU6	Missense_Mutation	SNP	ENST00000395889.2	hg19	CCDS35323.1	.	.	.	.	.	.	.	.	.	.	A	12.05	1.822596	0.32237	.	.	ENSG00000120498	ENST00000374333;ENST00000395889;ENST00000344304	T;T;T	0.39056	1.1;1.12;1.12	4.56	4.56	0.56223	Tetratricopeptide-like helical (1);	0.197085	0.33980	N	0.004373	T	0.55049	0.1896	L	0.49778	1.585	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.982	T	0.53215	-0.8470	9	.	.	.	-3.7026	11.0541	0.47907	1.0:0.0:0.0:0.0	.	137;152	Q8IYF3-3;Q8IYF3	.;TEX11_HUMAN	P	137;152;152	ENSP00000363453:L137P;ENSP00000379226:L152P;ENSP00000340995:L152P	.	L	-	2	0	TEX11	69989724	1.000000	0.71417	0.937000	0.37676	0.044000	0.14063	4.476000	0.60216	1.810000	0.52873	0.432000	0.28606	CTG	.	.		0.398	TEX11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359072.1			G	70072999	A	G	70072999	3	3	282	1	0	0	0	0	1	0	0	0	15789	188	7	2	2463	2	TEX11	23	70072999	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	648635	70072999	85197561	1374	41608										
OGT	8473	hgsc.bcm.edu	37	chrX	70775862	70775862	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tctgtgtcccacccatgcagActctctgaataacctagcca	6	15	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:70775862A>G	ENST00000373719.3	+	8	1200	c.983A>G	c.(982-984)gAc>gGc	p.D328G	OGT_ENST00000373701.3_Missense_Mutation_p.D318G	NM_181672.2|NM_181673.2	NP_858058.1|NP_858059.1	O15294	OGT1_HUMAN	O-linked N-acetylglucosamine (GlcNAc) transferase	328					apoptotic process (GO:0006915)|cellular response to retinoic acid (GO:0071300)|chromatin organization (GO:0006325)|circadian regulation of gene expression (GO:0032922)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of protein ubiquitination (GO:0031397)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of catalytic activity (GO:0043085)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of histone H3-K27 methylation (GO:0061087)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of proteolysis (GO:0045862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glycolytic process (GO:0006110)|regulation of insulin receptor signaling pathway (GO:0046626)|regulation of Rac protein signal transduction (GO:0035020)|response to insulin (GO:0032868)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone acetyltransferase complex (GO:0000123)|microtubule organizing center (GO:0005815)|mitochondrion (GO:0005739)|MLL5-L complex (GO:0070688)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	acetylglucosaminyltransferase activity (GO:0008375)|enzyme activator activity (GO:0008047)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein N-acetylglucosaminyltransferase activity (GO:0016262)|protein O-GlcNAc transferase activity (GO:0097363)			breast(6)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|liver(3)|lung(9)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Renal(35;0.156)					ACCCATGCAGACTCTCTGAAT	0.408																																					p.D328G		Atlas-SNP	.											.	OGT	207	.	0			c.A983G						.						155	128	137					X																	70775862		2203	4300	6503	SO:0001583	missense	8473	exon8			ATGCAGACTCTCT	U77413	CCDS14414.1, CCDS35502.1	Xq13	2013-07-24	2012-05-04		ENSG00000147162	ENSG00000147162	2.4.1.255	"Tetratricopeptide (TTC) repeat domain containing"	8127	protein-coding gene	gene with protein product	"UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase"	300255	"O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)"			9083068	Standard	NM_181672		Approved	O-GLCNAC, HRNT1, MGC22921, FLJ23071	uc004eaa.2	O15294	OTTHUMG00000033316	ENST00000373719.3:c.983A>G	chrX.hg19:g.70775862A>G	ENSP00000362824:p.Asp328Gly	162.0	0.0		119.0	5.0	NM_181672	Q7Z3K0|Q8WWM8|Q96CC1|Q9UG57	Missense_Mutation	SNP	ENST00000373719.3	hg19	CCDS14414.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.756306	0.89843	.	.	ENSG00000147162	ENST00000373719;ENST00000373701	T;T	0.60299	0.2;0.2	5.16	5.16	0.70880	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.77103	0.4081	M	0.83312	2.635	0.80722	D	1	D;D;D	0.71674	0.997;0.998;0.99	D;D;D	0.87578	0.998;0.996;0.993	T	0.80115	-0.1517	10	0.54805	T	0.06	-16.8643	14.1095	0.65113	1.0:0.0:0.0:0.0	.	202;318;328	Q548W1;O15294-3;O15294	.;.;OGT1_HUMAN	G	328;318	ENSP00000362824:D328G;ENSP00000362805:D318G	ENSP00000362805:D318G	D	+	2	0	OGT	70692587	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.081000	0.94049	1.907000	0.55213	0.486000	0.48141	GAC	.	.		0.408	OGT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000081829.3	NM_003605, NM_181672		G	70775862	A	G	70775862	3	3	282	1	0	0	0	0	1	0	0	0	10856	275	10	2	1013	2	OGT	23	70775862	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	702863	70775862	84494698	1375	41609										
NHSL2	340527	hgsc.bcm.edu	37	chrX	71359404	71359404	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agtcattgagtgcacccaagTtcagggcagctcagagtctc	11	11	4	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:71359404T>C	ENST00000373677.1	+	2	2170	c.908T>C	c.(907-909)gTt>gCt	p.V303A	NHSL2_ENST00000535692.1_Missense_Mutation_p.V303A|NHSL2_ENST00000540800.1_Missense_Mutation_p.V669A|NHSL2_ENST00000510661.1_Missense_Mutation_p.V438A			Q5HYW2	NHSL2_HUMAN	NHS-like 2	303	Ser-rich.									NS(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(10)|lung(7)|stomach(1)	28	Renal(35;0.156)					TGCACCCAAGTTCAGGGCAGC	0.557																																					p.V669A		Atlas-SNP	.											.	NHSL2	148	.	0			c.T2006C						.						74	58	63					X																	71359404		2203	4300	6503	SO:0001583	missense	340527	exon6			CCCAAGTTCAGGG			Xq13.1	2009-02-18			ENSG00000204131	ENSG00000204131			33737	protein-coding gene	gene with protein product							Standard	NM_001013627		Approved		uc011mqa.2	Q5HYW2	OTTHUMG00000021807	ENST00000373677.1:c.908T>C	chrX.hg19:g.71359404T>C	ENSP00000362781:p.Val303Ala	159.0	0.0		136.0	6.0	NM_001013627	B2RN94	Missense_Mutation	SNP	ENST00000373677.1	hg19		.	.	.	.	.	.	.	.	.	.	T	2.270	-0.367112	0.05069	.	.	ENSG00000204131	ENST00000540800;ENST00000373677;ENST00000510661;ENST00000535692	T;T;T;T	0.49139	1.44;0.86;0.79;0.86	5.77	3.39	0.38822	.	0.068183	0.64402	D	0.000018	T	0.31451	0.0797	L	0.45581	1.43	0.40595	D	0.981525	B;B;B	0.25809	0.126;0.135;0.041	B;B;B	0.20767	0.031;0.031;0.019	T	0.08207	-1.0733	10	0.12766	T	0.61	-8.9314	3.6473	0.08189	0.0:0.1771:0.1944:0.6285	.	669;438;303	F5H593;D6RBM4;Q5HYW2	.;.;NHSL2_HUMAN	A	669;303;438;303	ENSP00000444617:V669A;ENSP00000362781:V303A;ENSP00000424079:V438A;ENSP00000444914:V303A	ENSP00000362781:V303A	V	+	2	0	NHSL2	71276129	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	2.238000	0.43070	0.800000	0.34041	-0.354000	0.07668	GTT	.	.		0.557	NHSL2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000057170.1	NM_001013627		C	71359404	T	C	71359404	3	2	282	1	0	0	0	0	1	0	0	0	10421	1725	60	2	2028	2	NHSL2	23	71359404	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	583542	71359404	83911156	1376	41610										
KIAA2022	340533	hgsc.bcm.edu	37	chrX	73960376	73960376	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccatgggttcccaaaggggcTctatggaggccatcatgaat	12	10	2	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:73960376T>C	ENST00000055682.6	-	3	4627	c.4016A>G	c.(4015-4017)gAg>gGg	p.E1339G		NM_001008537.2	NP_001008537.1	Q5QGS0	K2022_HUMAN	KIAA2022	1339					base-excision repair, gap-filling (GO:0006287)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|nervous system development (GO:0007399)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)	delta DNA polymerase complex (GO:0043625)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|DNA-directed DNA polymerase activity (GO:0003887)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(23)|liver(1)|lung(41)|ovary(7)|pancreas(2)|prostate(4)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	109						CCAAAGGGGCTCTATGGAGGC	0.473																																					p.E1339G		Atlas-SNP	.											.	KIAA2022	262	.	0			c.A4016G						.						76	72	74					X																	73960376		2203	4300	6503	SO:0001583	missense	340533	exon3			AGGGGCTCTATGG		CCDS35337.1	Xq13.3	2014-02-19			ENSG00000050030	ENSG00000050030			29433	protein-coding gene	gene with protein product	"XLMR-related protein, neurite extension"	300524				15466006, 23615299	Standard	NM_001008537		Approved	XPN, MRX98	uc004eby.3	Q5QGS0	OTTHUMG00000021860	ENST00000055682.6:c.4016A>G	chrX.hg19:g.73960376T>C	ENSP00000055682:p.Glu1339Gly	144.0	0.0		113.0	5.0	NM_001008537	A7YY87|Q5JUX9|Q8IVE9	Missense_Mutation	SNP	ENST00000055682.6	hg19	CCDS35337.1	.	.	.	.	.	.	.	.	.	.	T	17.84	3.487508	0.63962	.	.	ENSG00000050030	ENST00000373468;ENST00000055682	T;T	0.33654	1.4;1.4	5.55	5.55	0.83447	.	0.206474	0.50627	D	0.000112	T	0.49898	0.1584	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.53151	-0.8479	10	0.87932	D	0	-15.4889	14.7048	0.69183	0.0:0.0:0.0:1.0	.	1339	Q5QGS0	K2022_HUMAN	G	1339	ENSP00000362567:E1339G;ENSP00000055682:E1339G	ENSP00000055682:E1339G	E	-	2	0	KIAA2022	73877101	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.698000	0.84413	1.853000	0.53794	0.441000	0.28932	GAG	.	.		0.473	KIAA2022-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057270.2	NM_001008537		C	73960376	T	C	73960376	3	2	282	1	0	0	0	0	1	0	0	0	8278	1551	54	2	542	2	KIAA2022	23	73960376	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2600972	73960376	81310184	1377	41611										
ABCB7	22	hgsc.bcm.edu	37	chrX	74282215	74282215	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cttcatcatagagtatgactGgggggtccttcaaaatggct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:74282215delG	ENST00000373394.3	-	14	1890	c.1883delC	c.(1882-1884)ccafs	p.P628fs	ABCB7_ENST00000253577.3_Frame_Shift_Del_p.P629fs|ABCB7_ENST00000339447.4_Frame_Shift_Del_p.P588fs|ABCB7_ENST00000534570.1_5'Flank			O75027	ABCB7_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 7	628	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular iron ion homeostasis (GO:0006879)|heme transport (GO:0015886)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|heme transporter activity (GO:0015232)			breast(1)|endometrium(5)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)	20						GAGTATGACTGGGGGGTCCTT	0.348																																					p.P629fs		Atlas-INDEL	.											.	ABCB7	69	.	0			c.1887delA						.						101	90	94					X																	74282215		2203	4300	6503	SO:0001589	frameshift_variant	22	exon14			.	AF038950	CCDS14428.1, CCDS65290.1, CCDS65291.1, CCDS75994.1	Xq13.3	2012-03-14			ENSG00000131269	ENSG00000131269		"ATP binding cassette transporters / subfamily B"	48	protein-coding gene	gene with protein product		300135		ABC7		9143506	Standard	NM_004299		Approved	EST140535, Atm1p, ASAT	uc004ebz.4	O75027	OTTHUMG00000021862	ENST00000373394.3:c.1883delC	chrX.hg19:g.74282215delG	ENSP00000362492:p.Pro628fs	225.0	0.0		179.0	13.0	NM_004299	G3XAC4|O75345|Q5VWY7|Q5VWY8|Q9BRE1|Q9UND1|Q9UP01	Frame_Shift_Del	DEL	ENST00000373394.3	hg19																																																																																				.	.		0.348	ABCB7-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000057274.1	NM_004299		-	74282215	G	-	74282215	7	5	282	1	0	1	0	1	0	0	0	0	46	1348	47	0	387	0	ABCB7	23	74282215	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	321839	74282215	80988345	1378	41612										
PGAM4	441531	hgsc.bcm.edu	37	chrX	77224433	77224433	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tttgcacaccgtctcttcatCccccagaaactgcatgggct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:77224433delC	ENST00000458128.1	-	1	702	c.703delG	c.(703-705)gatfs	p.D235fs	ATP7A_ENST00000341514.6_Intron|ATP7A_ENST00000350425.4_Intron|ATP7A_ENST00000343533.5_Intron	NM_001029891.2	NP_001025062.1	Q8N0Y7	PGAM4_HUMAN	phosphoglycerate mutase family member 4	235					glycolytic process (GO:0006096)|positive regulation of sperm motility (GO:1902093)	extracellular vesicular exosome (GO:0070062)|sperm principal piece (GO:0097228)	bisphosphoglycerate 2-phosphatase activity (GO:0004083)|bisphosphoglycerate mutase activity (GO:0004082)|phosphoglycerate mutase activity (GO:0004619)			endometrium(2)|lung(4)	6						GTCTCTTCATCCCCCAGAAAC	0.547																																					p.D235fs		Atlas-INDEL	.											.	PGAM4	28	.	0			c.704delA						.						69	66	67					X																	77224433		2203	4296	6499	SO:0001589	frameshift_variant	441531	exon1			.	AF465731	CCDS35338.1	Xq21.1	2011-02-09	2006-02-09		ENSG00000226784	ENSG00000226784			21731	protein-coding gene	gene with protein product		300567	"phosphoglycerate mutase family 4"			11961099, 9370262	Standard	NM_001029891		Approved	dJ1000K24.1, PGAM3, PGAM-B, PGAM1	uc004ecy.1	Q8N0Y7	OTTHUMG00000057865	ENST00000458128.1:c.703delG	chrX.hg19:g.77224433delC	ENSP00000412189:p.Asp235fs	226.0	0.0		151.0	11.0	NM_001029891	Q5JPN2|Q8NI24|Q8NI25|Q8NI26	Frame_Shift_Del	DEL	ENST00000458128.1	hg19	CCDS35338.1																																																																																			.	.		0.547	PGAM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128371.2	NM_001029891		-	77224433	C	-	77224433	7	5	282	1	0	1	0	1	0	0	0	0	11784	855	30	0	65	0	PGAM4	23	77224433	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	2942218	77224433	78046127	1379	41613										
SH3BGRL	6451	hgsc.bcm.edu	37	chrX	80532637	80532637	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cacaggttaccccctgccacCtcagattttcaatgaaagcc	6	15	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:80532637C>T	ENST00000373212.5	+	2	458	c.200C>T	c.(199-201)cCt>cTt	p.P67L	SH3BGRL_ENST00000481106.1_3'UTR	NM_003022.2	NP_003013.1	O75368	SH3L1_HUMAN	SH3 domain binding glutamate-rich protein like	67					positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	SH3/SH2 adaptor activity (GO:0005070)			endometrium(1)|lung(2)|ovary(1)	4		all_lung(315;5.94e-05)				CCCCTGCCACCTCAGATTTTC	0.388																																					p.P67L		Atlas-SNP	.											.	SH3BGRL	23	.	0			c.C200T						.						58	54	55					X																	80532637		2203	4300	6503	SO:0001583	missense	6451	exon2			TGCCACCTCAGAT	AF042081	CCDS14449.1	Xq13.3	2014-02-19	2014-02-19		ENSG00000131171	ENSG00000131171			10823	protein-coding gene	gene with protein product		300190	"SH3 domain binding glutamic acid-rich protein like"			9642120	Standard	NM_003022		Approved	MGC117402	uc004eef.3	O75368	OTTHUMG00000021910	ENST00000373212.5:c.200C>T	chrX.hg19:g.80532637C>T	ENSP00000362308:p.Pro67Leu	141.0	0.0		92.0	4.0	NM_003022	Q3SYL1|Q5JT50|Q6FIE8|Q9H0N8	Missense_Mutation	SNP	ENST00000373212.5	hg19	CCDS14449.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.634414	0.87660	.	.	ENSG00000131171	ENST00000373212	D	0.96265	-3.96	5.7	5.7	0.88788	Thioredoxin-like fold (2);	0.000000	0.85682	D	0.000000	D	0.98654	0.9549	M	0.93638	3.44	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.99734	1.1013	10	0.87932	D	0	-4.2429	17.6307	0.88106	0.0:1.0:0.0:0.0	.	19;66;67	B0AZV6;D3DTE6;O75368	.;.;SH3L1_HUMAN	L	67	ENSP00000362308:P67L	ENSP00000362308:P67L	P	+	2	0	SH3BGRL	80419293	1.000000	0.71417	1.000000	0.80357	0.744000	0.42396	7.182000	0.77689	2.380000	0.81148	0.600000	0.82982	CCT	.	.		0.388	SH3BGRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057350.1	NM_003022		T	80532637	C	T	80532637	3	4	282	1	0	0	0	0	1	0	0	0	14256	681	24	3	206	3	SH3BGRL	23	80532637	Missense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	3308204	80532637	74737923	1380	41614										
TCEAL6	158931	hgsc.bcm.edu	37	chrX	101395774	101395774	+	Missense_Mutation	SNP	T	T	C													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	actcccctgacaccccgttgTccccttgggcgaatggatcc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:101395774T>C	ENST00000372774.3	-	3	779	c.530A>G	c.(529-531)gAc>gGc	p.D177G	TCEAL6_ENST00000372773.1_Missense_Mutation_p.D177G	NM_001006938.2	NP_001006939.2	Q6IPX3	TCAL6_HUMAN	transcription elongation factor A (SII)-like 6	0					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	14						CACCCCGTTGTCCCCTTGGGC	0.507																																					p.D177G		Atlas-SNP	.											.	TCEAL6	27	.	0			c.A530G						.						19	18	19					X																	101395774		2197	4274	6471	SO:0001583	missense	158931	exon3			CCGTTGTCCCCTT	BC071675	CCDS43978.1	Xq22.1	2014-03-21			ENSG00000204071	ENSG00000204071			24553	protein-coding gene	gene with protein product						16221301	Standard	NM_001006938		Approved	WEX2	uc004eiq.3	Q6IPX3	OTTHUMG00000022050	ENST00000372774.3:c.530A>G	chrX.hg19:g.101395774T>C	ENSP00000361860:p.Asp177Gly	108.0	0.0		170.0	12.0	NM_001006938	Q5H9J8	Missense_Mutation	SNP	ENST00000372774.3	hg19	CCDS43978.1	.	.	.	.	.	.	.	.	.	.	A	0.755	-0.771235	0.02951	.	.	ENSG00000204071	ENST00000372774;ENST00000372773	T;T	0.23147	1.92;1.92	2.82	-3.23	0.05109	.	0.272209	0.20313	N	0.094788	T	0.11836	0.0288	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.08186	-1.0734	10	0.48119	T	0.1	.	3.3698	0.07216	0.1211:0.4969:0.222:0.1599	.	177	Q6IPX3-2	.	G	177	ENSP00000361860:D177G;ENSP00000361859:D177G	ENSP00000361859:D177G	D	-	2	0	TCEAL6	101282430	0.001000	0.12720	0.010000	0.14722	0.828000	0.46876	-1.039000	0.03550	-1.000000	0.03438	-0.742000	0.03525	GAC	.	.		0.507	TCEAL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057609.1	NM_001006938		C	101395774	T	C	101395774	3	2	282	1	0	0	0	0	1	0	0	0	15690	1667	58	2	25	2	TCEAL6	23	101395774	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	20863137	101395774	53874786	1381	41615	208	2								
TCEAL6	158931	hgsc.bcm.edu	37	chrX	101395778	101395778	+	Missense_Mutation	SNP	C	C	T													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccctgacaccccgttgtcccCttgggcgaatggatcctgta							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:101395778C>T	ENST00000372774.3	-	3	775	c.526G>A	c.(526-528)Ggg>Agg	p.G176R	TCEAL6_ENST00000372773.1_Missense_Mutation_p.G176R	NM_001006938.2	NP_001006939.2	Q6IPX3	TCAL6_HUMAN	transcription elongation factor A (SII)-like 6	0					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	14						CCGTTGTCCCCTTGGGCGAAT	0.502																																					p.G176R		Atlas-SNP	.											.	TCEAL6	27	.	0			c.G526A						.						13	13	13					X																	101395778		2197	4251	6448	SO:0001583	missense	158931	exon3			TGTCCCCTTGGGC	BC071675	CCDS43978.1	Xq22.1	2014-03-21			ENSG00000204071	ENSG00000204071			24553	protein-coding gene	gene with protein product						16221301	Standard	NM_001006938		Approved	WEX2	uc004eiq.3	Q6IPX3	OTTHUMG00000022050	ENST00000372774.3:c.526G>A	chrX.hg19:g.101395778C>T	ENSP00000361860:p.Gly176Arg	108.0	0.0		164.0	23.0	NM_001006938	Q5H9J8	Missense_Mutation	SNP	ENST00000372774.3	hg19	CCDS43978.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.605|9.605	1.129729|1.129729	0.21041|0.21041	.|.	.|.	ENSG00000204071|ENSG00000204071	ENST00000372774;ENST00000372773|ENST00000536102	T;T|.	0.40225|.	1.04;1.04|.	2.82|2.82	2.82|2.82	0.32997|0.32997	.|.	0.000000|.	0.39341|.	N|.	0.001392|.	T|T	0.27832|0.27832	0.0685|0.0685	L|L	0.32530|0.32530	0.975|0.975	0.09310|0.09310	N|N	1|1	D|.	0.57257|.	0.979|.	P|.	0.56563|.	0.801|.	T|T	0.22243|0.22243	-1.0222|-1.0222	10|6	0.54805|0.06365	T|T	0.06|0.9	.|.	8.3639|8.3639	0.32374|0.32374	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	176|.	Q6IPX3-2|.	.|.	R|K	176|175	ENSP00000361860:G176R;ENSP00000361859:G176R|.	ENSP00000361859:G176R|ENSP00000437364:R175K	G|R	-|-	1|2	0|0	TCEAL6|TCEAL6	101282434|101282434	0.007000|0.007000	0.16637|0.16637	0.089000|0.089000	0.20774|0.20774	0.743000|0.743000	0.42351|0.42351	1.059000|1.059000	0.30517|0.30517	1.692000|1.692000	0.51112|0.51112	0.468000|0.468000	0.43344|0.43344	GGG|AGG	.	.		0.502	TCEAL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057609.1	NM_001006938		T	101395778	C	T	101395778	3	4	282	1	0	0	0	0	1	0	0	0	15690	681	24	3	29	3	TCEAL6	23	101395778	Missense_Mutation	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	4	101395778	53874782	1382	41616	208	2								
GPRASP2	114928	hgsc.bcm.edu	37	chrX	101971961	101971961	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgattgccaactatatgtccGggtttctctccttattaacc	6	11	1	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:101971961G>A	ENST00000535209.1	+	4	2995	c.2164G>A	c.(2164-2166)Ggg>Agg	p.G722R	GPRASP2_ENST00000543253.1_Missense_Mutation_p.G722R|GPRASP2_ENST00000332262.5_Missense_Mutation_p.G722R			Q96D09	GASP2_HUMAN	G protein-coupled receptor associated sorting protein 2	722						cytoplasm (GO:0005737)	beta-amyloid binding (GO:0001540)			breast(3)|endometrium(5)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	30						CTATATGTCCGGGTTTCTCTC	0.413																																					p.G722R		Atlas-SNP	.											.	GPRASP2	89	.	0			c.G2164A						.						103	93	97					X																	101971961		2203	4300	6503	SO:0001583	missense	114928	exon4			ATGTCCGGGTTTC	AK094646	CCDS14501.1	Xq22.1	2014-03-21			ENSG00000158301	ENSG00000158301		"Armadillo repeat containing"	25169	protein-coding gene	gene with protein product						15086532, 16221301	Standard	NM_138437		Approved	GASP2, FLJ37327		Q96D09	OTTHUMG00000022059	ENST00000535209.1:c.2164G>A	chrX.hg19:g.101971961G>A	ENSP00000437394:p.Gly722Arg	215.0	0.0		167.0	138.0	NM_138437	D3DXA0|Q8NAB4	Missense_Mutation	SNP	ENST00000535209.1	hg19	CCDS14501.1	.	.	.	.	.	.	.	.	.	.	G	11.37	1.619652	0.28801	.	.	ENSG00000158301	ENST00000543253;ENST00000535209;ENST00000332262	T;T;T	0.28666	1.6;1.6;1.6	4.31	4.31	0.51392	Armadillo-like helical (1);Armadillo-type fold (1);	0.150817	0.31279	N	0.007934	T	0.49541	0.1563	M	0.69823	2.125	0.24777	N	0.992834	D	0.89917	1.0	D	0.73708	0.981	T	0.35051	-0.9804	10	0.28530	T	0.3	.	11.1272	0.48325	0.0:0.0:1.0:0.0	.	722	Q96D09	GASP2_HUMAN	R	722	ENSP00000437872:G722R;ENSP00000437394:G722R;ENSP00000339057:G722R	ENSP00000339057:G722R	G	+	1	0	GPRASP2	101858617	0.940000	0.31905	0.596000	0.28811	0.313000	0.28021	3.680000	0.54641	2.394000	0.81467	0.513000	0.50165	GGG	.	.		0.413	GPRASP2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057626.2	NM_138437		A	101971961	G	A	101971961	3	1	282	1	0	0	0	0	1	0	0	0	6732	1116	39	1	2166	1	GPRASP2	23	101971961	Missense_Mutation	SNP	G	TCGA-G3-A3CJ-01A-11D-A20W-10	576183	101971961	53298599	1383	41617										
TCEAL4	79921	hgsc.bcm.edu	37	chrX	102841623	102841623	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	catggaaaaactctacagtgAaaatgaaggaatggcttcaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:102841623delA	ENST00000472745.1	+	3	572	c.20delA	c.(19-21)gaafs	p.E7fs	TCEAL4_ENST00000415568.2_Frame_Shift_Del_p.E7fs|TCEAL4_ENST00000494801.1_Frame_Shift_Del_p.E7fs|TCEAL4_ENST00000468024.1_Frame_Shift_Del_p.E7fs|TCEAL4_ENST00000472484.1_Frame_Shift_Del_p.E7fs|TCEAL4_ENST00000372629.4_Frame_Shift_Del_p.E150fs			Q96EI5	TCAL4_HUMAN	transcription elongation factor A (SII)-like 4	7	Glu-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(2)|skin(2)	6						CTCTACAGTGAAAATGAAGGA	0.463																																					p.E7fs		Atlas-INDEL	.											.	TCEAL4	18	.	0			c.19delG						.						75	73	73					X																	102841623		2181	4286	6467	SO:0001589	frameshift_variant	79921	exon3			.	AF314542	CCDS14510.2, CCDS76004.1	Xq22.2	2014-03-21			ENSG00000133142	ENSG00000133142			26121	protein-coding gene	gene with protein product						14702039, 16221301	Standard	XM_005262192		Approved	FLJ21174, WEX7	uc004ekn.3	Q96EI5	OTTHUMG00000022103	ENST00000472745.1:c.20delA	chrX.hg19:g.102841623delA	ENSP00000424314:p.Glu7fs	208.0	0.0		150.0	11.0	NM_001006935	Q8WY12|Q9H2H1|Q9H775	Frame_Shift_Del	DEL	ENST00000472745.1	hg19	CCDS14510.2																																																																																			.	.		0.463	TCEAL4-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252339.2	NM_024863		-	102841623	A	-	102841623	7	5	282	1	0	1	0	1	0	0	0	0	15688	246	9	0	22	0	TCEAL4	23	102841623	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	869662	102841623	52428937	1384	41618										
NUP62CL	54830	hgsc.bcm.edu	37	chrX	106396417	106396417	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	cttacatctccacatgctccTcatctgcatcctgcagataa	4	15	3	1			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:106396417T>C	ENST00000372466.4	-	7	766	c.515A>G	c.(514-516)gAg>gGg	p.E172G	NUP62CL_ENST00000372461.3_3'UTR	NM_017681.2	NP_060151.2	Q9H1M0	N62CL_HUMAN	nucleoporin 62kDa C-terminal like	172					protein transport (GO:0015031)	nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			lung(4)	4						CACATGCTCCTCATCTGCATC	0.433																																					p.E172G		Atlas-SNP	.											.	NUP62CL	10	.	0			c.A515G						.						188	204	198					X																	106396417		2203	4300	6503	SO:0001583	missense	54830	exon7			TGCTCCTCATCTG	AK000137	CCDS14527.1	Xq22.3	2008-02-05			ENSG00000198088	ENSG00000198088			25960	protein-coding gene	gene with protein product						12477932	Standard	NM_017681		Approved	FLJ20130	uc004ena.3	Q9H1M0	OTTHUMG00000022159	ENST00000372466.4:c.515A>G	chrX.hg19:g.106396417T>C	ENSP00000361544:p.Glu172Gly	202.0	0.0		139.0	6.0	NM_017681	D3DUX4|Q8WVL6|Q9NXP2	Missense_Mutation	SNP	ENST00000372466.4	hg19	CCDS14527.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.76|13.76	2.332145|2.332145	0.41297|0.41297	.|.	.|.	ENSG00000198088|ENSG00000198088	ENST00000372466;ENST00000372465|ENST00000432145	T|.	0.78126|.	-1.15|.	5.44|5.44	1.48|1.48	0.22813|0.22813	Nucleoporin, NSP1-like, C-terminal (2);|.	0.287377|.	0.38778|.	N|.	0.001567|.	T|.	0.58380|.	0.2118|.	M|M	0.63428|0.63428	1.95|1.95	0.80722|0.80722	D|D	1|1	P|.	0.41188|.	0.741|.	P|.	0.53809|.	0.735|.	T|.	0.49844|.	-0.8896|.	10|.	0.33141|.	T|.	0.24|.	-0.0266|-0.0266	6.5555|6.5555	0.22458|0.22458	0.1472:0.0:0.3004:0.5524|0.1472:0.0:0.3004:0.5524	.|.	172|.	Q9H1M0|.	N62CL_HUMAN|.	G|W	172|103	ENSP00000361544:E172G|.	ENSP00000361543:E172G|.	E|X	-|-	2|3	0|0	NUP62CL|NUP62CL	106283073|106283073	1.000000|1.000000	0.71417|0.71417	0.001000|0.001000	0.08648|0.08648	0.195000|0.195000	0.23768|0.23768	3.221000|3.221000	0.51215|0.51215	-0.079000|-0.079000	0.12707|0.12707	-0.761000|-0.761000	0.03458|0.03458	GAG|TGA	.	.		0.433	NUP62CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057828.1	NM_017681		C	106396417	T	C	106396417	3	2	282	1	0	0	0	0	1	0	0	0	10778	1551	54	2	47	2	NUP62CL	23	106396417	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3554794	106396417	48874143	1385	41619										
NUP62CL	54830	hgsc.bcm.edu	37	chrX	106410964	106410964	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agtaaagccactggtgattgTggtagtagtgttggtggtga	16	3	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:106410964T>C	ENST00000372466.4	-	4	360	c.109A>G	c.(109-111)Aca>Gca	p.T37A	NUP62CL_ENST00000372461.3_Missense_Mutation_p.T37A	NM_017681.2	NP_060151.2	Q9H1M0	N62CL_HUMAN	nucleoporin 62kDa C-terminal like	37	Thr-rich.				protein transport (GO:0015031)	nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			lung(4)	4						Ctggtgattgtggtagtagtg	0.363																																					p.T37A		Atlas-SNP	.											.	NUP62CL	10	.	0			c.A109G						.						251	213	226					X																	106410964		2203	4300	6503	SO:0001583	missense	54830	exon4			TGATTGTGGTAGT	AK000137	CCDS14527.1	Xq22.3	2008-02-05			ENSG00000198088	ENSG00000198088			25960	protein-coding gene	gene with protein product						12477932	Standard	NM_017681		Approved	FLJ20130	uc004ena.3	Q9H1M0	OTTHUMG00000022159	ENST00000372466.4:c.109A>G	chrX.hg19:g.106410964T>C	ENSP00000361544:p.Thr37Ala	142.0	0.0		96.0	4.0	NM_017681	D3DUX4|Q8WVL6|Q9NXP2	Missense_Mutation	SNP	ENST00000372466.4	hg19	CCDS14527.1	.	.	.	.	.	.	.	.	.	.	T	2.105	-0.405143	0.04832	.	.	ENSG00000198088	ENST00000372466;ENST00000372465;ENST00000372461;ENST00000421752	T;T;T	0.59083	0.9;0.29;0.49	3.84	3.84	0.44239	Nucleoporin, NSP1-like, C-terminal (1);	0.756327	0.12760	N	0.441437	T	0.50803	0.1637	N	0.24115	0.695	0.09310	N	1	P	0.52842	0.956	P	0.50659	0.647	T	0.39522	-0.9610	10	0.87932	D	0	-0.9739	8.1143	0.30933	0.0:0.0:0.0:1.0	.	37	Q9H1M0	N62CL_HUMAN	A	37	ENSP00000361544:T37A;ENSP00000361539:T37A;ENSP00000405906:T37A	ENSP00000361539:T37A	T	-	1	0	NUP62CL	106297620	0.760000	0.28428	0.059000	0.19551	0.429000	0.31625	2.945000	0.49043	1.732000	0.51606	0.486000	0.48141	ACA	.	.		0.363	NUP62CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057828.1	NM_017681		C	106410964	T	C	106410964	3	2	282	1	0	0	0	0	1	0	0	0	10778	1696	59	2	465	2	NUP62CL	23	106410964	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	14547	106410964	48859596	1386	41620										
MID2	11043	hgsc.bcm.edu	37	chrX	107084012	107084012	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgcctagagttgtttgaagaCccccttctgctcccttgtgc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:107084012delC	ENST00000262843.6	+	2	665	c.117delC	c.(115-117)gacfs	p.D39fs	MID2_ENST00000443968.2_Frame_Shift_Del_p.D39fs	NM_012216.3|NM_052817.2	NP_036348.2|NP_438112.2	Q9UJV3	TRIM1_HUMAN	midline 2	39					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein localization to microtubule (GO:0035372)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	ligase activity (GO:0016874)|microtubule binding (GO:0008017)|phosphoprotein binding (GO:0051219)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)|ovary(1)|prostate(2)	19						TGTTTGAAGACCCCCTTCTGC	0.488																																					p.D39fs		Atlas-INDEL	.											.	MID2	122	.	0			c.116delA						.						188	178	182					X																	107084012		2203	4300	6503	SO:0001589	frameshift_variant	11043	exon2			.		CCDS14532.2, CCDS14533.2	Xq22.1-q22.2	2013-02-11			ENSG00000080561	ENSG00000080561		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Fibronectin type III domain containing"	7096	protein-coding gene	gene with protein product		300204				10400986	Standard	NM_012216		Approved	FXY2, TRIM1, RNF60	uc004enl.3	Q9UJV3	OTTHUMG00000022171	ENST00000262843.6:c.117delC	chrX.hg19:g.107084012delC	ENSP00000262843:p.Asp39fs	246.0	0.0		158.0	10.0	NM_012216	A6NEL8|A6PVI5|Q5JYF5|Q8WWK1|Q9UJR9	Frame_Shift_Del	DEL	ENST00000262843.6	hg19	CCDS14532.2																																																																																			.	.		0.488	MID2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057852.2	NM_012216		-	107084012	C	-	107084012	7	5	282	1	0	1	0	1	0	0	0	0	9587	506	18	0	123	0	MID2	23	107084012	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	673048	107084012	48186548	1387	41621										
CAPN6	827	hgsc.bcm.edu	37	chrX	110496327	110496327	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tccgttaatggtgggcaacaAgtcatcaatcaccacttcag	8	11	4	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:110496327A>G	ENST00000324068.1	-	4	582	c.415T>C	c.(415-417)Ttg>Ctg	p.L139L	CAPN6_ENST00000541758.1_5'UTR	NM_014289.3	NP_055104.2	Q9Y6Q1	CAN6_HUMAN	calpain 6	139	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				microtubule bundle formation (GO:0001578)|proteolysis (GO:0006508)|regulation of cytoskeleton organization (GO:0051493)	perinuclear region of cytoplasm (GO:0048471)|spindle microtubule (GO:0005876)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|microtubule binding (GO:0008017)			cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(25)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	47						GTGGGCAACAAGTCATCAATC	0.428																																					p.L139L		Atlas-SNP	.											.	CAPN6	120	.	0			c.T415C						.						155	131	139					X																	110496327		2203	4300	6503	SO:0001819	synonymous_variant	827	exon4			GCAACAAGTCATC	AF029232	CCDS14555.1	Xq23	2008-07-29			ENSG00000077274	ENSG00000077274			1483	protein-coding gene	gene with protein product		300146				9503024, 9339374	Standard	NM_014289		Approved	CAPNX, CalpM, CANPX	uc004epc.2	Q9Y6Q1	OTTHUMG00000022203	ENST00000324068.1:c.415T>C	chrX.hg19:g.110496327A>G		111.0	0.0		86.0	4.0	NM_014289	D3DUY7|Q9UEQ1|Q9UJA8	Silent	SNP	ENST00000324068.1	hg19	CCDS14555.1																																																																																			.	.		0.428	CAPN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057922.1			G	110496327	A	G	110496327	2	3	282	1	0	0	0	0	0	0	0	1	2632	69	3	2		2	CAPN6	23	110496327	Silent	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	3412315	110496327	44774233	1388	41622										
IL13RA2	3598	hgsc.bcm.edu	37	chrX	114248379	114248379	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agaagtacacctatgccaggTttccaagaacagagtaaata							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:114248379delT	ENST00000371936.1	-	6	723	c.474delA	c.(472-474)aaafs	p.K158fs	IL13RA2_ENST00000468224.1_5'Flank|IL13RA2_ENST00000243213.1_Frame_Shift_Del_p.K158fs			Q14627	I13R2_HUMAN	interleukin 13 receptor, alpha 2	158	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	cytokine receptor activity (GO:0004896)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(6)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	23						CTATGCCAGGTTTCCAAGAAC	0.308																																					p.P159fs		Atlas-INDEL	.											.	IL13RA2	66	.	0			c.475delC						.						76	68	71					X																	114248379		2203	4299	6502	SO:0001589	frameshift_variant	3598	exon5			.	X95302	CCDS14565.1	Xq23	2014-01-21			ENSG00000123496	ENSG00000123496		"Interleukins and interleukin receptors", "CD molecules"	5975	protein-coding gene	gene with protein product	"cancer/testis antigen 19"	300130				8663118, 9083087	Standard	NM_000640		Approved	IL-13R, IL13BP, CD213a2, CT19	uc004epx.3	Q14627	OTTHUMG00000022229	ENST00000371936.1:c.474delA	chrX.hg19:g.114248379delT	ENSP00000361004:p.Lys158fs	275.0	0.0		199.0	12.0	NM_000640	A8K7E2|O00667	Frame_Shift_Del	DEL	ENST00000371936.1	hg19	CCDS14565.1																																																																																			.	.		0.308	IL13RA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057966.1	NM_000640		-	114248379	T	-	114248379	7	5	282	1	0	1	0	1	0	0	0	0	7639	1722	60	0	692	0	IL13RA2	23	114248379	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3752052	114248379	41022181	1389	41623										
SLC6A14	11254	hgsc.bcm.edu	37	chrX	115577930	115577930	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gtatattttacagctcttttCccctatgtggtcctactcat							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:115577930delC	ENST00000371900.4	+	7	901	c.813delC	c.(811-813)ttcfs	p.F271fs		NM_007231.3	NP_009162.1	Q9UN76	S6A14_HUMAN	solute carrier family 6 (amino acid transporter), member 14	271					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)|transport (GO:0006810)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	amino acid transmembrane transporter activity (GO:0015171)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	23					L-Proline(DB00172)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	CAGCTCTTTTCCCCTATGTGG	0.338																																					p.F271fs		Atlas-INDEL	.											.	SLC6A14	56	.	0			c.812delT						.						105	104	104					X																	115577930		2203	4299	6502	SO:0001589	frameshift_variant	11254	exon7			.	AF151978	CCDS14570.1	Xq23	2013-05-22			ENSG00000087916	ENSG00000268104		"Solute carriers"	11047	protein-coding gene	gene with protein product		300444	"solute carrier family 6 (neurotransmitter transporter), member 14"			10446133	Standard	NM_007231		Approved		uc004eqi.3	Q9UN76	OTTHUMG00000022245	ENST00000371900.4:c.813delC	chrX.hg19:g.115577930delC	ENSP00000360967:p.Phe271fs	205.0	0.0		160.0	10.0	NM_007231	Q5H942	Frame_Shift_Del	DEL	ENST00000371900.4	hg19	CCDS14570.1																																																																																			.	.		0.338	SLC6A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057986.1			-	115577930	C	-	115577930	7	5	282	1	0	1	0	1	0	0	0	0	14692	854	30	0	839	0	SLC6A14	23	115577930	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	1329551	115577930	39692630	1390	41624										
KIAA1210	57481	hgsc.bcm.edu	37	chrX	118221022	118221022	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gaaccaattgtcagaattgcTctcaaaaacagatcgcctag	7	10	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:118221022T>C	ENST00000402510.2	-	11	4170	c.4171A>G	c.(4171-4173)Agc>Ggc	p.S1391G		NM_020721.1	NP_065772.1	Q9ULL0	K1210_HUMAN	KIAA1210	1391										breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(31)|ovary(4)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	64						TCAGAATTGCTCTCAAAAACA	0.453																																					p.S1391G		Atlas-SNP	.											.	KIAA1210	171	.	0			c.A4171G						.						126	122	124					X																	118221022		1908	4113	6021	SO:0001583	missense	57481	exon11			AATTGCTCTCAAA	AB033036	CCDS48156.1	Xq24	2012-10-04			ENSG00000250423	ENSG00000250423			29218	protein-coding gene	gene with protein product						10574462	Standard	NM_020721		Approved		uc004era.4	Q9ULL0	OTTHUMG00000162980	ENST00000402510.2:c.4171A>G	chrX.hg19:g.118221022T>C	ENSP00000384670:p.Ser1391Gly	79.0	0.0		71.0	4.0	NM_020721	B7ZCI8|Q5JPN4	Missense_Mutation	SNP	ENST00000402510.2	hg19	CCDS48156.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	6.643|6.643	0.487077|0.487077	0.12641|0.12641	.|.	.|.	ENSG00000248857|ENSG00000250423	ENST00000440399|ENST00000402510	.|T	.|0.10763	.|2.84	4.18|4.18	-1.1|-1.1	0.09872|0.09872	.|.	.|.	.|.	.|.	.|.	T|T	0.05227|0.05227	0.0139|0.0139	N|N	0.12182|0.12182	0.205|0.205	0.09310|0.09310	N|N	1|1	.|B	.|0.11235	.|0.004	.|B	.|0.11329	.|0.006	T|T	0.45644|0.45644	-0.9247|-0.9247	6|8	0.62326|.	D|.	0.03|.	.|.	7.3501|7.3501	0.26686|0.26686	0.0:0.4538:0.0:0.5462|0.0:0.4538:0.0:0.5462	.|.	.|1391	.|Q9ULL0	.|K1210_HUMAN	G|G	797|1391	.|ENSP00000384670:S1391G	ENSP00000393550:E797G|.	E|S	-|-	2|1	0|0	KIAA1210|RP13-347D8.6	118105050|118105050	0.001000|0.001000	0.12720|0.12720	0.001000|0.001000	0.08648|0.08648	0.008000|0.008000	0.06430|0.06430	-0.225000|-0.225000	0.09151|0.09151	-0.307000|-0.307000	0.08804|0.08804	0.417000|0.417000	0.27973|0.27973	GAG|AGC	.	.		0.453	KIAA1210-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371251.2	NM_020721		C	118221022	T	C	118221022	3	2	282	1	0	0	0	0	1	0	0	0	8223	1551	54	2	974	2	KIAA1210	23	118221022	Missense_Mutation	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	2643092	118221022	37049538	1391	41625										
RHOXF2	727940	hgsc.bcm.edu	37	chrX	119210952	119210952	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tgcgcgttgccaggctccagCcccccgacggcgccctgtgg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:119210952delC	ENST00000371402.2	-	2	570	c.381delG	c.(379-381)gggfs	p.G127fs	RP4-755D9.1_ENST00000553843.1_RNA	NM_001099685.1	NP_001093155.1	P0C7M4	RHF2B_HUMAN	Rhox homeobox family, member 2B	127					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			kidney(1)|large_intestine(2)|skin(3)|upper_aerodigestive_tract(1)	7						CAGGCTCCAGCCCCCCGACGG	0.657																																					p.L128fs		Atlas-INDEL	.											.	RHOXF2	19	.	0			c.382delC						.						5	6	6					X																	119210952		1460	3040	4500	SO:0001589	frameshift_variant	84528	exon2			.		CCDS43985.1	Xq24	2011-06-20			ENSG00000203989	ENSG00000203989		"Homeoboxes / PRD class"	33519	protein-coding gene	gene with protein product							Standard	NM_001099685		Approved		uc004esj.4	P0C7M4	OTTHUMG00000022288	ENST00000371402.2:c.381delG	chrX.hg19:g.119210952delC	ENSP00000360455:p.Gly127fs	214.0	0.0		174.0	11.0	NM_032498		Frame_Shift_Del	DEL	ENST00000371402.2	hg19	CCDS43985.1																																																																																			.	.		0.657	RHOXF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058081.2	NM_001099685		-	119210952	C	-	119210952	7	5	282	1	0	1	0	1	0	0	0	0	13363	726	26	0	497	0	RHOXF2	23	119210952	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	989930	119210952	36059608	1392	41626										
THOC2	57187	hgsc.bcm.edu	37	chrX	122802060	122802060	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ttctttctctcgctcatccaTtttttcagaagacaacacaa							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:122802060delT	ENST00000245838.8	-	10	998	c.967delA	c.(967-969)atgfs	p.M323fs	THOC2_ENST00000491737.1_Frame_Shift_Del_p.M208fs|THOC2_ENST00000355725.4_Frame_Shift_Del_p.M323fs	NM_001081550.1	NP_001075019.1	Q8NI27	THOC2_HUMAN	THO complex 2	323					mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						cgctcatccattttttcAGAA	0.343																																					p.M323fs		Atlas-INDEL	.											.	THOC2	310	.	0			c.968delT						.						186	166	172					X																	122802060		1819	4070	5889	SO:0001589	frameshift_variant	57187	exon10			.	AF441770	CCDS43988.1	Xq25-q26.3	2013-02-11	2004-08-09		ENSG00000125676	ENSG00000125676		"THO complex subunits"	19073	protein-coding gene	gene with protein product		300395	"chromosome X open reading frame 3"	CXorf3		11979277	Standard	NM_001081550		Approved	THO2, dJ506G2.1	uc004etu.3	Q8NI27	OTTHUMG00000022334	ENST00000245838.8:c.967delA	chrX.hg19:g.122802060delT	ENSP00000245838:p.Met323fs	220.0	0.0		163.0	10.0	NM_001081550	A6NM50|Q5JZ12|Q6IN92|Q9H8I6	Frame_Shift_Del	DEL	ENST00000245838.8	hg19	CCDS43988.1																																																																																			.	.		0.343	THOC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058153.3			-	122802060	T	-	122802060	7	5	282	1	0	1	0	1	0	0	0	0	15880	1493	52	0	3930	0	THOC2	23	122802060	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	3591108	122802060	32468500	1393	41627										
STAG2	10735	hgsc.bcm.edu	37	chrX	123195126	123195126	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	catgtgggactgtgctactgAgctgctgaaagactgggaat	14	7	0	3			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:123195126A>G	ENST00000371160.1	+	16	1759	c.1469A>G	c.(1468-1470)gAg>gGg	p.E490G	STAG2_ENST00000354548.5_Missense_Mutation_p.E421G|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Missense_Mutation_p.E490G|STAG2_ENST00000371157.3_Missense_Mutation_p.E490G|STAG2_ENST00000371144.3_Missense_Mutation_p.E490G|STAG2_ENST00000371145.3_Missense_Mutation_p.E490G	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	490					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						TGTGCTACTGAGCTGCTGAAA	0.383																																					p.E490G		Atlas-SNP	.											.	STAG2	309	.	0			c.A1469G						.						205	174	185					X																	123195126		2203	4300	6503	SO:0001583	missense	10735	exon16			CTACTGAGCTGCT	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.1469A>G	chrX.hg19:g.123195126A>G	ENSP00000360202:p.Glu490Gly	114.0	0.0		87.0	5.0	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Missense_Mutation	SNP	ENST00000371160.1	hg19	CCDS14607.1	.	.	.	.	.	.	.	.	.	.	A	17.57	3.423389	0.62733	.	.	ENSG00000101972	ENST00000218089;ENST00000455404;ENST00000354548;ENST00000371160;ENST00000371157;ENST00000371145;ENST00000371144	T;T;T;T;T;T;T	0.47869	1.8;0.83;1.41;1.4;1.4;1.8;1.4	5.28	5.28	0.74379	Armadillo-type fold (1);	0.049098	0.85682	D	0.000000	T	0.43853	0.1266	L	0.49455	1.56	0.58432	D	0.999999	B;B	0.21821	0.002;0.061	B;B	0.23150	0.004;0.044	T	0.30238	-0.9985	10	0.33141	T	0.24	-3.1734	14.4184	0.67165	1.0:0.0:0.0:0.0	.	490;490	Q8N3U4-2;Q8N3U4	.;STAG2_HUMAN	G	490;490;421;490;490;490;490	ENSP00000218089:E490G;ENSP00000397265:E490G;ENSP00000346555:E421G;ENSP00000360202:E490G;ENSP00000360199:E490G;ENSP00000360187:E490G;ENSP00000360186:E490G	ENSP00000218089:E490G	E	+	2	0	STAG2	123022807	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.283000	0.95860	1.853000	0.53794	0.441000	0.28932	GAG	.	.		0.383	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		G	123195126	A	G	123195126	3	3	282	1	0	0	0	0	1	0	0	0	15258	304	11	2	1523	2	STAG2	23	123195126	Missense_Mutation	SNP	A	TCGA-G3-A3CJ-01A-11D-A20W-10	393066	123195126	32075434	1394	41628										
SH2D1A	4068	hgsc.bcm.edu	37	chrX	123504064	123504064	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aaaagatatttccggaaaatAaaaaatctcatttcagcatt							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:123504064delA	ENST00000371139.4	+	3	539	c.240delA	c.(238-240)atafs	p.I80fs	STAG2_ENST00000469481.1_Intron|SH2D1A_ENST00000360027.4_Frame_Shift_Del_p.I80fs|SH2D1A_ENST00000491950.1_3'UTR|SH2D1A_ENST00000477673.2_Intron	NM_001114937.2|NM_002351.4	NP_001108409.1|NP_002342.1	O60880	SH21A_HUMAN	SH2 domain containing 1A	80	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|humoral immune response (GO:0006959)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)	SH3/SH2 adaptor activity (GO:0005070)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	10						TCCGGAAAATAAAAAATCTCA	0.368																																					p.I80fs		Atlas-INDEL	.											.	SH2D1A	23	.	0			c.239delT						.						104	103	103					X																	123504064		2203	4300	6503	SO:0001589	frameshift_variant	4068	exon3			.	AL023657	CCDS14608.1, CCDS48162.1	Xq25	2014-09-17	2010-04-21		ENSG00000183918	ENSG00000183918		"SH2 domain containing"	10820	protein-coding gene	gene with protein product	"Duncan's disease"	300490	"lymphoproliferative syndrome", "SH2 domain protein 1A"	IMD5, LYP		9771704, 9774102	Standard	NM_001114937		Approved	XLP, MTCP1, DSHP, XLPD, EBVS, SAP	uc004euf.4	O60880	OTTHUMG00000022344	ENST00000371139.4:c.240delA	chrX.hg19:g.123504064delA	ENSP00000360181:p.Ile80fs	283.0	0.0		209.0	15.0	NM_001114937	A8MSW0|O95383|O95384|O95385|O95386|Q6FGS6|Q9UNR0	Frame_Shift_Del	DEL	ENST00000371139.4	hg19	CCDS14608.1																																																																																			.	.		0.368	SH2D1A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058174.1	NM_002351		-	123504064	A	-	123504064	7	5	282	1	0	1	0	1	0	0	0	0	14245	352	13	0	250	0	SH2D1A	23	123504064	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	308938	123504064	31766496	1395	41629										
FHL1	2273	hgsc.bcm.edu	37	chrX	135288588	135288588	+	5'UTR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ccctccagctacaaggtgggCaccatggcggagaagtttga	13	11	0	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:135288588C>T	ENST00000345434.3	+	0	78				FHL1_ENST00000477080.1_3'UTR|FHL1_ENST00000535737.1_5'UTR|FHL1_ENST00000370676.3_Silent_p.G15G|FHL1_ENST00000394153.2_5'UTR|FHL1_ENST00000543669.1_5'UTR|FHL1_ENST00000394155.2_5'UTR|FHL1_ENST00000539015.1_Silent_p.G28G|FHL1_ENST00000370690.3_5'UTR|FHL1_ENST00000370683.1_Silent_p.G15G			Q13642	FHL1_HUMAN	four and a half LIM domains 1						cell differentiation (GO:0030154)|muscle organ development (GO:0007517)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of G2/M transition of mitotic cell cycle (GO:0010972)|organ morphogenesis (GO:0009887)|positive regulation of potassium ion transport (GO:0043268)|regulation of membrane depolarization (GO:0003254)|regulation of potassium ion transmembrane transporter activity (GO:1901016)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ion channel binding (GO:0044325)|zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	19	Acute lymphoblastic leukemia(192;0.000127)					ACAAGGTGGGCACCATGGCGG	0.582																																					p.G28G		Atlas-SNP	.											.	FHL1	114	.	0			c.C84T						.						121	111	115					X																	135288588		2203	4300	6503	SO:0001623	5_prime_UTR_variant	2273	exon2			GGTGGGCACCATG	U60115	CCDS14655.1, CCDS55505.1, CCDS55506.1, CCDS55507.1, CCDS76036.1	Xq26.3	2014-09-17			ENSG00000022267	ENSG00000022267			3702	protein-coding gene	gene with protein product	"Four-and-a-half LIM domains 1", "LIM protein SLIMMER"	300163				8753811, 9714789	Standard	NM_001449		Approved	SLIM1, KYO-T, bA535K18.1, FHL1B, XMPMA, FLH1A, MGC111107	uc004ezo.3	Q13642	OTTHUMG00000022504	ENST00000345434.3:c.-4C>T	chrX.hg19:g.135288588C>T		161.0	0.0		119.0	7.0	NM_001159701	B7Z5T4|B7Z793|O95212|Q13230|Q13645|Q5JXI7|Q5M7Y6|Q6IB30|Q9NZ40|Q9UKZ8|Q9Y630	Silent	SNP	ENST00000345434.3	hg19	CCDS55507.1																																																																																			.	.		0.582	FHL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058461.1	NM_001449		T	135288588	C	T	135288588	1	4	282	0	1	0	0	0	0	0	0	0	5886	697	25	3		3	FHL1	23	135288588	5'UTR	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10	11784524	135288588	19981972	1396	41630										
BCAP31	10134	hgsc.bcm.edu	37	chrX	152967544	152967544	+	Frame_Shift_Del	DEL	T	T	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tccgcatggccagaacctggTtttcagctttctctagttct							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:152967544delT	ENST00000345046.6	-	7	1027	c.620delA	c.(619-621)aacfs	p.N207fs	BCAP31_ENST00000458587.2_Frame_Shift_Del_p.N274fs|BCAP31_ENST00000441714.1_Frame_Shift_Del_p.N207fs	NM_001256447.1	NP_001243376.1	P51572	BAP31_HUMAN	B-cell receptor-associated protein 31	207					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|protein localization to endoplasmic reticulum exit site (GO:0070973)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lipid particle (GO:0005811)|membrane (GO:0016020)				endometrium(2)|large_intestine(2)|lung(2)|prostate(1)	7	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CAGAACCTGGTTTTCAGCTTT	0.502																																					p.N274fs		Atlas-INDEL	.											.	BCAP31	33	.	0			c.822delC						.						43	38	39					X																	152967544		2203	4297	6500	SO:0001589	frameshift_variant	10134	exon7			.	X81109	CCDS14727.1, CCDS48191.1	Xq28	2005-10-11			ENSG00000185825	ENSG00000185825			16695	protein-coding gene	gene with protein product		300398					Standard	NM_001139441		Approved	DXS1357E, BAP31, 6C6-Ag, CDM	uc011mza.1	P51572	OTTHUMG00000024218	ENST00000345046.6:c.620delA	chrX.hg19:g.152967544delT	ENSP00000343458:p.Asn207fs	214.0	0.0		145.0	10.0	NM_001139457	B3KQ79|D3DWV5|Q13836|Q96CF0	Frame_Shift_Del	DEL	ENST00000345046.6	hg19	CCDS14727.1																																																																																			.	.		0.502	BCAP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061071.1	NM_005745		-	152967544	T	-	152967544	7	5	282	1	0	1	0	1	0	0	0	0	1347	1725	60	0	128	0	BCAP31	23	152967544	Frame_Shift_Del	DEL	T	TCGA-G3-A3CJ-01A-11D-A20W-10	17678956	152967544	2303016	1397	41631										
PDZD4	57595	hgsc.bcm.edu	37	chrX	153073936	153073936	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	caggtcgtgacaggagctgtCcccccggaggcgggggctgc							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:153073936delC	ENST00000164640.4	-	2	366	c.175delG	c.(175-177)gacfs	p.D59fs	PDZD4_ENST00000393758.2_5'UTR|PDZD4_ENST00000475140.1_5'UTR|PDZD4_ENST00000544474.1_Intron	NM_032512.2	NP_115901.2	Q76G19	PDZD4_HUMAN	PDZ domain containing 4	59						cytoplasm (GO:0005737)				breast(3)|cervix(1)|endometrium(5)|lung(13)|skin(1)	23	all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CAGGAGCTGTCCCCCCGGAGG	0.657																																					p.D59fs		Atlas-INDEL	.											.	PDZD4	67	.	0			c.176delA						.						44	34	38					X																	153073936		2202	4296	6498	SO:0001589	frameshift_variant	57595	exon2			.	AK091444	CCDS14732.1	Xq28	2008-02-05		2006-01-24	ENSG00000067840	ENSG00000067840			21167	protein-coding gene	gene with protein product		300634		PDZK4		10819331, 15077175	Standard	NM_032512		Approved	KIAA1444, LU1, FLJ34125, PDZRN4L	uc004fiz.1	Q76G19	OTTHUMG00000024209	ENST00000164640.4:c.175delG	chrX.hg19:g.153073936delC	ENSP00000164640:p.Asp59fs	241.0	0.0		162.0	10.0	NM_032512	B3KXB1|B7ZKY3|Q8NB75|Q9BUH9|Q9P284	Frame_Shift_Del	DEL	ENST00000164640.4	hg19	CCDS14732.1																																																																																			.	.		0.657	PDZD4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061013.3	NM_032512		-	153073936	C	-	153073936	7	5	282	1	0	1	0	1	0	0	0	0	11712	855	30	0	2162	0	PDZD4	23	153073936	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	106392	153073936	2196624	1398	41632										
L1CAM	3897	hgsc.bcm.edu	37	chrX	153132510	153132510	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	tcagcccagggactctcaccTtccacgtgatgaccatattg	8	14	2	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:153132510T>C	ENST00000370060.1	-	18	2396	c.2207A>G	c.(2206-2208)aAg>aGg	p.K736R	L1CAM_ENST00000361981.3_Splice_Site_p.K731R|L1CAM_ENST00000538883.1_Splice_Site_p.K738R|L1CAM_ENST00000361699.4_Splice_Site_p.K736R|L1CAM_ENST00000543994.1_Splice_Site_p.K738R|L1CAM_ENST00000370055.1_Splice_Site_p.K731R|L1CAM_ENST00000370057.3_Splice_Site_p.K736R	NM_001278116.1	NP_001265045.1	P32004	L1CAM_HUMAN	L1 cell adhesion molecule	736	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cell-cell adhesion mediated by integrin (GO:0033631)|chemotaxis (GO:0006935)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|homotypic cell-cell adhesion (GO:0034109)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|nervous system development (GO:0007399)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	sialic acid binding (GO:0033691)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|liver(1)|lung(31)|ovary(13)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	81	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GACTCTCACCTTCCACGTGAT	0.542																																					p.K736R		Atlas-SNP	.											.	L1CAM	189	.	0			c.A2207G						.						336	270	292					X																	153132510		2203	4300	6503	SO:0001630	splice_region_variant	3897	exon17			CTCACCTTCCACG	M74387	CCDS14733.1, CCDS14734.1, CCDS48192.1	Xq28	2014-09-17	2003-04-07		ENSG00000198910	ENSG00000198910		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	6470	protein-coding gene	gene with protein product		308840	"antigen identified by monoclonal antibody R1"	HSAS1, SPG1, HSAS, MASA, MIC5, S10			Standard	NM_001278116		Approved	CD171	uc031tks.1	P32004	OTTHUMG00000024221	ENST00000370060.1:c.2208+1A>G	chrX.hg19:g.153132510T>C		202.0	0.0		157.0	7.0	NM_000425	A0AV65|A4ZYW4|B2RMU7|G3XAF4|Q8TA87	Missense_Mutation	SNP	ENST00000370060.1	hg19	CCDS14733.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.11|16.11	3.029383|3.029383	0.54790|0.54790	.|.	.|.	ENSG00000198910|ENSG00000198910	ENST00000370060;ENST00000543994;ENST00000370057;ENST00000538883;ENST00000361981;ENST00000370055;ENST00000361699|ENST00000455590	T;T;T;T;T;T;T|.	0.58358|.	0.34;0.34;0.34;0.34;0.34;0.34;0.34|.	5.77|5.77	5.77|5.77	0.91146|0.91146	Fibronectin, type III (4);Immunoglobulin-like fold (1);|.	0.080367|.	0.50627|.	D|.	0.000102|.	T|T	0.63070|0.63070	0.2480|0.2480	L|L	0.58302|0.58302	1.8|1.8	0.58432|0.58432	D|D	0.999993|0.999993	P;P;P|.	0.41710|.	0.717;0.563;0.76|.	B;B;B|.	0.44133|.	0.315;0.233;0.442|.	T|T	0.62590|0.62590	-0.6822|-0.6822	10|5	0.46703|.	T|.	0.11|.	.|.	10.4958|10.4958	0.44777|0.44777	0.0:0.0:0.1602:0.8397|0.0:0.0:0.1602:0.8397	.|.	731;736;736|.	G3XAF4;P32004-2;P32004|.	.;.;L1CAM_HUMAN|.	R|G	736;738;736;738;731;731;736|157	ENSP00000359077:K736R;ENSP00000438430:K738R;ENSP00000359074:K736R;ENSP00000439645:K738R;ENSP00000354712:K731R;ENSP00000359072:K731R;ENSP00000355380:K736R|.	ENSP00000355380:K736R|.	K|S	-|-	2|1	0|0	L1CAM|L1CAM	152785704|152785704	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.233000|0.233000	0.25261|0.25261	3.813000|3.813000	0.55636|0.55636	1.941000|1.941000	0.56285|0.56285	0.430000|0.430000	0.28490|0.28490	AAG|AGC	.	.		0.542	L1CAM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061094.2	NM_024003	Missense_Mutation	C	153132510	T	C	153132510	5	2	282	1	0	0	0	0	0	0	1	0	8597	1623	56	2	1614	2	L1CAM	23	153132510	Splice_Site	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	58574	153132510	2138050	1399	41633										
CTAG2	30848	hgsc.bcm.edu	37	chrX	153880814	153880814	+	Frame_Shift_Del	DEL	C	C	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	ggtgaagtccttcagaaccgCccctggtcgggggagaggtg							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:153880814delC	ENST00000247306.4	-	2	424	c.361delG	c.(361-363)gcgfs	p.A121fs	CTAG2_ENST00000369585.3_Frame_Shift_Del_p.A121fs	NM_020994.3	NP_066274.2	O75638	CTAG2_HUMAN	cancer/testis antigen 2	121						centrosome (GO:0005813)				central_nervous_system(1)|endometrium(1)|lung(6)|ovary(1)|pancreas(1)	10	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TTCAGAACCGCCCCTGGTCGG	0.647																																					p.A121fs		Atlas-INDEL	.											.	CTAG2	88	.	0			c.362delC						.						51	50	50					X																	153880814		2203	4297	6500	SO:0001589	frameshift_variant	30848	exon2			.	AJ012833	CCDS14759.1, CCDS35455.1	Xq28	2009-08-18			ENSG00000126890	ENSG00000126890			2492	protein-coding gene	gene with protein product	"CTL-recognized antigen on melanoma", "LAGE-1a protein", "cancer/testis antigen family 6, member 2a", "cancer/testis antigen family 6, member 2b"	300396				9626360, 10399963	Standard	NM_020994		Approved	LAGE-1, CAMEL, LAGE1, ESO2, MGC3803, MGC138724, CT6.2a, CT6.2b, LAGE-1a, LAGE-1b	uc004fmi.2	O75638	OTTHUMG00000024239	ENST00000247306.4:c.361delG	chrX.hg19:g.153880814delC	ENSP00000247306:p.Ala121fs	139.0	0.0		110.0	10.0	NM_020994	O75637|Q0VIL6|Q14CD6|Q2Z1N4|Q9BU80|Q9UJ89|Q9Y479	Frame_Shift_Del	DEL	ENST00000247306.4	hg19	CCDS14759.1																																																																																			.	.		0.647	CTAG2-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000061176.1	NM_020994		-	153880814	C	-	153880814	7	5	282	1	0	1	0	1	0	0	0	0	3993	739	26	0	414	0	CTAG2	23	153880814	Frame_Shift_Del	DEL	C	TCGA-G3-A3CJ-01A-11D-A20W-10	748304	153880814	1389746	1400	41634										
F8A1	474384	hgsc.bcm.edu	37	chrX	154687164	154687164	+	Frame_Shift_Del	DEL	G	G	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	gatcagactccctgtcctgaGggggagatggtttcttgcag							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:154687164delG	ENST00000369445.2	-	1	1112	c.1098delC	c.(1096-1098)cccfs	p.P366fs	MIR1184-3_ENST00000408676.1_RNA	NM_001007524.1	NP_001007525.1	P23610	F8I2_HUMAN	coagulation factor VIII-associated 3	366						nucleus (GO:0005634)						all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					CCTGTCCTGAGGGGGAGATGG	0.537																																					p.S367fs		Atlas-INDEL	.											.	.	.	.	0			c.1099delT						.						0	1	1					X																	154687164		0	2	2	SO:0001589	frameshift_variant	474383	exon1			.		CCDS35463.1	Xq28	2011-04-13	2011-04-13		ENSG00000185990	ENSG00000277150			31850	protein-coding gene	gene with protein product			"coagulation factor VIII-associated (intronic transcript) 3"				Standard	NM_001007524		Approved			P23610	OTTHUMG00000034289	ENST00000369445.2:c.1098delC	chrX.hg19:g.154687164delG	ENSP00000358454:p.Pro366fs	488.0	0.0		388.0	28.0	NM_001007523	Q5HY66|Q8IXP3	Frame_Shift_Del	DEL	ENST00000369445.2	hg19	CCDS35463.1																																																																																			.	.		0.537	F8A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082833.1	NM_001007524		-	154687164	G	-	154687164	7	5	282	1	0	1	0	1	0	0	0	0	5353	987	35	0	21	0	F8A1	23	154687164	Frame_Shift_Del	DEL	G	TCGA-G3-A3CJ-01A-11D-A20W-10	806350	154687164	583396	1401	41635										
ZFY	7544	hgsc.bcm.edu	37	chrY	2846064	2846064	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	agtctgctggccttggcagaCtggctaaacagaaaccaaag	11	10	1	2			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrY:2846064C>T	ENST00000155093.3	+	7	1486	c.1165C>T	c.(1165-1167)Ctg>Ttg	p.L389L	ZFY_ENST00000383052.1_Silent_p.L389L|ZFY-AS1_ENST00000417305.1_RNA|ZFY_ENST00000431102.1_Silent_p.L198L|ZFY_ENST00000449237.1_Silent_p.L312L|ZFY_ENST00000478783.1_3'UTR	NM_003411.3	NP_003402.2	P08048	ZFY_HUMAN	zinc finger protein, Y-linked	389					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			biliary_tract(1)|kidney(3)|large_intestine(1)|lung(3)	8						CCTTGGCAGACTGGCTAAACA	0.443																																					p.L389L		Atlas-SNP	.											.	ZFY	20	.	0			c.C1165T						.																																			SO:0001819	synonymous_variant	7544	exon7			GGCAGACTGGCTA	L10393	CCDS14774.1, CCDS48200.1, CCDS48201.1	Yp11.3	2013-01-08			ENSG00000067646	ENSG00000067646		"Zinc fingers, C2H2-type"	12870	protein-coding gene	gene with protein product		490000				2497060	Standard	NM_001145275		Approved	ZNF911	uc004fqj.3	P08048	OTTHUMG00000036159	ENST00000155093.3:c.1165C>T	chrY.hg19:g.2846064C>T		152.0	0.0		99.0	4.0	NM_003411	B4DVF7|Q14021|Q15558|Q1RME9|Q24JR0|Q96TF3	Silent	SNP	ENST00000155093.3	hg19	CCDS14774.1																																																																																			.	.		0.443	ZFY-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088063.1	NM_003411		T	2846064	C	T	2846064	2	4	282	1	0	0	0	0	0	0	0	1	17677	564	20	3		3	ZFY	24	2846064	Silent	SNP	C	TCGA-G3-A3CJ-01A-11D-A20W-10		2846064	56527502	1402	41636										
ZFY	7544	hgsc.bcm.edu	37	chrY	2847675	2847675	+	Frame_Shift_Del	DEL	A	A	-													0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	atgtggctgtccacaaaggtAaaaaaatgcaccaatgtaga							TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrY:2847675delA	ENST00000155093.3	+	8	2368	c.2047delA	c.(2047-2049)aaafs	p.K684fs	ZFY_ENST00000383052.1_Frame_Shift_Del_p.K684fs|ZFY-AS1_ENST00000417305.1_RNA|ZFY_ENST00000431102.1_Frame_Shift_Del_p.K493fs|ZFY_ENST00000449237.1_Frame_Shift_Del_p.K607fs	NM_003411.3	NP_003402.2	P08048	ZFY_HUMAN	zinc finger protein, Y-linked	684					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			biliary_tract(1)|kidney(3)|large_intestine(1)|lung(3)	8						CCACAAAGGTAAAAAAATGCA	0.398																																					p.G682fs		Atlas-INDEL	.											.	ZFY	20	.	0			c.2046delT						.						85	75	78					Y																	2847675		610	1971	2581	SO:0001589	frameshift_variant	7544	exon8			.	L10393	CCDS14774.1, CCDS48200.1, CCDS48201.1	Yp11.3	2013-01-08			ENSG00000067646	ENSG00000067646		"Zinc fingers, C2H2-type"	12870	protein-coding gene	gene with protein product		490000				2497060	Standard	NM_001145275		Approved	ZNF911	uc004fqj.3	P08048	OTTHUMG00000036159	ENST00000155093.3:c.2047delA	chrY.hg19:g.2847675delA	ENSP00000155093:p.Lys684fs	264.0	0.0		186.0	13.0	NM_003411	B4DVF7|Q14021|Q15558|Q1RME9|Q24JR0|Q96TF3	Frame_Shift_Del	DEL	ENST00000155093.3	hg19	CCDS14774.1																																																																																			.	.		0.398	ZFY-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088063.1	NM_003411		-	2847675	A	-	2847675	7	5	282	1	0	1	0	1	0	0	0	0	17677	363	13	0	2073	0	ZFY	24	2847675	Frame_Shift_Del	DEL	A	TCGA-G3-A3CJ-01A-11D-A20W-10	1611	2847675	56525891	1403	41637										
KDM5D	8284	hgsc.bcm.edu	37	chrY	21870223	21870223	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.005	7	1	0.619271473117263	0.353869413209865	0.70773882641973	0.0634674922600621	0.503688821553259	0	aatacctgcagctctagctgTctcagctcttccagccccac	6	17	3	0			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrY:21870223T>C	ENST00000317961.4	-	22	3439	c.3168A>G	c.(3166-3168)agA>agG	p.R1056R	KDM5D_ENST00000541639.1_Silent_p.R1087R|KDM5D_ENST00000382806.2_Silent_p.R999R	NM_004653.4	NP_004644.2	Q9BY66	KDM5D_HUMAN	lysine (K)-specific demethylase 5D	1056					histone H3-K4 demethylation (GO:0034720)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-K4 specific) (GO:0032453)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(9)|lung(6)|skin(1)	17					Vitamin C(DB00126)	GCTCTAGCTGTCTCAGCTCTT	0.547																																					p.R1087R		Atlas-SNP	.											.	KDM5D	40	.	0			c.A3261G						.						36	40	39					Y																	21870223		576	1907	2483	SO:0001819	synonymous_variant	8284	exon23			TAGCTGTCTCAGC	U52191	CCDS14794.1, CCDS55554.1, CCDS55555.1	Yq11	2013-01-28	2009-04-06	2009-04-06	ENSG00000012817	ENSG00000012817		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	11115	protein-coding gene	gene with protein product		426000	"Jumonji, AT rich interactive domain 1D (RBP2-like)", "Smcy homolog, Y-linked (mouse)", "jumonji, AT rich interactive domain 1D"	HYA, HY, SMCY, JARID1D		795123, 8841177	Standard	NM_001146705		Approved	KIAA0234	uc011naz.2	Q9BY66	OTTHUMG00000036508	ENST00000317961.4:c.3168A>G	chrY.hg19:g.21870223T>C		121.0	0.0		90.0	4.0	NM_001146705	A2RU19|A6H8V7|B7ZLX1|Q92509|Q92809|Q9HCU1	Silent	SNP	ENST00000317961.4	hg19	CCDS14794.1																																																																																			.	.		0.547	KDM5D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088790.1	NM_004653		C	21870223	T	C	21870223	2	2	282	1	0	0	0	0	0	0	0	1	8145	1664	58	2		2	KDM5D	24	21870223	Silent	SNP	T	TCGA-G3-A3CJ-01A-11D-A20W-10	19022548	21870223	37503343	1404	41638										
PRKCZ	5590	hgsc.bcm.edu	37	chr1	2103755	2103755	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	cacaggaaggcctgggccctGgtgacacaacgagcactttc	12	13	0	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr1:2103755G>T	ENST00000400921.2	+	10	1347	c.664G>T	c.(664-666)Ggt>Tgt	p.G222C	PRKCZ_ENST00000479263.1_3'UTR|PRKCZ_ENST00000400920.1_Missense_Mutation_p.G222C	NM_001033581.1	NP_001028753.1	Q05513	KPCZ_HUMAN	protein kinase C, zeta	405					actin cytoskeleton reorganization (GO:0031532)|activation of phospholipase D activity (GO:0031584)|activation of protein kinase B activity (GO:0032148)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|inflammatory response (GO:0006954)|insulin receptor signaling pathway (GO:0008286)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|membrane hyperpolarization (GO:0060081)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of apoptotic process (GO:0043066)|negative regulation of hydrolase activity (GO:0051346)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of protein complex assembly (GO:0031333)|neuron projection extension (GO:1990138)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glucose import (GO:0046326)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of interleukin-10 secretion (GO:2001181)|positive regulation of interleukin-13 secretion (GO:2000667)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 secretion (GO:2000664)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T-helper 2 cell cytokine production (GO:2000553)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|protein heterooligomerization (GO:0051291)|protein kinase C signaling (GO:0070528)|protein localization to plasma membrane (GO:0072659)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle transport along microtubule (GO:0047496)	apical cortex (GO:0045179)|apical plasma membrane (GO:0016324)|axon hillock (GO:0043203)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane raft (GO:0045121)|microtubule organizing center (GO:0005815)|myelin sheath abaxonal region (GO:0035748)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)	ATP binding (GO:0005524)|insulin receptor substrate binding (GO:0043560)|potassium channel regulator activity (GO:0015459)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(4)|endometrium(1)|large_intestine(5)|lung(5)|stomach(1)	18	all_cancers(77;0.000177)|all_epithelial(69;6.41e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.96e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.3e-23)|GBM - Glioblastoma multiforme(42;2.85e-08)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00294)|BRCA - Breast invasive adenocarcinoma(365;0.00493)|STAD - Stomach adenocarcinoma(132;0.00669)|KIRC - Kidney renal clear cell carcinoma(229;0.0411)|Lung(427;0.213)	Tamoxifen(DB00675)	CCTGGGCCCTGGTGACACAAC	0.642																																					p.G405C		Atlas-SNP	.											.	PRKCZ	84	.	0			c.G1213T						.						67	59	62					1																	2103755		2203	4300	6503	SO:0001583	missense	5590	exon13			GGCCCTGGTGACA	BC014270	CCDS37.1, CCDS41229.1, CCDS55563.1	1p36.33-p36.2	2009-07-10			ENSG00000067606	ENSG00000067606	2.7.11.1		9412	protein-coding gene	gene with protein product		176982					Standard	NM_001242874		Approved	PKC2	uc001aiq.3	Q05513	OTTHUMG00000001238	ENST00000400921.2:c.664G>T	chr1.hg19:g.2103755G>T	ENSP00000383712:p.Gly222Cys	124.0	0.0		104.0	25.0	NM_002744	A8K4N0|A8MU64|B7Z2J7|E9PCW2|Q15207|Q5SYT5|Q969S4	Missense_Mutation	SNP	ENST00000400921.2	hg19	CCDS41229.1	.	.	.	.	.	.	.	.	.	.	G	16.12	3.031664	0.54790	.	.	ENSG00000067606	ENST00000378567;ENST00000400921;ENST00000461106;ENST00000400920	T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23	5.21	5.21	0.72293	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.83635	0.5297	M	0.85777	2.775	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.998;0.998;0.999	D	0.86231	0.1637	10	0.87932	D	0	.	16.6546	0.85225	0.0:0.0:1.0:0.0	.	301;229;301;405	E9PCW2;B3KUN5;B7Z2J7;Q05513	.;.;.;KPCZ_HUMAN	C	405;222;301;222	ENSP00000367830:G405C;ENSP00000383712:G222C;ENSP00000426412:G301C;ENSP00000383711:G222C	ENSP00000367830:G405C	G	+	1	0	PRKCZ	2093615	1.000000	0.71417	0.131000	0.22000	0.005000	0.04900	8.822000	0.92013	2.599000	0.87857	0.650000	0.86243	GGT	.	.		0.642	PRKCZ-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000098533.3	NM_002744		T	2103755	G	T	2103755	3	4	283	1	0	0	0	0	1	0	0	0	12529	1348	47	3	1263	3	PRKCZ	1	2103755	Missense_Mutation	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10		2103755	247146866	1	41639										
CLCN6	1185	hgsc.bcm.edu	37	chr1	11896203	11896203	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gctcatcagcaacaacatcaAgttcaaggtaaagaaaacgg	8	9	4	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr1:11896203A>T	ENST00000346436.6	+	18	2025	c.1973A>T	c.(1972-1974)aAg>aTg	p.K658M	CLCN6_ENST00000312413.6_3'UTR|CLCN6_ENST00000376487.3_Missense_Mutation_p.K636M|CLCN6_ENST00000376496.3_Missense_Mutation_p.K658M	NM_001286.3	NP_001277	P51797	CLCN6_HUMAN	chloride channel, voltage-sensitive 6	658	CBS 1. {ECO:0000255|PROSITE- ProRule:PRU00703}.				cell volume homeostasis (GO:0006884)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|response to mechanical stimulus (GO:0009612)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|voltage-gated chloride channel activity (GO:0005247)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(4)	36	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		AACAACATCAAGTTCAAGGTA	0.567																																					p.K658M		Atlas-SNP	.											.	CLCN6	77	.	0			c.A1973T						.						77	69	71					1																	11896203		2203	4300	6503	SO:0001583	missense	1185	exon18			ACATCAAGTTCAA	X83378	CCDS138.1, CCDS57972.1	1p36	2012-09-26	2012-02-23		ENSG00000011021	ENSG00000011021		"Ion channels / Chloride channels : Voltage-sensitive"	2024	protein-coding gene	gene with protein product		602726	"chloride channel 6"			8543009	Standard	NM_001286		Approved	CLC-6, KIAA0046, ClC-6	uc001ate.5	P51797	OTTHUMG00000002299	ENST00000346436.6:c.1973A>T	chr1.hg19:g.11896203A>T	ENSP00000234488:p.Lys658Met	149.0	0.0		138.0	50.0	NM_001286	A8K1T4|B4DGT7|F8W9R3|O60818|O60819|O60820|O60821|P78520|P78521|Q17R81|Q5SNW2|Q5SNW3|Q5SNX1|Q5SNX2|Q5SNX3|Q99427|Q99428|Q99429	Missense_Mutation	SNP	ENST00000346436.6	hg19	CCDS138.1	.	.	.	.	.	.	.	.	.	.	A	13.99	2.400682	0.42613	.	.	ENSG00000011021	ENST00000346436;ENST00000376487;ENST00000376496	D;D;D	0.91996	-2.92;-2.91;-2.95	5.71	1.84	0.25277	Cystathionine beta-synthase, core (1);	0.254796	0.42964	D	0.000630	D	0.82291	0.5005	N	0.14661	0.345	0.80722	D	1	B;B	0.22146	0.065;0.039	B;B	0.21708	0.036;0.016	T	0.70234	-0.4928	10	0.36615	T	0.2	-13.6392	8.2988	0.32001	0.7356:0.0:0.2644:0.0	.	636;658	F8W9R3;P51797	.;CLCN6_HUMAN	M	658;636;658	ENSP00000234488:K658M;ENSP00000365670:K636M;ENSP00000365679:K658M	ENSP00000234488:K658M	K	+	2	0	CLCN6	11818790	0.990000	0.36364	0.910000	0.35882	0.907000	0.53573	2.069000	0.41481	0.051000	0.15978	0.379000	0.24179	AAG	.	.		0.567	CLCN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006639.2	NM_001286		T	11896203	A	T	11896203	3	4	283	1	0	0	0	0	1	0	0	0	3469	72	3	4	2053	4	CLCN6	1	11896203	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	9792448	11896203	237354418	2	41640										
UBR4	23352	hgsc.bcm.edu	37	chr1	19482082	19482082	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tttccctcctcattgaaaagGaaggtaacatctcttatctt	5	10	3	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr1:19482082G>T	ENST00000375254.3	-	43	6180	c.6153C>A	c.(6151-6153)ttC>ttA	p.F2051L	UBR4_ENST00000375226.2_Missense_Mutation_p.F2051L|UBR4_ENST00000375267.2_Missense_Mutation_p.F2051L|UBR4_ENST00000375217.2_Missense_Mutation_p.F2051L	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	2051					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		CATTGAAAAGGAAGGTAACAT	0.438																																					p.F2051L		Atlas-SNP	.											.	UBR4	415	.	0			c.C6153A						.						107	100	103					1																	19482082		2203	4300	6503	SO:0001583	missense	23352	exon43			GAAAAGGAAGGTA	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.6153C>A	chr1.hg19:g.19482082G>T	ENSP00000364403:p.Phe2051Leu	223.0	0.0		244.0	71.0	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	hg19	CCDS189.1	.	.	.	.	.	.	.	.	.	.	G	19.56	3.850305	0.71719	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000417040;ENST00000419533	T;T;T;T;T	0.20598	2.06;2.06;2.06;2.06;3.06	5.14	1.03	0.20045	.	0.000000	0.85682	D	0.000000	T	0.29914	0.0748	L	0.43701	1.375	0.80722	D	1	P	0.49447	0.924	P	0.57776	0.827	T	0.02464	-1.1155	10	0.56958	D	0.05	.	11.2082	0.48782	0.2556:0.0:0.7444:0.0	.	2051	Q5T4S7	UBR4_HUMAN	L	2051;2051;2051;2051;761;1267	ENSP00000364403:F2051L;ENSP00000364416:F2051L;ENSP00000364365:F2051L;ENSP00000364374:F2051L;ENSP00000404897:F761L	ENSP00000364365:F2051L	F	-	3	2	UBR4	19354669	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.762000	0.38451	0.362000	0.24319	0.650000	0.86243	TTC	.	.		0.438	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		T	19482082	G	T	19482082	3	4	283	1	0	0	0	0	1	0	0	0	16919	1165	41	3	9654	3	UBR4	1	19482082	Missense_Mutation	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	7585879	19482082	229768539	3	41641										
PIGV	55650	hgsc.bcm.edu	37	chr1	27124244	27124259	+	Frame_Shift_Del	DEL	GTTCTCCAGTCACACG	GTTCTCCAGTCACACG	-													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tttgtatcactggaaaacctGttctccagtcacacgataca							TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	GTTCTCCAGTCACACG	GTTCTCCAGTCACACG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr1:27124244_27124259delGTTCTCCAGTCACACG	ENST00000374145.1	+	4	2073_2088	c.1391_1406delGTTCTCCAGTCACACG	c.(1390-1407)tgttctccagtcacacgafs	p.CSPVTR464fs	PIGV_ENST00000078527.4_Frame_Shift_Del_p.CSPVTR464fs|PIGV_ENST00000449950.2_Frame_Shift_Del_p.CSPVTR236fs	NM_001202554.1	NP_001189483.1	Q9NUD9	PIGV_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class V	464					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	mannosyltransferase activity (GO:0000030)			NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(2)	14		all_cancers(24;3.93e-26)|all_epithelial(13;3.96e-23)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.26e-54)|Epithelial(14;2.85e-53)|OV - Ovarian serous cystadenocarcinoma(117;1.91e-30)|Colorectal(126;1.31e-09)|COAD - Colon adenocarcinoma(152;3.45e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000504)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.0222)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.153)|LUSC - Lung squamous cell carcinoma(448;0.227)		TGGAAAACCTGTTCTCCAGTCACACGATACATTCTA	0.5																																					p.464_469del		Atlas-Indel,Pindel	.											.	PIGV	47	.	0			c.1390_1405del						.																																			SO:0001589	frameshift_variant	55650	exon4			.	AK000484	CCDS287.1	1p36.11	2013-02-26	2006-06-28		ENSG00000060642	ENSG00000060642		"Dolichyl D-mannosyl phosphate dependent mannosyltransferases", "Phosphatidylinositol glycan anchor biosynthesis"	26031	protein-coding gene	gene with protein product	"GPI mannosyltransferase 2", "dol-P-Man dependent GPI mannosyltransferase"	610274	"phosphatidylinositol glycan, class V"			15623507	Standard	NM_017837		Approved	FLJ20477	uc001bmz.3	Q9NUD9	OTTHUMG00000004005	ENST00000374145.1:c.1391_1406delGTTCTCCAGTCACACG	chr1.hg19:g.27124244_27124259delGTTCTCCAGTCACACG	ENSP00000363260:p.Cys464fs	148.0	0.0		109.0	23.0	NM_001202554	D3DPL2|Q5JYG7|Q5JYG8|Q5JYG9|Q9NX26	Frame_Shift_Del	DEL	ENST00000374145.1	hg19	CCDS287.1																																																																																			.	.		0.5	PIGV-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011441.1	NM_017837		-	27124259	GTTCTCCAGTCACACG	-	27124244	7	5	283	1	0	1	0	1	0	0	0	0	11910	1377	48	0	1401	0	PIGV	1	27124244	Frame_Shift_Del	DEL	GTTCTCCAGTCACACG	TCGA-G3-A3CK-01A-11D-A20W-10	7642162	27124244	222126377	4	41642										
RCC1	1104	hgsc.bcm.edu	37	chr1	28861881	28861881	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	atttgccaaccgtggtggccGgcaaggcctcggtaagtggc	15	11	0	0	rs528320406		TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr1:28861881G>C	ENST00000373833.6	+	9	935	c.650G>C	c.(649-651)cGg>cCg	p.R217P	RCC1_ENST00000373831.3_Missense_Mutation_p.R248P|RCC1_ENST00000429051.1_3'UTR|RCC1_ENST00000398958.2_Missense_Mutation_p.R217P|RCC1_ENST00000373832.1_Missense_Mutation_p.R217P			P18754	RCC1_HUMAN	regulator of chromosome condensation 1	217					chromosome segregation (GO:0007059)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|positive regulation of Ran GTPase activity (GO:0032853)|regulation of mitosis (GO:0007088)|spindle assembly (GO:0051225)|viral process (GO:0016032)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|nucleosomal DNA binding (GO:0031492)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)	p.R217Q(1)		breast(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)	14		Colorectal(325;3.46e-05)|Lung NSC(340;0.000318)|all_lung(284;0.000434)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.00989)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)|Medulloblastoma(700;0.123)		Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|KIRC - Kidney renal clear cell carcinoma(1967;0.0101)|BRCA - Breast invasive adenocarcinoma(304;0.022)|READ - Rectum adenocarcinoma(331;0.0649)		CGTGGTGGCCGGCAAGGCCTC	0.602																																					p.R248P		Atlas-SNP	.											RCC1,caecum,carcinoma,0,1	RCC1	61	.	1	Substitution - Missense(1)	large_intestine(1)	c.G743C						.						69	66	67					1																	28861881		2203	4300	6503	SO:0001583	missense	1104	exon7			GTGGCCGGCAAGG	X12654	CCDS323.1, CCDS41295.1	1p35.3	2008-08-18	2005-05-09	2005-05-09	ENSG00000180198	ENSG00000180198			1913	protein-coding gene	gene with protein product		179710	"chromosome condensation 1"	CHC1		7851910	Standard	NM_001048199		Approved		uc001bqf.2	P18754	OTTHUMG00000003645	ENST00000373833.6:c.650G>C	chr1.hg19:g.28861881G>C	ENSP00000362939:p.Arg217Pro	105.0	1.0		123.0	43.0	NM_001048194	Q16269|Q6NT97	Missense_Mutation	SNP	ENST00000373833.6	hg19	CCDS323.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.916429	0.92249	.	.	ENSG00000180198	ENST00000398958;ENST00000427469;ENST00000434290;ENST00000373833;ENST00000419074;ENST00000373832;ENST00000373831;ENST00000411533;ENST00000430407	D;D;D;D;D;D;D;D;D	0.85088	-1.94;-1.94;-1.94;-1.94;-1.94;-1.94;-1.94;-1.94;-1.94	5.56	5.56	0.83823	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.099752	0.64402	D	0.000003	D	0.93249	0.7849	M	0.85542	2.76	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.85130	0.987;0.997;0.994	D	0.93541	0.6878	10	0.72032	D	0.01	-19.5465	18.2548	0.90016	0.0:0.0:1.0:0.0	.	248;234;217	P18754-2;E9PAT9;P18754	.;.;RCC1_HUMAN	P	217;217;253;217;217;217;248;234;217	ENSP00000381931:R217P;ENSP00000402740:R217P;ENSP00000405258:R253P;ENSP00000362939:R217P;ENSP00000402260:R217P;ENSP00000362938:R217P;ENSP00000362937:R248P;ENSP00000413644:R234P;ENSP00000394650:R217P	ENSP00000362937:R248P	R	+	2	0	RCC1	28734468	1.000000	0.71417	0.995000	0.50966	0.939000	0.58152	6.108000	0.71522	2.890000	0.99128	0.655000	0.94253	CGG	.	.		0.602	RCC1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010323.3	NM_001269		C	28861881	G	C	28861881	3	2	283	1	0	0	0	0	1	0	0	0	13188	1116	39	4	765	4	RCC1	1	28861881	Missense_Mutation	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	1737637	28861881	220388740	5	41643										
GJB5	2709	hgsc.bcm.edu	37	chr1	35223387	35223387	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ctctatgtgttccactcattCtaccccaaatatatcctccc	2	16	3	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr1:35223387C>A	ENST00000338513.1	+	2	629	c.456C>A	c.(454-456)ttC>ttA	p.F152L	GJB4_ENST00000339480.1_5'Flank	NM_005268.3	NP_005259.1	O95377	CXB5_HUMAN	gap junction protein, beta 5, 31.1kDa	152					cell communication (GO:0007154)|epidermis development (GO:0008544)|labyrinthine layer morphogenesis (GO:0060713)|spongiotrophoblast differentiation (GO:0060708)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|stomach(1)	10		Myeloproliferative disorder(586;0.0393)				TCCACTCATTCTACCCCAAAT	0.522																																					p.F152L		Atlas-SNP	.											.	GJB5	35	.	0			c.C456A						.						112	98	103					1																	35223387		2203	4300	6503	SO:0001583	missense	2709	exon2			CTCATTCTACCCC	BC004379	CCDS382.1	1p34.3	2008-05-14	2007-11-06		ENSG00000189280	ENSG00000189280		"Ion channels / Gap junction proteins (connexins)"	4287	protein-coding gene	gene with protein product	"connexin 31.1"	604493	"gap junction protein, beta 5 (connexin 31.1)", "gap junction protein, beta 5"			9843209	Standard	NM_005268		Approved	CX31.1	uc001bxu.4	O95377	OTTHUMG00000004053	ENST00000338513.1:c.456C>A	chr1.hg19:g.35223387C>A	ENSP00000340811:p.Phe152Leu	103.0	0.0		95.0	29.0	NM_005268	Q9UPA3	Missense_Mutation	SNP	ENST00000338513.1	hg19	CCDS382.1	.	.	.	.	.	.	.	.	.	.	C	0.025	-1.380752	0.01204	.	.	ENSG00000189280	ENST00000338513	D	0.90324	-2.65	5.89	2.81	0.32909	Gap junction protein, cysteine-rich domain (1);	0.287190	0.37348	N	0.002123	T	0.72252	0.3437	N	0.02412	-0.56	0.33889	D	0.637041	B	0.02656	0.0	B	0.06405	0.002	T	0.67273	-0.5712	10	0.02654	T	1	.	11.3043	0.49325	0.0:0.5903:0.3438:0.0658	.	152	O95377	CXB5_HUMAN	L	152	ENSP00000340811:F152L	ENSP00000340811:F152L	F	+	3	2	GJB5	34995974	0.489000	0.26004	0.971000	0.41717	0.036000	0.12997	-0.176000	0.09811	0.801000	0.34066	-0.254000	0.11334	TTC	.	.		0.522	GJB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011561.1	NM_005268		A	35223387	C	A	35223387	3	1	283	1	0	0	0	0	1	0	0	0	6419	912	32	3	458	3	GJB5	1	35223387	Missense_Mutation	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	6361506	35223387	214027234	6	41644										
WDR65	149465	hgsc.bcm.edu	37	chr1	43638463	43638463	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	cagacgctgcatgtttttggTcttcgatcccacgtggccaa	10	12	1	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr1:43638463T>C	ENST00000372492.4	+	2	363	c.39T>C	c.(37-39)ggT>ggC	p.G13G	EBNA1BP2_ENST00000431635.2_5'Flank|WDR65_ENST00000528956.1_Silent_p.G13G|EBNA1BP2_ENST00000236051.2_5'Flank|EBNA1BP2_ENST00000472982.1_5'Flank	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		13										NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				ATGTTTTTGGTCTTCGATCCC	0.478																																					p.G13G		Atlas-SNP	.											.	WDR65	76	.	0			c.T39C						.						145	128	134					1																	43638463		2203	4300	6503	SO:0001819	synonymous_variant	149465	exon2			TTTTGGTCTTCGA																												ENST00000372492.4:c.39T>C	chr1.hg19:g.43638463T>C		158.0	0.0		170.0	27.0	NM_152498	A6NKQ3|Q17RI9|Q5TAI0	Silent	SNP	ENST00000372492.4	hg19																																																																																				.	.		0.478	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1			C	43638463	T	C	43638463	2	2	283	1	0	0	0	0	0	0	0	1	17331	1654	58	2		2	WDR65	1	43638463	Silent	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	8415076	43638463	205612158	7	41645										
DMBX1	127343	hgsc.bcm.edu	37	chr1	46972704	46972704	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tgcagcactacggggtgaacGgctactcactgcacgccatg	12	13	1	1	rs150745846		TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr1:46972704G>A	ENST00000360032.3	+	1	36	c.22G>A	c.(22-24)Ggc>Agc	p.G8S	DMBX1_ENST00000371956.4_Missense_Mutation_p.G8S	NM_172225.1	NP_757379.1			diencephalon/mesencephalon homeobox 1											endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Acute lymphoblastic leukemia(166;0.155)					CGGGGTGAACGGCTACTCACT	0.632																																					p.G8S		Atlas-SNP	.											.	DMBX1	50	.	0			c.G22A						.	G	SER/GLY,SER/GLY	0,4406		0,0,2203	98	78	85		22,22	5.2	1	1	dbSNP_134	85	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	DMBX1	NM_147192.2,NM_172225.1	56,56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	8/383,8/378	46972704	1,13005	2203	4300	6503	SO:0001583	missense	127343	exon1			GTGAACGGCTACT	AB037699	CCDS536.1	1p34.1	2011-06-20	2004-03-29	2004-03-30	ENSG00000197587	ENSG00000197587		"Homeoboxes / PRD class"	19026	protein-coding gene	gene with protein product		607410	"orthodenticle homolog 3 (Drosophila)"	OTX3			Standard	NM_147192		Approved	PAXB	uc001cpx.3	Q8NFW5	OTTHUMG00000007982	ENST00000360032.3:c.22G>A	chr1.hg19:g.46972704G>A	ENSP00000353132:p.Gly8Ser	391.0	0.0		408.0	142.0	NM_147192		Missense_Mutation	SNP	ENST00000360032.3	hg19	CCDS536.1	.	.	.	.	.	.	.	.	.	.	G	35	5.546657	0.96488	0.0	1.16E-4	ENSG00000197587	ENST00000371956;ENST00000360032	D;D	0.95171	-3.39;-3.63	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	D	0.94781	0.8315	N	0.19112	0.55	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.983;0.993	D	0.95940	0.8946	10	0.72032	D	0.01	.	17.8482	0.88737	0.0:0.0:1.0:0.0	.	8;8	Q8NFW5;Q8NFW5-2	DMBX1_HUMAN;.	S	8	ENSP00000361024:G8S;ENSP00000353132:G8S	ENSP00000353132:G8S	G	+	1	0	DMBX1	46745291	1.000000	0.71417	0.986000	0.45419	0.994000	0.84299	7.408000	0.80041	2.453000	0.82957	0.655000	0.94253	GGC	.	G|1.000;A|0.000		0.632	DMBX1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021895.1			A	46972704	G	A	46972704	3	1	283	1	0	0	0	0	1	0	0	0	4580	1116	39	1	24	1	DMBX1	1	46972704	Missense_Mutation	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	3334241	46972704	202277917	8	41646										
NRD1	4898	hgsc.bcm.edu	37	chr1	52289359	52289359	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tggattgaaccactaaagtcAtgtaatgagaagagtagtaa	10	4	1	3			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr1:52289359A>G	ENST00000354831.7	-	9	1529	c.1340T>C	c.(1339-1341)aTg>aCg	p.M447T	NRD1_ENST00000352171.7_Missense_Mutation_p.M379T|NRD1_ENST00000539524.1_Missense_Mutation_p.M315T|NRD1_ENST00000485608.1_5'UTR|NRD1_ENST00000544028.1_Missense_Mutation_p.M247T	NM_002525.2	NP_002516.2	O43847	NRDC_HUMAN	nardilysin (N-arginine dibasic convertase)	378					cell migration (GO:0016477)|cell proliferation (GO:0008283)|neuromuscular junction development (GO:0007528)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)	cell surface (GO:0009986)|cytosol (GO:0005829)	epidermal growth factor binding (GO:0048408)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)	27						CACTAAAGTCATGTAATGAGA	0.378																																					p.M447T		Atlas-SNP	.											.	NRD1	89	.	0			c.T1340C						.						100	99	100					1																	52289359		2203	4300	6503	SO:0001583	missense	4898	exon9			AAAGTCATGTAAT	X93207	CCDS559.1, CCDS41335.1, CCDS55599.1	1p32.2-p32.1	2008-07-18			ENSG00000078618	ENSG00000078618			7995	protein-coding gene	gene with protein product		602651				9581555, 9479496	Standard	NM_002525		Approved	hNRD1, hNRD2	uc001ctc.4	O43847	OTTHUMG00000008278	ENST00000354831.7:c.1340T>C	chr1.hg19:g.52289359A>G	ENSP00000346890:p.Met447Thr	202.0	0.0		185.0	72.0	NM_002525	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	Missense_Mutation	SNP	ENST00000354831.7	hg19	CCDS559.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.262266	0.80358	.	.	ENSG00000078618	ENST00000352171;ENST00000354831;ENST00000539524;ENST00000546169;ENST00000544028	T;T;T;T	0.12569	2.67;2.67;2.67;2.67	5.53	5.53	0.82687	Peptidase M16, C-terminal (1);Peptidase M16, core (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.000000	0.85682	D	0.000000	T	0.51024	0.1650	H	0.95574	3.69	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.999	T	0.67074	-0.5762	10	0.87932	D	0	-11.9475	15.6605	0.77182	1.0:0.0:0.0:0.0	.	379;378;447	F5H6R2;O43847;B1AKJ5	.;NRDC_HUMAN;.	T	379;447;315;379;247	ENSP00000262679:M379T;ENSP00000346890:M447T;ENSP00000444416:M315T;ENSP00000442262:M247T	ENSP00000262679:M379T	M	-	2	0	NRD1	52061947	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.845000	0.92153	2.112000	0.64535	0.533000	0.62120	ATG	.	.		0.378	NRD1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023045.1	NM_002525		G	52289359	A	G	52289359	3	3	283	1	0	0	0	0	1	0	0	0	10654	217	8	2	2419	2	NRD1	1	52289359	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	5316655	52289359	196961262	9	41647										
L1TD1	54596	hgsc.bcm.edu	37	chr1	62676374	62676374	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	aagttcccattcaggtgtctTggaaattgaaaattcagtag	9	6	3	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr1:62676374T>C	ENST00000498273.1	+	4	2223	c.1928T>C	c.(1927-1929)tTg>tCg	p.L643S	Y_RNA_ENST00000363304.1_RNA	NM_001164835.1|NM_019079.4	NP_001158307.1|NP_061952.3	Q5T7N2	LITD1_HUMAN	LINE-1 type transposase domain containing 1	643										breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	35						tcaggtgtcttggaaattgaa	0.343																																					p.L643S		Atlas-SNP	.											.	L1TD1	114	.	0			c.T1928C						.						21	20	20					1																	62676374		2080	4001	6081	SO:0001583	missense	54596	exon5			GTGTCTTGGAAAT	BC060808	CCDS619.1	1p31.3	2009-01-12			ENSG00000240563	ENSG00000240563			25595	protein-coding gene	gene with protein product						12477932	Standard	NM_001164835		Approved	FLJ10884, ECAT11	uc001dae.4	Q5T7N2	OTTHUMG00000008914	ENST00000498273.1:c.1928T>C	chr1.hg19:g.62676374T>C	ENSP00000419901:p.Leu643Ser	161.0	0.0		155.0	48.0	NM_001164835	Q8NDA1|Q9NUV8|Q9NV78	Missense_Mutation	SNP	ENST00000498273.1	hg19	CCDS619.1	.	.	.	.	.	.	.	.	.	.	T	10.96	1.498565	0.26861	.	.	ENSG00000240563	ENST00000498273	T	0.23348	1.91	3.07	1.94	0.25998	.	.	.	.	.	T	0.30324	0.0761	M	0.71920	2.185	0.09310	N	1	P	0.39535	0.677	B	0.43536	0.423	T	0.23762	-1.0179	9	0.87932	D	0	.	4.8405	0.13487	0.0:0.1462:0.0:0.8538	.	643	Q5T7N2	LITD1_HUMAN	S	643	ENSP00000419901:L643S	ENSP00000419901:L643S	L	+	2	0	L1TD1	62448962	0.000000	0.05858	0.004000	0.12327	0.266000	0.26442	0.427000	0.21379	0.600000	0.29862	0.260000	0.18958	TTG	.	.		0.343	L1TD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024688.1	NM_019079		C	62676374	T	C	62676374	3	2	283	1	0	0	0	0	1	0	0	0	8598	1821	63	2	1934	2	L1TD1	1	62676374	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	10387015	62676374	186574247	10	41648										
ANGPTL3	27329	hgsc.bcm.edu	37	chr1	63070352	63070352	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	agaaaacaacctaaatggtaAatataacaaaccaagagcaa	5	7	0	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr1:63070352A>C	ENST00000371129.3	+	7	1327	c.1247A>C	c.(1246-1248)aAa>aCa	p.K416T	DOCK7_ENST00000404627.2_Intron|DOCK7_ENST00000340370.5_Intron|DOCK7_ENST00000251157.5_Intron	NM_014495.2	NP_055310.1	Q9Y5C1	ANGL3_HUMAN	angiopoietin-like 3	416	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				acylglycerol homeostasis (GO:0055090)|artery morphogenesis (GO:0048844)|cell-matrix adhesion (GO:0007160)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|fatty acid metabolic process (GO:0006631)|glycerol metabolic process (GO:0006071)|integrin-mediated signaling pathway (GO:0007229)|lipid homeostasis (GO:0055088)|lipid storage (GO:0019915)|negative regulation of lipoprotein lipase activity (GO:0051005)|negative regulation of phospholipase activity (GO:0010519)|phospholipid catabolic process (GO:0009395)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of lipid catabolic process (GO:0050996)|response to hormone (GO:0009725)|signal transduction (GO:0007165)|triglyceride homeostasis (GO:0070328)	cell surface (GO:0009986)|extracellular space (GO:0005615)	enzyme inhibitor activity (GO:0004857)|growth factor activity (GO:0008083)|integrin binding (GO:0005178)|phospholipase inhibitor activity (GO:0004859)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(3)|urinary_tract(1)	13						CTAAATGGTAAATATAACAAA	0.373																																					p.A416A		Atlas-SNP	.											.	ANGPTL3	42	.	0			c.C1247C						.						100	99	99					1																	63070352		2203	4300	6503	SO:0001583	missense	27329	exon7			ATGGTAAATATAA	AF152562	CCDS622.1	1p31.3	2013-02-06			ENSG00000132855	ENSG00000132855		"Fibrinogen C domain containing"	491	protein-coding gene	gene with protein product	"angiopoietin 5"	604774		ANGPT5		10644446	Standard	NM_014495		Approved		uc001das.2	Q9Y5C1	OTTHUMG00000009146	ENST00000371129.3:c.1247A>C	chr1.hg19:g.63070352A>C	ENSP00000360170:p.Lys416Thr	259.0	0.0		269.0	81.0	NM_014495	A0JLS0|B1ALJ0|B2RCW1	Silent	SNP	ENST00000371129.3	hg19	CCDS622.1	.	.	.	.	.	.	.	.	.	.	A	19.79	3.893670	0.72639	.	.	ENSG00000132855	ENST00000371129	T	0.78126	-1.15	5.4	5.4	0.78164	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 2 (1);	0.277044	0.46442	D	0.000290	T	0.80053	0.4553	M	0.69523	2.12	0.45427	D	0.998401	P	0.51147	0.942	P	0.54759	0.76	T	0.80329	-0.1428	10	0.40728	T	0.16	.	15.7054	0.77577	1.0:0.0:0.0:0.0	.	416	Q9Y5C1	ANGL3_HUMAN	T	416	ENSP00000360170:K416T	ENSP00000360170:K416T	K	+	2	0	ANGPTL3	62842940	1.000000	0.71417	0.999000	0.59377	0.966000	0.64601	3.514000	0.53422	2.164000	0.68074	0.477000	0.44152	AAA	.	.		0.373	ANGPTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025344.1	NM_014495		C	63070352	A	C	63070352	3	2	283	1	0	0	0	0	1	0	0	0	615	14	1	5	1273	5	ANGPTL3	1	63070352	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	393978	63070352	186180269	11	41649										
GBP3	2635	hgsc.bcm.edu	37	chr1	89480301	89480301	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	agagtgctgctcaggaggacGgccagggtgaagatccagga	17	8	1	3			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr1:89480301G>T	ENST00000370481.4	-	4	577	c.357C>A	c.(355-357)gcC>gcA	p.A119A	GBP3_ENST00000475853.2_5'Flank	NM_018284.2	NP_060754.2	Q8WXF7	ATLA1_HUMAN	guanylate binding protein 3	167	GB1/RHD3-type G.				axonogenesis (GO:0007409)|cell death (GO:0008219)|endoplasmic reticulum organization (GO:0007029)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi cis cisterna (GO:0000137)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	26		Lung NSC(277;0.123)		all cancers(265;0.0103)|Epithelial(280;0.0293)		TCAGGAGGACGGCCAGGGTGA	0.512																																					p.A119A		Atlas-SNP	.											.	GBP3	53	.	0			c.C357A						.						195	165	175					1																	89480301		2203	4300	6503	SO:0001819	synonymous_variant	2635	exon4			GAGGACGGCCAGG	BC063819	CCDS717.2	1p22.2	2008-02-05			ENSG00000117226	ENSG00000117226			4184	protein-coding gene	gene with protein product		600413				7518790	Standard	NM_018284		Approved	FLJ10961	uc001dmt.3	Q9H0R5	OTTHUMG00000010616	ENST00000370481.4:c.357C>A	chr1.hg19:g.89480301G>T		229.0	0.0		297.0	138.0	NM_018284	A6NND5|A8K2C0|G5E9T1|O95890|Q69YH7|Q96FK0	Silent	SNP	ENST00000370481.4	hg19	CCDS717.2																																																																																			.	.		0.512	GBP3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313541.3	NM_018284		T	89480301	G	T	89480301	2	4	283	1	0	0	0	0	0	0	0	1	6283	1103	39	1		1	GBP3	1	89480301	Silent	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	26409949	89480301	159770320	12	41650										
VAV3	10451	hgsc.bcm.edu	37	chr1	108322079	108322079	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	attcctgtggccaatgctatAggtgttcgagaaagtcgtga	12	7	0	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr1:108322079A>T	ENST00000370056.4	-	3	631	c.357T>A	c.(355-357)ccT>ccA	p.P119P	VAV3_ENST00000343258.4_5'UTR|VAV3_ENST00000371846.4_Silent_p.P54P|VAV3_ENST00000527011.1_Silent_p.P119P	NM_006113.4	NP_006104.4	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor	119	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of signal transduction (GO:0009967)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|vesicle fusion (GO:0006906)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|SH3/SH2 adaptor activity (GO:0005070)			NS(2)|breast(5)|endometrium(4)|kidney(2)|large_intestine(14)|lung(20)|ovary(6)|prostate(3)|stomach(1)|urinary_tract(1)	58		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)		CCAATGCTATAGGTGTTCGAG	0.328																																					p.P119P		Atlas-SNP	.											.	VAV3	176	.	0			c.T357A						.						117	110	113					1																	108322079		2203	4300	6503	SO:0001819	synonymous_variant	10451	exon3			TGCTATAGGTGTT	AF118886	CCDS785.1, CCDS44181.1	1p13.3	2013-02-14	2007-07-25		ENSG00000134215	ENSG00000134215		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "SH2 domain containing"	12659	protein-coding gene	gene with protein product		605541	"vav 3 oncogene"				Standard	NM_001079874		Approved		uc001dvk.1	Q9UKW4	OTTHUMG00000010995	ENST00000370056.4:c.357T>A	chr1.hg19:g.108322079A>T		83.0	0.0		112.0	39.0	NM_006113	B1AMM0|B1APV5|B4E232|B7ZLR1|E9PQ97|O60498|O95230|Q9Y5X8	Silent	SNP	ENST00000370056.4	hg19	CCDS785.1	.	.	.	.	.	.	.	.	.	.	A	8.499	0.863779	0.17250	.	.	ENSG00000134215	ENST00000490388	.	.	.	5.66	-1.36	0.09085	.	.	.	.	.	T	0.23766	0.0575	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.26710	-1.0095	4	.	.	.	.	1.9031	0.03272	0.432:0.2491:0.0737:0.2451	.	.	.	.	Q	114	.	.	L	-	2	0	VAV3	108123602	0.066000	0.20996	0.901000	0.35422	0.579000	0.36224	-0.941000	0.03925	-0.533000	0.06323	0.528000	0.53228	CTA	.	.		0.328	VAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030242.2	NM_006113		T	108322079	A	T	108322079	2	4	283	1	0	0	0	0	0	0	0	1	17148	407	15	4		4	VAV3	1	108322079	Silent	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	18841778	108322079	140928542	13	41651										
CELSR2	1952	hgsc.bcm.edu	37	chr1	109795272	109795272	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ttctacaccttccaaggaggCgacgatggagacggtgactt	12	10	1	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr1:109795272C>T	ENST00000271332.3	+	1	2632	c.2571C>T	c.(2569-2571)ggC>ggT	p.G857G		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	857	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		TCCAAGGAGGCGACGATGGAG	0.547																																					p.G857G	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-SNP	.											.	CELSR2	228	.	0			c.C2571T						.						113	104	107					1																	109795272		2203	4300	6503	SO:0001819	synonymous_variant	1952	exon1			AGGAGGCGACGAT	D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3231	protein-coding gene	gene with protein product		604265	"cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.2571C>T	chr1.hg19:g.109795272C>T		158.0	0.0		226.0	100.0	NM_001408	Q5T2Y7|Q92566	Silent	SNP	ENST00000271332.3	hg19	CCDS796.1																																																																																			.	.		0.547	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408		T	109795272	C	T	109795272	2	4	283	1	0	0	0	0	0	0	0	1	3224	755	27	1		1	CELSR2	1	109795272	Silent	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	1473193	109795272	139455349	14	41652										
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144921895	144921895	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tcgtgtgctgcagcctctacAaattgcacacattgtttggc	9	11	1	0	rs587609805		TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr1:144921895A>G	ENST00000369354.3	-	9	1323	c.1134T>C	c.(1132-1134)ttT>ttC	p.F378F	PDE4DIP_ENST00000313431.9_Silent_p.F541F|PDE4DIP_ENST00000479408.2_Silent_p.F165F|PDE4DIP_ENST00000530740.1_Silent_p.F515F|PDE4DIP_ENST00000369356.4_Silent_p.F378F|PDE4DIP_ENST00000369351.3_Silent_p.F378F|PDE4DIP_ENST00000313382.9_Silent_p.F444F|PDE4DIP_ENST00000369349.3_Silent_p.F378F|PDE4DIP_ENST00000529945.1_Silent_p.F541F|PDE4DIP_ENST00000369359.4_Silent_p.F515F			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	378					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		CAGCCTCTACAAATTGCACAC	0.438			T	PDGFRB	MPD																																p.F541F		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.T1623C						.						419	438	431					1																	144921895		2203	4296	6499	SO:0001819	synonymous_variant	9659	exon5			CTCTACAAATTGC	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"myomegalin"	608117	"cardiomyopathy associated 2"	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.1134T>C	chr1.hg19:g.144921895A>G		358.0	0.0		418.0	55.0	NM_001002811	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Silent	SNP	ENST00000369354.3	hg19	CCDS30824.1																																																																																			.	.		0.438	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		G	144921895	A	G	144921895	2	3	283	1	0	0	0	0	0	0	0	1	11652	127	5	2		2	PDE4DIP	1	144921895	Silent	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	35126623	144921895	104328726	15	41653										
RPRD2	23248	hgsc.bcm.edu	37	chr1	150437008	150437008	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tctttctgccaccaggggtcAgtcctgcatcaagaccttct	8	14	5	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr1:150437008A>G	ENST00000369068.4	+	10	1421	c.1417A>G	c.(1417-1419)Agt>Ggt	p.S473G	RPRD2_ENST00000492220.1_3'UTR|RPRD2_ENST00000539519.1_Missense_Mutation_p.S447G|RPRD2_ENST00000401000.4_Missense_Mutation_p.S447G	NM_015203.3	NP_056018.2	Q5VT52	RPRD2_HUMAN	regulation of nuclear pre-mRNA domain containing 2	473	Ser-rich.					DNA-directed RNA polymerase II, holoenzyme (GO:0016591)				central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						ACCAGGGGTCAGTCCTGCATC	0.478											OREG0013786	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S473G		Atlas-SNP	.											.	RPRD2	189	.	0			c.A1417G						.						45	57	53					1																	150437008		2062	4187	6249	SO:0001583	missense	23248	exon10			GGGGTCAGTCCTG	BX641025	CCDS44216.1, CCDS72907.1	1q21.2	2012-02-09	2008-08-15	2008-07-28	ENSG00000163125	ENSG00000163125			29039	protein-coding gene	gene with protein product		614695	"KIAA0460"	KIAA0460		22231121	Standard	XM_005245033		Approved	FLJ32145, HSPC099	uc009wlr.3	Q5VT52	OTTHUMG00000012808	ENST00000369068.4:c.1417A>G	chr1.hg19:g.150437008A>G	ENSP00000358064:p.Ser473Gly	34.0	0.0	1732	57.0	21.0	NM_015203	A8K6N8|B3KPT1|B4E2Q6|O75048|Q5VT51|Q5VT53|Q6MZL4|Q86XD2|Q9P0D7	Missense_Mutation	SNP	ENST00000369068.4	hg19	CCDS44216.1	.	.	.	.	.	.	.	.	.	.	A	25.7	4.663718	0.88251	.	.	ENSG00000163125	ENST00000401000;ENST00000539519;ENST00000369068	T;T;T	0.51817	0.72;0.74;0.69	5.34	5.34	0.76211	.	0.053884	0.85682	D	0.000000	T	0.56848	0.2013	M	0.61703	1.905	0.58432	D	0.999998	D;D;D	0.71674	0.99;0.996;0.998	P;P;D	0.66084	0.824;0.874;0.941	T	0.60429	-0.7265	10	0.56958	D	0.05	-10.5769	15.4877	0.75578	1.0:0.0:0.0:0.0	.	447;473;447	B4E2Q6;Q5VT52;Q5VT52-3	.;RPRD2_HUMAN;.	G	447;447;473	ENSP00000383785:S447G;ENSP00000445482:S447G;ENSP00000358064:S473G	ENSP00000358064:S473G	S	+	1	0	RPRD2	148703632	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.118000	0.89577	2.248000	0.74166	0.533000	0.62120	AGT	.	.		0.478	RPRD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000035844.1	NM_015203		G	150437008	A	G	150437008	3	3	283	1	0	0	0	0	1	0	0	0	13632	188	7	2	1455	2	RPRD2	1	150437008	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	5515113	150437008	98813613	16	41654										
PI4KB	5298	hgsc.bcm.edu	37	chr1	151280253	151280253	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	catcagggacttgatgaattCtctctcaggagccagtcgaa	10	10	3	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr1:151280253C>A	ENST00000368873.1	-	4	1147	c.979G>T	c.(979-981)Gaa>Taa	p.E327*	PI4KB_ENST00000271657.5_Nonsense_Mutation_p.E339*|PI4KB_ENST00000368872.1_Nonsense_Mutation_p.E312*|PI4KB_ENST00000368875.2_Nonsense_Mutation_p.E339*|PI4KB_ENST00000529142.1_5'UTR|PI4KB_ENST00000368874.4_Nonsense_Mutation_p.E312*			Q9UBF8	PI4KB_HUMAN	phosphatidylinositol 4-kinase, catalytic, beta	327					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi membrane (GO:0000139)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			breast(3)|endometrium(5)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	27	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			TTGATGAATTCTCTCTCAGGA	0.527																																					p.E339X	Colon(154;765 1838 9854 28443 37492)	Atlas-SNP	.											.	PI4KB	76	.	0			c.G1015T						.						79	78	78					1																	151280253		2203	4300	6503	SO:0001587	stop_gained	5298	exon5			TGAATTCTCTCTC	AB005910	CCDS993.1, CCDS55637.1, CCDS55638.1	1q21	2008-02-05	2007-08-14	2007-08-02	ENSG00000143393	ENSG00000143393			8984	protein-coding gene	gene with protein product		602758		PIK4CB		9020160, 9405938	Standard	NM_002651		Approved	PI4K-BETA, pi4K92	uc001exu.3	Q9UBF8	OTTHUMG00000012348	ENST00000368873.1:c.979G>T	chr1.hg19:g.151280253C>A	ENSP00000357867:p.Glu327*	219.0	0.0		226.0	105.0	NM_002651	B4DGI2|O15096|P78405|Q5VWB9|Q5VWC0|Q5VWC1|Q9BWR6	Nonsense_Mutation	SNP	ENST00000368873.1	hg19		.	.	.	.	.	.	.	.	.	.	C	41	9.065859	0.99053	.	.	ENSG00000143393	ENST00000368874;ENST00000368875;ENST00000271657;ENST00000368873;ENST00000368872	.	.	.	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-12.6846	18.82	0.92092	0.0:1.0:0.0:0.0	.	.	.	.	X	312;339;339;327;312	.	ENSP00000271657:E339X	E	-	1	0	PI4KB	149546877	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.409000	0.80053	2.797000	0.96272	0.563000	0.77884	GAA	.	.		0.527	PI4KB-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000034400.3	NM_002651		A	151280253	C	A	151280253	4	1	283	1	0	0	0	0	0	1	0	0	11883	922	32	3	1507	3	PI4KB	1	151280253	Nonsense_Mutation	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	843245	151280253	97970368	17	41655										
B4GALT3	8703	hgsc.bcm.edu	37	chr1	161141842	161141842	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	cagtgagttcatcccatcttGcgtccaggaattctgggtac	10	11	3	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr1:161141842G>T	ENST00000319769.5	-	8	1168	c.946C>A	c.(946-948)Caa>Aaa	p.Q316K	B4GALT3_ENST00000367998.1_Missense_Mutation_p.Q316K|PPOX_ENST00000495483.1_Intron|PPOX_ENST00000535223.1_Intron|PPOX_ENST00000432542.2_Intron|B4GALT3_ENST00000470882.1_5'UTR	NM_001199873.1|NM_003779.3	NP_001186802.1|NP_003770.1	O60512	B4GT3_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 3	316					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|galactosyltransferase activity (GO:0008378)|metal ion binding (GO:0046872)|N-acetyllactosamine synthase activity (GO:0003945)			cervix(1)|endometrium(5)|large_intestine(6)|lung(6)	18	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		N-Acetyl-D-glucosamine(DB00141)	ATCCCATCTTGCGTCCAGGAA	0.522																																					p.Q316K		Atlas-SNP	.											.	B4GALT3	39	.	0			c.C946A						.						75	78	77					1																	161141842		2203	4300	6503	SO:0001583	missense	8703	exon8			CATCTTGCGTCCA	BC006099	CCDS1222.1	1q21-q23	2013-02-19			ENSG00000158850	ENSG00000158850		"Beta 4-glycosyltransferases"	926	protein-coding gene	gene with protein product		604014				9405390, 9597550	Standard	NM_001199873		Approved	beta4Gal-T3	uc001fys.2	O60512	OTTHUMG00000034348	ENST00000319769.5:c.946C>A	chr1.hg19:g.161141842G>T	ENSP00000320965:p.Gln316Lys	114.0	0.0		143.0	40.0	NM_003779	D3DVG3|O60910|Q9BPZ4|Q9H8T2	Missense_Mutation	SNP	ENST00000319769.5	hg19	CCDS1222.1	.	.	.	.	.	.	.	.	.	.	G	5.768	0.326161	0.10900	.	.	ENSG00000158850	ENST00000319769;ENST00000407555;ENST00000367998;ENST00000367997	T;T	0.28255	1.62;1.62	5.28	5.28	0.74379	.	0.260915	0.40385	N	0.001105	T	0.04861	0.0131	N	0.03238	-0.38	0.34035	D	0.654243	B	0.10296	0.003	B	0.12837	0.008	T	0.16012	-1.0417	10	0.06625	T	0.88	.	13.5604	0.61786	0.0:0.1563:0.8437:0.0	.	316	O60512	B4GT3_HUMAN	K	316;293;316;316	ENSP00000320965:Q316K;ENSP00000356977:Q316K	ENSP00000320965:Q316K	Q	-	1	0	B4GALT3	159408466	1.000000	0.71417	0.989000	0.46669	0.994000	0.84299	4.881000	0.63114	2.746000	0.94184	0.655000	0.94253	CAA	.	.		0.522	B4GALT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083054.1	NM_003779		T	161141842	G	T	161141842	3	4	283	1	0	0	0	0	1	0	0	0	1272	1328	46	3	239	3	B4GALT3	1	161141842	Missense_Mutation	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	9861589	161141842	88108779	18	41656										
SCYL3	57147	hgsc.bcm.edu	37	chr1	169847817	169847817	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gccagcaatatgtcatagatCccagcacagacctctgcaga	8	13	2	3			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr1:169847817C>A	ENST00000367770.1	-	2	356	c.309G>T	c.(307-309)ggG>ggT	p.G103G	SCYL3_ENST00000367771.6_Silent_p.G103G|SCYL3_ENST00000470238.1_5'UTR|SCYL3_ENST00000367772.4_Silent_p.G103G			Q8IZE3	PACE1_HUMAN	SCY1-like 3 (S. cerevisiae)	103	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell migration (GO:0016477)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)	ATP binding (GO:0005524)|transferase activity, transferring phosphorus-containing groups (GO:0016772)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(5)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					TGTCATAGATCCCAGCACAGA	0.483																																					p.G103G		Atlas-SNP	.											.	SCYL3	116	.	0			c.G309T						.						129	125	126					1																	169847817		2203	4300	6503	SO:0001819	synonymous_variant	57147	exon3			ATAGATCCCAGCA	BC014662	CCDS1286.1, CCDS1287.1	1q24.2	2008-02-05			ENSG00000000457	ENSG00000000457			19285	protein-coding gene	gene with protein product	"ezrin-binding partner PACE-1"	608192				12651155	Standard	NM_020423		Approved	PACE-1, PACE1	uc001ggs.3	Q8IZE3	OTTHUMG00000035941	ENST00000367770.1:c.309G>T	chr1.hg19:g.169847817C>A		260.0	0.0		391.0	208.0	NM_020423	A8K8Z2|Q5THA6|Q5THA8|Q8IZN9|Q96C56|Q9UBK6	Silent	SNP	ENST00000367770.1	hg19	CCDS1287.1																																																																																			.	.		0.483	SCYL3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087550.4	NM_181093		A	169847817	C	A	169847817	2	1	283	1	0	0	0	0	0	0	0	1	13964	842	30	3		3	SCYL3	1	169847817	Silent	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	8705975	169847817	79402804	19	41657										
RASAL2	9462	hgsc.bcm.edu	37	chr1	178269226	178269226	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ccgagggtcagtttcccgagTacccaccagagggcgccact	12	15	1	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr1:178269226T>C	ENST00000367649.3	+	3	782	c.430T>C	c.(430-432)Tac>Cac	p.Y144H	RASAL2_ENST00000448150.3_Missense_Mutation_p.Y126H			Q9UJF2	NGAP_HUMAN	RAS protein activator like 2	0	PH.				negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Ras GTPase activator activity (GO:0005099)			biliary_tract(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(2)|lung(25)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54						GTTTCCCGAGTACCCACCAGA	0.483											OREG0014010	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y144H		Atlas-SNP	.											.	RASAL2	334	.	0			c.T430C						.						66	69	68					1																	178269226		2203	4300	6503	SO:0001583	missense	9462	exon3			CCCGAGTACCCAC	AF047711	CCDS1321.1, CCDS1322.1, CCDS1321.2	1q25	2013-01-10			ENSG00000075391	ENSG00000075391		"Pleckstrin homology (PH) domain containing"	9874	protein-coding gene	gene with protein product	"Ras GTPase activating protein-like", "Ras protein activator like 1"	606136				9877179	Standard	NM_004841		Approved	nGAP	uc001glq.3	Q9UJF2	OTTHUMG00000035022	ENST00000367649.3:c.430T>C	chr1.hg19:g.178269226T>C	ENSP00000356621:p.Tyr144His	74.0	0.0	1945	86.0	44.0	NM_170692	F8W755|O95174|Q2TB22|Q5TFU9	Missense_Mutation	SNP	ENST00000367649.3	hg19	CCDS1321.2	.	.	.	.	.	.	.	.	.	.	T	19.59	3.855975	0.71834	.	.	ENSG00000075391	ENST00000448150;ENST00000367649	T;T	0.20332	2.08;2.08	5.61	5.61	0.85477	.	0.074262	0.56097	D	0.000036	T	0.35913	0.0948	L	0.36672	1.1	0.46061	D	0.998844	D	0.69078	0.997	D	0.75484	0.986	T	0.03017	-1.1082	10	0.34782	T	0.22	.	15.0834	0.72133	0.0:0.0:0.0:1.0	.	144	F8W755	.	H	126;144	ENSP00000407768:Y126H;ENSP00000356621:Y144H	ENSP00000356621:Y144H	Y	+	1	0	RASAL2	176535849	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	5.728000	0.68531	2.254000	0.74563	0.533000	0.62120	TAC	.	.		0.483	RASAL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352415.1	NM_170692		C	178269226	T	C	178269226	3	2	283	1	0	0	0	0	1	0	0	0	13079	1638	57	2	440	2	RASAL2	1	178269226	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	8421409	178269226	70981395	20	41658										
TPR	7175	hgsc.bcm.edu	37	chr1	186295352	186295352	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	atcatcatcatcatcttcctCatcctcttcataatcctagt	1	14	8	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr1:186295352C>T	ENST00000367478.4	-	41	6201	c.5905G>A	c.(5905-5907)Gag>Aag	p.E1969K		NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	1969					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		tcatcttcctcatcctcttca	0.408			T	NTRK1	papillary thyroid																																p.E1969K		Atlas-SNP	.		Dom	yes		1	1q25	7175	translocated promoter region		E	.	TPR	441	.	0			c.G5905A						.						75	71	72					1																	186295352		2036	4192	6228	SO:0001583	missense	7175	exon41			CTTCCTCATCCTC	U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"translocated promoter region (to activated MET oncogene)"			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.5905G>A	chr1.hg19:g.186295352C>T	ENSP00000356448:p.Glu1969Lys	135.0	0.0		140.0	73.0	NM_003292	Q15655|Q5SWY0|Q99968	Missense_Mutation	SNP	ENST00000367478.4	hg19	CCDS41446.1	.	.	.	.	.	.	.	.	.	.	C	12.90	2.077916	0.36662	.	.	ENSG00000047410	ENST00000367478	T	0.26810	1.71	4.03	4.03	0.46877	.	0.388706	0.29100	N	0.013159	T	0.43986	0.1272	L	0.59436	1.845	0.46279	D	0.998969	P	0.52842	0.956	P	0.62184	0.899	T	0.22208	-1.0223	10	0.38643	T	0.18	.	16.1447	0.81559	0.0:1.0:0.0:0.0	.	1969	P12270	TPR_HUMAN	K	1969	ENSP00000356448:E1969K	ENSP00000356448:E1969K	E	-	1	0	TPR	184561975	1.000000	0.71417	0.997000	0.53966	0.815000	0.46073	3.231000	0.51294	2.544000	0.85801	0.655000	0.94253	GAG	.	.		0.408	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292		T	186295352	C	T	186295352	3	4	283	1	0	0	0	0	1	0	0	0	16431	835	29	3	1230	3	TPR	1	186295352	Missense_Mutation	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	8026126	186295352	62955269	21	41659										
GPR25	2848	hgsc.bcm.edu	37	chr1	200843249	200843249	+	Nonstop_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	acactgcctcggcctcctggTagctgccccgggccgctgga	13	17	0	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr1:200843249T>G	ENST00000304244.2	+	1	1167	c.1084T>G	c.(1084-1086)Tag>Gag	p.*362E		NM_005298.2	NP_005289.2	O00155	GPR25_HUMAN	G protein-coupled receptor 25	0					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			large_intestine(1)|lung(2)|ovary(1)|skin(1)	5						GGCCTCCTGGTAGCTGCCCCG	0.711																																					p.X362E		Atlas-SNP	.											.	GPR25	23	.	0			c.T1084G						.						6	5	5					1																	200843249		2051	4008	6059	SO:0001578	stop_lost	2848	exon1			TCCTGGTAGCTGC	U91939	CCDS1405.1	1q32.1	2012-08-21			ENSG00000170128	ENSG00000170128		"GPCR / Class A : Orphans"	4480	protein-coding gene	gene with protein product		602174				9020062	Standard	NM_005298		Approved		uc001gvn.2	O00155	OTTHUMG00000035788	ENST00000304244.2:c.1084T>G	chr1.hg19:g.200843249T>G	ENSP00000301917:p.*362Gluext*?	37.0	0.0		42.0	19.0	NM_005298	A0AVJ5	Missense_Mutation	SNP	ENST00000304244.2	hg19	CCDS1405.1	.	.	.	.	.	.	.	.	.	.	T	5.468	0.271420	0.10349	.	.	ENSG00000170128	ENST00000304244	.	.	.	2.79	0.44	0.16572	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.5235	0.16945	0.0:0.424:0.0:0.576	.	.	.	.	E	362	.	.	X	+	1	0	GPR25	199109872	0.000000	0.05858	0.001000	0.08648	0.059000	0.15707	-1.509000	0.02264	0.070000	0.16634	0.260000	0.18958	TAG	.	.		0.711	GPR25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087056.1	NM_005298		G	200843249	T	G	200843249	4	3	283	1	0	0	0	0	0	0	0	0	6691	1651	57	5	1086	5	GPR25	1	200843249	Nonstop_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	14547897	200843249	48407372	22	41660										
CNTN2	6900	hgsc.bcm.edu	37	chr1	205038645	205038645	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	cggtggcaccctcaggactcAgcggaggaggtggagccccc	16	14	2	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr1:205038645A>G	ENST00000331830.4	+	17	2436	c.2152A>G	c.(2152-2154)Agc>Ggc	p.S718G		NM_005076.3	NP_005067.1	Q02246	CNTN2_HUMAN	contactin 2 (axonal)	718	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|central nervous system myelination (GO:0022010)|cerebral cortex GABAergic interneuron migration (GO:0021853)|clustering of voltage-gated potassium channels (GO:0045163)|establishment of protein localization to juxtaparanode region of axon (GO:0071206)|learning (GO:0007612)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|positive regulation of protein processing (GO:0010954)|presynaptic membrane organization (GO:0097090)|receptor internalization (GO:0031623)|regulation of astrocyte differentiation (GO:0048710)|regulation of axon diameter (GO:0031133)|regulation of neuronal synaptic plasticity (GO:0048168)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|juxtaparanode region of axon (GO:0044224)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated potassium channel complex (GO:0008076)	carbohydrate binding (GO:0030246)|identical protein binding (GO:0042802)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(11)|lung(23)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	54	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			CTCAGGACTCAGCGGAGGAGG	0.597																																					p.S718G	Melanoma(183;2548 2817 37099 41192)	Atlas-SNP	.											.	CNTN2	116	.	0			c.A2152G						.						64	68	67					1																	205038645		2203	4300	6503	SO:0001583	missense	6900	exon17			GGACTCAGCGGAG	X67734	CCDS1449.1	1q32.1	2013-02-11			ENSG00000184144	ENSG00000184144		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2172	protein-coding gene	gene with protein product		190197		TAX, AXT		8307567, 8586965	Standard	NM_005076		Approved	TAG-1, TAX1	uc001hbr.3	Q02246	OTTHUMG00000037105	ENST00000331830.4:c.2152A>G	chr1.hg19:g.205038645A>G	ENSP00000330633:p.Ser718Gly	124.0	0.0		156.0	36.0	NM_005076	P78432|Q5T054	Missense_Mutation	SNP	ENST00000331830.4	hg19	CCDS1449.1	.	.	.	.	.	.	.	.	.	.	A	9.060	0.994363	0.19043	.	.	ENSG00000184144	ENST00000331830	T	0.59502	0.26	5.57	5.57	0.84162	Fibronectin, type III (5);Immunoglobulin-like fold (1);	0.090873	0.47852	D	0.000206	T	0.28764	0.0713	N	0.03281	-0.365	0.32149	N	0.584446	B;B	0.06786	0.0;0.001	B;B	0.09377	0.0;0.004	T	0.33343	-0.9872	10	0.10377	T	0.69	.	8.2247	0.31562	0.8504:0.0:0.1496:0.0	.	718;609	Q02246;Q68DA2	CNTN2_HUMAN;.	G	718	ENSP00000330633:S718G	ENSP00000330633:S718G	S	+	1	0	CNTN2	203305268	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	2.023000	0.41040	2.114000	0.64651	0.460000	0.39030	AGC	.	.		0.597	CNTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090080.3	NM_005076		G	205038645	A	G	205038645	3	3	283	1	0	0	0	0	1	0	0	0	3643	188	7	2	2214	2	CNTN2	1	205038645	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	4195396	205038645	44211976	23	41661										
EPRS	2058	hgsc.bcm.edu	37	chr1	220146578	220146578	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ataagcaattttaagaaactAccttgtgaaaagggtgacct	8	6	0	3			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr1:220146578A>G	ENST00000366923.3	-	29	4514		c.e29+1			NM_004446.2	NP_004437.2	P07814	SYEP_HUMAN	glutamyl-prolyl-tRNA synthetase						cellular response to interferon-gamma (GO:0071346)|gene expression (GO:0010467)|glutamyl-tRNA aminoacylation (GO:0006424)|negative regulation of translation (GO:0017148)|prolyl-tRNA aminoacylation (GO:0006433)|protein complex assembly (GO:0006461)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|GAIT complex (GO:0097452)|membrane (GO:0016020)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|glutamate-tRNA ligase activity (GO:0004818)|proline-tRNA ligase activity (GO:0004827)|RNA stem-loop binding (GO:0035613)			breast(2)|endometrium(11)|kidney(2)|large_intestine(13)|lung(24)|ovary(1)|prostate(3)|skin(2)|stomach(2)|urinary_tract(3)	63				GBM - Glioblastoma multiforme(131;0.0735)	L-Proline(DB00172)	TTAAGAAACTACCTTGTGAAA	0.418																																					.		Atlas-SNP	.											.	EPRS	140	.	0			c.4244+2T>C						.						156	150	152					1																	220146578		2203	4300	6503	SO:0001630	splice_region_variant	2058	exon30			GAAACTACCTTGT	X54326	CCDS31027.1	1q41	2011-07-01			ENSG00000136628	ENSG00000136628	6.1.1.15, 6.1.1.17	"Aminoacyl tRNA synthetases / Class I", "Aminoacyl tRNA synthetases / Class II"	3418	protein-coding gene	gene with protein product	"glutamate tRNA ligase", "proline tRNA ligase"	138295		QPRS, QARS		1988429	Standard	NM_004446		Approved	EARS, PARS, GLUPRORS	uc001hly.1	P07814	OTTHUMG00000037433	ENST00000366923.3:c.4244+1T>C	chr1.hg19:g.220146578A>G		150.0	0.0		135.0	21.0	NM_004446	A0AVA9|B9EGH3|Q05BP6|Q05DF8|Q5DSM1|Q5H9S5|Q6PD57|Q86X73	Splice_Site	SNP	ENST00000366923.3	hg19	CCDS31027.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.306983	0.81247	.	.	ENSG00000136628	ENST00000366923	.	.	.	5.91	5.91	0.95273	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3483	0.83171	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	EPRS	218213201	1.000000	0.71417	0.453000	0.27007	0.830000	0.47004	8.593000	0.90832	2.254000	0.74563	0.533000	0.62120	.	.	.		0.418	EPRS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091133.2	NM_004446	Intron	G	220146578	A	G	220146578	5	3	283	1	0	0	0	0	0	0	1	0	5193	405	14	2	308	2	EPRS	1	220146578	Splice_Site	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	15107933	220146578	29104043	24	41662										
LBR	3930	hgsc.bcm.edu	37	chr1	225611703	225611703	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ctgtcgtggctcagaatttcTacttcataataaagtgaact	7	8	3	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr1:225611703T>C	ENST00000338179.2	-	2	200	c.75A>G	c.(73-75)gtA>gtG	p.V25V	LBR_ENST00000272163.4_Silent_p.V25V	NM_194442.2	NP_919424.1	Q14739	LBR_HUMAN	lamin B receptor	25	Tudor.				cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|integral component of nuclear inner membrane (GO:0005639)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|lamin binding (GO:0005521)|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor (GO:0016628)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22	Breast(184;0.165)			GBM - Glioblastoma multiforme(131;0.117)		TCAGAATTTCTACTTCATAAT	0.393																																					p.V25V		Atlas-SNP	.											.	LBR	54	.	0			c.A75G						.						252	270	264					1																	225611703		2203	4300	6503	SO:0001819	synonymous_variant	3930	exon2			AATTTCTACTTCA	L25931	CCDS1545.1	1q42.1	2013-01-23			ENSG00000143815	ENSG00000143815		"Tudor domain containing"	6518	protein-coding gene	gene with protein product	"tudor domain containing 18"	600024				8157663, 9878250	Standard	NM_194442		Approved	DHCR14B, TDRD18	uc001hoy.3	Q14739	OTTHUMG00000037520	ENST00000338179.2:c.75A>G	chr1.hg19:g.225611703T>C		165.0	0.0		192.0	46.0	NM_194442	B2R5P3|Q14740|Q53GU7|Q59FE6	Silent	SNP	ENST00000338179.2	hg19	CCDS1545.1																																																																																			.	.		0.393	LBR-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091398.1	NM_002296		C	225611703	T	C	225611703	2	2	283	1	0	0	0	0	0	0	0	1	8661	1509	53	2		2	LBR	1	225611703	Silent	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	5465125	225611703	23638918	25	41663										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228469861	228469861	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gtgatgccggggaggtggtcTtctctgtgcggggcctcacc	17	11	3	1	rs189169421	byFrequency	TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr1:228469861T>C	ENST00000422127.1	+	31	8469	c.8425T>C	c.(8425-8427)Ttc>Ctc	p.F2809L	OBSCN_ENST00000570156.2_Missense_Mutation_p.F3238L|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000359599.6_Missense_Mutation_p.F1656L|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Missense_Mutation_p.F2809L	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	2809	Ig-like 27.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)	p.F3092V(1)|p.F2863V(1)		NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GGAGGTGGTCTTCTCTGTGCG	0.652																																					p.F3238L		Atlas-SNP	.											OBSCN_ENST00000359599,NS,carcinoma,0,2	OBSCN	2142	.	2	Substitution - Missense(2)	stomach(2)	c.T9712C						.						32	38	36					1																	228469861		1988	4152	6140	SO:0001583	missense	84033	exon36			GTGGTCTTCTCTG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.8425T>C	chr1.hg19:g.228469861T>C	ENSP00000409493:p.Phe2809Leu	254.0	0.0		303.0	172.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.225054	0.79576	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000359599;ENST00000366706;ENST00000366704	T;T;T	0.38560	1.13;1.13;1.13	4.21	4.21	0.49690	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000001	T	0.58538	0.2129	L	0.60455	1.87	0.80722	D	1	D;D;D	0.89917	0.991;1.0;0.998	P;D;D	0.87578	0.904;0.997;0.998	T	0.57412	-0.7816	10	0.36615	T	0.2	.	13.6084	0.62061	0.0:0.0:0.0:1.0	.	2809;2809;2809	Q5VST9;Q5VST9-2;Q5VST9-3	OBSCN_HUMAN;.;.	L	2809;2809;1656;508;215	ENSP00000284548:F2809L;ENSP00000409493:F2809L;ENSP00000352613:F1656L	ENSP00000284548:F2809L	F	+	1	0	OBSCN	226536484	1.000000	0.71417	1.000000	0.80357	0.396000	0.30629	7.599000	0.82757	1.679000	0.50963	0.379000	0.24179	TTC	.	T|0.999;G|0.001		0.652	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		C	228469861	T	C	228469861	3	2	283	1	0	0	0	0	1	0	0	0	10821	1609	56	2	8543	2	OBSCN	1	228469861	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	2858158	228469861	20780760	26	41664										
RAB4A	5867	hgsc.bcm.edu	37	chr1	229431599	229431599	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	agtataattcttccaggtccGtgacgagaagttattaccga	9	8	1	2	rs141754859		TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr1:229431599G>T	ENST00000366690.4	+	4	440	c.232G>T	c.(232-234)Gtg>Ttg	p.V78L	RAB4A_ENST00000473894.1_3'UTR	NM_004578.2	NP_004569.2	P20338	RAB4A_HUMAN	RAB4A, member RAS oncogene family	78					antigen processing and presentation (GO:0019882)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|regulation of endocytosis (GO:0030100)|small GTPase mediated signal transduction (GO:0007264)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|protein transporter activity (GO:0008565)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|skin(1)	11	Breast(184;0.0858)|Ovarian(103;0.103)	Prostate(94;0.178)				TTCCAGGTCCGTGACGAGAAG	0.502																																					p.V78L	Esophageal Squamous(11;250 603 9619 16563)	Atlas-SNP	.											.	RAB4A	29	.	0			c.G232T						.						78	81	80					1																	229431599		2203	4300	6503	SO:0001583	missense	5867	exon4			AGGTCCGTGACGA	BC004309	CCDS31050.1, CCDS73046.1	1q42-q43	2014-04-03		2002-02-28	ENSG00000168118	ENSG00000168118		"RAB, member RAS oncogene"	9781	protein-coding gene	gene with protein product		179511		RAB4			Standard	NM_004578		Approved	HRES-1/RAB4	uc001hth.4	P20338	OTTHUMG00000037627	ENST00000366690.4:c.232G>T	chr1.hg19:g.229431599G>T	ENSP00000355651:p.Val78Leu	110.0	0.0		125.0	32.0	NM_004578	Q5T7P7|Q9BQ44	Missense_Mutation	SNP	ENST00000366690.4	hg19	CCDS31050.1	.	.	.	.	.	.	.	.	.	.	G	15.01	2.705486	0.48412	.	.	ENSG00000168118	ENST00000366690	T	0.71461	-0.57	4.58	4.58	0.56647	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.63745	0.2537	N	0.11756	0.17	0.80722	D	1	B	0.31640	0.333	P	0.44561	0.453	T	0.68526	-0.5385	10	0.62326	D	0.03	.	14.572	0.68218	0.0:0.0:1.0:0.0	.	73	P20338	RAB4A_HUMAN	L	78	ENSP00000355651:V78L	ENSP00000355651:V78L	V	+	1	0	RAB4A	227498222	1.000000	0.71417	1.000000	0.80357	0.030000	0.12068	8.984000	0.93482	2.498000	0.84270	0.655000	0.94253	GTG	.	G|1.000;A|0.000		0.502	RAB4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091727.3	NM_004578		T	229431599	G	T	229431599	3	4	283	1	0	0	0	0	1	0	0	0	12961	1145	40	1	246	1	RAB4A	1	229431599	Missense_Mutation	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	961738	229431599	19819022	27	41665										
URB2	9816	hgsc.bcm.edu	37	chr1	229779359	229779359	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	acccaaatgttagaggttggGacgacagaggacttgaggct	14	7	0	3			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr1:229779359G>A	ENST00000258243.2	+	5	3850	c.3714G>A	c.(3712-3714)ggG>ggA	p.G1238G		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	1238						aggresome (GO:0016235)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(6)	73						TAGAGGTTGGGACGACAGAGG	0.498																																					p.G1238G		Atlas-SNP	.											.	URB2	152	.	0			c.G3714A						.						180	164	170					1																	229779359		2203	4300	6503	SO:0001819	synonymous_variant	9816	exon5			GGTTGGGACGACA	D50923	CCDS31052.1	1q42.13	2009-11-06	2008-10-01	2008-10-01	ENSG00000135763	ENSG00000135763			28967	protein-coding gene	gene with protein product	"nucleolar preribosomal-associated protein 1"		"KIAA0133"	KIAA0133		8590280	Standard	NM_014777		Approved	NPA2, NET10	uc001hts.1	Q14146	OTTHUMG00000039464	ENST00000258243.2:c.3714G>A	chr1.hg19:g.229779359G>A		208.0	0.0		253.0	127.0	NM_014777	Q5VYC9	Silent	SNP	ENST00000258243.2	hg19	CCDS31052.1																																																																																			.	.		0.498	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777		A	229779359	G	A	229779359	2	1	283	1	0	0	0	0	0	0	0	1	17040	1161	41	3		3	URB2	1	229779359	Silent	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	347760	229779359	19471262	28	41666										
KIAA1383	54627	hgsc.bcm.edu	37	chr1	232941381	232941381	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gccgtggccttccgcctgctGgacttccccacgctgttggt	12	16	0	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr1:232941381G>A	ENST00000418460.1	+	1	739	c.612G>A	c.(610-612)ctG>ctA	p.L204L		NM_019090.2	NP_061963.2	Q9P2G4	MAP10_HUMAN	microtubule-associated protein 10	62					cytoplasmic microtubule organization (GO:0031122)|positive regulation of cytokinesis (GO:0032467)|regulation of microtubule-based process (GO:0032886)|spindle midzone assembly involved in mitosis (GO:0051256)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|mitotic spindle pole (GO:0097431)	microtubule binding (GO:0008017)										TCCGCCTGCTGGACTTCCCCA	0.716																																					p.L204L		Atlas-SNP	.											.	.	.	.	0			c.G612A						.						5	7	6					1																	232941381		1949	4080	6029	SO:0001819	synonymous_variant	54627	exon1			CCTGCTGGACTTC	AB037804	CCDS44334.1	1q42.2	2013-02-12	2013-02-12	2013-02-12	ENSG00000212916	ENSG00000212916			29265	protein-coding gene	gene with protein product	"microtubule regulator 120 KDa"		"KIAA1383"	KIAA1383		23264731	Standard	NM_019090		Approved	MTR120	uc001hvh.2	Q9P2G4	OTTHUMG00000037819	ENST00000418460.1:c.612G>A	chr1.hg19:g.232941381G>A		31.0	0.0		50.0	4.0	NM_019090	A8K2F1|Q32MI1|Q58EZ9|Q5VV83	Silent	SNP	ENST00000418460.1	hg19	CCDS44334.1																																																																																			.	.		0.716	MAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092317.3	NM_019090		A	232941381	G	A	232941381	2	1	283	1	0	0	0	0	0	0	0	1	8237	1335	47	3		3	KIAA1383	1	232941381	Silent	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	3162022	232941381	16309240	29	41667										
BIRC6	57448	hgsc.bcm.edu	37	chr2	32654298	32654298	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	agtggatggatctctttctaAaggaatagaaccatcttcag	9	7	4	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr2:32654298A>C	ENST00000421745.2	+	11	3091	c.2957A>C	c.(2956-2958)aAa>aCa	p.K986T		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	986					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					TCTCTTTCTAAAGGAATAGAA	0.333																																					p.K986T	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.A2957C						.						54	52	53					2																	32654298		2202	4296	6498	SO:0001583	missense	57448	exon11			TTTCTAAAGGAAT	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.2957A>C	chr2.hg19:g.32654298A>C	ENSP00000393596:p.Lys986Thr	37.0	0.0		37.0	17.0	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	hg19	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	A	13.60	2.285916	0.40394	.	.	ENSG00000115760	ENST00000421745	T	0.75050	-0.9	4.91	4.91	0.64330	.	0.000000	0.85682	D	0.000000	T	0.59101	0.2169	L	0.29908	0.895	0.47698	D	0.999499	P	0.37781	0.608	B	0.24701	0.055	T	0.62501	-0.6841	10	0.38643	T	0.18	.	14.8359	0.70183	1.0:0.0:0.0:0.0	.	986	Q9NR09	BIRC6_HUMAN	T	986	ENSP00000393596:K986T	ENSP00000393596:K986T	K	+	2	0	BIRC6	32507802	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.038000	0.93771	1.957000	0.56846	0.460000	0.39030	AAA	.	.		0.333	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		C	32654298	A	C	32654298	3	2	283	1	0	0	0	0	1	0	0	0	1438	14	1	5	2999	5	BIRC6	2	32654298	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10		32654298	210545075	30	41668										
SRBD1	55133	hgsc.bcm.edu	37	chr2	45812829	45812829	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ctcttttctataacgtataaTgaagggaattgtgttatcat	7	5	3	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr2:45812829T>G	ENST00000263736.4	-	5	795	c.733A>C	c.(733-735)Att>Ctt	p.I245L		NM_018079.4	NP_060549.4	Q8N5C6	SRBD1_HUMAN	S1 RNA binding domain 1	245					nucleobase-containing compound metabolic process (GO:0006139)		hydrolase activity, acting on ester bonds (GO:0016788)|RNA binding (GO:0003723)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(13)|large_intestine(8)|lung(15)|skin(2)|stomach(1)|urinary_tract(1)	49		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	LUSC - Lung squamous cell carcinoma(58;0.0917)|Lung(47;0.154)			TAACGTATAATGAAGGGAATT	0.348																																					p.I245L		Atlas-SNP	.											.	SRBD1	107	.	0			c.A733C						.						112	115	114					2																	45812829		2203	4300	6503	SO:0001583	missense	55133	exon5			GTATAATGAAGGG	AK056536	CCDS1823.1	2p21	2008-02-05			ENSG00000068784	ENSG00000068784			25521	protein-coding gene	gene with protein product						12477932	Standard	NM_018079		Approved	FLJ10379	uc002rus.3	Q8N5C6	OTTHUMG00000128814	ENST00000263736.4:c.733A>C	chr2.hg19:g.45812829T>G	ENSP00000263736:p.Ile245Leu	134.0	0.0		104.0	25.0	NM_018079	Q53T56|Q96TA4|Q9NW11	Missense_Mutation	SNP	ENST00000263736.4	hg19	CCDS1823.1	.	.	.	.	.	.	.	.	.	.	T	15.95	2.985232	0.53934	.	.	ENSG00000068784	ENST00000263736	T	0.63580	-0.05	5.04	5.04	0.67666	Tex-like protein, N-terminal (1);Tex-like protein, HTH domain (1);	0.075235	0.53938	D	0.000059	T	0.72574	0.3477	M	0.93507	3.425	0.80722	D	1	B	0.25235	0.121	B	0.26416	0.069	T	0.76591	-0.2903	10	0.87932	D	0	.	14.6045	0.68466	0.0:0.0:0.0:1.0	.	245	Q8N5C6	SRBD1_HUMAN	L	245	ENSP00000263736:I245L	ENSP00000263736:I245L	I	-	1	0	SRBD1	45666333	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.851000	0.62896	2.113000	0.64589	0.455000	0.32223	ATT	.	.		0.348	SRBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250747.3	NM_018079		G	45812829	T	G	45812829	3	3	283	1	0	0	0	0	1	0	0	0	15148	1464	51	5	2322	5	SRBD1	2	45812829	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	13158531	45812829	197386544	31	41669										
STON1	11037	hgsc.bcm.edu	37	chr2	48818835	48818835	+	Frame_Shift_Del	DEL	A	A	-													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tcatacaaattagagcttggAtcagaccaagaaattccctc							TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr2:48818835delA	ENST00000406226.1	+	4	2169	c.1974delA	c.(1972-1974)ggafs	p.G658fs	STON1_ENST00000309835.3_Frame_Shift_Del_p.G658fs|STON1_ENST00000404752.1_Frame_Shift_Del_p.G658fs|STON1-GTF2A1L_ENST00000394754.1_Frame_Shift_Del_p.G658fs|STON1-GTF2A1L_ENST00000309827.2_Frame_Shift_Del_p.G658fs|STON1-GTF2A1L_ENST00000402114.2_Frame_Shift_Del_p.G658fs|STON1-GTF2A1L_ENST00000394751.3_Frame_Shift_Del_p.G658fs|STON1-GTF2A1L_ENST00000405008.1_Frame_Shift_Del_p.G658fs	NM_001198595.1	NP_001185524.1	Q9Y6Q2	STON1_HUMAN	stonin 1	658	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)	clathrin adaptor complex (GO:0030131)				NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(19)|prostate(3)|skin(2)	37		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TAGAGCTTGGATCAGACCAAG	0.428																																					p.G658fs		Atlas-INDEL	.											.	STON1-GTF2A1L	180	.	0			c.1973delG						.						192	185	187					2																	48818835		2203	4300	6503	SO:0001589	frameshift_variant	286749	exon3			.	AF026169	CCDS1841.1	2p16.3	2008-02-05			ENSG00000243244	ENSG00000243244			17003	protein-coding gene	gene with protein product	"stoned B homolog 1 (Drosophila)"	605357				14504226, 10364255	Standard	NM_001198595		Approved	SBLF, stoned-b1		Q9Y6Q2	OTTHUMG00000129169	ENST00000406226.1:c.1974delA	chr2.hg19:g.48818835delA	ENSP00000384615:p.Gly658fs	255.0	0.0		213.0	36.0	NM_172311	A8MXJ1|B5MCF5|B7ZL16|Q96JE3|Q9BYX3	Frame_Shift_Del	DEL	ENST00000406226.1	hg19	CCDS1841.1																																																																																			.	.		0.428	STON1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323848.2	NM_006873		-	48818835	A	-	48818835	7	5	283	1	0	1	0	1	0	0	0	0	15331	320	12	0	1980	0	STON1	2	48818835	Frame_Shift_Del	DEL	A	TCGA-G3-A3CK-01A-11D-A20W-10	3006006	48818835	194380538	32	41670	209	3								
STON1	11037	hgsc.bcm.edu	37	chr2	48818838	48818838	+	Silent	SNP	A	A	T													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tacaaattagagcttggatcAgaccaagaaattccctctga							TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr2:48818838A>T	ENST00000406226.1	+	4	2172	c.1977A>T	c.(1975-1977)tcA>tcT	p.S659S	STON1_ENST00000309835.3_Silent_p.S659S|STON1_ENST00000404752.1_Silent_p.S659S|STON1-GTF2A1L_ENST00000394754.1_Silent_p.S659S|STON1-GTF2A1L_ENST00000309827.2_Silent_p.S659S|STON1-GTF2A1L_ENST00000402114.2_Silent_p.S659S|STON1-GTF2A1L_ENST00000394751.3_Silent_p.S659S|STON1-GTF2A1L_ENST00000405008.1_Silent_p.S659S	NM_001198595.1	NP_001185524.1	Q9Y6Q2	STON1_HUMAN	stonin 1	659	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)	clathrin adaptor complex (GO:0030131)				NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(19)|prostate(3)|skin(2)	37		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AGCTTGGATCAGACCAAGAAA	0.428																																					p.S659S		Atlas-SNP	.											.	STON1	100	.	0			c.A1977T						.						191	185	187					2																	48818838		2203	4300	6503	SO:0001819	synonymous_variant	11037	exon4			TGGATCAGACCAA	AF026169	CCDS1841.1	2p16.3	2008-02-05			ENSG00000243244	ENSG00000243244			17003	protein-coding gene	gene with protein product	"stoned B homolog 1 (Drosophila)"	605357				14504226, 10364255	Standard	NM_001198595		Approved	SBLF, stoned-b1		Q9Y6Q2	OTTHUMG00000129169	ENST00000406226.1:c.1977A>T	chr2.hg19:g.48818838A>T		258.0	0.0		216.0	36.0	NM_001198595	A8MXJ1|B5MCF5|B7ZL16|Q96JE3|Q9BYX3	Silent	SNP	ENST00000406226.1	hg19	CCDS1841.1																																																																																			.	.		0.428	STON1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323848.2	NM_006873		T	48818838	A	T	48818838	2	4	283	1	0	0	0	0	0	0	0	1	15331	175	7	4		4	STON1	2	48818838	Silent	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	3	48818838	194380535	33	41671	209	3								
STON1	11037	hgsc.bcm.edu	37	chr2	48818840	48818841	+	Frame_Shift_Del	DEL	AC	AC	-													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	caaattagagcttggatcagAccaagaaattccctctgatt							TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr2:48818840_48818841delAC	ENST00000406226.1	+	4	2174_2175	c.1979_1980delAC	c.(1978-1980)gacfs	p.D660fs	STON1_ENST00000309835.3_Frame_Shift_Del_p.D660fs|STON1_ENST00000404752.1_Frame_Shift_Del_p.D660fs|STON1-GTF2A1L_ENST00000394754.1_Frame_Shift_Del_p.D660fs|STON1-GTF2A1L_ENST00000309827.2_Frame_Shift_Del_p.D660fs|STON1-GTF2A1L_ENST00000402114.2_Frame_Shift_Del_p.D660fs|STON1-GTF2A1L_ENST00000394751.3_Frame_Shift_Del_p.D660fs|STON1-GTF2A1L_ENST00000405008.1_Frame_Shift_Del_p.D660fs	NM_001198595.1	NP_001185524.1	Q9Y6Q2	STON1_HUMAN	stonin 1	660	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)	clathrin adaptor complex (GO:0030131)				NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(19)|prostate(3)|skin(2)	37		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			CTTGGATCAGACCAAGAAATTC	0.431																																					p.660_660del		Atlas-INDEL	.											.	STON1-GTF2A1L	180	.	0			c.1978_1979del						.																																			SO:0001589	frameshift_variant	286749	exon3			.	AF026169	CCDS1841.1	2p16.3	2008-02-05			ENSG00000243244	ENSG00000243244			17003	protein-coding gene	gene with protein product	"stoned B homolog 1 (Drosophila)"	605357				14504226, 10364255	Standard	NM_001198595		Approved	SBLF, stoned-b1		Q9Y6Q2	OTTHUMG00000129169	ENST00000406226.1:c.1979_1980delAC	chr2.hg19:g.48818840_48818841delAC	ENSP00000384615:p.Asp660fs	252.0	0.0		214.0	35.0	NM_172311	A8MXJ1|B5MCF5|B7ZL16|Q96JE3|Q9BYX3	Frame_Shift_Del	DEL	ENST00000406226.1	hg19	CCDS1841.1																																																																																			.	.		0.431	STON1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323848.2	NM_006873		-	48818841	AC	-	48818840	7	5	283	1	0	1	0	1	0	0	0	0	15331	275	10	0	1985	0	STON1	2	48818840	Frame_Shift_Del	DEL	AC	TCGA-G3-A3CK-01A-11D-A20W-10	2	48818840	194380533	34	41672	209	3								
ZNF638	27332	hgsc.bcm.edu	37	chr2	71577282	71577282	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	taccaaagttttcacatgctGatgcccagaagatgaagaga	9	8	1	5			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr2:71577282G>A	ENST00000409544.1	+	2	1828	c.1198G>A	c.(1198-1200)Gat>Aat	p.D400N	ZNF638_ENST00000410075.1_3'UTR|ZNF638_ENST00000355812.3_Missense_Mutation_p.D400N|ZNF638_ENST00000377802.2_Missense_Mutation_p.D400N|ZNF638_ENST00000264447.4_Missense_Mutation_p.D400N	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	400					regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						TTCACATGCTGATGCCCAGAA	0.408																																					p.D400N		Atlas-SNP	.											.	ZNF638	179	.	0			c.G1198A						.						142	140	141					2																	71577282		2203	4300	6503	SO:0001583	missense	27332	exon2			CATGCTGATGCCC	D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"RNA binding motif (RRM) containing"	17894	protein-coding gene	gene with protein product		614349	"zinc finger, matrin-like"	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.1198G>A	chr2.hg19:g.71577282G>A	ENSP00000386433:p.Asp400Asn	58.0	0.0		82.0	6.0	NM_014497	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Missense_Mutation	SNP	ENST00000409544.1	hg19	CCDS1917.1	.	.	.	.	.	.	.	.	.	.	G	13.54	2.266494	0.40095	.	.	ENSG00000075292	ENST00000410075;ENST00000544512;ENST00000355812;ENST00000377802;ENST00000264447;ENST00000409544	T;T;T;T;T;T	0.74842	-0.29;-0.88;0.3;-0.27;1.32;1.32	5.85	4.98	0.66077	.	0.377447	0.29335	N	0.012444	T	0.60379	0.2264	N	0.14661	0.345	0.28440	N	0.916847	D;P;P;P;P	0.56521	0.976;0.873;0.873;0.799;0.787	P;B;P;B;B	0.46452	0.517;0.42;0.517;0.272;0.42	T	0.54576	-0.8273	10	0.15499	T	0.54	-10.4049	12.5196	0.56052	0.08:0.0:0.92:0.0	.	506;400;400;400;400	F5H330;Q14966-4;Q14966-3;Q14966;Q14966-2	.;.;.;ZN638_HUMAN;.	N	400;506;400;400;400;400	ENSP00000386669:D400N;ENSP00000438189:D506N;ENSP00000348066:D400N;ENSP00000367033:D400N;ENSP00000264447:D400N;ENSP00000386433:D400N	ENSP00000264447:D400N	D	+	1	0	ZNF638	71430790	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.860000	0.48372	1.493000	0.48517	0.655000	0.94253	GAT	.	.		0.408	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497		A	71577282	G	A	71577282	3	1	283	1	0	0	0	0	1	0	0	0	18070	1290	45	3	1200	3	ZNF638	2	71577282	Missense_Mutation	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	22758442	71577282	171622091	35	41673										
AFF3	3899	hgsc.bcm.edu	37	chr2	100210640	100210640	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tttcaccgggttgtagtactGattgctctctgacccgtggc	11	11	2	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr2:100210640G>T	ENST00000409236.2	-	13	1595	c.1483C>A	c.(1483-1485)Cag>Aag	p.Q495K	AFF3_ENST00000356421.2_Missense_Mutation_p.Q520K|AFF3_ENST00000317233.4_Missense_Mutation_p.Q495K|AFF3_ENST00000409579.1_Missense_Mutation_p.Q520K			P51826	AFF3_HUMAN	AF4/FMR2 family, member 3	495					embryonic hindlimb morphogenesis (GO:0035116)|regulation of transcription, DNA-templated (GO:0006355)|response to tumor necrosis factor (GO:0034612)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)			NS(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(9)|kidney(4)|large_intestine(20)|liver(1)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(3)	86						TTGTAGTACTGATTGCTCTCT	0.498																																					p.Q520K		Atlas-SNP	.											.	AFF3	164	.	0			c.C1558A						.						144	161	156					2																	100210640		2203	4300	6503	SO:0001583	missense	3899	exon14			AGTACTGATTGCT	U34360	CCDS33258.1, CCDS42723.1	2q11.2-q12	2008-02-05	2005-06-27	2005-06-27	ENSG00000144218	ENSG00000144218			6473	protein-coding gene	gene with protein product		601464	"lymphoid nuclear protein related to AF4"	LAF4		8662235, 8555498	Standard	XM_005263945		Approved	MLLT2-like	uc002taf.3	P51826	OTTHUMG00000153011	ENST00000409236.2:c.1483C>A	chr2.hg19:g.100210640G>T	ENSP00000387207:p.Gln495Lys	279.0	0.0		244.0	72.0	NM_001025108	B7ZM46|B9EGL9|D3DVI6|Q53RD6|Q53S47|Q53SI6|Q53TB9|Q59F27|Q8IWJ5	Missense_Mutation	SNP	ENST00000409236.2	hg19	CCDS42723.1	.	.	.	.	.	.	.	.	.	.	G	12.78	2.040639	0.35989	.	.	ENSG00000144218	ENST00000317233;ENST00000356421;ENST00000409579;ENST00000409236;ENST00000433370;ENST00000444786;ENST00000432288	T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04	5.87	5.87	0.94306	.	0.162135	0.30383	N	0.009758	T	0.66167	0.2762	L	0.43152	1.355	0.38657	D	0.951992	P;D;B	0.53885	0.828;0.963;0.426	P;P;B	0.54401	0.621;0.751;0.085	T	0.60347	-0.7281	10	0.14656	T	0.56	.	17.9961	0.89184	0.0:0.0:1.0:0.0	.	648;495;520	B7Z4I6;P51826;P51826-2	.;AFF3_HUMAN;.	K	495;520;520;495;495;648;520	ENSP00000317421:Q495K;ENSP00000348793:Q520K;ENSP00000386834:Q520K;ENSP00000387207:Q495K	ENSP00000317421:Q495K	Q	-	1	0	AFF3	99577072	0.999000	0.42202	0.705000	0.30386	0.881000	0.50899	4.067000	0.57527	2.781000	0.95711	0.655000	0.94253	CAG	.	.		0.498	AFF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328982.3	NM_002285		T	100210640	G	T	100210640	3	4	283	1	0	0	0	0	1	0	0	0	358	1299	45	3	2241	3	AFF3	2	100210640	Missense_Mutation	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	28633358	100210640	142988733	36	41674										
ZC3H8	84524	hgsc.bcm.edu	37	chr2	112989510	112989510	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tgttcctgtatggtaaaactTacaaggatattcatgtaacc	7	7	1	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr2:112989510T>G	ENST00000409573.2	-	7	877	c.748A>C	c.(748-750)Aag>Cag	p.K250Q	ZC3H8_ENST00000272570.5_Missense_Mutation_p.K250Q|ZC3H8_ENST00000476902.1_5'Flank			Q8N5P1	ZC3H8_HUMAN	zinc finger CCCH-type containing 8	250					apoptotic process (GO:0006915)|negative regulation of T cell differentiation in thymus (GO:0033085)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|response to antibiotic (GO:0046677)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)|T cell homeostasis (GO:0043029)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)	7						TGGTAAAACTTACAAGGATAT	0.313																																					p.K250Q		Atlas-SNP	.											.	ZC3H8	17	.	0			c.A748C						.						89	88	88					2																	112989510		1889	4135	6024	SO:0001583	missense	84524	exon7			AAAACTTACAAGG	AF334161	CCDS46392.1	2q13	2012-07-05	2005-06-02	2005-06-02	ENSG00000144161	ENSG00000144161		"Zinc fingers, CCCH-type domain containing"	30941	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 8"	ZC3HDC8		12477932	Standard	NM_032494		Approved	Fliz1	uc021vmw.1	Q8N5P1	OTTHUMG00000153270	ENST00000409573.2:c.748A>C	chr2.hg19:g.112989510T>G	ENSP00000386488:p.Lys250Gln	63.0	0.0		74.0	24.0	NM_032494	Q9BZ75	Missense_Mutation	SNP	ENST00000409573.2	hg19	CCDS46392.1	.	.	.	.	.	.	.	.	.	.	T	17.77	3.470279	0.63625	.	.	ENSG00000144161	ENST00000409573;ENST00000272570	T;T	0.39787	1.06;1.06	4.73	4.73	0.59995	Zinc finger, CCCH-type (2);	1.625670	0.03800	N	0.264353	T	0.71384	0.3333	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.53781	-0.8390	10	0.72032	D	0.01	1.4205	14.3393	0.66614	0.0:0.0:0.0:1.0	.	250	Q8N5P1	ZC3H8_HUMAN	Q	250	ENSP00000386488:K250Q;ENSP00000272570:K250Q	ENSP00000272570:K250Q	K	-	1	0	ZC3H8	112705981	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.248000	0.78268	2.103000	0.63969	0.379000	0.24179	AAG	.	.		0.313	ZC3H8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330521.3	NM_032494		G	112989510	T	G	112989510	3	3	283	1	0	0	0	0	1	0	0	0	17589	1763	61	5	135	5	ZC3H8	2	112989510	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	12778870	112989510	130209863	37	41675										
PTPN18	26469	hgsc.bcm.edu	37	chr2	131117002	131117002	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	agcctggcctacattgccacGcaaggacccttgcctcacac	8	17	1	0	rs138461234	byFrequency	TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr2:131117002G>T	ENST00000175756.5	+	4	413	c.312G>T	c.(310-312)acG>acT	p.T104T	PTPN18_ENST00000347849.3_Intron|PTPN18_ENST00000420717.1_3'UTR	NM_014369.3	NP_055184.2	Q99952	PTN18_HUMAN	protein tyrosine phosphatase, non-receptor type 18 (brain-derived)	104	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)			endometrium(1)|kidney(3)|large_intestine(2)|lung(5)|ovary(3)|prostate(1)	15	Colorectal(110;0.1)					ACATTGCCACGCAAGGACCCT	0.607																																					p.T104T		Atlas-SNP	.											.	PTPN18	42	.	0			c.G312T						.						98	89	92					2																	131117002		2203	4300	6503	SO:0001819	synonymous_variant	26469	exon4			TGCCACGCAAGGA	X79568	CCDS2161.1, CCDS46410.1	2q21	2011-06-09			ENSG00000072135	ENSG00000072135		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9649	protein-coding gene	gene with protein product		606587				8950995	Standard	NM_014369		Approved	BDP1	uc002trc.3	Q99952	OTTHUMG00000131630	ENST00000175756.5:c.312G>T	chr2.hg19:g.131117002G>T		119.0	0.0		98.0	30.0	NM_014369	B4E1E6|Q53P42	Silent	SNP	ENST00000175756.5	hg19	CCDS2161.1																																																																																			.	G|0.996;C|0.004		0.607	PTPN18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254523.2			T	131117002	G	T	131117002	2	4	283	1	0	0	0	0	0	0	0	1	12797	1074	38	1		1	PTPN18	2	131117002	Silent	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	18127492	131117002	112082371	38	41676										
COBLL1	22837	hgsc.bcm.edu	37	chr2	165542496	165542496	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	caggggacatggaatggctgAgtcttgaccttccattcaca	11	10	2	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr2:165542496A>C	ENST00000392717.2	-	15	3579	c.3575T>G	c.(3574-3576)cTc>cGc	p.L1192R	COBLL1_ENST00000409184.3_Missense_Mutation_p.L1154R|SNORA70F_ENST00000384142.1_RNA|COBLL1_ENST00000342193.4_Missense_Mutation_p.L1154R|COBLL1_ENST00000375458.2_Missense_Mutation_p.L1116R|COBLL1_ENST00000194871.6_Missense_Mutation_p.L1221R			Q53SF7	COBL1_HUMAN	cordon-bleu WH2 repeat protein-like 1	1192						extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	47						GGAATGGCTGAGTCTTGACCT	0.438																																					p.L1154R		Atlas-SNP	.											.	COBLL1	122	.	0			c.T3461G						.						150	120	130					2																	165542496		2203	4300	6503	SO:0001583	missense	22837	exon14			TGGCTGAGTCTTG	AB023194	CCDS2223.2, CCDS63045.1	2q24.3	2012-12-07	2012-12-07		ENSG00000082438	ENSG00000082438			23571	protein-coding gene	gene with protein product		610318	"COBL-like 1"				Standard	NM_001278458		Approved	KIAA0977	uc002ucp.3	Q53SF7	OTTHUMG00000074019	ENST00000392717.2:c.3575T>G	chr2.hg19:g.165542496A>C	ENSP00000376478:p.Leu1192Arg	96.0	0.0		93.0	34.0	NM_014900	A6NMZ3|Q6IQ33|Q7Z3I6|Q9BRH4|Q9UG88|Q9Y2I3	Missense_Mutation	SNP	ENST00000392717.2	hg19		.	.	.	.	.	.	.	.	.	.	A	19.15	3.772607	0.69992	.	.	ENSG00000082438	ENST00000375458;ENST00000342193;ENST00000409184;ENST00000392717;ENST00000194871	.	.	.	5.62	5.62	0.85841	.	0.097389	0.45606	D	0.000345	T	0.77164	0.4090	M	0.66939	2.045	0.47374	D	0.999405	D;D;D	0.76494	0.998;0.998;0.999	D;D;D	0.69142	0.917;0.917;0.962	T	0.79771	-0.1663	9	0.87932	D	0	-1.6258	16.1219	0.81365	1.0:0.0:0.0:0.0	.	1192;1221;1154	Q53SF7;B7Z2P5;Q53SF7-2	COBL1_HUMAN;.;.	R	1116;1154;1154;1192;1221	.	ENSP00000194871:L1221R	L	-	2	0	COBLL1	165250742	1.000000	0.71417	0.982000	0.44146	0.909000	0.53808	3.275000	0.51639	2.254000	0.74563	0.528000	0.53228	CTC	.	.		0.438	COBLL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014900		C	165542496	A	C	165542496	3	2	283	1	0	0	0	0	1	0	0	0	3656	304	11	5	43	5	COBLL1	2	165542496	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	34425494	165542496	77656877	39	41677										
LRP2	4036	hgsc.bcm.edu	37	chr2	170033099	170033110	+	Splice_Site	DEL	CTAGTGGAAAAG	CTAGTGGAAAAG	-													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ggtaccacagggattgctcaCtagtggaaaaggaagaaaat					rs574497332		TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	CTAGTGGAAAAG	CTAGTGGAAAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr2:170033099_170033110delCTAGTGGAAAAG	ENST00000263816.3	-	54	10679		c.e54-1		LRP2_ENST00000461418.1_5'Flank	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2						cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	GGATTGCTCACTAGTGGAAAAGGAAGAAAATA	0.415																																					p.3465_3465del		Atlas-Indel,Pindel	.											.	LRP2	751	.	0			c.10394_10394del						.																																			SO:0001630	splice_region_variant	4036	exon54			.		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.10394-1CTTTTCCACTAG>-	chr2.hg19:g.170033099_170033110delCTAGTGGAAAAG		94.0	0.0		63.0	10.0	NM_004525	O00711|Q16215	Frame_Shift_Del	DEL	ENST00000263816.3	hg19	CCDS2232.1																																																																																			.	.		0.415	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	Intron	-	170033110	CTAGTGGAAAAG	-	170033099	8	5	283	1	0	1	0	1	0	0	1	0	8965	579	20	0	3678	0	LRP2	2	170033099	Splice_Site	DEL	CTAGTGGAAAAG	TCGA-G3-A3CK-01A-11D-A20W-10	4490603	170033099	73166274	40	41678										
GAD1	2571	hgsc.bcm.edu	37	chr2	171713607	171713607	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tgccaagattaaaaacagagAagaatttgagatggttttca	9	4	1	4			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr2:171713607A>G	ENST00000358196.3	+	15	2043	c.1493A>G	c.(1492-1494)gAa>gGa	p.E498G		NM_000817.2	NP_000808.2	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 (brain, 67kDa)	498					gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate catabolic process (GO:0006538)|glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|protein-pyridoxal-5-phosphate linkage (GO:0018352)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(15)|ovary(1)|urinary_tract(2)	35						AAAAACAGAGAAGAATTTGAG	0.418																																					p.E498G		Atlas-SNP	.											.	GAD1	79	.	0			c.A1493G						.						122	132	129					2																	171713607		2203	4300	6503	SO:0001583	missense	2571	exon15			ACAGAGAAGAATT		CCDS2239.1, CCDS2240.1	2q31	2008-02-05	2002-08-29		ENSG00000128683	ENSG00000128683	4.1.1.15		4092	protein-coding gene	gene with protein product		605363	"glutamate decarboxylase 1 (brain, 67kD)"	GAD		1549570	Standard	XM_005246443		Approved		uc002ugi.3	Q99259	OTTHUMG00000044175	ENST00000358196.3:c.1493A>G	chr2.hg19:g.171713607A>G	ENSP00000350928:p.Glu498Gly	67.0	0.0		87.0	25.0	NM_000817	Q49AK1|Q53TQ7|Q9BU91|Q9UHH4	Missense_Mutation	SNP	ENST00000358196.3	hg19	CCDS2239.1	.	.	.	.	.	.	.	.	.	.	A	18.04	3.533714	0.64972	.	.	ENSG00000128683	ENST00000358196	T	0.37584	1.19	5.75	5.75	0.90469	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.045953	0.85682	D	0.000000	T	0.39118	0.1066	L	0.46741	1.465	0.80722	D	1	B	0.29671	0.254	B	0.35073	0.195	T	0.29640	-1.0005	10	0.72032	D	0.01	-16.6059	16.0623	0.80847	1.0:0.0:0.0:0.0	.	498	Q99259	DCE1_HUMAN	G	498	ENSP00000350928:E498G	ENSP00000350928:E498G	E	+	2	0	GAD1	171421853	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.074000	0.76791	2.195000	0.70347	0.533000	0.62120	GAA	.	.		0.418	GAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102664.2			G	171713607	A	G	171713607	3	3	283	1	0	0	0	0	1	0	0	0	6187	246	9	2	1588	2	GAD1	2	171713607	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	1680508	171713607	71485766	41	41679										
SP3	6670	hgsc.bcm.edu	37	chr2	174820648	174820648	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	aatttgactgctttcttgatTtatacccccattatctgaag	5	9	2	3			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr2:174820648T>G	ENST00000310015.6	-	4	1122	c.592A>C	c.(592-594)Aat>Cat	p.N198H	SP3_ENST00000483084.1_5'Flank|SP3_ENST00000418194.2_Missense_Mutation_p.N130H|SP3_ENST00000455789.2_Missense_Mutation_p.N145H	NM_001172712.1|NM_003111.4	NP_001166183.1|NP_003102.1	Q02447	SP3_HUMAN	Sp3 transcription factor	198	Transactivation domain (Gln-rich).				B cell differentiation (GO:0030183)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|embryonic skeletal system development (GO:0048706)|enucleate erythrocyte differentiation (GO:0043353)|granulocyte differentiation (GO:0030851)|liver development (GO:0001889)|lung development (GO:0030324)|megakaryocyte differentiation (GO:0030219)|monocyte differentiation (GO:0030224)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|T cell differentiation (GO:0030217)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)		EWSR1/SP3(3)	NS(2)|large_intestine(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.185)			CTTTCTTGATTTATACCCCCA	0.428																																					p.N198H		Atlas-SNP	.											.	SP3	82	.	0			c.A592C						.						208	218	215					2																	174820648		2203	4300	6503	SO:0001583	missense	6670	exon4			CTTGATTTATACC	M97191	CCDS2254.1, CCDS46452.1	2q31	2013-01-08			ENSG00000172845	ENSG00000172845		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	11208	protein-coding gene	gene with protein product		601804				1341900, 1454515	Standard	NM_003111		Approved	SPR-2	uc002uig.3	Q02447	OTTHUMG00000132333	ENST00000310015.6:c.592A>C	chr2.hg19:g.174820648T>G	ENSP00000310301:p.Asn198His	208.0	0.0		193.0	63.0	NM_003111	A0AVL9|B4E2B7|Q69B26|Q69B27|Q8TD56|Q8WWU4|Q9BQR1	Missense_Mutation	SNP	ENST00000310015.6	hg19	CCDS2254.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.04|14.04	2.417320|2.417320	0.42918|0.42918	.|.	.|.	ENSG00000172845|ENSG00000172845	ENST00000310015;ENST00000455789;ENST00000418194|ENST00000416195	T;T;T|.	0.05025|.	3.52;3.51;3.51|.	5.95|5.95	5.95|5.95	0.96441|0.96441	.|.	0.204262|.	0.53938|.	D|.	0.000055|.	T|.	0.43634|.	0.1256|.	L|L	0.34521|0.34521	1.04|1.04	0.33341|0.33341	D|D	0.569885|0.569885	P;P;D|.	0.54964|.	0.947;0.913;0.969|.	P;B;P|.	0.50970|.	0.453;0.339;0.655|.	T|.	0.56062|.	-0.8041|.	10|.	0.56958|.	D|.	0.05|.	.|.	10.7032|10.7032	0.45939|0.45939	0.0:0.0708:0.0:0.9292|0.0:0.0708:0.0:0.9292	.|.	195;198;145|.	B7ZLN9;Q02447;Q02447-6|.	.;SP3_HUMAN;.|.	H|Y	198;145;130|154	ENSP00000310301:N198H;ENSP00000388903:N145H;ENSP00000406140:N130H|.	ENSP00000310301:N198H|.	N|X	-|-	1|3	0|2	SP3|SP3	174528894|174528894	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	2.149000|2.149000	0.42244|0.42244	2.272000|2.272000	0.75746|0.75746	0.460000|0.460000	0.39030|0.39030	AAT|TAA	.	.		0.428	SP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255452.1	NM_003111		G	174820648	T	G	174820648	3	3	283	1	0	0	0	0	1	0	0	0	14980	1841	64	5	1769	5	SP3	2	174820648	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	3107041	174820648	68378725	42	41680										
GTF3C3	9330	hgsc.bcm.edu	37	chr2	197643775	197643775	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	cttcaggattctgttctactAgtgttgtcaagagaggctag	11	7	4	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr2:197643775A>G	ENST00000263956.3	-	10	1324	c.1235T>C	c.(1234-1236)cTa>cCa	p.L412P		NM_012086.4	NP_036218.1	Q9Y5Q9	TF3C3_HUMAN	general transcription factor IIIC, polypeptide 3, 102kDa	412				LV -> HL (in Ref. 6; AAH15995). {ECO:0000305}.	5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(4)|endometrium(3)|kidney(1)|large_intestine(9)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						CTGTTCTACTAGTGTTGTCAA	0.378																																					p.L412P		Atlas-SNP	.											.	GTF3C3	96	.	0			c.T1235C						.						102	105	104					2																	197643775		2203	4300	6503	SO:0001583	missense	9330	exon10			TCTACTAGTGTTG	AF133123	CCDS2316.1, CCDS56153.1	2q33.1	2013-01-10	2002-08-29		ENSG00000119041	ENSG00000119041		"General transcription factors", "Tetratricopeptide (TTC) repeat domain containing"	4666	protein-coding gene	gene with protein product		604888	"general transcription factor IIIC, polypeptide 3 (102kD)"			10373544	Standard	NM_001206774		Approved	TFiiiC2-102, TFIIIC102	uc002uts.3	Q9Y5Q9	OTTHUMG00000154633	ENST00000263956.3:c.1235T>C	chr2.hg19:g.197643775A>G	ENSP00000263956:p.Leu412Pro	175.0	0.0		149.0	47.0	NM_012086	Q4ZG48|Q86XJ8|Q8WX84|Q96B44|Q9H5I8|Q9NT97	Missense_Mutation	SNP	ENST00000263956.3	hg19	CCDS2316.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.203397	0.79127	.	.	ENSG00000119041	ENST00000263956;ENST00000448087	T	0.58940	0.3	4.66	4.66	0.58398	Tetratricopeptide-like helical (1);	0.000000	0.64402	D	0.000002	T	0.70928	0.3280	L	0.55481	1.735	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.74262	-0.3722	10	0.72032	D	0.01	-10.0781	14.531	0.67926	1.0:0.0:0.0:0.0	.	412	Q9Y5Q9	TF3C3_HUMAN	P	412;97	ENSP00000263956:L412P	ENSP00000263956:L412P	L	-	2	0	GTF3C3	197352020	1.000000	0.71417	0.983000	0.44433	0.996000	0.88848	8.709000	0.91379	2.076000	0.62316	0.528000	0.53228	CTA	.	.		0.378	GTF3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256104.1			G	197643775	A	G	197643775	3	3	283	1	0	0	0	0	1	0	0	0	6883	420	15	2	1461	2	GTF3C3	2	197643775	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	22823127	197643775	45555598	43	41681										
MPP4	58538	hgsc.bcm.edu	37	chr2	202549803	202549803	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ttaccacttctctccgccagCccaccgtggatgatcctggc	8	17	1	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr2:202549803C>T	ENST00000409474.3	-	7	765	c.558G>A	c.(556-558)ggG>ggA	p.G186G	MPP4_ENST00000359962.5_Silent_p.G186G|MPP4_ENST00000315506.7_Silent_p.G186G|MPP4_ENST00000447335.2_Silent_p.G186G|MPP4_ENST00000428900.2_Silent_p.G186G|MPP4_ENST00000409143.1_Silent_p.G159G|MPP4_ENST00000396886.3_Silent_p.G142G	NM_033066.2	NP_149055	Q96JB8	MPP4_HUMAN	membrane protein, palmitoylated 4 (MAGUK p55 subfamily member 4)	186	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				protein localization to synapse (GO:0035418)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|presynaptic membrane (GO:0042734)				kidney(1)|lung(11)	12						TCTCCGCCAGCCCACCGTGGA	0.517																																					p.G186G		Atlas-SNP	.											.	MPP4	93	.	0			c.G558A						.						43	42	42					2																	202549803		1995	4190	6185	SO:0001819	synonymous_variant	58538	exon7			CGCCAGCCCACCG	AF316032	CCDS46491.1	2q33.2	2008-05-15			ENSG00000082126	ENSG00000082126			13680	protein-coding gene	gene with protein product		606575		DLG6		11414766	Standard	NM_033066		Approved		uc002uyk.4	Q96JB8	OTTHUMG00000154525	ENST00000409474.3:c.558G>A	chr2.hg19:g.202549803C>T		95.0	0.0		121.0	35.0	NM_033066	C9IZK4|Q53TT3|Q6ZNH6|Q96Q43|Q96Q44	Silent	SNP	ENST00000409474.3	hg19	CCDS46491.1																																																																																			.	.		0.517	MPP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335748.2			T	202549803	C	T	202549803	2	4	283	1	0	0	0	0	0	0	0	1	9745	726	26	3		3	MPP4	2	202549803	Silent	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	4906028	202549803	40649570	44	41682										
PECR	55825	hgsc.bcm.edu	37	chr2	216923626	216923626	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	aaaaacgcttacacagctaaTggaaatccagctttagtagg	8	8	0	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr2:216923626T>A	ENST00000265322.7	-	4	572	c.498A>T	c.(496-498)ccA>ccT	p.P166P	PECR_ENST00000497889.1_5'UTR	NM_018441.5	NP_060911.2	Q9BY49	PECR_HUMAN	peroxisomal trans-2-enoyl-CoA reductase	166					fatty acid biosynthetic process (GO:0006633)|oxidation-reduction process (GO:0055114)|phytol metabolic process (GO:0033306)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	receptor binding (GO:0005102)|trans-2-enoyl-CoA reductase (NADPH) activity (GO:0019166)			endometrium(2)|kidney(1)|liver(1)|lung(9)|stomach(1)	14		Renal(323;0.0327)		Epithelial(149;3.8e-06)|all cancers(144;0.000272)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Adenine(DB00173)	ACACAGCTAATGGAAATCCAG	0.378																																					p.P166P		Atlas-SNP	.											.	PECR	22	.	0			c.A498T						.						121	116	117					2																	216923626		2203	4300	6503	SO:0001819	synonymous_variant	55825	exon4			AGCTAATGGAAAT	AF119841	CCDS33375.1	2q35	2011-09-14			ENSG00000115425	ENSG00000115425	1.3.1.38	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	18281	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 29C, member 1"	605843				10811639, 11669066, 19027726	Standard	NM_018441		Approved	HSA250303, TERP, SDR29C1	uc002vft.3	Q9BY49	OTTHUMG00000154825	ENST00000265322.7:c.498A>T	chr2.hg19:g.216923626T>A		202.0	0.0		192.0	66.0	NM_018441	B2RE42|Q53TC4|Q6IAK9|Q9NRD4|Q9NY60|Q9P1A4	Silent	SNP	ENST00000265322.7	hg19	CCDS33375.1																																																																																			.	.		0.378	PECR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337277.1	NM_018441		A	216923626	T	A	216923626	2	1	283	1	0	0	0	0	0	0	0	1	11726	1451	51	4		4	PECR	2	216923626	Silent	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	14373823	216923626	26275747	45	41683										
CHPF	79586	hgsc.bcm.edu	37	chr2	220406586	220406586	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ggaggccaggctgaggtggcCagttaggcgtgccaggccgt	19	10	0	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr2:220406586C>T	ENST00000243776.6	-	2	888	c.640G>A	c.(640-642)Ggc>Agc	p.G214S	TMEM198_ENST00000344458.2_5'Flank|TMEM198_ENST00000373883.3_5'Flank|CHPF_ENST00000373891.2_Missense_Mutation_p.G214S|CHPF_ENST00000535926.1_Missense_Mutation_p.G52S	NM_024536.5	NP_078812	Q8IZ52	CHSS2_HUMAN	chondroitin polymerizing factor	214					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)	21		Renal(207;0.0183)		Epithelial(149;3.02e-08)|all cancers(144;3.41e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		CTGAGGTGGCCAGTTAGGCGT	0.697											OREG0015229	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G214S		Atlas-SNP	.											.	CHPF	56	.	0			c.G640A						.						29	24	26					2																	220406586		2201	4299	6500	SO:0001583	missense	79586	exon2			GGTGGCCAGTTAG	BC008878	CCDS2443.1, CCDS56169.1	2q35	2014-02-12			ENSG00000123989	ENSG00000123989	2.4.1.175, 2.4.1.226	"Beta 3-glycosyltransferases", "Beta 4-glycosyltransferases"	24291	protein-coding gene	gene with protein product	"chondroitin sulfate synthase 2"	610405				11230166, 12716890	Standard	NM_024536		Approved	CSS2, CHSY2	uc002vmc.4	Q8IZ52	OTTHUMG00000058929	ENST00000243776.6:c.640G>A	chr2.hg19:g.220406586C>T	ENSP00000243776:p.Gly214Ser	68.0	0.0	2266	125.0	39.0	NM_024536	B4DXU0|Q6UXD6|Q7L4G1|Q9H0F8|Q9H618	Missense_Mutation	SNP	ENST00000243776.6	hg19	CCDS2443.1	.	.	.	.	.	.	.	.	.	.	C	15.22	2.769714	0.49680	.	.	ENSG00000123989	ENST00000243776;ENST00000535926;ENST00000373891	T;T	0.10382	2.92;2.88	4.29	3.42	0.39159	.	0.290182	0.33327	N	0.005024	T	0.04092	0.0114	N	0.04820	-0.15	0.39060	D	0.960512	B;B	0.21606	0.046;0.058	B;B	0.21360	0.034;0.032	T	0.33394	-0.9870	10	0.08381	T	0.77	-22.8262	6.797	0.23731	0.294:0.6219:0.0:0.0841	.	214;214	F8W6H2;Q8IZ52	.;CHSS2_HUMAN	S	214;52;214	ENSP00000243776:G214S;ENSP00000445571:G52S	ENSP00000243776:G214S	G	-	1	0	CHPF	220114830	0.981000	0.34729	0.835000	0.33067	0.981000	0.71138	2.407000	0.44565	1.183000	0.42943	0.549000	0.68633	GGC	.	.		0.697	CHPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130268.1	NM_024536		T	220406586	C	T	220406586	3	4	283	1	0	0	0	0	1	0	0	0	3370	594	21	3	1699	3	CHPF	2	220406586	Missense_Mutation	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	3482960	220406586	22792787	46	41684										
UGT1A9	54600	hgsc.bcm.edu	37	chr2	234581246	234581246	+	Silent	SNP	T	T	A													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gaacatttattatgccaccgTtttttcaaaaatgccctaga							TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr2:234581246T>A	ENST00000354728.4	+	1	748	c.666T>A	c.(664-666)cgT>cgA	p.R222R	UGT1A10_ENST00000344644.5_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A1_ENST00000609637.1_Silent_p.R222R			O60656	UD19_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A9	222					cellular glucuronidation (GO:0052695)|cellular lipid metabolic process (GO:0044255)|drug metabolic process (GO:0017144)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|metabolic process (GO:0008152)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of fatty acid metabolic process (GO:0045922)|retinoic acid metabolic process (GO:0042573)|small molecule metabolic process (GO:0044281)|xenobiotic glucuronidation (GO:0052697)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)			breast(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	37		Breast(86;0.000766)|all_lung(227;0.00269)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0331)|Lung NSC(271;0.0459)|Lung SC(224;0.128)		Epithelial(121;1.26e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000436)|Lung(119;0.00347)|LUSC - Lung squamous cell carcinoma(224;0.00757)	Acetaminophen(DB00316)|Buprenorphine(DB00921)|Canagliflozin(DB08907)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Entacapone(DB00494)|Etodolac(DB00749)|Ezogabine(DB04953)|Flurbiprofen(DB00712)|Haloperidol(DB00502)|Human Serum Albumin(DB00062)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ketobemidone(DB06738)|Lumiracoxib(DB01283)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Nateglinide(DB00731)|Niflumic Acid(DB04552)|Oxazepam(DB00842)|Propofol(DB00818)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sulfamethoxazole(DB01015)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zileuton(DB00744)	TATGCCACCGTTTTTTCAAAA	0.433																																					p.R222R		Atlas-SNP	.											.	UGT1A9	79	.	0			c.T666A						.						215	224	221					2																	234581246		2203	4300	6503	SO:0001819	synonymous_variant	54600	exon1			CCACCGTTTTTTC	AF056188	CCDS2505.1	2q37	2010-03-05	2005-07-20		ENSG00000241119	ENSG00000241119		"UDP glucuronosyltransferases"	12541	other	complex locus constituent		606434	"UDP glycosyltransferase 1 family, polypeptide A9"			9295054, 1910331	Standard	NM_021027		Approved	HLUGP4, LUGP4, UGT1AI		O60656	OTTHUMG00000059124	ENST00000354728.4:c.666T>A	chr2.hg19:g.234581246T>A		414.0	0.0		341.0	117.0	NM_021027	B8K285|P36509|Q9HAX0	Silent	SNP	ENST00000354728.4	hg19	CCDS2505.1																																																																																			.	.		0.433	UGT1A9-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130995.1	NM_021027		A	234581246	T	A	234581246	2	1	283	1	0	0	0	0	0	0	0	1	16967	1712	60	4		4	UGT1A9	2	234581246	Silent	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	14174660	234581246	8618127	47	41685	210	2								
UGT1A9	54600	hgsc.bcm.edu	37	chr2	234581248	234581248	+	Missense_Mutation	SNP	T	T	A													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	acatttattatgccaccgttTtttcaaaaatgccctagaaa							TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr2:234581248T>A	ENST00000354728.4	+	1	750	c.668T>A	c.(667-669)tTt>tAt	p.F223Y	UGT1A10_ENST00000344644.5_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A1_ENST00000609637.1_Missense_Mutation_p.F223Y			O60656	UD19_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A9	223					cellular glucuronidation (GO:0052695)|cellular lipid metabolic process (GO:0044255)|drug metabolic process (GO:0017144)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|metabolic process (GO:0008152)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of fatty acid metabolic process (GO:0045922)|retinoic acid metabolic process (GO:0042573)|small molecule metabolic process (GO:0044281)|xenobiotic glucuronidation (GO:0052697)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)			breast(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	37		Breast(86;0.000766)|all_lung(227;0.00269)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0331)|Lung NSC(271;0.0459)|Lung SC(224;0.128)		Epithelial(121;1.26e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000436)|Lung(119;0.00347)|LUSC - Lung squamous cell carcinoma(224;0.00757)	Acetaminophen(DB00316)|Buprenorphine(DB00921)|Canagliflozin(DB08907)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Entacapone(DB00494)|Etodolac(DB00749)|Ezogabine(DB04953)|Flurbiprofen(DB00712)|Haloperidol(DB00502)|Human Serum Albumin(DB00062)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ketobemidone(DB06738)|Lumiracoxib(DB01283)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Nateglinide(DB00731)|Niflumic Acid(DB04552)|Oxazepam(DB00842)|Propofol(DB00818)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sulfamethoxazole(DB01015)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zileuton(DB00744)	TGCCACCGTTTTTTCAAAAAT	0.438																																					p.F223Y		Atlas-SNP	.											.	UGT1A9	79	.	0			c.T668A						.						214	223	220					2																	234581248		2203	4300	6503	SO:0001583	missense	54600	exon1			ACCGTTTTTTCAA	AF056188	CCDS2505.1	2q37	2010-03-05	2005-07-20		ENSG00000241119	ENSG00000241119		"UDP glucuronosyltransferases"	12541	other	complex locus constituent		606434	"UDP glycosyltransferase 1 family, polypeptide A9"			9295054, 1910331	Standard	NM_021027		Approved	HLUGP4, LUGP4, UGT1AI		O60656	OTTHUMG00000059124	ENST00000354728.4:c.668T>A	chr2.hg19:g.234581248T>A	ENSP00000346768:p.Phe223Tyr	411.0	0.0		336.0	113.0	NM_021027	B8K285|P36509|Q9HAX0	Missense_Mutation	SNP	ENST00000354728.4	hg19	CCDS2505.1	.	.	.	.	.	.	.	.	.	.	T	7.881	0.730240	0.15507	.	.	ENSG00000241119	ENST00000354728	T	0.61158	0.13	3.22	1.98	0.26296	.	.	.	.	.	T	0.43722	0.1260	L	0.47078	1.49	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.15052	0.012;0.012	T	0.28554	-1.0040	9	0.22706	T	0.39	.	3.6356	0.08147	0.1655:0.1881:0.0:0.6464	.	223;223	Q5DSZ5;O60656	.;UD19_HUMAN	Y	223	ENSP00000346768:F223Y	ENSP00000346768:F223Y	F	+	2	0	UGT1A9	234245987	0.000000	0.05858	0.003000	0.11579	0.034000	0.12701	-0.034000	0.12225	0.395000	0.25257	0.362000	0.22060	TTT	.	.		0.438	UGT1A9-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130995.1	NM_021027		A	234581248	T	A	234581248	3	1	283	1	0	0	0	0	1	0	0	0	16967	1841	64	4	670	4	UGT1A9	2	234581248	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	2	234581248	8618125	48	41686	210	2								
ITPR1	3708	hgsc.bcm.edu	37	chr3	4776907	4776907	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tgagtctggccgaggttcagTgtcaccttgacaaggagggg	16	8	3	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr3:4776907T>C	ENST00000443694.2	+	41	5368	c.5368T>C	c.(5368-5370)Tgt>Cgt	p.C1790R	ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000354582.6_Missense_Mutation_p.C1790R|ITPR1_ENST00000423119.2_Missense_Mutation_p.C1757R|ITPR1_ENST00000357086.4_Missense_Mutation_p.C1757R|ITPR1_ENST00000456211.2_Missense_Mutation_p.C1742R|ITPR1_ENST00000302640.8_Missense_Mutation_p.C1790R			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	1805					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	CGAGGTTCAGTGTCACCTTGA	0.493																																					p.C1790R		Atlas-SNP	.											.	ITPR1	659	.	0			c.T5368C						.						112	115	114					3																	4776907		2031	4182	6213	SO:0001583	missense	3708	exon43			GTTCAGTGTCACC	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"Ion channels / Inositol triphosphate receptors"	6180	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 94"	147265	"spinocerebellar ataxia 15", "spinocerebellar ataxia 16", "spinocerebellar ataxia 29"	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.5368T>C	chr3.hg19:g.4776907T>C	ENSP00000401671:p.Cys1790Arg	135.0	0.0		101.0	39.0	NM_001168272	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	hg19	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.661648	0.88154	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000426160;ENST00000357086;ENST00000456211;ENST00000443694	D;D;D;D;D;D	0.94897	-3.55;-3.55;-3.55;-3.55;-3.55;-3.55	5.09	5.09	0.68999	.	0.093975	0.85682	D	0.000000	D	0.97028	0.9029	M	0.80616	2.505	0.80722	D	1	D;D	0.89917	0.998;1.0	P;D	0.97110	0.901;1.0	D	0.96987	0.9719	10	0.45353	T	0.12	.	15.2238	0.73333	0.0:0.0:0.0:1.0	.	1805;1757	Q14643;G5E9P1	ITPR1_HUMAN;.	R	1805;1790;1790;1757;251;1757;1742;1790	ENSP00000306253:C1790R;ENSP00000346595:C1790R;ENSP00000405934:C1757R;ENSP00000349597:C1757R;ENSP00000397885:C1742R;ENSP00000401671:C1790R	ENSP00000306253:C1790R	C	+	1	0	ITPR1	4751907	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.587000	0.82613	2.056000	0.61249	0.477000	0.44152	TGT	.	.		0.493	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		C	4776907	T	C	4776907	3	2	283	1	0	0	0	0	1	0	0	0	7929	1696	59	2	5579	2	ITPR1	3	4776907	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10		4776907	193245523	49	41687										
ARPP21	10777	hgsc.bcm.edu	37	chr3	35763321	35763321	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gagtaccgggaagctgtccaAagcaggtagttagtactgaa	13	7	0	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr3:35763321A>C	ENST00000187397.4	+	14	1676	c.1220A>C	c.(1219-1221)aAa>aCa	p.K407T	ARPP21_ENST00000417925.1_Missense_Mutation_p.K373T|ARPP21_ENST00000337271.5_Missense_Mutation_p.K353T|ARPP21_ENST00000444190.1_Missense_Mutation_p.K353T|ARPP21_ENST00000458225.1_Missense_Mutation_p.K373T	NM_016300.4	NP_057384.2	Q9UBL0	ARP21_HUMAN	cAMP-regulated phosphoprotein, 21kDa	407	Ser-rich.				cellular response to heat (GO:0034605)	cytoplasm (GO:0005737)	nucleic acid binding (GO:0003676)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	61						AAGCTGTCCAAAGCAGGTAGT	0.498																																					p.K407T		Atlas-SNP	.											.	ARPP21	153	.	0			c.A1220C						.						26	23	24					3																	35763321		2203	4300	6503	SO:0001583	missense	10777	exon14			TGTCCAAAGCAGG	AA733082	CCDS2661.1, CCDS43063.1, CCDS58823.1, CCDS58824.1	3p24.3	2010-08-12			ENSG00000172995	ENSG00000172995			16968	protein-coding gene	gene with protein product	"R3H domain containing 3"	605488				8120638	Standard	NM_198399		Approved	ARPP-21, TARPP, R3HDM3	uc011axy.2	Q9UBL0	OTTHUMG00000130795	ENST00000187397.4:c.1220A>C	chr3.hg19:g.35763321A>C	ENSP00000187397:p.Lys407Thr	255.0	0.0		206.0	47.0	NM_016300	B4DG96|Q49AK3|Q49AS6|Q4G0V4|Q6NYC3|Q86V31|Q9UF93	Missense_Mutation	SNP	ENST00000187397.4	hg19	CCDS2661.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	28.5|28.5	4.924566|4.924566	0.92319|0.92319	.|.	.|.	ENSG00000172995|ENSG00000172995	ENST00000458225;ENST00000337271;ENST00000444190;ENST00000187397;ENST00000417925|ENST00000425289	T;T;T;T;T|.	0.52983|.	0.64;0.64;0.64;0.64;0.64|.	5.75|5.75	5.75|5.75	0.90469|0.90469	.|.	0.312522|.	0.31797|.	N|.	0.007041|.	T|T	0.76285|0.76285	0.3966|0.3966	M|M	0.77486|0.77486	2.375|2.375	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	0.997;0.996;1.0|.	D;D;D|.	0.73380|.	0.962;0.918;0.98|.	T|T	0.77189|0.77189	-0.2679|-0.2679	10|5	0.18710|.	T|.	0.47|.	-22.9268|-22.9268	16.0663|16.0663	0.80878|0.80878	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	373;407;353|.	Q9UBL0-3;Q9UBL0;Q9UBL0-4|.	.;ARP21_HUMAN;.|.	T|H	373;353;353;407;373|179	ENSP00000414351:K373T;ENSP00000337792:K353T;ENSP00000405276:K353T;ENSP00000187397:K407T;ENSP00000412326:K373T|.	ENSP00000187397:K407T|.	K|Q	+|+	2|3	0|2	ARPP21|ARPP21	35738325|35738325	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	9.287000|9.287000	0.95975|0.95975	2.201000|2.201000	0.70794|0.70794	0.533000|0.533000	0.62120|0.62120	AAA|CAA	.	.		0.498	ARPP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253334.2	NM_198399		C	35763321	A	C	35763321	3	2	283	1	0	0	0	0	1	0	0	0	978	14	1	5	1279	5	ARPP21	3	35763321	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	30986414	35763321	162259109	50	41688										
PLCD1	5333	hgsc.bcm.edu	37	chr3	38061825	38061825	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ccttcagcagcgcctgtagaTcctcatcatcctgtaggcct	8	15	3	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr3:38061825T>A	ENST00000334661.4	-	2	275	c.53A>T	c.(52-54)gAt>gTt	p.D18V	PLCD1_ENST00000463876.1_Missense_Mutation_p.D39V|PLCD1_ENST00000479619.1_5'Flank	NM_006225.3	NP_006216.2	P51178	PLCD1_HUMAN	phospholipase C, delta 1	18					angiogenesis (GO:0001525)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|labyrinthine layer blood vessel development (GO:0060716)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|GTPase activating protein binding (GO:0032794)|phosphatidic acid binding (GO:0070300)|phosphatidylinositol phosphate binding (GO:1901981)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylserine binding (GO:0001786)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(6)|prostate(1)|skin(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.0519)|Kidney(284;0.0653)		CGCCTGTAGATCCTCATCATC	0.567																																					p.D39V		Atlas-SNP	.											.	PLCD1	87	.	0			c.A116T						.						86	73	77					3																	38061825		2203	4300	6503	SO:0001583	missense	5333	exon2			TGTAGATCCTCAT		CCDS2671.1, CCDS46793.1	3p22-p21.3	2013-01-10			ENSG00000187091	ENSG00000187091	3.1.4.11	"EF-hand domain containing"	9060	protein-coding gene	gene with protein product		602142				9345909	Standard	NM_001130964		Approved		uc003chm.3	P51178	OTTHUMG00000130813	ENST00000334661.4:c.53A>T	chr3.hg19:g.38061825T>A	ENSP00000335600:p.Asp18Val	124.0	0.0		100.0	32.0	NM_001130964	B3KR14|Q86VN8	Missense_Mutation	SNP	ENST00000334661.4	hg19	CCDS2671.1	.	.	.	.	.	.	.	.	.	.	T	16.45	3.125712	0.56721	.	.	ENSG00000187091	ENST00000463876;ENST00000334661	T;T	0.61742	0.08;0.08	5.09	3.89	0.44902	Pleckstrin homology-type (1);	0.136584	0.64402	D	0.000004	T	0.69548	0.3123	M	0.69358	2.11	0.80722	D	1	D;D	0.89917	1.0;0.997	D;D	0.97110	1.0;0.973	T	0.65940	-0.6046	10	0.14252	T	0.57	.	12.0793	0.53662	0.0:0.0:0.1441:0.8559	.	18;39	P51178;B3KR14	PLCD1_HUMAN;.	V	39;18	ENSP00000430344:D39V;ENSP00000335600:D18V	ENSP00000335600:D18V	D	-	2	0	PLCD1	38036829	1.000000	0.71417	0.733000	0.30861	0.259000	0.26198	7.929000	0.87595	0.838000	0.34948	0.379000	0.24179	GAT	.	.		0.567	PLCD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253359.2			A	38061825	T	A	38061825	3	1	283	1	0	0	0	0	1	0	0	0	12040	1435	50	4	2273	4	PLCD1	3	38061825	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	2298504	38061825	159960605	51	41689										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266100	41266100	+	Missense_Mutation	SNP	T	T	C													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	agcaacagtcttacctggacTctggaatccattctggtgcc					rs121913416		TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr3:41266100T>C	ENST00000349496.5	+	3	377	c.97T>C	c.(97-99)Tct>Cct	p.S33P	CTNNB1_ENST00000396185.3_Missense_Mutation_p.S33P|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S33P|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S26P|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S33P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	33			Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> F (in PTR, MDB and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10666372}.|S -> L (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> Y (in colorectal cancer and PTR; enhances transactivation of target genes). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:9065402}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.S33P(47)|p.S33A(16)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.W25_D32del(4)|p.S33L(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S33N(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.D32fs*9(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.S29_H36del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.D32_S33insS(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.S33T(1)|p.D32_H36>D(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TTACCTGGACTCTGGAATCCA	0.488		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S33P	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,-1,1	CTNNB1	4904	.	212	Deletion - In frame(115)|Substitution - Missense(70)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)|Insertion - In frame(1)	liver(130)|large_intestine(20)|endometrium(14)|stomach(10)|pituitary(9)|pancreas(9)|central_nervous_system(8)|adrenal_gland(2)|small_intestine(2)|biliary_tract(2)|skin(2)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|breast(1)	c.T97C						.						93	77	82					3																	41266100		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	CTGGACTCTGGAA	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.97T>C	chr3.hg19:g.41266100T>C	ENSP00000344456:p.Ser33Pro	398.0	0.0		329.0	98.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.395782	0.83011	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.50548	0.74;0.74;0.74;0.74;0.74;0.74;0.74;0.74;0.74	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.70281	0.3206	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74509	-0.3642	10	0.87932	D	0	-10.7796	16.0677	0.80897	0.0:0.0:0.0:1.0	.	33	P35222	CTNB1_HUMAN	P	26;33;33;33;33;26;33;33;33	ENSP00000400508:S26P;ENSP00000385604:S33P;ENSP00000412219:S33P;ENSP00000379486:S33P;ENSP00000344456:S33P;ENSP00000411226:S26P;ENSP00000379488:S33P;ENSP00000409302:S33P;ENSP00000401599:S33P	ENSP00000344456:S33P	S	+	1	0	CTNNB1	41241104	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.201000	0.70794	0.533000	0.62120	TCT	.	.		0.488	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266100	T	C	41266100	3	2	283	1	0	0	0	0	1	0	0	0	4018	1551	54	2	103	2	CTNNB1	3	41266100	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	3204275	41266100	156756330	52	41690	211	2								
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266110	41266110	+	Missense_Mutation	SNP	A	A	C													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ttacctggactctggaatccAttctggtgccactaccacag					rs121913416		TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr3:41266110A>C	ENST00000349496.5	+	3	387	c.107A>C	c.(106-108)cAt>cCt	p.H36P	CTNNB1_ENST00000396185.3_Missense_Mutation_p.H36P|CTNNB1_ENST00000405570.1_Missense_Mutation_p.H36P|CTNNB1_ENST00000453024.1_Missense_Mutation_p.H29P|CTNNB1_ENST00000396183.3_Missense_Mutation_p.H36P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	36					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.H36P(24)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.V22_G38del(3)|p.H36R(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.I35_S37>T(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.D32_H36>D(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.I35_K170del(1)|p.H24_G38del(1)|p.S29_H36del(1)|p.I35_T41del(1)|p.I35_G38del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.D32fs*9(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.GIHS34?(1)|p.D32_H36del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TCTGGAATCCATTCTGGTGCC	0.498		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.H36P	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,carcinoma,0,1	CTNNB1	4904	.	159	Deletion - In frame(104)|Substitution - Missense(27)|Complex - deletion inframe(18)|Unknown(7)|Deletion - Frameshift(3)	liver(119)|large_intestine(20)|stomach(7)|kidney(6)|small_intestine(2)|skin(2)|adrenal_gland(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	c.A107C						.						95	80	85					3																	41266110		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	GAATCCATTCTGG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.107A>C	chr3.hg19:g.41266110A>C	ENSP00000344456:p.His36Pro	382.0	0.0		330.0	96.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	15.41	2.824526	0.50739	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88;0.88;0.88;0.88;0.88	5.76	5.76	0.90799	.	0.093481	0.85682	D	0.000000	T	0.51210	0.1661	M	0.64170	1.965	0.80722	D	1	P	0.40398	0.716	P	0.45946	0.498	T	0.54807	-0.8238	10	0.72032	D	0.01	-2.3155	16.0676	0.80897	1.0:0.0:0.0:0.0	.	36	P35222	CTNB1_HUMAN	P	29;36;36;36;36;29;36;36;36	ENSP00000400508:H29P;ENSP00000385604:H36P;ENSP00000412219:H36P;ENSP00000379486:H36P;ENSP00000344456:H36P;ENSP00000411226:H29P;ENSP00000379488:H36P;ENSP00000409302:H36P;ENSP00000401599:H36P	ENSP00000344456:H36P	H	+	2	0	CTNNB1	41241114	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.201000	0.70794	0.533000	0.62120	CAT	.	.		0.498	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266110	A	C	41266110	3	2	283	1	0	0	0	0	1	0	0	0	4018	217	8	5	113	5	CTNNB1	3	41266110	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	10	41266110	156756320	53	41691	211	2								
MANF	7873	hgsc.bcm.edu	37	chr3	51426503	51426503	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	atgcccccaaggcagccagtGcacggaccgatttgtagtct	11	13	1	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr3:51426503G>A	ENST00000528157.1	+	4	828	c.532G>A	c.(532-534)Gca>Aca	p.A178T	MANF_ENST00000470900.1_3'UTR|RBM15B_ENST00000323686.4_5'Flank	NM_006010.4	NP_006001.3	P55145	MANF_HUMAN	mesencephalic astrocyte-derived neurotrophic factor	178					response to unfolded protein (GO:0006986)|vasoconstriction of artery involved in ischemic response to lowering of systemic arterial blood pressure (GO:0002014)	extracellular space (GO:0005615)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	poly(A) RNA binding (GO:0044822)			lung(1)|ovary(1)	2						GGCAGCCAGTGCACGGACCGA	0.458											OREG0015594	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A178T		Atlas-SNP	.											.	MANF	8	.	0			c.G532A						.						29	30	30					3																	51426503		1909	4126	6035	SO:0001583	missense	7873	exon4			GCCAGTGCACGGA	M83751	CCDS46836.1, CCDS46836.2	3p21.1	2010-12-09	2009-06-04	2009-06-04	ENSG00000145050	ENSG00000145050			15461	protein-coding gene	gene with protein product		601916	"arginine-rich, mutated in early stage tumors"	ARMET		12794311	Standard	NM_006010		Approved	ARP	uc003dbc.3	P55145	OTTHUMG00000156897	ENST00000528157.1:c.532G>A	chr3.hg19:g.51426503G>A	ENSP00000432799:p.Ala178Thr	94.0	0.0	977	100.0	41.0	NM_006010	Q14CX4|Q86U67|Q96IS4	Missense_Mutation	SNP	ENST00000528157.1	hg19	CCDS46836.2	.	.	.	.	.	.	.	.	.	.	G	17.05	3.290296	0.59976	.	.	ENSG00000145050	ENST00000528157;ENST00000273628	.	.	.	5.7	4.69	0.59074	.	0.116838	0.56097	D	0.000033	T	0.62319	0.2418	M	0.62723	1.935	0.51482	D	0.999929	B	0.16166	0.016	B	0.28011	0.085	T	0.60505	-0.7250	9	0.49607	T	0.09	.	13.8252	0.63346	0.0:0.0:0.6339:0.3661	.	178	P55145	MANF_HUMAN	T	178;181	.	ENSP00000273628:A181T	A	+	1	0	MANF	51401543	1.000000	0.71417	0.947000	0.38551	0.992000	0.81027	3.461000	0.53035	1.220000	0.43490	0.655000	0.94253	GCA	.	.		0.458	MANF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346490.3	NM_006010		A	51426503	G	A	51426503	3	1	283	1	0	0	0	0	1	0	0	0	9232	1319	46	3	555	3	MANF	3	51426503	Missense_Mutation	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	10160393	51426503	146595927	54	41692										
ITIH1	3697	hgsc.bcm.edu	37	chr3	52823733	52823733	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	cctgggcagcatgacggcacGtacttcgggcggctgggaat	16	11	0	1	rs145442481		TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr3:52823733G>C	ENST00000273283.2	+	19	2208	c.2184G>C	c.(2182-2184)acG>acC	p.T728T	ITIH1_ENST00000540715.1_Silent_p.T586T|ITIH1_ENST00000542827.1_3'UTR|ITIH1_ENST00000537050.1_Silent_p.T440T|ITIH1_ENST00000405128.3_Silent_p.T94T	NM_002215.3	NP_002206.2	P19827	ITIH1_HUMAN	inter-alpha-trypsin inhibitor heavy chain 1	728	Hyaluronan-binding.				hyaluronan metabolic process (GO:0030212)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(16)|lung(18)|ovary(4)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	52				BRCA - Breast invasive adenocarcinoma(193;7.04e-05)|Kidney(197;0.000659)|KIRC - Kidney renal clear cell carcinoma(197;0.000795)|OV - Ovarian serous cystadenocarcinoma(275;0.0498)		ATGACGGCACGTACTTCGGGC	0.587																																					p.T728T		Atlas-SNP	.											.	ITIH1	108	.	0			c.G2184C						.						107	101	103					3																	52823733		2203	4300	6503	SO:0001819	synonymous_variant	3697	exon19			CGGCACGTACTTC		CCDS2864.1, CCDS54595.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055957	ENSG00000055957			6166	protein-coding gene	gene with protein product		147270	"inter-alpha (globulin) inhibitor, H1 polypeptide"			1385302, 10100603	Standard	NM_002215		Approved	H1P, IATIH, ITIH	uc003dfs.3	P19827	OTTHUMG00000150312	ENST00000273283.2:c.2184G>C	chr3.hg19:g.52823733G>C		112.0	0.0		110.0	40.0	NM_002215	A8K9N5|B2RAH9|B7Z558|B7Z8C0|F5H165|F5H7Y8|P78455|Q01746|Q562G1	Silent	SNP	ENST00000273283.2	hg19	CCDS2864.1																																																																																			.	G|1.000;A|0.000		0.587	ITIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317522.1	NM_002215		C	52823733	G	C	52823733	2	2	283	1	0	0	0	0	0	0	0	1	7912	1132	40	4		4	ITIH1	3	52823733	Silent	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	1397230	52823733	145198697	55	41693										
FLNB	2317	hgsc.bcm.edu	37	chr3	58141694	58141694	+	Nonsense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	cctgtcctcataggtaactaCgaggtgtccatcaagttcaa	8	11	3	0	rs541513836		TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr3:58141694C>G	ENST00000295956.4	+	41	6945	c.6780C>G	c.(6778-6780)taC>taG	p.Y2260*	FLNB_ENST00000357272.4_3'UTR|FLNB_ENST00000348383.5_Nonsense_Mutation_p.Y2219*|FLNB_ENST00000358537.3_Nonsense_Mutation_p.Y2236*|FLNB_ENST00000490882.1_Nonsense_Mutation_p.Y2291*|FLNB_ENST00000429972.2_Nonsense_Mutation_p.Y2249*|FLNB_ENST00000493452.1_Nonsense_Mutation_p.Y2067*|FLNB_ENST00000419752.2_Nonsense_Mutation_p.Y2080*	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	2260	Interaction with INPPL1.				actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		TAGGTAACTACGAGGTGTCCA	0.542																																					p.Y2291X		Atlas-SNP	.											.	FLNB	430	.	0			c.C6873G						.						80	71	74					3																	58141694		2203	4300	6503	SO:0001587	stop_gained	2317	exon42			TAACTACGAGGTG	AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"actin binding protein 278"	603381	"filamin B, beta (actin binding protein 278)", "Larsen syndrome 1 (autosomal dominant)"	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.6780C>G	chr3.hg19:g.58141694C>G	ENSP00000295956:p.Tyr2260*	75.0	0.0		69.0	20.0	NM_001164317	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Nonsense_Mutation	SNP	ENST00000295956.4	hg19	CCDS2885.1	.	.	.	.	.	.	.	.	.	.	C	49	15.163195	0.99824	.	.	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000493452;ENST00000419752	.	.	.	5.58	3.43	0.39272	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.4487	0.38712	0.0:0.7523:0.0:0.2477	.	.	.	.	X	2260;2291;2236;2249;2219;2067;2080	.	ENSP00000295956:Y2260X	Y	+	3	2	FLNB	58116734	0.995000	0.38212	1.000000	0.80357	0.983000	0.72400	0.362000	0.20284	1.502000	0.48669	0.655000	0.94253	TAC	.	.		0.542	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457		G	58141694	C	G	58141694	4	3	283	1	0	0	0	0	0	1	0	0	5942	547	19	4	7039	4	FLNB	3	58141694	Nonsense_Mutation	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	5317961	58141694	139880736	56	41694										
PHLDB2	90102	hgsc.bcm.edu	37	chr3	111632427	111632427	+	Frame_Shift_Del	DEL	T	T	-													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gtcagagcagtgccagcttcTttacccccaggagcaccagg							TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr3:111632427delT	ENST00000431670.2	+	3	2008	c.1597delT	c.(1597-1599)tttfs	p.F533fs	PHLDB2_ENST00000393925.3_Frame_Shift_Del_p.F533fs|PHLDB2_ENST00000495180.1_Frame_Shift_Del_p.F119fs|PHLDB2_ENST00000393923.3_Frame_Shift_Del_p.F560fs|PHLDB2_ENST00000412622.1_Frame_Shift_Del_p.F533fs|PHLDB2_ENST00000477695.1_Frame_Shift_Del_p.F533fs|PHLDB2_ENST00000481953.1_Frame_Shift_Del_p.F533fs	NM_001134438.1	NP_001127910.1	Q86SQ0	PHLB2_HUMAN	pleckstrin homology-like domain, family B, member 2	533						cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(8)|lung(23)|ovary(6)|skin(7)|stomach(1)	55						TGCCAGCTTCTTTACCCCCAG	0.567																																					p.F559fs		Atlas-Indel,Pindel	.											PHLDB2_ENST00000431670,NS,carcinoma,0,3	PHLDB2	449	.	0			c.1677delC						.						131	135	134					3																	111632427		2203	4300	6503	SO:0001589	frameshift_variant	90102	exon4			.		CCDS2962.1, CCDS46885.1, CCDS46886.1	3q13.13	2013-01-10			ENSG00000144824	ENSG00000144824		"Pleckstrin homology (PH) domain containing"	29573	protein-coding gene	gene with protein product		610298				12376540	Standard	NM_145753		Approved	LL5beta, FLJ21791, LL5b	uc003dyg.3	Q86SQ0	OTTHUMG00000159282	ENST00000431670.2:c.1597delT	chr3.hg19:g.111632427delT	ENSP00000405405:p.Phe533fs	115.0	0.0		144.0	51.0	NM_001134437	A5PKZ3|Q59EA8|Q68CY3|Q6NT98|Q8N8U8|Q8NAB1|Q8NCU5	Frame_Shift_Del	DEL	ENST00000431670.2	hg19	CCDS46886.1																																																																																			.	.		0.567	PHLDB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354337.1	NM_145753		-	111632427	T	-	111632427	7	5	283	1	0	1	0	1	0	0	0	0	11861	1609	56	0	1688	0	PHLDB2	3	111632427	Frame_Shift_Del	DEL	T	TCGA-G3-A3CK-01A-11D-A20W-10	53490733	111632427	86390003	57	41695										
KPNA1	3836	hgsc.bcm.edu	37	chr3	122146558	122146558	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tgatacaacccagttctactAggtacctaaatacaaagaat	5	9	1	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr3:122146558A>G	ENST00000344337.6	-	13	1432	c.1256T>C	c.(1255-1257)cTa>cCa	p.L419P	KPNA1_ENST00000466923.1_5'UTR|RP11-299J3.8_ENST00000609469.1_RNA|RP11-299J3.8_ENST00000608346.1_RNA|RP11-299J3.8_ENST00000608756.1_RNA|RP11-299J3.8_ENST00000608015.1_RNA	NM_002264.3	NP_002255.3	P52294	IMA5_HUMAN	karyopherin alpha 1 (importin alpha 5)	419	Binding to RAG1.				apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cytokine-mediated signaling pathway (GO:0019221)|intracellular transport of virus (GO:0075733)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein import into nucleus (GO:0042307)|regulation of DNA recombination (GO:0000018)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)|protein transporter activity (GO:0008565)			NS(1)|breast(1)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	21				GBM - Glioblastoma multiforme(114;0.0898)		CAGTTCTACTAGGTACCTAAA	0.388																																					p.L419P	Melanoma(12;340 801 11196 19797)	Atlas-SNP	.											.	KPNA1	42	.	0			c.T1256C						.						63	58	60					3																	122146558		2203	4300	6503	SO:0001583	missense	3836	exon13			TCTACTAGGTACC	S75295	CCDS3013.1	3q21	2013-02-14			ENSG00000114030	ENSG00000114030		"Importins", "Armadillo repeat containing"	6394	protein-coding gene	gene with protein product		600686				8052633	Standard	NM_002264		Approved	SRP1, RCH2, NPI-1, IPOA5	uc003efe.2	P52294	OTTHUMG00000159487	ENST00000344337.6:c.1256T>C	chr3.hg19:g.122146558A>G	ENSP00000343701:p.Leu419Pro	54.0	0.0		55.0	24.0	NM_002264	D3DN93|Q6IBQ9|Q9BQ56	Missense_Mutation	SNP	ENST00000344337.6	hg19	CCDS3013.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.618245	0.87359	.	.	ENSG00000114030	ENST00000344337	T	0.73789	-0.78	5.64	5.64	0.86602	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.90164	0.6926	H	0.95437	3.67	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92857	0.6302	10	0.87932	D	0	-7.5972	15.1937	0.73067	1.0:0.0:0.0:0.0	.	419	P52294	IMA1_HUMAN	P	419	ENSP00000343701:L419P	ENSP00000343701:L419P	L	-	2	0	KPNA1	123629248	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	9.109000	0.94291	2.367000	0.80283	0.528000	0.53228	CTA	.	.		0.388	KPNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355740.1	NM_002264		G	122146558	A	G	122146558	3	3	283	1	0	0	0	0	1	0	0	0	8438	420	15	2	368	2	KPNA1	3	122146558	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	10514131	122146558	75875872	58	41696										
C3orf79	152118	hgsc.bcm.edu	37	chr3	153202472	153202472	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	agagaaatcagtgtttgcttTacaaggtaaaacattgattt	8	4	1	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr3:153202472T>C	ENST00000446603.2	+	1	189	c.127T>C	c.(127-129)Tac>Cac	p.Y43H	RP11-23D24.2_ENST00000493214.2_RNA	NM_001101337.1	NP_001094807.1	P0CE67	CC079_HUMAN	chromosome 3 open reading frame 79	43										endometrium(1)|large_intestine(3)	4						GTGTTTGCTTTACAAGGTAAA	0.413																																					p.Y43H		Atlas-SNP	.											.	C3orf79	13	.	0			c.T127C						.						274	259	264					3																	153202472		1904	4133	6037	SO:0001583	missense	152118	exon1			TTGCTTTACAAGG	AF086445	CCDS46937.1	3q25.2	2009-09-30			ENSG00000237787	ENSG00000237787			37259	protein-coding gene	gene with protein product							Standard	NM_001101337		Approved		uc003ezt.3	P0CE67	OTTHUMG00000159629	ENST00000446603.2:c.127T>C	chr3.hg19:g.153202472T>C	ENSP00000389475:p.Tyr43His	152.0	0.0		138.0	45.0	NM_001101337		Missense_Mutation	SNP	ENST00000446603.2	hg19	CCDS46937.1	.	.	.	.	.	.	.	.	.	.	T	4.343	0.063024	0.08388	.	.	ENSG00000237787	ENST00000446603	.	.	.	3.66	-0.246	0.13022	.	.	.	.	.	T	0.16557	0.0398	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.11329	0.006	T	0.21552	-1.0242	8	0.87932	D	0	.	3.4367	0.07448	0.0:0.225:0.2029:0.5721	.	43	P0CE67	CC079_HUMAN	H	43	.	ENSP00000389475:Y43H	Y	+	1	0	C3orf79	154685162	0.003000	0.15002	0.001000	0.08648	0.262000	0.26303	0.633000	0.24598	-0.032000	0.13758	-0.256000	0.11100	TAC	.	.		0.413	C3orf79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356570.1	NM_001101337		C	153202472	T	C	153202472	3	2	283	1	0	0	0	0	1	0	0	0	2248	1754	61	2	129	2	C3orf79	3	153202472	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	31055914	153202472	44819958	59	41697										
SLC2A2	6514	hgsc.bcm.edu	37	chr3	170723139	170723139	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	cactagaataggctgtcggtAgctggaattggtgaagagct	14	6	0	3			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr3:170723139A>G	ENST00000314251.3	-	7	977	c.898T>C	c.(898-900)Tac>Cac	p.Y300H	SLC2A2_ENST00000382808.4_Missense_Mutation_p.Y181H	NM_000340.1	NP_000331.1	P11168	GTR2_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 2	300					carbohydrate metabolic process (GO:0005975)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transmembrane transport (GO:0035428)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	brush border (GO:0005903)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|hexose transmembrane transporter activity (GO:0015149)			central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)		Streptozocin(DB00428)	GGCTGTCGGTAGCTGGAATTG	0.413																																					p.Y300H		Atlas-SNP	.											.	SLC2A2	71	.	0			c.T898C						.						205	185	192					3																	170723139		2203	4300	6503	SO:0001583	missense	6514	exon7			GTCGGTAGCTGGA	J03810	CCDS3215.1	3q26.2-q27	2013-05-22			ENSG00000163581	ENSG00000163581		"Solute carriers"	11006	protein-coding gene	gene with protein product		138160		GLUT2		1852621	Standard	NM_000340		Approved		uc003fhe.1	P11168	OTTHUMG00000158997	ENST00000314251.3:c.898T>C	chr3.hg19:g.170723139A>G	ENSP00000323568:p.Tyr300His	215.0	0.0		198.0	65.0	NM_000340	A8K481|B2R936|B7Z547|F8W8V8|Q9UCW9	Missense_Mutation	SNP	ENST00000314251.3	hg19	CCDS3215.1	.	.	.	.	.	.	.	.	.	.	A	14.25	2.478654	0.44044	.	.	ENSG00000163581	ENST00000314251;ENST00000382808	T;T	0.75050	-0.9;-0.9	5.53	4.37	0.52481	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.105660	0.64402	N	0.000002	T	0.77405	0.4125	M	0.89163	3.01	0.58432	D	0.999992	P	0.42337	0.776	B	0.40134	0.32	T	0.78219	-0.2289	10	0.44086	T	0.13	.	11.4699	0.50261	0.9291:0.0:0.0709:0.0	.	300	P11168	GTR2_HUMAN	H	300;181	ENSP00000323568:Y300H;ENSP00000372258:Y181H	ENSP00000323568:Y300H	Y	-	1	0	SLC2A2	172205833	1.000000	0.71417	0.180000	0.23079	0.115000	0.19883	7.137000	0.77295	1.030000	0.39839	0.482000	0.46254	TAC	.	.		0.413	SLC2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352834.1	NM_000340		G	170723139	A	G	170723139	3	3	283	1	0	0	0	0	1	0	0	0	14559	420	15	2	696	2	SLC2A2	3	170723139	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	17520667	170723139	27299291	60	41698										
EIF4G1	1981	hgsc.bcm.edu	37	chr3	184040633	184040633	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gtggaagcctctaaacctagAggagaaaaaacgttacgacc	10	9	1	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr3:184040633A>G	ENST00000346169.2	+	13	2091	c.1820A>G	c.(1819-1821)gAg>gGg	p.E607G	EIF4G1_ENST00000350481.5_Missense_Mutation_p.E443G|EIF4G1_ENST00000319274.6_Missense_Mutation_p.E607G|EIF4G1_ENST00000411531.1_Missense_Mutation_p.E567G|EIF4G1_ENST00000342981.4_Missense_Mutation_p.E607G|EIF4G1_ENST00000434061.2_Missense_Mutation_p.E411G|EIF4G1_ENST00000352767.3_Missense_Mutation_p.E614G|EIF4G1_ENST00000424196.1_Missense_Mutation_p.E614G|EIF4G1_ENST00000414031.1_Missense_Mutation_p.E567G|EIF4G1_ENST00000382330.3_Missense_Mutation_p.E614G|EIF4G1_ENST00000427845.1_Missense_Mutation_p.E520G|SNORD66_ENST00000390856.1_RNA|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000441154.1_Missense_Mutation_p.E443G|EIF4G1_ENST00000435046.2_Missense_Mutation_p.E411G|EIF4G1_ENST00000392537.2_Missense_Mutation_p.E520G	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	607	EIF4E-binding.|MIF4G. {ECO:0000255|PROSITE- ProRule:PRU00698}.				cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|response to ethanol (GO:0045471)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	75	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			CTAAACCTAGAGGAGAAAAAA	0.463																																					p.E614G		Atlas-SNP	.											.	EIF4G1	151	.	0			c.A1841G						.						158	151	154					3																	184040633		2203	4300	6503	SO:0001583	missense	1981	exon14			ACCTAGAGGAGAA	D12686	CCDS3259.1, CCDS3260.1, CCDS3261.1, CCDS46970.1, CCDS46970.2, CCDS54687.1, CCDS54688.1	3q27.1	2013-09-19			ENSG00000114867	ENSG00000114867		"Parkinson disease"	3296	protein-coding gene	gene with protein product		600495		EIF4G, EIF4F		1429670, 9372926, 21907011	Standard	NM_182917		Approved	p220, PARK18	uc010hxy.3	Q04637	OTTHUMG00000156784	ENST00000346169.2:c.1820A>G	chr3.hg19:g.184040633A>G	ENSP00000316879:p.Glu607Gly	95.0	0.0		119.0	33.0	NM_001194946	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Missense_Mutation	SNP	ENST00000346169.2	hg19	CCDS3259.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.184374	0.78677	.	.	ENSG00000114867	ENST00000346169;ENST00000414031;ENST00000392537;ENST00000450424;ENST00000421110;ENST00000382330;ENST00000426123;ENST00000350481;ENST00000352767;ENST00000427845;ENST00000342981;ENST00000319274;ENST00000424196;ENST00000411531;ENST00000444861;ENST00000441154;ENST00000434061;ENST00000435046	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.51574	0.7;0.7;0.7;0.7;0.7;0.7;0.7;0.7;0.7;0.7;0.7;0.7;0.7;0.7;0.7;0.7;0.7;0.7	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.58004	0.2092	L	0.57536	1.79	0.80722	D	1	D;D;D;D	0.60160	0.987;0.972;0.987;0.972	P;P;P;P	0.55455	0.776;0.715;0.776;0.519	T	0.55218	-0.8175	10	0.31617	T	0.26	-19.4364	15.5933	0.76558	1.0:0.0:0.0:0.0	.	614;607;607;614	E9PFM1;D3DNT2;Q04637;B2RU10	.;.;IF4G1_HUMAN;.	G	607;567;520;607;614;614;548;443;614;520;607;607;614;567;443;443;411;411	ENSP00000316879:E607G;ENSP00000391935:E567G;ENSP00000376320:E520G;ENSP00000391412:E607G;ENSP00000413159:E614G;ENSP00000371767:E614G;ENSP00000403269:E548G;ENSP00000317600:E443G;ENSP00000338020:E614G;ENSP00000407682:E520G;ENSP00000343450:E607G;ENSP00000323737:E607G;ENSP00000416255:E614G;ENSP00000395974:E567G;ENSP00000398145:E443G;ENSP00000399858:E443G;ENSP00000411826:E411G;ENSP00000404754:E411G	ENSP00000323737:E607G	E	+	2	0	EIF4G1	185523327	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	8.761000	0.91691	2.270000	0.75569	0.460000	0.39030	GAG	.	.		0.463	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917		G	184040633	A	G	184040633	3	3	283	1	0	0	0	0	1	0	0	0	5038	304	11	2	1862	2	EIF4G1	3	184040633	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	13317494	184040633	13981797	61	41699										
BCL6	604	hgsc.bcm.edu	37	chr3	187449531	187449531	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	cttccggcaagtgtccacaaCatgctccatctgcaggtaca	8	14	1	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr3:187449531C>A	ENST00000406870.2	-	4	715	c.349G>T	c.(349-351)Gtt>Ttt	p.V117F	RP11-211G3.3_ENST00000437407.1_Intron|RP11-211G3.3_ENST00000449623.1_Intron|BCL6_ENST00000450123.2_Missense_Mutation_p.V117F|BCL6_ENST00000232014.4_Missense_Mutation_p.V117F	NM_001706.4	NP_001697.2	P41182	BCL6_HUMAN	B-cell CLL/lymphoma 6	117					actin cytoskeleton organization (GO:0030036)|B cell differentiation (GO:0030183)|cell morphogenesis (GO:0000902)|cellular response to DNA damage stimulus (GO:0006974)|erythrocyte development (GO:0048821)|germinal center formation (GO:0002467)|inflammatory response (GO:0006954)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of isotype switching to IgE isotypes (GO:0048294)|negative regulation of mast cell cytokine production (GO:0032764)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cellular component movement (GO:0051272)|protein import into nucleus, translocation (GO:0000060)|regulation of germinal center formation (GO:0002634)|regulation of immune response (GO:0050776)|regulation of inflammatory response (GO:0050727)|regulation of memory T cell differentiation (GO:0043380)|regulation of Rho GTPase activity (GO:0032319)|Rho protein signal transduction (GO:0007266)|spermatogenesis (GO:0007283)|type 2 immune response (GO:0042092)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|metal ion binding (GO:0046872)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(9)|lung(10)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	40	all_cancers(143;9.45e-12)|Ovarian(172;0.0418)		OV - Ovarian serous cystadenocarcinoma(80;1.76e-18)	GBM - Glioblastoma multiforme(93;0.0141)		GTGTCCACAACATGCTCCATC	0.527			"T, Mis"	"IG loci, ZNFN1A1, LCP1, PIM1, TFRC, CIITA, NACA, HSPCB, HSPCA, HIST1H4I, IL21R,  POU2AF1, ARHH, EIF4A2, SFRS3"	"NHL, CLL"																																p.V117F		Atlas-SNP	.		Dom	yes		3	3q27	604	B-cell CLL/lymphoma 6		L	.	BCL6	107	.	0			c.G349T						.						78	72	74					3																	187449531		2203	4300	6503	SO:0001583	missense	604	exon3			CCACAACATGCTC		CCDS3289.1, CCDS46975.1	3q27	2013-01-09	2008-08-01		ENSG00000113916	ENSG00000113916		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	1001	protein-coding gene	gene with protein product		109565	"zinc finger protein 51"	ZNF51			Standard	NM_001130845		Approved	ZBTB27, LAZ3, BCL5, BCL6A	uc003frq.2	P41182	OTTHUMG00000156441	ENST00000406870.2:c.349G>T	chr3.hg19:g.187449531C>A	ENSP00000384371:p.Val117Phe	155.0	0.0		180.0	65.0	NM_001134738	A7E241|B8PSA7|D3DNV5	Missense_Mutation	SNP	ENST00000406870.2	hg19	CCDS3289.1	.	.	.	.	.	.	.	.	.	.	C	34	5.327875	0.95733	.	.	ENSG00000113916	ENST00000406870;ENST00000232014;ENST00000450123;ENST00000430339	T;T;T;T	0.73469	-0.75;-0.75;-0.75;-0.75	5.76	5.76	0.90799	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	D	0.91202	0.7228	H	0.96015	3.755	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.998;0.998	D	0.93134	0.6535	10	0.87932	D	0	.	19.3276	0.94268	0.0:1.0:0.0:0.0	.	117;117	B8PSA7;P41182	.;BCL6_HUMAN	F	117	ENSP00000384371:V117F;ENSP00000232014:V117F;ENSP00000413122:V117F;ENSP00000415574:V117F	ENSP00000232014:V117F	V	-	1	0	BCL6	188932225	1.000000	0.71417	0.965000	0.40720	0.994000	0.84299	7.487000	0.81328	2.894000	0.99253	0.591000	0.81541	GTT	.	.		0.527	BCL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344202.1	NM_138931		A	187449531	C	A	187449531	3	1	283	1	0	0	0	0	1	0	0	0	1376	478	17	3	1799	3	BCL6	3	187449531	Missense_Mutation	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	3408898	187449531	10572899	62	41700										
DHX15	1665	hgsc.bcm.edu	37	chr4	24529578	24529578	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	aatattccttggattgaagtTtggcaatgatgcggtccaac	10	7	0	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr4:24529578T>G	ENST00000336812.4	-	14	2513	c.2357A>C	c.(2356-2358)aAa>aCa	p.K786T	DHX15_ENST00000508032.1_5'UTR	NM_001358.2	NP_001349.2	O43143	DHX15_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 15	786				KLQSKEYSQY -> QTSIQGIFTVLNSVLRTEVIERTALKD E (in Ref. 1; BAA23987). {ECO:0000305}.	mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|U12-type spliceosomal complex (GO:0005689)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(5)|liver(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	30		Breast(46;0.0503)				GGATTGAAGTTTGGCAATGAT	0.393																																					p.K786T		Atlas-SNP	.											DHX15,colon,carcinoma,0,1	DHX15	69	.	0			c.A2357C						.						154	138	144					4																	24529578		2203	4300	6503	SO:0001583	missense	1665	exon14			TGAAGTTTGGCAA	AB001636	CCDS33966.1	4p15.3	2013-05-13	2013-05-13	2003-06-20	ENSG00000109606	ENSG00000109606		"DEAH-boxes"	2738	protein-coding gene	gene with protein product		603403	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 15", "DEAH (Asp-Glu-Ala-His) box polypeptide 15"	DDX15		9388478	Standard	NM_001358		Approved	HRH2, DBP1, PRP43, PrPp43p, PRPF43	uc003gqx.3	O43143	OTTHUMG00000160304	ENST00000336812.4:c.2357A>C	chr4.hg19:g.24529578T>G	ENSP00000336741:p.Lys786Thr	141.0	0.0		173.0	65.0	NM_001358	Q9NQT7	Missense_Mutation	SNP	ENST00000336812.4	hg19	CCDS33966.1	.	.	.	.	.	.	.	.	.	.	T	15.70	2.910808	0.52439	.	.	ENSG00000109606	ENST00000336812;ENST00000535946	T	0.03212	4.01	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	T	0.04318	0.0119	N	0.24115	0.695	0.80722	D	1	B;B;B	0.12630	0.003;0.003;0.006	B;B;B	0.19148	0.011;0.011;0.024	T	0.48703	-0.9012	10	0.49607	T	0.09	-11.7458	16.4696	0.84102	0.0:0.0:0.0:1.0	.	786;775;775	O43143;B4E0S6;F5H6K0	DHX15_HUMAN;.;.	T	786;775	ENSP00000336741:K786T	ENSP00000336741:K786T	K	-	2	0	DHX15	24138676	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	2.289000	0.77006	0.482000	0.46254	AAA	.	.		0.393	DHX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360143.1	NM_001358		G	24529578	T	G	24529578	3	3	283	1	0	0	0	0	1	0	0	0	4503	1841	64	5	34	5	DHX15	4	24529578	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10		24529578	166624698	63	41701										
LIAS	6133	hgsc.bcm.edu	37	chr4	39460742	39460742	+	5'Flank	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tagtcctaaagaggaaatgtCtctacgctgcggggatgcag	13	8	1	1	rs372288500		TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr4:39460742C>A	ENST00000449470.2	-	0	0				LIAS_ENST00000381846.1_Missense_Mutation_p.S2Y|LIAS_ENST00000513731.1_Missense_Mutation_p.S2Y|RPL9_ENST00000295955.9_5'Flank|LIAS_ENST00000261434.3_Missense_Mutation_p.S2Y|LIAS_ENST00000515061.1_3'UTR|LIAS_ENST00000340169.2_Missense_Mutation_p.S2Y	NM_001024921.2	NP_001020092.1	P32969	RL9_HUMAN	ribosomal protein L9						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribosome (GO:0005840)	RNA binding (GO:0003723)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(1)|skin(1)	8						GAGGAAATGTCTCTACGCTGC	0.622																																					p.S2Y		Atlas-SNP	.											.	LIAS	26	.	0			c.C5A						.						62	61	62					4																	39460742		2203	4300	6503	SO:0001631	upstream_gene_variant	11019	exon1			AAATGTCTCTACG	D14531	CCDS3452.1	4p13	2011-04-06			ENSG00000163682	ENSG00000163682		"L ribosomal proteins"	10369	protein-coding gene	gene with protein product		603686				8597601, 8415001	Standard	XM_005262661		Approved	L9	uc021sso.1	P32969	OTTHUMG00000099367		chr4.hg19:g.39460742C>A	Exception_encountered	52.0	0.0		59.0	11.0	NM_194451		Missense_Mutation	SNP	ENST00000449470.2	hg19	CCDS3452.1	.	.	.	.	.	.	.	.	.	.	C	18.16	3.561934	0.65538	.	.	ENSG00000121897	ENST00000340169;ENST00000261434;ENST00000513731;ENST00000381846	T;T;T;T	0.79141	-1.15;-1.15;-1.24;-1.14	5.21	5.21	0.72293	.	0.421175	0.26574	N	0.023608	T	0.78929	0.4361	N	0.22421	0.69	0.26563	N	0.97371	D;P;P;P;P	0.65815	0.995;0.763;0.651;0.651;0.946	P;P;B;B;P	0.61201	0.885;0.533;0.248;0.248;0.735	T	0.72494	-0.4276	10	0.49607	T	0.09	-6.5397	15.9633	0.79948	0.0:1.0:0.0:0.0	.	2;2;2;2;2	B4E0L7;C9JCF6;D6RCP8;O43766;Q6P5Q6	.;.;.;LIAS_HUMAN;.	Y	2	ENSP00000340676:S2Y;ENSP00000261434:S2Y;ENSP00000425580:S2Y;ENSP00000371270:S2Y	ENSP00000261434:S2Y	S	+	2	0	LIAS	39137137	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	3.513000	0.53414	2.873000	0.98535	0.561000	0.74099	TCT	.	.		0.622	RPL9-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361018.1			A	39460742	C	A	39460742	1	1	283	0	1	0	0	0	0	0	0	0	8787	913	32	3		3	LIAS	4	39460742	5'Flank	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	14931164	39460742	151693534	64	41702										
TMEM33	55161	hgsc.bcm.edu	37	chr4	41941283	41941289	+	Frame_Shift_Del	DEL	CATCAAA	CATCAAA	-													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ttaccagtgctctgaggctgCatcaaagattaccacacttc							TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	CATCAAA	CATCAAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr4:41941283_41941289delCATCAAA	ENST00000504986.1	+	3	576_582	c.211_217delCATCAAA	c.(211-219)catcaaagafs	p.HQR71fs	TMEM33_ENST00000513702.1_Frame_Shift_Del_p.HQR71fs|TMEM33_ENST00000325094.5_Frame_Shift_Del_p.HQR71fs	NM_018126.2	NP_060596.2	P57088	TMM33_HUMAN	transmembrane protein 33	71						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)		p.H71Y(1)		endometrium(1)|large_intestine(3)|lung(4)|ovary(1)	9						TCTGAGGCTGCATCAAAGATTACCACA	0.459																																					p.70_72del		Atlas-INDEL	.											.	TMEM33	17	.	1	Substitution - Missense(1)	endometrium(1)	c.210_216del						.																																			SO:0001589	frameshift_variant	55161	exon3			.	BC000948	CCDS3464.1	4p14	2008-02-05			ENSG00000109133	ENSG00000109133			25541	protein-coding gene	gene with protein product						12477932	Standard	NM_018126		Approved	FLJ10525	uc003gwi.2	P57088	OTTHUMG00000099381	ENST00000504986.1:c.211_217delCATCAAA	chr4.hg19:g.41941283_41941289delCATCAAA	ENSP00000422473:p.His71fs	273.0	0.0		222.0	17.0	NM_018126	B3KSS8|Q9H953	Frame_Shift_Del	DEL	ENST00000504986.1	hg19	CCDS3464.1																																																																																			.	.		0.459	TMEM33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216834.2	NM_018126		-	41941289	CATCAAA	-	41941283	7	5	283	1	0	1	0	1	0	0	0	0	16171	710	25	0	221	0	TMEM33	4	41941283	Frame_Shift_Del	DEL	CATCAAA	TCGA-G3-A3CK-01A-11D-A20W-10	2480541	41941283	149212993	65	41703	212	2								
TMEM33	55161	hgsc.bcm.edu	37	chr4	41941291	41941298	+	Frame_Shift_Del	DEL	ATTACCAC	ATTACCAC	-													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gctctgaggctgcatcaaagAttaccacacttccagttaag							TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	ATTACCAC	ATTACCAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr4:41941291_41941298delATTACCAC	ENST00000504986.1	+	3	584_591	c.219_226delATTACCAC	c.(217-228)agattaccacacfs	p.LPH74fs	TMEM33_ENST00000513702.1_Frame_Shift_Del_p.LPH74fs|TMEM33_ENST00000325094.5_Frame_Shift_Del_p.LPH74fs	NM_018126.2	NP_060596.2	P57088	TMM33_HUMAN	transmembrane protein 33	74						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)				endometrium(1)|large_intestine(3)|lung(4)|ovary(1)	9						TGCATCAAAGATTACCACACTTCCAGTT	0.466																																					p.73_75del		Atlas-INDEL	.											.	TMEM33	17	.	0			c.218_225del						.																																			SO:0001589	frameshift_variant	55161	exon3			.	BC000948	CCDS3464.1	4p14	2008-02-05			ENSG00000109133	ENSG00000109133			25541	protein-coding gene	gene with protein product						12477932	Standard	NM_018126		Approved	FLJ10525	uc003gwi.2	P57088	OTTHUMG00000099381	ENST00000504986.1:c.219_226delATTACCAC	chr4.hg19:g.41941291_41941298delATTACCAC	ENSP00000422473:p.Leu74fs	274.0	0.0		217.0	17.0	NM_018126	B3KSS8|Q9H953	Frame_Shift_Del	DEL	ENST00000504986.1	hg19	CCDS3464.1																																																																																			.	.		0.466	TMEM33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216834.2	NM_018126		-	41941298	ATTACCAC	-	41941291	7	5	283	1	0	1	0	1	0	0	0	0	16171	330	12	0	229	0	TMEM33	4	41941291	Frame_Shift_Del	DEL	ATTACCAC	TCGA-G3-A3CK-01A-11D-A20W-10	8	41941291	149212985	66	41704	212	2								
LEF1	51176	hgsc.bcm.edu	37	chr4	109000723	109000723	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	caatagctggatgagggatgCcagttgtgtggggaccagga	17	6	0	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr4:109000723C>T	ENST00000265165.1	-	7	1424	c.770G>A	c.(769-771)gGc>gAc	p.G257D	LEF1_ENST00000438313.2_Missense_Mutation_p.G229D|LEF1_ENST00000379951.2_Missense_Mutation_p.G229D|LEF1_ENST00000510624.1_Missense_Mutation_p.G161D|LEF1_ENST00000503879.1_5'Flank	NM_016269.4	NP_057353.1	Q9UJU2	LEF1_HUMAN	lymphoid enhancer-binding factor 1	257	Pro-rich.				alpha-beta T cell differentiation (GO:0046632)|anatomical structure regression (GO:0060033)|apoptotic process involved in morphogenesis (GO:0060561)|apoptotic process involved in patterning of blood vessels (GO:1902262)|B cell proliferation (GO:0042100)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cell chemotaxis (GO:0060326)|cellular response to cytokine stimulus (GO:0071345)|cellular response to interleukin-4 (GO:0071353)|chorio-allantoic fusion (GO:0060710)|dentate gyrus development (GO:0021542)|embryonic limb morphogenesis (GO:0030326)|epithelial to mesenchymal transition (GO:0001837)|eye pigmentation (GO:0048069)|face morphogenesis (GO:0060325)|forebrain neuroblast division (GO:0021873)|forebrain neuron differentiation (GO:0021879)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|hypothalamus development (GO:0021854)|mammary gland development (GO:0030879)|muscle fiber development (GO:0048747)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic process in bone marrow (GO:0071866)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA binding (GO:0043392)|negative regulation of estrogen receptor binding (GO:0071899)|negative regulation of interleukin-13 production (GO:0032696)|negative regulation of interleukin-4 production (GO:0032713)|negative regulation of interleukin-5 production (GO:0032714)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell migration (GO:0001755)|neutrophil differentiation (GO:0030223)|odontoblast differentiation (GO:0071895)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|paraxial mesoderm formation (GO:0048341)|patterning of blood vessels (GO:0001569)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of cell cycle process (GO:0090068)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation in bone marrow (GO:0071864)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of gene expression (GO:0010628)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell-cell adhesion (GO:0022407)|regulation of striated muscle tissue development (GO:0016202)|sensory perception of taste (GO:0050909)|somitogenesis (GO:0001756)|sprouting angiogenesis (GO:0002040)|steroid hormone mediated signaling pathway (GO:0043401)|T cell receptor V(D)J recombination (GO:0033153)|T-helper 1 cell differentiation (GO:0045063)|tongue development (GO:0043586)|trachea gland development (GO:0061153)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|C2H2 zinc finger domain binding (GO:0070742)|chromatin binding (GO:0003682)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|enhancer binding (GO:0035326)|estrogen receptor activity (GO:0030284)|estrogen receptor binding (GO:0030331)|gamma-catenin binding (GO:0045295)|histone binding (GO:0042393)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(14)|prostate(1)|urinary_tract(1)	25				OV - Ovarian serous cystadenocarcinoma(123;0.000224)		ATGAGGGATGCCAGTTGTGTG	0.498																																					p.G257D		Atlas-SNP	.											.	LEF1	93	.	0			c.G770A						.						252	209	224					4																	109000723		2203	4300	6503	SO:0001583	missense	51176	exon7			GGGATGCCAGTTG		CCDS3679.1, CCDS47122.1, CCDS47123.1, CCDS54791.1	4q23-q25	2011-07-08			ENSG00000138795	ENSG00000138795			6551	protein-coding gene	gene with protein product		153245				1783375	Standard	NM_016269		Approved	TCF1ALPHA, TCF10, TCF7L3	uc003hyt.2	Q9UJU2	OTTHUMG00000131809	ENST00000265165.1:c.770G>A	chr4.hg19:g.109000723C>T	ENSP00000265165:p.Gly257Asp	174.0	0.0		141.0	58.0	NM_016269	B4DG38|B7Z8E2|E9PDK3|Q3ZCU4|Q9HAZ0	Missense_Mutation	SNP	ENST00000265165.1	hg19	CCDS3679.1	.	.	.	.	.	.	.	.	.	.	C	35	5.551944	0.96501	.	.	ENSG00000138795	ENST00000265165;ENST00000379951;ENST00000438313;ENST00000510624	D;D;D;D	0.99220	-5.58;-5.57;-5.55;-5.57	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	D	0.99492	0.9819	M	0.85373	2.75	0.80722	D	1	D;D;D;P;D	0.89917	1.0;0.994;1.0;0.83;0.998	D;P;D;P;D	0.91635	0.992;0.782;0.999;0.756;0.954	D	0.98951	1.0794	10	0.72032	D	0.01	.	20.1731	0.98165	0.0:1.0:0.0:0.0	.	161;114;229;229;257	E9PDK3;B4DZY5;Q9UJU2-6;Q9UJU2-5;Q9UJU2	.;.;.;.;LEF1_HUMAN	D	257;229;229;161	ENSP00000265165:G257D;ENSP00000369284:G229D;ENSP00000406176:G229D;ENSP00000422840:G161D	ENSP00000265165:G257D	G	-	2	0	LEF1	109220172	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.768000	0.95171	0.655000	0.94253	GGC	.	.		0.498	LEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254749.2			T	109000723	C	T	109000723	3	4	283	1	0	0	0	0	1	0	0	0	8723	739	26	3	533	3	LEF1	4	109000723	Missense_Mutation	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	67059432	109000723	82153553	67	41705										
VEGFC	7424	hgsc.bcm.edu	37	chr4	177608449	177608449	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ggggttgatttctggggcagGttcttttacatacacactgg	13	7	2	1	rs373146571		TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr4:177608449G>C	ENST00000280193.2	-	6	1452	c.1037C>G	c.(1036-1038)aCc>aGc	p.T346S	RP11-313E19.2_ENST00000509194.1_RNA|VEGFC_ENST00000507638.1_5'Flank|RP11-313E19.2_ENST00000504017.1_RNA	NM_005429.2	NP_005420	P49767	VEGFC_HUMAN	vascular endothelial growth factor C	346	4 X 16 AA repeats of C-X(10)-C-X-C- X(1,3)-C.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|induction of positive chemotaxis (GO:0050930)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of lymphangiogenesis (GO:1901492)|positive regulation of mast cell chemotaxis (GO:0060754)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein secretion (GO:0050714)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)|response to drug (GO:0042493)|signal transduction (GO:0007165)|substrate-dependent cell migration (GO:0006929)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	chemoattractant activity (GO:0042056)			biliary_tract(1)|cervix(1)|large_intestine(6)|lung(28)|pancreas(1)|prostate(2)|skin(2)	41		Breast(14;0.000223)|Renal(120;0.00988)|Prostate(90;0.00996)|Melanoma(52;0.0101)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;1.59e-18)|Epithelial(43;3.68e-16)|OV - Ovarian serous cystadenocarcinoma(60;8.52e-09)|GBM - Glioblastoma multiforme(59;0.000546)|STAD - Stomach adenocarcinoma(60;0.00308)|Colorectal(24;0.025)|COAD - Colon adenocarcinoma(29;0.0359)|LUSC - Lung squamous cell carcinoma(193;0.0397)		TCTGGGGCAGGTTCTTTTACA	0.433																																					p.T346S		Atlas-SNP	.											.	VEGFC	94	.	0			c.C1037G						.						264	235	244					4																	177608449		1849	4101	5950	SO:0001583	missense	7424	exon6			GGGCAGGTTCTTT	BC035212	CCDS43285.1	4q34.3	2013-02-18				ENSG00000150630			12682	protein-coding gene	gene with protein product	"vascular endothelial growth factor-related protein"	601528				8617204	Standard	NM_005429		Approved	VRP	uc003ius.1	P49767		ENST00000280193.2:c.1037C>G	chr4.hg19:g.177608449G>C	ENSP00000280193:p.Thr346Ser	257.0	0.0		230.0	89.0	NM_005429	B2R9Q8	Missense_Mutation	SNP	ENST00000280193.2	hg19	CCDS43285.1	.	.	.	.	.	.	.	.	.	.	G	10.34	1.322855	0.23994	.	.	ENSG00000150630	ENST00000280193	.	.	.	5.61	3.79	0.43588	.	0.184991	0.46442	D	0.000282	T	0.45856	0.1363	L	0.36672	1.1	0.34618	D	0.718292	B	0.17852	0.024	B	0.18561	0.022	T	0.52434	-0.8576	9	0.22109	T	0.4	-6.1851	13.1086	0.59261	0.0689:0.1239:0.8072:0.0	.	346	P49767	VEGFC_HUMAN	S	346	.	ENSP00000280193:T346S	T	-	2	0	VEGFC	177845443	0.950000	0.32346	0.994000	0.49952	0.923000	0.55619	1.903000	0.39858	1.364000	0.46038	0.650000	0.86243	ACC	.	.		0.433	VEGFC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361991.1	NM_005429		C	177608449	G	C	177608449	3	2	283	1	0	0	0	0	1	0	0	0	17167	1261	44	4	233	4	VEGFC	4	177608449	Missense_Mutation	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	68607726	177608449	13545827	68	41706										
KIAA0947	23379	hgsc.bcm.edu	37	chr5	5454677	5454677	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tttcacaggaaaagtgaaacTgcttctgaaggaactctggc	10	8	3	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr5:5454677T>C	ENST00000296564.7	+	11	839	c.617T>C	c.(616-618)cTg>cCg	p.L206P	KIAA0947_ENST00000512608.1_3'UTR	NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		206					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						AAAGTGAAACTGCTTCTGAAG	0.458																																					p.L206P		Atlas-SNP	.											.	KIAA0947	301	.	0			c.T617C						.						57	61	60					5																	5454677		1942	4148	6090	SO:0001583	missense	23379	exon11			TGAAACTGCTTCT																												ENST00000296564.7:c.617T>C	chr5.hg19:g.5454677T>C	ENSP00000296564:p.Leu206Pro	87.0	0.0		110.0	39.0	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Missense_Mutation	SNP	ENST00000296564.7	hg19	CCDS47187.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.184915	0.78677	.	.	ENSG00000164151	ENST00000296564	T	0.17054	2.3	5.25	5.25	0.73442	.	0.151623	0.42420	D	0.000711	T	0.28665	0.0710	L	0.27053	0.805	0.44880	D	0.997893	D	0.89917	1.0	D	0.75484	0.986	T	0.03898	-1.0994	10	0.72032	D	0.01	-8.8619	13.3984	0.60868	0.0:0.0:0.0:1.0	.	206	Q9Y2F5	K0947_HUMAN	P	206	ENSP00000296564:L206P	ENSP00000296564:L206P	L	+	2	0	KIAA0947	5507677	0.789000	0.28775	0.862000	0.33874	0.989000	0.77384	2.866000	0.48420	2.109000	0.64355	0.528000	0.53228	CTG	.	.		0.458	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1			C	5454677	T	C	5454677	3	2	283	1	0	0	0	0	1	0	0	0	8211	1580	55	2	659	2	KIAA0947	5	5454677	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10		5454677	175460583	69	41707										
ADCY2	108	hgsc.bcm.edu	37	chr5	7773106	7773106	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	cgtgttcctgcgggtaaactAtgagctgaagatgttgatca	12	7	1	4			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr5:7773106A>G	ENST00000338316.4	+	18	2365	c.2276A>G	c.(2275-2277)tAt>tGt	p.Y759C	ADCY2_ENST00000537121.1_Missense_Mutation_p.Y579C	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	759					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						CGGGTAAACTATGAGCTGAAG	0.507																																					p.Y759C		Atlas-SNP	.											.	ADCY2	337	.	0			c.A2276G						.						258	222	235					5																	7773106		2203	4300	6503	SO:0001583	missense	108	exon18			TAAACTATGAGCT	AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"Adenylate cyclases"	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.2276A>G	chr5.hg19:g.7773106A>G	ENSP00000342952:p.Tyr759Cys	344.0	0.0		358.0	128.0	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Missense_Mutation	SNP	ENST00000338316.4	hg19	CCDS3872.2	.	.	.	.	.	.	.	.	.	.	A	15.32	2.798226	0.50208	.	.	ENSG00000078295	ENST00000338316;ENST00000541993;ENST00000537121	T;D	0.81659	-1.05;-1.52	4.87	4.87	0.63330	.	0.135744	0.51477	D	0.000084	D	0.82273	0.5001	L	0.53249	1.67	0.54753	D	0.999989	D;P	0.63046	0.992;0.709	P;P	0.54965	0.765;0.571	T	0.79500	-0.1778	10	0.22109	T	0.4	.	12.7275	0.57178	1.0:0.0:0.0:0.0	.	579;759	B7Z2C1;Q08462	.;ADCY2_HUMAN	C	759;592;579	ENSP00000342952:Y759C;ENSP00000444803:Y579C	ENSP00000342952:Y759C	Y	+	2	0	ADCY2	7826106	1.000000	0.71417	0.751000	0.31187	0.915000	0.54546	6.605000	0.74155	1.835000	0.53391	0.383000	0.25322	TAT	.	.		0.507	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546		G	7773106	A	G	7773106	3	3	283	1	0	0	0	0	1	0	0	0	294	449	16	2	2346	2	ADCY2	5	7773106	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	2318429	7773106	173142154	70	41708										
CDH9	1007	hgsc.bcm.edu	37	chr5	26881298	26881298	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	atcggcaagttttttgaaacGaggcccccagtcactgaggt	11	10	1	2	rs568693690		TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr5:26881298G>T	ENST00000231021.4	-	12	2489	c.2317C>A	c.(2317-2319)Cgt>Agt	p.R773S		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	773					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						TTTTTGAAACGAGGCCCCCAG	0.408																																					p.R773S	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											.	CDH9	305	.	0			c.C2317A						.						128	124	126					5																	26881298		2203	4299	6502	SO:0001583	missense	1007	exon12			TGAAACGAGGCCC	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"Cadherins / Major cadherins"	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.2317C>A	chr5.hg19:g.26881298G>T	ENSP00000231021:p.Arg773Ser	128.0	0.0		139.0	44.0	NM_016279	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	hg19	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.379404	0.82682	.	.	ENSG00000113100	ENST00000231021	T	0.79653	-1.29	5.26	5.26	0.73747	Cadherin, cytoplasmic domain (1);	0.167045	0.56097	D	0.000037	D	0.92815	0.7715	H	0.96301	3.8	0.47476	D	0.99943	D;D	0.62365	0.991;0.991	D;D	0.66716	0.946;0.946	D	0.94980	0.8125	9	.	.	.	.	17.4441	0.87574	0.0:0.0:1.0:0.0	.	366;773	B4DFP0;Q9ULB4	.;CADH9_HUMAN	S	773	ENSP00000231021:R773S	.	R	-	1	0	CDH9	26917055	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	9.835000	0.99442	2.456000	0.83038	0.557000	0.71058	CGT	.	.		0.408	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		T	26881298	G	T	26881298	3	4	283	1	0	0	0	0	1	0	0	0	3119	1058	37	1	56	1	CDH9	5	26881298	Missense_Mutation	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	19108192	26881298	154033962	71	41709										
ITGA2	3673	hgsc.bcm.edu	37	chr5	52347345	52347345	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	acatcccagacatcccaataTggtggggacctcacaaacac	7	14	1	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr5:52347345T>C	ENST00000296585.5	+	7	878	c.735T>C	c.(733-735)taT>taC	p.Y245Y		NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	245	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular response to hormone stimulus (GO:0032870)|collagen-activated signaling pathway (GO:0038065)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|hepatocyte differentiation (GO:0070365)|hypotonic response (GO:0006971)|integrin-mediated signaling pathway (GO:0007229)|mammary gland development (GO:0030879)|mesodermal cell differentiation (GO:0048333)|organ morphogenesis (GO:0009887)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell projection organization (GO:0031346)|positive regulation of collagen binding (GO:0033343)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA binding (GO:0043388)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|response to amine (GO:0014075)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to muscle activity (GO:0014850)|response to organic cyclic compound (GO:0014070)|skin morphogenesis (GO:0043589)|substrate-dependent cell migration (GO:0006929)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	axon terminus (GO:0043679)|basal part of cell (GO:0045178)|cell outer membrane (GO:0009279)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin alpha2-beta1 complex (GO:0034666)|integrin complex (GO:0008305)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)			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)				CATCCCAATATGGTGGGGACC	0.348																																					p.Y245Y		Atlas-SNP	.											.	ITGA2	211	.	0			c.T735C						.						113	109	111					5																	52347345		2203	4300	6503	SO:0001819	synonymous_variant	3673	exon7			CCAATATGGTGGG		CCDS3957.1	5q11.2	2010-03-23			ENSG00000164171	ENSG00000164171		"CD molecules", "Integrins"	6137	protein-coding gene	gene with protein product		192974		CD49B			Standard	NM_002203		Approved	CD49b	uc003joy.3	P17301	OTTHUMG00000131165	ENST00000296585.5:c.735T>C	chr5.hg19:g.52347345T>C		158.0	0.0		165.0	50.0	NM_002203	Q14595	Silent	SNP	ENST00000296585.5	hg19	CCDS3957.1																																																																																			.	.		0.348	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203		C	52347345	T	C	52347345	2	2	283	1	0	0	0	0	0	0	0	1	7884	1471	51	2		2	ITGA2	5	52347345	Silent	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	25466047	52347345	128567915	72	41710										
CDC20B	166979	hgsc.bcm.edu	37	chr5	54442574	54442574	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gacagagccctagtttgactTtgctgccaccttgtggtaat	10	10	0	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr5:54442574T>G	ENST00000381375.2	-	3	382	c.237A>C	c.(235-237)caA>caC	p.Q79H	CDC20B_ENST00000296733.1_Missense_Mutation_p.Q79H|CDC20B_ENST00000322374.6_Missense_Mutation_p.Q79H|CDC20B_ENST00000331730.3_Missense_Mutation_p.Q58H|CDC20B_ENST00000334206.5_Missense_Mutation_p.Q79H			Q86Y33	CD20B_HUMAN	cell division cycle 20B	79										kidney(1)|large_intestine(5)|lung(7)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	19		Lung NSC(810;0.000744)|Breast(144;0.159)|Prostate(74;0.194)	LUSC - Lung squamous cell carcinoma(15;0.225)			TAGTTTGACTTTGCTGCCACC	0.517											OREG0016610	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q79H		Atlas-SNP	.											.	CDC20B	61	.	0			c.A237C						.						120	112	114					5																	54442574		2203	4300	6503	SO:0001583	missense	166979	exon3			TTGACTTTGCTGC	AB086378	CCDS3966.1, CCDS47207.1, CCDS54852.1	5q11.2	2013-01-17	2013-01-17		ENSG00000164287	ENSG00000164287		"WD repeat domain containing"	24222	protein-coding gene	gene with protein product			"CDC20 cell division cycle 20 homolog B (S. cerevisiae)", "cell division cycle 20 homolog B (S. cerevisiae)"				Standard	NM_152623		Approved	FLJ37927	uc003jpo.2	Q86Y33	OTTHUMG00000131185	ENST00000381375.2:c.237A>C	chr5.hg19:g.54442574T>G	ENSP00000370781:p.Gln79His	125.0	0.0	1000	114.0	42.0	NM_001170402	B7WNV8|B9EGL8|C9J6X8|C9JHE9|C9JKL5|Q86Y31|Q86Y32|Q8IUZ8|Q8N1S1|Q8NG56	Missense_Mutation	SNP	ENST00000381375.2	hg19	CCDS54852.1	.	.	.	.	.	.	.	.	.	.	T	14.97	2.695414	0.48202	.	.	ENSG00000164287	ENST00000334206;ENST00000296733;ENST00000381375;ENST00000322374;ENST00000331730	T;T;T;T;T	0.27104	3.11;3.11;3.11;3.11;1.69	4.79	-1.36	0.09085	.	0.147317	0.31450	N	0.007638	T	0.39009	0.1062	M	0.61703	1.905	0.09310	N	0.999994	D;D;D;D	0.89917	1.0;1.0;0.999;0.993	D;D;D;P	0.69479	0.964;0.961;0.915;0.891	T	0.17198	-1.0377	10	0.59425	D	0.04	-13.586	8.5261	0.33307	0.0:0.5087:0.0:0.4913	.	79;79;79;79	Q86Y33-4;Q86Y33-3;Q86Y33;Q86Y33-2	.;.;CD20B_HUMAN;.	H	79;79;79;79;58	ENSP00000335664:Q79H;ENSP00000296733:Q79H;ENSP00000370781:Q79H;ENSP00000315720:Q79H;ENSP00000330566:Q58H	ENSP00000296733:Q79H	Q	-	3	2	CDC20B	54478331	0.950000	0.32346	0.936000	0.37596	0.546000	0.35178	0.030000	0.13688	-0.103000	0.12175	0.528000	0.53228	CAA	.	.		0.517	CDC20B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369715.1	NM_152623		G	54442574	T	G	54442574	3	3	283	1	0	0	0	0	1	0	0	0	3062	1838	64	5	1362	5	CDC20B	5	54442574	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	2095229	54442574	126472686	73	41711										
SKIV2L2	23517	hgsc.bcm.edu	37	chr5	54619962	54619962	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	taaacaattctttttaagttTggcagacctgatgcccagag	8	8	1	3			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr5:54619962T>A	ENST00000230640.5	+	3	529	c.275T>A	c.(274-276)tTg>tAg	p.L92*	SKIV2L2_ENST00000545714.1_Intron|SKIV2L2_ENST00000504388.1_3'UTR	NM_015360.4	NP_056175.3	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2 (S. cerevisiae)	92					maturation of 5.8S rRNA (GO:0000460)|mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			NS(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|lung(12)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)				TTTTTAAGTTTGGCAGACCTG	0.358																																					p.L92X	Melanoma(2;92 134 23744 29976 33782)	Atlas-SNP	.											.	SKIV2L2	104	.	0			c.T275A						.						74	66	69					5																	54619962		2203	4299	6502	SO:0001587	stop_gained	23517	exon3			TAAGTTTGGCAGA	D29641	CCDS3967.1	5q11.2	2008-11-25	2005-02-18	2005-02-18	ENSG00000039123	ENSG00000039123			18734	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 118"		"KIAA0052"	KIAA0052			Standard	NM_015360		Approved	Mtr4, Dob1, fSAP118	uc003jpy.4	P42285	OTTHUMG00000097019	ENST00000230640.5:c.275T>A	chr5.hg19:g.54619962T>A	ENSP00000230640:p.Leu92*	85.0	0.0		115.0	51.0	NM_015360	Q2M386|Q6MZZ8|Q6P170|Q8N5R0|Q8TAG2	Nonsense_Mutation	SNP	ENST00000230640.5	hg19	CCDS3967.1	.	.	.	.	.	.	.	.	.	.	T	37	6.483372	0.97603	.	.	ENSG00000039123	ENST00000230640	.	.	.	5.55	5.55	0.83447	.	0.073017	0.56097	D	0.000026	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	-13.2739	14.6889	0.69070	0.0:0.0:0.0:1.0	.	.	.	.	X	92	.	ENSP00000230640:L92X	L	+	2	0	SKIV2L2	54655719	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	7.259000	0.78381	2.118000	0.64928	0.533000	0.62120	TTG	.	.		0.358	SKIV2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214108.1			A	54619962	T	A	54619962	4	1	283	1	0	0	0	0	0	1	0	0	14375	1821	63	4	285	4	SKIV2L2	5	54619962	Nonsense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	177388	54619962	126295298	74	41712										
IL6ST	3572	hgsc.bcm.edu	37	chr5	55259985	55259985	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tataactacctttatatacaGgatcaaaattgatatgatct	4	6	2	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr5:55259985G>T	ENST00000381298.2	-	6	959	c.647C>A	c.(646-648)cCt>cAt	p.P216H	IL6ST_ENST00000381293.2_Intron|IL6ST_ENST00000381294.3_Missense_Mutation_p.P216H|IL6ST_ENST00000336909.5_Missense_Mutation_p.P216H|IL6ST_ENST00000577363.1_5'Flank|IL6ST_ENST00000522633.2_Missense_Mutation_p.P216H|IL6ST_ENST00000381287.4_Missense_Mutation_p.P216H|IL6ST_ENST00000536319.1_Missense_Mutation_p.P216H|IL6ST_ENST00000381286.3_Intron|IL6ST_ENST00000502326.3_Missense_Mutation_p.P216H	NM_001190981.1|NM_002184.3|NM_175767.2	NP_001177910.1|NP_002175.2|NP_786943.1	P40189	IL6RB_HUMAN	interleukin 6 signal transducer	216	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|glycogen metabolic process (GO:0005977)|interleukin-27-mediated signaling pathway (GO:0070106)|interleukin-6-mediated signaling pathway (GO:0070102)|leukemia inhibitory factor signaling pathway (GO:0048861)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of Notch signaling pathway (GO:0008593)|response to cytokine (GO:0034097)|viral process (GO:0016032)	ciliary neurotrophic factor receptor complex (GO:0070110)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|interleukin-6 receptor complex (GO:0005896)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|oncostatin-M receptor complex (GO:0005900)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|interleukin-11 receptor activity (GO:0004921)|interleukin-27 receptor activity (GO:0045509)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(5)|kidney(5)|large_intestine(4)|liver(2)|lung(1)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)				TTTATATACAGGATCAAAATT	0.299			O		hepatocellular ca																																p.P216H		Atlas-SNP	.		Dom	yes		5	5q11	3572	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"		E	IL6ST,NS,carcinoma,0,1	IL6ST	75	.	0			c.C647A						.						93	91	92					5																	55259985		2203	4300	6503	SO:0001583	missense	3572	exon6			TATACAGGATCAA	M57230	CCDS3971.1, CCDS47209.1, CCDS54856.1	5q11.2	2014-04-04	2014-04-04		ENSG00000134352	ENSG00000134352		"Interleukins and interleukin receptors", "CD molecules", "Fibronectin type III domain containing"	6021	protein-coding gene	gene with protein product	"gp130, oncostatin M receptor"	600694	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"			2261637	Standard	NM_002184		Approved	GP130, CD130	uc003jqq.3	P40189	OTTHUMG00000097043	ENST00000381298.2:c.647C>A	chr5.hg19:g.55259985G>T	ENSP00000370698:p.Pro216His	198.0	0.0		225.0	78.0	NM_175767	A0N0L4|Q5FC04|Q9UQ41	Missense_Mutation	SNP	ENST00000381298.2	hg19	CCDS3971.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.140058	0.77775	.	.	ENSG00000134352	ENST00000381298;ENST00000336909;ENST00000381294;ENST00000381287;ENST00000536319;ENST00000522633;ENST00000542298	T;T;T;T;T;T	0.37752	1.18;1.18;1.18;1.18;1.18;1.18	6.17	6.17	0.99709	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.152023	0.64402	D	0.000010	T	0.62913	0.2467	M	0.82323	2.585	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.63699	-0.6578	10	0.51188	T	0.08	.	13.9957	0.64397	0.0685:0.0:0.9315:0.0	.	216;216;216	Q5FC04;P40189-2;P40189	.;.;IL6RB_HUMAN	H	216	ENSP00000370698:P216H;ENSP00000338799:P216H;ENSP00000370694:P216H;ENSP00000370687:P216H;ENSP00000444456:P216H;ENSP00000435399:P216H	ENSP00000338799:P216H	P	-	2	0	IL6ST	55295742	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.233000	0.78125	2.941000	0.99782	0.655000	0.94253	CCT	.	.		0.299	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184		T	55259985	G	T	55259985	3	4	283	1	0	0	0	0	1	0	0	0	7712	1000	35	3	2157	3	IL6ST	5	55259985	Missense_Mutation	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	640023	55259985	125655275	75	41713										
PLK2	10769	hgsc.bcm.edu	37	chr5	57752800	57752800	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tcaatatatcttgctttgtcTtttttgccaccaaaaagagc	5	9	3	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr5:57752800T>C	ENST00000274289.3	-	8	1428	c.1128A>G	c.(1126-1128)aaA>aaG	p.K376K	PLK2_ENST00000502671.1_5'UTR	NM_001252226.1|NM_006622.3	NP_001239155.1|NP_006613.2	Q9NYY3	PLK2_HUMAN	polo-like kinase 2	376					G1/S transition of mitotic cell cycle (GO:0000082)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|mitotic cell cycle checkpoint (GO:0007093)|mitotic spindle organization (GO:0007052)|negative regulation of apoptotic process (GO:0043066)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein phosphorylation (GO:0006468)|Rap protein signal transduction (GO:0032486)|Ras protein signal transduction (GO:0007265)|regulation of centriole replication (GO:0046599)|regulation of synaptic plasticity (GO:0048167)	centriole (GO:0005814)|centrosome (GO:0005813)|dendrite (GO:0030425)|intracellular (GO:0005622)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			endometrium(7)|large_intestine(7)|lung(5)|ovary(3)|prostate(2)|skin(2)	26		all_cancers(5;1.76e-12)|all_epithelial(5;2.09e-13)|all_lung(5;6.64e-05)|Lung NSC(5;0.000127)|Prostate(74;0.055)|Breast(144;0.0602)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;7.03e-37)		TTGCTTTGTCTTTTTTGCCAC	0.328																																					p.K376K		Atlas-SNP	.											.	PLK2	71	.	0			c.A1128G						.						70	73	72					5																	57752800		2203	4300	6503	SO:0001819	synonymous_variant	10769	exon8			TTTGTCTTTTTTG		CCDS3974.1, CCDS75250.1	5q12.1-q13.2	2013-01-18	2010-06-24		ENSG00000145632	ENSG00000145632			19699	protein-coding gene	gene with protein product	"serum-inducible kinase"	607023	"polo-like kinase 2 (Drosophila)"				Standard	NM_006622		Approved	SNK	uc003jrn.3	Q9NYY3	OTTHUMG00000097047	ENST00000274289.3:c.1128A>G	chr5.hg19:g.57752800T>C		96.0	0.0		145.0	53.0	NM_006622	O60679|Q96CV7|Q9UE61	Silent	SNP	ENST00000274289.3	hg19	CCDS3974.1	.	.	.	.	.	.	.	.	.	.	T	9.658	1.143357	0.21205	.	.	ENSG00000145632	ENST00000442330	.	.	.	5.28	1.75	0.24633	.	0.047044	0.85682	D	0.000000	T	0.38134	0.1029	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.05468	-1.0883	6	0.13108	T	0.6	-23.5228	6.9577	0.24580	0.0:0.3579:0.0:0.6421	.	.	.	.	R	362	.	ENSP00000401861:K362R	K	-	2	0	PLK2	57788557	0.986000	0.35501	1.000000	0.80357	0.999000	0.98932	0.216000	0.17585	0.862000	0.35528	0.533000	0.62120	AAG	.	.		0.328	PLK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214150.1	NM_006622		C	57752800	T	C	57752800	2	2	283	1	0	0	0	0	0	0	0	1	12105	1606	56	2		2	PLK2	5	57752800	Silent	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	2492815	57752800	123162460	76	41714										
FCHO2	115548	hgsc.bcm.edu	37	chr5	72377662	72377662	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gaatcttgcaacatactggaAatgtagtgctagcaccacag	9	9	1	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr5:72377662A>C	ENST00000430046.2	+	23	2149	c.2033A>C	c.(2032-2034)aAa>aCa	p.K678T	FCHO2_ENST00000512348.1_Missense_Mutation_p.K645T|FCHO2_ENST00000341845.6_Missense_Mutation_p.K678T	NM_001146032.1|NM_138782.2	NP_001139504.1|NP_620137.2	Q0JRZ9	FCHO2_HUMAN	FCH domain only 2	678	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.|Mediates interaction with DAB2, EPS15, EPS15R and ITSN1.				clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)|membrane invagination (GO:0010324)|protein localization to plasma membrane (GO:0072659)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(1)	17		Lung NSC(167;0.0465)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;4.6e-53)		ACATACTGGAAATGTAGTGCT	0.393																																					p.K678T		Atlas-SNP	.											.	FCHO2	96	.	0			c.A2033C						.						116	108	110					5																	72377662		1868	4109	5977	SO:0001583	missense	115548	exon23			ACTGGAAATGTAG	AL831971	CCDS47230.1, CCDS54868.1	5q13.2	2005-08-15			ENSG00000157107	ENSG00000157107			25180	protein-coding gene	gene with protein product		613438				15254787	Standard	NM_138782		Approved		uc003kcl.3	Q0JRZ9	OTTHUMG00000162413	ENST00000430046.2:c.2033A>C	chr5.hg19:g.72377662A>C	ENSP00000393776:p.Lys678Thr	153.0	0.0		151.0	51.0	NM_138782	A8K6W7|B2RNQ9|B4DHK0|E9PG79|Q0JTJ3|Q96CF5	Missense_Mutation	SNP	ENST00000430046.2	hg19	CCDS47230.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.269416	0.80469	.	.	ENSG00000157107	ENST00000430046;ENST00000341845;ENST00000512348	T;T;T	0.55588	0.51;0.51;0.51	5.65	4.49	0.54785	Muniscin C-terminal mu homology domain (1);	0.000000	0.85682	D	0.000000	T	0.71921	0.3397	M	0.81942	2.565	0.53005	D	0.999964	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.99	T	0.75286	-0.3371	10	0.87932	D	0	-23.8727	11.517	0.50526	0.9306:0.0:0.0694:0.0	.	645;678	E9PG79;Q0JRZ9	.;FCHO2_HUMAN	T	678;678;645	ENSP00000393776:K678T;ENSP00000344034:K678T;ENSP00000427296:K645T	ENSP00000344034:K678T	K	+	2	0	FCHO2	72413418	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.761000	0.91691	1.149000	0.42402	0.533000	0.62120	AAA	.	.		0.393	FCHO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368795.3	XM_291142		C	72377662	A	C	72377662	3	2	283	1	0	0	0	0	1	0	0	0	5796	14	1	5	2123	5	FCHO2	5	72377662	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	14624862	72377662	108537598	77	41715										
GPR98	84059	hgsc.bcm.edu	37	chr5	90079723	90079723	+	Missense_Mutation	SNP	T	T	C													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	agcggtccttgggcgccaccTagtgagcagaatcataatag							TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr5:90079723T>C	ENST00000405460.2	+	67	13598	c.13502T>C	c.(13501-13503)cTa>cCa	p.L4501P	GPR98_ENST00000425867.2_Missense_Mutation_p.L162P	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	4501					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		GGGCGCCACCTAGTGAGCAGA	0.443																																					p.L4501P		Atlas-SNP	.											.	GPR98	605	.	0			c.T13502C						.						59	57	58					5																	90079723		1839	4082	5921	SO:0001583	missense	84059	exon67			GCCACCTAGTGAG	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.13502T>C	chr5.hg19:g.90079723T>C	ENSP00000384582:p.Leu4501Pro	95.0	0.0		116.0	52.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	T	19.84	3.901167	0.72754	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.26957	1.7;1.7	5.97	5.97	0.96955	.	0.283287	0.34531	N	0.003900	T	0.51584	0.1683	M	0.76838	2.35	0.58432	D	0.999999	D;D;D	0.76494	0.998;0.996;0.999	D;P;D	0.68943	0.915;0.804;0.961	T	0.48768	-0.9006	10	0.33940	T	0.23	.	16.4454	0.83928	0.0:0.0:0.0:1.0	.	162;4501;162	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	P	4501;4501;162	ENSP00000384582:L4501P;ENSP00000392618:L162P	ENSP00000296619:L4501P	L	+	2	0	GPR98	90115479	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.908000	0.69916	2.275000	0.75901	0.533000	0.62120	CTA	.	.		0.443	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		C	90079723	T	C	90079723	3	2	283	1	0	0	0	0	1	0	0	0	6730	1522	53	2	13768	2	GPR98	5	90079723	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	17702061	90079723	90835537	78	41716	213	2								
GPR98	84059	hgsc.bcm.edu	37	chr5	90079728	90079728	+	Missense_Mutation	SNP	A	A	C													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tccttgggcgccacctagtgAgcagaatcataatagctaag							TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr5:90079728A>C	ENST00000405460.2	+	67	13603	c.13507A>C	c.(13507-13509)Agc>Cgc	p.S4503R	GPR98_ENST00000425867.2_Missense_Mutation_p.S164R	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	4503					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		CCACCTAGTGAGCAGAATCAT	0.428																																					p.S4503R		Atlas-SNP	.											GPR98,NS,carcinoma,0,2	GPR98	605	.	0			c.A13507C						.						60	58	59					5																	90079728		1838	4082	5920	SO:0001583	missense	84059	exon67			CTAGTGAGCAGAA	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.13507A>C	chr5.hg19:g.90079728A>C	ENSP00000384582:p.Ser4503Arg	103.0	0.0		119.0	21.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	A	15.04	2.714648	0.48622	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.27402	1.67;1.67	5.97	4.79	0.61399	.	0.177930	0.64402	D	0.000011	T	0.44973	0.1319	M	0.70595	2.14	0.30855	N	0.73417	P;P;P	0.50617	0.895;0.761;0.937	P;B;P	0.53809	0.548;0.276;0.735	T	0.55611	-0.8114	10	0.72032	D	0.01	.	10.3547	0.43956	0.7168:0.0:0.0:0.2832	.	164;4503;164	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	R	4503;4503;164	ENSP00000384582:S4503R;ENSP00000392618:S164R	ENSP00000296619:S4503R	S	+	1	0	GPR98	90115484	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	2.854000	0.48325	1.028000	0.39785	0.533000	0.62120	AGC	.	.		0.428	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		C	90079728	A	C	90079728	3	2	283	1	0	0	0	0	1	0	0	0	6730	304	11	5	13773	5	GPR98	5	90079728	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	5	90079728	90835532	79	41717	213	2								
ELL2	22936	hgsc.bcm.edu	37	chr5	95236720	95236720	+	Missense_Mutation	SNP	T	T	C													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tgtatccaggccagtctcttTgaagctctttaaaaacataa							TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr5:95236720T>C	ENST00000237853.4	-	6	1155	c.806A>G	c.(805-807)cAa>cGa	p.Q269R	ELL2_ENST00000431061.2_Intron	NM_012081.5	NP_036213.2	O00472	ELL2_HUMAN	elongation factor, RNA polymerase II, 2	269					regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|transcription elongation from RNA polymerase II promoter (GO:0006368)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)	24		all_cancers(142;2.04e-06)|all_epithelial(76;3.1e-09)|all_lung(232;0.00309)|Lung NSC(167;0.00454)|Ovarian(225;0.0165)|Colorectal(57;0.0343)|Breast(839;0.198)		all cancers(79;2.16e-15)		CCAGTCTCTTTGAAGCTCTTT	0.348																																					p.Q269R		Atlas-SNP	.											.	ELL2	63	.	0			c.A806G						.						78	83	82					5																	95236720		2202	4299	6501	SO:0001583	missense	22936	exon6			TCTCTTTGAAGCT	U88629	CCDS4080.1	5q15	2010-11-29			ENSG00000118985	ENSG00000118985			17064	protein-coding gene	gene with protein product		601874				9108030	Standard	NM_012081		Approved		uc003klr.4	O00472	OTTHUMG00000122085	ENST00000237853.4:c.806A>G	chr5.hg19:g.95236720T>C	ENSP00000237853:p.Gln269Arg	190.0	0.0		158.0	47.0	NM_012081	B4DNK7	Missense_Mutation	SNP	ENST00000237853.4	hg19	CCDS4080.1	.	.	.	.	.	.	.	.	.	.	T	19.12	3.765006	0.69878	.	.	ENSG00000118985	ENST00000237853;ENST00000513343	T;T	0.35048	1.33;1.33	5.52	5.52	0.82312	.	0.050304	0.85682	D	0.000000	T	0.59046	0.2165	M	0.81682	2.555	0.80722	D	1	D	0.61697	0.99	P	0.59487	0.858	T	0.65681	-0.6109	10	0.87932	D	0	-10.1971	15.2931	0.73882	0.0:0.0:0.0:1.0	.	269	O00472	ELL2_HUMAN	R	269;87	ENSP00000237853:Q269R;ENSP00000423915:Q87R	ENSP00000237853:Q269R	Q	-	2	0	ELL2	95262476	1.000000	0.71417	0.973000	0.42090	0.832000	0.47134	7.698000	0.84413	2.086000	0.62901	0.459000	0.35465	CAA	.	.		0.348	ELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242846.1	NM_012081		C	95236720	T	C	95236720	3	2	283	1	0	0	0	0	1	0	0	0	5065	1812	63	2	1144	2	ELL2	5	95236720	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	5156992	95236720	85678540	80	41718	214	2								
ELL2	22936	hgsc.bcm.edu	37	chr5	95236730	95236730	+	Nonsense_Mutation	SNP	T	T	A													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ccagtctctttgaagctcttTaaaaacataatcctttaagg							TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr5:95236730T>A	ENST00000237853.4	-	6	1145	c.796A>T	c.(796-798)Aaa>Taa	p.K266*	ELL2_ENST00000431061.2_Intron	NM_012081.5	NP_036213.2	O00472	ELL2_HUMAN	elongation factor, RNA polymerase II, 2	266					regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|transcription elongation from RNA polymerase II promoter (GO:0006368)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)	24		all_cancers(142;2.04e-06)|all_epithelial(76;3.1e-09)|all_lung(232;0.00309)|Lung NSC(167;0.00454)|Ovarian(225;0.0165)|Colorectal(57;0.0343)|Breast(839;0.198)		all cancers(79;2.16e-15)		TGAAGCTCTTTAAAAACATAA	0.348																																					p.K266X		Atlas-SNP	.											.	ELL2	63	.	0			c.A796T						.						74	79	77					5																	95236730		2202	4299	6501	SO:0001587	stop_gained	22936	exon6			GCTCTTTAAAAAC	U88629	CCDS4080.1	5q15	2010-11-29			ENSG00000118985	ENSG00000118985			17064	protein-coding gene	gene with protein product		601874				9108030	Standard	NM_012081		Approved		uc003klr.4	O00472	OTTHUMG00000122085	ENST00000237853.4:c.796A>T	chr5.hg19:g.95236730T>A	ENSP00000237853:p.Lys266*	192.0	0.0		149.0	45.0	NM_012081	B4DNK7	Nonsense_Mutation	SNP	ENST00000237853.4	hg19	CCDS4080.1	.	.	.	.	.	.	.	.	.	.	T	36	5.930280	0.97116	.	.	ENSG00000118985	ENST00000237853;ENST00000513343	.	.	.	5.52	5.52	0.82312	.	0.047215	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.4723	15.2931	0.73882	0.0:0.0:0.0:1.0	.	.	.	.	X	266;84	.	ENSP00000237853:K266X	K	-	1	0	ELL2	95262486	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	2.203000	0.42752	2.086000	0.62901	0.459000	0.35465	AAA	.	.		0.348	ELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242846.1	NM_012081		A	95236730	T	A	95236730	4	1	283	1	0	0	0	0	0	1	0	0	5065	1763	61	4	1154	4	ELL2	5	95236730	Nonsense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	10	95236730	85678530	81	41719	214	2								
PAIP2	51247	hgsc.bcm.edu	37	chr5	138704424	138704429	+	In_Frame_Del	DEL	CAAGAG	CAAGAG	-													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tatgtacttattttccaggtCaagagcaatctgaatccaaa							TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	CAAGAG	CAAGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr5:138704424_138704429delCAAGAG	ENST00000394795.2	+	4	1312_1317	c.321_326delCAAGAG	c.(319-327)gtcaagagc>gtc	p.KS108del	SLC23A1_ENST00000348729.3_Intron|PAIP2_ENST00000265192.4_In_Frame_Del_p.KS108del|PAIP2_ENST00000511706.1_In_Frame_Del_p.KS48del|PAIP2_ENST00000510080.1_In_Frame_Del_p.KS108del|SLC23A1_ENST00000353963.3_Intron|CTB-43P18.1_ENST00000503553.3_RNA|PAIP2_ENST00000511381.1_3'UTR			Q9BPZ3	PAIP2_HUMAN	poly(A) binding protein interacting protein 2	108	PABPC1-interacting motif-2 (PAM2).				memory (GO:0007613)|negative regulation of translational initiation (GO:0045947)|regulation of long-term synaptic potentiation (GO:1900271)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	mRNA binding (GO:0003729)|translation repressor activity (GO:0030371)			kidney(1)|large_intestine(2)|lung(2)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			TTTTCCAGGTCAAGAGCAATCTGAAT	0.374																																					p.107_109del		Atlas-Indel,Pindel	.											.	PAIP2	10	.	0			c.320_325del						.																																			SO:0001651	inframe_deletion	51247	exon4			.	AF151052	CCDS4211.1	5q32	2008-02-05			ENSG00000120727	ENSG00000120727			17970	protein-coding gene	gene with protein product		605604				11172725, 16804161	Standard	NM_016480		Approved	PAIP2A	uc003led.3	Q9BPZ3	OTTHUMG00000129227	ENST00000394795.2:c.321_326delCAAGAG	chr5.hg19:g.138704424_138704429delCAAGAG	ENSP00000378275:p.Lys108_Ser109del	162.0	0.0		132.0	25.0	NM_016480	B2RBI1|D3DQC6|Q49A06|Q9H0Y5|Q9P0Q8	In_Frame_Del	DEL	ENST00000394795.2	hg19	CCDS4211.1																																																																																			.	.		0.374	PAIP2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373002.1	NM_016480		-	138704429	CAAGAG	-	138704424	7	5	283	1	0	1	0	1	0	0	0	0	11406	813	29	0	331	0	PAIP2	5	138704424	In_Frame_Del	DEL	CAAGAG	TCGA-G3-A3CK-01A-11D-A20W-10	43467694	138704424	42210836	82	41720										
GRIA1	2890	hgsc.bcm.edu	37	chr5	153065884	153065884	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	aaatgaaacatgacggcatcCgaaaggtaaggtcccccttt	9	10	0	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr5:153065884C>T	ENST00000285900.5	+	8	1472	c.1129C>T	c.(1129-1131)Cga>Tga	p.R377*	GRIA1_ENST00000340592.5_Nonsense_Mutation_p.R377*|GRIA1_ENST00000448073.4_Nonsense_Mutation_p.R387*|GRIA1_ENST00000518783.1_Nonsense_Mutation_p.R387*|GRIA1_ENST00000518142.1_Nonsense_Mutation_p.R297*|GRIA1_ENST00000521843.2_Nonsense_Mutation_p.R308*	NM_000827.3|NM_001258019.1	NP_000818.2|NP_001244948.1	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1	377					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|axonal spine (GO:0044308)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|neuron spine (GO:0044309)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|PDZ domain binding (GO:0030165)	p.R377*(1)		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)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Perampanel(DB08883)|Sevoflurane(DB01236)	TGACGGCATCCGAAAGGTAAG	0.512																																					p.R387X		Atlas-SNP	.											GRIA1_ENST00000544403,NS,carcinoma,-1,1	GRIA1	321	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1159T						.						98	89	92					5																	153065884		2203	4300	6503	SO:0001587	stop_gained	2890	exon8			GGCATCCGAAAGG		CCDS4322.1, CCDS47318.1, CCDS58986.1, CCDS58987.1, CCDS58988.1, CCDS58989.1	5q33	2012-08-29			ENSG00000155511	ENSG00000155511		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4571	protein-coding gene	gene with protein product		138248		GLUR1		1652753, 1319477	Standard	NM_000827		Approved	GluA1, GLURA	uc011dcy.2	P42261	OTTHUMG00000130148	ENST00000285900.5:c.1129C>T	chr5.hg19:g.153065884C>T	ENSP00000285900:p.Arg377*	102.0	0.0		101.0	14.0	NM_001258021	B7Z2S0|B7Z2W8|B7Z3F6|B7Z9G9|D3DQI4|E7ESV8|Q2NKM6	Nonsense_Mutation	SNP	ENST00000285900.5	hg19	CCDS4322.1	.	.	.	.	.	.	.	.	.	.	C	37	6.492604	0.97612	.	.	ENSG00000155511	ENST00000285900;ENST00000544403;ENST00000518142;ENST00000537037;ENST00000340592;ENST00000521843;ENST00000544794;ENST00000518783;ENST00000448073	.	.	.	5.23	2.32	0.28847	.	0.061429	0.64402	D	0.000010	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.7135	0.62682	0.5498:0.4502:0.0:0.0	.	.	.	.	X	377;377;297;331;377;308;308;387;387	.	ENSP00000285900:R377X	R	+	1	2	GRIA1	153046077	0.541000	0.26417	0.999000	0.59377	0.727000	0.41649	0.800000	0.27042	0.159000	0.19401	-0.182000	0.12963	CGA	.	.		0.512	GRIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252456.3			T	153065884	C	T	153065884	4	4	283	1	0	0	0	0	0	1	0	0	6776	644	23	1	1159	1	GRIA1	5	153065884	Nonsense_Mutation	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	14361460	153065884	27849376	83	41721										
CCNG1	900	hgsc.bcm.edu	37	chr5	162866370	162866370	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	aaggtctgtggtttgagactAattgagtctgcacacgataa	11	6	2	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr5:162866370A>C	ENST00000340828.2	+	2	332	c.108A>C	c.(106-108)ctA>ctC	p.L36L	CCNG1_ENST00000511683.2_Intron|CCNG1_ENST00000512163.1_Intron|RP11-541P9.3_ENST00000458002.2_RNA|CCNG1_ENST00000510664.1_Intron|CCNG1_ENST00000504553.1_5'Flank|RP11-541P9.3_ENST00000503504.1_RNA|CCNG1_ENST00000393929.1_Silent_p.L36L	NM_004060.3	NP_004051.1	P51959	CCNG1_HUMAN	cyclin G1	36					brain development (GO:0007420)|cell growth (GO:0016049)|mitotic G2 DNA damage checkpoint (GO:0007095)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|response to organonitrogen compound (GO:0010243)|syncytium formation (GO:0006949)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(2)	12	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0597)|OV - Ovarian serous cystadenocarcinoma(192;0.107)|Epithelial(171;0.164)		GTTTGAGACTAATTGAGTCTG	0.438																																					p.L36L		Atlas-SNP	.											.	CCNG1	28	.	0			c.A108C						.						136	126	130					5																	162866370		2203	4300	6503	SO:0001819	synonymous_variant	900	exon3			GAGACTAATTGAG	D78341	CCDS4360.1	5q32-q34	2010-11-15			ENSG00000113328	ENSG00000113328			1592	protein-coding gene	gene with protein product		601578		CCNG		8954786, 8806701	Standard	NM_004060		Approved		uc003lzb.3	P51959	OTTHUMG00000130380	ENST00000340828.2:c.108A>C	chr5.hg19:g.162866370A>C		171.0	0.0		133.0	47.0	NM_199246	B2R7B2|B4DLW7|D3DQK7|Q15757|Q96L32	Silent	SNP	ENST00000340828.2	hg19	CCDS4360.1																																																																																			.	.		0.438	CCNG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252750.3	NM_004060		C	162866370	A	C	162866370	2	2	283	1	0	0	0	0	0	0	0	1	2925	349	13	5		5	CCNG1	5	162866370	Silent	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	9800486	162866370	18048890	84	41722										
RANBP17	64901	hgsc.bcm.edu	37	chr5	170346578	170346578	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	accagaaatcacgaaggcctTtatcacttctcggttggact	8	11	3	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr5:170346578T>G	ENST00000523189.1	+	11	1399	c.1235T>G	c.(1234-1236)tTt>tGt	p.F412C		NM_022897.3	NP_075048.1	Q9H2T7	RBP17_HUMAN	RAN binding protein 17	412					mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)	GTP binding (GO:0005525)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	50	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			ACGAAGGCCTTTATCACTTCT	0.368			T	TRD@	ALL																																p.F412C		Atlas-SNP	.		Dom	yes		5	5q34	64901	RAN binding protein 17		L	.	RANBP17	108	.	0			c.T1235G						.						165	162	163					5																	170346578		2203	4300	6503	SO:0001583	missense	64901	exon11			AGGCCTTTATCAC	AF222747	CCDS34287.1	5q34	2009-01-12			ENSG00000204764	ENSG00000204764			14428	protein-coding gene	gene with protein product		606141				11024021	Standard	NM_022897		Approved		uc003mba.3	Q9H2T7	OTTHUMG00000163203	ENST00000523189.1:c.1235T>G	chr5.hg19:g.170346578T>G	ENSP00000427975:p.Phe412Cys	190.0	0.0		193.0	73.0	NM_022897	Q8IU74	Missense_Mutation	SNP	ENST00000523189.1	hg19	CCDS34287.1	.	.	.	.	.	.	.	.	.	.	t	18.00	3.526548	0.64860	.	.	ENSG00000204764	ENST00000523189;ENST00000545246	T	0.66638	-0.22	5.68	3.1	0.35709	Armadillo-type fold (1);	0.188901	0.37483	N	0.002065	T	0.71417	0.3337	M	0.67397	2.05	0.46927	D	0.999256	D	0.60160	0.987	P	0.54372	0.75	T	0.72975	-0.4128	10	0.72032	D	0.01	-13.5708	9.1	0.36662	0.5695:0.0:0.0:0.4305	.	412	Q9H2T7	RBP17_HUMAN	C	412;308	ENSP00000427975:F412C	ENSP00000373770:F412C	F	+	2	0	RANBP17	170279183	1.000000	0.71417	0.995000	0.50966	0.855000	0.48748	5.654000	0.67974	0.942000	0.37525	0.477000	0.44152	TTT	.	.		0.368	RANBP17-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372036.1	NM_022897		G	170346578	T	G	170346578	3	3	283	1	0	0	0	0	1	0	0	0	13042	1841	64	5	1277	5	RANBP17	5	170346578	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	7480208	170346578	10568682	85	41723										
JARID2	3720	hgsc.bcm.edu	37	chr6	15468853	15468853	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tcgaggaggaagatgatgagAcagaagacgtcaaaacagcc	13	7	1	5			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr6:15468853A>T	ENST00000341776.2	+	5	818	c.574A>T	c.(574-576)Aca>Tca	p.T192S	JARID2_ENST00000541660.1_Missense_Mutation_p.T154S|JARID2_ENST00000397311.3_Missense_Mutation_p.T20S	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	192					central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	59	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				AGATGATGAGACAGAAGACGT	0.488																																					p.T192S		Atlas-SNP	.											.	JARID2	135	.	0			c.A574T						.						152	126	135					6																	15468853		2203	4300	6503	SO:0001583	missense	3720	exon5			GATGAGACAGAAG	U57592	CCDS4533.1, CCDS58996.1	6p24-p23	2008-02-05	2006-10-06	2004-01-30	ENSG00000008083	ENSG00000008083			6196	protein-coding gene	gene with protein product		601594	"jumonji (mouse) homolog", "Jumonji, AT rich interactive domain 2"	JMJ		8894700	Standard	NM_001267040		Approved		uc003nbj.4	Q92833	OTTHUMG00000014293	ENST00000341776.2:c.574A>T	chr6.hg19:g.15468853A>T	ENSP00000341280:p.Thr192Ser	175.0	0.0		209.0	90.0	NM_004973	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Missense_Mutation	SNP	ENST00000341776.2	hg19	CCDS4533.1	.	.	.	.	.	.	.	.	.	.	A	12.33	1.905084	0.33628	.	.	ENSG00000008083	ENST00000538175;ENST00000341776;ENST00000397311;ENST00000541660	T;T;T	0.34859	1.34;1.34;1.34	4.94	4.94	0.65067	.	0.432685	0.22979	N	0.053340	T	0.11793	0.0287	L	0.36672	1.1	0.25820	N	0.984297	P;P;B	0.36837	0.571;0.555;0.255	B;B;B	0.35770	0.21;0.138;0.104	T	0.08513	-1.0718	10	0.19590	T	0.45	-5.9259	9.7093	0.40236	0.8452:0.0:0.0:0.1548	.	154;56;192	F5H590;B7Z7X9;Q92833	.;.;JARD2_HUMAN	S	56;192;20;154	ENSP00000341280:T192S;ENSP00000380478:T20S;ENSP00000444623:T154S	ENSP00000341280:T192S	T	+	1	0	JARID2	15576832	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	2.856000	0.48341	1.858000	0.53909	0.529000	0.55759	ACA	.	.		0.488	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973		T	15468853	A	T	15468853	3	4	283	1	0	0	0	0	1	0	0	0	7954	275	10	4	592	4	JARID2	6	15468853	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10		15468853	155646214	86	41724										
SLC44A4	80736	hgsc.bcm.edu	37	chr6	31833747	31833747	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ggcaaaggctccagcgaggaCgcattggcccagggccagta	15	12	0	0	rs149591801	byFrequency	TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr6:31833747C>T	ENST00000229729.6	-	14	1410	c.1390G>A	c.(1390-1392)Gtc>Atc	p.V464I	SLC44A4_ENST00000544672.1_Missense_Mutation_p.V388I|SLC44A4_ENST00000375562.4_Missense_Mutation_p.V422I	NM_025257.2	NP_079533.2	Q53GD3	CTL4_HUMAN	solute carrier family 44, member 4	464					acetylcholine biosynthetic process (GO:0008292)|acetylcholine secretion (GO:0061526)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of cell growth (GO:0030307)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.V464I(2)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(1)|urinary_tract(2)	35					Choline(DB00122)	CCAGCGAGGACGCATTGGCCC	0.557													C|||	6	0.00119808	0	0	5008	,	,		19077	0		0	False		,,,				2504	0.0061				p.V464I		Atlas-SNP	.											SLC44A4,NS,carcinoma,0,2	SLC44A4	67	.	2	Substitution - Missense(2)	prostate(2)	c.G1390A						.	C	ILE/VAL,ILE/VAL,ILE/VAL	0,4406		0,0,2203	69	67	68		1264,1162,1390	4.3	1	6	dbSNP_134	68	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense,missense	SLC44A4	NM_001178044.1,NM_001178045.1,NM_025257.2	29,29,29	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging,probably-damaging,probably-damaging	422/669,388/635,464/711	31833747	2,13004	2203	4300	6503	SO:0001583	missense	80736	exon14			CGAGGACGCATTG	AF134726	CCDS4724.2, CCDS54989.1, CCDS54990.1	6p21.3	2014-02-17	2005-09-06	2005-09-06	ENSG00000204385	ENSG00000204385		"Solute carriers"	13941	protein-coding gene	gene with protein product		606107	"chromosome 6 open reading frame 29"	C6orf29		10677542, 15715662, 24379411	Standard	NM_025257		Approved	NG22, CTL4, FLJ14491, TPPT	uc010jti.3	Q53GD3	OTTHUMG00000031133	ENST00000229729.6:c.1390G>A	chr6.hg19:g.31833747C>T	ENSP00000229729:p.Val464Ile	113.0	0.0		122.0	48.0	NM_025257	A2BED3|B0UXX8|B0UZY8|B4DU94|B4DWM2|E9PEK7|Q5JP84|Q5JQ93|Q658S8|Q6UX89|Q8TEW4|Q96C58|Q96K59|Q9Y332	Missense_Mutation	SNP	ENST00000229729.6	hg19	CCDS4724.2	.	.	.	.	.	.	.	.	.	.	C	14.88	2.666032	0.47677	0.0	2.33E-4	ENSG00000204385	ENST00000229729;ENST00000375562;ENST00000544672	T;T;T	0.24350	1.86;1.86;1.86	5.21	4.34	0.51931	.	0.136893	0.49916	D	0.000127	T	0.19127	0.0459	L	0.58583	1.82	0.33101	D	0.539257	P	0.48503	0.911	P	0.46940	0.532	T	0.03957	-1.0989	10	0.46703	T	0.11	-17.9757	12.7587	0.57350	0.0:0.9198:0.0:0.0802	.	464	Q53GD3	CTL4_HUMAN	I	464;422;388	ENSP00000229729:V464I;ENSP00000364712:V422I;ENSP00000444109:V388I	ENSP00000229729:V464I	V	-	1	0	SLC44A4	31941726	0.995000	0.38212	1.000000	0.80357	0.863000	0.49368	2.759000	0.47573	1.434000	0.47414	0.655000	0.94253	GTC	.	C|1.000;T|0.000		0.557	SLC44A4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076234.3			T	31833747	C	T	31833747	3	4	283	1	0	0	0	0	1	0	0	0	14653	536	19	1	774	1	SLC44A4	6	31833747	Missense_Mutation	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	16364894	31833747	139281320	87	41725										
TAP1	6890	hgsc.bcm.edu	37	chr6	32821435	32821435	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ggcactcggacgccgtcccgGtcccggccgggcctgggact	16	17	0	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr6:32821435G>A	ENST00000354258.4	-	1	320	c.159C>T	c.(157-159)gaC>gaT	p.D53D	TAP1_ENST00000425148.2_5'Flank|PSMB9_ENST00000395330.1_Intron|PSMB9_ENST00000453265.2_5'Flank|PSMB9_ENST00000374859.2_5'Flank	NM_000593.5	NP_000584.2	Q03518	TAP1_HUMAN	transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)	53					antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytosol to ER transport (GO:0046967)|defense response (GO:0006952)|intracellular transport of viral protein in host cell (GO:0019060)|peptide transport (GO:0015833)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)|TAP complex (GO:0042825)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|MHC class Ib protein binding (GO:0023029)|peptide antigen binding (GO:0042605)|peptide transporter activity (GO:0015197)|protein homodimerization activity (GO:0042803)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(4)|prostate(1)|skin(1)	21					Lapatinib(DB01259)	CGCCGTCCCGGTCCCGGCCGG	0.736																																					p.D53D		Atlas-SNP	.											.	TAP1	39	.	0			c.C159T						.						7	9	8					6																	32821435		1458	2659	4117	SO:0001819	synonymous_variant	6890	exon1			GTCCCGGTCCCGG		CCDS4758.1	6p21.3	2014-09-17			ENSG00000168394	ENSG00000168394		"ATP binding cassette transporters / subfamily B"	43	protein-coding gene	gene with protein product		170260		ABCB2		1529427, 1946428	Standard	NM_000593		Approved	PSF1, RING4, D6S114E	uc003ocg.3	Q03518	OTTHUMG00000031067	ENST00000354258.4:c.159C>T	chr6.hg19:g.32821435G>A		32.0	0.0		41.0	16.0	NM_000593	Q16149|Q96CP4	Silent	SNP	ENST00000354258.4	hg19	CCDS4758.1																																																																																			.	.		0.736	TAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076087.2	NM_000593		A	32821435	G	A	32821435	2	1	283	1	0	0	0	0	0	0	0	1	15565	1252	44	3		3	TAP1	6	32821435	Silent	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	987688	32821435	138293632	88	41726										
RPS10	6204	hgsc.bcm.edu	37	chr6	34389539	34389539	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tccgtctgtaggtatctctgTcagcttcccctcttgtgagt	9	12	4	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr6:34389539T>C	ENST00000326199.8	-	4	461	c.368A>G	c.(367-369)gAc>gGc	p.D123G	RPS10-NUDT3_ENST00000605528.1_Missense_Mutation_p.D123G|RPS10_ENST00000344700.3_Missense_Mutation_p.D123G|RPS10_ENST00000494077.1_5'UTR	NM_001014.4|NM_001203245.2|NM_001204091.1	NP_001005.1|NP_001190174.1|NP_001191020.1	P46783	RS10_HUMAN	ribosomal protein S10	123					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(4)	9						GGTATCTCTGTCAGCTTCCCC	0.507																																					p.D123G	Colon(121;749 1624 4895 8687 22360)	Atlas-SNP	.											.	RPS10	15	.	0			c.A368G						.						255	258	257					6																	34389539		2203	4300	6503	SO:0001583	missense	6204	exon4			TCTCTGTCAGCTT	U14972	CCDS4792.1	6p21.31	2011-04-05			ENSG00000124614	ENSG00000124614		"S ribosomal proteins"	10383	protein-coding gene	gene with protein product		603632				7772601, 9582194	Standard	NM_001014		Approved	MGC88819, S10		P46783	OTTHUMG00000014546	ENST00000326199.8:c.368A>G	chr6.hg19:g.34389539T>C	ENSP00000347271:p.Asp123Gly	104.0	0.0		113.0	34.0	NM_001203245	B2R4E3|Q5TZC0	Missense_Mutation	SNP	ENST00000326199.8	hg19	CCDS4792.1	.	.	.	.	.	.	.	.	.	.	T	17.83	3.484904	0.63962	.	.	ENSG00000124614	ENST00000326199;ENST00000344700	T;T	0.80480	-1.33;-1.38	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.70518	0.3233	L	0.61387	1.9	0.80722	D	1	B	0.12630	0.006	B	0.12837	0.008	T	0.71090	-0.4693	10	0.49607	T	0.09	-15.5093	15.5772	0.76400	0.0:0.0:0.0:1.0	.	123	P46783	RS10_HUMAN	G	123	ENSP00000347271:D123G;ENSP00000363169:D123G	ENSP00000347271:D123G	D	-	2	0	RPS10	34497517	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.817000	0.86213	2.141000	0.66446	0.482000	0.46254	GAC	.	.		0.507	RPS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040230.1			C	34389539	T	C	34389539	3	2	283	1	0	0	0	0	1	0	0	0	13635	1667	58	2	141	2	RPS10	6	34389539	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	1568104	34389539	136725528	89	41727										
PGM3	5238	hgsc.bcm.edu	37	chr6	83896734	83896734	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gataactacataccatggaaTtgacctcctagaacagtcac	6	11	1	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr6:83896734T>C	ENST00000283977.4	-	3	333	c.207A>G	c.(205-207)caA>caG	p.Q69Q	PGM3_ENST00000506587.1_Silent_p.Q178Q|PGM3_ENST00000512866.1_Silent_p.Q150Q|PGM3_ENST00000513973.1_Silent_p.Q150Q					phosphoglucomutase 3											NS(1)|breast(1)|endometrium(2)|large_intestine(4)|lung(6)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	18		all_cancers(76;0.000504)|Acute lymphoblastic leukemia(125;3.85e-06)|all_hematologic(105;0.0017)|all_epithelial(107;0.068)		BRCA - Breast invasive adenocarcinoma(397;0.0478)		TACCATGGAATTGACCTCCTA	0.299																																					p.Q178Q		Atlas-SNP	.											.	PGM3	39	.	0			c.A534G						.						76	71	73					6																	83896734		2203	4300	6503	SO:0001819	synonymous_variant	5238	exon5			ATGGAATTGACCT	BC001258	CCDS4997.1, CCDS56435.1, CCDS56436.1, CCDS75487.1	6q14.1-q15	2012-10-02			ENSG00000013375	ENSG00000013375	5.4.2.3		8907	protein-coding gene	gene with protein product	"acetylglucosamine phosphomutase"	172100				12174217, 10721701	Standard	NM_001199917		Approved	AGM1, DKFZP434B187, PAGM	uc011dyz.2	O95394	OTTHUMG00000015110	ENST00000283977.4:c.207A>G	chr6.hg19:g.83896734T>C		216.0	0.0		246.0	74.0	NM_001199917		Silent	SNP	ENST00000283977.4	hg19																																																																																				.	.		0.299	PGM3-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000366385.2	NM_015599		C	83896734	T	C	83896734	2	2	283	1	0	0	0	0	0	0	0	1	11809	1490	52	2		2	PGM3	6	83896734	Silent	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	49507195	83896734	87218333	90	41728										
GABRR1	2569	hgsc.bcm.edu	37	chr6	89899882	89899890	+	Splice_Site	DEL	TCACAGCTT	TCACAGCTT	-													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gcccggggacaagtctactcAcagctttcaatttcaagaga							TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	TCACAGCTT	TCACAGCTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr6:89899882_89899890delTCACAGCTT	ENST00000454853.2	-	6	759_766	c.649_656delAAGCTGTGA	c.(649-657)aagctgtga>a	p.KL*217del	GABRR1_ENST00000435811.1_Splice_Site_p.KL*200del|GABRR1_ENST00000369451.3_Splice_Site_p.KL*130del	NM_001256704.1|NM_002042.4	NP_001243633.1|NP_002033.2	P24046	GBRR1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, rho 1	217					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(7)|lung(16)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	35		all_cancers(76;9.49e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.46e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.00917)	Adinazolam(DB00546)|Bromazepam(DB01558)|Cinolazepam(DB01594)|Clotiazepam(DB01559)|Diazepam(DB00829)|Estazolam(DB01215)|Fludiazepam(DB01567)|Flurazepam(DB00690)|Halazepam(DB00801)|Midazolam(DB00683)|Nitrazepam(DB01595)|Oxazepam(DB00842)|Prazepam(DB01588)|Quazepam(DB01589)|Temazepam(DB00231)|Triazolam(DB00897)	AAGTCTACTCACAGCTTTCAATTTCAAGA	0.455																																					p.218_219del		Atlas-Indel,Pindel	.											.	GABRR1	63	.	0			c.652_655del						.																																			SO:0001630	splice_region_variant	2569	exon6			.		CCDS5019.2, CCDS59028.1, CCDS59029.1	6q15	2012-06-22	2012-02-03		ENSG00000146276	ENSG00000146276		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4090	protein-coding gene	gene with protein product	"GABA(A) receptor, rho 1"	137161	"gamma-aminobutyric acid (GABA) receptor, rho 1"			1849271, 1315307	Standard	NM_002042		Approved		uc003pna.2	P24046	OTTHUMG00000015195	ENST00000454853.2:c.655+1AAGCTGTGA>-	chr6.hg19:g.89899882_89899890delTCACAGCTT		143.0	0.0		97.0	19.0	NM_002042	A1L401|B4DJK8|B4DQT5|B7ZBQ7|Q9BX06	Frame_Shift_Del	DEL	ENST00000454853.2	hg19	CCDS5019.2																																																																																			.	.		0.455	GABRR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041479.2		In_Frame_Del	-	89899890	TCACAGCTT	-	89899882	8	5	283	1	0	1	0	1	0	0	1	0	6184	173	6	0	802	0	GABRR1	6	89899882	Splice_Site	DEL	TCACAGCTT	TCGA-G3-A3CK-01A-11D-A20W-10	6003148	89899882	81215185	91	41729										
RNF146	81847	hgsc.bcm.edu	37	chr6	127608258	127608258	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tggacgtcgcaggaagattaAgcgagatataatagatatac	11	5	0	3			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr6:127608258A>C	ENST00000368314.1	+	3	924	c.500A>C	c.(499-501)aAg>aCg	p.K167T	ECHDC1_ENST00000488087.1_5'Flank|RNF146_ENST00000356799.2_3'UTR|RNF146_ENST00000608991.1_Missense_Mutation_p.K166T|RNF146_ENST00000610153.1_Missense_Mutation_p.K167T|RNF146_ENST00000309649.3_Missense_Mutation_p.K166T	NM_001242850.1|NM_001242851.1	NP_001229779.1|NP_001229780.1	Q9NTX7	RN146_HUMAN	ring finger protein 146	167	WWE. {ECO:0000255|PROSITE- ProRule:PRU00248}.				positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein autoubiquitination (GO:0051865)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly-ADP-D-ribose binding (GO:0072572)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	10				GBM - Glioblastoma multiforme(226;0.0407)|all cancers(137;0.2)		AGGAAGATTAAGCGAGATATA	0.413																																					p.K167T		Atlas-SNP	.											.	RNF146	31	.	0			c.A500C						.						72	73	72					6																	127608258		2203	4300	6503	SO:0001583	missense	81847	exon3			AGATTAAGCGAGA	AK027558	CCDS5136.1, CCDS56449.1	6q22.1-q22.33	2008-02-05			ENSG00000118518	ENSG00000118518		"RING-type (C3HC4) zinc fingers"	21336	protein-coding gene	gene with protein product		612137					Standard	NM_001242844		Approved	DKFZp434O1427, dactylidin, dJ351K20.1	uc021zes.1	Q9NTX7	OTTHUMG00000015522	ENST00000368314.1:c.500A>C	chr6.hg19:g.127608258A>C	ENSP00000357297:p.Lys167Thr	77.0	0.0		90.0	23.0	NM_001242850	E1P572|Q6FIB2|Q7L8H4|Q96K03|Q96T06|Q9NTX6	Missense_Mutation	SNP	ENST00000368314.1	hg19	CCDS56449.1	.	.	.	.	.	.	.	.	.	.	A	19.92	3.915839	0.73098	.	.	ENSG00000118518	ENST00000368314;ENST00000356799;ENST00000309649	T;T;T	0.54071	0.59;0.59;0.59	5.8	5.8	0.92144	WWE domain (2);WWE domain, subgroup (1);	0.046631	0.85682	D	0.000000	T	0.66366	0.2782	M	0.73319	2.225	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.70317	-0.4905	10	0.62326	D	0.03	-17.7046	16.1639	0.81739	1.0:0.0:0.0:0.0	.	167	Q9NTX7	RN146_HUMAN	T	167;166;166	ENSP00000357297:K167T;ENSP00000349253:K166T;ENSP00000309365:K166T	ENSP00000309365:K166T	K	+	2	0	RNF146	127649951	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.039000	0.93777	2.219000	0.72066	0.533000	0.62120	AAG	.	.		0.413	RNF146-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042112.1	NM_030963		C	127608258	A	C	127608258	3	2	283	1	0	0	0	0	1	0	0	0	13463	72	3	5	499	5	RNF146	6	127608258	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	37708376	127608258	43506809	92	41730										
SAMD3	154075	hgsc.bcm.edu	37	chr6	130536349	130536349	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	aaacaactcaccttgaaatcTatgaactagctctcctaaat	3	11	3	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr6:130536349T>C	ENST00000368134.2	-	5	678	c.70A>G	c.(70-72)Aga>Gga	p.R24G	SAMD3_ENST00000324172.6_Missense_Mutation_p.R24G|SAMD3_ENST00000457563.2_Missense_Mutation_p.R48G|SAMD3_ENST00000439090.2_Missense_Mutation_p.R24G|SAMD3_ENST00000532763.1_Missense_Mutation_p.R24G|SAMD3_ENST00000437477.2_Missense_Mutation_p.R24G|SAMD3_ENST00000533296.1_5'UTR	NM_001258275.1	NP_001245204.1	Q8N6K7	SAMD3_HUMAN	sterile alpha motif domain containing 3	24	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.									breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(3)|lung(15)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	29				GBM - Glioblastoma multiforme(226;0.00594)|OV - Ovarian serous cystadenocarcinoma(155;0.128)		CCTTGAAATCTATGAACTAGC	0.393																																					p.R24G		Atlas-SNP	.											.	SAMD3	98	.	0			c.A70G						.						95	95	95					6																	130536349		2203	4300	6503	SO:0001583	missense	154075	exon3			GAAATCTATGAAC	AK091351	CCDS34539.1, CCDS64525.1	6q23.1	2013-01-10			ENSG00000164483	ENSG00000164483		"Sterile alpha motif (SAM) domain containing"	21574	protein-coding gene	gene with protein product							Standard	NM_001017373		Approved	bA73O6.2, FLJ34032	uc031spp.1	Q8N6K7	OTTHUMG00000015556	ENST00000368134.2:c.70A>G	chr6.hg19:g.130536349T>C	ENSP00000357116:p.Arg24Gly	100.0	0.0		127.0	40.0	NM_001017373	B4DY20|E1P576|J3KQK4|Q4VXD8|Q8NAY1|Q8NB96	Missense_Mutation	SNP	ENST00000368134.2	hg19	CCDS34539.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.092704	0.76756	.	.	ENSG00000164483	ENST00000368134;ENST00000457563;ENST00000439090;ENST00000437477;ENST00000532763;ENST00000324172;ENST00000532309;ENST00000531544;ENST00000529723	T;T;T;T;T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79;0.79;0.79;0.79;0.79	5.9	5.9	0.94986	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.074521	0.64402	D	0.000019	T	0.45216	0.1331	N	0.24115	0.695	0.40848	D	0.983723	D;D;D	0.71674	0.998;0.976;0.961	D;P;P	0.67900	0.954;0.724;0.819	T	0.54754	-0.8246	10	0.87932	D	0	.	14.9005	0.70675	0.0:0.0:0.0:1.0	.	48;24;24	B4DY20;Q8N6K7-2;Q8N6K7	.;.;SAMD3_HUMAN	G	24;48;24;24;24;24;24;24;24	ENSP00000357116:R24G;ENSP00000402092:R48G;ENSP00000403565:R24G;ENSP00000391163:R24G;ENSP00000436088:R24G;ENSP00000324874:R24G;ENSP00000436115:R24G;ENSP00000435875:R24G;ENSP00000434139:R24G	ENSP00000324874:R24G	R	-	1	2	SAMD3	130578042	1.000000	0.71417	0.945000	0.38365	0.887000	0.51463	5.172000	0.65003	2.259000	0.74868	0.523000	0.50628	AGA	.	.		0.393	SAMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042197.3	NM_152552		C	130536349	T	C	130536349	3	2	283	1	0	0	0	0	1	0	0	0	13835	1530	53	2	1548	2	SAMD3	6	130536349	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	2928091	130536349	40578718	93	41731										
MEOX2	4223	hgsc.bcm.edu	37	chr7	15725601	15725601	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gtagtcccccggcgcgcacgCggccccagtcggggtgctgg	17	16	0	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr7:15725601C>T	ENST00000262041.5	-	1	836	c.427G>A	c.(427-429)Gcg>Acg	p.A143T	AC005550.4_ENST00000442176.1_lincRNA	NM_005924.4	NP_005915.2	P50222	MEOX2_HUMAN	mesenchyme homeobox 2	143					angiogenesis (GO:0001525)|blood circulation (GO:0008015)|limb development (GO:0060173)|multicellular organismal development (GO:0007275)|neuron death (GO:0070997)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle tissue development (GO:0007519)|somite specification (GO:0001757)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding (GO:0043565)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (126;0.0822)		GGCGCGCACGCGGCCCCAGTC	0.706																																					p.A143T	Esophageal Squamous(140;197 1769 16409 18257 29929)	Atlas-SNP	.											.	MEOX2	68	.	0			c.G427A						.						25	30	28					7																	15725601		2188	4266	6454	SO:0001583	missense	4223	exon1			CGCACGCGGCCCC		CCDS34605.1	7p22.1-p21.3	2014-07-15	2005-12-22		ENSG00000106511	ENSG00000106511		"Homeoboxes / ANTP class : HOXL subclass"	7014	protein-coding gene	gene with protein product	"growth arrest-specific homeobox"	600535	"mesenchyme homeo box 2 (growth arrest-specific homeo box)", "mesenchyme homeobox 2 (growth arrest-specific homeo box)"	GAX		7713505	Standard	NM_005924		Approved	MOX2	uc003stc.3	P50222	OTTHUMG00000152390	ENST00000262041.5:c.427G>A	chr7.hg19:g.15725601C>T	ENSP00000262041:p.Ala143Thr	48.0	0.0		82.0	35.0	NM_005924	B2R8I7|O75263|Q9UPL6	Missense_Mutation	SNP	ENST00000262041.5	hg19	CCDS34605.1	.	.	.	.	.	.	.	.	.	.	C	10.58	1.389997	0.25118	.	.	ENSG00000106511	ENST00000262041	D	0.90133	-2.62	5.43	1.28	0.21552	.	0.062950	0.64402	D	0.000005	T	0.77791	0.4183	N	0.19112	0.55	0.42799	D	0.993923	B	0.21147	0.052	B	0.08055	0.003	T	0.62067	-0.6932	10	0.14252	T	0.57	-4.8243	5.6014	0.17355	0.2734:0.572:0.0:0.1547	.	143	P50222	MEOX2_HUMAN	T	143	ENSP00000262041:A143T	ENSP00000262041:A143T	A	-	1	0	MEOX2	15692126	0.679000	0.27596	0.994000	0.49952	0.975000	0.68041	0.966000	0.29331	0.237000	0.21200	-0.824000	0.03097	GCG	.	.		0.706	MEOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326058.2	NM_005924		T	15725601	C	T	15725601	3	4	283	1	0	0	0	0	1	0	0	0	9483	768	27	1	499	1	MEOX2	7	15725601	Missense_Mutation	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10		15725601	143413062	94	41732										
EEPD1	80820	hgsc.bcm.edu	37	chr7	36336620	36336620	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	aggagaaaaggatgtcattaTcttaggggattttggccaag	13	4	2	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr7:36336620T>C	ENST00000242108.4	+	7	2052	c.1334T>C	c.(1333-1335)aTc>aCc	p.I445T	EEPD1_ENST00000534978.1_Missense_Mutation_p.I445T	NM_030636.2	NP_085139.2	Q7L9B9	EEPD1_HUMAN	endonuclease/exonuclease/phosphatase family domain containing 1	445					DNA repair (GO:0006281)		DNA binding (GO:0003677)			endometrium(2)|large_intestine(3)|lung(10)|ovary(1)|pancreas(1)|skin(1)	18						GATGTCATTATCTTAGGGGAT	0.468																																					p.I445T		Atlas-SNP	.											.	EEPD1	47	.	0			c.T1334C						.						87	83	85					7																	36336620		2203	4300	6503	SO:0001583	missense	80820	exon7			TCATTATCTTAGG	AK027386	CCDS34619.1	7p14.2	2007-12-07	2007-12-07		ENSG00000122547	ENSG00000122547			22223	protein-coding gene	gene with protein product							Standard	NM_030636		Approved	KIAA1706	uc003tfa.3	Q7L9B9	OTTHUMG00000154904	ENST00000242108.4:c.1334T>C	chr7.hg19:g.36336620T>C	ENSP00000242108:p.Ile445Thr	91.0	0.0		110.0	42.0	NM_030636	Q96K64|Q9C0F7	Missense_Mutation	SNP	ENST00000242108.4	hg19	CCDS34619.1	.	.	.	.	.	.	.	.	.	.	T	14.37	2.516577	0.44763	.	.	ENSG00000122547	ENST00000242108;ENST00000534978	D;D	0.95885	-3.84;-3.84	5.1	5.1	0.69264	Endonuclease/exonuclease/phosphatase (2);	0.293466	0.37348	N	0.002140	D	0.92873	0.7733	L	0.36672	1.1	0.24291	N	0.995165	B	0.21905	0.062	B	0.27715	0.082	D	0.87220	0.2253	10	0.87932	D	0	-3.6303	15.6062	0.76672	0.0:0.0:0.0:1.0	.	445	Q7L9B9	EEPD1_HUMAN	T	445	ENSP00000242108:I445T;ENSP00000442692:I445T	ENSP00000242108:I445T	I	+	2	0	EEPD1	36303145	0.994000	0.37717	0.341000	0.25589	0.748000	0.42578	7.788000	0.85771	2.231000	0.72958	0.459000	0.35465	ATC	.	.		0.468	EEPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337602.1	NM_030636		C	36336620	T	C	36336620	3	2	283	1	0	0	0	0	1	0	0	0	4934	1435	50	2	1356	2	EEPD1	7	36336620	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	20611019	36336620	122802043	95	41733										
NPC1L1	29881	hgsc.bcm.edu	37	chr7	44579886	44579886	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ctgggttcttcccacattcgTcatagaaggcgcagtagcca	10	12	2	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr7:44579886T>C	ENST00000289547.4	-	2	165	c.110A>G	c.(109-111)gAc>gGc	p.D37G	NPC1L1_ENST00000423141.1_Missense_Mutation_p.D37G|NPC1L1_ENST00000381160.3_Missense_Mutation_p.D37G|NPC1L1_ENST00000546276.1_Missense_Mutation_p.D37G	NM_013389.2	NP_037521.2	Q9UHC9	NPCL1_HUMAN	NPC1-like 1	37					cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intestinal cholesterol absorption (GO:0030299)|lipoprotein metabolic process (GO:0042157)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)	brush border membrane (GO:0031526)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|hedgehog receptor activity (GO:0008158)|myosin V binding (GO:0031489)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(7)|lung(27)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	57					Ezetimibe(DB00973)	CCCACATTCGTCATAGAAGGC	0.592																																					p.D37G		Atlas-SNP	.											.	NPC1L1	141	.	0			c.A110G						.						83	78	80					7																	44579886		2203	4300	6503	SO:0001583	missense	29881	exon2			CATTCGTCATAGA		CCDS5491.1, CCDS43575.1, CCDS75587.1	7p13	2012-11-15	2012-11-15		ENSG00000015520	ENSG00000015520			7898	protein-coding gene	gene with protein product		608010	"NPC1 (Niemann-Pick disease, type C1, gene)-like 1"			10783261	Standard	NM_013389		Approved		uc003tlb.3	Q9UHC9	OTTHUMG00000023691	ENST00000289547.4:c.110A>G	chr7.hg19:g.44579886T>C	ENSP00000289547:p.Asp37Gly	79.0	0.0		77.0	27.0	NM_001101648	A4D2J7|B7ZLE6|D3DVK9|Q17RV5|Q6R3Q4|Q9UHC8	Missense_Mutation	SNP	ENST00000289547.4	hg19	CCDS5491.1	.	.	.	.	.	.	.	.	.	.	t	0.118	-1.129137	0.01756	.	.	ENSG00000015520	ENST00000289547;ENST00000381160;ENST00000546276;ENST00000423141	T;T;T;T	0.77229	-1.08;-1.08;-1.08;-1.08	5.17	4.01	0.46588	.	0.467062	0.20698	N	0.087336	T	0.68769	0.3037	N	0.16656	0.425	0.36115	D	0.845046	B;P;B;B	0.40197	0.001;0.706;0.0;0.002	B;P;B;B	0.53360	0.003;0.724;0.007;0.005	T	0.66575	-0.5889	10	0.02654	T	1	-10.1182	8.9584	0.35832	0.0:0.0896:0.0:0.9104	.	37;37;37;37	B7ZLE6;Q9UHC9-3;Q17RV5;D3DVK9	.;.;.;.	G	37	ENSP00000289547:D37G;ENSP00000370552:D37G;ENSP00000438033:D37G;ENSP00000404670:D37G	ENSP00000289547:D37G	D	-	2	0	NPC1L1	44546411	0.960000	0.32886	0.055000	0.19348	0.465000	0.32709	2.637000	0.46553	0.810000	0.34279	0.459000	0.35465	GAC	.	.		0.592	NPC1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251256.1	NM_013389		C	44579886	T	C	44579886	3	2	283	1	0	0	0	0	1	0	0	0	10580	1667	58	2	4045	2	NPC1L1	7	44579886	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	8243266	44579886	114558777	96	41734										
IGFBP3	3486	hgsc.bcm.edu	37	chr7	45956856	45956856	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ggaggagaagttctgggtatCtgtgctctgagactcgtagt	15	6	3	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr7:45956856C>T	ENST00000275521.6	-	2	719	c.586G>A	c.(586-588)Gat>Aat	p.D196N	IGFBP3_ENST00000381083.4_Missense_Mutation_p.D202N|IGFBP3_ENST00000465642.1_5'UTR|IGFBP3_ENST00000381086.5_Missense_Mutation_p.D99N	NM_000598.4|NM_001013398.1	NP_000589.2|NP_001013416.1	P17936	IBP3_HUMAN	insulin-like growth factor binding protein 3	196	Ser/Thr-rich.				apoptotic process (GO:0006915)|cellular protein metabolic process (GO:0044267)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of signal transduction (GO:0009968)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell proliferation (GO:0048662)|osteoblast differentiation (GO:0001649)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of myoblast differentiation (GO:0045663)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of glucose metabolic process (GO:0010906)|type B pancreatic cell proliferation (GO:0044342)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|insulin-like growth factor binding protein complex (GO:0016942)|nucleus (GO:0005634)	insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|metal ion binding (GO:0046872)|protein tyrosine phosphatase activator activity (GO:0008160)			large_intestine(6)|lung(7)|pancreas(1)|prostate(3)	17					Mecasermin(DB01277)	TTCTGGGTATCTGTGCTCTGA	0.498											OREG0018049	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D202N		Atlas-SNP	.											.	IGFBP3	40	.	0			c.G604A						.						177	160	165					7																	45956856		2203	4300	6503	SO:0001583	missense	3486	exon2			GGGTATCTGTGCT		CCDS5505.1, CCDS34632.1	7p12.3	2014-09-17			ENSG00000146674	ENSG00000146674			5472	protein-coding gene	gene with protein product	"growth hormone-dependent binding protein", "acid stable subunit of the 140 K IGF complex", "binding protein 53", "binding protein 29", "IGF-binding protein 3"	146732				1695633	Standard	NM_000598		Approved	IBP3, BP-53	uc003tnr.3	P17936	OTTHUMG00000023769	ENST00000275521.6:c.586G>A	chr7.hg19:g.45956856C>T	ENSP00000275521:p.Asp196Asn	191.0	0.0	935	169.0	60.0	NM_001013398	A4D2F5|D3DVM0|Q2V509|Q6P1M6|Q9UCL4	Missense_Mutation	SNP	ENST00000275521.6	hg19	CCDS5505.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	33|33	5.269690|5.269690	0.95429|0.95429	.|.	.|.	ENSG00000146674|ENSG00000146674	ENST00000545032;ENST00000275521;ENST00000381086;ENST00000438491;ENST00000442142;ENST00000381083;ENST00000433047;ENST00000448817|ENST00000417621	T;T;T;T|.	0.26518|.	2.39;1.73;2.39;1.83|.	5.29|5.29	5.29|5.29	0.74685|0.74685	Thyroglobulin type-1 (1);|.	0.000000|.	0.85682|.	U|.	0.000000|.	T|T	0.78253|0.78253	0.4254|0.4254	M|M	0.84846|0.84846	2.72|2.72	0.48975|0.48975	D|D	0.999735|0.999735	P;D;P|.	0.67145|.	0.879;0.996;0.879|.	P;D;P|.	0.67900|.	0.496;0.954;0.566|.	T|T	0.80525|0.80525	-0.1344|-0.1344	10|5	0.37606|.	T|.	0.19|.	-53.1404|-53.1404	14.4394|14.4394	0.67306|0.67306	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	99;196;181|.	B3KWK7;P17936;B4DN53|.	.;IBP3_HUMAN;.|.	N|K	173;196;99;182;94;202;168;86|57	ENSP00000275521:D196N;ENSP00000370476:D99N;ENSP00000370473:D202N;ENSP00000389668:D86N|.	ENSP00000275521:D196N|.	D|R	-|-	1|2	0|0	IGFBP3|IGFBP3	45923381|45923381	0.994000|0.994000	0.37717|0.37717	0.978000|0.978000	0.43139|0.43139	0.995000|0.995000	0.86356|0.86356	2.960000|2.960000	0.49161|0.49161	2.463000|2.463000	0.83235|0.83235	0.655000|0.655000	0.94253|0.94253	GAT|AGA	.	.		0.498	IGFBP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251356.3	NM_001013398		T	45956856	C	T	45956856	3	4	283	1	0	0	0	0	1	0	0	0	7589	913	32	3	301	3	IGFBP3	7	45956856	Missense_Mutation	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	1376970	45956856	113181807	97	41735										
GUSB	2990	hgsc.bcm.edu	37	chr7	65425954	65425954	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gatacctggtttcattggcaAtcttccagtatctctctcgc	7	12	4	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr7:65425954A>T	ENST00000304895.4	-	12	2016	c.1886T>A	c.(1885-1887)aTt>aAt	p.I629N	GUSB_ENST00000345660.6_Missense_Mutation_p.I578N|GUSB_ENST00000421103.1_Missense_Mutation_p.I483N	NM_000181.3	NP_000172.2	P08236	BGLR_HUMAN	glucuronidase, beta	629					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-glucuronidase activity (GO:0004566)			breast(1)|cervix(2)|kidney(2)|large_intestine(4)|lung(10)|skin(1)	20						TTCATTGGCAATCTTCCAGTA	0.488																																					p.I629N		Atlas-SNP	.											.	GUSB	52	.	0			c.T1886A						.						259	234	243					7																	65425954		2203	4300	6503	SO:0001583	missense	2990	exon12			TTGGCAATCTTCC	M15182	CCDS5530.1, CCDS64665.1	7q11.21	2012-10-02			ENSG00000169919	ENSG00000169919	3.2.1.31		4696	protein-coding gene	gene with protein product		611499				3468507	Standard	NM_000181		Approved		uc003tun.3	P08236	OTTHUMG00000023735	ENST00000304895.4:c.1886T>A	chr7.hg19:g.65425954A>T	ENSP00000302728:p.Ile629Asn	308.0	0.0		276.0	85.0	NM_000181	B4E1F6|E9PCV0|Q549U0|Q96CL9	Missense_Mutation	SNP	ENST00000304895.4	hg19	CCDS5530.1	.	.	.	.	.	.	.	.	.	.	A	19.92	3.915919	0.73098	.	.	ENSG00000169919	ENST00000304895;ENST00000421103;ENST00000345660	D;D;D	0.95788	-3.81;-3.81;-3.81	5.87	5.87	0.94306	Glycoside hydrolase, superfamily (1);Glycoside hydrolase, family 2, TIM barrel (1);	0.328915	0.32640	N	0.005835	D	0.97309	0.9120	M	0.71871	2.18	0.45962	D	0.998785	D;D	0.76494	0.999;0.997	D;D	0.77004	0.989;0.971	D	0.97929	1.0319	10	0.87932	D	0	.	15.4554	0.75308	1.0:0.0:0.0:0.0	.	483;629	E9PCV0;P08236	.;BGLR_HUMAN	N	629;483;578	ENSP00000302728:I629N;ENSP00000391390:I483N;ENSP00000340734:I578N	ENSP00000302728:I629N	I	-	2	0	GUSB	65063389	1.000000	0.71417	0.267000	0.24556	0.685000	0.39939	9.326000	0.96389	2.253000	0.74438	0.533000	0.62120	ATT	.	.		0.488	GUSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251637.3	NM_000181		T	65425954	A	T	65425954	3	4	283	1	0	0	0	0	1	0	0	0	6911	101	4	4	73	4	GUSB	7	65425954	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	19469098	65425954	93712709	98	41736										
WBSCR22	114049	hgsc.bcm.edu	37	chr7	73105342	73105342	+	Splice_Site	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gcttctcttttttctgttctCgtgagtataagatcttctcc	6	10	5	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr7:73105342C>A	ENST00000265758.2	+	6	517	c.459C>A	c.(457-459)ctC>ctA	p.L153L	WBSCR22_ENST00000423497.1_Splice_Site_p.L153L|WBSCR22_ENST00000423166.2_Intron	NM_017528.4	NP_059998.2	O43709	WBS22_HUMAN	Williams Beuren syndrome chromosome region 22	153					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|rRNA processing (GO:0006364)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|large_intestine(2)|lung(9)|prostate(1)	13		Lung NSC(55;0.0908)|all_lung(88;0.198)				TTTCTGTTCTCGTGAGTATAA	0.473																																					p.L153L		Atlas-SNP	.											.	WBSCR22	27	.	0			c.C459A						.						238	225	230					7																	73105342		2203	4300	6503	SO:0001630	splice_region_variant	114049	exon6			TGTTCTCGTGAGT	AF420248	CCDS5557.1, CCDS56490.1	7q11.23	2012-06-12			ENSG00000071462	ENSG00000071462			16405	protein-coding gene	gene with protein product	"metastasis-related methyltransferase 1"	615733				12073013, 11978965, 21148752	Standard	NM_001202560		Approved	MGC19709, MGC2022, MGC5140, PP3381, WBMT, MERM1	uc003tyt.3	O43709	OTTHUMG00000023306	ENST00000265758.2:c.459+1C>A	chr7.hg19:g.73105342C>A		361.0	0.0		329.0	117.0	NM_001202560	A8K501|C9K060|Q96P12|Q9BQ58|Q9HBP9	Silent	SNP	ENST00000265758.2	hg19	CCDS5557.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.802309	0.90538	.	.	ENSG00000071462	ENST00000442099	.	.	.	5.37	-1.11	0.09840	.	.	.	.	.	T	0.55178	0.1904	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46803	-0.9165	4	.	.	.	-20.6338	9.4661	0.38813	0.0:0.2736:0.4255:0.3009	.	.	.	.	S	33	.	.	R	+	1	0	WBSCR22	72743278	1.000000	0.71417	0.912000	0.35992	0.793000	0.44817	1.556000	0.36288	-0.600000	0.05790	-0.657000	0.03884	CGT	.	.		0.473	WBSCR22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252303.1		Silent	A	73105342	C	A	73105342	5	1	283	1	0	0	0	0	0	0	1	0	17280	898	31	1	481	1	WBSCR22	7	73105342	Splice_Site	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	7679388	73105342	86033321	99	41737										
UPK3B	80761	hgsc.bcm.edu	37	chr7	76141019	76141019	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gacactggctgacattccggCctccccacagctgctgaccg	10	17	0	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr7:76141019C>T	ENST00000257632.5	+	2	574	c.446C>T	c.(445-447)gCc>gTc	p.A149V	UPK3B_ENST00000419923.2_Missense_Mutation_p.A149V|UPK3B_ENST00000443097.2_Missense_Mutation_p.A94V|UPK3B_ENST00000448265.3_Missense_Mutation_p.A149V|UPK3B_ENST00000394849.1_Missense_Mutation_p.A94V|UPK3B_ENST00000334348.3_Missense_Mutation_p.A94V			Q9BT76	UPK3B_HUMAN	uroplakin 3B	149					negative regulation of gene expression (GO:0010629)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(1)|lung(1)|skin(2)	8		Myeloproliferative disorder(862;0.204)				GACATTCCGGCCTCCCCACAG	0.657																																					p.A149V		Atlas-SNP	.											.	UPK3B	15	.	0			c.C446T						.						16	15	16					7																	76141019		2199	4292	6491	SO:0001583	missense	80761	exon2			TTCCGGCCTCCCC	BC004304	CCDS5588.1, CCDS5589.1, CCDS64693.1	7q11.2	2003-07-29			ENSG00000243566	ENSG00000243566			21444	protein-coding gene	gene with protein product	"uroplakin IIIb"	611887				12446744	Standard	XM_005250612		Approved	MGC10902, p35, UPIIIb, FLJ32198	uc003ufq.3	Q9BT76	OTTHUMG00000149929	ENST00000257632.5:c.446C>T	chr7.hg19:g.76141019C>T	ENSP00000257632:p.Ala149Val	415.0	0.0		416.0	109.0	NM_030570	A6NHH5|A8K231|A8MZA8|B3KPU5|Q75MM5|Q86W06	Missense_Mutation	SNP	ENST00000257632.5	hg19	CCDS5588.1	.	.	.	.	.	.	.	.	.	.	.	11.50	1.655888	0.29425	.	.	ENSG00000243566	ENST00000334348;ENST00000419923;ENST00000448265;ENST00000443097;ENST00000257632;ENST00000394849	T;T;T;T;T;T	0.55930	0.49;1.42;1.42;0.49;1.42;1.43	5.08	5.08	0.68730	.	0.528723	0.18103	N	0.151631	T	0.41003	0.1140	N	0.14661	0.345	0.20307	N	0.999912	P;P;P	0.49253	0.921;0.867;0.525	P;B;B	0.45913	0.497;0.295;0.165	T	0.25433	-1.0132	9	.	.	.	-13.7506	13.9688	0.64225	0.0:1.0:0.0:0.0	.	94;149;94	Q9BT76-2;Q9BT76;A6NHH5	.;UPK3B_HUMAN;.	V	94;149;149;94;149;94	ENSP00000334938:A94V;ENSP00000441602:A149V;ENSP00000441284:A149V;ENSP00000444585:A94V;ENSP00000257632:A149V;ENSP00000378319:A94V	.	A	+	2	0	UPK3B	75978955	0.000000	0.05858	0.151000	0.22473	0.045000	0.14185	0.370000	0.20433	2.362000	0.80069	0.467000	0.42956	GCC	.	.		0.657	UPK3B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000313978.2	NM_030570		T	76141019	C	T	76141019	3	4	283	1	0	0	0	0	1	0	0	0	17026	739	26	3	452	3	UPK3B	7	76141019	Missense_Mutation	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	3035677	76141019	82997644	100	41738										
MAGI2	9863	hgsc.bcm.edu	37	chr7	78130892	78130893	+	Splice_Site	INS	-	-	CT													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	aaagaaatgtgtgaaactcaINSctcaatgaagtagacttcgc							TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr7:78130892_78130893insCT	ENST00000354212.4	-	5	1219		c.e5+1		MAGI2_ENST00000535697.1_Splice_Site|MAGI2_ENST00000536571.1_Splice_Site|MAGI2_ENST00000522391.1_Splice_Site|MAGI2_ENST00000419488.1_Splice_Site	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2						cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|glomerular visceral epithelial cell development (GO:0072015)|mitotic cell cycle arrest (GO:0071850)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase B signaling (GO:0051898)|nerve growth factor signaling pathway (GO:0038180)|planar cell polarity pathway involved in axis elongation (GO:0003402)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of receptor internalization (GO:0002092)|protein heterooligomerization (GO:0051291)|receptor clustering (GO:0043113)|SMAD protein signal transduction (GO:0060395)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|late endosome (GO:0005770)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)|synapse (GO:0045202)|tight junction (GO:0005923)	beta-1 adrenergic receptor binding (GO:0031697)|phosphatase binding (GO:0019902)|receptor signaling complex scaffold activity (GO:0030159)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|type II activin receptor binding (GO:0070699)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(37)|ovary(5)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(3)	84		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				TGTGAAACTCACTCAATGAAGT	0.386																																					.		Atlas-Indel,Pindel	.											.	MAGI2	246	.	0			c.965+2->AG						.																																			SO:0001630	splice_region_variant	9863	exon6			.	AB014605	CCDS5594.1, CCDS75623.1	7q21	2005-08-09			ENSG00000187391	ENSG00000187391			18957	protein-coding gene	gene with protein product		606382				10681527, 9734811	Standard	XM_005250725		Approved	AIP1, ARIP1, KIAA0705, ACVRIP1, MAGI-2	uc003ugx.3	Q86UL8	OTTHUMG00000130697	ENST00000354212.4:c.965+1->AG	chr7.hg19:g.78130893_78130894dupCT		160.0	0.0		139.0	44.0	NM_012301	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Splice_Site	INS	ENST00000354212.4	hg19	CCDS5594.1																																																																																			.	.		0.386	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301	Intron	CT	78130893	-	CT	78130892	8	5	283	1	0	1	1	0	0	0	1	0	9200	173	6	0	3472	0	MAGI2	7	78130892	Splice_Site	INS	-	TCGA-G3-A3CK-01A-11D-A20W-10	1989873	78130892	81007771	101	41739										
MAGI2	9863	hgsc.bcm.edu	37	chr7	78130909	78130909	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ctcactcaatgaagtagactTcgcccttctctgtataggcc	7	13	3	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr7:78130909T>G	ENST00000354212.4	-	5	1203	c.950A>C	c.(949-951)gAa>gCa	p.E317A	MAGI2_ENST00000535697.1_Missense_Mutation_p.E154A|MAGI2_ENST00000536571.1_Missense_Mutation_p.E149A|MAGI2_ENST00000522391.1_Missense_Mutation_p.E317A|MAGI2_ENST00000419488.1_Missense_Mutation_p.E317A	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	317	Interaction with DDN.|WW 1. {ECO:0000255|PROSITE- ProRule:PRU00224}.				cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|glomerular visceral epithelial cell development (GO:0072015)|mitotic cell cycle arrest (GO:0071850)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase B signaling (GO:0051898)|nerve growth factor signaling pathway (GO:0038180)|planar cell polarity pathway involved in axis elongation (GO:0003402)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of receptor internalization (GO:0002092)|protein heterooligomerization (GO:0051291)|receptor clustering (GO:0043113)|SMAD protein signal transduction (GO:0060395)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|late endosome (GO:0005770)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)|synapse (GO:0045202)|tight junction (GO:0005923)	beta-1 adrenergic receptor binding (GO:0031697)|phosphatase binding (GO:0019902)|receptor signaling complex scaffold activity (GO:0030159)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|type II activin receptor binding (GO:0070699)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(37)|ovary(5)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(3)	84		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				GAAGTAGACTTCGCCCTTCTC	0.418																																					p.E317A		Atlas-SNP	.											.	MAGI2	246	.	0			c.A950C						.						233	196	208					7																	78130909		2203	4300	6503	SO:0001583	missense	9863	exon5			TAGACTTCGCCCT	AB014605	CCDS5594.1, CCDS75623.1	7q21	2005-08-09			ENSG00000187391	ENSG00000187391			18957	protein-coding gene	gene with protein product		606382				10681527, 9734811	Standard	XM_005250725		Approved	AIP1, ARIP1, KIAA0705, ACVRIP1, MAGI-2	uc003ugx.3	Q86UL8	OTTHUMG00000130697	ENST00000354212.4:c.950A>C	chr7.hg19:g.78130909T>G	ENSP00000346151:p.Glu317Ala	190.0	0.0		171.0	61.0	NM_012301	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Missense_Mutation	SNP	ENST00000354212.4	hg19	CCDS5594.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.556539	0.86231	.	.	ENSG00000187391	ENST00000419488;ENST00000354212;ENST00000536298;ENST00000522391;ENST00000536571;ENST00000535697	D;D;D;D;D	0.82344	-1.6;-1.6;-1.6;-1.6;-1.6	5.96	5.96	0.96718	WW/Rsp5/WWP (5);	0.000000	0.37483	U	0.002063	D	0.89663	0.6780	M	0.64080	1.96	0.80722	D	1	P;D;P;D	0.76494	0.845;0.967;0.917;0.999	P;P;P;D	0.81914	0.712;0.852;0.774;0.995	D	0.90113	0.4193	10	0.59425	D	0.04	.	15.6296	0.76893	0.0:0.0:0.0:1.0	.	154;149;317;317	F5GWH1;F5GWK7;Q86UL8-2;Q86UL8	.;.;.;MAGI2_HUMAN	A	317;317;317;317;149;154	ENSP00000405766:E317A;ENSP00000346151:E317A;ENSP00000428389:E317A;ENSP00000441584:E149A;ENSP00000441603:E154A	ENSP00000346151:E317A	E	-	2	0	MAGI2	77968845	1.000000	0.71417	0.998000	0.56505	0.981000	0.71138	7.698000	0.84413	2.285000	0.76669	0.533000	0.62120	GAA	.	.		0.418	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301		G	78130909	T	G	78130909	3	3	283	1	0	0	0	0	1	0	0	0	9200	1783	62	5	3489	5	MAGI2	7	78130909	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	17	78130909	81007754	102	41740										
ABCB1	5243	hgsc.bcm.edu	37	chr7	87148681	87148681	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tcatgagtttatgtgccaccAagtaggctccaaaccggaaa	9	10	1	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr7:87148681A>C	ENST00000265724.3	-	24	3305	c.2888T>G	c.(2887-2889)tTg>tGg	p.L963W	ABCB1_ENST00000488737.2_5'UTR|ABCB1_ENST00000543898.1_Missense_Mutation_p.L899W	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	963	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				drug transmembrane transport (GO:0006855)|G2/M transition of mitotic cell cycle (GO:0000086)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|stem cell proliferation (GO:0072089)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(14)|kidney(9)|large_intestine(14)|lung(48)|ovary(4)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	111	Esophageal squamous(14;0.00164)				Acebutolol(DB01193)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Adenosine triphosphate(DB00171)|ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Albendazole(DB00518)|Alfentanil(DB00802)|Alitretinoin(DB00523)|Amantadine(DB00915)|Aminohippurate(DB00345)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Amsacrine(DB00276)|Apixaban(DB06605)|Arsenic trioxide(DB01169)|Astemizole(DB00637)|Atazanavir(DB01072)|Atenolol(DB00335)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzocaine(DB01086)|Bepridil(DB01244)|Betamethasone(DB00443)|Biperiden(DB00810)|Boceprevir(DB08873)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Bromocriptine(DB01200)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Canagliflozin(DB08907)|Candesartan(DB00796)|Captopril(DB01197)|Carbamazepine(DB00564)|Carfilzomib(DB08889)|Carvedilol(DB01136)|Caspofungin(DB00520)|Chloroquine(DB00608)|Chlorpromazine(DB00477)|Chlorpropamide(DB00672)|Chlorprothixene(DB01239)|Cilazapril(DB01340)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisplatin(DB00515)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Clofazimine(DB00845)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabigatran etexilate(DB06695)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dipyridamole(DB00975)|Docetaxel(DB01248)|Domperidone(DB01184)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Dronedarone(DB04855)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Etravirine(DB06414)|Ezetimibe(DB00973)|Felodipine(DB01023)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fidaxomicin(DB08874)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluticasone furoate(DB08906)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gemcitabine(DB00441)|Glyburide(DB01016)|Gramicidin D(DB00027)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Imatinib(DB00619)|Imipramine(DB00458)|Indacaterol(DB05039)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketoconazole(DB01026)|Lamivudine(DB00709)|Lamotrigine(DB00555)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lenalidomide(DB00480)|Levetiracetam(DB01202)|Levofloxacin(DB01137)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Liothyronine(DB00279)|Liotrix(DB01583)|Lisinopril(DB00722)|Lomitapide(DB08827)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Mannitol(DB00742)|Maprotiline(DB00934)|Mebendazole(DB00643)|Mefloquine(DB00358)|Megestrol acetate(DB00351)|Meprobamate(DB00371)|Methadone(DB00333)|Methotrexate(DB00563)|Methylprednisolone(DB00959)|Metoprolol(DB00264)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mitomycin(DB00305)|Mitoxantrone(DB01204)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nadolol(DB01203)|Naloxone(DB01183)|Naltrexone(DB00704)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Neostigmine(DB01400)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nizatidine(DB00585)|Norethindrone(DB00717)|Olanzapine(DB00334)|Omeprazole(DB00338)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paroxetine(DB00715)|Pazopanib(DB06589)|Perindopril(DB00790)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Pitavastatin(DB08860)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pravastatin(DB00175)|Prazosin(DB00457)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Progesterone(DB00396)|Promethazine(DB01069)|Propafenone(DB01182)|Propranolol(DB00571)|Protriptyline(DB00344)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reboxetine(DB00234)|Regorafenib(DB08896)|Reserpine(DB00206)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Roxithromycin(DB00778)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Scopolamine(DB00747)|Selegiline(DB01037)|Sertraline(DB01104)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|SOFOSBUVIR(DB08934)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Streptozocin(DB00428)|Sulfinpyrazone(DB01138)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telaprevir(DB05521)|Telmisartan(DB00966)|Temsirolimus(DB06287)|Terazosin(DB01162)|Testosterone(DB00624)|Ticagrelor(DB08816)|Timolol(DB00373)|Tolvaptan(DB06212)|Topotecan(DB01030)|Toremifene(DB00539)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Vecuronium(DB01339)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voacamine(DB04877)|Zidovudine(DB00495)	ATGTGCCACCAAGTAGGCTCC	0.388																																					p.L963W		Atlas-SNP	.											.	ABCB1	263	.	0			c.T2888G						.						97	88	91					7																	87148681		2203	4300	6503	SO:0001583	missense	5243	exon24			GCCACCAAGTAGG	M14758	CCDS5608.1	7q21.12	2012-03-14	2004-05-12		ENSG00000085563	ENSG00000085563		"CD molecules", "ATP binding cassette transporters / subfamily B"	40	protein-coding gene	gene with protein product	"multidrug resistance protein 1"	171050	"colchicin sensitivity"	PGY1, MDR1, CLCS		3027054	Standard	NM_000927		Approved	P-gp, CD243, GP170, ABC20	uc003uiz.2	P08183	OTTHUMG00000023393	ENST00000265724.3:c.2888T>G	chr7.hg19:g.87148681A>C	ENSP00000265724:p.Leu963Trp	95.0	0.0		122.0	13.0	NM_000927	A8K294|B5AK60|Q12755|Q14812	Missense_Mutation	SNP	ENST00000265724.3	hg19	CCDS5608.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.225297	0.79576	.	.	ENSG00000085563	ENST00000543174;ENST00000265724;ENST00000543898	D;D	0.94000	-3.33;-3.33	5.79	4.61	0.57282	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.064892	0.64402	D	0.000008	D	0.97396	0.9148	H	0.94847	3.59	0.54753	D	0.999981	D;D	0.89917	0.999;1.0	D;D	0.91635	0.979;0.999	D	0.97515	1.0069	10	0.87932	D	0	-15.5609	12.1771	0.54192	0.8719:0.0:0.0:0.1281	.	899;963	B5AK60;P08183	.;MDR1_HUMAN	W	744;963;899	ENSP00000265724:L963W;ENSP00000444095:L899W	ENSP00000265724:L963W	L	-	2	0	ABCB1	86986617	0.998000	0.40836	1.000000	0.80357	0.938000	0.57974	9.146000	0.94640	0.971000	0.38288	0.459000	0.35465	TTG	.	.		0.388	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2	NM_000927		C	87148681	A	C	87148681	3	2	283	1	0	0	0	0	1	0	0	0	40	131	5	5	978	5	ABCB1	7	87148681	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	9017772	87148681	71989982	103	41741										
DLX5	1749	hgsc.bcm.edu	37	chr7	96651649	96651649	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tttctttggtttgccattcaCcattctcacctcgggctcgg	8	13	3	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr7:96651649C>T	ENST00000222598.4	-	2	861	c.388G>A	c.(388-390)Gtg>Atg	p.V130M	DLX5_ENST00000486603.2_Missense_Mutation_p.V130M|DLX5_ENST00000493764.1_Intron	NM_005221.5	NP_005212.1	P56178	DLX5_HUMAN	distal-less homeobox 5	130					anatomical structure formation involved in morphogenesis (GO:0048646)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|cell proliferation (GO:0008283)|cellular response to BMP stimulus (GO:0071773)|embryonic limb morphogenesis (GO:0030326)|endochondral ossification (GO:0001958)|epithelial cell differentiation (GO:0030855)|face morphogenesis (GO:0060325)|inner ear morphogenesis (GO:0042472)|nervous system development (GO:0007399)|olfactory pit development (GO:0060166)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription regulatory region DNA binding (GO:0044212)	p.M129_V130>IL(1)		central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)	20	all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858)					TTGCCATTCACCATTCTCACC	0.463																																					p.V130M		Atlas-SNP	.											.,1	DLX5	52	.	1	Complex - compound substitution(1)	lung(1)	c.G388A						.						130	126	127					7																	96651649		2203	4300	6503	SO:0001583	missense	1749	exon2			CATTCACCATTCT		CCDS5647.1	7q21.3	2011-06-20	2005-12-22		ENSG00000105880	ENSG00000105880		"Homeoboxes / ANTP class : NKL subclass"	2918	protein-coding gene	gene with protein product		600028	"distal-less homeo box 5"			7907794	Standard	XM_005250185		Approved		uc003uon.3	P56178	OTTHUMG00000154200	ENST00000222598.4:c.388G>A	chr7.hg19:g.96651649C>T	ENSP00000222598:p.Val130Met	79.0	0.0		67.0	33.0	NM_005221	B7Z4P3|Q9UPL1	Missense_Mutation	SNP	ENST00000222598.4	hg19	CCDS5647.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.984691	0.93044	.	.	ENSG00000105880	ENST00000222598	D	0.89875	-2.58	5.28	5.28	0.74379	Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.93321	0.7871	M	0.66439	2.03	0.80722	D	1	D;P	0.64830	0.994;0.834	D;P	0.62955	0.909;0.701	D	0.93410	0.6768	10	0.62326	D	0.03	-11.1905	18.7072	0.91643	0.0:1.0:0.0:0.0	.	130;130	B7Z4P3;P56178	.;DLX5_HUMAN	M	130	ENSP00000222598:V130M	ENSP00000222598:V130M	V	-	1	0	DLX5	96489585	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.582000	0.82546	2.752000	0.94435	0.467000	0.42956	GTG	.	.		0.463	DLX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334371.2			T	96651649	C	T	96651649	3	4	283	1	0	0	0	0	1	0	0	0	4576	507	18	3	489	3	DLX5	7	96651649	Missense_Mutation	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	9502968	96651649	62487014	104	41742										
CAPZA2	830	hgsc.bcm.edu	37	chr7	116544394	116544394	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	aacttcagtagaaactgctcTgagagcttacgtaaaagaac	8	8	2	3			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr7:116544394T>A	ENST00000361183.3	+	5	522	c.383T>A	c.(382-384)cTg>cAg	p.L128Q	CAPZA2_ENST00000458284.2_Missense_Mutation_p.L128Q|CAPZA2_ENST00000490693.1_Missense_Mutation_p.L128Q	NM_006136.2	NP_006127.1	P47755	CAZA2_HUMAN	capping protein (actin filament) muscle Z-line, alpha 2	128					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)	actin cytoskeleton (GO:0015629)|cortical cytoskeleton (GO:0030863)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|F-actin capping protein complex (GO:0008290)|membrane (GO:0016020)|WASH complex (GO:0071203)				endometrium(2)|kidney(3)|large_intestine(4)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	13	all_cancers(3;8.53e-08)|all_epithelial(6;7.79e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)		GBM - Glioblastoma multiforme(2;5.01e-06)|STAD - Stomach adenocarcinoma(10;0.000512)|all cancers(2;0.00326)			GAAACTGCTCTGAGAGCTTAC	0.403																																					p.L128Q		Atlas-SNP	.											.	CAPZA2	29	.	0			c.T383A						.						115	103	107					7																	116544394		2203	4300	6503	SO:0001583	missense	830	exon5			CTGCTCTGAGAGC		CCDS5768.1	7q31.2-q31.3	2008-07-18			ENSG00000198898	ENSG00000198898			1490	protein-coding gene	gene with protein product	"F-actin capping protein alpha-2 subunit"	601571					Standard	NM_006136		Approved	CAPZ, CAPPA2	uc003vil.3	P47755	OTTHUMG00000023185	ENST00000361183.3:c.383T>A	chr7.hg19:g.116544394T>A	ENSP00000354947:p.Leu128Gln	78.0	0.0		84.0	35.0	NM_006136	B4DG50	Missense_Mutation	SNP	ENST00000361183.3	hg19	CCDS5768.1	.	.	.	.	.	.	.	.	.	.	T	27.2	4.809458	0.90707	.	.	ENSG00000198898	ENST00000361183;ENST00000458284;ENST00000490693	.	.	.	5.42	5.42	0.78866	.	0.129181	0.52532	D	0.000063	T	0.79953	0.4535	M	0.80847	2.515	0.48452	D	0.999654	D	0.59767	0.986	D	0.74348	0.983	T	0.82896	-0.0230	9	0.72032	D	0.01	-4.8687	15.7455	0.77936	0.0:0.0:0.0:1.0	.	128	P47755	CAZA2_HUMAN	Q	128	.	ENSP00000354947:L128Q	L	+	2	0	CAPZA2	116331630	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.993000	0.88291	2.170000	0.68504	0.533000	0.62120	CTG	.	.		0.403	CAPZA2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059506.4	NM_006136		A	116544394	T	A	116544394	3	1	283	1	0	0	0	0	1	0	0	0	2643	1580	55	4	401	4	CAPZA2	7	116544394	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	19892745	116544394	42594269	105	41743										
C8orf79	57604	hgsc.bcm.edu	37	chr8	12879028	12879028	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	acagaagtttgggccagtagCactgtaacagtccagccttc	10	11	0	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr8:12879028C>A	ENST00000524591.2	+	5	1329	c.840C>A	c.(838-840)agC>agA	p.S280R	KIAA1456_ENST00000447063.2_Intron	NM_001099677.1|NM_020844.2	NP_001093147.1|NP_065895.2	Q9P272	K1456_HUMAN	KIAA1456	280							methyltransferase activity (GO:0008168)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	7						GGGCCAGTAGCACTGTAACAG	0.423																																					p.S280R		Atlas-SNP	.											.	KIAA1456	20	.	0			c.C840A						.						83	80	81					8																	12879028		1885	4106	5991	SO:0001583	missense	57604	exon5			CAGTAGCACTGTA	BC035082	CCDS47808.1	8p22	2013-10-04	2011-02-23	2011-02-23	ENSG00000250305	ENSG00000250305			26725	protein-coding gene	gene with protein product		615666	"chromosome 8 open reading frame 79"	C8orf79		23381944	Standard	NM_020844		Approved	FLJ36980	uc010lsq.3	Q8N9K7	OTTHUMG00000165477	ENST00000524591.2:c.840C>A	chr8.hg19:g.12879028C>A	ENSP00000432695:p.Ser280Arg	123.0	0.0		145.0	43.0	NM_020844	Q96AW6	Missense_Mutation	SNP	ENST00000524591.2	hg19	CCDS47808.1	.	.	.	.	.	.	.	.	.	.	C	13.13	2.144688	0.37825	.	.	ENSG00000250305	ENST00000524591;ENST00000529978	T	0.11604	2.76	5.18	4.3	0.51218	.	0.501510	0.24298	N	0.039744	T	0.14056	0.0340	M	0.64997	1.995	0.26851	N	0.968151	B	0.11235	0.004	B	0.10450	0.005	T	0.10200	-1.0640	10	0.72032	D	0.01	-5.7566	12.1134	0.53852	0.0:0.8569:0.0:0.1431	.	280	Q9P272	K1456_HUMAN	R	280;193	ENSP00000432695:S280R	ENSP00000432695:S280R	S	+	3	2	AC135352.2	12923399	0.000000	0.05858	0.087000	0.20705	0.013000	0.08279	0.381000	0.20619	1.552000	0.49463	0.655000	0.94253	AGC	.	.		0.423	KIAA1456-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383262.2	NM_001099677		A	12879028	C	A	12879028	3	1	283	1	0	0	0	0	1	0	0	0	2440	709	25	3	850	3	C8orf79	8	12879028	Missense_Mutation	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10		12879028	133484994	106	41744										
EPB49	2039	hgsc.bcm.edu	37	chr8	21924617	21924617	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	aaccacttacctcccccgggAgcgtgagcccctcccgagat	9	18	0	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr8:21924617A>G	ENST00000523266.1	+	3	502	c.40A>G	c.(40-42)Agc>Ggc	p.S14G	DMTN_ENST00000443491.2_Intron|DMTN_ENST00000519907.1_Missense_Mutation_p.S14G|DMTN_ENST00000517600.1_Intron|DMTN_ENST00000523782.2_Intron|DMTN_ENST00000358242.3_Missense_Mutation_p.S14G|DMTN_ENST00000432128.1_Missense_Mutation_p.S14G|DMTN_ENST00000415253.1_Missense_Mutation_p.S14G|DMTN_ENST00000265800.5_Missense_Mutation_p.S14G|DMTN_ENST00000381470.3_Missense_Mutation_p.S14G	NM_001978.2	NP_001969.2	Q08495	DEMA_HUMAN	dematin actin binding protein	14					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|actin filament capping (GO:0051693)|actin filament reorganization (GO:0090527)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cellular response to calcium ion (GO:0071277)|cellular response to cAMP (GO:0071320)|cytoskeleton organization (GO:0007010)|erythrocyte development (GO:0048821)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of blood coagulation (GO:0030194)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|positive regulation of platelet aggregation (GO:1901731)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of wound healing (GO:0090303)|protein complex assembly (GO:0006461)|protein secretion by platelet (GO:0070560)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)|regulation of lamellipodium assembly (GO:0010591)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cell projection membrane (GO:0031253)|cortical cytoskeleton (GO:0030863)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|protein self-association (GO:0043621)|receptor binding (GO:0005102)|spectrin binding (GO:0030507)										CTCCCCCGGGAGCGTGAGCCC	0.721																																					p.S14G		Atlas-SNP	.											.	EPB49	35	.	0			c.A40G						.						28	29	28					8																	21924617		2200	4298	6498	SO:0001583	missense	2039	exon3			CCCGGGAGCGTGA	U28389	CCDS6020.1, CCDS47820.1, CCDS47821.1	8p21.1	2013-05-03	2013-05-03	2013-05-03	ENSG00000158856	ENSG00000158856			3382	protein-coding gene	gene with protein product		125305	"erythrocyte membrane protein band 4.9 (dematin)"	EPB49		8341682, 12011427	Standard	NM_001978		Approved	DMT		Q08495	OTTHUMG00000097087	ENST00000523266.1:c.40A>G	chr8.hg19:g.21924617A>G	ENSP00000427866:p.Ser14Gly	227.0	0.0		200.0	62.0	NM_001978	A8K0T5|B3KP70|B3KRH3|E9PEJ0|Q13215|Q9BRE3	Missense_Mutation	SNP	ENST00000523266.1	hg19	CCDS6020.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.702006	0.88924	.	.	ENSG00000158856	ENST00000519850;ENST00000381470;ENST00000432128;ENST00000517804;ENST00000265800;ENST00000517418;ENST00000358242;ENST00000415253;ENST00000523266;ENST00000519907	T;T;T;T;T;T;T;T;T;T	0.50277	0.75;0.75;0.75;0.75;0.75;0.75;0.75;0.75;0.75;0.75	4.86	4.86	0.63082	.	.	.	.	.	T	0.63721	0.2535	M	0.68952	2.095	0.39049	D	0.960293	P;P	0.52842	0.956;0.954	P;D	0.63597	0.899;0.916	T	0.69847	-0.5034	9	0.87932	D	0	.	12.3993	0.55404	1.0:0.0:0.0:0.0	.	14;14	Q08495;Q08495-2	DEMA_HUMAN;.	G	14	ENSP00000430600:S14G;ENSP00000370879:S14G;ENSP00000416111:S14G;ENSP00000428415:S14G;ENSP00000265800:S14G;ENSP00000429948:S14G;ENSP00000350977:S14G;ENSP00000401291:S14G;ENSP00000427866:S14G;ENSP00000429377:S14G	ENSP00000265800:S14G	S	+	1	0	EPB49	21980563	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	6.653000	0.74382	1.824000	0.53156	0.379000	0.24179	AGC	.	.		0.721	DMTN-009	PUTATIVE	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375178.1	NM_001978		G	21924617	A	G	21924617	3	3	283	1	0	0	0	0	1	0	0	0	5161	304	11	2	46	2	EPB49	8	21924617	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	9045589	21924617	124439405	107	41745										
ELP3	55140	hgsc.bcm.edu	37	chr8	28013470	28013470	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tgtgtacagggatattccaaTgcctttagttagctcaggag	11	7	1	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr8:28013470T>C	ENST00000256398.8	+	11	1489	c.1112T>C	c.(1111-1113)aTg>aCg	p.M371T	ELP3_ENST00000380353.4_Missense_Mutation_p.M279T|ELP3_ENST00000542181.1_Missense_Mutation_p.M242T|ELP3_ENST00000524103.1_Missense_Mutation_p.M299T|ELP3_ENST00000537665.1_Missense_Mutation_p.M252T|ELP3_ENST00000521015.1_Missense_Mutation_p.M357T	NM_001284220.1|NM_001284226.1|NM_018091.5	NP_001271149.1|NP_001271155.1|NP_060561.3	Q9H9T3	ELP3_HUMAN	elongator acetyltransferase complex subunit 3	371					chromatin organization (GO:0006325)|positive regulation of cell migration (GO:0030335)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	histone acetyltransferase activity (GO:0004402)|iron-sulfur cluster binding (GO:0051536)|metal ion binding (GO:0046872)|phosphorylase kinase regulator activity (GO:0008607)			kidney(2)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.151)|Colorectal(74;0.183)		GATATTCCAATGCCTTTAGTT	0.403																																					p.M371T		Atlas-SNP	.											.	ELP3	36	.	0			c.T1112C						.						74	68	70					8																	28013470		2203	4300	6503	SO:0001583	missense	55140	exon11			TTCCAATGCCTTT		CCDS6065.1, CCDS64860.1, CCDS64861.1, CCDS75717.1, CCDS75718.1	8p21.1	2012-08-14	2012-08-08		ENSG00000134014	ENSG00000134014		"Chromatin-modifying enzymes / K-acetyltransferases", "Elongator acetyltransferase complex subunits"	20696	protein-coding gene	gene with protein product		612722	"elongation protein 3 homolog (S. cerevisiae)"			11714725	Standard	NM_018091		Approved	FLJ10422, KAT9	uc003xgo.4	Q9H9T3	OTTHUMG00000102124	ENST00000256398.8:c.1112T>C	chr8.hg19:g.28013470T>C	ENSP00000256398:p.Met371Thr	192.0	0.0		197.0	11.0	NM_018091	B4DE19|B4DIG1|E2QRI5|Q53G84|Q6AWB0|Q9BVF7|Q9NVZ1	Missense_Mutation	SNP	ENST00000256398.8	hg19	CCDS6065.1	.	.	.	.	.	.	.	.	.	.	T	16.72	3.202748	0.58234	.	.	ENSG00000134014	ENST00000521015;ENST00000256398;ENST00000542181;ENST00000524103;ENST00000537665;ENST00000380353	.	.	.	5.91	5.91	0.95273	Acyl-CoA N-acyltransferase (1);	0.000000	0.85682	D	0.000000	T	0.74635	0.3742	M	0.88906	2.99	0.80722	D	1	B;B	0.32893	0.029;0.389	B;B	0.40602	0.01;0.334	T	0.72481	-0.4280	9	0.17832	T	0.49	-29.4111	14.3004	0.66346	0.0:0.0:0.0:1.0	.	252;371	B4DE19;Q9H9T3	.;ELP3_HUMAN	T	357;371;242;299;252;279	.	ENSP00000256398:M371T	M	+	2	0	ELP3	28069389	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.705000	0.84606	2.254000	0.74563	0.533000	0.62120	ATG	.	.		0.403	ELP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219963.2	NM_018091		C	28013470	T	C	28013470	3	2	283	1	0	0	0	0	1	0	0	0	5083	1464	51	2	1154	2	ELP3	8	28013470	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	6088853	28013470	118350552	108	41746										
KIF13B	23303	hgsc.bcm.edu	37	chr8	28974375	28974375	+	Silent	SNP	T	T	C													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ccgtgaacattgacacagatTctcttgcgtaacaccagttg							TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr8:28974375T>C	ENST00000524189.1	-	31	3848	c.3810A>G	c.(3808-3810)agA>agG	p.R1270R	CTD-2647L4.1_ENST00000523661.1_RNA	NM_015254.3	NP_056069.2	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	1270					metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein targeting (GO:0006605)|regulation of axonogenesis (GO:0050770)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	axon (GO:0030424)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)			endometrium(6)|kidney(1)|lung(20)|urinary_tract(1)	28		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)		TGACACAGATTCTCTTGCGTA	0.582																																					p.R1270R		Atlas-SNP	.											.	KIF13B	192	.	0			c.A3810G						.						72	77	75					8																	28974375		2126	4240	6366	SO:0001819	synonymous_variant	23303	exon31			ACAGATTCTCTTG	AB014539	CCDS55217.1	8p21	2008-07-30				ENSG00000197892		"Kinesins"	14405	protein-coding gene	gene with protein product		607350				9734811, 10859302, 16864656	Standard	NM_015254		Approved	GAKIN, KIAA0639	uc003xhh.4	Q9NQT8		ENST00000524189.1:c.3810A>G	chr8.hg19:g.28974375T>C		262.0	0.0		234.0	74.0	NM_015254	B4DGY5|B5MC45|F8VPJ2|O75134|Q9BYJ6	Silent	SNP	ENST00000524189.1	hg19	CCDS55217.1																																																																																			.	.		0.582	KIF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376878.1			C	28974375	T	C	28974375	2	2	283	1	0	0	0	0	0	0	0	1	8284	1780	62	2		2	KIF13B	8	28974375	Silent	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	960905	28974375	117389647	109	41747	215	2								
KIF13B	23303	hgsc.bcm.edu	37	chr8	28974384	28974384	+	Silent	SNP	T	T	C													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ttgacacagattctcttgcgTaacaccagttgcatgtcagc							TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr8:28974384T>C	ENST00000524189.1	-	31	3839	c.3801A>G	c.(3799-3801)ttA>ttG	p.L1267L	CTD-2647L4.1_ENST00000523661.1_RNA	NM_015254.3	NP_056069.2	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	1267					metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein targeting (GO:0006605)|regulation of axonogenesis (GO:0050770)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	axon (GO:0030424)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)			endometrium(6)|kidney(1)|lung(20)|urinary_tract(1)	28		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)		TTCTCTTGCGTAACACCAGTT	0.592																																					p.L1267L		Atlas-SNP	.											.	KIF13B	192	.	0			c.A3801G						.						74	79	77					8																	28974384		2136	4243	6379	SO:0001819	synonymous_variant	23303	exon31			CTTGCGTAACACC	AB014539	CCDS55217.1	8p21	2008-07-30				ENSG00000197892		"Kinesins"	14405	protein-coding gene	gene with protein product		607350				9734811, 10859302, 16864656	Standard	NM_015254		Approved	GAKIN, KIAA0639	uc003xhh.4	Q9NQT8		ENST00000524189.1:c.3801A>G	chr8.hg19:g.28974384T>C		274.0	0.0		247.0	76.0	NM_015254	B4DGY5|B5MC45|F8VPJ2|O75134|Q9BYJ6	Silent	SNP	ENST00000524189.1	hg19	CCDS55217.1																																																																																			.	.		0.592	KIF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376878.1			C	28974384	T	C	28974384	2	2	283	1	0	0	0	0	0	0	0	1	8284	1635	57	2		2	KIF13B	8	28974384	Silent	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	9	28974384	117389638	110	41748	215	2								
PRKDC	5591	hgsc.bcm.edu	37	chr8	48856412	48856412	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tcattataaacagaatcctaCctgagggcacagcatatctc	6	11	2	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr8:48856412C>A	ENST00000523565.1	-	9	865		c.e9+1		PRKDC_ENST00000314191.2_Splice_Site|PRKDC_ENST00000338368.3_Splice_Site			P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic polypeptide						B cell lineage commitment (GO:0002326)|brain development (GO:0007420)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|ectopic germ cell programmed cell death (GO:0035234)|heart development (GO:0007507)|immunoglobulin V(D)J recombination (GO:0033152)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of protein phosphorylation (GO:0001933)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|pro-B cell differentiation (GO:0002328)|protein destabilization (GO:0031648)|regulation of circadian rhythm (GO:0042752)|response to gamma radiation (GO:0010332)|rhythmic process (GO:0048511)|signal transduction involved in mitotic G1 DNA damage checkpoint (GO:0072431)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell receptor V(D)J recombination (GO:0033153)|telomere maintenance (GO:0000723)	cytosol (GO:0005829)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription factor binding (GO:0008134)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(9)|cervix(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(30)|lung(56)|ovary(6)|pancreas(1)|prostate(8)|skin(7)	147		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)			Caffeine(DB00201)	CAGAATCCTACCTGAGGGCAC	0.294								Non-homologous end-joining																													.	Esophageal Squamous(79;1091 1253 12329 31680 40677)	Atlas-SNP	.											.	PRKDC	394	.	0			c.808+1G>T						.						34	33	33					8																	48856412		1806	4065	5871	SO:0001630	splice_region_variant	5591	exon10			ATCCTACCTGAGG		CCDS75734.1, CCDS75735.1	8q11	2014-09-17				ENSG00000253729	2.7.11.1		9413	protein-coding gene	gene with protein product		600899		HYRC, HYRC1		7638222	Standard	NM_001081640		Approved	DNPK1, p350, DNAPK, XRCC7, DNA-PKcs	uc003xqi.3	P78527		ENST00000523565.1:c.12643+1G>T	chr8.hg19:g.48856412C>A		136.0	0.0		133.0	40.0	NM_001081640	P78528|Q13327|Q13337|Q14175|Q59H99|Q7Z611|Q96SE6|Q9UME3	Splice_Site	SNP	ENST00000523565.1	hg19		.	.	.	.	.	.	.	.	.	.	C	21.7	4.184371	0.78677	.	.	ENSG00000253729	ENST00000314191;ENST00000338368	.	.	.	5.52	5.52	0.82312	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.4438	0.90676	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PRKDC	49018965	1.000000	0.71417	0.983000	0.44433	0.939000	0.58152	5.808000	0.69165	2.601000	0.87937	0.563000	0.77884	.	.	.		0.294	PRKDC-002	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000377896.1	NM_001081640	Intron	A	48856412	C	A	48856412	5	1	283	1	0	0	0	0	0	0	1	0	12533	521	18	3	11888	3	PRKDC	8	48856412	Splice_Site	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	19882028	48856412	97507610	111	41749										
PXDNL	137902	hgsc.bcm.edu	37	chr8	52323847	52323847	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	acagtgagcccctgcttcacAcgttcccgtatcagctgcag	9	15	2	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr8:52323847A>G	ENST00000356297.4	-	16	2125	c.2025T>C	c.(2023-2025)cgT>cgC	p.R675R	PXDNL_ENST00000543296.1_Silent_p.R675R	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	675					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				CCTGCTTCACACGTTCCCGTA	0.517																																					p.R675R		Atlas-SNP	.											.	PXDNL	414	.	0			c.T2025C						.						58	59	59					8																	52323847		2012	4180	6192	SO:0001819	synonymous_variant	137902	exon16			CTTCACACGTTCC		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"Immunoglobulin superfamily / I-set domain containing"	26359	protein-coding gene	gene with protein product	"polysomal ribonuclease 1 homolog (Xenopus)"	615904	"peroxidasin homolog-like (Drosophila)"			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.2025T>C	chr8.hg19:g.52323847A>G		179.0	0.0		227.0	71.0	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Silent	SNP	ENST00000356297.4	hg19	CCDS47855.1																																																																																			.	.		0.517	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		G	52323847	A	G	52323847	2	3	283	1	0	0	0	0	0	0	0	1	12863	146	6	2		2	PXDNL	8	52323847	Silent	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	3467435	52323847	94040175	112	41750										
RRS1	23212	hgsc.bcm.edu	37	chr8	67341483	67341483	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	cagtttgacctgggcaacctGctggcgtcggaccggaaccc	13	14	0	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr8:67341483G>A	ENST00000320270.2	+	1	221	c.117G>A	c.(115-117)ctG>ctA	p.L39L	RP11-346I3.4_ENST00000499642.1_lincRNA	NM_015169.3	NP_055984.1	Q15050	RRS1_HUMAN	RRS1 ribosome biogenesis regulator homolog (S. cerevisiae)	39					hematopoietic progenitor cell differentiation (GO:0002244)|mitotic metaphase plate congression (GO:0007080)|ribosome biogenesis (GO:0042254)	condensed nuclear chromosome (GO:0000794)|endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			kidney(2)|lung(2)	4		Lung NSC(129;0.197)	Epithelial(68;0.0391)|all cancers(69;0.0898)|BRCA - Breast invasive adenocarcinoma(89;0.111)|OV - Ovarian serous cystadenocarcinoma(28;0.226)			TGGGCAACCTGCTGGCGTCGG	0.672											OREG0018806	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L39L		Atlas-SNP	.											.	RRS1	13	.	0			c.G117A						.						49	39	43					8																	67341483		2186	4296	6482	SO:0001819	synonymous_variant	23212	exon1			CAACCTGCTGGCG	BC001811	CCDS6189.1	8q13.1	2013-10-22			ENSG00000179041	ENSG00000179041			17083	protein-coding gene	gene with protein product						7788527, 10688653	Standard	NM_015169		Approved	KIAA0112	uc003xwa.3	Q15050	OTTHUMG00000164765	ENST00000320270.2:c.117G>A	chr8.hg19:g.67341483G>A		161.0	0.0	1098	202.0	77.0	NM_015169	Q9BUX8	Silent	SNP	ENST00000320270.2	hg19	CCDS6189.1																																																																																			.	.		0.672	RRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380126.1	NM_015169		A	67341483	G	A	67341483	2	1	283	1	0	0	0	0	0	0	0	1	13707	1306	46	3		3	RRS1	8	67341483	Silent	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	15017636	67341483	79022539	113	41751										
ARFGEF1	10565	hgsc.bcm.edu	37	chr8	68130369	68130369	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	aagttgttgtcatccattcaGctttctggggaaaaaagtca	9	7	4	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr8:68130369G>A	ENST00000262215.3	-	31	4732	c.4343C>T	c.(4342-4344)gCt>gTt	p.A1448V	ARFGEF1_ENST00000518230.1_Missense_Mutation_p.A286V|ARFGEF1_ENST00000520381.1_Missense_Mutation_p.A902V	NM_006421.4	NP_006412.2	Q9Y6D6	BIG1_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)	1448					endomembrane system organization (GO:0010256)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein glycosylation in Golgi (GO:0090284)|positive regulation of wound healing (GO:0090303)|protein transport (GO:0015031)|regulation of ARF protein signal transduction (GO:0032012)|regulation of establishment of cell polarity (GO:2000114)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|small nuclear ribonucleoprotein complex (GO:0030532)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|guanyl-nucleotide exchange factor activity (GO:0005085)|myosin binding (GO:0017022)|protein kinase A regulatory subunit binding (GO:0034237)			breast(1)|endometrium(14)|kidney(4)|large_intestine(17)|lung(20)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)			CATCCATTCAGCTTTCTGGGG	0.274																																					p.A1448V		Atlas-SNP	.											.	ARFGEF1	196	.	0			c.C4343T						.						85	74	78					8																	68130369		2203	4300	6503	SO:0001583	missense	10565	exon31			CATTCAGCTTTCT	AF084520	CCDS6199.1	8q13	2011-08-18	2011-08-18		ENSG00000066777	ENSG00000066777			15772	protein-coding gene	gene with protein product		604141				10212200, 8917509	Standard	NM_006421		Approved	DKFZP434L057, BIG1, ARFGEP1, p200	uc003xxo.2	Q9Y6D6	OTTHUMG00000164626	ENST00000262215.3:c.4343C>T	chr8.hg19:g.68130369G>A	ENSP00000262215:p.Ala1448Val	196.0	0.0		138.0	46.0	NM_006421	Q9NV46|Q9UFV2|Q9UNL0	Missense_Mutation	SNP	ENST00000262215.3	hg19	CCDS6199.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.286513	0.80803	.	.	ENSG00000066777	ENST00000520381;ENST00000262215;ENST00000518230	T;T;T	0.65549	0.74;0.74;-0.16	5.48	5.48	0.80851	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.65112	0.2660	M	0.72479	2.2	0.58432	D	0.999999	P;B;B	0.41748	0.761;0.446;0.446	B;B;B	0.38106	0.265;0.15;0.15	T	0.71080	-0.4696	10	0.66056	D	0.02	.	19.7024	0.96060	0.0:0.0:1.0:0.0	.	1448;926;902	Q9Y6D6;Q59FY5;E5RIF2	BIG1_HUMAN;.;.	V	902;1448;286	ENSP00000428429:A902V;ENSP00000262215:A1448V;ENSP00000430891:A286V	ENSP00000262215:A1448V	A	-	2	0	ARFGEF1	68292923	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.813000	0.99286	2.724000	0.93272	0.655000	0.94253	GCT	.	.		0.274	ARFGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379441.4	NM_006421		A	68130369	G	A	68130369	3	1	283	1	0	0	0	0	1	0	0	0	852	971	34	3	1242	3	ARFGEF1	8	68130369	Missense_Mutation	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	788886	68130369	78233653	114	41752										
LACTB2	51110	hgsc.bcm.edu	37	chr8	71581340	71581340	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ggacagccgctcgacgcgctGcagtacagcagccattcccg	12	16	0	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr8:71581340G>A	ENST00000276590.4	-	1	52	c.16C>T	c.(16-18)Cag>Tag	p.Q6*	LACTB2_ENST00000522447.1_Nonsense_Mutation_p.Q6*|XKR9_ENST00000520030.1_5'Flank|XKR9_ENST00000408926.3_5'Flank	NM_016027.2	NP_057111.1	Q53H82	LACB2_HUMAN	lactamase, beta 2	6						mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			endometrium(2)|large_intestine(1)|liver(1)|lung(4)|ovary(1)|prostate(1)	10	Breast(64;0.0716)		Epithelial(68;0.00319)|all cancers(69;0.0175)|OV - Ovarian serous cystadenocarcinoma(28;0.0628)|BRCA - Breast invasive adenocarcinoma(89;0.166)			TCGACGCGCTGCAGTACAGCA	0.652											OREG0018822	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q6X		Atlas-SNP	.											.	LACTB2	26	.	0			c.C16T						.						27	25	26					8																	71581340		2199	4289	6488	SO:0001587	stop_gained	51110	exon1			CGCGCTGCAGTAC	AF151841	CCDS6208.1	8q13.3	2005-10-14			ENSG00000147592	ENSG00000147592			18512	protein-coding gene	gene with protein product							Standard	NM_016027		Approved	CGI-83	uc003xyp.3	Q53H82	OTTHUMG00000164430	ENST00000276590.4:c.16C>T	chr8.hg19:g.71581340G>A	ENSP00000276590:p.Gln6*	100.0	0.0	1131	98.0	7.0	NM_016027	A8K2D6|Q9Y392	Nonsense_Mutation	SNP	ENST00000276590.4	hg19	CCDS6208.1	.	.	.	.	.	.	.	.	.	.	G	36	5.839193	0.97009	.	.	ENSG00000147592	ENST00000522447;ENST00000276590	.	.	.	4.66	3.77	0.43336	.	0.111909	0.64402	D	0.000008	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	-2.6738	14.2343	0.65916	0.0:0.0:0.8497:0.1503	.	.	.	.	X	6	.	ENSP00000276590:Q6X	Q	-	1	0	LACTB2	71743894	1.000000	0.71417	0.977000	0.42913	0.037000	0.13140	7.091000	0.76923	1.167000	0.42706	0.650000	0.86243	CAG	.	.		0.652	LACTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378748.1	NM_016027		A	71581340	G	A	71581340	4	1	283	1	0	0	0	0	0	1	0	0	8607	1328	46	3	878	3	LACTB2	8	71581340	Nonsense_Mutation	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	3450971	71581340	74782682	115	41753										
INTS8	55656	hgsc.bcm.edu	37	chr8	95892461	95892461	+	Nonstop_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	aatggcaaaactttacttttAagcagttaaatttttttaac	4	5	0	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr8:95892461A>C	ENST00000523731.1	+	27	3120	c.2987A>C	c.(2986-2988)tAa>tCa	p.*996S	CCNE2_ENST00000308108.4_3'UTR|INTS8_ENST00000447247.1_Nonstop_Mutation_p.*979S|CCNE2_ENST00000520509.1_3'UTR	NM_017864.2	NP_060334.2	Q75QN2	INT8_HUMAN	integrator complex subunit 8	0					snRNA processing (GO:0016180)	integrator complex (GO:0032039)				breast(3)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	28	Breast(36;1.05e-06)					CTTTACTTTTAAGCAGttaaa	0.303																																					p.X996S		Atlas-SNP	.											.	INTS8	92	.	0			c.A2987C						.						39	40	40					8																	95892461		2203	4300	6503	SO:0001578	stop_lost	55656	exon27			ACTTTTAAGCAGT	AK091278	CCDS34925.1	8q22.1	2007-05-03	2006-03-15	2006-03-15	ENSG00000164941	ENSG00000164941			26048	protein-coding gene	gene with protein product		611351	"chromosome 8 open reading frame 52"	C8orf52		16239144	Standard	NM_017864		Approved	FLJ20530, INT8, MGC131633	uc003yhb.4	Q75QN2	OTTHUMG00000164695	ENST00000523731.1:c.2987A>C	chr8.hg19:g.95892461A>C	ENSP00000430338:p.*996Serext*6	88.0	0.0		107.0	36.0	NM_017864	B2RN92|Q5RKZ3|Q6P1R5|Q7Z314|Q9NVS6|Q9NWY7	Missense_Mutation	SNP	ENST00000523731.1	hg19	CCDS34925.1	.	.	.	.	.	.	.	.	.	.	a	19.04	3.750597	0.69533	.	.	ENSG00000164941	ENST00000523731;ENST00000447247	.	.	.	5.83	4.67	0.58626	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.7867	0.52047	0.9316:0.0:0.0684:0.0	.	.	.	.	S	996;979	.	.	X	+	2	2	INTS8	95961637	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	4.448000	0.60027	1.037000	0.40024	0.529000	0.55759	TAA	.	.		0.303	INTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379794.1	NM_017864		C	95892461	A	C	95892461	4	2	283	1	0	0	0	0	0	0	0	0	7793	369	13	5	3093	5	INTS8	8	95892461	Nonstop_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	24311121	95892461	50471561	116	41754										
RIMS2	9699	hgsc.bcm.edu	37	chr8	104898096	104898096	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gaggctcagggaccaagttcTtatgcacaaaggaccacaaa	10	10	2	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr8:104898096T>G	ENST00000436393.2	+	2	844	c.603T>G	c.(601-603)tcT>tcG	p.S201S	RIMS2_ENST00000507740.1_Silent_p.S231S|RIMS2_ENST00000262231.10_Silent_p.S231S|RIMS2_ENST00000406091.3_Silent_p.S423S			Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	454					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)	p.S231S(3)|p.S459S(2)|p.S201S(2)		NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			GACCAAGTTCTTATGCACAAA	0.478										HNSCC(12;0.0054)																											p.S423S		Atlas-SNP	.											RIMS2_ENST00000507740,NS,carcinoma,0,22	RIMS2	1357	.	7	Substitution - coding silent(7)	large_intestine(7)	c.T1269G						.						85	80	81					8																	104898096		1935	4137	6072	SO:0001819	synonymous_variant	9699	exon4			AAGTTCTTATGCA	AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"RAB3 interacting protein 3"	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000436393.2:c.603T>G	chr8.hg19:g.104898096T>G		81.0	0.0		68.0	28.0	NM_001100117	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Silent	SNP	ENST00000436393.2	hg19																																																																																				.	.		0.478	RIMS2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000367217.1	NM_001100117		G	104898096	T	G	104898096	2	3	283	1	0	0	0	0	0	0	0	1	13383	1596	56	5		5	RIMS2	8	104898096	Silent	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	9005635	104898096	41465926	117	41755										
RG9MTD3	158234	hgsc.bcm.edu	37	chr9	37776352	37776352	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	aatccaggaatacatggtcaGaaaccagaatgggaaaaact	9	7	1	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr9:37776352G>C	ENST00000297994.3	+	8	859	c.794G>C	c.(793-795)aGa>aCa	p.R265T	TRMT10B_ENST00000377753.2_Missense_Mutation_p.R187T|RP11-613M10.9_ENST00000540557.1_Intron|TRMT10B_ENST00000537911.1_Missense_Mutation_p.R214T|TRMT10B_ENST00000377754.2_Missense_Mutation_p.R170T	NM_144964.2	NP_659401.2	Q6PF06	TM10B_HUMAN	tRNA methyltransferase 10 homolog B (S. cerevisiae)	265	SAM-dependent MTase TRM10-type. {ECO:0000255|PROSITE-ProRule:PRU01012}.						methyltransferase activity (GO:0008168)										TACATGGTCAGAAACCAGAAT	0.443																																					p.R265T		Atlas-SNP	.											.	.	.	.	0			c.G794C						.						55	51	52					9																	37776352		1905	4133	6038	SO:0001583	missense	158234	exon8			TGGTCAGAAACCA	BC057774	CCDS43804.1, CCDS69598.1, CCDS69600.1, CCDS69601.1	9p13.1	2012-06-28	2012-06-28	2012-06-28	ENSG00000165275	ENSG00000165275			26454	protein-coding gene	gene with protein product			"RNA (guanine-9-) methyltransferase domain containing 3"	RG9MTD3		14702039	Standard	XM_005251373		Approved	FLJ31455, bA3J10.9	uc004aai.3	Q6PF06	OTTHUMG00000019933	ENST00000297994.3:c.794G>C	chr9.hg19:g.37776352G>C	ENSP00000297994:p.Arg265Thr	213.0	0.0		203.0	76.0	NM_144964	B7Z216|B7Z3D3|Q05DJ4|Q5QP83|Q8NAG2|Q96N36	Missense_Mutation	SNP	ENST00000297994.3	hg19	CCDS43804.1	.	.	.	.	.	.	.	.	.	.	G	13.45	2.240460	0.39598	.	.	ENSG00000165275	ENST00000377753;ENST00000537911;ENST00000377754;ENST00000297994	T;T;T;T	0.21361	2.01;2.01;2.01;2.01	5.28	-0.546	0.11840	.	0.245392	0.47093	D	0.000248	T	0.21387	0.0515	L	0.46157	1.445	0.80722	D	1	P;P;B;B;B	0.44344	0.485;0.833;0.408;0.026;0.316	B;P;B;B;B	0.49140	0.297;0.601;0.346;0.054;0.288	T	0.05257	-1.0896	10	0.20046	T	0.44	-3.1555	9.4421	0.38675	0.522:0.0:0.478:0.0	.	154;187;214;170;265	B7Z9F7;B7Z216;B7Z3D3;Q6PF06-2;Q6PF06	.;.;.;.;RG9D3_HUMAN	T	187;214;170;265	ENSP00000366982:R187T;ENSP00000444997:R214T;ENSP00000366983:R170T;ENSP00000297994:R265T	ENSP00000297994:R265T	R	+	2	0	RG9MTD3	37766352	0.625000	0.27111	0.141000	0.22245	0.466000	0.32739	0.737000	0.26144	-0.012000	0.14223	-0.136000	0.14681	AGA	.	.		0.443	TRMT10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052482.1	NM_144964		C	37776352	G	C	37776352	3	2	283	1	0	0	0	0	1	0	0	0	13288	942	33	4	820	4	RG9MTD3	9	37776352	Missense_Mutation	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10		37776352	103437079	118	41756										
TLE1	7088	hgsc.bcm.edu	37	chr9	84300807	84300807	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	cagtttctcacattccaattTaaggctaggaaaacaaaaca	5	9	1	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr9:84300807T>C	ENST00000376499.3	-	3	1194	c.130A>G	c.(130-132)Aaa>Gaa	p.K44E	TLE1_ENST00000376472.1_5'UTR|TLE1_ENST00000376463.1_5'UTR	NM_005077.3	NP_005068.2	Q04724	TLE1_HUMAN	transducin-like enhancer of split 1 (E(sp1) homolog, Drosophila)	44	Gln-rich.				multicellular organismal development (GO:0007275)|negative regulation of anoikis (GO:2000811)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation of gene expression (GO:0010628)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription factor binding (GO:0008134)			NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	29						CATTCCAATTTAAGGCTAGGA	0.348																																					p.K44E	NSCLC(155;1437 1995 30668 39354 45875)|Melanoma(16;266 781 14000 47728 51870)	Atlas-SNP	.											.	TLE1	81	.	0			c.A130G						.						111	100	104					9																	84300807		2202	4300	6502	SO:0001583	missense	7088	exon3			CCAATTTAAGGCT		CCDS6661.1	9q21.32	2013-01-10	2001-11-28		ENSG00000196781	ENSG00000196781		"WD repeat domain containing"	11837	protein-coding gene	gene with protein product	"enhancer of split groucho 1"	600189	"transducin-like enhancer of split 1, homolog of Drosophila E(sp1)"			8365415, 8808280	Standard	NM_005077		Approved	ESG1, GRG1, ESG	uc004aly.3	Q04724	OTTHUMG00000021008	ENST00000376499.3:c.130A>G	chr9.hg19:g.84300807T>C	ENSP00000365682:p.Lys44Glu	209.0	0.0		188.0	62.0	NM_005077	A8K495|Q5T3G4|Q969V9	Missense_Mutation	SNP	ENST00000376499.3	hg19	CCDS6661.1	.	.	.	.	.	.	.	.	.	.	T	29.0	4.965384	0.92855	.	.	ENSG00000196781	ENST00000376499;ENST00000355002;ENST00000418319	T;T	0.60040	0.22;0.93	5.69	5.69	0.88448	Groucho/TLE, N-terminal Q-rich domain (1);	0.000000	0.85682	D	0.000000	T	0.82263	0.4999	M	0.94021	3.485	0.80722	D	1	D;D;D;D;D;D	0.76494	0.997;0.999;0.999;0.996;0.987;0.998	D;D;D;D;D;D	0.91635	0.989;0.998;0.983;0.988;0.945;0.999	D	0.87160	0.2214	10	0.87932	D	0	-13.6039	15.9446	0.79784	0.0:0.0:0.0:1.0	.	44;44;44;71;44;44	B4E345;B4DEF9;A6NFH2;Q59EF7;Q5T3G3;Q04724	.;.;.;.;.;TLE1_HUMAN	E	44	ENSP00000365682:K44E;ENSP00000391347:K44E	ENSP00000347102:K44E	K	-	1	0	TLE1	83490627	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.040000	0.89188	2.158000	0.67659	0.459000	0.35465	AAA	.	.		0.348	TLE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055407.1	NM_005077		C	84300807	T	C	84300807	3	2	283	1	0	0	0	0	1	0	0	0	15953	1763	61	2	2254	2	TLE1	9	84300807	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	46524455	84300807	56912624	119	41757										
PTGR1	22949	hgsc.bcm.edu	37	chr9	114341085	114341086	+	Frame_Shift_Ins	INS	-	-	TT													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ttgtacttacattatcaaaaINStaacaatcataaccatcagg							TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr9:114341085_114341086insTT	ENST00000407693.2	-	7	903_904	c.641_642insAA	c.(640-642)tatfs	p.Y214fs	PTGR1_ENST00000538962.1_Frame_Shift_Ins_p.Y214fs|PTGR1_ENST00000238248.3_Frame_Shift_Ins_p.Y91fs|PTGR1_ENST00000309195.5_Frame_Shift_Ins_p.Y214fs	NM_001146108.1	NP_001139580.1	Q14914	PTGR1_HUMAN	prostaglandin reductase 1	214					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|leukotriene metabolic process (GO:0006691)|lipoxin metabolic process (GO:2001300)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	13-prostaglandin reductase activity (GO:0036132)|15-oxoprostaglandin 13-oxidase activity (GO:0047522)|2-alkenal reductase [NAD(P)] activity (GO:0032440)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(5)|lung(3)|ovary(1)	11						CATTATCAAAATAACAATCATA	0.376																																					p.Y214_F215delinsX	Ovarian(200;132 2151 7551 19220 46064)	Atlas-INDEL	.											.	PTGR1	23	.	0			c.642_643insAA						.																																			SO:0001589	frameshift_variant	22949	exon7			.	D49387	CCDS6779.1, CCDS55331.1	9q32	2008-06-04	2008-06-02	2008-06-02	ENSG00000106853	ENSG00000106853	1.3.1.74, 1.3.1.48		18429	protein-coding gene	gene with protein product	"zinc binding alcohol dehydrogenase domain containing 3"	601274	"leukotriene B4 12-hydroxydehydrogenase"	LTB4DH		8576264, 17449869	Standard	NM_001146109		Approved	ZADH3	uc004bfh.2	Q14914	OTTHUMG00000020493	ENST00000407693.2:c.641_642insAA	chr9.hg19:g.114341085_114341086insTT	ENSP00000385763:p.Tyr214fs	136.0	0.0		112.0	13.0	NM_001146108	A8K0N2|B4DPK3|F5GY50|Q8IYQ0|Q9H1X6	Frame_Shift_Ins	INS	ENST00000407693.2	hg19	CCDS6779.1																																																																																			.	.		0.376	PTGR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053647.2			TT	114341086	-	TT	114341085	7	5	283	1	0	1	1	0	0	0	0	0	12766	108	4	0	394	0	PTGR1	9	114341085	Frame_Shift_Ins	INS	-	TCGA-G3-A3CK-01A-11D-A20W-10	30040278	114341085	26872346	120	41758										
ZFP37	7539	hgsc.bcm.edu	37	chr9	115805892	115805892	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	agttctctgatgtacaacaaGgtgtgacttttggctaaagg	11	6	1	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr9:115805892G>C	ENST00000374227.3	-	4	1033	c.1006C>G	c.(1006-1008)Ctt>Gtt	p.L336V	ZFP37_ENST00000553380.1_Missense_Mutation_p.L351V|ZFP37_ENST00000555206.1_Missense_Mutation_p.L337V	NM_001282515.1|NM_001282518.1	NP_001269444.1|NP_001269447.1	Q9Y6Q3	ZFP37_HUMAN	ZFP37 zinc finger protein	336					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	38						TGTACAACAAGGTGTGACTTT	0.423																																					p.L336V		Atlas-SNP	.											.	ZFP37	93	.	0			c.C1006G						.						120	113	116					9																	115805892		2203	4300	6503	SO:0001583	missense	7539	exon4			CAACAAGGTGTGA	AF022158	CCDS6787.1, CCDS65109.1, CCDS65110.1	9q32	2013-01-08	2012-11-27		ENSG00000136866	ENSG00000136866		"Zinc fingers, C2H2-type", "-"	12863	protein-coding gene	gene with protein product		602951	"zinc finger protein homologous to Zfp37 in mouse", "zinc finger protein 37 homolog (mouse)"				Standard	NM_001282515		Approved	ZNF906	uc004bgm.1	Q9Y6Q3	OTTHUMG00000021019	ENST00000374227.3:c.1006C>G	chr9.hg19:g.115805892G>C	ENSP00000363344:p.Leu336Val	177.0	0.0		128.0	46.0	NM_003408	A0AVJ9|B4DVX4|G3V3L7|Q5T7Q4	Missense_Mutation	SNP	ENST00000374227.3	hg19	CCDS6787.1	.	.	.	.	.	.	.	.	.	.	G	11.09	1.537518	0.27475	.	.	ENSG00000136866	ENST00000374227;ENST00000555206;ENST00000553380	T;T;T	0.52983	0.64;0.64;0.64	4.0	4.0	0.46444	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.38272	N	0.001745	T	0.71558	0.3354	M	0.90814	3.15	0.31599	N	0.652919	B;B;D	0.67145	0.236;0.443;0.996	B;B;D	0.66196	0.17;0.233;0.942	T	0.78971	-0.1993	10	0.87932	D	0	-11.2728	14.4119	0.67119	0.0:0.0:1.0:0.0	.	337;351;336	G3V3L7;Q9Y6Q3-2;Q9Y6Q3	.;.;ZFP37_HUMAN	V	336;337;351	ENSP00000363344:L336V;ENSP00000451310:L337V;ENSP00000452552:L351V	ENSP00000363344:L336V	L	-	1	0	ZFP37	114845713	0.622000	0.27085	1.000000	0.80357	0.999000	0.98932	2.049000	0.41288	2.524000	0.85096	0.563000	0.77884	CTT	.	.		0.423	ZFP37-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055439.1	NM_003408		C	115805892	G	C	115805892	3	2	283	1	0	0	0	0	1	0	0	0	17663	1000	35	4	890	4	ZFP37	9	115805892	Missense_Mutation	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	1464807	115805892	25407539	121	41759										
ZNF618	114991	hgsc.bcm.edu	37	chr9	116770657	116770657	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	aggggcccctgagaaccgggCaggtaagtccttggtgtctg	16	10	1	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr9:116770657C>T	ENST00000374126.5	+	8	773	c.674C>T	c.(673-675)gCa>gTa	p.A225V	ZNF618_ENST00000288466.7_Missense_Mutation_p.A193V			Q5T7W0	ZN618_HUMAN	zinc finger protein 618	225					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|lung(10)|urinary_tract(1)	16						GAGAACCGGGCAGGTAAGTCC	0.632																																					p.A193V		Atlas-SNP	.											.	ZNF618	184	.	0			c.C578T						.						73	84	80					9																	116770657		1966	4131	6097	SO:0001583	missense	114991	exon7			ACCGGGCAGGTAA	BC012922	CCDS48008.1	9q33.1	2010-04-21			ENSG00000157657	ENSG00000157657		"Zinc fingers, C2H2-type"	29416	protein-coding gene	gene with protein product	"neural precursor cell expressed, developmentally down-regulated 10"					11853319	Standard	NM_133374		Approved	KIAA1952, NEDD10	uc004bic.3	Q5T7W0	OTTHUMG00000020532	ENST00000374126.5:c.674C>T	chr9.hg19:g.116770657C>T	ENSP00000363241:p.Ala225Val	123.0	0.0		112.0	34.0	NM_133374	B9EG82|Q4G0X6|Q5T7W1|Q6ZT53|Q7Z6B9|Q8TF49|Q96E49	Missense_Mutation	SNP	ENST00000374126.5	hg19		.	.	.	.	.	.	.	.	.	.	C	15.35	2.806307	0.50421	.	.	ENSG00000157657	ENST00000374126;ENST00000288466;ENST00000374124	T;T	0.19394	4.33;2.15	5.98	5.98	0.97165	.	0.144170	0.47852	D	0.000203	T	0.31295	0.0792	N	0.19112	0.55	0.27485	N	0.952452	D;B;B;B;P	0.63880	0.993;0.19;0.44;0.239;0.705	D;B;B;B;B	0.68192	0.956;0.068;0.118;0.167;0.359	T	0.10730	-1.0617	10	0.45353	T	0.12	-9.4771	15.9562	0.79889	0.0:1.0:0.0:0.0	.	193;193;225;193;193	B5MDS3;B9EG82;Q5T7W0;Q5T7W0-2;Q5T7W0-3	.;.;ZN618_HUMAN;.;.	V	225;193;193	ENSP00000288466:A193V;ENSP00000363239:A193V	ENSP00000288466:A193V	A	+	2	0	ZNF618	115810478	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	4.218000	0.58554	2.847000	0.97988	0.591000	0.81541	GCA	.	.		0.632	ZNF618-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000053749.1	XM_054983		T	116770657	C	T	116770657	3	4	283	1	0	0	0	0	1	0	0	0	18057	710	25	3	604	3	ZNF618	9	116770657	Missense_Mutation	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	964765	116770657	24442774	122	41760										
CEP110	11064	hgsc.bcm.edu	37	chr9	123922548	123922548	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	agaggaagaaaatcttcaggTtgttttaaggcagatgtcta	11	4	3	3			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr9:123922548T>C	ENST00000373855.1	+	32	5317	c.5057T>C	c.(5056-5058)gTt>gCt	p.V1686A	CNTRL_ENST00000373850.1_Missense_Mutation_p.V1134A|CNTRL_ENST00000373845.2_3'UTR|CNTRL_ENST00000373844.1_Missense_Mutation_p.V131A|CNTRL_ENST00000238341.5_Missense_Mutation_p.V1686A			Q7Z7A1	CNTRL_HUMAN	centriolin	1686					cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)				haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(2)|ovary(4)|skin(3)	20						AATCTTCAGGTTGTTTTAAGG	0.313																																					p.V1686A		Atlas-SNP	.											.	CNTRL	161	.	0			c.T5057C						.						73	86	82					9																	123922548		2203	4290	6493	SO:0001583	missense	11064	exon30			TTCAGGTTGTTTT	AF513978	CCDS35118.1	9q33.2	2014-02-20	2011-05-23	2011-05-23	ENSG00000119397	ENSG00000119397			1858	protein-coding gene	gene with protein product		605496	"centrosomal protein 1", "centrosomal protein 110kDa"	CEP1, CEP110		10688839	Standard	XM_005251679		Approved		uc004bkx.1	Q7Z7A1	OTTHUMG00000020581	ENST00000373855.1:c.5057T>C	chr9.hg19:g.123922548T>C	ENSP00000362962:p.Val1686Ala	234.0	0.0		200.0	56.0	NM_007018	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Missense_Mutation	SNP	ENST00000373855.1	hg19	CCDS35118.1	.	.	.	.	.	.	.	.	.	.	T	11.49	1.654806	0.29425	.	.	ENSG00000119397	ENST00000373855;ENST00000238341;ENST00000454238;ENST00000439778;ENST00000373850;ENST00000373845;ENST00000373844	T;T;T	0.27402	1.67;1.67;1.67	5.62	2.93	0.34026	.	.	.	.	.	T	0.20780	0.0500	L	0.60455	1.87	0.19300	N	0.99998	B	0.30741	0.293	B	0.22386	0.039	T	0.24548	-1.0157	9	0.07990	T	0.79	.	3.5789	0.07945	0.1242:0.0739:0.2282:0.5736	.	1686	Q7Z7A1	CNTRL_HUMAN	A	1686;1686;1686;442;1134;368;131	ENSP00000362962:V1686A;ENSP00000238341:V1686A;ENSP00000362956:V1134A	ENSP00000238341:V1686A	V	+	2	0	CNTRL	122962369	0.953000	0.32496	0.999000	0.59377	0.952000	0.60782	0.245000	0.18142	0.923000	0.37045	0.482000	0.46254	GTT	.	.		0.313	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018		C	123922548	T	C	123922548	3	2	283	1	0	0	0	0	1	0	0	0	3247	1725	60	2	5175	2	CEP110	9	123922548	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	7151891	123922548	17290883	123	41761										
GBGT1	26301	hgsc.bcm.edu	37	chr9	136029633	136029633	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gctgactccaggaaggactgGatgaaatgagtgtacctagt	13	7	0	3			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr9:136029633G>A	ENST00000372040.3	-	7	686	c.375C>T	c.(373-375)atC>atT	p.I125I	RALGDS_ENST00000542690.1_Intron|GBGT1_ENST00000372038.3_Missense_Mutation_p.P138S|GBGT1_ENST00000540636.1_Silent_p.I108I|GBGT1_ENST00000372043.3_Intron|GBGT1_ENST00000472281.1_5'UTR	NM_001282629.1	NP_001269558.1	Q8N5D6	GBGT1_HUMAN	globoside alpha-1,3-N-acetylgalactosaminyltransferase 1	125					glycolipid biosynthetic process (GO:0009247)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	globoside alpha-N-acetylgalactosaminyltransferase activity (GO:0047277)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(4)|lung(2)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(145;3.49e-06)|Epithelial(140;2.59e-05)		GGAAGGACTGGATGAAATGAG	0.607																																					p.I125I		Atlas-SNP	.											.	GBGT1	25	.	0			c.C375T						.						41	43	43					9																	136029633		2203	4299	6502	SO:0001819	synonymous_variant	26301	exon7			GGACTGGATGAAA	AY358175	CCDS6960.1, CCDS65175.1, CCDS65176.1	9q34.13-q34.3	2014-07-18			ENSG00000148288	ENSG00000148288		"Glycosyltransferase family 6 domain containing"	20460	protein-coding gene	gene with protein product	"Forssman glycolipid synthetase (FS)", "Forssman synthetase"	606074				10506200, 8855242	Standard	NM_021996		Approved	UDP-GalNAc, A3GALNT, MGC44848, FS		Q8N5D6	OTTHUMG00000020853	ENST00000372040.3:c.375C>T	chr9.hg19:g.136029633G>A		26.0	0.0		23.0	11.0	NM_021996	A8K633|B2RA95|B7Z8S5|Q45F07|Q5T7U9|Q5T7V1|Q8N2K4|Q9UKI5	Silent	SNP	ENST00000372040.3	hg19	CCDS6960.1	.	.	.	.	.	.	.	.	.	.	G	6.527	0.465514	0.12402	.	.	ENSG00000148288	ENST00000372038	T	0.38722	1.12	5.38	2.35	0.29111	.	.	.	.	.	T	0.38799	0.1054	.	.	.	0.18873	N	0.999989	.	.	.	.	.	.	T	0.25984	-1.0116	6	0.46703	T	0.11	-2.6927	7.4262	0.27100	0.1532:0.3919:0.4548:0.0	.	.	.	.	S	138	ENSP00000361108:P138S	ENSP00000361108:P138S	P	-	1	0	GBGT1	135019454	0.000000	0.05858	0.719000	0.30619	0.296000	0.27459	-0.499000	0.06413	0.186000	0.20125	0.491000	0.48974	CCA	.	.		0.607	GBGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054815.1	NM_021996		A	136029633	G	A	136029633	2	1	283	1	0	0	0	0	0	0	0	1	6280	1164	41	3		3	GBGT1	9	136029633	Silent	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	12107085	136029633	5183798	124	41762										
ZNF22	7570	hgsc.bcm.edu	37	chr10	45499035	45499035	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	agttcaactctttttcaacaCcagaagatccatactggaaa	5	10	3	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr10:45499035C>A	ENST00000298299.3	+	2	812	c.219C>A	c.(217-219)caC>caA	p.H73Q	CEP164P1_ENST00000456938.2_RNA|C10orf25_ENST00000298298.1_5'Flank	NM_006963.4	NP_008894.2	P17026	ZNF22_HUMAN	zinc finger protein 22	73					odontogenesis (GO:0042476)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(1)|kidney(2)|lung(2)	8		Prostate(175;0.0352)|all_neural(218;0.202)				TTTTTCAACACCAGAAGATCC	0.393																																					p.H73Q		Atlas-SNP	.											.	ZNF22	28	.	0			c.C219A						.						52	53	52					10																	45499035		2203	4300	6503	SO:0001583	missense	7570	exon2			TCAACACCAGAAG	BC041139	CCDS7211.1	10q11	2013-01-08	2012-07-12		ENSG00000165512	ENSG00000165512		"Zinc fingers, C2H2-type"	13012	protein-coding gene	gene with protein product		194529					Standard	NM_006963		Approved	KOX15, HKR-T1, ZNF422, Zfp422	uc001jbw.3	P17026	OTTHUMG00000018064	ENST00000298299.3:c.219C>A	chr10.hg19:g.45499035C>A	ENSP00000298299:p.His73Gln	47.0	0.0		43.0	12.0	NM_006963	Q5T741|Q96FM4	Missense_Mutation	SNP	ENST00000298299.3	hg19	CCDS7211.1	.	.	.	.	.	.	.	.	.	.	C	18.72	3.684432	0.68157	.	.	ENSG00000165512	ENST00000298299	D	0.99974	-10.2	5.12	0.975	0.19721	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.51477	D	0.000088	D	0.99971	0.9990	M	0.90922	3.16	0.42499	D	0.992926	D	0.89917	1.0	D	0.87578	0.998	D	0.94939	0.8089	10	0.87932	D	0	-29.3728	8.2413	0.31662	0.0:0.6166:0.0:0.3834	.	73	P17026	ZNF22_HUMAN	Q	73	ENSP00000298299:H73Q	ENSP00000298299:H73Q	H	+	3	2	ZNF22	44819041	0.008000	0.16893	1.000000	0.80357	0.993000	0.82548	-0.067000	0.11579	0.277000	0.22141	0.655000	0.94253	CAC	.	.		0.393	ZNF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047761.1	NM_006963		A	45499035	C	A	45499035	3	1	283	1	0	0	0	0	1	0	0	0	17789	506	18	3	221	3	ZNF22	10	45499035	Missense_Mutation	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10		45499035	90035712	125	41763										
ALOX5	240	hgsc.bcm.edu	37	chr10	45891384	45891384	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	aacacggcaaaaacaatatcGgtgagttatgacatcagatc	8	8	1	3			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr10:45891384G>T	ENST00000374391.2	+	3	484	c.431G>T	c.(430-432)cGa>cTa	p.R144L	ALOX5_ENST00000542434.1_Splice_Site_p.R144L	NM_000698.3|NM_001256153.1	NP_000689.1|NP_001243082.1	P09917	LOX5_HUMAN	arachidonate 5-lipoxygenase	144	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				arachidonic acid metabolic process (GO:0019369)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|leukotriene production involved in inflammatory response (GO:0002540)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular space (GO:0005615)|nuclear envelope (GO:0005635)|nuclear envelope lumen (GO:0005641)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)	arachidonate 5-lipoxygenase activity (GO:0004051)|iron ion binding (GO:0005506)			breast(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|pancreas(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		Lung SC(717;0.0257)			Aminosalicylic Acid(DB00233)|Balsalazide(DB01014)|Diclofenac(DB00586)|Diethylcarbamazine(DB00711)|Masoprocol(DB00179)|Meclofenamic acid(DB00939)|Mesalazine(DB00244)|Minocycline(DB01017)|Montelukast(DB00471)|Sulfasalazine(DB00795)|Vitamin E(DB00163)|Zileuton(DB00744)	AAACAATATCGGTGAGTTATG	0.443																																					p.R144L		Atlas-SNP	.											.	ALOX5	88	.	0			c.G431T						.						129	107	115					10																	45891384		2203	4300	6503	SO:0001630	splice_region_variant	240	exon3			AATATCGGTGAGT	J03571	CCDS7212.1, CCDS58078.1	10q11.2	2008-03-18			ENSG00000012779	ENSG00000012779	1.13.11.34	"Arachidonate lipoxygenases"	435	protein-coding gene	gene with protein product		152390				2565035	Standard	NM_001256153		Approved	5-LOX	uc001jce.4	P09917	OTTHUMG00000018081	ENST00000374391.2:c.431+1G>T	chr10.hg19:g.45891384G>T		150.0	0.0		132.0	42.0	NM_000698	B7ZLS0|E5FPY5|E5FPY7|E5FPY8|Q5JQ14	Missense_Mutation	SNP	ENST00000374391.2	hg19	CCDS7212.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.863720	0.91511	.	.	ENSG00000012779	ENST00000542434;ENST00000374391	D;D	0.90504	-2.68;-2.68	5.96	5.96	0.96718	Lipoxygenase, C-terminal (2);	0.173444	0.47852	D	0.000202	D	0.95252	0.8460	M	0.87381	2.88	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.997	P;P;P	0.62184	0.8;0.899;0.696	D	0.94819	0.7985	10	0.48119	T	0.1	-12.7091	15.9221	0.79583	0.0:0.0:1.0:0.0	.	144;144;144	B7ZLS0;E5FPY8;P09917	.;.;LOX5_HUMAN	L	144	ENSP00000437634:R144L;ENSP00000363512:R144L	ENSP00000363512:R144L	R	+	2	0	ALOX5	45211390	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	5.095000	0.64529	2.832000	0.97577	0.655000	0.94253	CGA	.	.		0.443	ALOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047780.1		Missense_Mutation	T	45891384	G	T	45891384	5	4	283	1	0	0	0	0	0	0	1	0	540	1130	39	1	441	1	ALOX5	10	45891384	Splice_Site	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	392349	45891384	89643363	126	41764										
LRRC27	80313	hgsc.bcm.edu	37	chr10	134161592	134161592	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gagctgtgaacgctcaggacCcagagggggctgtgatgaaa	16	8	1	4			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr10:134161592C>T	ENST00000368614.3	+	6	763	c.658C>T	c.(658-660)Cca>Tca	p.P220S	LRRC27_ENST00000368612.1_Missense_Mutation_p.P158S|LRRC27_ENST00000432555.2_Missense_Mutation_p.P93S|LRRC27_ENST00000368615.3_Missense_Mutation_p.P220S|LRRC27_ENST00000356571.4_3'UTR|LRRC27_ENST00000368613.4_Missense_Mutation_p.P220S|LRRC27_ENST00000368610.3_Missense_Mutation_p.P158S|LRRC27_ENST00000344079.5_Missense_Mutation_p.P220S|LRRC27_ENST00000392638.2_Missense_Mutation_p.P220S	NM_030626.2	NP_085129.1	Q9C0I9	LRC27_HUMAN	leucine rich repeat containing 27	220										breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)	18		all_cancers(35;6.28e-08)|all_epithelial(44;6.75e-06)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)|Colorectal(31;0.19)		OV - Ovarian serous cystadenocarcinoma(35;9.12e-05)|Epithelial(32;0.000116)|all cancers(32;0.000145)|BRCA - Breast invasive adenocarcinoma(275;0.218)		CGCTCAGGACCCAGAGGGGGC	0.577																																					p.P220S		Atlas-SNP	.											.	LRRC27	64	.	0			c.C658T						.						61	64	63					10																	134161592		2203	4300	6503	SO:0001583	missense	80313	exon6			CAGGACCCAGAGG	AB051461	CCDS31316.1, CCDS44496.1	10q26.3	2013-09-20			ENSG00000148814	ENSG00000148814			29346	protein-coding gene	gene with protein product						11214970	Standard	NM_030626		Approved	KIAA1674	uc010quw.1	Q9C0I9	OTTHUMG00000019284	ENST00000368614.3:c.658C>T	chr10.hg19:g.134161592C>T	ENSP00000357603:p.Pro220Ser	93.0	0.0		106.0	41.0	NM_001143757	A6NE72|A6NJB4|A6NKD3|D3DRH0|Q5SZH6|Q5SZH8|Q5SZH9|Q86XT5|Q8N7C8|Q8NA21	Missense_Mutation	SNP	ENST00000368614.3	hg19	CCDS31316.1	.	.	.	.	.	.	.	.	.	.	C	14.66	2.603052	0.46423	.	.	ENSG00000148814	ENST00000368615;ENST00000392638;ENST00000344079;ENST00000368614;ENST00000368613;ENST00000368612;ENST00000368610;ENST00000432555	T;T;T;T;T;T;T;T	0.45668	2.53;2.43;2.43;2.5;2.5;4.27;4.27;0.89	3.81	2.88	0.33553	.	1.545580	0.04074	N	0.308553	T	0.32704	0.0838	L	0.27053	0.805	0.09310	N	1	P;P;P;P;P	0.47910	0.804;0.782;0.902;0.51;0.774	B;B;B;B;B	0.42495	0.194;0.189;0.268;0.066;0.389	T	0.16394	-1.0404	10	0.10636	T	0.68	0.3322	10.0178	0.42024	0.0:0.7935:0.2065:0.0	.	220;93;158;220;220	Q9C0I9-4;B4DW88;Q9C0I9-2;Q9C0I9;Q9C0I9-3	.;.;.;LRC27_HUMAN;.	S	220;220;220;220;220;158;158;93	ENSP00000357604:P220S;ENSP00000376413:P220S;ENSP00000342641:P220S;ENSP00000357603:P220S;ENSP00000357602:P220S;ENSP00000357601:P158S;ENSP00000357599:P158S;ENSP00000407949:P93S	ENSP00000342641:P220S	P	+	1	0	LRRC27	134011582	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.268000	0.18571	0.875000	0.35847	0.655000	0.94253	CCA	.	.		0.577	LRRC27-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051058.2	XM_290462		T	134161592	C	T	134161592	3	4	283	1	0	0	0	0	1	0	0	0	8990	623	22	3	676	3	LRRC27	10	134161592	Missense_Mutation	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	88270208	134161592	1373155	127	41765										
C11orf42	160298	hgsc.bcm.edu	37	chr11	6231167	6231167	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	acctactgggtgtgctggtaAaacagtcccgcccagcccat	10	14	0	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr11:6231167A>C	ENST00000316375.2	+	2	210	c.160A>C	c.(160-162)Aaa>Caa	p.K54Q	FAM160A2_ENST00000529360.1_5'Flank	NM_173525.2	NP_775796.2	Q8N5U0	CK042_HUMAN	chromosome 11 open reading frame 42	54										endometrium(3)|kidney(3)|large_intestine(1)|lung(4)|ovary(2)|skin(1)|soft_tissue(1)	15		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.95e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGTGCTGGTAAAACAGTCCCG	0.617																																					p.K54Q		Atlas-SNP	.											.	C11orf42	35	.	0			c.A160C						.						131	106	115					11																	6231167		2201	4296	6497	SO:0001583	missense	160298	exon2			CTGGTAAAACAGT	BC031612	CCDS7759.1	11p15.4	2012-08-09			ENSG00000180878	ENSG00000180878			28541	protein-coding gene	gene with protein product						12477932	Standard	NM_173525		Approved	MGC34805	uc001mcj.3	Q8N5U0	OTTHUMG00000133377	ENST00000316375.2:c.160A>C	chr11.hg19:g.6231167A>C	ENSP00000321021:p.Lys54Gln	105.0	0.0		105.0	34.0	NM_173525		Missense_Mutation	SNP	ENST00000316375.2	hg19	CCDS7759.1	.	.	.	.	.	.	.	.	.	.	A	12.52	1.961200	0.34565	.	.	ENSG00000180878	ENST00000316375	T	0.62232	0.04	5.17	5.17	0.71159	.	0.000000	0.56097	D	0.000021	T	0.65873	0.2733	N	0.24115	0.695	0.31772	N	0.631935	D	0.76494	0.999	D	0.80764	0.994	T	0.71724	-0.4506	10	0.87932	D	0	-10.4063	11.314	0.49381	1.0:0.0:0.0:0.0	.	54	Q8N5U0	CK042_HUMAN	Q	54	ENSP00000321021:K54Q	ENSP00000321021:K54Q	K	+	1	0	C11orf42	6187743	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	4.583000	0.60964	2.168000	0.68352	0.477000	0.44152	AAA	.	.		0.617	C11orf42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257227.2	NM_173525		C	6231167	A	C	6231167	3	2	283	1	0	0	0	0	1	0	0	0	1643	15	1	5	166	5	C11orf42	11	6231167	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10		6231167	128775349	128	41766										
ZNF215	7762	hgsc.bcm.edu	37	chr11	6977459	6977459	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gaatgtgggagattcttcaaCcgacgtacaaaccttactaa	8	9	2	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr11:6977459C>A	ENST00000278319.5	+	7	1839	c.1251C>A	c.(1249-1251)aaC>aaA	p.N417K	ZNF215_ENST00000529903.1_Intron|ZNF215_ENST00000414517.2_Missense_Mutation_p.N417K	NM_013250.2	NP_037382.2	Q9UL58	ZN215_HUMAN	zinc finger protein 215	417					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(2)|skin(4)	32				Epithelial(150;6.33e-08)|BRCA - Breast invasive adenocarcinoma(625;0.134)		GATTCTTCAACCGACGTACAA	0.428																																					p.N417K		Atlas-SNP	.											.	ZNF215	72	.	0			c.C1251A						.						78	76	76					11																	6977459		2201	4296	6497	SO:0001583	missense	7762	exon7			CTTCAACCGACGT	AF056618	CCDS7775.1	11p15.4	2013-01-09			ENSG00000149054	ENSG00000149054		"Zinc fingers, C2H2-type", "-", "-", "-"	13007	protein-coding gene	gene with protein product		605016					Standard	XM_005253130		Approved	ZKSCAN11, ZSCAN43	uc001mey.3	Q9UL58	OTTHUMG00000165507	ENST00000278319.5:c.1251C>A	chr11.hg19:g.6977459C>A	ENSP00000278319:p.Asn417Lys	38.0	0.0		43.0	14.0	NM_013250	Q96C84	Missense_Mutation	SNP	ENST00000278319.5	hg19	CCDS7775.1	.	.	.	.	.	.	.	.	.	.	C	12.72	2.021184	0.35701	.	.	ENSG00000149054	ENST00000278319;ENST00000414517	T;T	0.14893	2.47;2.47	4.85	-1.48	0.08745	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.47093	D	0.000253	T	0.05640	0.0148	N	0.04669	-0.19	0.09310	N	1	B	0.29552	0.248	B	0.31245	0.126	T	0.21484	-1.0244	10	0.54805	T	0.06	-4.9298	1.5037	0.02482	0.1444:0.288:0.1408:0.4269	.	417	Q9UL58	ZN215_HUMAN	K	417	ENSP00000278319:N417K;ENSP00000393202:N417K	ENSP00000278319:N417K	N	+	3	2	ZNF215	6934035	0.000000	0.05858	0.046000	0.18839	0.579000	0.36224	-2.095000	0.01350	-0.131000	0.11578	-0.175000	0.13238	AAC	.	.		0.428	ZNF215-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384550.1			A	6977459	C	A	6977459	3	1	283	1	0	0	0	0	1	0	0	0	17786	506	18	3	1269	3	ZNF215	11	6977459	Missense_Mutation	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	746292	6977459	128029057	129	41767										
PDHX	8050	hgsc.bcm.edu	37	chr11	35006206	35006206	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gtggctgtggcaacagataaAggcttacttactccaatcat	9	9	1	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr11:35006206A>C	ENST00000227868.4	+	9	1197	c.1113A>C	c.(1111-1113)aaA>aaC	p.K371N	PDHX_ENST00000448838.3_Missense_Mutation_p.K356N|PDHX_ENST00000477173.3_3'UTR|PDHX_ENST00000430469.2_Missense_Mutation_p.K144N			O00330	ODPX_HUMAN	pyruvate dehydrogenase complex, component X	371					cellular metabolic process (GO:0044237)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	transferase activity, transferring acyl groups (GO:0016746)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)	16	all_epithelial(35;0.115)|Lung NSC(22;0.218)|all_lung(20;0.242)	all_hematologic(20;0.124)	STAD - Stomach adenocarcinoma(6;0.00113)			CAACAGATAAAGGCTTACTTA	0.403																																					p.K371N		Atlas-SNP	.											.	PDHX	40	.	0			c.A1113C						.						102	99	100					11																	35006206		2202	4298	6500	SO:0001583	missense	8050	exon9			AGATAAAGGCTTA	U82328	CCDS7896.1, CCDS44569.1, CCDS53616.1	11p13	2008-02-05			ENSG00000110435	ENSG00000110435			21350	protein-coding gene	gene with protein product		608769				9467010, 12372595	Standard	NM_003477		Approved	E3BP, proX, PDX1, OPDX, DLDBP	uc001mvt.3	O00330	OTTHUMG00000166491	ENST00000227868.4:c.1113A>C	chr11.hg19:g.35006206A>C	ENSP00000227868:p.Lys371Asn	140.0	0.0		131.0	28.0	NM_003477	B4DW62|D3DR11|E9PB14|E9PBP7|O60221|Q96FV8|Q99783	Missense_Mutation	SNP	ENST00000227868.4	hg19	CCDS7896.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	4.118|4.118	0.020021|0.020021	0.08006|0.08006	.|.	.|.	ENSG00000110435|ENSG00000110435	ENST00000448838;ENST00000227868;ENST00000430469|ENST00000526309	T;T;T|T	0.40756|0.43294	1.02;1.02;1.02|0.95	5.55|5.55	4.43|4.43	0.53597|0.53597	2-oxoacid dehydrogenase acyltransferase, catalytic domain (1);Chloramphenicol acetyltransferase-like domain (1);|.	0.469168|0.469168	0.24357|0.24357	N|N	0.039228|0.039228	T|T	0.28034|0.28034	0.0691|0.0691	N|N	0.20304|0.20304	0.555|0.555	0.43740|0.43740	D|D	0.996232|0.996232	P;B;B|.	0.35493|.	0.505;0.031;0.072|.	B;B;B|.	0.38296|.	0.27;0.11;0.043|.	T|T	0.06516|0.06516	-1.0822|-1.0822	10|8	0.25106|0.19590	T|T	0.35|0.45	-5.5828|-5.5828	6.172|6.172	0.20422|0.20422	0.7824:0.0:0.0758:0.1418|0.7824:0.0:0.0758:0.1418	.|.	144;356;371|.	E9PBP7;E9PB14;O00330|.	.;.;ODPX_HUMAN|.	N|T	356;371;144|59	ENSP00000389404:K356N;ENSP00000227868:K371N;ENSP00000415695:K144N|ENSP00000433204:K59T	ENSP00000227868:K371N|ENSP00000433204:K59T	K|K	+|+	3|2	2|0	PDHX|PDHX	34962782|34962782	1.000000|1.000000	0.71417|0.71417	0.981000|0.981000	0.43875|0.43875	0.546000|0.546000	0.35178|0.35178	2.450000|2.450000	0.44943|0.44943	0.932000|0.932000	0.37266|0.37266	-0.376000|-0.376000	0.06991|0.06991	AAA|AAG	.	.		0.403	PDHX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390017.1	NM_003477		C	35006206	A	C	35006206	3	2	283	1	0	0	0	0	1	0	0	0	11676	69	3	5	1266	5	PDHX	11	35006206	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	28028747	35006206	100000310	130	41768										
TMEM138	51524	hgsc.bcm.edu	37	chr11	61131920	61131920	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tgcagttcctgctgctgtccTatgacctctttgtcaattcc	7	13	2	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr11:61131920T>C	ENST00000278826.6	+	2	617	c.58T>C	c.(58-60)Tat>Cat	p.Y20H	TMEM138_ENST00000542946.1_Missense_Mutation_p.Y20H|CYB561A3_ENST00000426130.2_5'Flank|CYB561A3_ENST00000540317.1_5'Flank|CYB561A3_ENST00000294072.4_5'Flank|CYB561A3_ENST00000546151.1_5'Flank|TMEM138_ENST00000381787.2_5'Flank|CYB561A3_ENST00000544118.1_5'Flank|TMEM138_ENST00000540194.1_3'UTR|CYB561A3_ENST00000447532.2_5'Flank	NM_016464.4	NP_057548.1	Q9NPI0	TM138_HUMAN	transmembrane protein 138	20					cilium assembly (GO:0042384)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|vacuole (GO:0005773)				central_nervous_system(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	5						GCTGCTGTCCTATGACCTCTT	0.522																																					p.Y20H		Atlas-SNP	.											.	TMEM138	16	.	0			c.T58C						.						188	158	168					11																	61131920		2203	4299	6502	SO:0001583	missense	51524	exon2			CTGTCCTATGACC	AF151030	CCDS8005.1	11q12.2	2014-01-28			ENSG00000149483	ENSG00000149483			26944	protein-coding gene	gene with protein product		614459					Standard	NM_016464		Approved	HSPC196, JBTS16	uc001nrl.2	Q9NPI0	OTTHUMG00000168145	ENST00000278826.6:c.58T>C	chr11.hg19:g.61131920T>C	ENSP00000278826:p.Tyr20His	132.0	0.0		152.0	50.0	NM_016464	A6NGA7|B4E044|Q5JPE1	Missense_Mutation	SNP	ENST00000278826.6	hg19	CCDS8005.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.583514	0.86748	.	.	ENSG00000149483	ENST00000278826;ENST00000542946	D;T	0.88741	-2.42;-1.1	5.32	5.32	0.75619	.	0.237778	0.35585	N	0.003111	D	0.92034	0.7476	L	0.50333	1.59	0.80722	D	1	D;D;D	0.76494	0.999;0.993;0.988	D;P;P	0.67548	0.952;0.885;0.885	D	0.92136	0.5716	10	0.49607	T	0.09	-19.1299	14.9817	0.71316	0.0:0.0:0.0:1.0	.	20;20;20	B4E044;Q9NPI0-2;Q9NPI0	.;.;TM138_HUMAN	H	20	ENSP00000278826:Y20H;ENSP00000445792:Y20H	ENSP00000278826:Y20H	Y	+	1	0	TMEM138	60888496	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.705000	0.84606	2.010000	0.58986	0.460000	0.39030	TAT	.	.		0.522	TMEM138-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398399.2	NM_016464		C	61131920	T	C	61131920	3	2	283	1	0	0	0	0	1	0	0	0	16068	1522	53	2	60	2	TMEM138	11	61131920	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	26125714	61131920	73874596	131	41769										
TAF6L	10629	hgsc.bcm.edu	37	chr11	62554224	62554224	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gaccctggccgacatctaccGggagctctacgccttcttcg	10	16	3	0	rs377750789		TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr11:62554224G>C	ENST00000294168.3	+	11	1526	c.1325G>C	c.(1324-1326)cGg>cCg	p.R442P	RP11-727F15.12_ENST00000601484.1_RNA|TMEM179B_ENST00000533861.1_5'Flank|TMEM179B_ENST00000333449.4_5'Flank|TMEM223_ENST00000527073.1_Intron	NM_006473.3	NP_006464.1	Q9Y6J9	TAF6L_HUMAN	TAF6-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65kDa	442					chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|DNA-templated transcription, initiation (GO:0006352)|histone H3 acetylation (GO:0043966)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	histone deacetylase complex (GO:0000118)|STAGA complex (GO:0030914)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			endometrium(2)|large_intestine(5)|lung(4)|ovary(3)|prostate(1)|skin(1)	16						GACATCTACCGGGAGCTCTAC	0.711											OREG0021030	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R442P		Atlas-SNP	.											.	TAF6L	39	.	0			c.G1325C						.						18	21	20					11																	62554224		2201	4297	6498	SO:0001583	missense	10629	exon11			TCTACCGGGAGCT	BC008785	CCDS8035.1	11q12.3	2008-02-01	2002-08-29		ENSG00000162227	ENSG00000162227			17305	protein-coding gene	gene with protein product		602946	"TAF6-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65 kD"			9674425	Standard	NM_006473		Approved	PAF65A	uc001nvc.3	Q9Y6J9	OTTHUMG00000167610	ENST00000294168.3:c.1325G>C	chr11.hg19:g.62554224G>C	ENSP00000294168:p.Arg442Pro	47.0	0.0	1062	78.0	29.0	NM_006473	B2RAT0|Q96HA6	Missense_Mutation	SNP	ENST00000294168.3	hg19	CCDS8035.1	.	.	.	.	.	.	.	.	.	.	G	13.22	2.172347	0.38315	.	.	ENSG00000162227	ENST00000294168	T	0.47528	0.84	4.54	2.65	0.31530	.	0.417293	0.24334	N	0.039428	T	0.29850	0.0746	N	0.24115	0.695	0.80722	D	1	B	0.21147	0.052	B	0.19946	0.027	T	0.05649	-1.0872	10	0.33940	T	0.23	-3.5302	7.386	0.26882	0.2018:0.0:0.7982:0.0	.	442	Q9Y6J9	TAF6L_HUMAN	P	442	ENSP00000294168:R442P	ENSP00000294168:R442P	R	+	2	0	TAF6L	62310800	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.175000	0.42491	0.643000	0.30638	0.561000	0.74099	CGG	.	.		0.711	TAF6L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395352.1	NM_006473		C	62554224	G	C	62554224	3	2	283	1	0	0	0	0	1	0	0	0	15546	1116	39	4	1363	4	TAF6L	11	62554224	Missense_Mutation	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	1422304	62554224	72452292	132	41770										
SLC22A25	387601	hgsc.bcm.edu	37	chr11	62931493	62931493	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	taggatcatcatgagggaagCcagggctcccccaatattag	11	10	2	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr11:62931493C>A	ENST00000306494.6	-	9	1446	c.1447G>T	c.(1447-1449)Gct>Tct	p.A483S	SLC22A10_ENST00000525620.1_Intron|SLC22A10_ENST00000535888.1_Intron	NM_199352.3	NP_955384.3			solute carrier family 22, member 25											NS(2)|breast(2)|endometrium(4)|kidney(2)|large_intestine(7)|lung(7)|ovary(3)|skin(7)	34						ATGAGGGAAGCCAGGGCTCCC	0.463																																					p.A483S		Atlas-SNP	.											.	SLC22A25	87	.	0			c.G1447T						.						143	155	151					11																	62931493		2201	4298	6499	SO:0001583	missense	387601	exon9			GGGAAGCCAGGGC	AY437532	CCDS31592.1	11q12.3	2014-05-20			ENSG00000196600	ENSG00000196600		"Solute carriers"	32935	protein-coding gene	gene with protein product		610792	"MGI:2442751, MGI:2385316, MGI:3042283, MGI:3645714, MGI:3605624, MGI:2442750"			17714910	Standard	NM_199352		Approved	UST6, HIMTP, MGC120420	uc001nwr.1	Q6T423	OTTHUMG00000165340	ENST00000306494.6:c.1447G>T	chr11.hg19:g.62931493C>A	ENSP00000307443:p.Ala483Ser	295.0	0.0		286.0	97.0	NM_199352		Missense_Mutation	SNP	ENST00000306494.6	hg19	CCDS31592.1	.	.	.	.	.	.	.	.	.	.	C	12.67	2.008867	0.35415	.	.	ENSG00000196600	ENST00000306494	T	0.60299	0.2	4.56	-8.59	0.00893	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.329351	0.31041	N	0.008370	T	0.54532	0.1864	L	0.50847	1.595	0.09310	N	0.999999	P	0.40578	0.722	P	0.49012	0.598	T	0.59177	-0.7503	10	0.33141	T	0.24	.	17.4989	0.87726	0.8335:0.1665:0.0:0.0	.	483	Q6T423	S22AP_HUMAN	S	483	ENSP00000307443:A483S	ENSP00000307443:A483S	A	-	1	0	SLC22A25	62688069	0.011000	0.17503	0.000000	0.03702	0.001000	0.01503	-0.159000	0.10056	-1.918000	0.01072	-1.390000	0.01156	GCT	.	.		0.463	SLC22A25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383519.3	NM_199352		A	62931493	C	A	62931493	3	1	283	1	0	0	0	0	1	0	0	0	14469	739	26	3	200	3	SLC22A25	11	62931493	Missense_Mutation	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	377269	62931493	72075023	133	41771										
C11orf2	738	hgsc.bcm.edu	37	chr11	64877952	64877952	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	cagtacctctttttaccaccAggtggggctcctgtacgaag	10	12	1	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr11:64877952A>G	ENST00000279281.3	+	8	1970		c.e8-1		AP003068.9_ENST00000528887.1_RNA|TM7SF2_ENST00000279263.7_5'Flank|VPS51_ENST00000527646.1_Splice_Site|TM7SF2_ENST00000345348.5_5'Flank|TM7SF2_ENST00000540748.1_5'Flank	NM_013265.2	NP_037397.2	Q9UID3	VPS51_HUMAN	vacuolar protein sorting 51 homolog (S. cerevisiae)						autophagy (GO:0006914)|lipid transport (GO:0006869)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	GARP complex (GO:0000938)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)											TTTTACCACCAGGTGGGGCTC	0.597											OREG0021071	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.		Atlas-SNP	.											.	.	.	.	0			c.1879-2A>G						.						97	104	102					11																	64877952		2201	4297	6498	SO:0001630	splice_region_variant	738	exon8			ACCACCAGGTGGG	AF024631	CCDS8093.1	11q13.1	2012-07-19	2012-07-19	2012-07-19	ENSG00000149823	ENSG00000149823			1172	protein-coding gene	gene with protein product	"fat-free homolog (zebrafish)"	615738	"chromosome 11 open reading frame 3", "chromosome 11 open reading frame 2"	C11orf3, C11orf2		9286704, 20685960	Standard	NM_013265		Approved	ANG2, ANG3, FFR	uc001ocr.2	Q9UID3	OTTHUMG00000165600	ENST00000279281.3:c.1879-1A>G	chr11.hg19:g.64877952A>G		149.0	0.0	1079	148.0	59.0	NM_013265	Q6PJV5|Q7L8A6|Q8WZ35|Q96DF4|Q96GR3	Splice_Site	SNP	ENST00000279281.3	hg19	CCDS8093.1	.	.	.	.	.	.	.	.	.	.	A	16.21	3.060064	0.55432	.	.	ENSG00000149823	ENST00000279281;ENST00000526856	.	.	.	4.79	4.79	0.61399	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.5937	0.56456	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	C11orf2	64634528	1.000000	0.71417	0.999000	0.59377	0.571000	0.35966	8.770000	0.91746	2.141000	0.66446	0.402000	0.26972	.	.	.		0.597	VPS51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385217.1	NM_013265	Intron	G	64877952	A	G	64877952	5	3	283	1	0	0	0	0	0	0	1	0	1635	202	7	2	1907	2	C11orf2	11	64877952	Splice_Site	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	1946459	64877952	70128564	134	41772										
SCYL1	57410	hgsc.bcm.edu	37	chr11	65293085	65293085	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	catcttcgtctatgatgtgaAgcctggcgcggaagagcaga	13	9	2	4			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr11:65293085A>C	ENST00000270176.5	+	2	229	c.152A>C	c.(151-153)aAg>aCg	p.K51T	SCYL1_ENST00000524944.1_Missense_Mutation_p.K51T|SCYL1_ENST00000527009.1_5'UTR|SCYL1_ENST00000533862.1_Missense_Mutation_p.K51T|SCYL1_ENST00000279270.6_Missense_Mutation_p.K51T|SCYL1_ENST00000525364.1_Missense_Mutation_p.K51T|SCYL1_ENST00000420247.2_Missense_Mutation_p.K51T	NM_020680.3	NP_065731.3	Q96KG9	NTKL_HUMAN	SCY1-like 1 (S. cerevisiae)	51	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|transcription, DNA-templated (GO:0006351)	cis-Golgi network (GO:0005801)|COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|protein tyrosine kinase activity (GO:0004713)			ovary(1)|skin(1)	2						TATGATGTGAAGCCTGGCGCG	0.602																																					p.K51T		Atlas-SNP	.											.	SCYL1	76	.	0			c.A152C						.						37	42	40					11																	65293085		2020	4174	6194	SO:0001583	missense	57410	exon2			ATGTGAAGCCTGG	AF225424	CCDS41672.1, CCDS44646.1	11q11-q12	2008-07-21	2002-11-26	2002-11-29	ENSG00000142186	ENSG00000142186			14372	protein-coding gene	gene with protein product	"teratoma-associated tyrosine kinase", "telomerase transcriptional elements-interacting factor", "telomerase regulation-associated protein"	607982	"N-terminal kinase-like"	NTKL		11118629	Standard	NM_020680		Approved	HT019, P105, GKLP, NKTL, TAPK, TRAP, TEIF, MGC78454	uc001oea.1	Q96KG9	OTTHUMG00000166325	ENST00000270176.5:c.152A>C	chr11.hg19:g.65293085A>C	ENSP00000270176:p.Lys51Thr	109.0	0.0		122.0	38.0	NM_020680	A6NJF1|Q96G50|Q96KG8|Q96KH1|Q9HAW5|Q9HBL3|Q9NR53	Missense_Mutation	SNP	ENST00000270176.5	hg19	CCDS41672.1	.	.	.	.	.	.	.	.	.	.	A	14.77	2.634123	0.47049	.	.	ENSG00000142186	ENST00000270176;ENST00000525364;ENST00000420247;ENST00000533862;ENST00000527630;ENST00000349495;ENST00000279270;ENST00000524944;ENST00000417543	T;T;T;T;T;T;T	0.73789	-0.78;-0.78;-0.78;-0.78;-0.78;-0.78;-0.78	4.72	3.55	0.40652	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.348434	0.30593	N	0.009284	T	0.64594	0.2612	L	0.46567	1.45	0.30946	N	0.725326	B;P;B;B	0.36789	0.051;0.57;0.036;0.1	B;B;B;B	0.39258	0.141;0.295;0.037;0.217	T	0.65821	-0.6075	10	0.56958	D	0.05	0.1943	3.871	0.09036	0.7112:0.0:0.101:0.1878	.	51;51;51;51	E9PS17;Q96KG9-6;Q96KG9-2;Q96KG9	.;.;.;NTKL_HUMAN	T	51	ENSP00000270176:K51T;ENSP00000431635:K51T;ENSP00000408192:K51T;ENSP00000437254:K51T;ENSP00000433450:K51T;ENSP00000279270:K51T;ENSP00000432175:K51T	ENSP00000270176:K51T	K	+	2	0	SCYL1	65049661	1.000000	0.71417	0.983000	0.44433	0.987000	0.75469	3.685000	0.54678	0.596000	0.29794	0.448000	0.29417	AAG	.	.		0.602	SCYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389159.2	NM_020680		C	65293085	A	C	65293085	3	2	283	1	0	0	0	0	1	0	0	0	13962	72	3	5	158	5	SCYL1	11	65293085	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	415133	65293085	69713431	135	41773										
PC	5091	hgsc.bcm.edu	37	chr11	66618658	66618658	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	acgcctccggcacttcctgcCgcctccatgcccagcagcat	8	20	0	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr11:66618658C>G	ENST00000393958.2	-	16	2169	c.2076G>C	c.(2074-2076)gcG>gcC	p.A692A	PC_ENST00000393955.2_Silent_p.A692A|PC_ENST00000393960.1_Silent_p.A692A|PC_ENST00000529047.1_5'Flank|PC_ENST00000528224.1_5'Flank	NM_000920.3	NP_000911.2	P11498	PYC_HUMAN	pyruvate carboxylase	692	Carboxyltransferase.				biotin metabolic process (GO:0006768)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|oxaloacetate metabolic process (GO:0006107)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|pyruvate carboxylase activity (GO:0004736)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Melanoma(852;0.0525)		Lung(977;0.153)|LUSC - Lung squamous cell carcinoma(976;0.227)	Biotin(DB00121)|Pyruvic acid(DB00119)	CACTTCCTGCCGCCTCCATGC	0.587																																					p.A692A		Atlas-SNP	.											.	PC	116	.	0			c.G2076C						.						75	71	73					11																	66618658		2200	4295	6495	SO:0001819	synonymous_variant	5091	exon16			TCCTGCCGCCTCC	U04641	CCDS8152.1	11q13.4-q13.5	2012-07-11			ENSG00000173599	ENSG00000173599	6.4.1.1		8636	protein-coding gene	gene with protein product		608786				6548474	Standard	NM_022172		Approved	PCB	uc001ojn.1	P11498	OTTHUMG00000167099	ENST00000393958.2:c.2076G>C	chr11.hg19:g.66618658C>G		48.0	0.0		66.0	28.0	NM_000920	B4DN00|Q16705	Silent	SNP	ENST00000393958.2	hg19	CCDS8152.1																																																																																			.	.		0.587	PC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393115.1	NM_001040716		G	66618658	C	G	66618658	2	3	283	1	0	0	0	0	0	0	0	1	11506	639	23	4		4	PC	11	66618658	Silent	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	1325573	66618658	68387858	136	41774										
RAD9A	5883	hgsc.bcm.edu	37	chr11	67163617	67163618	+	Missense_Mutation	DNP	TC	TC	AG													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gcagagtcagcaaacttgaaTcttagcattcattttgatgc					rs185216264		TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr11:67163617_67163618TC>AG	ENST00000307980.2	+	8	798_799	c.705_706TC>AG	c.(703-708)aaTCtt>aaAGtt	p.235_236NL>KV	RAD9A_ENST00000535644.1_3'UTR|RNU6-1238P_ENST00000517215.1_RNA|PPP1CA_ENST00000532446.1_5'Flank	NM_001243224.1|NM_004584.2	NP_001230153.1|NP_004575.1	Q99638	RAD9A_HUMAN	RAD9 homolog A (S. pombe)	235					cellular response to DNA damage stimulus (GO:0006974)|cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|intra-S DNA damage checkpoint (GO:0031573)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)	checkpoint clamp complex (GO:0030896)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|enzyme binding (GO:0019899)|exodeoxyribonuclease III activity (GO:0008853)|histone deacetylase binding (GO:0042826)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)			lung(7)|upper_aerodigestive_tract(1)	8			BRCA - Breast invasive adenocarcinoma(15;8.53e-07)			CAAACTTGAATCTTAGCATTCA	0.594								Other conserved DNA damage response genes																													p.N235K|p.L236V		Atlas-SNP	.											.	RAD9A	15	.	0			c.T705A|c.C706G						.																																			SO:0001583	missense	5883	exon8			CTTGAATCTTAGC|TTGAATCTTAGCA	U53174	CCDS8159.1	11q13.1-q13.2	2008-02-05	2003-07-21	2003-07-23	ENSG00000172613	ENSG00000172613			9827	protein-coding gene	gene with protein product		603761	"RAD9 (S. pombe) homolog"	RAD9		8943031	Standard	NM_004584		Approved		uc001okr.3	Q99638	OTTHUMG00000167670	Exception_encountered	chr11.hg19:g.67163617_67163618delinsAG	ENSP00000311360:p.N235_L236delinsKV	145.0|141.0	0.0		142.0|140.0	51.0	NM_004584	B2RCZ8|Q6FI29|Q96C41	Missense_Mutation	SNP	ENST00000307980.2	hg19	CCDS8159.1																																																																																			.	.|C|1.000;T|0.000		0.594	RAD9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395481.2	NM_004584		AG	67163618	TC	AG	67163617	3	1	283	1	0	0	0	0	1	0	0	0	13010	1432	50	4	735	4	RAD9A	11	67163617	Missense_Mutation	DNP	TC	TCGA-G3-A3CK-01A-11D-A20W-10	544959	67163617	67842899	137	41775										
NUMA1	4926	hgsc.bcm.edu	37	chr11	71723462	71723628	+	Splice_Site	DEL	TCTCTGAAATACCTCTAGCTGCTCCACCTGTACATGGGGGAGGAGCAACAGAGACAGAGTGAGATGAGGCCAAAGAAGCACCAGCCCTGCTGCCAGGCTGACCTCACTGAGGCTCTGATACTTTCCCCTAAGGAGCTAGATTGACAGTAAGTTTAAAAATGCCAGTT	TCTCTGAAATACCTCTAGCTGCTCCACCTGTACATGGGGGAGGAGCAACAGAGACAGAGTGAGATGAGGCCAAAGAAGCACCAGCCCTGCTGCCAGGCTGACCTCACTGAGGCTCTGATACTTTCCCCTAAGGAGCTAGATTGACAGTAAGTTTAAAAATGCCAGTT	-													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	attacctgcttagtttgctcTctctgaaatacctctagctg					rs151297751|rs142887864|rs200067496|rs372055662|rs531160671|rs368603907|rs375081816|rs375099118	byFrequency	TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	TCTCTGAAATACCTCTAGCTGCTCCACCTGTACATGGGGGAGGAGCAACAGAGACAGAGTGAGATGAGGCCAAAGAAGCACCAGCCCTGCTGCCAGGCTGACCTCACTGAGGCTCTGATACTTTCCCCTAAGGAGCTAGATTGACAGTAAGTTTAAAAATGCCAGTT	TCTCTGAAATACCTCTAGCTGCTCCACCTGTACATGGGGGAGGAGCAACAGAGACAGAGTGAGATGAGGCCAAAGAAGCACCAGCCCTGCTGCCAGGCTGACCTCACTGAGGCTCTGATACTTTCCCCTAAGGAGCTAGATTGACAGTAAGTTTAAAAATGCCAGTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr11:71723462_71723628delTCTCTGAAATACCTCTAGCTGCTCCACCTGTACATGGGGGAGGAGCAACAGAGACAGAGTGAGATGAGGCCAAAGAAGCACCAGCCCTGCTGCCAGGCTGACCTCACTGAGGCTCTGATACTTTCCCCTAAGGAGCTAGATTGACAGTAAGTTTAAAAATGCCAGTT	ENST00000393695.3	-	16	4940_4966	c.4609_4635delAACTGGCATTTTTAAACTTACTGTCAATCTAGCTCCTTAGGGGAAAGTATCAGAGCCTCAGTGAGGTCAGCCTGGCAGCAGGGCTGGTGCTTCTTTGGCCTCATCTCACTCTGTCTCTGTTGCTCCTCCCCCATGTACAGGTGGAGCAGCTAGAGGTATTTCAGAGA	c.(4609-4635)aactggcatttttaaacttactgtcaadel	p.NWHF*TYCQ1537fs	NUMA1_ENST00000351960.6_Intron|RP11-849H4.4_ENST00000502284.1_RNA|NUMA1_ENST00000358965.6_Intron	NM_006185.2	NP_006176.2			nuclear mitotic apparatus protein 1											central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(12)|lung(20)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	65						TAGTTTGCTCTCTCTGAAATACCTCTAGCTGCTCCACCTGTACATGGGGGAGGAGCAACAGAGACAGAGTGAGATGAGGCCAAAGAAGCACCAGCCCTGCTGCCAGGCTGACCTCACTGAGGCTCTGATACTTTCCCCTAAGGAGCTAGATTGACAGTAAGTTTAAAAATGCCAGTTAGGCTGATTC	0.534			T	RARA	APL																																p.1537_1546del		Pindel	.		Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	.	NUMA1	142	.	0			c.4609_4636del						.																																			SO:0001630	splice_region_variant	4926	exon16			.	Z11584	CCDS31633.1, CCDS66156.1	11q13	2008-02-05				ENSG00000137497			8059	protein-coding gene	gene with protein product		164009				8406455	Standard	NM_006185		Approved		uc001orl.1	Q14980		ENST00000393695.3:c.4609-1AACTGGCATTTTTAAACTTACTGTCAATCTAGCTCCTTAGGGGAAAGTATCAGAGCCTCAGTGAGGTCAGCCTGGCAGCAGGGCTGGTGCTTCTTTGGCCTCATCTCACTCTGTCTCTGTTGCTCCTCCCCCATGTACAGGTGGAGCAGCTAGAGGTATTTCAGAGA>-	chr11.hg19:g.71723462_71723628delTCTCTGAAATACCTCTAGCTGCTCCACCTGTACATGGGGGAGGAGCAACAGAGACAGAGTGAGATGAGGCCAAAGAAGCACCAGCCCTGCTGCCAGGCTGACCTCACTGAGGCTCTGATACTTTCCCCTAAGGAGCTAGATTGACAGTAAGTTTAAAAATGCCAGTT		36.0	0.0		43.0	11.0	NM_006185		Frame_Shift_Del	DEL	ENST00000393695.3	hg19	CCDS31633.1																																																																																			.	.		0.534	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1		Frame_Shift_Del	-	71723628	TCTCTGAAATACCTCTAGCTGCTCCACCTGTACATGGGGGAGGAGCAACAGAGACAGAGTGAGATGAGGCCAAAGAAGCACCAGCCCTGCTGCCAGGCTGACCTCACTGAGGCTCTGATACTTTCCCCTAAGGAGCTAGATTGACAGTAAGTTTAAAAATGCCAGTT	-	71723462	8	5	283	1	0	1	0	1	0	0	1	0	10759	1548	54	0	1760	0	NUMA1	11	71723462	Splice_Site	DEL	TCTCTGAAATACCTCTAGCTGCTCCACCTGTACATGGGGGAGGAGCAACAGAGACAGAGTGAGATGAGGCCAAAGAAGCACCAGCCCTGCTGCCAGGCTGACCTCACTGAGGCTCTGATACTTTCCCCTAAGGAGCTAGATTGACAGTAAGTTTAAAAATGCCAGTT	TCGA-G3-A3CK-01A-11D-A20W-10	4559845	71723462	63283054	138	41776										
ZW10	9183	hgsc.bcm.edu	37	chr11	113619110	113619110	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	caatgggacagtagatgtttTttcattttccaggtcagtgt	10	6	2	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr11:113619110T>G	ENST00000200135.3	-	8	1102	c.958A>C	c.(958-960)Aaa>Caa	p.K320Q		NM_004724.3	NP_004715.1	O43264	ZW10_HUMAN	zw10 kinetochore protein	320					ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic metaphase plate congression (GO:0007080)|mitotic sister chromatid segregation (GO:0000070)|protein complex assembly (GO:0006461)|protein localization to kinetochore (GO:0034501)|protein transport (GO:0015031)|regulation of exit from mitosis (GO:0007096)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|nucleus (GO:0005634)|spindle pole (GO:0000922)	centromeric DNA binding (GO:0019237)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)	18		all_cancers(61;3.84e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000237)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.94e-06)|Epithelial(105;0.000103)|all cancers(92;0.000786)		GTAGATGTTTTTTCATTTTCC	0.378																																					p.K320Q		Atlas-SNP	.											.	ZW10	49	.	0			c.A958C						.						97	90	93					11																	113619110		2201	4296	6497	SO:0001583	missense	9183	exon8			ATGTTTTTTCATT	U54996	CCDS8363.1	11q23	2013-01-17	2012-12-13		ENSG00000086827	ENSG00000086827			13194	protein-coding gene	gene with protein product		603954	"ZW10 (Drosophila) homolog, centromere/kinetochore protein", "ZW10, kinetochore associated, homolog (Drosophila)"			9298984	Standard	NM_004724		Approved	KNTC1AP	uc001poe.3	O43264	OTTHUMG00000168190	ENST00000200135.3:c.958A>C	chr11.hg19:g.113619110T>G	ENSP00000200135:p.Lys320Gln	167.0	0.0		196.0	67.0	NM_004724	A1A528	Missense_Mutation	SNP	ENST00000200135.3	hg19	CCDS8363.1	.	.	.	.	.	.	.	.	.	.	T	12.18	1.859870	0.32884	.	.	ENSG00000086827	ENST00000200135	T	0.48522	0.81	5.49	5.49	0.81192	.	0.313273	0.35013	N	0.003503	T	0.42314	0.1197	L	0.57536	1.79	0.53005	D	0.999965	B	0.29136	0.234	B	0.34536	0.185	T	0.26643	-1.0097	10	0.13853	T	0.58	-8.3319	8.3543	0.32321	0.0:0.147:0.0:0.853	.	320	O43264	ZW10_HUMAN	Q	320	ENSP00000200135:K320Q	ENSP00000200135:K320Q	K	-	1	0	ZW10	113124320	1.000000	0.71417	0.663000	0.29738	0.073000	0.16967	3.217000	0.51184	2.218000	0.71995	0.533000	0.62120	AAA	.	.		0.378	ZW10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398700.1	NM_004724		G	113619110	T	G	113619110	3	3	283	1	0	0	0	0	1	0	0	0	18262	1850	64	5	1417	5	ZW10	11	113619110	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	41895648	113619110	21387406	139	41777										
ZBTB16	7704	hgsc.bcm.edu	37	chr11	114113007	114113007	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tacatctgcagtgagtgcaaCcgcaccttccccagccacac	7	17	1	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr11:114113007C>T	ENST00000335953.4	+	5	1952	c.1572C>T	c.(1570-1572)aaC>aaT	p.N524N	RP11-64D24.2_ENST00000544925.1_RNA|ZBTB16_ENST00000535379.1_3'UTR|ZBTB16_ENST00000392996.2_Silent_p.N524N	NM_006006.4	NP_005997.2	Q05516	ZBT16_HUMAN	zinc finger and BTB domain containing 16	524					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|cartilage development (GO:0051216)|central nervous system development (GO:0007417)|embryonic digit morphogenesis (GO:0042733)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic pattern specification (GO:0009880)|forelimb morphogenesis (GO:0035136)|hemopoiesis (GO:0030097)|male germ-line stem cell asymmetric division (GO:0048133)|mesonephros development (GO:0001823)|myeloid cell differentiation (GO:0030099)|negative regulation of cell proliferation (GO:0008285)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of ossification (GO:0045778)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to nucleus (GO:0034504)|protein ubiquitination (GO:0016567)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nuclear body (GO:0016604)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(2)|skin(1)|upper_aerodigestive_tract(2)	6		all_cancers(61;3.79e-18)|all_epithelial(67;2.32e-10)|all_hematologic(158;2.96e-05)|Melanoma(852;0.000362)|Acute lymphoblastic leukemia(157;0.00108)|Breast(348;0.0104)|all_neural(223;0.0294)|Prostate(24;0.0318)|Medulloblastoma(222;0.0438)		BRCA - Breast invasive adenocarcinoma(274;6.75e-06)|Epithelial(105;0.000181)|all cancers(92;0.0018)		GTGAGTGCAACCGCACCTTCC	0.632																																					p.N524N		Atlas-SNP	.											.	ZBTB16	101	.	0			c.C1572T						.						57	45	49					11																	114113007		2201	4296	6497	SO:0001819	synonymous_variant	7704	exon5			GTGCAACCGCACC	Z19002	CCDS8367.1	11q23	2013-10-17	2004-07-16	2004-07-16	ENSG00000109906	ENSG00000109906		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	12930	protein-coding gene	gene with protein product	"promyelocytic leukaemia zinc finger"	176797	"zinc finger protein 145 (Kruppel-like, expressed in promyelocytic leukemia)"	ZNF145			Standard	XM_006718899		Approved	PLZF	uc001poq.3	Q05516	OTTHUMG00000168243	ENST00000335953.4:c.1572C>T	chr11.hg19:g.114113007C>T		126.0	0.0		124.0	49.0	NM_006006	Q8TAL4	Silent	SNP	ENST00000335953.4	hg19	CCDS8367.1																																																																																			.	.		0.632	ZBTB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398940.1	NM_006006		T	114113007	C	T	114113007	2	4	283	1	0	0	0	0	0	0	0	1	17541	506	18	3		3	ZBTB16	11	114113007	Silent	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	493897	114113007	20893509	140	41778										
NOP2	4839	hgsc.bcm.edu	37	chr12	6673088	6673088	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ttcccgggccttctgcttccGagcagctctttcaatgggca	10	14	3	0	rs555886597		TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr12:6673088G>A	ENST00000322166.5	-	6	620	c.499C>T	c.(499-501)Cgg>Tgg	p.R167W	NOP2_ENST00000382421.3_Missense_Mutation_p.R200W|NOP2_ENST00000545200.1_Missense_Mutation_p.R163W|NOP2_ENST00000399466.2_Missense_Mutation_p.R163W|NOP2_ENST00000541778.1_Missense_Mutation_p.R163W|NOP2_ENST00000537442.1_Missense_Mutation_p.R167W|NOP2_ENST00000542015.1_Intron	NM_001258308.1|NM_006170.3	NP_001245237.1|NP_006161.2	P46087	NOP2_HUMAN	NOP2 nucleolar protein	167					positive regulation of cell proliferation (GO:0008284)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			breast(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	19						TTCTGCTTCCGAGCAGCTCTT	0.527											OREG0021630	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1	0.000199681	0	0.0014	5008	,	,		17442	0		0	False		,,,				2504	0				p.R200W		Atlas-SNP	.											.	NOP2	44	.	0			c.C598T						.						40	40	40					12																	6673088		1860	4107	5967	SO:0001583	missense	4839	exon7			GCTTCCGAGCAGC		CCDS44811.1, CCDS58202.1, CCDS58203.1, CCDS58204.1	12p13	2012-12-10	2012-12-10	2008-10-13	ENSG00000111641	ENSG00000111641		"NOP2/Sun domain containing"	7867	protein-coding gene	gene with protein product	"NOP2/Sun domain family, member 1"	164031	"nucleolar protein 1 (120kD)", "nucleolar protein 1, 120kDa", "nucleolar protein 2 homolog (yeast)", "NOP2 nucleolar protein homolog (yeast)"	NOL1		8088812	Standard	NM_006170		Approved	NOP120, NSUN1, p120	uc021qtz.2	P46087	OTTHUMG00000169163	ENST00000322166.5:c.499C>T	chr12.hg19:g.6673088G>A	ENSP00000313272:p.Arg167Trp	81.0	0.0	635	82.0	28.0	NM_001258309	A1A4Z3|B3KPD6|Q05BA7|Q0P5S5|Q3KQS4|Q58F30	Missense_Mutation	SNP	ENST00000322166.5	hg19	CCDS58203.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.447397	0.84101	.	.	ENSG00000111641	ENST00000537442;ENST00000382421;ENST00000545200;ENST00000399466;ENST00000322166;ENST00000541778;ENST00000542944;ENST00000542867;ENST00000536124	T;T;T;T;T;T;T;T;T	0.51071	2.43;2.33;2.45;2.43;2.43;2.43;0.86;0.8;0.72	5.83	5.83	0.93111	.	0.635618	0.16694	N	0.203439	T	0.58278	0.2111	L	0.46157	1.445	0.80722	D	1	D;D	0.71674	0.998;0.994	P;P	0.56474	0.549;0.799	T	0.55366	-0.8152	10	0.51188	T	0.08	-5.7531	16.8431	0.85973	0.0:0.0:1.0:0.0	.	200;163	Q3KQS4;P46087-2	.;.	W	167;200;163;163;167;163;43;163;167	ENSP00000444437:R167W;ENSP00000371858:R200W;ENSP00000439422:R163W;ENSP00000382392:R163W;ENSP00000313272:R167W;ENSP00000443150:R163W;ENSP00000440754:R43W;ENSP00000443035:R163W;ENSP00000442895:R167W	ENSP00000313272:R167W	R	-	1	2	NOP2	6543349	0.993000	0.37304	0.972000	0.41901	0.978000	0.69477	4.481000	0.60250	2.764000	0.94973	0.557000	0.71058	CGG	.	.		0.527	NOP2-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402614.1	NM_006170		A	6673088	G	A	6673088	3	1	283	1	0	0	0	0	1	0	0	0	10547	1057	37	1	1983	1	NOP2	12	6673088	Missense_Mutation	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10		6673088	127178807	141	41779										
A2M	2	hgsc.bcm.edu	37	chr12	9221388	9221388	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gctggtttcagatctcttacTgggacatcttgcagaaccgt	10	10	3	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr12:9221388T>C	ENST00000318602.7	-	34	4621	c.4314A>G	c.(4312-4314)ccA>ccG	p.P1438P	A2M-AS1_ENST00000499762.1_RNA	NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	1438					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|stem cell differentiation (GO:0048863)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	calcium-dependent protein binding (GO:0048306)|enzyme binding (GO:0019899)|growth factor binding (GO:0019838)|interleukin-1 binding (GO:0019966)|interleukin-8 binding (GO:0019959)|protease binding (GO:0002020)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|tumor necrosis factor binding (GO:0043120)			breast(1)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(17)|lung(30)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	77					Bacitracin(DB00626)|Becaplermin(DB00102)|Ocriplasmin(DB08888)	GATCTCTTACTGGGACATCTT	0.408																																					p.P1438P		Atlas-SNP	.											.	A2M	180	.	0			c.A4314G						.						70	68	68					12																	9221388		1878	4119	5997	SO:0001819	synonymous_variant	2	exon34			TCTTACTGGGACA	BX647329, X68728, M11313	CCDS44827.1	12p13.31	2010-02-24			ENSG00000175899	ENSG00000175899			7	protein-coding gene	gene with protein product		103950					Standard	XM_006719056		Approved	FWP007, S863-7, CPAMD5	uc001qvk.1	P01023	OTTHUMG00000150267	ENST00000318602.7:c.4314A>G	chr12.hg19:g.9221388T>C		178.0	0.0		163.0	33.0	NM_000014	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	Silent	SNP	ENST00000318602.7	hg19	CCDS44827.1																																																																																			.	.		0.408	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014		C	9221388	T	C	9221388	2	2	283	1	0	0	0	0	0	0	0	1	4	1567	55	2		2	A2M	12	9221388	Silent	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	2548300	9221388	124630507	142	41780										
ALG10B	144245	hgsc.bcm.edu	37	chr12	38714457	38714457	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	catgaagcctgtcttcatttTcctcaactattctacttttt	3	11	4	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr12:38714457T>C	ENST00000308742.4	+	3	1180	c.864T>C	c.(862-864)ttT>ttC	p.F288F	ALG10B_ENST00000551464.1_Intron|AC117372.1_ENST00000401168.2_RNA	NM_001013620.3	NP_001013642.1	Q5I7T1	AG10B_HUMAN	ALG10B, alpha-1,2-glucosyltransferase	288					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transferase activity, transferring hexosyl groups (GO:0016758)			breast(2)|kidney(3)|large_intestine(7)|lung(8)|ovary(4)|skin(1)	25	Esophageal squamous(101;0.187)	Lung NSC(34;0.204)|all_lung(34;0.235)				GTCTTCATTTTCCTCAACTAT	0.368																																					p.F288F		Atlas-SNP	.											.	ALG10B	58	.	0			c.T864C						.						136	140	139					12																	38714457		2203	4297	6500	SO:0001819	synonymous_variant	144245	exon3			TCATTTTCCTCAA	AY845858	CCDS31772.1	12q12	2013-03-04	2013-03-04		ENSG00000175548	ENSG00000175548	2.4.1.256		31088	protein-coding gene	gene with protein product	"potassium channel regulator 1", "dolichyl-P-Glc:Glc(2)Man(9)GlcNAc(2)-PP-dolichol alpha-1,2- glucosyltransferase"		"asparagine-linked glycosylation 10, alpha-1,2-glucosyltransferase homolog B (yeast)"				Standard	NM_001013620		Approved	KCR1	uc001rln.4	Q5I7T1	OTTHUMG00000169298	ENST00000308742.4:c.864T>C	chr12.hg19:g.38714457T>C		343.0	0.0		382.0	137.0	NM_001013620	B2RPF4	Silent	SNP	ENST00000308742.4	hg19	CCDS31772.1																																																																																			.	.		0.368	ALG10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403349.1	NM_001013620		C	38714457	T	C	38714457	2	2	283	1	0	0	0	0	0	0	0	1	512	1780	62	2		2	ALG10B	12	38714457	Silent	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	29493069	38714457	95137438	143	41781										
METTL7A	25840	hgsc.bcm.edu	37	chr12	51323788	51323788	+	Frame_Shift_Del	DEL	T	T	-													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	cctggatcctgcctggcaccTtctgtttgatgggtgcaacc							TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr12:51323788delT	ENST00000548553.1	+	3	1571	c.590delT	c.(589-591)cttfs	p.L198fs	METTL7A_ENST00000332160.4_Frame_Shift_Del_p.L198fs			Q9H8H3	MET7A_HUMAN	methyltransferase like 7A	198						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lipid particle (GO:0005811)|membrane (GO:0016020)	methyltransferase activity (GO:0008168)			endometrium(1)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)	10						GCCTGGCACCTTCTGTTTGAT	0.557																																					p.L197fs		Atlas-Indel,Pindel	.											.	METTL7A	19	.	0			c.589delC						.						124	121	122					12																	51323788		2203	4300	6503	SO:0001589	frameshift_variant	25840	exon2			.		CCDS8804.1	12q13.12	2013-06-20			ENSG00000185432	ENSG00000185432			24550	protein-coding gene	gene with protein product						12975309	Standard	XM_006719332		Approved	DKFZP586A0522	uc001rxb.3	Q9H8H3	OTTHUMG00000169484	ENST00000548553.1:c.590delT	chr12.hg19:g.51323788delT	ENSP00000448785:p.Leu198fs	128.0	0.0		100.0	24.0	NM_014033	Q9H7R3|Q9UHZ7|Q9Y422	Frame_Shift_Del	DEL	ENST00000548553.1	hg19	CCDS8804.1																																																																																			.	.		0.557	METTL7A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404294.2	NM_014033		-	51323788	T	-	51323788	7	5	283	1	0	1	0	1	0	0	0	0	9514	1609	56	0	596	0	METTL7A	12	51323788	Frame_Shift_Del	DEL	T	TCGA-G3-A3CK-01A-11D-A20W-10	12609331	51323788	82528107	144	41782	216	2								
METTL7A	25840	hgsc.bcm.edu	37	chr12	51323795	51323795	+	Silent	SNP	T	T	C													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	cctgcctggcaccttctgttTgatgggtgcaacctgaccag							TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr12:51323795T>C	ENST00000548553.1	+	3	1578	c.597T>C	c.(595-597)ttT>ttC	p.F199F	METTL7A_ENST00000332160.4_Silent_p.F199F			Q9H8H3	MET7A_HUMAN	methyltransferase like 7A	199						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lipid particle (GO:0005811)|membrane (GO:0016020)	methyltransferase activity (GO:0008168)			endometrium(1)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)	10						ACCTTCTGTTTGATGGGTGCA	0.562																																					p.F199F		Atlas-SNP	.											.	METTL7A	19	.	0			c.T597C						.						120	116	118					12																	51323795		2203	4300	6503	SO:0001819	synonymous_variant	25840	exon2			TCTGTTTGATGGG		CCDS8804.1	12q13.12	2013-06-20			ENSG00000185432	ENSG00000185432			24550	protein-coding gene	gene with protein product						12975309	Standard	XM_006719332		Approved	DKFZP586A0522	uc001rxb.3	Q9H8H3	OTTHUMG00000169484	ENST00000548553.1:c.597T>C	chr12.hg19:g.51323795T>C		112.0	0.0		97.0	26.0	NM_014033	Q9H7R3|Q9UHZ7|Q9Y422	Silent	SNP	ENST00000548553.1	hg19	CCDS8804.1																																																																																			.	.		0.562	METTL7A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404294.2	NM_014033		C	51323795	T	C	51323795	2	2	283	1	0	0	0	0	0	0	0	1	9514	1809	63	2		2	METTL7A	12	51323795	Silent	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	7	51323795	82528100	145	41783	216	2								
CNPY2	10330	hgsc.bcm.edu	37	chr12	56708923	56708923	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tgtgcctttacctccacagtGgagatcctggctcctccgag	10	14	0	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr12:56708923G>A	ENST00000273308.4	-	2	619	c.79C>T	c.(79-81)Cac>Tac	p.H27Y	CNPY2_ENST00000551720.1_5'UTR|RP11-977G19.11_ENST00000549860.1_RNA|PAN2_ENST00000549090.1_5'Flank|RP11-977G19.11_ENST00000549565.1_RNA|RP11-977G19.10_ENST00000549318.1_Missense_Mutation_p.H27Y	NM_014255.5	NP_055070.1	Q9Y2B0	CNPY2_HUMAN	canopy FGF signaling regulator 2	27	Saposin B-type. {ECO:0000255|PROSITE- ProRule:PRU00415}.				negative regulation of gene expression (GO:0010629)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|regulation of low-density lipoprotein particle clearance (GO:0010988)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)				large_intestine(2)|lung(2)	4						CCTCCACAGTGGAGATCCTGG	0.587																																					p.H27Y		Atlas-SNP	.											.	CNPY2	16	.	0			c.C79T						.						58	61	60					12																	56708923		2203	4300	6503	SO:0001583	missense	10330	exon2			CACAGTGGAGATC	AB015631	CCDS8914.1	12q15	2013-07-23	2013-07-23	2007-10-22		ENSG00000257727			13529	protein-coding gene	gene with protein product		605861	"transmembrane protein 4", "canopy 2 homolog (zebrafish)"	TMEM4		10072769, 15905959	Standard	NM_001190991		Approved	HP10390, ZSIG9, Cnpy2	uc001sku.2	Q9Y2B0	OTTHUMG00000170330	ENST00000273308.4:c.79C>T	chr12.hg19:g.56708923G>A	ENSP00000273308:p.His27Tyr	125.0	0.0		136.0	53.0	NM_014255	B2R7B9|Q9UHE9	Missense_Mutation	SNP	ENST00000273308.4	hg19	CCDS8914.1	.	.	.	.	.	.	.	.	.	.	G	17.17	3.322443	0.60634	.	.	ENSG00000144785;ENSG00000144785;ENSG00000144785;ENSG00000257727;ENSG00000257727	ENST00000549318;ENST00000547423;ENST00000548360;ENST00000273308;ENST00000551475	T;T;T;T;T	0.35421	1.31;1.31;1.31;1.31;1.31	5.17	5.17	0.71159	Saposin B (1);	0.107189	0.64402	D	0.000006	T	0.21307	0.0513	N	0.01576	-0.805	0.43300	D	0.995299	P;B	0.46912	0.886;0.002	P;B	0.46659	0.523;0.003	T	0.29579	-1.0007	10	0.30854	T	0.27	-20.3382	17.9755	0.89126	0.0:0.0:1.0:0.0	.	27;27	Q9Y2B0-2;Q9Y2B0	.;CNPY2_HUMAN	Y	27	ENSP00000446743:H27Y;ENSP00000446506:H27Y;ENSP00000447042:H27Y;ENSP00000273308:H27Y;ENSP00000448809:H27Y	ENSP00000273308:H27Y	H	-	1	0	RP11-977G19.10;CNPY2	54995190	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.846000	0.48262	2.865000	0.98341	0.655000	0.94253	CAC	.	.		0.587	CNPY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408546.1	NM_014255		A	56708923	G	A	56708923	3	1	283	1	0	0	0	0	1	0	0	0	3630	1348	47	3	489	3	CNPY2	12	56708923	Missense_Mutation	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	5385128	56708923	77142972	146	41784										
LRP1	4035	hgsc.bcm.edu	37	chr12	57601983	57601983	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	acgagccccacgccattgtgGtggacccactgagggggtgg	16	12	0	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr12:57601983G>A	ENST00000243077.3	+	77	12488	c.12022G>A	c.(12022-12024)Gtg>Atg	p.V4008M		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	4008					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	CGCCATTGTGGTGGACCCACT	0.667																																					p.V4008M		Atlas-SNP	.											.	LRP1	428	.	0			c.G12022A						.						39	33	35					12																	57601983		2202	4300	6502	SO:0001583	missense	4035	exon77			ATTGTGGTGGACC	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"CD molecules", "Low density lipoprotein receptors"	6692	protein-coding gene	gene with protein product		107770	"alpha-2-macroglobulin receptor"	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.12022G>A	chr12.hg19:g.57601983G>A	ENSP00000243077:p.Val4008Met	108.0	0.0		128.0	37.0	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	hg19	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	G	17.87	3.495477	0.64186	.	.	ENSG00000123384	ENST00000243077	D	0.97959	-4.63	4.19	4.19	0.49359	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.000000	0.64402	D	0.000019	D	0.98789	0.9592	M	0.89095	3.005	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99297	1.0900	10	0.62326	D	0.03	.	15.8163	0.78604	0.0:0.0:1.0:0.0	.	4008	Q07954	LRP1_HUMAN	M	4008	ENSP00000243077:V4008M	ENSP00000243077:V4008M	V	+	1	0	LRP1	55888250	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.457000	0.60088	2.325000	0.78763	0.655000	0.94253	GTG	.	.		0.667	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		A	57601983	G	A	57601983	3	1	283	1	0	0	0	0	1	0	0	0	8960	1261	44	3	12328	3	LRP1	12	57601983	Missense_Mutation	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	893060	57601983	76249912	147	41785										
MON2	23041	hgsc.bcm.edu	37	chr12	62929480	62929480	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ccaccactgcagctacacttTccaacaaatgtaagacaggc	6	14	0	1	rs201313378		TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr12:62929480T>C	ENST00000393632.2	+	14	2282	c.1891T>C	c.(1891-1893)Tcc>Ccc	p.S631P	MON2_ENST00000552115.1_Missense_Mutation_p.S631P|MON2_ENST00000546600.1_Missense_Mutation_p.S631P|MON2_ENST00000280379.6_Missense_Mutation_p.S631P|MON2_ENST00000552738.1_Intron|MON2_ENST00000393630.3_Missense_Mutation_p.S631P|MON2_ENST00000393629.2_Missense_Mutation_p.S631P	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	631					actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		AGCTACACTTTCCAACAAATG	0.388																																					p.S631P		Atlas-SNP	.											.	MON2	160	.	0			c.T1891C						.						102	98	99					12																	62929480		2203	4300	6503	SO:0001583	missense	23041	exon14			ACACTTTCCAACA		CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987			29177	protein-coding gene	gene with protein product			"MON2 homolog (yeast)"			16301316, 24285343	Standard	NM_015026		Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000393632.2:c.1891T>C	chr12.hg19:g.62929480T>C	ENSP00000377252:p.Ser631Pro	206.0	0.0		180.0	61.0	NM_015026	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Missense_Mutation	SNP	ENST00000393632.2	hg19	CCDS31849.1	.	.	.	.	.	.	.	.	.	.	T	11.36	1.615635	0.28801	.	.	ENSG00000061987	ENST00000393632;ENST00000393630;ENST00000280379;ENST00000546600;ENST00000261188;ENST00000393629;ENST00000552115	T;T;T;T;T;T	0.57907	0.38;0.37;0.38;0.38;0.38;0.39	5.35	4.17	0.49024	.	0.059325	0.64402	D	0.000001	T	0.33556	0.0867	N	0.11427	0.14	0.43662	D	0.996082	P;P;P	0.40250	0.586;0.709;0.709	B;B;B	0.39971	0.167;0.315;0.221	T	0.07424	-1.0773	9	.	.	.	-3.4905	12.5485	0.56214	0.0:0.0:0.1393:0.8607	.	631;631;631	B9EGP5;F8W1Z6;Q7Z3U7-4	.;.;.	P	631;631;631;631;559;631;631	ENSP00000377252:S631P;ENSP00000377250:S631P;ENSP00000280379:S631P;ENSP00000447407:S631P;ENSP00000377249:S631P;ENSP00000446635:S631P	.	S	+	1	0	MON2	61215747	1.000000	0.71417	0.994000	0.49952	0.353000	0.29299	2.615000	0.46368	0.928000	0.37168	0.533000	0.62120	TCC	.	T|0.999;G|0.001		0.388	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026		C	62929480	T	C	62929480	3	2	283	1	0	0	0	0	1	0	0	0	9709	1783	62	2	1945	2	MON2	12	62929480	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	5327497	62929480	70922415	148	41786										
PHLDA1	22822	hgsc.bcm.edu	37	chr12	76425350	76425350	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	agctgccgggcctctgccgtCctcttgcgagcgctcactga	12	16	3	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr12:76425350C>T	ENST00000266671.5	-	1	2362	c.172G>A	c.(172-174)Gac>Aac	p.D58N	PHLDA1_ENST00000602540.1_5'UTR|RP11-290L1.3_ENST00000552367.1_RNA|RP11-290L1.2_ENST00000547721.1_RNA			Q8WV24	PHLA1_HUMAN	pleckstrin homology-like domain, family A, member 1	58					apoptotic process (GO:0006915)|FasL biosynthetic process (GO:0045210)|forebrain neuron differentiation (GO:0021879)|positive regulation of apoptotic process (GO:0043065)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	14		Colorectal(145;0.09)				CCTCTGCCGTCCTCTTGCGAG	0.711																																					p.D58N		Atlas-SNP	.											.	PHLDA1	39	.	0			c.G172A						.						5	6	6					12																	76425350		1945	4058	6003	SO:0001583	missense	22822	exon1			TGCCGTCCTCTTG	Z50194	CCDS31861.1	12q15	2008-08-05				ENSG00000139289			8933	protein-coding gene	gene with protein product	"proline-histidine rich protein"	605335				12384558, 15037619	Standard	NM_007350		Approved	TDAG51, DT1P1B11, PHRIP	uc001sxu.3	Q8WV24		ENST00000266671.5:c.172G>A	chr12.hg19:g.76425350C>T	ENSP00000266671:p.Asp58Asn	122.0	0.0		155.0	66.0	NM_007350	A1A4G9|Q15184|Q2TAN2|Q9NZ17	Missense_Mutation	SNP	ENST00000266671.5	hg19	CCDS31861.1	.	.	.	.	.	.	.	.	.	.	C	14.56	2.573008	0.45798	.	.	ENSG00000139289	ENST00000266671	T	0.47177	0.85	4.37	2.36	0.29203	.	.	.	.	.	T	0.30541	0.0768	N	0.22421	0.69	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.23119	-1.0197	9	0.87932	D	0	.	4.6949	0.12799	0.0:0.6627:0.0:0.3373	.	58	Q8WV24	PHLA1_HUMAN	N	58	ENSP00000266671:D58N	ENSP00000266671:D58N	D	-	1	0	PHLDA1	74711617	0.000000	0.05858	0.918000	0.36340	0.766000	0.43426	-0.167000	0.09940	1.056000	0.40484	0.555000	0.69702	GAC	.	.		0.711	PHLDA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405846.2	NM_007350		T	76425350	C	T	76425350	3	4	283	1	0	0	0	0	1	0	0	0	11857	855	30	3	1037	3	PHLDA1	12	76425350	Missense_Mutation	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	13495870	76425350	57426545	149	41787										
EID3	493861	hgsc.bcm.edu	37	chr12	104698075	104698075	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	aatcagttagcattttgtgaCtttctgtttctgttcgtggg	10	6	3	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr12:104698075C>T	ENST00000527879.1	+	1	559	c.363C>T	c.(361-363)gaC>gaT	p.D121D	TXNRD1_ENST00000525566.1_Intron|TXNRD1_ENST00000526691.1_Intron|TXNRD1_ENST00000397736.2_Intron|TXNRD1_ENST00000429002.2_Intron|TXNRD1_ENST00000542918.1_Intron|TXNRD1_ENST00000388854.3_Intron|TXNRD1_ENST00000378070.4_Intron|TXNRD1_ENST00000529546.1_Intron|TXNRD1_ENST00000524698.1_Intron|TXNRD1_ENST00000526390.1_Intron|TXNRD1_ENST00000503506.2_Intron|TXNRD1_ENST00000540716.1_Intron|TXNRD1_ENST00000354940.6_Intron	NM_001008394.2	NP_001008395.1			EP300 interacting inhibitor of differentiation 3											large_intestine(5)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10						CATTTTGTGACTTTCTGTTTC	0.413																																					p.D121D		Atlas-SNP	.											.	EID3	28	.	0			c.C363T						.						212	210	211					12																	104698075		1973	4156	6129	SO:0001819	synonymous_variant	493861	exon1			TTGTGACTTTCTG	BC027612	CCDS53822.1	12q23.3	2006-11-24				ENSG00000255150			32961	protein-coding gene	gene with protein product		612986				15987788, 15752197	Standard	NM_001008394		Approved	FLJ25832, NSMCE4B, NSE4B	uc001tkw.3	Q8N140		ENST00000527879.1:c.363C>T	chr12.hg19:g.104698075C>T		218.0	0.0		251.0	80.0	NM_001008394		Silent	SNP	ENST00000527879.1	hg19	CCDS53822.1																																																																																			.	.		0.413	EID3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387034.1	NM_001008394		T	104698075	C	T	104698075	2	4	283	1	0	0	0	0	0	0	0	1	4991	564	20	3		3	EID3	12	104698075	Silent	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	28272725	104698075	29153820	150	41788										
SART3	9733	hgsc.bcm.edu	37	chr12	108932816	108932816	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gatcgccaattttcatctcaAaatcgatatatgcttgatat	5	8	2	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr12:108932816A>C	ENST00000228284.3	-	7	1190	c.956T>G	c.(955-957)tTt>tGt	p.F319C	SART3_ENST00000431469.2_Missense_Mutation_p.F319C	NM_014706.3	NP_055521.1	Q15020	SART3_HUMAN	squamous cell carcinoma antigen recognized by T cells 3	319					cell morphogenesis (GO:0000902)|hematopoietic stem cell proliferation (GO:0071425)|homeostasis of number of cells (GO:0048872)|regulation of gene expression (GO:0010468)|RNA processing (GO:0006396)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|stomach(1)	25						TTTCATCTCAAAATCGATATA	0.468									Porokeratosis																												p.F319C		Atlas-SNP	.											.	SART3	64	.	0			c.T956G						.						99	86	91					12																	108932816		2203	4300	6503	SO:0001583	missense	9733	exon7	Familial Cancer Database	incl.: Porokeratosis of Mibelli, Disseminated Superficial Actinic Porokertosis, Porokeratosis Palmaris Plantaris et Disseminata, Porokeratosis Punctata Palmaris et Plantaris, Linear Porokeratosis	ATCTCAAAATCGA	AB020880	CCDS9117.1	12q24.11	2013-02-12	2006-12-07			ENSG00000075856		"RNA binding motif (RRM) containing"	16860	protein-coding gene	gene with protein product		611684	"squamous cell carcinoma antigen recognised by T cells 3"			12032085, 15840095, 20595234	Standard	NM_014706		Approved	KIAA0156, RP11-13G14, TIP110, p110	uc001tmz.1	Q15020	OTTHUMG00000169449	ENST00000228284.3:c.956T>G	chr12.hg19:g.108932816A>C	ENSP00000228284:p.Phe319Cys	145.0	0.0		163.0	64.0	NM_014706	A8K2E4|Q2M2H0|Q58F06|Q8IUS1|Q96J95	Missense_Mutation	SNP	ENST00000228284.3	hg19	CCDS9117.1	.	.	.	.	.	.	.	.	.	.	A	27.4	4.828191	0.90955	.	.	ENSG00000075856	ENST00000228284;ENST00000431469;ENST00000412617;ENST00000546815	T;T;T	0.38887	1.11;1.11;1.11	6.06	6.06	0.98353	.	0.047341	0.85682	D	0.000000	T	0.67942	0.2947	M	0.85197	2.74	0.80722	D	1	D;D;D;D	0.76494	0.999;0.998;0.996;0.996	P;D;P;P	0.65573	0.906;0.936;0.784;0.847	T	0.73062	-0.4101	10	0.66056	D	0.02	-15.9919	16.6127	0.84892	1.0:0.0:0.0:0.0	.	267;337;319;319	E7EMI4;F8VV04;B7ZKM0;Q15020	.;.;.;SART3_HUMAN	C	319;319;267;337	ENSP00000228284:F319C;ENSP00000414453:F319C;ENSP00000449386:F337C	ENSP00000228284:F319C	F	-	2	0	SART3	107456946	1.000000	0.71417	0.976000	0.42696	0.996000	0.88848	4.498000	0.60373	2.322000	0.78497	0.528000	0.53228	TTT	.	.		0.468	SART3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404094.1			C	108932816	A	C	108932816	3	2	283	1	0	0	0	0	1	0	0	0	13862	14	1	5	1987	5	SART3	12	108932816	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	4234741	108932816	24919079	151	41789										
RXFP2	122042	hgsc.bcm.edu	37	chr13	32371491	32371491	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	cttttttatagtgttctctgAtgccatctgctggattcctg	8	9	2	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr13:32371491A>C	ENST00000298386.2	+	17	2011	c.1940A>C	c.(1939-1941)gAt>gCt	p.D647A	RXFP2_ENST00000380314.1_Missense_Mutation_p.D623A	NM_130806.3	NP_570718.1	Q8WXD0	RXFP2_HUMAN	relaxin/insulin-like family peptide receptor 2	647					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|oocyte maturation (GO:0001556)|positive regulation of cAMP biosynthetic process (GO:0030819)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	peptide hormone binding (GO:0017046)|protein-hormone receptor activity (GO:0016500)	p.D647A(1)		cervix(1)|endometrium(2)|large_intestine(15)|lung(13)|prostate(1)|stomach(1)	33		Lung SC(185;0.0262)		all cancers(112;0.000559)|Epithelial(112;0.0017)|OV - Ovarian serous cystadenocarcinoma(117;0.0145)|BRCA - Breast invasive adenocarcinoma(63;0.0535)		GTGTTCTCTGATGCCATCTGC	0.403																																					p.D647A		Atlas-SNP	.											RXFP2,colon,carcinoma,0,1	RXFP2	95	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1940C						.						221	213	216					13																	32371491		2203	4300	6503	SO:0001583	missense	122042	exon17			TCTCTGATGCCAT	AF403384	CCDS9342.1, CCDS53862.1	13q12.3	2012-08-08	2006-05-09	2006-05-09	ENSG00000133105	ENSG00000133105		"GPCR / Class A : Relaxin family peptide receptors"	17318	protein-coding gene	gene with protein product		606655	"leucine-rich repeat-containing G protein-coupled receptor 8"	LGR8		12217959, 12970298, 15956688, 16507880	Standard	NM_130806		Approved	GREAT, GPR106, INSL3R, RXFPR2	uc001utt.3	Q8WXD0	OTTHUMG00000016690	ENST00000298386.2:c.1940A>C	chr13.hg19:g.32371491A>C	ENSP00000298386:p.Asp647Ala	186.0	0.0		229.0	94.0	NM_130806	B1ALE9|Q3KU23	Missense_Mutation	SNP	ENST00000298386.2	hg19	CCDS9342.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.350196	0.82132	.	.	ENSG00000133105	ENST00000380314;ENST00000298386	T;T	0.36878	1.23;1.23	5.66	5.66	0.87406	GPCR, rhodopsin-like superfamily (1);	0.093559	0.64402	D	0.000001	T	0.64757	0.2627	M	0.88450	2.955	0.80722	D	1	D;D	0.57899	0.981;0.981	D;D	0.63192	0.912;0.912	T	0.72414	-0.4301	10	0.72032	D	0.01	.	15.8843	0.79232	1.0:0.0:0.0:0.0	.	623;647	Q3KU23;Q8WXD0	.;RXFP2_HUMAN	A	623;647	ENSP00000369670:D623A;ENSP00000298386:D647A	ENSP00000298386:D647A	D	+	2	0	RXFP2	31269491	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.753000	0.91637	2.164000	0.68074	0.533000	0.62120	GAT	.	.		0.403	RXFP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044399.1	NM_130806		C	32371491	A	C	32371491	3	2	283	1	0	0	0	0	1	0	0	0	13775	333	12	5	2006	5	RXFP2	13	32371491	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10		32371491	82798387	152	41790										
FREM2	341640	hgsc.bcm.edu	37	chr13	39263846	39263886	+	Frame_Shift_Del	DEL	CCGGGTCAAGAACTGGGCGTGGCTACTCGAGTGGCCCAGTT	CCGGGTCAAGAACTGGGCGTGGCTACTCGAGTGGCCCAGTT	-													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ataaaattgcttacagacccCcgggtcaagaactgggcgtg					rs145526450|rs369187680|rs140101984|rs377001164	byFrequency	TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	CCGGGTCAAGAACTGGGCGTGGCTACTCGAGTGGCCCAGTT	CCGGGTCAAGAACTGGGCGTGGCTACTCGAGTGGCCCAGTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr13:39263846_39263886delCCGGGTCAAGAACTGGGCGTGGCTACTCGAGTGGCCCAGTT	ENST00000280481.7	+	1	2581_2621	c.2365_2405delCCGGGTCAAGAACTGGGCGTGGCTACTCGAGTGGCCCAGTT	c.(2365-2406)ccgggtcaagaactgggcgtggctactcgagtggcccagttcfs	p.PGQELGVATRVAQF789fs		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	789					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.Q801H(1)|p.G790S(1)|p.P789P(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		TTACAGACCCCCGGGTCAAGAACTGGGCGTGGCTACTCGAGTGGCCCAGTTCCAGTTCCAG	0.552																																					p.788_802del		Atlas-Indel,Pindel	.											FREM2,caecum,carcinoma,0,1	FREM2	385	.	3	Substitution - Missense(2)|Substitution - coding silent(1)	skin(2)|endometrium(1)	c.2364_2404del						.																																			SO:0001589	frameshift_variant	341640	exon1			.	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.2365_2405delCCGGGTCAAGAACTGGGCGTGGCTACTCGAGTGGCCCAGTT	chr13.hg19:g.39263846_39263886delCCGGGTCAAGAACTGGGCGTGGCTACTCGAGTGGCCCAGTT	ENSP00000280481:p.Pro789fs	92.0	0.0		76.0	14.0	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Frame_Shift_Del	DEL	ENST00000280481.7	hg19	CCDS31960.1																																																																																			.	.		0.552	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		-	39263886	CCGGGTCAAGAACTGGGCGTGGCTACTCGAGTGGCCCAGTT	-	39263846	7	5	283	1	0	1	0	1	0	0	0	0	6053	623	22	0	2367	0	FREM2	13	39263846	Frame_Shift_Del	DEL	CCGGGTCAAGAACTGGGCGTGGCTACTCGAGTGGCCCAGTT	TCGA-G3-A3CK-01A-11D-A20W-10	6892355	39263846	75906032	153	41791										
ITM2B	9445	hgsc.bcm.edu	37	chr13	48832330	48832330	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	cctctgaacacttccattgtTatgccacccagaaacctact	4	15	1	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr13:48832330T>C	ENST00000378565.5	+	4	725	c.522T>C	c.(520-522)gtT>gtC	p.V174V	ITM2B_ENST00000378549.5_Intron	NM_021999.4	NP_068839.1	Q9Y287	ITM2B_HUMAN	integral membrane protein 2B	174	BRICHOS. {ECO:0000255|PROSITE- ProRule:PRU00255}.				extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|nervous system development (GO:0007399)	endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle membrane (GO:0030660)|integral component of organelle membrane (GO:0031301)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|beta-amyloid binding (GO:0001540)			endometrium(1)|large_intestine(2)|lung(3)	6		all_cancers(8;2.2e-31)|all_epithelial(8;6.77e-15)|all_lung(13;9.67e-07)|all_hematologic(8;9.72e-06)|Lung NSC(96;8.3e-05)|Breast(56;0.000141)|Acute lymphoblastic leukemia(8;0.00045)|Prostate(109;0.000669)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;1.97e-06)		CTTCCATTGTTATGCCACCCA	0.378																																					p.V174V		Atlas-SNP	.											.	ITM2B	24	.	0			c.T522C						.						178	164	168					13																	48832330		2203	4300	6503	SO:0001819	synonymous_variant	9445	exon4			CATTGTTATGCCA	AF092128	CCDS9409.1	13q14.2	2012-10-10			ENSG00000136156	ENSG00000136156		"BRICHOS domain containing"	6174	protein-coding gene	gene with protein product	"BRICHOS domain containing 2B"	603904				9795190	Standard	NM_021999		Approved	BRI, E25B, E3-16, BRICD2B	uc001vbz.3	Q9Y287	OTTHUMG00000016894	ENST00000378565.5:c.522T>C	chr13.hg19:g.48832330T>C		206.0	0.0		231.0	12.0	NM_021999	Q5W0A3|Q96B24|Q9NYH1	Silent	SNP	ENST00000378565.5	hg19	CCDS9409.1																																																																																			.	.		0.378	ITM2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044870.3	NM_021999		C	48832330	T	C	48832330	2	2	283	1	0	0	0	0	0	0	0	1	7922	1741	61	2		2	ITM2B	13	48832330	Silent	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	9568484	48832330	66337548	154	41792										
UBAC2	337867	hgsc.bcm.edu	37	chr13	99853763	99853763	+	Intron	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gttaggaagtcgtggcgaggGagcgcagctgtgctgctgga	19	7	0	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr13:99853763G>A	ENST00000403766.3	+	1	166				UBAC2_ENST00000376440.2_Missense_Mutation_p.G33E|UBAC2-AS1_ENST00000426037.2_lincRNA	NM_001144072.1	NP_001137544.1	Q8NBM4	UBAC2_HUMAN	UBA domain containing 2						protein localization to endoplasmic reticulum (GO:0070972)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)	10	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					CGTGGCGAGGGAGCGCAGCTG	0.498											OREG0022482	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G33E		Atlas-SNP	.											.	UBAC2	23	.	0			c.G98A						.						140	118	126					13																	99853763		2203	4300	6503	SO:0001627	intron_variant	337867	exon1			GCGAGGGAGCGCA	AK055110	CCDS9490.1, CCDS45064.1	13q32.3	2012-02-01	2007-04-20	2007-04-20	ENSG00000134882	ENSG00000134882			20486	protein-coding gene	gene with protein product			"phosphoglycerate dehydrogenase like 1"	PHGDHL1			Standard	NM_177967		Approved	FLJ30548, RP11-178C10.1	uc001voa.4	Q8NBM4	OTTHUMG00000017267	ENST00000403766.3:c.31+570G>A	chr13.hg19:g.99853763G>A		503.0	0.0	1346	501.0	166.0	NM_177967	B3KNV7|Q0VAB5|Q5W0W6|Q5W0W9|Q6GQR2|Q6P4B0|Q8N2E8|Q96NW2	Missense_Mutation	SNP	ENST00000403766.3	hg19	CCDS45064.1	.	.	.	.	.	.	.	.	.	.	g	12.25	1.881257	0.33255	.	.	ENSG00000134882	ENST00000376440	.	.	.	3.06	0.758	0.18432	.	.	.	.	.	T	0.22551	0.0544	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21690	-1.0238	6	.	.	.	.	4.478	0.11753	0.6724:0.0:0.3276:0.0	.	33	Q8NBM4-2	.	E	33	.	.	G	+	2	0	UBAC2	98651764	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	0.107000	0.15375	0.148000	0.19059	0.454000	0.30748	GGA	.	.		0.498	UBAC2-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045588.1	NM_177967		A	99853763	G	A	99853763	1	1	283	0	1	0	0	0	0	0	0	0	16850	1174	41	3		3	UBAC2	13	99853763	Intron	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	51021433	99853763	15316115	155	41793										
TNFSF13B	10673	hgsc.bcm.edu	37	chr13	108922722	108922722	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	agctccaggagaaggcaactCcagtcagaacagcagaaata	10	10	1	3			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr13:108922722C>T	ENST00000375887.4	+	2	552	c.374C>T	c.(373-375)tCc>tTc	p.S125F	TNFSF13B_ENST00000430559.1_Missense_Mutation_p.S125F|TNFSF13B_ENST00000542136.1_Missense_Mutation_p.S125F|TNFSF13B_ENST00000479435.1_3'UTR	NM_006573.4	NP_006564.1	Q9Y275	TN13B_HUMAN	tumor necrosis factor (ligand) superfamily, member 13b	125					B cell costimulation (GO:0031296)|B cell homeostasis (GO:0001782)|cell proliferation (GO:0008283)|immune response (GO:0006955)|immunoglobulin secretion (GO:0048305)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell proliferation (GO:0008284)|positive regulation of germinal center formation (GO:0002636)|positive regulation of T cell proliferation (GO:0042102)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			large_intestine(1)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	10	all_lung(23;0.000396)|all_neural(89;0.00256)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00902)|Lung SC(71;0.104)		all cancers(43;0.184)|BRCA - Breast invasive adenocarcinoma(86;0.19)		Belimumab(DB08879)	GAAGGCAACTCCAGTCAGAAC	0.463																																					p.S125F		Atlas-SNP	.											TNFSF13B,NS,malignant_melanoma,0,1	TNFSF13B	25	.	0			c.C374T						.						102	103	103					13																	108922722		2203	4300	6503	SO:0001583	missense	10673	exon2			GCAACTCCAGTCA	AF136293	CCDS9509.1, CCDS45067.1	13q32-q34	2008-05-14			ENSG00000102524	ENSG00000102524		"Tumor necrosis factor (ligand) superfamily", "CD molecules"	11929	protein-coding gene	gene with protein product		603969		TNFSF20		10331498, 10359578	Standard	NM_006573		Approved	BAFF, THANK, BLYS, TALL-1, TALL1, CD257	uc001vqr.3	Q9Y275	OTTHUMG00000017329	ENST00000375887.4:c.374C>T	chr13.hg19:g.108922722C>T	ENSP00000365048:p.Ser125Phe	97.0	0.0		93.0	33.0	NM_006573	E0ADT7|Q6FHD6|Q7Z5J2	Missense_Mutation	SNP	ENST00000375887.4	hg19	CCDS9509.1	.	.	.	.	.	.	.	.	.	.	C	6.527	0.465383	0.12402	.	.	ENSG00000102524	ENST00000430559;ENST00000375887;ENST00000542136	T;T;T	0.50813	0.73;0.73;0.73	5.17	3.45	0.39498	.	1.913480	0.01809	N	0.033334	T	0.44159	0.1280	L	0.36672	1.1	0.09310	N	0.999999	B;B	0.10296	0.003;0.001	B;B	0.11329	0.006;0.002	T	0.35500	-0.9786	10	0.66056	D	0.02	-2.8546	9.0086	0.36127	0.0:0.831:0.0:0.169	.	125;125	Q9Y275-2;Q9Y275	.;TN13B_HUMAN	F	125	ENSP00000389540:S125F;ENSP00000365048:S125F;ENSP00000445334:S125F	ENSP00000365048:S125F	S	+	2	0	TNFSF13B	107720723	0.155000	0.22806	0.575000	0.28536	0.146000	0.21551	1.164000	0.31810	0.582000	0.29556	0.655000	0.94253	TCC	.	.		0.463	TNFSF13B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045739.3			T	108922722	C	T	108922722	3	4	283	1	0	0	0	0	1	0	0	0	16321	855	30	3	380	3	TNFSF13B	13	108922722	Missense_Mutation	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	9068959	108922722	6247156	156	41794										
OR4Q3	441669	hgsc.bcm.edu	37	chr14	20215878	20215878	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	agagcatctctttttcaggaTgcctggcccagatctacttc	8	12	3	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr14:20215878T>C	ENST00000331723.1	+	1	292	c.292T>C	c.(292-294)Tgc>Cgc	p.C98R		NM_172194.1	NP_751944.1	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q, member 3	98						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(4)|endometrium(3)|kidney(2)|large_intestine(1)|lung(28)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	47	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TTTTTCAGGATGCCTGGCCCA	0.473																																					p.C98R		Atlas-SNP	.											.	OR4Q3	117	.	0			c.T292C						.						60	61	61					14																	20215878		2203	4297	6500	SO:0001583	missense	441669	exon1			TCAGGATGCCTGG	AF179768	CCDS32020.1	14p13	2012-08-09				ENSG00000182652		"GPCR / Class A : Olfactory receptors"	15426	protein-coding gene	gene with protein product				OR4Q4			Standard	NM_172194		Approved	C14orf13	uc010tkt.2	Q8NH05		ENST00000331723.1:c.292T>C	chr14.hg19:g.20215878T>C	ENSP00000330049:p.Cys98Arg	65.0	0.0		92.0	38.0	NM_172194	Q6IEX4	Missense_Mutation	SNP	ENST00000331723.1	hg19	CCDS32020.1	.	.	.	.	.	.	.	.	.	.	.	14.45	2.538683	0.45176	.	.	ENSG00000182652	ENST00000331723	T	0.00545	6.67	4.49	4.49	0.54785	GPCR, rhodopsin-like superfamily (1);	0.000000	0.43919	U	0.000514	T	0.04363	0.0120	H	0.98256	4.185	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.00409	-1.1757	10	0.87932	D	0	.	11.7648	0.51924	0.0:0.0:0.0:1.0	.	98	Q8NH05	OR4Q3_HUMAN	R	98	ENSP00000330049:C98R	ENSP00000330049:C98R	C	+	1	0	OR4Q3	19285718	1.000000	0.71417	0.998000	0.56505	0.270000	0.26580	7.648000	0.83479	1.880000	0.54463	0.416000	0.27883	TGC	.	.		0.473	OR4Q3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409818.2			C	20215878	T	C	20215878	3	2	283	1	0	0	0	0	1	0	0	0	11090	1464	51	2	294	2	OR4Q3	14	20215878	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10		20215878	87133662	157	41795										
AP1G2	8906	hgsc.bcm.edu	37	chr14	24031766	24031766	+	Frame_Shift_Del	DEL	C	C	-													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	cagcaggaggtccccatactCcccaatgcaccaggctgcca							TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr14:24031766delC	ENST00000308724.5	-	14	2202	c.1447delG	c.(1447-1449)gagfs	p.E483fs	AP1G2_ENST00000397120.3_Frame_Shift_Del_p.E483fs|AP1G2_ENST00000556277.1_5'Flank|RP11-66N24.3_ENST00000555968.1_RNA|RP11-66N24.4_ENST00000553985.1_RNA	NM_003917.2	NP_003908.1	O75843	AP1G2_HUMAN	adaptor-related protein complex 1, gamma 2 subunit	483					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	AP-1 adaptor complex (GO:0030121)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle (GO:0005798)|membrane (GO:0016020)|transport vesicle (GO:0030133)	protein transporter activity (GO:0008565)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	28	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00672)		TCCCCATACTCCCCAATGCAC	0.602											OREG0022605	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E483fs		Atlas-Indel,Pindel	.											.	AP1G2	75	.	0			c.1448delA						.						71	60	64					14																	24031766		2203	4300	6503	SO:0001589	frameshift_variant	8906	exon15			.	AB015318	CCDS9602.1	14q11.2	2008-07-03			ENSG00000213983	ENSG00000213983			556	protein-coding gene	gene with protein product		603534				9733768, 9762922	Standard	XM_005268167		Approved	G2AD	uc001wkl.2	O75843	OTTHUMG00000028760	ENST00000308724.5:c.1447delG	chr14.hg19:g.24031766delC	ENSP00000312442:p.Glu483fs	111.0	0.0	768	117.0	37.0	NM_003917	D3DS51|O75504	Frame_Shift_Del	DEL	ENST00000308724.5	hg19	CCDS9602.1																																																																																			.	.		0.602	AP1G2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071812.4	NM_003917		-	24031766	C	-	24031766	7	5	283	1	0	1	0	1	0	0	0	0	733	864	30	0	942	0	AP1G2	14	24031766	Frame_Shift_Del	DEL	C	TCGA-G3-A3CK-01A-11D-A20W-10	3815888	24031766	83317774	158	41796										
MBIP	51562	hgsc.bcm.edu	37	chr14	36785921	36785921	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gtaaatataaaatgtgttgtTcaagtgcactaaagagcaat	8	4	1	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr14:36785921T>G	ENST00000416007.4	-	2	314	c.227A>C	c.(226-228)gAa>gCa	p.E76A	MBIP_ENST00000318473.7_Missense_Mutation_p.E76A|MBIP_ENST00000359527.7_Missense_Mutation_p.E76A|MBIP_ENST00000603913.1_5'Flank	NM_001144891.1|NM_016586.2	NP_001138363.1|NP_057670.2	Q9NS73	MBIP1_HUMAN	MAP3K12 binding inhibitory protein 1	76					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|inactivation of MAPK activity involved in osmosensory signaling pathway (GO:0000173)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|protein kinase inhibitor activity (GO:0004860)			breast(2)|large_intestine(1)|lung(5)	8	all_cancers(3;1.55e-52)|all_epithelial(1;2.69e-62)|Breast(36;0.0505)|Hepatocellular(127;0.158)|Esophageal squamous(585;0.164)		Lung(8;1.28e-07)|LUAD - Lung adenocarcinoma(9;3e-07)|Epithelial(34;0.0303)|all cancers(34;0.0781)	GBM - Glioblastoma multiforme(112;0.0191)		AATGTGTTGTTCAAGTGCACT	0.368																																					p.E76A		Atlas-SNP	.											.	MBIP	25	.	0			c.A227C						.						68	68	68					14																	36785921		2203	4300	6503	SO:0001583	missense	51562	exon2			TGTTGTTCAAGTG	BC016821	CCDS9658.1, CCDS45096.1	14q13.2	2005-01-10			ENSG00000151332	ENSG00000151332			20427	protein-coding gene	gene with protein product		609431				10801814	Standard	NM_016586		Approved		uc001wtm.2	Q9NS73	OTTHUMG00000140222	ENST00000416007.4:c.227A>C	chr14.hg19:g.36785921T>G	ENSP00000399718:p.Glu76Ala	217.0	0.0		230.0	63.0	NM_016586	Q86TZ2|Q96AS5|Q9BS93|Q9NZE1	Missense_Mutation	SNP	ENST00000416007.4	hg19	CCDS9658.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.51|18.51	3.639703|3.639703	0.67244|0.67244	.|.	.|.	ENSG00000151332|ENSG00000151332	ENST00000416007;ENST00000318473;ENST00000359527;ENST00000396329;ENST00000553549;ENST00000556427|ENST00000553977	T;T;T|.	0.43688|.	0.94;0.94;0.94|.	5.17|5.17	5.17|5.17	0.71159|0.71159	.|.	0.050616|.	0.85682|.	D|.	0.000000|.	T|.	0.51736|.	0.1692|.	L|L	0.43152|0.43152	1.355|1.355	0.33315|0.33315	D|D	0.566546|0.566546	P;P;P|.	0.52316|.	0.873;0.952;0.873|.	B;B;B|.	0.43413|.	0.225;0.419;0.225|.	T|.	0.62263|.	-0.6891|.	10|.	0.66056|.	D|.	0.02|.	-15.4773|-15.4773	10.5384|10.5384	0.45018|0.45018	0.1443:0.0:0.0:0.8557|0.1443:0.0:0.0:0.8557	.|.	76;76;76|.	Q9NS73-5;Q9NS73-3;Q9NS73|.	.;.;MBIP1_HUMAN|.	A|C	76;76;76;76;55;34|72	ENSP00000399718:E76A;ENSP00000324444:E76A;ENSP00000352517:E76A|.	ENSP00000324444:E76A|.	E|X	-|-	2|3	0|0	MBIP|MBIP	35855672|35855672	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.983000|0.983000	0.72400|0.72400	5.740000|5.740000	0.68629|0.68629	2.092000|2.092000	0.63282|0.63282	0.477000|0.477000	0.44152|0.44152	GAA|TGA	.	.		0.368	MBIP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276685.2	NM_016586		G	36785921	T	G	36785921	3	3	283	1	0	0	0	0	1	0	0	0	9358	1783	62	5	839	5	MBIP	14	36785921	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	12754155	36785921	70563619	159	41797										
KIAA0586	9786	hgsc.bcm.edu	37	chr14	58895077	58895077	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ttctcaaaatcatggagatcAtttggttttgctgaaagatg	9	5	3	3			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr14:58895077A>G	ENST00000556134.1	+	2	324	c.50A>G	c.(49-51)cAt>cGt	p.H17R	RP11-517O13.1_ENST00000556734.1_RNA|KIAA0586_ENST00000354386.6_Missense_Mutation_p.H44R|TIMM9_ENST00000216463.4_5'Flank|TIMM9_ENST00000555593.1_5'Flank|TIMM9_ENST00000395159.2_5'Flank|TIMM9_ENST00000556007.2_5'Flank|KIAA0586_ENST00000261244.5_Missense_Mutation_p.H32R|KIAA0586_ENST00000423743.3_Intron|TIMM9_ENST00000555404.1_5'Flank	NM_001244190.1|NM_001244193.1	NP_001231119.1|NP_001231122.1	Q9BVV6	TALD3_HUMAN	KIAA0586	17					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|regulation of establishment of protein localization (GO:0070201)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				endometrium(4)|kidney(6)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CATGGAGATCATTTGGTTTTG	0.418																																					p.H44R		Atlas-SNP	.											.	KIAA0586	180	.	0			c.A131G						.						164	152	156					14																	58895077		2008	4187	6195	SO:0001583	missense	9786	exon2			GAGATCATTTGGT	AB011158	CCDS45115.1, CCDS58320.1, CCDS58321.1, CCDS58322.1, CCDS73639.1	14q23.1	2012-12-06			ENSG00000100578	ENSG00000100578			19960	protein-coding gene	gene with protein product		610178				16702409	Standard	NM_014749		Approved	Talpid3	uc010trr.2	Q9BVV6	OTTHUMG00000171141	ENST00000556134.1:c.50A>G	chr14.hg19:g.58895077A>G	ENSP00000452351:p.His17Arg	225.0	0.0		257.0	82.0	NM_001244189	B4DZB6|E7EWM8|J3KQH9|O60328|Q6NYC6|Q6UV20	Missense_Mutation	SNP	ENST00000556134.1	hg19	CCDS58321.1	.	.	.	.	.	.	.	.	.	.	A	7.070	0.568194	0.13560	.	.	ENSG00000100578	ENST00000354386;ENST00000556134;ENST00000261244	T;T;T	0.41065	1.01;1.03;1.03	5.08	2.7	0.31948	.	1.027060	0.07711	N	0.942010	T	0.30135	0.0755	.	.	.	0.09310	N	1	B;B;B	0.25667	0.131;0.035;0.035	B;B;B	0.23419	0.046;0.025;0.025	T	0.27839	-1.0062	9	0.41790	T	0.15	.	5.1913	0.15210	0.7271:0.1808:0.0921:0.0	.	44;32;17	E7EWM8;E9PGW8;Q9BVV6	.;.;K0586_HUMAN	R	44;17;32	ENSP00000346359:H44R;ENSP00000452351:H17R;ENSP00000261244:H32R	ENSP00000261244:H32R	H	+	2	0	KIAA0586	57964830	0.000000	0.05858	0.001000	0.08648	0.539000	0.34962	0.052000	0.14163	0.405000	0.25532	0.533000	0.62120	CAT	.	.		0.418	KIAA0586-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000411887.1	NM_014749		G	58895077	A	G	58895077	3	3	283	1	0	0	0	0	1	0	0	0	8195	217	8	2	97	2	KIAA0586	14	58895077	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	22109156	58895077	48454463	160	41798										
HSPA2	3306	hgsc.bcm.edu	37	chr14	65008467	65008467	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gtggacttctatacgtccatCacgcgcgcccgcttcgagga	11	14	2	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr14:65008467C>T	ENST00000394709.1	+	2	976	c.900C>T	c.(898-900)atC>atT	p.I300I	HSPA2_ENST00000247207.6_Silent_p.I300I|RP11-973N13.4_ENST00000554918.1_RNA			P54652	HSP72_HUMAN	heat shock 70kDa protein 2	300					male meiosis (GO:0007140)|male meiosis I (GO:0007141)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G2/M transition of mitotic cell cycle (GO:0031662)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)|spermatid development (GO:0007286)|synaptonemal complex disassembly (GO:0070194)	blood microparticle (GO:0072562)|CatSper complex (GO:0036128)|cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|glycolipid binding (GO:0051861)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	22				all cancers(60;0.00515)|OV - Ovarian serous cystadenocarcinoma(108;0.00584)|BRCA - Breast invasive adenocarcinoma(234;0.045)		ATACGTCCATCACGCGCGCCC	0.667																																					p.I300I	Pancreas(136;1211 1835 24894 31984 38227)	Atlas-SNP	.											.	HSPA2	83	.	0			c.C900T						.						20	21	20					14																	65008467		2203	4300	6503	SO:0001819	synonymous_variant	3306	exon1			GTCCATCACGCGC	L26336, BC001752	CCDS9766.1	14q23	2012-10-02	2002-08-29		ENSG00000126803	ENSG00000126803		"Heat shock proteins / HSP70"	5235	protein-coding gene	gene with protein product		140560	"heat shock 70kD protein 2"				Standard	NM_021979		Approved		uc001xhk.4	P54652	OTTHUMG00000141311	ENST00000394709.1:c.900C>T	chr14.hg19:g.65008467C>T		65.0	0.0		89.0	34.0	NM_021979	Q15508|Q53XM3|Q9UE78	Silent	SNP	ENST00000394709.1	hg19	CCDS9766.1																																																																																			.	.		0.667	HSPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280651.1			T	65008467	C	T	65008467	2	4	283	1	0	0	0	0	0	0	0	1	7420	816	29	3		3	HSPA2	14	65008467	Silent	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	6113390	65008467	42341073	161	41799										
FCF1	51077	hgsc.bcm.edu	37	chr14	75190045	75190045	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	cagaagtatcgagtggctctAaggtaggaaggaggtaaact	14	5	1	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr14:75190045A>C	ENST00000341162.4	+	5	417	c.363A>C	c.(361-363)ctA>ctC	p.L121L	FCF1_ENST00000534938.2_Silent_p.L109L|FCF1_ENST00000553615.1_Silent_p.L106L	NM_015962.4	NP_057046.1	Q9Y324	FCF1_HUMAN	FCF1 rRNA-processing protein	121	PINc.				rRNA processing (GO:0006364)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)	8				BRCA - Breast invasive adenocarcinoma(234;0.0037)		GAGTGGCTCTAAGGTAGGAAG	0.378																																					p.L121L		Atlas-SNP	.											.	FCF1	15	.	0			c.A363C						.						105	100	102					14																	75190045		2203	4300	6503	SO:0001819	synonymous_variant	51077	exon5			GGCTCTAAGGTAG	AF132969	CCDS9832.1	14q24.2	2013-05-03	2013-05-03	2007-01-30	ENSG00000119616	ENSG00000119616			20220	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 111", "FCF1 small subunit (SSU) processome component homolog (S. cerevisiae)"	C14orf111		16762320	Standard	XR_245690		Approved	CGI-35, Bka, UTP24	uc001xqh.3	Q9Y324		ENST00000341162.4:c.363A>C	chr14.hg19:g.75190045A>C		198.0	0.0		137.0	48.0	NM_015962	Q86TW8|Q8TBL8	Silent	SNP	ENST00000341162.4	hg19	CCDS9832.1																																																																																			.	.		0.378	FCF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413622.1	NM_015962		C	75190045	A	C	75190045	2	2	283	1	0	0	0	0	0	0	0	1	5785	349	13	5		5	FCF1	14	75190045	Silent	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	10181578	75190045	32159495	162	41800										
C14orf148	122945	hgsc.bcm.edu	37	chr14	77873885	77873885	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gtgtaaatttctacgcagatAttaggcagctgagacggcaa	11	7	1	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr14:77873885A>G	ENST00000380835.2	-	3	619	c.453T>C	c.(451-453)aaT>aaC	p.N151N	NOXRED1_ENST00000298358.3_Silent_p.N151N	NM_001113475.2	NP_001106946.1	Q6NXP6	NXRD1_HUMAN	NADP-dependent oxidoreductase domain containing 1	151					proline biosynthetic process (GO:0006561)		pyrroline-5-carboxylate reductase activity (GO:0004735)			NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)	9						CTACGCAGATATTAGGCAGCT	0.488																																					p.N151N		Atlas-SNP	.											.	NOXRED1	23	.	0			c.T453C						.						134	121	125					14																	77873885		2203	4300	6503	SO:0001819	synonymous_variant	122945	exon3			GCAGATATTAGGC	AK057371	CCDS45142.1	14q24.3	2011-09-30	2011-09-30	2011-09-30	ENSG00000165555	ENSG00000165555			20487	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 148"	C14orf148			Standard	NM_001113475		Approved	FLJ32809	uc001xtr.3	Q6NXP6	OTTHUMG00000171554	ENST00000380835.2:c.453T>C	chr14.hg19:g.77873885A>G		156.0	0.0		133.0	47.0	NM_001113475	B3KQ47|O95435	Silent	SNP	ENST00000380835.2	hg19	CCDS45142.1																																																																																			.	.		0.488	NOXRED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414103.1	NM_138791		G	77873885	A	G	77873885	2	3	283	1	0	0	0	0	0	0	0	1	1753	446	16	2		2	C14orf148	14	77873885	Silent	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	2683840	77873885	29475655	163	41801										
SPTLC2	9517	hgsc.bcm.edu	37	chr14	78021746	78021746	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ggccaaagtactccaccacaCcccggcctgtggggcccagg	12	17	0	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr14:78021746C>T	ENST00000216484.2	-	8	1266	c.1073G>A	c.(1072-1074)gGt>gAt	p.G358D	SPTLC2_ENST00000556264.1_5'Flank	NM_004863.3	NP_004854.1	O15270	SPTC2_HUMAN	serine palmitoyltransferase, long chain base subunit 2	358					ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphinganine biosynthetic process (GO:0046511)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|serine C-palmitoyltransferase complex (GO:0017059)	pyridoxal phosphate binding (GO:0030170)|serine C-palmitoyltransferase activity (GO:0004758)			kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(5)	19			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0346)	L-Serine(DB00133)	CTCCACCACACCCCGGCCTGT	0.517																																					p.G358D		Atlas-SNP	.											.	SPTLC2	55	.	0			c.G1073A						.						103	109	107					14																	78021746		2203	4300	6503	SO:0001583	missense	9517	exon8			ACCACACCCCGGC	AB011098	CCDS9865.1	14q24.3	2014-09-17			ENSG00000100596	ENSG00000100596	2.3.1.50		11278	protein-coding gene	gene with protein product		605713				8921873, 9363775	Standard	NM_004863		Approved	KIAA0526, LCB2, LCB2A, hLCB2a	uc001xub.3	O15270		ENST00000216484.2:c.1073G>A	chr14.hg19:g.78021746C>T	ENSP00000216484:p.Gly358Asp	164.0	0.0		127.0	46.0	NM_004863	Q16685	Missense_Mutation	SNP	ENST00000216484.2	hg19	CCDS9865.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.909563	0.92107	.	.	ENSG00000100596	ENST00000216484	D	0.96459	-4.02	4.89	4.89	0.63831	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.99162	0.9710	H	0.99682	4.7	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98556	1.0639	10	0.87932	D	0	-13.6121	18.6117	0.91288	0.0:1.0:0.0:0.0	.	358	O15270	SPTC2_HUMAN	D	358	ENSP00000216484:G358D	ENSP00000216484:G358D	G	-	2	0	SPTLC2	77091499	1.000000	0.71417	0.997000	0.53966	0.928000	0.56348	7.502000	0.81614	2.712000	0.92718	0.650000	0.86243	GGT	.	.		0.517	SPTLC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414030.1	NM_004863		T	78021746	C	T	78021746	3	4	283	1	0	0	0	0	1	0	0	0	15139	507	18	3	635	3	SPTLC2	14	78021746	Missense_Mutation	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	147861	78021746	29327794	164	41802										
RIN3	79890	hgsc.bcm.edu	37	chr14	93154522	93154523	+	Missense_Mutation	DNP	GC	GC	TT													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gacttccactttgtctaccgGcccctggacggtggtggcgg					rs554426241	byFrequency	TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr14:93154522_93154523GC>TT	ENST00000216487.7	+	10	3042_3043	c.2883_2884GC>TT	c.(2881-2886)cgGCcc>cgTTcc	p.P962S	RIN3_ENST00000418924.2_3'UTR	NM_024832.3	NP_079108.3	Q8TB24	RIN3_HUMAN	Ras and Rab interactor 3	962	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)	GTPase activator activity (GO:0005096)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(4)|kidney(2)|large_intestine(7)|lung(19)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36		all_cancers(154;0.0701)				TTGTCTACCGGCCCCTGGACGG	0.733																																					p.R961R|p.P962S		Atlas-SNP	.											.	RIN3	81	.	0			c.G2883T|c.C2884T						.																																			SO:0001583	missense	79890	exon10			CTACCGGCCCCTG|TACCGGCCCCTGG	BC025248	CCDS32144.1	14q32.13	2008-08-29				ENSG00000100599			18751	protein-coding gene	gene with protein product		610223				11733506	Standard	NM_024832		Approved	FLJ22439	uc001yap.3	Q8TB24		Exception_encountered	chr14.hg19:g.93154522_93154523delinsTT	ENSP00000216487:p.Pro962Ser	29.0	0.0		41.0|40.0	19.0	NM_024832	Q76LB3|Q8NF30|Q8TEE8|Q8WYP4|Q9H6A5|Q9HAG1	Silent|Missense_Mutation	SNP	ENST00000216487.7	hg19	CCDS32144.1																																																																																			.	.		0.733	RIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412269.1			TT	93154523	GC	TT	93154522	3	4	283	1	0	0	0	0	1	0	0	0	13388	1190	42	3	2921	3	RIN3	14	93154522	Missense_Mutation	DNP	GC	TCGA-G3-A3CK-01A-11D-A20W-10	15132776	93154522	14195018	165	41803										
PACS2	23241	hgsc.bcm.edu	37	chr14	105818768	105818768	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gtgctgccccccagtggacaAgtggagacagacctggccct	13	14	0	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr14:105818768A>C	ENST00000325438.8	+	3	765	c.261A>C	c.(259-261)caA>caC	p.Q87H	PACS2_ENST00000458164.2_Missense_Mutation_p.Q87H|PACS2_ENST00000447393.1_Missense_Mutation_p.Q87H|PACS2_ENST00000547217.1_Intron|PACS2_ENST00000430725.2_Missense_Mutation_p.Q20H			Q86VP3	PACS2_HUMAN	phosphofurin acidic cluster sorting protein 2	87					apoptotic process (GO:0006915)|autophagic vacuole assembly (GO:0000045)|protein localization to pre-autophagosomal structure (GO:0034497)|protein targeting to plasma membrane (GO:0072661)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)				endometrium(2)|kidney(2)|lung(7)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	21		all_cancers(154;0.0351)|all_epithelial(191;0.153)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.0145)|Epithelial(46;0.036)	Epithelial(152;0.138)		CCAGTGGACAAGTGGAGACAG	0.577											OREG0022968	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q87H		Atlas-SNP	.											PACS2,lower_third,carcinoma,0,2	PACS2	75	.	0			c.A261C						.						231	193	206					14																	105818768		2203	4300	6503	SO:0001583	missense	23241	exon3			TGGACAAGTGGAG	AB011174	CCDS32168.1, CCDS45178.1, CCDS45178.2, CCDS58339.1	14q32	2005-02-15	2005-02-15	2005-02-15		ENSG00000179364			23794	protein-coding gene	gene with protein product		610423	"phosphofurin acidic cluster sorting protein 1-like"	PACS1L		15692567	Standard	NM_001100913		Approved	KIAA0602	uc001yqu.3	Q86VP3	OTTHUMG00000170450	ENST00000325438.8:c.261A>C	chr14.hg19:g.105818768A>C	ENSP00000321834:p.Gln87His	212.0	0.0	1392	205.0	72.0	NM_001100913	A2VDJ9|G8JLK3|O60342|Q6P191|Q96FL7	Missense_Mutation	SNP	ENST00000325438.8	hg19	CCDS32168.1	.	.	.	.	.	.	.	.	.	.	A	8.958	0.969769	0.18659	.	.	ENSG00000179364	ENST00000430725;ENST00000325438;ENST00000458164;ENST00000447393;ENST00000546915	T;T;T;T	0.23348	1.93;1.91;1.91;1.91	4.71	0.966	0.19667	.	0.628217	0.15523	U	0.257917	T	0.08133	0.0203	N	0.02011	-0.69	0.35626	D	0.809808	B;B;B;B	0.13145	0.007;0.003;0.005;0.001	B;B;B;B	0.15052	0.009;0.012;0.006;0.002	T	0.21415	-1.0246	10	0.26408	T	0.33	-8.2172	5.0815	0.14659	0.545:0.2895:0.1654:0.0	.	87;87;87;96	E9PB38;Q86VP3-2;Q86VP3;Q86VP3-3	.;.;PACS2_HUMAN;.	H	20;87;87;87;20	ENSP00000393524:Q20H;ENSP00000321834:Q87H;ENSP00000399732:Q87H;ENSP00000393559:Q87H	ENSP00000321834:Q87H	Q	+	3	2	PACS2	104889813	0.000000	0.05858	0.999000	0.59377	0.981000	0.71138	-1.989000	0.01480	0.010000	0.14839	-0.379000	0.06801	CAA	.	.		0.577	PACS2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000409209.1	XM_377355		C	105818768	A	C	105818768	3	2	283	1	0	0	0	0	1	0	0	0	11382	69	3	5	271	5	PACS2	14	105818768	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	12664246	105818768	1530772	166	41804										
HERC2	8924	hgsc.bcm.edu	37	chr15	28482110	28482110	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	aaagcaaagattttcttactGgcacattcaatctcgacagg	7	9	3	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr15:28482110G>A	ENST00000261609.7	-	26	4110	c.4002C>T	c.(4000-4002)gcC>gcT	p.A1334A		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		TTTTCTTACTGGCACATTCAA	0.463																																					p.A1334A		Atlas-SNP	.											.	HERC2	501	.	0			c.C4002T						.						35	35	35					15																	28482110		2199	4287	6486	SO:0001630	splice_region_variant	8924	exon26			CTTACTGGCACAT	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.4003+1C>T	chr15.hg19:g.28482110G>A		300.0	0.0		306.0	107.0	NM_004667		Silent	SNP	ENST00000261609.7	hg19	CCDS10021.1																																																																																			.	.		0.463	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	Silent	A	28482110	G	A	28482110	5	1	283	1	0	0	0	0	0	0	1	0	7067	1362	47	3	10774	3	HERC2	15	28482110	Splice_Site	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10		28482110	74049282	167	41805										
TJP1	7082	hgsc.bcm.edu	37	chr15	30011153	30011153	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	agaaaactggtccgtatagcTtgaggactcgtatctgtatg	11	7	1	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr15:30011153T>C	ENST00000346128.6	-	21	3667	c.3193A>G	c.(3193-3195)Agc>Ggc	p.S1065G	TJP1_ENST00000356107.6_Missense_Mutation_p.S1065G|TJP1_ENST00000545208.2_Missense_Mutation_p.S985G|TJP1_ENST00000400011.2_Missense_Mutation_p.S989G	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	1065					apoptotic process (GO:0006915)|blastocyst formation (GO:0001825)|cell-cell junction assembly (GO:0007043)|cell-cell signaling involved in cell-cell junction organization (GO:1901350)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to glucose stimulus (GO:0071333)|hippo signaling (GO:0035329)|membrane organization (GO:0061024)|negative regulation of vascular permeability (GO:0043116)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to magnetism (GO:0071000)|sensory perception of sound (GO:0007605)	apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gap junction (GO:0005921)|intercalated disc (GO:0014704)|intercellular canaliculus (GO:0046581)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(4)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(1)	68		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)		TCCGTATAGCTTGAGGACTCG	0.463																																					p.S1065G	Melanoma(77;681 1843 6309 6570)	Atlas-SNP	.											.	TJP1	140	.	0			c.A3193G						.						312	308	310					15																	30011153		2071	4207	6278	SO:0001583	missense	7082	exon21			TATAGCTTGAGGA		CCDS42007.1, CCDS45199.1, CCDS73702.1	15q13	2012-07-12	2012-07-12		ENSG00000104067	ENSG00000104067			11827	protein-coding gene	gene with protein product	"zona occludens 1", "tight junction protein ZO-1"	601009				8825647	Standard	XM_005254616		Approved	ZO-1, MGC133289, DKFZp686M05161	uc001zcr.3	Q07157	OTTHUMG00000137397	ENST00000346128.6:c.3193A>G	chr15.hg19:g.30011153T>C	ENSP00000281537:p.Ser1065Gly	424.0	1.0		355.0	103.0	NM_003257	B4E3K1|Q2NKP3|Q4ZGJ6	Missense_Mutation	SNP	ENST00000346128.6	hg19	CCDS42007.1	.	.	.	.	.	.	.	.	.	.	T	0.176	-1.066831	0.01934	.	.	ENSG00000104067	ENST00000346128;ENST00000400011;ENST00000545208;ENST00000400007;ENST00000356107	T;T	0.05081	3.5;3.62	5.93	-0.31	0.12765	.	0.588912	0.21894	N	0.067548	T	0.03783	0.0107	N	0.25144	0.715	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.46884	-0.9159	10	0.10902	T	0.67	.	10.4411	0.44466	0.0:0.4047:0.0:0.5953	.	1058;985;1065;989	A9CQZ8;Q07157-2;Q07157;G5E9E7	.;.;ZO1_HUMAN;.	G	1065;989;1065;985;985	ENSP00000281537:S1065G;ENSP00000382890:S989G	ENSP00000281537:S1065G	S	-	1	0	TJP1	27798445	0.003000	0.15002	0.002000	0.10522	0.697000	0.40408	0.153000	0.16323	-0.077000	0.12752	0.460000	0.39030	AGC	.	.		0.463	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257		C	30011153	T	C	30011153	3	2	283	1	0	0	0	0	1	0	0	0	15944	1609	56	2	2085	2	TJP1	15	30011153	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	1529043	30011153	72520239	168	41806										
HERC1	8925	hgsc.bcm.edu	37	chr15	63943568	63943568	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gtgatcccaggctttcctcaGcatccccttccctagaatat	6	15	1	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr15:63943568G>A	ENST00000443617.2	-	53	10517	c.10430C>T	c.(10429-10431)gCt>gTt	p.A3477V		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	3477					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						GCTTTCCTCAGCATCCCCTTC	0.408																																					p.A3477V		Atlas-SNP	.											.	HERC1	624	.	0			c.C10430T						.						95	93	93					15																	63943568		1827	4083	5910	SO:0001583	missense	8925	exon53			TCCTCAGCATCCC	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.10430C>T	chr15.hg19:g.63943568G>A	ENSP00000390158:p.Ala3477Val	90.0	0.0		75.0	32.0	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	hg19	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	G	17.08	3.298859	0.60195	.	.	ENSG00000103657	ENST00000443617	T	0.24538	1.85	5.43	5.43	0.79202	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.378828	0.24031	N	0.042191	T	0.17874	0.0429	N	0.08118	0	0.31525	N	0.661906	B	0.15141	0.012	B	0.14023	0.01	T	0.12091	-1.0561	10	0.72032	D	0.01	.	19.258	0.93955	0.0:0.0:1.0:0.0	.	3477	Q15751	HERC1_HUMAN	V	3477	ENSP00000390158:A3477V	ENSP00000390158:A3477V	A	-	2	0	HERC1	61730621	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.476000	0.66793	2.554000	0.86153	0.655000	0.94253	GCT	.	.		0.408	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		A	63943568	G	A	63943568	3	1	283	1	0	0	0	0	1	0	0	0	7066	971	34	3	4259	3	HERC1	15	63943568	Missense_Mutation	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	33932415	63943568	38587824	169	41807										
HERC1	8925	hgsc.bcm.edu	37	chr15	63967194	63967194	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	cttcatgaacgccagtgagaTatgttaggtccagcagcaca	10	10	1	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr15:63967194T>A	ENST00000443617.2	-	38	7280	c.7193A>T	c.(7192-7194)tAt>tTt	p.Y2398F	RP11-317G6.1_ENST00000559303.2_RNA	NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	2398					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						GCCAGTGAGATATGTTAGGTC	0.488																																					p.Y2398F		Atlas-SNP	.											.	HERC1	624	.	0			c.A7193T						.						134	127	129					15																	63967194		2048	4207	6255	SO:0001583	missense	8925	exon38			GTGAGATATGTTA	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.7193A>T	chr15.hg19:g.63967194T>A	ENSP00000390158:p.Tyr2398Phe	317.0	0.0		260.0	83.0	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	hg19	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	T	14.78	2.637144	0.47049	.	.	ENSG00000103657	ENST00000443617	T	0.24151	1.87	5.51	5.51	0.81932	.	0.000000	0.64402	D	0.000001	T	0.19485	0.0468	L	0.29908	0.895	0.38422	D	0.94621	B	0.02656	0.0	B	0.04013	0.001	T	0.05801	-1.0863	10	0.40728	T	0.16	.	11.3945	0.49834	0.1353:0.0:0.0:0.8646	.	2398	Q15751	HERC1_HUMAN	F	2398	ENSP00000390158:Y2398F	ENSP00000390158:Y2398F	Y	-	2	0	HERC1	61754247	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.367000	0.52350	2.092000	0.63282	0.528000	0.53228	TAT	.	.		0.488	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		A	63967194	T	A	63967194	3	1	283	1	0	0	0	0	1	0	0	0	7066	1406	49	4	7556	4	HERC1	15	63967194	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	23626	63967194	38564198	170	41808										
PSMA4	5685	hgsc.bcm.edu	37	chr15	78837279	78837279	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	agcgctgtgtgatatcaaacAagcttatacacaatttggag	9	7	1	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr15:78837279A>T	ENST00000044462.7	+	6	506	c.356A>T	c.(355-357)cAa>cTa	p.Q119L	PSMA4_ENST00000413382.2_Missense_Mutation_p.Q48L|PSMA4_ENST00000559082.1_Missense_Mutation_p.Q119L|PSMA4_ENST00000557929.1_3'UTR|PSMA4_ENST00000558281.1_Missense_Mutation_p.Q119L|PSMA4_ENST00000560217.1_Missense_Mutation_p.Q88L|PSMA4_ENST00000558094.1_Missense_Mutation_p.Q31L|PSMA4_ENST00000558341.1_Intron	NM_002789.4	NP_002780.1	P25789	PSA4_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 4	119					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|proteasome core complex, alpha-subunit complex (GO:0019773)	threonine-type endopeptidase activity (GO:0004298)			kidney(2)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9						GATATCAAACAAGCTTATACA	0.313																																					p.Q119L		Atlas-SNP	.											.	PSMA4	17	.	0			c.A356T						.						86	84	85					15																	78837279		2196	4293	6489	SO:0001583	missense	5685	exon6			TCAAACAAGCTTA	BC005361	CCDS10303.1, CCDS45319.1	15q24.1	2004-01-19			ENSG00000041357	ENSG00000041357		"Proteasome (prosome, macropain) subunits"	9533	protein-coding gene	gene with protein product		176846				2025653	Standard	NM_002789		Approved	HC9, HsT17706	uc010blf.3	P25789	OTTHUMG00000143859	ENST00000044462.7:c.356A>T	chr15.hg19:g.78837279A>T	ENSP00000044462:p.Gln119Leu	93.0	0.0		73.0	23.0	NM_001102667	D3DW86|Q53XP2|Q567Q5|Q8TBD1	Missense_Mutation	SNP	ENST00000044462.7	hg19	CCDS10303.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.683284	0.88542	.	.	ENSG00000041357	ENST00000413382;ENST00000044462	T;T	0.24908	1.83;1.83	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.53883	0.1824	M	0.78223	2.4	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.58595	-0.7609	10	0.87932	D	0	-23.0772	16.1699	0.81801	1.0:0.0:0.0:0.0	.	119	P25789	PSA4_HUMAN	L	48;119	ENSP00000402118:Q48L;ENSP00000044462:Q119L	ENSP00000044462:Q119L	Q	+	2	0	PSMA4	76624334	1.000000	0.71417	1.000000	0.80357	0.627000	0.37826	9.072000	0.93986	2.217000	0.71921	0.533000	0.62120	CAA	.	.		0.313	PSMA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290107.5	NM_002789		T	78837279	A	T	78837279	3	4	283	1	0	0	0	0	1	0	0	0	12681	130	5	4	374	4	PSMA4	15	78837279	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	14870085	78837279	23694113	171	41809										
CIB1	10519	hgsc.bcm.edu	37	chr15	90773726	90773726	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ggggctgctgtcacaggacaAtcttaaaggagctgaacaag	13	8	2	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr15:90773726A>C	ENST00000328649.6	-	7	727	c.566T>G	c.(565-567)aTt>aGt	p.I189S		NM_006384.3	NP_006375.2	Q99828	CIB1_HUMAN	calcium and integrin binding 1 (calmyrin)	189					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell division (GO:0051301)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to growth factor stimulus (GO:0071363)|cellular response to nerve growth factor stimulus (GO:1990090)|cellular response to tumor necrosis factor (GO:0071356)|cytoplasmic microtubule organization (GO:0031122)|double-strand break repair (GO:0006302)|endomitotic cell cycle (GO:0007113)|extrinsic apoptotic signaling pathway (GO:0097191)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of megakaryocyte differentiation (GO:0045653)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of neuron projection development (GO:0010977)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|platelet formation (GO:0030220)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of male germ cell proliferation (GO:2000256)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of cell division (GO:0051302)|regulation of cell proliferation (GO:0042127)|response to ischemia (GO:0002931)|spermatid development (GO:0007286)|thrombopoietin-mediated signaling pathway (GO:0038163)	cell periphery (GO:0071944)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|protein anchor (GO:0043495)|Ras GTPase binding (GO:0017016)			lung(1)|prostate(1)	2	Melanoma(11;0.00551)|Lung NSC(78;0.0141)|all_lung(78;0.0303)		BRCA - Breast invasive adenocarcinoma(143;0.00269)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.217)			TCACAGGACAATCTTAAAGGA	0.557																																					p.I189S		Atlas-SNP	.											.	CIB1	8	.	0			c.T566G						.						68	64	66					15																	90773726		1819	3413	5232	SO:0001583	missense	10519	exon7			AGGACAATCTTAA	U82226	CCDS10360.1, CCDS73781.1	15q25.3-q26	2013-01-10			ENSG00000185043	ENSG00000185043		"EF-hand domain containing"	16920	protein-coding gene	gene with protein product		602293				9030514, 10826701	Standard	NM_006384		Approved	SIP2-28, CALMYRIN, CIB, KIP	uc031qtq.1	Q99828	OTTHUMG00000149808	ENST00000328649.6:c.566T>G	chr15.hg19:g.90773726A>C	ENSP00000333873:p.Ile189Ser	178.0	0.0		166.0	56.0	NM_006384	B5BU40|H6WJF3|O00693|O00735|Q6IB49|Q96J54|Q99971	Missense_Mutation	SNP	ENST00000328649.6	hg19	CCDS10360.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.499885	0.85176	.	.	ENSG00000185043	ENST00000328649	T	0.09911	2.93	5.67	5.67	0.87782	EF-hand-like domain (1);	0.049490	0.85682	D	0.000000	T	0.34221	0.0890	M	0.75615	2.305	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	T	0.07046	-1.0793	10	0.87932	D	0	-9.9203	15.1051	0.72315	1.0:0.0:0.0:0.0	.	189	Q99828	CIB1_HUMAN	S	189	ENSP00000333873:I189S	ENSP00000333873:I189S	I	-	2	0	CIB1	88574730	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.762000	0.55250	2.163000	0.67991	0.459000	0.35465	ATT	.	.		0.557	CIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313419.1			C	90773726	A	C	90773726	3	2	283	1	0	0	0	0	1	0	0	0	3422	101	4	5	13	5	CIB1	15	90773726	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	11936447	90773726	11757666	172	41810										
RAB40C	57799	hgsc.bcm.edu	37	chr16	677600	677600	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ccccccccagaactgctcgcGgagtaactgcaagatctcct	8	17	1	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr16:677600G>C	ENST00000248139.3	+	6	1027	c.824G>C	c.(823-825)cGg>cCg	p.R275P	RAB40C_ENST00000538492.1_Missense_Mutation_p.R275P|RAB40C_ENST00000539661.1_Missense_Mutation_p.R275P|RAB40C_ENST00000535977.1_Missense_Mutation_p.R275P	NM_021168.4	NP_066991.3	Q96S21	RB40C_HUMAN	RAB40C, member RAS oncogene family	275					protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)			NS(1)|endometrium(2)|large_intestine(1)|lung(1)|prostate(1)	6		Hepatocellular(780;0.0218)				AACTGCTCGCGGAGTAACTGC	0.697																																					p.R275P	Melanoma(123;1631 1690 28262 44104 44957)	Atlas-SNP	.											.	RAB40C	32	.	0			c.G824C						.						51	54	53					16																	677600		2201	4300	6501	SO:0001583	missense	57799	exon6			GCTCGCGGAGTAA	Z84779	CCDS10413.1	16p13.3	2008-07-28	2003-10-14		ENSG00000197562	ENSG00000197562		"RAB, member RAS oncogene"	18285	protein-coding gene	gene with protein product			"RAS-like, family 8, member C"	RASL8C		11697911, 18485483	Standard	NM_021168		Approved	RARL	uc021szv.1	Q96S21	OTTHUMG00000047854	ENST00000248139.3:c.824G>C	chr16.hg19:g.677600G>C	ENSP00000248139:p.Arg275Pro	90.0	0.0		81.0	24.0	NM_021168	A2IDE2|D3DU54|O60795|Q4TT41|Q5PXE8|Q6PIU5	Missense_Mutation	SNP	ENST00000248139.3	hg19	CCDS10413.1	.	.	.	.	.	.	.	.	.	.	G	10.51	1.371574	0.24771	.	.	ENSG00000197562	ENST00000535977;ENST00000539661;ENST00000538492;ENST00000248139	T;T;T;T	0.71341	-0.56;-0.56;-0.56;-0.56	4.85	4.85	0.62838	.	0.061993	0.64402	D	0.000013	T	0.65903	0.2736	L	0.36672	1.1	0.24015	N	0.99616	P;P	0.41041	0.736;0.586	B;B	0.41412	0.356;0.182	T	0.65409	-0.6175	10	0.87932	D	0	.	16.9555	0.86258	0.0:0.0:1.0:0.0	.	275;256	Q96S21;Q5PXE8	RB40C_HUMAN;.	P	275	ENSP00000438492:R275P;ENSP00000445050:R275P;ENSP00000438382:R275P;ENSP00000248139:R275P	ENSP00000248139:R275P	R	+	2	0	RAB40C	617601	0.711000	0.27906	0.053000	0.19242	0.839000	0.47603	4.008000	0.57103	2.228000	0.72767	0.561000	0.74099	CGG	.	.		0.697	RAB40C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109079.4	NM_021168		C	677600	G	C	677600	3	2	283	1	0	0	0	0	1	0	0	0	12957	1116	39	4	846	4	RAB40C	16	677600	Missense_Mutation	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10		677600	89677153	173	41811										
PKD1	5310	hgsc.bcm.edu	37	chr16	2140513	2140513	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ggactcggcaggacacagggTagagagcccagtcccagggc	16	12	0	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr16:2140513T>C	ENST00000262304.4	-	45	12425	c.12217A>G	c.(12217-12219)Acc>Gcc	p.T4073A	MIR1225_ENST00000408729.1_RNA|RP11-304L19.1_ENST00000570072.1_RNA|PKD1_ENST00000423118.1_Missense_Mutation_p.T4072A	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	4073					anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						GGACACAGGGTAGAGAGCCCA	0.667																																					p.T4073A		Atlas-SNP	.											.	PKD1	184	.	0			c.A12217G						.						26	29	28					16																	2140513		2182	4287	6469	SO:0001583	missense	5310	exon45			ACAGGGTAGAGAG	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"Voltage-gated ion channels / Transient receptor potential cation channels"	9008	protein-coding gene	gene with protein product	"polycystin 1", "transient receptor potential cation channel, subfamily P, member 1"	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.12217A>G	chr16.hg19:g.2140513T>C	ENSP00000262304:p.Thr4073Ala	52.0	0.0		76.0	28.0	NM_001009944	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	hg19	CCDS32369.1	.	.	.	.	.	.	.	.	.	.	t	7.338	0.620302	0.14193	.	.	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101	T;T	0.70986	-0.53;-0.53	4.27	-2.42	0.06542	Polycystin cation channel, PKD1/PKD2 (1);	0.571256	0.16534	N	0.210241	T	0.29389	0.0732	N	0.01267	-0.92	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.09377	0.002;0.004	T	0.36553	-0.9743	10	0.07482	T	0.82	.	4.277	0.10813	0.1093:0.5499:0.1216:0.2192	.	4072;4073	P98161-3;P98161	.;PKD1_HUMAN	A	4073;4072;3407	ENSP00000262304:T4073A;ENSP00000399501:T4072A	ENSP00000262304:T4073A	T	-	1	0	PKD1	2080514	0.000000	0.05858	0.051000	0.19133	0.008000	0.06430	0.060000	0.14342	-0.235000	0.09767	0.255000	0.18592	ACC	.	.		0.667	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			C	2140513	T	C	2140513	3	2	283	1	0	0	0	0	1	0	0	0	11972	1638	57	2	702	2	PKD1	16	2140513	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	1462913	2140513	88214240	174	41812										
GRIN2A	2903	hgsc.bcm.edu	37	chr16	10273990	10273990	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	aacacgaggccgtggatgcgTgccccggacatgaggtcgca	15	12	0	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr16:10273990T>C	ENST00000396573.2	-	3	588	c.279A>G	c.(277-279)gcA>gcG	p.A93A	GRIN2A_ENST00000330684.3_Silent_p.A93A|GRIN2A_ENST00000404927.2_Silent_p.A93A|GRIN2A_ENST00000562109.1_Silent_p.A93A|GRIN2A_ENST00000396575.2_Silent_p.A93A	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	93					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CGTGGATGCGTGCCCCGGACA	0.637																																					p.A93A		Atlas-SNP	.											.	GRIN2A	366	.	0			c.A279G						.						98	93	94					16																	10273990		2197	4300	6497	SO:0001819	synonymous_variant	2903	exon3			GATGCGTGCCCCG		CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.279A>G	chr16.hg19:g.10273990T>C		170.0	0.0		178.0	35.0	NM_000833	O00669|Q17RZ6	Silent	SNP	ENST00000396573.2	hg19	CCDS10539.1																																																																																			.	.		0.637	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			C	10273990	T	C	10273990	2	2	283	1	0	0	0	0	0	0	0	1	6788	1683	59	2		2	GRIN2A	16	10273990	Silent	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	8133477	10273990	80080763	175	41813										
LITAF	9516	hgsc.bcm.edu	37	chr16	11647418	11647418	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	cacaggctcccgcaggacagCcaggtcagagcaccggcgtt	13	15	1	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr16:11647418C>A	ENST00000571688.1	-	3	578	c.348G>T	c.(346-348)tgG>tgT	p.W116C	LITAF_ENST00000571459.1_Intron|LITAF_ENST00000571976.1_Missense_Mutation_p.W116C|LITAF_ENST00000576036.1_Missense_Mutation_p.W116C|LITAF_ENST00000381810.3_Missense_Mutation_p.W116C|LITAF_ENST00000570904.1_Missense_Mutation_p.W116C|LITAF_ENST00000413364.2_Missense_Mutation_p.W116C|LITAF_ENST00000574763.1_Missense_Mutation_p.W116C|LITAF_ENST00000572255.1_Missense_Mutation_p.W23C|LITAF_ENST00000339430.5_Missense_Mutation_p.W116C	NM_001136472.1	NP_001129944.1	Q99732	LITAF_HUMAN	lipopolysaccharide-induced TNF factor	116			W -> G (in CMT1C). {ECO:0000269|PubMed:12525712}.		aging (GO:0007568)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of cytokine production (GO:0001817)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)			endometrium(1)|large_intestine(1)|liver(1)|lung(3)|skin(1)	7						CGCAGGACAGCCAGGTCAGAG	0.602																																					p.W116C		Atlas-SNP	.											.	LITAF	16	.	0			c.G348T						.						60	48	52					16																	11647418		2197	4300	6497	SO:0001583	missense	9516	exon3			GGACAGCCAGGTC	AB034747	CCDS32386.1, CCDS45411.1	16p13.3-p12	2014-09-17							16841	protein-coding gene	gene with protein product		603795				9305847, 10200294	Standard	NM_004862		Approved	PIG7, SIMPLE, FLJ38636, TP53I7	uc002dbb.3	Q99732		ENST00000571688.1:c.348G>T	chr16.hg19:g.11647418C>A	ENSP00000459533:p.Trp116Cys	48.0	0.0		50.0	12.0	NM_001136473	D3DUG1|G5E9K0|Q05DW0|Q9C0L6	Missense_Mutation	SNP	ENST00000571688.1	hg19	CCDS32386.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.022741	0.75275	.	.	ENSG00000189067	ENST00000339430;ENST00000413364;ENST00000381810	D;D;D	0.88124	-2.34;-2.34;-2.34	5.48	5.48	0.80851	LPS-induced tumor necrosis factor alpha factor (2);	0.000000	0.85682	D	0.000000	D	0.93838	0.8029	M	0.83483	2.645	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.94299	0.7535	10	0.66056	D	0.02	-14.2553	16.8808	0.86062	0.0:1.0:0.0:0.0	.	116;116	G5E9K0;Q99732	.;LITAF_HUMAN	C	116	ENSP00000340118:W116C;ENSP00000397958:W116C;ENSP00000371231:W116C	ENSP00000340118:W116C	W	-	3	0	LITAF	11554919	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.373000	0.66162	2.572000	0.86782	0.655000	0.94253	TGG	.	.		0.602	LITAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436794.2	NM_004862		A	11647418	C	A	11647418	3	1	283	1	0	0	0	0	1	0	0	0	8839	740	26	3	231	3	LITAF	16	11647418	Missense_Mutation	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	1373428	11647418	78707335	176	41814										
KIAA0556	23247	hgsc.bcm.edu	37	chr16	27788950	27788950	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gctcctggtggacgacctgcTtgtgtacaatgggatcctgg	14	10	0	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr16:27788950T>G	ENST00000261588.4	+	26	4590	c.4571T>G	c.(4570-4572)cTt>cGt	p.L1524R		NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	1524						extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						GACGACCTGCTTGTGTACAAT	0.632																																					p.L1524R		Atlas-SNP	.											KIAA0556_ENST00000261588,caecum,carcinoma,0,2	KIAA0556	348	.	0			c.T4571G						.						105	91	96					16																	27788950		2197	4300	6497	SO:0001583	missense	23247	exon26			ACCTGCTTGTGTA	AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.4571T>G	chr16.hg19:g.27788950T>G	ENSP00000261588:p.Leu1524Arg	122.0	0.0		95.0	33.0	NM_015202	A7E2C2	Missense_Mutation	SNP	ENST00000261588.4	hg19	CCDS32415.1	.	.	.	.	.	.	.	.	.	.	T	15.46	2.841006	0.51057	.	.	ENSG00000047578	ENST00000261588	T	0.28454	1.61	4.75	4.75	0.60458	.	0.000000	0.64402	D	0.000011	T	0.60495	0.2273	M	0.87180	2.865	0.49389	D	0.999784	D	0.89917	1.0	D	0.97110	1.0	T	0.68941	-0.5276	10	0.87932	D	0	-39.4665	14.234	0.65913	0.0:0.0:0.0:1.0	.	1524	O60303	K0556_HUMAN	R	1524	ENSP00000261588:L1524R	ENSP00000261588:L1524R	L	+	2	0	KIAA0556	27696451	1.000000	0.71417	0.989000	0.46669	0.045000	0.14185	7.675000	0.84002	1.897000	0.54924	0.459000	0.35465	CTT	.	.		0.632	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202		G	27788950	T	G	27788950	3	3	283	1	0	0	0	0	1	0	0	0	8192	1609	56	5	4673	5	KIAA0556	16	27788950	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	16141532	27788950	62565803	177	41815										
N4BP1	9683	hgsc.bcm.edu	37	chr16	48596057	48596057	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ttgtgtaattgtctgcatggGcttcaacaaattgtttgaat	9	5	2	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr16:48596057G>A	ENST00000262384.3	-	2	733	c.497C>T	c.(496-498)gCc>gTc	p.A166V	RP11-44I10.3_ENST00000563994.1_RNA	NM_153029.3	NP_694574.3	O75113	N4BP1_HUMAN	NEDD4 binding protein 1	166					cellular response to UV (GO:0034644)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein ubiquitination (GO:0031397)	nucleolus (GO:0005730)|PML body (GO:0016605)				breast(3)|kidney(2)|lung(11)|urinary_tract(1)	17		all_cancers(37;0.179)|all_lung(18;0.11)				GTCTGCATGGGCTTCAACAAA	0.363																																					p.A166V		Atlas-SNP	.											.	N4BP1	121	.	0			c.C497T						.						107	98	101					16																	48596057		1852	4094	5946	SO:0001583	missense	9683	exon2			GCATGGGCTTCAA	AK026937	CCDS45479.1	16q12.1	2008-01-18				ENSG00000102921			29850	protein-coding gene	gene with protein product						9734811, 11717310	Standard	NM_153029		Approved		uc002efp.3	O75113		ENST00000262384.3:c.497C>T	chr16.hg19:g.48596057G>A	ENSP00000262384:p.Ala166Val	147.0	0.0		178.0	58.0	NM_153029	A7MD49|Q2YDX1	Missense_Mutation	SNP	ENST00000262384.3	hg19	CCDS45479.1	.	.	.	.	.	.	.	.	.	.	G	16.04	3.010246	0.54361	.	.	ENSG00000102921	ENST00000262384	T	0.47177	0.85	5.31	5.31	0.75309	.	0.335103	0.34959	N	0.003555	T	0.39860	0.1094	L	0.47716	1.5	0.37372	D	0.911662	P	0.39665	0.682	B	0.35550	0.205	T	0.43572	-0.9383	10	0.30078	T	0.28	-10.5521	14.2163	0.65795	0.0:0.0:0.8506:0.1494	.	166	O75113	N4BP1_HUMAN	V	166	ENSP00000262384:A166V	ENSP00000262384:A166V	A	-	2	0	N4BP1	47153558	1.000000	0.71417	0.955000	0.39395	0.996000	0.88848	4.177000	0.58276	2.632000	0.89209	0.655000	0.94253	GCC	.	.		0.363	N4BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429920.1	NM_014664		A	48596057	G	A	48596057	3	1	283	1	0	0	0	0	1	0	0	0	10118	1203	42	3	2217	3	N4BP1	16	48596057	Missense_Mutation	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	20807107	48596057	41758696	178	41816										
AMFR	267	hgsc.bcm.edu	37	chr16	56443342	56443342	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ggctaaaaactcacatattcAaatcgatccttgcagagctg	7	10	2	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr16:56443342A>G	ENST00000290649.5	-	3	717	c.507T>C	c.(505-507)ttT>ttC	p.F169F	RP11-413H22.2_ENST00000563090.1_RNA	NM_001144.5	NP_001135.3	Q9UKV5	AMFR_HUMAN	autocrine motility factor receptor, E3 ubiquitin protein ligase	169					aging (GO:0007568)|cellular component movement (GO:0006928)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|learning or memory (GO:0007611)|protein oligomerization (GO:0051259)|protein polyubiquitination (GO:0000209)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process (GO:0006511)	dendrite (GO:0030425)|endoplasmic reticulum membrane (GO:0005789)|growth cone (GO:0030426)|Hrd1p ubiquitin ligase complex (GO:0000836)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	ligase activity (GO:0016874)|receptor activity (GO:0004872)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17						TCACATATTCAAATCGATCCT	0.473																																					p.F169F	Pancreas(2;144 323 39528)	Atlas-SNP	.											.	AMFR	40	.	0			c.T507C						.						116	108	111					16																	56443342		2198	4300	6498	SO:0001819	synonymous_variant	267	exon3			ATATTCAAATCGA	L35233	CCDS10758.1	16q21	2013-01-09	2012-02-23		ENSG00000159461	ENSG00000159461		"RING-type (C3HC4) zinc fingers"	463	protein-coding gene	gene with protein product		603243	"autocrine motility factor receptor"			1649192	Standard	NM_001144		Approved	RNF45, gp78	uc002eiy.4	Q9UKV5	OTTHUMG00000133239	ENST00000290649.5:c.507T>C	chr16.hg19:g.56443342A>G		71.0	0.0		66.0	19.0	NM_001144	P26442|Q8IZ70	Silent	SNP	ENST00000290649.5	hg19	CCDS10758.1																																																																																			.	.		0.473	AMFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256978.2			G	56443342	A	G	56443342	2	3	283	1	0	0	0	0	0	0	0	1	571	127	5	2		2	AMFR	16	56443342	Silent	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	7847285	56443342	33911411	179	41817										
VPS53	55275	hgsc.bcm.edu	37	chr17	531471	531479	+	Splice_Site	DEL	TCTAGTAAA	TCTAGTAAA	-													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	attgctgggtcctcctggtcTctagtaaaacaaacatgtac					rs188572742	byFrequency	TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	TCTAGTAAA	TCTAGTAAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr17:531471_531479delTCTAGTAAA	ENST00000571805.1	-	9	824	c.688delTTTACTAGA	c.(688-690)ttt>tt	p.F230del	VPS53_ENST00000574029.1_Intron|VPS53_ENST00000576149.1_5'UTR|VPS53_ENST00000401468.3_Intron|VPS53_ENST00000446250.2_Splice_Site_p.F32del|VPS53_ENST00000291074.5_Splice_Site_p.F201del|VPS53_ENST00000437048.2_Splice_Site_p.F230del			Q5VIR6	VPS53_HUMAN	vacuolar protein sorting 53 homolog (S. cerevisiae)	230					protein transport (GO:0015031)	endosome (GO:0005768)|GARP complex (GO:0000938)|membrane (GO:0016020)				breast(1)|endometrium(4)|large_intestine(5)|lung(8)|prostate(1)	19				UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)		CCTCCTGGTCTCTAGTAAAACAAACATGT	0.407																																					p.230_230del		Atlas-Indel,Pindel	.											.	VPS53	109	.	0			c.688_689del						.																																			SO:0001630	splice_region_variant	55275	exon9			.		CCDS10995.1, CCDS45558.1	17p13.3	2007-07-13	2006-12-19			ENSG00000141252			25608	protein-coding gene	gene with protein product		615850	"vacuolar protein sorting 53 (yeast)"			15878329	Standard	NM_018289		Approved	FLJ10979, HCCS1	uc010cjo.2	Q5VIR6		ENST00000571805.1:c.688-1TTTACTAGA>-	chr17.hg19:g.531471_531479delTCTAGTAAA		100.0	0.0		68.0	20.0	NM_001128159	A8K2S8|B3FH42|Q8WYW3|Q9BRR2|Q9BY02|Q9NV25	Frame_Shift_Del	DEL	ENST00000571805.1	hg19																																																																																				.	.		0.407	VPS53-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000436940.2	NM_018289	In_Frame_Del	-	531479	TCTAGTAAA	-	531471	8	5	283	1	0	1	0	1	0	0	1	0	17230	1565	54	0	1881	0	VPS53	17	531471	Splice_Site	DEL	TCTAGTAAA	TCGA-G3-A3CK-01A-11D-A20W-10		531471	80663739	180	41818										
ZNF594	84622	hgsc.bcm.edu	37	chr17	5085970	5085970	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	atgtttgaggaaagctgtgcGccaaatgaagagcttcccac	11	9	0	3	rs181984106	byFrequency	TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr17:5085970G>T	ENST00000399604.4	-	1	1722	c.1582C>A	c.(1582-1584)Cgc>Agc	p.R528S	ZNF594_ENST00000575779.1_Missense_Mutation_p.R528S			Q96JF6	ZN594_HUMAN	zinc finger protein 594	528					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						AAAGCTGTGCGCCAAATGAAG	0.463																																					p.R528S		Atlas-SNP	.											.	ZNF594	89	.	0			c.C1582A						.						103	100	101					17																	5085970		2167	4290	6457	SO:0001583	missense	84622	exon2			CTGTGCGCCAAAT	AB058774	CCDS42241.1	17p13	2013-01-08			ENSG00000180626	ENSG00000180626		"Zinc fingers, C2H2-type"	29392	protein-coding gene	gene with protein product						11347906	Standard	NM_032530		Approved	KIAA1871	uc010cla.1	Q96JF6	OTTHUMG00000132059	ENST00000399604.4:c.1582C>A	chr17.hg19:g.5085970G>T	ENSP00000382513:p.Arg528Ser	166.0	0.0		160.0	61.0	NM_032530	Q6RFS0	Missense_Mutation	SNP	ENST00000399604.4	hg19	CCDS42241.1	.	.	.	.	.	.	.	.	.	.	G	0.001	-3.359912	0.00016	.	.	ENSG00000180626	ENST00000399604;ENST00000389222	T	0.14144	2.53	0.886	-1.77	0.07982	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05456	0.0144	N	0.17564	0.495	0.09310	N	1	B	0.28605	0.217	B	0.24394	0.053	T	0.40232	-0.9574	9	0.02654	T	1	.	6.1087	0.20087	0.4474:0.0:0.5526:0.0	.	528	Q96JF6	ZN594_HUMAN	S	528;123	ENSP00000382513:R528S	ENSP00000373874:R123S	R	-	1	0	ZNF594	5026694	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.225000	0.01212	-2.113000	0.00833	-2.108000	0.00357	CGC	.	G|0.999;A|0.001		0.463	ZNF594-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438996.1	XM_290737		T	5085970	G	T	5085970	3	4	283	1	0	0	0	0	1	0	0	0	18039	1087	38	1	845	1	ZNF594	17	5085970	Missense_Mutation	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	4554499	5085970	76109240	181	41819										
DNAH2	146754	hgsc.bcm.edu	37	chr17	7721651	7721651	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tggtcggctgttgatgcgcaTtggcgataaggaggtggaat	17	5	0	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr17:7721651T>C	ENST00000572933.1	+	69	11869	c.10409T>C	c.(10408-10410)aTt>aCt	p.I3470T	DNAH2_ENST00000389173.2_Missense_Mutation_p.I3470T			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	3470	AAA 5. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				TTGATGCGCATTGGCGATAAG	0.567																																					p.I3470T		Atlas-SNP	.											.	DNAH2	498	.	0			c.T10409C						.						220	196	204					17																	7721651		2203	4300	6503	SO:0001583	missense	146754	exon68			TGCGCATTGGCGA	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.10409T>C	chr17.hg19:g.7721651T>C	ENSP00000458355:p.Ile3470Thr	185.0	0.0		236.0	70.0	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	hg19	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	T	13.56	2.273274	0.40194	.	.	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.31510	1.49	5.0	3.92	0.45320	.	0.150858	0.44483	D	0.000459	T	0.45558	0.1348	M	0.82716	2.605	0.80722	D	1	P;P	0.37824	0.609;0.464	P;P	0.46585	0.521;0.471	T	0.47711	-0.9096	10	0.87932	D	0	.	9.8214	0.40885	0.0:0.0818:0.0:0.9182	.	3431;3470	Q9P225-2;Q9P225	.;DYH2_HUMAN	T	3431;3470	ENSP00000373825:I3470T	ENSP00000353818:I3431T	I	+	2	0	DNAH2	7662376	1.000000	0.71417	0.789000	0.31954	0.116000	0.19942	7.367000	0.79558	0.934000	0.37316	-0.256000	0.11100	ATT	.	.		0.567	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		C	7721651	T	C	7721651	3	2	283	1	0	0	0	0	1	0	0	0	4604	1493	52	2	10679	2	DNAH2	17	7721651	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	2635681	7721651	73473559	182	41820										
MYOCD	93649	hgsc.bcm.edu	37	chr17	12642602	12642602	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	agatgcggggaagcaggggcTtggcccccccagcaccccca	14	16	0	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr17:12642602T>G	ENST00000343344.4	+	7	674	c.674T>G	c.(673-675)cTt>cGt	p.L225R	AC005358.1_ENST00000609971.1_Missense_Mutation_p.L129R|MYOCD_ENST00000395988.1_3'UTR|MYOCD_ENST00000425538.1_Missense_Mutation_p.L225R			Q8IZQ8	MYCD_HUMAN	myocardin	225					cardiac muscle cell differentiation (GO:0055007)|cardiac ventricle development (GO:0003231)|cardiocyte differentiation (GO:0035051)|cell growth involved in cardiac muscle cell development (GO:0061049)|cellular component maintenance (GO:0043954)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hypoxia (GO:0071456)|digestive tract development (GO:0048565)|ductus arteriosus closure (GO:0097070)|hepatic stellate cell activation (GO:0035733)|lung alveolus development (GO:0048286)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of skeletal muscle cell differentiation (GO:2001015)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cardiac vascular smooth muscle cell differentiation (GO:2000724)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cell growth by extracellular stimulus (GO:0001560)|regulation of histone acetylation (GO:0035065)|regulation of myoblast differentiation (GO:0045661)|regulation of smooth muscle cell differentiation (GO:0051150)|response to hypoxia (GO:0001666)|smooth muscle cell differentiation (GO:0051145)|urinary bladder development (GO:0060157)|uterus development (GO:0060065)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(2)|lung(33)|ovary(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	70				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)		AAGCAGGGGCTTGGCCCCCCC	0.577																																					p.L225R		Atlas-SNP	.											.	MYOCD	291	.	0			c.T674G						.						56	52	53					17																	12642602		2203	4300	6503	SO:0001583	missense	93649	exon7			AGGGGCTTGGCCC	AF532596	CCDS11163.1, CCDS54091.1	17p11.2	2004-03-01			ENSG00000141052	ENSG00000141052			16067	protein-coding gene	gene with protein product		606127				11439182, 12397177	Standard	XM_005256863		Approved	MYCD	uc002gno.2	Q8IZQ8	OTTHUMG00000058767	ENST00000343344.4:c.674T>G	chr17.hg19:g.12642602T>G	ENSP00000341835:p.Leu225Arg	57.0	0.0		55.0	25.0	NM_001146312	Q5UBU5|Q8N7Q1	Missense_Mutation	SNP	ENST00000343344.4	hg19	CCDS11163.1	.	.	.	.	.	.	.	.	.	.	T	8.148	0.786697	0.16189	.	.	ENSG00000141052	ENST00000425538;ENST00000343344;ENST00000395988	T	0.46819	0.86	4.19	1.78	0.24846	.	0.549847	0.17527	N	0.171014	T	0.28167	0.0695	L	0.31926	0.97	0.09310	N	1	B;B;B	0.14012	0.004;0.009;0.007	B;B;B	0.12156	0.004;0.007;0.002	T	0.11470	-1.0586	10	0.15952	T	0.53	-13.1294	3.2337	0.06757	0.2748:0.1115:0.0:0.6137	.	129;225;225	Q8IZQ8-2;Q8IZQ8-3;Q8IZQ8	.;.;MYCD_HUMAN	R	225;225;129	ENSP00000341835:L225R	ENSP00000341835:L225R	L	+	2	0	MYOCD	12583327	0.002000	0.14202	0.039000	0.18376	0.463000	0.32649	0.417000	0.21214	0.766000	0.33244	0.482000	0.46254	CTT	.	.		0.577	MYOCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129950.1	NM_153604		G	12642602	T	G	12642602	3	3	283	1	0	0	0	0	1	0	0	0	10096	1609	56	5	700	5	MYOCD	17	12642602	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	4920951	12642602	68552608	183	41821										
FAM18B2	201158	hgsc.bcm.edu	37	chr17	15406305	15406305	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ataggcgggcgggcgccatcTgttggcagttgcctggagcc	17	11	1	0	rs141163711		TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr17:15406305T>A	ENST00000225576.3	-	6	799	c.704A>T	c.(703-705)cAg>cTg	p.Q235L	TVP23C_ENST00000519970.1_Intron|TVP23C-CDRT4_ENST00000522212.2_Intron	NM_145301.2	NP_660344.2	Q96ET8	TV23C_HUMAN	trans-golgi network vesicle protein 23 homolog C (S. cerevisiae)	235						integral component of membrane (GO:0016021)		p.Q235P(1)									GGGCGCCATCTGTTGGCAGTT	0.587																																					p.Q235L		Atlas-SNP	.											FAM18B2,NS,carcinoma,0,1	.	.	.	1	Substitution - Missense(1)	lung(1)	c.A704T						.						26	30	28					17																	15406305		2203	4300	6503	SO:0001583	missense	201158	exon6			GCCATCTGTTGGC	BC011952	CCDS11170.1, CCDS45617.1	17p12	2012-11-29	2012-11-29	2012-11-29	ENSG00000175106	ENSG00000175106			30453	protein-coding gene	gene with protein product			"family with sequence similarity 18, member B2"	FAM18B2			Standard	NM_001135036		Approved	MGC8763	uc002goq.2	Q96ET8	OTTHUMG00000171461	ENST00000225576.3:c.704A>T	chr17.hg19:g.15406305T>A	ENSP00000225576:p.Gln235Leu	148.0	0.0		132.0	36.0	NM_145301	Q3LIC7	Missense_Mutation	SNP	ENST00000225576.3	hg19	CCDS11170.1	.	.	.	.	.	.	.	.	.	.	T	14.82	2.649236	0.47362	.	.	ENSG00000175106	ENST00000225576	T	0.25912	1.77	3.65	2.54	0.30619	.	34.810200	0.00166	U	0.000001	T	0.20861	0.0502	N	0.22421	0.69	0.80722	D	1	P	0.47409	0.895	B	0.41332	0.354	T	0.15263	-1.0443	10	0.72032	D	0.01	-33.3475	6.0157	0.19601	0.0:0.1193:0.0:0.8807	.	235	Q96ET8	F18B2_HUMAN	L	235	ENSP00000225576:Q235L	ENSP00000225576:Q235L	Q	-	2	0	FAM18B2	15347030	0.932000	0.31603	0.718000	0.30602	0.101000	0.19017	1.117000	0.31234	0.752000	0.32923	0.377000	0.23210	CAG	.	T|1.000;C|0.000		0.587	TVP23C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000130705.2	NM_145301		A	15406305	T	A	15406305	3	1	283	1	0	0	0	0	1	0	0	0	5525	1580	55	4	130	4	FAM18B2	17	15406305	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	2763703	15406305	65788905	184	41822										
KSR1	8844	hgsc.bcm.edu	37	chr17	25928943	25928943	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	atctgctggccattgctggaAatgcctccttattgcagaaa	9	10	1	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr17:25928943A>C	ENST00000319524.6	+	12	1535	c.1535A>C	c.(1534-1536)aAa>aCa	p.K512T	KSR1_ENST00000581975.1_Intron|KSR1_ENST00000509603.2_Intron|KSR1_ENST00000268763.6_Missense_Mutation_p.K375T|KSR1_ENST00000398988.3_Missense_Mutation_p.K375T			Q8IVT5	KSR1_HUMAN	kinase suppressor of ras 1	512					Ras protein signal transduction (GO:0007265)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(12)|prostate(2)|urinary_tract(1)	28	Lung NSC(42;0.00836)		BRCA - Breast invasive adenocarcinoma(3;0.00122)	UCEC - Uterine corpus endometrioid carcinoma (53;0.168)		CATTGCTGGAAATGCCTCCTT	0.448											OREG0024261	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K375T	Esophageal Squamous(88;1120 1336 6324 10502 16832)	Atlas-SNP	.											.	KSR1	151	.	0			c.A1124C						.						58	56	56					17																	25928943		1949	4166	6115	SO:0001583	missense	8844	exon12			GCTGGAAATGCCT	U43586	CCDS58532.1	17q11.2	2012-05-23	2005-12-14	2005-12-14	ENSG00000141068	ENSG00000141068			6465	protein-coding gene	gene with protein product		601132	"kinase suppressor of ras"	KSR		8521512	Standard	XM_006722151		Approved	RSU2	uc031qzj.1	Q8IVT5	OTTHUMG00000132051	ENST00000319524.6:c.1535A>C	chr17.hg19:g.25928943A>C	ENSP00000323178:p.Lys512Thr	126.0	0.0	782	143.0	42.0	NM_014238	F8WEA9|H7BYU0|Q13476	Missense_Mutation	SNP	ENST00000319524.6	hg19		.	.	.	.	.	.	.	.	.	.	A	2.679	-0.275784	0.05679	.	.	ENSG00000141068	ENST00000319524;ENST00000268763;ENST00000398982	T;T	0.79653	-1.29;-1.26	4.74	2.5	0.30297	.	4.906310	0.00166	N	0.000009	T	0.56775	0.2008	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.54735	-0.8249	10	0.12430	T	0.62	.	4.9038	0.13788	0.7154:0.1882:0.0964:0.0	.	510	Q8IVT5	KSR1_HUMAN	T	512;375;375	ENSP00000323178:K512T;ENSP00000268763:K375T	ENSP00000268763:K375T	K	+	2	0	KSR1	22953070	0.014000	0.17966	0.001000	0.08648	0.001000	0.01503	0.416000	0.21198	0.399000	0.25367	-0.250000	0.11733	AAA	.	.		0.448	KSR1-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_014238		C	25928943	A	C	25928943	3	2	283	1	0	0	0	0	1	0	0	0	8590	14	1	5	1158	5	KSR1	17	25928943	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	10522638	25928943	55266267	185	41823										
NF1	4763	hgsc.bcm.edu	37	chr17	29496954	29496954	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gaagacaatgttgatgttcaTgatatagaattgttacagta	9	3	1	4			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr17:29496954T>C	ENST00000358273.4	+	5	908	c.525T>C	c.(523-525)caT>caC	p.H175H	NF1_ENST00000356175.3_Silent_p.H175H|NF1_ENST00000431387.4_Silent_p.H175H	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	175					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TTGATGTTCATGATATAGAAT	0.289			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																											p.H175H		Atlas-SNP	.	yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	.	NF1	1586	.	12	Whole gene deletion(8)|Unknown(4)	soft_tissue(7)|autonomic_ganglia(3)|central_nervous_system(2)	c.T525C						.						92	93	92					17																	29496954		2203	4299	6502	SO:0001819	synonymous_variant	4763	exon5	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	TGTTCATGATATA		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.525T>C	chr17.hg19:g.29496954T>C		64.0	0.0		84.0	28.0	NM_001128147	O00662|Q14284|Q14930|Q14931|Q9UMK3	Silent	SNP	ENST00000358273.4	hg19	CCDS42292.1																																																																																			.	.		0.289	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		C	29496954	T	C	29496954	2	2	283	1	0	0	0	0	0	0	0	1	10365	1461	51	2		2	NF1	17	29496954	Silent	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	3568011	29496954	51698256	186	41824										
ACACA	31	hgsc.bcm.edu	37	chr17	35631111	35631111	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ccatcatccacatctttcacAtaacctttttcatatagctc	1	14	4	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr17:35631111A>G	ENST00000394406.2	-	9	1060	c.870T>C	c.(868-870)taT>taC	p.Y290Y	ACACA_ENST00000353139.5_Silent_p.Y327Y|ACACA_ENST00000335166.5_Silent_p.Y212Y|ACACA_ENST00000360679.3_Silent_p.Y232Y	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	290	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.|Biotin carboxylation.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	CATCTTTCACATAACCTTTTT	0.428																																					p.Y327Y	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)	Atlas-SNP	.											.	ACACA	395	.	0			c.T981C						.						185	153	164					17																	35631111		2203	4300	6503	SO:0001819	synonymous_variant	31	exon9			TTTCACATAACCT	U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 1"	200350	"acetyl-Coenzyme A carboxylase alpha"	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.870T>C	chr17.hg19:g.35631111A>G		165.0	0.0		163.0	52.0	NM_198834	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Silent	SNP	ENST00000394406.2	hg19	CCDS11317.1																																																																																			.	.		0.428	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836		G	35631111	A	G	35631111	2	3	283	1	0	0	0	0	0	0	0	1	106	224	8	2		2	ACACA	17	35631111	Silent	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	6134157	35631111	45564099	187	41825										
KRT40	125115	hgsc.bcm.edu	37	chr17	39140461	39140461	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	cggagcagcttgaggcaggtGcacaaccggaagccgtgcca	15	12	0	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr17:39140461G>A	ENST00000398486.2	-	3	225	c.65C>T	c.(64-66)gCa>gTa	p.A22V	KRT40_ENST00000377755.4_Missense_Mutation_p.A22V	NM_182497.3	NP_872303.2	Q6A162	K1C40_HUMAN	keratin 40	22	Head.					intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9		Breast(137;0.00043)				TGAGGCAGGTGCACAACCGGA	0.572																																					p.A22V		Atlas-SNP	.											.	KRT40	27	.	0			c.C65T						.						33	42	39					17																	39140461		2093	4216	6309	SO:0001583	missense	125115	exon3			GCAGGTGCACAAC	AK093919	CCDS42320.1	17q21.2	2013-01-16			ENSG00000204889	ENSG00000204889		"-", "Intermediate filaments type I, keratins (acidic)"	26707	protein-coding gene	gene with protein product						16831889	Standard	NM_182497		Approved	FLJ36600, KA36	uc010cxh.1	Q6A162	OTTHUMG00000133596	ENST00000398486.2:c.65C>T	chr17.hg19:g.39140461G>A	ENSP00000381500:p.Ala22Val	109.0	0.0		140.0	59.0	NM_182497	Q6IFU5	Missense_Mutation	SNP	ENST00000398486.2	hg19	CCDS42320.1	.	.	.	.	.	.	.	.	.	.	G	7.463	0.645080	0.14451	.	.	ENSG00000204889	ENST00000377755;ENST00000398486	D;D	0.81908	-1.55;-1.55	4.79	2.74	0.32292	.	1.160560	0.06757	N	0.781005	T	0.78874	0.4352	L	0.57536	1.79	0.09310	N	1	B	0.23128	0.08	B	0.19946	0.027	T	0.60717	-0.7208	10	0.27785	T	0.31	.	6.747	0.23466	0.0837:0.0:0.6049:0.3113	.	22	Q6A162	K1C40_HUMAN	V	22	ENSP00000366984:A22V;ENSP00000381500:A22V	ENSP00000366984:A22V	A	-	2	0	KRT40	36393987	.	.	0.000000	0.03702	0.025000	0.11179	.	.	0.532000	0.28657	-0.500000	0.04577	GCA	.	.		0.572	KRT40-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257701.3	NM_182497		A	39140461	G	A	39140461	3	1	283	1	0	0	0	0	1	0	0	0	8487	1319	46	3	1258	3	KRT40	17	39140461	Missense_Mutation	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	3509350	39140461	42054749	188	41826										
ZNF652	22834	hgsc.bcm.edu	37	chr17	47390068	47390068	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	agaaaaacttaccaaccatgTgtttccgcacatgagccatg	7	11	0	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr17:47390068T>C	ENST00000362063.2	-	3	1358	c.1040A>G	c.(1039-1041)cAc>cGc	p.H347R	ZNF652_ENST00000430262.2_Missense_Mutation_p.H347R	NM_014897.2	NP_055712.1	Q9Y2D9	ZN652_HUMAN	zinc finger protein 652	347					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	20	all_cancers(4;6.81e-14)|Breast(4;4.97e-29)|all_epithelial(4;1.53e-17)		BRCA - Breast invasive adenocarcinoma(1;3.1e-14)|Epithelial(5;2.92e-06)|all cancers(6;3.15e-05)			ACCAACCATGTGTTTCCGCAC	0.383																																					p.H347R		Atlas-SNP	.											.	ZNF652	54	.	0			c.A1040G						.						71	71	71					17																	47390068		2203	4300	6503	SO:0001583	missense	22834	exon3			ACCATGTGTTTCC	AB023141	CCDS32677.1	17q21.32	2013-01-08				ENSG00000198740		"Zinc fingers, C2H2-type"	29147	protein-coding gene	gene with protein product		613907				10231032	Standard	NM_014897		Approved	KIAA0924	uc002iow.3	Q9Y2D9		ENST00000362063.2:c.1040A>G	chr17.hg19:g.47390068T>C	ENSP00000354686:p.His347Arg	80.0	0.0		121.0	32.0	NM_001145365	A4QPD9|Q5H9Q0	Missense_Mutation	SNP	ENST00000362063.2	hg19	CCDS32677.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.447319	0.84101	.	.	ENSG00000198740	ENST00000362063;ENST00000430262	D;D	0.86865	-2.18;-2.18	5.67	5.67	0.87782	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.95834	0.8644	H	0.97131	3.945	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.97268	0.9909	10	0.87932	D	0	-15.4672	15.5774	0.76404	0.0:0.0:0.0:1.0	.	347	Q9Y2D9	ZN652_HUMAN	R	347	ENSP00000354686:H347R;ENSP00000416305:H347R	ENSP00000354686:H347R	H	-	2	0	ZNF652	44745067	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.164000	0.68074	0.482000	0.46254	CAC	.	.		0.383	ZNF652-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364524.1	NM_014897		C	47390068	T	C	47390068	3	2	283	1	0	0	0	0	1	0	0	0	18080	1696	59	2	796	2	ZNF652	17	47390068	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	8249607	47390068	33805142	189	41827										
SLC35B1	10237	hgsc.bcm.edu	37	chr17	47781491	47781491	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gcagcaatgtcgaccaaaggTtgatgttcagcatcatgtgg	12	8	2	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr17:47781491T>G	ENST00000240333.6	-	6	747	c.626A>C	c.(625-627)aAc>aCc	p.N209T	SLC35B1_ENST00000415270.2_Missense_Mutation_p.N246T			P78383	S35B1_HUMAN	solute carrier family 35, member B1	209					transport (GO:0006810)|UDP-galactose transmembrane transport (GO:0072334)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	UDP-galactose transmembrane transporter activity (GO:0005459)			endometrium(1)|large_intestine(2)|lung(3)|urinary_tract(1)	7						CGACCAAAGGTTGATGTTCAG	0.532																																					p.N209T		Atlas-SNP	.											.	SLC35B1	21	.	0			c.A626C						.						232	184	201					17																	47781491		2203	4300	6503	SO:0001583	missense	10237	exon6			CAAAGGTTGATGT	D16978	CCDS11552.1, CCDS11552.2	17q21.32	2013-05-22			ENSG00000121073	ENSG00000121073		"Solute carriers"	20798	protein-coding gene	gene with protein product		610790				9010752	Standard	NM_005827		Approved	UGTREL1	uc002iph.1	P78383	OTTHUMG00000161638	ENST00000240333.6:c.626A>C	chr17.hg19:g.47781491T>G	ENSP00000240333:p.Asn209Thr	279.0	0.0		395.0	127.0	NM_005827	B4DEC4|J3KQV4|Q96EW7	Missense_Mutation	SNP	ENST00000240333.6	hg19	CCDS11552.1	.	.	.	.	.	.	.	.	.	.	T	29.3	4.998075	0.93227	.	.	ENSG00000121073	ENST00000240333;ENST00000415270;ENST00000504260;ENST00000502406;ENST00000503334;ENST00000508520;ENST00000502268;ENST00000435059;ENST00000514907;ENST00000515850	T;T;T;T;T;T	0.33438	1.41;1.41;1.41;1.41;1.41;1.41	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.61362	0.2341	M	0.86028	2.79	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.66184	-0.5987	10	0.59425	D	0.04	-0.5432	16.3021	0.82825	0.0:0.0:0.0:1.0	.	209;142;209	B4DJG9;D3DTX1;P78383	.;.;S35B1_HUMAN	T	209;246;85;85;142;212;85;209;178;243	ENSP00000240333:N209T;ENSP00000409548:N246T;ENSP00000423323:N142T;ENSP00000424367:N212T;ENSP00000426961:N178T;ENSP00000427689:N243T	ENSP00000240333:N209T	N	-	2	0	SLC35B1	45136490	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.993000	0.88291	2.326000	0.78906	0.533000	0.62120	AAC	.	.		0.532	SLC35B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365564.2	NM_005827		G	47781491	T	G	47781491	3	3	283	1	0	0	0	0	1	0	0	0	14590	1725	60	5	358	5	SLC35B1	17	47781491	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	391423	47781491	33413719	190	41828										
PDK2	5164	hgsc.bcm.edu	37	chr17	48174927	48174927	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ccgtgcagctggtgcagagcTggtgagacccctggctcagt	15	12	1	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr17:48174927T>C	ENST00000503176.1	+	2	420	c.259T>C	c.(259-261)Tgg>Cgg	p.W87R	PDK2_ENST00000007708.3_Splice_Site_p.W23R	NM_002611.4	NP_002602.2	Q15119	PDK2_HUMAN	pyruvate dehydrogenase kinase, isozyme 2	87					cellular metabolic process (GO:0044237)|cellular response to nutrient (GO:0031670)|cellular response to reactive oxygen species (GO:0034614)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|protein phosphorylation (GO:0006468)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of cellular ketone metabolic process (GO:0010565)|regulation of gluconeogenesis (GO:0006111)|regulation of glucose metabolic process (GO:0010906)|regulation of pH (GO:0006885)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrial pyruvate dehydrogenase complex (GO:0005967)	ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)			central_nervous_system(4)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	20						GGTGCAGAGCTGGTGAGACCC	0.617									Autosomal Dominant Polycystic Kidney Disease																												p.W87R		Atlas-SNP	.											.	PDK2	41	.	0			c.T259C						.						70	58	62					17																	48174927		2203	4300	6503	SO:0001630	splice_region_variant	5164	exon2	Familial Cancer Database	ADPKD	CAGAGCTGGTGAG	L42451	CCDS11559.1, CCDS56039.1	17q21.33	2012-07-18	2005-11-16		ENSG00000005882	ENSG00000005882			8810	protein-coding gene	gene with protein product		602525	"pyruvate dehydrogenase kinase, isoenzyme 2"			7499431	Standard	NM_001199898		Approved	PDHK2	uc002iqc.3	Q15119	OTTHUMG00000161948	ENST00000503176.1:c.260+1T>C	chr17.hg19:g.48174927T>C		42.0	0.0		62.0	16.0	NM_002611	A8K3A7|B3KNW0|Q6P515|Q9BS05	Missense_Mutation	SNP	ENST00000503176.1	hg19	CCDS11559.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.365910	0.82463	.	.	ENSG00000005882	ENST00000007708;ENST00000508030;ENST00000503176;ENST00000503614;ENST00000505440;ENST00000512238	T;T;T;T;T;T	0.35421	1.31;1.31;1.31;1.31;1.31;1.31	4.07	4.07	0.47477	Branched-chain alpha-ketoacid dehydrogenase kinase/Pyruvate dehydrogenase kinase, N-terminal (3);	0.158952	0.45606	D	0.000350	T	0.63965	0.2556	H	0.96547	3.84	0.80722	D	1	P	0.45078	0.85	P	0.53006	0.715	T	0.75331	-0.3355	10	0.66056	D	0.02	-1.2336	12.4738	0.55801	0.0:0.0:0.0:1.0	.	87	Q15119	PDK2_HUMAN	R	23;23;87;23;23;23	ENSP00000007708:W23R;ENSP00000427682:W23R;ENSP00000420927:W87R;ENSP00000425265:W23R;ENSP00000425615:W23R;ENSP00000421178:W23R	ENSP00000007708:W23R	W	+	1	0	PDK2	45529926	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.661000	0.83786	1.857000	0.53885	0.519000	0.50382	TGG	.	.		0.617	PDK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366492.2	NM_002611	Missense_Mutation	C	48174927	T	C	48174927	5	2	283	1	0	0	0	0	0	0	1	0	11685	1594	55	2	265	2	PDK2	17	48174927	Splice_Site	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	393436	48174927	33020283	191	41829										
MTMR4	9110	hgsc.bcm.edu	37	chr17	56584192	56584192	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	atcagcagcttttgaggagcTgctgtgctctccactccaga	10	12	2	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr17:56584192T>G	ENST00000323456.5	-	10	1027	c.903A>C	c.(901-903)gcA>gcC	p.A301A	MTMR4_ENST00000579925.1_Silent_p.A301A	NM_004687.4	NP_004678.3	Q9NYA4	MTMR4_HUMAN	myotubularin related protein 4	301	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|small molecule metabolic process (GO:0044281)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|early endosome membrane (GO:0031901)|extracellular space (GO:0005615)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(10)|endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|skin(5)	36	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TTTGAGGAGCTGCTGTGCTCT	0.572																																					p.A301A		Atlas-SNP	.											.	MTMR4	91	.	0			c.A903C						.						58	54	56					17																	56584192		2203	4300	6503	SO:0001819	synonymous_variant	9110	exon10			AGGAGCTGCTGTG	AB014547	CCDS11608.1	17q22-q23	2011-06-09				ENSG00000108389		"Zinc fingers, FYVE domain containing", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7452	protein-coding gene	gene with protein product		603559				9736772	Standard	NM_004687		Approved	KIAA0647, ZFYVE11	uc002iwj.2	Q9NYA4		ENST00000323456.5:c.903A>C	chr17.hg19:g.56584192T>G		80.0	0.0		114.0	18.0	NM_004687	D3DTZ6|Q8IV27|Q9Y4D5	Silent	SNP	ENST00000323456.5	hg19	CCDS11608.1																																																																																			.	.		0.572	MTMR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444721.1	NM_004687		G	56584192	T	G	56584192	2	3	283	1	0	0	0	0	0	0	0	1	9955	1567	55	5		5	MTMR4	17	56584192	Silent	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	8409265	56584192	24611018	192	41830										
AXIN2	8313	hgsc.bcm.edu	37	chr17	63534326	63534326	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	cctaggccgcattacctctcGgatctgctgcaggcgctcct	10	16	2	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr17:63534326G>A	ENST00000375702.5	-	4	1303	c.1195C>T	c.(1195-1197)Cga>Tga	p.R399*	CTD-2535L24.2_ENST00000577662.1_3'UTR|AXIN2_ENST00000307078.5_Nonsense_Mutation_p.R399*			Q9Y2T1	AXIN2_HUMAN	axin 2	399	Interaction with GSK3B. {ECO:0000250}.				bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to organic cyclic compound (GO:0071407)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|dorsal/ventral axis specification (GO:0009950)|intramembranous ossification (GO:0001957)|maintenance of DNA repeat elements (GO:0043570)|mRNA stabilization (GO:0048255)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell proliferation (GO:0008285)|negative regulation of osteoblast differentiation (GO:0045668)|odontogenesis (GO:0042476)|positive regulation of cell death (GO:0010942)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein phosphorylation (GO:0001934)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of chondrocyte development (GO:0061181)|regulation of mismatch repair (GO:0032423)|secondary heart field specification (GO:0003139)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)			NS(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	34						ATTACCTCTCGGATCTGCTGC	0.612									Oligodontia, Ectodermal Dysplasia and Colorectal Polyp syndrome																												p.R399X		Atlas-SNP	.											.	AXIN2	92	.	0			c.C1195T						.						68	55	59					17																	63534326		2203	4300	6503	SO:0001587	stop_gained	8313	exon5	Familial Cancer Database	Oligodontia-Colorectal Cancer syndrome, Tooth Agenesis-Colorectal Cancer Syndrome	CCTCTCGGATCTG	AF078165	CCDS11662.1	17q24.1	2014-09-17	2008-08-01		ENSG00000168646				904	protein-coding gene	gene with protein product	"conductin", "axil"	604025				10049590	Standard	NM_004655		Approved	MGC126582, DKFZp781B0869	uc002jfi.3	Q9Y2T1	OTTHUMG00000179353	ENST00000375702.5:c.1195C>T	chr17.hg19:g.63534326G>A	ENSP00000364854:p.Arg399*	173.0	0.0		204.0	55.0	NM_004655	Q3MJ88|Q9H3M6|Q9UH84	Nonsense_Mutation	SNP	ENST00000375702.5	hg19		.	.	.	.	.	.	.	.	.	.	G	36	5.646295	0.96704	.	.	ENSG00000168646	ENST00000307078;ENST00000375702	.	.	.	4.68	2.51	0.30379	.	0.291643	0.34652	N	0.003788	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.4675	11.9475	0.52936	0.0:0.0:0.491:0.509	.	.	.	.	X	399	.	ENSP00000302625:R399X	R	-	1	2	AXIN2	60964788	1.000000	0.71417	0.986000	0.45419	0.907000	0.53573	1.912000	0.39946	0.540000	0.28808	0.555000	0.69702	CGA	.	.		0.612	AXIN2-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000445901.1	NM_004655		A	63534326	G	A	63534326	4	1	283	1	0	0	0	0	0	1	0	0	1237	1124	39	1	1364	1	AXIN2	17	63534326	Nonsense_Mutation	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	6950134	63534326	17660884	193	41831										
CD300LB	124599	hgsc.bcm.edu	37	chr17	72518964	72518964	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tcagggaccctctgagacccCttcaaccagaggatggcagt	11	13	3	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr17:72518964C>G	ENST00000392621.1	-	4	634	c.630G>C	c.(628-630)aaG>aaC	p.K210N		NM_174892.2	NP_777552	A8K4G0	CLM7_HUMAN	CD300 molecule-like family member b	173					cellular response to lipopolysaccharide (GO:0071222)|innate immune response (GO:0045087)|neutrophil mediated immunity (GO:0002446)|positive regulation of mast cell activation (GO:0033005)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|skin(1)	21						TCTGAGACCCCTTCAACCAGA	0.532																																					p.K210N		Atlas-SNP	.											.	CD300LB	38	.	0			c.G630C						.						130	112	118					17																	72518964		2203	4300	6503	SO:0001583	missense	124599	exon4			AGACCCCTTCAAC	AF427618	CCDS11700.1, CCDS11700.2	17q25.1	2013-01-11	2006-03-29		ENSG00000178789	ENSG00000178789		"Immunoglobulin superfamily / V-set domain containing"	30811	protein-coding gene	gene with protein product	"triggering receptor expressed on myeloid cells 5"	610705	"CD300 antigen like family member B"			12975309	Standard	NM_174892		Approved	TREM5, CLM7	uc002jkx.2	A8K4G0	OTTHUMG00000067606	ENST00000392621.1:c.630G>C	chr17.hg19:g.72518964C>G	ENSP00000376397:p.Lys210Asn	229.0	0.0		307.0	86.0	NM_174892	Q1EG73|Q8IX40|Q8N6D1	Missense_Mutation	SNP	ENST00000392621.1	hg19	CCDS11700.1	.	.	.	.	.	.	.	.	.	.	C	7.214	0.595946	0.13875	.	.	ENSG00000178789	ENST00000392621;ENST00000314401	.	.	.	4.61	1.46	0.22682	.	0.544623	0.16395	N	0.216277	T	0.28433	0.0703	N	0.17345	0.48	0.35571	D	0.805457	B	0.22909	0.077	B	0.20955	0.032	T	0.16719	-1.0393	9	0.12430	T	0.62	-9.0403	5.4382	0.16494	0.0:0.6452:0.1652:0.1896	.	173	A8K4G0	CLM7_HUMAN	N	173;210	.	ENSP00000317337:K210N	K	-	3	2	CD300LB	70030559	0.265000	0.24102	0.204000	0.23530	0.395000	0.30598	0.352000	0.20113	0.244000	0.21351	-0.379000	0.06801	AAG	.	.		0.532	CD300LB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145082.2	NM_174892		G	72518964	C	G	72518964	3	3	283	1	0	0	0	0	1	0	0	0	3001	680	24	4	90	4	CD300LB	17	72518964	Missense_Mutation	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	8984638	72518964	8676246	194	41832										
CCDC137	339230	hgsc.bcm.edu	37	chr17	79639185	79639185	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	aggagcgtaagcaaggaccaGgtaagtggggcacggggaca	18	7	0	0	rs373550389		TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr17:79639185G>A	ENST00000329214.8	+	5	1063	c.660G>A	c.(658-660)caG>caA	p.Q220Q		NM_199287.2	NP_954981.1	Q6PK04	CC137_HUMAN	coiled-coil domain containing 137	220							poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(2)	12	all_neural(118;0.0878)|all_lung(278;0.23)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			GCAAGGACCAGGTAAGTGGGG	0.587																																					p.Q220Q		Atlas-SNP	.											.	CCDC137	27	.	0			c.G660A						.	G		0,4026		0,0,2013	40	44	42		660	4.8	0.9	17		42	1,8359		0,1,4179	no	coding-synonymous-near-splice	CCDC137	NM_199287.2		0,1,6192	AA,AG,GG		0.012,0.0,0.0081		220/290	79639185	1,12385	2013	4180	6193	SO:0001630	splice_region_variant	339230	exon5			GGACCAGGTAAGT	BC009369	CCDS42400.1	17q25.3	2008-07-04				ENSG00000185298			33451	protein-coding gene	gene with protein product		614271					Standard	NM_199287		Approved	MGC16597	uc002kbc.4	Q6PK04		ENST00000329214.8:c.660+1G>A	chr17.hg19:g.79639185G>A		128.0	0.0		140.0	77.0	NM_199287		Silent	SNP	ENST00000329214.8	hg19	CCDS42400.1																																																																																			.	.		0.587	CCDC137-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440387.1		Silent	A	79639185	G	A	79639185	5	1	283	1	0	0	0	0	0	0	1	0	2773	1014	35	3	678	3	CCDC137	17	79639185	Splice_Site	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	7120221	79639185	1556025	195	41833										
FASN	2194	hgsc.bcm.edu	37	chr17	80037282	80037282	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	cctcgccgtaggcgccacccGtcttggcgcgcagtagcatc	12	17	1	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr17:80037282G>A	ENST00000306749.2	-	42	7567	c.7349C>T	c.(7348-7350)aCg>aTg	p.T2450M	FASN_ENST00000579758.1_5'UTR	NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	2450	Thioesterase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	GGCGCCACCCGTCTTGGCGCG	0.652																																					p.T2450M	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.C7349T						.						82	70	74					17																	80037282		2203	4300	6503	SO:0001583	missense	2194	exon42			CCACCCGTCTTGG	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.7349C>T	chr17.hg19:g.80037282G>A	ENSP00000304592:p.Thr2450Met	150.0	0.0		185.0	51.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	hg19	CCDS11801.1	.	.	.	.	.	.	.	.	.	.	G	9.168	1.020442	0.19433	.	.	ENSG00000169710	ENST00000306749	T	0.26810	1.71	4.16	-0.264	0.12950	Thioesterase (1);	0.061993	0.64402	N	0.000005	T	0.20414	0.0491	M	0.73962	2.25	0.43439	D	0.995616	P	0.43024	0.798	B	0.34301	0.179	T	0.03325	-1.1048	10	0.48119	T	0.1	-6.2659	5.3654	0.16111	0.2357:0.0:0.6233:0.141	.	2450	P49327	FAS_HUMAN	M	2450	ENSP00000304592:T2450M	ENSP00000304592:T2450M	T	-	2	0	FASN	77630571	0.999000	0.42202	0.117000	0.21633	0.023000	0.10783	2.872000	0.48467	-0.084000	0.12595	0.561000	0.74099	ACG	.	.		0.652	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		A	80037282	G	A	80037282	3	1	283	1	0	0	0	0	1	0	0	0	5691	1145	40	1	194	1	FASN	17	80037282	Missense_Mutation	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	398097	80037282	1157928	196	41834										
FASN	2194	hgsc.bcm.edu	37	chr17	80039907	80039907	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gggaggccttcgtgccggcgTttctcacagatacgctccat	12	13	1	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr17:80039907T>G	ENST00000306749.2	-	36	6359	c.6141A>C	c.(6139-6141)aaA>aaC	p.K2047N	FASN_ENST00000579758.1_5'UTR	NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	2047	Beta-ketoacyl reductase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	CGTGCCGGCGTTTCTCACAGA	0.647																																					p.K2047N	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.A6141C						.						68	69	68					17																	80039907		2203	4300	6503	SO:0001583	missense	2194	exon36			CCGGCGTTTCTCA	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.6141A>C	chr17.hg19:g.80039907T>G	ENSP00000304592:p.Lys2047Asn	39.0	0.0		76.0	16.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	hg19	CCDS11801.1	.	.	.	.	.	.	.	.	.	.	T	14.48	2.548985	0.45383	.	.	ENSG00000169710	ENST00000306749	T	0.42513	0.97	4.77	2.73	0.32206	Polyketide synthase/Fatty acid synthase, KR (1);NAD(P)-binding domain (1);	0.349618	0.27433	N	0.019390	T	0.31420	0.0796	N	0.25957	0.775	0.32180	N	0.580527	B	0.20780	0.048	B	0.33254	0.16	T	0.33599	-0.9862	10	0.45353	T	0.12	-14.9167	8.1701	0.31249	0.0:0.7427:0.0:0.2573	.	2047	P49327	FAS_HUMAN	N	2047	ENSP00000304592:K2047N	ENSP00000304592:K2047N	K	-	3	2	FASN	77633196	1.000000	0.71417	0.985000	0.45067	0.570000	0.35934	2.389000	0.44407	0.407000	0.25591	0.260000	0.18958	AAA	.	.		0.647	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		G	80039907	T	G	80039907	3	3	283	1	0	0	0	0	1	0	0	0	5691	1722	60	5	1426	5	FASN	17	80039907	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	2625	80039907	1155303	197	41835										
ENOSF1	55556	hgsc.bcm.edu	37	chr18	683313	683313	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	cctcaatccacaatggcttgAacttggccagcttggacatc	8	13	1	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr18:683313A>C	ENST00000251101.7	-	11	897	c.809T>G	c.(808-810)tTc>tGc	p.F270C	ENOSF1_ENST00000383578.3_Missense_Mutation_p.F188C|ENOSF1_ENST00000580982.1_Missense_Mutation_p.F194C|ENOSF1_ENST00000319815.6_Missense_Mutation_p.F40C|ENOSF1_ENST00000583973.1_5'UTR|ENOSF1_ENST00000340116.7_Missense_Mutation_p.F291C	NM_017512.5	NP_059982.2	Q7L5Y1	ENOF1_HUMAN	enolase superfamily member 1	270					cellular amino acid catabolic process (GO:0009063)|cellular carbohydrate catabolic process (GO:0044275)	mitochondrion (GO:0005739)	isomerase activity (GO:0016853)|L-fuconate dehydratase activity (GO:0050023)|magnesium ion binding (GO:0000287)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	10						CAATGGCTTGAACTTGGCCAG	0.562																																					p.F291C		Atlas-SNP	.											.	ENOSF1	44	.	0			c.T872G						.						125	107	113					18																	683313		2203	4300	6503	SO:0001583	missense	55556	exon11			GGCTTGAACTTGG	X67098	CCDS11822.1, CCDS11823.1, CCDS45821.1	18p11.32	2005-01-26			ENSG00000132199	ENSG00000132199			30365	protein-coding gene	gene with protein product		607427				14508106	Standard	NM_001126123		Approved	HSRTSBETA, rTS, TYMSAS	uc002kku.4	Q7L5Y1	OTTHUMG00000131470	ENST00000251101.7:c.809T>G	chr18.hg19:g.683313A>C	ENSP00000251101:p.Phe270Cys	238.0	0.0		266.0	90.0	NM_202758	A6NMP3|A8K9R5|B3KSL6|B3KXE4|D3DUH0|Q15407|Q15594|Q15595|Q6ZS08|Q9HAS5|Q9HAS6	Missense_Mutation	SNP	ENST00000251101.7	hg19	CCDS11822.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.217209	0.79352	.	.	ENSG00000132199	ENST00000383578;ENST00000319815;ENST00000251101;ENST00000340116	T;T;T;T	0.47177	0.85;0.85;0.85;0.85	5.54	5.54	0.83059	Mandelate racemase/muconate lactonizing enzyme, conserved site (1);Mandelate racemase/muconate lactonizing enzyme, C-terminal (2);	0.095383	0.64402	D	0.000001	T	0.55497	0.1924	M	0.74258	2.255	0.80722	D	1	P;P;D;P;P	0.57571	0.948;0.837;0.98;0.948;0.647	P;B;P;P;B	0.49999	0.628;0.409;0.628;0.628;0.372	T	0.61028	-0.7145	10	0.56958	D	0.05	.	9.9774	0.41793	0.8486:0.0:0.0:0.1514	.	291;89;315;270;188	A6NMP3;B3KXE4;Q6ZS08;Q7L5Y1;Q7L5Y1-2	.;.;.;ENOF1_HUMAN;.	C	188;40;270;291	ENSP00000373072:F188C;ENSP00000313346:F40C;ENSP00000251101:F270C;ENSP00000345974:F291C	ENSP00000251101:F270C	F	-	2	0	ENOSF1	673313	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	6.834000	0.75339	2.096000	0.63516	0.477000	0.44152	TTC	.	.		0.562	ENOSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254312.2	NM_017512		C	683313	A	C	683313	3	2	283	1	0	0	0	0	1	0	0	0	5127	246	9	5	546	5	ENOSF1	18	683313	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10		683313	77393935	198	41836										
LAMA3	3909	hgsc.bcm.edu	37	chr18	21418835	21418835	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ccagttatgggcgatttgtcAatcaaaggtaatgtgtttcc	10	7	2	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr18:21418835A>G	ENST00000313654.9	+	26	3425	c.3184A>G	c.(3184-3186)Aat>Gat	p.N1062D	LAMA3_ENST00000399516.3_Missense_Mutation_p.N1062D	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	1062	Domain IV 1 (domain IV B).				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					GCGATTTGTCAATCAAAGGTA	0.418																																					p.N1062D		Atlas-SNP	.											.	LAMA3	397	.	0			c.A3184G						.						184	182	183					18																	21418835		1959	4142	6101	SO:0001583	missense	3909	exon26			TTTGTCAATCAAA	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"Laminins"	6483	protein-coding gene	gene with protein product		600805	"laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.3184A>G	chr18.hg19:g.21418835A>G	ENSP00000324532:p.Asn1062Asp	314.0	0.0		258.0	74.0	NM_001127717	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	hg19	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	A	2.951	-0.216710	0.06101	.	.	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000416669	T;T	0.17691	2.28;2.26	5.52	5.52	0.82312	.	.	.	.	.	T	0.14830	0.0358	L	0.59912	1.85	0.39731	D	0.971619	B;B	0.13145	0.004;0.007	B;B	0.09377	0.004;0.004	T	0.11397	-1.0589	9	0.11485	T	0.65	.	6.9956	0.24780	0.7668:0.1519:0.0813:0.0	.	1062;1062	Q6VU67;Q16787	.;LAMA3_HUMAN	D	1062;1062;1060	ENSP00000324532:N1062D;ENSP00000382432:N1062D	ENSP00000324532:N1062D	N	+	1	0	LAMA3	19672833	0.105000	0.21958	0.907000	0.35723	0.201000	0.24016	0.585000	0.23879	2.234000	0.73211	0.533000	0.62120	AAT	.	.		0.418	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		G	21418835	A	G	21418835	3	3	283	1	0	0	0	0	1	0	0	0	8616	130	5	2	3286	2	LAMA3	18	21418835	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	20735522	21418835	56658413	199	41837										
ZNF397	84307	hgsc.bcm.edu	37	chr18	32826113	32826113	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	atagtggggaggaaccttatCagtgtaatgaatgtggcaaa	13	4	1	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr18:32826113C>T	ENST00000330501.7	+	4	1597	c.1444C>T	c.(1444-1446)Cag>Tag	p.Q482*	ZNF397_ENST00000589420.1_Intron|ZNF397_ENST00000261333.6_Intron|ZNF397_ENST00000355632.4_Intron|ZNF397_ENST00000592264.1_Intron	NM_001135178.2	NP_001128650.1	Q8NF99	ZN397_HUMAN	zinc finger protein 397	482					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|large_intestine(3)|lung(5)|skin(1)	12						GGAACCTTATCAGTGTAATGA	0.398																																					p.Q482X		Atlas-SNP	.											.	ZNF397	51	.	0			c.C1444T						.						113	115	114					18																	32826113		692	1591	2283	SO:0001587	stop_gained	84307	exon4			CCTTATCAGTGTA	BC006172	CCDS32814.1, CCDS45852.1	18p12	2013-01-09	2003-07-22			ENSG00000186812		"-", "Zinc fingers, C2H2-type"	18818	protein-coding gene	gene with protein product		609601	"zinc finger protein 47"	ZNF47			Standard	NM_032347		Approved	ZSCAN15, MGC13250	uc010dmp.3	Q8NF99		ENST00000330501.7:c.1444C>T	chr18.hg19:g.32826113C>T	ENSP00000331577:p.Gln482*	172.0	0.0		169.0	64.0	NM_001135178	Q9BRM2	Nonsense_Mutation	SNP	ENST00000330501.7	hg19	CCDS45852.1	.	.	.	.	.	.	.	.	.	.	C	32	5.164590	0.94727	.	.	ENSG00000186812	ENST00000330501	.	.	.	4.31	3.35	0.38373	.	0.000000	0.32231	N	0.006391	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.9308	0.24439	0.1946:0.617:0.1884:0.0	.	.	.	.	X	482	.	.	Q	+	1	0	ZNF397	31080111	0.000000	0.05858	1.000000	0.80357	0.823000	0.46562	-0.637000	0.05459	2.392000	0.81423	0.305000	0.20034	CAG	.	.		0.398	ZNF397-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442398.1	NM_032347		T	32826113	C	T	32826113	4	4	283	1	0	0	0	0	0	1	0	0	17898	827	29	3	1454	3	ZNF397	18	32826113	Nonsense_Mutation	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	11407278	32826113	45251135	200	41838										
GALNT1	2589	hgsc.bcm.edu	37	chr18	33267146	33267146	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	aaggtgatcggactcttcctGtcaggtaattaatttgtcag	10	7	3	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr18:33267146G>C	ENST00000269195.5	+	5	959	c.856G>C	c.(856-858)Gtc>Ctc	p.V286L	GALNT1_ENST00000537549.1_Missense_Mutation_p.V226L	NM_020474.3	NP_065207.2	Q10472	GALT1_HUMAN	polypeptide N-acetylgalactosaminyltransferase 1	286	Catalytic subdomain B.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|protein O-linked glycosylation via serine (GO:0018242)|protein O-linked glycosylation via threonine (GO:0018243)	extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|manganese ion binding (GO:0030145)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(4)|stomach(1)	21						GACTCTTCCTGTCAGGTAATT	0.403																																					p.V286L		Atlas-SNP	.											.	GALNT1	53	.	0			c.G856C						.						121	121	121					18																	33267146		2203	4300	6503	SO:0001583	missense	2589	exon5			CTTCCTGTCAGGT		CCDS11915.1	18q12.1	2014-03-13	2014-03-13		ENSG00000141429	ENSG00000141429	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4123	protein-coding gene	gene with protein product	"protein-UDP acetylgalactosaminyltransferase 1", "polypeptide GalNAc transferase 1"	602273	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 1 (GalNAc-T1)"			7592619, 12199709	Standard	NM_020474		Approved	GalNAc-T1	uc002kzb.3	Q10472	OTTHUMG00000132567	ENST00000269195.5:c.856G>C	chr18.hg19:g.33267146G>C	ENSP00000269195:p.Val286Leu	135.0	0.0		88.0	21.0	NM_020474	Q86TJ7|Q9UM86	Missense_Mutation	SNP	ENST00000269195.5	hg19	CCDS11915.1	.	.	.	.	.	.	.	.	.	.	G	15.79	2.937040	0.52972	.	.	ENSG00000141429	ENST00000537748;ENST00000269195;ENST00000537549	T;T	0.61510	0.1;0.1	5.5	5.5	0.81552	Glycosyl transferase, family 2 (1);	0.000000	0.85682	D	0.000000	T	0.43809	0.1264	N	0.16368	0.405	0.80722	D	1	B	0.09022	0.002	B	0.11329	0.006	T	0.24048	-1.0171	10	0.30854	T	0.27	.	16.8858	0.86075	0.0:0.0:1.0:0.0	.	286	Q10472	GALT1_HUMAN	L	286;286;226	ENSP00000269195:V286L;ENSP00000440910:V226L	ENSP00000269195:V286L	V	+	1	0	GALNT1	31521144	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.869000	0.99810	2.595000	0.87683	0.585000	0.79938	GTC	.	.		0.403	GALNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255771.2	NM_020474		C	33267146	G	C	33267146	3	2	283	1	0	0	0	0	1	0	0	0	6215	1377	48	4	874	4	GALNT1	18	33267146	Missense_Mutation	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	441033	33267146	44810102	201	41839										
SCAMP4	113178	hgsc.bcm.edu	37	chr19	1924232	1924242	+	Frame_Shift_Del	DEL	GCCCGAGTACC	GCCCGAGTACC	-													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	aacttctcaggcaacagcctGcccgagtaccccactgtgcc							TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	GCCCGAGTACC	GCCCGAGTACC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr19:1924232_1924242delGCCCGAGTACC	ENST00000316097.8	+	7	906_916	c.639_649delGCCCGAGTACC	c.(637-651)ctgcccgagtaccccfs	p.PEYP214fs	SCAMP4_ENST00000409472.1_Frame_Shift_Del_p.PEYP180fs	NM_079834.2	NP_524558.1	Q969E2	SCAM4_HUMAN	secretory carrier membrane protein 4	214					protein transport (GO:0015031)	integral component of membrane (GO:0016021)							Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCAACAGCCTGCCCGAGTACCCCACTGTGCC	0.654																																					p.213_216del		Atlas-Indel,Pindel	.											.	SCAMP4	7	.	0			c.638_648del						.																																			SO:0001589	frameshift_variant	113178	exon7			.	AK091166	CCDS45903.1	19p13.3	2013-02-21			ENSG00000227500	ENSG00000227500		"Secretory carrier membrane proteins"	30385	protein-coding gene	gene with protein product		613764					Standard	NM_079834		Approved	FLJ33847	uc002luj.4	Q969E2	OTTHUMG00000154590	ENST00000316097.8:c.639_649delGCCCGAGTACC	chr19.hg19:g.1924232_1924242delGCCCGAGTACC	ENSP00000316007:p.Pro214fs	75.0	0.0		35.0	13.0	NM_079834	Q8N2N1|Q8NAV0	Frame_Shift_Del	DEL	ENST00000316097.8	hg19	CCDS45903.1																																																																																			.	.		0.654	SCAMP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336210.3	NM_079834		-	1924242	GCCCGAGTACC	-	1924232	7	5	283	1	0	1	0	1	0	0	0	0	13888	1306	46	0	661	0	SCAMP4	19	1924232	Frame_Shift_Del	DEL	GCCCGAGTACC	TCGA-G3-A3CK-01A-11D-A20W-10		1924232	57204751	202	41840										
FBN3	84467	hgsc.bcm.edu	37	chr19	8211044	8211044	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gcagctgggagccagcgtccCatccgcacaggtgcacaggt	14	14	0	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr19:8211044C>T	ENST00000600128.1	-	4	730	c.316G>A	c.(316-318)Ggg>Agg	p.G106R	FBN3_ENST00000270509.2_Missense_Mutation_p.G106R|FBN3_ENST00000601739.1_Missense_Mutation_p.G106R			Q75N90	FBN3_HUMAN	fibrillin 3	106						proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						GCCAGCGTCCCATCCGCACAG	0.657																																					p.G106R		Atlas-SNP	.											.	FBN3	300	.	0			c.G316A						.						28	27	28					19																	8211044		2200	4294	6494	SO:0001583	missense	84467	exon3			GCGTCCCATCCGC		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.316G>A	chr19.hg19:g.8211044C>T	ENSP00000470498:p.Gly106Arg	274.0	0.0		269.0	15.0	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	hg19	CCDS12196.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.270977	0.80469	.	.	ENSG00000142449	ENST00000270509	D	0.91577	-2.87	3.88	3.88	0.44766	.	0.149229	0.43919	U	0.000507	D	0.96140	0.8742	H	0.94462	3.54	0.48135	D	0.999592	D	0.89917	1.0	D	0.91635	0.999	D	0.96562	0.9416	10	0.87932	D	0	.	11.3274	0.49456	0.0:1.0:0.0:0.0	.	106	Q75N90	FBN3_HUMAN	R	106	ENSP00000270509:G106R	ENSP00000270509:G106R	G	-	1	0	FBN3	8117044	0.978000	0.34361	0.129000	0.21949	0.910000	0.53928	2.876000	0.48498	1.725000	0.51514	0.313000	0.20887	GGG	.	.		0.657	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447		T	8211044	C	T	8211044	3	4	283	1	0	0	0	0	1	0	0	0	5712	594	21	3	8357	3	FBN3	19	8211044	Missense_Mutation	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	6286812	8211044	50917939	203	41841										
ACTL9	284382	hgsc.bcm.edu	37	chr19	8807893	8807893	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gaaggcgcgcagggaggccaGgatggagcccccgatccata	16	12	0	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr19:8807893G>A	ENST00000324436.3	-	1	1279	c.1159C>T	c.(1159-1161)Ctg>Ttg	p.L387L		NM_178525.3	NP_848620.3	Q8TC94	ACTL9_HUMAN	actin-like 9	387						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(15)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	36						AGGGAGGCCAGGATGGAGCCC	0.647																																					p.L387L		Atlas-SNP	.											.	ACTL9	74	.	0			c.C1159T						.						35	38	37					19																	8807893		2203	4299	6502	SO:0001819	synonymous_variant	284382	exon1			AGGCCAGGATGGA		CCDS12207.1	19p13.2	2014-08-08			ENSG00000181786	ENSG00000181786			28494	protein-coding gene	gene with protein product							Standard	NM_178525		Approved	MGC33407	uc002mkl.2	Q8TC94	OTTHUMG00000182194	ENST00000324436.3:c.1159C>T	chr19.hg19:g.8807893G>A		107.0	0.0		102.0	29.0	NM_178525	A8K893|Q6X960	Silent	SNP	ENST00000324436.3	hg19	CCDS12207.1																																																																																			.	.		0.647	ACTL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459953.1	NM_178525		A	8807893	G	A	8807893	2	1	283	1	0	0	0	0	0	0	0	1	203	991	35	3		3	ACTL9	19	8807893	Silent	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	596849	8807893	50321090	204	41842										
ZNF560	147741	hgsc.bcm.edu	37	chr19	9578276	9578276	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ccattatgaactctcaaatgTccaaaaagagatgggtaaga	8	7	1	3			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr19:9578276T>C	ENST00000301480.4	-	10	1560	c.1347A>G	c.(1345-1347)ggA>ggG	p.G449G		NM_152476.2	NP_689689.2	Q96MR9	ZN560_HUMAN	zinc finger protein 560	449					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(16)|liver(2)|lung(24)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	65						CTCTCAAATGTCCAAAAAGAG	0.398																																					p.G449G		Atlas-SNP	.											.	ZNF560	162	.	0			c.A1347G						.						134	147	143					19																	9578276		2203	4300	6503	SO:0001819	synonymous_variant	147741	exon10			CAAATGTCCAAAA	AK056548	CCDS12214.1	19p13.2	2013-09-20			ENSG00000198028	ENSG00000198028		"Zinc fingers, C2H2-type", "-"	26484	protein-coding gene	gene with protein product							Standard	NM_152476		Approved	FLJ31986	uc002mlp.1	Q96MR9	OTTHUMG00000180130	ENST00000301480.4:c.1347A>G	chr19.hg19:g.9578276T>C		146.0	0.0		131.0	56.0	NM_152476	Q495S9|Q495T1	Silent	SNP	ENST00000301480.4	hg19	CCDS12214.1																																																																																			.	.		0.398	ZNF560-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449901.1	NM_152476		C	9578276	T	C	9578276	2	2	283	1	0	0	0	0	0	0	0	1	18006	1654	58	2		2	ZNF560	19	9578276	Silent	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	770383	9578276	49550707	205	41843										
PDE4A	5141	hgsc.bcm.edu	37	chr19	10531543	10531543	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ctcccccgcagcacctgtggCggcagcctcggacccccatc	10	21	0	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr19:10531543C>A	ENST00000352831.6	+	1	213	c.103C>A	c.(103-105)Cgg>Agg	p.R35R	PDE4A_ENST00000592685.1_Intron|PDE4A_ENST00000380702.2_Intron	NM_001111307.1	NP_001104777.1	P27815	PDE4A_HUMAN	phosphodiesterase 4A, cAMP-specific	35					cAMP catabolic process (GO:0006198)|cellular response to drug (GO:0035690)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of protein kinase A signaling (GO:0010738)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cytosol (GO:0005829)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	27			OV - Ovarian serous cystadenocarcinoma(20;5.8e-10)|Epithelial(33;7.58e-07)|all cancers(31;3.91e-06)		Caffeine(DB00201)|Dipyridamole(DB00975)|Drotaverine(DB06751)|Dyphylline(DB00651)|Enprofylline(DB00824)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Roflumilast(DB01656)|Theophylline(DB00277)|Tofisopam(DB08811)	GCACCTGTGGCGGCAGCCTCG	0.746																																					p.R35R		Atlas-SNP	.											.	PDE4A	236	.	0			c.C103A						.						6	7	7					19																	10531543		1211	3022	4233	SO:0001819	synonymous_variant	5141	exon1			CTGTGGCGGCAGC		CCDS12238.1, CCDS45961.1, CCDS45962.1, CCDS45963.1, CCDS58649.1	19p13.2	2010-06-24	2010-06-24			ENSG00000065989	3.1.4.17	"Phosphodiesterases"	8780	protein-coding gene	gene with protein product	"phosphodiesterase E2 dunce homolog (Drosophila)"	600126	"phosphodiesterase 4A, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E2)"	DPDE2		8009369	Standard	NM_006202		Approved		uc002moj.2	P27815		ENST00000352831.6:c.103C>A	chr19.hg19:g.10531543C>A		24.0	0.0		20.0	12.0	NM_001111307	O75522|O76092|Q16255|Q16691|Q5DM53|Q6PMT2|Q8IVA7|Q8WUQ3|Q9H3H2	Silent	SNP	ENST00000352831.6	hg19	CCDS45961.1																																																																																			.	.		0.746	PDE4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451244.1			A	10531543	C	A	10531543	2	1	283	1	0	0	0	0	0	0	0	1	11648	759	27	1		1	PDE4A	19	10531543	Silent	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	953267	10531543	48597440	206	41844										
KEAP1	9817	hgsc.bcm.edu	37	chr19	10602811	10602812	+	Frame_Shift_Ins	INS	-	-	CGTA													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gaaccgtcgctgttcgcagtINScgtacttgacccagttgatg							TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr19:10602811_10602812insCGTA	ENST00000171111.5	-	3	1313_1314	c.766_767insTACG	c.(766-768)gacfs	p.D256fs	KEAP1_ENST00000588024.1_5'UTR|CTC-429L19.3_ENST00000592671.1_RNA|KEAP1_ENST00000393623.2_Frame_Shift_Ins_p.D256fs	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	256	BACK.				cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)				breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	CTGTTCGCAGTCGTACTTGACC	0.634																																					p.D256fs		Atlas-Indel,Pindel	.											.	KEAP1	182	.	0			c.767_768insTACG						.																																			SO:0001589	frameshift_variant	9817	exon3			.	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"Kelch-like", "BTB/POZ domain containing"	23177	protein-coding gene	gene with protein product	"kelch-like family member 19"	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.763_766dupTACG	chr19.hg19:g.10602812_10602815dupCGTA	ENSP00000171111:p.Asp256fs	84.0	0.0		103.0	18.0	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Frame_Shift_Ins	INS	ENST00000171111.5	hg19	CCDS12239.1																																																																																			.	.		0.634	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289		CGTA	10602812	-	CGTA	10602811	7	5	283	1	0	1	1	0	0	0	0	0	8150	1667	58	0	1123	0	KEAP1	19	10602811	Frame_Shift_Ins	INS	-	TCGA-G3-A3CK-01A-11D-A20W-10	71268	10602811	48526172	207	41845										
KEAP1	9817	hgsc.bcm.edu	37	chr19	10610398	10610398	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	aacatggccttgaagacaggGctggatgaggccagcaccac	13	11	0	3			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr19:10610398G>T	ENST00000171111.5	-	2	859	c.312C>A	c.(310-312)agC>agA	p.S104R	KEAP1_ENST00000588024.1_5'Flank|KEAP1_ENST00000393623.2_Missense_Mutation_p.S104R	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	104	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)				breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	TGAAGACAGGGCTGGATGAGG	0.617																																					p.S104R		Atlas-SNP	.											.	KEAP1	182	.	0			c.C312A						.						83	67	73					19																	10610398		2203	4300	6503	SO:0001583	missense	9817	exon2			GACAGGGCTGGAT	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"Kelch-like", "BTB/POZ domain containing"	23177	protein-coding gene	gene with protein product	"kelch-like family member 19"	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.312C>A	chr19.hg19:g.10610398G>T	ENSP00000171111:p.Ser104Arg	145.0	0.0		157.0	55.0	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Missense_Mutation	SNP	ENST00000171111.5	hg19	CCDS12239.1	.	.	.	.	.	.	.	.	.	.	G	13.22	2.171438	0.38315	.	.	ENSG00000079999	ENST00000171111;ENST00000393623	D;D	0.85861	-2.04;-2.04	4.68	3.65	0.41850	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.099963	0.64402	D	0.000004	D	0.95046	0.8396	H	0.98754	4.32	0.58432	D	0.999997	D	0.89917	1.0	D	0.91635	0.999	D	0.95026	0.8165	10	0.87932	D	0	.	10.599	0.45356	0.0958:0.0:0.9042:0.0	.	104	Q14145	KEAP1_HUMAN	R	104	ENSP00000171111:S104R;ENSP00000377245:S104R	ENSP00000171111:S104R	S	-	3	2	KEAP1	10471398	1.000000	0.71417	0.998000	0.56505	0.108000	0.19459	2.606000	0.46291	0.980000	0.38523	-0.379000	0.06801	AGC	.	.		0.617	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289		T	10610398	G	T	10610398	3	4	283	1	0	0	0	0	1	0	0	0	8150	1194	42	3	1582	3	KEAP1	19	10610398	Missense_Mutation	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	7587	10610398	48518585	208	41846										
LPHN1	22859	hgsc.bcm.edu	37	chr19	14261860	14261860	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	agtagatttcgggggggccgGggggtgcgggagggggtggg	27	4	0	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr19:14261860G>T	ENST00000340736.6	-	24	4547	c.4250C>A	c.(4249-4251)cCc>cAc	p.P1417H	CTB-55O6.12_ENST00000588387.1_RNA|CTB-55O6.12_ENST00000588658.1_RNA|LPHN1_ENST00000361434.3_Missense_Mutation_p.P1412H	NM_001008701.2	NP_001008701.1	O94910	LPHN1_HUMAN	latrophilin 1	1417	Poly-Pro.				calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|heterophilic cell-cell adhesion (GO:0007157)|neuropeptide signaling pathway (GO:0007218)|positive regulation of synapse maturation (GO:0090129)	axon (GO:0030424)|cell junction (GO:0030054)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)			central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						GGGGGGGCCGGGGGGTGCGGG	0.726																																					p.P1417H		Atlas-SNP	.											.	LPHN1	107	.	0			c.C4250A						.						2	2	2					19																	14261860		1153	2788	3941	SO:0001583	missense	22859	exon24			GGGCCGGGGGGTG	AB020628	CCDS12307.1, CCDS32928.1	19p13.2	2014-08-08				ENSG00000072071		"-", "GPCR / Class B : Orphans"	20973	protein-coding gene	gene with protein product						10994649	Standard	NM_014921		Approved	KIAA0821, CIRL1, LEC2	uc010xnn.2	O94910		ENST00000340736.6:c.4250C>A	chr19.hg19:g.14261860G>T	ENSP00000340688:p.Pro1417His	41.0	0.0		91.0	42.0	NM_001008701	Q96IE7|Q9BU07|Q9HAR3	Missense_Mutation	SNP	ENST00000340736.6	hg19	CCDS32928.1	.	.	.	.	.	.	.	.	.	.	G	10.85	1.466249	0.26335	.	.	ENSG00000072071	ENST00000340736;ENST00000361434	T;T	0.70164	-0.46;-0.46	3.94	3.94	0.45596	GPCR, family 2, latrophilin, C-terminal (1);	0.241291	0.35179	N	0.003391	T	0.48642	0.1511	N	0.14661	0.345	0.37287	D	0.90808	P;P	0.44521	0.804;0.837	B;B	0.39590	0.202;0.304	T	0.60010	-0.7346	10	0.45353	T	0.12	.	13.4745	0.61301	0.0:0.0:1.0:0.0	.	1412;1417	O94910-2;O94910	.;LPHN1_HUMAN	H	1417;1412	ENSP00000340688:P1417H;ENSP00000355328:P1412H	ENSP00000340688:P1417H	P	-	2	0	LPHN1	14122860	0.991000	0.36638	0.927000	0.36925	0.179000	0.23085	2.178000	0.42519	1.764000	0.52075	0.205000	0.17691	CCC	.	.		0.726	LPHN1-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459696.1	NM_014921		T	14261860	G	T	14261860	3	4	283	1	0	0	0	0	1	0	0	0	8924	1232	43	3	178	3	LPHN1	19	14261860	Missense_Mutation	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	3651462	14261860	44867123	209	41847										
ZNF675	171392	hgsc.bcm.edu	37	chr19	23837293	23837293	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	attaaagactttcacatattTatcacattgaaacattttgc	3	7	2	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr19:23837293T>G	ENST00000359788.4	-	4	610	c.442A>C	c.(442-444)Aaa>Caa	p.K148Q	ZNF675_ENST00000600313.1_Intron|ZNF675_ENST00000601935.1_Intron|ZNF675_ENST00000596211.1_Intron	NM_138330.2	NP_612203.2	Q8TD23	ZN675_HUMAN	zinc finger protein 675	148				K -> E (in Ref. 1; AAK95822). {ECO:0000305}.	bone resorption (GO:0045453)|cytokine-mediated signaling pathway (GO:0019221)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of interleukin-1-mediated signaling pathway (GO:2000660)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	DNA binding (GO:0003677)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				TTCACATATTTATCACATTGA	0.308																																					p.K148Q		Atlas-SNP	.											.	ZNF675	88	.	0			c.A442C						.						68	68	68					19																	23837293		2202	4298	6500	SO:0001583	missense	171392	exon4			CATATTTATCACA		CCDS32981.1	19p12	2013-01-08						"Zinc fingers, C2H2-type", "-"	30768	protein-coding gene	gene with protein product	"TRAF6 inhibitory zinc finger"					11751921	Standard	NM_138330		Approved	TIZ, TBZF	uc002nri.3	Q8TD23		ENST00000359788.4:c.442A>C	chr19.hg19:g.23837293T>G	ENSP00000352836:p.Lys148Gln	97.0	0.0		119.0	6.0	NM_138330	Q8N211	Missense_Mutation	SNP	ENST00000359788.4	hg19	CCDS32981.1	.	.	.	.	.	.	.	.	.	.	.	9.941	1.217491	0.22373	.	.	ENSG00000197372	ENST00000359788	T	0.27256	1.68	0.916	-0.309	0.12769	.	.	.	.	.	T	0.24198	0.0586	M	0.65320	2	0.09310	N	1	B	0.32350	0.366	B	0.37304	0.246	T	0.28267	-1.0049	9	0.35671	T	0.21	.	3.793	0.08728	0.0:0.6215:0.0:0.3785	.	148	Q8TD23	ZN675_HUMAN	Q	148	ENSP00000352836:K148Q	ENSP00000352836:K148Q	K	-	1	0	ZNF675	23629133	0.000000	0.05858	0.292000	0.24919	0.289000	0.27227	-0.259000	0.08721	0.257000	0.21650	0.254000	0.18369	AAA	.	.		0.308	ZNF675-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466433.1	NM_138330		G	23837293	T	G	23837293	3	3	283	1	0	0	0	0	1	0	0	0	18097	1763	61	5	1268	5	ZNF675	19	23837293	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	9575433	23837293	35291690	210	41848										
ZFP82	284406	hgsc.bcm.edu	37	chr19	36884388	36884388	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	taaaggcttttccacactctTtacacacatagggtttctca	5	11	2	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr19:36884388T>G	ENST00000392161.3	-	5	1096	c.854A>C	c.(853-855)aAa>aCa	p.K285T	ZFP82_ENST00000392171.1_Missense_Mutation_p.K285T	NM_133466.2	NP_597723.1	Q8N141	ZFP82_HUMAN	ZFP82 zinc finger protein	285					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TCCACACTCTTTACACACATA	0.453																																					p.K285T		Atlas-SNP	.											.	ZFP82	71	.	0			c.A854C						.						150	147	148					19																	36884388		2203	4300	6503	SO:0001583	missense	284406	exon5			CACTCTTTACACA	AL834267	CCDS12493.1	19q13.13	2013-01-08	2012-11-27	2008-07-01		ENSG00000181007		"Zinc fingers, C2H2-type", "-"	28682	protein-coding gene	gene with protein product			"zinc finger protein 545", "zinc finger protein 82 homolog (mouse)", "zinc finger protein 82"	ZNF545		11853319	Standard	NM_133466		Approved	MGC45380, KIAA1948	uc002ody.1	Q8N141		ENST00000392161.3:c.854A>C	chr19.hg19:g.36884388T>G	ENSP00000431265:p.Lys285Thr	118.0	0.0		121.0	64.0	NM_133466	Q8NC63|Q8TF53	Missense_Mutation	SNP	ENST00000392161.3	hg19	CCDS12493.1	.	.	.	.	.	.	.	.	.	.	T	8.717	0.913484	0.17907	.	.	ENSG00000181007	ENST00000392161;ENST00000392171	T;T	0.08458	3.09;3.09	4.34	0.932	0.19466	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.336296	0.21375	N	0.075562	T	0.04998	0.0134	N	0.17248	0.465	0.21473	N	0.999675	B	0.06786	0.001	B	0.16289	0.015	T	0.35847	-0.9772	10	0.44086	T	0.13	.	8.0553	0.30602	0.0:0.094:0.5441:0.3619	.	285	Q8N141	ZFP82_HUMAN	T	285	ENSP00000431265:K285T;ENSP00000446080:K285T	ENSP00000431265:K285T	K	-	2	0	ZFP82	41576228	0.000000	0.05858	0.999000	0.59377	0.801000	0.45260	-2.029000	0.01430	0.301000	0.22738	-0.418000	0.06021	AAA	.	.		0.453	ZFP82-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109552.2	NM_133466		G	36884388	T	G	36884388	3	3	283	1	0	0	0	0	1	0	0	0	17668	1841	64	5	748	5	ZFP82	19	36884388	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	13047095	36884388	22244595	211	41849										
ZNF383	163087	hgsc.bcm.edu	37	chr19	37734483	37734484	+	Frame_Shift_Del	DEL	CC	CC	-													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gaattcacactggtgaaaagCcctataactgtaaggaatgt					rs149725989		TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	CC	CC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr19:37734483_37734484delCC	ENST00000589413.1	+	8	1928_1929	c.1345_1346delCC	c.(1345-1347)cccfs	p.P449fs	ZNF383_ENST00000590503.1_Frame_Shift_Del_p.P449fs|ZNF383_ENST00000352998.3_Frame_Shift_Del_p.P449fs			Q8NA42	ZN383_HUMAN	zinc finger protein 383	449					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(8)|ovary(1)|skin(1)	15			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TGGTGAAAAGCCCTATAACTGT	0.366																																					p.448_449del		Atlas-Indel,Pindel	.											.	ZNF383	42	.	0			c.1344_1345del						.																																			SO:0001589	frameshift_variant	163087	exon5			.	AY438646	CCDS12501.1	19q13.13	2013-01-08				ENSG00000188283		"Zinc fingers, C2H2-type", "-"	18609	protein-coding gene	gene with protein product							Standard	NM_152604		Approved	FLJ35863	uc002ofu.1	Q8NA42		ENST00000589413.1:c.1345_1346delCC	chr19.hg19:g.37734483_37734484delCC	ENSP00000464871:p.Pro449fs	78.0	0.0		63.0	20.0	NM_152604	Q6X2C7	Frame_Shift_Del	DEL	ENST00000589413.1	hg19	CCDS12501.1																																																																																			.	.		0.366	ZNF383-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458141.1	NM_152604		-	37734484	CC	-	37734483	7	5	283	1	0	1	0	1	0	0	0	0	17889	739	26	0	1359	0	ZNF383	19	37734483	Frame_Shift_Del	DEL	CC	TCGA-G3-A3CK-01A-11D-A20W-10	850095	37734483	21394500	212	41850										
POU2F2	5452	hgsc.bcm.edu	37	chr19	42599725	42599725	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	aactcttctctaaggcgaagCggacgtttgtctcgatgctg	11	10	3	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr19:42599725C>T	ENST00000526816.2	-	10	941	c.926G>A	c.(925-927)cGc>cAc	p.R309H	POU2F2_ENST00000389341.5_Missense_Mutation_p.R293H|POU2F2_ENST00000560398.1_Missense_Mutation_p.R315H|POU2F2_ENST00000560558.1_Missense_Mutation_p.R254H|POU2F2_ENST00000529952.1_Missense_Mutation_p.R309H|POU2F2_ENST00000533720.1_Missense_Mutation_p.R293H|POU2F2_ENST00000342301.4_Missense_Mutation_p.R309H|POU2F2_ENST00000529067.1_Missense_Mutation_p.R293H			P09086	PO2F2_HUMAN	POU class 2 homeobox 2	309					cell maturation (GO:0048469)|humoral immune response (GO:0006959)|immunoglobulin secretion involved in immune response (GO:0002380)|mature B cell differentiation (GO:0002335)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(5)|lung(4)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Prostate(69;0.059)			Dolutegravir(DB08930)	TAAGGCGAAGCGGACGTTTGT	0.672																																					p.R309H		Atlas-SNP	.											.	POU2F2	106	.	0			c.G926A						.						35	37	36					19																	42599725		2203	4300	6503	SO:0001583	missense	5452	exon10			GCGAAGCGGACGT		CCDS33035.1, CCDS56094.1, CCDS56095.1, CCDS58665.1	19q13.2	2011-06-20	2007-07-13					"Homeoboxes / POU class"	9213	protein-coding gene	gene with protein product		164176	"POU domain class 2, transcription factor 2"	OTF2			Standard	NM_001207026		Approved	OCT2	uc002osp.3	P09086		ENST00000526816.2:c.926G>A	chr19.hg19:g.42599725C>T	ENSP00000431603:p.Arg309His	88.0	0.0		77.0	11.0	NM_001207025	Q16648|Q7M4M8|Q9BRS4	Missense_Mutation	SNP	ENST00000526816.2	hg19	CCDS56095.1	.	.	.	.	.	.	.	.	.	.	C	33	5.254243	0.95336	.	.	ENSG00000028277	ENST00000389341;ENST00000342301;ENST00000292077;ENST00000533720;ENST00000526816;ENST00000529067;ENST00000529952	D;D;D;D;D	0.96232	-3.95;-3.95;-3.95;-3.95;-3.95	4.09	4.09	0.47781	Homeodomain-related (1);Homeobox (3);POU (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.98444	0.9482	M	0.92317	3.295	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.993;1.0	D	0.99453	1.0941	10	0.87932	D	0	.	15.6188	0.76790	0.0:1.0:0.0:0.0	.	293;309;293	P09086-4;P09086;P09086-3	.;PO2F2_HUMAN;.	H	293;309;309;293;308;293;309	ENSP00000373992:R293H;ENSP00000339369:R309H;ENSP00000437221:R293H;ENSP00000437224:R293H;ENSP00000436988:R309H	ENSP00000292077:R309H	R	-	2	0	POU2F2	47291565	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.774000	0.62339	2.271000	0.75665	0.655000	0.94253	CGC	.	.		0.672	POU2F2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387329.3			T	42599725	C	T	42599725	3	4	283	1	0	0	0	0	1	0	0	0	12281	768	27	1	533	1	POU2F2	19	42599725	Missense_Mutation	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	4865242	42599725	16529258	213	41851										
ERCC2	2068	hgsc.bcm.edu	37	chr19	45860557	45860557	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gaggcagacccgtgccagcgTcatggtgaaggttgccatgg	16	10	1	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr19:45860557T>C	ENST00000391945.4	-	15	1527	c.1450A>G	c.(1450-1452)Acg>Gcg	p.T484A	ERCC2_ENST00000391944.3_Missense_Mutation_p.T406A	NM_000400.3	NP_000391.1	P18074	ERCC2_HUMAN	excision repair cross-complementation group 2	484	Mediates interaction with MMS19.				7-methylguanosine mRNA capping (GO:0006370)|aging (GO:0007568)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|central nervous system myelin formation (GO:0032289)|chromosome segregation (GO:0007059)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|embryonic cleavage (GO:0040016)|erythrocyte maturation (GO:0043249)|extracellular matrix organization (GO:0030198)|gene expression (GO:0010467)|hair cell differentiation (GO:0035315)|hair follicle maturation (GO:0048820)|hematopoietic stem cell differentiation (GO:0060218)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|spinal cord development (GO:0021510)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)|viral process (GO:0016032)	cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|MMXD complex (GO:0071817)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			large_intestine(4)|lung(2)|ovary(1)|pancreas(1)|stomach(1)	9		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		CGTGCCAGCGTCATGGTGAAG	0.652			"Mis, N, F, S"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.T484A		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (D)	19	19q13.2-q13.3	2068	"excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D)"		E	.	ERCC2	78	.	0			c.A1450G						.						91	76	82					19																	45860557		2203	4300	6503	SO:0001583	missense	2068	exon15	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	CCAGCGTCATGGT		CCDS33049.1, CCDS46112.1	19q13.3	2014-09-17	2014-03-07		ENSG00000104884	ENSG00000104884	3.6.4.12	"General transcription factor IIH complex subunits"	3434	protein-coding gene	gene with protein product	"excision repair cross-complementing rodent repair deficiency, complementation group 2 protein", "TFIIH basal transcription factor complex helicase XPB subunit"	126340	"xeroderma pigmentosum complementary group D", "excision repair cross-complementing rodent repair deficiency, complementation group 2"	XPD		8413672, 2184031	Standard	NM_000400		Approved	MAG, EM9, MGC102762, MGC126218, MGC126219, TFIIH	uc002pbj.2	P18074	OTTHUMG00000048190	ENST00000391945.4:c.1450A>G	chr19.hg19:g.45860557T>C	ENSP00000375809:p.Thr484Ala	179.0	0.0		169.0	66.0	NM_000400	Q2TB78|Q2YDY2|Q7KZU6|Q8N721	Missense_Mutation	SNP	ENST00000391945.4	hg19	CCDS33049.1	.	.	.	.	.	.	.	.	.	.	T	25.1	4.606965	0.87157	.	.	ENSG00000104884	ENST00000391941;ENST00000391942;ENST00000391945;ENST00000391944	T;D	0.82344	-1.37;-1.6	5.27	5.27	0.74061	.	0.108809	0.64402	D	0.000008	D	0.88897	0.6562	M	0.93939	3.475	0.80722	D	1	B;P;P	0.42518	0.429;0.594;0.782	P;B;P	0.45681	0.49;0.354;0.472	D	0.90966	0.4816	10	0.87932	D	0	-20.816	11.5741	0.50852	0.0:0.0:0.0:1.0	.	406;484;177	E7EVE9;P18074;Q6ZNQ5	.;ERCC2_HUMAN;.	A	434;460;484;406	ENSP00000375809:T484A;ENSP00000375808:T406A	ENSP00000375805:T434A	T	-	1	0	ERCC2	50552397	1.000000	0.71417	0.999000	0.59377	0.982000	0.71751	6.731000	0.74785	1.991000	0.58162	0.533000	0.62120	ACG	.	.		0.652	ERCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109626.2	NM_000400		C	45860557	T	C	45860557	3	2	283	1	0	0	0	0	1	0	0	0	5215	1667	58	2	868	2	ERCC2	19	45860557	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	3260832	45860557	13268426	214	41852										
PRKD2	25865	hgsc.bcm.edu	37	chr19	47214295	47214320	+	Splice_Site	DEL	GCTGTAGGCGGAAAATAGGGGTGGAT	GCTGTAGGCGGAAAATAGGGGTGGAT	-													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	agtcctcgaaggtggccgagGctgtaggcggaaaatagggg							TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	GCTGTAGGCGGAAAATAGGGGTGGAT	GCTGTAGGCGGAAAATAGGGGTGGAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr19:47214295_47214320delGCTGTAGGCGGAAAATAGGGGTGGAT	ENST00000291281.4	-	3	605	c.380delATCCACCCCTATTTTCCGCCTACAGC	c.(379-381)gat>gt	p.D127fs	PRKD2_ENST00000433867.1_Splice_Site_p.D127fs|PRKD2_ENST00000601806.1_5'UTR|MIR320E_ENST00000390179.3_RNA|PRKD2_ENST00000595515.1_Splice_Site_p.D127fs|PRKD2_ENST00000600194.1_5'UTR			Q9BZL6	KPCD2_HUMAN	protein kinase D2	127					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial tube morphogenesis (GO:0061154)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(13)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	41		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000189)|all cancers(93;0.000545)|Epithelial(262;0.0219)|GBM - Glioblastoma multiforme(486;0.0353)		GGTGGCCGAGGCTGTAGGCGGAAAATAGGGGTGGATGCTTGAGGCG	0.593																																					p.127_127del		Atlas-INDEL	.											.	PRKD2	94	.	0			c.380_381del						.																																			SO:0001630	splice_region_variant	25865	exon3			.	AF151021	CCDS12689.1, CCDS59401.1	19q13.2	2013-01-10				ENSG00000105287		"Pleckstrin homology (PH) domain containing"	17293	protein-coding gene	gene with protein product		607074				11042152, 11062248	Standard	NM_001079880		Approved	PKD2, HSPC187, DKFZP586E0820	uc002pfj.3	Q9BZL6		ENST00000291281.4:c.380-1ATCCACCCCTATTTTCCGCCTACAGC>-	chr19.hg19:g.47214295_47214320delGCTGTAGGCGGAAAATAGGGGTGGAT		186.0	0.0		109.0	14.0	NM_016457	Q8TB08|Q9P0T6|Q9Y3X8	Frame_Shift_Del	DEL	ENST00000291281.4	hg19	CCDS12689.1																																																																																			.	.		0.593	PRKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466591.1	NM_016457	Frame_Shift_Del	-	47214320	GCTGTAGGCGGAAAATAGGGGTGGAT	-	47214295	8	5	283	1	0	1	0	1	0	0	1	0	12531	1217	42	0	2320	0	PRKD2	19	47214295	Splice_Site	DEL	GCTGTAGGCGGAAAATAGGGGTGGAT	TCGA-G3-A3CK-01A-11D-A20W-10	1353738	47214295	11914688	215	41853										
TEAD2	8463	hgsc.bcm.edu	37	chr19	49845749	49845749	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	atcatgtatcgctcaggcagCtgccgcaacttgtgcaagaa	10	11	2	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr19:49845749C>G	ENST00000311227.2	-	11	1266	c.1176G>C	c.(1174-1176)caG>caC	p.Q392H	TEAD2_ENST00000598810.1_Missense_Mutation_p.Q396H|TEAD2_ENST00000539846.1_Missense_Mutation_p.Q264H|CTC-301O7.4_ENST00000358234.4_lincRNA|TEAD2_ENST00000377214.4_Missense_Mutation_p.Q395H|TEAD2_ENST00000601519.1_Missense_Mutation_p.Q395H|TEAD2_ENST00000593945.1_Missense_Mutation_p.Q396H	NM_001256659.1|NM_003598.1	NP_001243588.1|NP_003589.1	Q15562	TEAD2_HUMAN	TEA domain family member 2	392	Transcriptional activation. {ECO:0000255}.				gene expression (GO:0010467)|hippo signaling (GO:0035329)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)	29		all_lung(116;7.65e-05)|Lung NSC(112;0.000132)|all_neural(266;0.0506)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00093)|GBM - Glioblastoma multiforme(486;0.0467)		GCTCAGGCAGCTGCCGCAACT	0.612																																					p.Q396H		Atlas-SNP	.											.	TEAD2	70	.	0			c.G1188C						.						73	66	68					19																	49845749		2203	4300	6503	SO:0001583	missense	8463	exon12			AGGCAGCTGCCGC	X94440	CCDS12761.1, CCDS58670.1, CCDS58671.1, CCDS59406.1	19q13.3	2008-07-22							11715	protein-coding gene	gene with protein product		601729				9889009, 8702974	Standard	NM_003598		Approved	TEF-4, ETF, TEF4	uc031rls.1	Q15562		ENST00000311227.2:c.1176G>C	chr19.hg19:g.49845749C>G	ENSP00000310701:p.Gln392His	154.0	0.0		181.0	63.0	NM_001256660	B4DTJ6|M0R1T9|Q8NA25|Q96IG3	Missense_Mutation	SNP	ENST00000311227.2	hg19	CCDS12761.1	.	.	.	.	.	.	.	.	.	.	C	1.446	-0.566263	0.03910	.	.	ENSG00000074219	ENST00000311227;ENST00000377214;ENST00000539846	T;T;T	0.28895	1.59;1.59;1.59	3.9	3.9	0.45041	.	0.105828	0.40728	N	0.001032	T	0.18045	0.0433	N	0.01809	-0.71	0.46416	D	0.999039	D;B;P	0.55385	0.971;0.0;0.948	P;B;P	0.55161	0.77;0.002;0.601	T	0.08086	-1.0739	10	0.02654	T	1	-21.84	14.2043	0.65725	0.0:1.0:0.0:0.0	.	264;392;395	B4DTJ6;Q15562;Q8NA25	.;TEAD2_HUMAN;.	H	392;395;264	ENSP00000310701:Q392H;ENSP00000366419:Q395H;ENSP00000437928:Q264H	ENSP00000310701:Q392H	Q	-	3	2	TEAD2	54537561	0.987000	0.35691	1.000000	0.80357	0.964000	0.63967	0.242000	0.18087	2.127000	0.65507	0.609000	0.83330	CAG	.	.		0.612	TEAD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465465.1	NM_003598		G	49845749	C	G	49845749	3	3	283	1	0	0	0	0	1	0	0	0	15754	796	28	4	175	4	TEAD2	19	49845749	Missense_Mutation	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	2631454	49845749	9283234	216	41854										
ZNF432	9668	hgsc.bcm.edu	37	chr19	52538392	52538392	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ctattggcttttgtacttacAgagaatttagctgcagaata	8	6	0	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr19:52538392A>T	ENST00000594154.1	-	5	752	c.540T>A	c.(538-540)tcT>tcA	p.S180S	ZNF432_ENST00000221315.5_Silent_p.S180S			O94892	ZN432_HUMAN	zinc finger protein 432	180					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	29		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.0054)|OV - Ovarian serous cystadenocarcinoma(262;0.0182)		TTGTACTTACAGAGAATTTAG	0.353																																					p.S180S		Atlas-SNP	.											.	ZNF432	172	.	0			c.T540A						.						66	65	65					19																	52538392		2203	4300	6503	SO:0001819	synonymous_variant	9668	exon5			ACTTACAGAGAAT	AB018341	CCDS12848.1	19q13.41	2013-01-08				ENSG00000256087		"Zinc fingers, C2H2-type", "-"	20810	protein-coding gene	gene with protein product						9872452	Standard	NM_014650		Approved	KIAA0798	uc002pyk.3	O94892		ENST00000594154.1:c.540T>A	chr19.hg19:g.52538392A>T		81.0	0.0		100.0	30.0	NM_014650		Silent	SNP	ENST00000594154.1	hg19	CCDS12848.1																																																																																			.	.		0.353	ZNF432-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462410.1	NM_014650		T	52538392	A	T	52538392	2	4	283	1	0	0	0	0	0	0	0	1	17921	175	7	4		4	ZNF432	19	52538392	Silent	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	2692643	52538392	6590591	217	41855										
NLRP11	204801	hgsc.bcm.edu	37	chr19	56320455	56320455	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tggtatccaaaggatgtctcAagaatctttctcctgtttgc	8	9	3	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr19:56320455A>C	ENST00000589093.1	-	3	1614	c.1521T>G	c.(1519-1521)ctT>ctG	p.L507L	NLRP11_ENST00000592953.1_Silent_p.L408L|NLRP11_ENST00000589824.2_Silent_p.L507L|NLRP11_ENST00000360133.3_Silent_p.L507L|NLRP11_ENST00000443188.1_Silent_p.L507L			P59045	NAL11_HUMAN	NLR family, pyrin domain containing 11	507							ATP binding (GO:0005524)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	66		Colorectal(82;0.0002)		GBM - Glioblastoma multiforme(193;0.0325)		AGGATGTCTCAAGAATCTTTC	0.418																																					p.L507L		Atlas-SNP	.											.	NLRP11	139	.	0			c.T1521G						.						118	117	118					19																	56320455		2203	4300	6503	SO:0001819	synonymous_variant	204801	exon5			TGTCTCAAGAATC	AY095145	CCDS12935.1, CCDS74458.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179873		"Nucleotide-binding domain and leucine rich repeat containing"	22945	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 11"	609664	"NACHT, leucine rich repeat and PYD containing 11"	NALP11		12563287, 12019269	Standard	NM_145007		Approved	PYPAF6, NOD17, PAN10, CLR19.6	uc010ygf.2	P59045		ENST00000589093.1:c.1521T>G	chr19.hg19:g.56320455A>C		189.0	0.0		177.0	58.0	NM_145007	C9JSF5|Q2TV85|Q2TV86|Q53ZZ0|Q8NBF5	Silent	SNP	ENST00000589093.1	hg19	CCDS12935.1																																																																																			.	.		0.418	NLRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453657.1	NM_145007		C	56320455	A	C	56320455	2	2	283	1	0	0	0	0	0	0	0	1	10482	117	5	5		5	NLRP11	19	56320455	Silent	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	3782063	56320455	2808528	218	41856										
TCF15	6939	hgsc.bcm.edu	37	chr20	590855	590855	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gggtacagcacgtgcgcgccGacgggccgcagcagcgcgaa	17	14	0	0	rs45526442		TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr20:590855G>A	ENST00000246080.3	-	1	187	c.27C>T	c.(25-27)gtC>gtT	p.V9V		NM_004609.3	NP_004600.2	Q12870	TCF15_HUMAN	transcription factor 15 (basic helix-loop-helix)	9					death (GO:0016265)|ear development (GO:0043583)|eating behavior (GO:0042755)|establishment of epithelial cell apical/basal polarity (GO:0045198)|mesenchymal to epithelial transition (GO:0060231)|mesoderm development (GO:0007498)|muscle organ morphogenesis (GO:0048644)|neuromuscular process controlling posture (GO:0050884)|paraxial mesoderm development (GO:0048339)|post-anal tail morphogenesis (GO:0036342)|regulation of gene expression involved in extracellular matrix organization (GO:1901311)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|respiratory system process (GO:0003016)|skeletal system morphogenesis (GO:0048705)|skin development (GO:0043588)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|lung(2)|prostate(1)	4		Breast(17;0.231)				CGTGCGCGCCGACGGGCCGCA	0.776																																					p.V9V		Atlas-SNP	.											.	TCF15	6	.	0			c.C27T						.						2	2	2					20																	590855		1302	2484	3786	SO:0001819	synonymous_variant	6939	exon1			CGCGCCGACGGGC		CCDS33432.1	20p13	2013-05-21			ENSG00000125878	ENSG00000125878		"Basic helix-loop-helix proteins"	11627	protein-coding gene	gene with protein product		601010				8825648, 8041747	Standard	NM_004609		Approved	EC2, PARAXIS, bHLHa40	uc002wdz.3	Q12870	OTTHUMG00000031640	ENST00000246080.3:c.27C>T	chr20.hg19:g.590855G>A		4.0	0.0		10.0	6.0	NM_004609	Q9NQQ1	Silent	SNP	ENST00000246080.3	hg19	CCDS33432.1																																																																																			.	G|0.950;A|0.050		0.776	TCF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077475.2	NM_004609		A	590855	G	A	590855	2	1	283	1	0	0	0	0	0	0	0	1	15703	1045	37	1		1	TCF15	20	590855	Silent	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10		590855	62434665	219	41857										
NOP56	10528	hgsc.bcm.edu	37	chr20	2633966	2633966	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ctgggcaaattccacagcatCgttcgtctggtggccttttg	11	11	1	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr20:2633966C>G	ENST00000329276.5	+	3	651	c.135C>G	c.(133-135)atC>atG	p.I45M	MIR1292_ENST00000408135.1_RNA|SNORD110_ENST00000408189.1_RNA|SNORD86_ENST00000391196.1_RNA|SNORA51_ENST00000606420.1_RNA	NM_006392.3	NP_006383.2	O00567	NOP56_HUMAN	NOP56 ribonucleoprotein	45					cell death (GO:0008219)|rRNA processing (GO:0006364)	box C/D snoRNP complex (GO:0031428)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|snoRNA binding (GO:0030515)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25						TCCACAGCATCGTTCGTCTGG	0.577																																					p.I45M		Atlas-SNP	.											.	NOP56	73	.	0			c.C135G						.						288	253	265					20																	2633966		2203	4300	6503	SO:0001583	missense	10528	exon3			CAGCATCGTTCGT	Y12065	CCDS13030.1	20p13	2012-12-10	2012-12-10	2009-01-13	ENSG00000101361	ENSG00000101361			15911	protein-coding gene	gene with protein product	"spinocerebellar ataxia 36"	614154	"nucleolar protein 5A (56kD with KKE/D repeat)", "nucleolar protein 5A (56kDa with KKE/D repeat)", "NOP56 ribonucleoprotein homolog (yeast)"	NOL5A		9372940, 21683323	Standard	NR_027700		Approved	SCA36	uc002wgh.3	O00567	OTTHUMG00000031703	ENST00000329276.5:c.135C>G	chr20.hg19:g.2633966C>G	ENSP00000370589:p.Ile45Met	303.0	0.0		261.0	44.0	NM_006392	Q2M3T6|Q9NQ05	Missense_Mutation	SNP	ENST00000329276.5	hg19	CCDS13030.1	.	.	.	.	.	.	.	.	.	.	C	10.74	1.434073	0.25813	.	.	ENSG00000101361	ENST00000329276;ENST00000445139	T;T	0.57907	0.37;0.94	5.59	2.39	0.29439	NOP5, N-terminal (1);	0.261492	0.47852	D	0.000213	T	0.31136	0.0787	N	0.20304	0.555	0.41476	D	0.988136	B	0.34313	0.448	B	0.37943	0.261	T	0.09207	-1.0685	10	0.07030	T	0.85	-8.1595	7.2301	0.26038	0.0:0.6963:0.1418:0.1619	.	45	O00567	NOP56_HUMAN	M	45	ENSP00000370589:I45M;ENSP00000388497:I45M	ENSP00000370589:I45M	I	+	3	3	NOP56	2581966	0.997000	0.39634	1.000000	0.80357	0.974000	0.67602	0.318000	0.19504	1.375000	0.46248	0.555000	0.69702	ATC	.	.		0.577	NOP56-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077631.2	NM_006392		G	2633966	C	G	2633966	3	3	283	1	0	0	0	0	1	0	0	0	10548	874	31	4	145	4	NOP56	20	2633966	Missense_Mutation	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	2043111	2633966	60391554	220	41858										
FAM83C	128876	hgsc.bcm.edu	37	chr20	33875240	33875240	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ctggaggaggggccgggagcGaggaagcagaggtgacccca	20	9	0	2	rs375816362		TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr20:33875240G>A	ENST00000374408.3	-	4	1438	c.1342C>T	c.(1342-1344)Cgc>Tgc	p.R448C	EIF6_ENST00000374450.3_5'Flank|EIF6_ENST00000374436.3_5'Flank|FAM83C-AS1_ENST00000429167.1_RNA|EIF6_ENST00000462894.1_5'Flank|EIF6_ENST00000374443.3_5'Flank	NM_178468.5	NP_848563.1	Q9BQN1	FA83C_HUMAN	family with sequence similarity 83, member C	448										central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(18;0.00252)			GGCCGGGAGCGAGGAAGCAGA	0.652													G|||	1	0.000199681	0	0	5008	,	,		17573	0		0	False		,,,				2504	0.001				p.R448C		Atlas-SNP	.											.	FAM83C	80	.	0			c.C1342T						.						41	36	38					20																	33875240		2203	4300	6503	SO:0001583	missense	128876	exon4			GGGAGCGAGGAAG	AL121753	CCDS13251.1	20q11.22	2011-04-01	2006-03-23	2006-03-23	ENSG00000125998	ENSG00000125998			16121	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 128"	C20orf128			Standard	NM_178468		Approved	dJ614O4.7	uc021wck.1	Q9BQN1	OTTHUMG00000032332	ENST00000374408.3:c.1342C>T	chr20.hg19:g.33875240G>A	ENSP00000363529:p.Arg448Cys	101.0	0.0		86.0	35.0	NM_178468	Q14D67|Q5JWN6|Q8N276	Missense_Mutation	SNP	ENST00000374408.3	hg19	CCDS13251.1	.	.	.	.	.	.	.	.	.	.	G	9.722	1.159888	0.21454	.	.	ENSG00000125998	ENST00000374408	T	0.07114	3.22	4.81	0.47	0.16747	.	0.888176	0.09695	N	0.767816	T	0.08088	0.0202	L	0.48877	1.53	0.09310	N	1	B	0.13145	0.007	B	0.06405	0.002	T	0.34551	-0.9824	10	0.72032	D	0.01	-17.195	5.4886	0.16763	0.1031:0.0:0.371:0.5259	.	448	Q9BQN1	FA83C_HUMAN	C	448	ENSP00000363529:R448C	ENSP00000363529:R448C	R	-	1	0	FAM83C	33338654	0.000000	0.05858	0.002000	0.10522	0.945000	0.59286	0.150000	0.16263	0.362000	0.24319	0.561000	0.74099	CGC	.	.		0.652	FAM83C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078854.3			A	33875240	G	A	33875240	3	1	283	1	0	0	0	0	1	0	0	0	5643	1058	37	1	905	1	FAM83C	20	33875240	Missense_Mutation	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	31241274	33875240	29150280	221	41859										
KIAA1755	85449	hgsc.bcm.edu	37	chr20	36848153	36848153	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	caaggctgtacaaggcagtgGctgcagccagatggctcctg	14	11	0	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr20:36848153G>A	ENST00000279024.4	-	11	2706	c.2435C>T	c.(2434-2436)gCc>gTc	p.A812V		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	812										breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				CAAGGCAGTGGCTGCAGCCAG	0.632																																					p.A812V		Atlas-SNP	.											.	KIAA1755	145	.	0			c.C2435T						.						108	102	104					20																	36848153		2203	4300	6503	SO:0001583	missense	85449	exon11			GCAGTGGCTGCAG	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.2435C>T	chr20.hg19:g.36848153G>A	ENSP00000279024:p.Ala812Val	86.0	0.0		97.0	25.0	NM_001029864	Q9C0A8	Missense_Mutation	SNP	ENST00000279024.4	hg19	CCDS33467.1	.	.	.	.	.	.	.	.	.	.	G	16.50	3.141898	0.57044	.	.	ENSG00000149633	ENST00000279024;ENST00000373398;ENST00000435901	T;T	0.22134	3.44;1.97	4.26	4.26	0.50523	.	0.000000	0.42053	D	0.000776	T	0.37839	0.1018	L	0.55017	1.72	0.35351	D	0.787336	D;D	0.89917	0.999;1.0	D;D	0.87578	0.994;0.998	T	0.33317	-0.9873	10	0.15066	T	0.55	.	14.5425	0.68005	0.0:0.0:1.0:0.0	.	812;320	Q5JYT7;E9PFS1	K1755_HUMAN;.	V	812;320;111	ENSP00000279024:A812V;ENSP00000393503:A111V	ENSP00000279024:A812V	A	-	2	0	KIAA1755	36281567	0.996000	0.38824	0.273000	0.24645	0.660000	0.38997	5.568000	0.67385	2.367000	0.80283	0.561000	0.74099	GCC	.	.		0.632	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864		A	36848153	G	A	36848153	3	1	283	1	0	0	0	0	1	0	0	0	8266	1203	42	3	1183	3	KIAA1755	20	36848153	Missense_Mutation	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	2972913	36848153	26177367	222	41860										
C21orf91	54149	hgsc.bcm.edu	37	chr21	19168929	19168942	+	Frame_Shift_Del	DEL	TCTGGACATTAGCC	TCTGGACATTAGCC	-													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gctgtaatgtggatgctgggTctggacattagcctctggac							TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	TCTGGACATTAGCC	TCTGGACATTAGCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr21:19168929_19168942delTCTGGACATTAGCC	ENST00000400558.3	-	3	711_724	c.621_634delGGCTAATGTCCAGA	c.(619-636)gaggctaatgtccagaccfs	p.EANVQT207fs	C21orf91_ENST00000493464.1_5'Flank|C21orf91_ENST00000400559.3_Frame_Shift_Del_p.EANVQT207fs|C21orf91_ENST00000284881.4_Frame_Shift_Del_p.EANVQT207fs|AL109761.5_ENST00000428689.1_RNA	NM_001100421.1	NP_001093891.1			chromosome 21 open reading frame 91											endometrium(2)|large_intestine(2)|lung(4)|ovary(1)	9				Epithelial(23;8.76e-05)|all cancers(11;0.000422)|OV - Ovarian serous cystadenocarcinoma(11;0.0107)|Lung(58;0.0129)|COAD - Colon adenocarcinoma(22;0.0303)|LUSC - Lung squamous cell carcinoma(23;0.0381)|Colorectal(24;0.0929)		GGATGCTGGGTCTGGACATTAGCCTCTGGACTAG	0.407																																					p.208_212del		Atlas-Indel,Pindel	.											.	C21orf91	21	.	0			c.622_635del						.																																			SO:0001589	frameshift_variant	54149	exon3			.	AF239726	CCDS42907.1, CCDS42908.1, CCDS42909.1	21q21.1	2011-12-12	2003-07-22		ENSG00000154642	ENSG00000154642			16459	protein-coding gene	gene with protein product	"cold sore susceptibility gene 1", "early undifferentiated retina and lens"		"chromosome 21 open reading frame 38"	C21orf38, C21orf14		22039568	Standard	NM_001100421		Approved	YG81, EURL, CSSG1	uc002yko.4	Q9NYK6	OTTHUMG00000074509	ENST00000400558.3:c.621_634delGGCTAATGTCCAGA	chr21.hg19:g.19168929_19168942delTCTGGACATTAGCC	ENSP00000383403:p.Glu207fs	261.0	0.0		250.0	50.0	NM_017447		Frame_Shift_Del	DEL	ENST00000400558.3	hg19	CCDS42909.1																																																																																			.	.		0.407	C21orf91-002	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000158214.1	NM_017447		-	19168942	TCTGGACATTAGCC	-	19168929	7	5	283	1	0	1	0	1	0	0	0	0	2136	1667	58	0	271	0	C21orf91	21	19168929	Frame_Shift_Del	DEL	TCTGGACATTAGCC	TCGA-G3-A3CK-01A-11D-A20W-10		19168929	28960966	223	41861										
SIM2	6493	hgsc.bcm.edu	37	chr21	38117328	38117328	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ctgccagccagcggtgaatgCcagtggcattatgccaaccc	11	14	0	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr21:38117328C>T	ENST00000290399.6	+	10	2080	c.1467C>T	c.(1465-1467)tgC>tgT	p.C489C	SIM2_ENST00000430056.3_Silent_p.C489C	NM_005069.3	NP_005060.1	Q14190	SIM2_HUMAN	single-minded family bHLH transcription factor 2	489	Single-minded C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00632}.				cell differentiation (GO:0030154)|embryonic pattern specification (GO:0009880)|lung development (GO:0030324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(6)|prostate(1)|skin(2)	16						GCGGTGAATGCCAGTGGCATT	0.587																																					p.C489C		Atlas-SNP	.											.	SIM2	55	.	0			c.C1467T						.						69	60	63					21																	38117328		2203	4300	6503	SO:0001819	synonymous_variant	6493	exon10			TGAATGCCAGTGG		CCDS13646.1	21q22.2	2013-10-17	2013-10-17		ENSG00000159263	ENSG00000159263		"Basic helix-loop-helix proteins"	10883	protein-coding gene	gene with protein product	"transcription factor SIM2"	600892	"single-minded (Drosophila) homolog 2", "single-minded homolog 2 (Drosophila)"	SIM		7485157	Standard	NM_009586		Approved	MGC119447, bHLHe15	uc002yvr.2	Q14190	OTTHUMG00000086637	ENST00000290399.6:c.1467C>T	chr21.hg19:g.38117328C>T		116.0	0.0		128.0	38.0	NM_005069	O60766|Q15470|Q15471|Q15472|Q15473|Q16532|Q2TBD8	Silent	SNP	ENST00000290399.6	hg19	CCDS13646.1	.	.	.	.	.	.	.	.	.	.	C	10.53	1.376642	0.24857	.	.	ENSG00000159263	ENST00000431229;ENST00000481730	.	.	.	4.74	4.74	0.60224	.	.	.	.	.	T	0.73984	0.3657	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.73842	-0.3855	4	.	.	.	.	18.1411	0.89639	0.0:1.0:0.0:0.0	.	.	.	.	S	427;86	.	.	P	+	1	0	SIM2	37039198	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.871000	0.56077	2.337000	0.79520	0.558000	0.71614	CCA	.	.		0.587	SIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194692.1	NM_009586		T	38117328	C	T	38117328	2	4	283	1	0	0	0	0	0	0	0	1	14339	747	26	3		3	SIM2	21	38117328	Silent	SNP	C	TCGA-G3-A3CK-01A-11D-A20W-10	18948399	38117328	10012567	224	41862										
KCNJ15	3772	hgsc.bcm.edu	37	chr21	39671772	39671772	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	atgggaagctgtgcttggtgAttcaggtagccaatatgagg	15	5	1	2			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr21:39671772A>G	ENST00000328656.4	+	4	892	c.589A>G	c.(589-591)Att>Gtt	p.I197V	KCNJ15_ENST00000398934.1_Missense_Mutation_p.I197V|KCNJ15_ENST00000398932.1_Missense_Mutation_p.I197V|KCNJ15_ENST00000398930.1_Missense_Mutation_p.I197V|KCNJ15_ENST00000398938.2_Missense_Mutation_p.I197V	NM_001276437.1|NM_001276438.1|NM_001276439.1|NM_002243.3	NP_001263366.1|NP_001263367.1|NP_001263368.1|NP_002234.2	Q99712	KCJ15_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 15	197					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	24					Yohimbine(DB01392)	GTGCTTGGTGATTCAGGTAGC	0.547																																					p.S197G		Atlas-SNP	.											.	KCNJ15	43	.	0			c.A589G						.						60	60	60					21																	39671772		2203	4300	6503	SO:0001583	missense	3772	exon3			TTGGTGATTCAGG	Y10745	CCDS13656.1	21q22.2	2011-07-05			ENSG00000157551	ENSG00000157551		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6261	protein-coding gene	gene with protein product		602106				9299242, 8995301, 16382105	Standard	NM_170736		Approved	Kir4.2, Kir1.3, IRKK	uc002ywx.4	Q99712	OTTHUMG00000090609	ENST00000328656.4:c.589A>G	chr21.hg19:g.39671772A>G	ENSP00000331698:p.Ile197Val	61.0	0.0		67.0	16.0	NM_170736	D3DSH5|O00564|Q96L28|Q99446	Missense_Mutation	SNP	ENST00000328656.4	hg19	CCDS13656.1	.	.	.	.	.	.	.	.	.	.	A	11.21	1.571641	0.28003	.	.	ENSG00000157551	ENST00000328656;ENST00000398938;ENST00000398932;ENST00000438657;ENST00000398930;ENST00000398934	D;D;D;D;D;D	0.91464	-2.85;-2.85;-2.85;-2.85;-2.85;-2.85	5.73	5.73	0.89815	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.062544	0.64402	D	0.000004	D	0.82870	0.5131	N	0.20986	0.625	0.38641	D	0.951609	B	0.16396	0.017	B	0.23275	0.045	T	0.78157	-0.2313	9	.	.	.	.	10.3723	0.44062	0.9272:0.0:0.0728:0.0	.	197	Q99712	IRK15_HUMAN	V	197	ENSP00000331698:I197V;ENSP00000381911:I197V;ENSP00000381905:I197V;ENSP00000414487:I197V;ENSP00000381904:I197V;ENSP00000381907:I197V	.	I	+	1	0	KCNJ15	38593642	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.435000	0.44811	2.190000	0.69967	0.533000	0.62120	ATT	.	.		0.547	KCNJ15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207181.2	NM_002243		G	39671772	A	G	39671772	3	3	283	1	0	0	0	0	1	0	0	0	8058	333	12	2	591	2	KCNJ15	21	39671772	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	1554444	39671772	8458123	225	41863										
IGSF5	150084	hgsc.bcm.edu	37	chr21	41160116	41160116	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tttcgtattcaatttcaaaaGtaagtttgaaaccacatcta	4	7	3	1			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr21:41160116G>A	ENST00000380588.4	+	6	1059		c.e6+1			NM_001080444.1	NP_001073913.1	Q9NSI5	IGSF5_HUMAN	immunoglobulin superfamily, member 5						single organismal cell-cell adhesion (GO:0016337)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(7)|skin(2)|stomach(1)	23		Prostate(19;5.35e-06)				AATTTCAAAAGTAAGTTTGAA	0.279																																					.		Atlas-SNP	.											.	IGSF5	62	.	0			c.956+1G>A						.						69	65	66					21																	41160116		2192	4294	6486	SO:0001630	splice_region_variant	150084	exon6			TCAAAAGTAAGTT		CCDS33562.1	21q22.2	2013-01-29			ENSG00000183067	ENSG00000183067		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5952	protein-coding gene	gene with protein product	"junctional adhesion molecule 4"	610638					Standard	NM_001080444		Approved	JAM4	uc002yyo.3	Q9NSI5	OTTHUMG00000086724	ENST00000380588.4:c.956+1G>A	chr21.hg19:g.41160116G>A		186.0	0.0		197.0	10.0	NM_001080444		Splice_Site	SNP	ENST00000380588.4	hg19	CCDS33562.1	.	.	.	.	.	.	.	.	.	.	G	8.937	0.964808	0.18583	.	.	ENSG00000183067	ENST00000380588	.	.	.	3.95	3.95	0.45737	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.82	0.52232	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	IGSF5	40081986	1.000000	0.71417	1.000000	0.80357	0.100000	0.18952	3.694000	0.54742	2.502000	0.84385	0.555000	0.69702	.	.	.		0.279	IGSF5-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195005.1		Intron	A	41160116	G	A	41160116	5	1	283	1	0	0	0	0	0	0	1	0	7611	1043	36	3	979	3	IGSF5	21	41160116	Splice_Site	SNP	G	TCGA-G3-A3CK-01A-11D-A20W-10	1488344	41160116	6969779	226	41864										
CYTSA	23384	hgsc.bcm.edu	37	chr22	24718668	24718668	+	Missense_Mutation	SNP	A	A	G													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	ccacagtggccagtgaccagAtagagatgaatcgcctgaag					rs200752862		TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr22:24718668A>G	ENST00000314328.9	+	5	2005	c.1720A>G	c.(1720-1722)Ata>Gta	p.I574V	SPECC1L_ENST00000437398.1_Missense_Mutation_p.I574V|SPECC1L-ADORA2A_ENST00000358654.2_Missense_Mutation_p.I574V|SPECC1L_ENST00000416735.1_Intron|SPECC1L_ENST00000541492.1_Missense_Mutation_p.I574V	NM_001254733.1|NM_015330.3	NP_001241662.1|NP_056145	Q69YQ0	CYTSA_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1-like	574					actin cytoskeleton organization (GO:0030036)|cell cycle (GO:0007049)|cell division (GO:0051301)|cell migration (GO:0016477)|negative regulation of actin filament depolymerization (GO:0030835)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|gap junction (GO:0005921)|microtubule organizing center (GO:0005815)				breast(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(6)|ovary(1)|prostate(1)|skin(3)|stomach(2)|urinary_tract(1)	27						CAGTGACCAGATAGAGATGAA	0.463																																					p.I574V		Atlas-SNP	.											.	SPECC1L	85	.	0			c.A1720G						.						65	66	65					22																	24718668		2203	4300	6503	SO:0001583	missense	23384	exon4			GACCAGATAGAGA	AK025531	CCDS33619.1, CCDS58797.1	22q11.23	2012-12-20	2010-09-17	2010-09-17	ENSG00000100014	ENSG00000100014			29022	protein-coding gene	gene with protein product	"cytokinesis and spindle organization A", "cytospin A"	614140	"SPECC1-like"			9205841	Standard	NM_001254733		Approved	KIAA0376, CYTSA	uc002zzv.4	Q69YQ0	OTTHUMG00000171450	ENST00000314328.9:c.1720A>G	chr22.hg19:g.24718668A>G	ENSP00000325785:p.Ile574Val	71.0	0.0		79.0	27.0	NM_001145468	B7Z758|F5H1H6|O15081	Missense_Mutation	SNP	ENST00000314328.9	hg19	CCDS33619.1	.	.	.	.	.	.	.	.	.	.	A	8.231	0.804758	0.16467	.	.	ENSG00000100014	ENST00000398280;ENST00000437398;ENST00000421374;ENST00000314328;ENST00000541492	T;T;T;T	0.60548	0.18;2.66;0.18;3.18	5.5	3.26	0.37387	.	0.147419	0.64402	D	0.000011	T	0.35307	0.0927	N	0.16368	0.405	0.34147	D	0.667089	B;B	0.20780	0.048;0.002	B;B	0.18871	0.023;0.001	T	0.39251	-0.9623	10	0.20046	T	0.44	-26.7237	8.2368	0.31631	0.7908:0.1353:0.0739:0.0	.	574;574	F5H1H6;Q69YQ0	.;CYTSA_HUMAN	V	602;574;574;574;574	ENSP00000393363:I574V;ENSP00000405671:I574V;ENSP00000325785:I574V;ENSP00000439633:I574V	ENSP00000325785:I574V	I	+	1	0	SPECC1L	23048668	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.508000	0.35769	2.099000	0.63709	0.533000	0.62120	ATA	.	.		0.463	SPECC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319986.2	NM_015330		G	24718668	A	G	24718668	3	3	283	1	0	0	0	0	1	0	0	0	4211	333	12	2	1730	2	CYTSA	22	24718668	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10		24718668	26585898	227	41865	217	2								
CYTSA	23384	hgsc.bcm.edu	37	chr22	24718674	24718674	+	Missense_Mutation	SNP	A	A	C													0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	tggccagtgaccagatagagAtgaatcgcctgaaggctcag							TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr22:24718674A>C	ENST00000314328.9	+	5	2011	c.1726A>C	c.(1726-1728)Atg>Ctg	p.M576L	SPECC1L_ENST00000437398.1_Missense_Mutation_p.M576L|SPECC1L-ADORA2A_ENST00000358654.2_Missense_Mutation_p.M576L|SPECC1L_ENST00000416735.1_Intron|SPECC1L_ENST00000541492.1_Missense_Mutation_p.M576L	NM_001254733.1|NM_015330.3	NP_001241662.1|NP_056145	Q69YQ0	CYTSA_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1-like	576					actin cytoskeleton organization (GO:0030036)|cell cycle (GO:0007049)|cell division (GO:0051301)|cell migration (GO:0016477)|negative regulation of actin filament depolymerization (GO:0030835)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|gap junction (GO:0005921)|microtubule organizing center (GO:0005815)				breast(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(6)|ovary(1)|prostate(1)|skin(3)|stomach(2)|urinary_tract(1)	27						CCAGATAGAGATGAATCGCCT	0.468																																					p.M576L		Atlas-SNP	.											.	SPECC1L	85	.	0			c.A1726C						.						67	69	68					22																	24718674		2203	4300	6503	SO:0001583	missense	23384	exon4			ATAGAGATGAATC	AK025531	CCDS33619.1, CCDS58797.1	22q11.23	2012-12-20	2010-09-17	2010-09-17	ENSG00000100014	ENSG00000100014			29022	protein-coding gene	gene with protein product	"cytokinesis and spindle organization A", "cytospin A"	614140	"SPECC1-like"			9205841	Standard	NM_001254733		Approved	KIAA0376, CYTSA	uc002zzv.4	Q69YQ0	OTTHUMG00000171450	ENST00000314328.9:c.1726A>C	chr22.hg19:g.24718674A>C	ENSP00000325785:p.Met576Leu	66.0	0.0		82.0	27.0	NM_001145468	B7Z758|F5H1H6|O15081	Missense_Mutation	SNP	ENST00000314328.9	hg19	CCDS33619.1	.	.	.	.	.	.	.	.	.	.	A	0.997	-0.692057	0.03303	.	.	ENSG00000100014	ENST00000398280;ENST00000437398;ENST00000421374;ENST00000314328;ENST00000541492	T;T;T;T	0.56941	0.43;2.9;0.43;3.43	5.5	1.9	0.25705	.	0.143693	0.64402	D	0.000005	T	0.13884	0.0336	N	0.00538	-1.39	0.31301	N	0.688266	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.35226	-0.9797	10	0.02654	T	1	-23.8918	6.1584	0.20350	0.6338:0.1386:0.2276:0.0	.	576;576	F5H1H6;Q69YQ0	.;CYTSA_HUMAN	L	604;576;576;576;576	ENSP00000393363:M576L;ENSP00000405671:M576L;ENSP00000325785:M576L;ENSP00000439633:M576L	ENSP00000325785:M576L	M	+	1	0	SPECC1L	23048674	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.481000	0.35476	0.405000	0.25532	0.533000	0.62120	ATG	.	.		0.468	SPECC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319986.2	NM_015330		C	24718674	A	C	24718674	3	2	283	1	0	0	0	0	1	0	0	0	4211	333	12	5	1736	5	CYTSA	22	24718674	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10	6	24718674	26585892	228	41866	217	2								
ADRBK2	157	hgsc.bcm.edu	37	chr22	26117279	26117279	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	actgacaatggaacagattcTctctgtggaagaaactcaaa	8	8	3	3			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chr22:26117279T>C	ENST00000324198.6	+	20	2012	c.1820T>C	c.(1819-1821)cTc>cCc	p.L607P		NM_005160.3	NP_005151.2	P35626	ARBK2_HUMAN	adrenergic, beta, receptor kinase 2	607	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				receptor internalization (GO:0031623)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)		ATP binding (GO:0005524)|beta-adrenergic receptor kinase activity (GO:0047696)|G-protein coupled receptor kinase activity (GO:0004703)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(14)|ovary(2)|skin(3)|stomach(2)	32					Adenosine triphosphate(DB00171)	GAACAGATTCTCTCTGTGGAA	0.279																																					p.L607P		Atlas-SNP	.											.	ADRBK2	78	.	0			c.T1820C						.						62	71	68					22																	26117279		2203	4296	6499	SO:0001583	missense	157	exon20			AGATTCTCTCTGT	X69117	CCDS13832.1	22q11	2013-01-10			ENSG00000100077	ENSG00000100077		"Pleckstrin homology (PH) domain containing"	290	protein-coding gene	gene with protein product		109636				7695743	Standard	NM_005160		Approved	GRK3, BARK2	uc003abx.4	P35626	OTTHUMG00000150280	ENST00000324198.6:c.1820T>C	chr22.hg19:g.26117279T>C	ENSP00000317578:p.Leu607Pro	266.0	0.0		336.0	113.0	NM_005160	Q9UGW9	Missense_Mutation	SNP	ENST00000324198.6	hg19	CCDS13832.1	.	.	.	.	.	.	.	.	.	.	T	12.97	2.096840	0.37048	.	.	ENSG00000100077	ENST00000324198	T	0.58358	0.34	5.68	5.68	0.88126	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.672824	0.14072	N	0.343311	T	0.44286	0.1286	N	0.22421	0.69	0.50632	D	0.999885	B	0.24132	0.098	B	0.30855	0.121	T	0.28808	-1.0032	10	0.33940	T	0.23	-1.2072	15.1109	0.72355	0.0:0.0:0.0:1.0	.	607	P35626	ARBK2_HUMAN	P	607	ENSP00000317578:L607P	ENSP00000317578:L607P	L	+	2	0	ADRBK2	24447279	0.836000	0.29430	0.214000	0.23707	0.981000	0.71138	5.504000	0.66968	2.165000	0.68154	0.533000	0.62120	CTC	.	.		0.279	ADRBK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317296.4	NM_005160		C	26117279	T	C	26117279	3	2	283	1	0	0	0	0	1	0	0	0	344	1551	54	2	1898	2	ADRBK2	22	26117279	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	1398605	26117279	25187287	229	41867										
WWC3	55841	hgsc.bcm.edu	37	chrX	10094158	10094158	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	cccgttctgtttgcagccacAtccgagtctatttgccccca	7	16	2	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chrX:10094158A>G	ENST00000380861.4	+	15	2309	c.1918A>G	c.(1918-1920)Atc>Gtc	p.I640V	WWC3_ENST00000454666.1_Missense_Mutation_p.I640V	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	640	C2.				negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(3)|endometrium(10)|kidney(1)|large_intestine(11)|lung(17)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	52						TTGCAGCCACATCCGAGTCTA	0.607																																					p.I640V		Atlas-SNP	.											.	WWC3	142	.	0			c.A1918G						.						180	177	178					X																	10094158		2203	4300	6503	SO:0001583	missense	55841	exon15			AGCCACATCCGAG	AK091936	CCDS14136.1	Xp22.32	2008-02-05			ENSG00000047644	ENSG00000047644		"WW, C2 and coiled-coil domain containing"	29237	protein-coding gene	gene with protein product						10574462	Standard	NM_015691		Approved	KIAA1280, BM042	uc004csx.4	Q9ULE0	OTTHUMG00000021123	ENST00000380861.4:c.1918A>G	chrX.hg19:g.10094158A>G	ENSP00000370242:p.Ile640Val	112.0	0.0		121.0	79.0	NM_015691	A8KA96|Q659C1|Q9BTQ1	Missense_Mutation	SNP	ENST00000380861.4	hg19	CCDS14136.1	.	.	.	.	.	.	.	.	.	.	A	3.393	-0.123822	0.06795	.	.	ENSG00000047644	ENST00000380861;ENST00000454666;ENST00000543412	T;T	0.23348	1.91;1.91	4.86	-0.459	0.12179	C2 calcium/lipid-binding domain, CaLB (1);	0.510624	0.22758	N	0.055985	T	0.15652	0.0377	L	0.31120	0.905	0.29179	N	0.876653	B	0.06786	0.001	B	0.12156	0.007	T	0.23976	-1.0173	9	.	.	.	-12.8248	10.3375	0.43858	0.5:0.0:0.5:0.0	.	640	Q9ULE0	WWC3_HUMAN	V	640;640;135	ENSP00000370242:I640V;ENSP00000399584:I640V	.	I	+	1	0	WWC3	10054158	0.995000	0.38212	0.611000	0.29010	0.045000	0.14185	0.883000	0.28200	-0.489000	0.06716	-0.314000	0.08810	ATC	.	.		0.607	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691		G	10094158	A	G	10094158	3	3	283	1	0	0	0	0	1	0	0	0	17428	217	8	2	1972	2	WWC3	23	10094158	Missense_Mutation	SNP	A	TCGA-G3-A3CK-01A-11D-A20W-10		10094158	145176402	230	41868										
SEPT6	23157	hgsc.bcm.edu	37	chrX	118827051	118827051	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0271493212669683	6	1	0.72908076643221	0.579525737420474	0.768758631272058	0.140866873065015	0.729941291585128	0	gcacttaccacctggcgagcTatatcggtcgctgccatcgc	10	15	0	0			TCGA-G3-A3CK-01A-11D-A20W-10	TCGA-G3-A3CK-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1127b561-ea40-4d5e-95df-daa0a5ebc1e4	b9244ba4-a36a-415f-8975-7e933dd7d8a4	g.chrX:118827051T>C	ENST00000343984.5	-	1	282	c.18A>G	c.(16-18)atA>atG	p.I6M	SEPT6_ENST00000394616.4_5'Flank|SEPT6_ENST00000360156.7_Missense_Mutation_p.I6M|SEPT6_ENST00000354228.4_Missense_Mutation_p.I6M|SEPT6_ENST00000394610.1_Missense_Mutation_p.I6M|SEPT6_ENST00000354416.3_Missense_Mutation_p.I6M|SEPT6_ENST00000489216.1_Missense_Mutation_p.I6M|SEPT6_ENST00000394617.2_Missense_Mutation_p.I6M	NM_015129.5	NP_055944.2	Q14141	SEPT6_HUMAN	septin 6	6					cytokinesis (GO:0000910)|viral process (GO:0016032)	axon terminus (GO:0043679)|kinetochore (GO:0000776)|septin complex (GO:0031105)|synaptic vesicle (GO:0008021)	GTP binding (GO:0005525)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(3)	17						CCTGGCGAGCTATATCGGTCG	0.682			T	MLL	AML																																p.I6M		Atlas-SNP	.		Dom	yes		X	Xq24	23157	septin 6		L	.	SEPT6	53	.	0			c.A18G						.						14	11	12					X																	118827051		2138	4179	6317	SO:0001583	missense	23157	exon1			GCGAGCTATATCG	D50918	CCDS14583.1, CCDS14584.1, CCDS14585.1	Xq24	2013-01-21			ENSG00000125354	ENSG00000125354		"Septins"	15848	protein-coding gene	gene with protein product		300683				8590280, 10744683	Standard	NM_015129		Approved	KIAA0128, SEP2, SEPT2, MGC16619, MGC20339	uc004erv.3	Q14141	OTTHUMG00000022280	ENST00000343984.5:c.18A>G	chrX.hg19:g.118827051T>C	ENSP00000341524:p.Ile6Met	185.0	0.0		122.0	77.0	NM_145802	Q5JTK0|Q969W5|Q96A13|Q96GR1|Q96P86|Q96P87	Missense_Mutation	SNP	ENST00000343984.5	hg19	CCDS14584.1	.	.	.	.	.	.	.	.	.	.	t	12.99	2.102449	0.37145	.	.	ENSG00000125354	ENST00000360156;ENST00000354228;ENST00000489216;ENST00000354416;ENST00000394610;ENST00000343984;ENST00000394617;ENST00000520510	T;T;T;T;T;T;T	0.54675	0.61;0.61;0.61;0.61;0.61;0.61;0.56	3.91	3.91	0.45181	.	.	.	.	.	T	0.30572	0.0769	N	0.16656	0.425	0.80722	D	1	P;P;B	0.37636	0.603;0.533;0.041	B;B;B	0.33521	0.165;0.109;0.057	T	0.06427	-1.0827	9	0.22706	T	0.39	.	8.2275	0.31577	0.0:0.0:0.0:1.0	.	6;6;6	F5H1J5;Q14141;Q548C9	.;SEPT6_HUMAN;.	M	6	ENSP00000353278:I6M;ENSP00000346169:I6M;ENSP00000418715:I6M;ENSP00000346397:I6M;ENSP00000378108:I6M;ENSP00000341524:I6M;ENSP00000378115:I6M	ENSP00000341524:I6M	I	-	3	3	SEPT6	118711079	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.598000	0.36740	1.759000	0.51996	0.478000	0.44815	ATA	.	.		0.682	SEPT6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058059.1	NM_145802		C	118827051	T	C	118827051	3	2	283	1	0	0	0	0	1	0	0	0	14083	1512	53	2	1348	2	SEPT6	23	118827051	Missense_Mutation	SNP	T	TCGA-G3-A3CK-01A-11D-A20W-10	108732893	118827051	36443509	231	41869										
PLEKHN1	84069	hgsc.bcm.edu	37	chr1	902177	902177	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	aagctcttccactacatcccGggcacggtgagcgcggcgtg	13	14	1	1	rs565222190	byFrequency	TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr1:902177G>T	ENST00000379409.2	+	2	207	c.177G>T	c.(175-177)ccG>ccT	p.P59P	PLEKHN1_ENST00000379410.3_Silent_p.P59P|PLEKHN1_ENST00000379407.3_Silent_p.P59P			Q494U1	PKHN1_HUMAN	pleckstrin homology domain containing, family N member 1	59										central_nervous_system(1)|endometrium(3)|kidney(1)|lung(2)|skin(1)|urinary_tract(1)	9	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.93e-23)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.00095)|Kidney(185;0.0023)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.199)		ACTACATCCCGGGCACGGTGA	0.721													G|||	3	0.000599042	0	0	5008	,	,		13646	0		0	False		,,,				2504	0.0031				p.P59P		Atlas-SNP	.											.	PLEKHN1	49	.	0			c.G177T						.						7	9	8					1																	902177		2087	4150	6237	SO:0001819	synonymous_variant	84069	exon2			CATCCCGGGCACG	AL136730	CCDS4.1, CCDS53256.1	1p36.33	2013-01-11			ENSG00000187583	ENSG00000187583		"Pleckstrin homology (PH) domain containing"	25284	protein-coding gene	gene with protein product						11230166	Standard	NM_032129		Approved	DKFZP434H2010	uc001acd.3	Q494U1	OTTHUMG00000040756	ENST00000379409.2:c.177G>T	chr1.hg19:g.902177G>T		6.0	0.0		4.0	4.0	NM_001160184	Q494U2|Q5SV98|Q9H0M7	Silent	SNP	ENST00000379409.2	hg19																																																																																				.	.		0.721	PLEKHN1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000473256.1	NM_032129		T	902177	G	T	902177	2	4	284	1	0	0	0	0	0	0	0	1	12092	1103	39	1		1	PLEKHN1	1	902177	Silent	SNP	G	TCGA-G3-A5SI-01A-31D-A27I-10		902177	248348444	1	41870										
TCHH	7062	hgsc.bcm.edu	37	chr1	152081091	152081138	+	In_Frame_Del	DEL	GAGGAATTTTCTCTGCCGTTGCTGGCGGTGCAGCTGCTGTTCCTCCTC	GAGGAATTTTCTCTGCCGTTGCTGGCGGTGCAGCTGCTGTTCCTCCTC	-													0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	cgcagctgctgttcctcctgGaggaattttctctgccgttg					rs573292568|rs200833723|rs544061610|rs539451789|rs75981854|rs555118497|rs189687085|rs553425100|rs185664717|rs574377133	byFrequency	TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	GAGGAATTTTCTCTGCCGTTGCTGGCGGTGCAGCTGCTGTTCCTCCTC	GAGGAATTTTCTCTGCCGTTGCTGGCGGTGCAGCTGCTGTTCCTCCTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr1:152081091_152081138delGAGGAATTTTCTCTGCCGTTGCTGGCGGTGCAGCTGCTGTTCCTCCTC	ENST00000368804.1	-	2	4554_4601	c.4555_4602delGAGGAGGAACAGCAGCTGCACCGCCAGCAACGGCAGAGAAAATTCCTC	c.(4555-4602)gaggaggaacagcagctgcaccgccagcaacggcagagaaaattcctcdel	p.EEEQQLHRQQRQRKFL1519del		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1519	23 X 26 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)	p.E1519Q(1)		NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GTTCCTCCTGGAGGAATTTTCTCTGCCGTTGCTGGCGGTGCAGCTGCTGTTCCTCCTCGAGGAATTTT	0.593																																					p.1519_1535del		Pindel	.											.	TCHH	275	.	1	Substitution - Missense(1)	lung(1)	c.4556_4603del						.																																			SO:0001651	inframe_deletion	7062	exon3			.	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"EF-hand domain containing"	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.4555_4602delGAGGAGGAACAGCAGCTGCACCGCCAGCAACGGCAGAGAAAATTCCTC	chr1.hg19:g.152081091_152081138delGAGGAATTTTCTCTGCCGTTGCTGGCGGTGCAGCTGCTGTTCCTCCTC	ENSP00000357794:p.Glu1519_Leu1534del	76.0	0.0		123.0	12.0	NM_007113	Q5VUI3	In_Frame_Del	DEL	ENST00000368804.1	hg19	CCDS41396.1																																																																																			.	.		0.593	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		-	152081138	GAGGAATTTTCTCTGCCGTTGCTGGCGGTGCAGCTGCTGTTCCTCCTC	-	152081091	7	5	284	1	0	1	0	1	0	0	0	0	15715	1161	41	0	1233	0	TCHH	1	152081091	In_Frame_Del	DEL	GAGGAATTTTCTCTGCCGTTGCTGGCGGTGCAGCTGCTGTTCCTCCTC	TCGA-G3-A5SI-01A-31D-A27I-10	151178914	152081091	97169530	2	41871			1	49		2	2	48	N	GAGGAATTTTCTCTGCCGTTGCTGGCGGTGCAGCTGCTGTTCCTCCTC_C	6.072804e-05
TCHH	7062	hgsc.bcm.edu	37	chr1	152081138	152081138	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	gtgcagctgctgttcctcctCgaggaattttctctctggtt	10	11	2	0	rs189687085	byFrequency	TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr1:152081138C>G	ENST00000368804.1	-	2	4554	c.4555G>C	c.(4555-4557)Gag>Cag	p.E1519Q		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1519	23 X 26 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)	p.E1519Q(1)		NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGTTCCTCCTCGAGGAATTTT	0.587																																					p.E1519Q		Atlas-SNP	.											TCHH,NS,carcinoma,0,1	TCHH	275	.	1	Substitution - Missense(1)	lung(1)	c.G4555C						.						53	55	54					1																	152081138		1885	4114	5999	SO:0001583	missense	7062	exon3			CCTCCTCGAGGAA	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"EF-hand domain containing"	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.4555G>C	chr1.hg19:g.152081138C>G	ENSP00000357794:p.Glu1519Gln	73.0	1.0		120.0	24.0	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	hg19	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	-	1.898	-0.453708	0.04540	.	.	ENSG00000159450	ENST00000368804	T	0.05382	3.45	0.113	0.113	0.14631	.	.	.	.	.	T	0.03739	0.0106	M	0.66939	2.045	0.09310	N	1	P	0.44281	0.831	P	0.47786	0.557	T	0.38802	-0.9644	8	0.23302	T	0.38	.	.	.	.	.	1519	Q07283	TRHY_HUMAN	Q	1519	ENSP00000357794:E1519Q	ENSP00000357794:E1519Q	E	-	1	0	TCHH	150347762	0.000000	0.05858	0.001000	0.08648	0.038000	0.13279	-0.405000	0.07196	0.183000	0.20059	0.186000	0.17326	GAG	.	C|1.000;T|0.000		0.587	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		G	152081138	C	G	152081138	3	3	284	1	0	0	0	0	1	0	0	0	15715	893	31	4	1280	4	TCHH	1	152081138	Missense_Mutation	SNP	C	TCGA-G3-A5SI-01A-31D-A27I-10	47	152081138	97169483	3	41872			1	49		2	2	48	N	GAGGAATTTTCTCTGCCGTTGCTGGCGGTGCAGCTGCTGTTCCTCCTC_C	6.072804e-05
CWC22	57703	hgsc.bcm.edu	37	chr2	180815590	180815590	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	atagaagtaaagaagttgatGgcaaaccgagtgtttcttgg	12	4	1	3			TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr2:180815590G>A	ENST00000410053.3	-	18	2180	c.1881C>T	c.(1879-1881)gcC>gcT	p.A627A	CWC22_ENST00000295749.6_Silent_p.A627A	NM_020943.2	NP_065994.1	Q9HCG8	CWC22_HUMAN	CWC22 spliceosome-associated protein	627					mRNA splicing, via spliceosome (GO:0000398)|regulation of mRNA splicing, via spliceosome (GO:0048024)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(8)|stomach(1)	30						AGAAGTTGATGGCAAACCGAG	0.318																																					p.A627A		Atlas-SNP	.											.	CWC22	62	.	0			c.C1881T						.						53	52	53					2																	180815590		1805	4077	5882	SO:0001819	synonymous_variant	57703	exon18			GTTGATGGCAAAC		CCDS46465.1	2q31.3	2014-07-03	2014-07-03		ENSG00000163510	ENSG00000163510			29322	protein-coding gene	gene with protein product	"functional spliceosome-associated protein b"	615186	"CWC22 spliceosome-associated protein homolog (S. cerevisiae)"			9136012, 23236153	Standard	NM_020943		Approved	KIAA1604, EIF4GL, fSAPb, NCM	uc010frh.1	Q9HCG8	OTTHUMG00000154244	ENST00000410053.3:c.1881C>T	chr2.hg19:g.180815590G>A		48.0	0.0		32.0	18.0	NM_020943	Q05DC2|Q4G135|Q52LF0|Q6PEX2|Q7Z6I0|Q9H5L3|Q9H6Q6	Silent	SNP	ENST00000410053.3	hg19	CCDS46465.1																																																																																			.	.		0.318	CWC22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334537.1	NM_020943		A	180815590	G	A	180815590	2	1	284	1	0	0	0	0	0	0	0	1	4070	1335	47	3		3	CWC22	2	180815590	Silent	SNP	G	TCGA-G3-A5SI-01A-31D-A27I-10		180815590	62383783	4	41873										
APEH	327	hgsc.bcm.edu	37	chr3	49719195	49719195	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	atcctgctgcagcctggcagCcctccagataagacccaagt	9	15	0	2			TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr3:49719195C>T	ENST00000296456.5	+	16	1879	c.1479C>T	c.(1477-1479)agC>agT	p.S493S	AC099668.5_ENST00000563780.1_RNA|APEH_ENST00000438011.1_Silent_p.S493S	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase	493					beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		AGCCTGGCAGCCCTCCAGATA	0.622																																					p.S493S		Atlas-SNP	.											.	APEH	45	.	0			c.C1479T						.						80	63	69					3																	49719195		2203	4300	6503	SO:0001819	synonymous_variant	327	exon16			TGGCAGCCCTCCA	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"acylaminoacyl-peptidase"	102645	"N-acylaminoacyl-peptide hydrolase"	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882	ENST00000296456.5:c.1479C>T	chr3.hg19:g.49719195C>T		187.0	0.0		166.0	21.0	NM_001640	Q9BQ33|Q9P0Y2	Silent	SNP	ENST00000296456.5	hg19	CCDS2801.1																																																																																			.	.		0.622	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2			T	49719195	C	T	49719195	2	4	284	1	0	0	0	0	0	0	0	1	768	738	26	3		3	APEH	3	49719195	Silent	SNP	C	TCGA-G3-A5SI-01A-31D-A27I-10		49719195	148303235	5	41874										
PBRM1	55193	hgsc.bcm.edu	37	chr3	52643631	52643631	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	tctctgcgtgtttcaagcagGactttgtgtagaacaagagc	11	8	2	2			TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr3:52643631G>T	ENST00000296302.7	-	16	2266	c.2265C>A	c.(2263-2265)gtC>gtA	p.V755V	PBRM1_ENST00000394830.3_Silent_p.V755V|PBRM1_ENST00000409057.1_Silent_p.V755V|PBRM1_ENST00000409767.1_Silent_p.V770V|PBRM1_ENST00000410007.1_Silent_p.V755V|PBRM1_ENST00000356770.4_Silent_p.V723V|PBRM1_ENST00000337303.4_Silent_p.V755V|PBRM1_ENST00000409114.3_Silent_p.V770V			Q86U86	PB1_HUMAN	polybromo 1	755					chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TTTCAAGCAGGACTTTGTGTA	0.423			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																p.V755V		Atlas-SNP	.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1	1252	.	0			c.C2265A						.						93	92	92					3																	52643631		2203	4300	6503	SO:0001819	synonymous_variant	55193	exon17			AAGCAGGACTTTG	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.2265C>A	chr3.hg19:g.52643631G>T		108.0	0.0		96.0	4.0	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Silent	SNP	ENST00000296302.7	hg19																																																																																				.	.		0.423	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165		T	52643631	G	T	52643631	2	4	284	1	0	0	0	0	0	0	0	1	11500	1161	41	3		3	PBRM1	3	52643631	Silent	SNP	G	TCGA-G3-A5SI-01A-31D-A27I-10	2924436	52643631	145378799	6	41875										
CLOCK	9575	hgsc.bcm.edu	37	chr4	56345032	56345032	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	tctgcagaacagtagatttgTccatctttctagcattacca	6	10	3	2			TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr4:56345032T>A	ENST00000309964.4	-	5	456	c.206A>T	c.(205-207)gAc>gTc	p.D69V	CLOCK_ENST00000513440.1_Missense_Mutation_p.D69V|CLOCK_ENST00000506923.1_5'UTR|CLOCK_ENST00000381322.1_Missense_Mutation_p.D69V	NM_004898.3	NP_004889.1	O15516	CLOCK_HUMAN	clock circadian regulator	69	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				cellular response to ionizing radiation (GO:0071479)|chromatin organization (GO:0006325)|circadian regulation of gene expression (GO:0032922)|circadian rhythm (GO:0007623)|DNA damage checkpoint (GO:0000077)|histone acetylation (GO:0016573)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of transcription, DNA-templated (GO:0045892)|photoperiodism (GO:0009648)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of hair cycle (GO:0042634)|regulation of insulin secretion (GO:0050796)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of type B pancreatic cell development (GO:2000074)|response to redox state (GO:0051775)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|chromosome (GO:0005694)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|histone acetyltransferase activity (GO:0004402)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(8)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38	Lung NSC(11;0.00335)|Glioma(25;0.08)|all_epithelial(27;0.0992)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(4;1.62e-07)|Lung(4;1.34e-06)|Epithelial(7;0.0107)			agtagatttgtccatctttct	0.323																																					p.D69V		Atlas-SNP	.											.	CLOCK	81	.	0			c.A206T						.						66	67	67					4																	56345032		2202	4299	6501	SO:0001583	missense	9575	exon6			GATTTGTCCATCT	AF011568	CCDS3500.1	4q12	2012-12-07	2012-12-07		ENSG00000134852	ENSG00000134852		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	2082	protein-coding gene	gene with protein product		601851	"clock (mouse) homolog", "clock homolog (mouse)"			10198158	Standard	NM_001267843		Approved	KIAA0334, KAT13D, bHLHe8	uc003hba.2	O15516	OTTHUMG00000102141	ENST00000309964.4:c.206A>T	chr4.hg19:g.56345032T>A	ENSP00000308741:p.Asp69Val	102.0	0.0		104.0	43.0	NM_004898	A0AV01|A2I2N9|O14516|Q9UIT8	Missense_Mutation	SNP	ENST00000309964.4	hg19	CCDS3500.1	.	.	.	.	.	.	.	.	.	.	T	25.8	4.673872	0.88445	.	.	ENSG00000134852	ENST00000309964;ENST00000381322;ENST00000513440	D;D;D	0.98044	-4.68;-4.68;-4.68	6.07	6.07	0.98685	Helix-loop-helix DNA-binding (5);	0.000000	0.85682	D	0.000000	D	0.98349	0.9452	M	0.84326	2.69	0.80722	D	1	P	0.45768	0.866	P	0.53988	0.739	D	0.99063	1.0831	10	0.72032	D	0.01	.	16.6407	0.85098	0.0:0.0:0.0:1.0	.	69	O15516	CLOCK_HUMAN	V	69	ENSP00000308741:D69V;ENSP00000370723:D69V;ENSP00000426983:D69V	ENSP00000308741:D69V	D	-	2	0	CLOCK	56039789	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.157000	0.77461	2.326000	0.78906	0.533000	0.62120	GAC	.	.		0.323	CLOCK-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361993.2	NM_004898		A	56345032	T	A	56345032	3	1	284	1	0	0	0	0	1	0	0	0	3551	1667	58	4	2406	4	CLOCK	4	56345032	Missense_Mutation	SNP	T	TCGA-G3-A5SI-01A-31D-A27I-10		56345032	134809244	7	41876										
CEP135	9662	hgsc.bcm.edu	37	chr4	56835289	56835289	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	aagaaacaatggcaaaacttCagctggtaagttgatgtcat	9	6	2	2			TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr4:56835289C>T	ENST00000257287.4	+	9	1229	c.1105C>T	c.(1105-1107)Cag>Tag	p.Q369*		NM_025009.4	NP_079285.2	Q66GS9	CP135_HUMAN	centrosomal protein 135kDa	369					centriole replication (GO:0007099)|centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)	protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(26)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	50	Glioma(25;0.08)|all_neural(26;0.101)					GGCAAAACTTCAGCTGGTAAG	0.368																																					p.Q369X		Atlas-SNP	.											.	CEP135	115	.	0			c.C1105T						.						70	72	71					4																	56835289		2203	4300	6503	SO:0001587	stop_gained	9662	exon9			AAACTTCAGCTGG	AB014535	CCDS33986.1	4q12	2014-02-20	2005-12-02	2005-12-02	ENSG00000174799	ENSG00000174799			29086	protein-coding gene	gene with protein product		611423	"KIAA0635", "centrosomal protein 4"	KIAA0635, CEP4		9734811, 14654843	Standard	NM_025009		Approved	FLJ13621	uc003hbi.4	Q66GS9	OTTHUMG00000160748	ENST00000257287.4:c.1105C>T	chr4.hg19:g.56835289C>T	ENSP00000257287:p.Gln369*	117.0	0.0		125.0	5.0	NM_025009	B2RMY0|O75130|Q58F25|Q9H8H7	Nonsense_Mutation	SNP	ENST00000257287.4	hg19	CCDS33986.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.901430	0.92035	.	.	ENSG00000174799	ENST00000257287	.	.	.	5.44	2.25	0.28309	.	0.260739	0.43260	D	0.000595	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	.	7.5616	0.27855	0.5176:0.3617:0.1207:0.0	.	.	.	.	X	369	.	ENSP00000257287:Q369X	Q	+	1	0	CEP135	56530046	1.000000	0.71417	0.929000	0.37066	0.201000	0.24016	2.151000	0.42263	0.585000	0.29608	0.563000	0.77884	CAG	.	.		0.368	CEP135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362092.2	NM_025009		T	56835289	C	T	56835289	4	4	284	1	0	0	0	0	0	1	0	0	3249	827	29	3	1135	3	CEP135	4	56835289	Nonsense_Mutation	SNP	C	TCGA-G3-A5SI-01A-31D-A27I-10	490257	56835289	134318987	8	41877										
UGT2B4	7363	hgsc.bcm.edu	37	chr4	70361558	70361580	+	Start_Codon_Del	DEL	CTGAAGTCCATTTCATAGACATC	CTGAAGTCCATTTCATAGACATC	-													0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	cagctgtatcagcagaagagCtgaagtccatttcatagaca					rs113676396|rs370125678|rs185779213|rs182850682	byFrequency	TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	CTGAAGTCCATTTCATAGACATC	CTGAAGTCCATTTCATAGACATC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr4:70361558_70361580delCTGAAGTCCATTTCATAGACATC	ENST00000305107.6	-	0	46_68				UGT2B4_ENST00000512583.1_Start_Codon_Del|UGT2B4_ENST00000381096.3_Intron|UGT2B4_ENST00000506580.1_5'UTR	NM_021139.2	NP_066962.2	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B4						cellular glucuronidation (GO:0052695)|estrogen catabolic process (GO:0006711)|metabolic process (GO:0008152)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)	p.M3L(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(29)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	47					Canagliflozin(DB08907)|Codeine(DB00318)|Dapagliflozin(DB06292)|Flurbiprofen(DB00712)|Ibuprofen(DB01050)|Morphine(DB00295)	AGCAGAAGAGCTGAAGTCCATTTCATAGACATCCTGATGCAAT	0.422																																					.		Pindel	.											.	UGT2B4	105	.	1	Substitution - Missense(1)	lung(1)	.						.																																			SO:0001582	initiator_codon_variant	7363	wholegene			.	BC026264	CCDS43234.1, CCDS75137.1	4q13	2008-02-05	2005-07-20			ENSG00000156096		"UDP glucuronosyltransferases"	12553	protein-coding gene	gene with protein product		600067	"UDP glycosyltransferase 2 family, polypeptide B4"			3109396, 7835904	Standard	NM_021139		Approved	UGT2B11	uc003hek.4	P06133			chr4.hg19:g.70361558_70361580delCTGAAGTCCATTTCATAGACATC		74.0	0.0		56.0	12.0	NM_021139	A6NCP7|B4DT75|G5E9X8|O60731|O60867|O75614|P36538|Q1HBF9|Q6QQX7	Frame_Shift_Del	DEL	ENST00000305107.6	hg19	CCDS43234.1																																																																																			.	.		0.422	UGT2B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365526.1	NM_021139		-	70361580	CTGAAGTCCATTTCATAGACATC	-	70361558	7	5	284	1	0	1	0	1	0	0	0	0	16976	797	28	0	1588	0	UGT2B4	4	70361558	Start_Codon_Del	DEL	CTGAAGTCCATTTCATAGACATC	TCGA-G3-A5SI-01A-31D-A27I-10	13526269	70361558	120792718	9	41878										
SKIV2L2	23517	hgsc.bcm.edu	37	chr5	54624616	54624616	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	ctagtatctgcacatacctcAgcgggaaaaacagtatgcgc	9	11	2	0			TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr5:54624616A>C	ENST00000230640.5	+	5	746	c.492A>C	c.(490-492)tcA>tcC	p.S164S	SKIV2L2_ENST00000545714.1_Silent_p.S63S	NM_015360.4	NP_056175.3	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2 (S. cerevisiae)	164	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				maturation of 5.8S rRNA (GO:0000460)|mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			NS(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|lung(12)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)				CACATACCTCAGCGGGAAAAA	0.363																																					p.S164S	Melanoma(2;92 134 23744 29976 33782)	Atlas-SNP	.											.	SKIV2L2	104	.	0			c.A492C						.						152	145	148					5																	54624616		2203	4300	6503	SO:0001819	synonymous_variant	23517	exon5			TACCTCAGCGGGA	D29641	CCDS3967.1	5q11.2	2008-11-25	2005-02-18	2005-02-18	ENSG00000039123	ENSG00000039123			18734	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 118"		"KIAA0052"	KIAA0052			Standard	NM_015360		Approved	Mtr4, Dob1, fSAP118	uc003jpy.4	P42285	OTTHUMG00000097019	ENST00000230640.5:c.492A>C	chr5.hg19:g.54624616A>C		76.0	0.0		66.0	27.0	NM_015360	Q2M386|Q6MZZ8|Q6P170|Q8N5R0|Q8TAG2	Silent	SNP	ENST00000230640.5	hg19	CCDS3967.1																																																																																			.	.		0.363	SKIV2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214108.1			C	54624616	A	C	54624616	2	2	284	1	0	0	0	0	0	0	0	1	14375	175	7	5		5	SKIV2L2	5	54624616	Silent	SNP	A	TCGA-G3-A5SI-01A-31D-A27I-10		54624616	126290644	10	41879										
ANXA6	309	hgsc.bcm.edu	37	chr5	150483246	150483246	+	Frame_Shift_Del	DEL	C	C	-													0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	tcagagtcttctcatctgtgCcagcaccctggtggagccag							TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr5:150483246delC	ENST00000354546.5	-	25	2074	c.1847delG	c.(1846-1848)ggcfs	p.G616fs	ANXA6_ENST00000356496.5_Frame_Shift_Del_p.G610fs|ANXA6_ENST00000521512.1_Frame_Shift_Del_p.G403fs|ANXA6_ENST00000377751.5_Frame_Shift_Del_p.G273fs|ANXA6_ENST00000523714.1_Frame_Shift_Del_p.G584fs	NM_001155.4	NP_001146.2	P08133	ANXA6_HUMAN	annexin A6	616					calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|protein homooligomerization (GO:0051260)|regulation of muscle contraction (GO:0006937)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|cholesterol binding (GO:0015485)|GTP binding (GO:0005525)|ligand-gated ion channel activity (GO:0015276)|lipid binding (GO:0008289)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(1)|lung(9)	12		Medulloblastoma(196;0.0912)|all_hematologic(541;0.208)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTCATCTGTGCCAGCACCCTG	0.532																																					p.G616fs		Atlas-Indel,Pindel	.											.	ANXA6	102	.	0			c.1848delC						.						30	31	31					5																	150483246		2102	4229	6331	SO:0001589	frameshift_variant	309	exon25			.	J03578	CCDS47315.1, CCDS54941.1	5q33.1	2008-02-05			ENSG00000197043	ENSG00000197043		"Annexins"	544	protein-coding gene	gene with protein product		114070		ANX6		3258820	Standard	NM_001155		Approved		uc003ltl.2	P08133	OTTHUMG00000164179	ENST00000354546.5:c.1847delG	chr5.hg19:g.150483246delC	ENSP00000346550:p.Gly616fs	85.0	0.0		53.0	22.0	NM_001155	B7Z8A7|D3DQH4|E9PGK1|Q6ZT79	Frame_Shift_Del	DEL	ENST00000354546.5	hg19	CCDS47315.1																																																																																			.	.		0.532	ANXA6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377668.2	NM_001155		-	150483246	C	-	150483246	7	5	284	1	0	1	0	1	0	0	0	0	722	739	26	0	182	0	ANXA6	5	150483246	Frame_Shift_Del	DEL	C	TCGA-G3-A5SI-01A-31D-A27I-10	95858630	150483246	30432014	11	41880										
DEK	7913	hgsc.bcm.edu	37	chr6	18249918	18249918	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	ttatcttcatcatctgaagaCtcttccttgtttttcttttc	3	10	6	2			TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr6:18249918C>T	ENST00000397239.3	-	7	1173	c.726G>A	c.(724-726)gaG>gaA	p.E242E	DEK_ENST00000244776.7_Silent_p.E208E	NM_003472.3	NP_003463.1	P35659	DEK_HUMAN	DEK proto-oncogene	242	Asp/Glu-rich (acidic).				chromatin modification (GO:0016568)|regulation of double-strand break repair (GO:2000779)|regulation of double-strand break repair via nonhomologous end joining (GO:2001032)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	7	Ovarian(93;0.00769)|Breast(50;0.0495)	all_hematologic(90;0.053)	OV - Ovarian serous cystadenocarcinoma(7;0.00291)|all cancers(50;0.031)|Epithelial(50;0.0332)			CATCTGAAGACTCTTCCTTGT	0.338			T	NUP214	AML																																p.E242E		Atlas-SNP	.		Dom	yes		6	6p23	7913	DEK oncogene (DNA binding)		L	.	DEK	31	.	0			c.G726A						.						89	81	84					6																	18249918		2203	4299	6502	SO:0001819	synonymous_variant	7913	exon7			TGAAGACTCTTCC	X64229	CCDS34344.1, CCDS47382.1	6p23	2014-06-25	2014-06-25		ENSG00000124795	ENSG00000124795			2768	protein-coding gene	gene with protein product		125264	"DEK oncogene (DNA binding)", "DEK oncogene"			1549122	Standard	NM_003472		Approved	D6S231E	uc003ncr.1	P35659	OTTHUMG00000014319	ENST00000397239.3:c.726G>A	chr6.hg19:g.18249918C>T		58.0	0.0		111.0	8.0	NM_003472	B2R6K6|B4DN37|Q5TGV4|Q5TGV5	Silent	SNP	ENST00000397239.3	hg19	CCDS34344.1																																																																																			.	.		0.338	DEK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039962.4			T	18249918	C	T	18249918	2	4	284	1	0	0	0	0	0	0	0	1	4426	564	20	3		3	DEK	6	18249918	Silent	SNP	C	TCGA-G3-A5SI-01A-31D-A27I-10		18249918	152865149	12	41881										
LATS1	9113	hgsc.bcm.edu	37	chr6	149997737	149997737	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	atataattgggagtcccaacCaaagaatgtgctagacatcg	9	8	0	2			TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr6:149997737C>T	ENST00000543571.1	-	6	3277	c.2730G>A	c.(2728-2730)ttG>ttA	p.L910L	LATS1_ENST00000542747.1_5'UTR|LATS1_ENST00000253339.5_Silent_p.L910L	NM_004690.3	NP_004681.1			large tumor suppressor kinase 1											central_nervous_system(1)|lung(5)	6		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116)		GAGTCCCAACCAAAGAATGTG	0.478																																					p.L910L		Atlas-SNP	.											.	LATS1	241	.	0			c.G2730A						.						74	73	73					6																	149997737		2203	4300	6503	SO:0001819	synonymous_variant	9113	exon6			CCCAACCAAAGAA	AF104413	CCDS34551.1, CCDS59040.1	6q25.1	2013-04-25	2013-04-25		ENSG00000131023	ENSG00000131023			6514	protein-coding gene	gene with protein product		603473	"LATS (large tumor suppressor, Drosophila) homolog 1", "LATS, large tumor suppressor, homolog 1 (Drosophila)"			9988268, 15122335	Standard	NM_004690		Approved	WARTS	uc003qmu.2	O95835	OTTHUMG00000016437	ENST00000543571.1:c.2730G>A	chr6.hg19:g.149997737C>T		75.0	0.0		69.0	4.0	NM_004690		Silent	SNP	ENST00000543571.1	hg19	CCDS34551.1																																																																																			.	.		0.478	LATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043923.4	NM_004690		T	149997737	C	T	149997737	2	4	284	1	0	0	0	0	0	0	0	1	8655	593	21	3		3	LATS1	6	149997737	Silent	SNP	C	TCGA-G3-A5SI-01A-31D-A27I-10	131747819	149997737	21117330	13	41882										
GLI3	2737	hgsc.bcm.edu	37	chr7	42116418	42116418	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	atgatgtctggcatcaattgGtacaggaggatggaaggcag	15	5	2	1			TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr7:42116418G>T	ENST00000395925.3	-	4	490	c.406C>A	c.(406-408)Cca>Aca	p.P136T	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	136					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						GCATCAATTGGTACAGGAGGA	0.413									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																												p.P136T		Atlas-SNP	.											.	GLI3	312	.	0			c.C406A						.						149	127	134					7																	42116418		2203	4300	6503	SO:0001583	missense	2737	exon4	Familial Cancer Database	;	CAATTGGTACAGG		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"Zinc fingers, C2H2-type"	4319	protein-coding gene	gene with protein product	"zinc finger protein GLI3", "oncogene GLI3", "DNA-binding protein"	165240	"Greig cephalopolysyndactyly syndrome", "GLI-Kruppel family member GLI3", "glioma-associated oncogene family zinc finger 3"	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.406C>A	chr7.hg19:g.42116418G>T	ENSP00000379258:p.Pro136Thr	161.0	0.0		175.0	33.0	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Missense_Mutation	SNP	ENST00000395925.3	hg19	CCDS5465.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.555198	0.86231	.	.	ENSG00000106571	ENST00000395925;ENST00000448703	T;T	0.76186	-1.0;-1.0	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.86091	0.5850	M	0.69358	2.11	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.86392	0.1736	10	0.87932	D	0	.	20.0781	0.97751	0.0:0.0:1.0:0.0	.	136	P10071	GLI3_HUMAN	T	136	ENSP00000379258:P136T;ENSP00000406135:P136T	ENSP00000379258:P136T	P	-	1	0	GLI3	42082943	1.000000	0.71417	0.724000	0.30704	0.987000	0.75469	9.174000	0.94824	2.817000	0.96982	0.563000	0.77884	CCA	.	.		0.413	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168		T	42116418	G	T	42116418	3	4	284	1	0	0	0	0	1	0	0	0	6447	1261	44	3	4384	3	GLI3	7	42116418	Missense_Mutation	SNP	G	TCGA-G3-A5SI-01A-31D-A27I-10		42116418	117022245	14	41883										
ZCWPW1	55063	hgsc.bcm.edu	37	chr7	100004329	100004329	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	gtgctcaccatgactgatagCtccagggacagctcctggaa	11	12	1	2			TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr7:100004329C>T	ENST00000398027.2	-	12	1405	c.1158G>A	c.(1156-1158)gaG>gaA	p.E386E	ZCWPW1_ENST00000490721.1_Silent_p.E266E|ZCWPW1_ENST00000360951.4_Silent_p.E387E|ZCWPW1_ENST00000324725.6_Silent_p.E266E	NM_017984.4	NP_060454.3	Q9H0M4	ZCPW1_HUMAN	zinc finger, CW type with PWWP domain 1	386							zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)	16	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TGACTGATAGCTCCAGGGACA	0.428																																					p.E387E		Atlas-SNP	.											.	ZCWPW1	41	.	0			c.G1161A						.						122	126	124					7																	100004329		1914	4126	6040	SO:0001819	synonymous_variant	55063	exon12			TGATAGCTCCAGG	AK000919	CCDS43623.1, CCDS59067.1	7q22.1	2012-02-10	2004-11-03		ENSG00000078487	ENSG00000078487			23486	protein-coding gene	gene with protein product			"zinc finger, CW-type with PWWP domain 1"			11230166, 14607086, 20826339	Standard	NM_017984		Approved	FLJ10057, DKFZp434N0510, ZCW1	uc003uut.4	Q9H0M4	OTTHUMG00000159537	ENST00000398027.2:c.1158G>A	chr7.hg19:g.100004329C>T		83.0	0.0		85.0	8.0	NM_001258008	A8MVF5|B4DUQ2|Q8NA98|Q9BUD0|Q9NWF7	Silent	SNP	ENST00000398027.2	hg19	CCDS43623.1																																																																																			.	.		0.428	ZCWPW1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356083.1	NM_017984		T	100004329	C	T	100004329	2	4	284	1	0	0	0	0	0	0	0	1	17612	796	28	3		3	ZCWPW1	7	100004329	Silent	SNP	C	TCGA-G3-A5SI-01A-31D-A27I-10	57887911	100004329	59134334	15	41884										
TAS2R3	50831	hgsc.bcm.edu	37	chr7	141464093	141464093	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	aagagaatgtctttgtctgaCttcatcatcaccaccctggc	7	12	5	2			TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr7:141464093C>G	ENST00000247879.2	+	1	197	c.135C>G	c.(133-135)gaC>gaG	p.D45E	SSBP1_ENST00000465582.1_Intron	NM_016943.2	NP_058639.1	Q9NYW6	TA2R3_HUMAN	taste receptor, type 2, member 3	45					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)	14	Melanoma(164;0.0171)					CTTTGTCTGACTTCATCATCA	0.418																																					p.D45E		Atlas-SNP	.											.	TAS2R3	40	.	0			c.C135G						.						265	254	258					7																	141464093		2203	4300	6503	SO:0001583	missense	50831	exon1			GTCTGACTTCATC	AF227130	CCDS5867.1	7q31.3-q32	2012-08-22			ENSG00000127362	ENSG00000127362		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14910	protein-coding gene	gene with protein product		604868					Standard	NM_016943		Approved	T2R3	uc003vwp.1	Q9NYW6	OTTHUMG00000157637	ENST00000247879.2:c.135C>G	chr7.hg19:g.141464093C>G	ENSP00000247879:p.Asp45Glu	172.0	0.0		148.0	6.0	NM_016943	A4D1U2|Q645W2|Q75MV6	Missense_Mutation	SNP	ENST00000247879.2	hg19	CCDS5867.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.026387	0.75390	.	.	ENSG00000127362	ENST00000247879	T	0.01139	5.28	6.17	3.31	0.37934	.	0.123149	0.51477	D	0.000084	T	0.07234	0.0183	M	0.91510	3.215	0.25960	N	0.982637	D	0.71674	0.998	D	0.69142	0.962	T	0.04855	-1.0922	10	0.87932	D	0	.	7.956	0.30042	0.1298:0.7287:0.0:0.1416	.	45	Q9NYW6	TA2R3_HUMAN	E	45	ENSP00000247879:D45E	ENSP00000247879:D45E	D	+	3	2	TAS2R3	141110562	0.231000	0.23751	1.000000	0.80357	0.928000	0.56348	0.019000	0.13444	0.924000	0.37069	-0.150000	0.13652	GAC	.	.		0.418	TAS2R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349288.1			G	141464093	C	G	141464093	3	3	284	1	0	0	0	0	1	0	0	0	15587	564	20	4	137	4	TAS2R3	7	141464093	Missense_Mutation	SNP	C	TCGA-G3-A5SI-01A-31D-A27I-10	41459764	141464093	17674570	16	41885										
SLC25A37	51312	hgsc.bcm.edu	37	chr8	23429092	23429092	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	ggcgggctggccggggccctCgccgcggccgccacgacccc	17	20	0	0			TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr8:23429092C>T	ENST00000519973.1	+	4	939	c.741C>T	c.(739-741)ctC>ctT	p.L247L	FP15737_ENST00000399967.3_5'Flank	NM_016612.2	NP_057696.2	Q9NYZ2	MFRN1_HUMAN	solute carrier family 25 (mitochondrial iron transporter), member 37	247					iron ion homeostasis (GO:0055072)|mitochondrial iron ion transport (GO:0048250)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	iron ion transmembrane transporter activity (GO:0005381)			NS(1)|endometrium(3)|large_intestine(2)|lung(8)|urinary_tract(1)	15		Prostate(55;0.114)		Colorectal(74;0.0198)|COAD - Colon adenocarcinoma(73;0.0751)		CCGGGGCCCTCGCCGCGGCCG	0.657																																					p.L247L		Atlas-SNP	.											.	SLC25A37	27	.	0			c.C741T						.						22	27	25					8																	23429092		1906	4104	6010	SO:0001819	synonymous_variant	51312	exon4			GGCCCTCGCCGCG	AF495725	CCDS47828.1	8p21.2	2013-05-22	2012-03-29		ENSG00000147454	ENSG00000147454		"Solute carriers"	29786	protein-coding gene	gene with protein product	"mitoferrin"	610387	"solute carrier family 25, member 37"			16511496	Standard	XM_006716352		Approved	MSCP, MFRN, MFRN1	uc003xdo.3	Q9NYZ2	OTTHUMG00000163865	ENST00000519973.1:c.741C>T	chr8.hg19:g.23429092C>T		39.0	0.0		33.0	16.0	NM_016612	A2RU93|Q53FT7|Q69YJ8|Q969S1|Q9P0J2	Silent	SNP	ENST00000519973.1	hg19	CCDS47828.1																																																																																			.	.		0.657	SLC25A37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376039.1	NM_016612		T	23429092	C	T	23429092	2	4	284	1	0	0	0	0	0	0	0	1	14516	871	31	1		1	SLC25A37	8	23429092	Silent	SNP	C	TCGA-G3-A5SI-01A-31D-A27I-10		23429092	122934930	17	41886										
KCNQ3	3786	hgsc.bcm.edu	37	chr8	133141974	133141974	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	ggtccccctcggggcaggttCacagggtcatgtgcaaaaaa	13	11	2	0			TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr8:133141974C>G	ENST00000388996.4	-	15	2574	c.2154G>C	c.(2152-2154)gtG>gtC	p.V718V	KCNQ3_ENST00000519445.1_Silent_p.V706V|KCNQ3_ENST00000521134.1_Silent_p.V598V	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	718					axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	70	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	GGGGCAGGTTCACAGGGTCAT	0.562																																					p.V718V		Atlas-SNP	.											.	KCNQ3	164	.	0			c.G2154C						.						44	44	44					8																	133141974		2203	4300	6503	SO:0001819	synonymous_variant	3786	exon15			CAGGTTCACAGGG	AB208890	CCDS34943.1, CCDS56554.1	8q24	2012-07-05			ENSG00000184156	ENSG00000184156		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6297	protein-coding gene	gene with protein product		602232		EBN2		9425900, 16382104	Standard	NM_004519		Approved	Kv7.3	uc003ytj.3	O43525	OTTHUMG00000137472	ENST00000388996.4:c.2154G>C	chr8.hg19:g.133141974C>G		176.0	0.0		304.0	89.0	NM_004519	A2VCT8|B4DJY4|E7EQ89	Silent	SNP	ENST00000388996.4	hg19	CCDS34943.1																																																																																			.	.		0.562	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519		G	133141974	C	G	133141974	2	3	284	1	0	0	0	0	0	0	0	1	8093	813	29	4		4	KCNQ3	8	133141974	Silent	SNP	C	TCGA-G3-A5SI-01A-31D-A27I-10	109712882	133141974	13222048	18	41887										
NFX1	4799	hgsc.bcm.edu	37	chr9	33295194	33295194	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	caccaaaacaggagggccacCgacatacaaacgcaggacac	9	14	0	0			TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr9:33295194C>T	ENST00000379540.3	+	2	864	c.802C>T	c.(802-804)Cga>Tga	p.R268*	NFX1_ENST00000379521.4_Nonsense_Mutation_p.R268*|NFX1_ENST00000318524.6_Nonsense_Mutation_p.R268*	NM_002504.4	NP_002495.2	Q12986	NFX1_HUMAN	nuclear transcription factor, X-box binding 1	268					inflammatory response (GO:0006954)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25			LUSC - Lung squamous cell carcinoma(29;0.00506)	GBM - Glioblastoma multiforme(74;0.224)		GGAGGGCCACCGACATACAAA	0.527																																					p.R268X		Atlas-SNP	.											NFX1,NS,haematopoietic_neoplasm,0,1	NFX1	85	.	0			c.C802T						.						121	111	115					9																	33295194		2203	4300	6503	SO:0001587	stop_gained	4799	exon2			GGCCACCGACATA	U19759	CCDS6538.1, CCDS6539.1, CCDS6540.1	9p12	2013-12-13			ENSG00000086102	ENSG00000086102			7803	protein-coding gene	gene with protein product		603255				7964459, 2511169	Standard	NM_002504		Approved	NFX2, MGC20369, Tex42, TEG-42	uc003zsq.3	Q12986	OTTHUMG00000019772	ENST00000379540.3:c.802C>T	chr9.hg19:g.33295194C>T	ENSP00000368856:p.Arg268*	146.0	1.0		127.0	7.0	NM_147134	A8K6H8|Q5VXW6|Q96EL5|Q9BXI1	Nonsense_Mutation	SNP	ENST00000379540.3	hg19	CCDS6538.1	.	.	.	.	.	.	.	.	.	.	C	16.96	3.265852	0.59540	.	.	ENSG00000086102	ENST00000379540;ENST00000379521;ENST00000536210;ENST00000318524	.	.	.	5.69	4.73	0.59995	.	0.285063	0.33732	N	0.004606	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.8523	0.57864	0.1944:0.8056:0.0:0.0	.	.	.	.	X	268	.	ENSP00000317695:R268X	R	+	1	2	NFX1	33285194	0.789000	0.28775	0.123000	0.21794	0.169000	0.22640	1.958000	0.40402	2.682000	0.91365	0.551000	0.68910	CGA	.	.		0.527	NFX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052069.1			T	33295194	C	T	33295194	4	4	284	1	0	0	0	0	0	1	0	0	10396	644	23	1	808	1	NFX1	9	33295194	Nonsense_Mutation	SNP	C	TCGA-G3-A5SI-01A-31D-A27I-10		33295194	107918237	19	41888										
OGN	4969	hgsc.bcm.edu	37	chr9	95152228	95152228	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	aggaagaactggaagttttaGtagttgattttcagcaagtg	12	3	1	2			TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr9:95152228G>C	ENST00000262551.4	-	5	958	c.538C>G	c.(538-540)Cta>Gta	p.L180V	CENPP_ENST00000375587.3_Intron|OGN_ENST00000375561.5_Missense_Mutation_p.L180V|OGN_ENST00000468743.1_5'UTR	NM_033014.2	NP_148935.1	P20774	MIME_HUMAN	osteoglycin	180					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|negative regulation of smooth muscle cell proliferation (GO:0048662)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|prostate(1)|urinary_tract(1)	13						GGAAGTTTTAGTAGTTGATTT	0.318																																					p.L180V		Atlas-SNP	.											.	OGN	26	.	0			c.C538G						.						119	122	121					9																	95152228		2202	4299	6501	SO:0001583	missense	4969	exon5			GTTTTAGTAGTTG	AI424992	CCDS6695.1	9q22	2008-02-05	2007-02-16		ENSG00000106809	ENSG00000106809		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	8126	protein-coding gene	gene with protein product	"mimecan proteoglycan"	602383	"osteoglycin (osteoinductive factor)"			2372374	Standard	NM_033014		Approved	mimecan, OIF, SLRR3A	uc004asa.3	P20774	OTTHUMG00000020224	ENST00000262551.4:c.538C>G	chr9.hg19:g.95152228G>C	ENSP00000262551:p.Leu180Val	56.0	0.0		29.0	14.0	NM_033014	Q6FIB0|Q9UF90|Q9UNK5	Missense_Mutation	SNP	ENST00000262551.4	hg19	CCDS6695.1	.	.	.	.	.	.	.	.	.	.	G	10.54	1.377437	0.24944	.	.	ENSG00000106809	ENST00000262551;ENST00000375561;ENST00000447356	D;D;D	0.83335	-1.71;-1.71;-1.71	5.27	-3.56	0.04626	.	0.417501	0.25854	N	0.027879	T	0.49541	0.1563	N	0.02539	-0.55	0.24841	N	0.99247	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.43637	-0.9379	10	0.26408	T	0.33	.	1.1245	0.01732	0.407:0.2378:0.1821:0.1731	.	238;180	B4DI63;P20774	.;MIME_HUMAN	V	180;180;238	ENSP00000262551:L180V;ENSP00000364711:L180V;ENSP00000396709:L238V	ENSP00000262551:L180V	L	-	1	2	OGN	94192049	0.000000	0.05858	0.982000	0.44146	0.998000	0.95712	-1.084000	0.03393	-0.304000	0.08843	0.655000	0.94253	CTA	.	.		0.318	OGN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053087.1	NM_024416		C	95152228	G	C	95152228	3	2	284	1	0	0	0	0	1	0	0	0	10855	1020	36	4	370	4	OGN	9	95152228	Missense_Mutation	SNP	G	TCGA-G3-A5SI-01A-31D-A27I-10	61857034	95152228	46061203	20	41889										
WT1	7490	hgsc.bcm.edu	37	chr11	32414248	32414248	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	gtgtcttttgagctggtctgAacgagaaaaccttcgttcac	10	9	3	3			TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr11:32414248A>G	ENST00000379079.2	-	8	940	c.667T>C	c.(667-669)Tca>Cca	p.S223P	WT1_ENST00000448076.3_Missense_Mutation_p.S435P|WT1_ENST00000332351.3_Missense_Mutation_p.S435P|WT1_ENST00000530998.1_Missense_Mutation_p.S206P	NM_001198551.1	NP_001185480.1	P19544	WT1_HUMAN	Wilms tumor 1	367			S -> N (in WT1). {ECO:0000269|PubMed:9529364}.		adrenal cortex formation (GO:0035802)|adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye development (GO:0043010)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|diaphragm development (GO:0060539)|epithelial cell differentiation (GO:0030855)|germ cell development (GO:0007281)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|gonad development (GO:0008406)|heart development (GO:0007507)|kidney development (GO:0001822)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|mesenchymal to epithelial transition (GO:0060231)|metanephric epithelium development (GO:0072207)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of female gonad development (GO:2000195)|negative regulation of metanephric glomerular mesangial cell proliferation (GO:0072302)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of heart growth (GO:0060421)|positive regulation of male gonad development (GO:2000020)|positive regulation of metanephric ureteric bud development (GO:2001076)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior mesonephric tubule development (GO:0072166)|regulation of organ formation (GO:0003156)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|sex determination (GO:0007530)|thorax and anterior abdomen determination (GO:0007356)|tissue development (GO:0009888)|ureteric bud development (GO:0001657)|vasculogenesis (GO:0001570)|visceral serous pericardium development (GO:0061032)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)		EWSR1/WT1(234)	NS(1)|haematopoietic_and_lymphoid_tissue(348)|kidney(149)|large_intestine(9)|lung(20)|peritoneum(1)|pleura(2)|skin(2)|upper_aerodigestive_tract(1)	533	Breast(20;0.247)		OV - Ovarian serous cystadenocarcinoma(30;0.128)			AGCTGGTCTGAACGAGAAAAC	0.443			"D, Mis, N, F, S"	EWSR1	"Wilms, desmoplastic small round cell tumor"	Wilms			Wilms' tumor-Aniridia-ambiguous Genitals-mental Retardation;Frasier syndrome;Familial Wilms' tumor;Denys-Drash syndrome																												p.S435P		Atlas-SNP	.	yes	Rec	yes	"Denys-Drash syndrome, Frasier syndrome, Familial Wilms tumor"	11	11p13	7490	Wilms tumour 1 gene		O	.	WT1	744	.	0			c.T1303C						.						188	158	168					11																	32414248		2202	4299	6501	SO:0001583	missense	7490	exon8	Familial Cancer Database	WAGR syndrome; ; ;incl.: Early Onset Nephrotic Syndrome-WT1 associated	GGTCTGAACGAGA		CCDS7878.2, CCDS44561.1, CCDS44562.1, CCDS55750.1, CCDS55751.1	11p13	2014-09-17			ENSG00000184937	ENSG00000184937		"Zinc fingers, C2H2-type"	12796	protein-coding gene	gene with protein product		607102		GUD		14681303	Standard	NM_024424		Approved	WAGR, WIT-2, AWT1	uc001mtn.2	P19544	OTTHUMG00000039556	ENST00000379079.2:c.667T>C	chr11.hg19:g.32414248A>G	ENSP00000368370:p.Ser223Pro	260.0	0.0		243.0	101.0	NM_024424	A8K6S1|B3KSA5|Q15881|Q16256|Q16575|Q4VXV4|Q4VXV5|Q4VXV6|Q8IYZ5	Missense_Mutation	SNP	ENST00000379079.2	hg19	CCDS55751.1	.	.	.	.	.	.	.	.	.	.	A	32	5.106549	0.94292	.	.	ENSG00000184937	ENST00000379079;ENST00000332351;ENST00000530998;ENST00000452863;ENST00000448076	T;T;T;T;T	0.36157	1.27;1.27;1.27;1.27;1.27	5.73	5.73	0.89815	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	U	0.000015	T	0.53738	0.1815	L	0.45228	1.405	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.997;0.998;0.998;0.998	D;D;D;D;D	0.91635	0.998;0.997;0.999;0.995;0.998	T	0.55062	-0.8199	10	0.72032	D	0.01	.	16.3143	0.82909	1.0:0.0:0.0:0.0	.	423;367;440;206;223	P19544-8;P19544;P19544-7;B3KSA5;P19544-6	.;WT1_HUMAN;.;.;.	P	223;435;206;418;435	ENSP00000368370:S223P;ENSP00000331327:S435P;ENSP00000435307:S206P;ENSP00000415516:S418P;ENSP00000413452:S435P	ENSP00000331327:S435P	S	-	1	0	WT1	32370824	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.284000	0.95882	2.313000	0.78055	0.454000	0.30748	TCA	.	.		0.443	WT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000095434.1	NM_000378		G	32414248	A	G	32414248	3	3	284	1	0	0	0	0	1	0	0	0	17423	246	9	2	262	2	WT1	11	32414248	Missense_Mutation	SNP	A	TCGA-G3-A5SI-01A-31D-A27I-10		32414248	102592268	21	41890										
CATSPER1	117144	hgsc.bcm.edu	37	chr11	65788038	65788038	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	caggggtgagtcctcacttgAggaagatgaagtactggatg	15	6	1	4			TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr11:65788038A>G	ENST00000312106.5	-	7	2125	c.1988T>C	c.(1987-1989)cTc>cCc	p.L663P		NM_053054.3	NP_444282.3	Q8NEC5	CTSR1_HUMAN	cation channel, sperm associated 1	663					calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|fusion of sperm to egg plasma membrane (GO:0007342)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|regulation of calcium ion transport (GO:0051924)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|central_nervous_system(1)|endometrium(9)|kidney(3)|large_intestine(6)|liver(3)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44						TCCTCACTTGAGGAAGATGAA	0.592																																					p.L663P		Atlas-SNP	.											.	CATSPER1	101	.	0			c.T1988C						.						94	97	96					11																	65788038		2201	4296	6497	SO:0001583	missense	117144	exon7			CACTTGAGGAAGA	AF407333	CCDS8127.1	11q12.1	2011-07-05			ENSG00000175294	ENSG00000175294		"Voltage-gated ion channels / Cation channels, sperm associated"	17116	protein-coding gene	gene with protein product		606389				11675491, 11595941, 16382101	Standard	NM_053054		Approved	CATSPER	uc001ogt.3	Q8NEC5	OTTHUMG00000166668	ENST00000312106.5:c.1988T>C	chr11.hg19:g.65788038A>G	ENSP00000309052:p.Leu663Pro	105.0	0.0		120.0	42.0	NM_053054	Q96P76	Missense_Mutation	SNP	ENST00000312106.5	hg19	CCDS8127.1	.	.	.	.	.	.	.	.	.	.	A	19.36	3.813138	0.70912	.	.	ENSG00000175294	ENST00000312106	D	0.99042	-5.36	5.23	5.23	0.72850	Ion transport (1);	0.000000	0.29616	U	0.011646	D	0.99230	0.9732	M	0.94101	3.495	0.58432	D	0.999999	P	0.49862	0.929	P	0.55965	0.788	D	0.99218	1.0878	10	0.87932	D	0	.	11.5111	0.50494	1.0:0.0:0.0:0.0	.	663	Q8NEC5	CTSR1_HUMAN	P	663	ENSP00000309052:L663P	ENSP00000309052:L663P	L	-	2	0	CATSPER1	65544614	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	5.564000	0.67359	1.974000	0.57490	0.459000	0.35465	CTC	.	.		0.592	CATSPER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391055.1	NM_053054		G	65788038	A	G	65788038	3	3	284	1	0	0	0	0	1	0	0	0	2689	304	11	2	378	2	CATSPER1	11	65788038	Missense_Mutation	SNP	A	TCGA-G3-A5SI-01A-31D-A27I-10	33373790	65788038	69218478	22	41891										
GPR84	53831	hgsc.bcm.edu	37	chr12	54756722	54756722	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	atgaagaatccggagctcttCtggctcctttaattggctgg	11	9	2	2			TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr12:54756722C>T	ENST00000551809.1	-	1	1549	c.914G>A	c.(913-915)aGa>aAa	p.R305K	GPR84_ENST00000267015.3_Missense_Mutation_p.R305K|RP11-753H16.5_ENST00000552785.1_RNA|RP11-753H16.3_ENST00000550474.1_RNA			Q9NQS5	GPR84_HUMAN	G protein-coupled receptor 84	305						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(2)|kidney(2)|large_intestine(6)|lung(5)|skin(1)|urinary_tract(1)	18						CGGAGCTCTTCTGGCTCCTTT	0.507																																					p.R305K		Atlas-SNP	.											.	GPR84	38	.	0			c.G914A						.						122	127	125					12																	54756722		2203	4300	6503	SO:0001583	missense	53831	exon2			GCTCTTCTGGCTC	AF237762	CCDS8878.1	12q13.13	2012-08-20						"GPCR / Class A : Fatty acid receptors"	4535	protein-coding gene	gene with protein product		606383				11273702	Standard	NM_020370		Approved	EX33	uc001sfu.3	Q9NQS5		ENST00000551809.1:c.914G>A	chr12.hg19:g.54756722C>T	ENSP00000450310:p.Arg305Lys	154.0	0.0		135.0	9.0	NM_020370	B6V9G7	Missense_Mutation	SNP	ENST00000551809.1	hg19	CCDS8878.1	.	.	.	.	.	.	.	.	.	.	c	0.005	-2.153377	0.00325	.	.	ENSG00000139572	ENST00000267015;ENST00000551809	T;T	0.37058	1.22;1.22	4.08	-6.13	0.02118	GPCR, rhodopsin-like superfamily (1);	2.058800	0.02794	N	0.122402	T	0.21468	0.0517	L	0.34521	1.04	0.09310	N	1	B	0.11235	0.004	B	0.14023	0.01	T	0.24728	-1.0152	10	0.07325	T	0.83	0.6568	6.2275	0.20716	0.0:0.2146:0.2622:0.5232	.	305	Q9NQS5	GPR84_HUMAN	K	305	ENSP00000267015:R305K;ENSP00000450310:R305K	ENSP00000267015:R305K	R	-	2	0	GPR84	53042989	0.000000	0.05858	0.011000	0.14972	0.110000	0.19582	-2.779000	0.00774	-1.350000	0.02199	-0.974000	0.02594	AGA	.	.		0.507	GPR84-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406156.1			T	54756722	C	T	54756722	3	4	284	1	0	0	0	0	1	0	0	0	6722	913	32	3	280	3	GPR84	12	54756722	Missense_Mutation	SNP	C	TCGA-G3-A5SI-01A-31D-A27I-10		54756722	79095173	23	41892										
NAB2	4665	hgsc.bcm.edu	37	chr12	57484963	57484963	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	tgggggagctgcagctgtacCgggtcctgcagcgcgccaac	16	13	0	0			TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr12:57484963C>T	ENST00000300131.3	+	2	517	c.139C>T	c.(139-141)Cgg>Tgg	p.R47W	NAB2_ENST00000342556.6_Missense_Mutation_p.R47W|NAB2_ENST00000357680.4_Missense_Mutation_p.R47W|NAB2_ENST00000554718.1_Intron	NM_005967.3	NP_005958.1	Q15742	NAB2_HUMAN	NGFI-A binding protein 2 (EGR1 binding protein 2)	47	NCD1.				cell proliferation (GO:0008283)|endochondral ossification (GO:0001958)|myelination (GO:0042552)|negative regulation of transcription from RNA polymerase III promoter (GO:0016480)|nervous system development (GO:0007399)|regulation of epidermis development (GO:0045682)|Schwann cell differentiation (GO:0014037)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	20						GCAGCTGTACCGGGTCCTGCA	0.647																																					p.R47W		Atlas-SNP	.											.	NAB2	47	.	0			c.C139T						.						61	64	63					12																	57484963		2203	4300	6503	SO:0001583	missense	4665	exon2			CTGTACCGGGTCC	BC065931	CCDS8930.1	12q13.3	2008-05-14				ENSG00000166886			7627	protein-coding gene	gene with protein product		602381				8668170, 8649813	Standard	XM_005268894		Approved	MADER	uc001smz.3	Q15742		ENST00000300131.3:c.139C>T	chr12.hg19:g.57484963C>T	ENSP00000300131:p.Arg47Trp	95.0	0.0		96.0	4.0	NM_005967	B2RAK3|O76006|Q14797	Missense_Mutation	SNP	ENST00000300131.3	hg19	CCDS8930.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.862548	0.91511	.	.	ENSG00000166886	ENST00000300131;ENST00000342556;ENST00000357680	D;D;D	0.82803	-1.65;-1.65;-1.65	4.49	4.49	0.54785	Nab, N-terminal (2);	0.000000	0.64402	D	0.000004	D	0.90235	0.6947	M	0.75447	2.3	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.91466	0.5193	10	0.87932	D	0	-12.742	14.7434	0.69472	0.0:1.0:0.0:0.0	.	47	Q15742	NAB2_HUMAN	W	47	ENSP00000300131:R47W;ENSP00000341491:R47W;ENSP00000350309:R47W	ENSP00000300131:R47W	R	+	1	2	NAB2	55771230	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.844000	0.69430	2.320000	0.78422	0.655000	0.94253	CGG	.	.		0.647	NAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412222.1	NM_005967		T	57484963	C	T	57484963	3	4	284	1	0	0	0	0	1	0	0	0	10141	643	23	1	145	1	NAB2	12	57484963	Missense_Mutation	SNP	C	TCGA-G3-A5SI-01A-31D-A27I-10	2728241	57484963	76366932	24	41893										
RB1	5925	hgsc.bcm.edu	37	chr13	48953741	48953742	+	Frame_Shift_Ins	INS	-	-	G													0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	gtttgtagcgatacaaacttINSggagttcgcttgtattaccg							TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr13:48953741_48953742insG	ENST00000267163.4	+	14	1482_1483	c.1344_1345insG	c.(1345-1347)ggafs	p.G449fs		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	449	Domain A.|Pocket; binds T and E1A.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(8)|p.G449R(1)|p.L448L(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(DB00071)|Insulin Regular(DB00030)"	GATACAAACTTGGAGTTCGCTT	0.347		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)																											p.L448fs		Atlas-INDEL	.	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	RB1,rectum,carcinoma,0,1	RB1	1068	.	25	Whole gene deletion(15)|Unknown(8)|Substitution - Missense(1)|Substitution - coding silent(1)	bone(11)|breast(5)|central_nervous_system(2)|adrenal_gland(1)|large_intestine(1)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)|lung(1)	c.1344_1345insG	GRCh37	CS071257	RB1	S		.																																			SO:0001589	frameshift_variant	5925	exon14	Familial Cancer Database		.	M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1346dupG	chr13.hg19:g.48953743_48953743dupG	ENSP00000267163:p.Gly449fs	91.0	0.0		25.0	19.0	NM_000321	A8K5E3|P78499|Q5VW46|Q8IZL4	Frame_Shift_Ins	INS	ENST00000267163.4	hg19	CCDS31973.1																																																																																			.	.		0.347	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			G	48953742	-	G	48953741	7	5	284	1	0	1	1	0	0	0	0	0	13113	1799	63	0	1398	0	RB1	13	48953741	Frame_Shift_Ins	INS	-	TCGA-G3-A5SI-01A-31D-A27I-10		48953741	66216137	25	41894										
KHNYN	23351	hgsc.bcm.edu	37	chr14	24901509	24901509	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	cctccctcctccagcggctcCacaatgggaatgcctctcct	7	19	1	0			TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr14:24901509C>A	ENST00000251343.5	+	3	1181	c.1042C>A	c.(1042-1044)Cac>Aac	p.H348N	CBLN3_ENST00000555436.1_5'Flank|KHNYN_ENST00000556842.1_Missense_Mutation_p.H348N|CBLN3_ENST00000267406.6_5'Flank|KHNYN_ENST00000554268.1_5'Flank|KHNYN_ENST00000553935.1_Missense_Mutation_p.H348N			O15037	KHNYN_HUMAN	KH and NYN domain containing	348							RNA binding (GO:0003723)			kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(3)	24						CCAGCGGCTCCACAATGGGAA	0.682											OREG0022627	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.H348N		Atlas-SNP	.											.	KHNYN	46	.	0			c.C1042A						.						49	55	53					14																	24901509		2203	4300	6503	SO:0001583	missense	23351	exon3			CGGCTCCACAATG	AB002321	CCDS32058.1	14q11.2	2010-11-23	2009-10-14	2009-10-14	ENSG00000100441	ENSG00000100441			20166	protein-coding gene	gene with protein product			"KIAA0323"	KIAA0323		17114934	Standard	NM_015299		Approved		uc001wph.4	O15037		ENST00000251343.5:c.1042C>A	chr14.hg19:g.24901509C>A	ENSP00000251343:p.His348Asn	174.0	0.0	774	150.0	8.0	NM_015299	Q86TZ6|Q8IUQ2|Q96BA9	Missense_Mutation	SNP	ENST00000251343.5	hg19	CCDS32058.1	.	.	.	.	.	.	.	.	.	.	C	13.47	2.246982	0.39697	.	.	ENSG00000100441	ENST00000251343;ENST00000556842;ENST00000553935	T;T;T	0.23552	1.9;1.9;1.9	5.27	4.29	0.51040	.	0.861964	0.10600	N	0.655769	T	0.18257	0.0438	L	0.27053	0.805	0.38383	D	0.94518	B;B	0.15141	0.012;0.005	B;B	0.09377	0.004;0.002	T	0.05801	-1.0863	10	0.15952	T	0.53	.	11.8273	0.52275	0.1868:0.8131:0.0:0.0	.	389;348	D3DS77;O15037	.;KHNYN_HUMAN	N	348	ENSP00000251343:H348N;ENSP00000451106:H348N;ENSP00000450799:H348N	ENSP00000251343:H348N	H	+	1	0	KHNYN	23971349	0.826000	0.29277	1.000000	0.80357	0.896000	0.52359	3.323000	0.52014	2.462000	0.83206	0.462000	0.41574	CAC	.	.		0.682	KHNYN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412928.1			A	24901509	C	A	24901509	3	1	284	1	0	0	0	0	1	0	0	0	8159	594	21	3	1048	3	KHNYN	14	24901509	Missense_Mutation	SNP	C	TCGA-G3-A5SI-01A-31D-A27I-10		24901509	82448031	26	41895										
CKB	1152	hgsc.bcm.edu	37	chr14	103986257	103986257	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	gccctgctccagccgctgctCcatctcgatgagcagcttca	9	17	2	1			TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr14:103986257C>T	ENST00000348956.2	-	8	1447	c.1090G>A	c.(1090-1092)Gag>Aag	p.E364K		NM_001823.4	NP_001814.2	P12277	KCRB_HUMAN	creatine kinase, brain	364	Phosphagen kinase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00843}.				cellular chloride ion homeostasis (GO:0030644)|cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|creatine kinase activity (GO:0004111)			lung(2)|prostate(1)	3		Melanoma(154;0.155)	Epithelial(46;0.14)		Creatine(DB00148)	AGCCGCTGCTCCATCTCGATG	0.637																																					p.E364K	Esophageal Squamous(186;2492 2823 49929 50127)	Atlas-SNP	.											.	CKB	9	.	0			c.G1090A						.						46	42	44					14																	103986257		2202	4300	6502	SO:0001583	missense	1152	exon8			GCTGCTCCATCTC		CCDS9981.1	14q32.32	2012-10-02			ENSG00000166165	ENSG00000166165	2.7.3.2		1991	protein-coding gene	gene with protein product		123280		CKBB			Standard	NM_001823		Approved		uc001ynf.2	P12277	OTTHUMG00000171786	ENST00000348956.2:c.1090G>A	chr14.hg19:g.103986257C>T	ENSP00000299198:p.Glu364Lys	47.0	0.0		43.0	16.0	NM_001823	A8K236|B2R5R4|Q2LE07|Q6FG40|Q9UC66	Missense_Mutation	SNP	ENST00000348956.2	hg19	CCDS9981.1	.	.	.	.	.	.	.	.	.	.	C	36	5.724393	0.96847	.	.	ENSG00000166165	ENST00000348956;ENST00000428256;ENST00000553610	T;T	0.38240	1.15;1.15	4.95	4.95	0.65309	ATP:guanido phosphotransferase, catalytic domain (2);Glutamine synthetase/guanido kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.73806	0.3634	H	0.97587	4.035	0.80722	D	1	D	0.69078	0.997	D	0.68483	0.958	D	0.84963	0.0878	10	0.87932	D	0	-15.8628	18.1883	0.89799	0.0:1.0:0.0:0.0	.	364	P12277	KCRB_HUMAN	K	364;329;162	ENSP00000299198:E364K;ENSP00000451426:E162K	ENSP00000299198:E364K	E	-	1	0	CKB	103056010	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.679000	0.84048	2.286000	0.76751	0.462000	0.41574	GAG	.	.		0.637	CKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415111.1			T	103986257	C	T	103986257	3	4	284	1	0	0	0	0	1	0	0	0	3448	864	30	3	59	3	CKB	14	103986257	Missense_Mutation	SNP	C	TCGA-G3-A5SI-01A-31D-A27I-10	79084748	103986257	3363283	27	41896										
IGDCC4	57722	hgsc.bcm.edu	37	chr15	65680865	65680865	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	cacctctgtgcgcgcccccaTcttgaagaagtaccgagtgt	10	14	2	2			TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr15:65680865T>A	ENST00000352385.2	-	16	2976	c.2767A>T	c.(2767-2769)Atg>Ttg	p.M923L	IGDCC4_ENST00000558048.1_5'Flank	NM_020962.1	NP_066013.1	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member 4	923	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	44						CGCGCCCCCATCTTGAAGAAG	0.617																																					p.M923L		Atlas-SNP	.											.	IGDCC4	95	.	0			c.A2767T						.						108	101	103					15																	65680865		2201	4299	6500	SO:0001583	missense	57722	exon16			CCCCCATCTTGAA		CCDS10206.1	15q22.31	2013-02-11			ENSG00000103742	ENSG00000103742		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	13770	protein-coding gene	gene with protein product	"likely ortholog of mouse neighbor of Punc E11"						Standard	NM_020962		Approved	NOPE, LOC57722	uc002aou.1	Q8TDY8	OTTHUMG00000133136	ENST00000352385.2:c.2767A>T	chr15.hg19:g.65680865T>A	ENSP00000319623:p.Met923Leu	101.0	0.0		82.0	30.0	NM_020962	Q9HCE4	Missense_Mutation	SNP	ENST00000352385.2	hg19	CCDS10206.1	.	.	.	.	.	.	.	.	.	.	T	15.85	2.954123	0.53293	.	.	ENSG00000103742	ENST00000352385;ENST00000356152	T	0.53423	0.62	5.16	5.16	0.70880	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.052891	0.85682	D	0.000000	T	0.35393	0.0930	N	0.16903	0.455	0.36920	D	0.89135	B	0.29955	0.263	B	0.31946	0.138	T	0.43475	-0.9389	10	0.48119	T	0.1	-32.3218	14.9867	0.71353	0.0:0.0:0.0:1.0	.	923	Q8TDY8	IGDC4_HUMAN	L	923;652	ENSP00000319623:M923L	ENSP00000319623:M923L	M	-	1	0	IGDCC4	63467918	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.518000	0.45537	1.946000	0.56461	0.459000	0.35465	ATG	.	.		0.617	IGDCC4-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256825.2	NM_020962		A	65680865	T	A	65680865	3	1	284	1	0	0	0	0	1	0	0	0	7578	1435	50	4	1005	4	IGDCC4	15	65680865	Missense_Mutation	SNP	T	TCGA-G3-A5SI-01A-31D-A27I-10		65680865	36850527	28	41897										
CACNA1H	8912	hgsc.bcm.edu	37	chr16	1263800	1263800	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	aggcccagcgccggccctacTatgccgactactcgcccacg	10	19	0	0			TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr16:1263800T>C	ENST00000348261.5	+	27	5046	c.4798T>C	c.(4798-4800)Tat>Cat	p.Y1600H	CACNA1H_ENST00000358590.4_Missense_Mutation_p.Y1594H|CACNA1H_ENST00000565831.1_Missense_Mutation_p.Y1594H	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	1600					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	CCGGCCCTACTATGCCGACTA	0.652																																					p.Y1600H		Atlas-SNP	.											.	CACNA1H	317	.	0			c.T4798C						.						50	48	49					16																	1263800		1999	4145	6144	SO:0001583	missense	8912	exon27			CCCTACTATGCCG	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.4798T>C	chr16.hg19:g.1263800T>C	ENSP00000334198:p.Tyr1600His	35.0	0.0		23.0	5.0	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	hg19	CCDS45375.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.228032	0.79576	.	.	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.97066	-4.23;-4.15	3.85	3.85	0.44370	.	0.141910	0.49305	D	0.000153	D	0.98333	0.9447	M	0.87456	2.885	0.48341	D	0.999633	D;D;D;P;D	0.89917	1.0;0.997;1.0;0.864;0.995	D;D;D;P;D	0.83275	0.996;0.96;0.971;0.671;0.929	D	0.99013	1.0815	10	0.87932	D	0	.	12.247	0.54576	0.0:0.0:0.0:1.0	.	346;335;341;1594;1600	A2SX38;A2SX35;A2SX37;O95180-2;O95180	.;.;.;.;CAC1H_HUMAN	H	1600;1594	ENSP00000334198:Y1600H;ENSP00000351401:Y1594H	ENSP00000334198:Y1600H	Y	+	1	0	CACNA1H	1203801	1.000000	0.71417	0.991000	0.47740	0.739000	0.42172	7.245000	0.78237	1.752000	0.51891	0.402000	0.26972	TAT	.	.		0.652	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407		C	1263800	T	C	1263800	3	2	284	1	0	0	0	0	1	0	0	0	2547	1522	53	2	4900	2	CACNA1H	16	1263800	Missense_Mutation	SNP	T	TCGA-G3-A5SI-01A-31D-A27I-10		1263800	89090953	29	41898										
ZNF263	10127	hgsc.bcm.edu	37	chr16	3335687	3335687	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	tctgtcaccttcagcattatCtgctccctggctttctcttt	5	14	5	0			TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr16:3335687C>G	ENST00000219069.5	+	3	1451	c.575C>G	c.(574-576)tCt>tGt	p.S192C	ZNF263_ENST00000538765.1_Intron|ZNF263_ENST00000573578.1_Missense_Mutation_p.L132V|ZNF263_ENST00000574253.1_Intron	NM_005741.4	NP_005732.2	O14978	ZN263_HUMAN	zinc finger protein 263	192					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)|skin(4)|urinary_tract(3)	20						TCAGCATTATCTGCTCCCTGG	0.473																																					p.S192C		Atlas-SNP	.											.	ZNF263	58	.	0			c.C575G						.						119	106	111					16																	3335687		2197	4300	6497	SO:0001583	missense	10127	exon3			CATTATCTGCTCC	AC004232	CCDS10499.1	16p13.3	2013-01-09			ENSG00000006194	ENSG00000006194		"Zinc fingers, C2H2-type", "-", "-", "-"	13056	protein-coding gene	gene with protein product		604191				9256059	Standard	NM_005741		Approved	FPM315, ZKSCAN12, ZSCAN44	uc002cuq.3	O14978	OTTHUMG00000129323	ENST00000219069.5:c.575C>G	chr16.hg19:g.3335687C>G	ENSP00000219069:p.Ser192Cys	133.0	0.0		142.0	27.0	NM_005741	B2R634|O43387|Q96H95	Missense_Mutation	SNP	ENST00000219069.5	hg19	CCDS10499.1	.	.	.	.	.	.	.	.	.	.	C	7.950	0.744671	0.15710	.	.	ENSG00000006194	ENST00000219069	T	0.05717	3.4	5.07	4.12	0.48240	.	0.407567	0.21597	N	0.072001	T	0.03651	0.0104	N	0.08118	0	0.80722	D	1	P	0.40000	0.698	B	0.38954	0.286	T	0.57888	-0.7733	10	0.30854	T	0.27	.	9.286	0.37758	0.0:0.9032:0.0:0.0968	.	192	O14978	ZN263_HUMAN	C	192	ENSP00000219069:S192C	ENSP00000219069:S192C	S	+	2	0	ZNF263	3275688	1.000000	0.71417	0.999000	0.59377	0.937000	0.57800	4.414000	0.59802	1.359000	0.45940	-0.136000	0.14681	TCT	.	.		0.473	ZNF263-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251463.2			G	3335687	C	G	3335687	3	3	284	1	0	0	0	0	1	0	0	0	17818	913	32	4	585	4	ZNF263	16	3335687	Missense_Mutation	SNP	C	TCGA-G3-A5SI-01A-31D-A27I-10	2071887	3335687	87019066	30	41899										
SMG6	23293	hgsc.bcm.edu	37	chr17	2203672	2203672	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	agactacgatcctcttgtccAgcagtcctaggaaaggattc	9	11	1	1			TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr17:2203672A>G	ENST00000263073.6	-	2	425	c.375T>C	c.(373-375)gcT>gcC	p.A125A	SMG6_ENST00000544865.1_Silent_p.A94A	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	125	Interaction with telomeric DNA.				gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|telomere maintenance (GO:0000723)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|telomeric DNA binding (GO:0042162)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(10)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						CCTCTTGTCCAGCAGTCCTAG	0.438																																					p.A125A	Melanoma(59;28 1088 11621 25887 46638 50814)	Atlas-SNP	.											.	SMG6	97	.	0			c.T375C						.						147	156	153					17																	2203672		2203	4300	6503	SO:0001819	synonymous_variant	23293	exon2			TTGTCCAGCAGTC	AB018275	CCDS11016.1, CCDS58498.1	17p13.3	2013-07-02	2013-07-02	2006-02-16	ENSG00000070366	ENSG00000070366			17809	protein-coding gene	gene with protein product	"EST1 telomerase component homolog A (S. cerevisiae)"	610963	"chromosome 17 open reading frame 31", "smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)"	C17orf31		12676087, 12699629	Standard	NM_017575		Approved	KIAA0732, SMG-6, EST1A	uc002fub.1	Q86US8	OTTHUMG00000177578	ENST00000263073.6:c.375T>C	chr17.hg19:g.2203672A>G		30.0	0.0		17.0	15.0	NM_017575	B7Z874|O94837|Q86VH6|Q9UF60	Silent	SNP	ENST00000263073.6	hg19	CCDS11016.1																																																																																			.	.		0.438	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437826.3			G	2203672	A	G	2203672	2	3	284	1	0	0	0	0	0	0	0	1	14812	175	7	2		2	SMG6	17	2203672	Silent	SNP	A	TCGA-G3-A5SI-01A-31D-A27I-10		2203672	78991538	31	41900										
DTNA	1837	hgsc.bcm.edu	37	chr18	32418068	32418068	+	Frame_Shift_Del	DEL	A	A	-													0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	tattaactagctctcctcccAaggacagtgaagtagagcag							TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr18:32418068delA	ENST00000399113.3	+	11	1105	c.1105delA	c.(1105-1107)aagfs	p.K369fs	DTNA_ENST00000269192.7_Frame_Shift_Del_p.K78fs|DTNA_ENST00000595022.1_Intron|DTNA_ENST00000598142.1_Intron|DTNA_ENST00000596745.1_Intron|DTNA_ENST00000556414.3_Intron|DTNA_ENST00000348997.5_Frame_Shift_Del_p.K366fs|DTNA_ENST00000399121.5_Intron|DTNA_ENST00000444659.1_Frame_Shift_Del_p.K369fs|DTNA_ENST00000283365.9_Intron|DTNA_ENST00000399097.3_Frame_Shift_Del_p.K48fs|DTNA_ENST00000269191.6_Frame_Shift_Del_p.K369fs|DTNA_ENST00000598334.1_Intron|DTNA_ENST00000599844.1_Intron|DTNA_ENST00000591182.1_Frame_Shift_Del_p.K48fs|DTNA_ENST00000269190.7_Frame_Shift_Del_p.K370fs|DTNA_ENST00000597599.1_Intron|DTNA_ENST00000597674.1_Intron|DTNA_ENST00000601125.1_Intron|DTNA_ENST00000598774.1_Intron			Q9Y4J8	DTNA_HUMAN	dystrobrevin, alpha	369					neuromuscular synaptic transmission (GO:0007274)|signal transduction (GO:0007165)|striated muscle contraction (GO:0006941)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(2)|lung(19)|prostate(1)|upper_aerodigestive_tract(1)	29						CTCTCCTCCCAAGGACAGTGA	0.483																																					p.P368fs		Atlas-Indel,Pindel	.											.	DTNA	321	.	0			c.1104delC						.						97	81	86					18																	32418068		2203	4300	6503	SO:0001589	frameshift_variant	1837	exon11			.	U84540	CCDS11908.1, CCDS11909.1, CCDS42426.1, CCDS45848.1, CCDS56060.1, CCDS56061.1, CCDS56062.1, CCDS56063.1, CCDS59309.1, CCDS59310.1, CCDS59311.1, CCDS59312.1, CCDS59313.1, CCDS59314.1	18q12	2014-09-17			ENSG00000134769	ENSG00000134769			3057	protein-coding gene	gene with protein product	"dystrophin-related protein 3"	601239				8081380, 15834686	Standard	NM_001390		Approved	D18S892E, DTN, DTN-1, DTN-2, DTN-3, DRP3	uc010dmn.1	Q9Y4J8	OTTHUMG00000132309	ENST00000399113.3:c.1105delA	chr18.hg19:g.32418068delA	ENSP00000382064:p.Lys369fs	113.0	0.0		92.0	25.0	NM_001391	A8K541|A8MSZ0|A8MUY4|B4DGS6|B4DIR0|B4DIU8|M0QYX6|M0R397|O15332|O15333|O75697|Q13197|Q13198|Q13199|Q13498|Q13499|Q13500|Q59GK7|Q9BS59	Frame_Shift_Del	DEL	ENST00000399113.3	hg19	CCDS59311.1																																																																																			.	.		0.483	DTNA-005	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255422.2	NM_001390		-	32418068	A	-	32418068	7	5	284	1	0	1	0	1	0	0	0	0	4790	131	5	0	1182	0	DTNA	18	32418068	Frame_Shift_Del	DEL	A	TCGA-G3-A5SI-01A-31D-A27I-10		32418068	45659180	32	41901										
LASS4	79603	hgsc.bcm.edu	37	chr19	8321909	8321909	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	ctacagtgccaacctgctgcGcattggctctctggtgctgc	11	14	1	0			TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr19:8321909G>A	ENST00000251363.5	+	9	989	c.689G>A	c.(688-690)cGc>cAc	p.R230H	CERS4_ENST00000559336.1_Missense_Mutation_p.R230H|CERS4_ENST00000559450.1_Missense_Mutation_p.R230H|CERS4_ENST00000558331.1_Missense_Mutation_p.R179H|CERS4_ENST00000595722.1_3'UTR	NM_024552.2	NP_078828.2	Q9HA82	CERS4_HUMAN	ceramide synthase 4	230	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										AACCTGCTGCGCATTGGCTCT	0.582																																					p.R230H		Atlas-SNP	.											.	.	.	.	0			c.G689A						.						257	242	247					19																	8321909		2203	4300	6503	SO:0001583	missense	79603	exon9			TGCTGCGCATTGG		CCDS12197.1	19p13.2	2014-09-11	2011-07-08	2011-07-08	ENSG00000090661	ENSG00000090661		"Homeoboxes / CERS class"	23747	protein-coding gene	gene with protein product		615334	"LAG1 longevity assurance homolog 4 (S. cerevisiae)", "LAG1 homolog, ceramide synthase 4"	LASS4			Standard	NM_024552		Approved	FLJ12089, Trh1	uc002mjg.3	Q9HA82	OTTHUMG00000172570	ENST00000251363.5:c.689G>A	chr19.hg19:g.8321909G>A	ENSP00000251363:p.Arg230His	215.0	0.0		212.0	17.0	NM_024552	D6W665	Missense_Mutation	SNP	ENST00000251363.5	hg19	CCDS12197.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.608073	0.87258	.	.	ENSG00000090661	ENST00000251363	D	0.86097	-2.07	4.92	4.92	0.64577	TRAM/LAG1/CLN8 homology domain (3);	0.000000	0.85682	D	0.000000	D	0.90528	0.7032	M	0.77103	2.36	0.80722	D	1	D;P	0.69078	0.997;0.931	P;P	0.57846	0.828;0.48	D	0.91585	0.5282	10	0.59425	D	0.04	-32.2793	15.5984	0.76606	0.0:0.0:1.0:0.0	.	230;230	Q53HF9;Q9HA82	.;CERS4_HUMAN	H	230	ENSP00000251363:R230H	ENSP00000251363:R230H	R	+	2	0	CERS4	8227909	1.000000	0.71417	1.000000	0.80357	0.477000	0.33069	8.383000	0.90157	2.271000	0.75665	0.561000	0.74099	CGC	.	.		0.582	CERS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419200.1	NM_024552		A	8321909	G	A	8321909	3	1	284	1	0	0	0	0	1	0	0	0	8650	1087	38	1	715	1	LASS4	19	8321909	Missense_Mutation	SNP	G	TCGA-G3-A5SI-01A-31D-A27I-10		8321909	50807074	33	41902										
C19orf43	79002	hgsc.bcm.edu	37	chr19	12845284	12845284	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	tgaacagctccaggaagctgCcgtcgttggcgaacaagttc	12	11	0	1			TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr19:12845284C>T	ENST00000242784.4	-	1	305	c.188G>A	c.(187-189)gGc>gAc	p.G63D	C19orf43_ENST00000588213.1_Missense_Mutation_p.G63D|C19orf43_ENST00000592273.1_Missense_Mutation_p.G63D|ASNA1_ENST00000591090.1_5'Flank	NM_024038.2	NP_076943.1	Q9BQ61	CS043_HUMAN	chromosome 19 open reading frame 43	63										endometrium(2)|large_intestine(2)	4						CAGGAAGCTGCCGTCGTTGGC	0.721																																					p.G63D		Atlas-SNP	.											.	C19orf43	13	.	0			c.G188A						.						8	6	7					19																	12845284		1936	3760	5696	SO:0001583	missense	79002	exon1			AAGCTGCCGTCGT	AK027588	CCDS12279.1	19p13.2	2011-11-24			ENSG00000123144	ENSG00000123144			28424	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 18"					12477932	Standard	NM_024038		Approved	MGC2803, fSAP18	uc002muu.3	Q9BQ61		ENST00000242784.4:c.188G>A	chr19.hg19:g.12845284C>T	ENSP00000242784:p.Gly63Asp	27.0	0.0		20.0	5.0	NM_024038		Missense_Mutation	SNP	ENST00000242784.4	hg19	CCDS12279.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.246052	0.80024	.	.	ENSG00000123144	ENST00000242784	.	.	.	4.41	4.41	0.53225	.	0.058840	0.64402	N	0.000002	T	0.62588	0.2440	L	0.31476	0.935	0.80722	D	1	D	0.67145	0.996	P	0.60345	0.873	T	0.67837	-0.5567	9	0.87932	D	0	-2.9497	16.3008	0.82811	0.0:1.0:0.0:0.0	.	63	Q9BQ61	CS043_HUMAN	D	63	.	ENSP00000242784:G63D	G	-	2	0	C19orf43	12706284	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.228000	0.72288	2.443000	0.82685	0.591000	0.81541	GGC	.	.		0.721	C19orf43-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450856.1	NM_024038		T	12845284	C	T	12845284	3	4	284	1	0	0	0	0	1	0	0	0	1928	739	26	3	354	3	C19orf43	19	12845284	Missense_Mutation	SNP	C	TCGA-G3-A5SI-01A-31D-A27I-10	4523375	12845284	46283699	34	41903										
USE1	55850	hgsc.bcm.edu	37	chr19	17330476	17330476	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	tgaaaatggcggaccagaacCtggagaaactgaagacggag	14	7	0	5			TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr19:17330476C>G	ENST00000263897.5	+	8	681	c.634C>G	c.(634-636)Ctg>Gtg	p.L212V	USE1_ENST00000596136.1_3'UTR|USE1_ENST00000445667.2_Missense_Mutation_p.L212V|USE1_ENST00000379776.4_3'UTR	NM_018467.3	NP_060937	Q9NZ43	USE1_HUMAN	unconventional SNARE in the ER 1 homolog (S. cerevisiae)	212					endoplasmic reticulum tubular network organization (GO:0071786)|lysosomal transport (GO:0007041)|protein catabolic process (GO:0030163)|protein transport (GO:0015031)|regulation of ER to Golgi vesicle-mediated transport (GO:0060628)|secretion by cell (GO:0032940)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|lung(3)	6						GGACCAGAACCTGGAGAAACT	0.547																																					p.L212V		Atlas-SNP	.											.	USE1	19	.	0			c.C634G						.						78	84	82					19																	17330476		2203	4298	6501	SO:0001583	missense	55850	exon8			CAGAACCTGGAGA	AF220052	CCDS46011.1	19p13.11	2007-08-20				ENSG00000053501			30882	protein-coding gene	gene with protein product	"Q-SNARE", "SNARE-like tail-anchored protein 1 homolog (S. cerevisiae)"	610675				16354670, 15029241	Standard	NM_018467		Approved	p31, SLT1, MDS032	uc002nfo.2	Q9NZ43		ENST00000263897.5:c.634C>G	chr19.hg19:g.17330476C>G	ENSP00000263897:p.Leu212Val	145.0	0.0		162.0	10.0	NM_018467	Q8NCK1|Q9BRT4	Missense_Mutation	SNP	ENST00000263897.5	hg19	CCDS46011.1	.	.	.	.	.	.	.	.	.	.	C	15.45	2.837606	0.50951	.	.	ENSG00000053501	ENST00000263897;ENST00000445667	T;T	0.54866	0.55;0.55	4.73	3.62	0.41486	.	0.111954	0.64402	D	0.000011	T	0.37100	0.0991	L	0.48642	1.525	0.80722	D	1	P	0.45044	0.849	B	0.40982	0.345	T	0.17930	-1.0353	10	0.15952	T	0.53	-15.0778	3.424	0.07403	0.0:0.6206:0.0:0.3794	.	212	Q9NZ43	USE1_HUMAN	V	212	ENSP00000263897:L212V;ENSP00000390287:L212V	ENSP00000263897:L212V	L	+	1	2	USE1	17191476	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	4.963000	0.63694	2.193000	0.70182	0.491000	0.48974	CTG	.	.		0.547	USE1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463295.1	NM_018467		G	17330476	C	G	17330476	3	3	284	1	0	0	0	0	1	0	0	0	17046	680	24	4	664	4	USE1	19	17330476	Missense_Mutation	SNP	C	TCGA-G3-A5SI-01A-31D-A27I-10	4485192	17330476	41798507	35	41904										
TMEM161A	54929	hgsc.bcm.edu	37	chr19	19245614	19245614	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	tgccgttacagagcagccagCgcgcgaaggagcagtgtggc	16	11	0	1	rs143085909		TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr19:19245614C>G	ENST00000162044.9	-	2	150	c.86G>C	c.(85-87)cGc>cCc	p.R29P	TMEM161A_ENST00000450333.2_Missense_Mutation_p.R29P|TMEM161A_ENST00000592147.1_Intron|TMEM161A_ENST00000587583.2_Missense_Mutation_p.R29P	NM_017814.2	NP_060284.1	Q9NX61	T161A_HUMAN	transmembrane protein 161A	29					cellular response to oxidative stress (GO:0034599)|cellular response to UV (GO:0034644)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|positive regulation of DNA repair (GO:0045739)|response to retinoic acid (GO:0032526)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	15			OV - Ovarian serous cystadenocarcinoma(5;1.19e-05)|Epithelial(12;0.0011)			GAGCAGCCAGCGCGCGAAGGA	0.706																																					p.R29P		Atlas-SNP	.											.	TMEM161A	37	.	0			c.G86C						.						15	13	14					19																	19245614		2190	4284	6474	SO:0001583	missense	54929	exon2			AGCCAGCGCGCGA	BC005210	CCDS12393.1, CCDS58656.1	19p13.11	2008-02-05				ENSG00000064545			26020	protein-coding gene	gene with protein product						12975309	Standard	NM_017814		Approved	FLJ39645, FLJ20422	uc002nlg.4	Q9NX61		ENST00000162044.9:c.86G>C	chr19.hg19:g.19245614C>G	ENSP00000162044:p.Arg29Pro	56.0	0.0		56.0	27.0	NM_001256766	B3KUE0|G5E9M6|Q7L2Y1	Missense_Mutation	SNP	ENST00000162044.9	hg19	CCDS12393.1	.	.	.	.	.	.	.	.	.	.	C	19.66	3.869176	0.72065	.	.	ENSG00000064545	ENST00000450333;ENST00000162044	.	.	.	4.63	4.63	0.57726	.	0.053328	0.64402	D	0.000001	T	0.78323	0.4265	M	0.76574	2.34	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.81466	-0.0920	9	0.72032	D	0.01	-6.0409	14.9691	0.71220	0.0:1.0:0.0:0.0	.	29;29;29	G5E9M6;B3KUE0;Q9NX61	.;.;T161A_HUMAN	P	29	.	ENSP00000162044:R29P	R	-	2	0	TMEM161A	19106614	1.000000	0.71417	0.911000	0.35937	0.238000	0.25445	7.131000	0.77243	2.142000	0.66516	0.313000	0.20887	CGC	.	C|1.000;A|0.000		0.706	TMEM161A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460089.2	NM_017814		G	19245614	C	G	19245614	3	3	284	1	0	0	0	0	1	0	0	0	16091	768	27	4	1397	4	TMEM161A	19	19245614	Missense_Mutation	SNP	C	TCGA-G3-A5SI-01A-31D-A27I-10	1915138	19245614	39883369	36	41905										
MYH14	79784	hgsc.bcm.edu	37	chr19	50766674	50766674	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	cagtggtggcggctgtttacCaaggtgagggcagcctgggg	19	8	0	1			TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr19:50766674C>T	ENST00000596571.1	+	19	2568	c.2568C>T	c.(2566-2568)acC>acT	p.T856T	MYH14_ENST00000262269.8_Silent_p.T897T|MYH14_ENST00000601313.1_Silent_p.T897T|MYH14_ENST00000376970.2_Silent_p.T889T|MYH14_ENST00000598205.1_Silent_p.T864T|MYH14_ENST00000440075.2_Silent_p.T897T|MYH14_ENST00000425460.1_Silent_p.T864T			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	856					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		GGCTGTTTACCAAGGTGAGGG	0.627																																					p.T897T		Atlas-SNP	.											.	MYH14	261	.	0			c.C2691T						.						14	18	17					19																	50766674		2188	4289	6477	SO:0001819	synonymous_variant	79784	exon22			GTTTACCAAGGTG	AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"Myosins / Myosin superfamily : Class II"	23212	protein-coding gene	gene with protein product		608568	"myosin, heavy polypeptide 14", "myosin, heavy chain 14"	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.2568C>T	chr19.hg19:g.50766674C>T		117.0	0.0		88.0	4.0	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Silent	SNP	ENST00000596571.1	hg19	CCDS59411.1																																																																																			.	.		0.627	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729		T	50766674	C	T	50766674	2	4	284	1	0	0	0	0	0	0	0	1	10042	581	21	3		3	MYH14	19	50766674	Silent	SNP	C	TCGA-G3-A5SI-01A-31D-A27I-10	31521060	50766674	8362309	37	41906										
TPX2	22974	hgsc.bcm.edu	37	chr20	30365347	30365347	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	atcagttgacttccacttccGcacagatgagcgaatcaaac	7	12	2	3	rs527354467		TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr20:30365347G>T	ENST00000300403.6	+	9	1316	c.788G>T	c.(787-789)cGc>cTc	p.R263L	TPX2_ENST00000340513.4_Missense_Mutation_p.R263L	NM_012112.4	NP_036244.2	Q9ULW0	TPX2_HUMAN	TPX2, microtubule-associated	263					activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|mitotic nuclear division (GO:0007067)|regulation of mitotic spindle organization (GO:0060236)	axon hillock (GO:0043203)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28			Epithelial(4;0.000771)|Colorectal(19;0.00306)|all cancers(5;0.004)|COAD - Colon adenocarcinoma(19;0.0347)|OV - Ovarian serous cystadenocarcinoma(3;0.0656)			TTCCACTTCCGCACAGATGAG	0.413																																					p.R263L		Atlas-SNP	.											.	TPX2	61	.	0			c.G788T						.						139	118	125					20																	30365347		2203	4300	6503	SO:0001583	missense	22974	exon9			ACTTCCGCACAGA	AF098158	CCDS13190.1	20q11.2	2013-07-23	2013-07-23	2003-10-08	ENSG00000088325	ENSG00000088325			1249	protein-coding gene	gene with protein product		605917	"chromosome 20 open reading frame 1", "TPX2, microtubule-associated, homolog (Xenopus laevis)"	C20orf2, C20orf1		9207457, 10393424	Standard	NM_012112		Approved	p100, DIL-2	uc002wwp.1	Q9ULW0	OTTHUMG00000032190	ENST00000300403.6:c.788G>T	chr20.hg19:g.30365347G>T	ENSP00000300403:p.Arg263Leu	169.0	0.0		153.0	68.0	NM_012112	Q9H1R4|Q9NRA3|Q9UFN9|Q9UL00|Q9Y2M1	Missense_Mutation	SNP	ENST00000300403.6	hg19	CCDS13190.1	.	.	.	.	.	.	.	.	.	.	G	12.68	2.010178	0.35415	.	.	ENSG00000088325	ENST00000300403;ENST00000340513	T	0.31510	1.49	5.36	-0.241	0.13043	.	0.826995	0.11539	N	0.553910	T	0.14917	0.0360	N	0.17082	0.46	0.28927	N	0.89182	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.001	T	0.25641	-1.0126	10	0.26408	T	0.33	5.0037	4.403	0.11395	0.2803:0.0:0.465:0.2547	.	263;263	Q96RR5;Q9ULW0	.;TPX2_HUMAN	L	263	ENSP00000341145:R263L	ENSP00000300403:R263L	R	+	2	0	TPX2	29829008	1.000000	0.71417	0.780000	0.31762	0.816000	0.46133	0.984000	0.29565	0.040000	0.15660	-0.140000	0.14226	CGC	.	.		0.413	TPX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078569.2			T	30365347	G	T	30365347	3	4	284	1	0	0	0	0	1	0	0	0	16447	1087	38	1	814	1	TPX2	20	30365347	Missense_Mutation	SNP	G	TCGA-G3-A5SI-01A-31D-A27I-10		30365347	32660173	38	41907										
PTPRT	11122	hgsc.bcm.edu	37	chr20	40730794	40730795	+	Frame_Shift_Ins	INS	-	-	GA													0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	ctgcgttgatgtaattgctgINSgattctccgtccactgagat							TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chr20:40730794_40730795insGA	ENST00000373187.1	-	26	3682_3683	c.3683_3684insTC	c.(3682-3684)tccfs	p.S1228fs	PTPRT_ENST00000373184.1_Frame_Shift_Ins_p.S1238fs|PTPRT_ENST00000373198.4_Frame_Shift_Ins_p.S1247fs|PTPRT_ENST00000356100.2_Frame_Shift_Ins_p.S1237fs|PTPRT_ENST00000373193.3_Frame_Shift_Ins_p.S1231fs|PTPRT_ENST00000373201.1_Frame_Shift_Ins_p.S1218fs|PTPRT_ENST00000373190.1_Frame_Shift_Ins_p.S1227fs			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	1228	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)			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)				TGTAATTGCTGGATTCTCCGTC	0.545																																					p.S1247fs		Atlas-INDEL	.											.	PTPRT	372	.	0			c.3741_3742insTC						.																																			SO:0001589	frameshift_variant	11122	exon27			.	AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.3682_3683dupTC	chr20.hg19:g.40730795_40730796dupGA	ENSP00000362283:p.Ser1228fs	173.0	0.0		140.0	63.0	NM_133170	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Frame_Shift_Ins	INS	ENST00000373187.1	hg19	CCDS42874.1																																																																																			.	.		0.545	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			GA	40730795	-	GA	40730794	7	5	284	1	0	1	1	0	0	0	0	0	12827	1335	47	0	665	0	PTPRT	20	40730794	Frame_Shift_Ins	INS	-	TCGA-G3-A5SI-01A-31D-A27I-10	10365447	40730794	22294726	39	41908										
PCDH11Y	83259	hgsc.bcm.edu	37	chrY	5605945	5605945	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.1	4	1	1.4247619047619	2.13714285714286	1.06857142857143	1	1	0	gccaacaggccagaccgtccAgaggtgattcccccattatg	10	14	0	3			TCGA-G3-A5SI-01A-31D-A27I-10	TCGA-G3-A5SI-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	93545962-11bc-4519-a539-fc6651d02b31	f7b392f4-f65f-496b-abcc-8b81bb38e24f	g.chrY:5605945A>T	ENST00000215473.6	+	6	3985	c.3985A>T	c.(3985-3987)Aga>Tga	p.R1329*				Q9BZA8	PC11Y_HUMAN	protocadherin 11 Y-linked	1329					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|kidney(2)|large_intestine(7)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						CAGACCGTCCAGAGGTGATTC	0.378																																					p.R1329X		Atlas-SNP	.											.	PCDH11Y	163	.	0			c.A3985T						.																																			SO:0001587	stop_gained	83259	exon5			CCGTCCAGAGGTG	AF332217	CCDS14776.1, CCDS14777.1, CCDS76066.1	Yp11.2	2010-01-26	2002-05-22	2002-05-24	ENSG00000099715	ENSG00000099715		"Cadherins / Protocadherins : Non-clustered"	15813	protein-coding gene	gene with protein product		400022	"protocadherin 22"	PCDH22		10644456, 11003707	Standard	NM_032971		Approved	PCDHY	uc004fqo.3	Q9BZA8	OTTHUMG00000035105	ENST00000215473.6:c.3985A>T	chrY.hg19:g.5605945A>T	ENSP00000215473:p.Arg1329*	241.0	1.0		242.0	220.0	NM_032973	Q70LR6|Q70LR8|Q70LS0|Q70LS1|Q70LS2|Q70LS3|Q70LS4|Q70LS5|Q8WY34|Q9BZA9|Q9H4E1	Nonsense_Mutation	SNP	ENST00000215473.6	hg19																																																																																				.	.		0.378	PCDH11Y-201	KNOWN	basic	protein_coding	protein_coding		NM_032973		T	5605945	A	T	5605945	4	4	284	1	0	0	0	0	0	1	0	0	11518	180	7	4	4061	4	PCDH11Y	24	5605945	Nonsense_Mutation	SNP	A	TCGA-G3-A5SI-01A-31D-A27I-10		5605945	53767621	40	41909										
MTOR	2475	hgsc.bcm.edu	37	chr1	11317091	11317091	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	ggtaaaagtgtcccctgccaTggcaagacggccaatggcct	12	12	0	1			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr1:11317091T>C	ENST00000361445.4	-	4	479	c.403A>G	c.(403-405)Atg>Gtg	p.M135V		NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	135	Interaction with NBN.		M -> T (in a metastatic melanoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	TCCCCTGCCATGGCAAGACGG	0.562																																					p.M135V		Atlas-SNP	.											.	MTOR	327	.	0			c.A403G						.						81	67	71					1																	11317091		2203	4300	6503	SO:0001583	missense	2475	exon4			CTGCCATGGCAAG	L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"FK506 binding protein 12-rapamycin associated protein 2", "rapamycin target protein", "FKBP12-rapamycin complex-associated protein 1", "FKBP-rapamycin associated protein", "rapamycin associated protein FRAP2", "dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)", "rapamycin and FKBP12 target 1", "mammalian target of rapamycin"	601231	"FK506 binding protein 12-rapamycin associated protein 1"	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.403A>G	chr1.hg19:g.11317091T>C	ENSP00000354558:p.Met135Val	603.0	2.0		231.0	157.0	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Missense_Mutation	SNP	ENST00000361445.4	hg19	CCDS127.1	.	.	.	.	.	.	.	.	.	.	T	4.534	0.099148	0.08681	.	.	ENSG00000198793	ENST00000361445;ENST00000539766	T	0.64260	-0.09	5.21	5.21	0.72293	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.48429	0.1499	N	0.20881	0.62	0.80722	D	1	B	0.06786	0.001	B	0.09377	0.004	T	0.39251	-0.9623	10	0.26408	T	0.33	-1.4542	15.0763	0.72080	0.0:0.0:0.0:1.0	.	135	P42345	MTOR_HUMAN	V	135	ENSP00000354558:M135V	ENSP00000354558:M135V	M	-	1	0	MTOR	11239678	1.000000	0.71417	1.000000	0.80357	0.814000	0.46013	4.841000	0.62824	1.965000	0.57142	0.455000	0.32223	ATG	.	.		0.562	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958		C	11317091	T	C	11317091	3	2	285	1	0	0	0	0	1	0	0	0	9963	1464	51	2	7466	2	MTOR	1	11317091	Missense_Mutation	SNP	T	TCGA-G3-A5SJ-01A-11D-A27I-10		11317091	237933530	1	41910										
ARHGEF10L	55160	hgsc.bcm.edu	37	chr1	17948399	17948422	+	In_Frame_Del	DEL	AAGGCAGCTACGTGGAGTCTCTGA	AAGGCAGCTACGTGGAGTCTCTGA	-													0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	gggctccatcgtgcagagcgAaggcagctacgtggagtctc					rs376652146|rs146595527		TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	AAGGCAGCTACGTGGAGTCTCTGA	AAGGCAGCTACGTGGAGTCTCTGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr1:17948399_17948422delAAGGCAGCTACGTGGAGTCTCTGA	ENST00000361221.3	+	11	1142_1165	c.983_1006delAAGGCAGCTACGTGGAGTCTCTGA	c.(982-1008)gaaggcagctacgtggagtctctgaag>gag	p.GSYVESLK329del	ARHGEF10L_ENST00000167825.4_In_Frame_Del_p.GSYVESLK107del|ARHGEF10L_ENST00000375420.3_In_Frame_Del_p.GSYVESLK87del|ARHGEF10L_ENST00000434513.1_In_Frame_Del_p.GSYVESLK329del|ARHGEF10L_ENST00000469726.1_3'UTR|ARHGEF10L_ENST00000452522.1_In_Frame_Del_p.GSYVESLK290del|ARHGEF10L_ENST00000375415.1_In_Frame_Del_p.GSYVESLK290del|ARHGEF10L_ENST00000375408.3_In_Frame_Del_p.GSYVESLK107del	NM_018125.3	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10-like	329	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.					cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.V332L(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	43		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)		GTGCAGAGCGAAGGCAGCTACGTGGAGTCTCTGAAGCGGATACT	0.594																																					p.328_335del		Atlas-Indel,Pindel	.											ARHGEF10L_ENST00000361221,rectum,carcinoma,0,2	ARHGEF10L	219	.	1	Substitution - Missense(1)	NS(1)	c.982_1005del						.																																			SO:0001651	inframe_deletion	55160	exon11			.	AB046846	CCDS182.1, CCDS30617.1	1p36.13	2011-11-16			ENSG00000074964	ENSG00000074964		"Rho guanine nucleotide exchange factors"	25540	protein-coding gene	gene with protein product	"GrinchGEF"	612494				10997877, 16112081	Standard	XM_005245923		Approved	FLJ10521, KIAA1626	uc001ban.3	Q9HCE6	OTTHUMG00000002514	ENST00000361221.3:c.983_1006delAAGGCAGCTACGTGGAGTCTCTGA	chr1.hg19:g.17948399_17948422delAAGGCAGCTACGTGGAGTCTCTGA	ENSP00000355060:p.Gly329_Lys336del	197.0	0.0		63.0	11.0	NM_018125	B7ZKS1|Q17RW1|Q3YFJ4|Q5VXI5|Q5VXI6|Q66K51|Q6P0L7|Q8NAV5|Q9NVT3	In_Frame_Del	DEL	ENST00000361221.3	hg19	CCDS182.1																																																																																			.	.		0.594	ARHGEF10L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007147.1	NM_018125		-	17948422	AAGGCAGCTACGTGGAGTCTCTGA	-	17948399	7	5	285	1	0	1	0	1	0	0	0	0	895	246	9	0	1021	0	ARHGEF10L	1	17948399	In_Frame_Del	DEL	AAGGCAGCTACGTGGAGTCTCTGA	TCGA-G3-A5SJ-01A-11D-A27I-10	6631308	17948399	231302222	2	41911										
UBR4	23352	hgsc.bcm.edu	37	chr1	19483269	19483269	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	ccggatttttacctttagccCacaaaccgccaagtagtctt	6	13	1	0			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr1:19483269C>T	ENST00000375254.3	-	41	5938	c.5911G>A	c.(5911-5913)Ggg>Agg	p.G1971R	UBR4_ENST00000375226.2_Missense_Mutation_p.G1971R|UBR4_ENST00000375217.2_Missense_Mutation_p.G1971R|UBR4_ENST00000375267.2_Missense_Mutation_p.G1971R	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	1971					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		ACCTTTAGCCCACAAACCGCC	0.453																																					p.G1971R		Atlas-SNP	.											.	UBR4	415	.	0			c.G5911A						.						90	92	91					1																	19483269		2203	4300	6503	SO:0001583	missense	23352	exon41			TTAGCCCACAAAC	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.5911G>A	chr1.hg19:g.19483269C>T	ENSP00000364403:p.Gly1971Arg	352.0	0.0		163.0	82.0	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	hg19	CCDS189.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.996249	0.93167	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000417040;ENST00000419533	T;T;T;T;T	0.21031	2.03;2.03;2.03;2.03;3.05	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.53481	0.1799	M	0.83603	2.65	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.57225	-0.7848	10	0.87932	D	0	.	19.8856	0.96911	0.0:1.0:0.0:0.0	.	1971	Q5T4S7	UBR4_HUMAN	R	1971;1971;1971;1971;681;1187	ENSP00000364403:G1971R;ENSP00000364416:G1971R;ENSP00000364365:G1971R;ENSP00000364374:G1971R;ENSP00000404897:G681R	ENSP00000364365:G1971R	G	-	1	0	UBR4	19355856	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	7.298000	0.78815	2.709000	0.92574	0.491000	0.48974	GGG	.	.		0.453	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		T	19483269	C	T	19483269	3	4	285	1	0	0	0	0	1	0	0	0	16919	594	21	3	9904	3	UBR4	1	19483269	Missense_Mutation	SNP	C	TCGA-G3-A5SJ-01A-11D-A27I-10	1534870	19483269	229767352	3	41912										
HS2ST1	9653	hgsc.bcm.edu	37	chr1	87563541	87563541	+	Frame_Shift_Del	DEL	A	A	-													0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	acctttgatgaatgtgtagcAgaaggtggctcagactgtgc							TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr1:87563541delA	ENST00000370550.5	+	5	972	c.609delA	c.(607-609)gcafs	p.A203fs	HS2ST1_ENST00000356813.4_Frame_Shift_Del_p.A177fs|HS2ST1_ENST00000370551.4_Frame_Shift_Del_p.A203fs|RP5-1052I5.2_ENST00000370548.2_Frame_Shift_Del_p.A177fs	NM_012262.3	NP_036394.1	Q7LGA3	HS2ST_HUMAN	heparan sulfate 2-O-sulfotransferase 1	203					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	sulfotransferase activity (GO:0008146)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)	9		Lung NSC(277;0.153)		all cancers(265;0.00699)|Epithelial(280;0.0261)		AATGTGTAGCAGAAGGTGGCT	0.443																																					p.A203fs		Atlas-INDEL	.											.	HS2ST1	43	.	0			c.608delC						.						159	148	151					1																	87563541		2203	4300	6503	SO:0001589	frameshift_variant	9653	exon5			.	AB007917	CCDS711.1, CCDS44171.1	1p22.3	2008-02-05			ENSG00000153936	ENSG00000153936		"Sulfotransferases, membrane-bound"	5193	protein-coding gene	gene with protein product		604844				9455484	Standard	NM_012262		Approved	KIAA0448	uc010osk.2	Q7LGA3	OTTHUMG00000010255	ENST00000370550.5:c.609delA	chr1.hg19:g.87563541delA	ENSP00000359581:p.Ala203fs	247.0	0.0		114.0	17.0	NM_012262	D3DT22|O75036|Q32NB5|Q8TAC5|Q9H441|Q9NUJ9	Frame_Shift_Del	DEL	ENST00000370550.5	hg19	CCDS711.1																																																																																			.	.		0.443	HS2ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028279.2	NM_012262		-	87563541	A	-	87563541	7	5	285	1	0	1	0	1	0	0	0	0	7371	175	7	0	627	0	HS2ST1	1	87563541	Frame_Shift_Del	DEL	A	TCGA-G3-A5SJ-01A-11D-A27I-10	68080272	87563541	161687080	4	41913	218	2								
HS2ST1	9653	hgsc.bcm.edu	37	chr1	87563544	87563544	+	Missense_Mutation	SNP	A	A	C													0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	tttgatgaatgtgtagcagaAggtggctcagactgtgctcc							TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr1:87563544A>C	ENST00000370550.5	+	5	975	c.612A>C	c.(610-612)gaA>gaC	p.E204D	HS2ST1_ENST00000356813.4_Missense_Mutation_p.E178D|HS2ST1_ENST00000370551.4_Missense_Mutation_p.E204D|RP5-1052I5.2_ENST00000370548.2_Missense_Mutation_p.E178D	NM_012262.3	NP_036394.1	Q7LGA3	HS2ST_HUMAN	heparan sulfate 2-O-sulfotransferase 1	204					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	sulfotransferase activity (GO:0008146)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)	9		Lung NSC(277;0.153)		all cancers(265;0.00699)|Epithelial(280;0.0261)		GTGTAGCAGAAGGTGGCTCAG	0.448																																					p.E204D		Atlas-SNP	.											.	HS2ST1	43	.	0			c.A612C						.						160	149	153					1																	87563544		2203	4300	6503	SO:0001583	missense	9653	exon5			AGCAGAAGGTGGC	AB007917	CCDS711.1, CCDS44171.1	1p22.3	2008-02-05			ENSG00000153936	ENSG00000153936		"Sulfotransferases, membrane-bound"	5193	protein-coding gene	gene with protein product		604844				9455484	Standard	NM_012262		Approved	KIAA0448	uc010osk.2	Q7LGA3	OTTHUMG00000010255	ENST00000370550.5:c.612A>C	chr1.hg19:g.87563544A>C	ENSP00000359581:p.Glu204Asp	258.0	0.0		121.0	17.0	NM_012262	D3DT22|O75036|Q32NB5|Q8TAC5|Q9H441|Q9NUJ9	Missense_Mutation	SNP	ENST00000370550.5	hg19	CCDS711.1	.	.	.	.	.	.	.	.	.	.	A	13.40	2.225926	0.39300	.	.	ENSG00000153936	ENST00000370551;ENST00000370550;ENST00000370548;ENST00000356813	T;T;T;T	0.72725	-0.68;-0.68;-0.68;-0.68	5.43	2.45	0.29901	.	0.049792	0.85682	D	0.000000	T	0.38852	0.1056	L	0.42744	1.35	0.26762	N	0.969977	B;B	0.21520	0.02;0.057	B;B	0.30943	0.079;0.122	T	0.32079	-0.9920	10	0.30078	T	0.28	-19.9645	4.9418	0.13969	0.2331:0.0:0.5359:0.231	.	204;178	Q7LGA3;Q7LGA3-2	HS2ST_HUMAN;.	D	204;204;178;178	ENSP00000359582:E204D;ENSP00000359581:E204D;ENSP00000359579:E178D;ENSP00000349268:E178D	ENSP00000349268:E178D	E	+	3	2	HS2ST1	87336132	0.998000	0.40836	1.000000	0.80357	0.990000	0.78478	0.460000	0.21924	0.352000	0.24053	-0.177000	0.13119	GAA	.	.		0.448	HS2ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028279.2	NM_012262		C	87563544	A	C	87563544	3	2	285	1	0	0	0	0	1	0	0	0	7371	69	3	5	630	5	HS2ST1	1	87563544	Missense_Mutation	SNP	A	TCGA-G3-A5SJ-01A-11D-A27I-10	3	87563544	161687077	5	41914	218	2								
ABCA4	24	hgsc.bcm.edu	37	chr1	94577092	94577092	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	cagaagatcccctggagccaCggcagcattcctgctgaggg	13	13	0	3	rs201725352		TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr1:94577092C>T	ENST00000370225.3	-	3	290	c.204G>A	c.(202-204)ccG>ccA	p.P68P	ABCA4_ENST00000535735.1_Silent_p.P68P	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	68			P -> L (in STGD1). {ECO:0000269|PubMed:10958763}.|P -> R (in STGD1).		phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			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)		CCTGGAGCCACGGCAGCATTC	0.493																																					p.P68P		Atlas-SNP	.											.	ABCA4	275	.	0			c.G204A						.						72	71	71					1																	94577092		2203	4300	6503	SO:0001819	synonymous_variant	24	exon3			GAGCCACGGCAGC	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.204G>A	chr1.hg19:g.94577092C>T		170.0	0.0		89.0	44.0	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Silent	SNP	ENST00000370225.3	hg19	CCDS747.1																																																																																			.	C|0.999;T|0.001		0.493	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		T	94577092	C	T	94577092	2	4	285	1	0	0	0	0	0	0	0	1	34	523	19	1		1	ABCA4	1	94577092	Silent	SNP	C	TCGA-G3-A5SJ-01A-11D-A27I-10	7013548	94577092	154673529	6	41915										
LRIG2	9860	hgsc.bcm.edu	37	chr1	113635842	113635842	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	gcctaggaaaatgaattacaAtgaactaacagaaatcccgt	7	8	0	3			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr1:113635842A>G	ENST00000361127.5	+	3	518	c.320A>G	c.(319-321)aAt>aGt	p.N107S		NM_014813.1	NP_055628.1	O94898	LRIG2_HUMAN	leucine-rich repeats and immunoglobulin-like domains 2	107					innervation (GO:0060384)|regulation of platelet-derived growth factor receptor signaling pathway (GO:0010640)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				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)		ATGAATTACAATGAACTAACA	0.303																																					p.N107S		Atlas-SNP	.											.	LRIG2	67	.	0			c.A320G						.						49	50	49					1																	113635842		2200	4293	6493	SO:0001583	missense	9860	exon3			ATTACAATGAACT	AB018349	CCDS30808.1	1p13.1	2013-01-11			ENSG00000198799	ENSG00000198799		"Immunoglobulin superfamily / I-set domain containing"	20889	protein-coding gene	gene with protein product		608869					Standard	XM_005271369		Approved	KIAA0806	uc001edf.1	O94898	OTTHUMG00000012133	ENST00000361127.5:c.320A>G	chr1.hg19:g.113635842A>G	ENSP00000355396:p.Asn107Ser	245.0	0.0		122.0	26.0	NM_014813	Q9NSN2	Missense_Mutation	SNP	ENST00000361127.5	hg19	CCDS30808.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.371797	0.82573	.	.	ENSG00000198799	ENST00000361127	T	0.26373	1.74	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.53094	0.1775	M	0.93283	3.4	0.80722	D	1	D	0.76494	0.999	D	0.66196	0.942	T	0.68172	-0.5479	10	0.87932	D	0	.	15.6116	0.76727	1.0:0.0:0.0:0.0	.	107	O94898	LRIG2_HUMAN	S	107	ENSP00000355396:N107S	ENSP00000355396:N107S	N	+	2	0	LRIG2	113437365	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	8.806000	0.91930	2.097000	0.63578	0.533000	0.62120	AAT	.	.		0.303	LRIG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033549.2	NM_014813		G	113635842	A	G	113635842	3	3	285	1	0	0	0	0	1	0	0	0	8954	101	4	2	330	2	LRIG2	1	113635842	Missense_Mutation	SNP	A	TCGA-G3-A5SJ-01A-11D-A27I-10	19058750	113635842	135614779	7	41916										
NOTCH2NL	388677	hgsc.bcm.edu	37	chr1	145281400	145281400	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	caatggaccgatgcctgcctGtctcatccctgtgcaaatgg	10	13	1	0			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr1:145281400G>T	ENST00000369340.3	+	5	774	c.330G>T	c.(328-330)ctG>ctT	p.L110L	NOTCH2NL_ENST00000362074.6_Silent_p.L110L|RP11-458D21.5_ENST00000468030.1_Silent_p.L110L|NOTCH2NL_ENST00000344859.3_Silent_p.L110L			Q7Z3S9	NT2NL_HUMAN	notch 2 N-terminal like	110	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|Notch signaling pathway (GO:0007219)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	27						ATGCCTGCCTGTCTCATCCCT	0.507																																					p.L110L		Atlas-SNP	.											.	NOTCH2NL	100	.	0			c.G330T						.						363	367	366					1																	145281400		2203	4299	6502	SO:0001819	synonymous_variant	388677	exon4			CTGCCTGTCTCAT		CCDS72880.1	1q21.2	2010-06-24	2010-06-24		ENSG00000213240	ENSG00000213240			31862	protein-coding gene	gene with protein product			"Notch homolog 2 (Drosophila) N-terminal like"			14673143	Standard	NM_203458		Approved	N2N	uc001emn.4	Q7Z3S9	OTTHUMG00000013754	ENST00000369340.3:c.330G>T	chr1.hg19:g.145281400G>T		2309.0	0.0		1094.0	78.0	NM_203458	Q5BKT8|Q5VTG9|Q5XG84|Q6P192|Q8NC23|Q8WUQ9|Q96FY1	Silent	SNP	ENST00000369340.3	hg19	CCDS909.1																																																																																			.	.		0.507	NOTCH2NL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000038546.1	NM_203458		T	145281400	G	T	145281400	2	4	285	1	0	0	0	0	0	0	0	1	10558	1364	48	3		3	NOTCH2NL	1	145281400	Silent	SNP	G	TCGA-G3-A5SJ-01A-11D-A27I-10	31645558	145281400	103969221	8	41917										
MAEL	84944	hgsc.bcm.edu	37	chr1	166990985	166990985	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	ttacccgcttactagagagcAtttccaattcttccagcaat	5	12	1	1			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr1:166990985A>G	ENST00000367872.4	+	12	1442	c.1198A>G	c.(1198-1200)Att>Gtt	p.I400V	MAEL_ENST00000491055.1_3'UTR|MAEL_ENST00000367870.2_Missense_Mutation_p.I369V	NM_032858.1	NP_116247.1	Q96JY0	MAEL_HUMAN	maelstrom spermatogenic transposon silencer	400					cell differentiation (GO:0030154)|cell morphogenesis (GO:0000902)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|piRNA metabolic process (GO:0034587)|regulation of organ growth (GO:0046620)|spermatogenesis (GO:0007283)|synapsis (GO:0007129)	autosome (GO:0030849)|chromatin (GO:0000785)|chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|perinuclear region of cytoplasm (GO:0048471)|piP-body (GO:0071547)|XY body (GO:0001741)	DNA binding (GO:0003677)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(12)|skin(4)	28						ACTAGAGAGCATTTCCAATTC	0.413																																					p.I400V		Atlas-SNP	.											.	MAEL	95	.	0			c.A1198G						.						137	131	133					1																	166990985		2203	4300	6503	SO:0001583	missense	84944	exon12			GAGAGCATTTCCA	AK027810, DQ076156	CCDS1257.1, CCDS65712.1, CCDS72975.1	1q24.1	2013-10-11	2012-12-18		ENSG00000143194	ENSG00000143194			25929	protein-coding gene	gene with protein product	"cancer/testis antigen 128", "spermatogenesis associated 35"	611368	"maelstrom homolog (Drosophila)"			19693694, 18694567	Standard	NM_001286378		Approved	FLJ14904, CT128, SPATA35	uc001gdy.1	Q96JY0	OTTHUMG00000034432	ENST00000367872.4:c.1198A>G	chr1.hg19:g.166990985A>G	ENSP00000356846:p.Ile400Val	395.0	0.0		153.0	44.0	NM_032858	B4DY43|E9JVC3|Q49AP9|Q5VZP8|Q9UIW6	Missense_Mutation	SNP	ENST00000367872.4	hg19	CCDS1257.1	.	.	.	.	.	.	.	.	.	.	A	12.61	1.988643	0.35131	.	.	ENSG00000143194	ENST00000367872;ENST00000367870;ENST00000537744	T;T	0.46451	0.87;0.89	5.23	2.89	0.33648	.	0.191758	0.36234	N	0.002714	T	0.09158	0.0226	N	0.24115	0.695	0.26690	N	0.971377	B;B	0.17038	0.003;0.02	B;B	0.18561	0.007;0.022	T	0.31166	-0.9953	10	0.23302	T	0.38	.	5.354	0.16051	0.7329:0.1774:0.0897:0.0	.	369;400	E9JVC3;Q96JY0	.;MAEL_HUMAN	V	400;369;122	ENSP00000356846:I400V;ENSP00000356844:I369V	ENSP00000356844:I369V	I	+	1	0	MAEL	165257609	0.952000	0.32445	0.996000	0.52242	0.997000	0.91878	0.564000	0.23563	0.436000	0.26393	0.533000	0.62120	ATT	.	.		0.413	MAEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083239.1	NM_032858		G	166990985	A	G	166990985	3	3	285	1	0	0	0	0	1	0	0	0	9163	217	8	2	1244	2	MAEL	1	166990985	Missense_Mutation	SNP	A	TCGA-G3-A5SJ-01A-11D-A27I-10	21709585	166990985	82259636	9	41918										
CR1L	1379	hgsc.bcm.edu	37	chr1	207872610	207872619	+	Splice_Site	DEL	GTGTGTGAAC	GTGTGTGAAC	-													0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	tttggaatagcagtgttccaGtgtgtgaacgtaagtaatag							TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	GTGTGTGAAC	GTGTGTGAAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr1:207872610_207872619delGTGTGTGAAC	ENST00000508064.2	+	8	1279_1288	c.1219_1228delGTGTGTGAAC	c.(1219-1230)gtgtgtgaacgt>gt	p.VCER407fs	CR1L_ENST00000530905.1_Intron	NM_175710.1	NP_783641.1	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like	407	Sushi 6. {ECO:0000255|PROSITE- ProRule:PRU00302}.					cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|receptor complex (GO:0043235)				endometrium(1)|kidney(1)|large_intestine(2)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						CAGTGTTCCAGTGTGTGAACGTAAGTAATA	0.395																																					p.406_409del		Atlas-INDEL	.											.	CR1L	97	.	0			c.1218_1227del						.																																			SO:0001630	splice_region_variant	1379	exon8			.	AY114160	CCDS44310.1	1q32.1	2008-02-05			ENSG00000197721	ENSG00000197721		"Complement system"	2335	protein-coding gene	gene with protein product		605886				2295627	Standard	NM_175710		Approved		uc001hga.4	Q2VPA4	OTTHUMG00000036354	ENST00000508064.2:c.1228+1GTGTGTGAAC>-	chr1.hg19:g.207872610_207872619delGTGTGTGAAC		394.0	0.0		108.0	12.0	NM_175710	Q32MC9|Q8NEU7	Frame_Shift_Del	DEL	ENST00000508064.2	hg19	CCDS44310.1																																																																																			.	.		0.395	CR1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390247.1	XM_114735	Frame_Shift_Del	-	207872619	GTGTGTGAAC	-	207872610	8	5	285	1	0	1	0	1	0	0	1	0	3843	1029	36	0	1249	0	CR1L	1	207872610	Splice_Site	DEL	GTGTGTGAAC	TCGA-G3-A5SJ-01A-11D-A27I-10	40881625	207872610	41378011	10	41919										
LYST	1130	hgsc.bcm.edu	37	chr1	235964399	235964399	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	tcagactttaagtctaccccTgaaaagagaaaagcgaaaga	8	8	2	4			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr1:235964399T>A	ENST00000389794.3	-	9	3887		c.e9-2		LYST_ENST00000536965.1_Splice_Site|LYST_ENST00000389793.2_Splice_Site			Q99698	LYST_HUMAN	lysosomal trafficking regulator						blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			AGTCTACCCCTGAAAAGAGAA	0.343																																					.		Atlas-SNP	.											.	LYST	370	.	0			c.3713-2A>T						.						66	69	68					1																	235964399		2202	4299	6501	SO:0001630	splice_region_variant	1130	exon10			TACCCCTGAAAAG	U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"WD repeat domain containing"	1968	protein-coding gene	gene with protein product		606897	"Chediak-Higashi syndrome 1"	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.3713-2A>T	chr1.hg19:g.235964399T>A		48.0	0.0		19.0	7.0	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Splice_Site	SNP	ENST00000389794.3	hg19	CCDS31062.1	.	.	.	.	.	.	.	.	.	.	T	12.15	1.852847	0.32699	.	.	ENSG00000143669	ENST00000389794;ENST00000389793;ENST00000536965	.	.	.	5.66	5.66	0.87406	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7694	0.69665	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	LYST	234031022	1.000000	0.71417	0.265000	0.24526	0.153000	0.21895	5.169000	0.64984	2.284000	0.76573	0.528000	0.53228	.	.	.		0.343	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5		Intron	A	235964399	T	A	235964399	5	1	285	1	0	0	0	0	0	0	1	0	9137	1594	55	4	7874	4	LYST	1	235964399	Splice_Site	SNP	T	TCGA-G3-A5SJ-01A-11D-A27I-10	28091789	235964399	13286222	11	41920										
CHRM3	1131	hgsc.bcm.edu	37	chr1	240072344	240072344	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	ttttggaatctgggctactgGctgtgctacatcaacagcac	10	10	2	0			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr1:240072344G>C	ENST00000255380.4	+	5	2372	c.1593G>C	c.(1591-1593)tgG>tgC	p.W531C		NM_000740.2	NP_000731.1	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	531					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|energy reserve metabolic process (GO:0006112)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of insulin secretion (GO:0050796)|regulation of vascular smooth muscle contraction (GO:0003056)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|smooth muscle contraction (GO:0006939)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)|receptor activity (GO:0004872)	p.W531S(2)		breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(19)|ovary(4)|prostate(1)|skin(12)|upper_aerodigestive_tract(1)	51	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Fesoterodine(DB06702)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Isopropamide(DB01625)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methacholine(DB06709)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tramadol(DB00193)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	TGGGCTACTGGCTGTGCTACA	0.483																																					p.W531C		Atlas-SNP	.											.	CHRM3	118	.	2	Substitution - Missense(2)	lung(2)	c.G1593C						.						118	99	106					1																	240072344		2203	4300	6503	SO:0001583	missense	1131	exon5			CTACTGGCTGTGC	U29589	CCDS1616.1	1q43	2012-09-20			ENSG00000133019	ENSG00000133019		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1952	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 3"	118494					Standard	XM_005273032		Approved		uc001hyp.3	P20309	OTTHUMG00000039649	ENST00000255380.4:c.1593G>C	chr1.hg19:g.240072344G>C	ENSP00000255380:p.Trp531Cys	367.0	0.0		96.0	32.0	NM_000740	Q0VAJ8|Q4QRI3|Q5VXY2|Q9HB60	Missense_Mutation	SNP	ENST00000255380.4	hg19	CCDS1616.1	.	.	.	.	.	.	.	.	.	.	G	18.02	3.529016	0.64860	.	.	ENSG00000133019	ENST00000255380	T	0.73789	-0.78	5.73	5.73	0.89815	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.88477	0.6447	M	0.84683	2.71	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89429	0.3715	10	0.87932	D	0	-8.1526	19.8984	0.96975	0.0:0.0:1.0:0.0	.	531	P20309	ACM3_HUMAN	C	531	ENSP00000255380:W531C	ENSP00000255380:W531C	W	+	3	0	CHRM3	238138967	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.713000	0.92767	0.655000	0.94253	TGG	.	.		0.483	CHRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095644.2	NM_000740		C	240072344	G	C	240072344	3	2	285	1	0	0	0	0	1	0	0	0	3380	1212	42	4	1595	4	CHRM3	1	240072344	Missense_Mutation	SNP	G	TCGA-G3-A5SJ-01A-11D-A27I-10	4107945	240072344	9178277	12	41921										
CLIP4	79745	hgsc.bcm.edu	37	chr2	29366660	29366660	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	tgacgccgcagccactgctaAggaaatcaagcagatgcttc	10	12	1	2			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr2:29366660A>G	ENST00000320081.5	+	7	989	c.734A>G	c.(733-735)aAg>aGg	p.K245R	CLIP4_ENST00000401617.2_Missense_Mutation_p.K138R|CLIP4_ENST00000401605.1_Missense_Mutation_p.K245R|CLIP4_ENST00000404424.1_Missense_Mutation_p.K245R	NM_024692.4	NP_078968.3	Q8N3C7	CLIP4_HUMAN	CAP-GLY domain containing linker protein family, member 4	245										endometrium(4)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|prostate(1)|skin(1)	26	Acute lymphoblastic leukemia(172;0.155)					GCCACTGCTAAGGAAATCAAG	0.463																																					p.K245R		Atlas-SNP	.											.	CLIP4	69	.	0			c.A734G						.						138	128	131					2																	29366660		2203	4300	6503	SO:0001583	missense	79745	exon7			CTGCTAAGGAAAT	AK024722	CCDS1770.1, CCDS74502.1	2p23	2013-01-10	2007-01-04	2007-01-04	ENSG00000115295	ENSG00000115295		"Ankyrin repeat domain containing"	26108	protein-coding gene	gene with protein product			"restin-like 2"	RSNL2			Standard	XM_005264562		Approved	FLJ21069	uc002rmv.3	Q8N3C7	OTTHUMG00000097837	ENST00000320081.5:c.734A>G	chr2.hg19:g.29366660A>G	ENSP00000327009:p.Lys245Arg	371.0	0.0		146.0	41.0	NM_024692	A0AV10|B2RMQ3|B7Z7N8|Q7Z4U3|Q96BR7|Q96MA5|Q9H7C0	Missense_Mutation	SNP	ENST00000320081.5	hg19	CCDS1770.1	.	.	.	.	.	.	.	.	.	.	A	16.65	3.182137	0.57800	.	.	ENSG00000115295	ENST00000401605;ENST00000401617;ENST00000404424;ENST00000402240;ENST00000320081;ENST00000379543;ENST00000530644	T;T;T;T	0.76968	-1.06;-0.78;-0.73;-0.73	5.64	5.64	0.86602	.	0.103874	0.64402	D	0.000005	D	0.87509	0.6195	M	0.74258	2.255	0.45295	D	0.998295	D;D	0.71674	0.998;0.998	D;D	0.77557	0.989;0.99	D	0.88258	0.2921	10	0.54805	T	0.06	.	15.8444	0.78876	1.0:0.0:0.0:0.0	.	245;245	A8K6D0;Q8N3C7	.;CLIP4_HUMAN	R	245;138;245;245;245;246;227	ENSP00000384242:K245R;ENSP00000385148:K138R;ENSP00000385594:K245R;ENSP00000327009:K245R	ENSP00000327009:K245R	K	+	2	0	CLIP4	29220164	1.000000	0.71417	0.375000	0.26029	0.163000	0.22366	6.297000	0.72757	2.144000	0.66660	0.528000	0.53228	AAG	.	.		0.463	CLIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215123.2	NM_024692		G	29366660	A	G	29366660	3	3	285	1	0	0	0	0	1	0	0	0	3537	72	3	2	756	2	CLIP4	2	29366660	Missense_Mutation	SNP	A	TCGA-G3-A5SJ-01A-11D-A27I-10		29366660	213832713	13	41922										
XDH	7498	hgsc.bcm.edu	37	chr2	31609400	31609400	+	Missense_Mutation	SNP	T	T	C													0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	cccttcaaatcgcagctgctTccgaggagtgtctttcagcc							TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr2:31609400T>C	ENST00000379416.3	-	9	721	c.673A>G	c.(673-675)Aag>Gag	p.K225E	XDH_ENST00000491727.1_5'UTR	NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	225					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|lactation (GO:0007595)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of gene expression (GO:0010629)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|negative regulation of vasculogenesis (GO:2001213)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)|xanthine catabolic process (GO:0009115)	cytosol (GO:0005829)|extracellular space (GO:0005615)|peroxisome (GO:0005777)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|protein homodimerization activity (GO:0042803)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)|xanthine oxidase activity (GO:0004855)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(31)|ovary(1)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(1)	74	Acute lymphoblastic leukemia(172;0.155)				Aldesleukin(DB00041)|Allopurinol(DB00437)|Azathioprine(DB00993)|Carboplatin(DB00958)|Carvedilol(DB01136)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|L-Carnitine(DB00583)|Menadione(DB00170)|Mercaptopurine(DB01033)|Nitrofural(DB00336)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Spermine(DB00127)|Trifluoperazine(DB00831)	CGCAGCTGCTTCCGAGGAGTG	0.507																																					p.K225E	Colon(66;682 1445 30109 40147)	Atlas-SNP	.											.	XDH	191	.	0			c.A673G						.						114	99	104					2																	31609400		2203	4300	6503	SO:0001583	missense	7498	exon9			GCTGCTTCCGAGG	D11456	CCDS1775.1	2p23.1	2009-07-10	2003-03-20		ENSG00000158125	ENSG00000158125	1.17.1.4		12805	protein-coding gene	gene with protein product		607633	"xanthene dehydrogenase"			8224915	Standard	NM_000379		Approved	XOR, XO	uc002rnv.1	P47989	OTTHUMG00000099385	ENST00000379416.3:c.673A>G	chr2.hg19:g.31609400T>C	ENSP00000368727:p.Lys225Glu	172.0	0.0		60.0	19.0	NM_000379	Q16681|Q16712|Q4PJ16	Missense_Mutation	SNP	ENST00000379416.3	hg19	CCDS1775.1	.	.	.	.	.	.	.	.	.	.	T	12.33	1.906243	0.33628	.	.	ENSG00000158125	ENST00000379416	T	0.21191	2.02	5.56	5.56	0.83823	FAD-binding, type 2, subdomain 1 (1);FAD-binding, type 2 (1);Xanthine dehydrogenase, small subunit (1);	0.366510	0.34223	N	0.004158	T	0.18676	0.0448	L	0.39633	1.23	0.36141	D	0.846803	B	0.17268	0.021	B	0.20767	0.031	T	0.14559	-1.0468	10	0.14656	T	0.56	.	14.749	0.69511	0.0:0.0:0.0:1.0	.	225	P47989	XDH_HUMAN	E	225	ENSP00000368727:K225E	ENSP00000368727:K225E	K	-	1	0	XDH	31462904	0.999000	0.42202	0.563000	0.28383	0.864000	0.49448	3.110000	0.50352	2.130000	0.65690	0.444000	0.29173	AAG	.	.		0.507	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379		C	31609400	T	C	31609400	3	2	285	1	0	0	0	0	1	0	0	0	17441	1792	62	2	3440	2	XDH	2	31609400	Missense_Mutation	SNP	T	TCGA-G3-A5SJ-01A-11D-A27I-10	2242740	31609400	211589973	14	41923	219	2								
XDH	7498	hgsc.bcm.edu	37	chr2	31609402	31609402	+	Missense_Mutation	SNP	C	C	G													0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	cttcaaatcgcagctgcttcCgaggagtgtctttcagcctc					rs112466737	byFrequency	TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr2:31609402C>G	ENST00000379416.3	-	9	719	c.671G>C	c.(670-672)cGg>cCg	p.R224P	XDH_ENST00000491727.1_5'UTR	NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	224					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|lactation (GO:0007595)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of gene expression (GO:0010629)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|negative regulation of vasculogenesis (GO:2001213)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)|xanthine catabolic process (GO:0009115)	cytosol (GO:0005829)|extracellular space (GO:0005615)|peroxisome (GO:0005777)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|protein homodimerization activity (GO:0042803)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)|xanthine oxidase activity (GO:0004855)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(31)|ovary(1)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(1)	74	Acute lymphoblastic leukemia(172;0.155)				Aldesleukin(DB00041)|Allopurinol(DB00437)|Azathioprine(DB00993)|Carboplatin(DB00958)|Carvedilol(DB01136)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|L-Carnitine(DB00583)|Menadione(DB00170)|Mercaptopurine(DB01033)|Nitrofural(DB00336)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Spermine(DB00127)|Trifluoperazine(DB00831)	CAGCTGCTTCCGAGGAGTGTC	0.507																																					p.R224P	Colon(66;682 1445 30109 40147)	Atlas-SNP	.											.	XDH	191	.	0			c.G671C						.						111	97	102					2																	31609402		2203	4300	6503	SO:0001583	missense	7498	exon9			TGCTTCCGAGGAG	D11456	CCDS1775.1	2p23.1	2009-07-10	2003-03-20		ENSG00000158125	ENSG00000158125	1.17.1.4		12805	protein-coding gene	gene with protein product		607633	"xanthene dehydrogenase"			8224915	Standard	NM_000379		Approved	XOR, XO	uc002rnv.1	P47989	OTTHUMG00000099385	ENST00000379416.3:c.671G>C	chr2.hg19:g.31609402C>G	ENSP00000368727:p.Arg224Pro	170.0	0.0		59.0	20.0	NM_000379	Q16681|Q16712|Q4PJ16	Missense_Mutation	SNP	ENST00000379416.3	hg19	CCDS1775.1	.	.	.	.	.	.	.	.	.	.	C	9.062	0.994856	0.19043	.	.	ENSG00000158125	ENST00000379416	T	0.21543	2.0	5.56	-3.95	0.04118	FAD-binding, type 2 (1);Xanthine dehydrogenase, small subunit (1);	0.732108	0.14037	N	0.345725	T	0.05868	0.0153	N	0.03224	-0.385	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.25152	-1.0140	10	0.25106	T	0.35	.	2.0551	0.03579	0.1047:0.2663:0.2113:0.4177	.	224	P47989	XDH_HUMAN	P	224	ENSP00000368727:R224P	ENSP00000368727:R224P	R	-	2	0	XDH	31462906	0.008000	0.16893	0.006000	0.13384	0.875000	0.50365	-1.636000	0.02016	-1.039000	0.03275	0.543000	0.68304	CGG	.	C|0.999;T|0.001		0.507	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379		G	31609402	C	G	31609402	3	3	285	1	0	0	0	0	1	0	0	0	17441	652	23	4	3442	4	XDH	2	31609402	Missense_Mutation	SNP	C	TCGA-G3-A5SJ-01A-11D-A27I-10	2	31609402	211589971	15	41924	219	2								
EMX1	2016	hgsc.bcm.edu	37	chr2	73160942	73160942	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	gtgtggttccagaaccggagGacaaagtacaaacggcagaa	13	8	0	2			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr2:73160942G>A	ENST00000258106.6	+	3	1110	c.732G>A	c.(730-732)agG>agA	p.R244R	EMX1_ENST00000394111.5_3'UTR	NM_004097.2	NP_004088.2	Q04741	EMX1_HUMAN	empty spiracles homeobox 1	211					brain morphogenesis (GO:0048854)|cerebral cortex neuron differentiation (GO:0021895)|cerebral cortex regionalization (GO:0021796)|in utero embryonic development (GO:0001701)|neuron projection extension (GO:1990138)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			cervix(1)|large_intestine(2)|lung(3)	6						AGAACCGGAGGACAAAGTACA	0.607																																					p.R244R		Atlas-SNP	.											EMX1,bladder,carcinoma,0,1	EMX1	12	.	0			c.G732A						.						61	69	66					2																	73160942		2062	4211	6273	SO:0001819	synonymous_variant	2016	exon3			CCGGAGGACAAAG	X68879	CCDS1921.2	2p13.2	2011-06-20	2007-02-15		ENSG00000135638	ENSG00000135638		"Homeoboxes / ANTP class : NKL subclass"	3340	protein-coding gene	gene with protein product		600034	"empty spiracles homolog 1 (Drosophila)"			7959790	Standard	XM_005264203		Approved		uc002sin.1	Q04741	OTTHUMG00000129778	ENST00000258106.6:c.732G>A	chr2.hg19:g.73160942G>A		161.0	0.0		56.0	17.0	NM_004097	Q0D2P0|Q53T30|Q86XB0	Silent	SNP	ENST00000258106.6	hg19	CCDS1921.2	.	.	.	.	.	.	.	.	.	.	G	13.97	2.395636	0.42512	.	.	ENSG00000135638	ENST00000394111	.	.	.	4.72	4.72	0.59763	.	.	.	.	.	T	0.76463	0.3991	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.79754	-0.1670	5	0.87932	D	0	-29.4034	16.7711	0.85537	0.0:0.0:1.0:0.0	.	.	.	.	N	197	.	ENSP00000377670:D197N	D	+	1	0	EMX1	73014450	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.808000	0.86044	2.635000	0.89317	0.484000	0.47621	GAC	.	.		0.607	EMX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251994.3			A	73160942	G	A	73160942	2	1	285	1	0	0	0	0	0	0	0	1	5109	1165	41	3		3	EMX1	2	73160942	Silent	SNP	G	TCGA-G3-A5SJ-01A-11D-A27I-10	41551540	73160942	170038431	16	41925										
NAT8	9027	hgsc.bcm.edu	37	chr2	73868277	73868277	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	cccgggcaaactggaggacaGtcctgaccagggcttttgct	13	12	0	1			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr2:73868277G>T	ENST00000272425.3	-	2	628	c.479C>A	c.(478-480)aCt>aAt	p.T160N		NM_003960.3|NM_016347.2	NP_003951.3|NP_057431.2			N-acetyltransferase 8 (GCN5-related, putative)											breast(1)|endometrium(2)|kidney(2)|lung(2)|ovary(1)|prostate(1)	9						CTGGAGGACAGTCCTGACCAG	0.567																																					p.T160N		Atlas-SNP	.											NAT8,NS,carcinoma,0,1	NAT8	26	.	0			c.C479A						.						75	77	76					2																	73868277		2203	4300	6503	SO:0001583	missense	9027	exon2			AGGACAGTCCTGA	AB013094	CCDS1926.1	2p13.2	2012-03-20	2008-09-24		ENSG00000144035	ENSG00000144035			18069	protein-coding gene	gene with protein product		606716	"N-acetyltransferase 8"			11397015, 9852678, 19011241	Standard	NM_003960		Approved	Hcml1, TSC501, GLA, ATase2	uc002sji.1	Q9UHE5	OTTHUMG00000129818	ENST00000272425.3:c.479C>A	chr2.hg19:g.73868277G>T	ENSP00000272425:p.Thr160Asn	296.0	1.0		107.0	44.0	NM_003960		Missense_Mutation	SNP	ENST00000272425.3	hg19	CCDS1926.1	.	.	.	.	.	.	.	.	.	.	G	16.92	3.255987	0.59321	.	.	ENSG00000144035	ENST00000272425	T	0.22945	1.93	3.86	2.97	0.34412	GCN5-related N-acetyltransferase (GNAT) domain (2);Acyl-CoA N-acyltransferase (2);	0.256438	0.37178	N	0.002214	T	0.42988	0.1227	M	0.69523	2.12	0.41732	D	0.989565	D	0.89917	1.0	D	0.75484	0.986	T	0.28996	-1.0026	10	0.49607	T	0.09	-23.6027	5.6538	0.17631	0.109:0.0:0.6987:0.1923	.	160	Q9UHE5	NAT8_HUMAN	N	160	ENSP00000272425:T160N	ENSP00000272425:T160N	T	-	2	0	NAT8	73721785	1.000000	0.71417	0.950000	0.38849	0.713000	0.41058	5.277000	0.65586	0.911000	0.36747	0.644000	0.83932	ACT	.	.		0.567	NAT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327854.1	NM_003960		T	73868277	G	T	73868277	3	4	285	1	0	0	0	0	1	0	0	0	10188	1029	36	3	208	3	NAT8	2	73868277	Missense_Mutation	SNP	G	TCGA-G3-A5SJ-01A-11D-A27I-10	707335	73868277	169331096	17	41926										
CCDC138	165055	hgsc.bcm.edu	37	chr2	109405347	109405347	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	tggagataaagttggttcatCgttaaaatattctgatgaaa	9	3	2	3			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr2:109405347C>A	ENST00000295124.4	+	3	251	c.191C>A	c.(190-192)tCg>tAg	p.S64*	CCDC138_ENST00000470608.1_3'UTR|CCDC138_ENST00000412964.2_Nonsense_Mutation_p.S64*	NM_144978.1	NP_659415.1	Q96M89	CC138_HUMAN	coiled-coil domain containing 138	64										endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	14						GTTGGTTCATCGTTAAAATAT	0.358																																					p.S64X		Atlas-SNP	.											.	CCDC138	49	.	0			c.C191A						.						169	163	165					2																	109405347		2203	4300	6503	SO:0001587	stop_gained	165055	exon3			GTTCATCGTTAAA	AK057307	CCDS2080.1	2q13	2008-02-05			ENSG00000163006	ENSG00000163006			26531	protein-coding gene	gene with protein product						12477932	Standard	NM_144978		Approved	FLJ32745	uc002ten.1	Q96M89	OTTHUMG00000130980	ENST00000295124.4:c.191C>A	chr2.hg19:g.109405347C>A	ENSP00000295124:p.Ser64*	140.0	0.0		54.0	14.0	NM_144978	Q05DF1|Q4ZG07|Q53TE1|Q6ZUY5|Q86VL7	Nonsense_Mutation	SNP	ENST00000295124.4	hg19	CCDS2080.1	.	.	.	.	.	.	.	.	.	.	C	13.32	2.203203	0.38905	.	.	ENSG00000163006	ENST00000412964;ENST00000295124	.	.	.	4.03	2.23	0.28157	.	0.352458	0.20938	N	0.082970	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.5115	6.3944	0.21605	0.0:0.7792:0.0:0.2208	.	.	.	.	X	64	.	ENSP00000295124:S64X	S	+	2	0	CCDC138	108771779	0.002000	0.14202	0.008000	0.14137	0.385000	0.30292	0.700000	0.25601	0.662000	0.31006	0.650000	0.86243	TCG	.	.		0.358	CCDC138-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253593.1	NM_144978		A	109405347	C	A	109405347	4	1	285	1	0	0	0	0	0	1	0	0	2774	893	31	1	201	1	CCDC138	2	109405347	Nonsense_Mutation	SNP	C	TCGA-G3-A5SJ-01A-11D-A27I-10	35537070	109405347	133794026	18	41927										
DPP10	57628	hgsc.bcm.edu	37	chr2	116497381	116497381	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	agaaagacttgccttcctgaTgataaatgactctttggtac	8	8	1	5			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr2:116497381T>C	ENST00000410059.1	+	9	1244	c.764T>C	c.(763-765)aTg>aCg	p.M255T	DPP10_ENST00000310323.8_Missense_Mutation_p.M248T|DPP10_ENST00000409163.1_Missense_Mutation_p.M205T|DPP10_ENST00000393147.2_Missense_Mutation_p.M259T	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	255						integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						GCCTTCCTGATGATAAATGAC	0.448																																					p.M259T		Atlas-SNP	.											.	DPP10	415	.	0			c.T776C						.						222	189	200					2																	116497381		2203	4299	6502	SO:0001583	missense	57628	exon9			TCCTGATGATAAA	AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"dipeptidylpeptidase 10", "dipeptidyl-peptidase 10"			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.764T>C	chr2.hg19:g.116497381T>C	ENSP00000386565:p.Met255Thr	414.0	0.0		197.0	52.0	NM_001178034	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Missense_Mutation	SNP	ENST00000410059.1	hg19	CCDS46400.1	.	.	.	.	.	.	.	.	.	.	T	1.242	-0.621064	0.03636	.	.	ENSG00000175497	ENST00000410059;ENST00000409163;ENST00000393146;ENST00000393147;ENST00000310323;ENST00000476155	T;T;T;T;T	0.28454	1.61;1.61;1.61;1.61;1.61	4.95	4.95	0.65309	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.215284	0.50627	D	0.000117	T	0.06280	0.0162	N	0.00242	-1.785	0.39244	D	0.963915	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.001;0.002;0.002;0.002	T	0.32587	-0.9901	10	0.02654	T	1	-33.0772	8.5707	0.33567	0.0:0.0948:0.0:0.9052	.	248;259;251;255	Q8N608-2;Q0GLB8;Q0GLB9;Q8N608	.;.;.;DPP10_HUMAN	T	255;205;251;259;248;205	ENSP00000386565:M255T;ENSP00000387038:M205T;ENSP00000376854:M251T;ENSP00000376855:M259T;ENSP00000309066:M248T	ENSP00000309066:M248T	M	+	2	0	DPP10	116213851	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	2.702000	0.47102	2.210000	0.71456	0.460000	0.39030	ATG	.	.		0.448	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868		C	116497381	T	C	116497381	3	2	285	1	0	0	0	0	1	0	0	0	4729	1464	51	2	969	2	DPP10	2	116497381	Missense_Mutation	SNP	T	TCGA-G3-A5SJ-01A-11D-A27I-10	7092034	116497381	126701992	19	41928										
PIKFYVE	200576	hgsc.bcm.edu	37	chr2	209190271	209190271	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	tacggtggaggttccatcccCtgggatcctgacatccctcc	10	15	0	1			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr2:209190271C>T	ENST00000264380.4	+	20	2894	c.2736C>T	c.(2734-2736)ccC>ccT	p.P912P		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	912					cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						GTTCCATCCCCTGGGATCCTG	0.507																																					p.P912P		Atlas-SNP	.											.	PIKFYVE	223	.	0			c.C2736T						.						82	75	78					2																	209190271		2203	4300	6503	SO:0001819	synonymous_variant	200576	exon20			CATCCCCTGGGAT	AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"Zinc fingers, FYVE domain containing"	23785	protein-coding gene	gene with protein product	"zinc finger, FYVE domain containing 29"	609414	"phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	ENST00000264380.4:c.2736C>T	chr2.hg19:g.209190271C>T		163.0	0.0		67.0	17.0	NM_015040	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Silent	SNP	ENST00000264380.4	hg19	CCDS2382.1																																																																																			.	.		0.507	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040		T	209190271	C	T	209190271	2	4	285	1	0	0	0	0	0	0	0	1	11933	668	24	3		3	PIKFYVE	2	209190271	Silent	SNP	C	TCGA-G3-A5SJ-01A-11D-A27I-10	92692890	209190271	34009102	20	41929										
USP40	55230	hgsc.bcm.edu	37	chr2	234438104	234438104	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	tttgcagttcaatgttagctGcatccatttcattcagtaaa	6	8	3	0			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr2:234438104G>T	ENST00000427112.2	-	11	1558	c.1523C>A	c.(1522-1524)gCa>gAa	p.A508E	USP40_ENST00000251722.6_Missense_Mutation_p.A508E|USP40_ENST00000450966.1_Missense_Mutation_p.A520E			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	508					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|endometrium(6)|kidney(5)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		AATGTTAGCTGCATCCATTTC	0.343																																					p.A520E		Atlas-SNP	.											.	USP40	174	.	0			c.C1559A						.						73	68	70					2																	234438104		1835	4070	5905	SO:0001583	missense	55230	exon11			TTAGCTGCATCCA	AK001647	CCDS46547.1	2q37.1	2005-08-08	2005-08-08		ENSG00000085982	ENSG00000085982		"Ubiquitin-specific peptidases"	20069	protein-coding gene	gene with protein product		610570	"ubiquitin specific protease 40"			12838346	Standard	NM_018218		Approved	FLJ10785	uc010zmr.2	Q9NVE5	OTTHUMG00000153199	ENST00000427112.2:c.1523C>A	chr2.hg19:g.234438104G>T	ENSP00000387898:p.Ala508Glu	61.0	0.0		24.0	8.0	NM_018218	Q6NX38|Q70EL0	Missense_Mutation	SNP	ENST00000427112.2	hg19	CCDS46547.1	.	.	.	.	.	.	.	.	.	.	G	7.098	0.573459	0.13623	.	.	ENSG00000085982	ENST00000450966;ENST00000251722;ENST00000427112	T;T;T	0.04454	3.62;3.62;3.62	5.76	2.81	0.32909	.	0.980252	0.08407	N	0.950515	T	0.05090	0.0136	L	0.38838	1.175	0.27224	N	0.959588	B;B	0.20780	0.028;0.048	B;B	0.14023	0.004;0.01	T	0.34625	-0.9821	10	0.25751	T	0.34	.	9.2049	0.37282	0.0667:0.0:0.5695:0.3639	.	508;520	Q9NVE5;Q9NVE5-3	UBP40_HUMAN;.	E	520;508;508	ENSP00000415434:A520E;ENSP00000251722:A508E;ENSP00000387898:A508E	ENSP00000251722:A508E	A	-	2	0	USP40	234102843	0.923000	0.31300	0.998000	0.56505	0.985000	0.73830	1.528000	0.35985	1.417000	0.47077	0.555000	0.69702	GCA	.	.		0.343	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294		T	234438104	G	T	234438104	3	4	285	1	0	0	0	0	1	0	0	0	17087	1319	46	3	2268	3	USP40	2	234438104	Missense_Mutation	SNP	G	TCGA-G3-A5SJ-01A-11D-A27I-10	25247833	234438104	8761269	21	41930										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41268760	41268760	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	tataatgaggacctatacttAcgaaaaactactgtggacca	7	8	0	1			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr3:41268760A>T	ENST00000349496.5	+	7	1278	c.998A>T	c.(997-999)tAc>tTc	p.Y333F	CTNNB1_ENST00000396185.3_Missense_Mutation_p.Y333F|CTNNB1_ENST00000453024.1_Missense_Mutation_p.Y326F|CTNNB1_ENST00000396183.3_Missense_Mutation_p.Y333F|CTNNB1_ENST00000405570.1_Missense_Mutation_p.Y333F	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	333					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		ACCTATACTTACGAAAAACTA	0.383		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.Y333F	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	.	CTNNB1	4904	.	0			c.A998T						.						107	106	106					3																	41268760		2203	4300	6503	SO:0001583	missense	1499	exon7	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	ATACTTACGAAAA	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.998A>T	chr3.hg19:g.41268760A>T	ENSP00000344456:p.Tyr333Phe	107.0	0.0		39.0	14.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	28.9	4.956688	0.92726	.	.	ENSG00000168036	ENST00000405570;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185	T;T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15;-0.15	5.5	5.5	0.81552	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.81522	0.4840	M	0.89478	3.035	0.80722	D	1	D;D	0.63046	0.97;0.992	P;D	0.66716	0.903;0.946	D	0.84926	0.0857	10	0.59425	D	0.04	-21.1058	15.5934	0.76558	1.0:0.0:0.0:0.0	.	261;333	B4DSW9;P35222	.;CTNB1_HUMAN	F	333;333;333;326;333	ENSP00000385604:Y333F;ENSP00000379486:Y333F;ENSP00000344456:Y333F;ENSP00000411226:Y326F;ENSP00000379488:Y333F	ENSP00000344456:Y333F	Y	+	2	0	CTNNB1	41243764	1.000000	0.71417	0.957000	0.39632	0.948000	0.59901	9.339000	0.96797	2.094000	0.63399	0.482000	0.46254	TAC	.	.		0.383	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41268760	A	T	41268760	3	4	285	1	0	0	0	0	1	0	0	0	4018	391	14	4	1020	4	CTNNB1	3	41268760	Missense_Mutation	SNP	A	TCGA-G3-A5SJ-01A-11D-A27I-10		41268760	156753670	22	41931										
ZPLD1	131368	hgsc.bcm.edu	37	chr3	102175049	102175049	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	tctaacaggtatccacaattCctggagtcagtgcttatgga	9	9	2	0			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr3:102175049C>T	ENST00000491959.1	+	11	1222	c.340C>T	c.(340-342)Cct>Tct	p.P114S	ZPLD1_ENST00000306176.1_Missense_Mutation_p.P130S|ZPLD1_ENST00000466937.1_Missense_Mutation_p.P114S			Q8TCW7	ZPLD1_HUMAN	zona pellucida-like domain containing 1	114	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.					integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(18)|ovary(2)|skin(3)	35						ATCCACAATTCCTGGAGTCAG	0.348																																					p.P130S		Atlas-SNP	.											.	ZPLD1	82	.	0			c.C388T						.						122	119	120					3																	102175049		2203	4300	6503	SO:0001583	missense	131368	exon4			ACAATTCCTGGAG	AY090780	CCDS2947.1	3q12.3	2009-03-25			ENSG00000170044	ENSG00000170044			27022	protein-coding gene	gene with protein product		615915				18632209	Standard	NM_175056		Approved		uc003dvt.1	Q8TCW7	OTTHUMG00000159229	ENST00000491959.1:c.340C>T	chr3.hg19:g.102175049C>T	ENSP00000420265:p.Pro114Ser	140.0	0.0		54.0	23.0	NM_175056	Q49AS1|Q8WU36	Missense_Mutation	SNP	ENST00000491959.1	hg19		.	.	.	.	.	.	.	.	.	.	C	12.63	1.995193	0.35226	.	.	ENSG00000170044	ENST00000491959;ENST00000306176;ENST00000466937	D;D;D	0.82167	-1.58;-1.58;-1.58	5.45	4.58	0.56647	Zona pellucida sperm-binding protein (3);	0.153821	0.64402	D	0.000013	T	0.73289	0.3568	L	0.34521	1.04	0.47949	D	0.999553	B;B	0.26547	0.152;0.137	B;B	0.27500	0.058;0.08	T	0.66563	-0.5892	10	0.08381	T	0.77	-8.7798	14.4134	0.67132	0.0:0.929:0.0:0.071	.	130;114	Q8TCW7-2;Q8TCW7	.;ZPLD1_HUMAN	S	114;130;114	ENSP00000420265:P114S;ENSP00000307801:P130S;ENSP00000418253:P114S	ENSP00000307801:P130S	P	+	1	0	ZPLD1	103657739	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.996000	0.40776	1.315000	0.45114	-0.137000	0.14449	CCT	.	.		0.348	ZPLD1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353984.1	NM_175056		T	102175049	C	T	102175049	3	4	285	1	0	0	0	0	1	0	0	0	18236	855	30	3	402	3	ZPLD1	3	102175049	Missense_Mutation	SNP	C	TCGA-G3-A5SJ-01A-11D-A27I-10	60906289	102175049	95847381	23	41932										
EPHB1	2047	hgsc.bcm.edu	37	chr3	134920510	134920510	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	ctccaggatgacacctcagaTcccacctacaccagctcctt	5	18	1	2			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr3:134920510T>G	ENST00000398015.3	+	12	2695	c.2325T>G	c.(2323-2325)gaT>gaG	p.D775E	EPHB1_ENST00000493838.1_Missense_Mutation_p.D336E	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	775	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|camera-type eye morphogenesis (GO:0048593)|cell chemotaxis (GO:0060326)|cell-substrate adhesion (GO:0031589)|central nervous system projection neuron axonogenesis (GO:0021952)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|neural precursor cell proliferation (GO:0061351)|neurogenesis (GO:0022008)|optic nerve morphogenesis (GO:0021631)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of JNK cascade (GO:0046328)|retinal ganglion cell axon guidance (GO:0031290)	axon (GO:0030424)|early endosome membrane (GO:0031901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(63)|ovary(8)|pancreas(2)|prostate(8)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	130						ACACCTCAGATCCCACCTACA	0.537																																					p.D775E		Atlas-SNP	.											.	EPHB1	519	.	0			c.T2325G						.						87	87	87					3																	134920510		2176	4297	6473	SO:0001583	missense	2047	exon12			CTCAGATCCCACC	L40636	CCDS46921.1	3q21-q23	2013-02-11	2004-10-28			ENSG00000154928		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3392	protein-coding gene	gene with protein product		600600	"EphB1"	EPHT2		8666391	Standard	NM_004441		Approved	Hek6	uc003eqt.3	P54762		ENST00000398015.3:c.2325T>G	chr3.hg19:g.134920510T>G	ENSP00000381097:p.Asp775Glu	393.0	1.0		175.0	60.0	NM_004441	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Missense_Mutation	SNP	ENST00000398015.3	hg19	CCDS46921.1	.	.	.	.	.	.	.	.	.	.	T	11.55	1.671933	0.29693	.	.	ENSG00000154928	ENST00000398015;ENST00000493838	D;D	0.82893	-1.66;-1.66	5.44	2.68	0.31781	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.66742	0.2820	N	0.05467	-0.045	0.54753	D	0.999989	P	0.46064	0.872	P	0.48227	0.571	T	0.65236	-0.6217	10	0.02654	T	1	.	9.1453	0.36928	0.0:0.6383:0.0:0.3617	.	775	P54762	EPHB1_HUMAN	E	775;336	ENSP00000381097:D775E;ENSP00000419574:D336E	ENSP00000381097:D775E	D	+	3	2	EPHB1	136403200	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.285000	0.33261	0.354000	0.24105	-0.468000	0.05107	GAT	.	.		0.537	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357671.1	NM_004441		G	134920510	T	G	134920510	3	3	285	1	0	0	0	0	1	0	0	0	5176	1432	50	5	2371	5	EPHB1	3	134920510	Missense_Mutation	SNP	T	TCGA-G3-A5SJ-01A-11D-A27I-10	32745461	134920510	63101920	24	41933										
PAQR9	344838	hgsc.bcm.edu	37	chr3	142682019	142682019	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	caggatgaagcactccacgaAgtcgtcgggcacctcgtccc	11	15	0	1			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr3:142682019A>C	ENST00000340634.3	-	1	159	c.160T>G	c.(160-162)Ttc>Gtc	p.F54V	RP11-372E1.6_ENST00000598139.1_RNA|RP11-372E1.6_ENST00000595248.1_RNA|RP11-372E1.6_ENST00000593321.1_RNA|RP11-372E1.6_ENST00000607937.1_RNA|RP11-372E1.6_ENST00000478823.1_RNA|RP11-372E1.6_ENST00000594095.1_RNA|RP11-372E1.6_ENST00000595774.1_RNA|RP11-372E1.6_ENST00000497652.1_RNA|RP11-372E1.6_ENST00000493825.1_RNA|RP11-372E1.6_ENST00000608686.1_RNA|RP11-372E1.6_ENST00000608349.1_RNA|RP11-372E1.6_ENST00000598787.1_RNA	NM_198504.2	NP_940906.1	Q6ZVX9	PAQR9_HUMAN	progestin and adipoQ receptor family member IX	54						integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			endometrium(2)|large_intestine(7)|lung(12)|prostate(1)	22						CACTCCACGAAGTCGTCGGGC	0.692																																					p.F54V		Atlas-SNP	.											.	PAQR9	57	.	0			c.T160G						.						30	30	30					3																	142682019		2198	4296	6494	SO:0001583	missense	344838	exon1			CCACGAAGTCGTC	AY424287	CCDS3128.1	3q23	2008-05-02			ENSG00000188582	ENSG00000188582			30131	protein-coding gene	gene with protein product		614580					Standard	NM_198504		Approved	FLJ41938	uc003evg.3	Q6ZVX9	OTTHUMG00000159313	ENST00000340634.3:c.160T>G	chr3.hg19:g.142682019A>C	ENSP00000341564:p.Phe54Val	105.0	0.0		67.0	19.0	NM_198504	Q147T6	Missense_Mutation	SNP	ENST00000340634.3	hg19	CCDS3128.1	.	.	.	.	.	.	.	.	.	.	A	10.55	1.381240	0.24944	.	.	ENSG00000188582	ENST00000340634	T	0.23950	1.88	4.25	4.25	0.50352	.	0.078533	0.51477	D	0.000085	T	0.28433	0.0703	M	0.61703	1.905	0.30608	N	0.759821	P	0.42483	0.781	B	0.40864	0.342	T	0.26643	-1.0097	10	0.34782	T	0.22	-20.6322	13.3044	0.60345	1.0:0.0:0.0:0.0	.	54	Q6ZVX9	PAQR9_HUMAN	V	54	ENSP00000341564:F54V	ENSP00000341564:F54V	F	-	1	0	PAQR9	144164709	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	0.922000	0.28734	1.681000	0.50988	0.421000	0.28195	TTC	.	.		0.692	PAQR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354538.1	NM_198504		C	142682019	A	C	142682019	3	2	285	1	0	0	0	0	1	0	0	0	11451	72	3	5	977	5	PAQR9	3	142682019	Missense_Mutation	SNP	A	TCGA-G3-A5SJ-01A-11D-A27I-10	7761509	142682019	55340411	25	41934										
KLHL6	89857	hgsc.bcm.edu	37	chr3	183209884	183209884	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	taacctcgttcttctcgtccCgcccgccggtgatgtagagc	10	15	2	2			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr3:183209884C>A	ENST00000341319.3	-	7	1732	c.1697G>T	c.(1696-1698)cGg>cTg	p.R566L		NM_130446.2	NP_569713.2	Q8WZ60	KLHL6_HUMAN	kelch-like family member 6	566					B cell receptor signaling pathway (GO:0050853)|germinal center formation (GO:0002467)					breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44	all_cancers(143;9.2e-12)|Ovarian(172;0.0172)		all cancers(12;1.29e-44)|Epithelial(37;1.24e-38)|LUSC - Lung squamous cell carcinoma(7;2.58e-24)|Lung(8;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.32e-22)			CTTCTCGTCCCGCCCGCCGGT	0.677																																					p.R566L		Atlas-SNP	.											.	KLHL6	100	.	0			c.G1697T						.						76	74	75					3																	183209884		2203	4300	6503	SO:0001583	missense	89857	exon7			TCGTCCCGCCCGC	AF441792	CCDS3245.2	3q27.3	2013-01-30	2013-01-30		ENSG00000172578	ENSG00000172578		"Kelch-like", "BTB/POZ domain containing"	18653	protein-coding gene	gene with protein product	"kelch-like protein KLHL6"	614214	"kelch-like 6 (Drosophila)"			11214971, 12617994	Standard	NM_130446		Approved	FLJ00029	uc003flr.3	Q8WZ60	OTTHUMG00000148673	ENST00000341319.3:c.1697G>T	chr3.hg19:g.183209884C>A	ENSP00000341342:p.Arg566Leu	122.0	0.0		92.0	5.0	NM_130446	B2RB31|D3DNS8|Q8N5I1|Q8N892	Missense_Mutation	SNP	ENST00000341319.3	hg19	CCDS3245.2	.	.	.	.	.	.	.	.	.	.	C	33	5.207252	0.95033	.	.	ENSG00000172578	ENST00000341319	T	0.78364	-1.17	5.42	5.42	0.78866	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	D	0.86590	0.5969	M	0.72353	2.195	0.50467	D	0.999878	D	0.76494	0.999	D	0.79108	0.992	T	0.82360	-0.0496	10	0.14656	T	0.56	.	19.2033	0.93720	0.0:1.0:0.0:0.0	.	566	Q8WZ60	KLHL6_HUMAN	L	566	ENSP00000341342:R566L	ENSP00000341342:R566L	R	-	2	0	KLHL6	184692578	0.998000	0.40836	0.980000	0.43619	0.965000	0.64279	5.907000	0.69908	2.557000	0.86248	0.491000	0.48974	CGG	.	.		0.677	KLHL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309024.1	NM_130446		A	183209884	C	A	183209884	3	1	285	1	0	0	0	0	1	0	0	0	8402	652	23	1	172	1	KLHL6	3	183209884	Missense_Mutation	SNP	C	TCGA-G3-A5SJ-01A-11D-A27I-10	40527865	183209884	14812546	26	41935										
ECE2	9718	hgsc.bcm.edu	37	chr3	183995039	183995039	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	ggccatgttccctaccacagAcccatcccacagcacctgcc	6	20	0	1			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr3:183995039A>G	ENST00000402825.3	+	4	617	c.617A>G	c.(616-618)gAc>gGc	p.D206G	ECE2_ENST00000404464.3_Splice_Site_p.D88G|ECE2_ENST00000359140.4_Splice_Site_p.D59G|ECE2_ENST00000357474.5_Splice_Site_p.D134G|EIF2B5_ENST00000444495.1_Intron	NM_014693.3	NP_055508.3	O60344	ECE2_HUMAN	endothelin converting enzyme 2	206	Endothelin-converting enzyme 2 region.				brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|cell-cell signaling (GO:0007267)|heart development (GO:0007507)|peptide hormone processing (GO:0016486)	cytoplasmic vesicle membrane (GO:0030659)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|methyltransferase activity (GO:0008168)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(13)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(4)	49	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			CCTACCACAGACCCATCCCAC	0.572																																					p.D206G		Atlas-SNP	.											.	ECE2	303	.	0			c.A617G						.						67	65	66					3																	183995039		2203	4300	6503	SO:0001630	splice_region_variant	9718	exon4			CCACAGACCCATC	AF428263	CCDS3255.1, CCDS33899.1, CCDS3256.2, CCDS43179.1, CCDS46969.1	3q27.1	2007-07-26			ENSG00000145194	ENSG00000145194			13275	protein-coding gene	gene with protein product		610145				11718899	Standard	NM_032331		Approved	KIAA0604, MGC2408	uc003fni.4	O60344	OTTHUMG00000150551	ENST00000402825.3:c.617-1A>G	chr3.hg19:g.183995039A>G		269.0	0.0		70.0	20.0	NM_014693	A5PLK8|Q6NTG7|Q6UW36|Q8NFD7|Q96NX3|Q96NX4|Q9BRZ8	Missense_Mutation	SNP	ENST00000402825.3	hg19	CCDS3256.2	.	.	.	.	.	.	.	.	.	.	A	14.47	2.544811	0.45280	.	.	ENSG00000145194	ENST00000402825;ENST00000359140;ENST00000404464;ENST00000357474;ENST00000430587	T;D;D;D;T	0.82803	-1.44;-1.64;-1.65;-1.65;-1.37	5.91	2.11	0.27256	.	0.392722	0.28958	N	0.013600	T	0.72598	0.3480	L	0.46157	1.445	0.54753	D	0.999985	B;B;B;B;B;B	0.11235	0.0;0.004;0.0;0.001;0.0;0.0	B;B;B;B;B;B	0.12837	0.003;0.008;0.001;0.008;0.0;0.002	T	0.62886	-0.6759	10	0.23891	T	0.37	.	6.0857	0.19966	0.7331:0.0:0.1432:0.1237	.	59;134;88;134;59;206	B4DKF3;B7Z1P1;O60344-2;O60344-5;O60344-3;O60344	.;.;.;.;.;ECE2_HUMAN	G	206;59;88;134;80	ENSP00000384223:D206G;ENSP00000352052:D59G;ENSP00000385846:D88G;ENSP00000350066:D134G;ENSP00000398444:D80G	ENSP00000350066:D134G	D	+	2	0	ECE2	185477733	0.617000	0.27043	1.000000	0.80357	0.993000	0.82548	0.818000	0.27295	1.073000	0.40885	0.533000	0.62120	GAC	.	.		0.572	ECE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318874.3	NM_014693	Missense_Mutation	G	183995039	A	G	183995039	5	3	285	1	0	0	0	0	0	0	1	0	4892	289	10	2	1195	2	ECE2	3	183995039	Splice_Site	SNP	A	TCGA-G3-A5SJ-01A-11D-A27I-10	785155	183995039	14027391	27	41936										
PCDH7	5099	hgsc.bcm.edu	37	chr4	30726026	30726026	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	ggcagtcctgacctggcaagGcattacaaatctagttcccc	9	13	1	1	rs370196952		TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr4:30726026G>T	ENST00000361762.2	+	1	3990	c.2982G>T	c.(2980-2982)agG>agT	p.R994S	PCDH7_ENST00000543491.1_Missense_Mutation_p.R994S	NM_002589.2	NP_002580.2	O60245	PCDH7_HUMAN	protocadherin 7	994					homophilic cell adhesion (GO:0007156)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(8)|liver(1)|lung(26)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	55						ACCTGGCAAGGCATTACAAAT	0.522																																					p.R994S		Atlas-SNP	.											.	PCDH7	215	.	0			c.G2982T						.	G	SER/ARG,SER/ARG,SER/ARG,SER/ARG	0,4406		0,0,2203	93	93	93		2982,2982,2982,2982	4.9	1	4		93	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	PCDH7	NM_001173523.1,NM_002589.2,NM_032456.2,NM_032457.3	110,110,110,110	0,1,6502	TT,TG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	994/1256,994/1070,994/1073,994/1248	30726026	1,13005	2203	4300	6503	SO:0001583	missense	5099	exon1			GGCAAGGCATTAC	AB006755	CCDS33971.1, CCDS75116.1	4p15	2014-06-13	2007-02-12			ENSG00000169851		"Cadherins / Protocadherins : Non-clustered"	8659	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 120"	602988	"BH-protocadherin (brain-heart)"			9615233	Standard	NM_002589		Approved	BH-Pcdh, PPP1R120	uc021xnd.1	O60245		ENST00000361762.2:c.2982G>T	chr4.hg19:g.30726026G>T	ENSP00000355243:p.Arg994Ser	222.0	0.0		100.0	36.0	NM_032457	O60246|O60247|Q4W5C4	Missense_Mutation	SNP	ENST00000361762.2	hg19	CCDS33971.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.44|14.44	2.535280|2.535280	0.45176|0.45176	0.0|0.0	1.16E-4|1.16E-4	ENSG00000169851|ENSG00000169851	ENST00000511884|ENST00000361762;ENST00000543491;ENST00000333135	.|T;T	.|0.39056	.|1.1;1.1	4.93|4.93	4.93|4.93	0.64822|0.64822	.|Protocadherin (1);	.|.	.|.	.|.	.|.	T|T	0.61714|0.61714	0.2369|0.2369	M|M	0.75615|0.75615	2.305|2.305	0.46167|0.46167	D|D	0.998904|0.998904	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.91635	.|0.999;0.99;0.999	T|T	0.64820|0.64820	-0.6317|-0.6317	5|9	.|0.87932	.|D	.|0	.|.	10.1696|10.1696	0.42902|0.42902	0.0769:0.1387:0.7844:0.0|0.0769:0.1387:0.7844:0.0	.|.	.|994;947;994	.|F5GWJ1;O60245-3;O60245	.|.;.;PCDH7_HUMAN	S|S	684|994;994;947	.|ENSP00000355243:R994S;ENSP00000441802:R994S	.|ENSP00000330302:R947S	A|R	+|+	1|3	0|2	PCDH7|PCDH7	30335124|30335124	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.951000|0.951000	0.60555|0.60555	2.256000|2.256000	0.43231|0.43231	2.567000|2.567000	0.86603|0.86603	0.561000|0.561000	0.74099|0.74099	GCA|AGG	.	.		0.522	PCDH7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360366.1	NM_032457, NM_002589		T	30726026	G	T	30726026	3	4	285	1	0	0	0	0	1	0	0	0	11525	1194	42	3	2984	3	PCDH7	4	30726026	Missense_Mutation	SNP	G	TCGA-G3-A5SJ-01A-11D-A27I-10		30726026	160428250	28	41937										
PDS5A	23244	hgsc.bcm.edu	37	chr4	39902096	39902096	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	gcgtacatggctccgaagcaTgttctgacacttccacattt	8	12	1	1			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr4:39902096T>C	ENST00000303538.8	-	14	2070	c.1531A>G	c.(1531-1533)Atg>Gtg	p.M511V	PDS5A_ENST00000503396.1_Missense_Mutation_p.M511V	NM_001100399.1	NP_001093869.1			PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae)											breast(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(14)|prostate(3)|skin(1)|urinary_tract(1)	39						CTCCGAAGCATGTTCTGACAC	0.358																																					p.M511V		Atlas-SNP	.											.	PDS5A	114	.	0			c.A1531G						.						68	66	67					4																	39902096		1922	4130	6052	SO:0001583	missense	23244	exon14			GAAGCATGTTCTG	AF294791	CCDS47045.1, CCDS54759.1	4p14	2007-06-20			ENSG00000121892	ENSG00000121892			29088	protein-coding gene	gene with protein product		613200				11076961, 15855230	Standard	NM_001100399		Approved	KIAA0648, PIG54, SCC-112	uc003guv.4	Q29RF7	OTTHUMG00000160582	ENST00000303538.8:c.1531A>G	chr4.hg19:g.39902096T>C	ENSP00000303427:p.Met511Val	93.0	0.0		34.0	16.0	NM_001100399		Missense_Mutation	SNP	ENST00000303538.8	hg19	CCDS47045.1	.	.	.	.	.	.	.	.	.	.	T	7.930	0.740385	0.15642	.	.	ENSG00000121892	ENST00000303538;ENST00000503396	T;T	0.66815	-0.06;-0.23	5.75	4.52	0.55395	Armadillo-like helical (1);Armadillo-type fold (1);	0.038952	0.85682	D	0.000000	T	0.61602	0.2360	L	0.35414	1.06	0.52501	D	0.999956	B;B	0.32302	0.003;0.363	B;B	0.42030	0.01;0.373	T	0.58691	-0.7592	9	.	.	.	-17.1339	14.1948	0.65662	0.0:0.0:0.1326:0.8674	.	511;511	Q29RF7-3;Q29RF7	.;PDS5A_HUMAN	V	511	ENSP00000303427:M511V;ENSP00000426749:M511V	.	M	-	1	0	PDS5A	39578491	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.196000	0.58407	2.196000	0.70406	0.402000	0.26972	ATG	.	.		0.358	PDS5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361287.1	NM_015200		C	39902096	T	C	39902096	3	2	285	1	0	0	0	0	1	0	0	0	11700	1464	51	2	2595	2	PDS5A	4	39902096	Missense_Mutation	SNP	T	TCGA-G3-A5SJ-01A-11D-A27I-10	9176070	39902096	151252180	29	41938										
ANKRD17	26057	hgsc.bcm.edu	37	chr4	74008379	74008379	+	Frame_Shift_Del	DEL	G	G	-													0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	tcaaacggtgagtaggatctGccccatgagccaaaagtagt							TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr4:74008379delG	ENST00000358602.4	-	12	2179	c.2063delC	c.(2062-2064)gcafs	p.A688fs	ANKRD17_ENST00000330838.6_Frame_Shift_Del_p.A688fs|ANKRD17_ENST00000509867.2_Frame_Shift_Del_p.A575fs|ANKRD17_ENST00000514252.1_5'UTR	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	688					blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			AGTAGGATCTGCCCCATGAGC	0.413																																					p.A688fs		Atlas-Indel,Pindel	.											.	ANKRD17	214	.	0			c.2064delA						.						130	122	125					4																	74008379		2203	4300	6503	SO:0001589	frameshift_variant	26057	exon12			.	AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"Ankyrin repeat domain containing"	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.2063delC	chr4.hg19:g.74008379delG	ENSP00000351416:p.Ala688fs	81.0	0.0		53.0	19.0	NM_198889	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Frame_Shift_Del	DEL	ENST00000358602.4	hg19	CCDS34004.1																																																																																			.	.		0.413	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217		-	74008379	G	-	74008379	7	5	285	1	0	1	0	1	0	0	0	0	646	1319	46	0	5840	0	ANKRD17	4	74008379	Frame_Shift_Del	DEL	G	TCGA-G3-A5SJ-01A-11D-A27I-10	34106283	74008379	117145897	30	41939	220	2								
ANKRD17	26057	hgsc.bcm.edu	37	chr4	74008384	74008384	+	Missense_Mutation	SNP	A	A	C													0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	cggtgagtaggatctgccccAtgagccaaaagtagttccac							TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr4:74008384A>C	ENST00000358602.4	-	12	2174	c.2058T>G	c.(2056-2058)caT>caG	p.H686Q	ANKRD17_ENST00000330838.6_Missense_Mutation_p.H686Q|ANKRD17_ENST00000509867.2_Missense_Mutation_p.H573Q|ANKRD17_ENST00000514252.1_5'UTR	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	686					blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GATCTGCCCCATGAGCCAAAA	0.428																																					p.H686Q		Atlas-SNP	.											.	ANKRD17	214	.	0			c.T2058G						.						129	121	124					4																	74008384		2203	4300	6503	SO:0001583	missense	26057	exon12			TGCCCCATGAGCC	AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"Ankyrin repeat domain containing"	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.2058T>G	chr4.hg19:g.74008384A>C	ENSP00000351416:p.His686Gln	93.0	0.0		57.0	20.0	NM_198889	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Missense_Mutation	SNP	ENST00000358602.4	hg19	CCDS34004.1	.	.	.	.	.	.	.	.	.	.	A	17.29	3.352546	0.61293	.	.	ENSG00000132466	ENST00000358602;ENST00000426990;ENST00000330838;ENST00000509867;ENST00000411811	T;T;T	0.64803	-0.12;-0.12;-0.12	5.94	-0.537	0.11872	Ankyrin repeat-containing domain (4);	0.000000	0.64402	D	0.000001	T	0.62877	0.2464	L	0.41824	1.3	0.27141	N	0.961652	D;B;P;P;P	0.65815	0.995;0.298;0.936;0.558;0.596	D;B;P;B;B	0.79784	0.993;0.234;0.698;0.444;0.316	T	0.58989	-0.7538	10	0.07325	T	0.83	.	11.5297	0.50601	0.6329:0.0:0.3671:0.0	.	207;686;686;686;573	B4DR08;O75179-2;G5E964;O75179;E7EUV3	.;.;.;ANR17_HUMAN;.	Q	686;686;686;573;686	ENSP00000351416:H686Q;ENSP00000332265:H686Q;ENSP00000427151:H573Q	ENSP00000332265:H686Q	H	-	3	2	ANKRD17	74227248	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	0.772000	0.26647	-0.064000	0.13043	-0.287000	0.09952	CAT	.	.		0.428	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217		C	74008384	A	C	74008384	3	2	285	1	0	0	0	0	1	0	0	0	646	214	8	5	5845	5	ANKRD17	4	74008384	Missense_Mutation	SNP	A	TCGA-G3-A5SJ-01A-11D-A27I-10	5	74008384	117145892	31	41940	220	2								
PTPN13	5783	hgsc.bcm.edu	37	chr4	87655497	87655497	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	atcctgacttaaaattaaccAaagtggccccagagggatgg	10	9	0	2			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr4:87655497A>G	ENST00000411767.2	+	13	1963	c.1900A>G	c.(1900-1902)Aaa>Gaa	p.K634E	PTPN13_ENST00000427191.2_Missense_Mutation_p.K634E|PTPN13_ENST00000316707.6_Missense_Mutation_p.K634E|PTPN13_ENST00000511467.1_Missense_Mutation_p.K634E|PTPN13_ENST00000436978.1_Missense_Mutation_p.K634E			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	634	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		AAAATTAACCAAAGTGGCCCC	0.284																																					p.K634E		Atlas-SNP	.											.	PTPN13	203	.	0			c.A1900G						.						51	49	49					4																	87655497		1788	4052	5840	SO:0001583	missense	5783	exon13			TTAACCAAAGTGG		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.1900A>G	chr4.hg19:g.87655497A>G	ENSP00000407249:p.Lys634Glu	105.0	0.0		38.0	10.0	NM_006264	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	hg19	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.753677	0.89753	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T;T	0.76060	-0.99;-0.99;-0.99;-0.99;-0.99	5.99	5.99	0.97316	FERM, N-terminal (1);Band 4.1 domain (1);FERM domain (1);	0.000000	0.52532	D	0.000067	D	0.85600	0.5734	M	0.71296	2.17	0.80722	D	1	P;D;D;D	0.89917	0.675;1.0;1.0;1.0	P;D;D;D	0.91635	0.733;0.999;0.999;0.999	D	0.86184	0.1608	10	0.54805	T	0.06	.	16.4943	0.84223	1.0:0.0:0.0:0.0	.	634;634;634;634	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	E	634;634;634;634;634;602	ENSP00000408368:K634E;ENSP00000394794:K634E;ENSP00000322675:K634E;ENSP00000407249:K634E;ENSP00000426626:K634E	ENSP00000322675:K634E	K	+	1	0	PTPN13	87874521	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.942000	0.92970	2.291000	0.77112	0.533000	0.62120	AAA	.	.		0.284	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			G	87655497	A	G	87655497	3	3	285	1	0	0	0	0	1	0	0	0	12795	131	5	2	1946	2	PTPN13	4	87655497	Missense_Mutation	SNP	A	TCGA-G3-A5SJ-01A-11D-A27I-10	13647113	87655497	103498779	32	41941										
GPRIN3	285513	hgsc.bcm.edu	37	chr4	90171127	90171127	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	gcaggggcacctgaaaagccAttggcattcttacacaggag	12	10	1	1	rs372513468	byFrequency	TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr4:90171127A>G	ENST00000609438.1	-	2	653	c.135T>C	c.(133-135)aaT>aaC	p.N45N	GPRIN3_ENST00000333209.4_Silent_p.N45N	NM_198281.2	NP_938022.2	Q6ZVF9	GRIN3_HUMAN	GPRIN family member 3	45										breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|prostate(2)|skin(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;5.67e-05)		CTGAAAAGCCATTGGCATTCT	0.557													A|||	2	0.000399361	0	0.0029	5008	,	,		19140	0		0	False		,,,				2504	0				p.N45N		Atlas-SNP	.											.	GPRIN3	90	.	0			c.T135C						.	A		1,4405	2.1+/-5.4	0,1,2202	62	64	63		135	2.8	1	4		63	0,8600		0,0,4300	no	coding-synonymous	GPRIN3	NM_198281.2		0,1,6502	GG,GA,AA		0.0,0.0227,0.0077		45/777	90171127	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	285513	exon2			AAAGCCATTGGCA	AK124616	CCDS34030.1	4q22.1	2006-08-24				ENSG00000185477			27733	protein-coding gene	gene with protein product		611241				15488195	Standard	NM_198281		Approved	GRIN3, FLJ42625	uc003hsm.1	Q6ZVF9		ENST00000609438.1:c.135T>C	chr4.hg19:g.90171127A>G		141.0	0.0		62.0	23.0	NM_198281	Q8IVE4	Silent	SNP	ENST00000609438.1	hg19	CCDS34030.1																																																																																			.	.		0.557	GPRIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363540.2	NM_198281		G	90171127	A	G	90171127	2	3	285	1	0	0	0	0	0	0	0	1	6740	214	8	2		2	GPRIN3	4	90171127	Silent	SNP	A	TCGA-G3-A5SJ-01A-11D-A27I-10	2515630	90171127	100983149	33	41942										
HHIP	64399	hgsc.bcm.edu	37	chr4	145568034	145568034	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	agtgggggagagatgctgtgCggtggcttctaccctcggct	17	9	1	1	rs200359445		TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr4:145568034C>T	ENST00000296575.3	+	1	862	c.207C>T	c.(205-207)tgC>tgT	p.C69C	HHIP-AS1_ENST00000508269.1_RNA|HHIP_ENST00000434550.2_Silent_p.C69C|HHIP-AS1_ENST00000512359.1_RNA|HHIP-AS1_ENST00000503066.1_RNA	NM_022475.2	NP_071920.1	Q96QV1	HHIP_HUMAN	hedgehog interacting protein	69					carbohydrate metabolic process (GO:0005975)|dorsal/ventral pattern formation (GO:0009953)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|negative regulation of signal transduction (GO:0009968)|negative regulation of smoothened signaling pathway (GO:0045879)|neuroblast proliferation (GO:0007405)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|skeletal system morphogenesis (GO:0048705)|smoothened signaling pathway (GO:0007224)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	hedgehog family protein binding (GO:0097108)|oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	33	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0185)		AGATGCTGTGCGGTGGCTTCT	0.632																																					p.C69C		Atlas-SNP	.											.	HHIP	100	.	0			c.C207T						.						66	70	68					4																	145568034		2203	4300	6503	SO:0001819	synonymous_variant	64399	exon1			GCTGTGCGGTGGC	AK024645	CCDS3762.1	4q31.21-q31.3	2008-08-29	2001-11-29		ENSG00000164161	ENSG00000164161			14866	protein-coding gene	gene with protein product		606178	"hedgehog-interacting protein"			11435703, 11731473	Standard	NM_022475		Approved	HIP, FLJ20992	uc003ijs.2	Q96QV1	OTTHUMG00000161428	ENST00000296575.3:c.207C>T	chr4.hg19:g.145568034C>T		195.0	0.0		72.0	4.0	NM_022475	Q6PK09|Q8NCI7|Q9BXK3|Q9H1J4|Q9H7E7	Silent	SNP	ENST00000296575.3	hg19	CCDS3762.1																																																																																			.	.		0.632	HHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364887.2			T	145568034	C	T	145568034	2	4	285	1	0	0	0	0	0	0	0	1	7101	776	27	1		1	HHIP	4	145568034	Silent	SNP	C	TCGA-G3-A5SJ-01A-11D-A27I-10	55396907	145568034	45586242	34	41943										
IQGAP2	10788	hgsc.bcm.edu	37	chr5	75888748	75888748	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	aggcaatattaataaagtcaAcagtaagtaatggatcgtat	8	4	1	0			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr5:75888748A>G	ENST00000274364.6	+	9	1202	c.905A>G	c.(904-906)aAc>aGc	p.N302S	IQGAP2_ENST00000379730.3_5'UTR	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	302					negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		AATAAAGTCAACAGTAAGTAA	0.353																																					p.N302S		Atlas-SNP	.											.	IQGAP2	186	.	0			c.A905G						.						144	154	151					5																	75888748		2203	4300	6503	SO:0001583	missense	10788	exon9			AAGTCAACAGTAA	U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.905A>G	chr5.hg19:g.75888748A>G	ENSP00000274364:p.Asn302Ser	336.0	0.0		165.0	49.0	NM_006633	A8K4V1|B7Z8A4|J3KR91	Missense_Mutation	SNP	ENST00000274364.6	hg19	CCDS34188.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.403643	0.83230	.	.	ENSG00000145703	ENST00000274364;ENST00000514350;ENST00000505766	T;T;T	0.48522	4.06;0.81;4.07	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.65760	0.2722	M	0.88570	2.965	0.80722	D	1	P	0.35714	0.517	P	0.45071	0.468	T	0.70880	-0.4752	10	0.66056	D	0.02	-21.7424	16.2537	0.82501	1.0:0.0:0.0:0.0	.	302	Q13576	IQGA2_HUMAN	S	302;275;252	ENSP00000274364:N302S;ENSP00000423672:N275S;ENSP00000421097:N252S	ENSP00000274364:N302S	N	+	2	0	IQGAP2	75924504	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	9.273000	0.95719	2.244000	0.73946	0.529000	0.55759	AAC	.	.		0.353	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633		G	75888748	A	G	75888748	3	3	285	1	0	0	0	0	1	0	0	0	7824	43	2	2	939	2	IQGAP2	5	75888748	Missense_Mutation	SNP	A	TCGA-G3-A5SJ-01A-11D-A27I-10		75888748	105026512	35	41944										
SRA1	8637	hgsc.bcm.edu	37	chr5	139930368	139930368	+	IGR	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	ttcattggctgcctcctctgAaaacagactcctcttttctg	6	13	4	2			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr5:139930368A>G	ENST00000310331.2	+	0	691				SRA1_ENST00000520427.1_5'UTR|SRA1_ENST00000336283.6_Missense_Mutation_p.S210P	NM_003732.2	NP_003723.1	O60516	4EBP3_HUMAN	eukaryotic translation initiation factor 4E binding protein 3						negative regulation of translational initiation (GO:0045947)	eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	translation repressor activity (GO:0030371)			endometrium(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCCTCCTCTGAAAACAGACTC	0.488																																					p.S210P		Atlas-SNP	.											.	SRA1	24	.	0			c.T628C						.						123	128	126					5																	139930368		2203	4300	6503	SO:0001628	intergenic_variant	10011	exon5			CCTCTGAAAACAG	AF038869	CCDS4226.1	5q31.3	2007-07-18			ENSG00000243056	ENSG00000243056			3290	protein-coding gene	gene with protein product		603483				9593750	Standard	NM_003732		Approved	4E-BP3	uc003lfy.1	O60516	OTTHUMG00000129498		chr5.hg19:g.139930368A>G		225.0	0.0		95.0	4.0	NM_001035235		Missense_Mutation	SNP	ENST00000310331.2	hg19	CCDS4226.1	.	.	.	.	.	.	.	.	.	.	A	16.90	3.250183	0.59212	.	.	ENSG00000213523	ENST00000336283;ENST00000520427	T	0.46063	0.88	5.74	4.52	0.55395	.	0.177394	0.38492	U	0.001664	T	0.31420	0.0796	L	0.42581	1.335	0.35534	D	0.802491	B	0.25007	0.116	B	0.28011	0.085	T	0.33828	-0.9853	9	.	.	.	.	5.933	0.19150	0.6556:0.14:0.0:0.2043	.	210	Q9HD15	SRA1_HUMAN	P	210;136	ENSP00000337513:S210P	.	S	-	1	0	SRA1	139910552	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	0.533000	0.23082	2.194000	0.70268	0.460000	0.39030	TCA	.	.		0.488	EIF4EBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251668.2	NM_003732		G	139930368	A	G	139930368	1	3	285	0	1	0	0	0	0	0	0	0	15147	246	9	2		2	SRA1	5	139930368	IGR	SNP	A	TCGA-G3-A5SJ-01A-11D-A27I-10	64041620	139930368	40984892	36	41945										
GPRIN1	114787	hgsc.bcm.edu	37	chr5	176024063	176024063	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	cacctccatggcggcgccgtAtacctcccacgtcatgccct	8	19	1	0			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr5:176024063A>G	ENST00000303991.4	-	2	2950	c.2773T>C	c.(2773-2775)Tac>Cac	p.Y925H		NM_052899.2	NP_443131.2	Q7Z2K8	GRIN1_HUMAN	G protein regulated inducer of neurite outgrowth 1	925	Interaction with GNAO1. {ECO:0000250}.				neuron projection development (GO:0031175)	cell projection (GO:0042995)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCGGCGCCGTATACCTCCCAC	0.726																																					p.Y925H		Atlas-SNP	.											.	GPRIN1	77	.	0			c.T2773C						.						50	52	52					5																	176024063		1732	3345	5077	SO:0001583	missense	114787	exon2			CGCCGTATACCTC	AB067480	CCDS4405.1	5q35.2	2008-02-05			ENSG00000169258	ENSG00000169258			24835	protein-coding gene	gene with protein product		611239				11572484	Standard	NM_052899		Approved	GRIN1, KIAA1893	uc003meo.1	Q7Z2K8	OTTHUMG00000130659	ENST00000303991.4:c.2773T>C	chr5.hg19:g.176024063A>G	ENSP00000305839:p.Tyr925His	21.0	0.0		18.0	8.0	NM_052899	C9JM70|Q8ND74|Q96PZ4	Missense_Mutation	SNP	ENST00000303991.4	hg19	CCDS4405.1	.	.	.	.	.	.	.	.	.	.	A	19.14	3.770534	0.69992	.	.	ENSG00000169258	ENST00000303991	T	0.55052	0.54	3.78	3.78	0.43462	.	.	.	.	.	T	0.64692	0.2621	L	0.48642	1.525	0.34637	D	0.720244	D	0.89917	1.0	D	0.87578	0.998	T	0.74487	-0.3649	9	0.66056	D	0.02	-2.8596	12.4842	0.55863	1.0:0.0:0.0:0.0	.	925	Q7Z2K8	GRIN1_HUMAN	H	925	ENSP00000305839:Y925H	ENSP00000305839:Y925H	Y	-	1	0	GPRIN1	175956669	1.000000	0.71417	0.998000	0.56505	0.853000	0.48598	8.446000	0.90329	1.338000	0.45544	0.260000	0.18958	TAC	.	.		0.726	GPRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253149.1	NM_052899		G	176024063	A	G	176024063	3	3	285	1	0	0	0	0	1	0	0	0	6738	449	16	2	257	2	GPRIN1	5	176024063	Missense_Mutation	SNP	A	TCGA-G3-A5SJ-01A-11D-A27I-10	36093695	176024063	4891197	37	41946										
NSD1	64324	hgsc.bcm.edu	37	chr5	176562395	176562395	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	gctgatggatcagaatccttTcaagaccctgaaaaaagtga	9	8	2	5			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr5:176562395T>G	ENST00000439151.2	+	2	336	c.291T>G	c.(289-291)ttT>ttG	p.F97L	NSD1_ENST00000361032.4_Missense_Mutation_p.F97L|NSD1_ENST00000511258.1_Intron|NSD1_ENST00000354179.4_Intron|NSD1_ENST00000347982.4_Intron	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	97					gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		CAGAATCCTTTCAAGACCCTG	0.443			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.F97L		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.T291G						.						83	81	81					5																	176562395		2203	4300	6503	SO:0001583	missense	64324	exon2	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	ATCCTTTCAAGAC	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	14234	protein-coding gene	gene with protein product		606681	"Sotos syndrome"	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.291T>G	chr5.hg19:g.176562395T>G	ENSP00000395929:p.Phe97Leu	142.0	0.0		51.0	16.0	NM_022455	Q96PD8|Q96RN7	Missense_Mutation	SNP	ENST00000439151.2	hg19	CCDS4412.1	.	.	.	.	.	.	.	.	.	.	T	8.137	0.784459	0.16189	.	.	ENSG00000165671	ENST00000439151;ENST00000361032	D;D	0.92149	-2.92;-2.98	5.23	4.07	0.47477	.	0.116384	0.39544	N	0.001335	T	0.79656	0.4483	N	0.08118	0	0.80722	D	1	B;B;B	0.11235	0.004;0.002;0.004	B;B;B	0.09377	0.004;0.002;0.003	T	0.69168	-0.5216	10	0.23302	T	0.38	.	5.3626	0.16095	0.0:0.0892:0.1775:0.7333	.	97;97;97	Q96L73-3;Q96L73;Q6PJ64	.;NSD1_HUMAN;.	L	97	ENSP00000395929:F97L;ENSP00000354310:F97L	ENSP00000354310:F97L	F	+	3	2	NSD1	176495001	1.000000	0.71417	1.000000	0.80357	0.144000	0.21451	1.836000	0.39191	1.008000	0.39264	0.454000	0.30748	TTT	.	.		0.443	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349		G	176562395	T	G	176562395	3	3	285	1	0	0	0	0	1	0	0	0	10678	1780	62	5	293	5	NSD1	5	176562395	Missense_Mutation	SNP	T	TCGA-G3-A5SJ-01A-11D-A27I-10	538332	176562395	4352865	38	41947										
DDAH2	23564	hgsc.bcm.edu	37	chr6	31695402	31695402	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	acccaggacgaagaaagagaCagtcagcagctgcgtcatct	11	11	3	2			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr6:31695402C>G	ENST00000375789.2	-	5	1289	c.659G>C	c.(658-660)tGt>tCt	p.C220S	DDAH2_ENST00000375792.3_Missense_Mutation_p.C220S|DDAH2_ENST00000375787.2_Missense_Mutation_p.C220S|DDAH2_ENST00000480913.1_5'UTR			O95865	DDAH2_HUMAN	dimethylarginine dimethylaminohydrolase 2	220					arginine catabolic process (GO:0006527)|citrulline metabolic process (GO:0000052)|negative regulation of apoptotic process (GO:0043066)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of nitric oxide biosynthetic process (GO:0045429)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|catalytic activity (GO:0003824)|dimethylargininase activity (GO:0016403)			endometrium(1)|large_intestine(3)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	11					L-Citrulline(DB00155)	AAGAAAGAGACAGTCAGCAGC	0.582																																					p.C220S		Atlas-SNP	.											.	DDAH2	15	.	0			c.G659C						.						185	159	168					6																	31695402		1511	2709	4220	SO:0001583	missense	23564	exon6			AAGAGACAGTCAG	AF070667	CCDS4718.1	6p21	2010-02-17			ENSG00000213722	ENSG00000213722	3.5.3.18		2716	protein-coding gene	gene with protein product		604744				10493931	Standard	XM_005248974		Approved		uc003nwq.3	O95865	OTTHUMG00000031212	ENST00000375789.2:c.659G>C	chr6.hg19:g.31695402C>G	ENSP00000364945:p.Cys220Ser	253.0	0.0		88.0	21.0	NM_013974	A2BEZ7	Missense_Mutation	SNP	ENST00000375789.2	hg19	CCDS4718.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.773911	0.90108	.	.	ENSG00000213722	ENST00000437288;ENST00000375789;ENST00000375787;ENST00000375792;ENST00000416410;ENST00000436437	.	.	.	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.72977	0.3528	M	0.67625	2.065	0.58432	D	0.999996	D	0.65815	0.995	D	0.91635	0.999	T	0.74999	-0.3472	9	0.62326	D	0.03	-14.2334	15.8242	0.78686	0.0:1.0:0.0:0.0	.	220	O95865	DDAH2_HUMAN	S	109;220;220;220;220;220	.	ENSP00000364943:C220S	C	-	2	0	DDAH2	31803381	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.424000	0.66464	2.586000	0.87340	0.655000	0.94253	TGT	.	.		0.582	DDAH2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076432.2			G	31695402	C	G	31695402	3	3	285	1	0	0	0	0	1	0	0	0	4324	478	17	4	206	4	DDAH2	6	31695402	Missense_Mutation	SNP	C	TCGA-G3-A5SJ-01A-11D-A27I-10		31695402	139419665	39	41948										
ZNF451	26036	hgsc.bcm.edu	37	chr6	57011983	57011983	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	aagaggttattgtccagattGcaatcaagtctttgtggatg	11	5	2	2			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr6:57011983G>T	ENST00000370706.4	+	10	1344	c.1100G>T	c.(1099-1101)tGc>tTc	p.C367F	RP11-203B9.4_ENST00000591553.1_RNA|RP11-203B9.4_ENST00000589549.1_RNA|ZNF451_ENST00000491832.2_Missense_Mutation_p.C367F|RP11-203B9.4_ENST00000587815.1_RNA|RP11-203B9.4_ENST00000586432.1_RNA|RP11-203B9.4_ENST00000586053.1_RNA|RP11-203B9.4_ENST00000588811.1_RNA|RP11-203B9.4_ENST00000585792.1_RNA|RP11-203B9.4_ENST00000592500.1_RNA|RP11-203B9.4_ENST00000416069.2_RNA|RP11-203B9.4_ENST00000592038.1_RNA|RP11-203B9.4_ENST00000586668.1_RNA|ZNF451_ENST00000357489.3_Missense_Mutation_p.C367F	NM_001031623.2	NP_001026794.1	Q9Y4E5	ZN451_HUMAN	zinc finger protein 451	367					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32	Lung NSC(77;0.145)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			TGTCCAGATTGCAATCAAGTC	0.408																																					p.C367F		Atlas-SNP	.											.	ZNF451	181	.	0			c.G1100T						.						91	86	88					6																	57011983		2203	4300	6503	SO:0001583	missense	26036	exon10			CAGATTGCAATCA	AB011148	CCDS4960.1, CCDS43477.1, CCDS59026.1	6p12.1	2012-08-08			ENSG00000112200	ENSG00000112200		"Zinc fingers, C2H2-type"	21091	protein-coding gene	gene with protein product		615708				9628581	Standard	NM_001031623		Approved	KIAA0576, COASTER, dJ417I1.1, KIAA1702	uc003pdm.2	Q9Y4E5	OTTHUMG00000014916	ENST00000370706.4:c.1100G>T	chr6.hg19:g.57011983G>T	ENSP00000359740:p.Cys367Phe	172.0	0.0		84.0	19.0	NM_001031623	Q5VVE9|Q5VVF1|Q86YE4|Q8N380|Q8TD15|Q9C0G1|Q9NQM1	Missense_Mutation	SNP	ENST00000370706.4	hg19	CCDS43477.1	.	.	.	.	.	.	.	.	.	.	G	19.42	3.824012	0.71143	.	.	ENSG00000112200	ENST00000370706;ENST00000357489;ENST00000491832	T;T;T	0.08008	3.14;3.14;3.14	5.6	5.6	0.85130	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	0.000000	0.85682	D	0.000000	T	0.24699	0.0599	M	0.74881	2.28	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;0.999	D;D;D;D	0.91635	0.999;0.998;0.999;0.998	T	0.01259	-1.1403	10	0.87932	D	0	-7.5559	19.6177	0.95640	0.0:0.0:1.0:0.0	.	367;367;367;367	Q9Y4E5-2;Q9Y4E5;E9PH99;Q4KMR5	.;ZN451_HUMAN;.;.	F	367	ENSP00000359740:C367F;ENSP00000350083:C367F;ENSP00000421645:C367F	ENSP00000350083:C367F	C	+	2	0	ZNF451	57119942	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.321000	0.89997	2.632000	0.89209	0.650000	0.86243	TGC	.	.		0.408	ZNF451-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041035.2	NM_015555		T	57011983	G	T	57011983	3	4	285	1	0	0	0	0	1	0	0	0	17937	1319	46	3	1138	3	ZNF451	6	57011983	Missense_Mutation	SNP	G	TCGA-G3-A5SJ-01A-11D-A27I-10	25316581	57011983	114103084	40	41949										
PGM3	5238	hgsc.bcm.edu	37	chr6	83881724	83881724	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	ctgttgtacagtcaagccctTcagagccaagattgcttcaa	8	11	3	2			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr6:83881724T>G	ENST00000283977.4	-	10	1180	c.1054A>C	c.(1054-1056)Aag>Cag	p.K352Q	PGM3_ENST00000512866.1_Missense_Mutation_p.K433Q|PGM3_ENST00000506587.1_Missense_Mutation_p.K461Q|PGM3_ENST00000513973.1_Missense_Mutation_p.K433Q					phosphoglucomutase 3											NS(1)|breast(1)|endometrium(2)|large_intestine(4)|lung(6)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	18		all_cancers(76;0.000504)|Acute lymphoblastic leukemia(125;3.85e-06)|all_hematologic(105;0.0017)|all_epithelial(107;0.068)		BRCA - Breast invasive adenocarcinoma(397;0.0478)		GTCAAGCCCTTCAGAGCCAAG	0.408																																					p.K461Q		Atlas-SNP	.											.	PGM3	39	.	0			c.A1381C						.						135	118	124					6																	83881724		2203	4300	6503	SO:0001583	missense	5238	exon12			AGCCCTTCAGAGC	BC001258	CCDS4997.1, CCDS56435.1, CCDS56436.1, CCDS75487.1	6q14.1-q15	2012-10-02			ENSG00000013375	ENSG00000013375	5.4.2.3		8907	protein-coding gene	gene with protein product	"acetylglucosamine phosphomutase"	172100				12174217, 10721701	Standard	NM_001199917		Approved	AGM1, DKFZP434B187, PAGM	uc011dyz.2	O95394	OTTHUMG00000015110	ENST00000283977.4:c.1054A>C	chr6.hg19:g.83881724T>G	ENSP00000283977:p.Lys352Gln	137.0	0.0		37.0	9.0	NM_001199917		Missense_Mutation	SNP	ENST00000283977.4	hg19		.	.	.	.	.	.	.	.	.	.	T	25.3	4.625256	0.87560	.	.	ENSG00000013375	ENST00000513973;ENST00000512866;ENST00000283977;ENST00000506587;ENST00000509219	T;T;T;T;T	0.47528	0.86;0.86;0.88;0.86;0.84	5.93	5.93	0.95920	.	0.084314	0.85682	D	0.000000	T	0.34337	0.0894	M	0.67700	2.07	0.58432	D	0.999998	P;P;B	0.38048	0.616;0.485;0.301	B;B;B	0.34242	0.178;0.15;0.062	T	0.28038	-1.0056	10	0.37606	T	0.19	-12.8053	16.3839	0.83495	0.0:0.0:0.0:1.0	.	461;461;433	E9PF86;B4DX94;O95394	.;.;AGM1_HUMAN	Q	433;433;352;461;64	ENSP00000424874:K433Q;ENSP00000421565:K433Q;ENSP00000283977:K352Q;ENSP00000425809:K461Q;ENSP00000423389:K64Q	ENSP00000283977:K352Q	K	-	1	0	PGM3	83938443	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.698000	0.84413	2.258000	0.74832	0.533000	0.62120	AAG	.	.		0.408	PGM3-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000366385.2	NM_015599		G	83881724	T	G	83881724	3	3	285	1	0	0	0	0	1	0	0	0	11809	1792	62	5	343	5	PGM3	6	83881724	Missense_Mutation	SNP	T	TCGA-G3-A5SJ-01A-11D-A27I-10	26869741	83881724	87233343	41	41950										
PRDM1	639	hgsc.bcm.edu	37	chr6	106554333	106554333	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	agctcgcccacctgcagaaaCactacctggtacacacggga	9	15	0	1			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr6:106554333C>T	ENST00000369096.4	+	6	2095	c.1861C>T	c.(1861-1863)Cac>Tac	p.H621Y	PRDM1_ENST00000369091.2_Missense_Mutation_p.H585Y|PRDM1_ENST00000369089.3_Missense_Mutation_p.H487Y	NM_001198.3	NP_001189.2	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain	621					cell fate commitment (GO:0045165)|eye photoreceptor cell development (GO:0042462)|germ cell development (GO:0007281)|intestinal epithelial cell development (GO:0060576)|maternal placenta development (GO:0001893)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gene expression (GO:0010628)|post-embryonic development (GO:0009791)|transcription, DNA-templated (GO:0006351)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(59)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(5)|urinary_tract(2)	94	Breast(9;0.022)	all_cancers(87;2.2e-31)|all_epithelial(87;2.03e-21)|Acute lymphoblastic leukemia(125;4.99e-11)|all_lung(197;7.55e-09)|all_hematologic(75;5.82e-08)|Lung NSC(302;1.28e-06)|Colorectal(196;0.0112)|Ovarian(999;0.0365)		all cancers(137;1.83e-46)|Epithelial(106;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(136;1.99e-20)|GBM - Glioblastoma multiforme(226;3.72e-11)|BRCA - Breast invasive adenocarcinoma(108;1.38e-05)		CCTGCAGAAACACTACCTGGT	0.512			"D, N, Mis, F, S"		DLBCL																																p.H621Y		Atlas-SNP	.		Rec	yes		6	6q21	639	"PR domain containing 1, with ZNF domain"		L	.	PRDM1	195	.	0			c.C1861T						.						125	103	110					6																	106554333		2203	4300	6503	SO:0001583	missense	639	exon6			CAGAAACACTACC		CCDS5054.2, CCDS34505.1	6q21	2013-01-08			ENSG00000057657	ENSG00000057657		"Zinc fingers, C2H2-type"	9346	protein-coding gene	gene with protein product		603423		BLIMP1		1851123	Standard	NM_001198		Approved	PRDI-BF1	uc003prd.2	O75626	OTTHUMG00000015299	ENST00000369096.4:c.1861C>T	chr6.hg19:g.106554333C>T	ENSP00000358092:p.His621Tyr	220.0	0.0		85.0	36.0	NM_001198	B2REA6|E1P5E0|Q86WM7	Missense_Mutation	SNP	ENST00000369096.4	hg19	CCDS5054.2	.	.	.	.	.	.	.	.	.	.	C	32	5.118073	0.94385	.	.	ENSG00000057657	ENST00000369091;ENST00000369096;ENST00000456278;ENST00000369089	D;D;D	0.86769	-2.17;-2.17;-2.17	5.44	5.44	0.79542	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.044901	0.85682	D	0.000000	D	0.95959	0.8684	H	0.97291	3.975	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.97110	0.993;1.0	D	0.97286	0.9921	10	0.87932	D	0	-34.9218	18.0362	0.89303	0.0:1.0:0.0:0.0	.	487;621	Q86WM7;O75626	.;PRDM1_HUMAN	Y	585;621;584;487	ENSP00000358087:H585Y;ENSP00000358092:H621Y;ENSP00000358085:H487Y	ENSP00000358085:H487Y	H	+	1	0	PRDM1	106661026	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.692000	0.84203	2.569000	0.86673	0.655000	0.94253	CAC	.	.		0.512	PRDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041661.3			T	106554333	C	T	106554333	3	4	285	1	0	0	0	0	1	0	0	0	12462	478	17	3	1896	3	PRDM1	6	106554333	Missense_Mutation	SNP	C	TCGA-G3-A5SJ-01A-11D-A27I-10	22672609	106554333	64560734	42	41951										
BCLAF1	9774	hgsc.bcm.edu	37	chr6	136599396	136599396	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	caggccaaatatcaccggatGtggctgatgacttattaaat	9	8	1	2			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr6:136599396G>T	ENST00000531224.1	-	4	875	c.623C>A	c.(622-624)aCa>aAa	p.T208K	BCLAF1_ENST00000530767.1_Missense_Mutation_p.T208K|BCLAF1_ENST00000527536.1_Missense_Mutation_p.T208K|BCLAF1_ENST00000392348.2_Missense_Mutation_p.T206K|BCLAF1_ENST00000353331.4_Missense_Mutation_p.T206K|BCLAF1_ENST00000527759.1_Missense_Mutation_p.T206K	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1	208					apoptotic process (GO:0006915)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA-templated transcription, initiation (GO:2000144)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of response to DNA damage stimulus (GO:2001022)|regulation of DNA-templated transcription in response to stress (GO:0043620)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			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)		ATCACCGGATGTGGCTGATGA	0.423																																					p.T208K	Colon(142;1534 1789 5427 7063 28491)	Atlas-SNP	.											.	BCLAF1	203	.	0			c.C623A						.						269	258	262					6																	136599396		2203	4300	6503	SO:0001583	missense	9774	exon4			CCGGATGTGGCTG	AF249273	CCDS5177.1, CCDS47485.1, CCDS47486.1, CCDS75525.1	6q22-q23	2007-03-02			ENSG00000029363	ENSG00000029363			16863	protein-coding gene	gene with protein product		612588				8724849, 10330179	Standard	NM_001077440		Approved	KIAA0164, BTF	uc003qgx.1	Q9NYF8	OTTHUMG00000033323	ENST00000531224.1:c.623C>A	chr6.hg19:g.136599396G>T	ENSP00000435210:p.Thr208Lys	165.0	0.0		72.0	10.0	NM_014739	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Missense_Mutation	SNP	ENST00000531224.1	hg19	CCDS5177.1	.	.	.	.	.	.	.	.	.	.	G	6.607	0.480474	0.12581	.	.	ENSG00000029363	ENST00000531224;ENST00000353331;ENST00000527536;ENST00000530767;ENST00000527759;ENST00000392348;ENST00000529826	T;T;T;T;T;T;T	0.13657	2.99;2.99;2.99;2.57;2.99;2.99;2.8	5.97	5.97	0.96955	.	0.170223	0.41194	D	0.000925	T	0.03871	0.0109	N	0.14661	0.345	0.80722	D	1	B;B;B;B	0.21905	0.018;0.062;0.018;0.018	B;B;B;B	0.14023	0.01;0.01;0.01;0.01	T	0.37686	-0.9695	10	0.32370	T	0.25	-6.4124	13.6035	0.62033	0.0707:0.0:0.9293:0.0	.	206;206;208;208	Q9NYF8-2;Q9NYF8-3;Q9NYF8;Q9NYF8-4	.;.;BCLF1_HUMAN;.	K	208;206;208;208;206;206;208	ENSP00000435210:T208K;ENSP00000229446:T206K;ENSP00000435441:T208K;ENSP00000436501:T208K;ENSP00000434826:T206K;ENSP00000376159:T206K;ENSP00000431734:T208K	ENSP00000229446:T206K	T	-	2	0	BCLAF1	136641089	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.800000	0.55537	2.834000	0.97654	0.650000	0.86243	ACA	.	.		0.423	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739		T	136599396	G	T	136599396	3	4	285	1	0	0	0	0	1	0	0	0	1383	1377	48	3	2179	3	BCLAF1	6	136599396	Missense_Mutation	SNP	G	TCGA-G3-A5SJ-01A-11D-A27I-10	30045063	136599396	34515671	43	41952										
ACAT2	39	hgsc.bcm.edu	37	chr6	160189612	160189612	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	cactgactgacagtatactcTgtgatggtcttacagatgca	9	9	2	4			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr6:160189612T>A	ENST00000367048.4	+	4	2202	c.442T>A	c.(442-444)Tgt>Agt	p.C148S	ACAT2_ENST00000541436.1_Missense_Mutation_p.C177S	NM_005891.2	NP_005882.2	Q9BWD1	THIC_HUMAN	acetyl-CoA acetyltransferase 2	148					lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleus (GO:0005634)	acetyl-CoA C-acetyltransferase activity (GO:0003985)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(1)	9		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.51e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		CAGTATACTCTGTGATGGTCT	0.398																																					p.C148S		Atlas-SNP	.											.	ACAT2	32	.	0			c.T442A						.						175	157	163					6																	160189612		2203	4300	6503	SO:0001583	missense	39	exon4			ATACTCTGTGATG	AF356877	CCDS5268.1	6q25.3	2014-05-19	2010-04-30		ENSG00000120437	ENSG00000120437	2.3.1.9		94	protein-coding gene	gene with protein product	"acetoacetyl Coenzyme A thiolase"	100678	"acetyl-Coenzyme A acetyltransferase 2 (acetoacetyl Coenzyme A thiolase)", "acetyl-Coenzyme A acetyltransferase 2"			2475872	Standard	NM_005891		Approved		uc010kjy.3	Q9BWD1	OTTHUMG00000015935	ENST00000367048.4:c.442T>A	chr6.hg19:g.160189612T>A	ENSP00000356015:p.Cys148Ser	206.0	0.0		69.0	22.0	NM_005891	B7Z233|E1P5B1|Q16146|Q5TCL7|Q8TDM4	Missense_Mutation	SNP	ENST00000367048.4	hg19	CCDS5268.1	.	.	.	.	.	.	.	.	.	.	T	7.104	0.574716	0.13623	.	.	ENSG00000120437	ENST00000367048;ENST00000541436	T;T	0.39997	1.05;1.05	5.64	1.86	0.25419	Thiolase, N-terminal (1);Thiolase-like (1);	0.498856	0.25689	N	0.028959	T	0.05364	0.0142	N	0.02111	-0.68	0.09310	N	0.999998	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.002	T	0.40553	-0.9557	10	0.30854	T	0.27	3.015	8.632	0.33926	0.0:0.3997:0.0:0.6003	.	177;148	B7Z233;Q9BWD1	.;THIC_HUMAN	S	148;177	ENSP00000356015:C148S;ENSP00000437850:C177S	ENSP00000356015:C148S	C	+	1	0	ACAT2	160109602	0.000000	0.05858	0.025000	0.17156	0.782000	0.44232	0.371000	0.20450	0.171000	0.19730	0.528000	0.53228	TGT	.	.		0.398	ACAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042912.1	NM_005891		A	160189612	T	A	160189612	3	1	285	1	0	0	0	0	1	0	0	0	122	1580	55	4	456	4	ACAT2	6	160189612	Missense_Mutation	SNP	T	TCGA-G3-A5SJ-01A-11D-A27I-10	23590216	160189612	10925455	44	41953										
GARS	2617	hgsc.bcm.edu	37	chr7	30673470	30673470	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	ggtaaaaaagagacaatcgaGgaatgaggacaattttgaca	11	4	0	3	rs537365362		TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr7:30673470G>T	ENST00000389266.3	+	17	2455	c.2214G>T	c.(2212-2214)gaG>gaT	p.E738D		NM_002047.2	NP_002038.2	P41250	SYG_HUMAN	glycyl-tRNA synthetase	738					cell death (GO:0008219)|diadenosine tetraphosphate biosynthetic process (GO:0015966)|gene expression (GO:0010467)|glycyl-tRNA aminoacylation (GO:0006426)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|secretory granule (GO:0030141)	ATP binding (GO:0005524)|glycine-tRNA ligase activity (GO:0004820)|protein dimerization activity (GO:0046983)			breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|skin(3)|urinary_tract(1)	24					Glycine(DB00145)	AGACAATCGAGGAATGAGGAC	0.393																																					p.E738D		Atlas-SNP	.											.	GARS	52	.	0			c.G2214T						.						95	87	89					7																	30673470		1877	4107	5984	SO:0001583	missense	2617	exon17			AATCGAGGAATGA	AK074524	CCDS43564.1	7p15	2014-09-17	2004-02-13		ENSG00000106105	ENSG00000106105	6.1.1.14	"Aminoacyl tRNA synthetases / Class II"	4162	protein-coding gene	gene with protein product	"glycine tRNA ligase"	600287	"Charcot-Marie-Tooth neuropathy 2D"	CMT2D		8595897, 8872480	Standard	NM_002047		Approved	GlyRS, DSMAV, SMAD1	uc003tbm.3	P41250	OTTHUMG00000152769	ENST00000389266.3:c.2214G>T	chr7.hg19:g.30673470G>T	ENSP00000373918:p.Glu738Asp	90.0	0.0		35.0	17.0	NM_002047	B3KQA2|B4DIA0|Q969Y1	Missense_Mutation	SNP	ENST00000389266.3	hg19	CCDS43564.1	.	.	.	.	.	.	.	.	.	.	G	13.06	2.125724	0.37533	.	.	ENSG00000106105	ENST00000389266	D	0.82344	-1.6	4.9	2.02	0.26589	.	.	.	.	.	T	0.76343	0.3974	L	0.53249	1.67	0.47819	D	0.999527	B	0.13594	0.008	B	0.10450	0.005	T	0.67031	-0.5773	9	0.36615	T	0.2	4.734	8.2635	0.31799	0.2789:0.0:0.7211:0.0	.	738	P41250	SYG_HUMAN	D	738	ENSP00000373918:E738D	ENSP00000373918:E738D	E	+	3	2	GARS	30639995	1.000000	0.71417	0.993000	0.49108	0.944000	0.59088	1.215000	0.32431	0.330000	0.23485	-0.145000	0.13849	GAG	.	.		0.393	GARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327735.1	NM_002047		T	30673470	G	T	30673470	3	4	285	1	0	0	0	0	1	0	0	0	6250	991	35	3	2280	3	GARS	7	30673470	Missense_Mutation	SNP	G	TCGA-G3-A5SJ-01A-11D-A27I-10		30673470	128465193	45	41954										
CCDC129	223075	hgsc.bcm.edu	37	chr7	31682701	31682701	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	tggggtttatggtaacccacGtcacagaaatgcaggacagt	12	8	1	1			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr7:31682701G>A	ENST00000407970.3	+	11	1755	c.1717G>A	c.(1717-1719)Gtc>Atc	p.V573I	CCDC129_ENST00000409210.1_Missense_Mutation_p.V481I|CCDC129_ENST00000319386.3_Missense_Mutation_p.V425I|CCDC129_ENST00000451887.2_Missense_Mutation_p.V599I	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	573										cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						GGTAACCCACGTCACAGAAAT	0.502																																					p.V599I		Atlas-SNP	.											.	CCDC129	127	.	0			c.G1795A						.						178	176	176					7																	31682701		2203	4300	6503	SO:0001583	missense	223075	exon11			ACCCACGTCACAG	AK128026	CCDS5435.2, CCDS59050.1, CCDS75577.1	7p14.3	2006-08-21			ENSG00000180347	ENSG00000180347			27363	protein-coding gene	gene with protein product						14702039	Standard	NM_001257967		Approved	FLJ38344	uc011kad.1	Q6ZRS4	OTTHUMG00000128611	ENST00000407970.3:c.1717G>A	chr7.hg19:g.31682701G>A	ENSP00000384416:p.Val573Ile	184.0	0.0		82.0	30.0	NM_001257968	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Missense_Mutation	SNP	ENST00000407970.3	hg19	CCDS5435.2	.	.	.	.	.	.	.	.	.	.	G	0.442	-0.898031	0.02472	.	.	ENSG00000180347	ENST00000319386;ENST00000407970;ENST00000451887;ENST00000538406;ENST00000409210	T;T;T;T	0.18502	2.21;2.48;2.47;2.22	5.6	-2.59	0.06209	.	1.100120	0.06868	N	0.800402	T	0.03095	0.0091	N	0.00621	-1.32	0.09310	N	1	B;B;B;B	0.09022	0.002;0.0;0.0;0.0	B;B;B;B	0.06405	0.002;0.001;0.001;0.001	T	0.40553	-0.9557	10	0.05721	T	0.95	-20.0766	1.6112	0.02694	0.4822:0.1344:0.2529:0.1305	.	599;583;573;425	F5H3V5;F5H2J8;Q6ZRS4;Q6ZRS4-2	.;.;CC129_HUMAN;.	I	425;573;599;583;481	ENSP00000313062:V425I;ENSP00000384416:V573I;ENSP00000395835:V599I;ENSP00000387214:V481I	ENSP00000313062:V425I	V	+	1	0	CCDC129	31649226	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.044000	0.12023	-0.065000	0.13021	-1.160000	0.01791	GTC	.	.		0.502	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300		A	31682701	G	A	31682701	3	1	285	1	0	0	0	0	1	0	0	0	2766	1145	40	1	1755	1	CCDC129	7	31682701	Missense_Mutation	SNP	G	TCGA-G3-A5SJ-01A-11D-A27I-10	1009231	31682701	127455962	46	41955										
ELMO1	9844	hgsc.bcm.edu	37	chr7	36895340	36895340	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	cgagtagcgcattcagtccaTccgtccagatacagtactgg	10	12	1	1			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr7:36895340T>C	ENST00000310758.4	-	22	2647	c.2000A>G	c.(1999-2001)gAt>gGt	p.D667G	ELMO1_ENST00000442504.1_Missense_Mutation_p.D667G|ELMO1_ENST00000448602.1_Missense_Mutation_p.D667G|ELMO1_ENST00000341056.3_Missense_Mutation_p.D369G|ELMO1_ENST00000396045.3_Missense_Mutation_p.D187G|ELMO1_ENST00000396040.2_Missense_Mutation_p.D187G	NM_001206480.1|NM_014800.10	NP_001193409.1|NP_055615.8	Q92556	ELMO1_HUMAN	engulfment and cell motility 1	667	PH.				actin cytoskeleton organization (GO:0030036)|apoptotic process (GO:0006915)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|phagocytosis, engulfment (GO:0006911)|Rac protein signal transduction (GO:0016601)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(28)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	58						ATTCAGTCCATCCGTCCAGAT	0.498																																					p.D667G		Atlas-SNP	.											.	ELMO1	141	.	0			c.A2000G						.						145	120	128					7																	36895340		2203	4300	6503	SO:0001583	missense	9844	exon22			AGTCCATCCGTCC	AF398885	CCDS5449.1, CCDS5450.1	7p14.1	2012-07-10	2006-01-20		ENSG00000155849	ENSG00000155849		"Engulfment and cell motility proteins"	16286	protein-coding gene	gene with protein product		606420	"engulfment and cell motility 1 (ced-12 homolog, C. elegans)"			11595183	Standard	NM_001039459		Approved	KIAA0281, CED12, ELMO-1, CED-12	uc003tfk.2	Q92556	OTTHUMG00000023701	ENST00000310758.4:c.2000A>G	chr7.hg19:g.36895340T>C	ENSP00000312185:p.Asp667Gly	312.0	0.0		135.0	38.0	NM_014800	A4D1X6|Q29R79|Q6ZTJ0|Q96PB0|Q9H0I1	Missense_Mutation	SNP	ENST00000310758.4	hg19	CCDS5449.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.951224	0.73787	.	.	ENSG00000155849	ENST00000341056;ENST00000396045;ENST00000310758;ENST00000361912;ENST00000396040;ENST00000442504;ENST00000448602	T;T;T;T;T;T	0.55413	0.52;0.52;0.52;0.52;0.52;0.52	4.88	4.88	0.63580	Pleckstrin homology-type (1);Pleckstrin homology domain (1);	0.059525	0.64402	D	0.000004	T	0.77177	0.4092	M	0.90814	3.15	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82818	-0.0269	10	0.87932	D	0	.	14.9719	0.71241	0.0:0.0:0.0:1.0	.	667	Q92556	ELMO1_HUMAN	G	369;187;667;571;187;667;667	ENSP00000342142:D369G;ENSP00000379360:D187G;ENSP00000312185:D667G;ENSP00000379355:D187G;ENSP00000406952:D667G;ENSP00000394458:D667G	ENSP00000312185:D667G	D	-	2	0	ELMO1	36861865	1.000000	0.71417	0.875000	0.34327	0.586000	0.36452	7.868000	0.87116	2.180000	0.69256	0.528000	0.53228	GAT	.	.		0.498	ELMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219830.4	NM_130442		C	36895340	T	C	36895340	3	2	285	1	0	0	0	0	1	0	0	0	5067	1435	50	2	187	2	ELMO1	7	36895340	Missense_Mutation	SNP	T	TCGA-G3-A5SJ-01A-11D-A27I-10	5212639	36895340	122243323	47	41956										
SUMF2	25870	hgsc.bcm.edu	37	chr7	56140741	56140741	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	gaagctgagatgtttggatgGagctttgtctttgaggactt	14	4	1	2			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr7:56140741G>C	ENST00000413756.1	+	3	299	c.276G>C	c.(274-276)tgG>tgC	p.W92C	SUMF2_ENST00000434526.2_Missense_Mutation_p.W111C|SUMF2_ENST00000275607.9_Missense_Mutation_p.W4C|SUMF2_ENST00000342190.6_Missense_Mutation_p.W111C|SUMF2_ENST00000437307.2_Missense_Mutation_p.W92C|SUMF2_ENST00000395435.2_Missense_Mutation_p.W111C|SUMF2_ENST00000395436.2_Missense_Mutation_p.W111C			Q8NBJ7	SUMF2_HUMAN	sulfatase modifying factor 2	92					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)	endoplasmic reticulum lumen (GO:0005788)	metal ion binding (GO:0046872)			breast(2)|endometrium(2)|large_intestine(1)|lung(6)|ovary(2)|skin(1)	14	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			TGTTTGGATGGAGCTTTGTCT	0.483																																					p.W111C		Atlas-SNP	.											.	SUMF2	56	.	0			c.G333C						.						139	138	138					7																	56140741		2203	4300	6503	SO:0001583	missense	25870	exon3			TGGATGGAGCTTT	AK075477	CCDS5524.2, CCDS43588.2, CCDS43589.2, CCDS47589.1, CCDS55111.1	7q11.1	2004-04-30			ENSG00000129103	ENSG00000129103			20415	protein-coding gene	gene with protein product		607940				12757706	Standard	NM_015411		Approved	DKFZp566I1024	uc003trv.3	Q8NBJ7	OTTHUMG00000129373	ENST00000413756.1:c.276G>C	chr7.hg19:g.56140741G>C	ENSP00000406445:p.Trp92Cys	178.0	0.0		84.0	20.0	NM_015411	B4DU41|B4DWQ0|Q14DW5|Q53ZE3|Q96BH2|Q9BRN3|Q9BWI1|Q9Y405	Missense_Mutation	SNP	ENST00000413756.1	hg19		.	.	.	.	.	.	.	.	.	.	G	19.37	3.814731	0.70912	.	.	ENSG00000129103	ENST00000395436;ENST00000434526;ENST00000275607;ENST00000395435;ENST00000413952;ENST00000342190;ENST00000437307;ENST00000413756;ENST00000451338	T;T;T;D;T;T;T;T;T	0.95035	0.97;0.97;0.97;-3.59;0.97;0.97;0.97;0.97;0.97	5.24	4.36	0.52297	C-type lectin fold (1);Formylglycine-generating sulphatase enzyme domain (2);	0.051131	0.85682	D	0.000000	D	0.97604	0.9215	M	0.92833	3.35	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.988;1.0	D;D;D;D;P;D	0.85130	0.997;0.993;0.993;0.993;0.714;0.992	D	0.97665	1.0163	10	0.40728	T	0.16	-19.5055	13.8015	0.63204	0.075:0.0:0.925:0.0	.	92;111;114;92;111;114	Q8NBJ7-5;A8MXB9;E7EMF9;Q8NBJ7;F8WA42;C9JL30	.;.;.;SUMF2_HUMAN;.;.	C	111;111;4;111;114;111;92;92;89	ENSP00000378824:W111C;ENSP00000400922:W111C;ENSP00000275607:W4C;ENSP00000378823:W111C;ENSP00000414434:W114C;ENSP00000341938:W111C;ENSP00000415989:W92C;ENSP00000406445:W92C;ENSP00000410796:W89C	ENSP00000275607:W4C	W	+	3	0	SUMF2	56108235	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.312000	0.78968	1.531000	0.49152	0.655000	0.94253	TGG	.	.		0.483	SUMF2-013	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000341457.2	NM_015411		C	56140741	G	C	56140741	3	2	285	1	0	0	0	0	1	0	0	0	15401	1183	41	4	343	4	SUMF2	7	56140741	Missense_Mutation	SNP	G	TCGA-G3-A5SJ-01A-11D-A27I-10	19245401	56140741	102997922	48	41957										
AKAP9	10142	hgsc.bcm.edu	37	chr7	91694746	91694746	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	gcaaaaccaagcattggaaaAgcagttagaaaaaatgagaa	9	5	0	2			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr7:91694746A>G	ENST00000359028.2	+	26	6440	c.6215A>G	c.(6214-6216)aAg>aGg	p.K2072R	AKAP9_ENST00000358100.2_Missense_Mutation_p.K2072R|AKAP9_ENST00000356239.3_Missense_Mutation_p.K2060R|AKAP9_ENST00000491695.1_3'UTR			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	2072	Glu-rich.				G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)	p.K2072R(1)|p.K2060R(1)		NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			GCATTGGAAAAGCAGTTAGAA	0.318			T	BRAF	papillary thyroid																																p.K2060R		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	AKAP9_ENST00000356239,NS,other,0,2	AKAP9	788	.	2	Substitution - Missense(2)	ovary(2)	c.A6179G						.						40	40	40					7																	91694746		2203	4298	6501	SO:0001583	missense	10142	exon25			TGGAAAAGCAGTT	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	379	protein-coding gene	gene with protein product	"A-kinase anchoring protein 450", "AKAP9-BRAF fusion protein", "AKAP120-like protein", "centrosome- and golgi-localized protein kinase N-associated protein", "protein kinase A anchoring protein 9", "A-kinase anchor protein, 350kDa", "protein phosphatase 1, regulatory subunit 45", "yotiao"	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.6215A>G	chr7.hg19:g.91694746A>G	ENSP00000351922:p.Lys2072Arg	100.0	1.0		50.0	23.0	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	hg19		.	.	.	.	.	.	.	.	.	.	A	19.13	3.768538	0.69878	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000265737	T;T;T	0.12465	2.7;2.71;2.68	5.62	5.62	0.85841	.	0.000000	0.43747	D	0.000529	T	0.40815	0.1132	M	0.80422	2.495	0.54753	D	0.999988	D;D;D	0.89917	0.997;0.998;1.0	D;D;D	0.87578	0.985;0.994;0.998	T	0.24440	-1.0160	10	0.46703	T	0.11	.	16.1177	0.81321	1.0:0.0:0.0:0.0	.	2072;2060;2060	Q99996;Q99996-2;Q99996-3	AKAP9_HUMAN;.;.	R	2060;2072;2072;2072;275	ENSP00000348573:K2060R;ENSP00000351922:K2072R;ENSP00000350813:K2072R	ENSP00000265737:K275R	K	+	2	0	AKAP9	91532682	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.269000	0.89878	2.267000	0.75376	0.528000	0.53228	AAG	.	.		0.318	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751		G	91694746	A	G	91694746	3	3	285	1	0	0	0	0	1	0	0	0	459	72	3	2	6277	2	AKAP9	7	91694746	Missense_Mutation	SNP	A	TCGA-G3-A5SJ-01A-11D-A27I-10	35554005	91694746	67443917	49	41958										
GCC1	79571	hgsc.bcm.edu	37	chr7	127222282	127222282	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	ccctgatgttcttttcgatgTggctctgcagggctgcaacc	11	12	2	1			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr7:127222282T>C	ENST00000321407.2	-	2	2538	c.2114A>G	c.(2113-2115)cAc>cGc	p.H705R	GCC1_ENST00000497650.1_5'Flank	NM_024523.5	NP_078799.2	Q96CN9	GCC1_HUMAN	GRIP and coiled-coil domain containing 1	705					protein targeting to Golgi (GO:0000042)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				breast(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(13)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						CTTTTCGATGTGGCTCTGCAG	0.582																																					p.H705R		Atlas-SNP	.											.	GCC1	83	.	0			c.A2114G						.						213	202	205					7																	127222282		2203	4300	6503	SO:0001583	missense	79571	exon2			TCGATGTGGCTCT	AF525417	CCDS5796.1	7q22.3	2004-03-05	2003-10-17		ENSG00000179562	ENSG00000179562			19095	protein-coding gene	gene with protein product		607418	"golgi coiled-coil 1"			10209125	Standard	NM_024523		Approved	FLJ22035, GCC88, GCC1P, MGC20706	uc003vma.3	Q96CN9	OTTHUMG00000023590	ENST00000321407.2:c.2114A>G	chr7.hg19:g.127222282T>C	ENSP00000318821:p.His705Arg	620.0	1.0		225.0	62.0	NM_024523	Q9H6N7	Missense_Mutation	SNP	ENST00000321407.2	hg19	CCDS5796.1	.	.	.	.	.	.	.	.	.	.	T	8.486	0.860825	0.17178	.	.	ENSG00000179562	ENST00000321407	T	0.11063	2.81	5.87	4.72	0.59763	.	0.199482	0.53938	N	0.000054	T	0.09818	0.0241	L	0.36672	1.1	0.33059	D	0.533798	B	0.06786	0.001	B	0.04013	0.001	T	0.04294	-1.0962	10	0.49607	T	0.09	-17.2003	10.4907	0.44750	0.0:0.0767:0.0:0.9233	.	705	Q96CN9	GCC1_HUMAN	R	705	ENSP00000318821:H705R	ENSP00000318821:H705R	H	-	2	0	GCC1	127009518	1.000000	0.71417	0.997000	0.53966	0.621000	0.37620	2.228000	0.42981	1.147000	0.42369	-0.290000	0.09829	CAC	.	.		0.582	GCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059911.3	NM_024523		C	127222282	T	C	127222282	3	2	285	1	0	0	0	0	1	0	0	0	6293	1696	59	2	217	2	GCC1	7	127222282	Missense_Mutation	SNP	T	TCGA-G3-A5SJ-01A-11D-A27I-10	35527536	127222282	31916381	50	41959										
SLC13A4	26266	hgsc.bcm.edu	37	chr7	135412217	135412217	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	gaccagcagcagcttccggaCtcggagcaggccctgcagca	13	15	0	0			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr7:135412217C>T	ENST00000354042.4	-	1	717	c.28G>A	c.(28-30)Gtc>Atc	p.V10I	FAM180A_ENST00000435869.1_5'Flank	NM_012450.2	NP_036582.2	Q9UKG4	S13A4_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 4	10					sodium ion transmembrane transport (GO:0035725)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	sodium:sulfate symporter activity (GO:0015382)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	24						AGCTTCCGGACTCGGAGCAGG	0.701																																					p.V10I		Atlas-SNP	.											.	SLC13A4	56	.	0			c.G28A						.						28	26	27					7																	135412217		1909	3624	5533	SO:0001583	missense	26266	exon1			TCCGGACTCGGAG	AF169301	CCDS5840.1	7q33	2013-07-18	2013-07-18		ENSG00000164707	ENSG00000164707		"Solute carriers"	15827	protein-coding gene	gene with protein product	"sulphate transporter 1"	604309	"solute carrier family 13 (sodium/sulphate symporters), member 4"			10535998	Standard	NM_012450		Approved	SUT-1, SUT1	uc003vta.3	Q9UKG4	OTTHUMG00000155539	ENST00000354042.4:c.28G>A	chr7.hg19:g.135412217C>T	ENSP00000297282:p.Val10Ile	8.0	0.0		26.0	11.0	NM_012450	A4D1Q4|Q8N631	Missense_Mutation	SNP	ENST00000354042.4	hg19	CCDS5840.1	.	.	.	.	.	.	.	.	.	.	C	16.95	3.262391	0.59431	.	.	ENSG00000164707	ENST00000354042	T	0.68025	-0.3	5.67	4.78	0.61160	.	0.407167	0.26560	N	0.023688	T	0.45478	0.1344	N	0.08118	0	0.09310	N	1	B	0.14012	0.009	B	0.12837	0.008	T	0.33317	-0.9873	10	0.34782	T	0.22	.	11.5152	0.50518	0.3258:0.6742:0.0:0.0	.	10	Q9UKG4	S13A4_HUMAN	I	10	ENSP00000297282:V10I	ENSP00000297282:V10I	V	-	1	0	SLC13A4	135062757	0.636000	0.27207	0.006000	0.13384	0.663000	0.39108	2.281000	0.43452	1.359000	0.45940	0.655000	0.94253	GTC	.	.		0.701	SLC13A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340558.1	NM_012450		T	135412217	C	T	135412217	3	4	285	1	0	0	0	0	1	0	0	0	14409	565	20	3	1916	3	SLC13A4	7	135412217	Missense_Mutation	SNP	C	TCGA-G3-A5SJ-01A-11D-A27I-10	8189935	135412217	23726446	51	41960										
MGAM	8972	hgsc.bcm.edu	37	chr7	141763307	141763307	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	tggcatttctaggatatgaaTgaaccatcaagcttcgtgaa	9	7	2	3	rs369807337		TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr7:141763307T>C	ENST00000549489.2	+	36	4361	c.4266T>C	c.(4264-4266)aaT>aaC	p.N1422N	MGAM_ENST00000475668.2_Silent_p.N1422N	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1422	Glucoamylase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	AGGATATGAATGAACCATCAA	0.463																																					p.N1422N		Atlas-SNP	.											.	MGAM	767	.	0			c.T4266C						.	T		0,3838		0,0,1919	56	53	54		4266	3	1	7		54	1,8245		0,1,4122	no	coding-synonymous	MGAM	NM_004668.2		0,1,6041	CC,CT,TT		0.0121,0.0,0.0083		1422/1858	141763307	1,12083	1919	4123	6042	SO:0001819	synonymous_variant	8972	exon36			TATGAATGAACCA	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.4266T>C	chr7.hg19:g.141763307T>C		157.0	0.0		70.0	21.0	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000549489.2	hg19	CCDS47727.1																																																																																			.	.		0.463	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			C	141763307	T	C	141763307	2	2	285	1	0	0	0	0	0	0	0	1	9550	1461	51	2		2	MGAM	7	141763307	Silent	SNP	T	TCGA-G3-A5SJ-01A-11D-A27I-10	6351090	141763307	17375356	52	41961										
ATAD2	29028	hgsc.bcm.edu	37	chr8	124408568	124408568	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	gaggccgcggagtggttgtgCagctccaagctgctgcggag	18	10	0	0			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr8:124408568C>T	ENST00000287394.5	-	1	137	c.30G>A	c.(28-30)ctG>ctA	p.L10L	ATAD2_ENST00000521903.1_Intron	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	10					ATP catabolic process (GO:0006200)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	48	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			AGTGGTTGTGCAGCTCCAAGC	0.682																																					p.L10L		Atlas-SNP	.											.	ATAD2	160	.	0			c.G30A						.						21	28	26					8																	124408568		2203	4300	6503	SO:0001819	synonymous_variant	29028	exon1			GTTGTGCAGCTCC	BC019909	CCDS6343.1	8q24.13	2014-01-21		2007-02-08	ENSG00000156802	ENSG00000156802		"ATPases / AAA-type"	30123	protein-coding gene	gene with protein product		611941				12477932	Standard	NM_014109		Approved	PRO2000, DKFZp667N1320, MGC5254, MGC29843, CT137	uc003yqh.4	Q6PL18	OTTHUMG00000165090	ENST00000287394.5:c.30G>A	chr8.hg19:g.124408568C>T		72.0	0.0		88.0	5.0	NM_014109	Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	Silent	SNP	ENST00000287394.5	hg19	CCDS6343.1																																																																																			.	.		0.682	ATAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381766.2	NM_014109		T	124408568	C	T	124408568	2	4	285	1	0	0	0	0	0	0	0	1	1071	697	25	3		3	ATAD2	8	124408568	Silent	SNP	C	TCGA-G3-A5SJ-01A-11D-A27I-10		124408568	21955454	53	41962										
NDRG1	10397	hgsc.bcm.edu	37	chr8	134270653	134270653	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	gcctgctcctgttcccatgcCaataatgcttttcagcctgg	8	14	1	0			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr8:134270653C>T	ENST00000414097.2	-	7	1273	c.406G>A	c.(406-408)Ggc>Agc	p.G136S	NDRG1_ENST00000354944.5_Intron|NDRG1_ENST00000537882.1_Missense_Mutation_p.G55S|NDRG1_ENST00000323851.7_Missense_Mutation_p.G136S|NDRG1_ENST00000518176.1_Intron|NDRG1_ENST00000518066.1_Intron|NDRG1_ENST00000522476.1_Missense_Mutation_p.G70S	NM_001135242.1	NP_001128714.1	Q92597	NDRG1_HUMAN	N-myc downstream regulated 1	136					cell death (GO:0008219)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|mast cell activation (GO:0045576)|peripheral nervous system myelin maintenance (GO:0032287)|positive regulation of spindle checkpoint (GO:0090232)|response to metal ion (GO:0010038)	cell-cell adherens junction (GO:0005913)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	cadherin binding (GO:0045296)|gamma-tubulin binding (GO:0043015)|microtubule binding (GO:0008017)|Rab GTPase binding (GO:0017137)		NDRG1/ERG(5)	endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|ovary(4)|prostate(1)|skin(1)	17	all_epithelial(106;4.26e-24)|Lung NSC(106;7.26e-07)|all_lung(105;2.77e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0107)			GTTCCCATGCCAATAATGCTT	0.438			T	ERG	prostate																																p.G136S		Atlas-SNP	.		Dom	yes		8	8q24.3	10397	N-myc downstream regulated 1		E	.	NDRG1	40	.	0			c.G406A						.						63	57	59					8																	134270653		2203	4300	6503	SO:0001583	missense	10397	exon7			CCATGCCAATAAT	X92845	CCDS34945.1, CCDS59112.1, CCDS59113.1	8q24	2014-09-17	2008-09-12		ENSG00000104419	ENSG00000104419			7679	protein-coding gene	gene with protein product		605262		CAP43		9251681, 8939898, 18455888	Standard	NM_006096		Approved	DRG1, RTP, TDD5, NDR1	uc003yue.2	Q92597	OTTHUMG00000164441	ENST00000414097.2:c.406G>A	chr8.hg19:g.134270653C>T	ENSP00000404854:p.Gly136Ser	270.0	0.0		212.0	65.0	NM_006096	B3KR80|B7Z446|O15207|Q6IBG2|Q9NYR6|Q9UK29	Missense_Mutation	SNP	ENST00000414097.2	hg19	CCDS34945.1	.	.	.	.	.	.	.	.	.	.	C	36	5.642439	0.96704	.	.	ENSG00000104419	ENST00000323851;ENST00000414097;ENST00000537882;ENST00000522476;ENST00000520230;ENST00000518480;ENST00000519228;ENST00000519580;ENST00000522890;ENST00000520943	T;T;T;T;T;T;T;T;T;T	0.29397	1.57;1.57;1.95;1.95;1.95;1.95;1.95;1.95;1.95;1.95	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.66567	0.2802	M	0.92833	3.35	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74728	-0.3567	10	0.66056	D	0.02	-40.9453	18.1007	0.89505	0.0:1.0:0.0:0.0	.	136	Q92597	NDRG1_HUMAN	S	136;136;55;70;153;70;136;136;136;147	ENSP00000319977:G136S;ENSP00000404854:G136S;ENSP00000437443:G55S;ENSP00000427894:G70S;ENSP00000428345:G153S;ENSP00000428802:G70S;ENSP00000429994:G136S;ENSP00000429272:G136S;ENSP00000428384:G136S;ENSP00000429840:G147S	ENSP00000319977:G136S	G	-	1	0	NDRG1	134339835	1.000000	0.71417	0.979000	0.43373	0.957000	0.61999	7.187000	0.77730	2.599000	0.87857	0.555000	0.69702	GGC	.	.		0.438	NDRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378805.1			T	134270653	C	T	134270653	3	4	285	1	0	0	0	0	1	0	0	0	10260	594	21	3	818	3	NDRG1	8	134270653	Missense_Mutation	SNP	C	TCGA-G3-A5SJ-01A-11D-A27I-10	9862085	134270653	12093369	54	41963										
PTK2	5747	hgsc.bcm.edu	37	chr8	141874456	141874456	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	ggcttatcttcagtaaactgGtttagaaatccttttggcaa	8	7	2	1			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr8:141874456G>C	ENST00000522684.1	-	5	634	c.405C>G	c.(403-405)aaC>aaG	p.N135K	PTK2_ENST00000395218.2_Missense_Mutation_p.N135K|PTK2_ENST00000521059.1_Missense_Mutation_p.N135K|PTK2_ENST00000340930.3_Missense_Mutation_p.N135K|PTK2_ENST00000519419.1_Missense_Mutation_p.N179K|PTK2_ENST00000535192.1_Missense_Mutation_p.N135K|PTK2_ENST00000517887.1_Missense_Mutation_p.N179K	NM_153831.3	NP_722560.1	Q05397	FAK1_HUMAN	protein tyrosine kinase 2	135	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell motility (GO:0048870)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|central nervous system neuron axonogenesis (GO:0021955)|embryo development (GO:0009790)|endothelial cell migration (GO:0043542)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|establishment of nucleus localization (GO:0040023)|extracellular matrix organization (GO:0030198)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|growth hormone receptor signaling pathway (GO:0060396)|heart morphogenesis (GO:0003007)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of organ growth (GO:0046621)|negative regulation of synapse assembly (GO:0051964)|netrin-activated signaling pathway (GO:0038007)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|placenta development (GO:0001890)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|regulation of endothelial cell migration (GO:0010594)|regulation of focal adhesion assembly (GO:0051893)|regulation of osteoblast differentiation (GO:0045667)|regulation of Rho GTPase activity (GO:0032319)|signal complex assembly (GO:0007172)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)	apical plasma membrane (GO:0016324)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|stress fiber (GO:0001725)	actin binding (GO:0003779)|ATP binding (GO:0005524)|JUN kinase binding (GO:0008432)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(6)|lung(23)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	48	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)			CAGTAAACTGGTTTAGAAATC	0.274																																					p.N157K		Atlas-SNP	.											.	PTK2	311	.	0			c.C471G						.						72	80	77					8																	141874456		2199	4291	6490	SO:0001583	missense	5747	exon5			AAACTGGTTTAGA	L13616	CCDS6381.1, CCDS56557.1	8q24.3	2013-02-18	2013-02-18		ENSG00000169398	ENSG00000169398	2.7.10.1	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9611	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 71"	600758	"PTK2 protein tyrosine kinase 2"			8422239	Standard	NM_153831		Approved	FAK, FADK, FAK1, PPP1R71	uc003yvt.3	Q05397	OTTHUMG00000067438	ENST00000522684.1:c.405C>G	chr8.hg19:g.141874456G>C	ENSP00000429911:p.Asn135Lys	169.0	0.0		90.0	32.0	NM_005607	B4E2N6|F5H4S4|Q14291|Q9UD85	Missense_Mutation	SNP	ENST00000522684.1	hg19	CCDS6381.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.87|12.87	2.066606|2.066606	0.36470|0.36470	.|.	.|.	ENSG00000169398|ENSG00000169398	ENST00000522684;ENST00000535192;ENST00000517887;ENST00000521059;ENST00000395214;ENST00000395218;ENST00000354438;ENST00000340930;ENST00000519419;ENST00000520828;ENST00000520475|ENST00000519654	T;T;T;T;T;T;T;T;T|.	0.40476|.	1.03;1.03;1.03;1.03;1.03;1.03;1.03;1.03;1.03|.	5.27|5.27	4.39|4.39	0.52855|0.52855	FERM central domain (1);Band 4.1 domain (1);FERM domain (1);|.	0.143624|.	0.64402|.	D|.	0.000009|.	T|T	0.42381|0.42381	0.1200|0.1200	N|N	0.22421|0.22421	0.69|0.69	0.80722|0.80722	D|D	1|1	B;P;B;B;B;B|.	0.35944|.	0.08;0.529;0.041;0.003;0.019;0.033|.	B;B;B;B;B;B|.	0.37422|.	0.051;0.249;0.051;0.026;0.036;0.043|.	T|T	0.22626|0.22626	-1.0211|-1.0211	10|5	0.56958|.	D|.	0.05|.	.|.	9.5112|9.5112	0.39078|0.39078	0.166:0.0:0.834:0.0|0.166:0.0:0.834:0.0	.|.	135;42;135;157;135;46|.	B4E2N6;Q59GN8;Q05397;Q658W2;Q8IYN9;Q59GM6|.	.;.;FAK1_HUMAN;.;.;.|.	K|A	135;135;179;135;45;135;42;135;179;34;135|146	ENSP00000429911:N135K;ENSP00000438009:N135K;ENSP00000429082:N179K;ENSP00000429474:N135K;ENSP00000378644:N135K;ENSP00000341189:N135K;ENSP00000429129:N179K;ENSP00000427762:N34K;ENSP00000428792:N135K|.	ENSP00000341189:N135K|.	N|P	-|-	3|1	2|0	PTK2|PTK2	141943638|141943638	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	1.013000|1.013000	0.29937|0.29937	1.207000|1.207000	0.43291|0.43291	0.313000|0.313000	0.20887|0.20887	AAC|CCA	.	.		0.274	PTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378054.5	NM_005607		C	141874456	G	C	141874456	3	2	285	1	0	0	0	0	1	0	0	0	12775	1252	44	4	2865	4	PTK2	8	141874456	Missense_Mutation	SNP	G	TCGA-G3-A5SJ-01A-11D-A27I-10	7603803	141874456	4489566	55	41964										
PTPRD	5789	hgsc.bcm.edu	37	chr9	8504350	8504350	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	gacggaaatagtataagctgTttggtttcagtccttgcagc	11	7	1	0			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr9:8504350T>C	ENST00000381196.4	-	20	2276	c.1733A>G	c.(1732-1734)aAc>aGc	p.N578S	PTPRD_ENST00000486161.1_Missense_Mutation_p.N578S|PTPRD_ENST00000397606.3_Missense_Mutation_p.N568S|PTPRD_ENST00000540109.1_Missense_Mutation_p.N578S|PTPRD_ENST00000355233.5_Missense_Mutation_p.N578S|PTPRD_ENST00000358503.5_Missense_Mutation_p.N565S|PTPRD_ENST00000360074.4_Missense_Mutation_p.N565S|PTPRD_ENST00000356435.5_Missense_Mutation_p.N578S|PTPRD_ENST00000397611.3_Missense_Mutation_p.N575S|PTPRD_ENST00000397617.3_Missense_Mutation_p.N568S|PTPRD_ENST00000537002.1_Missense_Mutation_p.N575S	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	578	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		GTATAAGCTGTTTGGTTTCAG	0.468										TSP Lung(15;0.13)																											p.N578S		Atlas-SNP	.											.	PTPRD	1348	.	0			c.A1733G						.						299	254	269					9																	8504350		2203	4300	6503	SO:0001583	missense	5789	exon12			AAGCTGTTTGGTT	X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.1733A>G	chr9.hg19:g.8504350T>C	ENSP00000370593:p.Asn578Ser	348.0	0.0		135.0	41.0	NM_130392	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Missense_Mutation	SNP	ENST00000381196.4	hg19	CCDS43786.1	.	.	.	.	.	.	.	.	.	.	T	13.13	2.144753	0.37825	.	.	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000355233;ENST00000397617;ENST00000397611;ENST00000537002;ENST00000346816;ENST00000540109;ENST00000486161;ENST00000397606	T;T;T;T;T;T;T;T;T;T;T	0.56611	0.45;0.45;0.45;0.45;0.45;0.45;0.45;0.45;0.45;0.45;0.45	5.53	5.53	0.82687	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.099895	0.64402	D	0.000002	T	0.52158	0.1717	L	0.35644	1.08	0.37285	D	0.908005	B;B;B;P;B;B;P;P;P	0.41265	0.361;0.361;0.018;0.542;0.003;0.312;0.744;0.744;0.613	B;B;B;B;B;B;P;P;P	0.47251	0.388;0.388;0.041;0.388;0.036;0.268;0.542;0.469;0.451	T	0.55617	-0.8113	9	.	.	.	.	15.6699	0.77264	0.0:0.0:0.0:1.0	.	568;572;578;578;575;575;565;578;578	Q3KPJ2;Q3KPI9;Q3KPJ0;Q3KPJ1;F5GWT7;F5GWY7;G3XAE2;Q2HXI4;P23468	.;.;.;.;.;.;.;.;PTPRD_HUMAN	S	578;578;565;565;578;568;575;575;578;578;578;568	ENSP00000370593:N578S;ENSP00000348812:N578S;ENSP00000353187:N565S;ENSP00000351293:N565S;ENSP00000347373:N578S;ENSP00000380741:N568S;ENSP00000380735:N575S;ENSP00000440515:N575S;ENSP00000438164:N578S;ENSP00000417093:N578S;ENSP00000380731:N568S	.	N	-	2	0	PTPRD	8494350	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	4.929000	0.63455	2.103000	0.63969	0.383000	0.25322	AAC	.	.		0.468	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3			C	8504350	T	C	8504350	3	2	285	1	0	0	0	0	1	0	0	0	12814	1725	60	2	4169	2	PTPRD	9	8504350	Missense_Mutation	SNP	T	TCGA-G3-A5SJ-01A-11D-A27I-10		8504350	132709081	56	41965										
SLC24A2	25769	hgsc.bcm.edu	37	chr9	19516230	19516230	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	acacaaagtagaggccaaacAtgatgaagcccaggattttg	10	8	0	3			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr9:19516230A>T	ENST00000341998.2	-	10	1968	c.1907T>A	c.(1906-1908)aTg>aAg	p.M636K	SLC24A2_ENST00000286344.3_Missense_Mutation_p.M619K	NM_001193288.2|NM_020344.3	NP_001180217.1|NP_065077.1	Q9UI40	NCKX2_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 2	636					cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)	cadmium ion binding (GO:0046870)|calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium, potassium:sodium antiporter activity (GO:0008273)|manganese ion binding (GO:0030145)|nickel cation binding (GO:0016151)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|symporter activity (GO:0015293)			endometrium(3)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33				GBM - Glioblastoma multiforme(1;1.67e-55)|Lung(42;0.0443)		GAGGCCAAACATGATGAAGCC	0.483																																					p.M636K		Atlas-SNP	.											.	SLC24A2	93	.	0			c.T1907A						.						159	149	152					9																	19516230		2203	4300	6503	SO:0001583	missense	25769	exon10			CCAAACATGATGA	AF097366	CCDS6493.1, CCDS55297.1	9p22.1	2013-05-22			ENSG00000155886	ENSG00000155886		"Solute carriers"	10976	protein-coding gene	gene with protein product		609838				10662833	Standard	NM_020344		Approved	NCKX2	uc003zoa.2	Q9UI40	OTTHUMG00000019646	ENST00000341998.2:c.1907T>A	chr9.hg19:g.19516230A>T	ENSP00000344801:p.Met636Lys	267.0	0.0		131.0	34.0	NM_020344	B7ZLL8|Q9NTN5|Q9NZQ4	Missense_Mutation	SNP	ENST00000341998.2	hg19	CCDS6493.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.450050	0.84101	.	.	ENSG00000155886	ENST00000341998;ENST00000286344	T;T	0.64991	-0.13;-0.13	5.21	5.21	0.72293	Sodium/calcium exchanger membrane region (1);	0.000000	0.85682	D	0.000000	D	0.85427	0.5694	H	0.96208	3.785	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.90234	0.4281	9	.	.	.	.	15.1006	0.72273	1.0:0.0:0.0:0.0	.	619;636	Q9UI40-2;Q9UI40	.;NCKX2_HUMAN	K	636;619	ENSP00000344801:M636K;ENSP00000286344:M619K	.	M	-	2	0	SLC24A2	19506230	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.282000	0.95840	1.975000	0.57531	0.533000	0.62120	ATG	.	.		0.483	SLC24A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051866.2	NM_020344		T	19516230	A	T	19516230	3	4	285	1	0	0	0	0	1	0	0	0	14481	217	8	4	82	4	SLC24A2	9	19516230	Missense_Mutation	SNP	A	TCGA-G3-A5SJ-01A-11D-A27I-10	11011880	19516230	121697201	57	41966										
DAB2IP	153090	hgsc.bcm.edu	37	chr9	124535286	124535286	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	cccagctgttggcaccgctcTccttccagaaccctgtgtac	8	17	1	1			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr9:124535286T>G	ENST00000408936.3	+	12	2661	c.2479T>G	c.(2479-2481)Tcc>Gcc	p.S827A	DAB2IP_ENST00000309989.1_Missense_Mutation_p.S703A|DAB2IP_ENST00000259371.2_Missense_Mutation_p.S799A			Q5VWQ8	DAB2P_HUMAN	DAB2 interacting protein	827	Necessary for interaction with AKT1.				activation of JUN kinase activity (GO:0007257)|activation of MAPKKK activity (GO:0000185)|angiogenesis (GO:0001525)|cell cycle (GO:0007049)|cell motility involved in cerebral cortex radial glia guided migration (GO:0021814)|cellular protein catabolic process (GO:0044257)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|layer formation in cerebral cortex (GO:0021819)|negative regulation of angiogenesis (GO:0016525)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of G0 to G1 transition (GO:0070317)|negative regulation of GTPase activity (GO:0034260)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphatidylinositol 3-kinase activity (GO:0043553)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of Ras GTPase activity (GO:0034261)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuron projection morphogenesis (GO:0048812)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of dendrite development (GO:1900006)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of synapse maturation (GO:0090129)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of ARF GTPase activity (GO:0032312)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein complex assembly (GO:0043254)|response to unfolded protein (GO:0006986)|transformed cell apoptotic process (GO:0006927)|tube formation (GO:0035148)|vascular endothelial growth factor receptor-2 signaling pathway (GO:0036324)	axon (GO:0030424)|cerebellar mossy fiber (GO:0044300)|climbing fiber (GO:0044301)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|neuronal cell body (GO:0043025)|neuronal cell body membrane (GO:0032809)|parallel fiber (GO:1990032)|plasma membrane (GO:0005886)	14-3-3 protein binding (GO:0071889)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|mitogen-activated protein kinase kinase binding (GO:0031434)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulatory subunit binding (GO:0036312)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein phosphatase 2A binding (GO:0051721)|Ras GTPase activator activity (GO:0005099)|SH3 domain binding (GO:0017124)|signaling adaptor activity (GO:0035591)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(8)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	27						GGCACCGCTCTCCTTCCAGAA	0.706																																					p.S799A		Atlas-SNP	.											.	DAB2IP	150	.	0			c.T2395G						.						29	29	29					9																	124535286		2159	4216	6375	SO:0001583	missense	153090	exon12			CCGCTCTCCTTCC	AF367051	CCDS6832.1, CCDS6833.2	9q33.1-q33.3	2008-07-21			ENSG00000136848	ENSG00000136848			17294	protein-coding gene	gene with protein product	"nGAP-like protein", "DOC-2/DAB2 interactive protein", "ASK-interacting protein", "ASK1-interacting protein 1"	609205				11944990, 11812785	Standard	XM_005251721		Approved	AF9Q34, DIP1/2, KIAA1743, AIP1	uc004bln.3	Q5VWQ8	OTTHUMG00000020595	ENST00000408936.3:c.2479T>G	chr9.hg19:g.124535286T>G	ENSP00000386183:p.Ser827Ala	41.0	0.0		32.0	11.0	NM_032552	A6H8V2|A6NHI9|B0QZB1|G3XA90|Q8TDL2|Q96SE1|Q9C0C0	Missense_Mutation	SNP	ENST00000408936.3	hg19		.	.	.	.	.	.	.	.	.	.	T	22.4	4.288620	0.80914	.	.	ENSG00000136848	ENST00000259371;ENST00000408936;ENST00000373782;ENST00000309989	T;T;T;T	0.28895	1.59;1.59;1.59;1.59	4.69	4.69	0.59074	.	0.000000	0.85682	D	0.000000	T	0.57095	0.2030	M	0.81942	2.565	0.53688	D	0.999972	D;D	0.89917	0.979;1.0	D;D	0.91635	0.982;0.999	T	0.63862	-0.6541	10	0.87932	D	0	.	13.6154	0.62105	0.0:0.0:0.0:1.0	.	827;799	Q5VWQ8;G3XA90	DAB2P_HUMAN;.	A	799;827;736;703	ENSP00000259371:S799A;ENSP00000386183:S827A;ENSP00000362887:S736A;ENSP00000310827:S703A	ENSP00000259371:S799A	S	+	1	0	DAB2IP	123575107	1.000000	0.71417	0.993000	0.49108	0.957000	0.61999	5.825000	0.69286	1.878000	0.54408	0.379000	0.24179	TCC	.	.		0.706	DAB2IP-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317857.1	NM_032552		G	124535286	T	G	124535286	3	3	285	1	0	0	0	0	1	0	0	0	4221	1551	54	5	2441	5	DAB2IP	9	124535286	Missense_Mutation	SNP	T	TCGA-G3-A5SJ-01A-11D-A27I-10	105019056	124535286	16678145	58	41967										
ITGA8	8516	hgsc.bcm.edu	37	chr10	15559199	15559199	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	tttgtcagctgttccctgtcGgtcatgtcctcctgaggagg	12	11	2	1	rs199977895	byFrequency	TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr10:15559199G>T	ENST00000378076.3	-	30	3503	c.3150C>A	c.(3148-3150)acC>acA	p.T1050T		NM_003638.1	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8	1050					brain development (GO:0007420)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|metanephros development (GO:0001656)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|substrate adhesion-dependent cell spreading (GO:0034446)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|dendritic spine membrane (GO:0032591)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integrin alpha8-beta1 complex (GO:0034678)|integrin complex (GO:0008305)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	metal ion binding (GO:0046872)			NS(2)|breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(57)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	96						GTTCCCTGTCGGTCATGTCCT	0.448													G|||	14	0.00279553	0	0	5008	,	,		14194	0		0	False		,,,				2504	0.0143				p.T1050T		Atlas-SNP	.											.	ITGA8	230	.	0			c.C3150A						.						85	82	83					10																	15559199		2203	4300	6503	SO:0001819	synonymous_variant	8516	exon30			CCTGTCGGTCATG	L36531	CCDS31155.1	10p13	2010-03-23			ENSG00000077943	ENSG00000077943		"Integrins"	6144	protein-coding gene	gene with protein product		604063				7768999	Standard	XM_005252633		Approved		uc001ioc.1	P53708	OTTHUMG00000017733	ENST00000378076.3:c.3150C>A	chr10.hg19:g.15559199G>T		65.0	0.0		42.0	18.0	NM_003638	B0YJ31|Q5VX94	Silent	SNP	ENST00000378076.3	hg19	CCDS31155.1																																																																																			.	G|0.999;T|0.001		0.448	ITGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046987.1	NM_003638		T	15559199	G	T	15559199	2	4	285	1	0	0	0	0	0	0	0	1	7891	1103	39	1		1	ITGA8	10	15559199	Silent	SNP	G	TCGA-G3-A5SJ-01A-11D-A27I-10		15559199	119975548	59	41968										
ZNF488	118738	hgsc.bcm.edu	37	chr10	48370889	48370889	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	gtggatgctcaggcccaggaGagggagcacgatgaccccac	15	12	1	2			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr10:48370889G>T	ENST00000395702.2	+	2	584	c.357G>T	c.(355-357)gaG>gaT	p.E119D	ZNF488_ENST00000494156.1_3'UTR|ZNF488_ENST00000586537.1_Missense_Mutation_p.E12D			Q96MN9	ZN488_HUMAN	zinc finger protein 488	119					negative regulation of transcription, DNA-templated (GO:0045892)|oligodendrocyte development (GO:0014003)|positive regulation of oligodendrocyte differentiation (GO:0048714)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|ovary(2)	14						AGGCCCAGGAGAGGGAGCACG	0.652																																					p.E119D		Atlas-SNP	.											.	ZNF488	38	.	0			c.G357T						.						38	39	39					10																	48370889		2202	4300	6502	SO:0001583	missense	118738	exon2			CCAGGAGAGGGAG	AK056666	CCDS73120.1	10q11.22	2014-04-10			ENSG00000165388	ENSG00000265763		"Zinc fingers, C2H2-type"	23535	protein-coding gene	gene with protein product							Standard	NM_153034		Approved	FLJ32104	uc001jex.3	Q96MN9	OTTHUMG00000188322	ENST00000395702.2:c.357G>T	chr10.hg19:g.48370889G>T	ENSP00000379054:p.Glu119Asp	232.0	0.0		75.0	34.0	NM_153034	Q05CE0	Missense_Mutation	SNP	ENST00000395702.2	hg19	CCDS7217.1	.	.	.	.	.	.	.	.	.	.	g	12.50	1.957986	0.34565	.	.	ENSG00000165388	ENST00000395702;ENST00000444585;ENST00000425196	T;T;T	0.37915	1.8;1.17;1.2	5.13	-7.36	0.01417	.	0.762403	0.11504	U	0.557418	T	0.20577	0.0495	L	0.50333	1.59	0.09310	N	1	B	0.12630	0.006	B	0.08055	0.003	T	0.24584	-1.0156	10	0.18710	T	0.47	.	3.2795	0.06909	0.4309:0.2614:0.2195:0.0882	.	119	Q96MN9	ZN488_HUMAN	D	119	ENSP00000379054:E119D;ENSP00000410326:E119D;ENSP00000412898:E119D	ENSP00000379054:E119D	E	+	3	2	ZNF488	47990895	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.017000	0.03630	-1.545000	0.01719	-0.376000	0.06991	GAG	.	.		0.652	ZNF488-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314632.1	NM_153034		T	48370889	G	T	48370889	3	4	285	1	0	0	0	0	1	0	0	0	17955	933	33	3	359	3	ZNF488	10	48370889	Missense_Mutation	SNP	G	TCGA-G3-A5SJ-01A-11D-A27I-10	32811690	48370889	87163858	60	41969										
SUPV3L1	6832	hgsc.bcm.edu	37	chr10	70955011	70955011	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	agaggatgggcctggaccagAgcacttctaggttggtggtc	16	8	1	2			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr10:70955011A>T	ENST00000359655.4	+	7	981	c.921A>T	c.(919-921)agA>agT	p.R307S		NM_003171.3	NP_003162.2	Q8IYB8	SUV3_HUMAN	suppressor of var1, 3-like 1 (S. cerevisiae)	307	Helicase ATP-binding.				ATP catabolic process (GO:0006200)|chromatin maintenance (GO:0070827)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|mitochondrial mRNA catabolic process (GO:0000958)|mitochondrial mRNA surveillance (GO:0035946)|mitochondrial ncRNA surveillance (GO:0035945)|mitochondrial RNA 3'-end processing (GO:0000965)|mitochondrial RNA surveillance (GO:2000827)|mitochondrion morphogenesis (GO:0070584)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell growth (GO:0030307)|positive regulation of mitochondrial RNA catabolic process (GO:0000962)|RNA catabolic process (GO:0006401)	mitochondrial degradosome (GO:0045025)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	3'-5' RNA helicase activity (GO:0034458)|ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						CCTGGACCAGAGCACTTCTAG	0.408																																					p.R307S		Atlas-SNP	.											.	SUPV3L1	61	.	0			c.A921T						.						77	77	77					10																	70955011		2203	4300	6503	SO:0001583	missense	6832	exon7			GACCAGAGCACTT	AF042169	CCDS7287.1	10q22.1	2008-08-01	2001-11-28		ENSG00000156502	ENSG00000156502			11471	protein-coding gene	gene with protein product		605122	"suppressor of var1 (S.cerevisiae) 3-like 1"			9925937, 16176273	Standard	XM_005270068		Approved	SUV3	uc001jpe.1	Q8IYB8	OTTHUMG00000018375	ENST00000359655.4:c.921A>T	chr10.hg19:g.70955011A>T	ENSP00000352678:p.Arg307Ser	150.0	0.0		39.0	20.0	NM_003171	A8K301|O43630	Missense_Mutation	SNP	ENST00000359655.4	hg19	CCDS7287.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.408968	0.83340	.	.	ENSG00000156502	ENST00000359655;ENST00000422378	T;T	0.33654	1.4;1.43	5.82	4.7	0.59300	.	0.000000	0.85682	D	0.000000	T	0.64638	0.2616	M	0.90595	3.13	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.69950	-0.5006	10	0.87932	D	0	-22.1198	10.4492	0.44511	0.8653:0.0:0.1347:0.0	.	307	Q8IYB8	SUV3_HUMAN	S	307;113	ENSP00000352678:R307S;ENSP00000409072:R113S	ENSP00000352678:R307S	R	+	3	2	SUPV3L1	70625017	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.559000	0.60796	1.043000	0.40175	0.528000	0.53228	AGA	.	.		0.408	SUPV3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048396.2	NM_003171		T	70955011	A	T	70955011	3	4	285	1	0	0	0	0	1	0	0	0	15417	301	11	4	947	4	SUPV3L1	10	70955011	Missense_Mutation	SNP	A	TCGA-G3-A5SJ-01A-11D-A27I-10	22584122	70955011	64579736	61	41970										
DLG5	9231	hgsc.bcm.edu	37	chr10	79577541	79577541	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	agtggtgcagttacccaggcGggcgctggagggcagtgagt	19	8	0	1			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr10:79577541G>C	ENST00000372391.2	-	18	3783	c.3778C>G	c.(3778-3780)Cgc>Ggc	p.R1260G	DLG5_ENST00000459739.1_5'UTR|DLG5_ENST00000372388.2_Missense_Mutation_p.R920G	NM_004747.3	NP_004738.3	Q8TDM6	DLG5_HUMAN	discs, large homolog 5 (Drosophila)	1260					apical protein localization (GO:0045176)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|intracellular signal transduction (GO:0035556)|metanephric collecting duct development (GO:0072205)|midbrain development (GO:0030901)|negative regulation of cell proliferation (GO:0008285)|polarized epithelial cell differentiation (GO:0030859)|protein complex assembly (GO:0006461)|protein localization to adherens junction (GO:0071896)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|zonula adherens assembly (GO:0045186)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cytoskeletal protein binding (GO:0008092)|receptor signaling complex scaffold activity (GO:0030159)			breast(9)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(17)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	60	all_cancers(46;0.0316)|all_epithelial(25;0.00147)|Breast(12;0.0015)|Prostate(51;0.0146)		Epithelial(14;0.00105)|OV - Ovarian serous cystadenocarcinoma(4;0.00151)|all cancers(16;0.00446)			TTACCCAGGCGGGCGCTGGAG	0.617																																					p.R1260G		Atlas-SNP	.											.	DLG5	154	.	0			c.C3778G						.						55	40	45					10																	79577541		2170	4243	6413	SO:0001583	missense	9231	exon18			CCAGGCGGGCGCT	U61843	CCDS7353.2	10q23	2008-07-09	2001-11-28		ENSG00000151208	ENSG00000151208			2904	protein-coding gene	gene with protein product		604090	"discs, large (Drosophila) homolog 5"			9738934	Standard	XM_005270276		Approved	P-dlg, KIAA0583	uc001jzk.3	Q8TDM6	OTTHUMG00000018548	ENST00000372391.2:c.3778C>G	chr10.hg19:g.79577541G>C	ENSP00000361467:p.Arg1260Gly	161.0	0.0		52.0	29.0	NM_004747	A6H8Y3|Q149N1|Q5T1H7|Q5T1H8|Q6DKG3|Q86WC0|Q8TDM7|Q9UE73|Q9Y4E3	Missense_Mutation	SNP	ENST00000372391.2	hg19	CCDS7353.2	.	.	.	.	.	.	.	.	.	.	G	13.56	2.273675	0.40194	.	.	ENSG00000151208	ENST00000372391;ENST00000424842;ENST00000372388	T;T;T	0.06687	3.27;3.32;3.49	5.8	3.86	0.44501	.	0.000000	0.39615	N	0.001314	T	0.15609	0.0376	L	0.46157	1.445	0.80722	D	1	D;D;B	0.76494	0.998;0.999;0.35	P;D;B	0.65233	0.899;0.933;0.203	T	0.12477	-1.0546	10	0.14656	T	0.56	.	9.247	0.37532	0.0775:0.0:0.7119:0.2107	.	1150;1260;920	Q8TDM6-4;Q8TDM6;Q8TDM6-2	.;DLG5_HUMAN;.	G	1260;221;920	ENSP00000361467:R1260G;ENSP00000394797:R221G;ENSP00000361464:R920G	ENSP00000361464:R920G	R	-	1	0	DLG5	79247547	1.000000	0.71417	1.000000	0.80357	0.879000	0.50718	3.546000	0.53656	1.459000	0.47892	0.655000	0.94253	CGC	.	.		0.617	DLG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048900.2			C	79577541	G	C	79577541	3	2	285	1	0	0	0	0	1	0	0	0	4560	1116	39	4	2041	4	DLG5	10	79577541	Missense_Mutation	SNP	G	TCGA-G3-A5SJ-01A-11D-A27I-10	8622530	79577541	55957206	62	41971										
BLNK	29760	hgsc.bcm.edu	37	chr10	97956734	97956734	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	taaatcgcacaggaatattaTatactcgcttattaaagaat	5	6	0	1			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr10:97956734T>C	ENST00000224337.5	-	16	1322	c.1181A>G	c.(1180-1182)tAt>tGt	p.Y394C	BLNK_ENST00000427367.2_Intron|BLNK_ENST00000413476.2_Intron|BLNK_ENST00000371176.2_Missense_Mutation_p.Y371C	NM_013314.3	NP_037446.1	Q8WV28	BLNK_HUMAN	B-cell linker	394	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				B cell differentiation (GO:0030183)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|positive regulation of signal transduction (GO:0009967)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|skin(2)|stomach(1)	14		Colorectal(252;0.083)		Epithelial(162;7.89e-08)|all cancers(201;2.27e-06)		AGGAATATTATATACTCGCTT	0.318																																					p.Y394C		Atlas-SNP	.											.	BLNK	46	.	0			c.A1181G						.						92	95	94					10																	97956734		2203	4299	6502	SO:0001583	missense	29760	exon16			ATATTATATACTC	AF068180	CCDS7446.1, CCDS44464.1, CCDS58091.1, CCDS73171.1	10q23.2-q23.33	2014-09-17			ENSG00000095585	ENSG00000095585		"SH2 domain containing"	14211	protein-coding gene	gene with protein product	"B-cell adapter containing a SH2 domain protein", "B-cell activation", "Src homology [SH2] domain-containing leukocyte protein of 65 kD", "B cell adaptor containing SH2 domain"	604515				9697839, 10583958	Standard	NM_013314		Approved	SLP65, Ly57, SLP-65, BLNK-s, BASH, bca	uc001kls.4	Q8WV28	OTTHUMG00000018827	ENST00000224337.5:c.1181A>G	chr10.hg19:g.97956734T>C	ENSP00000224337:p.Tyr394Cys	68.0	0.0		14.0	7.0	NM_013314	O75498|O75499|Q2MD49	Missense_Mutation	SNP	ENST00000224337.5	hg19	CCDS7446.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.0|20.0	3.929819|3.929819	0.73327|0.73327	.|.	.|.	ENSG00000095585|ENSG00000095585	ENST00000393889|ENST00000224337;ENST00000371176	.|D;D	.|0.88509	.|-2.39;-2.39	5.06|5.06	5.06|5.06	0.68205|0.68205	.|SH2 motif (4);	.|0.062767	.|0.64402	.|D	.|0.000003	D|D	0.94424|0.94424	0.8206|0.8206	M|M	0.83483|0.83483	2.645|2.645	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.97110	.|1.0;1.0;1.0	D|D	0.95153|0.95153	0.8274|0.8274	6|10	0.26408|0.87932	T|D	0.33|0	-15.7777|-15.7777	14.0992|14.0992	0.65044|0.65044	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|371;371;394	.|Q8WV28-2;Q2MD52;Q8WV28	.|.;.;BLNK_HUMAN	V|C	120|394;371	.|ENSP00000224337:Y394C;ENSP00000360218:Y371C	ENSP00000377467:I120V|ENSP00000224337:Y394C	I|Y	-|-	1|2	0|0	BLNK|BLNK	97946724|97946724	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	6.911000|6.911000	0.75746|0.75746	2.021000|2.021000	0.59480|0.59480	0.533000|0.533000	0.62120|0.62120	ATA|TAT	.	.		0.318	BLNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049593.1	NM_013314		C	97956734	T	C	97956734	3	2	285	1	0	0	0	0	1	0	0	0	1447	1406	49	2	197	2	BLNK	10	97956734	Missense_Mutation	SNP	T	TCGA-G3-A5SJ-01A-11D-A27I-10	18379193	97956734	37578013	63	41972										
PHRF1	57661	hgsc.bcm.edu	37	chr11	587380	587380	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	gagagctgcccaatctgtctCaacgcattcagagaccaggc	10	13	3	2			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr11:587380C>A	ENST00000264555.5	+	4	464	c.336C>A	c.(334-336)ctC>ctA	p.L112L	PHRF1_ENST00000416188.2_Silent_p.L112L|PHRF1_ENST00000533464.1_Silent_p.L108L|PHRF1_ENST00000413872.2_Silent_p.L111L	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	112					mRNA processing (GO:0006397)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)	RNA polymerase binding (GO:0070063)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|urinary_tract(2)	28						CAATCTGTCTCAACGCATTCA	0.557																																					p.L112L		Atlas-SNP	.											.	PHRF1	188	.	0			c.C336A						.						109	116	114					11																	587380		2067	4194	6261	SO:0001819	synonymous_variant	57661	exon4			CTGTCTCAACGCA	BC004950	CCDS44507.1, CCDS65987.1, CCDS65988.1, CCDS65989.1	11p15.5	2014-06-13			ENSG00000070047	ENSG00000070047		"RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	24351	protein-coding gene	gene with protein product	"CTD binding SR like protein rA9", "protein phosphatase 1, regulatory subunit 125"	611780		RNF221			Standard	XM_005253027		Approved	KIAA1542, PPP1R125	uc010qwc.2	Q9P1Y6	OTTHUMG00000165141	ENST00000264555.5:c.336C>A	chr11.hg19:g.587380C>A		222.0	0.0		49.0	24.0	NM_020901	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Silent	SNP	ENST00000264555.5	hg19																																																																																				.	.		0.557	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901		A	587380	C	A	587380	2	1	285	1	0	0	0	0	0	0	0	1	11870	813	29	3		3	PHRF1	11	587380	Silent	SNP	C	TCGA-G3-A5SJ-01A-11D-A27I-10		587380	134419136	64	41973										
KCNA5	3741	hgsc.bcm.edu	37	chr12	5153808	5153808	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	ctgaggaacgagtacttcttCgaccgcaaccggcccagctt	10	14	1	1			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr12:5153808C>T	ENST00000252321.3	+	1	724	c.495C>T	c.(493-495)ttC>ttT	p.F165F		NM_002234.3	NP_002225.2	P22460	KCNA5_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 5	165					atrial cardiac muscle cell action potential (GO:0086014)|membrane hyperpolarization (GO:0060081)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of potassium ion transport (GO:0043267)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of myoblast proliferation (GO:2000288)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transport (GO:0043266)|regulation of vasoconstriction (GO:0019229)|response to hypoxia (GO:0001666)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|intracellular canaliculus (GO:0046691)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|potassium channel inhibitor activity (GO:0019870)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization (GO:0086089)			NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(21)|ovary(5)|prostate(2)|upper_aerodigestive_tract(2)	52					Dalfampridine(DB06637)	AGTACTTCTTCGACCGCAACC	0.667																																					p.F165F		Atlas-SNP	.											.	KCNA5	138	.	0			c.C495T						.						38	41	40					12																	5153808		2203	4300	6503	SO:0001819	synonymous_variant	3741	exon1			CTTCTTCGACCGC	M83254	CCDS8536.1	12p13	2012-07-05				ENSG00000130037		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6224	protein-coding gene	gene with protein product		176267				16382104	Standard	NM_002234		Approved	Kv1.5, HK2, HPCN1	uc001qni.4	P22460		ENST00000252321.3:c.495C>T	chr12.hg19:g.5153808C>T		109.0	0.0		60.0	30.0	NM_002234	Q4KKT8|Q4VAJ1|Q4VAJ2|Q9UDA4	Silent	SNP	ENST00000252321.3	hg19	CCDS8536.1																																																																																			.	.		0.667	KCNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398925.2	NM_002234		T	5153808	C	T	5153808	2	4	285	1	0	0	0	0	0	0	0	1	8015	883	31	1		1	KCNA5	12	5153808	Silent	SNP	C	TCGA-G3-A5SJ-01A-11D-A27I-10		5153808	128698087	65	41974										
SCNN1A	6337	hgsc.bcm.edu	37	chr12	6483876	6483876	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	ccagcccctgctcctcacgcTtgttccccttcatgagccct	6	20	2	1			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr12:6483876T>C	ENST00000228916.2	-	2	172	c.74A>G	c.(73-75)aAg>aGg	p.K25R	SCNN1A_ENST00000360168.3_Missense_Mutation_p.K84R|SCNN1A_ENST00000543768.1_Missense_Mutation_p.K48R|LTBR_ENST00000539925.1_5'Flank|SCNN1A_ENST00000538979.1_Intron|SCNN1A_ENST00000396966.2_Missense_Mutation_p.K25R|SCNN1A_ENST00000358945.3_Missense_Mutation_p.K25R	NM_001038.5	NP_001029.1	P37088	SCNNA_HUMAN	sodium channel, non-voltage-gated 1 alpha subunit	25					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ciliary membrane (GO:0060170)|cortical actin cytoskeleton (GO:0030864)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|WW domain binding (GO:0050699)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(2)|lung(6)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Amiloride(DB00594)|Triamterene(DB00384)	CTCCTCACGCTTGTTCCCCTT	0.657																																					p.K84R		Atlas-SNP	.											.	SCNN1A	54	.	0			c.A251G						.						44	45	45					12																	6483876		2203	4300	6503	SO:0001583	missense	6337	exon1			TCACGCTTGTTCC	Z92978	CCDS8543.1, CCDS53738.1, CCDS53739.1	12p13	2012-02-28	2012-02-28		ENSG00000111319	ENSG00000111319		"Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels"	10599	protein-coding gene	gene with protein product		600228	"sodium channel, nonvoltage-gated 1 alpha", "sodium channel, non-voltage-gated 1 alpha"	SCNN1		7896277	Standard	NM_001038		Approved	ENaCalpha	uc001qnw.3	P37088	OTTHUMG00000168268	ENST00000228916.2:c.74A>G	chr12.hg19:g.6483876T>C	ENSP00000228916:p.Lys25Arg	67.0	0.0		35.0	16.0	NM_001159576	A5X2U9|B4E2Q5|C5HTZ0|O43271|Q6GSQ6|Q9UM64	Missense_Mutation	SNP	ENST00000228916.2	hg19	CCDS8543.1	.	.	.	.	.	.	.	.	.	.	T	12.33	1.906381	0.33628	.	.	ENSG00000111319	ENST00000360168;ENST00000358945;ENST00000228916;ENST00000396966;ENST00000543768;ENST00000536788	T;T;T;T;T;D	0.86432	-0.47;-0.52;-0.46;-0.14;-0.45;-2.12	4.95	3.8	0.43715	.	0.414043	0.23079	N	0.052175	T	0.81569	0.4850	M	0.64997	1.995	0.09310	N	1	P;B;B	0.35077	0.483;0.164;0.418	B;B;B	0.27887	0.084;0.06;0.083	T	0.72197	-0.4363	10	0.46703	T	0.11	-21.2032	7.4973	0.27496	0.0:0.0997:0.0:0.9003	.	48;25;84	B4E2Q5;P37088;P37088-2	.;SCNNA_HUMAN;.	R	84;25;25;25;48;46	ENSP00000353292:K84R;ENSP00000351825:K25R;ENSP00000228916:K25R;ENSP00000380166:K25R;ENSP00000438739:K48R;ENSP00000443434:K46R	ENSP00000228916:K25R	K	-	2	0	SCNN1A	6354137	0.008000	0.16893	0.005000	0.12908	0.111000	0.19643	1.341000	0.33907	0.739000	0.32628	0.482000	0.46254	AAG	.	.		0.657	SCNN1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399055.1			C	6483876	T	C	6483876	3	2	285	1	0	0	0	0	1	0	0	0	13942	1609	56	2	1983	2	SCNN1A	12	6483876	Missense_Mutation	SNP	T	TCGA-G3-A5SJ-01A-11D-A27I-10	1330068	6483876	127368019	66	41975										
CD163	9332	hgsc.bcm.edu	37	chr12	7640068	7640068	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	tgcagtgaaacatatgcctcCagatctgaccatttcctttt	6	11	1	3			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr12:7640068C>A	ENST00000359156.4	-	8	2139	c.1937G>T	c.(1936-1938)tGg>tTg	p.W646L	CD163_ENST00000432237.2_Missense_Mutation_p.W646L|CD163_ENST00000539632.1_5'Flank|CD163_ENST00000396620.3_Missense_Mutation_p.W679L|CD163_ENST00000541972.1_Missense_Mutation_p.W634L	NM_004244.5	NP_004235.4	Q86VB7	C163A_HUMAN	CD163 molecule	646	SRCR 6. {ECO:0000255|PROSITE- ProRule:PRU00196}.				acute-phase response (GO:0006953)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(6)|pancreas(2)|prostate(1)|skin(5)|urinary_tract(4)	76					WF10(DB05389)	CATATGCCTCCAGATCTGACC	0.488																																					p.W646L		Atlas-SNP	.											.	CD163	221	.	0			c.G1937T						.						151	135	141					12																	7640068		2203	4300	6503	SO:0001583	missense	9332	exon8			TGCCTCCAGATCT	Z22968	CCDS8578.1, CCDS53742.1	12p13	2006-03-28	2006-03-28		ENSG00000177575	ENSG00000177575		"CD molecules"	1631	protein-coding gene	gene with protein product		605545	"CD163 antigen"			10403791, 8370408	Standard	NM_004244		Approved	M130, MM130	uc001qsz.3	Q86VB7	OTTHUMG00000168353	ENST00000359156.4:c.1937G>T	chr12.hg19:g.7640068C>A	ENSP00000352071:p.Trp646Leu	334.0	1.0		149.0	58.0	NM_203416	C9JIG2|Q07898|Q07899|Q07900|Q07901|Q2VLH7	Missense_Mutation	SNP	ENST00000359156.4	hg19	CCDS8578.1	.	.	.	.	.	.	.	.	.	.	C	9.469	1.095028	0.20471	.	.	ENSG00000177575	ENST00000359156;ENST00000541972;ENST00000396620;ENST00000432237	T;T;T;T	0.29917	1.55;1.55;1.55;1.55	5.14	5.14	0.70334	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.177698	0.41712	N	0.000829	T	0.49236	0.1545	L	0.51422	1.61	0.47511	D	0.999446	D;D;D	0.89917	1.0;0.997;1.0	D;P;D	0.97110	1.0;0.844;1.0	T	0.26780	-1.0093	10	0.29301	T	0.29	.	16.4748	0.84129	0.0:1.0:0.0:0.0	.	679;646;646	C9JHR8;Q86VB7-3;Q86VB7	.;.;C163A_HUMAN	L	646;634;679;646	ENSP00000352071:W646L;ENSP00000444071:W634L;ENSP00000379863:W679L;ENSP00000403885:W646L	ENSP00000352071:W646L	W	-	2	0	CD163	7531335	1.000000	0.71417	1.000000	0.80357	0.865000	0.49528	2.164000	0.42387	2.561000	0.86390	0.655000	0.94253	TGG	.	.		0.488	CD163-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399396.2	NM_004244, NM_203416		A	7640068	C	A	7640068	3	1	285	1	0	0	0	0	1	0	0	0	2969	595	21	3	1569	3	CD163	12	7640068	Missense_Mutation	SNP	C	TCGA-G3-A5SJ-01A-11D-A27I-10	1156192	7640068	126211827	67	41976										
FLT1	2321	hgsc.bcm.edu	37	chr13	28963881	28963881	+	Intron	DEL	C	C	-													0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	tggtacaatcattccttgtgCttttaaatttggagatccga							TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr13:28963881delC	ENST00000282397.4	-	13	2221				FLT1_ENST00000541932.1_Intron	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1						blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	ATTCCTTGTGCTTTTAAATTT	0.353																																					p.S674fs		Atlas-Indel,Pindel	.											.	FLT1	393	.	0			c.2022delC						.						98	85	89					13																	28963881		1568	3582	5150	SO:0001627	intron_variant	2321	exon13			.	AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3763	protein-coding gene	gene with protein product	"vascular endothelial growth factor receptor 1", "vascular permeability factor receptor"	165070	"fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.1969+51G>-	chr13.hg19:g.28963881delC		50.0	0.0		33.0	15.0	NM_001159920	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Frame_Shift_Del	DEL	ENST00000282397.4	hg19	CCDS9330.1																																																																																			.	.		0.353	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1			-	28963881	C	-	28963881	6	5	285	0	1	1	0	1	0	0	0	0	5949	797	28	0		0	FLT1	13	28963881	Intron	DEL	C	TCGA-G3-A5SJ-01A-11D-A27I-10		28963881	86205997	68	41977										
NAA16	79612	hgsc.bcm.edu	37	chr13	41905450	41905450	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	caaatttatgaagaaattagTaagcagcaccccaaagcaat	6	8	0	2			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr13:41905450T>C	ENST00000379406.3	+	8	1176	c.852T>C	c.(850-852)agT>agC	p.S284S	NAA16_ENST00000403412.3_Silent_p.S284S|NAA16_ENST00000379367.3_Silent_p.S284S	NM_024561.4	NP_078837.3	Q6N069	NAA16_HUMAN	N(alpha)-acetyltransferase 16, NatA auxiliary subunit	284					N-terminal protein amino acid acetylation (GO:0006474)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NatA complex (GO:0031415)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ribosome binding (GO:0043022)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|urinary_tract(2)	31						AAGAAATTAGTAAGCAGCACC	0.313																																					p.S284S		Atlas-SNP	.											.	NAA16	74	.	0			c.T852C						.						81	89	86					13																	41905450		2203	4296	6499	SO:0001819	synonymous_variant	79612	exon8			AATTAGTAAGCAG	AL833341	CCDS9379.1, CCDS45044.1	13q14.11	2013-01-10	2010-01-14	2010-01-14	ENSG00000172766	ENSG00000172766		"N(alpha)-acetyltransferase subunits", "Tetratricopeptide (TTC) repeat domain containing"	26164	protein-coding gene	gene with protein product			"NMDA receptor regulated 1-like"	NARG1L		11483580, 19660095	Standard	NM_024561		Approved	FLJ22054, MGC40612, PRO2435	uc001uyf.2	Q6N069	OTTHUMG00000016791	ENST00000379406.3:c.852T>C	chr13.hg19:g.41905450T>C		115.0	0.0		64.0	20.0	NM_001110798	B0QZ59|Q5VSP9|Q6P2D5|Q8N5J3|Q8N870	Silent	SNP	ENST00000379406.3	hg19	CCDS9379.1																																																																																			.	.		0.313	NAA16-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044672.2	NM_018527		C	41905450	T	C	41905450	2	2	285	1	0	0	0	0	0	0	0	1	10128	1635	57	2		2	NAA16	13	41905450	Silent	SNP	T	TCGA-G3-A5SJ-01A-11D-A27I-10	12941569	41905450	73264428	69	41978										
SLITRK5	26050	hgsc.bcm.edu	37	chr13	88330185	88330185	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	gggaggacctgctgtcgccgGtgcaggacgccgaccgcttt	16	13	0	0			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr13:88330185G>A	ENST00000325089.6	+	2	2761	c.2542G>A	c.(2542-2544)Gtg>Atg	p.V848M	SLITRK5_ENST00000400028.3_Missense_Mutation_p.V607M	NM_015567.1	NP_056382.1	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5	848					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|cardiovascular system development (GO:0072358)|dendrite morphogenesis (GO:0048813)|grooming behavior (GO:0007625)|response to xenobiotic stimulus (GO:0009410)|skin development (GO:0043588)|striatum development (GO:0021756)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(14)|lung(40)|ovary(2)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(4)	81	all_neural(89;0.101)|Medulloblastoma(90;0.163)					GCTGTCGCCGGTGCAGGACGC	0.647																																					p.V848M		Atlas-SNP	.											.	SLITRK5	192	.	0			c.G2542A						.						25	26	26					13																	88330185		2200	4300	6500	SO:0001583	missense	26050	exon2			TCGCCGGTGCAGG	AB020725	CCDS9465.1	13q31.1	2004-04-16	2004-01-08		ENSG00000165300	ENSG00000165300			20295	protein-coding gene	gene with protein product		609680	"leucine rich repeat containing 11"	LRRC11		10048485, 14557068	Standard	NM_015567		Approved	bA364G4.2, KIAA0918	uc001vln.3	O94991	OTTHUMG00000017167	ENST00000325089.6:c.2542G>A	chr13.hg19:g.88330185G>A	ENSP00000366283:p.Val848Met	84.0	0.0		46.0	18.0	NM_015567	B3KNB8|B4DSH5|Q5VT81	Missense_Mutation	SNP	ENST00000325089.6	hg19	CCDS9465.1	.	.	.	.	.	.	.	.	.	.	G	9.997	1.232443	0.22626	.	.	ENSG00000165300	ENST00000325089;ENST00000400028	T;T	0.60040	0.22;0.56	5.57	4.54	0.55810	.	0.321942	0.27227	N	0.020325	T	0.47451	0.1446	L	0.44542	1.39	0.45806	D	0.998687	B;B	0.10296	0.003;0.002	B;B	0.08055	0.003;0.001	T	0.35351	-0.9792	9	.	.	.	-15.9477	12.5881	0.56428	0.0941:0.0:0.9059:0.0	.	607;848	B4DSH5;O94991	.;SLIK5_HUMAN	M	848;607	ENSP00000366283:V848M;ENSP00000442244:V607M	.	V	+	1	0	SLITRK5	87128186	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.740000	0.55082	2.618000	0.88619	0.561000	0.74099	GTG	.	.		0.647	SLITRK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045416.3			A	88330185	G	A	88330185	3	1	285	1	0	0	0	0	1	0	0	0	14761	1261	44	3	2544	3	SLITRK5	13	88330185	Missense_Mutation	SNP	G	TCGA-G3-A5SJ-01A-11D-A27I-10	46424735	88330185	26839693	70	41979										
MYH7	4625	hgsc.bcm.edu	37	chr14	23902342	23902342	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	tgaggttgtagagcaccgcgGgctcatgcaggaaggtcagc	16	9	2	2			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr14:23902342G>A	ENST00000355349.3	-	4	458	c.296C>T	c.(295-297)cCc>cTc	p.P99L		NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	99	Myosin motor.				adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		GAGCACCGCGGGCTCATGCAG	0.562																																					p.P99L		Atlas-SNP	.											.	MYH7	349	.	0			c.C296T						.						267	183	212					14																	23902342		2203	4300	6503	SO:0001583	missense	4625	exon4			ACCGCGGGCTCAT	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.296C>T	chr14.hg19:g.23902342G>A	ENSP00000347507:p.Pro99Leu	413.0	0.0		182.0	66.0	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Missense_Mutation	SNP	ENST00000355349.3	hg19	CCDS9601.1	.	.	.	.	.	.	.	.	.	.	g	18.59	3.656567	0.67586	.	.	ENSG00000092054	ENST00000355349;ENST00000544444	D	0.95588	-3.75	3.76	3.76	0.43208	Myosin head, motor domain (2);	.	.	.	.	D	0.96234	0.8772	M	0.89658	3.05	0.80722	D	1	B	0.19817	0.039	B	0.29524	0.103	D	0.96486	0.9360	9	0.72032	D	0.01	.	16.1486	0.81594	0.0:0.0:1.0:0.0	.	99	P12883	MYH7_HUMAN	L	99	ENSP00000347507:P99L	ENSP00000347507:P99L	P	-	2	0	MYH7	22972182	1.000000	0.71417	0.906000	0.35671	0.991000	0.79684	9.552000	0.98115	2.095000	0.63458	0.455000	0.32223	CCC	.	.		0.562	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257		A	23902342	G	A	23902342	3	1	285	1	0	0	0	0	1	0	0	0	10048	1232	43	3	5659	3	MYH7	14	23902342	Missense_Mutation	SNP	G	TCGA-G3-A5SJ-01A-11D-A27I-10		23902342	83447198	71	41980										
SLC8A3	6547	hgsc.bcm.edu	37	chr14	70634240	70634240	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	ttcccttccaggggcaccagGttcccatctagaaaatggga	10	12	1	1			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr14:70634240G>A	ENST00000381269.2	-	2	1653	c.900C>T	c.(898-900)aaC>aaT	p.N300N	SLC8A3_ENST00000528359.1_Silent_p.N300N|SLC8A3_ENST00000356921.2_Silent_p.N300N|SLC8A3_ENST00000534137.1_Silent_p.N300N|SLC8A3_ENST00000357887.3_Silent_p.N300N	NM_058240.2|NM_183002.1	NP_489479.1|NP_892114.1	P57103	NAC3_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 3	300					blood coagulation (GO:0007596)|calcium ion export from cell (GO:1990034)|calcium ion import into cell (GO:1990035)|calcium ion transport into cytosol (GO:0060402)|cell communication (GO:0007154)|cellular response to cAMP (GO:0071320)|hematopoietic progenitor cell differentiation (GO:0002244)|ion transport (GO:0006811)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	calcium:sodium antiporter activity (GO:0005432)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(18)|ovary(2)|pancreas(2)|prostate(3)|skin(6)	54				BRCA - Breast invasive adenocarcinoma(234;0.0079)|all cancers(60;0.0102)|OV - Ovarian serous cystadenocarcinoma(108;0.0555)		GGGGCACCAGGTTCCCATCTA	0.483																																					p.N300N		Atlas-SNP	.											SLC8A3_ENST00000357887,right_upper_lobe,carcinoma,0,2	SLC8A3	234	.	0			c.C900T						.						114	106	109					14																	70634240		2203	4300	6503	SO:0001819	synonymous_variant	6547	exon2			CACCAGGTTCCCA	AJ304852	CCDS9799.1, CCDS9800.1, CCDS35498.1, CCDS41967.1, CCDS45131.1, CCDS53904.1	14q24.1	2013-05-22	2008-09-02		ENSG00000100678	ENSG00000100678		"Solute carriers"	11070	protein-coding gene	gene with protein product		607991				8798769	Standard	XM_005268017		Approved	NCX3	uc001xly.3	P57103	OTTHUMG00000152342	ENST00000381269.2:c.900C>T	chr14.hg19:g.70634240G>A		95.0	0.0		23.0	7.0	NM_183002	Q5K3P6|Q5K3P7|Q8IUE9|Q8IUF0|Q8NFI7|Q96QG1|Q96QG2	Silent	SNP	ENST00000381269.2	hg19	CCDS35498.1																																																																																			.	.		0.483	SLC8A3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390736.1			A	70634240	G	A	70634240	2	1	285	1	0	0	0	0	0	0	0	1	14723	1252	44	3		3	SLC8A3	14	70634240	Silent	SNP	G	TCGA-G3-A5SJ-01A-11D-A27I-10	46731898	70634240	36715300	72	41981										
TC2N	123036	hgsc.bcm.edu	37	chr14	92265340	92265340	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	ctttattccttacccaggctTctgttactcccctgagaatt	5	13	1	1			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr14:92265340T>G	ENST00000435962.2	-	6	953	c.630A>C	c.(628-630)agA>agC	p.R210S	TC2N_ENST00000556018.1_Missense_Mutation_p.R210S|TC2N_ENST00000360594.5_Missense_Mutation_p.R210S|TC2N_ENST00000340892.5_Missense_Mutation_p.R210S	NM_001128596.1	NP_001122068	Q8N9U0	TAC2N_HUMAN	tandem C2 domains, nuclear	210					regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(5)|skin(1)|upper_aerodigestive_tract(2)	18				COAD - Colon adenocarcinoma(157;0.218)		TACCCAGGCTTCTGTTACTCC	0.313																																					p.R210S		Atlas-SNP	.											.	TC2N	49	.	0			c.A630C						.						45	48	47					14																	92265340		2203	4293	6496	SO:0001583	missense	123036	exon6			CAGGCTTCTGTTA	AA243837	CCDS9897.1, CCDS73679.1	14q32.12	2007-10-17	2007-08-17	2007-08-17		ENSG00000165929			19859	protein-coding gene	gene with protein product	"C2 calcium-dependent domain containing 1"		"chromosome 14 open reading frame 47", "membrane targeting (tandem) C2 domain containing 1"	C14orf47, MTAC2D1		11526914	Standard	NM_001128596		Approved	FLJ36557, Tac2-N, C2CD1	uc001xzt.4	Q8N9U0		ENST00000435962.2:c.630A>C	chr14.hg19:g.92265340T>G	ENSP00000387882:p.Arg210Ser	24.0	0.0		13.0	7.0	NM_001128596		Missense_Mutation	SNP	ENST00000435962.2	hg19	CCDS9897.1	.	.	.	.	.	.	.	.	.	.	T	12.36	1.913397	0.33815	.	.	ENSG00000165929	ENST00000435962;ENST00000340892;ENST00000360594;ENST00000556018;ENST00000556590	T;T;T;T;T	0.21734	3.37;3.37;3.37;2.26;1.99	5.13	1.45	0.22620	.	0.059245	0.64402	D	0.000002	T	0.24699	0.0599	L	0.27053	0.805	0.45733	D	0.998635	P;D	0.76494	0.948;0.999	P;D	0.80764	0.701;0.994	T	0.05733	-1.0867	10	0.17369	T	0.5	-20.5146	7.6139	0.28145	0.0:0.3795:0.0:0.6205	.	210;210	Q8N9U0-2;Q8N9U0	.;TAC2N_HUMAN	S	210;210;210;210;1	ENSP00000387882:R210S;ENSP00000343199:R210S;ENSP00000353802:R210S;ENSP00000451317:R210S;ENSP00000450922:R1S	ENSP00000343199:R210S	R	-	3	2	TC2N	91335093	1.000000	0.71417	1.000000	0.80357	0.002000	0.02628	1.163000	0.31798	0.267000	0.21916	-0.456000	0.05471	AGA	.	.		0.313	TC2N-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411778.1	NM_152332		G	92265340	T	G	92265340	3	3	285	1	0	0	0	0	1	0	0	0	15680	1780	62	5	870	5	TC2N	14	92265340	Missense_Mutation	SNP	T	TCGA-G3-A5SJ-01A-11D-A27I-10	21631100	92265340	15084200	73	41982										
TUBGCP5	114791	hgsc.bcm.edu	37	chr15	22848249	22848249	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	tcatttcaggttactttcagGagtgaaaaagctctttatat	7	6	4	1			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr15:22848249G>T	ENST00000283645.4	+	9	969	c.839G>T	c.(838-840)gGa>gTa	p.G280V	TUBGCP5_ENST00000453949.2_Missense_Mutation_p.G280V	NM_052903.4	NP_443135.3	Q96RT8	GCP5_HUMAN	tubulin, gamma complex associated protein 5	280					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gamma-tubulin ring complex (GO:0008274)|microtubule (GO:0005874)|nucleus (GO:0005634)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(5)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(23)|prostate(1)|skin(2)|urinary_tract(1)	46		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.86e-06)|Epithelial(43;2.63e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000949)		TTACTTTCAGGAGTGAAAAAG	0.284																																					p.G280V		Atlas-SNP	.											.	TUBGCP5	82	.	0			c.G839T						.						78	88	85					15																	22848249		2203	4299	6502	SO:0001583	missense	114791	exon9			TTTCAGGAGTGAA	AB067486	CCDS73697.1, CCDS73698.1	15q11.1	2014-04-17			ENSG00000153575	ENSG00000275835			18600	protein-coding gene	gene with protein product	"gamma-tubulin complex component GCP5"	608147				11694571	Standard	NM_052903		Approved	GCP5, KIAA1899	uc001yur.4	Q96RT8	OTTHUMG00000188371	ENST00000283645.4:c.839G>T	chr15.hg19:g.22848249G>T	ENSP00000283645:p.Gly280Val	129.0	0.0		40.0	11.0	NM_052903	E9PB12|Q6IQ52|Q96PY8	Missense_Mutation	SNP	ENST00000283645.4	hg19	CCDS10008.1	.	.	.	.	.	.	.	.	.	.	.	18.35	3.605398	0.66445	.	.	ENSG00000153575	ENST00000283645;ENST00000453949	T;T	0.60299	0.2;0.2	5.33	5.33	0.75918	.	0.058834	0.64402	D	0.000002	T	0.74061	0.3667	L	0.59436	1.845	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.73369	-0.4004	10	0.51188	T	0.08	-21.8386	19.2171	0.93782	0.0:0.0:1.0:0.0	.	280;280	Q96RT8;E9PB12	GCP5_HUMAN;.	V	280	ENSP00000283645:G280V;ENSP00000409217:G280V	ENSP00000283645:G280V	G	+	2	0	TUBGCP5	20399690	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.737000	0.74816	2.771000	0.95319	0.650000	0.86243	GGA	.	.		0.284	TUBGCP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250998.2	NM_052903		T	22848249	G	T	22848249	3	4	285	1	0	0	0	0	1	0	0	0	16784	1174	41	3	873	3	TUBGCP5	15	22848249	Missense_Mutation	SNP	G	TCGA-G3-A5SJ-01A-11D-A27I-10		22848249	79683143	74	41983										
VPS39	23339	hgsc.bcm.edu	37	chr15	42476724	42476724	+	Frame_Shift_Del	DEL	C	C	-													0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	gttggtctcacccatggccaCtggtatgtccgtccagttca							TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr15:42476724delC	ENST00000348544.4	-	9	741	c.742delG	c.(742-744)gtgfs	p.V248fs	VPS39_ENST00000318006.5_Frame_Shift_Del_p.V237fs			Q96JC1	VPS39_HUMAN	vacuolar protein sorting 39 homolog (S. cerevisiae)	248	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	endosome (GO:0005768)|HOPS complex (GO:0030897)|lysosomal membrane (GO:0005765)	small GTPase regulator activity (GO:0005083)			breast(2)|kidney(5)|large_intestine(4)|lung(8)|ovary(1)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		all_cancers(109;6.78e-16)|all_epithelial(112;1.81e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;3.05e-06)		CCCATGGCCACTGGTATGTCC	0.527																																					p.V237fs		Atlas-Indel,Pindel	.											.	VPS39	53	.	0			c.710delT						.						204	164	177					15																	42476724		2203	4299	6502	SO:0001589	frameshift_variant	23339	exon8			.	AF280814	CCDS10083.1, CCDS73710.1	15q14	2008-02-05	2006-12-19		ENSG00000166887	ENSG00000166887			20593	protein-coding gene	gene with protein product		612188	"vacuolar protein sorting 39 (yeast)"			11448994	Standard	XM_005254259		Approved	KIAA0770, VAM6	uc001zpc.3	Q96JC1	OTTHUMG00000130467	ENST00000348544.4:c.742delG	chr15.hg19:g.42476724delC	ENSP00000335193:p.Val248fs	263.0	0.0		114.0	41.0	NM_015289	O94869|Q71SQ6|Q7Z3V3|Q96B93|Q96RM0	Frame_Shift_Del	DEL	ENST00000348544.4	hg19	CCDS10083.1																																																																																			.	.		0.527	VPS39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000420472.1	NM_015289		-	42476724	C	-	42476724	7	5	285	1	0	1	0	1	0	0	0	0	17224	565	20	0	1990	0	VPS39	15	42476724	Frame_Shift_Del	DEL	C	TCGA-G3-A5SJ-01A-11D-A27I-10	19628475	42476724	60054668	75	41984										
MYEF2	50804	hgsc.bcm.edu	37	chr15	48458174	48458174	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	actaagatcatatttgttcaTagtttctagggctttcttta	6	6	4	1			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr15:48458174T>G	ENST00000324324.7	-	5	760	c.481A>C	c.(481-483)Atg>Ctg	p.M161L	MYEF2_ENST00000267836.6_Missense_Mutation_p.M161L	NM_016132.3	NP_057216	Q9P2K5	MYEF2_HUMAN	myelin expression factor 2	161	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				myotube differentiation (GO:0014902)|neuron differentiation (GO:0030182)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(1)|large_intestine(8)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	31		all_lung(180;0.00217)		all cancers(107;3.73e-10)|GBM - Glioblastoma multiforme(94;7.81e-07)		TATTTGTTCATAGTTTCTAGG	0.274																																					p.M161L		Atlas-SNP	.											.	MYEF2	67	.	0			c.A481C						.						60	74	69					15																	48458174		2184	4247	6431	SO:0001583	missense	50804	exon5			TGTTCATAGTTTC	AB037762	CCDS32230.1, CCDS73722.1	15q15.1	2013-07-16				ENSG00000104177		"RNA binding motif (RRM) containing"	17940	protein-coding gene	gene with protein product						10718198, 2601707	Standard	XM_005254422		Approved	MEF-2, FLJ11213, KIAA1341, HsT18564	uc001zwi.4	Q9P2K5		ENST00000324324.7:c.481A>C	chr15.hg19:g.48458174T>G	ENSP00000316950:p.Met161Leu	87.0	0.0		51.0	17.0	NM_016132	A7MCZ9|C9J921|C9K0J4|Q6NUM5|Q7L388|Q7Z4B7|Q9H922|Q9NUQ1	Missense_Mutation	SNP	ENST00000324324.7	hg19	CCDS32230.1	.	.	.	.	.	.	.	.	.	.	T	8.525	0.869597	0.17322	.	.	ENSG00000104177	ENST00000324324;ENST00000267836	T;T	0.69175	-0.38;-0.38	5.66	4.52	0.55395	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.44912	0.1316	N	0.05280	-0.08	0.80722	D	1	B;B	0.18741	0.003;0.03	B;B	0.23716	0.029;0.048	T	0.23940	-1.0174	10	0.19590	T	0.45	-9.65	12.8717	0.57968	0.0:0.0:0.1362:0.8638	.	161;161	Q9P2K5-2;Q9P2K5	.;MYEF2_HUMAN	L	161	ENSP00000316950:M161L;ENSP00000267836:M161L	ENSP00000267836:M161L	M	-	1	0	MYEF2	46245466	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	5.921000	0.70028	0.946000	0.37632	0.477000	0.44152	ATG	.	.		0.274	MYEF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416909.2	NM_016132		G	48458174	T	G	48458174	3	3	285	1	0	0	0	0	1	0	0	0	10033	1406	49	5	1373	5	MYEF2	15	48458174	Missense_Mutation	SNP	T	TCGA-G3-A5SJ-01A-11D-A27I-10	5981450	48458174	54073218	76	41985										
UBL7	84993	hgsc.bcm.edu	37	chr15	74742014	74742014	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	gagcccttcaaacaggaagcCacctggaggaggacgaacag	13	11	1	0			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr15:74742014C>A	ENST00000567435.1	-	8	1130	c.667G>T	c.(667-669)Ggc>Tgc	p.G223C	UBL7_ENST00000361351.4_Missense_Mutation_p.G223C|UBL7_ENST00000565335.1_Missense_Mutation_p.G223C|UBL7_ENST00000564488.1_Missense_Mutation_p.G223C|UBL7_ENST00000395081.2_Missense_Mutation_p.G223C			Q96S82	UBL7_HUMAN	ubiquitin-like 7	223										endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)	9						AACAGGAAGCCACCTGGAGGA	0.507																																					p.G223C		Atlas-SNP	.											.	UBL7	24	.	0			c.G667T						.						74	70	71					15																	74742014		2197	4296	6493	SO:0001583	missense	84993	exon8			GGAAGCCACCTGG	BC007913	CCDS10263.1	15q23	2014-03-06	2014-03-06		ENSG00000138629	ENSG00000138629			28221	protein-coding gene	gene with protein product	"bone marrow stromal cell-derived ubiquitin-like", " ubiquitin-like protein SB132"	609748	"ubiquitin-like 7 (bone marrow stromal cell-derived)"			12644319	Standard	NM_201265		Approved	BMSC-UbP, MGC14421	uc002axy.1	Q96S82	OTTHUMG00000139001	ENST00000567435.1:c.667G>T	chr15.hg19:g.74742014C>A	ENSP00000457703:p.Gly223Cys	191.0	0.0		79.0	4.0	NM_201265	D3DW57|Q96I03	Missense_Mutation	SNP	ENST00000567435.1	hg19	CCDS10263.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.508161	0.85282	.	.	ENSG00000138629	ENST00000361351;ENST00000395081	T;T	0.51071	0.72;0.72	5.22	5.22	0.72569	.	0.049061	0.85682	D	0.000000	T	0.63581	0.2523	L	0.60455	1.87	0.80722	D	1	D;D	0.71674	0.998;0.992	P;P	0.61328	0.887;0.826	T	0.62487	-0.6844	10	0.45353	T	0.12	-18.7737	18.7772	0.91915	0.0:1.0:0.0:0.0	.	263;223	D3DW56;Q96S82	.;UBL7_HUMAN	C	223	ENSP00000354883:G223C;ENSP00000378518:G223C	ENSP00000354883:G223C	G	-	1	0	UBL7	72529067	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.675000	0.68123	2.608000	0.88229	0.650000	0.86243	GGC	.	.		0.507	UBL7-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419627.1	NM_032907, NM_201265		A	74742014	C	A	74742014	3	1	285	1	0	0	0	0	1	0	0	0	16905	594	21	3	491	3	UBL7	15	74742014	Missense_Mutation	SNP	C	TCGA-G3-A5SJ-01A-11D-A27I-10	26283840	74742014	27789378	77	41986										
KLHDC4	54758	hgsc.bcm.edu	37	chr16	87741993	87741994	+	Frame_Shift_Del	DEL	GT	GT	-													0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	ctctcctctccgctgtcttcGtcgtcgaccccaccctcggc					rs371269644	byFrequency	TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	GT	GT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr16:87741993_87741994delGT	ENST00000270583.5	-	11	1584_1585	c.1526_1527delAC	c.(1525-1527)gacfs	p.D509fs	KLHDC4_ENST00000353170.5_Frame_Shift_Del_p.D452fs|KLHDC4_ENST00000347925.5_Frame_Shift_Del_p.D478fs|FLJ00104_ENST00000446344.1_5'Flank|KLHDC4_ENST00000566349.1_5'UTR	NM_017566.3	NP_060036.2	Q8TBB5	KLDC4_HUMAN	kelch domain containing 4	509										breast(2)|endometrium(3)|lung(10)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(2)	21				BRCA - Breast invasive adenocarcinoma(80;0.0283)		CGCTGTCTTCGTCGTCGACCCC	0.619																																					p.509_510del		Atlas-INDEL	.											.	KLHDC4	45	.	0			c.1527_1528del						.																																			SO:0001589	frameshift_variant	54758	exon11			.	AK001742	CCDS10963.1, CCDS54050.1, CCDS54051.1	16q24	2008-02-05			ENSG00000104731	ENSG00000104731			25272	protein-coding gene	gene with protein product							Standard	NM_001184854		Approved	DKFZp434G0522	uc002fki.3	Q8TBB5	OTTHUMG00000137657	ENST00000270583.5:c.1526_1527delAC	chr16.hg19:g.87741993_87741994delGT	ENSP00000270583:p.Asp509fs	98.0	0.0		44.0	10.0	NM_017566	D3DUN3|D3DUN4|D3DUN5|Q96F29|Q9BVN3	Frame_Shift_Del	DEL	ENST00000270583.5	hg19	CCDS10963.1																																																																																			.	.		0.619	KLHDC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269109.2	NM_017566		-	87741994	GT	-	87741993	7	5	285	1	0	1	0	1	0	0	0	0	8367	1136	40	0	39	0	KLHDC4	16	87741993	Frame_Shift_Del	DEL	GT	TCGA-G3-A5SJ-01A-11D-A27I-10		87741993	2612760	78	41987										
TP53	7157	hgsc.bcm.edu	37	chr17	7578513	7578513	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	cacagctgcacagggcaggtCttggccagttggcaaaacat	12	11	1	0			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr17:7578513C>A	ENST00000269305.4	-	5	606	c.417G>T	c.(415-417)aaG>aaT	p.K139N	TP53_ENST00000455263.2_Missense_Mutation_p.K139N|TP53_ENST00000420246.2_Missense_Mutation_p.K139N|TP53_ENST00000413465.2_Missense_Mutation_p.K139N|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.K139N|TP53_ENST00000445888.2_Missense_Mutation_p.K139N	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	139	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		K -> E (in sporadic cancers; somatic mutation).|K -> N (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:14660794}.|K -> Q (in sporadic cancers; somatic mutation).|K -> R (in sporadic cancers; somatic mutation).|K -> T (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.K139N(9)|p.0?(8)|p.K139K(7)|p.A138_P142delAKTCP(4)|p.C135fs*9(3)|p.K139_T140delKT(3)|p.N131fs*27(2)|p.L137_W146del10(1)|p.K139fs*9(1)|p.K46_T47delKT(1)|p.F134_T140>S(1)|p.A45_P49delAKTCP(1)|p.K7_T8delKT(1)|p.C3fs*9(1)|p.A6_P10delAKTCP(1)|p.A138_V143delAKTCPV(1)|p.K139fs*10(1)|p.K139fs*4(1)|p.C42fs*9(1)|p.Q136_K139delQLAK(1)|p.K139_C141>N(1)|p.C135_T140delCQLAKT(1)|p.K139fs*29(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CAGGGCAGGTCTTGGCCAGTT	0.567		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.K139N	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,bladder,carcinoma,0,5	TP53	33396	.	52	Deletion - In frame(15)|Deletion - Frameshift(9)|Substitution - Missense(9)|Whole gene deletion(8)|Substitution - coding silent(7)|Complex - deletion inframe(2)|Insertion - Frameshift(1)|Complex - frameshift(1)	breast(10)|ovary(9)|urinary_tract(6)|NS(5)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(4)|bone(4)|lung(3)|upper_aerodigestive_tract(2)|oesophagus(2)|stomach(1)|soft_tissue(1)|skin(1)	c.G417T						.						55	55	55					17																	7578513		2203	4300	6503	SO:0001583	missense	7157	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GCAGGTCTTGGCC	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.417G>T	chr17.hg19:g.7578513C>A	ENSP00000269305:p.Lys139Asn	111.0	0.0		48.0	24.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	15.00	2.702835	0.48307	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793	D;D;D;D;D;D;D;D;D	0.99818	-6.92;-6.92;-6.92;-6.92;-6.92;-6.92;-6.92;-6.92;-6.92	5.39	3.4	0.38934	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99704	0.9887	M	0.77406	2.37	0.58432	D	0.999991	P;D;D;P;D;P;P	0.69078	0.852;0.957;0.997;0.669;0.966;0.7;0.685	B;P;D;B;D;P;B	0.71414	0.426;0.831;0.973;0.211;0.928;0.894;0.187	D	0.97999	1.0359	10	0.87932	D	0	-25.2607	10.6631	0.45714	0.0:0.8408:0.0:0.1592	.	100;139;139;46;139;139;139	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	N	139;139;139;139;139;139;128;46;7;46;7;139	ENSP00000410739:K139N;ENSP00000352610:K139N;ENSP00000269305:K139N;ENSP00000398846:K139N;ENSP00000391127:K139N;ENSP00000391478:K139N;ENSP00000425104:K7N;ENSP00000423862:K46N;ENSP00000424104:K139N	ENSP00000269305:K139N	K	-	3	2	TP53	7519238	0.972000	0.33761	0.996000	0.52242	0.061000	0.15899	0.226000	0.17776	0.766000	0.33244	-0.137000	0.14449	AAG	.	.		0.567	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7578513	C	A	7578513	3	1	285	1	0	0	0	0	1	0	0	0	16396	912	32	3	881	3	TP53	17	7578513	Missense_Mutation	SNP	C	TCGA-G3-A5SJ-01A-11D-A27I-10		7578513	73616697	79	41988										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11573031	11573031	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	atgaaaattgatattcgaccCtttaaggcatctctgctgaa	7	8	1	3			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr17:11573031C>G	ENST00000262442.4	+	17	3341	c.3273C>G	c.(3271-3273)ccC>ccG	p.P1091P	DNAH9_ENST00000454412.2_Silent_p.P1091P	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	1091	Stem. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		ATATTCGACCCTTTAAGGCAT	0.443																																					p.P1091P		Atlas-SNP	.											.	DNAH9	695	.	0			c.C3273G						.						132	136	135					17																	11573031		2203	4300	6503	SO:0001819	synonymous_variant	1770	exon17			TCGACCCTTTAAG	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.3273C>G	chr17.hg19:g.11573031C>G		139.0	0.0		32.0	20.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	hg19	CCDS11160.1																																																																																			.	.		0.443	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		G	11573031	C	G	11573031	2	3	285	1	0	0	0	0	0	0	0	1	4610	668	24	4		4	DNAH9	17	11573031	Silent	SNP	C	TCGA-G3-A5SJ-01A-11D-A27I-10	3994518	11573031	69622179	80	41989										
RPL23A	6147	hgsc.bcm.edu	37	chr17	27049757	27049757	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	ccaggcttgaccactatgctAtcatcaagtttccgctgacc	7	14	2	2			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr17:27049757A>G	ENST00000422514.2	+	3	839	c.226A>G	c.(226-228)Atc>Gtc	p.I76V	SNORD42B_ENST00000458893.1_RNA|SNORD42A_ENST00000459584.1_RNA|AC010761.8_ENST00000582718.1_RNA|RPL23A_ENST00000472628.1_5'UTR|RPL23A_ENST00000394938.4_Missense_Mutation_p.I114V|RPL23A_ENST00000496182.1_5'UTR|SNORD4B_ENST00000459083.1_RNA|SNORD4A_ENST00000459174.1_RNA	NM_000984.5	NP_000975.2	P62750	RL23A_HUMAN	ribosomal protein L23a	76					cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			endometrium(1)|lung(3)|ovary(1)	5	Lung NSC(42;0.00431)					CCACTATGCTATCATCAAGTT	0.502																																					p.I76V		Atlas-SNP	.											.	RPL23A	13	.	0			c.A226G						.						67	67	67					17																	27049757		2203	4300	6503	SO:0001583	missense	6147	exon3			TATGCTATCATCA	U43701	CCDS11241.1	17q11.2	2011-04-06			ENSG00000198242	ENSG00000198242		"L ribosomal proteins"	10317	protein-coding gene	gene with protein product		602326				9417910	Standard	NM_000984		Approved	L23A	uc002hci.3	P62750	OTTHUMG00000132684	ENST00000422514.2:c.226A>G	chr17.hg19:g.27049757A>G	ENSP00000389103:p.Ile76Val	351.0	0.0		199.0	84.0	NM_000984	B2R5B2|P29316|P39024|Q92774	Missense_Mutation	SNP	ENST00000422514.2	hg19	CCDS11241.1	.	.	.	.	.	.	.	.	.	.	A	19.23	3.787187	0.70337	.	.	ENSG00000198242	ENST00000422514;ENST00000394938;ENST00000394935	T;T	0.41400	1.0;1.0	5.17	5.17	0.71159	Ribosomal protein L23/L15e (1);Nucleotide-binding, alpha-beta plait (1);	0.000000	0.36200	U	0.002730	T	0.37652	0.1011	L	0.28014	0.82	0.80722	D	1	B	0.24258	0.1	B	0.37387	0.248	T	0.21143	-1.0254	10	0.28530	T	0.3	2.3628	14.5334	0.67942	1.0:0.0:0.0:0.0	.	76	P62750	RL23A_HUMAN	V	76;114;78	ENSP00000389103:I76V;ENSP00000378396:I114V	ENSP00000378393:I78V	I	+	1	0	RPL23A	24073884	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	9.213000	0.95133	2.082000	0.62665	0.524000	0.50904	ATC	.	.		0.502	RPL23A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255975.1	NM_000984		G	27049757	A	G	27049757	3	3	285	1	0	0	0	0	1	0	0	0	13586	449	16	2	236	2	RPL23A	17	27049757	Missense_Mutation	SNP	A	TCGA-G3-A5SJ-01A-11D-A27I-10	15476726	27049757	54145453	81	41990										
CCT6B	10693	hgsc.bcm.edu	37	chr17	33281570	33281599	+	In_Frame_Del	DEL	TTATCTTTGCAGCTTCAAATCCTTCAGCTA	TTATCTTTGCAGCTTCAAATCCTTCAGCTA	-													0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	ctccaaaacttcaagtgcttTtatctttgcagcttcaaatc					rs373897477|rs116562403		TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	TTATCTTTGCAGCTTCAAATCCTTCAGCTA	TTATCTTTGCAGCTTCAAATCCTTCAGCTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr17:33281570_33281599delTTATCTTTGCAGCTTCAAATCCTTCAGCTA	ENST00000314144.5	-	4	471_500	c.356_385delTAGCTGAAGGATTTGAAGCTGCAAAGATAA	c.(355-387)atagctgaaggatttgaagctgcaaagataaaa>aaa	p.IAEGFEAAKI119del	CCT6B_ENST00000436961.3_In_Frame_Del_p.IAEGFEAAKI74del|CCT6B_ENST00000421975.3_In_Frame_Del_p.IAEGFEAAKI119del	NM_006584.3	NP_006575.2	Q92526	TCPW_HUMAN	chaperonin containing TCP1, subunit 6B (zeta 2)	119					chaperone-mediated protein complex assembly (GO:0051131)|protein folding (GO:0006457)|protein transport (GO:0015031)|spermatogenesis (GO:0007283)	chaperonin-containing T-complex (GO:0005832)	ATP binding (GO:0005524)|protein transporter activity (GO:0008565)|unfolded protein binding (GO:0051082)			NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)	20		Ovarian(249;0.17)				TCAAGTGCTTTTATCTTTGCAGCTTCAAATCCTTCAGCTATTATTCTAGG	0.33																																					p.119_129del		Pindel	.											.	CCT6B	63	.	0			c.357_386del						.																																			SO:0001651	inframe_deletion	10693	exon4			.	D78333	CCDS32617.1, CCDS54105.1, CCDS54106.1	17q	2011-09-02			ENSG00000132141	ENSG00000132141		"Heat Shock Proteins / Chaperonins"	1621	protein-coding gene	gene with protein product		610730				8812458, 9013858	Standard	NM_006584		Approved	Cctz2, TSA303	uc002hig.3	Q92526		ENST00000314144.5:c.356_385delTAGCTGAAGGATTTGAAGCTGCAAAGATAA	chr17.hg19:g.33281570_33281599delTTATCTTTGCAGCTTCAAATCCTTCAGCTA	ENSP00000327191:p.Ile119_Ile128del	95.0	0.0		36.0	10.0	NM_006584	B4DX20|B4DYB0|Q8TC34	In_Frame_Del	DEL	ENST00000314144.5	hg19	CCDS32617.1																																																																																			.	.		0.33	CCT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448014.1	NM_006584		-	33281599	TTATCTTTGCAGCTTCAAATCCTTCAGCTA	-	33281570	7	5	285	1	0	1	0	1	0	0	0	0	2960	1850	64	0	1251	0	CCT6B	17	33281570	In_Frame_Del	DEL	TTATCTTTGCAGCTTCAAATCCTTCAGCTA	TCGA-G3-A5SJ-01A-11D-A27I-10	6231813	33281570	47913640	82	41991										
UNC45B	146862	hgsc.bcm.edu	37	chr17	33486394	33486394	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	cccgtcctctttttcttcagAcaccaagaaggacctgaagc	7	14	3	3			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr17:33486394A>G	ENST00000268876.5	+	8	906	c.809A>G	c.(808-810)gAc>gGc	p.D270G	UNC45B_ENST00000433649.1_Splice_Site_p.D270G|UNC45B_ENST00000591048.1_Splice_Site_p.D270G|UNC45B_ENST00000378449.1_Splice_Site_p.D270G|UNC45B_ENST00000394570.2_Splice_Site_p.D270G	NM_173167.2	NP_775259.1	Q8IWX7	UN45B_HUMAN	unc-45 homolog B (C. elegans)	270					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(10)|lung(24)|ovary(3)|prostate(2)|skin(1)|stomach(1)|urinary_tract(3)	59		Ovarian(249;0.17)				TTTTCTTCAGACACCAAGAAG	0.512																																					p.D270G		Atlas-SNP	.											.	UNC45B	133	.	0			c.A809G						.						213	231	225					17																	33486394		2203	4300	6503	SO:0001630	splice_region_variant	146862	exon8			CTTCAGACACCAA	AW755253	CCDS11292.1, CCDS45648.1	17q12	2008-02-05	2005-11-17	2005-11-17	ENSG00000141161	ENSG00000141161			14304	protein-coding gene	gene with protein product		611220	"cardiomyopathy associated 4"	CMYA4		12356907	Standard	NM_001267052		Approved	UNC45	uc002hja.3	Q8IWX7	OTTHUMG00000132931	ENST00000268876.5:c.809-1A>G	chr17.hg19:g.33486394A>G		143.0	0.0		96.0	22.0	NM_001267052	Q495Q8|Q495Q9	Missense_Mutation	SNP	ENST00000268876.5	hg19	CCDS11292.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.593830	0.86953	.	.	ENSG00000141161	ENST00000394570;ENST00000268876;ENST00000433649;ENST00000378449	T;T;T;T	0.52983	0.64;3.16;0.64;3.15	5.87	5.87	0.94306	Armadillo-like helical (1);Armadillo-type fold (1);	0.096185	0.64402	D	0.000001	T	0.59432	0.2193	M	0.68952	2.095	0.80722	D	1	P;P;P	0.50156	0.845;0.932;0.897	P;P;P	0.52454	0.699;0.576;0.469	T	0.59413	-0.7459	9	.	.	.	.	15.7569	0.78037	1.0:0.0:0.0:0.0	.	270;270;270	Q8IWX7-2;Q8IWX7-3;Q8IWX7	.;.;UN45B_HUMAN	G	270	ENSP00000378071:D270G;ENSP00000268876:D270G;ENSP00000412840:D270G;ENSP00000367710:D270G	.	D	+	2	0	UNC45B	30510507	1.000000	0.71417	0.723000	0.30687	0.971000	0.66376	8.948000	0.93006	2.371000	0.80710	0.533000	0.62120	GAC	.	.		0.512	UNC45B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256458.2	NM_173167	Missense_Mutation	G	33486394	A	G	33486394	5	3	285	1	0	0	0	0	0	0	1	0	17004	289	10	2	835	2	UNC45B	17	33486394	Splice_Site	SNP	A	TCGA-G3-A5SJ-01A-11D-A27I-10	204824	33486394	47708816	83	41992										
KRT23	25984	hgsc.bcm.edu	37	chr17	39084785	39084785	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	atatcctccaggaccttaatCagatcttccctgggacctgt	7	13	2	1			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr17:39084785C>G	ENST00000209718.3	-	5	1135	c.711G>C	c.(709-711)ctG>ctC	p.L237L	KRT23_ENST00000436344.3_Silent_p.L100L|AC004231.2_ENST00000418393.1_RNA	NM_015515.3	NP_056330.3	Q9C075	K1C23_HUMAN	keratin 23 (histone deacetylase inducible)	237	Linker 12.|Rod.					intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21		Breast(137;0.000301)|Ovarian(249;0.15)				GGACCTTAATCAGATCTTCCC	0.383																																					p.L237L		Atlas-SNP	.											.	KRT23	59	.	0			c.G711C						.						198	192	194					17																	39084785		2203	4300	6503	SO:0001819	synonymous_variant	25984	exon5			CTTAATCAGATCT	AF102848	CCDS11380.1, CCDS62182.1	17q21.2	2013-01-16			ENSG00000108244	ENSG00000108244		"-", "Intermediate filaments type I, keratins (acidic)"	6438	protein-coding gene	gene with protein product		606194				11135429, 16831889	Standard	NM_015515		Approved	K23, DKFZP434G032, HAIK1, CK23, MGC26158	uc002hvm.1	Q9C075	OTTHUMG00000133376	ENST00000209718.3:c.711G>C	chr17.hg19:g.39084785C>G		168.0	0.0		74.0	18.0	NM_015515	A8K084|B7Z7J2|I3L3Q6|Q9NUR6	Silent	SNP	ENST00000209718.3	hg19	CCDS11380.1																																																																																			.	.		0.383	KRT23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257223.1			G	39084785	C	G	39084785	2	3	285	1	0	0	0	0	0	0	0	1	8469	813	29	4		4	KRT23	17	39084785	Silent	SNP	C	TCGA-G3-A5SJ-01A-11D-A27I-10	5598391	39084785	42110425	84	41993										
KRT39	390792	hgsc.bcm.edu	37	chr17	39118509	39118509	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	gcattgctgctgttgagagcTggtcaccacttgttgattca	11	9	2	2			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr17:39118509T>C	ENST00000355612.2	-	5	936	c.901A>G	c.(901-903)Agc>Ggc	p.S301G	AC004231.2_ENST00000418393.1_RNA	NM_213656.3	NP_998821.3	Q6A163	K1C39_HUMAN	keratin 39	301	Coil 2.|Rod.					intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	17		Breast(137;0.00043)|Ovarian(249;0.15)				TGTTGAGAGCTGGTCACCACT	0.468																																					p.S301G		Atlas-SNP	.											.	KRT39	53	.	0			c.A901G						.						216	203	208					17																	39118509		2203	4296	6499	SO:0001583	missense	390792	exon5			GAGAGCTGGTCAC	AJ786657	CCDS11382.1	17q21.2	2013-01-16			ENSG00000196859	ENSG00000196859		"-", "Intermediate filaments type I, keratins (acidic)"	32971	protein-coding gene	gene with protein product						16831889	Standard	NM_213656		Approved	KA35	uc002hvo.1	Q6A163	OTTHUMG00000133424	ENST00000355612.2:c.901A>G	chr17.hg19:g.39118509T>C	ENSP00000347823:p.Ser301Gly	132.0	0.0		76.0	32.0	NM_213656	B2RXK6|Q6IFU6	Missense_Mutation	SNP	ENST00000355612.2	hg19	CCDS11382.1	.	.	.	.	.	.	.	.	.	.	T	17.96	3.515661	0.64634	.	.	ENSG00000196859	ENST00000355612	D	0.89050	-2.46	5.7	4.6	0.57074	Filament (1);	0.119189	0.38837	N	0.001547	D	0.90546	0.7037	M	0.78801	2.425	0.28048	N	0.933473	P	0.44877	0.845	P	0.50825	0.651	D	0.85380	0.1119	10	0.52906	T	0.07	.	7.15	0.25606	0.0:0.0741:0.1488:0.7771	.	301	Q6A163	K1C39_HUMAN	G	301	ENSP00000347823:S301G	ENSP00000347823:S301G	S	-	1	0	KRT39	36372035	0.000000	0.05858	0.999000	0.59377	0.988000	0.76386	0.361000	0.20267	0.955000	0.37878	0.533000	0.62120	AGC	.	.		0.468	KRT39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257287.1	NM_213656		C	39118509	T	C	39118509	3	2	285	1	0	0	0	0	1	0	0	0	8485	1580	55	2	586	2	KRT39	17	39118509	Missense_Mutation	SNP	T	TCGA-G3-A5SJ-01A-11D-A27I-10	33724	39118509	42076701	85	41994										
HOXB5	3215	hgsc.bcm.edu	37	chr17	46669637	46669637	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	aatttgttgtccttcttccaCttcatgcgccggttctggaa	8	11	3	0			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr17:46669637C>G	ENST00000239151.5	-	2	1022	c.744G>C	c.(742-744)aaG>aaC	p.K248N	HOXB3_ENST00000472863.1_5'Flank|HOXB-AS3_ENST00000492897.3_RNA|HOXB-AS3_ENST00000467155.2_RNA|HOXB3_ENST00000476342.1_5'Flank|HOXB-AS3_ENST00000474040.1_RNA|HOXB3_ENST00000498678.1_5'Flank|HOXB3_ENST00000460160.1_5'Flank|HOXB-AS3_ENST00000465846.2_RNA|HOXB-AS3_ENST00000487849.3_RNA|HOXB-AS3_ENST00000429755.4_RNA|HOXB-AS3_ENST00000480872.1_RNA|HOXB3_ENST00000552000.2_Intron|HOXB-AS3_ENST00000476204.1_RNA	NM_002147.3	NP_002138.1	P09067	HXB5_HUMAN	homeobox B5	248					anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|endothelial cell differentiation (GO:0045446)	nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)			large_intestine(1)|lung(2)	3						CCTTCTTCCACTTCATGCGCC	0.622																																					p.K248N		Atlas-SNP	.											.	HOXB5	20	.	0			c.G744C						.						102	106	105					17																	46669637		2203	4300	6503	SO:0001583	missense	3215	exon2			CTTCCACTTCATG		CCDS11530.1	17q21.32	2011-06-20	2005-12-22		ENSG00000120075	ENSG00000120075		"Homeoboxes / ANTP class : HOXL subclass"	5116	protein-coding gene	gene with protein product		142960	"homeo box B5"	HOX2, HOX2A		1973146, 1358459	Standard	NM_002147		Approved		uc002inr.3	P09067	OTTHUMG00000159913	ENST00000239151.5:c.744G>C	chr17.hg19:g.46669637C>G	ENSP00000239151:p.Lys248Asn	164.0	0.0		104.0	48.0	NM_002147	B2RC69|P09069|Q17RP4	Missense_Mutation	SNP	ENST00000239151.5	hg19	CCDS11530.1	.	.	.	.	.	.	.	.	.	.	C	15.36	2.811996	0.50527	.	.	ENSG00000120075	ENST00000239151	D	0.97994	-4.65	5.4	1.76	0.24704	Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.98858	0.9614	H	0.97659	4.05	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97566	1.0101	9	.	.	.	.	5.3792	0.16181	0.1447:0.5546:0.0:0.3006	.	248	P09067	HXB5_HUMAN	N	248	ENSP00000239151:K248N	.	K	-	3	2	HOXB5	44024636	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.741000	0.26202	0.737000	0.32582	0.563000	0.77884	AAG	.	.		0.622	HOXB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358148.2			G	46669637	C	G	46669637	3	3	285	1	0	0	0	0	1	0	0	0	7313	564	20	4	69	4	HOXB5	17	46669637	Missense_Mutation	SNP	C	TCGA-G3-A5SJ-01A-11D-A27I-10	7551128	46669637	34525573	86	41995										
APPBP2	10513	hgsc.bcm.edu	37	chr17	58571884	58571884	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	tgcagcatctgattctgctaTataagagcaccgcctactga	8	11	2	3			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr17:58571884T>C	ENST00000083182.3	-	3	609	c.322A>G	c.(322-324)Ata>Gta	p.I108V		NM_001282476.1|NM_006380.2	NP_001269405.1|NP_006371.2	Q92624	APBP2_HUMAN	amyloid beta precursor protein (cytoplasmic tail) binding protein 2	108					intracellular protein transport (GO:0006886)|intracellular transport (GO:0046907)|metabolic process (GO:0008152)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	microtubule motor activity (GO:0003777)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(17)|pancreas(1)|urinary_tract(1)	25	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;3.67e-13)|all cancers(12;1.44e-11)|Colorectal(3;0.01)			GATTCTGCTATATAAGAGCAC	0.403																																					p.I108V		Atlas-SNP	.											.	APPBP2	48	.	0			c.A322G						.						97	95	96					17																	58571884		2203	4300	6503	SO:0001583	missense	10513	exon3			CTGCTATATAAGA	AF017782	CCDS32699.1	17q23.2	2012-09-20	2001-11-28		ENSG00000062725	ENSG00000062725			622	protein-coding gene	gene with protein product	"protein interacting with APP tail 1"	605324	"amyloid beta precursor protein (cytoplasmic tail)-binding protein 2"			9843960	Standard	NM_006380		Approved	KIAA0228, Hs.84084, PAT1	uc002iys.1	Q92624		ENST00000083182.3:c.322A>G	chr17.hg19:g.58571884T>C	ENSP00000083182:p.Ile108Val	100.0	0.0		77.0	44.0	NM_006380	A8K862|O95095|Q8WVC9	Missense_Mutation	SNP	ENST00000083182.3	hg19	CCDS32699.1	.	.	.	.	.	.	.	.	.	.	T	10.14	1.267404	0.23136	.	.	ENSG00000062725	ENST00000083182	D	0.81908	-1.55	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	T	0.78227	0.4250	L	0.36672	1.1	0.80722	D	1	B	0.22003	0.063	B	0.32090	0.14	T	0.72178	-0.4369	10	0.13853	T	0.58	0.0157	16.2762	0.82644	0.0:0.0:0.0:1.0	.	108	Q92624	APBP2_HUMAN	V	108	ENSP00000083182:I108V	ENSP00000083182:I108V	I	-	1	0	APPBP2	55926666	1.000000	0.71417	0.994000	0.49952	0.992000	0.81027	7.665000	0.83852	2.243000	0.73865	0.482000	0.46254	ATA	.	.		0.403	APPBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449465.1	NM_006380		C	58571884	T	C	58571884	3	2	285	1	0	0	0	0	1	0	0	0	816	1406	49	2	1479	2	APPBP2	17	58571884	Missense_Mutation	SNP	T	TCGA-G3-A5SJ-01A-11D-A27I-10	11902247	58571884	22623326	87	41996										
TEX2	55852	hgsc.bcm.edu	37	chr17	62230425	62230425	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	cgatcttctttttaataaacTctgtctctgttgctttttgg	6	8	4	0			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr17:62230425T>A	ENST00000583097.1	-	10	3192	c.3020A>T	c.(3019-3021)gAg>gTg	p.E1007V	TEX2_ENST00000581812.1_5'UTR|TEX2_ENST00000584379.1_Missense_Mutation_p.E1007V|TEX2_ENST00000258991.3_Missense_Mutation_p.E1014V			Q8IWB9	TEX2_HUMAN	testis expressed 2	1007					signal transduction (GO:0007165)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)				breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(8;1.33e-10)	READ - Rectum adenocarcinoma(1115;0.0689)		TTTAATAAACTCTGTCTCTGT	0.393																																					p.E1014V		Atlas-SNP	.											.	TEX2	89	.	0			c.A3041T						.						154	148	150					17																	62230425		2203	4300	6503	SO:0001583	missense	55852	exon10			ATAAACTCTGTCT	AB051525	CCDS11658.1, CCDS74131.1	17q23.3	2007-03-13	2007-03-13			ENSG00000136478			30884	protein-coding gene	gene with protein product	"transmembrane protein 96"		"testis expressed sequence 2"			11214970	Standard	XM_005257507		Approved	HT008, TMEM96, KIAA1738	uc002jee.3	Q8IWB9		ENST00000583097.1:c.3020A>T	chr17.hg19:g.62230425T>A	ENSP00000462665:p.Glu1007Val	115.0	0.0		66.0	28.0	NM_018469	Q6AHZ5|Q8N3L0|Q9C0C5	Missense_Mutation	SNP	ENST00000583097.1	hg19		.	.	.	.	.	.	.	.	.	.	T	15.46	2.840874	0.51057	.	.	ENSG00000136478	ENST00000258991	T	0.52295	0.67	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.68796	0.3040	M	0.72894	2.215	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.986	T	0.71866	-0.4463	10	0.87932	D	0	-23.7859	16.5582	0.84512	0.0:0.0:0.0:1.0	.	1014;1007	Q8IWB9-2;Q8IWB9	.;TEX2_HUMAN	V	1014	ENSP00000258991:E1014V	ENSP00000258991:E1014V	E	-	2	0	TEX2	59584157	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.698000	0.84413	2.308000	0.77769	0.533000	0.62120	GAG	.	.		0.393	TEX2-003	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000443745.1	NM_018469		A	62230425	T	A	62230425	3	1	285	1	0	0	0	0	1	0	0	0	15796	1551	54	4	375	4	TEX2	17	62230425	Missense_Mutation	SNP	T	TCGA-G3-A5SJ-01A-11D-A27I-10	3658541	62230425	18964785	88	41997										
SOX9	6662	hgsc.bcm.edu	37	chr17	70119055	70119055	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	atcttcaaggcgctgcaggcCgactcgccacactcctcctc	8	18	2	0			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr17:70119055C>T	ENST00000245479.2	+	2	999	c.627C>T	c.(625-627)gcC>gcT	p.A209A		NM_000346.3	NP_000337.1	P48436	SOX9_HUMAN	SRY (sex determining region Y)-box 9	209					astrocyte fate commitment (GO:0060018)|branching involved in ureteric bud morphogenesis (GO:0001658)|cAMP-mediated signaling (GO:0019933)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cell fate specification (GO:0001708)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to heparin (GO:0071504)|cellular response to interleukin-1 (GO:0071347)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|chondrocyte hypertrophy (GO:0003415)|chromatin remodeling (GO:0006338)|cochlea morphogenesis (GO:0090103)|cytoskeleton organization (GO:0007010)|endocardial cushion morphogenesis (GO:0003203)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation involved in prostatic bud elongation (GO:0060517)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|ERK1 and ERK2 cascade (GO:0070371)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|heart valve development (GO:0003170)|heart valve formation (GO:0003188)|heart valve morphogenesis (GO:0003179)|intestinal epithelial structure maintenance (GO:0060729)|intrahepatic bile duct development (GO:0035622)|limb bud formation (GO:0060174)|lung epithelial cell differentiation (GO:0060487)|male germ-line sex determination (GO:0019100)|male gonad development (GO:0008584)|mammary gland development (GO:0030879)|metanephric nephron tubule formation (GO:0072289)|morphogenesis of a branching epithelium (GO:0061138)|negative regulation of apoptotic process (GO:0043066)|negative regulation of biomineral tissue development (GO:0070168)|negative regulation of bone mineralization (GO:0030502)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of immune system process (GO:0002683)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of ossification (GO:0030279)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell development (GO:0014032)|notochord development (GO:0030903)|nucleosome assembly (GO:0006334)|oligodendrocyte differentiation (GO:0048709)|ossification (GO:0001503)|otic vesicle formation (GO:0030916)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of extracellular matrix assembly (GO:1901203)|positive regulation of kidney development (GO:0090184)|positive regulation of male gonad development (GO:2000020)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein complex assembly (GO:0006461)|protein kinase B signaling (GO:0043491)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in lung morphogenesis (GO:0061046)|regulation of cell adhesion (GO:0030155)|regulation of cell cycle process (GO:0010564)|regulation of cell proliferation (GO:0042127)|regulation of cell proliferation involved in tissue homeostasis (GO:0060784)|regulation of epithelial cell proliferation involved in lung morphogenesis (GO:2000794)|renal vesicle induction (GO:0072034)|retina development in camera-type eye (GO:0060041)|retinal rod cell differentiation (GO:0060221)|Sertoli cell development (GO:0060009)|Sertoli cell differentiation (GO:0060008)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|spermatogenesis (GO:0007283)|tissue homeostasis (GO:0001894)|transcription from RNA polymerase II promoter (GO:0006366)|ureter morphogenesis (GO:0072197)|ureter smooth muscle cell differentiation (GO:0072193)|ureter urothelium development (GO:0072190)	nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enhancer binding (GO:0035326)|enhancer sequence-specific DNA binding (GO:0001158)|pre-mRNA intronic binding (GO:0097157)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase activity (GO:0004672)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(4)|large_intestine(11)|lung(5)|pancreas(1)|upper_aerodigestive_tract(2)	26		Colorectal(1115;0.245)	STAD - Stomach adenocarcinoma(260;0.119)			CGCTGCAGGCCGACTCGCCAC	0.687																																					p.A209A	Pancreas(42;83 1041 2320 35205 39456)	Atlas-SNP	.											.	SOX9	91	.	0			c.C627T						.						65	71	69					17																	70119055		2203	4300	6503	SO:0001819	synonymous_variant	6662	exon2			GCAGGCCGACTCG	S74506	CCDS11689.1	17q24.3	2013-10-17	2008-07-31		ENSG00000125398	ENSG00000125398		"SRY (sex determining region Y)-boxes"	11204	protein-coding gene	gene with protein product		608160	"campomelic dysplasia, autosomal sex-reversal"	CMD1, CMPD1		8348155	Standard	NM_000346		Approved	SRA1	uc002jiw.3	P48436	OTTHUMG00000166300	ENST00000245479.2:c.627C>T	chr17.hg19:g.70119055C>T		116.0	0.0		87.0	49.0	NM_000346	Q53Y80	Silent	SNP	ENST00000245479.2	hg19	CCDS11689.1																																																																																			.	.		0.687	SOX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389032.1	NM_000346		T	70119055	C	T	70119055	2	4	285	1	0	0	0	0	0	0	0	1	14973	639	23	1		1	SOX9	17	70119055	Silent	SNP	C	TCGA-G3-A5SJ-01A-11D-A27I-10	7888630	70119055	11076155	89	41998										
RPTOR	57521	hgsc.bcm.edu	37	chr17	78857615	78857615	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	gggaaacctcattgccatctGcctggagcagctcaacgacc	10	14	3	0			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr17:78857615G>A	ENST00000306801.3	+	16	2047	c.1685G>A	c.(1684-1686)tGc>tAc	p.C562Y	RPTOR_ENST00000544334.2_Intron|RPTOR_ENST00000575542.1_3'UTR	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	562					cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nutrient levels (GO:0031669)|insulin receptor signaling pathway (GO:0008286)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|regulation of cell size (GO:0008361)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|TORC1 complex (GO:0031931)	14-3-3 protein binding (GO:0071889)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	44						ATTGCCATCTGCCTGGAGCAG	0.647																																					p.C562Y		Atlas-SNP	.											RPTOR,rectum,carcinoma,0,1	RPTOR	122	.	0			c.G1685A						.						87	81	83					17																	78857615		2203	4300	6503	SO:0001583	missense	57521	exon16			CCATCTGCCTGGA		CCDS11773.1, CCDS54175.1	17q25.3	2013-01-10				ENSG00000141564		"WD repeat domain containing"	30287	protein-coding gene	gene with protein product	"regulatory associated protein of mTOR"	607130				10718198, 12150926	Standard	NM_001163034		Approved	KOG1, Mip1, KIAA1303, raptor	uc002jyt.1	Q8N122		ENST00000306801.3:c.1685G>A	chr17.hg19:g.78857615G>A	ENSP00000307272:p.Cys562Tyr	96.0	0.0		60.0	17.0	NM_020761	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Missense_Mutation	SNP	ENST00000306801.3	hg19	CCDS11773.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.186631	0.78789	.	.	ENSG00000141564	ENST00000306801	T	0.35421	1.31	4.68	4.68	0.58851	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.69548	0.3123	M	0.92833	3.35	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.79339	-0.1844	10	0.87932	D	0	.	18.0063	0.89210	0.0:0.0:1.0:0.0	.	562	Q8N122	RPTOR_HUMAN	Y	562	ENSP00000307272:C562Y	ENSP00000307272:C562Y	C	+	2	0	RPTOR	76472210	1.000000	0.71417	1.000000	0.80357	0.859000	0.49053	9.159000	0.94728	2.322000	0.78497	0.558000	0.71614	TGC	.	.		0.647	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761		A	78857615	G	A	78857615	3	1	285	1	0	0	0	0	1	0	0	0	13680	1319	46	3	1747	3	RPTOR	17	78857615	Missense_Mutation	SNP	G	TCGA-G3-A5SJ-01A-11D-A27I-10	8738560	78857615	2337595	90	41999										
ATP5A1	498	hgsc.bcm.edu	37	chr18	43667458	43667458	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	caatggtgtacttcatggcaTctgagaaaatatattttaca	7	6	2	1			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr18:43667458T>A	ENST00000398752.6	-	7	921	c.800A>T	c.(799-801)gAt>gTt	p.D267V	ATP5A1_ENST00000282050.2_Splice_Site_p.D267V|ATP5A1_ENST00000590665.1_Splice_Site_p.D245V|ATP5A1_ENST00000593152.2_Splice_Site_p.D217V	NM_001001935.2|NM_004046.5	NP_001001935.1|NP_004037.1	P25705	ATPA_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle	267					ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|ATP hydrolysis coupled proton transport (GO:0015991)|cellular metabolic process (GO:0044237)|embryo development (GO:0009790)|lipid metabolic process (GO:0006629)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|negative regulation of endothelial cell proliferation (GO:0001937)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|proton-transporting ATP synthase complex, catalytic core F(1) (GO:0045261)	ATP binding (GO:0005524)|MHC class I protein binding (GO:0042288)|poly(A) RNA binding (GO:0044822)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transmembrane transporter activity (GO:0022857)			breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(8)|skin(1)|urinary_tract(1)	22						CTTCATGGCATCTGAGAAAAT	0.383																																					p.D267V		Atlas-SNP	.											.	ATP5A1	52	.	0			c.A800T						.						36	38	37					18																	43667458		2203	4300	6503	SO:0001630	splice_region_variant	498	exon7			ATGGCATCTGAGA	D14710	CCDS11927.1, CCDS58620.1, CCDS59315.1	18q21	2012-10-12	2006-01-13		ENSG00000152234	ENSG00000152234	3.6.1.14	"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	823	protein-coding gene	gene with protein product		164360	"ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 2, non-cardiac muscle-like 2", "ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 1, cardiac muscle"	ATP5AL2, ATPM		1830491	Standard	NM_001257334		Approved	ATP5A, hATP1, OMR, ORM	uc002lbr.2	P25705	OTTHUMG00000132637	ENST00000398752.6:c.800-1A>T	chr18.hg19:g.43667458T>A		256.0	0.0		90.0	21.0	NM_004046	A8K092|B4DY56|K7ENP3|Q53XX6|Q8IXV2|Q96FB4|Q96HW2|Q96IR6|Q9BTV8	Missense_Mutation	SNP	ENST00000398752.6	hg19	CCDS11927.1	.	.	.	.	.	.	.	.	.	.	T	19.11	3.764856	0.69878	.	.	ENSG00000152234	ENST00000282050;ENST00000398752;ENST00000542290	D;D	0.82344	-1.6;-1.6	4.47	4.47	0.54385	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.91005	0.7171	M	0.91717	3.235	0.80722	D	1	P	0.40834	0.73	P	0.53722	0.733	D	0.92741	0.6208	10	0.87932	D	0	.	13.7747	0.63046	0.0:0.0:0.0:1.0	.	267	P25705	ATPA_HUMAN	V	267;267;217	ENSP00000282050:D267V;ENSP00000381736:D267V	ENSP00000282050:D267V	D	-	2	0	ATP5A1	41921456	1.000000	0.71417	1.000000	0.80357	0.687000	0.40016	7.953000	0.87836	1.655000	0.50712	0.460000	0.39030	GAT	.	.		0.383	ATP5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255884.1	NM_004046	Missense_Mutation	A	43667458	T	A	43667458	5	1	285	1	0	0	0	0	0	0	1	0	1147	1449	50	4	885	4	ATP5A1	18	43667458	Splice_Site	SNP	T	TCGA-G3-A5SJ-01A-11D-A27I-10		43667458	34409790	91	42000										
DCC	1630	hgsc.bcm.edu	37	chr18	50450198	50450198	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	cctccaccaagttttacctgGttacgaggcgaggaagtcat	10	11	1	0			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr18:50450198G>T	ENST00000442544.2	+	4	1435	c.819G>T	c.(817-819)tgG>tgT	p.W273C	DCC_ENST00000412726.1_Missense_Mutation_p.W121C	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	273	Ig-like C2-type 3.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		GTTTTACCTGGTTACGAGGCG	0.378																																					p.W273C		Atlas-SNP	.											.	DCC	360	.	0			c.G819T						.						135	111	119					18																	50450198		2203	4300	6503	SO:0001583	missense	1630	exon4			TACCTGGTTACGA	X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2701	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 1"	120470	"deleted in colorectal carcinoma"			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.819G>T	chr18.hg19:g.50450198G>T	ENSP00000389140:p.Trp273Cys	264.0	0.0		137.0	36.0	NM_005215		Missense_Mutation	SNP	ENST00000442544.2	hg19	CCDS11952.1	.	.	.	.	.	.	.	.	.	.	G	12.28	1.891849	0.33442	.	.	ENSG00000187323	ENST00000442544;ENST00000304775;ENST00000412726	D;D	0.96300	-3.97;-3.97	5.74	5.74	0.90152	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.155107	0.46442	D	0.000293	D	0.99029	0.9668	H	0.98594	4.275	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99180	1.0867	10	0.87932	D	0	.	18.7545	0.91827	0.0:0.0:1.0:0.0	.	121;273	E7EQM8;P43146	.;DCC_HUMAN	C	273;206;121	ENSP00000389140:W273C;ENSP00000397322:W121C	ENSP00000304146:W206C	W	+	3	0	DCC	48704196	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	6.887000	0.75616	2.728000	0.93425	0.650000	0.86243	TGG	.	.		0.378	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215		T	50450198	G	T	50450198	3	4	285	1	0	0	0	0	1	0	0	0	4284	1270	44	3	833	3	DCC	18	50450198	Missense_Mutation	SNP	G	TCGA-G3-A5SJ-01A-11D-A27I-10	6782740	50450198	27627050	92	42001										
KIAA1683	80726	hgsc.bcm.edu	37	chr19	18368011	18368011	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	tagatgccaggccaatgcatGtgccgtgagctggccgaggg	16	10	0	2			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr19:18368011G>T	ENST00000600328.3	-	4	3715	c.3522C>A	c.(3520-3522)caC>caA	p.H1174Q	PDE4C_ENST00000355502.3_5'Flank|KIAA1683_ENST00000392413.4_Missense_Mutation_p.H1361Q|KIAA1683_ENST00000600359.3_Missense_Mutation_p.H1128Q|PDE4C_ENST00000596647.1_5'Flank			Q9H0B3	K1683_HUMAN	KIAA1683	1174						mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						GCCAATGCATGTGCCGTGAGC	0.597																																					p.H1361Q		Atlas-SNP	.											.	KIAA1683	190	.	0			c.C4083A						.						76	70	72					19																	18368011		2203	4300	6503	SO:0001583	missense	80726	exon4			ATGCATGTGCCGT	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.3522C>A	chr19.hg19:g.18368011G>T	ENSP00000470780:p.His1174Gln	115.0	0.0		39.0	13.0	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Missense_Mutation	SNP	ENST00000600328.3	hg19	CCDS32958.1	.	.	.	.	.	.	.	.	.	.	G	10.50	1.367347	0.24771	.	.	ENSG00000130518	ENST00000392413;ENST00000359737;ENST00000427634;ENST00000392412;ENST00000411671	T;T;T	0.03330	4.08;4.05;3.97	3.87	-0.861	0.10676	.	1.728120	0.03472	N	0.213781	T	0.07458	0.0188	L	0.34521	1.04	0.09310	N	1	D;D	0.67145	0.996;0.963	P;B	0.59115	0.852;0.444	T	0.24905	-1.0147	10	0.87932	D	0	-4.4094	2.5954	0.04853	0.3798:0.0:0.4046:0.2156	.	1361;1174	E9PDE0;Q9H0B3	.;K1683_HUMAN	Q	1361;1174;1128;438;788	ENSP00000376213:H1361Q;ENSP00000352774:H1174Q;ENSP00000404501:H1128Q	ENSP00000352774:H1174Q	H	-	3	2	KIAA1683	18229011	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.417000	0.21214	0.048000	0.15891	0.462000	0.41574	CAC	.	.		0.597	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3			T	18368011	G	T	18368011	3	4	285	1	0	0	0	0	1	0	0	0	8260	1368	48	3	24	3	KIAA1683	19	18368011	Missense_Mutation	SNP	G	TCGA-G3-A5SJ-01A-11D-A27I-10		18368011	40760972	93	42002										
SLC7A9	11136	hgsc.bcm.edu	37	chr19	33324221	33324221	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	gtcatcaagacgggaatgacTacgggcacctggagacgaaa	13	9	2	3			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr19:33324221T>A	ENST00000023064.4	-	12	1424	c.1233A>T	c.(1231-1233)gtA>gtT	p.V411V	SLC7A9_ENST00000587772.1_Silent_p.V411V|SLC7A9_ENST00000590341.1_Silent_p.V411V|CTD-2085J24.3_ENST00000590069.1_RNA	NM_001126335.1|NM_001243036.1|NM_014270.4	NP_001119807.1|NP_001229965.1|NP_055085.1	P82251	BAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, bo,+ system), member 9	411					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|leukocyte migration (GO:0050900)|neutral amino acid transport (GO:0015804)|protein complex assembly (GO:0006461)|transmembrane transport (GO:0055085)|transport (GO:0006810)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-cystine transmembrane transporter activity (GO:0015184)|neutral amino acid transmembrane transporter activity (GO:0015175)|peptide antigen binding (GO:0042605)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32	Esophageal squamous(110;0.137)				L-Cystine(DB00138)	CGGGAATGACTACGGGCACCT	0.408																																					p.V411V	GBM(181;1335 2108 9644 44178 46689)	Atlas-SNP	.											.	SLC7A9	78	.	0			c.A1233T						.						73	77	76					19																	33324221		2203	4300	6503	SO:0001819	synonymous_variant	11136	exon12			AATGACTACGGGC	AF141289	CCDS12425.1	19q13.11	2013-07-19	2013-07-19		ENSG00000021488	ENSG00000021488		"Solute carriers"	11067	protein-coding gene	gene with protein product		604144		CSNU3		10471498	Standard	NM_014270		Approved		uc021usa.1	P82251	OTTHUMG00000180287	ENST00000023064.4:c.1233A>T	chr19.hg19:g.33324221T>A		430.0	1.0		152.0	45.0	NM_001243036	B2R9A6	Silent	SNP	ENST00000023064.4	hg19	CCDS12425.1																																																																																			.	.		0.408	SLC7A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450585.1			A	33324221	T	A	33324221	2	1	285	1	0	0	0	0	0	0	0	1	14720	1509	53	4		4	SLC7A9	19	33324221	Silent	SNP	T	TCGA-G3-A5SJ-01A-11D-A27I-10	14956210	33324221	25804762	94	42003										
ZNF790	388536	hgsc.bcm.edu	37	chr19	37310028	37310029	+	Missense_Mutation	DNP	GC	GC	AT													0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	tgatgtcgagcaaggtgtgaGctccaaatataggctttccc							TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr19:37310028_37310029GC>AT	ENST00000356725.4	-	5	1337_1338	c.1217_1218GC>AT	c.(1216-1218)aGC>aAT	p.S406N	CTD-2162K18.5_ENST00000588906.1_RNA|CTD-2162K18.5_ENST00000587278.1_RNA	NM_001242802.1|NM_206894.3	NP_001229731.1|NP_996777.2	Q6PG37	ZN790_HUMAN	zinc finger protein 790	406					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			biliary_tract(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	32	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			CAAGGTGTGAGCTCCAAATATA	0.411																																					p.S406S|p.S406N		Atlas-SNP	.											.	ZNF790	89	.	0			c.C1218T|c.G1217A						.																																			SO:0001583	missense	388536	exon5			GTGTGAGCTCCAA|TGTGAGCTCCAAA	BC057245	CCDS12496.1	19q13.12	2013-01-08			ENSG00000197863	ENSG00000197863		"Zinc fingers, C2H2-type", "-"	33114	protein-coding gene	gene with protein product							Standard	NM_206894		Approved	MGC62100, FLJ20350	uc021utm.1	Q6PG37	OTTHUMG00000165616	ENST00000356725.4:c.1217_1218delinsAT	chr19.hg19:g.37310028_37310029delinsAT	ENSP00000349161:p.Ser406Asn	97.0|98.0	0.0		42.0	12.0	NM_206894		Silent|Missense_Mutation	SNP	ENST00000356725.4	hg19	CCDS12496.1																																																																																			.	.		0.411	ZNF790-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385341.2	NM_206894		AT	37310029	GC	AT	37310028	3	1	285	1	0	0	0	0	1	0	0	0	18177	962	34	3	696	3	ZNF790	19	37310028	Missense_Mutation	DNP	GC	TCGA-G3-A5SJ-01A-11D-A27I-10	3985807	37310028	21818955	95	42004										
ZNF420	147923	hgsc.bcm.edu	37	chr19	37582003	37582003	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	agatgtgatgttggagaactAtagcaacttggtatcactag	11	5	1	3			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr19:37582003A>G	ENST00000337995.3	+	4	331	c.116A>G	c.(115-117)tAt>tGt	p.Y39C	ZNF420_ENST00000304239.7_Missense_Mutation_p.Y39C|CTD-2293H3.1_ENST00000588369.1_RNA	NM_144689.3	NP_653290.2	Q8TAQ5	ZN420_HUMAN	zinc finger protein 420	39	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(2)|large_intestine(9)|lung(10)|prostate(1)|skin(3)	27			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TTGGAGAACTATAGCAACTTG	0.413																																					p.Y39C		Atlas-SNP	.											.	ZNF420	71	.	0			c.A116G						.						121	120	120					19																	37582003		2203	4300	6503	SO:0001583	missense	147923	exon4			AGAACTATAGCAA	AK056695	CCDS12498.1	19q13.12	2013-01-08			ENSG00000197050	ENSG00000197050		"Zinc fingers, C2H2-type", "-"	20649	protein-coding gene	gene with protein product							Standard	NM_144689		Approved	FLJ32191	uc002ofl.3	Q8TAQ5	OTTHUMG00000048168	ENST00000337995.3:c.116A>G	chr19.hg19:g.37582003A>G	ENSP00000338770:p.Tyr39Cys	151.0	0.0		90.0	21.0	NM_144689	B2RDY6|Q96ML5	Missense_Mutation	SNP	ENST00000337995.3	hg19	CCDS12498.1	.	.	.	.	.	.	.	.	.	.	.	11.47	1.648878	0.29336	.	.	ENSG00000197050	ENST00000304239;ENST00000337995	T;T	0.02525	4.26;4.26	4.36	2.2	0.27929	Krueppel-associated box (4);	.	.	.	.	T	0.06735	0.0172	M	0.89414	3.03	0.26380	N	0.976756	B	0.17852	0.024	B	0.18263	0.021	T	0.17930	-1.0353	9	0.66056	D	0.02	.	6.1975	0.20557	0.7891:0.0:0.2109:0.0	.	39	Q8TAQ5	ZN420_HUMAN	C	39	ENSP00000306102:Y39C;ENSP00000338770:Y39C	ENSP00000306102:Y39C	Y	+	2	0	ZNF420	42273843	0.993000	0.37304	0.916000	0.36221	0.816000	0.46133	4.273000	0.58914	0.197000	0.20387	0.482000	0.46254	TAT	.	.		0.413	ZNF420-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109587.3	NM_144689		G	37582003	A	G	37582003	3	3	285	1	0	0	0	0	1	0	0	0	17912	449	16	2	122	2	ZNF420	19	37582003	Missense_Mutation	SNP	A	TCGA-G3-A5SJ-01A-11D-A27I-10	271975	37582003	21546980	96	42005										
RBM39	9584	hgsc.bcm.edu	37	chr20	34319990	34319990	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	cctttctctgtctctacttcGcttccgttccttacttttgc	4	15	2	0			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr20:34319990G>A	ENST00000253363.6	-	4	192	c.169C>T	c.(169-171)Cga>Tga	p.R57*	RBM39_ENST00000407261.4_5'UTR|RBM39_ENST00000528062.3_Nonsense_Mutation_p.R57*|RBM39_ENST00000361162.6_Nonsense_Mutation_p.R57*			Q14498	RBM39_HUMAN	RNA binding motif protein 39	57	Arg/Ser-rich (RS domain).				mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	all_epithelial(2;0.00295)|Lung NSC(9;0.00453)|Breast(12;0.00544)|all_lung(11;0.00676)					TCTCTACTTCGCTTCCGTTCC	0.448																																					p.R57X		Atlas-SNP	.											.	RBM39	68	.	0			c.C169T						.						196	169	178					20																	34319990		2203	4300	6503	SO:0001587	stop_gained	9584	exon4			TACTTCGCTTCCG	L10910	CCDS13265.1, CCDS13266.1, CCDS56186.1	20q11.22	2014-07-03	2006-07-11	2006-07-11	ENSG00000131051	ENSG00000131051		"RNA binding motif (RRM) containing"	15923	protein-coding gene	gene with protein product	"coactivator of activating protein-1 and estrogen receptors", "functional spliceosome-associated protein 59"	604739	"RNA-binding region (RNP1, RRM) containing 2"	RNPC2		8227358, 15694343, 21551269	Standard	NM_184234		Approved	CC1.3, HCC1, CAPER, fSAP59, CAPERalpha	uc002xeb.3	Q14498	OTTHUMG00000032358	ENST00000253363.6:c.169C>T	chr20.hg19:g.34319990G>A	ENSP00000253363:p.Arg57*	143.0	0.0		57.0	18.0	NM_184234	A2RRD3|A5D8W2|B0BLV3|E1P5S0|E1P5S1|Q14499	Nonsense_Mutation	SNP	ENST00000253363.6	hg19	CCDS13266.1	.	.	.	.	.	.	.	.	.	.	g	26.7	4.761005	0.89932	.	.	ENSG00000131051	ENST00000253363;ENST00000361162;ENST00000528062;ENST00000374038;ENST00000427743;ENST00000434927	.	.	.	5.9	2.63	0.31362	.	0.236945	0.40640	N	0.001049	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.7554	0.69560	0.0:0.0:0.6008:0.3992	.	.	.	.	X	57	.	ENSP00000253363:R57X	R	-	1	2	RBM39	33783404	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.436000	0.52856	0.753000	0.32945	0.651000	0.88453	CGA	.	.		0.448	RBM39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078931.2	NM_184237		A	34319990	G	A	34319990	4	1	285	1	0	0	0	0	0	1	0	0	13148	1095	38	1	1479	1	RBM39	20	34319990	Nonsense_Mutation	SNP	G	TCGA-G3-A5SJ-01A-11D-A27I-10		34319990	28705530	97	42006										
KIAA0406	9675	hgsc.bcm.edu	37	chr20	36634716	36634716	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	gctcttctcaagagctgctgGtctttggttcaaatgacttc	9	10	4	2			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr20:36634716G>A	ENST00000373448.2	-	4	2624	c.2386C>T	c.(2386-2388)Cca>Tca	p.P796S	TTI1_ENST00000373447.3_Missense_Mutation_p.P796S|TTI1_ENST00000449821.1_Missense_Mutation_p.P796S	NM_014657.1	NP_055472.1	O43156	TTI1_HUMAN	TELO2 interacting protein 1	796					regulation of TOR signaling (GO:0032006)	cytoplasm (GO:0005737)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)				breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(6)|liver(1)|lung(18)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	47						AGAGCTGCTGGTCTTTGGTTC	0.463																																					p.P796S		Atlas-SNP	.											.	TTI1	104	.	0			c.C2386T						.						241	214	223					20																	36634716		2203	4300	6503	SO:0001583	missense	9675	exon4			CTGCTGGTCTTTG	BC013121	CCDS13300.1	20q11.23	2011-11-10	2011-11-10	2010-06-22	ENSG00000101407	ENSG00000101407			29029	protein-coding gene	gene with protein product	"smg-10 homolog, nonsense mediated mRNA decay factor (C. elegans)"	614425	"KIAA0406", "Tel2 interacting protein 1 homolog (S. pombe)"	KIAA0406		9455477, 20427287, 20371770	Standard	NM_014657		Approved	smg-10	uc002xhl.3	O43156	OTTHUMG00000032433	ENST00000373448.2:c.2386C>T	chr20.hg19:g.36634716G>A	ENSP00000362547:p.Pro796Ser	203.0	0.0		100.0	32.0	NM_014657	D6W4K3|Q5JX67|Q96A38|Q9BR47|Q9H4K0	Missense_Mutation	SNP	ENST00000373448.2	hg19	CCDS13300.1	.	.	.	.	.	.	.	.	.	.	G	5.811	0.333841	0.11013	.	.	ENSG00000101407	ENST00000373448;ENST00000373447;ENST00000449821	T;T;T	0.64991	-0.13;-0.13;-0.13	5.1	-3.88	0.04205	Armadillo-type fold (1);	0.741186	0.13471	N	0.385408	T	0.33177	0.0854	N	0.20401	0.57	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.26916	-1.0089	10	0.09084	T	0.74	1.5961	3.989	0.09529	0.1737:0.501:0.1975:0.1278	.	796	O43156	TTI1_HUMAN	S	796	ENSP00000362547:P796S;ENSP00000362546:P796S;ENSP00000407270:P796S	ENSP00000362546:P796S	P	-	1	0	TTI1	36068130	0.005000	0.15991	0.000000	0.03702	0.109000	0.19521	0.701000	0.25616	-0.498000	0.06632	0.557000	0.71058	CCA	.	.		0.463	TTI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079138.2	NM_014657		A	36634716	G	A	36634716	3	1	285	1	0	0	0	0	1	0	0	0	8182	1261	44	3	907	3	KIAA0406	20	36634716	Missense_Mutation	SNP	G	TCGA-G3-A5SJ-01A-11D-A27I-10	2314726	36634716	26390804	98	42007										
SHANK3	85358	hgsc.bcm.edu	37	chr22	51169547	51169547	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	gcagaagccgctgcagctctGgagcaagttcgacgtgggcg	16	11	1	1			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chr22:51169547G>T	ENST00000414786.2	+	23	5215	c.4988G>T	c.(4987-4989)tGg>tTg	p.W1663L	SHANK3_ENST00000445220.2_Missense_Mutation_p.W1679L|SHANK3_ENST00000262795.3_Missense_Mutation_p.W1684L			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	1668					adult behavior (GO:0030534)|alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|brain morphogenesis (GO:0048854)|dendritic spine morphogenesis (GO:0060997)|guanylate kinase-associated protein clustering (GO:0097117)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell volume (GO:0045794)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glutamate receptor signaling pathway (GO:1900451)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse structural plasticity (GO:0051835)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density assembly (GO:0097107)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of long term synaptic depression (GO:1900452)|regulation of long-term synaptic potentiation (GO:1900271)|social behavior (GO:0035176)|striatal medium spiny neuron differentiation (GO:0021773)|synapse assembly (GO:0007416)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)	8		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)		CTGCAGCTCTGGAGCAAGTTC	0.736																																					p.W1654L		Atlas-SNP	.											.	SHANK3	96	.	0			c.G4961T						.						3	4	4					22																	51169547		1427	2924	4351	SO:0001583	missense	85358	exon22			AGCTCTGGAGCAA	AB051437		22q13.3	2013-11-14			ENSG00000251322	ENSG00000251322		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	14294	protein-coding gene	gene with protein product	"proline rich synapse associated protein 2", "shank postsynaptic density protein"	606230				11258795, 11431708, 10806096, 17173049	Standard	NM_033517		Approved	SPANK-2, prosap2, KIAA1650, PSAP2	uc031ryd.1	Q9BYB0	OTTHUMG00000150169	ENST00000414786.2:c.4988G>T	chr22.hg19:g.51169547G>T	ENSP00000464552:p.Trp1663Leu	83.0	0.0		18.0	5.0	NM_033517	D7UT47|Q8TET3	Missense_Mutation	SNP	ENST00000414786.2	hg19		.	.	.	.	.	.	.	.	.	.	G	25.5	4.641109	0.87859	.	.	ENSG00000251322	ENST00000262795;ENST00000445220	T;T	0.74526	-0.85;-0.85	3.86	3.86	0.44501	.	0.135838	0.53938	D	0.000051	D	0.90648	0.7067	H	0.97852	4.09	0.37566	D	0.919243	D	0.76494	0.999	D	0.87578	0.998	D	0.94697	0.7879	10	0.87932	D	0	.	13.3157	0.60405	0.0:0.0:1.0:0.0	.	1684	F2Z3L0	.	L	1684;1679	ENSP00000442518:W1684L;ENSP00000446078:W1679L	ENSP00000442518:W1684L	W	+	2	0	SHANK3	49516413	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.985000	0.93487	1.986000	0.57962	0.305000	0.20034	TGG	.	.		0.736	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420		T	51169547	G	T	51169547	3	4	285	1	0	0	0	0	1	0	0	0	14281	1357	47	3	5141	3	SHANK3	22	51169547	Missense_Mutation	SNP	G	TCGA-G3-A5SJ-01A-11D-A27I-10		51169547	135019	99	42008										
ZNF711	7552	hgsc.bcm.edu	37	chrX	84526390	84526390	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	cacatcatatctgtccatacTaaggattttcctcacaaatg	4	11	3	0			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chrX:84526390T>C	ENST00000373165.3	+	9	2148	c.1842T>C	c.(1840-1842)acT>acC	p.T614T	ZNF711_ENST00000395402.1_Silent_p.T622T|ZNF711_ENST00000542798.1_Silent_p.T456T|ZNF711_ENST00000276123.3_Silent_p.T614T|ZNF711_ENST00000360700.4_Silent_p.T660T	NM_021998.4	NP_068838.3	Q9Y462	ZN711_HUMAN	zinc finger protein 711	614					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(14)|ovary(3)|skin(4)	28						CTGTCCATACTAAGGATTTTC	0.408																																					p.T614T		Atlas-SNP	.											.	ZNF711	198	.	0			c.T1842C						.						78	61	67					X																	84526390		2203	4300	6503	SO:0001819	synonymous_variant	7552	exon9			CCATACTAAGGAT	BC006349	CCDS35344.1	Xq21.1	2014-02-19	2006-06-29	2006-06-29	ENSG00000147180	ENSG00000147180		"Zinc fingers, C2H2-type"	13128	protein-coding gene	gene with protein product		314990	"zinc finger protein 6 (CMPX1)", "zinc finger protein 6"	ZNF6		19377476	Standard	XM_005262186		Approved	CMPX1, ZNF4, ZNF5, dJ75N13.1, Zfp711, MRX97	uc004eeo.3	Q9Y462	OTTHUMG00000021933	ENST00000373165.3:c.1842T>C	chrX.hg19:g.84526390T>C		200.0	1.0		85.0	49.0	NM_021998	B4DSV4|Q6NX42|Q9Y4J6	Silent	SNP	ENST00000373165.3	hg19	CCDS35344.1																																																																																			.	.		0.408	ZNF711-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057388.2	NM_021998		C	84526390	T	C	84526390	2	2	285	1	0	0	0	0	0	0	0	1	18131	1509	53	2		2	ZNF711	23	84526390	Silent	SNP	T	TCGA-G3-A5SJ-01A-11D-A27I-10		84526390	70744170	100	42009										
TCEAL8	90843	hgsc.bcm.edu	37	chrX	102508744	102508744	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	taaatccctggccaggctgaTtcggccctcctctggggttt	11	13	1	1			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chrX:102508744T>C	ENST00000372685.3	-	3	400	c.164A>G	c.(163-165)aAt>aGt	p.N55S	TCEAL8_ENST00000360000.4_Missense_Mutation_p.N55S	NM_153333.2	NP_699164.1	Q8IYN2	TCAL8_HUMAN	transcription elongation factor A (SII)-like 8	55					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				kidney(2)|lung(1)|ovary(1)	4						GCCAGGCTGATTCGGCCCTCC	0.522																																					p.N55S		Atlas-SNP	.											.	TCEAL8	15	.	0			c.A164G						.						166	143	151					X																	102508744		2203	4300	6503	SO:0001583	missense	90843	exon2			GGCTGATTCGGCC	AL833632	CCDS14504.1	Xq22.1	2014-03-21			ENSG00000180964	ENSG00000180964			28683	protein-coding gene	gene with protein product						16221301	Standard	NM_001006684		Approved	MGC45400, WEX3	uc004ejy.3	Q8IYN2	OTTHUMG00000022094	ENST00000372685.3:c.164A>G	chrX.hg19:g.102508744T>C	ENSP00000361770:p.Asn55Ser	184.0	0.0		75.0	4.0	NM_001006684		Missense_Mutation	SNP	ENST00000372685.3	hg19	CCDS14504.1	.	.	.	.	.	.	.	.	.	.	T	0.045	-1.269034	0.01433	.	.	ENSG00000180964	ENST00000360000;ENST00000372685	T;T	0.09073	3.02;3.02	4.52	-3.78	0.04333	.	1.008970	0.07967	N	0.983309	T	0.03871	0.0109	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43782	-0.9370	10	0.37606	T	0.19	-0.0505	6.925	0.24410	0.616:0.0:0.2472:0.1367	.	55	Q8IYN2	TCAL8_HUMAN	S	55	ENSP00000353093:N55S;ENSP00000361770:N55S	ENSP00000353093:N55S	N	-	2	0	TCEAL8	102395400	0.002000	0.14202	0.000000	0.03702	0.063000	0.16089	-0.118000	0.10692	-1.214000	0.02614	-0.991000	0.02546	AAT	.	.		0.522	TCEAL8-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057698.1	NM_153333		C	102508744	T	C	102508744	3	2	285	1	0	0	0	0	1	0	0	0	15692	1493	52	2	193	2	TCEAL8	23	102508744	Missense_Mutation	SNP	T	TCGA-G3-A5SJ-01A-11D-A27I-10	17982354	102508744	52761816	101	42010										
PHF6	84295	hgsc.bcm.edu	37	chrX	133527959	133527959	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0101010101010101	1	1	0.270459976105137	0.912802419354839	0	1	1	0	ggtctattgccgaaaacacaAgaaaactgcacataactccg	7	11	1	1			TCGA-G3-A5SJ-01A-11D-A27I-10	TCGA-G3-A5SJ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	92f0cb64-0a29-4ca2-92d0-94d1f0cf050b	b8cc644d-6325-45dc-bc23-58f5e69f8242	g.chrX:133527959A>G	ENST00000332070.3	+	5	597	c.395A>G	c.(394-396)aAg>aGg	p.K132R	PHF6_ENST00000416404.2_Missense_Mutation_p.K98R|PHF6_ENST00000394292.1_Missense_Mutation_p.K132R|PHF6_ENST00000370800.4_Missense_Mutation_p.K132R|PHF6_ENST00000370799.1_Missense_Mutation_p.K132R|PHF6_ENST00000370803.3_Missense_Mutation_p.K132R	NM_032458.2	NP_115834.1	Q8IWS0	PHF6_HUMAN	PHD finger protein 6	132					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone binding (GO:0042393)|histone deacetylase binding (GO:0042826)|phosphoprotein binding (GO:0051219)|poly(A) RNA binding (GO:0044822)|ribonucleoprotein complex binding (GO:0043021)|scaffold protein binding (GO:0097110)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(88)|kidney(2)|large_intestine(1)|liver(1)|lung(6)|ovary(1)|skin(1)|urinary_tract(1)	103	Acute lymphoblastic leukemia(192;0.000127)					CGAAAACACAAGAAAACTGCA	0.313			"F, N, Splice, Mis"		ETP ALL																																p.K132R	Colon(100;666 1493 6344 21231 35807)	Atlas-SNP	.		Rec	yes		X	Xq26.3	84295	PHD finger protein 6		L	.	PHF6	176	.	0			c.A395G						.						81	75	77					X																	133527959		2203	4300	6503	SO:0001583	missense	84295	exon5			AACACAAGAAAAC	AB058726	CCDS14639.1, CCDS14640.1	Xq26	2014-09-17			ENSG00000156531	ENSG00000156531		"Zinc fingers, PHD-type"	18145	protein-coding gene	gene with protein product	"centromere protein 31"	300414	"Borjeson-Forssman-Lehmann syndrome"	BFLS, BORJ		12415272, 15466013	Standard	NM_032335		Approved	KIAA1823, MGC14797, CENP-31	uc004exk.3	Q8IWS0	OTTHUMG00000022453	ENST00000332070.3:c.395A>G	chrX.hg19:g.133527959A>G	ENSP00000329097:p.Lys132Arg	126.0	0.0		51.0	27.0	NM_032335	A8K230|B4E0G4|D3DTG3|E9PC97|Q5JRC7|Q5JRC8|Q96JK3|Q9BRU0	Missense_Mutation	SNP	ENST00000332070.3	hg19	CCDS14639.1	.	.	.	.	.	.	.	.	.	.	A	11.79	1.743676	0.30865	.	.	ENSG00000156531	ENST00000370803;ENST00000332070;ENST00000394292;ENST00000370799;ENST00000416404;ENST00000370800	T;T;T;T;T;T	0.70282	-0.47;-0.47;-0.47;-0.47;-0.47;-0.47	4.92	4.92	0.64577	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type (1);	0.090698	0.64402	D	0.000001	T	0.44307	0.1287	N	0.05306	-0.075	0.41815	D	0.989997	B;B;B;B;B	0.14438	0.002;0.007;0.004;0.004;0.01	B;B;B;B;B	0.16289	0.002;0.005;0.015;0.015;0.013	T	0.43669	-0.9377	10	0.02654	T	1	-12.1591	11.6282	0.51158	1.0:0.0:0.0:0.0	.	98;132;132;132;132	B4E0G4;A8K230;Q8IWS0;E9PC97;Q8IWS0-2	.;.;PHF6_HUMAN;.;.	R	132;132;132;132;98;132	ENSP00000359839:K132R;ENSP00000329097:K132R;ENSP00000377831:K132R;ENSP00000359835:K132R;ENSP00000394480:K98R;ENSP00000359836:K132R	ENSP00000329097:K132R	K	+	2	0	PHF6	133355625	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.782000	0.62396	1.745000	0.51790	0.376000	0.23039	AAG	.	.		0.313	PHF6-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058367.1	NM_032458		G	133527959	A	G	133527959	3	3	285	1	0	0	0	0	1	0	0	0	11847	72	3	2	409	2	PHF6	23	133527959	Missense_Mutation	SNP	A	TCGA-G3-A5SJ-01A-11D-A27I-10	31019215	133527959	21742601	102	42011										
ZBTB40	9923	hgsc.bcm.edu	37	chr1	22848029	22848029	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	ccacaatcgaacccaccaccCtgacgtatttgctgctcaga	6	16	1	2			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr1:22848029C>A	ENST00000375647.4	+	15	3296	c.3089C>A	c.(3088-3090)cCt>cAt	p.P1030H	ZBTB40_ENST00000404138.1_Missense_Mutation_p.P1030H|ZBTB40-IT1_ENST00000438551.1_RNA|ZBTB40_ENST00000374651.4_Missense_Mutation_p.P918H	NM_014870.3	NP_055685.3	Q9NUA8	ZBT40_HUMAN	zinc finger and BTB domain containing 40	1030					bone mineralization (GO:0030282)|cellular response to DNA damage stimulus (GO:0006974)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(4)|large_intestine(6)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.86e-26)|Colorectal(126;8.55e-08)|COAD - Colon adenocarcinoma(152;4.1e-06)|GBM - Glioblastoma multiforme(114;1.39e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000712)|KIRC - Kidney renal clear cell carcinoma(1967;0.00374)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0693)|Lung(427;0.216)		ACCCACCACCCTGACGTATTT	0.493																																					p.P1030H		Atlas-SNP	.											.	ZBTB40	87	.	0			c.C3089A						.						149	122	131					1																	22848029		2203	4300	6503	SO:0001583	missense	9923	exon16			ACCACCCTGACGT	AB007947	CCDS224.1	1p36	2013-01-08			ENSG00000184677	ENSG00000184677		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	29045	protein-coding gene	gene with protein product		612106					Standard	NM_014870		Approved	KIAA0478, ZNF923	uc001bfu.2	Q9NUA8	OTTHUMG00000002897	ENST00000375647.4:c.3089C>A	chr1.hg19:g.22848029C>A	ENSP00000364798:p.Pro1030His	453.0	1.0		713.0	223.0	NM_001083621	O75066|Q5TFU5|Q8N1R1	Missense_Mutation	SNP	ENST00000375647.4	hg19	CCDS224.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.144244	0.77888	.	.	ENSG00000184677	ENST00000404138;ENST00000375647;ENST00000374651	T;T;T	0.10192	2.9;2.9;2.9	5.69	5.69	0.88448	.	0.000000	0.56097	D	0.000038	T	0.22859	0.0552	N	0.24115	0.695	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.01516	-1.1335	10	0.72032	D	0.01	-12.3833	18.4221	0.90594	0.0:1.0:0.0:0.0	.	918;1030	F8WAI8;Q9NUA8	.;ZBT40_HUMAN	H	1030;1030;918	ENSP00000384527:P1030H;ENSP00000364798:P1030H;ENSP00000363782:P918H	ENSP00000363782:P918H	P	+	2	0	ZBTB40	22720616	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.328000	0.79160	2.705000	0.92388	0.485000	0.47835	CCT	.	.		0.493	ZBTB40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008094.1	NM_014870		A	22848029	C	A	22848029	3	1	286	1	0	0	0	0	1	0	0	0	17557	681	24	3	3143	3	ZBTB40	1	22848029	Missense_Mutation	SNP	C	TCGA-G3-A5SK-01A-11D-A27I-10		22848029	226402592	1	42012										
KIAA0754	643314	hgsc.bcm.edu	37	chr1	39879769	39879769	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	cagcttcagtgcccacccccGaggagcctgcctccccagca	9	20	1	0			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr1:39879769G>A	ENST00000530275.1	+	1	3619	c.3424G>A	c.(3424-3426)Gag>Aag	p.E1142K	MACF1_ENST00000545844.1_Intron|MACF1_ENST00000564288.1_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000289893.4_Intron|MACF1_ENST00000372915.3_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000567887.1_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	1142	Ala-rich.									central_nervous_system(1)|large_intestine(6)|skin(1)	8	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			GCCCACCCCCGAGGAGCCTGC	0.667																																					p.E1278K		Atlas-SNP	.											.	KIAA0754	93	.	0			c.G3832A						.						13	15	14					1																	39879769		1997	4156	6153	SO:0001583	missense	643314	exon1			ACCCCCGAGGAGC			1p34.2	2009-07-09				ENSG00000255103			29111	protein-coding gene	gene with protein product						9872452	Standard	NM_015038		Approved		uc009vvt.1	O94854		ENST00000530275.1:c.3424G>A	chr1.hg19:g.39879769G>A	ENSP00000431179:p.Glu1142Lys	91.0	0.0		145.0	55.0	NM_015038	E9PMC2|Q6ZSB2	Missense_Mutation	SNP	ENST00000530275.1	hg19		.	.	.	.	.	.	.	.	.	.	G	12.43	1.935392	0.34189	.	.	ENSG00000255103	ENST00000530275	T	0.26223	1.75	3.7	0.687	0.18020	.	.	.	.	.	T	0.14184	0.0343	N	0.19112	0.55	0.09310	N	1	B	0.24533	0.105	B	0.15052	0.012	T	0.20874	-1.0262	9	0.51188	T	0.08	.	5.6751	0.17743	0.2889:0.1489:0.5622:0.0	.	1142	O94854	K0754_HUMAN	K	1142	ENSP00000431179:E1142K	ENSP00000431179:E1142K	E	+	1	0	RP4-562N20.1	39652356	0.049000	0.20398	0.005000	0.12908	0.011000	0.07611	0.754000	0.26390	-0.378000	0.07918	-2.039000	0.00418	GAG	.	.		0.667	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1	NM_015038		A	39879769	G	A	39879769	3	1	286	1	0	0	0	0	1	0	0	0	8201	1059	37	1	3834	1	KIAA0754	1	39879769	Missense_Mutation	SNP	G	TCGA-G3-A5SK-01A-11D-A27I-10	17031740	39879769	209370852	2	42013										
GJA8	2703	hgsc.bcm.edu	37	chr1	147381088	147381088	+	Frame_Shift_Del	DEL	C	C	-													0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	aagaagtggagggcgaggggCcgcctgcagaggagggagcc							TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr1:147381088delC	ENST00000369235.1	+	1	1006	c.1006delC	c.(1006-1008)ccgfs	p.P337fs	GJA8_ENST00000240986.4_Frame_Shift_Del_p.P337fs			P48165	CXA8_HUMAN	gap junction protein, alpha 8, 50kDa	337					cell-cell signaling (GO:0007267)|lens development in camera-type eye (GO:0002088)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of plasma membrane (GO:0005887)	channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)	37	all_hematologic(923;0.0276)					GGGCGAGGGGCCGCCTGCAGA	0.652																																					p.G335fs	Melanoma(76;1255 1795 8195 52096)	Atlas-Indel,Pindel	.											.	GJA8	108	.	0			c.1005delG						.						27	27	27					1																	147381088		2202	4299	6501	SO:0001589	frameshift_variant	2703	exon2			.	U34802	CCDS30834.1	1q21.1	2008-02-05	2007-01-16		ENSG00000121634	ENSG00000121634		"Ion channels / Gap junction proteins (connexins)"	4281	protein-coding gene	gene with protein product	"connexin 50"	600897	"gap junction protein, alpha 8, 50kD (connexin 50)", "gap junction protein, alpha 8, 50kDa (connexin 50)"	CAE1, CZP1, CAE		9497259, 7796604	Standard	NM_005267		Approved	CX50	uc001epu.2	P48165	OTTHUMG00000024085	ENST00000369235.1:c.1006delC	chr1.hg19:g.147381088delC	ENSP00000358238:p.Pro337fs	114.0	0.0		200.0	39.0	NM_005267	A7L5M5|Q5VVN9|Q9NP25	Frame_Shift_Del	DEL	ENST00000369235.1	hg19	CCDS30834.1																																																																																			.	.		0.652	GJA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060647.1	NM_005267		-	147381088	C	-	147381088	7	5	286	1	0	1	0	1	0	0	0	0	6413	739	26	0	1008	0	GJA8	1	147381088	Frame_Shift_Del	DEL	C	TCGA-G3-A5SK-01A-11D-A27I-10	107501319	147381088	101869533	3	42014										
S100A4	6275	hgsc.bcm.edu	37	chr1	153517143	153517143	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	cactcacccccaagaagctgGgcagctcccgggtcagcagc	11	17	2	1			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr1:153517143G>T	ENST00000368716.4	-	2	275	c.128C>A	c.(127-129)cCc>cAc	p.P43H	S100A4_ENST00000368715.1_Missense_Mutation_p.P43H|S100A4_ENST00000481009.1_5'UTR|S100A4_ENST00000354332.4_Missense_Mutation_p.P43H|S100A4_ENST00000368714.1_Missense_Mutation_p.P43H|S100A5_ENST00000368718.1_5'Flank|S100A5_ENST00000359215.1_5'Flank	NM_002961.2	NP_002952.1	P26447	S10A4_HUMAN	S100 calcium binding protein A4	43	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				epithelial to mesenchymal transition (GO:0001837)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)|RAGE receptor binding (GO:0050786)			large_intestine(2)|lung(1)|prostate(1)	4	all_lung(78;5.98e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)		Trifluoperazine(DB00831)	CAAGAAGCTGGGCAGCTCCCG	0.557																																					p.P43H		Atlas-SNP	.											.	S100A4	6	.	0			c.C128A						.						120	123	122					1																	153517143		2203	4300	6503	SO:0001583	missense	6275	exon2			AAGCTGGGCAGCT	BC016300	CCDS1042.1	1q12-q22	2013-01-10	2006-09-11		ENSG00000196154	ENSG00000196154		"S100 calcium binding proteins", "EF-hand domain containing"	10494	protein-coding gene	gene with protein product	"fibroblast-specific protein-1"	114210	"S100 calcium-binding protein A4 (calcium protein, calvasculin, metastasin, murine placental homolog)", "S100 calcium binding protein A4 (calcium protein, calvasculin, metastasin, murine placental homolog)"	MTS1, CAPL		3155863	Standard	NM_019554		Approved	P9KA, 18A2, PEL98, 42A, FSP1	uc001fbz.3	P26447	OTTHUMG00000013546	ENST00000368716.4:c.128C>A	chr1.hg19:g.153517143G>T	ENSP00000357705:p.Pro43His	109.0	0.0		179.0	53.0	NM_002961	A8K7R8|D3DV46|Q6ICP8	Missense_Mutation	SNP	ENST00000368716.4	hg19	CCDS1042.1	.	.	.	.	.	.	.	.	.	.	G	15.08	2.727143	0.48833	.	.	ENSG00000196154	ENST00000368715;ENST00000354332;ENST00000368716;ENST00000368714;ENST00000545360	T;T;T;T	0.13196	2.61;2.61;2.61;2.61	4.83	4.83	0.62350	S100/CaBP-9k-type, calcium binding, subdomain (1);EF-hand-like domain (1);	0.144460	0.47852	D	0.000205	T	0.12646	0.0307	M	0.71206	2.165	0.34055	D	0.656633	B	0.27700	0.186	B	0.38500	0.275	T	0.04294	-1.0962	10	0.41790	T	0.15	.	13.4438	0.61129	0.0:0.0:1.0:0.0	.	43	P26447	S10A4_HUMAN	H	43;43;43;43;32	ENSP00000357704:P43H;ENSP00000346294:P43H;ENSP00000357705:P43H;ENSP00000357703:P43H	ENSP00000346294:P43H	P	-	2	0	S100A4	151783767	0.649000	0.27322	1.000000	0.80357	0.959000	0.62525	2.148000	0.42235	2.235000	0.73313	0.561000	0.74099	CCC	.	.		0.557	S100A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037714.1	NM_002961		T	153517143	G	T	153517143	3	4	286	1	0	0	0	0	1	0	0	0	13795	1232	43	3	185	3	S100A4	1	153517143	Missense_Mutation	SNP	G	TCGA-G3-A5SK-01A-11D-A27I-10	6136055	153517143	95733478	4	42015										
SLC27A3	11000	hgsc.bcm.edu	37	chr1	153750269	153750269	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	tgctgaaatccaagttctcgGctggtcagttctgggaagat	12	8	3	2			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr1:153750269G>C	ENST00000368661.3	+	4	1275	c.1210G>C	c.(1210-1212)Gct>Cct	p.A404P	SLC27A3_ENST00000484014.1_3'UTR|SLC27A3_ENST00000271857.2_Missense_Mutation_p.A485P	NM_024330.1	NP_077306.1	Q5K4L6	S27A3_HUMAN	solute carrier family 27 (fatty acid transporter), member 3	404					fatty acid metabolic process (GO:0006631)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)	fatty-acyl-CoA synthase activity (GO:0004321)|ligase activity (GO:0016874)|nucleotide binding (GO:0000166)			NS(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	14	all_lung(78;6.47e-32)|Lung NSC(65;2.52e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			CAAGTTCTCGGCTGGTCAGTT	0.602																																					p.A404P		Atlas-SNP	.											.	SLC27A3	42	.	0			c.G1210C						.						75	69	71					1																	153750269		2203	4300	6503	SO:0001583	missense	11000	exon4			TTCTCGGCTGGTC	BC009916	CCDS1053.1	1q21.1	2013-05-22			ENSG00000143554	ENSG00000143554		"Acyl-CoA synthetase family", "Solute carriers"	10997	protein-coding gene	gene with protein product		604193				9671728	Standard	NM_024330		Approved	FATP3, MGC4365, ACSVL3	uc001fcz.3	Q5K4L6	OTTHUMG00000037155	ENST00000368661.3:c.1210G>C	chr1.hg19:g.153750269G>C	ENSP00000357650:p.Ala404Pro	105.0	0.0		267.0	12.0	NM_024330	Q5VUQ7|Q5VUQ8|Q5VUR3|Q6ZV16|Q8N2X7|Q8TEJ0|Q96SW5|Q9BTJ5|Q9BTY5	Missense_Mutation	SNP	ENST00000368661.3	hg19	CCDS1053.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.881771	0.91740	.	.	ENSG00000143554	ENST00000271857;ENST00000368661	T;T	0.08984	3.03;3.03	4.69	4.69	0.59074	AMP-dependent synthetase/ligase (1);	0.000000	0.64402	D	0.000001	T	0.27098	0.0664	M	0.88906	2.99	0.54753	D	0.999983	D	0.89917	1.0	D	0.97110	1.0	T	0.10474	-1.0628	10	0.87932	D	0	-10.2795	15.1428	0.72623	0.0:0.0:1.0:0.0	.	404	Q5K4L6	S27A3_HUMAN	P	485;404	ENSP00000271857:A485P;ENSP00000357650:A404P	ENSP00000271857:A485P	A	+	1	0	SLC27A3	152016893	1.000000	0.71417	0.814000	0.32528	0.951000	0.60555	7.517000	0.81783	2.437000	0.82529	0.491000	0.48974	GCT	.	.		0.602	SLC27A3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_024330		C	153750269	G	C	153750269	3	2	286	1	0	0	0	0	1	0	0	0	14542	1203	42	4	1224	4	SLC27A3	1	153750269	Missense_Mutation	SNP	G	TCGA-G3-A5SK-01A-11D-A27I-10	233126	153750269	95500352	5	42016										
CACNA1S	779	hgsc.bcm.edu	37	chr1	201058470	201058470	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	ccgaagttgtcgaagtgggtGatgccatggttgggccctgg	17	8	0	1			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr1:201058470G>A	ENST00000362061.3	-	6	1042	c.816C>T	c.(814-816)atC>atT	p.I272I	CACNA1S_ENST00000367338.3_Silent_p.I272I	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	272					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CGAAGTGGGTGATGCCATGGT	0.637																																					p.I272I		Atlas-SNP	.											.	CACNA1S	249	.	0			c.C816T						.						91	74	80					1																	201058470		2203	4300	6503	SO:0001819	synonymous_variant	779	exon6			GTGGGTGATGCCA	L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.816C>T	chr1.hg19:g.201058470G>A		202.0	0.0		419.0	170.0	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Silent	SNP	ENST00000362061.3	hg19	CCDS1407.1																																																																																			.	.		0.637	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069		A	201058470	G	A	201058470	2	1	286	1	0	0	0	0	0	0	0	1	2549	1280	45	3		3	CACNA1S	1	201058470	Silent	SNP	G	TCGA-G3-A5SK-01A-11D-A27I-10	47308201	201058470	48192151	6	42017										
USH2A	7399	hgsc.bcm.edu	37	chr1	215960064	215960064	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	tgaatggtttcttcggcagaTgaacacatttcttcaattga	8	7	3	4			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr1:215960064T>C	ENST00000307340.3	-	52	10721	c.10335A>G	c.(10333-10335)tcA>tcG	p.S3445S	USH2A_ENST00000366943.2_Silent_p.S3445S	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3445	Fibronectin type-III 19. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			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)		CTTCGGCAGATGAACACATTT	0.448										HNSCC(13;0.011)																											p.S3445S		Atlas-SNP	.											.	USH2A	1168	.	0			c.A10335G						.						195	161	173					1																	215960064		2203	4300	6503	SO:0001819	synonymous_variant	7399	exon52			GGCAGATGAACAC	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.10335A>G	chr1.hg19:g.215960064T>C		235.0	0.0		505.0	145.0	NM_206933	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	hg19	CCDS31025.1																																																																																			.	.		0.448	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		C	215960064	T	C	215960064	2	2	286	1	0	0	0	0	0	0	0	1	17051	1451	51	2		2	USH2A	1	215960064	Silent	SNP	T	TCGA-G3-A5SK-01A-11D-A27I-10	14901594	215960064	33290557	7	42018										
MOSC2	54996	hgsc.bcm.edu	37	chr1	220935024	220935024	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	tttggccttgacattaaaggCagagactgtggcaatgaggc	13	7	0	3			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr1:220935024C>T	ENST00000366913.3	+	3	669	c.471C>T	c.(469-471)ggC>ggT	p.G157G	MARC2_ENST00000359316.2_Silent_p.G157G	NM_017898.3	NP_060368.2	Q969Z3	MARC2_HUMAN	mitochondrial amidoxime reducing component 2	157					detoxification of nitrogen compound (GO:0051410)|nitrate metabolic process (GO:0042126)|oxidation-reduction process (GO:0055114)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)	molybdenum ion binding (GO:0030151)|molybdopterin cofactor binding (GO:0043546)|nitrate reductase activity (GO:0008940)|pyridoxal phosphate binding (GO:0030170)										ACATTAAAGGCAGAGACTGTG	0.403																																					p.G157G		Atlas-SNP	.											.	.	.	.	0			c.C471T						.						89	77	81					1																	220935024		2203	4300	6503	SO:0001819	synonymous_variant	54996	exon3			TAAAGGCAGAGAC		CCDS1525.1	1q41	2011-11-02	2011-11-02	2011-11-02	ENSG00000117791	ENSG00000117791			26064	protein-coding gene	gene with protein product		614127	"MOCO sulphurase C-terminal domain containing 2"	MOSC2		11886751	Standard	NM_017898		Approved	FLJ20605	uc001hmq.3	Q969Z3	OTTHUMG00000037354	ENST00000366913.3:c.471C>T	chr1.hg19:g.220935024C>T		134.0	0.0		269.0	137.0	NM_017898	B2D0R5|D3DTB3|Q0JSK7|Q5VT67|Q5VXC7|Q7L317|Q9H066|Q9NWU0	Silent	SNP	ENST00000366913.3	hg19	CCDS1525.1																																																																																			.	.		0.403	MARC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090911.1	NM_017898		T	220935024	C	T	220935024	2	4	286	1	0	0	0	0	0	0	0	1	9723	697	25	3		3	MOSC2	1	220935024	Silent	SNP	C	TCGA-G3-A5SK-01A-11D-A27I-10	4974960	220935024	28315597	8	42019										
PGBD5	79605	hgsc.bcm.edu	37	chr1	230468595	230468595	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	cggacccgcactcaccctgcTgcaccggggagtaggcgttg	14	15	1	0			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr1:230468595T>C	ENST00000525115.1	-	5	1084	c.1061A>G	c.(1060-1062)cAg>cGg	p.Q354R	PGBD5_ENST00000321327.2_Missense_Mutation_p.Q453R|PGBD5_ENST00000391860.1_Missense_Mutation_p.Q308R|PGBD5_ENST00000530424.1_5'UTR			Q8N414	PGBD5_HUMAN	piggyBac transposable element derived 5	354						integral component of membrane (GO:0016021)				biliary_tract(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(2)|skin(1)	33	Breast(184;0.0397)	Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;0.201)		CTCACCCTGCTGCACCGGGGA	0.617																																					p.Q423R		Atlas-SNP	.											.	PGBD5	73	.	0			c.A1268G						.						146	123	131					1																	230468595		2203	4300	6503	SO:0001583	missense	79605	exon5			CCCTGCTGCACCG	AK021475		1q42.13	2008-02-05			ENSG00000177614	ENSG00000177614			19405	protein-coding gene	gene with protein product							Standard	NM_001258311		Approved	DKFZp761A0620, FLJ11413	uc031psq.1	Q8N414	OTTHUMG00000037759	ENST00000525115.1:c.1061A>G	chr1.hg19:g.230468595T>C	ENSP00000431404:p.Gln354Arg	198.0	0.0		293.0	22.0	NM_001258311	A0PJF3|B9EK58|Q5SR37|Q6PJN2	Missense_Mutation	SNP	ENST00000525115.1	hg19		.	.	.	.	.	.	.	.	.	.	-	12.40	1.927392	0.34002	.	.	ENSG00000177614	ENST00000391860;ENST00000321327;ENST00000525115	T;T;T	0.18338	2.22;2.22;2.22	5.62	5.62	0.85841	.	0.099709	0.64402	D	0.000002	T	0.11239	0.0274	N	0.14661	0.345	0.37928	D	0.931928	B;B	0.19331	0.012;0.035	B;B	0.17433	0.011;0.018	T	0.20605	-1.0270	10	0.15499	T	0.54	-37.8999	15.921	0.79575	0.0:0.0:0.0:1.0	.	354;44	Q8N414;B4DM72	PGBD5_HUMAN;.	R	308;453;354	ENSP00000375733:Q308R;ENSP00000322530:Q453R;ENSP00000431404:Q354R	ENSP00000322530:Q453R	Q	-	2	0	PGBD5	228535218	1.000000	0.71417	1.000000	0.80357	0.760000	0.43138	4.885000	0.63142	2.164000	0.68074	0.472000	0.43445	CAG	.	.		0.617	PGBD5-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000382617.1	NM_024554		C	230468595	T	C	230468595	3	2	286	1	0	0	0	0	1	0	0	0	11793	1580	55	2	318	2	PGBD5	1	230468595	Missense_Mutation	SNP	T	TCGA-G3-A5SK-01A-11D-A27I-10	9533571	230468595	18782026	9	42020										
RYR2	6262	hgsc.bcm.edu	37	chr1	237823313	237823313	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	tggatggatttatggagaaaTatattcagactcttctaagg	10	4	3	2			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr1:237823313T>C	ENST00000366574.2	+	55	8554	c.8237T>C	c.(8236-8238)aTa>aCa	p.I2746T	RYR2_ENST00000542537.1_Missense_Mutation_p.I2730T|RYR2_ENST00000360064.6_Missense_Mutation_p.I2744T	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	2746	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TATGGAGAAATATATTCAGAC	0.289																																					p.I2746T		Atlas-SNP	.											.	RYR2	1273	.	0			c.T8237C						.						66	62	63					1																	237823313		1801	4062	5863	SO:0001583	missense	6262	exon55			GAGAAATATATTC	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.8237T>C	chr1.hg19:g.237823313T>C	ENSP00000355533:p.Ile2746Thr	57.0	0.0		63.0	19.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	T	5.473	0.272335	0.10349	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.91068	-2.78;-2.78;-2.78	5.63	4.51	0.55191	Ryanodine receptor Ryr (1);	0.367379	0.25558	N	0.029847	T	0.75510	0.3859	N	0.05230	-0.09	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.65245	-0.6215	10	0.07644	T	0.81	.	7.7902	0.29116	0.0:0.2054:0.0:0.7946	.	2746	Q92736	RYR2_HUMAN	T	2746;2744;2730	ENSP00000355533:I2746T;ENSP00000353174:I2744T;ENSP00000443798:I2730T	ENSP00000353174:I2744T	I	+	2	0	RYR2	235889936	0.032000	0.19561	1.000000	0.80357	0.990000	0.78478	0.779000	0.26746	0.966000	0.38159	0.383000	0.25322	ATA	.	.		0.289	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		C	237823313	T	C	237823313	3	2	286	1	0	0	0	0	1	0	0	0	13784	1406	49	2	8455	2	RYR2	1	237823313	Missense_Mutation	SNP	T	TCGA-G3-A5SK-01A-11D-A27I-10	7354718	237823313	11427308	10	42021										
OR2M7	391196	hgsc.bcm.edu	37	chr1	248487546	248487546	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	caacagaaagcattcggagcCaagcaatgatatatagaaga	9	7	0	4			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr1:248487546C>G	ENST00000317965.2	-	1	353	c.325G>C	c.(325-327)Ggc>Cgc	p.G109R		NM_001004691.1	NP_001004691.1	Q8NG81	OR2M7_HUMAN	olfactory receptor, family 2, subfamily M, member 7	109						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(6)|large_intestine(3)|lung(29)|skin(3)	42	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CATTCGGAGCCAAGCAATGAT	0.453																																					p.G109R		Atlas-SNP	.											OR2M7,right_upper_lobe,carcinoma,0,1	OR2M7	84	.	0			c.G325C						.						200	207	204					1																	248487546		2203	4300	6503	SO:0001583	missense	391196	exon1			CGGAGCCAAGCAA	BK004486	CCDS31111.1	1q44	2012-08-09			ENSG00000177186	ENSG00000177186		"GPCR / Class A : Olfactory receptors"	19594	protein-coding gene	gene with protein product							Standard	NM_001004691		Approved		uc010pzk.2	Q8NG81	OTTHUMG00000040461	ENST00000317965.2:c.325G>C	chr1.hg19:g.248487546C>G	ENSP00000324557:p.Gly109Arg	197.0	1.0		414.0	188.0	NM_001004691	B2RNL0|Q6IEX6	Missense_Mutation	SNP	ENST00000317965.2	hg19	CCDS31111.1	.	.	.	.	.	.	.	.	.	.	C	11.91	1.780995	0.31502	.	.	ENSG00000177186	ENST00000317965	T	0.09817	2.94	1.54	-0.407	0.12385	GPCR, rhodopsin-like superfamily (1);	0.247554	0.20872	U	0.084160	T	0.35158	0.0922	H	0.95365	3.66	0.09310	N	1	D	0.89917	1.0	D	0.74348	0.983	T	0.12218	-1.0556	10	0.87932	D	0	.	4.1603	0.10280	0.1889:0.552:0.0:0.2591	.	109	Q8NG81	OR2M7_HUMAN	R	109	ENSP00000324557:G109R	ENSP00000324557:G109R	G	-	1	0	OR2M7	246554169	0.000000	0.05858	0.002000	0.10522	0.080000	0.17528	-2.374000	0.01072	0.002000	0.14630	0.184000	0.17185	GGC	.	.		0.453	OR2M7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097357.1	NM_001004691		G	248487546	C	G	248487546	3	3	286	1	0	0	0	0	1	0	0	0	11023	594	21	4	616	4	OR2M7	1	248487546	Missense_Mutation	SNP	C	TCGA-G3-A5SK-01A-11D-A27I-10	10664233	248487546	763075	11	42022										
CCT4	10575	hgsc.bcm.edu	37	chr2	62107453	62107453	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	gcttggtacaagaatctaagAgggagccagcaatgatgact	12	7	1	4			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr2:62107453A>C	ENST00000394440.3	-	4	643	c.347T>G	c.(346-348)cTc>cGc	p.L116R	CCT4_ENST00000544185.1_Intron|CCT4_ENST00000544079.1_Missense_Mutation_p.L86R|CCT4_ENST00000538252.1_Missense_Mutation_p.L60R|AC107081.5_ENST00000425779.1_RNA	NM_006430.3	NP_006421.2	P50991	TCPD_HUMAN	chaperonin containing TCP1, subunit 4 (delta)	116					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(1)|large_intestine(2)|lung(6)|ovary(2)	11	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;6.5e-06)|Epithelial(17;0.0647)|all cancers(80;0.221)			AGAATCTAAGAGGGAGCCAGC	0.398																																					p.L116R		Atlas-SNP	.											.	CCT4	38	.	0			c.T347G						.						142	145	144					2																	62107453		2203	4300	6503	SO:0001583	missense	10575	exon4			TCTAAGAGGGAGC		CCDS33206.1, CCDS58711.1	2p15	2011-09-02			ENSG00000115484	ENSG00000115484		"Heat Shock Proteins / Chaperonins"	1617	protein-coding gene	gene with protein product		605142				9819444	Standard	NM_001256721		Approved	Cctd	uc002sbo.4	P50991	OTTHUMG00000152166	ENST00000394440.3:c.347T>G	chr2.hg19:g.62107453A>C	ENSP00000377958:p.Leu116Arg	78.0	0.0		117.0	32.0	NM_006430	B2R6I3|B7Z8B1|F5H5W3|O14870|Q53QP9|Q96C51	Missense_Mutation	SNP	ENST00000394440.3	hg19	CCDS33206.1	.	.	.	.	.	.	.	.	.	.	A	26.7	4.764973	0.90020	.	.	ENSG00000115484	ENST00000394440;ENST00000544079;ENST00000538252	D;D;D	0.87179	-2.22;-2.22;-2.22	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.97031	0.9030	H	0.99884	4.89	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.992;0.996	D	0.98991	1.0808	10	0.87932	D	0	-7.3028	15.5562	0.76196	1.0:0.0:0.0:0.0	.	86;116	F5H5W3;P50991	.;TCPD_HUMAN	R	116;86;60	ENSP00000377958:L116R;ENSP00000443061:L86R;ENSP00000442174:L60R	ENSP00000377958:L116R	L	-	2	0	CCT4	61960957	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.188000	0.94921	2.152000	0.67230	0.533000	0.62120	CTC	.	.		0.398	CCT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325548.2			C	62107453	A	C	62107453	3	2	286	1	0	0	0	0	1	0	0	0	2957	304	11	5	1316	5	CCT4	2	62107453	Missense_Mutation	SNP	A	TCGA-G3-A5SK-01A-11D-A27I-10		62107453	181091920	12	42023										
C2orf86	51057	hgsc.bcm.edu	37	chr2	63631475	63631475	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	cttgggtggcagcttattaaTgaaggcaaaagttcagtctg	12	6	2	1			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr2:63631475T>C	ENST00000272321.7	-	10	1670	c.1143A>G	c.(1141-1143)tcA>tcG	p.S381S	WDPCP_ENST00000409835.1_5'UTR|WDPCP_ENST00000409199.1_Silent_p.S189S|WDPCP_ENST00000409120.1_Silent_p.S189S|WDPCP_ENST00000409562.3_Silent_p.S381S|WDPCP_ENST00000398544.3_Silent_p.S222S	NM_015910.5	NP_056994.3	O95876	FRITZ_HUMAN	WD repeat containing planar cell polarity effector	381					auditory receptor cell morphogenesis (GO:0002093)|camera-type eye development (GO:0043010)|cardiovascular system development (GO:0072358)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|digestive system development (GO:0055123)|embryonic digit morphogenesis (GO:0042733)|establishment of protein localization (GO:0045184)|glomerular visceral epithelial cell migration (GO:0090521)|kidney development (GO:0001822)|palate development (GO:0060021)|regulation of embryonic cell shape (GO:0016476)|regulation of establishment of cell polarity (GO:2000114)|regulation of fibroblast migration (GO:0010762)|regulation of focal adhesion assembly (GO:0051893)|regulation of protein localization (GO:0032880)|regulation of ruffle assembly (GO:1900027)|respiratory system development (GO:0060541)|septin cytoskeleton organization (GO:0032185)|smoothened signaling pathway (GO:0007224)	axonemal basal plate (GO:0097541)|axoneme (GO:0005930)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(19)|ovary(1)|skin(1)	35						AGCTTATTAATGAAGGCAAAA	0.433																																					p.S381S		Atlas-SNP	.											.	WDPCP	79	.	0			c.A1143G						.						84	80	81					2																	63631475		1879	4109	5988	SO:0001819	synonymous_variant	51057	exon10			TATTAATGAAGGC		CCDS42688.1, CCDS46301.1	2p15	2014-04-24	2011-02-01	2011-02-01	ENSG00000143951	ENSG00000143951			28027	protein-coding gene	gene with protein product		613580	"chromosome 2 open reading frame 86"	C2orf86		15654087, 20671153	Standard	NM_015910		Approved	hFrtz, fritz, BBS15	uc002sch.3	O95876	OTTHUMG00000152566	ENST00000272321.7:c.1143A>G	chr2.hg19:g.63631475T>C		75.0	0.0		97.0	7.0	NM_015910	Q53RW4|Q7Z2Z3	Silent	SNP	ENST00000272321.7	hg19	CCDS42688.1																																																																																			.	.		0.433	WDPCP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326820.1	NM_015910		C	63631475	T	C	63631475	2	2	286	1	0	0	0	0	0	0	0	1	2203	1451	51	2		2	C2orf86	2	63631475	Silent	SNP	T	TCGA-G3-A5SK-01A-11D-A27I-10	1524022	63631475	179567898	13	42024										
CEP68	23177	hgsc.bcm.edu	37	chr2	65305033	65305033	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	agatatagatgaacatcagtCtctgacggagagtgtcttac	10	7	3	5			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr2:65305033C>G	ENST00000377990.2	+	5	2242	c.2039C>G	c.(2038-2040)tCt>tGt	p.S680C	RAB1A_ENST00000494188.1_Intron|CEP68_ENST00000260569.4_Missense_Mutation_p.S543C|CEP68_ENST00000546106.1_Intron	NM_015147.2	NP_055962.2	Q76N32	CEP68_HUMAN	centrosomal protein 68kDa	680					centriole-centriole cohesion (GO:0010457)|centrosome organization (GO:0051297)|protein localization to organelle (GO:0033365)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|endometrium(6)|kidney(8)|large_intestine(5)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32						GAACATCAGTCTCTGACGGAG	0.398																																					p.S680C		Atlas-SNP	.											.	CEP68	69	.	0			c.C2039G						.						89	90	90					2																	65305033		2203	4300	6503	SO:0001583	missense	23177	exon5			ATCAGTCTCTGAC	BC004873	CCDS1880.2	2p14	2014-02-20	2005-12-01	2005-12-01	ENSG00000011523	ENSG00000011523			29076	protein-coding gene	gene with protein product			"KIAA0582"	KIAA0582		9628581, 9847074, 14654843	Standard	NM_015147		Approved		uc002sdl.4	Q76N32	OTTHUMG00000129538	ENST00000377990.2:c.2039C>G	chr2.hg19:g.65305033C>G	ENSP00000367229:p.Ser680Cys	103.0	0.0		146.0	42.0	NM_015147	B4DRQ1|D6W5F1|D6W5F2|O60326|Q9BQ18|Q9UDM9	Missense_Mutation	SNP	ENST00000377990.2	hg19	CCDS1880.2	.	.	.	.	.	.	.	.	.	.	C	16.95	3.264123	0.59431	.	.	ENSG00000011523	ENST00000377990;ENST00000260569	T;T	0.79940	-1.32;-1.32	5.86	1.56	0.23342	.	0.836245	0.10874	N	0.624631	D	0.83764	0.5325	L	0.60455	1.87	0.80722	D	1	D;D	0.71674	0.998;0.998	P;P	0.61592	0.891;0.891	T	0.77943	-0.2398	10	0.66056	D	0.02	-2.5103	5.9154	0.19052	0.0:0.513:0.1385:0.3485	.	680;543	Q76N32;Q76N32-2	CEP68_HUMAN;.	C	680;543	ENSP00000367229:S680C;ENSP00000260569:S543C	ENSP00000260569:S543C	S	+	2	0	CEP68	65158537	0.778000	0.28640	0.996000	0.52242	0.806000	0.45545	0.421000	0.21280	0.068000	0.16574	0.563000	0.77884	TCT	.	.		0.398	CEP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251727.2	NM_015147		G	65305033	C	G	65305033	3	3	286	1	0	0	0	0	1	0	0	0	3260	913	32	4	2053	4	CEP68	2	65305033	Missense_Mutation	SNP	C	TCGA-G3-A5SK-01A-11D-A27I-10	1673558	65305033	177894340	14	42025										
NXPH2	11249	hgsc.bcm.edu	37	chr2	139428566	139428566	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	cttttgcacgagtttataatCaacactgtaaaaggcaatgt	7	7	1	0			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr2:139428566C>G	ENST00000272641.3	-	2	827	c.721G>C	c.(721-723)Gat>Cat	p.D241H		NM_007226.2	NP_009157.1	O95156	NXPH2_HUMAN	neurexophilin 2	241	V (Cys-rich).				neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)				endometrium(1)|large_intestine(3)|lung(6)|ovary(3)|prostate(3)|skin(3)|urinary_tract(3)	22				BRCA - Breast invasive adenocarcinoma(221;0.101)		AGTTTATAATCAACACTGTAA	0.458																																					p.D241H		Atlas-SNP	.											.	NXPH2	63	.	0			c.G721C						.						94	87	89					2																	139428566		1925	4136	6061	SO:0001583	missense	11249	exon2			TATAATCAACACT	AF043467	CCDS46421.1	2q22.1	2008-05-15			ENSG00000144227	ENSG00000144227			8076	protein-coding gene	gene with protein product		604635				9570794	Standard	NM_007226		Approved	NPH2	uc002tvi.3	O95156	OTTHUMG00000153636	ENST00000272641.3:c.721G>C	chr2.hg19:g.139428566C>G	ENSP00000272641:p.Asp241His	58.0	0.0		90.0	31.0	NM_007226	B7WP24|Q494R1|Q75QC3	Missense_Mutation	SNP	ENST00000272641.3	hg19	CCDS46421.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.147449	0.77888	.	.	ENSG00000144227	ENST00000272641	.	.	.	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.79464	0.4450	M	0.72894	2.215	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.77960	-0.2391	8	.	.	.	-20.6009	19.7866	0.96442	0.0:1.0:0.0:0.0	.	241	O95156	NXPH2_HUMAN	H	241	.	.	D	-	1	0	NXPH2	139145036	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.776000	0.85560	2.756000	0.94617	0.655000	0.94253	GAT	.	.		0.458	NXPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331901.1			G	139428566	C	G	139428566	3	3	286	1	0	0	0	0	1	0	0	0	10800	826	29	4	77	4	NXPH2	2	139428566	Missense_Mutation	SNP	C	TCGA-G3-A5SK-01A-11D-A27I-10	74123533	139428566	103770807	15	42026										
HOXD12	3238	hgsc.bcm.edu	37	chr2	176964643	176964643	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	aatggcggccagttggccgcGcttccccctatctcctaccc	9	18	1	0			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr2:176964643G>C	ENST00000406506.2	+	1	186	c.114G>C	c.(112-114)gcG>gcC	p.A38A	HOXD12_ENST00000404162.2_Silent_p.A38A			P35452	HXD12_HUMAN	homeobox D12	38				GGQLAALPPISYPRG -> AASLAFPLSPTRA (in Ref. 1; AAF79044). {ECO:0000305}.	embryonic digit morphogenesis (GO:0042733)|pattern specification process (GO:0007389)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|large_intestine(1)|lung(7)|ovary(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0521)|READ - Rectum adenocarcinoma(9;0.0678)		AGTTGGCCGCGCTTCCCCCTA	0.697																																					p.A38A		Atlas-SNP	.											.	HOXD12	25	.	0			c.G114C						.						36	40	39					2																	176964643		1816	4063	5879	SO:0001819	synonymous_variant	3238	exon1			GGCCGCGCTTCCC		CCDS46456.1	2q31.1	2011-06-20	2005-12-22		ENSG00000170178	ENSG00000170178		"Homeoboxes / ANTP class : HOXL subclass"	5135	protein-coding gene	gene with protein product		142988	"homeo box D12"	HOX4H		1675198, 1973146	Standard	NM_021193		Approved		uc010zev.1	P35452	OTTHUMG00000150358	ENST00000406506.2:c.114G>C	chr2.hg19:g.176964643G>C		39.0	0.0		48.0	10.0	NM_021193	B5MCP0|Q0VAD7|Q0VAD8|Q9NS03	Silent	SNP	ENST00000406506.2	hg19	CCDS46456.1																																																																																			.	.		0.697	HOXD12-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359253.2	NM_021193		C	176964643	G	C	176964643	2	2	286	1	0	0	0	0	0	0	0	1	7330	1074	38	4		4	HOXD12	2	176964643	Silent	SNP	G	TCGA-G3-A5SK-01A-11D-A27I-10	37536077	176964643	66234730	16	42027										
HIBCH	26275	hgsc.bcm.edu	37	chr2	191077767	191077767	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	ccatgagttgccttagtgtgAtctttagagatgttggagac	12	6	1	4			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr2:191077767A>C	ENST00000359678.5	-	12	1220	c.926T>G	c.(925-927)aTc>aGc	p.I309S	HIBCH_ENST00000410045.1_Missense_Mutation_p.I86S|HIBCH_ENST00000392332.3_Missense_Mutation_p.I309S|HIBCH_ENST00000486981.1_5'UTR	NM_014362.3|NM_198047.2	NP_055177.2|NP_932164.1	Q6NVY1	HIBCH_HUMAN	3-hydroxyisobutyryl-CoA hydrolase	309					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|valine catabolic process (GO:0006574)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	3-hydroxyisobutyryl-CoA hydrolase activity (GO:0003860)			NS(1)|breast(2)|endometrium(1)|large_intestine(1)|lung(5)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	13			OV - Ovarian serous cystadenocarcinoma(117;0.000586)|Epithelial(96;0.0286)|all cancers(119;0.0814)			CCTTAGTGTGATCTTTAGAGA	0.343																																					p.I309S		Atlas-SNP	.											.	HIBCH	28	.	0			c.T926G						.						93	98	96					2																	191077767		2203	4300	6503	SO:0001583	missense	26275	exon12			AGTGTGATCTTTA	U66669	CCDS2304.1, CCDS46475.1	2q32.3	2010-04-29	2010-04-29		ENSG00000198130	ENSG00000198130	3.1.2.4		4908	protein-coding gene	gene with protein product		610690	"3-hydroxyisobutyryl-Coenzyme A hydrolase"			8824301	Standard	NM_014362		Approved		uc002uru.3	Q6NVY1	OTTHUMG00000132673	ENST00000359678.5:c.926T>G	chr2.hg19:g.191077767A>C	ENSP00000352706:p.Ile309Ser	34.0	0.0		26.0	8.0	NM_014362	D3DPI4|Q53GA8|Q53GF2|Q53RF7|Q53TC6|Q92931|Q9BS94	Missense_Mutation	SNP	ENST00000359678.5	hg19	CCDS2304.1	.	.	.	.	.	.	.	.	.	.	A	16.77	3.214076	0.58452	.	.	ENSG00000198130	ENST00000392332;ENST00000359678;ENST00000410045;ENST00000416732;ENST00000409820	T;T;T;T;T	0.74526	-0.63;-0.63;-0.85;-0.85;-0.85	5.01	5.01	0.66863	.	0.231118	0.43110	D	0.000611	D	0.85741	0.5767	M	0.80028	2.48	0.58432	D	0.999998	D;D	0.76494	0.999;0.999	D;D	0.91635	0.997;0.999	D	0.87646	0.2525	10	0.87932	D	0	0.3696	12.711	0.57089	1.0:0.0:0.0:0.0	.	309;309	Q6NVY1-2;Q6NVY1	.;HIBCH_HUMAN	S	309;309;86;60;89	ENSP00000376144:I309S;ENSP00000352706:I309S;ENSP00000386274:I86S;ENSP00000399263:I60S;ENSP00000387098:I89S	ENSP00000352706:I309S	I	-	2	0	HIBCH	190786012	1.000000	0.71417	1.000000	0.80357	0.615000	0.37417	6.889000	0.75627	2.096000	0.63516	0.460000	0.39030	ATC	.	.		0.343	HIBCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255933.1			C	191077767	A	C	191077767	3	2	286	1	0	0	0	0	1	0	0	0	7109	333	12	5	246	5	HIBCH	2	191077767	Missense_Mutation	SNP	A	TCGA-G3-A5SK-01A-11D-A27I-10	14113124	191077767	52121606	17	42028										
CACNA2D3	55799	hgsc.bcm.edu	37	chr3	55108222	55108222	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	tccctctgcttttgatgctcTtctcaaggtgacactgactg	8	12	3	3			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr3:55108222T>G	ENST00000474759.1	+	38	3313	c.3265T>G	c.(3265-3267)Ttc>Gtc	p.F1089V	CACNA2D3_ENST00000415676.2_Missense_Mutation_p.F1089V|CACNA2D3_ENST00000478261.1_3'UTR|CACNA2D3_ENST00000490478.1_Missense_Mutation_p.F995V|CACNA2D3_ENST00000288197.5_Missense_Mutation_p.F1089V	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3	1089						integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(3)	59				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)	Amlodipine(DB00381)|Nilvadipine(DB06712)|Spironolactone(DB00421)	TTTGATGCTCTTCTCAAGGTG	0.498																																					p.F1089V		Atlas-SNP	.											.	CACNA2D3	159	.	0			c.T3265G						.						158	156	156					3																	55108222		2114	4217	6331	SO:0001583	missense	55799	exon38			ATGCTCTTCTCAA	AJ272268	CCDS54598.1	3p21.1	2010-10-05	2008-02-26		ENSG00000157445	ENSG00000157445		"Calcium channel subunits"	15460	protein-coding gene	gene with protein product		606399				11245980	Standard	XM_005265318		Approved	HSA272268	uc003dhf.3	Q8IZS8	OTTHUMG00000158580	ENST00000474759.1:c.3265T>G	chr3.hg19:g.55108222T>G	ENSP00000419101:p.Phe1089Val	118.0	0.0		208.0	10.0	NM_018398	B2RPL6|Q9NY16|Q9NY18	Missense_Mutation	SNP	ENST00000474759.1	hg19	CCDS54598.1	.	.	.	.	.	.	.	.	.	.	T	14.23	2.473012	0.43942	.	.	ENSG00000157445	ENST00000415676;ENST00000474759;ENST00000288197;ENST00000490478;ENST00000398624	T;T;T;T	0.08370	3.1;3.1;3.1;3.1	5.47	3.09	0.35607	.	0.175509	0.50627	D	0.000102	T	0.03959	0.0111	N	0.08118	0	0.39881	D	0.973642	B	0.06786	0.001	B	0.06405	0.002	T	0.45454	-0.9260	10	0.20046	T	0.44	-1.0083	8.5407	0.33390	0.0:0.1519:0.0:0.8481	.	1089	Q8IZS8	CA2D3_HUMAN	V	1089;1089;1089;995;996	ENSP00000389506:F1089V;ENSP00000419101:F1089V;ENSP00000288197:F1089V;ENSP00000417279:F995V	ENSP00000288197:F1089V	F	+	1	0	CACNA2D3	55083262	0.991000	0.36638	0.998000	0.56505	0.988000	0.76386	1.343000	0.33930	0.466000	0.27193	0.467000	0.42956	TTC	.	.		0.498	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351402.1			G	55108222	T	G	55108222	3	3	286	1	0	0	0	0	1	0	0	0	2552	1609	56	5	3415	5	CACNA2D3	3	55108222	Missense_Mutation	SNP	T	TCGA-G3-A5SK-01A-11D-A27I-10		55108222	142914208	18	42029										
KIAA2018	205717	hgsc.bcm.edu	37	chr3	113373818	113373818	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	gctgaactgcaatcatgaccTagaatatggcttatgttatg	9	7	1	3			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr3:113373818T>C	ENST00000478658.1	-	5	6728	c.6711A>G	c.(6709-6711)ctA>ctG	p.L2237L	KIAA2018_ENST00000316407.4_Silent_p.L2237L|KIAA2018_ENST00000491165.1_Intron			Q68DE3	K2018_HUMAN	KIAA2018	2237						membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(30)|ovary(8)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	80						AATCATGACCTAGAATATGGC	0.403																																					p.L2237L		Atlas-SNP	.											.	KIAA2018	180	.	0			c.A6711G						.						89	81	83					3																	113373818		1921	4136	6057	SO:0001819	synonymous_variant	205717	exon7			ATGACCTAGAATA	AB095938	CCDS43133.1	3q13.2	2014-01-02			ENSG00000176542	ENSG00000176542			30494	protein-coding gene	gene with protein product							Standard	XM_005247208		Approved		uc003eam.3	Q68DE3	OTTHUMG00000159322	ENST00000478658.1:c.6711A>G	chr3.hg19:g.113373818T>C		127.0	0.0		184.0	62.0	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	hg19	CCDS43133.1																																																																																			.	.		0.403	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		C	113373818	T	C	113373818	2	2	286	1	0	0	0	0	0	0	0	1	8277	1509	53	2		2	KIAA2018	3	113373818	Silent	SNP	T	TCGA-G3-A5SK-01A-11D-A27I-10	58265596	113373818	84648612	19	42030										
COL6A5	256076	hgsc.bcm.edu	37	chr3	130104098	130104098	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	attggggcagctaataaaatAgaactgcaagaaattgctgg	11	5	0	2			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr3:130104098A>G	ENST00000432398.2	+	5	2246	c.1752A>G	c.(1750-1752)atA>atG	p.I584M	COL6A5_ENST00000265379.6_Missense_Mutation_p.I584M	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	584	Nonhelical region.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						CTAATAAAATAGAACTGCAAG	0.438																																					p.I584M		Atlas-SNP	.											.	COL6A5	205	.	0			c.A1752G						.						42	38	39					3																	130104098		692	1590	2282	SO:0001583	missense	256076	exon5			TAAAATAGAACTG	AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"Collagens"	26674	protein-coding gene	gene with protein product	"von Willebrand factor A domain containing 4"	611916	"collagen, type XXIX, alpha 1"	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.1752A>G	chr3.hg19:g.130104098A>G	ENSP00000390895:p.Ile584Met	76.0	0.0		80.0	29.0	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	hg19		.	.	.	.	.	.	.	.	.	.	A	5.465	0.270854	0.10349	.	.	ENSG00000172752	ENST00000432398;ENST00000265379	D;D	0.83163	-1.69;-1.69	5.28	1.45	0.22620	.	.	.	.	.	T	0.67040	0.2851	N	0.20685	0.6	0.09310	N	1	B	0.15930	0.015	B	0.19666	0.026	T	0.54603	-0.8269	9	0.42905	T	0.14	.	1.9884	0.03441	0.5842:0.134:0.1523:0.1295	.	584	A8TX70-2	.	M	584	ENSP00000390895:I584M;ENSP00000265379:I584M	ENSP00000265379:I584M	I	+	3	3	COL6A5	131586788	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.044000	0.12023	0.348000	0.23949	0.455000	0.32223	ATA	.	.		0.438	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264		G	130104098	A	G	130104098	3	3	286	1	0	0	0	0	1	0	0	0	3704	410	15	2	1766	2	COL6A5	3	130104098	Missense_Mutation	SNP	A	TCGA-G3-A5SK-01A-11D-A27I-10	16730280	130104098	67918332	20	42031										
ACPP	55	hgsc.bcm.edu	37	chr3	132050504	132050504	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	cccatagctgggcatggagcAgcattatgaacttggagagt	13	8	0	2			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr3:132050504A>T	ENST00000336375.5	+	3	320	c.230A>T	c.(229-231)cAg>cTg	p.Q77L	ACPP_ENST00000475741.1_Missense_Mutation_p.Q77L|ACPP_ENST00000489084.1_3'UTR|ACPP_ENST00000351273.7_Missense_Mutation_p.Q77L	NM_001099.4	NP_001090.2	P15309	PPAP_HUMAN	acid phosphatase, prostate	77					adenosine metabolic process (GO:0046085)|dephosphorylation (GO:0016311)|nucleotide metabolic process (GO:0009117)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|purine nucleobase metabolic process (GO:0006144)|regulation of sensory perception of pain (GO:0051930)|thiamine metabolic process (GO:0006772)	apical part of cell (GO:0045177)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi cisterna (GO:0031985)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|vesicle membrane (GO:0012506)	5'-nucleotidase activity (GO:0008253)|acid phosphatase activity (GO:0003993)|choline binding (GO:0033265)|identical protein binding (GO:0042802)|lysophosphatidic acid phosphatase activity (GO:0052642)|phosphatase activity (GO:0016791)|thiamine phosphate phosphatase activity (GO:0042131)			NS(1)|breast(1)|endometrium(2)|large_intestine(5)|lung(13)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	27						GGCATGGAGCAGCATTATGAA	0.323																																					p.Q77L		Atlas-SNP	.											.	ACPP	118	.	0			c.A230T						.						45	49	48					3																	132050504		2198	4298	6496	SO:0001583	missense	55	exon3			TGGAGCAGCATTA		CCDS3073.1, CCDS46916.1	3q22.1	2012-05-16			ENSG00000014257	ENSG00000014257	3.1.3.2		125	protein-coding gene	gene with protein product		171790					Standard	NM_001099		Approved	ACP3, ACP-3	uc003eop.4	P15309	OTTHUMG00000159650	ENST00000336375.5:c.230A>T	chr3.hg19:g.132050504A>T	ENSP00000337471:p.Gln77Leu	94.0	0.0		90.0	27.0	NM_001099	D3DNC6|Q5FBY0|Q96KY0|Q96QK9|Q96QM0	Missense_Mutation	SNP	ENST00000336375.5	hg19	CCDS3073.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.344978	0.82022	.	.	ENSG00000014257	ENST00000336375;ENST00000475741;ENST00000351273	T;T;T	0.26223	1.75;1.75;1.75	5.58	5.58	0.84498	.	0.000000	0.64402	D	0.000008	T	0.57315	0.2045	M	0.88241	2.94	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.74023	0.966;0.942;0.982	T	0.66288	-0.5961	10	0.87932	D	0	.	14.7386	0.69437	1.0:0.0:0.0:0.0	.	77;77;77	P15309;P15309-2;Q5FBY0	PPAP_HUMAN;.;.	L	77	ENSP00000337471:Q77L;ENSP00000417744:Q77L;ENSP00000323036:Q77L	ENSP00000337471:Q77L	Q	+	2	0	ACPP	133533194	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.411000	0.66386	2.131000	0.65755	0.533000	0.62120	CAG	.	.		0.323	ACPP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000356699.2	NM_001099		T	132050504	A	T	132050504	3	4	286	1	0	0	0	0	1	0	0	0	167	188	7	4	240	4	ACPP	3	132050504	Missense_Mutation	SNP	A	TCGA-G3-A5SK-01A-11D-A27I-10	1946406	132050504	65971926	21	42032										
SR140	23350	hgsc.bcm.edu	37	chr3	142747437	142747437	+	Frame_Shift_Del	DEL	A	A	-													0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	tggaatgtcagaagagcaagAaacagaagcttttgtagagg							TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr3:142747437delA	ENST00000473835.2	+	16	1649	c.1559delA	c.(1558-1560)gaafs	p.E520fs	U2SURP_ENST00000493598.2_Frame_Shift_Del_p.E519fs|U2SURP_ENST00000397933.2_Frame_Shift_Del_p.E111fs	NM_001080415.1	NP_001073884.1	O15042	SR140_HUMAN	U2 snRNP-associated SURP domain containing	520					RNA processing (GO:0006396)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	31						GAAGAGCAAGAAACAGAAGCT	0.363																																					p.E520fs		Atlas-Indel,Pindel	.											.	U2SURP	66	.	0			c.1558delG						.						112	107	109					3																	142747437		1827	4082	5909	SO:0001589	frameshift_variant	23350	exon16			.	BK000564	CCDS46928.1	3q23	2013-02-12			ENSG00000163714	ENSG00000163714		"RNA binding motif (RRM) containing"	30855	protein-coding gene	gene with protein product	"functional spliceosome-associated protein a", "Ser/Arg-rich domain protein, 140 kDa", "U2 associated SR140 protein"					9205841, 12234937	Standard	NM_001080415		Approved	fSAPa, SR140	uc003evh.1	O15042	OTTHUMG00000159323	ENST00000473835.2:c.1559delA	chr3.hg19:g.142747437delA	ENSP00000418563:p.Glu520fs	219.0	0.0		246.0	84.0	NM_001080415	A0PJ60|Q0D2M1|Q2NKQ7|Q9BR70	Frame_Shift_Del	DEL	ENST00000473835.2	hg19	CCDS46928.1																																																																																			.	.		0.363	U2SURP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354603.2	NM_001080415		-	142747437	A	-	142747437	7	5	286	1	0	1	0	1	0	0	0	0	15146	246	9	0	1621	0	SR140	3	142747437	Frame_Shift_Del	DEL	A	TCGA-G3-A5SK-01A-11D-A27I-10	10696933	142747437	55274993	22	42033										
KIAA0232	9778	hgsc.bcm.edu	37	chr4	6864199	6864199	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	atggaccaaaaatagtgcctTtgaagaaaatgaacactgtt	8	6	0	3			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr4:6864199T>A	ENST00000307659.5	+	7	2545	c.2090T>A	c.(2089-2091)tTt>tAt	p.F697Y	KIAA0232_ENST00000425103.1_Missense_Mutation_p.F697Y	NM_014743.2	NP_055558.2	Q92628	K0232_HUMAN	KIAA0232	697							ATP binding (GO:0005524)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(12)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	41						AATAGTGCCTTTGAAGAAAAT	0.343																																					p.F697Y		Atlas-SNP	.											.	KIAA0232	102	.	0			c.T2090A						.						63	59	60					4																	6864199		1844	4098	5942	SO:0001583	missense	9778	exon7			GTGCCTTTGAAGA	D86985	CCDS43209.1	4p16.1	2012-11-29			ENSG00000170871	ENSG00000170871			28992	protein-coding gene	gene with protein product						9039502	Standard	NM_014743		Approved		uc003gjq.4	Q92628	OTTHUMG00000160072	ENST00000307659.5:c.2090T>A	chr4.hg19:g.6864199T>A	ENSP00000303928:p.Phe697Tyr	188.0	0.0		244.0	86.0	NM_014743	A7E2D2	Missense_Mutation	SNP	ENST00000307659.5	hg19	CCDS43209.1	.	.	.	.	.	.	.	.	.	.	T	19.22	3.786035	0.70337	.	.	ENSG00000170871	ENST00000425103;ENST00000307659	.	.	.	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.77824	0.4188	M	0.66939	2.045	0.58432	D	0.999996	D	0.76494	0.999	D	0.76071	0.987	T	0.80241	-0.1464	9	0.87932	D	0	-14.357	16.0174	0.80450	0.0:0.0:0.0:1.0	.	697	Q92628	K0232_HUMAN	Y	697	.	ENSP00000303928:F697Y	F	+	2	0	KIAA0232	6915100	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.765000	0.68834	2.186000	0.69663	0.533000	0.62120	TTT	.	.		0.343	KIAA0232-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359102.2	NM_014743		A	6864199	T	A	6864199	3	1	286	1	0	0	0	0	1	0	0	0	8172	1841	64	4	2108	4	KIAA0232	4	6864199	Missense_Mutation	SNP	T	TCGA-G3-A5SK-01A-11D-A27I-10		6864199	184290077	23	42034										
TXK	7294	hgsc.bcm.edu	37	chr4	48073678	48073678	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	tttccttctgtaaaaacttcCcacattaaaactcctgcaaa	2	12	1	0			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr4:48073678C>A	ENST00000264316.4	-	14	1456	c.1371G>T	c.(1369-1371)tgG>tgT	p.W457C	TXK_ENST00000507351.1_Missense_Mutation_p.W112C	NM_003328.2	NP_003319.2	P42681	TXK_HUMAN	TXK tyrosine kinase	457	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|adaptive immune response (GO:0002250)|cytokine production (GO:0001816)|interferon-gamma production (GO:0032609)|interleukin-4 production (GO:0032633)|NK T cell differentiation (GO:0001865)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|T cell receptor signaling pathway (GO:0050852)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|RNA polymerase II regulatory region DNA binding (GO:0001012)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|prostate(2)	25						TAAAAACTTCCCACATTAAAA	0.383																																					p.W457C		Atlas-SNP	.											.	TXK	58	.	0			c.G1371T						.						73	80	77					4																	48073678		2203	4300	6503	SO:0001583	missense	7294	exon14			AACTTCCCACATT	L27071	CCDS3480.1	4p12	2013-02-14	2003-04-01		ENSG00000074966	ENSG00000074966	2.7.10.1	"SH2 domain containing"	12434	protein-coding gene	gene with protein product		600058	"PTK4 protein tyrosine kinase 4"	PTK4		7951233, 7528718	Standard	NM_003328		Approved	TKL, PSCTK5, BTKL, RLK	uc003gxx.4	P42681	OTTHUMG00000102065	ENST00000264316.4:c.1371G>T	chr4.hg19:g.48073678C>A	ENSP00000264316:p.Trp457Cys	25.0	0.0		46.0	13.0	NM_003328	Q14220	Missense_Mutation	SNP	ENST00000264316.4	hg19	CCDS3480.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.854082	0.91355	.	.	ENSG00000074966	ENST00000264316;ENST00000507351	D;D	0.85955	-2.05;-2.05	5.45	5.45	0.79879	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000001	D	0.95017	0.8387	H	0.96239	3.79	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95108	0.8236	10	0.45353	T	0.12	.	18.4504	0.90702	0.0:1.0:0.0:0.0	.	144;457	B4DTB5;P42681	.;TXK_HUMAN	C	457;112	ENSP00000264316:W457C;ENSP00000423481:W112C	ENSP00000264316:W457C	W	-	3	0	TXK	47768435	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.651000	0.83577	2.836000	0.97738	0.655000	0.94253	TGG	.	.		0.383	TXK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219869.7	NM_003328		A	48073678	C	A	48073678	3	1	286	1	0	0	0	0	1	0	0	0	16801	624	22	3	220	3	TXK	4	48073678	Missense_Mutation	SNP	C	TCGA-G3-A5SK-01A-11D-A27I-10	41209479	48073678	143080598	24	42035										
CWH43	80157	hgsc.bcm.edu	37	chr4	49046853	49046853	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	tgtgaatacattatgtatcgAgggctgatcaggtgagcaca	12	6	1	3			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr4:49046853A>G	ENST00000226432.4	+	14	2037	c.1854A>G	c.(1852-1854)cgA>cgG	p.R618R	CWH43_ENST00000513409.1_Silent_p.R591R	NM_025087.2	NP_079363.2	Q9H720	PG2IP_HUMAN	cell wall biogenesis 43 C-terminal homolog (S. cerevisiae)	618	Required for function in lipid remodeling. {ECO:0000250}.				GPI anchor biosynthetic process (GO:0006506)	integral component of membrane (GO:0016021)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(26)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43						TTATGTATCGAGGGCTGATCA	0.373																																					p.R618R		Atlas-SNP	.											.	CWH43	101	.	0			c.A1854G						.						205	192	196					4																	49046853		2203	4300	6503	SO:0001819	synonymous_variant	80157	exon14			GTATCGAGGGCTG		CCDS3486.1, CCDS68697.1	4p12-p11	2010-09-21			ENSG00000109182	ENSG00000109182			26133	protein-coding gene	gene with protein product						17714445, 17761529	Standard	NM_025087		Approved	FLJ21511, CWH43-C	uc003gyv.3	Q9H720	OTTHUMG00000128627	ENST00000226432.4:c.1854A>G	chr4.hg19:g.49046853A>G		85.0	0.0		92.0	19.0	NM_025087	B2RPD7	Silent	SNP	ENST00000226432.4	hg19	CCDS3486.1																																																																																			.	.		0.373	CWH43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250496.2	NM_025087		G	49046853	A	G	49046853	2	3	286	1	0	0	0	0	0	0	0	1	4075	291	11	2		2	CWH43	4	49046853	Silent	SNP	A	TCGA-G3-A5SK-01A-11D-A27I-10	973175	49046853	142107423	25	42036										
SH3RF1	57630	hgsc.bcm.edu	37	chr4	170077556	170077556	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	aagcacattctacctttaccTttgcaaatggaaggcaatct	6	10	2	0			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr4:170077556T>G	ENST00000284637.9	-	3	1009	c.668A>C	c.(667-669)aAg>aCg	p.K223T	SH3RF1_ENST00000508685.1_5'UTR	NM_020870.3	NP_065921.2	Q7Z6J0	SH3R1_HUMAN	SH3 domain containing ring finger 1	223	SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.				negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|protein ubiquitination (GO:0016567)|regulation of JNK cascade (GO:0046328)	cell projection (GO:0042995)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	31		Prostate(90;0.00267)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)		TACCTTTACCTTTGCAAATGG	0.398																																					p.K223T		Atlas-SNP	.											.	SH3RF1	60	.	0			c.A668C						.						135	135	135					4																	170077556		2203	4300	6503	SO:0001630	splice_region_variant	57630	exon3			TTTACCTTTGCAA	BC033203	CCDS34099.1	4q32.3	2013-01-09	2006-02-13	2006-02-13	ENSG00000154447	ENSG00000154447		"RING-type (C3HC4) zinc fingers"	17650	protein-coding gene	gene with protein product	"plenty of SH3 domains"		"SH3 multiple domains 2"	SH3MD2		9482736	Standard	NM_020870		Approved	POSH, RNF142, KIAA1494	uc003isa.1	Q7Z6J0	OTTHUMG00000161010	ENST00000284637.9:c.669+1A>C	chr4.hg19:g.170077556T>G		184.0	0.0		253.0	92.0	NM_020870	Q05BT2|Q8IW46|Q9HAM2|Q9P234	Missense_Mutation	SNP	ENST00000284637.9	hg19	CCDS34099.1	.	.	.	.	.	.	.	.	.	.	T	16.50	3.139902	0.56936	.	.	ENSG00000154447	ENST00000284637	T	0.35973	1.28	5.76	5.76	0.90799	Src homology-3 domain (4);	0.000000	0.85682	D	0.000000	T	0.62502	0.2433	M	0.79123	2.44	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	T	0.66866	-0.5815	10	0.87932	D	0	-28.0384	16.3634	0.83296	0.0:0.0:0.0:1.0	.	223	Q7Z6J0	SH3R1_HUMAN	T	223	ENSP00000284637:K223T	ENSP00000284637:K223T	K	-	2	0	SH3RF1	170314131	1.000000	0.71417	1.000000	0.80357	0.101000	0.19017	7.655000	0.83696	2.324000	0.78689	0.533000	0.62120	AAG	.	.		0.398	SH3RF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363382.3	NM_020870	Missense_Mutation	G	170077556	T	G	170077556	5	3	286	1	0	0	0	0	0	0	1	0	14273	1623	56	5	2038	5	SH3RF1	4	170077556	Splice_Site	SNP	T	TCGA-G3-A5SK-01A-11D-A27I-10	121030703	170077556	21076720	26	42037										
ADAM29	11086	hgsc.bcm.edu	37	chr4	175897719	175897719	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	ccatgatgaggatacatgtcGttgttcacaacctagatgca	9	9	1	3	rs201308805		TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr4:175897719G>A	ENST00000359240.3	+	5	1713	c.1043G>A	c.(1042-1044)cGt>cAt	p.R348H	ADAM29_ENST00000404450.4_Missense_Mutation_p.R348H|RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000514159.1_Missense_Mutation_p.R348H|ADAM29_ENST00000445694.1_Missense_Mutation_p.R348H	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	348	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		GATACATGTCGTTGTTCACAA	0.373																																					p.R348H	Ovarian(140;1727 1835 21805 25838 41440)	Atlas-SNP	.											.	ADAM29	262	.	0			c.G1043A						.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	145	140	141		1043,1043,1043,1043	-7.2	0	4		141	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense,missense	ADAM29	NM_001130703.1,NM_001130704.1,NM_001130705.1,NM_014269.4	29,29,29,29	0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231	probably-damaging,probably-damaging,probably-damaging,probably-damaging	348/821,348/821,348/821,348/821	175897719	3,13003	2203	4300	6503	SO:0001583	missense	11086	exon4			CATGTCGTTGTTC	AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"ADAM metallopeptidase domain containing"	207	protein-coding gene	gene with protein product	"cancer/testis antigen 73"	604778	"a disintegrin and metalloproteinase domain 29"			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.1043G>A	chr4.hg19:g.175897719G>A	ENSP00000352177:p.Arg348His	149.0	0.0		172.0	13.0	NM_001130703	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Missense_Mutation	SNP	ENST00000359240.3	hg19	CCDS3823.1	.	.	.	.	.	.	.	.	.	.	G	10.29	1.308218	0.23821	2.27E-4	2.33E-4	ENSG00000168594	ENST00000359240;ENST00000445694;ENST00000404450;ENST00000514159	T;T;T;T	0.09538	2.97;2.97;2.97;2.97	3.6	-7.2	0.01495	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	4.010880	0.01831	U	0.034703	T	0.10594	0.0259	N	0.13168	0.305	0.09310	N	1	D	0.71674	0.998	P	0.61592	0.891	T	0.34129	-0.9841	9	.	.	.	.	1.6479	0.02766	0.1398:0.387:0.177:0.2961	.	348	Q9UKF5	ADA29_HUMAN	H	348	ENSP00000352177:R348H;ENSP00000414544:R348H;ENSP00000384229:R348H;ENSP00000423517:R348H	.	R	+	2	0	ADAM29	176134294	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.801000	0.00761	-2.197000	0.00750	-0.496000	0.04628	CGT	.	.		0.373	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding				A	175897719	G	A	175897719	3	1	286	1	0	0	0	0	1	0	0	0	247	1145	40	1	1045	1	ADAM29	4	175897719	Missense_Mutation	SNP	G	TCGA-G3-A5SK-01A-11D-A27I-10	5820163	175897719	15256557	27	42038										
ADAM29	11086	hgsc.bcm.edu	37	chr4	175898784	175898784	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	actttgtaaaaaaagtaaacCaataaaaaagcagcaagatg	6	5	0	1			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr4:175898784C>G	ENST00000359240.3	+	5	2778	c.2108C>G	c.(2107-2109)cCa>cGa	p.P703R	ADAM29_ENST00000404450.4_Missense_Mutation_p.P703R|RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000514159.1_Missense_Mutation_p.P703R|ADAM29_ENST00000445694.1_Missense_Mutation_p.P703R	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	703					spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		AAAAGTAAACCAATAAAAAAG	0.338																																					p.P703R	Ovarian(140;1727 1835 21805 25838 41440)	Atlas-SNP	.											.	ADAM29	262	.	0			c.C2108G						.						42	45	44					4																	175898784		2203	4300	6503	SO:0001583	missense	11086	exon4			GTAAACCAATAAA	AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"ADAM metallopeptidase domain containing"	207	protein-coding gene	gene with protein product	"cancer/testis antigen 73"	604778	"a disintegrin and metalloproteinase domain 29"			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.2108C>G	chr4.hg19:g.175898784C>G	ENSP00000352177:p.Pro703Arg	59.0	0.0		57.0	17.0	NM_001130703	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Missense_Mutation	SNP	ENST00000359240.3	hg19	CCDS3823.1	.	.	.	.	.	.	.	.	.	.	C	3.684	-0.064885	0.07273	.	.	ENSG00000168594	ENST00000359240;ENST00000445694;ENST00000404450;ENST00000514159	T;T;T;T	0.01871	4.59;4.59;4.59;4.59	2.63	-0.82	0.10826	.	.	.	.	.	T	0.01189	0.0039	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.49062	-0.8978	8	.	.	.	.	4.8219	0.13394	0.5584:0.2749:0.1667:0.0	.	703	Q9UKF5	ADA29_HUMAN	R	703	ENSP00000352177:P703R;ENSP00000414544:P703R;ENSP00000384229:P703R;ENSP00000423517:P703R	.	P	+	2	0	ADAM29	176135359	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.361000	0.00498	-0.227000	0.09884	0.643000	0.83706	CCA	.	.		0.338	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding				G	175898784	C	G	175898784	3	3	286	1	0	0	0	0	1	0	0	0	247	594	21	4	2110	4	ADAM29	4	175898784	Missense_Mutation	SNP	C	TCGA-G3-A5SK-01A-11D-A27I-10	1065	175898784	15255492	28	42039										
MTRR	4552	hgsc.bcm.edu	37	chr5	7892874	7892874	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	acccaggaaagctccattttGtcttcaacattgtggaattt	7	9	2	0			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr5:7892874G>C	ENST00000264668.2	+	11	1516	c.1486G>C	c.(1486-1488)Gtc>Ctc	p.V496L	MTRR_ENST00000440940.2_Missense_Mutation_p.V469L	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	496	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|DNA methylation (GO:0006306)|folic acid metabolic process (GO:0046655)|methionine biosynthetic process (GO:0009086)|methionine metabolic process (GO:0006555)|methylation (GO:0032259)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	[methionine synthase] reductase activity (GO:0030586)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|oxidoreductase activity, oxidizing metal ions, NAD or NADP as acceptor (GO:0016723)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(14)|ovary(1)|prostate(3)|stomach(1)	31					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	GCTCCATTTTGTCTTCAACAT	0.433																																					p.V496L		Atlas-SNP	.											.	MTRR	74	.	0			c.G1486C						.						188	169	176					5																	7892874		2203	4300	6503	SO:0001583	missense	4552	exon11			CATTTTGTCTTCA	AF025794	CCDS3874.1, CCDS47190.1	5p15.31	2011-05-12			ENSG00000124275	ENSG00000124275	1.16.1.8		7473	protein-coding gene	gene with protein product		602568				9501215	Standard	NM_024010		Approved	cblE	uc003jed.3	Q9UBK8	OTTHUMG00000090477	ENST00000264668.2:c.1486G>C	chr5.hg19:g.7892874G>C	ENSP00000264668:p.Val496Leu	150.0	0.0		213.0	14.0	NM_024010	O60471|Q32MA9|Q7Z4M8	Missense_Mutation	SNP	ENST00000264668.2	hg19	CCDS3874.1	.	.	.	.	.	.	.	.	.	.	G	14.54	2.565669	0.45694	.	.	ENSG00000124275	ENST00000264668;ENST00000440940	T;T	0.29655	1.56;1.56	4.89	0.53	0.17102	Riboflavin synthase-like beta-barrel (1);FAD-binding, type 1 (1);Ferredoxin reductase-type FAD-binding domain (1);	0.364021	0.30437	N	0.009621	T	0.34019	0.0883	M	0.62266	1.93	0.38294	D	0.942791	P	0.48834	0.916	P	0.48089	0.566	T	0.17653	-1.0362	10	0.51188	T	0.08	-8.869	8.9511	0.35790	0.3913:0.0:0.6087:0.0	.	496	Q9UBK8	MTRR_HUMAN	L	496;469	ENSP00000264668:V496L;ENSP00000402510:V469L	ENSP00000264668:V496L	V	+	1	0	MTRR	7945874	0.749000	0.28305	0.008000	0.14137	0.505000	0.33919	0.981000	0.29526	-0.219000	0.10003	-0.140000	0.14226	GTC	.	.		0.433	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1			C	7892874	G	C	7892874	3	2	286	1	0	0	0	0	1	0	0	0	9970	1377	48	4	1528	4	MTRR	5	7892874	Missense_Mutation	SNP	G	TCGA-G3-A5SK-01A-11D-A27I-10		7892874	173022386	29	42040										
RXFP3	51289	hgsc.bcm.edu	37	chr5	33938060	33938060	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	gcgctcaagagcctgctgtgGcgcatcgcgtctccttcgat	12	14	2	1			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr5:33938060G>A	ENST00000330120.3	+	1	1570	c.1215G>A	c.(1213-1215)tgG>tgA	p.W405*		NM_016568.3	NP_057652.1	Q9NSD7	RL3R1_HUMAN	relaxin/insulin-like family peptide receptor 3	405					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled peptide receptor activity (GO:0008528)|G-protein coupled receptor activity (GO:0004930)			endometrium(4)|large_intestine(9)|lung(24)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)	42						GCCTGCTGTGGCGCATCGCGT	0.682																																					p.W405X		Atlas-SNP	.											.	RXFP3	114	.	0			c.G1215A						.						53	54	53					5																	33938060		2203	4300	6503	SO:0001587	stop_gained	51289	exon1			GCTGTGGCGCATC	D88437	CCDS3900.1	5p15.1-p14	2012-08-08	2006-05-09	2006-03-15	ENSG00000182631	ENSG00000182631		"GPCR / Class A : Relaxin family peptide receptors"	24883	protein-coding gene	gene with protein product		609445	"relaxin 3 receptor 1", "relaxin family peptide receptor 3"	RLN3R1		15956688, 16507880	Standard	NM_016568		Approved	SALPR, GPCR135, RXFPR3	uc003jic.2	Q9NSD7	OTTHUMG00000090685	ENST00000330120.3:c.1215G>A	chr5.hg19:g.33938060G>A	ENSP00000328708:p.Trp405*	74.0	0.0		115.0	46.0	NM_016568	Q14DA5	Nonsense_Mutation	SNP	ENST00000330120.3	hg19	CCDS3900.1	.	.	.	.	.	.	.	.	.	.	G	41	8.931651	0.99008	.	.	ENSG00000182631	ENST00000330120	.	.	.	5.79	5.79	0.91817	.	0.553902	0.19673	N	0.108716	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.19147	T	0.46	-5.6355	20.0222	0.97508	0.0:0.0:1.0:0.0	.	.	.	.	X	405	.	ENSP00000328708:W405X	W	+	3	0	RXFP3	33973817	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.938000	0.87678	2.726000	0.93360	0.655000	0.94253	TGG	.	.		0.682	RXFP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207369.1	NM_016568		A	33938060	G	A	33938060	4	1	286	1	0	0	0	0	0	1	0	0	13776	1212	42	3	1217	3	RXFP3	5	33938060	Nonsense_Mutation	SNP	G	TCGA-G3-A5SK-01A-11D-A27I-10	26045186	33938060	146977200	30	42041										
ISL1	3670	hgsc.bcm.edu	37	chr5	50685666	50685666	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	agagatgacgggcctcagtcCccgtgtgatccgggtctggt	15	11	2	3			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr5:50685666C>A	ENST00000230658.7	+	4	1250	c.665C>A	c.(664-666)cCc>cAc	p.P222H	ISL1_ENST00000511384.1_Missense_Mutation_p.P222H|ISL1_ENST00000505475.2_3'UTR	NM_002202.2	NP_002193.2	P61371	ISL1_HUMAN	ISL LIM homeobox 1	222					atrial septum morphogenesis (GO:0060413)|axon regeneration (GO:0031103)|cardiac cell fate determination (GO:0060913)|cardiac muscle cell myoblast differentiation (GO:0060379)|cardiac right ventricle morphogenesis (GO:0003215)|cellular response to glucocorticoid stimulus (GO:0071385)|endocardial cushion morphogenesis (GO:0003203)|innervation (GO:0060384)|mesenchymal cell differentiation (GO:0048762)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of inflammatory response (GO:0050728)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of protein homodimerization activity (GO:0090074)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neuron fate specification (GO:0048665)|outflow tract morphogenesis (GO:0003151)|outflow tract septum morphogenesis (GO:0003148)|pancreas development (GO:0031016)|peripheral nervous system neuron axonogenesis (GO:0048936)|pharyngeal system development (GO:0060037)|pituitary gland development (GO:0021983)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of granulocyte colony-stimulating factor production (GO:0071657)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 alpha production (GO:0032730)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage colony-stimulating factor production (GO:1901258)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|retinal ganglion cell axon guidance (GO:0031290)|secondary heart field specification (GO:0003139)|sensory system development (GO:0048880)|spinal cord motor neuron cell fate specification (GO:0021520)|spinal cord motor neuron differentiation (GO:0021522)|trigeminal nerve development (GO:0021559)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral motor neuron differentiation (GO:0021524)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor binding (GO:0016922)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(11)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	31		Lung NSC(810;0.000845)|Breast(144;0.0411)				GGCCTCAGTCCCCGTGTGATC	0.562																																					p.P222H		Atlas-SNP	.											.	ISL1	65	.	0			c.C665A						.						63	75	71					5																	50685666		2203	4300	6503	SO:0001583	missense	3670	exon4			TCAGTCCCCGTGT	BC031213	CCDS43314.1	5q11.2	2012-03-09	2007-07-13		ENSG00000016082	ENSG00000016082		"Homeoboxes / LIM class"	6132	protein-coding gene	gene with protein product		600366	"ISL1 transcription factor, LIM/homeodomain, (islet-1)"			7912209	Standard	NM_002202		Approved	Isl-1, ISLET1	uc003jor.3	P61371	OTTHUMG00000162281	ENST00000230658.7:c.665C>A	chr5.hg19:g.50685666C>A	ENSP00000230658:p.Pro222His	148.0	0.0		256.0	84.0	NM_002202	P20663|P47894	Missense_Mutation	SNP	ENST00000230658.7	hg19	CCDS43314.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.713780	0.89112	.	.	ENSG00000016082	ENST00000230658;ENST00000503187;ENST00000511384	D;D	0.96168	-3.93;-3.93	5.73	5.73	0.89815	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.97832	0.9288	M	0.81802	2.56	0.80722	D	1	D	0.76494	0.999	D	0.76071	0.987	D	0.98225	1.0480	10	0.87932	D	0	.	19.8842	0.96908	0.0:1.0:0.0:0.0	.	222	P61371	ISL1_HUMAN	H	222	ENSP00000230658:P222H;ENSP00000422676:P222H	ENSP00000230658:P222H	P	+	2	0	ISL1	50721423	1.000000	0.71417	0.985000	0.45067	0.740000	0.42216	7.726000	0.84824	2.689000	0.91719	0.585000	0.79938	CCC	.	.		0.562	ISL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368413.3	NM_002202		A	50685666	C	A	50685666	3	1	286	1	0	0	0	0	1	0	0	0	7865	623	22	3	679	3	ISL1	5	50685666	Missense_Mutation	SNP	C	TCGA-G3-A5SK-01A-11D-A27I-10	16747606	50685666	130229594	31	42042										
KCTD16	57528	hgsc.bcm.edu	37	chr5	143853624	143853624	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	tcaaaattccagatcggtttCctgagagaaaacatccttgg	8	9	1	3			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr5:143853624C>T	ENST00000507359.3	+	3	2325	c.1234C>T	c.(1234-1236)Cct>Tct	p.P412S	KCTD16_ENST00000512467.1_Missense_Mutation_p.P412S	NM_020768.3	NP_065819.1	Q68DU8	KCD16_HUMAN	potassium channel tetramerization domain containing 16	412					protein homooligomerization (GO:0051260)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)				large_intestine(5)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	21		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)			AGATCGGTTTCCTGAGAGAAA	0.378																																					p.P412S		Atlas-SNP	.											.	KCTD16	70	.	0			c.C1234T						.						53	62	59					5																	143853624		2196	4298	6494	SO:0001583	missense	57528	exon4			CGGTTTCCTGAGA	AB037738	CCDS34260.1	5q32	2013-06-20	2013-06-20		ENSG00000183775	ENSG00000183775			29244	protein-coding gene	gene with protein product		613423	"potassium channel tetramerisation domain containing 16"			10718198	Standard	NM_020768		Approved	KIAA1317	uc003lnm.1	Q68DU8	OTTHUMG00000163172	ENST00000507359.3:c.1234C>T	chr5.hg19:g.143853624C>T	ENSP00000426548:p.Pro412Ser	92.0	0.0		91.0	25.0	NM_020768	Q9P2M9	Missense_Mutation	SNP	ENST00000507359.3	hg19	CCDS34260.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.696256	0.88830	.	.	ENSG00000183775	ENST00000512467;ENST00000507359	T;T	0.63913	-0.07;-0.07	6.17	6.17	0.99709	.	0.382752	0.29152	N	0.012981	T	0.74313	0.3700	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.74315	-0.3705	10	0.87932	D	0	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	412	Q68DU8	KCD16_HUMAN	S	412	ENSP00000424151:P412S;ENSP00000426548:P412S	ENSP00000426548:P412S	P	+	1	0	KCTD16	143833817	1.000000	0.71417	0.950000	0.38849	0.935000	0.57460	7.400000	0.79949	2.941000	0.99782	0.655000	0.94253	CCT	.	.		0.378	KCTD16-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371898.3	XM_098368		T	143853624	C	T	143853624	3	4	286	1	0	0	0	0	1	0	0	0	8112	855	30	3	1240	3	KCTD16	5	143853624	Missense_Mutation	SNP	C	TCGA-G3-A5SK-01A-11D-A27I-10	93167958	143853624	37061636	32	42043										
NSD1	64324	hgsc.bcm.edu	37	chr5	176721088	176721088	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	cactcacctggcagagcaatCaacaggaatggctgctcagg	11	12	3	1			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr5:176721088C>A	ENST00000439151.2	+	23	6764	c.6719C>A	c.(6718-6720)tCa>tAa	p.S2240*	NSD1_ENST00000347982.4_Nonsense_Mutation_p.S1971*|NSD1_ENST00000354179.4_Nonsense_Mutation_p.S1971*|NSD1_ENST00000361032.4_Nonsense_Mutation_p.S2137*	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	2240	Pro-rich.				gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		GCAGAGCAATCAACAGGAATG	0.572			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.S2240X		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.C6719A						.						77	77	77					5																	176721088		2203	4300	6503	SO:0001587	stop_gained	64324	exon23	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	AGCAATCAACAGG	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	14234	protein-coding gene	gene with protein product		606681	"Sotos syndrome"	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.6719C>A	chr5.hg19:g.176721088C>A	ENSP00000395929:p.Ser2240*	79.0	0.0		87.0	34.0	NM_022455	Q96PD8|Q96RN7	Nonsense_Mutation	SNP	ENST00000439151.2	hg19	CCDS4412.1	.	.	.	.	.	.	.	.	.	.	C	41	8.544165	0.98857	.	.	ENSG00000165671	ENST00000354179;ENST00000439151;ENST00000347982;ENST00000361032	.	.	.	5.58	5.58	0.84498	.	0.126320	0.36409	N	0.002606	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.6036	0.56511	0.0:0.834:0.166:0.0	.	.	.	.	X	1971;2240;1971;2137	.	ENSP00000343209:S1971X	S	+	2	0	NSD1	176653694	0.269000	0.24143	0.833000	0.33012	0.091000	0.18340	1.420000	0.34804	2.906000	0.99361	0.655000	0.94253	TCA	.	.		0.572	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349		A	176721088	C	A	176721088	4	1	286	1	0	0	0	0	0	1	0	0	10678	838	29	3	6805	3	NSD1	5	176721088	Nonsense_Mutation	SNP	C	TCGA-G3-A5SK-01A-11D-A27I-10	32867464	176721088	4194172	33	42044										
TRIM15	89870	hgsc.bcm.edu	37	chr6	30138285	30138285	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	aacctgtctgcaggtgtgagAtgaagacttttgtgagtcct	12	7	1	4			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr6:30138285A>C	ENST00000376694.4	+	5	1208	c.739A>C	c.(739-741)Atg>Ctg	p.M247L	TRIM15_ENST00000376688.1_Intron	NM_033229.2	NP_150232.2	Q9C019	TRI15_HUMAN	tripartite motif containing 15	247					innate immune response (GO:0045087)|mesodermal cell fate determination (GO:0007500)|negative regulation of intracellular transport of viral material (GO:1901253)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of RIG-I signaling pathway (GO:1900246)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of type I interferon production (GO:0032481)	intracellular (GO:0005622)	zinc ion binding (GO:0008270)			large_intestine(2)|lung(8)|prostate(2)|skin(1)|urinary_tract(1)	14						CAGGTGTGAGATGAAGACTTT	0.443																																					p.M247L		Atlas-SNP	.											.	TRIM15	34	.	0			c.A739C						.						99	95	97					6																	30138285		2203	4300	6503	SO:0001583	missense	89870	exon5			TGTGAGATGAAGA	AF220132, U34249	CCDS4677.1	6p21.33	2013-01-09	2011-01-25		ENSG00000204610	ENSG00000204610		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16284	protein-coding gene	gene with protein product			"zinc finger protein 178", "tripartite motif-containing 15"	ZNF178		11331580, 8304341, 8812418	Standard	NM_033229		Approved	ZNFB7, RNF93	uc010jrx.3	Q9C019	OTTHUMG00000031031	ENST00000376694.4:c.739A>C	chr6.hg19:g.30138285A>C	ENSP00000365884:p.Met247Leu	63.0	0.0		106.0	29.0	NM_033229	A2BEC9|O95604|Q8IUX9|Q9C018	Missense_Mutation	SNP	ENST00000376694.4	hg19	CCDS4677.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.805|9.805	1.181615|1.181615	0.21787|0.21787	.|.	.|.	ENSG00000204610|ENSG00000204610	ENST00000376695;ENST00000376694|ENST00000433744	T|.	0.51817|.	0.69|.	5.42|5.42	-0.0487|-0.0487	0.13837|0.13837	.|.	0.909841|.	0.09382|.	N|.	0.809779|.	T|T	0.05914|0.05914	0.0154|0.0154	N|N	0.12471|0.12471	0.22|0.22	0.09310|0.09310	N|N	0.999998|0.999998	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.39603|0.39603	-0.9606|-0.9606	10|5	0.28530|.	T|.	0.3|.	.|.	4.7476|4.7476	0.13045|0.13045	0.5314:0.3214:0.1472:0.0|0.5314:0.3214:0.1472:0.0	.|.	247|.	Q9C019|.	TRI15_HUMAN|.	L|S	178;247|83	ENSP00000365884:M247L|.	ENSP00000365884:M247L|.	M|R	+|+	1|3	0|2	TRIM15|TRIM15	30246264|30246264	0.035000|0.035000	0.19736|0.19736	0.151000|0.151000	0.22473|0.22473	0.823000|0.823000	0.46562|0.46562	0.389000|0.389000	0.20751|0.20751	0.045000|0.045000	0.15804|0.15804	0.472000|0.472000	0.43445|0.43445	ATG|AGA	.	.		0.443	TRIM15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076026.2	NM_033229		C	30138285	A	C	30138285	3	2	286	1	0	0	0	0	1	0	0	0	16505	333	12	5	757	5	TRIM15	6	30138285	Missense_Mutation	SNP	A	TCGA-G3-A5SK-01A-11D-A27I-10		30138285	140976782	34	42045										
EPB41L2	2037	hgsc.bcm.edu	37	chr6	131179313	131179313	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	cagccaactctgtttctttgTgtaccaccactcttgtgacc	6	14	3	1			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr6:131179313T>C	ENST00000337057.3	-	19	3162	c.2981A>G	c.(2980-2982)cAc>cGc	p.H994R	EPB41L2_ENST00000524581.1_Missense_Mutation_p.H372R|EPB41L2_ENST00000525271.1_Missense_Mutation_p.H662R|EPB41L2_ENST00000445890.2_Missense_Mutation_p.H736R|EPB41L2_ENST00000368128.2_Missense_Mutation_p.H994R|EPB41L2_ENST00000528282.1_Missense_Mutation_p.H736R|EPB41L2_ENST00000527659.1_Missense_Mutation_p.H800R|EPB41L2_ENST00000527411.1_Missense_Mutation_p.H924R|EPB41L2_ENST00000525193.1_Missense_Mutation_p.H695R|EPB41L2_ENST00000529208.1_Missense_Mutation_p.H924R|EPB41L2_ENST00000531410.1_Missense_Mutation_p.H115R|EPB41L2_ENST00000392427.3_Missense_Mutation_p.H662R|EPB41L2_ENST00000530757.1_Missense_Mutation_p.H190R|EPB41L2_ENST00000530481.1_Missense_Mutation_p.H841R	NM_001431.3	NP_001422.1	O43491	E41L2_HUMAN	erythrocyte membrane protein band 4.1-like 2	994	C-terminal (CTD).				cortical actin cytoskeleton organization (GO:0030866)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|spectrin (GO:0008091)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(23)|prostate(1)|skin(2)	44	Breast(56;0.0639)			OV - Ovarian serous cystadenocarcinoma(155;0.0271)|GBM - Glioblastoma multiforme(226;0.0355)		TGTTTCTTTGTGTACCACCAC	0.532																																					p.H994R		Atlas-SNP	.											.	EPB41L2	96	.	0			c.A2981G						.						353	256	289					6																	131179313		2203	4300	6503	SO:0001583	missense	2037	exon19			TCTTTGTGTACCA	AF027299	CCDS5141.1, CCDS47474.1, CCDS56450.1, CCDS59037.1	6q23	2008-08-29			ENSG00000079819	ENSG00000079819			3379	protein-coding gene	gene with protein product		603237				9598318, 9828140	Standard	NM_001431		Approved	4.1-G	uc003qch.2	O43491	OTTHUMG00000015560	ENST00000337057.3:c.2981A>G	chr6.hg19:g.131179313T>C	ENSP00000338481:p.His994Arg	146.0	0.0		193.0	69.0	NM_001431	B4DHI8|E9PPD9|Q5T4F0|Q68DV2	Missense_Mutation	SNP	ENST00000337057.3	hg19	CCDS5141.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.423681	0.83559	.	.	ENSG00000079819	ENST00000531410;ENST00000528282;ENST00000530481;ENST00000445890;ENST00000337057;ENST00000530757;ENST00000392427;ENST00000368128;ENST00000527411;ENST00000524581;ENST00000525271;ENST00000525193;ENST00000527659;ENST00000529208	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.78003	-1.14;-1.14;-1.14;-1.14;-1.14;-1.14;-1.14;-1.14;-1.14;-1.14;-1.14;-1.14;-1.14;-1.14	6.16	4.99	0.66335	Band 4.1, C-terminal (1);	0.043827	0.85682	D	0.000000	D	0.84419	0.5468	M	0.77820	2.39	0.49582	D	0.999802	P;P;D;P;D;P	0.89917	0.519;0.872;1.0;0.559;1.0;0.789	P;P;D;B;D;P	0.97110	0.635;0.636;0.999;0.435;1.0;0.596	D	0.86723	0.1943	10	0.66056	D	0.02	.	13.7045	0.62629	0.0:0.0:0.1286:0.8713	.	662;841;994;736;372;161	B4DHI8;E9PPD9;O43491;Q68DV2;Q6R5J7;Q9UG62	.;.;E41L2_HUMAN;.;.;.	R	115;736;841;736;994;190;662;994;924;372;662;695;800;924	ENSP00000434596:H115R;ENSP00000434308:H736R;ENSP00000434576:H841R;ENSP00000402041:H736R;ENSP00000338481:H994R;ENSP00000436349:H190R;ENSP00000376222:H662R;ENSP00000357110:H994R;ENSP00000436348:H924R;ENSP00000437207:H372R;ENSP00000432803:H662R;ENSP00000431988:H695R;ENSP00000431647:H800R;ENSP00000436641:H924R	ENSP00000338481:H994R	H	-	2	0	EPB41L2	131221006	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	7.673000	0.83973	1.129000	0.42072	-0.323000	0.08544	CAC	.	.		0.532	EPB41L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042204.3			C	131179313	T	C	131179313	3	2	286	1	0	0	0	0	1	0	0	0	5155	1696	59	2	40	2	EPB41L2	6	131179313	Missense_Mutation	SNP	T	TCGA-G3-A5SK-01A-11D-A27I-10	101041028	131179313	39935754	35	42046										
PLG	5340	hgsc.bcm.edu	37	chr6	161139737	161139737	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	tttttcagaaatttggatgaAaactactgccgcaatcctga	7	8	1	3			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr6:161139737A>G	ENST00000308192.9	+	9	1026	c.963A>G	c.(961-963)gaA>gaG	p.E321E		NM_000301.3	NP_000292.1	P00747	PLMN_HUMAN	plasminogen	321	Kringle 3. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of fibrinolysis (GO:0051918)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of fibrinolysis (GO:0051919)|tissue remodeling (GO:0048771)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	apolipoprotein binding (GO:0034185)|protein domain specific binding (GO:0019904)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)	59				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Alteplase(DB00009)|Aminocaproic Acid(DB00513)|Anistreplase(DB00029)|Aprotinin(DB06692)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Tranexamic Acid(DB00302)|Urokinase(DB00013)	ATTTGGATGAAAACTACTGCC	0.448																																					p.E321E		Atlas-SNP	.											.	PLG	150	.	0			c.A963G						.						62	67	65					6																	161139737		2203	4300	6503	SO:0001819	synonymous_variant	5340	exon9			GGATGAAAACTAC	M74220	CCDS5279.1, CCDS55074.1	6q26	2012-10-02			ENSG00000122194	ENSG00000122194			9071	protein-coding gene	gene with protein product		173350					Standard	NM_000301		Approved		uc003qtm.4	P00747	OTTHUMG00000015957	ENST00000308192.9:c.963A>G	chr6.hg19:g.161139737A>G		189.0	0.0		233.0	24.0	NM_000301	Q15146|Q5TEH4|Q6PA00	Silent	SNP	ENST00000308192.9	hg19	CCDS5279.1																																																																																			.	.		0.448	PLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042959.2	NM_000301		G	161139737	A	G	161139737	2	3	286	1	0	0	0	0	0	0	0	1	12095	11	1	2		2	PLG	6	161139737	Silent	SNP	A	TCGA-G3-A5SK-01A-11D-A27I-10	29960424	161139737	9975330	36	42047										
SDK1	221935	hgsc.bcm.edu	37	chr7	3658865	3658865	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	gctcaccacctacagcagcgAatataagtaattgatcgctt	7	11	1	1			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr7:3658865A>T	ENST00000404826.2	+	2	591	c.452A>T	c.(451-453)gAa>gTa	p.E151V	SDK1_ENST00000389531.3_Missense_Mutation_p.E151V	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	151	Ig-like C2-type 1.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		TACAGCAGCGAATATAAGTAA	0.448																																					p.E151V		Atlas-SNP	.											.	SDK1	361	.	0			c.A452T						.						86	73	77					7																	3658865		2203	4300	6503	SO:0001583	missense	221935	exon2			GCAGCGAATATAA	AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19307	protein-coding gene	gene with protein product		607216	"sidekick homolog 1 (chicken)", "sidekick homolog 1, cell adhesion molecule (chicken)"			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.452A>T	chr7.hg19:g.3658865A>T	ENSP00000385899:p.Glu151Val	90.0	0.0		152.0	47.0	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	hg19	CCDS34590.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.083102	0.76642	.	.	ENSG00000146555	ENST00000404826;ENST00000389531	T;T	0.12984	2.63;2.63	5.74	5.74	0.90152	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.123080	0.36134	N	0.002764	T	0.33527	0.0866	M	0.73598	2.24	0.58432	D	0.999993	P	0.51537	0.946	P	0.56916	0.809	T	0.03068	-1.1076	10	0.48119	T	0.1	.	16.0546	0.80788	1.0:0.0:0.0:0.0	.	151	Q7Z5N4	SDK1_HUMAN	V	151	ENSP00000385899:E151V;ENSP00000374182:E151V	ENSP00000374182:E151V	E	+	2	0	SDK1	3625391	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	8.723000	0.91458	2.191000	0.70037	0.528000	0.53228	GAA	.	.		0.448	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744		T	3658865	A	T	3658865	3	4	286	1	0	0	0	0	1	0	0	0	13983	246	9	4	458	4	SDK1	7	3658865	Missense_Mutation	SNP	A	TCGA-G3-A5SK-01A-11D-A27I-10		3658865	155479798	37	42048										
BBS9	27241	hgsc.bcm.edu	37	chr7	33397473	33397473	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	ctcttttattttaggcattcCgcgagttatccaatgtaaat	6	8	1	0			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr7:33397473C>T	ENST00000242067.6	+	16	2080	c.1559C>T	c.(1558-1560)cCg>cTg	p.P520L	BBS9_ENST00000355070.2_Missense_Mutation_p.P515L|BBS9_ENST00000350941.3_Missense_Mutation_p.P480L|BBS9_ENST00000396127.2_Missense_Mutation_p.P485L|BBS9_ENST00000354265.4_Missense_Mutation_p.P485L	NM_198428.2	NP_940820.1	Q3SYG4	PTHB1_HUMAN	Bardet-Biedl syndrome 9	520					cilium assembly (GO:0042384)|fat cell differentiation (GO:0045444)|protein transport (GO:0015031)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	BBSome (GO:0034464)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)			BBS9/PKD1L1(2)	NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	50			GBM - Glioblastoma multiforme(11;0.0894)			TTAGGCATTCCGCGAGTTATC	0.328									Bardet-Biedl syndrome																												p.P520L		Atlas-SNP	.											.	BBS9	194	.	0			c.C1559T						.						92	99	97					7																	33397473		2203	4299	6502	SO:0001583	missense	27241	exon16	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	GCATTCCGCGAGT		CCDS5441.1, CCDS34618.1, CCDS43566.1, CCDS47572.1	7p14	2014-06-17			ENSG00000122507	ENSG00000122507			30000	protein-coding gene	gene with protein product	"parathyroid hormone responsive B1 gene"	607968				16380913, 10221542	Standard	XM_005249701		Approved	B1, PTHB1	uc003tdn.1	Q3SYG4	OTTHUMG00000128659	ENST00000242067.6:c.1559C>T	chr7.hg19:g.33397473C>T	ENSP00000242067:p.Pro520Leu	39.0	0.0		46.0	17.0	NM_198428	E9PDC9|P78514|Q7KYS6|Q7KYS7|Q8N570|Q99844|Q99854|Q9Y699|Q9Y6A0	Missense_Mutation	SNP	ENST00000242067.6	hg19	CCDS43566.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.6|24.6	4.547960|4.547960	0.86022|0.86022	.|.	.|.	ENSG00000122507|ENSG00000122507	ENST00000242067;ENST00000350941;ENST00000396127;ENST00000355070;ENST00000354265;ENST00000396132|ENST00000537775	T;T;T;T;T|.	0.17691|.	2.26;2.26;2.26;2.26;2.26|.	5.94|5.94	5.94|5.94	0.96194|0.96194	.|.	0.052462|.	0.85682|.	D|.	0.000000|.	T|T	0.75102|0.75102	0.3804|0.3804	L|L	0.56769|0.56769	1.78|1.78	0.80722|0.80722	D|D	1|1	D;D;D;D;D|.	0.65815|.	0.995;0.989;0.989;0.989;0.989|.	D;D;P;D;P|.	0.65987|.	0.94;0.94;0.89;0.94;0.89|.	T|T	0.75147|0.75147	-0.3420|-0.3420	10|6	0.30854|0.72032	T|D	0.27|0.01	-18.1224|-18.1224	19.9763|19.9763	0.97309|0.97309	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	520;480;515;485;520|.	Q3SYG4-3;Q3SYG4-2;E9PDC9;Q3SYG4-4;Q3SYG4|.	.;.;.;.;PTHB1_HUMAN|.	L|C	520;480;485;515;485;520|398	ENSP00000242067:P520L;ENSP00000313122:P480L;ENSP00000379433:P485L;ENSP00000347182:P515L;ENSP00000346214:P485L|.	ENSP00000242067:P520L|ENSP00000441763:R398C	P|R	+|+	2|1	0|0	BBS9|BBS9	33363998|33363998	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	4.231000|4.231000	0.58639|0.58639	2.823000|2.823000	0.97156|0.97156	0.643000|0.643000	0.83706|0.83706	CCG|CGC	.	.		0.328	BBS9-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329064.1			T	33397473	C	T	33397473	3	4	286	1	0	0	0	0	1	0	0	0	1342	652	23	1	1617	1	BBS9	7	33397473	Missense_Mutation	SNP	C	TCGA-G3-A5SK-01A-11D-A27I-10	29738608	33397473	125741190	38	42049										
ZMIZ2	83637	hgsc.bcm.edu	37	chr7	44797559	44797559	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	aggaggggtaatgggcccctCtggcctctcccccttggcta	13	14	2	0			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr7:44797559C>G	ENST00000309315.4	+	6	788	c.665C>G	c.(664-666)tCt>tGt	p.S222C	ZMIZ2_ENST00000265346.7_Missense_Mutation_p.S222C|ZMIZ2_ENST00000441627.1_Missense_Mutation_p.S222C|ZMIZ2_ENST00000413916.1_Missense_Mutation_p.S190C|ZMIZ2_ENST00000433667.1_Missense_Mutation_p.S190C	NM_031449.3	NP_113637.3	Q8NF64	ZMIZ2_HUMAN	zinc finger, MIZ-type containing 2	222	Pro-rich.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|zinc ion binding (GO:0008270)			breast(3)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						ATGGGCCCCTCTGGCCTCTCC	0.622																																					p.S222C	NSCLC(20;604 852 1948 16908 50522)	Atlas-SNP	.											.	ZMIZ2	82	.	0			c.C665G						.						55	60	59					7																	44797559		1877	4096	5973	SO:0001583	missense	83637	exon5			GCCCCTCTGGCCT	AK090415	CCDS43576.1, CCDS43577.1, CCDS75591.1	7p13	2009-11-06			ENSG00000122515	ENSG00000122515		"Zinc fingers, MIZ-type"	22229	protein-coding gene	gene with protein product		611196					Standard	XM_005249866		Approved	KIAA1886, hZIMP7, ZIMP7, DKFZp761I2123, NET27	uc003tlr.3	Q8NF64	OTTHUMG00000155817	ENST00000309315.4:c.665C>G	chr7.hg19:g.44797559C>G	ENSP00000311778:p.Ser222Cys	91.0	0.0		124.0	41.0	NM_174929	A4D2K7|D3DVL1|O94790|Q0VGB4|Q659A8|Q6JKL5|Q8WTX8|Q96Q01|Q9BQH7	Missense_Mutation	SNP	ENST00000309315.4	hg19	CCDS43576.1	.	.	.	.	.	.	.	.	.	.	C	14.98	2.697355	0.48202	.	.	ENSG00000122515	ENST00000413916;ENST00000309315;ENST00000441627;ENST00000433667;ENST00000265346;ENST00000414051	T;T;T;T;T	0.32988	1.43;1.43;1.43;1.43;1.43	4.79	4.79	0.61399	.	0.539829	0.16950	N	0.192948	T	0.47525	0.1450	M	0.61703	1.905	0.23070	N	0.998344	D;D;D	0.67145	0.993;0.996;0.993	P;P;P	0.59288	0.855;0.827;0.855	T	0.36962	-0.9726	10	0.72032	D	0.01	-9.0171	12.7174	0.57123	0.1646:0.8354:0.0:0.0	.	222;222;190	Q8NF64-2;Q8NF64;Q8NF64-3	.;ZMIZ2_HUMAN;.	C	190;222;222;190;222;222	ENSP00000409648:S190C;ENSP00000311778:S222C;ENSP00000414723:S222C;ENSP00000396601:S190C;ENSP00000265346:S222C	ENSP00000265346:S222C	S	+	2	0	ZMIZ2	44764084	0.015000	0.18098	0.229000	0.23960	0.190000	0.23558	2.379000	0.44318	2.479000	0.83701	0.561000	0.74099	TCT	.	.		0.622	ZMIZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341790.1	NM_031449		G	44797559	C	G	44797559	3	3	286	1	0	0	0	0	1	0	0	0	17712	913	32	4	683	4	ZMIZ2	7	44797559	Missense_Mutation	SNP	C	TCGA-G3-A5SK-01A-11D-A27I-10	11400086	44797559	114341104	39	42050										
SLC26A4	5172	hgsc.bcm.edu	37	chr7	107342429	107342429	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	agtgaacgttcccaaagtgcCaatccatagccttgtgcttg	9	11	0	1			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr7:107342429C>T	ENST00000265715.3	+	17	2185	c.1961C>T	c.(1960-1962)cCa>cTa	p.P654L	SLC26A4_ENST00000544569.1_Missense_Mutation_p.P241L|SLC26A4_ENST00000543100.1_Missense_Mutation_p.P223L|SLC26A4_ENST00000541474.1_Missense_Mutation_p.P215L	NM_000441.1	NP_000432.1	O43511	S26A4_HUMAN	solute carrier family 26 (anion exchanger), member 4	654	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.				chloride transmembrane transport (GO:1902476)|inorganic anion transport (GO:0015698)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|regulation of protein localization (GO:0032880)|sensory perception of sound (GO:0007605)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	chloride transmembrane transporter activity (GO:0015108)|iodide transmembrane transporter activity (GO:0015111)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			central_nervous_system(2)|endometrium(1)|kidney(5)|large_intestine(8)|lung(16)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						CCCAAAGTGCCAATCCATAGC	0.443									Pendred syndrome																												p.P654L		Atlas-SNP	.											.	SLC26A4	117	.	0			c.C1961T						.						128	107	114					7																	107342429		2203	4300	6503	SO:0001583	missense	5172	exon17	Familial Cancer Database	Goiter-Deafness syndrome	AAGTGCCAATCCA	AF030880	CCDS5746.1	7q31	2013-07-18	2013-07-18		ENSG00000091137	ENSG00000091137		"Solute carriers"	8818	protein-coding gene	gene with protein product	"pendrin"	605646	"solute carrier family 26, member 4"	DFNB4		9500541, 11087667	Standard	NM_000441		Approved	PDS	uc003vep.3	O43511	OTTHUMG00000154807	ENST00000265715.3:c.1961C>T	chr7.hg19:g.107342429C>T	ENSP00000265715:p.Pro654Leu	212.0	0.0		263.0	83.0	NM_000441	B7Z266|O43170	Missense_Mutation	SNP	ENST00000265715.3	hg19	CCDS5746.1	.	.	.	.	.	.	.	.	.	.	C	19.00	3.742652	0.69418	.	.	ENSG00000091137	ENST00000265715;ENST00000541474;ENST00000544569;ENST00000543100	D;D;D;D	0.94280	-3.39;-3.39;-3.39;-3.39	5.74	5.74	0.90152	Sulphate transporter/antisigma-factor antagonist STAS (4);	0.133058	0.51477	D	0.000086	D	0.92299	0.7557	L	0.53249	1.67	0.54753	D	0.999989	P;P;B	0.46578	0.855;0.88;0.257	B;B;B	0.42462	0.251;0.388;0.216	D	0.91098	0.4912	10	0.33141	T	0.24	.	19.9351	0.97137	0.0:1.0:0.0:0.0	.	215;241;654	F5H104;B7Z6M6;O43511	.;.;S26A4_HUMAN	L	654;215;241;223	ENSP00000265715:P654L;ENSP00000439743:P215L;ENSP00000437427:P241L;ENSP00000441209:P223L	ENSP00000265715:P654L	P	+	2	0	SLC26A4	107129665	0.981000	0.34729	0.989000	0.46669	0.913000	0.54294	2.840000	0.48215	2.703000	0.92315	0.655000	0.94253	CCA	.	.		0.443	SLC26A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337148.1	NM_000441		T	107342429	C	T	107342429	3	4	286	1	0	0	0	0	1	0	0	0	14534	594	21	3	2023	3	SLC26A4	7	107342429	Missense_Mutation	SNP	C	TCGA-G3-A5SK-01A-11D-A27I-10	62544870	107342429	51796234	40	42051										
PTPRZ1	5803	hgsc.bcm.edu	37	chr7	121653216	121653216	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	tctgttcctataggaaatggGcatgttgccattacagctgt	10	8	1	0			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr7:121653216G>C	ENST00000393386.2	+	12	4527	c.4116G>C	c.(4114-4116)ggG>ggC	p.G1372G	PTPRZ1_ENST00000449182.1_Intron|PTPRZ1_ENST00000483028.1_3'UTR	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	1372					axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						TAGGAAATGGGCATGTTGCCA	0.418																																					p.G1372G		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.G4116C						.						185	181	182					7																	121653216		2203	4300	6503	SO:0001819	synonymous_variant	5803	exon12			AAATGGGCATGTT	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.4116G>C	chr7.hg19:g.121653216G>C		196.0	0.0		235.0	63.0	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Silent	SNP	ENST00000393386.2	hg19	CCDS34740.1																																																																																			.	.		0.418	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		C	121653216	G	C	121653216	2	2	286	1	0	0	0	0	0	0	0	1	12829	1190	42	4		4	PTPRZ1	7	121653216	Silent	SNP	G	TCGA-G3-A5SK-01A-11D-A27I-10	14310787	121653216	37485447	41	42052										
WDR86	349136	hgsc.bcm.edu	37	chr7	151093228	151093228	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	cccttgtccacactccagacCcgagctgtccggtcatagga	9	16	1	1			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr7:151093228C>G	ENST00000334493.6	-	3	790	c.360G>C	c.(358-360)cgG>cgC	p.R120R	WDR86_ENST00000469830.2_Silent_p.R120R|WDR86_ENST00000463000.1_5'Flank|WDR86_ENST00000477459.1_5'UTR	NM_001284262.1|NM_198285.2	NP_001271191.1|NP_938026.2	Q86TI4	WDR86_HUMAN	WD repeat domain 86	120										breast(1)|endometrium(2)|kidney(1)|lung(6)	10			OV - Ovarian serous cystadenocarcinoma(82;0.00419)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CACTCCAGACCCGAGCTGTCC	0.642																																					p.R120R		Atlas-SNP	.											.	WDR86	35	.	0			c.G360C						.						32	36	35					7																	151093228		2159	4270	6429	SO:0001819	synonymous_variant	349136	exon3			CCAGACCCGAGCT	AK125347	CCDS5925.2, CCDS64805.1, CCDS64806.1, CCDS75680.1	7q36.1	2013-01-09			ENSG00000187260	ENSG00000187260		"WD repeat domain containing"	28020	protein-coding gene	gene with protein product						12477932	Standard	NM_198285		Approved		uc003wkb.2	Q86TI4	OTTHUMG00000150764	ENST00000334493.6:c.360G>C	chr7.hg19:g.151093228C>G		54.0	0.0		84.0	24.0	NM_198285	B4DJF1|C9JAJ5|C9JXE3|Q3KNT1|Q6ZUS8	Silent	SNP	ENST00000334493.6	hg19	CCDS5925.2																																																																																			.	.		0.642	WDR86-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319999.3	NM_198285		G	151093228	C	G	151093228	2	3	286	1	0	0	0	0	0	0	0	1	17349	610	22	4		4	WDR86	7	151093228	Silent	SNP	C	TCGA-G3-A5SK-01A-11D-A27I-10	29440012	151093228	8045435	42	42053										
ESRP1	54845	hgsc.bcm.edu	37	chr8	95677274	95677274	+	Frame_Shift_Del	DEL	C	C	-													0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	gcacaaacatcacatggggaCccggtatattgaggtatgtc							TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr8:95677274delC	ENST00000433389.2	+	8	1065	c.875delC	c.(874-876)accfs	p.T292fs	ESRP1_ENST00000454170.2_Frame_Shift_Del_p.T292fs|ESRP1_ENST00000358397.5_Frame_Shift_Del_p.T292fs|ESRP1_ENST00000423620.2_Frame_Shift_Del_p.T292fs	NM_001034915.2|NM_017697.3	NP_001030087.2|NP_060167.2	Q6NXG1	ESRP1_HUMAN	epithelial splicing regulatory protein 1	292	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)		ESRP1/RAF1(4)	NS(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)|urinary_tract(2)	20						CACATGGGGACCCGGTATATT	0.483																																					p.T292fs		Atlas-Indel,Pindel	.											.	ESRP1	148	.	0			c.874delA						.						104	101	102					8																	95677274		1926	4141	6067	SO:0001589	frameshift_variant	54845	exon8			.	AK000178	CCDS47895.1, CCDS47896.1, CCDS47897.1, CCDS47898.1	8q22.1	2013-02-12	2009-03-10	2009-03-10	ENSG00000104413	ENSG00000104413		"RNA binding motif (RRM) containing"	25966	protein-coding gene	gene with protein product		612959	"RNA binding motif protein 35A"	RBM35A		12477932	Standard	NM_017697		Approved	FLJ20171	uc003ygq.4	Q6NXG1	OTTHUMG00000164587	ENST00000433389.2:c.875delC	chr8.hg19:g.95677274delC	ENSP00000405738:p.Thr292fs	231.0	0.0		275.0	86.0	NM_001122826	A6NHA8|A8MPX1|E9PB47|Q2M2B0|Q499G3|Q6PJ86|Q9NXL8	Frame_Shift_Del	DEL	ENST00000433389.2	hg19	CCDS47897.1																																																																																			.	.		0.483	ESRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379326.1	NM_017697		-	95677274	C	-	95677274	7	5	286	1	0	1	0	1	0	0	0	0	5260	507	18	0	905	0	ESRP1	8	95677274	Frame_Shift_Del	DEL	C	TCGA-G3-A5SK-01A-11D-A27I-10		95677274	50686748	43	42054										
NFKBIL2	4796	hgsc.bcm.edu	37	chr8	145668658	145668658	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	cccaggccctctgcagctccGtgtggttgcgcagggaatgt	14	13	1	0			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr8:145668658G>T	ENST00000409379.3	-	4	340	c.311C>A	c.(310-312)aCg>aAg	p.T104K		NM_013432.4	NP_038460.4	Q96HA7	TONSL_HUMAN	tonsoku-like, DNA repair protein	104					cytoplasmic sequestering of transcription factor (GO:0042994)|double-strand break repair via homologous recombination (GO:0000724)|regulation of RNA biosynthetic process (GO:2001141)|replication fork processing (GO:0031297)	cytoplasm (GO:0005737)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	histone binding (GO:0042393)|transcription corepressor activity (GO:0003714)	p.T104M(3)		biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|lung(14)|ovary(3)|prostate(1)|skin(1)	26						CTGCAGCTCCGTGTGGTTGCG	0.622																																					p.T104K		Atlas-SNP	.											TONSL_ENST00000409379,NS,haematopoietic_neoplasm,0,3	TONSL	128	.	3	Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(3)	c.C311A						.						90	95	93					8																	145668658		692	1591	2283	SO:0001583	missense	4796	exon4			AGCTCCGTGTGGT		CCDS34968.2	8q24.3	2013-01-10	2010-12-02	2010-11-30	ENSG00000160949	ENSG00000160949		"Ankyrin repeat domain containing"	7801	protein-coding gene	gene with protein product		604546	"nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 2"	NFKBIL2		7738005, 11246458	Standard	NM_013432		Approved	IKBR	uc011llg.2	Q96HA7	OTTHUMG00000153122	ENST00000409379.3:c.311C>A	chr8.hg19:g.145668658G>T	ENSP00000386239:p.Thr104Lys	111.0	0.0		197.0	61.0	NM_013432	B5MDP0|C9JKB1|C9JNV8|Q13006|Q9UGJ2	Missense_Mutation	SNP	ENST00000409379.3	hg19	CCDS34968.2	.	.	.	.	.	.	.	.	.	.	G	14.81	2.647335	0.47258	.	.	ENSG00000160949	ENST00000409379;ENST00000422691	T	0.75704	-0.96	4.81	1.5	0.22942	Tetratricopeptide-like helical (1);	.	.	.	.	T	0.54415	0.1857	N	0.22421	0.69	0.09310	N	1	P	0.43578	0.811	B	0.39904	0.313	T	0.41378	-0.9512	9	0.12103	T	0.63	.	7.0352	0.24989	0.3913:0.0:0.6087:0.0	.	104	Q96HA7	TONSL_HUMAN	K	104	ENSP00000386239:T104K	ENSP00000386239:T104K	T	-	2	0	TONSL	145639466	0.072000	0.21174	0.066000	0.19879	0.801000	0.45260	0.576000	0.23744	0.310000	0.22990	0.462000	0.41574	ACG	.	.		0.622	TONSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329668.2	NM_013432		T	145668658	G	T	145668658	3	4	286	1	0	0	0	0	1	0	0	0	10391	1145	40	1	3917	1	NFKBIL2	8	145668658	Missense_Mutation	SNP	G	TCGA-G3-A5SK-01A-11D-A27I-10	49991384	145668658	695364	44	42055										
DMRTA1	63951	hgsc.bcm.edu	37	chr9	22447695	22447695	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	gttccgcgacccccgctttcGaagttttccagcaagattat	8	13	0	1	rs558506579		TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr9:22447695G>T	ENST00000325870.2	+	1	856	c.631G>T	c.(631-633)Gaa>Taa	p.E211*		NM_022160.2	NP_071443.2	Q5VZB9	DMRTA_HUMAN	DMRT-like family A1	211					male mating behavior (GO:0060179)|ovarian follicle development (GO:0001541)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(3)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	15		all_cancers(5;4.09e-243)|Acute lymphoblastic leukemia(3;8.25e-150)|all_hematologic(3;4.25e-147)|Esophageal squamous(3;2.32e-09)|Renal(3;1.71e-07)|Breast(3;2.07e-06)|Hepatocellular(5;0.00563)		GBM - Glioblastoma multiforme(1;5.12e-278)|Lung(24;8.2e-52)|LUSC - Lung squamous cell carcinoma(38;1.46e-37)|OV - Ovarian serous cystadenocarcinoma(39;0.0517)		CCCCGCTTTCGAAGTTTTCCA	0.547																																					p.E211X		Atlas-SNP	.											.	DMRTA1	29	.	0			c.G631T						.						26	31	29					9																	22447695		2176	4295	6471	SO:0001587	stop_gained	63951	exon1			GCTTTCGAAGTTT	AJ290954	CCDS6514.1	9p21.3	2008-05-15			ENSG00000176399	ENSG00000176399			13826	protein-coding gene	gene with protein product		614803					Standard	NM_022160		Approved		uc003zpp.1	Q5VZB9	OTTHUMG00000019693	ENST00000325870.2:c.631G>T	chr9.hg19:g.22447695G>T	ENSP00000319651:p.Glu211*	136.0	0.0		148.0	42.0	NM_022160	A1L481|Q8N8Y9|Q9H4B9	Nonsense_Mutation	SNP	ENST00000325870.2	hg19	CCDS6514.1	.	.	.	.	.	.	.	.	.	.	G	37	6.162399	0.97338	.	.	ENSG00000176399	ENST00000325870	.	.	.	5.67	1.66	0.24008	.	0.603350	0.16754	N	0.200884	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.18710	T	0.47	-1.325	9.1383	0.36888	0.0806:0.4541:0.4653:0.0	.	.	.	.	X	211	.	ENSP00000319651:E211X	E	+	1	0	DMRTA1	22437695	0.121000	0.22262	0.015000	0.15790	0.034000	0.12701	0.712000	0.25779	0.037000	0.15575	0.655000	0.94253	GAA	.	.		0.547	DMRTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051935.2			T	22447695	G	T	22447695	4	4	286	1	0	0	0	0	0	1	0	0	4590	1059	37	1	633	1	DMRTA1	9	22447695	Nonsense_Mutation	SNP	G	TCGA-G3-A5SK-01A-11D-A27I-10		22447695	118765736	45	42056										
FAM166B	730112	hgsc.bcm.edu	37	chr9	35563264	35563264	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	atcttggaggccgaatgggaGgcagaagtgtgcggtggaca	18	6	1	1			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr9:35563264G>A	ENST00000399742.2	-	2	255	c.185C>T	c.(184-186)cCt>cTt	p.P62L	FAM166B_ENST00000492890.1_5'UTR	NM_001099951.2|NM_001164310.1	NP_001093421.1|NP_001157782.1	A8MTA8	F166B_HUMAN	family with sequence similarity 166, member B	62										kidney(3)|large_intestine(1)|lung(4)|ovary(1)	9						CCGAATGGGAGGCAGAAGTGT	0.617																																					p.P62L		Atlas-SNP	.											.	FAM166B	19	.	0			c.C185T						.						109	116	114					9																	35563264		2088	4227	6315	SO:0001583	missense	730112	exon2			ATGGGAGGCAGAA	BC129999	CCDS47963.1, CCDS56572.1	9p13.3	2008-06-10			ENSG00000215187	ENSG00000215187			34242	protein-coding gene	gene with protein product							Standard	NM_001099951		Approved		uc010mkr.3	A8MTA8	OTTHUMG00000019858	ENST00000399742.2:c.185C>T	chr9.hg19:g.35563264G>A	ENSP00000382646:p.Pro62Leu	134.0	0.0		178.0	53.0	NM_001099951	A1L3B2|B7ZBJ0	Missense_Mutation	SNP	ENST00000399742.2	hg19	CCDS56572.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.275430	0.80580	.	.	ENSG00000215187	ENST00000399742;ENST00000537504	.	.	.	5.9	5.9	0.94986	.	0.517299	0.14939	U	0.289603	T	0.78528	0.4297	M	0.65975	2.015	0.51482	D	0.999927	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.97110	1.0;0.998;0.986;0.999	T	0.77811	-0.2449	9	0.72032	D	0.01	-10.6523	15.7632	0.78103	0.0:0.0:1.0:0.0	.	62;62;62;62	B7ZW33;B7ZW26;A8MTA8;A8MTA8-2	.;.;F166B_HUMAN;.	L	62	.	ENSP00000382646:P62L	P	-	2	0	FAM166B	35553264	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.829000	0.55760	2.788000	0.95919	0.655000	0.94253	CCT	.	.		0.617	FAM166B-005	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336563.1	NM_001099951		A	35563264	G	A	35563264	3	1	286	1	0	0	0	0	1	0	0	0	5487	1000	35	3	481	3	FAM166B	9	35563264	Missense_Mutation	SNP	G	TCGA-G3-A5SK-01A-11D-A27I-10	13115569	35563264	105650167	46	42057										
TJP2	9414	hgsc.bcm.edu	37	chr9	71840272	71840272	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	gtaaaggaaatgacccgaacGggtctggcaactaaagatgg	13	7	1	2	rs140444730		TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr9:71840272G>T	ENST00000377245.4	+	6	1213	c.1005G>T	c.(1003-1005)acG>acT	p.T335T	TJP2_ENST00000265384.7_Silent_p.T335T|TJP2_ENST00000348208.4_Silent_p.T335T|TJP2_ENST00000539225.1_Silent_p.T366T|TJP2_ENST00000453658.2_Silent_p.T312T|TJP2_ENST00000535702.1_Silent_p.T339T	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	335	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|hippo signaling (GO:0035329)|nucleotide phosphorylation (GO:0046939)|response to organic substance (GO:0010033)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	guanylate kinase activity (GO:0004385)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(5)|lung(9)|prostate(3)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	35						TGACCCGAACGGGTCTGGCAA	0.463																																					p.T366T		Atlas-SNP	.											.	TJP2	120	.	0			c.G1098T						.						92	76	81					9																	71840272		2203	4300	6503	SO:0001819	synonymous_variant	9414	exon6			CCGAACGGGTCTG	L27476	CCDS6627.1, CCDS6628.1, CCDS55314.1, CCDS55315.1, CCDS55316.1, CCDS55317.1	9q13-q21	2012-07-12	2012-07-12		ENSG00000119139	ENSG00000119139			11828	protein-coding gene	gene with protein product	"Friedreich ataxia region gene X104 (tight junction protein ZO-2)", "zona occludens 2"	607709	"deafness, autosomal dominant 51"	DFNA51		7951235, 20602916	Standard	NM_001170630		Approved	ZO-2, X104, ZO2	uc011lrv.2	Q9UDY2	OTTHUMG00000019978	ENST00000377245.4:c.1005G>T	chr9.hg19:g.71840272G>T		94.0	0.0		121.0	47.0	NM_001170416	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Silent	SNP	ENST00000377245.4	hg19	CCDS6627.1																																																																																			.	G|1.000;A|0.000		0.463	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629		T	71840272	G	T	71840272	2	4	286	1	0	0	0	0	0	0	0	1	15945	1103	39	1		1	TJP2	9	71840272	Silent	SNP	G	TCGA-G3-A5SK-01A-11D-A27I-10	36277008	71840272	69373159	47	42058										
ADAMTS14	140766	hgsc.bcm.edu	37	chr10	72503886	72503886	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	caagtgtggagtctgcggggGtgacaactcccactgcagga	15	10	1	1			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr10:72503886G>T	ENST00000373207.1	+	14	2123	c.2123G>T	c.(2122-2124)gGt>gTt	p.G708V	ADAMTS14_ENST00000373208.1_Missense_Mutation_p.G711V	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	708	Cys-rich.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						GTCTGCGGGGGTGACAACTCC	0.657																																					p.G711V		Atlas-SNP	.											.	ADAMTS14	148	.	0			c.G2132T						.						38	33	35					10																	72503886		2186	4283	6469	SO:0001583	missense	140766	exon14			GCGGGGGTGACAA	AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"ADAM metallopeptidases with thrombospondin type 1 motif"	14899	protein-coding gene	gene with protein product		607506	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.2123G>T	chr10.hg19:g.72503886G>T	ENSP00000362303:p.Gly708Val	122.0	0.0		161.0	10.0	NM_139155	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Missense_Mutation	SNP	ENST00000373207.1	hg19	CCDS7306.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.893188	0.91889	.	.	ENSG00000138316	ENST00000373208;ENST00000373207	T;T	0.73363	-0.74;-0.74	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	D	0.92054	0.7482	H	0.98370	4.215	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.94881	0.8039	10	0.87932	D	0	.	18.4832	0.90819	0.0:0.0:1.0:0.0	.	641;708;711	Q8WXS8-2;Q8WXS8;Q5T4G1	.;ATS14_HUMAN;.	V	711;708	ENSP00000362304:G711V;ENSP00000362303:G708V	ENSP00000362303:G708V	G	+	2	0	ADAMTS14	72173892	1.000000	0.71417	0.828000	0.32881	0.995000	0.86356	9.125000	0.94402	2.688000	0.91661	0.591000	0.81541	GGT	.	.		0.657	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722		T	72503886	G	T	72503886	3	4	286	1	0	0	0	0	1	0	0	0	259	1261	44	3	2186	3	ADAMTS14	10	72503886	Missense_Mutation	SNP	G	TCGA-G3-A5SK-01A-11D-A27I-10		72503886	63030861	48	42059										
CYP2E1	1571	hgsc.bcm.edu	37	chr10	135340926	135340949	+	In_Frame_Del	DEL	CCTGCTGGTGTGGGCGGCCTTCCT	CCTGCTGGTGTGGGCGGCCTTCCT	-													0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	gccctcggagtcaccgtggcCctgctggtgtgggcggcctt					rs543066971|rs563043306|rs367957731|rs375169910		TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	CCTGCTGGTGTGGGCGGCCTTCCT	CCTGCTGGTGTGGGCGGCCTTCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr10:135340926_135340949delCCTGCTGGTGTGGGCGGCCTTCCT	ENST00000463117.2	+	3	299_322	c.27_50delCCTGCTGGTGTGGGCGGCCTTCCT	c.(25-51)gccctgctggtgtgggcggccttcctc>gcc	p.LLVWAAFL10del	SPRN_ENST00000541506.1_Intron|CYP2E1_ENST00000252945.3_In_Frame_Del_p.LLVWAAFL10del			P05181	CP2E1_HUMAN	cytochrome P450, family 2, subfamily E, polypeptide 1	10					drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|monoterpenoid metabolic process (GO:0016098)|oxidation-reduction process (GO:0055114)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to organonitrogen compound (GO:0010243)|response to ozone (GO:0010193)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|triglyceride metabolic process (GO:0006641)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|mitochondrion (GO:0005739)	enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)	p.A14V(1)		NS(1)|central_nervous_system(3)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(7)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)	Acetaminophen(DB00316)|Aldesleukin(DB00041)|Almotriptan(DB00918)|Alosetron(DB00969)|Aminophylline(DB01223)|Amitriptyline(DB00321)|Antipyrine(DB01435)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bifonazole(DB04794)|Bromazepam(DB01558)|Brompheniramine(DB00835)|Bupropion(DB01156)|Caffeine(DB00201)|Carbinoxamine(DB00748)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cimetidine(DB00501)|Citalopram(DB00215)|Clevidipine(DB04920)|Clofibrate(DB00636)|Clomifene(DB00882)|Clonazepam(DB01068)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Dacarbazine(DB00851)|Dalfampridine(DB06637)|Dapsone(DB00250)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Disulfiram(DB00822)|Econazole(DB01127)|Enflurane(DB00228)|Enfuvirtide(DB00109)|Estrone(DB00655)|Ethanol(DB00898)|Ethanolamine Oleate(DB06689)|Ethosuximide(DB00593)|Etoposide(DB00773)|Etoricoxib(DB01628)|Felbamate(DB00949)|Fingolimod(DB08868)|Flunitrazepam(DB01544)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluvoxamine(DB00176)|Folic Acid(DB00158)|Fomepizole(DB01213)|Glucosamine(DB01296)|Halothane(DB01159)|Hexobarbital(DB01355)|Iloperidone(DB04946)|Imipramine(DB00458)|Isoflurane(DB00753)|Isoniazid(DB00951)|Isosorbide Dinitrate(DB00883)|Itraconazole(DB01167)|Menadione(DB00170)|Meprobamate(DB00371)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Mexiletine(DB00379)|Miconazole(DB01110)|Midazolam(DB00683)|Mitoxantrone(DB01204)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nitrazepam(DB01595)|Nortriptyline(DB00540)|Ondansetron(DB00904)|Orphenadrine(DB01173)|Oxaliplatin(DB00526)|Paramethadione(DB00617)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Pimozide(DB01100)|Proguanil(DB01131)|Propofol(DB00818)|Quinidine(DB00908)|Quinine(DB00468)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rufinamide(DB06201)|S-Adenosylmethionine(DB00118)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sildenafil(DB00203)|Streptozocin(DB00428)|Sulfadiazine(DB00359)|Sulfanilamide(DB00259)|Tamoxifen(DB00675)|Thalidomide(DB01041)|Theobromine(DB01412)|Theophylline(DB00277)|Thiopental(DB00599)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Trimethadione(DB00347)|Ursodeoxycholic acid(DB01586)|Zafirlukast(DB00549)|Zopiclone(DB01198)	TCACCGTGGCCCTGCTGGTGTGGGCGGCCTTCCTCCTGCTGGTG	0.607									Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of																												p.9_17del		Pindel	.											.	CYP2E1	69	.	1	Substitution - Missense(1)	large_intestine(1)	c.26_49del						.																																			SO:0001651	inframe_deletion	1571	exon1	Familial Cancer Database	incl.: Familial Head and Neck Cancer	.	J02843	CCDS7686.1	10q26.3	2013-05-03	2003-01-14	2002-09-13	ENSG00000130649	ENSG00000130649		"Cytochrome P450s"	2631	protein-coding gene	gene with protein product		124040	"cytochrome P450, subfamily IIE (ethanol-inducible), polypeptide 1"	CYP2E			Standard	NM_000773		Approved		uc001lnj.1	P05181	OTTHUMG00000019322	ENST00000463117.2:c.27_50delCCTGCTGGTGTGGGCGGCCTTCCT	chr10.hg19:g.135340926_135340949delCCTGCTGGTGTGGGCGGCCTTCCT	ENSP00000440689:p.Leu10_Leu17del	66.0	0.0		35.0	12.0	NM_000773	Q5VZD5|Q6NWT9|Q9UK47	In_Frame_Del	DEL	ENST00000463117.2	hg19	CCDS7686.1																																																																																			.	.		0.607	CYP2E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051161.2	NM_000773		-	135340949	CCTGCTGGTGTGGGCGGCCTTCCT	-	135340926	7	5	286	1	0	1	0	1	0	0	0	0	4172	610	22	0	29	0	CYP2E1	10	135340926	In_Frame_Del	DEL	CCTGCTGGTGTGGGCGGCCTTCCT	TCGA-G3-A5SK-01A-11D-A27I-10	62837040	135340926	193821	49	42060										
DCDC1	341019	hgsc.bcm.edu	37	chr11	31312242	31312242	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	atctcatgcccatcctgcccCatgccattcttaaagaacag	5	15	2	1			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr11:31312242C>T	ENST00000452803.1	-	7	1113	c.912G>A	c.(910-912)atG>atA	p.M304I	DCDC1_ENST00000597505.1_Missense_Mutation_p.M304I	NM_181807.3	NP_861523.2	P59894	DCDC1_HUMAN	doublecortin domain containing 1	304					intracellular signal transduction (GO:0035556)					central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(17)|pancreas(2)|prostate(1)|skin(1)|stomach(1)	31	Lung SC(675;0.225)					CATCCTGCCCCATGCCATTCT	0.348																																					p.M304I		Atlas-SNP	.											.	DCDC1	74	.	0			c.G912A						.						78	80	79					11																	31312242		2202	4299	6501	SO:0001583	missense	341019	exon7			CTGCCCCATGCCA	AY247970	CCDS7872.1	11p14.1	2013-05-22			ENSG00000170959	ENSG00000170959			20625	protein-coding gene	gene with protein product		608062				12820024	Standard	NM_181807		Approved		uc001msv.3	P59894	OTTHUMG00000150144	ENST00000452803.1:c.912G>A	chr11.hg19:g.31312242C>T	ENSP00000389792:p.Met304Ile	125.0	0.0		161.0	11.0	NM_181807	A6PVL6|B7WNX6|Q6ZU04	Missense_Mutation	SNP	ENST00000452803.1	hg19	CCDS7872.1	.	.	.	.	.	.	.	.	.	.	C	10.24	1.294484	0.23564	.	.	ENSG00000188682	ENST00000452803	D	0.92805	-3.11	5.39	3.02	0.34903	Doublecortin domain (2);	0.394631	0.23770	N	0.044734	D	0.87589	0.6215	L	0.51422	1.61	0.23994	N	0.996237	B	0.09022	0.002	B	0.12156	0.007	T	0.76299	-0.3010	10	0.37606	T	0.19	-0.8357	8.2245	0.31560	0.0:0.6823:0.0:0.3177	.	304	P59894	DCDC1_HUMAN	I	304	ENSP00000389792:M304I	ENSP00000389792:M304I	M	-	3	0	DCDC1	31268818	0.898000	0.30612	1.000000	0.80357	0.984000	0.73092	1.351000	0.34022	0.479000	0.27511	-0.136000	0.14681	ATG	.	.		0.348	DCDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316531.1	NM_181807		T	31312242	C	T	31312242	3	4	286	1	0	0	0	0	1	0	0	0	4286	594	21	3	164	3	DCDC1	11	31312242	Missense_Mutation	SNP	C	TCGA-G3-A5SK-01A-11D-A27I-10		31312242	103694274	50	42061										
OR5T1	390155	hgsc.bcm.edu	37	chr11	56043388	56043388	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	attctacagttgtcactccaAaaatgttggtcaatttcctg	6	9	3	0			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr11:56043388A>G	ENST00000313033.2	+	1	360	c.274A>G	c.(274-276)Aaa>Gaa	p.K92E		NM_001004745.1	NP_001004745.1	Q8NG75	OR5T1_HUMAN	olfactory receptor, family 5, subfamily T, member 1	92						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(27)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	43	Esophageal squamous(21;0.00448)					TGTCACTCCAAAAATGTTGGT	0.373																																					p.K92E		Atlas-SNP	.											.	OR5T1	95	.	0			c.A274G						.						104	102	103					11																	56043388		2201	4296	6497	SO:0001583	missense	390155	exon1			ACTCCAAAAATGT	AB065962	CCDS31525.1	11q11	2012-08-09		2004-03-10	ENSG00000181698	ENSG00000181698		"GPCR / Class A : Olfactory receptors"	14821	protein-coding gene	gene with protein product				OR5T1P			Standard	NM_001004745		Approved		uc001nio.1	Q8NG75	OTTHUMG00000166853	ENST00000313033.2:c.274A>G	chr11.hg19:g.56043388A>G	ENSP00000323612:p.Lys92Glu	79.0	0.0		111.0	40.0	NM_001004745	B2RNM9	Missense_Mutation	SNP	ENST00000313033.2	hg19	CCDS31525.1	.	.	.	.	.	.	.	.	.	.	A	14.33	2.503231	0.44558	.	.	ENSG00000181698	ENST00000313033	T	0.01347	4.99	3.59	3.59	0.41128	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46442	D	0.000295	T	0.05547	0.0146	M	0.92412	3.305	0.09310	N	1	B	0.34372	0.451	B	0.40038	0.317	T	0.02526	-1.1146	10	0.87932	D	0	.	11.5033	0.50450	1.0:0.0:0.0:0.0	.	92	Q8NG75	OR5T1_HUMAN	E	92	ENSP00000323612:K92E	ENSP00000323612:K92E	K	+	1	0	OR5T1	55799964	0.023000	0.18921	0.021000	0.16686	0.084000	0.17831	2.746000	0.47467	1.648000	0.50643	0.381000	0.24937	AAA	.	.		0.373	OR5T1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391600.1	NM_001004745		G	56043388	A	G	56043388	3	3	286	1	0	0	0	0	1	0	0	0	11190	15	1	2	276	2	OR5T1	11	56043388	Missense_Mutation	SNP	A	TCGA-G3-A5SK-01A-11D-A27I-10	24731146	56043388	78963128	51	42062										
FAT3	120114	hgsc.bcm.edu	37	chr11	92538485	92538485	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	gtggaagtgagcgtcagtgaTgtgaatgacaatagcccagt	14	6	1	4			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr11:92538485T>C	ENST00000298047.6	+	10	9080	c.9063T>C	c.(9061-9063)gaT>gaC	p.D3021D	FAT3_ENST00000409404.2_Silent_p.D3021D|FAT3_ENST00000525166.1_Silent_p.D2871D			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	3021	Cadherin 27. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				GCGTCAGTGATGTGAATGACA	0.433										TCGA Ovarian(4;0.039)																											p.D3021D		Atlas-SNP	.											.	FAT3	1822	.	0			c.T9063C						.						63	64	63					11																	92538485		1958	4167	6125	SO:0001819	synonymous_variant	120114	exon10			CAGTGATGTGAAT	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.9063T>C	chr11.hg19:g.92538485T>C		198.0	0.0		230.0	71.0	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	hg19																																																																																				.	.		0.433	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		C	92538485	T	C	92538485	2	2	286	1	0	0	0	0	0	0	0	1	5699	1461	51	2		2	FAT3	11	92538485	Silent	SNP	T	TCGA-G3-A5SK-01A-11D-A27I-10	36495097	92538485	42468031	52	42063										
BIRC2	329	hgsc.bcm.edu	37	chr11	102221361	102221362	+	In_Frame_Ins	INS	-	-	TAG													0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	tctctagaaactctgaggttINStagcatttcaaatctgagca							TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr11:102221361_102221362insTAG	ENST00000227758.2	+	2	2175_2176	c.776_777insTAG	c.(775-780)tttagc>ttTAGtagc	p.260_261insS	BIRC2_ENST00000527910.1_3'UTR|BIRC2_ENST00000532672.1_In_Frame_Ins_p.239_240insS|BIRC2_ENST00000530675.1_In_Frame_Ins_p.211_212insS	NM_001166.4|NM_001256163.1	NP_001157.1|NP_001243092.1	Q13490	BIRC2_HUMAN	baculoviral IAP repeat containing 2	260					apoptotic process (GO:0006915)|cell surface receptor signaling pathway (GO:0007166)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein K48-linked ubiquitination (GO:1902524)|positive regulation of protein K63-linked ubiquitination (GO:1902523)|positive regulation of protein monoubiquitination (GO:1902527)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cell cycle (GO:0051726)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|regulation of cysteine-type endopeptidase activity (GO:2000116)|regulation of inflammatory response (GO:0050727)|regulation of innate immune response (GO:0045088)|regulation of necroptotic process (GO:0060544)|regulation of nucleotide-binding oligomerization domain containing signaling pathway (GO:0070424)|regulation of RIG-I signaling pathway (GO:0039535)|regulation of toll-like receptor signaling pathway (GO:0034121)|regulation of transcription, DNA-templated (GO:0006355)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|protein N-terminus binding (GO:0047485)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|liver(2)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|Epithelial(9;0.11)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0144)		ACTCTGAGGTTTAGCATTTCAA	0.441																																					p.F259delinsFS		Atlas-Indel,Pindel	.											.	BIRC2	51	.	0			c.776_777insTAG						.																																			SO:0001652	inframe_insertion	329	exon2			.	L49431	CCDS8316.1, CCDS58169.1	11q22	2011-01-25	2011-01-25		ENSG00000110330	ENSG00000110330		"Baculoviral IAP repeat containing", "RING-type (C3HC4) zinc fingers"	590	protein-coding gene	gene with protein product	"NFR2-TRAF signalling complex protein", "apoptosis inhibitor 1"	601712	"baculoviral IAP repeat-containing 2"	API1		8552191, 8548810	Standard	NM_001166		Approved	cIAP1, hiap-2, MIHB, RNF48, c-IAP1	uc010ruq.3	Q13490	OTTHUMG00000167325	ENST00000227758.2:c.777_779dupTAG	chr11.hg19:g.102221362_102221364dupTAG	ENSP00000227758:p.Ser261_Ser262dup	32.0	0.0		51.0	19.0	NM_001166	B4E026|Q16516|Q4TTG0	In_Frame_Ins	INS	ENST00000227758.2	hg19	CCDS8316.1																																																																																			.	.		0.441	BIRC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394170.1	NM_001166		TAG	102221362	-	TAG	102221361	7	5	286	1	0	1	1	0	0	0	0	0	1435	1841	64	0	778	0	BIRC2	11	102221361	In_Frame_Ins	INS	-	TCGA-G3-A5SK-01A-11D-A27I-10	9682876	102221361	32785155	53	42064										
EXPH5	23086	hgsc.bcm.edu	37	chr11	108383488	108383488	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	ttctctttctcctagcgatgGatctttgtctgaaggacttc	8	10	4	1			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr11:108383488G>T	ENST00000265843.4	-	6	2856	c.2746C>A	c.(2746-2748)Cca>Aca	p.P916T	EXPH5_ENST00000525344.1_Missense_Mutation_p.P909T|EXPH5_ENST00000428840.1_Missense_Mutation_p.P840T|EXPH5_ENST00000443411.1_Missense_Mutation_p.P728T|EXPH5_ENST00000524840.1_5'Flank	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	916					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		CCTAGCGATGGATCTTTGTCT	0.423																																					p.P916T		Atlas-SNP	.											.	EXPH5	193	.	0			c.C2746A						.						195	178	184					11																	108383488		2201	4298	6499	SO:0001583	missense	23086	exon6			GCGATGGATCTTT		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"synaptotagmin-like homologue lacking C2 domains b"	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.2746C>A	chr11.hg19:g.108383488G>T	ENSP00000265843:p.Pro916Thr	77.0	0.0		89.0	28.0	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	hg19	CCDS8341.1	.	.	.	.	.	.	.	.	.	.	G	15.59	2.877999	0.51801	.	.	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000526312;ENST00000533052	T;T;T;T;T;T	0.05319	4.06;3.98;3.83;4.06;3.88;3.46	5.89	3.94	0.45596	.	0.421653	0.22665	N	0.057160	T	0.13030	0.0316	M	0.65975	2.015	0.09310	N	1	P	0.52842	0.956	P	0.51016	0.656	T	0.06303	-1.0834	10	0.41790	T	0.15	-1.9558	9.6224	0.39730	0.0765:0.1403:0.7832:0.0	.	916	Q8NEV8	EXPH5_HUMAN	T	916;840;728;909;840;728	ENSP00000265843:P916T;ENSP00000391966:P840T;ENSP00000411390:P728T;ENSP00000432546:P909T;ENSP00000432683:P840T;ENSP00000446434:P728T	ENSP00000265843:P916T	P	-	1	0	EXPH5	107888698	0.000000	0.05858	0.240000	0.24138	0.603000	0.37013	-0.042000	0.12063	1.475000	0.48197	0.563000	0.77884	CCA	.	.		0.423	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065		T	108383488	G	T	108383488	3	4	286	1	0	0	0	0	1	0	0	0	5324	1174	41	3	3227	3	EXPH5	11	108383488	Missense_Mutation	SNP	G	TCGA-G3-A5SK-01A-11D-A27I-10	6162127	108383488	26623028	54	42065										
ARHGAP32	9743	hgsc.bcm.edu	37	chr11	128839106	128839106	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	tatgatggagtttgaggctaTgactcctctctggtttaggg	13	6	1	3			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr11:128839106T>C	ENST00000310343.9	-	22	5959	c.5960A>G	c.(5959-5961)cAt>cGt	p.H1987R	ARHGAP32_ENST00000527272.1_Missense_Mutation_p.H1638R|ARHGAP32_ENST00000392657.3_Missense_Mutation_p.H1638R|ARHGAP32_ENST00000524655.1_3'UTR	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	1987	Interaction with FYN.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)|phosphatidylinositol binding (GO:0035091)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(28)|ovary(3)|prostate(6)|urinary_tract(3)	60						TTTGAGGCTATGACTCCTCTC	0.552																																					p.H1987R		Atlas-SNP	.											.	ARHGAP32	307	.	0			c.A5960G						.						147	132	137					11																	128839106		2201	4297	6498	SO:0001583	missense	9743	exon22			AGGCTATGACTCC	AB018255	CCDS31718.1, CCDS44769.1	11q24.3	2011-06-29			ENSG00000134909	ENSG00000134909		"Rho GTPase activating proteins"	17399	protein-coding gene	gene with protein product		608541				12446789, 12819203, 17663722	Standard	NM_014715		Approved	GRIT, KIAA0712, MGC1892, RICS, GC-GAP	uc009zcp.3	A7KAX9	OTTHUMG00000165774	ENST00000310343.9:c.5960A>G	chr11.hg19:g.128839106T>C	ENSP00000310561:p.His1987Arg	198.0	0.0		266.0	25.0	NM_001142685	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Missense_Mutation	SNP	ENST00000310343.9	hg19	CCDS44769.1	.	.	.	.	.	.	.	.	.	.	T	17.72	3.458099	0.63401	.	.	ENSG00000134909	ENST00000310343;ENST00000392657;ENST00000527272	T;T;T	0.20069	2.1;2.1;2.1	5.83	4.7	0.59300	.	0.053099	0.64402	N	0.000001	T	0.23926	0.0579	M	0.64997	1.995	0.48288	D	0.999623	B	0.18461	0.028	B	0.15052	0.012	T	0.03051	-1.1078	10	0.87932	D	0	.	11.5602	0.50772	0.0:0.0693:0.0:0.9307	.	1987	A7KAX9	RHG32_HUMAN	R	1987;1638;1638	ENSP00000310561:H1987R;ENSP00000376425:H1638R;ENSP00000432862:H1638R	ENSP00000310561:H1987R	H	-	2	0	ARHGAP32	128344316	0.986000	0.35501	0.927000	0.36925	0.998000	0.95712	2.347000	0.44036	1.049000	0.40321	0.533000	0.62120	CAT	.	.		0.552	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715		C	128839106	T	C	128839106	3	2	286	1	0	0	0	0	1	0	0	0	881	1464	51	2	307	2	ARHGAP32	11	128839106	Missense_Mutation	SNP	T	TCGA-G3-A5SK-01A-11D-A27I-10	20455618	128839106	6167410	55	42066										
ARID2	196528	hgsc.bcm.edu	37	chr12	46244449	46244450	+	Frame_Shift_Ins	INS	-	-	A													0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	tcacaagatactgttatcatINSagcacccccacagtatgtaa							TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr12:46244449_46244450insA	ENST00000334344.6	+	15	2715_2716	c.2543_2544insA	c.(2542-2547)atagcafs	p.A849fs	ARID2_ENST00000422737.1_Frame_Shift_Ins_p.A700fs|ARID2_ENST00000457135.1_5'Flank|ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000444670.1_Frame_Shift_Ins_p.A459fs	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	849	Gln-rich.				chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		ACTGTTATCATAGCACCCCCAC	0.431			"N, S, F"		hepatocellular carcinoma																																p.I848fs		Pindel	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.,1	ARID2	311	.	0			c.2543_2544insA						.																																			SO:0001589	frameshift_variant	196528	exon15			.		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.2544dupA	chr12.hg19:g.46244450_46244450dupA	ENSP00000335044:p.Ala849fs	251.0	0.0		304.0	67.0	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Frame_Shift_Ins	INS	ENST00000334344.6	hg19	CCDS31783.1																																																																																			.	.		0.431	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		A	46244450	-	A	46244449	7	5	286	1	0	1	1	0	0	0	0	0	915	1406	49	0	2601	0	ARID2	12	46244449	Frame_Shift_Ins	INS	-	TCGA-G3-A5SK-01A-11D-A27I-10		46244449	87607446	56	42067										
IRAK3	11213	hgsc.bcm.edu	37	chr12	66611016	66611016	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	gagcttgaagttttactactGtgagtatgttttctctggaa	10	5	1	2			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr12:66611016G>T	ENST00000261233.4	+	6	1074		c.e6+1		IRAK3_ENST00000457197.2_Splice_Site	NM_007199.2	NP_009130.2			interleukin-1 receptor-associated kinase 3											breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(28;0.0203)		TTTTACTACTGTGAGTATGTT	0.353																																					.		Atlas-SNP	.											.	IRAK3	75	.	0			c.653+1G>T						.						452	482	472					12																	66611016		2203	4300	6503	SO:0001630	splice_region_variant	11213	exon6			ACTACTGTGAGTA	AF113136	CCDS8975.1, CCDS44937.1	12q13.13	2008-05-02			ENSG00000090376	ENSG00000090376			17020	protein-coding gene	gene with protein product		604459				10383454	Standard	NM_001142523		Approved	IRAK-M	uc001sth.3	Q9Y616	OTTHUMG00000169002	ENST00000261233.4:c.653+1G>T	chr12.hg19:g.66611016G>T		107.0	0.0		88.0	28.0	NM_007199		Splice_Site	SNP	ENST00000261233.4	hg19	CCDS8975.1	.	.	.	.	.	.	.	.	.	.	G	10.69	1.422174	0.25639	.	.	ENSG00000090376	ENST00000261233;ENST00000457197	.	.	.	5.39	5.39	0.77823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.6645	0.68896	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	IRAK3	64897283	1.000000	0.71417	1.000000	0.80357	0.136000	0.21042	4.738000	0.62073	2.514000	0.84764	0.563000	0.77884	.	.	.		0.353	IRAK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401908.1		Intron	T	66611016	G	T	66611016	5	4	286	1	0	0	0	0	0	0	1	0	7833	1391	48	3	676	3	IRAK3	12	66611016	Splice_Site	SNP	G	TCGA-G3-A5SK-01A-11D-A27I-10	20366567	66611016	67240879	57	42068										
IKBIP	121457	hgsc.bcm.edu	37	chr12	99028193	99028193	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	tgactgctgaaatacaaaccTggaaaagaaaagaaaaatca	7	6	1	4			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr12:99028193T>A	ENST00000342502.2	-	2	591		c.e2-2		IKBIP_ENST00000420861.1_Intron|IKBIP_ENST00000393042.3_Intron|IKBIP_ENST00000299157.4_Splice_Site	NM_201612.2	NP_963906.1	Q70UQ0	IKIP_HUMAN	IKBKB interacting protein						response to X-ray (GO:0010165)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(2)	6						AATACAAACCTGGAAAAGAAA	0.308																																					.		Atlas-SNP	.											.	IKBIP	46	.	0			c.180-2A>T						.						95	87	89					12																	99028193		2203	4300	6503	SO:0001630	splice_region_variant	121457	exon3			CAAACCTGGAAAA	AJ539425	CCDS9067.1, CCDS9068.1, CCDS41822.1	12q23.1	2010-02-17			ENSG00000166130	ENSG00000166130			26430	protein-coding gene	gene with protein product	"I kappa B kinase interacting protein"	609861				15389287	Standard	NM_153687		Approved	FLJ31051, IKIP	uc001tfx.4	Q70UQ0	OTTHUMG00000170213	ENST00000342502.2:c.180-2A>T	chr12.hg19:g.99028193T>A		45.0	0.0		35.0	15.0	NM_201612	Q6ZWH4|Q70UP9|Q86V91|Q96ND2	Splice_Site	SNP	ENST00000342502.2	hg19	CCDS9067.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.260584	0.80246	.	.	ENSG00000166130	ENST00000342502;ENST00000299157	.	.	.	5.97	5.97	0.96955	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.4608	0.84044	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	IKBIP	97552324	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.110000	0.64622	2.288000	0.76882	0.533000	0.62120	.	.	.		0.308	IKBIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000408003.2	NM_153687	Intron	A	99028193	T	A	99028193	5	1	286	1	0	0	0	0	0	0	1	0	7618	1594	55	4	1723	4	IKBIP	12	99028193	Splice_Site	SNP	T	TCGA-G3-A5SK-01A-11D-A27I-10	32417177	99028193	34823702	58	42069										
SLC39A9	55334	hgsc.bcm.edu	37	chr14	69925257	69925257	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	gccgcctggaagtggcagccCtggttctgggttgcctcatc	14	13	2	0			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr14:69925257C>G	ENST00000336643.5	+	7	1549	c.871C>G	c.(871-873)Ctg>Gtg	p.L291V	SLC39A9_ENST00000555245.1_3'UTR|SLC39A9_ENST00000031146.4_Missense_Mutation_p.L225V|SLC39A9_ENST00000557046.1_Missense_Mutation_p.L268V|SLC39A9_ENST00000556605.1_Intron	NM_018375.4	NP_060845.2	Q9NUM3	S39A9_HUMAN	solute carrier family 39, member 9	291					zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)			breast(1)|endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|skin(1)|stomach(1)	14				all cancers(60;0.00299)|BRCA - Breast invasive adenocarcinoma(234;0.0145)|OV - Ovarian serous cystadenocarcinoma(108;0.0373)		AGTGGCAGCCCTGGTTCTGGG	0.602																																					p.L291V		Atlas-SNP	.											.	SLC39A9	27	.	0			c.C871G						.						57	49	51					14																	69925257		2203	4300	6503	SO:0001583	missense	55334	exon7			GCAGCCCTGGTTC		CCDS9795.1, CCDS58327.1, CCDS58328.1	14q24.1	2013-07-17	2013-07-17			ENSG00000029364		"Solute carriers"	20182	protein-coding gene	gene with protein product							Standard	NM_018375		Approved	FLJ11274	uc001xle.3	Q9NUM3		ENST00000336643.5:c.871C>G	chr14.hg19:g.69925257C>G	ENSP00000336887:p.Leu291Val	73.0	0.0		143.0	48.0	NM_018375	G3V5J8|Q53HN3|Q5MJQ0|Q6P2Q1|Q86WY2	Missense_Mutation	SNP	ENST00000336643.5	hg19	CCDS9795.1	.	.	.	.	.	.	.	.	.	.	C	18.65	3.670638	0.67814	.	.	ENSG00000029364	ENST00000336643;ENST00000557046	T;T	0.47528	0.84;0.84	5.71	4.82	0.62117	.	0.000000	0.85682	D	0.000000	T	0.53465	0.1798	L	0.56199	1.76	0.58432	D	0.999999	P;D	0.58970	0.882;0.984	P;P	0.56612	0.495;0.802	T	0.50841	-0.8780	10	0.32370	T	0.25	-5.2008	8.9558	0.35816	0.0:0.7796:0.0:0.2204	.	268;291	Q9NUM3-2;Q9NUM3	.;S39A9_HUMAN	V	291;268	ENSP00000336887:L291V;ENSP00000451833:L268V	ENSP00000031146:L291V	L	+	1	2	SLC39A9	68995010	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.753000	0.47524	1.413000	0.46997	0.655000	0.94253	CTG	.	.		0.602	SLC39A9-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412446.1	NM_018375		G	69925257	C	G	69925257	3	3	286	1	0	0	0	0	1	0	0	0	14640	680	24	4	897	4	SLC39A9	14	69925257	Missense_Mutation	SNP	C	TCGA-G3-A5SK-01A-11D-A27I-10		69925257	37424283	59	42070										
CYP46A1	10858	hgsc.bcm.edu	37	chr14	100191750	100191750	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	cagcacctatgtcatggggcGgatggacacatactttgagg	13	9	1	1			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr14:100191750G>A	ENST00000261835.3	+	13	1303	c.1199G>A	c.(1198-1200)cGg>cAg	p.R400Q	CYP46A1_ENST00000423126.2_Missense_Mutation_p.R303Q|CYP46A1_ENST00000554176.1_Missense_Mutation_p.R237Q	NM_006668.1	NP_006659.1	Q9Y6A2	CP46A_HUMAN	cytochrome P450, family 46, subfamily A, polypeptide 1	400					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cholesterol catabolic process (GO:0006707)|nervous system development (GO:0007399)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	cholesterol 24-hydroxylase activity (GO:0033781)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid hydroxylase activity (GO:0008395)			breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|prostate(1)|skin(1)	25		Melanoma(154;0.0866)|all_epithelial(191;0.179)				GTCATGGGGCGGATGGACACA	0.607																																					p.R400Q		Atlas-SNP	.											.	CYP46A1	62	.	0			c.G1199A						.						120	103	109					14																	100191750		2203	4300	6503	SO:0001583	missense	10858	exon13			TGGGGCGGATGGA	AF094480	CCDS9954.1	14q32.2	2013-05-03	2003-02-14	2003-02-28	ENSG00000036530	ENSG00000036530		"Cytochrome P450s"	2641	protein-coding gene	gene with protein product		604087	"cytochrome P450, subfamily 46 (cholesterol 24-hydroxylase)"	CYP46		10377398	Standard	NM_006668		Approved		uc001ygo.3	Q9Y6A2	OTTHUMG00000171510	ENST00000261835.3:c.1199G>A	chr14.hg19:g.100191750G>A	ENSP00000261835:p.Arg400Gln	113.0	0.0		151.0	49.0	NM_006668	B4DHP8|E7EQG9|Q8N2B0	Missense_Mutation	SNP	ENST00000261835.3	hg19	CCDS9954.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.577747	0.86645	.	.	ENSG00000036530	ENST00000261835;ENST00000423126;ENST00000554176	T;D;D	0.82526	-0.83;-1.62;-1.62	4.48	4.48	0.54585	.	0.000000	0.85682	D	0.000000	D	0.89584	0.6757	M	0.70275	2.135	0.50467	D	0.999876	D;D	0.89917	1.0;1.0	D;D	0.91635	0.996;0.999	D	0.90506	0.4477	10	0.72032	D	0.01	.	13.0411	0.58899	0.0:0.0:1.0:0.0	.	237;400	Q8N2B0;Q9Y6A2	.;CP46A_HUMAN	Q	400;303;237	ENSP00000261835:R400Q;ENSP00000405779:R303Q;ENSP00000450553:R237Q	ENSP00000261835:R400Q	R	+	2	0	CYP46A1	99261503	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.402000	0.73260	2.218000	0.71995	0.563000	0.77884	CGG	.	.		0.607	CYP46A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413814.1			A	100191750	G	A	100191750	3	1	286	1	0	0	0	0	1	0	0	0	4184	1116	39	1	1249	1	CYP46A1	14	100191750	Missense_Mutation	SNP	G	TCGA-G3-A5SK-01A-11D-A27I-10	30266493	100191750	7157790	60	42071										
SPTBN5	51332	hgsc.bcm.edu	37	chr15	42159172	42159172	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	ctgacctgggttgcggcctgGgtgaagctggccatcagcag	16	11	1	2			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr15:42159172G>A	ENST00000320955.6	-	36	6692	c.6465C>T	c.(6463-6465)acC>acT	p.T2155T	MIR4310_ENST00000582950.1_RNA	NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	2155					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		TTGCGGCCTGGGTGAAGCTGG	0.657																																					p.T2120T		Atlas-SNP	.											.	SPTBN5	171	.	0			c.C6360T						.						9	13	12					15																	42159172		2082	4184	6266	SO:0001819	synonymous_variant	51332	exon36			GGCCTGGGTGAAG	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"beta V spectrin"	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.6465C>T	chr15.hg19:g.42159172G>A		78.0	0.0		102.0	43.0	NM_016642		Silent	SNP	ENST00000320955.6	hg19																																																																																				.	.		0.657	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642		A	42159172	G	A	42159172	2	1	286	1	0	0	0	0	0	0	0	1	15137	1219	43	3		3	SPTBN5	15	42159172	Silent	SNP	G	TCGA-G3-A5SK-01A-11D-A27I-10		42159172	60372220	61	42072										
KIAA0556	23247	hgsc.bcm.edu	37	chr16	27772791	27772791	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	gcactacctggggctcactgGcctggaagtggtgggcaagg	17	10	1	0			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr16:27772791G>A	ENST00000261588.4	+	19	3708	c.3689G>A	c.(3688-3690)gGc>gAc	p.G1230D		NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	1230						extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						GGGCTCACTGGCCTGGAAGTG	0.592																																					p.G1230D		Atlas-SNP	.											.	KIAA0556	348	.	0			c.G3689A						.						78	69	72					16																	27772791		2197	4300	6497	SO:0001583	missense	23247	exon19			TCACTGGCCTGGA	AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.3689G>A	chr16.hg19:g.27772791G>A	ENSP00000261588:p.Gly1230Asp	55.0	0.0		101.0	8.0	NM_015202	A7E2C2	Missense_Mutation	SNP	ENST00000261588.4	hg19	CCDS32415.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.799317	0.90538	.	.	ENSG00000047578	ENST00000261588	T	0.20069	2.1	4.56	4.56	0.56223	.	0.053288	0.85682	D	0.000000	T	0.56834	0.2012	M	0.92784	3.345	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.69580	-0.5107	10	0.59425	D	0.04	-15.1229	16.9555	0.86258	0.0:0.0:1.0:0.0	.	1230	O60303	K0556_HUMAN	D	1230	ENSP00000261588:G1230D	ENSP00000261588:G1230D	G	+	2	0	KIAA0556	27680292	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	9.703000	0.98714	2.086000	0.62901	0.561000	0.74099	GGC	.	.		0.592	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202		A	27772791	G	A	27772791	3	1	286	1	0	0	0	0	1	0	0	0	8192	1203	42	3	3763	3	KIAA0556	16	27772791	Missense_Mutation	SNP	G	TCGA-G3-A5SK-01A-11D-A27I-10		27772791	62581962	62	42073										
RNF166	115992	hgsc.bcm.edu	37	chr16	88764990	88764990	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	cttgtagctggggtccccccAgggcattgccgagcagatgg	15	12	0	1			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr16:88764990A>C	ENST00000312838.4	-	5	663	c.568T>G	c.(568-570)Tgg>Ggg	p.W190G	RP5-1142A6.5_ENST00000561699.1_RNA|RNF166_ENST00000562499.1_5'Flank|RNF166_ENST00000568683.1_Missense_Mutation_p.W81G|RNF166_ENST00000567844.1_Missense_Mutation_p.W109G|RNF166_ENST00000537718.2_Missense_Mutation_p.W81G|RNF166_ENST00000541206.2_Missense_Mutation_p.W81G	NM_178841.3	NP_849163.1	Q96A37	RN166_HUMAN	ring finger protein 166	190							zinc ion binding (GO:0008270)			endometrium(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0476)		GGGTCCCCCCAGGGCATTGCC	0.657																																					p.W190G		Atlas-SNP	.											.	RNF166	3	.	0			c.T568G						.						98	79	85					16																	88764990		2179	4283	6462	SO:0001583	missense	115992	exon5			CCCCCCAGGGCAT	AK057106	CCDS10969.1, CCDS54056.1, CCDS54057.1	16q24.3	2013-01-09			ENSG00000158717	ENSG00000158717		"RING-type (C3HC4) zinc fingers"	28856	protein-coding gene	gene with protein product						12477932	Standard	NM_178841		Approved	MGC2647, MGC14381	uc002flk.3	Q96A37	OTTHUMG00000137863	ENST00000312838.4:c.568T>G	chr16.hg19:g.88764990A>C	ENSP00000326095:p.Trp190Gly	79.0	0.0		141.0	6.0	NM_178841	B3KQ03|D3DX75|H3BTU8|Q96DM0	Missense_Mutation	SNP	ENST00000312838.4	hg19	CCDS10969.1	.	.	.	.	.	.	.	.	.	.	A	12.08	1.831010	0.32329	.	.	ENSG00000158717	ENST00000312838;ENST00000537718;ENST00000541206	T	0.16073	2.37	4.83	3.74	0.42951	Zinc finger, C2H2-like (1);	0.249988	0.43747	D	0.000529	T	0.12178	0.0296	L	0.31065	0.9	0.58432	D	0.999999	B	0.33807	0.426	B	0.35655	0.207	T	0.14476	-1.0471	10	0.17832	T	0.49	-3.4565	9.8527	0.41066	0.917:0.0:0.083:0.0	.	190	Q96A37	RN166_HUMAN	G	190;109;81	ENSP00000326095:W190G	ENSP00000326095:W190G	W	-	1	0	RNF166	87292491	1.000000	0.71417	1.000000	0.80357	0.410000	0.31052	7.077000	0.76814	0.712000	0.32039	0.165000	0.16767	TGG	.	.		0.657	RNF166-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269544.1	NM_178841		C	88764990	A	C	88764990	3	2	286	1	0	0	0	0	1	0	0	0	13472	188	7	5	153	5	RNF166	16	88764990	Missense_Mutation	SNP	A	TCGA-G3-A5SK-01A-11D-A27I-10	60992199	88764990	1589763	63	42074										
MYO1C	4641	hgsc.bcm.edu	37	chr17	1381960	1381960	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	gacgagccaggtaaaagtgcGgctgtacacagccttggcga	14	10	0	0			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr17:1381960G>A	ENST00000575158.1	-	10	1233	c.1057C>T	c.(1057-1059)Cgc>Tgc	p.R353C	MYO1C_ENST00000545534.2_Missense_Mutation_p.R364C|MYO1C_ENST00000359786.5_Missense_Mutation_p.R388C|MYO1C_ENST00000438665.2_Missense_Mutation_p.R369C|MYO1C_ENST00000361007.2_Missense_Mutation_p.R353C|MYO1C_ENST00000573198.1_5'Flank			Q12965	MYO1E_HUMAN	myosin IC	362	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|liver(2)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	17				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		GTAAAAGTGCGGCTGTACACA	0.642																																					p.R388C		Atlas-SNP	.											.	MYO1C	57	.	0			c.C1162T						.						107	88	94					17																	1381960		2203	4300	6503	SO:0001583	missense	4641	exon10			AAGTGCGGCTGTA	X98507	CCDS11003.1, CCDS42226.1, CCDS45562.1	17p13.3	2011-09-27			ENSG00000197879	ENSG00000197879		"Myosins / Myosin superfamily : Class I"	7597	protein-coding gene	gene with protein product		606538				9119401	Standard	NM_001080779		Approved	myr2	uc002fsp.3	O00159	OTTHUMG00000090323	ENST00000575158.1:c.1057C>T	chr17.hg19:g.1381960G>A	ENSP00000459174:p.Arg353Cys	124.0	0.0		145.0	6.0	NM_001080779	Q14778	Missense_Mutation	SNP	ENST00000575158.1	hg19	CCDS11003.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.655485	0.88056	.	.	ENSG00000197879	ENST00000359786;ENST00000438665;ENST00000535856;ENST00000361007;ENST00000545534;ENST00000535421	D;D;D;D	0.89681	-2.55;-2.55;-2.55;-2.55	5.69	5.69	0.88448	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.95557	0.8556	M	0.89414	3.03	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.998	D	0.95881	0.8899	10	0.87932	D	0	.	18.7983	0.92005	0.0:0.0:1.0:0.0	.	364;388;369	B7Z3E5;O00159;O00159-3	.;MYO1C_HUMAN;.	C	388;369;369;353;364;353	ENSP00000352834:R388C;ENSP00000412197:R369C;ENSP00000354283:R353C;ENSP00000437685:R364C	ENSP00000352834:R388C	R	-	1	0	MYO1C	1328710	1.000000	0.71417	0.997000	0.53966	0.299000	0.27559	7.894000	0.87336	2.696000	0.92011	0.655000	0.94253	CGC	.	.		0.642	MYO1C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438694.2			A	1381960	G	A	1381960	3	1	286	1	0	0	0	0	1	0	0	0	10079	1116	39	1	2121	1	MYO1C	17	1381960	Missense_Mutation	SNP	G	TCGA-G3-A5SK-01A-11D-A27I-10		1381960	79813250	64	42075										
TRPV1	7442	hgsc.bcm.edu	37	chr17	3481004	3481004	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	tggaagccacatactccttgAggtggctgaagtacagcacc	11	11	0	2			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr17:3481004A>C	ENST00000571088.1	-	11	1814	c.1601T>G	c.(1600-1602)cTc>cGc	p.L534R	RP11-235E17.3_ENST00000573568.1_RNA|TRPV1_ENST00000399756.4_Missense_Mutation_p.L534R|TRPV1_ENST00000399759.3_Missense_Mutation_p.L534R|SHPK_ENST00000572705.1_Missense_Mutation_p.L534R|TRPV1_ENST00000425167.2_Missense_Mutation_p.L545R|TRPV1_ENST00000576351.1_Missense_Mutation_p.L524R|TRPV1_ENST00000174621.6_Missense_Mutation_p.L532R|TRPV1_ENST00000310522.5_Missense_Mutation_p.L474R	NM_018727.5	NP_061197.4	Q8NER1	TRPV1_HUMAN	transient receptor potential cation channel, subfamily V, member 1	534					calcium ion transmembrane transport (GO:0070588)|cell surface receptor signaling pathway (GO:0007166)|cellular response to alkaloid (GO:0071312)|cellular response to ATP (GO:0071318)|chemosensory behavior (GO:0007635)|ion transmembrane transport (GO:0034220)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|calcium-release channel activity (GO:0015278)|excitatory extracellular ligand-gated ion channel activity (GO:0005231)|phosphoprotein binding (GO:0051219)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	17				Lung(1;0.055)|COAD - Colon adenocarcinoma(5;0.0896)|LUAD - Lung adenocarcinoma(1115;0.131)	Alpha-Linolenic Acid(DB00132)|Aspartame(DB00168)|Icosapent(DB00159)	ATACTCCTTGAGGTGGCTGAA	0.587																																					p.L534R	Melanoma(38;962 1762 15789)	Atlas-SNP	.											.	TRPV1	99	.	0			c.T1601G						.						40	46	44					17																	3481004		2090	4219	6309	SO:0001583	missense	7442	exon11			TCCTTGAGGTGGC	AJ272063	CCDS45576.1	17p13.2	2014-08-12	2002-01-29	2002-02-01	ENSG00000196689	ENSG00000262304		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	12716	protein-coding gene	gene with protein product		602076	"vanilloid receptor subtype 1"	VR1		9349813, 11549313, 16382100	Standard	NM_018727		Approved		uc010vrt.2	Q8NER1	OTTHUMG00000177649	ENST00000571088.1:c.1601T>G	chr17.hg19:g.3481004A>C	ENSP00000461007:p.Leu534Arg	149.0	0.0		171.0	89.0	NM_018727	A2RUA9|Q3LU47|Q9H0G9|Q9H303|Q9H304|Q9NQ74|Q9NY22	Missense_Mutation	SNP	ENST00000571088.1	hg19	CCDS45576.1	.	.	.	.	.	.	.	.	.	.	a	5.986	0.365878	0.11352	.	.	ENSG00000196689	ENST00000399759;ENST00000399756;ENST00000174621;ENST00000425167;ENST00000310522	D;D;D;D;D	0.86769	-2.17;-2.17;-2.17;-2.17;-2.17	5.23	-1.9	0.07665	Ion transport (1);	0.937438	0.09148	N	0.841989	T	0.60011	0.2236	N	0.01048	-1.04	0.19300	N	0.999976	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.0	T	0.52779	-0.8530	10	0.19590	T	0.45	-3.7513	4.0786	0.09916	0.3732:0.3516:0.0:0.2751	.	534;532;474;545	Q8NER1;E7EQ80;E7ESJ2;E7EQ78	TRPV1_HUMAN;.;.;.	R	534;534;532;545;474	ENSP00000382661:L534R;ENSP00000382659:L534R;ENSP00000174621:L532R;ENSP00000409627:L545R;ENSP00000311692:L474R	ENSP00000174621:L532R	L	-	2	0	TRPV1	3427753	0.000000	0.05858	0.122000	0.21767	0.720000	0.41350	-0.568000	0.05909	-0.206000	0.10203	-0.292000	0.09595	CTC	.	.		0.587	TRPV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438254.1	NM_018727		C	3481004	A	C	3481004	3	2	286	1	0	0	0	0	1	0	0	0	16610	304	11	5	615	5	TRPV1	17	3481004	Missense_Mutation	SNP	A	TCGA-G3-A5SK-01A-11D-A27I-10	2099044	3481004	77714206	65	42076										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11725907	11725907	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	cgcttcttgcagaacacagaGggcattgaggtgagagagaa	14	7	1	5			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr17:11725907G>T	ENST00000262442.4	+	47	9071	c.9003G>T	c.(9001-9003)gaG>gaT	p.E3001D	DNAH9_ENST00000454412.2_Missense_Mutation_p.E3001D	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	3001	AAA 4. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		AGAACACAGAGGGCATTGAGG	0.507																																					p.E3001D		Atlas-SNP	.											.	DNAH9	695	.	0			c.G9003T						.						103	101	102					17																	11725907		2203	4300	6503	SO:0001583	missense	1770	exon47			CACAGAGGGCATT	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.9003G>T	chr17.hg19:g.11725907G>T	ENSP00000262442:p.Glu3001Asp	115.0	0.0		123.0	51.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	hg19	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	G	2.852	-0.238060	0.05944	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.55052	0.54;0.54	3.68	-2.52	0.06346	Dynein heavy chain, P-loop containing D4 domain (1);	0.396595	0.23893	N	0.043532	T	0.31482	0.0798	L	0.31926	0.97	0.43846	D	0.99643	B	0.06786	0.001	B	0.18263	0.021	T	0.06844	-1.0804	10	0.16420	T	0.52	.	6.2515	0.20848	0.3157:0.3713:0.313:0.0	.	3001	Q9NYC9	DYH9_HUMAN	D	3001;3001;1583	ENSP00000262442:E3001D;ENSP00000414874:E3001D	ENSP00000262442:E3001D	E	+	3	2	DNAH9	11666632	0.006000	0.16342	0.023000	0.16930	0.529000	0.34654	0.066000	0.14489	-0.560000	0.06102	0.563000	0.77884	GAG	.	.		0.507	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		T	11725907	G	T	11725907	3	4	286	1	0	0	0	0	1	0	0	0	4610	991	35	3	9189	3	DNAH9	17	11725907	Missense_Mutation	SNP	G	TCGA-G3-A5SK-01A-11D-A27I-10	8244903	11725907	69469303	66	42077										
ZNF287	57336	hgsc.bcm.edu	37	chr17	16470785	16470785	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	agcaccagcagctccaaaatTtgttcctttgagtgaatctc	7	11	1	2			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr17:16470785T>G	ENST00000395824.1	-	2	878	c.261A>C	c.(259-261)caA>caC	p.Q87H	ZNF287_ENST00000395825.3_Missense_Mutation_p.Q87H|ZNF287_ENST00000461555.1_5'Flank			Q9HBT7	ZN287_HUMAN	zinc finger protein 287	80	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(5)|prostate(1)|urinary_tract(1)	20				UCEC - Uterine corpus endometrioid carcinoma (92;0.083)		GCTCCAAAATTTGTTCCTTTG	0.517																																					p.Q87H		Atlas-SNP	.											.	ZNF287	60	.	0			c.A261C						.						89	90	90					17																	16470785		2203	4300	6503	SO:0001583	missense	57336	exon2			CAAAATTTGTTCC	AF217227	CCDS11179.2	17p11.2	2013-01-09			ENSG00000141040	ENSG00000141040		"Zinc fingers, C2H2-type", "-", "-", "-"	13502	protein-coding gene	gene with protein product							Standard	NM_020653		Approved	ZKSCAN13, ZSCAN45	uc002gqi.2	Q9HBT7	OTTHUMG00000058993	ENST00000395824.1:c.261A>C	chr17.hg19:g.16470785T>G	ENSP00000379168:p.Gln87His	108.0	0.0		177.0	10.0	NM_020653	Q6IAG1	Missense_Mutation	SNP	ENST00000395824.1	hg19	CCDS11179.2	.	.	.	.	.	.	.	.	.	.	T	17.72	3.459326	0.63401	.	.	ENSG00000141040	ENST00000395825;ENST00000395824	T;T	0.09255	3.0;3.0	5.18	0.525	0.17072	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	0.000000	0.47093	D	0.000259	T	0.35422	0.0931	M	0.92970	3.365	0.28622	N	0.90814	D	0.69078	0.997	D	0.85130	0.997	T	0.17745	-1.0359	10	0.72032	D	0.01	.	7.8292	0.29332	0.0:0.5839:0.0:0.4161	.	80	Q9HBT7	ZN287_HUMAN	H	87	ENSP00000379169:Q87H;ENSP00000379168:Q87H	ENSP00000379168:Q87H	Q	-	3	2	ZNF287	16411510	0.997000	0.39634	0.998000	0.56505	0.980000	0.70556	0.119000	0.15626	-0.017000	0.14103	-0.250000	0.11733	CAA	.	.		0.517	ZNF287-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130504.1			G	16470785	T	G	16470785	3	3	286	1	0	0	0	0	1	0	0	0	17840	1838	64	5	2044	5	ZNF287	17	16470785	Missense_Mutation	SNP	T	TCGA-G3-A5SK-01A-11D-A27I-10	4744878	16470785	64724425	67	42078										
ALKBH5	54890	hgsc.bcm.edu	37	chr17	18110272	18110272	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	ccaccgcaaggcagaccctgAtgctgcccacaggtactcag	10	16	1	2			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr17:18110272A>T	ENST00000399138.4	+	3	1000	c.995A>T	c.(994-996)gAt>gTt	p.D332V	ALKBH5_ENST00000541285.1_De_novo_Start_OutOfFrame	NM_017758.3	NP_060228.3	Q6P6C2	ALKB5_HUMAN	AlkB family member 5, RNA demethylase	332					cell differentiation (GO:0030154)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|oxidative single-stranded RNA demethylation (GO:0035553)|response to hypoxia (GO:0001666)|spermatogenesis (GO:0007283)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|oxidative RNA demethylase activity (GO:0035515)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|ovary(1)|skin(1)	10	all_neural(463;0.228)					GCAGACCCTGATGCTGCCCAC	0.587																																					p.D332V	Ovarian(166;154 1953 40235 46283 46309)	Atlas-SNP	.											.	ALKBH5	24	.	0			c.A995T						.						127	131	130					17																	18110272		1939	4127	6066	SO:0001583	missense	54890	exon3			ACCCTGATGCTGC	AK000315	CCDS42272.1	17p11.2	2014-07-23	2014-07-23	2006-02-09	ENSG00000091542	ENSG00000091542	1.14.11.-	"Alkylation repair homologs"	25996	protein-coding gene	gene with protein product		613303	"oxoglutarate and iron-dependent oxygenase domain containing", "alkB, alkylation repair homolog 5 (E. coli)"	OFOXD1		11997338, 24778178	Standard	NM_017758		Approved	FLJ20308	uc010cpw.3	Q6P6C2	OTTHUMG00000059397	ENST00000399138.4:c.995A>T	chr17.hg19:g.18110272A>T	ENSP00000382091:p.Asp332Val	72.0	0.0		124.0	43.0	NM_017758	B4DVJ4|D3DXC6|Q9NXD6	Missense_Mutation	SNP	ENST00000399138.4	hg19	CCDS42272.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.591157	0.86851	.	.	ENSG00000091542	ENST00000261650;ENST00000500385;ENST00000399138	.	.	.	5.56	5.56	0.83823	.	0.046387	0.85682	D	0.000000	T	0.60856	0.2301	L	0.29908	0.895	0.80722	D	1	D	0.67145	0.996	P	0.59487	0.858	T	0.57154	-0.7860	9	0.24483	T	0.36	-3.5368	15.7046	0.77569	1.0:0.0:0.0:0.0	.	332	Q6P6C2-2	.	V	332;321;332	.	ENSP00000261650:D332V	D	+	2	0	ALKBH5	18050997	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.738000	0.84966	2.115000	0.64714	0.533000	0.62120	GAT	.	.		0.587	ALKBH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132069.3	NM_017758		T	18110272	A	T	18110272	3	4	286	1	0	0	0	0	1	0	0	0	530	333	12	4	1005	4	ALKBH5	17	18110272	Missense_Mutation	SNP	A	TCGA-G3-A5SK-01A-11D-A27I-10	1639487	18110272	63084938	68	42079										
CWC25	54883	hgsc.bcm.edu	37	chr17	36958366	36958366	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	catcttttcataaagttcttCtccagagctaccgaagttct	5	11	5	1			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr17:36958366C>T	ENST00000225428.5	-	10	1554	c.1257G>A	c.(1255-1257)gaG>gaA	p.E419E	PIP4K2B_ENST00000269554.3_5'Flank|CWC25_ENST00000536127.1_Silent_p.E356E|PIP4K2B_ENST00000311500.6_5'Flank	NM_017748.3	NP_060218.1	Q9NXE8	CWC25_HUMAN	CWC25 spliceosome-associated protein homolog (S. cerevisiae)	419										central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(1)|lung(4)|upper_aerodigestive_tract(1)	14						TAAAGTTCTTCTCCAGAGCTA	0.448																																					p.E419E		Atlas-SNP	.											.	CWC25	24	.	0			c.G1257A						.						70	67	68					17																	36958366		1860	4109	5969	SO:0001819	synonymous_variant	54883	exon10			GTTCTTCTCCAGA	AK000298	CCDS45663.1	17q12	2010-01-26	2010-01-26	2010-01-26		ENSG00000273559			25989	protein-coding gene	gene with protein product			"coiled-coil domain containing 49"	CCDC49		19941820	Standard	NM_017748		Approved	FLJ20291	uc002hqu.4	Q9NXE8		ENST00000225428.5:c.1257G>A	chr17.hg19:g.36958366C>T		65.0	0.0		118.0	35.0	NM_017748	A0JLM3|Q68DK5	Silent	SNP	ENST00000225428.5	hg19	CCDS45663.1																																																																																			.	.		0.448	CWC25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442186.6	NM_017748		T	36958366	C	T	36958366	2	4	286	1	0	0	0	0	0	0	0	1	4071	912	32	3		3	CWC25	17	36958366	Silent	SNP	C	TCGA-G3-A5SK-01A-11D-A27I-10	18848094	36958366	44236844	69	42080										
FKBP10	60681	hgsc.bcm.edu	37	chr17	39975544	39975544	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	ccgaaggacgctgtccagctAgagacgctggagctcccccc	12	16	0	1			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr17:39975544A>G	ENST00000321562.4	+	5	914	c.810A>G	c.(808-810)ctA>ctG	p.L270L	FKBP10_ENST00000544340.1_5'UTR	NM_021939.3	NP_068758.3	Q96AY3	FKB10_HUMAN	FK506 binding protein 10, 65 kDa	270					chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			cervix(1)|endometrium(3)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	14		Breast(137;0.00122)		BRCA - Breast invasive adenocarcinoma(366;0.148)		CTGTCCAGCTAGAGACGCTGG	0.642																																					p.L270L		Atlas-SNP	.											.	FKBP10	57	.	0			c.A810G						.						59	61	60					17																	39975544		2203	4300	6503	SO:0001819	synonymous_variant	60681	exon5			CCAGCTAGAGACG	AB045981	CCDS11409.1	17q21.2	2014-09-17	2002-08-29		ENSG00000141756	ENSG00000141756		"EF-hand domain containing"	18169	protein-coding gene	gene with protein product		607063	"FK506 binding protein 10 (65 kDa)"			11071917, 18786928	Standard	NM_021939		Approved	hFKBP65, FLJ22041, FKBP6, FLJ20683, FLJ23833	uc002hxv.2	Q96AY3	OTTHUMG00000133497	ENST00000321562.4:c.810A>G	chr17.hg19:g.39975544A>G		108.0	0.0		152.0	7.0	NM_021939	Q7Z3R4|Q9H3N3|Q9H6J3|Q9H6N5|Q9UF89	Silent	SNP	ENST00000321562.4	hg19	CCDS11409.1	.	.	.	.	.	.	.	.	.	.	A	6.798	0.516293	0.12944	.	.	ENSG00000141756	ENST00000455106	.	.	.	5.55	-0.884	0.10597	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-16.868	7.532	0.27689	0.3501:0.0:0.5488:0.1011	.	.	.	.	W	13	.	.	X	+	2	0	FKBP10	37229070	1.000000	0.71417	0.983000	0.44433	0.252000	0.25951	1.401000	0.34589	-0.001000	0.14495	0.459000	0.35465	TAG	.	.		0.642	FKBP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257410.2	NM_021939		G	39975544	A	G	39975544	2	3	286	1	0	0	0	0	0	0	0	1	5910	407	15	2		2	FKBP10	17	39975544	Silent	SNP	A	TCGA-G3-A5SK-01A-11D-A27I-10	3017178	39975544	41219666	70	42081										
ZACN	353174	hgsc.bcm.edu	37	chr17	74076379	74076379	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	agagcccccaggctcgagtaGaccaggacggccacgtgaag	14	13	0	3			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr17:74076379G>C	ENST00000334586.5	+	5	501	c.418G>C	c.(418-420)Gac>Cac	p.D140H	ZACN_ENST00000392503.2_Intron|EXOC7_ENST00000591724.1_5'Flank	NM_180990.3	NP_851321.2	Q401N2	ZACN_HUMAN	zinc activated ligand-gated ion channel	140					ion transmembrane transport (GO:0034220)|response to zinc ion (GO:0010043)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)|ligand-gated ion channel activity (GO:0015276)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	11						GGCTCGAGTAGACCAGGACGG	0.667																																					p.D140H		Atlas-SNP	.											.	ZACN	29	.	0			c.G418C						.						71	66	68					17																	74076379		2203	4300	6503	SO:0001583	missense	353174	exon5			CGAGTAGACCAGG	AK122638	CCDS11740.2	17q25.3	2012-01-18	2008-04-17	2008-04-17	ENSG00000186919	ENSG00000186919		"Ligand-gated ion channels / Zinc activated channels"	29504	protein-coding gene	gene with protein product		610935	"ligand-gated ion channel, zinc activated 1"	LGICZ1		12381728, 16083862	Standard	NM_180990		Approved	LGICZ, L2, ZAC, ZAC1	uc002jqn.2	Q401N2	OTTHUMG00000157186	ENST00000334586.5:c.418G>C	chr17.hg19:g.74076379G>C	ENSP00000334854:p.Asp140His	137.0	0.0		245.0	75.0	NM_180990	Q2TB29|Q6ZWK3|Q86YW4	Missense_Mutation	SNP	ENST00000334586.5	hg19	CCDS11740.2	.	.	.	.	.	.	.	.	.	.	G	6.198	0.404672	0.11754	.	.	ENSG00000186919	ENST00000334586	T	0.78481	-1.18	3.85	-0.834	0.10779	Neurotransmitter-gated ion-channel ligand-binding (3);	0.763550	0.12013	N	0.507714	T	0.62307	0.2417	L	0.46157	1.445	0.09310	N	0.999998	B	0.12013	0.005	B	0.12837	0.008	T	0.42120	-0.9470	10	0.11182	T	0.66	-10.5351	3.9401	0.09323	0.3459:0.3556:0.2985:0.0	.	140	Q401N2	ZACN_HUMAN	H	140	ENSP00000334854:D140H	ENSP00000334854:D140H	D	+	1	0	ZACN	71587974	0.796000	0.28864	0.001000	0.08648	0.020000	0.10135	0.902000	0.28459	0.020000	0.15106	-0.886000	0.02939	GAC	.	.		0.667	ZACN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347827.2	NM_180990		C	74076379	G	C	74076379	3	2	286	1	0	0	0	0	1	0	0	0	17525	942	33	4	436	4	ZACN	17	74076379	Missense_Mutation	SNP	G	TCGA-G3-A5SK-01A-11D-A27I-10	34100835	74076379	7118831	71	42082										
DNAH17	8632	hgsc.bcm.edu	37	chr17	76440846	76440846	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	agatccttcgatgtcactgtCcagatttttgaactcatcca	6	11	2	3			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr17:76440846C>A	ENST00000585328.1	-	71	11477	c.11353G>T	c.(11353-11355)Gac>Tac	p.D3785Y	DNAH17_ENST00000389840.5_Missense_Mutation_p.D3776Y|DNAH17_ENST00000586052.1_5'UTR	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	3776					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			ATGTCACTGTCCAGATTTTTG	0.582																																					p.D3790Y		Atlas-SNP	.											.	DNAH17	347	.	0			c.G11368T						.						67	61	63					17																	76440846		2203	4300	6503	SO:0001583	missense	8632	exon71			CACTGTCCAGATT	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"Axonemal dyneins"	2946	protein-coding gene	gene with protein product		610063	"dynein, axonemal, heavy polypeptide 17", "dynein, axonemal, heavy chain like 1", "dynein, axonemal, heavy like 1"	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.11353G>T	chr17.hg19:g.76440846C>A	ENSP00000465516:p.Asp3785Tyr	118.0	0.0		200.0	66.0	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Missense_Mutation	SNP	ENST00000585328.1	hg19		.	.	.	.	.	.	.	.	.	.	C	25.6	4.655751	0.88056	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.09163	3.01	4.99	4.99	0.66335	.	0.166015	0.41396	D	0.000893	T	0.36082	0.0954	M	0.87097	2.86	0.80722	D	1	D	0.56287	0.975	P	0.59221	0.854	T	0.36625	-0.9740	10	0.54805	T	0.06	.	18.2779	0.90089	0.0:1.0:0.0:0.0	.	3785	E7EUM8	.	Y	3785;3776	ENSP00000374490:D3776Y	ENSP00000300671:D3785Y	D	-	1	0	DNAH17	73952441	1.000000	0.71417	0.993000	0.49108	0.913000	0.54294	7.607000	0.82883	2.309000	0.77851	0.561000	0.74099	GAC	.	.		0.582	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		A	76440846	C	A	76440846	3	1	286	1	0	0	0	0	1	0	0	0	4603	855	30	3	2064	3	DNAH17	17	76440846	Missense_Mutation	SNP	C	TCGA-G3-A5SK-01A-11D-A27I-10	2364467	76440846	4754364	72	42083										
CDH7	1005	hgsc.bcm.edu	37	chr18	63489356	63489356	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	tccaaacatggatagagaggCtaaagaccagtatttgcttg	10	7	0	2			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr18:63489356C>T	ENST00000397968.2	+	5	1091	c.665C>T	c.(664-666)gCt>gTt	p.A222V	CDH7_ENST00000536984.2_Missense_Mutation_p.A222V|CDH7_ENST00000323011.3_Missense_Mutation_p.A222V	NM_004361.2	NP_004352.2	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2	222	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(43)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	80		Esophageal squamous(42;0.129)				GATAGAGAGGCTAAAGACCAG	0.403																																					p.A222V		Atlas-SNP	.											.	CDH7	362	.	0			c.C665T						.						139	109	119					18																	63489356		2203	4300	6503	SO:0001583	missense	1005	exon5			GAGAGGCTAAAGA	AB035301	CCDS11993.1	18q22.1	2010-01-26			ENSG00000081138	ENSG00000081138		"Cadherins / Major cadherins"	1766	protein-coding gene	gene with protein product		605806				9615235	Standard	NM_033646		Approved		uc002ljz.3	Q9ULB5	OTTHUMG00000132800	ENST00000397968.2:c.665C>T	chr18.hg19:g.63489356C>T	ENSP00000381058:p.Ala222Val	134.0	0.0		176.0	45.0	NM_004361	Q9H157	Missense_Mutation	SNP	ENST00000397968.2	hg19	CCDS11993.1	.	.	.	.	.	.	.	.	.	.	C	16.57	3.161054	0.57368	.	.	ENSG00000081138	ENST00000323011;ENST00000536984;ENST00000397966;ENST00000397968	T;T;T	0.51817	0.69;0.69;0.69	5.01	5.01	0.66863	Cadherin (4);Cadherin-like (1);	0.058450	0.64402	D	0.000003	T	0.31231	0.0790	N	0.11364	0.135	0.80722	D	1	B;B	0.18863	0.031;0.005	B;B	0.12837	0.008;0.003	T	0.08027	-1.0742	10	0.21014	T	0.42	.	18.69	0.91580	0.0:1.0:0.0:0.0	.	222;222	F5H5X9;Q9ULB5	.;CADH7_HUMAN	V	222	ENSP00000319166:A222V;ENSP00000443030:A222V;ENSP00000381058:A222V	ENSP00000319166:A222V	A	+	2	0	CDH7	61640336	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.627000	0.54252	2.473000	0.83533	0.591000	0.81541	GCT	.	.		0.403	CDH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256217.2	NM_033646		T	63489356	C	T	63489356	3	4	286	1	0	0	0	0	1	0	0	0	3117	797	28	3	679	3	CDH7	18	63489356	Missense_Mutation	SNP	C	TCGA-G3-A5SK-01A-11D-A27I-10		63489356	14587892	73	42084										
GALR1	2587	hgsc.bcm.edu	37	chr18	74980684	74980684	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	atcaccgcccactgcctggcGtacagcaattcctccgtgaa	8	16	1	1	rs199730182		TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr18:74980684G>T	ENST00000299727.3	+	3	876	c.876G>T	c.(874-876)gcG>gcT	p.A292A		NM_001480.3	NP_001471.2	P47211	GALR1_HUMAN	galanin receptor 1	292					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|digestion (GO:0007586)|negative regulation of adenylate cyclase activity (GO:0007194)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cortisol secretion (GO:0051464)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galanin receptor activity (GO:0004966)|neuropeptide binding (GO:0042923)|peptide hormone binding (GO:0017046)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.03e-06)|BRCA - Breast invasive adenocarcinoma(31;0.104)		ACTGCCTGGCGTACAGCAATT	0.493																																					p.A292A		Atlas-SNP	.											.	GALR1	53	.	0			c.G876T						.						84	83	83					18																	74980684		2203	4300	6503	SO:0001819	synonymous_variant	2587	exon3			CCTGGCGTACAGC	U90658	CCDS12012.1	18q23	2012-08-08			ENSG00000166573	ENSG00000166573		"GPCR / Class A : Galanin receptors"	4132	protein-coding gene	gene with protein product		600377		GALNR1, GALNR		7524088	Standard	NM_001480		Approved		uc002lms.4	P47211	OTTHUMG00000132875	ENST00000299727.3:c.876G>T	chr18.hg19:g.74980684G>T		76.0	0.0		124.0	41.0	NM_001480	Q4VBL7	Silent	SNP	ENST00000299727.3	hg19	CCDS12012.1																																																																																			.	G|0.999;A|0.001		0.493	GALR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256362.1			T	74980684	G	T	74980684	2	4	286	1	0	0	0	0	0	0	0	1	6235	1132	40	1		1	GALR1	18	74980684	Silent	SNP	G	TCGA-G3-A5SK-01A-11D-A27I-10	11491328	74980684	3096564	74	42085										
FFAR2	2867	hgsc.bcm.edu	37	chr19	35940974	35940974	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	tccccgtgcagtacaagctcTcccgccggcctctgtatgga	10	16	2	0			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr19:35940974T>G	ENST00000599180.2	+	2	438	c.358T>G	c.(358-360)Tcc>Gcc	p.S120A	FFAR2_ENST00000601590.1_Intron|FFAR2_ENST00000246549.2_Missense_Mutation_p.S120A			O15552	FFAR2_HUMAN	free fatty acid receptor 2	120					cell surface pattern recognition receptor signaling pathway (GO:0002752)|cellular response to fatty acid (GO:0071398)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|leukocyte chemotaxis involved in inflammatory response (GO:0002232)|lipid storage (GO:0019915)|mucosal immune response (GO:0002385)|positive regulation of acute inflammatory response to non-antigenic stimulus (GO:0002879)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine production involved in immune response (GO:0002720)|positive regulation of interleukin-8 secretion (GO:2000484)|regulation of acute inflammatory response (GO:0002673)|regulation of peptide hormone secretion (GO:0090276)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(6)|skin(1)|urinary_tract(1)	22	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			GTACAAGCTCTCCCGCCGGCC	0.562																																					p.S120A	GBM(40;139 809 9833 23358 48736)	Atlas-SNP	.											.	FFAR2	39	.	0			c.T358G						.						81	70	74					19																	35940974		2203	4300	6503	SO:0001583	missense	2867	exon1			AAGCTCTCCCGCC	AF024690	CCDS12461.1	19q13.1	2012-08-08	2006-02-15	2006-02-15		ENSG00000126262		"GPCR / Class A : Fatty acid receptors"	4501	protein-coding gene	gene with protein product		603823	"G protein-coupled receptor 43"	GPR43		9344866	Standard	NM_005306		Approved	FFA2R	uc010eea.3	O15552		ENST00000599180.2:c.358T>G	chr19.hg19:g.35940974T>G	ENSP00000473159:p.Ser120Ala	157.0	0.0		194.0	60.0	NM_005306	B0M0J9|Q4VAZ3|Q4VAZ5|Q4VBL5	Missense_Mutation	SNP	ENST00000599180.2	hg19	CCDS12461.1	.	.	.	.	.	.	.	.	.	.	T	3.881	-0.026016	0.07589	.	.	ENSG00000126262	ENST00000246549	T	0.71817	-0.6	5.72	2.16	0.27623	GPCR, rhodopsin-like superfamily (1);	0.440704	0.26522	N	0.023915	T	0.55513	0.1925	L	0.42686	1.345	0.23445	N	0.997662	B	0.06786	0.001	B	0.08055	0.003	T	0.34030	-0.9845	10	0.15499	T	0.54	-44.1769	7.4955	0.27487	0.1381:0.0:0.4283:0.4336	.	120	O15552	FFAR2_HUMAN	A	120	ENSP00000246549:S120A	ENSP00000246549:S120A	S	+	1	0	FFAR2	40632814	0.000000	0.05858	0.996000	0.52242	0.699000	0.40488	0.453000	0.21811	0.469000	0.27268	0.533000	0.62120	TCC	.	.		0.562	FFAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466120.3	NM_005306		G	35940974	T	G	35940974	3	3	286	1	0	0	0	0	1	0	0	0	5836	1551	54	5	360	5	FFAR2	19	35940974	Missense_Mutation	SNP	T	TCGA-G3-A5SK-01A-11D-A27I-10		35940974	23188009	75	42086										
MEIS3	56917	hgsc.bcm.edu	37	chr19	47910667	47910667	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	cgccagctgtttcttctgctCctccgaggggtacgggtgct	13	13	2	0			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr19:47910667C>G	ENST00000558555.1	-	9	1064	c.877G>C	c.(877-879)Gag>Cag	p.E293Q	MEIS3_ENST00000561293.1_Missense_Mutation_p.E339Q|MEIS3_ENST00000561096.1_Missense_Mutation_p.E381Q|MEIS3_ENST00000331559.5_Missense_Mutation_p.E322Q|MEIS3_ENST00000560253.1_5'UTR|MEIS3_ENST00000559524.1_Missense_Mutation_p.E339Q|MEIS3_ENST00000441740.2_Missense_Mutation_p.E276Q			Q99687	MEIS3_HUMAN	Meis homeobox 3	293					negative regulation of apoptotic signaling pathway (GO:2001234)|positive regulation of protein kinase B signaling (GO:0051897)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)			breast(1)|large_intestine(5)|lung(11)|prostate(1)|skin(2)	20		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;0.000198)|OV - Ovarian serous cystadenocarcinoma(262;0.000439)|Epithelial(262;0.0113)|GBM - Glioblastoma multiforme(486;0.0223)		TTCTTCTGCTCCTCCGAGGGG	0.697																																					p.E339Q		Atlas-SNP	.											.	MEIS3	40	.	0			c.G1015C						.						47	46	47					19																	47910667		2203	4298	6501	SO:0001583	missense	56917	exon9			TCTGCTCCTCCGA	BC025404	CCDS33064.1, CCDS46132.1, CCDS74406.1	19q13.32	2012-10-02	2007-02-15		ENSG00000105419	ENSG00000105419		"Homeoboxes / TALE class"	29537	protein-coding gene	gene with protein product			"Meis1, myeloid ecotropic viral integration site 1 homolog 3 (mouse)"			8950991	Standard	NM_020160		Approved	MRG2, DKFZp547H236	uc002pgt.4	Q99687	OTTHUMG00000172280	ENST00000558555.1:c.877G>C	chr19.hg19:g.47910667C>G	ENSP00000454073:p.Glu293Gln	39.0	0.0		79.0	20.0	NM_020160	A8K1N5|Q6NT73|Q8TC66|Q9NPW2	Missense_Mutation	SNP	ENST00000558555.1	hg19		.	.	.	.	.	.	.	.	.	.	C	23.1	4.380423	0.82682	.	.	ENSG00000105419	ENST00000331559;ENST00000441740	D	0.93488	-3.23	4.09	4.09	0.47781	Homeodomain-related (1);Homeobox (2);Homeobox KN domain (1);Homeodomain-like (1);	0.066555	0.56097	D	0.000023	D	0.93996	0.8077	L	0.33710	1.025	0.58432	D	0.999997	D;D;P;P;D	0.89917	1.0;0.997;0.503;0.949;0.992	D;D;B;P;P	0.72982	0.979;0.976;0.155;0.6;0.874	D	0.94630	0.7821	10	0.87932	D	0	-6.4022	14.1793	0.65564	0.0:1.0:0.0:0.0	.	185;293;276;339;168	Q8TCW1;Q99687;Q99687-3;Q99687-2;Q59FK5	.;MEIS3_HUMAN;.;.;.	Q	339;276	ENSP00000388667:E276Q	ENSP00000333552:E339Q	E	-	1	0	MEIS3	52602479	1.000000	0.71417	1.000000	0.80357	0.805000	0.45488	5.509000	0.67012	2.277000	0.76020	0.491000	0.48974	GAG	.	.		0.697	MEIS3-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000417642.1	XM_085929		G	47910667	C	G	47910667	3	3	286	1	0	0	0	0	1	0	0	0	9478	864	30	4	266	4	MEIS3	19	47910667	Missense_Mutation	SNP	C	TCGA-G3-A5SK-01A-11D-A27I-10	11969693	47910667	11218316	76	42087										
NOP56	10528	hgsc.bcm.edu	37	chr20	2635207	2635207	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	ccagactggaggagtcatagCtgagatcctgcgaggtgaga	15	8	1	3			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr20:2635207C>G	ENST00000329276.5	+	4	872	c.356C>G	c.(355-357)gCt>gGt	p.A119G	SNORD56_ENST00000413522.1_RNA|SNORD57_ENST00000448188.1_RNA|SNORA51_ENST00000606420.1_RNA|SNORD110_ENST00000408189.1_RNA|SNORD86_ENST00000391196.1_RNA|MIR1292_ENST00000408135.1_RNA	NM_006392.3	NP_006383.2	O00567	NOP56_HUMAN	NOP56 ribonucleoprotein	119					cell death (GO:0008219)|rRNA processing (GO:0006364)	box C/D snoRNP complex (GO:0031428)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|snoRNA binding (GO:0030515)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25						GGAGTCATAGCTGAGATCCTG	0.473																																					p.A119G		Atlas-SNP	.											.	NOP56	73	.	0			c.C356G						.						131	124	126					20																	2635207		2203	4300	6503	SO:0001583	missense	10528	exon4			TCATAGCTGAGAT	Y12065	CCDS13030.1	20p13	2012-12-10	2012-12-10	2009-01-13	ENSG00000101361	ENSG00000101361			15911	protein-coding gene	gene with protein product	"spinocerebellar ataxia 36"	614154	"nucleolar protein 5A (56kD with KKE/D repeat)", "nucleolar protein 5A (56kDa with KKE/D repeat)", "NOP56 ribonucleoprotein homolog (yeast)"	NOL5A		9372940, 21683323	Standard	NR_027700		Approved	SCA36	uc002wgh.3	O00567	OTTHUMG00000031703	ENST00000329276.5:c.356C>G	chr20.hg19:g.2635207C>G	ENSP00000370589:p.Ala119Gly	184.0	0.0		202.0	65.0	NM_006392	Q2M3T6|Q9NQ05	Missense_Mutation	SNP	ENST00000329276.5	hg19	CCDS13030.1	.	.	.	.	.	.	.	.	.	.	C	14.71	2.616358	0.46736	.	.	ENSG00000101361	ENST00000329276;ENST00000445139	T;T	0.58506	0.33;0.92	5.79	4.85	0.62838	.	0.092470	0.85682	D	0.000000	T	0.44871	0.1314	L	0.35593	1.075	0.58432	D	0.999996	B	0.10296	0.003	B	0.06405	0.002	T	0.30119	-0.9989	10	0.22109	T	0.4	-3.5696	12.384	0.55323	0.0:0.9187:0.0:0.0813	.	119	O00567	NOP56_HUMAN	G	119	ENSP00000370589:A119G;ENSP00000388497:A119G	ENSP00000370589:A119G	A	+	2	0	NOP56	2583207	0.998000	0.40836	0.867000	0.34043	0.984000	0.73092	3.837000	0.55820	1.434000	0.47414	0.555000	0.69702	GCT	.	.		0.473	NOP56-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077631.2	NM_006392		G	2635207	C	G	2635207	3	3	286	1	0	0	0	0	1	0	0	0	10548	797	28	4	370	4	NOP56	20	2635207	Missense_Mutation	SNP	C	TCGA-G3-A5SK-01A-11D-A27I-10		2635207	60390313	77	42088										
PLCB4	5332	hgsc.bcm.edu	37	chr20	9371192	9371192	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	ctccagcaaatatcaacagtAcaagatgtccaaatattgcg	6	10	1	1			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr20:9371192A>G	ENST00000378493.1	+	14	1268	c.1253A>G	c.(1252-1254)tAc>tGc	p.Y418C	PLCB4_ENST00000414679.2_Missense_Mutation_p.Y418C|PLCB4_ENST00000378501.2_Missense_Mutation_p.Y418C|PLCB4_ENST00000378473.3_Missense_Mutation_p.Y418C|PLCB4_ENST00000492632.1_3'UTR|PLCB4_ENST00000278655.4_Missense_Mutation_p.Y418C|PLCB4_ENST00000334005.3_Missense_Mutation_p.Y418C			Q15147	PLCB4_HUMAN	phospholipase C, beta 4	418	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|smooth endoplasmic reticulum (GO:0005790)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(2)|breast(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(11)|liver(4)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(19)|upper_aerodigestive_tract(1)	87						TATCAACAGTACAAGATGTCC	0.348																																					p.Y418C		Atlas-SNP	.											.	PLCB4	204	.	0			c.A1253G						.						68	67	67					20																	9371192		2203	4299	6502	SO:0001583	missense	5332	exon15			AACAGTACAAGAT		CCDS13104.1, CCDS13105.1, CCDS54447.1	20p12	2008-03-18			ENSG00000101333	ENSG00000101333	3.1.4.11		9059	protein-coding gene	gene with protein product		600810				8530101	Standard	NM_000933		Approved		uc021wam.1	Q15147	OTTHUMG00000031853	ENST00000378493.1:c.1253A>G	chr20.hg19:g.9371192A>G	ENSP00000367754:p.Tyr418Cys	94.0	0.0		107.0	29.0	NM_182797	B7ZLK6|E2QRH8|Q17R56|Q5JYS8|Q5JYS9|Q5JYT0|Q5JYT3|Q5JYT4|Q9BQW5|Q9BQW6|Q9BQW8|Q9UJQ2	Missense_Mutation	SNP	ENST00000378493.1	hg19	CCDS13105.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.939251	0.73557	.	.	ENSG00000101333	ENST00000334005;ENST00000378473;ENST00000278655;ENST00000378493;ENST00000378501;ENST00000414679	T;T;T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01;-0.01;-0.01	5.64	5.64	0.86602	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific , X domain (3);	0.561713	0.20248	N	0.096155	T	0.79167	0.4400	M	0.73962	2.25	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.87578	0.931;0.936;0.998;0.969	T	0.79848	-0.1630	10	0.51188	T	0.08	.	15.8569	0.78987	1.0:0.0:0.0:0.0	.	418;265;418;418	E2QRH8;Q15147-2;Q15147;Q15147-4	.;.;PLCB4_HUMAN;.	C	418;418;418;418;418;254	ENSP00000334105:Y418C;ENSP00000367734:Y418C;ENSP00000278655:Y418C;ENSP00000367754:Y418C;ENSP00000367762:Y418C;ENSP00000390616:Y254C	ENSP00000278655:Y418C	Y	+	2	0	PLCB4	9319192	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.214000	0.89760	2.136000	0.66102	0.477000	0.44152	TAC	.	.		0.348	PLCB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077948.2			G	9371192	A	G	9371192	3	3	286	1	0	0	0	0	1	0	0	0	12039	391	14	2	1307	2	PLCB4	20	9371192	Missense_Mutation	SNP	A	TCGA-G3-A5SK-01A-11D-A27I-10	6735985	9371192	53654328	78	42089										
CD93	22918	hgsc.bcm.edu	37	chr20	23065572	23065572	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	ctggcactgagtcccgtcctCcccggccaggacgtagccct	11	18	0	1			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr20:23065572C>T	ENST00000246006.4	-	1	1405	c.1258G>A	c.(1258-1260)Gag>Aag	p.E420K		NM_012072.3	NP_036204.2	Q9NPY3	C1QR1_HUMAN	CD93 molecule	420	EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				macrophage activation (GO:0042116)|phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|complement component C1q binding (GO:0001849)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(10)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	39	Colorectal(13;0.0352)|Lung NSC(19;0.0542)|all_lung(19;0.118)					GTCCCGTCCTCCCCGGCCAGG	0.642																																					p.E420K		Atlas-SNP	.											.	CD93	84	.	0			c.G1258A						.						42	46	45					20																	23065572		2203	4300	6503	SO:0001583	missense	22918	exon1			CGTCCTCCCCGGC	U94333	CCDS13149.1	20p11.21	2009-01-29	2006-03-28	2006-02-22	ENSG00000125810	ENSG00000125810		"CD molecules"	15855	protein-coding gene	gene with protein product		120577	"matrix-remodelling associated 4", "complement component 1, q subcomponent, receptor 1", "CD93 antigen"	MXRA4, C1QR1		9047234, 10648005	Standard	NM_012072		Approved	C1qRP, C1qR(P), dJ737E23.1, CDw93, ECSM3	uc002wsv.3	Q9NPY3	OTTHUMG00000032058	ENST00000246006.4:c.1258G>A	chr20.hg19:g.23065572C>T	ENSP00000246006:p.Glu420Lys	149.0	0.0		220.0	77.0	NM_012072	O00274	Missense_Mutation	SNP	ENST00000246006.4	hg19	CCDS13149.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.595530	0.86953	.	.	ENSG00000125810	ENST00000246006	D	0.85556	-2.0	5.18	4.17	0.49024	EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.293419	0.24128	N	0.041294	T	0.77103	0.4081	N	0.16266	0.395	0.35307	D	0.783579	P	0.47484	0.896	P	0.48270	0.572	T	0.76061	-0.3097	10	0.09338	T	0.73	-27.3807	14.2591	0.66073	0.0:0.7778:0.2222:0.0	.	420	Q9NPY3	C1QR1_HUMAN	K	420	ENSP00000246006:E420K	ENSP00000246006:E420K	E	-	1	0	CD93	23013572	0.008000	0.16893	0.070000	0.20053	0.034000	0.12701	0.668000	0.25127	2.557000	0.86248	0.650000	0.86243	GAG	.	.		0.642	CD93-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078312.2	NM_012072		T	23065572	C	T	23065572	3	4	286	1	0	0	0	0	1	0	0	0	3049	864	30	3	708	3	CD93	20	23065572	Missense_Mutation	SNP	C	TCGA-G3-A5SK-01A-11D-A27I-10	13694380	23065572	39959948	79	42090										
BPIL1	80341	hgsc.bcm.edu	37	chr20	31609598	31609598	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	tgtcgcccctgagatctttgTctatgaggtgagagcctttg	12	9	2	3			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr20:31609598T>C	ENST00000170150.3	+	15	1523	c.1328T>C	c.(1327-1329)gTc>gCc	p.V443A		NM_025227.1	NP_079503.1	Q8N4F0	BPIB2_HUMAN	BPI fold containing family B, member 2	443						extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)										GAGATCTTTGTCTATGAGGTG	0.582																																					p.V443A		Atlas-SNP	.											.	.	.	.	0			c.T1328C						.						145	130	135					20																	31609598		2203	4300	6503	SO:0001583	missense	80341	exon15			TCTTTGTCTATGA	AF465765	CCDS13210.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000078898	ENSG00000078898		"BPI fold containing"	16177	protein-coding gene	gene with protein product		614108	"bactericidal/permeability-increasing protein-like 1"	C20orf184, BPIL1		12185532, 21787333	Standard	NM_025227		Approved	dJ726C3.2, LPLUNC2	uc002wyj.4	Q8N4F0	OTTHUMG00000032232	ENST00000170150.3:c.1328T>C	chr20.hg19:g.31609598T>C	ENSP00000170150:p.Val443Ala	93.0	0.0		113.0	33.0	NM_025227	Q6UWN3|Q6ZME0|Q8NFQ7	Missense_Mutation	SNP	ENST00000170150.3	hg19	CCDS13210.1	.	.	.	.	.	.	.	.	.	.	T	16.34	3.095201	0.56075	.	.	ENSG00000078898	ENST00000170150	T	0.09445	2.98	4.49	4.49	0.54785	.	0.312255	0.22950	N	0.053664	T	0.12603	0.0306	L	0.32530	0.975	0.20764	N	0.999859	P	0.51240	0.943	P	0.48454	0.578	T	0.07214	-1.0784	10	0.56958	D	0.05	-20.169	10.7613	0.46266	0.0:0.0:0.0:1.0	.	443	Q8N4F0	BPIB2_HUMAN	A	443	ENSP00000170150:V443A	ENSP00000170150:V443A	V	+	2	0	BPIFB2	31073259	0.052000	0.20516	0.202000	0.23494	0.786000	0.44442	3.506000	0.53364	1.976000	0.57569	0.455000	0.32223	GTC	.	.		0.582	BPIFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078652.2	NM_025227		C	31609598	T	C	31609598	3	2	286	1	0	0	0	0	1	0	0	0	1493	1667	58	2	1382	2	BPIL1	20	31609598	Missense_Mutation	SNP	T	TCGA-G3-A5SK-01A-11D-A27I-10	8544026	31609598	31415922	80	42091										
ZSWIM3	140831	hgsc.bcm.edu	37	chr20	44506970	44506970	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	cagaagaagtaccagtacctCcttgggcccaatggggagct	12	11	0	2			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr20:44506970C>G	ENST00000255152.2	+	2	1982	c.1773C>G	c.(1771-1773)ctC>ctG	p.L591L	ZSWIM1_ENST00000372523.1_5'Flank|ZSWIM1_ENST00000372520.1_5'Flank|ZSWIM3_ENST00000454862.2_Silent_p.L585L	NM_080752.3	NP_542790.2	Q96MP5	ZSWM3_HUMAN	zinc finger, SWIM-type containing 3	591							zinc ion binding (GO:0008270)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	35		Myeloproliferative disorder(115;0.0122)				ACCAGTACCTCCTTGGGCCCA	0.592																																					p.L591L		Atlas-SNP	.											.	ZSWIM3	96	.	0			c.C1773G						.						81	69	73					20																	44506970		2203	4300	6503	SO:0001819	synonymous_variant	140831	exon2			GTACCTCCTTGGG	AL008726	CCDS13381.1	20q13.12	2014-06-13	2003-12-17	2003-12-19	ENSG00000132801	ENSG00000132801		"Zinc fingers, SWIM-type"	16157	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 174"		"chromosome 20 open reading frame 164"	C20orf164			Standard	NM_080752		Approved	dJ337O18.7, PPP1R174	uc002xqd.3	Q96MP5	OTTHUMG00000032627	ENST00000255152.2:c.1773C>G	chr20.hg19:g.44506970C>G		224.0	0.0		358.0	110.0	NM_080752	Q9BR13	Silent	SNP	ENST00000255152.2	hg19	CCDS13381.1																																																																																			.	.		0.592	ZSWIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079540.1	NM_080752		G	44506970	C	G	44506970	2	3	286	1	0	0	0	0	0	0	0	1	18257	842	30	4		4	ZSWIM3	20	44506970	Silent	SNP	C	TCGA-G3-A5SK-01A-11D-A27I-10	12897372	44506970	18518550	81	42092										
ELMO2	63916	hgsc.bcm.edu	37	chr20	45014770	45014770	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	gttttttactcacacctggaGgtgtgagatgagctgtccca	11	9	1	2	rs112131818	byFrequency	TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr20:45014770G>A	ENST00000290246.6	-	9	864	c.670C>T	c.(670-672)Ctc>Ttc	p.L224F	ELMO2_ENST00000352077.2_Missense_Mutation_p.L222F|ELMO2_ENST00000439931.2_Missense_Mutation_p.L224F|ELMO2_ENST00000488853.1_5'UTR|ELMO2_ENST00000445496.2_Missense_Mutation_p.L41F|ELMO2_ENST00000396391.1_Missense_Mutation_p.L224F|ELMO2_ENST00000372176.1_Missense_Mutation_p.L136F	NM_133171.3	NP_573403.1	Q96JJ3	ELMO2_HUMAN	engulfment and cell motility 2	224					apoptotic process (GO:0006915)|cell chemotaxis (GO:0060326)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	receptor tyrosine kinase binding (GO:0030971)			breast(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|urinary_tract(1)	16		Myeloproliferative disorder(115;0.0122)				CACACCTGGAGGTGTGAGATG	0.493													G|||	45	0.00898562	0.0318	0	5008	,	,		20924	0.001		0	False		,,,				2504	0.002				p.L224F		Atlas-SNP	.											.	ELMO2	51	.	0			c.C670T						.						115	109	111					20																	45014770		2203	4300	6503	SO:0001583	missense	63916	exon8			CCTGGAGGTGTGA	AF398886	CCDS13398.1	20q13	2010-03-18	2006-01-20		ENSG00000062598	ENSG00000062598		"Engulfment and cell motility proteins"	17233	protein-coding gene	gene with protein product		606421	"engulfment and cell motility 2 (ced-12 homolog, C. elegans)"			11595183	Standard	NM_133171		Approved	CED12, ELMO-2, CED-12, KIAA1834, FLJ11656	uc002xru.1	Q96JJ3	OTTHUMG00000033070	ENST00000290246.6:c.670C>T	chr20.hg19:g.45014770G>A	ENSP00000290246:p.Leu224Phe	103.0	0.0		116.0	6.0	NM_182764	E1P5T3|Q5JVZ6|Q7Z5G9|Q96CJ2|Q96ME5|Q96PA9|Q9H938|Q9H9L5|Q9HAH0|Q9NQQ6	Missense_Mutation	SNP	ENST00000290246.6	hg19	CCDS13398.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.291388	0.80914	.	.	ENSG00000062598	ENST00000290246;ENST00000372176;ENST00000396391;ENST00000439931;ENST00000445496;ENST00000352077;ENST00000425546;ENST00000450812	T;T;T;T;T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1;0.92;-0.1;0.52;-0.1	4.85	4.85	0.62838	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.69151	0.3079	L	0.49571	1.57	0.80722	D	1	P;P;P	0.50156	0.843;0.932;0.91	P;P;P	0.53912	0.737;0.708;0.737	T	0.70396	-0.4883	10	0.49607	T	0.09	-21.0836	17.1413	0.86754	0.0:0.0:1.0:0.0	.	224;224;224	B4DRL5;E9PBG2;Q96JJ3	.;.;ELMO2_HUMAN	F	224;136;224;224;41;222;12;224	ENSP00000290246:L224F;ENSP00000361249:L136F;ENSP00000379673:L224F;ENSP00000396519:L224F;ENSP00000409920:L41F;ENSP00000326172:L222F;ENSP00000388962:L12F;ENSP00000416181:L224F	ENSP00000290246:L224F	L	-	1	0	ELMO2	44448177	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.129000	0.71657	2.526000	0.85167	0.591000	0.81541	CTC	.	G|0.500;A|0.500		0.493	ELMO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080466.1	NM_022086		A	45014770	G	A	45014770	3	1	286	1	0	0	0	0	1	0	0	0	5068	1000	35	3	1548	3	ELMO2	20	45014770	Missense_Mutation	SNP	G	TCGA-G3-A5SK-01A-11D-A27I-10	507800	45014770	18010750	82	42093										
UMODL1	89766	hgsc.bcm.edu	37	chr21	43547324	43547324	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	cgtctagcaacgcccgggacCccatcaccttcagcttcatt	7	17	4	0			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chr21:43547324C>A	ENST00000408910.2	+	19	3502	c.3502C>A	c.(3502-3504)Ccc>Acc	p.P1168T	UMODL1_ENST00000400427.1_Missense_Mutation_p.P1224T|UMODL1_ENST00000400424.2_Missense_Mutation_p.P1096T|UMODL1_ENST00000408989.2_Missense_Mutation_p.P1296T|UMODL1_ENST00000400423.2_3'UTR	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	1168	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				adipose tissue development (GO:0060612)|cellular response to gonadotropin-releasing hormone (GO:0097211)|multicellular organismal reproductive process (GO:0048609)|regulation of apoptotic process (GO:0042981)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|peptidase inhibitor activity (GO:0030414)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(22)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	47						CGCCCGGGACCCCATCACCTT	0.562																																					p.P1296T	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.C3886A						.						54	55	55					21																	43547324		1947	4142	6089	SO:0001583	missense	89766	exon18			CGGGACCCCATCA		CCDS42935.1, CCDS42936.1, CCDS56214.1, CCDS56215.1	21q22.3	2008-07-04			ENSG00000177398	ENSG00000177398			12560	protein-coding gene	gene with protein product	"olfactorin"	613859				16026467	Standard	NM_173568		Approved		uc002zag.1	Q5DID0	OTTHUMG00000086788	ENST00000408910.2:c.3502C>A	chr21.hg19:g.43547324C>A	ENSP00000386147:p.Pro1168Thr	147.0	0.0		165.0	41.0	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Missense_Mutation	SNP	ENST00000408910.2	hg19	CCDS42936.1	.	.	.	.	.	.	.	.	.	.	C	14.35	2.508534	0.44660	.	.	ENSG00000177398	ENST00000400427;ENST00000400424;ENST00000408989;ENST00000408910;ENST00000434156	T;T;T;T	0.81247	-1.47;-1.47;-1.47;-1.47	3.43	3.43	0.39272	Zona pellucida sperm-binding protein (3);	0.158174	0.28958	N	0.013597	D	0.86422	0.5929	L	0.60012	1.86	0.44976	D	0.997999	P;D	0.89917	0.846;1.0	P;D	0.77557	0.624;0.99	D	0.86107	0.1560	9	.	.	.	-34.6306	14.312	0.66422	0.0:1.0:0.0:0.0	.	1296;1168	Q5DID0-2;Q5DID0	.;UROL1_HUMAN	T	1224;1096;1296;1168;53	ENSP00000383279:P1224T;ENSP00000383276:P1096T;ENSP00000386126:P1296T;ENSP00000386147:P1168T	.	P	+	1	0	UMODL1	42420393	0.989000	0.36119	0.995000	0.50966	0.336000	0.28762	2.012000	0.40932	2.219000	0.72066	0.462000	0.41574	CCC	.	.		0.562	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2			A	43547324	C	A	43547324	3	1	286	1	0	0	0	0	1	0	0	0	16995	623	22	3	3956	3	UMODL1	21	43547324	Missense_Mutation	SNP	C	TCGA-G3-A5SK-01A-11D-A27I-10		43547324	4582571	83	42094										
CXorf59	286464	hgsc.bcm.edu	37	chrX	36103589	36103589	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	ttcaagtcaatctttacctgTagataaccatgaaaaaaggg	7	7	3	2			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chrX:36103589T>C	ENST00000313548.4	+	5	761	c.575T>C	c.(574-576)gTa>gCa	p.V192A		NM_173695.2	NP_775966.1	Q8N9S7	CHDC2_HUMAN	calponin homology domain containing 2	192						integral component of membrane (GO:0016021)											TCTTTACCTGTAGATAACCAT	0.358																																					p.V192A		Atlas-SNP	.											.	.	.	.	0			c.T575C						.						82	76	78					X																	36103589		2202	4300	6502	SO:0001583	missense	286464	exon5			TACCTGTAGATAA	AK093920	CCDS14238.1	Xp21.1	2014-08-07	2012-11-28	2012-11-28	ENSG00000176034	ENSG00000176034			26708	protein-coding gene	gene with protein product			"chromosome X open reading frame 59"	CXorf59			Standard	NM_173695		Approved	FLJ36601, RP13-11B7.1	uc004ddk.1	Q8N9S7	OTTHUMG00000021351	ENST00000313548.4:c.575T>C	chrX.hg19:g.36103589T>C	ENSP00000324767:p.Val192Ala	58.0	0.0		69.0	52.0	NM_173695		Missense_Mutation	SNP	ENST00000313548.4	hg19	CCDS14238.1	.	.	.	.	.	.	.	.	.	.	T	2.062	-0.415058	0.04766	.	.	ENSG00000176034	ENST00000378660;ENST00000313548	.	.	.	5.9	-1.31	0.09230	.	1.343430	0.05103	N	0.487525	T	0.18087	0.0434	N	0.19112	0.55	0.09310	N	1	B	0.15473	0.013	B	0.08055	0.003	T	0.13899	-1.0492	9	0.16420	T	0.52	0.0922	0.2529	0.00208	0.2811:0.2452:0.1426:0.3311	.	192	Q8N9S7	CX059_HUMAN	A	192	.	ENSP00000324767:V192A	V	+	2	0	CXorf59	36013510	0.006000	0.16342	0.000000	0.03702	0.007000	0.05969	-0.218000	0.09240	-0.248000	0.09583	0.486000	0.48141	GTA	.	.		0.358	CHDC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_173695		C	36103589	T	C	36103589	3	2	286	1	0	0	0	0	1	0	0	0	4117	1638	57	2	589	2	CXorf59	23	36103589	Missense_Mutation	SNP	T	TCGA-G3-A5SK-01A-11D-A27I-10		36103589	119166971	84	42095										
KIAA2022	340533	hgsc.bcm.edu	37	chrX	73962088	73962088	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	tcagatagacgggaactgttTgatgtcccaggaataacttc	10	8	1	3			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chrX:73962088T>A	ENST00000055682.6	-	3	2915	c.2304A>T	c.(2302-2304)tcA>tcT	p.S768S		NM_001008537.2	NP_001008537.1	Q5QGS0	K2022_HUMAN	KIAA2022	768					base-excision repair, gap-filling (GO:0006287)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|nervous system development (GO:0007399)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)	delta DNA polymerase complex (GO:0043625)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|DNA-directed DNA polymerase activity (GO:0003887)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(23)|liver(1)|lung(41)|ovary(7)|pancreas(2)|prostate(4)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	109						GGGAACTGTTTGATGTCCCAG	0.418																																					p.S768S		Atlas-SNP	.											.	KIAA2022	262	.	0			c.A2304T						.						76	72	73					X																	73962088		2203	4298	6501	SO:0001819	synonymous_variant	340533	exon3			ACTGTTTGATGTC		CCDS35337.1	Xq13.3	2014-02-19			ENSG00000050030	ENSG00000050030			29433	protein-coding gene	gene with protein product	"XLMR-related protein, neurite extension"	300524				15466006, 23615299	Standard	NM_001008537		Approved	XPN, MRX98	uc004eby.3	Q5QGS0	OTTHUMG00000021860	ENST00000055682.6:c.2304A>T	chrX.hg19:g.73962088T>A		62.0	0.0		85.0	63.0	NM_001008537	A7YY87|Q5JUX9|Q8IVE9	Silent	SNP	ENST00000055682.6	hg19	CCDS35337.1																																																																																			.	.		0.418	KIAA2022-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057270.2	NM_001008537		A	73962088	T	A	73962088	2	1	286	1	0	0	0	0	0	0	0	1	8278	1799	63	4		4	KIAA2022	23	73962088	Silent	SNP	T	TCGA-G3-A5SK-01A-11D-A27I-10	37858499	73962088	81308472	85	42096										
SLITRK2	84631	hgsc.bcm.edu	37	chrX	144905414	144905414	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	ggtccttacctgataatataTttggggggacggccctaacc	11	10	0	1			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chrX:144905414T>A	ENST00000370490.1	+	1	5726	c.1471T>A	c.(1471-1473)Ttt>Att	p.F491I	SLITRK2_ENST00000413937.2_Missense_Mutation_p.F491I|SLITRK2_ENST00000434188.2_Missense_Mutation_p.F491I|SLITRK2_ENST00000428560.2_Missense_Mutation_p.F491I|SLITRK2_ENST00000447897.2_Missense_Mutation_p.F491I			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	491					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					TGATAATATATTTGGGGGGAC	0.453																																					p.F491I		Atlas-SNP	.											.	SLITRK2	221	.	0			c.T1471A						.						113	120	118					X																	144905414		2203	4300	6503	SO:0001583	missense	84631	exon5			AATATATTTGGGG	Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"slit-like 1 (Drosophila)"	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.1471T>A	chrX.hg19:g.144905414T>A	ENSP00000359521:p.Phe491Ile	41.0	0.0		121.0	38.0	NM_001144005	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Missense_Mutation	SNP	ENST00000370490.1	hg19	CCDS14680.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.189642	0.78789	.	.	ENSG00000185985	ENST00000335565;ENST00000447897;ENST00000370490;ENST00000434188;ENST00000413937;ENST00000428560	T;T;T;T;T;T	0.58797	0.31;0.31;0.31;0.31;0.31;0.31	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.81432	0.4821	M	0.93939	3.475	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	D	0.86052	0.1526	10	0.87932	D	0	-8.0912	12.9065	0.58156	0.0:0.0:0.0:1.0	.	491	Q9H156	SLIK2_HUMAN	I	491	ENSP00000334374:F491I;ENSP00000411681:F491I;ENSP00000359521:F491I;ENSP00000397015:F491I;ENSP00000407347:F491I;ENSP00000412010:F491I	ENSP00000334374:F491I	F	+	1	0	SLITRK2	144713106	1.000000	0.71417	1.000000	0.80357	0.808000	0.45660	8.040000	0.89188	1.955000	0.56771	0.486000	0.48141	TTT	.	.		0.453	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539		A	144905414	T	A	144905414	3	1	286	1	0	0	0	0	1	0	0	0	14758	1493	52	4	1473	4	SLITRK2	23	144905414	Missense_Mutation	SNP	T	TCGA-G3-A5SK-01A-11D-A27I-10	70943326	144905414	10365146	86	42097										
GABRQ	55879	hgsc.bcm.edu	37	chrX	151818957	151818957	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.25763862693323	1.84453665283541	0.76855693868142	0.592074592074592	1	0	taacagctaccttgtgcaagTctactggcctactgtcctca	7	13	2	0			TCGA-G3-A5SK-01A-11D-A27I-10	TCGA-G3-A5SK-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	30544c96-0217-45e7-98dc-3dcbf4cf5ab3	2acbefee-83af-414b-8ddf-9f823a91bb22	g.chrX:151818957T>C	ENST00000370306.2	+	7	835	c.815T>C	c.(814-816)gTc>gCc	p.V272A		NM_018558.2	NP_061028.3	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) A receptor, theta	272					neurotransmitter transport (GO:0006836)|signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|neurotransmitter transporter activity (GO:0005326)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(9)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	52	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CTTGTGCAAGTCTACTGGCCT	0.483																																					p.V272A		Atlas-SNP	.											.	GABRQ	131	.	0			c.T815C						.						367	297	321					X																	151818957		2203	4300	6503	SO:0001583	missense	55879	exon7			TGCAAGTCTACTG	U47334	CCDS14707.1	Xq28	2012-06-22	2012-02-03		ENSG00000147402	ENSG00000268089		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	14454	protein-coding gene	gene with protein product	"GABA(A) receptor, theta"	300349	"gamma-aminobutyric acid (GABA) receptor, theta"			10804200, 10449790	Standard	NM_018558		Approved	THETA	uc004ffp.1	Q9UN88	OTTHUMG00000022649	ENST00000370306.2:c.815T>C	chrX.hg19:g.151818957T>C	ENSP00000359329:p.Val272Ala	148.0	0.0		445.0	171.0	NM_018558	A6NFN1|Q32MB4|Q9NZK8	Missense_Mutation	SNP	ENST00000370306.2	hg19	CCDS14707.1	.	.	.	.	.	.	.	.	.	.	T	17.43	3.387602	0.61956	.	.	ENSG00000147402	ENST00000370306	D	0.85955	-2.05	6.01	4.88	0.63580	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.429650	0.19931	N	0.102873	T	0.76630	0.4014	L	0.28400	0.85	0.31351	N	0.682548	P	0.42456	0.78	B	0.43301	0.415	T	0.78575	-0.2151	10	0.66056	D	0.02	.	3.9603	0.09407	0.0:0.2646:0.0:0.7354	.	272	Q9UN88	GBRT_HUMAN	A	272	ENSP00000359329:V272A	ENSP00000359329:V272A	V	+	2	0	GABRQ	151569613	1.000000	0.71417	0.743000	0.31040	0.327000	0.28475	6.109000	0.71528	2.019000	0.59389	0.451000	0.29950	GTC	.	.		0.483	GABRQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058763.2	NM_018558		C	151818957	T	C	151818957	3	2	286	1	0	0	0	0	1	0	0	0	6183	1667	58	2	841	2	GABRQ	23	151818957	Missense_Mutation	SNP	T	TCGA-G3-A5SK-01A-11D-A27I-10	6913543	151818957	3451603	87	42098										
KIAA0562	9731	hgsc.bcm.edu	37	chr1	3750533	3750533	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	gtgagctgtttcaagtttacTcagtttatgtttaggaatat	9	4	2	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr1:3750533T>A	ENST00000378230.3	-	12	1876	c.1552A>T	c.(1552-1554)Agt>Tgt	p.S518C	CEP104_ENST00000460038.1_5'UTR	NM_014704.3	NP_055519.1	O60308	CE104_HUMAN	centrosomal protein 104kDa	518						centriole (GO:0005814)	glutamate binding (GO:0016595)|glycine binding (GO:0016594)|thienylcyclohexylpiperidine binding (GO:0016596)			breast(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(14)|lung(8)|prostate(1)|skin(3)	39						TCAAGTTTACTCAGTTTATGT	0.408																																					p.S518C		Atlas-SNP	.											.	CEP104	79	.	0			c.A1552T						.						125	116	119					1																	3750533		2203	4300	6503	SO:0001583	missense	9731	exon12			GTTTACTCAGTTT	AB011134	CCDS30571.1	1p36.32	2014-02-20	2011-05-06	2011-05-06	ENSG00000116198	ENSG00000116198			24866	protein-coding gene	gene with protein product	"glycine, glutamate, thienylcyclohexylpiperidine binding protein"		"KIAA0562"	KIAA0562		7488117, 21399614	Standard	NM_014704		Approved	GlyBP, RP1-286D6.4	uc001aky.2	O60308	OTTHUMG00000003507	ENST00000378230.3:c.1552A>T	chr1.hg19:g.3750533T>A	ENSP00000367476:p.Ser518Cys	148.0	0.0		93.0	30.0	NM_014704	Q5JSQ3|Q5SR24|Q5SR25|Q6PKF5|Q86W32|Q86X14	Missense_Mutation	SNP	ENST00000378230.3	hg19	CCDS30571.1	.	.	.	.	.	.	.	.	.	.	T	11.57	1.677602	0.29783	.	.	ENSG00000116198	ENST00000378230	T	0.35048	1.33	5.03	-3.6	0.04570	Armadillo-like helical (1);Armadillo-type fold (1);	0.242072	0.41605	D	0.000856	T	0.44540	0.1298	L	0.50333	1.59	0.26083	N	0.98106	D;P	0.61697	0.99;0.793	P;B	0.58970	0.849;0.386	T	0.51957	-0.8639	10	0.59425	D	0.04	.	15.3311	0.74212	0.0:0.8128:0.0:0.1872	.	518;518	O60308-3;O60308	.;CE104_HUMAN	C	518	ENSP00000367476:S518C	ENSP00000367476:S518C	S	-	1	0	CEP104	3740393	0.660000	0.27420	0.040000	0.18447	0.046000	0.14306	0.560000	0.23500	-0.605000	0.05753	0.383000	0.25322	AGT	.	.		0.408	CEP104-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009747.3	NM_014704		A	3750533	T	A	3750533	3	1	287	1	0	0	0	0	1	0	0	0	8193	1551	54	4	1269	4	KIAA0562	1	3750533	Missense_Mutation	SNP	T	TCGA-G3-A5SL-01A-11D-A27I-10		3750533	245500088	1	42099										
AKR7A2	8574	hgsc.bcm.edu	37	chr1	19634996	19634996	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	cagcgtctcttccaccggggTgccgtggtcaggtgcgtgta	15	12	2	0			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr1:19634996T>C	ENST00000235835.3	-	2	460	c.439A>G	c.(439-441)Acc>Gcc	p.T147A		NM_003689.3	NP_003680.2	O43488	ARK72_HUMAN	aldo-keto reductase family 7, member A2 (aflatoxin aldehyde reductase)	147					carbohydrate metabolic process (GO:0005975)|cellular aldehyde metabolic process (GO:0006081)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|electron carrier activity (GO:0009055)|phenanthrene-9,10-epoxide hydrolase activity (GO:0019119)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00461)|BRCA - Breast invasive adenocarcinoma(304;1.83e-05)|Kidney(64;0.000167)|GBM - Glioblastoma multiforme(114;0.00115)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		TCCACCGGGGTGCCGTGGTCA	0.612																																					p.T147A		Atlas-SNP	.											.	AKR7A2	19	.	0			c.A439G						.						60	61	61					1																	19634996		2203	4300	6503	SO:0001583	missense	8574	exon2			CCGGGGTGCCGTG	AF026947	CCDS194.1	1p36.13	2010-09-30			ENSG00000053371	ENSG00000053371		"Aldo-keto reductases"	389	protein-coding gene	gene with protein product		603418				9576847	Standard	NM_003689		Approved	AFAR	uc001bbw.3	O43488	OTTHUMG00000002522	ENST00000235835.3:c.439A>G	chr1.hg19:g.19634996T>C	ENSP00000235835:p.Thr147Ala	163.0	0.0		115.0	41.0	NM_003689	O75749|Q5TG63	Missense_Mutation	SNP	ENST00000235835.3	hg19	CCDS194.1	.	.	.	.	.	.	.	.	.	.	T	14.96	2.691947	0.48097	.	.	ENSG00000053371	ENST00000235835;ENST00000330072	T;T	0.04862	3.54;3.54	4.09	4.09	0.47781	NADP-dependent oxidoreductase domain (3);	0.048531	0.85682	D	0.000000	T	0.19406	0.0466	M	0.87971	2.92	0.38686	D	0.952661	B;B;B	0.32573	0.376;0.376;0.245	B;B;B	0.44315	0.353;0.446;0.353	T	0.03231	-1.1058	10	0.66056	D	0.02	.	12.3145	0.54948	0.0:0.0:0.0:1.0	.	118;118;147	C9JSL3;B4DZX4;O43488	.;.;ARK72_HUMAN	A	147;137	ENSP00000235835:T147A;ENSP00000339084:T137A	ENSP00000235835:T147A	T	-	1	0	AKR7A2	19507583	1.000000	0.71417	0.608000	0.28969	0.029000	0.11900	5.663000	0.68038	1.834000	0.53371	0.459000	0.35465	ACC	.	.		0.612	AKR7A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007165.2	NM_003689		C	19634996	T	C	19634996	3	2	287	1	0	0	0	0	1	0	0	0	475	1696	59	2	664	2	AKR7A2	1	19634996	Missense_Mutation	SNP	T	TCGA-G3-A5SL-01A-11D-A27I-10	15884463	19634996	229615625	2	42100										
NR0B2	8431	hgsc.bcm.edu	37	chr1	27240341	27240341	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	gctacggggtcgggggacagCcttgaggctggagctcagaa	18	9	1	2			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr1:27240341C>T	ENST00000254227.3	-	1	116	c.91G>A	c.(91-93)Gct>Act	p.A31T		NM_021969.2	NP_068804.1	Q15466	NR0B2_HUMAN	nuclear receptor subfamily 0, group B, member 2	31					cholesterol metabolic process (GO:0008203)|gene expression (GO:0010467)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ regeneration (GO:0031100)|positive regulation of insulin secretion (GO:0032024)|response to glucose (GO:0009749)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription corepressor activity (GO:0003714)			NS(1)|large_intestine(1)|lung(3)	5		all_cancers(24;1.23e-26)|all_epithelial(13;1.19e-23)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Breast(348;0.00017)|Renal(390;0.0007)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.01e-51)|OV - Ovarian serous cystadenocarcinoma(117;8.22e-30)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419)		CGGGGGACAGCCTTGAGGCTG	0.652																																					p.A31T		Atlas-SNP	.											.	NR0B2	14	.	0			c.G91A						.						42	43	42					1																	27240341		2203	4300	6503	SO:0001583	missense	8431	exon1			GGACAGCCTTGAG	AF044316	CCDS291.1	1p36.1	2013-01-16			ENSG00000131910	ENSG00000131910		"Nuclear hormone receptors"	7961	protein-coding gene	gene with protein product		604630				9603951	Standard	NM_021969		Approved	SHP	uc001bnf.3	Q15466	OTTHUMG00000004231	ENST00000254227.3:c.91G>A	chr1.hg19:g.27240341C>T	ENSP00000254227:p.Ala31Thr	41.0	0.0		34.0	10.0	NM_021969	F1D8P5|Q5QP36	Missense_Mutation	SNP	ENST00000254227.3	hg19	CCDS291.1	.	.	.	.	.	.	.	.	.	.	C	7.499	0.652276	0.14580	.	.	ENSG00000131910	ENST00000254227	D	0.84730	-1.89	5.15	0.621	0.17643	Nuclear hormone receptor, ligand-binding (2);	0.721913	0.14257	N	0.331062	T	0.65790	0.2725	N	0.16478	0.41	0.23043	N	0.99839	B	0.06786	0.001	B	0.04013	0.001	T	0.48234	-0.9053	10	0.08179	T	0.78	-11.7277	3.7527	0.08573	0.2341:0.2409:0.4392:0.0857	.	31	Q15466	NR0B2_HUMAN	T	31	ENSP00000254227:A31T	ENSP00000254227:A31T	A	-	1	0	NR0B2	27112928	0.017000	0.18338	0.990000	0.47175	0.711000	0.40976	-0.441000	0.06879	0.131000	0.18576	-0.311000	0.09066	GCT	.	.		0.652	NR0B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012185.1			T	27240341	C	T	27240341	3	4	287	1	0	0	0	0	1	0	0	0	10623	739	26	3	690	3	NR0B2	1	27240341	Missense_Mutation	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10	7605345	27240341	222010280	3	42101										
ANGPTL3	27329	hgsc.bcm.edu	37	chr1	63063267	63063267	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	attaagctccttctttttatTgttcctctagttatttcctc	3	10	2	0			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr1:63063267T>A	ENST00000371129.3	+	1	110	c.30T>A	c.(28-30)atT>atA	p.I10I	DOCK7_ENST00000251157.5_Intron|DOCK7_ENST00000340370.5_Intron|DOCK7_ENST00000404627.2_Intron	NM_014495.2	NP_055310.1	Q9Y5C1	ANGL3_HUMAN	angiopoietin-like 3	10					acylglycerol homeostasis (GO:0055090)|artery morphogenesis (GO:0048844)|cell-matrix adhesion (GO:0007160)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|fatty acid metabolic process (GO:0006631)|glycerol metabolic process (GO:0006071)|integrin-mediated signaling pathway (GO:0007229)|lipid homeostasis (GO:0055088)|lipid storage (GO:0019915)|negative regulation of lipoprotein lipase activity (GO:0051005)|negative regulation of phospholipase activity (GO:0010519)|phospholipid catabolic process (GO:0009395)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of lipid catabolic process (GO:0050996)|response to hormone (GO:0009725)|signal transduction (GO:0007165)|triglyceride homeostasis (GO:0070328)	cell surface (GO:0009986)|extracellular space (GO:0005615)	enzyme inhibitor activity (GO:0004857)|growth factor activity (GO:0008083)|integrin binding (GO:0005178)|phospholipase inhibitor activity (GO:0004859)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(3)|urinary_tract(1)	13						TTCTTTTTATTGTTCCTCTAG	0.338																																					p.X10X		Atlas-SNP	.											.	ANGPTL3	42	.	0			c.A30A						.						93	85	88					1																	63063267		2203	4299	6502	SO:0001819	synonymous_variant	27329	exon1			TTTTATTGTTCCT	AF152562	CCDS622.1	1p31.3	2013-02-06			ENSG00000132855	ENSG00000132855		"Fibrinogen C domain containing"	491	protein-coding gene	gene with protein product	"angiopoietin 5"	604774		ANGPT5		10644446	Standard	NM_014495		Approved		uc001das.2	Q9Y5C1	OTTHUMG00000009146	ENST00000371129.3:c.30T>A	chr1.hg19:g.63063267T>A		54.0	0.0		47.0	16.0	NM_014495	A0JLS0|B1ALJ0|B2RCW1	Silent	SNP	ENST00000371129.3	hg19	CCDS622.1																																																																																			.	.		0.338	ANGPTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025344.1	NM_014495		A	63063267	T	A	63063267	2	1	287	1	0	0	0	0	0	0	0	1	615	1800	63	4		4	ANGPTL3	1	63063267	Silent	SNP	T	TCGA-G3-A5SL-01A-11D-A27I-10	35822926	63063267	186187354	4	42102										
CLCA1	1179	hgsc.bcm.edu	37	chr1	86964423	86964423	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	ccaaatcaccgacctgaaggCggaaattcacgggggcagtc	12	12	2	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr1:86964423C>T	ENST00000234701.3	+	14	2633	c.2282C>T	c.(2281-2283)gCg>gTg	p.A761V	CLCA1_ENST00000394711.1_Missense_Mutation_p.A761V			A8K7I4	CLCA1_HUMAN	chloride channel accessory 1	761					calcium ion transport (GO:0006816)|cellular response to hypoxia (GO:0071456)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|zymogen granule membrane (GO:0042589)	chloride channel activity (GO:0005254)			NS(1)|breast(3)|endometrium(1)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Lung NSC(277;0.239)		all cancers(265;0.0249)|Epithelial(280;0.0476)		GACCTGAAGGCGGAAATTCAC	0.517																																					p.A761V		Atlas-SNP	.											.	CLCA1	109	.	0			c.C2282T						.						108	98	101					1																	86964423		2203	4300	6503	SO:0001583	missense	1179	exon13			TGAAGGCGGAAAT		CCDS709.1	1p22.3	2012-02-26	2009-01-29		ENSG00000016490	ENSG00000016490			2015	protein-coding gene	gene with protein product		603906	"chloride channel, calcium activated, family member 1", "chloride channel regulator 1"			9828122	Standard	NM_001285		Approved	CaCC, CLCRG1	uc001dlt.3	A8K7I4	OTTHUMG00000010254	ENST00000234701.3:c.2282C>T	chr1.hg19:g.86964423C>T	ENSP00000234701:p.Ala761Val	138.0	0.0		132.0	25.0	NM_001285	B2RAV5|O95151|Q5TDF4|Q9UNF6|Q9UPC6	Missense_Mutation	SNP	ENST00000234701.3	hg19	CCDS709.1	.	.	.	.	.	.	.	.	.	.	C	17.27	3.346440	0.61073	.	.	ENSG00000016490	ENST00000234701;ENST00000394711	T;T	0.38240	1.15;1.15	5.79	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.46308	0.1386	M	0.67953	2.075	0.37364	D	0.911347	D	0.89917	1.0	D	0.91635	0.999	T	0.45789	-0.9237	10	0.30854	T	0.27	-16.0434	14.7865	0.69808	0.1455:0.8545:0.0:0.0	.	761	A8K7I4	CLCA1_HUMAN	V	761	ENSP00000234701:A761V;ENSP00000378200:A761V	ENSP00000234701:A761V	A	+	2	0	CLCA1	86737011	0.962000	0.33011	0.878000	0.34440	0.469000	0.32828	3.238000	0.51352	1.400000	0.46741	0.655000	0.94253	GCG	.	.		0.517	CLCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028277.1	NM_001285		T	86964423	C	T	86964423	3	4	287	1	0	0	0	0	1	0	0	0	3459	768	27	1	2332	1	CLCA1	1	86964423	Missense_Mutation	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10	23901156	86964423	162286198	5	42103										
BCL9	607	hgsc.bcm.edu	37	chr1	147086412	147086412	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	gttttctactgagatggccaAtaagtaagttgatggctgtg	12	5	1	2			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr1:147086412A>G	ENST00000234739.3	+	6	1297	c.557A>G	c.(556-558)aAt>aGt	p.N186S	BCL9_ENST00000473292.1_3'UTR	NM_004326.2	NP_004317.2	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	186	Interacts with PYGO1.				canonical Wnt signaling pathway (GO:0060070)|myotube differentiation involved in skeletal muscle regeneration (GO:0014908)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				breast(1)|large_intestine(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	7	all_hematologic(923;0.115)					GAGATGGCCAATAAGTAAGTT	0.473			T	"IGH@, IGL@"	B-ALL																																p.N186S		Atlas-SNP	.		Dom	yes		1	1q21	607	B-cell CLL/lymphoma 9		L	.	BCL9	150	.	0			c.A557G						.						79	72	74					1																	147086412		2203	4300	6503	SO:0001583	missense	607	exon6			TGGCCAATAAGTA	Y13620	CCDS30833.1	1q21	2008-02-05			ENSG00000116128	ENSG00000116128			1008	protein-coding gene	gene with protein product		602597				9490669	Standard	NM_004326		Approved		uc001epq.3	O00512	OTTHUMG00000014031	ENST00000234739.3:c.557A>G	chr1.hg19:g.147086412A>G	ENSP00000234739:p.Asn186Ser	162.0	0.0		180.0	63.0	NM_004326	Q5T489	Missense_Mutation	SNP	ENST00000234739.3	hg19	CCDS30833.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.687915	0.88639	.	.	ENSG00000116128	ENST00000234739	T	0.67171	-0.25	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.74535	0.3729	L	0.57536	1.79	0.80722	D	1	D;D	0.63880	0.993;0.993	D;D	0.72625	0.978;0.978	T	0.77970	-0.2387	10	0.87932	D	0	-13.7433	15.8615	0.79026	1.0:0.0:0.0:0.0	.	186;186	Q1JQ81;O00512	.;BCL9_HUMAN	S	186	ENSP00000234739:N186S	ENSP00000234739:N186S	N	+	2	0	BCL9	145553036	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.735000	0.91549	2.333000	0.79357	0.533000	0.62120	AAT	.	.		0.473	BCL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039468.1	NM_004326		G	147086412	A	G	147086412	3	3	287	1	0	0	0	0	1	0	0	0	1381	101	4	2	567	2	BCL9	1	147086412	Missense_Mutation	SNP	A	TCGA-G3-A5SL-01A-11D-A27I-10	60121989	147086412	102164209	6	42104										
FCRL1	115350	hgsc.bcm.edu	37	chr1	157768011	157768011	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	gttgaggtaggtgaactcttGgggtagagggctgggaaggc	20	4	1	3			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr1:157768011G>T	ENST00000368176.3	-	8	1121	c.1054C>A	c.(1054-1056)Caa>Aaa	p.Q352K	FCRL1_ENST00000358292.3_Missense_Mutation_p.Q313K|FCRL1_ENST00000489998.1_5'UTR|FCRL1_ENST00000491942.1_Missense_Mutation_p.Q352K	NM_001159398.1|NM_052938.4	NP_001152870.1|NP_443170.1	Q96LA6	FCRL1_HUMAN	Fc receptor-like 1	352						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(24)|ovary(4)|prostate(1)|skin(6)	42	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			GTGAACTCTTGGGGTAGAGGG	0.498																																					p.Q352K	GBM(54;482 1003 11223 30131 35730)	Atlas-SNP	.											.	FCRL1	164	.	0			c.C1054A						.						118	113	114					1																	157768011		2203	4300	6503	SO:0001583	missense	115350	exon8			ACTCTTGGGGTAG	BC033690	CCDS1170.1, CCDS53382.1, CCDS53383.1	1q21-q22	2013-01-14			ENSG00000163534	ENSG00000163534		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18509	protein-coding gene	gene with protein product		606508				11493702, 11929751	Standard	NM_052938		Approved	FCRH1, IRTA5, IFGP1, CD307a	uc001frg.3	Q96LA6	OTTHUMG00000019398	ENST00000368176.3:c.1054C>A	chr1.hg19:g.157768011G>T	ENSP00000357158:p.Gln352Lys	78.0	0.0		173.0	10.0	NM_001159398	B2RE05|Q8N759|Q8NDI0|Q96PJ6	Missense_Mutation	SNP	ENST00000368176.3	hg19	CCDS1170.1	.	.	.	.	.	.	.	.	.	.	G	16.40	3.113035	0.56398	.	.	ENSG00000163534	ENST00000358292;ENST00000368176;ENST00000491942	T;T;T	0.42131	0.98;1.1;1.11	4.79	2.9	0.33743	.	3.842740	0.00397	N	0.000042	T	0.41190	0.1148	M	0.82323	2.585	0.09310	N	0.999997	P;D;B	0.61080	0.573;0.989;0.437	B;P;B	0.58620	0.23;0.842;0.115	T	0.16394	-1.0404	10	0.11794	T	0.64	.	6.0588	0.19826	0.0959:0.0:0.7183:0.1859	.	313;352;352	Q96LA6-3;Q96LA6-2;Q96LA6	.;.;FCRL1_HUMAN	K	313;352;352	ENSP00000351039:Q313K;ENSP00000357158:Q352K;ENSP00000418130:Q352K	ENSP00000351039:Q313K	Q	-	1	0	FCRL1	156034635	0.186000	0.23225	0.096000	0.21009	0.225000	0.24961	2.491000	0.45303	0.715000	0.32103	0.591000	0.81541	CAA	.	.		0.498	FCRL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051401.1	NM_052938		T	157768011	G	T	157768011	3	4	287	1	0	0	0	0	1	0	0	0	5802	1357	47	3	317	3	FCRL1	1	157768011	Missense_Mutation	SNP	G	TCGA-G3-A5SL-01A-11D-A27I-10	10681599	157768011	91482610	7	42105										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158614175	158614175	+	Frame_Shift_Del	DEL	C	C	-													0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	ctctcaacttgatcacagttCccctggaacatctatgagga							TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr1:158614175delC	ENST00000368147.4	-	30	4386	c.4206delG	c.(4204-4206)gggfs	p.G1402fs		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1402					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					GATCACAGTTCCCCTGGAACA	0.453																																					p.N1403fs		Atlas-Indel,Pindel	.											.	SPTA1	720	.	0			c.4207delA						.						93	90	91					1																	158614175		1953	4149	6102	SO:0001589	frameshift_variant	6708	exon30			.	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.4206delG	chr1.hg19:g.158614175delC	ENSP00000357129:p.Gly1402fs	77.0	0.0		163.0	42.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Frame_Shift_Del	DEL	ENST00000368147.4	hg19	CCDS41423.1																																																																																			.	.		0.453	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		-	158614175	C	-	158614175	7	5	287	1	0	1	0	1	0	0	0	0	15131	842	30	0	3145	0	SPTA1	1	158614175	Frame_Shift_Del	DEL	C	TCGA-G3-A5SL-01A-11D-A27I-10	846164	158614175	90636446	8	42106										
MNDA	4332	hgsc.bcm.edu	37	chr1	158813151	158813151	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	ggtcttgcggcacctgcaccCaccgcaagaaacaaactgac	9	15	1	2			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr1:158813151C>T	ENST00000368141.4	+	3	609	c.348C>T	c.(346-348)ccC>ccT	p.P116P		NM_002432.1	NP_002423.1	P41218	MNDA_HUMAN	myeloid cell nuclear differentiation antigen	116					B cell receptor signaling pathway (GO:0050853)|cellular defense response (GO:0006968)|cellular response to DNA damage stimulus (GO:0006974)|negative regulation of B cell proliferation (GO:0030889)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.P116P(1)		NS(2)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(26)|ovary(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	all_hematologic(112;0.0378)					CACCTGCACCCACCGCAAGAA	0.438																																					p.P116P		Atlas-SNP	.											MNDA,NS,carcinoma,0,1	MNDA	147	.	1	Substitution - coding silent(1)	lung(1)	c.C348T						.						60	54	56					1																	158813151		2203	4300	6503	SO:0001819	synonymous_variant	4332	exon3			TGCACCCACCGCA	BC032319	CCDS1177.1	1q22	2008-02-05			ENSG00000163563	ENSG00000163563			7183	protein-coding gene	gene with protein product		159553				1644857, 7512843	Standard	NM_002432		Approved	PYHIN3	uc001fsz.1	P41218	OTTHUMG00000022776	ENST00000368141.4:c.348C>T	chr1.hg19:g.158813151C>T		181.0	0.0		315.0	65.0	NM_002432		Silent	SNP	ENST00000368141.4	hg19	CCDS1177.1																																																																																			.	.		0.438	MNDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059069.1	NM_002432		T	158813151	C	T	158813151	2	4	287	1	0	0	0	0	0	0	0	1	9685	581	21	3		3	MNDA	1	158813151	Silent	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10	198976	158813151	90437470	9	42107										
TAGLN2	8407	hgsc.bcm.edu	37	chr1	159888612	159888612	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	agaggatctggcgtggcatcCcgtagccagtcatgcctgcc	13	13	2	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr1:159888612C>T	ENST00000368097.4	-	5	888	c.578G>A	c.(577-579)gGg>gAg	p.G193E	TAGLN2_ENST00000478033.1_5'UTR|TAGLN2_ENST00000320307.4_Missense_Mutation_p.G193E|TAGLN2_ENST00000368096.1_Missense_Mutation_p.G214E	NM_001277223.1|NM_003564.1	NP_001264152.1|NP_003555.1	P37802	TAGL2_HUMAN	transgelin 2	193					epithelial cell differentiation (GO:0030855)	extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)				endometrium(1)|large_intestine(2)|lung(6)	9	all_hematologic(112;0.0597)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GCGTGGCATCCCGTAGCCAGT	0.547																																					p.G193E		Atlas-SNP	.											.	TAGLN2	21	.	0			c.G578A						.						74	70	72					1																	159888612		2203	4300	6503	SO:0001583	missense	8407	exon5			GGCATCCCGTAGC	D21261	CCDS1189.1, CCDS60314.1	1q21-q25	2008-07-18			ENSG00000158710	ENSG00000158710			11554	protein-coding gene	gene with protein product	"SM22-alpha homolog"	604634				9693045	Standard	NM_001277223		Approved	KIAA0120, HA1756	uc031pqu.1	P37802	OTTHUMG00000022793	ENST00000368097.4:c.578G>A	chr1.hg19:g.159888612C>T	ENSP00000357077:p.Gly193Glu	151.0	0.0		134.0	84.0	NM_003564	E9KL39|Q5JRQ6|Q5JRQ7|Q6FGI1|Q9BUH5|Q9H4P0	Missense_Mutation	SNP	ENST00000368097.4	hg19	CCDS1189.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.897766	0.91962	.	.	ENSG00000158710	ENST00000368097;ENST00000368096;ENST00000320307	D;D;D	0.95307	-3.67;-3.67;-3.67	4.65	4.65	0.58169	Calponin homology domain (1);	0.000000	0.44688	U	0.000439	D	0.97920	0.9316	H	0.95504	3.68	0.80722	D	1	D	0.59767	0.986	D	0.72338	0.977	D	0.98696	1.0698	9	.	.	.	-20.4017	15.3984	0.74816	0.0:1.0:0.0:0.0	.	193	P37802	TAGL2_HUMAN	E	193;214;193	ENSP00000357077:G193E;ENSP00000357076:G214E;ENSP00000357075:G193E	.	G	-	2	0	TAGLN2	158155236	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.015000	0.76387	2.573000	0.86826	0.655000	0.94253	GGG	.	.		0.547	TAGLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059105.1	NM_003564		T	159888612	C	T	159888612	3	4	287	1	0	0	0	0	1	0	0	0	15554	623	22	3	25	3	TAGLN2	1	159888612	Missense_Mutation	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10	1075461	159888612	89362009	10	42108										
FAM5B	57795	hgsc.bcm.edu	37	chr1	177245347	177245347	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	tccccaggccttcaggtgctGctgcctgagtatctgcgtga	12	13	2	2			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr1:177245347G>A	ENST00000361539.4	+	6	1101	c.789G>A	c.(787-789)ctG>ctA	p.L263L	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	263	MACPF.				cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	extracellular region (GO:0005576)											TTCAGGTGCTGCTGCCTGAGT	0.557																																					p.L263L		Atlas-SNP	.											FAM5B,caecum,carcinoma,0,1	FAM5B	191	.	0			c.G789A						.						64	62	63					1																	177245347		2203	4300	6503	SO:0001819	synonymous_variant	57795	exon6			GGTGCTGCTGCCT		CCDS1320.1	1q24	2013-08-06	2013-08-06	2013-07-31	ENSG00000198797	ENSG00000198797			13746	protein-coding gene	gene with protein product			"family with sequence similarity 5, member B"	FAM5B		15193423	Standard	NM_021165		Approved	DBCCR1L2	uc001glf.3	Q9C0B6	OTTHUMG00000034953	ENST00000361539.4:c.789G>A	chr1.hg19:g.177245347G>A		143.0	0.0		240.0	27.0	NM_021165	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Silent	SNP	ENST00000361539.4	hg19	CCDS1320.1																																																																																			.	.		0.557	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1	NM_021165		A	177245347	G	A	177245347	2	1	287	1	0	0	0	0	0	0	0	1	5601	1306	46	3		3	FAM5B	1	177245347	Silent	SNP	G	TCGA-G3-A5SL-01A-11D-A27I-10	17356735	177245347	72005274	11	42109										
PLA2G4A	5321	hgsc.bcm.edu	37	chr1	186948508	186948508	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	tttgatatttttgatgacccAgaatcaccattttcaacctt	4	9	2	4			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr1:186948508A>G	ENST00000367466.3	+	17	2174	c.2022A>G	c.(2020-2022)ccA>ccG	p.P674P	PLA2G4A_ENST00000442353.2_Silent_p.P614P	NM_024420.2	NP_077734	P47712	PA24A_HUMAN	phospholipase A2, group IVA (cytosolic, calcium-dependent)	674	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid metabolic process (GO:0019369)|arachidonic acid secretion (GO:0050482)|blood coagulation (GO:0007596)|cardiolipin acyl-chain remodeling (GO:0035965)|cellular response to antibiotic (GO:0071236)|glycerophospholipid biosynthetic process (GO:0046474)|icosanoid biosynthetic process (GO:0046456)|icosanoid metabolic process (GO:0006690)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|platelet activation (GO:0030168)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|calcium-dependent phospholipid binding (GO:0005544)|lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|prostate(3)|skin(4)|stomach(1)	53					Aldesleukin(DB00041)|Carbachol(DB00411)|Carbenicillin(DB00578)|Epirubicin(DB00445)|Fluocinolone Acetonide(DB00591)|Fluticasone Propionate(DB00588)|Niflumic Acid(DB04552)|Orlistat(DB01083)|Quinacrine(DB01103)|Streptokinase(DB00086)|Suramin(DB04786)	TTGATGACCCAGAATCACCAT	0.343																																					p.P674P		Atlas-SNP	.											PLA2G4A,NS,carcinoma,0,1	PLA2G4A	125	.	0			c.A2022G						.						120	116	117					1																	186948508		2203	4300	6503	SO:0001819	synonymous_variant	5321	exon17			TGACCCAGAATCA	M72393	CCDS1372.1	1q25	2014-09-17			ENSG00000116711	ENSG00000116711	3.1.1.4, 3.1.1.5		9035	protein-coding gene	gene with protein product		600522		PLA2G4		8175726	Standard	NM_024420		Approved	cPLA2-alpha	uc001gsc.3	P47712	OTTHUMG00000035512	ENST00000367466.3:c.2022A>G	chr1.hg19:g.186948508A>G		180.0	0.0		168.0	80.0	NM_024420	B1AKG4|Q29R80	Silent	SNP	ENST00000367466.3	hg19	CCDS1372.1																																																																																			.	.		0.343	PLA2G4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086236.1	NM_024420		G	186948508	A	G	186948508	2	3	287	1	0	0	0	0	0	0	0	1	12010	175	7	2		2	PLA2G4A	1	186948508	Silent	SNP	A	TCGA-G3-A5SL-01A-11D-A27I-10	9703161	186948508	62302113	12	42110										
KCNK2	3776	hgsc.bcm.edu	37	chr1	215408294	215408294	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	agcgggccacctccatcaagCggaagctctcggcagaactg	12	14	2	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr1:215408294C>T	ENST00000444842.2	+	7	1237	c.1087C>T	c.(1087-1089)Cgg>Tgg	p.R363W	KCNK2_ENST00000391894.2_Missense_Mutation_p.R348W|KCNK2_ENST00000391895.2_Missense_Mutation_p.R359W	NM_001017425.2|NM_014217.3	NP_001017425.2|NP_055032.1	O95069	KCNK2_HUMAN	potassium channel, subfamily K, member 2	363	Required for basal channel activity. {ECO:0000250}.				G-protein coupled receptor signaling pathway (GO:0007186)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	outward rectifier potassium channel activity (GO:0015271)|potassium channel inhibitor activity (GO:0019870)|potassium ion leak channel activity (GO:0022841)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|upper_aerodigestive_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(81;0.0399)|all cancers(67;0.0556)|GBM - Glioblastoma multiforme(131;0.068)	Dofetilide(DB00204)|Dronedarone(DB04855)	CTCCATCAAGCGGAAGCTCTC	0.547																																					p.R363W		Atlas-SNP	.											.	KCNK2	135	.	0			c.C1087T						.						66	65	65					1																	215408294		2203	4300	6503	SO:0001583	missense	3776	exon7			ATCAAGCGGAAGC	AF004711	CCDS31024.1, CCDS41466.1, CCDS41467.1	1q41	2012-03-07			ENSG00000082482	ENSG00000082482		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6277	protein-coding gene	gene with protein product		603219				9721223, 16382106	Standard	NM_001017424		Approved	K2p2.1, TREK-1	uc001hkr.4	O95069	OTTHUMG00000037017	ENST00000444842.2:c.1087C>T	chr1.hg19:g.215408294C>T	ENSP00000394033:p.Arg363Trp	62.0	0.0		146.0	39.0	NM_001017425	A1Z1V3|A8K618|B2RCS4|B7ZL56|D3DTA5|Q5DP47|Q5DP48|Q9NRT2|Q9UNE3	Missense_Mutation	SNP	ENST00000444842.2	hg19	CCDS41467.1	.	.	.	.	.	.	.	.	.	.	C	18.27	3.587659	0.66105	.	.	ENSG00000082482	ENST00000391895;ENST00000391894;ENST00000444842	T;T;T	0.26957	1.7;1.72;1.7	5.72	2.48	0.30137	.	0.873374	0.09247	U	0.828466	T	0.40522	0.1120	L	0.29908	0.895	0.51482	D	0.999922	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.75484	0.986;0.952;0.986	T	0.27400	-1.0075	10	0.87932	D	0	.	13.9309	0.63994	0.5192:0.4808:0.0:0.0	.	348;363;359	O95069-2;O95069;O95069-3	.;KCNK2_HUMAN;.	W	359;348;363	ENSP00000375765:R359W;ENSP00000375764:R348W;ENSP00000394033:R363W	ENSP00000375764:R348W	R	+	1	2	KCNK2	213474917	0.999000	0.42202	0.999000	0.59377	0.969000	0.65631	1.624000	0.37018	0.726000	0.32339	-0.314000	0.08810	CGG	.	.		0.547	KCNK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089856.2	NM_014217		T	215408294	C	T	215408294	3	4	287	1	0	0	0	0	1	0	0	0	8075	759	27	1	1156	1	KCNK2	1	215408294	Missense_Mutation	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10	28459786	215408294	33842327	13	42111										
PQLC3	130814	hgsc.bcm.edu	37	chr2	11300640	11300640	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	tactatgggtatccgccgctGacctacctggagtaccccat	9	14	0	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr2:11300640G>C	ENST00000295083.3	+	2	367	c.192G>C	c.(190-192)ctG>ctC	p.L64L	PQLC3_ENST00000441908.2_Silent_p.L64L|PQLC3_ENST00000476787.1_3'UTR|PQLC3_ENST00000402361.1_Silent_p.L64L	NM_152391.3	NP_689604.1	Q8N755	PQLC3_HUMAN	PQ loop repeat containing 3	64						integral component of membrane (GO:0016021)				kidney(2)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	6	all_hematologic(175;0.0797)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.0978)|OV - Ovarian serous cystadenocarcinoma(76;0.132)		ATCCGCCGCTGACCTACCTGG	0.612																																					p.L64L		Atlas-SNP	.											.	PQLC3	8	.	0			c.G192C						.						159	135	143					2																	11300640		2203	4300	6503	SO:0001819	synonymous_variant	130814	exon2			GCCGCTGACCTAC	BC027625	CCDS1679.1, CCDS62856.1, CCDS62857.1	2p25.1	2004-02-05	2005-07-19	2005-07-19	ENSG00000162976	ENSG00000162976			28503	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 22"	C2orf22		12477932	Standard	NM_001282711		Approved	MGC33602	uc002rbc.3	Q8N755	OTTHUMG00000119055	ENST00000295083.3:c.192G>C	chr2.hg19:g.11300640G>C		212.0	0.0		134.0	7.0	NM_152391	B2R8K1|B4DWA4	Silent	SNP	ENST00000295083.3	hg19	CCDS1679.1	.	.	.	.	.	.	.	.	.	.	G	10.12	1.263258	0.23051	.	.	ENSG00000162976	ENST00000428481	.	.	.	5.01	-0.0192	0.13961	.	.	.	.	.	T	0.50854	0.1640	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35943	-0.9768	4	.	.	.	-25.8568	5.5394	0.17030	0.3671:0.3815:0.2514:0.0	.	.	.	.	H	44	.	.	D	+	1	0	PQLC3	11218091	0.990000	0.36364	0.996000	0.52242	0.988000	0.76386	0.143000	0.16115	-0.090000	0.12462	0.561000	0.74099	GAC	.	.		0.612	PQLC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239266.4	NM_152391		C	11300640	G	C	11300640	2	2	287	1	0	0	0	0	0	0	0	1	12432	1277	45	4		4	PQLC3	2	11300640	Silent	SNP	G	TCGA-G3-A5SL-01A-11D-A27I-10		11300640	231898733	14	42112										
ATL2	64225	hgsc.bcm.edu	37	chr2	38525447	38525447	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	taggccaatgaagccagtcaGtcctgagattatatacatag	9	8	1	2			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr2:38525447G>T	ENST00000378954.4	-	12	1472	c.1471C>A	c.(1471-1473)Ctg>Atg	p.L491M	ATL2_ENST00000452935.2_Missense_Mutation_p.L473M|ATL2_ENST00000419554.2_Missense_Mutation_p.L491M|ATL2_ENST00000402054.1_Missense_Mutation_p.L320M|ATL2_ENST00000406122.1_Missense_Mutation_p.L320M|ATL2_ENST00000546051.1_Missense_Mutation_p.L320M|ATL2_ENST00000332337.4_Missense_Mutation_p.L473M|ATL2_ENST00000539122.1_Missense_Mutation_p.L320M	NM_001135673.1|NM_022374.2	NP_001129145.1|NP_071769.2	Q8NHH9	ATLA2_HUMAN	atlastin GTPase 2	491					endoplasmic reticulum organization (GO:0007029)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	22						AAGCCAGTCAGTCCTGAGATT	0.393																																					p.L491M		Atlas-SNP	.											.	ATL2	49	.	0			c.C1471A						.						134	117	123					2																	38525447		2203	4300	6503	SO:0001583	missense	64225	exon12			CAGTCAGTCCTGA		CCDS1795.1, CCDS46260.1	2p22.3	2008-09-17	2008-09-17	2008-09-17	ENSG00000119787	ENSG00000119787			24047	protein-coding gene	gene with protein product		609368	"ADP-ribosylation factor-like 6 interacting protein 2"	ARL6IP2		10508919, 18270207	Standard	NM_022374		Approved		uc002rqq.3	Q8NHH9	OTTHUMG00000102074	ENST00000378954.4:c.1471C>A	chr2.hg19:g.38525447G>T	ENSP00000368237:p.Leu491Met	73.0	0.0		59.0	5.0	NM_001135673	B7Z1X2|B7Z7X8|Q4ZG30|Q7Z630|Q8NHH8|Q9H5M7	Missense_Mutation	SNP	ENST00000378954.4	hg19	CCDS46260.1	.	.	.	.	.	.	.	.	.	.	G	18.03	3.531447	0.64972	.	.	ENSG00000119787	ENST00000378954;ENST00000406122;ENST00000402054;ENST00000539122;ENST00000332337;ENST00000419554;ENST00000452935;ENST00000546051	D;D;D;D;D;D;D;D	0.91631	-2.88;-2.88;-2.88;-2.88;-2.88;-2.88;-2.88;-2.88	5.81	5.81	0.92471	.	0.198315	0.44285	D	0.000472	D	0.94079	0.8102	M	0.80183	2.485	0.54753	D	0.999982	P;B;P;P;B	0.51351	0.944;0.417;0.553;0.553;0.417	P;B;B;B;B	0.48063	0.565;0.146;0.281;0.281;0.146	D	0.94198	0.7447	10	0.56958	D	0.05	-9.7897	19.0794	0.93175	0.0:0.0:1.0:0.0	.	320;473;473;491;491	B5MCN0;B7Z7X8;Q8NHH9-4;Q8NHH9-2;Q8NHH9	.;.;.;.;ATLA2_HUMAN	M	491;320;320;320;473;491;473;320	ENSP00000368237:L491M;ENSP00000385446:L320M;ENSP00000384062:L320M;ENSP00000446192:L320M;ENSP00000333393:L473M;ENSP00000415336:L491M;ENSP00000390743:L473M;ENSP00000438938:L320M	ENSP00000333393:L473M	L	-	1	2	ATL2	38378951	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.805000	0.62561	2.746000	0.94184	0.591000	0.81541	CTG	.	.		0.393	ATL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219886.2	NM_022374		T	38525447	G	T	38525447	3	4	287	1	0	0	0	0	1	0	0	0	1107	1020	36	3	400	3	ATL2	2	38525447	Missense_Mutation	SNP	G	TCGA-G3-A5SL-01A-11D-A27I-10	27224807	38525447	204673926	15	42113										
CNNM4	26504	hgsc.bcm.edu	37	chr2	97428070	97428070	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	caagactatcactcgcttctAtaaccacccggtgcactttg	6	14	2	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr2:97428070A>G	ENST00000377075.2	+	1	1432	c.1334A>G	c.(1333-1335)tAt>tGt	p.Y445C		NM_020184.3	NP_064569.3	Q6P4Q7	CNNM4_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 4	445	CBS 2. {ECO:0000255|PROSITE- ProRule:PRU00703}.				biomineral tissue development (GO:0031214)|ion transport (GO:0006811)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)			breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)	20						ACTCGCTTCTATAACCACCCG	0.493																																					p.Y445C		Atlas-SNP	.											.	CNNM4	48	.	0			c.A1334G						.						127	122	124					2																	97428070		2203	4300	6503	SO:0001583	missense	26504	exon1			GCTTCTATAACCA	AB046812	CCDS2024.2	2q11.2	2014-08-08	2014-08-07		ENSG00000158158	ENSG00000158158			105	protein-coding gene	gene with protein product		607805	"cyclin M4"	ACDP4		21393841, 24194943	Standard	XM_005263914		Approved	KIAA1592	uc002swx.3	Q6P4Q7	OTTHUMG00000130532	ENST00000377075.2:c.1334A>G	chr2.hg19:g.97428070A>G	ENSP00000366275:p.Tyr445Cys	266.0	0.0		198.0	79.0	NM_020184	B7Z1U0|C7SQM3|C7SQM4|C7SQM5|Q53RE5|Q9H9G3|Q9HCI0|Q9NRN1	Missense_Mutation	SNP	ENST00000377075.2	hg19	CCDS2024.2	.	.	.	.	.	.	.	.	.	.	A	17.60	3.429345	0.62844	.	.	ENSG00000158158	ENST00000377075	D	0.93247	-3.19	5.13	5.13	0.70059	Cystathionine beta-synthase, core (2);	0.000000	0.64402	D	0.000001	D	0.96482	0.8852	M	0.81112	2.525	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97029	0.9749	10	0.87932	D	0	-0.0098	13.9468	0.64089	1.0:0.0:0.0:0.0	.	445	Q6P4Q7	CNNM4_HUMAN	C	445	ENSP00000366275:Y445C	ENSP00000366275:Y445C	Y	+	2	0	CNNM4	96791797	1.000000	0.71417	0.990000	0.47175	0.820000	0.46376	9.281000	0.95811	1.941000	0.56285	0.460000	0.39030	TAT	.	.		0.493	CNNM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252954.1	NM_020184		G	97428070	A	G	97428070	3	3	287	1	0	0	0	0	1	0	0	0	3617	449	16	2	1336	2	CNNM4	2	97428070	Missense_Mutation	SNP	A	TCGA-G3-A5SL-01A-11D-A27I-10	58902623	97428070	145771303	16	42114										
IL1F6	27179	hgsc.bcm.edu	37	chr2	113763592	113763592	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	agcaggggagcattcaggatAtcaatcatcgggtgtgggtt	15	6	3	0			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr2:113763592A>G	ENST00000259211.6	+	2	463	c.52A>G	c.(52-54)Atc>Gtc	p.I18V		NM_014440.1	NP_055255.1	Q9UHA7	IL36A_HUMAN	interleukin 36, alpha	18					immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of interleukin-6 production (GO:0032755)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	interleukin-1 receptor binding (GO:0005149)			large_intestine(1)|lung(3)|ovary(2)|skin(1)|stomach(2)	9						CATTCAGGATATCAATCATCG	0.478																																					p.I18V		Atlas-SNP	.											.	IL36A	17	.	0			c.A52G						.						102	106	105					2																	113763592		1949	4137	6086	SO:0001583	missense	27179	exon2			CAGGATATCAATC	AF201831	CCDS42734.1	2q12-q14.1	2011-07-14	2011-06-06	2011-06-06	ENSG00000136694	ENSG00000136694		"Interleukins and interleukin receptors"	15562	protein-coding gene	gene with protein product		605509	"interleukin 1 family, member 6 (epsilon)"	IL1F6		10625660	Standard	XM_005263639		Approved	FIL1, FIL1E, IL-1F6, IL1(EPSILON), MGC129553, MGC129552	uc010yxr.2	Q9UHA7	OTTHUMG00000153320	ENST00000259211.6:c.52A>G	chr2.hg19:g.113763592A>G	ENSP00000259211:p.Ile18Val	119.0	0.0		95.0	38.0	NM_014440	B2RAD9|Q53SR7|Q5BLR4|Q7RTZ8	Missense_Mutation	SNP	ENST00000259211.6	hg19	CCDS42734.1	.	.	.	.	.	.	.	.	.	.	A	1.173	-0.640291	0.03557	.	.	ENSG00000136694	ENST00000259211	T	0.16897	2.31	4.99	1.36	0.22044	.	0.995923	0.08141	N	0.991647	T	0.07188	0.0182	N	0.04260	-0.245	0.09310	N	1	B	0.18461	0.028	B	0.16722	0.016	T	0.39921	-0.9590	10	0.27082	T	0.32	-30.939	3.859	0.08988	0.4396:0.2648:0.0:0.2956	.	18	Q9UHA7	IL36A_HUMAN	V	18	ENSP00000259211:I18V	ENSP00000259211:I18V	I	+	1	0	IL36A	113480063	0.003000	0.15002	0.087000	0.20705	0.412000	0.31113	0.086000	0.14935	0.451000	0.26802	0.477000	0.44152	ATC	.	.		0.478	IL36A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330711.1	NM_014440		G	113763592	A	G	113763592	3	3	287	1	0	0	0	0	1	0	0	0	7663	449	16	2	58	2	IL1F6	2	113763592	Missense_Mutation	SNP	A	TCGA-G3-A5SL-01A-11D-A27I-10	16335522	113763592	129435781	17	42115										
BAZ2B	29994	hgsc.bcm.edu	37	chr2	160287506	160287506	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	gttacgaggtgttgagtgacCtgtgagactcatggaagggc	16	6	1	3			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr2:160287506C>G	ENST00000392783.2	-	10	2557	c.2062G>C	c.(2062-2064)Ggt>Cgt	p.G688R	BAZ2B_ENST00000355831.2_Missense_Mutation_p.G688R|BAZ2B_ENST00000343439.5_Intron|BAZ2B_ENST00000392782.1_Missense_Mutation_p.G686R	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	688					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						GTTGAGTGACCTGTGAGACTC	0.448																																					p.G688R		Atlas-SNP	.											.	BAZ2B	196	.	0			c.G2062C						.						230	221	224					2																	160287506		1919	4129	6048	SO:0001583	missense	29994	exon10			AGTGACCTGTGAG	AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636		"Zinc fingers, PHD-type"	963	protein-coding gene	gene with protein product		605683				10662543	Standard	XM_005246488		Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.2062G>C	chr2.hg19:g.160287506C>G	ENSP00000376534:p.Gly688Arg	122.0	0.0		135.0	8.0	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	hg19	CCDS2209.2	.	.	.	.	.	.	.	.	.	.	C	14.15	2.449032	0.43531	.	.	ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831	T;T;T	0.25250	2.05;1.81;2.05	5.86	5.86	0.93980	.	0.209070	0.23281	U	0.049912	T	0.21590	0.0520	N	0.08118	0	0.80722	D	1	B;B;B	0.25441	0.058;0.126;0.093	B;B;B	0.34873	0.058;0.191;0.045	T	0.17198	-1.0377	10	0.59425	D	0.04	-4.9903	20.178	0.98191	0.0:1.0:0.0:0.0	.	492;686;688	Q9UIF8-4;Q9UIF8-5;Q9UIF8	.;.;BAZ2B_HUMAN	R	686;688;688	ENSP00000376533:G686R;ENSP00000376534:G688R;ENSP00000348087:G688R	ENSP00000348087:G688R	G	-	1	0	BAZ2B	159995752	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.279000	0.72620	2.770000	0.95276	0.643000	0.83706	GGT	.	.		0.448	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2			G	160287506	C	G	160287506	3	3	287	1	0	0	0	0	1	0	0	0	1332	681	24	4	4556	4	BAZ2B	2	160287506	Missense_Mutation	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10	46523914	160287506	82911867	18	42116										
TTN	7273	hgsc.bcm.edu	37	chr2	179590290	179590290	+	Frame_Shift_Del	DEL	G	G	-													0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	ccactggacaaaaataggctGggcgccttctatggatgctt							TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr2:179590290delG	ENST00000591111.1	-	69	19914	c.19690delC	c.(19690-19692)cagfs	p.Q6564fs	TTN_ENST00000342175.6_Intron|TTN_ENST00000342992.6_Frame_Shift_Del_p.Q5637fs|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|RP11-171I2.1_ENST00000590024.1_RNA|TTN_ENST00000589042.1_Frame_Shift_Del_p.Q6881fs|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12167	Ig-like 47.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AAAATAGGCTGGGCGCCTTCT	0.428																																					p.Q6881fs		Atlas-INDEL	.											.	TTN	18412	.	0			c.20642delA						.						104	95	98					2																	179590290		1844	4107	5951	SO:0001589	frameshift_variant	7273	exon71			.	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.19690delC	chr2.hg19:g.179590290delG	ENSP00000465570:p.Gln6564fs	59.0	0.0		41.0	11.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Frame_Shift_Del	DEL	ENST00000591111.1	hg19																																																																																				.	.		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		-	179590290	G	-	179590290	7	5	287	1	0	1	0	1	0	0	0	0	16750	1357	47	0	84056	0	TTN	2	179590290	Frame_Shift_Del	DEL	G	TCGA-G3-A5SL-01A-11D-A27I-10	19302784	179590290	63609083	19	42117										
SLC4A3	6508	hgsc.bcm.edu	37	chr2	220503556	220503556	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	gctgttcccgccctcctcgtCctcatcctgatcttcatgga	7	17	3	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr2:220503556C>A	ENST00000358055.3	+	19	3500	c.2988C>A	c.(2986-2988)gtC>gtA	p.V996V	SLC4A3_ENST00000373762.3_Silent_p.V1023V|SLC4A3_ENST00000373760.2_Silent_p.V996V|SLC4A3_ENST00000317151.3_Silent_p.V996V|SLC4A3_ENST00000273063.6_Silent_p.V1023V			P48751	B3A3_HUMAN	solute carrier family 4 (anion exchanger), member 3	996	Membrane (anion exchange).				bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	51		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCCTCCTCGTCCTCATCCTGA	0.627																																					p.V1023V		Atlas-SNP	.											.	SLC4A3	144	.	0			c.C3069A						.						50	42	45					2																	220503556		2203	4300	6503	SO:0001819	synonymous_variant	6508	exon19			CCTCGTCCTCATC		CCDS2445.1, CCDS2446.1	2q35	2013-07-19	2013-07-19		ENSG00000114923	ENSG00000114923		"Solute carriers"	11029	protein-coding gene	gene with protein product	"Anion exchanger 3, neuronal"	106195	"solute carrier family 4, anion exchanger, member 3"			8001971	Standard	NM_005070		Approved	AE3, SLC2C	uc002vmo.4	P48751	OTTHUMG00000059238	ENST00000358055.3:c.2988C>A	chr2.hg19:g.220503556C>A		139.0	0.0		81.0	25.0	NM_201574	A6H8L2|A8K1Q9|B7ZVX6|B9EGD1|Q6YIQ9	Silent	SNP	ENST00000358055.3	hg19	CCDS2445.1																																																																																			.	.		0.627	SLC4A3-009	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316472.1	NM_005070		A	220503556	C	A	220503556	2	1	287	1	0	0	0	0	0	0	0	1	14670	842	30	3		3	SLC4A3	2	220503556	Silent	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10	40913266	220503556	22695817	20	42118										
FARP2	9855	hgsc.bcm.edu	37	chr2	242430491	242430491	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	tgcagcactcggctggagaaAgagaagtggatgctggacct	15	8	0	2			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr2:242430491A>G	ENST00000264042.3	+	23	2690	c.2520A>G	c.(2518-2520)aaA>aaG	p.K840K		NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	840	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton reorganization (GO:0031532)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|neuron remodeling (GO:0016322)|osteoclast differentiation (GO:0030316)|podosome assembly (GO:0071800)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of integrin activation (GO:0033623)|regulation of Rac GTPase activity (GO:0032314)|semaphorin-plexin signaling pathway (GO:0071526)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	43		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		GGCTGGAGAAAGAGAAGTGGA	0.647																																					p.K840K		Atlas-SNP	.											.	FARP2	92	.	0			c.A2520G						.						82	82	82					2																	242430491		2203	4300	6503	SO:0001819	synonymous_variant	9855	exon23			GGAGAAAGAGAAG	AB018336	CCDS33424.1, CCDS63197.1	2q37.3	2013-01-10			ENSG00000006607	ENSG00000006607		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	16460	protein-coding gene	gene with protein product						9872452, 12351724	Standard	NM_001282984		Approved	KIAA0793, FIR, PLEKHC3, FRG	uc002wbi.2	O94887	OTTHUMG00000151574	ENST00000264042.3:c.2520A>G	chr2.hg19:g.242430491A>G		442.0	1.0		243.0	79.0	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Silent	SNP	ENST00000264042.3	hg19	CCDS33424.1	.	.	.	.	.	.	.	.	.	.	A	7.670	0.686802	0.14973	.	.	ENSG00000006607	ENST00000444371	.	.	.	4.15	1.2	0.21068	.	.	.	.	.	T	0.57917	0.2086	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50931	-0.8769	4	.	.	.	.	9.7023	0.40194	0.2242:0.0:0.7758:0.0	.	.	.	.	G	34	.	.	R	+	1	2	FARP2	242079164	1.000000	0.71417	0.878000	0.34440	0.688000	0.40055	5.588000	0.67517	0.138000	0.18790	-0.904000	0.02843	AGA	.	.		0.647	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1			G	242430491	A	G	242430491	2	3	287	1	0	0	0	0	0	0	0	1	5685	69	3	2		2	FARP2	2	242430491	Silent	SNP	A	TCGA-G3-A5SL-01A-11D-A27I-10	21926935	242430491	768882	21	42119										
CHL1	10752	hgsc.bcm.edu	37	chr3	439928	439928	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	aggtaaaggtatcgggaagaTatcaggagtaaatcttactc	11	5	2	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr3:439928T>C	ENST00000256509.2	+	25	3755	c.3113T>C	c.(3112-3114)aTa>aCa	p.I1038T	CHL1_ENST00000397491.2_Missense_Mutation_p.I1022T	NM_001253387.1|NM_001253388.1|NM_006614.3	NP_001240316.1|NP_001240317.1|NP_006605.2	Q96FC9	DDX11_HUMAN	cell adhesion molecule L1-like	0					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			NS(1)|central_nervous_system(5)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|lung(31)|ovary(1)|prostate(4)|skin(10)|stomach(1)	93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		ATCGGGAAGATATCAGGAGTA	0.358																																					p.I1038T		Atlas-SNP	.											.	CHL1	242	.	0			c.T3113C						.						64	63	63					3																	439928		2203	4300	6503	SO:0001583	missense	10752	exon25			GGAAGATATCAGG	AF002246	CCDS2556.1, CCDS58812.1, CCDS74887.1	3p26	2013-05-01	2013-05-01		ENSG00000134121	ENSG00000134121		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	1939	protein-coding gene	gene with protein product	"neural cell adhesion molecule", "close homolog of L1"	607416	"cell adhesion molecule with homology to L1CAM (close homologue of L1)", "cell adhesion molecule with homology to L1CAM (close homolog of L1)"			9799093	Standard	NM_006614		Approved	CALL, L1CAM2, FLJ44930, MGC132578	uc003bot.3	O00533	OTTHUMG00000090601	ENST00000256509.2:c.3113T>C	chr3.hg19:g.439928T>C	ENSP00000256509:p.Ile1038Thr	83.0	0.0		69.0	12.0	NM_006614	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000256509.2	hg19	CCDS2556.1	.	.	.	.	.	.	.	.	.	.	T	10.21	1.287976	0.23478	.	.	ENSG00000134121	ENST00000256509;ENST00000397491	T;T	0.60424	0.19;0.2	5.72	4.52	0.55395	.	0.242716	0.39407	N	0.001367	T	0.39886	0.1095	L	0.29908	0.895	0.33202	D	0.552258	B;B	0.27679	0.085;0.185	B;B	0.27380	0.015;0.079	T	0.44620	-0.9316	10	0.12103	T	0.63	.	7.9446	0.29978	0.1351:0.0:0.1414:0.7235	.	1022;1038	O00533;O00533-2	CHL1_HUMAN;.	T	1038;1022	ENSP00000256509:I1038T;ENSP00000380628:I1022T	ENSP00000256509:I1038T	I	+	2	0	CHL1	414928	1.000000	0.71417	0.905000	0.35620	0.998000	0.95712	2.422000	0.44696	0.953000	0.37825	0.528000	0.53228	ATA	.	.		0.358	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614		C	439928	T	C	439928	3	2	287	1	0	0	0	0	1	0	0	0	3351	1406	49	2	3203	2	CHL1	3	439928	Missense_Mutation	SNP	T	TCGA-G3-A5SL-01A-11D-A27I-10		439928	197582502	22	42120										
NR2C2	7182	hgsc.bcm.edu	37	chr3	15062430	15062430	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	aatgcttagagatgggcatgAaaatggaatgtgagtaacaa	12	3	0	3			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr3:15062430A>G	ENST00000425241.1	+	5	909	c.547A>G	c.(547-549)Aaa>Gaa	p.K183E	NR2C2_ENST00000393102.3_Missense_Mutation_p.K183E|NR2C2_ENST00000406272.2_Missense_Mutation_p.K183E|NR2C2_ENST00000323373.6_Missense_Mutation_p.K202E			P49116	NR2C2_HUMAN	nuclear receptor subfamily 2, group C, member 2	183					cell differentiation (GO:0030154)|gene expression (GO:0010467)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(5)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						GATGGGCATGAAAATGGAATG	0.413																																					p.K202E		Atlas-SNP	.											.	NR2C2	44	.	0			c.A604G						.						74	71	72					3																	15062430		2203	4300	6503	SO:0001583	missense	7182	exon6			GGCATGAAAATGG	L27586	CCDS2621.1, CCDS74905.1	3p25	2013-01-16			ENSG00000177463	ENSG00000177463		"Nuclear hormone receptors"	7972	protein-coding gene	gene with protein product		601426		TR4		8661150, 8016112	Standard	XM_005265428		Approved	TAK1, TR2R1, hTAK1	uc003bzi.3	P49116	OTTHUMG00000129839	ENST00000425241.1:c.547A>G	chr3.hg19:g.15062430A>G	ENSP00000388387:p.Lys183Glu	68.0	0.0		77.0	4.0	NM_003298	A8K3H5|B6ZGT8|P55092	Missense_Mutation	SNP	ENST00000425241.1	hg19		.	.	.	.	.	.	.	.	.	.	A	26.7	4.759891	0.89932	.	.	ENSG00000177463	ENST00000425241;ENST00000323373;ENST00000393102;ENST00000437120;ENST00000406272	T;T;T;D;T	0.97186	0.4;0.4;0.4;-4.28;0.4	5.78	5.78	0.91487	Nuclear hormone receptor, ligand-binding (2);Zinc finger, nuclear hormone receptor-type (3);	0.000000	0.85682	D	0.000000	D	0.98372	0.9459	M	0.79926	2.475	0.80722	D	1	D;D	0.71674	0.998;0.997	D;D	0.79108	0.978;0.992	D	0.99521	1.0958	10	0.87932	D	0	.	16.4053	0.83662	1.0:0.0:0.0:0.0	.	183;202	P49116;F2YGU2	NR2C2_HUMAN;.	E	183;202;183;202;183	ENSP00000388387:K183E;ENSP00000320447:K202E;ENSP00000376814:K183E;ENSP00000401807:K202E;ENSP00000384463:K183E	ENSP00000320447:K202E	K	+	1	0	NR2C2	15037434	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	9.249000	0.95470	2.333000	0.79357	0.482000	0.46254	AAA	.	.		0.413	NR2C2-002	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000340729.1	NM_003298		G	15062430	A	G	15062430	3	3	287	1	0	0	0	0	1	0	0	0	10632	247	9	2	622	2	NR2C2	3	15062430	Missense_Mutation	SNP	A	TCGA-G3-A5SL-01A-11D-A27I-10	14622502	15062430	182960000	23	42121										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266098	41266098	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	gcagcaacagtcttacctggActctggaatccattctggtg	10	11	3	0	rs121913396|rs121913416		TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr3:41266098A>G	ENST00000349496.5	+	3	375	c.95A>G	c.(94-96)gAc>gGc	p.D32G	CTNNB1_ENST00000396183.3_Missense_Mutation_p.D32G|CTNNB1_ENST00000453024.1_Missense_Mutation_p.D25G|CTNNB1_ENST00000396185.3_Missense_Mutation_p.D32G|CTNNB1_ENST00000405570.1_Missense_Mutation_p.D32G	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	32			D -> A (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|D -> G (in PTR and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629}.|D -> Y (in PTR, hepatoblastoma and hepatocellular carcinoma; dbSNP:rs28931588). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:11703283, ECO:0000269|PubMed:9927029}.|Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.D32G(65)|p.A5_A80del(53)|p.D32V(33)|p.D32A(16)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.WQQQSYLD25?(5)|p.W25_D32del(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.S29_H36del(1)|p.D32del(1)|p.M14_S45del(1)|p.Q28_D32>H(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.D32fs*9(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TCTTACCTGGACTCTGGAATC	0.483	D32V(HEC265_ENDOMETRIUM)|D32V(HEC6_ENDOMETRIUM)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.D32G	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,+1,128	CTNNB1	4904	.	260	Deletion - In frame(120)|Substitution - Missense(114)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(154)|large_intestine(24)|pancreas(19)|central_nervous_system(16)|stomach(14)|endometrium(7)|skin(7)|ovary(4)|prostate(3)|pituitary(3)|small_intestine(2)|NS(2)|adrenal_gland(1)|soft_tissue(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)	c.A95G						.						92	77	82					3																	41266098		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	ACCTGGACTCTGG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.95A>G	chr3.hg19:g.41266098A>G	ENSP00000344456:p.Asp32Gly	170.0	0.0		232.0	73.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.308122	0.81247	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.50001	0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.69788	0.3150	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.74137	-0.3762	10	0.87932	D	0	0.3843	16.0676	0.80897	1.0:0.0:0.0:0.0	.	32	P35222	CTNB1_HUMAN	G	25;32;32;32;32;25;32;32;32	ENSP00000400508:D25G;ENSP00000385604:D32G;ENSP00000412219:D32G;ENSP00000379486:D32G;ENSP00000344456:D32G;ENSP00000411226:D25G;ENSP00000379488:D32G;ENSP00000409302:D32G;ENSP00000401599:D32G	ENSP00000344456:D32G	D	+	2	0	CTNNB1	41241102	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.201000	0.70794	0.533000	0.62120	GAC	.	.		0.483	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266098	A	G	41266098	3	3	287	1	0	0	0	0	1	0	0	0	4018	275	10	2	101	2	CTNNB1	3	41266098	Missense_Mutation	SNP	A	TCGA-G3-A5SL-01A-11D-A27I-10	26203668	41266098	156756332	24	42122										
CYP8B1	1582	hgsc.bcm.edu	37	chr3	42916920	42916920	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	tcaagccatcccccctcagaTgcttggtgctggctgagtgt	11	13	2	2			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr3:42916920T>A	ENST00000316161.4	-	1	713	c.389A>T	c.(388-390)cAt>cTt	p.H130L	KRBOX1_ENST00000426937.1_Intron|CYP8B1_ENST00000437102.1_Missense_Mutation_p.H130L|RP11-141M3.5_ENST00000471537.1_RNA	NM_004391.2	NP_004382.2	Q9UNU6	CP8B1_HUMAN	cytochrome P450, family 8, subfamily B, polypeptide 1	130					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	7alpha-hydroxycholest-4-en-3-one 12alpha-hydroxylase activity (GO:0033778)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|sterol 12-alpha-hydroxylase activity (GO:0008397)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(2)|prostate(2)|skin(5)	23				KIRC - Kidney renal clear cell carcinoma(284;0.213)|Kidney(284;0.249)		CCCCCTCAGATGCTTGGTGCT	0.498																																					p.H130L		Atlas-SNP	.											.	CYP8B1	59	.	0			c.A389T						.						118	110	112					3																	42916920		2203	4300	6503	SO:0001583	missense	1582	exon1			CTCAGATGCTTGG	AF090318	CCDS2707.1	3p22.1	2004-02-27	2003-01-14		ENSG00000180432	ENSG00000180432		"Cytochrome P450s"	2653	protein-coding gene	gene with protein product		602172	"cytochrome P450, subfamily VIIIB (sterol 12-alpha-hydroxylase), polypeptide 1"			10051404	Standard	NM_004391		Approved	CYP12	uc003cmh.3	Q9UNU6	OTTHUMG00000133047	ENST00000316161.4:c.389A>T	chr3.hg19:g.42916920T>A	ENSP00000318867:p.His130Leu	158.0	0.0		133.0	39.0	NM_004391	B2RCY3|O75958|Q6NWT2|Q6NWT3	Missense_Mutation	SNP	ENST00000316161.4	hg19	CCDS2707.1	.	.	.	.	.	.	.	.	.	.	T	12.01	1.809007	0.31961	.	.	ENSG00000180432	ENST00000437102;ENST00000316161	T;T	0.68025	-0.3;-0.3	5.57	4.38	0.52667	.	0.303187	0.34245	N	0.004136	T	0.62134	0.2403	L	0.35341	1.055	0.23346	N	0.997864	P;P	0.46142	0.873;0.787	P;P	0.54431	0.752;0.672	T	0.51834	-0.8655	10	0.08837	T	0.75	-0.7324	9.4875	0.38940	0.2818:0.0:0.0:0.7182	.	130;130	C9JFR9;Q9UNU6	.;CP8B1_HUMAN	L	130	ENSP00000404499:H130L;ENSP00000318867:H130L	ENSP00000318867:H130L	H	-	2	0	CYP8B1	42891924	0.991000	0.36638	0.035000	0.18076	0.013000	0.08279	3.800000	0.55537	0.911000	0.36747	0.459000	0.35465	CAT	.	.		0.498	CYP8B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256653.1	NM_004391		A	42916920	T	A	42916920	3	1	287	1	0	0	0	0	1	0	0	0	4200	1464	51	4	1120	4	CYP8B1	3	42916920	Missense_Mutation	SNP	T	TCGA-G3-A5SL-01A-11D-A27I-10	1650822	42916920	155105510	25	42123										
SLC38A3	10991	hgsc.bcm.edu	37	chr3	50251707	50251707	+	RNA	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	tcagaggggctgctcccggtCatcacccccatggcaggcaa	12	15	3	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr3:50251707C>T	ENST00000420502.1	+	0	229									solute carrier family 38, member 3											breast(1)|cervix(1)|endometrium(1)|lung(3)	6				BRCA - Breast invasive adenocarcinoma(193;0.000275)|KIRC - Kidney renal clear cell carcinoma(197;0.00548)|Kidney(197;0.00615)		TGCTCCCGGTCATCACCCCCA	0.622																																					p.V25V		Atlas-SNP	.											.	SLC38A3	22	.	0			c.C75T						.						42	44	44					3																	50251707		2065	4215	6280			10991	exon2			CCCGGTCATCACC	U49082	CCDS74940.1	3p21.3	2013-05-22			ENSG00000188338	ENSG00000188338		"Solute carriers"	18044	protein-coding gene	gene with protein product		604437				10619430, 10823827	Standard	XM_006712954		Approved	G17, SN1	uc003cyn.4	Q99624	OTTHUMG00000156764		chr3.hg19:g.50251707C>T		207.0	0.0		135.0	58.0	NM_006841		Silent	SNP	ENST00000420502.1	hg19																																																																																				.	.		0.622	SLC38A3-001	KNOWN	sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000345635.2	NM_006841		T	50251707	C	T	50251707	1	4	287	0	1	0	0	0	0	0	0	0	14620	813	29	3		3	SLC38A3	3	50251707	RNA	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10	7334787	50251707	147770723	26	42124										
CPB1	1360	hgsc.bcm.edu	37	chr3	148552327	148552327	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	ctgtcacacaaatcaaacctCacagtacagttgacttccgt	5	13	3	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr3:148552327C>A	ENST00000491148.1	+	4	524	c.190C>A	c.(190-192)Cac>Aac	p.H64N	CPB1_ENST00000282957.4_Missense_Mutation_p.H64N			P15086	CBPB1_HUMAN	carboxypeptidase B1 (tissue)	64						extracellular region (GO:0005576)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	38			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)			AATCAAACCTCACAGTACAGT	0.348																																					p.H64N		Atlas-SNP	.											.	CPB1	74	.	0			c.C190A						.						110	103	105					3																	148552327		2203	4300	6503	SO:0001583	missense	1360	exon3			AAACCTCACAGTA	AJ224866	CCDS33874.1	3q24	2012-02-10			ENSG00000153002	ENSG00000153002	3.4.17.2		2299	protein-coding gene	gene with protein product	"pancreatic carboxypeptidase B", "tissue carboxypeptidase B", "protaminase"	114852					Standard	XM_005247124		Approved		uc003ewl.3	P15086	OTTHUMG00000159520	ENST00000491148.1:c.190C>A	chr3.hg19:g.148552327C>A	ENSP00000417222:p.His64Asn	191.0	0.0		190.0	89.0	NM_001871	O60834|Q53XJ0|Q96BQ8	Missense_Mutation	SNP	ENST00000491148.1	hg19	CCDS33874.1	.	.	.	.	.	.	.	.	.	.	C	0.928	-0.713536	0.03206	.	.	ENSG00000153002	ENST00000491148;ENST00000462345;ENST00000282957;ENST00000468341	T;T;T;T	0.11930	2.73;2.73;2.73;2.73	5.03	4.13	0.48395	Proteinase inhibitor, propeptide (1);Proteinase inhibitor, carboxypeptidase propeptide (2);	0.398596	0.29846	N	0.011044	T	0.05960	0.0155	N	0.13098	0.295	0.27374	N	0.955609	B	0.02656	0.0	B	0.04013	0.001	T	0.40001	-0.9586	10	0.05620	T	0.96	.	7.1853	0.25797	0.163:0.5278:0.3092:0.0	.	64	P15086	CBPB1_HUMAN	N	64	ENSP00000417222:H64N;ENSP00000417117:H64N;ENSP00000282957:H64N;ENSP00000419427:H64N	ENSP00000282957:H64N	H	+	1	0	CPB1	150035017	0.983000	0.35010	0.828000	0.32881	0.517000	0.34286	2.134000	0.42102	2.319000	0.78375	0.471000	0.43371	CAC	.	.		0.348	CPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355928.1	NM_001871		A	148552327	C	A	148552327	3	1	287	1	0	0	0	0	1	0	0	0	3798	826	29	3	200	3	CPB1	3	148552327	Missense_Mutation	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10	98300620	148552327	49470103	27	42125										
PEX5L	51555	hgsc.bcm.edu	37	chr3	179592187	179592187	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	ctttttccaccactcagttcTggttgagatctgtgttctga	8	10	4	2			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr3:179592187T>C	ENST00000467460.1	-	7	984	c.654A>G	c.(652-654)ccA>ccG	p.P218P	PEX5L-AS1_ENST00000466064.1_RNA|PEX5L_ENST00000465751.1_Silent_p.P194P|PEX5L_ENST00000468741.1_Silent_p.P26P|PEX5L_ENST00000392649.3_Silent_p.P110P|PEX5L_ENST00000467440.2_5'UTR|PEX5L_ENST00000263962.8_Silent_p.P216P|PEX5L_ENST00000476138.1_Silent_p.P175P|PEX5L_ENST00000464614.1_Silent_p.P110P|PEX5L_ENST00000485199.1_Silent_p.P183P|PEX5L_ENST00000472994.1_Silent_p.P159P	NM_001256751.1|NM_016559.2	NP_001243680.1|NP_057643.1	Q8IYB4	PEX5R_HUMAN	peroxisomal biogenesis factor 5-like	218					maintenance of protein location (GO:0045185)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome matrix, docking (GO:0016560)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of membrane potential (GO:0042391)	cytosol (GO:0005829)|dendrite (GO:0030425)|peroxisomal membrane (GO:0005778)|receptor complex (GO:0043235)	peroxisome matrix targeting signal-1 binding (GO:0005052)|peroxisome targeting sequence binding (GO:0000268)|small GTPase binding (GO:0031267)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(23)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	all_cancers(143;3.94e-14)|Ovarian(172;0.0338)|Breast(254;0.183)		OV - Ovarian serous cystadenocarcinoma(80;1.75e-26)|GBM - Glioblastoma multiforme(14;0.000518)			CACTCAGTTCTGGTTGAGATC	0.408																																					p.P218P		Atlas-SNP	.											.	PEX5L	104	.	0			c.A654G						.						122	117	118					3																	179592187		2203	4300	6503	SO:0001819	synonymous_variant	51555	exon7			CAGTTCTGGTTGA	AJ245503	CCDS3236.1, CCDS58861.1, CCDS58862.1, CCDS58863.1, CCDS58864.1, CCDS58865.1, CCDS58866.1, CCDS58867.1	3q27.1	2013-01-10			ENSG00000114757	ENSG00000114757		"Tetratricopeptide (TTC) repeat domain containing"	30024	protein-coding gene	gene with protein product		611058				11463335	Standard	NM_016559		Approved	PEX5R, PXR2	uc003fki.2	Q8IYB4	OTTHUMG00000157363	ENST00000467460.1:c.654A>G	chr3.hg19:g.179592187T>C		39.0	0.0		51.0	17.0	NM_016559	B7Z2A5|B7Z305|B7Z318|B7Z5Z5|B7Z8P2|E7EUV8|E7EUZ0|E9PEC1|E9PH97|Q9NQD1|Q9P2U3|Q9P2U4	Silent	SNP	ENST00000467460.1	hg19	CCDS3236.1																																																																																			.	.		0.408	PEX5L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348577.1	NM_016559		C	179592187	T	C	179592187	2	2	287	1	0	0	0	0	0	0	0	1	11758	1567	55	2		2	PEX5L	3	179592187	Silent	SNP	T	TCGA-G3-A5SL-01A-11D-A27I-10	31039860	179592187	18430243	28	42126										
LGI2	55203	hgsc.bcm.edu	37	chr4	25005084	25005084	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	accacaccttcacaaacttaAgtcaacaattatatgttcaa	2	11	3	0			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr4:25005084A>C	ENST00000382114.4	-	8	1812	c.1627T>G	c.(1627-1629)Tta>Gta	p.L543V		NM_018176.3	NP_060646.2	Q8N0V4	LGI2_HUMAN	leucine-rich repeat LGI family, member 2	543						extracellular region (GO:0005576)				breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(15)|prostate(1)|skin(3)|stomach(2)	33		Breast(46;0.173)				CACAAACTTAAGTCAACAATT	0.388																																					p.L543V		Atlas-SNP	.											.	LGI2	62	.	0			c.T1627G						.						47	49	49					4																	25005084		2203	4299	6502	SO:0001583	missense	55203	exon8			AACTTAAGTCAAC	AJ487516	CCDS3431.1	4p15.31	2008-07-28			ENSG00000153012	ENSG00000153012			18710	protein-coding gene	gene with protein product		608301				12023020, 16014869	Standard	NM_018176		Approved	KIAA1916, FLJ10675	uc003grf.2	Q8N0V4	OTTHUMG00000097749	ENST00000382114.4:c.1627T>G	chr4.hg19:g.25005084A>C	ENSP00000371548:p.Leu543Val	77.0	0.0		46.0	15.0	NM_018176	Q3MIN2|Q8NDW6|Q96PX2|Q9NVK4	Missense_Mutation	SNP	ENST00000382114.4	hg19	CCDS3431.1	.	.	.	.	.	.	.	.	.	.	A	15.29	2.788376	0.49997	.	.	ENSG00000153012	ENST00000382114;ENST00000282970	T	0.69561	-0.41	5.57	0.42	0.16444	.	0.000000	0.64402	D	0.000001	T	0.76414	0.3984	M	0.77313	2.365	0.47065	D	0.999305	D	0.61080	0.989	D	0.63488	0.915	T	0.75028	-0.3462	10	0.87932	D	0	-18.4185	9.2079	0.37300	0.649:0.0:0.351:0.0	.	543	Q8N0V4	LGI2_HUMAN	V	543;191	ENSP00000371548:L543V	ENSP00000282970:L191V	L	-	1	2	LGI2	24614182	1.000000	0.71417	0.992000	0.48379	0.963000	0.63663	2.803000	0.47924	-0.127000	0.11661	-0.385000	0.06624	TTA	.	.		0.388	LGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214978.1			C	25005084	A	C	25005084	3	2	287	1	0	0	0	0	1	0	0	0	8761	69	3	5	14	5	LGI2	4	25005084	Missense_Mutation	SNP	A	TCGA-G3-A5SL-01A-11D-A27I-10		25005084	166149192	29	42127										
SEC24B	10427	hgsc.bcm.edu	37	chr4	110442575	110442575	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	ttttgatctttgttttctcaGcttataaaagacttactgaa	5	6	2	3			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr4:110442575G>A	ENST00000265175.5	+	14	2356		c.e14-1		SEC24B_ENST00000399100.2_Splice_Site|SEC24B_ENST00000504968.2_Splice_Site	NM_006323.2	NP_006314.2	O95487	SC24B_HUMAN	SEC24 family member B						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|aorta morphogenesis (GO:0035909)|auditory receptor cell stereocilium organization (GO:0060088)|cellular protein metabolic process (GO:0044267)|cochlear nucleus development (GO:0021747)|COPII vesicle coating (GO:0048208)|coronary artery morphogenesis (GO:0060982)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|lung lobe morphogenesis (GO:0060463)|membrane organization (GO:0061024)|neural tube closure (GO:0001843)|outflow tract morphogenesis (GO:0003151)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|pulmonary artery morphogenesis (GO:0061156)|regulation of cargo loading into COPII-coated vesicle (GO:1901301)|regulation of establishment of planar polarity involved in neural tube closure (GO:0090178)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|membrane (GO:0016020)	transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)		TGTTTTCTCAGCTTATAAAAG	0.353																																					.		Atlas-SNP	.											.	SEC24B	186	.	0			c.2302-1G>A						.						86	79	81					4																	110442575		1874	4089	5963	SO:0001630	splice_region_variant	10427	exon14			TTCTCAGCTTATA	AJ131245	CCDS43260.1, CCDS47124.1, CCDS75179.1	4q25	2013-10-21	2013-10-21		ENSG00000138802	ENSG00000138802			10704	protein-coding gene	gene with protein product		607184	"SEC24 (S. cerevisiae) related gene family, member B", "SEC24 family, member B (S. cerevisiae)"			10075675, 10329445	Standard	XM_005262688		Approved		uc003hzk.3	O95487	OTTHUMG00000161372	ENST00000265175.5:c.2302-1G>A	chr4.hg19:g.110442575G>A		123.0	0.0		69.0	16.0	NM_006323	B7ZKM8|B7ZKN4|Q0VG08	Splice_Site	SNP	ENST00000265175.5	hg19	CCDS47124.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.784398	0.90282	.	.	ENSG00000138802	ENST00000504968;ENST00000399100;ENST00000265175	.	.	.	5.78	5.78	0.91487	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.0139	0.97470	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SEC24B	110662024	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.807000	0.99171	2.724000	0.93272	0.563000	0.77884	.	.	.		0.353	SEC24B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364693.2		Intron	A	110442575	G	A	110442575	5	1	287	1	0	0	0	0	0	0	1	0	14010	985	34	3	2355	3	SEC24B	4	110442575	Splice_Site	SNP	G	TCGA-G3-A5SL-01A-11D-A27I-10	85437491	110442575	80711701	30	42128										
FGA	2243	hgsc.bcm.edu	37	chr4	155505929	155505929	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	actggatcccggtagcttgaTattgaaaatgccactttggg	11	8	0	2			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr4:155505929T>C	ENST00000302053.3	-	6	2026	c.1948A>G	c.(1948-1950)Atc>Gtc	p.I650V		NM_000508.3	NP_000499.1	P02671	FIBA_HUMAN	fibrinogen alpha chain	650	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				blood coagulation (GO:0007596)|blood coagulation, common pathway (GO:0072377)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|extracellular matrix organization (GO:0030198)|negative regulation of blood coagulation, common pathway (GO:2000261)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	structural molecule activity (GO:0005198)			NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	73	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)	GGTAGCTTGATATTGAAAATG	0.388																																					p.I650V	NSCLC(143;340 1922 20892 22370 48145)	Atlas-SNP	.											.	FGA	179	.	0			c.A1948G						.						47	48	48					4																	155505929		2203	4300	6503	SO:0001583	missense	2243	exon6			GCTTGATATTGAA		CCDS3787.1, CCDS47152.1	4q28	2014-09-17			ENSG00000171560	ENSG00000171560		"Fibrinogen C domain containing", "Endogenous ligands"	3661	protein-coding gene	gene with protein product		134820	"fibrinogen, A alpha polypeptide"				Standard	NM_000508		Approved		uc003iod.1	P02671	OTTHUMG00000150330	ENST00000302053.3:c.1948A>G	chr4.hg19:g.155505929T>C	ENSP00000306361:p.Ile650Val	29.0	0.0		39.0	18.0	NM_000508	A8K3E4|D3DP14|D3DP15|Q4QQH7|Q9BX62|Q9UCH2	Missense_Mutation	SNP	ENST00000302053.3	hg19	CCDS3787.1	.	.	.	.	.	.	.	.	.	.	T	11.35	1.613373	0.28712	.	.	ENSG00000171560	ENST00000302053	D	0.98207	-4.79	5.46	1.72	0.24424	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.088574	0.85682	N	0.000000	D	0.96488	0.8854	L	0.49455	1.56	0.80722	D	1	B	0.32526	0.374	B	0.40329	0.326	D	0.92665	0.6145	10	0.44086	T	0.13	.	9.1746	0.37105	0.0:0.2086:0.0:0.7914	.	650	P02671	FIBA_HUMAN	V	650	ENSP00000306361:I650V	ENSP00000306361:I650V	I	-	1	0	FGA	155725379	1.000000	0.71417	0.998000	0.56505	0.679000	0.39708	2.129000	0.42055	0.065000	0.16485	-0.280000	0.10049	ATC	.	.		0.388	FGA-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317593.1	NM_000508		C	155505929	T	C	155505929	3	2	287	1	0	0	0	0	1	0	0	0	5838	1406	49	2	656	2	FGA	4	155505929	Missense_Mutation	SNP	T	TCGA-G3-A5SL-01A-11D-A27I-10	45063354	155505929	35648347	31	42129										
WDR17	116966	hgsc.bcm.edu	37	chr4	177067183	177067183	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	gctgtgaagacacaaatgttCgtgtttattatgtagccacc	9	8	0	2			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr4:177067183C>T	ENST00000280190.4	+	13	1795	c.1639C>T	c.(1639-1641)Cgt>Tgt	p.R547C	WDR17_ENST00000508596.1_Missense_Mutation_p.R523C|WDR17_ENST00000507824.2_Missense_Mutation_p.R530C|WDR17_ENST00000393643.2_Missense_Mutation_p.R523C			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	547										breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(18)|lung(46)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	92		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)		CACAAATGTTCGTGTTTATTA	0.358																																					p.R547C		Atlas-SNP	.											WDR17,NS,carcinoma,0,1	WDR17	198	.	0			c.C1639T						.						120	113	115					4																	177067183		2203	4300	6503	SO:0001583	missense	116966	exon13			AATGTTCGTGTTT	AF492460	CCDS3825.1, CCDS43284.1, CCDS43284.2	4q34	2013-01-09			ENSG00000150627	ENSG00000150627		"WD repeat domain containing"	16661	protein-coding gene	gene with protein product		609005				12401215	Standard	NM_170710		Approved		uc003iuj.3	Q8IZU2	OTTHUMG00000160791	ENST00000280190.4:c.1639C>T	chr4.hg19:g.177067183C>T	ENSP00000280190:p.Arg547Cys	75.0	2.0		93.0	16.0	NM_170710	E7EQX0|Q0QD35	Missense_Mutation	SNP	ENST00000280190.4	hg19	CCDS3825.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.731452	0.89390	.	.	ENSG00000150627	ENST00000508596;ENST00000393643;ENST00000280190;ENST00000507824	T;T;T	0.68025	-0.3;-0.3;-0.3	5.49	5.49	0.81192	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.83995	0.5375	M	0.84082	2.675	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.85526	0.1206	10	0.62326	D	0.03	-20.7818	19.3758	0.94508	0.0:1.0:0.0:0.0	.	523;547	E7EQX0;Q8IZU2	.;WDR17_HUMAN	C	523;523;547;530	ENSP00000422763:R523C;ENSP00000377258:R523C;ENSP00000280190:R547C	ENSP00000280190:R547C	R	+	1	0	WDR17	177304177	1.000000	0.71417	0.980000	0.43619	0.951000	0.60555	7.138000	0.77305	2.579000	0.87056	0.563000	0.77884	CGT	.	.		0.358	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2			T	177067183	C	T	177067183	3	4	287	1	0	0	0	0	1	0	0	0	17292	884	31	1	1685	1	WDR17	4	177067183	Missense_Mutation	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10	21561254	177067183	14087093	32	42130										
BASP1	10409	hgsc.bcm.edu	37	chr5	17275846	17275846	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	cccagcttcagactcaaaacCcggcagctcggaggctgccc	10	17	2	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr5:17275846C>A	ENST00000322611.3	+	2	781	c.521C>A	c.(520-522)cCc>cAc	p.P174H		NM_001271606.1|NM_006317.3	NP_001258535.1|NP_006308.3	P80723	BASP1_HUMAN	brain abundant, membrane attached signal protein 1	174					diaphragm development (GO:0060539)|glomerular visceral epithelial cell differentiation (GO:0072112)|gonad development (GO:0008406)|mesenchymal to epithelial transition (GO:0060231)|metanephric mesenchyme development (GO:0072075)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of heart growth (GO:0060421)|positive regulation of metanephric ureteric bud development (GO:2001076)|substantia nigra development (GO:0021762)|thorax and anterior abdomen determination (GO:0007356)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|lung(8)	9						GACTCAAAACCCGGCAGCTCG	0.662																																					p.P174H		Atlas-SNP	.											.	BASP1	29	.	0			c.C521A						.						8	11	10					5																	17275846		2132	4200	6332	SO:0001583	missense	10409	exon2			CAAAACCCGGCAG	AF039656	CCDS3888.1	5p15.1	2010-12-03			ENSG00000176788	ENSG00000176788			957	protein-coding gene	gene with protein product		605940				9310187, 9749536	Standard	NM_001271606		Approved	NAP-22, NAP22, CAP23, CAP-23	uc031siz.1	P80723	OTTHUMG00000131061	ENST00000322611.3:c.521C>A	chr5.hg19:g.17275846C>A	ENSP00000319281:p.Pro174His	52.0	0.0		35.0	16.0	NM_006317	B4DJA8|D3DTD5|O43596|Q5U0S0|Q9BWA5	Missense_Mutation	SNP	ENST00000322611.3	hg19	CCDS3888.1	.	.	.	.	.	.	.	.	.	.	C	16.85	3.236152	0.58886	.	.	ENSG00000176788	ENST00000322611;ENST00000447228	T	0.67345	-0.26	4.51	4.51	0.55191	.	0.000000	0.51477	U	0.000098	T	0.78110	0.4232	L	0.54323	1.7	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.81072	-0.1098	10	0.87932	D	0	-7.1627	15.7977	0.78424	0.0:1.0:0.0:0.0	.	174	P80723	BASP1_HUMAN	H	174;120	ENSP00000319281:P174H	ENSP00000319281:P174H	P	+	2	0	BASP1	17328846	1.000000	0.71417	0.981000	0.43875	0.609000	0.37215	6.437000	0.73421	2.053000	0.61076	0.491000	0.48974	CCC	.	.		0.662	BASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253716.2			A	17275846	C	A	17275846	3	1	287	1	0	0	0	0	1	0	0	0	1317	623	22	3	523	3	BASP1	5	17275846	Missense_Mutation	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10		17275846	163639414	33	42131										
RAI14	26064	hgsc.bcm.edu	37	chr5	34824058	34824058	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	tgcactgtctgaaatgaagtCtcagtattcaaaagtgttga	9	6	3	3			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr5:34824058C>T	ENST00000265109.3	+	15	2398	c.2111C>T	c.(2110-2112)tCt>tTt	p.S704F	RAI14_ENST00000503673.1_Missense_Mutation_p.S704F|RAI14_ENST00000428746.2_Missense_Mutation_p.S704F|RAI14_ENST00000397449.1_Missense_Mutation_p.S697F|RAI14_ENST00000515799.1_Missense_Mutation_p.S707F|RAI14_ENST00000512629.1_Missense_Mutation_p.S675F|RAI14_ENST00000506376.1_Missense_Mutation_p.S696F	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	704						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(19)|lung(22)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(31;0.000191)					GAAATGAAGTCTCAGTATTCA	0.408																																					p.S707F		Atlas-SNP	.											.	RAI14	100	.	0			c.C2120T						.						89	87	87					5																	34824058		2203	4300	6503	SO:0001583	missense	26064	exon17			TGAAGTCTCAGTA	AB037755	CCDS34142.1, CCDS54837.1, CCDS54838.1, CCDS54839.1	5p13.3-p13.2	2013-01-10			ENSG00000039560	ENSG00000039560		"Ankyrin repeat domain containing"	14873	protein-coding gene	gene with protein product	"novel retinal pigment epithelial"	606586				11042181	Standard	NM_015577		Approved	NORPEG, KIAA1334, RAI13, DKFZp564G013	uc011coj.2	Q9P0K7	OTTHUMG00000162019	ENST00000265109.3:c.2111C>T	chr5.hg19:g.34824058C>T	ENSP00000265109:p.Ser704Phe	297.0	0.0		252.0	40.0	NM_001145525	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Missense_Mutation	SNP	ENST00000265109.3	hg19	CCDS34142.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.327857	0.81690	.	.	ENSG00000039560	ENST00000265109;ENST00000512629;ENST00000428746;ENST00000503673;ENST00000515799;ENST00000506376;ENST00000397449	T;T;T;T;T;T;T	0.37752	1.21;1.18;1.21;1.21;1.21;1.26;1.25	5.68	5.68	0.88126	.	.	.	.	.	T	0.47469	0.1447	L	0.32530	0.975	0.54753	D	0.999986	P;P;D;P	0.55385	0.937;0.938;0.971;0.938	P;P;P;P	0.57204	0.628;0.58;0.815;0.58	T	0.43766	-0.9371	9	0.72032	D	0.01	-4.0981	19.7964	0.96487	0.0:1.0:0.0:0.0	.	696;675;707;704	Q9P0K7-3;E9PED3;Q9P0K7-2;Q9P0K7	.;.;.;RAI14_HUMAN	F	704;675;704;704;707;696;697	ENSP00000265109:S704F;ENSP00000422377:S675F;ENSP00000388725:S704F;ENSP00000422942:S704F;ENSP00000427123:S707F;ENSP00000423854:S696F;ENSP00000380591:S697F	ENSP00000265109:S704F	S	+	2	0	RAI14	34859815	0.996000	0.38824	1.000000	0.80357	0.992000	0.81027	3.326000	0.52037	2.683000	0.91414	0.555000	0.69702	TCT	.	.		0.408	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577		T	34824058	C	T	34824058	3	4	287	1	0	0	0	0	1	0	0	0	13023	913	32	3	2230	3	RAI14	5	34824058	Missense_Mutation	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10	17548212	34824058	146091202	34	42132										
NIPBL	25836	hgsc.bcm.edu	37	chr5	37017238	37017238	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	ttacaagcaaaatggatcaaGgatctatagaacgcatttta	7	6	2	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr5:37017238G>C	ENST00000282516.8	+	24	5393	c.4894G>C	c.(4894-4896)Gga>Cga	p.G1632R	NIPBL_ENST00000448238.2_Missense_Mutation_p.G1632R	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	1632					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			AATGGATCAAGGATCTATAGA	0.343																																					p.G1632R		Atlas-SNP	.											.	NIPBL	513	.	0			c.G4894C						.						57	54	55					5																	37017238		2203	4300	6503	SO:0001583	missense	25836	exon24			GATCAAGGATCTA	AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"sister chromatid cohesion 2 homolog (yeast)"	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.4894G>C	chr5.hg19:g.37017238G>C	ENSP00000282516:p.Gly1632Arg	206.0	0.0		169.0	13.0	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Missense_Mutation	SNP	ENST00000282516.8	hg19	CCDS3920.1	.	.	.	.	.	.	.	.	.	.	G	11.46	1.645605	0.29246	.	.	ENSG00000164190	ENST00000282516;ENST00000448238	T;T	0.65732	-0.17;-0.17	5.45	5.45	0.79879	Armadillo-type fold (1);	0.181312	0.49305	D	0.000146	T	0.40839	0.1133	N	0.03324	-0.35	0.44660	D	0.997649	B;B	0.17852	0.024;0.005	B;B	0.15484	0.013;0.004	T	0.32798	-0.9893	10	0.14252	T	0.57	.	19.6495	0.95795	0.0:0.0:1.0:0.0	.	1632;1632	Q6KC79;Q6KC79-2	NIPBL_HUMAN;.	R	1632	ENSP00000282516:G1632R;ENSP00000406266:G1632R	ENSP00000282516:G1632R	G	+	1	0	NIPBL	37052995	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	5.298000	0.65710	2.717000	0.92951	0.585000	0.79938	GGA	.	.		0.343	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		C	37017238	G	C	37017238	3	2	287	1	0	0	0	0	1	0	0	0	10437	1001	35	4	4984	4	NIPBL	5	37017238	Missense_Mutation	SNP	G	TCGA-G3-A5SL-01A-11D-A27I-10	2193180	37017238	143898022	35	42133										
RASA1	5921	hgsc.bcm.edu	37	chr5	86672363	86672363	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	aaaaatcatgccagaagaagAgtacagtgaatttaaagagg	10	4	1	5			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr5:86672363A>C	ENST00000274376.6	+	16	2729	c.2165A>C	c.(2164-2166)gAg>gCg	p.E722A	RASA1_ENST00000456692.2_Missense_Mutation_p.E545A|RASA1_ENST00000506290.1_Missense_Mutation_p.E556A|RASA1_ENST00000512763.1_Missense_Mutation_p.E555A|CTC-428H11.2_ENST00000607486.1_RNA	NM_002890.2	NP_002881.1	P20936	RASA1_HUMAN	RAS p21 protein activator (GTPase activating protein) 1	722					blood vessel morphogenesis (GO:0048514)|embryo development (GO:0009790)|intracellular signal transduction (GO:0035556)|mitotic cytokinesis (GO:0000281)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|regulation of RNA metabolic process (GO:0051252)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|ruffle (GO:0001726)	glycoprotein binding (GO:0001948)|GTPase binding (GO:0051020)|potassium channel inhibitor activity (GO:0019870)|Ras GTPase activator activity (GO:0005099)|receptor binding (GO:0005102)			NS(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(12)|lung(13)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	48		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		CCAGAAGAAGAGTACAGTGAA	0.338																																					p.E722A		Atlas-SNP	.											.	RASA1	213	.	0			c.A2165C						.						70	69	70					5																	86672363		2203	4300	6503	SO:0001583	missense	5921	exon16			AAGAAGAGTACAG		CCDS34200.1, CCDS47243.1	5q13	2013-02-14			ENSG00000145715	ENSG00000145715		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	9871	protein-coding gene	gene with protein product	"capillary malformation-arteriovenous malformation"	139150		RASA		15917201	Standard	NM_022650		Approved	GAP, CM-AVM, p120GAP, p120RASGAP	uc003kiw.3	P20936	OTTHUMG00000162605	ENST00000274376.6:c.2165A>C	chr5.hg19:g.86672363A>C	ENSP00000274376:p.Glu722Ala	55.0	0.0		94.0	9.0	NM_002890	B2R6W3|Q9UDI1	Missense_Mutation	SNP	ENST00000274376.6	hg19	CCDS34200.1	.	.	.	.	.	.	.	.	.	.	A	17.67	3.447359	0.63178	.	.	ENSG00000145715	ENST00000274376;ENST00000534133;ENST00000456692;ENST00000512763;ENST00000506290	T;T;T;T	0.71461	-0.57;-0.57;-0.57;-0.57	5.54	5.54	0.83059	Rho GTPase activation protein (1);C2 calcium/lipid-binding domain, CaLB (1);Ras GTPase-activating protein (1);	0.195432	0.53938	D	0.000053	T	0.79452	0.4448	M	0.73962	2.25	0.80722	D	1	P;P;P;P;P	0.46578	0.797;0.477;0.797;0.871;0.88	P;B;P;P;P	0.51833	0.482;0.242;0.482;0.681;0.501	T	0.82275	-0.0538	10	0.72032	D	0.01	.	15.6717	0.77283	1.0:0.0:0.0:0.0	.	556;555;556;545;722	E9PGC0;B4DTL2;B4DTX4;P20936-2;P20936	.;.;.;.;RASA1_HUMAN	A	722;755;545;555;556	ENSP00000274376:E722A;ENSP00000411221:E545A;ENSP00000422008:E555A;ENSP00000420905:E556A	ENSP00000274376:E722A	E	+	2	0	RASA1	86708119	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.339000	0.96797	2.102000	0.63906	0.460000	0.39030	GAG	.	.		0.338	RASA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369729.1	NM_002890		C	86672363	A	C	86672363	3	2	287	1	0	0	0	0	1	0	0	0	13075	304	11	5	2239	5	RASA1	5	86672363	Missense_Mutation	SNP	A	TCGA-G3-A5SL-01A-11D-A27I-10	49655125	86672363	94242897	36	42134										
PCDHB10	56126	hgsc.bcm.edu	37	chr5	140572647	140572647	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	caaaactacacgatcagcccCaactcttttttccatattaa	2	13	2	0			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr5:140572647C>T	ENST00000239446.4	+	1	706	c.522C>T	c.(520-522)ccC>ccT	p.P174P		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	174	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGATCAGCCCCAACTCTTTTT	0.448																																					p.P174P		Atlas-SNP	.											.	PCDHB10	177	.	0			c.C522T						.						131	149	143					5																	140572647		2203	4300	6503	SO:0001819	synonymous_variant	56126	exon1			CAGCCCCAACTCT	AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"Cadherins / Protocadherins : Clustered"	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.522C>T	chr5.hg19:g.140572647C>T		323.0	0.0		186.0	67.0	NM_018930	Q96T99	Silent	SNP	ENST00000239446.4	hg19	CCDS4252.1																																																																																			.	.		0.448	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930		T	140572647	C	T	140572647	2	4	287	1	0	0	0	0	0	0	0	1	11544	581	21	3		3	PCDHB10	5	140572647	Silent	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10	53900284	140572647	40342613	37	42135										
DUSP22	56940	hgsc.bcm.edu	37	chr6	348175	348175	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	gtcactgactttggctgggaGgatgccctgcacaccgtgcg	14	12	1	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr6:348175G>C	ENST00000344450.5	+	6	779	c.336G>C	c.(334-336)gaG>gaC	p.E112D	DUSP22_ENST00000604971.1_Missense_Mutation_p.E9D|DUSP22_ENST00000605863.1_Missense_Mutation_p.E9D|DUSP22_ENST00000605035.1_Missense_Mutation_p.E9D|DUSP22_ENST00000605315.1_Missense_Mutation_p.E9D|DUSP22_ENST00000419235.2_Missense_Mutation_p.E112D|DUSP22_ENST00000603453.1_Missense_Mutation_p.E9D	NM_020185.3	NP_064570.1	Q9NRW4	DUS22_HUMAN	dual specificity phosphatase 22	112	Tyrosine-protein phosphatase.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|inactivation of MAPK activity (GO:0000188)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of JNK cascade (GO:0046330)|protein dephosphorylation (GO:0006470)|regulation of cell proliferation (GO:0042127)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(2)	26	all_hematologic(77;0.228)	Breast(5;0.0249)|all_hematologic(90;0.0489)		OV - Ovarian serous cystadenocarcinoma(45;0.0277)|BRCA - Breast invasive adenocarcinoma(62;0.0669)		TTGGCTGGGAGGATGCCCTGC	0.602																																					p.E112D		Atlas-SNP	.											.	DUSP22	55	.	0			c.G336C						.						179	162	168					6																	348175		2203	4300	6503	SO:0001583	missense	56940	exon6			CTGGGAGGATGCC	AF165519	CCDS4468.1, CCDS69035.1	6p25.3	2013-09-19			ENSG00000112679	ENSG00000112679		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	16077	protein-coding gene	gene with protein product						9205128, 11717427	Standard	NM_001286555		Approved	MKPX, JSP1, JKAP, VHX	uc003msx.3	Q9NRW4	OTTHUMG00000014113	ENST00000344450.5:c.336G>C	chr6.hg19:g.348175G>C	ENSP00000345281:p.Glu112Asp	305.0	0.0		273.0	15.0	NM_020185	B4DK56|Q59GW2|Q5VWR2|Q96AR1	Missense_Mutation	SNP	ENST00000344450.5	hg19	CCDS4468.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.01|17.01	3.280523|3.280523	0.59758|0.59758	.|.	.|.	ENSG00000112679|ENSG00000112679	ENST00000344450|ENST00000419235	D|.	0.85702|.	-2.02|.	5.82|5.82	-2.83|-2.83	0.05769|0.05769	Dual specificity phosphatase, catalytic domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);Dual specificity phosphatase, subgroup, catalytic domain (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.25901|0.25901	0.0631|0.0631	N|N	0.16862|0.16862	0.45|0.45	0.50171|0.50171	D|D	0.999852|0.999852	B;B;B|.	0.13145|.	0.003;0.007;0.004|.	B;B;B|.	0.19391|.	0.009;0.025;0.008|.	T|T	0.15492|0.15492	-1.0435|-1.0435	10|5	0.30078|.	T|.	0.28|.	.|.	13.5495|13.5495	0.61723|0.61723	0.4799:0.0:0.5201:0.0|0.4799:0.0:0.5201:0.0	.|.	112;69;112|.	Q9NRW4-2;B3KSA8;Q9NRW4|.	.;.;DUS22_HUMAN|.	D|R	112|50	ENSP00000345281:E112D|.	ENSP00000345281:E112D|.	E|G	+|+	3|1	2|0	DUSP22|DUSP22	293175|293175	0.996000|0.996000	0.38824|0.38824	0.835000|0.835000	0.33067|0.33067	0.983000|0.983000	0.72400|0.72400	0.436000|0.436000	0.21526|0.21526	-0.521000|-0.521000	0.06426|0.06426	0.655000|0.655000	0.94253|0.94253	GAG|GGA	.	.		0.602	DUSP22-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000039621.1	NM_020185		C	348175	G	C	348175	3	2	287	1	0	0	0	0	1	0	0	0	4823	991	35	4	358	4	DUSP22	6	348175	Missense_Mutation	SNP	G	TCGA-G3-A5SL-01A-11D-A27I-10		348175	170766892	38	42136										
RDBP	7936	hgsc.bcm.edu	37	chr6	31926222	31926223	+	Start_Codon_Ins	INS	-	-	T													0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	tccggggggtatcaccaacaINStggtggctcctagttcaggg							TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr6:31926222_31926223insT	ENST00000375429.3	-	0	227_228				NELFE_ENST00000375425.5_Frame_Shift_Ins_p.M8fs|MIR1236_ENST00000408340.1_RNA|SKIV2L_ENST00000544581.1_5'Flank|SKIV2L_ENST00000375394.2_5'Flank|NELFE_ENST00000444811.2_Start_Codon_Ins	NM_002904.5	NP_002895.3	P18615	NELFE_HUMAN	negative elongation factor complex member E						gene expression (GO:0010467)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	NELF complex (GO:0032021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)										TATCACCAACATGGTGGCTCCT	0.564																																					p.M1fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.2_3insA						.																																			SO:0001582	initiator_codon_variant	7936	exon2			.	M33230	CCDS4730.1	6p21.3	2013-02-12	2013-01-31	2013-01-31	ENSG00000204356	ENSG00000204356		"RNA binding motif (RRM) containing"	13974	protein-coding gene	gene with protein product		154040	"RD RNA-binding protein", "RD RNA binding protein"	RDBP			Standard	XM_006715205		Approved	RD, D6S45, NELF-E, RDP	uc003nyk.3	P18615	OTTHUMG00000031046	ENST00000375429.3:c.2dupA	chr6.hg19:g.31926223_31926223dupT		93.0	0.0		111.0	27.0	NM_002904	A2BE08|B4DUN1|B4DYX9|Q5JP74|Q5JP75|Q96F56|Q9NPK2	Frame_Shift_Ins	INS	ENST00000375429.3	hg19	CCDS4730.1																																																																																			.	.		0.564	NELFE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076047.4			T	31926223	-	T	31926222	7	5	287	1	0	1	1	0	0	0	0	0	13203	217	8	0	1180	0	RDBP	6	31926222	Start_Codon_Ins	INS	-	TCGA-G3-A5SL-01A-11D-A27I-10	31578047	31926222	139188845	39	42137										
TNXB	7148	hgsc.bcm.edu	37	chr6	32037394	32037394	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	tgcagcccgtagagcagcagCttgtacctgtgggcagggtc	15	11	0	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr6:32037394C>A	ENST00000375244.3	-	15	5724	c.5523G>T	c.(5521-5523)aaG>aaT	p.K1841N	TNXB_ENST00000375247.2_Missense_Mutation_p.K1841N			P22105	TENX_HUMAN	tenascin XB	1923	Fibronectin type-III 10. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						AGAGCAGCAGCTTGTACCTGT	0.667																																					p.K1841N		Atlas-SNP	.											.	TNXB	553	.	0			c.G5523T						.						27	33	31					6																	32037394		2173	4278	6451	SO:0001583	missense	7148	exon15			CAGCAGCTTGTAC	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.5523G>T	chr6.hg19:g.32037394C>A	ENSP00000364393:p.Lys1841Asn	55.0	0.0		79.0	8.0	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	hg19		.	.	.	.	.	.	.	.	.	.	C	21.3	4.134760	0.77662	.	.	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.56444	0.46;0.46	5.5	5.5	0.81552	.	0.000000	0.50627	D	0.000115	T	0.65037	0.2653	M	0.91872	3.25	0.25924	N	0.983075	D	0.89917	1.0	D	0.87578	0.998	T	0.63457	-0.6633	10	0.18710	T	0.47	.	10.4202	0.44346	0.0:0.9109:0.0:0.0891	.	1841	P22105-3	.	N	1841	ENSP00000364393:K1841N;ENSP00000364396:K1841N	ENSP00000364393:K1841N	K	-	3	2	TNXB	32145372	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	2.120000	0.41968	2.598000	0.87819	0.591000	0.81541	AAG	.	.		0.667	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		A	32037394	C	A	32037394	3	1	287	1	0	0	0	0	1	0	0	0	16361	796	28	3	9310	3	TNXB	6	32037394	Missense_Mutation	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10	111172	32037394	139077673	40	42138										
TNXB	7148	hgsc.bcm.edu	37	chr6	32041646	32041646	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	ggagaggcccacagagttggGggtcacatctgtcactgtca	14	10	4	2			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr6:32041646G>T	ENST00000375244.3	-	12	4660	c.4459C>A	c.(4459-4461)Ccc>Acc	p.P1487T	TNXB_ENST00000375247.2_Missense_Mutation_p.P1487T			P22105	TENX_HUMAN	tenascin XB	1574	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						ACAGAGTTGGGGGTCACATCT	0.612																																					p.P1487T		Atlas-SNP	.											.	TNXB	553	.	0			c.C4459A						.						30	33	32					6																	32041646		1268	2563	3831	SO:0001583	missense	7148	exon12			AGTTGGGGGTCAC	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.4459C>A	chr6.hg19:g.32041646G>T	ENSP00000364393:p.Pro1487Thr	111.0	0.0		134.0	31.0	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	hg19		.	.	.	.	.	.	.	.	.	.	G	11.56	1.674536	0.29693	.	.	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.56941	0.43;0.43	5.46	4.56	0.56223	.	0.414082	0.18364	N	0.143489	T	0.46737	0.1408	M	0.83384	2.64	0.27156	N	0.961295	B	0.34226	0.443	P	0.47299	0.543	T	0.51919	-0.8644	10	0.30854	T	0.27	.	6.0664	0.19866	0.1026:0.0:0.7139:0.1835	.	1487	P22105-3	.	T	1487	ENSP00000364393:P1487T;ENSP00000364396:P1487T	ENSP00000364393:P1487T	P	-	1	0	TNXB	32149624	0.985000	0.35326	0.926000	0.36857	0.533000	0.34776	1.184000	0.32053	1.212000	0.43366	0.543000	0.68304	CCC	.	.		0.612	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		T	32041646	G	T	32041646	3	4	287	1	0	0	0	0	1	0	0	0	16361	1232	43	3	10386	3	TNXB	6	32041646	Missense_Mutation	SNP	G	TCGA-G3-A5SL-01A-11D-A27I-10	4252	32041646	139073421	41	42139										
PKHD1	5314	hgsc.bcm.edu	37	chr6	51907882	51907882	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	aacctgcaagaactgggagtCaccagagaaaccagttccgg	11	11	1	2			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr6:51907882C>A	ENST00000371117.3	-	27	3147	c.2872G>T	c.(2872-2874)Gac>Tac	p.D958Y	PKHD1_ENST00000340994.4_Missense_Mutation_p.D958Y	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	958	IPT/TIG 4.				cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					AACTGGGAGTCACCAGAGAAA	0.368																																					p.D958Y		Atlas-SNP	.											.	PKHD1	927	.	0			c.G2872T						.						74	73	74					6																	51907882		2203	4300	6503	SO:0001583	missense	5314	exon27			GGGAGTCACCAGA	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.2872G>T	chr6.hg19:g.51907882C>A	ENSP00000360158:p.Asp958Tyr	55.0	0.0		139.0	33.0	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	hg19	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	C	15.72	2.916313	0.52546	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.90324	-2.65;-2.65	5.98	5.12	0.69794	Cell surface receptor IPT/TIG (1);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.429815	0.25984	N	0.027054	D	0.92254	0.7543	M	0.72118	2.19	0.09310	N	1	D;D	0.76494	0.996;0.999	P;D	0.72982	0.899;0.979	D	0.87537	0.2456	10	0.72032	D	0.01	.	12.1659	0.54129	0.0:0.9211:0.0:0.0789	.	958;958	P08F94-2;P08F94	.;PKHD1_HUMAN	Y	958	ENSP00000360158:D958Y;ENSP00000341097:D958Y	ENSP00000341097:D958Y	D	-	1	0	PKHD1	52015841	0.112000	0.22096	0.012000	0.15200	0.820000	0.46376	1.204000	0.32296	1.558000	0.49541	0.650000	0.86243	GAC	.	.		0.368	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		A	51907882	C	A	51907882	3	1	287	1	0	0	0	0	1	0	0	0	11980	826	29	3	9555	3	PKHD1	6	51907882	Missense_Mutation	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10	19866236	51907882	119207185	42	42140										
PHF10	55274	hgsc.bcm.edu	37	chr6	170112622	170112622	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	taatggcagataccgcagctCatctggtgagtacctgaagt	11	9	2	3			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr6:170112622C>A	ENST00000339209.4	-	8	940	c.817G>T	c.(817-819)Gag>Tag	p.E273*	PHF10_ENST00000366780.4_Nonsense_Mutation_p.E271*	NM_018288.3|NM_133325.2	NP_060758.2|NP_579866.2	Q8WUB8	PHF10_HUMAN	PHD finger protein 10	273	SAY.				nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	npBAF complex (GO:0071564)	zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|liver(3)|lung(4)|prostate(2)|urinary_tract(1)	14		Breast(66;5.08e-05)|Ovarian(120;0.208)		OV - Ovarian serous cystadenocarcinoma(33;1.4e-21)|BRCA - Breast invasive adenocarcinoma(81;1.4e-07)|GBM - Glioblastoma multiforme(31;0.00176)		TACCGCAGCTCATCTGGTGAG	0.428																																					p.E273X		Atlas-SNP	.											.	PHF10	76	.	0			c.G817T						.						116	113	114					6																	170112622		2203	4300	6503	SO:0001587	stop_gained	55274	exon8			GCAGCTCATCTGG	AF338735	CCDS5308.2, CCDS5309.2	6q27	2014-05-13			ENSG00000130024	ENSG00000130024		"Zinc fingers, PHD-type"	18250	protein-coding gene	gene with protein product		613069				11827455	Standard	NM_018288		Approved	FLJ10975, XAP135, BAF45a	uc011egy.2	Q8WUB8	OTTHUMG00000016058	ENST00000339209.4:c.817G>T	chr6.hg19:g.170112622C>A	ENSP00000341805:p.Glu273*	129.0	0.0		63.0	14.0	NM_018288	Q2YDA3|Q53HG8|Q9BXD2|Q9NV26	Nonsense_Mutation	SNP	ENST00000339209.4	hg19	CCDS5308.2	.	.	.	.	.	.	.	.	.	.	C	37	6.100383	0.97281	.	.	ENSG00000130024	ENST00000366780;ENST00000339209	.	.	.	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-30.6999	18.4165	0.90572	0.0:1.0:0.0:0.0	.	.	.	.	X	271;273	.	ENSP00000341805:E273X	E	-	1	0	PHF10	169854547	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.211000	0.77933	2.673000	0.90976	0.585000	0.79938	GAG	.	.		0.428	PHF10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346732.1	NM_018288		A	170112622	C	A	170112622	4	1	287	1	0	0	0	0	0	1	0	0	11830	835	29	3	699	3	PHF10	6	170112622	Nonsense_Mutation	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10	118204740	170112622	1002445	43	42141										
C7orf26	79034	hgsc.bcm.edu	37	chr7	6631388	6631388	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	tttcatcccttttcagccctCaagggaacaaagccgatgac	7	13	3	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr7:6631388C>T	ENST00000344417.5	+	2	571	c.304C>T	c.(304-306)Caa>Taa	p.Q102*	C7orf26_ENST00000359073.5_Nonsense_Mutation_p.Q83*|AC079742.4_ENST00000434951.1_RNA|C7orf26_ENST00000472693.1_3'UTR	NM_024067.2	NP_076972.2	Q96N11	CG026_HUMAN	chromosome 7 open reading frame 26	102										endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	11		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)		TTTCAGCCCTCAAGGGAACAA	0.498																																					p.Q102X		Atlas-SNP	.											.	C7orf26	33	.	0			c.C304T						.						145	149	148					7																	6631388		2203	4300	6503	SO:0001587	stop_gained	79034	exon2			AGCCCTCAAGGGA	BC005121	CCDS5353.1	7p22.1	2011-11-24			ENSG00000146576	ENSG00000146576			21702	protein-coding gene	gene with protein product							Standard	NM_024067		Approved	MGC2718	uc003sqo.1	Q96N11	OTTHUMG00000125517	ENST00000344417.5:c.304C>T	chr7.hg19:g.6631388C>T	ENSP00000340220:p.Gln102*	202.0	0.0		163.0	20.0	NM_024067	Q9BQ43	Nonsense_Mutation	SNP	ENST00000344417.5	hg19	CCDS5353.1	.	.	.	.	.	.	.	.	.	.	c	42	9.527965	0.99196	.	.	ENSG00000146576	ENST00000344417;ENST00000359073	.	.	.	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	-12.79	16.766	0.85524	0.0:1.0:0.0:0.0	.	.	.	.	X	102;83	.	ENSP00000340220:Q102X	Q	+	1	0	C7orf26	6597913	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.760000	0.85248	2.627000	0.88993	0.632000	0.83419	CAA	.	.		0.498	C7orf26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246844.2	NM_024067		T	6631388	C	T	6631388	4	4	287	1	0	0	0	0	0	1	0	0	2383	827	29	3	310	3	C7orf26	7	6631388	Nonsense_Mutation	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10		6631388	152507275	44	42142										
NT5C3	51251	hgsc.bcm.edu	37	chr7	33057096	33057100	+	Frame_Shift_Del	DEL	ATGAT	ATGAT	-													0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	gacacaactttgacattgggAtgataaacaccagcttgacg					rs104894027		TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	ATGAT	ATGAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr7:33057096_33057100delATGAT	ENST00000242210.7	-	7	735_739	c.659_663delATCAT	c.(658-663)tatcatfs	p.YH220fs	NT5C3A_ENST00000409787.1_Frame_Shift_Del_p.YH181fs|NT5C3A_ENST00000610140.1_Frame_Shift_Del_p.YH215fs|NT5C3A_ENST00000409467.1_Frame_Shift_Del_p.YH169fs|NT5C3A_ENST00000381626.2_Frame_Shift_Del_p.YH169fs|NT5C3A_ENST00000396152.2_Frame_Shift_Del_p.YH181fs|NT5C3A_ENST00000405342.1_Frame_Shift_Del_p.YH181fs|AVL9_ENST00000404479.1_Intron	NM_001002009.2|NM_001002010.2	NP_001002009.1|NP_001002010.1	Q9H0P0	5NT3A_HUMAN	5'-nucleotidase, cytosolic IIIA	220					dephosphorylation (GO:0016311)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside metabolic process (GO:0006213)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	2'-phosphotransferase activity (GO:0008665)|5'-nucleotidase activity (GO:0008253)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)										TGACATTGGGATGATAAACACCAGC	0.332																																					p.220_222del		Atlas-Indel,Pindel	.											.	.	.	.	0			c.660_664del	GRCh37	CM032297	NT5C3	M	rs104894027	.																																			SO:0001589	frameshift_variant	0	exon7			.	AF312735	CCDS34616.1, CCDS34617.1, CCDS55101.1	7p14.3	2013-03-06	2013-03-06	2013-03-06	ENSG00000122643	ENSG00000122643	3.1.3.5		17820	protein-coding gene	gene with protein product	"lupin"	606224	"5'-nucleotidase, cytosolic III"	NT5C3		11042152, 10942414	Standard	NM_001002010		Approved	UMPH1, PSN1, PN-I, UMPH, P5'N-1, cN-III, p36, POMP, hUMP1	uc003tdk.4	Q9H0P0	OTTHUMG00000152983	ENST00000242210.7:c.659_663delATCAT	chr7.hg19:g.33057096_33057100delATGAT	ENSP00000242210:p.Tyr220fs	154.0	0.0		134.0	24.0	NM_001002010	A8K253|B2RAA5|B8ZZC4|Q6IPZ1|Q6NXS6|Q7L3G6|Q9P0P5|Q9UC42|Q9UC43|Q9UC44|Q9UC45	Frame_Shift_Del	DEL	ENST00000242210.7	hg19	CCDS34616.1																																																																																			.	.		0.332	NT5C3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328880.1	NM_016489		-	33057100	ATGAT	-	33057096	7	5	287	1	0	1	0	1	0	0	0	0	10697	330	12	0	359	0	NT5C3	7	33057096	Frame_Shift_Del	DEL	ATGAT	TCGA-G3-A5SL-01A-11D-A27I-10	26425708	33057096	126081567	45	42143										
HGF	3082	hgsc.bcm.edu	37	chr7	81372744	81372744	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	ccatggcctcggctggccatCgggattgcggcaataattat	12	11	0	0			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr7:81372744C>A	ENST00000222390.5	-	7	1016	c.790G>T	c.(790-792)Gat>Tat	p.D264Y	HGF_ENST00000453411.1_Missense_Mutation_p.D259Y|HGF_ENST00000444829.2_Missense_Mutation_p.D264Y|HGF_ENST00000457544.2_Missense_Mutation_p.D259Y	NM_000601.4	NP_000592.3	P14210	HGF_HUMAN	hepatocyte growth factor (hepapoietin A; scatter factor)	264	Kringle 2. {ECO:0000255|PROSITE- ProRule:PRU00121}.				activation of MAPK activity (GO:0000187)|blood coagulation (GO:0007596)|cell chemotaxis (GO:0060326)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epithelial to mesenchymal transition (GO:0001837)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|hyaluronan metabolic process (GO:0030212)|liver development (GO:0001889)|mitotic nuclear division (GO:0007067)|myoblast proliferation (GO:0051450)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of hydrogen peroxide-mediated programmed cell death (GO:1901299)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|organ regeneration (GO:0031100)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of cell migration (GO:0030335)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	catalytic activity (GO:0003824)|chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|identical protein binding (GO:0042802)			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						GGCTGGCCATCGGGATTGCGG	0.488																																					p.D264Y		Atlas-SNP	.											HGF,NS,carcinoma,0,1	HGF	171	.	0			c.G790T						.						95	86	89					7																	81372744		2203	4300	6503	SO:0001583	missense	3082	exon7			GGCCATCGGGATT		CCDS5597.1, CCDS47626.1, CCDS47627.1, CCDS47628.1, CCDS47629.1	7q21.1	2009-09-11			ENSG00000019991	ENSG00000019991			4893	protein-coding gene	gene with protein product	"hepatopoietin A", "fibroblast-derived tumor cytotoxic factor", "scatter factor", "lung fibroblast-derived mitogen"	142409	"deafness, autosomal recessive 39"	DFNB39		1837206, 19576567	Standard	XM_006715956		Approved	SF, F-TCF, HGFB, HPTA	uc003uhl.3	P14210	OTTHUMG00000023804	ENST00000222390.5:c.790G>T	chr7.hg19:g.81372744C>A	ENSP00000222390:p.Asp264Tyr	85.0	0.0		181.0	23.0	NM_000601	A1L3U6|Q02935|Q13494|Q14519|Q3KRB2|Q8TCE2|Q9BYL9|Q9BYM0|Q9UDU6	Missense_Mutation	SNP	ENST00000222390.5	hg19	CCDS5597.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.265404	0.80358	.	.	ENSG00000019991	ENST00000222390;ENST00000457544;ENST00000444829;ENST00000453411;ENST00000394769	T;T;T;T	0.74002	-0.8;-0.8;-0.8;-0.8	5.75	5.75	0.90469	Kringle (5);Kringle-like fold (1);Kringle, conserved site (1);	0.049605	0.85682	D	0.000000	D	0.92397	0.7587	H	0.98333	4.205	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.996;0.992;0.993	D	0.94808	0.7976	10	0.87932	D	0	.	19.9474	0.97186	0.0:1.0:0.0:0.0	.	259;264;259;264	P14210-5;P14210-2;P14210-3;P14210	.;.;.;HGF_HUMAN	Y	264;259;264;259;264	ENSP00000222390:D264Y;ENSP00000391238:D259Y;ENSP00000389854:D264Y;ENSP00000408270:D259Y	ENSP00000222390:D264Y	D	-	1	0	HGF	81210680	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.386000	0.59620	2.724000	0.93272	0.655000	0.94253	GAT	.	.		0.488	HGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253315.2	NM_000601		A	81372744	C	A	81372744	3	1	287	1	0	0	0	0	1	0	0	0	7094	884	31	1	1456	1	HGF	7	81372744	Missense_Mutation	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10	48315648	81372744	77765919	46	42144										
PCLO	27445	hgsc.bcm.edu	37	chr7	82545309	82545309	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	tactaccaagatgggaaacaGcaaatgtgttatccgtagaa	9	7	0	2			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr7:82545309G>A	ENST00000333891.9	-	7	12330	c.11993C>T	c.(11992-11994)gCt>gTt	p.A3998V	PCLO_ENST00000437081.1_Missense_Mutation_p.A718V|PCLO_ENST00000423517.2_Missense_Mutation_p.A3998V	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						ATGGGAAACAGCAAATGTGTT	0.393																																					p.A3998V		Atlas-SNP	.											.	PCLO	1506	.	0			c.C11993T						.						354	331	338					7																	82545309		1910	4137	6047	SO:0001583	missense	27445	exon7			GAAACAGCAAATG	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.11993C>T	chr7.hg19:g.82545309G>A	ENSP00000334319:p.Ala3998Val	27.0	0.0		51.0	22.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	G	15.56	2.870130	0.51588	.	.	ENSG00000186472	ENST00000333891;ENST00000423517;ENST00000437081	T;T	0.19394	2.15;2.15	5.85	5.85	0.93711	.	.	.	.	.	T	0.39911	0.1096	L	0.54323	1.7	0.42635	D	0.99339	P;D;D	0.59767	0.799;0.986;0.986	B;P;P	0.56398	0.343;0.797;0.797	T	0.08911	-1.0699	9	0.87932	D	0	.	20.1542	0.98100	0.0:0.0:1.0:0.0	.	3929;3998;3998	Q9Y6V0;Q9Y6V0-5;Q9Y6V0-6	PCLO_HUMAN;.;.	V	3998;3998;718	ENSP00000334319:A3998V;ENSP00000388393:A3998V	ENSP00000334319:A3998V	A	-	2	0	PCLO	82383245	1.000000	0.71417	0.969000	0.41365	0.743000	0.42351	5.154000	0.64894	2.767000	0.95098	0.563000	0.77884	GCT	.	.		0.393	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82545309	G	A	82545309	3	1	287	1	0	0	0	0	1	0	0	0	11592	971	34	3	3528	3	PCLO	7	82545309	Missense_Mutation	SNP	G	TCGA-G3-A5SL-01A-11D-A27I-10	1172565	82545309	76593354	47	42145										
RELN	5649	hgsc.bcm.edu	37	chr7	103179563	103179563	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	ctgagcaggaggcagcgaagTctatctgtaggaaggaatcc	14	8	2	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr7:103179563T>C	ENST00000428762.1	-	45	7301	c.7142A>G	c.(7141-7143)gAc>gGc	p.D2381G	RELN_ENST00000424685.2_Missense_Mutation_p.D2381G|RELN_ENST00000343529.5_Missense_Mutation_p.D2381G	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	2381					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		GGCAGCGAAGTCTATCTGTAG	0.542																																					p.D2381G	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.A7142G						.						106	88	94					7																	103179563		2203	4300	6503	SO:0001583	missense	5649	exon45			GCGAAGTCTATCT		CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.7142A>G	chr7.hg19:g.103179563T>C	ENSP00000392423:p.Asp2381Gly	104.0	0.0		150.0	68.0	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	hg19	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	T	17.80	3.478959	0.63849	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.18657	2.2;2.2;2.2	5.35	5.35	0.76521	Neuraminidase (1);	0.000000	0.85682	D	0.000000	T	0.44705	0.1306	M	0.63843	1.955	0.58432	D	0.999999	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.992	T	0.40136	-0.9579	10	0.66056	D	0.02	.	15.3372	0.74266	0.0:0.0:0.0:1.0	.	2381;2381	P78509-2;P78509	.;RELN_HUMAN	G	2381	ENSP00000392423:D2381G;ENSP00000345694:D2381G;ENSP00000388446:D2381G	ENSP00000345694:D2381G	D	-	2	0	RELN	102966799	1.000000	0.71417	0.998000	0.56505	0.861000	0.49209	7.698000	0.84413	2.032000	0.59987	0.533000	0.62120	GAC	.	.		0.542	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		C	103179563	T	C	103179563	3	2	287	1	0	0	0	0	1	0	0	0	13235	1667	58	2	3324	2	RELN	7	103179563	Missense_Mutation	SNP	T	TCGA-G3-A5SL-01A-11D-A27I-10	20634254	103179563	55959100	48	42146										
RP1	6101	hgsc.bcm.edu	37	chr8	55534004	55534004	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	cacggagcctagtggtcttcAggaatggcgacccgaagacg	14	11	2	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr8:55534004A>G	ENST00000220676.1	+	2	626	c.478A>G	c.(478-480)Agg>Ggg	p.R160G		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	160	Doublecortin 2. {ECO:0000255|PROSITE- ProRule:PRU00072}.				axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			AGTGGTCTTCAGGAATGGCGA	0.662																																					p.R160G	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.A478G						.						63	66	65					8																	55534004		2203	4300	6503	SO:0001583	missense	6101	exon2			GTCTTCAGGAATG	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.478A>G	chr8.hg19:g.55534004A>G	ENSP00000220676:p.Arg160Gly	97.0	0.0		243.0	37.0	NM_006269		Missense_Mutation	SNP	ENST00000220676.1	hg19	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	A	13.08	2.129640	0.37630	.	.	ENSG00000104237	ENST00000220676	D	0.88975	-2.45	5.14	-2.13	0.07144	Doublecortin domain (4);	0.118204	0.37136	N	0.002238	D	0.91794	0.7404	M	0.84948	2.725	0.28950	N	0.890472	D	0.57257	0.979	P	0.52554	0.702	D	0.89781	0.3961	10	0.72032	D	0.01	-1.0676	16.2331	0.82357	0.4237:0.5763:0.0:0.0	.	160	P56715	RP1_HUMAN	G	160	ENSP00000220676:R160G	ENSP00000220676:R160G	R	+	1	2	RP1	55696557	0.732000	0.28121	0.119000	0.21687	0.172000	0.22775	0.880000	0.28159	-0.704000	0.05042	0.528000	0.53228	AGG	.	.		0.662	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		G	55534004	A	G	55534004	3	3	287	1	0	0	0	0	1	0	0	0	13547	179	7	2	480	2	RP1	8	55534004	Missense_Mutation	SNP	A	TCGA-G3-A5SL-01A-11D-A27I-10		55534004	90830018	49	42147										
TMEM67	91147	hgsc.bcm.edu	37	chr8	94817076	94817076	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	catgcagatactaatatggaAgaaatgaatatgaaccttaa	7	5	0	4			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr8:94817076A>G	ENST00000453321.3	+	23	2467	c.2409A>G	c.(2407-2409)gaA>gaG	p.E803E	TMEM67_ENST00000409623.3_Silent_p.E722E	NM_153704.5	NP_714915.3	Q5HYA8	MKS3_HUMAN	transmembrane protein 67	803					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of centrosome duplication (GO:0010826)	centrosome (GO:0005813)|ciliary membrane (GO:0060170)|cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)	filamin binding (GO:0031005)|unfolded protein binding (GO:0051082)			breast(3)|endometrium(8)|kidney(5)|large_intestine(4)|liver(2)|lung(15)|ovary(2)|skin(1)|urinary_tract(1)	41	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.00896)			CTAATATGGAAGAAATGAATA	0.303																																					p.E803E		Atlas-SNP	.											.	TMEM67	187	.	0			c.A2409G						.						113	110	111					8																	94817076		2203	4295	6498	SO:0001819	synonymous_variant	91147	exon23			TATGGAAGAAATG	BX648768	CCDS6258.2, CCDS47893.1	8q22.1	2014-09-17			ENSG00000164953	ENSG00000164953			28396	protein-coding gene	gene with protein product	"Meckelin"	609884	"Meckel syndrome, type 3"	MKS3		12384791, 16415887, 19508969	Standard	NM_153704		Approved	MGC26979, JBTS6, NPHP11	uc011lgk.2	Q5HYA8	OTTHUMG00000153119	ENST00000453321.3:c.2409A>G	chr8.hg19:g.94817076A>G		49.0	0.0		120.0	7.0	NM_153704	B3KRU5|B3KT47|G5E9H2|Q3ZCX3|Q7Z5T8|Q8IZ06	Silent	SNP	ENST00000453321.3	hg19	CCDS6258.2																																																																																			.	.		0.303	TMEM67-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329641.2	NM_153704		G	94817076	A	G	94817076	2	3	287	1	0	0	0	0	0	0	0	1	16211	69	3	2		2	TMEM67	8	94817076	Silent	SNP	A	TCGA-G3-A5SL-01A-11D-A27I-10	39283072	94817076	51546946	50	42148										
KIAA1429	25962	hgsc.bcm.edu	37	chr8	95523540	95523540	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	acattaaagaccaagtattaTtggccagagtctcttctgag	8	8	2	3			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr8:95523540T>C	ENST00000297591.5	-	13	3338	c.3263A>G	c.(3262-3264)aAt>aGt	p.N1088S	KIAA1429_ENST00000421249.2_Missense_Mutation_p.N1088S|KIAA1429_ENST00000523405.1_5'UTR|KIAA1429_ENST00000437199.1_Missense_Mutation_p.N1088S	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	1088					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			CCAAGTATTATTGGCCAGAGT	0.343																																					p.N1088S		Atlas-SNP	.											.	KIAA1429	176	.	0			c.A3263G						.						43	44	43					8																	95523540		2203	4300	6503	SO:0001583	missense	25962	exon13			GTATTATTGGCCA	AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 121"					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.3263A>G	chr8.hg19:g.95523540T>C	ENSP00000297591:p.Asn1088Ser	58.0	0.0		180.0	23.0	NM_015496	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Missense_Mutation	SNP	ENST00000297591.5	hg19	CCDS34923.1	.	.	.	.	.	.	.	.	.	.	T	10.61	1.397966	0.25205	.	.	ENSG00000164944	ENST00000297591;ENST00000437199;ENST00000421249	T;T;T	0.43294	0.95;0.95;0.95	5.38	2.95	0.34219	.	0.192146	0.53938	N	0.000056	T	0.21062	0.0507	N	0.12182	0.205	0.36989	D	0.894691	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.10894	-1.0610	10	0.17369	T	0.5	-20.6318	8.1915	0.31370	0.0:0.0699:0.1349:0.7952	.	1088;1088	Q69YN4-4;Q69YN4	.;VIR_HUMAN	S	1088	ENSP00000297591:N1088S;ENSP00000395600:N1088S;ENSP00000398390:N1088S	ENSP00000297591:N1088S	N	-	2	0	KIAA1429	95592716	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.565000	0.60836	0.413000	0.25759	0.528000	0.53228	AAT	.	.		0.343	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496		C	95523540	T	C	95523540	3	2	287	1	0	0	0	0	1	0	0	0	8240	1493	52	2	2277	2	KIAA1429	8	95523540	Missense_Mutation	SNP	T	TCGA-G3-A5SL-01A-11D-A27I-10	706464	95523540	50840482	51	42149										
KIAA1429	25962	hgsc.bcm.edu	37	chr8	95543221	95543221	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	cacaggatcatcttcatcatCatcaggtggagggggtcctg	12	10	6	0			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr8:95543221C>T	ENST00000297591.5	-	6	652	c.577G>A	c.(577-579)Gat>Aat	p.D193N	KIAA1429_ENST00000421249.2_Missense_Mutation_p.D193N|KIAA1429_ENST00000437199.1_Missense_Mutation_p.D193N|RP11-267M23.3_ENST00000521010.1_RNA	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	193	Pro-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			TCTTCATCATCATCAGGTGGA	0.453																																					p.D193N		Atlas-SNP	.											.	KIAA1429	176	.	0			c.G577A						.						121	111	115					8																	95543221		2203	4300	6503	SO:0001583	missense	25962	exon6			CATCATCATCAGG	AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 121"					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.577G>A	chr8.hg19:g.95543221C>T	ENSP00000297591:p.Asp193Asn	47.0	0.0		116.0	82.0	NM_015496	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Missense_Mutation	SNP	ENST00000297591.5	hg19	CCDS34923.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.971393	0.92919	.	.	ENSG00000164944	ENST00000297591;ENST00000437199;ENST00000421249	T;T;T	0.46063	0.89;0.89;0.88	5.24	5.24	0.73138	.	0.114985	0.56097	D	0.000021	T	0.59115	0.2170	L	0.44542	1.39	0.80722	D	1	D;D	0.67145	0.996;0.996	D;D	0.77557	0.99;0.99	T	0.61574	-0.7035	10	0.72032	D	0.01	-17.1239	18.8146	0.92072	0.0:1.0:0.0:0.0	.	193;193	Q69YN4-4;Q69YN4	.;VIR_HUMAN	N	193	ENSP00000297591:D193N;ENSP00000395600:D193N;ENSP00000398390:D193N	ENSP00000297591:D193N	D	-	1	0	KIAA1429	95612397	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	6.944000	0.75940	2.435000	0.82474	0.585000	0.79938	GAT	.	.		0.453	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496		T	95543221	C	T	95543221	3	4	287	1	0	0	0	0	1	0	0	0	8240	826	29	3	4991	3	KIAA1429	8	95543221	Missense_Mutation	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10	19681	95543221	50820801	52	42150										
UQCRB	7381	hgsc.bcm.edu	37	chr8	97245396	97245396	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	ctgcttacccagtttattgaAtcctgcagcattgtaatacc	6	11	0	1	rs376775585		TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr8:97245396A>C	ENST00000287022.5	-	2	182	c.79T>G	c.(79-81)Ttc>Gtc	p.F27V	UQCRB_ENST00000518406.1_Missense_Mutation_p.F27V|UQCRB_ENST00000517523.1_5'UTR|UQCRB_ENST00000523920.1_Missense_Mutation_p.F27V|KB-1043D8.6_ENST00000520575.1_RNA	NM_001199975.2|NM_006294.4	NP_001186904.1|NP_006285.1	P14927	QCR7_HUMAN	ubiquinol-cytochrome c reductase binding protein	27					aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|oxidation-reduction process (GO:0055114)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrial respiratory chain complex III (GO:0005750)				kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	10	Breast(36;5.16e-05)					AGTTTATTGAATCCTGCAGCA	0.328																																					p.F27V		Atlas-SNP	.											.	UQCRB	17	.	0			c.T79G						.	A	,VAL/PHE	0,4406		0,0,2203	115	107	110		,79	4.8	1	8		110	1,8599	1.2+/-3.3	0,1,4299	no	utr-5,missense	UQCRB	NM_001199975.1,NM_006294.3	,50	0,1,6502	CC,CA,AA		0.0116,0.0,0.0077	,possibly-damaging	,27/112	97245396	1,13005	2203	4300	6503	SO:0001583	missense	7381	exon2			TATTGAATCCTGC	X13585	CCDS6269.1, CCDS59107.1	8q22	2011-07-04			ENSG00000156467	ENSG00000156467		"Mitochondrial respiratory chain complex / Complex III"	12582	protein-coding gene	gene with protein product	"ubiquinol-cytochrome c reductase, complex III subunit VI", "cytochrome b-c1 complex subunit 7"	191330		UQBP		2167087, 2543413, 3056408	Standard	NM_006294		Approved	QP-C, QCR7, UQCR6	uc022ayx.1	P14927	OTTHUMG00000164711	ENST00000287022.5:c.79T>G	chr8.hg19:g.97245396A>C	ENSP00000287022:p.Phe27Val	40.0	0.0		145.0	14.0	NM_001254752	E5RJU0|Q6FGD1	Missense_Mutation	SNP	ENST00000287022.5	hg19	CCDS6269.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.428722	0.83667	0.0	1.16E-4	ENSG00000156467	ENST00000287022;ENST00000518406;ENST00000523920	T;T;T	0.48836	0.8;0.8;0.8	4.78	4.78	0.61160	.	0.048891	0.85682	D	0.000000	T	0.67059	0.2853	M	0.85945	2.785	0.80722	D	1	P	0.52842	0.956	P	0.58660	0.843	T	0.73760	-0.3881	10	0.87932	D	0	-0.4207	13.0389	0.58887	1.0:0.0:0.0:0.0	.	27	P14927	QCR7_HUMAN	V	27	ENSP00000287022:F27V;ENSP00000430494:F27V;ENSP00000430560:F27V	ENSP00000287022:F27V	F	-	1	0	UQCRB	97314572	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.413000	0.90235	2.030000	0.59900	0.533000	0.62120	TTC	.	.		0.328	UQCRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379863.1	NM_006294		C	97245396	A	C	97245396	3	2	287	1	0	0	0	0	1	0	0	0	17033	101	4	5	268	5	UQCRB	8	97245396	Missense_Mutation	SNP	A	TCGA-G3-A5SL-01A-11D-A27I-10	1702175	97245396	49118626	53	42151										
TRAPPC9	83696	hgsc.bcm.edu	37	chr8	141468638	141468638	+	5'Flank	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	gcttccccctgtgtggcgcgCggtcttgatccccagctggc	13	16	1	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr8:141468638C>T	ENST00000438773.2	-	0	0				TRAPPC9_ENST00000389328.4_Missense_Mutation_p.R9H|TRAPPC9_ENST00000389327.3_5'Flank	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9						cell differentiation (GO:0030154)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	47						GTGTGGCGCGCGGTCTTGATC	0.682																																					p.R9H		Atlas-SNP	.											.	TRAPPC9	114	.	0			c.G26A						.						9	10	9					8																	141468638		2156	4236	6392	SO:0001631	upstream_gene_variant	83696	exon1			GGCGCGCGGTCTT	BC006206	CCDS34946.1, CCDS55278.1	8q24.3	2010-10-22			ENSG00000167632	ENSG00000167632		"Trafficking protein particle complex"	30832	protein-coding gene	gene with protein product	"TRAPP 120 kDa subunit", "tularik gene 1"	611966				11572484	Standard	NM_031466		Approved	IKBKBBP, NIBP, KIAA1882, T1, TRS120, MRT13	uc003yvh.2	Q96Q05	OTTHUMG00000164187		chr8.hg19:g.141468638C>T	Exception_encountered	24.0	0.0		59.0	11.0	NM_031466	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Missense_Mutation	SNP	ENST00000438773.2	hg19	CCDS55278.1	.	.	.	.	.	.	.	.	.	.	C	9.421	1.083006	0.20309	.	.	ENSG00000167632	ENST00000389328	.	.	.	1.06	-0.054	0.13816	.	.	.	.	.	T	0.16171	0.0389	N	0.08118	0	0.09310	N	0.999994	B	0.02656	0.0	B	0.01281	0.0	T	0.20907	-1.0261	8	0.87932	D	0	.	2.7452	0.05264	0.0:0.3774:0.0:0.6226	.	9	Q96Q05-2	.	H	9	.	ENSP00000373979:R9H	R	-	2	0	TRAPPC9	141537820	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.268000	0.02836	-0.027000	0.13873	0.297000	0.19635	CGC	.	.		0.682	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466		T	141468638	C	T	141468638	1	4	287	0	1	0	0	0	0	0	0	0	16480	768	27	1		1	TRAPPC9	8	141468638	5'Flank	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10	44223242	141468638	4895384	54	42152										
BAI1	575	hgsc.bcm.edu	37	chr8	143623422	143623422	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	caaggggccgcccaccaattTcaacagcctgccggccaacg	10	17	1	0			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr8:143623422T>C	ENST00000517894.1	+	28	4721	c.3827T>C	c.(3826-3828)tTc>tCc	p.F1276S	BAI1_ENST00000323289.5_Missense_Mutation_p.F1276S			O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1	1276					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)|signal transduction (GO:0007165)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(28)|ovary(4)|pancreas(1)|prostate(7)	57	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					CCCACCAATTTCAACAGCCTG	0.677																																					p.F1276S		Atlas-SNP	.											.	BAI1	146	.	0			c.T3827C						.						19	24	23					8																	143623422		2102	4205	6307	SO:0001583	missense	575	exon27			CCAATTTCAACAG	AB005297	CCDS64985.1	8q24.3	2014-08-08			ENSG00000181790	ENSG00000181790		"-", "GPCR / Class B : Orphans"	943	protein-coding gene	gene with protein product		602682				9533023	Standard	NM_001702		Approved		uc003ywm.3	O14514	OTTHUMG00000164732	ENST00000517894.1:c.3827T>C	chr8.hg19:g.143623422T>C	ENSP00000430945:p.Phe1276Ser	85.0	0.0		138.0	13.0	NM_001702		Missense_Mutation	SNP	ENST00000517894.1	hg19		.	.	.	.	.	.	.	.	.	.	t	22.2	4.257991	0.80246	.	.	ENSG00000181790	ENST00000517894;ENST00000323289	T;T	0.44482	0.92;0.92	4.26	4.26	0.50523	.	0.000000	0.85682	U	0.000000	T	0.60418	0.2267	M	0.65975	2.015	0.42471	D	0.992823	D	0.76494	0.999	D	0.80764	0.994	T	0.63453	-0.6634	10	0.52906	T	0.07	.	12.565	0.56304	0.0:0.0:0.0:1.0	.	1276	E9PBK0	.	S	1276	ENSP00000430945:F1276S;ENSP00000313046:F1276S	ENSP00000313046:F1276S	F	+	2	0	BAI1	143620424	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	3.840000	0.55843	1.555000	0.49500	0.478000	0.44815	TTC	.	.		0.677	BAI1-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379963.3	NM_001702		C	143623422	T	C	143623422	3	2	287	1	0	0	0	0	1	0	0	0	1298	1783	62	2	3933	2	BAI1	8	143623422	Missense_Mutation	SNP	T	TCGA-G3-A5SL-01A-11D-A27I-10	2154784	143623422	2740600	55	42153										
NPR2	4882	hgsc.bcm.edu	37	chr9	35809218	35809218	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	agctaggatgcttccagctaGagcttcggggggatgtggaa	16	7	0	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr9:35809218G>A	ENST00000342694.2	+	21	3307	c.3052G>A	c.(3052-3054)Gag>Aag	p.E1018K	AL133410.1_ENST00000582432.1_RNA|SPAG8_ENST00000479751.1_5'Flank|SPAG8_ENST00000340291.2_Intron	NM_003995.3	NP_003986.2	P20594	ANPRB_HUMAN	natriuretic peptide receptor 2	1018					bone development (GO:0060348)|cell surface receptor signaling pathway (GO:0007166)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cGMP biosynthetic process (GO:0006182)|intracellular signal transduction (GO:0035556)|negative regulation of meiotic cell cycle (GO:0051447)|negative regulation of oocyte maturation (GO:1900194)|ossification (GO:0001503)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|signal transduction (GO:0007165)|single organism reproductive process (GO:0044702)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(2)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)		Erythrityl Tetranitrate(DB01613)|Nesiritide(DB04899)	CTTCCAGCTAGAGCTTCGGGG	0.547																																					p.E1018K		Atlas-SNP	.											.	NPR2	162	.	0			c.G3052A						.						108	109	108					9																	35809218		2203	4300	6503	SO:0001583	missense	4882	exon21			CAGCTAGAGCTTC	AJ005282	CCDS6590.1	9p21-p12	2014-03-03	2014-03-03		ENSG00000159899	ENSG00000159899			7944	protein-coding gene	gene with protein product	"guanylate cyclase B"	108961	"acromesomelic dysplasia, Maroteaux type", "atrionatriuretic peptide receptor B", "natriuretic peptide receptor B"	ANPRB, NPRB, AMDM		9634515, 15146390	Standard	XM_005251478		Approved	GUCY2B, ANPb	uc003zyd.3	P20594	OTTHUMG00000019871	ENST00000342694.2:c.3052G>A	chr9.hg19:g.35809218G>A	ENSP00000341083:p.Glu1018Lys	48.0	0.0		49.0	18.0	NM_003995	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	Missense_Mutation	SNP	ENST00000342694.2	hg19	CCDS6590.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.248090	0.80024	.	.	ENSG00000159899	ENST00000342694	T	0.81163	-1.46	5.97	5.97	0.96955	Adenylyl cyclase class-3/4/guanylyl cyclase (4);	0.000000	0.43747	D	0.000537	T	0.81772	0.4893	M	0.66297	2.02	0.80722	D	1	P	0.42456	0.78	B	0.40782	0.34	T	0.83351	-0.0003	10	0.62326	D	0.03	.	19.0168	0.92897	0.0:0.0:1.0:0.0	.	1018	P20594	ANPRB_HUMAN	K	1018	ENSP00000341083:E1018K	ENSP00000341083:E1018K	E	+	1	0	NPR2	35799218	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.985000	0.70556	2.836000	0.97738	0.655000	0.94253	GAG	.	.		0.547	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1			A	35809218	G	A	35809218	3	1	287	1	0	0	0	0	1	0	0	0	10604	943	33	3	3134	3	NPR2	9	35809218	Missense_Mutation	SNP	G	TCGA-G3-A5SL-01A-11D-A27I-10		35809218	105404213	56	42154										
TLR4	7099	hgsc.bcm.edu	37	chr9	120476662	120476662	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	tggtgtatctttgaatatgaGattgctcagacctggcagtt	11	6	2	3			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr9:120476662G>C	ENST00000355622.6	+	3	2357	c.2256G>C	c.(2254-2256)gaG>gaC	p.E752D	TLR4_ENST00000472304.1_3'UTR|TLR4_ENST00000394487.4_Missense_Mutation_p.E712D	NM_138554.4|NM_138557.2	NP_612564.1|NP_612567.1	O00206	TLR4_HUMAN	toll-like receptor 4	752	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				activation of MAPK activity (GO:0000187)|B cell proliferation involved in immune response (GO:0002322)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|detection of fungus (GO:0016046)|detection of lipopolysaccharide (GO:0032497)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|innate immune response (GO:0045087)|interferon-gamma production (GO:0032609)|intestinal epithelial structure maintenance (GO:0060729)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-23 production (GO:0032707)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of tumor necrosis factor production (GO:0032720)|nitric oxide production involved in inflammatory response (GO:0002537)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine production (GO:0032722)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 production (GO:0032732)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070430)|positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070434)|positive regulation of platelet activation (GO:0010572)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cytokine secretion (GO:0050707)|response to lipopolysaccharide (GO:0032496)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|lipopolysaccharide receptor complex (GO:0046696)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(66)|ovary(4)|pancreas(1)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	103					Naloxone(DB01183)	TTGAATATGAGATTGCTCAGA	0.502																																					p.E752D		Atlas-SNP	.											.	TLR4	220	.	0			c.G2256C						.						71	70	70					9																	120476662		2203	4300	6503	SO:0001583	missense	7099	exon3			ATATGAGATTGCT	U88880	CCDS6818.1	9q33.1	2013-01-23			ENSG00000136869	ENSG00000136869		"CD molecules"	11850	protein-coding gene	gene with protein product		603030				9435236, 9237759	Standard	NM_138554		Approved	hToll, CD284, TLR-4, ARMD10	uc004bjz.4	O00206	OTTHUMG00000021046	ENST00000355622.6:c.2256G>C	chr9.hg19:g.120476662G>C	ENSP00000363089:p.Glu752Asp	53.0	0.0		73.0	5.0	NM_138554	A8K1Y8|A9XLP9|A9XLQ0|A9XLQ1|B4E194|D1CS52|D1CS53|Q5VZI8|Q5VZI9|Q9UK78|Q9UM57	Missense_Mutation	SNP	ENST00000355622.6	hg19	CCDS6818.1	.	.	.	.	.	.	.	.	.	.	G	13.65	2.300056	0.40694	.	.	ENSG00000136869	ENST00000394487;ENST00000355622	T;T	0.08546	3.08;3.08	6.03	1.2	0.21068	Toll/interleukin-1 receptor homology (TIR) domain (4);	0.077760	0.53938	D	0.000043	T	0.04724	0.0128	N	0.11724	0.165	0.37533	D	0.918001	B	0.30889	0.299	B	0.37833	0.259	T	0.48864	-0.8997	10	0.19147	T	0.46	.	6.2635	0.20913	0.483:0.1392:0.3778:0.0	.	752	O00206	TLR4_HUMAN	D	712;752	ENSP00000377997:E712D;ENSP00000363089:E752D	ENSP00000363089:E752D	E	+	3	2	TLR4	119516483	0.993000	0.37304	1.000000	0.80357	0.998000	0.95712	0.274000	0.18680	0.305000	0.22832	0.655000	0.94253	GAG	.	.		0.502	TLR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055549.3	NM_138554		C	120476662	G	C	120476662	3	2	287	1	0	0	0	0	1	0	0	0	15968	933	33	4	2266	4	TLR4	9	120476662	Missense_Mutation	SNP	G	TCGA-G3-A5SL-01A-11D-A27I-10	84667444	120476662	20736769	57	42155										
CEP110	11064	hgsc.bcm.edu	37	chr9	123937425	123937425	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	aattggtcaccagcacctctGcagattcagcgtcatcaccc	7	15	5	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr9:123937425G>A	ENST00000373855.1	+	43	7137	c.6877G>A	c.(6877-6879)Gca>Aca	p.A2293T	CNTRL_ENST00000373850.1_Missense_Mutation_p.A1741T|CNTRL_ENST00000373845.2_3'UTR|CNTRL_ENST00000238341.5_Missense_Mutation_p.A2293T			Q7Z7A1	CNTRL_HUMAN	centriolin	2293	Sufficient for interaction with HOOK2.				cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)				haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(2)|ovary(4)|skin(3)	20						CAGCACCTCTGCAGATTCAGC	0.463																																					p.A2293T		Atlas-SNP	.											.	CNTRL	161	.	0			c.G6877A						.						118	110	113					9																	123937425		2203	4300	6503	SO:0001583	missense	11064	exon41			ACCTCTGCAGATT	AF513978	CCDS35118.1	9q33.2	2014-02-20	2011-05-23	2011-05-23	ENSG00000119397	ENSG00000119397			1858	protein-coding gene	gene with protein product		605496	"centrosomal protein 1", "centrosomal protein 110kDa"	CEP1, CEP110		10688839	Standard	XM_005251679		Approved		uc004bkx.1	Q7Z7A1	OTTHUMG00000020581	ENST00000373855.1:c.6877G>A	chr9.hg19:g.123937425G>A	ENSP00000362962:p.Ala2293Thr	71.0	0.0		105.0	14.0	NM_007018	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Missense_Mutation	SNP	ENST00000373855.1	hg19	CCDS35118.1	.	.	.	.	.	.	.	.	.	.	G	3.106	-0.183703	0.06340	.	.	ENSG00000119397	ENST00000373855;ENST00000238341;ENST00000454238;ENST00000394368;ENST00000373850;ENST00000373845	T;T;T	0.30714	1.82;1.82;1.52	5.33	1.28	0.21552	.	.	.	.	.	T	0.10294	0.0252	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.33675	-0.9859	9	0.13470	T	0.59	.	2.4271	0.04462	0.2299:0.1294:0.5078:0.1329	.	2293	Q7Z7A1	CNTRL_HUMAN	T	2293;2293;2293;450;1741;975	ENSP00000362962:A2293T;ENSP00000238341:A2293T;ENSP00000362956:A1741T	ENSP00000238341:A2293T	A	+	1	0	CNTRL	122977246	0.002000	0.14202	0.132000	0.22025	0.218000	0.24690	0.196000	0.17176	0.201000	0.20466	-0.266000	0.10368	GCA	.	.		0.463	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018		A	123937425	G	A	123937425	3	1	287	1	0	0	0	0	1	0	0	0	3247	1319	46	3	7039	3	CEP110	9	123937425	Missense_Mutation	SNP	G	TCGA-G3-A5SL-01A-11D-A27I-10	3460763	123937425	17276006	58	42156										
GOLGA1	2800	hgsc.bcm.edu	37	chr9	127685398	127685398	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	tgctttattttacttagttcCtgctgctggaacccctctaa	6	11	1	0	rs138655913		TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr9:127685398C>A	ENST00000373555.4	-	8	870	c.537G>T	c.(535-537)caG>caT	p.Q179H		NM_002077.3	NP_002068	Q92805	GOGA1_HUMAN	golgin A1	179					protein targeting to Golgi (GO:0000042)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)				NS(1)|endometrium(5)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)	20						TACTTAGTTCCTGCTGCTGGA	0.348																																					p.Q179H		Atlas-SNP	.											.	GOLGA1	60	.	0			c.G537T						.						166	149	155					9																	127685398		2203	4300	6503	SO:0001583	missense	2800	exon8			TAGTTCCTGCTGC	U51587	CCDS6860.1	9q34.11	2010-02-12	2010-02-12		ENSG00000136935	ENSG00000136935			4424	protein-coding gene	gene with protein product		602502	"golgi autoantigen, golgin subfamily a, 1"			9324025	Standard	NM_002077		Approved	golgin-97, MGC33154	uc004bpc.3	Q92805	OTTHUMG00000020665	ENST00000373555.4:c.537G>T	chr9.hg19:g.127685398C>A	ENSP00000362656:p.Gln179His	27.0	0.0		33.0	15.0	NM_002077	Q5T164|Q8IYZ9	Missense_Mutation	SNP	ENST00000373555.4	hg19	CCDS6860.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.931437	0.73442	.	.	ENSG00000136935	ENST00000373555	T	0.18016	2.24	5.42	4.53	0.55603	.	0.000000	0.42172	U	0.000752	T	0.41351	0.1155	M	0.76328	2.33	0.58432	D	0.999997	D;D	0.76494	0.999;0.998	D;D	0.85130	0.997;0.993	T	0.31364	-0.9946	10	0.52906	T	0.07	-15.526	13.3943	0.60840	0.0:0.924:0.0:0.076	.	78;179	Q59HA1;Q92805	.;GOGA1_HUMAN	H	179	ENSP00000362656:Q179H	ENSP00000362656:Q179H	Q	-	3	2	GOLGA1	126725219	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.108000	0.41854	1.296000	0.44742	0.591000	0.81541	CAG	.	C|1.000;T|0.000		0.348	GOLGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054049.1	NM_002077		A	127685398	C	A	127685398	3	1	287	1	0	0	0	0	1	0	0	0	6559	680	24	3	1830	3	GOLGA1	9	127685398	Missense_Mutation	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10	3747973	127685398	13528033	59	42157										
PPP2R4	5524	hgsc.bcm.edu	37	chr9	131898785	131898785	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	gcggaaactccagaaaacatAcaggatggagccagccggca	12	11	0	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr9:131898785A>G	ENST00000337738.1	+	8	968	c.701A>G	c.(700-702)tAc>tGc	p.Y234C	PPP2R4_ENST00000348141.5_Missense_Mutation_p.Y205C|PPP2R4_ENST00000357197.4_Missense_Mutation_p.Y170C|PPP2R4_ENST00000524946.2_5'Flank|PPP2R4_ENST00000358994.4_Missense_Mutation_p.Y199C|PPP2R4_ENST00000355007.3_Missense_Mutation_p.Y157C|PPP2R4_ENST00000423100.1_5'Flank|PPP2R4_ENST00000393370.2_Missense_Mutation_p.Y199C|PPP2R4_ENST00000452489.2_Missense_Mutation_p.Y234C|PPP2R4_ENST00000347048.4_Intron	NM_178001.2	NP_821068.1	Q15257	PTPA_HUMAN	protein phosphatase 2A activator, regulatory subunit 4	234					ATP catabolic process (GO:0006200)|mitotic spindle organization in nucleus (GO:0030472)|negative regulation of phosphoprotein phosphatase activity (GO:0032515)|negative regulation of protein dephosphorylation (GO:0035308)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein dephosphorylation (GO:0035307)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)|regulation of phosphoprotein phosphatase activity (GO:0043666)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	ATP binding (GO:0005524)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase type 2A regulator activity (GO:0008601)|protein tyrosine phosphatase activator activity (GO:0008160)|receptor binding (GO:0005102)			breast(3)|endometrium(1)|kidney(1)|lung(3)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	12		Medulloblastoma(224;0.235)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0178)		CAGAAAACATACAGGATGGAG	0.537																																					p.Y234C	Colon(158;2158 2504 4450 20433)	Atlas-SNP	.											.	PPP2R4	32	.	0			c.A701G						.						184	196	192					9																	131898785		2203	4300	6503	SO:0001583	missense	5524	exon8			AAACATACAGGAT	X73478	CCDS6920.1, CCDS65156.1, CCDS75917.1	9q34	2010-06-18	2007-01-22		ENSG00000119383	ENSG00000119383		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9308	protein-coding gene	gene with protein product	"phosphotyrosyl phosphatase activator", "PP2A phosphatase activator"	600756	"protein phosphatase 2A, regulatory subunit B' (PR 53)"			8530035	Standard	NM_021131		Approved	PTPA, PR53	uc004bxm.2	Q15257	OTTHUMG00000020774	ENST00000337738.1:c.701A>G	chr9.hg19:g.131898785A>G	ENSP00000337448:p.Tyr234Cys	179.0	0.0		134.0	51.0	NM_178001	A2A347|A9IZU4|B4DXM4|Q15258|Q53GZ3|Q5TZQ2|Q9BUK1|Q9NNZ7|Q9NNZ8|Q9NNZ9	Missense_Mutation	SNP	ENST00000337738.1	hg19		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	A|A|A	24.3|24.3|24.3	4.513174|4.513174|4.513174	0.85389|0.85389|0.85389	.|.|.	.|.|.	ENSG00000119383|ENSG00000119383|ENSG00000119383	ENST00000455240|ENST00000411917|ENST00000358994;ENST00000455292;ENST00000393370;ENST00000337738;ENST00000348141;ENST00000452489;ENST00000357197;ENST00000445241;ENST00000355007;ENST00000417728	.|.|T;T;T;T;T;T;T;T;T;T	.|.|0.60424	.|.|0.19;0.19;0.19;0.19;0.19;0.19;0.19;0.19;0.19;0.19	5.62|5.62|5.62	5.62|5.62|5.62	0.85841|0.85841|0.85841	.|.|.	.|.|0.000000	.|.|0.85682	.|.|D	.|.|0.000000	D|D|D	0.83954|0.83954|0.83954	0.5366|0.5366|0.5366	H|H|H	0.97240|0.97240|0.97240	3.965|3.965|3.965	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|.|D;D;D;D;D;D	.|.|0.89917	.|.|1.0;1.0;1.0;0.996;1.0;0.996	.|.|D;D;D;P;D;D	.|.|0.97110	.|.|1.0;0.999;1.0;0.908;1.0;0.959	D|D|D	0.89290|0.89290|0.89290	0.3618|0.3618|0.3618	5|5|10	.|.|0.87932	.|.|D	.|.|0	-24.3755|-24.3755|-24.3755	13.5753|13.5753|13.5753	0.61870|0.61870|0.61870	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.|.	.|.|157;170;234;157;234;199	.|.|B4DLX5;Q15257-3;B4DZF8;Q15257-4;Q15257;Q15257-2	.|.|.;.;.;.;PTPA_HUMAN;.	M|A|C	12|4|199;234;199;234;205;234;170;234;157;164	.|.|ENSP00000351885:Y199C;ENSP00000395499:Y234C;ENSP00000377036:Y199C;ENSP00000337448:Y234C;ENSP00000335200:Y205C;ENSP00000394338:Y234C;ENSP00000349726:Y170C;ENSP00000406997:Y234C;ENSP00000347109:Y157C;ENSP00000403542:Y164C	.|.|ENSP00000337448:Y234C	I|T|Y	+|+|+	3|1|2	3|0|0	PPP2R4|PPP2R4|PPP2R4	130938606|130938606|130938606	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.984000|0.984000|0.984000	0.44739|0.44739|0.44739	0.981000|0.981000|0.981000	0.71138|0.71138|0.71138	8.918000|8.918000|8.918000	0.92759|0.92759|0.92759	2.133000|2.133000|2.133000	0.65898|0.65898|0.65898	0.455000|0.455000|0.455000	0.32223|0.32223|0.32223	ATA|ACA|TAC	.	.		0.537	PPP2R4-201	KNOWN	basic	protein_coding	protein_coding		NM_021131		G	131898785	A	G	131898785	3	3	287	1	0	0	0	0	1	0	0	0	12403	391	14	2	731	2	PPP2R4	9	131898785	Missense_Mutation	SNP	A	TCGA-G3-A5SL-01A-11D-A27I-10	4213387	131898785	9314646	60	42158										
FRMD4A	55691	hgsc.bcm.edu	37	chr10	13708157	13708157	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	agacttgatgcggttctcatTgattgcattttcaatctcct	7	9	3	3			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr10:13708157T>G	ENST00000357447.2	-	18	1911	c.1543A>C	c.(1543-1545)Aat>Cat	p.N515H	FRMD4A_ENST00000378503.1_Missense_Mutation_p.N515H|FRMD4A_ENST00000358621.4_Missense_Mutation_p.N500H	NM_018027.3	NP_060497.3	Q9P2Q2	FRM4A_HUMAN	FERM domain containing 4A	515					establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)				breast(4)|endometrium(9)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	41						CGGTTCTCATTGATTGCATTT	0.522																																					p.N515H		Atlas-SNP	.											.	FRMD4A	108	.	0			c.A1543C						.						143	143	143					10																	13708157		2203	4300	6503	SO:0001583	missense	55691	exon18			TCTCATTGATTGC	AB037715	CCDS7101.1	10p14	2004-07-15	2004-07-15	2004-07-15	ENSG00000151474	ENSG00000151474			25491	protein-coding gene	gene with protein product			"FERM domain containing 4"	FRMD4		10718198	Standard	NM_018027		Approved	FLJ10210, KIAA1294, bA295P9.4	uc001ims.3	Q9P2Q2	OTTHUMG00000017708	ENST00000357447.2:c.1543A>C	chr10.hg19:g.13708157T>G	ENSP00000350032:p.Asn515His	81.0	0.0		64.0	28.0	NM_018027	A7E2Y3|Q5T377	Missense_Mutation	SNP	ENST00000357447.2	hg19	CCDS7101.1	.	.	.	.	.	.	.	.	.	.	T	18.46	3.629759	0.67015	.	.	ENSG00000151474	ENST00000358621;ENST00000357447;ENST00000378503	D;D;D	0.84800	-1.89;-1.9;-1.9	5.05	5.05	0.67936	.	0.042246	0.85682	D	0.000000	D	0.83413	0.5249	L	0.56199	1.76	0.80722	D	1	P	0.36495	0.556	B	0.38921	0.285	D	0.84349	0.0531	10	0.51188	T	0.08	-30.3368	14.9598	0.71147	0.0:0.0:0.0:1.0	.	515	Q9P2Q2	FRM4A_HUMAN	H	500;515;515	ENSP00000351438:N500H;ENSP00000350032:N515H;ENSP00000367764:N515H	ENSP00000350032:N515H	N	-	1	0	FRMD4A	13748163	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	7.867000	0.87062	2.134000	0.65973	0.459000	0.35465	AAT	.	.		0.522	FRMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046889.1	NM_018027		G	13708157	T	G	13708157	3	3	287	1	0	0	0	0	1	0	0	0	6059	1812	63	5	1604	5	FRMD4A	10	13708157	Missense_Mutation	SNP	T	TCGA-G3-A5SL-01A-11D-A27I-10		13708157	121826590	61	42159										
ITGA8	8516	hgsc.bcm.edu	37	chr10	15559170	15559170	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	tttcttgtcatgcctcagggGtcttgtcatttgtcagctgt	10	9	6	0			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr10:15559170G>C	ENST00000378076.3	-	30	3532	c.3179C>G	c.(3178-3180)aCc>aGc	p.T1060S		NM_003638.1	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8	1060					brain development (GO:0007420)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|metanephros development (GO:0001656)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|substrate adhesion-dependent cell spreading (GO:0034446)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|dendritic spine membrane (GO:0032591)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integrin alpha8-beta1 complex (GO:0034678)|integrin complex (GO:0008305)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	metal ion binding (GO:0046872)			NS(2)|breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(57)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	96						TGCCTCAGGGGTCTTGTCATT	0.418																																					p.T1060S		Atlas-SNP	.											.	ITGA8	230	.	0			c.C3179G						.						73	71	72					10																	15559170		2203	4300	6503	SO:0001583	missense	8516	exon30			TCAGGGGTCTTGT	L36531	CCDS31155.1	10p13	2010-03-23			ENSG00000077943	ENSG00000077943		"Integrins"	6144	protein-coding gene	gene with protein product		604063				7768999	Standard	XM_005252633		Approved		uc001ioc.1	P53708	OTTHUMG00000017733	ENST00000378076.3:c.3179C>G	chr10.hg19:g.15559170G>C	ENSP00000367316:p.Thr1060Ser	25.0	0.0		36.0	5.0	NM_003638	B0YJ31|Q5VX94	Missense_Mutation	SNP	ENST00000378076.3	hg19	CCDS31155.1	.	.	.	.	.	.	.	.	.	.	G	11.72	1.723763	0.30593	.	.	ENSG00000077943	ENST00000378076;ENST00000538044	T	0.68181	-0.31	5.89	2.6	0.31112	.	0.295809	0.36134	N	0.002776	T	0.41811	0.1175	N	0.12746	0.255	0.32435	N	0.547541	B;B	0.12013	0.005;0.003	B;B	0.15052	0.012;0.005	T	0.39881	-0.9592	10	0.11794	T	0.64	.	8.9387	0.35715	0.1507:0.1264:0.7228:0.0	.	1045;1060	F5H818;P53708	.;ITA8_HUMAN	S	1060;1045	ENSP00000367316:T1060S	ENSP00000367316:T1060S	T	-	2	0	ITGA8	15599176	1.000000	0.71417	0.899000	0.35326	0.632000	0.37999	3.859000	0.55987	0.835000	0.34877	0.563000	0.77884	ACC	.	.		0.418	ITGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046987.1	NM_003638		C	15559170	G	C	15559170	3	2	287	1	0	0	0	0	1	0	0	0	7891	1261	44	4	16	4	ITGA8	10	15559170	Missense_Mutation	SNP	G	TCGA-G3-A5SL-01A-11D-A27I-10	1851013	15559170	119975577	62	42160										
MAP3K8	1326	hgsc.bcm.edu	37	chr10	30747090	30747090	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	tacagcctgggggccacgctCatccacatgcagacgggcac	12	15	1	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr10:30747090C>A	ENST00000263056.1	+	7	1647	c.951C>A	c.(949-951)ctC>ctA	p.L317L	MAP3K8_ENST00000542547.1_Silent_p.L317L|MAP3K8_ENST00000375321.1_Silent_p.L317L	NM_001244134.1|NM_005204.3	NP_001231063.1|NP_005195.2	P41279	M3K8_HUMAN	mitogen-activated protein kinase kinase kinase 8	317	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|protein phosphorylation (GO:0006468)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		Prostate(175;0.151)				GGGCCACGCTCATCCACATGC	0.557																																					p.L317L		Atlas-SNP	.											.	MAP3K8	46	.	0			c.C951A						.						79	78	78					10																	30747090		2203	4300	6503	SO:0001819	synonymous_variant	1326	exon6			CACGCTCATCCAC	D14497	CCDS7166.1	10p11.2	2011-06-09			ENSG00000107968	ENSG00000107968		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6860	protein-coding gene	gene with protein product		191195		COT, ESTF		2072910, 8479752	Standard	NM_005204		Approved	Tpl-2, EST, c-COT, MEKK8	uc009xlf.2	P41279	OTTHUMG00000017889	ENST00000263056.1:c.951C>A	chr10.hg19:g.30747090C>A		147.0	0.0		150.0	54.0	NM_001244134	A8K2Q5|D3DRX1|Q14275|Q5T855|Q9HC81	Silent	SNP	ENST00000263056.1	hg19	CCDS7166.1																																																																																			.	.		0.557	MAP3K8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047416.2	NM_005204		A	30747090	C	A	30747090	2	1	287	1	0	0	0	0	0	0	0	1	9265	813	29	3		3	MAP3K8	10	30747090	Silent	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10	15187920	30747090	104787657	63	42161										
PRKG1	5592	hgsc.bcm.edu	37	chr10	54031194	54031194	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	tggacacaagacagcaggagCacatccgctcagagaagcag	12	11	1	2			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr10:54031194C>T	ENST00000401604.2	+	11	1407	c.1213C>T	c.(1213-1215)Cac>Tac	p.H405Y	PRKG1-AS1_ENST00000426785.2_RNA|PRKG1_ENST00000373985.1_Missense_Mutation_p.H393Y|PRKG1-AS1_ENST00000452247.2_RNA|PRKG1_ENST00000373980.4_Missense_Mutation_p.H420Y|PRKG1_ENST00000373975.2_Missense_Mutation_p.H123Y			Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I	405	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|dendrite development (GO:0016358)|forebrain development (GO:0030900)|negative regulation of platelet aggregation (GO:0090331)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|regulation of GTPase activity (GO:0043087)|relaxation of vascular smooth muscle (GO:0060087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	53		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		ACAGCAGGAGCACATCCGCTC	0.468																																					p.H420Y		Atlas-SNP	.											.	PRKG1	167	.	0			c.C1258T						.						85	79	81					10																	54031194		2203	4300	6503	SO:0001583	missense	5592	exon11			CAGGAGCACATCC		CCDS7244.1	10q11.2	2009-07-10			ENSG00000185532	ENSG00000185532	2.7.11.1		9414	protein-coding gene	gene with protein product		176894		PRKGR1B, PRKG1B		2792381, 1544322	Standard	NM_001098512		Approved	PGK, PKG	uc001jjo.3	Q13976	OTTHUMG00000018248	ENST00000401604.2:c.1213C>T	chr10.hg19:g.54031194C>T	ENSP00000384200:p.His405Tyr	42.0	0.0		100.0	32.0	NM_006258	A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	Missense_Mutation	SNP	ENST00000401604.2	hg19	CCDS44399.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.688039	0.88639	.	.	ENSG00000185532	ENST00000401604;ENST00000373985;ENST00000373980;ENST00000332193;ENST00000373975	T;T;T	0.65549	-0.16;-0.16;-0.16	4.92	4.92	0.64577	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.76307	0.3969	L	0.53671	1.685	0.80722	D	1	P;D;D	0.89917	0.908;1.0;1.0	P;D;D	0.91635	0.838;0.997;0.999	T	0.78909	-0.2018	10	0.87932	D	0	-14.0481	18.0731	0.89417	0.0:1.0:0.0:0.0	.	123;420;405	B3KSF3;Q13976-2;Q13976	.;.;KGP1_HUMAN	Y	405;393;420;123;17	ENSP00000384200:H405Y;ENSP00000363097:H393Y;ENSP00000363092:H420Y	ENSP00000327642:H123Y	H	+	1	0	PRKG1	53701200	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.349000	0.79376	2.435000	0.82474	0.551000	0.68910	CAC	.	.		0.468	PRKG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	54031194	C	T	54031194	3	4	287	1	0	0	0	0	1	0	0	0	12534	710	25	3	1570	3	PRKG1	10	54031194	Missense_Mutation	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10	23284104	54031194	81503553	64	42162										
SIRT3	23410	hgsc.bcm.edu	37	chr11	230535	230535	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	atgagcttcaaccagctttgAggcagggatgcccgacactg	12	11	1	2			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr11:230535A>C	ENST00000382743.4	-	4	826	c.724T>G	c.(724-726)Tca>Gca	p.S242A	SIRT3_ENST00000524564.1_Missense_Mutation_p.S178A|SIRT3_ENST00000532956.1_Missense_Mutation_p.S242A|SIRT3_ENST00000529382.1_Missense_Mutation_p.S100A|SIRT3_ENST00000525319.1_Missense_Mutation_p.S161A|SIRT3_ENST00000528702.1_5'UTR	NM_001017524.2|NM_012239.5	NP_001017524.1|NP_036371.1	Q9NTG7	SIR3_HUMAN	sirtuin 3	242	Deacetylase sirtuin-type. {ECO:0000255|PROSITE-ProRule:PRU00236}.				aerobic respiration (GO:0009060)|peptidyl-lysine deacetylation (GO:0034983)|protein ADP-ribosylation (GO:0006471)|protein deacetylation (GO:0006476)	membrane (GO:0016020)|mitochondrion (GO:0005739)	NAD+ ADP-ribosyltransferase activity (GO:0003950)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|zinc ion binding (GO:0008270)			endometrium(1)|lung(5)|urinary_tract(1)	7		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;3.66e-27)|Epithelial(43;2.02e-26)|OV - Ovarian serous cystadenocarcinoma(40;2.9e-21)|BRCA - Breast invasive adenocarcinoma(625;3.88e-05)|Lung(200;0.111)|LUSC - Lung squamous cell carcinoma(625;0.129)		ACCAGCTTTGAGGCAGGGATG	0.562																																					p.S242A		Atlas-SNP	.											.	SIRT3	28	.	0			c.T724G						.						101	88	92					11																	230535		2203	4300	6503	SO:0001583	missense	23410	exon4			GCTTTGAGGCAGG	AF083108	CCDS7691.1, CCDS53590.1	11p15.5	2010-06-25	2010-06-25		ENSG00000142082	ENSG00000142082			14931	protein-coding gene	gene with protein product		604481	"sirtuin (silent mating type information regulation 2, S.cerevisiae, homolog) 3", "sirtuin (silent mating type information regulation 2 homolog) 3 (S. cerevisiae)"			10381378, 18215119	Standard	NM_012239		Approved	SIR2L3	uc001lok.4	Q9NTG7	OTTHUMG00000119074	ENST00000382743.4:c.724T>G	chr11.hg19:g.230535A>C	ENSP00000372191:p.Ser242Ala	165.0	0.0		111.0	37.0	NM_012239	B7Z5U6|Q9Y6E8	Missense_Mutation	SNP	ENST00000382743.4	hg19	CCDS7691.1	.	.	.	.	.	.	.	.	.	.	A	18.17	3.563550	0.65651	.	.	ENSG00000142082	ENST00000382743;ENST00000525319;ENST00000524564;ENST00000532956;ENST00000529382	T;T;T;T;T	0.17854	2.25;2.25;2.25;2.25;2.25	5.31	2.81	0.32909	.	0.768733	0.11544	N	0.553454	T	0.23926	0.0579	L	0.56280	1.765	0.19300	N	0.999974	P;B;B;B;B	0.45986	0.87;0.142;0.026;0.211;0.13	P;P;B;P;B	0.49421	0.61;0.467;0.211;0.451;0.237	T	0.08827	-1.0703	10	0.56958	D	0.05	-1.8921	7.5964	0.28050	0.4772:0.3996:0.0:0.1232	.	242;242;161;178;242	E9PM75;B7Z7G4;E9PK80;E9PN58;Q9NTG7	.;.;.;.;SIRT3_HUMAN	A	242;161;178;242;100	ENSP00000372191:S242A;ENSP00000435464:S161A;ENSP00000432937:S178A;ENSP00000433077:S242A;ENSP00000437216:S100A	ENSP00000372191:S242A	S	-	1	0	SIRT3	220535	0.638000	0.27225	0.987000	0.45799	0.912000	0.54170	1.491000	0.35583	0.822000	0.34565	0.533000	0.62120	TCA	.	.		0.562	SIRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239288.3			C	230535	A	C	230535	3	2	287	1	0	0	0	0	1	0	0	0	14354	304	11	5	491	5	SIRT3	11	230535	Missense_Mutation	SNP	A	TCGA-G3-A5SL-01A-11D-A27I-10		230535	134775981	65	42163										
NUP98	4928	hgsc.bcm.edu	37	chr11	3797196	3797196	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	gatgtgctgccaaaaggattAgaggtggtatttgtggttcc	14	5	0	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr11:3797196A>T	ENST00000324932.7	-	5	831	c.411T>A	c.(409-411)tcT>tcA	p.S137S	NUP98_ENST00000359171.4_Silent_p.S137S|NUP98_ENST00000397007.4_Silent_p.S137S|NUP98_ENST00000397004.4_Silent_p.S137S|NUP98_ENST00000355260.3_Silent_p.S137S	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	137	FG repeats 1.|Gly/Thr-rich.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|DNA replication (GO:0006260)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore organization (GO:0006999)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nuclear pore outer ring (GO:0031080)|nucleoplasm (GO:0005654)	peptide binding (GO:0042277)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)	p.S137S(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		CAAAAGGATTAGAGGTGGTAT	0.383			T	"HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"	AML																																p.S137S		Atlas-SNP	.		Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	NUP98,NS,carcinoma,0,1	NUP98	149	.	1	Substitution - coding silent(1)	endometrium(1)	c.T411A						.						149	159	156					11																	3797196		2201	4298	6499	SO:0001819	synonymous_variant	4928	exon5			AGGATTAGAGGTG	AF071076, AF231130, BC012906, BG773331	CCDS7746.1, CCDS31347.1, CCDS41605.1, CCDS41606.1	11p15	2008-02-26	2002-08-29		ENSG00000110713	ENSG00000110713			8068	protein-coding gene	gene with protein product		601021	"nucleoporin 98kD"			9166830	Standard	NM_139131		Approved	NUP96	uc001lyh.3	P52948	OTTHUMG00000011846	ENST00000324932.7:c.411T>A	chr11.hg19:g.3797196A>T		200.0	0.0		163.0	37.0	NM_016320	Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Silent	SNP	ENST00000324932.7	hg19	CCDS7746.1																																																																																			.	.		0.383	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	NM_016320		T	3797196	A	T	3797196	2	4	287	1	0	0	0	0	0	0	0	1	10782	407	15	4		4	NUP98	11	3797196	Silent	SNP	A	TCGA-G3-A5SL-01A-11D-A27I-10	3566661	3797196	131209320	66	42164										
HBE1	3046	hgsc.bcm.edu	37	chr11	5291042	5291042	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	tgcttacctgcccaaggcttCacctccagcctcttccacat	5	18	2	0			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr11:5291042C>G	ENST00000380237.1	-	3	423	c.79G>C	c.(79-81)Gaa>Caa	p.E27Q	HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron|HBE1_ENST00000292896.2_Missense_Mutation_p.E27Q			P02100	HBE_HUMAN	hemoglobin, epsilon 1	27					blood coagulation (GO:0007596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein heterooligomerization (GO:0051291)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|hemoglobin complex (GO:0005833)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|oxygen transporter activity (GO:0005344)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|skin(1)	20		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.34e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CCCAAGGCTTCACCTCCAGCC	0.493																																					p.E27Q		Atlas-SNP	.											.	HBE1	42	.	0			c.G79C						.						116	103	108					11																	5291042		2201	4297	6498	SO:0001583	missense	3046	exon1			AGGCTTCACCTCC	BC015537	CCDS7756.1	11p15.5	2012-10-02			ENSG00000213931	ENSG00000213931			4830	protein-coding gene	gene with protein product		142100				2649166	Standard	NM_005330		Approved	HBE	uc001mal.1	P02100	OTTHUMG00000066675	ENST00000380237.1:c.79G>C	chr11.hg19:g.5291042C>G	ENSP00000369586:p.Glu27Gln	58.0	0.0		90.0	10.0	NM_005330	Q6FH44	Missense_Mutation	SNP	ENST00000380237.1	hg19	CCDS7756.1	.	.	.	.	.	.	.	.	.	.	C	19.30	3.800573	0.70567	.	.	ENSG00000213931	ENST00000380237;ENST00000292896;ENST00000396895	D;D;D	0.89617	-2.54;-2.54;-2.54	5.97	5.97	0.96955	Globin-like (1);Globin, structural domain (1);	0.397031	0.24016	U	0.042321	D	0.88566	0.6471	M	0.64630	1.985	0.43613	D	0.995989	B	0.31790	0.34	B	0.31390	0.129	D	0.86563	0.1842	10	0.51188	T	0.08	-29.7236	18.9809	0.92755	0.0:1.0:0.0:0.0	.	27	P02100	HBE_HUMAN	Q	27	ENSP00000369586:E27Q;ENSP00000292896:E27Q;ENSP00000380104:E27Q	ENSP00000292896:E27Q	E	-	1	0	HBE1	5247618	0.920000	0.31207	0.941000	0.38009	0.869000	0.49853	1.962000	0.40442	2.832000	0.97577	0.585000	0.79938	GAA	.	.		0.493	HBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142973.2	NM_005330		G	5291042	C	G	5291042	3	3	287	1	0	0	0	0	1	0	0	0	6989	835	29	4	376	4	HBE1	11	5291042	Missense_Mutation	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10	1493846	5291042	129715474	67	42165										
NELL1	4745	hgsc.bcm.edu	37	chr11	21555918	21555918	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	cttgtgtttttctctgaggcAgatattgatgaatgttcaga	10	5	2	5			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr11:21555918A>G	ENST00000357134.5	+	16	1797		c.e16-1		NELL1_ENST00000532434.1_Intron|NELL1_ENST00000529218.1_Splice_Site|NELL1_ENST00000298925.5_Splice_Site|NELL1_ENST00000325319.5_Splice_Site	NM_006157.3|NM_201551.1	NP_006148.2|NP_963845.1	Q92832	NELL1_HUMAN	NEL-like 1 (chicken)						cell differentiation (GO:0030154)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of osteoblast proliferation (GO:0033689)|nervous system development (GO:0007399)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of gene expression (GO:0010468)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(5)|kidney(3)|large_intestine(15)|lung(36)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	70						TCTCTGAGGCAGATATTGATG	0.433																																					.		Atlas-SNP	.											.	NELL1	179	.	0			c.1646-2A>G						.						129	121	124					11																	21555918		2203	4300	6503	SO:0001630	splice_region_variant	4745	exon16			TGAGGCAGATATT	AK127805	CCDS7855.1, CCDS44555.1, CCDS73267.1, CCDS73268.1	11p15.1	2008-02-01	2001-11-28		ENSG00000165973	ENSG00000165973			7750	protein-coding gene	gene with protein product		602319	"nel (chicken)-like 1"			8975702	Standard	NM_006157		Approved	IDH3GL, FLJ45906	uc001mqe.3	Q92832	OTTHUMG00000166042	ENST00000357134.5:c.1646-1A>G	chr11.hg19:g.21555918A>G		66.0	0.0		103.0	29.0	NM_006157	B2CKC1|Q4VB90|Q4VB91|Q6NSY8|Q9Y472	Splice_Site	SNP	ENST00000357134.5	hg19	CCDS7855.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.378103	0.82682	.	.	ENSG00000165973	ENST00000298925;ENST00000357134;ENST00000325319	.	.	.	5.37	5.37	0.77165	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3703	0.74557	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NELL1	21512494	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.581000	0.90788	2.040000	0.60383	0.377000	0.23210	.	.	.		0.433	NELL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387588.1	NM_006157	Intron	G	21555918	A	G	21555918	5	3	287	1	0	0	0	0	0	0	1	0	10342	202	7	2	1706	2	NELL1	11	21555918	Splice_Site	SNP	A	TCGA-G3-A5SL-01A-11D-A27I-10	16264876	21555918	113450598	68	42166										
SPRYD5	84767	hgsc.bcm.edu	37	chr11	55659022	55659022	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	gaaccgtgagctttgttgatGttgatcaaagttccctgata	10	7	1	4			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr11:55659022G>A	ENST00000449290.2	+	7	1365	c.1273G>A	c.(1273-1275)Gtt>Att	p.V425I	TRIM51_ENST00000244891.3_Missense_Mutation_p.V282I	NM_032681.3	NP_116070.2	Q9BSJ1	TRI51_HUMAN	tripartite motif-containing 51	425	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)										CTTTGTTGATGTTGATCAAAG	0.458																																					p.V425I		Atlas-SNP	.											.	.	.	.	0			c.G1273A						.						119	114	116					11																	55659022		2182	4238	6420	SO:0001583	missense	84767	exon7			GTTGATGTTGATC	BC005014		11p11	2013-01-09	2012-05-18	2012-05-18	ENSG00000124900	ENSG00000124900		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19023	protein-coding gene	gene with protein product			"SPRY domain containing 5"	SPRYD5			Standard	NM_032681		Approved	TRIM51A	uc010rip.2	Q9BSJ1	OTTHUMG00000156437	ENST00000449290.2:c.1273G>A	chr11.hg19:g.55659022G>A	ENSP00000395086:p.Val425Ile	34.0	0.0		39.0	12.0	NM_032681	A6NMG2	Missense_Mutation	SNP	ENST00000449290.2	hg19		.	.	.	.	.	.	.	.	.	.	.	15.40	2.823183	0.50739	.	.	ENSG00000124900	ENST00000449290;ENST00000244891	T;T	0.68903	-0.36;-0.36	1.36	1.36	0.22044	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	.	.	.	.	T	0.78188	0.4244	M	0.80616	2.505	0.09310	N	1	D	0.76494	0.999	D	0.73380	0.98	T	0.63143	-0.6703	9	0.49607	T	0.09	.	6.5498	0.22427	0.0:0.0:1.0:0.0	.	425	Q9BSJ1	SPRY5_HUMAN	I	425;282	ENSP00000395086:V425I;ENSP00000244891:V282I	ENSP00000244891:V282I	V	+	1	0	SPRYD5	55415598	0.983000	0.35010	0.004000	0.12327	0.355000	0.29361	2.035000	0.41155	0.646000	0.30693	0.162000	0.16502	GTT	.	.		0.458	TRIM51-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000391522.1	NM_032681		A	55659022	G	A	55659022	3	1	287	1	0	0	0	0	1	0	0	0	15126	1377	48	3	1295	3	SPRYD5	11	55659022	Missense_Mutation	SNP	G	TCGA-G3-A5SL-01A-11D-A27I-10	34103104	55659022	79347494	69	42167										
MAP3K11	399909	hgsc.bcm.edu	37	chr11	65380716	65380716	+	5'Flank	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	caatgatgttggggtgtgccAgcatggcgaagagccgggcc	17	9	0	2			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr11:65380716A>T	ENST00000355703.3	+	0	0				MAP3K11_ENST00000530153.1_5'Flank|MAP3K11_ENST00000309100.3_Missense_Mutation_p.L171Q	NM_032223.2	NP_115599.2	Q9H6A9	PCX3_HUMAN	pecanex-like 3 (Drosophila)							integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)	13						GGGGTGTGCCAGCATGGCGAA	0.647																																					p.L171Q		Atlas-SNP	.											MAP3K11,colon,carcinoma,0,1	MAP3K11	67	.	0			c.T512A						.						49	48	49					11																	65380716		2201	4297	6498	SO:0001631	upstream_gene_variant	4296	exon1			TGTGCCAGCATGG	BX640978	CCDS44650.1	11q12.1	2008-07-21			ENSG00000197136	ENSG00000197136			18760	protein-coding gene	gene with protein product						15146197	Standard	NM_032223		Approved	FLJ22427	uc001oey.2	Q9H6A9	OTTHUMG00000166539		chr11.hg19:g.65380716A>T	Exception_encountered	149.0	0.0		85.0	31.0	NM_002419	Q6MZN8	Missense_Mutation	SNP	ENST00000355703.3	hg19	CCDS44650.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.084318	0.76642	.	.	ENSG00000173327	ENST00000309100	D	0.95518	-3.73	3.79	3.79	0.43588	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.51477	D	0.000090	D	0.98036	0.9353	H	0.94503	3.545	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98344	1.0540	10	0.87932	D	0	.	10.5536	0.45103	1.0:0.0:0.0:0.0	.	171	Q16584	M3K11_HUMAN	Q	171	ENSP00000309597:L171Q	ENSP00000309597:L171Q	L	-	2	0	MAP3K11	65137292	1.000000	0.71417	0.998000	0.56505	0.929000	0.56500	8.951000	0.93025	1.594000	0.50039	0.460000	0.39030	CTG	.	.		0.647	PCNXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390321.1	NM_032223		T	65380716	A	T	65380716	1	4	287	0	1	0	0	0	0	0	0	0	9254	188	7	4		4	MAP3K11	11	65380716	5'Flank	SNP	A	TCGA-G3-A5SL-01A-11D-A27I-10	9721694	65380716	69625800	70	42168										
LRP5	4041	hgsc.bcm.edu	37	chr11	68216342	68216342	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	caccgacgtgtgtgacagcgActacagcgccagccgctgga	13	14	0	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr11:68216342A>T	ENST00000294304.7	+	23	4758	c.4652A>T	c.(4651-4653)gAc>gTc	p.D1551V	LRP5_ENST00000529481.1_3'UTR	NM_002335.2	NP_002326.2	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein 5	1551	Pro-rich.				adipose tissue development (GO:0060612)|anatomical structure regression (GO:0060033)|anterior/posterior pattern specification (GO:0009952)|apoptotic process involved in patterning of blood vessels (GO:1902262)|bone marrow development (GO:0048539)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|cell migration involved in gastrulation (GO:0042074)|cell-cell signaling involved in mammary gland development (GO:0060764)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic limb morphogenesis (GO:0030326)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocytosis (GO:0006897)|extracellular matrix-cell signaling (GO:0035426)|gastrulation with mouth forming second (GO:0001702)|glucose catabolic process (GO:0006007)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|osteoblast development (GO:0002076)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mitosis (GO:0045840)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of bone remodeling (GO:0046850)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to peptide hormone (GO:0043434)|retina morphogenesis in camera-type eye (GO:0060042)|retinal blood vessel morphogenesis (GO:0061304)|somatic stem cell maintenance (GO:0035019)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	coreceptor activity (GO:0015026)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(24)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TGTGACAGCGACTACAGCGCC	0.617																																					p.D1551V		Atlas-SNP	.											.	LRP5	136	.	0			c.A4652T						.						79	59	66					11																	68216342		2200	4294	6494	SO:0001583	missense	4041	exon23			ACAGCGACTACAG	AF064548	CCDS8181.1	11q13.4	2014-01-28	2003-03-12		ENSG00000162337	ENSG00000162337		"Low density lipoprotein receptors"	6697	protein-coding gene	gene with protein product		603506	"osteoporosis pseudoglioma syndrome", "exudative vitreoretinopathy 1"	LRP7, OPPG, EVR1		9714764, 10049586	Standard	XM_005273994		Approved	LR3, BMND1, HBM, OPS, OPTA1, VBCH2, EVR4	uc001ont.3	O75197	OTTHUMG00000167570	ENST00000294304.7:c.4652A>T	chr11.hg19:g.68216342A>T	ENSP00000294304:p.Asp1551Val	92.0	0.0		62.0	24.0	NM_002335	Q96TD6|Q9UES7|Q9UP66	Missense_Mutation	SNP	ENST00000294304.7	hg19	CCDS8181.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.95|15.95	2.984412|2.984412	0.53934|0.53934	.|.	.|.	ENSG00000162337|ENSG00000162337	ENST00000294304|ENST00000529702	D|.	0.94723|.	-3.5|.	4.73|4.73	4.73|4.73	0.59995|0.59995	.|.	0.000000|.	0.47455|.	U|.	0.000223|.	T|T	0.70351|0.70351	0.3214|0.3214	M|M	0.63428|0.63428	1.95|1.95	0.80722|0.80722	D|D	1|1	P;P|.	0.48294|.	0.908;0.908|.	P;P|.	0.46885|.	0.53;0.53|.	T|T	0.70230|0.70230	-0.4929|-0.4929	10|5	0.48119|.	T|.	0.1|.	.|.	14.4536|14.4536	0.67401|0.67401	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	1551;1551|.	Q9UES7;O75197|.	.;LRP5_HUMAN|.	V|S	1551|108	ENSP00000294304:D1551V|.	ENSP00000294304:D1551V|.	D|T	+|+	2|1	0|0	LRP5|LRP5	67972918|67972918	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.077000|0.077000	0.17291|0.17291	6.865000|6.865000	0.75500|0.75500	2.003000|2.003000	0.58678|0.58678	0.454000|0.454000	0.30748|0.30748	GAC|ACT	.	.		0.617	LRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395088.1	NM_002335		T	68216342	A	T	68216342	3	4	287	1	0	0	0	0	1	0	0	0	8969	275	10	4	4742	4	LRP5	11	68216342	Missense_Mutation	SNP	A	TCGA-G3-A5SL-01A-11D-A27I-10	2835626	68216342	66790174	71	42169										
MMP3	4314	hgsc.bcm.edu	37	chr11	102711281	102711281	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	gctgagtgaaagagacccagGgagtggccaatttcatgagc	14	8	1	4	rs375553123		TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr11:102711281G>T	ENST00000299855.5	-	5	925	c.669C>A	c.(667-669)tcC>tcA	p.S223S		NM_002422.3	NP_002413.1	P08254	MMP3_HUMAN	matrix metallopeptidase 3 (stromelysin 1, progelatinase)	223					cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|positive regulation of oxidative stress-induced cell death (GO:1903209)|proteolysis (GO:0006508)|regulation of cell migration (GO:0030334)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0142)	Marimastat(DB00786)	AGAGACCCAGGGAGTGGCCAA	0.403																																					p.S223S		Atlas-SNP	.											MMP3,colon,carcinoma,0,1	MMP3	60	.	0			c.C669A						.						113	111	111					11																	102711281		2203	4299	6502	SO:0001819	synonymous_variant	4314	exon5			ACCCAGGGAGTGG	X05232	CCDS8323.1	11q22.3	2012-10-02	2005-08-08		ENSG00000149968	ENSG00000149968	3.4.24.17		7173	protein-coding gene	gene with protein product		185250	"matrix metalloproteinase 3 (stromelysin 1, progelatinase)"	STMY1, STMY			Standard	NM_002422		Approved		uc001phj.1	P08254	OTTHUMG00000048254	ENST00000299855.5:c.669C>A	chr11.hg19:g.102711281G>T		101.0	0.0		65.0	3.0	NM_002422	B2R8B8|Q3B7S0|Q6GRF8	Silent	SNP	ENST00000299855.5	hg19	CCDS8323.1																																																																																			.	.		0.403	MMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109758.2	NM_002422		T	102711281	G	T	102711281	2	4	287	1	0	0	0	0	0	0	0	1	9675	1219	43	3		3	MMP3	11	102711281	Silent	SNP	G	TCGA-G3-A5SL-01A-11D-A27I-10	34494939	102711281	32295235	72	42170										
PDGFD	80310	hgsc.bcm.edu	37	chr11	103814257	103814257	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	tattctcaagatcttcttgcCatgactctggattgaagtac	7	9	4	3			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr11:103814257C>A	ENST00000393158.2	-	5	874	c.695G>T	c.(694-696)tGg>tTg	p.W232L	RP11-617B3.2_ENST00000527804.1_RNA|PDGFD_ENST00000302251.5_Missense_Mutation_p.W226L			Q9GZP0	PDGFD_HUMAN	platelet derived growth factor D	232					cellular response to amino acid stimulus (GO:0071230)|multicellular organismal development (GO:0007275)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell division (GO:0051781)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(8)|prostate(3)|upper_aerodigestive_tract(1)	23		Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Melanoma(852;0.0563)|all_neural(303;0.165)		BRCA - Breast invasive adenocarcinoma(274;0.00136)|Epithelial(105;0.111)		ATCTTCTTGCCATGACTCTGG	0.443																																					p.W232L		Atlas-SNP	.											PDGFD_ENST00000393158,colon,carcinoma,0,2	PDGFD	125	.	0			c.G695T						.						135	110	119					11																	103814257		2202	4299	6501	SO:0001583	missense	80310	exon5			TCTTGCCATGACT	AF113216	CCDS8326.1, CCDS41703.1	11q22.3	2008-02-05			ENSG00000170962	ENSG00000170962			30620	protein-coding gene	gene with protein product	"spinal cord derived growth factor B"	609673				11162582, 11980634	Standard	NM_033135		Approved	SCDGF-B, MSTP036, IEGF	uc001phq.3	Q9GZP0	OTTHUMG00000165953	ENST00000393158.2:c.695G>T	chr11.hg19:g.103814257C>A	ENSP00000376865:p.Trp232Leu	82.0	0.0		119.0	27.0	NM_025208	A8K9T6|Q9BWV5	Missense_Mutation	SNP	ENST00000393158.2	hg19	CCDS41703.1	.	.	.	.	.	.	.	.	.	.	C	18.22	3.575276	0.65878	.	.	ENSG00000170962	ENST00000393158;ENST00000302251	T;T	0.37411	1.2;1.22	5.53	5.53	0.82687	.	0.121611	0.64402	D	0.000011	T	0.42063	0.1186	M	0.63843	1.955	0.80722	D	1	B;B	0.19583	0.012;0.037	B;B	0.19148	0.006;0.024	T	0.30937	-0.9961	10	0.66056	D	0.02	-16.338	19.823	0.96605	0.0:1.0:0.0:0.0	.	232;226	Q9GZP0;Q9GZP0-2	PDGFD_HUMAN;.	L	232;226	ENSP00000376865:W232L;ENSP00000302193:W226L	ENSP00000302193:W226L	W	-	2	0	PDGFD	103319467	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	5.628000	0.67791	2.770000	0.95276	0.650000	0.86243	TGG	.	.		0.443	PDGFD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387231.2	NM_025208		A	103814257	C	A	103814257	3	1	287	1	0	0	0	0	1	0	0	0	11669	595	21	3	429	3	PDGFD	11	103814257	Missense_Mutation	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10	1102976	103814257	31192259	73	42171										
ZC3H12C	85463	hgsc.bcm.edu	37	chr11	110034060	110034060	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	tctggataattttctgaggaAgaaacctattgttcctgaac	8	7	2	3			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr11:110034060A>G	ENST00000278590.3	+	5	1262	c.1211A>G	c.(1210-1212)aAg>aGg	p.K404R	ZC3H12C_ENST00000528673.1_Missense_Mutation_p.K405R|ZC3H12C_ENST00000453089.2_Missense_Mutation_p.K373R	NM_033390.1	NP_203748.1	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	404							endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.72e-06)|BRCA - Breast invasive adenocarcinoma(274;1.17e-05)|all cancers(92;9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0279)		TTTCTGAGGAAGAAACCTATT	0.388																																					p.K404R		Atlas-SNP	.											.	ZC3H12C	83	.	0			c.A1211G						.						53	50	51					11																	110034060		1852	4090	5942	SO:0001583	missense	85463	exon5			TGAGGAAGAAACC		CCDS44727.1	11q22.3	2012-07-05			ENSG00000149289	ENSG00000149289		"Zinc fingers, CCCH-type domain containing"	29362	protein-coding gene	gene with protein product	"MCP induced protein 3"	615001				11214970, 18178554	Standard	NM_033390		Approved	KIAA1726, MCPIP3	uc009yxw.3	Q9C0D7	OTTHUMG00000166572	ENST00000278590.3:c.1211A>G	chr11.hg19:g.110034060A>G	ENSP00000278590:p.Lys404Arg	90.0	0.0		73.0	5.0	NM_033390	B4DI65|B4DR47	Missense_Mutation	SNP	ENST00000278590.3	hg19	CCDS44727.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.072879	0.76415	.	.	ENSG00000149289	ENST00000278590;ENST00000528673;ENST00000453089	T;T;T	0.38077	1.16;1.16;1.16	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.60340	0.2261	M	0.69823	2.125	0.53688	D	0.999975	P;D;P	0.76494	0.473;0.999;0.473	B;D;B	0.80764	0.081;0.994;0.081	T	0.62714	-0.6796	10	0.59425	D	0.04	-26.7066	16.1818	0.81909	1.0:0.0:0.0:0.0	.	405;404;404	B4DR47;B4DI65;Q9C0D7	.;.;ZC12C_HUMAN	R	404;405;373	ENSP00000278590:K404R;ENSP00000431821:K405R;ENSP00000413094:K373R	ENSP00000278590:K404R	K	+	2	0	ZC3H12C	109539270	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.225000	0.72522	0.459000	0.35465	AAG	.	.		0.388	ZC3H12C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390491.1	NM_033390		G	110034060	A	G	110034060	3	3	287	1	0	0	0	0	1	0	0	0	17578	72	3	2	1229	2	ZC3H12C	11	110034060	Missense_Mutation	SNP	A	TCGA-G3-A5SL-01A-11D-A27I-10	6219803	110034060	24972456	74	42172										
DSCAML1	57453	hgsc.bcm.edu	37	chr11	117321317	117321317	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	tggtgtacttgcggatcaccCcgttgggcttggtagggggg	18	8	1	0			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr11:117321317C>T	ENST00000321322.6	-	20	3837	c.3836G>A	c.(3835-3837)gGg>gAg	p.G1279E	DSCAML1_ENST00000527706.1_Missense_Mutation_p.G1009E	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1219	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.|Ig-like C2-type 10.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		GCGGATCACCCCGTTGGGCTT	0.567																																					p.G1279E		Atlas-SNP	.											.	DSCAML1	286	.	0			c.G3836A						.						61	57	58					11																	117321317		2201	4296	6497	SO:0001583	missense	57453	exon20			ATCACCCCGTTGG		CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.3836G>A	chr11.hg19:g.117321317C>T	ENSP00000315465:p.Gly1279Glu	69.0	0.0		47.0	9.0	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Missense_Mutation	SNP	ENST00000321322.6	hg19	CCDS8384.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.802243	0.90538	.	.	ENSG00000177103	ENST00000527706;ENST00000321322;ENST00000446508	T;T	0.64991	-0.13;-0.13	4.42	4.42	0.53409	Fibronectin, type III (4);Immunoglobulin-like fold (1);	.	.	.	.	D	0.84745	0.5540	H	0.94462	3.54	0.80722	D	1	D	0.67145	0.996	D	0.72625	0.978	D	0.89180	0.3543	9	0.87932	D	0	.	18.3455	0.90321	0.0:1.0:0.0:0.0	.	1219	Q8TD84	DSCL1_HUMAN	E	1009;1279;986	ENSP00000434335:G1009E;ENSP00000315465:G1279E	ENSP00000315465:G1279E	G	-	2	0	DSCAML1	116826527	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.643000	0.83403	2.741000	0.93983	0.585000	0.79938	GGG	.	.		0.567	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693		T	117321317	C	T	117321317	3	4	287	1	0	0	0	0	1	0	0	0	4771	623	22	3	2561	3	DSCAML1	11	117321317	Missense_Mutation	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10	7287257	117321317	17685199	75	42173										
AKAP3	10566	hgsc.bcm.edu	37	chr12	4737496	4737496	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	agccaggagccttgtctgggGcagcattcctggaacatgca	13	11	1	0			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr12:4737496G>A	ENST00000545990.2	-	5	1096	c.572C>T	c.(571-573)gCc>gTc	p.A191V	AKAP3_ENST00000228850.1_Missense_Mutation_p.A191V|RP11-500M8.7_ENST00000536588.1_Intron	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	191					acrosome reaction (GO:0007340)|cellular component movement (GO:0006928)|protein localization (GO:0008104)|single fertilization (GO:0007338)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	acrosomal vesicle (GO:0001669)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	protein kinase A binding (GO:0051018)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						CTTGTCTGGGGCAGCATTCCT	0.493																																					p.A191V		Atlas-SNP	.											.	AKAP3	212	.	0			c.C572T						.						111	106	107					12																	4737496		2203	4300	6503	SO:0001583	missense	10566	exon4			TCTGGGGCAGCAT	U85715	CCDS8531.1	12p13.3	2009-03-12				ENSG00000111254		"A-kinase anchor proteins"	373	protein-coding gene	gene with protein product	"Fibrous Sheath Protein of 95 kDa", "cancer/testis antigen 82"	604689				10334916, 10319321	Standard	NM_001278309		Approved	FSP95, SOB1, AKAP110, CT82	uc001qnb.4	O75969		ENST00000545990.2:c.572C>T	chr12.hg19:g.4737496G>A	ENSP00000440994:p.Ala191Val	102.0	0.0		94.0	37.0	NM_006422	O75945|Q86X01|Q9UM61	Missense_Mutation	SNP	ENST00000545990.2	hg19	CCDS8531.1	.	.	.	.	.	.	.	.	.	.	G	0.181	-1.061810	0.01950	.	.	ENSG00000111254	ENST00000228850;ENST00000545990	T;T	0.07800	3.16;3.16	4.87	-7.05	0.01573	A-kinase anchor 110kDa, C-terminal (1);	1.874110	0.02385	N	0.079148	T	0.05364	0.0142	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.32719	-0.9896	10	0.48119	T	0.1	.	4.711	0.12872	0.3967:0.0:0.2755:0.3278	.	191	O75969	AKAP3_HUMAN	V	191	ENSP00000228850:A191V;ENSP00000440994:A191V	ENSP00000228850:A191V	A	-	2	0	AKAP3	4607757	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	-0.142000	0.10311	-1.754000	0.01321	-0.806000	0.03193	GCC	.	.		0.493	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	NM_006422		A	4737496	G	A	4737496	3	1	287	1	0	0	0	0	1	0	0	0	452	1203	42	3	1997	3	AKAP3	12	4737496	Missense_Mutation	SNP	G	TCGA-G3-A5SL-01A-11D-A27I-10		4737496	129114399	76	42174										
PIK3C2G	5288	hgsc.bcm.edu	37	chr12	18691110	18691110	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	ggaccgagctcctttcatttTtacttcagagatggaatact	8	9	2	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr12:18691110T>G	ENST00000266497.5	+	23	3259	c.3221T>G	c.(3220-3222)tTt>tGt	p.F1074C	PIK3C2G_ENST00000433979.1_Missense_Mutation_p.F1074C|PIK3C2G_ENST00000538779.1_Missense_Mutation_p.F1115C			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	1074	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)			breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				CCTTTCATTTTTACTTCAGAG	0.368																																					p.F1074C		Atlas-SNP	.											.	PIK3C2G	315	.	0			c.T3221G						.						103	95	97					12																	18691110		1801	4074	5875	SO:0001583	missense	5288	exon24			TCATTTTTACTTC	AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"phosphoinositide-3-kinase, class 2, gamma polypeptide"			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.3221T>G	chr12.hg19:g.18691110T>G	ENSP00000266497:p.Phe1074Cys	25.0	0.0		70.0	26.0	NM_004570	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	hg19	CCDS44839.1	.	.	.	.	.	.	.	.	.	.	T	17.24	3.338549	0.60963	.	.	ENSG00000139144	ENST00000433979;ENST00000266497;ENST00000538779	T;T;T	0.76186	-1.0;-1.0;-1.0	3.78	3.78	0.43462	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.069387	0.56097	D	0.000021	D	0.85344	0.5675	M	0.81239	2.535	0.58432	D	0.999997	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.87468	0.2412	10	0.87932	D	0	-18.26	12.7158	0.57113	0.0:0.0:0.0:1.0	.	1114;1115;1074	B7ZLY6;F5H369;O75747	.;.;P3C2G_HUMAN	C	1074;1074;1115	ENSP00000404845:F1074C;ENSP00000266497:F1074C;ENSP00000445381:F1115C	ENSP00000266497:F1074C	F	+	2	0	PIK3C2G	18582377	1.000000	0.71417	1.000000	0.80357	0.813000	0.45954	7.700000	0.84556	1.955000	0.56771	0.482000	0.46254	TTT	.	.		0.368	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570		G	18691110	T	G	18691110	3	3	287	1	0	0	0	0	1	0	0	0	11920	1841	64	5	3311	5	PIK3C2G	12	18691110	Missense_Mutation	SNP	T	TCGA-G3-A5SL-01A-11D-A27I-10	13953614	18691110	115160785	77	42175										
ARID2	196528	hgsc.bcm.edu	37	chr12	46245723	46245723	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	tggagaacccgtcctgccgaCgaggagccacaaacaccagc	11	15	0	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr12:46245723C>T	ENST00000334344.6	+	15	3989	c.3817C>T	c.(3817-3819)Cga>Tga	p.R1273*	ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000444670.1_Nonsense_Mutation_p.R883*|ARID2_ENST00000457135.1_5'Flank|ARID2_ENST00000422737.1_Nonsense_Mutation_p.R1124*	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	1273					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		GTCCTGCCGACGAGGAGCCAC	0.428			"N, S, F"		hepatocellular carcinoma																																p.R1273X		Atlas-SNP	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	ARID2,NS,carcinoma,0,2	ARID2	311	.	0			c.C3817T						.						51	51	51					12																	46245723		2203	4300	6503	SO:0001587	stop_gained	196528	exon15			TGCCGACGAGGAG		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.3817C>T	chr12.hg19:g.46245723C>T	ENSP00000335044:p.Arg1273*	64.0	0.0		67.0	17.0	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Nonsense_Mutation	SNP	ENST00000334344.6	hg19	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	C	43	9.856911	0.99281	.	.	ENSG00000189079	ENST00000334344;ENST00000549153;ENST00000338636;ENST00000422737;ENST00000444670	.	.	.	6.17	5.21	0.72293	.	0.237030	0.43110	D	0.000616	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.2899	16.5817	0.84717	0.1917:0.8083:0.0:0.0	.	.	.	.	X	1273;390;390;1124;883	.	ENSP00000335044:R1273X	R	+	1	2	ARID2	44531990	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.429000	0.44758	2.941000	0.99782	0.655000	0.94253	CGA	.	.		0.428	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		T	46245723	C	T	46245723	4	4	287	1	0	0	0	0	0	1	0	0	915	528	19	1	3875	1	ARID2	12	46245723	Nonsense_Mutation	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10	27554613	46245723	87606172	78	42176										
COL2A1	1280	hgsc.bcm.edu	37	chr12	48391816	48391816	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	agatttctccctctcttaccTgaggcccaggaggtcctttg	9	13	2	2			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr12:48391816T>C	ENST00000380518.3	-	5	538	c.374A>G	c.(373-375)cAg>cGg	p.Q125R	COL2A1_ENST00000337299.6_Splice_Site_p.Q56R	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	125					axon guidance (GO:0007411)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to BMP stimulus (GO:0071773)|central nervous system development (GO:0007417)|chondrocyte differentiation (GO:0002062)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal joint morphogenesis (GO:0060272)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|limb bud formation (GO:0060174)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|notochord development (GO:0030903)|otic vesicle development (GO:0071599)|palate development (GO:0060021)|proteoglycan metabolic process (GO:0006029)|regulation of gene expression (GO:0010468)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|tissue homeostasis (GO:0001894)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen type II trimer (GO:0005585)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(3)	64		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	CTCTCTTACCTGAGGCCCAGG	0.527																																					p.Q125R		Atlas-SNP	.											.	COL2A1	368	.	0			c.A374G						.						107	112	110					12																	48391816		2203	4300	6503	SO:0001630	splice_region_variant	1280	exon5			CTTACCTGAGGCC	X16468	CCDS8759.1, CCDS41778.1	12q12-q13.2	2013-11-14	2008-02-04		ENSG00000139219	ENSG00000139219		"Collagens"	2200	protein-coding gene	gene with protein product		120140	"collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital)", "arthroophthalmopathy, progressive (Stickler syndrome)"	SEDC, AOM		1677770	Standard	NM_033150		Approved	STL1	uc001rqu.3	P02458	OTTHUMG00000149896	ENST00000380518.3:c.375+1A>G	chr12.hg19:g.48391816T>C		156.0	0.0		100.0	39.0	NM_001844	A6NGA0|Q12985|Q14009|Q14044|Q14045|Q14046|Q14047|Q14056|Q14058|Q16672|Q1JQ82|Q2V4X7|Q6LBY1|Q6LBY2|Q6LBY3|Q96IT5|Q99227|Q9UE38|Q9UE39|Q9UE40|Q9UE41|Q9UE42|Q9UE43	Missense_Mutation	SNP	ENST00000380518.3	hg19	CCDS41778.1	.	.	.	.	.	.	.	.	.	.	T	12.79	2.044709	0.36085	.	.	ENSG00000139219	ENST00000380518;ENST00000395281;ENST00000337299	D;D	0.92858	-3.12;-3.12	5.04	5.04	0.67666	.	0.277618	0.32301	N	0.006292	T	0.81153	0.4763	N	0.04724	-0.175	0.46874	D	0.999238	B;B	0.33919	0.231;0.432	B;B	0.31016	0.075;0.123	T	0.80238	-0.1465	10	0.16896	T	0.51	.	14.0685	0.64847	0.0:0.0:0.0:1.0	.	56;125	P02458-1;P02458	.;CO2A1_HUMAN	R	125;56;56	ENSP00000369889:Q125R;ENSP00000338213:Q56R	ENSP00000338213:Q56R	Q	-	2	0	COL2A1	46678083	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	3.777000	0.55364	2.047000	0.60756	0.454000	0.30748	CAG	.	.		0.527	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844	Missense_Mutation	C	48391816	T	C	48391816	5	2	287	1	0	0	0	0	0	0	1	0	3689	1594	55	2	4289	2	COL2A1	12	48391816	Splice_Site	SNP	T	TCGA-G3-A5SL-01A-11D-A27I-10	2146093	48391816	85460079	79	42177										
KRT72	140807	hgsc.bcm.edu	37	chr12	52979943	52979943	+	Frame_Shift_Del	DEL	G	G	-													0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	cctcctgccccagcattggtGctgctgatgacggctggaat					rs200611701		TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr12:52979943delG	ENST00000537672.2	-	9	1369	c.1359delC	c.(1357-1359)agcfs	p.S453fs	KRT72_ENST00000398066.3_Frame_Shift_Del_p.S265fs|KRT72_ENST00000293745.2_Frame_Shift_Del_p.S453fs|KRT72_ENST00000354310.4_Frame_Shift_Del_p.S411fs	NM_001146225.1	NP_001139697.1	Q14CN4	K2C72_HUMAN	keratin 72	453	Tail.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(357;0.195)		CAGCATTGGTGCTGCTGATGA	0.587																																					p.T454fs		Atlas-Indel,Pindel	.											.	KRT72	70	.	0			c.1360delA						.						42	39	40					12																	52979943		2203	4300	6503	SO:0001589	frameshift_variant	140807	exon9			.	AY033495	CCDS8833.1, CCDS53795.1	12q13.13	2013-06-25			ENSG00000170486	ENSG00000170486		"-", "Intermediate filaments type II, keratins (basic)"	28932	protein-coding gene	gene with protein product		608246				12648212, 11703281, 16831889	Standard	NM_080747		Approved	K6IRS2, KRT6IRS2, KRT6, K6irs	uc001saq.2	Q14CN4	OTTHUMG00000169744	ENST00000537672.2:c.1359delC	chr12.hg19:g.52979943delG	ENSP00000441160:p.Ser453fs	67.0	0.0		81.0	28.0	NM_080747	B4DEI8|H9KV51|Q8NA87|Q8WWY9|Q8WWZ0	Frame_Shift_Del	DEL	ENST00000537672.2	hg19	CCDS8833.1																																																																																			.	.		0.587	KRT72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405693.1	NM_080747		-	52979943	G	-	52979943	7	5	287	1	0	1	0	1	0	0	0	0	8494	1310	46	0	180	0	KRT72	12	52979943	Frame_Shift_Del	DEL	G	TCGA-G3-A5SL-01A-11D-A27I-10	4588127	52979943	80871952	80	42178										
ANAPC7	51434	hgsc.bcm.edu	37	chr12	110819712	110819712	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	gaatggccttggctcctaaaTagagggcccgggagtagcgt	15	9	0	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr12:110819712T>C	ENST00000455511.3	-	8	1079	c.1079A>G	c.(1078-1080)tAt>tGt	p.Y360C	ANAPC7_ENST00000481473.1_5'Flank|ANAPC7_ENST00000450008.2_Missense_Mutation_p.Y360C	NM_016238.2	NP_057322.2	Q9UJX3	APC7_HUMAN	anaphase promoting complex subunit 7	360					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)			breast(3)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)	19						GGCTCCTAAATAGAGGGCCCG	0.433																																					p.Y360C		Atlas-SNP	.											.	ANAPC7	68	.	0			c.A1079G						.						58	48	52					12																	110819712		2203	4300	6503	SO:0001583	missense	51434	exon8			CCTAAATAGAGGG	AF191340	CCDS9145.2, CCDS44971.1	12q13.12	2013-01-10			ENSG00000196510	ENSG00000196510		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	17380	protein-coding gene	gene with protein product		606949					Standard	NM_016238		Approved	APC7	uc001tqo.2	Q9UJX3	OTTHUMG00000157009	ENST00000455511.3:c.1079A>G	chr12.hg19:g.110819712T>C	ENSP00000394394:p.Tyr360Cys	64.0	0.0		47.0	18.0	NM_016238	Q96AC4|Q96GF4|Q9BU24|Q9NT16	Missense_Mutation	SNP	ENST00000455511.3	hg19	CCDS9145.2	.	.	.	.	.	.	.	.	.	.	T	22.5	4.298069	0.81025	.	.	ENSG00000196510	ENST00000455511;ENST00000450008;ENST00000471602;ENST00000548234	T;T	0.59364	0.27;0.27	6.17	6.17	0.99709	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.69744	0.3145	M	0.62723	1.935	0.58432	D	0.999999	D;P	0.61697	0.99;0.86	P;P	0.56474	0.799;0.516	T	0.71144	-0.4678	10	0.54805	T	0.06	-23.3973	16.8222	0.85835	0.0:0.0:0.0:1.0	.	360;360	Q9UJX3-2;Q9UJX3	.;APC7_HUMAN	C	360;360;53;62	ENSP00000394394:Y360C;ENSP00000402314:Y360C	ENSP00000402314:Y360C	Y	-	2	0	ANAPC7	109304095	1.000000	0.71417	1.000000	0.80357	0.807000	0.45602	7.698000	0.84413	2.371000	0.80710	0.533000	0.62120	TAT	.	.		0.433	ANAPC7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347075.3	NM_016238		C	110819712	T	C	110819712	3	2	287	1	0	0	0	0	1	0	0	0	606	1406	49	2	740	2	ANAPC7	12	110819712	Missense_Mutation	SNP	T	TCGA-G3-A5SL-01A-11D-A27I-10	57839769	110819712	23032183	81	42179										
XPO4	64328	hgsc.bcm.edu	37	chr13	21361634	21361634	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	tcttaccttaagaaagtgccGtgttgctagaaaaagtggtg	11	6	1	2			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr13:21361634G>C	ENST00000255305.6	-	21	3222	c.3151C>G	c.(3151-3153)Cgg>Ggg	p.R1051G	XPO4_ENST00000400602.2_Missense_Mutation_p.R1051G			Q9C0E2	XPO4_HUMAN	exportin 4	1051					positive regulation of protein export from nucleus (GO:0046827)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(10)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	41		all_cancers(29;5.05e-24)|all_epithelial(30;5.56e-20)|all_lung(29;2.38e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000521)|Epithelial(112;0.000892)|OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Lung(94;0.0189)|LUSC - Lung squamous cell carcinoma(192;0.0548)		AGAAAGTGCCGTGTTGCTAGA	0.453																																					p.R1051G		Atlas-SNP	.											XPO4,NS,carcinoma,0,1	XPO4	153	.	0			c.C3151G						.						126	125	126					13																	21361634		1923	4140	6063	SO:0001583	missense	64328	exon21			AGTGCCGTGTTGC	AB051508	CCDS41872.1	13q11	2011-04-13			ENSG00000132953	ENSG00000132953		"Exportins"	17796	protein-coding gene	gene with protein product		611449				11214970, 10944119	Standard	NM_022459		Approved	FLJ13046, KIAA1721	uc001unq.4	Q9C0E2	OTTHUMG00000016528	ENST00000255305.6:c.3151C>G	chr13.hg19:g.21361634G>C	ENSP00000255305:p.Arg1051Gly	139.0	0.0		92.0	31.0	NM_022459	Q5VUZ5|Q8N3V6|Q9H934	Missense_Mutation	SNP	ENST00000255305.6	hg19	CCDS41872.1	.	.	.	.	.	.	.	.	.	.	G	12.66	2.006111	0.35415	.	.	ENSG00000132953	ENST00000400602;ENST00000255305	T;T	0.25579	1.79;1.79	5.69	3.68	0.42216	Armadillo-like helical (1);Armadillo-type fold (1);Exportin 1, C-terminal (1);	0.119565	0.52532	D	0.000064	T	0.21387	0.0515	L	0.40543	1.245	0.58432	D	0.999992	B	0.14438	0.01	B	0.18871	0.023	T	0.04481	-1.0948	10	0.23302	T	0.38	-12.4956	13.6545	0.62330	0.0:0.0:0.6152:0.3848	.	1051	Q9C0E2	XPO4_HUMAN	G	1051	ENSP00000383444:R1051G;ENSP00000255305:R1051G	ENSP00000255305:R1051G	R	-	1	2	XPO4	20259634	0.986000	0.35501	0.996000	0.52242	0.977000	0.68977	1.802000	0.38853	1.524000	0.49035	0.655000	0.94253	CGG	.	.		0.453	XPO4-001	KNOWN	non_canonical_conserved|non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044096.1	NM_022459		C	21361634	G	C	21361634	3	2	287	1	0	0	0	0	1	0	0	0	17461	1144	40	4	316	4	XPO4	13	21361634	Missense_Mutation	SNP	G	TCGA-G3-A5SL-01A-11D-A27I-10		21361634	93808244	82	42180										
ACIN1	22985	hgsc.bcm.edu	37	chr14	23530298	23530298	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	aagaagagcactcacctggcTgtcagtcagtgggagccaat	12	10	3	2			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr14:23530298T>C	ENST00000262710.1	-	18	4021	c.3694A>G	c.(3694-3696)Agc>Ggc	p.S1232G	ACIN1_ENST00000397341.3_Missense_Mutation_p.S474G|ACIN1_ENST00000605057.1_Missense_Mutation_p.S1174G|ACIN1_ENST00000357481.2_Missense_Mutation_p.S474G|ACIN1_ENST00000557515.1_Missense_Mutation_p.S473G|ACIN1_ENST00000338631.6_Missense_Mutation_p.S505G|ACIN1_ENST00000555053.1_Missense_Mutation_p.S1219G|ACIN1_ENST00000457657.1_Missense_Mutation_p.S1192G	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	1232	Arg/Asp/Glu/Lys-rich.|Sufficient for interaction with RNPS1 and SAP18 and formation of th ASAP complex. {ECO:0000250}.				apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		CTCACCTGGCTGTCAGTCAGT	0.582																																					p.S1232G		Atlas-SNP	.											.	ACIN1	147	.	0			c.A3694G						.						104	88	93					14																	23530298		2203	4300	6503	SO:0001583	missense	22985	exon18			CCTGGCTGTCAGT	AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 152"	604562	"apoptotic chromatin condensation inducer in the nucleus"	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.3694A>G	chr14.hg19:g.23530298T>C	ENSP00000262710:p.Ser1232Gly	156.0	0.0		93.0	40.0	NM_014977	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Missense_Mutation	SNP	ENST00000262710.1	hg19	CCDS9587.1	.	.	.	.	.	.	.	.	.	.	T	14.82	2.650550	0.47362	.	.	ENSG00000100813	ENST00000557515;ENST00000338631;ENST00000357481;ENST00000262710;ENST00000457657;ENST00000397341;ENST00000555053	T;T;T;T;T;T;T	0.22336	1.96;1.96;1.96;1.96;1.96;1.96;1.96	5.03	3.81	0.43845	.	0.000000	0.47455	D	0.000240	T	0.10723	0.0262	N	0.14661	0.345	0.29355	N	0.865089	P;B;B;B;B	0.36249	0.545;0.41;0.41;0.065;0.065	B;B;B;B;B	0.35770	0.21;0.104;0.104;0.031;0.031	T	0.05500	-1.0881	10	0.46703	T	0.11	-8.5987	5.4923	0.16783	0.1548:0.0852:0.0:0.76	.	1219;1232;1192;505;474	G3V3M7;Q9UKV3;E7EQT4;Q9UKV3-2;Q9UKV3-3	.;ACINU_HUMAN;.;.;.	G	473;505;474;1232;1192;474;1219	ENSP00000451138:S473G;ENSP00000345541:S505G;ENSP00000350073:S474G;ENSP00000262710:S1232G;ENSP00000405677:S1192G;ENSP00000380502:S474G;ENSP00000451328:S1219G	ENSP00000262710:S1232G	S	-	1	0	ACIN1	22600138	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	3.357000	0.52277	2.237000	0.73441	0.460000	0.39030	AGC	.	.		0.582	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977		C	23530298	T	C	23530298	3	2	287	1	0	0	0	0	1	0	0	0	142	1580	55	2	339	2	ACIN1	14	23530298	Missense_Mutation	SNP	T	TCGA-G3-A5SL-01A-11D-A27I-10		23530298	83819242	83	42181										
MYH7	4625	hgsc.bcm.edu	37	chr14	23898464	23898464	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	gacattctgccccttggtgaCgtactcattgcccactttca	7	14	3	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr14:23898464C>T	ENST00000355349.3	-	13	1393	c.1231G>A	c.(1231-1233)Gtc>Atc	p.V411I		NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	411	Myosin motor.		V -> I (in CMH1). {ECO:0000269|PubMed:12974739, ECO:0000269|PubMed:12975413, ECO:0000269|PubMed:15858117}.		adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		CCCTTGGTGACGTACTCATTG	0.567																																					p.V411I		Atlas-SNP	.											.	MYH7	349	.	0			c.G1231A	GRCh37	CM032602	MYH7	M		.						158	134	142					14																	23898464		2203	4300	6503	SO:0001583	missense	4625	exon13			TGGTGACGTACTC	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.1231G>A	chr14.hg19:g.23898464C>T	ENSP00000347507:p.Val411Ile	215.0	0.0		169.0	62.0	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Missense_Mutation	SNP	ENST00000355349.3	hg19	CCDS9601.1	.	.	.	.	.	.	.	.	.	.	c	20.6	4.025763	0.75390	.	.	ENSG00000092054	ENST00000355349;ENST00000544444	D	0.88896	-2.44	4.04	4.04	0.47022	Myosin head, motor domain (2);	.	.	.	.	D	0.92218	0.7532	L	0.48362	1.52	0.80722	D	1	D	0.57571	0.98	D	0.77004	0.989	D	0.93171	0.6566	9	0.66056	D	0.02	.	16.3734	0.83374	0.0:1.0:0.0:0.0	.	411	P12883	MYH7_HUMAN	I	411	ENSP00000347507:V411I	ENSP00000347507:V411I	V	-	1	0	MYH7	22968304	1.000000	0.71417	0.937000	0.37676	0.551000	0.35334	5.787000	0.69013	2.077000	0.62373	0.455000	0.32223	GTC	.	.		0.567	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257		T	23898464	C	T	23898464	3	4	287	1	0	0	0	0	1	0	0	0	10048	536	19	1	4688	1	MYH7	14	23898464	Missense_Mutation	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10	368166	23898464	83451076	84	42182										
TINF2	26277	hgsc.bcm.edu	37	chr14	24709083	24709083	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	agaagggggtaggtattcacAgagagtgggtatcaaggtgt	17	3	2	2			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr14:24709083A>C	ENST00000267415.7	-	9	1617	c.1276T>G	c.(1276-1278)Tgt>Ggt	p.C426G	TINF2_ENST00000540705.1_Missense_Mutation_p.C391G|TINF2_ENST00000558566.1_3'UTR|TINF2_ENST00000558510.1_5'Flank|TINF2_ENST00000538777.1_3'UTR|TINF2_ENST00000399423.4_3'UTR	NM_001099274.1	NP_001092744.1	Q9BSI4	TINF2_HUMAN	TERF1 (TRF1)-interacting nuclear factor 2	426					negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of protein ADP-ribosylation (GO:0010836)|negative regulation of telomere maintenance via telomerase (GO:0032211)|positive regulation of telomere maintenance (GO:0032206)|protein localization to chromosome (GO:0034502)|protein localization to chromosome, telomeric region (GO:0070198)|telomere assembly (GO:0032202)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)	chromosome, telomeric region (GO:0000781)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinucleolar chromocenter (GO:0010370)	telomeric DNA binding (GO:0042162)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|prostate(1)|urinary_tract(1)	7				GBM - Glioblastoma multiforme(265;0.0185)		AGGTATTCACAGAGAGTGGGT	0.468									Congenital Dyskeratosis;Ataxia Pancytopenia syndrome																												p.C426G		Atlas-SNP	.											.	TINF2	61	.	0			c.T1276G						.						109	110	110					14																	24709083		1890	4120	6010	SO:0001583	missense	26277	exon9	Familial Cancer Database	Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita;Myelocerebellar disorder	ATTCACAGAGAGT	AF195512	CCDS41936.1, CCDS41937.1	14q12	2008-07-29				ENSG00000092330			11824	protein-coding gene	gene with protein product		604319				10581025, 18252230	Standard	NM_012461		Approved	TIN2	uc001woa.4	Q9BSI4		ENST00000267415.7:c.1276T>G	chr14.hg19:g.24709083A>C	ENSP00000267415:p.Cys426Gly	228.0	0.0		171.0	69.0	NM_001099274	B3W5Q7|Q9H904|Q9UHC2	Missense_Mutation	SNP	ENST00000267415.7	hg19	CCDS41936.1	.	.	.	.	.	.	.	.	.	.	A	9.587	1.125149	0.20959	.	.	ENSG00000092330	ENST00000267415;ENST00000540705	D;D	0.86627	-2.14;-2.15	5.76	4.62	0.57501	.	0.412421	0.20928	N	0.083148	D	0.82820	0.5120	L	0.53249	1.67	0.80722	D	1	B;B	0.25609	0.13;0.13	B;B	0.35039	0.194;0.194	T	0.71437	-0.4593	10	0.08179	T	0.78	-9.7461	8.3296	0.32178	0.9115:0.0:0.0885:0.0	.	391;426	B4DFJ1;Q9BSI4	.;TINF2_HUMAN	G	426;391	ENSP00000267415:C426G;ENSP00000442154:C391G	ENSP00000267415:C426G	C	-	1	0	TINF2	23778923	0.966000	0.33281	0.997000	0.53966	0.282000	0.26991	1.247000	0.32815	1.005000	0.39183	0.460000	0.39030	TGT	.	.		0.468	TINF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415406.2			C	24709083	A	C	24709083	3	2	287	1	0	0	0	0	1	0	0	0	15938	188	7	5	83	5	TINF2	14	24709083	Missense_Mutation	SNP	A	TCGA-G3-A5SL-01A-11D-A27I-10	810619	24709083	82640457	85	42183										
SGPP1	81537	hgsc.bcm.edu	37	chr14	64165361	64165361	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	gcagggaataagaatcagtcCatatataagagggtactaaa	10	5	1	2			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr14:64165361C>T	ENST00000247225.6	-	2	794	c.700G>A	c.(700-702)Gga>Aga	p.G234R		NM_030791.2	NP_110418.1	Q9BX95	SGPP1_HUMAN	sphingosine-1-phosphate phosphatase 1	234					extrinsic apoptotic signaling pathway (GO:0097191)|intrinsic apoptotic signaling pathway (GO:0097193)|small molecule metabolic process (GO:0044281)|sphinganine-1-phosphate metabolic process (GO:0006668)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	sphingosine-1-phosphate phosphatase activity (GO:0042392)	p.G234*(1)		central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(4)|skin(2)	10				OV - Ovarian serous cystadenocarcinoma(108;0.0056)|all cancers(60;0.0141)|BRCA - Breast invasive adenocarcinoma(234;0.103)		AGAATCAGTCCATATATAAGA	0.299																																					p.G234R		Atlas-SNP	.											SGPP1,NS,carcinoma,0,1	SGPP1	29	.	1	Substitution - Nonsense(1)	lung(1)	c.G700A						.						61	61	61					14																	64165361		2203	4294	6497	SO:0001583	missense	81537	exon2			TCAGTCCATATAT	AJ293294	CCDS9760.1	14q23.1	2003-09-17			ENSG00000126821	ENSG00000126821			17720	protein-coding gene	gene with protein product		612826				10859351	Standard	NM_030791		Approved		uc001xgj.3	Q9BX95	OTTHUMG00000029080	ENST00000247225.6:c.700G>A	chr14.hg19:g.64165361C>T	ENSP00000247225:p.Gly234Arg	158.0	0.0		94.0	24.0	NM_030791	B2RAH0|Q9H189	Missense_Mutation	SNP	ENST00000247225.6	hg19	CCDS9760.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.566056	0.86439	.	.	ENSG00000126821	ENST00000247225	T	0.54479	0.57	5.6	5.6	0.85130	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.76948	0.4059	M	0.86573	2.825	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75144	-0.3421	10	0.32370	T	0.25	-8.1847	19.5805	0.95465	0.0:1.0:0.0:0.0	.	234	Q9BX95	SGPP1_HUMAN	R	234	ENSP00000247225:G234R	ENSP00000247225:G234R	G	-	1	0	SGPP1	63235114	1.000000	0.71417	0.999000	0.59377	0.958000	0.62258	6.071000	0.71229	2.806000	0.96561	0.655000	0.94253	GGA	.	.		0.299	SGPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072626.3	NM_030791		T	64165361	C	T	64165361	3	4	287	1	0	0	0	0	1	0	0	0	14234	603	21	3	633	3	SGPP1	14	64165361	Missense_Mutation	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10	39456278	64165361	43184179	86	42184										
ZFYVE26	23503	hgsc.bcm.edu	37	chr14	68265045	68265045	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	ctgccttcacatggcttggcAttgtataagcaagggtcttt	10	9	2	0			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr14:68265045A>T	ENST00000347230.4	-	11	2072	c.1934T>A	c.(1933-1935)aTg>aAg	p.M645K	ZFYVE26_ENST00000555452.1_Missense_Mutation_p.M645K	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	645					cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		ATGGCTTGGCATTGTATAAGC	0.493																																					p.M645K		Atlas-SNP	.											.	ZFYVE26	223	.	0			c.T1934A						.						92	94	93					14																	68265045		2203	4300	6503	SO:0001583	missense	23503	exon11			CTTGGCATTGTAT	AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"Zinc fingers, FYVE domain containing"	20761	protein-coding gene	gene with protein product	"spastizin", "FYVE-CENT"	612012	"spastic paraplegia 15 (complicated, autosomal recessive)"	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.1934T>A	chr14.hg19:g.68265045A>T	ENSP00000251119:p.Met645Lys	163.0	0.0		121.0	54.0	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Missense_Mutation	SNP	ENST00000347230.4	hg19	CCDS9788.1	.	.	.	.	.	.	.	.	.	.	A	6.695	0.496957	0.12762	.	.	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000555452	T;T	0.26067	1.9;1.76	5.71	-1.1	0.09872	.	2.042190	0.01925	N	0.040776	T	0.11537	0.0281	N	0.08118	0	0.09310	N	1	B;B;B	0.19583	0.037;0.008;0.002	B;B;B	0.16722	0.003;0.016;0.0	T	0.20907	-1.0261	10	0.06099	T	0.92	7.9523	6.0455	0.19758	0.4395:0.1463:0.4143:0.0	.	645;645;645	Q68DK2-4;G3V2D8;Q68DK2	.;.;ZFY26_HUMAN	K	645;624;645	ENSP00000251119:M645K;ENSP00000450603:M645K	ENSP00000251119:M645K	M	-	2	0	ZFYVE26	67334798	0.000000	0.05858	0.000000	0.03702	0.582000	0.36321	0.479000	0.22228	-0.128000	0.11641	-0.250000	0.11733	ATG	.	.		0.493	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346		T	68265045	A	T	68265045	3	4	287	1	0	0	0	0	1	0	0	0	17683	217	8	4	5813	4	ZFYVE26	14	68265045	Missense_Mutation	SNP	A	TCGA-G3-A5SL-01A-11D-A27I-10	4099684	68265045	39084495	87	42185										
MPI	4351	hgsc.bcm.edu	37	chr15	75182913	75182914	+	Frame_Shift_Ins	INS	-	-	G													0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	cagtatgcctgggggaagatINSgggttccaacagcgaagtgg							TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr15:75182913_75182914insG	ENST00000352410.4	+	2	129_130	c.62_63insG	c.(61-66)atgggtfs	p.MG21fs	MPI_ENST00000563422.1_Frame_Shift_Ins_p.MG21fs|MPI_ENST00000564003.1_Intron|MPI_ENST00000566377.1_Frame_Shift_Ins_p.MG21fs|MPI_ENST00000535694.1_Intron|MPI_ENST00000563786.1_Start_Codon_Ins|MPI_ENST00000565576.1_Frame_Shift_Ins_p.MG21fs|MPI_ENST00000323744.6_Frame_Shift_Ins_p.MG21fs|MPI_ENST00000562606.1_Start_Codon_Ins			P34949	MPI_HUMAN	mannose phosphate isomerase	21					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	mannose-6-phosphate isomerase activity (GO:0004476)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|upper_aerodigestive_tract(1)	9						TGGGGGAAGATGGGTTCCAACA	0.609																																					p.M21fs		Atlas-Indel,Pindel	.											.	MPI	32	.	0			c.62_63insG						.																																			SO:0001589	frameshift_variant	4351	exon2			.		CCDS10272.1, CCDS73756.1, CCDS73757.1, CCDS73758.1	15q24.1	2013-09-19			ENSG00000178802	ENSG00000178802	5.3.1.8		7216	protein-coding gene	gene with protein product	"mannose-6-phosphate isomerase"	154550					Standard	NM_002435		Approved		uc002azc.1	P34949	OTTHUMG00000142826	ENST00000352410.4:c.65dupG	chr15.hg19:g.75182916_75182916dupG	ENSP00000318318:p.Met21fs	112.0	0.0		80.0	21.0	NM_002435	A8K8K9|Q96AB0	Frame_Shift_Ins	INS	ENST00000352410.4	hg19	CCDS10272.1																																																																																			.	.		0.609	MPI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286418.4			G	75182914	-	G	75182913	7	5	287	1	0	1	1	0	0	0	0	0	9738	1464	51	0	68	0	MPI	15	75182913	Frame_Shift_Ins	INS	-	TCGA-G3-A5SL-01A-11D-A27I-10		75182913	27348479	88	42186										
BTBD1	53339	hgsc.bcm.edu	37	chr15	83698992	83698992	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	cagcatcttggtcggtcaatGtattcaactcggggtttagg	12	8	3	0			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr15:83698992G>T	ENST00000261721.4	-	5	1153	c.951C>A	c.(949-951)taC>taA	p.Y317*	RP11-382A20.7_ENST00000570202.1_RNA|RP11-382A20.5_ENST00000566841.1_RNA|RP11-382A20.6_ENST00000568441.1_RNA|BTBD1_ENST00000560015.1_5'UTR|BTBD1_ENST00000379403.2_Nonsense_Mutation_p.Y317*	NM_001011885.1|NM_025238.3	NP_001011885.1|NP_079514.1	Q9H0C5	BTBD1_HUMAN	BTB (POZ) domain containing 1	317					protein ubiquitination (GO:0016567)|regulation of protein binding (GO:0043393)	cytoplasmic mRNA processing body (GO:0000932)|protein complex (GO:0043234)				central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)	10				all cancers(203;0.000186)		GTCGGTCAATGTATTCAACTC	0.453																																					p.Y317X		Atlas-SNP	.											.	BTBD1	32	.	0			c.C951A						.						198	198	198					15																	83698992		2203	4300	6503	SO:0001587	stop_gained	53339	exon5			GTCAATGTATTCA	AF355402	CCDS10322.1, CCDS32313.1	15q24	2013-01-08			ENSG00000064726	ENSG00000064726		"BTB/POZ domain containing"	1120	protein-coding gene	gene with protein product		608530					Standard	XM_006720573		Approved		uc002bjn.3	Q9H0C5	OTTHUMG00000147364	ENST00000261721.4:c.951C>A	chr15.hg19:g.83698992G>T	ENSP00000261721:p.Tyr317*	140.0	0.0		132.0	10.0	NM_025238	A6NMI8|Q9BX71|Q9NWN4	Nonsense_Mutation	SNP	ENST00000261721.4	hg19	CCDS10322.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.926990	0.92319	.	.	ENSG00000064726	ENST00000261721;ENST00000379403	.	.	.	5.15	3.28	0.37604	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.28530	T	0.3	-17.0624	7.0222	0.24920	0.3853:0.0:0.6147:0.0	.	.	.	.	X	317	.	ENSP00000261721:Y317X	Y	-	3	2	BTBD1	81489996	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	1.730000	0.38125	0.691000	0.31592	0.561000	0.74099	TAC	.	.		0.453	BTBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304008.1			T	83698992	G	T	83698992	4	4	287	1	0	0	0	0	0	1	0	0	1539	1372	48	3	513	3	BTBD1	15	83698992	Nonsense_Mutation	SNP	G	TCGA-G3-A5SL-01A-11D-A27I-10	8516079	83698992	18832400	89	42187										
CIITA	4261	hgsc.bcm.edu	37	chr16	11016299	11016300	+	Frame_Shift_Ins	INS	-	-	G													0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	ttcacggctgccggggcccaINSgcagctcgctgccagccttc							TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr16:11016299_11016300insG	ENST00000324288.8	+	18	3402_3403	c.3269_3270insG	c.(3268-3273)cagcagfs	p.Q1091fs	CIITA_ENST00000381835.5_Frame_Shift_Ins_p.Q507fs	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	1091					aging (GO:0007568)|cellular response to electrical stimulus (GO:0071257)|cellular response to exogenous dsRNA (GO:0071360)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to antibiotic (GO:0046677)|response to interferon-gamma (GO:0034341)|transcription, DNA-templated (GO:0006351)	cell surface (GO:0009986)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|GTP binding (GO:0005525)|kinase activity (GO:0016301)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transferase activity, transferring acyl groups (GO:0016746)			central_nervous_system(1)|large_intestine(7)|ovary(1)|skin(1)|stomach(2)	12						GCCGGGGCCCAGCAGCTCGCTG	0.639			T	"FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"	"PMBL, Hodgkin Lymphona, "																																p.Q1090fs		Pindel	.		Dom	yes		16	16p13	4261	"class II, major histocompatibility complex, transactivator"		L	.	CIITA	92	.	0			c.3269_3270insG						.																																			SO:0001589	frameshift_variant	4261	exon18			.	U18259	CCDS10544.1, CCDS66943.1, CCDS73826.1	16p13	2014-09-17	2005-08-12	2005-08-12	ENSG00000179583	ENSG00000179583		"Nucleotide-binding domain and leucine rich repeat containing"	7067	protein-coding gene	gene with protein product	"NLR family, acid domain containing", "nucleotide-binding oligomerization domain, leucine rich repeat and acid domain containing"	600005	"MHC class II transactivator"	MHC2TA		8402893	Standard	NM_000246		Approved	C2TA, NLRA	uc002dai.4	P33076	OTTHUMG00000129753	ENST00000324288.8:c.3270dupG	chr16.hg19:g.11016300_11016300dupG	ENSP00000316328:p.Gln1091fs	196.0	0.0		141.0	35.0	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Frame_Shift_Ins	INS	ENST00000324288.8	hg19	CCDS10544.1																																																																																			.	.		0.639	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246		G	11016300	-	G	11016299	7	5	287	1	0	1	1	0	0	0	0	0	3430	188	7	0	3339	0	CIITA	16	11016299	Frame_Shift_Ins	INS	-	TCGA-G3-A5SL-01A-11D-A27I-10		11016299	79338454	90	42188										
NOD2	64127	hgsc.bcm.edu	37	chr16	50745410	50745410	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	tgcatgccacccccccagacTcagcttcccaaggtctggga	9	17	2	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr16:50745410T>C	ENST00000300589.2	+	4	1693	c.1588T>C	c.(1588-1590)Tca>Cca	p.S530P	RP11-327F22.6_ENST00000602304.1_RNA	NM_022162.1	NP_071445.1	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain containing 2	530	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				activation of MAPK activity (GO:0000187)|activation of MAPK activity involved in innate immune response (GO:0035419)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to peptidoglycan (GO:0071224)|cytokine production involved in immune response (GO:0002367)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|detection of biotic stimulus (GO:0009595)|detection of muramyl dipeptide (GO:0032498)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|innate immune response (GO:0045087)|innate immune response in mucosa (GO:0002227)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|macrophage inflammatory protein-1 alpha production (GO:0071608)|maintenance of gastrointestinal epithelium (GO:0030277)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-18 production (GO:0032701)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of macrophage apoptotic process (GO:2000110)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell mediated immunity (GO:0002710)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of tumor necrosis factor production (GO:0032720)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of B cell activation (GO:0050871)|positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria (GO:0006965)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell cytokine production (GO:0002732)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gamma-delta T cell activation (GO:0046645)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of prostaglandin-E synthase activity (GO:2000363)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type 2 immune response (GO:0002830)|protein oligomerization (GO:0051259)|regulation of inflammatory response (GO:0050727)|regulation of neutrophil chemotaxis (GO:0090022)|response to exogenous dsRNA (GO:0043330)|response to lipopolysaccharide (GO:0032496)|response to muramyl dipeptide (GO:0032495)|response to nutrient (GO:0007584)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|enzyme binding (GO:0019899)|muramyl dipeptide binding (GO:0032500)|peptidoglycan binding (GO:0042834)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(30)|ovary(3)|skin(3)	52		all_cancers(37;0.0156)				CCCCCCAGACTCAGCTTCCCA	0.617																																					p.S530P		Atlas-SNP	.											.	NOD2	118	.	0			c.T1588C						.						43	47	46					16																	50745410		2198	4300	6498	SO:0001583	missense	64127	exon4			CCAGACTCAGCTT	AF178930	CCDS10746.1	16q12	2014-09-17	2006-12-08	2006-12-08	ENSG00000167207	ENSG00000167207		"Nucleotide-binding domain and leucine rich repeat containing"	5331	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 2", "NOD-like receptor C2", "NLR family, CARD domain containing 2"	605956	"caspase recruitment domain family, member 15"	IBD1, CARD15		7809109, 8587604	Standard	XM_005256084		Approved	BLAU, CD, PSORAS1, CLR16.3, NLRC2	uc002egm.1	Q9HC29	OTTHUMG00000133171	ENST00000300589.2:c.1588T>C	chr16.hg19:g.50745410T>C	ENSP00000300589:p.Ser530Pro	80.0	0.0		47.0	17.0	NM_022162	E2JEQ6|Q96RH5|Q96RH6|Q96RH8	Missense_Mutation	SNP	ENST00000300589.2	hg19	CCDS10746.1	.	.	.	.	.	.	.	.	.	.	T	4.331	0.060833	0.08339	.	.	ENSG00000167207	ENST00000526417;ENST00000300589	T	0.70399	-0.48	4.59	-9.19	0.00685	.	2.365230	0.01528	N	0.018640	T	0.57051	0.2027	L	0.57536	1.79	0.09310	N	1	B;P;P	0.34909	0.393;0.467;0.475	B;B;B	0.32864	0.099;0.154;0.073	T	0.49762	-0.8905	10	0.28530	T	0.3	.	3.403	0.07331	0.3258:0.0795:0.4293:0.1654	.	314;503;530	D6CHF9;Q9HC29-2;Q9HC29	.;.;NOD2_HUMAN	P	503;530	ENSP00000300589:S530P	ENSP00000300589:S530P	S	+	1	0	NOD2	49302911	0.000000	0.05858	0.000000	0.03702	0.048000	0.14542	-1.130000	0.03241	-1.404000	0.02050	-0.501000	0.04562	TCA	.	.		0.617	NOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256876.2	NM_022162		C	50745410	T	C	50745410	3	2	287	1	0	0	0	0	1	0	0	0	10526	1551	54	2	1602	2	NOD2	16	50745410	Missense_Mutation	SNP	T	TCGA-G3-A5SL-01A-11D-A27I-10	39729111	50745410	39609343	91	42189										
C16orf46	123775	hgsc.bcm.edu	37	chr16	81097428	81097428	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	cgtaatgtcactgacatcgaGaagacaataaacatgatttt	7	7	1	4			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr16:81097428G>A	ENST00000299578.5	-	3	368	c.133C>T	c.(133-135)Ctc>Ttc	p.L45F	C16orf46_ENST00000444657.3_Intron|C16orf46_ENST00000378611.4_Missense_Mutation_p.L45F|RP11-303E16.8_ENST00000564536.1_RNA	NM_152337.2	NP_689550.2	Q6P387	CP046_HUMAN	chromosome 16 open reading frame 46	45						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(2)|large_intestine(3)|lung(9)|prostate(1)|stomach(1)|urinary_tract(1)	18						CTGACATCGAGAAGACAATAA	0.358																																					p.L45F		Atlas-SNP	.											.	C16orf46	57	.	0			c.C133T						.						202	185	191					16																	81097428		2202	4300	6502	SO:0001583	missense	123775	exon2			CATCGAGAAGACA	BC064143	CCDS10932.1, CCDS42201.1	16q23.2	2012-10-09			ENSG00000166455	ENSG00000166455			26525	protein-coding gene	gene with protein product							Standard	NM_152337		Approved	FLJ32702	uc002fgc.4	Q6P387	OTTHUMG00000137629	ENST00000299578.5:c.133C>T	chr16.hg19:g.81097428G>A	ENSP00000299578:p.Leu45Phe	94.0	0.0		68.0	29.0	NM_001100873	Q96MA7	Missense_Mutation	SNP	ENST00000299578.5	hg19	CCDS10932.1	.	.	.	.	.	.	.	.	.	.	G	14.32	2.499950	0.44455	.	.	ENSG00000166455	ENST00000378611;ENST00000299578	T;T	0.31247	1.5;1.5	5.65	5.65	0.86999	.	0.000000	0.56097	D	0.000031	T	0.43853	0.1266	L	0.36672	1.1	0.37331	D	0.909981	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.46176	-0.9210	10	0.66056	D	0.02	.	11.0249	0.47739	0.0853:0.0:0.9147:0.0	.	45;45	Q6P387-2;Q6P387	.;CP046_HUMAN	F	45	ENSP00000367874:L45F;ENSP00000299578:L45F	ENSP00000299578:L45F	L	-	1	0	C16orf46	79654929	0.998000	0.40836	0.938000	0.37757	0.061000	0.15899	2.015000	0.40961	2.822000	0.97130	0.563000	0.77884	CTC	.	.		0.358	C16orf46-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269054.2	NM_152337		A	81097428	G	A	81097428	3	1	287	1	0	0	0	0	1	0	0	0	1817	942	33	3	1090	3	C16orf46	16	81097428	Missense_Mutation	SNP	G	TCGA-G3-A5SL-01A-11D-A27I-10	30352018	81097428	9257325	92	42190										
LRRC50	123872	hgsc.bcm.edu	37	chr16	84209627	84209627	+	Frame_Shift_Del	DEL	A	A	-													0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	cacgtcactccctgtgctggAaaacctccccacagacactc							TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr16:84209627delA	ENST00000378553.5	+	11	1911	c.1787delA	c.(1786-1788)gaafs	p.E596fs	DNAAF1_ENST00000563818.1_3'UTR	NM_178452.4	NP_848547.4	Q8NEP3	DAAF1_HUMAN	dynein, axonemal, assembly factor 1	596					axonemal dynein complex assembly (GO:0070286)|cilium morphogenesis (GO:0060271)|cilium movement (GO:0003341)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|inner dynein arm assembly (GO:0036159)|left/right pattern formation (GO:0060972)|lung development (GO:0030324)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)|regulation of cilium beat frequency (GO:0003356)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dynein binding (GO:0045502)			NS(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(4)|urinary_tract(1)	41						CCTGTGCTGGAAAACCTCCCC	0.458											OREG0023983	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E596fs		Atlas-Indel,Pindel	.											.	DNAAF1	81	.	0			c.1786delG						.						83	75	77					16																	84209627		2200	4300	6500	SO:0001589	frameshift_variant	123872	exon11			.	BC024009	CCDS10943.2	16q24.1	2012-05-03	2011-06-09	2011-06-09	ENSG00000154099	ENSG00000154099			30539	protein-coding gene	gene with protein product	"outer row dynein assembly 7 homolog (Chlamydomonas)"	613190	"leucine rich repeat containing 50"	LRRC50		19944405	Standard	NM_178452		Approved	FLJ25330, ODA7, CILD13	uc002fhl.4	Q8NEP3	OTTHUMG00000128517	ENST00000378553.5:c.1787delA	chr16.hg19:g.84209627delA	ENSP00000367815:p.Glu596fs	193.0	0.0	1227	99.0	33.0	NM_178452	B4DJA3|Q69YI8|Q69YJ0|Q69YW5|Q96LP3|Q96MB6	Frame_Shift_Del	DEL	ENST00000378553.5	hg19	CCDS10943.2																																																																																			.	.		0.458	DNAAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250328.3	NM_178452		-	84209627	A	-	84209627	7	5	287	1	0	1	0	1	0	0	0	0	9018	246	9	0	1829	0	LRRC50	16	84209627	Frame_Shift_Del	DEL	A	TCGA-G3-A5SL-01A-11D-A27I-10	3112199	84209627	6145126	93	42191										
AIPL1	23746	hgsc.bcm.edu	37	chr17	6328940	6328940	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	gtggctctgcgggaggctgcGtggcaccctggctcagcatg	17	12	2	0			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr17:6328940G>C	ENST00000381129.3	-	6	1075	c.995C>G	c.(994-996)aCg>aGg	p.T332R	AIPL1_ENST00000576307.1_Missense_Mutation_p.T272R|AIPL1_ENST00000576776.1_Missense_Mutation_p.T308R|AIPL1_ENST00000570466.1_Missense_Mutation_p.T310R|AIPL1_ENST00000575265.1_3'UTR|AIPL1_ENST00000574506.1_Missense_Mutation_p.T320R|AIPL1_ENST00000250087.5_Missense_Mutation_p.T269R	NM_001033055.1|NM_014336.3	NP_001028227.1|NP_055151.3	Q9NZN9	AIPL1_HUMAN	aryl hydrocarbon receptor interacting protein-like 1	332					negative regulation of apoptotic process (GO:0043066)|phototransduction, visible light (GO:0007603)|protein farnesylation (GO:0018343)|protein folding (GO:0006457)|regulation of cGMP metabolic process (GO:0030823)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|photoreceptor inner segment (GO:0001917)	farnesylated protein binding (GO:0001918)|unfolded protein binding (GO:0051082)			NS(1)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|skin(1)	12				COAD - Colon adenocarcinoma(228;0.141)		gggaggctGCGTGGCACCCTG	0.677																																					p.T332R		Atlas-SNP	.											.	AIPL1	34	.	0			c.C995G						.						91	79	83					17																	6328940		2203	4300	6503	SO:0001583	missense	23746	exon6			GGCTGCGTGGCAC	AF148864	CCDS11075.1, CCDS32539.1, CCDS32540.1, CCDS67130.1, CCDS67131.1, CCDS67132.1, CCDS67133.1	17p13.1	2013-01-08	2001-11-29		ENSG00000129221	ENSG00000129221			359	protein-coding gene	gene with protein product		604392	"aryl hydrocarbon receptor-interacting protein-like 1"	LCA4		10615133, 14555765, 15365173	Standard	NM_001285402		Approved		uc002gcp.3	Q9NZN9	OTTHUMG00000102043	ENST00000381129.3:c.995C>G	chr17.hg19:g.6328940G>C	ENSP00000370521:p.Thr332Arg	26.0	0.0		26.0	11.0	NM_014336	D3DTM4|Q659W3|Q659W4|Q6ZZB6|Q8N6A0|Q9H873|Q9NS10	Missense_Mutation	SNP	ENST00000381129.3	hg19	CCDS11075.1	.	.	.	.	.	.	.	.	.	.	G	9.013	0.982945	0.18889	.	.	ENSG00000129221	ENST00000381129;ENST00000381128;ENST00000250087	D;D	0.88124	-2.34;-2.23	2.78	-1.75	0.08031	.	1.682670	0.06116	U	0.668047	T	0.69006	0.3063	N	0.08118	0	0.09310	N	1	B;B;P;P;B	0.35307	0.361;0.233;0.494;0.494;0.233	B;B;B;B;B	0.19666	0.008;0.008;0.026;0.018;0.008	T	0.56691	-0.7937	10	0.23302	T	0.38	.	9.6405	0.39835	0.0:0.6617:0.3383:0.0	.	308;310;269;272;332	Q659W3;Q659W4;Q9NZN9-3;Q9NZN9-2;Q9NZN9	.;.;.;.;AIPL1_HUMAN	R	332;272;269	ENSP00000370521:T332R;ENSP00000250087:T269R	ENSP00000250087:T269R	T	-	2	0	AIPL1	6269664	0.000000	0.05858	0.001000	0.08648	0.023000	0.10783	-1.401000	0.02502	-0.037000	0.13646	0.462000	0.41574	ACG	.	.		0.677	AIPL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219828.3	NM_014336		C	6328940	G	C	6328940	3	2	287	1	0	0	0	0	1	0	0	0	436	1145	40	4	163	4	AIPL1	17	6328940	Missense_Mutation	SNP	G	TCGA-G3-A5SL-01A-11D-A27I-10		6328940	74866270	94	42192										
SLC47A1	55244	hgsc.bcm.edu	37	chr17	19445791	19445791	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	caagctggagctggatgcagTcacgctggcaatcgcggtac	14	11	1	0			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr17:19445791T>G	ENST00000270570.4	+	2	307	c.221T>G	c.(220-222)gTc>gGc	p.V74G	SLC47A1_ENST00000395585.1_Missense_Mutation_p.V74G|SLC47A1_ENST00000575023.1_Missense_Mutation_p.V74G|SLC47A1_ENST00000436810.2_Missense_Mutation_p.V74G|SLC47A1_ENST00000571335.1_5'UTR|SLC47A1_ENST00000457293.1_Missense_Mutation_p.V74G|SLC47A1_ENST00000584348.1_3'UTR|SLC47A1_ENST00000542886.1_Missense_Mutation_p.V74G	NM_018242.2	NP_060712.2	Q96FL8	S47A1_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 1	74					organic cation transport (GO:0015695)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane-bounded vesicle (GO:0031988)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|monovalent cation:proton antiporter activity (GO:0005451)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(4)|lung(5)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	23	all_cancers(12;2.49e-05)|all_epithelial(12;0.00263)|Hepatocellular(7;0.00345)				Aciclovir(DB00787)|Bromodiphenhydramine(DB01237)|Cephalexin(DB00567)|Cimetidine(DB00501)|Metformin(DB00331)|Sirolimus(DB00877)	CTGGATGCAGTCACGCTGGCA	0.512																																					p.V74G		Atlas-SNP	.											.	SLC47A1	55	.	0			c.T221G						.						172	129	143					17																	19445791		2203	4300	6503	SO:0001583	missense	55244	exon2			ATGCAGTCACGCT		CCDS11209.1	17p11.2	2013-07-17	2013-07-17		ENSG00000142494	ENSG00000142494		"Solute carriers"	25588	protein-coding gene	gene with protein product	"multidrug and toxin extrusion 1"	609832				16330770, 16996621, 16928787	Standard	NM_018242		Approved	FLJ10847, MATE1	uc002gvy.1	Q96FL8	OTTHUMG00000059466	ENST00000270570.4:c.221T>G	chr17.hg19:g.19445791T>G	ENSP00000270570:p.Val74Gly	148.0	0.0		94.0	13.0	NM_018242	Q53HF5|Q6PD77|Q86VL4|Q9NVA3	Missense_Mutation	SNP	ENST00000270570.4	hg19	CCDS11209.1	.	.	.	.	.	.	.	.	.	.	T	16.16	3.045646	0.55110	.	.	ENSG00000142494	ENST00000436810;ENST00000270570;ENST00000457293;ENST00000542886;ENST00000395585	T;T;T;T;T	0.38077	1.3;1.16;1.16;1.16;1.16	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	T	0.57169	0.2035	M	0.63843	1.955	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.998;0.997	D;D;D;D	0.97110	1.0;1.0;0.989;0.987	T	0.60414	-0.7268	10	0.66056	D	0.02	-22.0268	14.2177	0.65805	0.0:0.0:0.0:1.0	.	74;74;74;74	E7EX57;B4DYV3;Q96FL8;Q96FL8-3	.;.;S47A1_HUMAN;.	G	74	ENSP00000407155:V74G;ENSP00000270570:V74G;ENSP00000415586:V74G;ENSP00000440435:V74G;ENSP00000378951:V74G	ENSP00000270570:V74G	V	+	2	0	SLC47A1	19386383	1.000000	0.71417	0.988000	0.46212	0.172000	0.22775	7.207000	0.77899	1.975000	0.57531	0.528000	0.53228	GTC	.	.		0.512	SLC47A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132250.1	NM_018242		G	19445791	T	G	19445791	3	3	287	1	0	0	0	0	1	0	0	0	14662	1667	58	5	227	5	SLC47A1	17	19445791	Missense_Mutation	SNP	T	TCGA-G3-A5SL-01A-11D-A27I-10	13116851	19445791	61749419	95	42193										
UTP6	55813	hgsc.bcm.edu	37	chr17	30190389	30190389	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	tcttcatcttcataaatggcCagtctgatgcatagcatgtt	7	9	5	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr17:30190389C>G	ENST00000261708.4	-	19	1920	c.1783G>C	c.(1783-1785)Ggc>Cgc	p.G595R		NM_018428.2	NP_060898.2	Q9NYH9	UTP6_HUMAN	UTP6, small subunit (SSU) processome component, homolog (yeast)	595					rRNA processing (GO:0006364)	nucleolus (GO:0005730)				breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|skin(1)	21		all_hematologic(16;0.0149)|Ovarian(249;0.021)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|Breast(31;0.231)				CATAAATGGCCAGTCTGATGC	0.438																																					p.G595R		Atlas-SNP	.											.	UTP6	46	.	0			c.G1783C						.						168	166	167					17																	30190389		2203	4300	6503	SO:0001583	missense	55813	exon19			AATGGCCAGTCTG	AF116631	CCDS11269.1	17q11.2	2010-06-24	2006-05-16	2006-05-16	ENSG00000108651	ENSG00000108651			18279	protein-coding gene	gene with protein product	"hepatocellular carcinoma associated antigen 66"		"chromosome 17 open reading frame 40"	C17orf40		10843809, 16138909	Standard	NM_018428		Approved	HCA66	uc002hgr.3	Q9NYH9	OTTHUMG00000132815	ENST00000261708.4:c.1783G>C	chr17.hg19:g.30190389C>G	ENSP00000261708:p.Gly595Arg	132.0	0.0		101.0	6.0	NM_018428	Q8IX96|Q96BL2|Q9NQ91	Missense_Mutation	SNP	ENST00000261708.4	hg19	CCDS11269.1	.	.	.	.	.	.	.	.	.	.	c	24.1	4.498991	0.85069	.	.	ENSG00000108651	ENST00000261708	T	0.43294	0.95	5.54	5.54	0.83059	.	0.243352	0.47852	D	0.000207	T	0.66992	0.2846	M	0.79805	2.47	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.64506	0.926;0.926	T	0.71227	-0.4655	10	0.87932	D	0	-1.2623	19.0741	0.93151	0.0:1.0:0.0:0.0	.	595;595	B3KQ21;Q9NYH9	.;UTP6_HUMAN	R	595	ENSP00000261708:G595R	ENSP00000261708:G595R	G	-	1	0	UTP6	27214502	1.000000	0.71417	1.000000	0.80357	0.520000	0.34377	3.781000	0.55394	2.606000	0.88127	0.586000	0.80456	GGC	.	.		0.438	UTP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256265.2	NM_018428		G	30190389	C	G	30190389	3	3	287	1	0	0	0	0	1	0	0	0	17117	594	21	4	14	4	UTP6	17	30190389	Missense_Mutation	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10	10744598	30190389	51004821	96	42194										
COL1A1	1277	hgsc.bcm.edu	37	chr17	48264129	48264129	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	tgagggtggtgtccacctcgAggtcacggtcacgaaccaca	13	12	2	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr17:48264129A>T	ENST00000225964.5	-	48	3804	c.3686T>A	c.(3685-3687)cTc>cAc	p.L1229H		NM_000088.3	NP_000079	P02452	CO1A1_HUMAN	collagen, type I, alpha 1	1229	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|bone trabecula formation (GO:0060346)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to amino acid stimulus (GO:0071230)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal system development (GO:0048706)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|leukocyte migration (GO:0050900)|negative regulation of cell-substrate adhesion (GO:0010812)|osteoblast differentiation (GO:0001649)|platelet activation (GO:0030168)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterotrimerization (GO:0070208)|protein localization to nucleus (GO:0034504)|protein transport (GO:0015031)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to estradiol (GO:0032355)|response to hydrogen peroxide (GO:0042542)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|tooth mineralization (GO:0034505)|visual perception (GO:0007601)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)		COL1A1/PDGFB(429)	NS(1)|breast(3)|central_nervous_system(8)|endometrium(3)|kidney(4)|large_intestine(17)|liver(3)|lung(18)|ovary(1)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	71					Collagenase(DB00048)	GTCCACCTCGAGGTCACGGTC	0.627			T	"PDGFB, USP6"	"dermatofibrosarcoma protuberans, aneurysmal bone cyst "		Osteogenesis imperfecta																														p.L1229H		Atlas-SNP	.		Dom	yes		17	17q21.31-q22	1277	"collagen, type I, alpha 1"	yes	M	.	COL1A1	158	.	0			c.T3686A						.						158	150	152					17																	48264129		2203	4300	6503	SO:0001583	missense	1277	exon48			ACCTCGAGGTCAC	Z74615	CCDS11561.1	17q21.33	2014-09-17			ENSG00000108821	ENSG00000108821		"Collagens"	2197	protein-coding gene	gene with protein product		120150				3178743, 2857713	Standard	NM_000088		Approved	OI4	uc002iqm.3	P02452	OTTHUMG00000148674	ENST00000225964.5:c.3686T>A	chr17.hg19:g.48264129A>T	ENSP00000225964:p.Leu1229His	137.0	0.0		87.0	42.0	NM_000088	O76045|P78441|Q13896|Q13902|Q13903|Q14037|Q14992|Q15176|Q15201|Q16050|Q59F64|Q7KZ30|Q7KZ34|Q8IVI5|Q8N473|Q9UML6|Q9UMM7	Missense_Mutation	SNP	ENST00000225964.5	hg19	CCDS11561.1	.	.	.	.	.	.	.	.	.	.	A	9.353	1.066030	0.20067	.	.	ENSG00000108821	ENST00000225964	D	0.89681	-2.55	4.03	4.03	0.46877	Fibrillar collagen, C-terminal (2);	0.083285	0.49305	D	0.000142	D	0.84763	0.5544	M	0.71036	2.16	0.38553	D	0.949504	B	0.10296	0.003	B	0.04013	0.001	T	0.77659	-0.2505	10	0.13853	T	0.58	.	7.8053	0.29198	0.8138:0.0:0.0:0.1862	.	1229	P02452	CO1A1_HUMAN	H	1229	ENSP00000225964:L1229H	ENSP00000225964:L1229H	L	-	2	0	COL1A1	45619128	0.999000	0.42202	1.000000	0.80357	0.985000	0.73830	3.972000	0.56838	1.676000	0.50930	0.260000	0.18958	CTC	.	.		0.627	COL1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309036.2			T	48264129	A	T	48264129	3	4	287	1	0	0	0	0	1	0	0	0	3679	304	11	4	724	4	COL1A1	17	48264129	Missense_Mutation	SNP	A	TCGA-G3-A5SL-01A-11D-A27I-10	18073740	48264129	32931081	97	42195										
DDX42	11325	hgsc.bcm.edu	37	chr17	61864631	61864631	+	Splice_Site	DEL	G	G	-													0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	aactttgatgaagaaaatgcGtaagtggtaattcctggtag							TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr17:61864631delG	ENST00000578681.1	+	3	822		c.e3+1		DDX42_ENST00000583590.1_Splice_Site|DDX42_ENST00000359353.5_Intron|DDX42_ENST00000457800.2_Splice_Site|DDX42_ENST00000389924.2_Splice_Site	NM_007372.2	NP_031398.2	Q86XP3	DDX42_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 42						protein localization (GO:0008104)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)	46						AAGAAAATGCGTAAGTGGTAA	0.378																																					p.A74fs		Atlas-Indel,Pindel	.											DDX42,NS,carcinoma,0,1	DDX42	86	.	0			c.221delC						.						60	62	61					17																	61864631		2203	4300	6503	SO:0001630	splice_region_variant	11325	exon3			.	BC015505	CCDS32704.1	17q23	2014-02-14	2013-05-13			ENSG00000198231		"DEAD-boxes"	18676	protein-coding gene	gene with protein product	"splicing factor 3b, subunit 8"	613369	"DEAD (Asp-Glu-Ala-Asp) box polypeptide 42"			10727850, 16397294	Standard	NM_007372		Approved	RNAHP, RHELP, SF3b125, SF3B8	uc002jbv.3	Q86XP3		ENST00000578681.1:c.221+1G>-	chr17.hg19:g.61864631delG		115.0	0.0		95.0	25.0	NM_007372	A6NML1|A8KA43|O75619|Q68G51|Q96BK1|Q96HR7|Q9Y3V8	Frame_Shift_Del	DEL	ENST00000578681.1	hg19	CCDS32704.1																																																																																			.	.		0.378	DDX42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444368.1	NM_007372	Intron	-	61864631	G	-	61864631	8	5	287	1	0	1	0	1	0	0	1	0	4364	1159	40	0	224	0	DDX42	17	61864631	Splice_Site	DEL	G	TCGA-G3-A5SL-01A-11D-A27I-10	13600502	61864631	19330579	98	42196										
FASN	2194	hgsc.bcm.edu	37	chr17	80040959	80040959	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	atcagcttgggtttggccccCttcagcactgcctccggctc	10	16	2	0			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr17:80040959C>T	ENST00000306749.2	-	33	5816	c.5598G>A	c.(5596-5598)aaG>aaA	p.K1866K	FASN_ENST00000579758.1_5'UTR	NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	1866	Beta-ketoacyl reductase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	GTTTGGCCCCCTTCAGCACTG	0.667																																					p.K1866K	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.G5598A						.						80	78	79					17																	80040959		2198	4298	6496	SO:0001819	synonymous_variant	2194	exon33			GGCCCCCTTCAGC	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.5598G>A	chr17.hg19:g.80040959C>T		80.0	0.0		69.0	35.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Silent	SNP	ENST00000306749.2	hg19	CCDS11801.1																																																																																			.	.		0.667	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		T	80040959	C	T	80040959	2	4	287	1	0	0	0	0	0	0	0	1	5691	680	24	3		3	FASN	17	80040959	Silent	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10	18176328	80040959	1154251	99	42197										
LAMA3	3909	hgsc.bcm.edu	37	chr18	21441703	21441703	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	gcaacagtatggtggcggatCtccaggagctgcccgcaacc	13	13	1	0			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr18:21441703C>A	ENST00000313654.9	+	35	4757	c.4516C>A	c.(4516-4518)Ctc>Atc	p.L1506I	LAMA3_ENST00000399516.3_Missense_Mutation_p.L1506I	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	1506	Laminin IV type A. {ECO:0000255|PROSITE- ProRule:PRU00458}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					GGTGGCGGATCTCCAGGAGCT	0.587																																					p.L1506I		Atlas-SNP	.											.	LAMA3	397	.	0			c.C4516A						.						41	44	43					18																	21441703		2032	4186	6218	SO:0001583	missense	3909	exon35			GCGGATCTCCAGG	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"Laminins"	6483	protein-coding gene	gene with protein product		600805	"laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.4516C>A	chr18.hg19:g.21441703C>A	ENSP00000324532:p.Leu1506Ile	125.0	0.0		136.0	58.0	NM_001127717	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	hg19	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	C	11.35	1.613046	0.28712	.	.	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000416669	T;T	0.19806	2.13;2.12	5.5	1.38	0.22167	Laminin B type IV (1);Growth factor, receptor (1);	.	.	.	.	T	0.14960	0.0361	L	0.39898	1.24	0.80722	D	1	B;B	0.10296	0.002;0.003	B;B	0.09377	0.002;0.004	T	0.06661	-1.0814	9	0.36615	T	0.2	.	6.6861	0.23146	0.3415:0.291:0.3675:0.0	.	1506;1506	Q6VU67;Q16787	.;LAMA3_HUMAN	I	1506;1506;1504	ENSP00000324532:L1506I;ENSP00000382432:L1506I	ENSP00000324532:L1506I	L	+	1	0	LAMA3	19695701	1.000000	0.71417	0.988000	0.46212	0.251000	0.25915	1.414000	0.34736	0.589000	0.29677	0.555000	0.69702	CTC	.	.		0.587	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		A	21441703	C	A	21441703	3	1	287	1	0	0	0	0	1	0	0	0	8616	913	32	3	4654	3	LAMA3	18	21441703	Missense_Mutation	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10		21441703	56635545	100	42198										
HOOK2	29911	hgsc.bcm.edu	37	chr19	12886218	12886218	+	Splice_Site	DEL	C	C	-													0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	tagccccgccccacgacctaCccaggtgagcagagacccgc							TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr19:12886218delC	ENST00000397668.3	-	1	119		c.e1+1		HOOK2_ENST00000264827.5_Splice_Site|HOOK2_ENST00000589965.1_Splice_Site	NM_013312.2	NP_037444.2	Q96ED9	HOOK2_HUMAN	hook microtubule-tethering protein 2						early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|protein transport (GO:0015031)	centrosome (GO:0005813)|FHF complex (GO:0070695)|microtubule (GO:0005874)	identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(5)|skin(1)	20						CCACGACCTACCCAGGTGAGC	0.682																																					.		Atlas-Indel,Pindel	.											.	HOOK2	73	.	0			c.45+2G>-						.						23	29	27					19																	12886218		1943	4125	6068	SO:0001630	splice_region_variant	29911	exon2			.	AF044924	CCDS42507.1, CCDS42508.1	19p13.2	2013-08-21	2013-08-21						19885	protein-coding gene	gene with protein product		607824	"hook homolog 2 (Drosophila)"			9927460	Standard	NM_013312		Approved	HK2	uc002muy.2	Q96ED9		ENST00000397668.3:c.45+1G>-	chr19.hg19:g.12886218delC		130.0	0.0		95.0	26.0	NM_001100176	O60562	Splice_Site	DEL	ENST00000397668.3	hg19	CCDS42508.1																																																																																			.	.		0.682	HOOK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451008.1	NM_013312	Intron	-	12886218	C	-	12886218	8	5	287	1	0	1	0	1	0	0	1	0	7292	521	18	0	2205	0	HOOK2	19	12886218	Splice_Site	DEL	C	TCGA-G3-A5SL-01A-11D-A27I-10		12886218	46242765	101	42199										
GLT25D1	79709	hgsc.bcm.edu	37	chr19	17691557	17691557	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	agcaccccgagaaggctgtgCctcgcgtgaggaacctggtg	15	12	0	2			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr19:17691557C>T	ENST00000252599.4	+	11	1564	c.1444C>T	c.(1444-1446)Cct>Tct	p.P482S		NM_024656.2	NP_078932.2	Q8NBJ5	GT251_HUMAN	collagen beta(1-O)galactosyltransferase 1	482					extracellular matrix organization (GO:0030198)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum lumen (GO:0005788)|membrane (GO:0016020)	procollagen galactosyltransferase activity (GO:0050211)										GAAGGCTGTGCCTCGCGTGAG	0.662																																					p.P482S		Atlas-SNP	.											.	.	.	.	0			c.C1444T						.						72	64	66					19																	17691557		2203	4300	6503	SO:0001583	missense	79709	exon11			GCTGTGCCTCGCG	AK075541	CCDS12363.1	19p13.11	2013-02-27	2013-02-27	2013-02-27	ENSG00000130309	ENSG00000130309			26182	protein-coding gene	gene with protein product			"glycosyltransferase 25 domain containing 1"	GLT25D1		19075007	Standard	NM_024656		Approved	FLJ22329	uc002nhc.1	Q8NBJ5		ENST00000252599.4:c.1444C>T	chr19.hg19:g.17691557C>T	ENSP00000252599:p.Pro482Ser	99.0	0.0		71.0	29.0	NM_024656	Q8NC64	Missense_Mutation	SNP	ENST00000252599.4	hg19	CCDS12363.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.661793	0.88154	.	.	ENSG00000130309	ENST00000379714;ENST00000252599	T	0.78924	-1.22	5.24	5.24	0.73138	.	0.107265	0.64402	D	0.000004	D	0.84229	0.5426	L	0.55481	1.735	0.80722	D	1	B;D;P	0.67145	0.275;0.996;0.949	B;D;P	0.68621	0.147;0.959;0.719	T	0.81805	-0.0764	10	0.28530	T	0.3	4.5113	16.2945	0.82763	0.0:1.0:0.0:0.0	.	11;210;482	B3KQ10;E9PC06;Q8NBJ5	.;.;GT251_HUMAN	S	210;482	ENSP00000252599:P482S	ENSP00000252599:P482S	P	+	1	0	GLT25D1	17552557	0.993000	0.37304	0.998000	0.56505	0.971000	0.66376	2.437000	0.44828	2.456000	0.83038	0.491000	0.48974	CCT	.	.		0.662	COLGALT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464216.1	NM_024656		T	17691557	C	T	17691557	3	4	287	1	0	0	0	0	1	0	0	0	6474	739	26	3	1486	3	GLT25D1	19	17691557	Missense_Mutation	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10	4805339	17691557	41437426	102	42200										
APLP1	333	hgsc.bcm.edu	37	chr19	36363455	36363455	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	cctggggaaatcagtgagcaCgaggggttcctgagggccaa	16	9	1	2			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr19:36363455C>T	ENST00000221891.4	+	7	1113	c.921C>T	c.(919-921)caC>caT	p.H307H	APLP1_ENST00000537454.2_Silent_p.H268H|APLP1_ENST00000586861.1_Silent_p.H301H	NM_001024807.1|NM_005166.3	NP_001019978.1|NP_005157.1	P51693	APLP1_HUMAN	amyloid beta (A4) precursor-like protein 1	307					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular response to norepinephrine stimulus (GO:0071874)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|mRNA polyadenylation (GO:0006378)|negative regulation of cAMP biosynthetic process (GO:0030818)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|regulation of translation (GO:0006417)	basement membrane (GO:0005604)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|alpha-2B adrenergic receptor binding (GO:0031695)|alpha-2C adrenergic receptor binding (GO:0031696)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|transition metal ion binding (GO:0046914)			breast(4)|endometrium(2)|kidney(2)|large_intestine(12)|liver(1)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	33	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TCAGTGAGCACGAGGGGTTCC	0.572																																					p.H307H		Atlas-SNP	.											.	APLP1	77	.	0			c.C921T						.						146	143	144					19																	36363455		2203	4300	6503	SO:0001819	synonymous_variant	333	exon7			TGAGCACGAGGGG	U48437	CCDS32997.1	19q	2008-07-15							597	protein-coding gene	gene with protein product	"amyloid-like protein 1", "amyloid precursor-like protein 1"	104775				8432545	Standard	NM_001024807		Approved	APLP	uc002ocf.3	P51693		ENST00000221891.4:c.921C>T	chr19.hg19:g.36363455C>T		160.0	0.0		126.0	50.0	NM_005166	O00113|Q96A92	Silent	SNP	ENST00000221891.4	hg19	CCDS32997.1																																																																																			.	.		0.572	APLP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452564.1	NM_001024807		T	36363455	C	T	36363455	2	4	287	1	0	0	0	0	0	0	0	1	778	535	19	1		1	APLP1	19	36363455	Silent	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10	18671898	36363455	22765528	103	42201										
ZNF816A	125893	hgsc.bcm.edu	37	chr19	53453569	53453569	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	tcttcgactaaaaaccttgcCacattcattacatgtgtaag	5	10	2	0			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr19:53453569C>A	ENST00000357666.4	-	5	1759	c.1459G>T	c.(1459-1461)Ggc>Tgc	p.G487C	ZNF816_ENST00000444460.2_Missense_Mutation_p.G487C|ZNF816_ENST00000434371.2_Intron|ZNF321P_ENST00000391777.3_Intron	NM_001031665.2	NP_001026835.1	Q0VGE8	ZN816_HUMAN	zinc finger protein 816	487					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(10)|lung(9)|stomach(1)|urinary_tract(2)	27						AAAACCTTGCCACATTCATTA	0.403																																					p.G487C		Atlas-SNP	.											.	ZNF816	73	.	0			c.G1459T						.						96	96	96					19																	53453569		2203	4300	6503	SO:0001583	missense	125893	exon4			CCTTGCCACATTC	BC063805	CCDS33096.1	19q13.41	2013-01-08	2010-07-23	2010-07-23		ENSG00000180257		"Zinc fingers, C2H2-type", "-"	26995	protein-coding gene	gene with protein product			"zinc finger protein 816A"	ZNF816A			Standard	NM_001031665		Approved		uc002qam.2	Q0VGE8		ENST00000357666.4:c.1459G>T	chr19.hg19:g.53453569C>A	ENSP00000350295:p.Gly487Cys	68.0	0.0		52.0	10.0	NM_001202457	A8K7H5|Q3KR39|Q659B3	Missense_Mutation	SNP	ENST00000357666.4	hg19	CCDS33096.1	.	.	.	.	.	.	.	.	.	.	-	10.83	1.461443	0.26248	.	.	ENSG00000180257	ENST00000357666;ENST00000444460	T;T	0.23754	1.89;1.89	1.85	1.85	0.25348	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.57636	0.2067	H	0.94734	3.575	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.67738	-0.5593	9	0.87932	D	0	.	10.6734	0.45772	0.0:1.0:0.0:0.0	.	487	Q0VGE8	ZN816_HUMAN	C	487	ENSP00000350295:G487C;ENSP00000403266:G487C	ENSP00000350295:G487C	G	-	1	0	ZNF816	58145381	0.319000	0.24607	0.501000	0.27601	0.074000	0.17049	1.906000	0.39887	1.006000	0.39211	0.313000	0.20887	GGC	.	.		0.403	ZNF816-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396132.1	NM_001031665		A	53453569	C	A	53453569	3	1	287	1	0	0	0	0	1	0	0	0	18192	594	21	3	500	3	ZNF816A	19	53453569	Missense_Mutation	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10	17090114	53453569	5675414	104	42202										
ZNF471	57573	hgsc.bcm.edu	37	chr19	57036179	57036179	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	agccttcaagcaaaggcaacAccttgctcaacatcacagaa	6	13	3	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr19:57036179A>G	ENST00000308031.5	+	5	876	c.743A>G	c.(742-744)cAc>cGc	p.H248R	ZNF471_ENST00000591537.1_Missense_Mutation_p.T108A|ZNF471_ENST00000593197.1_Intron	NM_020813.2	NP_065864.2	Q9BX82	ZN471_HUMAN	zinc finger protein 471	248					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(8)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0307)		CAAAGGCAACACCTTGCTCAA	0.388																																					p.H248R	Colon(65;957 1402 6678 10163)|Esophageal Squamous(159;2295 2541 15408 21211)	Atlas-SNP	.											.	ZNF471	99	.	0			c.A743G						.						83	89	87					19																	57036179		2203	4300	6503	SO:0001583	missense	57573	exon5			GGCAACACCTTGC	AB037817	CCDS12945.1	19q13.43	2013-01-08				ENSG00000196263		"Zinc fingers, C2H2-type", "-"	23226	protein-coding gene	gene with protein product						10718198	Standard	NM_020813		Approved	KIAA1396, Z1971	uc002qnh.3	Q9BX82		ENST00000308031.5:c.743A>G	chr19.hg19:g.57036179A>G	ENSP00000309161:p.His248Arg	79.0	0.0		80.0	34.0	NM_020813	B4DF32|O75260|Q08AD6|Q08AD7|Q8N3V1|Q9P2F1	Missense_Mutation	SNP	ENST00000308031.5	hg19	CCDS12945.1	.	.	.	.	.	.	.	.	.	.	A	9.469	1.095196	0.20471	.	.	ENSG00000196263	ENST00000308031	T	0.12984	2.63	4.29	2.05	0.26809	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.16300	0.0392	N	0.17838	0.53	0.09310	N	1	D	0.89917	1.0	D	0.83275	0.996	T	0.20438	-1.0275	9	0.20519	T	0.43	.	4.0866	0.09950	0.6715:0.0:0.1647:0.1638	.	248	Q9BX82	ZN471_HUMAN	R	248	ENSP00000309161:H248R	ENSP00000309161:H248R	H	+	2	0	ZNF471	61727991	.	.	0.295000	0.24960	0.953000	0.61014	.	.	0.652000	0.30806	0.379000	0.24179	CAC	.	.		0.388	ZNF471-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458405.1	NM_020813		G	57036179	A	G	57036179	3	3	287	1	0	0	0	0	1	0	0	0	17945	159	6	2	757	2	ZNF471	19	57036179	Missense_Mutation	SNP	A	TCGA-G3-A5SL-01A-11D-A27I-10	3582610	57036179	2092804	105	42203										
ZNF17	7565	hgsc.bcm.edu	37	chr19	57931234	57931234	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	ggagcatcttagagagaagcTcaccagaagtgatgaaggga	14	6	2	5			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr19:57931234T>G	ENST00000601808.1	+	3	587	c.374T>G	c.(373-375)cTc>cGc	p.L125R	ZNF17_ENST00000307658.7_Missense_Mutation_p.L127R|AC004076.7_ENST00000597410.1_Intron|AC003002.6_ENST00000596400.1_Missense_Mutation_p.L137R|ZNF17_ENST00000595206.1_3'UTR	NM_006959.2	NP_008890.2	P17021	ZNF17_HUMAN	zinc finger protein 17	125					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0234)|GBM - Glioblastoma multiforme(193;0.000426)|Lung(386;0.176)		AGAGAGAAGCTCACCAGAAGT	0.502																																					p.L125R	Melanoma(149;1637 1853 29914 42869 44988)	Atlas-SNP	.											.	ZNF17	49	.	0			c.T374G						.						124	126	125					19																	57931234		2203	4300	6503	SO:0001583	missense	7565	exon3			AGAAGCTCACCAG	X52341	CCDS42636.1	19q13.43	2013-01-08	2006-05-10			ENSG00000186272		"Zinc fingers, C2H2-type", "-"	12958	protein-coding gene	gene with protein product			"zinc finger protein 17 (HPF3, KOX 10)"			2115127, 2014798	Standard	NM_006959		Approved	HPF3, KOX10, KIAA1947, FLJ40864, FLJ46058, FLJ46615	uc002qoo.1	P17021		ENST00000601808.1:c.374T>G	chr19.hg19:g.57931234T>G	ENSP00000471905:p.Leu125Arg	187.0	0.0		162.0	10.0	NM_006959	B3KXU2|B3KY20|Q8N7M1|Q8N893|Q8TF54	Missense_Mutation	SNP	ENST00000601808.1	hg19	CCDS42636.1	.	.	.	.	.	.	.	.	.	.	T	8.816	0.936305	0.18206	.	.	ENSG00000186272	ENST00000307658	.	.	.	1.7	0.503	0.16940	.	.	.	.	.	T	0.28830	0.0715	L	0.33137	0.985	0.09310	N	1	P;B	0.50066	0.931;0.114	P;B	0.47430	0.547;0.021	T	0.11941	-1.0567	8	0.39692	T	0.17	.	5.0105	0.14310	0.627:0.0:0.0:0.373	.	127;125	P17021-2;P17021	.;ZNF17_HUMAN	R	125	.	ENSP00000302455:L125R	L	+	2	0	ZNF17	62623046	0.000000	0.05858	0.001000	0.08648	0.315000	0.28087	-2.175000	0.01263	0.037000	0.15575	0.528000	0.53228	CTC	.	.		0.502	ZNF17-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466384.1	NM_006959		G	57931234	T	G	57931234	3	3	287	1	0	0	0	0	1	0	0	0	17758	1551	54	5	384	5	ZNF17	19	57931234	Missense_Mutation	SNP	T	TCGA-G3-A5SL-01A-11D-A27I-10	895055	57931234	1197749	106	42204										
PTPRA	5786	hgsc.bcm.edu	37	chr20	3002002	3002002	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	caaggctgctggacctatggGaatattcgggtgtctgtaga	14	7	1	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr20:3002002G>A	ENST00000216877.6	+	13	1462	c.1062G>A	c.(1060-1062)ggG>ggA	p.G354G	PTPRA_ENST00000380393.3_Silent_p.G363G|PTPRA_ENST00000358719.4_Silent_p.G219G|PTPRA_ENST00000425918.2_Silent_p.G374G|PTPRA_ENST00000399903.2_Silent_p.G363G|PTPRA_ENST00000318266.5_Silent_p.G354G|PTPRA_ENST00000356147.3_Silent_p.G354G	NM_080840.2	NP_543030.1	P18433	PTPRA_HUMAN	protein tyrosine phosphatase, receptor type, A	363	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axon guidance (GO:0007411)|insulin receptor signaling pathway (GO:0008286)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein phosphorylation (GO:0006468)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						GGACCTATGGGAATATTCGGG	0.522																																					p.G363G		Atlas-SNP	.											.	PTPRA	75	.	0			c.G1089A						.						203	165	178					20																	3002002		2203	4300	6503	SO:0001819	synonymous_variant	5786	exon18			CTATGGGAATATT		CCDS13038.1, CCDS13039.1	20p13	2011-06-09			ENSG00000132670	ENSG00000132670		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9664	protein-coding gene	gene with protein product		176884		PTPRL2, PTPA		2172030, 2169617	Standard	NM_080840		Approved	LRP, HLPR, HPTPA, RPTPA	uc002whn.3	P18433	OTTHUMG00000031718	ENST00000216877.6:c.1062G>A	chr20.hg19:g.3002002G>A		264.0	0.0		223.0	78.0	NM_002836	A8K2G8|D3DVX5|Q14513|Q7Z2I2|Q96TD9	Silent	SNP	ENST00000216877.6	hg19	CCDS13039.1																																																																																			.	.		0.522	PTPRA-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077682.3			A	3002002	G	A	3002002	2	1	287	1	0	0	0	0	0	0	0	1	12810	1161	41	3		3	PTPRA	20	3002002	Silent	SNP	G	TCGA-G3-A5SL-01A-11D-A27I-10		3002002	60023518	107	42205										
TMPRSS15	5651	hgsc.bcm.edu	37	chr21	19647566	19647566	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	ctgcacatatcatattttcaGtaatgttatattctggcatc	5	8	3	0			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr21:19647566G>T	ENST00000284885.3	-	24	2885	c.2852C>A	c.(2851-2853)aCt>aAt	p.T951N		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	951	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						CATATTTTCAGTAATGTTATA	0.388																																					p.T951N		Atlas-SNP	.											.	TMPRSS15	189	.	0			c.C2852A						.						179	171	173					21																	19647566		2203	4300	6503	SO:0001583	missense	5651	exon24			TTTTCAGTAATGT		CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"Serine peptidases / Transmembrane"	9490	protein-coding gene	gene with protein product	"proenterokinase", "enteropeptidase"	606635	"protease, serine, 7 (enterokinase)"	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.2852C>A	chr21.hg19:g.19647566G>T	ENSP00000284885:p.Thr951Asn	92.0	0.0		91.0	4.0	NM_002772	Q2NKL7	Missense_Mutation	SNP	ENST00000284885.3	hg19	CCDS13571.1	.	.	.	.	.	.	.	.	.	.	G	13.75	2.329538	0.41297	.	.	ENSG00000154646	ENST00000284885	D	0.90324	-2.65	5.46	3.61	0.41365	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.121220	0.53938	D	0.000050	D	0.88220	0.6378	M	0.62016	1.91	0.43338	D	0.995382	B	0.22414	0.069	B	0.27170	0.077	T	0.82474	-0.0439	9	.	.	.	.	11.9069	0.52717	0.0:0.1325:0.7295:0.138	.	951	P98073	ENTK_HUMAN	N	951	ENSP00000284885:T951N	.	T	-	2	0	TMPRSS15	18569437	1.000000	0.71417	0.984000	0.44739	0.989000	0.77384	5.360000	0.66086	0.752000	0.32923	-0.158000	0.13435	ACT	.	.		0.388	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772		T	19647566	G	T	19647566	3	4	287	1	0	0	0	0	1	0	0	0	16261	1029	36	3	215	3	TMPRSS15	21	19647566	Missense_Mutation	SNP	G	TCGA-G3-A5SL-01A-11D-A27I-10		19647566	28482329	108	42206										
PRDM15	63977	hgsc.bcm.edu	37	chr21	43221871	43221871	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	gtcacatttgggtcacccagGgtcaccactacctggaagat	10	12	3	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr21:43221871G>A	ENST00000269844.3	-	31	4163	c.4053C>T	c.(4051-4053)acC>acT	p.T1351T	PRDM15_ENST00000398548.1_Silent_p.T1022T|PRDM15_ENST00000447207.2_Silent_p.T985T|PRDM15_ENST00000538201.1_Silent_p.T1005T|PRDM15_ENST00000470586.1_5'UTR|PRDM15_ENST00000422911.1_Silent_p.T1042T	NM_022115.3	NP_071398.3	P57071	PRD15_HUMAN	PR domain containing 15	1351					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(3)|skin(2)|stomach(2)|urinary_tract(1)	43						GGTCACCCAGGGTCACCACTA	0.527																																					p.T1351T		Atlas-SNP	.											.	PRDM15	110	.	0			c.C4053T						.						66	69	68					21																	43221871		2203	4300	6503	SO:0001819	synonymous_variant	63977	exon31			ACCCAGGGTCACC	AF276513	CCDS13676.1, CCDS42932.1, CCDS63370.1	21q22.3	2013-01-08	2002-07-31		ENSG00000141956	ENSG00000141956		"Zinc fingers, C2H2-type"	13999	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 83"	ZNF298, C21orf83		12036297, 12036298	Standard	NM_022115		Approved		uc002yzq.1	P57071	OTTHUMG00000086781	ENST00000269844.3:c.4053C>T	chr21.hg19:g.43221871G>A		271.0	0.0		182.0	31.0	NM_022115	E9PDJ6|E9PF37|E9PGL3|Q4W8S0|Q4W8S3|Q4W8S4|Q4W8S5|Q8N0X3|Q8NEX0|Q9NQV3	Silent	SNP	ENST00000269844.3	hg19	CCDS13676.1																																																																																			.	.		0.527	PRDM15-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022115		A	43221871	G	A	43221871	2	1	287	1	0	0	0	0	0	0	0	1	12468	1219	43	3		3	PRDM15	21	43221871	Silent	SNP	G	TCGA-G3-A5SL-01A-11D-A27I-10	23574305	43221871	4908024	109	42207										
COL18A1	80781	hgsc.bcm.edu	37	chr21	46888317	46888317	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	acttccccagcctcttcttcCgtgacttctcactgctgttc	5	17	3	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr21:46888317C>T	ENST00000359759.4	+	2	1534	c.1513C>T	c.(1513-1515)Cgt>Tgt	p.R505C	COL18A1_ENST00000400337.2_Missense_Mutation_p.R90C|COL18A1_ENST00000355480.5_Missense_Mutation_p.R270C			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	505	Laminin G-like.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		CCTCTTCTTCCGTGACTTCTC	0.647																																					p.R270C		Atlas-SNP	.											.	COL18A1	129	.	0			c.C808T						.						81	94	90					21																	46888317		2072	4208	6280	SO:0001583	missense	80781	exon2			TTCTTCCGTGACT		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"Collagens"	2195	protein-coding gene	gene with protein product	"endostatin"	120328	"Knobloch syndrome, type 1"	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.1513C>T	chr21.hg19:g.46888317C>T	ENSP00000352798:p.Arg505Cys	226.0	0.0		126.0	38.0	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000359759.4	hg19		.	.	.	.	.	.	.	.	.	.	C	11.31	1.599866	0.28534	.	.	ENSG00000182871	ENST00000400337;ENST00000400347;ENST00000355480;ENST00000359759;ENST00000539645	T;T;T	0.74002	-0.8;-0.8;-0.8	4.65	2.44	0.29823	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);Laminin G, thrombospondin-type, N-terminal (1);	0.067657	0.56097	D	0.000021	T	0.81278	0.4789	M	0.64997	1.995	0.58432	D	0.99999	D;D;D	0.89917	1.0;0.999;0.999	D;P;P	0.64595	0.927;0.88;0.809	T	0.82737	-0.0309	10	0.87932	D	0	.	11.7042	0.51587	0.4477:0.5523:0.0:0.0	.	505;270;90	P39060;P39060-1;P39060-2	COIA1_HUMAN;.;.	C	90;90;270;505;505	ENSP00000383191:R90C;ENSP00000347665:R270C;ENSP00000352798:R505C	ENSP00000347665:R270C	R	+	1	0	COL18A1	45712745	0.976000	0.34144	0.820000	0.32676	0.457000	0.32468	0.952000	0.29149	1.051000	0.40369	0.655000	0.94253	CGT	.	.		0.647	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1			T	46888317	C	T	46888317	3	4	287	1	0	0	0	0	1	0	0	0	3677	652	23	1	1633	1	COL18A1	21	46888317	Missense_Mutation	SNP	C	TCGA-G3-A5SL-01A-11D-A27I-10	3666446	46888317	1241578	110	42208										
ADORA2A	135	hgsc.bcm.edu	37	chr22	24837383	24837383	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	acgtggagctccttagccatGagctcaagggagtgtgccca	13	11	1	1	rs201827862		TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr22:24837383G>A	ENST00000337539.7	+	3	1624	c.1165G>A	c.(1165-1167)Gag>Aag	p.E389K	ADORA2A-AS1_ENST00000427813.2_RNA|SPECC1L-ADORA2A_ENST00000358654.2_3'UTR|ADORA2A-AS1_ENST00000543438.1_RNA|ADORA2A-AS1_ENST00000326341.4_RNA	NM_000675.4|NM_001278497.1|NM_001278498.1|NM_001278499.1|NM_001278500.1	NP_000666.2|NP_001265426.1|NP_001265427.1|NP_001265428.1|NP_001265429.1	P29274	AA2AR_HUMAN	adenosine A2a receptor	389					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|apoptotic process (GO:0006915)|blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cAMP biosynthetic process (GO:0006171)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|central nervous system development (GO:0007417)|inflammatory response (GO:0006954)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phagocytosis (GO:0006909)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|sensory perception (GO:0007600)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|G-protein coupled adenosine receptor activity (GO:0001609)|identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(7)|skin(1)	21	Colorectal(2;0.196)				Adenosine(DB00640)|Caffeine(DB00201)|Defibrotide(DB04932)|Dyphylline(DB00651)|Enprofylline(DB00824)|Mefloquine(DB00358)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Regadenoson(DB06213)|Theobromine(DB01412)|Theophylline(DB00277)	CCTTAGCCATGAGCTCAAGGG	0.632																																					p.E389K		Atlas-SNP	.											.	ADORA2A	44	.	0			c.G1165A						.						28	27	27					22																	24837383		2203	4300	6503	SO:0001583	missense	135	exon3			AGCCATGAGCTCA	X68486	CCDS13826.1	22q11.23	2012-08-08			ENSG00000128271	ENSG00000128271		"GPCR / Class A : Adenosine receptors"	263	protein-coding gene	gene with protein product		102776		ADORA2		1662665, 2541503	Standard	NM_001278497		Approved	RDC8	uc002zzy.4	P29274	OTTHUMG00000150761	ENST00000337539.7:c.1165G>A	chr22.hg19:g.24837383G>A	ENSP00000336630:p.Glu389Lys	234.0	0.0		160.0	59.0	NM_000675	B2R7E0	Missense_Mutation	SNP	ENST00000337539.7	hg19	CCDS13826.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.686871	0.88639	.	.	ENSG00000128271	ENST00000541988;ENST00000337539;ENST00000417596	T	0.64438	-0.1	4.41	4.41	0.53225	.	0.468674	0.18687	N	0.133987	T	0.54208	0.1844	L	0.56769	1.78	0.23221	N	0.998092	B	0.27498	0.18	B	0.25884	0.064	T	0.45396	-0.9264	10	0.06757	T	0.87	-13.0096	14.5397	0.67984	0.0:0.0:1.0:0.0	.	389	P29274	AA2AR_HUMAN	K	389	ENSP00000336630:E389K	ENSP00000336630:E389K	E	+	1	0	ADORA2A	23167383	1.000000	0.71417	0.055000	0.19348	0.919000	0.55068	4.367000	0.59498	2.206000	0.71126	0.462000	0.41574	GAG	.	.		0.632	ADORA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319971.2	NM_000675		A	24837383	G	A	24837383	3	1	287	1	0	0	0	0	1	0	0	0	327	1291	45	3	1171	3	ADORA2A	22	24837383	Missense_Mutation	SNP	G	TCGA-G3-A5SL-01A-11D-A27I-10		24837383	26467183	111	42209										
BPIL2	254240	hgsc.bcm.edu	37	chr22	32810334	32810335	+	Frame_Shift_Ins	INS	-	-	A													0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	tgtctgcttatcaggttcagINSaccttcccatacgtggaaac							TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr22:32810334_32810335insA	ENST00000397452.1	-	16	1589_1590	c.1479_1480insT	c.(1477-1482)ggtctgfs	p.L494fs	BPIFC_ENST00000534972.1_Frame_Shift_Ins_p.L218fs|BPIFC_ENST00000300399.3_Frame_Shift_Ins_p.L494fs|RTCB_ENST00000451746.2_5'Flank|RTCB_ENST00000216038.5_5'Flank|BPIFC_ENST00000432451.2_Frame_Shift_Ins_p.L251fs			Q8NFQ6	BPIFC_HUMAN	BPI fold containing family C	494						extracellular region (GO:0005576)	lipopolysaccharide binding (GO:0001530)|phospholipid binding (GO:0005543)										ATCAGGTTCAGACCTTCCCATA	0.475																																					p.L494fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.1480_1481insT						.																																			SO:0001589	frameshift_variant	254240	exon15			.	AF465766	CCDS13906.1	22q12.3	2011-08-04	2011-08-01	2011-08-01	ENSG00000184459	ENSG00000184459		"BPI fold containing"	16503	protein-coding gene	gene with protein product		614109	"bactericidal/permeability-increasing protein-like 2"	BPIL2			Standard	NM_174932		Approved	dJ149A16.7	uc003amn.2	Q8NFQ6	OTTHUMG00000058273	ENST00000397452.1:c.1480dupT	chr22.hg19:g.32810335_32810335dupA	ENSP00000380594:p.Leu494fs	202.0	0.0		209.0	22.0	NM_174932	A2RRF1	Frame_Shift_Ins	INS	ENST00000397452.1	hg19	CCDS13906.1																																																																																			.	.		0.475	BPIFC-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129029.2	NM_174932		A	32810335	-	A	32810334	7	5	287	1	0	1	1	0	0	0	0	0	1494	933	33	0	47	0	BPIL2	22	32810334	Frame_Shift_Ins	INS	-	TCGA-G3-A5SL-01A-11D-A27I-10	7972951	32810334	18494232	112	42210										
CARD10	29775	hgsc.bcm.edu	37	chr22	37888678	37888678	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	gcacacttggaagtccagccGggagctgggcaggtctagca	15	11	1	0			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr22:37888678G>A	ENST00000403299.1	-	18	2824	c.2608C>T	c.(2608-2610)Cgg>Tgg	p.R870W	CARD10_ENST00000406271.3_Missense_Mutation_p.R584W|CARD10_ENST00000251973.5_Missense_Mutation_p.R870W			Q9BWT7	CAR10_HUMAN	caspase recruitment domain family, member 10	870					activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein complex assembly (GO:0006461)|regulation of apoptotic process (GO:0042981)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)	receptor signaling complex scaffold activity (GO:0030159)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	Melanoma(58;0.0574)					AAGTCCAGCCGGGAGCTGGGC	0.687																																					p.R870W		Atlas-SNP	.											.	CARD10	55	.	0			c.C2608T						.						25	25	25					22																	37888678		2201	4296	6497	SO:0001583	missense	29775	exon17			CCAGCCGGGAGCT	AF086324	CCDS13948.1	22q13.1	2008-05-22			ENSG00000100065	ENSG00000100065			16422	protein-coding gene	gene with protein product		607209				11259443, 11356195	Standard	NM_014550		Approved	CARMA3, BIMP1	uc003asu.1	Q9BWT7	OTTHUMG00000150592	ENST00000403299.1:c.2608C>T	chr22.hg19:g.37888678G>A	ENSP00000384570:p.Arg870Trp	154.0	0.0		119.0	5.0	NM_014550	Q14CQ8|Q5TFG6|Q8NC81|Q9UGR5|Q9UGR6|Q9Y3H0	Missense_Mutation	SNP	ENST00000403299.1	hg19	CCDS13948.1	.	.	.	.	.	.	.	.	.	.	G	18.79	3.698057	0.68386	.	.	ENSG00000100065	ENST00000403299;ENST00000406271;ENST00000251973	T;T;T	0.41400	1.0;2.69;1.0	4.81	2.67	0.31697	.	0.072818	0.56097	D	0.000024	T	0.49304	0.1549	L	0.41236	1.265	0.33332	D	0.56865	D;P	0.71674	0.998;0.669	P;B	0.58970	0.849;0.049	T	0.62426	-0.6857	10	0.62326	D	0.03	-24.5752	13.536	0.61646	0.0:0.0:0.7112:0.2888	.	870;584	Q9BWT7;Q8NC81	CAR10_HUMAN;.	W	870;584;870	ENSP00000384570:R870W;ENSP00000385799:R584W;ENSP00000251973:R870W	ENSP00000251973:R870W	R	-	1	2	CARD10	36218624	1.000000	0.71417	0.998000	0.56505	0.919000	0.55068	2.526000	0.45607	0.222000	0.20900	-0.808000	0.03180	CGG	.	.		0.687	CARD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318997.1	NM_014550		A	37888678	G	A	37888678	3	1	287	1	0	0	0	0	1	0	0	0	2646	1115	39	1	506	1	CARD10	22	37888678	Missense_Mutation	SNP	G	TCGA-G3-A5SL-01A-11D-A27I-10	5078344	37888678	13415888	113	42211										
LDOC1L	84247	hgsc.bcm.edu	37	chr22	44893045	44893045	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	ccacacgctcggcctcacccGggaagcgggaggcctggaag	15	15	1	0			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr22:44893045G>A	ENST00000341255.3	-	2	901	c.392C>T	c.(391-393)cCg>cTg	p.P131L		NM_032287.2	NP_115663.2	Q6ICC9	LDOCL_HUMAN	leucine zipper, down-regulated in cancer 1-like	131										breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(3)|prostate(2)	11		Ovarian(80;0.024)|all_neural(38;0.0416)		LUAD - Lung adenocarcinoma(64;0.0161)		GGCCTCACCCGGGAAGCGGGA	0.637																																					p.P131L		Atlas-SNP	.											.	LDOC1L	24	.	0			c.C392T						.						38	42	41					22																	44893045		2203	4300	6503	SO:0001583	missense	84247	exon2			TCACCCGGGAAGC	CR456439	CCDS33662.1	22q13.3	2006-09-06			ENSG00000188636	ENSG00000188636			13343	protein-coding gene	gene with protein product						15716091, 16093683	Standard	NM_032287		Approved	dJ1033E15.2, DKFZp761O17121, Mart6, Mar6	uc003beu.1	Q6ICC9	OTTHUMG00000150465	ENST00000341255.3:c.392C>T	chr22.hg19:g.44893045G>A	ENSP00000340434:p.Pro131Leu	64.0	0.0		55.0	30.0	NM_032287	Q6ZTR1	Missense_Mutation	SNP	ENST00000341255.3	hg19	CCDS33662.1	.	.	.	.	.	.	.	.	.	.	G	19.26	3.793126	0.70452	.	.	ENSG00000188636	ENST00000341255	T	0.22539	1.95	3.27	3.27	0.37495	.	0.284835	0.22798	N	0.055509	T	0.29223	0.0727	L	0.29908	0.895	0.40101	D	0.976373	D	0.89917	1.0	D	0.66716	0.946	T	0.03157	-1.1066	10	0.51188	T	0.08	-18.2845	10.3019	0.43656	0.0:0.0:1.0:0.0	.	131	Q6ICC9	LDOCL_HUMAN	L	131	ENSP00000340434:P131L	ENSP00000340434:P131L	P	-	2	0	LDOC1L	43271709	0.992000	0.36948	0.728000	0.30774	0.956000	0.61745	3.769000	0.55303	2.139000	0.66308	0.591000	0.81541	CCG	.	.		0.637	LDOC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318222.1	NM_032287		A	44893045	G	A	44893045	3	1	287	1	0	0	0	0	1	0	0	0	8719	1116	39	1	331	1	LDOC1L	22	44893045	Missense_Mutation	SNP	G	TCGA-G3-A5SL-01A-11D-A27I-10	7004367	44893045	6411521	114	42212										
SBF1	6305	hgsc.bcm.edu	37	chr22	50886721	50886721	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	gtgctggtgctgcggcgggcAgcctgacgggagccggatgt	20	10	0	1			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chr22:50886721A>T	ENST00000390679.3	-	37	5410	c.5226T>A	c.(5224-5226)gcT>gcA	p.A1742A	SBF1_ENST00000348911.6_Silent_p.A1743A|SBF1_ENST00000380817.3_Silent_p.A1768A			O95248	MTMR5_HUMAN	SET binding factor 1	1742					cell death (GO:0008219)|positive regulation of Rab GTPase activity (GO:0032851)|protein dephosphorylation (GO:0006470)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(8)|large_intestine(3)|lung(18)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	43		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)		TGCGGCGGGCAGCCTGACGGG	0.642																																					p.A1768A		Atlas-SNP	.											.	SBF1	211	.	0			c.T5304A						.						39	47	44					22																	50886721		2083	4209	6292	SO:0001819	synonymous_variant	6305	exon38			GCGGGCAGCCTGA	U93181	CCDS14091.1, CCDS14091.2	22q13.33	2013-01-10			ENSG00000100241	ENSG00000100241		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins", "DENN/MADD domain containing", "Pleckstrin homology (PH) domain containing"	10542	protein-coding gene	gene with protein product	"myotubularin related 5", "DENN/MADD domain containing 7A"	603560				9537414, 9736772	Standard	NM_002972		Approved	MTMR5, DENND7A	uc003blh.3	O95248	OTTHUMG00000150204	ENST00000390679.3:c.5226T>A	chr22.hg19:g.50886721A>T		161.0	1.0		90.0	61.0	NM_002972	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Silent	SNP	ENST00000390679.3	hg19		.	.	.	.	.	.	.	.	.	.	A	11.59	1.685202	0.29872	.	.	ENSG00000100241	ENST00000418590	.	.	.	3.61	-7.22	0.01485	.	.	.	.	.	T	0.43456	0.1248	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45687	-0.9244	4	.	.	.	.	4.7953	0.13269	0.4376:0.0:0.3039:0.2585	.	.	.	.	S	290	.	.	C	-	1	0	SBF1	49233587	0.000000	0.05858	0.972000	0.41901	0.982000	0.71751	-3.375000	0.00493	-1.290000	0.02372	0.402000	0.26972	TGC	.	.		0.642	SBF1-201	KNOWN	basic	protein_coding	protein_coding				T	50886721	A	T	50886721	2	4	287	1	0	0	0	0	0	0	0	1	13873	175	7	4		4	SBF1	22	50886721	Silent	SNP	A	TCGA-G3-A5SL-01A-11D-A27I-10	5993676	50886721	417845	115	42213										
MAGEE2	139599	hgsc.bcm.edu	37	chrX	75003638	75003638	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0862068965517241	10	1	1.4664005322688	1.97964071856287	1.31976047904192	0.245077461269365	0.896214637779148	0	gacattggcctctttgacacGgttgcccatcaggaagatca	10	11	3	2			TCGA-G3-A5SL-01A-11D-A27I-10	TCGA-G3-A5SL-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	70422e6d-cb1f-4284-8be9-1d4517ffad60	a38d4467-c3e5-4639-ad4f-88bcd7ab9f26	g.chrX:75003638G>A	ENST00000373359.2	-	1	1441	c.1249C>T	c.(1249-1251)Cgt>Tgt	p.R417C		NM_138703.4	NP_619648.1	Q8TD90	MAGE2_HUMAN	melanoma antigen family E, 2	417	MAGE 2. {ECO:0000255|PROSITE- ProRule:PRU00127}.									autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						TCTTTGACACGGTTGCCCATC	0.473																																					p.R417C		Atlas-SNP	.											.	MAGEE2	94	.	0			c.C1249T						.						146	124	132					X																	75003638		2203	4300	6503	SO:0001583	missense	139599	exon1			TGACACGGTTGCC	AF490509	CCDS14431.1	Xq13	2008-02-05			ENSG00000186675	ENSG00000186675			24935	protein-coding gene	gene with protein product		300760				11454705	Standard	NM_138703		Approved	HCA3	uc004ecj.2	Q8TD90	OTTHUMG00000021870	ENST00000373359.2:c.1249C>T	chrX.hg19:g.75003638G>A	ENSP00000362457:p.Arg417Cys	96.0	0.0		91.0	62.0	NM_138703	Q5JSI5	Missense_Mutation	SNP	ENST00000373359.2	hg19	CCDS14431.1	.	.	.	.	.	.	.	.	.	.	G	10.23	1.292589	0.23564	.	.	ENSG00000186675	ENST00000373359	T	0.04862	3.54	2.5	1.62	0.23740	.	.	.	.	.	T	0.03608	0.0103	N	0.16708	0.43	0.37083	D	0.899066	B	0.29671	0.254	B	0.24848	0.056	T	0.44174	-0.9345	9	0.56958	D	0.05	.	4.583	0.12267	0.1922:0.0:0.8078:0.0	.	417	Q8TD90	MAGE2_HUMAN	C	417	ENSP00000362457:R417C	ENSP00000362457:R417C	R	-	1	0	MAGEE2	74920363	1.000000	0.71417	0.988000	0.46212	0.697000	0.40408	1.339000	0.33885	0.468000	0.27243	0.422000	0.28245	CGT	.	.		0.473	MAGEE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057288.1	NM_138703		A	75003638	G	A	75003638	3	1	287	1	0	0	0	0	1	0	0	0	9195	1116	39	1	326	1	MAGEE2	23	75003638	Missense_Mutation	SNP	G	TCGA-G3-A5SL-01A-11D-A27I-10		75003638	80266922	116	42214										
SESN2	83667	hgsc.bcm.edu	37	chr1	28598805	28598805	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	acctccgcaggctgccgcccGccatcagtgttcttacctgg	10	17	2	0			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr1:28598805G>A	ENST00000253063.3	+	4	686	c.365G>A	c.(364-366)cGc>cAc	p.R122H		NM_031459.4	NP_113647.1	P58004	SESN2_HUMAN	sestrin 2	122					autophagy (GO:0006914)|fatty acid beta-oxidation (GO:0006635)|glucose import (GO:0046323)|mitochondrial DNA metabolic process (GO:0032042)|protein kinase B signaling (GO:0043491)|regulation of cAMP-dependent protein kinase activity (GO:2000479)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of response to reactive oxygen species (GO:1901031)|response to glucose (GO:0009749)|response to insulin (GO:0032868)|triglyceride homeostasis (GO:0070328)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|endometrium(3)|large_intestine(5)|lung(7)|ovary(2)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	27		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;4.76e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;2.98e-22)|Colorectal(126;3.04e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00279)|STAD - Stomach adenocarcinoma(196;0.00303)|BRCA - Breast invasive adenocarcinoma(304;0.00595)|READ - Rectum adenocarcinoma(331;0.0649)		GCTGCCGCCCGCCATCAGTGT	0.642																																					p.R122H		Atlas-SNP	.											SESN2,NS,carcinoma,0,2	SESN2	51	.	0			c.G365A						.						61	62	62					1																	28598805		2203	4300	6503	SO:0001583	missense	83667	exon4			CCGCCCGCCATCA	AY123223	CCDS321.1	1p35.2	2008-02-05			ENSG00000130766	ENSG00000130766			20746	protein-coding gene	gene with protein product		607767				12607115, 12203114	Standard	NM_031459		Approved	SES2, DKFZp761M0212, HI95, SEST2	uc001bps.3	P58004	OTTHUMG00000003532	ENST00000253063.3:c.365G>A	chr1.hg19:g.28598805G>A	ENSP00000253063:p.Arg122His	68.0	0.0		51.0	10.0	NM_031459	Q5T7D0|Q96SI5	Missense_Mutation	SNP	ENST00000253063.3	hg19	CCDS321.1	.	.	.	.	.	.	.	.	.	.	G	31	5.059292	0.93846	.	.	ENSG00000130766	ENST00000253063	T	0.52295	0.67	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.73713	0.3622	M	0.85777	2.775	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.78071	-0.2347	10	0.87932	D	0	-31.6762	18.9052	0.92458	0.0:0.0:1.0:0.0	.	122	P58004	SESN2_HUMAN	H	122	ENSP00000253063:R122H	ENSP00000253063:R122H	R	+	2	0	SESN2	28471392	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.557000	0.82243	2.568000	0.86640	0.591000	0.81541	CGC	.	.		0.642	SESN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009840.1			A	28598805	G	A	28598805	3	1	288	1	0	0	0	0	1	0	0	0	14140	1087	38	1	379	1	SESN2	1	28598805	Missense_Mutation	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10		28598805	220651816	1	42215										
TTF2	8458	hgsc.bcm.edu	37	chr1	117644020	117644020	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	agatttgtttgtgagggaacAgtagaagaaaagatcttaca	11	3	1	5			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr1:117644020A>G	ENST00000369466.4	+	23	3407	c.3363A>G	c.(3361-3363)acA>acG	p.T1121T	TTF2_ENST00000480701.1_3'UTR	NM_003594.3	NP_003585.3	Q9UNY4	TTF2_HUMAN	transcription termination factor, RNA polymerase II	1121	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(24)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	50	Lung SC(450;0.225)	all_cancers(81;4.23e-06)|all_epithelial(167;3.65e-07)|all_lung(203;2.81e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0553)|Colorectal(144;0.179)|LUSC - Lung squamous cell carcinoma(189;0.19)		GTGAGGGAACAGTAGAAGAAA	0.338																																					p.T1121T		Atlas-SNP	.											.	TTF2	92	.	0			c.A3363G						.						88	101	97					1																	117644020		2203	4300	6503	SO:0001819	synonymous_variant	8458	exon23			GGGAACAGTAGAA	AF073771	CCDS892.1	1p13.1	2014-02-18			ENSG00000116830	ENSG00000116830			12398	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 6"	604718				9748214	Standard	NM_003594		Approved	HuF2, ZGRF6	uc001egy.3	Q9UNY4	OTTHUMG00000012030	ENST00000369466.4:c.3363A>G	chr1.hg19:g.117644020A>G		21.0	0.0		24.0	8.0	NM_003594	A8K4Q2|O75921|Q5T2K7|Q5VVU8|Q8N6I8	Silent	SNP	ENST00000369466.4	hg19	CCDS892.1																																																																																			.	.		0.338	TTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033277.3			G	117644020	A	G	117644020	2	3	288	1	0	0	0	0	0	0	0	1	16734	175	7	2		2	TTF2	1	117644020	Silent	SNP	A	TCGA-G3-A5SM-01A-12D-A28X-10	89045215	117644020	131606601	2	42216										
C1orf125	126859	hgsc.bcm.edu	37	chr1	179504037	179504037	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	gagaagtaaaagaagaagaaGaacaacaagaagaagaagaa	11	2	0	9	rs200097954|rs368406759|rs6425573	byFrequency	TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr1:179504037G>C	ENST00000367618.3	+	25	3358	c.2971G>C	c.(2971-2973)Gaa>Caa	p.E991Q		NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	991	Glu-rich.		E -> Q (in dbSNP:rs6425573).					p.E991_Q992delEQ(1)		NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(27)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	59						agaagaagaagaacaacaaga	0.318													G|||	14	0.00279553	0	0.0058	5008	,	,		17137	0.002		0.004	False		,,,				2504	0.0041				p.E991Q		Atlas-SNP	.											.	AXDND1	142	.	1	Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	c.G2971C						.						49	51	50					1																	179504037		2152	4286	6438	SO:0001583	missense	126859	exon25			GAAGAAGAACAAC	BX647935	CCDS30948.1	1q25.2	2011-02-18	2011-02-18	2011-02-18	ENSG00000162779	ENSG00000162779			26564	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 125"	C1orf125		14702039	Standard	NM_144696		Approved	FLJ32940	uc001gmo.3	Q5T1B0	OTTHUMG00000035266	ENST00000367618.3:c.2971G>C	chr1.hg19:g.179504037G>C	ENSP00000356590:p.Glu991Gln	220.0	0.0		268.0	20.0	NM_144696	Q6AWB2|Q96LJ3|Q96M01	Missense_Mutation	SNP	ENST00000367618.3	hg19	CCDS30948.1	.	.	.	.	.	.	.	.	.	.	G	9.300	1.052898	0.19907	.	.	ENSG00000162779	ENST00000367618;ENST00000360322;ENST00000434088	T;T	0.19105	2.17;2.17	4.89	-6.02	0.02192	.	0.508747	0.16499	N	0.211773	T	0.08980	0.0222	N	0.24115	0.695	0.09310	N	1	B;B	0.24186	0.099;0.099	B;B	0.10450	0.003;0.005	T	0.15838	-1.0423	10	0.28530	T	0.3	-2.8152	6.1976	0.20557	0.4456:0.3814:0.173:0.0	rs6425573	875;991	E9PCJ4;Q5T1B0	.;AXDN1_HUMAN	Q	991;875;851	ENSP00000356590:E991Q;ENSP00000391716:E851Q	ENSP00000353471:E875Q	E	+	1	0	AXDND1	177770660	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.365000	0.20348	-1.164000	0.02790	-1.047000	0.02352	GAA	.	G|1.000;|0.000		0.318	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	NM_144696		C	179504037	G	C	179504037	3	2	288	1	0	0	0	0	1	0	0	0	1995	943	33	4	3065	4	C1orf125	1	179504037	Missense_Mutation	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	61860017	179504037	69746584	3	42217										
CR2	1380	hgsc.bcm.edu	37	chr1	207644362	207644362	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	tggcagcgtgtgaagctacaGgaaggcaactcttgacaaaa	12	8	1	2			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr1:207644362G>A	ENST00000367058.3	+	8	1612	c.1423G>A	c.(1423-1425)Gga>Aga	p.G475R	CR2_ENST00000367059.3_Missense_Mutation_p.G475R|CR2_ENST00000458541.2_Missense_Mutation_p.G475R|CR2_ENST00000367057.3_Missense_Mutation_p.G475R	NM_001877.4	NP_001868.2	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus) receptor 2	475	Sushi 8. {ECO:0000255|PROSITE- ProRule:PRU00302}.				B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|complement activation, classical pathway (GO:0006958)|immune response (GO:0006955)|innate immune response (GO:0045087)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	complement binding (GO:0001848)|complement receptor activity (GO:0004875)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|breast(3)|endometrium(4)|kidney(3)|large_intestine(12)|lung(26)|ovary(1)|pancreas(1)|prostate(1)|skin(12)|upper_aerodigestive_tract(3)|urinary_tract(1)	69						TGAAGCTACAGGAAGGCAACT	0.433																																					p.G475R		Atlas-SNP	.											.	CR2	164	.	0			c.G1423A						.						157	151	153					1																	207644362		2203	4300	6503	SO:0001583	missense	1380	exon8			GCTACAGGAAGGC	M26004	CCDS1478.1, CCDS31007.1	1q32	2014-09-17			ENSG00000117322	ENSG00000117322		"CD molecules", "Complement system"	2336	protein-coding gene	gene with protein product		120650					Standard	NM_001006658		Approved	CD21	uc001hfv.3	P20023	OTTHUMG00000036307	ENST00000367058.3:c.1423G>A	chr1.hg19:g.207644362G>A	ENSP00000356025:p.Gly475Arg	192.0	0.0		238.0	27.0	NM_001006658	C9JHD2|Q13866|Q14212|Q53EL2|Q5BKT9|Q5SR46|Q5SR48	Missense_Mutation	SNP	ENST00000367058.3	hg19	CCDS1478.1	.	.	.	.	.	.	.	.	.	.	G	12.87	2.067016	0.36470	.	.	ENSG00000117322	ENST00000367058;ENST00000367057;ENST00000367059;ENST00000458541	T;T;T;T	0.35048	1.39;1.33;1.4;1.39	4.89	4.89	0.63831	Sushi/SCR/CCP (1);	.	.	.	.	T	0.48768	0.1518	L	0.51422	1.61	0.09310	N	1	P;P;P	0.47191	0.644;0.458;0.891	P;P;P	0.55222	0.585;0.532;0.771	T	0.34925	-0.9809	9	0.49607	T	0.09	.	14.284	0.66232	0.0:0.0:1.0:0.0	.	475;475;475	Q5SR47;P20023;P20023-3	.;CR2_HUMAN;.	R	475	ENSP00000356025:G475R;ENSP00000356024:G475R;ENSP00000356026:G475R;ENSP00000404222:G475R	ENSP00000356024:G475R	G	+	1	0	CR2	205710985	0.175000	0.23083	0.008000	0.14137	0.002000	0.02628	3.872000	0.56085	2.646000	0.89796	0.655000	0.94253	GGA	.	.		0.433	CR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000088274.1	NM_001877		A	207644362	G	A	207644362	3	1	288	1	0	0	0	0	1	0	0	0	3844	1001	35	3	1453	3	CR2	1	207644362	Missense_Mutation	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	28140325	207644362	41606259	4	42218										
KIF26B	55083	hgsc.bcm.edu	37	chr1	245849809	245849809	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	cctgagcaccacgatggtgaCggtgcagcagccactggagc	14	13	0	2	rs202113373		TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr1:245849809C>T	ENST00000407071.2	+	12	3964	c.3524C>T	c.(3523-3525)aCg>aTg	p.T1175M	KIF26B_ENST00000366518.4_Missense_Mutation_p.T794M	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	1175					establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			ACGATGGTGACGGTGCAGCAG	0.627																																					p.T1175M		Atlas-SNP	.											.	KIF26B	343	.	0			c.C3524T						.	C	MET/THR	0,4374		0,0,2187	27	34	32		3524	5.8	1	1		32	1,8533		0,1,4266	yes	missense	KIF26B	NM_018012.3	81	0,1,6453	TT,TC,CC		0.0117,0.0,0.0077	probably-damaging	1175/2109	245849809	1,12907	2187	4267	6454	SO:0001583	missense	55083	exon12			TGGTGACGGTGCA	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"Kinesins"	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.3524C>T	chr1.hg19:g.245849809C>T	ENSP00000385545:p.Thr1175Met	134.0	0.0		177.0	17.0	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Missense_Mutation	SNP	ENST00000407071.2	hg19	CCDS44342.1	.	.	.	.	.	.	.	.	.	.	C	15.42	2.827666	0.50845	0.0	1.17E-4	ENSG00000162849	ENST00000407071;ENST00000366518;ENST00000413001	D;D	0.81659	-1.52;-1.52	5.77	5.77	0.91146	.	.	.	.	.	T	0.77864	0.4194	M	0.62088	1.915	0.39707	D	0.97127	D;D	0.53312	0.959;0.959	B;B	0.35655	0.207;0.207	T	0.82252	-0.0549	9	0.54805	T	0.06	.	19.9961	0.97386	0.0:1.0:0.0:0.0	.	794;1175	B7WPD9;Q2KJY2	.;KI26B_HUMAN	M	1175;794;791	ENSP00000385545:T1175M;ENSP00000355475:T794M	ENSP00000355475:T794M	T	+	2	0	KIF26B	243916432	0.997000	0.39634	0.957000	0.39632	0.974000	0.67602	3.441000	0.52893	2.744000	0.94065	0.561000	0.74099	ACG	.	.		0.627	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354		T	245849809	C	T	245849809	3	4	288	1	0	0	0	0	1	0	0	0	8304	536	19	1	3570	1	KIF26B	1	245849809	Missense_Mutation	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	38205447	245849809	3400812	5	42219										
EXOC6B	23233	hgsc.bcm.edu	37	chr2	72692418	72692418	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	agctgtaggaactggtcaatCttctggtttaagttggtata	11	5	3	0			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr2:72692418C>A	ENST00000272427.6	-	18	1981	c.1851G>T	c.(1849-1851)aaG>aaT	p.K617N	EXOC6B_ENST00000410104.1_Missense_Mutation_p.K617N	NM_015189.1	NP_056004.1	Q9Y2D4	EXC6B_HUMAN	exocyst complex component 6B	617					protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	exocyst (GO:0000145)				breast(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	10						ACTGGTCAATCTTCTGGTTTA	0.398																																					p.K617N		Atlas-SNP	.											.	EXOC6B	93	.	0			c.G1851T						.						120	116	118					2																	72692418		1925	4131	6056	SO:0001583	missense	23233	exon18			GTCAATCTTCTGG	AB023136	CCDS46333.1	2p13.2	2013-01-22	2006-11-07	2006-11-07	ENSG00000144036	ENSG00000144036			17085	protein-coding gene	gene with protein product		607880	"SEC15-like 2 (S. cerevisiae)", "SEC15 homolog B (S. cerevisiae)"	SEC15L2, SEC15B		10231032, 11406615	Standard	NM_015189		Approved	KIAA0919	uc010fep.3	Q9Y2D4	OTTHUMG00000152723	ENST00000272427.6:c.1851G>T	chr2.hg19:g.72692418C>A	ENSP00000272427:p.Lys617Asn	149.0	0.0		136.0	57.0	NM_015189	B8ZZY3	Missense_Mutation	SNP	ENST00000272427.6	hg19	CCDS46333.1	.	.	.	.	.	.	.	.	.	.	C	18.80	3.700731	0.68501	.	.	ENSG00000144036	ENST00000272427;ENST00000410104;ENST00000290144	T;T	0.59364	0.27;0.27	5.33	2.55	0.30701	.	0.000000	0.85682	D	0.000000	T	0.74854	0.3771	M	0.85859	2.78	0.80722	D	1	P;D	0.76494	0.503;0.999	B;D	0.81914	0.175;0.995	T	0.75235	-0.3389	10	0.87932	D	0	.	9.7205	0.40300	0.0:0.7715:0.0:0.2285	.	617;617	Q9Y2D4;Q9Y2D4-2	EXC6B_HUMAN;.	N	617	ENSP00000272427:K617N;ENSP00000386698:K617N	ENSP00000272427:K617N	K	-	3	2	EXOC6B	72545926	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.111000	0.41883	0.328000	0.23435	0.591000	0.81541	AAG	.	.		0.398	EXOC6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327558.1	XM_039570		A	72692418	C	A	72692418	3	1	288	1	0	0	0	0	1	0	0	0	5311	912	32	3	604	3	EXOC6B	2	72692418	Missense_Mutation	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10		72692418	170506955	6	42220										
RGPD4	285190	hgsc.bcm.edu	37	chr2	108488192	108488192	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	cccaatcctgaaaacactggGcccacattagaatgggataa	8	11	0	2			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr2:108488192G>C	ENST00000408999.3	+	20	3809	c.3732G>C	c.(3730-3732)ggG>ggC	p.G1244G	RGPD4_ENST00000354986.4_Silent_p.G1244G	NM_182588.2	NP_872394.2	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4	1244					protein targeting to Golgi (GO:0000042)					breast(1)|endometrium(7)|kidney(4)|lung(23)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(3)	43						AAAACACTGGGCCCACATTAG	0.448																																					p.G1244G		Atlas-SNP	.											.	RGPD4	112	.	0			c.G3732C						.						57	44	48					2																	108488192		692	1590	2282	SO:0001819	synonymous_variant	285190	exon20			CACTGGGCCCACA	BX537861	CCDS46381.1	2q12.3	2013-01-10			ENSG00000196862	ENSG00000196862		"Tetratricopeptide (TTC) repeat domain containing"	32417	protein-coding gene	gene with protein product		612707				15710750, 15815621	Standard	NM_182588		Approved	RGP4, DKFZp686P0288	uc010ywk.2	Q7Z3J3	OTTHUMG00000153208	ENST00000408999.3:c.3732G>C	chr2.hg19:g.108488192G>C		493.0	0.0		508.0	80.0	NM_182588	B9A029	Silent	SNP	ENST00000408999.3	hg19	CCDS46381.1																																																																																			.	.		0.448	RGPD4-001	NOVEL	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330096.2	XM_496581		C	108488192	G	C	108488192	2	2	288	1	0	0	0	0	0	0	0	1	13303	1190	42	4		4	RGPD4	2	108488192	Silent	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	35795774	108488192	134711181	7	42221										
DAPL1	92196	hgsc.bcm.edu	37	chr2	159651944	159651944	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	gggggacatcctcctgcaggTaggctgccacctgccctcag	13	15	1	0			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr2:159651944T>A	ENST00000309950.3	+	1	114		c.e1+2		DAPL1_ENST00000409042.1_Splice_Site	NM_001017920.2	NP_001017920.2	A0PJW8	DAPL1_HUMAN	death associated protein-like 1						apoptotic process (GO:0006915)|cell differentiation (GO:0030154)					prostate(1)	1						CTCCTGCAGGTAGGCTGCCAC	0.607																																					.		Atlas-SNP	.											.	DAPL1	11	.	0			c.58+2T>A						.						60	36	44					2																	159651944		2190	4270	6460	SO:0001630	splice_region_variant	92196	exon1			TGCAGGTAGGCTG		CCDS33307.1	2q24	2007-06-26			ENSG00000163331	ENSG00000163331			21490	protein-coding gene	gene with protein product							Standard	NM_001017920		Approved		uc002uaf.3	A0PJW8	OTTHUMG00000153970	ENST00000309950.3:c.58+2T>A	chr2.hg19:g.159651944T>A		271.0	0.0		237.0	32.0	NM_001017920	A0PJW9|B9EIK6	Splice_Site	SNP	ENST00000309950.3	hg19	CCDS33307.1	.	.	.	.	.	.	.	.	.	.	T	18.10	3.549625	0.65311	.	.	ENSG00000163331	ENST00000309950;ENST00000409042	.	.	.	5.85	5.85	0.93711	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.6221	0.56610	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	DAPL1	159360190	1.000000	0.71417	1.000000	0.80357	0.865000	0.49528	3.736000	0.55052	2.233000	0.73108	0.533000	0.62120	.	.	.		0.607	DAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333265.1	NM_001017920	Intron	A	159651944	T	A	159651944	5	1	288	1	0	0	0	0	0	0	1	0	4240	1652	57	4	62	4	DAPL1	2	159651944	Splice_Site	SNP	T	TCGA-G3-A5SM-01A-12D-A28X-10	51163752	159651944	83547429	8	42222										
LY75	4065	hgsc.bcm.edu	37	chr2	160664981	160664981	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	aacagaatgttgagataatcCaagccaaactctcatggtaa	7	8	1	2			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr2:160664981C>T	ENST00000263636.4	-	33	4828	c.4801G>A	c.(4801-4803)Gga>Aga	p.G1601R	LY75_ENST00000554112.1_Missense_Mutation_p.G1601R|LY75-CD302_ENST00000505052.1_Missense_Mutation_p.G1601R|LY75_ENST00000553424.1_Missense_Mutation_p.G1601R|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.G1601R	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	1601	C-type lectin 10. {ECO:0000255|PROSITE- ProRule:PRU00040}.				endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		TGAGATAATCCAAGCCAAACT	0.348																																					p.G1601R		Atlas-SNP	.											.	LY75	151	.	0			c.G4801A						.						209	203	205					2																	160664981		2202	4299	6501	SO:0001583	missense	4065	exon33			ATAATCCAAGCCA	AF011333	CCDS2211.1	2q24	2011-08-30			ENSG00000054219	ENSG00000054219		"CD molecules", "C-type lectin domain containing"	6729	protein-coding gene	gene with protein product		604524				9553150	Standard	NM_002349		Approved	DEC-205, CLEC13B, CD205		O60449	OTTHUMG00000132025	ENST00000263636.4:c.4801G>A	chr2.hg19:g.160664981C>T	ENSP00000263636:p.Gly1601Arg	94.0	0.0		104.0	20.0	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	hg19	CCDS2211.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.452915	0.84209	.	.	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.38077	1.16;1.16;1.16;1.16;1.16	5.55	5.55	0.83447	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.000000	0.33057	U	0.005337	T	0.72374	0.3452	H	0.94620	3.56	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	T	0.80701	-0.1265	10	0.87932	D	0	-17.6567	19.0954	0.93248	0.0:1.0:0.0:0.0	.	1601;1601;1601	O60449-3;O60449;O60449-2	.;LY75_HUMAN;.	R	1601	ENSP00000451511:G1601R;ENSP00000451446:G1601R;ENSP00000263636:G1601R;ENSP00000423463:G1601R;ENSP00000421035:G1601R	ENSP00000423463:G1601R	G	-	1	0	LY75;LY75-CD302	160373227	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	5.165000	0.64959	2.606000	0.88127	0.491000	0.48974	GGA	.	.		0.348	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1			T	160664981	C	T	160664981	3	4	288	1	0	0	0	0	1	0	0	0	9108	603	21	3	379	3	LY75	2	160664981	Missense_Mutation	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	1013037	160664981	82534392	9	42223										
TTN	7273	hgsc.bcm.edu	37	chr2	179560835	179560835	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	tggttctacctccagttcgtCataaggttcttcgaaagatt	8	9	3	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr2:179560835C>T	ENST00000591111.1	-	112	30237	c.30013G>A	c.(30013-30015)Gac>Aac	p.D10005N	TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.D10322N|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.D9078N|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589830.1_RNA			Q8WZ42	TITIN_HUMAN	titin	0	Glu-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCCAGTTCGTCATAAGGTTCT	0.373																																					p.D10322N		Atlas-SNP	.											.	TTN	18412	.	0			c.G30964A						.						131	110	117					2																	179560835		1781	3897	5678	SO:0001583	missense	7273	exon114			GTTCGTCATAAGG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.30013G>A	chr2.hg19:g.179560835C>T	ENSP00000465570:p.Asp10005Asn	140.0	0.0		116.0	38.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	17.96	3.516402	0.64634	.	.	ENSG00000155657	ENST00000342992;ENST00000414766	T	0.64438	-0.1	5.78	5.78	0.91487	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.60366	0.2263	L	0.47716	1.5	0.80722	D	1	B;P	0.37330	0.048;0.59	B;B	0.39904	0.031;0.313	T	0.64343	-0.6430	9	0.87932	D	0	.	15.5205	0.75862	0.0:1.0:0.0:0.0	.	10005;10005	Q8WZ42;Q8WZ42-5	TITIN_HUMAN;.	N	9078;200	ENSP00000343764:D9078N	ENSP00000343764:D9078N	D	-	1	0	TTN	179269080	0.995000	0.38212	0.765000	0.31456	0.871000	0.50021	3.839000	0.55835	2.729000	0.93468	0.650000	0.86243	GAC	.	.		0.373	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179560835	C	T	179560835	3	4	288	1	0	0	0	0	1	0	0	0	16750	826	29	3	73561	3	TTN	2	179560835	Missense_Mutation	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	18895854	179560835	63638538	10	42224										
CRYGD	1421	hgsc.bcm.edu	37	chr2	208988981	208988981	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	agcagccgctgtccacgcgcGccgagttgcagcggctcaag	14	15	1	0	rs200234608		TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr2:208988981G>A	ENST00000264376.4	-	2	134	c.107C>T	c.(106-108)gCg>gTg	p.A36V		NM_006891.3	NP_008822.2	P07320	CRGD_HUMAN	crystallin, gamma D	36	Beta/gamma crystallin 'Greek key' 1. {ECO:0000255|PROSITE-ProRule:PRU00028}.				cellular response to reactive oxygen species (GO:0034614)|lens development in camera-type eye (GO:0002088)|lens fiber cell differentiation (GO:0070306)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	structural constituent of eye lens (GO:0005212)			breast(1)|endometrium(1)|lung(3)	5				LUSC - Lung squamous cell carcinoma(261;0.0703)|Epithelial(149;0.0858)|Lung(261;0.133)		GTCCACGCGCGCCGAGTTGCA	0.652																																					p.A36V		Atlas-SNP	.											CRYGD,NS,neuroblastoma,0,1	CRYGD	18	.	0			c.C107T						.						11	13	12					2																	208988981		2179	4274	6453	SO:0001583	missense	1421	exon2			ACGCGCGCCGAGT		CCDS2378.1	2q33.3	2013-02-14			ENSG00000118231	ENSG00000118231			2411	protein-coding gene	gene with protein product		123690		CRYG4			Standard	NM_006891		Approved		uc002vcn.4	P07320	OTTHUMG00000132944	ENST00000264376.4:c.107C>T	chr2.hg19:g.208988981G>A	ENSP00000264376:p.Ala36Val	187.0	2.0		135.0	8.0	NM_006891	Q17RF7|Q53R51|Q99681	Missense_Mutation	SNP	ENST00000264376.4	hg19	CCDS2378.1	.	.	.	.	.	.	.	.	.	.	G	11.40	1.627591	0.28978	.	.	ENSG00000118231	ENST00000264376	T	0.72051	-0.62	4.35	3.19	0.36642	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.184420	0.36703	N	0.002444	T	0.29389	0.0732	N	0.00166	-1.94	0.09310	N	0.999995	B	0.02656	0.0	B	0.01281	0.0	T	0.34875	-0.9811	10	0.32370	T	0.25	.	8.1681	0.31239	0.9021:0.0:0.0979:0.0	.	36	P07320	CRGD_HUMAN	V	36	ENSP00000264376:A36V	ENSP00000264376:A36V	A	-	2	0	CRYGD	208697226	0.280000	0.24249	0.067000	0.19924	0.966000	0.64601	2.073000	0.41519	0.695000	0.31675	-0.573000	0.04149	GCG	.	G|0.998;A|0.002		0.652	CRYGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256476.2	NM_006891		A	208988981	G	A	208988981	3	1	288	1	0	0	0	0	1	0	0	0	3919	1087	38	1	425	1	CRYGD	2	208988981	Missense_Mutation	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	29428146	208988981	34210392	11	42225										
CHRND	1144	hgsc.bcm.edu	37	chr2	233390976	233390976	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	ctggctgccctggcggtgtgTggtaagggaagacaccctcc	15	12	0	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr2:233390976T>C	ENST00000258385.3	+	1	83	c.51T>C	c.(49-51)tgT>tgC	p.C17C	CHRND_ENST00000457943.2_5'UTR|CHRND_ENST00000536614.1_Splice_Site_p.C17C|CHRND_ENST00000543200.1_Splice_Site_p.C17C	NM_000751.2	NP_000742.1	Q07001	ACHD_HUMAN	cholinergic receptor, nicotinic, delta (muscle)	17					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|muscle contraction (GO:0006936)|musculoskeletal movement (GO:0050881)|neuromuscular process (GO:0050905)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|skeletal muscle tissue growth (GO:0048630)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)	34		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;1.89e-16)|BRCA - Breast invasive adenocarcinoma(100;0.00078)|Lung(119;0.00579)|LUSC - Lung squamous cell carcinoma(224;0.00754)	Galantamine(DB00674)	TGGCGGTGTGTGGTAAGGGAA	0.657																																					p.C17C		Atlas-SNP	.											.	CHRND	67	.	0			c.T51C						.						56	54	55					2																	233390976		2203	4300	6503	SO:0001630	splice_region_variant	1144	exon1			GGTGTGTGGTAAG	X55019	CCDS2494.1, CCDS58754.1	2q37.1	2012-02-11	2012-02-07		ENSG00000135902	ENSG00000135902		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1965	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, delta (muscle)"	100720	"cholinergic receptor, nicotinic, delta"	ACHRD			Standard	NM_000751		Approved		uc002vsw.4	Q07001	OTTHUMG00000133261	ENST00000258385.3:c.52+1T>C	chr2.hg19:g.233390976T>C		197.0	0.0		214.0	24.0	NM_000751	A8K661|B4DT92|Q52LH4	Silent	SNP	ENST00000258385.3	hg19	CCDS2494.1																																																																																			.	.		0.657	CHRND-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257038.2		Silent	C	233390976	T	C	233390976	5	2	288	1	0	0	0	0	0	0	1	0	3396	1710	59	2	53	2	CHRND	2	233390976	Splice_Site	SNP	T	TCGA-G3-A5SM-01A-12D-A28X-10	24401995	233390976	9808397	12	42226										
CHL1	10752	hgsc.bcm.edu	37	chr3	403447	403447	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	cagtggttgggtacagtgctTtcttacattgcgagttcttt	11	7	2	0			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr3:403447T>C	ENST00000256509.2	+	13	2014	c.1372T>C	c.(1372-1374)Ttc>Ctc	p.F458L	CHL1-AS1_ENST00000608098.1_RNA|CHL1-AS1_ENST00000417612.1_RNA|CHL1_ENST00000397491.2_Missense_Mutation_p.F442L	NM_001253387.1|NM_001253388.1|NM_006614.3	NP_001240316.1|NP_001240317.1|NP_006605.2	Q96FC9	DDX11_HUMAN	cell adhesion molecule L1-like	0					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			NS(1)|central_nervous_system(5)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|lung(31)|ovary(1)|prostate(4)|skin(10)|stomach(1)	93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		GTACAGTGCTTTCTTACATTG	0.403																																					p.F458L		Atlas-SNP	.											.	CHL1	242	.	0			c.T1372C						.						239	224	229					3																	403447		2203	4300	6503	SO:0001583	missense	10752	exon11			AGTGCTTTCTTAC	AF002246	CCDS2556.1, CCDS58812.1, CCDS74887.1	3p26	2013-05-01	2013-05-01		ENSG00000134121	ENSG00000134121		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	1939	protein-coding gene	gene with protein product	"neural cell adhesion molecule", "close homolog of L1"	607416	"cell adhesion molecule with homology to L1CAM (close homologue of L1)", "cell adhesion molecule with homology to L1CAM (close homolog of L1)"			9799093	Standard	NM_006614		Approved	CALL, L1CAM2, FLJ44930, MGC132578	uc003bot.3	O00533	OTTHUMG00000090601	ENST00000256509.2:c.1372T>C	chr3.hg19:g.403447T>C	ENSP00000256509:p.Phe458Leu	126.0	0.0		126.0	59.0	NM_001253388	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000256509.2	hg19	CCDS2556.1	.	.	.	.	.	.	.	.	.	.	T	6.380	0.438243	0.12104	.	.	ENSG00000134121	ENST00000256509;ENST00000397491	T;T	0.25912	1.77;1.77	5.24	5.24	0.73138	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.103501	0.64402	D	0.000002	T	0.13927	0.0337	N	0.21097	0.63	0.33495	D	0.589144	B;B;B	0.24186	0.008;0.008;0.099	B;B;B	0.25291	0.034;0.034;0.059	T	0.15206	-1.0445	10	0.02654	T	1	.	9.0535	0.36392	0.0:0.0846:0.0:0.9153	.	442;442;458	B3KX75;O00533;O00533-2	.;CHL1_HUMAN;.	L	458;442	ENSP00000256509:F458L;ENSP00000380628:F442L	ENSP00000256509:F458L	F	+	1	0	CHL1	378447	0.922000	0.31269	0.607000	0.28956	0.912000	0.54170	2.115000	0.41921	2.095000	0.63458	0.460000	0.39030	TTC	.	.		0.403	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614		C	403447	T	C	403447	3	2	288	1	0	0	0	0	1	0	0	0	3351	1841	64	2	1414	2	CHL1	3	403447	Missense_Mutation	SNP	T	TCGA-G3-A5SM-01A-12D-A28X-10		403447	197618983	13	42227										
FGD5	152273	hgsc.bcm.edu	37	chr3	14862981	14862981	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	gccagggctggcgcgttcacGaagctgtttgaagatcagag	15	9	2	3			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr3:14862981G>T	ENST00000285046.5	+	1	2513	c.2403G>T	c.(2401-2403)acG>acT	p.T801T	FGD5_ENST00000543601.1_Silent_p.T560T	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	801					actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			NS(2)|breast(2)|endometrium(3)|kidney(5)|large_intestine(10)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(1)	54						GCGCGTTCACGAAGCTGTTTG	0.522																																					p.T801T		Atlas-SNP	.											.	FGD5	248	.	0			c.G2403T						.						86	90	89					3																	14862981		2076	4234	6310	SO:0001819	synonymous_variant	152273	exon1			GTTCACGAAGCTG	AK097276	CCDS46767.1	3p25.1	2013-01-10			ENSG00000154783	ENSG00000154783		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	19117	protein-coding gene	gene with protein product		614788					Standard	NM_152536		Approved	ZFYVE23, FLJ39957, FLJ00274	uc003bzc.3	Q6ZNL6	OTTHUMG00000155556	ENST00000285046.5:c.2403G>T	chr3.hg19:g.14862981G>T		81.0	0.0		80.0	32.0	NM_152536	B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	Silent	SNP	ENST00000285046.5	hg19	CCDS46767.1	.	.	.	.	.	.	.	.	.	.	G	4.897	0.166768	0.09339	.	.	ENSG00000154783	ENST00000457774	.	.	.	5.03	-7.79	0.01218	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-25.8753	1.4612	0.02396	0.3217:0.3005:0.2279:0.1499	.	.	.	.	X	15	.	.	E	+	1	0	FGD5	14837985	0.000000	0.05858	0.775000	0.31657	0.710000	0.40934	-5.607000	0.00110	-1.205000	0.02645	-0.229000	0.12294	GAA	.	.		0.522	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340628.1	NM_152536		T	14862981	G	T	14862981	2	4	288	1	0	0	0	0	0	0	0	1	5844	1045	37	1		1	FGD5	3	14862981	Silent	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	14459534	14862981	183159449	14	42228										
SLC22A14	9389	hgsc.bcm.edu	37	chr3	38357904	38357904	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	ccagaccccctccctcctgcCcatctttctctgctgcgtct	5	21	3	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr3:38357904C>A	ENST00000273173.4	+	9	1713	c.1622C>A	c.(1621-1623)cCc>cAc	p.P541H	SLC22A14_ENST00000448498.1_Missense_Mutation_p.P541H	NM_004803.3	NP_004794.2	Q9Y267	S22AE_HUMAN	solute carrier family 22, member 14	541					organic cation transport (GO:0015695)	integral component of plasma membrane (GO:0005887)	organic cation transmembrane transporter activity (GO:0015101)			central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(5)|prostate(2)|skin(1)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0554)|Kidney(284;0.0696)		TCCCTCCTGCCCATCTTTCTC	0.617																																					p.P541H		Atlas-SNP	.											.	SLC22A14	64	.	0			c.C1622A						.						121	91	101					3																	38357904		2203	4300	6503	SO:0001583	missense	9389	exon9			TCCTGCCCATCTT	AB011082	CCDS2677.1	3p21.3	2013-05-22	2008-01-11	2003-10-15	ENSG00000144671	ENSG00000144671		"Solute carriers"	8495	protein-coding gene	gene with protein product		604048	"organic cationic transporter-like 4", "solute carrier family 22 (organic cation transporter), member 14"	ORCTL4		10072596	Standard	NM_004803		Approved	OCTL2	uc003cib.2	Q9Y267	OTTHUMG00000131082	ENST00000273173.4:c.1622C>A	chr3.hg19:g.38357904C>A	ENSP00000273173:p.Pro541His	87.0	0.0		125.0	25.0	NM_004803	A0AVS9|A1L4H6|B2RCX3|Q6DJT3	Missense_Mutation	SNP	ENST00000273173.4	hg19	CCDS2677.1	.	.	.	.	.	.	.	.	.	.	C	15.48	2.845781	0.51164	.	.	ENSG00000144671	ENST00000448498;ENST00000423219;ENST00000273173	T;T	0.74209	-0.82;-0.82	4.2	4.2	0.49525	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.380298	0.29668	N	0.011513	D	0.86986	0.6065	M	0.88512	2.96	0.09310	N	0.999999	D	0.89917	1.0	D	0.85130	0.997	T	0.78971	-0.1993	10	0.87932	D	0	.	12.3339	0.55056	0.0:1.0:0.0:0.0	.	541	Q9Y267	S22AE_HUMAN	H	541;526;541	ENSP00000396283:P541H;ENSP00000273173:P541H	ENSP00000273173:P541H	P	+	2	0	SLC22A14	38332908	0.006000	0.16342	0.006000	0.13384	0.005000	0.04900	1.816000	0.38992	2.610000	0.88304	0.655000	0.94253	CCC	.	.		0.617	SLC22A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253742.3	NM_004803		A	38357904	C	A	38357904	3	1	288	1	0	0	0	0	1	0	0	0	14460	623	22	3	1656	3	SLC22A14	3	38357904	Missense_Mutation	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	23494923	38357904	159664526	15	42229										
KIF15	56992	hgsc.bcm.edu	37	chr3	44843455	44843455	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	taaggaatgagattcaaactCtgcgagaacaagtgagtata	10	5	2	3			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr3:44843455C>A	ENST00000326047.4	+	13	1647	c.1498C>A	c.(1498-1500)Ctg>Atg	p.L500M	KIF15_ENST00000425755.1_Missense_Mutation_p.L135M	NM_020242.2	NP_064627.1	Q9NS87	KIF15_HUMAN	kinesin family member 15	500					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|plus-end kinesin complex (GO:0005873)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(5)	36				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)		GATTCAAACTCTGCGAGAACA	0.378																																					p.L500M		Atlas-SNP	.											.	KIF15	103	.	0			c.C1498A						.						25	28	27					3																	44843455		2203	4300	6503	SO:0001583	missense	56992	exon13			CAAACTCTGCGAG	AB035898	CCDS33744.1	3p21.31	2008-03-03	2005-03-15	2005-03-17	ENSG00000163808	ENSG00000163808		"Kinesins"	17273	protein-coding gene	gene with protein product			"kinesin-like 7"	KNSL7		10878014	Standard	NM_020242		Approved	HKLP2, NY-BR-62	uc003cnx.4	Q9NS87	OTTHUMG00000156307	ENST00000326047.4:c.1498C>A	chr3.hg19:g.44843455C>A	ENSP00000324020:p.Leu500Met	88.0	0.0		107.0	23.0	NM_020242	Q17RV9|Q69YL6|Q96JX7|Q9H280	Missense_Mutation	SNP	ENST00000326047.4	hg19	CCDS33744.1	.	.	.	.	.	.	.	.	.	.	C	16.45	3.127473	0.56721	.	.	ENSG00000163808	ENST00000326047;ENST00000481166;ENST00000396031;ENST00000425755	T;D;T	0.83506	-0.88;-1.73;0.17	5.32	3.54	0.40534	Kinesin-like, KLP2 (1);	0.000000	0.41097	D	0.000959	D	0.88325	0.6406	M	0.66939	2.045	0.41210	D	0.986435	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.87087	0.2170	10	0.59425	D	0.04	.	9.1616	0.37025	0.0:0.7772:0.0:0.2228	.	135;500	C9JKA9;Q9NS87	.;KIF15_HUMAN	M	500;272;499;135	ENSP00000324020:L500M;ENSP00000425499:L272M;ENSP00000389982:L135M	ENSP00000324020:L500M	L	+	1	2	KIF15	44818459	0.326000	0.24669	0.966000	0.40874	0.963000	0.63663	0.870000	0.28010	0.633000	0.30452	-0.379000	0.06801	CTG	.	.		0.378	KIF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343831.2			A	44843455	C	A	44843455	3	1	288	1	0	0	0	0	1	0	0	0	8286	912	32	3	1548	3	KIF15	3	44843455	Missense_Mutation	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	6485551	44843455	153178975	16	42230										
OR5K4	403278	hgsc.bcm.edu	37	chr3	98073262	98073262	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	ttccactgtatagactctccTgtacagatccttctattaat	4	11	2	2			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr3:98073262T>A	ENST00000354924.2	+	1	565	c.565T>A	c.(565-567)Tgt>Agt	p.C189S	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005517.1	NP_001005517.1	A6NMS3	OR5K4_HUMAN	olfactory receptor, family 5, subfamily K, member 4	189						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(13)|upper_aerodigestive_tract(1)	21						TAGACTCTCCTGTACAGATCC	0.328																																					p.C189S		Atlas-SNP	.											.	OR5K4	75	.	0			c.T565A						.						75	82	80					3																	98073262		2203	4300	6503	SO:0001583	missense	403278	exon1			CTCTCCTGTACAG		CCDS33802.1	3q11.2	2013-09-23			ENSG00000196098	ENSG00000196098		"GPCR / Class A : Olfactory receptors"	31291	protein-coding gene	gene with protein product							Standard	NM_001005517		Approved		uc011bgv.2	A6NMS3	OTTHUMG00000160081	ENST00000354924.2:c.565T>A	chr3.hg19:g.98073262T>A	ENSP00000347003:p.Cys189Ser	79.0	0.0		94.0	21.0	NM_001005517		Missense_Mutation	SNP	ENST00000354924.2	hg19	CCDS33802.1	.	.	.	.	.	.	.	.	.	.	T	15.88	2.962589	0.53400	.	.	ENSG00000196098	ENST00000354924	T	0.00450	7.36	4.82	3.65	0.41850	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35466	U	0.003181	T	0.01156	0.0038	M	0.87617	2.895	0.32590	N	0.527343	D	0.67145	0.996	D	0.72075	0.976	T	0.17077	-1.0381	10	0.72032	D	0.01	-37.8397	8.734	0.34516	0.0:0.0914:0.0:0.9086	.	189	A6NMS3	OR5K4_HUMAN	S	189	ENSP00000347003:C189S	ENSP00000347003:C189S	C	+	1	0	OR5K4	99555952	1.000000	0.71417	0.872000	0.34217	0.752000	0.42762	7.116000	0.77119	0.950000	0.37743	0.491000	0.48974	TGT	.	.		0.328	OR5K4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359114.1			A	98073262	T	A	98073262	3	1	288	1	0	0	0	0	1	0	0	0	11178	1580	55	4	567	4	OR5K4	3	98073262	Missense_Mutation	SNP	T	TCGA-G3-A5SM-01A-12D-A28X-10	53229807	98073262	99949168	17	42231										
BBX	56987	hgsc.bcm.edu	37	chr3	107491987	107491987	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	tccacacccaagaagacttgCaaaaagaggcagtcttcgga	9	11	1	3			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr3:107491987C>T	ENST00000325805.8	+	11	1706	c.1419C>T	c.(1417-1419)tgC>tgT	p.C473C	BBX_ENST00000402543.1_Silent_p.C473C|BBX_ENST00000406780.1_Silent_p.C473C|BBX_ENST00000415149.2_Silent_p.C473C|BBX_ENST00000416476.2_Intron			Q8WY36	BBX_HUMAN	bobby sox homolog (Drosophila)	473	Lys-rich.				bone development (GO:0060348)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(18)|ovary(4)|pancreas(1)|skin(2)	49			OV - Ovarian serous cystadenocarcinoma(3;0.112)			AGAAGACTTGCAAAAAGAGGC	0.418																																					p.C473C		Atlas-SNP	.											.	BBX	156	.	0			c.C1419T						.						64	67	66					3																	107491987		2203	4299	6502	SO:0001819	synonymous_variant	56987	exon11			GACTTGCAAAAAG	AF168718	CCDS2950.1, CCDS46881.1, CCDS63712.1	3q13.1	2008-07-18			ENSG00000114439	ENSG00000114439			14422	protein-coding gene	gene with protein product	"x 001 protein"					11680820	Standard	NM_001142568		Approved	MDS001, HSPC339, HBP2	uc010hpr.4	Q8WY36	OTTHUMG00000150360	ENST00000325805.8:c.1419C>T	chr3.hg19:g.107491987C>T		255.0	0.0		265.0	101.0	NM_001142568	A2RRM7|Q2TAJ1|Q7L3J8|Q7LBY8|Q8NDB0|Q8WY35|Q9H0J6	Silent	SNP	ENST00000325805.8	hg19	CCDS46881.1																																																																																			.	.		0.418	BBX-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317820.1	NM_020235		T	107491987	C	T	107491987	2	4	288	1	0	0	0	0	0	0	0	1	1343	718	25	3		3	BBX	3	107491987	Silent	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	9418725	107491987	90530443	18	42232										
CCDC52	152185	hgsc.bcm.edu	37	chr3	113212077	113212077	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	ggttctatgacagactcattAaagatagattgggtgatagg	12	4	2	5			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr3:113212077A>G	ENST00000295872.4	-	6	727	c.468T>C	c.(466-468)ttT>ttC	p.F156F		NM_144718.3	NP_653319.1	Q8N0Z3	SPICE_HUMAN	spindle and centriole associated protein 1	156					metaphase plate congression (GO:0051310)|regulation of centriole replication (GO:0046599)|spindle assembly involved in mitosis (GO:0090307)	centriole (GO:0005814)|centrosome (GO:0005813)|spindle (GO:0005819)				NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(3)|large_intestine(9)|lung(10)|ovary(2)|skin(2)|urinary_tract(1)	33						CAGACTCATTAAAGATAGATT	0.408																																					p.F156F		Atlas-SNP	.											.	SPICE1	130	.	0			c.T468C						.						109	107	107					3																	113212077		2203	4300	6503	SO:0001819	synonymous_variant	152185	exon6			CTCATTAAAGATA	AY099107	CCDS2973.1	3q13.2	2010-09-01	2010-09-01	2010-09-01	ENSG00000163611	ENSG00000163611			25083	protein-coding gene	gene with protein product	"spindle and centriole protein"	613447	"coiled-coil domain containing 52"	CCDC52		20736305	Standard	NM_144718		Approved	SPICE	uc003eag.4	Q8N0Z3	OTTHUMG00000159261	ENST00000295872.4:c.468T>C	chr3.hg19:g.113212077A>G		104.0	0.0		98.0	4.0	NM_144718	D3DN72|Q8WUX6	Silent	SNP	ENST00000295872.4	hg19	CCDS2973.1																																																																																			.	.		0.408	SPICE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354177.2	NM_144718		G	113212077	A	G	113212077	2	3	288	1	0	0	0	0	0	0	0	1	2824	359	13	2		2	CCDC52	3	113212077	Silent	SNP	A	TCGA-G3-A5SM-01A-12D-A28X-10	5720090	113212077	84810353	19	42233										
CLSTN2	64084	hgsc.bcm.edu	37	chr3	140123517	140123517	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	gacagcattctgcaggtggaGgccattgacgaggactgctc	14	10	1	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr3:140123517G>A	ENST00000458420.3	+	4	736	c.546G>A	c.(544-546)gaG>gaA	p.E182E	AC092988.1_ENST00000580582.1_RNA	NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	182	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						TGCAGGTGGAGGCCATTGACG	0.517										HNSCC(16;0.037)																											p.E182E	GBM(45;858 913 3709 36904 37282)	Atlas-SNP	.											.	CLSTN2	190	.	0			c.G546A						.						153	123	133					3																	140123517		2203	4300	6503	SO:0001819	synonymous_variant	64084	exon4			GGTGGAGGCCATT	AJ278018	CCDS3112.1	3q23	2011-07-01			ENSG00000158258	ENSG00000158258		"Cadherins / Cadherin-related"	17448	protein-coding gene	gene with protein product	"cadherin-related family member 13"	611323				12498782	Standard	NM_022131		Approved	CSTN2, CS2, FLJ39113, CDHR13	uc003etn.3	Q9H4D0	OTTHUMG00000160139	ENST00000458420.3:c.546G>A	chr3.hg19:g.140123517G>A		260.0	0.0		235.0	84.0	NM_022131	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Silent	SNP	ENST00000458420.3	hg19	CCDS3112.1																																																																																			.	.		0.517	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131		A	140123517	G	A	140123517	2	1	288	1	0	0	0	0	0	0	0	1	3564	991	35	3		3	CLSTN2	3	140123517	Silent	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	26911440	140123517	57898913	20	42234										
MECOM	2122	hgsc.bcm.edu	37	chr3	168810745	168810745	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	aaaagtaaaagacagctttaCctctcctccacattcctggg	6	12	1	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr3:168810745C>A	ENST00000464456.1	-	12	3774		c.e12+1		MECOM_ENST00000468789.1_Splice_Site|MECOM_ENST00000472280.1_Splice_Site|MECOM_ENST00000392736.3_Splice_Site|MECOM_ENST00000460814.1_Splice_Site|MECOM_ENST00000494292.1_Splice_Site|MECOM_ENST00000433243.2_Splice_Site|MECOM_ENST00000264674.3_Splice_Site	NM_001164000.1	NP_001157472.1	Q13465	MDS1_HUMAN	MDS1 and EVI1 complex locus						regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	85						GACAGCTTTACCTCTCCTCCA	0.388																																					.		Atlas-SNP	.											.	MECOM	216	.	0			c.2795+1G>T						.						108	99	102					3																	168810745		2203	4300	6503	SO:0001630	splice_region_variant	2122	exon15			GCTTTACCTCTCC	S82592, AF164154	CCDS3205.1, CCDS54669.1, CCDS54670.1	3q26.2	2013-01-08	2009-08-07	2009-08-07	ENSG00000085276	ENSG00000085276		"Zinc fingers, C2H2-type"	3498	protein-coding gene	gene with protein product		165215	"myelodysplasia syndrome 1", "ecotropic viral integration site 1"	MDS1, EVI1		2115646, 8171026, 8643684	Standard	NM_001105077		Approved	MDS1-EVI1, PRDM3	uc011bpj.1	Q03112	OTTHUMG00000158596	ENST00000464456.1:c.2573+1G>T	chr3.hg19:g.168810745C>A		43.0	0.0		78.0	13.0	NM_001105077	Q13466|Q6FH90	Splice_Site	SNP	ENST00000464456.1	hg19	CCDS54669.1	.	.	.	.	.	.	.	.	.	.	C	15.88	2.963671	0.53507	.	.	ENSG00000085276	ENST00000264674;ENST00000392736;ENST00000464456;ENST00000472280;ENST00000494292;ENST00000468789;ENST00000460814;ENST00000433243	.	.	.	5.41	5.41	0.78517	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.2024	0.93715	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MECOM	170293439	1.000000	0.71417	1.000000	0.80357	0.350000	0.29205	7.163000	0.77524	2.527000	0.85204	0.460000	0.39030	.	.	.		0.388	MECOM-020	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351519.1	NM_005241, NM_004991	Intron	A	168810745	C	A	168810745	5	1	288	1	0	0	0	0	0	0	1	0	9431	521	18	3	570	3	MECOM	3	168810745	Splice_Site	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	28687228	168810745	29211685	21	42235										
HTRA3	94031	hgsc.bcm.edu	37	chr4	8295868	8295868	+	Missense_Mutation	SNP	G	G	T													0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	tcacggctggcatctcctttGccatcccctcagaccgcatc							TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr4:8295868G>T	ENST00000307358.2	+	6	1195	c.991G>T	c.(991-993)Gcc>Tcc	p.A331S	HTRA3_ENST00000382512.3_Missense_Mutation_p.A331S	NM_053044.3	NP_444272.1	P83110	HTRA3_HUMAN	HtrA serine peptidase 3	331	Serine protease.				negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.A331T(1)		central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|ovary(2)|prostate(1)|urinary_tract(1)	18						CATCTCCTTTGCCATCCCCTC	0.592																																					p.A331S		Atlas-SNP	.											HTRA3,NS,carcinoma,0,1	HTRA3	39	.	1	Substitution - Missense(1)	ovary(1)	c.G991T						.						135	90	106					4																	8295868		2203	4299	6502	SO:0001583	missense	94031	exon6			TCCTTTGCCATCC	AY040094	CCDS3400.1, CCDS75105.1	4p16.1	2008-02-05			ENSG00000170801	ENSG00000170801			30406	protein-coding gene	gene with protein product	"pregnancy-related serine protease"	608785				12513693, 14500695	Standard	XM_005248040		Approved	Tasp, Prsp	uc003gla.3	P83110	OTTHUMG00000090561	ENST00000307358.2:c.991G>T	chr4.hg19:g.8295868G>T	ENSP00000303766:p.Ala331Ser	121.0	0.0		139.0	17.0	NM_053044	Q7Z7A2	Missense_Mutation	SNP	ENST00000307358.2	hg19	CCDS3400.1	.	.	.	.	.	.	.	.	.	.	G	19.24	3.790384	0.70337	.	.	ENSG00000170801	ENST00000307358;ENST00000382512	D;D	0.90620	-2.7;-2.7	3.33	3.33	0.38152	Peptidase cysteine/serine, trypsin-like (1);	0.000000	0.85682	U	0.000000	D	0.94703	0.8291	M	0.85777	2.775	0.80722	D	1	D;P	0.56287	0.975;0.843	P;P	0.61070	0.883;0.798	D	0.95592	0.8655	10	0.87932	D	0	-10.3834	14.6368	0.68696	0.0:0.0:1.0:0.0	.	331;331	P83110;P83110-2	HTRA3_HUMAN;.	S	331	ENSP00000303766:A331S;ENSP00000371952:A331S	ENSP00000303766:A331S	A	+	1	0	HTRA3	8346768	1.000000	0.71417	0.999000	0.59377	0.665000	0.39181	8.992000	0.93519	1.410000	0.46936	0.313000	0.20887	GCC	.	.		0.592	HTRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092669.1	NM_053044		T	8295868	G	T	8295868	3	4	288	1	0	0	0	0	1	0	0	0	7464	1319	46	3	1013	3	HTRA3	4	8295868	Missense_Mutation	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10		8295868	182858408	22	42236	221	2								
HTRA3	94031	hgsc.bcm.edu	37	chr4	8295870	8295870	+	Silent	SNP	C	C	T													0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	acggctggcatctcctttgcCatcccctcagaccgcatcac							TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr4:8295870C>T	ENST00000307358.2	+	6	1197	c.993C>T	c.(991-993)gcC>gcT	p.A331A	HTRA3_ENST00000382512.3_Silent_p.A331A	NM_053044.3	NP_444272.1	P83110	HTRA3_HUMAN	HtrA serine peptidase 3	331	Serine protease.				negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|ovary(2)|prostate(1)|urinary_tract(1)	18						TCTCCTTTGCCATCCCCTCAG	0.592																																					p.A331A		Atlas-SNP	.											.	HTRA3	39	.	0			c.C993T						.						135	90	106					4																	8295870		2203	4299	6502	SO:0001819	synonymous_variant	94031	exon6			CTTTGCCATCCCC	AY040094	CCDS3400.1, CCDS75105.1	4p16.1	2008-02-05			ENSG00000170801	ENSG00000170801			30406	protein-coding gene	gene with protein product	"pregnancy-related serine protease"	608785				12513693, 14500695	Standard	XM_005248040		Approved	Tasp, Prsp	uc003gla.3	P83110	OTTHUMG00000090561	ENST00000307358.2:c.993C>T	chr4.hg19:g.8295870C>T		121.0	0.0		136.0	17.0	NM_053044	Q7Z7A2	Silent	SNP	ENST00000307358.2	hg19	CCDS3400.1																																																																																			.	.		0.592	HTRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092669.1	NM_053044		T	8295870	C	T	8295870	2	4	288	1	0	0	0	0	0	0	0	1	7464	581	21	3		3	HTRA3	4	8295870	Silent	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	2	8295870	182858406	23	42237	221	2								
PCDH7	5099	hgsc.bcm.edu	37	chr4	30726251	30726251	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	ccaaatatatttaaatatccCagggagggctaataactctg	7	8	1	0			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr4:30726251C>T	ENST00000361762.2	+	1	4182				PCDH7_ENST00000543491.1_Intron	NM_002589.2	NP_002580.2	O60245	PCDH7_HUMAN	protocadherin 7						homophilic cell adhesion (GO:0007156)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(8)|liver(1)|lung(26)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	55						TTAAATATCCCAGGGAGGGCT	0.318																																					p.P1069P		Atlas-SNP	.											.	PCDH7	215	.	0			c.C3207T						.						32	32	32					4																	30726251		1975	4186	6161	SO:0001627	intron_variant	5099	exon1			ATATCCCAGGGAG	AB006755	CCDS33971.1, CCDS75116.1	4p15	2014-06-13	2007-02-12			ENSG00000169851		"Cadherins / Protocadherins : Non-clustered"	8659	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 120"	602988	"BH-protocadherin (brain-heart)"			9615233	Standard	NM_002589		Approved	BH-Pcdh, PPP1R120	uc021xnd.1	O60245		ENST00000361762.2:c.3174+33C>T	chr4.hg19:g.30726251C>T		49.0	0.0		39.0	12.0	NM_032456	O60246|O60247|Q4W5C4	Silent	SNP	ENST00000361762.2	hg19	CCDS33971.1																																																																																			.	.		0.318	PCDH7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360366.1	NM_032457, NM_002589		T	30726251	C	T	30726251	1	4	288	0	1	0	0	0	0	0	0	0	11525	581	21	3		3	PCDH7	4	30726251	Intron	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	22430381	30726251	160428025	24	42238										
N4BP2	55728	hgsc.bcm.edu	37	chr4	40103840	40103840	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	aaacgtcctgaagaagagagTgaagattcaaaaatggattc	10	5	1	5			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr4:40103840T>G	ENST00000261435.6	+	4	791	c.375T>G	c.(373-375)agT>agG	p.S125R		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	125					nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|endonuclease activity (GO:0004519)			breast(4)|endometrium(3)|kidney(12)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	60						AAGAAGAGAGTGAAGATTCAA	0.373																																					p.S125R		Atlas-SNP	.											.	N4BP2	166	.	0			c.T375G						.						98	94	96					4																	40103840		2203	4300	6503	SO:0001583	missense	55728	exon4			AGAGAGTGAAGAT	AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"BCL-3 binding protein"					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.375T>G	chr4.hg19:g.40103840T>G	ENSP00000261435:p.Ser125Arg	117.0	0.0		98.0	38.0	NM_018177	A0AVR3|Q9NVK2|Q9P2D4	Missense_Mutation	SNP	ENST00000261435.6	hg19	CCDS3457.1	.	.	.	.	.	.	.	.	.	.	T	8.463	0.855782	0.17106	.	.	ENSG00000078177	ENST00000261435;ENST00000381804;ENST00000515550	T;T	0.78707	-1.2;-1.2	5.55	-3.76	0.04359	.	1.043650	0.07522	N	0.910740	T	0.52645	0.1747	N	0.14661	0.345	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.08055	0.003;0.001	T	0.30475	-0.9977	10	0.23302	T	0.38	0.0651	1.8642	0.03195	0.1084:0.2008:0.2164:0.4745	.	125;125	Q86UW6-2;Q86UW6	.;N4BP2_HUMAN	R	125;45;45	ENSP00000261435:S125R;ENSP00000422057:S45R	ENSP00000261435:S125R	S	+	3	2	N4BP2	39780235	0.001000	0.12720	0.008000	0.14137	0.553000	0.35397	-0.087000	0.11215	-0.303000	0.08856	0.482000	0.46254	AGT	.	.		0.373	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177		G	40103840	T	G	40103840	3	3	288	1	0	0	0	0	1	0	0	0	10119	1693	59	5	381	5	N4BP2	4	40103840	Missense_Mutation	SNP	T	TCGA-G3-A5SM-01A-12D-A28X-10	9377589	40103840	151050436	25	42239										
GABRG1	2565	hgsc.bcm.edu	37	chr4	46060284	46060284	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	tattgatccaaaaagacaccCaagaaagaacaactgtcaga	6	9	1	5			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr4:46060284C>A	ENST00000295452.4	-	7	1033	c.866G>T	c.(865-867)tGg>tTg	p.W289L		NM_173536.3	NP_775807.2	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 1	289					gamma-aminobutyric acid signaling pathway (GO:0007214)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(2)|central_nervous_system(5)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(2)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	76				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	AAAAGACACCCAAGAAAGAAC	0.343																																					p.W289L		Atlas-SNP	.											.	GABRG1	172	.	0			c.G866T						.						102	100	101					4																	46060284		2203	4300	6503	SO:0001583	missense	2565	exon7			GACACCCAAGAAA	BC031087	CCDS3470.1	4p12	2012-06-22			ENSG00000163285	ENSG00000163285		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4086	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma"	137166				1321425	Standard	NM_173536		Approved		uc003gxb.3	Q8N1C3	OTTHUMG00000128609	ENST00000295452.4:c.866G>T	chr4.hg19:g.46060284C>A	ENSP00000295452:p.Trp289Leu	196.0	0.0		185.0	39.0	NM_173536	Q5H9T8	Missense_Mutation	SNP	ENST00000295452.4	hg19	CCDS3470.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.724255	0.89298	.	.	ENSG00000163285	ENST00000295452;ENST00000540030	D	0.84298	-1.83	5.38	5.38	0.77491	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.94974	0.8374	H	0.95470	3.675	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96078	0.9051	10	0.87932	D	0	.	18.5473	0.91052	0.0:1.0:0.0:0.0	.	289	Q8N1C3	GBRG1_HUMAN	L	289	ENSP00000295452:W289L	ENSP00000295452:W289L	W	-	2	0	GABRG1	45755041	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	5.983000	0.70540	2.702000	0.92279	0.549000	0.68633	TGG	.	.		0.343	GABRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250470.1	NM_173536		A	46060284	C	A	46060284	3	1	288	1	0	0	0	0	1	0	0	0	6179	595	21	3	543	3	GABRG1	4	46060284	Missense_Mutation	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	5956444	46060284	145093992	26	42240										
TRPC3	7222	hgsc.bcm.edu	37	chr4	122836092	122836092	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	gctgctggcagttgggatgaGccacaaactattgggagaga	15	7	0	2			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr4:122836092G>A	ENST00000379645.3	-	4	1257	c.1184C>T	c.(1183-1185)gCt>gTt	p.A395V	TRPC3_ENST00000264811.5_Missense_Mutation_p.A322V|TRPC3_ENST00000513531.1_Intron	NM_001130698.1	NP_001124170.1	Q13507	TRPC3_HUMAN	transient receptor potential cation channel, subfamily C, member 3	310					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|phototransduction (GO:0007602)|platelet activation (GO:0030168)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cardiac muscle hypertrophy in response to stress (GO:1903244)|response to ATP (GO:0033198)|response to calcium ion (GO:0051592)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(12)|lung(13)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						GTTGGGATGAGCCACAAACTA	0.463																																					p.A395V		Atlas-SNP	.											.	TRPC3	201	.	0			c.C1184T						.						77	62	67					4																	122836092		2203	4300	6503	SO:0001583	missense	7222	exon4			GGATGAGCCACAA	Y13758	CCDS3725.1, CCDS47130.1	4q27	2011-12-14			ENSG00000138741	ENSG00000138741		"Voltage-gated ion channels / Transient receptor potential cation channels"	12335	protein-coding gene	gene with protein product		602345				8646775, 16382100	Standard	NM_003305		Approved		uc003ieg.2	Q13507	OTTHUMG00000133069	ENST00000379645.3:c.1184C>T	chr4.hg19:g.122836092G>A	ENSP00000368966:p.Ala395Val	104.0	0.0		69.0	13.0	NM_001130698	A7VJS1|E9PCJ9|O00593|Q15660|Q52M35|Q5G1L5	Missense_Mutation	SNP	ENST00000379645.3	hg19	CCDS47130.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.829710	0.91036	.	.	ENSG00000138741	ENST00000264811;ENST00000379645	T;T	0.73258	-0.73;-0.73	5.5	5.5	0.81552	.	0.146455	0.47093	D	0.000243	D	0.84754	0.5542	M	0.92649	3.33	0.80722	D	1	D;P	0.55800	0.973;0.864	P;P	0.51974	0.686;0.456	D	0.88696	0.3212	10	0.87932	D	0	-5.8817	19.3937	0.94596	0.0:0.0:1.0:0.0	.	310;395	Q13507;Q5G1L5	TRPC3_HUMAN;.	V	322;395	ENSP00000264811:A322V;ENSP00000368966:A395V	ENSP00000264811:A322V	A	-	2	0	TRPC3	123055542	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.753000	0.98904	2.586000	0.87340	0.655000	0.94253	GCT	.	.		0.463	TRPC3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364252.1	NM_003305		A	122836092	G	A	122836092	3	1	288	1	0	0	0	0	1	0	0	0	16594	971	34	3	1617	3	TRPC3	4	122836092	Missense_Mutation	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	76775808	122836092	68318184	27	42241										
SLC6A18	348932	hgsc.bcm.edu	37	chr5	1244795	1244795	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	cggctgacctggagggtggtCagtcccctgctgctgaccat	14	13	1	2			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr5:1244795C>T	ENST00000324642.3	+	11	1692	c.1569C>T	c.(1567-1569)gtC>gtT	p.V523V		NM_182632.2	NP_872438.2	Q96N87	S6A18_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 18	523					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)			endometrium(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(4)|upper_aerodigestive_tract(1)	34	all_cancers(3;2.99e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.76e-10)		Epithelial(17;0.000356)|all cancers(22;0.00124)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			GGAGGGTGGTCAGTCCCCTGC	0.592																																					p.V523V		Atlas-SNP	.											.	SLC6A18	84	.	0			c.C1569T						.						62	61	62					5																	1244795		2203	4300	6503	SO:0001819	synonymous_variant	348932	exon11			GGTGGTCAGTCCC	AK055798	CCDS3860.1	5p15	2013-07-19	2013-07-19		ENSG00000164363	ENSG00000164363		"Solute carriers"	26441	protein-coding gene	gene with protein product		610300	"solute carrier family 6 (neurotransmitter transporter), member 18", "solute carrier family 6, member 18"			19478081	Standard	NM_182632		Approved	FLJ31236, Xtrp2	uc003jby.2	Q96N87	OTTHUMG00000090356	ENST00000324642.3:c.1569C>T	chr5.hg19:g.1244795C>T		118.0	0.0		142.0	33.0	NM_182632		Silent	SNP	ENST00000324642.3	hg19	CCDS3860.1																																																																																			.	.		0.592	SLC6A18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206728.3	NM_182632		T	1244795	C	T	1244795	2	4	288	1	0	0	0	0	0	0	0	1	14696	813	29	3		3	SLC6A18	5	1244795	Silent	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10		1244795	179670465	28	42242										
FBXO4	26272	hgsc.bcm.edu	37	chr5	41927119	41927119	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	ctttcttctgtttcagattgAtgtacagctatatattttgt	6	6	3	2			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr5:41927119A>T	ENST00000281623.3	+	2	250	c.194A>T	c.(193-195)gAt>gTt	p.D65V	FBXO4_ENST00000509134.1_Missense_Mutation_p.D65V|FBXO4_ENST00000296812.2_Missense_Mutation_p.D65V	NM_012176.2	NP_036308.1	Q9UKT5	FBX4_HUMAN	F-box protein 4	65	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				positive regulation of protein ubiquitination (GO:0031398)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|telomere maintenance (GO:0000723)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	protein homodimerization activity (GO:0042803)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(11)|prostate(1)|stomach(1)|urinary_tract(2)	27		Lung NSC(810;4.15e-05)|Breast(839;0.00093)|Ovarian(839;0.00965)|Myeloproliferative disorder(839;0.0255)|all_neural(839;0.0604)				TTTCAGATTGATGTACAGCTA	0.333																																					p.D65V		Atlas-SNP	.											.	FBXO4	42	.	0			c.A194T						.						107	106	106					5																	41927119		2203	4300	6503	SO:0001583	missense	26272	exon2			AGATTGATGTACA	AF129534	CCDS3938.1, CCDS3939.1, CCDS75238.1	5p12	2008-02-05	2004-06-15		ENSG00000151876	ENSG00000151876		"F-boxes /  "other""	13583	protein-coding gene	gene with protein product		609090	"F-box only protein 4"			10531035, 10531037	Standard	NM_033484		Approved	FBX4	uc003jmq.3	Q9UKT5	OTTHUMG00000094799	ENST00000281623.3:c.194A>T	chr5.hg19:g.41927119A>T	ENSP00000281623:p.Asp65Val	70.0	0.0		67.0	10.0	NM_033484	Q68CU8|Q86VT8|Q9UK98	Missense_Mutation	SNP	ENST00000281623.3	hg19	CCDS3938.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.223973	0.79576	.	.	ENSG00000151876	ENST00000296812;ENST00000281623;ENST00000509134	T;T;T	0.58652	0.32;0.32;0.32	5.3	5.3	0.74995	F-box domain, cyclin-like (3);F-box domain, Skp2-like (1);	0.098369	0.64402	D	0.000002	T	0.75932	0.3917	M	0.81341	2.54	0.80722	D	1	D;D;D	0.63880	0.993;0.993;0.992	D;D;P	0.65874	0.939;0.919;0.868	T	0.79985	-0.1572	10	0.72032	D	0.01	-5.4731	15.2454	0.73502	1.0:0.0:0.0:0.0	.	65;65;65	D6RAJ6;Q9UKT5;Q9UKT5-2	.;FBX4_HUMAN;.	V	65	ENSP00000296812:D65V;ENSP00000281623:D65V;ENSP00000421749:D65V	ENSP00000281623:D65V	D	+	2	0	FBXO4	41962876	1.000000	0.71417	0.995000	0.50966	0.949000	0.60115	6.839000	0.75364	2.010000	0.58986	0.533000	0.62120	GAT	.	.		0.333	FBXO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211614.1			T	41927119	A	T	41927119	3	4	288	1	0	0	0	0	1	0	0	0	5756	333	12	4	200	4	FBXO4	5	41927119	Missense_Mutation	SNP	A	TCGA-G3-A5SM-01A-12D-A28X-10	40682324	41927119	138988141	29	42243										
HMGCR	3156	hgsc.bcm.edu	37	chr5	74646693	74646693	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	aaacagtacagcagatacttCtaaggtttcattaggactgg	9	7	2	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr5:74646693C>A	ENST00000287936.4	+	9	1016	c.860C>A	c.(859-861)tCt>tAt	p.S287Y	HMGCR_ENST00000343975.5_Missense_Mutation_p.S287Y|HMGCR_ENST00000511206.1_Missense_Mutation_p.S287Y	NM_000859.2	NP_000850.1	P04035	HMDH_HUMAN	3-hydroxy-3-methylglutaryl-CoA reductase	287					aging (GO:0007568)|cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|coenzyme A metabolic process (GO:0015936)|isoprenoid biosynthetic process (GO:0008299)|myoblast differentiation (GO:0045445)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of striated muscle cell apoptotic process (GO:0010664)|negative regulation of vasodilation (GO:0045908)|negative regulation of wound healing (GO:0061045)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein tetramerization (GO:0051262)|response to ethanol (GO:0045471)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|ubiquinone metabolic process (GO:0006743)|visual learning (GO:0008542)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|peroxisomal membrane (GO:0005778)	coenzyme binding (GO:0050662)|hydroxymethylglutaryl-CoA reductase (NADPH) activity (GO:0004420)|hydroxymethylglutaryl-CoA reductase activity (GO:0042282)|NADPH binding (GO:0070402)			breast(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	20		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;2.24e-54)	Atorvastatin(DB01076)|Fluvastatin(DB01095)|Lovastatin(DB00227)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rosuvastatin(DB01098)|Simvastatin(DB00641)	GCAGATACTTCTAAGGTTTCA	0.373																																					p.S287Y		Atlas-SNP	.											.	HMGCR	53	.	0			c.C860A						.						116	116	116					5																	74646693		2203	4300	6503	SO:0001583	missense	3156	exon9			ATACTTCTAAGGT		CCDS4027.1, CCDS47234.1	5q13.3-q14	2012-10-02	2010-04-30		ENSG00000113161	ENSG00000113161	1.1.1.88, 1.1.1.34		5006	protein-coding gene	gene with protein product	"hydroxymethylglutaryl-CoA reductase", "3-hydroxy-3-methylglutaryl CoA reductase (NADPH)"	142910	"3-hydroxy-3-methylglutaryl-Coenzyme A reductase"				Standard	NM_000859		Approved		uc003kdp.3	P04035	OTTHUMG00000102069	ENST00000287936.4:c.860C>A	chr5.hg19:g.74646693C>A	ENSP00000287936:p.Ser287Tyr	88.0	0.0		64.0	18.0	NM_001130996	B7Z3Y9|Q8N190	Missense_Mutation	SNP	ENST00000287936.4	hg19	CCDS4027.1	.	.	.	.	.	.	.	.	.	.	C	15.46	2.841321	0.51057	.	.	ENSG00000113161	ENST00000511206;ENST00000544469;ENST00000287936;ENST00000343975	T;T;T	0.46819	0.88;0.88;0.86	5.92	5.92	0.95590	.	0.587928	0.19863	N	0.104367	T	0.41328	0.1154	L	0.43152	1.355	0.29215	N	0.874344	B;B;B;B	0.34181	0.44;0.44;0.224;0.116	B;B;B;B	0.29353	0.086;0.034;0.101;0.034	T	0.49021	-0.8982	10	0.59425	D	0.04	-2.9611	15.0866	0.72158	0.1417:0.8583:0.0:0.0	.	287;287;287;287	B2R649;A8KA27;P04035-2;P04035	.;.;.;HMDH_HUMAN	Y	287;218;287;287	ENSP00000426745:S287Y;ENSP00000287936:S287Y;ENSP00000340816:S287Y	ENSP00000287936:S287Y	S	+	2	0	HMGCR	74682449	0.979000	0.34478	0.480000	0.27341	0.780000	0.44128	4.741000	0.62095	2.818000	0.97014	0.655000	0.94253	TCT	.	.		0.373	HMGCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219877.2			A	74646693	C	A	74646693	3	1	288	1	0	0	0	0	1	0	0	0	7240	913	32	3	890	3	HMGCR	5	74646693	Missense_Mutation	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	32719574	74646693	106268567	30	42244										
BRD8	10902	hgsc.bcm.edu	37	chr5	137501703	137501703	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	cactcttctttgatagaattGatgatcatggatatttcact	6	7	4	4			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr5:137501703G>A	ENST00000254900.5	-	11	1463	c.1092C>T	c.(1090-1092)atC>atT	p.I364I	BRD8_ENST00000515014.1_5'Flank|BRD8_ENST00000402931.1_Silent_p.I364I|BRD8_ENST00000455658.2_Silent_p.I323I|BRD8_ENST00000411594.2_Silent_p.I367I|BRD8_ENST00000230901.5_Silent_p.I437I	NM_139199.1	NP_631938	Q9H0E9	BRD8_HUMAN	bromodomain containing 8	364					cell surface receptor signaling pathway (GO:0007166)|chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|intracellular receptor signaling pathway (GO:0030522)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Swr1 complex (GO:0000812)	sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid hormone receptor activity (GO:0004887)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(3)|urinary_tract(1)	35			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TGATAGAATTGATGATCATGG	0.478																																					p.I437I		Atlas-SNP	.											.	BRD8	192	.	0			c.C1311T						.						149	142	144					5																	137501703		2203	4300	6503	SO:0001819	synonymous_variant	10902	exon12			AGAATTGATGATC	AF016270	CCDS4198.1, CCDS34241.1, CCDS54907.1	5q31	2008-02-05			ENSG00000112983	ENSG00000112983			19874	protein-coding gene	gene with protein product		602848				8611617, 9368056	Standard	NM_001164326		Approved	SMAP, p120	uc003lcf.1	Q9H0E9	OTTHUMG00000129204	ENST00000254900.5:c.1092C>T	chr5.hg19:g.137501703G>A		79.0	0.0		61.0	18.0	NM_006696	O43178|Q15355|Q58AB0|Q59GN0|Q969M9	Silent	SNP	ENST00000254900.5	hg19	CCDS4198.1	.	.	.	.	.	.	.	.	.	.	G	6.476	0.456051	0.12283	.	.	ENSG00000112983	ENST00000441656	.	.	.	5.65	1.28	0.21552	.	.	.	.	.	T	0.51669	0.1688	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35871	-0.9771	4	.	.	.	-11.4674	5.5038	0.16842	0.3681:0.0:0.4923:0.1396	.	.	.	.	L	358	.	.	S	-	2	0	BRD8	137529602	1.000000	0.71417	0.999000	0.59377	0.957000	0.61999	0.854000	0.27791	0.059000	0.16252	-1.004000	0.02495	TCA	.	.		0.478	BRD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251282.3	NM_006696		A	137501703	G	A	137501703	2	1	288	1	0	0	0	0	0	0	0	1	1508	1280	45	3		3	BRD8	5	137501703	Silent	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	62855010	137501703	43413557	31	42245										
PCDHB8	56128	hgsc.bcm.edu	37	chr5	140558833	140558833	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	aacttttacaccctactaacAgagacaccactagacagaga	5	12	0	3			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr5:140558833A>G	ENST00000239444.2	+	1	1463	c.1218A>G	c.(1216-1218)acA>acG	p.T406T	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	406	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(14)|liver(1)|lung(38)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCCTACTAACAGAGACACCAC	0.468																																					p.T406T		Atlas-SNP	.											.	PCDHB8	199	.	0			c.A1218G						.						118	152	140					5																	140558833		2203	4300	6503	SO:0001819	synonymous_variant	56128	exon1			ACTAACAGAGACA	AF152501	CCDS4250.1	5q31	2010-01-26			ENSG00000120322	ENSG00000120322		"Cadherins / Protocadherins : Clustered"	8693	other	protocadherin		606334				10380929	Standard	NM_019120		Approved	PCDH-BETA8, PCDH3I	uc011dai.2	Q9UN66	OTTHUMG00000129621	ENST00000239444.2:c.1218A>G	chr5.hg19:g.140558833A>G		533.0	0.0		508.0	98.0	NM_019120	B9EGV1	Silent	SNP	ENST00000239444.2	hg19	CCDS4250.1																																																																																			.	.		0.468	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120		G	140558833	A	G	140558833	2	3	288	1	0	0	0	0	0	0	0	1	11557	175	7	2		2	PCDHB8	5	140558833	Silent	SNP	A	TCGA-G3-A5SM-01A-12D-A28X-10	3057130	140558833	40356427	32	42246										
PCDHGC5	26025	hgsc.bcm.edu	37	chr5	140871340	140871340	+	Intron	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	ccgcccgtcctcataagggaTtgaacttgcatccactcctc	7	16	1	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr5:140871340T>A	ENST00000252085.3	+	2	2566				PCDHGC4_ENST00000306593.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGC5_ENST00000252087.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGC3_ENST00000308177.3_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB3_ENST00000576222.1_Intron	NM_003735.2|NM_032094.1	NP_003726.1|NP_115265.1	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12						homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(23)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	58			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCATAAGGGATTGAACTTGCA	0.672																																					p.L845M		Atlas-SNP	.											.	PCDHGC5	199	.	0			c.T2533A						.						11	15	13					5																	140871340		1092	2139	3231	SO:0001627	intron_variant	56097	exon1			AAGGGATTGAACT	AF152506	CCDS4260.1, CCDS75346.1	5q31	2010-01-26	2002-05-23		ENSG00000253159	ENSG00000253159		"Cadherins / Protocadherins : Clustered"	8699	other	protocadherin	"fibroblast cadherin FIB3"	603059	"cadherin 21"	CDH21		10380929	Standard	NM_003735		Approved	KIAA0588, FIB3, PCDH-GAMMA-A12		O60330	OTTHUMG00000129611	ENST00000252085.3:c.2425-3034T>A	chr5.hg19:g.140871340T>A		144.0	0.0		119.0	11.0	NM_032407	O15100|Q6UW70|Q9Y5D7	Missense_Mutation	SNP	ENST00000252085.3	hg19	CCDS4260.1																																																																																			.	.		0.672	PCDHGA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251806.2	NM_003735		A	140871340	T	A	140871340	1	1	288	0	1	0	0	0	0	0	0	0	11580	1490	52	4		4	PCDHGC5	5	140871340	Intron	SNP	T	TCGA-G3-A5SM-01A-12D-A28X-10	312507	140871340	40043920	33	42247										
DHX16	8449	hgsc.bcm.edu	37	chr6	30627550	30627550	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	ccaggatatccccagggggcTgggtcacatggatctgcaac	13	12	2	0			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr6:30627550T>A	ENST00000376442.3	-	11	2012	c.1817A>T	c.(1816-1818)cAg>cTg	p.Q606L	DHX16_ENST00000376437.5_Missense_Mutation_p.Q125L|DHX16_ENST00000480966.1_5'UTR	NM_001164239.1|NM_003587.4	NP_001157711.1|NP_003578.2	O60231	DHX16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 16	606	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			kidney(2)|ovary(2)	4						CCCAGGGGGCTGGGTCACATG	0.582																																					p.Q606L		Atlas-SNP	.											.	DHX16	119	.	0			c.A1817T						.						90	86	87					6																	30627550		2203	4300	6503	SO:0001583	missense	8449	exon11			GGGGGCTGGGTCA	AB001601	CCDS4685.1	6p21.3	2010-02-17	2003-06-13	2003-06-20	ENSG00000204560	ENSG00000204560		"DEAH-boxes"	2739	protein-coding gene	gene with protein product		603405	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 16"	DDX16		9547260	Standard	NM_003587		Approved	DBP2, Prp2, PRPF2	uc003nqz.3	O60231	OTTHUMG00000031060	ENST00000376442.3:c.1817A>T	chr6.hg19:g.30627550T>A	ENSP00000365625:p.Gln606Leu	109.0	0.0		72.0	10.0	NM_003587	O60322|Q5JP45|Q969X7|Q96QC1	Missense_Mutation	SNP	ENST00000376442.3	hg19	CCDS4685.1	.	.	.	.	.	.	.	.	.	.	T	26.2	4.718166	0.89205	.	.	ENSG00000204560	ENST00000376442;ENST00000376437	T;T	0.08102	3.13;3.13	4.96	4.96	0.65561	Helicase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.15912	0.0383	L	0.58969	1.84	0.80722	D	1	D;D;D	0.76494	0.999;0.968;0.996	D;P;P	0.69142	0.962;0.749;0.776	T	0.00411	-1.1756	10	0.87932	D	0	.	14.0286	0.64601	0.0:0.0:0.0:1.0	.	546;606;125	B4DZ28;O60231;Q5SQH5	.;DHX16_HUMAN;.	L	606;125	ENSP00000365625:Q606L;ENSP00000365620:Q125L	ENSP00000365620:Q125L	Q	-	2	0	DHX16	30735529	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	3.825000	0.55730	2.212000	0.71576	0.374000	0.22700	CAG	.	.		0.582	DHX16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076076.2	NM_003587		A	30627550	T	A	30627550	3	1	288	1	0	0	0	0	1	0	0	0	4504	1580	55	4	1348	4	DHX16	6	30627550	Missense_Mutation	SNP	T	TCGA-G3-A5SM-01A-12D-A28X-10		30627550	140487517	34	42248										
TTBK1	84630	hgsc.bcm.edu	37	chr6	43220563	43220563	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	aatgtggccctcaaggtggaGtcagcccagcagcccaagca	12	13	2	0			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr6:43220563G>A	ENST00000259750.4	+	3	278	c.195G>A	c.(193-195)gaG>gaA	p.E65E	TTBK1_ENST00000304139.5_Silent_p.E14E	NM_032538.1	NP_115927.1	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	65	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(10)|liver(1)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)			TCAAGGTGGAGTCAGCCCAGC	0.592																																					p.E65E		Atlas-SNP	.											.	TTBK1	124	.	0			c.G195A						.						101	94	96					6																	43220563		2203	4300	6503	SO:0001819	synonymous_variant	84630	exon3			GGTGGAGTCAGCC	AB058758	CCDS34455.1	6p21.1	2008-02-05			ENSG00000146216	ENSG00000146216			19140	protein-coding gene	gene with protein product						11347906	Standard	XM_006715229		Approved	KIAA1855	uc003ouq.1	Q5TCY1	OTTHUMG00000014725	ENST00000259750.4:c.195G>A	chr6.hg19:g.43220563G>A		77.0	0.0		62.0	13.0	NM_032538	A2A2U5|Q2L6C6|Q6ZNH0|Q8N444|Q96JH2	Silent	SNP	ENST00000259750.4	hg19	CCDS34455.1																																																																																			.	.		0.592	TTBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040584.3			A	43220563	G	A	43220563	2	1	288	1	0	0	0	0	0	0	0	1	16691	1020	36	3		3	TTBK1	6	43220563	Silent	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	12593013	43220563	127894504	35	42249										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152768757	152768757	+	Splice_Site	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	ggtaacaccatttctgatctCctgaaatgagagaacacttt	7	9	2	4			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr6:152768757C>G	ENST00000367255.5	-	29	4106	c.3505G>C	c.(3505-3507)Gag>Cag	p.E1169Q	SYNE1_ENST00000341594.5_Splice_Site_p.E1235Q|SYNE1_ENST00000448038.1_Splice_Site_p.E1176Q|SYNE1_ENST00000265368.4_Splice_Site_p.E1169Q|SYNE1_ENST00000423061.1_Splice_Site_p.E1176Q|SYNE1_ENST00000367253.4_Splice_Site_p.E1169Q|SYNE1_ENST00000413186.2_Splice_Site_p.E1169Q|SYNE1_ENST00000367248.3_Splice_Site_p.E1159Q	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1169					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TTTCTGATCTCCTGAAATGAG	0.423										HNSCC(10;0.0054)																											p.E1176Q		Atlas-SNP	.											.	SYNE1	3227	.	0			c.G3526C						.						102	100	101					6																	152768757		2203	4300	6503	SO:0001630	splice_region_variant	23345	exon29			TGATCTCCTGAAA	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.3505-1G>C	chr6.hg19:g.152768757C>G		52.0	0.0		36.0	6.0	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	19.59	3.856819	0.71834	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000367253;ENST00000367248;ENST00000413186	T;T;T;T;T;T;T;T	0.36699	1.24;1.24;1.24;1.24;1.24;1.24;1.24;1.24	6.05	6.05	0.98169	.	0.191068	0.36444	N	0.002592	T	0.42720	0.1215	L	0.51422	1.61	0.80722	D	1	D;P;D;D;P;P	0.67145	0.991;0.5;0.987;0.996;0.5;0.633	P;B;P;D;B;B	0.63703	0.77;0.156;0.854;0.917;0.156;0.417	T	0.02789	-1.1110	10	0.19590	T	0.45	.	18.7818	0.91937	0.0:1.0:0.0:0.0	.	1152;1169;1159;1169;1169;1176	B3W695;Q8NF91;F5GXQ8;Q8NF91-6;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.;.;.	Q	1169;1176;1169;1176;1235;1169;1159;1169	ENSP00000356224:E1169Q;ENSP00000396024:E1176Q;ENSP00000265368:E1169Q;ENSP00000390975:E1176Q;ENSP00000341887:E1235Q;ENSP00000356222:E1169Q;ENSP00000356217:E1159Q;ENSP00000414510:E1169Q	ENSP00000265368:E1169Q	E	-	1	0	SYNE1	152810450	1.000000	0.71417	1.000000	0.80357	0.583000	0.36354	2.935000	0.48963	2.878000	0.98634	0.650000	0.86243	GAG	.	.		0.423	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	Missense_Mutation	G	152768757	C	G	152768757	5	3	288	1	0	0	0	0	0	0	1	0	15460	869	30	4	23433	4	SYNE1	6	152768757	Splice_Site	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	109548194	152768757	18346310	36	42250										
FNDC1	84624	hgsc.bcm.edu	37	chr6	159655441	159655441	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	accccgatgctgtccttgcgCcagaggatgatgcatgccag	12	13	0	2			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr6:159655441C>A	ENST00000297267.9	+	11	4097	c.3897C>A	c.(3895-3897)cgC>cgA	p.R1299R	FNDC1_ENST00000340366.6_Silent_p.R1236R	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1299					cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		TGTCCTTGCGCCAGAGGATGA	0.597																																					p.R1299R		Atlas-SNP	.											.	FNDC1	250	.	0			c.C3897A						.						27	29	28					6																	159655441		2067	4151	6218	SO:0001819	synonymous_variant	84624	exon11			CTTGCGCCAGAGG	AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"Fibronectin type III domain containing"	21184	protein-coding gene	gene with protein product		609991	"fibronectin type III domain containing 2"	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.3897C>A	chr6.hg19:g.159655441C>A		189.0	0.0		154.0	15.0	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Silent	SNP	ENST00000297267.9	hg19	CCDS47512.1	.	.	.	.	.	.	.	.	.	.	C	7.331	0.618973	0.14129	.	.	ENSG00000164694	ENST00000329629	.	.	.	5.43	-2.5	0.06384	.	.	.	.	.	T	0.31199	0.0789	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35051	-0.9804	4	.	.	.	-19.8688	4.6058	0.12376	0.1199:0.2471:0.5018:0.1312	.	.	.	.	T	1195	.	.	P	+	1	0	FNDC1	159575431	0.989000	0.36119	1.000000	0.80357	0.499000	0.33736	-0.009000	0.12765	-0.312000	0.08741	0.557000	0.71058	CCA	.	.		0.597	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532		A	159655441	C	A	159655441	2	1	288	1	0	0	0	0	0	0	0	1	5976	726	26	3		3	FNDC1	6	159655441	Silent	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	6886684	159655441	11459626	37	42251										
PCLO	27445	hgsc.bcm.edu	37	chr7	82791801	82791801	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	gcctccatgccggccgggatCgcggtgtgagaggggctccc	17	14	0	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr7:82791801C>A	ENST00000333891.9	-	1	445	c.108G>T	c.(106-108)gcG>gcT	p.A36A	PCLO_ENST00000423517.2_Silent_p.A36A	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						CGGCCGGGATCGCGGTGTGAG	0.697																																					p.A36A		Atlas-SNP	.											.	PCLO	1506	.	0			c.G108T						.						17	21	20					7																	82791801		1980	4130	6110	SO:0001819	synonymous_variant	27445	exon1			CGGGATCGCGGTG	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.108G>T	chr7.hg19:g.82791801C>A		110.0	0.0		75.0	41.0	NM_014510		Silent	SNP	ENST00000333891.9	hg19	CCDS47630.1																																																																																			.	.		0.697	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82791801	C	A	82791801	2	1	288	1	0	0	0	0	0	0	0	1	11592	871	31	1		1	PCLO	7	82791801	Silent	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10		82791801	76346862	38	42252										
COG5	10466	hgsc.bcm.edu	37	chr7	106921825	106921827	+	In_Frame_Del	DEL	CAG	CAG	-													0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	taatgtgaggtttgtatcaaCagcagcaacatttagttcac							TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	CAG	CAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr7:106921825_106921827delCAG	ENST00000347053.3	-	14	1636_1638	c.1586_1588delCTG	c.(1585-1590)gctgtt>gtt	p.A529del	COG5_ENST00000297135.3_In_Frame_Del_p.A529del|COG5_ENST00000393603.2_In_Frame_Del_p.A529del	NM_181733.2	NP_859422.2	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5	529					intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|skin(4)|stomach(1)	40						TTTGTATCAACAGCAGCAACATT	0.34																																					p.529_530del		Atlas-Indel,Pindel	.											.	COG5	78	.	0			c.1587_1589del						.																																			SO:0001651	inframe_deletion	10466	exon14			.	AF058718	CCDS5742.1, CCDS5743.1, CCDS55152.1	7q31	2010-06-24	2001-12-07	2002-05-10	ENSG00000164597	ENSG00000164597		"Components of oligomeric golgi complex"	14857	protein-coding gene	gene with protein product		606821	"golgi transport complex 1 (90 kDa subunit)"	GOLTC1		9792665, 11980916	Standard	NM_006348		Approved	GTC90	uc003vec.2	Q9UP83	OTTHUMG00000023895	ENST00000347053.3:c.1586_1588delCTG	chr7.hg19:g.106921828_106921830delCAG	ENSP00000334703:p.Ala529del	98.0	0.0		114.0	19.0	NM_001161520	A4D0R6|A4D0R7|O14555|O95008|Q6NUL5	In_Frame_Del	DEL	ENST00000347053.3	hg19	CCDS5743.1																																																																																			.	.		0.34	COG5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060216.4			-	106921827	CAG	-	106921825	7	5	288	1	0	1	0	1	0	0	0	0	3663	478	17	0	1034	0	COG5	7	106921825	In_Frame_Del	DEL	CAG	TCGA-G3-A5SM-01A-12D-A28X-10	24130024	106921825	52216838	39	42253										
NRCAM	4897	hgsc.bcm.edu	37	chr7	107799966	107799966	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	ctggatttcagggtcagcatGggcatcttccttttctttaa	9	9	4	0			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr7:107799966G>A	ENST00000425651.2	-	29	3618	c.3619C>T	c.(3619-3621)Cat>Tat	p.H1207Y	NRCAM_ENST00000413765.2_Missense_Mutation_p.H1083Y|NRCAM_ENST00000379028.3_Missense_Mutation_p.H1207Y|NRCAM_ENST00000379024.4_Missense_Mutation_p.H1095Y|NRCAM_ENST00000379022.4_Missense_Mutation_p.H1207Y|NRCAM_ENST00000351718.4_Missense_Mutation_p.H1086Y|NRCAM_ENST00000522550.2_5'Flank	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	1207					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						GGGTCAGCATGGGCATCTTCC	0.403																																					p.H1207Y		Atlas-SNP	.											.	NRCAM	267	.	0			c.C3619T						.						170	153	159					7																	107799966		2203	4299	6502	SO:0001583	missense	4897	exon29			CAGCATGGGCATC		CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7994	protein-coding gene	gene with protein product	"NgCAM-related cell adhesion molecule"	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.3619C>T	chr7.hg19:g.107799966G>A	ENSP00000401244:p.His1207Tyr	89.0	0.0		90.0	38.0	NM_001037132	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Missense_Mutation	SNP	ENST00000425651.2	hg19	CCDS47686.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.883682	0.91740	.	.	ENSG00000091129	ENST00000379032;ENST00000379028;ENST00000413765;ENST00000537765;ENST00000437386;ENST00000351718;ENST00000379024;ENST00000425651;ENST00000379022	D;D;D;D;D;D	0.85773	-2.03;-2.03;-2.03;-2.03;-2.03;-2.03	5.74	5.74	0.90152	.	0.097095	0.64402	D	0.000001	D	0.91613	0.7350	M	0.73598	2.24	0.80722	D	1	D;P;D;D;D;D	0.64830	0.991;0.832;0.966;0.984;0.98;0.994	P;P;P;P;P;D	0.64506	0.786;0.625;0.786;0.808;0.786;0.926	D	0.89107	0.3493	10	0.28530	T	0.3	.	19.9187	0.97077	0.0:0.0:1.0:0.0	.	1207;53;1083;1095;1086;1207	Q92823-5;B4DFP9;Q92823-3;E9PDA4;Q92823-4;Q92823	.;.;.;.;.;NRCAM_HUMAN	Y	1207;1207;1083;1114;51;1086;1095;1207;1207	ENSP00000368314:H1207Y;ENSP00000407858:H1083Y;ENSP00000325269:H1086Y;ENSP00000368310:H1095Y;ENSP00000401244:H1207Y;ENSP00000368308:H1207Y	ENSP00000325269:H1086Y	H	-	1	0	NRCAM	107587202	1.000000	0.71417	0.753000	0.31225	0.932000	0.56968	9.869000	0.99810	2.702000	0.92279	0.591000	0.81541	CAT	.	.		0.403	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132		A	107799966	G	A	107799966	3	1	288	1	0	0	0	0	1	0	0	0	10653	1348	47	3	333	3	NRCAM	7	107799966	Missense_Mutation	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	878141	107799966	51338697	40	42254										
TMEM176A	55365	hgsc.bcm.edu	37	chr7	150501448	150501448	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	ggccttggccctctgtccccAggccttgttcagaacccttc	9	17	2	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr7:150501448A>G	ENST00000484928.1	+	6	1136		c.e6-1		TMEM176A_ENST00000461345.1_Splice_Site|TMEM176A_ENST00000004103.3_Splice_Site|TMEM176B_ENST00000447204.2_5'Flank			Q96HP8	T176A_HUMAN	transmembrane protein 176A						negative regulation of dendritic cell differentiation (GO:2001199)	integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|lung(7)|ovary(2)|stomach(1)	12			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CTCTGTCCCCAGGCCTTGTTC	0.547																																					.		Atlas-SNP	.											.	TMEM176A	35	.	0			c.556-2A>G						.						136	111	119					7																	150501448		2203	4300	6503	SO:0001630	splice_region_variant	55365	exon6			GTCCCCAGGCCTT	AF258340	CCDS5909.1	7q36.1	2006-09-04			ENSG00000002933	ENSG00000002933			24930	protein-coding gene	gene with protein product		610334				12097419, 8889548	Standard	NM_018487		Approved	HCA112	uc003whx.1	Q96HP8	OTTHUMG00000158114	ENST00000484928.1:c.556-1A>G	chr7.hg19:g.150501448A>G		104.0	0.0		112.0	21.0	NM_018487	D3DX00|Q9NYC7	Splice_Site	SNP	ENST00000484928.1	hg19	CCDS5909.1	.	.	.	.	.	.	.	.	.	.	A	15.08	2.727426	0.48833	.	.	ENSG00000002933	ENST00000484928;ENST00000004103;ENST00000461345;ENST00000475536	.	.	.	4.51	4.51	0.55191	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.5109	0.44862	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TMEM176A	150132381	1.000000	0.71417	0.998000	0.56505	0.822000	0.46500	3.199000	0.51043	1.804000	0.52760	0.533000	0.62120	.	.	.		0.547	TMEM176A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350222.1	NM_018487	Intron	G	150501448	A	G	150501448	5	3	288	1	0	0	0	0	0	0	1	0	16107	202	7	2	572	2	TMEM176A	7	150501448	Splice_Site	SNP	A	TCGA-G3-A5SM-01A-12D-A28X-10	42701482	150501448	8637215	41	42255										
MLL3	58508	hgsc.bcm.edu	37	chr7	151860411	151860411	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	gctctttgtctatctacctcCtgcatgagttggatccgttg	9	11	3	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr7:151860411C>T	ENST00000262189.6	-	43	10469	c.10251G>A	c.(10249-10251)caG>caA	p.Q3417Q	KMT2C_ENST00000355193.2_Silent_p.Q3417Q	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	3417	Gln-rich.				histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										TATCTACCTCCTGCATGAGTT	0.448																																					p.Q3417Q		Atlas-SNP	.											.	MLL3	1564	.	0			c.G10251A						.						316	275	289					7																	151860411		2203	4300	6503	SO:0001819	synonymous_variant	58508	exon43			TACCTCCTGCATG	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.10251G>A	chr7.hg19:g.151860411C>T		200.0	0.0		230.0	87.0	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Silent	SNP	ENST00000262189.6	hg19	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	C	5.430	0.264411	0.10294	.	.	ENSG00000055609	ENST00000360104	.	.	.	5.18	-5.15	0.02866	.	.	.	.	.	T	0.52917	0.1764	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53107	-0.8485	4	.	.	.	.	10.172	0.42915	0.0:0.5193:0.1106:0.3701	.	.	.	.	R	923	.	.	G	-	1	0	MLL3	151491344	0.021000	0.18746	0.432000	0.26747	0.846000	0.48090	-0.827000	0.04424	-1.345000	0.02214	-0.238000	0.12139	GGA	.	.		0.448	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			T	151860411	C	T	151860411	2	4	288	1	0	0	0	0	0	0	0	1	9631	680	24	3		3	MLL3	7	151860411	Silent	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	1358963	151860411	7278252	42	42256										
RP1L1	94137	hgsc.bcm.edu	37	chr8	10468548	10468548	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	gctccctctggctctgggtcCtggccggggtccccttccag	13	17	2	0			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr8:10468548C>T	ENST00000382483.3	-	4	3283	c.3060G>A	c.(3058-3060)caG>caA	p.Q1020Q		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1020					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		GCTCTGGGTCCTGGCCGGGGT	0.672																																					p.Q1020Q		Atlas-SNP	.											.	RP1L1	453	.	0			c.G3060A						.						21	23	23					8																	10468548		1834	4027	5861	SO:0001819	synonymous_variant	94137	exon4			TGGGTCCTGGCCG	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.3060G>A	chr8.hg19:g.10468548C>T		104.0	0.0		85.0	40.0	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	hg19	CCDS43708.1																																																																																			.	.		0.672	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			T	10468548	C	T	10468548	2	4	288	1	0	0	0	0	0	0	0	1	13548	680	24	3		3	RP1L1	8	10468548	Silent	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10		10468548	135895474	43	42257										
EFHA2	286097	hgsc.bcm.edu	37	chr8	16921654	16921654	+	Frame_Shift_Del	DEL	G	G	-													0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	tgccacatctcgggagaggcGatttcgtttatttgcttcta							TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr8:16921654delG	ENST00000318063.5	+	2	485	c.443delG	c.(442-444)cgafs	p.R148fs		NM_181723.2	NP_859074.1	Q86XE3	MICU3_HUMAN	mitochondrial calcium uptake family, member 3	148						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)										CGGGAGAGGCGATTTCGTTTA	0.388																																					p.R148fs		Atlas-Indel,Pindel	.											EFHA2,NS,carcinoma,0,2	EFHA2	60	.	0			c.442delC						.						188	166	174					8																	16921654		2203	4300	6503	SO:0001589	frameshift_variant	286097	exon2			.	BC032868	CCDS5999.1	8p22	2013-03-26	2013-03-26	2013-03-14	ENSG00000155970	ENSG00000155970		"EF-hand domain containing"	27820	protein-coding gene	gene with protein product		610633	"EF hand domain family A2", "EF-hand domain family, member A2"	EFHA2		23409044	Standard	NM_181723		Approved	DKFZp313A0139	uc003wxd.2	Q86XE3	OTTHUMG00000096965	ENST00000318063.5:c.443delG	chr8.hg19:g.16921654delG	ENSP00000321455:p.Arg148fs	94.0	0.0		74.0	14.0	NM_181723	Q8IYZ3	Frame_Shift_Del	DEL	ENST00000318063.5	hg19	CCDS5999.1																																																																																			.	.		0.388	MICU3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214031.1	NM_181723		-	16921654	G	-	16921654	7	5	288	1	0	1	0	1	0	0	0	0	4946	1058	37	0	449	0	EFHA2	8	16921654	Frame_Shift_Del	DEL	G	TCGA-G3-A5SM-01A-12D-A28X-10	6453106	16921654	129442368	44	42258										
C8orf41	80185	hgsc.bcm.edu	37	chr8	33370119	33370119	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	cgatggggcttccagagcgcTgtcaagctccattcctgact	11	13	1	2			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr8:33370119T>C	ENST00000431156.2	-	2	631	c.13A>G	c.(13-15)Agc>Ggc	p.S5G	SNORD13_ENST00000459299.1_RNA|TTI2_ENST00000519356.1_5'Flank|TTI2_ENST00000520636.1_Missense_Mutation_p.S5G|TTI2_ENST00000360742.5_Missense_Mutation_p.S5G	NM_001102401.2	NP_001095871.1	Q6NXR4	TTI2_HUMAN	TELO2 interacting protein 2	5																	TCCAGAGCGCTGTCAAGCTCC	0.557																																					p.S5G		Atlas-SNP	.											.	.	.	.	0			c.A13G						.						48	50	49					8																	33370119		2203	4294	6497	SO:0001583	missense	80185	exon2			GAGCGCTGTCAAG	AK026916	CCDS6090.1	8p12	2011-11-10	2011-11-10	2011-09-22		ENSG00000129696			26262	protein-coding gene	gene with protein product		614426	"chromosome 8 open reading frame 41", "Tel2 interacting protein 2 homolog (S. pombe)"	C8orf41		20801936, 20810650	Standard	NM_025115		Approved	FLJ23263	uc003xjm.5	Q6NXR4		ENST00000431156.2:c.13A>G	chr8.hg19:g.33370119T>C	ENSP00000411169:p.Ser5Gly	39.0	0.0		38.0	18.0	NM_001265581	D3DSV7|Q96IM2|Q9H5N4	Missense_Mutation	SNP	ENST00000431156.2	hg19	CCDS6090.1	.	.	.	.	.	.	.	.	.	.	T	8.203	0.798525	0.16397	.	.	ENSG00000129696	ENST00000360742;ENST00000431156;ENST00000522668;ENST00000520636;ENST00000520397;ENST00000523305	T;T;T;T	0.58940	0.33;0.33;0.3;0.68	3.54	-7.07	0.01563	.	1.511920	0.04180	N	0.326383	T	0.35970	0.0950	L	0.28400	0.85	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.10917	-1.0609	10	0.33141	T	0.24	-0.8541	0.7161	0.00932	0.2238:0.1332:0.2251:0.4179	.	5;5;5	E5RH83;Q6NXR4;E5RIH5	.;TTI2_HUMAN;.	G	5	ENSP00000353971:S5G;ENSP00000411169:S5G;ENSP00000428401:S5G;ENSP00000428569:S5G	ENSP00000353971:S5G	S	-	1	0	C8orf41	33489661	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-6.566000	0.00061	-2.317000	0.00644	-0.366000	0.07423	AGC	.	.		0.557	TTI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376555.1	NM_025115		C	33370119	T	C	33370119	3	2	288	1	0	0	0	0	1	0	0	0	2429	1580	55	2	1541	2	C8orf41	8	33370119	Missense_Mutation	SNP	T	TCGA-G3-A5SM-01A-12D-A28X-10	16448465	33370119	112993903	45	42259										
CHD7	55636	hgsc.bcm.edu	37	chr8	61764754	61764754	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	gacggcggcctcgagaggaaGtgagagctctggaagcggaa	18	8	1	2			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr8:61764754G>A	ENST00000423902.2	+	29	6321	c.5842G>A	c.(5842-5844)Gtg>Atg	p.V1948M	CHD7_ENST00000524602.1_Intron	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	1948					adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			TCGAGAGGAAGTGAGAGCTCT	0.537																																					p.V1948M		Atlas-SNP	.											.	CHD7	534	.	0			c.G5842A						.						54	58	57					8																	61764754		1886	4091	5977	SO:0001583	missense	55636	exon29			GAGGAAGTGAGAG	AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"CHARGE association"	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.5842G>A	chr8.hg19:g.61764754G>A	ENSP00000392028:p.Val1948Met	112.0	0.0		127.0	53.0	NM_017780	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Missense_Mutation	SNP	ENST00000423902.2	hg19	CCDS47865.1	.	.	.	.	.	.	.	.	.	.	G	13.35	2.209770	0.39003	.	.	ENSG00000171316	ENST00000307121;ENST00000423902	D	0.86956	-2.19	5.18	5.18	0.71444	.	0.152794	0.42548	D	0.000689	D	0.85630	0.5741	N	0.25332	0.735	0.39940	D	0.974391	D	0.54772	0.968	P	0.50860	0.652	D	0.85789	0.1366	10	0.36615	T	0.2	-19.0624	19.0585	0.93076	0.0:0.0:1.0:0.0	.	1948	Q9P2D1	CHD7_HUMAN	M	1948	ENSP00000392028:V1948M	ENSP00000307304:V1948M	V	+	1	0	CHD7	61927308	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.139000	0.71728	2.583000	0.87209	0.655000	0.94253	GTG	.	.		0.537	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762		A	61764754	G	A	61764754	3	1	288	1	0	0	0	0	1	0	0	0	3332	1029	36	3	5952	3	CHD7	8	61764754	Missense_Mutation	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	28394635	61764754	84599268	46	42260										
LRRC67	286187	hgsc.bcm.edu	37	chr8	67926750	67926750	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	tgggtcagatttgtggcataAttcaggttagtgatttgact	12	4	2	3			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr8:67926750A>G	ENST00000324682.5	-	3	351	c.207T>C	c.(205-207)aaT>aaC	p.N69N	PPP1R42_ENST00000522909.1_Silent_p.N69N|PPP1R42_ENST00000517834.1_Intron	NM_001013626.2	NP_001013648.1	Q7Z4L9	PPR42_HUMAN	protein phosphatase 1, regulatory subunit 42	69					regulation of phosphatase activity (GO:0010921)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|manchette (GO:0002177)|microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)	actin binding (GO:0003779)|dynein binding (GO:0045502)|tubulin binding (GO:0015631)										TTGTGGCATAATTCAGGTTAG	0.313																																					p.N69N		Atlas-SNP	.											.	PPP1R42	2	.	0			c.T207C						.						96	107	103					8																	67926750		2203	4289	6492	SO:0001819	synonymous_variant	286187	exon3			GGCATAATTCAGG	BC055413	CCDS34902.1	8q13.1-q13.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000178125	ENSG00000178125		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	33732	protein-coding gene	gene with protein product	"testis leucine-rich repeat"		"leucine rich repeat containing 67"	LRRC67			Standard	NM_001013626		Approved	dtr, TLLR	uc003xxc.3	Q7Z4L9	OTTHUMG00000164745	ENST00000324682.5:c.207T>C	chr8.hg19:g.67926750A>G		89.0	0.0		83.0	11.0	NM_001013626		Silent	SNP	ENST00000324682.5	hg19	CCDS34902.1																																																																																			.	.		0.313	PPP1R42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380034.2	NM_001013626		G	67926750	A	G	67926750	2	3	288	1	0	0	0	0	0	0	0	1	9028	98	4	2		2	LRRC67	8	67926750	Silent	SNP	A	TCGA-G3-A5SM-01A-12D-A28X-10	6161996	67926750	78437272	47	42261										
PGCP	10404	hgsc.bcm.edu	37	chr8	97847252	97847252	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	tttcgatgaactgcagagaaGggcctcagaagcaagaggga	14	7	1	4			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr8:97847252G>C	ENST00000220763.5	+	3	695	c.485G>C	c.(484-486)aGg>aCg	p.R162T		NM_016134.2	NP_057218.1	Q9Y646	CBPQ_HUMAN	carboxypeptidase Q	162					peptide catabolic process (GO:0043171)|proteolysis (GO:0006508)|thyroid hormone generation (GO:0006590)|tissue regeneration (GO:0042246)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)	carboxypeptidase activity (GO:0004180)|metal ion binding (GO:0046872)|metallodipeptidase activity (GO:0070573)|protein homodimerization activity (GO:0042803)										CTGCAGAGAAGGGCCTCAGAA	0.473																																					p.R162T		Atlas-SNP	.											.	.	.	.	0			c.G485C						.						121	112	115					8																	97847252		2203	4300	6503	SO:0001583	missense	10404	exon3			AGAGAAGGGCCTC	AF107834	CCDS6273.1	8q22.2	2012-02-17			ENSG00000104324	ENSG00000104324			16910	protein-coding gene	gene with protein product	"lysosomal dipeptidase", "Ser-Met dipeptidase", "plasma glutamate carboxypeptidase"					10206990	Standard	NM_016134		Approved	LDP, PGCP	uc003yhw.3	Q9Y646	OTTHUMG00000164690	ENST00000220763.5:c.485G>C	chr8.hg19:g.97847252G>C	ENSP00000220763:p.Arg162Thr	215.0	0.0		235.0	88.0	NM_016134	B2RD88|Q8NBZ1|Q9UNM8|Q9Y5X6	Missense_Mutation	SNP	ENST00000220763.5	hg19	CCDS6273.1	.	.	.	.	.	.	.	.	.	.	G	12.14	1.848311	0.32699	.	.	ENSG00000104324	ENST00000220763;ENST00000517742	T;T	0.45668	0.94;0.89	5.74	4.87	0.63330	.	0.047455	0.85682	D	0.000000	T	0.49457	0.1558	L	0.55103	1.725	0.39093	D	0.961145	P;D	0.55172	0.893;0.97	P;P	0.54759	0.76;0.67	T	0.47699	-0.9097	10	0.22706	T	0.39	-25.4327	12.6301	0.56653	0.0758:0.0:0.9242:0.0	.	162;162	B5MDX4;Q9Y646	.;PGCP_HUMAN	T	162	ENSP00000220763:R162T;ENSP00000429146:R162T	ENSP00000220763:R162T	R	+	2	0	AC010859.1	97916428	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	4.876000	0.63079	1.418000	0.47098	0.655000	0.94253	AGG	.	.		0.473	CPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379757.2	NM_016134		C	97847252	G	C	97847252	3	2	288	1	0	0	0	0	1	0	0	0	11795	1000	35	4	491	4	PGCP	8	97847252	Missense_Mutation	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	29920502	97847252	48516770	48	42262										
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110447476	110447476	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	tggacatgcccccgttgctgTgtccatggctgatgttggac	13	11	0	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr8:110447476T>G	ENST00000378402.5	+	29	3502	c.3398T>G	c.(3397-3399)gTg>gGg	p.V1133G		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	1133	IPT/TIG 4.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			CCCGTTGCTGTGTCCATGGCT	0.423										HNSCC(38;0.096)																											p.V1133G		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.T3398G						.						175	175	175					8																	110447476		1865	4121	5986	SO:0001583	missense	93035	exon29			TTGCTGTGTCCAT	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.3398T>G	chr8.hg19:g.110447476T>G	ENSP00000367655:p.Val1133Gly	115.0	0.0		120.0	6.0	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	hg19	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	T	14.21	2.467625	0.43839	.	.	ENSG00000205038	ENST00000378402	D	0.81908	-1.55	6.07	6.07	0.98685	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.074683	0.52532	D	0.000065	D	0.90823	0.7118	M	0.84082	2.675	0.46901	D	0.999245	D	0.67145	0.996	D	0.68765	0.96	D	0.91925	0.5550	10	0.87932	D	0	.	13.0325	0.58851	0.0:0.0:0.0:1.0	.	1133	Q86WI1	PKHL1_HUMAN	G	1133	ENSP00000367655:V1133G	ENSP00000367655:V1133G	V	+	2	0	PKHD1L1	110516652	1.000000	0.71417	0.994000	0.49952	0.026000	0.11368	3.959000	0.56744	2.326000	0.78906	0.533000	0.62120	GTG	.	.		0.423	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		G	110447476	T	G	110447476	3	3	288	1	0	0	0	0	1	0	0	0	11981	1696	59	5	3512	5	PKHD1L1	8	110447476	Missense_Mutation	SNP	T	TCGA-G3-A5SM-01A-12D-A28X-10	12600224	110447476	35916546	49	42263										
PUF60	22827	hgsc.bcm.edu	37	chr8	144899577	144899577	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	ggctgggccagggtcagtgcTggggacaccagtccaggtgt	18	10	1	0			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr8:144899577T>A	ENST00000526683.1	-	10	1623	c.1068A>T	c.(1066-1068)ccA>ccT	p.P356P	PUF60_ENST00000456095.2_Silent_p.P327P|SCRIB_ENST00000320476.3_5'Flank|SCRIB_ENST00000356994.2_5'Flank|PUF60_ENST00000313352.7_Silent_p.P296P|PUF60_ENST00000453551.2_Silent_p.P313P|PUF60_ENST00000527197.1_Silent_p.P310P|PUF60_ENST00000524570.1_5'UTR|SCRIB_ENST00000377533.3_5'Flank|PUF60_ENST00000349157.6_Silent_p.P339P	NM_001271098.1|NM_078480.2	NP_001258027.1|NP_510965.1	Q9UHX1	PUF60_HUMAN	poly-U binding splicing factor 60KDa	356	Inhibits homodimerization.|Inhibits transcriptional repression, interaction with ERCC3 and apoptosis induction.				apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(1)|kidney(3)|lung(7)|prostate(2)	14	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;6.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			GGGTCAGTGCTGGGGACACCA	0.637																																					p.P356P		Atlas-SNP	.											.	PUF60	26	.	0			c.A1068T						.						20	24	23					8																	144899577		2167	4281	6448	SO:0001819	synonymous_variant	22827	exon10			CAGTGCTGGGGAC	AF114818	CCDS47933.1, CCDS47934.1, CCDS47935.1, CCDS59514.1, CCDS59515.1, CCDS59516.1	8q24.3	2013-02-12	2007-07-27		ENSG00000179950	ENSG00000179950		"RNA binding motif (RRM) containing"	17042	protein-coding gene	gene with protein product	"siah binding protein 1", "FBP interacting repressor", "pyrimidine tract binding splicing factor", "Ro ribonucleoprotein binding protein 1"	604819				10668799, 10882074, 17579712	Standard	NM_078480		Approved	FIR, SIAHBP1, RoBPI	uc003yzs.4	Q9UHX1	OTTHUMG00000165155	ENST00000526683.1:c.1068A>T	chr8.hg19:g.144899577T>A		151.0	0.0		187.0	84.0	NM_078480	A8K8K8|Q969E7|Q96D94|Q96H63|Q99628|Q9NZA0|Q9UJY7	Silent	SNP	ENST00000526683.1	hg19	CCDS47934.1	.	.	.	.	.	.	.	.	.	.	T	9.483	1.098705	0.20552	.	.	ENSG00000179950	ENST00000532884	.	.	.	3.96	-1.84	0.07809	.	.	.	.	.	T	0.39655	0.1086	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.29366	-1.0014	4	.	.	.	.	1.7799	0.03029	0.4723:0.1027:0.1016:0.3233	.	.	.	.	L	226	.	.	Q	-	2	0	PUF60	144971565	0.735000	0.28153	0.987000	0.45799	0.990000	0.78478	-0.368000	0.07543	-0.113000	0.11958	0.459000	0.35465	CAG	.	.		0.637	PUF60-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382222.1	NM_014281		A	144899577	T	A	144899577	2	1	288	1	0	0	0	0	0	0	0	1	12839	1567	55	4		4	PUF60	8	144899577	Silent	SNP	T	TCGA-G3-A5SM-01A-12D-A28X-10	34452101	144899577	1464445	50	42264										
PARP10	84875	hgsc.bcm.edu	37	chr8	145059302	145059302	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	gcccattgtcacagtccctgCaccctgcagagccgtcacca	8	18	2	1	rs199611396		TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr8:145059302C>A	ENST00000313028.7	-	5	962	c.868G>T	c.(868-870)Gca>Tca	p.A290S	PARP10_ENST00000525773.1_Missense_Mutation_p.A302S|PARP10_ENST00000533665.1_5'UTR|PARP10_ENST00000524918.1_Missense_Mutation_p.A290S	NM_032789.3	NP_116178.2	Q53GL7	PAR10_HUMAN	poly (ADP-ribose) polymerase family, member 10	290					negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of gene expression (GO:0010629)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of protein K63-linked ubiquitination (GO:1900045)|negative regulation of viral genome replication (GO:0045071)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein poly-ADP-ribosylation (GO:0070212)|regulation of chromatin assembly (GO:0010847)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	K63-linked polyubiquitin binding (GO:0070530)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(4)|pancreas(1)|upper_aerodigestive_tract(2)	27	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.31e-40)|Epithelial(56;1.16e-39)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			ACAGTCCCTGCACCCTGCAGA	0.627																																					p.A290S		Atlas-SNP	.											.	PARP10	57	.	0			c.G868T						.						84	82	83					8																	145059302		2203	4300	6503	SO:0001583	missense	84875	exon5			TCCCTGCACCCTG	AK027370	CCDS34960.1	8q24	2010-02-16				ENSG00000178685		"Poly (ADP-ribose) polymerases"	25895	protein-coding gene	gene with protein product		609564				15273990	Standard	NM_032789		Approved	FLJ14464	uc003zal.4	Q53GL7		ENST00000313028.7:c.868G>T	chr8.hg19:g.145059302C>A	ENSP00000325618:p.Ala290Ser	75.0	0.0		81.0	13.0	NM_032789	Q8N2I0|Q8WV05|Q96CH7|Q96K72	Missense_Mutation	SNP	ENST00000313028.7	hg19	CCDS34960.1	.	.	.	.	.	.	.	.	.	.	C	8.863	0.947293	0.18356	.	.	ENSG00000178685	ENST00000524918;ENST00000313028;ENST00000525773;ENST00000313059	T;T;T;T	0.57107	2.61;2.55;2.53;0.42	3.01	-6.03	0.02185	.	1.668030	0.04232	U	0.335399	T	0.27278	0.0669	N	0.19112	0.55	0.09310	N	1	B;B;B	0.22800	0.035;0.028;0.075	B;B;B	0.17433	0.018;0.007;0.018	T	0.10042	-1.0647	10	0.15499	T	0.54	.	0.9804	0.01435	0.1384:0.2593:0.2557:0.3466	.	302;290;290	E9PNI7;E9PK67;Q53GL7	.;.;PAR10_HUMAN	S	290;290;302;205	ENSP00000431620:A290S;ENSP00000325618:A290S;ENSP00000434776:A302S;ENSP00000314320:A205S	ENSP00000325618:A290S	A	-	1	0	PARP10	145131290	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.212000	0.09319	-1.108000	0.03000	-0.488000	0.04728	GCA	.	.		0.627	PARP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383866.1	NM_032789		A	145059302	C	A	145059302	3	1	288	1	0	0	0	0	1	0	0	0	11464	710	25	3	2237	3	PARP10	8	145059302	Missense_Mutation	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	159725	145059302	1304720	51	42265										
DNAI1	27019	hgsc.bcm.edu	37	chr9	34514529	34514529	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	tggacagtgaagatctgggaCcacaccatcaagtgaggggc	14	9	2	3			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr9:34514529C>T	ENST00000242317.4	+	17	1878	c.1707C>T	c.(1705-1707)gaC>gaT	p.D569D		NM_001281428.1|NM_012144.2	NP_001268357.1|NP_036276.1	Q9UI46	DNAI1_HUMAN	dynein, axonemal, intermediate chain 1	569					cell projection organization (GO:0030030)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	motor activity (GO:0003774)			autonomic_ganglia(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(13)|prostate(1)|skin(2)|urinary_tract(1)	34	all_epithelial(49;0.244)		LUSC - Lung squamous cell carcinoma(29;0.0107)|STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.0222)		AGATCTGGGACCACACCATCA	0.597									Kartagener syndrome																												p.D569D		Atlas-SNP	.											.	DNAI1	72	.	0			c.C1707T						.						117	111	113					9																	34514529		2203	4300	6503	SO:0001819	synonymous_variant	27019	exon17	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CTGGGACCACACC	AF091619	CCDS6557.1, CCDS75829.1	9p13.3	2013-02-19	2006-09-04		ENSG00000122735	ENSG00000122735		"Axonemal dyneins", "WD repeat domain containing"	2954	protein-coding gene	gene with protein product		604366	"dynein, axonemal, intermediate polypeptide 1"			10577904, 21953912	Standard	NM_012144		Approved	DIC1, PCD, CILD1	uc003zum.3	Q9UI46	OTTHUMG00000019825	ENST00000242317.4:c.1707C>T	chr9.hg19:g.34514529C>T		91.0	0.0		90.0	14.0	NM_012144	B7Z7U1|Q5T8G7|Q8NHQ7|Q9UEZ8	Silent	SNP	ENST00000242317.4	hg19	CCDS6557.1	.	.	.	.	.	.	.	.	.	.	C	7.842	0.722142	0.15372	.	.	ENSG00000122735	ENST00000442556	.	.	.	5.57	4.67	0.58626	.	.	.	.	.	T	0.58047	0.2095	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56165	-0.8024	4	.	.	.	.	7.5718	0.27911	0.1617:0.7545:0.0:0.0838	.	.	.	.	I	73	.	.	T	+	2	0	DNAI1	34504529	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.112000	0.31172	1.352000	0.45808	0.561000	0.74099	ACC	.	.		0.597	DNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052192.1			T	34514529	C	T	34514529	2	4	288	1	0	0	0	0	0	0	0	1	4611	506	18	3		3	DNAI1	9	34514529	Silent	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10		34514529	106698902	52	42266										
TLE4	7091	hgsc.bcm.edu	37	chr9	82320836	82320837	+	Missense_Mutation	DNP	GG	GG	TT													0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	gagaaaagtgatgacaacttGgtggttgacgtttccaatga							TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr9:82320836_82320837GG>TT	ENST00000376552.2	+	10	1780_1781	c.762_763GG>TT	c.(760-765)ttGGtg>ttTTtg	p.254_255LV>FL	TLE4_ENST00000376544.3_Intron|TLE4_ENST00000265284.6_Missense_Mutation_p.229_230LV>FL|TLE4_ENST00000376537.4_Missense_Mutation_p.254_255LV>FL|TLE4_ENST00000376520.4_Missense_Mutation_p.254_255LV>FL|TLE4_ENST00000376534.4_5'UTR	NM_007005.3	NP_008936.2	Q04727	TLE4_HUMAN	transducin-like enhancer of split 4	254	CCN domain.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|Wnt signaling pathway (GO:0016055)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	39						ATGACAACTTGGTGGTTGACGT	0.401																																					p.L254F|p.V255L		Atlas-SNP	.											.	TLE4	187	.	0			c.G762T|c.G763T						.																																			SO:0001583	missense	7091	exon10			CAACTTGGTGGTT|AACTTGGTGGTTG	M99439	CCDS43837.1, CCDS65069.1, CCDS65070.1, CCDS75851.1	9q21.32	2014-03-07	2014-03-07		ENSG00000106829	ENSG00000106829		"WD repeat domain containing"	11840	protein-coding gene	gene with protein product		605132	"transducin-like enhancer of split 4, homolog of Drosophila E(sp1)", "transducin-like enhancer of split 4 (E(sp1) homolog, Drosophila)"			8365415	Standard	XM_005252167		Approved	E(spI), ESG, GRG4	uc004alc.3	Q04727	OTTHUMG00000020072	Exception_encountered	chr9.hg19:g.82320836_82320837delinsTT	ENSP00000365735:p.L254_V255delinsFL	326.0|322.0	0.0		166.0|161.0	52.0|49.0	NM_007005	F8W6T6|Q3ZCS1|Q5T1Y2|Q6PCB3|Q9BZ07|Q9BZ08|Q9BZ09|Q9NSL3|Q9ULF9	Missense_Mutation	SNP	ENST00000376552.2	hg19	CCDS43837.1																																																																																			.	.		0.401	TLE4-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052792.4	XM_212237		TT	82320837	GG	TT	82320836	3	4	288	1	0	0	0	0	1	0	0	0	15956	1339	47	3	800	3	TLE4	9	82320836	Missense_Mutation	DNP	GG	TCGA-G3-A5SM-01A-12D-A28X-10	47806307	82320836	58892595	53	42267										
ABCA1	19	hgsc.bcm.edu	37	chr9	107607783	107607783	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	gggccagagtcccaagactaTgcagcaatgtttttgtggct	12	9	0	2			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr9:107607783T>C	ENST00000374736.3	-	8	1182	c.788A>G	c.(787-789)cAt>cGt	p.H263R		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	263					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	CCCAAGACTATGCAGCAATGT	0.448																																					p.H263R		Atlas-SNP	.											.	ABCA1	244	.	0			c.A788G						.						117	105	109					9																	107607783		2203	4300	6503	SO:0001583	missense	19	exon8			AGACTATGCAGCA	AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"ATP binding cassette transporters / subfamily A"	29	protein-coding gene	gene with protein product	"Tangier disease"	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.788A>G	chr9.hg19:g.107607783T>C	ENSP00000363868:p.His263Arg	87.0	0.0		79.0	21.0	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Missense_Mutation	SNP	ENST00000374736.3	hg19	CCDS6762.1	.	.	.	.	.	.	.	.	.	.	T	7.197	0.592676	0.13875	.	.	ENSG00000165029	ENST00000374736	D	0.87571	-2.27	5.62	3.26	0.37387	.	0.583335	0.19928	N	0.102936	T	0.75221	0.3820	N	0.14661	0.345	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.66280	-0.5963	10	0.56958	D	0.05	.	8.4518	0.32875	0.0:0.1534:0.0:0.8466	.	263	O95477	ABCA1_HUMAN	R	263	ENSP00000363868:H263R	ENSP00000363868:H263R	H	-	2	0	ABCA1	106647604	0.260000	0.24053	0.452000	0.26994	0.123000	0.20343	3.305000	0.51873	0.413000	0.25759	-0.361000	0.07541	CAT	.	.		0.448	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502		C	107607783	T	C	107607783	3	2	288	1	0	0	0	0	1	0	0	0	28	1464	51	2	6169	2	ABCA1	9	107607783	Missense_Mutation	SNP	T	TCGA-G3-A5SM-01A-12D-A28X-10	25286947	107607783	33605648	54	42268										
TPRN	286262	hgsc.bcm.edu	37	chr9	140093940	140093940	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	ctctgccacctaatagcccgGtcagcgagggcggtggctgt	14	13	2	0			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr9:140093940G>T	ENST00000409012.4	-	1	1310	c.1224C>A	c.(1222-1224)gaC>gaA	p.D408E	TPRN_ENST00000321773.2_Missense_Mutation_p.D347E|TPRN_ENST00000541945.1_Intron	NM_001128228.2	NP_001121700.2	Q4KMQ1	TPRN_HUMAN	taperin	408					sensory perception of sound (GO:0007605)	stereocilium (GO:0032420)				breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)	8						TAATAGCCCGGTCAGCGAGGG	0.697																																					p.D408E		Atlas-SNP	.											.	TPRN	28	.	0			c.C1224A						.						9	12	11					9																	140093940		2181	4279	6460	SO:0001583	missense	286262	exon1			AGCCCGGTCAGCG	AK074735	CCDS56594.1	9q34.3	2011-01-06	2010-03-24	2010-03-24	ENSG00000176058	ENSG00000176058			26894	protein-coding gene	gene with protein product		613354	"chromosome 9 open reading frame 75", "deafness, autosomal recessive 79"	C9orf75, DFNB79		20170898, 20170899	Standard	NM_001128228		Approved	FLJ90254	uc004clu.3	Q4KMQ1	OTTHUMG00000020984	ENST00000409012.4:c.1224C>A	chr9.hg19:g.140093940G>T	ENSP00000387100:p.Asp408Glu	102.0	0.0		75.0	33.0	NM_001128228	B7ZKU5|Q5VSG5|Q5VSG6|Q6IPP2|Q8NCH2	Missense_Mutation	SNP	ENST00000409012.4	hg19	CCDS56594.1	.	.	.	.	.	.	.	.	.	.	G	0.005	-2.152969	0.00325	.	.	ENSG00000176058	ENST00000333046;ENST00000409012;ENST00000321773	.	.	.	3.47	1.43	0.22495	.	2.020920	0.02495	N	0.089907	T	0.34221	0.0890	L	0.43923	1.385	0.09310	N	1	B	0.24618	0.107	B	0.20577	0.03	T	0.12682	-1.0538	9	0.28530	T	0.3	.	4.0337	0.09721	0.1489:0.2767:0.5745:0.0	.	408	Q4KMQ1	TPRN_HUMAN	E	206;408;347	.	ENSP00000313704:D347E	D	-	3	2	TPRN	139213761	0.472000	0.25870	0.162000	0.22713	0.120000	0.20174	0.966000	0.29331	0.653000	0.30826	0.456000	0.33151	GAC	.	.		0.697	TPRN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055323.3	NM_173691		T	140093940	G	T	140093940	3	4	288	1	0	0	0	0	1	0	0	0	16436	1252	44	3	1007	3	TPRN	9	140093940	Missense_Mutation	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	32486157	140093940	1119491	55	42269										
VIM	7431	hgsc.bcm.edu	37	chr10	17271663	17271663	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	gcccggggtgcggctcctgcAggactcggtggacttctcgc	16	14	1	0			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr10:17271663A>T	ENST00000224237.5	+	1	387	c.242A>T	c.(241-243)cAg>cTg	p.Q81L	VIM_ENST00000485947.1_3'UTR|VIM_ENST00000544301.1_Missense_Mutation_p.Q81L|VIM-AS1_ENST00000605833.1_RNA|VIM-AS1_ENST00000437232.1_RNA			P08670	VIME_HUMAN	vimentin	81	Head.				apoptotic process (GO:0006915)|astrocyte development (GO:0014002)|Bergmann glial cell differentiation (GO:0060020)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular component movement (GO:0006928)|intermediate filament organization (GO:0045109)|lens fiber cell development (GO:0070307)|muscle filament sliding (GO:0030049)|negative regulation of neuron projection development (GO:0010977)|positive regulation of gene expression (GO:0010628)|viral process (GO:0016032)	cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|neuron projection (GO:0043005)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	double-stranded RNA binding (GO:0003725)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(2)|lung(18)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CGGCTCCTGCAGGACTCGGTG	0.677																																					p.Q81L		Atlas-SNP	.											.	VIM	71	.	0			c.A242T						.						15	15	15					10																	17271663		2168	4246	6414	SO:0001583	missense	7431	exon2			TCCTGCAGGACTC	M14144	CCDS7120.1	10p13	2013-01-16			ENSG00000026025	ENSG00000026025		"Intermediate filaments type III"	12692	protein-coding gene	gene with protein product		193060					Standard	NM_003380		Approved		uc001iou.2	P08670	OTTHUMG00000017744	ENST00000224237.5:c.242A>T	chr10.hg19:g.17271663A>T	ENSP00000224237:p.Gln81Leu	108.0	0.0		98.0	34.0	NM_003380	B0YJC2|D3DRU4|Q15867|Q15868|Q15869|Q548L2|Q6LER9|Q8N850|Q96ML2|Q9NTM3	Missense_Mutation	SNP	ENST00000224237.5	hg19	CCDS7120.1	.	.	.	.	.	.	.	.	.	.	A	10.51	1.369899	0.24771	.	.	ENSG00000026025	ENST00000544301;ENST00000224237;ENST00000545533	D;D	0.82255	-1.59;-1.59	5.29	4.12	0.48240	Intermediate filament head, DNA-binding domain (1);	0.153499	0.30383	N	0.009749	T	0.68778	0.3038	N	0.19112	0.55	0.35531	D	0.802231	B;B;B;B;B	0.06786	0.0;0.0;0.001;0.001;0.0	B;B;B;B;B	0.11329	0.004;0.002;0.004;0.006;0.004	T	0.64918	-0.6294	10	0.33141	T	0.24	.	7.5003	0.27513	0.7098:0.1484:0.0:0.1418	.	81;68;68;81;81	Q53HU8;F5H288;B3KRK8;B0YJC4;P08670	.;.;.;.;VIME_HUMAN	L	81;81;68	ENSP00000446007:Q81L;ENSP00000224237:Q81L	ENSP00000224237:Q81L	Q	+	2	0	VIM	17311669	1.000000	0.71417	0.998000	0.56505	0.928000	0.56348	4.392000	0.59659	0.809000	0.34255	0.450000	0.29827	CAG	.	.		0.677	VIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047015.1	NM_003380		T	17271663	A	T	17271663	3	4	288	1	0	0	0	0	1	0	0	0	17181	188	7	4	244	4	VIM	10	17271663	Missense_Mutation	SNP	A	TCGA-G3-A5SM-01A-12D-A28X-10		17271663	118263084	56	42270										
MYO3A	53904	hgsc.bcm.edu	37	chr10	26409644	26409644	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	gcatactcgctgcaatcttgAatgttggcaacattgaattt	8	8	1	2			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr10:26409644A>T	ENST00000265944.5	+	18	1982	c.1816A>T	c.(1816-1818)Aat>Tat	p.N606Y	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	606	Myosin motor.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						TGCAATCTTGAATGTTGGCAA	0.403																																					p.N606Y		Atlas-SNP	.											.	MYO3A	371	.	0			c.A1816T						.						186	155	165					10																	26409644		2203	4300	6503	SO:0001583	missense	53904	exon18			ATCTTGAATGTTG	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.1816A>T	chr10.hg19:g.26409644A>T	ENSP00000265944:p.Asn606Tyr	113.0	0.0		82.0	27.0	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	hg19	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	A	26.9	4.779314	0.90195	.	.	ENSG00000095777	ENST00000265944	T	0.71222	-0.55	5.96	5.96	0.96718	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	T	0.79341	0.4429	L	0.39467	1.215	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	T	0.81219	-0.1032	10	0.87932	D	0	.	16.4447	0.83919	1.0:0.0:0.0:0.0	.	606	Q8NEV4	MYO3A_HUMAN	Y	606	ENSP00000265944:N606Y	ENSP00000265944:N606Y	N	+	1	0	MYO3A	26449650	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.339000	0.96797	2.284000	0.76573	0.528000	0.53228	AAT	.	.		0.403	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		T	26409644	A	T	26409644	3	4	288	1	0	0	0	0	1	0	0	0	10085	246	9	4	1878	4	MYO3A	10	26409644	Missense_Mutation	SNP	A	TCGA-G3-A5SM-01A-12D-A28X-10	9137981	26409644	109125103	57	42271										
A1CF	29974	hgsc.bcm.edu	37	chr10	52575807	52575807	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	taatggctctgttgctgagaTgtcctttggtggctgggaaa	14	6	1	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr10:52575807T>C	ENST00000373993.1	-	7	1144	c.1100A>G	c.(1099-1101)cAt>cGt	p.H367R	A1CF_ENST00000374001.2_Missense_Mutation_p.H367R|A1CF_ENST00000395489.2_Missense_Mutation_p.H360R|ASAH2B_ENST00000483649.1_3'UTR|A1CF_ENST00000493415.1_5'UTR|A1CF_ENST00000373997.3_Missense_Mutation_p.H367R|A1CF_ENST00000282641.2_Missense_Mutation_p.H367R|A1CF_ENST00000395495.1_Missense_Mutation_p.H312R|A1CF_ENST00000373995.3_Missense_Mutation_p.H375R			Q9NQ94	A1CF_HUMAN	APOBEC1 complementation factor	367	Required for nuclear localization. {ECO:0000269|PubMed:12896982}.				cytidine to uridine editing (GO:0016554)|gene expression (GO:0010467)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|protein stabilization (GO:0050821)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			NS(1)|breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(14)|prostate(2)|skin(3)	29						GTTGCTGAGATGTCCTTTGGT	0.473																																					p.H375R		Atlas-SNP	.											.	A1CF	190	.	0			c.A1124G						.						155	150	152					10																	52575807		2203	4300	6503	SO:0001583	missense	29974	exon10			CTGAGATGTCCTT	AF271790	CCDS7241.1, CCDS7242.1, CCDS7243.1, CCDS73133.1	10q21.1	2013-02-12			ENSG00000148584	ENSG00000148584		"RNA binding motif (RRM) containing"	24086	protein-coding gene	gene with protein product						11815617, 11072063	Standard	NM_014576		Approved	ACF, ASP, ACF64, ACF65, APOBEC1CF	uc001jjj.3	Q9NQ94	OTTHUMG00000018240	ENST00000373993.1:c.1100A>G	chr10.hg19:g.52575807T>C	ENSP00000363105:p.His367Arg	205.0	0.0		177.0	50.0	NM_001198820	A1L4F2|A8K7G7|B7ZM14|Q5SZQ0|Q9NQ93|Q9NQX8|Q9NQX9|Q9NXC9|Q9NZD3	Missense_Mutation	SNP	ENST00000373993.1	hg19	CCDS7242.1	.	.	.	.	.	.	.	.	.	.	T	15.91	2.973237	0.53614	.	.	ENSG00000148584	ENST00000374001;ENST00000373993;ENST00000373997;ENST00000373995;ENST00000282641;ENST00000395495;ENST00000395488;ENST00000395489	T;T;T;T;T;T;T	0.10960	2.88;2.94;2.88;2.88;2.94;2.82;2.94	5.78	3.26	0.37387	.	0.428194	0.29348	N	0.012402	T	0.07954	0.0199	L	0.29908	0.895	0.38326	D	0.943653	B;B;B;B	0.22003	0.063;0.012;0.008;0.0	B;B;B;B	0.21360	0.034;0.006;0.009;0.004	T	0.24190	-1.0167	10	0.21014	T	0.42	.	11.3109	0.49364	0.0:0.0:0.2317:0.7683	.	360;367;367;375	F8W9F8;Q9NQ94;Q9NQ94-2;Q9NQ94-4	.;A1CF_HUMAN;.;.	R	367;367;367;375;367;312;350;360	ENSP00000363113:H367R;ENSP00000363105:H367R;ENSP00000363109:H367R;ENSP00000363107:H375R;ENSP00000282641:H367R;ENSP00000378873:H312R;ENSP00000378868:H360R	ENSP00000282641:H367R	H	-	2	0	A1CF	52245813	0.995000	0.38212	0.998000	0.56505	0.989000	0.77384	2.389000	0.44407	2.214000	0.71695	0.528000	0.53228	CAT	.	.		0.473	A1CF-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048086.2	NM_014576		C	52575807	T	C	52575807	3	2	288	1	0	0	0	0	1	0	0	0	2	1464	51	2	704	2	A1CF	10	52575807	Missense_Mutation	SNP	T	TCGA-G3-A5SM-01A-12D-A28X-10	26166163	52575807	82958940	58	42272										
TMEM26	219623	hgsc.bcm.edu	37	chr10	63212687	63212687	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	cgcttgaacttgagggtgagCgcagtctccaggaagagcaa	14	9	1	4			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr10:63212687C>T	ENST00000399298.3	-	1	521	c.153G>A	c.(151-153)gcG>gcA	p.A51A	TMEM26_ENST00000399293.1_Silent_p.A51A|RP11-809M12.1_ENST00000389640.4_RNA	NM_178505.6	NP_848600.2	Q6ZUK4	TMM26_HUMAN	transmembrane protein 26	51						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	18	Prostate(12;0.0112)					TGAGGGTGAGCGCAGTCTCCA	0.637																																					p.A51A		Atlas-SNP	.											.	TMEM26	47	.	0			c.G153A						.						74	86	82					10																	63212687		2032	4182	6214	SO:0001819	synonymous_variant	219623	exon1			GGTGAGCGCAGTC	BC042872	CCDS41530.1	10q21.3	2008-10-20			ENSG00000196932	ENSG00000196932			28550	protein-coding gene	gene with protein product						12477932	Standard	NM_178505		Approved	MGC35010, Em:AC068892.1	uc001jlo.2	Q6ZUK4	OTTHUMG00000018293	ENST00000399298.3:c.153G>A	chr10.hg19:g.63212687C>T		207.0	0.0		212.0	27.0	NM_178505	Q6ZVM0|Q8IVN9	Silent	SNP	ENST00000399298.3	hg19	CCDS41530.1																																																																																			.	.		0.637	TMEM26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359121.1	NM_178505		T	63212687	C	T	63212687	2	4	288	1	0	0	0	0	0	0	0	1	16166	755	27	1		1	TMEM26	10	63212687	Silent	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	10636880	63212687	72322060	59	42273										
STOX1	219736	hgsc.bcm.edu	37	chr10	70644911	70644911	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	attagactggagaaacacccCaagctccctgctacacagcc	7	15	0	2			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr10:70644911C>T	ENST00000298596.6	+	3	1442	c.1359C>T	c.(1357-1359)ccC>ccT	p.P453P	STOX1_ENST00000399169.4_Silent_p.P453P|STOX1_ENST00000421961.2_Silent_p.P343P|STOX1_ENST00000399162.2_Intron|STOX1_ENST00000399165.4_Intron	NM_152709.4	NP_689922.3	Q6ZVD7	STOX1_HUMAN	storkhead box 1	453						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|prostate(1)|skin(3)	28						AGAAACACCCCAAGCTCCCTG	0.488																																					p.P453P		Atlas-SNP	.											.	STOX1	75	.	0			c.C1359T						.						106	109	108					10																	70644911		1908	4114	6022	SO:0001819	synonymous_variant	219736	exon3			ACACCCCAAGCTC	AK057891	CCDS41535.1, CCDS44416.1, CCDS44417.1	10q22.1	2005-11-29	2005-04-04	2005-04-04	ENSG00000165730	ENSG00000165730			23508	protein-coding gene	gene with protein product		609397	"chromosome 10 open reading frame 24"	C10orf24			Standard	NM_152709		Approved	FLJ25162	uc001joq.3	Q6ZVD7	OTTHUMG00000018367	ENST00000298596.6:c.1359C>T	chr10.hg19:g.70644911C>T		101.0	0.0		112.0	16.0	NM_152709	A2A3Q9|A5D6Y7|B0QZA4|B0QZA5|B0QZA6|Q4F8Q6|Q5I946|Q5I947|Q5I948|Q5VX38|Q5VX39|Q6ZRY3|Q96LR3|Q96LS0	Silent	SNP	ENST00000298596.6	hg19	CCDS41535.1																																																																																			.	.		0.488	STOX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276849.3	NM_152709		T	70644911	C	T	70644911	2	4	288	1	0	0	0	0	0	0	0	1	15334	581	21	3		3	STOX1	10	70644911	Silent	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	7432224	70644911	64889836	60	42274										
HKDC1	80201	hgsc.bcm.edu	37	chr10	71007177	71007177	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	acctgggtctggaaccgtctGaggctgactgcattgccgtc	13	12	2	2			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr10:71007177G>A	ENST00000354624.5	+	9	1226	c.1093G>A	c.(1093-1095)Gag>Aag	p.E365K	HKDC1_ENST00000395086.2_Missense_Mutation_p.E365K	NM_025130.3	NP_079406	Q2TB90	HKDC1_HUMAN	hexokinase domain containing 1	365	Hexokinase type-2 1.				carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)	cytosol (GO:0005829)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|mannokinase activity (GO:0019158)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						GGAACCGTCTGAGGCTGACTG	0.572																																					p.E365K		Atlas-SNP	.											.	HKDC1	98	.	0			c.G1093A						.						126	122	123					10																	71007177		2203	4300	6503	SO:0001583	missense	80201	exon9			CCGTCTGAGGCTG		CCDS7288.1	10q22.1	2006-10-24			ENSG00000156510	ENSG00000156510			23302	protein-coding gene	gene with protein product						12477932	Standard	NM_025130		Approved	FLJ37767, FLJ22761	uc001jpf.4	Q2TB90	OTTHUMG00000018371	ENST00000354624.5:c.1093G>A	chr10.hg19:g.71007177G>A	ENSP00000346643:p.Glu365Lys	177.0	0.0		190.0	51.0	NM_025130	B5MDN9|Q2TB91|Q5VTC7|Q7Z373|Q8WU37|Q96EH2|Q9H5Y9	Missense_Mutation	SNP	ENST00000354624.5	hg19	CCDS7288.1	.	.	.	.	.	.	.	.	.	.	G	13.73	2.324364	0.41197	.	.	ENSG00000156510	ENST00000354624;ENST00000395087;ENST00000395086	D;D	0.96265	-3.96;-3.96	4.84	4.84	0.62591	Hexokinase, C-terminal (1);	0.390122	0.28209	N	0.016190	D	0.93360	0.7883	L	0.33792	1.035	0.40601	D	0.981589	B	0.23591	0.088	B	0.30943	0.122	D	0.90623	0.4561	10	0.12766	T	0.61	-26.9802	18.1044	0.89516	0.0:0.0:1.0:0.0	.	365	Q2TB90	HKDC1_HUMAN	K	365	ENSP00000346643:E365K;ENSP00000378521:E365K	ENSP00000346643:E365K	E	+	1	0	HKDC1	70677183	1.000000	0.71417	0.919000	0.36401	0.746000	0.42486	4.420000	0.59841	2.498000	0.84270	0.561000	0.74099	GAG	.	.		0.572	HKDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048389.1	NM_025130		A	71007177	G	A	71007177	3	1	288	1	0	0	0	0	1	0	0	0	7202	1291	45	3	1127	3	HKDC1	10	71007177	Missense_Mutation	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	362266	71007177	64527570	61	42275										
SORCS1	114815	hgsc.bcm.edu	37	chr10	108367021	108367021	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	tgggtaagccagggagcaccGccaccaggatgtgctggcct	15	12	0	0			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr10:108367021G>A	ENST00000263054.6	-	23	3075	c.3068C>T	c.(3067-3069)gCg>gTg	p.A1023V	SORCS1_ENST00000369698.1_Missense_Mutation_p.A558V|SORCS1_ENST00000344440.6_Missense_Mutation_p.A1023V|SORCS1_ENST00000478809.2_5'UTR	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	1023					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		AGGGAGCACCGCCACCAGGAT	0.552																																					p.A1023V		Atlas-SNP	.											.	SORCS1	534	.	0			c.C3068T						.						66	63	64					10																	108367021		2203	4300	6503	SO:0001583	missense	114815	exon23			AGCACCGCCACCA	AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.3068C>T	chr10.hg19:g.108367021G>A	ENSP00000263054:p.Ala1023Val	90.0	0.0		78.0	24.0	NM_001206572	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	hg19	CCDS7559.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.37|13.37	2.217666|2.217666	0.39201|0.39201	.|.	.|.	ENSG00000108018|ENSG00000108018	ENST00000369698;ENST00000263054;ENST00000344440|ENST00000452214	T;T;T|.	0.20881|.	2.04;2.57;2.59|.	5.92|5.92	5.92|5.92	0.95590|0.95590	.|.	0.059080|.	0.64402|.	D|.	0.000002|.	T|T	0.65450|0.65450	0.2692|0.2692	L|L	0.35249|0.35249	1.045|1.045	0.58432|0.58432	D|D	0.999998|0.999998	B;P;P;B;P|.	0.37038|.	0.443;0.579;0.579;0.443;0.579|.	B;B;B;B;B|.	0.31290|.	0.06;0.127;0.127;0.06;0.127|.	T|T	0.58487|0.58487	-0.7628|-0.7628	9|5	.|.	.|.	.|.	-22.0366|-22.0366	19.9164|19.9164	0.97064|0.97064	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1023;1023;1023;1023;1023|.	A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2|.	.;.;.;SORC1_HUMAN;.|.	V|W	558;1023;1023|38	ENSP00000358712:A558V;ENSP00000263054:A1023V;ENSP00000345964:A1023V|.	.|.	A|R	-|-	2|1	0|2	SORCS1|SORCS1	108357011|108357011	1.000000|1.000000	0.71417|0.71417	0.968000|0.968000	0.41197|0.41197	0.742000|0.742000	0.42306|0.42306	8.452000|8.452000	0.90346|0.90346	2.804000|2.804000	0.96469|0.96469	0.655000|0.655000	0.94253|0.94253	GCG|CGG	.	.		0.552	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918		A	108367021	G	A	108367021	3	1	288	1	0	0	0	0	1	0	0	0	14945	1087	38	1	688	1	SORCS1	10	108367021	Missense_Mutation	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	37359844	108367021	27167726	62	42276										
OR4A15	81328	hgsc.bcm.edu	37	chr11	55135547	55135547	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	tgtcacattcttactaatctAcatggtgacgataatgggca	8	8	3	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr11:55135547A>T	ENST00000314706.3	+	1	188	c.188A>T	c.(187-189)tAc>tTc	p.Y63F		NM_001005275.1	NP_001005275.1	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A, member 15	63						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(48)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	71						TTACTAATCTACATGGTGACG	0.423																																					p.Y63F		Atlas-SNP	.											.	OR4A15	161	.	0			c.A188T						.						93	85	88					11																	55135547		2201	4296	6497	SO:0001583	missense	81328	exon1			TAATCTACATGGT	AB065776	CCDS31500.1	11q11	2012-08-09			ENSG00000181958	ENSG00000181958		"GPCR / Class A : Olfactory receptors"	15152	protein-coding gene	gene with protein product							Standard	NM_001005275		Approved		uc010rif.2	Q8NGL6	OTTHUMG00000166711	ENST00000314706.3:c.188A>T	chr11.hg19:g.55135547A>T	ENSP00000325065:p.Tyr63Phe	108.0	0.0		123.0	17.0	NM_001005275	Q6IFL4|Q96R65	Missense_Mutation	SNP	ENST00000314706.3	hg19	CCDS31500.1	.	.	.	.	.	.	.	.	.	.	a	15.58	2.874859	0.51695	.	.	ENSG00000181958	ENST00000314706	T	0.04406	3.63	3.48	3.48	0.39840	.	0.000000	0.45606	D	0.000359	T	0.11623	0.0283	M	0.84156	2.68	0.34689	D	0.725566	B	0.33528	0.416	B	0.40285	0.325	T	0.04976	-1.0914	10	0.72032	D	0.01	.	10.0107	0.41984	1.0:0.0:0.0:0.0	.	63	Q8NGL6	O4A15_HUMAN	F	63	ENSP00000325065:Y63F	ENSP00000325065:Y63F	Y	+	2	0	OR4A15	54892123	0.997000	0.39634	0.544000	0.28141	0.021000	0.10359	5.616000	0.67709	1.456000	0.47831	0.403000	0.27427	TAC	.	.		0.423	OR4A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391161.1	NM_001005275		T	55135547	A	T	55135547	3	4	288	1	0	0	0	0	1	0	0	0	11049	391	14	4	190	4	OR4A15	11	55135547	Missense_Mutation	SNP	A	TCGA-G3-A5SM-01A-12D-A28X-10		55135547	79870969	63	42277										
OR4C11	219429	hgsc.bcm.edu	37	chr11	55371775	55371775	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	aaaattaagaagattacaaaCactattttctgcctcaaggg	6	7	2	2			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr11:55371775C>A	ENST00000302231.4	-	1	99	c.75G>T	c.(73-75)gtG>gtT	p.V25V		NM_001004700.2	NP_001004700.2	Q6IEV9	OR4CB_HUMAN	olfactory receptor, family 4, subfamily C, member 11	25						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(1)|large_intestine(5)|lung(23)|ovary(1)|prostate(1)|skin(1)	33						AGATTACAAACACTATTTTCT	0.408																																					p.V25V		Atlas-SNP	.											.	OR4C11	73	.	0			c.G75T						.						70	66	68					11																	55371775		2177	3998	6175	SO:0001819	synonymous_variant	219429	exon1			TACAAACACTATT	AB065774	CCDS31503.1	11q11	2012-08-09		2004-03-10	ENSG00000172188	ENSG00000172188		"GPCR / Class A : Olfactory receptors"	15167	protein-coding gene	gene with protein product				OR4C11P			Standard	NM_001004700		Approved		uc010rii.2	Q6IEV9	OTTHUMG00000165290	ENST00000302231.4:c.75G>T	chr11.hg19:g.55371775C>A		95.0	0.0		84.0	15.0	NM_001004700	B9EIL4|Q8NGL8	Silent	SNP	ENST00000302231.4	hg19	CCDS31503.1																																																																																			.	.		0.408	OR4C11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383268.1	NM_001004700		A	55371775	C	A	55371775	2	1	288	1	0	0	0	0	0	0	0	1	11054	465	17	3		3	OR4C11	11	55371775	Silent	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	236228	55371775	79634741	64	42278										
OR8K1	390157	hgsc.bcm.edu	37	chr11	56114194	56114194	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	tctcatatcctacatgtttaTtctagtggccattctcagaa	5	10	3	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr11:56114194T>G	ENST00000279783.2	+	1	774	c.680T>G	c.(679-681)aTt>aGt	p.I227S		NM_001002907.1	NP_001002907.1	Q8NGG5	OR8K1_HUMAN	olfactory receptor, family 8, subfamily K, member 1	227						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(8)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33	Esophageal squamous(21;0.00448)					TACATGTTTATTCTAGTGGCC	0.398										HNSCC(65;0.19)																											p.I227S		Atlas-SNP	.											.	OR8K1	93	.	0			c.T680G						.						98	89	92					11																	56114194		2201	4296	6497	SO:0001583	missense	390157	exon1			TGTTTATTCTAGT	AB065835	CCDS31528.1	11q11	2012-08-09			ENSG00000150261	ENSG00000150261		"GPCR / Class A : Olfactory receptors"	14831	protein-coding gene	gene with protein product							Standard	NM_001002907		Approved		uc010rjg.2	Q8NGG5	OTTHUMG00000166858	ENST00000279783.2:c.680T>G	chr11.hg19:g.56114194T>G	ENSP00000279783:p.Ile227Ser	96.0	0.0		105.0	51.0	NM_001002907	B9EJB1|Q6IFC3|Q96RC1	Missense_Mutation	SNP	ENST00000279783.2	hg19	CCDS31528.1	.	.	.	.	.	.	.	.	.	.	T	17.87	3.494499	0.64186	.	.	ENSG00000150261	ENST00000279783	T	0.00384	7.6	5.0	5.0	0.66597	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49916	D	0.000137	T	0.02012	0.0063	H	0.98446	4.235	0.50632	D	0.99988	D	0.76494	0.999	D	0.70487	0.969	T	0.05500	-1.0881	10	0.87932	D	0	-20.7066	14.7062	0.69191	0.0:0.0:0.0:1.0	.	227	Q8NGG5	OR8K1_HUMAN	S	227	ENSP00000279783:I227S	ENSP00000279783:I227S	I	+	2	0	OR8K1	55870770	1.000000	0.71417	0.021000	0.16686	0.613000	0.37349	7.351000	0.79395	1.862000	0.54008	0.448000	0.29417	ATT	.	.		0.398	OR8K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391605.1	NM_001002907		G	56114194	T	G	56114194	3	3	288	1	0	0	0	0	1	0	0	0	11252	1493	52	5	682	5	OR8K1	11	56114194	Missense_Mutation	SNP	T	TCGA-G3-A5SM-01A-12D-A28X-10	742419	56114194	78892322	65	42279										
TSKU	25987	hgsc.bcm.edu	37	chr11	76507685	76507685	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	ggccctgcactgcgtagacaCccgggattctgctgccaggg	14	14	1	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr11:76507685C>A	ENST00000527881.1	+	2	2051	c.1025C>A	c.(1024-1026)aCc>aAc	p.T342N	TSKU_ENST00000333090.4_Missense_Mutation_p.T342N			Q8WUA8	TSK_HUMAN	tsukushi, small leucine rich proteoglycan	342					anterior commissure morphogenesis (GO:0021960)|ciliary body morphogenesis (GO:0061073)|corpus callosum morphogenesis (GO:0021540)|lateral ventricle development (GO:0021670)|negative regulation of Wnt signaling pathway (GO:0030178)|regulation of gene expression (GO:0010468)	extracellular space (GO:0005615)				NS(1)|large_intestine(4)|lung(6)|urinary_tract(1)	12	Ovarian(111;0.112)					TGCGTAGACACCCGGGATTCT	0.677																																					p.T342N		Atlas-SNP	.											.	TSKU	26	.	0			c.C1025A						.						8	14	12					11																	76507685		2016	4002	6018	SO:0001583	missense	25987	exon2			TAGACACCCGGGA	AK075476	CCDS8246.1	11q13.5	2012-12-05	2012-12-05	2006-11-21	ENSG00000182704	ENSG00000182704			28850	protein-coding gene	gene with protein product		608015	"leucine rich repeat containing 54", "tsukushin", "tsukushi small leucine rich proteoglycan homolog (Xenopus laevis)"	LRRC54		11085516, 19710929, 22880013	Standard	NM_001258210		Approved	E2IG4, TSK	uc031qcw.1	Q8WUA8		ENST00000527881.1:c.1025C>A	chr11.hg19:g.76507685C>A	ENSP00000434847:p.Thr342Asn	55.0	0.0		38.0	11.0	NM_015516	B3KQT7|Q6UXK1|Q9UG10|Q9UJX9	Missense_Mutation	SNP	ENST00000527881.1	hg19	CCDS8246.1	.	.	.	.	.	.	.	.	.	.	C	12.73	2.024939	0.35701	.	.	ENSG00000182704	ENST00000333090;ENST00000439807;ENST00000527881	T;T	0.33216	1.42;1.42	4.63	1.26	0.21427	.	0.934295	0.09039	N	0.857533	T	0.15565	0.0375	N	0.19112	0.55	0.09310	N	1	B	0.23650	0.089	B	0.18263	0.021	T	0.33033	-0.9884	10	0.11485	T	0.65	-7.6346	4.7821	0.13208	0.0:0.5036:0.2745:0.2219	.	342	Q8WUA8	TSK_HUMAN	N	342;310;342	ENSP00000332668:T342N;ENSP00000434847:T342N	ENSP00000332668:T342N	T	+	2	0	TSKU	76185333	0.003000	0.15002	0.003000	0.11579	0.613000	0.37349	0.981000	0.29526	0.492000	0.27815	0.556000	0.70494	ACC	.	.		0.677	TSKU-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382871.1	NM_015516		A	76507685	C	A	76507685	3	1	288	1	0	0	0	0	1	0	0	0	16642	507	18	3	1027	3	TSKU	11	76507685	Missense_Mutation	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	20393491	76507685	58498831	66	42280										
CAPN5	726	hgsc.bcm.edu	37	chr11	76834775	76834775	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	aaggatgaatttctgggccaGgtgcacctaaaggctgaccc	12	10	1	2			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr11:76834775G>A	ENST00000278559.3	+	13	1971	c.1782G>A	c.(1780-1782)caG>caA	p.Q594Q	CAPN5_ENST00000456580.2_Silent_p.Q634Q|CAPN5_ENST00000531028.1_Splice_Site|CAPN5_ENST00000529629.1_Silent_p.Q594Q	NM_004055.4	NP_004046.2	O15484	CAN5_HUMAN	calpain 5	594	C2.				proteolysis (GO:0006508)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(1)|breast(2)|endometrium(2)|large_intestine(7)|lung(17)|urinary_tract(1)	30						TTCTGGGCCAGGTGCACCTAA	0.607																																					p.Q594Q		Atlas-SNP	.											.	CAPN5	67	.	0			c.G1782A						.						117	116	116					11																	76834775		2200	4292	6492	SO:0001819	synonymous_variant	726	exon13			GGGCCAGGTGCAC		CCDS8248.1	11q14	2014-01-29				ENSG00000149260			1482	protein-coding gene	gene with protein product		602537	"vitreoretinopathy, neovascular inflammatory"	VRNI		9503024, 9367857, 23055945	Standard	NM_004055		Approved	nCL-3, HTRA3, ADNIV	uc001oxx.3	O15484		ENST00000278559.3:c.1782G>A	chr11.hg19:g.76834775G>A		136.0	0.0		144.0	29.0	NM_004055	O00263	Silent	SNP	ENST00000278559.3	hg19	CCDS8248.1																																																																																			.	.		0.607	CAPN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382564.2	NM_004055		A	76834775	G	A	76834775	2	1	288	1	0	0	0	0	0	0	0	1	2631	991	35	3		3	CAPN5	11	76834775	Silent	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	327090	76834775	58171741	67	42281										
DSCAML1	57453	hgsc.bcm.edu	37	chr11	117342745	117342745	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	gtgtggactgcttgaagtccCaggaatctggagagaagaca	14	7	1	3			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr11:117342745C>T	ENST00000321322.6	-	15	2973	c.2972G>A	c.(2971-2973)tGg>tAg	p.W991*	DSCAML1_ENST00000527706.1_Nonsense_Mutation_p.W721*	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	931	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		CTTGAAGTCCCAGGAATCTGG	0.522																																					p.W991X		Atlas-SNP	.											.	DSCAML1	286	.	0			c.G2972A						.						143	122	129					11																	117342745		2201	4296	6497	SO:0001587	stop_gained	57453	exon15			AAGTCCCAGGAAT		CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.2972G>A	chr11.hg19:g.117342745C>T	ENSP00000315465:p.Trp991*	163.0	0.0		178.0	12.0	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Nonsense_Mutation	SNP	ENST00000321322.6	hg19	CCDS8384.1	.	.	.	.	.	.	.	.	.	.	C	39	7.714800	0.98450	.	.	ENSG00000177103	ENST00000527706;ENST00000321322;ENST00000446508	.	.	.	4.31	4.31	0.51392	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.9945	0.86363	0.0:1.0:0.0:0.0	.	.	.	.	X	721;991;698	.	ENSP00000315465:W991X	W	-	2	0	DSCAML1	116847955	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.645000	0.83430	2.226000	0.72624	0.455000	0.32223	TGG	.	.		0.522	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693		T	117342745	C	T	117342745	4	4	288	1	0	0	0	0	0	1	0	0	4771	595	21	3	3445	3	DSCAML1	11	117342745	Nonsense_Mutation	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	40507970	117342745	17663771	68	42282										
HYOU1	10525	hgsc.bcm.edu	37	chr11	118924950	118924950	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	tgtcatagaacatgatattcTgtagagatatcaaggcaact	8	6	3	3			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr11:118924950T>C	ENST00000404233.3	-	8	803		c.e8-2		HYOU1_ENST00000529972.1_Splice_Site|HYOU1_ENST00000525859.1_Splice_Site|HYOU1_ENST00000543287.1_Splice_Site	NM_001130991.1|NM_006389.3	NP_001124463.1|NP_006380.1	Q9Y4L1	HYOU1_HUMAN	hypoxia up-regulated 1						activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|response to ischemia (GO:0002931)|response to stress (GO:0006950)	endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(10)|prostate(1)|skin(2)	33	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.78e-05)		CATGATATTCTGTAGAGATAT	0.522																																					.		Atlas-SNP	.											.	HYOU1	88	.	0			c.679-2A>G						.						65	55	59					11																	118924950		2200	4295	6495	SO:0001630	splice_region_variant	10525	exon9			ATATTCTGTAGAG	U65785	CCDS8408.1	11q23.1-q23.3	2011-09-02			ENSG00000149428	ENSG00000149428		"Heat shock proteins / HSP70"	16931	protein-coding gene	gene with protein product	"glucose-regulated protein 170"	601746				9020069, 10037731	Standard	XM_005271390		Approved	ORP150, HSP12A, Grp170	uc001pux.3	Q9Y4L1	OTTHUMG00000166354	ENST00000404233.3:c.679-2A>G	chr11.hg19:g.118924950T>C		86.0	0.0		79.0	15.0	NM_001130991	A8C1Z0|B7Z909|Q2I204|Q53H25	Splice_Site	SNP	ENST00000404233.3	hg19	CCDS8408.1	.	.	.	.	.	.	.	.	.	.	T	16.94	3.261262	0.59431	.	.	ENSG00000149428	ENST00000404233;ENST00000353883;ENST00000529972;ENST00000536103;ENST00000535579;ENST00000525859;ENST00000544701;ENST00000543287;ENST00000530473	.	.	.	4.46	4.46	0.54185	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.9041	0.63823	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	HYOU1	118430160	1.000000	0.71417	0.872000	0.34217	0.730000	0.41778	7.466000	0.80914	1.879000	0.54435	0.460000	0.39030	.	.	.		0.522	HYOU1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389353.1	NM_006389	Intron	C	118924950	T	C	118924950	5	2	288	1	0	0	0	0	0	0	1	0	7479	1594	55	2	2398	2	HYOU1	11	118924950	Splice_Site	SNP	T	TCGA-G3-A5SM-01A-12D-A28X-10	1582205	118924950	16081566	69	42283										
CACNA1C	775	hgsc.bcm.edu	37	chr12	2774038	2774038	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	catcatgctggcctgcatgcCaggcaagaagtgtgccccag	12	13	1	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr12:2774038C>T	ENST00000347598.4	+	37	4424	c.4424C>T	c.(4423-4425)cCa>cTa	p.P1475L	CACNA1C_ENST00000399655.1_Missense_Mutation_p.P1427L|CACNA1C_ENST00000399637.1_Missense_Mutation_p.P1427L|CACNA1C_ENST00000399595.1_Missense_Mutation_p.P1416L|CACNA1C_ENST00000399603.1_Missense_Mutation_p.P1427L|CACNA1C_ENST00000399641.1_Missense_Mutation_p.P1427L|CACNA1C_ENST00000406454.3_Missense_Mutation_p.P1427L|CACNA1C_ENST00000399606.1_Missense_Mutation_p.P1447L|CACNA1C_ENST00000399597.1_Missense_Mutation_p.P1427L|CACNA1C_ENST00000327702.7_Missense_Mutation_p.P1427L|CACNA1C_ENST00000399634.1_Missense_Mutation_p.P1427L|CACNA1C_ENST00000399621.1_Missense_Mutation_p.P1427L|CACNA1C_ENST00000399644.1_Missense_Mutation_p.P1427L|CACNA1C_ENST00000399591.1_Missense_Mutation_p.P1416L|CACNA1C_ENST00000399601.1_Missense_Mutation_p.P1427L|CACNA1C_ENST00000399649.1_Missense_Mutation_p.P1414L|CACNA1C_ENST00000402845.3_Missense_Mutation_p.P1427L|CACNA1C_ENST00000399629.1_Missense_Mutation_p.P1444L|CACNA1C_ENST00000335762.5_Missense_Mutation_p.P1452L|CACNA1C_ENST00000399638.1_Missense_Mutation_p.P1455L|CACNA1C_ENST00000399617.1_Missense_Mutation_p.P1427L|CACNA1C_ENST00000344100.3_Missense_Mutation_p.P1449L	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	1475					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	GCCTGCATGCCAGGCAAGAAG	0.597																																					p.P1475L		Atlas-SNP	.											.	CACNA1C	1023	.	0			c.C4424T						.						37	40	39					12																	2774038		2185	4299	6484	SO:0001583	missense	775	exon37			GCATGCCAGGCAA	AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.4424C>T	chr12.hg19:g.2774038C>T	ENSP00000266376:p.Pro1475Leu	69.0	0.0		77.0	30.0	NM_199460	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Missense_Mutation	SNP	ENST00000347598.4	hg19	CCDS44788.1	.	.	.	.	.	.	.	.	.	.	C	15.19	2.758790	0.49468	.	.	ENSG00000151067	ENST00000335762;ENST00000399655;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595;ENST00000322367	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97016	-4.21;-4.21;-4.21;-4.21;-4.21;-4.21;-4.21;-4.21;-4.21;-4.21;-4.21;-4.21;-4.21;-4.21;-4.21;-4.21;-4.21;-4.21;-4.21;-4.21;-4.21;-4.21	4.07	4.07	0.47477	Ion transport (1);	0.121117	0.56097	D	0.000024	D	0.97324	0.9125	L	0.54323	1.7	0.80722	D	1	B;D;B;B;D;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.89917	0.113;0.999;0.012;0.383;1.0;0.018;0.012;0.018;0.189;0.077;0.002;0.005;0.018;0.009;0.005;0.011;0.004;0.094;0.033;0.016;0.027;0.007;0.007;0.016;0.005	B;D;B;B;D;B;B;B;P;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.87578	0.132;0.991;0.02;0.344;0.998;0.027;0.02;0.036;0.447;0.099;0.013;0.009;0.029;0.026;0.011;0.044;0.006;0.087;0.027;0.028;0.013;0.02;0.02;0.013;0.009	D	0.98100	1.0414	10	0.72032	D	0.01	.	16.8336	0.85951	0.0:1.0:0.0:0.0	.	118;1449;1424;1475;1427;1427;1427;1444;1455;1427;1447;1427;1387;1475;1427;1427;1427;1416;1414;1416;1416;1427;1427;1427;1427	B7Z7Z5;Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-23;Q13936-28;Q13936-11;E9PDJ1;E9PDJ0;F5GY28;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;Q13936-12	.;.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	L	1452;1427;1427;1455;1427;1427;1427;1416;1427;1475;1447;1427;1449;1444;1427;1414;1427;1427;1427;1427;1427;1416;1257	ENSP00000336982:P1452L;ENSP00000382563:P1427L;ENSP00000382552:P1427L;ENSP00000382547:P1455L;ENSP00000382506:P1427L;ENSP00000382530:P1427L;ENSP00000382546:P1427L;ENSP00000382500:P1416L;ENSP00000382549:P1427L;ENSP00000266376:P1475L;ENSP00000382515:P1447L;ENSP00000382510:P1427L;ENSP00000341092:P1449L;ENSP00000382537:P1444L;ENSP00000329877:P1427L;ENSP00000382557:P1414L;ENSP00000385724:P1427L;ENSP00000382512:P1427L;ENSP00000382542:P1427L;ENSP00000382526:P1427L;ENSP00000385896:P1427L;ENSP00000382504:P1416L	ENSP00000323129:P1257L	P	+	2	0	CACNA1C	2644299	0.997000	0.39634	0.999000	0.59377	0.993000	0.82548	3.681000	0.54648	2.264000	0.75181	0.561000	0.74099	CCA	.	.		0.597	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719		T	2774038	C	T	2774038	3	4	288	1	0	0	0	0	1	0	0	0	2542	594	21	3	4744	3	CACNA1C	12	2774038	Missense_Mutation	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10		2774038	131077857	70	42284										
SOX5	6660	hgsc.bcm.edu	37	chr12	24048842	24048842	+	Missense_Mutation	SNP	A	A	C													0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	gaaaactcacatgcaagggaAggtgaaaggctgggagcccg							TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr12:24048842A>C	ENST00000451604.2	-	2	256	c.155T>G	c.(154-156)cTt>cGt	p.L52R	SOX5_ENST00000545921.1_Missense_Mutation_p.L42R|SOX5_ENST00000309359.1_Missense_Mutation_p.L39R|SOX5_ENST00000541536.1_Missense_Mutation_p.L39R|SOX5_ENST00000381381.2_Missense_Mutation_p.L39R|SOX5_ENST00000537393.1_Missense_Mutation_p.L52R|SOX5_ENST00000546136.1_Missense_Mutation_p.L39R|SOX5_ENST00000441133.2_Missense_Mutation_p.L52R|SOX5_ENST00000541847.1_Missense_Mutation_p.L42R			P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5	52					cartilage development (GO:0051216)|cell fate commitment (GO:0045165)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system neuron differentiation (GO:0021953)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|oligodendrocyte differentiation (GO:0048709)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of timing of neuron differentiation (GO:0060164)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear transcription factor complex (GO:0044798)	sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(25)|ovary(5)|skin(2)|upper_aerodigestive_tract(3)	57						ATGCAAGGGAAGGTGAAAGGC	0.532																																					p.L52R		Atlas-SNP	.											.	SOX5	134	.	0			c.T155G						.						251	238	242					12																	24048842		2203	4300	6503	SO:0001583	missense	6660	exon2			AAGGGAAGGTGAA	AB081589	CCDS8699.1, CCDS41761.1, CCDS44844.1, CCDS58216.1, CCDS58217.1	12p12.1	2010-04-20			ENSG00000134532	ENSG00000134532		"SRY (sex determining region Y)-boxes"	11201	protein-coding gene	gene with protein product		604975				8812465	Standard	NM_006940		Approved	L-SOX5, MGC35153	uc001rfw.3	P35711	OTTHUMG00000169026	ENST00000451604.2:c.155T>G	chr12.hg19:g.24048842A>C	ENSP00000398273:p.Leu52Arg	133.0	0.0		120.0	37.0	NM_006940	B7Z8V0|F5H5B0|Q86UK8|Q8J017|Q8J018|Q8J019|Q8J020|Q8N1D9|Q8N7E0|Q8TEA4	Missense_Mutation	SNP	ENST00000451604.2	hg19	CCDS8699.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.005010	0.74932	.	.	ENSG00000134532	ENST00000546136;ENST00000309359;ENST00000381381;ENST00000451604;ENST00000435266;ENST00000537393;ENST00000541536;ENST00000545921;ENST00000541847;ENST00000441133;ENST00000538083	D;D;D;D;D;D;D	0.99105	-5.36;-5.36;-5.43;-5.38;-4.5;-5.43;-5.36	6.01	6.01	0.97437	.	0.000000	0.85682	D	0.000000	D	0.99199	0.9722	M	0.76328	2.33	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;0.997;1.0	D;D;D;D	0.97110	0.996;1.0;0.991;0.999	D	0.99768	1.1023	10	0.87932	D	0	.	16.5285	0.84344	1.0:0.0:0.0:0.0	.	52;52;39;52	G3V0H1;F5H0I3;P35711-4;P35711	.;.;.;SOX5_HUMAN	R	39;39;39;52;39;52;39;42;42;52;39	ENSP00000437487:L39R;ENSP00000308927:L39R;ENSP00000370788:L39R;ENSP00000398273:L52R;ENSP00000439832:L52R;ENSP00000441973:L39R;ENSP00000443520:L42R	ENSP00000308927:L39R	L	-	2	0	SOX5	23940109	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.343000	0.90052	2.307000	0.77673	0.528000	0.53228	CTT	.	.		0.532	SOX5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402006.2	NM_006940		C	24048842	A	C	24048842	3	2	288	1	0	0	0	0	1	0	0	0	14969	72	3	5	2202	5	SOX5	12	24048842	Missense_Mutation	SNP	A	TCGA-G3-A5SM-01A-12D-A28X-10	21274804	24048842	109803053	71	42285	222	2								
SOX5	6660	hgsc.bcm.edu	37	chr12	24048849	24048849	+	Missense_Mutation	SNP	A	A	C													0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	cacatgcaagggaaggtgaaAggctgggagcccgtcactct							TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr12:24048849A>C	ENST00000451604.2	-	2	249	c.148T>G	c.(148-150)Ttt>Gtt	p.F50V	SOX5_ENST00000545921.1_Missense_Mutation_p.F40V|SOX5_ENST00000309359.1_Missense_Mutation_p.F37V|SOX5_ENST00000541536.1_Missense_Mutation_p.F37V|SOX5_ENST00000381381.2_Missense_Mutation_p.F37V|SOX5_ENST00000537393.1_Missense_Mutation_p.F50V|SOX5_ENST00000546136.1_Missense_Mutation_p.F37V|SOX5_ENST00000441133.2_Missense_Mutation_p.F50V|SOX5_ENST00000541847.1_Missense_Mutation_p.F40V			P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5	50					cartilage development (GO:0051216)|cell fate commitment (GO:0045165)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system neuron differentiation (GO:0021953)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|oligodendrocyte differentiation (GO:0048709)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of timing of neuron differentiation (GO:0060164)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear transcription factor complex (GO:0044798)	sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(25)|ovary(5)|skin(2)|upper_aerodigestive_tract(3)	57						GGAAGGTGAAAGGCTGGGAGC	0.537																																					p.F50V		Atlas-SNP	.											.	SOX5	134	.	0			c.T148G						.						251	238	242					12																	24048849		2203	4300	6503	SO:0001583	missense	6660	exon2			GGTGAAAGGCTGG	AB081589	CCDS8699.1, CCDS41761.1, CCDS44844.1, CCDS58216.1, CCDS58217.1	12p12.1	2010-04-20			ENSG00000134532	ENSG00000134532		"SRY (sex determining region Y)-boxes"	11201	protein-coding gene	gene with protein product		604975				8812465	Standard	NM_006940		Approved	L-SOX5, MGC35153	uc001rfw.3	P35711	OTTHUMG00000169026	ENST00000451604.2:c.148T>G	chr12.hg19:g.24048849A>C	ENSP00000398273:p.Phe50Val	132.0	0.0		118.0	33.0	NM_006940	B7Z8V0|F5H5B0|Q86UK8|Q8J017|Q8J018|Q8J019|Q8J020|Q8N1D9|Q8N7E0|Q8TEA4	Missense_Mutation	SNP	ENST00000451604.2	hg19	CCDS8699.1	.	.	.	.	.	.	.	.	.	.	A	17.11	3.305198	0.60305	.	.	ENSG00000134532	ENST00000546136;ENST00000309359;ENST00000381381;ENST00000451604;ENST00000435266;ENST00000537393;ENST00000541536;ENST00000545921;ENST00000541847;ENST00000441133;ENST00000538083	D;D;D;D;D;D;D	0.96685	-4.07;-4.07;-4.08;-4.08;-4.09;-4.08;-4.07	6.01	6.01	0.97437	.	0.055402	0.64402	D	0.000001	D	0.93268	0.7855	L	0.34521	1.04	0.44123	D	0.996903	B;B;B;B	0.24368	0.048;0.05;0.102;0.066	B;B;B;B	0.21151	0.015;0.022;0.033;0.017	D	0.90370	0.4380	10	0.37606	T	0.19	.	16.5285	0.84344	1.0:0.0:0.0:0.0	.	50;50;37;50	G3V0H1;F5H0I3;P35711-4;P35711	.;.;.;SOX5_HUMAN	V	37;37;37;50;37;50;37;40;40;50;37	ENSP00000437487:F37V;ENSP00000308927:F37V;ENSP00000370788:F37V;ENSP00000398273:F50V;ENSP00000439832:F50V;ENSP00000441973:F37V;ENSP00000443520:F40V	ENSP00000308927:F37V	F	-	1	0	SOX5	23940116	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.162000	0.71874	2.307000	0.77673	0.528000	0.53228	TTT	.	.		0.537	SOX5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402006.2	NM_006940		C	24048849	A	C	24048849	3	2	288	1	0	0	0	0	1	0	0	0	14969	72	3	5	2209	5	SOX5	12	24048849	Missense_Mutation	SNP	A	TCGA-G3-A5SM-01A-12D-A28X-10	7	24048849	109803046	72	42286	222	2								
KRT2	3849	hgsc.bcm.edu	37	chr12	53041619	53041619	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	ctgtctccatgtctcccgacAgtcacctggagctcctcata	7	16	4	0			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr12:53041619A>G	ENST00000309680.3	-	6	1164	c.1143T>C	c.(1141-1143)acT>acC	p.T381T		NM_000423.2	NP_000414.2	P35908	K22E_HUMAN	keratin 2	381	Coil 2.|Rod.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte activation (GO:0032980)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(18)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32				BRCA - Breast invasive adenocarcinoma(357;0.19)		GTCTCCCGACAGTCACCTGGA	0.537																																					p.T381T		Atlas-SNP	.											.	KRT2	94	.	0			c.T1143C						.						74	59	64					12																	53041619		2203	4300	6503	SO:0001819	synonymous_variant	3849	exon6			CCCGACAGTCACC		CCDS8835.1	12q13.13	2013-01-16	2008-08-01	2006-07-17	ENSG00000172867	ENSG00000172867		"-", "Intermediate filaments type II, keratins (basic)"	6439	protein-coding gene	gene with protein product	"epidermal ichthyosis bullosa of Siemens"	600194	"keratin 2A (epidermal ichthyosis bullosa of Siemens)"	KRT2A		7524919, 16831889	Standard	NM_000423		Approved	KRTE	uc001sat.3	P35908	OTTHUMG00000169748	ENST00000309680.3:c.1143T>C	chr12.hg19:g.53041619A>G		91.0	0.0		82.0	21.0	NM_000423	Q4VAQ2	Silent	SNP	ENST00000309680.3	hg19	CCDS8835.1																																																																																			.	.		0.537	KRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405704.1	NM_000423		G	53041619	A	G	53041619	2	3	288	1	0	0	0	0	0	0	0	1	8466	175	7	2		2	KRT2	12	53041619	Silent	SNP	A	TCGA-G3-A5SM-01A-12D-A28X-10	28992770	53041619	80810276	73	42287										
TENC1	23371	hgsc.bcm.edu	37	chr12	53448150	53448150	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	gccgccttccccgcgcggccCgatgaacagcggcaccgggg	15	18	0	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr12:53448150C>G	ENST00000314250.6	+	7	737	c.447C>G	c.(445-447)ccC>ccG	p.P149P	RP11-983P16.4_ENST00000551890.1_RNA|TENC1_ENST00000451358.1_Silent_p.P149P|TENC1_ENST00000314276.3_Silent_p.P159P|TENC1_ENST00000549700.1_Silent_p.P149P|RP11-983P16.4_ENST00000550601.1_RNA|TENC1_ENST00000379902.3_Silent_p.P25P|RP11-983P16.4_ENST00000546793.1_RNA|TENC1_ENST00000552570.1_Silent_p.P149P|TENC1_ENST00000546602.1_Silent_p.P149P	NM_170754.2	NP_736610.2	Q63HR2	TENC1_HUMAN	tensin like C1 domain containing phosphatase (tensin 2)	149	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				cellular homeostasis (GO:0019725)|collagen metabolic process (GO:0032963)|intracellular signal transduction (GO:0035556)|kidney development (GO:0001822)|multicellular organism growth (GO:0035264)|multicellular organismal homeostasis (GO:0048871)|negative regulation of cell proliferation (GO:0008285)|response to muscle activity (GO:0014850)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(19)|ovary(1)|pancreas(1)|stomach(3)	34						CCGCGCGGCCCGATGAACAGC	0.687																																					p.P159P		Atlas-SNP	.											.	TENC1	148	.	0			c.C477G						.						22	24	23					12																	53448150		2202	4292	6494	SO:0001819	synonymous_variant	23371	exon7			GCGGCCCGATGAA	AF518729	CCDS8842.1, CCDS8843.1, CCDS8844.1	12q13.13	2013-02-14	2004-03-05			ENSG00000111077		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	19737	protein-coding gene	gene with protein product	"tensin 2"	607717	"tensin like C1 domain-containing phosphatase"				Standard	NM_015319		Approved	KIAA1075, C1-TEN, TNS2	uc001sbp.3	Q63HR2	OTTHUMG00000169730	ENST00000314250.6:c.447C>G	chr12.hg19:g.53448150C>G		144.0	0.0		48.0	4.0	NM_015319	A2VDF2|A2VDF3|A2VDI8|A5PKY4|Q2NL80|Q76MW6|Q7Z5T9|Q8NFF9|Q8NFG0|Q96P25|Q9NT29|Q9UPS7	Silent	SNP	ENST00000314250.6	hg19	CCDS8843.1																																																																																			.	.		0.687	TENC1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405779.1	NM_170754		G	53448150	C	G	53448150	2	3	288	1	0	0	0	0	0	0	0	1	15773	639	23	4		4	TENC1	12	53448150	Silent	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	406531	53448150	80403745	74	42288										
ITGA7	3679	hgsc.bcm.edu	37	chr12	56092544	56092544	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	gagtagccaaagccggaggtCaggcgctccccagacagcat	13	13	1	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr12:56092544C>G	ENST00000555728.1	-	7	1108	c.1080G>C	c.(1078-1080)ctG>ctC	p.L360L	ITGA7_ENST00000347027.6_Silent_p.L316L|ITGA7_ENST00000394229.2_Silent_p.L316L|ITGA7_ENST00000257879.6_Silent_p.L316L|ITGA7_ENST00000553804.1_Silent_p.L320L|ITGA7_ENST00000257880.7_Silent_p.L360L|ITGA7_ENST00000394230.2_Silent_p.L320L|ITGA7_ENST00000452168.2_Silent_p.L223L			Q13683	ITA7_HUMAN	integrin, alpha 7	360					blood vessel morphogenesis (GO:0048514)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|regulation of cell shape (GO:0008360)|skeletal muscle tissue development (GO:0007519)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integrin alpha7-beta1 complex (GO:0034677)|muscle tendon junction (GO:0005927)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(16)|ovary(2)|prostate(2)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						AGCCGGAGGTCAGGCGCTCCC	0.652																																					p.L320L		Atlas-SNP	.											.	ITGA7	194	.	0			c.G960C						.						68	55	60					12																	56092544		2203	4300	6503	SO:0001819	synonymous_variant	3679	exon6			GGAGGTCAGGCGC		CCDS8888.1, CCDS44914.1, CCDS55832.1	12q13	2014-09-17				ENSG00000135424		"Integrins"	6143	protein-coding gene	gene with protein product		600536				7607681	Standard	NM_002206		Approved		uc001shh.3	Q13683		ENST00000555728.1:c.1080G>C	chr12.hg19:g.56092544C>G		175.0	0.0		152.0	26.0	NM_001144996	B4E3U0|C9JMD3|C9JMZ6|O43197|Q86W93|Q9NY89|Q9UET0|Q9UEV2	Silent	SNP	ENST00000555728.1	hg19																																																																																				.	.		0.652	ITGA7-014	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000410138.1	NM_002206		G	56092544	C	G	56092544	2	3	288	1	0	0	0	0	0	0	0	1	7890	813	29	4		4	ITGA7	12	56092544	Silent	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	2644394	56092544	77759351	75	42289										
ANKRD52	283373	hgsc.bcm.edu	37	chr12	56638565	56638565	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	gacattgtccgcgaaggcagCggcgtgaaggggggtcctgt	18	9	0	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr12:56638565C>T	ENST00000267116.7	-	24	2714	c.2593G>A	c.(2593-2595)Gct>Act	p.A865T	ANKRD52_ENST00000548241.1_5'Flank	NM_173595.3	NP_775866.2	Q8NB46	ANR52_HUMAN	ankyrin repeat domain 52	865										endometrium(9)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)|skin(1)	29						GCGAAGGCAGCGGCGTGAAGG	0.582																																					p.A865T		Atlas-SNP	.											ANKRD52,NS,carcinoma,0,1	ANKRD52	81	.	0			c.G2593A						.						60	61	61					12																	56638565		2103	4232	6335	SO:0001583	missense	283373	exon24			AGGCAGCGGCGTG	AK091555	CCDS44920.1	12q13.3	2013-01-10			ENSG00000139645	ENSG00000139645		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits", "Ankyrin repeat domain containing"	26614	protein-coding gene	gene with protein product	"protein phosphatase 6 ankyrin repeat subunit C"						Standard	NM_173595		Approved	FLJ34236, PP6-ARS-C	uc001skm.4	Q8NB46	OTTHUMG00000170329	ENST00000267116.7:c.2593G>A	chr12.hg19:g.56638565C>T	ENSP00000267116:p.Ala865Thr	73.0	0.0		59.0	8.0	NM_173595	A6NE79|B1Q2K2	Missense_Mutation	SNP	ENST00000267116.7	hg19	CCDS44920.1	.	.	.	.	.	.	.	.	.	.	C	33	5.226030	0.95173	.	.	ENSG00000139645	ENST00000267116;ENST00000417002	T	0.81163	-1.46	4.53	4.53	0.55603	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	D	0.91264	0.7246	M	0.90483	3.12	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.92745	0.6211	9	.	.	.	.	16.5704	0.84611	0.0:1.0:0.0:0.0	.	865	Q8NB46	ANR52_HUMAN	T	865	ENSP00000267116:A865T	.	A	-	1	0	ANKRD52	54924832	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.629000	0.83207	2.527000	0.85204	0.655000	0.94253	GCT	.	.		0.582	ANKRD52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408539.1	NM_173595		T	56638565	C	T	56638565	3	4	288	1	0	0	0	0	1	0	0	0	678	768	27	1	657	1	ANKRD52	12	56638565	Missense_Mutation	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	546021	56638565	77213330	76	42290										
B4GALNT1	2583	hgsc.bcm.edu	37	chr12	58020643	58020643	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	ggcgtaagtctctgctccggCatcccttgatgtccaaggca	11	13	1	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr12:58020643C>T	ENST00000341156.4	-	11	2070	c.1486G>A	c.(1486-1488)Gcc>Acc	p.A496T	B4GALNT1_ENST00000418555.2_Missense_Mutation_p.A441T	NM_001478.3	NP_001469.1	Q00973	B4GN1_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 1	496					carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|ganglioside biosynthetic process (GO:0001574)|glycosphingolipid metabolic process (GO:0006687)|lipid glycosylation (GO:0030259)|lipid storage (GO:0019915)|protein glycosylation (GO:0006486)|spermatogenesis (GO:0007283)	integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|plasma membrane (GO:0005886)	(N-acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase activity (GO:0003947)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)|urinary_tract(1)	20	Melanoma(17;0.122)		BRCA - Breast invasive adenocarcinoma(9;0.109)			TCTGCTCCGGCATCCCTTGAT	0.572																																					p.D496N		Atlas-SNP	.											B4GALNT1,NS,carcinoma,0,1	B4GALNT1	53	.	0			c.G1486A						.						134	103	114					12																	58020643		2203	4300	6503	SO:0001583	missense	2583	exon11			CTCCGGCATCCCT	M83651	CCDS8950.1, CCDS61170.1, CCDS61171.1	12q13.3	2013-09-11	2006-01-08	2006-01-08	ENSG00000135454	ENSG00000135454	2.4.1.92	"Beta 4-glycosyltransferases", "Glycosyltransferase family 2 domain containing"	4117	protein-coding gene	gene with protein product	"GD2 synthase, GM2 synthase"	601873	"UDP-N-acetyl-alpha-D-galactosamine:(N-acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase (GalNAc-T)", "UDP-Gal:betaGlcNAc beta-1,4-N-acetylgalactosaminyltransferase transferase 1", "spastic paraplegia 26"	GALGT, SPG26		1601877, 23746551	Standard	NM_001478		Approved	beta1-4GalNAc-T	uc001spg.2	Q00973	OTTHUMG00000170190	ENST00000341156.4:c.1486G>A	chr12.hg19:g.58020643C>T	ENSP00000341562:p.Ala496Thr	157.0	0.0		121.0	28.0	NM_001478	B4DE26|Q8N636	Missense_Mutation	SNP	ENST00000341156.4	hg19	CCDS8950.1	.	.	.	.	.	.	.	.	.	.	.	3.499	-0.102300	0.06967	.	.	ENSG00000135454	ENST00000341156;ENST00000418555	T;T	0.24908	1.83;1.83	4.6	-2.01	0.07410	.	0.986029	0.08259	N	0.973367	T	0.12561	0.0305	L	0.27053	0.805	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.35968	-0.9767	10	0.12766	T	0.61	-8.2877	2.3241	0.04218	0.2739:0.1614:0.4339:0.1308	.	441;496	B4DE26;Q00973	.;B4GN1_HUMAN	T	496;441	ENSP00000341562:A496T;ENSP00000401601:A441T	ENSP00000341562:A496T	A	-	1	0	B4GALNT1	56306910	0.000000	0.05858	0.005000	0.12908	0.227000	0.25037	-0.340000	0.07821	-0.240000	0.09696	0.467000	0.42956	GCC	.	.		0.572	B4GALNT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407853.1	NM_001478		T	58020643	C	T	58020643	3	4	288	1	0	0	0	0	1	0	0	0	1266	710	25	3	119	3	B4GALNT1	12	58020643	Missense_Mutation	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	1382078	58020643	75831252	77	42291										
XPOT	11260	hgsc.bcm.edu	37	chr12	64813854	64813854	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	gcgttttgtattttaggaggCtcgtaggaatactctcataa	10	6	1	0			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr12:64813854C>T	ENST00000332707.5	+	7	1023	c.494C>T	c.(493-495)gCt>gTt	p.A165V		NM_007235.4	NP_009166.2	O43592	XPOT_HUMAN	exportin, tRNA	165	Necessary for interaction with Ran, nuclear localization and nuclear import.				intracellular protein transport (GO:0006886)|tRNA export from nucleus (GO:0006409)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(7)|lung(12)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				GBM - Glioblastoma multiforme(28;0.0404)		TTTTAGGAGGCTCGTAGGAAT	0.333																																					p.A165V		Atlas-SNP	.											.	XPOT	105	.	0			c.C494T						.						62	61	61					12																	64813854		2203	4300	6503	SO:0001583	missense	11260	exon7			AGGAGGCTCGTAG	AF039022	CCDS31852.1	12q14.1	2012-10-17	2012-10-17		ENSG00000184575	ENSG00000184575		"Exportins"	12826	protein-coding gene	gene with protein product		603180	"exportin, tRNA (nuclear export receptor for tRNAs)"			9660920, 9512417	Standard	NM_007235		Approved	XPO3	uc001ssb.3	O43592	OTTHUMG00000168794	ENST00000332707.5:c.494C>T	chr12.hg19:g.64813854C>T	ENSP00000327821:p.Ala165Val	53.0	0.0		42.0	5.0	NM_007235	A6NLH1|O43784|Q8WUG2|Q9BVS7	Missense_Mutation	SNP	ENST00000332707.5	hg19	CCDS31852.1	.	.	.	.	.	.	.	.	.	.	C	14.32	2.498967	0.44455	.	.	ENSG00000184575	ENST00000332707;ENST00000400935	T;T	0.44083	0.93;0.93	4.79	4.79	0.61399	Exportin-1/Importin-beta-like (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.153219	0.64402	D	0.000017	T	0.37348	0.1000	L	0.41415	1.275	0.46044	D	0.998839	B	0.16802	0.019	B	0.19666	0.026	T	0.12837	-1.0532	9	.	.	.	.	18.7197	0.91688	0.0:1.0:0.0:0.0	.	165	O43592	XPOT_HUMAN	V	165	ENSP00000327821:A165V;ENSP00000383722:A165V	.	A	+	2	0	XPOT	63100121	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.921000	0.70028	2.593000	0.87608	0.655000	0.94253	GCT	.	.		0.333	XPOT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401122.1	NM_007235		T	64813854	C	T	64813854	3	4	288	1	0	0	0	0	1	0	0	0	17465	797	28	3	516	3	XPOT	12	64813854	Missense_Mutation	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	6793211	64813854	69038041	78	42292										
FAM71C	196472	hgsc.bcm.edu	37	chr12	100042218	100042218	+	Missense_Mutation	SNP	C	C	T													0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	acctgatgtcatgctgctggCccgaccagctgctgtctgtg							TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr12:100042218C>T	ENST00000324341.1	+	1	688	c.266C>T	c.(265-267)gCc>gTc	p.A89V	ANKS1B_ENST00000329257.7_Intron|ANKS1B_ENST00000547010.1_Intron|ANKS1B_ENST00000547776.2_Intron	NM_153364.3	NP_699195.1	Q8NEG0	FA71C_HUMAN	family with sequence similarity 71, member C	89										breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				OV - Ovarian serous cystadenocarcinoma(2;0.00733)|Epithelial(2;0.0385)|all cancers(2;0.19)		ATGCTGCTGGCCCGACCAGCT	0.562																																					p.A89V		Atlas-SNP	.											.	FAM71C	48	.	0			c.C266T						.						93	85	88					12																	100042218		2203	4300	6503	SO:0001583	missense	196472	exon1			TGCTGGCCCGACC		CCDS9072.1	12q23.1	2006-02-03				ENSG00000180219			28594	protein-coding gene	gene with protein product						12477932	Standard	NM_153364		Approved	MGC39520	uc001tgn.3	Q8NEG0		ENST00000324341.1:c.266C>T	chr12.hg19:g.100042218C>T	ENSP00000315247:p.Ala89Val	119.0	0.0		122.0	18.0	NM_153364	B2R6Y6	Missense_Mutation	SNP	ENST00000324341.1	hg19	CCDS9072.1	.	.	.	.	.	.	.	.	.	.	C	15.71	2.913571	0.52439	.	.	ENSG00000180219	ENST00000324341	T	0.32988	1.43	3.94	1.94	0.25998	.	0.000000	0.64402	D	0.000012	T	0.47673	0.1458	M	0.72479	2.2	0.20074	N	0.999934	D	0.89917	1.0	D	0.91635	0.999	T	0.21211	-1.0252	9	.	.	.	-18.162	6.4957	0.22140	0.2078:0.5908:0.2014:0.0	.	89	Q8NEG0	FA71C_HUMAN	V	89	ENSP00000315247:A89V	.	A	+	2	0	FAM71C	98566349	0.657000	0.27393	0.465000	0.27155	0.589000	0.36550	0.870000	0.28010	0.530000	0.28619	0.555000	0.69702	GCC	.	.		0.562	FAM71C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408458.1	NM_153364		T	100042218	C	T	100042218	3	4	288	1	0	0	0	0	1	0	0	0	5617	739	26	3	268	3	FAM71C	12	100042218	Missense_Mutation	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	35228364	100042218	33809677	79	42293	223	3								
FAM71C	196472	hgsc.bcm.edu	37	chr12	100042220	100042221	+	Frame_Shift_Del	DEL	CG	CG	-													0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	ctgatgtcatgctgctggccCgaccagctgctgtctgtgac					rs141451941|rs181913768	byFrequency	TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	CG	CG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr12:100042220_100042221delCG	ENST00000324341.1	+	1	690_691	c.268_269delCG	c.(268-270)cgafs	p.R90fs	ANKS1B_ENST00000329257.7_Intron|ANKS1B_ENST00000547010.1_Intron|ANKS1B_ENST00000547776.2_Intron	NM_153364.3	NP_699195.1	Q8NEG0	FA71C_HUMAN	family with sequence similarity 71, member C	90										breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				OV - Ovarian serous cystadenocarcinoma(2;0.00733)|Epithelial(2;0.0385)|all cancers(2;0.19)		GCTGCTGGCCCGACCAGCTGCT	0.559																																					p.89_90del		Atlas-INDEL	.											.	FAM71C	48	.	0			c.267_268del						.																																			SO:0001589	frameshift_variant	196472	exon1			.		CCDS9072.1	12q23.1	2006-02-03				ENSG00000180219			28594	protein-coding gene	gene with protein product						12477932	Standard	NM_153364		Approved	MGC39520	uc001tgn.3	Q8NEG0		ENST00000324341.1:c.268_269delCG	chr12.hg19:g.100042220_100042221delCG	ENSP00000315247:p.Arg90fs	114.0	0.0		117.0	18.0	NM_153364	B2R6Y6	Frame_Shift_Del	DEL	ENST00000324341.1	hg19	CCDS9072.1																																																																																			.	.		0.559	FAM71C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408458.1	NM_153364		-	100042221	CG	-	100042220	7	5	288	1	0	1	0	1	0	0	0	0	5617	644	23	0	270	0	FAM71C	12	100042220	Frame_Shift_Del	DEL	CG	TCGA-G3-A5SM-01A-12D-A28X-10	2	100042220	33809675	80	42294	223	3								
FAM71C	196472	hgsc.bcm.edu	37	chr12	100042223	100042223	+	Missense_Mutation	SNP	C	C	T													0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	atgtcatgctgctggcccgaCcagctgctgtctgtgacaat							TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr12:100042223C>T	ENST00000324341.1	+	1	693	c.271C>T	c.(271-273)Cca>Tca	p.P91S	ANKS1B_ENST00000329257.7_Intron|ANKS1B_ENST00000547010.1_Intron|ANKS1B_ENST00000547776.2_Intron	NM_153364.3	NP_699195.1	Q8NEG0	FA71C_HUMAN	family with sequence similarity 71, member C	91										breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				OV - Ovarian serous cystadenocarcinoma(2;0.00733)|Epithelial(2;0.0385)|all cancers(2;0.19)		GCTGGCCCGACCAGCTGCTGT	0.552																																					p.P91S		Atlas-SNP	.											.	FAM71C	48	.	0			c.C271T						.						90	83	85					12																	100042223		2203	4300	6503	SO:0001583	missense	196472	exon1			GCCCGACCAGCTG		CCDS9072.1	12q23.1	2006-02-03				ENSG00000180219			28594	protein-coding gene	gene with protein product						12477932	Standard	NM_153364		Approved	MGC39520	uc001tgn.3	Q8NEG0		ENST00000324341.1:c.271C>T	chr12.hg19:g.100042223C>T	ENSP00000315247:p.Pro91Ser	111.0	0.0		120.0	19.0	NM_153364	B2R6Y6	Missense_Mutation	SNP	ENST00000324341.1	hg19	CCDS9072.1	.	.	.	.	.	.	.	.	.	.	C	10.81	1.455266	0.26161	.	.	ENSG00000180219	ENST00000324341	T	0.11385	2.78	3.94	2.02	0.26589	.	0.218998	0.31082	N	0.008300	T	0.24044	0.0582	M	0.70595	2.14	0.09310	N	1	D	0.76494	0.999	D	0.73380	0.98	T	0.03193	-1.1062	9	.	.	.	-13.4292	4.5197	0.11954	0.2189:0.6653:0.0:0.1158	.	91	Q8NEG0	FA71C_HUMAN	S	91	ENSP00000315247:P91S	.	P	+	1	0	FAM71C	98566354	0.000000	0.05858	0.004000	0.12327	0.119000	0.20118	-0.632000	0.05489	0.567000	0.29293	0.555000	0.69702	CCA	.	.		0.552	FAM71C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408458.1	NM_153364		T	100042223	C	T	100042223	3	4	288	1	0	0	0	0	1	0	0	0	5617	507	18	3	273	3	FAM71C	12	100042223	Missense_Mutation	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	3	100042223	33809672	81	42295	223	3								
DIS3	22894	hgsc.bcm.edu	37	chr13	73336102	73336102	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	tgtgtgtatattggagacgcTaagccatagtgatgaaaatc	11	5	0	3			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr13:73336102T>G	ENST00000377767.4	-	17	2401	c.2301A>C	c.(2299-2301)ttA>ttC	p.L767F	DIS3_ENST00000545453.1_Missense_Mutation_p.L605F|DIS3_ENST00000377780.4_Missense_Mutation_p.L737F	NM_014953.3	NP_055768.3	Q9Y2L1	RRP44_HUMAN	DIS3 exosome endoribonuclease and 3'-5' exoribonuclease	767					CUT catabolic process (GO:0071034)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of GTPase activity (GO:0043547)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA catabolic process (GO:0016075)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|membrane (GO:0016020)|nuclear exosome (RNase complex) (GO:0000176)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|endonuclease activity (GO:0004519)|guanyl-nucleotide exchange factor activity (GO:0005085)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(7)|kidney(5)|large_intestine(10)|lung(6)|prostate(2)|skin(1)	35		Breast(118;0.0074)|Acute lymphoblastic leukemia(28;0.0195)		GBM - Glioblastoma multiforme(99;0.000181)		TTGGAGACGCTAAGCCATAGT	0.328										Multiple Myeloma(4;0.011)																											p.L767F		Atlas-SNP	.											.	DIS3	103	.	0			c.A2301C						.						94	90	91					13																	73336102		2203	4300	6503	SO:0001583	missense	22894	exon17			AGACGCTAAGCCA	AB023225	CCDS9447.1, CCDS45057.1	13q21.32	2014-03-05	2014-03-05	2007-01-12	ENSG00000083520	ENSG00000083520			20604	protein-coding gene	gene with protein product	"exosome component 11"	607533	"KIAA1008", "DIS3 mitotic control homolog (S. cerevisiae)"	KIAA1008		11935316, 9562621	Standard	XM_005266294		Approved	dis3p, RRP44, EXOSC11	uc001vix.4	Q9Y2L1	OTTHUMG00000017070	ENST00000377767.4:c.2301A>C	chr13.hg19:g.73336102T>G	ENSP00000366997:p.Leu767Phe	93.0	0.0		61.0	18.0	NM_014953	A6NI21|B2RBL2|Q5W0P7|Q5W0P8|Q658Z7|Q7Z481|Q8WWI2|Q9UG36	Missense_Mutation	SNP	ENST00000377767.4	hg19	CCDS9447.1	.	.	.	.	.	.	.	.	.	.	T	16.85	3.237751	0.58886	.	.	ENSG00000083520	ENST00000377767;ENST00000377780;ENST00000545453	T;T;T	0.71341	-0.56;-0.56;-0.56	5.68	3.24	0.37175	Ribonuclease II/R, conserved site (1);Ribonuclease II/R (2);	0.000000	0.85682	D	0.000000	D	0.90246	0.6950	H	0.99770	4.765	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.90372	0.4381	10	0.87932	D	0	.	10.126	0.42649	0.0:0.1357:0.0:0.8643	.	737;767	Q9Y2L1-2;Q9Y2L1	.;RRP44_HUMAN	F	767;737;605	ENSP00000366997:L767F;ENSP00000367011:L737F;ENSP00000440058:L605F	ENSP00000366997:L767F	L	-	3	2	DIS3	72234103	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	1.646000	0.37249	0.428000	0.26173	-0.451000	0.05528	TTA	.	.		0.328	DIS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045250.2	NM_014953		G	73336102	T	G	73336102	3	3	288	1	0	0	0	0	1	0	0	0	4537	1519	53	5	595	5	DIS3	13	73336102	Missense_Mutation	SNP	T	TCGA-G3-A5SM-01A-12D-A28X-10		73336102	41833776	82	42296										
RNASE2	6036	hgsc.bcm.edu	37	chr14	21423958	21423958	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	caaaactgttcacttcccaaAtttgtctgcttcttctgttg	5	11	4	0			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr14:21423958A>G	ENST00000304625.2	+	2	118	c.28A>G	c.(28-30)Att>Gtt	p.I10V		NM_002934.2	NP_002925.1	P10153	RNAS2_HUMAN	ribonuclease, RNase A family, 2 (liver, eosinophil-derived neurotoxin)	10					chemotaxis (GO:0006935)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	nucleic acid binding (GO:0003676)|pancreatic ribonuclease activity (GO:0004522)|ribonuclease activity (GO:0004540)			breast(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(1)|stomach(1)	17	all_cancers(95;0.00381)		OV - Ovarian serous cystadenocarcinoma(11;6.3e-09)|Epithelial(56;1.42e-07)|all cancers(55;5.48e-07)	GBM - Glioblastoma multiforme(265;0.0187)		CACTTCCCAAATTTGTCTGCT	0.463																																					p.I10V		Atlas-SNP	.											.	RNASE2	26	.	0			c.A28G						.						99	107	104					14																	21423958		2203	4297	6500	SO:0001583	missense	6036	exon2			TCCCAAATTTGTC	X55988	CCDS9561.1	14q11.2	2014-03-13			ENSG00000169385	ENSG00000169385		"Ribonucleases, RNase A"	10045	protein-coding gene	gene with protein product		131410		RNS2		1577491, 2734298	Standard	NM_002934		Approved	EDN	uc001vyl.1	P10153	OTTHUMG00000029607	ENST00000304625.2:c.28A>G	chr14.hg19:g.21423958A>G	ENSP00000303276:p.Ile10Val	138.0	0.0		142.0	33.0	NM_002934	Q52M39|Q9H2B7|Q9UCG7	Missense_Mutation	SNP	ENST00000304625.2	hg19	CCDS9561.1	.	.	.	.	.	.	.	.	.	.	a	4.437	0.080951	0.08533	.	.	ENSG00000169385	ENST00000304625	T	0.05996	3.36	2.23	1.29	0.21616	.	1.581710	0.04558	U	0.391135	T	0.05868	0.0153	L	0.38531	1.155	0.09310	N	1	B	0.34241	0.444	B	0.27380	0.079	T	0.38972	-0.9636	10	0.41790	T	0.15	.	5.9076	0.19010	0.3353:0.6647:0.0:0.0	.	10	P10153	RNAS2_HUMAN	V	10	ENSP00000303276:I10V	ENSP00000303276:I10V	I	+	1	0	RNASE2	20493798	0.001000	0.12720	0.002000	0.10522	0.009000	0.06853	0.097000	0.15168	0.473000	0.27368	-0.666000	0.03841	ATT	.	.		0.463	RNASE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073799.2			G	21423958	A	G	21423958	3	3	288	1	0	0	0	0	1	0	0	0	13419	101	4	2	30	2	RNASE2	14	21423958	Missense_Mutation	SNP	A	TCGA-G3-A5SM-01A-12D-A28X-10		21423958	85925582	83	42297										
LTB4R	1241	hgsc.bcm.edu	37	chr14	24785243	24785243	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	ctttgtgtcccagaagctacGcaccaaggcgatggcccggc	12	14	0	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr14:24785243G>T	ENST00000396789.4	+	2	2111	c.386G>T	c.(385-387)cGc>cTc	p.R129L	LTB4R_ENST00000396782.2_Missense_Mutation_p.R129L|LTB4R_ENST00000345363.3_Missense_Mutation_p.R129L	NM_181657.3	NP_858043.1	Q15722	LT4R1_HUMAN	leukotriene B4 receptor	129					cellular component movement (GO:0006928)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|muscle contraction (GO:0006936)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	leukotriene B4 receptor activity (GO:0001632)|leukotriene receptor activity (GO:0004974)|nucleotide binding (GO:0000166)			endometrium(1)|kidney(2)|large_intestine(1)|lung(3)|stomach(1)	8				GBM - Glioblastoma multiforme(265;0.018)		CAGAAGCTACGCACCAAGGCG	0.637																																					p.R129L		Atlas-SNP	.											.	LTB4R	18	.	0			c.G386T						.						42	44	43					14																	24785243		2203	4300	6503	SO:0001583	missense	1241	exon2			AGCTACGCACCAA	X98356	CCDS9626.1	14q11.2-q12	2012-08-10			ENSG00000213903	ENSG00000213903		"GPCR / Class A : Leukotriene receptors"	6713	protein-coding gene	gene with protein product		601531		P2RY7, GPR16, CMKRL1		8921391, 8702478	Standard	NM_181657		Approved	BLTR, P2Y7, LTB4R1	uc001wos.3	Q15722	OTTHUMG00000029346	ENST00000396789.4:c.386G>T	chr14.hg19:g.24785243G>T	ENSP00000380008:p.Arg129Leu	68.0	0.0		74.0	12.0	NM_181657	Q13305|Q53XV5|Q92641|Q9BSU5	Missense_Mutation	SNP	ENST00000396789.4	hg19	CCDS9626.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.353581	0.82243	.	.	ENSG00000213903	ENST00000345363;ENST00000396789;ENST00000556141;ENST00000396782	T;T;T;T	0.37235	1.21;1.21;1.21;1.21	5.89	5.89	0.94794	GPCR, rhodopsin-like superfamily (1);	0.063953	0.64402	U	0.000011	T	0.66177	0.2763	M	0.86268	2.805	0.58432	D	0.999997	D	0.89917	1.0	D	0.97110	1.0	T	0.70099	-0.4965	10	0.87932	D	0	.	17.7301	0.88375	0.0:0.0:1.0:0.0	.	129	Q15722	LT4R1_HUMAN	L	129;129;29;129	ENSP00000307445:R129L;ENSP00000380008:R129L;ENSP00000451929:R29L;ENSP00000380002:R129L	ENSP00000307445:R129L	R	+	2	0	LTB4R	23855083	0.060000	0.20803	0.992000	0.48379	0.090000	0.18270	1.812000	0.38952	2.789000	0.95967	0.655000	0.94253	CGC	.	.		0.637	LTB4R-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073198.4			T	24785243	G	T	24785243	3	4	288	1	0	0	0	0	1	0	0	0	9080	1087	38	1	388	1	LTB4R	14	24785243	Missense_Mutation	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	3361285	24785243	82564297	84	42298										
MLH3	27030	hgsc.bcm.edu	37	chr14	75505047	75505047	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	taaactccattcttacctgcCtcgccattctcttcagtctt	3	15	4	0			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr14:75505047C>A	ENST00000556740.1	-	5	3674	c.3639G>T	c.(3637-3639)gaG>gaT	p.E1213D	MLH3_ENST00000555671.1_5'Flank|MLH3_ENST00000556257.1_Intron|MLH3_ENST00000355774.2_Missense_Mutation_p.E1213D|MLH3_ENST00000238662.7_Missense_Mutation_p.E1213D|MLH3_ENST00000380968.2_Missense_Mutation_p.E159D|MLH3_ENST00000544985.1_Missense_Mutation_p.E173D			Q9UHC1	MLH3_HUMAN	mutL homolog 3	1213					ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44				BRCA - Breast invasive adenocarcinoma(234;0.00688)		TCTTACCTGCCTCGCCATTCT	0.353								Mismatch excision repair (MMR)																													p.E1213D		Atlas-SNP	.											.	MLH3	200	.	0			c.G3639T						.						127	116	120					14																	75505047		2203	4300	6503	SO:0001583	missense	27030	exon6			ACCTGCCTCGCCA	AF195657	CCDS9837.1, CCDS32123.1	14q24.3	2014-09-17	2013-09-12			ENSG00000119684			7128	protein-coding gene	gene with protein product		604395	"mutL (E. coli) homolog 3", "mutL homolog 3 (E. coli)"			10615123	Standard	XR_245681		Approved		uc001xrd.1	Q9UHC1		ENST00000556740.1:c.3639G>T	chr14.hg19:g.75505047C>A	ENSP00000452316:p.Glu1213Asp	64.0	0.0		65.0	4.0	NM_014381	P49751|Q56DK9|Q9P292|Q9UHC0	Missense_Mutation	SNP	ENST00000556740.1	hg19	CCDS32123.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.72|13.72	2.322843|2.322843	0.41096|0.41096	.|.	.|.	ENSG00000119684|ENSG00000119684	ENST00000355774;ENST00000380968;ENST00000238662;ENST00000556740;ENST00000544985|ENST00000553713	T;T;T;T;T|.	0.81330|.	-1.47;0.58;-1.48;-1.47;0.44|.	5.58|5.58	0.0763|0.0763	0.14402|0.14402	MutL, C-terminal, dimerisation (1);|.	0.834230|.	0.11104|.	N|.	0.599366|.	T|T	0.19046|0.19046	0.0457|0.0457	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	B;B|.	0.16603|.	0.018;0.005|.	B;B|.	0.21151|.	0.019;0.033|.	T|T	0.28427|0.28427	-1.0044|-1.0044	10|5	0.49607|.	T|.	0.09|.	0.0621|0.0621	5.9608|5.9608	0.19299|0.19299	0.1247:0.3891:0.0:0.4862|0.1247:0.3891:0.0:0.4862	.|.	1213;1213|.	Q9UHC1-2;Q9UHC1|.	.;MLH3_HUMAN|.	D|M	1213;159;1213;1213;173|237	ENSP00000348020:E1213D;ENSP00000370355:E159D;ENSP00000238662:E1213D;ENSP00000452316:E1213D;ENSP00000441371:E173D|.	ENSP00000238662:E1213D|.	E|R	-|-	3|2	2|0	MLH3|MLH3	74574800|74574800	0.000000|0.000000	0.05858|0.05858	0.380000|0.380000	0.26093|0.26093	0.935000|0.935000	0.57460|0.57460	-1.227000|-1.227000	0.02950|0.02950	0.194000|0.194000	0.20326|0.20326	0.561000|0.561000	0.74099|0.74099	GAG|AGG	.	.		0.353	MLH3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415006.1	NM_014381		A	75505047	C	A	75505047	3	1	288	1	0	0	0	0	1	0	0	0	9627	680	24	3	754	3	MLH3	14	75505047	Missense_Mutation	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	50719804	75505047	31844493	85	42299										
ITPK1	3705	hgsc.bcm.edu	37	chr14	93542960	93542960	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	ctgcacaacctccatccctcGcttcctgtggagaaaaacaa	6	15	0	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr14:93542960G>A	ENST00000267615.6	-	3	273	c.100C>T	c.(100-102)Cga>Tga	p.R34*	ITPK1_ENST00000354313.3_Nonsense_Mutation_p.R34*|ITPK1_ENST00000555495.1_Intron|ITPK1_ENST00000556603.2_Nonsense_Mutation_p.R34*			Q13572	ITPK1_HUMAN	inositol-tetrakisphosphate 1-kinase	34					blood coagulation (GO:0007596)|dephosphorylation (GO:0016311)|inositol phosphate metabolic process (GO:0043647)|inositol trisphosphate metabolic process (GO:0032957)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|inositol tetrakisphosphate 1-kinase activity (GO:0047325)|inositol-1,3,4,5,6-pentakisphosphate 1-phosphatase activity (GO:0052825)|inositol-1,3,4,6-tetrakisphosphate 1-phosphatase activity (GO:0052831)|inositol-1,3,4,6-tetrakisphosphate 6-phosphatase activity (GO:0052830)|inositol-1,3,4-trisphosphate 5-kinase activity (GO:0052726)|inositol-1,3,4-trisphosphate 6-kinase activity (GO:0052725)|inositol-3,4,6-trisphosphate 1-kinase activity (GO:0052835)|isomerase activity (GO:0016853)|magnesium ion binding (GO:0000287)			endometrium(1)|large_intestine(3)|lung(6)|ovary(1)	11		all_cancers(154;0.077)|all_epithelial(191;0.247)		Epithelial(152;0.124)|all cancers(159;0.169)		TCCATCCCTCGCTTCCTGTGG	0.582																																					p.R34X		Atlas-SNP	.											.	ITPK1	53	.	0			c.C100T						.						158	123	135					14																	93542960		2203	4300	6503	SO:0001587	stop_gained	3705	exon3			TCCCTCGCTTCCT	U51336	CCDS9907.1, CCDS45157.1	14q32.12	2012-08-16	2011-04-28		ENSG00000100605	ENSG00000100605	2.7.1.134		6177	protein-coding gene	gene with protein product		601838	"inositol 1,3,4-triphosphate 5/6 kinase"			8662638, 11042108	Standard	NM_014216		Approved		uc001ybh.3	Q13572	OTTHUMG00000171226	ENST00000267615.6:c.100C>T	chr14.hg19:g.93542960G>A	ENSP00000267615:p.Arg34*	167.0	0.0		164.0	55.0	NM_001142593	Q9BTL6|Q9H2E7	Nonsense_Mutation	SNP	ENST00000267615.6	hg19	CCDS9907.1	.	.	.	.	.	.	.	.	.	.	G	36	5.790703	0.96945	.	.	ENSG00000100605	ENST00000354313;ENST00000556603;ENST00000267615;ENST00000311458;ENST00000554999;ENST00000555553;ENST00000553452;ENST00000557309	.	.	.	3.7	3.7	0.42460	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.3871	11.2719	0.49144	0.0:0.0:1.0:0.0	.	.	.	.	X	34	.	ENSP00000267615:R34X	R	-	1	2	ITPK1	92612713	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	3.694000	0.54742	2.372000	0.80975	0.561000	0.74099	CGA	.	.		0.582	ITPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412421.2	NM_014216		A	93542960	G	A	93542960	4	1	288	1	0	0	0	0	0	1	0	0	7925	1095	38	1	1228	1	ITPK1	14	93542960	Nonsense_Mutation	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	18037913	93542960	13806580	86	42300										
KIF26A	26153	hgsc.bcm.edu	37	chr14	104641634	104641634	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	cccgagacgcagaccacttcCgctgcagcaccttcgcggag	11	17	0	2			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr14:104641634C>T	ENST00000423312.2	+	12	2509	c.2509C>T	c.(2509-2511)Cgc>Tgc	p.R837C	KIF26A_ENST00000315264.7_Missense_Mutation_p.R698C	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	837					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|enteric nervous system development (GO:0048484)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of signal transduction (GO:0009968)|regulation of cell growth by extracellular stimulus (GO:0001560)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	21		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767)	Epithelial(46;0.152)	Epithelial(152;0.161)		AGACCACTTCCGCTGCAGCAC	0.677																																					p.R837C		Atlas-SNP	.											.	KIF26A	84	.	0			c.C2509T						.						15	18	17					14																	104641634		2025	4166	6191	SO:0001583	missense	26153	exon12			CACTTCCGCTGCA	AB033062	CCDS45171.1	14q32.33	2009-03-19			ENSG00000066735	ENSG00000066735		"Kinesins"	20226	protein-coding gene	gene with protein product		613231				10574462, 11416179	Standard	NM_015656		Approved	KIAA1236, DKFZP434N178	uc001yos.4	Q9ULI4	OTTHUMG00000154986	ENST00000423312.2:c.2509C>T	chr14.hg19:g.104641634C>T	ENSP00000388241:p.Arg837Cys	77.0	0.0		18.0	8.0	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Missense_Mutation	SNP	ENST00000423312.2	hg19	CCDS45171.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.406843	0.83230	.	.	ENSG00000066735	ENST00000423312;ENST00000315264	T;T	0.80033	-1.33;-1.33	3.81	2.7	0.31948	.	.	.	.	.	T	0.80486	0.4632	L	0.47716	1.5	0.43673	D	0.996106	D	0.76494	0.999	P	0.54924	0.764	T	0.81245	-0.1020	9	0.87932	D	0	.	8.962	0.35854	0.53:0.47:0.0:0.0	.	837	Q9ULI4	KI26A_HUMAN	C	837;698	ENSP00000388241:R837C;ENSP00000325452:R698C	ENSP00000325452:R698C	R	+	1	0	KIF26A	103711387	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	5.441000	0.66569	1.835000	0.53391	0.462000	0.41574	CGC	.	.		0.677	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1			T	104641634	C	T	104641634	3	4	288	1	0	0	0	0	1	0	0	0	8303	652	23	1	2555	1	KIF26A	14	104641634	Missense_Mutation	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	11098674	104641634	2707906	87	42301										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105420945	105420945	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	ctaggttcgtaggcctctgaCgagctgtgtgacctctgggg	15	10	2	2	rs376708808	byFrequency	TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr14:105420945C>T	ENST00000333244.5	-	7	962	c.843G>A	c.(841-843)tcG>tcA	p.S281S	AHNAK2_ENST00000557457.1_5'Flank	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	281						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				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)			AGGCCTCTGACGAGCTGTGTG	0.612																																					p.S281S		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G843A						.						35	38	37					14																	105420945		2077	4190	6267	SO:0001819	synonymous_variant	113146	exon7			CTCTGACGAGCTG	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.843G>A	chr14.hg19:g.105420945C>T		74.0	0.0		48.0	28.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	hg19	CCDS45177.1																																																																																			.	.		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		T	105420945	C	T	105420945	2	4	288	1	0	0	0	0	0	0	0	1	415	523	19	1		1	AHNAK2	14	105420945	Silent	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	779311	105420945	1928595	88	42302										
VPS39	23339	hgsc.bcm.edu	37	chr15	42454640	42454641	+	Frame_Shift_Ins	INS	-	-	G													0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	ggccccaggcagtgaatgctINSggggggcgacaggtacatcc							TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr15:42454640_42454641insG	ENST00000348544.4	-	23	2246_2247	c.2247_2248insC	c.(2245-2250)cccagcfs	p.S750fs	VPS39_ENST00000318006.5_Frame_Shift_Ins_p.S739fs			Q96JC1	VPS39_HUMAN	vacuolar protein sorting 39 homolog (S. cerevisiae)	750					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	endosome (GO:0005768)|HOPS complex (GO:0030897)|lysosomal membrane (GO:0005765)	small GTPase regulator activity (GO:0005083)			breast(2)|kidney(5)|large_intestine(4)|lung(8)|ovary(1)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		all_cancers(109;6.78e-16)|all_epithelial(112;1.81e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;3.05e-06)		CAGTGAATGCTGGGGGGCGACA	0.589																																					p.S739fs		Atlas-Indel,Pindel	.											.	VPS39	53	.	0			c.2215_2216insC						.																																			SO:0001589	frameshift_variant	23339	exon22			.	AF280814	CCDS10083.1, CCDS73710.1	15q14	2008-02-05	2006-12-19		ENSG00000166887	ENSG00000166887			20593	protein-coding gene	gene with protein product		612188	"vacuolar protein sorting 39 (yeast)"			11448994	Standard	XM_005254259		Approved	KIAA0770, VAM6	uc001zpc.3	Q96JC1	OTTHUMG00000130467	ENST00000348544.4:c.2248dupC	chr15.hg19:g.42454646_42454646dupG	ENSP00000335193:p.Ser750fs	135.0	0.0		103.0	35.0	NM_015289	O94869|Q71SQ6|Q7Z3V3|Q96B93|Q96RM0	Frame_Shift_Ins	INS	ENST00000348544.4	hg19	CCDS10083.1																																																																																			.	.		0.589	VPS39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000420472.1	NM_015289		G	42454641	-	G	42454640	7	5	288	1	0	1	1	0	0	0	0	0	17224	1580	55	0	428	0	VPS39	15	42454640	Frame_Shift_Ins	INS	-	TCGA-G3-A5SM-01A-12D-A28X-10		42454640	60076752	89	42303										
HCN4	10021	hgsc.bcm.edu	37	chr15	73617654	73617654	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	ctcacctcccgcaggggctcGcttagctcgcccaggatgct	11	17	1	0			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr15:73617654G>A	ENST00000261917.3	-	5	2715	c.1722C>T	c.(1720-1722)agC>agT	p.S574S		NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	574					blood circulation (GO:0008015)|cation transport (GO:0006812)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)	cAMP binding (GO:0030552)|cation channel activity (GO:0005261)|identical protein binding (GO:0042802)|intracellular cAMP activated cation channel activity (GO:0005222)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(13)|liver(1)|lung(18)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				COAD - Colon adenocarcinoma(1;0.142)		GCAGGGGCTCGCTTAGCTCGC	0.677																																					p.S574S		Atlas-SNP	.											.	HCN4	150	.	0			c.C1722T						.						41	46	44					15																	73617654		2198	4297	6495	SO:0001819	synonymous_variant	10021	exon5			GGGCTCGCTTAGC	AJ132429	CCDS10248.1	15q24.1	2011-07-05			ENSG00000138622	ENSG00000138622		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	16882	protein-coding gene	gene with protein product		605206				10228147, 10430953, 16382102	Standard	NM_005477		Approved		uc002avp.3	Q9Y3Q4	OTTHUMG00000137563	ENST00000261917.3:c.1722C>T	chr15.hg19:g.73617654G>A		160.0	0.0		113.0	80.0	NM_005477	Q9UMQ7	Silent	SNP	ENST00000261917.3	hg19	CCDS10248.1																																																																																			.	.		0.677	HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268900.2	NM_005477		A	73617654	G	A	73617654	2	1	288	1	0	0	0	0	0	0	0	1	7008	1078	38	1		1	HCN4	15	73617654	Silent	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	31163014	73617654	28913738	90	42304										
ITFG3	83986	hgsc.bcm.edu	37	chr16	314814	314814	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	gtcccccaccctgcagccgtCctgtttgagccaagccgcca	9	19	0	1	rs140101617		TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr16:314814C>A	ENST00000399932.3	+	13	1903	c.1452C>A	c.(1450-1452)gtC>gtA	p.V484V	ITFG3_ENST00000450082.2_Silent_p.V484V|ITFG3_ENST00000301678.3_Silent_p.V484V|ITFG3_ENST00000600536.1_Intron|ITFG3_ENST00000442458.2_Intron|ITFG3_ENST00000301679.2_Silent_p.V484V	NM_001284497.1	NP_001271426.1	Q9H0X4	ITFG3_HUMAN	integrin alpha FG-GAP repeat containing 3	484						cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(3)|endometrium(2)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	16		all_cancers(16;0.000129)|all_epithelial(16;0.000206)|Hepatocellular(16;0.00264)|Lung NSC(18;0.0626)|all_lung(18;0.13)				CTGCAGCCGTCCTGTTTGAGC	0.687																																					p.V484V		Atlas-SNP	.											.	ITFG3	42	.	0			c.C1452A						.						17	21	20					16																	314814		2093	4211	6304	SO:0001819	synonymous_variant	83986	exon13			AGCCGTCCTGTTT	AL136542	CCDS10402.1	16p13.3	2006-03-31	2006-03-31	2006-03-31	ENSG00000167930	ENSG00000167930			14163	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 9"	C16orf9			Standard	XM_005255622		Approved	DKFZP761D0211, FLJ32603	uc002cgf.3	Q9H0X4	OTTHUMG00000060728	ENST00000399932.3:c.1452C>A	chr16.hg19:g.314814C>A		58.0	0.0		48.0	12.0	NM_032039	D3DU45|Q7L416|Q96FR1|Q96MC7|Q96S30	Silent	SNP	ENST00000399932.3	hg19	CCDS10402.1	.	.	.	.	.	.	.	.	.	.	C	0.718	-0.784727	0.02907	.	.	ENSG00000167930	ENST00000424016	.	.	.	5.0	2.97	0.34412	.	.	.	.	.	T	0.54886	0.1886	.	.	.	0.51482	D	0.999924	.	.	.	.	.	.	T	0.49916	-0.8888	4	.	.	.	-18.7667	6.4344	0.21815	0.0:0.58:0.3073:0.1126	.	.	.	.	Y	124	.	.	S	+	2	0	ITFG3	254815	0.235000	0.23794	0.270000	0.24601	0.826000	0.46750	0.395000	0.20850	1.102000	0.41551	0.555000	0.69702	TCC	.	C|1.000;T|0.000		0.687	ITFG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134227.2	NM_032039		A	314814	C	A	314814	2	1	288	1	0	0	0	0	0	0	0	1	7880	842	30	3		3	ITFG3	16	314814	Silent	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10		314814	90039939	91	42305										
PTX4	390667	hgsc.bcm.edu	37	chr16	1535964	1535964	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	ggacagcgttccaggcaggtGcagttggccccctgcacaaa	13	13	0	0			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr16:1535964G>A	ENST00000447419.2	-	3	1438	c.1413C>T	c.(1411-1413)tgC>tgT	p.C471C	PTX4_ENST00000293922.1_Silent_p.C466C|PTX4_ENST00000440447.2_3'UTR			Q96A99	PTX4_HUMAN	pentraxin 4, long	471						extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						CCAGGCAGGTGCAGTTGGCCC	0.652																																					p.C466C		Atlas-SNP	.											.	PTX4	46	.	0			c.C1398T						.						28	29	29					16																	1535964		2198	4300	6498	SO:0001819	synonymous_variant	390667	exon3			GCAGGTGCAGTTG		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"chromosome 16 open reading frame 38"	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.1413C>T	chr16.hg19:g.1535964G>A		58.0	0.0		66.0	11.0	NM_001013658		Silent	SNP	ENST00000447419.2	hg19																																																																																				.	.		0.652	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658		A	1535964	G	A	1535964	2	1	288	1	0	0	0	0	0	0	0	1	12838	1311	46	3		3	PTX4	16	1535964	Silent	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	1221150	1535964	88818789	92	42306										
PKD1	5310	hgsc.bcm.edu	37	chr16	2157970	2157970	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	gccagccgccagccgctcccGtggaatggtgaccgtgctgc	14	16	0	1	rs184394342	byFrequency	TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr16:2157970G>T	ENST00000262304.4	-	16	7187	c.6979C>A	c.(6979-6981)Cgg>Agg	p.R2327R	PKD1_ENST00000561991.1_5'Flank|PKD1_ENST00000423118.1_Silent_p.R2327R	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	2327	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						AGCCGCTCCCGTGGAATGGTG	0.701																																					p.R2327R		Atlas-SNP	.											.	PKD1	184	.	0			c.C6979A						.						5	5	5					16																	2157970		1955	3980	5935	SO:0001819	synonymous_variant	5310	exon16			GCTCCCGTGGAAT	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"Voltage-gated ion channels / Transient receptor potential cation channels"	9008	protein-coding gene	gene with protein product	"polycystin 1", "transient receptor potential cation channel, subfamily P, member 1"	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.6979C>A	chr16.hg19:g.2157970G>T		112.0	0.0		53.0	4.0	NM_000296	Q15140|Q15141	Silent	SNP	ENST00000262304.4	hg19	CCDS32369.1																																																																																			.	G|0.999;A|0.001		0.701	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			T	2157970	G	T	2157970	2	4	288	1	0	0	0	0	0	0	0	1	11972	1144	40	1		1	PKD1	16	2157970	Silent	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	622006	2157970	88196783	93	42307										
MLST8	64223	hgsc.bcm.edu	37	chr16	2257268	2257268	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	acagaccacaacgagcagctGatccctgagcccgaggtctc	10	15	1	3			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr16:2257268G>T	ENST00000569417.1	+	6	849	c.495G>T	c.(493-495)ctG>ctT	p.L165L	MLST8_ENST00000564088.1_Silent_p.L165L|MLST8_ENST00000397124.1_Silent_p.L165L|MLST8_ENST00000301724.10_Silent_p.L165L|MLST8_ENST00000561651.1_3'UTR|AC009065.3_ENST00000517149.1_RNA|MLST8_ENST00000565250.1_Silent_p.L165L|MLST8_ENST00000382450.4_Silent_p.L164L|MLST8_ENST00000301725.7_Silent_p.L184L	NM_022372.4	NP_071767.3	Q9BVC4	LST8_HUMAN	MTOR associated protein, LST8 homolog (S. cerevisiae)	165					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of TOR signaling (GO:0032008)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of Rac GTPase activity (GO:0032314)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|cytosol (GO:0005829)				large_intestine(3)|lung(2)|skin(1)	6						ACGAGCAGCTGATCCCTGAGC	0.617																																					p.L165L		Atlas-SNP	.											.	MLST8	60	.	0			c.G495T						.						158	174	169					16																	2257268		2159	4256	6415	SO:0001819	synonymous_variant	64223	exon6			GCAGCTGATCCCT		CCDS10462.2, CCDS58409.1	16p13.3	2013-01-09			ENSG00000167965	ENSG00000167965		"WD repeat domain containing"	24825	protein-coding gene	gene with protein product	"G protein beta subunit like"	612190				12477932	Standard	NM_022372		Approved	Lst8, Pop3, GBL, GbetaL	uc002cpc.3	Q9BVC4	OTTHUMG00000128827	ENST00000569417.1:c.495G>T	chr16.hg19:g.2257268G>T		180.0	0.0		220.0	87.0	NM_001199174	B3KMM4|B4DY00|D3DU88|Q5M800|Q86Y18|Q8WUI5|Q9HA66|Q9UJV6	Silent	SNP	ENST00000569417.1	hg19	CCDS10462.2																																																																																			.	.		0.617	MLST8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250763.2	NM_022372		T	2257268	G	T	2257268	2	4	288	1	0	0	0	0	0	0	0	1	9643	1277	45	3		3	MLST8	16	2257268	Silent	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	99298	2257268	88097485	94	42308										
NMRAL1	57407	hgsc.bcm.edu	37	chr16	4519432	4519432	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	accttgaatgtcccatcttcCaggagtgtgcgggccacgga	12	12	1	1	rs11557237		TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr16:4519432C>T	ENST00000574733.1	-	3	804	c.75G>A	c.(73-75)ctG>ctA	p.L25L	NMRAL1_ENST00000572391.1_Intron|NMRAL1_ENST00000283429.6_Silent_p.L25L|NMRAL1_ENST00000574425.1_Silent_p.L25L|NMRAL1_ENST00000404295.3_Silent_p.L25L			Q9HBL8	NMRL1_HUMAN	NmrA-like family domain containing 1	25						cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|prostate(2)|stomach(1)	15						TCCCATCTTCCAGGAGTGTGC	0.562																																					p.L25L		Atlas-SNP	.											.	NMRAL1	31	.	0			c.G75A						.						218	197	204					16																	4519432		2197	4300	6497	SO:0001819	synonymous_variant	57407	exon3			ATCTTCCAGGAGT	AF225419	CCDS10516.1	16p13.3	2013-10-11			ENSG00000153406	ENSG00000153406		"Short chain dehydrogenase/reductase superfamily / Atypical members"	24987	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 48A, member 1"					19027726	Standard	NM_020677		Approved	FLJ25918, HSCARG, SDR48A1	uc002cwo.3	Q9HBL8	OTTHUMG00000129468	ENST00000574733.1:c.75G>A	chr16.hg19:g.4519432C>T		73.0	0.0		81.0	36.0	NM_020677		Silent	SNP	ENST00000574733.1	hg19	CCDS10516.1																																																																																			.	.		0.562	NMRAL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438579.1	NM_020677		T	4519432	C	T	4519432	2	4	288	1	0	0	0	0	0	0	0	1	10510	581	21	3		3	NMRAL1	16	4519432	Silent	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	2262164	4519432	85835321	95	42309										
CP110	9738	hgsc.bcm.edu	37	chr16	19551992	19551992	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	ttttcagaaagcgaggagttActaaaaagcaagatgttagc	10	5	1	2			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr16:19551992A>G	ENST00000381396.5	+	5	2179	c.1932A>G	c.(1930-1932)ttA>ttG	p.L644L	CCP110_ENST00000396208.2_Silent_p.L644L|CCP110_ENST00000396212.2_Silent_p.L644L	NM_001199022.1	NP_001185951	O43303	CP110_HUMAN	centriolar coiled coil protein 110kDa	644					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of cytokinesis (GO:0032465)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|protein complex (GO:0043234)				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|stomach(3)|urinary_tract(1)	21						GCGAGGAGTTACTAAAAAGCA	0.358																																					p.L644L		Atlas-SNP	.											.	CCP110	57	.	0			c.A1932G						.						64	63	63					16																	19551992		2197	4300	6497	SO:0001819	synonymous_variant	9738	exon5			GGAGTTACTAAAA	AB007879	CCDS10579.1, CCDS55992.1	16p12.3	2014-02-20	2011-05-27		ENSG00000103540	ENSG00000103540			24342	protein-coding gene	gene with protein product		609544				9455477, 12361598, 16760425	Standard	NM_014711		Approved	KIAA0419, CP110	uc002dgl.4	O43303	OTTHUMG00000131459	ENST00000381396.5:c.1932A>G	chr16.hg19:g.19551992A>G		298.0	0.0		337.0	133.0	NM_001199022	B7WP23|O43335|Q68DV9|Q8NE13	Silent	SNP	ENST00000381396.5	hg19	CCDS55992.1																																																																																			.	.		0.358	CCP110-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254284.2	NM_014711		G	19551992	A	G	19551992	2	3	288	1	0	0	0	0	0	0	0	1	3790	388	14	2		2	CP110	16	19551992	Silent	SNP	A	TCGA-G3-A5SM-01A-12D-A28X-10	15032560	19551992	70802761	96	42310										
WDR81	124997	hgsc.bcm.edu	37	chr17	1630783	1630783	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	cagagaggggcaagctggacCaactgtttgagtacaggcct	14	9	0	2			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr17:1630783C>T	ENST00000409644.1	+	1	2530	c.2530C>T	c.(2530-2532)Caa>Taa	p.Q844*	WDR81_ENST00000545662.1_5'Flank|WDR81_ENST00000437219.2_Intron|WDR81_ENST00000419248.1_Intron|WDR81_ENST00000446363.1_Intron|WDR81_ENST00000309182.5_Intron|RP11-961A15.1_ENST00000576540.1_RNA	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	844					negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		CAAGCTGGACCAACTGTTTGA	0.632																																					p.Q844X		Atlas-SNP	.											.	WDR81	180	.	0			c.C2530T						.						34	39	37					17																	1630783		692	1589	2281	SO:0001587	stop_gained	124997	exon1			CTGGACCAACTGT	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"WD repeat domain containing"	26600	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 166"	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.2530C>T	chr17.hg19:g.1630783C>T	ENSP00000386609:p.Gln844*	109.0	0.0		66.0	26.0	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Nonsense_Mutation	SNP	ENST00000409644.1	hg19	CCDS54062.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.683694	0.88639	.	.	ENSG00000167716	ENST00000409644	.	.	.	5.38	4.39	0.52855	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.13853	T	0.58	.	15.359	0.74453	0.0:0.8599:0.1401:0.0	.	.	.	.	X	844	.	ENSP00000386609:Q844X	Q	+	1	0	WDR81	1577533	0.004000	0.15560	0.044000	0.18714	0.098000	0.18820	1.483000	0.35497	1.358000	0.45922	0.555000	0.69702	CAA	.	.		0.632	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348		T	1630783	C	T	1630783	4	4	288	1	0	0	0	0	0	1	0	0	17345	595	21	3	2594	3	WDR81	17	1630783	Nonsense_Mutation	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10		1630783	79564427	97	42311										
SMG6	23293	hgsc.bcm.edu	37	chr17	2076069	2076069	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	gtgaggtcatcatccgggtcCttgtacagtggcacctcaga	12	11	3	2			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr17:2076069C>G	ENST00000263073.6	-	13	3290	c.3240G>C	c.(3238-3240)aaG>aaC	p.K1080N	SMG6_ENST00000544865.1_Missense_Mutation_p.K1049N|SMG6_ENST00000536871.2_Missense_Mutation_p.K172N|SMG6_ENST00000354901.4_Missense_Mutation_p.K172N	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	1080					gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|telomere maintenance (GO:0000723)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|telomeric DNA binding (GO:0042162)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(10)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						CATCCGGGTCCTTGTACAGTG	0.537																																					p.K1080N	Melanoma(59;28 1088 11621 25887 46638 50814)	Atlas-SNP	.											.	SMG6	97	.	0			c.G3240C						.						128	104	112					17																	2076069		2203	4300	6503	SO:0001583	missense	23293	exon13			CGGGTCCTTGTAC	AB018275	CCDS11016.1, CCDS58498.1	17p13.3	2013-07-02	2013-07-02	2006-02-16	ENSG00000070366	ENSG00000070366			17809	protein-coding gene	gene with protein product	"EST1 telomerase component homolog A (S. cerevisiae)"	610963	"chromosome 17 open reading frame 31", "smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)"	C17orf31		12676087, 12699629	Standard	NM_017575		Approved	KIAA0732, SMG-6, EST1A	uc002fub.1	Q86US8	OTTHUMG00000177578	ENST00000263073.6:c.3240G>C	chr17.hg19:g.2076069C>G	ENSP00000263073:p.Lys1080Asn	134.0	0.0		127.0	57.0	NM_017575	B7Z874|O94837|Q86VH6|Q9UF60	Missense_Mutation	SNP	ENST00000263073.6	hg19	CCDS11016.1	.	.	.	.	.	.	.	.	.	.	C	11.52	1.661901	0.29515	.	.	ENSG00000070366	ENST00000263073;ENST00000544865;ENST00000536871	T;T;T	0.29917	1.55;1.55;1.55	6.02	5.06	0.68205	.	0.000000	0.85682	D	0.000000	T	0.28333	0.0700	L	0.40543	1.245	0.40679	D	0.982284	D	0.52996	0.957	B	0.43658	0.426	T	0.04242	-1.0966	10	0.33141	T	0.24	-12.8458	13.5637	0.61804	0.0:0.9286:0.0:0.0714	.	1080	Q86US8	EST1A_HUMAN	N	1080;1049;172	ENSP00000263073:K1080N;ENSP00000443920:K1049N;ENSP00000440283:K172N	ENSP00000263073:K1080N	K	-	3	2	SMG6	2022819	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.970000	0.40520	1.568000	0.49683	0.549000	0.68633	AAG	.	.		0.537	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437826.3			G	2076069	C	G	2076069	3	3	288	1	0	0	0	0	1	0	0	0	14812	680	24	4	1047	4	SMG6	17	2076069	Missense_Mutation	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	445286	2076069	79119141	98	42312										
SPNS3	201305	hgsc.bcm.edu	37	chr17	4348361	4348361	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	ctgctgctgtctgcacctgtGtttggctacctgggcgaccg	13	13	1	0			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr17:4348361G>T	ENST00000355530.2	+	3	580	c.300G>T	c.(298-300)gtG>gtT	p.V100V	SPNS3_ENST00000576069.1_Intron|SPNS3_ENST00000333476.2_Intron	NM_182538.4	NP_872344.3	Q6ZMD2	SPNS3_HUMAN	spinster homolog 3 (Drosophila)	100					lipid transport (GO:0006869)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				NS(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(6)|stomach(2)	28						CTGCACCTGTGTTTGGCTACC	0.617																																					p.V100V		Atlas-SNP	.											.	SPNS3	52	.	0			c.G300T						.						231	181	198					17																	4348361		2203	4300	6503	SO:0001819	synonymous_variant	201305	exon3			ACCTGTGTTTGGC		CCDS11045.1	17p13.2	2014-08-12			ENSG00000182557	ENSG00000182557			28433	protein-coding gene	gene with protein product		611701					Standard	NM_182538		Approved	MGC29671	uc002fxt.3	Q6ZMD2	OTTHUMG00000177737	ENST00000355530.2:c.300G>T	chr17.hg19:g.4348361G>T		156.0	0.0		113.0	5.0	NM_182538	Q8IZ31	Silent	SNP	ENST00000355530.2	hg19	CCDS11045.1																																																																																			.	.		0.617	SPNS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438793.1	NM_182538		T	4348361	G	T	4348361	2	4	288	1	0	0	0	0	0	0	0	1	15091	1364	48	3		3	SPNS3	17	4348361	Silent	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	2272292	4348361	76846849	99	42313										
PITPNM3	83394	hgsc.bcm.edu	37	chr17	6381970	6381970	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	catcctggtactgcggggagGagatggccaacaggggaagg	18	8	0	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr17:6381970G>C	ENST00000262483.8	-	7	761	c.674C>G	c.(673-675)tCc>tGc	p.S225C	PITPNM3_ENST00000421306.3_Missense_Mutation_p.S189C	NM_031220.3	NP_112497.2	Q9BZ71	PITM3_HUMAN	PITPNM family member 3	225					phosphatidylinositol metabolic process (GO:0046488)|phospholipid transport (GO:0015914)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|phosphatidylinositol transporter activity (GO:0008526)|receptor tyrosine kinase binding (GO:0030971)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(3)|skin(2)	36				Colorectal(2;0.000372)|READ - Rectum adenocarcinoma(2;0.0276)|LUAD - Lung adenocarcinoma(2;0.0836)|COAD - Colon adenocarcinoma(228;0.185)		CTGCGGGGAGGAGATGGCCAA	0.632																																					p.S225C		Atlas-SNP	.											.	PITPNM3	91	.	0			c.C674G						.						64	53	57					17																	6381970		2203	4300	6503	SO:0001583	missense	83394	exon7			GGGGAGGAGATGG	AF334586	CCDS11076.1, CCDS54080.1	17p13	2013-07-18	2013-07-18	2013-07-18	ENSG00000091622	ENSG00000091622		"GPCR / Class A : Chemokine receptors : Atypical"	21043	protein-coding gene	gene with protein product	"atypical chemokine receptor 6"	608921	"cone rod dystrophy 5"	CORD5		10022914	Standard	NM_031220		Approved	NIR1, RDGBA3, ACKR6	uc002gdd.4	Q9BZ71	OTTHUMG00000102039	ENST00000262483.8:c.674C>G	chr17.hg19:g.6381970G>C	ENSP00000262483:p.Ser225Cys	114.0	0.0		81.0	36.0	NM_031220	A1A5D0|F8WEW5|Q59GH9|Q9NPQ4	Missense_Mutation	SNP	ENST00000262483.8	hg19	CCDS11076.1	.	.	.	.	.	.	.	.	.	.	G	19.06	3.753172	0.69648	.	.	ENSG00000091622	ENST00000262483;ENST00000421306	T;T	0.20598	2.06;2.06	3.89	3.89	0.44902	.	0.273259	0.42420	D	0.000716	T	0.37571	0.1008	L	0.46157	1.445	0.43902	D	0.996533	D;D	0.89917	1.0;0.993	D;P	0.72982	0.979;0.635	T	0.08889	-1.0700	10	0.52906	T	0.07	.	14.1702	0.65506	0.0:0.0:1.0:0.0	.	189;225	F8WEW5;Q9BZ71	.;PITM3_HUMAN	C	225;189	ENSP00000262483:S225C;ENSP00000407882:S189C	ENSP00000262483:S225C	S	-	2	0	PITPNM3	6322694	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.312000	0.78968	2.477000	0.83638	0.455000	0.32223	TCC	.	.		0.632	PITPNM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219824.2	NM_031220		C	6381970	G	C	6381970	3	2	288	1	0	0	0	0	1	0	0	0	11961	1174	41	4	2306	4	PITPNM3	17	6381970	Missense_Mutation	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	2033609	6381970	74813240	100	42314										
TP53	7157	hgsc.bcm.edu	37	chr17	7574035	7574035	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	agcgctcacgcccacggatcTgcagcaacagaggaggggga	15	12	2	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr17:7574035T>C	ENST00000269305.4	-	10	1183		c.e10-2		TP53_ENST00000455263.2_Splice_Site|TP53_ENST00000413465.2_Intron|TP53_ENST00000359597.4_Intron|TP53_ENST00000420246.2_Splice_Site|TP53_ENST00000445888.2_Splice_Site	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53						apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.?(10)|p.0?(8)|p.I332fs*49(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CCCACGGATCTGCAGCAACAG	0.507		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											.	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000269305,NS,carcinoma,0,13	TP53	33396	.	19	Unknown(10)|Whole gene deletion(8)|Insertion - Frameshift(1)	lung(5)|haematopoietic_and_lymphoid_tissue(4)|bone(4)|central_nervous_system(2)|liver(2)|stomach(1)|breast(1)	c.994-2A>G						.						44	36	38					17																	7574035		2203	4300	6503	SO:0001630	splice_region_variant	7157	exon11	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	CGGATCTGCAGCA	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.994-2A>G	chr17.hg19:g.7574035T>C		110.0	0.0		82.0	35.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Splice_Site	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	12.31	1.898270	0.33535	.	.	ENSG00000141510	ENST00000269305;ENST00000445888;ENST00000396473	.	.	.	5.13	5.13	0.70059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.1784	0.59641	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	TP53	7514760	1.000000	0.71417	0.937000	0.37676	0.131000	0.20780	6.590000	0.74085	2.061000	0.61500	0.459000	0.35465	.	.	.		0.507	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	Intron	C	7574035	T	C	7574035	5	2	288	1	0	0	0	0	0	0	1	0	16396	1594	55	2	197	2	TP53	17	7574035	Splice_Site	SNP	T	TCGA-G3-A5SM-01A-12D-A28X-10	1192065	7574035	73621175	101	42315										
KRTAP1-3	81850	hgsc.bcm.edu	37	chr17	39190602	39190602	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	ctcacaggagtagcagcagcAgactgggcggcagcaggact	15	11	1	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr17:39190602A>G	ENST00000344363.5	-	1	505	c.472T>C	c.(472-474)Tgc>Cgc	p.C158R		NM_030966.1	NP_112228.1	Q8IUG1	KRA13_HUMAN	keratin associated protein 1-3	168						keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(6)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			TAGCAGCAGCAGACTGGGCGG	0.542																																					p.C158R		Atlas-SNP	.											.	KRTAP1-3	18	.	0			c.T472C						.						36	43	40					17																	39190602		2029	4178	6207	SO:0001583	missense	81850	exon1			AGCAGCAGACTGG	AJ406927	CCDS42323.1	17q21.2	2013-06-20			ENSG00000221880	ENSG00000221880		"Keratin associated proteins"	16771	protein-coding gene	gene with protein product		608820				11279113	Standard	NM_030966		Approved	KAP1.3	uc002hvv.3	Q8IUG1	OTTHUMG00000133583	ENST00000344363.5:c.472T>C	chr17.hg19:g.39190602A>G	ENSP00000344420:p.Cys158Arg	294.0	0.0		263.0	46.0	NM_030966	Q07628|Q8IUG0|Q9BYS2	Missense_Mutation	SNP	ENST00000344363.5	hg19	CCDS42323.1	.	.	.	.	.	.	.	.	.	.	A	16.44	3.122611	0.56613	.	.	ENSG00000221880	ENST00000344363	T	0.50001	0.76	4.52	4.52	0.55395	.	.	.	.	.	T	0.66742	0.2820	.	.	.	0.58432	D	0.999998	D	0.62365	0.991	D	0.77557	0.99	T	0.70905	-0.4745	8	0.87932	D	0	.	10.7883	0.46417	1.0:0.0:0.0:0.0	.	168	Q8IUG1	KRA13_HUMAN	R	158	ENSP00000344420:C158R	ENSP00000344420:C158R	C	-	1	0	KRTAP1-3	36444128	1.000000	0.71417	1.000000	0.80357	0.633000	0.38033	3.489000	0.53237	1.971000	0.57363	0.523000	0.50628	TGC	.	.		0.542	KRTAP1-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257687.1			G	39190602	A	G	39190602	3	3	288	1	0	0	0	0	1	0	0	0	8512	188	7	2	35	2	KRTAP1-3	17	39190602	Missense_Mutation	SNP	A	TCGA-G3-A5SM-01A-12D-A28X-10	31616567	39190602	42004608	102	42316										
ITGA3	3675	hgsc.bcm.edu	37	chr17	48148866	48148866	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	gcagcgccattgccctggcaGacctgaacaatgatgggtga	13	11	0	4			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr17:48148866G>A	ENST00000320031.8	+	6	1273	c.943G>A	c.(943-945)Gac>Aac	p.D315N	ITGA3_ENST00000007722.7_Missense_Mutation_p.D315N|ITGA3_ENST00000544892.1_Missense_Mutation_p.D90N	NM_002204.2|NM_005501.2	NP_002195.1|NP_005492.1	P26006	ITA3_HUMAN	integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3 receptor)	315					blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|lung development (GO:0030324)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|negative regulation of cell projection organization (GO:0031345)|nephron development (GO:0072006)|neuron migration (GO:0001764)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|regulation of BMP signaling pathway (GO:0030510)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of Wnt signaling pathway (GO:0030111)|renal filtration (GO:0097205)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|skin development (GO:0043588)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integrin alpha3-beta1 complex (GO:0034667)|integrin complex (GO:0008305)|invadopodium membrane (GO:0071438)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	glycoprotein binding (GO:0001948)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)			endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)	31						TGCCCTGGCAGACCTGAACAA	0.637																																					p.D315N		Atlas-SNP	.											.	ITGA3	128	.	0			c.G943A						.						26	26	26					17																	48148866		2203	4298	6501	SO:0001583	missense	3675	exon6			CTGGCAGACCTGA	M59911	CCDS11557.1, CCDS11558.1	17q21.33	2010-03-23	2003-10-13		ENSG00000005884	ENSG00000005884		"CD molecules", "Integrins"	6139	protein-coding gene	gene with protein product		605025	"antigen identified by monoclonal antibody J143"	MSK18		1655803, 9704023	Standard	NM_005501		Approved	CD49c, VLA3a, VCA-2, GAP-B3	uc010dbm.3	P26006	OTTHUMG00000161890	ENST00000320031.8:c.943G>A	chr17.hg19:g.48148866G>A	ENSP00000315190:p.Asp315Asn	21.0	0.0		26.0	7.0	NM_005501	A7E246|B7ZM80|B9EGQ1|D3DTX4|D3DTX5	Missense_Mutation	SNP	ENST00000320031.8	hg19	CCDS11558.1	.	.	.	.	.	.	.	.	.	.	G	33	5.198081	0.94997	.	.	ENSG00000005884	ENST00000544892;ENST00000007722;ENST00000538917;ENST00000320031	D;D;D	0.94897	-3.55;-3.55;-3.55	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	D	0.98460	0.9487	H	0.98068	4.14	0.51767	D	0.999937	D;D	0.89917	0.999;1.0	D;D	0.79784	0.936;0.993	D	0.99716	1.1008	10	0.87932	D	0	.	18.0766	0.89428	0.0:0.0:1.0:0.0	.	315;315	P26006-1;P26006	.;ITA3_HUMAN	N	90;315;301;315	ENSP00000446133:D90N;ENSP00000007722:D315N;ENSP00000315190:D315N	ENSP00000007722:D315N	D	+	1	0	ITGA3	45503865	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	9.093000	0.94163	2.566000	0.86566	0.563000	0.77884	GAC	.	.		0.637	ITGA3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000366298.1	NM_005501		A	48148866	G	A	48148866	3	1	288	1	0	0	0	0	1	0	0	0	7886	942	33	3	965	3	ITGA3	17	48148866	Missense_Mutation	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	8958264	48148866	33046344	103	42317										
KIF2B	84643	hgsc.bcm.edu	37	chr17	51901739	51901739	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	agttttccctcgttgatttaGctgggaatgaaagaggagca	12	6	0	3			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr17:51901739G>T	ENST00000268919.4	+	1	1501	c.1345G>T	c.(1345-1347)Gct>Tct	p.A449S		NM_032559.4	NP_115948.4	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	449	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(15)|lung(58)|ovary(5)|prostate(4)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						CGTTGATTTAGCTGGGAATGA	0.488																																					p.A449S		Atlas-SNP	.											.	KIF2B	254	.	0			c.G1345T						.						55	50	52					17																	51901739		2203	4300	6503	SO:0001583	missense	84643	exon1			GATTTAGCTGGGA	AF333335	CCDS32685.1	17q22	2014-08-12			ENSG00000141200	ENSG00000141200		"Kinesins"	29443	protein-coding gene	gene with protein product		615142				11416179	Standard	NM_032559		Approved		uc002iua.2	Q8N4N8	OTTHUMG00000177756	ENST00000268919.4:c.1345G>T	chr17.hg19:g.51901739G>T	ENSP00000268919:p.Ala449Ser	101.0	0.0		94.0	16.0	NM_032559	Q96MA2|Q9BXG6	Missense_Mutation	SNP	ENST00000268919.4	hg19	CCDS32685.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.700253	0.88924	.	.	ENSG00000141200	ENST00000268919;ENST00000416491	D	0.86956	-2.19	5.73	5.73	0.89815	Kinesin, motor domain (5);Kinesin, motor region, conserved site (1);	0.000000	0.44688	D	0.000437	D	0.96926	0.8996	H	0.99535	4.615	0.58432	D	0.999998	D	0.89917	1.0	D	0.87578	0.998	D	0.98245	1.0490	10	0.87932	D	0	.	19.2577	0.93952	0.0:0.0:1.0:0.0	.	449	Q8N4N8	KIF2B_HUMAN	S	449;337	ENSP00000268919:A449S	ENSP00000268919:A449S	A	+	1	0	KIF2B	49256738	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	9.813000	0.99286	2.854000	0.98071	0.655000	0.94253	GCT	.	.		0.488	KIF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438854.1	NM_032559		T	51901739	G	T	51901739	3	4	288	1	0	0	0	0	1	0	0	0	8307	971	34	3	1347	3	KIF2B	17	51901739	Missense_Mutation	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	3752873	51901739	29293471	104	42318										
TEX14	56155	hgsc.bcm.edu	37	chr17	56700253	56700253	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	gtcaaagcccaagtcttcggGttttgacccctctcatcgtg	9	13	3	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr17:56700253G>T	ENST00000240361.8	-	4	457	c.372C>A	c.(370-372)aaC>aaA	p.N124K	TEX14_ENST00000349033.5_Missense_Mutation_p.N124K|TEX14_ENST00000389934.3_Missense_Mutation_p.N124K			Q8IWB6	TEX14_HUMAN	testis expressed 14	124					attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)			breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					AAGTCTTCGGGTTTTGACCCC	0.562																																					p.N124K		Atlas-SNP	.											.	TEX14	343	.	0			c.C372A						.						117	86	96					17																	56700253		2203	4300	6503	SO:0001583	missense	56155	exon4			CTTCGGGTTTTGA	AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"cancer/testis antigen 113"	605792	"testis expressed sequence 14"			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.372C>A	chr17.hg19:g.56700253G>T	ENSP00000240361:p.Asn124Lys	135.0	0.0		129.0	56.0	NM_198393	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Missense_Mutation	SNP	ENST00000240361.8	hg19	CCDS56042.1	.	.	.	.	.	.	.	.	.	.	G	9.071	0.996974	0.19043	.	.	ENSG00000121101	ENST00000240361;ENST00000389934;ENST00000349033	T;T;T	0.33865	1.39;1.39;1.39	5.12	-5.34	0.02705	Ankyrin repeat-containing domain (3);	0.245125	0.35291	N	0.003309	T	0.23649	0.0572	L	0.34521	1.04	0.21499	N	0.999668	B;B;B	0.25809	0.083;0.135;0.135	B;B;B	0.21917	0.017;0.037;0.037	T	0.11060	-1.0603	10	0.66056	D	0.02	-6.3684	14.5577	0.68113	0.7121:0.0:0.2879:0.0	.	124;124;124	Q8IWB6;Q8IWB6-3;Q8IWB6-2	TEX14_HUMAN;.;.	K	124	ENSP00000240361:N124K;ENSP00000374584:N124K;ENSP00000268910:N124K	ENSP00000240361:N124K	N	-	3	2	TEX14	54055252	0.000000	0.05858	0.007000	0.13788	0.478000	0.33099	-0.907000	0.04067	-0.915000	0.03823	-0.768000	0.03414	AAC	.	.		0.562	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1			T	56700253	G	T	56700253	3	4	288	1	0	0	0	0	1	0	0	0	15793	1252	44	3	4223	3	TEX14	17	56700253	Missense_Mutation	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	4798514	56700253	24494957	105	42319										
CD300E	342510	hgsc.bcm.edu	37	chr17	72613454	72613454	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	ccaccttctcttctcccttgGtctccacaatgctctcacat	3	18	4	0	rs201462551		TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr17:72613454G>C	ENST00000328630.3	-	2	231	c.191C>G	c.(190-192)aCc>aGc	p.T64S	CD300E_ENST00000426295.2_Missense_Mutation_p.T105S|CD300E_ENST00000392619.1_Missense_Mutation_p.T91S			Q496F6	CLM2_HUMAN	CD300e molecule	64	Ig-like V-type.				innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|kidney(3)|large_intestine(4)|lung(4)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	19						TTCTCCCTTGGTCTCCACAAT	0.522																																					p.T64S		Atlas-SNP	.											.	CD300E	70	.	0			c.C191G						.						245	156	186					17																	72613454		2203	4300	6503	SO:0001583	missense	342510	exon2			CCCTTGGTCTCCA	BX648376	CCDS11702.1	17q25.1	2013-01-11	2006-03-28	2006-02-22	ENSG00000186407	ENSG00000186407		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	28874	protein-coding gene	gene with protein product		609801	"CD300 antigen like family member E", "CD300e antigen"	CD300LE		15549731, 15557162	Standard	NM_181449		Approved	IREM2, CLM2	uc002jlb.2	Q496F6	OTTHUMG00000067605	ENST00000328630.3:c.191C>G	chr17.hg19:g.72613454G>C	ENSP00000329942:p.Thr64Ser	150.0	0.0		164.0	18.0	NM_181449	B4DNS1|Q7Z7I3	Missense_Mutation	SNP	ENST00000328630.3	hg19	CCDS11702.1	.	.	.	.	.	.	.	.	.	.	G	16.47	3.133156	0.56828	.	.	ENSG00000186407	ENST00000392619;ENST00000426295;ENST00000328630;ENST00000412268	T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17	4.74	3.77	0.43336	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.47455	D	0.000235	T	0.73442	0.3587	M	0.63428	1.95	0.27250	N	0.958922	D	0.89917	1.0	D	0.91635	0.999	T	0.65294	-0.6203	10	0.87932	D	0	-16.4136	9.5171	0.39113	0.1012:0.0:0.8988:0.0	.	64	Q496F6	CLM2_HUMAN	S	91;105;64;66	ENSP00000376395:T91S;ENSP00000416642:T105S;ENSP00000329942:T64S;ENSP00000415488:T66S	ENSP00000329942:T64S	T	-	2	0	CD300E	70125049	0.224000	0.23674	0.447000	0.26932	0.004000	0.04260	2.338000	0.43957	1.312000	0.45043	-0.229000	0.12294	ACC	.	G|1.000;A|0.000		0.522	CD300E-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_181449		C	72613454	G	C	72613454	3	2	288	1	0	0	0	0	1	0	0	0	3000	1261	44	4	438	4	CD300E	17	72613454	Missense_Mutation	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	15913201	72613454	8581756	106	42320										
GALNT1	2589	hgsc.bcm.edu	37	chr18	33267144	33267144	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	gaaaggtgatcggactcttcCtgtcaggtaattaatttgtc	10	7	2	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr18:33267144C>T	ENST00000269195.5	+	5	957	c.854C>T	c.(853-855)cCt>cTt	p.P285L	GALNT1_ENST00000537549.1_Missense_Mutation_p.P225L	NM_020474.3	NP_065207.2	Q10472	GALT1_HUMAN	polypeptide N-acetylgalactosaminyltransferase 1	285	Catalytic subdomain B.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|protein O-linked glycosylation via serine (GO:0018242)|protein O-linked glycosylation via threonine (GO:0018243)	extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|manganese ion binding (GO:0030145)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(4)|stomach(1)	21						CGGACTCTTCCTGTCAGGTAA	0.408																																					p.P285L		Atlas-SNP	.											.	GALNT1	53	.	0			c.C854T						.						128	126	126					18																	33267144		2203	4300	6503	SO:0001583	missense	2589	exon5			CTCTTCCTGTCAG		CCDS11915.1	18q12.1	2014-03-13	2014-03-13		ENSG00000141429	ENSG00000141429	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4123	protein-coding gene	gene with protein product	"protein-UDP acetylgalactosaminyltransferase 1", "polypeptide GalNAc transferase 1"	602273	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 1 (GalNAc-T1)"			7592619, 12199709	Standard	NM_020474		Approved	GalNAc-T1	uc002kzb.3	Q10472	OTTHUMG00000132567	ENST00000269195.5:c.854C>T	chr18.hg19:g.33267144C>T	ENSP00000269195:p.Pro285Leu	129.0	0.0		133.0	17.0	NM_020474	Q86TJ7|Q9UM86	Missense_Mutation	SNP	ENST00000269195.5	hg19	CCDS11915.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.019438	0.93462	.	.	ENSG00000141429	ENST00000537748;ENST00000269195;ENST00000537549	T;T	0.61392	0.11;0.11	5.5	5.5	0.81552	Glycosyl transferase, family 2 (1);	0.000000	0.85682	D	0.000000	T	0.81912	0.4923	M	0.92507	3.315	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.86191	0.1612	10	0.87932	D	0	.	16.8858	0.86075	0.0:1.0:0.0:0.0	.	285	Q10472	GALT1_HUMAN	L	285;285;225	ENSP00000269195:P285L;ENSP00000440910:P225L	ENSP00000269195:P285L	P	+	2	0	GALNT1	31521142	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.818000	0.86416	2.595000	0.87683	0.585000	0.79938	CCT	.	.		0.408	GALNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255771.2	NM_020474		T	33267144	C	T	33267144	3	4	288	1	0	0	0	0	1	0	0	0	6215	681	24	3	872	3	GALNT1	18	33267144	Missense_Mutation	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10		33267144	44810104	107	42321										
FHOD3	80206	hgsc.bcm.edu	37	chr18	34156482	34156482	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	accgcaatgaaaccattcagTggctgtacactctcattggg	9	11	2	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr18:34156482T>C	ENST00000359247.4	+	6	580	c.580T>C	c.(580-582)Tgg>Cgg	p.W194R	FHOD3_ENST00000591635.1_5'UTR|FHOD3_ENST00000445677.1_Missense_Mutation_p.W194R|FHOD3_ENST00000590592.1_Missense_Mutation_p.W194R|FHOD3_ENST00000257209.4_Missense_Mutation_p.W194R	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	194	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)				NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				AACCATTCAGTGGCTGTACAC	0.388																																					p.W194R		Atlas-SNP	.											.	FHOD3	210	.	0			c.T580C						.						137	121	127					18																	34156482		2203	4300	6503	SO:0001583	missense	80206	exon6			ATTCAGTGGCTGT	AK091899	CCDS32816.1, CCDS62418.1, CCDS62419.1	18q12	2007-08-02				ENSG00000134775			26178	protein-coding gene	gene with protein product		609691				11214970	Standard	NM_025135		Approved	FHOS2, KIAA1695, FLJ22297, FLJ22717	uc021uiv.1	Q2V2M9		ENST00000359247.4:c.580T>C	chr18.hg19:g.34156482T>C	ENSP00000352186:p.Trp194Arg	188.0	0.0		180.0	24.0	NM_025135	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Missense_Mutation	SNP	ENST00000359247.4	hg19		.	.	.	.	.	.	.	.	.	.	T	22.9	4.351935	0.82132	.	.	ENSG00000134775	ENST00000257209;ENST00000359247;ENST00000445677	T;T;T	0.25749	1.78;1.78;1.78	5.73	5.73	0.89815	GTPase-binding/formin homology 3 (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.51483	0.1677	M	0.74467	2.265	0.52501	D	0.99995	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.996;1.0;0.997	T	0.55360	-0.8153	10	0.87932	D	0	.	13.9605	0.64175	0.0:0.0:0.0:1.0	.	194;194;194	Q2V2M9;Q2V2M9-3;E5F5Q0	FHOD3_HUMAN;.;.	R	194	ENSP00000257209:W194R;ENSP00000352186:W194R;ENSP00000411430:W194R	ENSP00000257209:W194R	W	+	1	0	FHOD3	32410480	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.645000	0.83430	2.176000	0.68965	0.533000	0.62120	TGG	.	.		0.388	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114		C	34156482	T	C	34156482	3	2	288	1	0	0	0	0	1	0	0	0	5891	1696	59	2	602	2	FHOD3	18	34156482	Missense_Mutation	SNP	T	TCGA-G3-A5SM-01A-12D-A28X-10	889338	34156482	43920766	108	42322										
DOK6	220164	hgsc.bcm.edu	37	chr18	67425047	67425047	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	caaatcaatatctcttcctcGcagcgcgtactggcatcaca	6	14	3	0			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr18:67425047G>A	ENST00000382713.5	+	7	984	c.794G>A	c.(793-795)cGc>cAc	p.R265H		NM_152721.5	NP_689934.2	Q6PKX4	DOK6_HUMAN	docking protein 6	265										central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	20		Colorectal(73;0.083)|Esophageal squamous(42;0.131)				TCTCTTCCTCGCAGCGCGTAC	0.398																																					p.R265H		Atlas-SNP	.											DOK6,NS,carcinoma,0,1	DOK6	56	.	0			c.G794A						.						129	110	117					18																	67425047		2203	4300	6503	SO:0001583	missense	220164	exon7			TTCCTCGCAGCGC	AK057795	CCDS32841.1	18q22.2	2013-01-10	2005-01-18	2005-01-18		ENSG00000206052		"Pleckstrin homology (PH) domain containing"	28301	protein-coding gene	gene with protein product		611402	"docking protein 5-like"	DOK5L		15286081	Standard	NM_152721		Approved	MGC20785, HsT3226	uc002lkl.3	Q6PKX4		ENST00000382713.5:c.794G>A	chr18.hg19:g.67425047G>A	ENSP00000372160:p.Arg265His	85.0	1.0		97.0	42.0	NM_152721	A6NNG3|Q4V9S3|Q8WUZ8|Q96HI2|Q96LU2	Missense_Mutation	SNP	ENST00000382713.5	hg19	CCDS32841.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.877349	0.91664	.	.	ENSG00000206052	ENST00000382713	D	0.82803	-1.65	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	D	0.87661	0.6233	L	0.38175	1.15	0.58432	D	0.999998	D	0.89917	1.0	D	0.91635	0.999	D	0.87903	0.2692	10	0.54805	T	0.06	-17.7497	18.4033	0.90525	0.0:0.0:1.0:0.0	.	265	Q6PKX4	DOK6_HUMAN	H	265	ENSP00000372160:R265H	ENSP00000372160:R265H	R	+	2	0	DOK6	65576027	1.000000	0.71417	0.958000	0.39756	0.974000	0.67602	7.786000	0.85741	2.681000	0.91329	0.561000	0.74099	CGC	.	.		0.398	DOK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442969.1	NM_152721		A	67425047	G	A	67425047	3	1	288	1	0	0	0	0	1	0	0	0	4703	1087	38	1	820	1	DOK6	18	67425047	Missense_Mutation	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	33268565	67425047	10652201	109	42323										
SALL3	27164	hgsc.bcm.edu	37	chr18	76754132	76754132	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	caagtgcaagatctgcggccGcgccttcaccaccaagggca	11	15	2	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr18:76754132G>T	ENST00000537592.2	+	2	2141	c.2141G>T	c.(2140-2142)cGc>cTc	p.R714L	SALL3_ENST00000575389.2_Missense_Mutation_p.R714L|SALL3_ENST00000536229.3_Missense_Mutation_p.R581L	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	714					forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|negative regulation of smoothened signaling pathway (GO:0045879)|olfactory bulb interneuron development (GO:0021891)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(40)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)		ATCTGCGGCCGCGCCTTCACC	0.657																																					p.R714L		Atlas-SNP	.											.	SALL3	162	.	0			c.G2141T						.						39	36	37					18																	76754132		2203	4299	6502	SO:0001583	missense	27164	exon2			GCGGCCGCGCCTT	AJ007421	CCDS12013.1	18q23	2013-10-17	2013-10-17		ENSG00000256463	ENSG00000256463		"Zinc fingers, C2H2-type"	10527	protein-coding gene	gene with protein product		605079	"sal (Drosophila)-like 3", "sal-like 3 (Drosophila)"			10610715	Standard	NM_171999		Approved	ZNF796	uc002lmt.3	Q9BXA9	OTTHUMG00000132896	ENST00000537592.2:c.2141G>T	chr18.hg19:g.76754132G>T	ENSP00000441823:p.Arg714Leu	133.0	0.0		75.0	17.0	NM_171999	Q9UGH1	Missense_Mutation	SNP	ENST00000537592.2	hg19	CCDS12013.1	.	.	.	.	.	.	.	.	.	.	G	14.53	2.561897	0.45590	.	.	ENSG00000256463	ENST00000537592;ENST00000536229;ENST00000543056	T	0.19105	2.17	5.33	5.33	0.75918	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.56097	D	0.000022	T	0.42921	0.1224	L	0.48362	1.52	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.29336	-1.0015	10	0.87932	D	0	-49.9595	19.053	0.93053	0.0:0.0:1.0:0.0	.	446;714	F5GXY4;Q9BXA9	.;SALL3_HUMAN	L	714;714;446	ENSP00000441823:R714L	ENSP00000299466:R714L	R	+	2	0	SALL3	74855120	1.000000	0.71417	0.997000	0.53966	0.692000	0.40212	9.787000	0.99055	2.499000	0.84300	0.655000	0.94253	CGC	.	.		0.657	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256397.1	NM_171999		T	76754132	G	T	76754132	3	4	288	1	0	0	0	0	1	0	0	0	13827	1087	38	1	2147	1	SALL3	18	76754132	Missense_Mutation	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	9329085	76754132	1323116	110	42324										
PSG11	5680	hgsc.bcm.edu	37	chr19	43528932	43528932	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	tgtaggatcctgcgtcctccCgggtgacattctggatcagc	12	12	2	1	rs111739483	byFrequency	TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr19:43528932C>A	ENST00000401740.1	-	2	444	c.341G>T	c.(340-342)cGg>cTg	p.R114L	PSG11_ENST00000403486.1_Intron|PSG11_ENST00000320078.7_Missense_Mutation_p.R114L|PSG11_ENST00000306322.7_Intron			Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 11	114	Ig-like V-type.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	26		Prostate(69;0.00682)				TGCGTCCTCCCGGGTGACATT	0.443																																					p.R114L		Atlas-SNP	.											.	PSG11	57	.	0			c.G341T						.						157	153	154					19																	43528932		2198	4295	6493	SO:0001583	missense	5680	exon2			TCCTCCCGGGTGA	U25988	CCDS12614.2, CCDS12615.2	19q13.2	2013-01-29			ENSG00000243130	ENSG00000243130		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9516	protein-coding gene	gene with protein product	"pregnancy specific beta-1-glycoprotein 13"	176401		PSG13, PSG14		7794280	Standard	NM_001113410		Approved	MGC22484	uc002ovm.1	Q9UQ72	OTTHUMG00000151546	ENST00000401740.1:c.341G>T	chr19.hg19:g.43528932C>A	ENSP00000384995:p.Arg114Leu	292.0	0.0		364.0	44.0	NM_002785	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Missense_Mutation	SNP	ENST00000401740.1	hg19	CCDS12614.2	.	.	.	.	.	.	.	.	.	.	t	0.187	-1.056764	0.01965	.	.	ENSG00000243130	ENST00000320078;ENST00000401740	T;T	0.63096	-0.02;-0.02	0.929	-1.86	0.07760	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.33818	0.0876	N	0.11131	0.1	0.09310	N	1	B	0.10296	0.003	B	0.22152	0.038	T	0.13656	-1.0501	9	0.22109	T	0.4	.	1.4589	0.02391	0.3155:0.2605:0.0:0.424	.	114	Q9UQ72	PSG11_HUMAN	L	114	ENSP00000319140:R114L;ENSP00000384995:R114L	ENSP00000319140:R114L	R	-	2	0	PSG11	48220772	0.000000	0.05858	0.024000	0.17045	0.008000	0.06430	-2.383000	0.01063	-1.324000	0.02272	-1.109000	0.02080	CGG	.	C|0.977;T|0.023		0.443	PSG11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323079.1	NM_002785		A	43528932	C	A	43528932	3	1	288	1	0	0	0	0	1	0	0	0	12666	652	23	1	682	1	PSG11	19	43528932	Missense_Mutation	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10		43528932	15600051	111	42325										
KLK1	3816	hgsc.bcm.edu	37	chr19	51322605	51322605	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	cagcgggccccctgaatcacCctgggagcacaaggtgggag	15	13	1	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr19:51322605C>T	ENST00000301420.2	-	5	669	c.634G>A	c.(634-636)Ggt>Agt	p.G212S	CTD-2568A17.5_ENST00000326989.5_lincRNA|KLK1_ENST00000448701.2_Splice_Site_p.G110S	NM_002257.2	NP_002248.1	P06870	KLK1_HUMAN	kallikrein 1	212	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)			breast(1)|large_intestine(4)|lung(7)|urinary_tract(1)	13		all_neural(266;0.0199)		OV - Ovarian serous cystadenocarcinoma(262;0.00224)|GBM - Glioblastoma multiforme(134;0.00399)	Aprotinin(DB06692)	CCTGAATCACCCTGGGAGCAC	0.627																																					p.G212S		Atlas-SNP	.											.	KLK1	27	.	0			c.G634A						.						50	49	49					19																	51322605		2203	4300	6503	SO:0001630	splice_region_variant	3816	exon5			AATCACCCTGGGA	L10038	CCDS12804.1	19q13.3	2008-02-05	2006-10-27			ENSG00000167748	3.4.21.35	"Kallikreins"	6357	protein-coding gene	gene with protein product		147910	"kallikrein 1, renal/pancreas/salivary"			1684954, 16800724, 16800723	Standard	NM_002257		Approved	Klk6	uc002ptk.1	P06870		ENST00000301420.2:c.634-1G>A	chr19.hg19:g.51322605C>T		63.0	0.0		79.0	5.0	NM_002257	Q66US9|Q86U61|Q8TCV8|Q9BS53|Q9NQU4|Q9UD19|Q9UMJ1	Missense_Mutation	SNP	ENST00000301420.2	hg19	CCDS12804.1	.	.	.	.	.	.	.	.	.	.	c	22.8	4.336266	0.81801	.	.	ENSG00000167748	ENST00000301420;ENST00000448701	D;D	0.97924	-4.61;-4.61	3.66	3.66	0.41972	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	D	0.98623	0.9539	M	0.88512	2.96	0.43959	D	0.996635	D	0.89917	1.0	D	0.91635	0.999	D	0.98667	1.0686	9	0.87932	D	0	.	11.1408	0.48402	0.0:1.0:0.0:0.0	.	212	P06870	KLK1_HUMAN	S	212;110	ENSP00000301420:G212S;ENSP00000400994:G110S	ENSP00000301420:G212S	G	-	1	0	KLK1	56014417	1.000000	0.71417	0.999000	0.59377	0.567000	0.35839	4.291000	0.59025	2.334000	0.79466	0.561000	0.74099	GGT	.	.		0.627	KLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464135.2	NM_002257	Missense_Mutation	T	51322605	C	T	51322605	5	4	288	1	0	0	0	0	0	0	1	0	8406	637	22	3	158	3	KLK1	19	51322605	Splice_Site	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	7793673	51322605	7806378	112	42326										
ZNF528	84436	hgsc.bcm.edu	37	chr19	52919064	52919064	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	acgacatcaaaaaattcataCtggagagaaaccttacagtt	6	8	2	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr19:52919064C>A	ENST00000360465.3	+	7	1385	c.959C>A	c.(958-960)aCt>aAt	p.T320N	ZNF528_ENST00000391788.2_3'UTR	NM_032423.2	NP_115799.2	Q3MIS6	ZN528_HUMAN	zinc finger protein 528	320					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(6)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	39				GBM - Glioblastoma multiforme(134;0.00249)|OV - Ovarian serous cystadenocarcinoma(262;0.00817)		AAAATTCATACTGGAGAGAAA	0.378																																					p.T320N		Atlas-SNP	.											.	ZNF528	95	.	0			c.C959A						.						49	52	51					19																	52919064		2203	4299	6502	SO:0001583	missense	84436	exon7			TTCATACTGGAGA	AB058730	CCDS33091.1	19q13	2013-01-08			ENSG00000167555	ENSG00000167555		"Zinc fingers, C2H2-type", "-"	29384	protein-coding gene	gene with protein product		615580				11347906	Standard	NM_032423		Approved	KIAA1827	uc002pzh.3	Q3MIS6	OTTHUMG00000156494	ENST00000360465.3:c.959C>A	chr19.hg19:g.52919064C>A	ENSP00000353652:p.Thr320Asn	89.0	0.0		90.0	7.0	NM_032423	B3KPN4|Q86T88|Q96JK0	Missense_Mutation	SNP	ENST00000360465.3	hg19	CCDS33091.1	.	.	.	.	.	.	.	.	.	.	C	19.41	3.822683	0.71028	.	.	ENSG00000167555	ENST00000360465	T	0.26067	1.76	1.85	-1.06	0.10002	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.21631	0.0521	L	0.45137	1.4	0.23076	N	0.998334	P	0.43857	0.819	B	0.44133	0.442	T	0.14755	-1.0461	9	0.72032	D	0.01	.	4.6207	0.12449	0.211:0.6502:0.0:0.1388	.	320	Q3MIS6	ZN528_HUMAN	N	320	ENSP00000353652:T320N	ENSP00000353652:T320N	T	+	2	0	ZNF528	57610876	0.016000	0.18221	0.007000	0.13788	0.787000	0.44495	0.494000	0.22467	-0.357000	0.08175	0.491000	0.48974	ACT	.	.		0.378	ZNF528-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344336.1	NM_032423		A	52919064	C	A	52919064	3	1	288	1	0	0	0	0	1	0	0	0	17984	565	20	3	973	3	ZNF528	19	52919064	Missense_Mutation	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	1596459	52919064	6209919	113	42327										
ZNF835	90485	hgsc.bcm.edu	37	chr19	57175244	57175244	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	caggtgtagggccgctcgccCgtgtgcgtgcgctggtgcag	18	12	0	0			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr19:57175244C>T	ENST00000537055.2	-	2	1554	c.1323G>A	c.(1321-1323)acG>acA	p.T441T		NM_001005850.2	NP_001005850.2	Q9Y2P0	ZN835_HUMAN	zinc finger protein 835	441					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(22)|pancreas(3)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	47						GCCGCTCGCCCGTGTGCGTGC	0.667																																					p.T441T		Atlas-SNP	.											.	ZNF835	106	.	0			c.G1323A						.						44	49	47					19																	57175244		2201	4297	6498	SO:0001819	synonymous_variant	90485	exon2			CTCGCCCGTGTGC	AK023017	CCDS56105.1	19q13.43	2013-01-08			ENSG00000127903	ENSG00000127903		"Zinc fingers, C2H2-type"	34332	protein-coding gene	gene with protein product							Standard	NM_001005850		Approved	BC37295_3	uc010ygn.2	Q9Y2P0		ENST00000537055.2:c.1323G>A	chr19.hg19:g.57175244C>T		60.0	0.0		35.0	10.0	NM_001005850	B7Z5Y0|G3V1S0	Silent	SNP	ENST00000537055.2	hg19	CCDS56105.1																																																																																			.	.		0.667	ZNF835-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459800.1	NM_001005850		T	57175244	C	T	57175244	2	4	288	1	0	0	0	0	0	0	0	1	18201	639	23	1		1	ZNF835	19	57175244	Silent	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	4256180	57175244	1953739	114	42328										
PREX1	57580	hgsc.bcm.edu	37	chr20	47269978	47269978	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	catcgttcatcacgttgctgCcattgaccttcagaatgcac	7	13	3	2			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr20:47269978C>T	ENST00000371941.3	-	20	2289	c.2267G>A	c.(2266-2268)gGc>gAc	p.G756D	PREX1_ENST00000396220.1_Missense_Mutation_p.G756D	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	756					actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			CACGTTGCTGCCATTGACCTT	0.587																																					p.G756D		Atlas-SNP	.											.	PREX1	441	.	0			c.G2267A						.						126	114	118					20																	47269978		2203	4300	6503	SO:0001583	missense	57580	exon20			TTGCTGCCATTGA	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.2267G>A	chr20.hg19:g.47269978C>T	ENSP00000361009:p.Gly756Asp	67.0	0.0		63.0	18.0	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	hg19	CCDS13410.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.023153	0.75275	.	.	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.28895	1.59;1.59	5.08	5.08	0.68730	PDZ/DHR/GLGF (2);	0.000000	0.56097	U	0.000034	T	0.60818	0.2298	M	0.84511	2.7	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.992;0.994	T	0.68093	-0.5500	10	0.87932	D	0	.	16.7473	0.85476	0.0:1.0:0.0:0.0	.	756;53	Q8TCU6;Q8TCU6-2	PREX1_HUMAN;.	D	756	ENSP00000361009:G756D;ENSP00000379522:G756D	ENSP00000361009:G756D	G	-	2	0	PREX1	46703385	1.000000	0.71417	0.997000	0.53966	0.338000	0.28826	7.015000	0.76387	2.382000	0.81193	0.456000	0.33151	GGC	.	.		0.587	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		T	47269978	C	T	47269978	3	4	288	1	0	0	0	0	1	0	0	0	12488	739	26	3	2796	3	PREX1	20	47269978	Missense_Mutation	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10		47269978	15755542	115	42329										
KRTAP8-1	337879	hgsc.bcm.edu	37	chr21	32185533	32185533	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	gccccggggaagttgtcgcaGagcatggtgtcgggagtgga	19	8	0	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr21:32185533G>C	ENST00000329621.4	-	1	37	c.6C>G	c.(4-6)ctC>ctG	p.L2L		NM_175857.3	NP_787053.1	Q8IUC2	KRA81_HUMAN	keratin associated protein 8-1	2						intermediate filament (GO:0005882)				central_nervous_system(1)|large_intestine(1)|lung(4)	6						AGTTGTCGCAGAGCATGGTGT	0.552																																					p.L2L		Atlas-SNP	.											.	KRTAP8-1	20	.	0			c.C6G						.						75	65	68					21																	32185533		2203	4300	6503	SO:0001819	synonymous_variant	337879	exon1			GTCGCAGAGCATG	AJ457064	CCDS13607.1	21q22.1	2006-03-13			ENSG00000183640	ENSG00000183640		"Keratin associated proteins"	18935	protein-coding gene	gene with protein product						12359730	Standard	NM_175857		Approved	KAP8.1	uc002you.3	Q8IUC2	OTTHUMG00000057771	ENST00000329621.4:c.6C>G	chr21.hg19:g.32185533G>C		190.0	0.0		173.0	52.0	NM_175857	Q3LI57	Silent	SNP	ENST00000329621.4	hg19	CCDS13607.1																																																																																			.	.		0.552	KRTAP8-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128223.1			C	32185533	G	C	32185533	2	2	288	1	0	0	0	0	0	0	0	1	8581	929	33	4		4	KRTAP8-1	21	32185533	Silent	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10		32185533	15944362	116	42330										
BACE2	25825	hgsc.bcm.edu	37	chr21	42598204	42598204	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	acataaaagctacagattctCgttgacactggaagcagtaa	8	8	1	2			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr21:42598204C>A	ENST00000330333.6	+	2	787	c.324C>A	c.(322-324)ctC>ctA	p.L108L	BACE2_ENST00000347667.5_Silent_p.L108L|BACE2_ENST00000328735.6_Silent_p.L108L	NM_012105.3	NP_036237.2	Q9Y5Z0	BACE2_HUMAN	beta-site APP-cleaving enzyme 2	108					membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(2)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14		Prostate(19;1.57e-07)|all_epithelial(19;0.0251)				TACAGATTCTCGTTGACACTG	0.398																																					p.L108L		Atlas-SNP	.											.	BACE2	45	.	0			c.C324A						.						86	87	87					21																	42598204		2203	4300	6503	SO:0001819	synonymous_variant	25825	exon2			GATTCTCGTTGAC	AF117892	CCDS13668.1, CCDS13669.1, CCDS13670.1	21q22.3	2011-08-11			ENSG00000182240	ENSG00000182240			934	protein-coding gene	gene with protein product		605668		AEPLC		10965118, 10830953	Standard	NM_138991		Approved	CEAP1, DRAP, ALP56	uc002yyw.3	Q9Y5Z0	OTTHUMG00000086742	ENST00000330333.6:c.324C>A	chr21.hg19:g.42598204C>A		160.0	0.0		200.0	14.0	NM_138992	A8K7P1|Q5DIH8|Q8N2D4|Q9H2V8|Q9NZL1|Q9NZL2|Q9UJT6	Silent	SNP	ENST00000330333.6	hg19	CCDS13668.1																																																																																			.	.		0.398	BACE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195056.1			A	42598204	C	A	42598204	2	1	288	1	0	0	0	0	0	0	0	1	1282	871	31	1		1	BACE2	21	42598204	Silent	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	10412671	42598204	5531691	117	42331										
RRP1B	23076	hgsc.bcm.edu	37	chr21	45107710	45107710	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	agcccgagggcccacagggaAatgttggaatcagcagtgtt	14	9	1	0			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chr21:45107710A>T	ENST00000340648.4	+	13	1572	c.1455A>T	c.(1453-1455)gaA>gaT	p.E485D		NM_015056.2	NP_055871.1	Q14684	RRP1B_HUMAN	ribosomal RNA processing 1B	485					negative regulation of phosphatase activity (GO:0010923)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|euchromatin (GO:0000791)|heterochromatin (GO:0000792)|nucleolus (GO:0005730)|nucleus (GO:0005634)|preribosome, small subunit precursor (GO:0030688)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(3)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(1)	21				STAD - Stomach adenocarcinoma(101;0.178)		CCCACAGGGAAATGTTGGAAT	0.617																																					p.E485D		Atlas-SNP	.											.	RRP1B	51	.	0			c.A1455T						.						50	56	54					21																	45107710		2203	4297	6500	SO:0001583	missense	23076	exon13			CAGGGAAATGTTG	AK124620	CCDS33577.1	21q22.3	2014-06-13	2013-07-02	2007-03-26	ENSG00000160208	ENSG00000160208			23818	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 136"	610654	"KIAA0179", "ribosomal RNA processing 1 homolog B (S. cerevisiae)"	KIAA0179			Standard	NM_015056		Approved	Nnp1, RRP1, PPP1R136	uc002zdk.3	Q14684	OTTHUMG00000086872	ENST00000340648.4:c.1455A>T	chr21.hg19:g.45107710A>T	ENSP00000339145:p.Glu485Asp	120.0	0.0		131.0	25.0	NM_015056	Q8TBZ4	Missense_Mutation	SNP	ENST00000340648.4	hg19	CCDS33577.1	.	.	.	.	.	.	.	.	.	.	A	10.84	1.465065	0.26335	.	.	ENSG00000160208	ENST00000340648	T	0.01192	5.2	4.41	2.52	0.30459	.	0.412177	0.22580	N	0.058227	T	0.01092	0.0036	L	0.32530	0.975	0.09310	N	1	P	0.37466	0.596	B	0.32864	0.154	T	0.51252	-0.8729	10	0.87932	D	0	-0.0083	8.8103	0.34963	0.198:0.0:0.802:0.0	.	485	Q14684	RRP1B_HUMAN	D	485	ENSP00000339145:E485D	ENSP00000339145:E485D	E	+	3	2	RRP1B	43932138	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	0.587000	0.23909	0.945000	0.37605	-0.366000	0.07423	GAA	.	.		0.617	RRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195651.1	NM_015056		T	45107710	A	T	45107710	3	4	288	1	0	0	0	0	1	0	0	0	13703	11	1	4	1505	4	RRP1B	21	45107710	Missense_Mutation	SNP	A	TCGA-G3-A5SM-01A-12D-A28X-10	2509506	45107710	3022185	118	42332										
MAGED1	9500	hgsc.bcm.edu	37	chrX	51638377	51638377	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	caaaaggcccaaatggtgtcTatgatttctctcaggctcat	8	10	4	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chrX:51638377T>C	ENST00000375722.1	+	3	526	c.274T>C	c.(274-276)Tat>Cat	p.Y92H	MAGED1_ENST00000375695.2_Missense_Mutation_p.Y148H|MAGED1_ENST00000326587.7_Missense_Mutation_p.Y92H|MAGED1_ENST00000375772.3_Missense_Mutation_p.Y92H|MAGED1_ENST00000494718.1_3'UTR			Q9Y5V3	MAGD1_HUMAN	melanoma antigen family D, 1	92					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|circadian regulation of gene expression (GO:0032922)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of circadian rhythm (GO:0042752)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	transcription coactivator activity (GO:0003713)			breast(1)|endometrium(4)|large_intestine(10)|lung(13)|ovary(3)|upper_aerodigestive_tract(1)	32	Ovarian(276;0.236)					AAATGGTGTCTATGATTTCTC	0.507										Multiple Myeloma(10;0.10)																											p.Y148H		Atlas-SNP	.											.	MAGED1	84	.	0			c.T442C						.						47	38	42					X																	51638377		2203	4300	6503	SO:0001583	missense	9500	exon4			GGTGTCTATGATT	AF124440	CCDS14337.1, CCDS35279.1	Xp11.23	2008-08-01			ENSG00000179222	ENSG00000179222			6813	protein-coding gene	gene with protein product		300224				10409427	Standard	NM_006986		Approved	NRAGE, DLXIN-1	uc004dpn.3	Q9Y5V3	OTTHUMG00000021540	ENST00000375722.1:c.274T>C	chrX.hg19:g.51638377T>C	ENSP00000364874:p.Tyr92His	127.0	0.0		120.0	19.0	NM_001005333	Q5VSH6|Q8IZ84|Q8WY92|Q9H352|Q9HBT4|Q9UF36	Missense_Mutation	SNP	ENST00000375722.1	hg19	CCDS14337.1	.	.	.	.	.	.	.	.	.	.	T	15.19	2.759515	0.49468	.	.	ENSG00000179222	ENST00000375772;ENST00000375722;ENST00000326587;ENST00000375695;ENST00000430189	T;T;T;T	0.56275	0.47;0.47;0.47;0.47	3.43	3.43	0.39272	.	0.000000	0.33959	N	0.004388	T	0.52709	0.1751	L	0.29908	0.895	0.25094	N	0.990835	D;P;D	0.76494	0.999;0.77;0.998	D;P;D	0.78314	0.974;0.611;0.991	T	0.38866	-0.9641	10	0.15952	T	0.53	.	7.6184	0.28171	0.0:0.0:0.0:1.0	.	92;148;92	B4DQ04;Q9Y5V3-2;Q9Y5V3	.;.;MAGD1_HUMAN	H	92;92;92;148;92	ENSP00000364927:Y92H;ENSP00000364874:Y92H;ENSP00000325333:Y92H;ENSP00000364847:Y148H	ENSP00000325333:Y92H	Y	+	1	0	MAGED1	51655117	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.396000	0.34531	1.611000	0.50210	0.372000	0.22366	TAT	.	.		0.507	MAGED1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056593.1	NM_001005332		C	51638377	T	C	51638377	3	2	288	1	0	0	0	0	1	0	0	0	9192	1522	53	2	452	2	MAGED1	23	51638377	Missense_Mutation	SNP	T	TCGA-G3-A5SM-01A-12D-A28X-10		51638377	103632183	119	42333										
KDM5C	8242	hgsc.bcm.edu	37	chrX	53246991	53246991	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	tccttaccacaaggttggctCcagactggtacatttcatag	8	11	1	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chrX:53246991C>A	ENST00000375401.3	-	4	1041	c.509G>T	c.(508-510)gGa>gTa	p.G170V	KDM5C_ENST00000404049.3_Missense_Mutation_p.G170V|KDM5C_ENST00000375379.3_Missense_Mutation_p.G170V|KDM5C_ENST00000452825.3_Missense_Mutation_p.G103V|KDM5C_ENST00000375383.3_Missense_Mutation_p.G129V	NM_001282622.1|NM_004187.3	NP_001269551.1|NP_004178.2	P41229	KDM5C_HUMAN	lysine (K)-specific demethylase 5C	170					histone H3-K4 demethylation (GO:0034720)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-K4 specific) (GO:0032453)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(30)|large_intestine(9)|lung(17)|oesophagus(1)|ovary(6)|prostate(1)|salivary_gland(1)|skin(1)|upper_aerodigestive_tract(2)	82						AAGGTTGGCTCCAGACTGGTA	0.498			"N, F, S"		clear cell renal carcinoma																																p.G170V		Atlas-SNP	.		Rec	yes		X	Xp11.22-p11.21	8242	lysine (K)-specific demethylase 5C (JARID1C)		E	.	KDM5C	385	.	0			c.G509T						.						98	72	81					X																	53246991		2203	4300	6503	SO:0001583	missense	8242	exon4			TTGGCTCCAGACT	Z29650	CCDS14351.1, CCDS55417.1, CCDS65269.1	Xp11.22-p11.21	2014-01-31	2009-04-06	2009-04-06	ENSG00000126012	ENSG00000126012		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	11114	protein-coding gene	gene with protein product		314690	"Jumonji, AT rich interactive domain 1C (RBP2-like)", "Smcy homolog, X-linked (mouse)", "jumonji, AT rich interactive domain 1C", "mental retardation, X-linked 13"	SMCX, JARID1C, MRX13		7951230, 8162017, 19826449	Standard	NM_004187		Approved	DXS1272E, XE169	uc004drz.3	P41229	OTTHUMG00000021606	ENST00000375401.3:c.509G>T	chrX.hg19:g.53246991C>A	ENSP00000364550:p.Gly170Val	241.0	0.0		227.0	43.0	NM_004187	B0QZ44|B4E3I2|F5H3T1|Q5JUX3|Q5JUX4|Q5JUX5|Q7Z5S5	Missense_Mutation	SNP	ENST00000375401.3	hg19	CCDS14351.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.203222	0.79127	.	.	ENSG00000126012	ENST00000452825;ENST00000375401;ENST00000404049;ENST00000375379;ENST00000375383	T;T;T;T;T	0.64085	-0.08;-0.08;-0.08;-0.08;-0.08	5.21	5.21	0.72293	ARID/BRIGHT DNA-binding domain (3);	0.000000	0.85682	D	0.000000	T	0.80649	0.4663	M	0.84846	2.72	0.80722	D	1	D;D;D	0.67145	0.982;0.996;0.996	D;D;D	0.70016	0.927;0.923;0.967	D	0.84188	0.0443	10	0.87932	D	0	-15.3935	15.4283	0.75072	0.0:1.0:0.0:0.0	.	103;170;170	F5H3T1;B0QZ44;P41229	.;.;KDM5C_HUMAN	V	103;170;170;170;129	ENSP00000445176:G103V;ENSP00000364550:G170V;ENSP00000385394:G170V;ENSP00000364528:G170V;ENSP00000364532:G129V	ENSP00000364528:G170V	G	-	2	0	KDM5C	53263716	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.657000	0.83745	2.323000	0.78572	0.529000	0.55759	GGA	.	.		0.498	KDM5C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056737.2	NM_004187		A	53246991	C	A	53246991	3	1	288	1	0	0	0	0	1	0	0	0	8144	855	30	3	4363	3	KDM5C	23	53246991	Missense_Mutation	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	1608614	53246991	102023569	120	42334										
IQSEC2	23096	hgsc.bcm.edu	37	chrX	53277365	53277365	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	ggatatgggactggaacttcCggagcgcatcatccagatcc	12	11	1	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chrX:53277365C>T	ENST00000375368.5	-	6	2683	c.2483G>A	c.(2482-2484)cGg>cAg	p.R828Q	IQSEC2_ENST00000396435.3_Missense_Mutation_p.R838Q|IQSEC2_ENST00000375365.2_Missense_Mutation_p.R633Q			Q5JU85	IQEC2_HUMAN	IQ motif and Sec7 domain 2	828	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(10)|ovary(4)|skin(1)	29						CTGGAACTTCCGGAGCGCATC	0.562																																					p.R838Q		Atlas-SNP	.											.	IQSEC2	195	.	0			c.G2513A						.						92	55	67					X																	53277365		2203	4300	6503	SO:0001583	missense	23096	exon7			AACTTCCGGAGCG	AB011094	CCDS35298.1, CCDS48130.1	Xp11.23	2014-01-31			ENSG00000124313	ENSG00000124313			29059	protein-coding gene	gene with protein product		300522	"mental retardation, X-linked 1 (non-dysmorphic)"	MRX1		9628581, 20473311	Standard	NM_001243197		Approved	KIAA0522	uc004dsd.3	Q5JU85	OTTHUMG00000021608	ENST00000375368.5:c.2483G>A	chrX.hg19:g.53277365C>T	ENSP00000364517:p.Arg828Gln	150.0	0.0		158.0	11.0	NM_001111125	B3KT97|C7SDG1|O60275|Q5JUX1	Missense_Mutation	SNP	ENST00000375368.5	hg19		.	.	.	.	.	.	.	.	.	.	C	31	5.080058	0.94050	.	.	ENSG00000124313	ENST00000396435;ENST00000375368;ENST00000375365	T;T;T	0.71461	-0.57;-0.57;-0.57	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	D	0.90188	0.6933	H	0.97265	3.97	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.99	D	0.93523	0.6863	10	0.87932	D	0	.	17.5783	0.87957	0.0:1.0:0.0:0.0	.	838;633	Q5JU85-2;Q5JU85-3	.;.	Q	838;828;633	ENSP00000379712:R838Q;ENSP00000364517:R828Q;ENSP00000364514:R633Q	ENSP00000364514:R633Q	R	-	2	0	IQSEC2	53294090	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.818000	0.86416	2.422000	0.82143	0.600000	0.82982	CGG	.	.		0.562	IQSEC2-201	KNOWN	basic	protein_coding	protein_coding		XM_291345		T	53277365	C	T	53277365	3	4	288	1	0	0	0	0	1	0	0	0	7827	652	23	1	1989	1	IQSEC2	23	53277365	Missense_Mutation	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	30374	53277365	101993195	121	42335										
GLRA4	441509	hgsc.bcm.edu	37	chrX	102973919	102973919	+	Intron	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	ggtaaatggtgagcaggaggGcacattgggatgaatgggaa	18	3	0	2			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chrX:102973919G>T	ENST00000372617.4	-	7	1354				GLRA4_ENST00000469567.1_5'Flank	NM_001024452.2	NP_001019623.2	Q5JXX5	GLRA4_HUMAN	glycine receptor, alpha 4							cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|glycine binding (GO:0016594)|transmitter-gated ion channel activity (GO:0022824)			cervix(1)|endometrium(2)|large_intestine(2)|lung(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	21						GAGCAGGAGGGCACATTGGGA	0.502																																					p.C333X		Atlas-SNP	.											.	GLRA4	86	.	0			c.C999A						.																																			SO:0001627	intron_variant	441509	exon7			AGGAGGGCACATT	Z93848	CCDS43980.2	Xq22.2	2012-01-16			ENSG00000188828	ENSG00000188828		"Ligand-gated ion channels / Glycine receptors"	31715	protein-coding gene	gene with protein product							Standard	NM_001024452		Approved		uc011mse.2	Q5JXX5	OTTHUMG00000022110	ENST00000372617.4:c.933+65C>A	chrX.hg19:g.102973919G>T		189.0	0.0		180.0	67.0	NM_001172285		Nonsense_Mutation	SNP	ENST00000372617.4	hg19	CCDS43980.2																																																																																			.	.		0.502	GLRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057742.2	NM_001024452		T	102973919	G	T	102973919	1	4	288	0	1	0	0	0	0	0	0	0	6465	1195	42	3		3	GLRA4	23	102973919	Intron	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	49696554	102973919	52296641	122	42336										
IRS4	8471	hgsc.bcm.edu	37	chrX	107977917	107977917	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	cacctgaaccgtgcccacctGcggtgccctggccatctcta	9	18	1	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chrX:107977917G>A	ENST00000372129.2	-	1	1734	c.1658C>T	c.(1657-1659)gCa>gTa	p.A553V	RP6-24A23.3_ENST00000436013.1_RNA|RP6-24A23.3_ENST00000608811.1_RNA|RP6-24A23.6_ENST00000563887.1_5'Flank	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	553					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						GTGCCCACCTGCGGTGCCCTG	0.642																																					p.A553V		Atlas-SNP	.											.	IRS4	253	.	0			c.C1658T						.						115	117	117					X																	107977917		2203	4300	6503	SO:0001583	missense	8471	exon1			CCACCTGCGGTGC	AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.1658C>T	chrX.hg19:g.107977917G>A	ENSP00000361202:p.Ala553Val	56.0	0.0		41.0	8.0	NM_003604		Missense_Mutation	SNP	ENST00000372129.2	hg19	CCDS14544.1	.	.	.	.	.	.	.	.	.	.	G	8.057	0.767257	0.15983	.	.	ENSG00000133124	ENST00000372129	T	0.35421	1.31	4.76	4.76	0.60689	.	0.526496	0.20003	N	0.101297	T	0.31796	0.0808	L	0.51422	1.61	0.23831	N	0.996729	B	0.06786	0.001	B	0.09377	0.004	T	0.10405	-1.0631	10	0.25106	T	0.35	0.3699	12.071	0.53616	0.0:0.0:1.0:0.0	.	553	O14654	IRS4_HUMAN	V	553	ENSP00000361202:A553V	ENSP00000361202:A553V	A	-	2	0	IRS4	107864573	0.003000	0.15002	0.948000	0.38648	0.130000	0.20726	1.176000	0.31957	2.335000	0.79485	0.600000	0.82982	GCA	.	.		0.642	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604		A	107977917	G	A	107977917	3	1	288	1	0	0	0	0	1	0	0	0	7851	1319	46	3	2119	3	IRS4	23	107977917	Missense_Mutation	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	5003998	107977917	47292643	123	42337										
STAG2	10735	hgsc.bcm.edu	37	chrX	123195634	123195634	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	tttttagcactaacagatagGcaagagagtgctctgattga	10	6	1	4			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chrX:123195634G>A	ENST00000371160.1	+	17	1838	c.1548G>A	c.(1546-1548)agG>agA	p.R516R	STAG2_ENST00000218089.9_Silent_p.R516R|STAG2_ENST00000371157.3_Silent_p.R516R|STAG2_ENST00000371144.3_Silent_p.R516R|STAG2_ENST00000371145.3_Silent_p.R516R|STAG2_ENST00000354548.5_Silent_p.R447R|STAG2_ENST00000469481.1_Intron	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	516					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						TAACAGATAGGCAAGAGAGTG	0.363																																					p.R516R		Atlas-SNP	.											.	STAG2	309	.	0			c.G1548A						.						57	53	54					X																	123195634		2203	4300	6503	SO:0001819	synonymous_variant	10735	exon17			AGATAGGCAAGAG	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.1548G>A	chrX.hg19:g.123195634G>A		152.0	0.0		138.0	22.0	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Silent	SNP	ENST00000371160.1	hg19	CCDS14607.1																																																																																			.	.		0.363	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		A	123195634	G	A	123195634	2	1	288	1	0	0	0	0	0	0	0	1	15258	1194	42	3		3	STAG2	23	123195634	Silent	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	15217717	123195634	32074926	124	42338										
PLXNB3	5365	hgsc.bcm.edu	37	chrX	153035892	153035892	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	tgccgtccaggccttggaggCggctgccccgtgagtccctg	15	15	0	1			TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chrX:153035892C>A	ENST00000361971.5	+	9	2000	c.1886C>A	c.(1885-1887)gCg>gAg	p.A629E	PLXNB3_ENST00000538966.1_Missense_Mutation_p.A652E|PLXNB3_ENST00000538776.1_Missense_Mutation_p.A282E|PLXNB3_ENST00000538543.1_Missense_Mutation_p.A179E|PLXNB3_ENST00000538282.1_Missense_Mutation_p.A239E	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	629	PSI 2.				axon guidance (GO:0007411)|cell chemotaxis (GO:0060326)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|negative regulation of GTPase activity (GO:0034260)|negative regulation of lamellipodium assembly (GO:0010593)|positive chemotaxis (GO:0050918)|positive regulation of endothelial cell proliferation (GO:0001938)|semaphorin-plexin signaling pathway (GO:0071526)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)			central_nervous_system(1)|endometrium(7)|large_intestine(2)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					GCCTTGGAGGCGGCTGCCCCG	0.657																																					p.A652E		Atlas-SNP	.											.	PLXNB3	208	.	0			c.C1955A						.						56	41	46					X																	153035892		2192	4296	6488	SO:0001583	missense	5365	exon10			TGGAGGCGGCTGC	AF149019	CCDS14729.1, CCDS55536.1	Xq28	2008-02-05			ENSG00000198753	ENSG00000198753		"Plexins"	9105	protein-coding gene	gene with protein product		300214		PLXN6		10520995	Standard	NM_005393		Approved	PLEXR, PLEXB3	uc010nuk.2	Q9ULL4	OTTHUMG00000024217	ENST00000361971.5:c.1886C>A	chrX.hg19:g.153035892C>A	ENSP00000355378:p.Ala629Glu	181.0	0.0		165.0	67.0	NM_001163257	B7Z3E6|F5H773|Q9HDA4	Missense_Mutation	SNP	ENST00000361971.5	hg19	CCDS14729.1	.	.	.	.	.	.	.	.	.	.	c	0.003	-2.406058	0.00193	.	.	ENSG00000198753	ENST00000538966;ENST00000361971;ENST00000538776;ENST00000538543;ENST00000538282	T;T;T;T;T	0.65732	5.38;5.34;4.75;2.03;-0.17	5.1	-5.79	0.02354	.	1.048160	0.07454	N	0.899545	T	0.39911	0.1096	N	0.19112	0.55	0.09310	N	1	B;B;B;B;B	0.30914	0.045;0.3;0.144;0.077;0.007	B;B;B;B;B	0.36534	0.024;0.039;0.227;0.109;0.031	T	0.36720	-0.9736	10	0.02654	T	1	.	8.4457	0.32841	0.0:0.4929:0.1237:0.3834	.	282;311;179;652;629	B7Z3H9;B7Z9A5;F5GZZ4;F5H773;Q9ULL4	.;.;.;.;PLXB3_HUMAN	E	652;629;282;179;239	ENSP00000442736:A652E;ENSP00000355378:A629E;ENSP00000445569:A282E;ENSP00000444086:A179E;ENSP00000441919:A239E	ENSP00000355378:A629E	A	+	2	0	PLXNB3	152689086	0.000000	0.05858	0.005000	0.12908	0.015000	0.08874	-3.653000	0.00402	-1.807000	0.01236	-1.326000	0.01283	GCG	.	.		0.657	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1			A	153035892	C	A	153035892	3	1	288	1	0	0	0	0	1	0	0	0	12134	768	27	1	2034	1	PLXNB3	23	153035892	Missense_Mutation	SNP	C	TCGA-G3-A5SM-01A-12D-A28X-10	29840258	153035892	2234668	125	42339										
PLXNB3	5365	hgsc.bcm.edu	37	chrX	153042728	153042728	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0655737704918033	8	1	1.09807327001357	2.26477611940299	0.838805970149254	0.666846143491722	1	0	ggcacctggtgaaagccaccGaggagccagaaggggccaag	16	11	0	2	rs372327696		TCGA-G3-A5SM-01A-12D-A28X-10	TCGA-G3-A5SM-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e2dae934-c940-4712-976d-68a9cce2b2c2	e6086fb4-e933-4934-8437-5c592d7bf553	g.chrX:153042728G>A	ENST00000361971.5	+	30	5107	c.4993G>A	c.(4993-4995)Gag>Aag	p.E1665K	PLXNB3_ENST00000538966.1_Missense_Mutation_p.E1688K|PLXNB3_ENST00000538776.1_Missense_Mutation_p.E1318K|SRPK3_ENST00000489426.1_5'UTR|PLXNB3_ENST00000485980.1_3'UTR	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	1665					axon guidance (GO:0007411)|cell chemotaxis (GO:0060326)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|negative regulation of GTPase activity (GO:0034260)|negative regulation of lamellipodium assembly (GO:0010593)|positive chemotaxis (GO:0050918)|positive regulation of endothelial cell proliferation (GO:0001938)|semaphorin-plexin signaling pathway (GO:0071526)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)			central_nervous_system(1)|endometrium(7)|large_intestine(2)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					GAAAGCCACCGAGGAGCCAGA	0.657													G|||	1	0.000264901	8e-04	0	3775	,	,		12328	0		0	False		,,,				2504	0				p.E1688K		Atlas-SNP	.											.	PLXNB3	208	.	0			c.G5062A						.	G	LYS/GLU,LYS/GLU	0,3816		0,0,1628,560	29	21	24		5062,4993	5	0.5	X		24	1,6714		0,1,2426,1861	no	missense,missense	PLXNB3	NM_001163257.1,NM_005393.2	56,56	0,1,4054,2421	AA,AG,GG,G		0.0149,0.0,0.0095	probably-damaging,probably-damaging	1688/1933,1665/1910	153042728	1,10530	2188	4288	6476	SO:0001583	missense	5365	exon31			GCCACCGAGGAGC	AF149019	CCDS14729.1, CCDS55536.1	Xq28	2008-02-05			ENSG00000198753	ENSG00000198753		"Plexins"	9105	protein-coding gene	gene with protein product		300214		PLXN6		10520995	Standard	NM_005393		Approved	PLEXR, PLEXB3	uc010nuk.2	Q9ULL4	OTTHUMG00000024217	ENST00000361971.5:c.4993G>A	chrX.hg19:g.153042728G>A	ENSP00000355378:p.Glu1665Lys	138.0	0.0		121.0	45.0	NM_001163257	B7Z3E6|F5H773|Q9HDA4	Missense_Mutation	SNP	ENST00000361971.5	hg19	CCDS14729.1	.	.	.	.	.	.	.	.	.	.	G	29.5	5.014283	0.93404	0.0	1.49E-4	ENSG00000198753	ENST00000538966;ENST00000361971;ENST00000538776	T;T;T	0.12361	2.69;2.69;2.69	4.99	4.99	0.66335	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.43100	0.1232	M	0.84846	2.72	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.997;0.995;0.998	T	0.50092	-0.8868	10	0.72032	D	0.01	.	16.3453	0.83126	0.0:0.0:1.0:0.0	.	1318;1688;1665	B7Z3H9;F5H773;Q9ULL4	.;.;PLXB3_HUMAN	K	1688;1665;1318	ENSP00000442736:E1688K;ENSP00000355378:E1665K;ENSP00000445569:E1318K	ENSP00000355378:E1665K	E	+	1	0	PLXNB3	152695922	1.000000	0.71417	0.539000	0.28077	0.567000	0.35839	9.785000	0.99042	2.200000	0.70718	0.529000	0.55759	GAG	.	.		0.657	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1			A	153042728	G	A	153042728	3	1	288	1	0	0	0	0	1	0	0	0	12134	1059	37	1	5225	1	PLXNB3	23	153042728	Missense_Mutation	SNP	G	TCGA-G3-A5SM-01A-12D-A28X-10	6836	153042728	2227832	126	42340										
LCK	3932	hgsc.bcm.edu	37	chr1	32740006	32740006	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	tgtgtgagaactgccattatCccatagtcccactggatggc	10	11	0	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr1:32740006C>G	ENST00000336890.5	+	2	214	c.76C>G	c.(76-78)Ccc>Gcc	p.P26A	LCK_ENST00000333070.4_Missense_Mutation_p.P26A|LCK_ENST00000373564.3_Missense_Mutation_p.P26A	NM_005356.3	NP_005347.3	P06239	LCK_HUMAN	LCK proto-oncogene, Src family tyrosine kinase	26	Interactions with CD4 and CD8. {ECO:0000250}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|aging (GO:0007568)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular zinc ion homeostasis (GO:0006882)|dephosphorylation (GO:0016311)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hemopoiesis (GO:0030097)|innate immune response (GO:0045087)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of gene expression (GO:0010628)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|positive regulation of uterine smooth muscle contraction (GO:0070474)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of defense response to virus by virus (GO:0050690)|regulation of lymphocyte activation (GO:0051249)|release of sequestered calcium ion into cytosol (GO:0051209)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to zinc ion (GO:0010043)|T cell costimulation (GO:0031295)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|pericentriolar material (GO:0000242)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|ATP binding (GO:0005524)|ATPase binding (GO:0051117)|CD4 receptor binding (GO:0042609)|CD8 receptor binding (GO:0042610)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine kinase activity (GO:0004713)|SH2 domain binding (GO:0042169)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	37		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.212)			Dasatinib(DB01254)|Ponatinib(DB08901)	CTGCCATTATCCCATAGTCCC	0.552			T	TRB@	T-ALL																																p.P26A		Atlas-SNP	.		Dom	yes		1	1p35-p34.3	3932	lymphocyte-specific protein tyrosine kinase		L	.	LCK	124	.	0			c.C76G						.						109	94	99					1																	32740006		2203	4300	6503	SO:0001583	missense	3932	exon2			CATTATCCCATAG	M36881	CCDS359.1	1p34.3	2014-09-17	2014-06-25		ENSG00000182866	ENSG00000182866	2.7.10.1	"SH2 domain containing"	6524	protein-coding gene	gene with protein product		153390	"lymphocyte-specific protein tyrosine kinase"			2787474	Standard	XM_005270862		Approved		uc001buy.3	P06239	OTTHUMG00000007463	ENST00000336890.5:c.76C>G	chr1.hg19:g.32740006C>G	ENSP00000337825:p.Pro26Ala	79.0	0.0		95.0	46.0	NM_005356	D3DPP8|P07100|Q12850|Q13152|Q5TDH8|Q5TDH9|Q7RTZ3|Q96DW4|Q9NYT8	Missense_Mutation	SNP	ENST00000336890.5	hg19	CCDS359.1	.	.	.	.	.	.	.	.	.	.	c	28.0	4.878279	0.91664	.	.	ENSG00000182866	ENST00000336890;ENST00000482949;ENST00000495610;ENST00000461712;ENST00000373562;ENST00000477031;ENST00000373557;ENST00000333070;ENST00000436824;ENST00000373564	T;T;T;T;T;T;T;T;T	0.54479	0.57;0.57;0.57;0.57;0.57;0.57;0.57;0.57;0.57	5.03	5.03	0.67393	.	0.000000	0.64402	D	0.000009	T	0.71213	0.3313	M	0.68593	2.085	0.49687	D	0.999815	D;D;D;D	0.89917	0.966;1.0;0.988;0.987	P;D;P;P	0.83275	0.577;0.996;0.876;0.808	T	0.72557	-0.4257	10	0.52906	T	0.07	.	17.3642	0.87359	0.0:1.0:0.0:0.0	.	70;26;26;26	E7EN21;Q573B4;P06239-3;P06239	.;.;.;LCK_HUMAN	A	26;26;26;26;26;70;70;26;70;26	ENSP00000337825:P26A;ENSP00000431517:P26A;ENSP00000435605:P26A;ENSP00000434525:P26A;ENSP00000362663:P26A;ENSP00000436554:P70A;ENSP00000362658:P70A;ENSP00000328213:P26A;ENSP00000362665:P26A	ENSP00000328213:P26A	P	+	1	0	LCK	32512593	1.000000	0.71417	0.998000	0.56505	0.972000	0.66771	5.815000	0.69215	2.519000	0.84933	0.487000	0.48397	CCC	.	.		0.552	LCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019616.4	NM_005356		G	32740006	C	G	32740006	3	3	289	1	0	0	0	0	1	0	0	0	8685	855	30	4	78	4	LCK	1	32740006	Missense_Mutation	SNP	C	TCGA-G3-A6UC-01A-21D-A33K-10		32740006	216510615	1	42341										
GTF2B	2959	hgsc.bcm.edu	37	chr1	89325566	89325566	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	aacaaagctaaaaacttaccTttaaatgtcctaggaacccc	4	11	0	0			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr1:89325566T>C	ENST00000370500.5	-	5	652	c.534A>G	c.(532-534)aaA>aaG	p.K178K	GTF2B_ENST00000494819.1_5'UTR	NM_001514.5	NP_001505.1	Q00403	TF2B_HUMAN	general transcription factor IIB	178					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	nucleoplasm (GO:0005654)	core promoter binding (GO:0001047)|thyroid hormone receptor binding (GO:0046966)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	10		Lung NSC(277;0.123)		all cancers(265;0.0131)|Epithelial(280;0.0255)		AAAACTTACCTTTAAATGTCC	0.413																																					p.K178K		Atlas-SNP	.											.	GTF2B	32	.	0			c.A534G						.						116	122	120					1																	89325566		2203	4300	6503	SO:0001630	splice_region_variant	2959	exon5			CTTACCTTTAAAT	M76766	CCDS715.1	1p22-p21	2010-03-23			ENSG00000137947	ENSG00000137947		"General transcription factors"	4648	protein-coding gene	gene with protein product		189963				1876184, 8162052	Standard	NM_001514		Approved	TFIIB	uc001dmo.4	Q00403	OTTHUMG00000010611	ENST00000370500.5:c.535+1A>G	chr1.hg19:g.89325566T>C		50.0	0.0		68.0	28.0	NM_001514	A8K1A7|Q5JS30	Silent	SNP	ENST00000370500.5	hg19	CCDS715.1																																																																																			.	.		0.413	GTF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029279.1	NM_001514	Silent	C	89325566	T	C	89325566	5	2	289	1	0	0	0	0	0	0	1	0	6864	1623	56	2	428	2	GTF2B	1	89325566	Splice_Site	SNP	T	TCGA-G3-A6UC-01A-21D-A33K-10	56585560	89325566	159925055	2	42342										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103548452	103548452	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	ttagaattctttctgtttgtGcaaaatcccgttgtttttga	7	6	2	2			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr1:103548452G>C	ENST00000370096.3	-	2	495	c.183C>G	c.(181-183)tgC>tgG	p.C61W	COL11A1_ENST00000512756.1_Missense_Mutation_p.C61W|COL11A1_ENST00000358392.2_Missense_Mutation_p.C61W|COL11A1_ENST00000353414.4_Missense_Mutation_p.C61W	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	61					cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)	p.C61*(2)		NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		TTCTGTTTGTGCAAAATCCCG	0.363																																					p.C61W		Atlas-SNP	.											COL11A1_ENST00000370096,NS,carcinoma,0,2	COL11A1	972	.	2	Substitution - Nonsense(2)	lung(2)	c.C183G						.						128	130	129					1																	103548452		2203	4300	6503	SO:0001583	missense	1301	exon2			GTTTGTGCAAAAT	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.183C>G	chr1.hg19:g.103548452G>C	ENSP00000359114:p.Cys61Trp	47.0	0.0		62.0	25.0	NM_001190709	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	hg19	CCDS778.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.755733	0.49362	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000512756;ENST00000427239	T;T;T;T;T	0.02301	4.35;4.35;4.35;4.35;4.35	5.7	5.7	0.88788	Concanavalin A-like lectin/glucanase (1);Laminin G, thrombospondin-type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.12646	0.0307	M	0.88704	2.975	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;1.0;0.999	D;D;D;D	0.85130	0.993;0.997;0.997;0.993	T	0.01276	-1.1398	10	0.87932	D	0	.	19.8365	0.96659	0.0:0.0:1.0:0.0	.	61;61;61;61	E9PCU0;P12107-3;P12107-2;P12107	.;.;.;COBA1_HUMAN	W	61	ENSP00000359114:C61W;ENSP00000351163:C61W;ENSP00000302551:C61W;ENSP00000426533:C61W;ENSP00000408640:C61W	ENSP00000302551:C61W	C	-	3	2	COL11A1	103321040	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	3.383000	0.52471	2.694000	0.91930	0.467000	0.42956	TGC	.	.		0.363	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		C	103548452	G	C	103548452	3	2	289	1	0	0	0	0	1	0	0	0	3669	1311	46	4	5658	4	COL11A1	1	103548452	Missense_Mutation	SNP	G	TCGA-G3-A6UC-01A-21D-A33K-10	14222886	103548452	145702169	3	42343										
PHGDH	26227	hgsc.bcm.edu	37	chr1	120284487	120284487	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	gcggatgtgaacttggtgaaCgctaagctgctggtgaaaga	15	6	0	4			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr1:120284487C>A	ENST00000369409.4	+	10	1312	c.1176C>A	c.(1174-1176)aaC>aaA	p.N392K	PHGDH_ENST00000482968.1_3'UTR|PHGDH_ENST00000369407.3_Missense_Mutation_p.N358K	NM_006623.3	NP_006614.2	O43175	SERA_HUMAN	phosphoglycerate dehydrogenase	392					brain development (GO:0007420)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|G1 to G0 transition (GO:0070314)|gamma-aminobutyric acid metabolic process (GO:0009448)|glial cell development (GO:0021782)|glutamine metabolic process (GO:0006541)|glycine metabolic process (GO:0006544)|L-serine biosynthetic process (GO:0006564)|neural tube development (GO:0021915)|neuron projection development (GO:0031175)|regulation of gene expression (GO:0010468)|small molecule metabolic process (GO:0044281)|spinal cord development (GO:0021510)|taurine metabolic process (GO:0019530)|threonine metabolic process (GO:0006566)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	electron carrier activity (GO:0009055)|NAD binding (GO:0051287)|phosphoglycerate dehydrogenase activity (GO:0004617)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)	18	all_cancers(5;1.18e-09)|all_epithelial(5;2.16e-10)|Melanoma(3;1.93e-05)|all_neural(166;0.219)	all_lung(203;3.66e-05)|Lung NSC(69;0.000202)|all_epithelial(167;0.0347)		Lung(183;0.0111)|LUSC - Lung squamous cell carcinoma(189;0.0593)		ACTTGGTGAACGCTAAGCTGC	0.582																																					p.N392K		Atlas-SNP	.											.	PHGDH	51	.	0			c.C1176A						.						87	74	79					1																	120284487		2203	4300	6503	SO:0001583	missense	26227	exon10			GGTGAACGCTAAG	BC011262	CCDS904.1	1p12	2008-02-05			ENSG00000092621	ENSG00000092621	1.1.1.95		8923	protein-coding gene	gene with protein product		606879					Standard	NM_006623		Approved	SERA, PGDH, PDG	uc001ehz.3	O43175	OTTHUMG00000012100	ENST00000369409.4:c.1176C>A	chr1.hg19:g.120284487C>A	ENSP00000358417:p.Asn392Lys	50.0	0.0		43.0	15.0	NM_006623	B2RD08|Q5SZU3|Q9BQ01	Missense_Mutation	SNP	ENST00000369409.4	hg19	CCDS904.1	.	.	.	.	.	.	.	.	.	.	.	14.32	2.501598	0.44455	.	.	ENSG00000092621	ENST00000369409;ENST00000537497;ENST00000369407	D;D	0.90504	-2.68;-2.68	5.54	-3.06	0.05379	.	0.085714	0.85682	D	0.000000	D	0.90253	0.6952	M	0.70275	2.135	0.38969	D	0.958714	D;D;D;D	0.89917	0.999;0.999;1.0;1.0	D;D;D;D	0.81914	0.973;0.973;0.995;0.985	D	0.88158	0.2855	10	0.87932	D	0	-24.6842	7.549	0.27783	0.0:0.345:0.1181:0.5368	.	358;358;265;392	B3KSC3;Q5SZU1;F5H634;O43175	.;.;.;SERA_HUMAN	K	392;265;358	ENSP00000358417:N392K;ENSP00000358415:N358K	ENSP00000358415:N358K	N	+	3	2	PHGDH	120086010	0.842000	0.29525	0.887000	0.34795	0.011000	0.07611	-0.254000	0.08781	-0.444000	0.07170	-0.140000	0.14226	AAC	.	.		0.582	PHGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033464.1	NM_006623		A	120284487	C	A	120284487	3	1	289	1	0	0	0	0	1	0	0	0	11850	535	19	1	1214	1	PHGDH	1	120284487	Missense_Mutation	SNP	C	TCGA-G3-A6UC-01A-21D-A33K-10	16736035	120284487	128966134	4	42344										
PDZK1	5174	hgsc.bcm.edu	37	chr1	145748546	145748546	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	ccggctctgctatctcgtgaAggaaggaggcagctatggct	14	10	2	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr1:145748546A>G	ENST00000344770.2	+	3	492	c.419A>G	c.(418-420)aAg>aGg	p.K140R	PDZK1_ENST00000451928.2_Missense_Mutation_p.K140R|PDZK1_ENST00000417171.1_Missense_Mutation_p.K140R	NM_002614.4	NP_002605.2	Q5T2W1	NHRF3_HUMAN	PDZ domain containing 1	140	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				carnitine transport (GO:0015879)|cell proliferation (GO:0008283)|drug transport (GO:0015893)|establishment of protein localization to plasma membrane (GO:0090002)|positive regulation of ion transmembrane transport (GO:0034767)|positive regulation of protein targeting to membrane (GO:0090314)|regulation of anion transport (GO:0044070)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|transporter activity (GO:0005215)			NS(1)|endometrium(1)|large_intestine(1)|lung(3)|pancreas(1)	7	all_hematologic(18;0.00473)|Acute lymphoblastic leukemia(18;0.0786)		KIRC - Kidney renal clear cell carcinoma(6;0.0764)|Kidney(552;0.118)|Colorectal(543;0.229)			TATCTCGTGAAGGAAGGAGGC	0.522																																					p.K140R		Atlas-SNP	.											.	PDZK1	15	.	0			c.A419G						.						80	84	83					1																	145748546		2203	4300	6503	SO:0001583	missense	5174	exon4			TCGTGAAGGAAGG	AF012281	CCDS72859.1, CCDS72860.1	1q21	2009-08-21			ENSG00000174827	ENSG00000174827			8821	protein-coding gene	gene with protein product		603831				9461128	Standard	NM_002614		Approved	PDZD1, NHERF3	uc001eoo.2	Q5T2W1	OTTHUMG00000013735	ENST00000344770.2:c.419A>G	chr1.hg19:g.145748546A>G	ENSP00000342143:p.Lys140Arg	284.0	0.0		467.0	268.0	NM_002614	B4DPB9|E7EU02|O60450|Q5T5P6|Q9BQ41	Missense_Mutation	SNP	ENST00000344770.2	hg19	CCDS924.1	.	.	.	.	.	.	.	.	.	.	A	15.98	2.994037	0.54041	.	.	ENSG00000174827	ENST00000443667;ENST00000417171;ENST00000451928;ENST00000344770	T;T;T;T	0.32753	1.64;1.64;1.44;1.64	5.84	5.84	0.93424	PDZ/DHR/GLGF (3);	0.050633	0.85682	D	0.000000	T	0.32315	0.0825	L	0.52011	1.625	0.47905	D	0.999542	P;D	0.89917	0.924;1.0	P;D	0.85130	0.791;0.997	T	0.18178	-1.0345	10	0.07813	T	0.8	-12.1142	14.1607	0.65446	1.0:0.0:0.0:0.0	.	140;140	E7EU02;Q5T2W1	.;NHRF3_HUMAN	R	140	ENSP00000409291:K140R;ENSP00000394485:K140R;ENSP00000403422:K140R;ENSP00000342143:K140R	ENSP00000342143:K140R	K	+	2	0	PDZK1	144459903	1.000000	0.71417	1.000000	0.80357	0.003000	0.03518	7.578000	0.82498	2.233000	0.73108	0.482000	0.46254	AAG	.	.		0.522	PDZK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038502.2	NM_002614		G	145748546	A	G	145748546	3	3	289	1	0	0	0	0	1	0	0	0	11716	72	3	2	425	2	PDZK1	1	145748546	Missense_Mutation	SNP	A	TCGA-G3-A6UC-01A-21D-A33K-10	25464059	145748546	103502075	5	42345										
HIST2H2BE	8349	hgsc.bcm.edu	37	chr1	149858163	149858163	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	cttggagccctttttaggggCcggagcggattttgccggtt	15	9	0	0			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr1:149858163C>A	ENST00000369155.2	-	1	69	c.28G>T	c.(28-30)Gcc>Tcc	p.A10S	HIST2H2AC_ENST00000331380.2_5'Flank|BOLA1_ENST00000369153.2_5'Flank	NM_003528.2	NP_003519.1	Q16778	H2B2E_HUMAN	histone cluster 2, H2be	10					antibacterial humoral response (GO:0019731)|chromatin organization (GO:0006325)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|nucleosome assembly (GO:0006334)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	14	Breast(34;0.0124)|all_hematologic(923;0.127)		STAD - Stomach adenocarcinoma(528;0.133)|LUSC - Lung squamous cell carcinoma(543;0.221)			TTTTTAGGGGCCGGAGCGGAT	0.512																																					p.A10S		Atlas-SNP	.											HIST2H2BE,NS,carcinoma,0,1	HIST2H2BE	33	.	0			c.G28T						.						67	69	68					1																	149858163		2203	4300	6503	SO:0001583	missense	8349	exon1			TAGGGGCCGGAGC	AY131979	CCDS936.1	1q21.2	2011-01-27	2006-10-11	2003-03-07	ENSG00000184678	ENSG00000184678		"Histones / Replication-dependent"	4760	protein-coding gene	gene with protein product		601831	"H2B histone family, member Q", "histone 2, H2be"	H2B, H2BFQ		1469070, 12408966	Standard	NM_003528		Approved	H2B/q, H2B.1	uc001etc.3	Q16778	OTTHUMG00000012095	ENST00000369155.2:c.28G>T	chr1.hg19:g.149858163C>A	ENSP00000358151:p.Ala10Ser	125.0	1.0		192.0	59.0	NM_003528	A3KMC7|A8K110|Q4KMY1|Q5QNX0|Q9UE88	Missense_Mutation	SNP	ENST00000369155.2	hg19	CCDS936.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.099168	0.76983	.	.	ENSG00000184678	ENST00000369155	T	0.22539	1.95	5.99	5.99	0.97316	Histone-fold (2);	0.000000	0.85682	D	0.000000	T	0.19127	0.0459	M	0.76433	2.335	0.41464	D	0.988064	B	0.09022	0.002	B	0.04013	0.001	T	0.01444	-1.1353	10	0.48119	T	0.1	.	19.1154	0.93336	0.0:1.0:0.0:0.0	.	10	Q16778	H2B2E_HUMAN	S	10	ENSP00000358151:A10S	ENSP00000358151:A10S	A	-	1	0	HIST2H2BE	148124787	1.000000	0.71417	0.944000	0.38274	0.907000	0.53573	6.253000	0.72453	2.857000	0.98124	0.650000	0.86243	GCC	.	.		0.512	HIST2H2BE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033455.1	NM_003528		A	149858163	C	A	149858163	3	1	289	1	0	0	0	0	1	0	0	0	7188	739	26	3	356	3	HIST2H2BE	1	149858163	Missense_Mutation	SNP	C	TCGA-G3-A6UC-01A-21D-A33K-10	4109617	149858163	99392458	6	42346										
FLG	2312	hgsc.bcm.edu	37	chr1	152282595	152282595	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	tgactaacactggatccctgGcgcctgcttgtcttggaccc	10	14	1	1	rs368218057		TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr1:152282595G>T	ENST00000368799.1	-	3	4802	c.4767C>A	c.(4765-4767)cgC>cgA	p.R1589R	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1589	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGGATCCCTGGCGCCTGCTTG	0.582									Ichthyosis																												p.R1589R		Atlas-SNP	.											.	FLG	900	.	0			c.C4767A						.	G		0,4406		0,0,2203	152	164	160		4767	-4.6	0	1		160	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FLG	NM_002016.1		0,1,6502	TT,TG,GG		0.0116,0.0,0.0077		1589/4062	152282595	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TCCCTGGCGCCTG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.4767C>A	chr1.hg19:g.152282595G>T		136.0	0.0		142.0	39.0	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	hg19	CCDS30860.1																																																																																			.	.		0.582	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		T	152282595	G	T	152282595	2	4	289	1	0	0	0	0	0	0	0	1	5930	1190	42	3		3	FLG	1	152282595	Silent	SNP	G	TCGA-G3-A6UC-01A-21D-A33K-10	2424432	152282595	96968026	7	42347										
LAMC1	3915	hgsc.bcm.edu	37	chr1	183111767	183111767	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	tcagcgatcttgataggaaaGtgtctgacctggagaatgaa	12	6	3	4			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr1:183111767G>A	ENST00000258341.4	+	28	4929	c.4672G>A	c.(4672-4674)Gtg>Atg	p.V1558M	RP11-181K3.4_ENST00000457852.3_RNA	NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	1558	Domain II and I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						TGATAGGAAAGTGTCTGACCT	0.468																																					p.V1558M		Atlas-SNP	.											.	LAMC1	176	.	0			c.G4672A						.						111	90	97					1																	183111767		2203	4300	6503	SO:0001583	missense	3915	exon28			AGGAAAGTGTCTG	J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"Laminins"	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.4672G>A	chr1.hg19:g.183111767G>A	ENSP00000258341:p.Val1558Met	71.0	0.0		125.0	37.0	NM_002293	Q5VYE7	Missense_Mutation	SNP	ENST00000258341.4	hg19	CCDS1351.1	.	.	.	.	.	.	.	.	.	.	G	15.25	2.778657	0.49786	.	.	ENSG00000135862	ENST00000258341	T	0.31247	1.5	5.57	5.57	0.84162	.	0.065064	0.64402	D	0.000006	T	0.23054	0.0557	N	0.25426	0.745	0.53005	D	0.999969	B	0.26195	0.144	B	0.19148	0.024	T	0.02821	-1.1106	10	0.36615	T	0.2	.	15.0699	0.72026	0.0:0.1415:0.8585:0.0	.	1558	P11047	LAMC1_HUMAN	M	1558	ENSP00000258341:V1558M	ENSP00000258341:V1558M	V	+	1	0	LAMC1	181378390	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.364000	0.73086	2.611000	0.88343	0.655000	0.94253	GTG	.	.		0.468	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293		A	183111767	G	A	183111767	3	1	289	1	0	0	0	0	1	0	0	0	8623	1029	36	3	4782	3	LAMC1	1	183111767	Missense_Mutation	SNP	G	TCGA-G3-A6UC-01A-21D-A33K-10	30829172	183111767	66138854	8	42348										
PLA2G4A	5321	hgsc.bcm.edu	37	chr1	186839647	186839648	+	Splice_Site	DNP	GC	GC	AA													0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	aagggggcctttggtgacatGcgtaagtgccctttttttct							TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr1:186839647_186839648GC>AA	ENST00000367466.3	+	3	266_267	c.114_115GC>AA	c.(112-117)atGCtt>atAAtt	p.38_39ML>II	PLA2G4A_ENST00000442353.2_Splice_Site_p.38_39ML>II|PLA2G4A_ENST00000466600.1_3'UTR	NM_024420.2	NP_077734	P47712	PA24A_HUMAN	phospholipase A2, group IVA (cytosolic, calcium-dependent)	38	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.|Phospholipid binding. {ECO:0000305}.				arachidonic acid metabolic process (GO:0019369)|arachidonic acid secretion (GO:0050482)|blood coagulation (GO:0007596)|cardiolipin acyl-chain remodeling (GO:0035965)|cellular response to antibiotic (GO:0071236)|glycerophospholipid biosynthetic process (GO:0046474)|icosanoid biosynthetic process (GO:0046456)|icosanoid metabolic process (GO:0006690)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|platelet activation (GO:0030168)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|calcium-dependent phospholipid binding (GO:0005544)|lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|prostate(3)|skin(4)|stomach(1)	53					Aldesleukin(DB00041)|Carbachol(DB00411)|Carbenicillin(DB00578)|Epirubicin(DB00445)|Fluocinolone Acetonide(DB00591)|Fluticasone Propionate(DB00588)|Niflumic Acid(DB04552)|Orlistat(DB01083)|Quinacrine(DB01103)|Streptokinase(DB00086)|Suramin(DB04786)	TTGGTGACATGCGTAAGTGCCC	0.426																																					p.M38I|p.L39I		Atlas-SNP	.											.	PLA2G4A	125	.	0			c.G114A|c.C115A						.																																			SO:0001630	splice_region_variant	5321	exon3			TGACATGCGTAAG|GACATGCGTAAGT	M72393	CCDS1372.1	1q25	2014-09-17			ENSG00000116711	ENSG00000116711	3.1.1.4, 3.1.1.5		9035	protein-coding gene	gene with protein product		600522		PLA2G4		8175726	Standard	NM_024420		Approved	cPLA2-alpha	uc001gsc.3	P47712	OTTHUMG00000035512	Exception_encountered	chr1.hg19:g.186839647_186839648delinsAA		57.0|55.0	0.0		113.0|112.0	30.0	NM_024420	B1AKG4|Q29R80	Missense_Mutation	SNP	ENST00000367466.3	hg19	CCDS1372.1																																																																																			.	.		0.426	PLA2G4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086236.1	NM_024420	Missense_Mutation	AA	186839648	GC	AA	186839647	5	1	289	1	0	0	0	0	0	0	1	0	12010	1333	46	3	120	3	PLA2G4A	1	186839647	Splice_Site	DNP	GC	TCGA-G3-A6UC-01A-21D-A33K-10	3727880	186839647	62410974	9	42349										
FAM5C	339479	hgsc.bcm.edu	37	chr1	190067609	190067609	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	tgtcttccatttgttccccaGagttaatgtccagttataac	6	10	1	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr1:190067609G>T	ENST00000367462.3	-	8	2071	c.1840C>A	c.(1840-1842)Ctg>Atg	p.L614M	BRINP3_ENST00000534846.1_Missense_Mutation_p.L512M	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	614					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)											TTGTTCCCCAGAGTTAATGTC	0.443																																					p.L614M		Atlas-SNP	.											.	FAM5C	343	.	0			c.C1840A						.						244	256	252					1																	190067609		2203	4300	6503	SO:0001583	missense	339479	exon8			TCCCCAGAGTTAA	AB111893	CCDS1373.1	1q31.1	2013-09-18	2013-09-18	2013-09-18	ENSG00000162670	ENSG00000162670			22393	protein-coding gene	gene with protein product			"family with sequence similarity 5, member C"	FAM5C		16018821, 15193423	Standard	NM_199051		Approved	DBCCR1L, DBCCR1L1	uc001gse.1	Q76B58	OTTHUMG00000035533	ENST00000367462.3:c.1840C>A	chr1.hg19:g.190067609G>T	ENSP00000356432:p.Leu614Met	67.0	0.0		73.0	21.0	NM_199051	B3KVP1|B7Z260|O95726|Q2M330	Missense_Mutation	SNP	ENST00000367462.3	hg19	CCDS1373.1	.	.	.	.	.	.	.	.	.	.	G	13.05	2.122327	0.37436	.	.	ENSG00000162670	ENST00000367462;ENST00000534846	T;T	0.32272	1.7;1.46	5.61	2.65	0.31530	.	0.078660	0.51477	D	0.000082	T	0.39332	0.1074	M	0.69823	2.125	0.38339	D	0.944007	P;P	0.52061	0.95;0.917	P;P	0.52424	0.698;0.502	T	0.39272	-0.9622	10	0.87932	D	0	.	5.3923	0.16251	0.2414:0.1484:0.6102:0.0	.	512;614	B7Z260;Q76B58	.;FAM5C_HUMAN	M	614;512	ENSP00000356432:L614M;ENSP00000438022:L512M	ENSP00000356432:L614M	L	-	1	2	FAM5C	188334232	0.996000	0.38824	0.921000	0.36526	0.972000	0.66771	1.772000	0.38552	0.706000	0.31912	0.585000	0.79938	CTG	.	.		0.443	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086278.1	NM_199051		T	190067609	G	T	190067609	3	4	289	1	0	0	0	0	1	0	0	0	5602	933	33	3	464	3	FAM5C	1	190067609	Missense_Mutation	SNP	G	TCGA-G3-A6UC-01A-21D-A33K-10	3227962	190067609	59183012	10	42350										
TTC13	79573	hgsc.bcm.edu	37	chr1	231096999	231096999	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	aagcaaggagtcacagggtgAtgatcccttgggttcgcagt	14	8	1	2			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr1:231096999A>C	ENST00000366661.4	-	2	329	c.322T>G	c.(322-324)Tca>Gca	p.S108A	TTC13_ENST00000414259.1_Missense_Mutation_p.S108A|TTC13_ENST00000366662.4_Missense_Mutation_p.S108A	NM_024525.4	NP_078801.3	Q8NBP0	TTC13_HUMAN	tetratricopeptide repeat domain 13	108										central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	39	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)		COAD - Colon adenocarcinoma(196;0.243)		TCACAGGGTGATGATCCCTTG	0.423																																					p.S108A		Atlas-SNP	.											.	TTC13	74	.	0			c.T322G						.						124	113	117					1																	231096999		2203	4300	6503	SO:0001583	missense	79573	exon2			AGGGTGATGATCC		CCDS1588.1, CCDS44332.1, CCDS44332.2	1q42.2	2013-01-10			ENSG00000143643	ENSG00000143643		"Tetratricopeptide (TTC) repeat domain containing"	26204	protein-coding gene	gene with protein product							Standard	NM_024525		Approved	FLJ22584	uc001huf.4	Q8NBP0	OTTHUMG00000037788	ENST00000366661.4:c.322T>G	chr1.hg19:g.231096999A>C	ENSP00000355621:p.Ser108Ala	67.0	0.0		106.0	27.0	NM_001122835	B1AQI1|B1AQI2|Q8IVP8|Q8NBI0|Q8ND20	Missense_Mutation	SNP	ENST00000366661.4	hg19	CCDS1588.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	0.583|0.583	-0.836257|-0.836257	0.02692|0.02692	.|.	.|.	ENSG00000143643|ENSG00000143643	ENST00000522821|ENST00000366661;ENST00000366662;ENST00000414259	.|T;T;T	.|0.42900	.|1.02;0.96;0.96	5.27|5.27	2.28|2.28	0.28536|0.28536	.|.	.|0.371098	.|0.30714	.|N	.|0.009033	T|T	0.16428|0.16428	0.0395|0.0395	N|N	0.03608|0.03608	-0.345|-0.345	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.06786	.|0.0;0.001;0.0	.|B;B;B	.|0.06405	.|0.0;0.001;0.002	T|T	0.28138|0.28138	-1.0053|-1.0053	5|10	.|0.08837	.|T	.|0.75	-0.9707|-0.9707	9.4866|9.4866	0.38933|0.38933	0.0769:0.2799:0.6433:0.0|0.0769:0.2799:0.6433:0.0	.|.	.|108;108;108	.|E9PGV4;Q8NBP0-2;Q8NBP0	.|.;.;TTC13_HUMAN	Q|A	96|108	.|ENSP00000355621:S108A;ENSP00000355622:S108A;ENSP00000416631:S108A	.|ENSP00000355621:S108A	H|S	-|-	3|1	2|0	TTC13|TTC13	229163622|229163622	0.547000|0.547000	0.26465|0.26465	0.120000|0.120000	0.21714|0.21714	0.811000|0.811000	0.45836|0.45836	0.535000|0.535000	0.23114|0.23114	0.197000|0.197000	0.20387|0.20387	-0.237000|-0.237000	0.12165|0.12165	CAT|TCA	.	.		0.423	TTC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092229.2	NM_024525		C	231096999	A	C	231096999	3	2	289	1	0	0	0	0	1	0	0	0	16695	333	12	5	2348	5	TTC13	1	231096999	Missense_Mutation	SNP	A	TCGA-G3-A6UC-01A-21D-A33K-10	41029390	231096999	18153622	11	42351										
OR2W5	441932	hgsc.bcm.edu	37	chr1	247655247	247655247	+	RNA	DEL	T	T	-													0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	actcccaagatcaggggaagTtcctgactctcttctacacc							TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr1:247655247delT	ENST00000522351.1	+	0	878							A6NFC9	OR2W5_HUMAN	olfactory receptor, family 2, subfamily W, member 5							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(24)|ovary(1)|skin(4)	39	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.222)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			TCAGGGGAAGTTCCTGACTCT	0.512																																					p.V273fs		Atlas-Indel,Pindel	.											.	OR2W5	97	.	0			c.817delG						.						129	115	120					1																	247655247		2203	4300	6503			441932	exon1			.			1q44	2013-03-27		2004-03-10	ENSG00000203664	ENSG00000203664		"GPCR / Class A : Olfactory receptors"	15424	other	unknown				OR2W5P		12213199	Standard	NM_001004698		Approved	OST722	uc001icz.2	A6NFC9	OTTHUMG00000040573		chr1.hg19:g.247655247delT		180.0	0.0		301.0	101.0	NM_001004698	B9EH85	Frame_Shift_Del	DEL	ENST00000522351.1	hg19																																																																																				.	.		0.512	OR2W5-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000375789.1	NM_001004698		-	247655247	T	-	247655247	6	5	289	0	1	1	0	1	0	0	0	0	11043	1725	60	0		0	OR2W5	1	247655247	RNA	DEL	T	TCGA-G3-A6UC-01A-21D-A33K-10	16558248	247655247	1595374	12	42352										
OR6F1	343169	hgsc.bcm.edu	37	chr1	247875237	247875237	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	ccacagtgttcaggacgtggAcagctttgatcagatccaag	11	10	2	2			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr1:247875237A>G	ENST00000302084.2	-	1	868	c.821T>C	c.(820-822)gTc>gCc	p.V274A	RP11-634B7.4_ENST00000449298.1_RNA	NM_001005286.1	NP_001005286.1	Q8NGZ6	OR6F1_HUMAN	olfactory receptor, family 6, subfamily F, member 1	274						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(1)|large_intestine(5)|lung(34)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)	47	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.0168)			CAGGACGTGGACAGCTTTGAT	0.478																																					p.V274A		Atlas-SNP	.											.	OR6F1	88	.	0			c.T821C						.						116	113	114					1																	247875237		2203	4300	6503	SO:0001583	missense	343169	exon1			ACGTGGACAGCTT	BK004460	CCDS31095.1	1q44	2012-08-09			ENSG00000169214	ENSG00000169214		"GPCR / Class A : Olfactory receptors"	15027	protein-coding gene	gene with protein product							Standard	NM_001005286		Approved	OST731	uc001idj.1	Q8NGZ6	OTTHUMG00000040213	ENST00000302084.2:c.821T>C	chr1.hg19:g.247875237A>G	ENSP00000305640:p.Val274Ala	69.0	0.0		93.0	30.0	NM_001005286	B2RNV6|Q6IF02|Q96R39	Missense_Mutation	SNP	ENST00000302084.2	hg19	CCDS31095.1	.	.	.	.	.	.	.	.	.	.	A	11.49	1.652864	0.29336	.	.	ENSG00000169214	ENST00000302084	T	0.39406	1.08	3.49	3.49	0.39957	GPCR, rhodopsin-like superfamily (1);	0.657383	0.12629	N	0.452358	T	0.27169	0.0666	N	0.12853	0.265	0.09310	N	1	P	0.38745	0.645	B	0.41946	0.371	T	0.08472	-1.0720	10	0.51188	T	0.08	-34.2103	6.4793	0.22053	0.8855:0.0:0.1145:0.0	.	274	Q8NGZ6	OR6F1_HUMAN	A	274	ENSP00000305640:V274A	ENSP00000305640:V274A	V	-	2	0	OR6F1	245941860	0.002000	0.14202	0.002000	0.10522	0.059000	0.15707	1.722000	0.38042	1.574000	0.49760	0.482000	0.46254	GTC	.	.		0.478	OR6F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096870.1	NM_001005286		G	247875237	A	G	247875237	3	3	289	1	0	0	0	0	1	0	0	0	11210	275	10	2	109	2	OR6F1	1	247875237	Missense_Mutation	SNP	A	TCGA-G3-A6UC-01A-21D-A33K-10	219990	247875237	1375384	13	42353										
ROCK2	9475	hgsc.bcm.edu	37	chr2	11348447	11348447	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	catctttctgtttaaggagcTcatttattttctgctgtgac	7	8	4	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr2:11348447T>A	ENST00000315872.6	-	19	2778	c.2330A>T	c.(2329-2331)gAg>gTg	p.E777V	ROCK2_ENST00000401753.1_Missense_Mutation_p.E534V	NM_004850.3	NP_004841.2	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein kinase 2	777	Interaction with PPP1R12A.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|neural tube closure (GO:0001843)|positive regulation of centrosome duplication (GO:0010825)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of circadian rhythm (GO:0042752)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|rhythmic process (GO:0048511)|smooth muscle contraction (GO:0006939)	centrosome (GO:0005813)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole centrosome (GO:0031616)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(6)|lung(10)|prostate(1)|skin(4)|stomach(3)|urinary_tract(2)	43	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)		TTTAAGGAGCTCATTTATTTT	0.318																																					p.E777V		Atlas-SNP	.											.	ROCK2	224	.	0			c.A2330T						.						85	78	81					2																	11348447		1811	4069	5880	SO:0001583	missense	9475	exon19			AGGAGCTCATTTA	D87931	CCDS42654.1	2p24	2013-01-10			ENSG00000134318	ENSG00000134318	2.7.11.1	"Pleckstrin homology (PH) domain containing"	10252	protein-coding gene	gene with protein product		604002				9933571	Standard	NM_004850		Approved		uc002rbd.1	O75116	OTTHUMG00000149916	ENST00000315872.6:c.2330A>T	chr2.hg19:g.11348447T>A	ENSP00000317985:p.Glu777Val	38.0	0.0		49.0	18.0	NM_004850	Q53QZ0|Q53SJ7|Q9UQN5	Missense_Mutation	SNP	ENST00000315872.6	hg19	CCDS42654.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.254813	0.80135	.	.	ENSG00000134318	ENST00000315872;ENST00000401753;ENST00000399089	T;T	0.64438	-0.1;0.95	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.65863	0.2732	L	0.57536	1.79	0.58432	D	0.999995	P	0.46859	0.885	P	0.46885	0.53	T	0.68236	-0.5462	10	0.49607	T	0.09	.	15.7982	0.78428	0.0:0.0:0.0:1.0	.	777	O75116	ROCK2_HUMAN	V	777;534;135	ENSP00000317985:E777V;ENSP00000385509:E534V	ENSP00000317985:E777V	E	-	2	0	ROCK2	11265898	1.000000	0.71417	0.996000	0.52242	0.994000	0.84299	5.952000	0.70282	2.132000	0.65825	0.533000	0.62120	GAG	.	.		0.318	ROCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313886.3			A	11348447	T	A	11348447	3	1	289	1	0	0	0	0	1	0	0	0	13533	1551	54	4	1896	4	ROCK2	2	11348447	Missense_Mutation	SNP	T	TCGA-G3-A6UC-01A-21D-A33K-10		11348447	231850926	14	42354										
ADCY3	109	hgsc.bcm.edu	37	chr2	25141567	25141567	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	tgtcgctggagaagaccacaGcacacatgaccaccacgtag	10	13	0	3			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr2:25141567G>T	ENST00000260600.5	-	1	1141	c.290C>A	c.(289-291)gCt>gAt	p.A97D		NM_004036.3	NP_004027.2	O60266	ADCY3_HUMAN	adenylate cyclase 3	97					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			NS(1)|breast(5)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|prostate(4)|skin(2)	44	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					GAAGACCACAGCACACATGAC	0.567																																					p.A97D		Atlas-SNP	.											.	ADCY3	114	.	0			c.C290A						.						109	114	112					2																	25141567		2203	4300	6503	SO:0001583	missense	109	exon1			ACCACAGCACACA	AF033861	CCDS1715.1	2p23.3	2013-02-04			ENSG00000138031	ENSG00000138031	4.6.1.1	"Adenylate cyclases"	234	protein-coding gene	gene with protein product		600291				9920776	Standard	NM_004036		Approved	AC3	uc002rfs.4	O60266	OTTHUMG00000094765	ENST00000260600.5:c.290C>A	chr2.hg19:g.25141567G>T	ENSP00000260600:p.Ala97Asp	147.0	0.0		138.0	52.0	NM_004036	B3KT86|Q53T54|Q9UDB1	Missense_Mutation	SNP	ENST00000260600.5	hg19	CCDS1715.1	.	.	.	.	.	.	.	.	.	.	G	18.42	3.620799	0.66787	.	.	ENSG00000138031	ENST00000260600;ENST00000415879;ENST00000435135;ENST00000438445	T;T;T	0.81163	-1.46;-1.08;0.44	4.8	3.85	0.44370	.	0.000000	0.85682	D	0.000000	T	0.75715	0.3887	M	0.67953	2.075	0.80722	D	1	B;B	0.31318	0.139;0.319	B;B	0.24006	0.03;0.05	T	0.75326	-0.3357	10	0.33940	T	0.23	.	13.1935	0.59726	0.0:0.1611:0.8389:0.0	.	97;97	B7ZLX9;O60266	.;ADCY3_HUMAN	D	97;72;97;97	ENSP00000260600:A97D;ENSP00000389799:A97D;ENSP00000406153:A97D	ENSP00000260600:A97D	A	-	2	0	ADCY3	24995071	0.999000	0.42202	0.939000	0.37840	0.987000	0.75469	7.429000	0.80309	2.211000	0.71520	0.563000	0.77884	GCT	.	.		0.567	ADCY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211574.2			T	25141567	G	T	25141567	3	4	289	1	0	0	0	0	1	0	0	0	295	971	34	3	3228	3	ADCY3	2	25141567	Missense_Mutation	SNP	G	TCGA-G3-A6UC-01A-21D-A33K-10	13793120	25141567	218057806	15	42355										
PEX13	5194	hgsc.bcm.edu	37	chr2	61258660	61258660	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	cacagcagacaggaagtagcAgtgtgaacacttttagacct	10	9	0	3			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr2:61258660A>G	ENST00000295030.5	+	2	237	c.199A>G	c.(199-201)Agt>Ggt	p.S67G	PEX13_ENST00000472678.1_3'UTR	NM_002618.3	NP_002609.1	Q92968	PEX13_HUMAN	peroxisomal biogenesis factor 13	67					cerebral cortex cell migration (GO:0021795)|fatty acid alpha-oxidation (GO:0001561)|locomotory behavior (GO:0007626)|microtubule-based peroxisome localization (GO:0060152)|neuron migration (GO:0001764)|protein import into peroxisome matrix, docking (GO:0016560)|suckling behavior (GO:0001967)	integral component of peroxisomal membrane (GO:0005779)|membrane (GO:0016020)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)				endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10			LUSC - Lung squamous cell carcinoma(5;2.05e-06)|Lung(5;3.13e-05)|Epithelial(17;0.114)			AGGAAGTAGCAGTGTGAACAC	0.428																																					p.S67G		Atlas-SNP	.											.	PEX13	27	.	0			c.A199G						.						122	120	121					2																	61258660		2203	4300	6503	SO:0001583	missense	5194	exon2			AGTAGCAGTGTGA	U71374	CCDS1866.1	2p16.1	2008-08-26	2008-08-26		ENSG00000162928	ENSG00000162928			8855	protein-coding gene	gene with protein product		601789	"peroxisome biogenesis factor 13"			9878256	Standard	NM_002618		Approved		uc002sau.4	Q92968	OTTHUMG00000129422	ENST00000295030.5:c.199A>G	chr2.hg19:g.61258660A>G	ENSP00000295030:p.Ser67Gly	78.0	0.0		92.0	31.0	NM_002618	B2RCS1	Missense_Mutation	SNP	ENST00000295030.5	hg19	CCDS1866.1	.	.	.	.	.	.	.	.	.	.	A	10.98	1.503485	0.26949	.	.	ENSG00000162928	ENST00000295030	T	0.76578	-1.03	5.85	5.85	0.93711	.	0.792914	0.12121	N	0.497700	T	0.58104	0.2099	N	0.08118	0	0.54753	D	0.999982	B	0.02656	0.0	B	0.01281	0.0	T	0.53408	-0.8443	10	0.22109	T	0.4	-3.5224	8.567	0.33545	0.8572:0.0:0.1428:0.0	.	67	Q92968	PEX13_HUMAN	G	67	ENSP00000295030:S67G	ENSP00000295030:S67G	S	+	1	0	PEX13	61112164	0.638000	0.27225	0.865000	0.33974	0.986000	0.74619	2.334000	0.43920	2.222000	0.72286	0.533000	0.62120	AGT	.	.		0.428	PEX13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251581.3	NM_002618		G	61258660	A	G	61258660	3	3	289	1	0	0	0	0	1	0	0	0	11750	188	7	2	205	2	PEX13	2	61258660	Missense_Mutation	SNP	A	TCGA-G3-A6UC-01A-21D-A33K-10	36117093	61258660	181940713	16	42356										
CNGA3	1261	hgsc.bcm.edu	37	chr2	98996755	98996755	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	gccgagcttaaggaggtgtcCagccaagaaagcaatgccca	12	11	0	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr2:98996755C>A	ENST00000272602.2	+	3	372	c.333C>A	c.(331-333)tcC>tcA	p.S111S	CNGA3_ENST00000436404.2_Silent_p.S111S|CNGA3_ENST00000393504.1_Silent_p.S111S|CNGA3_ENST00000409937.1_Silent_p.S115S			Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3	111					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to magnesium ion (GO:0032026)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|photoreceptor outer segment membrane (GO:0042622)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(17)|ovary(5)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	49						AGGAGGTGTCCAGCCAAGAAA	0.592																																					p.S111S		Atlas-SNP	.											.	CNGA3	118	.	0			c.C333A						.						71	67	69					2																	98996755		2203	4300	6503	SO:0001819	synonymous_variant	1261	exon4			GGTGTCCAGCCAA	S76069	CCDS2034.1, CCDS42719.1	2q11.2	2013-01-08			ENSG00000144191	ENSG00000144191		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2150	protein-coding gene	gene with protein product		600053		CNCG3, ACHM2		7532814, 9517456, 16382102	Standard	NM_001298		Approved	CCNC1, CCNCa, CNG3	uc002syt.3	Q16281	OTTHUMG00000130561	ENST00000272602.2:c.333C>A	chr2.hg19:g.98996755C>A		115.0	0.0		90.0	38.0	NM_001298	E9PF93|Q4VAP7|Q53RD2|Q6ZNA7|Q9UP64	Silent	SNP	ENST00000272602.2	hg19	CCDS2034.1																																																																																			.	.		0.592	CNGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252986.1	NM_001298		A	98996755	C	A	98996755	2	1	289	1	0	0	0	0	0	0	0	1	3600	581	21	3		3	CNGA3	2	98996755	Silent	SNP	C	TCGA-G3-A6UC-01A-21D-A33K-10	37738095	98996755	144202618	17	42357										
CCDC74A	90557	hgsc.bcm.edu	37	chr2	132290493	132290493	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	aggccccaggcagccccggaGgaagctagctttcccaggtg	14	14	0	0			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr2:132290493G>A	ENST00000295171.6	+	6	1071	c.933G>A	c.(931-933)gaG>gaA	p.E311E	CCDC74A_ENST00000467992.2_3'UTR|CCDC74A_ENST00000409856.3_Silent_p.E245E	NM_001258304.1|NM_001258305.1|NM_138770.2	NP_001245233.1|NP_001245234.1|NP_620125.1	Q96AQ1	CC74A_HUMAN	coiled-coil domain containing 74A	311										endometrium(4)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						CAGCCCCGGAGGAAGCTAGCT	0.667																																					p.R247K		Atlas-SNP	.											.	CCDC74A	44	.	0			c.G740A						.						58	68	65					2																	132290493		2203	4300	6503	SO:0001819	synonymous_variant	90557	exon5			CCCGGAGGAAGCT		CCDS2167.1, CCDS58732.1, CCDS74578.1	2q21.1	2008-02-05		2006-02-16	ENSG00000163040	ENSG00000163040			25197	protein-coding gene	gene with protein product						12477932	Standard	NM_138770		Approved	FLJ40345	uc002ttb.4	Q96AQ1	OTTHUMG00000131667	ENST00000295171.6:c.933G>A	chr2.hg19:g.132290493G>A		260.0	0.0		218.0	42.0	NM_001258305	Q6P4I5	Missense_Mutation	SNP	ENST00000295171.6	hg19	CCDS2167.1	.	.	.	.	.	.	.	.	.	.	.	13.86	2.362848	0.41902	.	.	ENSG00000163040	ENST00000434330	T	0.51325	0.71	3.35	3.35	0.38373	.	.	.	.	.	T	0.56016	0.1957	.	.	.	0.35196	D	0.773865	.	.	.	.	.	.	T	0.69235	-0.5198	6	0.87932	D	0	.	10.5645	0.45165	0.0:0.0:1.0:0.0	.	.	.	.	K	200	ENSP00000406839:R200K	ENSP00000406839:R200K	R	+	2	0	CCDC74A	132006963	0.295000	0.24389	0.294000	0.24946	0.011000	0.07611	0.925000	0.28791	1.586000	0.49944	0.430000	0.28490	AGG	.	.		0.667	CCDC74A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254570.2	NM_138770		A	132290493	G	A	132290493	2	1	289	1	0	0	0	0	0	0	0	1	2849	991	35	3		3	CCDC74A	2	132290493	Silent	SNP	G	TCGA-G3-A6UC-01A-21D-A33K-10	33293738	132290493	110908880	18	42358										
PKP4	8502	hgsc.bcm.edu	37	chr2	159526271	159526271	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	cctggtcaaccggctccccgGcggcaatggccccagtgtct	12	17	2	0			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr2:159526271G>A	ENST00000389759.3	+	17	2880	c.2768G>A	c.(2767-2769)gGc>gAc	p.G923D	PKP4_ENST00000389757.3_Missense_Mutation_p.G923D|AC005042.4_ENST00000342892.4_RNA	NM_003628.3	NP_003619.2	Q99569	PKP4_HUMAN	plakophilin 4	923					cell-cell junction assembly (GO:0007043)|cell-cell signaling (GO:0007267)|positive regulation of cytokinesis (GO:0032467)|positive regulation of gene expression (GO:0010628)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell adhesion (GO:0030155)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|desmosome (GO:0030057)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)				breast(2)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(21)|ovary(6)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	61						CGGCTCCCCGGCGGCAATGGC	0.522										HNSCC(62;0.18)																											p.G923D		Atlas-SNP	.											.	PKP4	133	.	0			c.G2768A						.						50	53	52					2																	159526271		2203	4300	6503	SO:0001583	missense	8502	exon17			TCCCCGGCGGCAA	X81889	CCDS33305.1, CCDS33306.1	2q24.1	2013-02-14			ENSG00000144283	ENSG00000144283		"Armadillo repeat containing"	9026	protein-coding gene	gene with protein product		604276				9342840, 8937994	Standard	NM_003628		Approved	p0071	uc002tzv.3	Q99569	OTTHUMG00000153969	ENST00000389759.3:c.2768G>A	chr2.hg19:g.159526271G>A	ENSP00000374409:p.Gly923Asp	224.0	0.0		186.0	83.0	NM_001005476	Q86W91	Missense_Mutation	SNP	ENST00000389759.3	hg19	CCDS33305.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.812128	0.90707	.	.	ENSG00000144283	ENST00000389757;ENST00000389759	T;T	0.38887	1.11;1.11	5.82	5.82	0.92795	Armadillo-like helical (1);Armadillo-type fold (1);	0.051797	0.85682	D	0.000000	T	0.61413	0.2345	L	0.46819	1.47	0.80722	D	1	D;D;D	0.89917	0.995;1.0;0.997	D;D;D	0.97110	0.949;1.0;0.953	T	0.60454	-0.7260	10	0.66056	D	0.02	-11.2665	20.0989	0.97860	0.0:0.0:1.0:0.0	.	878;923;923	Q4W5T8;Q99569-2;Q99569	.;.;PKP4_HUMAN	D	923	ENSP00000374407:G923D;ENSP00000374409:G923D	ENSP00000374407:G923D	G	+	2	0	PKP4	159234517	1.000000	0.71417	0.083000	0.20561	0.927000	0.56198	9.756000	0.98918	2.764000	0.94973	0.650000	0.86243	GGC	.	.		0.522	PKP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333250.1			A	159526271	G	A	159526271	3	1	289	1	0	0	0	0	1	0	0	0	11996	1203	42	3	2830	3	PKP4	2	159526271	Missense_Mutation	SNP	G	TCGA-G3-A6UC-01A-21D-A33K-10	27235778	159526271	83673102	19	42359										
SP3	6670	hgsc.bcm.edu	37	chr2	174820558	174820558	+	Frame_Shift_Del	DEL	T	T	-													0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	gacttgaccagtctgtggtaTgagattctggatgttagcag							TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr2:174820558delT	ENST00000310015.6	-	4	1212	c.682delA	c.(682-684)atafs	p.I228fs	SP3_ENST00000455789.2_Frame_Shift_Del_p.I175fs|SP3_ENST00000418194.2_Frame_Shift_Del_p.I160fs|SP3_ENST00000483084.1_5'Flank	NM_001172712.1|NM_003111.4	NP_001166183.1|NP_003102.1	Q02447	SP3_HUMAN	Sp3 transcription factor	228	Transactivation domain (Gln-rich).				B cell differentiation (GO:0030183)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|embryonic skeletal system development (GO:0048706)|enucleate erythrocyte differentiation (GO:0043353)|granulocyte differentiation (GO:0030851)|liver development (GO:0001889)|lung development (GO:0030324)|megakaryocyte differentiation (GO:0030219)|monocyte differentiation (GO:0030224)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|T cell differentiation (GO:0030217)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)		EWSR1/SP3(3)	NS(2)|large_intestine(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.185)			GTCTGTGGTATGAGATTCTGG	0.453																																					p.I228fs		Atlas-Indel,Pindel	.											.	SP3	82	.	0			c.683delT						.						141	144	143					2																	174820558		2203	4300	6503	SO:0001589	frameshift_variant	6670	exon4			.	M97191	CCDS2254.1, CCDS46452.1	2q31	2013-01-08			ENSG00000172845	ENSG00000172845		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	11208	protein-coding gene	gene with protein product		601804				1341900, 1454515	Standard	NM_003111		Approved	SPR-2	uc002uig.3	Q02447	OTTHUMG00000132333	ENST00000310015.6:c.682delA	chr2.hg19:g.174820558delT	ENSP00000310301:p.Ile228fs	71.0	0.0		63.0	32.0	NM_003111	A0AVL9|B4E2B7|Q69B26|Q69B27|Q8TD56|Q8WWU4|Q9BQR1	Frame_Shift_Del	DEL	ENST00000310015.6	hg19	CCDS2254.1																																																																																			.	.		0.453	SP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255452.1	NM_003111		-	174820558	T	-	174820558	7	5	289	1	0	1	0	1	0	0	0	0	14980	1464	51	0	1679	0	SP3	2	174820558	Frame_Shift_Del	DEL	T	TCGA-G3-A6UC-01A-21D-A33K-10	15294287	174820558	68378815	20	42360										
TTN	7273	hgsc.bcm.edu	37	chr2	179484523	179484523	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	cttagccattggacttccacCttatctttattgagttctgc	6	11	2	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr2:179484523C>A	ENST00000591111.1	-	200	41822	c.41598G>T	c.(41596-41598)aaG>aaT	p.K13866N	TTN-AS1_ENST00000604956.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.K15507N|TTN_ENST00000342992.6_Missense_Mutation_p.K12939N|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589907.1_RNA|RP11-171I2.4_ENST00000605334.1_lincRNA|TTN_ENST00000342175.6_Missense_Mutation_p.K6634N|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.K6567N|TTN_ENST00000460472.2_Missense_Mutation_p.K6442N|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13866					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGACTTCCACCTTATCTTTAT	0.403																																					p.K15507N		Atlas-SNP	.											.	TTN	18412	.	0			c.G46521T						.						177	169	171					2																	179484523		1862	4093	5955	SO:0001583	missense	7273	exon250			TTCCACCTTATCT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.41598G>T	chr2.hg19:g.179484523C>A	ENSP00000465570:p.Lys13866Asn	62.0	0.0		77.0	40.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	11.73	1.724819	0.30593	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3	5.82	1.97	0.26223	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.46444	0.1393	N	0.05351	-0.065	0.35338	D	0.78619	P;P;P;P	0.36354	0.549;0.549;0.549;0.549	B;B;B;B	0.43623	0.258;0.258;0.425;0.258	T	0.52668	-0.8545	9	0.87932	D	0	.	2.2597	0.04064	0.1204:0.3516:0.1177:0.4103	.	6442;6567;6634;13866	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	N	12939;6442;6634;6567;6442	ENSP00000343764:K12939N;ENSP00000434586:K6442N;ENSP00000340554:K6634N;ENSP00000352154:K6567N	ENSP00000340554:K6634N	K	-	3	2	TTN	179192768	0.001000	0.12720	1.000000	0.80357	0.998000	0.95712	-1.524000	0.02233	0.373000	0.24621	0.655000	0.94253	AAG	.	.		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179484523	C	A	179484523	3	1	289	1	0	0	0	0	1	0	0	0	16750	680	24	3	61624	3	TTN	2	179484523	Missense_Mutation	SNP	C	TCGA-G3-A6UC-01A-21D-A33K-10	4663965	179484523	63714850	21	42361										
AOX1	316	hgsc.bcm.edu	37	chr2	201531449	201531449	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	tcatggatgttggctgcagtAtaaatccagccattgacata	9	8	1	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr2:201531449A>G	ENST00000374700.2	+	32	3824	c.3583A>G	c.(3583-3585)Ata>Gta	p.I1195V	AOX1_ENST00000485106.1_3'UTR	NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	1195					inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)			breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	TGGCTGCAGTATAAATCCAGC	0.383																																					p.I1195V		Atlas-SNP	.											.	AOX1	152	.	0			c.A3583G						.						113	105	108					2																	201531449		2203	4300	6503	SO:0001583	missense	316	exon32			TGCAGTATAAATC	AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356			553	protein-coding gene	gene with protein product		602841				7570184	Standard	NM_001159		Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	ENST00000374700.2:c.3583A>G	chr2.hg19:g.201531449A>G	ENSP00000363832:p.Ile1195Val	73.0	0.0		83.0	39.0	NM_001159	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	Missense_Mutation	SNP	ENST00000374700.2	hg19	CCDS33360.1	.	.	.	.	.	.	.	.	.	.	A	14.49	2.550506	0.45383	.	.	ENSG00000138356	ENST00000374700;ENST00000260930;ENST00000439380	T;T;T	0.39787	1.06;1.06;1.06	5.09	2.6	0.31112	Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding (3);	0.220508	0.44902	D	0.000401	T	0.53802	0.1819	M	0.87682	2.9	0.46167	D	0.998901	B	0.32382	0.368	B	0.40444	0.329	T	0.58719	-0.7587	10	0.66056	D	0.02	-31.141	12.137	0.53977	0.6741:0.3259:0.0:0.0	.	1195	Q06278	ADO_HUMAN	V	1195;81;35	ENSP00000363832:I1195V;ENSP00000260930:I81V;ENSP00000413326:I35V	ENSP00000260930:I81V	I	+	1	0	AOX1	201239694	0.791000	0.28800	0.992000	0.48379	0.976000	0.68499	0.659000	0.24994	0.423000	0.26033	0.383000	0.25322	ATA	.	.		0.383	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335844.1	NM_001159		G	201531449	A	G	201531449	3	3	289	1	0	0	0	0	1	0	0	0	729	449	16	2	3709	2	AOX1	2	201531449	Missense_Mutation	SNP	A	TCGA-G3-A6UC-01A-21D-A33K-10	22046926	201531449	41667924	22	42362										
ABCA12	26154	hgsc.bcm.edu	37	chr2	215813394	215813394	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	ttcttccacagttaccaggtCatctaaggcatcttcctgag	7	12	4	1	rs373723120		TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr2:215813394C>T	ENST00000272895.7	-	47	7249	c.7030G>A	c.(7030-7032)Gac>Aac	p.D2344N	ABCA12_ENST00000389661.4_Missense_Mutation_p.D2026N|AC072062.1_ENST00000607412.1_RNA	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	2344	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		GTTACCAGGTCATCTAAGGCA	0.383																																					p.D2344N	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											.	ABCA12	368	.	0			c.G7030A						.	C	ASN/ASP,ASN/ASP	0,4406		0,0,2203	102	94	97		6076,7030	5.5	1	2		97	1,8599		0,1,4299	no	missense,missense	ABCA12	NM_015657.3,NM_173076.2	23,23	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	2026/2278,2344/2596	215813394	1,13005	2203	4300	6503	SO:0001583	missense	26154	exon47			CCAGGTCATCTAA	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.7030G>A	chr2.hg19:g.215813394C>T	ENSP00000272895:p.Asp2344Asn	140.0	0.0		159.0	59.0	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	hg19	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.282329	0.80692	0.0	1.16E-4	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.93763	-3.28;-3.28	5.48	5.48	0.80851	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.64402	D	0.000004	D	0.92100	0.7496	L	0.39147	1.195	0.80722	D	1	B;P	0.40794	0.437;0.729	B;B	0.43251	0.241;0.413	D	0.92755	0.6219	10	0.72032	D	0.01	.	19.387	0.94560	0.0:1.0:0.0:0.0	.	2344;2026	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	N	2344;2026	ENSP00000272895:D2344N;ENSP00000374312:D2026N	ENSP00000272895:D2344N	D	-	1	0	ABCA12	215521639	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.521000	0.45563	2.572000	0.86782	0.655000	0.94253	GAC	.	.		0.383	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		T	215813394	C	T	215813394	3	4	289	1	0	0	0	0	1	0	0	0	30	826	29	3	785	3	ABCA12	2	215813394	Missense_Mutation	SNP	C	TCGA-G3-A6UC-01A-21D-A33K-10	14281945	215813394	27385979	23	42363										
SP140	11262	hgsc.bcm.edu	37	chr2	231090583	231090583	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	gcccagcagggccagcagggGcagatggcaagtggagacag	18	10	0	2			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr2:231090583G>A	ENST00000392045.3	+	1	138	c.24G>A	c.(22-24)ggG>ggA	p.G8G	SP110_ENST00000540870.1_5'Flank|SP140_ENST00000343805.6_Silent_p.G8G|SP140_ENST00000420434.3_Silent_p.G8G|SP140_ENST00000350136.5_5'UTR|SP140_ENST00000417495.3_Silent_p.G8G|SP140_ENST00000373645.3_Silent_p.G8G|SP140_ENST00000486687.2_Silent_p.G8G	NM_007237.4	NP_009168.4	Q13342	SP140_HUMAN	SP140 nuclear body protein	8					defense response (GO:0006952)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.G8G(2)		NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	12		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		GCCAGCAGGGGCAGATGGCAA	0.547																																					p.G8G		Atlas-SNP	.											SP140_ENST00000392045,NS,carcinoma,+1,2	SP140	121	.	2	Substitution - coding silent(2)	lung(2)	c.G24A						.						160	130	140					2																	231090583		2203	4300	6503	SO:0001819	synonymous_variant	11262	exon1			GCAGGGGCAGATG	U63420	CCDS33392.1, CCDS42831.1, CCDS63149.1, CCDS63150.1, CCDS63151.1	2q37.1	2013-01-28			ENSG00000079263	ENSG00000079263		"Zinc fingers, PHD-type"	17133	protein-coding gene	gene with protein product		608602				8695863, 8910577, 12368356	Standard	NM_001005176		Approved	LYSP100-B, LYSP100-A	uc002vql.3	Q13342	OTTHUMG00000153670	ENST00000392045.3:c.24G>A	chr2.hg19:g.231090583G>A		72.0	1.0		100.0	38.0	NM_007237	E7ESH9|E7EUR5|E9PFJ6|Q0VGE5|Q13341|Q3KR17|Q4ZG66|Q53TG1|Q6NSG4|Q92881|Q96TG3	Silent	SNP	ENST00000392045.3	hg19	CCDS42831.1																																																																																			.	.		0.547	SP140-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000332015.1	NM_007237		A	231090583	G	A	231090583	2	1	289	1	0	0	0	0	0	0	0	1	14977	1190	42	3		3	SP140	2	231090583	Silent	SNP	G	TCGA-G3-A6UC-01A-21D-A33K-10	15277189	231090583	12108790	24	42364										
CNTN6	27255	hgsc.bcm.edu	37	chr3	1189706	1189706	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	agtggaaatgaggttgctatGgaaactggtaattctgctgc	13	5	1	1	rs144055237		TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr3:1189706G>A	ENST00000446702.2	+	2	641	c.14G>A	c.(13-15)tGg>tAg	p.W5*	CNTN6_ENST00000539053.1_Intron|CNTN6_ENST00000350110.2_Nonsense_Mutation_p.W5*			Q9UQ52	CNTN6_HUMAN	contactin 6	5					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		AGGTTGCTATGGAAACTGGTA	0.343																																					p.W5X		Atlas-SNP	.											.	CNTN6	245	.	0			c.G14A						.						117	122	120					3																	1189706		2203	4300	6503	SO:0001587	stop_gained	27255	exon2			TGCTATGGAAACT	AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	2176	protein-coding gene	gene with protein product	"neural adhesion molecule"	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.14G>A	chr3.hg19:g.1189706G>A	ENSP00000407822:p.Trp5*	122.0	0.0		171.0	62.0	NM_014461	Q2KHM2	Nonsense_Mutation	SNP	ENST00000446702.2	hg19	CCDS2557.1	.	.	.	.	.	.	.	.	.	.	G	40	8.466839	0.98825	.	.	ENSG00000134115	ENST00000446702;ENST00000350110	.	.	.	5.49	5.49	0.81192	.	0.484634	0.19560	N	0.111341	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	17.5615	0.87909	0.0:0.0:1.0:0.0	.	.	.	.	X	5	.	ENSP00000341882:W5X	W	+	2	0	CNTN6	1164706	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.679000	0.68160	2.571000	0.86741	0.655000	0.94253	TGG	.	G|1.000;C|0.000		0.343	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461		A	1189706	G	A	1189706	4	1	289	1	0	0	0	0	0	1	0	0	3647	1357	47	3	16	3	CNTN6	3	1189706	Nonsense_Mutation	SNP	G	TCGA-G3-A6UC-01A-21D-A33K-10		1189706	196832724	25	42365										
FANCD2	2177	hgsc.bcm.edu	37	chr3	10136948	10136948	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	gctgcttcatcacctgtgtgGgcattccaaggtaagaaggg	13	9	2	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr3:10136948G>A	ENST00000419585.1	+	41	4189	c.4028G>A	c.(4027-4029)gGg>gAg	p.G1343E	FANCD2_ENST00000287647.3_Missense_Mutation_p.G1343E|FANCD2_ENST00000383807.1_Missense_Mutation_p.G1343E|FANCD2OS_ENST00000524279.1_Intron|FANCD2OS_ENST00000436517.1_5'UTR|FANCD2_ENST00000383806.1_3'UTR			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2	1343					DNA repair (GO:0006281)|gamete generation (GO:0007276)|response to gamma radiation (GO:0010332)|synapsis (GO:0007129)	condensed chromosome (GO:0000793)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA polymerase binding (GO:0070182)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	51				OV - Ovarian serous cystadenocarcinoma(96;0.148)		CACCTGTGTGGGCATTCCAAG	0.463			"D, Mis, N, F"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.G1343E		Atlas-SNP	.	yes	Rec		Fanconi anaemia D2	3	3p26	2177	"Fanconi anemia, complementation group D2"		L	.	FANCD2	253	.	0			c.G4028A						.						79	74	76					3																	10136948		2203	4300	6503	SO:0001583	missense	2177	exon41	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TGTGTGGGCATTC	AF340183	CCDS2595.1, CCDS33696.1	3p25.3	2014-09-17		2001-10-05	ENSG00000144554	ENSG00000144554		"Fanconi anemia, complementation groups"	3585	protein-coding gene	gene with protein product		613984		FACD, FANCD		7581463, 11239453, 18475298	Standard	XM_005264946		Approved	FAD, FA-D2	uc003buw.3	Q9BXW9	OTTHUMG00000128670	ENST00000419585.1:c.4028G>A	chr3.hg19:g.10136948G>A	ENSP00000398754:p.Gly1343Glu	110.0	0.0		117.0	58.0	NM_001018115	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	Missense_Mutation	SNP	ENST00000419585.1	hg19	CCDS33696.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.041157	0.93685	.	.	ENSG00000144554	ENST00000287647;ENST00000383807;ENST00000419585	T;T;T	0.65178	-0.14;-0.14;-0.14	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.81054	0.4743	M	0.80982	2.52	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.81974	-0.0687	10	0.66056	D	0.02	.	17.9953	0.89181	0.0:0.0:1.0:0.0	.	1343;1343	Q9BXW9-2;Q9BXW9	.;FACD2_HUMAN	E	1343	ENSP00000287647:G1343E;ENSP00000373318:G1343E;ENSP00000398754:G1343E	ENSP00000287647:G1343E	G	+	2	0	FANCD2	10111948	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.409000	0.97331	2.856000	0.98102	0.644000	0.83932	GGG	.	.		0.463	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339873.1			A	10136948	G	A	10136948	3	1	289	1	0	0	0	0	1	0	0	0	5673	1232	43	3	4186	3	FANCD2	3	10136948	Missense_Mutation	SNP	G	TCGA-G3-A6UC-01A-21D-A33K-10	8947242	10136948	187885482	26	42366										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266100	41266100	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	agcaacagtcttacctggacTctggaatccattctggtgcc	9	12	3	0	rs121913416		TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr3:41266100T>C	ENST00000349496.5	+	3	377	c.97T>C	c.(97-99)Tct>Cct	p.S33P	CTNNB1_ENST00000396183.3_Missense_Mutation_p.S33P|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S33P|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S33P|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S26P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	33			Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> F (in PTR, MDB and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10666372}.|S -> L (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> Y (in colorectal cancer and PTR; enhances transactivation of target genes). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:9065402}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.S33P(47)|p.S33A(16)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.W25_D32del(4)|p.S33L(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S33N(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.D32fs*9(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.S29_H36del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.D32_S33insS(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.S33T(1)|p.D32_H36>D(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TTACCTGGACTCTGGAATCCA	0.488		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S33P	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,-1,1	CTNNB1	4904	.	212	Deletion - In frame(115)|Substitution - Missense(70)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)|Insertion - In frame(1)	liver(130)|large_intestine(20)|endometrium(14)|stomach(10)|pituitary(9)|pancreas(9)|central_nervous_system(8)|adrenal_gland(2)|small_intestine(2)|biliary_tract(2)|skin(2)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|breast(1)	c.T97C						.						93	77	82					3																	41266100		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	CTGGACTCTGGAA	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.97T>C	chr3.hg19:g.41266100T>C	ENSP00000344456:p.Ser33Pro	183.0	0.0		154.0	70.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.395782	0.83011	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.50548	0.74;0.74;0.74;0.74;0.74;0.74;0.74;0.74;0.74	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.70281	0.3206	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74509	-0.3642	10	0.87932	D	0	-10.7796	16.0677	0.80897	0.0:0.0:0.0:1.0	.	33	P35222	CTNB1_HUMAN	P	26;33;33;33;33;26;33;33;33	ENSP00000400508:S26P;ENSP00000385604:S33P;ENSP00000412219:S33P;ENSP00000379486:S33P;ENSP00000344456:S33P;ENSP00000411226:S26P;ENSP00000379488:S33P;ENSP00000409302:S33P;ENSP00000401599:S33P	ENSP00000344456:S33P	S	+	1	0	CTNNB1	41241104	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.201000	0.70794	0.533000	0.62120	TCT	.	.		0.488	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266100	T	C	41266100	3	2	289	1	0	0	0	0	1	0	0	0	4018	1551	54	2	103	2	CTNNB1	3	41266100	Missense_Mutation	SNP	T	TCGA-G3-A6UC-01A-21D-A33K-10	31129152	41266100	156756330	27	42367										
DNAH1	25981	hgsc.bcm.edu	37	chr3	52434364	52434364	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	cactatcaaccacaggacacTctaccaactatgtcattgct	4	14	3	0			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr3:52434364T>A	ENST00000420323.2	+	78	12961	c.12700T>A	c.(12700-12702)Tct>Act	p.S4234T		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	4299					cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		CACAGGACACTCTACCAACTA	0.557																																					p.S4234T		Atlas-SNP	.											.	DNAH1	534	.	0			c.T12700A						.						211	219	217					3																	52434364		2111	4254	6365	SO:0001583	missense	25981	exon78			GGACACTCTACCA	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.12700T>A	chr3.hg19:g.52434364T>A	ENSP00000401514:p.Ser4234Thr	87.0	0.0		78.0	34.0	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	hg19	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	T	34	5.324886	0.95708	.	.	ENSG00000114841	ENST00000420323	T	0.62639	0.01	5.73	5.73	0.89815	.	0.000000	0.49916	D	0.000137	D	0.86251	0.5888	H	0.96943	3.91	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90918	0.4781	10	0.87932	D	0	.	16.0101	0.80396	0.0:0.0:0.0:1.0	.	4234	C9JXH6	.	T	4234	ENSP00000401514:S4234T	ENSP00000401514:S4234T	S	+	1	0	DNAH1	52409404	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.010000	0.88615	2.185000	0.69588	0.533000	0.62120	TCT	.	.		0.557	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		A	52434364	T	A	52434364	3	1	289	1	0	0	0	0	1	0	0	0	4599	1551	54	4	13006	4	DNAH1	3	52434364	Missense_Mutation	SNP	T	TCGA-G3-A6UC-01A-21D-A33K-10	11168264	52434364	145588066	28	42368										
PBRM1	55193	hgsc.bcm.edu	37	chr3	52598201	52598201	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	tgtcattttctggtatttcaGttggcctgcaggagaggaag	13	6	3	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr3:52598201G>A	ENST00000296302.7	-	23	3741	c.3740C>T	c.(3739-3741)aCt>aTt	p.T1247I	PBRM1_ENST00000409767.1_Missense_Mutation_p.T1262I|SMIM4_ENST00000476842.1_Intron|PBRM1_ENST00000409057.1_Missense_Mutation_p.T1247I|PBRM1_ENST00000409114.3_Missense_Mutation_p.T1262I|PBRM1_ENST00000337303.4_Missense_Mutation_p.T1247I|PBRM1_ENST00000394830.3_Missense_Mutation_p.T1222I|PBRM1_ENST00000356770.4_Missense_Mutation_p.T1215I|PBRM1_ENST00000410007.1_Missense_Mutation_p.T1222I			Q86U86	PB1_HUMAN	polybromo 1	1247	BAH 2. {ECO:0000255|PROSITE- ProRule:PRU00370}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TGGTATTTCAGTTGGCCTGCA	0.398			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																p.T1222I		Atlas-SNP	.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1	1252	.	0			c.C3665T						.						96	95	95					3																	52598201		2203	4300	6503	SO:0001583	missense	55193	exon24			ATTTCAGTTGGCC	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.3740C>T	chr3.hg19:g.52598201G>A	ENSP00000296302:p.Thr1247Ile	79.0	0.0		70.0	31.0	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Missense_Mutation	SNP	ENST00000296302.7	hg19		.	.	.	.	.	.	.	.	.	.	G	27.6	4.846718	0.91277	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351	D;D;D;D;D;D;D;D;D	0.85484	-1.99;-1.99;-1.99;-1.99;-1.99;-1.99;-1.99;-1.99;-1.99	5.43	5.43	0.79202	Bromo adjacent homology (BAH) domain (3);	0.000000	0.85682	D	0.000000	D	0.91382	0.7281	L	0.56769	1.78	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;0.999;1.0;0.999;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.97110	0.998;0.994;0.997;0.994;0.999;1.0;0.997;0.996	D	0.91831	0.5475	10	0.72032	D	0.01	-11.6219	19.2735	0.94021	0.0:0.0:1.0:0.0	.	1222;1222;1247;1262;1262;1247;1215;1247	Q86U86-9;Q86U86-4;Q86U86-2;Q86U86-8;Q86U86-7;Q86U86;Q86U86-3;Q86U86-5	.;.;.;.;.;PB1_HUMAN;.;.	I	1215;1222;1247;1247;1247;1222;1262;1262;1246	ENSP00000349213:T1215I;ENSP00000378307:T1222I;ENSP00000296302:T1247I;ENSP00000338302:T1247I;ENSP00000386593:T1247I;ENSP00000386529:T1222I;ENSP00000386643:T1262I;ENSP00000386601:T1262I;ENSP00000387775:T1246I	ENSP00000296302:T1247I	T	-	2	0	PBRM1	52573241	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.549000	0.85964	0.655000	0.94253	ACT	.	.		0.398	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165		A	52598201	G	A	52598201	3	1	289	1	0	0	0	0	1	0	0	0	11500	1029	36	3	1192	3	PBRM1	3	52598201	Missense_Mutation	SNP	G	TCGA-G3-A6UC-01A-21D-A33K-10	163837	52598201	145424229	29	42369										
NSUN3	63899	hgsc.bcm.edu	37	chr3	93802963	93802963	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	atttctagggagatactaacAtctccatcatgctggcaata	7	9	3	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr3:93802963A>G	ENST00000314622.4	+	3	346	c.135A>G	c.(133-135)acA>acG	p.T45T		NM_022072.3	NP_071355.1	Q9H649	NSUN3_HUMAN	NOP2/Sun domain family, member 3	45							methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|skin(1)	18						AGATACTAACATCTCCATCAT	0.343																																					p.T45T		Atlas-SNP	.											.	NSUN3	33	.	0			c.A135G						.						41	42	41					3																	93802963		2202	4300	6502	SO:0001819	synonymous_variant	63899	exon3			ACTAACATCTCCA	BC020602	CCDS2927.1	3q11.2	2009-11-23	2009-11-23		ENSG00000178694	ENSG00000178694		"NOP2/Sun domain containing"	26208	protein-coding gene	gene with protein product			"NOL1/NOP2/Sun domain family 3", "NOL1/NOP2/Sun domain family, member 3"			12477932	Standard	NM_022072		Approved	FLJ22609	uc003drl.1	Q9H649	OTTHUMG00000159025	ENST00000314622.4:c.135A>G	chr3.hg19:g.93802963A>G		126.0	0.0		117.0	48.0	NM_022072	Q6PG41|Q8IXG9|Q9H6M2	Silent	SNP	ENST00000314622.4	hg19	CCDS2927.1																																																																																			.	.		0.343	NSUN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352934.1	NM_022072		G	93802963	A	G	93802963	2	3	289	1	0	0	0	0	0	0	0	1	10688	204	8	2		2	NSUN3	3	93802963	Silent	SNP	A	TCGA-G3-A6UC-01A-21D-A33K-10	41204762	93802963	104219467	30	42370										
SENP7	57337	hgsc.bcm.edu	37	chr3	101058948	101058948	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	attgtacttacttaaggtaaAaatcaatgattacatcatta	4	5	2	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr3:101058948A>T	ENST00000394095.2	-	16	2401	c.2348T>A	c.(2347-2349)tTt>tAt	p.F783Y	SENP7_ENST00000314261.7_Missense_Mutation_p.F717Y|SENP7_ENST00000394094.2_Missense_Mutation_p.F718Y|SENP7_ENST00000348610.3_Missense_Mutation_p.F750Y|SENP7_ENST00000358203.3_Missense_Mutation_p.F619Y|SENP7_ENST00000394091.1_Missense_Mutation_p.F619Y	NM_001282802.1|NM_020654.3	NP_001269731.1|NP_065705.3	Q9BQF6	SENP7_HUMAN	SUMO1/sentrin specific peptidase 7	783	Protease.					intracellular (GO:0005622)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)			breast(2)|endometrium(1)|kidney(1)|large_intestine(16)|lung(15)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						CTTAAGGTAAAAATCAATGAT	0.299																																					p.F783Y		Atlas-SNP	.											.	SENP7	170	.	0			c.T2348A						.						44	42	43					3																	101058948		2201	4285	6486	SO:0001583	missense	57337	exon16			AGGTAAAAATCAA		CCDS2941.2, CCDS43121.1, CCDS63704.1, CCDS63705.1, CCDS63706.1	3q12	2008-02-05	2005-08-17		ENSG00000138468	ENSG00000138468			30402	protein-coding gene	gene with protein product		612846	"SUMO1/sentrin specific protease 7"			11214970, 11230166	Standard	NM_001282802		Approved		uc003dut.3	Q9BQF6	OTTHUMG00000149927	ENST00000394095.2:c.2348T>A	chr3.hg19:g.101058948A>T	ENSP00000377655:p.Phe783Tyr	258.0	0.0		293.0	116.0	NM_020654	A1L3A5|A8MW39|B7WNW8|Q7Z3F4|Q96PS5|Q9C0F6|Q9HBT5	Missense_Mutation	SNP	ENST00000394095.2	hg19	CCDS2941.2	.	.	.	.	.	.	.	.	.	.	A	25.7	4.666480	0.88251	.	.	ENSG00000138468	ENST00000394095;ENST00000394094;ENST00000314261;ENST00000394091;ENST00000358203;ENST00000348610	T;T;T;T;T;T	0.38722	1.12;1.12;1.12;1.12;1.12;1.12	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.69133	0.3077	M	0.87328	2.875	0.80722	D	1	D;D;D;P	0.89917	1.0;1.0;1.0;0.886	D;D;D;P	0.97110	0.997;1.0;0.999;0.863	T	0.75852	-0.3171	10	0.87932	D	0	-14.6007	15.1096	0.72346	1.0:0.0:0.0:0.0	.	619;717;750;783	Q9BQF6-4;Q9BQF6-5;Q9BQF6-2;Q9BQF6	.;.;.;SENP7_HUMAN	Y	783;718;717;619;619;750	ENSP00000377655:F783Y;ENSP00000377654:F718Y;ENSP00000313624:F717Y;ENSP00000377651:F619Y;ENSP00000350936:F619Y;ENSP00000342159:F750Y	ENSP00000313624:F717Y	F	-	2	0	SENP7	102541638	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.215000	0.89762	2.106000	0.64143	0.460000	0.39030	TTT	.	.		0.299	SENP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313957.2	NM_020654		T	101058948	A	T	101058948	3	4	289	1	0	0	0	0	1	0	0	0	14066	14	1	4	840	4	SENP7	3	101058948	Missense_Mutation	SNP	A	TCGA-G3-A6UC-01A-21D-A33K-10	7255985	101058948	96963482	31	42371										
ZDHHC23	254887	hgsc.bcm.edu	37	chr3	113667674	113667674	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	cacagaagggcagtatgaagCctgtgaagaaaaagaaaacc	11	7	0	5			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr3:113667674C>T	ENST00000330212.3	+	2	324	c.25C>T	c.(25-27)Cct>Tct	p.P9S	ZDHHC23_ENST00000498275.1_Missense_Mutation_p.P3S|RP11-255E6.6_ENST00000609657.1_RNA	NM_173570.3	NP_775841.2	Q8IYP9	ZDH23_HUMAN	zinc finger, DHHC-type containing 23	9					protein localization to plasma membrane (GO:0072659)|protein palmitoylation (GO:0018345)	integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|urinary_tract(2)	16						CAGTATGAAGCCTGTGAAGAA	0.468																																					p.P9S		Atlas-SNP	.											.	ZDHHC23	38	.	0			c.C25T						.						128	128	128					3																	113667674		2203	4300	6503	SO:0001583	missense	254887	exon2			ATGAAGCCTGTGA	AK127025	CCDS33827.1	3q13.31	2008-05-02			ENSG00000184307	ENSG00000184307		"Zinc fingers, DHHC-type"	28654	protein-coding gene	gene with protein product						12477932	Standard	NM_173570		Approved	MGC42530	uc003eau.3	Q8IYP9	OTTHUMG00000159335	ENST00000330212.3:c.25C>T	chr3.hg19:g.113667674C>T	ENSP00000330485:p.Pro9Ser	48.0	0.0		65.0	29.0	NM_173570	D3DN76	Missense_Mutation	SNP	ENST00000330212.3	hg19	CCDS33827.1	.	.	.	.	.	.	.	.	.	.	C	14.87	2.663884	0.47572	.	.	ENSG00000184307	ENST00000330212;ENST00000498275;ENST00000491556	T;T;T	0.41400	1.01;1.02;1.0	4.86	1.83	0.25207	.	0.667620	0.14416	N	0.320967	T	0.20373	0.0490	N	0.08118	0	0.29581	N	0.84919	B	0.02656	0.0	B	0.04013	0.001	T	0.12319	-1.0552	10	0.49607	T	0.09	-2.555	5.7672	0.18233	0.1978:0.6182:0.0:0.184	.	9	Q8IYP9	ZDH23_HUMAN	S	9;3;9	ENSP00000330485:P9S;ENSP00000417840:P3S;ENSP00000420292:P9S	ENSP00000330485:P9S	P	+	1	0	ZDHHC23	115150364	0.695000	0.27747	0.945000	0.38365	0.632000	0.37999	0.490000	0.22403	0.650000	0.30769	0.591000	0.81541	CCT	.	.		0.468	ZDHHC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354702.1	NM_173570		T	113667674	C	T	113667674	3	4	289	1	0	0	0	0	1	0	0	0	17629	739	26	3	27	3	ZDHHC23	3	113667674	Missense_Mutation	SNP	C	TCGA-G3-A6UC-01A-21D-A33K-10	12608726	113667674	84354756	32	42372										
QTRTD1	79691	hgsc.bcm.edu	37	chr3	113785076	113785076	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	ttttctgttttgcttacagaGcagaacatcatgaagtcttg	8	7	3	3			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr3:113785076G>A	ENST00000281273.4	+	4	459	c.202G>A	c.(202-204)Gca>Aca	p.A68T	QTRTD1_ENST00000479882.1_5'UTR|QTRTD1_ENST00000493014.1_Intron|QTRTD1_ENST00000485050.1_Splice_Site_p.A80T|QTRTD1_ENST00000466050.1_3'UTR	NM_024638.3	NP_078914.1			queuine tRNA-ribosyltransferase domain containing 1											central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|skin(2)	10						TGCTTACAGAGCAGAACATCA	0.328																																					p.A80T		Atlas-SNP	.											.	QTRTD1	29	.	0			c.G238A						.						121	122	122					3																	113785076		2203	4300	6503	SO:0001630	splice_region_variant	79691	exon3			TACAGAGCAGAAC	AK023022	CCDS33828.1, CCDS58846.1, CCDS58845.1, CCDS58844.1	3q13.31	2010-11-16			ENSG00000151576	ENSG00000151576			25771	protein-coding gene	gene with protein product						12477932	Standard	NM_024638		Approved	FLJ12960	uc003eaz.4	Q9H974	OTTHUMG00000159336	ENST00000281273.4:c.201-1G>A	chr3.hg19:g.113785076G>A		50.0	0.0		59.0	27.0	NM_001256835		Missense_Mutation	SNP	ENST00000281273.4	hg19	CCDS33828.1	.	.	.	.	.	.	.	.	.	.	G	17.54	3.414500	0.62511	.	.	ENSG00000151576	ENST00000472599;ENST00000485050;ENST00000281273;ENST00000482307	.	.	.	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.61887	0.2383	L	0.58302	1.8	0.80722	D	1	P;B	0.45986	0.87;0.23	P;B	0.44561	0.453;0.082	T	0.62393	-0.6864	9	0.45353	T	0.12	-15.1412	19.9595	0.97236	0.0:0.0:1.0:0.0	.	82;68	C9JJ71;Q9H974	.;QTRD1_HUMAN	T	82;80;68;68	.	ENSP00000281273:A68T	A	+	1	0	QTRTD1	115267766	1.000000	0.71417	1.000000	0.80357	0.298000	0.27526	8.486000	0.90451	2.706000	0.92434	0.563000	0.77884	GCA	.	.		0.328	QTRTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354708.2	NM_024638	Missense_Mutation	A	113785076	G	A	113785076	5	1	289	1	0	0	0	0	0	0	1	0	12901	985	34	3	208	3	QTRTD1	3	113785076	Splice_Site	SNP	G	TCGA-G3-A6UC-01A-21D-A33K-10	117402	113785076	84237354	33	42373										
COL6A5	256076	hgsc.bcm.edu	37	chr3	130129336	130129336	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	gtagaagtggacagaaagggGtgcaaggcagtcctagttcc	15	7	0	2	rs371782483		TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr3:130129336G>T	ENST00000432398.2	+	20	5124	c.4630G>T	c.(4630-4632)Gtg>Ttg	p.V1544L	COL6A5_ENST00000265379.6_Missense_Mutation_p.V1544L	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	1544	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						ACAGAAAGGGGTGCAAGGCAG	0.398																																					p.V1544L		Atlas-SNP	.											.	COL6A5	205	.	0			c.G4630T						.						106	86	92					3																	130129336		692	1591	2283	SO:0001583	missense	256076	exon20			AAAGGGGTGCAAG	AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"Collagens"	26674	protein-coding gene	gene with protein product	"von Willebrand factor A domain containing 4"	611916	"collagen, type XXIX, alpha 1"	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.4630G>T	chr3.hg19:g.130129336G>T	ENSP00000390895:p.Val1544Leu	98.0	0.0		129.0	57.0	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	hg19		.	.	.	.	.	.	.	.	.	.	G	2.169	-0.390423	0.04932	.	.	ENSG00000172752	ENST00000432398;ENST00000265379	D;D	0.93763	-3.22;-3.28	5.73	-8.29	0.01009	.	.	.	.	.	T	0.80717	0.4676	N	0.05158	-0.105	0.09310	N	1	B	0.06786	0.001	B	0.11329	0.006	T	0.67473	-0.5662	9	0.25106	T	0.35	.	9.7336	0.40376	0.189:0.1004:0.6119:0.0987	.	1544	A8TX70-2	.	L	1544	ENSP00000390895:V1544L;ENSP00000265379:V1544L	ENSP00000265379:V1544L	V	+	1	0	COL6A5	131612026	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-1.003000	0.03682	-1.514000	0.01786	-0.806000	0.03193	GTG	.	.		0.398	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264		T	130129336	G	T	130129336	3	4	289	1	0	0	0	0	1	0	0	0	3704	1261	44	3	4704	3	COL6A5	3	130129336	Missense_Mutation	SNP	G	TCGA-G3-A6UC-01A-21D-A33K-10	16344260	130129336	67893094	34	42374										
CLSTN2	64084	hgsc.bcm.edu	37	chr3	140281700	140281700	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	aggtgctacatcacatccgcTaccgcaactggcgtccggct	10	15	1	0			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr3:140281700T>G	ENST00000458420.3	+	14	2450	c.2260T>G	c.(2260-2262)Tac>Gac	p.Y754D		NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	754					homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						TCACATCCGCTACCGCAACTG	0.557										HNSCC(16;0.037)																											p.Y754D	GBM(45;858 913 3709 36904 37282)	Atlas-SNP	.											.	CLSTN2	190	.	0			c.T2260G						.						58	55	56					3																	140281700		2203	4300	6503	SO:0001583	missense	64084	exon14			ATCCGCTACCGCA	AJ278018	CCDS3112.1	3q23	2011-07-01			ENSG00000158258	ENSG00000158258		"Cadherins / Cadherin-related"	17448	protein-coding gene	gene with protein product	"cadherin-related family member 13"	611323				12498782	Standard	NM_022131		Approved	CSTN2, CS2, FLJ39113, CDHR13	uc003etn.3	Q9H4D0	OTTHUMG00000160139	ENST00000458420.3:c.2260T>G	chr3.hg19:g.140281700T>G	ENSP00000402460:p.Tyr754Asp	116.0	0.0		121.0	47.0	NM_022131	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Missense_Mutation	SNP	ENST00000458420.3	hg19	CCDS3112.1	.	.	.	.	.	.	.	.	.	.	T	16.61	3.172363	0.57584	.	.	ENSG00000158258	ENST00000458420	T	0.34859	1.34	4.83	4.83	0.62350	.	0.000000	0.85682	D	0.000000	T	0.62612	0.2442	M	0.86097	2.795	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.67979	-0.5530	9	.	.	.	-29.2093	12.6334	0.56669	0.0:0.0:0.0:1.0	.	754	Q9H4D0	CSTN2_HUMAN	D	754	ENSP00000402460:Y754D	.	Y	+	1	0	CLSTN2	141764390	1.000000	0.71417	0.994000	0.49952	0.177000	0.22998	7.997000	0.88414	1.926000	0.55796	0.460000	0.39030	TAC	.	.		0.557	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131		G	140281700	T	G	140281700	3	3	289	1	0	0	0	0	1	0	0	0	3564	1522	53	5	2314	5	CLSTN2	3	140281700	Missense_Mutation	SNP	T	TCGA-G3-A6UC-01A-21D-A33K-10	10152364	140281700	57740730	35	42375										
CCDC39	339829	hgsc.bcm.edu	37	chr3	180359906	180359906	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	tgttttcttttttctagggaAagaacttcttctgccttact	6	8	4	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr3:180359906A>T	ENST00000442201.2	-	13	1868	c.1749T>A	c.(1747-1749)ctT>ctA	p.L583L	CCDC39_ENST00000273654.4_Silent_p.L667L	NM_181426.1	NP_852091.1	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	583					axonemal dynein complex assembly (GO:0070286)|cilium-dependent cell motility (GO:0060285)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)				NS(1)|breast(1)|endometrium(4)|large_intestine(9)|lung(22)|ovary(6)|prostate(2)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			TTTCTAGGGAAAGAACTTCTT	0.348																																					p.L583L		Atlas-SNP	.											.	CCDC39	242	.	0			c.T1749A						.						143	126	132					3																	180359906		1836	4087	5923	SO:0001819	synonymous_variant	339829	exon13			TAGGGAAAGAACT	BC047103	CCDS46964.1	3q26.33	2012-07-27			ENSG00000145075	ENSG00000145075			25244	protein-coding gene	gene with protein product		613798				21131972	Standard	NM_181426		Approved	DKFZp434A128, CILD14, FAP59	uc010hxe.3	Q9UFE4	OTTHUMG00000157857	ENST00000442201.2:c.1749T>A	chr3.hg19:g.180359906A>T		83.0	0.0		102.0	42.0	NM_181426	B4E2H1	Silent	SNP	ENST00000442201.2	hg19	CCDS46964.1																																																																																			.	.		0.348	CCDC39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349783.3	XM_291028		T	180359906	A	T	180359906	2	4	289	1	0	0	0	0	0	0	0	1	2813	1	1	4		4	CCDC39	3	180359906	Silent	SNP	A	TCGA-G3-A6UC-01A-21D-A33K-10	40078206	180359906	17662524	36	42376										
MAP6D1	79929	hgsc.bcm.edu	37	chr3	183543020	183543020	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	ggcgccgggcgcaggtggcgCggaggactgcgcggaggatt	22	10	0	0			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr3:183543020C>T	ENST00000318631.3	-	1	346	c.316G>A	c.(316-318)Gcg>Acg	p.A106T	MAP6D1_ENST00000431348.1_Missense_Mutation_p.A106T|MAP6D1_ENST00000463801.1_5'Flank	NM_024871.2	NP_079147.1	Q9H9H5	MA6D1_HUMAN	MAP6 domain containing 1	106					dendrite morphogenesis (GO:0048813)|lysosome localization (GO:0032418)|microtubule cytoskeleton organization (GO:0000226)|N-terminal peptidyl-L-cysteine N-palmitoylation (GO:0018009)|negative regulation of microtubule depolymerization (GO:0007026)	cis-Golgi network (GO:0005801)|Golgi-associated vesicle (GO:0005798)|microtubule (GO:0005874)				endometrium(1)|lung(1)	2	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;5.15e-42)|Epithelial(37;4.29e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			GCAGGTGGCGCGGAGGACTGC	0.761																																					p.A106T		Atlas-SNP	.											.	MAP6D1	2	.	0			c.G316A						.						2	3	3					3																	183543020		1478	3110	4588	SO:0001583	missense	79929	exon1			GTGGCGCGGAGGA	BC006434	CCDS3247.1	3q27.1	2005-12-22			ENSG00000180834	ENSG00000180834			25753	protein-coding gene	gene with protein product		610593				12477932	Standard	NM_024871		Approved	FLJ12748	uc003fmc.2	Q9H9H5	OTTHUMG00000156900	ENST00000318631.3:c.316G>A	chr3.hg19:g.183543020C>T	ENSP00000314560:p.Ala106Thr	30.0	0.0		23.0	10.0	NM_024871		Missense_Mutation	SNP	ENST00000318631.3	hg19	CCDS3247.1	.	.	.	.	.	.	.	.	.	.	C	12.11	1.841073	0.32513	.	.	ENSG00000180834	ENST00000318631;ENST00000431348	T;T	0.17370	2.28;2.28	2.46	2.46	0.29980	.	.	.	.	.	T	0.20047	0.0482	N	0.17082	0.46	0.24707	N	0.993226	D	0.71674	0.998	D	0.64410	0.925	T	0.09100	-1.0690	9	0.41790	T	0.15	.	7.2828	0.26320	0.0:0.7231:0.2769:0.0	.	106	Q9H9H5	MA6D1_HUMAN	T	106	ENSP00000314560:A106T;ENSP00000388945:A106T	ENSP00000314560:A106T	A	-	1	0	MAP6D1	185025714	.	.	0.017000	0.16124	0.053000	0.15095	.	.	1.684000	0.51022	0.455000	0.32223	GCG	.	.		0.761	MAP6D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346516.1	NM_024871		T	183543020	C	T	183543020	3	4	289	1	0	0	0	0	1	0	0	0	9274	768	27	1	295	1	MAP6D1	3	183543020	Missense_Mutation	SNP	C	TCGA-G3-A6UC-01A-21D-A33K-10	3183114	183543020	14479410	37	42377										
UBXN7	26043	hgsc.bcm.edu	37	chr3	196159225	196159226	+	In_Frame_Ins	INS	-	-	CCC													0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	gtggtgaactgttgaattaaINSccccttcagcgccgaggacg							TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr3:196159225_196159226insCCC	ENST00000296328.4	-	1	119_120	c.45_46insGGG	c.(43-48)gggtta>gggGGGtta	p.15_16insG	UBXN7_ENST00000535858.1_5'UTR|UBXN7_ENST00000428095.1_5'UTR|UBXN7-AS1_ENST00000442941.1_RNA|UBXN7-AS1_ENST00000598881.1_RNA	NM_015562.1	NP_056377.1	O94888	UBXN7_HUMAN	UBX domain protein 7	15						Cdc48p-Npl4p-Ufd1p AAA ATPase complex (GO:0034098)|nucleus (GO:0005634)	transcription factor binding (GO:0008134)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)			NS(1)|endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	18						TGTTGAATTAACCCCTTCAGCG	0.668																																					p.L16delinsGL		Atlas-Indel,Pindel	.											.	UBXN7	43	.	0			c.46_47insGGG						.																																			SO:0001652	inframe_insertion	26043	exon1			.	AB018337	CCDS43191.1	3q29	2012-07-06	2008-07-25	2008-07-25	ENSG00000163960	ENSG00000163960		"UBX domain containing"	29119	protein-coding gene	gene with protein product			"UBX domain containing 7"	UBXD7		9872452, 22537386	Standard	NM_015562		Approved	KIAA0794	uc003fwm.4	O94888	OTTHUMG00000155639	ENST00000296328.4:c.43_45dupGGG	chr3.hg19:g.196159226_196159228dupCCC	ENSP00000296328:p.Gly15_Gly15dup	154.0	0.0		152.0	58.0	NM_015562	D3DXB3|Q6ZP77|Q86X20|Q8N327	In_Frame_Ins	INS	ENST00000296328.4	hg19	CCDS43191.1																																																																																			.	.		0.668	UBXN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340938.2	XM_087353		CCC	196159226	-	CCC	196159225	7	5	289	1	0	1	1	0	0	0	0	0	16933	40	2	0	1467	0	UBXN7	3	196159225	In_Frame_Ins	INS	-	TCGA-G3-A6UC-01A-21D-A33K-10	12616205	196159225	1863205	38	42378										
HTT	3064	hgsc.bcm.edu	37	chr4	3241784	3241784	+	Nonstop_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	tccacaaggtcaccacctgcTgagcgccatggtgggagaga	13	12	1	2			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr4:3241784T>A	ENST00000355072.5	+	67	9572	c.9427T>A	c.(9427-9429)Tga>Aga	p.*3143R		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	0					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		CACCACCTGCTGAGCGCCATG	0.622																																					p.X3143R		Atlas-SNP	.											.	HTT	221	.	0			c.T9427A						.						27	29	28					4																	3241784		2042	4182	6224	SO:0001578	stop_lost	3064	exon67			ACCTGCTGAGCGC	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.9427T>A	chr4.hg19:g.3241784T>A	ENSP00000347184:p.*3143Argext*8	88.0	0.0		81.0	44.0	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	hg19	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	T	11.71	1.720000	0.30503	.	.	ENSG00000197386	ENST00000355072	.	.	.	5.32	4.06	0.47325	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.2101	0.48793	0.0:0.0:0.1534:0.8466	.	.	.	.	R	3143	.	.	X	+	1	0	HTT	3211582	1.000000	0.71417	0.980000	0.43619	0.329000	0.28539	5.982000	0.70532	1.984000	0.57885	0.533000	0.62120	TGA	.	.		0.622	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		A	3241784	T	A	3241784	4	1	289	1	0	0	0	0	0	0	0	0	7466	1593	55	4	9693	4	HTT	4	3241784	Nonstop_Mutation	SNP	T	TCGA-G3-A6UC-01A-21D-A33K-10		3241784	187912492	39	42379										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79373018	79373018	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	gagaaggcaacagattgattGacaagtcattttccatcagc	9	8	2	4			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr4:79373018G>C	ENST00000264895.6	+	46	6996	c.6556G>C	c.(6556-6558)Gac>Cac	p.D2186H		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	2186					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						CAGATTGATTGACAAGTCATT	0.348																																					p.D2186H		Atlas-SNP	.											.	FRAS1	779	.	0			c.G6556C						.						115	108	110					4																	79373018		1841	4095	5936	SO:0001583	missense	80144	exon46			TTGATTGACAAGT	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.6556G>C	chr4.hg19:g.79373018G>C	ENSP00000264895:p.Asp2186His	56.0	0.0		55.0	20.0	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000264895.6	hg19	CCDS54771.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.2|20.2	3.943607|3.943607	0.73672|0.73672	.|.	.|.	ENSG00000138759|ENSG00000138759	ENST00000264895|ENST00000512123	T|.	0.56776|.	0.44|.	5.65|5.65	4.81|4.81	0.61882|0.61882	.|.	0.280610|.	0.38272|.	N|.	0.001743|.	T|.	0.74884|.	0.3775|.	M|M	0.78916|0.78916	2.43|2.43	0.80722|0.80722	D|D	1|1	B|.	0.25955|.	0.138|.	B|.	0.14578|.	0.011|.	T|.	0.76350|.	-0.2991|.	10|.	0.72032|.	D|.	0.01|.	.|.	14.5744|14.5744	0.68235|0.68235	0.0706:0.0:0.9294:0.0|0.0706:0.0:0.9294:0.0	.|.	2186|.	E9PHH6|.	.|.	H|S	2186|414	ENSP00000264895:D2186H|.	ENSP00000264895:D2186H|.	D|X	+|+	1|2	0|2	FRAS1|FRAS1	79592042|79592042	1.000000|1.000000	0.71417|0.71417	0.060000|0.060000	0.19600|0.19600	0.886000|0.886000	0.51366|0.51366	5.672000|5.672000	0.68102|0.68102	1.390000|1.390000	0.46547|0.46547	0.591000|0.591000	0.81541|0.81541	GAC|TGA	.	.		0.348	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	79373018	G	C	79373018	3	2	289	1	0	0	0	0	1	0	0	0	6050	1290	45	4	6813	4	FRAS1	4	79373018	Missense_Mutation	SNP	G	TCGA-G3-A6UC-01A-21D-A33K-10	76131234	79373018	111781258	40	42380										
PRDM8	56978	hgsc.bcm.edu	37	chr4	81123282	81123282	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	cagcaggaggcacctttaggCccgggtcccaagttttgcaa	12	12	0	0			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr4:81123282C>A	ENST00000504452.1	+	8	1505	c.666C>A	c.(664-666)ggC>ggA	p.G222G	PRDM8_ENST00000415738.2_Silent_p.G222G|PRDM8_ENST00000339711.4_Silent_p.G222G			Q9NQV8	PRDM8_HUMAN	PR domain containing 8	222	Gly-rich.				corpus callosum morphogenesis (GO:0021540)|corticospinal tract morphogenesis (GO:0021957)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(2)	10						CACCTTTAGGCCCGGGTCCCA	0.701											OREG0016246	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G222G		Atlas-SNP	.											.	PRDM8	44	.	0			c.C666A						.						16	22	20					4																	81123282		2003	4165	6168	SO:0001819	synonymous_variant	56978	exon4			TTTAGGCCCGGGT	AF275815	CCDS43243.1	4q21	2008-08-21				ENSG00000152784			13993	protein-coding gene	gene with protein product							Standard	NM_020226		Approved		uc003hmc.4	Q9NQV8		ENST00000504452.1:c.666C>A	chr4.hg19:g.81123282C>A		213.0	0.0	1203	154.0	67.0	NM_001099403	A8K7X2|Q6IQ36	Silent	SNP	ENST00000504452.1	hg19	CCDS43243.1																																																																																			.	.		0.701	PRDM8-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362793.1			A	81123282	C	A	81123282	2	1	289	1	0	0	0	0	0	0	0	1	12474	726	26	3		3	PRDM8	4	81123282	Silent	SNP	C	TCGA-G3-A6UC-01A-21D-A33K-10	1750264	81123282	110030994	41	42381										
DSPP	1834	hgsc.bcm.edu	37	chr4	88537080	88537088	+	In_Frame_Del	DEL	ACAGCAGCA	ACAGCAGCA	-													0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	tgaaagcagtgatagcagtgAcagcagcaatagcagtgaca					rs367717407|rs201754564|rs370267258|rs553101049	byFrequency	TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	ACAGCAGCA	ACAGCAGCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr4:88537080_88537088delACAGCAGCA	ENST00000282478.7	+	4	3299_3307	c.3266_3274delACAGCAGCA	c.(3265-3276)gacagcagcaat>gat	p.SSN1090del	DSPP_ENST00000399271.1_In_Frame_Del_p.SSN1090del|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1090	Asp/Ser-rich.			Missing (in Ref. 1; AAF42472 and 3; AAD16120). {ECO:0000305}.	biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			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)		gatagcagtgacagcagcaatagcagtga	0.536																																					p.1089_1091del		Atlas-INDEL	.											.	DSPP	174	.	0			c.3265_3273del						.			1444,630		641,162,234						0.5	0			23	2259,1617		893,473,572	no	coding	DSPP	NM_014208.3		1534,635,806	A1A1,A1R,RR		41.7183,30.3761,37.7647				3703,2247				SO:0001651	inframe_deletion	1834	exon5			.	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3266_3274delACAGCAGCA	chr4.hg19:g.88537080_88537088delACAGCAGCA	ENSP00000282478:p.Ser1090_Asn1092del	75.0	0.0		84.0	20.0	NM_014208	A8MUI0|O95815	In_Frame_Del	DEL	ENST00000282478.7	hg19	CCDS43248.1																																																																																			.	.		0.536	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		-	88537088	ACAGCAGCA	-	88537080	7	5	289	1	0	1	0	1	0	0	0	0	4784	275	10	0	3280	0	DSPP	4	88537080	In_Frame_Del	DEL	ACAGCAGCA	TCGA-G3-A6UC-01A-21D-A33K-10	7413798	88537080	102617196	42	42382										
PPAP2A	8611	hgsc.bcm.edu	37	chr5	54763785	54763785	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	gatttttgaccaatctggatCacaaacatccaagaagtgag	8	8	2	3			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr5:54763785C>T	ENST00000307259.8	-	3	823	c.403G>A	c.(403-405)Gat>Aat	p.D135N	PPAP2A_ENST00000264775.5_Missense_Mutation_p.D136N|PPAP2A_ENST00000515132.1_5'UTR	NM_003711.2	NP_003702.2	O14494	LPP1_HUMAN	phosphatidic acid phosphatase type 2A	135					androgen receptor signaling pathway (GO:0030521)|germ cell migration (GO:0008354)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|lipid metabolic process (GO:0006629)|negative regulation of cell proliferation (GO:0008285)|phospholipid dephosphorylation (GO:0046839)|protein dephosphorylation (GO:0006470)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of lipid metabolic process (GO:0019216)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidate phosphatase activity (GO:0008195)			breast(2)|endometrium(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)	9		Lung NSC(810;4.08e-05)|Prostate(74;0.0181)|Breast(144;0.0544)				CAATCTGGATCACAAACATCC	0.433																																					p.D136N		Atlas-SNP	.											.	PPAP2A	42	.	0			c.G406A						.						148	144	145					5																	54763785		2203	4300	6503	SO:0001583	missense	8611	exon3			CTGGATCACAAAC	AB000888	CCDS34159.1, CCDS34160.1	5q11	2009-05-27			ENSG00000067113	ENSG00000067113	3.1.3.4		9228	protein-coding gene	gene with protein product		607124				9305923	Standard	NM_003711		Approved	PAP-2a, LPP1	uc003jpz.4	O14494	OTTHUMG00000162240	ENST00000307259.8:c.403G>A	chr5.hg19:g.54763785C>T	ENSP00000302229:p.Asp135Asn	83.0	0.0		76.0	31.0	NM_176895	B7ZKN8|G3XA95|O60457|O60463|Q17RZ4	Missense_Mutation	SNP	ENST00000307259.8	hg19	CCDS34159.1	.	.	.	.	.	.	.	.	.	.	C	11.07	1.530184	0.27387	.	.	ENSG00000067113	ENST00000264775;ENST00000307259	T;T	0.74737	-0.87;-0.87	5.58	1.53	0.23141	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.388937	0.31976	N	0.006774	T	0.50565	0.1623	N	0.17723	0.515	0.26385	N	0.97668	B;B	0.06786	0.001;0.001	B;B	0.11329	0.006;0.006	T	0.23261	-1.0193	10	0.10902	T	0.67	-10.4161	5.3051	0.15799	0.0:0.3753:0.2239:0.4009	.	135;136	O14494;G3XA95	LPP1_HUMAN;.	N	136;135	ENSP00000264775:D136N;ENSP00000302229:D135N	ENSP00000264775:D136N	D	-	1	0	PPAP2A	54799542	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	2.492000	0.45311	0.395000	0.25257	0.573000	0.79308	GAT	.	.		0.433	PPAP2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368073.1			T	54763785	C	T	54763785	3	4	289	1	0	0	0	0	1	0	0	0	12299	826	29	3	467	3	PPAP2A	5	54763785	Missense_Mutation	SNP	C	TCGA-G3-A6UC-01A-21D-A33K-10		54763785	126151475	43	42383										
ANKRD55	79722	hgsc.bcm.edu	37	chr5	55472050	55472050	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	aatattggctcccatcttcaAcagcagcttcactgtgtccg	7	13	3	0			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr5:55472050A>G	ENST00000341048.4	-	4	392	c.241T>C	c.(241-243)Ttg>Ctg	p.L81L	ANKRD55_ENST00000504958.2_Silent_p.L81L|ANKRD55_ENST00000513241.2_Silent_p.L52L	NM_024669.2	NP_078945.2	Q3KP44	ANR55_HUMAN	ankyrin repeat domain 55	81										breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(1)	34		Lung NSC(810;8.69e-05)|Prostate(74;0.00634)|Breast(144;0.0334)|Ovarian(174;0.223)				CCCATCTTCAACAGCAGCTTC	0.507																																					p.L81L		Atlas-SNP	.											.	ANKRD55	70	.	0			c.T241C						.						180	152	161					5																	55472050		2203	4300	6503	SO:0001819	synonymous_variant	79722	exon4			TCTTCAACAGCAG	AK021857	CCDS34161.1	5q11.2	2013-01-10			ENSG00000164512	ENSG00000164512		"Ankyrin repeat domain containing"	25681	protein-coding gene	gene with protein product		615189					Standard	XM_005248599		Approved	FLJ11795	uc003jqu.3	Q3KP44	OTTHUMG00000162305	ENST00000341048.4:c.241T>C	chr5.hg19:g.55472050A>G		76.0	0.0		100.0	41.0	NM_024669	B3KVT8|Q3KP45|Q9HAD3	Silent	SNP	ENST00000341048.4	hg19	CCDS34161.1																																																																																			.	.		0.507	ANKRD55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368510.4	NM_024669		G	55472050	A	G	55472050	2	3	289	1	0	0	0	0	0	0	0	1	681	40	2	2		2	ANKRD55	5	55472050	Silent	SNP	A	TCGA-G3-A6UC-01A-21D-A33K-10	708265	55472050	125443210	44	42384										
ALDH7A1	501	hgsc.bcm.edu	37	chr5	125896800	125896800	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	atggcattgtttcctccaagTtccaacagacttctccctta	5	13	1	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr5:125896800T>C	ENST00000409134.3	-	10	1107	c.888A>G	c.(886-888)gaA>gaG	p.E296E	ALDH7A1_ENST00000447989.2_Silent_p.E323E|ALDH7A1_ENST00000553117.1_Silent_p.E296E	NM_001182.4|NM_001201377.1	NP_001173.2|NP_001188306.1	P49419	AL7A1_HUMAN	aldehyde dehydrogenase 7 family, member A1	296					cellular aldehyde metabolic process (GO:0006081)|cellular nitrogen compound metabolic process (GO:0034641)|glycine betaine biosynthetic process from choline (GO:0019285)|lysine catabolic process (GO:0006554)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|betaine-aldehyde dehydrogenase activity (GO:0008802)|L-aminoadipate-semialdehyde dehydrogenase activity (GO:0004043)			endometrium(1)|kidney(4)|large_intestine(4)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	16		all_cancers(142;0.24)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0417)|OV - Ovarian serous cystadenocarcinoma(64;0.068)|all cancers(49;0.109)		TTCCTCCAAGTTCCAACAGAC	0.353																																					p.E323E		Atlas-SNP	.											.	ALDH7A1	57	.	0			c.A969G						.						116	111	113					5																	125896800		2203	4300	6503	SO:0001819	synonymous_variant	501	exon10			TCCAAGTTCCAAC	S74728	CCDS4137.2, CCDS56380.1	5q31	2013-06-03			ENSG00000164904	ENSG00000164904	1.2.1.31	"Aldehyde dehydrogenases"	877	protein-coding gene	gene with protein product	"antiquitin 1", "26g turgor protein homolog", "alpha-aminoadipic semialdehyde dehydrogenase", "alpha-AASA dehydrogenase", "delta1-piperideine-6-carboxylate dehydrogenease", "P6c dehydrogenase"	107323		ATQ1		9417906	Standard	NM_001182		Approved	EPD, PDE	uc003ktx.3	P49419	OTTHUMG00000128942	ENST00000409134.3:c.888A>G	chr5.hg19:g.125896800T>C		473.0	0.0		505.0	172.0	NM_001202404	B2R669|B4DIC7|B4DMA0|E7EPT3|O14619|Q6IPU8|Q9BUL4	Silent	SNP	ENST00000409134.3	hg19	CCDS4137.2																																																																																			.	.		0.353	ALDH7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250921.2	NM_001182		C	125896800	T	C	125896800	2	2	289	1	0	0	0	0	0	0	0	1	504	1722	60	2		2	ALDH7A1	5	125896800	Silent	SNP	T	TCGA-G3-A6UC-01A-21D-A33K-10	70424750	125896800	55018460	45	42385										
PRSS16	10279	hgsc.bcm.edu	37	chr6	27222637	27222637	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	gacccctggggctaacaaagTgctgtttgttaatggtgagc	13	8	0	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr6:27222637T>C	ENST00000230582.3	+	10	1331	c.1316T>C	c.(1315-1317)gTg>gCg	p.V439A	PRSS16_ENST00000377456.2_Intron|PRSS16_ENST00000421826.2_Missense_Mutation_p.V182A	NM_005865.3	NP_005856.1	Q9NQE7	TSSP_HUMAN	protease, serine, 16 (thymus)	439					protein catabolic process (GO:0030163)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|lysosome (GO:0005764)	serine-type peptidase activity (GO:0008236)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	26						GCTAACAAAGTGCTGTTTGTT	0.552																																					p.V439A	NSCLC(178;1118 2105 17078 23587 44429)	Atlas-SNP	.											.	PRSS16	66	.	0			c.T1316C						.						90	85	87					6																	27222637		2203	4300	6503	SO:0001583	missense	10279	exon10			ACAAAGTGCTGTT	AF052514	CCDS4623.1	6p21	2010-05-07			ENSG00000112812	ENSG00000112812		"Serine peptidases / Serine peptidases"	9480	protein-coding gene	gene with protein product		607169				10527559	Standard	NM_005865		Approved	TSSP	uc003nja.3	Q9NQE7	OTTHUMG00000016167	ENST00000230582.3:c.1316T>C	chr6.hg19:g.27222637T>C	ENSP00000230582:p.Val439Ala	55.0	0.0		181.0	63.0	NM_005865	O75416	Missense_Mutation	SNP	ENST00000230582.3	hg19	CCDS4623.1	.	.	.	.	.	.	.	.	.	.	T	18.40	3.616447	0.66672	.	.	ENSG00000112812	ENST00000421826;ENST00000230582	T;T	0.22336	1.96;1.96	4.68	4.68	0.58851	.	0.353251	0.29908	N	0.010891	T	0.39462	0.1079	M	0.88979	2.995	0.34944	D	0.750551	D;P	0.67145	0.996;0.926	D;P	0.66847	0.947;0.56	T	0.52909	-0.8512	10	0.87932	D	0	-25.4079	10.7158	0.46011	0.0:0.0:0.0:1.0	.	182;439	F2Z2N5;Q9NQE7	.;TSSP_HUMAN	A	182;439	ENSP00000404349:V182A;ENSP00000230582:V439A	ENSP00000230582:V439A	V	+	2	0	PRSS16	27330616	0.997000	0.39634	0.622000	0.29159	0.875000	0.50365	3.619000	0.54196	2.106000	0.64143	0.455000	0.32223	GTG	.	.		0.552	PRSS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043418.2			C	27222637	T	C	27222637	3	2	289	1	0	0	0	0	1	0	0	0	12628	1696	59	2	1354	2	PRSS16	6	27222637	Missense_Mutation	SNP	T	TCGA-G3-A6UC-01A-21D-A33K-10		27222637	143892430	46	42386										
ATF6B	1388	hgsc.bcm.edu	37	chr6	32084267	32084267	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	aaagagttaccattgggggcCatggcaggcatcaccaggga	14	9	1	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr6:32084267C>T	ENST00000375203.3	-	17	1904	c.1872G>A	c.(1870-1872)atG>atA	p.M624I	ATF6B_ENST00000375201.4_Missense_Mutation_p.M621I	NM_001136153.1|NM_004381.4	NP_001129625.1|NP_004372.3	Q99941	ATF6B_HUMAN	activating transcription factor 6 beta	624					response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.M624I(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	22						CATTGGGGGCCATGGCAGGCA	0.632																																					p.M624I		Atlas-SNP	.											ATF6B,NS,carcinoma,0,1	ATF6B	40	.	1	Substitution - Missense(1)	kidney(1)	c.G1872A						.						114	92	100					6																	32084267		2203	4300	6503	SO:0001583	missense	1388	exon17			GGGGGCCATGGCA		CCDS47408.1, CCDS4737.1	6p21.3	2013-01-10	2008-10-21	2008-10-21	ENSG00000213676	ENSG00000213676		"basic leucine zipper proteins"	2349	protein-coding gene	gene with protein product		600984	"cAMP responsive element binding protein-like 1"	CREBL1		11256944, 14973138	Standard	NM_004381		Approved	G13	uc003nzn.3	Q99941	OTTHUMG00000031296	ENST00000375203.3:c.1872G>A	chr6.hg19:g.32084267C>T	ENSP00000364349:p.Met624Ile	61.0	0.0		175.0	54.0	NM_004381	B0UYX6|Q13269|Q14343|Q14345|Q5SSW7|Q99635|Q99637|Q9H3V9|Q9H3W1|Q9NPL0	Missense_Mutation	SNP	ENST00000375203.3	hg19	CCDS4737.1	.	.	.	.	.	.	.	.	.	.	C	15.66	2.898994	0.52227	.	.	ENSG00000213676	ENST00000375203;ENST00000375201	T;T	0.56611	0.45;1.2	5.45	5.45	0.79879	.	0.000000	0.85682	U	0.000000	T	0.46983	0.1421	N	0.25485	0.75	0.51482	D	0.999929	D;P;D	0.58268	0.982;0.533;0.969	D;B;D	0.68943	0.961;0.186;0.914	T	0.32052	-0.9921	10	0.13853	T	0.58	-14.2841	16.7853	0.85573	0.0:1.0:0.0:0.0	.	621;624;624	Q99941-2;Q99941;Q6AZW6	.;ATF6B_HUMAN;.	I	624;621	ENSP00000364349:M624I;ENSP00000364347:M621I	ENSP00000364347:M621I	M	-	3	0	ATF6B	32192245	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	2.646000	0.46630	2.574000	0.86865	0.467000	0.42956	ATG	.	.		0.632	ATF6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076638.2			T	32084267	C	T	32084267	3	4	289	1	0	0	0	0	1	0	0	0	1085	594	21	3	247	3	ATF6B	6	32084267	Missense_Mutation	SNP	C	TCGA-G3-A6UC-01A-21D-A33K-10	4861630	32084267	139030800	47	42387										
NOTCH4	4855	hgsc.bcm.edu	37	chr6	32166274	32166274	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	agcatggctgcctgagggagCgccccacagccaccactcag	12	16	1	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr6:32166274C>A	ENST00000375023.3	-	26	4818	c.4680G>T	c.(4678-4680)gcG>gcT	p.A1560A	NOTCH4_ENST00000443903.2_5'Flank|GPSM3_ENST00000375043.3_5'Flank	NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	1560					cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						CCTGAGGGAGCGCCCCACAGC	0.582																																					p.A1560A		Atlas-SNP	.											.	NOTCH4	201	.	0			c.G4680T						.						64	54	58					6																	32166274		1511	2709	4220	SO:0001819	synonymous_variant	4855	exon26			AGGGAGCGCCCCA		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"Ankyrin repeat domain containing"	7884	protein-coding gene	gene with protein product		164951	"Notch (Drosophila) homolog 4", "Notch homolog 4 (Drosophila)"	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.4680G>T	chr6.hg19:g.32166274C>A		99.0	0.0		176.0	67.0	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Silent	SNP	ENST00000375023.3	hg19	CCDS34420.1																																																																																			.	.		0.582	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2			A	32166274	C	A	32166274	2	1	289	1	0	0	0	0	0	0	0	1	10560	755	27	1		1	NOTCH4	6	32166274	Silent	SNP	C	TCGA-G3-A6UC-01A-21D-A33K-10	82007	32166274	138948793	48	42388										
ZNF318	24149	hgsc.bcm.edu	37	chr6	43306248	43306248	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	ttcagcctctttgtcaatcaTtagcaagttgggctgtttta	8	8	4	0			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr6:43306248T>G	ENST00000361428.2	-	10	5565	c.5488A>C	c.(5488-5490)Atg>Ctg	p.M1830L	ZNF318_ENST00000318149.3_Intron	NM_014345.2	NP_055160.2	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	1830					meiotic nuclear division (GO:0007126)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(21)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	61			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)			TTGTCAATCATTAGCAAGTTG	0.413																																					p.M1830L		Atlas-SNP	.											.	ZNF318	175	.	0			c.A5488C						.						152	139	143					6																	43306248		2203	4300	6503	SO:0001583	missense	24149	exon10			CAATCATTAGCAA	AF090114	CCDS4895.2	6p21.1	2013-09-19			ENSG00000171467	ENSG00000171467		"Zinc fingers, C2H2-type"	13578	protein-coding gene	gene with protein product						10873617	Standard	NM_014345		Approved	HRIHFB2436, ZFP318	uc003oux.3	Q5VUA4	OTTHUMG00000014732	ENST00000361428.2:c.5488A>C	chr6.hg19:g.43306248T>G	ENSP00000354964:p.Met1830Leu	136.0	0.0		272.0	61.0	NM_014345	O94796|Q4G0E4|Q8NEM6|Q9UNU8|Q9Y2W9	Missense_Mutation	SNP	ENST00000361428.2	hg19	CCDS4895.2	.	.	.	.	.	.	.	.	.	.	T	7.537	0.659805	0.14645	.	.	ENSG00000171467	ENST00000361428	T	0.11277	2.79	5.3	1.44	0.22558	.	0.595915	0.16372	N	0.217300	T	0.01765	0.0056	N	0.24115	0.695	0.09310	N	0.999993	B	0.12630	0.006	B	0.08055	0.003	T	0.45234	-0.9275	10	0.46703	T	0.11	0.3088	2.6744	0.05077	0.1478:0.0808:0.1544:0.617	.	1830	Q5VUA4	ZN318_HUMAN	L	1830	ENSP00000354964:M1830L	ENSP00000354964:M1830L	M	-	1	0	ZNF318	43414226	0.000000	0.05858	0.017000	0.16124	0.497000	0.33675	-0.005000	0.12855	0.073000	0.16731	0.455000	0.32223	ATG	.	.		0.413	ZNF318-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040601.2	NM_014345		G	43306248	T	G	43306248	3	3	289	1	0	0	0	0	1	0	0	0	17851	1493	52	5	1355	5	ZNF318	6	43306248	Missense_Mutation	SNP	T	TCGA-G3-A6UC-01A-21D-A33K-10	11139974	43306248	127808819	49	42389										
ZUFSP	221302	hgsc.bcm.edu	37	chr6	116972883	116972883	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	catagattgaatttttggaaTgcaaggaatcaacataccta	7	6	1	2			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr6:116972883T>A	ENST00000368576.3	-	7	1411	c.1168A>T	c.(1168-1170)Att>Ttt	p.I390F	ZUFSP_ENST00000471919.1_5'Flank	NM_145062.2	NP_659499.2	Q96AP4	ZUFSP_HUMAN	zinc finger with UFM1-specific peptidase domain	390							metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(6)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	21				GBM - Glioblastoma multiforme(226;0.0258)|all cancers(137;0.0368)|OV - Ovarian serous cystadenocarcinoma(136;0.0464)|Epithelial(106;0.186)		ATTTTTGGAATGCAAGGAATC	0.368																																					p.I390F		Atlas-SNP	.											.	ZUFSP	46	.	0			c.A1168T						.						64	62	62					6																	116972883		2203	4300	6503	SO:0001583	missense	221302	exon7			TTGGAATGCAAGG	AK054582	CCDS5110.1	6q22.31	2013-01-28	2008-03-25	2008-03-25	ENSG00000153975	ENSG00000153975		"Zinc fingers, C2H2-type"	21224	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 113"	C6orf113			Standard	NM_145062		Approved	dJ412I7.3	uc003pxf.2	Q96AP4	OTTHUMG00000015445	ENST00000368576.3:c.1168A>T	chr6.hg19:g.116972883T>A	ENSP00000357565:p.Ile390Phe	29.0	0.0		51.0	46.0	NM_145062	Q5TD92|Q6PJH7|Q96NV6	Missense_Mutation	SNP	ENST00000368576.3	hg19	CCDS5110.1	.	.	.	.	.	.	.	.	.	.	T	26.3	4.725083	0.89298	.	.	ENSG00000153975	ENST00000368576	T	0.42900	0.96	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.66228	0.2768	M	0.91818	3.245	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.73883	-0.3842	10	0.52906	T	0.07	-17.8576	15.8443	0.78876	0.0:0.0:0.0:1.0	.	390	Q96AP4	ZUFSP_HUMAN	F	390	ENSP00000357565:I390F	ENSP00000357565:I390F	I	-	1	0	ZUFSP	117079576	1.000000	0.71417	0.998000	0.56505	0.981000	0.71138	4.601000	0.61090	2.194000	0.70268	0.528000	0.53228	ATT	.	.		0.368	ZUFSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041961.1	NM_145062		A	116972883	T	A	116972883	3	1	289	1	0	0	0	0	1	0	0	0	18261	1464	51	4	584	4	ZUFSP	6	116972883	Missense_Mutation	SNP	T	TCGA-G3-A6UC-01A-21D-A33K-10	73666635	116972883	54142184	50	42390										
ZBTB2	57621	hgsc.bcm.edu	37	chr6	151687721	151687722	+	Missense_Mutation	DNP	CC	CC	TA													0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	cttatcctggaggtctgtggCcgtggatctcgcccgagttt							TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr6:151687721_151687722CC>TA	ENST00000325144.4	-	3	619_620	c.479_480GG>TA	c.(478-480)cGG>cTA	p.R160L		NM_020861.1	NP_065912.1	Q8N680	ZBTB2_HUMAN	zinc finger and BTB domain containing 2	160					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|large_intestine(2)|lung(6)|skin(1)	12			BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.63e-11)		AGGTCTGTGGCCGTGGATCTCG	0.525																																					p.R160R|p.R160L		Atlas-SNP	.											.	ZBTB2	30	.	0			c.G480A|c.G479T						.																																			SO:0001583	missense	57621	exon3			CTGTGGCCGTGGA|TGTGGCCGTGGAT	BC020172	CCDS5231.1	6q25.1	2013-01-09			ENSG00000181472	ENSG00000181472		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	20868	protein-coding gene	gene with protein product						10819331	Standard	NM_020861		Approved	KIAA1483, ZNF437, bA351K16.2	uc003qoh.3	Q8N680	OTTHUMG00000015834	ENST00000325144.4:c.479_480delinsTA	chr6.hg19:g.151687721_151687722delinsTA	ENSP00000323183:p.Arg160Leu	95.0|96.0	0.0		54.0	46.0	NM_020861	A8K7C7|Q5SZ81|Q9P245	Silent|Missense_Mutation	SNP	ENST00000325144.4	hg19	CCDS5231.1																																																																																			.	.		0.525	ZBTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042715.1	NM_020861		TA	151687722	CC	TA	151687721	3	4	289	1	0	0	0	0	1	0	0	0	17543	726	26	3	1068	3	ZBTB2	6	151687721	Missense_Mutation	DNP	CC	TCGA-G3-A6UC-01A-21D-A33K-10	34714838	151687721	19427346	51	42391										
TNRC18	84629	hgsc.bcm.edu	37	chr7	5352548	5352548	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	gaggaggaggaggaggaggaTgaggacgaggaagaggagga	24	1	0	2	rs112615228		TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr7:5352548T>G	ENST00000430969.1	-	27	8322	c.7974A>C	c.(7972-7974)tcA>tcC	p.S2658S	TNRC18_ENST00000399537.4_Silent_p.S2658S	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2658	Ser-rich.						chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		aggaggaggatgaggacgagg	0.617																																					p.S2658S		Atlas-SNP	.											.	TNRC18	311	.	0			c.A7974C						.						7	7	7					7																	5352548		1528	3528	5056	SO:0001819	synonymous_variant	84629	exon27			GGAGGATGAGGAC	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"Trinucleotide (CAG) repeat containing"	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.7974A>C	chr7.hg19:g.5352548T>G		32.0	0.0		28.0	14.0	NM_001080495	A8MX41|Q96JH1|Q96K91	Silent	SNP	ENST00000430969.1	hg19	CCDS47534.1	.	.	.	.	.	.	.	.	.	.	N	0.011	-1.737644	0.00681	.	.	ENSG00000182095	ENST00000399544	.	.	.	.	.	.	.	.	.	.	.	T	0.63379	0.2506	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63655	-0.6588	3	0.87932	D	0	.	.	.	.	.	.	.	.	P	1171	.	ENSP00000382459:H1171P	H	-	2	0	TNRC18	5319074	0.757000	0.28394	0.042000	0.18584	0.026000	0.11368	0.000000	0.12993	0.000000	0.14550	0.000000	0.15137	CAT	.	T|0.500;A|0.500		0.617	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				G	5352548	T	G	5352548	2	3	289	1	0	0	0	0	0	0	0	1	16354	1451	51	5		5	TNRC18	7	5352548	Silent	SNP	T	TCGA-G3-A6UC-01A-21D-A33K-10		5352548	153786115	52	42392										
TRA2A	29896	hgsc.bcm.edu	37	chr7	23545860	23545860	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	acctccacctccaccgccgcCgcctcctccaccacccccac	3	28	0	0			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr7:23545860C>G	ENST00000297071.4	-	6	883	c.667G>C	c.(667-669)Ggc>Cgc	p.G223R	TRA2A_ENST00000474586.1_5'Flank|TRA2A_ENST00000538367.1_Missense_Mutation_p.G122R|TRA2A_ENST00000392502.4_Missense_Mutation_p.G122R	NM_013293.3	NP_037425.1	Q13595	TRA2A_HUMAN	transformer 2 alpha homolog (Drosophila)	223	Linker.				mRNA splicing, via spliceosome (GO:0000398)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	10						ccaccgccgccgcctcctcca	0.448																																					p.G223R	Pancreas(121;2137 2973 46590)	Atlas-SNP	.											TRA2A,NS,carcinoma,0,1	TRA2A	29	.	0			c.G667C						.						40	40	40					7																	23545860		2203	4300	6503	SO:0001583	missense	29896	exon6			CGCCGCCGCCTCC	U53209	CCDS5383.1, CCDS64609.1, CCDS75569.1	7p15.3	2014-02-12			ENSG00000164548	ENSG00000164548		"RNA binding motif (RRM) containing"	16645	protein-coding gene	gene with protein product		602718				8799144, 9546399	Standard	XM_005249725		Approved	htra-2-alpha, tra2a, AWMS1	uc003swi.3	Q13595	OTTHUMG00000128459	ENST00000297071.4:c.667G>C	chr7.hg19:g.23545860C>G	ENSP00000297071:p.Gly223Arg	76.0	0.0		116.0	40.0	NM_013293	B4DUA9	Missense_Mutation	SNP	ENST00000297071.4	hg19	CCDS5383.1	.	.	.	.	.	.	.	.	.	.	C	12.48	1.951265	0.34471	.	.	ENSG00000164548	ENST00000297071;ENST00000392502;ENST00000538367	T;T;T	0.75050	-0.9;-0.9;-0.9	5.33	5.33	0.75918	.	0.289069	0.37095	N	0.002242	T	0.75568	0.3867	N	0.17474	0.49	0.80722	D	1	D	0.71674	0.998	D	0.71656	0.974	T	0.71384	-0.4609	10	0.15952	T	0.53	-4.9705	18.6991	0.91614	0.0:1.0:0.0:0.0	.	223	Q13595	TRA2A_HUMAN	R	223;122;122	ENSP00000297071:G223R;ENSP00000376290:G122R;ENSP00000441116:G122R	ENSP00000297071:G223R	G	-	1	0	TRA2A	23512385	0.964000	0.33143	0.502000	0.27614	0.046000	0.14306	2.321000	0.43805	2.499000	0.84300	0.585000	0.79938	GGC	.	.		0.448	TRA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250257.1	NM_013293		G	23545860	C	G	23545860	3	3	289	1	0	0	0	0	1	0	0	0	16448	652	23	4	193	4	TRA2A	7	23545860	Missense_Mutation	SNP	C	TCGA-G3-A6UC-01A-21D-A33K-10	18193312	23545860	135592803	53	42393										
BLVRA	644	hgsc.bcm.edu	37	chr7	43846653	43846653	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	cttccatttcaagtctgggtCcttggagaatgtgccaaatg	10	9	2	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr7:43846653C>G	ENST00000402924.1	+	9	873	c.710C>G	c.(709-711)tCc>tGc	p.S237C	BLVRA_ENST00000265523.4_Missense_Mutation_p.S237C	NM_001253823.1	NP_001240752.1	P53004	BIEA_HUMAN	biliverdin reductase A	237					heme catabolic process (GO:0042167)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound metabolic process (GO:0006778)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	biliverdin reductase activity (GO:0004074)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(4)|lung(4)|ovary(1)|stomach(2)	12						AAGTCTGGGTCCTTGGAGAAT	0.378																																					p.S237C		Atlas-SNP	.											.	BLVRA	26	.	0			c.C710G						.						63	62	62					7																	43846653		2203	4300	6503	SO:0001583	missense	644	exon9			CTGGGTCCTTGGA	BC008456	CCDS5472.1	7p13	2012-10-02			ENSG00000106605	ENSG00000106605	1.3.1.24		1062	protein-coding gene	gene with protein product		109750		BLVR			Standard	NM_001253823		Approved		uc003tir.3	P53004	OTTHUMG00000128953	ENST00000402924.1:c.710C>G	chr7.hg19:g.43846653C>G	ENSP00000385757:p.Ser237Cys	56.0	0.0		72.0	26.0	NM_001253823	A8K747|O95019|Q86UX0|Q96QL4|Q9BRW8	Missense_Mutation	SNP	ENST00000402924.1	hg19	CCDS5472.1	.	.	.	.	.	.	.	.	.	.	C	9.002	0.980396	0.18812	.	.	ENSG00000106605	ENST00000265523;ENST00000402924	T;T	0.24350	1.86;1.86	4.25	3.29	0.37713	Biliverdin reductase, catalytic (2);	0.405752	0.28847	N	0.013951	T	0.14442	0.0349	N	0.24115	0.695	0.24634	N	0.9936	B	0.11235	0.004	B	0.08055	0.003	T	0.07849	-1.0751	10	0.45353	T	0.12	.	5.3361	0.15959	0.0:0.6038:0.2765:0.1197	.	237	P53004	BIEA_HUMAN	C	237	ENSP00000265523:S237C;ENSP00000385757:S237C	ENSP00000265523:S237C	S	+	2	0	BLVRA	43813178	0.309000	0.24518	0.998000	0.56505	0.985000	0.73830	1.394000	0.34509	2.076000	0.62316	0.462000	0.41574	TCC	.	.		0.378	BLVRA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339006.1	NM_000712		G	43846653	C	G	43846653	3	3	289	1	0	0	0	0	1	0	0	0	1451	855	30	4	736	4	BLVRA	7	43846653	Missense_Mutation	SNP	C	TCGA-G3-A6UC-01A-21D-A33K-10	20300793	43846653	115292010	54	42394										
ZNF716	441234	hgsc.bcm.edu	37	chr7	57529339	57529339	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	atgtggcaaagcctttagctTaccctcaaccttcacttacc	5	14	2	0			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr7:57529339T>A	ENST00000420713.1	+	4	1284	c.1172T>A	c.(1171-1173)tTa>tAa	p.L391*		NM_001159279.1	NP_001152751.1	A6NP11	ZN716_HUMAN	zinc finger protein 716	391					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|kidney(1)|lung(20)|ovary(2)	24						GCCTTTAGCTTACCCTCAACC	0.428																																					p.L391X		Atlas-SNP	.											.	ZNF716	207	.	0			c.T1172A						.						41	40	41					7																	57529339		692	1591	2283	SO:0001587	stop_gained	441234	exon4			TTAGCTTACCCTC	AK131575	CCDS55112.1	7p11.1	2013-01-08			ENSG00000182111	ENSG00000182111		"Zinc fingers, C2H2-type", "-"	32458	protein-coding gene	gene with protein product							Standard	NM_001159279		Approved	FLJ46189	uc011kdi.1	A6NP11	OTTHUMG00000156689	ENST00000420713.1:c.1172T>A	chr7.hg19:g.57529339T>A	ENSP00000394248:p.Leu391*	78.0	0.0		73.0	33.0	NM_001159279		Nonsense_Mutation	SNP	ENST00000420713.1	hg19	CCDS55112.1	.	.	.	.	.	.	.	.	.	.	T	10.73	1.432343	0.25813	.	.	ENSG00000182111	ENST00000420713;ENST00000418732	.	.	.	0.195	-0.39	0.12450	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.09843	T	0.71	.	2.9185	0.05761	0.2385:0.0:0.4737:0.2877	.	.	.	.	X	391;379	.	ENSP00000387687:L379X	L	+	2	0	ZNF716	57533281	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.090000	0.03372	-3.452000	0.00160	-3.579000	0.00029	TTA	.	.		0.428	ZNF716-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345309.1	NM_001159279		A	57529339	T	A	57529339	4	1	289	1	0	0	0	0	0	1	0	0	18134	1764	61	4	1186	4	ZNF716	7	57529339	Nonsense_Mutation	SNP	T	TCGA-G3-A6UC-01A-21D-A33K-10	13682686	57529339	101609324	55	42395										
COL1A2	1278	hgsc.bcm.edu	37	chr7	94027070	94027070	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	ttttctacagctttacaagaGgtgagtaaaactttttttag	7	5	1	2			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr7:94027070G>A	ENST00000297268.6	+	2	552	c.81G>A	c.(79-81)gaG>gaA	p.E27E		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	27					blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	CTTTACAAGAGGTGAGTAAAA	0.284										HNSCC(75;0.22)																											p.E27E		Atlas-SNP	.											.	COL1A2	240	.	0			c.G81A						.						31	33	32					7																	94027070		2111	4194	6305	SO:0001630	splice_region_variant	1278	exon2			ACAAGAGGTGAGT	Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"Collagens"	2198	protein-coding gene	gene with protein product	"alpha 2(I)-collagen", "alpha-2 collagen type I", "type I procollagen", "collagen I, alpha-2 polypeptide", "collagen of skin, tendon and bone, alpha-2 chain"	120160	"osteogenesis imperfecta type IV"	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.81+1G>A	chr7.hg19:g.94027070G>A		148.0	0.0		301.0	83.0	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Silent	SNP	ENST00000297268.6	hg19	CCDS34682.1																																																																																			.	.		0.284	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089	Silent	A	94027070	G	A	94027070	5	1	289	1	0	0	0	0	0	0	1	0	3680	1014	35	3	87	3	COL1A2	7	94027070	Splice_Site	SNP	G	TCGA-G3-A6UC-01A-21D-A33K-10	36497731	94027070	65111593	56	42396										
PPP1R3A	5506	hgsc.bcm.edu	37	chr7	113558467	113558467	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	ccatctttttgataaggaggAaccaatacaatcttaaagga	7	7	2	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr7:113558467A>T	ENST00000284601.3	-	1	653	c.585T>A	c.(583-585)gtT>gtA	p.V195V		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	195	CBM21. {ECO:0000255|PROSITE- ProRule:PRU00491}.				glycogen metabolic process (GO:0005977)	integral component of membrane (GO:0016021)				NS(2)|breast(8)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|liver(1)|lung(43)|ovary(10)|pancreas(7)|prostate(3)|skin(15)|stomach(1)|upper_aerodigestive_tract(2)	121						GATAAGGAGGAACCAATACAA	0.333																																					p.V195V		Atlas-SNP	.											.	PPP1R3A	317	.	0			c.T585A						.						100	94	96					7																	113558467		2203	4299	6502	SO:0001819	synonymous_variant	5506	exon1			AGGAGGAACCAAT	AF024578	CCDS5759.1	7q31.1	2012-04-17	2011-10-04	2001-07-02	ENSG00000154415	ENSG00000154415	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9291	protein-coding gene	gene with protein product	"glycogen-associated regulatory subunit of protein phosphatase-1", "protein phosphatase 1 regulatory subunit GM"	600917	"protein phosphatase 1, regulatory (inhibitor) subunit 3A (glycogen and sarcoplasmic reticulum binding subunit, skeletal muscle)", "protein phosphatase 1, regulatory (inhibitor) subunit 3A"	PPP1R3		7926294	Standard	NM_002711		Approved	GM	uc010ljy.1	Q16821	OTTHUMG00000156944	ENST00000284601.3:c.585T>A	chr7.hg19:g.113558467A>T		75.0	0.0		126.0	39.0	NM_002711	A0AVQ2|A4D0T6|O43476|Q75LN8|Q7KYM8|Q86UI6	Silent	SNP	ENST00000284601.3	hg19	CCDS5759.1																																																																																			.	.		0.333	PPP1R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346724.1	NM_002711		T	113558467	A	T	113558467	2	4	289	1	0	0	0	0	0	0	0	1	12383	233	9	4		4	PPP1R3A	7	113558467	Silent	SNP	A	TCGA-G3-A6UC-01A-21D-A33K-10	19531397	113558467	45580196	57	42397										
PLXNA4	91584	hgsc.bcm.edu	37	chr7	131829964	131829964	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	aggaagtcaaacatgtacttGatggccaggggcagggcaga	15	7	1	2			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr7:131829964G>T	ENST00000359827.3	-	29	6101	c.5139C>A	c.(5137-5139)atC>atA	p.I1713I	PLXNA4_ENST00000321063.4_Silent_p.I1713I			Q9HCM2	PLXA4_HUMAN	plexin A4	1713					anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						ACATGTACTTGATGGCCAGGG	0.547																																					p.I1713I		Atlas-SNP	.											.	PLXNA4	873	.	0			c.C5139A						.						102	101	102					7																	131829964		2203	4300	6503	SO:0001819	synonymous_variant	91584	exon29			GTACTTGATGGCC	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"Plexins"	9102	protein-coding gene	gene with protein product		604280	"plexin A4, A", "plexin A4, B"	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.5139C>A	chr7.hg19:g.131829964G>T		136.0	0.0		195.0	44.0	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Silent	SNP	ENST00000359827.3	hg19	CCDS43646.1																																																																																			.	.		0.547	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		T	131829964	G	T	131829964	2	4	289	1	0	0	0	0	0	0	0	1	12131	1280	45	3		3	PLXNA4	7	131829964	Silent	SNP	G	TCGA-G3-A6UC-01A-21D-A33K-10	18271497	131829964	27308699	58	42398										
C8orf41	80185	hgsc.bcm.edu	37	chr8	33361419	33361419	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	agtgcagggttttctccaggAtggggaataaatccagcaga	13	7	1	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr8:33361419A>T	ENST00000431156.2	-	5	1580	c.962T>A	c.(961-963)aTc>aAc	p.I321N	TTI2_ENST00000360742.5_Missense_Mutation_p.I321N|TTI2_ENST00000519356.1_5'UTR|TTI2_ENST00000520636.1_Missense_Mutation_p.I290N	NM_001102401.2	NP_001095871.1	Q6NXR4	TTI2_HUMAN	TELO2 interacting protein 2	321																	TTTCTCCAGGATGGGGAATAA	0.522																																					p.I321N		Atlas-SNP	.											.	.	.	.	0			c.T962A						.						76	69	72					8																	33361419		2203	4300	6503	SO:0001583	missense	80185	exon5			TCCAGGATGGGGA	AK026916	CCDS6090.1	8p12	2011-11-10	2011-11-10	2011-09-22		ENSG00000129696			26262	protein-coding gene	gene with protein product		614426	"chromosome 8 open reading frame 41", "Tel2 interacting protein 2 homolog (S. pombe)"	C8orf41		20801936, 20810650	Standard	NM_025115		Approved	FLJ23263	uc003xjm.5	Q6NXR4		ENST00000431156.2:c.962T>A	chr8.hg19:g.33361419A>T	ENSP00000411169:p.Ile321Asn	87.0	0.0		47.0	39.0	NM_001265581	D3DSV7|Q96IM2|Q9H5N4	Missense_Mutation	SNP	ENST00000431156.2	hg19	CCDS6090.1	.	.	.	.	.	.	.	.	.	.	A	17.21	3.332123	0.60853	.	.	ENSG00000129696	ENST00000360742;ENST00000431156;ENST00000522668;ENST00000520636	T;T;T	0.77229	-1.08;-1.08;-1.08	5.78	4.62	0.57501	.	0.726885	0.12391	N	0.473009	D	0.83487	0.5265	L	0.54323	1.7	0.80722	D	1	D;D	0.65815	0.995;0.989	P;P	0.60541	0.876;0.691	T	0.80924	-0.1165	10	0.87932	D	0	-2.6669	11.5253	0.50576	0.9295:0.0:0.0705:0.0	.	321;290	Q6NXR4;E5RIH5	TTI2_HUMAN;.	N	321;321;321;290	ENSP00000353971:I321N;ENSP00000411169:I321N;ENSP00000428401:I290N	ENSP00000353971:I321N	I	-	2	0	C8orf41	33480961	1.000000	0.71417	0.563000	0.28383	0.250000	0.25880	7.703000	0.84585	1.018000	0.39521	0.528000	0.53228	ATC	.	.		0.522	TTI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376555.1	NM_025115		T	33361419	A	T	33361419	3	4	289	1	0	0	0	0	1	0	0	0	2429	333	12	4	580	4	C8orf41	8	33361419	Missense_Mutation	SNP	A	TCGA-G3-A6UC-01A-21D-A33K-10		33361419	113002603	59	42399										
C8orf86	389649	hgsc.bcm.edu	37	chr8	38386043	38386043	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	ttagtctcttgctcccaagcTcctcagccagcttcccggac	7	17	2	0			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr8:38386043T>C	ENST00000358138.1	-	1	137	c.113A>G	c.(112-114)gAg>gGg	p.E38G	C8orf86_ENST00000437935.2_Missense_Mutation_p.E38G	NM_207412.1	NP_997295.1	Q6ZUL3	CH086_HUMAN	chromosome 8 open reading frame 86	38										breast(1)|endometrium(1)|large_intestine(1)|lung(1)|prostate(1)	5						GCTCCCAAGCTCCTCAGCCAG	0.537																																					p.E38G		Atlas-SNP	.											.	C8orf86	17	.	0			c.A113G						.						124	109	114					8																	38386043		2203	4300	6503	SO:0001583	missense	389649	exon1			CCAAGCTCCTCAG	BC137511	CCDS6108.1	8p12-p11.23	2009-03-03			ENSG00000196166	ENSG00000196166			33774	protein-coding gene	gene with protein product							Standard	NM_207412		Approved	FLJ43582	uc003xlx.1	Q6ZUL3	OTTHUMG00000163992	ENST00000358138.1:c.113A>G	chr8.hg19:g.38386043T>C	ENSP00000350856:p.Glu38Gly	74.0	0.0		47.0	32.0	NM_207412	A4QPB7	Missense_Mutation	SNP	ENST00000358138.1	hg19	CCDS6108.1	.	.	.	.	.	.	.	.	.	.	T	6.908	0.537031	0.13188	.	.	ENSG00000196166	ENST00000358138;ENST00000437935	T;T	0.56275	0.52;0.47	4.81	-0.392	0.12442	.	.	.	.	.	T	0.27731	0.0682	N	0.08118	0	0.09310	N	1	B	0.20550	0.046	B	0.18871	0.023	T	0.19516	-1.0303	9	0.87932	D	0	.	4.1761	0.10353	0.0:0.2906:0.1737:0.5357	.	38	Q6ZUL3	CH086_HUMAN	G	38	ENSP00000350856:E38G;ENSP00000389615:E38G	ENSP00000350856:E38G	E	-	2	0	C8orf86	38505200	0.000000	0.05858	0.001000	0.08648	0.017000	0.09413	0.034000	0.13776	-0.127000	0.11661	-0.290000	0.09829	GAG	.	.		0.537	C8orf86-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376668.1	NM_207412		C	38386043	T	C	38386043	3	2	289	1	0	0	0	0	1	0	0	0	2444	1551	54	2	570	2	C8orf86	8	38386043	Missense_Mutation	SNP	T	TCGA-G3-A6UC-01A-21D-A33K-10	5024624	38386043	107977979	60	42400										
ZNF7	7553	hgsc.bcm.edu	37	chr8	146067786	146067786	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	tctctcgcctgagtcagcatCagctgattcacactggagag	10	12	4	3	rs370205689		TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr8:146067786C>T	ENST00000528372.1	+	5	1534	c.1294C>T	c.(1294-1296)Cag>Tag	p.Q432*	ZNF7_ENST00000525266.1_Intron|ZNF7_ENST00000544249.1_Nonsense_Mutation_p.Q336*|ZNF7_ENST00000446747.2_Nonsense_Mutation_p.Q443*|ZNF7_ENST00000325241.6_Nonsense_Mutation_p.Q432*|ZNF7_ENST00000325217.5_Intron			P17097	ZNF7_HUMAN	zinc finger protein 7	432					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|ovary(5)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.0812)|Ovarian(118;0.0822)|Acute lymphoblastic leukemia(644;0.143)	Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;2.11e-07)		GAGTCAGCATCAGCTGATTCA	0.448																																					p.Q432X		Atlas-SNP	.											.	ZNF7	62	.	0			c.C1294T						.						70	74	73					8																	146067786		2203	4299	6502	SO:0001587	stop_gained	7553	exon5			CAGCATCAGCTGA	AB209619	CCDS6435.1, CCDS64996.1, CCDS64998.1, CCDS64999.1	8q24	2013-01-08	2006-05-09		ENSG00000147789	ENSG00000147789		"Zinc fingers, C2H2-type", "-"	13139	protein-coding gene	gene with protein product		194531	"zinc finger protein 7 (KOX 4, clone HF.16)"			2106481, 1946370	Standard	NM_003416		Approved	KOX4, HF.16	uc003zeg.4	P17097	OTTHUMG00000165200	ENST00000528372.1:c.1294C>T	chr8.hg19:g.146067786C>T	ENSP00000432724:p.Gln432*	36.0	0.0		59.0	20.0	NM_003416	B4DT08|D3DWN6|P17015|Q8N8Y4	Nonsense_Mutation	SNP	ENST00000528372.1	hg19	CCDS6435.1	.	.	.	.	.	.	.	.	.	.	C	36	5.917306	0.97105	.	.	ENSG00000147789	ENST00000325241;ENST00000446747;ENST00000544249;ENST00000528372	.	.	.	4.9	4.9	0.64082	.	0.000000	0.44483	D	0.000457	.	.	.	.	.	.	0.58432	D	0.999998	.	.	.	.	.	.	.	.	.	.	.	.	.	-18.5174	17.0043	0.86388	0.0:1.0:0.0:0.0	.	.	.	.	X	432;443;336;432	.	.	Q	+	1	0	ZNF7	146038590	0.006000	0.16342	0.382000	0.26119	0.968000	0.65278	1.568000	0.36418	2.553000	0.86117	0.561000	0.74099	CAG	.	.		0.448	ZNF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382660.1	NM_003416		T	146067786	C	T	146067786	4	4	289	1	0	0	0	0	0	1	0	0	18117	827	29	3	1308	3	ZNF7	8	146067786	Nonsense_Mutation	SNP	C	TCGA-G3-A6UC-01A-21D-A33K-10	107681743	146067786	296236	61	42401										
SLC1A1	6505	hgsc.bcm.edu	37	chr9	4544613	4544613	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	gaacacagcaacctctcaacTctagagaaattctactttgc	5	12	3	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr9:4544613T>C	ENST00000262352.3	+	2	374	c.138T>C	c.(136-138)acT>acC	p.T46T		NM_004170.5	NP_004161.4	P43005	EAA3_HUMAN	solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1	46					D-aspartate import (GO:0070779)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glutamate binding (GO:0016595)|glutamate:sodium symporter activity (GO:0015501)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|pancreas(1)|skin(1)	15		Acute lymphoblastic leukemia(2;0.0359)|Breast(48;0.0457)		GBM - Glioblastoma multiforme(50;0.0124)|Lung(218;0.183)	L-Aspartic Acid(DB00128)|Pregabalin(DB00230)	ACCTCTCAACTCTAGAGAAAT	0.398																																					p.T46T		Atlas-SNP	.											SLC1A1,caecum,carcinoma,0,1	SLC1A1	43	.	0			c.T138C						.						150	148	149					9																	4544613		2203	4300	6503	SO:0001819	synonymous_variant	6505	exon2			CTCAACTCTAGAG		CCDS6452.1	9p24	2013-05-22			ENSG00000106688	ENSG00000106688		"Solute carriers"	10939	protein-coding gene	gene with protein product		133550				8020993	Standard	NM_004170		Approved	EAAC1, EAAT3	uc003zij.2	P43005	OTTHUMG00000019468	ENST00000262352.3:c.138T>C	chr9.hg19:g.4544613T>C		137.0	0.0		204.0	51.0	NM_004170	O75587|Q5VZ24|Q8N199|Q9UEW2	Silent	SNP	ENST00000262352.3	hg19	CCDS6452.1																																																																																			.	.		0.398	SLC1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051571.1			C	4544613	T	C	4544613	2	2	289	1	0	0	0	0	0	0	0	1	14446	1538	54	2		2	SLC1A1	9	4544613	Silent	SNP	T	TCGA-G3-A6UC-01A-21D-A33K-10		4544613	136668818	62	42402										
KDM4C	23081	hgsc.bcm.edu	37	chr9	7103697	7103698	+	Missense_Mutation	DNP	TG	TG	GA													0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	ccttccagaaatgcatcttcTgcagacaccgggttaagagg							TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	T|G	T|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr9:7103697_7103698TG>GA	ENST00000381309.3	+	18	3002_3003	c.2437_2438TG>GA	c.(2437-2439)TGc>GAc	p.C813D	KDM4C_ENST00000536108.1_Missense_Mutation_p.A596T|KDM4C_ENST00000442236.2_Missense_Mutation_p.C558D|KDM4C_ENST00000381306.3_Missense_Mutation_p.C813D|KDM4C_ENST00000428870.2_Missense_Mutation_p.C500D	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	813					histone H3-K9 demethylation (GO:0033169)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	androgen receptor binding (GO:0050681)|dioxygenase activity (GO:0051213)|enzyme binding (GO:0019899)|histone demethylase activity (H3-K9 specific) (GO:0032454)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43						ATGCATCTTCTGCAGACACCGG	0.49																																					p.C813G|p.C813Y		Atlas-SNP	.											.	KDM4C	186	.	0			c.T2437G|c.G2438A						.																																			SO:0001583	missense	23081	exon18			ATCTTCTGCAGAC|TCTTCTGCAGACA	AB018323	CCDS6471.1, CCDS55285.1, CCDS55286.1, CCDS55287.1	9p24-p23	2013-01-23	2009-04-06	2009-04-06	ENSG00000107077	ENSG00000107077		"Chromatin-modifying enzymes / K-demethylases", "Tudor domain containing"	17071	protein-coding gene	gene with protein product	"tudor domain containing 14C"	605469	"jumonji domain containing 2C"	JMJD2C		9872452, 15138608	Standard	NM_015061		Approved	GASC1, KIAA0780, TDRD14C	uc003zkh.3	Q9H3R0	OTTHUMG00000019536	Exception_encountered	chr9.hg19:g.7103697_7103698delinsGA	ENSP00000370710:p.Cys813Asp	63.0|60.0	0.0		106.0|105.0	15.0|14.0	NM_001146694	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Missense_Mutation	SNP	ENST00000381309.3	hg19	CCDS6471.1																																																																																			.	.		0.49	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061		GA	7103698	TG	GA	7103697	3	3	289	1	0	0	0	0	1	0	0	0	8139	1580	55	5	2595	5	KDM4C	9	7103697	Missense_Mutation	DNP	TG	TCGA-G3-A6UC-01A-21D-A33K-10	2559084	7103697	134109734	63	42403										
KLHL9	55958	hgsc.bcm.edu	37	chr9	21334479	21334479	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	tttgtaaaaagctagcagctTcaagtgtgtcctgaagattg	10	6	1	2			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr9:21334479T>C	ENST00000359039.4	-	1	900	c.380A>G	c.(379-381)gAa>gGa	p.E127G	KLHL9_ENST00000537938.1_Missense_Mutation_p.E59G			Q9P2J3	KLHL9_HUMAN	kelch-like family member 9	127					cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|midbody (GO:0030496)				endometrium(9)|large_intestine(7)|lung(10)|ovary(4)|skin(2)	32				Lung(24;8.52e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.118)		GCTAGCAGCTTCAAGTGTGTC	0.348																																					p.E127G		Atlas-SNP	.											.	KLHL9	61	.	0			c.A380G						.						51	56	54					9																	21334479		2203	4300	6503	SO:0001583	missense	55958	exon1			GCAGCTTCAAGTG	AB037775	CCDS6503.1	9p22	2013-01-30	2013-01-30		ENSG00000198642	ENSG00000198642		"Kelch-like", "BTB/POZ domain containing"	18732	protein-coding gene	gene with protein product		611201	"kelch-like 9 (Drosophila)"				Standard	NM_018847		Approved	KIAA1354, FLJ13568	uc003zoy.3	Q9P2J3	OTTHUMG00000019669	ENST00000359039.4:c.380A>G	chr9.hg19:g.21334479T>C	ENSP00000351933:p.Glu127Gly	107.0	0.0		116.0	46.0	NM_018847	Q8TCQ2	Missense_Mutation	SNP	ENST00000359039.4	hg19	CCDS6503.1	.	.	.	.	.	.	.	.	.	.	T	10.85	1.467979	0.26335	.	.	ENSG00000198642	ENST00000359039;ENST00000537938	T;T	0.69175	-0.38;-0.38	5.22	5.22	0.72569	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	T	0.73705	0.3621	M	0.70787	2.145	0.80722	D	1	P	0.34909	0.475	P	0.47251	0.542	T	0.71869	-0.4462	10	0.31617	T	0.26	.	13.3655	0.60680	0.0:0.0:0.0:1.0	.	127	Q9P2J3	KLHL9_HUMAN	G	127;59	ENSP00000351933:E127G;ENSP00000437733:E59G	ENSP00000351933:E127G	E	-	2	0	KLHL9	21324479	1.000000	0.71417	0.997000	0.53966	0.949000	0.60115	7.959000	0.87885	2.114000	0.64651	0.533000	0.62120	GAA	.	.		0.348	KLHL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051898.2	NM_018847		C	21334479	T	C	21334479	3	2	289	1	0	0	0	0	1	0	0	0	8405	1783	62	2	1477	2	KLHL9	9	21334479	Missense_Mutation	SNP	T	TCGA-G3-A6UC-01A-21D-A33K-10	14230782	21334479	119878952	64	42404										
ZBTB5	9925	hgsc.bcm.edu	37	chr9	37440805	37440805	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	agatgccctggtcaactgtgGagggccaggctgggaaggat	17	8	1	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr9:37440805G>T	ENST00000307750.4	-	2	1932	c.1744C>A	c.(1744-1746)Cca>Aca	p.P582T		NM_014872.2	NP_055687.1	O15062	ZBTB5_HUMAN	zinc finger and BTB domain containing 5	582					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)	8				GBM - Glioblastoma multiforme(29;0.00733)|Lung(182;0.226)		GTCAACTGTGGAGGGCCAGGC	0.498																																					p.P582T		Atlas-SNP	.											.	ZBTB5	43	.	0			c.C1744A						.						73	70	71					9																	37440805		2203	4300	6503	SO:0001583	missense	9925	exon2			ACTGTGGAGGGCC	AB002352	CCDS6610.1	9p13.1	2013-01-09			ENSG00000168795	ENSG00000168795		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	23836	protein-coding gene	gene with protein product						9205841	Standard	NM_014872		Approved	KIAA0354	uc003zzx.3	O15062	OTTHUMG00000019918	ENST00000307750.4:c.1744C>A	chr9.hg19:g.37440805G>T	ENSP00000307604:p.Pro582Thr	70.0	0.0		71.0	36.0	NM_014872		Missense_Mutation	SNP	ENST00000307750.4	hg19	CCDS6610.1	.	.	.	.	.	.	.	.	.	.	G	17.50	3.406198	0.62288	.	.	ENSG00000168795	ENST00000307750	T	0.10860	2.83	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.19565	0.0470	L	0.27053	0.805	0.80722	D	1	D	0.59357	0.985	D	0.66196	0.942	T	0.06110	-1.0845	10	0.14252	T	0.57	.	18.8456	0.92205	0.0:0.0:1.0:0.0	.	582	O15062	ZBTB5_HUMAN	T	582	ENSP00000307604:P582T	ENSP00000307604:P582T	P	-	1	0	ZBTB5	37430805	1.000000	0.71417	0.992000	0.48379	0.997000	0.91878	9.137000	0.94496	2.785000	0.95823	0.655000	0.94253	CCA	.	.		0.498	ZBTB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052462.1	NM_014872		T	37440805	G	T	37440805	3	4	289	1	0	0	0	0	1	0	0	0	17566	1174	41	3	293	3	ZBTB5	9	37440805	Missense_Mutation	SNP	G	TCGA-G3-A6UC-01A-21D-A33K-10	16106326	37440805	103772626	65	42405										
PSMB7	5695	hgsc.bcm.edu	37	chr9	127174695	127174695	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	gggaagacggccagtggagaGggagtggagctccaggttgg	21	6	0	2			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr9:127174695G>C	ENST00000259457.3	-	4	344	c.331C>G	c.(331-333)Ctc>Gtc	p.L111V	PSMB7_ENST00000498485.1_5'UTR|PSMB7_ENST00000536392.1_Missense_Mutation_p.L111V	NM_002799.3	NP_002790.1	Q99436	PSB7_HUMAN	proteasome (prosome, macropain) subunit, beta type, 7	111					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)			breast(1)|endometrium(1)|kidney(1)|lung(1)|pancreas(1)	5						CCAGTGGAGAGGGAGTGGAGC	0.478																																					p.L111V		Atlas-SNP	.											.	PSMB7	11	.	0			c.C331G						.						160	163	162					9																	127174695		2203	4300	6503	SO:0001583	missense	5695	exon4			TGGAGAGGGAGTG	AJ420455	CCDS6855.1	9q34.11-q34.12	2008-02-05			ENSG00000136930	ENSG00000136930		"Proteasome (prosome, macropain) subunits"	9544	protein-coding gene	gene with protein product		604030				8811196	Standard	NM_002799		Approved	Z	uc004boj.4	Q99436	OTTHUMG00000021042	ENST00000259457.3:c.331C>G	chr9.hg19:g.127174695G>C	ENSP00000259457:p.Leu111Val	85.0	0.0		109.0	54.0	NM_002799	B4E0P1|Q5TBG6|Q96AG8|Q9BWA7	Missense_Mutation	SNP	ENST00000259457.3	hg19	CCDS6855.1	.	.	.	.	.	.	.	.	.	.	G	31	5.069081	0.93950	.	.	ENSG00000136930	ENST00000259457;ENST00000536392;ENST00000441097	T;T;T	0.26373	1.74;1.74;1.74	4.88	4.88	0.63580	.	0.000000	0.85682	D	0.000000	T	0.49779	0.1577	M	0.84433	2.695	0.80722	D	1	P;P	0.38745	0.645;0.526	P;B	0.50537	0.643;0.431	T	0.54262	-0.8320	10	0.59425	D	0.04	-11.6855	17.5569	0.87894	0.0:0.0:1.0:0.0	.	111;111	B4E0P1;Q99436	.;PSB7_HUMAN	V	111	ENSP00000259457:L111V;ENSP00000440247:L111V;ENSP00000393157:L111V	ENSP00000259457:L111V	L	-	1	0	PSMB7	126214516	1.000000	0.71417	0.993000	0.49108	0.998000	0.95712	5.506000	0.66993	2.688000	0.91661	0.655000	0.94253	CTC	.	.		0.478	PSMB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055525.1	NM_002799		C	127174695	G	C	127174695	3	2	289	1	0	0	0	0	1	0	0	0	12694	1000	35	4	522	4	PSMB7	9	127174695	Missense_Mutation	SNP	G	TCGA-G3-A6UC-01A-21D-A33K-10	89733890	127174695	14038736	66	42406										
ZBTB43	23099	hgsc.bcm.edu	37	chr9	129595723	129595723	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	ggctgatgaaagcaattatgAtgagcaggtggatttctatg	13	4	1	4			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr9:129595723A>T	ENST00000373464.4	+	3	1199	c.935A>T	c.(934-936)gAt>gTt	p.D312V	ZBTB43_ENST00000373457.1_Missense_Mutation_p.D312V|ZBTB43_ENST00000449886.1_Missense_Mutation_p.D312V	NM_014007.3	NP_054726.1	O43298	ZBT43_HUMAN	zinc finger and BTB domain containing 43	312					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14						AGCAATTATGATGAGCAGGTG	0.522																																					p.D312V		Atlas-SNP	.											.	ZBTB43	25	.	0			c.A935T						.						71	74	73					9																	129595723		2203	4300	6503	SO:0001583	missense	23099	exon2			ATTATGATGAGCA	AF049907	CCDS6867.1	9q33.3	2013-01-09	2006-04-12	2006-04-12	ENSG00000169155	ENSG00000169155		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	17908	protein-coding gene	gene with protein product			"zinc finger protein 297B"	ZNF297B			Standard	NM_014007		Approved	KIAA0414, ZNF-X, FLJ22470, ZBTB22B	uc010mxf.3	O43298	OTTHUMG00000020693	ENST00000373464.4:c.935A>T	chr9.hg19:g.129595723A>T	ENSP00000362563:p.Asp312Val	51.0	0.0		56.0	18.0	NM_001135776	Q5JU96	Missense_Mutation	SNP	ENST00000373464.4	hg19	CCDS6867.1	.	.	.	.	.	.	.	.	.	.	A	9.432	1.085873	0.20390	.	.	ENSG00000169155	ENST00000449886;ENST00000373464;ENST00000373457	T;T;T	0.11063	2.81;2.81;2.81	5.51	4.35	0.52113	.	0.058394	0.64402	D	0.000003	T	0.08358	0.0208	L	0.27053	0.805	0.51482	D	0.999929	B	0.28933	0.228	B	0.27608	0.081	T	0.27191	-1.0081	10	0.30078	T	0.28	.	12.1389	0.53986	0.8715:0.0:0.0:0.1285	.	312	O43298	ZBT43_HUMAN	V	312	ENSP00000390344:D312V;ENSP00000362563:D312V;ENSP00000362556:D312V	ENSP00000362556:D312V	D	+	2	0	ZBTB43	128635544	1.000000	0.71417	0.403000	0.26384	0.845000	0.48019	7.082000	0.76851	1.004000	0.39156	0.379000	0.24179	GAT	.	.		0.522	ZBTB43-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054124.1	NM_001135776		T	129595723	A	T	129595723	3	4	289	1	0	0	0	0	1	0	0	0	17559	333	12	4	937	4	ZBTB43	9	129595723	Missense_Mutation	SNP	A	TCGA-G3-A6UC-01A-21D-A33K-10	2421028	129595723	11617708	67	42407										
ASS1	445	hgsc.bcm.edu	37	chr9	133327679	133327679	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	tggacacctcgtgcatcctcGtgtggctgaaggaacaaggc	13	11	0	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr9:133327679G>T	ENST00000372394.1	+	3	545	c.64G>T	c.(64-66)Gtg>Ttg	p.V22L	snoU13_ENST00000458976.1_RNA|ASS1_ENST00000372393.3_Missense_Mutation_p.V22L|ASS1_ENST00000352480.5_Missense_Mutation_p.V22L			P00966	ASSY_HUMAN	argininosuccinate synthase 1	22					acute-phase response (GO:0006953)|aging (GO:0007568)|arginine biosynthetic process (GO:0006526)|argininosuccinate metabolic process (GO:0000053)|aspartate metabolic process (GO:0006531)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to amine stimulus (GO:0071418)|cellular response to amino acid stimulus (GO:0071230)|cellular response to ammonium ion (GO:0071242)|cellular response to cAMP (GO:0071320)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to glucagon stimulus (GO:0071377)|cellular response to interferon-gamma (GO:0071346)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to oleic acid (GO:0071400)|cellular response to tumor necrosis factor (GO:0071356)|citrulline metabolic process (GO:0000052)|diaphragm development (GO:0060539)|kidney development (GO:0001822)|liver development (GO:0001889)|midgut development (GO:0007494)|negative regulation of leukocyte cell-cell adhesion (GO:1903038)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to growth hormone (GO:0060416)|response to mycotoxin (GO:0010046)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)|perikaryon (GO:0043204)	amino acid binding (GO:0016597)|argininosuccinate synthase activity (GO:0004055)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|toxic substance binding (GO:0015643)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	17				OV - Ovarian serous cystadenocarcinoma(145;0.000514)	Adenosine triphosphate(DB00171)|L-Arginine(DB00125)|L-Aspartic Acid(DB00128)|L-Citrulline(DB00155)	GTGCATCCTCGTGTGGCTGAA	0.597																																					p.V22L		Atlas-SNP	.											.	ASS1	37	.	0			c.G64T						.						142	124	130					9																	133327679		2203	4300	6503	SO:0001583	missense	445	exon2			ATCCTCGTGTGGC	X01630	CCDS6933.1	9q34.1	2012-10-02	2010-04-20	2006-08-24	ENSG00000130707	ENSG00000130707	6.3.4.5		758	protein-coding gene	gene with protein product		603470	"argininosuccinate synthetase"	ASS		3513483, 852520	Standard	NM_054012		Approved	CTLN1	uc004bzm.3	P00966	OTTHUMG00000020806	ENST00000372394.1:c.64G>T	chr9.hg19:g.133327679G>T	ENSP00000361471:p.Val22Leu	68.0	0.0		53.0	26.0	NM_054012	Q6LDL2|Q86UZ0|Q96GT4	Missense_Mutation	SNP	ENST00000372394.1	hg19	CCDS6933.1	.	.	.	.	.	.	.	.	.	.	G	14.21	2.468813	0.43839	.	.	ENSG00000130707	ENST00000334909;ENST00000352480;ENST00000372394;ENST00000372393;ENST00000422569;ENST00000443588	D;D;D;D;D	0.94613	-3.47;-3.47;-3.47;-3.47;-3.47	4.95	4.04	0.47022	Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.64402	U	0.000004	D	0.92110	0.7499	L	0.52206	1.635	0.58432	D	0.999996	B;B;B	0.14012	0.004;0.009;0.009	B;B;B	0.16289	0.01;0.015;0.015	D	0.89284	0.3614	10	0.66056	D	0.02	.	14.6152	0.68544	0.0:0.1467:0.8533:0.0	.	22;22;22	A8KAP9;Q5T6L4;P00966	.;.;ASSY_HUMAN	L	22	ENSP00000253004:V22L;ENSP00000361471:V22L;ENSP00000361469:V22L;ENSP00000394212:V22L;ENSP00000397785:V22L	ENSP00000361470:V22L	V	+	1	0	ASS1	132317500	1.000000	0.71417	1.000000	0.80357	0.863000	0.49368	7.162000	0.77515	1.170000	0.42753	0.462000	0.41574	GTG	.	.		0.597	ASS1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054652.1	NM_000050		T	133327679	G	T	133327679	3	4	289	1	0	0	0	0	1	0	0	0	1061	1145	40	1	66	1	ASS1	9	133327679	Missense_Mutation	SNP	G	TCGA-G3-A6UC-01A-21D-A33K-10	3731956	133327679	7885752	68	42408										
USP54	159195	hgsc.bcm.edu	37	chr10	75276369	75276369	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	gtgccccatgcttaagctgaGaatcacagaaccttgtgata	9	10	1	3			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr10:75276369G>C	ENST00000339859.4	-	19	3915	c.3815C>G	c.(3814-3816)tCt>tGt	p.S1272C	USP54_ENST00000428547.1_Missense_Mutation_p.S1122C|RP11-137L10.6_ENST00000595069.1_RNA|RP11-137L10.6_ENST00000600206.1_RNA|USP54_ENST00000497106.1_5'UTR|RP11-137L10.6_ENST00000593790.1_RNA|USP54_ENST00000422491.2_Missense_Mutation_p.S454C|USP54_ENST00000408019.1_Missense_Mutation_p.S1272C|RP11-137L10.6_ENST00000597958.1_RNA|USP54_ENST00000394811.2_Missense_Mutation_p.S360C			Q70EL1	UBP54_HUMAN	ubiquitin specific peptidase 54	1272					ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitinyl hydrolase activity (GO:0036459)			breast(5)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)	30	Prostate(51;0.0112)					CTTAAGCTGAGAATCACAGAA	0.478																																					p.S1272C	Colon(195;880 2046 8854 25025 38456)	Atlas-SNP	.											.	USP54	178	.	0			c.C3815G						.						99	101	101					10																	75276369		2203	4300	6503	SO:0001583	missense	159195	exon18			AGCTGAGAATCAC	AJ583820	CCDS7329.2	10q22.3	2006-09-26	2005-08-08	2004-01-30	ENSG00000166348	ENSG00000166348		"Ubiquitin-specific peptidases"	23513	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 29", "ubiquitin specific protease 54"	C10orf29		14715245	Standard	NM_152586		Approved	FLJ37318, bA137L10.3, bA137L10.4	uc001juo.3	Q70EL1	OTTHUMG00000018469	ENST00000339859.4:c.3815C>G	chr10.hg19:g.75276369G>C	ENSP00000345216:p.Ser1272Cys	57.0	0.0		70.0	24.0	NM_152586	A1L4Q4|A3KFK3|A3KFK5|A3KFK6|A3KFK7|A6PVS4|A6PVS5|A6PVS6|A6PVS7|B3KVY1|B9ZVM1|Q5F2F4|Q6P1N6|Q6ZSP1|Q6ZSR1|Q6ZTM0|Q8N1X2	Missense_Mutation	SNP	ENST00000339859.4	hg19	CCDS7329.2	.	.	.	.	.	.	.	.	.	.	G	14.29	2.491503	0.44249	.	.	ENSG00000166348	ENST00000339859;ENST00000408019;ENST00000428547;ENST00000394811;ENST00000422491	T;T;T;T;T	0.33654	1.57;1.57;1.54;1.4;1.44	6.03	5.12	0.69794	.	.	.	.	.	T	0.44829	0.1312	L	0.34521	1.04	0.80722	D	1	D;D	0.89917	1.0;0.997	D;P	0.68943	0.961;0.819	T	0.32929	-0.9888	9	0.39692	T	0.17	-9.0972	10.2685	0.43468	0.0676:0.0:0.7979:0.1346	.	454;1272	E7EW90;Q70EL1	.;UBP54_HUMAN	C	1272;1272;1122;360;454	ENSP00000345216:S1272C;ENSP00000386080:S1272C;ENSP00000408714:S1122C;ENSP00000378290:S360C;ENSP00000407368:S454C	ENSP00000345216:S1272C	S	-	2	0	USP54	74946375	1.000000	0.71417	1.000000	0.80357	0.821000	0.46438	4.943000	0.63554	1.560000	0.49568	-0.150000	0.13652	TCT	.	.		0.478	USP54-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316563.2	NM_152586		C	75276369	G	C	75276369	3	2	289	1	0	0	0	0	1	0	0	0	17100	942	33	4	1259	4	USP54	10	75276369	Missense_Mutation	SNP	G	TCGA-G3-A6UC-01A-21D-A33K-10		75276369	60258378	69	42409										
PTEN	5728	hgsc.bcm.edu	37	chr10	89653856	89653857	+	Frame_Shift_Ins	INS	-	-	ATGTAGTAAGGTAAGAATGCTTTGATTTTCTATTTCAA													0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	atacaggaacaatattgatgINSatgtagtaaggtaagaatgc							TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr10:89653856_89653857insATGTAGTAAGGTAAGAATGCTTTGATTTTCTATTTCAA	ENST00000371953.3	+	2	1511_1512	c.154_155insATGTAGTAAGGTAAGAATGCTTTGATTTTCTATTTCAA	c.(154-156)gatfs	p.-52fs		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog						activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(8)|p.Y27fs*1(2)|p.D52del(2)|p.D52N(1)|p.D52G(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		CAATATTGATGATGTAGTAAGG	0.297		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																											p.D52_V53delinsDVVRX		Pindel	.	yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	PTEN,caecum,carcinoma,-2,2	PTEN	3652	.	51	Whole gene deletion(37)|Unknown(8)|Substitution - Missense(2)|Deletion - In frame(2)|Deletion - Frameshift(2)	prostate(14)|skin(9)|central_nervous_system(8)|haematopoietic_and_lymphoid_tissue(4)|lung(4)|endometrium(3)|ovary(3)|breast(2)|soft_tissue(1)|urinary_tract(1)|NS(1)|kidney(1)	c.154_155insATGTAGTAAGGTAAGAATGCTTTGATTTTCTATTTCAA	GRCh37	CD075524	PTEN	D		.																																			SO:0001589	frameshift_variant	5728	exon2	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	Exception_encountered	chr10.hg19:g.89653856_89653857insATGTAGTAAGGTAAGAATGCTTTGATTTTCTATTTCAA	ENSP00000361021:p.Asp52fs	51.0	0.0		63.0	10.0	NM_000314	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Frame_Shift_Ins	INS	ENST00000371953.3	hg19	CCDS31238.1																																																																																			.	.		0.297	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		ATGTAGTAAGGTAAGAATGCTTTGATTTTCTATTTCAA	89653857	-	ATGTAGTAAGGTAAGAATGCTTTGATTTTCTATTTCAA	89653856	7	5	289	1	0	1	1	0	0	0	0	0	12750	1290	45	0	160	0	PTEN	10	89653856	Frame_Shift_Ins	INS	-	TCGA-G3-A6UC-01A-21D-A33K-10	14377487	89653856	45880891	70	42410										
WNT8B	7479	hgsc.bcm.edu	37	chr10	102239757	102239757	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	tgcagctgtccagccatggtGggcttcgcagtggtaagaaa	14	9	0	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr10:102239757G>A	ENST00000343737.5	+	3	357	c.229G>A	c.(229-231)Ggg>Agg	p.G77R		NM_003393.3	NP_003384.2	Q93098	WNT8B_HUMAN	wingless-type MMTV integration site family, member 8B	77					cell fate commitment (GO:0045165)|cellular response to retinoic acid (GO:0071300)|determination of dorsal identity (GO:0048263)|gastrulation (GO:0007369)|negative regulation of gene expression (GO:0010629)|nervous system development (GO:0007399)|neuron differentiation (GO:0030182)|positive regulation of gene expression (GO:0010628)|response to estradiol (GO:0032355)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(1)|large_intestine(1)|ovary(1)|skin(1)	4		Colorectal(252;0.117)		Epithelial(162;1.87e-10)|all cancers(201;1.64e-08)		CAGCCATGGTGGGCTTCGCAG	0.587																																					p.G77R		Atlas-SNP	.											.	WNT8B	31	.	0			c.G229A						.						54	49	51					10																	102239757		2203	4300	6503	SO:0001583	missense	7479	exon3			CATGGTGGGCTTC	X91940	CCDS7494.1	10q24	2003-11-12			ENSG00000075290	ENSG00000075290		"Wingless-type MMTV integration sites"	12789	protein-coding gene	gene with protein product		601396				8661156	Standard	NM_003393		Approved		uc001krb.3	Q93098	OTTHUMG00000018912	ENST00000343737.5:c.229G>A	chr10.hg19:g.102239757G>A	ENSP00000340677:p.Gly77Arg	41.0	0.0		36.0	16.0	NM_003393	O00771|Q5VX55|Q8WYK9	Missense_Mutation	SNP	ENST00000343737.5	hg19	CCDS7494.1	.	.	.	.	.	.	.	.	.	.	G	11.35	1.612903	0.28712	.	.	ENSG00000075290	ENST00000343737	T	0.75367	-0.93	5.7	5.7	0.88788	.	1.622190	0.03427	N	0.207152	T	0.64516	0.2605	N	0.10733	0.035	0.50467	D	0.999878	B	0.14805	0.011	B	0.20577	0.03	T	0.13764	-1.0497	10	0.12103	T	0.63	.	19.8354	0.96655	0.0:0.0:1.0:0.0	.	77	Q93098	WNT8B_HUMAN	R	77	ENSP00000340677:G77R	ENSP00000340677:G77R	G	+	1	0	WNT8B	102229747	1.000000	0.71417	0.969000	0.41365	0.762000	0.43233	6.062000	0.71155	2.686000	0.91538	0.555000	0.69702	GGG	.	.		0.587	WNT8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049867.1	NM_003393		A	102239757	G	A	102239757	3	1	289	1	0	0	0	0	1	0	0	0	17412	1348	47	3	239	3	WNT8B	10	102239757	Missense_Mutation	SNP	G	TCGA-G3-A6UC-01A-21D-A33K-10	12585901	102239757	33294990	71	42411										
SPI1	6688	hgsc.bcm.edu	37	chr11	47381480	47381480	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	gctccagctccatgtggcggTagagctgctgcagctgcggg	16	12	0	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr11:47381480T>C	ENST00000378538.3	-	3	476	c.254A>G	c.(253-255)tAc>tGc	p.Y85C	SPI1_ENST00000227163.4_Missense_Mutation_p.Y86C|SPI1_ENST00000533030.1_Intron|SPI1_ENST00000533968.1_Missense_Mutation_p.Y85C	NM_001080547.1|NM_003120.2	NP_001074016.1|NP_003111.2	P17947	SPI1_HUMAN	Spi-1 proto-oncogene	85					anatomical structure regression (GO:0060033)|apoptotic process involved in patterning of blood vessels (GO:1902262)|erythrocyte differentiation (GO:0030218)|granulocyte differentiation (GO:0030851)|histone H3 acetylation (GO:0043966)|hypermethylation of CpG island (GO:0044027)|lymphocyte differentiation (GO:0030098)|lymphoid progenitor cell differentiation (GO:0002320)|macrophage differentiation (GO:0030225)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of histone H4 acetylation (GO:0090241)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of erythrocyte differentiation (GO:0045646)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|somatic stem cell maintenance (GO:0035019)	nuclear chromatin (GO:0000790)	core promoter binding (GO:0001047)|NFAT protein binding (GO:0051525)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(2)|lung(4)|ovary(1)	8				Lung(87;0.0967)		CATGTGGCGGTAGAGCTGCTG	0.652																																					p.Y86C		Atlas-SNP	.											.	SPI1	21	.	0			c.A257G						.						55	47	50					11																	47381480		2200	4297	6497	SO:0001583	missense	6688	exon3			TGGCGGTAGAGCT	X52056	CCDS7933.2, CCDS44591.1	11p12-p11.22	2014-06-25	2014-06-25		ENSG00000066336	ENSG00000066336			11241	protein-coding gene	gene with protein product	"hematopoietic transcription factor PU.1", "31 kDa transforming protein"	165170	"spleen focus forming virus (SFFV) proviral integration oncogene"			1693183	Standard	NM_003120		Approved	PU.1, SPI-A, OF, SFPI1, SPI-1	uc001nfb.1	P17947	OTTHUMG00000150150	ENST00000378538.3:c.254A>G	chr11.hg19:g.47381480T>C	ENSP00000367799:p.Tyr85Cys	25.0	0.0		28.0	11.0	NM_001080547		Missense_Mutation	SNP	ENST00000378538.3	hg19	CCDS7933.2	.	.	.	.	.	.	.	.	.	.	T	17.58	3.424117	0.62733	.	.	ENSG00000066336	ENST00000378538;ENST00000227163;ENST00000533968	T;T;T	0.32515	1.45;1.45;1.45	3.59	3.59	0.41128	.	0.502444	0.20700	N	0.087289	T	0.52709	0.1751	M	0.73962	2.25	0.44024	D	0.996741	D;D;D	0.89917	1.0;0.977;0.991	D;P;P	0.69479	0.964;0.764;0.849	T	0.58470	-0.7631	10	0.72032	D	0.01	-22.9164	12.6475	0.56744	0.0:0.0:0.0:1.0	.	85;85;86	F5H3K6;P17947;P17947-2	.;SPI1_HUMAN;.	C	85;86;85	ENSP00000367799:Y85C;ENSP00000227163:Y86C;ENSP00000438846:Y85C	ENSP00000227163:Y86C	Y	-	2	0	SPI1	47338056	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.984000	0.40658	1.617000	0.50277	0.533000	0.62120	TAC	.	.		0.652	SPI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316571.1	NM_003120		C	47381480	T	C	47381480	3	2	289	1	0	0	0	0	1	0	0	0	15064	1638	57	2	570	2	SPI1	11	47381480	Missense_Mutation	SNP	T	TCGA-G3-A6UC-01A-21D-A33K-10		47381480	87625036	72	42412										
OR9Q2	219957	hgsc.bcm.edu	37	chr11	57958110	57958110	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	caggcatgatcctcctgatcCgtggcgatcgtcggctccac	11	15	0	2			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr11:57958110C>T	ENST00000311591.3	+	1	205	c.148C>T	c.(148-150)Cgt>Tgt	p.R50C		NM_001005283.2	NP_001005283.1	Q8NGE9	OR9Q2_HUMAN	olfactory receptor, family 9, subfamily Q, member 2	50						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(2)|endometrium(1)|large_intestine(3)|lung(24)|ovary(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	41		Breast(21;0.0589)				CCTCCTGATCCGTGGCGATCG	0.512																																					p.R50C		Atlas-SNP	.											.	OR9Q2	78	.	0			c.C148T						.						116	88	97					11																	57958110		2201	4296	6497	SO:0001583	missense	219957	exon1			CTGATCCGTGGCG	AB065859	CCDS31544.1	11q12.1	2012-08-09		2004-03-10	ENSG00000186513	ENSG00000186513		"GPCR / Class A : Olfactory receptors"	15328	protein-coding gene	gene with protein product				OR9Q2P			Standard	NM_001005283		Approved		uc010rka.2	Q8NGE9	OTTHUMG00000167414	ENST00000311591.3:c.148C>T	chr11.hg19:g.57958110C>T	ENSP00000308714:p.Arg50Cys	126.0	0.0		91.0	44.0	NM_001005283		Missense_Mutation	SNP	ENST00000311591.3	hg19	CCDS31544.1	.	.	.	.	.	.	.	.	.	.	C	3.282	-0.146763	0.06627	.	.	ENSG00000186513	ENST00000311591	T	0.01084	5.36	5.43	-1.2	0.09554	GPCR, rhodopsin-like superfamily (1);	0.896444	0.09421	N	0.804391	T	0.00875	0.0029	L	0.28274	0.84	0.20403	N	0.999908	B	0.12630	0.006	B	0.04013	0.001	T	0.48364	-0.9042	10	0.38643	T	0.18	-0.0824	1.4131	0.02295	0.129:0.2122:0.2527:0.4061	.	50	Q8NGE9	OR9Q2_HUMAN	C	50	ENSP00000308714:R50C	ENSP00000308714:R50C	R	+	1	0	OR9Q2	57714686	0.000000	0.05858	0.153000	0.22517	0.060000	0.15804	-1.258000	0.02863	0.080000	0.16959	0.655000	0.94253	CGT	.	.		0.512	OR9Q2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394540.1	NM_001005283		T	57958110	C	T	57958110	3	4	289	1	0	0	0	0	1	0	0	0	11265	652	23	1	150	1	OR9Q2	11	57958110	Missense_Mutation	SNP	C	TCGA-G3-A6UC-01A-21D-A33K-10	10576630	57958110	77048406	73	42413										
SUV420H1	51111	hgsc.bcm.edu	37	chr11	67953257	67953257	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	ctgaaaattacctagtattcAttttgtgtgtttgaaaacct	6	6	1	2			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr11:67953257A>C	ENST00000304363.4	-	3	652	c.299T>G	c.(298-300)aTg>aGg	p.M100R	SUV420H1_ENST00000405515.1_Missense_Mutation_p.M100R|SUV420H1_ENST00000402789.1_Missense_Mutation_p.M100R|SUV420H1_ENST00000402185.2_Missense_Mutation_p.M100R|SUV420H1_ENST00000401547.2_Missense_Mutation_p.M100R	NM_017635.3	NP_060105	Q4FZB7	SV421_HUMAN	suppressor of variegation 4-20 homolog 1 (Drosophila)	100					histone H4-K20 trimethylation (GO:0034773)|muscle organ development (GO:0007517)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome, centromeric region (GO:0000780)	histone methyltransferase activity (H4-K20 specific) (GO:0042799)|histone-lysine N-methyltransferase activity (GO:0018024)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(15)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46						CCTAGTATTCATTTTGTGTGT	0.348																																					p.M100R		Atlas-SNP	.											.	SUV420H1	125	.	0			c.T299G						.						88	90	89					11																	67953257		2200	4294	6494	SO:0001583	missense	51111	exon3			GTATTCATTTTGT	AL512763	CCDS31623.1, CCDS44660.1	11q13.2	2011-07-01			ENSG00000110066	ENSG00000110066		"Chromatin-modifying enzymes / K-methyltransferases"	24283	protein-coding gene	gene with protein product		610881				10810093, 11401438	Standard	NM_016028		Approved	CGI-85, KMT5B	uc001onm.1	Q4FZB7	OTTHUMG00000150484	ENST00000304363.4:c.299T>G	chr11.hg19:g.67953257A>C	ENSP00000305899:p.Met100Arg	70.0	0.0		98.0	38.0	NM_017635	B7WNX7|Q3SX56|Q4V775|Q6P150|Q96E44|Q9BUL0|Q9H022|Q9H2K3|Q9NXV3|Q9Y393	Missense_Mutation	SNP	ENST00000304363.4	hg19	CCDS31623.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.217173	0.79352	.	.	ENSG00000110066	ENST00000304363;ENST00000401547;ENST00000405515;ENST00000402789;ENST00000402185;ENST00000453170;ENST00000458496;ENST00000434573	T;T;T;T;T;T;T;T	0.54479	0.92;0.92;0.92;0.92;0.57;0.92;0.92;0.92	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.59905	0.2228	N	0.19112	0.55	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.96;0.999	D;D;D;D	0.91635	0.987;0.999;0.962;0.996	T	0.64884	-0.6302	10	0.66056	D	0.02	-39.6175	16.0399	0.80667	1.0:0.0:0.0:0.0	.	100;100;100;100	B7WNX0;B5MCB3;Q4FZB7-2;Q4FZB7	.;.;.;SV421_HUMAN	R	100;100;100;100;100;29;29;100	ENSP00000305899:M100R;ENSP00000385965:M100R;ENSP00000385640:M100R;ENSP00000385005:M100R;ENSP00000384724:M100R;ENSP00000406377:M29R;ENSP00000403233:M29R;ENSP00000402921:M100R	ENSP00000305899:M100R	M	-	2	0	SUV420H1	67709833	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.139000	0.94554	2.371000	0.80710	0.533000	0.62120	ATG	.	.		0.348	SUV420H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318319.1	NM_017635		C	67953257	A	C	67953257	3	2	289	1	0	0	0	0	1	0	0	0	15429	217	8	5	2402	5	SUV420H1	11	67953257	Missense_Mutation	SNP	A	TCGA-G3-A6UC-01A-21D-A33K-10	9995147	67953257	67053259	74	42414										
FAT3	120114	hgsc.bcm.edu	37	chr11	92531036	92531036	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	atgtttaagatcgaaccggtCctaggcatcatcaccatttg	8	10	2	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr11:92531036C>T	ENST00000298047.6	+	9	4874	c.4857C>T	c.(4855-4857)gtC>gtT	p.V1619V	FAT3_ENST00000409404.2_Silent_p.V1619V|FAT3_ENST00000525166.1_Silent_p.V1469V			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	1619	Cadherin 15. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				TCGAACCGGTCCTAGGCATCA	0.433										TCGA Ovarian(4;0.039)																											p.V1619V		Atlas-SNP	.											.	FAT3	1822	.	0			c.C4857T						.						116	111	113					11																	92531036		1984	4160	6144	SO:0001819	synonymous_variant	120114	exon9			ACCGGTCCTAGGC	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.4857C>T	chr11.hg19:g.92531036C>T		182.0	0.0		174.0	75.0	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	hg19																																																																																				.	.		0.433	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		T	92531036	C	T	92531036	2	4	289	1	0	0	0	0	0	0	0	1	5699	842	30	3		3	FAT3	11	92531036	Silent	SNP	C	TCGA-G3-A6UC-01A-21D-A33K-10	24577779	92531036	42475480	75	42415										
EXPH5	23086	hgsc.bcm.edu	37	chr11	108381599	108381599	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	ctctctgtcatatttgcctcCtgacttctttgaggtaattc	6	11	3	2			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr11:108381599C>T	ENST00000265843.4	-	6	4745	c.4635G>A	c.(4633-4635)caG>caA	p.Q1545Q	EXPH5_ENST00000525344.1_Silent_p.Q1538Q|EXPH5_ENST00000428840.1_Silent_p.Q1469Q|EXPH5_ENST00000443411.1_Silent_p.Q1357Q|EXPH5_ENST00000524840.1_5'Flank	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	1545					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		TATTTGCCTCCTGACTTCTTT	0.428																																					p.Q1545Q		Atlas-SNP	.											.	EXPH5	193	.	0			c.G4635A						.						82	77	79					11																	108381599		2201	4298	6499	SO:0001819	synonymous_variant	23086	exon6			TGCCTCCTGACTT		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"synaptotagmin-like homologue lacking C2 domains b"	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.4635G>A	chr11.hg19:g.108381599C>T		89.0	0.0		89.0	43.0	NM_015065	Q2KHM1|Q9Y4D6	Silent	SNP	ENST00000265843.4	hg19	CCDS8341.1																																																																																			.	.		0.428	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065		T	108381599	C	T	108381599	2	4	289	1	0	0	0	0	0	0	0	1	5324	680	24	3		3	EXPH5	11	108381599	Silent	SNP	C	TCGA-G3-A6UC-01A-21D-A33K-10	15850563	108381599	26624917	76	42416										
UBE4A	9354	hgsc.bcm.edu	37	chr11	118245829	118245829	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	ggtgctgctctcctgaagctAtgccagccattttgcaaacc	9	13	1	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr11:118245829A>G	ENST00000431736.2	+	9	1428	c.1356A>G	c.(1354-1356)ctA>ctG	p.L452L	UBE4A_ENST00000252108.3_Silent_p.L445L					ubiquitination factor E4A											autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(7)|liver(2)|lung(14)|ovary(3)|prostate(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	56	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)		TCCTGAAGCTATGCCAGCCAT	0.453																																					p.L452L		Atlas-SNP	.											.	UBE4A	97	.	0			c.A1356G						.						92	86	88					11																	118245829		2200	4296	6496	SO:0001819	synonymous_variant	9354	exon9			GAAGCTATGCCAG	D50916	CCDS8396.1, CCDS55790.1	11q23.3	2013-01-28	2011-05-19					"U-box domain containing"	12499	protein-coding gene	gene with protein product		603753	"ubiquitination factor E4A (homologous to yeast UFD2)", "ubiquitination factor E4A (UFD2 homolog, yeast)"			10089879	Standard	NM_004788		Approved	UBOX2, UFD2, KIAA0126, E4	uc001psv.3	Q14139	OTTHUMG00000168100	ENST00000431736.2:c.1356A>G	chr11.hg19:g.118245829A>G		91.0	0.0		111.0	53.0	NM_004788		Silent	SNP	ENST00000431736.2	hg19	CCDS8396.1																																																																																			.	.		0.453	UBE4A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398143.1	NM_004788		G	118245829	A	G	118245829	2	3	289	1	0	0	0	0	0	0	0	1	16897	436	16	2		2	UBE4A	11	118245829	Silent	SNP	A	TCGA-G3-A6UC-01A-21D-A33K-10	9864230	118245829	16760687	77	42417										
PDZRN4	29951	hgsc.bcm.edu	37	chr12	41949558	41949558	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	tcgagaaggggatcggatttTgcaagtaggtggtatagtaa	15	3	0	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr12:41949558T>A	ENST00000402685.2	+	7	1369	c.1361T>A	c.(1360-1362)tTg>tAg	p.L454*	PDZRN4_ENST00000298919.7_Nonsense_Mutation_p.L194*|PDZRN4_ENST00000539469.2_Nonsense_Mutation_p.L196*	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	454	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.						ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				GATCGGATTTTGCAAGTAGGT	0.398																																					p.L454X		Atlas-SNP	.											.	PDZRN4	346	.	0			c.T1361A						.						158	153	155					12																	41949558		2203	4300	6503	SO:0001587	stop_gained	29951	exon7			GGATTTTGCAAGT	AK094690	CCDS8739.1, CCDS53777.1	12q12	2008-08-14	2008-08-14			ENSG00000165966		"RING-type (C3HC4) zinc fingers"	30552	protein-coding gene	gene with protein product	"similar to semaF cytoplasmic domain associated protein 3"	609730				11230166, 15010864	Standard	NM_013377		Approved	DKFZp434B0417, LNX4, FLJ33777, IMAGE5767589	uc010skn.2	Q6ZMN7		ENST00000402685.2:c.1361T>A	chr12.hg19:g.41949558T>A	ENSP00000384197:p.Leu454*	72.0	0.0		71.0	31.0	NM_001164595	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Nonsense_Mutation	SNP	ENST00000402685.2	hg19	CCDS53777.1	.	.	.	.	.	.	.	.	.	.	T	41	8.607313	0.98884	.	.	ENSG00000165966	ENST00000402685;ENST00000539469;ENST00000298919	.	.	.	5.25	4.09	0.47781	.	0.101520	0.42964	D	0.000623	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.0601	12.8531	0.57869	0.0:0.0:0.1365:0.8635	.	.	.	.	X	454;196;194	.	ENSP00000298919:L194X	L	+	2	0	PDZRN4	40235825	1.000000	0.71417	0.999000	0.59377	0.979000	0.70002	7.932000	0.87634	1.062000	0.40625	0.528000	0.53228	TTG	.	.		0.398	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377		A	41949558	T	A	41949558	4	1	289	1	0	0	0	0	0	1	0	0	11719	1821	63	4	1460	4	PDZRN4	12	41949558	Nonsense_Mutation	SNP	T	TCGA-G3-A6UC-01A-21D-A33K-10		41949558	91902337	78	42418										
PRICKLE1	144165	hgsc.bcm.edu	37	chr12	42858275	42858275	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	caggtctgacagacactccaGggaatcttcataccactgtg	9	12	3	2			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr12:42858275G>C	ENST00000455697.1	-	7	1846	c.1561C>G	c.(1561-1563)Ctg>Gtg	p.L521V	PRICKLE1_ENST00000552240.1_Missense_Mutation_p.L521V|PRICKLE1_ENST00000345127.3_Missense_Mutation_p.L521V|RP11-328C8.4_ENST00000547824.1_RNA|PRICKLE1_ENST00000548696.1_Missense_Mutation_p.L521V|PRICKLE1_ENST00000445766.2_Missense_Mutation_p.L521V	NM_001144882.1|NM_001144883.1	NP_001138354.1|NP_001138355.1	Q96MT3	PRIC1_HUMAN	prickle homolog 1 (Drosophila)	521					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell myoblast differentiation (GO:2000691)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(13)|ovary(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	47	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)		AGACACTCCAGGGAATCTTCA	0.478																																					p.L521V		Atlas-SNP	.											.	PRICKLE1	105	.	0			c.C1561G						.						122	117	119					12																	42858275		2203	4300	6503	SO:0001583	missense	144165	exon7			ACTCCAGGGAATC	AK056499	CCDS8742.1	12p11-q12	2010-08-13	2006-09-12			ENSG00000139174			17019	protein-coding gene	gene with protein product		608500	"prickle-like 1 (Drosophila)"			12525887, 18976727	Standard	NM_153026		Approved	FLJ31937, EPM1B	uc010skv.2	Q96MT3		ENST00000455697.1:c.1561C>G	chr12.hg19:g.42858275G>C	ENSP00000401060:p.Leu521Val	89.0	0.0		108.0	47.0	NM_001144882	Q14C83|Q71QF8|Q96N00	Missense_Mutation	SNP	ENST00000455697.1	hg19	CCDS8742.1	.	.	.	.	.	.	.	.	.	.	G	13.13	2.146368	0.37923	.	.	ENSG00000139174	ENST00000455697;ENST00000445766;ENST00000548696;ENST00000345127;ENST00000552240	T;T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16;-0.16	5.76	1.75	0.24633	.	0.133960	0.49916	D	0.000129	T	0.55386	0.1917	M	0.70275	2.135	0.48236	D	0.999616	B	0.13145	0.007	B	0.08055	0.003	T	0.57723	-0.7762	10	0.87932	D	0	-9.1716	6.1408	0.20259	0.2769:0.1284:0.5947:0.0	.	521	Q96MT3	PRIC1_HUMAN	V	521	ENSP00000401060:L521V;ENSP00000398947:L521V;ENSP00000448359:L521V;ENSP00000345064:L521V;ENSP00000449819:L521V	ENSP00000345064:L521V	L	-	1	2	PRICKLE1	41144542	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.470000	0.35354	0.898000	0.36418	0.650000	0.86243	CTG	.	.		0.478	PRICKLE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404069.1			C	42858275	G	C	42858275	3	2	289	1	0	0	0	0	1	0	0	0	12498	991	35	4	942	4	PRICKLE1	12	42858275	Missense_Mutation	SNP	G	TCGA-G3-A6UC-01A-21D-A33K-10	908717	42858275	90993620	79	42419										
C12orf68	387856	hgsc.bcm.edu	37	chr12	48578199	48578200	+	Missense_Mutation	DNP	CC	CC	AA													0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	attatgaccactgcgccccgCcagggcggcttgggcgtggt							TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr12:48578199_48578200CC>AA	ENST00000316554.3	+	1	834_835	c.294_295CC>AA	c.(292-297)cgCCag>cgAAag	p.Q99K		NM_001013635.3	NP_001013657.3	Q52MB2	CC184_HUMAN		99						cytoplasm (GO:0005737)				central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)	4						CTGCGCCCCGCCAGGGCGGCTT	0.678																																					p.R98R|p.Q99K		Atlas-SNP	.											.|C12orf68,NS,carcinoma,0,1	C12orf68	11	.	0			c.C294A|c.C295A						.																																			SO:0001583	missense	387856	exon1			GCCCCGCCAGGGC|CCCCGCCAGGGCG																												Exception_encountered	chr12.hg19:g.48578199_48578200delinsAA	ENSP00000320849:p.Gln99Lys	19.0	0.0		25.0	13.0	NM_001013635	Q96MK5|Q96N39	Silent|Missense_Mutation	SNP	ENST00000316554.3	hg19	CCDS31785.1																																																																																			.	.		0.678	C12orf68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406514.1			AA	48578200	CC	AA	48578199	3	1	289	1	0	0	0	0	1	0	0	0	1712	726	26	3	296	3	C12orf68	12	48578199	Missense_Mutation	DNP	CC	TCGA-G3-A6UC-01A-21D-A33K-10	5719924	48578199	85273696	80	42420										
CAND1	55832	hgsc.bcm.edu	37	chr12	67699851	67699851	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	tcttattattccattgccaaAtgtgtagctgcccttactcg	6	11	1	0			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr12:67699851A>C	ENST00000545606.1	+	10	2840	c.2403A>C	c.(2401-2403)aaA>aaC	p.K801N		NM_018448.3	NP_060918.2	Q86VP6	CAND1_HUMAN	cullin-associated and neddylation-dissociated 1	801					cell differentiation (GO:0030154)|negative regulation of catalytic activity (GO:0043086)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|protein ubiquitination (GO:0016567)|SCF complex assembly (GO:0010265)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				NS(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)	35			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)		CCATTGCCAAATGTGTAGCTG	0.428																																					p.K801N		Atlas-SNP	.											.	CAND1	100	.	0			c.A2403C						.						98	89	92					12																	67699851		2203	4300	6503	SO:0001583	missense	55832	exon10			TGCCAAATGTGTA		CCDS8977.1	12q14	2008-02-05			ENSG00000111530	ENSG00000111530			30688	protein-coding gene	gene with protein product	"TBP interacting protein"	607727				10048485, 8954946	Standard	NM_018448		Approved	TIP120A, DKFZp434M1414, KIAA0829, TIP120	uc001stn.2	Q86VP6	OTTHUMG00000169060	ENST00000545606.1:c.2403A>C	chr12.hg19:g.67699851A>C	ENSP00000442318:p.Lys801Asn	63.0	0.0		80.0	38.0	NM_018448	B2RAU3|O94918|Q6PIY4|Q8NDJ4|Q96JZ9|Q96T19|Q9BTC4|Q9H0G2|Q9P0H7|Q9UF85	Missense_Mutation	SNP	ENST00000545606.1	hg19	CCDS8977.1	.	.	.	.	.	.	.	.	.	.	A	15.34	2.805411	0.50315	.	.	ENSG00000111530	ENST00000545606;ENST00000299218;ENST00000544619	T;T	0.66815	-0.23;-0.23	5.62	3.29	0.37713	Armadillo-like helical (1);Armadillo-type fold (1);	0.094546	0.64402	D	0.000001	T	0.81856	0.4911	M	0.89601	3.045	0.80722	D	1	D;D	0.89917	1.0;0.992	D;P	0.68039	0.955;0.776	T	0.81885	-0.0727	9	.	.	.	-18.8306	9.7089	0.40233	0.8602:0.0:0.1398:0.0	.	633;801	Q86VP6-2;Q86VP6	.;CAND1_HUMAN	N	801;801;341	ENSP00000442318:K801N;ENSP00000444089:K341N	.	K	+	3	2	CAND1	65986118	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	2.591000	0.46163	0.432000	0.26286	-0.256000	0.11100	AAA	.	.		0.428	CAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402105.1	NM_018448		C	67699851	A	C	67699851	3	2	289	1	0	0	0	0	1	0	0	0	2617	98	4	5	2441	5	CAND1	12	67699851	Missense_Mutation	SNP	A	TCGA-G3-A6UC-01A-21D-A33K-10	19121652	67699851	66152044	81	42421										
ZFC3H1	196441	hgsc.bcm.edu	37	chr12	72017346	72017346	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	tggttttaaggtattcagctActattccatcattagcagat	7	7	2	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr12:72017346A>C	ENST00000378743.3	-	24	4896	c.4538T>G	c.(4537-4539)gTa>gGa	p.V1513G		NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	1513					RNA processing (GO:0006396)	extracellular space (GO:0005615)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						GTATTCAGCTACTATTCCATC	0.303																																					p.V1513G		Atlas-SNP	.											.	ZFC3H1	172	.	0			c.T4538G						.						87	80	82					12																	72017346		1833	4079	5912	SO:0001583	missense	196441	exon24			TCAGCTACTATTC	AB011118	CCDS41813.1	12q21.1	2013-01-25	2008-10-01	2008-10-01		ENSG00000133858		"Zinc finger, C3H1-type containing"	28328	protein-coding gene	gene with protein product			"proline/serine-rich coiled-coil 2", "coiled-coil domain containing 131"	PSRC2, CCDC131		9628581	Standard	NM_144982		Approved	MGC23401, KIAA0546	uc001swo.2	O60293	OTTHUMG00000169545	ENST00000378743.3:c.4538T>G	chr12.hg19:g.72017346A>C	ENSP00000368017:p.Val1513Gly	61.0	0.0		96.0	48.0	NM_144982	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Missense_Mutation	SNP	ENST00000378743.3	hg19	CCDS41813.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.108600	0.77096	.	.	ENSG00000133858	ENST00000378743	T	0.33654	1.4	5.11	5.11	0.69529	.	0.596788	0.16463	N	0.213326	T	0.35278	0.0926	L	0.27053	0.805	0.80722	D	1	D	0.56521	0.976	P	0.47864	0.559	T	0.24154	-1.0168	10	0.87932	D	0	.	14.905	0.70711	1.0:0.0:0.0:0.0	.	1513	O60293	ZC3H1_HUMAN	G	1513	ENSP00000368017:V1513G	ENSP00000368017:V1513G	V	-	2	0	ZFC3H1	70303613	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	6.267000	0.72546	1.924000	0.55735	0.533000	0.62120	GTA	.	.		0.303	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982		C	72017346	A	C	72017346	3	2	289	1	0	0	0	0	1	0	0	0	17648	391	14	5	1479	5	ZFC3H1	12	72017346	Missense_Mutation	SNP	A	TCGA-G3-A6UC-01A-21D-A33K-10	4317495	72017346	61834549	82	42422										
P2RX2	22953	hgsc.bcm.edu	37	chr12	133197658	133197658	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	gcatcggagtgcaaccccaaGtactccttccggaggcttga	11	13	0	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr12:133197658G>A	ENST00000389110.3	+	8	883	c.846G>A	c.(844-846)aaG>aaA	p.K282K	P2RX2_ENST00000343948.4_Silent_p.K282K|P2RX2_ENST00000352418.4_Silent_p.K210K|P2RX2_ENST00000348800.5_Silent_p.K282K|P2RX2_ENST00000351222.4_Silent_p.K190K|P2RX2_ENST00000350048.5_Silent_p.K258K|P2RX2_ENST00000449132.2_Silent_p.K248K	NM_170682.2|NM_170683.2|NM_174873.1	NP_733782.1|NP_733783.1|NP_777362.1	Q9UBL9	P2RX2_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 2	282					behavioral response to pain (GO:0048266)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of hypoxic conditions in blood by carotid body chemoreceptor signaling (GO:0003029)|ion transmembrane transport (GO:0034220)|neuromuscular junction development (GO:0007528)|neuromuscular synaptic transmission (GO:0007274)|neuronal action potential (GO:0019228)|peristalsis (GO:0030432)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|response to ATP (GO:0033198)|response to carbohydrate (GO:0009743)|response to hypoxia (GO:0001666)|sensory perception of sound (GO:0007605)|sensory perception of taste (GO:0050909)|skeletal muscle fiber development (GO:0048741)|urinary bladder smooth muscle contraction (GO:0014832)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|dendritic spine (GO:0043197)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|cadmium ion binding (GO:0046870)|cobalt ion binding (GO:0050897)|copper ion binding (GO:0005507)|drug binding (GO:0008144)|extracellular ATP-gated cation channel activity (GO:0004931)|identical protein binding (GO:0042802)|ligand-gated ion channel activity (GO:0015276)|mercury ion binding (GO:0045340)|nickel cation binding (GO:0016151)|phosphatidylinositol binding (GO:0035091)|purinergic nucleotide receptor activity (GO:0001614)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|kidney(2)|large_intestine(2)|liver(2)|lung(8)|ovary(1)|prostate(3)	20	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0767)		OV - Ovarian serous cystadenocarcinoma(86;2.32e-08)|Epithelial(86;8.62e-08)|all cancers(50;4.5e-06)		GCAACCCCAAGTACTCCTTCC	0.592																																					p.K282K		Atlas-SNP	.											.	P2RX2	49	.	0			c.G846A						.						123	99	107					12																	133197658		2203	4300	6503	SO:0001819	synonymous_variant	22953	exon8			CCCCAAGTACTCC	AF109387	CCDS31930.1, CCDS31931.1, CCDS31932.1, CCDS31933.1, CCDS31934.1, CCDS31935.1, CCDS61286.1, CCDS73548.1	12q24.33	2013-03-22			ENSG00000187848	ENSG00000187848		"Purinergic receptors", "Ligand-gated ion channels / Purinergic receptors, ionotropic"	15459	protein-coding gene	gene with protein product		600844	"deafness, autosomal dominant 41"	DFNA41		10570044, 7523952, 23345450	Standard	XM_005266154		Approved	P2X2	uc001ukk.1	Q9UBL9	OTTHUMG00000168018	ENST00000389110.3:c.846G>A	chr12.hg19:g.133197658G>A		50.0	0.0		42.0	24.0	NM_170683	A6NGB4|A6NH93|A6NHC2|A6NHU3|A6NIG9|Q6V9R6|Q9NR37|Q9NR38|Q9UHD5|Q9UHD6|Q9UHD7|Q9Y637|Q9Y638	Silent	SNP	ENST00000389110.3	hg19	CCDS31931.1																																																																																			.	.		0.592	P2RX2-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397542.1			A	133197658	G	A	133197658	2	1	289	1	0	0	0	0	0	0	0	1	11349	1020	36	3		3	P2RX2	12	133197658	Silent	SNP	G	TCGA-G3-A6UC-01A-21D-A33K-10	61180312	133197658	654237	83	42423										
ZDHHC20	253832	hgsc.bcm.edu	37	chr13	21974596	21974597	+	Frame_Shift_Ins	INS	-	-	A													0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	acaataaaaacagcaggaagINSaatttgtaattagaaaatcc							TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr13:21974596_21974597insA	ENST00000400590.3	-	7	707_708	c.509_510insT	c.(508-510)ttcfs	p.F170fs	ZDHHC20_ENST00000320220.9_Frame_Shift_Ins_p.F170fs|ZDHHC20_ENST00000494731.1_5'UTR|ZDHHC20_ENST00000382466.3_Frame_Shift_Ins_p.F170fs|ZDHHC20_ENST00000542645.1_Frame_Shift_Ins_p.F107fs|ZDHHC20_ENST00000415724.1_Frame_Shift_Ins_p.F170fs			Q5W0Z9	ZDH20_HUMAN	zinc finger, DHHC-type containing 20	170					protein palmitoylation (GO:0018345)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	9		all_cancers(29;8.1e-16)|all_epithelial(30;3.63e-14)|all_lung(29;2.04e-13)|Lung SC(185;0.0367)		all cancers(112;0.000268)|Epithelial(112;0.000735)|OV - Ovarian serous cystadenocarcinoma(117;0.00517)|Lung(94;0.171)		ACAGCAGGAAGAATTTGTAATT	0.307																																					p.F170fs		Atlas-Indel,Pindel	.											.	ZDHHC20	36	.	0			c.510_511insT						.																																			SO:0001589	frameshift_variant	253832	exon7			.	AK090979	CCDS45017.1, CCDS73551.1	13q12.11	2008-10-21			ENSG00000180776	ENSG00000180776		"Zinc fingers, DHHC-type"	20749	protein-coding gene	gene with protein product							Standard	NM_153251		Approved	FLJ25952	uc001uoa.2	Q5W0Z9	OTTHUMG00000017410	ENST00000400590.3:c.510dupT	chr13.hg19:g.21974598_21974598dupA	ENSP00000383433:p.Phe170fs	332.0	0.0		405.0	177.0	NM_153251	A8MTV9|C9JG20|I6L9D4|Q2TB82|Q6NVU8	Frame_Shift_Ins	INS	ENST00000400590.3	hg19																																																																																				.	.		0.307	ZDHHC20-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000045994.1	NM_153251		A	21974597	-	A	21974596	7	5	289	1	0	1	1	0	0	0	0	0	17626	933	33	0	578	0	ZDHHC20	13	21974596	Frame_Shift_Ins	INS	-	TCGA-G3-A6UC-01A-21D-A33K-10		21974596	93195282	84	42424										
ATP8A2	51761	hgsc.bcm.edu	37	chr13	26273415	26273416	+	Missense_Mutation	DNP	GC	GC	TT													0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	ggccacaccctgaagtacgcGctctccttcgaagtccggag							TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr13:26273415_26273416GC>TT	ENST00000381655.2	+	25	2458_2459	c.2316_2317GC>TT	c.(2314-2319)gcGCtc>gcTTtc	p.L773F	ATP8A2_ENST00000255283.8_Missense_Mutation_p.L733F|ATP8A2_ENST00000491840.1_3'UTR	NM_016529.4	NP_057613.4	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8A, member 2	733					aging (GO:0007568)|axonogenesis (GO:0007409)|detection of light stimulus involved in visual perception (GO:0050908)|eating behavior (GO:0042755)|inner ear morphogenesis (GO:0042472)|involuntary skeletal muscle contraction (GO:0003011)|negative regulation of cell proliferation (GO:0008285)|neurofilament cytoskeleton organization (GO:0060052)|neuromuscular process controlling posture (GO:0050884)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phospholipid translocation (GO:0061092)|response to auditory stimulus (GO:0010996)|retina layer formation (GO:0010842)|skin development (GO:0043588)	cell projection (GO:0042995)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(17)|lung(31)|ovary(4)|skin(3)|stomach(1)|urinary_tract(1)	72		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		TGAAGTACGCGCTCTCCTTCGA	0.55																																					p.A772A|p.L773F		Atlas-SNP	.											.	ATP8A2	181	.	0			c.G2316T|c.C2317T						.																																			SO:0001583	missense	51761	exon25			GTACGCGCTCTCC|TACGCGCTCTCCT	AL137256	CCDS41873.1	13q12	2010-04-20	2010-03-31		ENSG00000132932	ENSG00000132932	3.6.3.1	"ATPases / P-type"	13533	protein-coding gene	gene with protein product		605870	"ATPase, aminophospholipid transporter-like, Class I, type 8A, member 2", "ATPase, aminophospholipid transporter-like, class I, type 8A, member 2"			11015572, 19778899	Standard	NM_016529		Approved	ATPIB, ML-1	uc001uqk.3	Q9NTI2	OTTHUMG00000016611	Exception_encountered	chr13.hg19:g.26273415_26273416delinsTT	ENSP00000371070:p.Leu773Phe	68.0|66.0	0.0		57.0	19.0|16.0	NM_016529	Q9H527|Q9NPU6|Q9NTL2|Q9NYM3	Silent|Missense_Mutation	SNP	ENST00000381655.2	hg19	CCDS41873.1																																																																																			.	.		0.55	ATP8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044236.2	NM_016529		TT	26273416	GC	TT	26273415	3	4	289	1	0	0	0	0	1	0	0	0	1193	1074	38	1	2414	1	ATP8A2	13	26273415	Missense_Mutation	DNP	GC	TCGA-G3-A6UC-01A-21D-A33K-10	4298819	26273415	88896463	85	42425										
FAM124A	220108	hgsc.bcm.edu	37	chr13	51854702	51854702	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	ccaagccatacacctggcagCagccagcagtccccgctcaa	8	18	1	0			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr13:51854702C>A	ENST00000322475.8	+	4	1086	c.951C>A	c.(949-951)agC>agA	p.S317R	FAM124A_ENST00000280057.6_Missense_Mutation_p.S353R	NM_001242312.1	NP_001229241.1	Q86V42	F124A_HUMAN	family with sequence similarity 124A	317										breast(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|skin(1)	26		Acute lymphoblastic leukemia(7;0.000334)|Breast(56;0.00156)|Prostate(109;0.00538)|Lung NSC(96;0.0216)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;4.25e-07)		CACCTGGCAGCAGCCAGCAGT	0.597																																					p.S353R		Atlas-SNP	.											.	FAM124A	61	.	0			c.C1059A						.						63	65	64					13																	51854702		2203	4300	6503	SO:0001583	missense	220108	exon5			TGGCAGCAGCCAG	AK096364	CCDS9427.1, CCDS55900.1	13q14.3	2006-08-11			ENSG00000150510	ENSG00000150510			26413	protein-coding gene	gene with protein product						12975309	Standard	NM_145019		Approved	FLJ30707	uc001vff.2	Q86V42	OTTHUMG00000016942	ENST00000322475.8:c.951C>A	chr13.hg19:g.51854702C>A	ENSP00000324625:p.Ser317Arg	49.0	0.0		44.0	13.0	NM_145019	A2A324|Q8N8P9|Q8NE66|Q96NJ9	Missense_Mutation	SNP	ENST00000322475.8	hg19	CCDS55900.1	.	.	.	.	.	.	.	.	.	.	C	14.43	2.531674	0.45073	.	.	ENSG00000150510	ENST00000322475;ENST00000280057	T;T	0.46451	0.87;0.87	4.97	4.12	0.48240	.	0.633137	0.16201	N	0.224936	T	0.34454	0.0898	L	0.50333	1.59	0.09310	N	1	B;B	0.33583	0.418;0.218	B;B	0.33521	0.162;0.165	T	0.15435	-1.0437	10	0.21014	T	0.42	.	8.7056	0.34351	0.0:0.8257:0.0:0.1743	.	317;353	Q86V42;Q86V42-2	F124A_HUMAN;.	R	317;353	ENSP00000324625:S317R;ENSP00000280057:S353R	ENSP00000280057:S353R	S	+	3	2	FAM124A	50752703	0.002000	0.14202	0.003000	0.11579	0.395000	0.30598	1.610000	0.36869	1.081000	0.41110	0.655000	0.94253	AGC	.	.		0.597	FAM124A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045019.3	NM_145019		A	51854702	C	A	51854702	3	1	289	1	0	0	0	0	1	0	0	0	5430	709	25	3	1077	3	FAM124A	13	51854702	Missense_Mutation	SNP	C	TCGA-G3-A6UC-01A-21D-A33K-10	25581287	51854702	63315176	86	42426										
TEP1	7011	hgsc.bcm.edu	37	chr14	20876328	20876328	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	atgtccatgtggtttctccaTggtcttcaggtcagaaagtg	11	8	4	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr14:20876328T>G	ENST00000262715.5	-	2	311	c.271A>C	c.(271-273)Atg>Ctg	p.M91L	TEP1_ENST00000556935.1_Missense_Mutation_p.M91L	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	91					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		GGTTTCTCCATGGTCTTCAGG	0.537																																					p.M91L		Atlas-SNP	.											.	TEP1	224	.	0			c.A271C						.						114	111	112					14																	20876328		2203	4300	6503	SO:0001583	missense	7011	exon2			TCTCCATGGTCTT		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"WD repeat domain containing"	11726	protein-coding gene	gene with protein product	"TROVE domain family, member 1"	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.271A>C	chr14.hg19:g.20876328T>G	ENSP00000262715:p.Met91Leu	173.0	0.0		182.0	75.0	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	hg19	CCDS9548.1	.	.	.	.	.	.	.	.	.	.	T	0.016	-1.526510	0.00959	.	.	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935;ENST00000556549	T;T;T	0.33438	1.41;1.41;1.41	4.98	-6.3	0.02007	.	0.991696	0.08208	N	0.981217	T	0.08670	0.0215	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.32719	-0.9896	10	0.02654	T	1	-0.6589	1.1701	0.01823	0.2437:0.1546:0.369:0.2328	.	91;91	G3V5X7;Q99973	.;TEP1_HUMAN	L	91	ENSP00000262715:M91L;ENSP00000452574:M91L;ENSP00000452240:M91L	ENSP00000262715:M91L	M	-	1	0	TEP1	19946168	0.000000	0.05858	0.000000	0.03702	0.343000	0.28985	-0.362000	0.07602	-1.245000	0.02513	-1.437000	0.01076	ATG	.	.		0.537	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		G	20876328	T	G	20876328	3	3	289	1	0	0	0	0	1	0	0	0	15774	1464	51	5	7828	5	TEP1	14	20876328	Missense_Mutation	SNP	T	TCGA-G3-A6UC-01A-21D-A33K-10		20876328	86473212	87	42427										
YLPM1	56252	hgsc.bcm.edu	37	chr14	75230510	75230510	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	tggcagccgccaccgccaccGatgcccccgccacccgggcc	11	23	0	0			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr14:75230510G>T	ENST00000552421.1	+	1	442	c.318G>T	c.(316-318)ccG>ccT	p.P106P	YLPM1_ENST00000325680.7_Silent_p.P106P|YLPM1_ENST00000238571.3_Silent_p.P106P			P49750	YLPM1_HUMAN	YLP motif containing 1	106	Pro-rich.				regulation of telomere maintenance (GO:0032204)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	62			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		CACCGCCACCGATGCCCCCGC	0.692																																					p.P106P		Atlas-SNP	.											.	YLPM1	298	.	0			c.G318T						.						27	34	32					14																	75230510		1889	4100	5989	SO:0001819	synonymous_variant	56252	exon1			GCCACCGATGCCC	AK090435	CCDS45135.1	14q24.3	2014-06-13	2004-07-15	2004-07-15	ENSG00000119596	ENSG00000119596			17798	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 169"		"chromosome 14 open reading frame 170"	C14orf170		7596406	Standard	NM_019589		Approved	ZAP, PPP1R169	uc001xqj.4	P49750	OTTHUMG00000172503	ENST00000552421.1:c.318G>T	chr14.hg19:g.75230510G>T		38.0	0.0		45.0	15.0	NM_019589	P49752|Q96I64|Q9P1V7	Silent	SNP	ENST00000552421.1	hg19																																																																																				.	.		0.692	YLPM1-008	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404450.1	NM_019589		T	75230510	G	T	75230510	2	4	289	1	0	0	0	0	0	0	0	1	17501	1045	37	1		1	YLPM1	14	75230510	Silent	SNP	G	TCGA-G3-A6UC-01A-21D-A33K-10	54354182	75230510	32119030	88	42428										
NEK9	91754	hgsc.bcm.edu	37	chr14	75590868	75590868	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	tctcattcaaggcatcacgaCgttccttctcagacagccgg	8	14	4	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr14:75590868C>T	ENST00000238616.5	-	2	436	c.278G>A	c.(277-279)cGt>cAt	p.R93H	RP11-950C14.7_ENST00000556236.1_RNA	NM_033116.4	NP_149107.4	Q8TD19	NEK9_HUMAN	NIMA-related kinase 9	93	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			endometrium(4)|kidney(2)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	31				BRCA - Breast invasive adenocarcinoma(234;0.00718)		GGCATCACGACGTTCCTTCTC	0.468																																					p.R93H		Atlas-SNP	.											.	NEK9	64	.	0			c.G278A						.						188	141	157					14																	75590868		2203	4300	6503	SO:0001583	missense	91754	exon2			TCACGACGTTCCT	AY048580	CCDS9839.1	14q24.2	2012-11-15	2012-11-15		ENSG00000119638	ENSG00000119638			18591	protein-coding gene	gene with protein product		609798	"NIMA (never in mitosis gene a)- related kinase 9"			11864968	Standard	NM_033116		Approved	Nek8, NERCC, DKFZp434D0935, MGC16714	uc001xrl.3	Q8TD19	OTTHUMG00000171768	ENST00000238616.5:c.278G>A	chr14.hg19:g.75590868C>T	ENSP00000238616:p.Arg93His	131.0	0.0		134.0	13.0	NM_033116	Q52LK6|Q8NCN0|Q8TCY4|Q9UPI4|Q9Y6S4|Q9Y6S5|Q9Y6S6	Missense_Mutation	SNP	ENST00000238616.5	hg19	CCDS9839.1	.	.	.	.	.	.	.	.	.	.	C	36	5.825949	0.96996	.	.	ENSG00000119638	ENST00000238616;ENST00000540227	T	0.66460	-0.21	6.17	6.17	0.99709	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.097256	0.64402	D	0.000001	T	0.82240	0.4994	M	0.76433	2.335	0.80722	D	1	D	0.76494	0.999	D	0.64506	0.926	T	0.82281	-0.0535	10	0.87932	D	0	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	93	Q8TD19	NEK9_HUMAN	H	93;75	ENSP00000238616:R93H	ENSP00000238616:R93H	R	-	2	0	NEK9	74660621	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.752000	0.85141	2.941000	0.99782	0.655000	0.94253	CGT	.	.		0.468	NEK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415021.1	NM_033116		T	75590868	C	T	75590868	3	4	289	1	0	0	0	0	1	0	0	0	10340	536	19	1	2745	1	NEK9	14	75590868	Missense_Mutation	SNP	C	TCGA-G3-A6UC-01A-21D-A33K-10	360358	75590868	31758672	89	42429										
FLRT2	23768	hgsc.bcm.edu	37	chr14	86089139	86089139	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	atttctgaacggatccagctCtctatccattttgtgaatga	7	9	2	3			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr14:86089139C>A	ENST00000330753.4	+	2	2048	c.1281C>A	c.(1279-1281)ctC>ctA	p.L427L	FLRT2_ENST00000554746.1_Silent_p.L427L	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	427	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		GGATCCAGCTCTCTATCCATT	0.488																																					p.L427L		Atlas-SNP	.											.	FLRT2	168	.	0			c.C1281A						.						65	64	64					14																	86089139		2203	4300	6503	SO:0001819	synonymous_variant	23768	exon2			CCAGCTCTCTATC	AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070		"Fibronectin type III domain containing"	3761	protein-coding gene	gene with protein product		604807				10644439, 16872596	Standard	XM_005267490		Approved		uc001xvr.3	O43155		ENST00000330753.4:c.1281C>A	chr14.hg19:g.86089139C>A		171.0	0.0		137.0	58.0	NM_013231	A0AV84|B7ZLP3	Silent	SNP	ENST00000330753.4	hg19	CCDS9877.1																																																																																			.	.		0.488	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1			A	86089139	C	A	86089139	2	1	289	1	0	0	0	0	0	0	0	1	5947	900	32	3		3	FLRT2	14	86089139	Silent	SNP	C	TCGA-G3-A6UC-01A-21D-A33K-10	10498271	86089139	21260401	90	42430										
FMN1	342184	hgsc.bcm.edu	37	chr15	33359765	33359765	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	gtccctgcttcttttctctgActtccctctgattctgtctc	5	15	5	2			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr15:33359765A>G	ENST00000559047.1	-	3	2043				FMN1_ENST00000561249.1_Intron|FMN1_ENST00000559150.1_Intron|FMN1_ENST00000334528.9_Silent_p.S107S|FMN1_ENST00000558197.1_Silent_p.S107S			Q68DA7	FMN1_HUMAN	formin 1						actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		CTTTTCTCTGACTTCCCTCTG	0.498																																					p.S107S		Atlas-SNP	.											.	FMN1	174	.	0			c.T321C						.						90	90	90					15																	33359765		1945	4156	6101	SO:0001627	intron_variant	342184	exon1			TCTCTGACTTCCC	AH002864	CCDS45209.1, CCDS61581.1, CCDS61582.1	15q13.3	2013-06-13	2005-01-20	2005-01-22	ENSG00000248905	ENSG00000248905			3768	protein-coding gene	gene with protein product	"limb deformity protein"	136535	"formin (limb deformity)"	LD, FMN		1673046	Standard	NM_001277313		Approved	DKFZP686C2281, FLJ45135, MGC125288, MGC125289	uc031qrh.1	Q68DA7	OTTHUMG00000172201	ENST00000559047.1:c.2044-2490T>C	chr15.hg19:g.33359765A>G		111.0	0.0		166.0	44.0	NM_001103184	Q3B7I6|Q3ZAR4|Q6ZSY1	Silent	SNP	ENST00000559047.1	hg19																																																																																				.	.		0.498	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184		G	33359765	A	G	33359765	1	3	289	0	1	0	0	0	0	0	0	0	5957	272	10	2		2	FMN1	15	33359765	Intron	SNP	A	TCGA-G3-A6UC-01A-21D-A33K-10		33359765	69171627	91	42431										
FMN1	342184	hgsc.bcm.edu	37	chr15	33359984	33359984	+	Intron	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	aacccaaatagggatttcatAgagaacttactcaggatcga	8	8	2	1	rs184741064		TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr15:33359984A>T	ENST00000559047.1	-	3	2043				FMN1_ENST00000561249.1_Intron|FMN1_ENST00000559150.1_Intron|FMN1_ENST00000334528.9_Silent_p.S34S|FMN1_ENST00000558197.1_Silent_p.S34S			Q68DA7	FMN1_HUMAN	formin 1						actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		GGGATTTCATAGAGAACTTAC	0.433																																					p.S34S		Atlas-SNP	.											.	FMN1	174	.	0			c.T102A						.						75	71	72					15																	33359984		1902	4129	6031	SO:0001627	intron_variant	342184	exon1			TTTCATAGAGAAC	AH002864	CCDS45209.1, CCDS61581.1, CCDS61582.1	15q13.3	2013-06-13	2005-01-20	2005-01-22	ENSG00000248905	ENSG00000248905			3768	protein-coding gene	gene with protein product	"limb deformity protein"	136535	"formin (limb deformity)"	LD, FMN		1673046	Standard	NM_001277313		Approved	DKFZP686C2281, FLJ45135, MGC125288, MGC125289	uc031qrh.1	Q68DA7	OTTHUMG00000172201	ENST00000559047.1:c.2044-2709T>A	chr15.hg19:g.33359984A>T		79.0	0.0		127.0	39.0	NM_001103184	Q3B7I6|Q3ZAR4|Q6ZSY1	Silent	SNP	ENST00000559047.1	hg19																																																																																				.	A|1.000;G|0.000		0.433	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184		T	33359984	A	T	33359984	1	4	289	0	1	0	0	0	0	0	0	0	5957	407	15	4		4	FMN1	15	33359984	Intron	SNP	A	TCGA-G3-A6UC-01A-21D-A33K-10	219	33359984	69171408	92	42432										
CGNL1	84952	hgsc.bcm.edu	37	chr15	57731023	57731023	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	agaaaaccaggccagatgttCttcccttccggcgacaggat	10	12	1	2			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr15:57731023C>T	ENST00000281282.5	+	2	904	c.826C>T	c.(826-828)Ctt>Ttt	p.L276F		NM_001252335.1|NM_032866.4	NP_001239264.1|NP_116255.2	Q0VF96	CGNL1_HUMAN	cingulin-like 1	276	Head.					myosin complex (GO:0016459)|tight junction (GO:0005923)	motor activity (GO:0003774)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(14)|ovary(4)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)	60				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)		GCCAGATGTTCTTCCCTTCCG	0.617																																					p.L276F		Atlas-SNP	.											.	CGNL1	125	.	0			c.C826T						.						55	59	58					15																	57731023		2192	4292	6484	SO:0001583	missense	84952	exon3			GATGTTCTTCCCT	AY274808	CCDS10161.1	15q21.3	2011-06-10			ENSG00000128849	ENSG00000128849			25931	protein-coding gene	gene with protein product		607856				11214970	Standard	NM_001252335		Approved	FLJ14957, JACOP, KIAA1749, paracingulin	uc002aeg.3	Q0VF96	OTTHUMG00000166485	ENST00000281282.5:c.826C>T	chr15.hg19:g.57731023C>T	ENSP00000281282:p.Leu276Phe	196.0	0.0		237.0	58.0	NM_001252335	Q05BZ4|Q52LR0|Q695C7|Q7Z2L3|Q96JV2|Q96MN6|Q9C0B4	Missense_Mutation	SNP	ENST00000281282.5	hg19	CCDS10161.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.631990	0.87660	.	.	ENSG00000128849	ENST00000281282	T	0.55588	0.51	5.27	5.27	0.74061	.	0.000000	0.45606	D	0.000346	T	0.71160	0.3307	M	0.62723	1.935	0.54753	D	0.999985	D	0.89917	1.0	D	0.85130	0.997	T	0.69971	-0.5000	10	0.46703	T	0.11	-15.6301	19.0822	0.93187	0.0:1.0:0.0:0.0	.	276	Q0VF96	CGNL1_HUMAN	F	276	ENSP00000281282:L276F	ENSP00000281282:L276F	L	+	1	0	CGNL1	55518315	1.000000	0.71417	0.878000	0.34440	0.814000	0.46013	6.992000	0.76238	2.722000	0.93159	0.655000	0.94253	CTT	.	.		0.617	CGNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255482.2	NM_032866		T	57731023	C	T	57731023	3	4	289	1	0	0	0	0	1	0	0	0	3306	913	32	3	828	3	CGNL1	15	57731023	Missense_Mutation	SNP	C	TCGA-G3-A6UC-01A-21D-A33K-10	24371039	57731023	44800369	93	42433										
SALL1	6299	hgsc.bcm.edu	37	chr16	51173435	51173435	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	acccactgaggatgaatcatTggtcaggacatccccctcga	9	13	2	2			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr16:51173435T>C	ENST00000251020.4	-	2	2731	c.2698A>G	c.(2698-2700)Aat>Gat	p.N900D	SALL1_ENST00000566102.1_Intron|SALL1_ENST00000440970.1_Missense_Mutation_p.N803D|SALL1_ENST00000541611.1_Intron	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	900					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			GATGAATCATTGGTCAGGACA	0.547																																					p.N900D	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											.	SALL1	301	.	0			c.A2698G						.						99	77	85					16																	51173435		2198	4300	6498	SO:0001583	missense	6299	exon2			AATCATTGGTCAG	X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"Zinc fingers, C2H2-type"	10524	protein-coding gene	gene with protein product		602218	"sal (Drosophila)-like 1", "sal-like 1 (Drosophila)"	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.2698A>G	chr16.hg19:g.51173435T>C	ENSP00000251020:p.Asn900Asp	67.0	0.0		65.0	25.0	NM_002968	Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	hg19	CCDS10747.1	.	.	.	.	.	.	.	.	.	.	T	13.83	2.354902	0.41700	.	.	ENSG00000103449	ENST00000251020;ENST00000440970;ENST00000457559	T;T	0.78595	-1.19;-1.19	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	D	0.85678	0.5752	M	0.80332	2.49	0.80722	D	1	D	0.63046	0.992	P	0.55785	0.784	D	0.87543	0.2460	10	0.59425	D	0.04	.	15.6025	0.76636	0.0:0.0:0.0:1.0	.	900	Q9NSC2	SALL1_HUMAN	D	900;803;864	ENSP00000251020:N900D;ENSP00000407914:N803D	ENSP00000251020:N900D	N	-	1	0	SALL1	49730936	1.000000	0.71417	0.999000	0.59377	0.089000	0.18198	8.040000	0.89188	2.085000	0.62840	0.455000	0.32223	AAT	.	.		0.547	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968		C	51173435	T	C	51173435	3	2	289	1	0	0	0	0	1	0	0	0	13825	1812	63	2	1284	2	SALL1	16	51173435	Missense_Mutation	SNP	T	TCGA-G3-A6UC-01A-21D-A33K-10		51173435	39181318	94	42434										
USP6	9098	hgsc.bcm.edu	37	chr17	5072174	5072174	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	tgcttttttggtaccacgagAcccggccctctgccagcata	9	14	1	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr17:5072174A>G	ENST00000574788.1	+	35	5571	c.3341A>G	c.(3340-3342)gAc>gGc	p.D1114G	USP6_ENST00000304328.5_Missense_Mutation_p.D797G|USP6_ENST00000250066.6_Missense_Mutation_p.D1114G|USP6_ENST00000332776.4_3'UTR			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	1114	USP.				cellular protein modification process (GO:0006464)|protein deubiquitination (GO:0016579)|regulation of vesicle-mediated transport (GO:0060627)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	calmodulin binding (GO:0005516)|cysteine-type endopeptidase activity (GO:0004197)|nucleic acid binding (GO:0003676)|Rab GTPase activator activity (GO:0005097)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						GTACCACGAGACCCGGCCCTC	0.473			T	"COL1A1, CDH11, ZNF9, OMD"	aneurysmal bone cysts																																p.D1114G		Atlas-SNP	.		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	.	USP6	213	.	0			c.A3341G						.						108	117	114					17																	5072174		2203	4300	6503	SO:0001583	missense	9098	exon27			CACGAGACCCGGC	X63547	CCDS11069.2	17p13	2014-06-12	2014-06-12		ENSG00000129204	ENSG00000129204	3.4.19.12	"Ubiquitin-specific peptidases"	12629	protein-coding gene	gene with protein product	"ubiquitin carboxyl-terminal hydrolase 6", "TBC1D3 and USP32 fusion", "Tre-2 oncogene"	604334	"ubiquitin specific protease 6 (Tre-2 oncogene)", "TRE oncogene, Smith Magenis syndrome chromosome region", "ubiquitin specific peptidase 6 (Tre-2 oncogene)"	HRP1, TRESMCR		12838346, 1349106	Standard	NM_004505		Approved	Tre-2, TRE17, Tre2	uc002gav.1	P35125	OTTHUMG00000099449	ENST00000574788.1:c.3341A>G	chr17.hg19:g.5072174A>G	ENSP00000460380:p.Asp1114Gly	218.0	1.0		188.0	88.0	NM_004505	Q15634|Q86WP6|Q8IWT4	Missense_Mutation	SNP	ENST00000574788.1	hg19	CCDS11069.2	.	.	.	.	.	.	.	.	.	.	A	6.157	0.397222	0.11638	.	.	ENSG00000129204	ENST00000250066;ENST00000304328	T;T	0.31769	1.48;1.48	2.35	1.16	0.20824	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.144593	0.64402	D	0.000006	T	0.16385	0.0394	N	0.24115	0.695	0.36649	D	0.877306	B;B	0.14438	0.004;0.01	B;B	0.19666	0.009;0.026	T	0.07693	-1.0759	10	0.51188	T	0.08	.	2.7335	0.05234	0.5608:0.2776:0.1616:0.0	.	797;1114	P35125-2;P35125	.;UBP6_HUMAN	G	1114;797	ENSP00000250066:D1114G;ENSP00000305473:D797G	ENSP00000250066:D1114G	D	+	2	0	USP6	5012898	1.000000	0.71417	0.957000	0.39632	0.072000	0.16883	4.658000	0.61497	0.133000	0.18654	0.155000	0.16302	GAC	.	.		0.473	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505		G	5072174	A	G	5072174	3	3	289	1	0	0	0	0	1	0	0	0	17101	275	10	2	3443	2	USP6	17	5072174	Missense_Mutation	SNP	A	TCGA-G3-A6UC-01A-21D-A33K-10		5072174	76123036	95	42435										
MYH1	4619	hgsc.bcm.edu	37	chr17	10399270	10399270	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	tctattattacatgcacctgGgtgtgcaggagctgaacacg	11	9	1	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr17:10399270G>C	ENST00000226207.5	-	35	5260	c.5166C>G	c.(5164-5166)acC>acG	p.T1722T	RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	1722					muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						CATGCACCTGGGTGTGCAGGA	0.448																																					p.T1722T		Atlas-SNP	.											.	MYH1	403	.	0			c.C5166G						.						66	62	63					17																	10399270		2203	4300	6503	SO:0001819	synonymous_variant	4619	exon35			CACCTGGGTGTGC		CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"Myosins / Myosin superfamily : Class II"	7567	protein-coding gene	gene with protein product	"myosin heavy chain IIx/d"	160730	"myosin, heavy polypeptide 1, skeletal muscle, adult"			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.5166C>G	chr17.hg19:g.10399270G>C		63.0	0.0		59.0	28.0	NM_005963	Q14CA4|Q9Y622	Silent	SNP	ENST00000226207.5	hg19	CCDS11155.1																																																																																			.	.		0.448	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963		C	10399270	G	C	10399270	2	2	289	1	0	0	0	0	0	0	0	1	10038	1219	43	4		4	MYH1	17	10399270	Silent	SNP	G	TCGA-G3-A6UC-01A-21D-A33K-10	5327096	10399270	70795940	96	42436										
MYH1	4619	hgsc.bcm.edu	37	chr17	10408340	10408340	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	cagggccagtgcttcacattCatgaaggcacggacattgta	11	10	2	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr17:10408340C>T	ENST00000226207.5	-	22	2572	c.2478G>A	c.(2476-2478)atG>atA	p.M826I	RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	826					muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						GCTTCACATTCATGAAGGCAC	0.423																																					p.M826I		Atlas-SNP	.											.	MYH1	403	.	0			c.G2478A						.						98	92	94					17																	10408340		2203	4300	6503	SO:0001583	missense	4619	exon22			CACATTCATGAAG		CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"Myosins / Myosin superfamily : Class II"	7567	protein-coding gene	gene with protein product	"myosin heavy chain IIx/d"	160730	"myosin, heavy polypeptide 1, skeletal muscle, adult"			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.2478G>A	chr17.hg19:g.10408340C>T	ENSP00000226207:p.Met826Ile	85.0	0.0		67.0	31.0	NM_005963	Q14CA4|Q9Y622	Missense_Mutation	SNP	ENST00000226207.5	hg19	CCDS11155.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.011166	0.75046	.	.	ENSG00000109061	ENST00000226207	T	0.71103	-0.54	5.47	5.47	0.80525	.	0.000000	0.52532	U	0.000072	T	0.72061	0.3414	M	0.66439	2.03	0.58432	D	0.999999	B	0.13594	0.008	B	0.18263	0.021	T	0.67722	-0.5597	10	0.48119	T	0.1	.	19.6961	0.96026	0.0:1.0:0.0:0.0	.	826	P12882	MYH1_HUMAN	I	826	ENSP00000226207:M826I	ENSP00000226207:M826I	M	-	3	0	MYH1	10349065	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.963000	0.70372	2.745000	0.94114	0.650000	0.86243	ATG	.	.		0.423	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963		T	10408340	C	T	10408340	3	4	289	1	0	0	0	0	1	0	0	0	10038	826	29	3	3417	3	MYH1	17	10408340	Missense_Mutation	SNP	C	TCGA-G3-A6UC-01A-21D-A33K-10	9070	10408340	70786870	97	42437										
SLFN13	146857	hgsc.bcm.edu	37	chr17	33769276	33769276	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	cagctccttccagagggactCtggagtacattccaaatgtc	9	12	1	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr17:33769276C>A	ENST00000285013.6	-	5	1503	c.1228G>T	c.(1228-1230)Gag>Tag	p.E410*	SLFN13_ENST00000542635.1_Nonsense_Mutation_p.E410*|SLFN13_ENST00000533791.1_Nonsense_Mutation_p.E410*|SLFN13_ENST00000534689.1_Nonsense_Mutation_p.E92*|SLFN13_ENST00000526861.1_Nonsense_Mutation_p.E410*|SLFN13_ENST00000360502.2_Nonsense_Mutation_p.E92*	NM_144682.5	NP_653283.3	Q68D06	SLN13_HUMAN	schlafen family member 13	410						intracellular (GO:0005622)	ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(1)|large_intestine(10)|lung(8)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	31				UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		CAGAGGGACTCTGGAGTACAT	0.403																																					p.E410X		Atlas-SNP	.											.	SLFN13	79	.	0			c.G1228T						.						58	56	56					17																	33769276		2203	4300	6503	SO:0001587	stop_gained	146857	exon5			GGGACTCTGGAGT	AL832726	CCDS32620.1	17q12	2006-04-05				ENSG00000154760			26481	protein-coding gene	gene with protein product		614957				9846487	Standard	NM_144682		Approved	FLJ31952	uc002hjl.2	Q68D06		ENST00000285013.6:c.1228G>T	chr17.hg19:g.33769276C>A	ENSP00000285013:p.Glu410*	41.0	0.0		43.0	19.0	NM_144682	E1P645|Q658M1|Q6ZS51|Q96A81	Nonsense_Mutation	SNP	ENST00000285013.6	hg19	CCDS32620.1	.	.	.	.	.	.	.	.	.	.	c	25.7	4.662025	0.88251	.	.	ENSG00000154760	ENST00000285013;ENST00000360502;ENST00000526861;ENST00000542635;ENST00000534689;ENST00000532210	.	.	.	3.21	-0.296	0.12824	.	0.600105	0.14848	N	0.294891	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	3.469	0.07561	0.0:0.5194:0.2148:0.2657	.	.	.	.	X	410;92;410;410;92;79	.	ENSP00000285013:E410X	E	-	1	0	SLFN13	30793389	0.002000	0.14202	0.000000	0.03702	0.030000	0.12068	0.253000	0.18296	-0.121000	0.11787	0.407000	0.27541	GAG	.	.		0.403	SLFN13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381883.1	NM_144682		A	33769276	C	A	33769276	4	1	289	1	0	0	0	0	0	1	0	0	14751	922	32	3	1473	3	SLFN13	17	33769276	Nonsense_Mutation	SNP	C	TCGA-G3-A6UC-01A-21D-A33K-10	23360936	33769276	47425934	98	42438										
PIGW	284098	hgsc.bcm.edu	37	chr17	34894023	34894034	+	In_Frame_Del	DEL	AAGTAAATGTAG	AAGTAAATGTAG	-													0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	catatctctttacgtagttcAagtaaatgtagaagcagtat					rs138980777|rs551293655	byFrequency	TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	AAGTAAATGTAG	AAGTAAATGTAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr17:34894023_34894034delAAGTAAATGTAG	ENST00000592983.1	+	2	1653_1664	c.1073_1084delAAGTAAATGTAG	c.(1072-1086)caagtaaatgtagaa>caa	p.VNVE359del	MYO19_ENST00000590081.1_Intron|PIGW_ENST00000328396.2_In_Frame_Del_p.VNVE359del			Q7Z7B1	PIGW_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class W	359					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transferase activity, transferring acyl groups (GO:0016746)			breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TACGTAGTTCAAGTAAATGTAGAAGCAGTATC	0.34																																					p.358_361del		Atlas-Indel,Pindel	.											.	PIGW	50	.	0			c.1072_1083del						.																																			SO:0001651	inframe_deletion	284098	exon2			.	AB097818	CCDS11313.1	17q21.1	2014-05-06	2006-06-28		ENSG00000184886	ENSG00000277161		"Phosphatidylinositol glycan anchor biosynthesis"	23213	protein-coding gene	gene with protein product		610275	"phosphatidylinositol glycan, class W"			14517336, 12714589	Standard	XM_005257238		Approved	Gwt1, FLJ37433	uc002hmz.1	Q7Z7B1	OTTHUMG00000188438	ENST00000592983.1:c.1073_1084delAAGTAAATGTAG	chr17.hg19:g.34894023_34894034delAAGTAAATGTAG	ENSP00000468778:p.Val359_Glu362del	53.0	0.0		53.0	12.0	NM_178517	Q8N9G3	In_Frame_Del	DEL	ENST00000592983.1	hg19	CCDS11313.1																																																																																			.	.		0.34	PIGW-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451318.1	NM_178517		-	34894034	AAGTAAATGTAG	-	34894023	7	5	289	1	0	1	0	1	0	0	0	0	11911	130	5	0	1075	0	PIGW	17	34894023	In_Frame_Del	DEL	AAGTAAATGTAG	TCGA-G3-A6UC-01A-21D-A33K-10	1124747	34894023	46301187	99	42439										
SOCS7	30837	hgsc.bcm.edu	37	chr17	36508355	36508355	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	gggccgggggtcaagacagtCggtgggggttgctgcccgtg	21	9	1	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr17:36508355C>T	ENST00000577233.1	+	1	228	c.228C>T	c.(226-228)gtC>gtT	p.V76V	SOCS7_ENST00000331159.5_Silent_p.V76V	NM_014598.2	NP_055413.1	O14512	SOCS7_HUMAN	suppressor of cytokine signaling 7	76					fat cell differentiation (GO:0045444)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|negative regulation of signal transduction (GO:0009968)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	SH3 domain binding (GO:0017124)			central_nervous_system(1)|endometrium(1)|kidney(1)|prostate(1)|skin(5)	9	Breast(7;3.47e-17)					TCAAGACAGTCGGTGGGGGTT	0.766																																					p.V76V		Atlas-SNP	.											.	SOCS7	22	.	0			c.C228T						.						2	4	3					17																	36508355		1355	2657	4012	SO:0001819	synonymous_variant	30837	exon1			GACAGTCGGTGGG	AB005216	CCDS32637.1	17q12	2014-08-12			ENSG00000274211	ENSG00000274211		"Suppressors of cytokine signaling", "SH2 domain containing"	29846	protein-coding gene	gene with protein product	"Nck, Ash and phospholipase C binding protein", "NCK-associated protein 4"	608788				9344857, 12076535	Standard	XM_005257264		Approved	NAP4, NCKAP4	uc002hqa.3	O14512	OTTHUMG00000188546	ENST00000577233.1:c.228C>T	chr17.hg19:g.36508355C>T		28.0	0.0		38.0	12.0	NM_014598	A2VCU2|Q0IJ63	Silent	SNP	ENST00000577233.1	hg19	CCDS32637.1																																																																																			.	.		0.766	SOCS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440486.4	XM_371052		T	36508355	C	T	36508355	2	4	289	1	0	0	0	0	0	0	0	1	14934	871	31	1		1	SOCS7	17	36508355	Silent	SNP	C	TCGA-G3-A6UC-01A-21D-A33K-10	1614332	36508355	44686855	100	42440										
FHOD3	80206	hgsc.bcm.edu	37	chr18	34156492	34156492	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	aaccattcagtggctgtacaCtctcattgggtcaaaggtaa	9	9	3	0	rs147225084		TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr18:34156492C>A	ENST00000359247.4	+	6	590	c.590C>A	c.(589-591)aCt>aAt	p.T197N	FHOD3_ENST00000445677.1_Missense_Mutation_p.T197N|FHOD3_ENST00000591635.1_5'UTR|FHOD3_ENST00000257209.4_Missense_Mutation_p.T197N|FHOD3_ENST00000590592.1_Missense_Mutation_p.T197N	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	197	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)				NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				TGGCTGTACACTCTCATTGGG	0.393																																					p.T197N		Atlas-SNP	.											.	FHOD3	210	.	0			c.C590A						.						127	113	118					18																	34156492		2203	4300	6503	SO:0001583	missense	80206	exon6			TGTACACTCTCAT	AK091899	CCDS32816.1, CCDS62418.1, CCDS62419.1	18q12	2007-08-02				ENSG00000134775			26178	protein-coding gene	gene with protein product		609691				11214970	Standard	NM_025135		Approved	FHOS2, KIAA1695, FLJ22297, FLJ22717	uc021uiv.1	Q2V2M9		ENST00000359247.4:c.590C>A	chr18.hg19:g.34156492C>A	ENSP00000352186:p.Thr197Asn	82.0	0.0		86.0	32.0	NM_025135	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Missense_Mutation	SNP	ENST00000359247.4	hg19		.	.	.	.	.	.	.	.	.	.	C	20.4	3.981161	0.74474	.	.	ENSG00000134775	ENST00000257209;ENST00000359247;ENST00000445677	T;T;T	0.23950	1.88;1.88;1.88	5.73	5.73	0.89815	GTPase-binding/formin homology 3 (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.050173	0.85682	D	0.000000	T	0.44746	0.1308	M	0.68317	2.08	0.32471	N	0.542826	D;D;P	0.59357	0.982;0.985;0.74	P;P;P	0.55260	0.664;0.772;0.583	T	0.56384	-0.7988	10	0.72032	D	0.01	.	17.3817	0.87406	0.0:1.0:0.0:0.0	.	197;197;197	Q2V2M9;Q2V2M9-3;E5F5Q0	FHOD3_HUMAN;.;.	N	197	ENSP00000257209:T197N;ENSP00000352186:T197N;ENSP00000411430:T197N	ENSP00000257209:T197N	T	+	2	0	FHOD3	32410490	1.000000	0.71417	0.981000	0.43875	0.975000	0.68041	4.458000	0.60095	2.694000	0.91930	0.655000	0.94253	ACT	.	C|1.000;T|0.000		0.393	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114		A	34156492	C	A	34156492	3	1	289	1	0	0	0	0	1	0	0	0	5891	565	20	3	612	3	FHOD3	18	34156492	Missense_Mutation	SNP	C	TCGA-G3-A6UC-01A-21D-A33K-10		34156492	43920756	101	42441										
TXNL1	9352	hgsc.bcm.edu	37	chr18	54285333	54285333	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	aagacattcacaaccagcttTgttaataaaaggcattaaat	5	7	1	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr18:54285333T>C	ENST00000217515.6	-	4	598	c.394A>G	c.(394-396)Aaa>Gaa	p.K132E	TXNL1_ENST00000540155.1_Missense_Mutation_p.K9E|TXNL1_ENST00000590954.1_Missense_Mutation_p.K132E	NM_004786.2	NP_004777.1	O43396	TXNL1_HUMAN	thioredoxin-like 1	132	PITH. {ECO:0000255|PROSITE- ProRule:PRU00864}.				cell redox homeostasis (GO:0045454)|glycerol ether metabolic process (GO:0006662)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	disulfide oxidoreductase activity (GO:0015036)|protein disulfide oxidoreductase activity (GO:0015035)			endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4				READ - Rectum adenocarcinoma(59;0.193)|Colorectal(16;0.211)		CAACCAGCTTTGTTAATAAAA	0.308																																					p.K132E		Atlas-SNP	.											.	TXNL1	30	.	0			c.A394G						.						102	94	97					18																	54285333		2202	4300	6502	SO:0001583	missense	9352	exon4			CAGCTTTGTTAAT	AF003938	CCDS11961.1	18q21.31	2011-01-17	2004-05-06	2004-05-07	ENSG00000091164	ENSG00000091164			12436	protein-coding gene	gene with protein product	"thioredoxin-like, 32kD"	603049	"thioredoxin-like, 32kDa"	TXNL		9473519, 9668102	Standard	NM_004786		Approved	Txl, TRP32	uc002lgg.3	O43396	OTTHUMG00000132722	ENST00000217515.6:c.394A>G	chr18.hg19:g.54285333T>C	ENSP00000217515:p.Lys132Glu	47.0	0.0		51.0	23.0	NM_004786		Missense_Mutation	SNP	ENST00000217515.6	hg19	CCDS11961.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.197784	0.79015	.	.	ENSG00000091164	ENST00000217515;ENST00000540155	T	0.18016	2.24	5.69	5.69	0.88448	Proteasome-interacting thioredoxin-like domain, C-terminal (1);Galactose-binding domain-like (1);	0.041576	0.85682	D	0.000000	T	0.35189	0.0923	M	0.84846	2.72	0.80722	D	1	P;P	0.43750	0.816;0.514	P;P	0.48425	0.577;0.502	T	0.16335	-1.0406	10	0.30854	T	0.27	.	15.5967	0.76587	0.0:0.0:0.0:1.0	.	132;132	B2R960;O43396	.;TXNL1_HUMAN	E	132;9	ENSP00000217515:K132E	ENSP00000217515:K132E	K	-	1	0	TXNL1	52436331	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.613000	0.82986	2.160000	0.67779	0.482000	0.46254	AAA	.	.		0.308	TXNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256064.2			C	54285333	T	C	54285333	3	2	289	1	0	0	0	0	1	0	0	0	16819	1821	63	2	495	2	TXNL1	18	54285333	Missense_Mutation	SNP	T	TCGA-G3-A6UC-01A-21D-A33K-10	20128841	54285333	23791915	102	42442										
TSHZ3	57616	hgsc.bcm.edu	37	chr19	31768705	31768705	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	tggggctgttctcctggctgCggaagcccccatcgctggat	14	13	1	0			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr19:31768705C>T	ENST00000240587.4	-	2	2321	c.1994G>A	c.(1993-1995)cGc>cAc	p.R665H		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	665					in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					CTCCTGGCTGCGGAAGCCCCC	0.662																																					p.R665H		Atlas-SNP	.											.	TSHZ3	549	.	0			c.G1994A						.						17	19	18					19																	31768705		2198	4284	6482	SO:0001583	missense	57616	exon2			TGGCTGCGGAAGC	AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	30700	protein-coding gene	gene with protein product	"teashirt 3"	614119	"zinc finger protein 537", "teashirt family zinc finger 3"	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.1994G>A	chr19.hg19:g.31768705C>T	ENSP00000240587:p.Arg665His	65.0	0.0		44.0	18.0	NM_020856	Q9H0G6|Q9P254	Missense_Mutation	SNP	ENST00000240587.4	hg19	CCDS12421.2	.	.	.	.	.	.	.	.	.	.	C	5.503	0.277747	0.10403	.	.	ENSG00000121297	ENST00000240587	T	0.43294	0.95	5.35	3.16	0.36331	.	0.342599	0.33895	N	0.004445	T	0.21387	0.0515	N	0.14661	0.345	0.21064	N	0.999793	P	0.34892	0.474	B	0.22386	0.039	T	0.08106	-1.0738	10	0.51188	T	0.08	-1.0788	9.744	0.40435	0.0:0.1399:0.0:0.8601	.	665	Q63HK5	TSH3_HUMAN	H	665	ENSP00000240587:R665H	ENSP00000240587:R665H	R	-	2	0	TSHZ3	36460545	0.897000	0.30589	0.792000	0.32020	0.009000	0.06853	1.223000	0.32527	0.321000	0.23259	-1.223000	0.01593	CGC	.	.		0.662	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856		T	31768705	C	T	31768705	3	4	289	1	0	0	0	0	1	0	0	0	16640	768	27	1	1255	1	TSHZ3	19	31768705	Missense_Mutation	SNP	C	TCGA-G3-A6UC-01A-21D-A33K-10		31768705	27360278	103	42443										
PRKD2	25865	hgsc.bcm.edu	37	chr19	47192900	47192900	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	tctccatcaccacaaacactTtctcaggcgtctcgaacatg	5	15	4	0			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr19:47192900T>A	ENST00000291281.4	-	14	2090	c.1865A>T	c.(1864-1866)aAa>aTa	p.K622I	PRKD2_ENST00000600194.1_Missense_Mutation_p.K465I|PRKD2_ENST00000595515.1_Missense_Mutation_p.K622I|RN7SL364P_ENST00000473668.2_RNA|PRKD2_ENST00000433867.1_Missense_Mutation_p.K622I|PRKD2_ENST00000601806.1_Missense_Mutation_p.K465I			Q9BZL6	KPCD2_HUMAN	protein kinase D2	622	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial tube morphogenesis (GO:0061154)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(13)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	41		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000189)|all cancers(93;0.000545)|Epithelial(262;0.0219)|GBM - Glioblastoma multiforme(486;0.0353)		CACAAACACTTTCTCAGGCGT	0.597																																					p.K622I		Atlas-SNP	.											.	PRKD2	94	.	0			c.A1865T						.						160	140	147					19																	47192900		2203	4300	6503	SO:0001583	missense	25865	exon14			AACACTTTCTCAG	AF151021	CCDS12689.1, CCDS59401.1	19q13.2	2013-01-10				ENSG00000105287		"Pleckstrin homology (PH) domain containing"	17293	protein-coding gene	gene with protein product		607074				11042152, 11062248	Standard	NM_001079880		Approved	PKD2, HSPC187, DKFZP586E0820	uc002pfj.3	Q9BZL6		ENST00000291281.4:c.1865A>T	chr19.hg19:g.47192900T>A	ENSP00000291281:p.Lys622Ile	128.0	0.0		103.0	47.0	NM_016457	Q8TB08|Q9P0T6|Q9Y3X8	Missense_Mutation	SNP	ENST00000291281.4	hg19	CCDS12689.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.067811	0.76301	.	.	ENSG00000105287	ENST00000291281;ENST00000433867	T;T	0.67171	-0.25;-0.25	5.06	4.04	0.47022	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000001	T	0.71358	0.3330	L	0.48877	1.53	0.41386	D	0.987585	P;P;P	0.52842	0.769;0.564;0.956	P;P;P	0.62649	0.611;0.515;0.905	T	0.71751	-0.4498	10	0.72032	D	0.01	-31.8831	7.4521	0.27244	0.0:0.1733:0.0:0.8267	.	622;107;622	E7ER94;A0JLT6;Q9BZL6	.;.;KPCD2_HUMAN	I	622	ENSP00000291281:K622I;ENSP00000393978:K622I	ENSP00000291281:K622I	K	-	2	0	PRKD2	51884740	0.997000	0.39634	0.995000	0.50966	0.902000	0.53008	1.628000	0.37060	0.878000	0.35920	0.533000	0.62120	AAA	.	.		0.597	PRKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466591.1	NM_016457		A	47192900	T	A	47192900	3	1	289	1	0	0	0	0	1	0	0	0	12531	1841	64	4	791	4	PRKD2	19	47192900	Missense_Mutation	SNP	T	TCGA-G3-A6UC-01A-21D-A33K-10	15424195	47192900	11936083	104	42444										
ZNF331	55422	hgsc.bcm.edu	37	chr19	54080362	54080362	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	acatcaaaaaattcatactgGggagaagccctacgaatgta	8	8	2	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr19:54080362G>T	ENST00000253144.9	+	7	1881	c.548G>T	c.(547-549)gGg>gTg	p.G183V	ZNF331_ENST00000513999.1_Missense_Mutation_p.G183V|ZNF331_ENST00000511593.2_Missense_Mutation_p.G183V|ZNF331_ENST00000449416.1_Missense_Mutation_p.G183V|ZNF331_ENST00000511154.1_Missense_Mutation_p.G183V|ZNF331_ENST00000411977.2_Missense_Mutation_p.G183V|ZNF331_ENST00000512387.1_Missense_Mutation_p.G183V|ZNF331_ENST00000513265.1_Intron	NM_001253801.1|NM_018555.5	NP_001240730.1|NP_061025.5	Q9NQX6	ZN331_HUMAN	zinc finger protein 331	183					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(1)|lung(1)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	10				GBM - Glioblastoma multiforme(134;0.00555)		ATTCATACTGGGGAGAAGCCC	0.418			T	?	follicular thyroid adenoma																																p.G183V		Atlas-SNP	.		Dom	yes		19	19q13.3-q13.4	55422	zinc finger protein 331		E	.	ZNF331	66	.	0			c.G548T						.						75	82	80					19																	54080362		2203	4300	6503	SO:0001583	missense	55422	exon5			ATACTGGGGAGAA	AF251515	CCDS33102.1	19q13	2013-12-10				ENSG00000130844		"Zinc fingers, C2H2-type", "-"	15489	protein-coding gene	gene with protein product	"rearranged in thyroid adenomas"	606043					Standard	NM_001079906		Approved	RITA, ZNF463, ZNF361	uc021uzh.1	Q9NQX6		ENST00000253144.9:c.548G>T	chr19.hg19:g.54080362G>T	ENSP00000253144:p.Gly183Val	113.0	0.0		100.0	51.0	NM_001253801	Q96GJ4	Missense_Mutation	SNP	ENST00000253144.9	hg19	CCDS33102.1	.	.	.	.	.	.	.	.	.	.	G	17.02	3.281458	0.59758	.	.	ENSG00000130844	ENST00000253144;ENST00000511593;ENST00000449416;ENST00000411977;ENST00000511154;ENST00000513999;ENST00000512387	T;T;T;T;T;T;T	0.23552	1.9;1.9;1.9;1.9;1.9;1.9;1.9	3.68	3.68	0.42216	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.35739	N	0.003019	T	0.51193	0.1660	M	0.79805	2.47	0.47698	D	0.999498	D	0.89917	1.0	D	0.76575	0.988	T	0.59091	-0.7519	10	0.87932	D	0	.	13.245	0.60018	0.0:0.0:1.0:0.0	.	183	Q9NQX6	ZN331_HUMAN	V	183	ENSP00000253144:G183V;ENSP00000427439:G183V;ENSP00000393817:G183V;ENSP00000393336:G183V;ENSP00000421014:G183V;ENSP00000423156:G183V;ENSP00000421728:G183V	ENSP00000253144:G183V	G	+	2	0	ZNF331	58772174	0.782000	0.28689	0.709000	0.30452	0.863000	0.49368	1.991000	0.40727	2.049000	0.60858	0.563000	0.77884	GGG	.	.		0.418	ZNF331-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371366.1	NM_018555		T	54080362	G	T	54080362	3	4	289	1	0	0	0	0	1	0	0	0	17864	1232	43	3	558	3	ZNF331	19	54080362	Missense_Mutation	SNP	G	TCGA-G3-A6UC-01A-21D-A33K-10	6887462	54080362	5048621	105	42445										
ZNF543	125919	hgsc.bcm.edu	37	chr19	57839129	57839129	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	ttctcacctggccttgcctgAggaagtcttactccaggaac	9	13	2	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr19:57839129A>G	ENST00000321545.4	+	4	644	c.299A>G	c.(298-300)gAg>gGg	p.E100G		NM_213598.3	NP_998763.2	Q08ER8	ZN543_HUMAN	zinc finger protein 543	100					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|kidney(2)|large_intestine(8)|lung(11)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	28		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		GCCTTGCCTGAGGAAGTCTTA	0.473																																					p.E100G		Atlas-SNP	.											.	ZNF543	61	.	0			c.A299G						.						75	76	76					19																	57839129		2203	4300	6503	SO:0001583	missense	125919	exon4			TGCCTGAGGAAGT	AL834534	CCDS33130.1	19q13.43	2013-01-08				ENSG00000178229		"Zinc fingers, C2H2-type", "-"	25281	protein-coding gene	gene with protein product							Standard	NM_213598		Approved	DKFZp434H055	uc002qoi.2	Q08ER8		ENST00000321545.4:c.299A>G	chr19.hg19:g.57839129A>G	ENSP00000322545:p.Glu100Gly	239.0	0.0		220.0	46.0	NM_213598	Q495U9|Q495V0|Q6ZMP4|Q8NCX4	Missense_Mutation	SNP	ENST00000321545.4	hg19	CCDS33130.1	.	.	.	.	.	.	.	.	.	.	A	10.73	1.431699	0.25813	.	.	ENSG00000178229	ENST00000321545	T	0.27720	1.65	2.87	1.7	0.24286	.	.	.	.	.	T	0.22085	0.0532	L	0.38175	1.15	0.09310	N	1	B	0.12630	0.006	B	0.08055	0.003	T	0.16928	-1.0386	9	0.51188	T	0.08	.	6.4979	0.22152	0.5794:0.4206:0.0:0.0	.	100	Q08ER8	ZN543_HUMAN	G	100	ENSP00000322545:E100G	ENSP00000322545:E100G	E	+	2	0	ZNF543	62530941	0.007000	0.16637	0.013000	0.15412	0.236000	0.25371	1.190000	0.32126	1.320000	0.45209	0.454000	0.30748	GAG	.	.		0.473	ZNF543-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465780.1	XM_064865		G	57839129	A	G	57839129	3	3	289	1	0	0	0	0	1	0	0	0	17991	304	11	2	313	2	ZNF543	19	57839129	Missense_Mutation	SNP	A	TCGA-G3-A6UC-01A-21D-A33K-10	3758767	57839129	1289854	106	42446										
ZSCAN1	284312	hgsc.bcm.edu	37	chr19	58549467	58549467	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	ggtgctggagcagttcctggGcgcgctgcccagcaagatgc	16	12	0	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr19:58549467G>A	ENST00000282326.1	+	3	510	c.263G>A	c.(262-264)gGc>gAc	p.G88D	ZSCAN1_ENST00000601162.1_Missense_Mutation_p.G88D|ZSCAN1_ENST00000391700.1_Missense_Mutation_p.G88D	NM_182572.3	NP_872378.3	Q8NBB4	ZSCA1_HUMAN	zinc finger and SCAN domain containing 1	88	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)		CAGTTCCTGGGCGCGCTGCCC	0.697																																					p.G88D		Atlas-SNP	.											.	ZSCAN1	102	.	0			c.G263A						.						18	18	18					19																	58549467		2197	4293	6490	SO:0001583	missense	284312	exon3			TCCTGGGCGCGCT	AK091098	CCDS12969.1	19q13.43	2013-06-13	2004-04-21		ENSG00000152467	ENSG00000152467		"-", "Zinc fingers, C2H2-type"	23712	protein-coding gene	gene with protein product			"zinc finger with SCAN domain 1"			12477932	Standard	NM_182572		Approved	FLJ33779, ZNF915	uc002qrc.1	Q8NBB4	OTTHUMG00000183381	ENST00000282326.1:c.263G>A	chr19.hg19:g.58549467G>A	ENSP00000282326:p.Gly88Asp	19.0	0.0		37.0	21.0	NM_182572	Q3B798|Q6WLH8|Q86WS8	Missense_Mutation	SNP	ENST00000282326.1	hg19	CCDS12969.1	.	.	.	.	.	.	.	.	.	.	G	14.69	2.611798	0.46631	.	.	ENSG00000152467	ENST00000391700;ENST00000282326	T;T	0.04119	3.7;3.7	2.09	0.814	0.18756	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	.	.	.	.	T	0.07007	0.0178	L	0.46157	1.445	0.09310	N	1	P;D	0.56287	0.624;0.975	B;P	0.48815	0.425;0.591	T	0.34054	-0.9844	9	0.56958	D	0.05	.	5.8004	0.18410	0.0:0.3406:0.6594:0.0	.	88;88	Q8NBB4;Q8NBB4-2	ZSCA1_HUMAN;.	D	88	ENSP00000375581:G88D;ENSP00000282326:G88D	ENSP00000282326:G88D	G	+	2	0	ZSCAN1	63241279	0.124000	0.22315	0.574000	0.28523	0.970000	0.65996	0.194000	0.17135	1.170000	0.42753	0.407000	0.27541	GGC	.	.		0.697	ZSCAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466427.1	NM_182572		A	58549467	G	A	58549467	3	1	289	1	0	0	0	0	1	0	0	0	18241	1203	42	3	265	3	ZSCAN1	19	58549467	Missense_Mutation	SNP	G	TCGA-G3-A6UC-01A-21D-A33K-10	710338	58549467	579516	107	42447										
PANK2	80025	hgsc.bcm.edu	37	chr20	3893207	3893207	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	cgtggagatagcaccaaagtGgataaactagtacgagatat	11	6	0	2			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr20:3893207G>A	ENST00000316562.4	+	4	1344	c.1338G>A	c.(1336-1338)gtG>gtA	p.V446V	PANK2_ENST00000497424.1_Silent_p.V155V|PANK2_ENST00000610179.1_Silent_p.V323V|PANK2_ENST00000464452.1_3'UTR	NM_153638.2	NP_705902.2	Q9BZ23	PANK2_HUMAN	pantothenate kinase 2	446					aerobic respiration (GO:0009060)|cell death (GO:0008219)|coenzyme A biosynthetic process (GO:0015937)|coenzyme biosynthetic process (GO:0009108)|mitochondrion morphogenesis (GO:0070584)|pantothenate metabolic process (GO:0015939)|regulation of mitochondrial membrane potential (GO:0051881)|small molecule metabolic process (GO:0044281)|spermatid development (GO:0007286)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial intermembrane space (GO:0005758)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						GCACCAAAGTGGATAAACTAG	0.463																																					p.V446V		Atlas-SNP	.											.	PANK2	37	.	0			c.G1338A						.						131	138	135					20																	3893207		2203	4300	6503	SO:0001819	synonymous_variant	80025	exon4			CAAAGTGGATAAA	AK021791	CCDS13071.2, CCDS13072.1	20p13	2008-07-31	2008-07-31	2002-09-06	ENSG00000125779	ENSG00000125779	2.7.1.33		15894	protein-coding gene	gene with protein product	"Hallervorden-Spatz syndrome"	606157	"neurodegeneration with brain iron accumulation 1 (Hallervorden-Spatz syndrome)"	C20orf48, NBIA1		8944032, 11479594	Standard	XM_005260835		Approved	HSS, FLJ11729, PKAN, HARP	uc002wkc.3	Q9BZ23	OTTHUMG00000031768	ENST00000316562.4:c.1338G>A	chr20.hg19:g.3893207G>A		77.0	0.0		121.0	36.0	NM_153638	B1AK33|B2Z3X0|D3DVZ0|Q5T7I2|Q5T7I4|Q7RTX5|Q8N7Q4|Q8TCR5|Q9BYW5|Q9HAF2	Silent	SNP	ENST00000316562.4	hg19	CCDS13071.2																																																																																			.	.		0.463	PANK2-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077793.2	NM_024960		A	3893207	G	A	3893207	2	1	289	1	0	0	0	0	0	0	0	1	11426	1335	47	3		3	PANK2	20	3893207	Silent	SNP	G	TCGA-G3-A6UC-01A-21D-A33K-10		3893207	59132313	108	42448										
CEP250	11190	hgsc.bcm.edu	37	chr20	34057783	34057783	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	agattatgaaaagatgataaAggctctgagagagacagtgg	13	3	1	6			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr20:34057783A>G	ENST00000397527.1	+	10	1640	c.920A>G	c.(919-921)aAg>aGg	p.K307R	CEP250_ENST00000397524.1_Missense_Mutation_p.K307R|CEP250_ENST00000342580.4_Missense_Mutation_p.K307R	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	307					centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of centriole-centriole cohesion (GO:0030997)	centriole (GO:0005814)|centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)|spindle pole centrosome (GO:0031616)	protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			AAGATGATAAAGGCTCTGAGA	0.468																																					p.K307R		Atlas-SNP	.											.	CEP250	141	.	0			c.A920G						.						97	89	92					20																	34057783		2203	4300	6503	SO:0001583	missense	11190	exon10			TGATAAAGGCTCT	AF022655	CCDS13255.1	20q11.22	2014-02-20	2006-01-11	2006-01-11	ENSG00000126001	ENSG00000126001			1859	protein-coding gene	gene with protein product		609689	"centrosomal protein 2"	CEP2		9506584, 9647649	Standard	NM_007186		Approved	C-NAP1	uc021wco.1	Q9BV73	OTTHUMG00000032343	ENST00000397527.1:c.920A>G	chr20.hg19:g.34057783A>G	ENSP00000380661:p.Lys307Arg	66.0	0.0		85.0	38.0	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Missense_Mutation	SNP	ENST00000397527.1	hg19	CCDS13255.1	.	.	.	.	.	.	.	.	.	.	A	16.21	3.059726	0.55325	.	.	ENSG00000126001	ENST00000397527;ENST00000342580;ENST00000397524;ENST00000425934	T;T;T;T	0.46063	2.85;2.93;0.88;1.96	5.59	3.2	0.36748	.	2.494980	0.01519	N	0.018286	T	0.42966	0.1226	L	0.55834	1.745	0.27549	N	0.950548	B;P	0.44044	0.302;0.825	B;B	0.41813	0.053;0.367	T	0.23726	-1.0180	10	0.34782	T	0.22	.	6.2298	0.20728	0.7832:0.0:0.0758:0.141	.	307;307	A6PVI9;Q9BV73	.;CP250_HUMAN	R	307	ENSP00000380661:K307R;ENSP00000341541:K307R;ENSP00000380658:K307R;ENSP00000413827:K307R	ENSP00000341541:K307R	K	+	2	0	CEP250	33521197	1.000000	0.71417	0.994000	0.49952	0.995000	0.86356	1.601000	0.36773	0.943000	0.37553	0.533000	0.62120	AAG	.	.		0.468	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186		G	34057783	A	G	34057783	3	3	289	1	0	0	0	0	1	0	0	0	3254	72	3	2	946	2	CEP250	20	34057783	Missense_Mutation	SNP	A	TCGA-G3-A6UC-01A-21D-A33K-10	30164576	34057783	28967737	109	42449										
FAM83D	81610	hgsc.bcm.edu	37	chr20	37580989	37580998	+	Frame_Shift_Del	DEL	CAAAGAGCGG	CAAAGAGCGG	-													0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	gactcacttagaaacttgaaCaaagagcggcaattccactt					rs147472094|rs545956434	byFrequency	TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	CAAAGAGCGG	CAAAGAGCGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr20:37580989_37580998delCAAAGAGCGG	ENST00000217429.4	+	4	1715_1724	c.1674_1683delCAAAGAGCGG	c.(1672-1683)aacaaagagcggfs	p.NKER558fs		NM_030919.2	NP_112181.2	Q9H4H8	FA83D_HUMAN	family with sequence similarity 83, member D	528					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.R561W(1)		endometrium(2)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)|stomach(1)	28		Myeloproliferative disorder(115;0.00878)				GAAACTTGAACAAAGAGCGGCAATTCCACT	0.505																																					p.558_561del		Atlas-Indel,Pindel	.											FAM83D,NS,carcinoma,0,1	FAM83D	60	.	1	Substitution - Missense(1)	large_intestine(1)	c.1673_1682del						.																																			SO:0001589	frameshift_variant	81610	exon4			.	AL023803	CCDS42872.1	20q11.23	2014-03-13	2006-03-23	2006-03-23	ENSG00000101447	ENSG00000101447			16122	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 129"	C20orf129		23205133	Standard	NM_030919		Approved	dJ616B8.3	uc002xjg.3	Q9H4H8	OTTHUMG00000032462	ENST00000217429.4:c.1674_1683delCAAAGAGCGG	chr20.hg19:g.37580989_37580998delCAAAGAGCGG	ENSP00000217429:p.Asn558fs	125.0	0.0		89.0	16.0	NM_030919	B4E1I7|Q5THR2|Q68EN1|Q6P457|Q7Z6H0|Q96DF5|Q96N89|Q9BVM8	Frame_Shift_Del	DEL	ENST00000217429.4	hg19	CCDS42872.1																																																																																			.	.		0.505	FAM83D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079211.1			-	37580998	CAAAGAGCGG	-	37580989	7	5	289	1	0	1	0	1	0	0	0	0	5644	477	17	0	1688	0	FAM83D	20	37580989	Frame_Shift_Del	DEL	CAAAGAGCGG	TCGA-G3-A6UC-01A-21D-A33K-10	3523206	37580989	25444531	110	42450										
PLCG1	5335	hgsc.bcm.edu	37	chr20	39792440	39792440	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	ggacaccatgaacaaccctcTttcccactactggatctcct	5	16	2	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr20:39792440T>C	ENST00000373271.1	+	10	1382	c.977T>C	c.(976-978)cTt>cCt	p.L326P	PLCG1_ENST00000373272.2_Missense_Mutation_p.L326P|PLCG1_ENST00000244007.3_Missense_Mutation_p.L326P	NM_182811.1	NP_877963.1	P19174	PLCG1_HUMAN	phospholipase C, gamma 1	326	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|cell migration (GO:0016477)|cellular response to epidermal growth factor stimulus (GO:0071364)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phospholipid catabolic process (GO:0009395)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cell projection (GO:0042995)|cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|protein kinase binding (GO:0019901)|receptor signaling protein activity (GO:0005057)			breast(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(16)|skin(6)|urinary_tract(2)	46		Myeloproliferative disorder(115;0.00878)				AACAACCCTCTTTCCCACTAC	0.547																																					p.L326P		Atlas-SNP	.											.	PLCG1	111	.	0			c.T977C						.						143	134	137					20																	39792440		2203	4300	6503	SO:0001583	missense	5335	exon10			ACCCTCTTTCCCA	M34667	CCDS13313.1, CCDS13314.1	20q12-q13.1	2013-02-14	2004-01-29		ENSG00000124181	ENSG00000124181	3.1.4.11	"Pleckstrin homology (PH) domain containing", "EF-hand domain containing", "SH2 domain containing"	9065	protein-coding gene	gene with protein product		172420	"phospholipase C, gamma 1 (formerly subtype 148)"	PLC1		2167438, 3254788	Standard	NM_182811		Approved	PLC148, PLC-II, PLCgamma1, NCKAP3	uc002xjo.1	P19174	OTTHUMG00000033082	ENST00000373271.1:c.977T>C	chr20.hg19:g.39792440T>C	ENSP00000362368:p.Leu326Pro	73.0	0.0		82.0	39.0	NM_182811	B7ZLY7|B9EGH4|E1P5W4|Q2V575	Missense_Mutation	SNP	ENST00000373271.1	hg19	CCDS13314.1	.	.	.	.	.	.	.	.	.	.	T	16.11	3.030122	0.54790	.	.	ENSG00000124181	ENST00000244007;ENST00000373271;ENST00000373272	T;T;T	0.71579	-0.58;-0.58;-0.58	5.69	4.59	0.56863	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific , X domain (3);	0.000000	0.85682	D	0.000000	D	0.89887	0.6845	H	0.98833	4.345	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.91999	0.5609	10	0.87932	D	0	.	11.7443	0.51811	0.0:0.069:0.0:0.931	.	326;326	P19174;A2A284	PLCG1_HUMAN;.	P	326	ENSP00000244007:L326P;ENSP00000362368:L326P;ENSP00000362369:L326P	ENSP00000244007:L326P	L	+	2	0	PLCG1	39225854	1.000000	0.71417	0.059000	0.19551	0.513000	0.34164	6.295000	0.72744	0.978000	0.38470	-0.274000	0.10170	CTT	.	.		0.547	PLCG1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080514.3	NM_182811		C	39792440	T	C	39792440	3	2	289	1	0	0	0	0	1	0	0	0	12044	1609	56	2	1015	2	PLCG1	20	39792440	Missense_Mutation	SNP	T	TCGA-G3-A6UC-01A-21D-A33K-10	2211451	39792440	23233080	111	42451										
MYBL2	4605	hgsc.bcm.edu	37	chr20	42338684	42338684	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	aagaacgccctggagaagtaCggacccctgaagcccctggt	12	13	0	3			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr20:42338684C>T	ENST00000217026.4	+	10	1714	c.1587C>T	c.(1585-1587)taC>taT	p.Y529Y	MYBL2_ENST00000396863.4_Silent_p.Y505Y	NM_002466.2	NP_002457.1	P10244	MYBB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 2	529					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|spindle assembly involved in mitosis (GO:0090307)	Myb complex (GO:0031523)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	46		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			TGGAGAAGTACGGACCCCTGA	0.592																																					p.Y529Y		Atlas-SNP	.											.	MYBL2	82	.	0			c.C1587T						.						153	151	152					20																	42338684		2203	4300	6503	SO:0001819	synonymous_variant	4605	exon10			GAAGTACGGACCC		CCDS13322.1, CCDS63276.1	20q13.1	2013-07-09	2013-07-09		ENSG00000101057	ENSG00000101057			7548	protein-coding gene	gene with protein product		601415				8812502	Standard	NM_002466		Approved	BMYB, B-MYB	uc002xlb.1	P10244	OTTHUMG00000033062	ENST00000217026.4:c.1587C>T	chr20.hg19:g.42338684C>T		103.0	0.0		71.0	16.0	NM_002466	B2RBS5|B7Z8D9|F8W6N6|Q53F07	Silent	SNP	ENST00000217026.4	hg19	CCDS13322.1																																																																																			.	.		0.592	MYBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080408.1	NM_002466		T	42338684	C	T	42338684	2	4	289	1	0	0	0	0	0	0	0	1	10019	547	19	1		1	MYBL2	20	42338684	Silent	SNP	C	TCGA-G3-A6UC-01A-21D-A33K-10	2546244	42338684	20686836	112	42452										
LAMA5	3911	hgsc.bcm.edu	37	chr20	60892042	60892042	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	gttggaggcctcgatggcccTctgggtgaggcggtcctggt	18	10	1	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr20:60892042T>C	ENST00000252999.3	-	56	7615	c.7549A>G	c.(7549-7551)Agg>Ggg	p.R2517G		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2517	Domain II and I.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			TCGATGGCCCTCTGGGTGAGG	0.682																																					p.R2517G		Atlas-SNP	.											.	LAMA5	268	.	0			c.A7549G						.						59	53	55					20																	60892042		2186	4281	6467	SO:0001583	missense	3911	exon56			TGGCCCTCTGGGT	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"Laminins"	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.7549A>G	chr20.hg19:g.60892042T>C	ENSP00000252999:p.Arg2517Gly	23.0	0.0		32.0	17.0	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	hg19	CCDS33502.1	.	.	.	.	.	.	.	.	.	.	-	9.580	1.123238	0.20959	.	.	ENSG00000130702	ENST00000252999	T	0.19394	2.15	4.26	0.783	0.18572	.	0.090855	0.41500	U	0.000878	T	0.28001	0.0690	M	0.61703	1.905	0.80722	D	1	P	0.47762	0.9	P	0.47044	0.535	T	0.05241	-1.0897	10	0.46703	T	0.11	.	14.192	0.65644	0.0:0.0:0.232:0.768	.	2517	O15230	LAMA5_HUMAN	G	2517	ENSP00000252999:R2517G	ENSP00000252999:R2517G	R	-	1	2	LAMA5	60325437	0.965000	0.33210	0.994000	0.49952	0.375000	0.29983	0.386000	0.20702	-0.156000	0.11079	0.235000	0.17854	AGG	.	.		0.682	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		C	60892042	T	C	60892042	3	2	289	1	0	0	0	0	1	0	0	0	8618	1550	54	2	3638	2	LAMA5	20	60892042	Missense_Mutation	SNP	T	TCGA-G3-A6UC-01A-21D-A33K-10	18553358	60892042	2133478	113	42453										
DIDO1	11083	hgsc.bcm.edu	37	chr20	61525548	61525548	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	tctgcggagggaacctggccTgaagaaggcgaggaaaggct	17	8	1	2			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr20:61525548T>A	ENST00000266070.4	-	12	2898		c.e12-2		DIDO1_ENST00000395343.1_Splice_Site|DIDO1_ENST00000395335.2_Splice_Site|DIDO1_ENST00000395340.1_Splice_Site	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1						apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					GAACCTGGCCTGAAGAAGGCG	0.473																																					.	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											.	DIDO1	321	.	0			c.2573-2A>T						.						62	72	69					20																	61525548		2161	4265	6426	SO:0001630	splice_region_variant	11083	exon13			CTGGCCTGAAGAA	AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"Zinc fingers, PHD-type"	2680	protein-coding gene	gene with protein product		604140	"chromosome 20 open reading frame 158", "death associated transcription factor 1"	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.2573-2A>T	chr20.hg19:g.61525548T>A		41.0	0.0		38.0	17.0	NM_001193369	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Splice_Site	SNP	ENST00000266070.4	hg19	CCDS33506.1	.	.	.	.	.	.	.	.	.	.	T	13.26	2.183011	0.38511	.	.	ENSG00000101191	ENST00000266070;ENST00000395343;ENST00000395340;ENST00000395335	.	.	.	5.88	5.88	0.94601	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.2987	0.82793	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	DIDO1	60995993	1.000000	0.71417	0.996000	0.52242	0.171000	0.22731	6.755000	0.74914	2.257000	0.74773	0.459000	0.35465	.	.	.		0.473	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796	Intron	A	61525548	T	A	61525548	5	1	289	1	0	0	0	0	0	0	1	0	4524	1594	55	4	4200	4	DIDO1	20	61525548	Splice_Site	SNP	T	TCGA-G3-A6UC-01A-21D-A33K-10	633506	61525548	1499972	114	42454										
ZGPAT	84619	hgsc.bcm.edu	37	chr20	62340049	62340049	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	caggctgacctgcgccagctGcagggggacctgaaggagct	16	12	0	2			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr20:62340049G>A	ENST00000328969.5	+	2	244	c.117G>A	c.(115-117)ctG>ctA	p.L39L	ARFRP1_ENST00000359715.5_5'Flank|ZGPAT_ENST00000448100.2_Silent_p.L39L|ARFRP1_ENST00000324228.2_5'Flank|RP4-583P15.15_ENST00000490623.2_5'Flank|ZGPAT_ENST00000355969.6_Silent_p.L39L|ARFRP1_ENST00000609142.1_5'Flank|ARFRP1_ENST00000440854.1_5'Flank|ZGPAT_ENST00000357119.4_Silent_p.L39L|ARFRP1_ENST00000607873.1_5'Flank|ZGPAT_ENST00000369967.3_Silent_p.L39L	NM_032527.4	NP_115916.3	Q8N5A5	ZGPAT_HUMAN	zinc finger, CCCH-type with G patch domain	39					negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)	14	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					TGCGCCAGCTGCAGGGGGACC	0.677																																					p.L39L		Atlas-SNP	.											.	ZGPAT	57	.	0			c.G117A						.						35	38	37					20																	62340049		2202	4293	6495	SO:0001819	synonymous_variant	84619	exon2			CCAGCTGCAGGGG	AK027878	CCDS13534.1, CCDS13535.1, CCDS56203.1	20q13.3	2013-01-28	2004-12-01	2004-12-01	ENSG00000197114	ENSG00000197114		"Zinc fingers, CCCH-type domain containing", "G patch domain containing"	15948	protein-coding gene	gene with protein product			"KIAA1847"	KIAA1847		16952911	Standard	NM_181485		Approved	dJ583P15.3, MGC44880, FLJ14972, ZC3HDC9, ZC3H9, GPATC6, GPATCH6, ZIP	uc002ygk.3	Q8N5A5	OTTHUMG00000032998	ENST00000328969.5:c.117G>A	chr20.hg19:g.62340049G>A		43.0	0.0		41.0	15.0	NM_032527	E1P5K1|Q4VXN9|Q5JWI9|Q5JWJ0|Q8NC55|Q8WUV4|Q96JI0|Q96JU4|Q9H401	Silent	SNP	ENST00000328969.5	hg19	CCDS13534.1																																																																																			.	.		0.677	ZGPAT-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080214.1	NM_181484		A	62340049	G	A	62340049	2	1	289	1	0	0	0	0	0	0	0	1	17689	1306	46	3		3	ZGPAT	20	62340049	Silent	SNP	G	TCGA-G3-A6UC-01A-21D-A33K-10	814501	62340049	685471	115	42455										
DGCR14	8220	hgsc.bcm.edu	37	chr22	19124884	19124884	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	acgtagggcgtttccgacccTtcaactctcaagggtgtgtt	11	11	2	0			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr22:19124884T>C	ENST00000252137.6	-	8	1030	c.987A>G	c.(985-987)gaA>gaG	p.E329E		NM_022719.2	NP_073210.1	Q96DF8	DGC14_HUMAN	DiGeorge syndrome critical region gene 14	329					mRNA splicing, via spliceosome (GO:0000398)|nervous system development (GO:0007399)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)	16	Colorectal(54;0.0993)					TTTCCGACCCTTCAACTCTCA	0.592																																					p.E329E		Atlas-SNP	.											.	DGCR14	43	.	0			c.A987G						.						227	197	207					22																	19124884		2203	4300	6503	SO:0001819	synonymous_variant	8220	exon8			CGACCCTTCAACT	L77566	CCDS13756.1	22q11.21	2007-02-20			ENSG00000100056	ENSG00000100056			16817	protein-coding gene	gene with protein product		601755	"DiGeorge syndrome critical region gene 13"	DGCR13		8776594, 9063747	Standard	NM_022719		Approved	DGSI, Es2el, ES2, DGS-H	uc002zou.3	Q96DF8	OTTHUMG00000150119	ENST00000252137.6:c.987A>G	chr22.hg19:g.19124884T>C		148.0	0.0		126.0	52.0	NM_022719	Q49AH7|Q9BTZ4	Silent	SNP	ENST00000252137.6	hg19	CCDS13756.1																																																																																			.	.		0.592	DGCR14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316432.2			C	19124884	T	C	19124884	2	2	289	1	0	0	0	0	0	0	0	1	4462	1606	56	2		2	DGCR14	22	19124884	Silent	SNP	T	TCGA-G3-A6UC-01A-21D-A33K-10		19124884	32179682	116	42456										
MORC2	22880	hgsc.bcm.edu	37	chr22	31328358	31328358	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	agactcaccagaggaaaagaTattagctcatctgaattcat	7	8	4	4			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr22:31328358T>C	ENST00000397641.3	-	24	3237	c.2829A>G	c.(2827-2829)atA>atG	p.I943M	MORC2_ENST00000215862.4_Missense_Mutation_p.I881M|MORC2-AS1_ENST00000441558.1_RNA			Q9Y6X9	MORC2_HUMAN	MORC family CW-type zinc finger 2	943						cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	21						GAGGAAAAGATATTAGCTCAT	0.468																																					p.I881M		Atlas-SNP	.											.	MORC2	78	.	0			c.A2643G						.						138	126	130					22																	31328358		2203	4300	6503	SO:0001583	missense	22880	exon25			AAAAGATATTAGC	AB020659	CCDS33636.1	22q12.2	2005-06-15	2005-06-15	2005-06-15	ENSG00000133422	ENSG00000133422			23573	protein-coding gene	gene with protein product			"zinc finger, CW-type with coiled-coil domain 1", "zinc finger, CW type with coiled-coil domain 1"	ZCWCC1		14607086	Standard	XM_005261391		Approved	ZCW3, KIAA0852, AC004542.C22.1	uc003aje.1	Q9Y6X9	OTTHUMG00000151193	ENST00000397641.3:c.2829A>G	chr22.hg19:g.31328358T>C	ENSP00000380763:p.Ile943Met	69.0	0.0		54.0	30.0	NM_014941	B2RNB1|Q9UF28|Q9Y6V2	Missense_Mutation	SNP	ENST00000397641.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.12|14.12	2.439573|2.439573	0.43326|0.43326	.|.	.|.	ENSG00000133422|ENSG00000133422	ENST00000397641;ENST00000215862|ENST00000445980	T;T|.	0.12569|.	2.67;2.67|.	5.48|5.48	-1.46|-1.46	0.08800|0.08800	.|.	0.235047|0.235047	0.47455|0.47455	D|D	0.000232|0.000232	T|T	0.24851|0.24851	0.0603|0.0603	N|N	0.12182|0.12182	0.205|0.205	0.80722|0.80722	D|D	1|1	B|.	0.26195|.	0.144|.	B|.	0.14023|.	0.01|.	T|T	0.27054|0.27054	-1.0085|-1.0085	10|7	0.45353|0.02654	T|T	0.12|1	.|.	7.8002|7.8002	0.29170|0.29170	0.0:0.1088:0.5719:0.3193|0.0:0.1088:0.5719:0.3193	.|.	943|.	Q9Y6X9|.	MORC2_HUMAN|.	M|V	943;881|105	ENSP00000380763:I943M;ENSP00000215862:I881M|.	ENSP00000215862:I881M|ENSP00000402602:I105V	I|I	-|-	3|1	3|0	MORC2|MORC2	29658358|29658358	0.998000|0.998000	0.40836|0.40836	0.812000|0.812000	0.32479|0.32479	0.977000|0.977000	0.68977|0.68977	0.541000|0.541000	0.23207|0.23207	-0.158000|-0.158000	0.11040|0.11040	0.533000|0.533000	0.62120|0.62120	ATA|ATC	.	.		0.468	MORC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000321710.2	NM_014941		C	31328358	T	C	31328358	3	2	289	1	0	0	0	0	1	0	0	0	9711	1396	49	2	281	2	MORC2	22	31328358	Missense_Mutation	SNP	T	TCGA-G3-A6UC-01A-21D-A33K-10	12203474	31328358	19976208	117	42457										
HDAC10	83933	hgsc.bcm.edu	37	chr22	50688856	50688856	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	gtgtgtccggggacacgcacCgggtggaagtagatggcgtc	18	9	0	1			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chr22:50688856C>A	ENST00000216271.5	-	3	643	c.291G>T	c.(289-291)ccG>ccT	p.P97P	HDAC10_ENST00000498366.1_Intron|HDAC10_ENST00000448072.1_Splice_Site_p.P97P|HDAC10_ENST00000349505.4_Splice_Site_p.P97P|MAPK12_ENST00000497036.1_5'UTR	NM_001159286.1|NM_032019.5	NP_001152758.1|NP_114408.3	Q969S8	HDA10_HUMAN	histone deacetylase 10	97	Histone deacetylase.				chromatin modification (GO:0016568)|histone deacetylation (GO:0016575)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|oligodendrocyte development (GO:0014003)|protein deacetylation (GO:0006476)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)			endometrium(2)|kidney(2)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	8		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|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)		GGACACGCACCGGGTGGAAGT	0.637																																					p.P97P		Atlas-SNP	.											.	HDAC10	29	.	0			c.G291T						.						122	95	104					22																	50688856		2201	4300	6501	SO:0001630	splice_region_variant	83933	exon3			ACGCACCGGGTGG	AF393962	CCDS14088.1, CCDS54545.1	22q13.31	2008-06-10			ENSG00000100429	ENSG00000100429			18128	protein-coding gene	gene with protein product		608544				11677242, 11726666	Standard	NM_032019		Approved	DKFZP761B039	uc003bkg.3	Q969S8	OTTHUMG00000044647	ENST00000216271.5:c.291+1G>T	chr22.hg19:g.50688856C>A		68.0	0.0		57.0	36.0	NM_032019	Q08AP4|Q6STF9|Q96P77|Q96P78|Q9H028|Q9UGX1|Q9UGX2	Silent	SNP	ENST00000216271.5	hg19	CCDS14088.1																																																																																			.	.		0.637	HDAC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104141.4	NM_032019	Silent	A	50688856	C	A	50688856	5	1	289	1	0	0	0	0	0	0	1	0	7014	666	23	1	1790	1	HDAC10	22	50688856	Splice_Site	SNP	C	TCGA-G3-A6UC-01A-21D-A33K-10	19360498	50688856	615710	118	42458										
ITM2A	9452	hgsc.bcm.edu	37	chrX	78618461	78618461	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	tttcaaagtcatgaataattGctgcagggtcactatcagag	9	7	4	2			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chrX:78618461G>C	ENST00000373298.2	-	3	562	c.419C>G	c.(418-420)gCa>gGa	p.A140G	ITM2A_ENST00000469541.1_5'UTR|ITM2A_ENST00000434584.2_Missense_Mutation_p.A96G	NM_004867.4	NP_004858.1	O43736	ITM2A_HUMAN	integral membrane protein 2A	140	BRICHOS. {ECO:0000255|PROSITE- ProRule:PRU00255}.					integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	18						ATGAATAATTGCTGCAGGGTC	0.408																																					p.A140G		Atlas-SNP	.											.	ITM2A	51	.	0			c.C419G						.						88	77	80					X																	78618461		2203	4300	6503	SO:0001583	missense	9452	exon3			ATAATTGCTGCAG	BC034485	CCDS14444.1, CCDS55455.1	Xq13.3-q21.2	2012-10-10			ENSG00000078596	ENSG00000078596		"BRICHOS domain containing"	6173	protein-coding gene	gene with protein product	"BRICHOS domain containing 2A"	300222				9892734, 8702637	Standard	NM_004867		Approved	BRICD2A, E25A	uc004edh.3	O43736	OTTHUMG00000021900	ENST00000373298.2:c.419C>G	chrX.hg19:g.78618461G>C	ENSP00000362395:p.Ala140Gly	140.0	1.0		157.0	140.0	NM_004867	B2R7X5|B4E062|Q6IBC9	Missense_Mutation	SNP	ENST00000373298.2	hg19	CCDS14444.1	.	.	.	.	.	.	.	.	.	.	g	11.67	1.706964	0.30232	.	.	ENSG00000078596	ENST00000373298;ENST00000434584	T;T	0.79554	-1.28;-1.28	4.38	3.49	0.39957	BRICHOS (2);	0.136419	0.50627	D	0.000116	T	0.82066	0.4956	L	0.41236	1.265	0.42052	D	0.991127	B;D	0.64830	0.182;0.994	B;D	0.64506	0.102;0.926	T	0.77284	-0.2645	10	0.22706	T	0.39	-9.0789	11.5645	0.50796	0.0:0.0:0.8199:0.1801	.	96;140	B4E062;O43736	.;ITM2A_HUMAN	G	140;96	ENSP00000362395:A140G;ENSP00000415533:A96G	ENSP00000362395:A140G	A	-	2	0	ITM2A	78505117	1.000000	0.71417	0.998000	0.56505	0.962000	0.63368	4.184000	0.58323	0.634000	0.30469	0.534000	0.68092	GCA	.	.		0.408	ITM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057329.1	NM_004867		C	78618461	G	C	78618461	3	2	289	1	0	0	0	0	1	0	0	0	7921	1319	46	4	388	4	ITM2A	23	78618461	Missense_Mutation	SNP	G	TCGA-G3-A6UC-01A-21D-A33K-10		78618461	76652099	119	42459										
PABPC5	140886	hgsc.bcm.edu	37	chrX	90690655	90690655	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	tgtacgtgggtgacttggacCcagatgtcaccgaggacatg	14	9	1	2			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chrX:90690655C>T	ENST00000312600.3	+	2	293	c.79C>T	c.(79-81)Cca>Tca	p.P27S	PABPC5_ENST00000373105.1_Intron|PABPC5-AS1_ENST00000456187.1_RNA	NM_080832.2	NP_543022.1	Q96DU9	PABP5_HUMAN	poly(A) binding protein, cytoplasmic 5	27	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.					mitochondrion (GO:0005739)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(20)|ovary(1)|pancreas(1)	42						TGACTTGGACCCAGATGTCAC	0.592																																					p.P27S		Atlas-SNP	.											.	PABPC5	92	.	0			c.C79T						.						70	54	60					X																	90690655		2203	4300	6503	SO:0001583	missense	140886	exon2			TTGGACCCAGATG	AJ278963	CCDS14460.1	Xq21.3	2013-02-12	2001-11-28		ENSG00000174740	ENSG00000174740		"RNA binding motif (RRM) containing"	13629	protein-coding gene	gene with protein product		300407	"poly(A)-binding protein, cytoplasmic 5"			11374897	Standard	NM_080832		Approved	PABP5	uc004efg.3	Q96DU9	OTTHUMG00000021959	ENST00000312600.3:c.79C>T	chrX.hg19:g.90690655C>T	ENSP00000308012:p.Pro27Ser	61.0	0.0		62.0	15.0	NM_080832	A8K240|Q5JQF4|Q6P529|Q9UFE5	Missense_Mutation	SNP	ENST00000312600.3	hg19	CCDS14460.1	.	.	.	.	.	.	.	.	.	.	C	17.38	3.374970	0.61735	.	.	ENSG00000174740	ENST00000312600	T	0.16897	2.31	4.43	4.43	0.53597	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.050090	0.85682	D	0.000000	T	0.18130	0.0435	L	0.52206	1.635	0.80722	D	1	B	0.22080	0.064	B	0.22880	0.042	T	0.02691	-1.1123	10	0.40728	T	0.16	.	13.8904	0.63736	0.0:1.0:0.0:0.0	.	27	Q96DU9	PABP5_HUMAN	S	27	ENSP00000308012:P27S	ENSP00000308012:P27S	P	+	1	0	PABPC5	90577311	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.485000	0.60279	2.450000	0.82876	0.600000	0.82982	CCA	.	.		0.592	PABPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057429.1	NM_080832		T	90690655	C	T	90690655	3	4	289	1	0	0	0	0	1	0	0	0	11376	623	22	3	81	3	PABPC5	23	90690655	Missense_Mutation	SNP	C	TCGA-G3-A6UC-01A-21D-A33K-10	12072194	90690655	64579905	120	42460										
IRS4	8471	hgsc.bcm.edu	37	chrX	107977380	107977380	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	cttcaaaaggggatcgagagTggcgcttttttgaagcagag	14	6	1	3			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chrX:107977380T>C	ENST00000372129.2	-	1	2271	c.2195A>G	c.(2194-2196)cAc>cGc	p.H732R	RP6-24A23.6_ENST00000563887.1_5'Flank|RP6-24A23.3_ENST00000436013.1_RNA|RP6-24A23.3_ENST00000608811.1_RNA	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	732	CRK-binding.				positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						GGATCGAGAGTGGCGCTTTTT	0.502																																					p.H732R		Atlas-SNP	.											.	IRS4	253	.	0			c.A2195G						.						71	72	72					X																	107977380		2203	4300	6503	SO:0001583	missense	8471	exon1			CGAGAGTGGCGCT	AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.2195A>G	chrX.hg19:g.107977380T>C	ENSP00000361202:p.His732Arg	115.0	0.0		85.0	78.0	NM_003604		Missense_Mutation	SNP	ENST00000372129.2	hg19	CCDS14544.1	.	.	.	.	.	.	.	.	.	.	T	12.44	1.939889	0.34189	.	.	ENSG00000133124	ENST00000372129	T	0.18174	2.23	5.33	4.16	0.48862	.	0.665344	0.14620	N	0.308478	T	0.27313	0.0670	L	0.57536	1.79	0.09310	N	1	D	0.67145	0.996	P	0.59595	0.86	T	0.07986	-1.0744	10	0.12430	T	0.62	-19.4821	8.3647	0.32380	0.0:0.1562:0.0:0.8438	.	732	O14654	IRS4_HUMAN	R	732	ENSP00000361202:H732R	ENSP00000361202:H732R	H	-	2	0	IRS4	107864036	1.000000	0.71417	0.765000	0.31456	0.970000	0.65996	2.867000	0.48428	1.955000	0.56771	0.486000	0.48141	CAC	.	.		0.502	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604		C	107977380	T	C	107977380	3	2	289	1	0	0	0	0	1	0	0	0	7851	1696	59	2	1582	2	IRS4	23	107977380	Missense_Mutation	SNP	T	TCGA-G3-A6UC-01A-21D-A33K-10	17286725	107977380	47293180	121	42461										
MAGEA6	4105	hgsc.bcm.edu	37	chrX	151870008	151870008	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0573770491803279	7	1	1.25444444444444	1.43365079365079	1.19470899470899	0.361455108359133	1	0	tgtgttagaggtgtttgaggGgagggaagacagtatcttcg	17	3	1	3			TCGA-G3-A6UC-01A-21D-A33K-10	TCGA-G3-A6UC-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec3c8a89-d074-4f74-afca-6f67a8fb7ce4	fe550293-61ff-43cb-aace-8ff6e6889a33	g.chrX:151870008G>T	ENST00000329342.5	+	3	923	c.698G>T	c.(697-699)gGg>gTg	p.G233V		NM_005363.2	NP_005354.1	P43360	MAGA6_HUMAN	melanoma antigen family A, 6	233	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.									breast(1)|endometrium(3)|large_intestine(3)|lung(16)|prostate(3)|skin(1)|urinary_tract(1)	28	Acute lymphoblastic leukemia(192;6.56e-05)					GTGTTTGAGGGGAGGGAAGAC	0.537																																					p.G233V		Atlas-SNP	.											.	MAGEA6	53	.	0			c.G698T						.						161	156	158					X																	151870008		2202	4300	6502	SO:0001583	missense	4105	exon3			TTGAGGGGAGGGA		CCDS76050.1	Xq28	2009-03-13			ENSG00000197172	ENSG00000197172			6804	protein-coding gene	gene with protein product	"MAGE-6 antigen", "melanoma-associated antigen 6", "melanoma antigen family A 6", "cancer/testis antigen family 1, member 6"	300176		MAGE6		8575766	Standard	NM_005363		Approved	CT1.6	uc004ffq.1	P43360	OTTHUMG00000022642	ENST00000329342.5:c.698G>T	chrX.hg19:g.151870008G>T	ENSP00000329199:p.Gly233Val	134.0	0.0		222.0	10.0	NM_005363	A8IF93|Q6NW44	Missense_Mutation	SNP	ENST00000329342.5	hg19	CCDS14708.1	.	.	.	.	.	.	.	.	.	.	g	9.860	1.196128	0.22037	.	.	ENSG00000197172	ENST00000329342;ENST00000457643	T;T	0.05513	3.43;3.43	0.605	0.605	0.17553	.	.	.	.	.	T	0.30103	0.0754	H	0.95043	3.615	0.19300	N	0.999979	D	0.55605	0.972	D	0.65987	0.94	T	0.04708	-1.0932	8	0.87932	D	0	.	.	.	.	.	233	P43360	MAGA6_HUMAN	V	233	ENSP00000329199:G233V;ENSP00000401806:G233V	ENSP00000329199:G233V	G	+	2	0	MAGEA6	151620664	0.000000	0.05858	0.007000	0.13788	0.130000	0.20726	-1.239000	0.02916	0.573000	0.29400	0.181000	0.17075	GGG	.	.		0.537	MAGEA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058747.2	NM_005363		T	151870008	G	T	151870008	3	4	289	1	0	0	0	0	1	0	0	0	9179	1232	43	3	700	3	MAGEA6	23	151870008	Missense_Mutation	SNP	G	TCGA-G3-A6UC-01A-21D-A33K-10	43892628	151870008	3400552	122	42462										
SAMD11	148398	hgsc.bcm.edu	37	chr1	878348	878348	+	Frame_Shift_Del	DEL	G	G	-													0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	ctccgggccaagctccagctGgaggggccggcgccgagggg							TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:878348delG	ENST00000342066.3	+	11	1557	c.1474delG	c.(1474-1476)ggafs	p.G493fs		NM_152486.2	NP_689699	Q96NU1	SAM11_HUMAN	sterile alpha motif domain containing 11	493					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.74e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.93e-23)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.000472)|Kidney(185;0.0023)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.199)		AGCTCCAGCTGGAGGGGCCGG	0.687																																					p.A491fs		Atlas-Indel,Pindel	.											.	SAMD11	34	.	0			c.1473delT						.						4	5	4					1																	878348		2043	4093	6136	SO:0001589	frameshift_variant	148398	exon11			.	BC024295	CCDS2.2	1p36.33	2013-01-10			ENSG00000187634	ENSG00000187634		"Sterile alpha motif (SAM) domain containing"	28706	protein-coding gene	gene with protein product						12477932	Standard	NM_152486		Approved	MGC45873	uc001abw.1	Q96NU1	OTTHUMG00000040719	ENST00000342066.3:c.1474delG	chr1.hg19:g.878348delG	ENSP00000342313:p.Gly493fs	93.0	0.0		61.0	27.0	NM_152486	A2AA76|I7FV78|I7FV81|I7G0Z6|Q5SV96|Q5SV99|Q5SVA0|Q8N195|Q8TB59	Frame_Shift_Del	DEL	ENST00000342066.3	hg19	CCDS2.2																																																																																			.	.		0.687	SAMD11-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276866.2	NM_152486		-	878348	G	-	878348	7	5	290	1	0	1	0	1	0	0	0	0	13831	1349	47	0	1512	0	SAMD11	1	878348	Frame_Shift_Del	DEL	G	TCGA-G3-A7M5-01A-11D-A33Q-10		878348	248372273	1	42463										
LOC440563	0	hgsc.bcm.edu	37	chr1	13183341	13183341	+	IGR	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	cttaatggcctgaaggtcatCtcctttcagctttccagact	7	12	3	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:13183341C>T								RP13-221M14.3 (18873 upstream) : PRAMEF26 (33014 downstream)																							TGAAGGTCATCTCCTTTCAGC	0.453																																					p.D178N		Atlas-SNP	.											.	.	.	.	0			c.G532A						.						96	67	76					1																	13183341		692	1591	2283	SO:0001628	intergenic_variant	0	exon2			GGTCATCTCCTTT																													chr1.hg19:g.13183341C>T		130.0	0.0		170.0	21.0	NM_001136561		Missense_Mutation	SNP		hg19																																																																																				.	.	0	0.453									T	13183341	C	T	13183341	1	4	290	0	1	0	0	0	0	0	0	0	8888	913	32	3		3	LOC440563	1	13183341	IGR	SNP	C	TCGA-G3-A7M5-01A-11D-A33Q-10	12304993	13183341	236067280	2	42464										
IPP	3652	hgsc.bcm.edu	37	chr1	46184955	46184955	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tcgaagctacagttgtccacTgtttagtaactggatcatag	9	8	1	0			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:46184955T>G	ENST00000396478.3	-	6	1208	c.1106A>C	c.(1105-1107)cAg>cCg	p.Q369P		NM_005897.2	NP_005888.1	Q9Y573	IPP_HUMAN	intracisternal A particle-promoted polypeptide	369						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	actin binding (GO:0003779)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|stomach(2)	20	Acute lymphoblastic leukemia(166;0.155)					AGTTGTCCACTGTTTAGTAAC	0.363																																					p.Q369P		Atlas-SNP	.											.	IPP	66	.	0			c.A1106C						.						127	106	113					1																	46184955		2203	4300	6503	SO:0001583	missense	3652	exon6			GTCCACTGTTTAG	BC032544	CCDS30702.1, CCDS44132.1	1p34-p32	2013-01-30			ENSG00000197429	ENSG00000197429		"Kelch-like", "BTB/POZ domain containing"	6108	protein-coding gene	gene with protein product	"kelch-like family member 27"	147485				1905535, 8432546	Standard	NM_005897		Approved	KLHL27	uc001cou.3	Q9Y573	OTTHUMG00000008004	ENST00000396478.3:c.1106A>C	chr1.hg19:g.46184955T>G	ENSP00000379739:p.Gln369Pro	68.0	0.0		72.0	43.0	NM_001145349	A2A6V4|D3DQ11|Q8N5C3	Missense_Mutation	SNP	ENST00000396478.3	hg19	CCDS30702.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.061563	0.76187	.	.	ENSG00000197429	ENST00000359942;ENST00000396478	T;T	0.79141	-1.24;-1.24	5.84	5.84	0.93424	Galactose oxidase, beta-propeller (1);	0.107275	0.64402	D	0.000004	D	0.87051	0.6081	M	0.83953	2.67	0.80722	D	1	P;D	0.61080	0.832;0.989	P;P	0.58172	0.699;0.834	D	0.88807	0.3289	10	0.66056	D	0.02	.	16.216	0.82217	0.0:0.0:0.0:1.0	.	369;369	Q9Y573;A2A6V3	IPP_HUMAN;.	P	369	ENSP00000353024:Q369P;ENSP00000379739:Q369P	ENSP00000353024:Q369P	Q	-	2	0	IPP	45957542	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.597000	0.82733	2.228000	0.72767	0.482000	0.46254	CAG	.	.		0.363	IPP-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021974.3	NM_005897		G	46184955	T	G	46184955	3	3	290	1	0	0	0	0	1	0	0	0	7809	1580	55	5	766	5	IPP	1	46184955	Missense_Mutation	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	33001614	46184955	203065666	3	42465										
LRRC7	57554	hgsc.bcm.edu	37	chr1	70505455	70505455	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	caacagctgcttagacatatAgaagctagacggttagacag	10	8	0	4			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:70505455A>G	ENST00000035383.5	+	19	3864	c.3834A>G	c.(3832-3834)atA>atG	p.I1278M	LRRC7_ENST00000415775.2_Missense_Mutation_p.I562M|LRRC7_ENST00000310961.5_Missense_Mutation_p.I1283M	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	1278						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)				breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						TTAGACATATAGAAGCTAGAC	0.443																																					p.I1278M		Atlas-SNP	.											.	LRRC7	400	.	0			c.A3834G						.						92	91	91					1																	70505455		2203	4300	6503	SO:0001583	missense	57554	exon19			ACATATAGAAGCT		CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.3834A>G	chr1.hg19:g.70505455A>G	ENSP00000035383:p.Ile1278Met	65.0	0.0		66.0	14.0	NM_020794	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Missense_Mutation	SNP	ENST00000035383.5	hg19	CCDS645.1	.	.	.	.	.	.	.	.	.	.	A	16.83	3.230527	0.58777	.	.	ENSG00000033122	ENST00000310961;ENST00000035383;ENST00000415775;ENST00000370957	T;T;T	0.63255	0.17;-0.03;1.15	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.62036	0.2395	N	0.24115	0.695	0.49389	D	0.99978	D;D;D	0.89917	1.0;1.0;0.996	D;D;P	0.85130	0.991;0.997;0.823	T	0.69427	-0.5148	10	0.72032	D	0.01	.	15.9872	0.80168	1.0:0.0:0.0:0.0	.	562;1278;1278	F8WE45;Q96NW7-2;Q96NW7	.;.;LRRC7_HUMAN	M	1283;1278;562;1101	ENSP00000309245:I1283M;ENSP00000035383:I1278M;ENSP00000394867:I562M	ENSP00000035383:I1278M	I	+	3	3	LRRC7	70278043	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.530000	0.60595	2.367000	0.80283	0.528000	0.53228	ATA	.	.		0.443	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794		G	70505455	A	G	70505455	3	3	290	1	0	0	0	0	1	0	0	0	9029	410	15	2	3908	2	LRRC7	1	70505455	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	24320500	70505455	178745166	4	42466										
SLC44A5	204962	hgsc.bcm.edu	37	chr1	75716965	75716965	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	gtaacaggttaaagtaaaacAaaatggtcttgttcctgtta	8	5	1	0			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:75716965A>T	ENST00000370855.5	-	7	388	c.275T>A	c.(274-276)tTg>tAg	p.L92*	SLC44A5_ENST00000469525.1_5'UTR|SLC44A5_ENST00000370859.3_Nonsense_Mutation_p.L92*|SLC44A5_ENST00000535611.1_5'UTR	NM_152697.4	NP_689910.2	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5	92					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				kidney(1)|large_intestine(13)|lung(35)|ovary(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61						AAAGTAAAACAAAATGGTCTT	0.398																																					p.L92X		Atlas-SNP	.											.	SLC44A5	231	.	0			c.T275A						.						106	94	98					1																	75716965		2203	4300	6503	SO:0001587	stop_gained	204962	exon7			TAAAACAAAATGG	BC034580	CCDS667.1, CCDS44164.1	1p31.1	2013-05-22			ENSG00000137968	ENSG00000137968		"Solute carriers"	28524	protein-coding gene	gene with protein product						15715662	Standard	NM_152697		Approved	MGC34032, CTL5	uc001dgu.3	Q8NCS7	OTTHUMG00000009721	ENST00000370855.5:c.275T>A	chr1.hg19:g.75716965A>T	ENSP00000359892:p.Leu92*	65.0	0.0		78.0	24.0	NM_001130058	B5MCU3|Q4G0K0|Q8NA44|Q8NB86	Nonsense_Mutation	SNP	ENST00000370855.5	hg19	CCDS667.1	.	.	.	.	.	.	.	.	.	.	A	34	5.322037	0.95708	.	.	ENSG00000137968	ENST00000370859;ENST00000536707;ENST00000370855;ENST00000535790	.	.	.	4.78	4.78	0.61160	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.2814	13.9805	0.64301	1.0:0.0:0.0:0.0	.	.	.	.	X	92;131;92;85	.	ENSP00000359892:L92X	L	-	2	0	SLC44A5	75489553	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	6.972000	0.76110	2.094000	0.63399	0.528000	0.53228	TTG	.	.		0.398	SLC44A5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026921.1	NM_152697		T	75716965	A	T	75716965	4	4	290	1	0	0	0	0	0	1	0	0	14654	131	5	4	2067	4	SLC44A5	1	75716965	Nonsense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	5211510	75716965	173533656	5	42467										
CLCA2	9635	hgsc.bcm.edu	37	chr1	86919189	86919189	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	gcccccaccctgatgtgtttCcaccatgcaaaattattgac	6	14	0	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:86919189C>A	ENST00000370565.4	+	13	2455	c.2293C>A	c.(2293-2295)Cca>Aca	p.P765T	CLCA2_ENST00000498802.1_3'UTR	NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	765					cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)			NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		TGATGTGTTTCCACCATGCAA	0.517																																					p.P765T	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											.	CLCA2	102	.	0			c.C2293A						.						89	91	90					1																	86919189		2203	4300	6503	SO:0001583	missense	9635	exon13			GTGTTTCCACCAT		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"chloride channel, calcium activated, family member 2", "chloride channel regulator 2"				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.2293C>A	chr1.hg19:g.86919189C>A	ENSP00000359596:p.Pro765Thr	40.0	0.0		65.0	29.0	NM_006536	A8K2T3|Q9Y6N2	Missense_Mutation	SNP	ENST00000370565.4	hg19	CCDS708.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.022242	0.75275	.	.	ENSG00000137975	ENST00000370565	T	0.07444	3.19	5.76	5.76	0.90799	.	0.209202	0.40385	N	0.001105	T	0.18923	0.0454	M	0.86028	2.79	0.37261	D	0.906973	D	0.59767	0.986	P	0.55785	0.784	T	0.00829	-1.1549	10	0.87932	D	0	-10.101	14.7385	0.69434	0.1448:0.8552:0.0:0.0	.	765	Q9UQC9	CLCA2_HUMAN	T	765	ENSP00000359596:P765T	ENSP00000359596:P765T	P	+	1	0	CLCA2	86691777	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	3.533000	0.53561	2.871000	0.98454	0.655000	0.94253	CCA	.	.		0.517	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536		A	86919189	C	A	86919189	3	1	290	1	0	0	0	0	1	0	0	0	3460	855	30	3	2343	3	CLCA2	1	86919189	Missense_Mutation	SNP	C	TCGA-G3-A7M5-01A-11D-A33Q-10	11202224	86919189	162331432	6	42468										
BTBD8	284697	hgsc.bcm.edu	37	chr1	92554445	92554445	+	Frame_Shift_Del	DEL	T	T	-													0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	aagctttagaatttagaacgTttttacagtaagtgctttct							TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:92554445delT	ENST00000342818.3	+	2	576	c.340delT	c.(340-342)tttfs	p.F114fs	BTBD8_ENST00000370382.3_Frame_Shift_Del_p.F114fs|BTBD8_ENST00000540648.1_Frame_Shift_Del_p.F114fs	NM_183242.3	NP_899065.2	Q5XKL5	BTBD8_HUMAN	BTB (POZ) domain containing 8	114	BTB 1. {ECO:0000255|PROSITE- ProRule:PRU00037}.					nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)	16		all_lung(203;0.0484)|Lung NSC(277;0.126)|Glioma(108;0.222)		all cancers(265;0.0153)|Epithelial(280;0.0982)		ATTTAGAACGTTTTTACAGTA	0.274																																					p.T113fs		Atlas-Indel,Pindel	.											.	BTBD8	32	.	0			c.339delG						.						85	79	81					1																	92554445		2202	4299	6501	SO:0001589	frameshift_variant	284697	exon2			.	AY346333	CCDS737.1	1p22.1	2013-01-08			ENSG00000189195	ENSG00000189195		"BTB/POZ domain containing"	21019	protein-coding gene	gene with protein product						14654994	Standard	NM_183242		Approved		uc001doo.3	Q5XKL5	OTTHUMG00000010289	ENST00000342818.3:c.340delT	chr1.hg19:g.92554445delT	ENSP00000343686:p.Phe114fs	107.0	0.0		90.0	49.0	NM_183242	Q6V9S5	Frame_Shift_Del	DEL	ENST00000342818.3	hg19	CCDS737.1																																																																																			.	.		0.274	BTBD8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028372.1	NM_183242		-	92554445	T	-	92554445	7	5	290	1	0	1	0	1	0	0	0	0	1549	1725	60	0	346	0	BTBD8	1	92554445	Frame_Shift_Del	DEL	T	TCGA-G3-A7M5-01A-11D-A33Q-10	5635256	92554445	156696176	7	42469										
VAV3	10451	hgsc.bcm.edu	37	chr1	108152569	108152569	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	ttaccagggttggcaagaatAatctactggtttgggcacct	11	8	1	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:108152569A>T	ENST00000370056.4	-	22	2273	c.1999T>A	c.(1999-2001)Tat>Aat	p.Y667N	VAV3_ENST00000527011.1_Missense_Mutation_p.Y667N|VAV3_ENST00000415432.2_Missense_Mutation_p.Y107N|VAV3_ENST00000343258.4_5'UTR|VAV3_ENST00000544443.1_Missense_Mutation_p.Y71N	NM_006113.4	NP_006104.4	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor	667	Sufficient for interaction with ROS1.				angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of signal transduction (GO:0009967)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|vesicle fusion (GO:0006906)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|SH3/SH2 adaptor activity (GO:0005070)			NS(2)|breast(5)|endometrium(4)|kidney(2)|large_intestine(14)|lung(20)|ovary(6)|prostate(3)|stomach(1)|urinary_tract(1)	58		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)		TGGCAAGAATAATCTACTGGT	0.363																																					p.Y667N		Atlas-SNP	.											.	VAV3	176	.	0			c.T1999A						.						99	95	96					1																	108152569		2203	4300	6503	SO:0001583	missense	10451	exon22			AAGAATAATCTAC	AF118886	CCDS785.1, CCDS44181.1	1p13.3	2013-02-14	2007-07-25		ENSG00000134215	ENSG00000134215		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "SH2 domain containing"	12659	protein-coding gene	gene with protein product		605541	"vav 3 oncogene"				Standard	NM_001079874		Approved		uc001dvk.1	Q9UKW4	OTTHUMG00000010995	ENST00000370056.4:c.1999T>A	chr1.hg19:g.108152569A>T	ENSP00000359073:p.Tyr667Asn	93.0	0.0		114.0	43.0	NM_006113	B1AMM0|B1APV5|B4E232|B7ZLR1|E9PQ97|O60498|O95230|Q9Y5X8	Missense_Mutation	SNP	ENST00000370056.4	hg19	CCDS785.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.035887	0.75617	.	.	ENSG00000134215	ENST00000370056;ENST00000527011;ENST00000544443;ENST00000415432	T;D;T;T	0.92545	1.77;-3.06;1.77;1.77	5.14	5.14	0.70334	SH2 motif (1);	0.116765	0.64402	D	0.000012	D	0.95014	0.8386	M	0.80616	2.505	0.80722	D	1	D;D;D;D	0.89917	0.998;0.999;0.984;1.0	D;D;D;D	0.87578	0.991;0.988;0.95;0.998	D	0.94910	0.8064	10	0.48119	T	0.1	.	13.8104	0.63260	1.0:0.0:0.0:0.0	.	667;71;667;107	E9PQ97;B7Z3Z5;Q9UKW4;Q9UKW4-3	.;.;VAV3_HUMAN;.	N	667;667;71;107	ENSP00000359073:Y667N;ENSP00000432540:Y667N;ENSP00000446404:Y71N;ENSP00000394897:Y107N	ENSP00000359073:Y667N	Y	-	1	0	VAV3	107954092	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.368000	0.79567	2.074000	0.62210	0.477000	0.44152	TAT	.	.		0.363	VAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030242.2	NM_006113		T	108152569	A	T	108152569	3	4	290	1	0	0	0	0	1	0	0	0	17148	362	13	4	568	4	VAV3	1	108152569	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	15598124	108152569	141098052	8	42470										
LRIG2	9860	hgsc.bcm.edu	37	chr1	113657138	113657138	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	gcatagctggagggagtcctGcccctcgtctcaactggact	12	13	1	0			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:113657138G>A	ENST00000361127.5	+	15	2368	c.2170G>A	c.(2170-2172)Gcc>Acc	p.A724T	LRIG2_ENST00000492207.1_3'UTR	NM_014813.1	NP_055628.1	O94898	LRIG2_HUMAN	leucine-rich repeats and immunoglobulin-like domains 2	724	Ig-like C2-type 3.				innervation (GO:0060384)|regulation of platelet-derived growth factor receptor signaling pathway (GO:0010640)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				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)		AGGGAGTCCTGCCCCTCGTCT	0.493																																					p.A724T		Atlas-SNP	.											.	LRIG2	67	.	0			c.G2170A						.						99	91	94					1																	113657138		2203	4300	6503	SO:0001583	missense	9860	exon15			AGTCCTGCCCCTC	AB018349	CCDS30808.1	1p13.1	2013-01-11			ENSG00000198799	ENSG00000198799		"Immunoglobulin superfamily / I-set domain containing"	20889	protein-coding gene	gene with protein product		608869					Standard	XM_005271369		Approved	KIAA0806	uc001edf.1	O94898	OTTHUMG00000012133	ENST00000361127.5:c.2170G>A	chr1.hg19:g.113657138G>A	ENSP00000355396:p.Ala724Thr	57.0	0.0		69.0	21.0	NM_014813	Q9NSN2	Missense_Mutation	SNP	ENST00000361127.5	hg19	CCDS30808.1	.	.	.	.	.	.	.	.	.	.	G	14.34	2.505537	0.44558	.	.	ENSG00000198799	ENST00000361127	T	0.66099	-0.19	5.3	2.34	0.29019	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.173530	0.50627	D	0.000110	T	0.20333	0.0489	N	0.11341	0.13	0.42584	D	0.993225	B	0.09022	0.002	B	0.16722	0.016	T	0.04255	-1.0965	10	0.27785	T	0.31	.	8.1469	0.31117	0.1378:0.0:0.7352:0.127	.	724	O94898	LRIG2_HUMAN	T	724	ENSP00000355396:A724T	ENSP00000355396:A724T	A	+	1	0	LRIG2	113458661	0.997000	0.39634	0.962000	0.40283	0.950000	0.60333	2.272000	0.43373	0.593000	0.29745	0.561000	0.74099	GCC	.	.		0.493	LRIG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033549.2	NM_014813		A	113657138	G	A	113657138	3	1	290	1	0	0	0	0	1	0	0	0	8954	1319	46	3	2228	3	LRIG2	1	113657138	Missense_Mutation	SNP	G	TCGA-G3-A7M5-01A-11D-A33Q-10	5504569	113657138	135593483	9	42471										
RPTN	126638	hgsc.bcm.edu	37	chr1	152128332	152128332	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	ttgtcggtccatctgactgtAgtgggaactctggccttgtc	12	10	2	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:152128332A>T	ENST00000316073.3	-	3	1307	c.1243T>A	c.(1243-1245)Tac>Aac	p.Y415N		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	415	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						ATCTGACTGTAGTGGGAACTC	0.517																																					p.Y415N		Atlas-SNP	.											.	RPTN	123	.	0			c.T1243A						.						784	679	711					1																	152128332		1568	3582	5150	SO:0001583	missense	126638	exon3			GACTGTAGTGGGA	AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"EF-hand domain containing"	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.1243T>A	chr1.hg19:g.152128332A>T	ENSP00000317895:p.Tyr415Asn	106.0	0.0		172.0	88.0	NM_001122965	B7ZBZ3	Missense_Mutation	SNP	ENST00000316073.3	hg19	CCDS41397.1	.	.	.	.	.	.	.	.	.	.	a	14.18	2.458554	0.43634	.	.	ENSG00000215853	ENST00000316073;ENST00000541545	T	0.11930	2.73	4.65	0.906	0.19314	.	.	.	.	.	T	0.03915	0.0110	M	0.78916	2.43	0.09310	N	1	P	0.50617	0.937	B	0.33392	0.163	T	0.37663	-0.9696	9	0.28530	T	0.3	.	4.3063	0.10949	0.4809:0.3424:0.1768:0.0	.	415	Q6XPR3	RPTN_HUMAN	N	415;70	ENSP00000317895:Y415N	ENSP00000317895:Y415N	Y	-	1	0	RPTN	150394956	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.330000	0.07925	-0.105000	0.12132	0.323000	0.21402	TAC	.	.		0.517	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312		T	152128332	A	T	152128332	3	4	290	1	0	0	0	0	1	0	0	0	13679	420	15	4	1115	4	RPTN	1	152128332	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	38471194	152128332	97122289	10	42472										
FCRL2	79368	hgsc.bcm.edu	37	chr1	157740434	157740434	+	Frame_Shift_Del	DEL	G	G	-													0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tctccttcgaagacagaagaGggcgccacaagggtcagcga							TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:157740434delG	ENST00000361516.3	-	3	123	c.75delC	c.(73-75)cccfs	p.P25fs	FCRL2_ENST00000368181.4_Frame_Shift_Del_p.P25fs|FCRL2_ENST00000469986.1_5'Flank|FCRL2_ENST00000392274.3_Frame_Shift_Del_p.P25fs	NM_030764.3	NP_110391.2	Q96LA5	FCRL2_HUMAN	Fc receptor-like 2	25	Ig-like C2-type 1.				cell-cell signaling (GO:0007267)|positive regulation of signal transduction (GO:0009967)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|skin(2)	51	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			AGACAGAAGAGGGCGCCACAA	0.483																																					p.S26fs		Atlas-Indel,Pindel	.											.	FCRL2	104	.	0			c.76delT						.						40	39	39					1																	157740434		2203	4300	6503	SO:0001589	frameshift_variant	79368	exon3			.	AF319438	CCDS1168.1	1q23.1	2013-01-14	2002-01-14	2005-03-23	ENSG00000132704	ENSG00000132704		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14875	protein-coding gene	gene with protein product		606509	"SH2 domain-containing phosphatase anchor protein 1"	SPAP1		11162587	Standard	NM_030764		Approved	FCRH2, IRTA4, CD307b	uc001fre.2	Q96LA5	OTTHUMG00000019399	ENST00000361516.3:c.75delC	chr1.hg19:g.157740434delG	ENSP00000355157:p.Pro25fs	49.0	0.0		59.0	27.0	NM_030764	A0N0M5|A1L307|A6NMS0|Q6NTA1|Q9BZI4|Q9BZI5|Q9BZI6	Frame_Shift_Del	DEL	ENST00000361516.3	hg19	CCDS1168.1																																																																																			.	.		0.483	FCRL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051408.2	NM_030764		-	157740434	G	-	157740434	7	5	290	1	0	1	0	1	0	0	0	0	5803	987	35	0	1491	0	FCRL2	1	157740434	Frame_Shift_Del	DEL	G	TCGA-G3-A7M5-01A-11D-A33Q-10	5612102	157740434	91510187	11	42473										
DARC	2532	hgsc.bcm.edu	37	chr1	159175433	159175433	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	ctgcccttcttcatcctcacCagtgtcctgggtatcctagc	7	16	3	0	rs375137235		TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:159175433C>T	ENST00000368122.2	+	2	883	c.204C>T	c.(202-204)acC>acT	p.T68T	DARC_ENST00000537147.1_Silent_p.T68T|DARC_ENST00000368121.2_Silent_p.T70T|CTA-134P22.2_ENST00000609696.1_RNA	NM_002036.3	NP_002027.2	Q16570	ACKR1_HUMAN		68					chemokine-mediated signaling pathway (GO:0070098)|defense response (GO:0006952)|inflammatory response (GO:0006954)|regulation of chemokine production (GO:0032642)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C-C chemokine binding (GO:0019957)|G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			large_intestine(2)|lung(1)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	8	all_hematologic(112;0.0429)					TCATCCTCACCAGTGTCCTGG	0.587																																					p.T70T		Atlas-SNP	.											.	DARC	76	.	0			c.C210T						.	C	,	1,4405	2.1+/-5.4	0,1,2202	133	119	124		210,204	4.8	0.4	1		124	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	DARC	NM_001122951.2,NM_002036.3	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	70/339,68/337	159175433	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	2532	exon1			CCTCACCAGTGTC																												ENST00000368122.2:c.204C>T	chr1.hg19:g.159175433C>T		70.0	0.0		64.0	28.0	NM_001122951	A8YPG5|O75898|Q16300|Q8WWE3|Q9UJP0|Q9UKZ5|Q9UKZ6|Q9UQE1	Silent	SNP	ENST00000368122.2	hg19	CCDS1183.1																																																																																			.	.		0.587	DARC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090338.2			T	159175433	C	T	159175433	2	4	290	1	0	0	0	0	0	0	0	1	4242	581	21	3		3	DARC	1	159175433	Silent	SNP	C	TCGA-G3-A7M5-01A-11D-A33Q-10	1434999	159175433	90075188	12	42474										
DUSP12	11266	hgsc.bcm.edu	37	chr1	161723027	161723027	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	gtacagtggatggaatctgcTttgttgggagtgatggatgg	17	3	1	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:161723027T>G	ENST00000367943.4	+	5	869	c.837T>G	c.(835-837)gcT>gcG	p.A279A		NM_007240.1	NP_009171.1	Q9UNI6	DUS12_HUMAN	dual specificity phosphatase 12	279					cellular protein modification process (GO:0006464)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of glucokinase activity (GO:0033133)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|lung(1)	5	all_hematologic(112;0.0359)		BRCA - Breast invasive adenocarcinoma(70;0.00634)			TGGAATCTGCTTTGTTGGGAG	0.368																																					p.A279A		Atlas-SNP	.											.	DUSP12	20	.	0			c.T837G						.						247	204	219					1																	161723027		2203	4300	6503	SO:0001819	synonymous_variant	11266	exon5			ATCTGCTTTGTTG	AF119226	CCDS1234.1	1q21-q22	2011-06-09			ENSG00000081721	ENSG00000081721		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	3067	protein-coding gene	gene with protein product	"serine/threonine specific protein phosphatase", "YVH1 protein-tyrosine phosphatase (S. cerevisiae) ortholog"	604835				10446167	Standard	XM_005244862		Approved	YVH1, DUSP1	uc001gbo.3	Q9UNI6	OTTHUMG00000034540	ENST00000367943.4:c.837T>G	chr1.hg19:g.161723027T>G		88.0	0.0		94.0	35.0	NM_007240	Q5VXA8	Silent	SNP	ENST00000367943.4	hg19	CCDS1234.1																																																																																			.	.		0.368	DUSP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083588.1	NM_007240		G	161723027	T	G	161723027	2	3	290	1	0	0	0	0	0	0	0	1	4814	1596	56	5		5	DUSP12	1	161723027	Silent	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	2547594	161723027	87527594	13	42475										
RGS4	5999	hgsc.bcm.edu	37	chr1	163043349	163043349	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	aagaaaatcaaatcaccatcTaaactaagtcccaaggccaa	4	11	3	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:163043349T>A	ENST00000367909.6	+	4	655	c.315T>A	c.(313-315)tcT>tcA	p.S105S	RGS4_ENST00000491263.1_3'UTR|RGS4_ENST00000527809.1_Silent_p.S87S|RGS4_ENST00000367906.3_Silent_p.S87S|RGS4_ENST00000367908.4_Intron|RGS4_ENST00000531057.1_Silent_p.S105S|RGS4_ENST00000421743.2_Silent_p.S202S	NM_001113380.1|NM_005613.5	NP_001106851.1|NP_005604.1	P49798	RGS4_HUMAN	regulator of G-protein signaling 4	105	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				inactivation of MAPK activity (GO:0000188)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|upper_aerodigestive_tract(2)	21						AATCACCATCTAAACTAAGTC	0.368																																					p.S202S	Ovarian(76;1257 1738 3039 6086)	Atlas-SNP	.											.	RGS4	97	.	0			c.T606A						.						103	95	98					1																	163043349		2203	4300	6503	SO:0001819	synonymous_variant	5999	exon5			ACCATCTAAACTA	BC051869	CCDS1243.1, CCDS44270.1, CCDS44271.1, CCDS44272.1	1q23.3	2008-05-14	2007-08-14		ENSG00000117152	ENSG00000117152		"Regulators of G-protein signaling"	10000	protein-coding gene	gene with protein product		602516	"regulator of G-protein signalling 4", "schizophrenia disorder 9"	SCZD9		8602223, 8756726	Standard	NM_001102445		Approved		uc001gcl.4	P49798	OTTHUMG00000034417	ENST00000367909.6:c.315T>A	chr1.hg19:g.163043349T>A		242.0	0.0		259.0	101.0	NM_001102445	A7XA56|A7XA58|A7XA59|A7YVV7|B1APZ3	Silent	SNP	ENST00000367909.6	hg19	CCDS1243.1																																																																																			.	.		0.368	RGS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083197.2	NM_005613		A	163043349	T	A	163043349	2	1	290	1	0	0	0	0	0	0	0	1	13322	1509	53	4		4	RGS4	1	163043349	Silent	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	1320322	163043349	86207272	14	42476										
ASTN1	460	hgsc.bcm.edu	37	chr1	176838062	176838062	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	atagtggtagaggacccggtGtaaggtgggggaacccagat	17	6	0	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:176838062G>A	ENST00000367654.3	-	22	3800	c.3589C>T	c.(3589-3591)Cac>Tac	p.H1197Y	ASTN1_ENST00000367657.3_Missense_Mutation_p.H1189Y|ASTN1_ENST00000424564.2_Missense_Mutation_p.H1189Y|ASTN1_ENST00000361833.2_Missense_Mutation_p.H1189Y	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	1197					locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						AGGACCCGGTGTAAGGTGGGG	0.488																																					p.H1189Y		Atlas-SNP	.											.	ASTN1	314	.	0			c.C3565T						.						157	147	151					1																	176838062		2203	4300	6503	SO:0001583	missense	460	exon22			CCCGGTGTAAGGT	AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"astrotactin"	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.3589C>T	chr1.hg19:g.176838062G>A	ENSP00000356626:p.His1197Tyr	174.0	0.0		204.0	68.0	NM_004319	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Missense_Mutation	SNP	ENST00000367654.3	hg19		.	.	.	.	.	.	.	.	.	.	G	14.25	2.480535	0.44044	.	.	ENSG00000152092	ENST00000367657;ENST00000361833;ENST00000367654;ENST00000424564;ENST00000541808	T;T;T;T	0.11495	2.77;3.18;3.18;2.77	5.7	5.7	0.88788	.	0.042709	0.85682	D	0.000000	T	0.11367	0.0277	L	0.27053	0.805	0.80722	D	1	B;B	0.34103	0.437;0.232	B;B	0.40375	0.327;0.248	T	0.09400	-1.0676	10	0.07644	T	0.81	-17.1324	19.4429	0.94831	0.0:0.0:1.0:0.0	.	1189;1189	O14525-2;B1AJS1	.;.	Y	1189;1189;1197;1189;1189	ENSP00000356629:H1189Y;ENSP00000354536:H1189Y;ENSP00000356626:H1197Y;ENSP00000395041:H1189Y	ENSP00000354536:H1189Y	H	-	1	0	ASTN1	175104685	1.000000	0.71417	0.507000	0.27676	0.142000	0.21351	7.782000	0.85680	2.698000	0.92095	0.655000	0.94253	CAC	.	.		0.488	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319		A	176838062	G	A	176838062	3	1	290	1	0	0	0	0	1	0	0	0	1064	1377	48	3	331	3	ASTN1	1	176838062	Missense_Mutation	SNP	G	TCGA-G3-A7M5-01A-11D-A33Q-10	13794713	176838062	72412559	15	42477										
TDRD5	163589	hgsc.bcm.edu	37	chr1	179600021	179600021	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	aaaggacaccaagacttactAgtgtttgatgcggataagaa	10	6	0	3			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:179600021A>T	ENST00000367614.1	+	7	1451	c.1092A>T	c.(1090-1092)ctA>ctT	p.L364L	TDRD5_ENST00000294848.8_Silent_p.L364L|TDRD5_ENST00000444136.1_Silent_p.L364L	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	364	HTH OST-type 3. {ECO:0000255|PROSITE- ProRule:PRU00975}.				DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)				NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						AAGACTTACTAGTGTTTGATG	0.398																																					p.L364L		Atlas-SNP	.											.	TDRD5	149	.	0			c.A1092T						.						137	128	131					1																	179600021		2203	4300	6503	SO:0001819	synonymous_variant	163589	exon7			CTTACTAGTGTTT	AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"Tudor domain containing"	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.1092A>T	chr1.hg19:g.179600021A>T		275.0	0.0		286.0	104.0	NM_173533	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Silent	SNP	ENST00000367614.1	hg19	CCDS1332.1																																																																																			.	.		0.398	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533		T	179600021	A	T	179600021	2	4	290	1	0	0	0	0	0	0	0	1	15748	407	15	4		4	TDRD5	1	179600021	Silent	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	2761959	179600021	69650600	16	42478										
KIAA1614	57710	hgsc.bcm.edu	37	chr1	180904396	180904396	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	gcccctcgccgtcgcacgtgCgctttgaggatgagtccgcc	13	16	0	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:180904396C>A	ENST00000367588.4	+	5	1406	c.1351C>A	c.(1351-1353)Cgc>Agc	p.R451S	KIAA1614_ENST00000367587.1_Missense_Mutation_p.R72S	NM_020950.1	NP_066001.1	Q5VZ46	K1614_HUMAN	KIAA1614	451										NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	33						GTCGCACGTGCGCTTTGAGGA	0.701																																					p.R451S		Atlas-SNP	.											.	KIAA1614	75	.	0			c.C1351A						.						9	12	11					1																	180904396		2054	4152	6206	SO:0001583	missense	57710	exon5			CACGTGCGCTTTG	AB046834	CCDS41442.1	1q25.3	2008-02-05			ENSG00000135835	ENSG00000135835			29327	protein-coding gene	gene with protein product							Standard	NM_020950		Approved		uc001gok.2	Q5VZ46	OTTHUMG00000035183	ENST00000367588.4:c.1351C>A	chr1.hg19:g.180904396C>A	ENSP00000356560:p.Arg451Ser	39.0	0.0		66.0	26.0	NM_020950	Q5VZ45|Q9HCF8	Missense_Mutation	SNP	ENST00000367588.4	hg19	CCDS41442.1	.	.	.	.	.	.	.	.	.	.	c	18.39	3.612668	0.66672	.	.	ENSG00000135835	ENST00000367588;ENST00000367587	T;T	0.63744	0.22;-0.06	4.83	4.83	0.62350	.	0.137394	0.49305	D	0.000150	T	0.76463	0.3991	L	0.61218	1.895	0.28098	N	0.9315370000000001	D	0.89917	1.0	D	0.91635	0.999	T	0.79276	-0.1870	9	0.51188	T	0.08	-22.1444	16.0625	0.80847	0.0:1.0:0.0:0.0	.	451	Q5VZ46	K1614_HUMAN	S	451;72	ENSP00000356560:R451S;ENSP00000356559:R72S	ENSP00000356559:R72S	R	+	1	0	KIAA1614	179171019	0.997000	0.39634	0.748000	0.31131	0.120000	0.20174	3.946000	0.56644	2.383000	0.81215	0.457000	0.33378	CGC	.	.		0.701	KIAA1614-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085151.1	XM_046531		A	180904396	C	A	180904396	3	1	290	1	0	0	0	0	1	0	0	0	8257	768	27	1	1369	1	KIAA1614	1	180904396	Missense_Mutation	SNP	C	TCGA-G3-A7M5-01A-11D-A33Q-10	1304375	180904396	68346225	17	42479										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181689967	181689967	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	gcaaattttgataccttcccTgcagccatcatgactgtgtt	7	11	1	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:181689967T>A	ENST00000367573.2	+	15	1932	c.1932T>A	c.(1930-1932)ccT>ccA	p.P644P	CACNA1E_ENST00000357570.5_Silent_p.P595P|CACNA1E_ENST00000358338.5_Silent_p.P595P|CACNA1E_ENST00000367567.4_Silent_p.P251P|CACNA1E_ENST00000367570.1_Silent_p.P644P|CACNA1E_ENST00000526775.1_Silent_p.P644P|CACNA1E_ENST00000360108.3_Silent_p.P644P	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	644					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						ATACCTTCCCTGCAGCCATCA	0.428																																					p.P644P		Atlas-SNP	.											.	CACNA1E	778	.	0			c.T1932A						.						69	67	68					1																	181689967		1894	4125	6019	SO:0001819	synonymous_variant	777	exon15			CTTCCCTGCAGCC	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.1932T>A	chr1.hg19:g.181689967T>A		27.0	0.0		46.0	13.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Silent	SNP	ENST00000367573.2	hg19	CCDS55664.1																																																																																			.	.		0.428	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		A	181689967	T	A	181689967	2	1	290	1	0	0	0	0	0	0	0	1	2544	1567	55	4		4	CACNA1E	1	181689967	Silent	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	785571	181689967	67560654	18	42480										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181702886	181702886	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tggactcaaccgtggtgcacAgtgagagcacagtccctgtt	12	11	1	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:181702886A>T	ENST00000367573.2	+	21	3262	c.3262A>T	c.(3262-3264)Att>Ttt	p.I1088F	CACNA1E_ENST00000357570.5_Splice_Site_p.I1039F|CACNA1E_ENST00000358338.5_Splice_Site_p.I1020F|CACNA1E_ENST00000367567.4_Splice_Site_p.I695F|CACNA1E_ENST00000367570.1_Splice_Site_p.I1088F|CACNA1E_ENST00000526775.1_Splice_Site_p.I1069F|CACNA1E_ENST00000360108.3_Splice_Site_p.I1069F	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1088					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						CGTGGTGCACAGTGAGAGCAC	0.622																																					p.I1088F		Atlas-SNP	.											.	CACNA1E	778	.	0			c.A3262T						.						32	35	34					1																	181702886		2136	4221	6357	SO:0001630	splice_region_variant	777	exon21			GTGCACAGTGAGA	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.3262+1A>T	chr1.hg19:g.181702886A>T		114.0	0.0		160.0	61.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	A	14.05	2.420767	0.42918	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.96427	-3.95;-3.95;-3.96;-3.95;-4.01;-3.96;-3.96	4.88	4.88	0.63580	.	0.604131	0.19018	N	0.124893	D	0.92325	0.7565	N	0.08118	0	0.49687	D	0.99981	P;P;P	0.50819	0.775;0.939;0.557	B;P;B	0.47299	0.256;0.543;0.221	D	0.93529	0.6868	10	0.66056	D	0.02	.	14.1472	0.65357	1.0:0.0:0.0:0.0	.	1069;1088;1088	Q15878-2;Q15878;Q15878-3	.;CAC1E_HUMAN;.	F	1088;1069;1039;1020;695;1069;1088	ENSP00000356542:I1088F;ENSP00000434814:I1069F;ENSP00000350183:I1039F;ENSP00000351101:I1020F;ENSP00000356539:I695F;ENSP00000353222:I1069F;ENSP00000356545:I1088F	ENSP00000350183:I1039F	I	+	1	0	CACNA1E	179969509	1.000000	0.71417	1.000000	0.80357	0.438000	0.31896	5.000000	0.63940	1.832000	0.53329	0.459000	0.35465	ATT	.	.		0.622	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721	Missense_Mutation	T	181702886	A	T	181702886	5	4	290	1	0	0	0	0	0	0	1	0	2544	202	7	4	3344	4	CACNA1E	1	181702886	Splice_Site	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	12919	181702886	67547735	19	42481										
LAMC2	3918	hgsc.bcm.edu	37	chr1	183207463	183207463	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	aatcagatcagctgctttccCgtgccaatcttgctaaaagc	7	12	3	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:183207463C>A	ENST00000264144.4	+	19	2841	c.2776C>A	c.(2776-2778)Cgt>Agt	p.R926S	LAMC2_ENST00000493293.1_Missense_Mutation_p.R926S	NM_005562.2	NP_005553.2	Q13753	LAMC2_HUMAN	laminin, gamma 2	926	Domain II and I.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	cell cortex (GO:0005938)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-2 complex (GO:0005607)|laminin-5 complex (GO:0005610)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	heparin binding (GO:0008201)			breast(2)|endometrium(6)|kidney(8)|large_intestine(11)|lung(18)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55						GCTGCTTTCCCGTGCCAATCT	0.413																																					p.R926S		Atlas-SNP	.											LAMC2,colon,carcinoma,0,1	LAMC2	113	.	0			c.C2776A						.						132	122	125					1																	183207463		2203	4300	6503	SO:0001583	missense	3918	exon19			CTTTCCCGTGCCA	Z15008	CCDS1352.1, CCDS44285.1	1q25-q31	2013-03-01	2002-08-29		ENSG00000058085	ENSG00000058085		"Laminins"	6493	protein-coding gene	gene with protein product		150292	"laminin, gamma 2 (nicein (100kD), kalinin (105kD), BM600 (100kD), Herlitz junctional epidermolysis bullosa))"	EBR2, LAMB2T, LAMNB2, EBR2A		1383240	Standard	NM_005562		Approved	nicein-100kDa, kalinin-105kDa, BM600-100kDa	uc001gqa.2	Q13753	OTTHUMG00000035520	ENST00000264144.4:c.2776C>A	chr1.hg19:g.183207463C>A	ENSP00000264144:p.Arg926Ser	37.0	0.0		84.0	35.0	NM_005562	Q02536|Q02537|Q13752|Q14941|Q14DF7|Q2M1N2|Q5VYE8	Missense_Mutation	SNP	ENST00000264144.4	hg19	CCDS1352.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.280939	0.80692	.	.	ENSG00000058085	ENST00000493293;ENST00000537180;ENST00000264144	T;T	0.17854	2.4;2.25	5.19	4.21	0.49690	.	0.000000	0.64402	D	0.000002	T	0.42921	0.1224	M	0.83483	2.645	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.73708	0.956;0.956;0.981	T	0.41698	-0.9494	10	0.62326	D	0.03	.	12.8485	0.57844	0.1627:0.8373:0.0:0.0	.	926;926;926	Q2M1N2;Q13753;Q13753-2	.;LAMC2_HUMAN;.	S	926	ENSP00000432063:R926S;ENSP00000264144:R926S	ENSP00000264144:R926S	R	+	1	0	LAMC2	181474086	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.525000	0.53502	2.558000	0.86282	0.655000	0.94253	CGT	.	.		0.413	LAMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086258.1	NM_005562		A	183207463	C	A	183207463	3	1	290	1	0	0	0	0	1	0	0	0	8624	652	23	1	2850	1	LAMC2	1	183207463	Missense_Mutation	SNP	C	TCGA-G3-A7M5-01A-11D-A33Q-10	1504577	183207463	66043158	20	42482										
C1orf26	54823	hgsc.bcm.edu	37	chr1	185137519	185137519	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tataatataaaaagaagacaAggactgaaaaggtaaatttc	7	3	0	3			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:185137519A>T	ENST00000367500.4	+	4	378	c.213A>T	c.(211-213)caA>caT	p.Q71H	SWT1_ENST00000367501.3_Missense_Mutation_p.Q71H	NM_017673.6	NP_060143.4	Q5T5J6	SWT1_HUMAN	SWT1 RNA endoribonuclease homolog (S. cerevisiae)	71										breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(16)|ovary(1)|prostate(1)|urinary_tract(1)	41						AAAGAAGACAAGGACTGAAAA	0.234																																					p.Q71H		Atlas-SNP	.											.	SWT1	88	.	0			c.A213T						.						31	37	35					1																	185137519		2169	4271	6440	SO:0001583	missense	54823	exon4			AAGACAAGGACTG	AF288392	CCDS1367.1	1q25	2013-08-29	2011-01-24	2011-01-24	ENSG00000116668	ENSG00000116668			16785	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 26"	C1orf26		11318611, 19127978, 23768067	Standard	NM_017673		Approved	FLJ20121, HsSwt1	uc001grg.4	Q5T5J6	OTTHUMG00000035390	ENST00000367500.4:c.213A>T	chr1.hg19:g.185137519A>T	ENSP00000356470:p.Gln71His	274.0	0.0		357.0	173.0	NM_017673	Q8NEK9|Q9BZQ7|Q9NXQ0	Missense_Mutation	SNP	ENST00000367500.4	hg19	CCDS1367.1	.	.	.	.	.	.	.	.	.	.	A	2.824	-0.244237	0.05906	.	.	ENSG00000116668	ENST00000367501;ENST00000367500;ENST00000450350	T;T;T	0.46819	2.21;2.21;0.86	4.7	-3.61	0.04556	.	0.717261	0.12541	N	0.459923	T	0.29749	0.0743	L	0.43152	1.355	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.18808	-1.0325	10	0.41790	T	0.15	.	1.8988	0.03263	0.3507:0.1518:0.3588:0.1387	.	71	Q5T5J6	SWT1_HUMAN	H	71	ENSP00000356471:Q71H;ENSP00000356470:Q71H;ENSP00000401413:Q71H	ENSP00000356470:Q71H	Q	+	3	2	SWT1	183404142	0.933000	0.31639	0.023000	0.16930	0.050000	0.14768	0.106000	0.15354	-0.574000	0.05990	0.459000	0.35465	CAA	.	.		0.234	SWT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085790.1	NM_017673		T	185137519	A	T	185137519	3	4	290	1	0	0	0	0	1	0	0	0	2037	69	3	4	223	4	C1orf26	1	185137519	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	1930056	185137519	64113102	21	42483										
RGS18	64407	hgsc.bcm.edu	37	chr1	192129516	192129516	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tttcttgtacagagtctcccCtgaagaggcagtgaaatggg	12	8	2	4			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:192129516C>T	ENST00000367460.3	+	3	411	c.230C>T	c.(229-231)cCt>cTt	p.P77L	RGS18_ENST00000481707.1_3'UTR	NM_130782.2	NP_570138.1	Q9NS28	RGS18_HUMAN	regulator of G-protein signaling 18	77					G-protein coupled receptor signaling pathway (GO:0007186)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			kidney(1)|large_intestine(2)|lung(15)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						AGAGTCTCCCCTGAAGAGGCA	0.358																																					p.P77L		Atlas-SNP	.											.	RGS18	54	.	0			c.C230T						.						110	101	104					1																	192129516		2203	4300	6503	SO:0001583	missense	64407	exon3			TCTCCCCTGAAGA	AF268036	CCDS1374.1	1q31.2	2008-02-05	2007-08-14		ENSG00000150681	ENSG00000150681		"Regulators of G-protein signaling"	14261	protein-coding gene	gene with protein product		607192	"regulator of G-protein signalling 18"			11042171	Standard	NM_130782		Approved	RGS13	uc001gsg.3	Q9NS28	OTTHUMG00000035592	ENST00000367460.3:c.230C>T	chr1.hg19:g.192129516C>T	ENSP00000356430:p.Pro77Leu	115.0	0.0		133.0	58.0	NM_130782	B2RD23	Missense_Mutation	SNP	ENST00000367460.3	hg19	CCDS1374.1	.	.	.	.	.	.	.	.	.	.	C	14.24	2.477014	0.44044	.	.	ENSG00000150681	ENST00000367460	T	0.62498	0.02	5.91	4.01	0.46588	Regulator of G protein signalling superfamily (1);Regulator of G-protein signaling, domain 1 (1);	0.142711	0.64402	N	0.000004	T	0.53802	0.1819	L	0.52364	1.645	0.80722	D	1	B	0.15930	0.015	B	0.18871	0.023	T	0.46555	-0.9183	10	0.31617	T	0.26	.	10.3565	0.43967	0.1349:0.7942:0.0:0.071	.	77	Q9NS28	RGS18_HUMAN	L	77	ENSP00000356430:P77L	ENSP00000356430:P77L	P	+	2	0	RGS18	190396139	1.000000	0.71417	0.991000	0.47740	0.984000	0.73092	3.383000	0.52471	0.797000	0.33971	0.655000	0.94253	CCT	.	.		0.358	RGS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086382.1	NM_130782		T	192129516	C	T	192129516	3	4	290	1	0	0	0	0	1	0	0	0	13315	681	24	3	240	3	RGS18	1	192129516	Missense_Mutation	SNP	C	TCGA-G3-A7M5-01A-11D-A33Q-10	6991997	192129516	57121105	22	42484										
PLXNA2	5362	hgsc.bcm.edu	37	chr1	208252776	208252776	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	ccgcagctctcccgctgggcTgcacacttgtagagatggac	12	14	1	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:208252776T>A	ENST00000367033.3	-	12	3172	c.2415A>T	c.(2413-2415)gcA>gcT	p.A805A		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	805			A -> G (in dbSNP:rs17011882).		axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)	p.A805A(1)		NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		CCCGCTGGGCTGCACACTTGT	0.587																																					p.A805A		Atlas-SNP	.											PLXNA2,NS,carcinoma,0,1	PLXNA2	178	.	1	Substitution - coding silent(1)	lung(1)	c.A2415T						.						20	21	21					1																	208252776		2202	4300	6502	SO:0001819	synonymous_variant	5362	exon12			CTGGGCTGCACAC	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"Plexins"	9100	protein-coding gene	gene with protein product	"plexin 2", "plexin-A2", "semaphorin receptor OCT", "transmembrane protein OCT"	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.2415A>T	chr1.hg19:g.208252776T>A		72.0	0.0		85.0	33.0	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Silent	SNP	ENST00000367033.3	hg19	CCDS31013.1																																																																																			.	.		0.587	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179		A	208252776	T	A	208252776	2	1	290	1	0	0	0	0	0	0	0	1	12129	1567	55	4		4	PLXNA2	1	208252776	Silent	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	16123260	208252776	40997845	23	42485										
FAM71A	149647	hgsc.bcm.edu	37	chr1	212798434	212798434	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tgtccgtatggtgaccatggGcattgcacgtaccagcccca	11	13	0	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:212798434G>C	ENST00000294829.3	+	1	646	c.215G>C	c.(214-216)gGc>gCc	p.G72A	RP11-338C15.5_ENST00000427949.1_RNA	NM_153606.3	NP_705834.2	Q8IYT1	FA71A_HUMAN	family with sequence similarity 71, member A	72						nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(7)|liver(1)|lung(12)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(81;0.00631)|all cancers(67;0.00981)|GBM - Glioblastoma multiforme(131;0.0715)|Epithelial(68;0.094)		GTGACCATGGGCATTGCACGT	0.542																																					p.G72A		Atlas-SNP	.											.	FAM71A	87	.	0			c.G215C						.						149	125	133					1																	212798434		2203	4300	6503	SO:0001583	missense	149647	exon1			CCATGGGCATTGC		CCDS1507.1	1q32.3	2008-02-05			ENSG00000162771	ENSG00000162771			26541	protein-coding gene	gene with protein product						12477932	Standard	NM_153606		Approved	FLJ32796	uc010pth.1	Q8IYT1	OTTHUMG00000041084	ENST00000294829.3:c.215G>C	chr1.hg19:g.212798434G>C	ENSP00000294829:p.Gly72Ala	93.0	0.0		105.0	36.0	NM_153606	Q5VTZ1	Missense_Mutation	SNP	ENST00000294829.3	hg19	CCDS1507.1	.	.	.	.	.	.	.	.	.	.	G	11.06	1.527504	0.27299	.	.	ENSG00000162771	ENST00000294829	T	0.12774	2.65	4.41	3.46	0.39613	.	0.182460	0.34245	N	0.004134	T	0.30792	0.0776	M	0.66439	2.03	0.35263	D	0.779787	D	0.61080	0.989	D	0.67548	0.952	T	0.41215	-0.9521	10	0.59425	D	0.04	-31.17	10.2591	0.43416	0.0:0.2011:0.7989:0.0	.	72	Q8IYT1	FA71A_HUMAN	A	72	ENSP00000294829:G72A	ENSP00000294829:G72A	G	+	2	0	FAM71A	210865057	1.000000	0.71417	0.996000	0.52242	0.383000	0.30230	2.912000	0.48782	1.176000	0.42840	0.460000	0.39030	GGC	.	.		0.542	FAM71A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098529.1	NM_153606		C	212798434	G	C	212798434	3	2	290	1	0	0	0	0	1	0	0	0	5615	1203	42	4	217	4	FAM71A	1	212798434	Missense_Mutation	SNP	G	TCGA-G3-A7M5-01A-11D-A33Q-10	4545658	212798434	36452187	24	42486										
EXOC8	149371	hgsc.bcm.edu	37	chr1	231471360	231471360	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	gattcacacgaataagtctaGatgcattcctcagatcttgg	8	9	4	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:231471360G>C	ENST00000360394.2	-	1	2218	c.2132C>G	c.(2131-2133)tCt>tGt	p.S711C	SPRTN_ENST00000391858.4_5'Flank|EXOC8_ENST00000366645.1_Missense_Mutation_p.S707C|SPRTN_ENST00000295050.7_5'Flank|SPRTN_ENST00000008440.9_5'Flank	NM_175876.3	NP_787072.2	Q8IYI6	EXOC8_HUMAN	exocyst complex component 8	711					cellular protein localization (GO:0034613)|cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|exocyst (GO:0000145)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(2)|endometrium(1)|large_intestine(2)|liver(1)|lung(5)|prostate(1)|skin(1)|stomach(1)	14	Breast(184;0.0871)	all_cancers(173;0.151)|Prostate(94;0.183)				AATAAGTCTAGATGCATTCCT	0.403																																					p.S711C		Atlas-SNP	.											.	EXOC8	42	.	0			c.C2132G						.						155	145	148					1																	231471360		2203	4300	6503	SO:0001583	missense	149371	exon1			AGTCTAGATGCAT	AL117352	CCDS1593.1	1q42.2	2013-01-22			ENSG00000116903	ENSG00000116903			24659	protein-coding gene	gene with protein product		615283				12477932	Standard	NM_175876		Approved	SEC84, EXO84, Exo84p	uc001huq.3	Q8IYI6	OTTHUMG00000038025	ENST00000360394.2:c.2132C>G	chr1.hg19:g.231471360G>C	ENSP00000353564:p.Ser711Cys	145.0	0.0		203.0	72.0	NM_175876	B3KU33|Q5TE82	Missense_Mutation	SNP	ENST00000360394.2	hg19	CCDS1593.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.689005	0.88735	.	.	ENSG00000116903	ENST00000360394;ENST00000366645	T;T	0.78364	-1.17;-1.16	5.43	5.43	0.79202	.	0.062472	0.64402	D	0.000004	T	0.72162	0.3426	N	0.19112	0.55	0.80722	D	1	P	0.50943	0.94	P	0.46975	0.533	T	0.72950	-0.4136	10	0.38643	T	0.18	-15.1838	19.5966	0.95541	0.0:0.0:1.0:0.0	.	711	Q8IYI6	EXOC8_HUMAN	C	711;707	ENSP00000353564:S711C;ENSP00000355605:S707C	ENSP00000353564:S711C	S	-	2	0	EXOC8	229537983	1.000000	0.71417	0.237000	0.24090	0.994000	0.84299	9.378000	0.97191	2.698000	0.92095	0.655000	0.94253	TCT	.	.		0.403	EXOC8-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_175876		C	231471360	G	C	231471360	3	2	290	1	0	0	0	0	1	0	0	0	5313	942	33	4	49	4	EXOC8	1	231471360	Missense_Mutation	SNP	G	TCGA-G3-A7M5-01A-11D-A33Q-10	18672926	231471360	17779261	25	42487										
RYR2	6262	hgsc.bcm.edu	37	chr1	237804197	237804197	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	ttttgaaacattcatgaaagTgacacagaggaggaggaaga	12	4	1	5			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:237804197T>G	ENST00000366574.2	+	47	7433	c.7116T>G	c.(7114-7116)ctT>ctG	p.L2372L	RYR2_ENST00000360064.6_Splice_Site_p.L2370L|RYR2_ENST00000542537.1_Splice_Site_p.L2356L	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	2372	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TTCATGAAAGTGACACAGAGG	0.428																																					p.L2372L		Atlas-SNP	.											.	RYR2	1273	.	0			c.T7116G						.						121	115	117					1																	237804197		2011	4196	6207	SO:0001630	splice_region_variant	6262	exon47			TGAAAGTGACACA	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.7116-1T>G	chr1.hg19:g.237804197T>G		26.0	0.0		35.0	6.0	NM_001035	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	hg19	CCDS55691.1																																																																																			.	.		0.428	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	Silent	G	237804197	T	G	237804197	5	3	290	1	0	0	0	0	0	0	1	0	13784	1710	59	5	7302	5	RYR2	1	237804197	Splice_Site	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	6332837	237804197	11446424	26	42488										
PXDN	7837	hgsc.bcm.edu	37	chr2	1652347	1652347	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	cgtgtggccaaacctgaaggCcgcggtggcgaaggcgttga	17	10	0	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr2:1652347C>A	ENST00000252804.4	-	17	3255	c.3205G>T	c.(3205-3207)Gcc>Tcc	p.A1069S		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	1069					extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.A1069T(1)		breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		AACCTGAAGGCCGCGGTGGCG	0.597																																					p.A1069S		Atlas-SNP	.											PXDN,NS,carcinoma,0,1	PXDN	255	.	1	Substitution - Missense(1)	kidney(1)	c.G3205T						.						54	66	62					2																	1652347		2189	4280	6469	SO:0001583	missense	7837	exon17			TGAAGGCCGCGGT	AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"Immunoglobulin superfamily / I-set domain containing"	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.3205G>T	chr2.hg19:g.1652347C>A	ENSP00000252804:p.Ala1069Ser	46.0	0.0		41.0	19.0	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Missense_Mutation	SNP	ENST00000252804.4	hg19	CCDS46221.1	.	.	.	.	.	.	.	.	.	.	C	17.97	3.519345	0.64634	.	.	ENSG00000130508	ENST00000252804	T	0.79940	-1.32	5.72	4.84	0.62591	.	0.000000	0.85682	D	0.000000	D	0.93900	0.8048	H	0.98542	4.26	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.96345	0.9254	10	0.87932	D	0	-37.893	16.2512	0.82489	0.1337:0.8663:0.0:0.0	.	1069	Q92626	PXDN_HUMAN	S	1069	ENSP00000252804:A1069S	ENSP00000252804:A1069S	A	-	1	0	PXDN	1631354	1.000000	0.71417	0.953000	0.39169	0.341000	0.28922	5.896000	0.69822	1.411000	0.46957	0.650000	0.86243	GCC	.	.		0.597	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455		A	1652347	C	A	1652347	3	1	290	1	0	0	0	0	1	0	0	0	12862	739	26	3	1262	3	PXDN	2	1652347	Missense_Mutation	SNP	C	TCGA-G3-A7M5-01A-11D-A33Q-10		1652347	241547026	27	42489										
PLB1	151056	hgsc.bcm.edu	37	chr2	28752185	28752185	+	Splice_Site	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	aaaccagttctctctttagtCctttcagacatcatcagata	4	11	5	2	rs542670180		TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr2:28752185C>A	ENST00000327757.5	+	7	371	c.327C>A	c.(325-327)gtC>gtA	p.V109V	PLB1_ENST00000422425.2_Splice_Site_p.V109V	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	109	4 X 308-326 AA approximate repeats.				glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(31)|ovary(6)|prostate(1)|skin(7)|stomach(2)	69	Acute lymphoblastic leukemia(172;0.155)					TCTCTTTAGTCCTTTCAGACA	0.502																																					p.V109V		Atlas-SNP	.											.	PLB1	255	.	0			c.C327A						.						173	151	158					2																	28752185		2203	4300	6503	SO:0001630	splice_region_variant	151056	exon7			TTTAGTCCTTTCA		CCDS33168.1, CCDS54340.1	2p23.3	2014-03-14			ENSG00000163803	ENSG00000163803	3.1.1.4, 3.1.1.5		30041	protein-coding gene	gene with protein product		610179				12150957	Standard	NM_153021		Approved	PLB, FLJ30866	uc002rmb.2	Q6P1J6	OTTHUMG00000152014	ENST00000327757.5:c.326-1C>A	chr2.hg19:g.28752185C>A		44.0	0.0		44.0	18.0	NM_001170585	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Silent	SNP	ENST00000327757.5	hg19	CCDS33168.1	.	.	.	.	.	.	.	.	.	.	C	9.578	1.122947	0.20959	.	.	ENSG00000163803	ENST00000404858	.	.	.	5.49	2.26	0.28386	.	.	.	.	.	T	0.53514	0.1801	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44832	-0.9302	4	.	.	.	.	5.7636	0.18213	0.0:0.6184:0.0:0.3816	.	.	.	.	Y	108	.	.	S	+	2	0	PLB1	28605689	0.995000	0.38212	0.998000	0.56505	0.566000	0.35808	0.403000	0.20982	0.668000	0.31126	0.655000	0.94253	TCC	.	.		0.502	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2		Silent	A	28752185	C	A	28752185	5	1	290	1	0	0	0	0	0	0	1	0	12033	869	30	3	353	3	PLB1	2	28752185	Splice_Site	SNP	C	TCGA-G3-A7M5-01A-11D-A33Q-10	27099838	28752185	214447188	28	42490										
FAM179A	165186	hgsc.bcm.edu	37	chr2	29226440	29226440	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	catcgtgatcccacccatccCaaaggccaggacggttgcag	10	15	0	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr2:29226440C>T	ENST00000379558.4	+	6	1073	c.722C>T	c.(721-723)cCa>cTa	p.P241L	FAM179A_ENST00000403861.2_Missense_Mutation_p.P241L	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	241										breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						CCACCCATCCCAAAGGCCAGG	0.647																																					p.P241L		Atlas-SNP	.											.	FAM179A	106	.	0			c.C722T						.						37	43	41					2																	29226440		2051	4171	6222	SO:0001583	missense	165186	exon6			CCATCCCAAAGGC	AK125239, AK125744	CCDS1769.2	2p23.2	2008-10-30			ENSG00000189350	ENSG00000189350			33715	protein-coding gene	gene with protein product						16344560	Standard	NM_199280		Approved	FLJ43249, LOC165186	uc010ezl.3	Q6ZUX3	OTTHUMG00000128432	ENST00000379558.4:c.722C>T	chr2.hg19:g.29226440C>T	ENSP00000368876:p.Pro241Leu	118.0	0.0		178.0	14.0	NM_199280	Q6ZUF5	Missense_Mutation	SNP	ENST00000379558.4	hg19	CCDS1769.2	.	.	.	.	.	.	.	.	.	.	C	3.463	-0.109477	0.06924	.	.	ENSG00000189350	ENST00000379558;ENST00000403861	T;T	0.14766	2.98;2.48	5.16	0.17	0.15021	.	.	.	.	.	T	0.07458	0.0188	N	0.19112	0.55	0.09310	N	1	B;B	0.29301	0.241;0.041	B;B	0.29598	0.104;0.028	T	0.38067	-0.9678	9	0.32370	T	0.25	.	4.2617	0.10744	0.1483:0.5091:0.0:0.3426	.	241;241	F8W8E4;Q6ZUX3	.;F179A_HUMAN	L	241	ENSP00000368876:P241L;ENSP00000384699:P241L	ENSP00000368876:P241L	P	+	2	0	FAM179A	29079944	0.009000	0.17119	0.004000	0.12327	0.003000	0.03518	0.234000	0.17930	-0.030000	0.13804	-0.424000	0.05967	CCA	.	.		0.647	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280		T	29226440	C	T	29226440	3	4	290	1	0	0	0	0	1	0	0	0	5510	594	21	3	740	3	FAM179A	2	29226440	Missense_Mutation	SNP	C	TCGA-G3-A7M5-01A-11D-A33Q-10	474255	29226440	213972933	29	42491										
EML4	27436	hgsc.bcm.edu	37	chr2	42530527	42530527	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tcttgacatgtgctcaggacAggcaggtgtgcctgtggaac	14	9	2	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr2:42530527A>T	ENST00000318522.5	+	16	2102	c.1840A>T	c.(1840-1842)Agg>Tgg	p.R614W	EML4_ENST00000401738.3_Missense_Mutation_p.R625W|EML4_ENST00000453191.2_De_novo_Start_OutOfFrame|EML4_ENST00000402711.2_Missense_Mutation_p.R556W	NM_019063.3	NP_061936	Q9HC35	EMAL4_HUMAN	echinoderm microtubule associated protein like 4	614					microtubule-based process (GO:0007017)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|mitotic spindle (GO:0072686)			EML4/ALK(543)	NS(2)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	12						TGCTCAGGACAGGCAGGTGTG	0.468			T	ALK	NSCLC																																p.R614W		Atlas-SNP	.		Dom	yes		2	2p21	27436	echinoderm microtubule associated protein like 4		E	.	EML4	92	.	0			c.A1840T						.						131	121	124					2																	42530527		2203	4300	6503	SO:0001583	missense	27436	exon16			CAGGACAGGCAGG	AF177377	CCDS1807.1, CCDS46266.1	2p21	2013-01-10		2002-02-15	ENSG00000143924	ENSG00000143924		"WD repeat domain containing"	1316	protein-coding gene	gene with protein product		607442		C2orf2			Standard	NM_019063		Approved	ROPP120, ELP120	uc002rsi.3	Q9HC35	OTTHUMG00000128603	ENST00000318522.5:c.1840A>T	chr2.hg19:g.42530527A>T	ENSP00000320663:p.Arg614Trp	125.0	0.0		143.0	62.0	NM_019063	A6H8Y6|B2RBK3|B2RTW7|B5MCW9|Q3SWW0|Q53R29|Q53TW8|Q6PJ45|Q9NV40	Missense_Mutation	SNP	ENST00000318522.5	hg19	CCDS1807.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.072079	0.76415	.	.	ENSG00000143924	ENST00000318522;ENST00000402711;ENST00000401738	T;T;T	0.61742	0.08;0.08;0.08	5.01	3.83	0.44106	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.083457	0.85682	D	0.000000	T	0.79275	0.4418	M	0.93062	3.375	0.80722	D	1	D;D;D	0.76494	0.992;0.999;0.996	D;D;D	0.72625	0.949;0.978;0.97	T	0.82497	-0.0428	10	0.72032	D	0.01	-12.6355	11.2629	0.49093	0.8467:0.1533:0.0:0.0	.	556;625;614	B5MCW9;B5MBZ0;Q9HC35	.;.;EMAL4_HUMAN	W	614;556;625	ENSP00000320663:R614W;ENSP00000385059:R556W;ENSP00000384939:R625W	ENSP00000320663:R614W	R	+	1	2	EML4	42384031	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.387000	0.52501	0.905000	0.36596	0.528000	0.53228	AGG	.	.		0.468	EML4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250463.3	NM_019063		T	42530527	A	T	42530527	3	4	290	1	0	0	0	0	1	0	0	0	5101	179	7	4	1902	4	EML4	2	42530527	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	13304087	42530527	200668846	30	42492										
USP34	9736	hgsc.bcm.edu	37	chr2	61520656	61520656	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	ccagaattaaaaatttctaaTaactgttgaagccctccagc	5	10	1	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr2:61520656T>C	ENST00000398571.2	-	33	4567	c.4491A>G	c.(4489-4491)ttA>ttG	p.L1497L		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	1497					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			AAATTTCTAATAACTGTTGAA	0.348																																					p.L1497L		Atlas-SNP	.											.	USP34	334	.	0			c.A4491G						.						84	76	79					2																	61520656		1814	4075	5889	SO:0001819	synonymous_variant	9736	exon33			TTCTAATAACTGT	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"Ubiquitin-specific peptidases"	20066	protein-coding gene	gene with protein product		615295	"ubiquitin specific protease 34"			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.4491A>G	chr2.hg19:g.61520656T>C		177.0	0.0		235.0	50.0	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Silent	SNP	ENST00000398571.2	hg19	CCDS42686.1																																																																																			.	.		0.348	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			C	61520656	T	C	61520656	2	2	290	1	0	0	0	0	0	0	0	1	17080	1403	49	2		2	USP34	2	61520656	Silent	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	18990129	61520656	181678717	31	42493										
ARHGAP25	9938	hgsc.bcm.edu	37	chr2	69034418	69034418	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tcctcagcagtgtttggccaGcgcttggatgagactgtggc	14	10	1	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr2:69034418G>A	ENST00000295381.3	+	5	896	c.477G>A	c.(475-477)caG>caA	p.Q159Q	ARHGAP25_ENST00000497079.1_Silent_p.Q153Q|ARHGAP25_ENST00000544262.1_Silent_p.Q134Q|ARHGAP25_ENST00000409030.3_Silent_p.Q152Q|ARHGAP25_ENST00000409220.1_Silent_p.Q153Q|ARHGAP25_ENST00000456116.2_3'UTR|ARHGAP25_ENST00000467265.1_Silent_p.Q120Q|ARHGAP25_ENST00000409202.3_Silent_p.Q160Q	NM_001007231.2	NP_001007232.2	P42331	RHG25_HUMAN	Rho GTPase activating protein 25	159	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(20)|ovary(3)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	52						TGTTTGGCCAGCGCTTGGATG	0.527																																					p.Q160Q		Atlas-SNP	.											.	ARHGAP25	175	.	0			c.G480A						.						90	84	86					2																	69034418		2203	4300	6503	SO:0001819	synonymous_variant	9938	exon5			TGGCCAGCGCTTG	D29642	CCDS33214.1, CCDS46312.1, CCDS33214.2, CCDS54363.1, CCDS54364.1	2p13.3	2013-01-10			ENSG00000163219	ENSG00000163219		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	28951	protein-coding gene	gene with protein product		610587				7584044	Standard	NM_001007231		Approved	KIAA0053	uc010fdg.3	P42331	OTTHUMG00000152621	ENST00000295381.3:c.477G>A	chr2.hg19:g.69034418G>A		196.0	0.0		186.0	72.0	NM_001007231	A8K2Y1|B7Z498|E9PFQ7|G5E9G2|Q8IXQ2	Silent	SNP	ENST00000295381.3	hg19		.	.	.	.	.	.	.	.	.	.	G	9.044	0.990388	0.18966	.	.	ENSG00000163219	ENST00000497259	.	.	.	4.88	4.01	0.46588	.	.	.	.	.	T	0.64649	0.2617	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.66972	-0.5788	5	0.87932	D	0	.	8.3561	0.32331	0.2439:0.0:0.7561:0.0	.	.	.	.	N	19	.	ENSP00000420427:S92N	S	+	2	0	ARHGAP25	68887922	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	3.082000	0.50128	1.301000	0.44836	-0.234000	0.12200	AGC	.	.		0.527	ARHGAP25-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014882		A	69034418	G	A	69034418	2	1	290	1	0	0	0	0	0	0	0	1	874	962	34	3		3	ARHGAP25	2	69034418	Silent	SNP	G	TCGA-G3-A7M5-01A-11D-A33Q-10	7513762	69034418	174164955	32	42494										
ZNF638	27332	hgsc.bcm.edu	37	chr2	71650150	71650150	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tgaaactttggagcttgaaaCtcaaggagaggaggtcaaag	13	5	2	3			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr2:71650150C>G	ENST00000409544.1	+	22	4136	c.3506C>G	c.(3505-3507)aCt>aGt	p.T1169S	ZNF638_ENST00000264447.4_Missense_Mutation_p.T1169S|ZNF638_ENST00000355812.3_Intron|ZNF638_ENST00000409407.1_Missense_Mutation_p.T109S	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	1169	Glu-rich.				regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						GAGCTTGAAACTCAAGGAGAG	0.418																																					p.T1169S		Atlas-SNP	.											.	ZNF638	179	.	0			c.C3506G						.						95	94	94					2																	71650150		2203	4300	6503	SO:0001583	missense	27332	exon22			TTGAAACTCAAGG	D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"RNA binding motif (RRM) containing"	17894	protein-coding gene	gene with protein product		614349	"zinc finger, matrin-like"	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.3506C>G	chr2.hg19:g.71650150C>G	ENSP00000386433:p.Thr1169Ser	102.0	0.0		133.0	45.0	NM_014497	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Missense_Mutation	SNP	ENST00000409544.1	hg19	CCDS1917.1	.	.	.	.	.	.	.	.	.	.	C	1.044	-0.677871	0.03378	.	.	ENSG00000075292	ENST00000394137;ENST00000264447;ENST00000409544;ENST00000409407;ENST00000462695	T;T;T	0.28895	1.59;1.59;1.92	5.69	2.66	0.31614	.	0.584093	0.16588	N	0.207891	T	0.16128	0.0388	L	0.27053	0.805	0.43673	D	0.996101	B;B;B	0.22346	0.068;0.017;0.01	B;B;B	0.15484	0.006;0.013;0.006	T	0.06058	-1.0848	10	0.12430	T	0.62	-3.8445	5.5923	0.17307	0.3903:0.5178:0.0:0.092	.	1169;1169;1169	A8K583;Q14966-3;Q14966	.;.;ZN638_HUMAN	S	748;1169;1169;109;109	ENSP00000264447:T1169S;ENSP00000386433:T1169S;ENSP00000386813:T109S	ENSP00000264447:T1169S	T	+	2	0	ZNF638	71503658	0.007000	0.16637	0.998000	0.56505	0.127000	0.20565	0.361000	0.20267	1.469000	0.48083	0.655000	0.94253	ACT	.	.		0.418	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497		G	71650150	C	G	71650150	3	3	290	1	0	0	0	0	1	0	0	0	18070	565	20	4	3588	4	ZNF638	2	71650150	Missense_Mutation	SNP	C	TCGA-G3-A7M5-01A-11D-A33Q-10	2615732	71650150	171549223	33	42495										
DNAH6	1768	hgsc.bcm.edu	37	chr2	84880551	84880551	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	agacaaaatcttcagcctgaGatgtgtatggttagaaaggt	11	5	2	3			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr2:84880551G>C	ENST00000237449.6	+	33	5195	c.5187G>C	c.(5185-5187)gaG>gaC	p.E1729D	DNAH6_ENST00000389394.3_Missense_Mutation_p.E1729D|DNAH6_ENST00000398278.2_Missense_Mutation_p.E1729D			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	1729	AAA 2. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						TTCAGCCTGAGATGTGTATGG	0.393																																					p.E1729D		Atlas-SNP	.											.	DNAH6	194	.	0			c.G5187C						.						56	49	51					2																	84880551		692	1591	2283	SO:0001583	missense	1768	exon34			GCCTGAGATGTGT	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.5187G>C	chr2.hg19:g.84880551G>C	ENSP00000237449:p.Glu1729Asp	84.0	0.0		95.0	38.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	hg19	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	G	11.29	1.594698	0.28445	.	.	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.40476	1.03;1.03;1.03	5.03	2.2	0.27929	.	.	.	.	.	T	0.31231	0.0790	L	0.39467	1.215	0.20926	N	0.999824	P	0.37955	0.612	B	0.33846	0.171	T	0.08493	-1.0719	9	0.44086	T	0.13	.	9.6334	0.39793	0.2407:0.0:0.7593:0.0	.	1729	Q9C0G6	DYH6_HUMAN	D	1729	ENSP00000374045:E1729D;ENSP00000381326:E1729D;ENSP00000237449:E1729D	ENSP00000237449:E1729D	E	+	3	2	DNAH6	84734062	0.186000	0.23225	0.592000	0.28758	0.991000	0.79684	0.314000	0.19432	0.526000	0.28541	0.544000	0.68410	GAG	.	.		0.393	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		C	84880551	G	C	84880551	3	2	290	1	0	0	0	0	1	0	0	0	4607	933	33	4	5317	4	DNAH6	2	84880551	Missense_Mutation	SNP	G	TCGA-G3-A7M5-01A-11D-A33Q-10	13230401	84880551	158318822	34	42496										
GLI2	2736	hgsc.bcm.edu	37	chr2	121728098	121728099	+	Missense_Mutation	DNP	CC	CC	AA													0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	ccctcacccaccttcctggcCcagcagcccatggccctcac							TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr2:121728098_121728099CC>AA	ENST00000452319.1	+	7	1035_1036	c.975_976CC>AA	c.(973-978)gcCCag>gcAAag	p.Q326K	GLI2_ENST00000361492.4_Missense_Mutation_p.Q326K|GLI2_ENST00000314490.11_5'UTR|GLI2_ENST00000435313.2_3'UTR					GLI family zinc finger 2											NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				CCTTCCTGGCCCAGCAGCCCAT	0.639																																					p.A325A|p.Q326K		Atlas-SNP	.											.	GLI2	187	.	0			c.C975A|c.C976A						.																																			SO:0001583	missense	2736	exon6			CCTGGCCCAGCAG|CTGGCCCAGCAGC		CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"Zinc fingers, C2H2-type"	4318	protein-coding gene	gene with protein product	"tax-responsive element-2 holding protein", "tax helper protein 1", "tax helper protein 2"	165230	"GLI-Kruppel family member GLI2", "glioma-associated oncogene family zinc finger 2"			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	Exception_encountered	chr2.hg19:g.121728098_121728099delinsAA	ENSP00000390436:p.Gln326Lys	98.0|95.0	0.0		126.0|125.0	57.0	NM_005270		Silent|Missense_Mutation	SNP	ENST00000452319.1	hg19	CCDS33283.1																																																																																			.	.		0.639	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270		AA	121728099	CC	AA	121728098	3	1	290	1	0	0	0	0	1	0	0	0	6446	610	22	3	997	3	GLI2	2	121728098	Missense_Mutation	DNP	CC	TCGA-G3-A7M5-01A-11D-A33Q-10	36847547	121728098	121471275	35	42497										
ACVR2A	92	hgsc.bcm.edu	37	chr2	148653868	148653868	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tattgtttttattatcttatAggtgctatacttggtagatc	7	4	1	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr2:148653868A>T	ENST00000241416.7	+	2	691		c.e2-1		ACVR2A_ENST00000535787.1_Intron|ACVR2A_ENST00000404590.1_Splice_Site	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA						activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		ATTATCTTATAGGTGCTATAC	0.323																																					.		Atlas-SNP	.											.	ACVR2A	125	.	0			c.56-2A>T						.						65	70	68					2																	148653868		2203	4299	6502	SO:0001630	splice_region_variant	92	exon2			TCTTATAGGTGCT		CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"activin A receptor, type II"	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.56-1A>T	chr2.hg19:g.148653868A>T		49.0	0.0		72.0	35.0	NM_001616	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	Splice_Site	SNP	ENST00000241416.7	hg19	CCDS33301.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.113429	0.77210	.	.	ENSG00000121989	ENST00000241416;ENST00000404590	.	.	.	5.17	5.17	0.71159	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0153	0.71578	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ACVR2A	148370338	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	9.280000	0.95786	1.942000	0.56320	0.533000	0.62120	.	.	.		0.323	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616	Intron	T	148653868	A	T	148653868	5	4	290	1	0	0	0	0	0	0	1	0	223	434	15	4	60	4	ACVR2A	2	148653868	Splice_Site	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	26925770	148653868	94545505	36	42498										
ACVR2A	92	hgsc.bcm.edu	37	chr2	148653984	148653984	+	Frame_Shift_Del	DEL	G	G	-													0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	ttatggtgacaaagataaacGgcggcattgttttgctacct							TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr2:148653984delG	ENST00000241416.7	+	2	806	c.170delG	c.(169-171)cggfs	p.R58fs	ACVR2A_ENST00000535787.1_5'UTR|AC009480.3_ENST00000402410.2_RNA|ACVR2A_ENST00000404590.1_Frame_Shift_Del_p.R58fs	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	58					activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		AAAGATAAACGGCGGCATTGT	0.388																																					p.R57fs		Atlas-INDEL	.											ACVR2A,colon,carcinoma,0,1	ACVR2A	125	.	0			c.169delC						.						177	173	175					2																	148653984		2203	4300	6503	SO:0001589	frameshift_variant	92	exon2			.		CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"activin A receptor, type II"	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.170delG	chr2.hg19:g.148653984delG	ENSP00000241416:p.Arg58fs	74.0	0.0		95.0	23.0	NM_001616	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	Frame_Shift_Del	DEL	ENST00000241416.7	hg19	CCDS33301.1																																																																																			.	.		0.388	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616		-	148653984	G	-	148653984	7	5	290	1	0	1	0	1	0	0	0	0	223	1116	39	0	176	0	ACVR2A	2	148653984	Frame_Shift_Del	DEL	G	TCGA-G3-A7M5-01A-11D-A33Q-10	116	148653984	94545389	37	42499	224	3								
ACVR2A	92	hgsc.bcm.edu	37	chr2	148653985	148653987	+	In_Frame_Del	DEL	GCG	GCG	-													0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tatggtgacaaagataaacgGcggcattgttttgctacctg							TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	GCG	GCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr2:148653985_148653987delGCG	ENST00000241416.7	+	2	807_809	c.171_173delGCG	c.(169-174)cggcgg>cgg	p.57_58RR>R	ACVR2A_ENST00000535787.1_5'UTR|AC009480.3_ENST00000402410.2_RNA|ACVR2A_ENST00000404590.1_In_Frame_Del_p.57_58RR>R	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	57					activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		AAGATAAACGGCGGCATTGTTTT	0.394																																					p.57_58del		Pindel	.											.	ACVR2A	125	.	0			c.170_172del						.																																			SO:0001651	inframe_deletion	92	exon2			.		CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"activin A receptor, type II"	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.171_173delGCG	chr2.hg19:g.148653985_148653987delGCG	ENSP00000241416:p.Arg58del	73.0	0.0		96.0	15.0	NM_001616	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	In_Frame_Del	DEL	ENST00000241416.7	hg19	CCDS33301.1																																																																																			.	.		0.394	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616		-	148653987	GCG	-	148653985	7	5	290	1	0	1	0	1	0	0	0	0	223	1190	42	0	177	0	ACVR2A	2	148653985	In_Frame_Del	DEL	GCG	TCGA-G3-A7M5-01A-11D-A33Q-10	1	148653985	94545388	38	42500	224	3								
ACVR2A	92	hgsc.bcm.edu	37	chr2	148653987	148653987	+	Missense_Mutation	SNP	G	G	C													0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tggtgacaaagataaacggcGgcattgttttgctacctgga							TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr2:148653987G>C	ENST00000241416.7	+	2	809	c.173G>C	c.(172-174)cGg>cCg	p.R58P	ACVR2A_ENST00000535787.1_5'UTR|AC009480.3_ENST00000402410.2_RNA|ACVR2A_ENST00000404590.1_Missense_Mutation_p.R58P	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	58					activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		GATAAACGGCGGCATTGTTTT	0.393																																					p.R58P		Atlas-SNP	.											.	ACVR2A	125	.	0			c.G173C						.						176	173	174					2																	148653987		2203	4300	6503	SO:0001583	missense	92	exon2			AACGGCGGCATTG		CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"activin A receptor, type II"	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.173G>C	chr2.hg19:g.148653987G>C	ENSP00000241416:p.Arg58Pro	73.0	0.0		96.0	25.0	NM_001616	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	Missense_Mutation	SNP	ENST00000241416.7	hg19	CCDS33301.1	.	.	.	.	.	.	.	.	.	.	G	16.41	3.115003	0.56505	.	.	ENSG00000121989	ENST00000241416;ENST00000404590	D;D	0.98313	-4.86;-4.86	5.58	5.58	0.84498	TGF-beta receptor/activin receptor, type I/II (1);	0.064020	0.64402	D	0.000006	D	0.95007	0.8384	N	0.24115	0.695	0.80722	D	1	B	0.02656	0.0	B	0.09377	0.004	D	0.91890	0.5523	10	0.29301	T	0.29	.	14.4061	0.67083	0.0:0.0:0.8524:0.1476	.	58	P27037	AVR2A_HUMAN	P	58	ENSP00000241416:R58P;ENSP00000384338:R58P	ENSP00000241416:R58P	R	+	2	0	ACVR2A	148370457	1.000000	0.71417	0.990000	0.47175	0.876000	0.50452	5.554000	0.67294	2.619000	0.88677	0.655000	0.94253	CGG	.	.		0.393	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616		C	148653987	G	C	148653987	3	2	290	1	0	0	0	0	1	0	0	0	223	1116	39	4	179	4	ACVR2A	2	148653987	Missense_Mutation	SNP	G	TCGA-G3-A7M5-01A-11D-A33Q-10	2	148653987	94545386	39	42501	224	3								
ZNF804A	91752	hgsc.bcm.edu	37	chr2	185800725	185800725	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	agcaaaaaataaccaagttgGggatcaagcccaggggattc	11	8	1	0	rs371202844		TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr2:185800725G>T	ENST00000302277.6	+	4	1196	c.602G>T	c.(601-603)gGg>gTg	p.G201V		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	201							metal ion binding (GO:0046872)			NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						AACCAAGTTGGGGATCAAGCC	0.408																																					p.G201V		Atlas-SNP	.											.	ZNF804A	322	.	0			c.G602T						.						65	68	67					2																	185800725		2203	4300	6503	SO:0001583	missense	91752	exon4			AAGTTGGGGATCA	AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.602G>T	chr2.hg19:g.185800725G>T	ENSP00000303252:p.Gly201Val	109.0	0.0		128.0	40.0	NM_194250	A7E253|Q6ZN26	Missense_Mutation	SNP	ENST00000302277.6	hg19	CCDS2291.1	.	.	.	.	.	.	.	.	.	.	G	11.86	1.763984	0.31228	.	.	ENSG00000170396	ENST00000302277	T	0.07216	3.21	5.32	2.48	0.30137	.	0.225677	0.31102	N	0.008252	T	0.08670	0.0215	M	0.65975	2.015	0.45205	D	0.998216	B	0.28512	0.214	B	0.23852	0.049	T	0.16100	-1.0414	10	0.87932	D	0	-1.7274	3.1123	0.06363	0.1506:0.1409:0.5623:0.1462	.	201	Q7Z570	Z804A_HUMAN	V	201	ENSP00000303252:G201V	ENSP00000303252:G201V	G	+	2	0	ZNF804A	185508970	1.000000	0.71417	0.018000	0.16275	0.986000	0.74619	3.921000	0.56454	0.219000	0.20840	0.467000	0.42956	GGG	.	.		0.408	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250		T	185800725	G	T	185800725	3	4	290	1	0	0	0	0	1	0	0	0	18185	1232	43	3	616	3	ZNF804A	2	185800725	Missense_Mutation	SNP	G	TCGA-G3-A7M5-01A-11D-A33Q-10	37146738	185800725	57398648	40	42502										
ZSWIM2	151112	hgsc.bcm.edu	37	chr2	187697904	187697904	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tctcatttttagtatctatgTattttacaacttcatctgct	3	8	4	0			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr2:187697904T>A	ENST00000295131.2	-	7	923	c.884A>T	c.(883-885)tAc>tTc	p.Y295F		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	295					apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			AGTATCTATGTATTTTACAAC	0.308																																					p.Y295F		Atlas-SNP	.											.	ZSWIM2	119	.	0			c.A884T						.						117	111	113					2																	187697904		2198	4294	6492	SO:0001583	missense	151112	exon7			TCTATGTATTTTA	AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"Zinc fingers, SWIM-type", "Zinc fingers, ZZ-type"	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.884A>T	chr2.hg19:g.187697904T>A	ENSP00000295131:p.Tyr295Phe	169.0	0.0		193.0	65.0	NM_182521	B3KXV6|Q53SI3|Q57ZY3	Missense_Mutation	SNP	ENST00000295131.2	hg19	CCDS33348.1	.	.	.	.	.	.	.	.	.	.	T	0.789	-0.759367	0.03019	.	.	ENSG00000163012	ENST00000295131	T	0.22945	1.93	5.44	0.537	0.17144	.	0.638228	0.13952	N	0.351408	T	0.19127	0.0459	L	0.42245	1.32	0.09310	N	1	B	0.25007	0.116	B	0.22880	0.042	T	0.18871	-1.0323	10	0.34782	T	0.22	-1.0638	7.8676	0.29545	0.0:0.3365:0.0:0.6635	.	295	Q8NEG5	ZSWM2_HUMAN	F	295	ENSP00000295131:Y295F	ENSP00000295131:Y295F	Y	-	2	0	ZSWIM2	187406149	0.233000	0.23772	0.003000	0.11579	0.086000	0.17979	0.368000	0.20399	0.075000	0.16796	0.477000	0.44152	TAC	.	.		0.308	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521		A	187697904	T	A	187697904	3	1	290	1	0	0	0	0	1	0	0	0	18256	1638	57	4	1029	4	ZSWIM2	2	187697904	Missense_Mutation	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	1897179	187697904	55501469	41	42503										
PLCL1	5334	hgsc.bcm.edu	37	chr2	198948585	198948585	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	aaatgactgcatcagcttcaTgcaagctggctgtgagttga	11	8	2	3			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr2:198948585T>A	ENST00000428675.1	+	2	742	c.344T>A	c.(343-345)aTg>aAg	p.M115K	PLCL1_ENST00000437704.2_Missense_Mutation_p.M17K	NM_006226.3	NP_006217.3	Q15111	PLCL1_HUMAN	phospholipase C-like 1	115	Interaction with PPP1C.|PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				gamma-aminobutyric acid signaling pathway (GO:0007214)|intracellular signal transduction (GO:0035556)|lipid metabolic process (GO:0006629)|positive regulation of receptor binding (GO:1900122)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|inositol 1,4,5 trisphosphate binding (GO:0070679)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(14)|lung(44)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	80					Quinacrine(DB01103)	ATCAGCTTCATGCAAGCTGGC	0.453																																					p.M115K		Atlas-SNP	.											.	PLCL1	358	.	0			c.T344A						.						78	73	75					2																	198948585		2203	4300	6503	SO:0001583	missense	5334	exon2			GCTTCATGCAAGC	D42108	CCDS2326.1, CCDS2326.2	2q33	2014-06-13	2002-02-18	2002-02-22	ENSG00000115896	ENSG00000115896			9063	protein-coding gene	gene with protein product	"phospholipase C related, but catalytically inactive protein", "protein phosphatase 1, regulatory subunit 127"	600597	"phospholipase C, epsilon"	PLCE		7633416	Standard	NM_006226		Approved	PLC-L, PLCL, PRIP, PPP1R127	uc010fsp.3	Q15111	OTTHUMG00000132750	ENST00000428675.1:c.344T>A	chr2.hg19:g.198948585T>A	ENSP00000402861:p.Met115Lys	105.0	0.0		90.0	34.0	NM_006226	Q3MJ90|Q53SD3|Q7Z3S3	Missense_Mutation	SNP	ENST00000428675.1	hg19	CCDS2326.2	.	.	.	.	.	.	.	.	.	.	T	25.8	4.674636	0.88445	.	.	ENSG00000115896	ENST00000428675;ENST00000437704	T;T	0.64260	-0.09;-0.09	5.67	5.67	0.87782	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.85682	D	0.000000	D	0.82967	0.5152	M	0.90650	3.135	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.99;0.999	D	0.86392	0.1736	9	.	.	.	.	16.215	0.82206	0.0:0.0:0.0:1.0	.	115;41	Q15111;B4DYZ4	PLCL1_HUMAN;.	K	115;17	ENSP00000402861:M115K;ENSP00000414138:M17K	.	M	+	2	0	PLCL1	198656830	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.986000	0.88173	2.288000	0.76882	0.533000	0.62120	ATG	.	.		0.453	PLCL1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340210.1	NM_006226		A	198948585	T	A	198948585	3	1	290	1	0	0	0	0	1	0	0	0	12048	1464	51	4	350	4	PLCL1	2	198948585	Missense_Mutation	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	11250681	198948585	44250788	42	42504										
CNTN4	152330	hgsc.bcm.edu	37	chr3	3084827	3084827	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	cccctctagtgcaacagtcaAtgtgacaacccgaaagccac	7	15	2	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr3:3084827A>T	ENST00000397461.1	+	21	3062	c.2678A>T	c.(2677-2679)aAt>aTt	p.N893I	CNTN4-AS1_ENST00000442749.2_RNA|CNTN4_ENST00000448906.2_Missense_Mutation_p.N565I|CNTN4_ENST00000358480.3_Missense_Mutation_p.N674I|CNTN4_ENST00000427331.1_Missense_Mutation_p.N893I|CNTN4_ENST00000397459.2_Missense_Mutation_p.N565I|CNTN4_ENST00000418658.1_Missense_Mutation_p.N893I	NM_001206955.1	NP_001193884.1	Q8IWV2	CNTN4_HUMAN	contactin 4	893	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|brain development (GO:0007420)|negative regulation of neuron differentiation (GO:0045665)|nervous system development (GO:0007399)|neuron cell-cell adhesion (GO:0007158)|neuron projection development (GO:0031175)|regulation of synaptic plasticity (GO:0048167)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(19)|ovary(2)|pancreas(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		GCAACAGTCAATGTGACAACC	0.433																																					p.N893I		Atlas-SNP	.											.	CNTN4	335	.	0			c.A2678T						.						82	80	81					3																	3084827		2203	4300	6503	SO:0001583	missense	152330	exon22			CAGTCAATGTGAC	AW665944	CCDS2558.1, CCDS43041.1	3p26.3	2013-02-11			ENSG00000144619	ENSG00000144619		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2174	protein-coding gene	gene with protein product		607280				8586965, 12202991	Standard	NM_175607		Approved	BIG-2	uc003bpc.3	Q8IWV2	OTTHUMG00000119031	ENST00000397461.1:c.2678A>T	chr3.hg19:g.3084827A>T	ENSP00000380602:p.Asn893Ile	480.0	1.0		424.0	108.0	NM_175607	B2RAX3|Q8IX14|Q8TC35	Missense_Mutation	SNP	ENST00000397461.1	hg19	CCDS43041.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.374002	0.82573	.	.	ENSG00000144619	ENST00000418658;ENST00000397461;ENST00000427331;ENST00000358480;ENST00000397459;ENST00000448906	T;T;T;T;T;T	0.53206	0.63;0.63;0.63;0.63;0.63;0.63	5.22	5.22	0.72569	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.58595	0.2133	L	0.54908	1.71	0.80722	D	1	B;P	0.40731	0.309;0.728	P;P	0.53809	0.677;0.735	T	0.55679	-0.8103	9	.	.	.	.	15.3899	0.74735	1.0:0.0:0.0:0.0	.	892;893	Q8IWV2-3;Q8IWV2	.;CNTN4_HUMAN	I	893;893;893;674;565;565	ENSP00000396010:N893I;ENSP00000380602:N893I;ENSP00000413642:N893I;ENSP00000351267:N674I;ENSP00000380600:N565I;ENSP00000392077:N565I	.	N	+	2	0	CNTN4	3059827	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.219000	0.78000	2.106000	0.64143	0.533000	0.62120	AAT	.	.		0.433	CNTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239236.2			T	3084827	A	T	3084827	3	4	290	1	0	0	0	0	1	0	0	0	3645	101	4	4	2752	4	CNTN4	3	3084827	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10		3084827	194937603	43	42505										
CACNA2D3	55799	hgsc.bcm.edu	37	chr3	54880437	54880437	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	cagttagggattcacggttaTgcctttgcaatcacaaataa	8	8	2	0	rs368852689		TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr3:54880437T>A	ENST00000474759.1	+	17	1617	c.1569T>A	c.(1567-1569)taT>taA	p.Y523*	CACNA2D3_ENST00000490478.1_Nonsense_Mutation_p.Y429*|CACNA2D3_ENST00000288197.5_Nonsense_Mutation_p.Y523*|CACNA2D3_ENST00000415676.2_Nonsense_Mutation_p.Y523*	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3	523	Cache.					integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(3)	59				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)	Amlodipine(DB00381)|Nilvadipine(DB06712)|Spironolactone(DB00421)	TTCACGGTTATGCCTTTGCAA	0.408																																					p.Y523X		Atlas-SNP	.											.	CACNA2D3	159	.	0			c.T1569A						.						90	84	86					3																	54880437		1882	4108	5990	SO:0001587	stop_gained	55799	exon17			CGGTTATGCCTTT	AJ272268	CCDS54598.1	3p21.1	2010-10-05	2008-02-26		ENSG00000157445	ENSG00000157445		"Calcium channel subunits"	15460	protein-coding gene	gene with protein product		606399				11245980	Standard	XM_005265318		Approved	HSA272268	uc003dhf.3	Q8IZS8	OTTHUMG00000158580	ENST00000474759.1:c.1569T>A	chr3.hg19:g.54880437T>A	ENSP00000419101:p.Tyr523*	50.0	0.0		60.0	14.0	NM_018398	B2RPL6|Q9NY16|Q9NY18	Nonsense_Mutation	SNP	ENST00000474759.1	hg19	CCDS54598.1	.	.	.	.	.	.	.	.	.	.	T	37	6.197801	0.97367	.	.	ENSG00000157445	ENST00000415676;ENST00000474759;ENST00000288197;ENST00000490478;ENST00000398624;ENST00000438476	.	.	.	5.47	4.27	0.50696	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.3557	10.3003	0.43648	0.0:0.076:0.0:0.924	.	.	.	.	X	523;523;523;429;429;422	.	ENSP00000288197:Y523X	Y	+	3	2	CACNA2D3	54855477	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.958000	0.29227	0.859000	0.35456	0.454000	0.30748	TAT	.	.		0.408	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351402.1			A	54880437	T	A	54880437	4	1	290	1	0	0	0	0	0	1	0	0	2552	1471	51	4	1635	4	CACNA2D3	3	54880437	Nonsense_Mutation	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	51795610	54880437	143141993	44	42506										
IL17RD	54756	hgsc.bcm.edu	37	chr3	57148802	57148802	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	atggtgatattctgggcgtcAgcaatcacatgcttccccac	9	12	3	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr3:57148802A>T	ENST00000296318.7	-	3	316	c.228T>A	c.(226-228)gcT>gcA	p.A76A	IL17RD_ENST00000479825.1_5'UTR|IL17RD_ENST00000320057.5_5'UTR|IL17RD_ENST00000463523.1_5'UTR|IL17RD_ENST00000427856.2_Silent_p.A52A	NM_017563.3	NP_060033.3	Q8NFM7	I17RD_HUMAN	interleukin 17 receptor D	76					signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)	16				KIRC - Kidney renal clear cell carcinoma(284;0.0173)|Kidney(284;0.0204)		TCTGGGCGTCAGCAATCACAT	0.453																																					p.A76A		Atlas-SNP	.											.	IL17RD	93	.	0			c.T228A						.						72	73	72					3																	57148802		1937	4144	6081	SO:0001819	synonymous_variant	54756	exon3			GGCGTCAGCAATC	AF494208	CCDS2880.2	3p21.1	2008-02-05			ENSG00000144730	ENSG00000144730		"Interleukins and interleukin receptors"	17616	protein-coding gene	gene with protein product		606807				11802164, 12604616	Standard	NM_017563		Approved	SEF, IL17RLM, FLJ35755, IL-17RD	uc003dil.3	Q8NFM7	OTTHUMG00000150171	ENST00000296318.7:c.228T>A	chr3.hg19:g.57148802A>T		53.0	0.0		65.0	35.0	NM_017563	Q2NKP7|Q58EZ7|Q6RVF4|Q6UWI5|Q8N113|Q8NFS0|Q9UFA0	Silent	SNP	ENST00000296318.7	hg19	CCDS2880.2																																																																																			.	.		0.453	IL17RD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316680.1	NM_017563		T	57148802	A	T	57148802	2	4	290	1	0	0	0	0	0	0	0	1	7651	175	7	4		4	IL17RD	3	57148802	Silent	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	2268365	57148802	140873628	45	42507										
PRICKLE2	166336	hgsc.bcm.edu	37	chr3	64084768	64084768	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	gctcttctgtcttttcctgcTgtgcaactgtcctctgccac	7	15	4	0			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr3:64084768T>A	ENST00000295902.6	-	8	3079	c.2494A>T	c.(2494-2496)Agc>Tgc	p.S832C	PRICKLE2-AS1_ENST00000460946.1_RNA|PRICKLE2-AS1_ENST00000476308.1_RNA|RP11-129B22.1_ENST00000482609.1_RNA|PRICKLE2_ENST00000564377.1_Missense_Mutation_p.S888C	NM_198859.3	NP_942559.1	Q7Z3G6	PRIC2_HUMAN	prickle homolog 2 (Drosophila)	832					establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|neuron projection development (GO:0031175)	apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(9)|liver(1)|lung(10)|ovary(4)|prostate(2)|skin(2)|stomach(1)	32		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000971)|KIRC - Kidney renal clear cell carcinoma(15;0.00443)|Kidney(15;0.00497)		CTTTTCCTGCTGTGCAACTGT	0.468																																					p.S832C		Atlas-SNP	.											.	PRICKLE2	88	.	0			c.A2494T						.						107	105	106					3																	64084768		2203	4300	6503	SO:0001583	missense	166336	exon8			TCCTGCTGTGCAA	AK127839	CCDS2902.1	3p14.3	2006-09-12	2006-09-12		ENSG00000163637	ENSG00000163637			20340	protein-coding gene	gene with protein product		608501	"prickle-like 2 (Drosophila)"			12525887	Standard	NM_198859		Approved	DKFZp686D143	uc003dmf.3	Q7Z3G6	OTTHUMG00000158789	ENST00000295902.6:c.2494A>T	chr3.hg19:g.64084768T>A	ENSP00000295902:p.Ser832Cys	86.0	0.0		75.0	15.0	NM_198859	Q0VF44	Missense_Mutation	SNP	ENST00000295902.6	hg19	CCDS2902.1	.	.	.	.	.	.	.	.	.	.	T	15.88	2.962224	0.53400	.	.	ENSG00000163637	ENST00000295902	D	0.86432	-2.12	5.83	3.44	0.39384	.	0.059918	0.64402	D	0.000002	D	0.83963	0.5368	L	0.44542	1.39	0.42333	D	0.9923	D	0.57899	0.981	P	0.46796	0.527	T	0.82851	-0.0253	10	0.72032	D	0.01	-26.1787	10.3142	0.43727	0.0:0.1304:0.0:0.8696	.	832	Q7Z3G6	PRIC2_HUMAN	C	832	ENSP00000295902:S832C	ENSP00000295902:S832C	S	-	1	0	PRICKLE2	64059808	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.660000	0.46749	0.474000	0.27392	0.533000	0.62120	AGC	.	.		0.468	PRICKLE2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352219.1	NM_198859		A	64084768	T	A	64084768	3	1	290	1	0	0	0	0	1	0	0	0	12499	1580	55	4	44	4	PRICKLE2	3	64084768	Missense_Mutation	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	6935966	64084768	133937662	46	42508										
OR5H6	79295	hgsc.bcm.edu	37	chr3	97983418	97983418	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	atccacagtgactccgaagaTgctgatcaacttcttagcta	7	11	2	3			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr3:97983418T>G	ENST00000383696.2	+	1	331	c.290T>G	c.(289-291)aTg>aGg	p.M97R	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005479.1	NP_001005479.1	Q8NGV6	OR5H6_HUMAN	olfactory receptor, family 5, subfamily H, member 6 (gene/pseudogene)	97						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(2)|endometrium(1)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						ACTCCGAAGATGCTGATCAAC	0.408																																					p.M97R		Atlas-SNP	.											.	OR5H6	89	.	0			c.T290G						.						141	146	144					3																	97983418		2203	4300	6503	SO:0001583	missense	79295	exon1			CGAAGATGCTGAT	BK004374	CCDS33800.1	3q12.1	2013-10-10	2013-10-10		ENSG00000230301	ENSG00000230301		"GPCR / Class A : Olfactory receptors"	14767	protein-coding gene	gene with protein product			"olfactory receptor, family 5, subfamily H, member 6"				Standard	NM_001005479		Approved		uc003dsi.1	Q8NGV6	OTTHUMG00000160078	ENST00000383696.2:c.290T>G	chr3.hg19:g.97983418T>G	ENSP00000373196:p.Met97Arg	137.0	0.0		122.0	30.0	NM_001005479	Q6IF88	Missense_Mutation	SNP	ENST00000383696.2	hg19	CCDS33800.1	.	.	.	.	.	.	.	.	.	.	-	12.86	2.065491	0.36470	.	.	ENSG00000230301	ENST00000383696	T	0.06068	3.35	2.19	0.902	0.19290	GPCR, rhodopsin-like superfamily (1);	0.218873	0.32218	N	0.006411	T	0.27594	0.0678	H	0.97390	3.995	0.09310	N	1	D	0.56968	0.978	P	0.58266	0.836	T	0.15206	-1.0445	10	0.87932	D	0	.	6.3694	0.21473	0.0:0.0:0.2532:0.7467	.	97	Q8NGV6	OR5H6_HUMAN	R	97	ENSP00000373196:M97R	ENSP00000373196:M97R	M	+	2	0	OR5H6	99466108	0.008000	0.16893	0.002000	0.10522	0.007000	0.05969	1.769000	0.38522	0.092000	0.17331	0.163000	0.16589	ATG	.	.		0.408	OR5H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359111.2			G	97983418	T	G	97983418	3	3	290	1	0	0	0	0	1	0	0	0	11172	1464	51	5	292	5	OR5H6	3	97983418	Missense_Mutation	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	33898650	97983418	100039012	47	42509										
NR1I2	8856	hgsc.bcm.edu	37	chr3	119530549	119530549	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	atgaaaacctttgacactacCttctcccatttcaagaattt	3	11	2	3			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr3:119530549C>G	ENST00000337940.4	+	4	660	c.612C>G	c.(610-612)acC>acG	p.T204T	NR1I2_ENST00000466380.1_Silent_p.T165T|NR1I2_ENST00000393716.2_Silent_p.T165T	NM_022002.2	NP_071285.1	O75469	NR1I2_HUMAN	nuclear receptor subfamily 1, group I, member 2	165	Hinge.				drug export (GO:0046618)|exogenous drug catabolic process (GO:0042738)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|steroid metabolic process (GO:0008202)|transcription initiation from RNA polymerase II promoter (GO:0006367)|xenobiotic metabolic process (GO:0006805)|xenobiotic transport (GO:0042908)	nucleoplasm (GO:0005654)	drug binding (GO:0008144)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(2)|prostate(2)|skin(3)	23				GBM - Glioblastoma multiforme(114;0.175)	Docetaxel(DB01248)|Erlotinib(DB00530)|Estradiol(DB00783)|Ethinyl Estradiol(DB00977)|Paclitaxel(DB01229)|Rifampicin(DB01045)|Rifaximin(DB01220)|Rilpivirine(DB08864)|Vitamin E(DB00163)	TTGACACTACCTTCTCCCATT	0.532																																					p.T204T		Atlas-SNP	.											.	NR1I2	44	.	0			c.C612G						.						107	93	98					3																	119530549		2203	4300	6503	SO:0001819	synonymous_variant	8856	exon4			CACTACCTTCTCC	AF061056	CCDS2995.1, CCDS43136.1, CCDS54627.1	3q12-q13.3	2013-03-25			ENSG00000144852	ENSG00000144852		"Nuclear hormone receptors"	7968	protein-coding gene	gene with protein product	"pregnane X receptor", "orphan nuclear receptor PXR"	603065				9727070, 9770465	Standard	NM_003889		Approved	ONR1, PXR, BXR, SXR, PAR2	uc003edk.3	O75469	OTTHUMG00000159400	ENST00000337940.4:c.612C>G	chr3.hg19:g.119530549C>G		50.0	0.0		58.0	28.0	NM_022002	Q006P5|Q008C8|Q96AC7|Q9UJ22|Q9UJ23|Q9UJ24|Q9UJ25|Q9UJ26|Q9UJ27|Q9UNW4	Silent	SNP	ENST00000337940.4	hg19	CCDS2995.1																																																																																			.	.		0.532	NR1I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355126.1			G	119530549	C	G	119530549	2	3	290	1	0	0	0	0	0	0	0	1	10629	668	24	4		4	NR1I2	3	119530549	Silent	SNP	C	TCGA-G3-A7M5-01A-11D-A33Q-10	21547131	119530549	78491881	48	42510										
ILDR1	286676	hgsc.bcm.edu	37	chr3	121712452	121712452	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	ccaagactttggcccccggtCctggagctcctggtggaaat	12	13	0	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr3:121712452C>A	ENST00000344209.5	-	7	1270	c.1144G>T	c.(1144-1146)Gac>Tac	p.D382Y	ILDR1_ENST00000462014.1_Missense_Mutation_p.D350Y|ILDR1_ENST00000460554.1_5'UTR|ILDR1_ENST00000393631.1_Missense_Mutation_p.D293Y|ILDR1_ENST00000273691.3_Missense_Mutation_p.D338Y	NM_001199799.1	NP_001186728.1	Q86SU0	ILDR1_HUMAN	immunoglobulin-like domain containing receptor 1	382					positive regulation of peptide hormone secretion (GO:0090277)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-density lipoprotein particle receptor activity (GO:0070506)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				GBM - Glioblastoma multiforme(114;0.156)		GGCCCCCGGTCCTGGAGCTCC	0.597																																					p.D382Y		Atlas-SNP	.											.	ILDR1	120	.	0			c.G1144T						.						66	65	65					3																	121712452		2203	4300	6503	SO:0001583	missense	286676	exon7			CCCGGTCCTGGAG	BC044240	CCDS3008.1, CCDS56270.1, CCDS56271.1	3q21.1	2013-10-11			ENSG00000145103	ENSG00000145103			28741	protein-coding gene	gene with protein product		609739	"deafness, autosomal recessive 42"	DFNB42		15641023, 21255762	Standard	NM_175924		Approved	MGC50831	uc003ees.3	Q86SU0	OTTHUMG00000159481	ENST00000344209.5:c.1144G>T	chr3.hg19:g.121712452C>A	ENSP00000345667:p.Asp382Tyr	102.0	0.0		111.0	58.0	NM_001199799	Q6ZP61|Q7Z578	Missense_Mutation	SNP	ENST00000344209.5	hg19	CCDS56271.1	.	.	.	.	.	.	.	.	.	.	C	11.26	1.585387	0.28268	.	.	ENSG00000145103	ENST00000273691;ENST00000344209;ENST00000393631;ENST00000462014	T;T;T;T	0.80480	-0.86;-0.64;-1.38;-0.46	5.59	1.45	0.22620	.	0.643972	0.15526	N	0.257764	T	0.80358	0.4608	L	0.54323	1.7	0.09310	N	0.999996	P;B;P;P	0.52692	0.946;0.0;0.892;0.955	P;B;P;P	0.55161	0.77;0.0;0.643;0.643	T	0.67945	-0.5539	10	0.44086	T	0.13	-7.8368	5.2014	0.15267	0.1369:0.5202:0.266:0.0769	.	293;382;338;350	Q86SU0-5;Q86SU0;Q86SU0-2;Q86SU0-6	.;ILDR1_HUMAN;.;.	Y	338;382;293;350	ENSP00000273691:D338Y;ENSP00000345667:D382Y;ENSP00000377251:D293Y;ENSP00000419414:D350Y	ENSP00000273691:D338Y	D	-	1	0	ILDR1	123195142	0.401000	0.25303	0.124000	0.21820	0.181000	0.23173	0.985000	0.29578	0.272000	0.22027	-0.143000	0.13931	GAC	.	.		0.597	ILDR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355666.1	NM_175924		A	121712452	C	A	121712452	3	1	290	1	0	0	0	0	1	0	0	0	7718	855	30	3	504	3	ILDR1	3	121712452	Missense_Mutation	SNP	C	TCGA-G3-A7M5-01A-11D-A33Q-10	2181903	121712452	76309978	49	42511										
CCDC37	348807	hgsc.bcm.edu	37	chr3	126135180	126135180	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	aacggcagcagcagaagacgAtgcgggtgcaccagaagatg	15	9	0	4			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr3:126135180A>T	ENST00000352312.1	+	5	346	c.247A>T	c.(247-249)Atg>Ttg	p.M83L	CCDC37_ENST00000505024.1_Missense_Mutation_p.M83L|CCDC37_ENST00000393425.1_Missense_Mutation_p.M83L	NM_182628.2	NP_872434.2	Q494V2	CCD37_HUMAN	coiled-coil domain containing 37	83										NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|skin(3)	23				GBM - Glioblastoma multiforme(114;0.166)		GCAGAAGACGATGCGGGTGCA	0.682																																					p.M83L		Atlas-SNP	.											.	CCDC37	69	.	0			c.A247T						.						37	33	34					3																	126135180		2202	4298	6500	SO:0001583	missense	348807	exon5			AAGACGATGCGGG	AK097402	CCDS3037.1	3q21.2	2014-07-31			ENSG00000163885	ENSG00000163885			26842	protein-coding gene	gene with protein product						23569216	Standard	NM_182628		Approved	FLJ40083, MIA1	uc003eiu.1	Q494V2	OTTHUMG00000162691	ENST00000352312.1:c.247A>T	chr3.hg19:g.126135180A>T	ENSP00000344749:p.Met83Leu	89.0	0.0		76.0	22.0	NM_182628	D3DNA8|Q494V1|Q494V4|Q8N838	Missense_Mutation	SNP	ENST00000352312.1	hg19	CCDS3037.1	.	.	.	.	.	.	.	.	.	.	A	0.006	-2.093653	0.00364	.	.	ENSG00000163885	ENST00000352312;ENST00000393425;ENST00000505024	T;T;T	0.25579	1.79;1.79;1.79	4.59	0.872	0.19113	.	0.303339	0.32386	N	0.006161	T	0.04952	0.0133	N	0.00742	-1.23	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.39663	-0.9603	10	0.02654	T	1	-17.6983	5.3001	0.15773	0.404:0.4415:0.0:0.1545	.	83;83	Q494V2-2;Q494V2	.;CCD37_HUMAN	L	83	ENSP00000344749:M83L;ENSP00000377076:M83L;ENSP00000423046:M83L	ENSP00000344749:M83L	M	+	1	0	CCDC37	127617870	0.000000	0.05858	0.013000	0.15412	0.034000	0.12701	-0.597000	0.05713	-0.090000	0.12462	-0.680000	0.03767	ATG	.	.		0.682	CCDC37-001	KNOWN	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000370099.4	NM_182628		T	126135180	A	T	126135180	3	4	290	1	0	0	0	0	1	0	0	0	2811	333	12	4	261	4	CCDC37	3	126135180	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	4422728	126135180	71887250	50	42512										
STAG1	10274	hgsc.bcm.edu	37	chr3	136196226	136196226	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tactccaatttcttcaatacAaatggctctaatctcagcaa	3	11	4	0			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr3:136196226A>T	ENST00000383202.2	-	10	1187	c.931T>A	c.(931-933)Tgt>Agt	p.C311S	STAG1_ENST00000236698.5_Missense_Mutation_p.C311S|STAG1_ENST00000434713.2_Missense_Mutation_p.C85S	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	311	SCD. {ECO:0000255|PROSITE- ProRule:PRU00750}.				chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						TCTTCAATACAAATGGCTCTA	0.348																																					p.C311S		Atlas-SNP	.											.	STAG1	135	.	0			c.T931A						.						120	114	116					3																	136196226		2203	4299	6502	SO:0001583	missense	10274	exon10			CAATACAAATGGC	Z75330	CCDS3090.1	3q22.2-q22.3	2011-08-12			ENSG00000118007	ENSG00000118007			11354	protein-coding gene	gene with protein product		604358				9305759	Standard	XM_006713471		Approved	SA-1, SCC3A	uc003era.1	Q8WVM7	OTTHUMG00000159798	ENST00000383202.2:c.931T>A	chr3.hg19:g.136196226A>T	ENSP00000372689:p.Cys311Ser	43.0	0.0		54.0	26.0	NM_005862	O00539|Q6P275	Missense_Mutation	SNP	ENST00000383202.2	hg19	CCDS3090.1	.	.	.	.	.	.	.	.	.	.	A	26.7	4.766467	0.90020	.	.	ENSG00000118007	ENST00000383202;ENST00000236698;ENST00000434713	T;T;T	0.31510	1.49;1.49;1.49	5.09	5.09	0.68999	Stromalin conservative domain (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.57740	0.2074	M	0.82823	2.61	0.80722	D	1	D;P;D	0.76494	0.999;0.948;0.999	D;P;D	0.70935	0.971;0.63;0.971	T	0.62253	-0.6893	10	0.46703	T	0.11	.	15.1528	0.72713	1.0:0.0:0.0:0.0	.	328;311;311	Q4LE48;Q6P275;Q8WVM7	.;.;STAG1_HUMAN	S	311;311;85	ENSP00000372689:C311S;ENSP00000236698:C311S;ENSP00000404396:C85S	ENSP00000236698:C311S	C	-	1	0	STAG1	137678916	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.287000	0.95975	2.031000	0.59945	0.533000	0.62120	TGT	.	.		0.348	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357366.1	NM_005862		T	136196226	A	T	136196226	3	4	290	1	0	0	0	0	1	0	0	0	15257	130	5	4	2945	4	STAG1	3	136196226	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	10061046	136196226	61826204	51	42513										
P2RY1	5028	hgsc.bcm.edu	37	chr3	152553693	152553693	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	cgccgtctcctcgtcgttcaAatgcgccttgaccaagacgg	10	15	2	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr3:152553693A>T	ENST00000305097.3	+	1	958	c.122A>T	c.(121-123)aAa>aTa	p.K41I		NM_002563.3	NP_002554.1	P47900	P2RY1_HUMAN	purinergic receptor P2Y, G-protein coupled, 1	41					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|aging (GO:0007568)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cell surface receptor signaling pathway (GO:0007166)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of binding (GO:0051100)|negative regulation of norepinephrine secretion (GO:0010700)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of hormone secretion (GO:0046887)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of ion transport (GO:0043270)|positive regulation of penile erection (GO:0060406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to plasma membrane (GO:0072659)|regulation of receptor activity (GO:0010469)|regulation of vasodilation (GO:0042312)|relaxation of muscle (GO:0090075)|response to growth factor (GO:0070848)|response to mechanical stimulus (GO:0009612)|sensory perception of pain (GO:0019233)|signal transduction involved in regulation of gene expression (GO:0023019)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell body (GO:0044297)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ADP binding (GO:0043531)|ADP-activated nucleotide receptor activity (GO:0045032)|ATP binding (GO:0005524)|ATP-activated nucleotide receptor activity (GO:0045031)|G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|receptor activity (GO:0004872)|scaffold protein binding (GO:0097110)			breast(1)|endometrium(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)	23			LUSC - Lung squamous cell carcinoma(72;0.0628)|Lung(72;0.11)			TCGTCGTTCAAATGCGCCTTG	0.622																																					p.K41I		Atlas-SNP	.											.	P2RY1	49	.	0			c.A122T						.						83	73	76					3																	152553693		2203	4300	6503	SO:0001583	missense	5028	exon1			CGTTCAAATGCGC	U42029	CCDS3169.1	3q25.2	2012-08-08			ENSG00000169860	ENSG00000169860		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	8539	protein-coding gene	gene with protein product		601167				8579591	Standard	NM_002563		Approved	P2Y1	uc003ezq.3	P47900	OTTHUMG00000159694	ENST00000305097.3:c.122A>T	chr3.hg19:g.152553693A>T	ENSP00000304767:p.Lys41Ile	112.0	0.0		112.0	59.0	NM_002563		Missense_Mutation	SNP	ENST00000305097.3	hg19	CCDS3169.1	.	.	.	.	.	.	.	.	.	.	A	10.24	1.294501	0.23564	.	.	ENSG00000169860	ENST00000305097	T	0.36520	1.25	5.37	-7.62	0.01294	.	0.758261	0.12413	N	0.471082	T	0.15696	0.0378	N	0.08118	0	0.09310	N	1	B	0.16603	0.018	B	0.18871	0.023	T	0.17048	-1.0382	10	0.46703	T	0.11	.	11.3924	0.49822	0.7134:0.1016:0.1849:0.0	.	41	P47900	P2RY1_HUMAN	I	41	ENSP00000304767:K41I	ENSP00000304767:K41I	K	+	2	0	P2RY1	154036383	0.001000	0.12720	0.000000	0.03702	0.281000	0.26958	-0.174000	0.09839	-1.876000	0.01131	-0.256000	0.11100	AAA	.	.		0.622	P2RY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356943.1	NM_002563		T	152553693	A	T	152553693	3	4	290	1	0	0	0	0	1	0	0	0	11355	14	1	4	124	4	P2RY1	3	152553693	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	16357467	152553693	45468737	52	42514										
MECOM	2122	hgsc.bcm.edu	37	chr3	168840403	168840403	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	acattcatagtgctttccacTgtcatgtgacatctggtggc	9	10	3	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr3:168840403T>A	ENST00000464456.1	-	5	1579	c.379A>T	c.(379-381)Agt>Tgt	p.S127C	MECOM_ENST00000472280.1_Missense_Mutation_p.S127C|MECOM_ENST00000433243.2_Missense_Mutation_p.S127C|MECOM_ENST00000264674.3_Missense_Mutation_p.S191C|MECOM_ENST00000468789.1_Missense_Mutation_p.S127C|MECOM_ENST00000460814.1_Missense_Mutation_p.S127C|MECOM_ENST00000392736.3_Missense_Mutation_p.S127C|MECOM_ENST00000494292.1_Missense_Mutation_p.S315C	NM_001164000.1	NP_001157472.1	Q13465	MDS1_HUMAN	MDS1 and EVI1 complex locus	0					regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	85						TGCTTTCCACTGTCATGTGAC	0.433																																					p.S315C		Atlas-SNP	.											.	MECOM	216	.	0			c.A943T						.						222	185	198					3																	168840403		2203	4300	6503	SO:0001583	missense	2122	exon6			TTCCACTGTCATG	S82592, AF164154	CCDS3205.1, CCDS54669.1, CCDS54670.1	3q26.2	2013-01-08	2009-08-07	2009-08-07	ENSG00000085276	ENSG00000085276		"Zinc fingers, C2H2-type"	3498	protein-coding gene	gene with protein product		165215	"myelodysplasia syndrome 1", "ecotropic viral integration site 1"	MDS1, EVI1		2115646, 8171026, 8643684	Standard	NM_001105077		Approved	MDS1-EVI1, PRDM3	uc011bpj.1	Q03112	OTTHUMG00000158596	ENST00000464456.1:c.379A>T	chr3.hg19:g.168840403T>A	ENSP00000419770:p.Ser127Cys	121.0	0.0		95.0	45.0	NM_004991	Q13466|Q6FH90	Missense_Mutation	SNP	ENST00000464456.1	hg19	CCDS54669.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.282114	0.80692	.	.	ENSG00000085276	ENST00000264674;ENST00000392736;ENST00000464456;ENST00000472280;ENST00000494292;ENST00000468789;ENST00000460814;ENST00000433243;ENST00000492586	T;T;T;T;T;T;T;T;T	0.15952	2.38;2.38;2.38;2.38;2.38;2.38;2.38;2.38;2.38	5.68	4.52	0.55395	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.263556	0.29892	N	0.010924	T	0.33118	0.0852	L	0.51422	1.61	0.58432	D	0.999995	D;D;D;D;D	0.76494	0.999;0.996;0.998;0.998;0.997	D;P;P;P;P	0.66847	0.947;0.794;0.862;0.891;0.817	T	0.03008	-1.1083	10	0.87932	D	0	-11.5787	11.6019	0.51008	0.0:0.0695:0.0:0.9305	.	315;127;315;191;127	Q03112-3;Q03112-6;E7EQ57;Q03112-4;Q03112	.;.;.;.;EVI1_HUMAN	C	191;127;127;127;315;127;127;127;102	ENSP00000264674:S191C;ENSP00000376493:S127C;ENSP00000419770:S127C;ENSP00000420048:S127C;ENSP00000417899:S315C;ENSP00000419995:S127C;ENSP00000420466:S127C;ENSP00000394302:S127C;ENSP00000417506:S102C	ENSP00000264674:S191C	S	-	1	0	MECOM	170323097	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	0.989000	0.38761	0.533000	0.62120	AGT	.	.		0.433	MECOM-020	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351519.1	NM_005241, NM_004991		A	168840403	T	A	168840403	3	1	290	1	0	0	0	0	1	0	0	0	9431	1580	55	4	2827	4	MECOM	3	168840403	Missense_Mutation	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	16286710	168840403	29182027	53	42515										
GPR160	26996	hgsc.bcm.edu	37	chr3	169802417	169802417	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	ataacttcctatatgaatgaAactatcttatattttccttt	2	7	1	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr3:169802417A>C	ENST00000355897.5	+	4	1265	c.657A>C	c.(655-657)gaA>gaC	p.E219D		NM_014373.2	NP_055188.1	Q9UJ42	GP160_HUMAN	G protein-coupled receptor 160	219						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			breast(1)|cervix(1)|kidney(1)|large_intestine(3)|lung(2)	8	all_cancers(22;3.26e-22)|all_epithelial(15;5.71e-27)|all_lung(20;8.41e-17)|Lung NSC(18;3.49e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)			ATATGAATGAAACTATCTTAT	0.333																																					p.E219D		Atlas-SNP	.											.	GPR160	26	.	0			c.A657C						.						82	82	82					3																	169802417		2203	4300	6503	SO:0001583	missense	26996	exon4			GAATGAAACTATC	AB083583	CCDS3211.1	3q26.2-q27	2012-08-21			ENSG00000173890	ENSG00000173890		"GPCR / Class A : Orphans"	23693	protein-coding gene	gene with protein product						12044878	Standard	NM_014373		Approved	GPCR150, GPCR1	uc003fgi.3	Q9UJ42	OTTHUMG00000158776	ENST00000355897.5:c.657A>C	chr3.hg19:g.169802417A>C	ENSP00000348161:p.Glu219Asp	65.0	0.0		70.0	35.0	NM_014373	D3DNQ2	Missense_Mutation	SNP	ENST00000355897.5	hg19	CCDS3211.1	.	.	.	.	.	.	.	.	.	.	A	10.88	1.474890	0.26511	.	.	ENSG00000173890	ENST00000355897	.	.	.	5.7	1.62	0.23740	GPCR, rhodopsin-like superfamily (1);	0.289956	0.29587	N	0.011725	T	0.45135	0.1327	L	0.43152	1.355	0.23036	N	0.998391	D	0.61697	0.99	P	0.55749	0.783	T	0.34403	-0.9830	9	0.51188	T	0.08	.	9.8917	0.41294	0.2784:0.0:0.7216:0.0	.	219	Q9UJ42	GP160_HUMAN	D	219	.	ENSP00000348161:E219D	E	+	3	2	GPR160	171285111	1.000000	0.71417	0.117000	0.21633	0.110000	0.19582	3.045000	0.49838	0.004000	0.14682	-0.408000	0.06270	GAA	.	.		0.333	GPR160-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352167.1	NM_014373		C	169802417	A	C	169802417	3	2	290	1	0	0	0	0	1	0	0	0	6672	11	1	5	659	5	GPR160	3	169802417	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	962014	169802417	28220013	54	42516										
KLHL24	54800	hgsc.bcm.edu	37	chr3	183381339	183381339	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	actgagtgctacgatcctgtAacaggagaatggaagtcttt	11	7	1	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr3:183381339A>T	ENST00000454652.2	+	5	1400	c.1014A>T	c.(1012-1014)gtA>gtT	p.V338V	KLHL24_ENST00000242810.6_Silent_p.V338V|KLHL24_ENST00000476808.1_Silent_p.V338V	NM_017644.3	NP_060114.2	Q6TFL4	KLH24_HUMAN	kelch-like family member 24	338						cell projection (GO:0042995)|cytoplasm (GO:0005737)				NS(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(10)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27	all_cancers(143;2.88e-10)|Ovarian(172;0.0303)		all cancers(12;1.43e-42)|Epithelial(37;1.73e-36)|OV - Ovarian serous cystadenocarcinoma(80;8.75e-22)			ACGATCCTGTAACAGGAGAAT	0.413																																					p.V338V		Atlas-SNP	.											.	KLHL24	56	.	0			c.A1014T						.						149	137	141					3																	183381339		2203	4300	6503	SO:0001819	synonymous_variant	54800	exon4			TCCTGTAACAGGA		CCDS3246.1	3q27.1	2013-02-22	2013-02-22		ENSG00000114796	ENSG00000114796		"Kelch-like", "BTB/POZ domain containing"	25947	protein-coding gene	gene with protein product		611295	"kelch-like 24 (Drosophila)"				Standard	XM_005247552		Approved	DRE1, FLJ20059	uc003flv.3	Q6TFL4	OTTHUMG00000156911	ENST00000454652.2:c.1014A>T	chr3.hg19:g.183381339A>T		75.0	0.0		70.0	40.0	NM_017644	A5PLN8|Q9H620|Q9NXT9	Silent	SNP	ENST00000454652.2	hg19	CCDS3246.1																																																																																			.	.		0.413	KLHL24-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346586.2	NM_017644		T	183381339	A	T	183381339	2	4	290	1	0	0	0	0	0	0	0	1	8388	349	13	4		4	KLHL24	3	183381339	Silent	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	13578922	183381339	14641091	55	42517										
SLIT2	9353	hgsc.bcm.edu	37	chr4	20487848	20487848	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tcaacaataacaacattactAgactttctgtggcaagtttc	5	9	2	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr4:20487848A>T	ENST00000504154.1	+	7	817	c.565A>T	c.(565-567)Aga>Tga	p.R189*	SLIT2_ENST00000503837.1_Nonsense_Mutation_p.R189*|SLIT2_ENST00000503823.1_Nonsense_Mutation_p.R189*|SLIT2_ENST00000273739.5_Nonsense_Mutation_p.R189*	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	189					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)			NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						CAACATTACTAGACTTTCTGT	0.274																																					p.R189X		Atlas-SNP	.											.	SLIT2	290	.	0			c.A565T						.						73	74	74					4																	20487848		2202	4299	6501	SO:0001587	stop_gained	9353	exon7			ATTACTAGACTTT	AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"slit (Drosophila) homolog 2"	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.565A>T	chr4.hg19:g.20487848A>T	ENSP00000422591:p.Arg189*	311.0	0.0		330.0	251.0	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Nonsense_Mutation	SNP	ENST00000504154.1	hg19	CCDS3426.1	.	.	.	.	.	.	.	.	.	.	A	35	5.496967	0.96355	.	.	ENSG00000145147	ENST00000503823;ENST00000504154;ENST00000273739;ENST00000382173;ENST00000503837	.	.	.	5.3	4.03	0.46877	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18710	T	0.47	.	10.8909	0.46994	0.6576:0.3424:0.0:0.0	.	.	.	.	X	189	.	ENSP00000273739:R189X	R	+	1	2	SLIT2	20096946	1.000000	0.71417	0.939000	0.37840	0.992000	0.81027	3.618000	0.54188	2.120000	0.65058	0.459000	0.35465	AGA	.	.		0.274	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2			T	20487848	A	T	20487848	4	4	290	1	0	0	0	0	0	1	0	0	14755	412	15	4	591	4	SLIT2	4	20487848	Nonsense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10		20487848	170666428	56	42518										
TMEM156	80008	hgsc.bcm.edu	37	chr4	38995620	38995620	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	gatcctctcctgataagaacTagaaagtgattaagaaaatg	8	6	1	5			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr4:38995620T>A	ENST00000381938.3	-	3	466		c.e3-2			NM_024943.1	NP_079219.1	Q8N614	TM156_HUMAN	transmembrane protein 156							integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|stomach(1)	10						TGATAAGAACTAGAAAGTGAT	0.328																																					.		Atlas-SNP	.											.	TMEM156	31	.	0			c.359-2A>T						.						63	64	64					4																	38995620		2202	4300	6502	SO:0001630	splice_region_variant	80008	exon4			AAGAACTAGAAAG	AK026888	CCDS3448.1	4p14	2008-02-05			ENSG00000121895	ENSG00000121895			26260	protein-coding gene	gene with protein product						12477932	Standard	NM_024943		Approved	FLJ23235	uc003gto.3	Q8N614	OTTHUMG00000128582	ENST00000381938.3:c.359-2A>T	chr4.hg19:g.38995620T>A		131.0	0.0		111.0	85.0	NM_024943	Q9H5N9	Splice_Site	SNP	ENST00000381938.3	hg19	CCDS3448.1	.	.	.	.	.	.	.	.	.	.	T	16.89	3.246822	0.59103	.	.	ENSG00000121895	ENST00000381938;ENST00000344606	.	.	.	5.21	5.21	0.72293	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.3895	0.49806	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	TMEM156	38672015	0.996000	0.38824	0.950000	0.38849	0.794000	0.44872	4.025000	0.57225	2.174000	0.68829	0.533000	0.62120	.	.	.		0.328	TMEM156-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250435.3	NM_024943	Intron	A	38995620	T	A	38995620	5	1	290	1	0	0	0	0	0	0	1	0	16088	1536	53	4	549	4	TMEM156	4	38995620	Splice_Site	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	18507772	38995620	152158656	57	42519										
GRXCR1	389207	hgsc.bcm.edu	37	chr4	43032535	43032535	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	caatgaaaatggtcttcagcGttgtaagaactgtgctggtt	11	6	2	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr4:43032535G>A	ENST00000399770.2	+	4	851	c.851G>A	c.(850-852)cGt>cAt	p.R284H		NM_001080476.2	NP_001073945.1	A8MXD5	GRCR1_HUMAN	glutaredoxin, cysteine rich 1	284					auditory receptor cell differentiation (GO:0042491)|cell redox homeostasis (GO:0045454)|inner ear receptor cell development (GO:0060119)|inner ear receptor stereocilium organization (GO:0060122)|negative regulation of phosphatase activity (GO:0010923)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of sound (GO:0007605)|vestibular receptor cell development (GO:0060118)	kinocilium (GO:0060091)|stereocilium (GO:0032420)	electron carrier activity (GO:0009055)|protein disulfide oxidoreductase activity (GO:0015035)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(22)|ovary(1)|prostate(2)|skin(1)	32						GGTCTTCAGCGTTGTAAGAAC	0.393																																					p.R284H		Atlas-SNP	.											.	GRXCR1	78	.	0			c.G851A						.						143	134	136					4																	43032535		1891	4118	6009	SO:0001583	missense	389207	exon4			TTCAGCGTTGTAA		CCDS43225.1	4p14	2014-06-12			ENSG00000215203	ENSG00000215203			31673	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 88"	613283	"deafness, autosomal recessive 25"	DFNB25		20137778	Standard	NM_001080476		Approved	PPP1R88	uc003gwt.3	A8MXD5	OTTHUMG00000160434	ENST00000399770.2:c.851G>A	chr4.hg19:g.43032535G>A	ENSP00000382670:p.Arg284His	75.0	0.0		93.0	17.0	NM_001080476		Missense_Mutation	SNP	ENST00000399770.2	hg19	CCDS43225.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.405470	0.83230	.	.	ENSG00000215203	ENST00000399770	T	0.21932	1.98	5.64	5.64	0.86602	.	0.173392	0.39909	U	0.001231	T	0.39937	0.1097	M	0.81682	2.555	0.53688	D	0.999975	D	0.67145	0.996	P	0.49502	0.613	T	0.42275	-0.9461	10	0.72032	D	0.01	-11.3334	18.6692	0.91504	0.0:0.0:1.0:0.0	.	284	A8MXD5	GRCR1_HUMAN	H	284	ENSP00000382670:R284H	ENSP00000382670:R284H	R	+	2	0	GRXCR1	42727292	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	6.834000	0.75339	2.649000	0.89929	0.579000	0.79373	CGT	.	.		0.393	GRXCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360576.1	NM_001080476		A	43032535	G	A	43032535	3	1	290	1	0	0	0	0	1	0	0	0	6821	1145	40	1	865	1	GRXCR1	4	43032535	Missense_Mutation	SNP	G	TCGA-G3-A7M5-01A-11D-A33Q-10	4036915	43032535	148121741	58	42520										
GK2	2712	hgsc.bcm.edu	37	chr4	80327914	80327914	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	aaatcgttccatcctgagaaCtgacaaagcctggggttcaa	9	10	1	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr4:80327914C>T	ENST00000358842.3	-	1	1458	c.1441G>A	c.(1441-1443)Gtt>Att	p.V481I		NM_033214.2	NP_149991.2	Q01415	GALK2_HUMAN	glycerol kinase 2	0					carbohydrate metabolic process (GO:0005975)|galactose metabolic process (GO:0006012)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|galactokinase activity (GO:0004335)|N-acetylgalactosamine kinase activity (GO:0033858)			autonomic_ganglia(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	39						ATCCTGAGAACTGACAAAGCC	0.498																																					p.V481I		Atlas-SNP	.											.	GK2	102	.	0			c.G1441A						.						129	123	125					4																	80327914		2203	4300	6503	SO:0001583	missense	2712	exon1			TGAGAACTGACAA	BC029820	CCDS3585.1	4q13	2008-02-05	2002-10-03	2002-10-04	ENSG00000196475	ENSG00000196475		"Glycerol kinases"	4291	protein-coding gene	gene with protein product		600148	"glycerol kinase pseudogene 2"	GKP2		7987308	Standard	NM_033214		Approved	GKTA	uc003hlu.3	Q14410	OTTHUMG00000130199	ENST00000358842.3:c.1441G>A	chr4.hg19:g.80327914C>T	ENSP00000351706:p.Val481Ile	154.0	0.0		130.0	27.0	NM_033214	Q7Z4Q4	Missense_Mutation	SNP	ENST00000358842.3	hg19	CCDS3585.1	.	.	.	.	.	.	.	.	.	.	C	0.179	-1.064393	0.01934	.	.	ENSG00000196475	ENST00000358842	T	0.14516	2.5	4.11	-4.57	0.03421	.	0.711220	0.13539	N	0.380325	T	0.06371	0.0164	N	0.19112	0.55	0.09310	N	1	B	0.11235	0.004	B	0.17098	0.017	T	0.24512	-1.0158	10	0.54805	T	0.06	-16.3104	2.8385	0.05522	0.1143:0.3204:0.1124:0.4529	.	481	Q14410	GLPK2_HUMAN	I	481	ENSP00000351706:V481I	ENSP00000351706:V481I	V	-	1	0	GK2	80546938	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.214000	0.09292	-1.253000	0.02488	0.585000	0.79938	GTT	.	.		0.498	GK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252517.2	NM_033214		T	80327914	C	T	80327914	3	4	290	1	0	0	0	0	1	0	0	0	6429	565	20	3	224	3	GK2	4	80327914	Missense_Mutation	SNP	C	TCGA-G3-A7M5-01A-11D-A33Q-10	37295379	80327914	110826362	59	42521										
ADAMTS12	81792	hgsc.bcm.edu	37	chr5	33576426	33576426	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tcagtaaccatcccctcaacTctgggtgtcccagtttcgga	8	14	3	0			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr5:33576426T>C	ENST00000504830.1	-	19	4040	c.3705A>G	c.(3703-3705)agA>agG	p.R1235R	ADAMTS12_ENST00000352040.3_Silent_p.R1150R|ADAMTS12_ENST00000504582.1_5'Flank	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	1235	Spacer 2.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						TCCCCTCAACTCTGGGTGTCC	0.577										HNSCC(64;0.19)																											p.R1235R		Atlas-SNP	.											.	ADAMTS12	464	.	0			c.A3705G						.						129	127	128					5																	33576426		2203	4300	6503	SO:0001819	synonymous_variant	81792	exon19			CTCAACTCTGGGT	AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"ADAM metallopeptidases with thrombospondin type 1 motif"	14605	protein-coding gene	gene with protein product		606184	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.3705A>G	chr5.hg19:g.33576426T>C		129.0	0.0		196.0	98.0	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Silent	SNP	ENST00000504830.1	hg19	CCDS34140.1																																																																																			.	.		0.577	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		C	33576426	T	C	33576426	2	2	290	1	0	0	0	0	0	0	0	1	257	1548	54	2		2	ADAMTS12	5	33576426	Silent	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10		33576426	147338834	60	42522										
HCN1	348980	hgsc.bcm.edu	37	chr5	45353293	45353293	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	catagtaatcatgtatcttcTgacgcatatcagctggtaac	7	9	4	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr5:45353293T>A	ENST00000303230.4	-	5	1343	c.1286A>T	c.(1285-1287)cAg>cTg	p.Q429L		NM_021072.3	NP_066550.2	O60741	HCN1_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 1	429					apical protein localization (GO:0045176)|cellular response to cAMP (GO:0071320)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|retinal cone cell development (GO:0046549)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|intracellular cAMP activated cation channel activity (GO:0005222)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(3)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(21)|liver(1)|lung(98)|ovary(1)|prostate(7)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(5)	156						ATGTATCTTCTGACGCATATC	0.333																																					p.Q429L		Atlas-SNP	.											.	HCN1	298	.	0			c.A1286T						.						160	147	151					5																	45353293		2203	4299	6502	SO:0001583	missense	348980	exon5			ATCTTCTGACGCA	AF064876	CCDS3952.1	5p12	2011-07-05			ENSG00000164588	ENSG00000164588		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	4845	protein-coding gene	gene with protein product		602780		BCNG1		9405696, 9630217, 16382102	Standard	NM_021072		Approved	BCNG-1, HAC-2	uc003jok.3	O60741	OTTHUMG00000131155	ENST00000303230.4:c.1286A>T	chr5.hg19:g.45353293T>A	ENSP00000307342:p.Gln429Leu	50.0	0.0		82.0	30.0	NM_021072		Missense_Mutation	SNP	ENST00000303230.4	hg19	CCDS3952.1	.	.	.	.	.	.	.	.	.	.	T	19.04	3.750570	0.69533	.	.	ENSG00000164588	ENST00000303230	D	0.96459	-4.02	5.97	5.97	0.96955	Cyclic nucleotide-binding-like (1);	0.000000	0.64402	D	0.000005	D	0.94857	0.8338	L	0.60845	1.875	0.80722	D	1	B	0.22909	0.077	B	0.13407	0.009	D	0.92407	0.5934	10	0.59425	D	0.04	.	16.4473	0.83942	0.0:0.0:0.0:1.0	.	429	O60741	HCN1_HUMAN	L	429	ENSP00000307342:Q429L	ENSP00000307342:Q429L	Q	-	2	0	HCN1	45389050	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.033000	0.88852	2.281000	0.76405	0.533000	0.62120	CAG	.	.		0.333	HCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253847.1	NM_021072		A	45353293	T	A	45353293	3	1	290	1	0	0	0	0	1	0	0	0	7005	1580	55	4	1402	4	HCN1	5	45353293	Missense_Mutation	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	11776867	45353293	135561967	61	42523										
POC5	134359	hgsc.bcm.edu	37	chr5	74981226	74981226	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tggtaagggcatcggaggagCtgaaggatccaaatgagcag	16	6	0	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr5:74981226C>G	ENST00000428202.2	-	10	1402	c.1213G>C	c.(1213-1215)Gct>Cct	p.A405P	POC5_ENST00000510798.1_Missense_Mutation_p.A288P|POC5_ENST00000514838.2_Missense_Mutation_p.A377P|POC5_ENST00000380475.2_Missense_Mutation_p.A288P|POC5_ENST00000446329.2_Missense_Mutation_p.A380P	NM_001099271.1	NP_001092741.1	Q8NA72	POC5_HUMAN	POC5 centriolar protein	405					cell cycle (GO:0007049)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						ATCGGAGGAGCTGAAGGATCC	0.498																																					p.A405P		Atlas-SNP	.											.	POC5	82	.	0			c.G1213C						.						177	193	188					5																	74981226		2018	4198	6216	SO:0001583	missense	134359	exon10			GAGGAGCTGAAGG	AK093098	CCDS47236.1, CCDS47237.1	5q13.3	2013-08-05	2013-08-05	2010-03-26	ENSG00000152359	ENSG00000152359			26658	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 37", "POC5 centriolar protein homolog (Chlamydomonas)"	C5orf37		19349582	Standard	NM_152408		Approved	FLJ35779, MGC120442, MGC120443, MGC120444, hPOC5	uc003keh.4	Q8NA72	OTTHUMG00000162487	ENST00000428202.2:c.1213G>C	chr5.hg19:g.74981226C>G	ENSP00000410216:p.Ala405Pro	105.0	0.0		97.0	32.0	NM_001099271	B4DJG7|Q494X7|Q494X9|Q6P085	Missense_Mutation	SNP	ENST00000428202.2	hg19	CCDS47236.1	.	.	.	.	.	.	.	.	.	.	C	12.91	2.079968	0.36662	.	.	ENSG00000152359	ENST00000428202;ENST00000514838;ENST00000380475;ENST00000510798;ENST00000446329	T;T;T;T;T	0.46063	1.83;1.42;0.88;0.88;1.82	4.14	2.27	0.28462	.	0.838861	0.10828	N	0.629672	T	0.52208	0.1720	L	0.54323	1.7	0.09310	N	1	D;D;B	0.55385	0.971;0.971;0.026	P;P;B	0.58454	0.779;0.839;0.009	T	0.35773	-0.9775	10	0.54805	T	0.06	-3.6516	9.0897	0.36603	0.4146:0.5854:0.0:0.0	.	288;405;380	Q8NA72-2;Q8NA72;Q8NA72-3	.;POC5_HUMAN;.	P	405;377;288;288;380	ENSP00000410216:A405P;ENSP00000420971:A377P;ENSP00000369842:A288P;ENSP00000426796:A288P;ENSP00000399481:A380P	ENSP00000369842:A288P	A	-	1	0	POC5	75016982	0.004000	0.15560	0.003000	0.11579	0.035000	0.12851	1.879000	0.39618	0.634000	0.30469	0.561000	0.74099	GCT	.	.		0.498	POC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369124.1	NM_152408		G	74981226	C	G	74981226	3	3	290	1	0	0	0	0	1	0	0	0	12186	797	28	4	526	4	POC5	5	74981226	Missense_Mutation	SNP	C	TCGA-G3-A7M5-01A-11D-A33Q-10	29627933	74981226	105934034	62	42524										
PPIP5K2	23262	hgsc.bcm.edu	37	chr5	102515845	102515845	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	cagagccaattcatatacacAggaagtctccacttccaaga	6	12	2	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr5:102515845A>T	ENST00000358359.3	+	24	3387	c.2878A>T	c.(2878-2880)Agg>Tgg	p.R960W	PPIP5K2_ENST00000513500.1_3'UTR|PPIP5K2_ENST00000414217.1_Missense_Mutation_p.R960W|PPIP5K2_ENST00000321521.9_Missense_Mutation_p.R960W	NM_001276277.1	NP_001263206.1	O43314	VIP2_HUMAN	diphosphoinositol pentakisphosphate kinase 2	960					inositol metabolic process (GO:0006020)|inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	acid phosphatase activity (GO:0003993)|ATP binding (GO:0005524)|diphosphoinositol-pentakisphosphate kinase activity (GO:0033857)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol-1,3,4,5,6-pentakisphosphate kinase activity (GO:0000827)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						TCATATACACAGGAAGTCTCC	0.323																																					p.R960W		Atlas-SNP	.											.	PPIP5K2	98	.	0			c.A2878T						.						90	88	89					5																	102515845		2203	4300	6503	SO:0001583	missense	23262	exon23			ATACACAGGAAGT	AB007893	CCDS34207.1, CCDS64212.1, CCDS75283.1	5q21.1	2014-05-06	2010-01-26	2010-01-26	ENSG00000145725	ENSG00000145725	2.7.4.24		29035	protein-coding gene	gene with protein product		611648	"histidine acid phosphatase domain containing 1"	HISPPD1		9455477, 17690096, 18981179	Standard	NM_001276277		Approved	KIAA0433, VIP2	uc003koe.4	O43314	OTTHUMG00000181461	ENST00000358359.3:c.2878A>T	chr5.hg19:g.102515845A>T	ENSP00000351126:p.Arg960Trp	73.0	0.0		113.0	26.0	NM_015216	A1NI53|A6NGS8|Q8TB50	Missense_Mutation	SNP	ENST00000358359.3	hg19		.	.	.	.	.	.	.	.	.	.	A	23.4	4.406314	0.83230	.	.	ENSG00000145725	ENST00000321521;ENST00000358359;ENST00000451606;ENST00000414217;ENST00000509597	T;T;T;T	0.26373	2.31;2.3;2.31;1.74	5.98	5.98	0.97165	.	0.062501	0.64402	D	0.000004	T	0.47801	0.1465	M	0.69358	2.11	0.45129	D	0.99814	D;D;D	0.60160	0.987;0.957;0.984	P;P;P	0.62885	0.877;0.908;0.901	T	0.47911	-0.9080	10	0.87932	D	0	.	15.0407	0.71788	1.0:0.0:0.0:0.0	.	975;960;960	E9PGM8;O43314-2;O43314	.;.;VIP2_HUMAN	W	960;960;975;960;234	ENSP00000313070:R960W;ENSP00000351126:R960W;ENSP00000416016:R960W;ENSP00000424948:R234W	ENSP00000313070:R960W	R	+	1	2	PPIP5K2	102543744	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.839000	0.55835	2.289000	0.77006	0.482000	0.46254	AGG	.	.		0.323	PPIP5K2-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000370487.1	NM_015216		T	102515845	A	T	102515845	3	4	290	1	0	0	0	0	1	0	0	0	12345	179	7	4	2968	4	PPIP5K2	5	102515845	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	27534619	102515845	78399415	63	42525										
DMXL1	1657	hgsc.bcm.edu	37	chr5	118407346	118407346	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	gcagcattggcgaccagcgcTtcacggtgagtgagggaggc	17	10	1	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr5:118407346T>G	ENST00000311085.8	+	1	162	c.82T>G	c.(82-84)Ttc>Gtc	p.F28V	CTB-161M19.4_ENST00000510128.1_RNA|CTB-161M19.4_ENST00000504820.1_RNA|DMXL1_ENST00000539542.1_Missense_Mutation_p.F28V|snoU13_ENST00000458753.1_RNA	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	28										breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		CGACCAGCGCTTCACGGTGAG	0.687																																					p.F28V		Atlas-SNP	.											.	DMXL1	268	.	0			c.T82G						.						44	35	38					5																	118407346		2193	4293	6486	SO:0001583	missense	1657	exon1			CAGCGCTTCACGG	AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"WD repeat domain containing"	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.82T>G	chr5.hg19:g.118407346T>G	ENSP00000309690:p.Phe28Val	62.0	0.0		94.0	18.0	NM_005509		Missense_Mutation	SNP	ENST00000311085.8	hg19	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	T	17.59	3.428424	0.62844	.	.	ENSG00000172869	ENST00000503802;ENST00000311085;ENST00000539542	T;T;T	0.12879	2.82;2.64;2.82	4.46	4.46	0.54185	WD40 repeat-like-containing domain (1);	0.054402	0.64402	D	0.000001	T	0.21103	0.0508	M	0.79693	2.465	0.44227	D	0.997069	B;B	0.09022	0.002;0.001	B;B	0.18263	0.021;0.005	T	0.03630	-1.1018	10	0.52906	T	0.07	-9.652	13.0056	0.58703	0.0:0.0:0.0:1.0	.	28;28	F5H269;Q9Y485	.;DMXL1_HUMAN	V	28	ENSP00000427692:F28V;ENSP00000309690:F28V;ENSP00000439479:F28V	ENSP00000309690:F28V	F	+	1	0	DMXL1	118435245	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.351000	0.44071	1.768000	0.52137	0.459000	0.35465	TTC	.	.		0.687	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		G	118407346	T	G	118407346	3	3	290	1	0	0	0	0	1	0	0	0	4596	1609	56	5	84	5	DMXL1	5	118407346	Missense_Mutation	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	15891501	118407346	62507914	64	42526										
TGFBI	7045	hgsc.bcm.edu	37	chr5	135388630	135388630	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	cacatcttgaagtcagctatGtgtgctgaagccatcgttgc	10	10	2	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr5:135388630G>C	ENST00000442011.2	+	8	1109	c.948G>C	c.(946-948)atG>atC	p.M316I	TGFBI_ENST00000305126.8_Missense_Mutation_p.M316I	NM_000358.2	NP_000349.1	Q15582	BGH3_HUMAN	transforming growth factor, beta-induced, 68kDa	316	FAS1 2. {ECO:0000255|PROSITE- ProRule:PRU00082}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|chondrocyte differentiation (GO:0002062)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	collagen binding (GO:0005518)|extracellular matrix binding (GO:0050840)|integrin binding (GO:0005178)			breast(6)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			AGTCAGCTATGTGTGCTGAAG	0.572																																					p.M316I		Atlas-SNP	.											.	TGFBI	76	.	0			c.G948C						.						69	77	74					5																	135388630		2147	4245	6392	SO:0001583	missense	7045	exon8			AGCTATGTGTGCT	M77349	CCDS47266.1	5q31	2008-02-05	2002-08-29		ENSG00000120708	ENSG00000120708			11771	protein-coding gene	gene with protein product		601692	"transforming growth factor, beta-induced, 68kD"	CSD3, LCD1, CSD1, CSD2		9463327	Standard	NM_000358		Approved	BIGH3, CDB1, CDGG1	uc003lbf.4	Q15582	OTTHUMG00000163213	ENST00000442011.2:c.948G>C	chr5.hg19:g.135388630G>C	ENSP00000416330:p.Met316Ile	100.0	0.0		148.0	48.0	NM_000358	D3DQB1|O14471|O14472|O14476|O43216|O43217|O43218|O43219|Q53XM1	Missense_Mutation	SNP	ENST00000442011.2	hg19	CCDS47266.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.07|16.07	3.017612|3.017612	0.54576|0.54576	.|.	.|.	ENSG00000120708|ENSG00000120708	ENST00000442011;ENST00000398813;ENST00000305126|ENST00000514554	D;D|.	0.90788|.	-2.73;-2.73|.	5.65|5.65	5.65|5.65	0.86999|0.86999	FAS1 domain (5);|.	0.218491|.	0.56097|.	D|.	0.000027|.	T|T	0.45256|0.45256	0.1333|0.1333	N|N	0.04655|0.04655	-0.195|-0.195	0.44985|0.44985	D|D	0.998|0.998	P;P|.	0.45212|.	0.853;0.807|.	P;P|.	0.47376|.	0.545;0.475|.	T|T	0.40776|0.40776	-0.9545|-0.9545	10|5	0.20519|.	T|.	0.43|.	-12.9086|-12.9086	20.073|20.073	0.97731|0.97731	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	49;316|.	B9ZVW9;Q15582|.	.;BGH3_HUMAN|.	I|L	316;49;316|34	ENSP00000416330:M316I;ENSP00000306306:M316I|.	ENSP00000306306:M316I|.	M|V	+|+	3|1	0|0	TGFBI|TGFBI	135416529|135416529	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.862000|0.862000	0.49288|0.49288	4.670000|4.670000	0.61583|0.61583	2.811000|2.811000	0.96726|0.96726	0.655000|0.655000	0.94253|0.94253	ATG|GTG	.	.		0.572	TGFBI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372108.1			C	135388630	G	C	135388630	3	2	290	1	0	0	0	0	1	0	0	0	15835	1377	48	4	978	4	TGFBI	5	135388630	Missense_Mutation	SNP	G	TCGA-G3-A7M5-01A-11D-A33Q-10	16981284	135388630	45526630	65	42527										
ANKHD1	54882	hgsc.bcm.edu	37	chr5	139838859	139838859	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	ttattaaggcaggggctgatAtagaacttggctgctccaca	11	8	0	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr5:139838859A>G	ENST00000360839.2	+	9	1745	c.1591A>G	c.(1591-1593)Ata>Gta	p.I531V	ANKHD1_ENST00000394722.3_Missense_Mutation_p.I520V|ANKHD1_ENST00000394723.3_Missense_Mutation_p.I531V|ANKHD1-EIF4EBP3_ENST00000532219.1_Missense_Mutation_p.I531V|ANKHD1_ENST00000297183.6_Missense_Mutation_p.I531V	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	531						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGGGCTGATATAGAACTTGG	0.453																																					p.I531V		Atlas-SNP	.											.	ANKHD1	233	.	0			c.A1591G						.						91	94	93					5																	139838859		2203	4300	6503	SO:0001583	missense	54882	exon9			GCTGATATAGAAC	AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503		"Ankyrin repeat domain containing"	24714	protein-coding gene	gene with protein product		610500				10470851, 11230166, 16098192	Standard	NM_017747		Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.1591A>G	chr5.hg19:g.139838859A>G	ENSP00000354085:p.Ile531Val	100.0	0.0		138.0	42.0	NM_024668	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Missense_Mutation	SNP	ENST00000360839.2	hg19	CCDS4225.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.80|14.80	2.643079|2.643079	0.47153|0.47153	.|.	.|.	ENSG00000131503|ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000254996	ENST00000246149|ENST00000360839;ENST00000422011;ENST00000297183;ENST00000253810;ENST00000310356;ENST00000421134;ENST00000394723;ENST00000394722;ENST00000532219	.|T;T;T;T;T;T	.|0.62788	.|0.02;0.02;0.0;0.0;0.0;0.02	5.51|5.51	5.51|5.51	0.81932|0.81932	.|Ankyrin repeat-containing domain (4);	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.54967|0.54967	0.1891|0.1891	N|N	0.13299|0.13299	0.325|0.325	0.58432|0.58432	D|D	0.999994|0.999994	.|B;P;P;B;B	.|0.47677	.|0.296;0.899;0.777;0.35;0.424	.|B;P;P;B;B	.|0.51101	.|0.101;0.659;0.566;0.101;0.263	T|T	0.53070|0.53070	-0.8490|-0.8490	6|10	.|0.21014	.|T	.|0.42	.|.	15.6258|15.6258	0.76855|0.76855	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|531;531;531;520;531	.|Q8IWZ3-5;Q8IWZ2;Q8IWZ3;Q8IWZ3-3;Q8IWZ3-2	.|.;.;ANKH1_HUMAN;.;.	M|V	6|531;545;531;531;46;531;531;520;531	.|ENSP00000354085:I531V;ENSP00000297183:I531V;ENSP00000394489:I531V;ENSP00000378212:I531V;ENSP00000378211:I520V;ENSP00000432016:I531V	.|ENSP00000432016:I531V	I|I	+|+	3|1	3|0	ANKHD1|ANKHD1-EIF4EBP3;ANKHD1	139819043|139819043	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	5.890000|5.890000	0.69774|0.69774	2.105000|2.105000	0.64084|0.64084	0.454000|0.454000	0.30748|0.30748	ATA|ATA	.	.		0.453	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747		G	139838859	A	G	139838859	3	3	290	1	0	0	0	0	1	0	0	0	628	449	16	2	1625	2	ANKHD1	5	139838859	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	4450229	139838859	41076401	66	42528										
AFAP1L1	134265	hgsc.bcm.edu	37	chr5	148682070	148682070	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	ctgggacccggcaagtcgccTgagtacatcagctcccacag	11	15	1	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr5:148682070T>C	ENST00000296721.4	+	5	515	c.417T>C	c.(415-417)ccT>ccC	p.P139P	AFAP1L1_ENST00000515000.1_Silent_p.P139P|AFAP1L1_ENST00000522492.1_3'UTR	NM_001146337.1|NM_152406.2	NP_001139809.1|NP_689619.1	Q8TED9	AF1L1_HUMAN	actin filament associated protein 1-like 1	139						cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(10)|ovary(1)|pancreas(1)|skin(2)	26			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCAAGTCGCCTGAGTACATCA	0.597																																					p.P139P		Atlas-SNP	.											.	AFAP1L1	86	.	0			c.T417C						.						27	24	25					5																	148682070		2202	4294	6496	SO:0001819	synonymous_variant	134265	exon5			GTCGCCTGAGTAC	AK094067	CCDS34274.1, CCDS54932.1	5q33.1	2013-01-10			ENSG00000157510	ENSG00000157510		"Pleckstrin homology (PH) domain containing"	26714	protein-coding gene	gene with protein product		614410					Standard	NM_152406		Approved	FLJ36748	uc003lqh.3	Q8TED9	OTTHUMG00000163441	ENST00000296721.4:c.417T>C	chr5.hg19:g.148682070T>C		51.0	0.0		59.0	17.0	NM_001146337	Q08AN4|Q08AN5|Q8IW82|Q8N8Z5|Q8N9Q4	Silent	SNP	ENST00000296721.4	hg19	CCDS34274.1																																																																																			.	.		0.597	AFAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373443.1	NM_152406		C	148682070	T	C	148682070	2	2	290	1	0	0	0	0	0	0	0	1	354	1567	55	2		2	AFAP1L1	5	148682070	Silent	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	8843211	148682070	32233190	67	42529										
FAT2	2196	hgsc.bcm.edu	37	chr5	150946663	150946663	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	ccggagaaatgatttagatcAaaatactctagttcattgcc	7	8	3	3			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr5:150946663A>T	ENST00000261800.5	-	1	1842	c.1830T>A	c.(1828-1830)ttT>ttA	p.F610L		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	610	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GATTTAGATCAAAATACTCTA	0.418																																					p.F610L		Atlas-SNP	.											.	FAT2	465	.	0			c.T1830A						.						104	106	106					5																	150946663		2203	4300	6503	SO:0001583	missense	2196	exon1			TAGATCAAAATAC	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.1830T>A	chr5.hg19:g.150946663A>T	ENSP00000261800:p.Phe610Leu	88.0	0.0		126.0	42.0	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	hg19	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	A	14.23	2.474515	0.43942	.	.	ENSG00000086570	ENST00000261800	T	0.70749	-0.51	5.75	-1.01	0.10169	Cadherin (4);Cadherin-like (1);	0.087556	0.49916	D	0.000121	D	0.82962	0.5151	M	0.88704	2.975	0.47341	D	0.999396	D	0.76494	0.999	D	0.83275	0.996	T	0.81549	-0.0882	10	0.72032	D	0.01	.	10.008	0.41968	0.6136:0.0:0.3864:0.0	.	610	Q9NYQ8	FAT2_HUMAN	L	610	ENSP00000261800:F610L	ENSP00000261800:F610L	F	-	3	2	FAT2	150926856	0.932000	0.31603	0.035000	0.18076	0.475000	0.33008	1.745000	0.38278	-0.408000	0.07565	-0.250000	0.11733	TTT	.	.		0.418	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		T	150946663	A	T	150946663	3	4	290	1	0	0	0	0	1	0	0	0	5698	127	5	4	11311	4	FAT2	5	150946663	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	2264593	150946663	29968597	68	42530										
CYFIP2	26999	hgsc.bcm.edu	37	chr5	156816275	156816275	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tgtccatgttcgaggtcatcCtgacccgcattcggagctac	10	13	1	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr5:156816275C>T	ENST00000521420.1	+	28	3299	c.3208C>T	c.(3208-3210)Ctg>Ttg	p.L1070L	CYFIP2_ENST00000442283.2_3'UTR|CYFIP2_ENST00000347377.6_Silent_p.L1096L|CYFIP2_ENST00000318218.6_Silent_p.L1121L|CYFIP2_ENST00000541131.1_Silent_p.L1021L|CYFIP2_ENST00000377576.3_Silent_p.L1096L|CYFIP2_ENST00000522463.1_Silent_p.L900L|CYFIP2_ENST00000435847.2_Silent_p.L795L					cytoplasmic FMR1 interacting protein 2											breast(1)|endometrium(12)|kidney(2)|lung(23)	38	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CGAGGTCATCCTGACCCGCAT	0.617																																					p.L1096L		Atlas-SNP	.											.	CYFIP2	354	.	0			c.C3286T						.						69	78	75					5																	156816275		2190	4289	6479	SO:0001819	synonymous_variant	26999	exon29			GTCATCCTGACCC	AF160973	CCDS75364.1	5q34	2008-07-18				ENSG00000055163			13760	protein-coding gene	gene with protein product	"p53 inducible protein"	606323				11438699	Standard	NM_001037333		Approved	PIR121	uc021ygm.1	Q96F07		ENST00000521420.1:c.3208C>T	chr5.hg19:g.156816275C>T		61.0	0.0		96.0	57.0	NM_001037332		Silent	SNP	ENST00000521420.1	hg19																																																																																				.	.		0.617	CYFIP2-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000373710.1	NM_001037332		T	156816275	C	T	156816275	2	4	290	1	0	0	0	0	0	0	0	1	4140	680	24	3		3	CYFIP2	5	156816275	Silent	SNP	C	TCGA-G3-A7M5-01A-11D-A33Q-10	5869612	156816275	24098985	69	42531										
JARID2	3720	hgsc.bcm.edu	37	chr6	15496721	15496722	+	Frame_Shift_Ins	INS	-	-	G													0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	aagtcatgcactaaggaggtINSgggggggcggcagctgcggg					rs554145993		TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr6:15496721_15496722insG	ENST00000341776.2	+	7	1509_1510	c.1265_1266insG	c.(1264-1269)gtggggfs	p.VG422fs	JARID2_ENST00000541660.1_Frame_Shift_Ins_p.VG384fs|JARID2_ENST00000397311.3_Frame_Shift_Ins_p.VG250fs	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	422					central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	59	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				ACTAAGGAGGTGGGGGGGCGGC	0.668																																					p.V422fs		Atlas-INDEL	.											.,1	JARID2	135	.	0			c.1265_1266insG						.																																			SO:0001589	frameshift_variant	3720	exon7			.	U57592	CCDS4533.1, CCDS58996.1	6p24-p23	2008-02-05	2006-10-06	2004-01-30	ENSG00000008083	ENSG00000008083			6196	protein-coding gene	gene with protein product		601594	"jumonji (mouse) homolog", "Jumonji, AT rich interactive domain 2"	JMJ		8894700	Standard	NM_001267040		Approved		uc003nbj.4	Q92833	OTTHUMG00000014293	ENST00000341776.2:c.1272dupG	chr6.hg19:g.15496728_15496728dupG	ENSP00000341280:p.Val422fs	58.0	0.0		75.0	11.0	NM_004973	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Frame_Shift_Ins	INS	ENST00000341776.2	hg19	CCDS4533.1																																																																																			.	.		0.668	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973		G	15496722	-	G	15496721	7	5	290	1	0	1	1	0	0	0	0	0	7954	1696	59	0	1291	0	JARID2	6	15496721	Frame_Shift_Ins	INS	-	TCGA-G3-A7M5-01A-11D-A33Q-10		15496721	155618346	70	42532										
KIF13A	63971	hgsc.bcm.edu	37	chr6	17794911	17794911	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	aatatggagatccacatttcTattcttcgcgttacttcatt	5	9	3	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr6:17794911T>A	ENST00000259711.6	-	24	3072	c.2967A>T	c.(2965-2967)atA>atT	p.I989I	KIF13A_ENST00000378843.2_Silent_p.I989I|KIF13A_ENST00000378814.5_Silent_p.I989I|KIF13A_ENST00000378816.5_Silent_p.I989I|KIF13A_ENST00000378826.2_Silent_p.I989I	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	989					ATP catabolic process (GO:0006200)|cargo loading into vesicle (GO:0035459)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|Golgi to plasma membrane protein transport (GO:0043001)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)	centrosome (GO:0005813)|endosome membrane (GO:0010008)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|trans-Golgi network membrane (GO:0032588)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	64	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			TCCACATTTCTATTCTTCGCG	0.418																																					p.I989I		Atlas-SNP	.											.	KIF13A	276	.	0			c.A2967T						.						102	99	100					6																	17794911		1960	4150	6110	SO:0001819	synonymous_variant	63971	exon24			CATTTCTATTCTT	AJ291578	CCDS47380.1, CCDS47381.1, CCDS54967.1, CCDS54968.1, CCDS58998.1	6p23	2008-10-21			ENSG00000137177	ENSG00000137177		"Kinesins"	14566	protein-coding gene	gene with protein product		605433				11106728	Standard	NM_022113		Approved	bA500C11.2	uc003ncg.4	Q9H1H9	OTTHUMG00000014313	ENST00000259711.6:c.2967A>T	chr6.hg19:g.17794911T>A		43.0	0.0		83.0	31.0	NM_001105567	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Silent	SNP	ENST00000259711.6	hg19	CCDS47381.1	.	.	.	.	.	.	.	.	.	.	T	12.17	1.858692	0.32791	.	.	ENSG00000137177	ENST00000358380	.	.	.	5.45	-2.51	0.06365	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.7765	0.29041	0.2149:0.0:0.3669:0.4183	.	.	.	.	L	383	.	.	X	-	2	0	KIF13A	17902890	1.000000	0.71417	0.950000	0.38849	0.992000	0.81027	0.553000	0.23391	-0.183000	0.10585	0.533000	0.62120	TAG	.	.		0.418	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4			A	17794911	T	A	17794911	2	1	290	1	0	0	0	0	0	0	0	1	8283	1512	53	4		4	KIF13A	6	17794911	Silent	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	2298190	17794911	153320156	71	42533										
HLA-DPB1	3115	hgsc.bcm.edu	37	chr6	33053994	33054040	+	Stop_Codon_Del	DEL	TTATATAACCTTTCGTCTTTCATTTCAGTTCAACGAGGATCTGCATA	TTATATAACCTTTCGTCTTTCATTTCAGTTCAACGAGGATCTGCATA	-													0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	aacctttcgtctttcatttcAgttcaacgaggatctgcata					rs201552902|rs150818884|rs67523850	byFrequency	TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	TTATATAACCTTTCGTCTTTCATTTCAGTTCAACGAGGATCTGCATA	TTATATAACCTTTCGTCTTTCATTTCAGTTCAACGAGGATCTGCATA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr6:33053994_33054040delTTATATAACCTTTCGTCTTTCATTTCAGTTCAACGAGGATCTGCATA	ENST00000418931.2	+	0	873_897					NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)	p.R255P(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						CTTTCATTTCAGTTCAACGAGGATCTGCATAAACAGGTAATATTCCTGCTTTGATTTCCTTGTGGGG	0.429																																					p.253_259del		Pindel	.											.	HLA-DPB1	28	.	1	Substitution - Missense(1)	cervix(1)	c.758_775del						.																																			SO:0001567	stop_retained_variant	3115	exon5			.		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	Exception_encountered	chr6.hg19:g.33053994_33054040delTTATATAACCTTTCGTCTTTCATTTCAGTTCAACGAGGATCTGCATA		59.0	0.0		76.0	10.0	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	In_Frame_Del	DEL	ENST00000418931.2	hg19	CCDS4765.1																																																																																			.	.		0.429	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121		-	33054040	TTATATAACCTTTCGTCTTTCATTTCAGTTCAACGAGGATCTGCATA	-	33053994	7	5	290	1	0	1	0	1	0	0	0	0	7212	202	7	0	774	0	HLA-DPB1	6	33053994	Stop_Codon_Del	DEL	TTATATAACCTTTCGTCTTTCATTTCAGTTCAACGAGGATCTGCATA	TCGA-G3-A7M5-01A-11D-A33Q-10	15259083	33053994	138061073	72	42534										
ITPR3	3710	hgsc.bcm.edu	37	chr6	33643557	33643557	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	caccatgcacgactatgcgcCgctggtctcgggtgccctgc	12	16	1	0			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr6:33643557C>T	ENST00000374316.5	+	26	4266	c.3206C>T	c.(3205-3207)cCg>cTg	p.P1069L	ITPR3_ENST00000605930.1_Missense_Mutation_p.P1069L			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	1069					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	GACTATGCGCCGCTGGTCTCG	0.642																																					p.P1069L		Atlas-SNP	.											.	ITPR3	409	.	0			c.C3206T						.						40	31	34					6																	33643557		2203	4300	6503	SO:0001583	missense	3710	exon25			ATGCGCCGCTGGT	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"Ion channels / Inositol triphosphate receptors"	6182	protein-coding gene	gene with protein product		147267	"inositol 1,4,5-triphosphate receptor, type 3"			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.3206C>T	chr6.hg19:g.33643557C>T	ENSP00000363435:p.Pro1069Leu	93.0	0.0		111.0	34.0	NM_002224	Q14649|Q5TAQ2	Missense_Mutation	SNP	ENST00000374316.5	hg19	CCDS4783.1	.	.	.	.	.	.	.	.	.	.	C	15.01	2.706114	0.48412	.	.	ENSG00000096433	ENST00000374316	D	0.92647	-3.08	5.67	4.79	0.61399	.	0.249581	0.41194	N	0.000936	D	0.90000	0.6878	M	0.83774	2.66	0.80722	D	1	B	0.21071	0.051	B	0.19391	0.025	D	0.89456	0.3733	10	0.87932	D	0	-39.1943	14.9016	0.70684	0.0:0.9304:0.0:0.0696	.	1069	Q14573	ITPR3_HUMAN	L	1069	ENSP00000363435:P1069L	ENSP00000363435:P1069L	P	+	2	0	ITPR3	33751535	1.000000	0.71417	0.374000	0.26016	0.183000	0.23260	6.082000	0.71318	2.697000	0.92050	0.655000	0.94253	CCG	.	.		0.642	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224		T	33643557	C	T	33643557	3	4	290	1	0	0	0	0	1	0	0	0	7931	652	23	1	3304	1	ITPR3	6	33643557	Missense_Mutation	SNP	C	TCGA-G3-A7M5-01A-11D-A33Q-10	589563	33643557	137471510	73	42535										
KLHDC3	116138	hgsc.bcm.edu	37	chr6	42986094	42986094	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tgcccagggcagccctgcacGctggagggacttccactcag	13	15	1	0			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr6:42986094G>A	ENST00000326974.4	+	6	728	c.533G>A	c.(532-534)cGc>cAc	p.R178H	KLHDC3_ENST00000244670.8_Missense_Mutation_p.R44H|KLHDC3_ENST00000332245.8_Missense_Mutation_p.R119H	NM_057161.3	NP_476502.1	Q9BQ90	KLDC3_HUMAN	kelch domain containing 3	178					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|reciprocal meiotic recombination (GO:0007131)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)	chromatin binding (GO:0003682)			cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9			Colorectal(64;0.00237)|all cancers(41;0.0034)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0539)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			AGCCCTGCACGCTGGAGGGAC	0.552																																					p.R178H		Atlas-SNP	.											.	KLHDC3	23	.	0			c.G533A						.						40	35	37					6																	42986094		2203	4300	6503	SO:0001583	missense	116138	exon6			CTGCACGCTGGAG	AB055925	CCDS4880.1	6p21.1	2003-06-12			ENSG00000124702	ENSG00000124702			20704	protein-coding gene	gene with protein product		611248				12444059, 12606021	Standard	NM_057161		Approved	PEAS, hPeas, dJ20C7.3	uc003otl.3	Q9BQ90	OTTHUMG00000014714	ENST00000326974.4:c.533G>A	chr6.hg19:g.42986094G>A	ENSP00000313995:p.Arg178His	47.0	0.0		60.0	32.0	NM_057161	A8K2W9	Missense_Mutation	SNP	ENST00000326974.4	hg19	CCDS4880.1	.	.	.	.	.	.	.	.	.	.	G	16.52	3.146365	0.57044	.	.	ENSG00000124702	ENST00000326974;ENST00000432243;ENST00000244670;ENST00000394096;ENST00000426116;ENST00000332245	T;T;T	0.67171	-0.25;-0.25;-0.25	5.64	4.77	0.60923	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.56232	0.1971	L	0.49640	1.575	0.80722	D	1	P;P;P;D	0.64830	0.603;0.593;0.765;0.994	B;B;B;P	0.52856	0.063;0.045;0.147;0.711	T	0.56774	-0.7923	10	0.13853	T	0.58	.	14.4033	0.67065	0.0709:0.0:0.9291:0.0	.	178;119;44;178	E7ENU0;E7ERR0;F8W6A4;Q9BQ90	.;.;.;KLDC3_HUMAN	H	178;178;44;178;151;119	ENSP00000313995:R178H;ENSP00000244670:R44H;ENSP00000331562:R119H	ENSP00000244670:R44H	R	+	2	0	KLHDC3	43094072	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	9.102000	0.94226	1.394000	0.46624	0.561000	0.74099	CGC	.	.		0.552	KLHDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040570.1	NM_057161		A	42986094	G	A	42986094	3	1	290	1	0	0	0	0	1	0	0	0	8366	1087	38	1	551	1	KLHDC3	6	42986094	Missense_Mutation	SNP	G	TCGA-G3-A7M5-01A-11D-A33Q-10	9342537	42986094	128128973	74	42536										
GRM1	2911	hgsc.bcm.edu	37	chr6	146720714	146720714	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	ccaagcctgagaggaatgtcCgcagtgccttcaccacctct	9	15	2	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr6:146720714C>G	ENST00000282753.1	+	7	2774	c.2539C>G	c.(2539-2541)Cgc>Ggc	p.R847G	GRM1_ENST00000492807.2_Missense_Mutation_p.R847G|GRM1_ENST00000355289.4_Missense_Mutation_p.R847G|GRM1_ENST00000507907.1_Missense_Mutation_p.R847G|GRM1_ENST00000392299.2_Missense_Mutation_p.R847G|GRM1_ENST00000361719.2_Missense_Mutation_p.R847G			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	847					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		GAGGAATGTCCGCAGTGCCTT	0.512																																					p.R847G		Atlas-SNP	.											.	GRM1	419	.	0			c.C2539G						.						106	87	93					6																	146720714		2203	4300	6503	SO:0001583	missense	2911	exon8			AATGTCCGCAGTG	U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4593	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 85"	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	ENST00000282753.1:c.2539C>G	chr6.hg19:g.146720714C>G	ENSP00000282753:p.Arg847Gly	94.0	0.0		49.0	37.0	NM_000838	B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Missense_Mutation	SNP	ENST00000282753.1	hg19	CCDS5209.1	.	.	.	.	.	.	.	.	.	.	C	19.78	3.891888	0.72524	.	.	ENSG00000152822	ENST00000361719;ENST00000392299;ENST00000492807;ENST00000282753;ENST00000355289;ENST00000507907	D;D;D;D;D;D	0.89415	-2.48;-2.51;-2.51;-2.48;-2.51;-2.51	5.68	5.68	0.88126	GPCR, family 3, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.94453	0.8215	M	0.81341	2.54	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;0.997;1.0	D	0.94259	0.7500	10	0.66056	D	0.02	.	19.7753	0.96389	0.0:1.0:0.0:0.0	.	847;847;847	F8W805;Q13255;Q13255-2	.;GRM1_HUMAN;.	G	847	ENSP00000354896:R847G;ENSP00000376119:R847G;ENSP00000424095:R847G;ENSP00000282753:R847G;ENSP00000347437:R847G;ENSP00000425599:R847G	ENSP00000282753:R847G	R	+	1	0	GRM1	146762407	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.686000	0.91538	0.585000	0.79938	CGC	.	.		0.512	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838		G	146720714	C	G	146720714	3	3	290	1	0	0	0	0	1	0	0	0	6805	652	23	4	2565	4	GRM1	6	146720714	Missense_Mutation	SNP	C	TCGA-G3-A7M5-01A-11D-A33Q-10	103734620	146720714	24394353	75	42537										
TMEM184A	202915	hgsc.bcm.edu	37	chr7	1586662	1586663	+	In_Frame_Ins	INS	-	-	GCC													0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	ctcccgccggagccgccgctINSggggtgggtgccgggcctgg					rs3837151|rs3779607	byFrequency	TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr7:1586662_1586663insGCC	ENST00000297477.5	-	9	1483_1484	c.1167_1168insGGC	c.(1165-1170)cccagc>cccGGCagc	p.389_390PS>PGS	TMEM184A_ENST00000449955.1_5'Flank	NM_001097620.1	NP_001091089.1	Q6ZMB5	T184A_HUMAN	transmembrane protein 184A	389			S -> G (in dbSNP:rs3779607). {ECO:0000269|PubMed:15489334}.		germ-line sex determination (GO:0018992)|regulation of protein localization (GO:0032880)|regulation of secretion (GO:0051046)	early endosome membrane (GO:0031901)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	12		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;5.88e-15)		GAGCCGCCGCTGGGGTGGGTGC	0.703																																					p.S390delinsGS		Atlas-INDEL	.											.,1	TMEM184A	35	.	0			c.1168_1169insGGC						.			1912,2170		535,842,664						-3.6	0		dbSNP_132	17	3872,4214		1028,1816,1199	no	coding	TMEM184A	NM_001097620.1		1563,2658,1863	A1A1,A1R,RR		47.8852,46.8398,47.5345				5784,6384				SO:0001652	inframe_insertion	202915	exon9			.		CCDS43537.1	7p22.3	2008-05-02			ENSG00000164855	ENSG00000164855			28797	protein-coding gene	gene with protein product						12477932	Standard	NM_001097620		Approved	MGC9712	uc003skv.4	Q6ZMB5	OTTHUMG00000119025	ENST00000297477.5:c.1167_1168insGGC	chr7.hg19:g.1586662_1586663insGCC	ENSP00000297477:p.Pro389_Ser390insGly	10.0	0.0		18.0	11.0	NM_001097620	Q8TBQ6	In_Frame_Ins	INS	ENST00000297477.5	hg19	CCDS43537.1																																																																																			.	.		0.703	TMEM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239229.4	NM_152689		GCC	1586663	-	GCC	1586662	7	5	290	1	0	1	1	0	0	0	0	0	16119	1580	55	0	77	0	TMEM184A	7	1586662	In_Frame_Ins	INS	-	TCGA-G3-A7M5-01A-11D-A33Q-10		1586662	157552001	76	42538										
PDE1C	5137	hgsc.bcm.edu	37	chr7	31855598	31855599	+	Frame_Shift_Del	DEL	CA	CA	-													0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	gtttttcccacgagggttgtCacttttgtttgcccgtgttc							TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr7:31855598_31855599delCA	ENST00000396191.1	-	15	2207_2208	c.1752_1753delTG	c.(1750-1755)agtgacfs	p.SD584fs	PDE1C_ENST00000321453.7_Frame_Shift_Del_p.SD584fs|PDE1C_ENST00000396193.1_Frame_Shift_Del_p.SD644fs|PDE1C_ENST00000479980.1_5'UTR|PDE1C_ENST00000396182.2_Frame_Shift_Del_p.SD584fs|PDE1C_ENST00000396184.3_Frame_Shift_Del_p.SD584fs	NM_001191057.1	NP_001177986.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	584					activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)	cytosol (GO:0005829)	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	81			GBM - Glioblastoma multiforme(11;0.216)		Caffeine(DB00201)	CGAGGGTTGTCACTTTTGTTTG	0.48																																					p.645_645del		Atlas-Indel,Pindel	.											.	PDE1C	465	.	0			c.1933_1934del						.																																			SO:0001589	frameshift_variant	5137	exon16			.	U40371	CCDS5437.1, CCDS55099.1, CCDS55100.1	7p15.1-p14.3	2008-05-15	2002-08-29		ENSG00000154678	ENSG00000154678	3.1.4.17	"Phosphodiesterases"	8776	protein-coding gene	gene with protein product		602987	"phosphodiesterase 1C, calmodulin-dependent (70kD)"			8557689	Standard	XM_005249769		Approved	Hcam3	uc003tco.2	Q14123	OTTHUMG00000023836	ENST00000396191.1:c.1752_1753delTG	chr7.hg19:g.31855598_31855599delCA	ENSP00000379494:p.Ser584fs	112.0	0.0		161.0	48.0	NM_001191058	B3KPC6|E9PE92|Q14124|Q8NB10	Frame_Shift_Del	DEL	ENST00000396191.1	hg19	CCDS55099.1																																																																																			.	.		0.48	PDE1C-006	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328458.1			-	31855599	CA	-	31855598	7	5	290	1	0	1	0	1	0	0	0	0	11644	826	29	0	163	0	PDE1C	7	31855598	Frame_Shift_Del	DEL	CA	TCGA-G3-A7M5-01A-11D-A33Q-10	30268936	31855598	127283065	77	42539										
ZNF479	90827	hgsc.bcm.edu	37	chr7	57194367	57194367	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	aattccgctgagcacaatccAggcattgccattcctccaga	7	14	0	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr7:57194367A>T	ENST00000331162.4	-	3	368	c.98T>A	c.(97-99)cTg>cAg	p.L33Q		NM_033273.1	NP_150376.1	Q96JC4	ZN479_HUMAN	zinc finger protein 479	33	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(53)|ovary(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	84			GBM - Glioblastoma multiforme(1;9.18e-12)			AGCACAATCCAGGCATTGCCA	0.408																																					p.L33Q		Atlas-SNP	.											.	ZNF479	193	.	0			c.T98A						.						59	60	60					7																	57194367		2181	4288	6469	SO:0001583	missense	90827	exon3			CAATCCAGGCATT	AF277624	CCDS43590.1	7p11.2	2013-01-08			ENSG00000185177	ENSG00000185177		"Zinc fingers, C2H2-type", "-"	23258	protein-coding gene	gene with protein product						11410164	Standard	NM_033273		Approved	KR19	uc010kzo.3	Q96JC4	OTTHUMG00000156682	ENST00000331162.4:c.98T>A	chr7.hg19:g.57194367A>T	ENSP00000333776:p.Leu33Gln	326.0	0.0		467.0	122.0	NM_033273		Missense_Mutation	SNP	ENST00000331162.4	hg19	CCDS43590.1	.	.	.	.	.	.	.	.	.	.	a	11.64	1.698177	0.30142	.	.	ENSG00000185177	ENST00000331162	T	0.19250	2.16	1.25	1.25	0.21368	Krueppel-associated box (4);	.	.	.	.	T	0.56906	0.2017	H	0.98068	4.14	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.44757	-0.9307	9	0.87932	D	0	.	6.2934	0.21073	1.0:0.0:0.0:0.0	.	33	Q96JC4	ZN479_HUMAN	Q	33	ENSP00000333776:L33Q	ENSP00000333776:L33Q	L	-	2	0	ZNF479	57198309	0.694000	0.27738	0.096000	0.21009	0.021000	0.10359	3.306000	0.51881	0.558000	0.29135	0.324000	0.21423	CTG	.	.		0.408	ZNF479-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345302.1	XM_291202		T	57194367	A	T	57194367	3	4	290	1	0	0	0	0	1	0	0	0	17948	188	7	4	1488	4	ZNF479	7	57194367	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	25338769	57194367	101944296	78	42540										
RABGEF1	27342	hgsc.bcm.edu	37	chr7	66270375	66270375	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	gagaggatggctactatttcAccaatctggtgagtaagtga	12	6	2	3			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr7:66270375A>T	ENST00000284957.5	+	8	1146	c.1069A>T	c.(1069-1071)Acc>Tcc	p.T357S	RABGEF1_ENST00000439720.2_Missense_Mutation_p.T370S|KCTD7_ENST00000510829.2_Missense_Mutation_p.T357S|KCTD7_ENST00000451741.2_Missense_Mutation_p.T357S|RABGEF1_ENST00000484547.2_3'UTR|RABGEF1_ENST00000450873.2_Missense_Mutation_p.T357S|KCTD7_ENST00000380828.2_Missense_Mutation_p.T397S|RABGEF1_ENST00000437078.2_Missense_Mutation_p.T371S			Q9UJ41	RABX5_HUMAN	RAB guanine nucleotide exchange factor (GEF) 1	574					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|protein targeting to membrane (GO:0006612)	early endosome (GO:0005769)	DNA binding (GO:0003677)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|stomach(1)	27						CTACTATTTCACCAATCTGGT	0.502																																					p.T357S		Atlas-SNP	.											.	RABGEF1	56	.	0			c.A1069T						.						85	75	78					7																	66270375		2203	4300	6503	SO:0001583	missense	27342	exon8			TATTTCACCAATC	AJ250042	CCDS5535.1, CCDS69308.1, CCDS75610.1	7q11.21	2010-07-09			ENSG00000154710	ENSG00000154710			17676	protein-coding gene	gene with protein product		609700				12505986, 11098082	Standard	NM_014504		Approved	rabex-5, RABEX5	uc003tvh.3	Q9UJ41	OTTHUMG00000129547	ENST00000284957.5:c.1069A>T	chr7.hg19:g.66270375A>T	ENSP00000284957:p.Thr357Ser	50.0	0.0		82.0	20.0	NM_014504	B4DZM7|Q3HKR2|Q3HKR3|Q53FG0	Missense_Mutation	SNP	ENST00000284957.5	hg19	CCDS5535.1	.	.	.	.	.	.	.	.	.	.	A	32	5.149651	0.94645	.	.	ENSG00000243335;ENSG00000243335;ENSG00000243335;ENSG00000243335;ENSG00000243335;ENSG00000154710;ENSG00000154710;ENSG00000154710;ENSG00000154710	ENST00000380827;ENST00000380828;ENST00000510829;ENST00000451741;ENST00000539561;ENST00000284957;ENST00000450873;ENST00000439720;ENST00000437078	T;T;T;T;T;T;T	0.39229	1.09;1.09;1.09;1.09;1.09;1.09;1.09	5.6	5.6	0.85130	Vacuolar sorting protein 9, subgroup (1);Vacuolar sorting protein 9 (2);	0.000000	0.85682	D	0.000000	T	0.61464	0.2349	M	0.72624	2.21	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.58233	-0.7672	10	0.17832	T	0.49	-20.5411	14.9658	0.71193	1.0:0.0:0.0:0.0	.	371;191;574	B4DZM7;B3KMF1;Q9UJ41	.;.;RABX5_HUMAN	S	441;397;357;357;273;357;357;370;371	ENSP00000370208:T397S;ENSP00000421124:T357S;ENSP00000398177:T357S;ENSP00000284957:T357S;ENSP00000415815:T357S;ENSP00000403429:T370S;ENSP00000390480:T371S	ENSP00000370207:T441S	T	+	1	0	RABGEF1;KCTD7	65907810	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.802000	0.91910	2.135000	0.66039	0.533000	0.62120	ACC	.	.		0.502	RABGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251737.3	NM_014504		T	66270375	A	T	66270375	3	4	290	1	0	0	0	0	1	0	0	0	12981	159	6	4	1095	4	RABGEF1	7	66270375	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	9076008	66270375	92868288	79	42541										
WBSCR17	64409	hgsc.bcm.edu	37	chr7	71142287	71142287	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tccgtgccatggctggggacCacaggtaggagctcgtctct	14	12	1	0			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr7:71142287C>A	ENST00000333538.5	+	9	2130	c.1496C>A	c.(1495-1497)cCa>cAa	p.P499Q	WBSCR17_ENST00000498380.2_3'UTR	NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17	499	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(5)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(7)|large_intestine(22)|lung(45)|ovary(2)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	100		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				GGCTGGGGACCACAGGTAGGA	0.532																																					p.P499Q		Atlas-SNP	.											.	WBSCR17	208	.	0			c.C1496A						.						151	149	150					7																	71142287		2203	4300	6503	SO:0001583	missense	64409	exon9			GGGGACCACAGGT	AF410457	CCDS5540.1	7q11.23	2014-03-13			ENSG00000185274	ENSG00000185274		"Glycosyltransferase family 2 domain containing"	16347	protein-coding gene	gene with protein product	"polypeptide N-acetylgalactosaminyltransferase-like 3", "polypeptide GalNAc transferase 3"	615137				12073013, 15744064, 22787146	Standard	NM_022479		Approved	GALNTL3, GalNAc-T5L	uc003tvy.4	Q6IS24	OTTHUMG00000129783	ENST00000333538.5:c.1496C>A	chr7.hg19:g.71142287C>A	ENSP00000329654:p.Pro499Gln	64.0	0.0		103.0	56.0	NM_022479	Q8NFV9|Q9NTA8	Missense_Mutation	SNP	ENST00000333538.5	hg19	CCDS5540.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.566464	0.86439	.	.	ENSG00000185274	ENST00000333538	T	0.25085	1.82	5.35	5.35	0.76521	Ricin B-related lectin (1);Ricin B lectin (3);	0.283398	0.27876	N	0.017499	T	0.48926	0.1527	L	0.58428	1.81	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.34004	-0.9846	10	0.49607	T	0.09	.	18.2305	0.89934	0.0:1.0:0.0:0.0	.	499	Q6IS24	GLTL3_HUMAN	Q	499	ENSP00000329654:P499Q	ENSP00000329654:P499Q	P	+	2	0	WBSCR17	70780223	1.000000	0.71417	0.973000	0.42090	0.897000	0.52465	7.203000	0.77864	2.779000	0.95612	0.650000	0.86243	CCA	.	.		0.532	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252006.1	NM_022479		A	71142287	C	A	71142287	3	1	290	1	0	0	0	0	1	0	0	0	17279	594	21	3	1530	3	WBSCR17	7	71142287	Missense_Mutation	SNP	C	TCGA-G3-A7M5-01A-11D-A33Q-10	4871912	71142287	87996376	80	42542										
COL1A2	1278	hgsc.bcm.edu	37	chr7	94029552	94029552	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	gatggtgaagatggtcccacAggccctcctggtccacctgg	13	13	0	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr7:94029552A>T	ENST00000297268.6	+	5	648	c.177A>T	c.(175-177)acA>acT	p.T59T		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	59			T -> P (in dbSNP:rs1800221). {ECO:0000269|PubMed:4011429}.		blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	ATGGTCCCACAGGCCCTCCTG	0.532										HNSCC(75;0.22)																											p.T59T		Atlas-SNP	.											.	COL1A2	240	.	0			c.A177T						.						94	92	92					7																	94029552		2203	4300	6503	SO:0001819	synonymous_variant	1278	exon5			TCCCACAGGCCCT	Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"Collagens"	2198	protein-coding gene	gene with protein product	"alpha 2(I)-collagen", "alpha-2 collagen type I", "type I procollagen", "collagen I, alpha-2 polypeptide", "collagen of skin, tendon and bone, alpha-2 chain"	120160	"osteogenesis imperfecta type IV"	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.177A>T	chr7.hg19:g.94029552A>T		81.0	0.0		123.0	67.0	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Silent	SNP	ENST00000297268.6	hg19	CCDS34682.1																																																																																			.	.		0.532	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089		T	94029552	A	T	94029552	2	4	290	1	0	0	0	0	0	0	0	1	3680	175	7	4		4	COL1A2	7	94029552	Silent	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	22887265	94029552	65109111	81	42543										
OR2F2	135948	hgsc.bcm.edu	37	chr7	143633139	143633139	+	Frame_Shift_Del	DEL	A	A	-													0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	gtccctcagtccttcaagagAagctgatctctgtcttctat							TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr7:143633139delA	ENST00000408955.2	+	1	881	c.814delA	c.(814-816)aagfs	p.K272fs		NM_001004685.1	NP_001004685.1	O95006	OR2F2_HUMAN	olfactory receptor, family 2, subfamily F, member 2	272						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(19)|ovary(3)|skin(2)|stomach(1)|urinary_tract(1)	32	Melanoma(164;0.0903)					CCTTCAAGAGAAGCTGATCTC	0.498																																					p.E271fs		Atlas-Indel,Pindel	.											.	OR2F2	63	.	0			c.813delG						.						100	102	101					7																	143633139		2197	4300	6497	SO:0001589	frameshift_variant	135948	exon1			.		CCDS43666.1	7q33-q35	2012-08-09			ENSG00000221910	ENSG00000221910		"GPCR / Class A : Olfactory receptors"	8247	protein-coding gene	gene with protein product							Standard	NM_001004685		Approved	OR7-1	uc011ktv.2	O95006	OTTHUMG00000157768	ENST00000408955.2:c.814delA	chr7.hg19:g.143633139delA	ENSP00000386222:p.Lys272fs	91.0	0.0		150.0	87.0	NM_001004685	A4D2G0|Q6IFP8	Frame_Shift_Del	DEL	ENST00000408955.2	hg19	CCDS43666.1																																																																																			.	.		0.498	OR2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349570.1			-	143633139	A	-	143633139	7	5	290	1	0	1	0	1	0	0	0	0	11006	247	9	0	816	0	OR2F2	7	143633139	Frame_Shift_Del	DEL	A	TCGA-G3-A7M5-01A-11D-A33Q-10	49603587	143633139	15505524	82	42544										
LRRC61	65999	hgsc.bcm.edu	37	chr7	150034126	150034126	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	cctgggcctggagtggctggAcctatcaggcaacgcgctca	14	13	2	0			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr7:150034126A>G	ENST00000359623.4	+	3	764	c.176A>G	c.(175-177)gAc>gGc	p.D59G	LRRC61_ENST00000493307.1_Missense_Mutation_p.D59G|LRRC61_ENST00000323078.7_Missense_Mutation_p.D59G	NM_001142928.1	NP_001136400.1	Q9BV99	LRC61_HUMAN	leucine rich repeat containing 61	59										endometrium(2)|large_intestine(1)|skin(1)|upper_aerodigestive_tract(1)	5			OV - Ovarian serous cystadenocarcinoma(82;0.011)			GAGTGGCTGGACCTATCAGGC	0.652																																					p.D59G		Atlas-SNP	.											.	LRRC61	17	.	0			c.A176G						.						67	57	60					7																	150034126		2201	4298	6499	SO:0001583	missense	65999	exon2			GGCTGGACCTATC	BC001354	CCDS5901.1	7q31-q35	2006-02-07			ENSG00000127399	ENSG00000127399			21704	protein-coding gene	gene with protein product							Standard	NM_023942		Approved	MGC3036, FLJ31392, HSPC295	uc003wgv.4	Q9BV99	OTTHUMG00000158326	ENST00000359623.4:c.176A>G	chr7.hg19:g.150034126A>G	ENSP00000352642:p.Asp59Gly	26.0	0.0		38.0	17.0	NM_023942	B3KUW0|D3DWY8	Missense_Mutation	SNP	ENST00000359623.4	hg19	CCDS5901.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.036052	0.75617	.	.	ENSG00000127399	ENST00000323078;ENST00000359623;ENST00000493307	T;T;T	0.11821	2.74;2.74;2.74	4.97	4.97	0.65823	.	0.000000	0.85682	D	0.000000	T	0.34250	0.0891	M	0.73217	2.22	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.04103	-1.0977	10	0.33141	T	0.24	-34.5686	12.6413	0.56711	1.0:0.0:0.0:0.0	.	59	Q9BV99	LRC61_HUMAN	G	59	ENSP00000339047:D59G;ENSP00000352642:D59G;ENSP00000420560:D59G	ENSP00000339047:D59G	D	+	2	0	LRRC61	149665059	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	6.318000	0.72866	1.878000	0.54408	0.454000	0.30748	GAC	.	.		0.652	LRRC61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350696.1	NM_023942		G	150034126	A	G	150034126	3	3	290	1	0	0	0	0	1	0	0	0	9026	275	10	2	178	2	LRRC61	7	150034126	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	6400987	150034126	9104537	83	42545										
KCNB2	9312	hgsc.bcm.edu	37	chr8	73480433	73480433	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	gaacgaagaactgaggcgagAggcagagactatgcgagagc	16	7	0	5			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr8:73480433A>T	ENST00000523207.1	+	2	1052	c.464A>T	c.(463-465)gAg>gTg	p.E155V		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	155					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.E155V(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	CTGAGGCGAGAGGCAGAGACT	0.453																																					p.E155V		Atlas-SNP	.											KCNB2,acral,malignant_melanoma,+1,1	KCNB2	228	.	1	Substitution - Missense(1)	prostate(1)	c.A464T						.						134	141	138					8																	73480433		2203	4300	6503	SO:0001583	missense	9312	exon2			GGCGAGAGGCAGA	U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.464A>T	chr8.hg19:g.73480433A>T	ENSP00000430846:p.Glu155Val	72.0	0.0		103.0	39.0	NM_004770	Q7Z7D0|Q9BXD3	Missense_Mutation	SNP	ENST00000523207.1	hg19	CCDS6209.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.419981	0.83559	.	.	ENSG00000182674	ENST00000523207	D	0.97752	-4.52	6.07	6.07	0.98685	.	0.000000	0.33813	U	0.004527	D	0.96716	0.8928	L	0.58101	1.795	0.80722	D	1	P	0.34462	0.454	B	0.37601	0.254	D	0.96476	0.9352	10	0.66056	D	0.02	.	16.3141	0.82909	1.0:0.0:0.0:0.0	.	155	Q92953	KCNB2_HUMAN	V	155	ENSP00000430846:E155V	ENSP00000430846:E155V	E	+	2	0	KCNB2	73642987	1.000000	0.71417	1.000000	0.80357	0.798000	0.45092	9.339000	0.96797	2.326000	0.78906	0.533000	0.62120	GAG	.	.		0.453	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770		T	73480433	A	T	73480433	3	4	290	1	0	0	0	0	1	0	0	0	8022	304	11	4	466	4	KCNB2	8	73480433	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10		73480433	72883589	84	42546										
TRMT12	55039	hgsc.bcm.edu	37	chr8	125464081	125464081	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	agctctcaaatattgcagatAgggtgatcctggggctgatt	12	7	1	3			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr8:125464081A>T	ENST00000328599.3	+	1	1034	c.913A>T	c.(913-915)Agg>Tgg	p.R305W	TRMT12_ENST00000521443.1_Intron	NM_017956.3	NP_060426.2	Q53H54	TYW2_HUMAN	tRNA methyltransferase 12 homolog (S. cerevisiae)	305					tRNA processing (GO:0008033)		transferase activity (GO:0016740)			breast(2)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			TATTGCAGATAGGGTGATCCT	0.463																																					p.R305W		Atlas-SNP	.											.	TRMT12	28	.	0			c.A913T						.						80	80	80					8																	125464081		2203	4300	6503	SO:0001583	missense	55039	exon1			GCAGATAGGGTGA	AF313041	CCDS6349.1	8q24.13	2011-05-09	2006-11-16		ENSG00000183665	ENSG00000183665			26091	protein-coding gene	gene with protein product	"tRNA-yW synthesizing protein 2"	611244	"tRNA methyltranferase 12 homolog (S. cerevisiae)"			16005430, 17150819	Standard	NM_017956		Approved	FLJ20772, Trm12, TYW2	uc003yra.4	Q53H54	OTTHUMG00000165022	ENST00000328599.3:c.913A>T	chr8.hg19:g.125464081A>T	ENSP00000329858:p.Arg305Trp	45.0	0.0		60.0	24.0	NM_017956	Q6PKB9|Q96F21|Q9NWK6	Missense_Mutation	SNP	ENST00000328599.3	hg19	CCDS6349.1	.	.	.	.	.	.	.	.	.	.	A	19.64	3.866351	0.71949	.	.	ENSG00000183665	ENST00000328599	T	0.30981	1.51	5.41	1.5	0.22942	.	0.000000	0.85682	D	0.000000	T	0.64962	0.2646	H	0.95917	3.74	0.58432	D	0.999996	D	0.89917	1.0	D	0.97110	1.0	T	0.72462	-0.4286	10	0.87932	D	0	-18.3481	11.9586	0.52995	0.5774:0.4226:0.0:0.0	.	305	Q53H54	TYW2_HUMAN	W	305	ENSP00000329858:R305W	ENSP00000329858:R305W	R	+	1	2	TRMT12	125533262	1.000000	0.71417	0.982000	0.44146	0.969000	0.65631	1.868000	0.39509	0.077000	0.16863	0.459000	0.35465	AGG	.	.		0.463	TRMT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381465.1	NM_017956		T	125464081	A	T	125464081	3	4	290	1	0	0	0	0	1	0	0	0	16579	411	15	4	915	4	TRMT12	8	125464081	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	51983648	125464081	20899941	85	42547										
ASPN	54829	hgsc.bcm.edu	37	chr9	95232978	95232978	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	gaagtgagtcctttaaaatcAttttctttgatttccttaat	5	6	2	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr9:95232978A>T	ENST00000375544.3	-	3	603	c.360T>A	c.(358-360)aaT>aaA	p.N120K	ASPN_ENST00000375543.1_Missense_Mutation_p.N120K|ASPN_ENST00000395538.3_Missense_Mutation_p.N120K|CENPP_ENST00000375587.3_Intron	NM_017680.4	NP_060150	Q9BXN1	ASPN_HUMAN	asporin	120					bone mineralization (GO:0030282)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|skin(1)	9						CTTTAAAATCATTTTCTTTGA	0.289																																					p.N120K		Atlas-SNP	.											.	ASPN	52	.	0			c.T360A						.						79	82	81					9																	95232978		2201	4289	6490	SO:0001583	missense	54829	exon3			AAAATCATTTTCT	AF316824		9q22.31	2008-05-14	2007-02-15		ENSG00000106819	ENSG00000106819		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	14872	protein-coding gene	gene with protein product	"asporin proteoglycan"	608135	"asporin (LRR class 1)"				Standard	NM_017680		Approved	FLJ20129, SLRR1C, PLAP1	uc004ase.2	Q9BXN1	OTTHUMG00000020227	ENST00000375544.3:c.360T>A	chr9.hg19:g.95232978A>T	ENSP00000364694:p.Asn120Lys	93.0	0.0		72.0	42.0	NM_001193335	Q5TBF3|Q96K79|Q96LD0|Q9NXP3	Missense_Mutation	SNP	ENST00000375544.3	hg19		.	.	.	.	.	.	.	.	.	.	A	14.50	2.553652	0.45487	.	.	ENSG00000106819	ENST00000375544;ENST00000375543;ENST00000395538	T;T;T	0.56941	0.43;0.43;0.43	5.7	-4.31	0.03698	.	0.134360	0.64402	D	0.000002	T	0.29423	0.0733	N	0.25825	0.765	0.32875	D	0.509751	B;B	0.17465	0.02;0.022	B;B	0.23852	0.049;0.049	T	0.02167	-1.1202	10	0.49607	T	0.09	.	3.383	0.07261	0.3018:0.2095:0.3862:0.1025	.	120;120	Q5TBF2;Q9BXN1	.;ASPN_HUMAN	K	120	ENSP00000364694:N120K;ENSP00000364693:N120K;ENSP00000378909:N120K	ENSP00000364693:N120K	N	-	3	2	ASPN	94272799	0.509000	0.26163	0.988000	0.46212	0.995000	0.86356	-0.147000	0.10234	-0.333000	0.08476	-0.256000	0.11100	AAT	.	.		0.289	ASPN-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000053094.1	NM_017680		T	95232978	A	T	95232978	3	4	290	1	0	0	0	0	1	0	0	0	1057	214	8	4	806	4	ASPN	9	95232978	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10		95232978	45980453	86	42548										
WNK2	65268	hgsc.bcm.edu	37	chr9	96079849	96079849	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	atgccacgtctgcccccagcGcccggccctctgtccaccac	8	22	2	0			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr9:96079849G>A	ENST00000297954.4	+	29	6675	c.6675G>A	c.(6673-6675)gcG>gcA	p.A2225A	WNK2_ENST00000395477.2_Silent_p.A2188A|WNK2_ENST00000471076.1_3'UTR|WNK2_ENST00000427277.2_Silent_p.A1800A|WNK2_ENST00000395475.2_3'UTR|WNK2_ENST00000349097.3_Silent_p.A1837A|WNK2_ENST00000356055.3_3'UTR	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	2225					intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						TGCCCCCAGCGCCCGGCCCTC	0.647																																					p.A2188A		Atlas-SNP	.											.	WNK2	277	.	0			c.G6564A						.						71	64	67					9																	96079849		2203	4300	6503	SO:0001819	synonymous_variant	65268	exon28			CCCAGCGCCCGGC	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"serologically defined colon cancer antigen 43"	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.6675G>A	chr9.hg19:g.96079849G>A		45.0	0.0		24.0	15.0	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Silent	SNP	ENST00000297954.4	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	1.105|1.105	-0.659938|-0.659938	0.03454|0.03454	.|.	.|.	ENSG00000165238|ENSG00000165238	ENST00000411624|ENST00000432730;ENST00000448251	T|.	0.61859|.	0.07|.	5.8|5.8	-7.3|-7.3	0.01446|0.01446	.|.	0.891771|.	0.09390|.	N|.	0.808668|.	T|T	0.28167|0.28167	0.0695|0.0695	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.31447|0.31447	-0.9943|-0.9943	7|4	0.23891|.	T|.	0.37|.	.|.	9.7361|9.7361	0.40388|0.40388	0.5466:0.0949:0.3585:0.0|0.5466:0.0949:0.3585:0.0	.|.	.|.	.|.	.|.	T|H	1680|2184;985	ENSP00000414622:A1680T|.	ENSP00000414622:A1680T|.	A|R	+|+	1|2	0|0	WNK2|WNK2	95119670|95119670	0.061000|0.061000	0.20836|0.20836	0.000000|0.000000	0.03702|0.03702	0.030000|0.030000	0.12068|0.12068	0.288000|0.288000	0.18939|0.18939	-2.221000|-2.221000	0.00728|0.00728	-0.753000|-0.753000	0.03488|0.03488	GCC|CGC	.	.		0.647	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648		A	96079849	G	A	96079849	2	1	290	1	0	0	0	0	0	0	0	1	17393	1074	38	1		1	WNK2	9	96079849	Silent	SNP	G	TCGA-G3-A7M5-01A-11D-A33Q-10	846871	96079849	45133582	87	42549										
COL15A1	1306	hgsc.bcm.edu	37	chr9	101777823	101777823	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	ggctcccctcacagccaccaTggcccctgagcgggcagtca	11	18	2	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr9:101777823T>C	ENST00000375001.3	+	10	1901	c.1478T>C	c.(1477-1479)aTg>aCg	p.M493T		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	493	4 X tandem repeats.|Nonhelical region 1 (NC1).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				ACAGCCACCATGGCCCCTGAG	0.572																																					p.M493T		Atlas-SNP	.											.	COL15A1	211	.	0			c.T1478C						.						54	48	50					9																	101777823		2203	4300	6503	SO:0001583	missense	1306	exon10			CCACCATGGCCCC	L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2192	protein-coding gene	gene with protein product	"collagen type XV proteoglycan"	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.1478T>C	chr9.hg19:g.101777823T>C	ENSP00000364140:p.Met493Thr	46.0	0.0		30.0	25.0	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Missense_Mutation	SNP	ENST00000375001.3	hg19	CCDS35081.1	.	.	.	.	.	.	.	.	.	.	T	1.194	-0.634417	0.03584	.	.	ENSG00000204291	ENST00000375001;ENST00000536083	D	0.89196	-2.48	3.76	-7.51	0.01346	.	.	.	.	.	T	0.73705	0.3621	N	0.14661	0.345	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.60357	-0.7279	9	0.13108	T	0.6	2.6614	10.3435	0.43893	0.0:0.1623:0.116:0.7216	.	493	P39059	COFA1_HUMAN	T	493;463	ENSP00000364140:M493T	ENSP00000364140:M493T	M	+	2	0	COL15A1	100817644	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.946000	0.00167	-2.145000	0.00801	-0.911000	0.02809	ATG	.	.		0.572	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855		C	101777823	T	C	101777823	3	2	290	1	0	0	0	0	1	0	0	0	3674	1464	51	2	1516	2	COL15A1	9	101777823	Missense_Mutation	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	5697974	101777823	39435608	88	42550										
USP20	10868	hgsc.bcm.edu	37	chr9	132636872	132636872	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	cagatcctgtgcattcacctAaagcgctttcggcacgaggt	10	12	1	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr9:132636872A>T	ENST00000315480.4	+	18	1916	c.1758A>T	c.(1756-1758)ctA>ctT	p.L586L	USP20_ENST00000358355.1_Silent_p.L586L|USP20_ENST00000372429.3_Silent_p.L586L			Q9Y2K6	UBP20_HUMAN	ubiquitin specific peptidase 20	586	USP.				endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|urinary_tract(1)	11		Ovarian(14;0.00556)				GCATTCACCTAAAGCGCTTTC	0.607																																					p.L586L		Atlas-SNP	.											.	USP20	186	.	0			c.A1758T						.						61	66	65					9																	132636872		2118	4237	6355	SO:0001819	synonymous_variant	10868	exon18			TCACCTAAAGCGC	AB023220	CCDS43892.1	9q34.2	2014-07-15	2005-08-08		ENSG00000136878	ENSG00000136878		"Ubiquitin-specific peptidases"	12619	protein-coding gene	gene with protein product		615143	"ubiquitin specific protease 20"			12838346	Standard	NM_006676		Approved	KIAA1003	uc004byr.3	Q9Y2K6	OTTHUMG00000020793	ENST00000315480.4:c.1758A>T	chr9.hg19:g.132636872A>T		93.0	0.0		62.0	44.0	NM_001008563	Q541F1|Q8IXQ1|Q96LG5|Q9UQN8|Q9UQP0	Silent	SNP	ENST00000315480.4	hg19	CCDS43892.1																																																																																			.	.		0.607	USP20-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054604.2			T	132636872	A	T	132636872	2	4	290	1	0	0	0	0	0	0	0	1	17067	349	13	4		4	USP20	9	132636872	Silent	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	30859049	132636872	8576559	89	42551										
KIAA1217	56243	hgsc.bcm.edu	37	chr10	24813464	24813464	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	ggttcgccacgcgcagagctCccctgtggtcatccagccct	11	17	1	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr10:24813464C>G	ENST00000376454.3	+	13	2699	c.2669C>G	c.(2668-2670)tCc>tGc	p.S890C	KIAA1217_ENST00000396446.1_Missense_Mutation_p.S573C|KIAA1217_ENST00000307544.6_Missense_Mutation_p.S573C|KIAA1217_ENST00000376462.1_Missense_Mutation_p.S810C|KIAA1217_ENST00000376451.2_Missense_Mutation_p.S573C|KIAA1217_ENST00000376452.3_Missense_Mutation_p.S855C|KIAA1217_ENST00000430453.2_Intron|KIAA1217_ENST00000458595.1_Missense_Mutation_p.S855C|KIAA1217_ENST00000396445.1_Missense_Mutation_p.S573C	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	890					embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						GCGCAGAGCTCCCCTGTGGTC	0.662																																					p.S890C		Atlas-SNP	.											.	KIAA1217	235	.	0			c.C2669G						.						66	54	58					10																	24813464		2203	4300	6503	SO:0001583	missense	56243	exon13			AGAGCTCCCCTGT	BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"sickle tail"					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.2669C>G	chr10.hg19:g.24813464C>G	ENSP00000365637:p.Ser890Cys	47.0	0.0		46.0	21.0	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Missense_Mutation	SNP	ENST00000376454.3	hg19	CCDS31165.1	.	.	.	.	.	.	.	.	.	.	C	18.10	3.548084	0.65311	.	.	ENSG00000120549	ENST00000376462;ENST00000376456;ENST00000458595;ENST00000442879;ENST00000376454;ENST00000376452;ENST00000438429;ENST00000307544;ENST00000450158;ENST00000396445;ENST00000376451;ENST00000396446	T;T;T;T;T;T;T;T;T;T	0.55052	0.54;0.54;0.54;0.54;0.54;0.54;0.54;0.54;0.54;0.54	5.42	5.42	0.78866	.	0.120213	0.64402	D	0.000020	T	0.71143	0.3305	M	0.66939	2.045	0.58432	D	0.999999	D;D;D;D;D;D;D;D	0.76494	0.999;0.998;0.992;0.994;0.998;0.992;0.983;0.99	D;P;P;P;D;P;P;P	0.65773	0.913;0.838;0.867;0.889;0.938;0.877;0.839;0.81	T	0.73341	-0.4013	10	0.66056	D	0.02	.	19.2009	0.93711	0.0:1.0:0.0:0.0	.	855;855;573;573;573;573;890;890	Q5T5P2-7;A6NLF3;Q5T5P2-4;Q5T5P2-8;Q5T5P2-3;Q5T5P2-6;Q5T5P2;Q5T5P2-2	.;.;.;.;.;.;SKT_HUMAN;.	C	810;855;855;573;890;855;705;573;573;573;573;573	ENSP00000365645:S810C;ENSP00000365639:S855C;ENSP00000392625:S855C;ENSP00000365637:S890C;ENSP00000365635:S855C;ENSP00000404798:S705C;ENSP00000302343:S573C;ENSP00000379722:S573C;ENSP00000365634:S573C;ENSP00000379723:S573C	ENSP00000302343:S573C	S	+	2	0	KIAA1217	24853470	1.000000	0.71417	0.800000	0.32199	0.059000	0.15707	7.287000	0.78681	2.549000	0.85964	0.491000	0.48974	TCC	.	.		0.662	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590		G	24813464	C	G	24813464	3	3	290	1	0	0	0	0	1	0	0	0	8225	855	30	4	2719	4	KIAA1217	10	24813464	Missense_Mutation	SNP	C	TCGA-G3-A7M5-01A-11D-A33Q-10		24813464	110721283	90	42552										
FAM21C	253725	hgsc.bcm.edu	37	chr10	46272808	46272808	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	ttggagtgaagtctgtggatAagaaggttgagagtgccaag	16	3	1	3			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr10:46272808A>T	ENST00000336378.4	+	22	2342	c.2224A>T	c.(2224-2226)Aag>Tag	p.K742*	FAM21C_ENST00000374362.2_Nonsense_Mutation_p.K744*|FAM21C_ENST00000540872.1_Nonsense_Mutation_p.K744*|FAM21C_ENST00000359860.4_Nonsense_Mutation_p.K686*|FAM21C_ENST00000537517.1_Intron	NM_015262.2	NP_056077.2	Q9Y4E1	FA21C_HUMAN	family with sequence similarity 21, member C	742					retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|endosome (GO:0005768)|plasma membrane (GO:0005886)|WASH complex (GO:0071203)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	28						GTCTGTGGATAAGAAGGTTGA	0.423																																					p.K744X		Atlas-SNP	.											.	FAM21C	68	.	0			c.A2230T						.						134	133	133					10																	46272808		1816	4048	5864	SO:0001587	stop_gained	253725	exon22			GTGGATAAGAAGG		CCDS44374.1, CCDS44374.2, CCDS53528.1, CCDS53529.1	10q11.22	2014-05-09			ENSG00000172661	ENSG00000172661			23414	protein-coding gene	gene with protein product		613631				20498093	Standard	NM_015262		Approved	Em:AC012044.3, KIAA0592	uc001jcu.3	Q9Y4E1	OTTHUMG00000018089	ENST00000336378.4:c.2224A>T	chr10.hg19:g.46272808A>T	ENSP00000337541:p.Lys742*	384.0	0.0		389.0	157.0	NM_015262	B4DZQ6|B9EK53|F5H0J6|F5H871|Q5SQU4|Q5SQU5|Q7L521|Q9UG79	Nonsense_Mutation	SNP	ENST00000336378.4	hg19		.	.	.	.	.	.	.	.	.	.	A	26.4	4.732498	0.89482	.	.	ENSG00000172661	ENST00000336378;ENST00000540872;ENST00000374362;ENST00000399588;ENST00000359860;ENST00000436993	.	.	.	3.01	-1.42	0.08913	.	1.772090	0.02631	N	0.104260	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.2029	5.1852	0.15180	0.3039:0.5442:0.1519:0.0	.	.	.	.	X	742;744;744;744;686;656	.	ENSP00000337541:K742X	K	+	1	0	FAM21C	45592814	0.005000	0.15991	0.002000	0.10522	0.371000	0.29859	-0.267000	0.08619	-0.368000	0.08040	0.241000	0.17934	AAG	.	.		0.423	FAM21C-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding				T	46272808	A	T	46272808	4	4	290	1	0	0	0	0	0	1	0	0	5547	363	13	4	2316	4	FAM21C	10	46272808	Nonsense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	21459344	46272808	89261939	91	42553										
PCDH15	65217	hgsc.bcm.edu	37	chr10	55912909	55912909	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tgcttggaccgtgagtgcgtAagtccgcccgactatcattt	11	11	1	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr10:55912909A>T	ENST00000320301.6	-	14	2129	c.1735T>A	c.(1735-1737)Tac>Aac	p.Y579N	PCDH15_ENST00000373965.2_Missense_Mutation_p.Y586N|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000373955.1_Missense_Mutation_p.Y579N|PCDH15_ENST00000409834.1_Missense_Mutation_p.Y190N|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000361849.3_Missense_Mutation_p.Y579N|PCDH15_ENST00000373957.3_Missense_Mutation_p.Y557N|PCDH15_ENST00000395438.1_Missense_Mutation_p.Y579N|PCDH15_ENST00000437009.1_Missense_Mutation_p.Y579N|PCDH15_ENST00000395445.1_Missense_Mutation_p.Y586N|PCDH15_ENST00000395433.1_Missense_Mutation_p.Y557N|PCDH15_ENST00000414778.1_Missense_Mutation_p.Y584N|PCDH15_ENST00000395430.1_Missense_Mutation_p.Y579N|PCDH15_ENST00000395446.1_Missense_Mutation_p.Y579N|PCDH15_ENST00000395432.2_Missense_Mutation_p.Y542N	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	579	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				GTGAGTGCGTAAGTCCGCCCG	0.483										HNSCC(58;0.16)																											p.Y584N		Atlas-SNP	.											.	PCDH15	1715	.	0			c.T1750A						.						137	119	125					10																	55912909		2203	4300	6503	SO:0001583	missense	65217	exon15			GTGCGTAAGTCCG	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.1735T>A	chr10.hg19:g.55912909A>T	ENSP00000322604:p.Tyr579Asn	88.0	0.0		88.0	18.0	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	hg19	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	A	16.44	3.123189	0.56613	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395446;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000373957;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009;ENST00000373955	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.70164	-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46	5.83	5.83	0.93111	Cadherin (5);Cadherin-like (1);	.	.	.	.	D	0.88051	0.6333	H	0.97131	3.945	0.58432	D	0.999997	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.999;1.0;0.999;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.91635	0.995;0.998;0.997;0.999;0.997;0.998;0.995;0.995;0.997;0.998;0.99;0.995;0.986;0.982;0.998	D	0.91955	0.5574	9	0.87932	D	0	.	15.8727	0.79132	1.0:0.0:0.0:0.0	.	557;579;579;584;579;542;579;579;586;586;579;584;579;557;579	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;A2A3D8;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	N	586;584;579;579;190;586;579;542;579;557;557;579;579;584;579;579	ENSP00000363076:Y586N;ENSP00000410304:Y584N;ENSP00000378826:Y579N;ENSP00000386693:Y190N;ENSP00000378832:Y586N;ENSP00000378833:Y579N;ENSP00000378820:Y542N;ENSP00000354950:Y579N;ENSP00000378821:Y557N;ENSP00000363068:Y557N;ENSP00000322604:Y579N;ENSP00000378818:Y579N;ENSP00000412628:Y579N;ENSP00000363066:Y579N	ENSP00000322604:Y579N	Y	-	1	0	PCDH15	55582915	1.000000	0.71417	0.192000	0.23308	0.112000	0.19704	8.740000	0.91579	2.231000	0.72958	0.528000	0.53228	TAC	.	.		0.483	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		T	55912909	A	T	55912909	3	4	290	1	0	0	0	0	1	0	0	0	11520	362	13	4	5831	4	PCDH15	10	55912909	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	9640101	55912909	79621838	92	42554										
RHOBTB1	9886	hgsc.bcm.edu	37	chr10	62647978	62647978	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	cggcccactcacccgagaacGttcccttgctgagacactct	8	17	2	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr10:62647978G>A	ENST00000337910.5	-	6	1785	c.1448C>T	c.(1447-1449)aCg>aTg	p.T483M	RHOBTB1_ENST00000357917.4_Missense_Mutation_p.T483M	NM_001242359.1|NM_014836.4	NP_001229288.1|NP_055651.1	O94844	RHBT1_HUMAN	Rho-related BTB domain containing 1	483					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			endometrium(4)|large_intestine(6)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	Prostate(12;0.0112)					ACCCGAGAACGTTCCCTTGCT	0.468																																					p.T483M		Atlas-SNP	.											.	RHOBTB1	61	.	0			c.C1448T						.						81	78	79					10																	62647978		2203	4300	6503	SO:0001583	missense	9886	exon6			GAGAACGTTCCCT	AB018283	CCDS7261.1	10q22.1	2013-01-08			ENSG00000072422	ENSG00000072422		"BTB/POZ domain containing"	18738	protein-coding gene	gene with protein product		607351				11222756	Standard	NM_014836		Approved	KIAA0740	uc001jlh.3	O94844	OTTHUMG00000018292	ENST00000337910.5:c.1448C>T	chr10.hg19:g.62647978G>A	ENSP00000338671:p.Thr483Met	77.0	0.0		70.0	35.0	NM_014836		Missense_Mutation	SNP	ENST00000337910.5	hg19	CCDS7261.1	.	.	.	.	.	.	.	.	.	.	G	17.79	3.475541	0.63737	.	.	ENSG00000072422	ENST00000357917;ENST00000337910	T;T	0.68025	-0.3;-0.3	5.75	5.75	0.90469	BTB/POZ (1);BTB/POZ fold (2);	0.066716	0.64402	D	0.000008	D	0.83055	0.5171	M	0.80746	2.51	0.58432	D	0.999999	D	0.89917	1.0	D	0.79108	0.992	T	0.80854	-0.1196	10	0.34782	T	0.22	.	19.9525	0.97208	0.0:0.0:1.0:0.0	.	483	O94844	RHBT1_HUMAN	M	483	ENSP00000350595:T483M;ENSP00000338671:T483M	ENSP00000338671:T483M	T	-	2	0	RHOBTB1	62317984	1.000000	0.71417	0.955000	0.39395	0.687000	0.40016	7.631000	0.83237	2.719000	0.93026	0.655000	0.94253	ACG	.	.		0.468	RHOBTB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048220.1			A	62647978	G	A	62647978	3	1	290	1	0	0	0	0	1	0	0	0	13348	1145	40	1	666	1	RHOBTB1	10	62647978	Missense_Mutation	SNP	G	TCGA-G3-A7M5-01A-11D-A33Q-10	6735069	62647978	72886769	93	42555										
DDX21	9188	hgsc.bcm.edu	37	chr10	70730090	70730090	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	agcccaggagctgtcccagaAttcagctataaagcaggttg	11	10	1	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr10:70730090A>T	ENST00000354185.4	+	8	1468	c.1370A>T	c.(1369-1371)aAt>aTt	p.N457I		NM_001256910.1|NM_004728.3	NP_001243839.1|NP_004719.2	Q9NR30	DDX21_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 21	457	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|osteoblast differentiation (GO:0001649)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	20						CTGTCCCAGAATTCAGCTATA	0.453																																					p.N457I		Atlas-SNP	.											.	DDX21	57	.	0			c.A1370T						.						68	66	67					10																	70730090		2203	4300	6503	SO:0001583	missense	9188	exon8			CCCAGAATTCAGC	U41387	CCDS31211.1, CCDS73144.1	10q21	2013-05-13	2012-02-23		ENSG00000165732	ENSG00000165732		"DEAD-boxes"	2744	protein-coding gene	gene with protein product		606357	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 21", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 21"			8614622, 18180292	Standard	NM_004728		Approved	RH-II/GU, GURDB	uc001jov.2	Q9NR30	OTTHUMG00000018366	ENST00000354185.4:c.1370A>T	chr10.hg19:g.70730090A>T	ENSP00000346120:p.Asn457Ile	73.0	0.0		91.0	14.0	NM_004728	B2RDL0|Q13436|Q5VX41|Q68D35	Missense_Mutation	SNP	ENST00000354185.4	hg19	CCDS31211.1	.	.	.	.	.	.	.	.	.	.	A	17.88	3.496376	0.64186	.	.	ENSG00000165732	ENST00000354185	T	0.04406	3.63	5.73	-0.928	0.10448	Helicase, C-terminal (2);	0.172541	0.64402	D	0.000009	T	0.05456	0.0144	N	0.16478	0.41	0.44966	D	0.997984	P	0.52692	0.955	P	0.55871	0.786	T	0.44436	-0.9328	10	0.52906	T	0.07	-27.1742	6.759	0.23530	0.4783:0.1307:0.391:0.0	.	457	Q9NR30	DDX21_HUMAN	I	457	ENSP00000346120:N457I	ENSP00000346120:N457I	N	+	2	0	DDX21	70400096	0.987000	0.35691	0.091000	0.20842	0.625000	0.37756	2.869000	0.48444	-0.105000	0.12132	0.533000	0.62120	AAT	.	.		0.453	DDX21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048374.1	NM_004728		T	70730090	A	T	70730090	3	4	290	1	0	0	0	0	1	0	0	0	4351	101	4	4	1400	4	DDX21	10	70730090	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	8082112	70730090	64804657	94	42556										
CNNM1	26507	hgsc.bcm.edu	37	chr10	101124744	101124744	+	Frame_Shift_Del	DEL	G	G	-													0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	ggaaggttggaagtctggctGgatcttctgtctttcgtatg							TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr10:101124744delG	ENST00000356713.4	+	6	2450	c.2161delG	c.(2161-2163)ggafs	p.G721fs	CNNM1_ENST00000370534.4_Frame_Shift_Del_p.G356fs|CNNM1_ENST00000370528.3_Frame_Shift_Del_p.G650fs|CNNM1_ENST00000446890.1_Frame_Shift_Del_p.G650fs	NM_020348.2	NP_065081.2	Q9NRU3	CNNM1_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 1	721					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(5)|ovary(1)|prostate(1)|skin(1)	25		Colorectal(252;0.234)		Epithelial(162;6.82e-10)|all cancers(201;5.62e-08)		AAGTCTGGCTGGATCTTCTGT	0.517																																					p.A720fs		Atlas-Indel,Pindel	.											.	CNNM1	101	.	0			c.2160delT						.						201	161	174					10																	101124744		2203	4300	6503	SO:0001589	frameshift_variant	26507	exon6			.	AF169226	CCDS7478.2	10q24.2	2014-08-08	2014-08-07		ENSG00000119946	ENSG00000119946			102	protein-coding gene	gene with protein product		607802	"cyclin M1"	ACDP1		21393841	Standard	NM_020348		Approved		uc001kpp.4	Q9NRU3	OTTHUMG00000018881	ENST00000356713.4:c.2161delG	chr10.hg19:g.101124744delG	ENSP00000349147:p.Gly721fs	56.0	0.0		50.0	35.0	NM_020348	Q4QQG7|Q4QQH8|Q4QQP9|Q9NT45	Frame_Shift_Del	DEL	ENST00000356713.4	hg19	CCDS7478.2																																																																																			.	.		0.517	CNNM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049792.2	NM_020348		-	101124744	G	-	101124744	7	5	290	1	0	1	0	1	0	0	0	0	3614	1349	47	0	2183	0	CNNM1	10	101124744	Frame_Shift_Del	DEL	G	TCGA-G3-A7M5-01A-11D-A33Q-10	30394654	101124744	34410003	95	42557										
TDRD1	56165	hgsc.bcm.edu	37	chr10	115959029	115959029	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tccagggctcttcacctcctTaggacctcctcttcggtcca	7	17	3	0			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr10:115959029T>C	ENST00000369280.1	+	4	942	c.482T>C	c.(481-483)tTa>tCa	p.L161S	TDRD1_ENST00000422662.1_5'UTR|TDRD1_ENST00000369282.1_Missense_Mutation_p.L161S|TDRD1_ENST00000251864.2_Missense_Mutation_p.L161S|TDRD1_ENST00000369281.2_Missense_Mutation_p.L161S			Q9BXT4	TDRD1_HUMAN	tudor domain containing 1	161					DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|germ cell development (GO:0007281)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|P granule (GO:0043186)|pi-body (GO:0071546)	metal ion binding (GO:0046872)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(5)	48		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0343)|all cancers(201;0.0754)		TTCACCTCCTTAGGACCTCCT	0.418																																					p.L161S		Atlas-SNP	.											.	TDRD1	126	.	0			c.T482C						.						149	137	141					10																	115959029		2203	4300	6503	SO:0001583	missense	56165	exon4			CCTCCTTAGGACC	AF285606	CCDS7588.1	10q26.11	2013-01-23			ENSG00000095627	ENSG00000095627		"Tudor domain containing"	11712	protein-coding gene	gene with protein product	"cancer/testis antigen 41.1"	605796				11279525	Standard	NM_198795		Approved	CT41.1	uc001lbg.1	Q9BXT4	OTTHUMG00000019083	ENST00000369280.1:c.482T>C	chr10.hg19:g.115959029T>C	ENSP00000358286:p.Leu161Ser	150.0	0.0		161.0	86.0	NM_198795	A6NEN3|A6NMN2|B3KVI4|B4E2L5|D3DRC2|Q4G0Y8|Q6P518|Q9H7B3	Missense_Mutation	SNP	ENST00000369280.1	hg19		.	.	.	.	.	.	.	.	.	.	T	17.12	3.307334	0.60305	.	.	ENSG00000095627	ENST00000369282;ENST00000251864;ENST00000369281;ENST00000369280	T;T;T;T	0.20881	2.93;2.9;2.04;2.93	6.05	6.05	0.98169	.	0.252959	0.34046	N	0.004315	T	0.37046	0.0989	L	0.36672	1.1	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;1.0;1.0	D;D;D;D	0.91635	0.997;0.997;0.999;0.992	T	0.08006	-1.0743	10	0.59425	D	0.04	-12.3224	14.1164	0.65156	0.0:0.0:0.0:1.0	.	161;161;161;161	Q9BXT4;B7WPM2;Q9BXT4-3;Q9BXT4-2	TDRD1_HUMAN;.;.;.	S	161	ENSP00000358288:L161S;ENSP00000251864:L161S;ENSP00000358287:L161S;ENSP00000358286:L161S	ENSP00000251864:L161S	L	+	2	0	TDRD1	115949019	0.982000	0.34865	0.994000	0.49952	0.396000	0.30629	4.890000	0.63178	2.320000	0.78422	0.528000	0.53228	TTA	.	.		0.418	TDRD1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050457.2			C	115959029	T	C	115959029	3	2	290	1	0	0	0	0	1	0	0	0	15745	1764	61	2	492	2	TDRD1	10	115959029	Missense_Mutation	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	14834285	115959029	19575718	96	42558										
VWA2	340706	hgsc.bcm.edu	37	chr10	116048949	116048949	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	cccctacctaggtggggtggGctcagccggcaccgccctgc	14	17	1	0			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr10:116048949G>T	ENST00000392982.3	+	12	2073	c.1823G>T	c.(1822-1824)gGc>gTc	p.G608V	VWA2_ENST00000603594.1_Missense_Mutation_p.G608V			Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	608	VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				calcium-independent cell-matrix adhesion (GO:0007161)|protein homooligomerization (GO:0051260)|regulation of insulin receptor signaling pathway (GO:0046626)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Epithelial(162;0.036)|all cancers(201;0.0793)		GGTGGGGTGGGCTCAGCCGGC	0.657																																					p.G608V		Atlas-SNP	.											.	VWA2	64	.	0			c.G1823T						.						32	30	31					10																	116048949		2201	4300	6501	SO:0001583	missense	340706	exon12			GGGTGGGCTCAGC	AK127756	CCDS7589.1, CCDS7589.2	10q25.3	2009-11-06			ENSG00000165816	ENSG00000165816			24709	protein-coding gene	gene with protein product						15580307, 14506275	Standard	NM_001272046		Approved	FLJ45857, FLJ16213, CCSP-2, AMACO, NET42	uc001lbl.2	Q5GFL6	OTTHUMG00000019082	ENST00000392982.3:c.1823G>T	chr10.hg19:g.116048949G>T	ENSP00000376708:p.Gly608Val	45.0	0.0		30.0	15.0	NM_001272046	A1A5D4|B5MDJ8|Q6ZS39|Q6ZWJ7|Q708C5|Q70UZ8	Missense_Mutation	SNP	ENST00000392982.3	hg19		.	.	.	.	.	.	.	.	.	.	G	15.76	2.929055	0.52759	.	.	ENSG00000165816	ENST00000392982;ENST00000298715	T	0.77877	-1.13	5.29	5.29	0.74685	von Willebrand factor, type A (3);	0.061486	0.64402	D	0.000005	D	0.84973	0.5591	M	0.66939	2.045	0.58432	D	0.999998	P;D;D	0.71674	0.876;0.998;0.998	P;D;P	0.65323	0.734;0.934;0.892	D	0.86107	0.1560	10	0.66056	D	0.02	.	12.7097	0.57082	0.0:0.2158:0.7842:0.0	.	304;608;608	Q5GFL6-3;Q5GFL6;Q5GFL6-2	.;VWA2_HUMAN;.	V	608	ENSP00000376708:G608V	ENSP00000298715:G608V	G	+	2	0	VWA2	116038939	1.000000	0.71417	0.901000	0.35422	0.454000	0.32378	3.872000	0.56085	2.460000	0.83146	0.655000	0.94253	GGC	.	.		0.657	VWA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050456.3	NM_198496		T	116048949	G	T	116048949	3	4	290	1	0	0	0	0	1	0	0	0	17254	1203	42	3	1865	3	VWA2	10	116048949	Missense_Mutation	SNP	G	TCGA-G3-A7M5-01A-11D-A33Q-10	89920	116048949	19485798	97	42559										
OR56B1	387748	hgsc.bcm.edu	37	chr11	5758461	5758461	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	actctgtacttagactgaacTcagctgaagctgcagccaag	9	11	2	3			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr11:5758461T>A	ENST00000317121.3	+	1	781	c.715T>A	c.(715-717)Tca>Aca	p.S239T	TRIM5_ENST00000380027.1_Intron	NM_001005180.2	NP_001005180.1	Q8NGI3	O56B1_HUMAN	olfactory receptor, family 56, subfamily B, member 1	239						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|prostate(1)|skin(1)	13		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.086)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.184)		TAGACTGAACTCAGCTGAAGC	0.418																																					p.S239T		Atlas-SNP	.											.	OR56B1	38	.	0			c.T715A						.						128	122	124					11																	5758461		2201	4297	6498	SO:0001583	missense	387748	exon1			CTGAACTCAGCTG	BK004386	CCDS31395.1	11p15.4	2012-08-09		2004-03-10	ENSG00000181023	ENSG00000181023		"GPCR / Class A : Olfactory receptors"	15245	protein-coding gene	gene with protein product				OR56B1P			Standard	NM_001005180		Approved		uc001mbt.2	Q8NGI3	OTTHUMG00000066891	ENST00000317121.3:c.715T>A	chr11.hg19:g.5758461T>A	ENSP00000322939:p.Ser239Thr	56.0	0.0		53.0	24.0	NM_001005180	B2RNY6|B3KV42|Q6IF76	Missense_Mutation	SNP	ENST00000317121.3	hg19	CCDS31395.1	.	.	.	.	.	.	.	.	.	.	T	16.14	3.039125	0.55003	.	.	ENSG00000181023	ENST00000317121	T	0.00325	8.1	5.87	5.87	0.94306	GPCR, rhodopsin-like superfamily (1);	0.215458	0.23303	U	0.049649	T	0.00637	0.0021	M	0.83692	2.655	0.09310	N	1	D	0.59357	0.985	D	0.66847	0.947	T	0.46484	-0.9188	10	0.59425	D	0.04	.	9.5113	0.39078	0.1572:0.0:0.0:0.8428	.	239	Q8NGI3	O56B1_HUMAN	T	239	ENSP00000322939:S239T	ENSP00000322939:S239T	S	+	1	0	OR56B1	5715037	0.460000	0.25776	0.054000	0.19295	0.923000	0.55619	2.027000	0.41078	2.253000	0.74438	0.533000	0.62120	TCA	.	.		0.418	OR56B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143354.1	NM_001005180		A	5758461	T	A	5758461	3	1	290	1	0	0	0	0	1	0	0	0	11146	1551	54	4	717	4	OR56B1	11	5758461	Missense_Mutation	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10		5758461	129248055	98	42560										
MICAL2	9645	hgsc.bcm.edu	37	chr11	12265545	12265545	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tctgtgcagaataaactactCtctaaaggcctgtctcatac	6	11	3	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr11:12265545C>T	ENST00000256194.4	+	21	2958	c.2670C>T	c.(2668-2670)ctC>ctT	p.L890L	MICAL2_ENST00000342902.5_Silent_p.L890L|MICAL2_ENST00000379612.3_Intron|MICAL2_ENST00000527546.1_Intron|MICAL2_ENST00000537344.1_Intron	NM_001282663.1|NM_014632.2	NP_001269592.1|NP_055447.1	O94851	MICA2_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 2	890					actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|heart development (GO:0007507)|heart looping (GO:0001947)|oxidation-reduction process (GO:0055114)|positive regulation of transcription via serum response element binding (GO:0010735)|sulfur oxidation (GO:0019417)	nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|NADPH:sulfur oxidoreductase activity (GO:0043914)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	47				Epithelial(150;0.00552)		ATAAACTACTCTCTAAAGGCC	0.478																																					p.L890L		Atlas-SNP	.											.	MICAL2	114	.	0			c.C2670T						.						327	283	298					11																	12265545		2201	4294	6495	SO:0001819	synonymous_variant	9645	exon21			ACTACTCTCTAAA	AB018293	CCDS7809.1, CCDS60726.1, CCDS60727.1, CCDS60728.1	11p15.3	2014-08-12	2013-03-26		ENSG00000133816	ENSG00000133816			24693	protein-coding gene	gene with protein product		608881				12110185	Standard	XM_005253249		Approved	KIAA0750	uc001mjz.3	O94851	OTTHUMG00000165744	ENST00000256194.4:c.2670C>T	chr11.hg19:g.12265545C>T		112.0	0.0		133.0	10.0	NM_014632	B4DGZ0|B7Z849|D3DQW5|G3XAC8|Q5KTR3|Q5KTR4|Q7Z3A8	Silent	SNP	ENST00000256194.4	hg19	CCDS7809.1																																																																																			.	.		0.478	MICAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385993.1	NM_014632		T	12265545	C	T	12265545	2	4	290	1	0	0	0	0	0	0	0	1	9579	900	32	3		3	MICAL2	11	12265545	Silent	SNP	C	TCGA-G3-A7M5-01A-11D-A33Q-10	6507084	12265545	122740971	99	42561										
SAA4	6291	hgsc.bcm.edu	37	chr11	18253952	18253952	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tctgtgttacctgatgagttTagcagcccagacacccccag	9	13	1	3			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr11:18253952T>C	ENST00000278222.4	-	3	400	c.220A>G	c.(220-222)Aaa>Gaa	p.K74E	SAA2-SAA4_ENST00000524555.1_RNA	NM_006512.3	NP_006503.2	P35542	SAA4_HUMAN	serum amyloid A4, constitutive	74					acute-phase response (GO:0006953)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(6)|skin(1)|stomach(1)	13						CTGATGAGTTTAGCAGCCCAG	0.507																																					p.K152E		Atlas-SNP	.											.	.	.	.	0			c.A454G						.						164	164	164					11																	18253952		2199	4293	6492	SO:0001583	missense	100528017	exon5			TGAGTTTAGCAGC	M81349	CCDS7832.1	11p15.1-p14	2008-07-21			ENSG00000148965	ENSG00000148965			10516	protein-coding gene	gene with protein product		104752				8325654	Standard	NM_006512		Approved	C-SAA, CSAA		P35542	OTTHUMG00000166483	ENST00000278222.4:c.220A>G	chr11.hg19:g.18253952T>C	ENSP00000278222:p.Lys74Glu	113.0	0.0		120.0	37.0	NM_001199744	Q6FHJ4	Missense_Mutation	SNP	ENST00000278222.4	hg19	CCDS7832.1	.	.	.	.	.	.	.	.	.	.	T	10.81	1.456689	0.26161	.	.	ENSG00000148965	ENST00000278222	T	0.10099	2.91	3.58	0.437	0.16555	.	.	.	.	.	T	0.04407	0.0121	N	0.11284	0.12	0.24179	N	0.995592	B	0.31256	0.316	B	0.28991	0.097	T	0.44832	-0.9302	9	0.13470	T	0.59	9.7551	5.3805	0.16189	0.0:0.3737:0.0:0.6263	.	74	P35542	SAA4_HUMAN	E	74	ENSP00000278222:K74E	ENSP00000278222:K74E	K	-	1	0	SAA4	18210528	0.000000	0.05858	0.340000	0.25575	0.732000	0.41865	-0.462000	0.06704	0.292000	0.22492	0.383000	0.25322	AAA	.	.		0.507	SAA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389988.1	NM_006512		C	18253952	T	C	18253952	3	2	290	1	0	0	0	0	1	0	0	0	13815	1763	61	2	180	2	SAA4	11	18253952	Missense_Mutation	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	5988407	18253952	116752564	100	42562										
MRGPRX2	117194	hgsc.bcm.edu	37	chr11	19077115	19077115	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	aaaagagcccacgaagaagtAaatgatggggttggcactgc	13	7	0	3			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr11:19077115A>T	ENST00000329773.2	-	2	922	c.835T>A	c.(835-837)Tac>Aac	p.Y279N		NM_054030.2	NP_473371.1	Q96LB1	MRGX2_HUMAN	MAS-related GPR, member X2	279					positive regulation of cytokinesis (GO:0032467)|sensory perception of pain (GO:0019233)|sleep (GO:0030431)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide binding (GO:0042923)			NS(1)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	15						ACGAAGAAGTAAATGATGGGG	0.478																																					p.Y279N	GBM(198;1966 2199 4849 37227 49954)	Atlas-SNP	.											.	MRGPRX2	42	.	0			c.T835A						.						70	75	73					11																	19077115		2199	4293	6492	SO:0001583	missense	117194	exon2			AGAAGTAAATGAT		CCDS7847.1	11p15.1	2013-10-10			ENSG00000183695	ENSG00000183695		"GPCR / Class A : Orphans"	17983	protein-coding gene	gene with protein product		607228				11551509	Standard	NM_054030		Approved	MRGX2	uc001mph.3	Q96LB1	OTTHUMG00000166098	ENST00000329773.2:c.835T>A	chr11.hg19:g.19077115A>T	ENSP00000333800:p.Tyr279Asn	77.0	0.0		81.0	28.0	NM_054030	B5B0C7|Q4QXW4|Q4QXW7|Q4QXX0|Q4QXX2|Q4QXX3|Q4QXX4|Q4QXX6|Q4QXX7	Missense_Mutation	SNP	ENST00000329773.2	hg19	CCDS7847.1	.	.	.	.	.	.	.	.	.	.	.	23.9	4.472045	0.84533	.	.	ENSG00000183695	ENST00000329773	D	0.93307	-3.2	5.26	5.26	0.73747	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000026	D	0.97573	0.9205	H	0.95679	3.705	0.39544	D	0.968865	D	0.89917	1.0	D	0.91635	0.999	D	0.99387	1.0924	10	0.87932	D	0	.	13.4552	0.61195	1.0:0.0:0.0:0.0	.	279	Q96LB1	MRGX2_HUMAN	N	279	ENSP00000333800:Y279N	ENSP00000333800:Y279N	Y	-	1	0	MRGPRX2	19033691	1.000000	0.71417	0.999000	0.59377	0.942000	0.58702	7.385000	0.79763	2.343000	0.79666	0.533000	0.62120	TAC	.	.		0.478	MRGPRX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387819.1	NM_054030		T	19077115	A	T	19077115	3	4	290	1	0	0	0	0	1	0	0	0	9776	362	13	4	161	4	MRGPRX2	11	19077115	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	823163	19077115	115929401	101	42563										
OR4X1	390113	hgsc.bcm.edu	37	chr11	48285788	48285788	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	accgctatgtggccatctgcAagcccttgcactacatggcc	9	15	1	0			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr11:48285788A>T	ENST00000320048.1	+	1	376	c.376A>T	c.(376-378)Aag>Tag	p.K126*		NM_001004726.1	NP_001004726.1	Q8NH49	OR4X1_HUMAN	olfactory receptor, family 4, subfamily X, member 1 (gene/pseudogene)	126						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(1)	28						GGCCATCTGCAAGCCCTTGCA	0.552																																					p.K126X		Atlas-SNP	.											.	OR4X1	75	.	0			c.A376T						.						87	79	82					11																	48285788		2201	4298	6499	SO:0001587	stop_gained	390113	exon1			ATCTGCAAGCCCT	AB065544	CCDS31487.1	11p11.2	2013-10-10	2013-10-10		ENSG00000176567	ENSG00000176567		"GPCR / Class A : Olfactory receptors"	14854	protein-coding gene	gene with protein product			"olfactory receptor, family 4, subfamily X, member 1"				Standard	NM_001004726		Approved		uc010rht.2	Q8NH49	OTTHUMG00000165301	ENST00000320048.1:c.376A>T	chr11.hg19:g.48285788A>T	ENSP00000321506:p.Lys126*	70.0	0.0		94.0	33.0	NM_001004726	Q6IF74	Nonsense_Mutation	SNP	ENST00000320048.1	hg19	CCDS31487.1	.	.	.	.	.	.	.	.	.	.	A	12.52	1.963728	0.34659	.	.	ENSG00000176567	ENST00000320048	.	.	.	4.26	4.26	0.50523	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.0635	0.30646	0.794:0.206:0.0:0.0	.	.	.	.	X	126	.	ENSP00000321506:K126X	K	+	1	0	OR4X1	48242364	0.118000	0.22208	1.000000	0.80357	0.229000	0.25112	1.709000	0.37909	1.911000	0.55334	0.456000	0.33151	AAG	.	.		0.552	OR4X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383373.1	NM_001004726		T	48285788	A	T	48285788	4	4	290	1	0	0	0	0	0	1	0	0	11093	131	5	4	378	4	OR4X1	11	48285788	Nonsense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	29208673	48285788	86720728	102	42564										
OR4C11	219429	hgsc.bcm.edu	37	chr11	55371245	55371245	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	aactacttgagcaaattgccCcactgttagacaccaacagc	6	13	0	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr11:55371245C>T	ENST00000302231.4	-	1	629	c.605G>A	c.(604-606)gGg>gAg	p.G202E		NM_001004700.2	NP_001004700.2	Q6IEV9	OR4CB_HUMAN	olfactory receptor, family 4, subfamily C, member 11	202						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(1)|large_intestine(5)|lung(23)|ovary(1)|prostate(1)|skin(1)	33						GCAAATTGCCCCACTGTTAGA	0.403																																					p.G202E		Atlas-SNP	.											.	OR4C11	73	.	0			c.G605A						.						88	73	78					11																	55371245		2179	4012	6191	SO:0001583	missense	219429	exon1			ATTGCCCCACTGT	AB065774	CCDS31503.1	11q11	2012-08-09		2004-03-10	ENSG00000172188	ENSG00000172188		"GPCR / Class A : Olfactory receptors"	15167	protein-coding gene	gene with protein product				OR4C11P			Standard	NM_001004700		Approved		uc010rii.2	Q6IEV9	OTTHUMG00000165290	ENST00000302231.4:c.605G>A	chr11.hg19:g.55371245C>T	ENSP00000306651:p.Gly202Glu	115.0	0.0		161.0	25.0	NM_001004700	B9EIL4|Q8NGL8	Missense_Mutation	SNP	ENST00000302231.4	hg19	CCDS31503.1	.	.	.	.	.	.	.	.	.	.	C	12.43	1.935284	0.34189	.	.	ENSG00000172188	ENST00000302231	T	0.38401	1.14	4.34	4.34	0.51931	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49305	U	0.000143	T	0.64940	0.2644	M	0.89095	3.005	0.27902	N	0.938934	D	0.89917	1.0	D	0.83275	0.996	T	0.63377	-0.6651	10	0.87932	D	0	.	14.0633	0.64812	0.0:1.0:0.0:0.0	.	202	Q6IEV9	OR4CB_HUMAN	E	202	ENSP00000306651:G202E	ENSP00000306651:G202E	G	-	2	0	OR4C11	55127821	0.000000	0.05858	0.917000	0.36280	0.049000	0.14656	-0.188000	0.09642	2.425000	0.82216	0.478000	0.44815	GGG	.	.		0.403	OR4C11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383268.1	NM_001004700		T	55371245	C	T	55371245	3	4	290	1	0	0	0	0	1	0	0	0	11054	623	22	3	329	3	OR4C11	11	55371245	Missense_Mutation	SNP	C	TCGA-G3-A7M5-01A-11D-A33Q-10	7085457	55371245	79635271	103	42565										
OR4C6	219432	hgsc.bcm.edu	37	chr11	55433436	55433436	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	gcctgtggtcactcaccccaTagacaaggcaatggctgtgt	11	12	2	1	rs367617569		TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr11:55433436T>C	ENST00000314259.3	+	1	823	c.794T>C	c.(793-795)aTa>aCa	p.I265T		NM_001004704.1	NP_001004704.1	Q8NH72	OR4C6_HUMAN	olfactory receptor, family 4, subfamily C, member 6	265						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|lung(49)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	71						ACTCACCCCATAGACAAGGCA	0.473																																					p.I265T		Atlas-SNP	.											.	OR4C6	114	.	0			c.T794C						.	T	THR/ILE	0,4400		0,0,2200	105	102	103		794	2.9	0.9	11		103	1,8591	1.2+/-3.3	0,1,4295	no	missense	OR4C6	NM_001004704.1	89	0,1,6495	CC,CT,TT		0.0116,0.0,0.0077	possibly-damaging	265/310	55433436	1,12991	2200	4296	6496	SO:0001583	missense	219432	exon1			ACCCCATAGACAA	CR593785	CCDS31506.1	11q11	2012-08-09			ENSG00000181903	ENSG00000181903		"GPCR / Class A : Olfactory receptors"	14743	protein-coding gene	gene with protein product							Standard	NM_001004704		Approved		uc010rik.2	Q8NH72	OTTHUMG00000166800	ENST00000314259.3:c.794T>C	chr11.hg19:g.55433436T>C	ENSP00000324769:p.Ile265Thr	76.0	0.0		74.0	27.0	NM_001004704	B2RP11|Q6IFD2	Missense_Mutation	SNP	ENST00000314259.3	hg19	CCDS31506.1	.	.	.	.	.	.	.	.	.	.	T	12.40	1.927195	0.34002	0.0	1.16E-4	ENSG00000181903	ENST00000314259	T	0.00115	8.71	4.07	2.86	0.33363	GPCR, rhodopsin-like superfamily (1);	0.167338	0.27927	N	0.017287	T	0.00144	0.0004	N	0.16368	0.405	0.09310	N	1	P	0.42296	0.775	P	0.48873	0.593	T	0.42682	-0.9437	10	0.51188	T	0.08	.	4.637	0.12530	0.1705:0.0995:0.0:0.7299	.	265	Q8NH72	OR4C6_HUMAN	T	265	ENSP00000324769:I265T	ENSP00000324769:I265T	I	+	2	0	OR4C6	55190012	0.000000	0.05858	0.937000	0.37676	0.540000	0.34992	-5.249000	0.00137	1.484000	0.48361	0.444000	0.29173	ATA	.	.		0.473	OR4C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391504.1	NM_001004704		C	55433436	T	C	55433436	3	2	290	1	0	0	0	0	1	0	0	0	11061	1406	49	2	796	2	OR4C6	11	55433436	Missense_Mutation	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	62191	55433436	79573080	104	42566										
OR5AS1	219447	hgsc.bcm.edu	37	chr11	55798176	55798176	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tccaggaaaagcatctctccTtatgggtgtgcactacaaat	8	10	1	0			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr11:55798176T>A	ENST00000313555.1	+	1	282	c.282T>A	c.(280-282)ccT>ccA	p.P94P		NM_001001921.1	NP_001001921.1	Q8N127	O5AS1_HUMAN	olfactory receptor, family 5, subfamily AS, member 1	94						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(7)|large_intestine(7)|liver(1)|lung(22)|ovary(3)|prostate(4)|skin(3)|stomach(1)	48	Esophageal squamous(21;0.00693)					GCATCTCTCCTTATGGGTGTG	0.433																																					p.P94P		Atlas-SNP	.											.	OR5AS1	121	.	0			c.T282A						.						87	77	80					11																	55798176		2201	4296	6497	SO:0001819	synonymous_variant	219447	exon1			CTCTCCTTATGGG	AB065543	CCDS31516.1	11q11	2012-08-09			ENSG00000181785	ENSG00000181785		"GPCR / Class A : Olfactory receptors"	15261	protein-coding gene	gene with protein product							Standard	NM_001001921		Approved		uc010riw.2	Q8N127	OTTHUMG00000166830	ENST00000313555.1:c.282T>A	chr11.hg19:g.55798176T>A		46.0	0.0		75.0	35.0	NM_001001921	Q6IFB8	Silent	SNP	ENST00000313555.1	hg19	CCDS31516.1																																																																																			.	.		0.433	OR5AS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391538.1	NM_001001921		A	55798176	T	A	55798176	2	1	290	1	0	0	0	0	0	0	0	1	11155	1596	56	4		4	OR5AS1	11	55798176	Silent	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	364740	55798176	79208340	105	42567										
OR8J3	81168	hgsc.bcm.edu	37	chr11	55905001	55905001	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	caagattgatgatagctagaTgtctcaggaaaaagtacatg	10	5	1	4			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr11:55905001T>A	ENST00000301529.1	-	1	193	c.194A>T	c.(193-195)cAt>cTt	p.H65L		NM_001004064.1	NP_001004064.1	Q8NGG0	OR8J3_HUMAN	olfactory receptor, family 8, subfamily J, member 3	65						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(1)|lung(38)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	59	Esophageal squamous(21;0.00693)					GATAGCTAGATGTCTCAGGAA	0.438																																					p.H65L		Atlas-SNP	.											.	OR8J3	112	.	0			c.A194T						.						144	140	141					11																	55905001		2201	4296	6497	SO:0001583	missense	81168	exon1			GCTAGATGTCTCA		CCDS31520.1	11q12.2	2012-08-09			ENSG00000167822	ENSG00000167822		"GPCR / Class A : Olfactory receptors"	15312	protein-coding gene	gene with protein product							Standard	NM_001004064		Approved		uc010riz.2	Q8NGG0	OTTHUMG00000166834	ENST00000301529.1:c.194A>T	chr11.hg19:g.55905001T>A	ENSP00000301529:p.His65Leu	94.0	0.0		133.0	57.0	NM_001004064	Q6IFB6|Q96RC2	Missense_Mutation	SNP	ENST00000301529.1	hg19	CCDS31520.1	.	.	.	.	.	.	.	.	.	.	T	10.12	1.262808	0.23051	.	.	ENSG00000167822	ENST00000301529	T	0.02944	4.1	3.26	1.81	0.25067	GPCR, rhodopsin-like superfamily (1);	0.185693	0.38058	N	0.001835	T	0.07503	0.0189	M	0.81802	2.56	0.09310	N	1	P	0.51653	0.947	P	0.49451	0.611	T	0.07829	-1.0752	10	0.87932	D	0	.	8.367	0.32393	0.2358:0.0:0.0:0.7642	.	65	Q8NGG0	OR8J3_HUMAN	L	65	ENSP00000301529:H65L	ENSP00000301529:H65L	H	-	2	0	OR8J3	55661577	0.000000	0.05858	0.002000	0.10522	0.070000	0.16714	0.882000	0.28186	1.268000	0.44264	0.240000	0.17902	CAT	.	.		0.438	OR8J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391542.1	NM_001004064		A	55905001	T	A	55905001	3	1	290	1	0	0	0	0	1	0	0	0	11251	1464	51	4	755	4	OR8J3	11	55905001	Missense_Mutation	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	106825	55905001	79101515	106	42568										
OR5M10	390167	hgsc.bcm.edu	37	chr11	56344760	56344760	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	aagccatacatgtaaggcacAgtgaccagagagatgcaaat	10	8	0	3			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr11:56344760A>T	ENST00000526812.2	-	1	503	c.438T>A	c.(436-438)acT>acA	p.T146T		NM_001004741.1	NP_001004741.1	Q6IEU7	OR5MA_HUMAN	olfactory receptor, family 5, subfamily M, member 10	146						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(15)|upper_aerodigestive_tract(2)|urinary_tract(2)	25						TGTAAGGCACAGTGACCAGAG	0.453																																					p.T146T		Atlas-SNP	.											.	OR5M10	56	.	0			c.T438A						.						182	172	175					11																	56344760		2017	4203	6220	SO:0001819	synonymous_variant	390167	exon1			AGGCACAGTGACC	BK004515	CCDS53630.1	11q11	2012-08-09				ENSG00000254834		"GPCR / Class A : Olfactory receptors"	15290	protein-coding gene	gene with protein product							Standard	NM_001004741		Approved		uc001niz.1	Q6IEU7		ENST00000526812.2:c.438T>A	chr11.hg19:g.56344760A>T		117.0	0.0		157.0	60.0	NM_001004741	B9EIL9	Silent	SNP	ENST00000526812.2	hg19	CCDS53630.1																																																																																			.	.		0.453	OR5M10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391609.1	NM_001004741		T	56344760	A	T	56344760	2	4	290	1	0	0	0	0	0	0	0	1	11182	175	7	4		4	OR5M10	11	56344760	Silent	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	439759	56344760	78661756	107	42569										
PRG3	10394	hgsc.bcm.edu	37	chr11	57147137	57147137	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	atcctcaaagttgtcttgacAggcagaagccttgacctcct	8	12	2	3			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr11:57147137A>T	ENST00000287143.2	-	3	314	c.205T>A	c.(205-207)Tgt>Agt	p.C69S		NM_006093.3	NP_006084.2	Q8TBJ4	LPPR1_HUMAN	proteoglycan 3	0					nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)			large_intestine(3)|lung(5)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	13						TTGTCTTGACAGGCAGAAGCC	0.542																																					p.C69S	Melanoma(154;1456 2519 19358 45229)	Atlas-SNP	.											.	PRG3	35	.	0			c.T205A						.						118	99	105					11																	57147137		2201	4296	6497	SO:0001583	missense	10394	exon3			CTTGACAGGCAGA	AF132209	CCDS7954.1	11q12.1	2008-02-05			ENSG00000156575	ENSG00000156575			9363	protein-coding gene	gene with protein product		606814				10318872, 11170744	Standard	NM_006093		Approved	MBPH	uc001njv.2	Q9Y2Y8	OTTHUMG00000167026	ENST00000287143.2:c.205T>A	chr11.hg19:g.57147137A>T	ENSP00000287143:p.Cys69Ser	81.0	0.0		114.0	33.0	NM_006093	Q5VX23|Q9NXE2	Missense_Mutation	SNP	ENST00000287143.2	hg19	CCDS7954.1	.	.	.	.	.	.	.	.	.	.	A	6.244	0.413080	0.11812	.	.	ENSG00000156575	ENST00000287143	T	0.38240	1.15	4.61	-9.23	0.00672	.	2.082990	0.02179	N	0.060318	T	0.10809	0.0264	N	0.02916	-0.46	0.09310	N	1	B	0.14012	0.009	B	0.09377	0.004	T	0.13926	-1.0491	10	0.20046	T	0.44	4.6396	0.8412	0.01150	0.154:0.2949:0.2088:0.3423	.	69	Q9Y2Y8	PRG3_HUMAN	S	69	ENSP00000287143:C69S	ENSP00000287143:C69S	C	-	1	0	PRG3	56903713	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.816000	0.04477	-1.358000	0.02177	-1.476000	0.00998	TGT	.	.		0.542	PRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392467.1	NM_006093		T	57147137	A	T	57147137	3	4	290	1	0	0	0	0	1	0	0	0	12492	188	7	4	488	4	PRG3	11	57147137	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	802377	57147137	77859379	108	42570										
PCNXL3	399909	hgsc.bcm.edu	37	chr11	65391690	65391690	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	acaactgggtgatcgcgtacAgccgtcctgtctacttctgc	10	13	2	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr11:65391690A>T	ENST00000355703.3	+	14	3108	c.2569A>T	c.(2569-2571)Agc>Tgc	p.S857C		NM_032223.2	NP_115599.2	Q9H6A9	PCX3_HUMAN	pecanex-like 3 (Drosophila)	857						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)	13						GATCGCGTACAGCCGTCCTGT	0.632																																					p.S857C		Atlas-SNP	.											.	PCNXL3	140	.	0			c.A2569T						.						55	61	59					11																	65391690		2182	4273	6455	SO:0001583	missense	399909	exon14			GCGTACAGCCGTC	BX640978	CCDS44650.1	11q12.1	2008-07-21			ENSG00000197136	ENSG00000197136			18760	protein-coding gene	gene with protein product						15146197	Standard	NM_032223		Approved	FLJ22427	uc001oey.2	Q9H6A9	OTTHUMG00000166539	ENST00000355703.3:c.2569A>T	chr11.hg19:g.65391690A>T	ENSP00000347931:p.Ser857Cys	26.0	0.0		42.0	14.0	NM_032223	Q6MZN8	Missense_Mutation	SNP	ENST00000355703.3	hg19	CCDS44650.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.756911	0.89843	.	.	ENSG00000197136	ENST00000355703	T	0.60424	0.19	4.75	4.75	0.60458	.	.	.	.	.	T	0.74906	0.3778	M	0.81341	2.54	0.49051	D	0.999749	D	0.69078	0.997	D	0.70935	0.971	T	0.78912	-0.2017	9	0.87932	D	0	.	12.1857	0.54236	1.0:0.0:0.0:0.0	.	857	Q9H6A9	PCX3_HUMAN	C	857	ENSP00000347931:S857C	ENSP00000347931:S857C	S	+	1	0	PCNXL3	65148266	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.497000	0.90488	1.783000	0.52377	0.379000	0.24179	AGC	.	.		0.632	PCNXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390321.1	NM_032223		T	65391690	A	T	65391690	3	4	290	1	0	0	0	0	1	0	0	0	11602	188	7	4	2623	4	PCNXL3	11	65391690	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	8244553	65391690	69614826	109	42571										
GRIA4	2893	hgsc.bcm.edu	37	chr11	105769114	105769114	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	atggatcgctggaagaaactAgatcagagagagtatccagg	13	6	1	4			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr11:105769114A>T	ENST00000530497.1	+	6	846	c.846A>T	c.(844-846)ctA>ctT	p.L282L	GRIA4_ENST00000393125.2_Silent_p.L282L|GRIA4_ENST00000428631.2_Silent_p.L282L|GRIA4_ENST00000393127.2_Silent_p.L282L|GRIA4_ENST00000282499.5_Silent_p.L282L|GRIA4_ENST00000525187.1_Silent_p.L282L			P48058	GRIA4_HUMAN	glutamate receptor, ionotropic, AMPA 4	282					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(24)|liver(2)|lung(25)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	82		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)		GGAAGAAACTAGATCAGAGAG	0.348																																					p.L282L		Atlas-SNP	.											.	GRIA4	380	.	0			c.A846T						.						60	62	61					11																	105769114		2202	4299	6501	SO:0001819	synonymous_variant	2893	exon7			GAAACTAGATCAG	U16129	CCDS8333.1, CCDS41706.1, CCDS41707.1	11q22	2012-08-29	2012-02-03		ENSG00000152578	ENSG00000152578		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4574	protein-coding gene	gene with protein product		138246	"glutamate receptor, ionotrophic, AMPA 4"	GLUR4			Standard	NM_001077244		Approved	GluA4, GLURD	uc001pix.2	P48058	OTTHUMG00000166236	ENST00000530497.1:c.846A>T	chr11.hg19:g.105769114A>T		151.0	0.0		173.0	72.0	NM_001077244	Q86XE8	Silent	SNP	ENST00000530497.1	hg19	CCDS8333.1																																																																																			.	.		0.348	GRIA4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388593.1			T	105769114	A	T	105769114	2	4	290	1	0	0	0	0	0	0	0	1	6779	407	15	4		4	GRIA4	11	105769114	Silent	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	40377424	105769114	29237402	110	42572										
SCN3B	55800	hgsc.bcm.edu	37	chr11	123524465	123524465	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tggtacttaccccagtagatAagcacgagagaagccagggg	13	9	0	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr11:123524465A>T	ENST00000392770.2	-	1	847	c.45T>A	c.(43-45)ctT>ctA	p.L15L	SCN3B_ENST00000299333.3_Silent_p.L15L|SCN3B_ENST00000530277.1_Silent_p.L15L	NM_018400.3	NP_060870.1	Q9NY72	SCN3B_HUMAN	sodium channel, voltage-gated, type III, beta subunit	15					atrial cardiac muscle cell action potential (GO:0086014)|axon guidance (GO:0007411)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|positive regulation of heart rate (GO:0010460)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|ventricular cardiac muscle cell action potential (GO:0086005)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	ion channel binding (GO:0044325)|sodium channel regulator activity (GO:0017080)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(16)|ovary(2)|skin(2)	26		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0227)	Valproic Acid(DB00313)|Zonisamide(DB00909)	CCCAGTAGATAAGCACGAGAG	0.493																																					p.L15L		Atlas-SNP	.											.	SCN3B	53	.	0			c.T45A						.						202	203	203					11																	123524465		2202	4299	6501	SO:0001819	synonymous_variant	55800	exon1			GTAGATAAGCACG	AJ243396	CCDS8442.1	11q24.1	2014-09-17	2012-02-28		ENSG00000166257	ENSG00000166257		"Sodium channels", "Voltage-gated ion channels / Sodium channels", "Immunoglobulin superfamily / V-set domain containing"	20665	protein-coding gene	gene with protein product		608214	"sodium channel, voltage-gated, type III, beta"			10688874	Standard	XR_428980		Approved	HSA243396	uc001pzb.1	Q9NY72	OTTHUMG00000166006	ENST00000392770.2:c.45T>A	chr11.hg19:g.123524465A>T		77.0	0.0		70.0	36.0	NM_018400	A5H1I5|Q17RL3|Q9ULR2	Silent	SNP	ENST00000392770.2	hg19	CCDS8442.1																																																																																			.	.		0.493	SCN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387412.1	NM_018400		T	123524465	A	T	123524465	2	4	290	1	0	0	0	0	0	0	0	1	13934	349	13	4		4	SCN3B	11	123524465	Silent	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	17755351	123524465	11482051	111	42573										
NFRKB	4798	hgsc.bcm.edu	37	chr11	129751620	129751644	+	Splice_Site	DEL	AAAAAAGAGCATCTTACCTCGACTT	AAAAAAGAGCATCTTACCTCGACTT	-													0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	cctacaaaaaagagcatcttAcctcgactttctccagcaag							TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	AAAAAAGAGCATCTTACCTCGACTT	AAAAAAGAGCATCTTACCTCGACTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr11:129751620_129751644delAAAAAAGAGCATCTTACCTCGACTT	ENST00000446488.3	-	11	1399_1422	c.1296_1319delAAGTCGAGGTAAGATGCTCTTTTTT	c.(1294-1320)caaagtcgaggtaagatgctctttttt>cat	p.QSRGKMLFF432fs	NFRKB_ENST00000304521.5_Splice_Site_p.QSRGKMLFF432fs|NFRKB_ENST00000524746.1_Splice_Site_p.QSRGKMLFF432fs|NFRKB_ENST00000524794.1_Splice_Site_p.QSRGKMLFF457fs	NM_001143835.1	NP_001137307.1	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein	432	Winged-helix like domain.				DNA recombination (GO:0006310)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protease binding (GO:0002020)	p.R464P(1)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(13)|ovary(4)|skin(3)|urinary_tract(1)	32	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0167)|Lung(977;0.171)|LUSC - Lung squamous cell carcinoma(976;0.184)		AGAGCATCTTACCTCGACTTTCTCCAGCAAGATACTGCAGGGCTG	0.48											OREG0021512	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.463_465del		Atlas-Indel,Pindel	.											.	NFRKB	101	.	1	Substitution - Missense(1)	lung(1)	c.1387_1393del						.																																			SO:0001630	splice_region_variant	4798	exon10			.		CCDS8483.1, CCDS44770.1	11q24-q25	2011-07-06			ENSG00000170322	ENSG00000170322		"INO80 complex subunits"	7802	protein-coding gene	gene with protein product	"nuclear factor related to kappa B binding protein", "DNA-binding protein R kappa B", "INO80 complex subunit G"	164013				1427843	Standard	NM_006165		Approved	DKFZp547B2013, INO80G	uc001qfg.3	Q6P4R8	OTTHUMG00000165761	ENST00000446488.3:c.1318+1AAGTCGAGGTAAGATGCTCTTTTTT>-	chr11.hg19:g.129751620_129751644delAAAAAAGAGCATCTTACCTCGACTT		80.0	0.0	1574	76.0	11.0	NM_006165	Q12869|Q15312|Q9H048	Frame_Shift_Del	DEL	ENST00000446488.3	hg19	CCDS44770.1																																																																																			.	.		0.48	NFRKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386063.2	NM_006165	Frame_Shift_Del	-	129751644	AAAAAAGAGCATCTTACCTCGACTT	-	129751620	8	5	290	1	0	1	0	1	0	0	1	0	10393	405	14	0	2643	0	NFRKB	11	129751620	Splice_Site	DEL	AAAAAAGAGCATCTTACCTCGACTT	TCGA-G3-A7M5-01A-11D-A33Q-10	6227155	129751620	5254896	112	42574										
PDE3A	5139	hgsc.bcm.edu	37	chr12	20523005	20523005	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	aacaaatcttgccgcagtccGcggaggcggctccaagggag	14	12	1	0			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr12:20523005G>T	ENST00000359062.3	+	1	827	c.787G>T	c.(787-789)Gcg>Tcg	p.A263S	RP11-284H19.1_ENST00000535755.1_RNA	NM_000921.4|NM_001244683.1	NP_000912.3|NP_001231612.1	Q14432	PDE3A_HUMAN	phosphodiesterase 3A, cGMP-inhibited	263					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP-mediated signaling (GO:0019934)|diterpenoid metabolic process (GO:0016101)|lipid metabolic process (GO:0006629)|negative regulation of apoptotic process (GO:0043066)|negative regulation of vascular permeability (GO:0043116)|oocyte maturation (GO:0001556)|positive regulation of oocyte development (GO:0060282)|positive regulation of vascular permeability (GO:0043117)|regulation of meiosis (GO:0040020)|response to cAMP (GO:0051591)|response to drug (GO:0042493)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(7)|lung(29)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	58	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Caffeine(DB00201)|Cilostazol(DB01166)|Enoximone(DB04880)|Ibudilast(DB05266)|Levosimendan(DB00922)|Milrinone(DB00235)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Tofisopam(DB08811)	GCCGCAGTCCGCGGAGGCGGC	0.612																																					p.A263S		Atlas-SNP	.											.	PDE3A	184	.	0			c.G787T						.						31	36	34					12																	20523005		2198	4299	6497	SO:0001583	missense	5139	exon1			CAGTCCGCGGAGG		CCDS31754.1	12p12.2	2011-04-15			ENSG00000172572	ENSG00000172572	3.1.4.17	"Phosphodiesterases"	8778	protein-coding gene	gene with protein product		123805				1315035, 10679291	Standard	NM_000921		Approved	CGI-PDE	uc001reh.2	Q14432	OTTHUMG00000168962	ENST00000359062.3:c.787G>T	chr12.hg19:g.20523005G>T	ENSP00000351957:p.Ala263Ser	29.0	0.0		37.0	22.0	NM_000921	O60865|Q13348|Q17RD1	Missense_Mutation	SNP	ENST00000359062.3	hg19	CCDS31754.1	.	.	.	.	.	.	.	.	.	.	G	11.78	1.741618	0.30865	.	.	ENSG00000172572	ENST00000359062	T	0.61742	0.08	4.06	-1.52	0.08637	.	3.626890	0.00465	N	0.000107	T	0.26810	0.0656	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.10132	-1.0643	10	0.20519	T	0.43	.	2.1787	0.03868	0.1553:0.1102:0.3239:0.4106	.	263	Q14432	PDE3A_HUMAN	S	263	ENSP00000351957:A263S	ENSP00000351957:A263S	A	+	1	0	PDE3A	20414272	0.000000	0.05858	0.665000	0.29768	0.995000	0.86356	-0.540000	0.06106	-0.182000	0.10602	0.650000	0.86243	GCG	.	.		0.612	PDE3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401756.2			T	20523005	G	T	20523005	3	4	290	1	0	0	0	0	1	0	0	0	11646	1087	38	1	789	1	PDE3A	12	20523005	Missense_Mutation	SNP	G	TCGA-G3-A7M5-01A-11D-A33Q-10		20523005	113328890	113	42575										
NR4A1	3164	hgsc.bcm.edu	37	chr12	52452600	52452600	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	gctgcctgtcacgtctgttgGgcaaactgcccgagctgcgg	14	13	2	0	rs577412593		TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr12:52452600G>C	ENST00000243050.1	+	8	1983	c.1669G>C	c.(1669-1671)Ggc>Cgc	p.G557R	NR4A1_ENST00000360284.3_Missense_Mutation_p.G570R|NR4A1_ENST00000394824.2_Missense_Mutation_p.G557R|NR4A1_ENST00000394825.1_Missense_Mutation_p.G557R|NR4A1_ENST00000550082.1_Missense_Mutation_p.G570R|RP11-1100L3.8_ENST00000564363.1_lincRNA|NR4A1_ENST00000545748.1_Missense_Mutation_p.G611R	NM_002135.4	NP_002126.2	P22736	NR4A1_HUMAN	nuclear receptor subfamily 4, group A, member 1	557					cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial cell chemotaxis (GO:0035767)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)	16				BRCA - Breast invasive adenocarcinoma(357;0.0967)		ACGTCTGTTGGGCAAACTGCC	0.652																																					p.G570R		Atlas-SNP	.											.	NR4A1	77	.	0			c.G1708C						.						46	42	44					12																	52452600		2203	4300	6503	SO:0001583	missense	3164	exon8			CTGTTGGGCAAAC	L13740	CCDS8818.1, CCDS55828.1, CCDS73471.1	12q13	2013-01-16			ENSG00000123358	ENSG00000123358		"Nuclear hormone receptors"	7980	protein-coding gene	gene with protein product		139139		HMR, GFRP1		2626032	Standard	NM_002135		Approved	TR3, N10, NAK-1, NGFIB, NUR77	uc001rzt.3	P22736	OTTHUMG00000150393	ENST00000243050.1:c.1669G>C	chr12.hg19:g.52452600G>C	ENSP00000243050:p.Gly557Arg	44.0	0.0		41.0	23.0	NM_001202233	B4DML7|Q15627|Q53Y00|Q6IBU8	Missense_Mutation	SNP	ENST00000243050.1	hg19	CCDS8818.1	.	.	.	.	.	.	.	.	.	.	G	15.49	2.849188	0.51270	.	.	ENSG00000123358	ENST00000360284;ENST00000545748;ENST00000550082;ENST00000243050;ENST00000394825;ENST00000394824	D;D;D;D;D;D	0.96587	-4.06;-4.06;-4.06;-4.06;-4.06;-4.06	5.06	5.06	0.68205	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.052982	0.85682	D	0.000000	D	0.97424	0.9157	M	0.81802	2.56	0.54753	D	0.999986	D;B	0.76494	0.999;0.307	P;B	0.62435	0.902;0.095	D	0.96736	0.9543	10	0.51188	T	0.08	.	11.7688	0.51945	0.0846:0.0:0.9154:0.0	.	570;557	B4DML7;P22736	.;NR4A1_HUMAN	R	570;611;570;557;557;557	ENSP00000353427:G570R;ENSP00000440864:G611R;ENSP00000449539:G570R;ENSP00000243050:G557R;ENSP00000378302:G557R;ENSP00000378301:G557R	ENSP00000243050:G557R	G	+	1	0	NR4A1	50738867	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.564000	0.67359	2.813000	0.96785	0.655000	0.94253	GGC	.	.		0.652	NR4A1-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000317922.2			C	52452600	G	C	52452600	3	2	290	1	0	0	0	0	1	0	0	0	10641	1232	43	4	1691	4	NR4A1	12	52452600	Missense_Mutation	SNP	G	TCGA-G3-A7M5-01A-11D-A33Q-10	31929595	52452600	81399295	114	42576										
LGR5	8549	hgsc.bcm.edu	37	chr12	71977559	71977560	+	Nonsense_Mutation	DNP	CC	CC	AA													0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	cagatcccctctgtacatttCccccattaaactgttaattg							TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr12:71977559_71977560CC>AA	ENST00000266674.5	+	18	2080_2081	c.1769_1770CC>AA	c.(1768-1770)tCC>tAA	p.S590*	RP11-186F10.2_ENST00000546601.1_RNA|LGR5_ENST00000540815.2_Nonsense_Mutation_p.S566*|LGR5_ENST00000536515.1_Nonsense_Mutation_p.S518*			O75473	LGR5_HUMAN	leucine-rich repeat containing G protein-coupled receptor 5	590					G-protein coupled receptor signaling pathway (GO:0007186)|inner ear development (GO:0048839)|positive regulation of canonical Wnt signaling pathway (GO:0090263)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)		NUP107/LGR5(2)	endometrium(2)|kidney(3)|large_intestine(2)|lung(24)|ovary(1)|pancreas(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(3)	48						CTGTACATTTCCCCCATTAAAC	0.5																																					p.S590Y|p.S590S		Atlas-SNP	.											.	LGR5	103	.	0			c.C1769A|c.C1770A						.																																			SO:0001587	stop_gained	8549	exon18			ACATTTCCCCCAT|CATTTCCCCCATT	AF062006	CCDS9000.1, CCDS61194.1, CCDS61195.1	12q22-q23	2012-08-21	2011-01-25	2004-11-12				"GPCR / Class A : Orphans"	4504	protein-coding gene	gene with protein product		606667	"G protein-coupled receptor 49", "leucine-rich repeat-containing G protein-coupled receptor 5"	GPR67, GPR49		9642114	Standard	NM_003667		Approved	HG38, FEX	uc001swl.4	O75473	OTTHUMG00000169543	Exception_encountered	chr12.hg19:g.71977559_71977560delinsAA	ENSP00000266674:p.Ser590*	148.0|146.0	0.0		161.0|160.0	67.0|66.0	NM_003667	D8MCT0|Q4VAM0|Q4VAM2|Q9UP75	Missense_Mutation|Silent	SNP	ENST00000266674.5	hg19	CCDS9000.1																																																																																			.	.		0.5	LGR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404744.1	NM_003667		AA	71977560	CC	AA	71977559	4	1	290	1	0	0	0	0	0	1	0	0	8766	855	30	3	1839	3	LGR5	12	71977559	Nonsense_Mutation	DNP	CC	TCGA-G3-A7M5-01A-11D-A33Q-10	19524959	71977559	61874336	115	42577										
LRRIQ1	84125	hgsc.bcm.edu	37	chr12	85554467	85554467	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	aaatcaccaaagatggtacaGcccagaagagatggttactt	9	8	1	3			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr12:85554467G>T	ENST00000393217.2	+	24	4858	c.4797G>T	c.(4795-4797)caG>caT	p.Q1599H	LRRIQ1_ENST00000528777.3_3'UTR	NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	1599										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		AGATGGTACAGCCCAGAAGAG	0.308																																					p.Q1599H		Atlas-SNP	.											.	LRRIQ1	512	.	0			c.G4797T						.						120	108	112					12																	85554467		1823	4079	5902	SO:0001583	missense	84125	exon24			GGTACAGCCCAGA	AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.4797G>T	chr12.hg19:g.85554467G>T	ENSP00000376910:p.Gln1599His	68.0	0.0		105.0	44.0	NM_001079910	Q567P4|Q9BS17|Q9HA36	Missense_Mutation	SNP	ENST00000393217.2	hg19	CCDS41816.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	1.853|1.853	-0.464480|-0.464480	0.04476|0.04476	.|.	.|.	ENSG00000133640|ENSG00000133640	ENST00000393217|ENST00000526363	T|.	0.53640|.	0.61|.	4.77|4.77	-1.33|-1.33	0.09172|0.09172	.|.	.|.	.|.	.|.	.|.	T|T	0.19604|0.19604	0.0471|0.0471	N|N	0.24115|0.24115	0.695|0.695	0.09310|0.09310	N|N	1|1	B|.	0.14805|.	0.011|.	B|.	0.14023|.	0.01|.	T|T	0.25398|0.25398	-1.0133|-1.0133	9|5	0.41790|.	T|.	0.15|.	.|.	2.7392|2.7392	0.05249|0.05249	0.234:0.12:0.5228:0.1232|0.234:0.12:0.5228:0.1232	.|.	1599|.	Q96JM4|.	LRIQ1_HUMAN|.	H|I	1599|20	ENSP00000376910:Q1599H|.	ENSP00000376910:Q1599H|.	Q|S	+|+	3|2	2|0	LRRIQ1|LRRIQ1	84078598|84078598	0.001000|0.001000	0.12720|0.12720	0.015000|0.015000	0.15790|0.15790	0.347000|0.347000	0.29111|0.29111	0.366000|0.366000	0.20365|0.20365	-0.136000|-0.136000	0.11475|0.11475	0.557000|0.557000	0.71058|0.71058	CAG|AGC	.	.		0.308	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165		T	85554467	G	T	85554467	3	4	290	1	0	0	0	0	1	0	0	0	9038	962	34	3	4891	3	LRRIQ1	12	85554467	Missense_Mutation	SNP	G	TCGA-G3-A7M5-01A-11D-A33Q-10	13576908	85554467	48297428	116	42578										
AMDHD1	144193	hgsc.bcm.edu	37	chr12	96360279	96360279	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	gagatctcattatcatcaatTcatcccggtgagtgtgcttc	8	10	4	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr12:96360279T>G	ENST00000266736.2	+	8	1292	c.1186T>G	c.(1186-1188)Tca>Gca	p.S396A		NM_152435.2	NP_689648.2	Q96NU7	HUTI_HUMAN	amidohydrolase domain containing 1	396					cellular nitrogen compound metabolic process (GO:0034641)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	imidazolonepropionase activity (GO:0050480)|metal ion binding (GO:0046872)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|skin(1)	22						TATCATCAATTCATCCCGGTG	0.448																																					p.S396A		Atlas-SNP	.											.	AMDHD1	56	.	0			c.T1186G						.						220	206	211					12																	96360279		2203	4300	6503	SO:0001583	missense	144193	exon8			ATCAATTCATCCC	AB075878	CCDS9057.1	12q23.1	2006-02-02				ENSG00000139344			28577	protein-coding gene	gene with protein product							Standard	NM_152435		Approved	MGC35366	uc001tel.2	Q96NU7	OTTHUMG00000170353	ENST00000266736.2:c.1186T>G	chr12.hg19:g.96360279T>G	ENSP00000266736:p.Ser396Ala	37.0	0.0		75.0	18.0	NM_152435	A8K463|Q68CI8	Missense_Mutation	SNP	ENST00000266736.2	hg19	CCDS9057.1	.	.	.	.	.	.	.	.	.	.	T	0.369	-0.934822	0.02340	.	.	ENSG00000139344	ENST00000266736	T	0.71103	-0.54	5.82	-1.44	0.08856	Metal-dependent hydrolase, composite domain (1);	0.784314	0.12321	N	0.479276	T	0.46308	0.1386	N	0.02802	-0.49	0.24577	N	0.99389	B	0.02656	0.0	B	0.01281	0.0	T	0.13683	-1.0500	10	0.12430	T	0.62	-7.277	20.0123	0.97464	0.0:0.0:0.7636:0.2364	.	396	Q96NU7	HUTI_HUMAN	A	396	ENSP00000266736:S396A	ENSP00000266736:S396A	S	+	1	0	AMDHD1	94884410	0.173000	0.23056	0.975000	0.42487	0.390000	0.30446	-0.267000	0.08619	-0.496000	0.06650	-0.396000	0.06452	TCA	.	.		0.448	AMDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408640.1	NM_152435		G	96360279	T	G	96360279	3	3	290	1	0	0	0	0	1	0	0	0	567	1783	62	5	1216	5	AMDHD1	12	96360279	Missense_Mutation	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	10805812	96360279	37491616	117	42579										
RASAL1	8437	hgsc.bcm.edu	37	chr12	113553065	113553065	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	gaacggaagagggtgttgggGtccactgggaggacaggagg	21	5	0	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr12:113553065G>T	ENST00000261729.5	-	12	1323	c.1008C>A	c.(1006-1008)gaC>gaA	p.D336E	RASAL1_ENST00000548055.1_Missense_Mutation_p.D336E|RASAL1_ENST00000446861.3_Missense_Mutation_p.D336E|RASAL1_ENST00000546530.1_Missense_Mutation_p.D336E|RASAL1_ENST00000418411.2_5'UTR			O95294	RASL1_HUMAN	RAS protein activator like 1 (GAP1 like)	336	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|phospholipid binding (GO:0005543)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(3)|prostate(2)|skin(2)	43						GGGTGTTGGGGTCCACTGGGA	0.567																																					p.D336E		Atlas-SNP	.											.	RASAL1	89	.	0			c.C1008A						.						176	182	180					12																	113553065		2203	4300	6503	SO:0001583	missense	8437	exon12			GTTGGGGTCCACT	AF086713	CCDS9165.1, CCDS55888.1, CCDS55889.1, CCDS73529.1	12q23-q24	2013-01-10			ENSG00000111344	ENSG00000111344		"Pleckstrin homology (PH) domain containing"	9873	protein-coding gene	gene with protein product		604118				9751798	Standard	NM_001193520		Approved	RASAL	uc001tul.3	O95294	OTTHUMG00000169705	ENST00000261729.5:c.1008C>A	chr12.hg19:g.113553065G>T	ENSP00000261729:p.Asp336Glu	93.0	0.0		153.0	40.0	NM_004658	B7ZKM4|C9JFK5|F8VQX1|Q52M03|Q59H24|Q96CC7	Missense_Mutation	SNP	ENST00000261729.5	hg19	CCDS9165.1	.	.	.	.	.	.	.	.	.	.	G	11.55	1.671794	0.29693	.	.	ENSG00000111344	ENST00000546530;ENST00000261729;ENST00000446861;ENST00000548055	T;T;T;T	0.17054	2.3;2.3;2.3;2.3	4.78	1.42	0.22433	Rho GTPase activation protein (1);Ras GTPase-activating protein (4);	0.000000	0.85682	D	0.000000	T	0.25457	0.0619	L	0.42632	1.34	0.42957	D	0.994399	D;D;D;D;P;P;D	0.89917	1.0;1.0;1.0;1.0;0.46;0.655;1.0	D;D;D;D;B;P;D	0.97110	0.998;1.0;0.996;1.0;0.327;0.557;0.999	T	0.06862	-1.0803	10	0.19147	T	0.46	.	7.3437	0.26652	0.4556:0.0:0.5444:0.0	.	336;336;336;348;336;336;336	B7ZKM4;B4DG06;F8VRH9;Q59H24;F8VQX1;O95294;O95294-2	.;.;.;.;.;RASL1_HUMAN;.	E	336	ENSP00000450244:D336E;ENSP00000261729:D336E;ENSP00000395920:D336E;ENSP00000448510:D336E	ENSP00000261729:D336E	D	-	3	2	RASAL1	112037448	1.000000	0.71417	0.999000	0.59377	0.428000	0.31595	0.807000	0.27140	0.449000	0.26747	-0.424000	0.05967	GAC	.	.		0.567	RASAL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405522.2	NM_004658		T	113553065	G	T	113553065	3	4	290	1	0	0	0	0	1	0	0	0	13078	1252	44	3	1450	3	RASAL1	12	113553065	Missense_Mutation	SNP	G	TCGA-G3-A7M5-01A-11D-A33Q-10	17192786	113553065	20298830	118	42580										
VPS33A	65082	hgsc.bcm.edu	37	chr12	122717409	122717409	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	agtggggccctgggaggatgCggaggacctcctcgatgctc	17	11	0	0			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr12:122717409C>A	ENST00000267199.4	-	12	1659	c.1547G>T	c.(1546-1548)cGc>cTc	p.R516L	RP11-512M8.5_ENST00000535844.1_Missense_Mutation_p.R477L	NM_022916.4	NP_075067.2	Q96AX1	VP33A_HUMAN	vacuolar protein sorting 33 homolog A (S. cerevisiae)	516					lysosome localization (GO:0032418)|melanosome localization (GO:0032400)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of developmental pigmentation (GO:0048070)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	early endosome (GO:0005769)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)				NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(13)|ovary(1)|skin(2)	28	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000336)|Epithelial(86;0.000606)|BRCA - Breast invasive adenocarcinoma(302;0.23)		TGGGAGGATGCGGAGGACCTC	0.592																																					p.R516L		Atlas-SNP	.											.	VPS33A	61	.	0			c.G1547T						.						45	42	43					12																	122717409		2203	4300	6503	SO:0001583	missense	65082	exon12			AGGATGCGGAGGA	AK026048	CCDS9231.1	12q24.31	2008-06-23	2006-04-04		ENSG00000139719	ENSG00000139719			18179	protein-coding gene	gene with protein product		610034	"vacuolar protein sorting 33A (yeast)"			11250079	Standard	NM_022916		Approved		uc001ucd.3	Q96AX1	OTTHUMG00000168920	ENST00000267199.4:c.1547G>T	chr12.hg19:g.122717409C>A	ENSP00000267199:p.Arg516Leu	83.0	0.0		118.0	41.0	NM_022916	Q547V4|Q9H5Q0	Missense_Mutation	SNP	ENST00000267199.4	hg19	CCDS9231.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.168288	0.78339	.	.	ENSG00000139719	ENST00000267199	T	0.29142	1.58	5.54	4.54	0.55810	.	0.052923	0.64402	D	0.000001	T	0.27832	0.0685	M	0.65498	2.005	0.80722	D	1	P	0.34587	0.458	B	0.34824	0.19	T	0.23547	-1.0185	10	0.51188	T	0.08	-24.5461	3.6122	0.08065	0.0:0.6492:0.0:0.3508	.	516	Q96AX1	VP33A_HUMAN	L	516	ENSP00000267199:R516L	ENSP00000446319:R477L	R	-	2	0	VPS33A	121283362	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.182000	0.71995	2.596000	0.87737	0.655000	0.94253	CGC	.	.		0.592	VPS33A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401607.2			A	122717409	C	A	122717409	3	1	290	1	0	0	0	0	1	0	0	0	17216	768	27	1	251	1	VPS33A	12	122717409	Missense_Mutation	SNP	C	TCGA-G3-A7M5-01A-11D-A33Q-10	9164344	122717409	11134486	119	42581										
SACS	26278	hgsc.bcm.edu	37	chr13	23910455	23910455	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	ttttctttctgcccaaattcTgtgccaagtgttgtaaaaca	6	9	3	0			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr13:23910455T>G	ENST00000382292.3	-	9	7833	c.7560A>C	c.(7558-7560)acA>acC	p.T2520T	SACS_ENST00000382298.3_Silent_p.T2520T|SACS_ENST00000402364.1_Silent_p.T1770T			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	2520					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		GCCCAAATTCTGTGCCAAGTG	0.398																																					p.T2520T		Atlas-SNP	.											.	SACS	871	.	0			c.A7560C						.						118	114	115					13																	23910455		2203	4299	6502	SO:0001819	synonymous_variant	26278	exon10			AAATTCTGTGCCA	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.7560A>C	chr13.hg19:g.23910455T>G		98.0	0.0		77.0	26.0	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	hg19	CCDS9300.2																																																																																			.	.		0.398	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		G	23910455	T	G	23910455	2	3	290	1	0	0	0	0	0	0	0	1	13819	1567	55	5		5	SACS	13	23910455	Silent	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10		23910455	91259423	120	42582										
PARP4	143	hgsc.bcm.edu	37	chr13	25043232	25043232	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	ctaggtactcttgctgggctTcttccttctctttaatctgg	8	11	4	0			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr13:25043232T>A	ENST00000381989.3	-	17	2168	c.2063A>T	c.(2062-2064)gAa>gTa	p.E688V		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	688	VIT. {ECO:0000255|PROSITE- ProRule:PRU00801}.				cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		TTGCTGGGCTTCTTCCTTCTC	0.443																																					p.E688V		Atlas-SNP	.											.	PARP4	142	.	0			c.A2063T						.						110	102	105					13																	25043232		2203	4300	6503	SO:0001583	missense	143	exon17			TGGGCTTCTTCCT	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"Poly (ADP-ribose) polymerases"	271	protein-coding gene	gene with protein product	"von Willebrand factor A domain containing 5C"	607519	"ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.2063A>T	chr13.hg19:g.25043232T>A	ENSP00000371419:p.Glu688Val	53.0	0.0		44.0	9.0	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	hg19	CCDS9307.1	.	.	.	.	.	.	.	.	.	.	T	6.476	0.456029	0.12283	.	.	ENSG00000102699	ENST00000381989	T	0.23754	1.89	4.08	-1.28	0.09318	Vault protein inter-alpha-trypsin (2);Vault protein inter-alpha-trypsin, metazoa (1);	0.824151	0.11071	N	0.602925	T	0.17831	0.0428	L	0.42744	1.35	0.27802	N	0.942462	B	0.14012	0.009	B	0.15052	0.012	T	0.27365	-1.0076	10	0.66056	D	0.02	-0.5016	3.071	0.06230	0.125:0.0921:0.1621:0.6207	.	688	Q9UKK3	PARP4_HUMAN	V	688	ENSP00000371419:E688V	ENSP00000371419:E688V	E	-	2	0	PARP4	23941232	0.984000	0.35163	0.789000	0.31954	0.152000	0.21847	0.917000	0.28665	-0.389000	0.07786	0.369000	0.22263	GAA	.	.		0.443	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437		A	25043232	T	A	25043232	3	1	290	1	0	0	0	0	1	0	0	0	11472	1783	62	4	3183	4	PARP4	13	25043232	Missense_Mutation	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	1132777	25043232	90126646	121	42583										
FREM2	341640	hgsc.bcm.edu	37	chr13	39454462	39454462	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tatatacatacgatctatacAgtgagatcgaaagacaatgc	7	7	1	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr13:39454462A>T	ENST00000280481.7	+	24	9264	c.9048A>T	c.(9046-9048)acA>acT	p.T3016T		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	3016					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		CGATCTATACAGTGAGATCGA	0.433																																					p.T3016T		Atlas-SNP	.											.	FREM2	385	.	0			c.A9048T						.						94	90	91					13																	39454462		2203	4300	6503	SO:0001819	synonymous_variant	341640	exon24			CTATACAGTGAGA	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.9048A>T	chr13.hg19:g.39454462A>T		85.0	0.0		46.0	18.0	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	hg19	CCDS31960.1																																																																																			.	.		0.433	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		T	39454462	A	T	39454462	2	4	290	1	0	0	0	0	0	0	0	1	6053	175	7	4		4	FREM2	13	39454462	Silent	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	14411230	39454462	75715416	122	42584										
TTC5	91875	hgsc.bcm.edu	37	chr14	20760207	20760207	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	aatggctacagagtctccaaTgagcactccccagctctgca	8	14	2	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr14:20760207T>G	ENST00000258821.3	-	9	1194	c.1138A>C	c.(1138-1140)Att>Ctt	p.I380L		NM_138376.2	NP_612385.2	Q8N0Z6	TTC5_HUMAN	tetratricopeptide repeat domain 5	380					DNA repair (GO:0006281)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	15	all_cancers(95;0.00092)		Epithelial(56;1.1e-06)|all cancers(55;8.07e-06)	GBM - Glioblastoma multiforme(265;0.0106)		GAGTCTCCAATGAGCACTCCC	0.473																																					p.I380L		Atlas-SNP	.											.	TTC5	34	.	0			c.A1138C						.						106	89	95					14																	20760207		2203	4300	6503	SO:0001583	missense	91875	exon9			CTCCAATGAGCAC	BC008647	CCDS9546.1	14q11.2	2013-01-11			ENSG00000136319	ENSG00000136319		"Tetratricopeptide (TTC) repeat domain containing"	19274	protein-coding gene	gene with protein product						11511361	Standard	NM_138376		Approved	Strap	uc001vwt.3	Q8N0Z6	OTTHUMG00000029506	ENST00000258821.3:c.1138A>C	chr14.hg19:g.20760207T>G	ENSP00000258821:p.Ile380Leu	52.0	0.0		66.0	29.0	NM_138376	A8MQ18|Q96HF9	Missense_Mutation	SNP	ENST00000258821.3	hg19	CCDS9546.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.3|25.3	4.626093|4.626093	0.87560|0.87560	.|.	.|.	ENSG00000136319|ENSG00000136319	ENST00000423949|ENST00000258821	.|T	.|0.35605	.|1.3	4.71|4.71	4.71|4.71	0.59529|0.59529	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.46833|0.46833	0.1413|0.1413	M|M	0.71036|0.71036	2.16|2.16	0.58432|0.58432	D|D	0.999999|0.999999	.|B	.|0.31548	.|0.328	.|B	.|0.41619	.|0.361	T|T	0.52990|0.52990	-0.8501|-0.8501	5|10	.|0.72032	.|D	.|0.01	.|.	13.6327|13.6327	0.62204|0.62204	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|380	.|Q8N0Z6	.|TTC5_HUMAN	P|L	324|380	.|ENSP00000258821:I380L	.|ENSP00000258821:I380L	H|I	-|-	2|1	0|0	TTC5|TTC5	19830047|19830047	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.895000|0.895000	0.52256|0.52256	6.239000|6.239000	0.72356|0.72356	2.123000|2.123000	0.65237|0.65237	0.456000|0.456000	0.33151|0.33151	CAT|ATT	.	.		0.473	TTC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073529.4	NM_138376		G	20760207	T	G	20760207	3	3	290	1	0	0	0	0	1	0	0	0	16726	1464	51	5	192	5	TTC5	14	20760207	Missense_Mutation	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10		20760207	86589333	123	42585										
SLC10A1	6554	hgsc.bcm.edu	37	chr14	70245100	70245110	+	Frame_Shift_Del	DEL	AGCCCTTCTCC	AGCCCTTCTCC	-													0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	aaaatatggcaatgaggagaAgcccttctccaagctggaaa					rs376884319|rs201076064|rs202023002		TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	AGCCCTTCTCC	AGCCCTTCTCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr14:70245100_70245110delAGCCCTTCTCC	ENST00000216540.4	-	4	1016_1026	c.883_893delGGAGAAGGGCT	c.(883-894)ggagaagggcttfs	p.GEGL295fs		NM_003049.3	NP_003040.1	Q14973	NTCP_HUMAN	solute carrier family 10 (sodium/bile acid cotransporter), member 1	295					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bile acid:sodium symporter activity (GO:0008508)			NS(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)	14				all cancers(60;0.00228)|BRCA - Breast invasive adenocarcinoma(234;0.0137)|OV - Ovarian serous cystadenocarcinoma(108;0.0226)	Bumetanide(DB00887)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Ethinyl Estradiol(DB00977)|Indomethacin(DB00328)|Liothyronine(DB00279)|Liotrix(DB01583)|Pitavastatin(DB08860)|Probenecid(DB01032)|Progesterone(DB00396)|Testosterone(DB00624)|Ursodeoxycholic acid(DB01586)	AATGAGGAGAAGCCCTTCTCCAAGCTGGAAA	0.441																																					p.295_298del		Atlas-Indel,Pindel	.											.	SLC10A1	32	.	0			c.884_894del						.																																			SO:0001589	frameshift_variant	6554	exon4			.	L21893	CCDS9797.1	14q24.2	2013-07-18	2013-07-18		ENSG00000100652	ENSG00000100652		"Solute carriers"	10905	protein-coding gene	gene with protein product		182396				8132774	Standard	NM_003049		Approved	NTCP	uc001xlr.2	Q14973	OTTHUMG00000171236	ENST00000216540.4:c.883_893delGGAGAAGGGCT	chr14.hg19:g.70245100_70245110delAGCCCTTCTCC	ENSP00000216540:p.Gly295fs	94.0	0.0		100.0	26.0	NM_003049	B9EGB6|Q2TU29	Frame_Shift_Del	DEL	ENST00000216540.4	hg19	CCDS9797.1																																																																																			.	.		0.441	SLC10A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412464.1			-	70245110	AGCCCTTCTCC	-	70245100	7	5	290	1	0	1	0	1	0	0	0	0	14388	72	3	0	164	0	SLC10A1	14	70245100	Frame_Shift_Del	DEL	AGCCCTTCTCC	TCGA-G3-A7M5-01A-11D-A33Q-10	49484893	70245100	37104440	124	42586										
ADAM20	8748	hgsc.bcm.edu	37	chr14	70990228	70990228	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	agtcacattcctccccttctTcaaccactagattcccacag	3	17	3	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr14:70990228T>A	ENST00000256389.3	-	2	1641	c.1397A>T	c.(1396-1398)gAa>gTa	p.E466V	RP11-486O13.4_ENST00000556646.1_lincRNA	NM_003814.4	NP_003805.3	O43506	ADA20_HUMAN	ADAM metallopeptidase domain 20	416	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(2)	27			KIRC - Kidney renal clear cell carcinoma(12;0.133)|Kidney(31;0.188)	all cancers(60;0.00294)|BRCA - Breast invasive adenocarcinoma(234;0.00668)|OV - Ovarian serous cystadenocarcinoma(108;0.0344)		CTCCCCTTCTTCAACCACTAG	0.438																																					p.E466V		Atlas-SNP	.											.	ADAM20	59	.	0			c.A1397T						.						141	123	129					14																	70990228		2203	4300	6503	SO:0001583	missense	8748	exon2			CCTTCTTCAACCA	AF029899	CCDS32111.1	14q24.2	2012-04-30	2005-08-18		ENSG00000134007	ENSG00000134007		"ADAM metallopeptidase domain containing"	199	protein-coding gene	gene with protein product		603712	"a disintegrin and metalloproteinase domain 20"			9469942	Standard	NM_003814		Approved		uc001xme.3	O43506	OTTHUMG00000167548	ENST00000256389.3:c.1397A>T	chr14.hg19:g.70990228T>A	ENSP00000256389:p.Glu466Val	127.0	0.0		130.0	47.0	NM_003814	Q6GTZ1|Q9UKJ9	Missense_Mutation	SNP	ENST00000256389.3	hg19	CCDS32111.1	.	.	.	.	.	.	.	.	.	.	T	15.27	2.784097	0.49997	.	.	ENSG00000134007	ENST00000256389	T	0.22743	1.94	4.54	4.54	0.55810	Blood coagulation inhibitor, Disintegrin (4);	0.000000	0.37809	U	0.001923	T	0.65069	0.2656	H	0.99273	4.495	0.35140	D	0.768745	D	0.89917	1.0	D	0.91635	0.999	D	0.85266	0.1053	10	0.87932	D	0	.	14.1752	0.65537	0.0:0.0:0.0:1.0	.	416	O43506	ADA20_HUMAN	V	466	ENSP00000256389:E466V	ENSP00000256389:E466V	E	-	2	0	ADAM20	70059981	1.000000	0.71417	0.974000	0.42286	0.121000	0.20230	5.619000	0.67729	1.803000	0.52742	0.455000	0.32223	GAA	.	.		0.438	ADAM20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395004.2			A	70990228	T	A	70990228	3	1	290	1	0	0	0	0	1	0	0	0	242	1783	62	4	937	4	ADAM20	14	70990228	Missense_Mutation	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	745128	70990228	36359312	125	42587										
CLMN	79789	hgsc.bcm.edu	37	chr14	95677202	95677202	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	aactgcccgcaaagtcctgcAccgccacgccatacctgaag	8	17	0	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr14:95677202A>T	ENST00000298912.4	-	7	736	c.623T>A	c.(622-624)gTg>gAg	p.V208E		NM_024734.3	NP_079010.2	Q96JQ2	CLMN_HUMAN	calmin (calponin-like, transmembrane)	208	Actin-binding.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				negative regulation of cell proliferation (GO:0008285)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(17)|prostate(3)|skin(3)	44				Epithelial(152;0.193)		AAAGTCCTGCACCGCCACGCC	0.582																																					p.V208E		Atlas-SNP	.											.	CLMN	103	.	0			c.T623A						.						85	91	89					14																	95677202		2203	4300	6503	SO:0001583	missense	79789	exon7			TCCTGCACCGCCA	AB033014	CCDS9933.1	14q32.13	2012-10-02			ENSG00000165959	ENSG00000165959			19972	protein-coding gene	gene with protein product		611121				11386753	Standard	NM_024734		Approved	FLJ12383, KIAA1188, KIAA0500	uc001yef.2	Q96JQ2	OTTHUMG00000171629	ENST00000298912.4:c.623T>A	chr14.hg19:g.95677202A>T	ENSP00000298912:p.Val208Glu	68.0	0.0		85.0	37.0	NM_024734	B2RAR7|Q9H713|Q9HA23|Q9HA57|Q9UFP4|Q9ULN2	Missense_Mutation	SNP	ENST00000298912.4	hg19	CCDS9933.1	.	.	.	.	.	.	.	.	.	.	A	27.9	4.872604	0.91587	.	.	ENSG00000165959	ENST00000298912	T	0.64438	-0.1	5.93	5.93	0.95920	Calponin homology domain (5);	0.000000	0.35838	N	0.002959	D	0.84142	0.5407	M	0.92649	3.33	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88028	0.2773	10	0.87932	D	0	.	16.3721	0.83368	1.0:0.0:0.0:0.0	.	208	Q96JQ2	CLMN_HUMAN	E	208	ENSP00000298912:V208E	ENSP00000298912:V208E	V	-	2	0	CLMN	94746955	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.962000	0.93254	2.257000	0.74773	0.533000	0.62120	GTG	.	.		0.582	CLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414518.2			T	95677202	A	T	95677202	3	4	290	1	0	0	0	0	1	0	0	0	3544	159	6	4	2413	4	CLMN	14	95677202	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	24686974	95677202	11672338	126	42588										
AK7	122481	hgsc.bcm.edu	37	chr14	96875253	96875253	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	actgtcgacggtgatgacttGggcgcgctccaaagccctgg	14	12	0	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr14:96875253G>A	ENST00000267584.4	+	4	517	c.473G>A	c.(472-474)tGg>tAg	p.W158*	AK7_ENST00000554313.1_3'UTR	NM_152327.3	NP_689540.2	Q96M32	KAD7_HUMAN	adenylate kinase 7	158					axoneme assembly (GO:0035082)|brain development (GO:0007420)|epithelial cilium movement (GO:0003351)|inflammatory response to antigenic stimulus (GO:0002437)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)			breast(2)|cervix(2)|endometrium(3)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)		GTGATGACTTGGGCGCGCTCC	0.468																																					p.W158X		Atlas-SNP	.											.	AK7	69	.	0			c.G473A						.						90	87	88					14																	96875253		2203	4300	6503	SO:0001587	stop_gained	122481	exon4			TGACTTGGGCGCG	AK057426	CCDS9945.1	14q32.31	2012-08-15			ENSG00000140057	ENSG00000140057		"Adenylate kinases"	20091	protein-coding gene	gene with protein product		615364					Standard	NM_152327		Approved	FLJ32864	uc001yfn.3	Q96M32	OTTHUMG00000171421	ENST00000267584.4:c.473G>A	chr14.hg19:g.96875253G>A	ENSP00000267584:p.Trp158*	105.0	0.0		147.0	53.0	NM_152327	Q8IYP6	Nonsense_Mutation	SNP	ENST00000267584.4	hg19	CCDS9945.1	.	.	.	.	.	.	.	.	.	.	G	17.50	3.404954	0.62288	.	.	ENSG00000140057	ENST00000267584	.	.	.	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.7302	15.7785	0.78242	0.0:0.0:1.0:0.0	.	.	.	.	X	158	.	ENSP00000267584:W158X	W	+	2	0	AK7	95945006	1.000000	0.71417	0.996000	0.52242	0.037000	0.13140	6.236000	0.72339	2.535000	0.85469	0.655000	0.94253	TGG	.	.		0.468	AK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413340.1			A	96875253	G	A	96875253	4	1	290	1	0	0	0	0	0	1	0	0	444	1357	47	3	487	3	AK7	14	96875253	Nonsense_Mutation	SNP	G	TCGA-G3-A7M5-01A-11D-A33Q-10	1198051	96875253	10474287	127	42589										
RYR3	6263	hgsc.bcm.edu	37	chr15	34109120	34109120	+	Frame_Shift_Del	DEL	G	G	-													0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	agattttggatagaaacagaGgagtattcctttgaagagaa							TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr15:34109120delG	ENST00000389232.4	+	75	10630	c.10560delG	c.(10558-10560)gagfs	p.E3521fs	RYR3_ENST00000415757.3_Frame_Shift_Del_p.E3516fs	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3521					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			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)		TAGAAACAGAGGAGTATTCCT	0.458																																					p.E3520fs		Atlas-Indel,Pindel	.											.	RYR3	760	.	0			c.10559delA						.						70	67	68					15																	34109120		1865	4108	5973	SO:0001589	frameshift_variant	6263	exon75			.		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.10560delG	chr15.hg19:g.34109120delG	ENSP00000373884:p.Glu3521fs	94.0	0.0		110.0	42.0	NM_001036	O15175|Q15412	Frame_Shift_Del	DEL	ENST00000389232.4	hg19	CCDS45210.1																																																																																			.	.		0.458	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			-	34109120	G	-	34109120	7	5	290	1	0	1	0	1	0	0	0	0	13785	991	35	0	10858	0	RYR3	15	34109120	Frame_Shift_Del	DEL	G	TCGA-G3-A7M5-01A-11D-A33Q-10		34109120	68422272	128	42590										
ZFP106	64397	hgsc.bcm.edu	37	chr15	42729475	42729475	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	ttatctgctgaacaggtataTagcaagttcccaaatatctg	7	8	2	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr15:42729475T>C	ENST00000263805.4	-	10	4958	c.4632A>G	c.(4630-4632)ctA>ctG	p.L1544L	ZNF106_ENST00000565380.1_Silent_p.L772L|ZNF106_ENST00000565611.1_Silent_p.L729L	NM_001284306.1|NM_001284307.1|NM_022473.1	NP_001271235.1|NP_001271236.1|NP_071918.1	Q9H2Y7	ZN106_HUMAN	zinc finger protein 106	1544					insulin receptor signaling pathway (GO:0008286)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										AACAGGTATATAGCAAGTTCC	0.398																																					p.L1544L		Atlas-SNP	.											.	ZFP106	117	.	0			c.A4632G						.						145	138	140					15																	42729475		2203	4299	6502	SO:0001819	synonymous_variant	64397	exon10			GGTATATAGCAAG	AF205632	CCDS32208.1, CCDS61602.1, CCDS61603.1	15q15.1	2012-11-27	2012-11-27		ENSG00000103994	ENSG00000103994		"Zinc fingers, C2H2-type"	12886	protein-coding gene	gene with protein product	"SH3-domain binding protein 3"		"zinc finger protein 106 homolog (mouse)"	ZFP106			Standard	XM_005254591		Approved	ZNF474, SH3BP3	uc001zpw.3	Q9H2Y7	OTTHUMG00000173244	ENST00000263805.4:c.4632A>G	chr15.hg19:g.42729475T>C		81.0	0.0		91.0	23.0	NM_022473	B4DZ40|E9PE29|Q6NSD9|Q6PEK1|Q86T43|Q86T45|Q86T50|Q86T58|Q86TA9|Q96M37|Q9H7B8	Silent	SNP	ENST00000263805.4	hg19	CCDS32208.1																																																																																			.	.		0.398	ZNF106-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422587.1	NM_022473		C	42729475	T	C	42729475	2	2	290	1	0	0	0	0	0	0	0	1	17652	1393	49	2		2	ZFP106	15	42729475	Silent	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	8620355	42729475	59801917	129	42591										
SEMA6D	80031	hgsc.bcm.edu	37	chr15	48058329	48058329	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	attgcatctcgtgacccgtaTtgtggctggttaagccaggg	13	9	1	1	rs113249348		TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr15:48058329T>A	ENST00000316364.5	+	15	2035	c.1596T>A	c.(1594-1596)taT>taA	p.Y532*	SEMA6D_ENST00000389433.2_Nonsense_Mutation_p.Y532*|SEMA6D_ENST00000558816.1_Nonsense_Mutation_p.Y532*|SEMA6D_ENST00000536845.2_Nonsense_Mutation_p.Y532*|SEMA6D_ENST00000537942.1_Nonsense_Mutation_p.Y532*|SEMA6D_ENST00000355997.3_Nonsense_Mutation_p.Y532*|SEMA6D_ENST00000354744.4_Nonsense_Mutation_p.Y532*|SEMA6D_ENST00000358066.4_Nonsense_Mutation_p.Y532*|SEMA6D_ENST00000389428.3_Nonsense_Mutation_p.Y532*|SEMA6D_ENST00000558014.1_Nonsense_Mutation_p.Y532*|SEMA6D_ENST00000389432.2_Nonsense_Mutation_p.Y532*	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	532	PSI.				axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		GTGACCCGTATTGTGGCTGGT	0.463																																					p.Y532X		Atlas-SNP	.											.	SEMA6D	322	.	0			c.T1596A						.						103	91	95					15																	48058329		2198	4297	6495	SO:0001587	stop_gained	80031	exon15			CCCGTATTGTGGC	AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"Semaphorins"	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.1596T>A	chr15.hg19:g.48058329T>A	ENSP00000324857:p.Tyr532*	98.0	0.0		125.0	13.0	NM_153617	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Nonsense_Mutation	SNP	ENST00000316364.5	hg19	CCDS32225.1	.	.	.	.	.	.	.	.	.	.	T	41	8.907301	0.98998	.	.	ENSG00000137872	ENST00000537942;ENST00000536845;ENST00000316364;ENST00000389433;ENST00000389432;ENST00000354744;ENST00000358066;ENST00000389428;ENST00000355997	.	.	.	5.89	-0.111	0.13576	.	0.055415	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.4731	0.44648	0.0:0.5971:0.0:0.4029	.	.	.	.	X	532	.	ENSP00000324857:Y532X	Y	+	3	2	SEMA6D	45845621	1.000000	0.71417	0.952000	0.39060	0.996000	0.88848	0.886000	0.28241	-0.276000	0.09206	-0.290000	0.09829	TAT	.	T|0.500;C|0.500		0.463	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966		A	48058329	T	A	48058329	4	1	290	1	0	0	0	0	0	1	0	0	14057	1500	52	4	1654	4	SEMA6D	15	48058329	Nonsense_Mutation	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	5328854	48058329	54473063	130	42592										
SLC12A1	6557	hgsc.bcm.edu	37	chr15	48513119	48513119	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	ataccgcttctatccacaggTaagatgcatgctgaacatct	7	11	2	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr15:48513119T>A	ENST00000558405.1	+	3	568	c.554T>A	c.(553-555)gTa>gAa	p.V185E	SLC12A1_ENST00000561031.1_Splice_Site_p.V185E|SLC12A1_ENST00000396577.3_Splice_Site_p.V185E|SLC12A1_ENST00000380993.3_Splice_Site_p.V185E|SLC12A1_ENST00000330289.6_Splice_Site_p.V185E			Q13621	S12A1_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 1	185					cell death (GO:0008219)|chemical homeostasis (GO:0048878)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|kidney development (GO:0001822)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:potassium:chloride symporter activity (GO:0008511)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|prostate(2)|skin(1)	59		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Potassium Chloride(DB00761)|Quinethazone(DB01325)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	TATCCACAGGTAAGATGCATG	0.473																																					p.V185E		Atlas-SNP	.											.	SLC12A1	243	.	0			c.T554A						.						120	113	115					15																	48513119		2198	4297	6495	SO:0001630	splice_region_variant	6557	exon4			CACAGGTAAGATG		CCDS10129.2, CCDS53940.1	15q15-q21	2013-07-18	2013-07-18		ENSG00000074803	ENSG00000074803		"Solute carriers"	10910	protein-coding gene	gene with protein product		600839				8640224	Standard	NM_000338		Approved	NKCC2	uc010bem.3	Q13621	OTTHUMG00000131495	ENST00000558405.1:c.553-1T>A	chr15.hg19:g.48513119T>A		104.0	0.0		135.0	58.0	NM_001184832	A8JYA2|E9PDW4	Missense_Mutation	SNP	ENST00000558405.1	hg19	CCDS10129.2	.	.	.	.	.	.	.	.	.	.	T	28.2	4.898311	0.91962	.	.	ENSG00000074803	ENST00000380993;ENST00000396577;ENST00000330289	D;D;D	0.99023	-5.34;-5.34;-5.34	5.96	5.96	0.96718	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.99450	0.9805	M	0.92970	3.365	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.81914	0.986;0.995	D	0.98519	1.0622	10	0.87932	D	0	.	16.4484	0.83959	0.0:0.0:0.0:1.0	.	185;185	Q8IUN5;Q13621	.;S12A1_HUMAN	E	185	ENSP00000370381:V185E;ENSP00000379822:V185E;ENSP00000331550:V185E	ENSP00000331550:V185E	V	+	2	0	SLC12A1	46300411	1.000000	0.71417	0.994000	0.49952	0.845000	0.48019	7.698000	0.84413	2.285000	0.76669	0.533000	0.62120	GTA	.	.		0.473	SLC12A1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417131.1		Missense_Mutation	A	48513119	T	A	48513119	5	1	290	1	0	0	0	0	0	0	1	0	14397	1652	57	4	564	4	SLC12A1	15	48513119	Splice_Site	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	454790	48513119	54018273	131	42593										
IGDCC3	9543	hgsc.bcm.edu	37	chr15	65621468	65621468	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	ctgggtctcctcacacggagCgggggctgcaggatcctgct	15	13	2	0	rs149849455		TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr15:65621468C>T	ENST00000327987.4	-	14	2475	c.2224G>A	c.(2224-2226)Gct>Act	p.A742T	IGDCC3_ENST00000559231.1_5'Flank	NM_004884.3	NP_004875.2	Q8IVU1	IGDC3_HUMAN	immunoglobulin superfamily, DCC subclass, member 3	742					neuromuscular process controlling balance (GO:0050885)	integral component of plasma membrane (GO:0005887)				breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(9)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						TCACACGGAGCGGGGGCTGCA	0.672																																					p.A742T		Atlas-SNP	.											.	IGDCC3	82	.	0			c.G2224A						.	C	THR/ALA	0,4402		0,0,2201	15	18	17		2224	-2.6	0	15	dbSNP_134	17	1,8595		0,1,4297	no	missense	IGDCC3	NM_004884.3	58	0,1,6498	TT,TC,CC		0.0116,0.0,0.0077	benign	742/815	65621468	1,12997	2201	4298	6499	SO:0001583	missense	9543	exon14			ACGGAGCGGGGGC	AF063936	CCDS10205.1	15q22.3-q23	2013-02-11	2009-01-08	2009-01-08	ENSG00000174498	ENSG00000174498		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9700	protein-coding gene	gene with protein product		604184	"putative neuronal cell adhesion molecule"	PUNC		9922388	Standard	NM_004884		Approved	HsT18880	uc002aos.2	Q8IVU1	OTTHUMG00000133137	ENST00000327987.4:c.2224G>A	chr15.hg19:g.65621468C>T	ENSP00000332773:p.Ala742Thr	62.0	0.0		67.0	37.0	NM_004884	O95215	Missense_Mutation	SNP	ENST00000327987.4	hg19	CCDS10205.1	.	.	.	.	.	.	.	.	.	.	C	12.90	2.077256	0.36662	0.0	1.16E-4	ENSG00000174498	ENST00000327987;ENST00000443278	T	0.65364	-0.15	5.3	-2.6	0.06190	.	2.424390	0.01794	N	0.032480	T	0.47820	0.1466	N	0.19112	0.55	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.35151	-0.9800	10	0.36615	T	0.2	-0.1839	10.404	0.44246	0.0:0.4979:0.0:0.5021	.	742	Q8IVU1	IGDC3_HUMAN	T	742;565	ENSP00000332773:A742T	ENSP00000332773:A742T	A	-	1	0	IGDCC3	63408521	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.706000	0.01895	-0.793000	0.04475	-0.145000	0.13849	GCT	.	C|1.000;T|0.000		0.672	IGDCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256826.1	NM_004884		T	65621468	C	T	65621468	3	4	290	1	0	0	0	0	1	0	0	0	7577	768	27	1	224	1	IGDCC3	15	65621468	Missense_Mutation	SNP	C	TCGA-G3-A7M5-01A-11D-A33Q-10	17108349	65621468	36909924	132	42594										
EDC3	80153	hgsc.bcm.edu	37	chr15	74925259	74925259	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	gggcaatccaggcagttgatGaccaggtccacagggctagt	14	10	0	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr15:74925259G>A	ENST00000315127.4	-	7	1402	c.1221C>T	c.(1219-1221)gtC>gtT	p.V407V	EDC3_ENST00000568176.1_Silent_p.V407V|EDC3_ENST00000426797.3_Silent_p.V407V	NM_001142444.1|NM_025083.3	NP_001135916.1|NP_079359.2	Q96F86	EDC3_HUMAN	enhancer of mRNA decapping 3	407	YjeF N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00719}.				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)|membrane (GO:0016020)	identical protein binding (GO:0042802)|RNA binding (GO:0003723)			breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	16						GGCAGTTGATGACCAGGTCCA	0.597											OREG0023286	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V407V		Atlas-SNP	.											.	EDC3	32	.	0			c.C1221T						.						68	48	55					15																	74925259		2197	4296	6493	SO:0001819	synonymous_variant	80153	exon8			GTTGATGACCAGG	BC011534	CCDS10267.1	15q24.1	2013-05-02	2013-05-02	2006-07-07	ENSG00000179151	ENSG00000179151			26114	protein-coding gene	gene with protein product		609842	"yjeF domain containing (E.coli)", "LSM16 homolog (EDC3, S. cerevisiae)", "enhancer of mRNA decapping 3 homolog (S. cerevisiae)"	YJDC, LSM16		15225602, 17533573, 22483619	Standard	NM_025083		Approved	FLJ21128, hYjeF_N2-15q23, YJEFN2	uc002aym.3	Q96F86	OTTHUMG00000142815	ENST00000315127.4:c.1221C>T	chr15.hg19:g.74925259G>A		67.0	0.0	1156	85.0	23.0	NM_001142444	B3KPH0|D3DW61|Q9H797	Silent	SNP	ENST00000315127.4	hg19	CCDS10267.1																																																																																			.	.		0.597	EDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286399.1	NM_025083		A	74925259	G	A	74925259	2	1	290	1	0	0	0	0	0	0	0	1	4909	1277	45	3		3	EDC3	15	74925259	Silent	SNP	G	TCGA-G3-A7M5-01A-11D-A33Q-10	9303791	74925259	27606133	133	42595										
ACAN	176	hgsc.bcm.edu	37	chr15	89402447	89402447	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	gtcacacctcgcagctgggcGttgtcatcagcaccagcatc	10	15	3	0	rs533925391		TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr15:89402447G>A	ENST00000561243.1	+	11	6631	c.6631G>A	c.(6631-6633)Gtt>Att	p.V2211I	ACAN_ENST00000559004.1_Missense_Mutation_p.V2211I|ACAN_ENST00000439576.2_Missense_Mutation_p.V2211I|ACAN_ENST00000352105.7_Missense_Mutation_p.V2211I			P16112	PGCA_HUMAN	aggrecan	2096	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.|G3.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			GCAGCTGGGCGTTGTCATCAG	0.597													G|||	1	0.000199681	8e-04	0	5008	,	,		18793	0		0	False		,,,				2504	0				p.V2211I		Atlas-SNP	.											.	ACAN	220	.	0			c.G6631A						.						44	50	48					15																	89402447		2134	4239	6373	SO:0001583	missense	176	exon12			CTGGGCGTTGTCA	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	319	protein-coding gene	gene with protein product	"aggrecan proteoglycan"	155760	"chondroitin sulfate proteoglycan 1", "aggrecan 1"	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.6631G>A	chr15.hg19:g.89402447G>A	ENSP00000453342:p.Val2211Ile	111.0	0.0		130.0	53.0	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	hg19	CCDS53970.1	.	.	.	.	.	.	.	.	.	.	G	0.119	-1.128582	0.01756	.	.	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	T;T	0.02606	4.36;4.23	5.12	-1.75	0.08031	.	0.642182	0.11888	N	0.519845	T	0.01765	0.0056	N	0.21583	0.68	0.09310	N	1	P;B	0.39311	0.667;0.304	B;B	0.37780	0.258;0.06	T	0.45963	-0.9225	10	0.21540	T	0.41	-2.0E-4	3.0641	0.06209	0.2863:0.11:0.4916:0.1121	.	2211;2211	E7ENV9;E7EX88	.;.	I	2211;2211;2097	ENSP00000387356:V2211I;ENSP00000341615:V2211I	ENSP00000268134:V2097I	V	+	1	0	ACAN	87203451	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-0.782000	0.04643	-0.274000	0.09232	-1.342000	0.01247	GTT	.	.		0.597	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135		A	89402447	G	A	89402447	3	1	290	1	0	0	0	0	1	0	0	0	117	1145	40	1	6673	1	ACAN	15	89402447	Missense_Mutation	SNP	G	TCGA-G3-A7M5-01A-11D-A33Q-10	14477188	89402447	13128945	134	42596										
FURIN	5045	hgsc.bcm.edu	37	chr15	91424605	91424605	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	aagtcctcgatacgcactatAgcaccgagaatgacgtggag	11	10	0	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr15:91424605A>G	ENST00000268171.3	+	16	2161	c.1882A>G	c.(1882-1884)Agc>Ggc	p.S628G		NM_002569.2	NP_002560.1	P09958	FURIN_HUMAN	furin (paired basic amino acid cleaving enzyme)	628					cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of low-density lipoprotein particle receptor catabolic process (GO:0032804)|negative regulation of transforming growth factor beta1 production (GO:0032911)|nerve growth factor processing (GO:0032455)|nerve growth factor production (GO:0032902)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|post-translational protein modification (GO:0043687)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)|regulation of protein catabolic process (GO:0042176)|secretion by cell (GO:0032940)|signal peptide processing (GO:0006465)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|nerve growth factor binding (GO:0048406)|peptidase activity (GO:0008233)|peptide binding (GO:0042277)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(4)|endometrium(4)|large_intestine(3)|liver(2)|lung(13)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	36	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			TACGCACTATAGCACCGAGAA	0.657																																					p.S628G		Atlas-SNP	.											.	FURIN	85	.	0			c.A1882G						.						74	69	71					15																	91424605		2197	4297	6494	SO:0001583	missense	5045	exon16			CACTATAGCACCG	X17094	CCDS10364.1	15q26.1	2007-01-24	2002-12-04	2002-12-06	ENSG00000140564	ENSG00000140564			8568	protein-coding gene	gene with protein product		136950	"paired basic amino acid cleaving enzyme (furin, membrane associated receptor protein)"	PCSK3, FUR, PACE		2251280, 1741956	Standard	NM_002569		Approved	SPC1	uc002bpu.1	P09958	OTTHUMG00000149831	ENST00000268171.3:c.1882A>G	chr15.hg19:g.91424605A>G	ENSP00000268171:p.Ser628Gly	68.0	0.0		73.0	16.0	NM_002569	Q14336|Q6LBS3|Q9UCZ5	Missense_Mutation	SNP	ENST00000268171.3	hg19	CCDS10364.1	.	.	.	.	.	.	.	.	.	.	A	10.10	1.258843	0.23051	.	.	ENSG00000140564	ENST00000268171	D	0.85861	-2.04	5.02	3.88	0.44766	Growth factor, receptor (1);	0.199858	0.52532	D	0.000062	T	0.70298	0.3208	N	0.15975	0.35	0.25058	N	0.991089	B	0.06786	0.001	B	0.06405	0.002	T	0.55186	-0.8180	10	0.21014	T	0.42	-26.9162	9.8671	0.41150	0.8561:0.0:0.1439:0.0	.	628	P09958	FURIN_HUMAN	G	628	ENSP00000268171:S628G	ENSP00000268171:S628G	S	+	1	0	FURIN	89225609	.	.	1.000000	0.80357	0.572000	0.35998	.	.	1.893000	0.54813	0.454000	0.30748	AGC	.	.		0.657	FURIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313492.1	NM_002569		G	91424605	A	G	91424605	3	3	290	1	0	0	0	0	1	0	0	0	6107	420	15	2	1940	2	FURIN	15	91424605	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	2022158	91424605	11106787	135	42597										
SEPT12	124404	hgsc.bcm.edu	37	chr16	4827877	4827877	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tggtcagctgtcctggggagGccggggccaggttcacccag	17	12	2	0			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr16:4827877G>C	ENST00000268231.8	-	10	1261	c.998C>G	c.(997-999)gCc>gGc	p.A333G	SEPT12_ENST00000396693.5_Missense_Mutation_p.A287G	NM_144605.4	NP_653206.2	Q8IYM1	SEP12_HUMAN	septin 12	333					cell cycle (GO:0007049)|cell division (GO:0051301)	cleavage furrow (GO:0032154)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|septin complex (GO:0031105)|sperm annulus (GO:0097227)|spindle (GO:0005819)|stress fiber (GO:0001725)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)			NS(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|skin(2)|stomach(3)	23						TCCTGGGGAGGCCGGGGCCAG	0.632																																					p.A333G		Atlas-SNP	.											.	SEPT12	40	.	0			c.C998G						.						28	29	29					16																	4827877		2175	4272	6447	SO:0001583	missense	124404	exon10			GGGGAGGCCGGGG	AK058139	CCDS10522.1, CCDS53987.1	16p13.3	2013-01-21			ENSG00000140623	ENSG00000140623		"Septins"	26348	protein-coding gene	gene with protein product		611562				14611653, 15915442	Standard	NM_001154458		Approved	FLJ25410	uc002cxq.3	Q8IYM1	OTTHUMG00000129481	ENST00000268231.8:c.998C>G	chr16.hg19:g.4827877G>C	ENSP00000268231:p.Ala333Gly	127.0	0.0		112.0	56.0	NM_144605	Q0P6B0|Q1PBH0|Q96LL0	Missense_Mutation	SNP	ENST00000268231.8	hg19	CCDS10522.1	.	.	.	.	.	.	.	.	.	.	G	13.72	2.320559	0.41096	.	.	ENSG00000140623	ENST00000396693;ENST00000268231	T;T	0.55413	0.52;0.55	4.59	2.57	0.30868	.	0.824903	0.10352	N	0.684976	T	0.29684	0.0741	N	0.08118	0	0.09310	N	1	B;B	0.31769	0.288;0.339	B;B	0.30572	0.117;0.076	T	0.17992	-1.0351	10	0.49607	T	0.09	.	5.4604	0.16614	0.184:0.1627:0.6533:0.0	.	287;333	Q8IYM1-2;Q8IYM1	.;SEP12_HUMAN	G	287;333	ENSP00000379922:A287G;ENSP00000268231:A333G	ENSP00000268231:A333G	A	-	2	0	SEPT12	4767878	0.011000	0.17503	0.091000	0.20842	0.418000	0.31294	1.466000	0.35310	0.636000	0.30508	0.462000	0.41574	GCC	.	.		0.632	SEPT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251645.2	NM_144605		C	4827877	G	C	4827877	3	2	290	1	0	0	0	0	1	0	0	0	14077	1203	42	4	82	4	SEPT12	16	4827877	Missense_Mutation	SNP	G	TCGA-G3-A7M5-01A-11D-A33Q-10		4827877	85526876	136	42598										
MKL2	57496	hgsc.bcm.edu	37	chr16	14304134	14304134	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	ctgcaacaaaggaggacgagAgaacaactagtggaccaggg	14	8	0	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr16:14304134A>G	ENST00000341243.5	+	2	156	c.156A>G	c.(154-156)agA>agG	p.R52R	MKL2_ENST00000571589.1_Silent_p.R63R|MKL2_ENST00000572567.1_Silent_p.R52R|MKL2_ENST00000573051.1_Silent_p.R12R|MKL2_ENST00000318282.5_Silent_p.R63R|MKL2_ENST00000574045.1_Silent_p.R63R			Q9ULH7	MKL2_HUMAN	MKL/myocardin-like 2	52					blood vessel morphogenesis (GO:0048514)|cardiac muscle tissue development (GO:0048738)|embryonic organ development (GO:0048568)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|muscle organ development (GO:0007517)|positive regulation of striated muscle tissue development (GO:0045844)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(6)|liver(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						GGAGGACGAGAGAACAACTAG	0.488																																					p.R63R		Atlas-SNP	.											.	MKL2	103	.	0			c.A189G						.						178	137	151					16																	14304134		2197	4300	6497	SO:0001819	synonymous_variant	57496	exon4			GACGAGAGAACAA	AB033069	CCDS32391.1	16p13.12	2012-11-29			ENSG00000186260	ENSG00000186260			29819	protein-coding gene	gene with protein product		609463				10574462	Standard	NM_014048		Approved	MRTF-B, FLJ31823	uc002dcg.3	Q9ULH7	OTTHUMG00000177379	ENST00000341243.5:c.156A>G	chr16.hg19:g.14304134A>G		91.0	0.0		86.0	39.0	NM_014048	A6ND53|B4DGT8|Q68CT1|Q6UB16|Q86WW2|Q8N226	Silent	SNP	ENST00000341243.5	hg19																																																																																				.	.		0.488	MKL2-202	KNOWN	basic	protein_coding	protein_coding		NM_014048		G	14304134	A	G	14304134	2	3	290	1	0	0	0	0	0	0	0	1	9611	301	11	2		2	MKL2	16	14304134	Silent	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	9476257	14304134	76050619	137	42599										
DNAH3	55567	hgsc.bcm.edu	37	chr16	21071601	21071601	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	ttaccttgacatatgcttcaAtcccaagtccaatgacttct	4	12	2	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr16:21071601A>T	ENST00000261383.3	-	26	3796	c.3797T>A	c.(3796-3798)aTt>aAt	p.I1266N	DNAH3_ENST00000415178.1_Missense_Mutation_p.I1266N	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1266	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			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)		ATATGCTTCAATCCCAAGTCC	0.498																																					p.I1266N		Atlas-SNP	.											.	DNAH3	1142	.	0			c.T3797A						.						212	199	203					16																	21071601		2201	4300	6501	SO:0001583	missense	55567	exon26			GCTTCAATCCCAA	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"Axonemal dyneins"	2949	protein-coding gene	gene with protein product		603334	"dynein, axonemal, heavy polypeptide 3"			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.3797T>A	chr16.hg19:g.21071601A>T	ENSP00000261383:p.Ile1266Asn	127.0	0.0		64.0	11.0	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	hg19	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	A	13.74	2.327509	0.41197	.	.	ENSG00000158486	ENST00000261383;ENST00000415178	T;T	0.61742	0.08;0.08	5.47	5.47	0.80525	Dynein heavy chain, domain-2 (1);	0.223435	0.39687	N	0.001289	T	0.72078	0.3416	M	0.71296	2.17	0.52099	D	0.999941	D	0.69078	0.997	P	0.60541	0.876	T	0.74185	-0.3747	10	0.49607	T	0.09	.	15.5585	0.76219	1.0:0.0:0.0:0.0	.	1266	Q8TD57	DYH3_HUMAN	N	1266	ENSP00000261383:I1266N;ENSP00000394245:I1266N	ENSP00000261383:I1266N	I	-	2	0	DNAH3	20979102	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.473000	0.90410	2.088000	0.63022	0.519000	0.50382	ATT	.	.		0.498	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		T	21071601	A	T	21071601	3	4	290	1	0	0	0	0	1	0	0	0	4605	101	4	4	8700	4	DNAH3	16	21071601	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	6767467	21071601	69283152	138	42600										
HS3ST4	9951	hgsc.bcm.edu	37	chr16	26147301	26147301	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tgtggaccccgccggggaaaTggccaaagtacaggattttc	13	10	0	0			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr16:26147301T>A	ENST00000331351.5	+	2	1495	c.1103T>A	c.(1102-1104)aTg>aAg	p.M368K	HS3ST4_ENST00000475436.1_3'UTR	NM_006040.2	NP_006031.2	Q9Y661	HS3S4_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	368					heparan sulfate proteoglycan metabolic process (GO:0030201)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)			breast(2)|endometrium(3)|large_intestine(1)|lung(9)	15				GBM - Glioblastoma multiforme(48;0.0988)		GCCGGGGAAATGGCCAAAGTA	0.493																																					p.M368K		Atlas-SNP	.											.	HS3ST4	120	.	0			c.T1103A						.						84	82	82					16																	26147301		1568	3582	5150	SO:0001583	missense	9951	exon2			GGGAAATGGCCAA	AF105378	CCDS53995.1	16p11.2	2008-03-12			ENSG00000182601	ENSG00000182601	2.8.2.23	"Sulfotransferases, membrane-bound"	5200	protein-coding gene	gene with protein product		604059				9988767	Standard	NM_006040		Approved	3OST4	uc002dof.3	Q9Y661	OTTHUMG00000059978	ENST00000331351.5:c.1103T>A	chr16.hg19:g.26147301T>A	ENSP00000330606:p.Met368Lys	121.0	0.0		135.0	70.0	NM_006040	Q5QI42|Q8NDC2	Missense_Mutation	SNP	ENST00000331351.5	hg19	CCDS53995.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.786606	0.90367	.	.	ENSG00000182601	ENST00000331351	D	0.82893	-1.66	5.56	5.56	0.83823	Sulfotransferase domain (1);	0.058199	0.64402	U	0.000005	D	0.92149	0.7511	M	0.91663	3.23	0.80722	D	1	D	0.62365	0.991	D	0.63957	0.92	D	0.93807	0.7106	10	0.87932	D	0	.	14.8801	0.70525	0.0:0.0:0.0:1.0	.	368	Q9Y661	HS3S4_HUMAN	K	368	ENSP00000330606:M368K	ENSP00000330606:M368K	M	+	2	0	HS3ST4	26054802	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.004000	0.88535	2.102000	0.63906	0.533000	0.62120	ATG	.	.		0.493	HS3ST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133286.2	NM_006040		A	26147301	T	A	26147301	3	1	290	1	0	0	0	0	1	0	0	0	7376	1464	51	4	1109	4	HS3ST4	16	26147301	Missense_Mutation	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	5075700	26147301	64207452	139	42601										
MT1E	4493	hgsc.bcm.edu	37	chr16	56660821	56660821	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	cctgctgccccgtgggctgtGccaagtgtgcccagggctgc	15	15	0	0			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr16:56660821G>T	ENST00000306061.6	+	3	501	c.124G>T	c.(124-126)Gcc>Tcc	p.A42S	MT1E_ENST00000330439.6_3'UTR|MT1E_ENST00000568293.1_Missense_Mutation_p.A20S	NM_175617.3	NP_783316.2	P04732	MT1E_HUMAN	metallothionein 1E	42	Alpha.				cellular response to cadmium ion (GO:0071276)|cellular response to zinc ion (GO:0071294)|negative regulation of growth (GO:0045926)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)										CGTGGGCTGTGCCAAGTGTGC	0.592																																					p.A42S		Atlas-SNP	.											.	MT1E	7	.	0			c.G124T						.						142	136	138					16																	56660821		2198	4300	6498	SO:0001583	missense	4493	exon3			GGCTGTGCCAAGT	BC009699	CCDS10764.2	16q13	2008-08-11	2007-03-02		ENSG00000169715	ENSG00000169715		"Metallothioneins"	7397	protein-coding gene	gene with protein product		156351		MT1		6089206, 2581970	Standard	XM_005255956		Approved	MTD	uc002ejl.3	P04732	OTTHUMG00000133014	ENST00000306061.6:c.124G>T	chr16.hg19:g.56660821G>T	ENSP00000307706:p.Ala42Ser	43.0	0.0		39.0	23.0	NM_175617	A2RRF7|Q86YX4|Q8TD51	Missense_Mutation	SNP	ENST00000306061.6	hg19	CCDS10764.2	.	.	.	.	.	.	.	.	.	.	G	11.00	1.509995	0.27036	.	.	ENSG00000169715	ENST00000306061	T	0.09445	2.98	2.39	1.39	0.22231	Metallothionein domain, vertebrate (1);Metallothionein domain (1);	.	.	.	.	T	0.07638	0.0192	.	.	.	0.80722	D	1	B	0.17038	0.02	B	0.18871	0.023	T	0.21280	-1.0250	8	0.40728	T	0.16	.	5.6138	0.17420	0.2906:0.0:0.7094:0.0	.	42	P04732	MT1E_HUMAN	S	42	ENSP00000307706:A42S	ENSP00000307706:A42S	A	+	1	0	MT1E	55218322	0.288000	0.24324	0.995000	0.50966	0.831000	0.47069	0.203000	0.17315	0.327000	0.23409	0.306000	0.20318	GCC	.	.		0.592	MT1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256600.1	NM_175617		T	56660821	G	T	56660821	3	4	290	1	0	0	0	0	1	0	0	0	9908	1319	46	3	134	3	MT1E	16	56660821	Missense_Mutation	SNP	G	TCGA-G3-A7M5-01A-11D-A33Q-10	30513520	56660821	33693932	140	42602										
KCNG4	93107	hgsc.bcm.edu	37	chr16	84270675	84270675	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tcctcctggaaggacagcgcGcacatctcctgcagaagcac	10	15	1	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr16:84270675G>A	ENST00000308251.4	-	2	485	c.417C>T	c.(415-417)tgC>tgT	p.C139C	KCNG4_ENST00000568181.1_Silent_p.C139C	NM_172347.2	NP_758857.1	Q8TDN1	KCNG4_HUMAN	potassium voltage-gated channel, subfamily G, member 4	139					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.C139C(2)		breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	31						AGGACAGCGCGCACATCTCCT	0.652																																					p.C139C		Atlas-SNP	.											KCNG4,rectum,carcinoma,0,2	KCNG4	71	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C417T						.						47	49	48					16																	84270675		2200	4300	6500	SO:0001819	synonymous_variant	93107	exon2			CAGCGCGCACATC	AF348984	CCDS10945.1	16q24.1	2011-07-05			ENSG00000168418	ENSG00000168418		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	19697	protein-coding gene	gene with protein product		607603				12060745, 16382104	Standard	NM_172347		Approved	Kv6.4	uc010voc.2	Q8TDN1	OTTHUMG00000137638	ENST00000308251.4:c.417C>T	chr16.hg19:g.84270675G>A		64.0	1.0		68.0	33.0	NM_172347	Q96H24	Silent	SNP	ENST00000308251.4	hg19	CCDS10945.1																																																																																			.	.		0.652	KCNG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269079.2	NM_172347		A	84270675	G	A	84270675	2	1	290	1	0	0	0	0	0	0	0	1	8039	1079	38	1		1	KCNG4	16	84270675	Silent	SNP	G	TCGA-G3-A7M5-01A-11D-A33Q-10	27609854	84270675	6084078	141	42603										
KIAA0513	9764	hgsc.bcm.edu	37	chr16	85114999	85114999	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	aagcgatctcccactaccagGtaggagcaaagtgtggcccc	11	13	1	0			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr16:85114999G>A	ENST00000566428.1	+	9	1611		c.e9+1		KIAA0513_ENST00000258180.3_Splice_Site|KIAA0513_ENST00000538274.1_Splice_Site			O60268	K0513_HUMAN	KIAA0513							cytoplasm (GO:0005737)				breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|liver(2)|lung(9)|pancreas(1)	18				BRCA - Breast invasive adenocarcinoma(80;0.234)		CCACTACCAGGTAGGAGCAAA	0.537																																					.		Atlas-SNP	.											.	KIAA0513	43	.	0			c.980+1G>A						.						49	37	41					16																	85114999		2195	4294	6489	SO:0001630	splice_region_variant	9764	exon9			TACCAGGTAGGAG	AB011085	CCDS32499.1, CCDS67091.1, CCDS73919.1	16q24.1	2012-11-29			ENSG00000135709	ENSG00000135709			29058	protein-coding gene	gene with protein product		611675				9628581	Standard	XM_005256265		Approved		uc002fiu.3	O60268	OTTHUMG00000176597	ENST00000566428.1:c.980+1G>A	chr16.hg19:g.85114999G>A		64.0	0.0		73.0	30.0	NM_014732	B4DSS5|D3DUM2|Q8N6G0	Splice_Site	SNP	ENST00000566428.1	hg19	CCDS32499.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.516209	0.85495	.	.	ENSG00000135709	ENST00000538274;ENST00000258180	.	.	.	4.75	4.75	0.60458	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.7052	0.85370	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	KIAA0513	83672500	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.068000	0.93961	2.350000	0.79820	0.561000	0.74099	.	.	.		0.537	KIAA0513-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432736.1	NM_014732	Intron	A	85114999	G	A	85114999	5	1	290	1	0	0	0	0	0	0	1	0	8190	1275	44	3	1011	3	KIAA0513	16	85114999	Splice_Site	SNP	G	TCGA-G3-A7M5-01A-11D-A33Q-10	844324	85114999	5239754	142	42604										
ALKBH5	54890	hgsc.bcm.edu	37	chr17	18088100	18088100	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	aagctggtggagcaccgcgtCatccccgagggcttcgtcaa	13	13	2	0			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr17:18088100C>T	ENST00000399138.4	+	1	548	c.543C>T	c.(541-543)gtC>gtT	p.V181V	RP11-258F1.1_ENST00000583062.1_RNA|RP11-258F1.1_ENST00000577847.1_RNA|ALKBH5_ENST00000541285.1_Intron	NM_017758.3	NP_060228.3	Q6P6C2	ALKB5_HUMAN	AlkB family member 5, RNA demethylase	181					cell differentiation (GO:0030154)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|oxidative single-stranded RNA demethylation (GO:0035553)|response to hypoxia (GO:0001666)|spermatogenesis (GO:0007283)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|oxidative RNA demethylase activity (GO:0035515)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|ovary(1)|skin(1)	10	all_neural(463;0.228)					AGCACCGCGTCATCCCCGAGG	0.677																																					p.V181V	Ovarian(166;154 1953 40235 46283 46309)	Atlas-SNP	.											.	ALKBH5	24	.	0			c.C543T						.						36	42	40					17																	18088100		2094	4200	6294	SO:0001819	synonymous_variant	54890	exon1			CCGCGTCATCCCC	AK000315	CCDS42272.1	17p11.2	2014-07-23	2014-07-23	2006-02-09	ENSG00000091542	ENSG00000091542	1.14.11.-	"Alkylation repair homologs"	25996	protein-coding gene	gene with protein product		613303	"oxoglutarate and iron-dependent oxygenase domain containing", "alkB, alkylation repair homolog 5 (E. coli)"	OFOXD1		11997338, 24778178	Standard	NM_017758		Approved	FLJ20308	uc010cpw.3	Q6P6C2	OTTHUMG00000059397	ENST00000399138.4:c.543C>T	chr17.hg19:g.18088100C>T		47.0	0.0		81.0	37.0	NM_017758	B4DVJ4|D3DXC6|Q9NXD6	Silent	SNP	ENST00000399138.4	hg19	CCDS42272.1																																																																																			.	.		0.677	ALKBH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132069.3	NM_017758		T	18088100	C	T	18088100	2	4	290	1	0	0	0	0	0	0	0	1	530	813	29	3		3	ALKBH5	17	18088100	Silent	SNP	C	TCGA-G3-A7M5-01A-11D-A33Q-10		18088100	63107110	143	42605										
TMEM132E	124842	hgsc.bcm.edu	37	chr17	32964875	32964875	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	gctgcgggtgcaaggagagcTgtcgccgccagcaggcaacc	16	13	0	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr17:32964875T>A	ENST00000321639.5	+	10	2907	c.2579T>A	c.(2578-2580)cTg>cAg	p.L860Q		NM_207313.1	NP_997196.1	Q6IEE7	T132E_HUMAN	transmembrane protein 132E	860						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(28)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	57				BRCA - Breast invasive adenocarcinoma(366;0.231)		CAAGGAGAGCTGTCGCCGCCA	0.697																																					p.L860Q		Atlas-SNP	.											.	TMEM132E	122	.	0			c.T2579A						.						25	27	26					17																	32964875		2166	4225	6391	SO:0001583	missense	124842	exon10			GAGAGCTGTCGCC	BN000149	CCDS11283.1	17q12	2012-11-01			ENSG00000181291	ENSG00000181291			26991	protein-coding gene	gene with protein product							Standard	NM_207313		Approved		uc002hif.3	Q6IEE7	OTTHUMG00000132927	ENST00000321639.5:c.2579T>A	chr17.hg19:g.32964875T>A	ENSP00000316532:p.Leu860Gln	28.0	0.0		33.0	18.0	NM_207313	Q8WUF4|Q8WVA5	Missense_Mutation	SNP	ENST00000321639.5	hg19	CCDS11283.1	.	.	.	.	.	.	.	.	.	.	T	12.41	1.930269	0.34096	.	.	ENSG00000181291	ENST00000321639	T	0.06449	3.3	4.73	4.73	0.59995	.	0.000000	0.64402	D	0.000001	T	0.18841	0.0452	L	0.55743	1.74	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.01309	-1.1389	10	0.30854	T	0.27	-31.6467	13.5748	0.61868	0.0:0.0:0.0:1.0	.	860	Q6IEE7	T132E_HUMAN	Q	860	ENSP00000316532:L860Q	ENSP00000316532:L860Q	L	+	2	0	TMEM132E	29988988	1.000000	0.71417	1.000000	0.80357	0.035000	0.12851	6.101000	0.71479	1.993000	0.58246	0.523000	0.50628	CTG	.	.		0.697	TMEM132E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256440.2	NM_207313		A	32964875	T	A	32964875	3	1	290	1	0	0	0	0	1	0	0	0	16063	1580	55	4	2617	4	TMEM132E	17	32964875	Missense_Mutation	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	14876775	32964875	48230335	144	42606										
KRT27	342574	hgsc.bcm.edu	37	chr17	38937443	38937443	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tcttcagctctacttactttAgtctgaagtcatcagctgtt	6	10	6	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr17:38937443A>T	ENST00000301656.3	-	2	564	c.524T>A	c.(523-525)cTa>cAa	p.L175Q		NM_181537.3	NP_853515.2			keratin 27											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(3)|skin(1)|stomach(1)	21		Breast(137;0.000812)				TACTTACTTTAGTCTGAAGTC	0.338																																					p.L175Q		Atlas-SNP	.											.	KRT27	41	.	0			c.T524A						.						89	77	81					17																	38937443		2203	4299	6502	SO:0001583	missense	342574	exon2			TACTTTAGTCTGA	AJ564206	CCDS11375.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000171446	ENSG00000171446		"-", "Intermediate filaments type I, keratins (acidic)"	30841	protein-coding gene	gene with protein product			"keratin 25C"	KRT25C		16831889	Standard	NM_181537		Approved		uc002hvg.3	Q7Z3Y8	OTTHUMG00000133371	ENST00000301656.3:c.524T>A	chr17.hg19:g.38937443A>T	ENSP00000301656:p.Leu175Gln	92.0	0.0		100.0	29.0	NM_181537		Missense_Mutation	SNP	ENST00000301656.3	hg19	CCDS11375.1	.	.	.	.	.	.	.	.	.	.	A	16.90	3.249692	0.59212	.	.	ENSG00000171446	ENST00000301656	D	0.82711	-1.64	5.58	5.58	0.84498	Filament (1);	0.273139	0.26359	N	0.024826	D	0.84946	0.5585	L	0.56769	1.78	0.09310	N	0.999999	P	0.37233	0.588	P	0.46685	0.524	T	0.79811	-0.1646	10	0.54805	T	0.06	.	13.7809	0.63081	1.0:0.0:0.0:0.0	.	175	Q7Z3Y8	K1C27_HUMAN	Q	175	ENSP00000301656:L175Q	ENSP00000301656:L175Q	L	-	2	0	KRT27	36190969	0.034000	0.19679	0.223000	0.23860	0.962000	0.63368	3.090000	0.50191	2.248000	0.74166	0.528000	0.53228	CTA	.	.		0.338	KRT27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257216.1	NM_181537		T	38937443	A	T	38937443	3	4	290	1	0	0	0	0	1	0	0	0	8473	420	15	4	883	4	KRT27	17	38937443	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	5972568	38937443	42257767	145	42607										
KCNJ16	3773	hgsc.bcm.edu	37	chr17	68128987	68128987	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	ctggtcaccccggtaactatTgtccatgaaattgaccatga	8	11	1	3			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr17:68128987T>A	ENST00000589377.1	+	2	922	c.759T>A	c.(757-759)atT>atA	p.I253I	KCNJ16_ENST00000283936.1_Silent_p.I253I|KCNJ16_ENST00000585558.1_Silent_p.I288I|KCNJ16_ENST00000586462.1_Silent_p.I292I|KCNJ16_ENST00000392671.1_Silent_p.I253I|KCNJ16_ENST00000392670.1_Silent_p.I253I	NM_001270422.1	NP_001257351.1	Q9NPI9	KCJ16_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 16	253					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)			breast(3)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	32	Breast(10;2.96e-09)					CGGTAACTATTGTCCATGAAA	0.438																																					p.I253I		Atlas-SNP	.											.	KCNJ16	72	.	0			c.T759A						.						125	117	120					17																	68128987		2203	4300	6503	SO:0001819	synonymous_variant	3773	exon6			AACTATTGTCCAT	AF153815	CCDS11687.1, CCDS74141.1	17q24.3	2011-07-05				ENSG00000153822		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6262	protein-coding gene	gene with protein product		605722				11240146, 16382105	Standard	NM_018658		Approved	Kir5.1, BIR9	uc002jio.4	Q9NPI9		ENST00000589377.1:c.759T>A	chr17.hg19:g.68128987T>A		62.0	0.0		83.0	41.0	NM_001270422		Silent	SNP	ENST00000589377.1	hg19	CCDS11687.1																																																																																			.	.		0.438	KCNJ16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450880.1	NM_018658		A	68128987	T	A	68128987	2	1	290	1	0	0	0	0	0	0	0	1	8059	1800	63	4		4	KCNJ16	17	68128987	Silent	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	29191544	68128987	13066223	146	42608										
LAMA1	284217	hgsc.bcm.edu	37	chr18	6978215	6978215	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tggccatggtggagtcctgcAgaagctggtgtgtctctcgt	15	9	1	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr18:6978215A>T	ENST00000389658.3	-	43	6263	c.6170T>A	c.(6169-6171)cTg>cAg	p.L2057Q		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2057	Domain II and I.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				GGAGTCCTGCAGAAGCTGGTG	0.587																																					p.L2057Q		Atlas-SNP	.											.	LAMA1	458	.	0			c.T6170A						.						231	201	211					18																	6978215		2203	4300	6503	SO:0001583	missense	284217	exon43			TCCTGCAGAAGCT	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.6170T>A	chr18.hg19:g.6978215A>T	ENSP00000374309:p.Leu2057Gln	75.0	0.0		64.0	30.0	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	hg19	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	A	19.93	3.917552	0.73098	.	.	ENSG00000101680	ENST00000389658	T	0.51325	0.71	5.65	5.65	0.86999	Laminin II (1);	0.272595	0.28748	N	0.014265	T	0.61311	0.2337	M	0.65975	2.015	0.09310	N	1	D	0.55800	0.973	P	0.56163	0.793	T	0.57271	-0.7840	10	0.35671	T	0.21	.	16.183	0.81925	1.0:0.0:0.0:0.0	.	2057	P25391	LAMA1_HUMAN	Q	2057	ENSP00000374309:L2057Q	ENSP00000374309:L2057Q	L	-	2	0	LAMA1	6968215	0.999000	0.42202	0.048000	0.18961	0.021000	0.10359	6.242000	0.72376	2.282000	0.76494	0.533000	0.62120	CTG	.	.		0.587	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		T	6978215	A	T	6978215	3	4	290	1	0	0	0	0	1	0	0	0	8614	188	7	4	3141	4	LAMA1	18	6978215	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10		6978215	71099033	147	42609										
C18orf26	284254	hgsc.bcm.edu	37	chr18	52262216	52262216	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	ggctcacagttccatatgctGgtgtctaccttcaaatgata	8	10	3	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr18:52262216G>A	ENST00000321600.1	+	2	228	c.182G>A	c.(181-183)tGg>tAg	p.W61*	DYNAP_ENST00000585973.1_Intron	NM_173629.1	NP_775900.1	Q8N1N2	DYNAP_HUMAN	dynactin associated protein	61					activation of protein kinase B activity (GO:0032148)|cellular response to ergosterol (GO:1901625)|positive regulation of cell proliferation (GO:0008284)|regulation of apoptotic process (GO:0042981)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)											TCCATATGCTGGTGTCTACCT	0.463																																					p.W61X		Atlas-SNP	.											.	.	.	.	0			c.G182A						.						196	181	186					18																	52262216		2203	4300	6503	SO:0001587	stop_gained	284254	exon2			TATGCTGGTGTCT	AK096425	CCDS11957.1	18q21.2	2012-10-24	2012-10-24	2012-10-24	ENSG00000178690	ENSG00000178690			26808	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 26"	C18orf26		20978158	Standard	NM_173629		Approved	FLJ39106	uc002lfq.1	Q8N1N2	OTTHUMG00000132709	ENST00000321600.1:c.182G>A	chr18.hg19:g.52262216G>A	ENSP00000315265:p.Trp61*	92.0	0.0		92.0	52.0	NM_173629		Nonsense_Mutation	SNP	ENST00000321600.1	hg19	CCDS11957.1	.	.	.	.	.	.	.	.	.	.	.	14.85	2.657331	0.47467	.	.	ENSG00000178690	ENST00000321600	.	.	.	4.24	2.43	0.29744	.	0.628433	0.13361	N	0.393641	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.1587	5.2196	0.15362	0.1044:0.0:0.6932:0.2025	.	.	.	.	X	61	.	ENSP00000315265:W61X	W	+	2	0	C18orf26	50413214	0.014000	0.17966	0.003000	0.11579	0.086000	0.17979	1.058000	0.30504	0.725000	0.32318	-0.251000	0.11542	TGG	.	.		0.463	DYNAP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256007.1	NM_173629		A	52262216	G	A	52262216	4	1	290	1	0	0	0	0	0	1	0	0	1902	1357	47	3	188	3	C18orf26	18	52262216	Nonsense_Mutation	SNP	G	TCGA-G3-A7M5-01A-11D-A33Q-10	45284001	52262216	25815032	148	42610										
MATK	4145	hgsc.bcm.edu	37	chr19	3784140	3784140	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	acggcatgaggctgagcttgGggtctgcggagagggcctcc	18	10	1	3			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr19:3784140G>A	ENST00000310132.6	-	5	742	c.344C>T	c.(343-345)cCc>cTc	p.P115L	MATK_ENST00000585778.1_Missense_Mutation_p.P115L|MATK_ENST00000395040.2_Missense_Mutation_p.P74L|MATK_ENST00000395045.2_Missense_Mutation_p.P116L	NM_139355.2	NP_647612.1	P42679	MATK_HUMAN	megakaryocyte-associated tyrosine kinase	115					cell proliferation (GO:0008283)|mesoderm development (GO:0007498)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)	cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|skin(2)|stomach(2)|urinary_tract(1)	26		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)		GCTGAGCTTGGGGTCTGCGGA	0.682																																					p.P116L		Atlas-SNP	.											.	MATK	108	.	0			c.C347T						.						30	34	33					19																	3784140		2201	4298	6499	SO:0001583	missense	4145	exon5			AGCTTGGGGTCTG	L18974	CCDS12113.1, CCDS12114.1, CCDS42468.1	19p13.3	2013-02-14						"SH2 domain containing"	6906	protein-coding gene	gene with protein product	"Csk-homologous kinase", "tyrosine-protein kinase CTK", "protein kinase HYL", "hematopoietic consensus tyrosine-lacking kinase", "tyrosylprotein kinase", "hydroxyaryl-protein kinase", "Csk-type protein tyrosine kinase", "HYL tyrosine kinase", "tyrosine kinase MATK", "leukocyte carboxyl-terminal src kinase related"	600038				8288563, 7530249	Standard	NM_139355		Approved	HYLTK, CTK, HYL, Lsk, CHK, HHYLTK, DKFZp434N1212, MGC1708, MGC2101	uc002lyt.3	P42679		ENST00000310132.6:c.344C>T	chr19.hg19:g.3784140G>A	ENSP00000308734:p.Pro115Leu	35.0	0.0		41.0	21.0	NM_002378	B3KNZ9|Q9NST8	Missense_Mutation	SNP	ENST00000310132.6	hg19	CCDS12114.1	.	.	.	.	.	.	.	.	.	.	g	19.29	3.799137	0.70567	.	.	ENSG00000007264	ENST00000395045;ENST00000310132;ENST00000395040	T;T;T	0.16743	2.32;2.32;2.32	4.25	4.25	0.50352	Src homology-3 domain (1);	0.000000	0.85682	D	0.000000	T	0.30603	0.0770	L	0.39514	1.22	0.80722	D	1	D;D;D	0.71674	0.998;0.998;0.998	P;P;P	0.61940	0.896;0.896;0.896	T	0.06041	-1.0849	10	0.66056	D	0.02	-29.0344	16.0026	0.80306	0.0:0.0:1.0:0.0	.	115;116;115	F1T0G6;B3KNZ9;P42679	.;.;MATK_HUMAN	L	116;115;74	ENSP00000378485:P116L;ENSP00000308734:P115L;ENSP00000378481:P74L	ENSP00000308734:P115L	P	-	2	0	MATK	3735140	1.000000	0.71417	0.964000	0.40570	0.663000	0.39108	3.524000	0.53495	2.067000	0.61834	0.306000	0.20318	CCC	.	.		0.682	MATK-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453639.1	NM_139355		A	3784140	G	A	3784140	3	1	290	1	0	0	0	0	1	0	0	0	9341	1232	43	3	1219	3	MATK	19	3784140	Missense_Mutation	SNP	G	TCGA-G3-A7M5-01A-11D-A33Q-10		3784140	55344843	149	42611										
MUC16	94025	hgsc.bcm.edu	37	chr19	9062327	9062327	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	gatgtggctttgggtgtctcTgagtcagataggacagaaga	15	5	2	4			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr19:9062327T>A	ENST00000397910.4	-	3	25322	c.25119A>T	c.(25117-25119)tcA>tcT	p.S8373S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	8375	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGGGTGTCTCTGAGTCAGATA	0.478																																					p.S8373S		Atlas-SNP	.											.	MUC16	4315	.	0			c.A25119T						.						178	173	175					19																	9062327		2079	4206	6285	SO:0001819	synonymous_variant	94025	exon3			TGTCTCTGAGTCA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.25119A>T	chr19.hg19:g.9062327T>A		68.0	0.0		66.0	25.0	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9062327	T	A	9062327	2	1	290	1	0	0	0	0	0	0	0	1	9982	1567	55	4		4	MUC16	19	9062327	Silent	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	5278187	9062327	50066656	150	42612										
MUC16	94025	hgsc.bcm.edu	37	chr19	9082590	9082590	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	gatgttggagaaagtgtcagAgctgaagtctgaagatgcac	14	5	2	5			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr19:9082590A>T	ENST00000397910.4	-	1	9428	c.9225T>A	c.(9223-9225)gcT>gcA	p.A3075A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3076	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AAAGTGTCAGAGCTGAAGTCT	0.498																																					p.A3075A		Atlas-SNP	.											.	MUC16	4315	.	0			c.T9225A						.						154	156	156					19																	9082590		1948	4136	6084	SO:0001819	synonymous_variant	94025	exon1			TGTCAGAGCTGAA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.9225T>A	chr19.hg19:g.9082590A>T		103.0	0.0		155.0	66.0	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.498	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9082590	A	T	9082590	2	4	290	1	0	0	0	0	0	0	0	1	9982	291	11	4		4	MUC16	19	9082590	Silent	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	20263	9082590	50046393	151	42613										
ZNF486	90649	hgsc.bcm.edu	37	chr19	20307961	20307961	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	gacttaaccaatgtttgacaActacccagagcaaaatattt	5	9	0	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr19:20307961A>T	ENST00000335117.8	+	4	499	c.442A>T	c.(442-444)Act>Tct	p.T148S	CTC-260E6.6_ENST00000586657.1_RNA|CTC-260E6.6_ENST00000585498.1_RNA|CTC-260E6.6_ENST00000593655.1_RNA	NM_052852.3	NP_443084.2	Q96H40	ZN486_HUMAN	zinc finger protein 486	148					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	11						ATGTTTGACAACTACCCAGAG	0.318																																					p.T148S		Atlas-SNP	.											.	ZNF486	74	.	0			c.A442T						.						69	75	73					19																	20307961		2187	4294	6481	SO:0001583	missense	90649	exon4			TTGACAACTACCC	BC008936	CCDS46029.1	19p12	2014-02-13	2003-12-16	2003-12-17	ENSG00000256229	ENSG00000256229		"Zinc fingers, C2H2-type", "-"	20807	protein-coding gene	gene with protein product			"KRAB domain only 2"	KRBO2			Standard	NM_052852		Approved	MGC2396	uc002nou.3	Q96H40	OTTHUMG00000179731	ENST00000335117.8:c.442A>T	chr19.hg19:g.20307961A>T	ENSP00000335042:p.Thr148Ser	174.0	0.0		249.0	94.0	NM_052852	Q0VG00	Missense_Mutation	SNP	ENST00000335117.8	hg19	CCDS46029.1	.	.	.	.	.	.	.	.	.	.	a	6.228	0.410191	0.11812	.	.	ENSG00000256229	ENST00000545779;ENST00000335117	T	0.47528	0.84	0.149	0.149	0.14863	.	.	.	.	.	T	0.40171	0.1106	L	0.43923	1.385	0.21355	N	0.999719	P	0.45078	0.85	P	0.46208	0.507	T	0.23332	-1.0191	8	0.27082	T	0.32	.	.	.	.	.	148	Q96H40	ZN486_HUMAN	S	187;148	ENSP00000335042:T148S	ENSP00000335042:T148S	T	+	1	0	ZNF486	20168961	0.001000	0.12720	0.052000	0.19188	0.052000	0.14988	1.065000	0.30592	0.166000	0.19597	0.164000	0.16699	ACT	.	.		0.318	ZNF486-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447843.2	NM_052852		T	20307961	A	T	20307961	3	4	290	1	0	0	0	0	1	0	0	0	17954	43	2	4	456	4	ZNF486	19	20307961	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	11225371	20307961	38821022	152	42614										
ZNF568	374900	hgsc.bcm.edu	37	chr19	37440867	37440867	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tcttattacacatcagaaaaTtcatactggggaaaaaccgt	6	8	3	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr19:37440867T>A	ENST00000333987.7	+	7	1318	c.812T>A	c.(811-813)aTt>aAt	p.I271N	ZNF568_ENST00000455427.2_Intron|ZNF568_ENST00000415168.1_Missense_Mutation_p.I207N|ZNF568_ENST00000427117.1_Intron	NM_001204835.1|NM_198539.3	NP_001191764.1|NP_940941.2	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	271					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(9)|ovary(1)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CATCAGAAAATTCATACTGGG	0.363																																					p.I271N		Atlas-SNP	.											.	ZNF568	106	.	0			c.T812A						.						37	41	39					19																	37440867		2123	4245	6368	SO:0001583	missense	374900	exon7			AGAAAATTCATAC	BX640681	CCDS42558.1, CCDS56092.1, CCDS56093.1, CCDS74351.1	19q13.12	2013-09-20			ENSG00000198453	ENSG00000198453		"Zinc fingers, C2H2-type", "-"	25392	protein-coding gene	gene with protein product							Standard	NM_198539		Approved	DKFZp686B0797	uc002ofc.3	Q3ZCX4	OTTHUMG00000048160	ENST00000333987.7:c.812T>A	chr19.hg19:g.37440867T>A	ENSP00000334685:p.Ile271Asn	80.0	0.0		112.0	49.0	NM_198539	B4DS92|E7ER33|Q6N060|Q8NA64	Missense_Mutation	SNP	ENST00000333987.7	hg19	CCDS42558.1	.	.	.	.	.	.	.	.	.	.	T	14.59	2.580163	0.46006	.	.	ENSG00000198453	ENST00000333987;ENST00000415168	T;T	0.09073	3.02;3.02	3.95	3.95	0.45737	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.37483	N	0.002071	T	0.19087	0.0458	L	0.56769	1.78	0.58432	D	0.999999	D	0.57571	0.98	D	0.65573	0.936	T	0.00555	-1.1673	10	0.87932	D	0	.	6.0896	0.19987	0.0:0.1155:0.0:0.8845	.	271	Q3ZCX4	ZN568_HUMAN	N	271;207	ENSP00000334685:I271N;ENSP00000394514:I207N	ENSP00000334685:I271N	I	+	2	0	ZNF568	42132707	0.000000	0.05858	0.724000	0.30704	0.999000	0.98932	-0.359000	0.07632	1.775000	0.52247	0.533000	0.62120	ATT	.	.		0.363	ZNF568-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109572.2	NM_198539		A	37440867	T	A	37440867	3	1	290	1	0	0	0	0	1	0	0	0	18014	1493	52	4	830	4	ZNF568	19	37440867	Missense_Mutation	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	17132906	37440867	21688116	153	42615										
PLD3	23646	hgsc.bcm.edu	37	chr19	40877640	40877640	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tggctcgagacctgaccaagAtctttgaggcctactggttc	11	11	1	4			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr19:40877640A>T	ENST00000409587.1	+	9	1136	c.739A>T	c.(739-741)Atc>Ttc	p.I247F	PLD3_ENST00000409419.1_Missense_Mutation_p.I247F|PLD3_ENST00000409281.1_Missense_Mutation_p.I247F|PLD3_ENST00000356508.5_Missense_Mutation_p.I247F|PLD3_ENST00000409735.4_Missense_Mutation_p.I247F			Q8IV08	PLD3_HUMAN	phospholipase D family, member 3	247					cell death (GO:0008219)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phospholipase D activity (GO:0004630)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	20			Lung(22;0.000636)|LUSC - Lung squamous cell carcinoma(20;0.00248)			CCTGACCAAGATCTTTGAGGC	0.587																																					p.I247F		Atlas-SNP	.											.	PLD3	71	.	0			c.A739T						.						100	67	78					19																	40877640		2203	4300	6503	SO:0001583	missense	23646	exon9			ACCAAGATCTTTG	BC000553	CCDS33027.1	19q13.2	2014-03-14	2005-05-20		ENSG00000105223	ENSG00000105223			17158	protein-coding gene	gene with protein product		615698	"phospholipase D3"			9140189, 15794758	Standard	XM_005258704		Approved	HU-K4	uc002onj.4	Q8IV08	OTTHUMG00000152736	ENST00000409587.1:c.739A>T	chr19.hg19:g.40877640A>T	ENSP00000387050:p.Ile247Phe	74.0	0.0		86.0	31.0	NM_012268	Q92853|Q9BW87	Missense_Mutation	SNP	ENST00000409587.1	hg19	CCDS33027.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.176795	0.78564	.	.	ENSG00000105223	ENST00000409419;ENST00000409587;ENST00000356508;ENST00000536031;ENST00000409735;ENST00000409281	T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67	5.77	4.7	0.59300	Phospholipase D/viral envelope (1);	0.106329	0.64402	D	0.000005	T	0.65749	0.2721	M	0.83223	2.63	0.80722	D	1	D	0.67145	0.996	D	0.71414	0.973	T	0.68796	-0.5314	10	0.56958	D	0.05	-11.9012	7.2566	0.26179	0.872:0.0:0.128:0.0	.	247	Q8IV08	PLD3_HUMAN	F	247;247;247;228;247;247	ENSP00000386293:I247F;ENSP00000387050:I247F;ENSP00000348901:I247F;ENSP00000386938:I247F;ENSP00000387022:I247F	ENSP00000348901:I247F	I	+	1	0	PLD3	45569480	1.000000	0.71417	1.000000	0.80357	0.658000	0.38924	4.239000	0.58694	2.215000	0.71742	0.459000	0.35465	ATC	.	.		0.587	PLD3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327721.1	NM_012268		T	40877640	A	T	40877640	3	4	290	1	0	0	0	0	1	0	0	0	12056	333	12	4	765	4	PLD3	19	40877640	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	3436773	40877640	18251343	154	42616										
LIG1	3978	hgsc.bcm.edu	37	chr19	48643272	48643273	+	Missense_Mutation	DNP	CC	CC	AA													0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	gaaggacaccatcacccacgCcaagctccaggccctgctgg							TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr19:48643272_48643273CC>AA	ENST00000263274.7	-	12	1461_1462	c.1042_1043GG>TT	c.(1042-1044)GGc>TTc	p.G348F	LIG1_ENST00000427526.2_Missense_Mutation_p.G317F|LIG1_ENST00000536218.1_Missense_Mutation_p.G280F	NM_000234.1	NP_000225.1	P18858	DNLI1_HUMAN	ligase I, DNA, ATP-dependent	348					anatomical structure morphogenesis (GO:0009653)|base-excision repair (GO:0006284)|cell division (GO:0051301)|DNA biosynthetic process (GO:0071897)|DNA ligation involved in DNA repair (GO:0051103)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|response to hydrogen peroxide (GO:0042542)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(22)|prostate(2)|skin(1)	44		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)	ATCACCCACGCCAAGCTCCAGG	0.634								Nucleotide excision repair (NER)																													p.G348V|p.G348C		Atlas-SNP	.											.	LIG1	151	.	0			c.G1043T|c.G1042T						.																																			SO:0001583	missense	3978	exon12			CCCACGCCAAGCT|CCACGCCAAGCTC		CCDS12711.1, CCDS74409.1, CCDS74410.1	19q13.2-q13.3	2014-09-17				ENSG00000105486	6.5.1.1		6598	protein-coding gene	gene with protein product		126391					Standard	XM_005258934		Approved		uc002pia.1	P18858		ENST00000263274.7:c.1042_1043delinsAA	chr19.hg19:g.48643272_48643273delinsAA	ENSP00000263274:p.Gly348Phe	54.0	0.0		85.0	27.0|26.0	NM_000234	B2RAI8|Q2TB12|Q32P23	Missense_Mutation	SNP	ENST00000263274.7	hg19	CCDS12711.1																																																																																			.	.		0.634	LIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465575.1	NM_000234		AA	48643273	CC	AA	48643272	3	1	290	1	0	0	0	0	1	0	0	0	8790	739	26	3	1784	3	LIG1	19	48643272	Missense_Mutation	DNP	CC	TCGA-G3-A7M5-01A-11D-A33Q-10	7765632	48643272	10485711	155	42617										
C19orf48	84798	hgsc.bcm.edu	37	chr19	51301354	51301354	+	Stop_Codon_Del	DEL	A	A	-													0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	gcacttcctgaatgcagctcAaaccaggagcagctccccca							TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr19:51301354delA	ENST00000598463.1	-	0	1450				C19orf48_ENST00000345523.4_Stop_Codon_Del|C19orf48_ENST00000391812.1_Stop_Codon_Del|C19orf48_ENST00000595794.1_5'Flank|SNORD88A_ENST00000408314.1_RNA|C19orf48_ENST00000596655.1_Stop_Codon_Del|SNORD88B_ENST00000408454.1_RNA			Q6RUI8	CS048_HUMAN	chromosome 19 open reading frame 48											endometrium(1)|kidney(1)|lung(1)|ovary(1)	4		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00531)|GBM - Glioblastoma multiforme(134;0.0145)		AATGCAGCTCAAACCAGGAGC	0.627																																					p.X118X		Atlas-Indel,Pindel	.											.	C19orf48	11	.	0			c.353delG						.						83	85	85					19																	51301354		2203	4300	6503	SO:0001567	stop_retained_variant	84798	exon5			.	BC037227	CCDS12803.1	19q13.33	2012-10-26			ENSG00000167747	ENSG00000167747			29667	protein-coding gene	gene with protein product	"multidrug resistance-related protein"					12452007	Standard	NM_001290154		Approved	MGC13170	uc002ptg.3	Q6RUI8		Exception_encountered	chr19.hg19:g.51301354delA	Exception_encountered	33.0	0.0		52.0	27.0	NM_199249		In_Frame_Del	DEL	ENST00000598463.1	hg19	CCDS12803.1																																																																																			.	.		0.627	C19orf48-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464107.1	NM_032712		-	51301354	A	-	51301354	7	5	290	1	0	1	0	1	0	0	0	0	1933	143	5	0	5	0	C19orf48	19	51301354	Stop_Codon_Del	DEL	A	TCGA-G3-A7M5-01A-11D-A33Q-10	2658082	51301354	7827629	156	42618										
KIR2DL3	3804	hgsc.bcm.edu	37	chr19	55263853	55263853	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	agaccctcaggaggtgacatAtgcacagttgaatcactgcg	11	10	2	3			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr19:55263853A>T	ENST00000342376.3	+	8	939	c.908A>T	c.(907-909)tAt>tTt	p.Y303F	KIR3DL1_ENST00000541392.1_Intron|KIR2DL4_ENST00000396284.2_Intron|KIR3DL1_ENST00000538269.1_Intron|CTB-61M7.1_ENST00000400864.3_RNA|KIR2DL3_ENST00000434419.2_Intron|KIR3DL1_ENST00000402254.2_Intron	NM_015868.2	NP_056952.2	P43628	KI2L3_HUMAN	killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail, 3	303					immune response (GO:0006955)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|large_intestine(1)|lung(11)|ovary(3)|pancreas(1)|skin(2)|urinary_tract(1)	21				GBM - Glioblastoma multiforme(193;0.0192)		GAGGTGACATATGCACAGTTG	0.488																																					p.Y303F		Atlas-SNP	.											.	KIR2DL3	68	.	0			c.A908T						.						212	218	216					19																	55263853		2049	4015	6064	SO:0001583	missense	3804	exon8			TGACATATGCACA	L41268	CCDS33107.1	19q13.4	2013-01-29				ENSG00000243772		"Killer cell immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6331	protein-coding gene	gene with protein product		604938				7749980, 8662091	Standard	XM_006725426		Approved	cl-6, nkat2, nkat2a, nkat2b, p58, CD158B2		P43628	OTTHUMG00000065887	ENST00000342376.3:c.908A>T	chr19.hg19:g.55263853A>T	ENSP00000342215:p.Tyr303Phe	113.0	0.0		130.0	66.0	NM_015868	O43472|P78402|Q14944|Q14945|Q9UM51|Q9UQ70	Missense_Mutation	SNP	ENST00000342376.3	hg19	CCDS33107.1	.	.	.	.	.	.	.	.	.	.	A	12.08	1.830010	0.32329	.	.	ENSG00000243772	ENST00000342376	T	0.00584	6.4	1.06	1.06	0.20224	.	.	.	.	.	T	0.03053	0.0090	H	0.94847	3.59	0.09310	N	0.999999	P;D;D	0.54964	0.927;0.969;0.969	D;P;P	0.67725	0.953;0.45;0.45	T	0.25328	-1.0135	9	0.87932	D	0	.	4.3665	0.11227	1.0:0.0:0.0:0.0	.	205;303;303	P43628-2;P43628;E3NZD8	.;KI2L3_HUMAN;.	F	303	ENSP00000342215:Y303F	ENSP00000342215:Y303F	Y	+	2	0	KIR2DL3	59955665	0.220000	0.23631	0.049000	0.19019	0.074000	0.17049	1.289000	0.33307	0.739000	0.32628	0.248000	0.18094	TAT	.	.		0.488	KIR2DL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000141150.1			T	55263853	A	T	55263853	3	4	290	1	0	0	0	0	1	0	0	0	8326	449	16	4	938	4	KIR2DL3	19	55263853	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	3962499	55263853	3865130	157	42619										
NLRP5	126206	hgsc.bcm.edu	37	chr19	56538847	56538847	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	agagacgtgggcacagagaaGctcaagtcagaggtcgtgtc	15	8	2	3			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr19:56538847G>T	ENST00000390649.3	+	7	1248	c.1248G>T	c.(1246-1248)aaG>aaT	p.K416N		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	416	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|ovary(5)|skin(2)|stomach(4)|upper_aerodigestive_tract(2)	25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		GCACAGAGAAGCTCAAGTCAG	0.557																																					p.K416N		Atlas-SNP	.											.	NLRP5	217	.	0			c.G1248T						.						48	49	49					19																	56538847		2091	4209	6300	SO:0001583	missense	126206	exon7			AGAGAAGCTCAAG	AY154460	CCDS12938.1	19q13.43	2008-10-30	2006-12-08	2006-12-08	ENSG00000171487	ENSG00000171487		"Nucleotide-binding domain and leucine rich repeat containing"	21269	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 5"	609658	"NACHT, leucine rich repeat and PYD containing 5"	NALP5		12563287, 11925379	Standard	NM_153447		Approved	PYPAF8, MATER, PAN11, CLR19.8	uc002qmj.3	P59047	OTTHUMG00000149887	ENST00000390649.3:c.1248G>T	chr19.hg19:g.56538847G>T	ENSP00000375063:p.Lys416Asn	58.0	0.0		90.0	20.0	NM_153447	A8MTY4|Q86W29	Missense_Mutation	SNP	ENST00000390649.3	hg19	CCDS12938.1	.	.	.	.	.	.	.	.	.	.	G	13.38	2.219706	0.39201	.	.	ENSG00000171487	ENST00000390649	T	0.78364	-1.17	3.35	1.01	0.19927	.	1.816140	0.03225	N	0.178137	T	0.78629	0.4313	L	0.54965	1.715	0.09310	N	1	B	0.30526	0.283	B	0.39465	0.3	T	0.63497	-0.6624	10	0.45353	T	0.12	.	9.1235	0.36801	0.0:0.443:0.557:0.0	.	416	P59047	NALP5_HUMAN	N	416	ENSP00000375063:K416N	ENSP00000375063:K416N	K	+	3	2	NLRP5	61230659	0.026000	0.19158	0.007000	0.13788	0.005000	0.04900	-0.017000	0.12590	0.352000	0.24053	0.655000	0.94253	AAG	.	.		0.557	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447		T	56538847	G	T	56538847	3	4	290	1	0	0	0	0	1	0	0	0	10489	962	34	3	1274	3	NLRP5	19	56538847	Missense_Mutation	SNP	G	TCGA-G3-A7M5-01A-11D-A33Q-10	1274994	56538847	2590136	158	42620										
ZNF667	63934	hgsc.bcm.edu	37	chr19	56953879	56953879	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	ctcctgtatgaatgttctgaTgaagtttaagagagaagctt	10	5	1	5			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr19:56953879T>A	ENST00000504904.3	-	7	1204	c.485A>T	c.(484-486)cAt>cTt	p.H162L	ZNF667_ENST00000292069.6_Missense_Mutation_p.H162L|ZNF667_ENST00000591790.1_3'UTR|ZNF667_ENST00000342634.3_Missense_Mutation_p.H290L			Q5HYK9	ZN667_HUMAN	zinc finger protein 667	162					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	38		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0615)		AATGTTCTGATGAAGTTTAAG	0.373																																					p.H162L		Atlas-SNP	.											.	ZNF667	95	.	0			c.A485T						.						83	87	86					19																	56953879		2203	4299	6502	SO:0001583	missense	63934	exon5			TTCTGATGAAGTT		CCDS12944.1	19q13.43	2013-01-08				ENSG00000198046		"Zinc fingers, C2H2-type", "-"	28854	protein-coding gene	gene with protein product		611024					Standard	NM_022103		Approved	FLJ14011	uc002qnd.3	Q5HYK9		ENST00000504904.3:c.485A>T	chr19.hg19:g.56953879T>A	ENSP00000439402:p.His162Leu	109.0	0.0		139.0	60.0	NM_022103	B2RMS6|B9EK36|Q6B093|Q9H807	Missense_Mutation	SNP	ENST00000504904.3	hg19	CCDS12944.1	.	.	.	.	.	.	.	.	.	.	T	14.82	2.650751	0.47362	.	.	ENSG00000198046	ENST00000342634;ENST00000504904;ENST00000292069;ENST00000360227	D;D;D	0.86865	-2.18;-2.18;-2.18	4.86	4.86	0.63082	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.45867	D	0.000339	D	0.95906	0.8667	H	0.98333	4.205	0.47659	D	0.999487	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.995	D	0.96963	0.9703	10	0.87932	D	0	-9.2598	12.4411	0.55625	0.0:0.0:0.0:1.0	.	290;162	E7EPS0;Q5HYK9	.;ZN667_HUMAN	L	290;162;162;36	ENSP00000344699:H290L;ENSP00000439402:H162L;ENSP00000292069:H162L	ENSP00000292069:H162L	H	-	2	0	ZNF667	61645691	1.000000	0.71417	0.752000	0.31206	0.002000	0.02628	5.373000	0.66162	2.037000	0.60232	0.477000	0.44152	CAT	.	.		0.373	ZNF667-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458394.1	NM_022103		A	56953879	T	A	56953879	3	1	290	1	0	0	0	0	1	0	0	0	18089	1464	51	4	1351	4	ZNF667	19	56953879	Missense_Mutation	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	415032	56953879	2175104	159	42621										
CHGB	1114	hgsc.bcm.edu	37	chr20	5904188	5904188	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	ccacaaggtgcgtggaaagaGctggacagaaattatctcaa	11	8	1	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr20:5904188G>A	ENST00000378961.4	+	4	1602	c.1398G>A	c.(1396-1398)gaG>gaA	p.E466E		NM_001819.2	NP_001810.2	P05060	SCG1_HUMAN	chromogranin B (secretogranin 1)	466						extracellular region (GO:0005576)|secretory granule (GO:0030141)	hormone activity (GO:0005179)			breast(7)|kidney(2)|large_intestine(8)|lung(19)|ovary(1)|pancreas(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	47						CGTGGAAAGAGCTGGACAGAA	0.522																																					p.E466E		Atlas-SNP	.											.	CHGB	112	.	0			c.G1398A						.						98	101	100					20																	5904188		2203	4300	6503	SO:0001819	synonymous_variant	1114	exon4			GAAAGAGCTGGAC		CCDS13092.1	20p12.3	2013-09-19			ENSG00000089199	ENSG00000089199			1930	protein-coding gene	gene with protein product	"secretogranin B"	118920		SCG1		3608978	Standard	NM_001819		Approved		uc002wmg.3	P05060	OTTHUMG00000031821	ENST00000378961.4:c.1398G>A	chr20.hg19:g.5904188G>A		55.0	0.0		92.0	40.0	NM_001819	A8K021|Q59EU9|Q6IBS6|Q9BQV6|Q9UC25|Q9UJA6	Silent	SNP	ENST00000378961.4	hg19	CCDS13092.1																																																																																			.	.		0.522	CHGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077897.2	NM_001819		A	5904188	G	A	5904188	2	1	290	1	0	0	0	0	0	0	0	1	3341	962	34	3		3	CHGB	20	5904188	Silent	SNP	G	TCGA-G3-A7M5-01A-11D-A33Q-10		5904188	57121332	160	42622										
PLCB1	23236	hgsc.bcm.edu	37	chr20	8713899	8713899	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	actcagacctggctatgcaaAtaaatatggggatgtatgaa	10	6	1	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr20:8713899A>G	ENST00000338037.6	+	19	1930	c.1903A>G	c.(1903-1905)Ata>Gta	p.I635V	PLCB1_ENST00000378637.2_Missense_Mutation_p.I635V|PLCB1_ENST00000494924.1_3'UTR|PLCB1_ENST00000378641.3_Missense_Mutation_p.I635V	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	635	PI-PLC Y-box. {ECO:0000255|PROSITE- ProRule:PRU00271}.				activation of meiosis involved in egg activation (GO:0060466)|cerebral cortex development (GO:0021987)|fat cell differentiation (GO:0045444)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G2/M transition of mitotic cell cycle (GO:0000086)|glutamate receptor signaling pathway (GO:0007215)|inositol phosphate metabolic process (GO:0043647)|insulin-like growth factor receptor signaling pathway (GO:0048009)|interleukin-1-mediated signaling pathway (GO:0070498)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-15-mediated signaling pathway (GO:0035723)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|memory (GO:0007613)|negative regulation of monocyte extravasation (GO:2000438)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of CD24 biosynthetic process (GO:2000560)|positive regulation of developmental growth (GO:0048639)|positive regulation of embryonic development (GO:0040019)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of GTPase activity (GO:0043547)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fertilization (GO:0080154)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						GGCTATGCAAATAAATATGGG	0.393																																					p.P635A		Atlas-SNP	.											.	PLCB1	394	.	0			c.C1903G						.						123	117	119					20																	8713899		2203	4300	6503	SO:0001583	missense	23236	exon19			ATGCAAATAAATA	AB011153	CCDS13102.1, CCDS13103.1	20p12	2008-03-18			ENSG00000182621	ENSG00000182621	3.1.4.11		15917	protein-coding gene	gene with protein product		607120				10760467, 11118617	Standard	NM_015192		Approved	KIAA0581, PLC-I, PLC154	uc002wnb.4	Q9NQ66	OTTHUMG00000031849	ENST00000338037.6:c.1903A>G	chr20.hg19:g.8713899A>G	ENSP00000338185:p.Ile635Val	90.0	0.0		110.0	56.0	NM_015192	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Missense_Mutation	SNP	ENST00000338037.6	hg19	CCDS13102.1	.	.	.	.	.	.	.	.	.	.	A	13.25	2.181469	0.38511	.	.	ENSG00000182621	ENST00000378641;ENST00000338037;ENST00000378637;ENST00000441163;ENST00000535719	T;T;T	0.66460	-0.21;-0.21;-0.21	5.19	4.03	0.46877	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific, Y domain (3);	0.127350	0.53938	D	0.000041	T	0.47600	0.1454	N	0.13299	0.325	0.33361	D	0.57238	B;B	0.18013	0.014;0.025	B;B	0.26416	0.069;0.041	T	0.56038	-0.8045	10	0.46703	T	0.11	.	7.9853	0.30207	0.7282:0.1385:0.0:0.1333	.	635;635	Q9NQ66;Q9NQ66-2	PLCB1_HUMAN;.	V	635;635;635;555;555	ENSP00000367908:I635V;ENSP00000338185:I635V;ENSP00000367904:I635V	ENSP00000338185:I635V	I	+	1	0	PLCB1	8661899	1.000000	0.71417	0.579000	0.28588	0.975000	0.68041	2.337000	0.43947	2.075000	0.62263	0.528000	0.53228	ATA	.	.		0.393	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3			G	8713899	A	G	8713899	3	3	290	1	0	0	0	0	1	0	0	0	12036	101	4	2	1977	2	PLCB1	20	8713899	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	2809711	8713899	54311621	161	42623										
CRNKL1	51340	hgsc.bcm.edu	37	chr20	20033133	20033133	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	caggactgacctttgacctcTcgcttgagccgtgacggagg	13	12	1	4			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr20:20033133T>A	ENST00000377340.2	-	2	368	c.337A>T	c.(337-339)Aga>Tga	p.R113*	CRNKL1_ENST00000536226.1_5'Flank|C20orf26_ENST00000377309.2_5'Flank|C20orf26_ENST00000377306.1_5'Flank|C20orf26_ENST00000389656.3_5'Flank|CRNKL1_ENST00000377327.4_Nonsense_Mutation_p.R101*|C20orf26_ENST00000245957.5_5'Flank	NM_001278628.1|NM_016652.4	NP_001265557.1|NP_057736.4	Q9BZJ0	CRNL1_HUMAN	crooked neck pre-mRNA splicing factor 1	113					mRNA splicing, via spliceosome (GO:0000398)|spliceosomal complex assembly (GO:0000245)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|cervix(2)|endometrium(7)|large_intestine(11)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(6)	45						CTTTGACCTCTCGCTTGAGCC	0.597																																					p.R113X		Atlas-SNP	.											.	CRNKL1	101	.	0			c.A337T						.						79	76	77					20																	20033133		2203	4300	6503	SO:0001587	stop_gained	51340	exon2			GACCTCTCGCTTG	AF255443	CCDS33446.1, CCDS63238.1, CCDS63239.1	20p11.2	2013-10-03	2013-10-03		ENSG00000101343	ENSG00000101343			15762	protein-coding gene	gene with protein product	"SYF3 pre-mRNA-splicing factor"	610952	"crooked neck (Drosophila Crn homolog)-like 1", "Crn, crooked neck-like 1 (Drosophila)", "crooked neck pre-mRNA splicing factor-like 1 (Drosophila)"				Standard	NM_016652		Approved	CRN, CLF, SYF3, Clf1	uc002wrs.3	Q9BZJ0	OTTHUMG00000032000	ENST00000377340.2:c.337A>T	chr20.hg19:g.20033133T>A	ENSP00000366557:p.Arg113*	81.0	0.0		100.0	34.0	NM_016652	A8K9T4|Q5JY64|Q8WYI5|Q9BZI9|Q9BZJ1|Q9BZJ2|Q9GZW7|Q9H8F8|Q9NQH5|Q9NYD8	Nonsense_Mutation	SNP	ENST00000377340.2	hg19	CCDS33446.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.012309	0.75046	.	.	ENSG00000101343	ENST00000377327;ENST00000377340	.	.	.	5.38	-10.8	0.00216	.	1.951080	0.02912	N	0.136770	.	.	.	.	.	.	0.09310	N	0.999995	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.0425	1.2283	0.01938	0.3008:0.1367:0.1404:0.4221	.	.	.	.	X	101;113	.	ENSP00000366544:R101X	R	-	1	2	CRNKL1	19981133	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-1.371000	0.02573	-3.650000	0.00126	-1.292000	0.01352	AGA	.	.		0.597	CRNKL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000127787.1			A	20033133	T	A	20033133	4	1	290	1	0	0	0	0	0	1	0	0	3893	1559	54	4	2265	4	CRNKL1	20	20033133	Nonsense_Mutation	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	11319234	20033133	42992387	162	42624										
RALGAPA2	57186	hgsc.bcm.edu	37	chr20	20563863	20563863	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	agagttgtgtcactgttggtActttcacctggtacaatgga	11	7	2	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr20:20563863A>T	ENST00000202677.7	-	20	2545	c.2538T>A	c.(2536-2538)agT>agA	p.S846R		NM_020343.3	NP_065076.2	Q2PPJ7	RGPA2_HUMAN	Ral GTPase activating protein, alpha subunit 2 (catalytic)	846					activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(25)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	54						CACTGTTGGTACTTTCACCTG	0.433																																					p.S846R		Atlas-SNP	.											.	RALGAPA2	274	.	0			c.T2538A						.						80	77	78					20																	20563863		1903	4124	6027	SO:0001583	missense	57186	exon20			GTTGGTACTTTCA	AL078634, DQ310704	CCDS46584.1	20p11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000188559	ENSG00000188559			16207	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 74"	C20orf74		16490346, 19520869	Standard	NM_020343		Approved	dJ1049G11.4, AS250, KIAA1272, RapGAPalpha2	uc002wrz.3	Q2PPJ7	OTTHUMG00000032010	ENST00000202677.7:c.2538T>A	chr20.hg19:g.20563863A>T	ENSP00000202677:p.Ser846Arg	77.0	0.0		88.0	41.0	NM_020343	Q4VXU6|Q5JUA3|Q5JUA4|Q5T9K3|Q96CX9|Q9BQT7|Q9H9D9|Q9ULE8	Missense_Mutation	SNP	ENST00000202677.7	hg19	CCDS46584.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.20|14.20	2.464979|2.464979	0.43839|0.43839	.|.	.|.	ENSG00000188559|ENSG00000188559	ENST00000202677|ENST00000430436	T|.	0.70282|.	-0.47|.	6.07|6.07	2.66|2.66	0.31614|0.31614	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.62877|0.62877	0.2464|0.2464	M|M	0.68317|0.68317	2.08|2.08	0.40371|0.40371	D|D	0.979341|0.979341	D;B|.	0.56746|.	0.977;0.053|.	P;B|.	0.54312|.	0.748;0.019|.	T|T	0.60265|0.60265	-0.7297|-0.7297	10|5	0.23891|.	T|.	0.37|.	.|.	9.32|9.32	0.37957|0.37957	0.7959:0.0:0.2041:0.0|0.7959:0.0:0.2041:0.0	.|.	684;846|.	A8MSM5;Q2PPJ7|.	.;RGPA2_HUMAN|.	R|E	846|663	ENSP00000202677:S846R|.	ENSP00000202677:S846R|.	S|V	-|-	3|2	2|0	RALGAPA2|RALGAPA2	20511863|20511863	1.000000|1.000000	0.71417|0.71417	0.984000|0.984000	0.44739|0.44739	0.949000|0.949000	0.60115|0.60115	2.317000|2.317000	0.43770|0.43770	0.539000|0.539000	0.28788|0.28788	0.533000|0.533000	0.62120|0.62120	AGT|GTA	.	.		0.433	RALGAPA2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471941.1	NM_020343		T	20563863	A	T	20563863	3	4	290	1	0	0	0	0	1	0	0	0	13029	388	14	4	3163	4	RALGAPA2	20	20563863	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	530730	20563863	42461657	163	42625										
SFRS6	6431	hgsc.bcm.edu	37	chr20	42089474	42089474	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	aagcagatctaaggatgagtAtgagaaatctcgaagcaggt	12	5	2	3			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr20:42089474A>G	ENST00000244020.3	+	6	912	c.806A>G	c.(805-807)tAt>tGt	p.Y269C		NM_006275.5	NP_006266.2	Q13247	SRSF6_HUMAN	serine/arginine-rich splicing factor 6	269	Arg/Ser-rich (RS domain).				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of cell death (GO:0060548)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of keratinocyte proliferation (GO:0010837)|regulation of wound healing (GO:0061041)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)	p.Y269C(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|upper_aerodigestive_tract(2)	5						AAGGATGAGTATGAGAAATCT	0.453																																					p.Y269C		Atlas-SNP	.											SRSF6_ENST00000244020,NS,carcinoma,0,1	SRSF6	37	.	1	Substitution - Missense(1)	lung(1)	c.A806G						.						55	56	56					20																	42089474		2203	4300	6503	SO:0001583	missense	6431	exon6			ATGAGTATGAGAA	U30883	CCDS13318.1	20q12-q13.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000124193	ENSG00000124193		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10788	protein-coding gene	gene with protein product	"pre-mRNA splicing factor SRP55", "SR splicing factor 6"	601944	"splicing factor, arginine/serine-rich 6"	SFRS6		7556075, 20516191	Standard	NM_006275		Approved	SRP55, B52	uc010zwg.2	Q13247	OTTHUMG00000032502	ENST00000244020.3:c.806A>G	chr20.hg19:g.42089474A>G	ENSP00000244020:p.Tyr269Cys	111.0	0.0		136.0	20.0	NM_006275	B7Z6J3|E1P5W6|Q13244|Q13245|Q96J06|Q9UJB8|Q9Y3N7	Missense_Mutation	SNP	ENST00000244020.3	hg19	CCDS13318.1	.	.	.	.	.	.	.	.	.	.	A	7.519	0.656340	0.14580	.	.	ENSG00000124193	ENST00000244020	T	0.11169	2.8	5.83	4.75	0.60458	.	0.350840	0.26784	N	0.022505	T	0.09774	0.0240	L	0.36672	1.1	0.20873	N	0.999833	B	0.28512	0.214	B	0.26693	0.072	T	0.17961	-1.0352	10	0.48119	T	0.1	.	11.4682	0.50252	0.7846:0.2154:0.0:0.0	.	269	Q13247	SRSF6_HUMAN	C	269	ENSP00000244020:Y269C	ENSP00000244020:Y269C	Y	+	2	0	SRSF6	41522888	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.101000	0.50283	2.217000	0.71921	0.477000	0.44152	TAT	.	.		0.453	SRSF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079292.1	NM_006275		G	42089474	A	G	42089474	3	3	290	1	0	0	0	0	1	0	0	0	14196	449	16	2	828	2	SFRS6	20	42089474	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	21525611	42089474	20936046	164	42626										
ZNF334	55713	hgsc.bcm.edu	37	chr20	45130663	45130663	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tttcgtacataaaaattttcCacattgactgcattcatagg	5	8	1	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr20:45130663C>T	ENST00000347606.4	-	5	1497	c.1315G>A	c.(1315-1317)Gga>Aga	p.G439R	ZNF334_ENST00000457685.2_Missense_Mutation_p.G401R|ZNF334_ENST00000593880.1_Missense_Mutation_p.G462R	NM_018102.4	NP_060572.3	Q9HCZ1	ZN334_HUMAN	zinc finger protein 334	439					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G439R(1)		NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0122)				AAAAATTTTCCACATTGACTG	0.378																																					p.G439R		Atlas-SNP	.											ZNF334,NS,carcinoma,0,1	ZNF334	101	.	1	Substitution - Missense(1)	kidney(1)	c.G1315A						.						115	113	114					20																	45130663		2203	4299	6502	SO:0001583	missense	55713	exon5			ATTTTCCACATTG	AK001331	CCDS33480.1, CCDS74736.1	20q13.12	2013-09-20			ENSG00000198185	ENSG00000198185		"Zinc fingers, C2H2-type", "-"	15806	protein-coding gene	gene with protein product							Standard	NM_018102		Approved	bA179N14.1	uc002xsc.4	Q9HCZ1	OTTHUMG00000032654	ENST00000347606.4:c.1315G>A	chr20.hg19:g.45130663C>T	ENSP00000255129:p.Gly439Arg	55.0	0.0		87.0	28.0	NM_018102	Q5T6U2|Q9NVW4	Missense_Mutation	SNP	ENST00000347606.4	hg19	CCDS33480.1	.	.	.	.	.	.	.	.	.	.	C	12.68	2.009792	0.35415	.	.	ENSG00000198185	ENST00000457685;ENST00000347606	T;T	0.22743	1.94;1.94	3.24	0.129	0.14739	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.25044	0.0608	M	0.81239	2.535	0.35114	D	0.766422	B;B;B	0.26547	0.152;0.152;0.152	B;B;B	0.28232	0.087;0.087;0.087	T	0.18555	-1.0333	9	0.87932	D	0	.	7.0128	0.24871	0.0:0.6653:0.0:0.3347	.	401;439;462	B3KQ93;Q9HCZ1;Q8N3P8	.;ZN334_HUMAN;.	R	401;439	ENSP00000402582:G401R;ENSP00000255129:G439R	ENSP00000255129:G439R	G	-	1	0	ZNF334	44564070	0.296000	0.24398	0.009000	0.14445	0.977000	0.68977	0.397000	0.20883	-0.062000	0.13088	-0.216000	0.12614	GGA	.	.		0.378	ZNF334-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079575.1			T	45130663	C	T	45130663	3	4	290	1	0	0	0	0	1	0	0	0	17866	603	21	3	731	3	ZNF334	20	45130663	Missense_Mutation	SNP	C	TCGA-G3-A7M5-01A-11D-A33Q-10	3041189	45130663	17894857	165	42627										
IGSF5	150084	hgsc.bcm.edu	37	chr21	41151111	41151111	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	ggcaaagttggacttggactAgcaggcaccatgcttctgac	12	10	1	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr21:41151111A>T	ENST00000380588.4	+	5	916	c.813A>T	c.(811-813)ctA>ctT	p.L271L	IGSF5_ENST00000479378.1_3'UTR	NM_001080444.1	NP_001073913.1	Q9NSI5	IGSF5_HUMAN	immunoglobulin superfamily, member 5	271					single organismal cell-cell adhesion (GO:0016337)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(7)|skin(2)|stomach(1)	23		Prostate(19;5.35e-06)				GACTTGGACTAGCAGGCACCA	0.488																																					p.L271L		Atlas-SNP	.											.	IGSF5	62	.	0			c.A813T						.						121	113	116					21																	41151111		2203	4300	6503	SO:0001819	synonymous_variant	150084	exon5			TGGACTAGCAGGC		CCDS33562.1	21q22.2	2013-01-29			ENSG00000183067	ENSG00000183067		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5952	protein-coding gene	gene with protein product	"junctional adhesion molecule 4"	610638					Standard	NM_001080444		Approved	JAM4	uc002yyo.3	Q9NSI5	OTTHUMG00000086724	ENST00000380588.4:c.813A>T	chr21.hg19:g.41151111A>T		49.0	0.0		81.0	34.0	NM_001080444		Silent	SNP	ENST00000380588.4	hg19	CCDS33562.1																																																																																			.	.		0.488	IGSF5-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195005.1			T	41151111	A	T	41151111	2	4	290	1	0	0	0	0	0	0	0	1	7611	407	15	4		4	IGSF5	21	41151111	Silent	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10		41151111	6978784	166	42628										
FTCD	10841	hgsc.bcm.edu	37	chr21	47566181	47566181	+	Splice_Site	DEL	C	C	-													0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	cgggagggcagaggctcactCgatgatccgctccttagggc					rs374048282		TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr21:47566181delC	ENST00000291670.5	-	8	1010	c.967delG	c.(967-969)gag>ag	p.E323fs	FTCD_ENST00000397748.1_Splice_Site_p.E323fs|FTCD_ENST00000359679.2_Splice_Site_p.E323fs|FTCD_ENST00000355384.2_Splice_Site_p.E323fs|FTCD_ENST00000498355.2_5'UTR|FTCD_ENST00000397743.1_Splice_Site_p.E323fs|FTCD_ENST00000397746.3_Splice_Site_p.E323fs	NM_006657.2	NP_006648.1	O95954	FTCD_HUMAN	formimidoyltransferase cyclodeaminase	323	Formiminotransferase C-subdomain. {ECO:0000250}.				cellular nitrogen compound metabolic process (GO:0034641)|cytoskeleton organization (GO:0007010)|folic acid-containing compound metabolic process (GO:0006760)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	folic acid binding (GO:0005542)|formimidoyltetrahydrofolate cyclodeaminase activity (GO:0030412)|glutamate formimidoyltransferase activity (GO:0030409)			endometrium(1)|large_intestine(2)|lung(9)|pancreas(1)|prostate(3)|skin(3)	19	Breast(49;0.214)			Colorectal(79;0.235)	Tetrahydrofolic acid(DB00116)	GAGGCTCACTCGATGATCCGC	0.697																																					p.E323fs		Atlas-Indel,Pindel	.											.	FTCD	59	.	0			c.968delA						.						68	67	67					21																	47566181		2159	4279	6438	SO:0001630	splice_region_variant	10841	exon8			.	U91541	CCDS13731.1	21q22.3	2013-06-10	2013-06-10		ENSG00000160282	ENSG00000160282	2.1.2.5, 4.3.1.4		3974	protein-coding gene	gene with protein product		606806	"formiminotransferase cyclodeaminase"			10029623, 10773664	Standard	NM_006657		Approved		uc002zif.3	O95954	OTTHUMG00000090488	ENST00000291670.5:c.968+1G>-	chr21.hg19:g.47566181delC		100.0	0.0		113.0	51.0	NM_206965	B9EGD0|Q86V03|Q9HCT4|Q9HCT5|Q9HCT6|Q9UHJ2	Frame_Shift_Del	DEL	ENST00000291670.5	hg19	CCDS13731.1																																																																																			.	.		0.697	FTCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206962.1	NM_006657	Frame_Shift_Del	-	47566181	C	-	47566181	8	5	290	1	0	1	0	1	0	0	1	0	6089	898	31	0	686	0	FTCD	21	47566181	Splice_Site	DEL	C	TCGA-G3-A7M5-01A-11D-A33Q-10	6415070	47566181	563714	167	42629										
CHEK2	11200	hgsc.bcm.edu	37	chr22	29130468	29130468	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	gctcctcaggttcttggtccTcaggttcttggtcctcagga	11	12	5	0			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr22:29130468T>G	ENST00000405598.1	-	3	433	c.242A>C	c.(241-243)gAg>gCg	p.E81A	CHEK2_ENST00000544772.1_5'UTR|CHEK2_ENST00000402731.1_Missense_Mutation_p.E81A|CHEK2_ENST00000382580.2_Missense_Mutation_p.E81A|CHEK2_ENST00000382578.1_Missense_Mutation_p.E81A|CHEK2_ENST00000348295.3_Missense_Mutation_p.E81A|CHEK2_ENST00000382566.1_Missense_Mutation_p.E81A|CHEK2_ENST00000328354.6_Missense_Mutation_p.E81A|CHEK2_ENST00000404276.1_Missense_Mutation_p.E81A|CHEK2_ENST00000382565.1_Missense_Mutation_p.E81A|CHEK2_ENST00000403642.1_Missense_Mutation_p.E81A			O96017	CHK2_HUMAN	checkpoint kinase 2	81					cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						TTCTTGGTCCTCAGGTTCTTG	0.522			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																													p.E81A		Atlas-SNP	.	yes	Rec		familial breast cancer	22	22q12.1	11200	CHK2 checkpoint homolog (S. pombe)		E	.	CHEK2	438	.	0			c.A242C						.						70	74	72					22																	29130468		2203	4300	6503	SO:0001583	missense	11200	exon2			TGGTCCTCAGGTT	AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"CHK2 (checkpoint, S.pombe) homolog", "CHK2 checkpoint homolog (S. pombe)"	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.242A>C	chr22.hg19:g.29130468T>G	ENSP00000386087:p.Glu81Ala	96.0	0.0		72.0	15.0	NM_145862	A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Missense_Mutation	SNP	ENST00000405598.1	hg19	CCDS13843.1	.	.	.	.	.	.	.	.	.	.	T	16.74	3.206881	0.58343	.	.	ENSG00000183765	ENST00000348295;ENST00000382578;ENST00000382565;ENST00000382566;ENST00000328354;ENST00000404276;ENST00000405598;ENST00000382580;ENST00000403642;ENST00000402731;ENST00000447421;ENST00000439200;ENST00000398017	T;T;T;D;T;T;T;T;T;T;T;T;D	0.93488	0.84;-0.2;-0.26;-3.23;-0.12;-0.12;-0.12;2.27;-0.2;0.84;0.32;2.27;-2.27	5.41	5.41	0.78517	.	.	.	.	.	D	0.91703	0.7377	L	0.29908	0.895	0.40775	D	0.983123	D;D;D;D;P;D	0.60160	0.967;0.987;0.976;0.986;0.944;0.974	P;P;P;P;B;P	0.56163	0.716;0.754;0.541;0.793;0.437;0.793	D	0.89126	0.3506	9	0.09338	T	0.73	.	14.9223	0.70847	0.0:0.0:0.0:1.0	.	81;81;81;81;81;81	O96017-7;O96017-4;A8JZZ5;O96017-12;O96017;O96017-9	.;.;.;.;CHK2_HUMAN;.	A	81;81;81;81;81;81;81;81;81;81;81;81;91	ENSP00000329012:E81A;ENSP00000372021:E81A;ENSP00000372006:E81A;ENSP00000372007:E81A;ENSP00000329178:E81A;ENSP00000385747:E81A;ENSP00000386087:E81A;ENSP00000372023:E81A;ENSP00000384919:E81A;ENSP00000384835:E81A;ENSP00000397478:E81A;ENSP00000408065:E81A;ENSP00000381099:E91A	ENSP00000329178:E81A	E	-	2	0	CHEK2	27460468	1.000000	0.71417	0.969000	0.41365	0.982000	0.71751	5.187000	0.65087	2.180000	0.69256	0.528000	0.53228	GAG	.	.		0.522	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735		G	29130468	T	G	29130468	3	3	290	1	0	0	0	0	1	0	0	0	3337	1551	54	5	1578	5	CHEK2	22	29130468	Missense_Mutation	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10		29130468	22174098	168	42630										
MCM5	4174	hgsc.bcm.edu	37	chr22	35812706	35812706	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	cagtgttcggccgctgggatGagacgaagggggaggacaac	18	8	0	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr22:35812706G>C	ENST00000216122.4	+	12	1643	c.1489G>C	c.(1489-1491)Gag>Cag	p.E497Q	MCM5_ENST00000382011.5_Missense_Mutation_p.E454Q	NM_006739.3	NP_006730.2	P33992	MCM5_HUMAN	minichromosome maintenance complex component 5	497	MCM.				DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29						CCGCTGGGATGAGACGAAGGG	0.567																																					p.E497Q		Atlas-SNP	.											.	MCM5	54	.	0			c.G1489C						.						118	92	101					22																	35812706		2203	4300	6503	SO:0001583	missense	4174	exon12			TGGGATGAGACGA		CCDS13915.1	22q13.1-q13.2	2007-04-04	2007-04-04		ENSG00000100297	ENSG00000100297			6948	protein-coding gene	gene with protein product		602696	"minichromosome maintenance deficient (S. cerevisiae) 5 (cell division cycle 46)", "MCM5 minichromosome maintenance deficient 5, cell division cycle 46 (S. cerevisiae)"	CDC46		8751386, 10591208	Standard	NM_006739		Approved		uc003anu.4	P33992	OTTHUMG00000150961	ENST00000216122.4:c.1489G>C	chr22.hg19:g.35812706G>C	ENSP00000216122:p.Glu497Gln	69.0	0.0		63.0	25.0	NM_006739	O60785|Q14578|Q9BTJ4|Q9BWL8	Missense_Mutation	SNP	ENST00000216122.4	hg19	CCDS13915.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.892370	0.91889	.	.	ENSG00000100297	ENST00000216122;ENST00000382011	T;T	0.06528	3.29;3.29	5.77	4.73	0.59995	.	0.148087	0.64402	D	0.000010	T	0.13628	0.0330	L	0.37507	1.11	0.47547	D	0.999451	P;P;P;P	0.37276	0.589;0.589;0.589;0.589	P;P;P;P	0.50136	0.632;0.632;0.565;0.632	T	0.02676	-1.1125	10	0.87932	D	0	-27.8061	16.6228	0.84934	0.0:0.1302:0.8698:0.0	.	497;497;454;497	B1AHB0;Q53FG5;B1AHB1;P33992	.;.;.;MCM5_HUMAN	Q	497;454	ENSP00000216122:E497Q;ENSP00000371441:E454Q	ENSP00000216122:E497Q	E	+	1	0	MCM5	34142706	1.000000	0.71417	0.990000	0.47175	0.954000	0.61252	3.776000	0.55356	1.403000	0.46800	0.650000	0.86243	GAG	.	.		0.567	MCM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320661.3			C	35812706	G	C	35812706	3	2	290	1	0	0	0	0	1	0	0	0	9399	1291	45	4	1531	4	MCM5	22	35812706	Missense_Mutation	SNP	G	TCGA-G3-A7M5-01A-11D-A33Q-10	6682238	35812706	15491860	169	42631										
PHEX	5251	hgsc.bcm.edu	37	chrX	22056646	22056646	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	actgcctgaagccagaatgcAtcgaagcgggtaagtcacag	12	10	1	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chrX:22056646A>C	ENST00000379374.4	+	2	743	c.178A>C	c.(178-180)Atc>Ctc	p.I60L	PHEX_ENST00000537599.1_Missense_Mutation_p.I60L|PHEX_ENST00000535894.1_5'UTR	NM_000444.4	NP_000435.3	P78562	PHEX_HUMAN	phosphate regulating endopeptidase homolog, X-linked	60					bone mineralization (GO:0030282)|cell-cell signaling (GO:0007267)|cellular protein modification process (GO:0006464)|organophosphate metabolic process (GO:0019637)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|cervix(2)|endometrium(2)|large_intestine(12)|liver(1)|lung(19)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	42						GCCAGAATGCATCGAAGCGGG	0.418																																					p.I60L		Atlas-SNP	.											.	PHEX	95	.	0			c.A178C						.						230	204	213					X																	22056646		2203	4300	6503	SO:0001583	missense	5251	exon2			GAATGCATCGAAG	U82970	CCDS14204.1	Xp22.2-p22.1	2008-07-31	2008-07-31		ENSG00000102174	ENSG00000102174			8918	protein-coding gene	gene with protein product		300550	"phosphate regulating gene with homologies to endopeptidases on the X chromosome (hypophosphatemia, vitamin D resistant rickets)"	HYP, HPDR		7550339, 9070861	Standard	NM_000444		Approved	PEX, HPDR1, HYP1, XLH	uc004dah.3	P78562	OTTHUMG00000021241	ENST00000379374.4:c.178A>C	chrX.hg19:g.22056646A>C	ENSP00000368682:p.Ile60Leu	39.0	0.0		38.0	28.0	NM_000444	O00678|Q13646|Q2M325|Q93032|Q99827	Missense_Mutation	SNP	ENST00000379374.4	hg19	CCDS14204.1	.	.	.	.	.	.	.	.	.	.	A	15.01	2.705829	0.48412	.	.	ENSG00000102174	ENST00000379374;ENST00000537599	D;D	0.82081	-1.57;-1.57	5.58	1.82	0.25136	.	0.306400	0.39909	N	0.001234	T	0.67608	0.2911	N	0.14661	0.345	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.57283	-0.7838	10	0.66056	D	0.02	.	9.0666	0.36467	0.7843:0.0:0.2157:0.0	.	60;60	F5GXU4;P78562	.;PHEX_HUMAN	L	60	ENSP00000368682:I60L;ENSP00000440362:I60L	ENSP00000368682:I60L	I	+	1	0	PHEX	21966567	1.000000	0.71417	0.640000	0.29408	0.987000	0.75469	2.298000	0.43602	-0.031000	0.13781	-0.335000	0.08231	ATC	.	.		0.418	PHEX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056035.1	NM_000444		C	22056646	A	C	22056646	3	2	290	1	0	0	0	0	1	0	0	0	11828	217	8	5	184	5	PHEX	23	22056646	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10		22056646	133213914	170	42632										
KLHL15	80311	hgsc.bcm.edu	37	chrX	24006693	24006693	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	agaaagtctcatctctggttCtgcctgctacggcgtaaata	9	10	3	1			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chrX:24006693C>A	ENST00000328046.8	-	4	1415	c.1160G>T	c.(1159-1161)aGa>aTa	p.R387I		NM_030624.2	NP_085127.2	Q96M94	KLH15_HUMAN	kelch-like family member 15	387					protein ubiquitination (GO:0016567)					autonomic_ganglia(1)|breast(1)|endometrium(8)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)	22						ATCTCTGGTTCTGCCTGCTAC	0.433																																					p.R387I		Atlas-SNP	.											.	KLHL15	50	.	0			c.G1160T						.						158	133	141					X																	24006693		2203	4300	6503	SO:0001583	missense	80311	exon4			CTGGTTCTGCCTG	AB051464	CCDS35217.1	Xp22.1-p21	2013-01-30	2013-01-30		ENSG00000174010	ENSG00000174010		"Kelch-like", "BTB/POZ domain containing"	29347	protein-coding gene	gene with protein product			"kelch-like 15 (Drosophila)"			11214970, 14702039	Standard	NM_030624		Approved	KIAA1677	uc004dba.4	Q96M94	OTTHUMG00000021261	ENST00000328046.8:c.1160G>T	chrX.hg19:g.24006693C>A	ENSP00000332791:p.Arg387Ile	97.0	0.0		102.0	91.0	NM_030624	Q32MN3|Q8NDA3|Q96BM6|Q9C0I6	Missense_Mutation	SNP	ENST00000328046.8	hg19	CCDS35217.1	.	.	.	.	.	.	.	.	.	.	C	15.87	2.961028	0.53400	.	.	ENSG00000174010	ENST00000328046	T	0.78481	-1.18	5.49	5.49	0.81192	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	D	0.83899	0.5354	L	0.42487	1.325	0.80722	D	1	D	0.71674	0.998	D	0.65874	0.939	D	0.84113	0.0402	10	0.49607	T	0.09	.	18.6167	0.91305	0.0:1.0:0.0:0.0	.	387	Q96M94	KLH15_HUMAN	I	387	ENSP00000332791:R387I	ENSP00000332791:R387I	R	-	2	0	KLHL15	23916614	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.294000	0.78760	2.426000	0.82243	0.506000	0.49869	AGA	.	.		0.433	KLHL15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056078.1	XM_040383		A	24006693	C	A	24006693	3	1	290	1	0	0	0	0	1	0	0	0	8380	913	32	3	658	3	KLHL15	23	24006693	Missense_Mutation	SNP	C	TCGA-G3-A7M5-01A-11D-A33Q-10	1950047	24006693	131263867	171	42633										
DCAF8L1	139425	hgsc.bcm.edu	37	chrX	27999289	27999289	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	gttcaggaaaccaccatcccTggtatcaccaccatctccgg	7	16	3	0			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chrX:27999289T>A	ENST00000441525.1	-	1	277	c.163A>T	c.(163-165)Agg>Tgg	p.R55W		NM_001017930.1	NP_001017930.1	A6NGE4	DC8L1_HUMAN	DDB1 and CUL4 associated factor 8-like 1	55										NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(24)|ovary(3)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	56						CCACCATCCCTGGTATCACCA	0.527																																					p.R55W		Atlas-SNP	.											.	DCAF8L1	121	.	0			c.A163T						.						135	99	111					X																	27999289		2202	4300	6502	SO:0001583	missense	139425	exon1			CATCCCTGGTATC		CCDS35222.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17	ENSG00000226372	ENSG00000226372		"WD repeat domain containing"	31810	protein-coding gene	gene with protein product			"WD repeat domain 42B"	WDR42B			Standard	NM_001017930		Approved		uc004dbx.1	A6NGE4	OTTHUMG00000021312	ENST00000441525.1:c.163A>T	chrX.hg19:g.27999289T>A	ENSP00000405222:p.Arg55Trp	93.0	0.0		108.0	91.0	NM_001017930	B3KXX1	Missense_Mutation	SNP	ENST00000441525.1	hg19	CCDS35222.1	.	.	.	.	.	.	.	.	.	.	T	10.30	1.312153	0.23821	.	.	ENSG00000226372	ENST00000441525	T	0.64618	-0.11	0.842	-1.08	0.09936	.	1.668810	0.04494	U	0.380061	T	0.55513	0.1925	L	0.50333	1.59	0.09310	N	1	D	0.59357	0.985	B	0.43754	0.43	T	0.50338	-0.8840	10	0.62326	D	0.03	.	4.4695	0.11704	0.0:0.0:0.3321:0.6679	.	55	A6NGE4	DC8L1_HUMAN	W	55	ENSP00000405222:R55W	ENSP00000405222:R55W	R	-	1	2	DCAF8L1	27909210	0.002000	0.14202	0.006000	0.13384	0.101000	0.19017	0.053000	0.14184	-0.346000	0.08312	0.235000	0.17854	AGG	.	.		0.527	DCAF8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056150.2	XM_066690		A	27999289	T	A	27999289	3	1	290	1	0	0	0	0	1	0	0	0	4279	1579	55	4	1643	4	DCAF8L1	23	27999289	Missense_Mutation	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	3992596	27999289	127271271	172	42634										
CCNB3	85417	hgsc.bcm.edu	37	chrX	50053768	50053768	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tggccttgcaggagaagcccAgcattgagcaggaggccctc	14	12	0	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chrX:50053768A>T	ENST00000376042.1	+	6	2897	c.2599A>T	c.(2599-2601)Agc>Tgc	p.S867C	CCNB3_ENST00000376038.1_Intron|CCNB3_ENST00000348603.2_Intron|CCNB3_ENST00000276014.7_Missense_Mutation_p.S867C			Q8WWL7	CCNB3_HUMAN	cyclin B3	867					meiotic nuclear division (GO:0007126)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)	nucleus (GO:0005634)				breast(3)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Ovarian(276;0.236)					GGAGAAGCCCAGCATTGAGCA	0.537																																					p.S867C		Atlas-SNP	.											.	CCNB3	367	.	0			c.A2599T						.						45	38	40					X																	50053768		2203	4300	6503	SO:0001583	missense	85417	exon5			AAGCCCAGCATTG	AJ314764	CCDS14331.1, CCDS14332.1	Xp11	2008-07-03			ENSG00000147082	ENSG00000147082			18709	protein-coding gene	gene with protein product		300456				11846420, 12185076	Standard	XM_006724610		Approved		uc004doy.3	Q8WWL7	OTTHUMG00000021519	ENST00000376042.1:c.2599A>T	chrX.hg19:g.50053768A>T	ENSP00000365210:p.Ser867Cys	84.0	0.0		111.0	94.0	NM_033031	B1AQI5|B1AQI6|Q96SB5|Q96SB6|Q96SB7|Q9NT38	Missense_Mutation	SNP	ENST00000376042.1	hg19	CCDS14331.1	.	.	.	.	.	.	.	.	.	.	A	14.68	2.606232	0.46527	.	.	ENSG00000147082	ENST00000376042;ENST00000276014	T;T	0.35973	1.28;1.28	4.07	0.0577	0.14324	.	60.879100	0.00166	N	0.000000	T	0.32556	0.0833	L	0.38175	1.15	0.09310	N	1	D	0.60160	0.987	P	0.48189	0.57	T	0.11324	-1.0592	9	.	.	.	.	0.7114	0.00925	0.467:0.2082:0.1198:0.205	.	867	Q8WWL7	CCNB3_HUMAN	C	867	ENSP00000365210:S867C;ENSP00000276014:S867C	.	S	+	1	0	CCNB3	50070508	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.136000	0.10405	-0.081000	0.12662	0.430000	0.28490	AGC	.	.		0.537	CCNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056558.1			T	50053768	A	T	50053768	3	4	290	1	0	0	0	0	1	0	0	0	2916	188	7	4	2613	4	CCNB3	23	50053768	Missense_Mutation	SNP	A	TCGA-G3-A7M5-01A-11D-A33Q-10	22054479	50053768	105216792	173	42635										
PHKA1	5255	hgsc.bcm.edu	37	chrX	71804110	71804110	+	Frame_Shift_Del	DEL	T	T	-													0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	gactcttacctctctagtggTagaggaaggaaggacaaacc							TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chrX:71804110delT	ENST00000373542.4	-	30	3445	c.3286delA	c.(3286-3288)accfs	p.T1097fs	PHKA1_ENST00000339490.3_Frame_Shift_Del_p.T1084fs|PHKA1_ENST00000541944.1_Frame_Shift_Del_p.T1025fs|PHKA1_ENST00000373539.3_Frame_Shift_Del_p.T1114fs|PHKA1_ENST00000373545.3_Frame_Shift_Del_p.T1055fs	NM_002637.3	NP_002628.2	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle)	1097					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(2)|lung(18)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	52	Renal(35;0.156)					TCTCTAGTGGTAGAGGAAGGA	0.393																																					p.T1096fs		Pindel	.											.	PHKA1	129	.	0			c.3287delC						.						118	94	103					X																	71804110		2203	4300	6503	SO:0001589	frameshift_variant	5255	exon30			.		CCDS14421.1, CCDS48137.1, CCDS55453.1	Xq12-q13	2009-07-10			ENSG00000067177	ENSG00000067177	2.7.11.19		8925	protein-coding gene	gene with protein product		311870		PHKA			Standard	NM_002637		Approved		uc004eax.4	P46020	OTTHUMG00000022696	ENST00000373542.4:c.3286delA	chrX.hg19:g.71804110delT	ENSP00000362643:p.Thr1097fs	267.0	0.0		313.0	115.0	NM_002637	B7ZL05|B7ZL07|Q2M3D7	Frame_Shift_Del	DEL	ENST00000373542.4	hg19	CCDS14421.1																																																																																			.	.		0.393	PHKA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058896.1			-	71804110	T	-	71804110	7	5	290	1	0	1	0	1	0	0	0	0	11852	1638	57	0	397	0	PHKA1	23	71804110	Frame_Shift_Del	DEL	T	TCGA-G3-A7M5-01A-11D-A33Q-10	21750342	71804110	83466450	174	42636										
GABRA3	2556	hgsc.bcm.edu	37	chrX	151336877	151336877	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	tcctgcacgtaggtggccttGggtgaagcaatgattgttgg	15	7	0	2			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chrX:151336877G>C	ENST00000370314.4	-	10	1540	c.1302C>G	c.(1300-1302)ccC>ccG	p.P434P	GABRA3_ENST00000535043.1_Silent_p.P434P|RP11-329E24.6_ENST00000453915.1_RNA	NM_000808.3	NP_000799.1	P34903	GBRA3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 3	434					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|skin(6)	37	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zolpidem(DB00425)|Zopiclone(DB01198)	AGGTGGCCTTGGGTGAAGCAA	0.532																																					p.P434P	NSCLC(142;2578 2613 10251 16743)	Atlas-SNP	.											.	GABRA3	97	.	0			c.C1302G						.						305	240	262					X																	151336877		2203	4300	6503	SO:0001819	synonymous_variant	2556	exon10			GGCCTTGGGTGAA		CCDS14706.1	Xq28	2012-06-22			ENSG00000011677	ENSG00000011677		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4077	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 3"	305660					Standard	NM_000808		Approved		uc010ntk.1	P34903	OTTHUMG00000024183	ENST00000370314.4:c.1302C>G	chrX.hg19:g.151336877G>C		127.0	0.0		273.0	71.0	NM_000808	Q8TAF9	Silent	SNP	ENST00000370314.4	hg19	CCDS14706.1																																																																																			.	.		0.532	GABRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060921.1	NM_000808		C	151336877	G	C	151336877	2	2	290	1	0	0	0	0	0	0	0	1	6170	1335	47	4		4	GABRA3	23	151336877	Silent	SNP	G	TCGA-G3-A7M5-01A-11D-A33Q-10	79532767	151336877	3933683	175	42637										
MECP2	4204	hgsc.bcm.edu	37	chrX	153295883	153295883	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0402298850574713	7	1	1.16897089397089	1.54150007996162	0.98960498960499	1	1	0	ctctctgtttggccttggcaTggaggatgaaacaatgtctt	11	8	2	1	rs267608630		TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chrX:153295883T>A	ENST00000303391.6	-	4	1645	c.1396A>T	c.(1396-1398)Atg>Ttg	p.M466L	MECP2_ENST00000460227.1_5'Flank|MECP2_ENST00000453960.2_Missense_Mutation_p.M478L	NM_004992.3	NP_004983.1	P51608	MECP2_HUMAN	methyl CpG binding protein 2	466				M -> V (in Ref. 7; CAD97991). {ECO:0000305}.	adult locomotory behavior (GO:0008344)|behavioral fear response (GO:0001662)|cardiolipin metabolic process (GO:0032048)|catecholamine secretion (GO:0050432)|cerebellum development (GO:0021549)|chromatin silencing (GO:0006342)|dendrite development (GO:0016358)|glucocorticoid metabolic process (GO:0008211)|glutamine metabolic process (GO:0006541)|histone acetylation (GO:0016573)|histone methylation (GO:0016571)|inositol metabolic process (GO:0006020)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|negative regulation of histone acetylation (GO:0035067)|negative regulation of histone methylation (GO:0031061)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurological system process involved in regulation of systemic arterial blood pressure (GO:0001976)|neuron maturation (GO:0042551)|pathogenesis (GO:0009405)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of cell proliferation (GO:0008284)|positive regulation of synapse assembly (GO:0051965)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|proprioception (GO:0019230)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|sensory perception of pain (GO:0019233)|social behavior (GO:0035176)|startle response (GO:0001964)|synapse assembly (GO:0007416)|transcription, DNA-templated (GO:0006351)|ventricular system development (GO:0021591)|visual learning (GO:0008542)	cytosol (GO:0005829)|extracellular space (GO:0005615)|heterochromatin (GO:0000792)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|double-stranded methylated DNA binding (GO:0010385)|methyl-CpG binding (GO:0008327)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|protein N-terminus binding (GO:0047485)|sequence-specific DNA binding transcription factor activity (GO:0003700)|siRNA binding (GO:0035197)|transcription corepressor activity (GO:0003714)			breast(2)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(8)|prostate(2)|urinary_tract(1)	23	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GGCCTTGGCATGGAGGATGAA	0.582																																					p.M478L		Atlas-SNP	.											.	MECP2	41	.	0			c.A1432T						.						253	219	230					X																	153295883		2203	4300	6503	SO:0001583	missense	4204	exon3			TTGGCATGGAGGA	AF158180	CCDS14741.1, CCDS48193.1	Xq28	2014-09-17	2014-06-18		ENSG00000169057	ENSG00000169057			6990	protein-coding gene	gene with protein product		300005	"mental retardation, X-linked 16", "mental retardation, X-linked 79", "Rett syndrome", "methyl CpG binding protein 2 (Rett syndrome)"	RTT, MRX16, MRX79		1606614, 10508514	Standard	NM_004992		Approved		uc004fjw.2	P51608	OTTHUMG00000024229	ENST00000303391.6:c.1396A>T	chrX.hg19:g.153295883T>A	ENSP00000301948:p.Met466Leu	48.0	0.0		116.0	52.0	NM_001110792	O15233|Q6QHH9|Q7Z384	Missense_Mutation	SNP	ENST00000303391.6	hg19	CCDS14741.1	.	.	.	.	.	.	.	.	.	.	T	12.35	1.911461	0.33721	.	.	ENSG00000169057	ENST00000303391;ENST00000453960	D;D	0.88354	-2.37;-2.36	5.67	4.48	0.54585	.	0.160656	0.56097	N	0.000025	T	0.77253	0.4103	N	0.19112	0.55	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.65442	-0.6167	10	0.23302	T	0.38	-12.9611	5.0745	0.14625	0.0:0.0937:0.1833:0.7231	.	478;466	P51608-2;P51608	.;MECP2_HUMAN	L	466;478	ENSP00000301948:M466L;ENSP00000395535:M478L	ENSP00000301948:M466L	M	-	1	0	MECP2	152949077	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.156000	0.31712	0.737000	0.32582	0.417000	0.27973	ATG	.	.		0.582	MECP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061144.1	NM_004992		A	153295883	T	A	153295883	3	1	290	1	0	0	0	0	1	0	0	0	9432	1464	51	4	68	4	MECP2	23	153295883	Missense_Mutation	SNP	T	TCGA-G3-A7M5-01A-11D-A33Q-10	1959006	153295883	1974677	176	42638										
EPHA8	2046	hgsc.bcm.edu	37	chr1	22915685	22915685	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	ggccgctgtggtcaacatcaCcacgaaccaggcaggtaggc	13	13	2	0			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr1:22915685C>T	ENST00000166244.3	+	5	1373	c.1301C>T	c.(1300-1302)aCc>aTc	p.T434I	EPHA8_ENST00000374644.4_Missense_Mutation_p.T434I|EPHA8_ENST00000538803.1_Missense_Mutation_p.T434I	NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8	434	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GTCAACATCACCACGAACCAG	0.657																																					p.T434I		Atlas-SNP	.											.	EPHA8	221	.	0			c.C1301T						.						36	35	35					1																	22915685		2203	4300	6503	SO:0001583	missense	2046	exon5			ACATCACCACGAA	BC038796	CCDS225.1, CCDS30626.1	1p36.12	2013-02-11	2004-10-28		ENSG00000070886	ENSG00000070886	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3391	protein-coding gene	gene with protein product		176945	"EphA8"	EEK		1648701	Standard	NM_001006943		Approved	Hek3	uc001bfx.1	P29322	OTTHUMG00000002892	ENST00000166244.3:c.1301C>T	chr1.hg19:g.22915685C>T	ENSP00000166244:p.Thr434Ile	104.0	0.0		99.0	28.0	NM_020526	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Missense_Mutation	SNP	ENST00000166244.3	hg19	CCDS225.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.636454	0.87760	.	.	ENSG00000070886	ENST00000166244;ENST00000374644;ENST00000538803	T;T;T	0.55930	0.49;4.89;4.89	4.52	4.52	0.55395	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.75831	0.3903	M	0.86502	2.82	0.80722	D	1	B;D	0.89917	0.28;1.0	B;D	0.78314	0.044;0.991	T	0.81163	-0.1058	10	0.87932	D	0	.	16.3069	0.82852	0.0:1.0:0.0:0.0	.	434;434	P29322;P29322-2	EPHA8_HUMAN;.	I	434	ENSP00000166244:T434I;ENSP00000363775:T434I;ENSP00000440274:T434I	ENSP00000166244:T434I	T	+	2	0	EPHA8	22788272	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	5.756000	0.68757	2.498000	0.84270	0.436000	0.28706	ACC	.	.		0.657	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526		T	22915685	C	T	22915685	3	4	291	1	0	0	0	0	1	0	0	0	5175	507	18	3	1319	3	EPHA8	1	22915685	Missense_Mutation	SNP	C	TCGA-G3-A7M6-01A-11D-A33Q-10		22915685	226334936	1	42639										
C1QC	714	hgsc.bcm.edu	37	chr1	22970634	22970634	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	acgggatcccagggatgcccGgcctgcccggggcaccaggg	17	15	0	0			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr1:22970634G>A	ENST00000374639.3	+	2	236	c.118G>A	c.(118-120)Ggc>Agc	p.G40S	C1QC_ENST00000374637.1_Missense_Mutation_p.G40S|C1QC_ENST00000374640.4_Missense_Mutation_p.G40S	NM_001114101.1	NP_001107573.1	P02747	C1QC_HUMAN	complement component 1, q subcomponent, C chain	40	Collagen-like.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|immune response (GO:0006955)|innate immune response (GO:0045087)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of macrophage differentiation (GO:0045650)	blood microparticle (GO:0072562)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	15		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;6.21e-27)|Colorectal(126;1.5e-07)|COAD - Colon adenocarcinoma(152;1.12e-05)|GBM - Glioblastoma multiforme(114;1.61e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000538)|KIRC - Kidney renal clear cell carcinoma(1967;0.00269)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.196)	Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	AGGGATGCCCGGCCTGCCCGG	0.692																																					p.G40S	Ovarian(26;671 750 8290 29071 43278)	Atlas-SNP	.											.	C1QC	35	.	0			c.G118A						.						15	17	16					1																	22970634		2193	4278	6471	SO:0001583	missense	714	exon2			ATGCCCGGCCTGC	AK057792	CCDS227.1	1p36.11	2014-09-17	2006-02-09	2006-02-09	ENSG00000159189	ENSG00000159189		"Complement system"	1245	protein-coding gene	gene with protein product		120575	"complement component 1, q subcomponent, gamma polypeptide"	C1QG		1706597	Standard	NM_001114101		Approved		uc001bga.4	P02747	OTTHUMG00000002891	ENST00000374639.3:c.118G>A	chr1.hg19:g.22970634G>A	ENSP00000363770:p.Gly40Ser	115.0	0.0		99.0	37.0	NM_001114101	Q7Z502|Q96DL2|Q96H05	Missense_Mutation	SNP	ENST00000374639.3	hg19	CCDS227.1	.	.	.	.	.	.	.	.	.	.	G	35	5.572044	0.96553	.	.	ENSG00000159189	ENST00000374640;ENST00000374639;ENST00000374637	D;D;D	0.99607	-6.27;-6.27;-6.27	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	D	0.99725	0.9893	M	0.94101	3.495	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97524	1.0075	10	0.59425	D	0.04	.	17.4377	0.87557	0.0:0.0:1.0:0.0	.	40	P02747	C1QC_HUMAN	S	40	ENSP00000363771:G40S;ENSP00000363770:G40S;ENSP00000363768:G40S	ENSP00000363768:G40S	G	+	1	0	C1QC	22843221	1.000000	0.71417	0.980000	0.43619	0.991000	0.79684	8.000000	0.88501	2.460000	0.83146	0.561000	0.74099	GGC	.	.		0.692	C1QC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008083.1	NM_172369		A	22970634	G	A	22970634	3	1	291	1	0	0	0	0	1	0	0	0	1959	1116	39	1	120	1	C1QC	1	22970634	Missense_Mutation	SNP	G	TCGA-G3-A7M6-01A-11D-A33Q-10	54949	22970634	226279987	2	42640										
CSMD2	114784	hgsc.bcm.edu	37	chr1	34258042	34258042	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	acatgtagagaactgtcttcTggtccccatcctgaccacca	7	14	2	2			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr1:34258042T>C	ENST00000338325.1	-	5	768	c.356A>G	c.(355-357)cAg>cGg	p.Q119R	CSMD2_ENST00000373381.4_Missense_Mutation_p.Q511R			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	471	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				AACTGTCTTCTGGTCCCCATC	0.567																																					p.Q471R		Atlas-SNP	.											.	CSMD2	946	.	0			c.A1412G						.						209	167	181					1																	34258042		2203	4300	6503	SO:0001583	missense	114784	exon11			GTCTTCTGGTCCC	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000338325.1:c.356A>G	chr1.hg19:g.34258042T>C	ENSP00000340311:p.Gln119Arg	151.0	0.0		113.0	38.0	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000338325.1	hg19		.	.	.	.	.	.	.	.	.	.	T	12.47	1.948465	0.34377	.	.	ENSG00000121904	ENST00000373381;ENST00000338325	T;T	0.23950	1.88;3.75	5.2	5.2	0.72013	CUB (5);	0.000000	0.85682	D	0.000000	T	0.29093	0.0723	N	0.21324	0.655	0.80722	D	1	P;P	0.51653	0.947;0.888	P;P	0.57846	0.828;0.762	T	0.03433	-1.1037	10	0.16896	T	0.51	.	13.0709	0.59061	0.0:0.0:0.0:1.0	.	471;511	Q7Z408;E7EUA6	CSMD2_HUMAN;.	R	511;119	ENSP00000362479:Q511R;ENSP00000340311:Q119R	ENSP00000241312:Q471R	Q	-	2	0	CSMD2	34030629	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.676000	0.61627	1.995000	0.58328	0.378000	0.23410	CAG	.	.		0.567	CSMD2-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000036404.2	NM_052896		C	34258042	T	C	34258042	3	2	291	1	0	0	0	0	1	0	0	0	3947	1580	55	2	9287	2	CSMD2	1	34258042	Missense_Mutation	SNP	T	TCGA-G3-A7M6-01A-11D-A33Q-10	11287408	34258042	214992579	3	42641										
COL8A2	1296	hgsc.bcm.edu	37	chr1	36564429	36564429	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	tggtcctggcaaccctgctgCccctgggactcccacaccgt	10	18	0	0			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr1:36564429C>T	ENST00000397799.1	-	4	1077	c.853G>A	c.(853-855)Gca>Aca	p.A285T	COL8A2_ENST00000481785.1_Missense_Mutation_p.A220T|COL8A2_ENST00000303143.4_Missense_Mutation_p.A285T			P25067	CO8A2_HUMAN	collagen, type VIII, alpha 2	285	Triple-helical region.				angiogenesis (GO:0001525)|camera-type eye morphogenesis (GO:0048593)|collagen catabolic process (GO:0030574)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			NS(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				AACCCTGCTGCCCCTGGGACT	0.697																																					p.A285T		Atlas-SNP	.											.	COL8A2	41	.	0			c.G853A						.						15	18	17					1																	36564429		2186	4280	6466	SO:0001583	missense	1296	exon2			CTGCTGCCCCTGG	M60832	CCDS403.1, CCDS72756.1	1p34.2-p32.3	2014-02-14			ENSG00000171812	ENSG00000171812		"Collagens"	2216	protein-coding gene	gene with protein product		120252		FECD		11689488	Standard	XM_005270477		Approved	PPCD, FECD1, PPCD2	uc001bzv.2	P25067	OTTHUMG00000007665	ENST00000397799.1:c.853G>A	chr1.hg19:g.36564429C>T	ENSP00000380901:p.Ala285Thr	61.0	0.0		57.0	17.0	NM_005202	Q5JV31|Q8TEJ5	Missense_Mutation	SNP	ENST00000397799.1	hg19	CCDS403.1	.	.	.	.	.	.	.	.	.	.	C	5.834	0.338113	0.11013	.	.	ENSG00000171812	ENST00000303143;ENST00000397799;ENST00000481785	D;D;D	0.97505	-4.41;-4.41;-4.41	3.7	1.66	0.24008	.	0.691089	0.14127	N	0.339654	D	0.92987	0.7768	L	0.33753	1.03	0.32016	N	0.601443	B	0.16396	0.017	B	0.20184	0.028	D	0.86474	0.1787	10	0.15499	T	0.54	.	11.3827	0.49768	0.5109:0.4891:0.0:0.0	.	285	P25067	CO8A2_HUMAN	T	285;285;220	ENSP00000305913:A285T;ENSP00000380901:A285T;ENSP00000436433:A220T	ENSP00000305913:A285T	A	-	1	0	COL8A2	36337016	0.000000	0.05858	0.998000	0.56505	0.917000	0.54804	-0.100000	0.10990	0.172000	0.19760	0.205000	0.17691	GCA	.	.		0.697	COL8A2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313674.1	NM_005202		T	36564429	C	T	36564429	3	4	291	1	0	0	0	0	1	0	0	0	3708	739	26	3	1262	3	COL8A2	1	36564429	Missense_Mutation	SNP	C	TCGA-G3-A7M6-01A-11D-A33Q-10	2306387	36564429	212686192	4	42642										
PRPF38B	55119	hgsc.bcm.edu	37	chr1	109241956	109241956	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	agaaagaacggcgaagatccCgaagtattgaccgggggtta	14	7	0	4			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr1:109241956C>G	ENST00000370025.4	+	6	1224	c.955C>G	c.(955-957)Cga>Gga	p.R319G	PRPF38B_ENST00000370021.1_Missense_Mutation_p.R208G	NM_018061.2	NP_060531.2	Q5VTL8	PR38B_HUMAN	pre-mRNA processing factor 38B	319	Arg-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			NS(1)|kidney(3)|large_intestine(5)|lung(8)|prostate(1)|skin(1)	19		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0149)|Lung(183;0.0888)|COAD - Colon adenocarcinoma(174;0.113)|Epithelial(280;0.161)		GCGAAGATCCCGAAGTATTGA	0.502																																					p.R319G		Atlas-SNP	.											.	PRPF38B	55	.	0			c.C955G						.						89	89	89					1																	109241956		2203	4300	6503	SO:0001583	missense	55119	exon6			AGATCCCGAAGTA	AL833950	CCDS788.1	1p13.3	2013-10-03	2013-10-03		ENSG00000134186	ENSG00000134186			25512	protein-coding gene	gene with protein product			"PRP38 pre-mRNA processing factor 38 (yeast) domain containing B"				Standard	NM_018061		Approved	FLJ10330, NET1	uc001dvv.4	Q5VTL8	OTTHUMG00000010991	ENST00000370025.4:c.955C>G	chr1.hg19:g.109241956C>G	ENSP00000359042:p.Arg319Gly	159.0	0.0		238.0	49.0	NM_018061	Q05DD6|Q32Q58|Q5VTL9|Q6PK39|Q7Z6E2|Q86WF3|Q8IWG9|Q9NW40	Missense_Mutation	SNP	ENST00000370025.4	hg19	CCDS788.1	.	.	.	.	.	.	.	.	.	.	C	5.593	0.294227	0.10567	.	.	ENSG00000134186	ENST00000370025;ENST00000370021	T;T	0.13778	2.56;2.56	5.69	4.75	0.60458	.	0.000000	0.85682	D	0.000000	T	0.15609	0.0376	L	0.34521	1.04	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	T	0.02352	-1.1172	10	0.44086	T	0.13	.	13.4404	0.61109	0.3161:0.6839:0.0:0.0	.	319	Q5VTL8	PR38B_HUMAN	G	319;208	ENSP00000359042:R319G;ENSP00000359038:R208G	ENSP00000359038:R208G	R	+	1	2	PRPF38B	109043479	0.999000	0.42202	1.000000	0.80357	0.151000	0.21798	3.189000	0.50965	1.326000	0.45319	0.591000	0.81541	CGA	.	.		0.502	PRPF38B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030231.1	NM_018061		G	109241956	C	G	109241956	3	3	291	1	0	0	0	0	1	0	0	0	12580	644	23	4	977	4	PRPF38B	1	109241956	Missense_Mutation	SNP	C	TCGA-G3-A7M6-01A-11D-A33Q-10	72677527	109241956	140008665	5	42643										
OR10X1	128367	hgsc.bcm.edu	37	chr1	158549068	158549068	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	aatgaattctgtgtggttacTgtctatacaagacagcctaa	8	7	2	2			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr1:158549068T>C	ENST00000368150.1	-	1	621	c.622A>G	c.(622-624)Agt>Ggt	p.S208G		NM_001004477.1	NP_001004477.1	Q8NGY0	O10X1_HUMAN	olfactory receptor, family 10, subfamily X, member 1 (gene/pseudogene)	208						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(2)|large_intestine(6)|lung(22)|ovary(2)|skin(2)|urinary_tract(1)	37	all_hematologic(112;0.0378)					GTGTGGTTACTGTCTATACAA	0.428																																					p.S208G		Atlas-SNP	.											.	OR10X1	96	.	0			c.A622G						.						91	91	91					1																	158549068		2203	4300	6503	SO:0001583	missense	128367	exon1			GGTTACTGTCTAT	BK004194	CCDS30900.1	1q23.1	2013-10-10	2013-10-10	2004-03-10	ENSG00000186400	ENSG00000186400		"GPCR / Class A : Olfactory receptors"	14995	protein-coding gene	gene with protein product			"olfactory receptor, family 10, subfamily X, member 1"	OR10X1P			Standard	NM_001004477		Approved		uc010pin.2	Q8NGY0	OTTHUMG00000019635	ENST00000368150.1:c.622A>G	chr1.hg19:g.158549068T>C	ENSP00000357132:p.Ser208Gly	161.0	0.0		273.0	57.0	NM_001004477	Q6IFR8	Missense_Mutation	SNP	ENST00000368150.1	hg19	CCDS30900.1	.	.	.	.	.	.	.	.	.	.	T	4.296	0.054209	0.08291	.	.	ENSG00000186400	ENST00000368150	T	0.00188	8.59	4.8	3.6	0.41247	GPCR, rhodopsin-like superfamily (1);	0.106927	0.42294	D	0.000733	T	0.00073	0.0002	L	0.29908	0.895	0.09310	N	1	B	0.16166	0.016	B	0.17098	0.017	T	0.32268	-0.9913	10	0.87932	D	0	.	10.8539	0.46786	0.0:0.0:0.1574:0.8425	.	208	Q8NGY0	O10X1_HUMAN	G	208	ENSP00000357132:S208G	ENSP00000357132:S208G	S	-	1	0	OR10X1	156815692	0.024000	0.19004	0.750000	0.31169	0.015000	0.08874	1.212000	0.32394	1.998000	0.58463	0.455000	0.32223	AGT	.	.		0.428	OR10X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051850.2	NM_001004477		C	158549068	T	C	158549068	3	2	291	1	0	0	0	0	1	0	0	0	10931	1580	55	2	353	2	OR10X1	1	158549068	Missense_Mutation	SNP	T	TCGA-G3-A7M6-01A-11D-A33Q-10	49307112	158549068	90701553	6	42644										
XCL2	6846	hgsc.bcm.edu	37	chr1	168510343	168510343	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	tcagcacagacttttaggccAcgtttggtaataaaactgta	8	8	1	1			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr1:168510343A>G	ENST00000367819.2	-	3	224	c.192T>C	c.(190-192)cgT>cgC	p.R64R		NM_003175.3	NP_003166.1	Q9UBD3	XCL2_HUMAN	chemokine (C motif) ligand 2	64					blood circulation (GO:0008015)|cell chemotaxis (GO:0060326)|immune response (GO:0006955)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)			large_intestine(1)|lung(6)|ovary(1)	8	all_hematologic(923;0.215)					CTTTTAGGCCACGTTTGGTAA	0.473																																					p.R64R		Atlas-SNP	.											.	XCL2	18	.	0			c.T192C						.						165	143	150					1																	168510343		2203	4300	6503	SO:0001819	synonymous_variant	6846	exon3			TAGGCCACGTTTG	BC070309	CCDS1273.1	1q24.2	2013-02-28	2002-08-22	2002-08-23	ENSG00000143185	ENSG00000143185		"Endogenous ligands"	10646	protein-coding gene	gene with protein product		604828	"small inducible cytokine subfamily C, member 2"	SCYC2		7875320	Standard	NM_003175		Approved	SCM-1b	uc001gfn.4	Q9UBD3	OTTHUMG00000034549	ENST00000367819.2:c.192T>C	chr1.hg19:g.168510343A>G		107.0	0.0		169.0	22.0	NM_003175		Silent	SNP	ENST00000367819.2	hg19	CCDS1273.1																																																																																			.	.		0.473	XCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083613.1	NM_003175		G	168510343	A	G	168510343	2	3	291	1	0	0	0	0	0	0	0	1	17439	146	6	2		2	XCL2	1	168510343	Silent	SNP	A	TCGA-G3-A7M6-01A-11D-A33Q-10	9961275	168510343	80740278	7	42645										
GLUL	2752	hgsc.bcm.edu	37	chr1	182353689	182353689	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	ctggccaacagtccggggaaTgcgtatgctggcgctacgat	14	11	0	0			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr1:182353689T>C	ENST00000331872.6	-	7	1513	c.973A>G	c.(973-975)Att>Gtt	p.I325V	GLUL_ENST00000491322.1_5'UTR|GLUL_ENST00000417584.2_Missense_Mutation_p.I325V|GLUL_ENST00000339526.4_Missense_Mutation_p.I325V|GLUL_ENST00000311223.5_Missense_Mutation_p.I325V	NM_001033044.2	NP_001028216.1	P15104	GLNA_HUMAN	glutamate-ammonia ligase	325					cell proliferation (GO:0008283)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to starvation (GO:0009267)|glutamate catabolic process (GO:0006538)|glutamine biosynthetic process (GO:0006542)|neurotransmitter uptake (GO:0001504)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of insulin secretion (GO:0032024)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein homooligomerization (GO:0051260)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon terminus (GO:0043679)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glial cell projection (GO:0097386)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perikaryon (GO:0043204)|protein complex (GO:0043234)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|glutamate-ammonia ligase activity (GO:0004356)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)			endometrium(2)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(1)	16					Ceftriaxone(DB01212)|Diazoxide(DB01119)|L-Glutamine(DB00130)|L-Methionine(DB00134)|Pegvisomant(DB00082)	GTCCGGGGAATGCGTATGCTG	0.557																																					p.I325V		Atlas-SNP	.											.	GLUL	38	.	0			c.A973G						.						100	91	94					1																	182353689		2203	4300	6503	SO:0001583	missense	2752	exon7			GGGGAATGCGTAT	AL161952	CCDS1344.1	1q31	2010-05-04	2010-05-04		ENSG00000135821	ENSG00000135821	6.3.1.2		4341	protein-coding gene	gene with protein product	"glutamine synthetase"	138290	"glutamate-ammonia ligase (glutamine synthase)"	GLNS		1681907, 2888076	Standard	NM_002065		Approved		uc001gpa.2	P15104	OTTHUMG00000037407	ENST00000331872.6:c.973A>G	chr1.hg19:g.182353689T>C	ENSP00000356537:p.Ile325Val	83.0	0.0		95.0	41.0	NM_001033056	Q499Y9|Q5T9Z1|Q7Z3W4|Q8IZ17	Missense_Mutation	SNP	ENST00000331872.6	hg19	CCDS1344.1	.	.	.	.	.	.	.	.	.	.	T	17.38	3.374949	0.61735	.	.	ENSG00000135821	ENST00000331872;ENST00000311223;ENST00000417584;ENST00000339526	D;D;D;D	0.86769	-2.17;-2.17;-2.17;-2.17	5.34	5.34	0.76211	Glutamine synthetase, catalytic domain (1);Glutamine synthetase/guanido kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.85239	0.5651	L	0.58583	1.82	0.80722	D	1	B	0.30406	0.278	B	0.36186	0.219	T	0.81236	-0.1024	10	0.15499	T	0.54	-20.0742	14.1051	0.65083	0.0:0.0:0.0:1.0	.	325	P15104	GLNA_HUMAN	V	325	ENSP00000356537:I325V;ENSP00000307900:I325V;ENSP00000398320:I325V;ENSP00000344958:I325V	ENSP00000307900:I325V	I	-	1	0	GLUL	180620312	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.516000	0.81772	2.011000	0.59026	0.460000	0.39030	ATT	.	.		0.557	GLUL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091043.1	NM_002065		C	182353689	T	C	182353689	3	2	291	1	0	0	0	0	1	0	0	0	6486	1464	51	2	152	2	GLUL	1	182353689	Missense_Mutation	SNP	T	TCGA-G3-A7M6-01A-11D-A33Q-10	13843346	182353689	66896932	8	42646										
PLXNA2	5362	hgsc.bcm.edu	37	chr1	208219318	208219318	+	Frame_Shift_Del	DEL	C	C	-													0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	gtagtagataaacttggtgtCgttgtaaattagcaaggatt							TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr1:208219318delC	ENST00000367033.3	-	18	4157	c.3400delG	c.(3400-3402)gacfs	p.D1134fs		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	1134	IPT/TIG 3.				axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		AACTTGGTGTCGTTGTAAATT	0.493																																					p.D1134fs		Atlas-Indel,Pindel	.											.	PLXNA2	178	.	0			c.3401delA						.						181	173	175					1																	208219318		2203	4300	6503	SO:0001589	frameshift_variant	5362	exon18			.	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"Plexins"	9100	protein-coding gene	gene with protein product	"plexin 2", "plexin-A2", "semaphorin receptor OCT", "transmembrane protein OCT"	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.3400delG	chr1.hg19:g.208219318delC	ENSP00000356000:p.Asp1134fs	196.0	0.0		168.0	132.0	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Frame_Shift_Del	DEL	ENST00000367033.3	hg19	CCDS31013.1																																																																																			.	.		0.493	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179		-	208219318	C	-	208219318	7	5	291	1	0	1	0	1	0	0	0	0	12129	884	31	0	2344	0	PLXNA2	1	208219318	Frame_Shift_Del	DEL	C	TCGA-G3-A7M6-01A-11D-A33Q-10	25865629	208219318	41031303	9	42647										
MIA3	375056	hgsc.bcm.edu	37	chr1	222802341	222802341	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	caccctaacgcatccagagaCagtgtggagggagacgcttt	12	11	0	2			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr1:222802341C>G	ENST00000344922.5	+	4	1804	c.1779C>G	c.(1777-1779)gaC>gaG	p.D593E	MIA3_ENST00000344441.6_Missense_Mutation_p.D593E|MIA3_ENST00000470521.1_3'UTR|MIA3_ENST00000344507.1_Intron	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	593					chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|exocytosis (GO:0006887)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|positive regulation of bone mineralization (GO:0030501)|positive regulation of leukocyte migration (GO:0002687)|protein transport (GO:0015031)|wound healing (GO:0042060)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(5)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(15)|lung(37)|ovary(5)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|urinary_tract(1)	80				GBM - Glioblastoma multiforme(131;0.0199)		CATCCAGAGACAGTGTGGAGG	0.473																																					p.D593E		Atlas-SNP	.											.	MIA3	167	.	0			c.C1779G						.						76	80	78					1																	222802341		2042	4183	6225	SO:0001583	missense	375056	exon4			CAGAGACAGTGTG		CCDS41470.1, CCDS73035.1	1p36.33	2012-12-13		2006-07-25	ENSG00000154305	ENSG00000154305			24008	protein-coding gene	gene with protein product	"C219 reactive peptide", "transport and golgi organization"	613455				15183315	Standard	XM_005273121		Approved	UNQ6077, FLJ39207, KIAA0268, TANGO	uc001hnl.3	Q5JRA6	OTTHUMG00000037543	ENST00000344922.5:c.1779C>G	chr1.hg19:g.222802341C>G	ENSP00000340900:p.Asp593Glu	98.0	0.0		131.0	23.0	NM_198551	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Missense_Mutation	SNP	ENST00000344922.5	hg19	CCDS41470.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.86|14.86	2.660504|2.660504	0.47572|0.47572	.|.	.|.	ENSG00000154305|ENSG00000154305	ENST00000344922;ENST00000344441;ENST00000320831|ENST00000354906	T;T|.	0.05139|.	3.49;3.49|.	4.32|4.32	-7.94|-7.94	0.01152|0.01152	.|.	.|.	.|.	.|.	.|.	T|T	0.32315|0.32315	0.0825|0.0825	L|L	0.58101|0.58101	1.795|1.795	0.09310|0.09310	N|N	1|1	B;B|.	0.19200|.	0.002;0.034|.	B;B|.	0.16722|.	0.007;0.016|.	T|T	0.39921|0.39921	-0.9590|-0.9590	9|5	0.49607|.	T|.	0.09|.	.|.	1.3612|1.3612	0.02192|0.02192	0.1357:0.244:0.2721:0.3482|0.1357:0.244:0.2721:0.3482	.|.	593;593|.	Q5JRA6-2;Q5JRA6|.	.;MIA3_HUMAN|.	E|E	593|176	ENSP00000340900:D593E;ENSP00000340587:D593E|.	ENSP00000325973:D593E|.	D|Q	+|+	3|1	2|0	MIA3|MIA3	220868964|220868964	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.285000|0.285000	0.27093|0.27093	-0.418000|-0.418000	0.07080|0.07080	-1.026000|-1.026000	0.03330|0.03330	0.305000|0.305000	0.20034|0.20034	GAC|CAG	.	.		0.473	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551		G	222802341	C	G	222802341	3	3	291	1	0	0	0	0	1	0	0	0	9574	477	17	4	1793	4	MIA3	1	222802341	Missense_Mutation	SNP	C	TCGA-G3-A7M6-01A-11D-A33Q-10	14583023	222802341	26448280	10	42648										
ZNF678	339500	hgsc.bcm.edu	37	chr1	227843314	227843314	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	ttagtaagcataagagaattCatactgaagagaaaccctac	7	7	1	3			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr1:227843314C>A	ENST00000343776.5	+	4	1708	c.1363C>A	c.(1363-1365)Cat>Aat	p.H455N	ZNF678_ENST00000397097.3_Missense_Mutation_p.H510N|ZNF678_ENST00000608949.1_Intron	NM_178549.3	NP_848644.2	Q5SXM1	ZN678_HUMAN	zinc finger protein 678	455					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|pancreas(1)|prostate(1)	24		Prostate(94;0.0885)				TAAGAGAATTCATACTGAAGA	0.373																																					p.H510N		Atlas-SNP	.											.	ZNF678	137	.	0			c.C1528A						.						39	43	42					1																	227843314		2202	4296	6498	SO:0001583	missense	339500	exon4			AGAATTCATACTG	BC042500		1q42.13	2013-01-08			ENSG00000181450	ENSG00000181450		"Zinc fingers, C2H2-type", "-"	28652	protein-coding gene	gene with protein product	"hypothetical protein MGC42493"					12477932	Standard	NM_178549		Approved	MGC42493	uc021pjy.1	Q5SXM1	OTTHUMG00000037700	ENST00000343776.5:c.1363C>A	chr1.hg19:g.227843314C>A	ENSP00000344828:p.His455Asn	66.0	0.0		79.0	16.0	NM_178549	Q8IVQ9	Missense_Mutation	SNP	ENST00000343776.5	hg19		.	.	.	.	.	.	.	.	.	.	C	13.25	2.182006	0.38511	.	.	ENSG00000181450	ENST00000343776;ENST00000397097	T;T	0.67345	-0.26;-0.26	1.63	0.606	0.17559	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.80319	0.4601	M	0.87269	2.87	0.30291	N	0.790393	D	0.89917	1.0	D	0.91635	0.999	T	0.73145	-0.4075	9	0.87932	D	0	.	6.2562	0.20876	0.0:0.8068:0.0:0.1932	.	455	Q5SXM1	ZN678_HUMAN	N	455;510	ENSP00000344828:H455N;ENSP00000440403:H510N	ENSP00000344828:H455N	H	+	1	0	ZNF678	225909937	0.999000	0.42202	0.003000	0.11579	0.001000	0.01503	5.623000	0.67757	-0.034000	0.13713	-0.192000	0.12808	CAT	.	.		0.373	ZNF678-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000091976.2	NM_178549		A	227843314	C	A	227843314	3	1	291	1	0	0	0	0	1	0	0	0	18100	826	29	3	1542	3	ZNF678	1	227843314	Missense_Mutation	SNP	C	TCGA-G3-A7M6-01A-11D-A33Q-10	5040973	227843314	21407307	11	42649										
RYR2	6262	hgsc.bcm.edu	37	chr1	237875069	237875069	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	tcaaaagagaagagcagaacTtcgttgtacagaatgaaatc	9	6	1	5			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr1:237875069T>G	ENST00000366574.2	+	71	10572	c.10255T>G	c.(10255-10257)Ttc>Gtc	p.F3419V	RYR2_ENST00000360064.6_Missense_Mutation_p.F3417V|RYR2_ENST00000609119.1_3'UTR|RYR2_ENST00000542537.1_Missense_Mutation_p.F3403V	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	3419					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			AGAGCAGAACTTCGTTGTACA	0.333																																					p.F3419V		Atlas-SNP	.											.	RYR2	1273	.	0			c.T10255G						.						52	51	51					1																	237875069		1824	4069	5893	SO:0001583	missense	6262	exon71			CAGAACTTCGTTG	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.10255T>G	chr1.hg19:g.237875069T>G	ENSP00000355533:p.Phe3419Val	185.0	0.0		208.0	18.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.503513	0.85176	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537;ENST00000542288	D;D;D	0.98419	-4.92;-4.9;-4.92	4.97	4.97	0.65823	.	0.000000	0.64402	U	0.000012	D	0.98893	0.9625	M	0.84846	2.72	0.80722	D	1	D	0.76494	0.999	D	0.75020	0.985	D	0.99782	1.1028	10	0.87932	D	0	.	14.6613	0.68873	0.0:0.0:0.0:1.0	.	3419	Q92736	RYR2_HUMAN	V	3419;3417;3403;374	ENSP00000355533:F3419V;ENSP00000353174:F3417V;ENSP00000443798:F3403V	ENSP00000353174:F3417V	F	+	1	0	RYR2	235941692	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	8.040000	0.89188	1.880000	0.54463	0.482000	0.46254	TTC	.	.		0.333	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		G	237875069	T	G	237875069	3	3	291	1	0	0	0	0	1	0	0	0	13784	1609	56	5	10537	5	RYR2	1	237875069	Missense_Mutation	SNP	T	TCGA-G3-A7M6-01A-11D-A33Q-10	10031755	237875069	11375552	12	42650										
APOB	338	hgsc.bcm.edu	37	chr2	21252519	21252519	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	tgtggactttaccttgtcttTaggctccattttccgcagag	9	10	1	1			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr2:21252519T>C	ENST00000233242.1	-	12	1736	c.1609A>G	c.(1609-1611)Aaa>Gaa	p.K537E	APOB_ENST00000399256.4_Missense_Mutation_p.K537E	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	537	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.				artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ACCTTGTCTTTAGGCTCCATT	0.423																																					p.K537E		Atlas-SNP	.											.	APOB	761	.	0			c.A1609G						.						179	166	170					2																	21252519		2203	4300	6503	SO:0001583	missense	338	exon12			TGTCTTTAGGCTC	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.1609A>G	chr2.hg19:g.21252519T>C	ENSP00000233242:p.Lys537Glu	50.0	0.0		36.0	13.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	T	2.217	-0.379363	0.05000	.	.	ENSG00000084674	ENST00000233242;ENST00000535079;ENST00000399256	T;T	0.39406	1.08;1.08	5.28	1.63	0.23807	Lipid transport protein, N-terminal (3);Vitellinogen, superhelical (2);	1.061170	0.07360	N	0.883872	T	0.30823	0.0777	L	0.44542	1.39	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.30327	-0.9982	10	0.02654	T	1	.	8.9237	0.35628	0.0:0.212:0.0:0.788	.	537	P04114	APOB_HUMAN	E	537	ENSP00000233242:K537E;ENSP00000382200:K537E	ENSP00000233242:K537E	K	-	1	0	APOB	21106024	0.003000	0.15002	0.000000	0.03702	0.122000	0.20287	1.433000	0.34947	0.097000	0.17492	-0.411000	0.06167	AAA	.	.		0.423	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			C	21252519	T	C	21252519	3	2	291	1	0	0	0	0	1	0	0	0	785	1763	61	2	12154	2	APOB	2	21252519	Missense_Mutation	SNP	T	TCGA-G3-A7M6-01A-11D-A33Q-10		21252519	221946854	13	42651										
SLC30A6	55676	hgsc.bcm.edu	37	chr2	32396397	32396397	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	aaaccacaaagatcctttttTggcaagttgttacgggaatt	8	7	0	1			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr2:32396397T>A	ENST00000282587.5	+	2	82	c.45T>A	c.(43-45)ttT>ttA	p.F15L	SLC30A6_ENST00000357055.3_5'UTR|SLC30A6_ENST00000379343.2_Missense_Mutation_p.F15L|SLC30A6_ENST00000435660.1_Missense_Mutation_p.F15L|SLC30A6_ENST00000538303.1_Intron|SLC30A6_ENST00000406369.1_Intron	NM_017964.3	NP_060434.2	Q6NXT4	ZNT6_HUMAN	solute carrier family 30 (zinc transporter), member 6	15					cellular protein metabolic process (GO:0044267)|Golgi to endosome transport (GO:0006895)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(4)|lung(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					GATCCTTTTTTGGCAAGTTGT	0.333																																					p.F15L		Atlas-SNP	.											.	SLC30A6	37	.	0			c.T45A						.						107	106	106					2																	32396397		2203	4300	6503	SO:0001583	missense	55676	exon2			CTTTTTTGGCAAG	AK055663	CCDS1780.1, CCDS54341.1, CCDS54342.1, CCDS54343.1	2p22.3	2013-05-22			ENSG00000152683	ENSG00000152683		"Solute carriers"	19305	protein-coding gene	gene with protein product		611148					Standard	NM_017964		Approved	FLJ31101, ZNT6	uc002rof.2	Q6NXT4	OTTHUMG00000128456	ENST00000282587.5:c.45T>A	chr2.hg19:g.32396397T>A	ENSP00000282587:p.Phe15Leu	100.0	0.0		89.0	33.0	NM_001193513	A5YM45|B7Z901|Q8N5C9|Q96NC3	Missense_Mutation	SNP	ENST00000282587.5	hg19	CCDS1780.1	.	.	.	.	.	.	.	.	.	.	T	13.62	2.290116	0.40494	.	.	ENSG00000152683	ENST00000379343;ENST00000282587;ENST00000435660	T	0.75938	-0.98	5.32	5.32	0.75619	.	0.241870	0.42548	D	0.000690	T	0.50973	0.1647	N	0.08118	0	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.001;0.003;0.001	T	0.48636	-0.9018	10	0.11485	T	0.65	-13.8268	10.4496	0.44513	0.0:0.0:0.1634:0.8366	.	15;15;15	Q6NXT4-3;Q6NXT4-2;Q6NXT4	.;.;ZNT6_HUMAN	L	15	ENSP00000282587:F15L	ENSP00000282587:F15L	F	+	3	2	SLC30A6	32249901	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.392000	0.44433	2.009000	0.58944	0.459000	0.35465	TTT	.	.		0.333	SLC30A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250254.2			A	32396397	T	A	32396397	3	1	291	1	0	0	0	0	1	0	0	0	14574	1809	63	4	51	4	SLC30A6	2	32396397	Missense_Mutation	SNP	T	TCGA-G3-A7M6-01A-11D-A33Q-10	11143878	32396397	210802976	14	42652										
ANAPC1	64682	hgsc.bcm.edu	37	chr2	112550033	112550033	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	cgttttcatgtgtaagaagcGacaaagctgcaaaaccttta	8	8	1	1			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr2:112550033G>A	ENST00000341068.3	-	38	5390	c.4618C>T	c.(4618-4620)Cgc>Tgc	p.R1540C		NM_022662.3	NP_073153.1	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1	1540					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)				NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(7)|lung(16)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	49						TGTAAGAAGCGACAAAGCTGC	0.483																																					p.R1540C		Atlas-SNP	.											.	ANAPC1	116	.	0			c.C4618T						.						18	20	19					2																	112550033		2183	4261	6444	SO:0001583	missense	64682	exon38			AGAAGCGACAAAG	AJ278357	CCDS2093.1	2q12.1	2011-06-15			ENSG00000153107	ENSG00000153107		"Anaphase promoting complex subunits"	19988	protein-coding gene	gene with protein product		608473				11179667	Standard	NM_022662		Approved	MCPR, TSG24, APC1	uc002ssh.3	Q9H1A4	OTTHUMG00000131277	ENST00000341068.3:c.4618C>T	chr2.hg19:g.112550033G>A	ENSP00000339109:p.Arg1540Cys	521.0	1.0		389.0	125.0	NM_022662	Q2M3H8|Q9BSE6|Q9H8D0	Missense_Mutation	SNP	ENST00000341068.3	hg19	CCDS2093.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.2|25.2	4.610427|4.610427	0.87258|0.87258	.|.	.|.	ENSG00000153107|ENSG00000153107	ENST00000341068|ENST00000427997	.|.	.|.	.|.	4.57|4.57	4.57|4.57	0.56435|0.56435	.|.	0.000000|.	0.35870|.	U|.	0.002932|.	D|D	0.85044|0.85044	0.5607|0.5607	M|M	0.91196|0.91196	3.185|3.185	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.80764|.	0.994|.	D|D	0.88956|0.88956	0.3390|0.3390	9|5	0.87932|.	D|.	0|.	-11.7322|-11.7322	17.698|17.698	0.88286|0.88286	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1540|.	Q9H1A4|.	APC1_HUMAN|.	C|L	1540|1074	.|.	ENSP00000339109:R1540C|.	R|S	-|-	1|2	0|0	ANAPC1|ANAPC1	112266504|112266504	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	6.639000|6.639000	0.74314|0.74314	2.237000|2.237000	0.73441|0.73441	0.585000|0.585000	0.79938|0.79938	CGC|TCG	.	.		0.483	ANAPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254045.2	NM_022662		A	112550033	G	A	112550033	3	1	291	1	0	0	0	0	1	0	0	0	598	1058	37	1	1260	1	ANAPC1	2	112550033	Missense_Mutation	SNP	G	TCGA-G3-A7M6-01A-11D-A33Q-10	80153636	112550033	130649340	15	42653										
PSD4	23550	hgsc.bcm.edu	37	chr2	113949983	113949983	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	tctgaggacaccgatgaactCttcttggcttcctgggagcc	11	12	3	2			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr2:113949983C>T	ENST00000245796.6	+	6	1850	c.1655C>T	c.(1654-1656)tCt>tTt	p.S552F	PSD4_ENST00000441564.3_Missense_Mutation_p.S524F	NM_012455.2	NP_036587.2	Q8NDX1	PSD4_HUMAN	pleckstrin and Sec7 domain containing 4	552	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			cervix(1)|endometrium(2)|large_intestine(4)|lung(13)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CCGATGAACTCTTCTTGGCTT	0.547																																					p.S552F		Atlas-SNP	.											.	PSD4	74	.	0			c.C1655T						.						187	192	191					2																	113949983		2203	4300	6503	SO:0001583	missense	23550	exon6			TGAACTCTTCTTG	U63127	CCDS33276.1	2q13	2013-01-10			ENSG00000125637	ENSG00000125637		"Pleckstrin homology (PH) domain containing"	19096	protein-coding gene	gene with protein product		614442				12082148	Standard	XM_005263634		Approved	TIC, EFA6B	uc002tjc.3	Q8NDX1	OTTHUMG00000153339	ENST00000245796.6:c.1655C>T	chr2.hg19:g.113949983C>T	ENSP00000245796:p.Ser552Phe	62.0	0.0		45.0	11.0	NM_012455	A6NEG7|A8K1Y0|O95621|Q4ZG34|Q6GPH8|Q8IYP4	Missense_Mutation	SNP	ENST00000245796.6	hg19	CCDS33276.1	.	.	.	.	.	.	.	.	.	.	c	10.86	1.469554	0.26423	.	.	ENSG00000125637	ENST00000245796;ENST00000441564	T;T	0.11930	2.73;2.82	5.51	-0.711	0.11230	.	0.590962	0.15539	N	0.257041	T	0.04318	0.0119	N	0.02539	-0.55	0.18873	N	0.999989	B;B;B	0.11235	0.0;0.004;0.002	B;B;B	0.08055	0.001;0.003;0.001	T	0.45011	-0.9290	10	0.15066	T	0.55	.	9.063	0.36447	0.0:0.3329:0.0:0.6671	.	210;524;552	Q59HG0;Q8NDX1-2;Q8NDX1	.;.;PSD4_HUMAN	F	552;524	ENSP00000245796:S552F;ENSP00000413997:S524F	ENSP00000245796:S552F	S	+	2	0	PSD4	113666454	0.135000	0.22499	0.002000	0.10522	0.033000	0.12548	-0.159000	0.10056	-0.044000	0.13491	0.553000	0.69018	TCT	.	.		0.547	PSD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330789.1	NM_012455		T	113949983	C	T	113949983	3	4	291	1	0	0	0	0	1	0	0	0	12661	913	32	3	1673	3	PSD4	2	113949983	Missense_Mutation	SNP	C	TCGA-G3-A7M6-01A-11D-A33Q-10	1399950	113949983	129249390	16	42654										
TTN	7273	hgsc.bcm.edu	37	chr2	179615005	179615005	+	Intron	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	ctgggactttatgtgctttgAcatcatgtttttgttttgct	9	6	1	1			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr2:179615005A>T	ENST00000591111.1	-	45	10585				TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000360870.5_Missense_Mutation_p.V4041D|TTN_ENST00000460472.2_Intron|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000342992.6_Intron			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATGTGCTTTGACATCATGTTT	0.383																																					p.V4041D		Atlas-SNP	.											.	TTN	18412	.	0			c.T12122A						.						207	177	187					2																	179615005		2203	4300	6503	SO:0001627	intron_variant	7273	exon46			GCTTTGACATCAT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10360+2845T>A	chr2.hg19:g.179615005A>T		110.0	0.0		84.0	31.0	NM_133379	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	10.38	1.333636	0.24167	.	.	ENSG00000155657	ENST00000360870	T	0.58940	0.3	5.33	-1.9	0.07665	.	.	.	.	.	T	0.28466	0.0704	N	0.14661	0.345	0.09310	N	1	B	0.27416	0.178	B	0.24541	0.054	T	0.18209	-1.0344	9	0.12103	T	0.63	.	1.9774	0.03418	0.3999:0.1329:0.3378:0.1294	.	4041	Q8WZ42-6	.	D	4041	ENSP00000354117:V4041D	ENSP00000354117:V4041D	V	-	2	0	TTN	179323250	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.471000	0.22100	-0.137000	0.11455	0.533000	0.62120	GTC	.	.		0.383	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179615005	A	T	179615005	1	4	291	0	1	0	0	0	0	0	0	0	16750	275	10	4		4	TTN	2	179615005	Intron	SNP	A	TCGA-G3-A7M6-01A-11D-A33Q-10	65665022	179615005	63584368	17	42655										
CASP10	843	hgsc.bcm.edu	37	chr2	202082364	202082364	+	Intron	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	caacgatgatgtgagtcgaaGagtggacaaacagggaacaa	13	6	0	3			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr2:202082364G>C	ENST00000272879.5	+	9	1599				CASP10_ENST00000448480.1_Intron|CASP10_ENST00000286186.6_Missense_Mutation_p.R490T|CASP10_ENST00000360132.3_3'UTR|CASP10_ENST00000313728.7_Missense_Mutation_p.R423T|CASP10_ENST00000346817.5_Missense_Mutation_p.R447T|CASP10_ENST00000492363.1_3'UTR	NM_032974.4	NP_116756.2	Q92851	CASPA_HUMAN	caspase 10, apoptosis-related cysteine peptidase						apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|innate immune response (GO:0045087)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of apoptotic process (GO:0042981)	CD95 death-inducing signaling complex (GO:0031265)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097199)|death effector domain binding (GO:0035877)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	27						GTGAGTCGAAGAGTGGACAAA	0.418																																					p.R490T		Atlas-SNP	.											.	CASP10	95	.	0			c.G1469C						.						133	118	123					2																	202082364		2203	4300	6503	SO:0001627	intron_variant	843	exon10			GTCGAAGAGTGGA	U60519	CCDS2338.1, CCDS2339.1, CCDS2340.1, CCDS56159.1, CCDS56160.1	2q33-q34	2014-09-17	2005-08-17		ENSG00000003400	ENSG00000003400	3.4.22.63	"Caspases"	1500	protein-coding gene	gene with protein product		601762	"caspase 10, apoptosis-related cysteine protease"			8755496	Standard	NM_032974		Approved	MCH4	uc002uxj.1	Q92851	OTTHUMG00000132818	ENST00000272879.5:c.1415+8079G>C	chr2.hg19:g.202082364G>C		197.0	0.0		162.0	53.0	NM_032977	Q68HC0|Q6KF62|Q6KF63|Q8IUP5|Q8WYQ8|Q99845|Q9Y2U6|Q9Y2U7	Missense_Mutation	SNP	ENST00000272879.5	hg19	CCDS2338.1	.	.	.	.	.	.	.	.	.	.	G	13.41	2.227754	0.39399	.	.	ENSG00000003400	ENST00000286186;ENST00000346817;ENST00000313728	T;T;T	0.80393	-1.37;-1.37;-1.37	5.3	-5.3	0.02738	.	0.987548	0.08267	N	0.972144	T	0.78541	0.4299	.	.	.	0.09310	N	1	P;D;P	0.56035	0.551;0.974;0.835	B;P;P	0.56916	0.433;0.809;0.466	T	0.69658	-0.5086	9	0.25751	T	0.34	.	7.5148	0.27593	0.3348:0.0:0.4654:0.1998	.	423;447;490	Q92851-6;Q92851-2;Q92851-4	.;.;.	T	490;447;423	ENSP00000286186:R490T;ENSP00000237865:R447T;ENSP00000314599:R423T	ENSP00000286186:R490T	R	+	2	0	CASP10	201790609	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	0.427000	0.21379	-0.560000	0.06102	-0.302000	0.09304	AGA	.	.		0.418	CASP10-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256273.1	NM_032977		C	202082364	G	C	202082364	1	2	291	0	1	0	0	0	0	0	0	0	2671	942	33	4		4	CASP10	2	202082364	Intron	SNP	G	TCGA-G3-A7M6-01A-11D-A33Q-10	22467359	202082364	41117009	18	42656										
ATP2B2	491	hgsc.bcm.edu	37	chr3	10401666	10401666	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	cttgcgcacggagttgaaggTgtacactttgtacaacttct	10	9	1	1			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr3:10401666T>A	ENST00000352432.4	-	12	1870	c.1801A>T	c.(1801-1803)Acc>Tcc	p.T601S	ATP2B2_ENST00000397077.1_Missense_Mutation_p.T556S|ATP2B2_ENST00000383800.4_Missense_Mutation_p.T556S|ATP2B2_ENST00000360273.2_Missense_Mutation_p.T601S|ATP2B2_ENST00000343816.4_Missense_Mutation_p.T587S			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	601					auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						GAGTTGAAGGTGTACACTTTG	0.577																																					p.T601S	Ovarian(125;1619 1709 15675 19819 38835)	Atlas-SNP	.											.	ATP2B2	304	.	0			c.A1801T						.						104	84	91					3																	10401666		2203	4300	6503	SO:0001583	missense	491	exon13			TGAAGGTGTACAC	X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"ATPases / P-type"	815	protein-coding gene	gene with protein product	"plasma membrane Ca2+ pump 2", "plasma membrane calcium-transporting ATPase 2"	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.1801A>T	chr3.hg19:g.10401666T>A	ENSP00000324172:p.Thr601Ser	33.0	0.0		30.0	11.0	NM_001001331	O00766|Q12994|Q16818	Missense_Mutation	SNP	ENST00000352432.4	hg19	CCDS33701.1	.	.	.	.	.	.	.	.	.	.	T	29.2	4.986075	0.93044	.	.	ENSG00000157087	ENST00000352432;ENST00000383800;ENST00000397077;ENST00000360273;ENST00000343816;ENST00000535386;ENST00000452124;ENST00000342354	T;T;T;T;T;T	0.70045	-0.45;-0.45;-0.45;-0.45;-0.45;-0.45	4.93	4.93	0.64822	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.85682	D	0.000000	T	0.78953	0.4365	M	0.63169	1.94	0.80722	D	1	D;B;D	0.63046	0.992;0.363;0.992	D;B;D	0.74674	0.984;0.386;0.946	T	0.80991	-0.1135	10	0.62326	D	0.03	-43.1335	14.5887	0.68347	0.0:0.0:0.0:1.0	.	536;568;601	F5H7F7;Q4LE63;Q01814	.;.;AT2B2_HUMAN	S	601;556;556;601;587;536;457;601	ENSP00000324172:T601S;ENSP00000373311:T556S;ENSP00000380267:T556S;ENSP00000353414:T601S;ENSP00000344677:T587S;ENSP00000414854:T457S	ENSP00000342954:T601S	T	-	1	0	ATP2B2	10376666	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.040000	0.89188	1.844000	0.53588	0.482000	0.46254	ACC	.	.		0.577	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683		A	10401666	T	A	10401666	3	1	291	1	0	0	0	0	1	0	0	0	1140	1696	59	4	1974	4	ATP2B2	3	10401666	Missense_Mutation	SNP	T	TCGA-G3-A7M6-01A-11D-A33Q-10		10401666	187620764	19	42657										
MST1R	4486	hgsc.bcm.edu	37	chr3	49933287	49933287	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	ggccgcaccactctacccagGatatgacattcaccatctac	6	16	3	1	rs201143544		TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr3:49933287G>A	ENST00000296474.3	-	12	2850	c.2823C>T	c.(2821-2823)atC>atT	p.I941I	MST1R_ENST00000344206.4_Silent_p.I892I	NM_002447.2	NP_002438	Q04912	RON_HUMAN	macrophage stimulating 1 receptor (c-met-related tyrosine kinase)	941					cellular component movement (GO:0006928)|defense response (GO:0006952)|innate immune response (GO:0045087)|macrophage colony-stimulating factor signaling pathway (GO:0038145)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|response to virus (GO:0009615)|signal transduction (GO:0007165)|single fertilization (GO:0007338)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|macrophage colony-stimulating factor receptor activity (GO:0005011)			cervix(1)|endometrium(5)|large_intestine(3)|lung(17)|ovary(5)|prostate(2)|skin(1)|urinary_tract(3)	37				BRCA - Breast invasive adenocarcinoma(193;4.65e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)		CTCTACCCAGGATATGACATT	0.632																																					p.I941I		Atlas-SNP	.											.	MST1R	205	.	0			c.C2823T						.						63	61	62					3																	49933287		2203	4299	6502	SO:0001819	synonymous_variant	4486	exon12			ACCCAGGATATGA	X70040	CCDS2807.1, CCDS58833.1	3p21	2008-08-18			ENSG00000164078	ENSG00000164078		"CD molecules"	7381	protein-coding gene	gene with protein product		600168	"PTK8 protein tyrosine kinase 8"	RON, PTK8		8386824	Standard	NM_002447		Approved	CDw136, CD136	uc003cxy.4	Q04912	OTTHUMG00000156709	ENST00000296474.3:c.2823C>T	chr3.hg19:g.49933287G>A		39.0	0.0		44.0	12.0	NM_002447	B5A944|B5A945|B5A946|B5A947	Silent	SNP	ENST00000296474.3	hg19	CCDS2807.1																																																																																			.	G|0.999;A|0.001		0.632	MST1R-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345403.1			A	49933287	G	A	49933287	2	1	291	1	0	0	0	0	0	0	0	1	9900	1164	41	3		3	MST1R	3	49933287	Silent	SNP	G	TCGA-G3-A7M6-01A-11D-A33Q-10	39531621	49933287	148089143	20	42658										
DNAH12	201625	hgsc.bcm.edu	37	chr3	57356458	57356458	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	aggagattcagccgaagaccCgtgggaggttcattagtcat	13	8	3	2			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr3:57356458C>T	ENST00000351747.2	-	50	8013	c.7833G>A	c.(7831-7833)acG>acA	p.T2611T	DNAH12_ENST00000344804.4_Silent_p.T244T	NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	2611	AAA 4. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						GCCGAAGACCCGTGGGAGGTT	0.403																																					p.T2611T		Atlas-SNP	.											.	DNAH12	182	.	0			c.G7833A						.						136	128	130					3																	57356458		692	1591	2283	SO:0001819	synonymous_variant	201625	exon50			AAGACCCGTGGGA	U53532, AK126276	CCDS33771.1	3p21.1	2009-02-04	2006-09-04		ENSG00000174844	ENSG00000174844		"Axonemal dyneins"	2943	protein-coding gene	gene with protein product		603340	"dynein, axonemal, heavy polypeptide 12", "dynein heavy chain domain 2", "dynein heavy domain 2", "dynein, axonemal, heavy chain 12-like", "dynein, axonemal, heavy chain 7-like"	DNHD2, DNAH12L, DNAH7L		8812413, 8666668	Standard	NM_198564		Approved	DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290	uc003dit.2	Q6ZR08	OTTHUMG00000158598	ENST00000351747.2:c.7833G>A	chr3.hg19:g.57356458C>T		74.0	0.0		67.0	23.0	NM_178504	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Silent	SNP	ENST00000351747.2	hg19		.	.	.	.	.	.	.	.	.	.	C	8.276	0.814503	0.16607	.	.	ENSG00000174844	ENST00000462199	.	.	.	5.53	-6.61	0.01818	.	.	.	.	.	T	0.47377	0.1442	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49735	-0.8908	4	.	.	.	.	7.3368	0.26615	0.2631:0.1989:0.0:0.538	.	.	.	.	R	302	.	.	G	-	1	0	DNAH12	57331498	0.017000	0.18338	0.791000	0.31998	0.990000	0.78478	-0.900000	0.04097	-1.365000	0.02158	-0.484000	0.04775	GGG	.	.		0.403	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504		T	57356458	C	T	57356458	2	4	291	1	0	0	0	0	0	0	0	1	4602	639	23	1		1	DNAH12	3	57356458	Silent	SNP	C	TCGA-G3-A7M6-01A-11D-A33Q-10	7423171	57356458	140665972	21	42659										
CD80	941	hgsc.bcm.edu	37	chr3	119263583	119263583	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	ccatatattcatgtccccagAcatcatagtcagcaccattt	4	13	3	1			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr3:119263583A>T	ENST00000264246.3	-	3	594	c.232T>A	c.(232-234)Tct>Act	p.S78T	CD80_ENST00000383669.3_Missense_Mutation_p.S78T|CD80_ENST00000383668.3_Missense_Mutation_p.S78T|CD80_ENST00000478182.1_Missense_Mutation_p.S78T	NM_005191.3	NP_005182.1	P33681	CD80_HUMAN	CD80 molecule	78	Ig-like V-type.				cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045425)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of signal transduction (GO:0009967)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|positive regulation of transcription, DNA-templated (GO:0045893)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|viral process (GO:0016032)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)	12					Abatacept(DB01281)|Belatacept(DB06681)	ATGTCCCCAGACATCATAGTC	0.478																																					p.S78T	Melanoma(132;135 1764 1806 5833 14593)	Atlas-SNP	.											.	CD80	35	.	0			c.T232A						.						187	164	172					3																	119263583		2203	4300	6503	SO:0001583	missense	941	exon3			CCCCAGACATCAT		CCDS2989.1	3q13.3-q21	2013-01-11	2006-03-31		ENSG00000121594	ENSG00000121594		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing"	1700	protein-coding gene	gene with protein product	"B-lymphocyte activation antigen B7"	112203	"CD80 antigen (CD28 antigen ligand 1, B7-1 antigen)", "CD80 molecule "	CD28LG, CD28LG1		1370389	Standard	NM_005191		Approved	B7.1, B7-1	uc003ecq.3	P33681	OTTHUMG00000159419	ENST00000264246.3:c.232T>A	chr3.hg19:g.119263583A>T	ENSP00000264246:p.Ser78Thr	132.0	0.0		93.0	34.0	NM_005191	Q5DTA9|Q5DTB0	Missense_Mutation	SNP	ENST00000264246.3	hg19	CCDS2989.1	.	.	.	.	.	.	.	.	.	.	A	13.60	2.286632	0.40494	.	.	ENSG00000121594	ENST00000264246;ENST00000478182;ENST00000383669;ENST00000383668	T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1	5.13	-5.64	0.02466	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.004310	0.08020	N	0.991846	T	0.49474	0.1559	M	0.69358	2.11	0.09310	N	1	P;P;P;P	0.43431	0.807;0.552;0.714;0.714	B;B;B;B	0.41813	0.367;0.183;0.295;0.295	T	0.44711	-0.9310	10	0.25106	T	0.35	-2.6639	0.3927	0.00413	0.2245:0.2618:0.2576:0.2562	.	78;78;78;78	Q5DTA9;Q5DTB0;A0N0P2;P33681	.;.;.;CD80_HUMAN	T	78	ENSP00000264246:S78T;ENSP00000418364:S78T;ENSP00000373165:S78T;ENSP00000373164:S78T	ENSP00000264246:S78T	S	-	1	0	CD80	120746273	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.161000	0.10026	-0.885000	0.03971	-0.297000	0.09499	TCT	.	.		0.478	CD80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355196.1	NM_005191		T	119263583	A	T	119263583	3	4	291	1	0	0	0	0	1	0	0	0	3040	275	10	4	650	4	CD80	3	119263583	Missense_Mutation	SNP	A	TCGA-G3-A7M6-01A-11D-A33Q-10	61907125	119263583	78758847	22	42660										
MECOM	2122	hgsc.bcm.edu	37	chr3	168833394	168833394	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	tggaggcttggaggggactgGagtcaagggcttctcatcct	16	8	2	0			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr3:168833394G>C	ENST00000464456.1	-	7	2902	c.1702C>G	c.(1702-1704)Cca>Gca	p.P568A	MECOM_ENST00000460814.1_Missense_Mutation_p.P568A|MECOM_ENST00000494292.1_Missense_Mutation_p.P756A|MECOM_ENST00000433243.2_Missense_Mutation_p.P569A|MECOM_ENST00000264674.3_Missense_Mutation_p.P633A|MECOM_ENST00000472280.1_Missense_Mutation_p.P569A|MECOM_ENST00000468789.1_Missense_Mutation_p.P568A|MECOM_ENST00000392736.3_Missense_Mutation_p.P568A	NM_001164000.1	NP_001157472.1	Q13465	MDS1_HUMAN	MDS1 and EVI1 complex locus	0					regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	85						GAGGGGACTGGAGTCAAGGGC	0.547																																					p.P756A		Atlas-SNP	.											.	MECOM	216	.	0			c.C2266G						.						173	160	164					3																	168833394		2203	4300	6503	SO:0001583	missense	2122	exon8			GGACTGGAGTCAA	S82592, AF164154	CCDS3205.1, CCDS54669.1, CCDS54670.1	3q26.2	2013-01-08	2009-08-07	2009-08-07	ENSG00000085276	ENSG00000085276		"Zinc fingers, C2H2-type"	3498	protein-coding gene	gene with protein product		165215	"myelodysplasia syndrome 1", "ecotropic viral integration site 1"	MDS1, EVI1		2115646, 8171026, 8643684	Standard	NM_001105077		Approved	MDS1-EVI1, PRDM3	uc011bpj.1	Q03112	OTTHUMG00000158596	ENST00000464456.1:c.1702C>G	chr3.hg19:g.168833394G>C	ENSP00000419770:p.Pro568Ala	77.0	0.0		67.0	26.0	NM_004991	Q13466|Q6FH90	Missense_Mutation	SNP	ENST00000464456.1	hg19	CCDS54669.1	.	.	.	.	.	.	.	.	.	.	G	0.088	-1.171858	0.01646	.	.	ENSG00000085276	ENST00000264674;ENST00000392736;ENST00000464456;ENST00000472280;ENST00000494292;ENST00000468789;ENST00000460814;ENST00000433243;ENST00000492586	T;T;T;T;T;T;T;T;T	0.08984	3.44;3.43;3.32;3.53;3.31;3.43;3.3;3.53;3.03	5.61	3.8	0.43715	.	1.705140	0.03194	N	0.173793	T	0.12092	0.0294	L	0.47190	1.495	0.25726	N	0.985325	B;B;B;B;B	0.26081	0.141;0.015;0.087;0.038;0.009	B;B;B;B;B	0.26693	0.072;0.013;0.033;0.022;0.006	T	0.44711	-0.9310	10	0.27082	T	0.32	0.0208	11.6441	0.51250	0.1458:0.0:0.8542:0.0	.	756;569;756;633;568	Q03112-3;Q03112-6;E7EQ57;Q03112-4;Q03112	.;.;.;.;EVI1_HUMAN	A	633;568;568;569;756;568;568;569;219	ENSP00000264674:P633A;ENSP00000376493:P568A;ENSP00000419770:P568A;ENSP00000420048:P569A;ENSP00000417899:P756A;ENSP00000419995:P568A;ENSP00000420466:P568A;ENSP00000394302:P569A;ENSP00000417506:P219A	ENSP00000264674:P633A	P	-	1	0	MECOM	170316088	1.000000	0.71417	0.808000	0.32385	0.006000	0.05464	2.867000	0.48428	0.709000	0.31976	0.655000	0.94253	CCA	.	.		0.547	MECOM-020	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351519.1	NM_005241, NM_004991		C	168833394	G	C	168833394	3	2	291	1	0	0	0	0	1	0	0	0	9431	1174	41	4	1493	4	MECOM	3	168833394	Missense_Mutation	SNP	G	TCGA-G3-A7M6-01A-11D-A33Q-10	49569811	168833394	29189036	23	42661										
TIGD2	166815	hgsc.bcm.edu	37	chr4	90035650	90035650	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	ataaattggtattaaggaggCttcggaccataataagaaaa	9	4	0	1			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr4:90035650C>T	ENST00000317005.2	+	1	1683	c.1525C>T	c.(1525-1527)Ctt>Ttt	p.L509F	RP11-84C13.1_ENST00000603357.1_lincRNA	NM_145715.2	NP_663761.1	Q4W5G0	TIGD2_HUMAN	tigger transposable element derived 2	509						nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	14		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;3.86e-05)		ATTAAGGAGGCTTCGGACCAT	0.333																																					p.L509F		Atlas-SNP	.											.	TIGD2	36	.	0			c.C1525T						.						65	72	69					4																	90035650		2203	4300	6503	SO:0001583	missense	166815	exon1			AGGAGGCTTCGGA	AK027653	CCDS3633.1	4q21.3	2013-02-21			ENSG00000180346	ENSG00000180346			18333	protein-coding gene	gene with protein product		612973					Standard	NM_145715		Approved		uc003hsk.3	Q4W5G0	OTTHUMG00000130946	ENST00000317005.2:c.1525C>T	chr4.hg19:g.90035650C>T	ENSP00000317170:p.Leu509Phe	110.0	0.0		80.0	34.0	NM_145715		Missense_Mutation	SNP	ENST00000317005.2	hg19	CCDS3633.1	.	.	.	.	.	.	.	.	.	.	C	10.46	1.356143	0.24598	.	.	ENSG00000180346	ENST00000317005	T	0.38401	1.14	4.31	3.46	0.39613	.	0.000000	0.40728	N	0.001021	T	0.30727	0.0774	L	0.54323	1.7	0.25198	N	0.990079	B	0.14012	0.009	B	0.12837	0.008	T	0.19353	-1.0308	10	0.39692	T	0.17	-4.7504	8.0617	0.30638	0.0:0.889:0.0:0.111	.	509	Q4W5G0	TIGD2_HUMAN	F	509	ENSP00000317170:L509F	ENSP00000317170:L509F	L	+	1	0	TIGD2	90254673	1.000000	0.71417	0.916000	0.36221	0.843000	0.47879	2.496000	0.45346	1.019000	0.39547	0.467000	0.42956	CTT	.	.		0.333	TIGD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253545.2	NM_145715		T	90035650	C	T	90035650	3	4	291	1	0	0	0	0	1	0	0	0	15911	797	28	3	1527	3	TIGD2	4	90035650	Missense_Mutation	SNP	C	TCGA-G3-A7M6-01A-11D-A33Q-10		90035650	101118626	24	42662										
FSTL5	56884	hgsc.bcm.edu	37	chr4	162431553	162431553	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	ataattcaacttagtaccttCttctctccataatatgttag	3	9	3	0			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr4:162431553C>A	ENST00000306100.5	-	11	1772	c.1336G>T	c.(1336-1338)Gaa>Taa	p.E446*	FSTL5_ENST00000427802.2_Intron|FSTL5_ENST00000379164.4_Nonsense_Mutation_p.E445*|FSTL5_ENST00000536695.1_Nonsense_Mutation_p.E445*	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	446						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(18)|lung(43)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	91	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		TTAGTACCTTCTTCTCTCCAT	0.249																																					p.E446X		Atlas-SNP	.											.	FSTL5	207	.	0			c.G1336T						.						46	46	46					4																	162431553		2191	4268	6459	SO:0001587	stop_gained	56884	exon11			TACCTTCTTCTCT	BC036502	CCDS3802.1, CCDS47157.1, CCDS47158.1	4q32.3	2013-01-11			ENSG00000168843	ENSG00000168843		"EF-hand domain containing", "Immunoglobulin superfamily / I-set domain containing"	21386	protein-coding gene	gene with protein product						10574462, 15527507	Standard	NM_020116		Approved	DKFZp566D234, KIAA1263	uc003iqh.4	Q8N475	OTTHUMG00000161397	ENST00000306100.5:c.1336G>T	chr4.hg19:g.162431553C>A	ENSP00000305334:p.Glu446*	346.0	0.0		308.0	103.0	NM_020116	E9PCP6|Q9NSW7|Q9ULF7	Nonsense_Mutation	SNP	ENST00000306100.5	hg19	CCDS3802.1	.	.	.	.	.	.	.	.	.	.	C	41	8.663030	0.98905	.	.	ENSG00000168843	ENST00000306100;ENST00000379164;ENST00000536695	.	.	.	5.4	5.4	0.78164	.	0.048523	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	.	12.4534	0.55688	0.0:0.8314:0.1686:0.0	.	.	.	.	X	446;445;445	.	ENSP00000305334:E446X	E	-	1	0	FSTL5	162651003	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	3.102000	0.50291	2.522000	0.85027	0.557000	0.71058	GAA	.	.		0.249	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116		A	162431553	C	A	162431553	4	1	291	1	0	0	0	0	0	1	0	0	6088	922	32	3	1231	3	FSTL5	4	162431553	Nonsense_Mutation	SNP	C	TCGA-G3-A7M6-01A-11D-A33Q-10	72395903	162431553	28722723	25	42663										
AHRR	57491	hgsc.bcm.edu	37	chr5	427999	427999	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	tcaggagccatgctcccgccGcggctgtcgctgttctgcat	12	15	2	0			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr5:427999G>A	ENST00000505113.1	+	8	842	c.798G>A	c.(796-798)ccG>ccA	p.P266P	AHRR_ENST00000512529.1_Silent_p.P112P|AHRR_ENST00000316418.5_Silent_p.P284P|AHRR_ENST00000506456.1_Silent_p.P122P	NM_001242412.1	NP_001229341.1	A9YTQ3	AHRR_HUMAN	aryl-hydrocarbon receptor repressor	266					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of protein sumoylation (GO:0033235)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(2)|endometrium(4)|large_intestine(1)|lung(12)|prostate(1)	20			Epithelial(17;0.0011)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00354)|Lung(60;0.0863)			TGCTCCCGCCGCGGCTGTCGC	0.557																																					p.P284P		Atlas-SNP	.											.	AHRR	67	.	0			c.G852A						.						24	28	27					5																	427999		1897	4106	6003	SO:0001819	synonymous_variant	57491	exon9			CCCGCCGCGGCTG	AB033060	CCDS43297.1, CCDS56355.1	5p15.33	2013-05-21	2003-09-11	2003-09-12	ENSG00000063438	ENSG00000063438		"Basic helix-loop-helix proteins"	346	protein-coding gene	gene with protein product		606517	"aryl hydrocarbon receptor regulator"	AHH, AHHR		1070014, 11423533	Standard	NM_020731		Approved	KIAA1234, bHLHe77	uc003jaw.3	A9YTQ3	OTTHUMG00000162171	ENST00000505113.1:c.798G>A	chr5.hg19:g.427999G>A		93.0	0.0		130.0	20.0	NM_020731	A7MBN5|D6RAZ1|Q9HAZ3|Q9ULI6	Silent	SNP	ENST00000505113.1	hg19	CCDS56355.1																																																																																			.	.		0.557	AHRR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367720.1	NM_020731		A	427999	G	A	427999	2	1	291	1	0	0	0	0	0	0	0	1	417	1074	38	1		1	AHRR	5	427999	Silent	SNP	G	TCGA-G3-A7M6-01A-11D-A33Q-10		427999	180487261	26	42664										
AP3B1	8546	hgsc.bcm.edu	37	chr5	77298849	77298849	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	tccactgtgactagcatcaaTgacccactgtgcacagtttt	7	12	1	2			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr5:77298849T>C	ENST00000255194.6	-	27	3337	c.3162A>G	c.(3160-3162)tcA>tcG	p.S1054S	AP3B1_ENST00000519295.1_Silent_p.S1005S	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	1054					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein targeting to lysosome (GO:0006622)	AP-3 adaptor complex (GO:0030123)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|protein phosphatase binding (GO:0019903)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(12)|lung(12)|prostate(1)|skin(2)|urinary_tract(1)	39		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		CTAGCATCAATGACCCACTGT	0.438									Hermansky-Pudlak syndrome																												p.S1054S		Atlas-SNP	.											.	AP3B1	94	.	0			c.A3162G						.						119	115	116					5																	77298849		2203	4300	6503	SO:0001819	synonymous_variant	8546	exon27	Familial Cancer Database	HPS, HPS1-8	CATCAATGACCCA	U81504	CCDS4041.1, CCDS64186.1	5q14.1	2014-09-17			ENSG00000132842	ENSG00000132842			566	protein-coding gene	gene with protein product		603401				9182526, 9151686	Standard	NM_003664		Approved	ADTB3A, HPS2	uc003kfj.4	O00203	OTTHUMG00000106919	ENST00000255194.6:c.3162A>G	chr5.hg19:g.77298849T>C		39.0	0.0		42.0	17.0	NM_003664	E5RJ68|O00580|Q7Z393|Q9HD66	Silent	SNP	ENST00000255194.6	hg19	CCDS4041.1																																																																																			.	.		0.438	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2			C	77298849	T	C	77298849	2	2	291	1	0	0	0	0	0	0	0	1	744	1451	51	2		2	AP3B1	5	77298849	Silent	SNP	T	TCGA-G3-A7M6-01A-11D-A33Q-10	76870850	77298849	103616411	27	42665										
PCDHB6	56130	hgsc.bcm.edu	37	chr5	140530762	140530762	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	agaaaggctttggattttgaGgaaattcagtcttatgacgt	11	4	2	3			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr5:140530762G>A	ENST00000231136.1	+	1	924	c.924G>A	c.(922-924)gaG>gaA	p.E308E	PCDHB6_ENST00000543635.1_Silent_p.E172E	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	308	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGGATTTTGAGGAAATTCAGT	0.458																																					p.E308E		Atlas-SNP	.											.	PCDHB6	161	.	0			c.G924A						.						90	98	95					5																	140530762		2203	4300	6503	SO:0001819	synonymous_variant	56130	exon1			TTTTGAGGAAATT	AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"Cadherins / Protocadherins : Clustered"	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.924G>A	chr5.hg19:g.140530762G>A		91.0	0.0		46.0	7.0	NM_018939	B2R8R9	Silent	SNP	ENST00000231136.1	hg19	CCDS4248.1																																																																																			.	.		0.458	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939		A	140530762	G	A	140530762	2	1	291	1	0	0	0	0	0	0	0	1	11555	991	35	3		3	PCDHB6	5	140530762	Silent	SNP	G	TCGA-G3-A7M6-01A-11D-A33Q-10	63231913	140530762	40384498	28	42666										
EBF1	1879	hgsc.bcm.edu	37	chr5	158135124	158135124	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	aggagaagatgcccgaggagCtgctgcagttggaggggagg	20	6	0	2			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr5:158135124C>T	ENST00000313708.6	-	15	1889	c.1607G>A	c.(1606-1608)aGc>aAc	p.S536N	EBF1_ENST00000380654.4_Missense_Mutation_p.S505N|EBF1_ENST00000517373.1_Missense_Mutation_p.S468N|EBF1_ENST00000518836.1_5'UTR	NM_024007.3	NP_076870.1	Q9UH73	COE1_HUMAN	early B-cell factor 1	536	Pro/Ser/Thr-rich.				multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)		HMGA2/EBF1(2)	breast(3)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(18)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42	Renal(175;0.00196)	Acute lymphoblastic leukemia(3;2.99e-06)|all_hematologic(3;0.000772)|Medulloblastoma(196;0.037)|all_neural(177;0.143)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GCCCGAGGAGCTGCTGCAGTT	0.577			T	HMGA2	lipoma																																p.S536N		Atlas-SNP	.		Dom	yes		5	5q34	1879	early B-cell factor 1		M	.	EBF1	110	.	0			c.G1607A						.						70	65	67					5																	158135124		2203	4298	6501	SO:0001583	missense	1879	exon15			GAGGAGCTGCTGC	AF208502	CCDS4343.1	5q34	2008-02-05	2006-09-26	2006-09-26	ENSG00000164330	ENSG00000164330			3126	protein-coding gene	gene with protein product		164343	"early B-cell factor"	EBF		8012110	Standard	NM_024007		Approved	OLF1	uc010jip.3	Q9UH73	OTTHUMG00000130304	ENST00000313708.6:c.1607G>A	chr5.hg19:g.158135124C>T	ENSP00000322898:p.Ser536Asn	72.0	0.0		25.0	12.0	NM_024007	Q8IW11	Missense_Mutation	SNP	ENST00000313708.6	hg19	CCDS4343.1	.	.	.	.	.	.	.	.	.	.	C	17.17	3.322259	0.60634	.	.	ENSG00000164330	ENST00000318060;ENST00000313708;ENST00000380654;ENST00000517373	T;T;T	0.45668	0.89;0.89;0.89	5.22	5.22	0.72569	.	0.219909	0.47093	D	0.000259	T	0.42810	0.1219	L	0.50333	1.59	0.37580	D	0.919754	B;B;B;B	0.09022	0.0;0.0;0.001;0.002	B;B;B;B	0.15052	0.001;0.001;0.005;0.012	T	0.43956	-0.9359	10	0.59425	D	0.04	-8.8208	18.8129	0.92065	0.0:1.0:0.0:0.0	.	536;523;536;505	A8K0Z7;B4E2U8;Q9UH73;Q9UH73-2	.;.;COE1_HUMAN;.	N	536;536;505;468	ENSP00000322898:S536N;ENSP00000370029:S505N;ENSP00000428020:S468N	ENSP00000322898:S536N	S	-	2	0	EBF1	158067702	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.265000	0.51561	2.437000	0.82529	0.655000	0.94253	AGC	.	.		0.577	EBF1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000252649.1	NM_024007		T	158135124	C	T	158135124	3	4	291	1	0	0	0	0	1	0	0	0	4882	797	28	3	176	3	EBF1	5	158135124	Missense_Mutation	SNP	C	TCGA-G3-A7M6-01A-11D-A33Q-10	17604362	158135124	22780136	29	42667										
SERPINB6	5269	hgsc.bcm.edu	37	chr6	2954826	2954826	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	gaataacaatacattttcacCttctgtcttttcagctaccc	3	12	4	0			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr6:2954826C>T	ENST00000380520.1	-	3	2424	c.430G>A	c.(430-432)Ggt>Agt	p.G144S	SERPINB6_ENST00000335686.5_Splice_Site_p.G144S|SERPINB6_ENST00000380539.1_Splice_Site_p.G144S|SERPINB6_ENST00000380546.3_Splice_Site_p.G144S|SERPINB6_ENST00000380529.1_Splice_Site_p.G144S|SERPINB6_ENST00000380524.1_Splice_Site_p.G144S			P35237	SPB6_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 6	144					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(8)|stomach(1)|upper_aerodigestive_tract(2)	17	Ovarian(93;0.0412)	all_hematologic(90;0.0895)			Drotrecogin alfa(DB00055)	ACATTTTCACCTTCTGTCTTT	0.363																																					p.G163S		Atlas-SNP	.											SERPINB6,colon,carcinoma,0,1	SERPINB6	31	.	0			c.G487A						.						167	158	161					6																	2954826		2203	4300	6503	SO:0001630	splice_region_variant	5269	exon4			TTTCACCTTCTGT	Z22658	CCDS4479.1, CCDS75386.1, CCDS75387.1	6p25.2	2014-02-18	2005-08-18		ENSG00000124570	ENSG00000124570		"Serine (or cysteine) peptidase inhibitors"	8950	protein-coding gene	gene with protein product	"cytoplasmic antiproteinase"	173321	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 6", "deafness, autosomal recessive 91"	PI6, DFNB91		8415716, 9858835, 20451170, 24172014	Standard	NM_004568		Approved	PTI, CAP	uc031smo.1	P35237	OTTHUMG00000016170	ENST00000380520.1:c.430+1G>A	chr6.hg19:g.2954826C>T		45.0	0.0		43.0	12.0	NM_001271823	B2RBA8|Q59F97|Q5TD06|Q7Z2Y7|Q96J44|Q9UDI7	Missense_Mutation	SNP	ENST00000380520.1	hg19	CCDS4479.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.467576	0.84533	.	.	ENSG00000124570	ENST00000380524;ENST00000380520;ENST00000335686;ENST00000380529;ENST00000380539;ENST00000380546	D;D;D;D;D;D	0.86497	-2.13;-2.13;-2.13;-2.13;-2.13;-2.13	5.22	5.22	0.72569	Serpin domain (3);	0.149558	0.64402	D	0.000014	D	0.92378	0.7581	M	0.77313	2.365	0.47905	D	0.99954	D	0.71674	0.998	D	0.70016	0.967	D	0.91422	0.5159	9	.	.	.	.	18.2123	0.89874	0.0:1.0:0.0:0.0	.	144	P35237	SPB6_HUMAN	S	144	ENSP00000369896:G144S;ENSP00000369891:G144S;ENSP00000338358:G144S;ENSP00000369901:G144S;ENSP00000369912:G144S;ENSP00000369919:G144S	.	G	-	1	0	SERPINB6	2899825	1.000000	0.71417	1.000000	0.80357	0.712000	0.41017	3.299000	0.51826	2.820000	0.97059	0.650000	0.86243	GGT	.	.		0.363	SERPINB6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043422.1		Missense_Mutation	T	2954826	C	T	2954826	5	4	291	1	0	0	0	0	0	0	1	0	14120	695	24	3	716	3	SERPINB6	6	2954826	Splice_Site	SNP	C	TCGA-G3-A7M6-01A-11D-A33Q-10		2954826	168160241	30	42668										
DSP	1832	hgsc.bcm.edu	37	chr6	7576541	7576541	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	ccccaggttatgggacctggAgaaacaaatcaagcaattga	10	9	1	2			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr6:7576541A>G	ENST00000379802.3	+	19	2986	c.2645A>G	c.(2644-2646)gAg>gGg	p.E882G	DSP_ENST00000418664.2_Missense_Mutation_p.E882G	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	882	Globular 1.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		TGGGACCTGGAGAAACAAATC	0.373																																					p.E882G		Atlas-SNP	.											.	DSP	306	.	0			c.A2645G						.						90	92	91					6																	7576541		2203	4300	6503	SO:0001583	missense	1832	exon19			ACCTGGAGAAACA	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"desmoplakin (DPI, DPII)"			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.2645A>G	chr6.hg19:g.7576541A>G	ENSP00000369129:p.Glu882Gly	103.0	0.0		85.0	30.0	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Missense_Mutation	SNP	ENST00000379802.3	hg19	CCDS4501.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.465892	0.84425	.	.	ENSG00000096696	ENST00000379802;ENST00000418664;ENST00000397483	T;T	0.41400	1.0;1.0	6.02	6.02	0.97574	.	0.000000	0.64402	D	0.000002	T	0.55433	0.1920	M	0.69823	2.125	0.58432	D	0.999999	D;D	0.76494	0.999;0.999	D;D	0.64144	0.922;0.922	T	0.61068	-0.7137	10	0.87932	D	0	.	16.5446	0.84426	1.0:0.0:0.0:0.0	.	929;882	Q4LE79;P15924	.;DESP_HUMAN	G	882;882;687	ENSP00000369129:E882G;ENSP00000396591:E882G	ENSP00000369129:E882G	E	+	2	0	DSP	7521540	1.000000	0.71417	1.000000	0.80357	0.719000	0.41307	8.392000	0.90180	2.311000	0.77944	0.533000	0.62120	GAG	.	.		0.373	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		G	7576541	A	G	7576541	3	3	291	1	0	0	0	0	1	0	0	0	4783	304	11	2	2719	2	DSP	6	7576541	Missense_Mutation	SNP	A	TCGA-G3-A7M6-01A-11D-A33Q-10	4621715	7576541	163538526	31	42669										
JARID2	3720	hgsc.bcm.edu	37	chr6	15468865	15468865	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	atgatgagacagaagacgtcAaaacagccaccaacaatgct	8	10	1	4			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr6:15468865A>C	ENST00000341776.2	+	5	830	c.586A>C	c.(586-588)Aaa>Caa	p.K196Q	JARID2_ENST00000397311.3_Missense_Mutation_p.K24Q|JARID2_ENST00000541660.1_Missense_Mutation_p.K158Q	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	196					central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	59	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				AGAAGACGTCAAAACAGCCAC	0.512																																					p.K196Q		Atlas-SNP	.											.	JARID2	135	.	0			c.A586C						.						155	127	136					6																	15468865		2203	4300	6503	SO:0001583	missense	3720	exon5			GACGTCAAAACAG	U57592	CCDS4533.1, CCDS58996.1	6p24-p23	2008-02-05	2006-10-06	2004-01-30	ENSG00000008083	ENSG00000008083			6196	protein-coding gene	gene with protein product		601594	"jumonji (mouse) homolog", "Jumonji, AT rich interactive domain 2"	JMJ		8894700	Standard	NM_001267040		Approved		uc003nbj.4	Q92833	OTTHUMG00000014293	ENST00000341776.2:c.586A>C	chr6.hg19:g.15468865A>C	ENSP00000341280:p.Lys196Gln	102.0	0.0		82.0	29.0	NM_004973	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Missense_Mutation	SNP	ENST00000341776.2	hg19	CCDS4533.1	.	.	.	.	.	.	.	.	.	.	A	19.41	3.822559	0.71028	.	.	ENSG00000008083	ENST00000538175;ENST00000341776;ENST00000397311;ENST00000541660	T;T;T	0.36340	1.26;1.26;1.26	4.89	4.89	0.63831	.	0.285984	0.38005	N	0.001849	T	0.38957	0.1060	L	0.44542	1.39	0.32940	D	0.518328	D;D;D	0.76494	0.999;0.998;0.985	D;P;P	0.66351	0.943;0.852;0.715	T	0.39840	-0.9594	10	0.56958	D	0.05	-6.9403	14.5584	0.68118	1.0:0.0:0.0:0.0	.	158;60;196	F5H590;B7Z7X9;Q92833	.;.;JARD2_HUMAN	Q	60;196;24;158	ENSP00000341280:K196Q;ENSP00000380478:K24Q;ENSP00000444623:K158Q	ENSP00000341280:K196Q	K	+	1	0	JARID2	15576844	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.433000	0.73404	1.842000	0.53543	0.529000	0.55759	AAA	.	.		0.512	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973		C	15468865	A	C	15468865	3	2	291	1	0	0	0	0	1	0	0	0	7954	131	5	5	604	5	JARID2	6	15468865	Missense_Mutation	SNP	A	TCGA-G3-A7M6-01A-11D-A33Q-10	7892324	15468865	155646202	32	42670										
CFB	629	hgsc.bcm.edu	37	chr6	31915210	31915210	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	gaagacagcgtcacctaccaCtgcagccgggggcttaccct	11	15	1	1			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr6:31915210C>T	ENST00000425368.2	+	4	1083	c.570C>T	c.(568-570)caC>caT	p.H190H	CFB_ENST00000456570.1_Silent_p.H692H|CFB_ENST00000556679.1_Silent_p.H692H|CFB_ENST00000477310.1_Silent_p.H541H	NM_001710.5	NP_001701.2	P00751	CFAB_HUMAN	complement factor B	190	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	complement binding (GO:0001848)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(10)|pancreas(1)|skin(1)|urinary_tract(1)	21						TCACCTACCACTGCAGCCGGG	0.637																																					p.H190H		Atlas-SNP	.											.	CFB	33	.	0			c.C570T						.						112	111	112					6																	31915210		1510	2707	4217	SO:0001819	synonymous_variant	629	exon4			CTACCACTGCAGC	L15702	CCDS4729.1	6p21.33	2014-09-17	2006-02-10	2006-02-10	ENSG00000243649	ENSG00000243649	3.4.21.47	"Complement system"	1037	protein-coding gene	gene with protein product		138470	"B-factor, properdin"	BFD, BF			Standard	NM_001710		Approved	H2-Bf	uc011dor.2	P00751	OTTHUMG00000031198	ENST00000425368.2:c.570C>T	chr6.hg19:g.31915210C>T		50.0	0.0		35.0	15.0	NM_001710	B0QZQ6|O15006|Q29944|Q53F89|Q5JP67|Q5ST50|Q96HX6|Q9BTF5|Q9BX92	Silent	SNP	ENST00000425368.2	hg19	CCDS4729.1																																																																																			.	.		0.637	CFB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076395.3	NM_001710		T	31915210	C	T	31915210	2	4	291	1	0	0	0	0	0	0	0	1	3280	564	20	3		3	CFB	6	31915210	Silent	SNP	C	TCGA-G3-A7M6-01A-11D-A33Q-10	16446345	31915210	139199857	33	42671										
AGPAT1	10554	hgsc.bcm.edu	37	chr6	32138234	32138234	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	cagggtctgggcgacctcagAcatgacactgatggcatccc	12	13	2	3			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr6:32138234A>G	ENST00000395499.1	-	4	1057	c.478T>C	c.(478-480)Tct>Cct	p.S160P	AGPAT1_ENST00000375107.3_Missense_Mutation_p.S160P|AGPAT1_ENST00000336984.6_Missense_Mutation_p.S160P|AGPAT1_ENST00000395496.1_Missense_Mutation_p.S160P|PPT2-EGFL8_ENST00000422437.1_3'UTR|AGPAT1_ENST00000490711.1_Intron|AGPAT1_ENST00000375104.2_Missense_Mutation_p.S160P|AGPAT1_ENST00000412465.2_Missense_Mutation_p.S48P|AGPAT1_ENST00000395497.1_Missense_Mutation_p.S160P			Q99943	PLCA_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 1	160					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of cellular metabolic process (GO:0031325)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			central_nervous_system(1)|large_intestine(3)|lung(6)|ovary(2)	12						GCGACCTCAGACATGACACTG	0.582																																					p.S160P		Atlas-SNP	.											.	AGPAT1	22	.	0			c.T478C						.						81	83	82					6																	32138234		1511	2709	4220	SO:0001583	missense	10554	exon4			CCTCAGACATGAC	U56417	CCDS4744.1	6p21.3	2013-02-05	2013-02-05		ENSG00000204310	ENSG00000204310	2.3.1.51	"1-acylglycerol-3-phosphate O-acyltransferases"	324	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, alpha"	603099	"1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha)"			9461603, 9291118	Standard	NM_032741		Approved	LPAAT-alpha	uc003oae.3	Q99943	OTTHUMG00000031210	ENST00000395499.1:c.478T>C	chr6.hg19:g.32138234A>G	ENSP00000378877:p.Ser160Pro	39.0	0.0		37.0	15.0	NM_006411	A2BFI5|Q5BL03	Missense_Mutation	SNP	ENST00000395499.1	hg19	CCDS4744.1	.	.	.	.	.	.	.	.	.	.	A	19.66	3.869730	0.72065	.	.	ENSG00000204310	ENST00000395496;ENST00000375107;ENST00000395499;ENST00000375104;ENST00000395497;ENST00000336984;ENST00000412465;ENST00000538952	D;D;D;D;D;D;D	0.93547	-3.24;-3.24;-3.24;-3.24;-3.24;-3.24;-3.24	5.89	4.78	0.61160	Phospholipid/glycerol acyltransferase (2);1-acyl-sn-glycerol-3-phosphate acyltransferase (1);	0.453294	0.25130	N	0.032911	D	0.90442	0.7007	M	0.68317	2.08	0.44899	D	0.997912	P;P	0.48230	0.907;0.637	P;B	0.51266	0.664;0.435	D	0.88744	0.3245	10	0.30854	T	0.27	-12.0463	5.8796	0.18848	0.6424:0.2161:0.0:0.1415	.	124;160	B4DRH1;Q99943	.;PLCA_HUMAN	P	160;160;160;160;160;160;48;64	ENSP00000378874:S160P;ENSP00000364248:S160P;ENSP00000378877:S160P;ENSP00000364245:S160P;ENSP00000378875:S160P;ENSP00000337463:S160P;ENSP00000410473:S48P	ENSP00000337463:S160P	S	-	1	0	AGPAT1	32246212	0.713000	0.27926	1.000000	0.80357	0.999000	0.98932	-0.000000	0.12993	2.254000	0.74563	0.533000	0.62120	TCT	.	.		0.582	AGPAT1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268941.1	NM_006411		G	32138234	A	G	32138234	3	3	291	1	0	0	0	0	1	0	0	0	386	275	10	2	389	2	AGPAT1	6	32138234	Missense_Mutation	SNP	A	TCGA-G3-A7M6-01A-11D-A33Q-10	223024	32138234	138976833	34	42672										
CAPN11	11131	hgsc.bcm.edu	37	chr6	44137245	44137245	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	ccaactccaaaaatgtgcagAacatctcctggcagcggccc	8	15	1	1			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr6:44137245A>G	ENST00000398776.1	+	3	354	c.316A>G	c.(316-318)Aac>Gac	p.N106D	CAPN11_ENST00000542245.1_Missense_Mutation_p.N106D	NM_007058.3	NP_008989.2	Q9UMQ6	CAN11_HUMAN	calpain 11	106	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|peptidase activity (GO:0008233)			breast(3)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)	36	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			AAATGTGCAGAACATCTCCTG	0.542																																					p.N106D		Atlas-SNP	.											.	CAPN11	66	.	0			c.A316G						.						19	21	20					6																	44137245		1894	4121	6015	SO:0001583	missense	11131	exon3			GTGCAGAACATCT	AJ242832	CCDS47436.1	6p12	2013-01-10			ENSG00000137225	ENSG00000137225		"EF-hand domain containing"	1478	protein-coding gene	gene with protein product		604822				10409436	Standard	NM_007058		Approved		uc003owt.1	Q9UMQ6	OTTHUMG00000014758	ENST00000398776.1:c.316A>G	chr6.hg19:g.44137245A>G	ENSP00000381758:p.Asn106Asp	151.0	0.0		118.0	39.0	NM_007058	B2RA64|Q5T3G1|Q8N4R5	Missense_Mutation	SNP	ENST00000398776.1	hg19	CCDS47436.1	.	.	.	.	.	.	.	.	.	.	A	8.632	0.893884	0.17613	.	.	ENSG00000137225	ENST00000398776;ENST00000542245;ENST00000532171	D;D;D	0.87334	-2.24;-2.24;-2.24	4.31	0.57	0.17347	Peptidase C2, calpain, catalytic domain (3);	0.121320	0.37809	N	0.001940	T	0.66268	0.2772	L	0.45228	1.405	0.24481	N	0.994344	B	0.10296	0.003	B	0.12156	0.007	T	0.60895	-0.7172	10	0.46703	T	0.11	.	7.8633	0.29522	0.5116:0.0:0.4884:0.0	.	106	Q9UMQ6	CAN11_HUMAN	D	106;106;136	ENSP00000381758:N106D;ENSP00000441078:N106D;ENSP00000432420:N136D	ENSP00000381758:N106D	N	+	1	0	CAPN11	44245223	0.510000	0.26171	0.736000	0.30914	0.032000	0.12392	1.878000	0.39608	0.098000	0.17522	-0.263000	0.10527	AAC	.	.		0.542	CAPN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040714.3			G	44137245	A	G	44137245	3	3	291	1	0	0	0	0	1	0	0	0	2626	246	9	2	326	2	CAPN11	6	44137245	Missense_Mutation	SNP	A	TCGA-G3-A7M6-01A-11D-A33Q-10	11999011	44137245	126977822	35	42673										
AIM1	202	hgsc.bcm.edu	37	chr6	106967133	106967133	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	ctgccaccaaaatctccttaTttgaaaacaaacggacaaac	4	12	1	1			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr6:106967133T>C	ENST00000369066.3	+	2	1313	c.826T>C	c.(826-828)Ttt>Ctt	p.F276L		NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		AATCTCCTTATTTGAAAACAA	0.433																																					p.F276L		Atlas-SNP	.											.	AIM1	161	.	0			c.T826C						.						56	55	55					6																	106967133		2203	4300	6503	SO:0001583	missense	202	exon2			TCCTTATTTGAAA	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"suppression of tumorigenicity 4", "beta-gamma crystallin domain containing 1"	601797	"suppression of tumorigenicity 4 (malignant melanoma)"	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.826T>C	chr6.hg19:g.106967133T>C	ENSP00000358062:p.Phe276Leu	138.0	0.0		100.0	35.0	NM_001624	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000369066.3	hg19	CCDS34506.1	.	.	.	.	.	.	.	.	.	.	T	28.6	4.935332	0.92458	.	.	ENSG00000112297	ENST00000285105;ENST00000369066	D	0.83914	-1.78	5.59	5.59	0.84812	.	0.000000	0.44097	D	0.000481	D	0.87442	0.6178	M	0.63843	1.955	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.87929	0.2709	10	0.49607	T	0.09	.	15.7563	0.78030	0.0:0.0:0.0:1.0	.	276	Q9Y4K1	AIM1_HUMAN	L	684;276	ENSP00000358062:F276L	ENSP00000285105:F684L	F	+	1	0	AIM1	107073826	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.503000	0.66962	2.129000	0.65627	0.454000	0.30748	TTT	.	.		0.433	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1			C	106967133	T	C	106967133	3	2	291	1	0	0	0	0	1	0	0	0	430	1493	52	2	832	2	AIM1	6	106967133	Missense_Mutation	SNP	T	TCGA-G3-A7M6-01A-11D-A33Q-10	62829888	106967133	64147934	36	42674										
KIAA1244	57221	hgsc.bcm.edu	37	chr6	138655844	138655844	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	atccaccccatccaccggggGcttctctgggaaagaaaccc	9	16	1	1			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr6:138655844G>C	ENST00000251691.4	+	33	6027	c.5861G>C	c.(5860-5862)gGc>gCc	p.G1954A		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		TCCACCGGGGGCTTCTCTGGG	0.622																																					p.G1954A		Atlas-SNP	.											.	KIAA1244	236	.	0			c.G5861C						.						24	25	25					6																	138655844		2203	4300	6503	SO:0001583	missense	57221	exon33			CCGGGGGCTTCTC	AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	21213	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 33"		"chromosome 6 open reading frame 92"	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.5861G>C	chr6.hg19:g.138655844G>C	ENSP00000251691:p.Gly1954Ala	50.0	0.0		46.0	12.0	NM_020340		Missense_Mutation	SNP	ENST00000251691.4	hg19	CCDS5189.2	.	.	.	.	.	.	.	.	.	.	G	17.60	3.428918	0.62844	.	.	ENSG00000112379	ENST00000251691;ENST00000367706	T	0.21031	2.03	5.87	5.87	0.94306	.	3.981390	0.00397	N	0.000045	T	0.12646	0.0307	L	0.32530	0.975	0.58432	D	0.999992	P	0.37441	0.595	B	0.34931	0.192	T	0.48681	-0.9014	10	0.20046	T	0.44	-24.2261	20.2011	0.98259	0.0:0.0:1.0:0.0	.	1954	Q5TH69	BIG3_HUMAN	A	1954;119	ENSP00000251691:G1954A	ENSP00000251691:G1954A	G	+	2	0	KIAA1244	138697537	1.000000	0.71417	0.999000	0.59377	0.437000	0.31866	7.625000	0.83145	2.780000	0.95670	0.543000	0.68304	GGC	.	.		0.622	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340		C	138655844	G	C	138655844	3	2	291	1	0	0	0	0	1	0	0	0	8226	1203	42	4	5991	4	KIAA1244	6	138655844	Missense_Mutation	SNP	G	TCGA-G3-A7M6-01A-11D-A33Q-10	31688711	138655844	32459223	37	42675										
ACAT2	39	hgsc.bcm.edu	37	chr6	160197285	160197285	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	actgatggaacgggaacagtCaccccagccaatgcttcagg	11	12	2	1			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr6:160197285C>T	ENST00000367048.4	+	6	2498	c.738C>T	c.(736-738)gtC>gtT	p.V246V	ACAT2_ENST00000541436.1_Silent_p.V275V|ACAT2_ENST00000472052.1_3'UTR	NM_005891.2	NP_005882.2	Q9BWD1	THIC_HUMAN	acetyl-CoA acetyltransferase 2	246					lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleus (GO:0005634)	acetyl-CoA C-acetyltransferase activity (GO:0003985)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(1)	9		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.51e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		CGGGAACAGTCACCCCAGCCA	0.393																																					p.V246V		Atlas-SNP	.											.	ACAT2	32	.	0			c.C738T						.						67	66	66					6																	160197285		2203	4300	6503	SO:0001819	synonymous_variant	39	exon6			AACAGTCACCCCA	AF356877	CCDS5268.1	6q25.3	2014-05-19	2010-04-30		ENSG00000120437	ENSG00000120437	2.3.1.9		94	protein-coding gene	gene with protein product	"acetoacetyl Coenzyme A thiolase"	100678	"acetyl-Coenzyme A acetyltransferase 2 (acetoacetyl Coenzyme A thiolase)", "acetyl-Coenzyme A acetyltransferase 2"			2475872	Standard	NM_005891		Approved		uc010kjy.3	Q9BWD1	OTTHUMG00000015935	ENST00000367048.4:c.738C>T	chr6.hg19:g.160197285C>T		90.0	0.0		62.0	15.0	NM_005891	B7Z233|E1P5B1|Q16146|Q5TCL7|Q8TDM4	Silent	SNP	ENST00000367048.4	hg19	CCDS5268.1																																																																																			.	.		0.393	ACAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042912.1	NM_005891		T	160197285	C	T	160197285	2	4	291	1	0	0	0	0	0	0	0	1	122	813	29	3		3	ACAT2	6	160197285	Silent	SNP	C	TCGA-G3-A7M6-01A-11D-A33Q-10	21541441	160197285	10917782	38	42676										
ZNF736	728927	hgsc.bcm.edu	37	chr7	63796756	63796756	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	gagaactatggaaacctggtCtccttgggtgagaataactt	11	7	1	2			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr7:63796756C>G	ENST00000423484.2	+	2	245	c.123C>G	c.(121-123)gtC>gtG	p.V41V	ZNF736_ENST00000355095.4_Silent_p.V41V			B4DX44	ZN736_HUMAN	zinc finger protein 736	41	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|stomach(1)|urinary_tract(1)	9						GAAACCTGGTCTCCTTGGGTG	0.383																																					p.V41V		Atlas-SNP	.											.	ZNF736	33	.	0			c.C123G						.						63	64	64					7																	63796756		692	1591	2283	SO:0001819	synonymous_variant	728927	exon3			CCTGGTCTCCTTG		CCDS55114.1	7q11.21	2013-01-08			ENSG00000234444	ENSG00000234444		"Zinc fingers, C2H2-type", "-"	32467	protein-coding gene	gene with protein product							Standard	XM_006716104		Approved		uc011kdo.2	B4DX44	OTTHUMG00000156537	ENST00000423484.2:c.123C>G	chr7.hg19:g.63796756C>G		27.0	0.0		25.0	6.0	NM_001170905		Silent	SNP	ENST00000423484.2	hg19	CCDS55114.1																																																																																			.	.		0.383	ZNF736-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000344559.2	NM_001170905		G	63796756	C	G	63796756	2	3	291	1	0	0	0	0	0	0	0	1	18140	900	32	4		4	ZNF736	7	63796756	Silent	SNP	C	TCGA-G3-A7M6-01A-11D-A33Q-10		63796756	95341907	39	42677										
ZNF107	51427	hgsc.bcm.edu	37	chr7	64167242	64167242	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	aattcatactgaagagaaacCcaacaaatgtgaagaatgtg	8	6	1	4	rs199803183		TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr7:64167242C>A	ENST00000395391.1	+	4	1935	c.560C>A	c.(559-561)cCc>cAc	p.P187H	ZNF107_ENST00000344930.3_Missense_Mutation_p.P187H|ZNF107_ENST00000423627.1_Missense_Mutation_p.P187H			Q9UII5	ZN107_HUMAN	zinc finger protein 107	187					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(18)|ovary(1)|stomach(1)	37		Lung NSC(55;0.00948)|all_lung(88;0.0249)				GAAGAGAAACCCAACAAATGT	0.368																																					p.P187H		Atlas-SNP	.											.	ZNF107	107	.	0			c.C560A						.						34	37	36					7																	64167242		2200	4299	6499	SO:0001583	missense	51427	exon7			AGAAACCCAACAA	AB027251	CCDS5527.1, CCDS75605.1, CCDS75606.1	7q11.2	2013-01-08	2007-06-26			ENSG00000196247		"Zinc fingers, C2H2-type"	12887	protein-coding gene	gene with protein product		603989	"zinc finger protein 588", "zinc finger protein 107 (Y8)"	ZNF588		8467795	Standard	NM_016220		Approved	ZFD25, smap-7	uc003tte.3	Q9UII5		ENST00000395391.1:c.560C>A	chr7.hg19:g.64167242C>A	ENSP00000378789:p.Pro187His	63.0	0.0		73.0	27.0	NM_016220		Missense_Mutation	SNP	ENST00000395391.1	hg19	CCDS5527.1	.	.	.	.	.	.	.	.	.	.	.	12.13	1.847049	0.32606	.	.	ENSG00000196247	ENST00000344930;ENST00000423627;ENST00000395391	T;T;T	0.29397	1.57;1.57;1.57	1.38	1.38	0.22167	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.47097	0.1427	M	0.88310	2.945	0.36086	D	0.843146	D	0.55800	0.973	P	0.52267	0.694	T	0.61078	-0.7135	8	.	.	.	.	8.2014	0.31428	0.0:1.0:0.0:0.0	.	187	Q9UII5	ZN107_HUMAN	H	187	ENSP00000343443:P187H;ENSP00000400037:P187H;ENSP00000378789:P187H	.	P	+	2	0	ZNF107	63804677	0.058000	0.20735	0.010000	0.14722	0.037000	0.13140	1.469000	0.35343	0.712000	0.32039	0.448000	0.29417	CCC	.	C|0.999;T|0.001		0.368	ZNF107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251593.1	NM_016220		A	64167242	C	A	64167242	3	1	291	1	0	0	0	0	1	0	0	0	17730	623	22	3	566	3	ZNF107	7	64167242	Missense_Mutation	SNP	C	TCGA-G3-A7M6-01A-11D-A33Q-10	370486	64167242	94971421	40	42678										
WRN	7486	hgsc.bcm.edu	37	chr8	31030549	31030549	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	aagagacgattacctgtgtgGtttgccaaaggaagtgatac	12	6	0	2			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr8:31030549G>A	ENST00000298139.5	+	35	4479	c.4230G>A	c.(4228-4230)tgG>tgA	p.W1410*	RP11-363L24.3_ENST00000523365.1_RNA|RP11-363L24.3_ENST00000521252.1_RNA	NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN	Werner syndrome, RecQ helicase-like	1410					aging (GO:0007568)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to starvation (GO:0009267)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|double-strand break repair (GO:0006302)|multicellular organismal aging (GO:0010259)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleolus to nucleoplasm transport (GO:0032066)|positive regulation of hydrolase activity (GO:0051345)|regulation of apoptotic process (GO:0042981)|regulation of growth rate (GO:0040009)|replication fork processing (GO:0031297)|replicative cell aging (GO:0001302)|response to oxidative stress (GO:0006979)|response to UV-C (GO:0010225)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	3'-5' DNA helicase activity (GO:0043138)|3'-5' exonuclease activity (GO:0008408)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|exonuclease activity (GO:0004527)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|Y-form DNA binding (GO:0000403)			central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(13)|lung(28)|ovary(3)|skin(3)|upper_aerodigestive_tract(3)	60		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		TACCTGTGTGGTTTGCCAAAG	0.368			"Mis, N, F, S"			"osteosarcoma, meningioma, others"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome																												p.W1410X	Ovarian(18;161 598 2706 14834 27543)	Atlas-SNP	.	yes	Rec		Werner Syndrome	8	8p12-p11.2	7486	Werner syndrome (RECQL2)		"L, E, M, O"	.	WRN	116	.	0			c.G4230A						.						97	92	94					8																	31030549		2203	4300	6503	SO:0001587	stop_gained	7486	exon35	Familial Cancer Database	WS, Adult Progeria	TGTGTGGTTTGCC		CCDS6082.1	8p12	2014-09-17	2009-03-19		ENSG00000165392	ENSG00000165392			12791	protein-coding gene	gene with protein product		604611	"Werner syndrome"			9288107	Standard	NM_000553		Approved	RECQL2, RECQ3	uc003xio.4	Q14191	OTTHUMG00000163894	ENST00000298139.5:c.4230G>A	chr8.hg19:g.31030549G>A	ENSP00000298139:p.Trp1410*	80.0	0.0		35.0	16.0	NM_000553	A1KYY9	Nonsense_Mutation	SNP	ENST00000298139.5	hg19	CCDS6082.1	.	.	.	.	.	.	.	.	.	.	G	40	8.441325	0.98813	.	.	ENSG00000165392	ENST00000298139	.	.	.	3.96	3.96	0.45880	.	0.000000	0.52532	D	0.000076	.	.	.	.	.	.	0.53005	D	0.999968	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.9772	11.8351	0.52319	0.0:0.0:1.0:0.0	.	.	.	.	X	1410	.	ENSP00000298139:W1410X	W	+	3	0	WRN	31150091	1.000000	0.71417	0.985000	0.45067	0.042000	0.13812	3.470000	0.53100	2.501000	0.84356	0.591000	0.81541	TGG	.	.		0.368	WRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376248.1			A	31030549	G	A	31030549	4	1	291	1	0	0	0	0	0	1	0	0	17417	1270	44	3	4364	3	WRN	8	31030549	Nonsense_Mutation	SNP	G	TCGA-G3-A7M6-01A-11D-A33Q-10		31030549	115333473	41	42679										
JPH1	56704	hgsc.bcm.edu	37	chr8	75227318	75227318	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	tcttgttatttgcccactccCcttcatacttcatgccattg	4	14	3	0			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr8:75227318C>G	ENST00000342232.4	-	2	957	c.917G>C	c.(916-918)gGg>gCg	p.G306A		NM_020647.2	NP_065698.1	Q9HDC5	JPH1_HUMAN	junctophilin 1	306					calcium ion transport into cytosol (GO:0060402)|muscle organ development (GO:0007517)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	24	Breast(64;0.00576)		BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.0728)|all cancers(69;0.176)			TGCCCACTCCCCTTCATACTT	0.522																																					p.G306A		Atlas-SNP	.											.	JPH1	77	.	0			c.G917C						.						132	129	130					8																	75227318		2203	4300	6503	SO:0001583	missense	56704	exon2			CACTCCCCTTCAT	AB042634	CCDS6217.1	8q21	2008-07-03			ENSG00000104369	ENSG00000104369			14201	protein-coding gene	gene with protein product		605266				10891348, 10949023	Standard	XM_005251273		Approved	JP-1	uc003yae.3	Q9HDC5	OTTHUMG00000164524	ENST00000342232.4:c.917G>C	chr8.hg19:g.75227318C>G	ENSP00000344488:p.Gly306Ala	133.0	0.0		176.0	34.0	NM_020647	B2RTZ0	Missense_Mutation	SNP	ENST00000342232.4	hg19	CCDS6217.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.812911	0.90707	.	.	ENSG00000104369	ENST00000342232	D	0.95482	-3.72	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	D	0.98538	0.9512	H	0.95079	3.62	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99349	1.0914	10	0.87932	D	0	.	19.1608	0.93531	0.0:1.0:0.0:0.0	.	306	Q9HDC5	JPH1_HUMAN	A	306	ENSP00000344488:G306A	ENSP00000344488:G306A	G	-	2	0	JPH1	75389873	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.597000	0.82733	2.749000	0.94314	0.655000	0.94253	GGG	.	.		0.522	JPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379102.1			G	75227318	C	G	75227318	3	3	291	1	0	0	0	0	1	0	0	0	7969	623	22	4	1084	4	JPH1	8	75227318	Missense_Mutation	SNP	C	TCGA-G3-A7M6-01A-11D-A33Q-10	44196769	75227318	71136704	42	42680										
C9orf93	203238	hgsc.bcm.edu	37	chr9	15777776	15777776	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	gcccatggacttcataaagtAaacacactggccctgaaata	7	11	1	1			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr9:15777776A>G	ENST00000380701.3	+	19	3178	c.2850A>G	c.(2848-2850)gtA>gtG	p.V950V	CCDC171_ENST00000297641.3_Silent_p.V950V|RNU6-14P_ENST00000384630.1_RNA	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	950																	TTCATAAAGTAAACACACTGG	0.408																																					p.V950V		Atlas-SNP	.											.	.	.	.	0			c.A2850G						.						77	79	78					9																	15777776		2203	4300	6503	SO:0001819	synonymous_variant	203238	exon19			TAAAGTAAACACA	AY422473	CCDS6481.1	9p22.2	2012-03-26	2012-03-26	2012-03-26	ENSG00000164989	ENSG00000164989			29828	protein-coding gene	gene with protein product	"myosin tail domain containing protein"		"chromosome 9 open reading frame 93"	C9orf93		14702039	Standard	NM_173550		Approved	FLJ39267, FLJ46740, Em:AL513423.1, bA778P13.1, bA536D16.1	uc003zmd.3	Q6TFL3	OTTHUMG00000019584	ENST00000380701.3:c.2850A>G	chr9.hg19:g.15777776A>G		72.0	0.0		62.0	29.0	NM_173550	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	Silent	SNP	ENST00000380701.3	hg19	CCDS6481.1																																																																																			.	.		0.408	CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051768.4	NM_173550		G	15777776	A	G	15777776	2	3	291	1	0	0	0	0	0	0	0	1	2508	349	13	2		2	C9orf93	9	15777776	Silent	SNP	A	TCGA-G3-A7M6-01A-11D-A33Q-10		15777776	125435655	43	42681										
CNTLN	54875	hgsc.bcm.edu	37	chr9	17342344	17342344	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	actgaaatcaggaaaataaaGagagcagatccccaacaact	7	9	1	3			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr9:17342344G>T	ENST00000380647.3	+	12	1872	c.1788G>T	c.(1786-1788)aaG>aaT	p.K596N	CNTLN_ENST00000262360.5_Missense_Mutation_p.K596N|CNTLN_ENST00000425824.1_Missense_Mutation_p.K596N			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	596					centriole-centriole cohesion (GO:0010457)|protein localization to organelle (GO:0033365)	centriole (GO:0005814)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)|protein binding, bridging (GO:0030674)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(6)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53				GBM - Glioblastoma multiforme(50;6.14e-10)		GGAAAATAAAGAGAGCAGATC	0.323																																					p.K596N		Atlas-SNP	.											.	CNTLN	128	.	0			c.G1788T						.						67	63	64					9																	17342344		1828	4076	5904	SO:0001583	missense	54875	exon12			AATAAAGAGAGCA	AK000283	CCDS43789.1, CCDS47953.1	9p22.2-p22.1	2008-11-11	2008-02-08	2008-02-08	ENSG00000044459	ENSG00000044459			23432	protein-coding gene	gene with protein product		611870	"chromosome 9 open reading frame 101", "chromosome 9 open reading frame 39"	C9orf101, C9orf39		18086554	Standard	XM_005251492		Approved	FLJ20276, bA340N12.1, OTTHUMG00000019597	uc003zmy.3	Q9NXG0	OTTHUMG00000019599	ENST00000380647.3:c.1788G>T	chr9.hg19:g.17342344G>T	ENSP00000370021:p.Lys596Asn	193.0	0.0		140.0	45.0	NM_017738	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Missense_Mutation	SNP	ENST00000380647.3	hg19	CCDS43789.1	.	.	.	.	.	.	.	.	.	.	G	13.02	2.112371	0.37242	.	.	ENSG00000044459	ENST00000380647;ENST00000425824;ENST00000262360	T;T;T	0.11821	2.74;2.74;2.74	5.45	5.45	0.79879	.	.	.	.	.	T	0.15132	0.0365	L	0.56769	1.78	0.37828	D	0.928632	P;P;P	0.41848	0.634;0.763;0.763	B;B;B	0.36608	0.167;0.229;0.167	T	0.04467	-1.0949	9	0.48119	T	0.1	.	12.6018	0.56501	0.0759:0.0:0.9241:0.0	.	596;596;596	Q9NXG0;C9J1F9;Q9NXG0-2	CNTLN_HUMAN;.;.	N	596	ENSP00000370021:K596N;ENSP00000392798:K596N;ENSP00000262360:K596N	ENSP00000262360:K596N	K	+	3	2	CNTLN	17332344	1.000000	0.71417	0.978000	0.43139	0.495000	0.33615	2.644000	0.46613	2.550000	0.86006	0.563000	0.77884	AAG	.	.		0.323	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738		T	17342344	G	T	17342344	3	4	291	1	0	0	0	0	1	0	0	0	3641	933	33	3	1864	3	CNTLN	9	17342344	Missense_Mutation	SNP	G	TCGA-G3-A7M6-01A-11D-A33Q-10	1564568	17342344	123871087	44	42682										
HKDC1	80201	hgsc.bcm.edu	37	chr10	71025434	71025434	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	atcgtggtgaaggaggtgtgCggagccgtgtcccggcgggc	20	9	0	1	rs373165480		TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr10:71025434C>T	ENST00000354624.5	+	17	2599	c.2466C>T	c.(2464-2466)tgC>tgT	p.C822C	RP11-227H15.5_ENST00000413220.1_RNA	NM_025130.3	NP_079406	Q2TB90	HKDC1_HUMAN	hexokinase domain containing 1	822	Hexokinase type-2 2.				carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)	cytosol (GO:0005829)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|mannokinase activity (GO:0019158)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						AGGAGGTGTGCGGAGCCGTGT	0.642													C|||	1	0.000199681	0	0	5008	,	,		16556	0		0	False		,,,				2504	0.001				p.C822C		Atlas-SNP	.											.	HKDC1	98	.	0			c.C2466T						.						58	55	56					10																	71025434		2203	4299	6502	SO:0001819	synonymous_variant	80201	exon17			GGTGTGCGGAGCC		CCDS7288.1	10q22.1	2006-10-24			ENSG00000156510	ENSG00000156510			23302	protein-coding gene	gene with protein product						12477932	Standard	NM_025130		Approved	FLJ37767, FLJ22761	uc001jpf.4	Q2TB90	OTTHUMG00000018371	ENST00000354624.5:c.2466C>T	chr10.hg19:g.71025434C>T		87.0	0.0		80.0	38.0	NM_025130	B5MDN9|Q2TB91|Q5VTC7|Q7Z373|Q8WU37|Q96EH2|Q9H5Y9	Silent	SNP	ENST00000354624.5	hg19	CCDS7288.1																																																																																			.	.		0.642	HKDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048389.1	NM_025130		T	71025434	C	T	71025434	2	4	291	1	0	0	0	0	0	0	0	1	7202	776	27	1		1	HKDC1	10	71025434	Silent	SNP	C	TCGA-G3-A7M6-01A-11D-A33Q-10		71025434	64509313	45	42683										
ANO9	338440	hgsc.bcm.edu	37	chr11	428795	428795	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	atggccggagcttgtagtcgGggcagttaatgagctgaagt	16	6	0	2			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr11:428795G>A	ENST00000332826.6	-	12	1031	c.947C>T	c.(946-948)cCc>cTc	p.P316L		NM_001012302.2	NP_001012302	A1A5B4	ANO9_HUMAN	anoctamin 9	316					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|negative regulation of intracellular calcium activated chloride channel activity (GO:1902939)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)			central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|lung(5)|ovary(1)|prostate(4)|skin(4)	21						CTTGTAGTCGGGGCAGTTAAT	0.612																																					p.P316L		Atlas-SNP	.											.	ANO9	61	.	0			c.C947T						.						254	185	209					11																	428795		2198	4296	6494	SO:0001583	missense	338440	exon12			TAGTCGGGGCAGT	U33271	CCDS31326.1	11p15.5	2014-04-09	2008-08-28	2008-08-28	ENSG00000185101	ENSG00000185101		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	20679	protein-coding gene	gene with protein product			"tumor protein p53 inducible protein 5", "transmembrane protein 16J"	TP53I5, TMEM16J		9305847, 24692353	Standard	NM_001012302		Approved	PIG5	uc001lpi.2	A1A5B4	OTTHUMG00000165446	ENST00000332826.6:c.947C>T	chr11.hg19:g.428795G>A	ENSP00000332788:p.Pro316Leu	60.0	0.0		42.0	12.0	NM_001012302	B3KUC4|B4E134|Q8TEN4	Missense_Mutation	SNP	ENST00000332826.6	hg19	CCDS31326.1	.	.	.	.	.	.	.	.	.	.	G	3.960	-0.010449	0.07727	.	.	ENSG00000185101	ENST00000332826	T	0.62232	0.04	3.62	2.68	0.31781	.	4.560930	0.00622	N	0.000454	T	0.55689	0.1936	L	0.41710	1.295	0.09310	N	1	B;B	0.19200	0.013;0.034	B;B	0.18561	0.009;0.022	T	0.32666	-0.9898	10	0.23891	T	0.37	.	8.9508	0.35788	0.0877:0.15:0.7623:0.0	.	17;316	A1A5B4-2;A1A5B4	.;ANO9_HUMAN	L	316	ENSP00000332788:P316L	ENSP00000332788:P316L	P	-	2	0	ANO9	418795	0.016000	0.18221	0.021000	0.16686	0.037000	0.13140	1.853000	0.39358	0.848000	0.35191	0.462000	0.41574	CCC	.	.		0.612	ANO9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384116.1	NM_001012302		A	428795	G	A	428795	3	1	291	1	0	0	0	0	1	0	0	0	704	1232	43	3	1449	3	ANO9	11	428795	Missense_Mutation	SNP	G	TCGA-G3-A7M6-01A-11D-A33Q-10		428795	134577721	46	42684										
SYT9	143425	hgsc.bcm.edu	37	chr11	7273526	7273526	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	gccaggatttcatttaccacCtgcgggaccgtgccagaccc	10	15	1	1	rs146068689		TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr11:7273526C>T	ENST00000318881.6	+	1	346	c.109C>T	c.(109-111)Ctg>Ttg	p.L37L	SYT9_ENST00000396716.2_Intron	NM_175733.3	NP_783860.1	Q86SS6	SYT9_HUMAN	synaptotagmin IX	37					positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of insulin secretion (GO:0050796)	cell junction (GO:0030054)|dense core granule (GO:0031045)|integral component of membrane (GO:0016021)|secretory granule membrane (GO:0030667)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)			NS(1)|endometrium(2)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	38				Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)		CATTTACCACCTGCGGGACCG	0.716																																					p.L37L		Atlas-SNP	.											.	SYT9	91	.	0			c.C109T						.						13	13	13					11																	7273526		2156	4206	6362	SO:0001819	synonymous_variant	143425	exon1			TACCACCTGCGGG	AK055003	CCDS7778.1	11p15.4	2013-01-21			ENSG00000170743	ENSG00000170743		"Synaptotagmins"	19265	protein-coding gene	gene with protein product		613528				11543631	Standard	NM_175733		Approved		uc001mfe.3	Q86SS6	OTTHUMG00000165499	ENST00000318881.6:c.109C>T	chr11.hg19:g.7273526C>T		52.0	0.0		57.0	23.0	NM_175733		Silent	SNP	ENST00000318881.6	hg19	CCDS7778.1																																																																																			.	C|1.000;G|0.000		0.716	SYT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384483.1	NM_175733		T	7273526	C	T	7273526	2	4	291	1	0	0	0	0	0	0	0	1	15496	680	24	3		3	SYT9	11	7273526	Silent	SNP	C	TCGA-G3-A7M6-01A-11D-A33Q-10	6844731	7273526	127732990	47	42685										
OR5D18	219438	hgsc.bcm.edu	37	chr11	55587833	55587833	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	caaagccttctccacctgtgCctcccacctgactgccatca	5	19	2	1			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr11:55587833C>T	ENST00000333976.4	+	1	748	c.728C>T	c.(727-729)gCc>gTc	p.A243V		NM_001001952.1	NP_001001952.1	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D, member 18	243						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(3)|large_intestine(6)|lung(33)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		all_epithelial(135;0.208)				TCCACCTGTGCCTCCCACCTG	0.517																																					p.A243V		Atlas-SNP	.											.	OR5D18	121	.	0			c.C728T						.						131	112	119					11																	55587833		2200	4296	6496	SO:0001583	missense	219438	exon1			CCTGTGCCTCCCA	AB065781	CCDS31510.1	11q11	2012-08-09			ENSG00000186119	ENSG00000186119		"GPCR / Class A : Olfactory receptors"	15285	protein-coding gene	gene with protein product							Standard	NM_001001952		Approved		uc010rin.2	Q8NGL1	OTTHUMG00000166811	ENST00000333976.4:c.728C>T	chr11.hg19:g.55587833C>T	ENSP00000335025:p.Ala243Val	87.0	0.0		70.0	20.0	NM_001001952	Q6IF67|Q6IFD3|Q96RB3	Missense_Mutation	SNP	ENST00000333976.4	hg19	CCDS31510.1	.	.	.	.	.	.	.	.	.	.	.	15.83	2.948752	0.53186	.	.	ENSG00000186119	ENST00000333976	T	0.38560	1.13	4.9	1.92	0.25849	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39210	N	0.001428	T	0.51143	0.1657	M	0.74389	2.26	0.26071	N	0.981222	P	0.37330	0.59	P	0.51079	0.658	T	0.48768	-0.9006	10	0.66056	D	0.02	-12.1998	4.7313	0.12966	0.1443:0.4973:0.2798:0.0786	.	243	Q8NGL1	OR5DI_HUMAN	V	243	ENSP00000335025:A243V	ENSP00000335025:A243V	A	+	2	0	OR5D18	55344409	0.000000	0.05858	0.966000	0.40874	0.964000	0.63967	-0.131000	0.10482	0.211000	0.20683	0.573000	0.79308	GCC	.	.		0.517	OR5D18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391515.1	NM_001001952		T	55587833	C	T	55587833	3	4	291	1	0	0	0	0	1	0	0	0	11166	739	26	3	730	3	OR5D18	11	55587833	Missense_Mutation	SNP	C	TCGA-G3-A7M6-01A-11D-A33Q-10	48314307	55587833	79418683	48	42686										
OR5B12	390191	hgsc.bcm.edu	37	chr11	58207024	58207025	+	Missense_Mutation	DNP	CC	CC	AA													0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	aaagaggtcattgaatcccaCcacaaaaaaaataaccatct							TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr11:58207024_58207025CC>AA	ENST00000302572.2	-	1	621_622	c.600_601GG>TT	c.(598-603)gtGGtg>gtTTtg	p.V201L		NM_001004733.2	NP_001004733.1	Q96R08	OR5BC_HUMAN	olfactory receptor, family 5, subfamily B, member 12	201						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(6)|liver(1)|lung(28)|ovary(1)|prostate(3)|skin(1)	40	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				TTGAATCCCACCACAAAAAAAA	0.396																																					p.V201L|p.V200V		Atlas-SNP	.											.	OR5B12	80	.	0			c.G601T|c.G600T						.																																			SO:0001583	missense	390191	exon1			ATCCCACCACAAA|TCCCACCACAAAA	AB065851	CCDS31551.1	11q12.1	2012-08-09		2004-03-10	ENSG00000172362	ENSG00000172362		"GPCR / Class A : Olfactory receptors"	15432	protein-coding gene	gene with protein product				OR5B12P, OR5B16		12213199	Standard	NM_001004733		Approved	OST743	uc010rkh.2	Q96R08	OTTHUMG00000167543	ENST00000302572.2:c.600_601delinsAA	chr11.hg19:g.58207024_58207025delinsAA	ENSP00000306657:p.Val201Leu	106.0|105.0	0.0		94.0|95.0	44.0	NM_001004733	B2RNL2|Q6IEV5	Missense_Mutation|Silent	SNP	ENST00000302572.2	hg19	CCDS31551.1																																																																																			.	.		0.396	OR5B12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394987.1	NM_001004733		AA	58207025	CC	AA	58207024	3	1	291	1	0	0	0	0	1	0	0	0	11157	507	18	3	347	3	OR5B12	11	58207024	Missense_Mutation	DNP	CC	TCGA-G3-A7M6-01A-11D-A33Q-10	2619191	58207024	76799492	49	42687										
VWF	7450	hgsc.bcm.edu	37	chr12	6125791	6125791	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	atggtggtgatgcttccataCtgcagcactgacacctgagt	11	10	0	3			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr12:6125791C>T	ENST00000261405.5	-	30	5456	c.5202G>A	c.(5200-5202)caG>caA	p.Q1734Q		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	1734	VWFA 3; main binding site for collagens type I and III. {ECO:0000255|PROSITE- ProRule:PRU00219}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	TGCTTCCATACTGCAGCACTG	0.537																																					p.Q1734Q		Atlas-SNP	.											.	VWF	338	.	0			c.G5202A						.						86	80	82					12																	6125791		2203	4300	6503	SO:0001819	synonymous_variant	7450	exon30			TCCATACTGCAGC		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"Endogenous ligands"	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.5202G>A	chr12.hg19:g.6125791C>T		102.0	0.0		111.0	28.0	NM_000552	Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	hg19	CCDS8539.1																																																																																			.	.		0.537	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		T	6125791	C	T	6125791	2	4	291	1	0	0	0	0	0	0	0	1	17261	564	20	3		3	VWF	12	6125791	Silent	SNP	C	TCGA-G3-A7M6-01A-11D-A33Q-10		6125791	127726104	50	42688										
GCN1L1	10985	hgsc.bcm.edu	37	chr12	120580319	120580320	+	Frame_Shift_Ins	INS	-	-	A													0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	aggaaactcaccgttctcttINSatctgcacacgtgctggcca							TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr12:120580319_120580320insA	ENST00000300648.6	-	44	5832_5833	c.5820_5821insT	c.(5818-5823)gataagfs	p.K1941fs		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	1941					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					ACCGTTCTCTTATCTGCACACG	0.569																																					p.K1941_R1942delinsX		Atlas-Indel,Pindel	.											.	GCN1L1	207	.	0			c.5821_5822insT						.																																			SO:0001589	frameshift_variant	10985	exon44			.	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.5821dupT	chr12.hg19:g.120580320_120580320dupA	ENSP00000300648:p.Lys1941fs	87.0	0.0		90.0	36.0	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Frame_Shift_Ins	INS	ENST00000300648.6	hg19	CCDS41847.1																																																																																			.	.		0.569	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1			A	120580320	-	A	120580319	7	5	291	1	0	1	1	0	0	0	0	0	6307	1763	61	0	2254	0	GCN1L1	12	120580319	Frame_Shift_Ins	INS	-	TCGA-G3-A7M6-01A-11D-A33Q-10	114454528	120580319	13271576	51	42689										
NPAS3	64067	hgsc.bcm.edu	37	chr14	33684417	33684417	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	attgagaaaggagaaatcccGagatgctgctcgctcccgcc	11	12	0	3			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr14:33684417G>T	ENST00000356141.4	+	3	170	c.170G>T	c.(169-171)cGa>cTa	p.R57L	NPAS3_ENST00000341321.4_Missense_Mutation_p.R57L|NPAS3_ENST00000548645.1_Missense_Mutation_p.R27L|NPAS3_ENST00000547068.1_5'UTR|NPAS3_ENST00000346562.2_Missense_Mutation_p.R27L|NPAS3_ENST00000551008.1_5'Flank|NPAS3_ENST00000357798.5_Missense_Mutation_p.R27L|NPAS3_ENST00000551492.1_Missense_Mutation_p.R64L			Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3	57	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|positive regulation of transcription, DNA-templated (GO:0045893)|startle response (GO:0001964)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(4)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	40	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)		GAGAAATCCCGAGATGCTGCT	0.443																																					p.R57L		Atlas-SNP	.											.	NPAS3	266	.	0			c.G170T						.						54	61	59					14																	33684417		2203	4300	6503	SO:0001583	missense	64067	exon3			AATCCCGAGATGC	AF164438	CCDS9645.1, CCDS53891.1, CCDS53892.1, CCDS55912.1	14q13.1	2013-08-23			ENSG00000151322	ENSG00000151322		"Basic helix-loop-helix proteins"	19311	protein-coding gene	gene with protein product		609430					Standard	NM_022123		Approved	MOP6, PASD6, bHLHe12	uc001wru.3	Q8IXF0	OTTHUMG00000140215	ENST00000356141.4:c.170G>T	chr14.hg19:g.33684417G>T	ENSP00000348460:p.Arg57Leu	93.0	0.0		95.0	26.0	NM_001164749	Q86US6|Q86US7|Q8IXF2|Q9BY81|Q9H323|Q9Y4L8	Missense_Mutation	SNP	ENST00000356141.4	hg19	CCDS53891.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.892889	0.91889	.	.	ENSG00000151322	ENST00000551634;ENST00000551492;ENST00000346562;ENST00000341321;ENST00000548645;ENST00000356141;ENST00000357798	T;T;T;D;T;T;T	0.97924	3.19;2.0;3.14;-4.61;3.13;2.0;2.98	5.96	5.96	0.96718	Helix-loop-helix DNA-binding (4);	0.000000	0.56097	D	0.000025	D	0.98617	0.9537	M	0.71871	2.18	0.80722	D	1	D;D;D;D	0.76494	0.999;0.998;0.999;0.999	D;D;D;D	0.79108	0.992;0.981;0.992;0.992	D	0.99486	1.0949	10	0.87932	D	0	.	20.4008	0.98991	0.0:0.0:1.0:0.0	.	27;57;27;27	Q8IXF0-2;Q8IXF0;Q8IXF0-4;Q8IXF0-3	.;NPAS3_HUMAN;.;.	L	34;64;27;57;27;57;27	ENSP00000448373:R34L;ENSP00000450392:R64L;ENSP00000319610:R27L;ENSP00000344158:R57L;ENSP00000448916:R27L;ENSP00000348460:R57L;ENSP00000350446:R27L	ENSP00000344158:R57L	R	+	2	0	NPAS3	32754168	1.000000	0.71417	1.000000	0.80357	0.833000	0.47200	9.845000	0.99498	2.826000	0.97356	0.655000	0.94253	CGA	.	.		0.443	NPAS3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276645.1			T	33684417	G	T	33684417	3	4	291	1	0	0	0	0	1	0	0	0	10573	1058	37	1	180	1	NPAS3	14	33684417	Missense_Mutation	SNP	G	TCGA-G3-A7M6-01A-11D-A33Q-10		33684417	73665123	52	42690										
OTX2	5015	hgsc.bcm.edu	37	chr14	57268479	57268479	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	aacctggaatttccacgaggAtgtctgatctttataatcca	7	9	2	1			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr14:57268479A>T	ENST00000555006.1	-	4	1252	c.844T>A	c.(844-846)Tcc>Acc	p.S282T	RP11-1085N6.6_ENST00000602485.1_lincRNA|OTX2_ENST00000408990.3_Missense_Mutation_p.S282T|OTX2_ENST00000339475.5_Missense_Mutation_p.S290T			P32243	OTX2_HUMAN	orthodenticle homeobox 2	282					axon guidance (GO:0007411)|cell fate specification (GO:0001708)|diencephalon morphogenesis (GO:0048852)|dorsal/ventral pattern formation (GO:0009953)|endoderm development (GO:0007492)|eye photoreceptor cell fate commitment (GO:0042706)|forebrain development (GO:0030900)|inner ear morphogenesis (GO:0042472)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|neuron fate determination (GO:0048664)|positive regulation of embryonic development (GO:0040019)|positive regulation of gastrulation (GO:2000543)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|primitive streak formation (GO:0090009)|protein complex assembly (GO:0006461)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of smoothened signaling pathway (GO:0008589)|somite rostral/caudal axis specification (GO:0032525)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|nucleus (GO:0005634)|protein complex (GO:0043234)	eukaryotic initiation factor 4E binding (GO:0008190)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	19	Medulloblastoma(1;0.00184)|all_neural(1;0.00414)					TTCCACGAGGATGTCTGATCT	0.413																																					p.S290T		Atlas-SNP	.											.	OTX2	47	.	0			c.T868A						.						64	68	67					14																	57268479		2203	4300	6503	SO:0001583	missense	5015	exon3			ACGAGGATGTCTG	AF298117	CCDS9728.1, CCDS41960.1	14q22.3	2014-09-17	2007-02-15		ENSG00000165588	ENSG00000165588		"Homeoboxes / PRD class"	8522	protein-coding gene	gene with protein product		600037	"orthodenticle homolog 2 (Drosophila)"			7959790	Standard	NM_021728		Approved		uc031qor.1	P32243	OTTHUMG00000152338	ENST00000555006.1:c.844T>A	chr14.hg19:g.57268479A>T	ENSP00000452336:p.Ser282Thr	101.0	0.0		72.0	33.0	NM_001270525	B2RAN5|Q6GTV3|Q9HAW3|Q9P2R1	Missense_Mutation	SNP	ENST00000555006.1	hg19	CCDS41960.1	.	.	.	.	.	.	.	.	.	.	A	12.32	1.901855	0.33535	.	.	ENSG00000165588	ENST00000339475;ENST00000408990;ENST00000555006	D;D;D	0.90444	-2.67;-2.65;-2.65	5.65	5.65	0.86999	.	0.312780	0.23272	N	0.050008	D	0.82788	0.5113	N	0.11560	0.145	0.35723	D	0.81732	B;B	0.12013	0.005;0.001	B;B	0.10450	0.004;0.005	T	0.82592	-0.0381	10	0.72032	D	0.01	.	15.2098	0.73214	1.0:0.0:0.0:0.0	.	290;282	F1T0D1;P32243	.;OTX2_HUMAN	T	290;282;282	ENSP00000343819:S290T;ENSP00000386185:S282T;ENSP00000452336:S282T	ENSP00000343819:S290T	S	-	1	0	OTX2	56338232	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.231000	0.78106	2.371000	0.80710	0.533000	0.62120	TCC	.	.		0.413	OTX2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411522.1	NM_021728.		T	57268479	A	T	57268479	3	4	291	1	0	0	0	0	1	0	0	0	11330	333	12	4	29	4	OTX2	14	57268479	Missense_Mutation	SNP	A	TCGA-G3-A7M6-01A-11D-A33Q-10	23584062	57268479	50081061	53	42691										
UBE3A	7337	hgsc.bcm.edu	37	chr15	25616615	25616615	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	tctggtgtagacccttctaaTggcatcaatatccacagaca	7	11	3	2			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr15:25616615T>C	ENST00000397954.2	-	4	714	c.715A>G	c.(715-717)Att>Gtt	p.I239V	UBE3A_ENST00000566215.1_Missense_Mutation_p.I216V|UBE3A_ENST00000428984.2_Missense_Mutation_p.I216V|UBE3A_ENST00000232165.3_Missense_Mutation_p.I236V|SNHG14_ENST00000554726.1_RNA|UBE3A_ENST00000438097.1_Missense_Mutation_p.I216V			Q05086	UBE3A_HUMAN	ubiquitin protein ligase E3A	239					androgen receptor signaling pathway (GO:0030521)|brain development (GO:0007420)|ovarian follicle development (GO:0001541)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland growth (GO:0060736)|protein autoubiquitination (GO:0051865)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|proteolysis (GO:0006508)|sperm entry (GO:0035037)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(13)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	38		all_cancers(20;3.47e-21)|Breast(32;0.00123)		all cancers(64;2.78e-08)|Epithelial(43;8.85e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0155)|Lung(196;0.0616)		ACCCTTCTAATGGCATCAATA	0.408																																					p.I239V		Atlas-SNP	.											.	UBE3A	109	.	0			c.A715G						.						148	147	147					15																	25616615		2203	4300	6503	SO:0001583	missense	7337	exon7			TTCTAATGGCATC	AF002224	CCDS32177.1, CCDS45191.1, CCDS45192.1	15q11.2	2014-09-17	2008-07-31		ENSG00000114062	ENSG00000114062	6.3.2.19		12496	protein-coding gene	gene with protein product	"Angelman syndrome"	601623	"human papilloma virus E6-associated protein"	EPVE6AP, HPVE6A		8221889	Standard	NM_130838		Approved	AS, ANCR, E6-AP, FLJ26981	uc001zas.3	Q05086		ENST00000397954.2:c.715A>G	chr15.hg19:g.25616615T>C	ENSP00000381045:p.Ile239Val	59.0	0.0		69.0	29.0	NM_000462	A8K8Z9|P78355|Q93066|Q9UEP4|Q9UEP5|Q9UEP6|Q9UEP7|Q9UEP8|Q9UEP9	Missense_Mutation	SNP	ENST00000397954.2	hg19	CCDS45192.1	.	.	.	.	.	.	.	.	.	.	T	1.304	-0.604168	0.03717	.	.	ENSG00000114062	ENST00000232165;ENST00000356465;ENST00000397954;ENST00000438097;ENST00000428984	T;T;T;T	0.15487	2.42;2.42;2.42;2.42	5.8	0.901	0.19284	.	0.161068	0.56097	N	0.000036	T	0.02688	0.0081	N	0.00210	-1.845	0.32995	D	0.525486	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44907	-0.9297	10	0.02654	T	1	.	8.6434	0.33991	0.0:0.515:0.0:0.485	.	236;239	Q05086-3;Q05086	.;UBE3A_HUMAN	V	236;236;239;216;216	ENSP00000232165:I236V;ENSP00000381045:I239V;ENSP00000411258:I216V;ENSP00000401265:I216V	ENSP00000232165:I236V	I	-	1	0	UBE3A	23167708	0.998000	0.40836	0.761000	0.31378	0.991000	0.79684	2.105000	0.41825	0.121000	0.18284	0.477000	0.44152	ATT	.	.		0.408	UBE3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000434203.1	NM_000462		C	25616615	T	C	25616615	3	2	291	1	0	0	0	0	1	0	0	0	16894	1464	51	2	1944	2	UBE3A	15	25616615	Missense_Mutation	SNP	T	TCGA-G3-A7M6-01A-11D-A33Q-10		25616615	76914777	54	42692										
MGA	23269	hgsc.bcm.edu	37	chr15	41961695	41961695	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	cactctatgcatcgttacctGccgaggcttcatttggtgcc	9	13	2	0			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr15:41961695G>A	ENST00000570161.1	+	1	603	c.603G>A	c.(601-603)ctG>ctA	p.L201L	MGA_ENST00000219905.7_Silent_p.L201L|MGA_ENST00000568630.1_Intron|MGA_ENST00000566586.1_Silent_p.L201L|MGA_ENST00000389936.4_Silent_p.L201L|MGA_ENST00000545763.1_Silent_p.L201L			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	Maltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	ATCGTTACCTGCCGAGGCTTC	0.438																																					p.L201L		Atlas-SNP	.											.	MGA	264	.	0			c.G603A						.						135	133	134					15																	41961695		1979	4159	6138	SO:0001819	synonymous_variant	23269	exon2			TTACCTGCCGAGG	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.603G>A	chr15.hg19:g.41961695G>A		92.0	0.0		90.0	23.0	NM_001080541	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000570161.1	hg19	CCDS55959.1																																																																																			.	.		0.438	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		A	41961695	G	A	41961695	2	1	291	1	0	0	0	0	0	0	0	1	9549	1306	46	3		3	MGA	15	41961695	Silent	SNP	G	TCGA-G3-A7M6-01A-11D-A33Q-10	16345080	41961695	60569697	55	42693										
MYO5C	55930	hgsc.bcm.edu	37	chr15	52521421	52521421	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	ggtgttggagttgcatcttcTcatccttgagagctttaatt	10	7	2	1			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr15:52521421T>C	ENST00000261839.7	-	25	3277	c.3116A>G	c.(3115-3117)gAg>gGg	p.E1039G		NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	1039						extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(7)|large_intestine(15)|lung(12)|ovary(7)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66				all cancers(107;0.0137)		TTGCATCTTCTCATCCTTGAG	0.478																																					p.E1039G		Atlas-SNP	.											.	MYO5C	162	.	0			c.A3116G						.						134	128	130					15																	52521421		1905	4114	6019	SO:0001583	missense	55930	exon25			ATCTTCTCATCCT	AF272390	CCDS42036.1	15q21	2011-09-27				ENSG00000128833		"Myosins / Myosin superfamily : Class V"	7604	protein-coding gene	gene with protein product	"myosin 5C"	610022				11870218	Standard	NM_018728		Approved	MGC74969	uc010bff.3	Q9NQX4		ENST00000261839.7:c.3116A>G	chr15.hg19:g.52521421T>C	ENSP00000261839:p.Glu1039Gly	62.0	0.0		37.0	14.0	NM_018728	Q6P1W8	Missense_Mutation	SNP	ENST00000261839.7	hg19	CCDS42036.1	.	.	.	.	.	.	.	.	.	.	T	18.14	3.558584	0.65538	.	.	ENSG00000128833	ENST00000261839	T	0.18657	2.2	5.88	5.88	0.94601	.	0.058580	0.64402	D	0.000002	T	0.22859	0.0552	N	0.19112	0.55	0.80722	D	1	D	0.56968	0.978	P	0.54499	0.754	T	0.02450	-1.1157	10	0.66056	D	0.02	.	9.8877	0.41272	0.0:0.0754:0.0:0.9246	.	1039	Q9NQX4	MYO5C_HUMAN	G	1039	ENSP00000261839:E1039G	ENSP00000261839:E1039G	E	-	2	0	MYO5C	50308713	1.000000	0.71417	0.963000	0.40424	0.528000	0.34623	4.697000	0.61782	2.243000	0.73865	0.528000	0.53228	GAG	.	.		0.478	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728		C	52521421	T	C	52521421	3	2	291	1	0	0	0	0	1	0	0	0	10089	1551	54	2	2180	2	MYO5C	15	52521421	Missense_Mutation	SNP	T	TCGA-G3-A7M6-01A-11D-A33Q-10	10559726	52521421	50009971	56	42694										
SCAPER	49855	hgsc.bcm.edu	37	chr15	77057677	77057677	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	attaattttcaaatgccagaCcttttacgagagggtgaaga	9	6	1	4			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr15:77057677C>A	ENST00000563290.1	-	13	1709		c.e13+1		SCAPER_ENST00000324767.7_Splice_Site|SCAPER_ENST00000538941.2_Splice_Site			Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER							endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(16)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	39						AAATGCCAGACCTTTTACGAG	0.398																																					.		Atlas-SNP	.											.	SCAPER	160	.	0			c.1613+1G>T						.						73	65	68					15																	77057677		1838	4085	5923	SO:0001630	splice_region_variant	49855	exon13			GCCAGACCTTTTA	AB040887, AF242528	CCDS53961.1, CCDS53962.1	15q24.3	2012-10-05	2009-03-11	2007-08-20	ENSG00000140386	ENSG00000140386		"Zinc fingers, C2H2-type"	13081	protein-coding gene	gene with protein product		611611	"zinc finger protein 291"	ZNF291		17698606	Standard	NM_020843		Approved	Zfp291	uc002bby.3	Q9BY12	OTTHUMG00000172655	ENST00000563290.1:c.1613+1G>T	chr15.hg19:g.77057677C>A		125.0	0.0		95.0	26.0	NM_020843	F5H7X8|H3BNR7|Q3B7X7|Q96BS9|Q9H3D8|Q9NT03|Q9P274	Splice_Site	SNP	ENST00000563290.1	hg19	CCDS53962.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.530342	0.85706	.	.	ENSG00000140386	ENST00000324767;ENST00000538941;ENST00000303521	.	.	.	5.64	5.64	0.86602	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.6939	0.96016	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SCAPER	74844732	1.000000	0.71417	1.000000	0.80357	0.894000	0.52154	7.487000	0.81328	2.660000	0.90430	0.455000	0.32223	.	.	.		0.398	SCAPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419698.1	NM_020843	Intron	A	77057677	C	A	77057677	5	1	291	1	0	0	0	0	0	0	1	0	13893	521	18	3	2668	3	SCAPER	15	77057677	Splice_Site	SNP	C	TCGA-G3-A7M6-01A-11D-A33Q-10	24536256	77057677	25473715	57	42695										
ERI2	6296	hgsc.bcm.edu	37	chr16	20802201	20802219	+	Intron	DEL	GTCCCCTGAGGCCAGATCA	GTCCCCTGAGGCCAGATCA	-													0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	tgctgaagaaaagcatgctgGtcccctgaggccagatcact					rs145561309|rs372613008|rs368001171		TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	GTCCCCTGAGGCCAGATCA	GTCCCCTGAGGCCAGATCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr16:20802201_20802219delGTCCCCTGAGGCCAGATCA	ENST00000289416.5	+	10	1801				ACSM3_ENST00000450120.2_Intron|ACSM3_ENST00000567387.1_Intron|ERI2_ENST00000300005.3_Frame_Shift_Del_p.SDLASGD256fs	NM_005622.3	NP_005613.2	Q53FZ2	ACSM3_HUMAN	acyl-CoA synthetase medium-chain family member 3						cholesterol homeostasis (GO:0042632)|fatty acid biosynthetic process (GO:0006633)|regulation of blood pressure (GO:0008217)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty acid ligase activity (GO:0015645)|metal ion binding (GO:0046872)	p.G261G(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)	21						AAGCATGCTGGTCCCCTGAGGCCAGATCACTGTTCCAGG	0.443																																					p.257_263del		Atlas-Indel,Pindel	.											.	ERI2	50	.	1	Substitution - coding silent(1)	kidney(1)	c.769_787del						.																																			SO:0001627	intron_variant	112479	exon9			.	D16350	CCDS10589.1, CCDS45435.1	16p13.11	2006-02-08	2005-09-08	2005-09-08	ENSG00000005187	ENSG00000005187		"Acyl-CoA synthetase family"	10522	protein-coding gene	gene with protein product		145505	"SA (rat hypertension-associated) homolog", "SA hypertension-associated homolog (rat)"	SAH		7843754, 7907320, 11470804	Standard	NM_005622		Approved	SA	uc002dhr.3	Q53FZ2	OTTHUMG00000131552	ENST00000289416.5:c.1326+191GTCCCCTGAGGCCAGATCA>-	chr16.hg19:g.20802201_20802219delGTCCCCTGAGGCCAGATCA		376.0	0.0		263.0	48.0	NM_080663	O60363|Q13732|Q15425|Q7KYM6|Q9BUA2	Frame_Shift_Del	DEL	ENST00000289416.5	hg19	CCDS10589.1																																																																																			.	.		0.443	ACSM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254414.2	NM_005622		-	20802219	GTCCCCTGAGGCCAGATCA	-	20802201	6	5	291	0	1	1	0	1	0	0	0	0	5230	1252	44	0		0	ERI2	16	20802201	Intron	DEL	GTCCCCTGAGGCCAGATCA	TCGA-G3-A7M6-01A-11D-A33Q-10		20802201	69552552	58	42696										
TRPV3	162514	hgsc.bcm.edu	37	chr17	3446875	3446875	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	cggctgcaaagatgcgcttcTtcagccgcctctttttcctc	8	15	3	1			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr17:3446875T>G	ENST00000576742.1	-	5	680	c.359A>C	c.(358-360)aAg>aCg	p.K120T	TRPV3_ENST00000301365.4_Missense_Mutation_p.K120T|TRPV3_ENST00000572519.1_Missense_Mutation_p.K120T	NM_001258205.1|NM_145068.3	NP_001245134.1|NP_659505.1	Q8NET8	TRPV3_HUMAN	transient receptor potential cation channel, subfamily V, member 3	120					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|negative regulation of hair cycle (GO:0042636)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium channel activity (GO:0005262)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(12)|ovary(5)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	35					Menthol(DB00825)	GATGCGCTTCTTCAGCCGCCT	0.547																																					p.K120T		Atlas-SNP	.											.	TRPV3	85	.	0			c.A359C						.						110	106	108					17																	3446875		2203	4300	6503	SO:0001583	missense	162514	exon5			CGCTTCTTCAGCC	AF514998	CCDS11029.1, CCDS58500.1	17p13.3	2013-01-10			ENSG00000167723	ENSG00000167723		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	18084	protein-coding gene	gene with protein product		607066				12016205, 12077606, 16382100	Standard	NM_001258205		Approved	VRL3	uc002fvr.3	Q8NET8	OTTHUMG00000090695	ENST00000576742.1:c.359A>C	chr17.hg19:g.3446875T>G	ENSP00000461518:p.Lys120Thr	60.0	0.0		26.0	20.0	NM_001258205	Q8NDW7|Q8NET9|Q8NFH2	Missense_Mutation	SNP	ENST00000576742.1	hg19	CCDS11029.1	.	.	.	.	.	.	.	.	.	.	T	13.59	2.283203	0.40394	.	.	ENSG00000167723	ENST00000381913;ENST00000301365;ENST00000430263	D	0.88509	-2.39	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	D	0.92802	0.7711	M	0.64170	1.965	0.35700	D	0.815542	D;B;P;B;D;P;P	0.76494	0.999;0.215;0.946;0.215;0.999;0.713;0.665	D;B;P;B;D;P;B	0.80764	0.994;0.135;0.809;0.135;0.994;0.518;0.384	D	0.95196	0.8312	10	0.59425	D	0.04	-5.1433	12.9536	0.58415	0.0:0.0:0.0:1.0	.	104;104;120;104;120;120;120	E7EV24;B7ZKP9;Q2M3L1;B7ZKP6;Q8NET8-3;Q8NET8;Q8NET8-2	.;.;.;.;.;TRPV3_HUMAN;.	T	120;120;104	ENSP00000301365:K120T	ENSP00000301365:K120T	K	-	2	0	TRPV3	3393625	1.000000	0.71417	1.000000	0.80357	0.101000	0.19017	4.411000	0.59781	2.060000	0.61445	0.459000	0.35465	AAG	.	.		0.547	TRPV3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207379.2	NM_145068		G	3446875	T	G	3446875	3	3	291	1	0	0	0	0	1	0	0	0	16612	1609	56	5	2069	5	TRPV3	17	3446875	Missense_Mutation	SNP	T	TCGA-G3-A7M6-01A-11D-A33Q-10		3446875	77748335	59	42697										
TP53	7157	hgsc.bcm.edu	37	chr17	7578205	7578205	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	gctcatagggcaccaccacaCtatgtcgaaaagtgtttctg	9	11	2	0	rs587782177		TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr17:7578205C>T	ENST00000269305.4	-	6	833	c.644G>A	c.(643-645)aGt>aAt	p.S215N	TP53_ENST00000420246.2_Missense_Mutation_p.S215N|TP53_ENST00000445888.2_Missense_Mutation_p.S215N|TP53_ENST00000413465.2_Missense_Mutation_p.S215N|TP53_ENST00000574684.1_Intron|TP53_ENST00000359597.4_Missense_Mutation_p.S215N|TP53_ENST00000455263.2_Missense_Mutation_p.S215N	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	215	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		S -> C (in sporadic cancers; somatic mutation).|S -> G (in sporadic cancers; somatic mutation).|S -> I (in sporadic cancers; somatic mutation).|S -> K (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|S -> N (in sporadic cancers; somatic mutation).|S -> R (in sporadic cancers; somatic mutation).|S -> T (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.S215I(18)|p.S215N(9)|p.0?(8)|p.?(5)|p.S215T(3)|p.S215fs*32(3)|p.H214fs*5(2)|p.S122N(1)|p.S215fs*27(1)|p.S215del(1)|p.S215fs*29(1)|p.D208_V216delDRNTFRHSV(1)|p.S83I(1)|p.S83N(1)|p.T211_S215delTFRHS(1)|p.D208fs*1(1)|p.S215fs*31(1)|p.T211fs*28(1)|p.R213_S215>X(1)|p.S122I(1)|p.D207_V216del10(1)|p.S215_V218>M(1)|p.R209fs*6(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CACCACCACACTATGTCGAAA	0.537		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.S215N	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,lymphoid_neoplasm,+1,1	TP53	33396	.	64	Substitution - Missense(34)|Deletion - Frameshift(10)|Whole gene deletion(8)|Unknown(5)|Deletion - In frame(4)|Complex - deletion inframe(2)|Complex - frameshift(1)	biliary_tract(10)|oesophagus(10)|lung(9)|large_intestine(6)|ovary(6)|bone(5)|upper_aerodigestive_tract(4)|haematopoietic_and_lymphoid_tissue(4)|central_nervous_system(3)|liver(2)|breast(2)|stomach(1)|kidney(1)|skin(1)	c.G644A						.						125	112	116					17																	7578205		2203	4300	6503	SO:0001583	missense	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	ACCACACTATGTC	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.644G>A	chr17.hg19:g.7578205C>T	ENSP00000269305:p.Ser215Asn	108.0	1.0		51.0	29.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.996533	0.93167	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99854	-7.19;-7.19;-7.19;-7.19;-7.19;-7.19;-7.19;-7.19	5.28	5.28	0.74379	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99825	0.9922	M	0.73598	2.24	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;0.999;0.996;0.999;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	0.993;1.0;0.973;0.992;1.0;1.0;0.999	D	0.96641	0.9474	10	0.87932	D	0	-18.3023	16.7921	0.85592	0.0:1.0:0.0:0.0	.	176;215;215;122;215;215;215	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	N	215;215;215;215;215;215;204;122;83;122;83	ENSP00000410739:S215N;ENSP00000352610:S215N;ENSP00000269305:S215N;ENSP00000398846:S215N;ENSP00000391127:S215N;ENSP00000391478:S215N;ENSP00000425104:S83N;ENSP00000423862:S122N	ENSP00000269305:S215N	S	-	2	0	TP53	7518930	1.000000	0.71417	0.567000	0.28434	0.964000	0.63967	6.042000	0.70996	2.634000	0.89283	0.563000	0.77884	AGT	.	.		0.537	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7578205	C	T	7578205	3	4	291	1	0	0	0	0	1	0	0	0	16396	565	20	3	650	3	TP53	17	7578205	Missense_Mutation	SNP	C	TCGA-G3-A7M6-01A-11D-A33Q-10	4131330	7578205	73617005	60	42698										
CBX4	8535	hgsc.bcm.edu	37	chr17	77808750	77808751	+	Frame_Shift_Ins	INS	-	-	G													0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	ggggccggcatcattccgttINSgggggggcccttctcggagc							TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr17:77808750_77808751insG	ENST00000269397.4	-	5	867_868	c.690_691insC	c.(688-693)cccaacfs	p.N231fs		NM_003655.2	NP_003646.2	O00257	CBX4_HUMAN	chromobox homolog 4	231	Interaction with BMI1.				chromatin modification (GO:0016568)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein sumoylation (GO:0016925)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|single-stranded RNA binding (GO:0003727)|SUMO binding (GO:0032183)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			ATCATTCCGTTGGGGGGGCCCT	0.639											OREG0024799	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N231fs		Atlas-Indel,Pindel	.											.,1	CBX4	40	.	0			c.691_692insC						.																																			SO:0001589	frameshift_variant	8535	exon5			.	AF013956	CCDS32758.1	17q25.3	2010-07-06	2010-06-24		ENSG00000141582	ENSG00000141582			1554	protein-coding gene	gene with protein product	"NS5ATP1-binding protein 16", "Pc class 2 homolog (Drosophila)"	603079	"chromobox homolog 4 (Drosophila Pc class)"			9315667	Standard	NM_003655		Approved	hPC2, PC2, NBP16	uc002jxe.3	O00257	OTTHUMG00000150415	ENST00000269397.4:c.691dupC	chr17.hg19:g.77808757_77808757dupG	ENSP00000269397:p.Asn231fs	120.0	0.0	1178	123.0	14.0	NM_003655	B1PJR7|Q6TPI8|Q96C04	Frame_Shift_Ins	INS	ENST00000269397.4	hg19	CCDS32758.1																																																																																			.	.		0.639	CBX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318007.1	NM_003655		G	77808751	-	G	77808750	7	5	291	1	0	1	1	0	0	0	0	0	2722	1812	63	0	995	0	CBX4	17	77808750	Frame_Shift_Ins	INS	-	TCGA-G3-A7M6-01A-11D-A33Q-10	70230545	77808750	3386460	61	42699										
AATK	9625	hgsc.bcm.edu	37	chr17	79094718	79094718	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	ttctctgggcctgaggtggcCtcggcctcagcctcgaggtc	14	14	2	1	rs546580102		TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr17:79094718C>G	ENST00000326724.4	-	11	3042	c.3018G>C	c.(3016-3018)gaG>gaC	p.E1006D	AATK_ENST00000417379.1_Missense_Mutation_p.E903D	NM_001080395.2	NP_001073864.2	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	1006					brain development (GO:0007420)|negative regulation of axon extension (GO:0030517)|neuron apoptotic process (GO:0051402)|peptidyl-tyrosine autophosphorylation (GO:0038083)|Rab protein signal transduction (GO:0032482)	axonal growth cone (GO:0044295)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(2)|lung(8)|ovary(3)|prostate(1)|stomach(4)|upper_aerodigestive_tract(1)	21	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			CTGAGGTGGCCTCGGCCTCAG	0.672																																					p.E1006D		Atlas-SNP	.											.	AATK	102	.	0			c.G3018C						.						17	19	18					17																	79094718		1875	4098	5973	SO:0001583	missense	9625	exon11			GGTGGCCTCGGCC	AB014541	CCDS45807.1, CCDS58607.1	17q25.3	2014-06-12			ENSG00000181409	ENSG00000181409			21	protein-coding gene	gene with protein product	"lemur tyrosine kinase 1", "protein phosphatase 1, regulatory subunit 77"	605276				9734811, 10083745	Standard	NM_001080395		Approved	AATYK, KIAA0641, LMTK1, LMR1, AATYK1, PPP1R77	uc010dia.3	Q6ZMQ8	OTTHUMG00000132717	ENST00000326724.4:c.3018G>C	chr17.hg19:g.79094718C>G	ENSP00000324196:p.Glu1006Asp	64.0	0.0		71.0	21.0	NM_001080395	O75136|Q6ZN31|Q86X28	Missense_Mutation	SNP	ENST00000326724.4	hg19	CCDS45807.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.64|10.64	1.407952|1.407952	0.25378|0.25378	.|.	.|.	ENSG00000181409|ENSG00000181409	ENST00000326724|ENST00000417379	T|.	0.11063|.	2.81|.	5.2|5.2	-0.0483|-0.0483	0.13839|0.13839	.|.	28.962000|.	0.00166|.	N|.	0.000005|.	T|T	0.21387|0.21387	0.0515|0.0515	N|N	0.21142|0.21142	0.635|0.635	0.22017|0.22017	N|N	0.999411|0.999411	B|.	0.30664|.	0.289|.	B|.	0.23275|.	0.045|.	T|T	0.26326|0.26326	-1.0106|-1.0106	10|5	0.15066|.	T|.	0.55|.	.|.	4.7113|4.7113	0.12873|0.12873	0.0:0.4439:0.3194:0.2367|0.0:0.4439:0.3194:0.2367	.|.	1006|.	Q6ZMQ8|.	LMTK1_HUMAN|.	D|T	1006|959	ENSP00000324196:E1006D|.	ENSP00000324196:E1006D|.	E|R	-|-	3|2	2|0	AATK|AATK	76709313|76709313	0.011000|0.011000	0.17503|0.17503	0.007000|0.007000	0.13788|0.13788	0.009000|0.009000	0.06853|0.06853	-0.040000|-0.040000	0.12104|0.12104	0.003000|0.003000	0.14656|0.14656	0.462000|0.462000	0.41574|0.41574	GAG|AGG	.	.		0.672	AATK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256055.1	NM_004920		G	79094718	C	G	79094718	3	3	291	1	0	0	0	0	1	0	0	0	26	680	24	4	1122	4	AATK	17	79094718	Missense_Mutation	SNP	C	TCGA-G3-A7M6-01A-11D-A33Q-10	1285968	79094718	2100492	62	42700										
EMILIN2	84034	hgsc.bcm.edu	37	chr18	2885054	2885054	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	tcctggctttagagggggagAttgccaagaaggtcccaaag	14	8	0	3			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr18:2885054A>G	ENST00000254528.3	+	3	509	c.350A>G	c.(349-351)gAt>gGt	p.D117G		NM_032048.2	NP_114437.2	Q9BXX0	EMIL2_HUMAN	elastin microfibril interfacer 2	117	EMI. {ECO:0000255|PROSITE- ProRule:PRU00384}.				cell adhesion (GO:0007155)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix constituent conferring elasticity (GO:0030023)			breast(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(4)	48				READ - Rectum adenocarcinoma(2;0.1)		AGAGGGGGAGATTGCCAAGAA	0.522																																					p.D117G		Atlas-SNP	.											.	EMILIN2	97	.	0			c.A350G						.						101	92	95					18																	2885054		2203	4300	6503	SO:0001583	missense	84034	exon3			GGGGAGATTGCCA	AF270513	CCDS11828.1	18p11.3	2008-02-05			ENSG00000132205	ENSG00000132205		"EMI domain containing"	19881	protein-coding gene	gene with protein product		608928					Standard	NM_032048		Approved	FLJ33200, FOAP-10	uc002kln.3	Q9BXX0	OTTHUMG00000128525	ENST00000254528.3:c.350A>G	chr18.hg19:g.2885054A>G	ENSP00000254528:p.Asp117Gly	76.0	0.0		59.0	22.0	NM_032048	B2RMY3|Q8NBH3|Q96JQ4	Missense_Mutation	SNP	ENST00000254528.3	hg19	CCDS11828.1	.	.	.	.	.	.	.	.	.	.	A	27.5	4.833821	0.91036	.	.	ENSG00000132205	ENST00000254528	T	0.37752	1.18	5.83	5.83	0.93111	EMI domain (1);	0.217303	0.39407	N	0.001363	T	0.49490	0.1560	L	0.47716	1.5	0.58432	D	0.999999	P	0.50272	0.933	P	0.57057	0.812	T	0.44406	-0.9330	10	0.51188	T	0.08	-29.7081	16.2121	0.82168	1.0:0.0:0.0:0.0	.	117	Q9BXX0	EMIL2_HUMAN	G	117	ENSP00000254528:D117G	ENSP00000254528:D117G	D	+	2	0	EMILIN2	2875054	1.000000	0.71417	0.996000	0.52242	0.994000	0.84299	6.750000	0.74888	2.223000	0.72356	0.528000	0.53228	GAT	.	.		0.522	EMILIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250337.2	NM_032048		G	2885054	A	G	2885054	3	3	291	1	0	0	0	0	1	0	0	0	5096	333	12	2	360	2	EMILIN2	18	2885054	Missense_Mutation	SNP	A	TCGA-G3-A7M6-01A-11D-A33Q-10		2885054	75192194	63	42701										
ZNF43	7594	hgsc.bcm.edu	37	chr19	22000753	22000753	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	aggctctttttcttgctccaGacaggtgatcaggtctggct	11	10	4	2			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr19:22000753G>A	ENST00000354959.4	-	3	335	c.166C>T	c.(166-168)Ctg>Ttg	p.L56L	ZNF43_ENST00000595461.1_Silent_p.L50L|ZNF43_ENST00000598381.1_Silent_p.L50L|ZNF43_ENST00000598288.1_Silent_p.L50L|ZNF43_ENST00000594012.1_Silent_p.L50L	NM_003423.3	NP_003414.2	P17038	ZNF43_HUMAN	zinc finger protein 43	56	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2)	51		Renal(1328;0.000219)|Hepatocellular(1079;0.121)		GBM - Glioblastoma multiforme(1328;5.97e-05)|STAD - Stomach adenocarcinoma(1328;0.0127)		TCTTGCTCCAGACAGGTGATC	0.408																																					p.L65L		Atlas-SNP	.											.	ZNF43	152	.	0			c.C193T						.						156	157	156					19																	22000753		2203	4300	6503	SO:0001819	synonymous_variant	7594	exon3			GCTCCAGACAGGT	X59244	CCDS12413.2, CCDS59367.1, CCDS74321.1	19p13.1-p12	2013-01-08	2006-05-11		ENSG00000198521	ENSG00000198521		"Zinc fingers, C2H2-type", "-"	13109	protein-coding gene	gene with protein product		603972	"zinc finger protein 39-like 1 (KOX 27)", "zinc finger protein 43 (HTF6)"	ZNF39L1		1711675	Standard	NM_001256649		Approved	HTF6, KOX27	uc031rka.1	P17038	OTTHUMG00000128543	ENST00000354959.4:c.166C>T	chr19.hg19:g.22000753G>A		61.0	0.0		52.0	34.0	NM_001256653	A8K5N8|P28160|Q53XQ2|Q5H9T3|Q96DG1	Silent	SNP	ENST00000354959.4	hg19	CCDS12413.2																																																																																			.	.		0.408	ZNF43-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250380.2	NM_003423		A	22000753	G	A	22000753	2	1	291	1	0	0	0	0	0	0	0	1	17918	933	33	3		3	ZNF43	19	22000753	Silent	SNP	G	TCGA-G3-A7M6-01A-11D-A33Q-10		22000753	37128230	64	42702										
KCNJ14	3770	hgsc.bcm.edu	37	chr19	48965315	48965315	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	gcctggccttctggctcattGcctcgctgcacggcgacctg	12	16	2	0			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr19:48965315G>A	ENST00000391884.1	+	1	810	c.334G>A	c.(334-336)Gcc>Acc	p.A112T	KCNJ14_ENST00000342291.2_Missense_Mutation_p.A112T			Q9UNX9	KCJ14_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 14	112					potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)			cervix(1)|endometrium(2)|large_intestine(2)|lung(2)|skin(2)|urinary_tract(1)	10		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000109)|all cancers(93;0.000129)|Epithelial(262;0.0081)|GBM - Glioblastoma multiforme(486;0.0222)	Yohimbine(DB01392)	CTGGCTCATTGCCTCGCTGCA	0.692																																					p.G112S	NSCLC(148;170 3504 35216)	Atlas-SNP	.											.	KCNJ14	28	.	0			c.G334A						.						46	26	33					19																	48965315		2203	4300	6503	SO:0001583	missense	3770	exon2			CTCATTGCCTCGC	BC042033	CCDS12721.1	19q13	2011-07-05				ENSG00000182324		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6260	protein-coding gene	gene with protein product		603953				9592090, 10723734, 16382105	Standard	NM_013348		Approved	Kir2.4, IRK4	uc002pje.2	Q9UNX9		ENST00000391884.1:c.334G>A	chr19.hg19:g.48965315G>A	ENSP00000375756:p.Ala112Thr	22.0	0.0		43.0	26.0	NM_013348		Missense_Mutation	SNP	ENST00000391884.1	hg19	CCDS12721.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.665038	0.88251	.	.	ENSG00000182324	ENST00000342291;ENST00000391884	D;D	0.96685	-4.09;-4.09	4.45	3.4	0.38934	Potassium channel, inwardly rectifying, Kir, conserved region 2 (2);	0.000000	0.85682	D	0.000000	D	0.97851	0.9294	M	0.89601	3.045	0.54753	D	0.999983	D	0.54397	0.966	P	0.62089	0.898	D	0.97931	1.0320	10	0.87932	D	0	.	10.6938	0.45886	0.0959:0.0:0.9041:0.0	.	112	Q9UNX9	IRK14_HUMAN	T	112	ENSP00000341479:A112T;ENSP00000375756:A112T	ENSP00000341479:A112T	A	+	1	0	KCNJ14	53657127	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	9.786000	0.99046	1.008000	0.39264	0.591000	0.81541	GCC	.	.		0.692	KCNJ14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466127.1	NM_013348		A	48965315	G	A	48965315	3	1	291	1	0	0	0	0	1	0	0	0	8057	1319	46	3	336	3	KCNJ14	19	48965315	Missense_Mutation	SNP	G	TCGA-G3-A7M6-01A-11D-A33Q-10	26964562	48965315	10163668	65	42703										
SLC24A3	57419	hgsc.bcm.edu	37	chr20	19560719	19560719	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	ccttggaaaagatctgtgagGtacgtgcctcacattcttgg	11	9	3	2			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr20:19560719G>C	ENST00000328041.6	+	4	620		c.e4+1			NM_020689.3	NP_065740.2	Q9HC58	NCKX3_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 3						ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|liver(1)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						GATCTGTGAGGTACGTGCCTC	0.532																																					.		Atlas-SNP	.											.	SLC24A3	92	.	0			c.423+1G>C						.						381	258	300					20																	19560719		2203	4300	6503	SO:0001630	splice_region_variant	57419	exon4			TGTGAGGTACGTG	AF169257	CCDS13140.1	20p13	2013-05-22			ENSG00000185052	ENSG00000185052		"Solute carriers"	10977	protein-coding gene	gene with protein product		609839					Standard	NM_020689		Approved		uc002wrl.3	Q9HC58	OTTHUMG00000031993	ENST00000328041.6:c.423+1G>C	chr20.hg19:g.19560719G>C		101.0	0.0		105.0	58.0	NM_020689	B1AKV7|Q9BQJ9|Q9BQL7|Q9BQY3|Q9H519	Splice_Site	SNP	ENST00000328041.6	hg19	CCDS13140.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.839821	0.91117	.	.	ENSG00000185052	ENST00000328041	.	.	.	5.34	5.34	0.76211	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.9079	0.86133	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC24A3	19508719	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.269000	0.95684	2.664000	0.90586	0.655000	0.94253	.	.	.		0.532	SLC24A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078207.4	NM_020689	Intron	C	19560719	G	C	19560719	5	2	291	1	0	0	0	0	0	0	1	0	14482	1275	44	4	438	4	SLC24A3	20	19560719	Splice_Site	SNP	G	TCGA-G3-A7M6-01A-11D-A33Q-10		19560719	43464801	66	42704										
ZSWIM1	90204	hgsc.bcm.edu	37	chr20	44512235	44512235	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	ctccctcaatgccatctgcaCagggccagcagcccaactgt	8	17	2	0			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr20:44512235C>T	ENST00000372523.1	+	2	1099	c.1004C>T	c.(1003-1005)aCa>aTa	p.T335I	ZSWIM1_ENST00000372520.1_Missense_Mutation_p.T335I	NM_080603.4	NP_542170.3	Q9BR11	ZSWM1_HUMAN	zinc finger, SWIM-type containing 1	335						nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	13		Myeloproliferative disorder(115;0.028)				GCCATCTGCACAGGGCCAGCA	0.557																																					p.T335I		Atlas-SNP	.											.	ZSWIM1	35	.	0			c.C1004T						.						108	99	102					20																	44512235		2203	4300	6503	SO:0001583	missense	90204	exon2			TCTGCACAGGGCC	AL008726	CCDS13382.2	20q13.12	2013-09-20	2003-12-17	2003-12-19	ENSG00000168612	ENSG00000168612		"Zinc fingers, SWIM-type"	16155	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 162"	C20orf162			Standard	NM_080603		Approved	dJ337O18.5	uc010ghi.3	Q9BR11	OTTHUMG00000074023	ENST00000372523.1:c.1004C>T	chr20.hg19:g.44512235C>T	ENSP00000361601:p.Thr335Ile	77.0	0.0		96.0	51.0	NM_080603	Q5JZH2|Q9BR12|Q9BV30	Missense_Mutation	SNP	ENST00000372523.1	hg19	CCDS13382.2	.	.	.	.	.	.	.	.	.	.	C	9.401	1.078054	0.20227	.	.	ENSG00000168612	ENST00000372523;ENST00000372520	T;T	0.24723	1.84;1.84	5.03	3.11	0.35812	.	0.231898	0.28742	U	0.014285	T	0.12689	0.0308	N	0.14661	0.345	0.26741	N	0.970397	B	0.29988	0.264	B	0.23150	0.044	T	0.15578	-1.0432	10	0.34782	T	0.22	-3.017	8.4234	0.32714	0.0:0.7659:0.0:0.2341	.	335	Q9BR11	ZSWM1_HUMAN	I	335	ENSP00000361601:T335I;ENSP00000361598:T335I	ENSP00000361598:T335I	T	+	2	0	ZSWIM1	43945642	0.870000	0.30015	0.755000	0.31263	0.997000	0.91878	1.441000	0.35035	0.717000	0.32145	0.655000	0.94253	ACA	.	.		0.557	ZSWIM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157064.2	NM_080603		T	44512235	C	T	44512235	3	4	291	1	0	0	0	0	1	0	0	0	18255	478	17	3	1006	3	ZSWIM1	20	44512235	Missense_Mutation	SNP	C	TCGA-G3-A7M6-01A-11D-A33Q-10	24951516	44512235	18513285	67	42705										
C21orf29	54084	hgsc.bcm.edu	37	chr21	45941865	45941865	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	aaggtgttggccaccaccagGaacgagtagggccccacact	12	13	0	0	rs201105425		TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr21:45941865G>C	ENST00000323084.4	-	9	1532	c.1467C>G	c.(1465-1467)ttC>ttG	p.F489L	C21orf90_ENST00000465978.1_Intron|TSPEAR_ENST00000397916.1_Missense_Mutation_p.F421L	NM_001272037.1|NM_144991.2	NP_001258966.1|NP_659428.2	Q8WU66	TSEAR_HUMAN	thrombospondin-type laminin G domain and EAR repeats	489					sensory perception of sound (GO:0007605)	cell surface (GO:0009986)|ciliary membrane (GO:0060170)|extracellular region (GO:0005576)|stereocilium (GO:0032420)				breast(1)|central_nervous_system(6)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	37						CCACCACCAGGAACGAGTAGG	0.627																																					p.F489L		Atlas-SNP	.											.	TSPEAR	110	.	0			c.C1467G						.						183	184	183					21																	45941865		2203	4300	6503	SO:0001583	missense	54084	exon9			CACCAGGAACGAG	AJ487962	CCDS13712.1, CCDS74801.1	21q22.3	2012-10-30	2011-01-25	2011-01-25	ENSG00000175894	ENSG00000175894			1268	protein-coding gene	gene with protein product		612920	"chromosome 21 open reading frame 29", "deafness, autosomal recessive 98"	C21orf29, DFNB98		12095917, 22678063	Standard	NM_144991		Approved	MGC11251, TSP-EAR	uc002zfe.1	Q8WU66	OTTHUMG00000041215	ENST00000323084.4:c.1467C>G	chr21.hg19:g.45941865G>C	ENSP00000321987:p.Phe489Leu	119.0	0.0		123.0	43.0	NM_144991		Missense_Mutation	SNP	ENST00000323084.4	hg19	CCDS13712.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.062996	0.76187	.	.	ENSG00000175894	ENST00000323084;ENST00000397918;ENST00000397916;ENST00000341581	T;T	0.31769	1.48;1.57	5.18	2.98	0.34508	.	0.109447	0.64402	D	0.000003	T	0.52581	0.1743	M	0.82823	2.61	0.80722	D	1	D	0.65815	0.995	D	0.63283	0.913	T	0.59648	-0.7415	10	0.72032	D	0.01	-11.0242	10.935	0.47241	0.1982:0.0:0.8018:0.0	.	489	Q8WU66	TSEAR_HUMAN	L	489;342;421;490	ENSP00000321987:F489L;ENSP00000381012:F421L	ENSP00000321987:F489L	F	-	3	2	TSPEAR	44766293	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.433000	0.34947	1.327000	0.45338	0.563000	0.77884	TTC	.	G|0.999;A|0.001		0.627	TSPEAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098761.1	NM_144991		C	45941865	G	C	45941865	3	2	291	1	0	0	0	0	1	0	0	0	2126	1165	41	4	558	4	C21orf29	21	45941865	Missense_Mutation	SNP	G	TCGA-G3-A7M6-01A-11D-A33Q-10		45941865	2188030	68	42706										
POTEH	23784	hgsc.bcm.edu	37	chr22	16279260	16279260	+	Frame_Shift_Del	DEL	T	T	-													0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	aaaaatttcaccacttgctgTttttgctcatgtacaccaag							TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr22:16279260delT	ENST00000343518.6	-	4	1014	c.963delA	c.(961-963)aaafs	p.K321fs	POTEH-AS1_ENST00000422014.1_RNA|RNU6-816P_ENST00000390914.1_RNA	NM_001136213.1	NP_001129685.1	Q6S545	POTEH_HUMAN	POTE ankyrin domain family, member H	321								p.K321K(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(20)|ovary(1)|skin(7)|urinary_tract(2)	37						CCACTTGCTGTTTTTGCTCAT	0.323																																					p.Q322fs		Atlas-INDEL	.											.	POTEH	114	.	1	Substitution - coding silent(1)	urinary_tract(1)	c.964delC						.																																			SO:0001589	frameshift_variant	23784	exon4			.	AY462874	CCDS74808.1	22q11.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000198062	ENSG00000198062		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	133	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 7"	608913	"actin, beta-like 1", "ANKRD26-like family C, member 3"	ACTBL1, A26C3		10591208, 15276201, 21439273	Standard	NM_001136213		Approved	POTE22, CT104.7	uc010gqp.2	Q6S545	OTTHUMG00000140314	ENST00000343518.6:c.963delA	chr22.hg19:g.16279260delT	ENSP00000340610:p.Lys321fs	384.0	0.0		387.0	41.0	NM_001136213	A2CEK4|A6NCI1|A9Z1W0	Frame_Shift_Del	DEL	ENST00000343518.6	hg19	CCDS46658.1																																																																																			.	.		0.323	POTEH-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276918.4	NM_001136213		-	16279260	T	-	16279260	7	5	291	1	0	1	0	1	0	0	0	0	12276	1722	60	0	702	0	POTEH	22	16279260	Frame_Shift_Del	DEL	T	TCGA-G3-A7M6-01A-11D-A33Q-10		16279260	35025306	69	42707										
LIMK2	3985	hgsc.bcm.edu	37	chr22	31669449	31669449	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	ttccccaaggaaagagctatGatgagacggtggatatcttc	11	8	1	3			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr22:31669449G>C	ENST00000331728.4	+	14	1684	c.1570G>C	c.(1570-1572)Gat>Cat	p.D524H	LIMK2_ENST00000444929.2_Missense_Mutation_p.D278H|LIMK2_ENST00000467301.1_3'UTR|LIMK2_ENST00000340552.4_Missense_Mutation_p.D503H|LIMK2_ENST00000333611.4_Missense_Mutation_p.D503H|LIMK2_ENST00000406516.1_Missense_Mutation_p.D446H	NM_005569.3	NP_005560.1	P53671	LIMK2_HUMAN	LIM domain kinase 2	524	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				phosphorylation (GO:0016310)|spermatogenesis (GO:0007283)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			endometrium(7)|kidney(3)|large_intestine(6)|lung(6)|ovary(2)|prostate(4)|skin(1)	29						AAAGAGCTATGATGAGACGGT	0.532											OREG0026477	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D524H		Atlas-SNP	.											.	LIMK2	101	.	0			c.G1570C						.						276	190	220					22																	31669449		2203	4300	6503	SO:0001583	missense	3985	exon14			AGCTATGATGAGA	D45906	CCDS13891.1, CCDS13892.1, CCDS33637.1	22q12	2005-01-21			ENSG00000182541	ENSG00000182541			6614	protein-coding gene	gene with protein product		601988				8537403, 10591208	Standard	NM_005569		Approved		uc003akh.3	P53671	OTTHUMG00000151251	ENST00000331728.4:c.1570G>C	chr22.hg19:g.31669449G>C	ENSP00000332687:p.Asp524His	62.0	0.0	826	54.0	14.0	NM_005569	A8K6H5|Q7KZ80|Q7L3H5|Q96E10|Q99464|Q9UFU0	Missense_Mutation	SNP	ENST00000331728.4	hg19	CCDS13891.1	.	.	.	.	.	.	.	.	.	.	.	22.7	4.323944	0.81580	.	.	ENSG00000182541	ENST00000406516;ENST00000444929;ENST00000331728;ENST00000436394;ENST00000333611;ENST00000340552	D;D;D;D;D	0.90261	-2.64;-2.64;-2.64;-2.64;-2.64	5.53	4.52	0.55395	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.95188	0.8440	M	0.83384	2.64	0.58432	D	0.999995	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.87578	0.997;0.996;0.998;0.998;0.989	D	0.95580	0.8645	10	0.87932	D	0	-20.9085	13.5652	0.61813	0.0749:0.0:0.9251:0.0	.	556;503;278;524;446	F5GY29;Q7L3H5;E7EUC1;P53671;B5MC51	.;.;.;LIMK2_HUMAN;.	H	446;278;524;556;503;503	ENSP00000384602:D446H;ENSP00000409522:D278H;ENSP00000332687:D524H;ENSP00000330470:D503H;ENSP00000339916:D503H	ENSP00000332687:D524H	D	+	1	0	LIMK2	29999449	1.000000	0.71417	0.996000	0.52242	0.994000	0.84299	9.476000	0.97823	1.329000	0.45376	0.563000	0.77884	GAT	.	.		0.532	LIMK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321911.1	NM_016733		C	31669449	G	C	31669449	3	2	291	1	0	0	0	0	1	0	0	0	8811	1290	45	4	1681	4	LIMK2	22	31669449	Missense_Mutation	SNP	G	TCGA-G3-A7M6-01A-11D-A33Q-10	15390189	31669449	19635117	70	42708										
SREBF2	6721	hgsc.bcm.edu	37	chr22	42273946	42273946	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	gctgagacgctccttcttagGttctgggggctggtttgact	14	9	2	2			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chr22:42273946G>T	ENST00000361204.4	+	9	1746	c.1580G>T	c.(1579-1581)gGt>gTt	p.G527V		NM_004599.2	NP_004590.2	Q12772	SRBP2_HUMAN	sterol regulatory element binding transcription factor 2	527					cellular lipid metabolic process (GO:0044255)|cellular response to laminar fluid shear stress (GO:0071499)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cholesterol homeostasis (GO:2000188)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|response to low-density lipoprotein particle (GO:0055098)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SREBP-SCAP-Insig complex (GO:0032937)	E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(6)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	38						TCCTTCTTAGGTTCTGGGGGC	0.532																																					p.G527V		Atlas-SNP	.											.	SREBF2	99	.	0			c.G1580T						.						156	149	152					22																	42273946		2203	4300	6503	SO:0001630	splice_region_variant	6721	exon9			TCTTAGGTTCTGG	U02031	CCDS14023.1	22q13.2	2013-05-21			ENSG00000198911	ENSG00000198911		"Basic helix-loop-helix proteins"	11290	protein-coding gene	gene with protein product		600481				7903453	Standard	NM_004599		Approved	SREBP2, bHLHd2	uc003bbi.3	Q12772	OTTHUMG00000151261	ENST00000361204.4:c.1580-1G>T	chr22.hg19:g.42273946G>T		45.0	0.0		34.0	14.0	NM_004599	Q05BD5|Q6GTH7|Q86V36|Q9UH04	Missense_Mutation	SNP	ENST00000361204.4	hg19	CCDS14023.1	.	.	.	.	.	.	.	.	.	.	G	13.30	2.194588	0.38806	.	.	ENSG00000198911	ENST00000361204;ENST00000444813;ENST00000457567	T	0.55052	0.54	4.96	3.94	0.45596	.	0.478366	0.25786	N	0.028315	T	0.33000	0.0848	L	0.29908	0.895	0.80722	D	1	P	0.40144	0.704	B	0.32289	0.143	T	0.08932	-1.0698	9	.	.	.	.	8.6039	0.33762	0.1892:0.0:0.8108:0.0	.	527	Q12772	SRBP2_HUMAN	V	527	ENSP00000354476:G527V	.	G	+	2	0	SREBF2	40603892	1.000000	0.71417	0.985000	0.45067	0.872000	0.50106	4.109000	0.57824	1.318000	0.45170	0.549000	0.68633	GGT	.	.		0.532	SREBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321956.1	NM_004599	Missense_Mutation	T	42273946	G	T	42273946	5	4	291	1	0	0	0	0	0	0	1	0	15157	1275	44	3	1614	3	SREBF2	22	42273946	Splice_Site	SNP	G	TCGA-G3-A7M6-01A-11D-A33Q-10	10604497	42273946	9030620	71	42709										
TLR8	51311	hgsc.bcm.edu	37	chrX	12937389	12937389	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	gtctgataatttcatcacacAcataacgaatgaatcatttc	4	9	4	2			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chrX:12937389A>G	ENST00000218032.6	+	2	317	c.230A>G	c.(229-231)cAc>cGc	p.H77R	TLR8_ENST00000311912.5_Missense_Mutation_p.H95R	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	77					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	TTCATCACACACATAACGAAT	0.418																																					p.H77R		Atlas-SNP	.											.	TLR8	134	.	0			c.A230G						.						110	103	105					X																	12937389		2203	4300	6503	SO:0001583	missense	51311	exon2			TCACACACATAAC	AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"CD molecules"	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.230A>G	chrX.hg19:g.12937389A>G	ENSP00000218032:p.His77Arg	394.0	0.0		306.0	99.0	NM_138636	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Missense_Mutation	SNP	ENST00000218032.6	hg19	CCDS14152.1	.	.	.	.	.	.	.	.	.	.	A	0	-2.694149	0.00098	.	.	ENSG00000101916	ENST00000218032;ENST00000311912	T;T	0.56275	0.47;0.47	4.52	-2.75	0.05914	.	1.094670	0.07150	N	0.848986	T	0.29914	0.0748	N	0.16708	0.43	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.09377	0.004;0.004	T	0.31194	-0.9952	10	0.06494	T	0.89	.	9.4329	0.38622	0.5549:0.0:0.4451:0.0	.	77;95	Q9NR97;D1CS70	TLR8_HUMAN;.	R	77;95	ENSP00000218032:H77R;ENSP00000312082:H95R	ENSP00000218032:H77R	H	+	2	0	TLR8	12847310	0.000000	0.05858	0.000000	0.03702	0.066000	0.16364	0.233000	0.17911	-0.878000	0.04007	-0.434000	0.05882	CAC	.	.		0.418	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610		G	12937389	A	G	12937389	3	3	291	1	0	0	0	0	1	0	0	0	15972	159	6	2	236	2	TLR8	23	12937389	Missense_Mutation	SNP	A	TCGA-G3-A7M6-01A-11D-A33Q-10		12937389	142333171	72	42710										
GEMIN8	54960	hgsc.bcm.edu	37	chrX	14027290	14027290	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	tccagctgctgctgccgcccTgagaacaaacacgaacgtga	10	14	0	2			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chrX:14027290T>A	ENST00000380523.4	-	5	791		c.e5-2		GEMIN8_ENST00000398355.3_Splice_Site	NM_017856.2	NP_060326.1	Q9NWZ8	GEMI8_HUMAN	gem (nuclear organelle) associated protein 8						spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	9						GCTGCCGCCCTGAGAACAAAC	0.587																																					.		Atlas-SNP	.											.	GEMIN8	19	.	0			c.473-2A>T						.						50	44	46					X																	14027290		2203	4300	6503	SO:0001630	splice_region_variant	54960	exon5			CCGCCCTGAGAAC	BC020785	CCDS14159.1	Xp22	2010-03-16	2006-11-24	2006-11-24	ENSG00000046647	ENSG00000046647			26044	protein-coding gene	gene with protein product			"family with sequence similarity 51, member A1"	FAM51A1		16434402	Standard	NM_017856		Approved	FLJ20514	uc004cwd.3	Q9NWZ8	OTTHUMG00000021160	ENST00000380523.4:c.473-2A>T	chrX.hg19:g.14027290T>A		103.0	0.0		81.0	25.0	NM_001042480	C4AMC4|Q2LJ66|Q6ZV27	Splice_Site	SNP	ENST00000380523.4	hg19	CCDS14159.1	.	.	.	.	.	.	.	.	.	.	T	18.83	3.707967	0.68615	.	.	ENSG00000046647	ENST00000380523;ENST00000398355;ENST00000332885	.	.	.	5.39	5.39	0.77823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.6477	0.62292	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	GEMIN8	13937211	1.000000	0.71417	0.984000	0.44739	0.669000	0.39330	7.503000	0.81632	1.818000	0.53035	0.486000	0.48141	.	.	.		0.587	GEMIN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055815.1	NM_017856	Intron	A	14027290	T	A	14027290	5	1	291	1	0	0	0	0	0	0	1	0	6342	1594	55	4	261	4	GEMIN8	23	14027290	Splice_Site	SNP	T	TCGA-G3-A7M6-01A-11D-A33Q-10	1089901	14027290	141243270	73	42711										
PDK3	5165	hgsc.bcm.edu	37	chrX	24513001	24513001	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	gtgggattggttcagagttgGtaagtaaacaatgtggctta	14	3	1	1			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chrX:24513001G>C	ENST00000379162.4	+	2	483		c.e2+1		PDK3_ENST00000441463.2_Splice_Site|PDK3_ENST00000493226.1_Splice_Site	NM_005391.4	NP_005382.1	Q15120	PDK3_HUMAN	pyruvate dehydrogenase kinase, isozyme 3						cell death (GO:0008219)|cellular metabolic process (GO:0044237)|cellular response to fatty acid (GO:0071398)|cellular response to glucose stimulus (GO:0071333)|glucose metabolic process (GO:0006006)|hypoxia-inducible factor-1alpha signaling pathway (GO:0097411)|peptidyl-serine phosphorylation (GO:0018105)|peroxisome proliferator activated receptor signaling pathway (GO:0035357)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of glucose metabolic process (GO:0010906)|regulation of reactive oxygen species metabolic process (GO:2000377)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)			NS(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						TTCAGAGTTGGTAAGTAAACA	0.448																																					.		Atlas-SNP	.											.	PDK3	86	.	0			c.248+1G>C						.						64	54	57					X																	24513001		2203	4300	6503	SO:0001630	splice_region_variant	5165	exon2			GAGTTGGTAAGTA	L42452	CCDS14212.1, CCDS48088.1	Xp22.12	2008-02-05	2005-11-16		ENSG00000067992	ENSG00000067992			8811	protein-coding gene	gene with protein product		300906	"pyruvate dehydrogenase kinase, isoenzyme 3"			7499431	Standard	NM_001142386		Approved		uc004dbh.3	Q15120	OTTHUMG00000021269	ENST00000379162.4:c.248+1G>C	chrX.hg19:g.24513001G>C		110.0	0.0		76.0	24.0	NM_001142386	B4DXG6	Splice_Site	SNP	ENST00000379162.4	hg19	CCDS14212.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.545625	0.86022	.	.	ENSG00000067992	ENST00000379162;ENST00000441463	.	.	.	5.77	5.77	0.91146	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.1444	0.93459	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PDK3	24422922	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.779000	0.99018	2.557000	0.86248	0.594000	0.82650	.	.	.		0.448	PDK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056097.1	NM_005391	Intron	C	24513001	G	C	24513001	5	2	291	1	0	0	0	0	0	0	1	0	11686	1275	44	4	255	4	PDK3	23	24513001	Splice_Site	SNP	G	TCGA-G3-A7M6-01A-11D-A33Q-10	10485711	24513001	130757559	74	42712										
TFE3	7030	hgsc.bcm.edu	37	chrX	48895554	48895554	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	ccgtgctggggagctgcagtCctgtggtgcctccgggcaga	17	12	0	1			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chrX:48895554C>T	ENST00000315869.7	-	5	1125	c.866G>A	c.(865-867)gGa>gAa	p.G289E	TFE3_ENST00000487451.1_5'UTR	NM_006521.4	NP_006512.2	P19532	TFE3_HUMAN	transcription factor binding to IGHM enhancer 3	289					humoral immune response (GO:0006959)|positive regulation of cell adhesion (GO:0045785)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of osteoclast differentiation (GO:0045670)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)		NONO/TFE3(2)|PRCC/TFE3(25)|SFPQ/TFE3(6)|CLTC/TFE3(2)|ASPSCR1/TFE3(167)	central_nervous_system(1)	1						GAGCTGCAGTCCTGTGGTGCC	0.502			T	"SFPQ, ASPSCR1, PRCC, NONO, CLTC"	"papillary renal, alveolar soft part sarcoma, renal"																																p.G289E		Atlas-SNP	.		Dom	yes		X	Xp11.22	7030	transcription factor binding to IGHM enhancer 3		E	.	TFE3	93	.	0			c.G866A						.						65	42	50					X																	48895554		2202	4299	6501	SO:0001583	missense	7030	exon5			TGCAGTCCTGTGG	X96717	CCDS14315.3	Xp11.22	2013-05-21			ENSG00000068323	ENSG00000068323		"Basic helix-loop-helix proteins"	11752	protein-coding gene	gene with protein product	transcription factor E family, member A	314310				1672758, 1685140	Standard	NM_006521		Approved	TFEA, bHLHe33	uc004dmb.3	P19532	OTTHUMG00000022690	ENST00000315869.7:c.866G>A	chrX.hg19:g.48895554C>T	ENSP00000314129:p.Gly289Glu	144.0	0.0		130.0	46.0	NM_006521	A8MZL6|Q5JU74|Q92757|Q92758|Q99964	Missense_Mutation	SNP	ENST00000315869.7	hg19	CCDS14315.3	.	.	.	.	.	.	.	.	.	.	c	19.81	3.895958	0.72639	.	.	ENSG00000068323	ENST00000315869	T	0.12984	2.63	5.89	5.89	0.94794	.	0.050565	0.85682	D	0.000000	T	0.27134	0.0665	L	0.39245	1.2	0.80722	D	1	D	0.76494	0.999	D	0.69824	0.966	T	0.02546	-1.1143	10	0.12103	T	0.63	-18.792	17.8426	0.88719	0.0:1.0:0.0:0.0	.	289	P19532	TFE3_HUMAN	E	289	ENSP00000314129:G289E	ENSP00000314129:G289E	G	-	2	0	TFE3	48782498	0.000000	0.05858	0.541000	0.28102	0.931000	0.56810	-0.081000	0.11321	2.488000	0.83962	0.509000	0.49947	GGA	.	.		0.502	TFE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058872.2	NM_006521		T	48895554	C	T	48895554	3	4	291	1	0	0	0	0	1	0	0	0	15815	855	30	3	885	3	TFE3	23	48895554	Missense_Mutation	SNP	C	TCGA-G3-A7M6-01A-11D-A33Q-10	24382553	48895554	106375006	75	42713										
MAGED1	9500	hgsc.bcm.edu	37	chrX	51639742	51639742	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	cagctaggcagaccccaccaGcctggcagaacccagtcgct	10	17	0	2			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chrX:51639742G>A	ENST00000375722.1	+	4	1243	c.991G>A	c.(991-993)Gcc>Acc	p.A331T	MAGED1_ENST00000326587.7_Missense_Mutation_p.A331T|MAGED1_ENST00000375772.3_Missense_Mutation_p.A331T|MAGED1_ENST00000494718.1_3'UTR|MAGED1_ENST00000375695.2_Missense_Mutation_p.A387T			Q9Y5V3	MAGD1_HUMAN	melanoma antigen family D, 1	331	22 X 6 AA tandem repeats of W-[PQ]-X-P-X- X.|Pro-rich.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|circadian regulation of gene expression (GO:0032922)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of circadian rhythm (GO:0042752)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	transcription coactivator activity (GO:0003713)			breast(1)|endometrium(4)|large_intestine(10)|lung(13)|ovary(3)|upper_aerodigestive_tract(1)	32	Ovarian(276;0.236)					GACCCCACCAGCCTGGCAGAA	0.612										Multiple Myeloma(10;0.10)																											p.A387T		Atlas-SNP	.											.	MAGED1	84	.	0			c.G1159A						.						61	58	59					X																	51639742		2203	4300	6503	SO:0001583	missense	9500	exon5			CCACCAGCCTGGC	AF124440	CCDS14337.1, CCDS35279.1	Xp11.23	2008-08-01			ENSG00000179222	ENSG00000179222			6813	protein-coding gene	gene with protein product		300224				10409427	Standard	NM_006986		Approved	NRAGE, DLXIN-1	uc004dpn.3	Q9Y5V3	OTTHUMG00000021540	ENST00000375722.1:c.991G>A	chrX.hg19:g.51639742G>A	ENSP00000364874:p.Ala331Thr	158.0	0.0		113.0	48.0	NM_001005333	Q5VSH6|Q8IZ84|Q8WY92|Q9H352|Q9HBT4|Q9UF36	Missense_Mutation	SNP	ENST00000375722.1	hg19	CCDS14337.1	.	.	.	.	.	.	.	.	.	.	G	12.25	1.881762	0.33255	.	.	ENSG00000179222	ENST00000375772;ENST00000375722;ENST00000326587;ENST00000375695	T;T;T;T	0.52526	0.66;0.66;0.66;0.66	3.67	0.96	0.19631	.	0.240725	0.21627	N	0.071556	T	0.24353	0.0590	L	0.38175	1.15	0.27670	N	0.946784	P;P	0.37731	0.607;0.473	B;B	0.30782	0.12;0.056	T	0.10706	-1.0618	10	0.15066	T	0.55	.	2.1382	0.03768	0.4275:0.0:0.3268:0.2457	.	387;331	Q9Y5V3-2;Q9Y5V3	.;MAGD1_HUMAN	T	331;331;331;387	ENSP00000364927:A331T;ENSP00000364874:A331T;ENSP00000325333:A331T;ENSP00000364847:A387T	ENSP00000325333:A331T	A	+	1	0	MAGED1	51656482	0.904000	0.30761	1.000000	0.80357	0.969000	0.65631	0.164000	0.16542	0.110000	0.17919	0.284000	0.19432	GCC	.	.		0.612	MAGED1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056593.1	NM_001005332		A	51639742	G	A	51639742	3	1	291	1	0	0	0	0	1	0	0	0	9192	971	34	3	1173	3	MAGED1	23	51639742	Missense_Mutation	SNP	G	TCGA-G3-A7M6-01A-11D-A33Q-10	2744188	51639742	103630818	76	42714										
CPXCR1	53336	hgsc.bcm.edu	37	chrX	88008954	88008954	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	aaagcgaaaatatatagcatGtctttaccatccaaatagtt	5	7	1	0			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chrX:88008954G>A	ENST00000276127.4	+	3	798	c.539G>A	c.(538-540)tGt>tAt	p.C180Y	CPXCR1_ENST00000373111.1_Missense_Mutation_p.C180Y	NM_033048.5	NP_149037	Q8N123	CPXCR_HUMAN	CPX chromosome region, candidate 1	180							metal ion binding (GO:0046872)			NS(1)|cervix(1)|kidney(1)|large_intestine(11)|liver(1)|lung(20)|ovary(3)|upper_aerodigestive_tract(2)	40						TATATAGCATGTCTTTACCAT	0.433																																					p.C180Y		Atlas-SNP	.											.	CPXCR1	83	.	0			c.G539A						.						69	54	59					X																	88008954		2203	4300	6503	SO:0001583	missense	53336	exon3			TAGCATGTCTTTA	AL031116	CCDS14458.1	Xq21.3	2009-08-06			ENSG00000147183	ENSG00000147183			2332	protein-coding gene	gene with protein product	"cancer/testis antigen 77"					11499681	Standard	NM_033048		Approved	CT77	uc004efc.4	Q8N123	OTTHUMG00000021950	ENST00000276127.4:c.539G>A	chrX.hg19:g.88008954G>A	ENSP00000276127:p.Cys180Tyr	183.0	0.0		142.0	54.0	NM_001184771	B2R9F9|D3DTE7|Q96RS3	Missense_Mutation	SNP	ENST00000276127.4	hg19	CCDS14458.1	.	.	.	.	.	.	.	.	.	.	G	5.338	0.247607	0.10130	.	.	ENSG00000147183	ENST00000276127;ENST00000373111	T;T	0.41758	0.99;0.99	3.06	1.9	0.25705	.	0.732237	0.11244	N	0.584366	T	0.23492	0.0568	N	0.19112	0.55	0.09310	N	1	B	0.26876	0.162	B	0.22880	0.042	T	0.20140	-1.0284	9	.	.	.	-2.2053	5.6224	0.17465	0.0:0.0:0.304:0.696	.	180	Q8N123	CPXCR_HUMAN	Y	180	ENSP00000276127:C180Y;ENSP00000362203:C180Y	.	C	+	2	0	CPXCR1	87895610	0.002000	0.14202	0.000000	0.03702	0.034000	0.12701	0.670000	0.25157	0.437000	0.26423	-0.325000	0.08501	TGT	.	.		0.433	CPXCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057418.1	NM_033048		A	88008954	G	A	88008954	3	1	291	1	0	0	0	0	1	0	0	0	3838	1377	48	3	541	3	CPXCR1	23	88008954	Missense_Mutation	SNP	G	TCGA-G3-A7M6-01A-11D-A33Q-10	36369212	88008954	67261606	77	42715										
BTK	695	hgsc.bcm.edu	37	chrX	100608970	100608970	+	Silent	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	cttgtgtattcatcatccagGacatacctgcaagggattca	8	10	3	0			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chrX:100608970G>C	ENST00000308731.7	-	17	1801	c.1638C>G	c.(1636-1638)gtC>gtG	p.V546V	BTK_ENST00000372880.1_Silent_p.V370V	NM_000061.2	NP_000052.1	Q06187	BTK_HUMAN	Bruton agammaglobulinemia tyrosine kinase	546	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adaptive immune response (GO:0002250)|apoptotic signaling pathway (GO:0097190)|B cell activation (GO:0042113)|B cell receptor signaling pathway (GO:0050853)|calcium-mediated signaling (GO:0019722)|cell maturation (GO:0048469)|Fc-epsilon receptor signaling pathway (GO:0038095)|histamine secretion by mast cell (GO:0002553)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of B cell apoptotic process (GO:0002902)|regulation of B cell cytokine production (GO:0002721)|response to organic substance (GO:0010033)|response to reactive oxygen species (GO:0000302)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mast cell granule (GO:0042629)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein tyrosine kinase activity (GO:0004713)			breast(4)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(25)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50						CATCATCCAGGACATACCTGC	0.468									Agammaglobulinemia, X-linked																												p.V546V		Atlas-SNP	.											.	BTK	87	.	0			c.C1638G						.						128	121	123					X																	100608970		2203	4300	6503	SO:0001819	synonymous_variant	695	exon17	Familial Cancer Database	Bruton Type Agammaglobulinemia	ATCCAGGACATAC	AK057105	CCDS14482.1, CCDS76002.1, CCDS76003.1	Xq21.33-q22	2014-09-17			ENSG00000010671	ENSG00000010671	2.7.10.1	"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	1133	protein-coding gene	gene with protein product		300300		AGMX1, IMD1		8380905	Standard	NM_000061		Approved	ATK, XLA, PSCTK1	uc004ehg.2	Q06187	OTTHUMG00000022022	ENST00000308731.7:c.1638C>G	chrX.hg19:g.100608970G>C		58.0	0.0		57.0	16.0	NM_000061	B2RAW1|Q32ML5	Silent	SNP	ENST00000308731.7	hg19	CCDS14482.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.256|7.256	0.604286|0.604286	0.14002|0.14002	.|.	.|.	ENSG00000010671|ENSG00000010671	ENST00000443591|ENST00000372869	.|.	.|.	.|.	5.46|5.46	1.21|1.21	0.21127|0.21127	.|.	.|.	.|.	.|.	.|.	T|T	0.69043|0.69043	0.3067|0.3067	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.67444|0.67444	-0.5669|-0.5669	5|5	0.87932|0.87932	D|D	0|0	.|.	10.0043|10.0043	0.41949|0.41949	0.3506:0.0:0.6494:0.0|0.3506:0.0:0.6494:0.0	.|.	.|.	.|.	.|.	A|C	196|66	.|.	ENSP00000416302:P196A|ENSP00000361960:S66C	P|S	-|-	1|2	0|0	BTK|BTK	100495626|100495626	0.537000|0.537000	0.26386|0.26386	0.993000|0.993000	0.49108|0.49108	0.858000|0.858000	0.48976|0.48976	-0.178000|-0.178000	0.09782|0.09782	-0.206000|-0.206000	0.10203|0.10203	0.600000|0.600000	0.82982|0.82982	CCT|TCC	.	.		0.468	BTK-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057532.2	NM_000061		C	100608970	G	C	100608970	2	2	291	1	0	0	0	0	0	0	0	1	1559	1161	41	4		4	BTK	23	100608970	Silent	SNP	G	TCGA-G3-A7M6-01A-11D-A33Q-10	12600016	100608970	54661590	78	42716										
HTR2C	3358	hgsc.bcm.edu	37	chrX	114141284	114141284	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	agctttcttcataccgctgaCgattatggtgattacgtatt	8	8	2	2			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chrX:114141284C>G	ENST00000276198.1	+	6	1411	c.683C>G	c.(682-684)aCg>aGg	p.T228R	HTR2C_ENST00000371951.1_Missense_Mutation_p.T228R|HTR2C_ENST00000371950.3_Missense_Mutation_p.D196E	NM_000868.2	NP_000859.1	P28335	5HT2C_HUMAN	5-hydroxytryptamine (serotonin) receptor 2C, G protein-coupled	228					behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|cGMP biosynthetic process (GO:0006182)|feeding behavior (GO:0007631)|locomotory behavior (GO:0007626)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|phospholipase C-activating serotonin receptor signaling pathway (GO:0007208)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|regulation of appetite (GO:0032098)|regulation of corticotropin-releasing hormone secretion (GO:0043397)|regulation of neurological system process (GO:0031644)|release of sequestered calcium ion into cytosol (GO:0051209)|response to drug (GO:0042493)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding (GO:0071886)|drug binding (GO:0008144)|Gq/11-coupled serotonin receptor activity (GO:0001587)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(15)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	50					Agomelatine(DB06594)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Clomipramine(DB01242)|Clozapine(DB00363)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Dexfenfluramine(DB01191)|Doxepin(DB01142)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Lorcaserin(DB04871)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Pramipexole(DB00413)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Sertindole(DB06144)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)	ATACCGCTGACGATTATGGTG	0.502																																					p.T228R		Atlas-SNP	.											.	HTR2C	117	.	0			c.C683G						.						373	316	336					X																	114141284		2203	4300	6503	SO:0001583	missense	3358	exon6			CGCTGACGATTAT		CCDS14564.1, CCDS59174.1	Xq23	2013-12-19	2012-02-03		ENSG00000147246	ENSG00000147246		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5295	protein-coding gene	gene with protein product		312861	"5-hydroxytryptamine (serotonin) receptor 2C"	HTR1C		7895773	Standard	NM_000868		Approved	5-HT2C, 5HTR2C	uc004epu.1	P28335	OTTHUMG00000022226	ENST00000276198.1:c.683C>G	chrX.hg19:g.114141284C>G	ENSP00000276198:p.Thr228Arg	164.0	0.0		113.0	42.0	NM_000868	B1AMW4|Q5VUF8|Q9NP28	Missense_Mutation	SNP	ENST00000276198.1	hg19	CCDS14564.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.67|14.67	2.604386|2.604386	0.46423|0.46423	.|.	.|.	ENSG00000147246|ENSG00000147246	ENST00000371950|ENST00000276198;ENST00000371951	T|T;T	0.52295|0.38077	0.67|1.16;1.16	4.87|4.87	3.74|3.74	0.42951|0.42951	.|GPCR, rhodopsin-like superfamily (1);	.|0.226336	.|0.38164	.|N	.|0.001794	T|T	0.57286|0.57286	0.2043|0.2043	M|M	0.89353|0.89353	3.025|3.025	0.19300|0.19300	N|N	0.99998|0.99998	P|D	0.43094|0.71674	0.799|0.998	B|D	0.42798|0.70227	0.398|0.968	T|T	0.52381|0.52381	-0.8583|-0.8583	9|10	0.66056|0.46703	D|T	0.02|0.11	.|.	4.3412|4.3412	0.11110|0.11110	0.0:0.6903:0.0:0.3097|0.0:0.6903:0.0:0.3097	.|.	196|228	B1AMW4|P28335	.|5HT2C_HUMAN	E|R	196|228	ENSP00000361018:D196E|ENSP00000276198:T228R;ENSP00000361019:T228R	ENSP00000361018:D196E|ENSP00000276198:T228R	D|T	+|+	3|2	2|0	HTR2C|HTR2C	114047540|114047540	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.926000|0.926000	0.56050|0.56050	3.862000|3.862000	0.56009|0.56009	2.135000|2.135000	0.66039|0.66039	0.538000|0.538000	0.68166|0.68166	GAC|ACG	.	.		0.502	HTR2C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057962.1	NM_000868		G	114141284	C	G	114141284	3	3	291	1	0	0	0	0	1	0	0	0	7452	536	19	4	697	4	HTR2C	23	114141284	Missense_Mutation	SNP	C	TCGA-G3-A7M6-01A-11D-A33Q-10	13532314	114141284	41129276	79	42717										
UPF3B	65109	hgsc.bcm.edu	37	chrX	118971720	118971720	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	agtttaatgacaagcagcacCttgtttcttattcgatctct	6	9	2	1			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chrX:118971720C>G	ENST00000276201.2	-	10	1371	c.1302G>C	c.(1300-1302)aaG>aaC	p.K434N	UPF3B_ENST00000345865.2_Splice_Site_p.K421N|UPF3B_ENST00000478840.1_5'Flank	NM_080632.2	NP_542199.1	Q9BZI7	REN3B_HUMAN	UPF3 regulator of nonsense transcripts homolog B (yeast)	434	Necessary for interaction with RBM8A and for activating NMD.|Sufficient for association with EJC core.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(12)|ovary(2)|prostate(1)	30						CAAGCAGCACCTTGTTTCTTA	0.358																																					p.K434N		Atlas-SNP	.											.	UPF3B	74	.	0			c.G1302C						.						168	154	159					X																	118971720		2203	4300	6503	SO:0001630	splice_region_variant	65109	exon10			CAGCACCTTGTTT	AF318576	CCDS14587.1, CCDS14588.1	Xq25-q26	2014-01-31			ENSG00000125351	ENSG00000125351			20439	protein-coding gene	gene with protein product		300298	"mental retardation, X-linked 62"	MRX62		11113196, 11163187, 19238151	Standard	NM_023010		Approved	RENT3B, UPF3X, HUPF3B	uc004erz.2	Q9BZI7	OTTHUMG00000022282	ENST00000276201.2:c.1302+1G>C	chrX.hg19:g.118971720C>G		56.0	0.0		55.0	19.0	NM_080632	D3DWI3|D3DWI4|Q0VAK8|Q9H1J0	Missense_Mutation	SNP	ENST00000276201.2	hg19	CCDS14588.1	.	.	.	.	.	.	.	.	.	.	C	18.26	3.583624	0.65992	.	.	ENSG00000125351	ENST00000276201;ENST00000345865	D;D	0.94046	-3.34;-3.21	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	D	0.96846	0.8970	M	0.82823	2.61	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.83275	0.996;0.991	D	0.96956	0.9698	9	.	.	.	.	17.42	0.87512	0.0:1.0:0.0:0.0	.	421;434	Q9BZI7-2;Q9BZI7	.;REN3B_HUMAN	N	434;421	ENSP00000276201:K434N;ENSP00000245418:K421N	.	K	-	3	2	UPF3B	118855748	1.000000	0.71417	1.000000	0.80357	0.501000	0.33797	6.942000	0.75928	2.328000	0.79073	0.526000	0.51066	AAG	.	.		0.358	UPF3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058068.1		Missense_Mutation	G	118971720	C	G	118971720	5	3	291	1	0	0	0	0	0	0	1	0	17021	695	24	4	157	4	UPF3B	23	118971720	Splice_Site	SNP	C	TCGA-G3-A7M6-01A-11D-A33Q-10	4830436	118971720	36298840	80	42718										
SLC10A3	8273	hgsc.bcm.edu	37	chrX	153715955	153715955	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0740740740740741	6	1	0.990956072351421	1.42037037037037	0.760912698412698	1	1	0	gggcctgggaggcatagtcaGcttgaaggcggcggagggat	20	7	1	1			TCGA-G3-A7M6-01A-11D-A33Q-10	TCGA-G3-A7M6-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b169ab6b-42d8-4868-bfc2-8f08e8d8a0f6	23b38a16-e459-4735-8033-cc843860bb38	g.chrX:153715955G>T	ENST00000393587.4	-	3	1588	c.1325C>A	c.(1324-1326)gCt>gAt	p.A442D	SLC10A3_ENST00000393586.1_Missense_Mutation_p.A497D|UBL4A_ENST00000369653.4_5'Flank|UBL4A_ENST00000477777.1_5'Flank|SLC10A3_ENST00000369649.4_Missense_Mutation_p.A413D|UBL4A_ENST00000369660.4_5'Flank|SLC10A3_ENST00000263512.4_Missense_Mutation_p.A442D	NM_001142391.1|NM_001142392.1	NP_001135863.1|NP_001135864.1	P09131	P3_HUMAN	solute carrier family 10, member 3	442					response to retinoic acid (GO:0032526)	integral component of membrane (GO:0016021)	bile acid:sodium symporter activity (GO:0008508)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GGCATAGTCAGCTTGAAGGCG	0.632																																					p.A442D		Atlas-SNP	.											.	SLC10A3	42	.	0			c.C1325A						.						46	43	44					X																	153715955		2203	4300	6503	SO:0001583	missense	8273	exon3			TAGTCAGCTTGAA	X12458	CCDS14755.1, CCDS48195.1	Xq28	2013-07-18	2013-07-18		ENSG00000126903	ENSG00000126903		"Solute carriers"	22979	protein-coding gene	gene with protein product		312090				8733135	Standard	NM_019848		Approved	P3, DXS253E	uc004flq.3	P09131	OTTHUMG00000013369	ENST00000393587.4:c.1325C>A	chrX.hg19:g.153715955G>T	ENSP00000377212:p.Ala442Asp	130.0	0.0		124.0	37.0	NM_001142392	Q5HY79|Q9BSL2	Missense_Mutation	SNP	ENST00000393587.4	hg19	CCDS14755.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.028336	0.75390	.	.	ENSG00000126903	ENST00000369649;ENST00000393586;ENST00000263512;ENST00000393587	T;T;T;T	0.11495	2.94;2.77;2.79;2.79	5.1	4.23	0.50019	.	0.000000	0.64402	U	0.000001	T	0.26846	0.0657	L	0.53561	1.675	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.00783	-1.1568	10	0.87932	D	0	-20.2371	11.6956	0.51542	0.0906:0.0:0.9094:0.0	.	413;442	Q9BSL2;P09131	.;P3_HUMAN	D	413;497;442;442	ENSP00000358663:A413D;ENSP00000377211:A497D;ENSP00000263512:A442D;ENSP00000377212:A442D	ENSP00000263512:A442D	A	-	2	0	SLC10A3	153369149	1.000000	0.71417	0.599000	0.28851	0.972000	0.66771	8.439000	0.90308	1.036000	0.39998	0.513000	0.50165	GCT	.	.		0.632	SLC10A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037235.3	NM_019848		T	153715955	G	T	153715955	3	4	291	1	0	0	0	0	1	0	0	0	14390	971	34	3	112	3	SLC10A3	23	153715955	Missense_Mutation	SNP	G	TCGA-G3-A7M6-01A-11D-A33Q-10	34744235	153715955	1554605	81	42719										
PRDM2	7799	hgsc.bcm.edu	37	chr1	14105806	14105806	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.121212121212121	4	1	1.57333333333333	0	1.96666666666667	0.0285714285714286	0.304738562091504	0	gacggcatcagcgtagagttCacgaacgtcatctgattccc	10	12	4	2			TCGA-G3-A7M7-01A-12D-A34Z-10	TCGA-G3-A7M7-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e2d5d14-93c7-44fb-bee9-d6bf7c286368	3a264183-655d-4ab5-ade1-24ffbfd0cdb0	g.chr1:14105806C>T	ENST00000235372.7	+	8	2372	c.1516C>T	c.(1516-1518)Cac>Tac	p.H506Y	PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000413440.1_Missense_Mutation_p.H305Y|PRDM2_ENST00000503842.1_Intron|PRDM2_ENST00000311066.5_Missense_Mutation_p.H506Y|PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000343137.4_Missense_Mutation_p.H305Y	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	506					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		GCGTAGAGTTCACGAACGTCA	0.478																																					p.H506Y		Atlas-SNP	.											.	PRDM2	147	.	0			c.C1516T						.						43	43	43					1																	14105806		2203	4300	6503	SO:0001583	missense	7799	exon8			AGAGTTCACGAAC	U17838	CCDS150.1, CCDS151.1, CCDS30603.1, CCDS44061.1	1p36	2011-07-01			ENSG00000116731	ENSG00000116731		"Chromatin-modifying enzymes / K-methyltransferases"	9347	protein-coding gene	gene with protein product	"retinoblastoma protein-binding zinc finger protein", "retinoblastoma protein-interacting zinc finger protein", "MTE-binding protein", "zinc-finger DNA-binding protein", "GATA-3 binding protein G3B"	601196				7538672	Standard	NM_012231		Approved	RIZ, RIZ1, RIZ2, KMT8, MTB-ZF, HUMHOXY1	uc001avi.3	Q13029	OTTHUMG00000007917	ENST00000235372.7:c.1516C>T	chr1.hg19:g.14105806C>T	ENSP00000235372:p.His506Tyr	82.0	0.0		39.0	13.0	NM_015866	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Missense_Mutation	SNP	ENST00000235372.7	hg19	CCDS150.1	.	.	.	.	.	.	.	.	.	.	C	16.57	3.158860	0.57368	.	.	ENSG00000116731	ENST00000235372;ENST00000311066;ENST00000400800;ENST00000413440;ENST00000343137	D;D;D;D	0.85955	-2.05;-2.05;-2.05;-2.05	5.62	5.62	0.85841	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);	0.000000	0.85682	D	0.000000	D	0.89086	0.6615	L	0.34521	1.04	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	D	0.90131	0.4206	10	0.87932	D	0	.	18.2252	0.89915	0.0:1.0:0.0:0.0	.	506;364;506;506	A8MW16;Q5THJ0;Q13029;Q13029-2	.;.;PRDM2_HUMAN;.	Y	506;506;506;305;305	ENSP00000235372:H506Y;ENSP00000312352:H506Y;ENSP00000411103:H305Y;ENSP00000341621:H305Y	ENSP00000235372:H506Y	H	+	1	0	PRDM2	13978393	1.000000	0.71417	0.113000	0.21522	0.980000	0.70556	7.487000	0.81328	2.633000	0.89246	0.655000	0.94253	CAC	.	.		0.478	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231		T	14105806	C	T	14105806	3	4	292	1	0	0	0	0	1	0	0	0	12470	826	29	3	1542	3	PRDM2	1	14105806	Missense_Mutation	SNP	C	TCGA-G3-A7M7-01A-12D-A34Z-10		14105806	235144815	1	42720										
COL24A1	255631	hgsc.bcm.edu	37	chr1	86554879	86554879	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.121212121212121	4	1	1.57333333333333	0	1.96666666666667	0.0285714285714286	0.304738562091504	0	tatcaccttgcataccagggGggcccattaatccagaaagg	10	11	1	1			TCGA-G3-A7M7-01A-12D-A34Z-10	TCGA-G3-A7M7-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e2d5d14-93c7-44fb-bee9-d6bf7c286368	3a264183-655d-4ab5-ade1-24ffbfd0cdb0	g.chr1:86554879G>A	ENST00000370571.2	-	7	2051	c.1685C>T	c.(1684-1686)cCc>cTc	p.P562L	COL24A1_ENST00000436319.1_Missense_Mutation_p.P562L	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	562	Collagen-like 2.				extracellular matrix organization (GO:0030198)|hematopoietic progenitor cell differentiation (GO:0002244)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			NS(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(9)|liver(1)|lung(56)|ovary(4)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	101				all cancers(265;0.0627)|Epithelial(280;0.0689)		CATACCAGGGGGGCCCATTAA	0.328																																					p.P562L		Atlas-SNP	.											.	COL24A1	202	.	0			c.C1685T						.						78	77	77					1																	86554879		1805	4063	5868	SO:0001583	missense	255631	exon7			CCAGGGGGGCCCA	AF410793	CCDS41353.1	1p22.3-p22.2	2013-01-16			ENSG00000171502	ENSG00000171502		"Collagens"	20821	protein-coding gene	gene with protein product		610025					Standard	NM_152890		Approved		uc001dlj.3	Q17RW2	OTTHUMG00000010629	ENST00000370571.2:c.1685C>T	chr1.hg19:g.86554879G>A	ENSP00000359603:p.Pro562Leu	188.0	0.0		160.0	40.0	NM_152890	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Missense_Mutation	SNP	ENST00000370571.2	hg19	CCDS41353.1	.	.	.	.	.	.	.	.	.	.	G	6.261	0.416198	0.11870	.	.	ENSG00000171502	ENST00000370571;ENST00000436319	D;T	0.96685	-4.09;2.33	5.41	4.5	0.54988	.	0.390052	0.18954	N	0.126616	D	0.88291	0.6397	L	0.42529	1.33	0.58432	D	0.99999	P;B	0.41848	0.763;0.001	B;B	0.39465	0.3;0.005	D	0.86991	0.2110	10	0.08837	T	0.75	.	10.1227	0.42630	0.09:0.0:0.91:0.0	.	562;562	F8WDM8;Q17RW2	.;COOA1_HUMAN	L	562	ENSP00000359603:P562L;ENSP00000392531:P562L	ENSP00000359603:P562L	P	-	2	0	COL24A1	86327467	0.999000	0.42202	0.945000	0.38365	0.351000	0.29236	3.506000	0.53364	1.529000	0.49120	-0.291000	0.09656	CCC	.	.		0.328	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	NM_152890		A	86554879	G	A	86554879	3	1	292	1	0	0	0	0	1	0	0	0	3685	1232	43	3	3675	3	COL24A1	1	86554879	Missense_Mutation	SNP	G	TCGA-G3-A7M7-01A-12D-A34Z-10	72449073	86554879	162695742	2	42721										
PGBD2	267002	hgsc.bcm.edu	37	chr1	249211312	249211312	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.121212121212121	4	1	1.57333333333333	0	1.96666666666667	0.0285714285714286	0.304738562091504	0	tcaatttgagtcttacggctCaggaattgaagtgtgttttg	11	5	3	2			TCGA-G3-A7M7-01A-12D-A34Z-10	TCGA-G3-A7M7-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e2d5d14-93c7-44fb-bee9-d6bf7c286368	3a264183-655d-4ab5-ade1-24ffbfd0cdb0	g.chr1:249211312C>T	ENST00000329291.5	+	3	676	c.529C>T	c.(529-531)Cag>Tag	p.Q177*	PGBD2_ENST00000462488.1_Intron|PGBD2_ENST00000355360.4_Intron|PGBD2_ENST00000539153.1_Nonsense_Mutation_p.Q174*	NM_170725.2	NP_733843.1	Q6P3X8	PGBD2_HUMAN	piggyBac transposable element derived 2	177										NS(1)|endometrium(3)|lung(6)|ovary(1)|skin(3)	14	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.012)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			TCTTACGGCTCAGGAATTGAA	0.368																																					p.Q177X		Atlas-SNP	.											.	PGBD2	103	.	0			c.C529T						.						146	150	149					1																	249211312		2203	4300	6503	SO:0001587	stop_gained	267002	exon3			ACGGCTCAGGAAT	AF229602	CCDS31128.1, CCDS31129.1	1q	2008-02-05			ENSG00000185220	ENSG00000185220			19399	protein-coding gene	gene with protein product							Standard	XM_005270333		Approved		uc001ifh.3	Q6P3X8	OTTHUMG00000040424	ENST00000329291.5:c.529C>T	chr1.hg19:g.249211312C>T	ENSP00000331643:p.Gln177*	47.0	0.0		46.0	12.0	NM_170725	B3KVR8|Q6MZF8	Nonsense_Mutation	SNP	ENST00000329291.5	hg19	CCDS31128.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.322177	0.81580	.	.	ENSG00000185220	ENST00000329291;ENST00000539153	.	.	.	4.04	4.04	0.47022	.	0.000000	0.33792	N	0.004560	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06891	T	0.86	-13.8225	11.9052	0.52708	0.0:1.0:0.0:0.0	.	.	.	.	X	177;174	.	ENSP00000331643:Q177X	Q	+	1	0	PGBD2	247177935	0.739000	0.28196	0.939000	0.37840	0.528000	0.34623	0.864000	0.27926	2.243000	0.73865	0.655000	0.94253	CAG	.	.		0.368	PGBD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000097318.1			T	249211312	C	T	249211312	4	4	292	1	0	0	0	0	0	1	0	0	11790	827	29	3	535	3	PGBD2	1	249211312	Nonsense_Mutation	SNP	C	TCGA-G3-A7M7-01A-12D-A34Z-10	162656433	249211312	39309	3	42722										
LHCGR	3973	hgsc.bcm.edu	37	chr2	48950602	48950602	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.121212121212121	4	1	1.57333333333333	0	1.96666666666667	0.0285714285714286	0.304738562091504	0	ggagtttactcacagtgttaCagattcattattcatccctt	6	9	3	1			TCGA-G3-A7M7-01A-12D-A34Z-10	TCGA-G3-A7M7-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e2d5d14-93c7-44fb-bee9-d6bf7c286368	3a264183-655d-4ab5-ade1-24ffbfd0cdb0	g.chr2:48950602C>A	ENST00000294954.7	-	6	550	c.529G>T	c.(529-531)Gta>Tta	p.V177L	LHCGR_ENST00000401907.1_Missense_Mutation_p.V177L|LHCGR_ENST00000403273.1_Missense_Mutation_p.V177L|STON1-GTF2A1L_ENST00000402114.2_Intron|LHCGR_ENST00000405626.1_Missense_Mutation_p.V177L|LHCGR_ENST00000344775.3_Missense_Mutation_p.V177L	NM_000233.3	NP_000224.2	P22888	LSHR_HUMAN	luteinizing hormone/choriogonadotropin receptor	177					activation of adenylate cyclase activity (GO:0007190)|cellular response to gonadotropin stimulus (GO:0071371)|cognition (GO:0050890)|development of secondary male sexual characteristics (GO:0046544)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|ovarian follicle development (GO:0001541)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|regulation of steroid hormone biosynthetic process (GO:0090030)|seminiferous tubule development (GO:0072520)|spermatogenesis (GO:0007283)|uterus development (GO:0060065)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	choriogonadotropin hormone binding (GO:0038106)|choriogonadotropin hormone receptor activity (GO:0035472)|luteinizing hormone receptor activity (GO:0004964)			NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(3)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	56		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Buserelin(DB06719)|Cetrorelix(DB00050)|Choriogonadotropin alfa(DB00097)|Goserelin(DB00014)|Lutropin alfa(DB00044)|Menotropins(DB00032)	CACAGTGTTACAGATTCATTA	0.383																																					p.V177L		Atlas-SNP	.											.	LHCGR	154	.	0			c.G529T						.						114	104	108					2																	48950602		2203	4300	6503	SO:0001583	missense	3973	exon6			GTGTTACAGATTC		CCDS1842.1	2p21	2012-08-10			ENSG00000138039	ENSG00000138039		"GPCR / Class A : Gonadotropin and TSH receptors"	6585	protein-coding gene	gene with protein product		152790	"hypergonadotropic hypogonadism"	HHG			Standard	NM_000233		Approved	LHR, LCGR, LGR2, ULG5	uc002rwu.4	P22888	OTTHUMG00000129257	ENST00000294954.7:c.529G>T	chr2.hg19:g.48950602C>A	ENSP00000294954:p.Val177Leu	82.0	0.0		55.0	11.0	NM_000233	Q14751|Q15996|Q9UEW9	Missense_Mutation	SNP	ENST00000294954.7	hg19	CCDS1842.1	.	.	.	.	.	.	.	.	.	.	C	8.709	0.911526	0.17833	.	.	ENSG00000138039	ENST00000344775;ENST00000294954;ENST00000405626;ENST00000403273;ENST00000401907;ENST00000428232	D;D;T;D;D;T	0.91843	-2.92;-2.92;-1.19;-2.92;-2.92;-1.19	5.62	-5.23	0.02798	.	0.688144	0.15640	N	0.251926	T	0.76877	0.4049	N	0.13003	0.285	0.18873	N	0.999983	B	0.06786	0.001	B	0.08055	0.003	T	0.65092	-0.6252	9	.	.	.	.	3.6028	0.08031	0.1807:0.4397:0.1135:0.2661	.	177	P22888	LSHR_HUMAN	L	177;177;177;177;177;143	ENSP00000344301:V177L;ENSP00000294954:V177L;ENSP00000386033:V177L;ENSP00000385847:V177L;ENSP00000385406:V177L;ENSP00000403748:V143L	.	V	-	1	0	LHCGR	48804106	0.000000	0.05858	0.978000	0.43139	0.948000	0.59901	-1.301000	0.02749	-0.364000	0.08088	-1.124000	0.02001	GTA	.	.		0.383	LHCGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251364.4	NM_000233.3		A	48950602	C	A	48950602	3	1	292	1	0	0	0	0	1	0	0	0	8771	478	17	3	1594	3	LHCGR	2	48950602	Missense_Mutation	SNP	C	TCGA-G3-A7M7-01A-12D-A34Z-10		48950602	194248771	4	42723										
FARSB	10056	hgsc.bcm.edu	37	chr2	223494886	223494886	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.121212121212121	4	1	1.57333333333333	0	1.96666666666667	0.0285714285714286	0.304738562091504	0	tgacaataatatcaagaactAtttttgcctgcaaagaaaag	6	6	1	3			TCGA-G3-A7M7-01A-12D-A34Z-10	TCGA-G3-A7M7-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e2d5d14-93c7-44fb-bee9-d6bf7c286368	3a264183-655d-4ab5-ade1-24ffbfd0cdb0	g.chr2:223494886A>G	ENST00000281828.6	-	9	1057	c.794T>C	c.(793-795)aTa>aCa	p.I265T	FARSB_ENST00000536361.1_Missense_Mutation_p.I166T	NM_005687.3	NP_005678.3	Q9NSD9	SYFB_HUMAN	phenylalanyl-tRNA synthetase, beta subunit	265					gene expression (GO:0010467)|phenylalanyl-tRNA aminoacylation (GO:0006432)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|phenylalanine-tRNA ligase activity (GO:0004826)|RNA binding (GO:0003723)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	24		Renal(207;0.0183)		Epithelial(121;3.47e-10)|all cancers(144;1.86e-07)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.011)	L-Phenylalanine(DB00120)	ATCAAGAACTATTTTTGCCTG	0.303																																					p.I265T		Atlas-SNP	.											.	FARSB	49	.	0			c.T794C						.						92	89	90					2																	223494886		2202	4300	6502	SO:0001583	missense	10056	exon9			AGAACTATTTTTG	AF042346	CCDS2454.1	2q36.2	2011-07-01	2007-02-23	2007-02-23	ENSG00000116120	ENSG00000116120	6.1.1.20	"Aminoacyl tRNA synthetases / Class II"	17800	protein-coding gene	gene with protein product	"phenylalanine tRNA ligase 1, beta, cytoplasmic"	609690	"phenylalanyl-tRNA synthetase-like, beta subunit"	FARSLB		10049785	Standard	NM_005687		Approved	PheHB, FRSB	uc002vne.1	Q9NSD9	OTTHUMG00000133155	ENST00000281828.6:c.794T>C	chr2.hg19:g.223494886A>G	ENSP00000281828:p.Ile265Thr	143.0	0.0		111.0	36.0	NM_005687	B4DFM0|O95708|Q4ZFX1|Q57ZJ5|Q9NZZ6	Missense_Mutation	SNP	ENST00000281828.6	hg19	CCDS2454.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.001283	0.74818	.	.	ENSG00000116120	ENST00000281828;ENST00000536361	T;T	0.28069	1.63;1.63	5.57	5.57	0.84162	B3/B4 tRNA-binding domain (2);Phenylalanyl-tRNA synthetase, B3/B4 (1);	0.041677	0.85682	D	0.000000	T	0.43545	0.1252	M	0.75447	2.3	0.80722	D	1	P;B	0.42973	0.796;0.43	P;P	0.46026	0.501;0.501	T	0.40232	-0.9574	10	0.45353	T	0.12	-15.0248	15.7429	0.77914	1.0:0.0:0.0:0.0	.	265;265	A8K666;Q9NSD9	.;SYFB_HUMAN	T	265;166	ENSP00000281828:I265T;ENSP00000442950:I166T	ENSP00000281828:I265T	I	-	2	0	FARSB	223203130	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.961000	0.76042	2.118000	0.64928	0.528000	0.53228	ATA	.	.		0.303	FARSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256855.2	NM_005687		G	223494886	A	G	223494886	3	3	292	1	0	0	0	0	1	0	0	0	5688	449	16	2	1011	2	FARSB	2	223494886	Missense_Mutation	SNP	A	TCGA-G3-A7M7-01A-12D-A34Z-10	174544284	223494886	19704487	5	42724										
TRPM8	79054	hgsc.bcm.edu	37	chr2	234839334	234839334	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.121212121212121	4	1	1.57333333333333	0	1.96666666666667	0.0285714285714286	0.304738562091504	0	acttggtgaattttattcaaGcaaattttaagaaacgagaa	7	4	1	3			TCGA-G3-A7M7-01A-12D-A34Z-10	TCGA-G3-A7M7-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e2d5d14-93c7-44fb-bee9-d6bf7c286368	3a264183-655d-4ab5-ade1-24ffbfd0cdb0	g.chr2:234839334G>A	ENST00000324695.4	+	3	179	c.139G>A	c.(139-141)Gca>Aca	p.A47T	TRPM8_ENST00000409625.1_5'UTR|TRPM8_ENST00000355722.4_5'UTR|TRPM8_ENST00000433712.2_5'UTR	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8	47					calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|protein homotetramerization (GO:0051289)|protein homotrimerization (GO:0070207)|response to cold (GO:0009409)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(2)|lung(27)|prostate(2)|skin(7)|stomach(2)	66		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)	TTTTATTCAAGCAAATTTTAA	0.328																																					p.A47T		Atlas-SNP	.											.	TRPM8	146	.	0			c.G139A						.						105	112	110					2																	234839334		2203	4299	6502	SO:0001583	missense	79054	exon3			ATTCAAGCAAATT	AC005538	CCDS33407.1	2q37	2011-12-14			ENSG00000144481	ENSG00000144481		"Voltage-gated ion channels / Transient receptor potential cation channels"	17961	protein-coding gene	gene with protein product		606678				16382100	Standard	NM_024080		Approved		uc002vvh.3	Q7Z2W7	OTTHUMG00000059129	ENST00000324695.4:c.139G>A	chr2.hg19:g.234839334G>A	ENSP00000323926:p.Ala47Thr	92.0	0.0		57.0	13.0	NM_024080	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Missense_Mutation	SNP	ENST00000324695.4	hg19	CCDS33407.1	.	.	.	.	.	.	.	.	.	.	G	15.87	2.960578	0.53400	.	.	ENSG00000144481	ENST00000324695	T	0.61392	0.11	5.51	4.63	0.57726	.	0.150706	0.45361	N	0.000377	T	0.41096	0.1144	N	0.20685	0.6	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18777	-1.0326	10	0.21014	T	0.42	-0.4364	13.1702	0.59593	0.0773:0.0:0.9227:0.0	.	47	Q7Z2W7	TRPM8_HUMAN	T	47	ENSP00000323926:A47T	ENSP00000323926:A47T	A	+	1	0	TRPM8	234504073	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	4.752000	0.62176	1.320000	0.45209	0.650000	0.86243	GCA	.	.		0.328	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080		A	234839334	G	A	234839334	3	1	292	1	0	0	0	0	1	0	0	0	16607	971	34	3	145	3	TRPM8	2	234839334	Missense_Mutation	SNP	G	TCGA-G3-A7M7-01A-12D-A34Z-10	11344448	234839334	8360039	6	42725										
BOC	91653	hgsc.bcm.edu	37	chr3	113005642	113005642	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.121212121212121	4	1	1.57333333333333	0	1.96666666666667	0.0285714285714286	0.304738562091504	0	ggcctacgtaggacaggaacCtggaatgcagctctccccgg	13	13	1	0			TCGA-G3-A7M7-01A-12D-A34Z-10	TCGA-G3-A7M7-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e2d5d14-93c7-44fb-bee9-d6bf7c286368	3a264183-655d-4ab5-ade1-24ffbfd0cdb0	g.chr3:113005642C>A	ENST00000495514.1	+	20	3982	c.3278C>A	c.(3277-3279)cCt>cAt	p.P1093H	BOC_ENST00000355385.3_Missense_Mutation_p.P1093H|BOC_ENST00000273395.4_Missense_Mutation_p.P1094H			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	1093					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			GGACAGGAACCTGGAATGCAG	0.542																																					p.P1093H		Atlas-SNP	.											.	BOC	139	.	0			c.C3278A						.						112	120	117					3																	113005642		2203	4300	6503	SO:0001583	missense	91653	exon20			AGGAACCTGGAAT	AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	17173	protein-coding gene	gene with protein product	"brother of CDO", "brother of CDON", "cell adhesion associated, oncogene regulated 2"	608708	"Boc homolog (mouse)"			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.3278C>A	chr3.hg19:g.113005642C>A	ENSP00000418663:p.Pro1093His	60.0	0.0		33.0	12.0	NM_033254	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Missense_Mutation	SNP	ENST00000495514.1	hg19	CCDS2971.1	.	.	.	.	.	.	.	.	.	.	C	11.05	1.524587	0.27299	.	.	ENSG00000144857	ENST00000495514;ENST00000273395;ENST00000355385	T;T;T	0.59638	0.25;0.25;0.25	6.17	-0.237	0.13061	.	0.542823	0.18213	N	0.148136	T	0.34048	0.0884	N	0.24115	0.695	0.09310	N	1	B;B	0.12013	0.005;0.003	B;B	0.10450	0.005;0.002	T	0.10730	-1.0617	10	0.39692	T	0.17	.	2.384	0.04361	0.1335:0.4771:0.1308:0.2585	.	1094;1093	Q9BWV1-3;Q9BWV1	.;BOC_HUMAN	H	1093;1094;1093	ENSP00000418663:P1093H;ENSP00000273395:P1094H;ENSP00000347546:P1093H	ENSP00000273395:P1094H	P	+	2	0	BOC	114488332	0.000000	0.05858	0.002000	0.10522	0.400000	0.30750	-0.119000	0.10676	-0.106000	0.12110	0.655000	0.94253	CCT	.	.		0.542	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254		A	113005642	C	A	113005642	3	1	292	1	0	0	0	0	1	0	0	0	1481	681	24	3	3348	3	BOC	3	113005642	Missense_Mutation	SNP	C	TCGA-G3-A7M7-01A-12D-A34Z-10		113005642	85016788	7	42726										
ATR	545	hgsc.bcm.edu	37	chr3	142275251	142275251	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.121212121212121	4	1	1.57333333333333	0	1.96666666666667	0.0285714285714286	0.304738562091504	0	atcttgggaactctgttacaAgaattctgctgctgcaataa	8	8	3	1			TCGA-G3-A7M7-01A-12D-A34Z-10	TCGA-G3-A7M7-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e2d5d14-93c7-44fb-bee9-d6bf7c286368	3a264183-655d-4ab5-ade1-24ffbfd0cdb0	g.chr3:142275251A>C	ENST00000350721.4	-	9	2173	c.2052T>G	c.(2050-2052)tcT>tcG	p.S684S	ATR_ENST00000383101.3_Silent_p.S620S	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	684					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						CTCTGTTACAAGAATTCTGCT	0.388								Other conserved DNA damage response genes																													p.S684S		Atlas-SNP	.											.	ATR	285	.	0			c.T2052G						.						70	77	74					3																	142275251		2203	4300	6503	SO:0001819	synonymous_variant	545	exon9			GTTACAAGAATTC	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.2052T>G	chr3.hg19:g.142275251A>C		87.0	0.0		77.0	18.0	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Silent	SNP	ENST00000350721.4	hg19	CCDS3124.1																																																																																			.	.		0.388	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		C	142275251	A	C	142275251	2	2	292	1	0	0	0	0	0	0	0	1	1204	59	3	5		5	ATR	3	142275251	Silent	SNP	A	TCGA-G3-A7M7-01A-12D-A34Z-10	29269609	142275251	55747179	8	42727										
PCDHB5	26167	hgsc.bcm.edu	37	chr5	140516880	140516880	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.121212121212121	4	1	1.57333333333333	0	1.96666666666667	0.0285714285714286	0.304738562091504	0	gcatgtgggcgcacaatggcGaggtgcgcaccgccaggctg	17	12	0	0			TCGA-G3-A7M7-01A-12D-A34Z-10	TCGA-G3-A7M7-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e2d5d14-93c7-44fb-bee9-d6bf7c286368	3a264183-655d-4ab5-ade1-24ffbfd0cdb0	g.chr5:140516880G>C	ENST00000231134.5	+	1	2081	c.1864G>C	c.(1864-1866)Gag>Cag	p.E622Q		NM_015669.2	NP_056484.1	Q9Y5E4	PCDB5_HUMAN	protocadherin beta 5	622	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|kidney(1)|large_intestine(18)|lung(25)|ovary(3)|prostate(6)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	81			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GCACAATGGCGAGGTGCGCAC	0.706																																					p.E622Q		Atlas-SNP	.											.	PCDHB5	184	.	0			c.G1864C						.						44	46	45					5																	140516880		2155	4208	6363	SO:0001583	missense	26167	exon1			AATGGCGAGGTGC	AF152498	CCDS4247.1	5q31	2010-01-26			ENSG00000113209	ENSG00000113209		"Cadherins / Protocadherins : Clustered"	8690	other	protocadherin		606331				10380929	Standard	NM_015669		Approved	DKFZp586B0217, PCDH-BETA5	uc003liq.3	Q9Y5E4	OTTHUMG00000129616	ENST00000231134.5:c.1864G>C	chr5.hg19:g.140516880G>C	ENSP00000231134:p.Glu622Gln	9.0	0.0		11.0	4.0	NM_015669	Q549F4|Q9UFU9	Missense_Mutation	SNP	ENST00000231134.5	hg19	CCDS4247.1	.	.	.	.	.	.	.	.	.	.	G	18.56	3.650117	0.67472	.	.	ENSG00000113209	ENST00000231134	T	0.53423	0.62	4.65	4.65	0.58169	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.70954	0.3283	M	0.84156	2.68	0.36717	D	0.880998	D	0.65815	0.995	D	0.68039	0.955	T	0.80763	-0.1237	9	0.87932	D	0	.	17.92	0.88963	0.0:0.0:1.0:0.0	.	622	Q9Y5E4	PCDB5_HUMAN	Q	622	ENSP00000231134:E622Q	ENSP00000231134:E622Q	E	+	1	0	PCDHB5	140497064	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	3.522000	0.53480	2.301000	0.77427	0.430000	0.28490	GAG	.	.		0.706	PCDHB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251811.1	NM_015669		C	140516880	G	C	140516880	3	2	292	1	0	0	0	0	1	0	0	0	11554	1059	37	4	1866	4	PCDHB5	5	140516880	Missense_Mutation	SNP	G	TCGA-G3-A7M7-01A-12D-A34Z-10		140516880	40398380	9	42728										
MFAP3	4238	hgsc.bcm.edu	37	chr5	153429404	153429404	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.121212121212121	4	1	1.57333333333333	0	1.96666666666667	0.0285714285714286	0.304738562091504	0	agcaaatcgtagttcttacaAtgcatcctttccctcaagct	5	12	2	0			TCGA-G3-A7M7-01A-12D-A34Z-10	TCGA-G3-A7M7-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e2d5d14-93c7-44fb-bee9-d6bf7c286368	3a264183-655d-4ab5-ade1-24ffbfd0cdb0	g.chr5:153429404A>G	ENST00000436816.1	+	2	341	c.122A>G	c.(121-123)aAt>aGt	p.N41S	MFAP3_ENST00000322602.5_Missense_Mutation_p.N41S|MFAP3_ENST00000439768.2_Intron	NM_001242336.1|NM_005927.4	NP_001229265.1|NP_005918.1	P55082	MFAP3_HUMAN	microfibrillar-associated protein 3	41					extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|kidney(2)|large_intestine(1)|lung(2)|pancreas(1)	7	Renal(175;0.00488)	Lung NSC(249;0.00145)|all_lung(500;0.00226)|all_neural(177;0.122)|Breast(839;0.14)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)	OV - Ovarian serous cystadenocarcinoma(192;9.69e-06)|GBM - Glioblastoma multiforme(465;0.0201)		AGTTCTTACAATGCATCCTTT	0.423																																					p.N41S		Atlas-SNP	.											.	MFAP3	20	.	0			c.A122G						.						107	95	99					5																	153429404		2203	4300	6503	SO:0001583	missense	4238	exon2			CTTACAATGCATC		CCDS4324.1, CCDS47319.1	5q32-q33.2	2013-01-11			ENSG00000037749	ENSG00000037749		"Immunoglobulin superfamily / I-set domain containing"	7034	protein-coding gene	gene with protein product		600491				7782085	Standard	NM_005927		Approved		uc010jib.2	P55082	OTTHUMG00000130149	ENST00000436816.1:c.122A>G	chr5.hg19:g.153429404A>G	ENSP00000409933:p.Asn41Ser	120.0	0.0		84.0	21.0	NM_005927	B2RDK0|B4DKA1|Q9NXA7	Missense_Mutation	SNP	ENST00000436816.1	hg19	CCDS4324.1	.	.	.	.	.	.	.	.	.	.	A	18.77	3.694667	0.68386	.	.	ENSG00000037749	ENST00000522782;ENST00000436816;ENST00000322602;ENST00000522177	T;T	0.19250	2.16;2.16	5.8	5.8	0.92144	.	0.350970	0.33092	N	0.005295	T	0.18593	0.0446	L	0.29908	0.895	0.42581	D	0.993218	B	0.26876	0.162	B	0.21917	0.037	T	0.02498	-1.1150	10	0.62326	D	0.03	-28.0662	16.1512	0.81624	1.0:0.0:0.0:0.0	.	41	P55082	MFAP3_HUMAN	S	41	ENSP00000409933:N41S;ENSP00000322956:N41S	ENSP00000322956:N41S	N	+	2	0	MFAP3	153409597	0.998000	0.40836	0.811000	0.32455	0.919000	0.55068	2.503000	0.45407	2.222000	0.72286	0.533000	0.62120	AAT	.	.		0.423	MFAP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252457.2	NM_005927		G	153429404	A	G	153429404	3	3	292	1	0	0	0	0	1	0	0	0	9524	101	4	2	124	2	MFAP3	5	153429404	Missense_Mutation	SNP	A	TCGA-G3-A7M7-01A-12D-A34Z-10	12912524	153429404	27485856	10	42729										
ESR1	2099	hgsc.bcm.edu	37	chr6	152415519	152415519	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.121212121212121	4	1	1.57333333333333	0	1.96666666666667	0.0285714285714286	0.304738562091504	0	actctctctctgcgcattcaGgagtgtacacatttctgtcc	7	13	4	0			TCGA-G3-A7M7-01A-12D-A34Z-10	TCGA-G3-A7M7-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e2d5d14-93c7-44fb-bee9-d6bf7c286368	3a264183-655d-4ab5-ade1-24ffbfd0cdb0	g.chr6:152415519G>A	ENST00000206249.3	+	7	1731		c.e7-1		ESR1_ENST00000456483.2_Splice_Site|ESR1_ENST00000406599.1_Splice_Site|ESR1_ENST00000440973.1_Splice_Site|ESR1_ENST00000443427.1_Splice_Site|ESR1_ENST00000338799.5_Splice_Site|ESR1_ENST00000427531.2_Intron	NM_000125.3	NP_000116.2	P03372	ESR1_HUMAN	estrogen receptor 1						androgen metabolic process (GO:0008209)|antral ovarian follicle growth (GO:0001547)|cellular response to estradiol stimulus (GO:0071392)|chromatin remodeling (GO:0006338)|epithelial cell development (GO:0002064)|epithelial cell proliferation involved in mammary gland duct elongation (GO:0060750)|gene expression (GO:0010467)|intracellular estrogen receptor signaling pathway (GO:0030520)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|male gonad development (GO:0008584)|mammary gland alveolus development (GO:0060749)|mammary gland branching involved in pregnancy (GO:0060745)|negative regulation of gene expression (GO:0010629)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|uterus development (GO:0060065)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|transcriptionally active chromatin (GO:0035327)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enzyme binding (GO:0019899)|estrogen receptor activity (GO:0030284)|estrogen response element binding (GO:0034056)|estrogen-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0038052)|identical protein binding (GO:0042802)|nitric-oxide synthase regulator activity (GO:0030235)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(19)|ovary(1)|prostate(2)|skin(1)	49		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Allylestrenol(DB01431)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Estropipate(DB04574)|Ethinyl Estradiol(DB00977)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Ospemifene(DB04938)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)|Trilostane(DB01108)	TGCGCATTCAGGAGTGTACAC	0.502																																					.		Atlas-SNP	.											.	ESR1	94	.	0			c.1370-1G>A						.						121	122	122					6																	152415519		2203	4300	6503	SO:0001630	splice_region_variant	2099	exon9			CATTCAGGAGTGT	X03635	CCDS5234.1	6q24-q27	2013-01-16			ENSG00000091831	ENSG00000091831		"Nuclear hormone receptors"	3467	protein-coding gene	gene with protein product		133430		ESR		3754034	Standard	NM_000125		Approved	NR3A1, Era	uc003qon.4	P03372	OTTHUMG00000016103	ENST00000206249.3:c.1370-1G>A	chr6.hg19:g.152415519G>A		49.0	0.0		38.0	10.0	NM_001122742	Q13511|Q14276|Q5T5H7|Q6MZQ9|Q9NU51|Q9UDZ7|Q9UIS7	Splice_Site	SNP	ENST00000206249.3	hg19	CCDS5234.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.743328	0.89663	.	.	ENSG00000091831	ENST00000440973;ENST00000338799;ENST00000456483;ENST00000443427;ENST00000206249;ENST00000406599;ENST00000431590	.	.	.	5.43	5.43	0.79202	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.2505	0.93923	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ESR1	152457212	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.888000	0.92464	2.555000	0.86185	0.555000	0.69702	.	.	.		0.502	ESR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043308.1		Intron	A	152415519	G	A	152415519	5	1	292	1	0	0	0	0	0	0	1	0	5258	1014	35	3	1395	3	ESR1	6	152415519	Splice_Site	SNP	G	TCGA-G3-A7M7-01A-12D-A34Z-10		152415519	18699548	11	42730										
SAMD9	54809	hgsc.bcm.edu	37	chr7	92733863	92733863	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.121212121212121	4	1	1.57333333333333	0	1.96666666666667	0.0285714285714286	0.304738562091504	0	ttcctgacatcagaagctctTtctctttgccaggaacttgg	8	11	3	2			TCGA-G3-A7M7-01A-12D-A34Z-10	TCGA-G3-A7M7-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e2d5d14-93c7-44fb-bee9-d6bf7c286368	3a264183-655d-4ab5-ade1-24ffbfd0cdb0	g.chr7:92733863T>A	ENST00000379958.2	-	3	1817	c.1548A>T	c.(1546-1548)gaA>gaT	p.E516D		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	516						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			CAGAAGCTCTTTCTCTTTGCC	0.393																																					p.E516D		Atlas-SNP	.											.	SAMD9	239	.	0			c.A1548T						.						92	95	94					7																	92733863		2203	4300	6503	SO:0001583	missense	54809	exon2			AGCTCTTTCTCTT	AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"Sterile alpha motif (SAM) domain containing"	1348	protein-coding gene	gene with protein product		610456	"chromosome 7 open reading frame 5"	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.1548A>T	chr7.hg19:g.92733863T>A	ENSP00000369292:p.Glu516Asp	71.0	0.0		51.0	18.0	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Missense_Mutation	SNP	ENST00000379958.2	hg19	CCDS34680.1	.	.	.	.	.	.	.	.	.	.	T	7.051	0.564393	0.13498	.	.	ENSG00000205413	ENST00000379958;ENST00000446617	T;T	0.13778	2.56;2.56	4.08	0.513	0.17000	.	0.178248	0.33959	U	0.004389	T	0.07052	0.0179	L	0.28192	0.835	0.23449	N	0.997659	B	0.25272	0.122	B	0.25614	0.062	T	0.32666	-0.9898	10	0.21014	T	0.42	.	3.8598	0.08991	0.1589:0.2907:0.0:0.5504	.	516	Q5K651	SAMD9_HUMAN	D	516	ENSP00000369292:E516D;ENSP00000414529:E516D	ENSP00000369292:E516D	E	-	3	2	SAMD9	92571799	0.610000	0.26983	1.000000	0.80357	0.996000	0.88848	-0.004000	0.12878	0.249000	0.21456	0.491000	0.48974	GAA	.	.		0.393	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654		A	92733863	T	A	92733863	3	1	292	1	0	0	0	0	1	0	0	0	13841	1838	64	4	3225	4	SAMD9	7	92733863	Missense_Mutation	SNP	T	TCGA-G3-A7M7-01A-12D-A34Z-10		92733863	66404800	12	42731										
OR2F1	26211	hgsc.bcm.edu	37	chr7	143657370	143657370	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.121212121212121	4	1	1.57333333333333	0	1.96666666666667	0.0285714285714286	0.304738562091504	0	gctgtgcagcccagttatttTtctccctggccttgggtggg	13	11	1	0			TCGA-G3-A7M7-01A-12D-A34Z-10	TCGA-G3-A7M7-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e2d5d14-93c7-44fb-bee9-d6bf7c286368	3a264183-655d-4ab5-ade1-24ffbfd0cdb0	g.chr7:143657370T>C	ENST00000392899.1	+	1	344	c.307T>C	c.(307-309)Ttc>Ctc	p.F103L	RP4-669B10.3_ENST00000466281.1_lincRNA	NM_012369.2	NP_036501.2	Q13607	OR2F1_HUMAN	olfactory receptor, family 2, subfamily F, member 1 (gene/pseudogene)	103					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|skin(4)	34	Melanoma(164;0.0903)					CCAGTTATTTTTCTCCCTGGC	0.527																																					p.F103L		Atlas-SNP	.											.	OR2F1	71	.	0			c.T307C						.						158	144	149					7																	143657370		2203	4300	6503	SO:0001583	missense	26211	exon1			TTATTTTTCTCCC	U56421	CCDS5887.1	7q35	2013-06-03	2013-06-03		ENSG00000213215	ENSG00000213215		"GPCR / Class A : Olfactory receptors"	8246	protein-coding gene	gene with protein product		608497	"olfactory receptor, family 2, subfamily F, member 1"	OR2F4, OR2F5, OR2F3, OR2F3P		9500546	Standard	NM_012369		Approved	OLF3, OR7-140, OR7-139, OR14-60	uc003wds.1	Q13607	OTTHUMG00000157771	ENST00000392899.1:c.307T>C	chr7.hg19:g.143657370T>C	ENSP00000376633:p.Phe103Leu	95.0	0.0		62.0	17.0	NM_012369	A4D2G1|Q6IFP7|Q96R49|Q9UDX1	Missense_Mutation	SNP	ENST00000392899.1	hg19	CCDS5887.1	.	.	.	.	.	.	.	.	.	.	T	8.542	0.873541	0.17322	.	.	ENSG00000213215	ENST00000392899	T	0.00495	6.99	5.41	1.62	0.23740	GPCR, rhodopsin-like superfamily (1);	0.111768	0.40908	N	0.000987	T	0.00271	0.0008	N	0.12853	0.265	0.32041	N	0.598204	B	0.12630	0.006	B	0.10450	0.005	T	0.19451	-1.0305	10	0.15952	T	0.53	-43.3321	5.7545	0.18164	0.2791:0.0:0.2897:0.4313	.	103	Q13607	OR2F1_HUMAN	L	103	ENSP00000376633:F103L	ENSP00000376633:F103L	F	+	1	0	OR2F1	143288303	0.000000	0.05858	0.987000	0.45799	0.857000	0.48899	0.123000	0.15708	0.115000	0.18071	0.533000	0.62120	TTC	.	.		0.527	OR2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349581.1			C	143657370	T	C	143657370	3	2	292	1	0	0	0	0	1	0	0	0	11005	1841	64	2	309	2	OR2F1	7	143657370	Missense_Mutation	SNP	T	TCGA-G3-A7M7-01A-12D-A34Z-10	50923507	143657370	15481293	13	42732										
ADAMTSL1	92949	hgsc.bcm.edu	37	chr9	18639393	18639393	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.121212121212121	4	1	1.57333333333333	0	1.96666666666667	0.0285714285714286	0.304738562091504	0	aatggctggaccactcacagCagatttcattgtcaaggtga	10	9	3	2			TCGA-G3-A7M7-01A-12D-A34Z-10	TCGA-G3-A7M7-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e2d5d14-93c7-44fb-bee9-d6bf7c286368	3a264183-655d-4ab5-ade1-24ffbfd0cdb0	g.chr9:18639393C>T	ENST00000380548.4	+	7	1157	c.818C>T	c.(817-819)gCa>gTa	p.A273V	ADAMTSL1_ENST00000276935.6_Missense_Mutation_p.A273V|ADAMTSL1_ENST00000327883.7_Missense_Mutation_p.A273V|ADAMTSL1_ENST00000380566.4_Missense_Mutation_p.A273V	NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	273						proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(2)|lung(17)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(50;1.29e-17)		CCACTCACAGCAGATTTCATT	0.428																																					p.A273V		Atlas-SNP	.											.	ADAMTSL1	306	.	0			c.C818T						.						60	62	61					9																	18639393		2203	4299	6502	SO:0001583	missense	92949	exon7			TCACAGCAGATTT	AF176313	CCDS6485.1, CCDS47954.1	9p21.3	2013-01-11			ENSG00000178031	ENSG00000178031		"Immunoglobulin superfamily / I-set domain containing"	14632	protein-coding gene	gene with protein product	"punctin"	609198	"chromosome 9 open reading frame 94"	C9orf94		9628581, 11805097	Standard	NM_001040272		Approved	ADAMTSR1, FLJ35283	uc003zne.4	Q8N6G6	OTTHUMG00000019604	ENST00000380548.4:c.818C>T	chr9.hg19:g.18639393C>T	ENSP00000369921:p.Ala273Val	56.0	0.0		44.0	16.0	NM_052866	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Missense_Mutation	SNP	ENST00000380548.4	hg19	CCDS47954.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.169730	0.78452	.	.	ENSG00000178031	ENST00000380548;ENST00000327883;ENST00000380566;ENST00000276935	T;T;T;T	0.64085	-0.08;0.65;0.65;0.65	5.77	5.77	0.91146	.	.	.	.	.	T	0.73450	0.3588	L	0.55481	1.735	0.80722	D	1	D;D	0.71674	0.998;0.971	P;P	0.59703	0.862;0.818	T	0.67968	-0.5533	9	0.32370	T	0.25	.	20.3472	0.98799	0.0:1.0:0.0:0.0	.	273;273	Q8N6G6;Q8N6G6-2	ATL1_HUMAN;.	V	273	ENSP00000369921:A273V;ENSP00000327887:A273V;ENSP00000369940:A273V;ENSP00000276935:A273V	ENSP00000276935:A273V	A	+	2	0	ADAMTSL1	18629393	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.879000	0.75572	2.890000	0.99128	0.650000	0.86243	GCA	.	.		0.428	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1			T	18639393	C	T	18639393	3	4	292	1	0	0	0	0	1	0	0	0	274	710	25	3	844	3	ADAMTSL1	9	18639393	Missense_Mutation	SNP	C	TCGA-G3-A7M7-01A-12D-A34Z-10		18639393	122574038	14	42733										
IFNA14	3448	hgsc.bcm.edu	37	chr9	21239523	21239523	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.121212121212121	4	1	1.57333333333333	0	1.96666666666667	0.0285714285714286	0.304738562091504	0	cttcacagccaggatggagtCctcattcatcaggggagtct	11	11	5	0			TCGA-G3-A7M7-01A-12D-A34Z-10	TCGA-G3-A7M7-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e2d5d14-93c7-44fb-bee9-d6bf7c286368	3a264183-655d-4ab5-ade1-24ffbfd0cdb0	g.chr9:21239523C>A	ENST00000380222.2	-	1	455	c.412G>T	c.(412-414)Gac>Tac	p.D138Y		NM_002172.2	NP_002163.2	P01570	IFN14_HUMAN	interferon, alpha 14	138					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|cytokine receptor binding (GO:0005126)|type I interferon receptor binding (GO:0005132)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(7)	11				Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)		AGGATGGAGTCCTCATTCATC	0.448																																					p.D138Y		Atlas-SNP	.											.	IFNA14	29	.	0			c.G412T						.						205	208	207					9																	21239523		2203	4297	6500	SO:0001583	missense	3448	exon1			TGGAGTCCTCATT		CCDS6501.1	9p22	2010-08-24			ENSG00000228083	ENSG00000228083		"Interferons"	5420	protein-coding gene	gene with protein product		147579				1385305	Standard	NM_002172		Approved	LEIF2H, IFN-alphaH	uc010mis.3	P01570	OTTHUMG00000019665	ENST00000380222.2:c.412G>T	chr9.hg19:g.21239523C>A	ENSP00000369571:p.Asp138Tyr	103.0	0.0		47.0	18.0	NM_002172	Q5VZ56|Q7M4S1	Missense_Mutation	SNP	ENST00000380222.2	hg19	CCDS6501.1	.	.	.	.	.	.	.	.	.	.	-	13.87	2.366666	0.41902	.	.	ENSG00000228083	ENST00000380222	T	0.06608	3.28	3.38	0.263	0.15602	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.540907	0.17422	N	0.174794	T	0.23054	0.0557	M	0.91406	3.205	0.09310	N	1	D	0.57571	0.98	D	0.71414	0.973	T	0.06320	-1.0833	10	0.87932	D	0	.	3.0236	0.06084	0.181:0.5317:0.1769:0.1103	.	138	P01570	IFN14_HUMAN	Y	138	ENSP00000369571:D138Y	ENSP00000369571:D138Y	D	-	1	0	IFNA14	21229523	0.000000	0.05858	0.017000	0.16124	0.375000	0.29983	0.259000	0.18405	0.216000	0.20781	0.398000	0.26397	GAC	.	.		0.448	IFNA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051894.1	NM_002172		A	21239523	C	A	21239523	3	1	292	1	0	0	0	0	1	0	0	0	7543	855	30	3	161	3	IFNA14	9	21239523	Missense_Mutation	SNP	C	TCGA-G3-A7M7-01A-12D-A34Z-10	2600130	21239523	119973908	15	42734										
KIF24	347240	hgsc.bcm.edu	37	chr9	34310818	34310818	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.121212121212121	4	1	1.57333333333333	0	1.96666666666667	0.0285714285714286	0.304738562091504	0	cccccagtattgcagaaaggTaatttggtgaaaagagtgaa	11	6	0	4			TCGA-G3-A7M7-01A-12D-A34Z-10	TCGA-G3-A7M7-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e2d5d14-93c7-44fb-bee9-d6bf7c286368	3a264183-655d-4ab5-ade1-24ffbfd0cdb0	g.chr9:34310818T>C	ENST00000402558.2	-	1	551	c.527A>G	c.(526-528)tAc>tGc	p.Y176C	KIF24_ENST00000379174.3_Missense_Mutation_p.Y176C|KIF24_ENST00000379166.2_Missense_Mutation_p.Y176C|KIF24_ENST00000345050.2_Missense_Mutation_p.Y176C			Q5T7B8	KIF24_HUMAN	kinesin family member 24	176					ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)	centriole (GO:0005814)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|liver(1)|lung(13)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	32			LUSC - Lung squamous cell carcinoma(29;0.0107)			TGCAGAAAGGTAATTTGGTGA	0.388																																					p.Y176C		Atlas-SNP	.											.	KIF24	64	.	0			c.A527G						.						203	194	197					9																	34310818		1859	4101	5960	SO:0001583	missense	347240	exon2			GAAAGGTAATTTG	AK001795	CCDS6551.2	9p13.3	2013-01-10			ENSG00000186638	ENSG00000186638		"Kinesins", "Sterile alpha motif (SAM) domain containing"	19916	protein-coding gene	gene with protein product		613747	"chromosome 9 open reading frame 48"	C9orf48		12477932	Standard	NM_194313		Approved	bA571F15.4, FLJ10933, FLJ43884	uc003zua.4	Q5T7B8	OTTHUMG00000019810	ENST00000402558.2:c.527A>G	chr9.hg19:g.34310818T>C	ENSP00000384433:p.Tyr176Cys	174.0	0.0		133.0	34.0	NM_194313	Q2TB93|Q5T7B5|Q5T7B7|Q6ZU97|Q6ZUZ2|Q86XZ0|Q9NV43	Missense_Mutation	SNP	ENST00000402558.2	hg19	CCDS6551.2	.	.	.	.	.	.	.	.	.	.	T	10.59	1.392350	0.25118	.	.	ENSG00000186638	ENST00000402558;ENST00000379174;ENST00000379166;ENST00000345050;ENST00000420188	T;T;T;T	0.71461	-0.36;-0.57;-0.36;-0.57	5.48	3.03	0.35002	.	0.859366	0.09781	N	0.756736	T	0.58552	0.2130	N	0.19112	0.55	0.09310	N	1	D;D	0.58970	0.984;0.973	P;B	0.46452	0.517;0.319	T	0.48833	-0.9000	10	0.72032	D	0.01	.	5.5086	0.16868	0.2587:0.0714:0.0:0.6698	.	176;176	Q5T7B8-4;Q5T7B8	.;KIF24_HUMAN	C	176	ENSP00000384433:Y176C;ENSP00000368472:Y176C;ENSP00000368464:Y176C;ENSP00000340179:Y176C	ENSP00000340179:Y176C	Y	-	2	0	KIF24	34300818	0.953000	0.32496	0.988000	0.46212	0.110000	0.19582	1.345000	0.33953	0.333000	0.23563	0.528000	0.53228	TAC	.	.		0.388	KIF24-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052150.5			C	34310818	T	C	34310818	3	2	292	1	0	0	0	0	1	0	0	0	8301	1638	57	2	3627	2	KIF24	9	34310818	Missense_Mutation	SNP	T	TCGA-G3-A7M7-01A-12D-A34Z-10	13071295	34310818	106902613	16	42735										
PTGR1	22949	hgsc.bcm.edu	37	chr9	114348335	114348335	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.121212121212121	4	1	1.57333333333333	0	1.96666666666667	0.0285714285714286	0.304738562091504	0	gtattgtgtctggccactctGtcagcagcttttccagatct	9	11	4	1			TCGA-G3-A7M7-01A-12D-A34Z-10	TCGA-G3-A7M7-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e2d5d14-93c7-44fb-bee9-d6bf7c286368	3a264183-655d-4ab5-ade1-24ffbfd0cdb0	g.chr9:114348335G>A	ENST00000407693.2	-	5	582	c.320C>T	c.(319-321)aCa>aTa	p.T107I	PTGR1_ENST00000538962.1_Missense_Mutation_p.T107I|PTGR1_ENST00000309195.5_Missense_Mutation_p.T107I|PTGR1_ENST00000238248.3_5'UTR	NM_001146108.1	NP_001139580.1	Q14914	PTGR1_HUMAN	prostaglandin reductase 1	107					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|leukotriene metabolic process (GO:0006691)|lipoxin metabolic process (GO:2001300)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	13-prostaglandin reductase activity (GO:0036132)|15-oxoprostaglandin 13-oxidase activity (GO:0047522)|2-alkenal reductase [NAD(P)] activity (GO:0032440)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(5)|lung(3)|ovary(1)	11						TGGCCACTCTGTCAGCAGCTT	0.463																																					p.T107I	Ovarian(200;132 2151 7551 19220 46064)	Atlas-SNP	.											.	PTGR1	23	.	0			c.C320T						.						138	109	119					9																	114348335		2203	4300	6503	SO:0001583	missense	22949	exon5			CACTCTGTCAGCA	D49387	CCDS6779.1, CCDS55331.1	9q32	2008-06-04	2008-06-02	2008-06-02	ENSG00000106853	ENSG00000106853	1.3.1.74, 1.3.1.48		18429	protein-coding gene	gene with protein product	"zinc binding alcohol dehydrogenase domain containing 3"	601274	"leukotriene B4 12-hydroxydehydrogenase"	LTB4DH		8576264, 17449869	Standard	NM_001146109		Approved	ZADH3	uc004bfh.2	Q14914	OTTHUMG00000020493	ENST00000407693.2:c.320C>T	chr9.hg19:g.114348335G>A	ENSP00000385763:p.Thr107Ile	110.0	0.0		70.0	18.0	NM_001146108	A8K0N2|B4DPK3|F5GY50|Q8IYQ0|Q9H1X6	Missense_Mutation	SNP	ENST00000407693.2	hg19	CCDS6779.1	.	.	.	.	.	.	.	.	.	.	G	9.614	1.132170	0.21041	.	.	ENSG00000106853	ENST00000538962;ENST00000309195;ENST00000407693;ENST00000333580;ENST00000422125	T;T;T;T	0.51817	0.69;0.69;0.69;0.85	4.74	0.169	0.15017	GroES-like (1);	1.008970	0.07932	N	0.977675	T	0.39545	0.1082	L	0.46819	1.47	0.09310	N	0.999995	B;B;B	0.18741	0.03;0.001;0.029	B;B;B	0.17722	0.019;0.003;0.01	T	0.34428	-0.9829	10	0.37606	T	0.19	-8.3056	8.3144	0.32091	0.0759:0.0:0.5129:0.4113	.	107;107;107	F5GY50;B4DPK3;Q14914	.;.;PTGR1_HUMAN	I	107;107;107;88;88	ENSP00000440281:T107I;ENSP00000311572:T107I;ENSP00000385763:T107I;ENSP00000395965:T88I	ENSP00000311572:T107I	T	-	2	0	PTGR1	113388156	0.005000	0.15991	0.003000	0.11579	0.909000	0.53808	1.506000	0.35747	0.211000	0.20683	-0.310000	0.09108	ACA	.	.		0.463	PTGR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053647.2			A	114348335	G	A	114348335	3	1	292	1	0	0	0	0	1	0	0	0	12766	1377	48	3	724	3	PTGR1	9	114348335	Missense_Mutation	SNP	G	TCGA-G3-A7M7-01A-12D-A34Z-10	80037517	114348335	26865096	17	42736										
ARHGAP12	94134	hgsc.bcm.edu	37	chr10	32150410	32150410	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.121212121212121	4	1	1.57333333333333	0	1.96666666666667	0.0285714285714286	0.304738562091504	0	ttccaagttctttcctgtgtCcctctgttatagtaatagca	6	10	2	0			TCGA-G3-A7M7-01A-12D-A34Z-10	TCGA-G3-A7M7-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e2d5d14-93c7-44fb-bee9-d6bf7c286368	3a264183-655d-4ab5-ade1-24ffbfd0cdb0	g.chr10:32150410C>G	ENST00000344936.2	-	4	1095	c.861G>C	c.(859-861)ggG>ggC	p.G287G	ARHGAP12_ENST00000375245.4_Silent_p.G287G|ARHGAP12_ENST00000396144.4_Silent_p.G287G|ARHGAP12_ENST00000311380.4_Silent_p.G287G|ARHGAP12_ENST00000375250.5_Silent_p.G287G	NM_001270697.1|NM_018287.6	NP_001257626.1|NP_060757.4	Q8IWW6	RHG12_HUMAN	Rho GTPase activating protein 12	287	WW 1. {ECO:0000255|PROSITE- ProRule:PRU00224}.				morphogenesis of an epithelial sheet (GO:0002011)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(11)|lung(10)|skin(1)|urinary_tract(2)	31		Prostate(175;0.0199)				TTTCCTGTGTCCCTCTGTTAT	0.473																																					p.G287G		Atlas-SNP	.											.	ARHGAP12	79	.	0			c.G861C						.						112	100	104					10																	32150410		2203	4300	6503	SO:0001819	synonymous_variant	94134	exon4			CTGTGTCCCTCTG	AY033594	CCDS7170.1, CCDS59214.1, CCDS59215.1, CCDS59216.1, CCDS73082.1	10p11.22	2013-01-10			ENSG00000165322	ENSG00000165322		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	16348	protein-coding gene	gene with protein product		610577				11854031	Standard	NM_001270695		Approved	FLJ20737, FLJ10971, FLJ21785	uc001ivz.2	Q8IWW6	OTTHUMG00000017911	ENST00000344936.2:c.861G>C	chr10.hg19:g.32150410C>G		122.0	0.0		121.0	29.0	NM_001270696	B1ANY0|B1ANY1|B1ANY2|Q504X1|Q86UB3|Q8IWW7|Q8N3L1|Q9NT76	Silent	SNP	ENST00000344936.2	hg19	CCDS7170.1																																																																																			.	.		0.473	ARHGAP12-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047465.1			G	32150410	C	G	32150410	2	3	292	1	0	0	0	0	0	0	0	1	865	842	30	4		4	ARHGAP12	10	32150410	Silent	SNP	C	TCGA-G3-A7M7-01A-12D-A34Z-10		32150410	103384337	18	42737										
CBARA1	10367	hgsc.bcm.edu	37	chr10	74326487	74326487	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.121212121212121	4	1	1.57333333333333	0	1.96666666666667	0.0285714285714286	0.304738562091504	0	tctggatgggctgtgatcctCcatggtaccatcgagaaccc	11	12	1	2			TCGA-G3-A7M7-01A-12D-A34Z-10	TCGA-G3-A7M7-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e2d5d14-93c7-44fb-bee9-d6bf7c286368	3a264183-655d-4ab5-ade1-24ffbfd0cdb0	g.chr10:74326487C>A	ENST00000361114.5	-	2	161	c.65G>T	c.(64-66)gGa>gTa	p.G22V	MICU1_ENST00000401998.3_Missense_Mutation_p.G22V|MICU1_ENST00000604025.1_5'UTR|MICU1_ENST00000398761.4_Missense_Mutation_p.G22V	NM_001195518.1|NM_006077.3	NP_001182447.1|NP_006068.2	Q9BPX6	MICU1_HUMAN	mitochondrial calcium uptake 1	22					calcium ion import (GO:0070509)|calcium ion transmembrane import into mitochondrion (GO:0036444)|defense response (GO:0006952)|mitochondrial calcium ion homeostasis (GO:0051560)|mitochondrial calcium ion transport (GO:0006851)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|protein homooligomerization (GO:0051260)	calcium channel complex (GO:0034704)|integral component of mitochondrial membrane (GO:0032592)|intracellular (GO:0005622)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|uniplex complex (GO:1990246)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)										CTGTGATCCTCCATGGTACCA	0.483																																					p.G22V		Atlas-SNP	.											.	.	.	.	0			c.G65T						.						71	71	71					10																	74326487		1950	4164	6114	SO:0001583	missense	10367	exon2			GATCCTCCATGGT	Y17711	CCDS55714.1, CCDS55715.1	10q22.1	2013-01-10	2011-06-23	2011-06-23	ENSG00000107745	ENSG00000107745		"EF-hand domain containing"	1530	protein-coding gene	gene with protein product		605084	"calcium binding atopy-related autoantigen 1"	CBARA1		9806765, 20693986	Standard	NM_006077		Approved	CALC, EFHA3, FLJ12684	uc001jtb.2	Q9BPX6	OTTHUMG00000018437	ENST00000361114.5:c.65G>T	chr10.hg19:g.74326487C>A	ENSP00000354415:p.Gly22Val	77.0	0.0		45.0	17.0	NM_001195518	A8MV96|B3KN20|B4DJH9|B4DPI1|B5MBY3|D3YTJ3|O75785|Q9H9N6|Q9UFX0	Missense_Mutation	SNP	ENST00000361114.5	hg19	CCDS55715.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.779263	0.90195	.	.	ENSG00000107745	ENST00000361114;ENST00000398761;ENST00000401998	D;D;D	0.81908	-1.54;-1.55;-1.54	5.91	5.91	0.95273	.	0.115517	0.64402	D	0.000011	T	0.80166	0.4573	L	0.48642	1.525	0.80722	D	1	P	0.36222	0.544	B	0.33339	0.162	T	0.81252	-0.1017	10	0.87932	D	0	.	19.0678	0.93119	0.0:1.0:0.0:0.0	.	22	Q9BPX6	MICU1_HUMAN	V	22	ENSP00000354415:G22V;ENSP00000381745:G22V;ENSP00000384068:G22V	ENSP00000354415:G22V	G	-	2	0	MICU1	73996493	0.994000	0.37717	1.000000	0.80357	0.989000	0.77384	3.430000	0.52807	2.813000	0.96785	0.655000	0.94253	GGA	.	.		0.483	MICU1-002	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048586.1	NM_006077		A	74326487	C	A	74326487	3	1	292	1	0	0	0	0	1	0	0	0	2698	855	30	3	1415	3	CBARA1	10	74326487	Missense_Mutation	SNP	C	TCGA-G3-A7M7-01A-12D-A34Z-10	42176077	74326487	61208260	19	42738										
CYP2C8	1558	hgsc.bcm.edu	37	chr10	96796969	96796969	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.121212121212121	4	1	1.57333333333333	0	1.96666666666667	0.0285714285714286	0.304738562091504	0	gtagtattgaggttctttaaAtcatcaacagatttcaggtt	8	5	4	2			TCGA-G3-A7M7-01A-12D-A34Z-10	TCGA-G3-A7M7-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e2d5d14-93c7-44fb-bee9-d6bf7c286368	3a264183-655d-4ab5-ade1-24ffbfd0cdb0	g.chr10:96796969A>G	ENST00000371270.3	-	9	1483	c.1389T>C	c.(1387-1389)gaT>gaC	p.D463D	CYP2C8_ENST00000535898.1_Silent_p.D361D	NM_000770.3|NM_001198853.1|NM_001198855.1	NP_000761.3|NP_001185782.1|NP_001185784.1	P10632	CP2C8_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 8	463					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|omega-hydroxylase P450 pathway (GO:0097267)|organic acid metabolic process (GO:0006082)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|caffeine oxidase activity (GO:0034875)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)			breast(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|skin(3)	21		Colorectal(252;0.0397)		all cancers(201;6.21e-05)	Abiraterone(DB05812)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Almotriptan(DB00918)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amprenavir(DB00701)|Antipyrine(DB01435)|Apixaban(DB06605)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bezafibrate(DB01393)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Buprenorphine(DB00921)|Bupropion(DB01156)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Candesartan(DB00796)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Cisapride(DB00604)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Colchicine(DB01394)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dapsone(DB00250)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Diltiazem(DB00343)|Domperidone(DB01184)|Eltrombopag(DB06210)|Enzalutamide(DB08899)|Erlotinib(DB00530)|Estradiol(DB00783)|Eszopiclone(DB00402)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Felodipine(DB01023)|Fenofibrate(DB01039)|Fluorouracil(DB00544)|Fluvastatin(DB01095)|Fosphenytoin(DB01320)|Gemfibrozil(DB01241)|Halofantrine(DB01218)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Ifosfamide(DB01181)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Liotrix(DB01583)|Loperamide(DB00836)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Medroxyprogesterone Acetate(DB00603)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Methadone(DB00333)|Metronidazole(DB00916)|Mirtazapine(DB00370)|Mometasone(DB00764)|Montelukast(DB00471)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Naloxone(DB01183)|Naproxen(DB00788)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Omeprazole(DB00338)|Oxybutynin(DB01062)|Paclitaxel(DB01229)|Paramethadione(DB00617)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Perphenazine(DB00850)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenprocoumon(DB00946)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Propafenone(DB01182)|Propofol(DB00818)|Pyrimethamine(DB00205)|Quinidine(DB00908)|Quinine(DB00468)|Raloxifene(DB00481)|Regorafenib(DB08896)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rifapentine(DB01201)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Salmeterol(DB00938)|Saquinavir(DB01232)|Secobarbital(DB00418)|Selegiline(DB01037)|Simvastatin(DB00641)|Sitagliptin(DB01261)|Sorafenib(DB00398)|Spironolactone(DB00421)|Sulfadiazine(DB00359)|Sulfamethoxazole(DB01015)|Sulfaphenazole(DB06729)|Sulfinpyrazone(DB01138)|Tamoxifen(DB00675)|Tazarotene(DB00799)|Temazepam(DB00231)|Terbinafine(DB00857)|Testosterone(DB00624)|Theophylline(DB00277)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tolbutamide(DB01124)|Torasemide(DB00214)|Trametinib(DB08911)|Tretinoin(DB00755)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Verapamil(DB00661)|Vismodegib(DB08828)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zidovudine(DB00495)|Zopiclone(DB01198)	GGTTCTTTAAATCATCAACAG	0.413																																					p.D463D		Atlas-SNP	.											.	CYP2C8	73	.	0			c.T1389C						.						132	136	134					10																	96796969		2203	4300	6503	SO:0001819	synonymous_variant	1558	exon9			CTTTAAATCATCA	M17397	CCDS7438.1, CCDS55721.1, CCDS73166.1	10q24.1	2007-12-14	2003-01-14		ENSG00000138115	ENSG00000138115		"Cytochrome P450s"	2622	protein-coding gene	gene with protein product		601129	"cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 8"			7841444	Standard	NM_001198853		Approved	CPC8	uc001kkb.3	P10632	OTTHUMG00000018804	ENST00000371270.3:c.1389T>C	chr10.hg19:g.96796969A>G		92.0	0.0		64.0	16.0	NM_000770	A8K9N8|B0AZN2|B7Z1F6|Q5VX93|Q8WWB1|Q9UCZ9	Silent	SNP	ENST00000371270.3	hg19	CCDS7438.1																																																																																			.	.		0.413	CYP2C8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049499.2	NM_000770		G	96796969	A	G	96796969	2	3	292	1	0	0	0	0	0	0	0	1	4169	98	4	2		2	CYP2C8	10	96796969	Silent	SNP	A	TCGA-G3-A7M7-01A-12D-A34Z-10	22470482	96796969	38737778	20	42739										
ABLIM1	3983	hgsc.bcm.edu	37	chr10	116417809	116417809	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.121212121212121	4	1	1.57333333333333	0	1.96666666666667	0.0285714285714286	0.304738562091504	0	gatagtggcacgcctatgagCggtgaaggaggtcccagaga	16	8	0	3			TCGA-G3-A7M7-01A-12D-A34Z-10	TCGA-G3-A7M7-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e2d5d14-93c7-44fb-bee9-d6bf7c286368	3a264183-655d-4ab5-ade1-24ffbfd0cdb0	g.chr10:116417809C>A	ENST00000277895.5	-	1	248	c.151G>T	c.(151-153)Gct>Tct	p.A51S	ABLIM1_ENST00000369252.4_Intron|ABLIM1_ENST00000533213.2_Intron|snoU13_ENST00000458910.1_RNA	NM_002313.5	NP_002304.3	O14639	ABLM1_HUMAN	actin binding LIM protein 1	51					axon guidance (GO:0007411)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|visual perception (GO:0007601)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	30		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)		CGCCTATGAGCGGTGAAGGAG	0.517																																					p.A51S		Atlas-SNP	.											ABLIM1_ENST00000336585,colon,carcinoma,0,1	ABLIM1	131	.	0			c.G151T						.						95	87	90					10																	116417809		2203	4300	6503	SO:0001583	missense	3983	exon1			TATGAGCGGTGAA	AF005654	CCDS7590.1, CCDS31289.1	10q25	2008-07-07		2002-09-13	ENSG00000099204	ENSG00000099204			78	protein-coding gene	gene with protein product		602330		LIMAB1, ABLIM		9245787	Standard	NM_002313		Approved	abLIM, limatin	uc021pyw.1	O14639	OTTHUMG00000019088	ENST00000277895.5:c.151G>T	chr10.hg19:g.116417809C>A	ENSP00000277895:p.Ala51Ser	64.0	0.0		55.0	17.0	NM_002313	A6NI16|A6NJ06|A8MXA9|B3KVH2|Q15039|Q5JVV1|Q5JVV2|Q5T6N2|Q5T6N3|Q5T6N5|Q68CQ9|Q9BUP1	Missense_Mutation	SNP	ENST00000277895.5	hg19	CCDS7590.1	.	.	.	.	.	.	.	.	.	.	C	12.14	1.849365	0.32699	.	.	ENSG00000099204	ENST00000336585;ENST00000369262;ENST00000277895	T	0.27720	1.65	5.77	-1.77	0.07982	.	1.937130	0.03007	N	0.148935	T	0.18509	0.0444	N	0.14661	0.345	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.25433	-1.0132	10	0.41790	T	0.15	.	6.4267	0.21773	0.0:0.1746:0.4573:0.3681	.	51	O14639	ABLM1_HUMAN	S	51	ENSP00000277895:A51S	ENSP00000277895:A51S	A	-	1	0	ABLIM1	116407799	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.873000	0.04214	-0.019000	0.14055	-0.219000	0.12488	GCT	.	.		0.517	ABLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050469.3			A	116417809	C	A	116417809	3	1	292	1	0	0	0	0	1	0	0	0	94	768	27	1	2361	1	ABLIM1	10	116417809	Missense_Mutation	SNP	C	TCGA-G3-A7M7-01A-12D-A34Z-10	19620840	116417809	19116938	21	42740										
RARG	5916	hgsc.bcm.edu	37	chr12	53609161	53609161	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.121212121212121	4	1	1.57333333333333	0	1.96666666666667	0.0285714285714286	0.304738562091504	0	caccttgttgatgatacagtTtttgtcgcggtgacacgtgt	11	8	0	3			TCGA-G3-A7M7-01A-12D-A34Z-10	TCGA-G3-A7M7-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e2d5d14-93c7-44fb-bee9-d6bf7c286368	3a264183-655d-4ab5-ade1-24ffbfd0cdb0	g.chr12:53609161T>C	ENST00000425354.2	-	5	878	c.391A>G	c.(391-393)Aac>Gac	p.N131D	RARG_ENST00000394426.1_Missense_Mutation_p.N131D|RARG_ENST00000338561.5_Missense_Mutation_p.N120D|RARG_ENST00000543762.1_5'UTR|RARG_ENST00000543726.1_Missense_Mutation_p.N109D|RARG_ENST00000327550.3_Missense_Mutation_p.N59D	NM_000966.5	NP_000957.1	P13631	RARG_HUMAN	retinoic acid receptor, gamma	131					anterior/posterior pattern specification (GO:0009952)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|embryonic camera-type eye development (GO:0031076)|embryonic eye morphogenesis (GO:0048048)|embryonic hindlimb morphogenesis (GO:0035116)|face development (GO:0060324)|gene expression (GO:0010467)|glandular epithelial cell development (GO:0002068)|growth plate cartilage chondrocyte growth (GO:0003430)|Harderian gland development (GO:0070384)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of programmed cell death (GO:0043068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of cell size (GO:0008361)|regulation of myelination (GO:0031641)|response to retinoic acid (GO:0032526)|retinal pigment epithelium development (GO:0003406)|retinoic acid receptor signaling pathway (GO:0048384)|trachea cartilage development (GO:0060534)|transcription initiation from RNA polymerase II promoter (GO:0006367)	integral component of membrane (GO:0016021)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|retinoic acid receptor activity (GO:0003708)|retinoid X receptor binding (GO:0046965)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Tazarotene(DB00799)|Tretinoin(DB00755)	ATGATACAGTTTTTGTCGCGG	0.527																																					p.N131D		Atlas-SNP	.											.	RARG	53	.	0			c.A391G						.						257	199	219					12																	53609161		2203	4300	6503	SO:0001583	missense	5916	exon5			TACAGTTTTTGTC	M57707	CCDS8850.1, CCDS41790.1, CCDS58236.1, CCDS58237.1	12q13	2013-01-16			ENSG00000172819	ENSG00000172819		"Nuclear hormone receptors"	9866	protein-coding gene	gene with protein product		180190				1849262	Standard	NM_001042728		Approved	RARC, NR1B3	uc001scf.3	P13631	OTTHUMG00000048077	ENST00000425354.2:c.391A>G	chr12.hg19:g.53609161T>C	ENSP00000388510:p.Asn131Asp	39.0	0.0		25.0	6.0	NM_000966	B7Z492|B7Z4F1|B7ZAE4|J3KNP6|P22932|Q15281|Q52LZ8|Q9BYX8|Q9H1I3|Q9UJ38	Missense_Mutation	SNP	ENST00000425354.2	hg19	CCDS8850.1	.	.	.	.	.	.	.	.	.	.	T	17.35	3.367774	0.61513	.	.	ENSG00000172819	ENST00000425354;ENST00000394426;ENST00000327550;ENST00000338561;ENST00000543726;ENST00000550265	D;D;D;D;D	0.97066	-4.0;-4.0;-4.0;-4.0;-4.23	4.43	4.43	0.53597	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (3);	0.000000	0.85682	D	0.000000	D	0.95875	0.8657	N	0.20881	0.62	0.80722	D	1	P;D;D;P	0.67145	0.928;0.992;0.996;0.755	P;P;D;P	0.67382	0.775;0.906;0.951;0.809	D	0.93560	0.6894	10	0.13853	T	0.58	.	13.1019	0.59224	0.0:0.0:0.0:1.0	.	168;109;131;120	F8VR45;B7Z4F1;P13631;F1D8P1	.;.;RARG_HUMAN;.	D	131;131;59;120;109;168	ENSP00000388510:N131D;ENSP00000377947:N131D;ENSP00000332695:N59D;ENSP00000343698:N120D;ENSP00000444335:N109D	ENSP00000332695:N59D	N	-	1	0	RARG	51895428	1.000000	0.71417	1.000000	0.80357	0.844000	0.47949	7.798000	0.85924	1.992000	0.58205	0.472000	0.43445	AAC	.	.		0.527	RARG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109404.2	NM_000966		C	53609161	T	C	53609161	3	2	292	1	0	0	0	0	1	0	0	0	13069	1841	64	2	997	2	RARG	12	53609161	Missense_Mutation	SNP	T	TCGA-G3-A7M7-01A-12D-A34Z-10		53609161	80242734	22	42741										
SOHLH2	54937	hgsc.bcm.edu	37	chr13	36747869	36747869	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.121212121212121	4	1	1.57333333333333	0	1.96666666666667	0.0285714285714286	0.304738562091504	0	gagctctctgcatcaggagtGgagcacccattccagcacgt	11	13	2	0	rs572238180		TCGA-G3-A7M7-01A-12D-A34Z-10	TCGA-G3-A7M7-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e2d5d14-93c7-44fb-bee9-d6bf7c286368	3a264183-655d-4ab5-ade1-24ffbfd0cdb0	g.chr13:36747869G>A	ENST00000379881.3	-	9	1048	c.960C>T	c.(958-960)tcC>tcT	p.S320S	CCDC169-SOHLH2_ENST00000511166.1_Silent_p.S397S|SOHLH2_ENST00000554962.1_Silent_p.S397S	NM_017826.2	NP_060296.2	Q9NX45	SOLH2_HUMAN	spermatogenesis and oogenesis specific basic helix-loop-helix 2	320					multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;4.63e-08)|Epithelial(112;2.67e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00272)|BRCA - Breast invasive adenocarcinoma(63;0.00685)|GBM - Glioblastoma multiforme(144;0.0273)		CATCAGGAGTGGAGCACCCAT	0.522													G|||	1	0.000199681	0	0.0014	5008	,	,		19309	0		0	False		,,,				2504	0				p.S397S		Atlas-SNP	.											.	.	.	.	0			c.C1191T						.						122	109	113					13																	36747869		2203	4300	6503	SO:0001819	synonymous_variant	100526761	exon14			AGGAGTGGAGCAC	AK000456	CCDS9355.1, CCDS61309.1	13q13.3	2013-05-21			ENSG00000120669	ENSG00000120669		"Basic helix-loop-helix proteins"	26026	protein-coding gene	gene with protein product	"spermatogenesis associated 28"					12477932	Standard	NM_017826		Approved	FLJ20449, TEB1, bHLHe81, SPATA28		Q9NX45	OTTHUMG00000016728	ENST00000379881.3:c.960C>T	chr13.hg19:g.36747869G>A		50.0	0.0		38.0	9.0	NM_001198910	B4DX90|Q5EGC3|Q8TC74|Q96QX4	Silent	SNP	ENST00000379881.3	hg19	CCDS9355.1																																																																																			.	.		0.522	SOHLH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044477.2	NM_017826		A	36747869	G	A	36747869	2	1	292	1	0	0	0	0	0	0	0	1	14939	1335	47	3		3	SOHLH2	13	36747869	Silent	SNP	G	TCGA-G3-A7M7-01A-12D-A34Z-10		36747869	78422009	23	42742										
NDRG2	57447	hgsc.bcm.edu	37	chr14	21486186	21486186	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.121212121212121	4	1	1.57333333333333	0	1.96666666666667	0.0285714285714286	0.304738562091504	0	aagtacttgaaggcctcggtCagcttgcctggctgcggaag	14	10	1	1			TCGA-G3-A7M7-01A-12D-A34Z-10	TCGA-G3-A7M7-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e2d5d14-93c7-44fb-bee9-d6bf7c286368	3a264183-655d-4ab5-ade1-24ffbfd0cdb0	g.chr14:21486186C>T	ENST00000556147.1	-	15	1849	c.909G>A	c.(907-909)ctG>ctA	p.L303L	NDRG2_ENST00000397851.2_Silent_p.L303L|NDRG2_ENST00000298687.5_Silent_p.L303L|NDRG2_ENST00000554143.1_Silent_p.L289L|NDRG2_ENST00000553503.1_Silent_p.L289L|NDRG2_ENST00000350792.3_Silent_p.L289L|NDRG2_ENST00000397856.3_Silent_p.L273L|NDRG2_ENST00000554104.1_Silent_p.L216L|NDRG2_ENST00000555158.1_Silent_p.L289L|NDRG2_ENST00000298684.5_Silent_p.L260L|NDRG2_ENST00000397853.3_Silent_p.L303L|NDRG2_ENST00000397855.3_Silent_p.L260L|NDRG2_ENST00000397847.2_Silent_p.L292L|NDRG2_ENST00000360463.3_Silent_p.L289L|NDRG2_ENST00000397844.2_Silent_p.L273L|NDRG2_ENST00000554277.1_5'Flank|NDRG2_ENST00000403829.3_Silent_p.L299L|NDRG2_ENST00000397858.1_Silent_p.L303L			Q9UN36	NDRG2_HUMAN	NDRG family member 2	303					cell differentiation (GO:0030154)|negative regulation of cytokine production (GO:0001818)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of smooth muscle cell proliferation (GO:0048662)|regulation of platelet-derived growth factor production (GO:0090361)|regulation of vascular endothelial growth factor production (GO:0010574)|substantia nigra development (GO:0021762)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)				breast(2)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	23	all_cancers(95;0.00185)		OV - Ovarian serous cystadenocarcinoma(11;6.85e-11)|Epithelial(56;9.49e-09)|all cancers(55;3.84e-08)	GBM - Glioblastoma multiforme(265;0.0191)		AGGCCTCGGTCAGCTTGCCTG	0.592																																					p.L303L		Atlas-SNP	.											.	NDRG2	37	.	0			c.G909A						.						182	172	175					14																	21486186		2203	4300	6503	SO:0001819	synonymous_variant	57447	exon15			CTCGGTCAGCTTG	AB033074	CCDS9564.1, CCDS9565.1, CCDS61384.1, CCDS61386.1, CCDS73613.1	14q11.2	2008-07-09			ENSG00000165795	ENSG00000165795			14460	protein-coding gene	gene with protein product		605272				10831399	Standard	NM_201535		Approved	KIAA1248, SYLD	uc001vyx.3	Q9UN36	OTTHUMG00000029619	ENST00000556147.1:c.909G>A	chr14.hg19:g.21486186C>T		29.0	0.0		27.0	15.0	NM_201537	B3KUE3|B4DE86|B7WP11|B7WPD5|D3DS07|D3DS10|Q567T1|Q68DW2|Q86U08|Q86U46|Q96FD3|Q96FT0|Q96JU0|Q96PN0|Q9BQH5|Q9ULH2	Silent	SNP	ENST00000556147.1	hg19	CCDS9565.1																																																																																			.	.		0.592	NDRG2-013	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411717.1			T	21486186	C	T	21486186	2	4	292	1	0	0	0	0	0	0	0	1	10261	813	29	3		3	NDRG2	14	21486186	Silent	SNP	C	TCGA-G3-A7M7-01A-12D-A34Z-10		21486186	85863354	24	42743										
ACAN	176	hgsc.bcm.edu	37	chr15	89385015	89385015	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.121212121212121	4	1	1.57333333333333	0	1.96666666666667	0.0285714285714286	0.304738562091504	0	aggctgctatggagacaaggAtgagtttcctggtgtgagga	16	5	0	3			TCGA-G3-A7M7-01A-12D-A34Z-10	TCGA-G3-A7M7-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e2d5d14-93c7-44fb-bee9-d6bf7c286368	3a264183-655d-4ab5-ade1-24ffbfd0cdb0	g.chr15:89385015A>G	ENST00000561243.1	+	4	674	c.674A>G	c.(673-675)gAt>gGt	p.D225G	ACAN_ENST00000439576.2_Missense_Mutation_p.D225G|ACAN_ENST00000558207.1_Missense_Mutation_p.D225G|ACAN_ENST00000559004.1_Missense_Mutation_p.D225G|ACAN_ENST00000352105.7_Missense_Mutation_p.D225G			P16112	PGCA_HUMAN	aggrecan	225	G1-B.|Link 1. {ECO:0000255|PROSITE- ProRule:PRU00323}.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			GGAGACAAGGATGAGTTTCCT	0.577																																					p.D225G		Atlas-SNP	.											.	ACAN	220	.	0			c.A674G						.						171	182	178					15																	89385015		2092	4206	6298	SO:0001583	missense	176	exon5			ACAAGGATGAGTT	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	319	protein-coding gene	gene with protein product	"aggrecan proteoglycan"	155760	"chondroitin sulfate proteoglycan 1", "aggrecan 1"	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.674A>G	chr15.hg19:g.89385015A>G	ENSP00000453342:p.Asp225Gly	44.0	0.0		34.0	17.0	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	hg19	CCDS53970.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.005082	0.74932	.	.	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	T;T	0.02446	4.53;4.29	5.61	5.61	0.85477	.	.	.	.	.	T	0.09379	0.0231	L	0.39020	1.185	0.51482	D	0.999925	D;D;D	0.89917	1.0;1.0;0.994	D;D;D	0.79784	0.993;0.993;0.953	T	0.20273	-1.0280	9	0.45353	T	0.12	-21.726	14.6404	0.68720	1.0:0.0:0.0:0.0	.	225;225;225	E7ENV9;E7EX88;Q6PID9	.;.;.	G	225	ENSP00000387356:D225G;ENSP00000341615:D225G	ENSP00000268134:D225G	D	+	2	0	ACAN	87186019	1.000000	0.71417	0.992000	0.48379	0.993000	0.82548	6.048000	0.71046	2.134000	0.65973	0.482000	0.46254	GAT	.	.		0.577	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135		G	89385015	A	G	89385015	3	3	292	1	0	0	0	0	1	0	0	0	117	333	12	2	688	2	ACAN	15	89385015	Missense_Mutation	SNP	A	TCGA-G3-A7M7-01A-12D-A34Z-10		89385015	13146377	25	42744										
CHD2	1106	hgsc.bcm.edu	37	chr15	93510735	93510735	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.121212121212121	4	1	1.57333333333333	0	1.96666666666667	0.0285714285714286	0.304738562091504	0	atgtcagcccttcagaaacaGtattacaagtaagttcttgt	7	8	3	1			TCGA-G3-A7M7-01A-12D-A34Z-10	TCGA-G3-A7M7-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e2d5d14-93c7-44fb-bee9-d6bf7c286368	3a264183-655d-4ab5-ade1-24ffbfd0cdb0	g.chr15:93510735G>C	ENST00000394196.4	+	17	3249	c.2181G>C	c.(2179-2181)caG>caC	p.Q727H	CHD2_ENST00000557381.1_Missense_Mutation_p.Q727H	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	727					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			TTCAGAAACAGTATTACAAGT	0.393																																					p.Q727H		Atlas-SNP	.											.	CHD2	280	.	0			c.G2181C						.						75	68	70					15																	93510735		2197	4298	6495	SO:0001583	missense	1106	exon17			GAAACAGTATTAC	AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.2181G>C	chr15.hg19:g.93510735G>C	ENSP00000377747:p.Gln727His	63.0	0.0		59.0	13.0	NM_001271	C6G482|Q96IP5	Missense_Mutation	SNP	ENST00000394196.4	hg19	CCDS10374.2	.	.	.	.	.	.	.	.	.	.	G	20.7	4.041729	0.75732	.	.	ENSG00000173575	ENST00000394196;ENST00000557381	D;D	0.92647	-3.08;-3.08	5.83	5.83	0.93111	SNF2-related (1);	0.000000	0.32769	U	0.005678	D	0.95755	0.8619	M	0.65498	2.005	0.80722	D	1	D;D	0.89917	0.997;1.0	D;D	0.74023	0.966;0.982	D	0.95610	0.8671	10	0.87932	D	0	-29.2142	20.115	0.97926	0.0:0.0:1.0:0.0	.	727;727	O14647;O14647-2	CHD2_HUMAN;.	H	727	ENSP00000377747:Q727H;ENSP00000451366:Q727H	ENSP00000377747:Q727H	Q	+	3	2	CHD2	91311739	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.144000	0.50616	2.761000	0.94854	0.650000	0.86243	CAG	.	.		0.393	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271		C	93510735	G	C	93510735	3	2	292	1	0	0	0	0	1	0	0	0	3327	1020	36	4	2247	4	CHD2	15	93510735	Missense_Mutation	SNP	G	TCGA-G3-A7M7-01A-12D-A34Z-10	4125720	93510735	9020657	26	42745										
CREBBP	1387	hgsc.bcm.edu	37	chr16	3830772	3830772	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.121212121212121	4	1	1.57333333333333	0	1.96666666666667	0.0285714285714286	0.304738562091504	0	tccgcaggtcctgagtgacaTgttcgtgccagcctttcctt	10	13	0	2			TCGA-G3-A7M7-01A-12D-A34Z-10	TCGA-G3-A7M7-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e2d5d14-93c7-44fb-bee9-d6bf7c286368	3a264183-655d-4ab5-ade1-24ffbfd0cdb0	g.chr16:3830772T>C	ENST00000262367.5	-	8	2593	c.1784A>G	c.(1783-1785)cAt>cGt	p.H595R	CREBBP_ENST00000382070.3_Missense_Mutation_p.H557R	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	595	KIX. {ECO:0000255|PROSITE- ProRule:PRU00311}.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		CTGAGTGACATGTTCGTGCCA	0.473			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																														p.H595R		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP	546	.	0			c.A1784G						.						117	96	104					16																	3830772		2197	4300	6497	SO:0001583	missense	1387	exon8			GTGACATGTTCGT	U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.1784A>G	chr16.hg19:g.3830772T>C	ENSP00000262367:p.His595Arg	73.0	0.0		43.0	10.0	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	hg19	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	T	18.52	3.641647	0.67244	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070	D;D	0.82984	-1.67;-1.6	5.65	5.65	0.86999	Coactivator CBP, KIX (4);	0.000000	0.85682	D	0.000000	D	0.86117	0.5856	L	0.29908	0.895	0.80722	D	1	D;D	0.76494	0.966;0.999	D;D	0.83275	0.972;0.996	D	0.86055	0.1528	10	0.40728	T	0.16	-19.1248	15.8672	0.79074	0.0:0.0:0.0:1.0	.	625;595	Q4LE28;Q92793	.;CBP_HUMAN	R	595;625;557	ENSP00000262367:H595R;ENSP00000371502:H557R	ENSP00000262367:H595R	H	-	2	0	CREBBP	3770773	1.000000	0.71417	0.976000	0.42696	0.990000	0.78478	7.932000	0.87634	2.156000	0.67533	0.482000	0.46254	CAT	.	.		0.473	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		C	3830772	T	C	3830772	3	2	292	1	0	0	0	0	1	0	0	0	3863	1464	51	2	5640	2	CREBBP	16	3830772	Missense_Mutation	SNP	T	TCGA-G3-A7M7-01A-12D-A34Z-10		3830772	86523981	27	42746										
N4BP1	9683	hgsc.bcm.edu	37	chr16	48595832	48595832	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.121212121212121	4	1	1.57333333333333	0	1.96666666666667	0.0285714285714286	0.304738562091504	0	taagctcagaaacaggagtcCcagctttatttcttgcctct	7	11	3	1	rs374516858		TCGA-G3-A7M7-01A-12D-A34Z-10	TCGA-G3-A7M7-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e2d5d14-93c7-44fb-bee9-d6bf7c286368	3a264183-655d-4ab5-ade1-24ffbfd0cdb0	g.chr16:48595832C>A	ENST00000262384.3	-	2	958	c.722G>T	c.(721-723)gGg>gTg	p.G241V	RP11-44I10.3_ENST00000563994.1_RNA	NM_153029.3	NP_694574.3	O75113	N4BP1_HUMAN	NEDD4 binding protein 1	241					cellular response to UV (GO:0034644)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein ubiquitination (GO:0031397)	nucleolus (GO:0005730)|PML body (GO:0016605)				breast(3)|kidney(2)|lung(11)|urinary_tract(1)	17		all_cancers(37;0.179)|all_lung(18;0.11)				AACAGGAGTCCCAGCTTTATT	0.413																																					p.G241V		Atlas-SNP	.											N4BP1_ENST00000262384,NS,carcinoma,0,2	N4BP1	121	.	0			c.G722T						.						75	72	73					16																	48595832		1871	4083	5954	SO:0001583	missense	9683	exon2			GGAGTCCCAGCTT	AK026937	CCDS45479.1	16q12.1	2008-01-18				ENSG00000102921			29850	protein-coding gene	gene with protein product						9734811, 11717310	Standard	NM_153029		Approved		uc002efp.3	O75113		ENST00000262384.3:c.722G>T	chr16.hg19:g.48595832C>A	ENSP00000262384:p.Gly241Val	129.0	0.0		81.0	24.0	NM_153029	A7MD49|Q2YDX1	Missense_Mutation	SNP	ENST00000262384.3	hg19	CCDS45479.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.017658	0.75161	.	.	ENSG00000102921	ENST00000262384	T	0.52526	0.66	5.61	5.61	0.85477	.	0.388030	0.26871	N	0.022074	T	0.56499	0.1989	L	0.29908	0.895	0.58432	D	0.999999	D	0.69078	0.997	P	0.59643	0.861	T	0.59637	-0.7417	10	0.87932	D	0	-6.7919	19.6397	0.95753	0.0:1.0:0.0:0.0	.	241	O75113	N4BP1_HUMAN	V	241	ENSP00000262384:G241V	ENSP00000262384:G241V	G	-	2	0	N4BP1	47153333	0.756000	0.28383	0.997000	0.53966	0.959000	0.62525	4.141000	0.58038	2.632000	0.89209	0.655000	0.94253	GGG	.	.		0.413	N4BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429920.1	NM_014664		A	48595832	C	A	48595832	3	1	292	1	0	0	0	0	1	0	0	0	10118	623	22	3	1992	3	N4BP1	16	48595832	Missense_Mutation	SNP	C	TCGA-G3-A7M7-01A-12D-A34Z-10	44765060	48595832	41758921	28	42747										
BRCA1	672	hgsc.bcm.edu	37	chr17	41245778	41245778	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.121212121212121	4	1	1.57333333333333	0	1.96666666666667	0.0285714285714286	0.304738562091504	0	tcgagttccatattgcttatActgctgcttataggttcagc	8	9	1	0	rs80359886		TCGA-G3-A7M7-01A-12D-A34Z-10	TCGA-G3-A7M7-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e2d5d14-93c7-44fb-bee9-d6bf7c286368	3a264183-655d-4ab5-ade1-24ffbfd0cdb0	g.chr17:41245778A>G	ENST00000357654.3	-	10	1888	c.1770T>C	c.(1768-1770)agT>agC	p.S590S	BRCA1_ENST00000346315.3_Silent_p.S590S|BRCA1_ENST00000491747.2_Intron|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000351666.3_Intron|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000468300.1_Intron|BRCA1_ENST00000309486.4_Silent_p.S294S|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000352993.3_Intron|BRCA1_ENST00000471181.2_Silent_p.S590S|BRCA1_ENST00000354071.3_Silent_p.S590S|BRCA1_ENST00000493795.1_Silent_p.S543S	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	590					androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		TATTGCTTATACTGCTGCTTA	0.368			"D, Mis, N, F, S"		ovarian	"breast, ovarian"		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																											p.S590S		Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	.	BRCA1	304	.	0			c.T1770C						.						89	88	88					17																	41245778		2202	4298	6500	SO:0001819	synonymous_variant	672	exon10	Familial Cancer Database		GCTTATACTGCTG	U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1100	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 1", "protein phosphatase 1, regulatory subunit 53"	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.1770T>C	chr17.hg19:g.41245778A>G		173.0	0.0		136.0	13.0	NM_007300	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Silent	SNP	ENST00000357654.3	hg19	CCDS11453.1																																																																																			.	.		0.368	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294		G	41245778	A	G	41245778	2	3	292	1	0	0	0	0	0	0	0	1	1500	388	14	2		2	BRCA1	17	41245778	Silent	SNP	A	TCGA-G3-A7M7-01A-12D-A34Z-10		41245778	39949432	29	42748										
ZNF616	90317	hgsc.bcm.edu	37	chr19	52618825	52618825	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.121212121212121	4	1	1.57333333333333	0	1.96666666666667	0.0285714285714286	0.304738562091504	0	ttgcaaaagctgaacggtcaCtgaagaccttgccacattct	8	11	2	3			TCGA-G3-A7M7-01A-12D-A34Z-10	TCGA-G3-A7M7-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e2d5d14-93c7-44fb-bee9-d6bf7c286368	3a264183-655d-4ab5-ade1-24ffbfd0cdb0	g.chr19:52618825C>A	ENST00000600228.1	-	4	1853	c.1592G>T	c.(1591-1593)aGt>aTt	p.S531I	ZNF616_ENST00000330123.5_3'UTR	NM_178523.3	NP_848618.2	Q08AN1	ZN616_HUMAN	zinc finger protein 616	531					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(14)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	48				GBM - Glioblastoma multiforme(134;0.00392)|OV - Ovarian serous cystadenocarcinoma(262;0.0189)		TGAACGGTCACTGAAGACCTT	0.443																																					p.S531I		Atlas-SNP	.											.	ZNF616	109	.	0			c.G1592T						.						99	96	97					19																	52618825		2203	4300	6503	SO:0001583	missense	90317	exon4			CGGTCACTGAAGA	AK092266	CCDS33090.1	19q13.41	2013-01-08				ENSG00000204611		"Zinc fingers, C2H2-type", "-"	28062	protein-coding gene	gene with protein product							Standard	NM_178523		Approved	MGC45556	uc002pym.3	Q08AN1		ENST00000600228.1:c.1592G>T	chr19.hg19:g.52618825C>A	ENSP00000471000:p.Ser531Ile	61.0	0.0		58.0	10.0	NM_178523	B3KRV1|Q0P658|Q658V7	Missense_Mutation	SNP	ENST00000600228.1	hg19	CCDS33090.1	.	.	.	.	.	.	.	.	.	.	C	6.113	0.389086	0.11581	.	.	ENSG00000204611	ENST00000330123	.	.	.	1.08	-2.15	0.07102	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.15132	0.0365	N	0.17594	0.5	0.09310	N	1	P	0.41784	0.762	B	0.41619	0.361	T	0.10019	-1.0648	8	0.33141	T	0.24	.	1.8145	0.03097	0.1737:0.2287:0.4384:0.1591	.	531	Q08AN1	ZN616_HUMAN	I	531	.	ENSP00000328722:S531I	S	-	2	0	ZNF616	57310637	0.000000	0.05858	0.000000	0.03702	0.803000	0.45373	-8.110000	0.00025	-0.756000	0.04703	0.305000	0.20034	AGT	.	.		0.443	ZNF616-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462451.1	XM_030892		A	52618825	C	A	52618825	3	1	292	1	0	0	0	0	1	0	0	0	18056	565	20	3	757	3	ZNF616	19	52618825	Missense_Mutation	SNP	C	TCGA-G3-A7M7-01A-12D-A34Z-10		52618825	6510158	30	42749										
GNAS	2778	hgsc.bcm.edu	37	chr20	57484420	57484420	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.121212121212121	4	1	1.57333333333333	0	1.96666666666667	0.0285714285714286	0.304738562091504	0	ttcaggacctgcttcgctgcCgtgtcctgacttctggaatc	10	13	2	1	rs11554273		TCGA-G3-A7M7-01A-12D-A34Z-10	TCGA-G3-A7M7-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e2d5d14-93c7-44fb-bee9-d6bf7c286368	3a264183-655d-4ab5-ade1-24ffbfd0cdb0	g.chr20:57484420C>T	ENST00000371085.3	+	8	1025	c.601C>T	c.(601-603)Cgt>Tgt	p.R201C	GNAS_ENST00000464624.2_3'UTR|GNAS_ENST00000354359.7_Missense_Mutation_p.R202C|GNAS_ENST00000371075.3_3'UTR|GNAS_ENST00000371102.4_Missense_Mutation_p.R830C|GNAS_ENST00000371100.4_Missense_Mutation_p.R844C|GNAS_ENST00000371095.3_Missense_Mutation_p.R187C|GNAS_ENST00000313949.7_3'UTR|GNAS_ENST00000306090.10_Missense_Mutation_p.R187C|GNAS_ENST00000265620.7_Missense_Mutation_p.R186C	NM_000516.4	NP_000507.1	P63092	GNAS2_HUMAN	GNAS complex locus	201			R -> C (in MAS and somatotrophinoma; dbSNP:rs11554273). {ECO:0000269|PubMed:1944469, ECO:0000269|PubMed:2549426}.|R -> G (in MAS). {ECO:0000269|PubMed:10571700}.|R -> H (in MAS, somatotrophinoma and AIMAH1). {ECO:0000269|PubMed:12727968, ECO:0000269|PubMed:1594625, ECO:0000269|PubMed:1944469, ECO:0000269|PubMed:2549426}.|R -> L (in non-MAS endocrine tumors). {ECO:0000269|PubMed:7751320}.|R -> S (in AIMAH1, pituitary tumor and polyostotic fibrous dysplasia). {ECO:0000269|PubMed:12727968, ECO:0000269|PubMed:8766942, ECO:0000269|PubMed:9267696}.		activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|bone development (GO:0060348)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|cognition (GO:0050890)|developmental growth (GO:0048589)|energy reserve metabolic process (GO:0006112)|hair follicle placode formation (GO:0060789)|intracellular transport (GO:0046907)|platelet aggregation (GO:0070527)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of insulin secretion (GO:0050796)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intrinsic component of membrane (GO:0031224)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	adenylate cyclase activity (GO:0004016)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)	p.R201C(228)|p.R844C(9)|p.R201S(5)		adrenal_gland(12)|autonomic_ganglia(1)|biliary_tract(5)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(37)|liver(9)|lung(9)|ovary(16)|pancreas(56)|parathyroid(5)|pituitary(228)|prostate(2)|small_intestine(1)|stomach(1)|testis(2)|thyroid(35)|upper_aerodigestive_tract(3)|urinary_tract(1)	441	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			GCTTCGCTGCCGTGTCCTGAC	0.428			Mis		pituitary adenoma		"McCune-Albright syndrome; pseudohypoparathyroidism, type IA"			TSP Lung(22;0.16)																											p.R844C	Colon(117;935 1597 6045 8307 46442)	Atlas-SNP	.		Dom	yes		20	20q13.2	2778	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	yes	E	GNAS_ENST00000371100,NS,adenocarcinoma,0,338	GNAS	867	.	242	Substitution - Missense(242)	pituitary(141)|pancreas(35)|large_intestine(14)|ovary(12)|thyroid(10)|adrenal_gland(7)|biliary_tract(6)|parathyroid(5)|liver(3)|kidney(3)|testis(2)|upper_aerodigestive_tract(2)|autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)	c.C2530T						.						80	78	79					20																	57484420		2203	4300	6503	SO:0001583	missense	2778	exon8			CGCTGCCGTGTCC	M21142	CCDS13471.1, CCDS13472.1, CCDS42892.1, CCDS46622.1, CCDS46623.1, CCDS46624.1	20q13.2-q13.3	2010-03-01	2001-12-19	2001-12-20	ENSG00000087460	ENSG00000087460			4392	protein-coding gene	gene with protein product	"secretogranin VI"	139320	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	GNAS1			Standard	NM_000516		Approved	NESP55, NESP, GNASXL, GPSA, SCG6	uc002xzw.3	O95467	OTTHUMG00000033069	ENST00000371085.3:c.601C>T	chr20.hg19:g.57484420C>T	ENSP00000360126:p.Arg201Cys	74.0	0.0		46.0	18.0	NM_080425	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Missense_Mutation	SNP	ENST00000371085.3	hg19	CCDS13472.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.215896	0.79352	.	.	ENSG00000087460	ENST00000371100;ENST00000371102;ENST00000371095;ENST00000371085;ENST00000354359;ENST00000265620;ENST00000306090	D;D;D;D;D;D;D	0.99466	-5.95;-5.95;-5.95;-5.95;-5.95;-2.99;-5.95	5.53	4.53	0.55603	G protein alpha subunit, helical insertion (2);	0.000000	0.85682	D	0.000000	D	0.99775	0.9907	H	0.99732	4.735	0.80722	D	1	D;D;D;D	0.89917	0.999;0.983;0.979;1.0	D;P;P;D	0.97110	0.939;0.845;0.643;1.0	D	0.96814	0.9599	10	0.87932	D	0	.	13.0593	0.58997	0.2437:0.7563:0.0:0.0	rs11554273	201;202;186;844	P63092;A6NI00;P63092-3;Q5JWF2	GNAS2_HUMAN;.;.;GNAS1_HUMAN	C	844;830;187;201;202;186;187	ENSP00000360141:R844C;ENSP00000360143:R830C;ENSP00000360136:R187C;ENSP00000360126:R201C;ENSP00000346328:R202C;ENSP00000265620:R186C;ENSP00000304472:R187C	ENSP00000265620:R186C	R	+	1	0	GNAS	56917815	1.000000	0.71417	0.998000	0.56505	0.941000	0.58515	4.055000	0.57441	2.596000	0.87737	0.563000	0.77884	CGT	.	C|1.000		0.428	GNAS-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080431.2	NM_000516		T	57484420	C	T	57484420	3	4	292	1	0	0	0	0	1	0	0	0	6518	652	23	1	3448	1	GNAS	20	57484420	Missense_Mutation	SNP	C	TCGA-G3-A7M7-01A-12D-A34Z-10		57484420	5541100	31	42750										
DGCR6L	85359	hgsc.bcm.edu	37	chr22	20307214	20307214	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.121212121212121	4	1	1.57333333333333	0	1.96666666666667	0.0285714285714286	0.304738562091504	0	ttgtacaggctcttttcggtGaggtgctggatctccagtag	13	8	2	1			TCGA-G3-A7M7-01A-12D-A34Z-10	TCGA-G3-A7M7-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e2d5d14-93c7-44fb-bee9-d6bf7c286368	3a264183-655d-4ab5-ade1-24ffbfd0cdb0	g.chr22:20307214G>A	ENST00000248879.3	-	2	310	c.219C>T	c.(217-219)ctC>ctT	p.L73L	XXbac-B444P24.13_ENST00000608275.1_RNA|DGCR6L_ENST00000405465.3_Missense_Mutation_p.S69L|XXbac-B444P24.14_ENST00000609632.1_lincRNA	NM_033257.3	NP_150282.2	Q9BY27	DGC6L_HUMAN	DiGeorge syndrome critical region gene 6-like	73						nucleus (GO:0005634)				endometrium(1)|kidney(1)|lung(2)|stomach(1)	5	Colorectal(54;0.0993)					TCTTTTCGGTGAGGTGCTGGA	0.672																																					p.L73L		Atlas-SNP	.											.	DGCR6L	9	.	0			c.C219T						.						35	32	33					22																	20307214		2201	4298	6499	SO:0001819	synonymous_variant	85359	exon2			TTCGGTGAGGTGC	AF228708	CCDS13778.1	22q11.21	2013-02-19			ENSG00000128185	ENSG00000128185			18551	protein-coding gene	gene with protein product		609459				11157784	Standard	NM_033257		Approved	FLJ10666	uc002zrx.3	Q9BY27	OTTHUMG00000150583	ENST00000248879.3:c.219C>T	chr22.hg19:g.20307214G>A		73.0	0.0		54.0	9.0	NM_033257	A8K1N7|B3KMC0|D3DX29|Q9BW33	Silent	SNP	ENST00000248879.3	hg19	CCDS13778.1	.	.	.	.	.	.	.	.	.	.	G	8.733	0.917160	0.17982	.	.	ENSG00000128185	ENST00000405465	T	0.35421	1.31	2.49	0.0108	0.14084	.	.	.	.	.	T	0.24851	0.0603	.	.	.	0.18873	N	0.999986	.	.	.	.	.	.	T	0.27536	-1.0071	5	.	.	.	-12.8707	5.5677	0.17180	0.0:0.4196:0.3673:0.2131	.	.	.	.	L	69	ENSP00000386052:S69L	.	S	-	2	0	DGCR6L	18687214	1.000000	0.71417	0.988000	0.46212	0.087000	0.18053	1.239000	0.32719	-0.051000	0.13334	0.306000	0.20318	TCA	.	.		0.672	DGCR6L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318970.3	NM_033257		A	20307214	G	A	20307214	2	1	292	1	0	0	0	0	0	0	0	1	4465	1277	45	3		3	DGCR6L	22	20307214	Silent	SNP	G	TCGA-G3-A7M7-01A-12D-A34Z-10		20307214	30997352	32	42751										
TMEM187	8269	hgsc.bcm.edu	37	chrX	153247691	153247691	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.121212121212121	4	1	1.57333333333333	0	1.96666666666667	0.0285714285714286	0.304738562091504	0	ccatgccgttcaactcactcGtgaacatggcctacacgctg	8	15	2	1			TCGA-G3-A7M7-01A-12D-A34Z-10	TCGA-G3-A7M7-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e2d5d14-93c7-44fb-bee9-d6bf7c286368	3a264183-655d-4ab5-ade1-24ffbfd0cdb0	g.chrX:153247691G>A	ENST00000369982.4	+	2	925	c.178G>A	c.(178-180)Gtg>Atg	p.V60M	MIR3202-1_ENST00000580198.1_RNA	NM_003492.2	NP_003483.1	Q14656	TM187_HUMAN	transmembrane protein 187	60						integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)				breast(1)|large_intestine(1)|lung(1)|prostate(2)	5	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CAACTCACTCGTGAACATGGC	0.652																																					p.V60M		Atlas-SNP	.											.	TMEM187	21	.	0			c.G178A						.						48	48	48					X																	153247691		2203	4300	6503	SO:0001583	missense	8269	exon2			TCACTCGTGAACA	X92475	CCDS14739.1	Xq28	2007-03-14	2007-03-14	2007-03-14	ENSG00000177854	ENSG00000177854			13705	protein-coding gene	gene with protein product		300059	"chromosome X open reading frame 12"	CXorf12		8661027	Standard	NM_003492		Approved	ITBA1, DXS9878E	uc004fjq.2	Q14656	OTTHUMG00000024220	ENST00000369982.4:c.178G>A	chrX.hg19:g.153247691G>A	ENSP00000358999:p.Val60Met	38.0	0.0		36.0	23.0	NM_003492	B2RC47|Q6IAV7	Missense_Mutation	SNP	ENST00000369982.4	hg19	CCDS14739.1	.	.	.	.	.	.	.	.	.	.	G	12.65	2.002389	0.35320	.	.	ENSG00000177854	ENST00000369982;ENST00000425274	T;T	0.35048	1.33;1.33	4.13	-7.34	0.01427	.	0.899723	0.08783	U	0.894396	T	0.47544	0.1451	M	0.63843	1.955	0.09310	N	1	D	0.67145	0.996	P	0.55667	0.781	T	0.61242	-0.7102	10	0.87932	D	0	.	16.9406	0.86217	0.1944:0.0:0.8056:0.0	.	60	Q14656	TM187_HUMAN	M	60	ENSP00000358999:V60M;ENSP00000390108:V60M	ENSP00000358999:V60M	V	+	1	0	TMEM187	152900885	0.015000	0.18098	0.000000	0.03702	0.006000	0.05464	0.079000	0.14782	-1.849000	0.01171	0.436000	0.28706	GTG	.	.		0.652	TMEM187-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061093.1	NM_003492		A	153247691	G	A	153247691	3	1	292	1	0	0	0	0	1	0	0	0	16124	1145	40	1	180	1	TMEM187	23	153247691	Missense_Mutation	SNP	G	TCGA-G3-A7M7-01A-12D-A34Z-10		153247691	2022869	33	42752										
PAPPA2	60676	hgsc.bcm.edu	37	chr1	176709306	176709306	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	1	1	0.842672413793103	0	0.963054187192118	1	1	0	agtaactgcatctcagaggaCgaggggcagaatcatcaggg	14	8	3	2	rs376458121		TCGA-G3-A7M8-01A-11D-A33Q-10	TCGA-G3-A7M8-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ebbad8e2-34d1-4dfb-9d3b-96d717f3c94d	5ce7cd8f-dec6-4766-bc13-35f2ff250c92	g.chr1:176709306C>T	ENST00000367662.3	+	14	5289	c.4125C>T	c.(4123-4125)gaC>gaT	p.D1375D		NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	1375					bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						TCTCAGAGGACGAGGGGCAGA	0.483																																					p.D1375D		Atlas-SNP	.											PAPPA2,caecum,carcinoma,0,2	PAPPA2	665	.	0			c.C4125T						.	C		9,3955		0,9,1973	86	83	84		4125	-10.4	0	1		84	0,8330		0,0,4165	no	coding-synonymous	PAPPA2	NM_020318.2		0,9,6138	TT,TC,CC		0.0,0.227,0.0732		1375/1792	176709306	9,12285	1982	4165	6147	SO:0001819	synonymous_variant	60676	exon14			AGAGGACGAGGGG	BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"placenta-specific 3"	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.4125C>T	chr1.hg19:g.176709306C>T		81.0	0.0		69.0	9.0	NM_020318	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Silent	SNP	ENST00000367662.3	hg19	CCDS41438.1																																																																																			.	.		0.483	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1			T	176709306	C	T	176709306	2	4	293	1	0	0	0	0	0	0	0	1	11442	535	19	1		1	PAPPA2	1	176709306	Silent	SNP	C	TCGA-G3-A7M8-01A-11D-A33Q-10		176709306	72541315	1	42753										
ASPM	259266	hgsc.bcm.edu	37	chr1	197071915	197071915	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.05	1	1	0.842672413793103	0	0.963054187192118	1	1	0	cttttcacgctgcattttacCttgataatatgctctacatc	4	11	2	1			TCGA-G3-A7M8-01A-11D-A33Q-10	TCGA-G3-A7M8-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ebbad8e2-34d1-4dfb-9d3b-96d717f3c94d	5ce7cd8f-dec6-4766-bc13-35f2ff250c92	g.chr1:197071915C>G	ENST00000367409.4	-	18	6722	c.6466G>C	c.(6466-6468)Ggt>Cgt	p.G2156R	ASPM_ENST00000294732.7_Intron|ASPM_ENST00000367408.1_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	2156					developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						TGCATTTTACCTTGATAATAT	0.338																																					p.G2156R		Atlas-SNP	.											.	ASPM	444	.	0			c.G6466C						.						131	126	128					1																	197071915		2203	4300	6503	SO:0001583	missense	259266	exon18			TTTTACCTTGATA	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"microcephaly, primary autosomal recessive 5", "asp (abnormal spindle)-like, microcephaly associated (Drosophila)"	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.6466G>C	chr1.hg19:g.197071915C>G	ENSP00000356379:p.Gly2156Arg	57.0	0.0		51.0	18.0	NM_018136	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	hg19	CCDS1389.1	.	.	.	.	.	.	.	.	.	.	c	17.41	3.383832	0.61845	.	.	ENSG00000066279	ENST00000367409	T	0.63417	-0.04	5.48	5.48	0.80851	.	0.000000	0.64402	D	0.000001	T	0.74313	0.3700	L	0.58810	1.83	0.80722	D	1	D	0.67145	0.996	D	0.70487	0.969	T	0.67245	-0.5719	10	0.11182	T	0.66	.	19.3495	0.94378	0.0:1.0:0.0:0.0	.	2156	Q8IZT6	ASPM_HUMAN	R	2156	ENSP00000356379:G2156R	ENSP00000356379:G2156R	G	-	1	0	ASPM	195338538	0.996000	0.38824	0.434000	0.26772	0.890000	0.51754	3.222000	0.51223	2.587000	0.87381	0.639000	0.83563	GGT	.	.		0.338	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136		G	197071915	C	G	197071915	3	3	293	1	0	0	0	0	1	0	0	0	1056	681	24	4	4011	4	ASPM	1	197071915	Missense_Mutation	SNP	C	TCGA-G3-A7M8-01A-11D-A33Q-10	20362609	197071915	52178706	2	42754										
PLEKHA6	22874	hgsc.bcm.edu	37	chr1	204214797	204214797	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.05	1	1	0.842672413793103	0	0.963054187192118	1	1	0	gttgttcttcctcagcccctCcatcacgtcctggatcctcc	6	18	3	0			TCGA-G3-A7M8-01A-11D-A33Q-10	TCGA-G3-A7M8-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ebbad8e2-34d1-4dfb-9d3b-96d717f3c94d	5ce7cd8f-dec6-4766-bc13-35f2ff250c92	g.chr1:204214797C>A	ENST00000272203.3	-	14	2294	c.1978G>T	c.(1978-1980)Gag>Tag	p.E660*	PLEKHA6_ENST00000414478.1_Nonsense_Mutation_p.E680*	NM_014935.4	NP_055750.2	Q9Y2H5	PKHA6_HUMAN	pleckstrin homology domain containing, family A member 6	660										breast(2)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_cancers(21;0.0222)|Breast(84;0.179)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.229)			CTCAGCCCCTCCATCACGTCC	0.597																																					p.E660X		Atlas-SNP	.											.	PLEKHA6	115	.	0			c.G1978T						.						138	117	124					1																	204214797		2203	4300	6503	SO:0001587	stop_gained	22874	exon14			GCCCCTCCATCAC	AB023186	CCDS1444.1	1q32	2013-01-10			ENSG00000143850	ENSG00000143850		"Pleckstrin homology (PH) domain containing"	17053	protein-coding gene	gene with protein product		607771				11001876	Standard	NM_014935		Approved	PEPP3, KIAA0969	uc001hau.4	Q9Y2H5	OTTHUMG00000036057	ENST00000272203.3:c.1978G>T	chr1.hg19:g.204214797C>A	ENSP00000272203:p.Glu660*	35.0	0.0		34.0	11.0	NM_014935	A7MD51|Q5VTI6	Nonsense_Mutation	SNP	ENST00000272203.3	hg19	CCDS1444.1	.	.	.	.	.	.	.	.	.	.	C	42	9.820152	0.99272	.	.	ENSG00000143850	ENST00000272203;ENST00000414478	.	.	.	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-23.9479	17.357	0.87338	0.0:1.0:0.0:0.0	.	.	.	.	X	660;680	.	ENSP00000272203:E660X	E	-	1	0	PLEKHA6	202481420	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.158000	0.77470	2.406000	0.81754	0.563000	0.77884	GAG	.	.		0.597	PLEKHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087889.3	NM_014935		A	204214797	C	A	204214797	4	1	293	1	0	0	0	0	0	1	0	0	12069	864	30	3	1204	3	PLEKHA6	1	204214797	Nonsense_Mutation	SNP	C	TCGA-G3-A7M8-01A-11D-A33Q-10	7142882	204214797	45035824	3	42755										
APOB	338	hgsc.bcm.edu	37	chr2	21230621	21230625	+	Frame_Shift_Del	DEL	GAAAA	GAAAA	-													0.05	1	1	0.842672413793103	0	0.963054187192118	1	1	0	tgatctcaaatggctgggctGaaaagaaaagagaatttttc							TCGA-G3-A7M8-01A-11D-A33Q-10	TCGA-G3-A7M8-10A-01D-A33Q-10	GAAAA	GAAAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ebbad8e2-34d1-4dfb-9d3b-96d717f3c94d	5ce7cd8f-dec6-4766-bc13-35f2ff250c92	g.chr2:21230621_21230625delGAAAA	ENST00000233242.1	-	26	9242_9246	c.9115_9119delTTTTC	c.(9115-9120)ttttcafs	p.FS3039fs		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	3039					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGGCTGGGCTGAAAAGAAAAGAGAA	0.405																																					p.3039_3040del		Atlas-Indel,Pindel	.											.	APOB	761	.	0			c.9116_9120del						.			0,4266		0,0,2133						-1.4	0.3			53	4,8246		1,2,4122	no	frameshift	APOB	NM_000384.2		1,2,6255	A1A1,A1R,RR		0.0485,0.0,0.032				4,12512				SO:0001589	frameshift_variant	338	exon26			.	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.9115_9119delTTTTC	chr2.hg19:g.21230626_21230630delGAAAA	ENSP00000233242:p.Phe3039fs	161.0	0.0		120.0	38.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Frame_Shift_Del	DEL	ENST00000233242.1	hg19	CCDS1703.1																																																																																			.	.		0.405	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			-	21230625	GAAAA	-	21230621	7	5	293	1	0	1	0	1	0	0	0	0	785	1294	45	0	4588	0	APOB	2	21230621	Frame_Shift_Del	DEL	GAAAA	TCGA-G3-A7M8-01A-11D-A33Q-10		21230621	221968752	4	42756										
LRPPRC	10128	hgsc.bcm.edu	37	chr2	44209519	44209519	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	1	1	0.842672413793103	0	0.963054187192118	1	1	0	gaaaaagtggactcctcttgAatatctttttctttggcagc	8	8	3	1			TCGA-G3-A7M8-01A-11D-A33Q-10	TCGA-G3-A7M8-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ebbad8e2-34d1-4dfb-9d3b-96d717f3c94d	5ce7cd8f-dec6-4766-bc13-35f2ff250c92	g.chr2:44209519A>G	ENST00000260665.7	-	2	261	c.204T>C	c.(202-204)atT>atC	p.I68I	LRPPRC_ENST00000409946.1_Silent_p.I68I|LRPPRC_ENST00000409659.1_Silent_p.I68I	NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	68					mitochondrion transport along microtubule (GO:0047497)|mRNA transport (GO:0051028)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of mitochondrial translation (GO:0070129)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(3)|endometrium(3)|kidney(5)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|skin(2)	41		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				ACTCCTCTTGAATATCTTTTT	0.378																																					p.I68I		Atlas-SNP	.											.	LRPPRC	105	.	0			c.T204C						.						50	55	54					2																	44209519		2203	4300	6503	SO:0001819	synonymous_variant	10128	exon2			CTCTTGAATATCT	M92439	CCDS33189.1	2p21	2012-02-24	2012-02-24		ENSG00000138095	ENSG00000138095			15714	protein-coding gene	gene with protein product		607544	"Leigh syndrome, French-Canadian type (cytochrome oxidase deficiency)"	LSFC		8012652, 8619474, 22045337	Standard	NM_133259		Approved	GP130, LRP130	uc002rtr.2	P42704	OTTHUMG00000152782	ENST00000260665.7:c.204T>C	chr2.hg19:g.44209519A>G		253.0	0.0		207.0	12.0	NM_133259	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Silent	SNP	ENST00000260665.7	hg19	CCDS33189.1																																																																																			.	.		0.378	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259		G	44209519	A	G	44209519	2	3	293	1	0	0	0	0	0	0	0	1	8974	242	9	2		2	LRPPRC	2	44209519	Silent	SNP	A	TCGA-G3-A7M8-01A-11D-A33Q-10	22978898	44209519	198989854	5	42757										
BCL11A	53335	hgsc.bcm.edu	37	chr2	60687855	60687855	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	1	1	0.842672413793103	0	0.963054187192118	1	1	0	cctcttttgagctgggcctgCccgggcccggaccactaata	11	15	1	1			TCGA-G3-A7M8-01A-11D-A33Q-10	TCGA-G3-A7M8-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ebbad8e2-34d1-4dfb-9d3b-96d717f3c94d	5ce7cd8f-dec6-4766-bc13-35f2ff250c92	g.chr2:60687855C>T	ENST00000335712.6	-	4	2419	c.2192G>A	c.(2191-2193)gGc>gAc	p.G731D	BCL11A_ENST00000537768.1_Missense_Mutation_p.G400D|BCL11A_ENST00000359629.5_Intron|BCL11A_ENST00000477659.1_5'UTR|BCL11A_ENST00000356842.4_Missense_Mutation_p.G731D|BCL11A_ENST00000538214.1_Missense_Mutation_p.G697D|BCL11A_ENST00000358510.4_Missense_Mutation_p.G697D	NM_022893.3	NP_075044.2	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A (zinc finger protein)	731					B cell differentiation (GO:0030183)|negative regulation of axon extension (GO:0030517)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|negative regulation of protein homooligomerization (GO:0032463)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of dendrite development (GO:0050773)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription corepressor activity (GO:0003714)	p.G731fs*>40(1)|p.G731fs*56(1)		NS(1)|breast(6)|central_nervous_system(6)|endometrium(4)|kidney(1)|large_intestine(8)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	59			LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199)			GCTGGGCCTGCCCGGGCCCGG	0.627			T	IGH@	B-CLL																																p.G731D		Atlas-SNP	.		Dom	yes		2	2p13	53335	B-cell CLL/lymphoma 11A		L	.	BCL11A	298	.	2	Deletion - Frameshift(2)	lung(2)	c.G2192A						.						67	73	71					2																	60687855		2203	4300	6503	SO:0001583	missense	53335	exon4			GGCCTGCCCGGGC	AJ404611	CCDS1861.1, CCDS1862.1, CCDS46295.1	2p16.1	2013-01-08	2002-05-08		ENSG00000119866	ENSG00000119866		"Zinc fingers, C2H2-type"	13221	protein-coding gene	gene with protein product		606557	"ecotropic viral integration site 9"	EVI9		11719382, 18245381	Standard	NM_018014		Approved	BCL11A-XL, BCL11A-L, BCL11A-S, CTIP1, HBFQTL5, ZNF856	uc002sae.1	Q9H165	OTTHUMG00000129420	ENST00000335712.6:c.2192G>A	chr2.hg19:g.60687855C>T	ENSP00000338774:p.Gly731Asp	54.0	0.0		47.0	12.0	NM_018014	D6W5D7|Q86W14|Q8WU92|Q96JL6|Q9H163|Q9H164|Q9H3G9|Q9NWA7	Missense_Mutation	SNP	ENST00000335712.6	hg19	CCDS1862.1	.	.	.	.	.	.	.	.	.	.	C	14.71	2.615713	0.46631	.	.	ENSG00000119866	ENST00000356842;ENST00000378117;ENST00000538214;ENST00000537768;ENST00000335712;ENST00000358510	T;T;T;T;T	0.39056	1.49;3.1;1.1;3.17;3.08	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.63094	0.2482	L	0.57536	1.79	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.998;0.999;1.0;1.0	T	0.54344	-0.8308	10	0.31617	T	0.26	-2.8724	20.3312	0.98718	0.0:1.0:0.0:0.0	.	697;400;697;731;731	F5H2Y4;B4DT16;Q9H165-6;Q9H165;D9YZV9	.;.;.;BC11A_HUMAN;.	D	731;756;697;400;731;697	ENSP00000349300:G731D;ENSP00000438303:G697D;ENSP00000443712:G400D;ENSP00000338774:G731D;ENSP00000351307:G697D	ENSP00000338774:G731D	G	-	2	0	BCL11A	60541359	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	5.759000	0.68785	2.797000	0.96272	0.655000	0.94253	GGC	.	.		0.627	BCL11A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251579.2	NM_022893		T	60687855	C	T	60687855	3	4	293	1	0	0	0	0	1	0	0	0	1363	739	26	3	425	3	BCL11A	2	60687855	Missense_Mutation	SNP	C	TCGA-G3-A7M8-01A-11D-A33Q-10	16478336	60687855	182511518	6	42758										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178952085	178952085	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	1	1	0.842672413793103	0	0.963054187192118	1	1	0	gaaacaaatgaatgatgcacAtcatggtggctggacaacaa	10	7	1	2	rs121913279		TCGA-G3-A7M8-01A-11D-A33Q-10	TCGA-G3-A7M8-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ebbad8e2-34d1-4dfb-9d3b-96d717f3c94d	5ce7cd8f-dec6-4766-bc13-35f2ff250c92	g.chr3:178952085A>G	ENST00000263967.3	+	21	3297	c.3140A>G	c.(3139-3141)cAt>cGt	p.H1047R	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1047	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		H -> L (in BC; unknown pathological significance). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16353168}.|H -> R (in CLOVE, KERSEB, CRC, BC and OC; also found in an endometrial carcinoma sample; shows an increase in lipid kinase activity; oncogenic in vivo; requires binding to p85 regulatory subunit to induce cellular transformation but not interaction with RAS; may mimic the conformatitonal change triggered by the interaction with RAS; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells; increases lipid kinase activity; may alter the interaction of the PI3K/ PI4K kinase domain with the cell membrane). {ECO:0000269|PubMed:15016963, ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16114017, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|H -> Y (in MCAP; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.H1047R(1387)|p.H1047L(194)|p.H1047P(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AATGATGCACATCATGGTGGC	0.378	H1047L(EFM19_BREAST)|H1047R(BT20_BREAST)|H1047R(CAL29_URINARY_TRACT)|H1047R(CAL33_UPPER_AERODIGESTIVE_TRACT)|H1047R(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|H1047R(HCC1954_BREAST)|H1047R(HCT116_LARGE_INTESTINE)|H1047R(HSC2_UPPER_AERODIGESTIVE_TRACT)|H1047R(LS180_LARGE_INTESTINE)|H1047R(MCAS_OVARY)|H1047R(MDAMB453_BREAST)|H1047R(NCIH1048_LUNG)|H1047R(RKO_LARGE_INTESTINE)|H1047R(SKOV3_OVARY)|H1047R(T47D_BREAST)	57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											p.H1047R	Colon(199;1504 1750 3362 26421 31210 32040)	Atlas-SNP	.		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	PIK3CA_ENST00000263967,NS,adenocarcinoma,0,2044	PIK3CA	8460	.	1582	Substitution - Missense(1582)	breast(961)|large_intestine(245)|endometrium(114)|ovary(77)|urinary_tract(36)|upper_aerodigestive_tract(26)|lung(19)|central_nervous_system(19)|stomach(19)|haematopoietic_and_lymphoid_tissue(11)|thyroid(10)|NS(9)|liver(7)|kidney(6)|soft_tissue(6)|skin(4)|prostate(4)|pituitary(3)|pancreas(3)|meninges(1)|cervix(1)|bone(1)	c.A3140G						.						99	89	92					3																	178952085		1912	4130	6042	SO:0001583	missense	5290	exon21			ATGCACATCATGG		CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3140A>G	chr3.hg19:g.178952085A>G	ENSP00000263967:p.His1047Arg	93.0	0.0		77.0	22.0	NM_006218	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	hg19	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	14.34	2.506328	0.44558	.	.	ENSG00000121879	ENST00000263967	T	0.80214	-1.35	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	T	0.62466	0.2430	N	0.08118	0	0.80722	D	1	P	0.38597	0.639	B	0.28011	0.085	T	0.67526	-0.5648	10	0.40728	T	0.16	-21.2893	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1047	P42336	PK3CA_HUMAN	R	1047	ENSP00000263967:H1047R	ENSP00000263967:H1047R	H	+	2	0	PIK3CA	180434779	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	8.859000	0.92264	2.333000	0.79357	0.482000	0.46254	CAT	.	.		0.378	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			G	178952085	A	G	178952085	3	3	293	1	0	0	0	0	1	0	0	0	11922	217	8	2	3218	2	PIK3CA	3	178952085	Missense_Mutation	SNP	A	TCGA-G3-A7M8-01A-11D-A33Q-10		178952085	19070345	7	42759										
GRIA2	2891	hgsc.bcm.edu	37	chr4	158242731	158242731	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.05	1	1	0.842672413793103	0	0.963054187192118	1	1	0	aagaaaaagaataccctggaGctcacacaacaacaattaag	6	9	1	2	rs147349807		TCGA-G3-A7M8-01A-11D-A33Q-10	TCGA-G3-A7M8-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ebbad8e2-34d1-4dfb-9d3b-96d717f3c94d	5ce7cd8f-dec6-4766-bc13-35f2ff250c92	g.chr4:158242731G>T	ENST00000264426.9	+	6	1141	c.862G>T	c.(862-864)Gct>Tct	p.A288S	GRIA2_ENST00000393815.2_Missense_Mutation_p.A241S|GRIA2_ENST00000507898.1_Missense_Mutation_p.A241S|GRIA2_ENST00000449365.1_Missense_Mutation_p.A241S|GRIA2_ENST00000296526.7_Missense_Mutation_p.A288S	NM_001083619.1	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2	288					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(2)|lung(32)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	79	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	ATACCCTGGAGCTCACACAAC	0.373																																					p.A288S		Atlas-SNP	.											.	GRIA2	358	.	0			c.G862T						.	G	SER/ALA,SER/ALA,SER/ALA	0,4406		0,0,2203	115	124	121		862,862,721	4.6	1	4	dbSNP_134	121	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	GRIA2	NM_000826.3,NM_001083619.1,NM_001083620.1	99,99,99	0,1,6502	TT,TG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging	288/884,288/884,241/837	158242731	1,13005	2203	4300	6503	SO:0001583	missense	2891	exon6			CCTGGAGCTCACA		CCDS3797.1, CCDS43274.1, CCDS43275.1	4q32.1	2012-08-29			ENSG00000120251	ENSG00000120251		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4572	protein-coding gene	gene with protein product		138247		GLUR2		1311100	Standard	NM_001083619		Approved	GluA2, GLURB	uc003ipl.4	P42262	OTTHUMG00000133836	ENST00000264426.9:c.862G>T	chr4.hg19:g.158242731G>T	ENSP00000264426:p.Ala288Ser	109.0	0.0		81.0	23.0	NM_000826	A8MT92|I6L997|Q96FP6	Missense_Mutation	SNP	ENST00000264426.9	hg19	CCDS43274.1	.	.	.	.	.	.	.	.	.	.	G	18.55	3.648812	0.67358	0.0	1.16E-4	ENSG00000120251	ENST00000507898;ENST00000393815;ENST00000296526;ENST00000264426;ENST00000449365	D;D;D;D;D	0.83419	-1.72;-1.72;-1.72;-1.72;-1.72	5.46	4.59	0.56863	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.85517	0.5715	L	0.32530	0.975	0.80722	D	1	B;D;D	0.63880	0.165;0.957;0.993	B;P;D	0.83275	0.345;0.875;0.996	T	0.82323	-0.0514	10	0.20046	T	0.44	.	15.3237	0.74144	0.0:0.0:0.8591:0.1409	.	288;288;241	P42262;P42262-2;A8MT92	GRIA2_HUMAN;.;.	S	241;241;288;288;241	ENSP00000426845:A241S;ENSP00000377403:A241S;ENSP00000296526:A288S;ENSP00000264426:A288S;ENSP00000389837:A241S	ENSP00000264426:A288S	A	+	1	0	GRIA2	158462181	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	9.238000	0.95380	1.227000	0.43598	0.591000	0.81541	GCT	.	G|1.000;T|0.000		0.373	GRIA2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000258367.2			T	158242731	G	T	158242731	3	4	293	1	0	0	0	0	1	0	0	0	6777	971	34	3	884	3	GRIA2	4	158242731	Missense_Mutation	SNP	G	TCGA-G3-A7M8-01A-11D-A33Q-10		158242731	32911545	8	42760										
NSUN2	54888	hgsc.bcm.edu	37	chr5	6602579	6602579	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	1	1	0.842672413793103	0	0.963054187192118	1	1	0	cgtgtactgacttacgcagaAtctggttcatacttcagcac	8	11	3	2			TCGA-G3-A7M8-01A-11D-A33Q-10	TCGA-G3-A7M8-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ebbad8e2-34d1-4dfb-9d3b-96d717f3c94d	5ce7cd8f-dec6-4766-bc13-35f2ff250c92	g.chr5:6602579A>G	ENST00000264670.6	-	18	2303	c.1992T>C	c.(1990-1992)gaT>gaC	p.D664D	NSUN2_ENST00000506139.1_Silent_p.D629D|NSUN2_ENST00000539938.1_Silent_p.D428D	NM_017755.5	NP_060225.4	Q08J23	NSUN2_HUMAN	NOP2/Sun RNA methyltransferase family, member 2	664					mitotic nuclear division (GO:0007067)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|tRNA (cytosine-5-)-methyltransferase activity (GO:0016428)|tRNA binding (GO:0000049)			breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	41						CTTACGCAGAATCTGGTTCAT	0.493																																					p.D664D		Atlas-SNP	.											.	NSUN2	82	.	0			c.T1992C						.						390	332	352					5																	6602579		2203	4300	6503	SO:0001819	synonymous_variant	54888	exon18			CGCAGAATCTGGT	AK000310	CCDS3869.1, CCDS54832.1	5p15.32	2014-01-31	2012-06-12		ENSG00000037474	ENSG00000037474		"NOP2/Sun domain containing"	25994	protein-coding gene	gene with protein product	"tRNA methyltransferase 4 homolog (S. cerevisiae)", "Myc-induced SUN-domain-containing protein"	610916	"NOL1/NOP2/Sun domain family, member 2", "NOP2/Sun domain family, member 2", "mental retardation, non-syndromic, autosomal recessive, 5"	MRT5		17071714, 22541559	Standard	NM_017755		Approved	FLJ20303, TRM4, Misu	uc003jdu.3	Q08J23	OTTHUMG00000090455	ENST00000264670.6:c.1992T>C	chr5.hg19:g.6602579A>G		91.0	0.0		72.0	25.0	NM_017755	A8K529|B2RNR4|B3KP09|B4DQW2|G3V1R4|Q9BVN4|Q9H858|Q9NXD9	Silent	SNP	ENST00000264670.6	hg19	CCDS3869.1																																																																																			.	.		0.493	NSUN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206902.1	NM_017755		G	6602579	A	G	6602579	2	3	293	1	0	0	0	0	0	0	0	1	10687	98	4	2		2	NSUN2	5	6602579	Silent	SNP	A	TCGA-G3-A7M8-01A-11D-A33Q-10		6602579	174312681	9	42761										
AHNAK	79026	hgsc.bcm.edu	37	chr11	62286773	62286773	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.05	1	1	0.842672413793103	0	0.963054187192118	1	1	0	cattcaggtcaaatccctgtTttttggccttaatcttagga	7	9	3	0			TCGA-G3-A7M8-01A-11D-A33Q-10	TCGA-G3-A7M8-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ebbad8e2-34d1-4dfb-9d3b-96d717f3c94d	5ce7cd8f-dec6-4766-bc13-35f2ff250c92	g.chr11:62286773T>A	ENST00000378024.4	-	5	15390	c.15116A>T	c.(15115-15117)aAa>aTa	p.K5039I	AHNAK_ENST00000525875.1_5'Flank|AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	5039					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				AAATCCCTGTTTTTTGGCCTT	0.448																																					p.K5039I		Atlas-SNP	.											.	AHNAK	532	.	0			c.A15116T						.						163	169	167					11																	62286773		2202	4299	6501	SO:0001583	missense	79026	exon5			CCCTGTTTTTTGG	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.15116A>T	chr11.hg19:g.62286773T>A	ENSP00000367263:p.Lys5039Ile	137.0	0.0		126.0	28.0	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	hg19	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	T	13.94	2.386748	0.42308	.	.	ENSG00000124942	ENST00000378024	T	0.00678	5.87	4.87	3.74	0.42951	.	0.000000	0.45126	D	0.000398	T	0.03348	0.0097	M	0.77103	2.36	0.29150	N	0.87844	D	0.71674	0.998	D	0.66847	0.947	T	0.08617	-1.0713	10	0.41790	T	0.15	-8.3472	10.3304	0.43818	0.0:0.0794:0.0:0.9206	.	5039	Q09666	AHNK_HUMAN	I	5039	ENSP00000367263:K5039I	ENSP00000367263:K5039I	K	-	2	0	AHNAK	62043349	0.998000	0.40836	0.703000	0.30354	0.968000	0.65278	2.010000	0.40913	0.820000	0.34516	0.448000	0.29417	AAA	.	.		0.448	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		A	62286773	T	A	62286773	3	1	293	1	0	0	0	0	1	0	0	0	414	1841	64	4	2676	4	AHNAK	11	62286773	Missense_Mutation	SNP	T	TCGA-G3-A7M8-01A-11D-A33Q-10		62286773	72719743	10	42762										
UTP20	27340	hgsc.bcm.edu	37	chr12	101679570	101679570	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	1	1	0.842672413793103	0	0.963054187192118	1	1	0	gacaaatgccaatcattcaaTcagttggtgtatcaccaaaa	6	9	4	0			TCGA-G3-A7M8-01A-11D-A33Q-10	TCGA-G3-A7M8-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ebbad8e2-34d1-4dfb-9d3b-96d717f3c94d	5ce7cd8f-dec6-4766-bc13-35f2ff250c92	g.chr12:101679570T>C	ENST00000261637.4	+	4	411	c.237T>C	c.(235-237)aaT>aaC	p.N79N		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	79					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						AATCATTCAATCAGTTGGTGT	0.363																																					p.N79N		Atlas-SNP	.											.	UTP20	222	.	0			c.T237C						.						100	100	100					12																	101679570		2203	4300	6503	SO:0001819	synonymous_variant	27340	exon4			ATTCAATCAGTTG	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"down regulated in metastasis"	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.237T>C	chr12.hg19:g.101679570T>C		85.0	0.0		89.0	32.0	NM_014503	Q9H3H4	Silent	SNP	ENST00000261637.4	hg19	CCDS9081.1																																																																																			.	.		0.363	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		C	101679570	T	C	101679570	2	2	293	1	0	0	0	0	0	0	0	1	17114	1432	50	2		2	UTP20	12	101679570	Silent	SNP	T	TCGA-G3-A7M8-01A-11D-A33Q-10		101679570	32172325	11	42763										
PTGDR	5729	hgsc.bcm.edu	37	chr14	52735240	52735240	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.05	1	1	0.842672413793103	0	0.963054187192118	1	1	0	cggcggctgcagcggcacccGcgctcctgcaccagggactg	15	17	0	0			TCGA-G3-A7M8-01A-11D-A33Q-10	TCGA-G3-A7M8-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ebbad8e2-34d1-4dfb-9d3b-96d717f3c94d	5ce7cd8f-dec6-4766-bc13-35f2ff250c92	g.chr14:52735240G>A	ENST00000306051.2	+	1	810	c.708G>A	c.(706-708)ccG>ccA	p.P236P	PTGDR_ENST00000553372.1_Silent_p.P236P	NM_000953.2	NP_000944.1	Q13258	PD2R_HUMAN	prostaglandin D2 receptor (DP)	236					adenosine metabolic process (GO:0046085)|cellular response to prostaglandin D stimulus (GO:0071799)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|male sex determination (GO:0030238)|sleep (GO:0030431)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	prostaglandin D receptor activity (GO:0004956)|prostaglandin J receptor activity (GO:0001785)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(15)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Breast(41;0.0639)|all_epithelial(31;0.0887)				Nedocromil(DB00716)	AGCGGCACCCGCGCTCCTGCA	0.706																																					p.P236P		Atlas-SNP	.											.	PTGDR	58	.	0			c.G708A						.						34	34	34					14																	52735240		2201	4298	6499	SO:0001819	synonymous_variant	5729	exon1			GCACCCGCGCTCC	U31332	CCDS9707.1, CCDS61454.1	14q22.1	2012-08-08			ENSG00000168229	ENSG00000168229		"GPCR / Class A : Prostanoid receptors"	9591	protein-coding gene	gene with protein product		604687				7642548	Standard	NM_000953		Approved	DP, DP1, PTGDR1	uc001wzq.3	Q13258	OTTHUMG00000140299	ENST00000306051.2:c.708G>A	chr14.hg19:g.52735240G>A		34.0	0.0		48.0	12.0	NM_000953	G3V5L3|Q13250|Q13251|Q1ZZ52	Silent	SNP	ENST00000306051.2	hg19	CCDS9707.1																																																																																			.	.		0.706	PTGDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276889.1	NM_000953		A	52735240	G	A	52735240	2	1	293	1	0	0	0	0	0	0	0	1	12753	1074	38	1		1	PTGDR	14	52735240	Silent	SNP	G	TCGA-G3-A7M8-01A-11D-A33Q-10		52735240	54614300	12	42764										
PGBD4	161779	hgsc.bcm.edu	37	chr15	34394935	34394935	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	1	1	0.842672413793103	0	0.963054187192118	1	1	0	aaagagctctacatcaagtgActcagggcgctccatgaaat	9	10	3	3			TCGA-G3-A7M8-01A-11D-A33Q-10	TCGA-G3-A7M8-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ebbad8e2-34d1-4dfb-9d3b-96d717f3c94d	5ce7cd8f-dec6-4766-bc13-35f2ff250c92	g.chr15:34394935A>C	ENST00000397766.2	+	1	662	c.203A>C	c.(202-204)gAc>gCc	p.D68A	EMC7_ENST00000256545.4_5'Flank|EMC7_ENST00000532113.1_5'Flank	NM_152595.4	NP_689808.2	Q96DM1	PGBD4_HUMAN	piggyBac transposable element derived 4	68										breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|pancreas(1)|prostate(1)	16		all_lung(180;1.76e-08)		all cancers(64;1.22e-17)|GBM - Glioblastoma multiforme(113;1.78e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0242)		ACATCAAGTGACTCAGGGCGC	0.443																																					p.D68A		Atlas-SNP	.											.	PGBD4	58	.	0			c.A203C						.						78	74	75					15																	34394935		2201	4298	6499	SO:0001583	missense	161779	exon1			CAAGTGACTCAGG	AK057200	CCDS10033.1	15q13.1	2002-10-25			ENSG00000182405	ENSG00000182405			19401	protein-coding gene	gene with protein product							Standard	NM_152595		Approved	FLJ32638, FLJ37497	uc001zho.3	Q96DM1	OTTHUMG00000129370	ENST00000397766.2:c.203A>C	chr15.hg19:g.34394935A>C	ENSP00000380872:p.Asp68Ala	63.0	0.0		64.0	25.0	NM_152595	A1L487|A8K0C6|Q8N9E8	Missense_Mutation	SNP	ENST00000397766.2	hg19	CCDS10033.1	.	.	.	.	.	.	.	.	.	.	a	0.008	-1.915541	0.00503	.	.	ENSG00000182405	ENST00000397766	T	0.17370	2.28	0.774	0.774	0.18521	.	419.160000	0.01268	U	0.009394	T	0.07908	0.0198	N	0.08118	0	0.09310	N	1	B	0.22414	0.069	B	0.12837	0.008	T	0.24621	-1.0155	10	0.09338	T	0.73	.	3.8175	0.08821	1.0:0.0:0.0:0.0	.	68	Q96DM1	PGBD4_HUMAN	A	68	ENSP00000380872:D68A	ENSP00000380872:D68A	D	+	2	0	PGBD4	32182227	0.006000	0.16342	0.015000	0.15790	0.051000	0.14879	0.540000	0.23191	0.602000	0.29896	0.248000	0.18094	GAC	.	.		0.443	PGBD4-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251522.1			C	34394935	A	C	34394935	3	2	293	1	0	0	0	0	1	0	0	0	11792	275	10	5	205	5	PGBD4	15	34394935	Missense_Mutation	SNP	A	TCGA-G3-A7M8-01A-11D-A33Q-10		34394935	68136457	13	42765										
LRRC49	54839	hgsc.bcm.edu	37	chr15	71329548	71329548	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	1	1	0.842672413793103	0	0.963054187192118	1	1	0	tttcggtatctactagaatcCaaaggaaaaaaacctggtat	7	7	1	1			TCGA-G3-A7M8-01A-11D-A33Q-10	TCGA-G3-A7M8-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ebbad8e2-34d1-4dfb-9d3b-96d717f3c94d	5ce7cd8f-dec6-4766-bc13-35f2ff250c92	g.chr15:71329548C>T	ENST00000260382.5	+	15	1994	c.1734C>T	c.(1732-1734)tcC>tcT	p.S578S	LRRC49_ENST00000443425.2_Silent_p.S534S|LRRC49_ENST00000560158.2_Silent_p.S266S|LRRC49_ENST00000436542.2_3'UTR|LRRC49_ENST00000544974.2_Silent_p.S568S|LRRC49_ENST00000560691.1_Silent_p.S284S|LRRC49_ENST00000560369.1_Silent_p.S583S	NM_001199017.1|NM_017691.3	NP_001185946.1|NP_060161.2	Q8IUZ0	LRC49_HUMAN	leucine rich repeat containing 49	578						cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(3)|skin(3)	34						TACTAGAATCCAAAGGAAAAA	0.308																																					p.S583S		Atlas-SNP	.											.	LRRC49	73	.	0			c.C1749T						.						81	88	85					15																	71329548		2199	4293	6492	SO:0001819	synonymous_variant	54839	exon15			AGAATCCAAAGGA		CCDS32282.1, CCDS55971.1, CCDS58376.1, CCDS61694.1	15q23	2005-08-09				ENSG00000137821			25965	protein-coding gene	gene with protein product						12477932	Standard	NM_001199017		Approved	FLJ20156	uc010ukf.2	Q8IUZ0		ENST00000260382.5:c.1734C>T	chr15.hg19:g.71329548C>T		407.0	0.0		349.0	31.0	NM_001199017	B3KVX1|B7Z366|F5H1J4|G5E9T5|H0YLN4|Q9NXM6	Silent	SNP	ENST00000260382.5	hg19	CCDS32282.1																																																																																			.	.		0.308	LRRC49-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417209.3	NM_017691		T	71329548	C	T	71329548	2	4	293	1	0	0	0	0	0	0	0	1	9015	581	21	3		3	LRRC49	15	71329548	Silent	SNP	C	TCGA-G3-A7M8-01A-11D-A33Q-10	36934613	71329548	31201844	14	42766										
C17orf68	80169	hgsc.bcm.edu	37	chr17	8139600	8139600	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.05	1	1	0.842672413793103	0	0.963054187192118	1	1	0	gatcttggacactcgcagttCtgtcagcacataggctgtac	10	11	3	0			TCGA-G3-A7M8-01A-11D-A33Q-10	TCGA-G3-A7M8-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ebbad8e2-34d1-4dfb-9d3b-96d717f3c94d	5ce7cd8f-dec6-4766-bc13-35f2ff250c92	g.chr17:8139600C>T	ENST00000315684.8	-	6	860	c.853G>A	c.(853-855)Gaa>Aaa	p.E285K	CTC1_ENST00000581671.1_5'UTR	NM_025099.5	NP_079375.3	Q2NKJ3	CTC1_HUMAN	CTS telomere maintenance complex component 1	285					bone marrow development (GO:0048539)|cellular response to DNA damage stimulus (GO:0006974)|hematopoietic stem cell proliferation (GO:0071425)|multicellular organism growth (GO:0035264)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|replicative senescence (GO:0090399)|spleen development (GO:0048536)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)|thymus development (GO:0048538)	nuclear chromosome, telomeric region (GO:0000784)|nucleus (GO:0005634)|Stn1-Ten1 complex (GO:0070188)	single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|skin(4)	29						ACTCGCAGTTCTGTCAGCACA	0.577																																					p.E285K		Atlas-SNP	.											.	CTC1	75	.	0			c.G853A						.						46	48	47					17																	8139600		2103	4212	6315	SO:0001583	missense	80169	exon6			GCAGTTCTGTCAG	AL831955	CCDS42259.1	17p13.1	2011-02-21	2011-02-21	2011-02-21	ENSG00000178971	ENSG00000178971			26169	protein-coding gene	gene with protein product	"conserved telomere maintenance component 1", "alpha accessory factor 132", "conserved telomere capping protein 1"	613129	"tmp494178", "chromosome 17 open reading frame 68"	C17orf68		19854130, 19854131	Standard	NM_025099		Approved	FLJ22170, AAF132	uc002gkq.4	Q2NKJ3		ENST00000315684.8:c.853G>A	chr17.hg19:g.8139600C>T	ENSP00000313759:p.Glu285Lys	39.0	0.0		36.0	7.0	NM_025099	B3KR66|C9JEX5|Q1PCD1|Q2TBE3|Q8N3S6|Q9H6L0	Missense_Mutation	SNP	ENST00000315684.8	hg19	CCDS42259.1	.	.	.	.	.	.	.	.	.	.	c	5.638	0.302300	0.10678	.	.	ENSG00000178971	ENST00000315684;ENST00000449476	D;D	0.82619	-1.63;-1.63	4.76	1.66	0.24008	.	0.978962	0.08388	N	0.953444	T	0.64305	0.2586	N	0.13043	0.29	0.09310	N	1	B	0.16396	0.017	B	0.14578	0.011	T	0.50701	-0.8797	10	0.06757	T	0.87	-0.1245	5.7761	0.18279	0.0:0.66:0.0:0.34	.	285	Q2NKJ3	CTC1_HUMAN	K	285;250	ENSP00000313759:E285K;ENSP00000396018:E250K	ENSP00000313759:E285K	E	-	1	0	CTC1	8080325	0.302000	0.24454	0.355000	0.25773	0.502000	0.33828	0.616000	0.24344	0.696000	0.31696	0.556000	0.70494	GAA	.	.		0.577	CTC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442012.1	NM_025099		T	8139600	C	T	8139600	3	4	293	1	0	0	0	0	1	0	0	0	1878	922	32	3	2872	3	C17orf68	17	8139600	Missense_Mutation	SNP	C	TCGA-G3-A7M8-01A-11D-A33Q-10		8139600	73055610	15	42767										
HOXB7	3217	hgsc.bcm.edu	37	chr17	46688035	46688035	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.05	1	1	0.842672413793103	0	0.963054187192118	1	1	0	cagtgcatgttgaaggaactCggctcgagcccatagccggc	13	12	0	1			TCGA-G3-A7M8-01A-11D-A33Q-10	TCGA-G3-A7M8-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ebbad8e2-34d1-4dfb-9d3b-96d717f3c94d	5ce7cd8f-dec6-4766-bc13-35f2ff250c92	g.chr17:46688035C>A	ENST00000239165.7	-	1	344	c.246G>T	c.(244-246)ccG>ccT	p.P82P	HOXB7_ENST00000567101.2_Intron	NM_004502.3	NP_004493.3	P09629	HXB7_HUMAN	homeobox B7	82					anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|multicellular organismal development (GO:0007275)|myeloid cell differentiation (GO:0030099)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	8						TGAAGGAACTCGGCTCGAGCC	0.711																																					p.P82P		Atlas-SNP	.											.	HOXB7	15	.	0			c.G246T						.						8	6	7					17																	46688035		2102	4108	6210	SO:0001819	synonymous_variant	3217	exon1			GGAACTCGGCTCG		CCDS11532.1	17q21.32	2013-05-22	2005-12-22					"Homeoboxes / ANTP class : HOXL subclass"	5118	protein-coding gene	gene with protein product		142962	"homeo box B7"	HOX2, HOX2C		1973146, 1358459	Standard	NM_004502		Approved		uc002inv.3	P09629	OTTHUMG00000170231	ENST00000239165.7:c.246G>T	chr17.hg19:g.46688035C>A		156.0	0.0		127.0	34.0	NM_004502	A8K3N8|Q15957|Q53FN3|Q96BQ6	Silent	SNP	ENST00000239165.7	hg19	CCDS11532.1																																																																																			.	.		0.711	HOXB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358097.3			A	46688035	C	A	46688035	2	1	293	1	0	0	0	0	0	0	0	1	7315	871	31	1		1	HOXB7	17	46688035	Silent	SNP	C	TCGA-G3-A7M8-01A-11D-A33Q-10	38548435	46688035	34507175	16	42768										
APOH	350	hgsc.bcm.edu	37	chr17	64210603	64210603	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.05	1	1	0.842672413793103	0	0.963054187192118	1	1	0	tggggacttcgatagtgccaTctatacactgagcatcctct	9	11	2	1			TCGA-G3-A7M8-01A-11D-A33Q-10	TCGA-G3-A7M8-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ebbad8e2-34d1-4dfb-9d3b-96d717f3c94d	5ce7cd8f-dec6-4766-bc13-35f2ff250c92	g.chr17:64210603T>G	ENST00000205948.6	-	7	987	c.950A>C	c.(949-951)gAt>gCt	p.D317A		NM_000042.2	NP_000033.2	P02749	APOH_HUMAN	apolipoprotein H (beta-2-glycoprotein I)	317	Sushi-like.				blood coagulation, intrinsic pathway (GO:0007597)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood coagulation (GO:0030195)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of myeloid cell apoptotic process (GO:0033033)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|plasminogen activation (GO:0031639)|positive regulation of blood coagulation (GO:0030194)|positive regulation of lipoprotein lipase activity (GO:0051006)|regulation of fibrinolysis (GO:0051917)|triglyceride metabolic process (GO:0006641)|triglyceride transport (GO:0034197)	cell surface (GO:0009986)|chylomicron (GO:0042627)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipid binding (GO:0005543)			central_nervous_system(1)|kidney(3)|large_intestine(5)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(6;9.74e-08)			GATAGTGCCATCTATACACTG	0.403																																					p.D317A	Melanoma(155;624 1882 16869 48804 51309)	Atlas-SNP	.											.	APOH	45	.	0			c.A950C						.						194	157	169					17																	64210603		2203	4300	6503	SO:0001583	missense	350	exon7			GTGCCATCTATAC		CCDS11663.1	17q24.2	2013-01-24				ENSG00000091583		"Apolipoproteins"	616	protein-coding gene	gene with protein product	"beta-2-glycoprotein I"	138700		B2G1		1582254	Standard	NM_000042		Approved	BG	uc002jfn.4	P02749		ENST00000205948.6:c.950A>C	chr17.hg19:g.64210603T>G	ENSP00000205948:p.Asp317Ala	197.0	0.0		130.0	9.0	NM_000042	B2R9M3|Q9UCN7	Missense_Mutation	SNP	ENST00000205948.6	hg19	CCDS11663.1	.	.	.	.	.	.	.	.	.	.	t	14.15	2.448700	0.43531	.	.	ENSG00000091583	ENST00000205948	T	0.41400	1.0	5.5	5.5	0.81552	Complement control module (2);Beta-2-glycoprotein-1 fifth domain (2);	0.092847	0.64402	D	0.000001	T	0.65080	0.2657	M	0.78049	2.395	0.44000	D	0.996709	D	0.76494	0.999	D	0.74348	0.983	T	0.69165	-0.5217	10	0.62326	D	0.03	.	14.6578	0.68847	0.0:0.0:0.0:1.0	.	317	P02749	APOH_HUMAN	A	317	ENSP00000205948:D317A	ENSP00000205948:D317A	D	-	2	0	APOH	61641065	0.905000	0.30787	0.348000	0.25681	0.087000	0.18053	5.549000	0.67261	2.104000	0.64026	0.529000	0.55759	GAT	.	.		0.403	APOH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446926.1	NM_000042		G	64210603	T	G	64210603	3	3	293	1	0	0	0	0	1	0	0	0	804	1435	50	5	95	5	APOH	17	64210603	Missense_Mutation	SNP	T	TCGA-G3-A7M8-01A-11D-A33Q-10	17522568	64210603	16984607	17	42769										
FZR1	51343	hgsc.bcm.edu	37	chr19	3532454	3532454	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	1	1	0.842672413793103	0	0.963054187192118	1	1	0	cgagcctgagccccgtgcagCagtacacggagcacctggcg	14	15	0	1			TCGA-G3-A7M8-01A-11D-A33Q-10	TCGA-G3-A7M8-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ebbad8e2-34d1-4dfb-9d3b-96d717f3c94d	5ce7cd8f-dec6-4766-bc13-35f2ff250c92	g.chr19:3532454C>T	ENST00000395095.3	+	10	1048	c.1048C>T	c.(1048-1050)Cag>Tag	p.Q350*	FZR1_ENST00000313639.8_Nonsense_Mutation_p.Q261*|FZR1_ENST00000441788.2_Nonsense_Mutation_p.Q350*	NM_001136198.1	NP_001129670.1	Q9UM11	FZR_HUMAN	fizzy/cell division cycle 20 related 1 (Drosophila)	350					activation of anaphase-promoting complex activity (GO:0051488)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|DNA repair (GO:0006281)|G2 DNA damage checkpoint (GO:0031572)|lens fiber cell differentiation (GO:0070306)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of cell aging (GO:0090344)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of meiosis (GO:0040020)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(1)|kidney(4)|liver(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(2)	13				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00253)|STAD - Stomach adenocarcinoma(1328;0.18)		CCCCGTGCAGCAGTACACGGA	0.701																																					p.Q350X		Atlas-SNP	.											.	FZR1	42	.	0			c.C1048T						.						22	25	24					19																	3532454		2200	4297	6497	SO:0001587	stop_gained	51343	exon10			GTGCAGCAGTACA	AF083810	CCDS12109.1, CCDS45916.1, CCDS45917.1	19p13.3	2013-01-10				ENSG00000105325		"WD repeat domain containing"	24824	protein-coding gene	gene with protein product		603619				9734353, 11003657	Standard	NM_016263		Approved	HCDH1, CDH1, HCDH, FZR, FZR2, KIAA1242, CDC20C	uc010dtk.2	Q9UM11		ENST00000395095.3:c.1048C>T	chr19.hg19:g.3532454C>T	ENSP00000378529:p.Gln350*	68.0	0.0		51.0	18.0	NM_001136198	O75869|Q86U66|Q96NW8|Q9UI96|Q9ULH8|Q9UM10|Q9UNQ1|Q9Y2T8	Nonsense_Mutation	SNP	ENST00000395095.3	hg19	CCDS45916.1	.	.	.	.	.	.	.	.	.	.	c	38	6.673294	0.97751	.	.	ENSG00000105325	ENST00000441788;ENST00000395095;ENST00000313639	.	.	.	5.39	5.39	0.77823	.	0.051202	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-35.2661	17.7131	0.88327	0.0:1.0:0.0:0.0	.	.	.	.	X	350;350;261	.	ENSP00000321800:Q261X	Q	+	1	0	FZR1	3483454	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.468000	0.80943	2.531000	0.85337	0.543000	0.68304	CAG	.	.		0.701	FZR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452869.2	NM_016263		T	3532454	C	T	3532454	4	4	293	1	0	0	0	0	0	1	0	0	6146	711	25	3	1086	3	FZR1	19	3532454	Nonsense_Mutation	SNP	C	TCGA-G3-A7M8-01A-11D-A33Q-10		3532454	55596529	18	42770										
INSR	3643	hgsc.bcm.edu	37	chr19	7120659	7120659	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.05	1	1	0.842672413793103	0	0.963054187192118	1	1	0	agaagaagtggtgaagacccCatccttcagggactccggtg	13	10	1	4			TCGA-G3-A7M8-01A-11D-A33Q-10	TCGA-G3-A7M8-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ebbad8e2-34d1-4dfb-9d3b-96d717f3c94d	5ce7cd8f-dec6-4766-bc13-35f2ff250c92	g.chr19:7120659C>T	ENST00000302850.5	-	20	3773	c.3631G>A	c.(3631-3633)Ggg>Agg	p.G1211R	INSR_ENST00000341500.5_Missense_Mutation_p.G1199R	NM_000208.2	NP_000199.2	P06213	INSR_HUMAN	insulin receptor	1211	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|carbohydrate metabolic process (GO:0005975)|cellular response to growth factor stimulus (GO:0071363)|cellular response to insulin stimulus (GO:0032869)|epidermis development (GO:0008544)|exocrine pancreas development (GO:0031017)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|insulin receptor signaling pathway (GO:0008286)|male sex determination (GO:0030238)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of developmental growth (GO:0048639)|positive regulation of DNA replication (GO:0045740)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of respiratory burst (GO:0060267)|protein autophosphorylation (GO:0046777)|protein heterotetramerization (GO:0051290)|regulation of embryonic development (GO:0045995)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction by phosphorylation (GO:0023014)|transformation of host cell by virus (GO:0019087)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|insulin receptor complex (GO:0005899)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|insulin binding (GO:0043559)|insulin receptor substrate binding (GO:0043560)|insulin-activated receptor activity (GO:0005009)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor II binding (GO:0031995)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|PTB domain binding (GO:0051425)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(1)|central_nervous_system(4)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(4)|prostate(4)|skin(3)|stomach(2)|urinary_tract(2)	66					"""Insulin(DB00071)|""Insulin(DB08914)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"	GTGAAGACCCCATCCTTCAGG	0.552																																					p.G1211R		Atlas-SNP	.											.	INSR	265	.	0			c.G3631A						.						133	108	117					19																	7120659		2203	4300	6503	SO:0001583	missense	3643	exon20			AGACCCCATCCTT	M10051	CCDS12176.1, CCDS42487.1	19p13.3-p13.2	2013-02-11				ENSG00000171105		"CD molecules", "Fibronectin type III domain containing"	6091	protein-coding gene	gene with protein product		147670				2983222	Standard	NM_000208		Approved	CD220	uc002mgd.1	P06213		ENST00000302850.5:c.3631G>A	chr19.hg19:g.7120659C>T	ENSP00000303830:p.Gly1211Arg	110.0	0.0		88.0	37.0	NM_000208	Q17RW0|Q59H98|Q9UCB7|Q9UCB8|Q9UCB9	Missense_Mutation	SNP	ENST00000302850.5	hg19	CCDS12176.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.442872	0.83993	.	.	ENSG00000171105	ENST00000302850;ENST00000341500	D;D	0.82526	-1.62;-1.62	4.41	4.41	0.53225	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.43260	U	0.000592	D	0.88273	0.6392	L	0.49571	1.57	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.993;0.998	D	0.89578	0.3818	10	0.87932	D	0	.	14.8438	0.70246	0.0:1.0:0.0:0.0	.	1199;1211	P06213-2;P06213	.;INSR_HUMAN	R	1211;1199	ENSP00000303830:G1211R;ENSP00000342838:G1199R	ENSP00000303830:G1211R	G	-	1	0	INSR	7071659	1.000000	0.71417	0.979000	0.43373	0.734000	0.41952	7.446000	0.80609	2.166000	0.68216	0.455000	0.32223	GGG	.	.		0.552	INSR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458544.1			T	7120659	C	T	7120659	3	4	293	1	0	0	0	0	1	0	0	0	7782	594	21	3	529	3	INSR	19	7120659	Missense_Mutation	SNP	C	TCGA-G3-A7M8-01A-11D-A33Q-10	3588205	7120659	52008324	19	42771										
KIAA1210	57481	hgsc.bcm.edu	37	chrX	118281508	118281508	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.05	1	1	0.842672413793103	0	0.963054187192118	1	1	0	ggcccactatcctggccagaTccccaagattaccagcaatc	7	16	0	2			TCGA-G3-A7M8-01A-11D-A33Q-10	TCGA-G3-A7M8-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ebbad8e2-34d1-4dfb-9d3b-96d717f3c94d	5ce7cd8f-dec6-4766-bc13-35f2ff250c92	g.chrX:118281508T>C	ENST00000402510.2	-	2	337	c.338A>G	c.(337-339)gAt>gGt	p.D113G		NM_020721.1	NP_065772.1	Q9ULL0	K1210_HUMAN	KIAA1210	113										breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(31)|ovary(4)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	64						CCTGGCCAGATCCCCAAGATT	0.463																																					p.D113G		Atlas-SNP	.											.	KIAA1210	171	.	0			c.A338G						.						98	88	91					X																	118281508		2008	4179	6187	SO:0001583	missense	57481	exon2			GCCAGATCCCCAA	AB033036	CCDS48156.1	Xq24	2012-10-04			ENSG00000250423	ENSG00000250423			29218	protein-coding gene	gene with protein product						10574462	Standard	NM_020721		Approved		uc004era.4	Q9ULL0	OTTHUMG00000162980	ENST00000402510.2:c.338A>G	chrX.hg19:g.118281508T>C	ENSP00000384670:p.Asp113Gly	55.0	0.0		62.0	9.0	NM_020721	B7ZCI8|Q5JPN4	Missense_Mutation	SNP	ENST00000402510.2	hg19	CCDS48156.1	.	.	.	.	.	.	.	.	.	.	T	8.983	0.975914	0.18736	.	.	ENSG00000250423	ENST00000402510	T	0.13657	2.57	3.11	-4.96	0.03038	.	.	.	.	.	T	0.05318	0.0141	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.36407	-0.9749	9	0.66056	D	0.02	.	3.1402	0.06453	0.4857:0.252:0.0:0.2624	.	113	Q9ULL0	K1210_HUMAN	G	113	ENSP00000384670:D113G	ENSP00000384670:D113G	D	-	2	0	RP13-347D8.6	118165536	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.006000	0.12833	-1.283000	0.02393	-1.372000	0.01188	GAT	.	.		0.463	KIAA1210-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371251.2	NM_020721		C	118281508	T	C	118281508	3	2	293	1	0	0	0	0	1	0	0	0	8223	1435	50	2	4843	2	KIAA1210	23	118281508	Missense_Mutation	SNP	T	TCGA-G3-A7M8-01A-11D-A33Q-10		118281508	36989052	20	42772										
KIF21B	23046	hgsc.bcm.edu	37	chr1	200945972	200945972	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	ggccgtctgggtgaccgtcaGgcacatcacagggccgatgt	15	12	3	1			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr1:200945972G>A	ENST00000422435.2	-	32	4691	c.4375C>T	c.(4375-4377)Ctg>Ttg	p.L1459L	KIF21B_ENST00000332129.2_Silent_p.L1446L|KIF21B_ENST00000461742.2_Silent_p.L1459L|KIF21B_ENST00000360529.5_Silent_p.L1446L	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	1459					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						GTGACCGTCAGGCACATCACA	0.627																																					p.L1459L		Atlas-SNP	.											.	KIF21B	208	.	0			c.C4375T						.						45	40	42					1																	200945972		2203	4300	6503	SO:0001819	synonymous_variant	23046	exon32			CCGTCAGGCACAT	BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"Kinesins", "WD repeat domain containing"	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.4375C>T	chr1.hg19:g.200945972G>A		52.0	0.0		33.0	13.0	NM_001252102	B2RP62|B7ZMI0|Q5T4J3	Silent	SNP	ENST00000422435.2	hg19	CCDS58056.1																																																																																			.	.		0.627	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332		A	200945972	G	A	200945972	2	1	294	1	0	0	0	0	0	0	0	1	8298	991	35	3		3	KIF21B	1	200945972	Silent	SNP	G	TCGA-G3-A7M9-01A-23D-A34Z-10		200945972	48304649	1	42773										
ITPKB	3707	hgsc.bcm.edu	37	chr1	226923399	226923399	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	ggcaggttgccccgagggctTccctgcgtctcctccaaggc	13	16	1	0			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr1:226923399T>G	ENST00000272117.3	-	1	1760	c.1761A>C	c.(1759-1761)ggA>ggC	p.G587G	ITPKB_ENST00000366784.1_Silent_p.G587G|ITPKB_ENST00000429204.1_Silent_p.G587G			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	587					cell surface receptor signaling pathway (GO:0007166)|inositol phosphate metabolic process (GO:0043647)|MAPK cascade (GO:0000165)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of Ras protein signal transduction (GO:0046579)|positive thymic T cell selection (GO:0045059)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(1)	30		Prostate(94;0.0773)				CCCGAGGGCTTCCCTGCGTCT	0.602																																					p.G587G	Colon(84;110 1851 5306 33547)	Atlas-SNP	.											.	ITPKB	158	.	0			c.A1761C						.						54	49	51					1																	226923399		2203	4300	6503	SO:0001819	synonymous_variant	3707	exon2			AGGGCTTCCCTGC	AJ242780	CCDS1555.1	1q42.12	2011-04-28	2011-04-28		ENSG00000143772	ENSG00000143772	2.7.1.127		6179	protein-coding gene	gene with protein product		147522	"inositol 1,4,5-trisphosphate 3-kinase B"			1654894, 1330886	Standard	NM_002221		Approved	IP3KB, IP3-3KB	uc010pvo.2	P27987	OTTHUMG00000037582	ENST00000272117.3:c.1761A>C	chr1.hg19:g.226923399T>G		40.0	0.0		40.0	15.0	NM_002221	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	Silent	SNP	ENST00000272117.3	hg19	CCDS1555.1																																																																																			.	.		0.602	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221		G	226923399	T	G	226923399	2	3	294	1	0	0	0	0	0	0	0	1	7927	1770	62	5		5	ITPKB	1	226923399	Silent	SNP	T	TCGA-G3-A7M9-01A-23D-A34Z-10	25977427	226923399	22327222	2	42774										
GREB1	9687	hgsc.bcm.edu	37	chr2	11716535	11716535	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	gcttctgttacttcacggaaTtctccaatcatataaatctg	5	10	5	0			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr2:11716535T>C	ENST00000381486.2	+	5	811	c.511T>C	c.(511-513)Ttc>Ctc	p.F171L	GREB1_ENST00000381483.2_Missense_Mutation_p.F171L|GREB1_ENST00000389825.3_Missense_Mutation_p.F61L|GREB1_ENST00000234142.5_Missense_Mutation_p.F171L|GREB1_ENST00000263834.5_Missense_Mutation_p.F171L	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	171						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		CTTCACGGAATTCTCCAATCA	0.393																																					p.F171L	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											.	GREB1	308	.	0			c.T511C						.						135	140	138					2																	11716535		2203	4300	6503	SO:0001583	missense	9687	exon5			ACGGAATTCTCCA		CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"gene regulated by estrogen in breast cancer"	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.511T>C	chr2.hg19:g.11716535T>C	ENSP00000370896:p.Phe171Leu	147.0	0.0		165.0	37.0	NM_148903	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	hg19	CCDS42655.1	.	.	.	.	.	.	.	.	.	.	T	28.5	4.929320	0.92389	.	.	ENSG00000196208	ENST00000381486;ENST00000263834;ENST00000389825;ENST00000381483;ENST00000234142	T;D;D;D;T	0.81821	2.77;-1.54;-1.54;-1.54;2.77	4.88	4.88	0.63580	.	0.000000	0.85682	D	0.000000	D	0.88621	0.6486	M	0.73962	2.25	0.80722	D	1	D;D;P;P	0.76494	0.995;0.999;0.954;0.95	D;D;P;P	0.85130	0.917;0.997;0.654;0.73	D	0.88557	0.3120	10	0.42905	T	0.14	-36.4097	14.6441	0.68748	0.0:0.0:0.0:1.0	.	171;61;171;171	Q4ZG55-2;F8W6E5;Q4ZG55-3;Q4ZG55	.;.;.;GREB1_HUMAN	L	171;171;61;171;171	ENSP00000370896:F171L;ENSP00000263834:F171L;ENSP00000374475:F61L;ENSP00000370892:F171L;ENSP00000234142:F171L	ENSP00000234142:F171L	F	+	1	0	GREB1	11633986	1.000000	0.71417	0.916000	0.36221	0.880000	0.50808	7.726000	0.84824	2.049000	0.60858	0.533000	0.62120	TTC	.	.		0.393	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668		C	11716535	T	C	11716535	3	2	294	1	0	0	0	0	1	0	0	0	6769	1493	52	2	525	2	GREB1	2	11716535	Missense_Mutation	SNP	T	TCGA-G3-A7M9-01A-23D-A34Z-10		11716535	231482838	3	42775										
FAHD2B	151313	hgsc.bcm.edu	37	chr2	97751541	97751541	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	gcgtcttgttagccagtcacGagcactcacgtcatgagcca	10	13	4	1			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr2:97751541G>A	ENST00000414820.1	-	6	850	c.580C>T	c.(580-582)Cgt>Tgt	p.R194C	FAHD2B_ENST00000272610.3_Missense_Mutation_p.R194C|FAHD2B_ENST00000440566.2_Missense_Mutation_p.R194C|FAHD2B_ENST00000468548.1_5'Flank			Q6P2I3	FAH2B_HUMAN	fumarylacetoacetate hydrolase domain containing 2B	194							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			kidney(5)|large_intestine(2)|lung(3)|skin(2)	12						AGCCAGTCACGAGCACTCACG	0.582																																					p.R194C		Atlas-SNP	.											.	FAHD2B	34	.	0			c.C580T						.						114	102	106					2																	97751541		2203	4300	6503	SO:0001583	missense	151313	exon5			AGTCACGAGCACT		CCDS2030.1	2q11.2	2012-06-29			ENSG00000144199	ENSG00000144199			25318	protein-coding gene	gene with protein product							Standard	NM_199336		Approved	DKFZp434N062	uc002sxm.3	Q6P2I3	OTTHUMG00000130533	ENST00000414820.1:c.580C>T	chr2.hg19:g.97751541G>A	ENSP00000410470:p.Arg194Cys	137.0	0.0		98.0	44.0	NM_199336	D3DXH7|Q8NDK1	Missense_Mutation	SNP	ENST00000414820.1	hg19	CCDS2030.1	.	.	.	.	.	.	.	.	.	.	g	18.38	3.610637	0.66558	.	.	ENSG00000144199	ENST00000414820;ENST00000272610;ENST00000440566	D;D;D	0.99226	-5.59;-5.59;-5.59	0.624	-1.25	0.09405	Fumarylacetoacetase, C-terminal-related (2);Fumarylacetoacetase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.99348	0.9771	H	0.95574	3.69	0.58432	D	0.999991	D	0.89917	1.0	D	0.91635	0.999	D	0.98323	1.0529	10	0.87932	D	0	.	4.9789	0.14155	0.0:0.0:0.6568:0.3432	.	194	Q6P2I3	FAH2B_HUMAN	C	194	ENSP00000410470:R194C;ENSP00000272610:R194C;ENSP00000444599:R194C	ENSP00000272610:R194C	R	-	1	0	FAHD2B	97115268	1.000000	0.71417	0.792000	0.32020	0.673000	0.39480	1.987000	0.40687	-0.423000	0.07394	0.306000	0.20318	CGT	.	.		0.582	FAHD2B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339482.1	NM_199336		A	97751541	G	A	97751541	3	1	294	1	0	0	0	0	1	0	0	0	5379	1058	37	1	380	1	FAHD2B	2	97751541	Missense_Mutation	SNP	G	TCGA-G3-A7M9-01A-23D-A34Z-10	86035006	97751541	145447832	4	42776										
RNF149	284996	hgsc.bcm.edu	37	chr2	101911551	101911551	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	atgccgggtgccaacccctaTggtcatcgttactggaattc	10	12	1	0			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr2:101911551T>C	ENST00000295317.3	-	2	660	c.553A>G	c.(553-555)Ata>Gta	p.I185V		NM_173647.3	NP_775918.2	Q8NC42	RN149_HUMAN	ring finger protein 149	185					cellular response to drug (GO:0035690)|negative regulation of MAPK cascade (GO:0043409)|regulation of protein stability (GO:0031647)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	12						CCAACCCCTATGGTCATCGTT	0.453																																					p.I185V	Colon(25;331 612 6521 7355 31028)	Atlas-SNP	.											.	RNF149	25	.	0			c.A553G						.						153	140	144					2																	101911551		2203	4300	6503	SO:0001583	missense	284996	exon2			CCCCTATGGTCAT	AK074985	CCDS2051.1	2q12.1	2013-01-09			ENSG00000163162	ENSG00000163162		"RING-type (C3HC4) zinc fingers"	23137	protein-coding gene	gene with protein product							Standard	NM_173647		Approved	FLJ90504	uc002taz.2	Q8NC42	OTTHUMG00000130685	ENST00000295317.3:c.553A>G	chr2.hg19:g.101911551T>C	ENSP00000295317:p.Ile185Val	89.0	0.0		66.0	14.0	NM_173647	Q53S14|Q8N5I8|Q8NBY5|Q8WUU3	Missense_Mutation	SNP	ENST00000295317.3	hg19	CCDS2051.1	.	.	.	.	.	.	.	.	.	.	T	12.68	2.009826	0.35415	.	.	ENSG00000163162	ENST00000295317	T	0.07688	3.17	5.26	4.1	0.47936	.	0.082861	0.48767	D	0.000172	T	0.07773	0.0195	L	0.45051	1.395	0.46028	D	0.998825	P	0.43750	0.816	B	0.36766	0.232	T	0.21999	-1.0229	10	0.44086	T	0.13	.	10.9748	0.47459	0.0:0.0733:0.0:0.9267	.	185	Q8NC42	RN149_HUMAN	V	185	ENSP00000295317:I185V	ENSP00000295317:I185V	I	-	1	0	RNF149	101277983	1.000000	0.71417	0.217000	0.23759	0.157000	0.22087	5.073000	0.64395	0.841000	0.35020	0.482000	0.46254	ATA	.	.		0.453	RNF149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253180.2	NM_173647		C	101911551	T	C	101911551	3	2	294	1	0	0	0	0	1	0	0	0	13465	1464	51	2	673	2	RNF149	2	101911551	Missense_Mutation	SNP	T	TCGA-G3-A7M9-01A-23D-A34Z-10	4160010	101911551	141287822	5	42777										
STEAP3	55240	hgsc.bcm.edu	37	chr2	120005515	120005515	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	aacaagttcttcaagctgccCgtgtccgtggtcaacaccac	8	14	3	0	rs372658109		TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr2:120005515C>A	ENST00000354888.5	+	4	1257	c.753C>A	c.(751-753)ccC>ccA	p.P251P	STEAP3_ENST00000425223.2_Silent_p.P251P|STEAP3_ENST00000393110.2_Silent_p.P261P|STEAP3_ENST00000409811.1_Silent_p.P251P|STEAP3-AS1_ENST00000454260.1_RNA|STEAP3_ENST00000393107.2_Silent_p.P251P|STEAP3_ENST00000393108.2_Silent_p.P251P|STEAP3_ENST00000450943.2_Silent_p.P251P|STEAP3_ENST00000393106.2_Silent_p.P251P	NM_182915.2	NP_878919.2	Q658P3	STEA3_HUMAN	STEAP family member 3, metalloreductase	251					apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cellular iron ion homeostasis (GO:0006879)|copper ion import (GO:0015677)|exosomal secretion (GO:1990182)|ferric iron import into cell (GO:0097461)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902167)|protein secretion (GO:0009306)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)	cupric reductase activity (GO:0008823)|ferric-chelate reductase (NADPH) activity (GO:0052851)|ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	17						TCAAGCTGCCCGTGTCCGTGG	0.627																																					p.P261P		Atlas-SNP	.											.	STEAP3	44	.	0			c.C783A						.						120	115	116					2																	120005515		2203	4300	6503	SO:0001819	synonymous_variant	55240	exon4			GCTGCCCGTGTCC	AY029585	CCDS2125.1, CCDS42738.1	2q14.2	2011-09-30	2011-09-30		ENSG00000115107	ENSG00000115107			24592	protein-coding gene	gene with protein product		609671				12606722	Standard	NM_182915		Approved	TSAP6, dudlin-2, STMP3	uc002tlr.3	Q658P3	OTTHUMG00000131402	ENST00000354888.5:c.753C>A	chr2.hg19:g.120005515C>A		32.0	0.0		43.0	21.0	NM_182915	A8K6E3|Q4VBR2|Q4ZG36|Q53SQ8|Q7Z389|Q86SF6|Q8NEW6|Q8TDP3|Q8TF03|Q9NVB5	Silent	SNP	ENST00000354888.5	hg19	CCDS2125.1																																																																																			.	.		0.627	STEAP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254193.1	NM_018234		A	120005515	C	A	120005515	2	1	294	1	0	0	0	0	0	0	0	1	15294	639	23	1		1	STEAP3	2	120005515	Silent	SNP	C	TCGA-G3-A7M9-01A-23D-A34Z-10	18093964	120005515	123193858	6	42778										
FIGN	55137	hgsc.bcm.edu	37	chr2	164468244	164468244	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	caactttgtgggcaggagacCgagtggttgaggtgatgtca	16	6	1	3			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr2:164468244C>G	ENST00000333129.3	-	3	412	c.98G>C	c.(97-99)cGg>cCg	p.R33P	FIGN_ENST00000409634.1_Intron|FIGN_ENST00000482917.1_5'UTR	NM_018086.2	NP_060556.2	Q5HY92	FIGN_HUMAN	fidgetin	33					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)	p.R33Q(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(1)|prostate(2)|skin(1)	47						GGCAGGAGACCGAGTGGTTGA	0.517																																					p.R33P		Atlas-SNP	.											FIGN,NS,carcinoma,0,1	FIGN	106	.	1	Substitution - Missense(1)	breast(1)	c.G98C						.						100	101	100					2																	164468244		2082	4234	6316	SO:0001583	missense	55137	exon3			GGAGACCGAGTGG	AK001267	CCDS2221.2	2q24	2010-04-21			ENSG00000182263	ENSG00000182263		"ATPases / AAA-type"	13285	protein-coding gene	gene with protein product		605295				11017077	Standard	XM_005246661		Approved		uc002uck.1	Q5HY92	OTTHUMG00000074059	ENST00000333129.3:c.98G>C	chr2.hg19:g.164468244C>G	ENSP00000333836:p.Arg33Pro	77.0	1.0		64.0	21.0	NM_018086	B3KWM0|Q9H6M5|Q9NVZ9	Missense_Mutation	SNP	ENST00000333129.3	hg19	CCDS2221.2	.	.	.	.	.	.	.	.	.	.	C	17.37	3.371699	0.61624	.	.	ENSG00000182263	ENST00000333129	T	0.25414	1.8	6.17	6.17	0.99709	.	0.000000	0.85682	U	0.000000	T	0.47116	0.1428	L	0.48362	1.52	0.80722	D	1	D	0.71674	0.998	D	0.77004	0.989	T	0.03148	-1.1067	10	0.31617	T	0.26	-14.7367	20.8794	0.99867	0.0:1.0:0.0:0.0	.	33	Q5HY92	FIGN_HUMAN	P	33	ENSP00000333836:R33P	ENSP00000333836:R33P	R	-	2	0	FIGN	164176490	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.487000	0.81328	2.941000	0.99782	0.655000	0.94253	CGG	.	.		0.517	FIGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157220.2	NM_018086		G	164468244	C	G	164468244	3	3	294	1	0	0	0	0	1	0	0	0	5899	652	23	4	2185	4	FIGN	2	164468244	Missense_Mutation	SNP	C	TCGA-G3-A7M9-01A-23D-A34Z-10	44462729	164468244	78731129	7	42779										
FN1	2335	hgsc.bcm.edu	37	chr2	216256381	216256381	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	agaccactgcattgtctgaaGgagaaattgacaactctgca	9	9	2	4			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr2:216256381G>T	ENST00000359671.1	-	25	4218	c.3953C>A	c.(3952-3954)cCt>cAt	p.P1318H	FN1_ENST00000357867.4_Missense_Mutation_p.P1318H|FN1_ENST00000446046.1_Missense_Mutation_p.P1318H|FN1_ENST00000357009.2_Missense_Mutation_p.P1318H|FN1_ENST00000346544.3_Missense_Mutation_p.P1318H|FN1_ENST00000421182.1_Missense_Mutation_p.P1318H|FN1_ENST00000323926.6_Missense_Mutation_p.P1409H|FN1_ENST00000345488.5_Missense_Mutation_p.P1318H|FN1_ENST00000443816.1_Missense_Mutation_p.P1318H|FN1_ENST00000356005.4_Missense_Mutation_p.P1318H|FN1_ENST00000354785.4_Missense_Mutation_p.P1409H|FN1_ENST00000432072.2_Missense_Mutation_p.P1409H|FN1_ENST00000336916.4_Missense_Mutation_p.P1318H			P02751	FINC_HUMAN	fibronectin 1	1318	Cell-attachment.|Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316, ECO:0000255|PROSITE-ProRule:PRU00478, ECO:0000255|PROSITE-ProRule:PRU00479}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	ATTGTCTGAAGGAGAAATTGA	0.403																																					p.P1409H		Atlas-SNP	.											.	FN1	521	.	0			c.C4226A						.						134	126	129					2																	216256381		2203	4300	6503	SO:0001583	missense	2335	exon26			TCTGAAGGAGAAA		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"Fibronectin type III domain containing", "Endogenous ligands"	3778	protein-coding gene	gene with protein product	"migration-stimulating factor", "cold-insoluble globulin"	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.3953C>A	chr2.hg19:g.216256381G>T	ENSP00000352696:p.Pro1318His	44.0	0.0		66.0	21.0	NM_212482	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Missense_Mutation	SNP	ENST00000359671.1	hg19		.	.	.	.	.	.	.	.	.	.	G	18.76	3.691754	0.68271	.	.	ENSG00000115414	ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000359671;ENST00000346544;ENST00000345488;ENST00000357009;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005;ENST00000456923	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.58358	0.34;0.34;0.34;0.34;0.34;0.34;0.34;0.34;0.34;0.34;0.34;0.34;0.34;0.34	5.62	5.62	0.85841	.	0.000000	0.64402	D	0.000003	T	0.75170	0.3813	M	0.80982	2.52	0.45515	D	0.99847	D;D;D;D;D;D;D;D;D	0.89917	1.0;0.988;0.999;1.0;1.0;0.999;1.0;1.0;0.999	D;P;D;D;D;D;D;D;D	0.97110	0.999;0.899;0.985;1.0;1.0;0.967;0.999;0.999;0.972	T	0.73795	-0.3870	10	0.38643	T	0.18	.	19.6604	0.95864	0.0:0.0:1.0:0.0	.	1409;1409;1318;1318;1318;1318;1318;1318;1409	P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;P02751-9;P02751-14;P02751-15	.;.;.;.;.;.;.;.;.	H	1318;1409;1318;1318;1409;1318;1318;1318;1318;1318;1318;1409;1318;125	ENSP00000394423:P1318H;ENSP00000323534:P1409H;ENSP00000338200:P1318H;ENSP00000350534:P1318H;ENSP00000346839:P1409H;ENSP00000352696:P1318H;ENSP00000265312:P1318H;ENSP00000273049:P1318H;ENSP00000349509:P1318H;ENSP00000410422:P1318H;ENSP00000415018:P1318H;ENSP00000399538:P1409H;ENSP00000348285:P1318H;ENSP00000416139:P125H	ENSP00000323534:P1409H	P	-	2	0	FN1	215964626	1.000000	0.71417	0.997000	0.53966	0.923000	0.55619	7.627000	0.83176	2.648000	0.89879	0.655000	0.94253	CCT	.	.		0.403	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		T	216256381	G	T	216256381	3	4	294	1	0	0	0	0	1	0	0	0	5970	1000	35	3	3291	3	FN1	2	216256381	Missense_Mutation	SNP	G	TCGA-G3-A7M9-01A-23D-A34Z-10	51788137	216256381	26942992	8	42780										
PRSS50	29122	hgsc.bcm.edu	37	chr3	46755757	46755757	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	acagtgcagcgggaatggtcCttcaacacatagtccgtgcc	11	12	1	0			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr3:46755757C>A	ENST00000460241.1	-	9	2375	c.705G>T	c.(703-705)aaG>aaT	p.K235N	PRSS50_ENST00000315170.7_Missense_Mutation_p.K235N			Q9UI38	TSP50_HUMAN	protease, serine, 50	235	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)	serine-type endopeptidase activity (GO:0004252)|threonine-type endopeptidase activity (GO:0004298)			endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11						GGGAATGGTCCTTCAACACAT	0.597																																					p.K235N	Pancreas(41;915 1239 11561 17469)	Atlas-SNP	.											.	PRSS50	35	.	0			c.G705T						.						121	91	101					3																	46755757		2202	4300	6502	SO:0001583	missense	29122	exon4			ATGGTCCTTCAAC	AF100707	CCDS2745.1	3p21.31	2011-05-24			ENSG00000206549	ENSG00000206549		"Serine peptidases / Serine peptidases"	17910	protein-coding gene	gene with protein product	"cancer/testis antigen 20", "testes specific protease 50"	607950				10397268	Standard	NM_013270		Approved	TSP50, CT20	uc003cqe.1	Q9UI38	OTTHUMG00000164067	ENST00000460241.1:c.705G>T	chr3.hg19:g.46755757C>A	ENSP00000418875:p.Lys235Asn	31.0	0.0		39.0	20.0	NM_013270		Missense_Mutation	SNP	ENST00000460241.1	hg19	CCDS2745.1	.	.	.	.	.	.	.	.	.	.	C	15.95	2.983530	0.53827	.	.	ENSG00000206549	ENST00000455218;ENST00000315170;ENST00000460241	D;D	0.89196	-2.48;-2.48	3.6	1.81	0.25067	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.735756	0.11871	N	0.521475	T	0.79317	0.4425	N	0.19112	0.55	0.22199	N	0.9993	B	0.30634	0.288	B	0.34038	0.174	T	0.66909	-0.5804	10	0.33141	T	0.24	.	5.9328	0.19148	0.0:0.7625:0.0:0.2375	.	235	Q9UI38	TSP50_HUMAN	N	149;235;235	ENSP00000326598:K235N;ENSP00000418875:K235N	ENSP00000326598:K235N	K	-	3	2	PRSS50	46730761	0.007000	0.16637	0.972000	0.41901	0.019000	0.09904	0.282000	0.18829	0.533000	0.28675	-0.381000	0.06696	AAG	.	.		0.597	PRSS50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354544.1			A	46755757	C	A	46755757	3	1	294	1	0	0	0	0	1	0	0	0	12643	680	24	3	464	3	PRSS50	3	46755757	Missense_Mutation	SNP	C	TCGA-G3-A7M9-01A-23D-A34Z-10		46755757	151266673	9	42781										
CHDH	55349	hgsc.bcm.edu	37	chr3	53851908	53851908	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	tgccttctctgcgatcatgaTtgtgggggcgttcaggttgc	14	9	3	1			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr3:53851908T>C	ENST00000315251.6	-	9	2118	c.1681A>G	c.(1681-1683)Atc>Gtc	p.I561V		NM_018397.4	NP_060867.2	Q8NE62	CHDH_HUMAN	choline dehydrogenase	561					glycine betaine biosynthetic process from choline (GO:0019285)	mitochondrial inner membrane (GO:0005743)	choline dehydrogenase activity (GO:0008812)|flavin adenine dinucleotide binding (GO:0050660)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	17		Hepatocellular(537;0.152)		BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)	Choline(DB00122)	GCGATCATGATTGTGGGGGCG	0.597																																					p.I561V		Atlas-SNP	.											.	CHDH	34	.	0			c.A1681G						.						98	80	86					3																	53851908		2203	4300	6503	SO:0001583	missense	55349	exon9			TCATGATTGTGGG	AJ272267	CCDS2873.1	3p21	2004-11-24			ENSG00000016391	ENSG00000016391	1.1.99.1		24288	protein-coding gene	gene with protein product							Standard	NM_018397		Approved		uc003dgz.3	Q8NE62	OTTHUMG00000158281	ENST00000315251.6:c.1681A>G	chr3.hg19:g.53851908T>C	ENSP00000319851:p.Ile561Val	88.0	0.0		56.0	25.0	NM_018397	Q9NY17	Missense_Mutation	SNP	ENST00000315251.6	hg19	CCDS2873.1	.	.	.	.	.	.	.	.	.	.	T	11.41	1.630713	0.28978	.	.	ENSG00000016391	ENST00000315251	T	0.41758	0.99	5.69	1.48	0.22813	Glucose-methanol-choline oxidoreductase, C-terminal (1);	0.120942	0.56097	N	0.000039	T	0.32734	0.0839	L	0.39898	1.24	0.47037	D	0.999293	B	0.19073	0.033	B	0.21708	0.036	T	0.11421	-1.0588	10	0.62326	D	0.03	-24.6102	9.8993	0.41338	0.0:0.2126:0.0:0.7874	.	561	Q8NE62	CHDH_HUMAN	V	561	ENSP00000319851:I561V	ENSP00000319851:I561V	I	-	1	0	CHDH	53826948	0.995000	0.38212	0.181000	0.23098	0.410000	0.31052	2.417000	0.44653	0.017000	0.15025	-0.290000	0.09829	ATC	.	.		0.597	CHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350567.2	NM_018397		C	53851908	T	C	53851908	3	2	294	1	0	0	0	0	1	0	0	0	3335	1493	52	2	107	2	CHDH	3	53851908	Missense_Mutation	SNP	T	TCGA-G3-A7M9-01A-23D-A34Z-10	7096151	53851908	144170522	10	42782										
TMPRSS7	344805	hgsc.bcm.edu	37	chr3	111764772	111764772	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	agggactggctgtggacatgGactctgtggtactaaatggt	15	6	1	0			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr3:111764772G>C	ENST00000452346.2	+	5	676	c.673G>C	c.(673-675)Gac>Cac	p.D225H	TMPRSS7_ENST00000419127.1_Missense_Mutation_p.D112H			Q7RTY8	TMPS7_HUMAN	transmembrane protease, serine 7	225	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.				proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(2)|endometrium(6)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						TGTGGACATGGACTCTGTGGT	0.473																																					p.D112H		Atlas-SNP	.											.	TMPRSS7	126	.	0			c.G334C						.						241	214	222					3																	111764772		692	1591	2283	SO:0001583	missense	344805	exon4			GACATGGACTCTG	BN000125	CCDS43129.2	3q13.2	2010-04-13	2004-03-16		ENSG00000176040	ENSG00000176040		"Serine peptidases / Transmembrane"	30846	protein-coding gene	gene with protein product			"type II transmembrane serine protease 7"			12838346	Standard	NM_001042575		Approved		uc010hqb.2	Q7RTY8	OTTHUMG00000157148	ENST00000452346.2:c.673G>C	chr3.hg19:g.111764772G>C	ENSP00000398236:p.Asp225His	177.0	0.0		151.0	45.0	NM_001042575	C9J8P7|E9PAS3|Q17RH4	Missense_Mutation	SNP	ENST00000452346.2	hg19		.	.	.	.	.	.	.	.	.	.	G	21.4	4.150002	0.78001	.	.	ENSG00000176040	ENST00000452346;ENST00000443106;ENST00000437906;ENST00000419127;ENST00000460599	T;T;T	0.35973	1.28;1.28;1.28	5.06	5.06	0.68205	.	.	.	.	.	T	0.40619	0.1124	N	0.08118	0	0.50039	D	0.999841	D	0.89917	1.0	D	0.91635	0.999	T	0.48031	-0.9070	9	0.52906	T	0.07	.	15.8068	0.78520	0.0:0.0:1.0:0.0	.	112	Q7RTY8-2	.	H	225;212;212;112;88	ENSP00000398236:D225H;ENSP00000411645:D112H;ENSP00000447563:D88H	ENSP00000411645:D112H	D	+	1	0	TMPRSS7	113247462	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.709000	0.84645	2.763000	0.94921	0.655000	0.94253	GAC	.	.		0.473	TMPRSS7-003	NOVEL	NAGNAG_splice_site|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000347592.2	XM_293599		C	111764772	G	C	111764772	3	2	294	1	0	0	0	0	1	0	0	0	16267	1174	41	4	344	4	TMPRSS7	3	111764772	Missense_Mutation	SNP	G	TCGA-G3-A7M9-01A-23D-A34Z-10	57912864	111764772	86257658	11	42783										
PTX3	5806	hgsc.bcm.edu	37	chr3	157160183	157160183	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	acagctattttattcccaatGcgttccaagaagatttttgg	7	8	0	2			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr3:157160183G>A	ENST00000295927.3	+	3	706	c.561G>A	c.(559-561)atG>atA	p.M187I	VEPH1_ENST00000392833.2_Intron|VEPH1_ENST00000362010.2_Intron|VEPH1_ENST00000392832.2_Intron|VEPH1_ENST00000543418.1_Intron	NM_002852.3	NP_002843.2	P26022	PTX3_HUMAN	pentraxin 3, long	187	Pentaxin.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of exo-alpha-sialidase activity (GO:1903016)|negative regulation of glycoprotein metabolic process (GO:1903019)|negative regulation of viral entry into host cell (GO:0046597)|opsonization (GO:0008228)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phagocytosis (GO:0050766)|response to yeast (GO:0001878)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	(1->3)-beta-D-glucan binding (GO:0001872)|complement component C1q binding (GO:0001849)|virion binding (GO:0046790)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(4)|stomach(1)	10			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)			TATTCCCAATGCGTTCCAAGA	0.348																																					p.M187I		Atlas-SNP	.											.	PTX3	27	.	0			c.G561A						.						54	54	54					3																	157160183		2203	4300	6503	SO:0001583	missense	5806	exon3			CCCAATGCGTTCC	X63613	CCDS3180.1	3q25	2010-03-11	2010-03-11		ENSG00000163661	ENSG00000163661			9692	protein-coding gene	gene with protein product		602492	"pentaxin-related gene, rapidly induced by IL-1 beta", "tumor necrosis factor, alpha-induced protein 5", "pentraxin-related gene, rapidly induced by IL-1 beta"	TNFAIP5		1429570	Standard	NM_002852		Approved	TSG-14	uc003fbl.4	P26022	OTTHUMG00000158750	ENST00000295927.3:c.561G>A	chr3.hg19:g.157160183G>A	ENSP00000295927:p.Met187Ile	27.0	0.0		34.0	11.0	NM_002852	B2R6T6|Q38M82	Missense_Mutation	SNP	ENST00000295927.3	hg19	CCDS3180.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.105810	0.77096	.	.	ENSG00000163661	ENST00000295927	T	0.06218	3.33	5.5	5.5	0.81552	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.037066	0.85682	D	0.000000	T	0.29028	0.0721	M	0.82630	2.6	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	T	0.01520	-1.1334	10	0.31617	T	0.26	-36.0161	19.3998	0.94623	0.0:0.0:1.0:0.0	.	187	P26022	PTX3_HUMAN	I	187	ENSP00000295927:M187I	ENSP00000295927:M187I	M	+	3	0	PTX3	158642877	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.238000	0.78173	2.586000	0.87340	0.655000	0.94253	ATG	.	.		0.348	PTX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352028.1	NM_002852		A	157160183	G	A	157160183	3	1	294	1	0	0	0	0	1	0	0	0	12837	1319	46	3	571	3	PTX3	3	157160183	Missense_Mutation	SNP	G	TCGA-G3-A7M9-01A-23D-A34Z-10	45395411	157160183	40862247	12	42784										
SI	6476	hgsc.bcm.edu	37	chr3	164737493	164737493	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	aaccatatatatattctgatGgcaggcgagtcgatatttga	9	6	1	2			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr3:164737493G>T	ENST00000264382.3	-	28	3382	c.3320C>A	c.(3319-3321)cCa>cAa	p.P1107Q		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	1107	Sucrase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)			NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	ATATTCTGATGGCAGGCGAGT	0.408										HNSCC(35;0.089)																											p.P1107Q		Atlas-SNP	.											.	SI	500	.	0			c.C3320A						.						102	99	100					3																	164737493		2203	4299	6502	SO:0001583	missense	6476	exon28			TCTGATGGCAGGC	X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"Oligosaccharide alpha-1,6-glucosidase"	609845	"sucrase-isomaltase"			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.3320C>A	chr3.hg19:g.164737493G>T	ENSP00000264382:p.Pro1107Gln	84.0	0.0		73.0	23.0	NM_001041	A2RUC3|Q1JQ80|Q1RMC2	Missense_Mutation	SNP	ENST00000264382.3	hg19	CCDS3196.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.349569	0.82132	.	.	ENSG00000090402	ENST00000264382	D	0.86497	-2.13	4.46	4.46	0.54185	Glycoside hydrolase-type carbohydrate-binding (1);	0.075502	0.64402	D	0.000020	D	0.95127	0.8421	M	0.93898	3.47	0.54753	D	0.999982	D	0.89917	1.0	D	0.79784	0.993	D	0.96547	0.9405	10	0.87932	D	0	.	17.305	0.87192	0.0:0.0:1.0:0.0	.	1107	P14410	SUIS_HUMAN	Q	1107	ENSP00000264382:P1107Q	ENSP00000264382:P1107Q	P	-	2	0	SI	166220187	1.000000	0.71417	0.996000	0.52242	0.922000	0.55478	8.963000	0.93385	2.293000	0.77203	0.591000	0.81541	CCA	.	.		0.408	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041		T	164737493	G	T	164737493	3	4	294	1	0	0	0	0	1	0	0	0	14312	1348	47	3	2247	3	SI	3	164737493	Missense_Mutation	SNP	G	TCGA-G3-A7M9-01A-23D-A34Z-10	7577310	164737493	33284937	13	42785										
TP63	8626	hgsc.bcm.edu	37	chr3	189526152	189526152	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	tccctataacacagaccacgCgcagaacagcgtcacggcgc	9	16	1	2			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr3:189526152C>T	ENST00000264731.3	+	4	505	c.416C>T	c.(415-417)gCg>gTg	p.A139V	TP63_ENST00000418709.2_Missense_Mutation_p.A139V|TP63_ENST00000456148.1_Missense_Mutation_p.A45V|TP63_ENST00000382063.4_Intron|TP63_ENST00000437221.1_Missense_Mutation_p.A45V|TP63_ENST00000354600.5_Missense_Mutation_p.A45V|TP63_ENST00000392463.2_Missense_Mutation_p.A45V|TP63_ENST00000392460.3_Missense_Mutation_p.A139V|TP63_ENST00000449992.1_Intron|TP63_ENST00000320472.5_Missense_Mutation_p.A139V|TP63_ENST00000392461.3_Missense_Mutation_p.A45V|TP63_ENST00000440651.2_Missense_Mutation_p.A139V	NM_001114978.1|NM_003722.4	NP_001108450.1|NP_003713.3	Q9H3D4	P63_HUMAN	tumor protein p63	139					apoptotic process (GO:0006915)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|cloacal septation (GO:0060197)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|ectoderm and mesoderm interaction (GO:0007499)|embryonic limb morphogenesis (GO:0030326)|epidermal cell division (GO:0010481)|epithelial cell development (GO:0002064)|establishment of planar polarity (GO:0001736)|establishment of skin barrier (GO:0061436)|female genitalia morphogenesis (GO:0048807)|hair follicle morphogenesis (GO:0031069)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|keratinocyte differentiation (GO:0030216)|keratinocyte proliferation (GO:0043616)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organismal aging (GO:0010259)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular senescence (GO:2000773)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of mesoderm development (GO:2000381)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|polarized epithelial cell differentiation (GO:0030859)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell cycle G1/S phase transition (GO:1902808)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-anal tail morphogenesis (GO:0036342)|prostatic bud formation (GO:0060513)|protein homotetramerization (GO:0051289)|proximal/distal pattern formation (GO:0009954)|regulation of epidermal cell division (GO:0010482)|regulation of neuron apoptotic process (GO:0043523)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|skeletal system development (GO:0001501)|smooth muscle tissue development (GO:0048745)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|sympathetic nervous system development (GO:0048485)|urinary bladder development (GO:0060157)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region DNA binding (GO:0044212)|WW domain binding (GO:0050699)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(5)|large_intestine(12)|lung(15)|ovary(2)|skin(9)|upper_aerodigestive_tract(6)	61	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)		ACAGACCACGCGCAGAACAGC	0.612										HNSCC(45;0.13)																											p.A139V		Atlas-SNP	.											.	TP63	187	.	0			c.C416T						.						184	137	153					3																	189526152		2203	4300	6503	SO:0001583	missense	8626	exon4			ACCACGCGCAGAA	AB010153	CCDS3293.1, CCDS46976.1, CCDS46977.1, CCDS46978.1, CCDS46979.1, CCDS46980.1	3q27-q29	2014-09-17			ENSG00000073282	ENSG00000073282			15979	protein-coding gene	gene with protein product		603273	"tumor protein p73-like", "tumor protein p53-like", "tumor protein p53-competing protein"	TP73L, TP53L, TP53CP		9774969, 9662378, 11181441, 11181451	Standard	NM_003722		Approved	p51, SHFM4, EEC3, p63, p73L, OFC8, KET, p73H, NBP, p53CP	uc003fry.2	Q9H3D4	OTTHUMG00000156313	ENST00000264731.3:c.416C>T	chr3.hg19:g.189526152C>T	ENSP00000264731:p.Ala139Val	62.0	0.0		59.0	15.0	NM_001114979	O75080|O75195|O75922|O76078|Q6VEG2|Q6VEG3|Q6VEG4|Q6VFJ1|Q6VFJ2|Q6VFJ3|Q6VH20|Q7LDI3|Q7LDI4|Q7LDI5|Q96KR0|Q9H3D2|Q9H3D3|Q9H3P8|Q9NPH7|Q9P1B4|Q9P1B5|Q9P1B6|Q9P1B7|Q9UBV9|Q9UE10|Q9UP26|Q9UP27|Q9UP28|Q9UP74	Missense_Mutation	SNP	ENST00000264731.3	hg19	CCDS3293.1	.	.	.	.	.	.	.	.	.	.	C	35	5.567392	0.96540	.	.	ENSG00000073282	ENST00000264731;ENST00000418709;ENST00000320472;ENST00000392460;ENST00000440651;ENST00000354600;ENST00000434928;ENST00000437221;ENST00000392463;ENST00000392461;ENST00000456148	D;D;D;D;D;D;T;D;D;D;D	0.99793	-6.51;-6.77;-6.76;-6.76;-6.53;-6.43;-1.13;-6.63;-6.66;-6.64;-6.46	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	D	0.99483	0.9816	L	0.32530	0.975	0.80722	D	1	D;D;D;D;D;D;D;D;D	0.76494	0.999;0.999;0.999;0.997;0.997;0.989;0.999;0.998;0.999	D;D;P;P;P;P;D;D;D	0.69307	0.949;0.963;0.908;0.815;0.815;0.522;0.963;0.919;0.963	D	0.99250	1.0887	9	.	.	.	-3.5143	19.122	0.93367	0.0:1.0:0.0:0.0	.	139;139;45;45;45;45;139;139;139	Q9H3D4-7;Q9H3D4-11;Q9H3D4-4;Q9H3D4-2;Q9H3D4-6;C9D7C9;Q9H3D4-3;Q9H3D4;Q9H3D4-5	.;.;.;.;.;.;.;P63_HUMAN;.	V	139;139;139;139;139;45;45;45;45;45;45	ENSP00000264731:A139V;ENSP00000407144:A139V;ENSP00000317510:A139V;ENSP00000376253:A139V;ENSP00000394337:A139V;ENSP00000346614:A45V;ENSP00000401661:A45V;ENSP00000392488:A45V;ENSP00000376256:A45V;ENSP00000376254:A45V;ENSP00000389485:A45V	.	A	+	2	0	TP63	191008846	1.000000	0.71417	0.934000	0.37439	0.991000	0.79684	7.487000	0.81328	2.770000	0.95276	0.655000	0.94253	GCG	.	.		0.612	TP63-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000343865.1	NM_003722		T	189526152	C	T	189526152	3	4	294	1	0	0	0	0	1	0	0	0	16407	768	27	1	476	1	TP63	3	189526152	Missense_Mutation	SNP	C	TCGA-G3-A7M9-01A-23D-A34Z-10	24788659	189526152	8496278	14	42786										
WFS1	7466	hgsc.bcm.edu	37	chr4	6303650	6303650	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	gcttcaagtacgtccgcgtgActgacatcgacaacagcgcc	10	14	1	2			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr4:6303650A>C	ENST00000226760.1	+	8	2298	c.2128A>C	c.(2128-2130)Act>Cct	p.T710P	WFS1_ENST00000503569.1_Missense_Mutation_p.T710P	NM_001145853.1|NM_006005.3	NP_001139325.1|NP_005996.2	O76024	WFS1_HUMAN	Wolfram syndrome 1 (wolframin)	710					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|calcium ion homeostasis (GO:0055074)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glucose homeostasis (GO:0042593)|kidney development (GO:0001822)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of programmed cell death (GO:0043069)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neurological system process (GO:0050877)|olfactory behavior (GO:0042048)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of growth (GO:0045927)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of proteolysis (GO:0045862)|protein maturation by protein folding (GO:0022417)|protein stabilization (GO:0050821)|renal water homeostasis (GO:0003091)|response to endoplasmic reticulum stress (GO:0034976)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	activating transcription factor binding (GO:0033613)|ATPase binding (GO:0051117)|transporter activity (GO:0005215)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	21				Colorectal(103;0.0512)		CGTCCGCGTGACTGACATCGA	0.642																																					p.T710P		Atlas-SNP	.											.	WFS1	71	.	0			c.A2128C						.						39	34	36					4																	6303650		2203	4300	6503	SO:0001583	missense	7466	exon8			CGCGTGACTGACA	AF084481	CCDS3386.1	4p16.1	2014-06-18			ENSG00000109501	ENSG00000109501			12762	protein-coding gene	gene with protein product		606201		DFNA6, DFNA14, DFNA38		7987399, 9771706	Standard	NM_006005		Approved	DIDMOAD, WFS	uc003gix.3	O76024	OTTHUMG00000090431	ENST00000226760.1:c.2128A>C	chr4.hg19:g.6303650A>C	ENSP00000226760:p.Thr710Pro	31.0	0.0		34.0	11.0	NM_001145853	B2R797|D3DVT1|Q8N6I3|Q9UNW6	Missense_Mutation	SNP	ENST00000226760.1	hg19	CCDS3386.1	.	.	.	.	.	.	.	.	.	.	A	12.51	1.959340	0.34565	.	.	ENSG00000109501	ENST00000503569;ENST00000226760;ENST00000540337	D;D	0.97575	-4.44;-4.44	5.49	5.49	0.81192	.	0.050606	0.85682	D	0.000000	D	0.97986	0.9337	M	0.75447	2.3	0.48087	D	0.999588	D	0.71674	0.998	D	0.65010	0.931	D	0.98602	1.0659	10	0.62326	D	0.03	-39.7433	14.7629	0.69619	1.0:0.0:0.0:0.0	.	710	O76024	WFS1_HUMAN	P	710;710;88	ENSP00000423337:T710P;ENSP00000226760:T710P	ENSP00000226760:T710P	T	+	1	0	WFS1	6354551	1.000000	0.71417	0.975000	0.42487	0.213000	0.24496	3.589000	0.53972	2.092000	0.63282	0.459000	0.35465	ACT	.	.		0.642	WFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206863.1			C	6303650	A	C	6303650	3	2	294	1	0	0	0	0	1	0	0	0	17375	275	10	5	2154	5	WFS1	4	6303650	Missense_Mutation	SNP	A	TCGA-G3-A7M9-01A-23D-A34Z-10		6303650	184850626	15	42787										
GUF1	60558	hgsc.bcm.edu	37	chr4	44693809	44693809	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	tgaaatccctatcttctggaTatgctaggtaaaaaaataat	6	6	2	1			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr4:44693809T>C	ENST00000281543.5	+	13	1800	c.1606T>C	c.(1606-1608)Tat>Cat	p.Y536H	GUF1_ENST00000506793.1_3'UTR|RP11-700J17.1_ENST00000610260.1_RNA	NM_021927.2	NP_068746.2			GUF1 GTPase homolog (S. cerevisiae)											breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	19						ATCTTCTGGATATGCTAGGTA	0.279																																					p.Y536H		Atlas-SNP	.											.	GUF1	72	.	0			c.T1606C						.						91	107	102					4																	44693809		2201	4283	6484	SO:0001583	missense	60558	exon13			TCTGGATATGCTA		CCDS3468.1	4p13	2006-02-16			ENSG00000151806	ENSG00000151806			25799	protein-coding gene	gene with protein product						8553703	Standard	NM_021927		Approved	FLJ13220	uc003gww.4	Q8N442	OTTHUMG00000128608	ENST00000281543.5:c.1606T>C	chr4.hg19:g.44693809T>C	ENSP00000281543:p.Tyr536His	59.0	0.0		41.0	15.0	NM_021927		Missense_Mutation	SNP	ENST00000281543.5	hg19	CCDS3468.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.168090	0.78339	.	.	ENSG00000151806	ENST00000281543	T	0.63913	-0.07	4.87	4.87	0.63330	Elongation factor G/III/V (1);Translation elongation factor EFG/EF2, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.84515	0.5489	H	0.95712	3.71	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89165	0.3533	10	0.87932	D	0	-13.5349	13.9439	0.64073	0.0:0.0:0.0:1.0	.	536	Q8N442	GUF1_HUMAN	H	536	ENSP00000281543:Y536H	ENSP00000281543:Y536H	Y	+	1	0	GUF1	44388566	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.562000	0.82300	1.952000	0.56665	0.533000	0.62120	TAT	.	.		0.279	GUF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250469.3	NM_021927		C	44693809	T	C	44693809	3	2	294	1	0	0	0	0	1	0	0	0	6908	1406	49	2	1656	2	GUF1	4	44693809	Missense_Mutation	SNP	T	TCGA-G3-A7M9-01A-23D-A34Z-10	38390159	44693809	146460467	16	42788										
NFXL1	152518	hgsc.bcm.edu	37	chr4	47850329	47850329	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	cttccgacgacccttcagtcTgttttcaaaagcttctagtt	6	12	4	0			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr4:47850329T>A	ENST00000507489.1	-	23	2763	c.2587A>T	c.(2587-2589)Aga>Tga	p.R863*	NFXL1_ENST00000381538.3_Nonsense_Mutation_p.R863*	NM_001278624.1	NP_001265553.1	Q6ZNB6	NFXL1_HUMAN	nuclear transcription factor, X-box binding-like 1	863						integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(4)	27						CCCTTCAGTCTGTTTTCAAAA	0.328																																					p.R863X		Atlas-SNP	.											.	NFXL1	79	.	0			c.A2587T						.						122	119	120					4																	47850329		2203	4300	6503	SO:0001587	stop_gained	152518	exon23			TCAGTCTGTTTTC	AY134856	CCDS3478.2	4p12	2008-02-05			ENSG00000170448	ENSG00000170448			18726	protein-coding gene	gene with protein product	"ovarian zinc finger protein"						Standard	NM_152995		Approved	HOZFP	uc003gxp.3	Q6ZNB6	OTTHUMG00000128621	ENST00000507489.1:c.2587A>T	chr4.hg19:g.47850329T>A	ENSP00000422037:p.Arg863*	146.0	0.0		114.0	36.0	NM_152995	B1Q2K1|Q86VG1|Q8WVH1	Nonsense_Mutation	SNP	ENST00000507489.1	hg19	CCDS3478.2	.	.	.	.	.	.	.	.	.	.	T	37	6.286246	0.97444	.	.	ENSG00000170448	ENST00000381538;ENST00000507489	.	.	.	5.66	4.41	0.53225	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-22.0455	12.1758	0.54184	0.0:0.0:0.1426:0.8574	.	.	.	.	X	863	.	ENSP00000370949:R863X	R	-	1	2	NFXL1	47545086	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.341000	0.33907	2.158000	0.67659	0.528000	0.53228	AGA	.	.		0.328	NFXL1-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361636.1	NM_152995		A	47850329	T	A	47850329	4	1	294	1	0	0	0	0	0	1	0	0	10397	1588	55	4	152	4	NFXL1	4	47850329	Nonsense_Mutation	SNP	T	TCGA-G3-A7M9-01A-23D-A34Z-10	3156520	47850329	143303947	17	42789										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79295351	79295351	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	tcctcttggaagcccagtgtGtccaggaatgtgggaagggg	16	8	1	0			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr4:79295351G>T	ENST00000325942.6	+	25	3537	c.3097G>T	c.(3097-3099)Gtc>Ttc	p.V1033F	FRAS1_ENST00000264895.6_Missense_Mutation_p.V1033F	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	1033					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						AGCCCAGTGTGTCCAGGAATG	0.502																																					p.V1033F		Atlas-SNP	.											.	FRAS1	779	.	0			c.G3097T						.						125	123	123					4																	79295351		1948	4160	6108	SO:0001583	missense	80144	exon25			CAGTGTGTCCAGG	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.3097G>T	chr4.hg19:g.79295351G>T	ENSP00000326330:p.Val1033Phe	59.0	0.0		33.0	21.0	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000325942.6	hg19	CCDS54772.1	.	.	.	.	.	.	.	.	.	.	G	15.15	2.748993	0.49257	.	.	ENSG00000138759	ENST00000325942;ENST00000264895	D;D	0.87334	-2.24;-2.24	5.94	4.93	0.64822	.	0.063513	0.64402	D	0.000008	D	0.93429	0.7904	M	0.86097	2.795	0.80722	D	1	D;D	0.64830	0.983;0.994	P;D	0.65684	0.873;0.937	D	0.94029	0.7299	10	0.87932	D	0	.	15.7332	0.77822	0.0767:0.0:0.9233:0.0	.	1033;1033	E9PHH6;A2RRR8	.;.	F	1033	ENSP00000326330:V1033F;ENSP00000264895:V1033F	ENSP00000264895:V1033F	V	+	1	0	FRAS1	79514375	1.000000	0.71417	0.999000	0.59377	0.001000	0.01503	5.694000	0.68272	2.820000	0.97059	0.650000	0.86243	GTC	.	.		0.502	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2			T	79295351	G	T	79295351	3	4	294	1	0	0	0	0	1	0	0	0	6050	1377	48	3	3195	3	FRAS1	4	79295351	Missense_Mutation	SNP	G	TCGA-G3-A7M9-01A-23D-A34Z-10	31445022	79295351	111858925	18	42790										
DSPP	1834	hgsc.bcm.edu	37	chr4	88535262	88535262	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	tgctaattcagaaagtgacaAtaacagcagtagccgaggag	11	7	1	2			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr4:88535262A>G	ENST00000282478.7	+	4	1481	c.1448A>G	c.(1447-1449)aAt>aGt	p.N483S	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Missense_Mutation_p.N483S			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	483	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			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)		GAAAGTGACAATAACAGCAGT	0.383																																					p.N483S		Atlas-SNP	.											.	DSPP	174	.	0			c.A1448G						.						126	119	121					4																	88535262		2008	4181	6189	SO:0001583	missense	1834	exon5			GTGACAATAACAG	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.1448A>G	chr4.hg19:g.88535262A>G	ENSP00000282478:p.Asn483Ser	87.0	0.0		37.0	24.0	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	hg19	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	A	5.630	0.300953	0.10678	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.89050	-2.46;-2.46	4.74	2.17	0.27698	.	0.713649	0.11506	N	0.557210	D	0.82669	0.5087	M	0.64997	1.995	0.09310	N	1	B	0.28713	0.22	B	0.23574	0.047	T	0.65417	-0.6173	10	0.08599	T	0.76	-16.9559	5.7554	0.18170	0.7372:0.169:0.0938:0.0	.	483	Q9NZW4	DSPP_HUMAN	S	483	ENSP00000382213:N483S;ENSP00000282478:N483S	ENSP00000282478:N483S	N	+	2	0	DSPP	88754286	0.000000	0.05858	0.006000	0.13384	0.107000	0.19398	0.581000	0.23819	0.684000	0.31448	0.366000	0.22137	AAT	.	.		0.383	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		G	88535262	A	G	88535262	3	3	294	1	0	0	0	0	1	0	0	0	4784	101	4	2	1462	2	DSPP	4	88535262	Missense_Mutation	SNP	A	TCGA-G3-A7M9-01A-23D-A34Z-10	9239911	88535262	102619014	19	42791										
NPY5R	4889	hgsc.bcm.edu	37	chr4	164272303	164272303	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	aagaagatatagcaagaagaCagcatgtgtgttacctgctc	10	7	0	4	rs146231711		TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr4:164272303C>T	ENST00000515560.1	+	4	2400	c.878C>T	c.(877-879)aCa>aTa	p.T293I	NPY5R_ENST00000506953.1_Missense_Mutation_p.T293I|NPY5R_ENST00000338566.3_Missense_Mutation_p.T293I			Q15761	NPY5R_HUMAN	neuropeptide Y receptor Y5	293					cardiac left ventricle morphogenesis (GO:0003214)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|generation of ovulation cycle rhythm (GO:0060112)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neuropeptide signaling pathway (GO:0007218)|outflow tract morphogenesis (GO:0003151)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of smooth muscle cell proliferation (GO:0048661)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)|pancreatic polypeptide receptor activity (GO:0001602)|peptide YY receptor activity (GO:0001601)			NS(2)|biliary_tract(1)|breast(1)|endometrium(3)|large_intestine(4)|lung(26)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_hematologic(180;0.166)	Prostate(90;0.109)				AGCAAGAAGACAGCATGTGTG	0.428																																					p.T293I	Melanoma(139;1287 1774 9781 19750 25599)	Atlas-SNP	.											.	NPY5R	101	.	0			c.C878T						.	C	ILE/THR	1,4405	2.1+/-5.4	0,1,2202	99	99	99		878	2.7	0.8	4	dbSNP_134	99	0,8600		0,0,4300	no	missense	NPY5R	NM_006174.2	89	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	293/446	164272303	1,13005	2203	4300	6503	SO:0001583	missense	4889	exon4			AGAAGACAGCATG	BC042416	CCDS3804.1	4q31-q32	2012-08-08				ENSG00000164129		"GPCR / Class A : Neuropeptide receptors : Y"	7958	protein-coding gene	gene with protein product		602001				8700207, 9417917	Standard	NM_006174		Approved	NPYR5	uc003iqn.3	Q15761		ENST00000515560.1:c.878C>T	chr4.hg19:g.164272303C>T	ENSP00000423917:p.Thr293Ile	55.0	0.0		15.0	9.0	NM_006174	Q6GTR7|Q92916	Missense_Mutation	SNP	ENST00000515560.1	hg19	CCDS3804.1	.	.	.	.	.	.	.	.	.	.	C	10.37	1.332690	0.24167	2.27E-4	0.0	ENSG00000164129	ENST00000338566;ENST00000515560;ENST00000506953	T;T;T	0.71817	-0.6;-0.6;-0.6	4.49	2.7	0.31948	GPCR, rhodopsin-like superfamily (1);	0.166788	0.27126	N	0.020803	T	0.63920	0.2552	L	0.43152	1.355	0.30306	N	0.789	P	0.45396	0.857	B	0.43623	0.425	T	0.62388	-0.6865	10	0.30078	T	0.28	.	13.6284	0.62181	0.2831:0.7169:0.0:0.0	.	293	Q15761	NPY5R_HUMAN	I	293	ENSP00000339377:T293I;ENSP00000423917:T293I;ENSP00000423474:T293I	ENSP00000339377:T293I	T	+	2	0	NPY5R	164491753	0.857000	0.29778	0.849000	0.33467	0.724000	0.41520	1.591000	0.36665	0.555000	0.29079	0.467000	0.42956	ACA	.	C|1.000;T|0.000		0.428	NPY5R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364633.1	NM_006174		T	164272303	C	T	164272303	3	4	294	1	0	0	0	0	1	0	0	0	10619	478	17	3	880	3	NPY5R	4	164272303	Missense_Mutation	SNP	C	TCGA-G3-A7M9-01A-23D-A34Z-10	75737041	164272303	26881973	20	42792										
HELT	391723	hgsc.bcm.edu	37	chr4	185941802	185941802	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	agtgccgctcgctagcccagCgcagcagcacagccccttcc	10	19	0	0			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr4:185941802C>T	ENST00000515777.1	+	4	693	c.605C>T	c.(604-606)gCg>gTg	p.A202V	HELT_ENST00000505610.1_Missense_Mutation_p.A201V|HELT_ENST00000338875.4_Missense_Mutation_p.A287V			A6NFD8	HELT_HUMAN	helt bHLH transcription factor	202	Pro-rich.				central nervous system development (GO:0007417)|GABAergic neuron differentiation in basal ganglia (GO:0021858)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|suckling behavior (GO:0001967)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(2)	14		all_lung(41;9.65e-12)|Lung NSC(41;1.64e-11)|Colorectal(36;0.0215)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;8.92e-26)|Epithelial(43;3.02e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.59e-11)|Colorectal(24;4.79e-05)|BRCA - Breast invasive adenocarcinoma(30;7.72e-05)|GBM - Glioblastoma multiforme(59;0.000274)|COAD - Colon adenocarcinoma(29;0.000362)|STAD - Stomach adenocarcinoma(60;0.000756)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.155)		GCTAGCCCAGCGCAGCAGCAC	0.726																																					p.A287V		Atlas-SNP	.											.	HELT	34	.	0			c.C860T						.						16	18	17					4																	185941802		2200	4290	6490	SO:0001583	missense	391723	exon4			GCCCAGCGCAGCA	BC144567	CCDS75214.1, CCDS75215.1	4q35.1	2014-07-17	2011-09-12		ENSG00000187821	ENSG00000187821		"Basic helix-loop-helix proteins"	33783	protein-coding gene	gene with protein product	"megane bHLH factor", "HES-like"		"Hey-like transcription factor (zebrafish)", "HES/HEY-like transcription factor"			14764602, 17611227	Standard	XM_005262989		Approved	HESL, HCM1228, Mgn, bHLHb44, MEGANE	uc011ckq.2	A6NFD8	OTTHUMG00000160484	ENST00000515777.1:c.605C>T	chr4.hg19:g.185941802C>T	ENSP00000426033:p.Ala202Val	11.0	0.0		16.0	13.0	NM_001029887	B2RTS5|B7ZMI7|B7ZMI8	Missense_Mutation	SNP	ENST00000515777.1	hg19		.	.	.	.	.	.	.	.	.	.	C	10.59	1.393785	0.25205	.	.	ENSG00000187821	ENST00000505610;ENST00000515777;ENST00000338875	T;T;T	0.64991	-0.13;-0.12;1.81	4.96	3.22	0.36961	.	0.134936	0.49916	D	0.000123	T	0.38904	0.1058	L	0.27053	0.805	0.26792	N	0.969387	P;B;B	0.41131	0.739;0.063;0.104	B;B;B	0.22753	0.041;0.016;0.036	T	0.16719	-1.0393	10	0.34782	T	0.22	.	10.6558	0.45673	0.1224:0.5445:0.333:0.0	.	287;202;201	A6NFD8;B7ZMI7;A6NFD8-2	HELT_HUMAN;.;.	V	201;202;287	ENSP00000422140:A201V;ENSP00000426033:A202V;ENSP00000343464:A287V	ENSP00000343464:A287V	A	+	2	0	HELT	186178796	0.975000	0.34042	0.924000	0.36721	0.088000	0.18126	2.287000	0.43505	0.493000	0.27837	0.561000	0.74099	GCG	.	.		0.726	HELT-002	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000360792.1	NM_001300781		T	185941802	C	T	185941802	3	4	294	1	0	0	0	0	1	0	0	0	7057	768	27	1	874	1	HELT	4	185941802	Missense_Mutation	SNP	C	TCGA-G3-A7M9-01A-23D-A34Z-10	21669499	185941802	5212474	21	42793										
GPR98	84059	hgsc.bcm.edu	37	chr5	89948314	89948314	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	aagcaaaaccaatcattctcCatgcttttccagataaaatt	3	10	2	1			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr5:89948314C>T	ENST00000405460.2	+	19	3664	c.3568C>T	c.(3568-3570)Cat>Tat	p.H1190Y		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	1190	Calx-beta 9. {ECO:0000305|PubMed:11606593}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		AATCATTCTCCATGCTTTTCC	0.348																																					p.H1190Y		Atlas-SNP	.											.	GPR98	605	.	0			c.C3568T						.						90	82	85					5																	89948314		1878	4115	5993	SO:0001583	missense	84059	exon19			ATTCTCCATGCTT	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.3568C>T	chr5.hg19:g.89948314C>T	ENSP00000384582:p.His1190Tyr	148.0	0.0		72.0	39.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.32|15.32	2.797986|2.797986	0.50208|0.50208	.|.	.|.	ENSG00000164199|ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000399043|ENST00000504142	T|.	0.26957|.	1.7|.	6.07|6.07	6.07|6.07	0.98685|0.98685	.|.	0.247806|.	0.47852|.	D|.	0.000218|.	T|T	0.57621|0.57621	0.2066|0.2066	N|N	0.24115|0.24115	0.695|0.695	0.80722|0.80722	D|D	1|1	P|.	0.40230|.	0.708|.	B|.	0.31191|.	0.125|.	T|T	0.48399|0.48399	-0.9039|-0.9039	10|5	0.66056|.	D|.	0.02|.	.|.	20.6525|20.6525	0.99598|0.99598	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1190|.	Q8WXG9|.	GPR98_HUMAN|.	Y|L	1190|778	ENSP00000384582:H1190Y|.	ENSP00000296619:H1190Y|.	H|P	+|+	1|2	0|0	GPR98|GPR98	89984070|89984070	0.975000|0.975000	0.34042|0.34042	0.994000|0.994000	0.49952|0.49952	0.861000|0.861000	0.49209|0.49209	2.369000|2.369000	0.44231|0.44231	2.890000|2.890000	0.99128|0.99128	0.585000|0.585000	0.79938|0.79938	CAT|CCA	.	.		0.348	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		T	89948314	C	T	89948314	3	4	294	1	0	0	0	0	1	0	0	0	6730	594	21	3	3642	3	GPR98	5	89948314	Missense_Mutation	SNP	C	TCGA-G3-A7M9-01A-23D-A34Z-10		89948314	90966946	22	42794										
SLCO6A1	133482	hgsc.bcm.edu	37	chr5	101813521	101813521	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	ttttgattggaatgatatacCactgctctggcaaccactga	8	9	1	3			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr5:101813521C>T	ENST00000506729.1	-	3	832	c.661G>A	c.(661-663)Ggt>Agt	p.G221S	SLCO6A1_ENST00000379807.3_Missense_Mutation_p.G221S|SLCO6A1_ENST00000514551.1_Intron|SLCO6A1_ENST00000379810.1_Intron|SLCO6A1_ENST00000389019.3_Intron|SLCO6A1_ENST00000513675.1_Intron			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	221						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(17)|lung(22)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	60		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)		AATGATATACCACTGCTCTGG	0.338																																					p.G221S		Atlas-SNP	.											.	SLCO6A1	153	.	0			c.G661A						.						170	166	168					5																	101813521		2203	4300	6503	SO:0001583	missense	133482	exon3			ATATACCACTGCT	AF505657	CCDS34206.1, CCDS75282.1	5q21.2	2013-05-22			ENSG00000205359	ENSG00000205359		"Solute carriers"	23613	protein-coding gene	gene with protein product	"cancer/testis antigen 48"	613365					Standard	XM_005271874		Approved	OATP6A1, OATPY, MGC26949, CT48	uc003knp.3	Q86UG4	OTTHUMG00000162759	ENST00000506729.1:c.661G>A	chr5.hg19:g.101813521C>T	ENSP00000421339:p.Gly221Ser	95.0	0.0		25.0	17.0	NM_173488	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Missense_Mutation	SNP	ENST00000506729.1	hg19	CCDS34206.1	.	.	.	.	.	.	.	.	.	.	C	4.681	0.126682	0.08931	.	.	ENSG00000205359	ENST00000506729;ENST00000379807	T;T	0.37235	1.21;1.21	4.84	-3.85	0.04243	Major facilitator superfamily domain, general substrate transporter (1);	5.373610	0.00754	N	0.001085	T	0.10294	0.0252	N	0.01576	-0.805	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.14699	-1.0463	10	0.08599	T	0.76	.	0.3132	0.00291	0.2792:0.1788:0.1454:0.3966	.	221	Q86UG4	SO6A1_HUMAN	S	221	ENSP00000421339:G221S;ENSP00000369135:G221S	ENSP00000369135:G221S	G	-	1	0	SLCO6A1	101841420	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.636000	0.05465	-0.485000	0.06754	-0.229000	0.12294	GGT	.	.		0.338	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488		T	101813521	C	T	101813521	3	4	294	1	0	0	0	0	1	0	0	0	14747	594	21	3	1542	3	SLCO6A1	5	101813521	Missense_Mutation	SNP	C	TCGA-G3-A7M9-01A-23D-A34Z-10	11865207	101813521	79101739	23	42795										
AQPEP	206338	hgsc.bcm.edu	37	chr5	115323605	115323605	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	ttctcttttctggaggatttGtttaatatcagttactctct	6	7	4	0			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr5:115323605G>C	ENST00000357872.4	+	4	1198	c.1074G>C	c.(1072-1074)ttG>ttC	p.L358F	AQPEP_ENST00000395528.2_5'UTR	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		358						integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)										TGGAGGATTTGTTTAATATCA	0.423																																					p.L358F		Atlas-SNP	.											.	.	.	.	0			c.G1074C						.						166	158	161					5																	115323605		2202	4300	6502	SO:0001583	missense	0	exon4			GGATTTGTTTAAT																												ENST00000357872.4:c.1074G>C	chr5.hg19:g.115323605G>C	ENSP00000350541:p.Leu358Phe	186.0	0.0		95.0	13.0	NM_173800	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Missense_Mutation	SNP	ENST00000357872.4	hg19	CCDS4124.1	.	.	.	.	.	.	.	.	.	.	G	9.466	1.094306	0.20471	.	.	ENSG00000172901	ENST00000357872;ENST00000379578	T	0.02631	4.22	5.14	1.06	0.20224	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.289067	0.24323	N	0.039539	T	0.04679	0.0127	L	0.31926	0.97	0.80722	D	1	D	0.53312	0.959	P	0.56960	0.81	T	0.55360	-0.8153	10	0.22706	T	0.39	.	7.9111	0.29791	0.6546:0.0:0.3454:0.0	.	358	Q6Q4G3	AMPQ_HUMAN	F	358;347	ENSP00000350541:L358F	ENSP00000350541:L358F	L	+	3	2	AC010282.1	115351504	0.929000	0.31497	0.998000	0.56505	0.981000	0.71138	0.051000	0.14141	-0.103000	0.12175	-0.471000	0.05019	TTG	.	.		0.423	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1			C	115323605	G	C	115323605	3	2	294	1	0	0	0	0	1	0	0	0	834	1368	48	4	1088	4	AQPEP	5	115323605	Missense_Mutation	SNP	G	TCGA-G3-A7M9-01A-23D-A34Z-10	13510084	115323605	65591655	24	42796										
PCDHA7	56141	hgsc.bcm.edu	37	chr5	140215989	140215989	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	gtcgctggtggaaagcggccAggcaccaaaggcgtcgtcgc	16	12	0	0	rs370529939		TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr5:140215989A>T	ENST00000525929.1	+	1	2021	c.2021A>T	c.(2020-2022)cAg>cTg	p.Q674L	PCDHA7_ENST00000378125.3_Missense_Mutation_p.Q674L|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018910.2	NP_061733.1	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7	674	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|biliary_tract(1)|breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAAAGCGGCCAGGCACCAAAG	0.657																																					p.Q674L	NSCLC(160;258 2013 5070 22440 28951)	Atlas-SNP	.											.	PCDHA7	367	.	0			c.A2021T						.						77	75	76					5																	140215989		2203	4299	6502	SO:0001583	missense	56141	exon1			GCGGCCAGGCACC	AF152485	CCDS54918.1	5q31	2010-11-26				ENSG00000204963		"Cadherins / Protocadherins : Clustered"	8673	other	complex locus constituent	"KIAA0345-like 7", "ortholog to mouse CNR4"	606313		CNRS4		10380929, 10662547	Standard	NM_018910		Approved	CNR4, CRNR4		Q9UN72		ENST00000525929.1:c.2021A>T	chr5.hg19:g.140215989A>T	ENSP00000436426:p.Gln674Leu	26.0	0.0		24.0	15.0	NM_031852	O75282	Missense_Mutation	SNP	ENST00000525929.1	hg19	CCDS54918.1	.	.	.	.	.	.	.	.	.	.	A	2.151	-0.394480	0.04899	.	.	ENSG00000204963	ENST00000525929;ENST00000378125	T;T	0.52295	0.67;0.7	3.57	2.36	0.29203	Cadherin (2);	0.298550	0.17684	U	0.165532	T	0.44829	0.1312	M	0.69358	2.11	0.09310	N	1	B;B	0.16802	0.019;0.011	B;B	0.23150	0.044;0.013	T	0.45145	-0.9281	10	0.62326	D	0.03	.	8.7292	0.34489	0.63:0.37:0.0:0.0	.	674;674	Q9UN72-2;Q9UN72	.;PCDA7_HUMAN	L	674	ENSP00000436426:Q674L;ENSP00000367365:Q674L	ENSP00000367365:Q674L	Q	+	2	0	PCDHA7	140196173	0.000000	0.05858	0.024000	0.17045	0.008000	0.06430	-0.103000	0.10940	0.513000	0.28278	0.379000	0.24179	CAG	.	.		0.657	PCDHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372887.2	NM_018910		T	140215989	A	T	140215989	3	4	294	1	0	0	0	0	1	0	0	0	11538	188	7	4	2023	4	PCDHA7	5	140215989	Missense_Mutation	SNP	A	TCGA-G3-A7M9-01A-23D-A34Z-10	24892384	140215989	40699271	25	42797										
PCDHB10	56126	hgsc.bcm.edu	37	chr5	140573688	140573688	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	gccctcaggtcgctggactaCgaggccctgcaggctttcga	13	14	1	0			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr5:140573688C>A	ENST00000239446.4	+	1	1747	c.1563C>A	c.(1561-1563)taC>taA	p.Y521*		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	521	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGCTGGACTACGAGGCCCTGC	0.706																																					p.Y521X		Atlas-SNP	.											.	PCDHB10	177	.	0			c.C1563A						.						93	111	105					5																	140573688		2203	4298	6501	SO:0001587	stop_gained	56126	exon1			GGACTACGAGGCC	AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"Cadherins / Protocadherins : Clustered"	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.1563C>A	chr5.hg19:g.140573688C>A	ENSP00000239446:p.Tyr521*	71.0	0.0		59.0	17.0	NM_018930	Q96T99	Nonsense_Mutation	SNP	ENST00000239446.4	hg19	CCDS4252.1	.	.	.	.	.	.	.	.	.	.	c	36	5.833420	0.97003	.	.	ENSG00000120324	ENST00000239446	.	.	.	3.53	0.623	0.17654	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.8578	0.18730	0.0:0.4142:0.0:0.5858	.	.	.	.	X	521	.	ENSP00000239446:Y521X	Y	+	3	2	PCDHB10	140553872	0.000000	0.05858	0.960000	0.40013	0.961000	0.63080	-2.742000	0.00798	0.289000	0.22422	0.549000	0.68633	TAC	.	.		0.706	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930		A	140573688	C	A	140573688	4	1	294	1	0	0	0	0	0	1	0	0	11544	547	19	1	1565	1	PCDHB10	5	140573688	Nonsense_Mutation	SNP	C	TCGA-G3-A7M9-01A-23D-A34Z-10	357699	140573688	40341572	26	42798										
DDR1	780	hgsc.bcm.edu	37	chr6	30866689	30866689	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	agttcacgactgcgagtgacGtgtgggcctttggtgtgacc	15	9	1	2			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr6:30866689G>T	ENST00000324771.8	+	19	3024	c.2476G>T	c.(2476-2478)Gtg>Ttg	p.V826L	DDR1_ENST00000508312.1_Missense_Mutation_p.V807L|DDR1_ENST00000376575.3_Missense_Mutation_p.V832L|DDR1_ENST00000376568.3_Missense_Mutation_p.V826L|DDR1_ENST00000452441.1_Missense_Mutation_p.V826L|DDR1_ENST00000376570.4_Missense_Mutation_p.V789L|DDR1_ENST00000446312.1_3'UTR|DDR1_ENST00000513240.1_Missense_Mutation_p.V832L|DDR1_ENST00000361741.4_Intron|DDR1_ENST00000376567.2_Missense_Mutation_p.V789L|DDR1_ENST00000454612.2_Missense_Mutation_p.V789L|DDR1_ENST00000376569.3_Missense_Mutation_p.V789L|DDR1_ENST00000418800.2_Missense_Mutation_p.V789L			Q08345	DDR1_HUMAN	discoidin domain receptor tyrosine kinase 1	826	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|ear development (GO:0043583)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine autophosphorylation (GO:0038083)|protein autophosphorylation (GO:0046777)|regulation of cell growth (GO:0001558)|regulation of cell-matrix adhesion (GO:0001952)|regulation of extracellular matrix disassembly (GO:0010715)|smooth muscle cell migration (GO:0014909)|smooth muscle cell-matrix adhesion (GO:0061302)|wound healing, spreading of cells (GO:0044319)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(1)|prostate(1)|skin(1)	29					Imatinib(DB00619)	TGCGAGTGACGTGTGGGCCTT	0.597																																					p.V832L		Atlas-SNP	.											.	DDR1	213	.	0			c.G2494T						.						169	132	144					6																	30866689		2203	4300	6503	SO:0001583	missense	780	exon16			AGTGACGTGTGGG	X99031	CCDS4690.1, CCDS34385.1, CCDS47396.1, CCDS56411.1, CCDS75419.1	6p21.33	2010-02-17	2008-01-23		ENSG00000204580	ENSG00000204580	2.7.10.1	"CD molecules"	2730	protein-coding gene	gene with protein product		600408	"discoidin domain receptor family, member 1"	NTRK4, PTK3A, NEP, CAK, EDDR1		7789998	Standard	NM_001954		Approved	RTK6, CD167	uc003nrv.3	Q08345	OTTHUMG00000031236	ENST00000324771.8:c.2476G>T	chr6.hg19:g.30866689G>T	ENSP00000318217:p.Val826Leu	83.0	0.0		78.0	31.0	NM_013994	B5A975|B5A976|B7Z2K0|Q14196|Q16562|Q2L6H3|Q4LE50|Q5ST11|Q5ST12|Q6NSK4|Q9UD35|Q9UD36|Q9UD37|Q9UD86|Q9UDL2	Missense_Mutation	SNP	ENST00000324771.8	hg19	CCDS34385.1	.	.	.	.	.	.	.	.	.	.	G	15.86	2.957658	0.53400	.	.	ENSG00000204580	ENST00000324771;ENST00000418800;ENST00000454612;ENST00000376569;ENST00000376575;ENST00000376570;ENST00000376568;ENST00000452441;ENST00000508312;ENST00000376567;ENST00000513240	D;D;D;D;D;D;D;D;D;D;D	0.87809	-2.3;-2.3;-2.3;-2.3;-2.3;-2.3;-2.3;-2.3;-2.3;-2.3;-2.3	4.89	4.89	0.63831	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000002	D	0.86209	0.5878	M	0.80422	2.495	0.80722	D	1	B;B;B;B	0.25206	0.003;0.12;0.023;0.003	B;B;B;B	0.34722	0.012;0.188;0.082;0.017	D	0.87341	0.2331	10	0.87932	D	0	.	15.5589	0.76223	0.0:0.0:1.0:0.0	.	807;290;832;826	B7Z2K0;A2ABL4;Q08345-5;Q08345	.;.;.;DDR1_HUMAN	L	826;789;789;789;832;789;826;826;807;789;832	ENSP00000318217:V826L;ENSP00000407699:V789L;ENSP00000406091:V789L;ENSP00000365753:V789L;ENSP00000365759:V832L;ENSP00000365754:V789L;ENSP00000365752:V826L;ENSP00000405039:V826L;ENSP00000422442:V807L;ENSP00000365751:V789L;ENSP00000427552:V832L	ENSP00000318217:V826L	V	+	1	0	DDR1	30974668	1.000000	0.71417	0.990000	0.47175	0.515000	0.34225	9.823000	0.99369	2.256000	0.74724	0.467000	0.42956	GTG	.	.		0.597	DDR1-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076494.3	NM_013994		T	30866689	G	T	30866689	3	4	294	1	0	0	0	0	1	0	0	0	4338	1145	40	1	2556	1	DDR1	6	30866689	Missense_Mutation	SNP	G	TCGA-G3-A7M9-01A-23D-A34Z-10		30866689	140248378	27	42799										
ITPR3	3710	hgsc.bcm.edu	37	chr6	33639857	33639857	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	ggggcacatgatgtccaccaTggtgctgagccgcaagcagt	14	11	0	2			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr6:33639857T>C	ENST00000374316.5	+	23	3840	c.2780T>C	c.(2779-2781)aTg>aCg	p.M927T	ITPR3_ENST00000605930.1_Missense_Mutation_p.M927T			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	927					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	ATGTCCACCATGGTGCTGAGC	0.612																																					p.M927T		Atlas-SNP	.											.	ITPR3	409	.	0			c.T2780C						.						93	81	85					6																	33639857		2203	4300	6503	SO:0001583	missense	3710	exon22			CCACCATGGTGCT	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"Ion channels / Inositol triphosphate receptors"	6182	protein-coding gene	gene with protein product		147267	"inositol 1,4,5-triphosphate receptor, type 3"			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.2780T>C	chr6.hg19:g.33639857T>C	ENSP00000363435:p.Met927Thr	33.0	0.0		31.0	11.0	NM_002224	Q14649|Q5TAQ2	Missense_Mutation	SNP	ENST00000374316.5	hg19	CCDS4783.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.576476	0.86645	.	.	ENSG00000096433	ENST00000374316	D	0.92348	-3.02	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	D	0.93177	0.7827	M	0.79926	2.475	0.58432	D	0.999998	P	0.47910	0.902	P	0.51229	0.663	D	0.94018	0.7290	10	0.66056	D	0.02	-47.7924	15.5417	0.76057	0.0:0.0:0.0:1.0	.	927	Q14573	ITPR3_HUMAN	T	927	ENSP00000363435:M927T	ENSP00000363435:M927T	M	+	2	0	ITPR3	33747835	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.698000	0.84413	2.072000	0.62099	0.533000	0.62120	ATG	.	.		0.612	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224		C	33639857	T	C	33639857	3	2	294	1	0	0	0	0	1	0	0	0	7931	1464	51	2	2866	2	ITPR3	6	33639857	Missense_Mutation	SNP	T	TCGA-G3-A7M9-01A-23D-A34Z-10	2773168	33639857	137475210	28	42800										
C6orf221	154288	hgsc.bcm.edu	37	chr6	74072885	74072886	+	Missense_Mutation	DNP	GG	GG	TT													0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	ttgattcacgtgaatcgattGgaccctaacggcgaggctga							TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr6:74072885_74072886GG>TT	ENST00000370367.3	+	2	290_291	c.237_238GG>TT	c.(235-240)ttGGac>ttTTac	p.79_80LD>FY		NM_001017361.2	NP_001017361.1	Q587J8	KHD3L_HUMAN	KH domain containing 3-like, subcortical maternal complex member	79	KH; atypical.						RNA binding (GO:0003723)										TGAATCGATTGGACCCTAACGG	0.569																																					p.L79F|p.D80Y		Atlas-SNP	.											.	.	.	.	0			c.G237T|c.G238T						.																																			SO:0001583	missense	154288	exon2			TCGATTGGACCCT|CGATTGGACCCTA	AB211062	CCDS34484.1	6q13	2012-06-25	2012-06-25	2012-06-25	ENSG00000203908	ENSG00000203908			33699	protein-coding gene	gene with protein product	"ES cell associated transcript 1"	611687	"chromosome 6 open reading frame 221"	C6orf221		21885028	Standard	NM_001017361		Approved	ECAT1	uc003pgt.4	Q587J8	OTTHUMG00000015024	Exception_encountered	chr6.hg19:g.74072885_74072886delinsTT	ENSP00000359392:p.L79_D80delinsFY	43.0	0.0		32.0|33.0	10.0|11.0	NM_001017361	B2RNW7	Missense_Mutation	SNP	ENST00000370367.3	hg19	CCDS34484.1																																																																																			.	.		0.569	KHDC3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041202.3	NM_001017361		TT	74072886	GG	TT	74072885	3	4	294	1	0	0	0	0	1	0	0	0	2357	1339	47	3	243	3	C6orf221	6	74072885	Missense_Mutation	DNP	GG	TCGA-G3-A7M9-01A-23D-A34Z-10	40433028	74072885	97042182	29	42801										
IMPG1	3617	hgsc.bcm.edu	37	chr6	76720891	76720891	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	tctcttacttacctaaatccTaacacatggatttttttgaa	3	9	1	1			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr6:76720891T>A	ENST00000369950.3	-	8	1047	c.858A>T	c.(856-858)ttA>ttT	p.L286F	IMPG1_ENST00000369963.3_3'UTR	NM_001282368.1|NM_001563.2	NP_001269297.1|NP_001554.2			interphotoreceptor matrix proteoglycan 1											breast(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(8)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	63		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				ACCTAAATCCTAACACATGGA	0.313																																					p.L286F	Pancreas(37;839 1141 2599 26037)	Atlas-SNP	.											.	IMPG1	143	.	0			c.A858T						.						50	54	53					6																	76720891		2200	4297	6497	SO:0001583	missense	3617	exon8			AAATCCTAACACA	AF017776	CCDS4985.1, CCDS75483.1	6q14.2-q15	2008-02-05	2004-05-25		ENSG00000112706	ENSG00000112706			6055	protein-coding gene	gene with protein product		602870	"sialoprotein associated with cones and rods"	SPACR			Standard	NM_001282368		Approved	IPM150, GP147	uc003pik.1	Q17R60	OTTHUMG00000015063	ENST00000369950.3:c.858A>T	chr6.hg19:g.76720891T>A	ENSP00000358966:p.Leu286Phe	116.0	0.0		86.0	36.0	NM_001563		Missense_Mutation	SNP	ENST00000369950.3	hg19	CCDS4985.1	.	.	.	.	.	.	.	.	.	.	T	18.42	3.619027	0.66787	.	.	ENSG00000112706	ENST00000369950	T	0.44881	0.91	5.56	1.55	0.23275	SEA (3);	0.275088	0.25978	N	0.027093	T	0.47820	0.1466	M	0.73962	2.25	0.80722	D	1	D	0.71674	0.998	D	0.76575	0.988	T	0.50398	-0.8833	10	0.59425	D	0.04	.	8.2252	0.31564	0.0:0.2951:0.0:0.7049	.	286	Q17R60	IMPG1_HUMAN	F	286	ENSP00000358966:L286F	ENSP00000358966:L286F	L	-	3	2	IMPG1	76777611	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.498000	0.22530	0.487000	0.27698	0.528000	0.53228	TTA	.	.		0.313	IMPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041288.1	NM_001563		A	76720891	T	A	76720891	3	1	294	1	0	0	0	0	1	0	0	0	7737	1519	53	4	1575	4	IMPG1	6	76720891	Missense_Mutation	SNP	T	TCGA-G3-A7M9-01A-23D-A34Z-10	2648006	76720891	94394176	30	42802										
MAP3K7	6885	hgsc.bcm.edu	37	chr6	91269811	91269811	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	ttactttggtggtttcaggtCcctgtgaattagcgctttgg	12	7	1	1			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr6:91269811C>A	ENST00000369329.3	-	5	627	c.466G>T	c.(466-468)Gac>Tac	p.D156Y	MAP3K7_ENST00000369327.3_Missense_Mutation_p.D156Y|MAP3K7_ENST00000369325.3_Missense_Mutation_p.D156Y|MAP3K7_ENST00000369332.3_Missense_Mutation_p.D156Y	NM_145331.2	NP_663304.1	O43318	M3K7_HUMAN	mitogen-activated protein kinase kinase kinase 7	156	Interaction with MAPK8IP1. {ECO:0000250}.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|Fc-epsilon receptor signaling pathway (GO:0038095)|histone H3 acetylation (GO:0043966)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of ripoptosome assembly involved in necroptotic process (GO:1902443)|neural tube formation (GO:0001841)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|regulation of reactive oxygen species metabolic process (GO:2000377)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase activity (GO:0004708)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|scaffold protein binding (GO:0097110)			endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	28		all_cancers(76;6.4e-08)|Acute lymphoblastic leukemia(125;1.43e-09)|Prostate(29;9.32e-09)|all_hematologic(105;3.69e-06)|all_epithelial(107;0.000187)|Ovarian(999;0.0164)		OV - Ovarian serous cystadenocarcinoma(136;2.05e-11)|all cancers(137;3.25e-11)|GBM - Glioblastoma multiforme(226;0.0416)|BRCA - Breast invasive adenocarcinoma(108;0.0429)		GGTTTCAGGTCCCTGTGAATT	0.478																																					p.D156Y		Atlas-SNP	.											.	MAP3K7	100	.	0			c.G466T						.						239	217	225					6																	91269811		2203	4300	6503	SO:0001583	missense	6885	exon5			TCAGGTCCCTGTG	AB009356	CCDS5027.1, CCDS5028.1, CCDS5029.1, CCDS5030.1	6q15	2011-06-09			ENSG00000135341	ENSG00000135341		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6859	protein-coding gene	gene with protein product		602614		TAK1		9466656	Standard	NM_003188		Approved	MEKK7	uc003pnz.2	O43318	OTTHUMG00000015217	ENST00000369329.3:c.466G>T	chr6.hg19:g.91269811C>A	ENSP00000358335:p.Asp156Tyr	169.0	0.0		93.0	46.0	NM_145333	B2RE27|E1P523|O43317|O43319|Q5TDN2|Q5TDN3|Q5TDT7|Q9NTR3|Q9NZ70	Missense_Mutation	SNP	ENST00000369329.3	hg19	CCDS5028.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.417423	0.83449	.	.	ENSG00000135341	ENST00000369332;ENST00000369329;ENST00000369325;ENST00000369327	T;T;T;T	0.61742	0.08;0.08;0.08;0.08	5.11	5.11	0.69529	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.86657	0.5985	H	0.99675	4.695	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.92805	0.6259	10	0.87932	D	0	.	18.8863	0.92379	0.0:1.0:0.0:0.0	.	156;156;156;156	O43318-4;O43318-2;O43318-3;O43318	.;.;.;M3K7_HUMAN	Y	156	ENSP00000358338:D156Y;ENSP00000358335:D156Y;ENSP00000358331:D156Y;ENSP00000358333:D156Y	ENSP00000358331:D156Y	D	-	1	0	MAP3K7	91326532	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.776000	0.85560	2.530000	0.85305	0.585000	0.79938	GAC	.	.		0.478	MAP3K7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041530.1	NM_145331		A	91269811	C	A	91269811	3	1	294	1	0	0	0	0	1	0	0	0	9264	855	30	3	1406	3	MAP3K7	6	91269811	Missense_Mutation	SNP	C	TCGA-G3-A7M9-01A-23D-A34Z-10	14548920	91269811	79845256	31	42803										
EPHA7	2045	hgsc.bcm.edu	37	chr6	94120578	94120578	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	tctttctttcaccaaggtcaCcttgggtaaaactttcatct	5	11	6	0			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr6:94120578C>T	ENST00000369303.4	-	3	657	c.473G>A	c.(472-474)gGt>gAt	p.G158D	EPHA7_ENST00000369297.1_Missense_Mutation_p.G158D	NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	158	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|ephrin receptor signaling pathway (GO:0048013)|negative chemotaxis (GO:0050919)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cell-cell adhesion (GO:0022407)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of protein autophosphorylation (GO:0031952)|retinal ganglion cell axon guidance (GO:0031290)	dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|chemorepellent activity (GO:0045499)|GPI-linked ephrin receptor activity (GO:0005004)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(1)|central_nervous_system(7)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|lung(43)|ovary(8)|pancreas(1)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(13)|urinary_tract(1)	112		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		ACCAAGGTCACCTTGGGTAAA	0.398																																					p.G158D		Atlas-SNP	.											.	EPHA7	251	.	0			c.G473A						.						135	135	135					6																	94120578		2203	4300	6503	SO:0001583	missense	2045	exon3			AGGTCACCTTGGG	L36642	CCDS5031.1, CCDS75494.1	6q16.3	2013-02-11	2004-10-28		ENSG00000135333	ENSG00000135333		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3390	protein-coding gene	gene with protein product		602190	"EphA7"			9267020	Standard	NM_004440		Approved	Hek11	uc003poe.3	Q15375	OTTHUMG00000015228	ENST00000369303.4:c.473G>A	chr6.hg19:g.94120578C>T	ENSP00000358309:p.Gly158Asp	131.0	0.0		80.0	28.0	NM_004440	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Missense_Mutation	SNP	ENST00000369303.4	hg19	CCDS5031.1	.	.	.	.	.	.	.	.	.	.	C	17.05	3.288944	0.59976	.	.	ENSG00000135333	ENST00000369303;ENST00000369297	T;T	0.09350	2.99;2.99	5.32	5.32	0.75619	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	T	0.22975	0.0555	L	0.55103	1.725	0.58432	D	0.999991	D;D;D;D	0.89917	0.983;1.0;1.0;1.0	P;D;D;D	0.97110	0.644;1.0;1.0;1.0	T	0.00503	-1.1701	10	0.52906	T	0.07	.	19.4211	0.94721	0.0:1.0:0.0:0.0	.	158;158;158;158	Q15375-4;Q15375-3;Q15375-2;Q15375	.;.;.;EPHA7_HUMAN	D	158	ENSP00000358309:G158D;ENSP00000358303:G158D	ENSP00000358303:G158D	G	-	2	0	EPHA7	94177299	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.744000	0.62118	2.676000	0.91093	0.650000	0.86243	GGT	.	.		0.398	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1			T	94120578	C	T	94120578	3	4	294	1	0	0	0	0	1	0	0	0	5174	507	18	3	2583	3	EPHA7	6	94120578	Missense_Mutation	SNP	C	TCGA-G3-A7M9-01A-23D-A34Z-10	2850767	94120578	76994489	32	42804										
ASCC3	10973	hgsc.bcm.edu	37	chr6	101166124	101166124	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	tatcatactctgtgtggattCcacctatatggattatttta	6	7	2	0			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr6:101166124C>T	ENST00000369162.2	-	12	2250	c.1906G>A	c.(1906-1908)Gaa>Aaa	p.E636K	ASCC3_ENST00000522650.1_Missense_Mutation_p.E636K	NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	636	Helicase ATP-binding 1. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		TGTGTGGATTCCACCTATATG	0.303																																					p.E636K		Atlas-SNP	.											.	ASCC3	205	.	0			c.G1906A						.						83	83	83					6																	101166124		2203	4300	6503	SO:0001583	missense	10973	exon12			TGGATTCCACCTA	AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"RNA helicase family"	614217	"helicase, ATP binding 1"	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.1906G>A	chr6.hg19:g.101166124C>T	ENSP00000358159:p.Glu636Lys	75.0	0.0		49.0	19.0	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Missense_Mutation	SNP	ENST00000369162.2	hg19	CCDS5046.1	.	.	.	.	.	.	.	.	.	.	C	32	5.148786	0.94603	.	.	ENSG00000112249	ENST00000369162;ENST00000522650	T;T	0.14640	2.49;2.49	5.36	5.36	0.76844	DEAD-like helicase (2);ATPase, AAA+ type, core (1);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.119748	0.56097	D	0.000034	T	0.34164	0.0888	M	0.81614	2.55	0.80722	D	1	D;D	0.71674	0.998;0.992	D;D	0.73380	0.98;0.954	T	0.18524	-1.0334	10	0.66056	D	0.02	.	19.0903	0.93224	0.0:1.0:0.0:0.0	.	636;636	E7EW23;Q8N3C0	.;HELC1_HUMAN	K	636	ENSP00000358159:E636K;ENSP00000430769:E636K	ENSP00000358159:E636K	E	-	1	0	ASCC3	101272845	1.000000	0.71417	1.000000	0.80357	0.723000	0.41478	7.818000	0.86416	2.499000	0.84300	0.585000	0.79938	GAA	.	.		0.303	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828		T	101166124	C	T	101166124	3	4	294	1	0	0	0	0	1	0	0	0	1033	864	30	3	4826	3	ASCC3	6	101166124	Missense_Mutation	SNP	C	TCGA-G3-A7M9-01A-23D-A34Z-10	7045546	101166124	69948943	33	42805										
TAAR1	134864	hgsc.bcm.edu	37	chr6	132966704	132966704	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	aacagcagggacactccaacTaatgaagatcatcacacaaa	6	11	2	2			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr6:132966704T>C	ENST00000275216.1	-	1	438	c.439A>G	c.(439-441)Agt>Ggt	p.S147G		NM_138327.1	NP_612200.1	Q96RJ0	TAAR1_HUMAN	trace amine associated receptor 1	147					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|trace-amine receptor activity (GO:0001594)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)	18	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00616)|GBM - Glioblastoma multiforme(226;0.0154)	Amphetamine(DB00182)|Dextroamphetamine(DB01576)|Methamphetamine(DB01577)|Propylhexedrine(DB06714)	ACACTCCAACTAATGAAGATC	0.393																																					p.S147G		Atlas-SNP	.											.	TAAR1	41	.	0			c.A439G						.						58	57	57					6																	132966704		2203	4300	6503	SO:0001583	missense	134864	exon1			TCCAACTAATGAA	AY180374	CCDS5158.1	6q23.1	2012-08-08	2005-02-23	2005-02-24	ENSG00000146399	ENSG00000146399		"GPCR / Class A : Trace amine associated receptors"	17734	protein-coding gene	gene with protein product		609333	"trace amine receptor 1"	TRAR1		11459929, 15718104	Standard	NM_138327		Approved	TAR1, TA1	uc003qdm.1	Q96RJ0	OTTHUMG00000015583	ENST00000275216.1:c.439A>G	chr6.hg19:g.132966704T>C	ENSP00000275216:p.Ser147Gly	77.0	0.0		49.0	17.0	NM_138327	Q2M1W5|Q3MIH8|Q5VUQ1	Missense_Mutation	SNP	ENST00000275216.1	hg19	CCDS5158.1	.	.	.	.	.	.	.	.	.	.	T	16.07	3.019627	0.54576	.	.	ENSG00000146399	ENST00000275216	T	0.72051	-0.62	5.73	2.02	0.26589	GPCR, rhodopsin-like superfamily (1);	0.043249	0.85682	D	0.000000	T	0.59569	0.2203	M	0.82132	2.575	0.38986	D	0.95904	B	0.33841	0.428	B	0.39068	0.289	T	0.58317	-0.7657	10	0.45353	T	0.12	-9.8524	9.6416	0.39842	0.0:0.1977:0.0:0.8023	.	147	Q96RJ0	TAAR1_HUMAN	G	147	ENSP00000275216:S147G	ENSP00000275216:S147G	S	-	1	0	TAAR1	133008397	0.963000	0.33076	0.684000	0.30055	0.952000	0.60782	2.005000	0.40864	0.113000	0.18004	0.454000	0.30748	AGT	.	.		0.393	TAAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042259.1	NM_138327		C	132966704	T	C	132966704	3	2	294	1	0	0	0	0	1	0	0	0	15504	1522	53	2	584	2	TAAR1	6	132966704	Missense_Mutation	SNP	T	TCGA-G3-A7M9-01A-23D-A34Z-10	31800580	132966704	38148363	34	42806										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48431663	48431663	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	tggacaacctcaccgtccggGaacatttgctgctctttgct	9	13	2	0			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr7:48431663G>T	ENST00000435803.1	+	38	11824	c.11800G>T	c.(11800-11802)Gaa>Taa	p.E3934*		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	3934	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.E3879K(1)|p.E3934K(1)		breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						CACCGTCCGGGAACATTTGCT	0.517																																					p.E3934X		Atlas-SNP	.											ABCA13_ENST00000435803,trunk,malignant_melanoma,0,2	ABCA13	1192	.	2	Substitution - Missense(2)	skin(2)	c.G11800T						.						124	127	126					7																	48431663		2021	4180	6201	SO:0001587	stop_gained	154664	exon38			GTCCGGGAACATT	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.11800G>T	chr7.hg19:g.48431663G>T	ENSP00000411096:p.Glu3934*	67.0	0.0		56.0	21.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Nonsense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	G	52	19.415468	0.99919	.	.	ENSG00000179869	ENST00000435803	.	.	.	5.32	5.32	0.75619	.	0.000000	0.41294	U	0.000908	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	15.7134	0.77649	0.0:0.0:1.0:0.0	.	.	.	.	X	3934	.	ENSP00000411096:E3934X	E	+	1	0	ABCA13	48402209	1.000000	0.71417	0.046000	0.18839	0.049000	0.14656	8.042000	0.89430	2.485000	0.83878	0.467000	0.42956	GAA	.	.		0.517	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		T	48431663	G	T	48431663	4	4	294	1	0	0	0	0	0	1	0	0	31	1175	41	3	11779	3	ABCA13	7	48431663	Nonsense_Mutation	SNP	G	TCGA-G3-A7M9-01A-23D-A34Z-10		48431663	110707000	35	42807										
PCLO	27445	hgsc.bcm.edu	37	chr7	82531973	82531973	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	atgatttgctttacctgaaaCtgtgtgatcctttgagtctc	8	8	1	4			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr7:82531973C>T	ENST00000333891.9	-	9	13859	c.13522G>A	c.(13522-13524)Gtt>Att	p.V4508I	PCLO_ENST00000423517.2_Missense_Mutation_p.V4508I	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TTACCTGAAACTGTGTGATCC	0.279																																					p.V4508I		Atlas-SNP	.											.	PCLO	1506	.	0			c.G13522A						.						217	185	195					7																	82531973		1814	4082	5896	SO:0001583	missense	27445	exon9			CTGAAACTGTGTG	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.13522G>A	chr7.hg19:g.82531973C>T	ENSP00000334319:p.Val4508Ile	119.0	0.0		78.0	27.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	C	13.22	2.173092	0.38413	.	.	ENSG00000186472	ENST00000333891;ENST00000423517	T;T	0.16897	2.31;2.32	5.7	4.82	0.62117	.	.	.	.	.	T	0.13457	0.0326	L	0.28115	0.83	0.80722	D	1	B;B	0.10296	0.003;0.003	B;B	0.12156	0.007;0.007	T	0.03773	-1.1005	9	0.87932	D	0	.	11.4181	0.49965	0.0:0.862:0.0:0.138	.	4508;4508	Q9Y6V0-5;Q9Y6V0-6	.;.	I	4508	ENSP00000334319:V4508I;ENSP00000388393:V4508I	ENSP00000334319:V4508I	V	-	1	0	PCLO	82369909	0.997000	0.39634	1.000000	0.80357	0.987000	0.75469	3.627000	0.54252	2.694000	0.91930	0.467000	0.42956	GTT	.	.		0.279	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		T	82531973	C	T	82531973	3	4	294	1	0	0	0	0	1	0	0	0	11592	565	20	3	1991	3	PCLO	7	82531973	Missense_Mutation	SNP	C	TCGA-G3-A7M9-01A-23D-A34Z-10	34100310	82531973	76606690	36	42808										
HEPACAM2	253012	hgsc.bcm.edu	37	chr7	92837990	92837990	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	tccattgtcttctgggctacTttctcagatgcaacttctaa	6	11	4	1			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr7:92837990T>A	ENST00000394468.2	-	4	992	c.915A>T	c.(913-915)aaA>aaT	p.K305N	HEPACAM2_ENST00000341723.4_Missense_Mutation_p.K293N|HEPACAM2_ENST00000440868.1_Missense_Mutation_p.K293N|HEPACAM2_ENST00000453812.2_Missense_Mutation_p.K328N	NM_001039372.1	NP_001034461.1	A8MVW5	HECA2_HUMAN	HEPACAM family member 2	305	Ig-like C2-type 2.				centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|midbody (GO:0030496)|spindle (GO:0005819)				breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|ovary(4)|skin(1)	28						TCTGGGCTACTTTCTCAGATG	0.443																																					p.K305N		Atlas-SNP	.											.	HEPACAM2	132	.	0			c.A915T						.						167	147	154					7																	92837990		2203	4300	6503	SO:0001583	missense	253012	exon4			GGCTACTTTCTCA	AK096002	CCDS5629.1, CCDS43616.1, CCDS75631.1, CCDS75632.1	7q21.3	2013-01-29	2008-07-11		ENSG00000188175	ENSG00000188175		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	27364	protein-coding gene	gene with protein product		614133				12975309	Standard	NM_001288804		Approved	FLJ38683	uc003umm.3	A8MVW5	OTTHUMG00000131732	ENST00000394468.2:c.915A>T	chr7.hg19:g.92837990T>A	ENSP00000377980:p.Lys305Asn	134.0	0.0		97.0	32.0	NM_001039372	B3KTT4|B4DPJ1|B9EG93|E9PDV5|Q6UXI0	Missense_Mutation	SNP	ENST00000394468.2	hg19	CCDS43616.1	.	.	.	.	.	.	.	.	.	.	T	12.04	1.817667	0.32145	.	.	ENSG00000188175	ENST00000394468;ENST00000341723;ENST00000440868;ENST00000453812	T;T;T;T	0.12569	2.67;2.67;2.67;2.67	5.23	-2.05	0.07321	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.394694	0.29631	N	0.011605	T	0.10337	0.0253	N	0.24115	0.695	0.26828	N	0.968639	P;P;B;B	0.49307	0.922;0.801;0.379;0.178	P;P;B;B	0.49528	0.614;0.494;0.196;0.145	T	0.28299	-1.0048	10	0.30854	T	0.27	-3.3532	8.3344	0.32206	0.0:0.1251:0.4308:0.444	.	328;293;305;293	E9PDV5;C9JN07;A8MVW5;A8MVW5-2	.;.;HECA2_HUMAN;.	N	305;293;293;328	ENSP00000377980:K305N;ENSP00000340532:K293N;ENSP00000389592:K293N;ENSP00000390204:K328N	ENSP00000340532:K293N	K	-	3	2	HEPACAM2	92675926	0.720000	0.27996	0.984000	0.44739	0.018000	0.09664	0.183000	0.16919	-0.089000	0.12484	-1.151000	0.01829	AAA	.	.		0.443	HEPACAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254651.1	NM_198151		A	92837990	T	A	92837990	3	1	294	1	0	0	0	0	1	0	0	0	7062	1606	56	4	501	4	HEPACAM2	7	92837990	Missense_Mutation	SNP	T	TCGA-G3-A7M9-01A-23D-A34Z-10	10306017	92837990	66300673	37	42809										
TNKS	8658	hgsc.bcm.edu	37	chr8	9538246	9538246	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	tttttataggagtggtaatgAagaaaaactaatggctttac	9	3	0	2			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr8:9538246A>T	ENST00000310430.6	+	5	1069	c.1043A>T	c.(1042-1044)gAa>gTa	p.E348V	TNKS_ENST00000520408.1_Missense_Mutation_p.E348V|TNKS_ENST00000518027.1_3'UTR|TNKS_ENST00000518281.1_Missense_Mutation_p.E111V	NM_003747.2	NP_003738.2	O95271	TNKS1_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	348					mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|mRNA transport (GO:0051028)|negative regulation of DNA binding (GO:0043392)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein poly-ADP-ribosylation (GO:0070212)|protein polyubiquitination (GO:0000209)|protein transport (GO:0015031)|regulation of telomere maintenance via telomerase (GO:0032210)|spindle assembly (GO:0051225)|Wnt signaling pathway (GO:0016055)	chromosome, centromeric region (GO:0000775)|chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nuclear chromosome, telomeric region (GO:0000784)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	NAD+ ADP-ribosyltransferase activity (GO:0003950)|zinc ion binding (GO:0008270)			NS(1)|endometrium(10)|kidney(6)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	49				COAD - Colon adenocarcinoma(149;0.0467)		AGTGGTAATGAAGAAAAACTA	0.303																																					p.E348V		Atlas-SNP	.											.	TNKS	198	.	0			c.A1043T						.						81	87	85					8																	9538246		2203	4300	6503	SO:0001583	missense	8658	exon5			GTAATGAAGAAAA	AF082556	CCDS5974.1	8p23.1	2013-01-10			ENSG00000173273	ENSG00000173273		"Poly (ADP-ribose) polymerases", "Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	11941	protein-coding gene	gene with protein product		603303				9822378, 10198177	Standard	XM_006716263		Approved	TIN1, TINF1, TNKS1, PARP-5a, PARP5A, pART5	uc003wss.3	O95271	OTTHUMG00000090481	ENST00000310430.6:c.1043A>T	chr8.hg19:g.9538246A>T	ENSP00000311579:p.Glu348Val	143.0	0.0		121.0	46.0	NM_003747	O95272|Q4G0F2	Missense_Mutation	SNP	ENST00000310430.6	hg19	CCDS5974.1	.	.	.	.	.	.	.	.	.	.	A	18.20	3.570510	0.65765	.	.	ENSG00000173273	ENST00000520408;ENST00000310430;ENST00000518281	T;T;T	0.62639	0.01;0.01;0.01	5.83	5.83	0.93111	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.77025	0.4070	M	0.69358	2.11	0.80722	D	1	D;P	0.71674	0.998;0.956	D;P	0.71184	0.972;0.809	T	0.77130	-0.2701	10	0.45353	T	0.12	.	16.1967	0.82036	1.0:0.0:0.0:0.0	.	348;348	E7EWY6;O95271	.;TNKS1_HUMAN	V	348;348;111	ENSP00000428299:E348V;ENSP00000311579:E348V;ENSP00000429890:E111V	ENSP00000311579:E348V	E	+	2	0	TNKS	9575656	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.483000	0.90442	2.217000	0.71921	0.477000	0.44152	GAA	.	.		0.303	TNKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206935.1	NM_003747		T	9538246	A	T	9538246	3	4	294	1	0	0	0	0	1	0	0	0	16334	246	9	4	1061	4	TNKS	8	9538246	Missense_Mutation	SNP	A	TCGA-G3-A7M9-01A-23D-A34Z-10		9538246	136825776	38	42810										
GATA4	2626	hgsc.bcm.edu	37	chr8	11615852	11615852	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	gggccctccatccaccctgtCctctcggccctgaagctctc	8	20	2	1			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr8:11615852C>T	ENST00000335135.4	+	7	1755	c.1197C>T	c.(1195-1197)gtC>gtT	p.V399V	GATA4_ENST00000532059.1_Silent_p.V400V|GATA4_ENST00000528712.1_Silent_p.V193V	NM_002052.3	NP_002043.2	P43694	GATA4_HUMAN	GATA binding protein 4	399					atrial septum morphogenesis (GO:0060413)|atrial septum primum morphogenesis (GO:0003289)|atrial septum secundum morphogenesis (GO:0003290)|atrioventricular valve morphogenesis (GO:0003181)|blood coagulation (GO:0007596)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac ventricle morphogenesis (GO:0003208)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell-cell signaling (GO:0007267)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to glucose stimulus (GO:0071333)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic foregut morphogenesis (GO:0048617)|embryonic heart tube anterior/posterior pattern specification (GO:0035054)|endocardial cushion development (GO:0003197)|endoderm development (GO:0007492)|endoderm formation (GO:0001706)|epithelial cell fate commitment (GO:0072148)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|intestinal epithelial cell differentiation (GO:0060575)|lung lobe formation (GO:0060464)|male gonad development (GO:0008584)|negative regulation of autophagy (GO:0010507)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to mechanical stimulus (GO:0009612)|seminiferous tubule development (GO:0072520)|Sertoli cell differentiation (GO:0060008)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular cardiac muscle tissue development (GO:0003229)|ventricular septum development (GO:0003281)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|co-SMAD binding (GO:0070410)|DNA binding (GO:0003677)|enhancer sequence-specific DNA binding (GO:0001158)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(10)	13	all_epithelial(15;0.0839)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.199)		TCCACCCTGTCCTCTCGGCCC	0.602																																					p.V399V		Atlas-SNP	.											.	GATA4	29	.	0			c.C1197T						.						154	134	141					8																	11615852		2203	4300	6503	SO:0001819	synonymous_variant	2626	exon7			CCCTGTCCTCTCG	AK097060	CCDS5983.1	8p23.1-p22	2013-01-25	2001-11-28		ENSG00000136574	ENSG00000136574		"GATA zinc finger domain containing"	4173	protein-coding gene	gene with protein product		600576	"GATA-binding protein 4"			7665171	Standard	NM_002052		Approved		uc003wuc.2	P43694	OTTHUMG00000090800	ENST00000335135.4:c.1197C>T	chr8.hg19:g.11615852C>T		43.0	0.0		40.0	15.0	NM_002052	B7ZKX0|B7ZKZ4|Q3MJ45|Q5IFM8	Silent	SNP	ENST00000335135.4	hg19	CCDS5983.1																																																																																			.	.		0.602	GATA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207587.2	NM_002052		T	11615852	C	T	11615852	2	4	294	1	0	0	0	0	0	0	0	1	6264	842	30	3		3	GATA4	8	11615852	Silent	SNP	C	TCGA-G3-A7M9-01A-23D-A34Z-10	2077606	11615852	134748170	39	42811										
ADAM18	8749	hgsc.bcm.edu	37	chr8	39505913	39505913	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	ctgcagcatgcacgactataGatattttgtttcaaaatttg	7	7	1	1			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr8:39505913G>C	ENST00000265707.5	+	12	1142	c.1097G>C	c.(1096-1098)aGa>aCa	p.R366T	ADAM18_ENST00000541111.1_Intron|ADAM18_ENST00000379866.1_Missense_Mutation_p.R342T	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	366	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(31)|ovary(1)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)	71		all_cancers(7;1.32e-05)|all_epithelial(6;3.08e-10)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00769)|Breast(189;0.0112)	LUSC - Lung squamous cell carcinoma(45;0.000199)			CACGACTATAGATATTTTGTT	0.348																																					p.R366T		Atlas-SNP	.											.	ADAM18	169	.	0			c.G1097C						.						62	63	63					8																	39505913		2203	4300	6503	SO:0001583	missense	8749	exon12			ACTATAGATATTT	AJ133004	CCDS6113.1, CCDS55225.1	8p11.22	2008-08-07	2005-08-18		ENSG00000168619	ENSG00000168619		"ADAM metallopeptidase domain containing"	196	protein-coding gene	gene with protein product			"a disintegrin and metalloproteinase domain 18"			12200459	Standard	NM_014237		Approved	tMDCIII, ADAM27	uc003xni.3	Q9Y3Q7	OTTHUMG00000164040	ENST00000265707.5:c.1097G>C	chr8.hg19:g.39505913G>C	ENSP00000265707:p.Arg366Thr	146.0	0.0		163.0	12.0	NM_014237	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Missense_Mutation	SNP	ENST00000265707.5	hg19	CCDS6113.1	.	.	.	.	.	.	.	.	.	.	G	5.674	0.308908	0.10733	.	.	ENSG00000168619	ENST00000265707;ENST00000379866;ENST00000522198	T;T	0.63580	-0.05;-0.05	5.4	-5.51	0.02568	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.930373	0.08987	N	0.864945	T	0.43831	0.1265	L	0.52364	1.645	0.09310	N	1	B;B	0.14805	0.009;0.011	B;B	0.18263	0.012;0.021	T	0.34527	-0.9825	10	0.22109	T	0.4	.	0.9863	0.01447	0.3381:0.3169:0.1508:0.1942	.	342;366	Q9Y3Q7-2;Q9Y3Q7	.;ADA18_HUMAN	T	366;342;298	ENSP00000265707:R366T;ENSP00000369195:R342T	ENSP00000265707:R366T	R	+	2	0	ADAM18	39625070	0.002000	0.14202	0.000000	0.03702	0.034000	0.12701	-0.404000	0.07205	-0.904000	0.03876	0.585000	0.79938	AGA	.	.		0.348	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237		C	39505913	G	C	39505913	3	2	294	1	0	0	0	0	1	0	0	0	239	942	33	4	1143	4	ADAM18	8	39505913	Missense_Mutation	SNP	G	TCGA-G3-A7M9-01A-23D-A34Z-10	27890061	39505913	106858109	40	42812										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77768145	77768145	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	aacatagggaagcctttcatGatcaatcaaggcggaacgga	11	8	3	1			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr8:77768145G>A	ENST00000521891.2	+	10	9436	c.8988G>A	c.(8986-8988)atG>atA	p.M2996I	ZFHX4_ENST00000455469.2_Missense_Mutation_p.M2951I|ZFHX4_ENST00000518282.1_Missense_Mutation_p.M2970I|ZFHX4_ENST00000050961.6_Missense_Mutation_p.M2951I	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2951					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			AGCCTTTCATGATCAATCAAG	0.473										HNSCC(33;0.089)																											p.M2996I		Atlas-SNP	.											.	ZFHX4	878	.	0			c.G8988A						.						45	44	44					8																	77768145		1909	4123	6032	SO:0001583	missense	79776	exon10			TTTCATGATCAAT		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.8988G>A	chr8.hg19:g.77768145G>A	ENSP00000430497:p.Met2996Ile	55.0	0.0		52.0	20.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	hg19	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	G	12.08	1.830677	0.32329	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.48201	0.82;0.87;0.84;0.83	5.17	5.17	0.71159	.	0.000000	0.53938	U	0.000049	T	0.54967	0.1891	N	0.24115	0.695	0.54753	D	0.999981	P;P;P	0.51653	0.913;0.947;0.947	P;P;D	0.68192	0.746;0.871;0.956	T	0.47736	-0.9094	10	0.24483	T	0.36	.	18.8517	0.92235	0.0:0.0:1.0:0.0	.	2951;2951;2996	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	I	2996;2980;2951;2951;2970	ENSP00000430497:M2996I;ENSP00000399605:M2951I;ENSP00000050961:M2951I;ENSP00000430848:M2970I	ENSP00000050961:M2951I	M	+	3	0	ZFHX4	77930700	1.000000	0.71417	1.000000	0.80357	0.407000	0.30961	7.665000	0.83852	2.687000	0.91594	0.643000	0.83706	ATG	.	.		0.473	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		A	77768145	G	A	77768145	3	1	294	1	0	0	0	0	1	0	0	0	17650	1290	45	3	9022	3	ZFHX4	8	77768145	Missense_Mutation	SNP	G	TCGA-G3-A7M9-01A-23D-A34Z-10	38262232	77768145	68595877	41	42813										
INSL4	3641	hgsc.bcm.edu	37	chr9	5231621	5231621	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	agagctgaggggatgtggtcCccgatttggaaaacacttgc	14	8	0	2			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr9:5231621C>A	ENST00000239316.4	+	1	203	c.98C>A	c.(97-99)cCc>cAc	p.P33H		NM_002195.1	NP_002186.1	Q14641	INSL4_HUMAN	insulin-like 4 (placenta)	33					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|female pregnancy (GO:0007565)|multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	insulin-like growth factor receptor binding (GO:0005159)|receptor binding (GO:0005102)			endometrium(2)|lung(2)|skin(1)|urinary_tract(1)	6	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0201)|Lung(218;0.14)		GGATGTGGTCCCCGATTTGGA	0.562																																					p.P33H		Atlas-SNP	.											.	INSL4	20	.	0			c.C98A						.						96	84	88					9																	5231621		2203	4300	6503	SO:0001583	missense	3641	exon1			GTGGTCCCCGATT		CCDS6459.1	9p24	2008-02-05			ENSG00000120211	ENSG00000120211			6087	protein-coding gene	gene with protein product		600910				8666396, 9730618	Standard	NM_002195		Approved	EPIL	uc003ziy.3	Q14641	OTTHUMG00000019494	ENST00000239316.4:c.98C>A	chr9.hg19:g.5231621C>A	ENSP00000239316:p.Pro33His	55.0	0.0		48.0	11.0	NM_002195	A8K678|Q5W127	Missense_Mutation	SNP	ENST00000239316.4	hg19	CCDS6459.1	.	.	.	.	.	.	.	.	.	.	C	5.242	0.230205	0.09969	.	.	ENSG00000120211	ENST00000239316	D	0.84516	-1.86	1.8	-3.59	0.04583	.	0.850582	0.08754	U	0.898665	T	0.65080	0.2657	N	0.08118	0	0.09310	N	1	B	0.14438	0.01	B	0.06405	0.002	T	0.47686	-0.9098	10	0.59425	D	0.04	.	2.6307	0.04943	0.4657:0.2892:0.0:0.245	.	33	Q14641	INSL4_HUMAN	H	33	ENSP00000239316:P33H	ENSP00000239316:P33H	P	+	2	0	INSL4	5221621	0.000000	0.05858	0.000000	0.03702	0.037000	0.13140	-2.654000	0.00855	-1.510000	0.01796	0.205000	0.17691	CCC	.	.		0.562	INSL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051616.2	NM_002195		A	5231621	C	A	5231621	3	1	294	1	0	0	0	0	1	0	0	0	7777	623	22	3	100	3	INSL4	9	5231621	Missense_Mutation	SNP	C	TCGA-G3-A7M9-01A-23D-A34Z-10		5231621	135981810	42	42814										
DNAJB5	25822	hgsc.bcm.edu	37	chr9	34993331	34993331	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	ggccttgaagtaccacccagAcaagaataaagaacccaacg	8	12	0	4			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr9:34993331A>C	ENST00000541010.1	+	1	3113	c.101A>C	c.(100-102)gAc>gCc	p.D34A	DNAJB5_ENST00000335998.3_Missense_Mutation_p.D68A|DNAJB5_ENST00000312316.5_Missense_Mutation_p.D34A|DNAJB5_ENST00000545841.1_Missense_Mutation_p.D34A|DNAJB5_ENST00000453597.3_Missense_Mutation_p.D148A|DNAJB5_ENST00000454002.2_Missense_Mutation_p.D106A			O75953	DNJB5_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 5	34	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein folding (GO:0006457)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|nucleus (GO:0005634)	chaperone binding (GO:0051087)			kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(32;0.00575)			TACCACCCAGACAAGAATAAA	0.478																																					p.D148A		Atlas-SNP	.											.	DNAJB5	69	.	0			c.A443C						.						140	138	139					9																	34993331		2203	4300	6503	SO:0001583	missense	25822	exon3			ACCCAGACAAGAA	AF088982	CCDS35007.1, CCDS47959.1, CCDS47960.1, CCDS47960.2	9p	2011-09-02			ENSG00000137094	ENSG00000137094		"Heat shock proteins / DNAJ (HSP40)"	14887	protein-coding gene	gene with protein product		611328				10570961, 11147971	Standard	NM_001135004		Approved	Hsc40	uc003zvs.4	O75953	OTTHUMG00000019840	ENST00000541010.1:c.101A>C	chr9.hg19:g.34993331A>C	ENSP00000443151:p.Asp34Ala	46.0	0.0		43.0	16.0	NM_001135004	B3KN14|B4DSA6|J3KQM9|J3KR08|Q5T656|Q8TDR7|Q96EM4	Missense_Mutation	SNP	ENST00000541010.1	hg19	CCDS35007.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.118223	0.77323	.	.	ENSG00000137094	ENST00000453597;ENST00000335998;ENST00000378751;ENST00000312316;ENST00000541010;ENST00000454002;ENST00000545841;ENST00000539059;ENST00000443266	D;D;D;D;D;D;D;D	0.91521	-2.86;-2.86;-2.86;-2.86;-2.86;-2.86;-2.86;-2.86	5.31	5.31	0.75309	Heat shock protein DnaJ, N-terminal (5);	0.000000	0.85682	D	0.000000	D	0.96796	0.8954	H	0.96460	3.825	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97952	1.0332	10	0.87932	D	0	.	14.5924	0.68378	1.0:0.0:0.0:0.0	.	106;34	B4DSA6;O75953	.;DNJB5_HUMAN	A	148;68;34;34;34;106;34;70;34	ENSP00000404079:D148A;ENSP00000337626:D68A;ENSP00000312517:D34A;ENSP00000443151:D34A;ENSP00000413684:D106A;ENSP00000441999:D34A;ENSP00000445536:D70A;ENSP00000396332:D34A	ENSP00000312517:D34A	D	+	2	0	DNAJB5	34983331	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.761000	0.91691	2.234000	0.73211	0.459000	0.35465	GAC	.	.		0.478	DNAJB5-008	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401397.1			C	34993331	A	C	34993331	3	2	294	1	0	0	0	0	1	0	0	0	4625	275	10	5	323	5	DNAJB5	9	34993331	Missense_Mutation	SNP	A	TCGA-G3-A7M9-01A-23D-A34Z-10	29761710	34993331	106220100	43	42815										
TLE4	7091	hgsc.bcm.edu	37	chr9	82267541	82267541	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	cccagcatttatcacatggaCatggtctccccgtacctctg	7	15	3	0			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr9:82267541C>A	ENST00000376552.2	+	7	1442	c.424C>A	c.(424-426)Cat>Aat	p.H142N	TLE4_ENST00000265284.6_Missense_Mutation_p.H117N|TLE4_ENST00000376537.4_Missense_Mutation_p.H142N|TLE4_ENST00000376544.3_Missense_Mutation_p.H142N|TLE4_ENST00000376520.4_Missense_Mutation_p.H142N|TLE4_ENST00000376534.4_De_novo_Start_InFrame|TLE4_ENST00000455913.1_3'UTR	NM_007005.3	NP_008936.2	Q04727	TLE4_HUMAN	transducin-like enhancer of split 4	142	Gly/Pro-rich (GP domain).				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|Wnt signaling pathway (GO:0016055)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	39						ATCACATGGACATGGTCTCCC	0.552																																					p.H142N		Atlas-SNP	.											.	TLE4	187	.	0			c.C424A						.						110	119	116					9																	82267541		2057	4188	6245	SO:0001583	missense	7091	exon7			CATGGACATGGTC	M99439	CCDS43837.1, CCDS65069.1, CCDS65070.1, CCDS75851.1	9q21.32	2014-03-07	2014-03-07		ENSG00000106829	ENSG00000106829		"WD repeat domain containing"	11840	protein-coding gene	gene with protein product		605132	"transducin-like enhancer of split 4, homolog of Drosophila E(sp1)", "transducin-like enhancer of split 4 (E(sp1) homolog, Drosophila)"			8365415	Standard	XM_005252167		Approved	E(spI), ESG, GRG4	uc004alc.3	Q04727	OTTHUMG00000020072	ENST00000376552.2:c.424C>A	chr9.hg19:g.82267541C>A	ENSP00000365735:p.His142Asn	88.0	0.0		69.0	16.0	NM_007005	F8W6T6|Q3ZCS1|Q5T1Y2|Q6PCB3|Q9BZ07|Q9BZ08|Q9BZ09|Q9NSL3|Q9ULF9	Missense_Mutation	SNP	ENST00000376552.2	hg19	CCDS43837.1	.	.	.	.	.	.	.	.	.	.	C	18.83	3.707990	0.68615	.	.	ENSG00000106829	ENST00000376552;ENST00000376544;ENST00000376520;ENST00000399288;ENST00000435650;ENST00000414465;ENST00000376537;ENST00000265284;ENST00000425506;ENST00000428713;ENST00000490347	T;T;T;T;T;T;T;T;T	0.52057	0.7;0.68;0.74;0.85;0.73;0.82;0.8;1.35;1.62	6.17	6.17	0.99709	.	0.096408	0.64402	D	0.000001	T	0.61022	0.2314	M	0.78049	2.395	0.80722	D	1	P;B;B;B	0.40875	0.731;0.027;0.38;0.059	P;B;B;B	0.44860	0.462;0.015;0.197;0.038	T	0.61053	-0.7140	10	0.52906	T	0.07	-20.9074	20.8794	0.99867	0.0:1.0:0.0:0.0	.	117;142;142;142	F8W6T6;Q04727-2;Q04727-3;Q04727	.;.;.;TLE4_HUMAN	N	142;142;142;156;156;128;142;117;140;127;12	ENSP00000365735:H142N;ENSP00000365727:H142N;ENSP00000365703:H142N;ENSP00000415423:H156N;ENSP00000365720:H142N;ENSP00000265284:H117N;ENSP00000412567:H140N;ENSP00000409313:H127N;ENSP00000417844:H12N	ENSP00000265284:H117N	H	+	1	0	TLE4	81457361	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	7.155000	0.77445	2.941000	0.99782	0.655000	0.94253	CAT	.	.		0.552	TLE4-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052792.4	XM_212237		A	82267541	C	A	82267541	3	1	294	1	0	0	0	0	1	0	0	0	15956	478	17	3	450	3	TLE4	9	82267541	Missense_Mutation	SNP	C	TCGA-G3-A7M9-01A-23D-A34Z-10	47274210	82267541	58945890	44	42816										
ZCCHC6	79670	hgsc.bcm.edu	37	chr9	88967620	88967620	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	cttcctgcttccatttctgaCgtggtttctaggcttgttag	9	10	2	1			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr9:88967620C>A	ENST00000375963.3	-	2	667	c.495G>T	c.(493-495)acG>acT	p.T165T	ZCCHC6_ENST00000375960.2_Silent_p.T165T|ZCCHC6_ENST00000375961.2_Silent_p.T165T|ZCCHC6_ENST00000375947.1_5'UTR|ZCCHC6_ENST00000277141.6_5'UTR	NM_001185059.1|NM_024617.3	NP_001171988.1|NP_078893.2	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6	165					RNA 3'-end processing (GO:0031123)		poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	46						CCATTTCTGACGTGGTTTCTA	0.403																																					p.T165T		Atlas-SNP	.											.	ZCCHC6	105	.	0			c.G495T						.						155	157	156					9																	88967620		2203	4300	6503	SO:0001819	synonymous_variant	79670	exon2			TTCTGACGTGGTT	AL832026	CCDS35057.1, CCDS55323.1	9q21	2014-03-05			ENSG00000083223	ENSG00000083223		"Zinc fingers, CCHC domain containing"	25817	protein-coding gene	gene with protein product	"TUTase7"					11214970	Standard	NM_001185059		Approved	KIAA1711, FLJ13409, PAPD6, TUT7	uc004aoq.3	Q5VYS8	OTTHUMG00000020137	ENST00000375963.3:c.495G>T	chr9.hg19:g.88967620C>A		201.0	0.0		140.0	37.0	NM_024617	Q5H9T0|Q5VYS5|Q5VYS7|Q658Z9|Q659A2|Q6MZJ3|Q8N5F0|Q96N57|Q96NE8|Q9C0F2|Q9H8M6	Silent	SNP	ENST00000375963.3	hg19	CCDS35057.1																																																																																			.	.		0.403	ZCCHC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052918.1	NM_024617		A	88967620	C	A	88967620	2	1	294	1	0	0	0	0	0	0	0	1	17607	523	19	1		1	ZCCHC6	9	88967620	Silent	SNP	C	TCGA-G3-A7M9-01A-23D-A34Z-10	6700079	88967620	52245811	45	42817										
LOC645961	645961	hgsc.bcm.edu	37	chr9	90746827	90746827	+	IGR	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	gacgcagggcaagctactccAgtgttcttcatcggggatag	13	10	2	0			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr9:90746827A>G								U6 (133577 upstream) : U3 (242356 downstream)																							AAGCTACTCCAGTGTTCTTCA	0.512																																					p.T375T		Atlas-SNP	.											.	.	.	.	0			c.T1125C						.						10	10	10					9																	90746827		686	1582	2268	SO:0001628	intergenic_variant	645961	exon4			TACTCCAGTGTTC																													chr9.hg19:g.90746827A>G		87.0	0.0		73.0	38.0	NM_001166137		Silent	SNP		hg19																																																																																				.	.	0	0.512									G	90746827	A	G	90746827	1	3	294	0	1	0	0	0	0	0	0	0	8892	175	7	2		2	LOC645961	9	90746827	IGR	SNP	A	TCGA-G3-A7M9-01A-23D-A34Z-10	1779207	90746827	50466604	46	42818										
TSTD2	158427	hgsc.bcm.edu	37	chr9	100365038	100365038	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	ctggtcccagcgggctccacAgtatgaacactctggggagg	14	12	1	1			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr9:100365038A>G	ENST00000341170.4	-	10	1646	c.1264T>C	c.(1264-1266)Tgt>Cgt	p.C422R		NM_139246.4	NP_640339.4	Q5T7W7	TSTD2_HUMAN	thiosulfate sulfurtransferase (rhodanese)-like domain containing 2	422										large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	15						CGGGCTCCACAGTATGAACAC	0.517																																					p.C422R		Atlas-SNP	.											.	TSTD2	42	.	0			c.T1264C						.						57	57	57					9																	100365038		2203	4300	6503	SO:0001583	missense	158427	exon10			CTCCACAGTATGA	AF258575	CCDS6727.2	9q22.33	2013-09-20	2009-08-12	2009-08-12	ENSG00000136925	ENSG00000136925			30087	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 97"	C9orf97		12477932	Standard	NM_139246		Approved	PP4189	uc004axn.3	Q5T7W7	OTTHUMG00000020328	ENST00000341170.4:c.1264T>C	chr9.hg19:g.100365038A>G	ENSP00000342499:p.Cys422Arg	91.0	0.0		63.0	26.0	NM_139246	A6NMJ4|A8K584|Q6ZQZ6|Q8IYM3|Q8WY73|Q96ML6|Q96MU1	Missense_Mutation	SNP	ENST00000341170.4	hg19	CCDS6727.2	.	.	.	.	.	.	.	.	.	.	A	22.6	4.307103	0.81247	.	.	ENSG00000136925	ENST00000375173;ENST00000375172;ENST00000341170	T;T	0.33654	1.4;1.4	5.75	5.75	0.90469	Rhodanese-like (2);	0.000000	0.85682	D	0.000000	T	0.68696	0.3029	M	0.93197	3.39	0.80722	D	1	D	0.76494	0.999	D	0.66196	0.942	T	0.77686	-0.2495	10	0.66056	D	0.02	-12.5258	16.0276	0.80553	1.0:0.0:0.0:0.0	.	422	Q5T7W7	TSTD2_HUMAN	R	18;196;422	ENSP00000364316:C18R;ENSP00000342499:C422R	ENSP00000342499:C422R	C	-	1	0	TSTD2	99404859	1.000000	0.71417	1.000000	0.80357	0.853000	0.48598	8.850000	0.92190	2.326000	0.78906	0.533000	0.62120	TGT	.	.		0.517	TSTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053325.4	NM_139246		G	100365038	A	G	100365038	3	3	294	1	0	0	0	0	1	0	0	0	16690	188	7	2	290	2	TSTD2	9	100365038	Missense_Mutation	SNP	A	TCGA-G3-A7M9-01A-23D-A34Z-10	9618211	100365038	40848393	47	42819										
COL5A1	1289	hgsc.bcm.edu	37	chr9	137630354	137630354	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	gggcccgcctggcccagaagGccccgcggtgagtatccggc	16	16	0	2			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr9:137630354G>A	ENST00000371817.3	+	10	1838	c.1424G>A	c.(1423-1425)gGc>gAc	p.G475D		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	475	Interrupted collagenous region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		GGCCCAGAAGGCCCCGCGGTG	0.632																																					p.G475D		Atlas-SNP	.											.	COL5A1	323	.	0			c.G1424A						.						44	47	46					9																	137630354		2203	4300	6503	SO:0001583	missense	1289	exon10			CAGAAGGCCCCGC	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"Collagens"	2209	protein-coding gene	gene with protein product	"alpha 1 type V collagen"	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.1424G>A	chr9.hg19:g.137630354G>A	ENSP00000360882:p.Gly475Asp	37.0	0.0		40.0	26.0	NM_000093	Q15094|Q5SUX4	Missense_Mutation	SNP	ENST00000371817.3	hg19	CCDS6982.1	.	.	.	.	.	.	.	.	.	.	G	14.39	2.521900	0.44866	.	.	ENSG00000130635	ENST00000371817	D	0.99353	-5.77	4.69	4.69	0.59074	.	0.000000	0.85682	U	0.000000	D	0.99711	0.9889	H	0.99197	4.465	0.58432	D	0.999994	D	0.89917	1.0	D	0.87578	0.998	D	0.97007	0.9733	10	0.66056	D	0.02	.	16.3829	0.83481	0.0:0.0:1.0:0.0	.	475	P20908	CO5A1_HUMAN	D	475	ENSP00000360882:G475D	ENSP00000360882:G475D	G	+	2	0	COL5A1	136770175	1.000000	0.71417	0.999000	0.59377	0.201000	0.24016	5.554000	0.67294	2.166000	0.68216	0.491000	0.48974	GGC	.	.		0.632	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093		A	137630354	G	A	137630354	3	1	294	1	0	0	0	0	1	0	0	0	3698	1203	42	3	1462	3	COL5A1	9	137630354	Missense_Mutation	SNP	G	TCGA-G3-A7M9-01A-23D-A34Z-10	37265316	137630354	3583077	48	42820										
COBRA1	25920	hgsc.bcm.edu	37	chr9	140158810	140158810	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	ggccaggagcaggtgctgggGtgagggtcggctccacgagg	21	9	0	1			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr9:140158810G>T	ENST00000343053.4	+	6	1233		c.e6+1			NM_015456.3	NP_056271.2	Q8WX92	NELFB_HUMAN	negative elongation factor complex member B						gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|NELF complex (GO:0032021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											AGGTGCTGGGGTGAGGGTCGG	0.657																																					.		Atlas-SNP	.											.	.	.	.	0			c.896+1G>T						.						51	52	52					9																	140158810		2192	4296	6488	SO:0001630	splice_region_variant	25920	exon6			GCTGGGGTGAGGG	AF464935	CCDS7040.1	9q34	2013-01-31	2013-01-31	2013-01-31	ENSG00000188986	ENSG00000188986			24324	protein-coding gene	gene with protein product		611180	"cofactor of BRCA1"	COBRA1		11230166, 10574461, 17910036, 17659869	Standard	NM_015456		Approved	KIAA1182, NELF-B	uc004cmm.4	Q8WX92	OTTHUMG00000131778	ENST00000343053.4:c.896+1G>T	chr9.hg19:g.140158810G>T		22.0	0.0		30.0	19.0	NM_015456	A2BFA3|Q96EW5|Q9H9R4|Q9ULN8|Q9Y3W0	Splice_Site	SNP	ENST00000343053.4	hg19	CCDS7040.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.153040	0.78001	.	.	ENSG00000188986	ENST00000343053	.	.	.	4.41	4.41	0.53225	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.902	0.79384	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	COBRA1	139278631	1.000000	0.71417	1.000000	0.80357	0.859000	0.49053	9.611000	0.98342	2.134000	0.65973	0.313000	0.20887	.	.	.		0.657	NELFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254710.1	NM_015456	Intron	T	140158810	G	T	140158810	5	4	294	1	0	0	0	0	0	0	1	0	3657	1275	44	3	919	3	COBRA1	9	140158810	Splice_Site	SNP	G	TCGA-G3-A7M9-01A-23D-A34Z-10	2528456	140158810	1054621	49	42821										
DIP2C	22982	hgsc.bcm.edu	37	chr10	375432	375432	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	cagctccatcacggagtaggAgcaaaacgtgtctcggactt	11	11	2	0			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr10:375432A>G	ENST00000280886.6	-	30	3781	c.3694T>C	c.(3694-3696)Tcc>Ccc	p.S1232P		NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	1232						nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(8)|endometrium(6)|kidney(10)|large_intestine(13)|lung(26)|ovary(3)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	81		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		ACGGAGTAGGAGCAAAACGTG	0.597																																					p.S1232P		Atlas-SNP	.											.	DIP2C	195	.	0			c.T3694C						.						64	54	58					10																	375432		2203	4300	6503	SO:0001583	missense	22982	exon30			AGTAGGAGCAAAA	BC035216	CCDS7054.1	10p15.3	2006-01-13	2006-01-13	2006-01-13	ENSG00000151240	ENSG00000151240			29150	protein-coding gene	gene with protein product		611380	"KIAA0934"	KIAA0934			Standard	NM_014974		Approved		uc001ifp.3	Q9Y2E4	OTTHUMG00000017532	ENST00000280886.6:c.3694T>C	chr10.hg19:g.375432A>G	ENSP00000280886:p.Ser1232Pro	30.0	0.0		16.0	7.0	NM_014974	B4DPI5|Q5SS78	Missense_Mutation	SNP	ENST00000280886.6	hg19	CCDS7054.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	34|34	5.409065|5.409065	0.96072|0.96072	.|.	.|.	ENSG00000151240|ENSG00000151240	ENST00000434695|ENST00000280886;ENST00000535541;ENST00000381503	.|T	.|0.39997	.|1.05	5.84|5.84	5.84|5.84	0.93424|0.93424	.|AMP-dependent synthetase/ligase (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.44519|0.44519	0.1297|0.1297	L|L	0.33668|0.33668	1.02|1.02	0.80722|0.80722	D|D	1|1	.|P	.|0.41475	.|0.751	.|P	.|0.54060	.|0.741	T|T	0.21793|0.21793	-1.0235|-1.0235	5|10	.|0.02654	.|T	.|1	-29.0651|-29.0651	16.2141|16.2141	0.82191|0.82191	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|1232	.|Q9Y2E4	.|DIP2C_HUMAN	P|P	37|1232;157;81	.|ENSP00000280886:S1232P	.|ENSP00000280886:S1232P	L|S	-|-	2|1	0|0	DIP2C|DIP2C	365432|365432	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.958000|0.958000	0.62258|0.62258	9.339000|9.339000	0.96797|0.96797	2.230000|2.230000	0.72887|0.72887	0.528000|0.528000	0.53228|0.53228	CTC|TCC	.	.		0.597	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974		G	375432	A	G	375432	3	3	294	1	0	0	0	0	1	0	0	0	4531	304	11	2	1008	2	DIP2C	10	375432	Missense_Mutation	SNP	A	TCGA-G3-A7M9-01A-23D-A34Z-10		375432	135159315	50	42822										
TRDMT1	1787	hgsc.bcm.edu	37	chr10	17202313	17202313	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	gtgatacctacagaggttggAgataatagaaactcttggta	11	5	1	4			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr10:17202313A>G	ENST00000377799.3	-	6	497	c.450T>C	c.(448-450)tcT>tcC	p.S150S	TRDMT1_ENST00000452380.2_5'UTR|TRDMT1_ENST00000351358.4_Silent_p.S104S|TRDMT1_ENST00000457442.2_Silent_p.S69S|TRDMT1_ENST00000377766.5_Missense_Mutation_p.S79P|TRDMT1_ENST00000488990.1_Intron|TRDMT1_ENST00000412821.3_Silent_p.S126S|TRDMT1_ENST00000358282.7_3'UTR	NM_004412.5	NP_004403.1	O14717	TRDMT_HUMAN	tRNA aspartic acid methyltransferase 1	150	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				C-5 methylation of cytosine (GO:0090116)|response to amphetamine (GO:0001975)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|RNA binding (GO:0003723)|tRNA methyltransferase activity (GO:0008175)			breast(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(4)|ovary(1)|prostate(1)	18					Pentamidine(DB00738)	CAGAGGTTGGAGATAATAGAA	0.284																																					p.S150S		Atlas-SNP	.											.	TRDMT1	46	.	0			c.T450C						.						25	25	25					10																	17202313		2201	4289	6490	SO:0001819	synonymous_variant	1787	exon6			GGTTGGAGATAAT	AJ223333	CCDS7114.1	10p15.1	2006-10-23	2006-10-23	2006-10-23	ENSG00000107614	ENSG00000107614	2.1.1.37		2977	protein-coding gene	gene with protein product		602478	"DNA (cytosine-5-)-methyltransferase 2"	DNMT2		9425235, 9763678, 16424344	Standard	NM_004412		Approved	RNMT1	uc001iop.3	O14717	OTTHUMG00000017745	ENST00000377799.3:c.450T>C	chr10.hg19:g.17202313A>G		198.0	0.0		121.0	38.0	NM_004412	B0YJ02|B0YJ03|B0YJ07|B0YJ08|O43669|Q86WW6	Silent	SNP	ENST00000377799.3	hg19	CCDS7114.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.63|15.63	2.889911|2.889911	0.52014|0.52014	.|.	.|.	ENSG00000107614|ENSG00000107614	ENST00000436968|ENST00000377766;ENST00000313936	.|T	.|0.44482	.|0.92	5.79|5.79	3.29|3.29	0.37713|0.37713	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.48892|0.48892	0.1525|0.1525	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.49051|0.49051	-0.8979|-0.8979	4|7	.|0.72032	.|D	.|0.01	-23.1687|-23.1687	7.4582|7.4582	0.27278|0.27278	0.7095:0.1486:0.0:0.142|0.7095:0.1486:0.0:0.142	.|.	.|.	.|.	.|.	P|P	58|79;84	.|ENSP00000324263:S84P	.|ENSP00000324263:S84P	L|S	-|-	2|1	0|0	TRDMT1|TRDMT1	17242319|17242319	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	2.014000|2.014000	0.40951|0.40951	0.977000|0.977000	0.38444|0.38444	0.455000|0.455000	0.32223|0.32223	CTC|TCC	.	.		0.284	TRDMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047024.3	NM_004412		G	17202313	A	G	17202313	2	3	294	1	0	0	0	0	0	0	0	1	16482	291	11	2		2	TRDMT1	10	17202313	Silent	SNP	A	TCGA-G3-A7M9-01A-23D-A34Z-10	16826881	17202313	118332434	51	42823										
MYO3A	53904	hgsc.bcm.edu	37	chr10	26462717	26462717	+	Frame_Shift_Del	DEL	C	C	-													0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	tttcaaacctgaagaggaaaCcaccaatgctgtggagagta							TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr10:26462717delC	ENST00000265944.5	+	30	3690	c.3524delC	c.(3523-3525)accfs	p.T1176fs	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	1176					ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						GAAGAGGAAACCACCAATGCT	0.373																																					p.T1175fs		Atlas-Indel,Pindel	.											.	MYO3A	371	.	0			c.3523delA						.						64	62	63					10																	26462717		2203	4300	6503	SO:0001589	frameshift_variant	53904	exon30			.	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.3524delC	chr10.hg19:g.26462717delC	ENSP00000265944:p.Thr1176fs	73.0	0.0		59.0	27.0	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Frame_Shift_Del	DEL	ENST00000265944.5	hg19	CCDS7148.1																																																																																			.	.		0.373	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		-	26462717	C	-	26462717	7	5	294	1	0	1	0	1	0	0	0	0	10085	507	18	0	3634	0	MYO3A	10	26462717	Frame_Shift_Del	DEL	C	TCGA-G3-A7M9-01A-23D-A34Z-10	9260404	26462717	109072030	52	42824										
FAM13C	220965	hgsc.bcm.edu	37	chr10	61028335	61028335	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	ggtatttcttttcttgttcaAatttttcttcaaatttccga	4	7	5	0			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr10:61028335A>G	ENST00000373868.2	-	8	1007	c.920T>C	c.(919-921)tTt>tCt	p.F307S	FAM13C_ENST00000468840.2_Missense_Mutation_p.F224S|FAM13C_ENST00000277705.6_Missense_Mutation_p.F328S|FAM13C_ENST00000419214.2_Missense_Mutation_p.F307S|FAM13C_ENST00000435852.2_Missense_Mutation_p.F307S|FAM13C_ENST00000442566.3_Missense_Mutation_p.F328S|FAM13C_ENST00000373867.3_Missense_Mutation_p.F224S|FAM13C_ENST00000422313.2_Missense_Mutation_p.F307S	NM_198215.3	NP_937858.2	Q8NE31	FA13C_HUMAN	family with sequence similarity 13, member C	307										NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(19)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						TTCTTGTTCAAATTTTTCTTC	0.498																																					p.F307S		Atlas-SNP	.											.	FAM13C	124	.	0			c.T920C						.						89	89	89					10																	61028335		2203	4300	6503	SO:0001583	missense	220965	exon8			TGTTCAAATTTTT	U79304	CCDS31207.1, CCDS44406.1, CCDS7255.1, CCDS53538.1	10q21	2009-09-15	2009-01-20	2009-01-20	ENSG00000148541	ENSG00000148541			19371	protein-coding gene	gene with protein product			"family with sequence similarity 13, member C1"	FAM13C1			Standard	NM_001001971		Approved		uc001jkn.3	Q8NE31	OTTHUMG00000018277	ENST00000373868.2:c.920T>C	chr10.hg19:g.61028335A>G	ENSP00000362975:p.Phe307Ser	92.0	0.0		66.0	13.0	NM_198215	B7ZB77|Q5T631|Q6P2M3|Q99787	Missense_Mutation	SNP	ENST00000373868.2	hg19	CCDS7255.1	.	.	.	.	.	.	.	.	.	.	A	29.2	4.983183	0.93044	.	.	ENSG00000148541	ENST00000373867;ENST00000373868;ENST00000442566;ENST00000277705;ENST00000419214;ENST00000468840;ENST00000435852;ENST00000422313;ENST00000468696	T;T;T;T;T;T;T;T;T	0.76448	-1.02;-1.02;-1.02;-1.02;-0.26;-1.02;-1.02;-1.02;-1.02	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.89174	0.6640	M	0.83483	2.645	0.50813	D	0.999891	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.999;0.998;0.999	D	0.90406	0.4406	10	0.87932	D	0	-15.8349	16.8222	0.85835	1.0:0.0:0.0:0.0	.	307;224;307;307;307	B7Z2K3;B7ZB77;Q8NE31-2;Q8NE31-3;Q8NE31	.;.;.;.;FA13C_HUMAN	S	224;307;328;328;307;224;307;307;85	ENSP00000362974:F224S;ENSP00000362975:F307S;ENSP00000395661:F328S;ENSP00000277705:F328S;ENSP00000391993:F307S;ENSP00000423896:F224S;ENSP00000392302:F307S;ENSP00000400241:F307S;ENSP00000445068:F85S	ENSP00000277705:F328S	F	-	2	0	FAM13C	60698341	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.207000	0.89746	2.371000	0.80710	0.533000	0.62120	TTT	.	.		0.498	FAM13C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048162.2			G	61028335	A	G	61028335	3	3	294	1	0	0	0	0	1	0	0	0	5459	14	1	2	865	2	FAM13C	10	61028335	Missense_Mutation	SNP	A	TCGA-G3-A7M9-01A-23D-A34Z-10	34565618	61028335	74506412	53	42825										
SORCS1	114815	hgsc.bcm.edu	37	chr10	108459041	108459041	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	acattctccaaggccagggtGaagtagacaccacgtgtgtc	11	11	1	2			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr10:108459041G>A	ENST00000263054.6	-	9	1351	c.1344C>T	c.(1342-1344)ttC>ttT	p.F448F	SORCS1_ENST00000369698.1_5'UTR|SORCS1_ENST00000344440.6_Silent_p.F448F	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	448					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		AGGCCAGGGTGAAGTAGACAC	0.517																																					p.F448F		Atlas-SNP	.											.	SORCS1	534	.	0			c.C1344T						.						263	197	219					10																	108459041		2203	4300	6503	SO:0001819	synonymous_variant	114815	exon9			CAGGGTGAAGTAG	AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.1344C>T	chr10.hg19:g.108459041G>A		92.0	0.0		51.0	19.0	NM_001206572	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Silent	SNP	ENST00000263054.6	hg19	CCDS7559.1																																																																																			.	.		0.517	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918		A	108459041	G	A	108459041	2	1	294	1	0	0	0	0	0	0	0	1	14945	1281	45	3		3	SORCS1	10	108459041	Silent	SNP	G	TCGA-G3-A7M9-01A-23D-A34Z-10	47430706	108459041	27075706	54	42826										
OR4C46	119749	hgsc.bcm.edu	37	chr11	51515655	51515655	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	tgaccactatgtggccatctGcaagcccttgcactatatga	8	12	1	2			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr11:51515655G>T	ENST00000328188.1	+	1	374	c.374G>T	c.(373-375)tGc>tTc	p.C125F		NM_001004703.1	NP_001004703.1	A6NHA9	O4C46_HUMAN	olfactory receptor, family 4, subfamily C, member 46	125						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(5)|large_intestine(5)|lung(31)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	48						GTGGCCATCTGCAAGCCCTTG	0.483																																					p.C125F		Atlas-SNP	.											.	OR4C46	96	.	0			c.G374T						.						159	157	157					11																	51515655		2201	4296	6497	SO:0001583	missense	119749	exon1			CCATCTGCAAGCC		CCDS73288.1	11p11.12	2012-08-09			ENSG00000185926	ENSG00000185926		"GPCR / Class A : Olfactory receptors"	31271	protein-coding gene	gene with protein product		614273					Standard	NM_001004703		Approved		uc010ric.2	A6NHA9	OTTHUMG00000166705	ENST00000328188.1:c.374G>T	chr11.hg19:g.51515655G>T	ENSP00000329056:p.Cys125Phe	100.0	0.0		70.0	38.0	NM_001004703		Missense_Mutation	SNP	ENST00000328188.1	hg19	CCDS31498.1	.	.	.	.	.	.	.	.	.	.	.	10.61	1.398440	0.25205	.	.	ENSG00000185926	ENST00000328188	T	0.34472	1.36	2.63	1.69	0.24217	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49916	D	0.000127	T	0.68476	0.3005	H	0.98901	4.365	0.35436	D	0.79443	D	0.76494	0.999	D	0.63488	0.915	T	0.76677	-0.2871	10	0.87932	D	0	.	7.4418	0.27187	0.1419:0.0:0.8581:0.0	.	125	A6NHA9	O4C46_HUMAN	F	125	ENSP00000329056:C125F	ENSP00000329056:C125F	C	+	2	0	OR4C46	51372231	1.000000	0.71417	0.974000	0.42286	0.038000	0.13279	7.151000	0.77411	0.463000	0.27118	0.134000	0.15878	TGC	.	.		0.483	OR4C46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391155.1	NM_001004703		T	51515655	G	T	51515655	3	4	294	1	0	0	0	0	1	0	0	0	11060	1319	46	3	376	3	OR4C46	11	51515655	Missense_Mutation	SNP	G	TCGA-G3-A7M9-01A-23D-A34Z-10		51515655	83490861	55	42827										
TNKS1BP1	85456	hgsc.bcm.edu	37	chr11	57080487	57080489	+	In_Frame_Del	DEL	CCC	CCC	-													0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	tgggaattgaggttgactctCcccatcgcccttctgggtga					rs564910885	byFrequency	TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	CCC	CCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr11:57080487_57080489delCCC	ENST00000532437.1	-	4	1984_1986	c.1673_1675delGGG	c.(1672-1677)ggggag>gag	p.G558del	TNKS1BP1_ENST00000358252.3_In_Frame_Del_p.G558del|TNKS1BP1_ENST00000530920.1_5'Flank			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	558	Acidic.|Pro-rich.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)			breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				GGTTGACTCTCCCCATCGCCCTT	0.591																																					p.558_559del		Atlas-Indel,Pindel	.											.	TNKS1BP1	148	.	0			c.1674_1676del						.																																			SO:0001651	inframe_deletion	85456	exon5			.	AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.1673_1675delGGG	chr11.hg19:g.57080487_57080489delCCC	ENSP00000437271:p.Gly558del	68.0	0.0		43.0	15.0	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	In_Frame_Del	DEL	ENST00000532437.1	hg19	CCDS7951.1																																																																																			.	.		0.591	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396		-	57080489	CCC	-	57080487	7	5	294	1	0	1	0	1	0	0	0	0	16335	864	30	0	3542	0	TNKS1BP1	11	57080487	In_Frame_Del	DEL	CCC	TCGA-G3-A7M9-01A-23D-A34Z-10	5564832	57080487	77926029	56	42828										
SLCO1C1	53919	hgsc.bcm.edu	37	chr12	20893142	20893145	+	Frame_Shift_Del	DEL	GGAA	GGAA	-													0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	tttacaactgcacttgtgtgGgaattgcagcttctaaatcc					rs558577357		TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	GGAA	GGAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr12:20893142_20893145delGGAA	ENST00000266509.2	+	12	1941_1944	c.1573_1576delGGAA	c.(1573-1578)ggaattfs	p.GI525fs	SLCO1C1_ENST00000381552.1_Frame_Shift_Del_p.GI525fs|SLCO1C1_ENST00000545102.1_Frame_Shift_Del_p.GI407fs|SLCO1C1_ENST00000545604.1_Frame_Shift_Del_p.GI525fs|SLCO1C1_ENST00000540354.1_Frame_Shift_Del_p.GI476fs	NM_017435.4	NP_059131.1	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family, member 1C1	525	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			NS(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	60	Esophageal squamous(101;0.149)				Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Meclofenamic acid(DB00939)|Methotrexate(DB00563)|Ouabain(DB01092)|Phenytoin(DB00252)|Probenecid(DB01032)	CACTTGTGTGGGAATTGCAGCTTC	0.343																																					p.524_525del		Atlas-Indel,Pindel	.											.	SLCO1C1	216	.	0			c.1572_1575del						.																																			SO:0001589	frameshift_variant	53919	exon12			.	AF260704	CCDS8683.1, CCDS53757.1, CCDS53758.1, CCDS53759.1	12p12.2	2013-05-22	2003-11-25	2003-11-26	ENSG00000139155	ENSG00000139155		"Solute carriers"	13819	protein-coding gene	gene with protein product		613389	"solute carrier family 21 (organic anion transporter), member 14"	SLC21A14			Standard	NM_017435		Approved	OATP-F, OATP1C1, OATP1	uc010sii.2	Q9NYB5	OTTHUMG00000168966	ENST00000266509.2:c.1573_1576delGGAA	chr12.hg19:g.20893142_20893145delGGAA	ENSP00000266509:p.Gly525fs	99.0	0.0		77.0	28.0	NM_017435	B7Z251|B7Z3Q3|B7Z8P1|F5GZD6|Q5JPA4	Frame_Shift_Del	DEL	ENST00000266509.2	hg19	CCDS8683.1																																																																																			.	.		0.343	SLCO1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401765.1	NM_017435		-	20893145	GGAA	-	20893142	7	5	294	1	0	1	0	1	0	0	0	0	14740	1233	43	0	1615	0	SLCO1C1	12	20893142	Frame_Shift_Del	DEL	GGAA	TCGA-G3-A7M9-01A-23D-A34Z-10		20893142	112958753	57	42829										
PPFIBP1	8496	hgsc.bcm.edu	37	chr12	27787982	27787982	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	atggaaacagatgagaaagaAggcttgagatgccagatccc	12	7	0	5			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr12:27787982A>T	ENST00000318304.8	+	4	487	c.204A>T	c.(202-204)gaA>gaT	p.E68D	PPFIBP1_ENST00000545334.1_Missense_Mutation_p.E68D|PPFIBP1_ENST00000537927.1_Intron|PPFIBP1_ENST00000542629.1_Missense_Mutation_p.E68D|PPFIBP1_ENST00000228425.6_Missense_Mutation_p.E68D|PPFIBP1_ENST00000535047.1_Missense_Mutation_p.E68D	NM_001198916.1|NM_177444.2	NP_001185845.1|NP_803193	Q86W92	LIPB1_HUMAN	PTPRF interacting protein, binding protein 1 (liprin beta 1)	68					cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)			PPFIBP1/ALK(3)	central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(13)|prostate(2)|skin(1)	32	Lung SC(9;0.0873)					ATGAGAAAGAAGGCTTGAGAT	0.463																																					p.E68D		Atlas-SNP	.											.	PPFIBP1	153	.	0			c.A204T						.						102	104	104					12																	27787982		2203	4300	6503	SO:0001583	missense	8496	exon4			GAAAGAAGGCTTG	AF034802	CCDS8713.1, CCDS55812.1, CCDS55813.1, CCDS55814.1	12p12.1	2013-01-10						"Sterile alpha motif (SAM) domain containing"	9249	protein-coding gene	gene with protein product		603141				9624153, 11836260	Standard	NM_003622		Approved	L2, hSGT2, hSgt2p, SGT2	uc001ric.2	Q86W92		ENST00000318304.8:c.204A>T	chr12.hg19:g.27787982A>T	ENSP00000314724:p.Glu68Asp	78.0	0.0		91.0	33.0	NM_003622	O75336|Q86X70|Q9NY03|Q9ULJ0	Missense_Mutation	SNP	ENST00000318304.8	hg19	CCDS55812.1	.	.	.	.	.	.	.	.	.	.	A	10.05	1.245443	0.22796	.	.	ENSG00000110841	ENST00000543820;ENST00000545381;ENST00000545334;ENST00000318304;ENST00000535047;ENST00000542629;ENST00000228425;ENST00000535575;ENST00000542187	T;T;T;T;T	0.14766	2.48;2.48;2.48;2.48;2.48	4.53	0.91	0.19337	.	0.000000	0.33005	U	0.005396	T	0.05686	0.0149	N	0.11064	0.09	0.35587	D	0.80678	B;B;B;B;B	0.21452	0.002;0.056;0.004;0.003;0.039	B;B;B;B;B	0.23574	0.005;0.027;0.012;0.006;0.047	T	0.38607	-0.9653	10	0.19147	T	0.46	-22.965	5.2389	0.15462	0.5106:0.1516:0.3378:0.0	.	68;68;68;68;68	Q86W92;Q86W92-2;Q86W92-4;Q86W92-5;F5H0E0	LIPB1_HUMAN;.;.;.;.	D	68;68;68;68;68;68;68;68;81	ENSP00000445822:E68D;ENSP00000314724:E68D;ENSP00000444046:E68D;ENSP00000443442:E68D;ENSP00000228425:E68D	ENSP00000228425:E68D	E	+	3	2	PPFIBP1	27679249	0.972000	0.33761	0.999000	0.59377	0.856000	0.48823	0.226000	0.17776	0.006000	0.14734	0.254000	0.18369	GAA	.	.		0.463	PPFIBP1-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402877.1	NM_003622		T	27787982	A	T	27787982	3	4	294	1	0	0	0	0	1	0	0	0	12322	69	3	4	210	4	PPFIBP1	12	27787982	Missense_Mutation	SNP	A	TCGA-G3-A7M9-01A-23D-A34Z-10	6894840	27787982	106063913	58	42830										
IPO8	10526	hgsc.bcm.edu	37	chr12	30816574	30816574	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	ttcaaagaactaaatgcatgAagtacccagcaagactgtat	7	8	1	3			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr12:30816574A>C	ENST00000256079.4	-	14	1781	c.1443T>G	c.(1441-1443)ctT>ctG	p.L481L	IPO8_ENST00000544829.1_Silent_p.L276L	NM_006390.3	NP_006381.2	O15397	IPO8_HUMAN	importin 8	481					intracellular protein transport (GO:0006886)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	Ran GTPase binding (GO:0008536)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(16)|liver(1)|lung(22)|prostate(2)|skin(2)|urinary_tract(2)	52	all_lung(12;6.66e-10)|Lung NSC(12;4.84e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					TAAATGCATGAAGTACCCAGC	0.338																																					p.L481L		Atlas-SNP	.											.	IPO8	105	.	0			c.T1443G						.						76	73	74					12																	30816574		2203	4300	6503	SO:0001819	synonymous_variant	10526	exon14			TGCATGAAGTACC	U77494	CCDS8719.1, CCDS53773.1	12p11.21	2011-05-23	2003-03-11	2003-03-14	ENSG00000133704	ENSG00000133704		"Importins"	9853	protein-coding gene	gene with protein product		605600	"RAN binding protein 8"	RANBP8		9214382	Standard	NM_006390		Approved	IMP8	uc001rjd.3	O15397	OTTHUMG00000169172	ENST00000256079.4:c.1443T>G	chr12.hg19:g.30816574A>C		22.0	0.0		28.0	13.0	NM_006390	B7Z7M3	Silent	SNP	ENST00000256079.4	hg19	CCDS8719.1																																																																																			.	.		0.338	IPO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402700.2	NM_006390		C	30816574	A	C	30816574	2	2	294	1	0	0	0	0	0	0	0	1	7807	233	9	5		5	IPO8	12	30816574	Silent	SNP	A	TCGA-G3-A7M9-01A-23D-A34Z-10	3028592	30816574	103035321	59	42831										
XPOT	11260	hgsc.bcm.edu	37	chr12	64814173	64814173	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	gtcatatgtcaatagaagttCtacgggaagaagcatgtgac	11	6	3	3			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr12:64814173C>A	ENST00000332707.5	+	8	1244	c.715C>A	c.(715-717)Cta>Ata	p.L239I		NM_007235.4	NP_009166.2	O43592	XPOT_HUMAN	exportin, tRNA	239	Necessary for interaction with Ran, nuclear localization and nuclear import.				intracellular protein transport (GO:0006886)|tRNA export from nucleus (GO:0006409)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(7)|lung(12)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				GBM - Glioblastoma multiforme(28;0.0404)		AATAGAAGTTCTACGGGAAGA	0.318																																					p.L239I		Atlas-SNP	.											.	XPOT	105	.	0			c.C715A						.						69	72	71					12																	64814173		2203	4298	6501	SO:0001583	missense	11260	exon8			GAAGTTCTACGGG	AF039022	CCDS31852.1	12q14.1	2012-10-17	2012-10-17		ENSG00000184575	ENSG00000184575		"Exportins"	12826	protein-coding gene	gene with protein product		603180	"exportin, tRNA (nuclear export receptor for tRNAs)"			9660920, 9512417	Standard	NM_007235		Approved	XPO3	uc001ssb.3	O43592	OTTHUMG00000168794	ENST00000332707.5:c.715C>A	chr12.hg19:g.64814173C>A	ENSP00000327821:p.Leu239Ile	76.0	0.0		72.0	25.0	NM_007235	A6NLH1|O43784|Q8WUG2|Q9BVS7	Missense_Mutation	SNP	ENST00000332707.5	hg19	CCDS31852.1	.	.	.	.	.	.	.	.	.	.	C	33	5.226256	0.95173	.	.	ENSG00000184575	ENST00000332707	T	0.68765	-0.35	4.89	4.89	0.63831	Exportin-1/Importin-beta-like (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.135823	0.51477	D	0.000099	T	0.78641	0.4315	M	0.64404	1.975	0.80722	D	1	D	0.61080	0.989	P	0.62740	0.906	T	0.77624	-0.2518	9	.	.	.	.	18.9398	0.92601	0.0:1.0:0.0:0.0	.	239	O43592	XPOT_HUMAN	I	239	ENSP00000327821:L239I	.	L	+	1	2	XPOT	63100440	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.657000	0.83745	2.649000	0.89929	0.655000	0.94253	CTA	.	.		0.318	XPOT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401122.1	NM_007235		A	64814173	C	A	64814173	3	1	294	1	0	0	0	0	1	0	0	0	17465	912	32	3	741	3	XPOT	12	64814173	Missense_Mutation	SNP	C	TCGA-G3-A7M9-01A-23D-A34Z-10	33997599	64814173	69037722	60	42832										
SLC6A15	55117	hgsc.bcm.edu	37	chr12	85277689	85277689	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	gccaagcaaaccatgacccaGgcagccaacaagcagatggt	10	13	0	2			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr12:85277689G>T	ENST00000266682.5	-	5	1246	c.705C>A	c.(703-705)gcC>gcA	p.A235A	SLC6A15_ENST00000450363.3_Silent_p.A235A|SLC6A15_ENST00000552192.1_Silent_p.A128A|SLC6A15_ENST00000551388.1_Intron	NM_182767.5	NP_877499.1	Q9H2J7	S6A15_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 15	235					amino acid transport (GO:0006865)|ion transport (GO:0006811)|leucine transport (GO:0015820)|neurotransmitter transport (GO:0006836)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)|proline:sodium symporter activity (GO:0005298)			kidney(1)|large_intestine(18)|lung(15)|ovary(1)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	44						CCATGACCCAGGCAGCCAACA	0.443																																					p.A235A		Atlas-SNP	.											.	SLC6A15	159	.	0			c.C705A						.						82	73	76					12																	85277689		2203	4300	6503	SO:0001819	synonymous_variant	55117	exon5			GACCCAGGCAGCC	AF265577	CCDS9026.1, CCDS9027.1, CCDS53816.1	12q21.31	2013-07-15	2008-09-02		ENSG00000072041	ENSG00000072041		"Solute carriers"	13621	protein-coding gene	gene with protein product	"homolog of rat orphan transporter v7-3", "sodium/chloride dependent neurotransmitter transporter Homo sapiens orphan neurotransmitter transporter NTT7"	607971	"solute carrier family 6 (neurotransmitter transporter), member 15"			10471414, 11112352, 16185194	Standard	NM_182767		Approved	hv7-3, NTT73, FLJ10316, V7-3, SBAT1	uc001szv.4	Q9H2J7	OTTHUMG00000169742	ENST00000266682.5:c.705C>A	chr12.hg19:g.85277689G>T		60.0	0.0		48.0	21.0	NM_018057	A8K592|B7Z2P7|E7ESJ5|Q9H9F5	Silent	SNP	ENST00000266682.5	hg19	CCDS9026.1																																																																																			.	.		0.443	SLC6A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405678.1	NM_018057, NM_182767		T	85277689	G	T	85277689	2	4	294	1	0	0	0	0	0	0	0	1	14693	987	35	3		3	SLC6A15	12	85277689	Silent	SNP	G	TCGA-G3-A7M9-01A-23D-A34Z-10	20463516	85277689	48574206	61	42833										
ACTR6	64431	hgsc.bcm.edu	37	chr12	100594687	100594687	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	ccaaaatcggttacagccatGaaaatgtgtcgtaagtactt	8	8	0	1			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr12:100594687G>A	ENST00000188312.2	+	1	823	c.58G>A	c.(58-60)Gaa>Aaa	p.E20K	ACTR6_ENST00000550813.1_3'UTR|ACTR6_ENST00000552376.1_Missense_Mutation_p.E20K|ACTR6_ENST00000551617.1_5'UTR|ACTR6_ENST00000546902.1_5'UTR	NM_022496.4	NP_071941.1	Q9GZN1	ARP6_HUMAN	ARP6 actin-related protein 6 homolog (yeast)	20						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|skin(1)	14						TTACAGCCATGAAAATGTGTC	0.463																																					p.E20K		Atlas-SNP	.											.	ACTR6	29	.	0			c.G58A						.						238	193	208					12																	100594687		2203	4300	6503	SO:0001583	missense	64431	exon1			AGCCATGAAAATG	AF212251	CCDS9074.1	12q23.1	2012-07-09			ENSG00000075089	ENSG00000075089			24025	protein-coding gene	gene with protein product						11368909	Standard	NM_022496		Approved	ARP6, FLJ13433	uc001thb.2	Q9GZN1	OTTHUMG00000170245	ENST00000188312.2:c.58G>A	chr12.hg19:g.100594687G>A	ENSP00000188312:p.Glu20Lys	43.0	0.0		43.0	11.0	NM_022496	B3KW37|B4DLG9|Q53GH2|Q9BY39|Q9H8H6	Missense_Mutation	SNP	ENST00000188312.2	hg19	CCDS9074.1	.	.	.	.	.	.	.	.	.	.	G	15.10	2.732152	0.48939	.	.	ENSG00000075089	ENST00000188312;ENST00000552376	D;D	0.96104	-3.91;-3.91	5.5	4.6	0.57074	.	0.251983	0.45126	D	0.000385	D	0.95121	0.8419	M	0.79011	2.435	0.80722	D	1	P;B;B	0.35242	0.492;0.098;0.119	B;B;B	0.38225	0.268;0.107;0.171	D	0.95250	0.8359	10	0.87932	D	0	.	14.4601	0.67442	0.0722:0.0:0.9278:0.0	.	20;20;20	B4DLG9;F8W057;Q9GZN1	.;.;ARP6_HUMAN	K	20	ENSP00000188312:E20K;ENSP00000447237:E20K	ENSP00000188312:E20K	E	+	1	0	ACTR6	99118818	1.000000	0.71417	0.996000	0.52242	0.301000	0.27625	4.773000	0.62331	2.854000	0.98071	0.655000	0.94253	GAA	.	.		0.463	ACTR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408159.1	NM_022496		A	100594687	G	A	100594687	3	1	294	1	0	0	0	0	1	0	0	0	216	1291	45	3	60	3	ACTR6	12	100594687	Missense_Mutation	SNP	G	TCGA-G3-A7M9-01A-23D-A34Z-10	15316998	100594687	33257208	62	42834										
SH2B3	10019	hgsc.bcm.edu	37	chr12	111885820	111885820	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	ggtcctcttccctttctcccTtcctcactgggattcagagt	7	15	4	1	rs537932422	byFrequency	TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr12:111885820T>C	ENST00000341259.2	+	8	1799	c.1442T>C	c.(1441-1443)cTt>cCt	p.L481P	SH2B3_ENST00000538307.1_Missense_Mutation_p.L279P	NM_005475.2	NP_005466.1	Q9UQQ2	SH2B3_HUMAN	SH2B adaptor protein 3	481					blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|embryonic hemopoiesis (GO:0035162)|intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)	phosphate ion binding (GO:0042301)|signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	10					Pazopanib(DB06589)	CCTTTCTCCCTTCCTCACTGG	0.567																																					p.L481P		Atlas-SNP	.											.	SH2B3	62	.	0			c.T1442C						.						236	195	209					12																	111885820		2203	4300	6503	SO:0001583	missense	10019	exon8			TCTCCCTTCCTCA	AF055581	CCDS9153.1	12q24.12	2014-09-17				ENSG00000111252		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	29605	protein-coding gene	gene with protein product	"lymphocyte adaptor protein"	605093				10799879	Standard	NM_005475		Approved	LNK, IDDM20	uc001tse.3	Q9UQQ2		ENST00000341259.2:c.1442T>C	chr12.hg19:g.111885820T>C	ENSP00000345492:p.Leu481Pro	47.0	0.0		32.0	9.0	NM_005475	B9EGG5|O95184	Missense_Mutation	SNP	ENST00000341259.2	hg19	CCDS9153.1	.	.	.	.	.	.	.	.	.	.	T	9.555	1.116826	0.20795	.	.	ENSG00000111252	ENST00000341259;ENST00000551001;ENST00000538307	T;T	0.35421	1.32;1.31	4.96	4.96	0.65561	.	0.312186	0.30347	N	0.009823	T	0.21145	0.0509	N	0.14661	0.345	0.80722	D	1	B;B;B	0.29612	0.023;0.017;0.251	B;B;B	0.21917	0.032;0.009;0.037	T	0.06826	-1.0805	10	0.42905	T	0.14	.	11.5822	0.50898	0.0:0.0:0.1491:0.8509	.	279;345;481	F5GYM4;Q59H48;Q9UQQ2	.;.;SH2B3_HUMAN	P	481;291;279	ENSP00000345492:L481P;ENSP00000440597:L279P	ENSP00000345492:L481P	L	+	2	0	SH2B3	110370203	0.886000	0.30341	0.953000	0.39169	0.567000	0.35839	3.418000	0.52721	2.002000	0.58637	0.379000	0.24179	CTT	.	.		0.567	SH2B3-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000404779.1	NM_005475		C	111885820	T	C	111885820	3	2	294	1	0	0	0	0	1	0	0	0	14244	1609	56	2	1468	2	SH2B3	12	111885820	Missense_Mutation	SNP	T	TCGA-G3-A7M9-01A-23D-A34Z-10	11291133	111885820	21966075	63	42835										
TMEM132B	114795	hgsc.bcm.edu	37	chr12	125834213	125834213	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	ttatcaatgccagctatggcCcattttcagtggagaagata	9	8	2	2			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr12:125834213C>T	ENST00000299308.3	+	2	276	c.268C>T	c.(268-270)Cca>Tca	p.P90S	TMEM132B_ENST00000418253.2_3'UTR	NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	90						integral component of membrane (GO:0016021)				NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		CAGCTATGGCCCATTTTCAGT	0.498																																					p.P90S		Atlas-SNP	.											.	TMEM132B	207	.	0			c.C268T						.						107	105	106					12																	125834213		1872	4105	5977	SO:0001583	missense	114795	exon2			TATGGCCCATTTT	AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.268C>T	chr12.hg19:g.125834213C>T	ENSP00000299308:p.Pro90Ser	51.0	0.0		67.0	20.0	NM_052907	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Missense_Mutation	SNP	ENST00000299308.3	hg19	CCDS41859.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.288066	0.80803	.	.	ENSG00000139364	ENST00000299308	T	0.11495	2.77	5.41	5.41	0.78517	.	.	.	.	.	T	0.26122	0.0637	L	0.39245	1.2	0.80722	D	1	D	0.89917	1.0	D	0.68621	0.959	T	0.00422	-1.1749	9	0.49607	T	0.09	.	19.1923	0.93672	0.0:1.0:0.0:0.0	.	90	Q14DG7	T132B_HUMAN	S	90	ENSP00000299308:P90S	ENSP00000299308:P90S	P	+	1	0	TMEM132B	124400166	0.998000	0.40836	0.975000	0.42487	0.910000	0.53928	3.491000	0.53252	2.514000	0.84764	0.591000	0.81541	CCA	.	.		0.498	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907		T	125834213	C	T	125834213	3	4	294	1	0	0	0	0	1	0	0	0	16061	623	22	3	274	3	TMEM132B	12	125834213	Missense_Mutation	SNP	C	TCGA-G3-A7M9-01A-23D-A34Z-10	13948393	125834213	8017682	64	42836										
FREM2	341640	hgsc.bcm.edu	37	chr13	39263789	39263789	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	tgactgacaacccctcagtcGtggtgacccattttacccaa	7	14	1	3	rs7327915	byFrequency	TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr13:39263789G>T	ENST00000280481.7	+	1	2524	c.2308G>T	c.(2308-2310)Gtg>Ttg	p.V770L		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	770			V -> M (in dbSNP:rs7327915).		cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		CCCCTCAGTCGTGGTGACCCA	0.537																																					p.V770L		Atlas-SNP	.											.	FREM2	385	.	0			c.G2308T						.						84	87	86					13																	39263789		2203	4300	6503	SO:0001583	missense	341640	exon1			TCAGTCGTGGTGA	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.2308G>T	chr13.hg19:g.39263789G>T	ENSP00000280481:p.Val770Leu	52.0	0.0		35.0	18.0	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	hg19	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	G	7.127	0.579210	0.13686	.	.	ENSG00000150893	ENST00000280481	T	0.41400	1.0	5.8	1.81	0.25067	.	0.599178	0.17790	N	0.161915	T	0.28433	0.0703	L	0.34521	1.04	0.80722	P	0.0	B	0.10296	0.003	B	0.09377	0.004	T	0.25117	-1.0141	9	0.28530	T	0.3	.	8.671	0.34149	0.1301:0.2312:0.6386:0.0	.	770	Q5SZK8	FREM2_HUMAN	L	770	ENSP00000280481:V770L	ENSP00000280481:V770L	V	+	1	0	FREM2	38161789	0.018000	0.18449	0.310000	0.25168	0.901000	0.52897	1.470000	0.35354	0.330000	0.23485	0.655000	0.94253	GTG	.	G|0.960;A|0.040		0.537	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		T	39263789	G	T	39263789	3	4	294	1	0	0	0	0	1	0	0	0	6053	1145	40	1	2310	1	FREM2	13	39263789	Missense_Mutation	SNP	G	TCGA-G3-A7M9-01A-23D-A34Z-10		39263789	75906089	65	42837										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64593080	64593089	+	Frame_Shift_Del	DEL	TAAAAAATTG	TAAAAAATTG	-													0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	gaagcatatatcaatttggaTaaaaaattgtttgaactatt							TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	TAAAAAATTG	TAAAAAATTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr14:64593080_64593089delTAAAAAATTG	ENST00000344113.4	+	72	13802_13811	c.13590_13599delTAAAAAATTG	c.(13588-13599)gataaaaaattgfs	p.DKKL4530fs	SYNE2_ENST00000358025.3_Frame_Shift_Del_p.DKKL4530fs|SYNE2_ENST00000554584.1_Frame_Shift_Del_p.DKKL4481fs|SYNE2_ENST00000394768.2_Frame_Shift_Del_p.DKKL915fs|SYNE2_ENST00000555002.1_Frame_Shift_Del_p.DKKL1164fs|SYNE2_ENST00000357395.3_Frame_Shift_Del_p.DKKL915fs|ESR2_ENST00000542956.1_Intron	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	4530					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		TCAATTTGGATAAAAAATTGTTTGAACTAT	0.41																																					p.4530_4533del		Atlas-Indel,Pindel	.											.	SYNE2	577	.	0			c.13589_13598del						.																																			SO:0001589	frameshift_variant	23224	exon72			.	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.13590_13599delTAAAAAATTG	chr14.hg19:g.64593080_64593089delTAAAAAATTG	ENSP00000341781:p.Asp4530fs	65.0	0.0		58.0	18.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Frame_Shift_Del	DEL	ENST00000344113.4	hg19	CCDS41963.1																																																																																			.	.		0.41	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		-	64593089	TAAAAAATTG	-	64593080	7	5	294	1	0	1	0	1	0	0	0	0	15461	1403	49	0	13872	0	SYNE2	14	64593080	Frame_Shift_Del	DEL	TAAAAAATTG	TCGA-G3-A7M9-01A-23D-A34Z-10		64593080	42756460	66	42838										
DYNC1H1	1778	hgsc.bcm.edu	37	chr14	102446826	102446826	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	agcccggaagttctcctgacTctggatatcttgaaacatgg	10	10	3	2			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr14:102446826T>G	ENST00000360184.4	+	5	1064	c.900T>G	c.(898-900)acT>acG	p.T300T		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	300	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						TTCTCCTGACTCTGGATATCT	0.448																																					p.T300T		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.T900G						.						72	73	72					14																	102446826		2203	4300	6503	SO:0001819	synonymous_variant	1778	exon5			CCTGACTCTGGAT	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"Cytoplasmic dyneins"	2961	protein-coding gene	gene with protein product		600112	"dynein, cytoplasmic, heavy polypeptide 1"	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.900T>G	chr14.hg19:g.102446826T>G		50.0	0.0		28.0	11.0	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Silent	SNP	ENST00000360184.4	hg19	CCDS9966.1																																																																																			.	.		0.448	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		G	102446826	T	G	102446826	2	3	294	1	0	0	0	0	0	0	0	1	4843	1538	54	5		5	DYNC1H1	14	102446826	Silent	SNP	T	TCGA-G3-A7M9-01A-23D-A34Z-10	37853746	102446826	4902714	67	42839										
HSP90AA1	3320	hgsc.bcm.edu	37	chr14	102548666	102548670	+	Frame_Shift_Del	DEL	GTTGA	GTTGA	-													0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	ttgctgccatgtaacccattGttgagttgtctcttagggct							TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	GTTGA	GTTGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr14:102548666_102548670delGTTGA	ENST00000216281.8	-	10	2072_2076	c.1867_1871delTCAAC	c.(1867-1872)tcaacafs	p.ST623fs	HSP90AA1_ENST00000334701.7_Frame_Shift_Del_p.ST745fs	NM_005348.3	NP_005339.3	P07900	HS90A_HUMAN	heat shock protein 90kDa alpha (cytosolic), class A member 1	623					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone-mediated protein complex assembly (GO:0051131)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|mitochondrial transport (GO:0006839)|mitotic cell cycle (GO:0000278)|nitric oxide metabolic process (GO:0046209)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|protein import into mitochondrial outer membrane (GO:0045040)|protein refolding (GO:0042026)|regulation of nitric-oxide synthase activity (GO:0050999)|response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|identical protein binding (GO:0042802)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|TPR domain binding (GO:0030911)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(6)|large_intestine(3)|liver(1)|lung(10)|ovary(2)|prostate(1)	28					Nedocromil(DB00716)|Rifabutin(DB00615)	GTAACCCATTGTTGAGTTGTCTCTT	0.444																																					p.745_746del		Pindel	.											.	HSP90AA1	65	.	0			c.2234_2238del						.																																			SO:0001589	frameshift_variant	3320	exon11			.	M27024	CCDS9967.1, CCDS32160.1	14q32.33	2011-09-02	2006-02-24	2006-02-24	ENSG00000080824	ENSG00000080824		"Heat shock proteins / HSPC"	5253	protein-coding gene	gene with protein product		140571	"heat shock 90kD protein 1, alpha", "heat shock 90kDa protein 1, alpha"	HSPC1, HSPCA		2527334, 16269234	Standard	NM_001017963		Approved	Hsp89, Hsp90, FLJ31884, HSP90N	uc001ykv.4	P07900		ENST00000216281.8:c.1867_1871delTCAAC	chr14.hg19:g.102548666_102548670delGTTGA	ENSP00000216281:p.Ser623fs	82.0	0.0		63.0	18.0	NM_001017963	A8K500|B3KPJ9|Q2PP14|Q5CAQ6|Q5CAQ7|Q9BVQ5	Frame_Shift_Del	DEL	ENST00000216281.8	hg19	CCDS9967.1																																																																																			.	.		0.444	HSP90AA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414952.2	NM_005348		-	102548670	GTTGA	-	102548666	7	5	294	1	0	1	0	1	0	0	0	0	7410	1377	48	0	335	0	HSP90AA1	14	102548666	Frame_Shift_Del	DEL	GTTGA	TCGA-G3-A7M9-01A-23D-A34Z-10	101840	102548666	4800874	68	42840										
PLD4	122618	hgsc.bcm.edu	37	chr14	105398614	105398614	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	agaaagtcttcatcgtgccgGtggggaaccattccaacatc	10	11	2	1			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr14:105398614G>T	ENST00000392593.4	+	10	1411	c.1243G>T	c.(1243-1245)Gtg>Ttg	p.V415L	PLD4_ENST00000553861.1_5'UTR|PLD4_ENST00000540372.1_Missense_Mutation_p.V422L	NM_138790.2	NP_620145.2	Q96BZ4	PLD4_HUMAN	phospholipase D family, member 4	415					glycerophospholipid biosynthetic process (GO:0046474)|hematopoietic progenitor cell differentiation (GO:0002244)|inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phagocytosis (GO:0006909)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|trans-Golgi network membrane (GO:0032588)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase D activity (GO:0004630)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	13		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.00067)|OV - Ovarian serous cystadenocarcinoma(23;0.00976)|Epithelial(46;0.0201)|GBM - Glioblastoma multiforme(11;0.116)			CATCGTGCCGGTGGGGAACCA	0.627																																					p.V415L		Atlas-SNP	.											.	PLD4	46	.	0			c.G1243T						.						47	53	51					14																	105398614		2100	4218	6318	SO:0001583	missense	122618	exon10			GTGCCGGTGGGGA		CCDS9995.2	14q32.33	2014-01-28	2005-05-20	2005-05-20	ENSG00000166428	ENSG00000166428			23792	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 175"	C14orf175			Standard	XM_006720024		Approved		uc001ypu.1	Q96BZ4	OTTHUMG00000144167	ENST00000392593.4:c.1243G>T	chr14.hg19:g.105398614G>T	ENSP00000376372:p.Val415Leu	39.0	0.0		34.0	13.0	NM_138790	Q6UWD2	Missense_Mutation	SNP	ENST00000392593.4	hg19	CCDS9995.2	.	.	.	.	.	.	.	.	.	.	G	12.87	2.067649	0.36470	.	.	ENSG00000166428	ENST00000540372;ENST00000392593	T;T	0.22945	1.93;1.93	4.51	2.67	0.31697	.	0.085365	0.47093	D	0.000245	T	0.24198	0.0586	M	0.64404	1.975	0.80722	D	1	B;B	0.20988	0.044;0.05	B;B	0.24974	0.034;0.057	T	0.05209	-1.0899	10	0.37606	T	0.19	-18.6312	7.1021	0.25343	0.3452:0.0:0.6548:0.0	.	422;415	F5H2B5;Q96BZ4	.;PLD4_HUMAN	L	422;415	ENSP00000438677:V422L;ENSP00000376372:V415L	ENSP00000376372:V415L	V	+	1	0	PLD4	104469659	0.746000	0.28272	0.927000	0.36925	0.678000	0.39670	2.109000	0.41863	0.908000	0.36671	0.550000	0.68814	GTG	.	.		0.627	PLD4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000291348.2	NM_138790		T	105398614	G	T	105398614	3	4	294	1	0	0	0	0	1	0	0	0	12057	1261	44	3	1277	3	PLD4	14	105398614	Missense_Mutation	SNP	G	TCGA-G3-A7M9-01A-23D-A34Z-10	2849948	105398614	1950926	69	42841										
RYR3	6263	hgsc.bcm.edu	37	chr15	33895514	33895514	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	aaggatggggaggcaatggtGttggtgacgacctgtactcc	16	7	0	1	rs552872767		TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr15:33895514G>T	ENST00000389232.4	+	18	2183	c.2113G>T	c.(2113-2115)Gtt>Ttt	p.V705F	RYR3_ENST00000415757.3_Missense_Mutation_p.V705F	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	705	B30.2/SPRY 1. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			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)		AGGCAATGGTGTTGGTGACGA	0.532																																					p.V705F		Atlas-SNP	.											.	RYR3	760	.	0			c.G2113T						.						243	254	250					15																	33895514		2136	4245	6381	SO:0001583	missense	6263	exon18			AATGGTGTTGGTG		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.2113G>T	chr15.hg19:g.33895514G>T	ENSP00000373884:p.Val705Phe	100.0	0.0		41.0	29.0	NM_001243996	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	hg19	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.996826	0.93167	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	T;T	0.62364	0.03;0.03	5.42	5.42	0.78866	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.64402	D	0.000001	D	0.83811	0.5335	M	0.90542	3.125	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	D	0.86455	0.1775	10	0.87932	D	0	.	19.4732	0.94971	0.0:0.0:1.0:0.0	.	705;705	Q15413-2;Q15413	.;RYR3_HUMAN	F	705	ENSP00000373884:V705F;ENSP00000399610:V705F	ENSP00000354735:V705F	V	+	1	0	RYR3	31682806	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	9.539000	0.98076	2.831000	0.97527	0.644000	0.83932	GTT	.	.		0.532	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			T	33895514	G	T	33895514	3	4	294	1	0	0	0	0	1	0	0	0	13785	1377	48	3	2183	3	RYR3	15	33895514	Missense_Mutation	SNP	G	TCGA-G3-A7M9-01A-23D-A34Z-10		33895514	68635878	70	42842										
TP53	7157	hgsc.bcm.edu	37	chr17	7578264	7578270	+	Frame_Shift_Del	DEL	GATAAGA	GATAAGA	-													0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	cgcaaatttccttccactcgGataagatgctgaggaggggc					rs370216745|rs587780071		TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	GATAAGA	GATAAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr17:7578264_7578270delGATAAGA	ENST00000269305.4	-	6	768_774	c.579_585delTCTTATC	c.(577-585)catcttatcfs	p.HLI193fs	TP53_ENST00000574684.1_Intron|TP53_ENST00000413465.2_Frame_Shift_Del_p.HLI193fs|TP53_ENST00000455263.2_Frame_Shift_Del_p.HLI193fs|TP53_ENST00000445888.2_Frame_Shift_Del_p.HLI193fs|TP53_ENST00000420246.2_Frame_Shift_Del_p.HLI193fs|TP53_ENST00000359597.4_Frame_Shift_Del_p.HLI193fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	193	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		H -> D (in sporadic cancers; somatic mutation).|H -> L (in sporadic cancers; somatic mutation).|H -> N (in sporadic cancers; somatic mutation).|H -> P (in sporadic cancers; somatic mutation).|H -> Q (in sporadic cancers; somatic mutation).|H -> R (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7887414}.|H -> Y (in sporadic cancers; somatic mutation).|QH -> HN (in a sporadic cancer; somatic mutation).|QH -> HY (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.I195T(69)|p.L194R(47)|p.I195F(20)|p.L194F(17)|p.I195N(12)|p.I195S(10)|p.L194P(8)|p.0?(8)|p.L194H(8)|p.R196*(7)|p.I195fs*14(6)|p.I195fs*52(6)|p.?(6)|p.L101R(5)|p.L62R(5)|p.L194L(4)|p.A189_V197delAPPQHLIRV(4)|p.P191_E198>Q(3)|p.I195M(3)|p.P191fs*53(2)|p.I102S(2)|p.L194fs*15(2)|p.I102T(2)|p.H193H(2)|p.I63T(2)|p.I63S(2)|p.L194V(1)|p.L194fs*14(1)|p.P191fs*6(1)|p.I102fs*52(1)|p.H193_I195delHLI(1)|p.P59_E66>Q(1)|p.I102fs*14(1)|p.I195fs*12(1)|p.L101H(1)|p.I63fs*14(1)|p.I195fs*50(1)|p.I102M(1)|p.I102F(1)|p.I63F(1)|p.I195_G199delIRVEG(1)|p.P98_E105>Q(1)|p.A189fs*53(1)|p.I63fs*>28(1)|p.L62H(1)|p.L194I(1)|p.I63M(1)|p.I195L(1)|p.L194fs*52(1)|p.H193_I195>AP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CTTCCACTCGGATAAGATGCTGAGGAG	0.551		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.194_196del	Pancreas(47;798 1329 9957 10801)	Pindel	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,adenocarcinoma,0,1	TP53	33396	.	286	Substitution - Missense(221)|Deletion - Frameshift(15)|Insertion - Frameshift(10)|Whole gene deletion(8)|Substitution - Nonsense(7)|Deletion - In frame(6)|Complex - deletion inframe(6)|Unknown(6)|Substitution - coding silent(6)|Complex - frameshift(1)	ovary(52)|breast(42)|lung(35)|large_intestine(34)|haematopoietic_and_lymphoid_tissue(18)|upper_aerodigestive_tract(14)|oesophagus(14)|skin(14)|biliary_tract(13)|urinary_tract(11)|stomach(10)|central_nervous_system(8)|liver(6)|bone(4)|pancreas(4)|endometrium(3)|soft_tissue(2)|eye(1)|prostate(1)	c.580_586del						.																																			SO:0001589	frameshift_variant	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	.	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.579_585delTCTTATC	chr17.hg19:g.7578264_7578270delGATAAGA	ENSP00000269305:p.His193fs	60.0	0.0		24.0	10.0	NM_001126112	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Del	DEL	ENST00000269305.4	hg19	CCDS11118.1																																																																																			.	.		0.551	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		-	7578270	GATAAGA	-	7578264	7	5	294	1	0	1	0	1	0	0	0	0	16396	1164	41	0	709	0	TP53	17	7578264	Frame_Shift_Del	DEL	GATAAGA	TCGA-G3-A7M9-01A-23D-A34Z-10		7578264	73616946	71	42843										
NGFR	4804	hgsc.bcm.edu	37	chr17	47587941	47587941	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	cccagcccgtggtgacccgaGgcaccaccgacaacctcatc	9	19	1	1			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr17:47587941G>C	ENST00000172229.3	+	4	861	c.736G>C	c.(736-738)Ggc>Cgc	p.G246R	NGFR_ENST00000504201.1_Missense_Mutation_p.G152R|RP5-1029K10.2_ENST00000514506.1_RNA	NM_002507.3	NP_002498.1	P08138	TNR16_HUMAN	nerve growth factor receptor	246	Ser/Thr-rich.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|central nervous system development (GO:0007417)|circadian regulation of gene expression (GO:0032922)|detection of temperature stimulus (GO:0016048)|glucose homeostasis (GO:0042593)|hair follicle morphogenesis (GO:0031069)|intracellular protein transport (GO:0006886)|membrane protein intracellular domain proteolysis (GO:0031293)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell cycle (GO:0045786)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of hair follicle development (GO:0051799)|nerve development (GO:0021675)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of axonogenesis (GO:0050772)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of odontogenesis of dentin-containing tooth (GO:0042488)|regulation of axonogenesis (GO:0050770)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of glucose import in response to insulin stimulus (GO:2001273)	cell surface (GO:0009986)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|neuronal postsynaptic density (GO:0097481)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	death receptor activity (GO:0005035)|Rab GTPase binding (GO:0017137)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)	17	all_cancers(4;1.45e-13)|Breast(4;6.34e-28)|all_epithelial(4;4.95e-17)					GGTGACCCGAGGCACCACCGA	0.607																																					p.G246R		Atlas-SNP	.											.	NGFR	46	.	0			c.G736C						.						109	99	102					17																	47587941		2203	4300	6503	SO:0001583	missense	4804	exon4			ACCCGAGGCACCA	M14764	CCDS11549.1	17q21-q22	2013-05-22	2010-04-28		ENSG00000064300	ENSG00000064300		"Tumor necrosis factor receptor superfamily", "CD molecules"	7809	protein-coding gene	gene with protein product	"low affinity nerve growth factor receptor", "TNFR superfamily, member 16"	162010	"nerve growth factor receptor (TNFR superfamily, member 16)"			3022937, 3006050	Standard	NM_002507		Approved	TNFRSF16, CD271, p75NTR	uc002ioz.4	P08138	OTTHUMG00000161495	ENST00000172229.3:c.736G>C	chr17.hg19:g.47587941G>C	ENSP00000172229:p.Gly246Arg	33.0	0.0		30.0	15.0	NM_002507	B2R961|B4E096	Missense_Mutation	SNP	ENST00000172229.3	hg19	CCDS11549.1	.	.	.	.	.	.	.	.	.	.	G	14.15	2.449678	0.43531	.	.	ENSG00000064300	ENST00000172229;ENST00000504201	D;D	0.91295	-2.74;-2.82	4.85	4.85	0.62838	.	0.168500	0.51477	D	0.000088	D	0.88328	0.6407	M	0.65975	2.015	0.34770	D	0.733639	P	0.38617	0.64	B	0.33121	0.158	D	0.91457	0.5186	10	0.33940	T	0.23	-48.9827	16.0977	0.81139	0.0:0.0:1.0:0.0	.	246	P08138	TNR16_HUMAN	R	246;152	ENSP00000172229:G246R;ENSP00000421731:G152R	ENSP00000172229:G246R	G	+	1	0	NGFR	44942940	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	8.372000	0.90127	2.397000	0.81536	0.650000	0.86243	GGC	.	.		0.607	NGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365150.1			C	47587941	G	C	47587941	3	2	294	1	0	0	0	0	1	0	0	0	10405	1000	35	4	750	4	NGFR	17	47587941	Missense_Mutation	SNP	G	TCGA-G3-A7M9-01A-23D-A34Z-10	40009677	47587941	33607269	72	42844										
TOB1	10140	hgsc.bcm.edu	37	chr17	48940660	48940661	+	Frame_Shift_Ins	INS	-	-	GC													0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	tggctgctgctgttgctgtgINSgctgctgctggctacccaag					rs372275994		TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr17:48940660_48940661insGC	ENST00000268957.3	-	3	1146_1147	c.718_719insGC	c.(718-720)ccafs	p.P240fs	TOB1_ENST00000499247.2_Frame_Shift_Ins_p.P240fs|TOB1_ENST00000509385.1_5'Flank	NM_001243877.1	NP_001230806.1	P50616	TOB1_HUMAN	transducer of ERBB2, 1	240	Poly-Gln.				negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell proliferation (GO:0008285)|negative regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060212)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of translation (GO:0017148)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of signal transduction (GO:0009967)|SMAD protein import into nucleus (GO:0007184)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	receptor tyrosine kinase binding (GO:0030971)|SH3/SH2 adaptor activity (GO:0005070)|transcription corepressor activity (GO:0003714)			breast(1)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13			BRCA - Breast invasive adenocarcinoma(22;1.09e-08)			ctgttgctgtggctgctgctgG	0.55																																					p.P240fs	NSCLC(144;643 1919 24513 29423 40686)	Atlas-INDEL	.											.	TOB1	40	.	0			c.719_720insGC						.																																			SO:0001589	frameshift_variant	10140	exon2			.	D38305	CCDS11576.1	17q21.33	2012-08-14			ENSG00000141232	ENSG00000141232			11979	protein-coding gene	gene with protein product		605523		TROB1		8632892, 17785442	Standard	NM_005749		Approved	TOB, TROB	uc002isw.3	P50616	OTTHUMG00000162277	ENST00000268957.3:c.717_718dupGC	chr17.hg19:g.48940661_48940662dupGC	ENSP00000268957:p.Pro240fs	36.0	0.0		29.0	10.0	NM_005749	B2R9T0|D3DTY3|Q4KMQ0	Frame_Shift_Ins	INS	ENST00000268957.3	hg19	CCDS11576.1																																																																																			.	.		0.55	TOB1-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000368364.1			GC	48940661	-	GC	48940660	7	5	294	1	0	1	1	0	0	0	0	0	16362	1348	47	0	322	0	TOB1	17	48940660	Frame_Shift_Ins	INS	-	TCGA-G3-A7M9-01A-23D-A34Z-10	1352719	48940660	32254550	73	42845										
ABCA5	23461	hgsc.bcm.edu	37	chr17	67287403	67287403	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	agaatattcatcaatgtactCtttcctgttccactgtggcc	6	11	3	1			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr17:67287403C>T	ENST00000392676.3	-	12	1624	c.1560G>A	c.(1558-1560)aaG>aaA	p.K520K	ABCA5_ENST00000588877.1_Silent_p.K520K|ABCA5_ENST00000392677.2_Silent_p.K520K			Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 5	520	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cholesterol efflux (GO:0033344)|high-density lipoprotein particle remodeling (GO:0034375)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|reverse cholesterol transport (GO:0043691)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(18)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	54	Breast(10;3.72e-11)				Tacrolimus(DB00864)	TCAATGTACTCTTTCCTGTTC	0.333																																					p.K520K		Atlas-SNP	.											.	ABCA5	162	.	0			c.G1560A						.						94	91	92					17																	67287403		2203	4300	6503	SO:0001819	synonymous_variant	23461	exon11			TGTACTCTTTCCT	U66672	CCDS11685.1	17q24.3	2012-03-14			ENSG00000154265	ENSG00000154265		"ATP binding cassette transporters / subfamily A"	35	protein-coding gene	gene with protein product		612503				8894702	Standard	NM_172232		Approved	EST90625	uc002jig.2	Q8WWZ7		ENST00000392676.3:c.1560G>A	chr17.hg19:g.67287403C>T		101.0	0.0		58.0	18.0	NM_018672	Q8IVJ2|Q96LJ1|Q96MS4|Q96PZ9|Q9NY14	Silent	SNP	ENST00000392676.3	hg19	CCDS11685.1																																																																																			.	.		0.333	ABCA5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450654.1	NM_018672		T	67287403	C	T	67287403	2	4	294	1	0	0	0	0	0	0	0	1	35	912	32	3		3	ABCA5	17	67287403	Silent	SNP	C	TCGA-G3-A7M9-01A-23D-A34Z-10	18346743	67287403	13907807	74	42846										
ITGB4	3691	hgsc.bcm.edu	37	chr17	73723340	73723340	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	tccgtgtggataaggactgcGcctactgcacagacgaggtg	14	10	0	1	rs146966502	byFrequency	TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr17:73723340G>T	ENST00000200181.3	+	3	332	c.145G>T	c.(145-147)Gcc>Tcc	p.A49S	ITGB4_ENST00000339591.3_Missense_Mutation_p.A49S|ITGB4_ENST00000579662.1_Missense_Mutation_p.A49S|ITGB4_ENST00000450894.3_Missense_Mutation_p.A49S|ITGB4_ENST00000449880.2_Missense_Mutation_p.A49S|ITGB4_ENST00000584558.1_3'UTR	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	49	PSI.				amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			TAAGGACTGCGCCTACTGCAC	0.602																																					p.A49S		Atlas-SNP	.											.	ITGB4	165	.	0			c.G145T						.						78	65	69					17																	73723340		2203	4300	6503	SO:0001583	missense	3691	exon3			GACTGCGCCTACT		CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"CD molecules", "Integrins", "Fibronectin type III domain containing"	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.145G>T	chr17.hg19:g.73723340G>T	ENSP00000200181:p.Ala49Ser	46.0	0.0		36.0	11.0	NM_001005731	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Missense_Mutation	SNP	ENST00000200181.3	hg19	CCDS11727.1	.	.	.	.	.	.	.	.	.	.	G	13.19	2.164637	0.38217	.	.	ENSG00000132470	ENST00000200181;ENST00000339591;ENST00000449880	D;D;D	0.86497	-2.13;-2.13;-2.13	5.36	5.36	0.76844	Integrin beta subunit, N-terminal (2);	0.063342	0.64402	D	0.000007	D	0.86740	0.6005	L	0.52364	1.645	0.51012	D	0.999901	B;P;P;P	0.45768	0.247;0.651;0.866;0.866	B;B;P;P	0.49276	0.279;0.354;0.605;0.605	D	0.85406	0.1134	10	0.36615	T	0.2	.	12.2711	0.54706	0.0:0.0:0.7128:0.2872	.	49;49;49;49	P16144-5;P16144-3;A0AVL6;P16144	.;.;.;ITB4_HUMAN	S	49	ENSP00000200181:A49S;ENSP00000344079:A49S;ENSP00000400217:A49S	ENSP00000200181:A49S	A	+	1	0	ITGB4	71234935	1.000000	0.71417	0.995000	0.50966	0.881000	0.50899	4.928000	0.63447	2.505000	0.84491	0.655000	0.94253	GCC	.	A|0.000;G|1.000		0.602	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1			T	73723340	G	T	73723340	3	4	294	1	0	0	0	0	1	0	0	0	7906	1087	38	1	151	1	ITGB4	17	73723340	Missense_Mutation	SNP	G	TCGA-G3-A7M9-01A-23D-A34Z-10	6435937	73723340	7471870	75	42847										
SPHK1	8877	hgsc.bcm.edu	37	chr17	74382080	74382096	+	Frame_Shift_Del	DEL	GGCGTGCTCCCGCGGCC	GGCGTGCTCCCGCGGCC	-													0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	tctcagcgggcggcccccggGgcgtgctcccgcggccctgc					rs373986019		TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	GGCGTGCTCCCGCGGCC	GGCGTGCTCCCGCGGCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr17:74382080_74382096delGGCGTGCTCCCGCGGCC	ENST00000545180.1	+	5	834_850	c.25_41delGGCGTGCTCCCGCGGCC	c.(25-42)ggcgtgctcccgcggcccfs	p.GVLPRP9fs	SPHK1_ENST00000592299.1_Frame_Shift_Del_p.GVLPRP9fs|SPHK1_ENST00000392496.3_Frame_Shift_Del_p.GVLPRP9fs|SPHK1_ENST00000590959.1_Frame_Shift_Del_p.GVLPRP23fs|SPHK1_ENST00000323374.4_Frame_Shift_Del_p.GVLPRP95fs			Q9NYA1	SPHK1_HUMAN	sphingosine kinase 1	9					'de novo' posttranslational protein folding (GO:0051084)|blood vessel development (GO:0001568)|brain development (GO:0007420)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|female pregnancy (GO:0007565)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|lipid phosphorylation (GO:0046834)|negative regulation of apoptotic process (GO:0043066)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neurotransmitter secretion (GO:0001956)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of smooth muscle contraction (GO:0045987)|protein folding (GO:0006457)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of interleukin-1 beta production (GO:0032651)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|response to amine (GO:0014075)|response to ATP (GO:0033198)|response to interleukin-1 (GO:0070555)|response to magnesium ion (GO:0032026)|response to progesterone (GO:0032570)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingoid catabolic process (GO:0046521)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|D-erythro-sphingosine kinase activity (GO:0017050)|diacylglycerol kinase activity (GO:0004143)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|NAD+ kinase activity (GO:0003951)|protein phosphatase 2A binding (GO:0051721)|sphinganine kinase activity (GO:0008481)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)	11					Fingolimod(DB08868)	CGGCCCCCGGGGCGTGCTCCCGCGGCCCTGCCGCGTG	0.659											OREG0024750	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.94_100del	GBM(90;966 1307 27369 33775 44498)	Atlas-INDEL	.											.	SPHK1	24	.	0			c.282_298del						.																																			SO:0001589	frameshift_variant	8877	exon3			.	BC030553	CCDS11744.1, CCDS45785.1, CCDS59297.1	17q25.2	2004-02-18				ENSG00000176170			11240	protein-coding gene	gene with protein product		603730				9726979	Standard	NM_182965		Approved	SPHK	uc002jrj.2	Q9NYA1		ENST00000545180.1:c.25_41delGGCGTGCTCCCGCGGCC	chr17.hg19:g.74382080_74382096delGGCGTGCTCCCGCGGCC	ENSP00000440970:p.Gly9fs	32.0	0.0	1152	26.0	10.0	NM_182965	Q8N632|Q96GK1|Q9HD92|Q9NY70|Q9NYL3	Frame_Shift_Del	DEL	ENST00000545180.1	hg19	CCDS45785.1																																																																																			.	.		0.659	SPHK1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450113.1	NM_182965, NM_021972		-	74382096	GGCGTGCTCCCGCGGCC	-	74382080	7	5	294	1	0	1	0	1	0	0	0	0	15061	1232	43	0	335	0	SPHK1	17	74382080	Frame_Shift_Del	DEL	GGCGTGCTCCCGCGGCC	TCGA-G3-A7M9-01A-23D-A34Z-10	658740	74382080	6813130	76	42848										
SEPT9	10801	hgsc.bcm.edu	37	chr17	75303253	75303253	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	gacctccagtggccggctccGgaggcttggtgactccagtg	15	13	0	1			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr17:75303253G>C	ENST00000427177.1	+	2	176	c.50G>C	c.(49-51)cGg>cCg	p.R17P	SEPT9_ENST00000591198.1_Intron|SEPT9_ENST00000449803.2_5'UTR|SEPT9_ENST00000431235.2_5'UTR	NM_001113491.1	NP_001106963.1	Q9UHD8	SEPT9_HUMAN	septin 9	17					cell cycle (GO:0007049)|cell division (GO:0051301)|GTP catabolic process (GO:0006184)|protein heterooligomerization (GO:0051291)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|perinuclear region of cytoplasm (GO:0048471)|stress fiber (GO:0001725)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			autonomic_ganglia(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|prostate(2)	16			BRCA - Breast invasive adenocarcinoma(99;0.153)			GGCCGGCTCCGGAGGCTTGGT	0.622																																					p.R17P		Atlas-SNP	.											.	SEPT9	105	.	0			c.G50C						.						90	89	90					17																	75303253		1568	3582	5150	SO:0001583	missense	10801	exon2			GGCTCCGGAGGCT	AB023208	CCDS45790.1, CCDS45791.1, CCDS45792.1, CCDS45793.1, CCDS45794.1, CCDS45795.1, CCDS74166.1	17q25.3	2014-09-17	2005-01-11	2005-01-12	ENSG00000184640	ENSG00000184640		"Septins"	7323	protein-coding gene	gene with protein product	"Ov/Br septin"	604061	"MLL septin-like fusion"	MSF		10339604, 10485469	Standard	NM_006640		Approved	MSF1, KIAA0991, PNUTL4, AF17q25, SeptD1	uc002jts.4	Q9UHD8		ENST00000427177.1:c.50G>C	chr17.hg19:g.75303253G>C	ENSP00000391249:p.Arg17Pro	42.0	0.0		33.0	17.0	NM_001113491	A8K2V3|B3KPM0|B4DTL9|B4E0N2|B4E274|B7Z654|Q96QF3|Q96QF4|Q96QF5|Q9HA04|Q9UG40|Q9Y5W4	Missense_Mutation	SNP	ENST00000427177.1	hg19	CCDS45790.1	.	.	.	.	.	.	.	.	.	.	g	15.13	2.742457	0.49151	.	.	ENSG00000184640	ENST00000427177	T	0.37915	1.17	3.66	2.69	0.31865	.	.	.	.	.	T	0.28333	0.0700	N	0.08118	0	0.80722	D	1	D	0.67145	0.996	P	0.55455	0.776	T	0.12192	-1.0557	9	0.87932	D	0	.	7.1862	0.25801	0.1219:0.0:0.8781:0.0	.	17	Q9UHD8	SEPT9_HUMAN	P	17	ENSP00000391249:R17P	ENSP00000391249:R17P	R	+	2	0	SEPT9	72814848	1.000000	0.71417	1.000000	0.80357	0.751000	0.42716	4.328000	0.59253	1.132000	0.42129	-0.265000	0.10407	CGG	.	.		0.622	SEPT9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000436304.2	NM_006640		C	75303253	G	C	75303253	3	2	294	1	0	0	0	0	1	0	0	0	14086	1116	39	4	56	4	SEPT9	17	75303253	Missense_Mutation	SNP	G	TCGA-G3-A7M9-01A-23D-A34Z-10	921173	75303253	5891957	77	42849										
CBX4	8535	hgsc.bcm.edu	37	chr17	77808471	77808471	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	ctcctccctcctcttgggcgGcgcctccaccttcttctcct	6	21	3	0	rs138355116		TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr17:77808471G>A	ENST00000269397.4	-	5	1147	c.970C>T	c.(970-972)Ccg>Tcg	p.P324S		NM_003655.2	NP_003646.2	O00257	CBX4_HUMAN	chromobox homolog 4	324	Interaction with BMI1.				chromatin modification (GO:0016568)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein sumoylation (GO:0016925)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|single-stranded RNA binding (GO:0003727)|SUMO binding (GO:0032183)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)	p.P324S(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			CTCTTGGGCGGCGCCTCCACC	0.672											OREG0024799	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P324S		Atlas-SNP	.											CBX4,abdomen,malignant_melanoma,0,1	CBX4	40	.	1	Substitution - Missense(1)	skin(1)	c.C970T						.						26	26	26					17																	77808471		2202	4300	6502	SO:0001583	missense	8535	exon5			TGGGCGGCGCCTC	AF013956	CCDS32758.1	17q25.3	2010-07-06	2010-06-24		ENSG00000141582	ENSG00000141582			1554	protein-coding gene	gene with protein product	"NS5ATP1-binding protein 16", "Pc class 2 homolog (Drosophila)"	603079	"chromobox homolog 4 (Drosophila Pc class)"			9315667	Standard	NM_003655		Approved	hPC2, PC2, NBP16	uc002jxe.3	O00257	OTTHUMG00000150415	ENST00000269397.4:c.970C>T	chr17.hg19:g.77808471G>A	ENSP00000269397:p.Pro324Ser	39.0	0.0	1178	27.0	11.0	NM_003655	B1PJR7|Q6TPI8|Q96C04	Missense_Mutation	SNP	ENST00000269397.4	hg19	CCDS32758.1	.	.	.	.	.	.	.	.	.	.	g	8.228	0.803951	0.16467	.	.	ENSG00000141582	ENST00000269397	.	.	.	3.67	1.54	0.23209	.	0.686289	0.10318	U	0.689154	T	0.26629	0.0651	L	0.44542	1.39	0.18873	N	0.999981	B	0.16802	0.019	B	0.14578	0.011	T	0.30995	-0.9959	9	0.10636	T	0.68	-24.3783	1.2937	0.02065	0.1348:0.1775:0.3268:0.361	.	324	O00257	CBX4_HUMAN	S	324	.	ENSP00000269397:P324S	P	-	1	0	CBX4	75423066	0.781000	0.28676	0.003000	0.11579	0.868000	0.49771	1.202000	0.32271	0.059000	0.16252	-0.851000	0.03033	CCG	.	.		0.672	CBX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318007.1	NM_003655		A	77808471	G	A	77808471	3	1	294	1	0	0	0	0	1	0	0	0	2722	1203	42	3	716	3	CBX4	17	77808471	Missense_Mutation	SNP	G	TCGA-G3-A7M9-01A-23D-A34Z-10	2505218	77808471	3386739	78	42850										
VAV1	7409	hgsc.bcm.edu	37	chr19	6833726	6833726	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	ctttaccctcccgtagatttCccaggaactatgaagaaggt	8	11	0	3			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr19:6833726C>A	ENST00000602142.1	+	18	1795	c.1713C>A	c.(1711-1713)ttC>ttA	p.F571L	VAV1_ENST00000304076.2_Missense_Mutation_p.F571L|VAV1_ENST00000599806.1_Missense_Mutation_p.F516L|VAV1_ENST00000596764.1_Missense_Mutation_p.F539L|VAV1_ENST00000539284.1_Missense_Mutation_p.F474L	NM_005428.3	NP_005419.2	P15498	VAV_HUMAN	vav 1 guanine nucleotide exchange factor	571					apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|reactive oxygen species metabolic process (GO:0072593)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(16)|lung(18)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	62						CCGTAGATTTCCCAGGAACTA	0.537																																					p.F571L		Atlas-SNP	.											.	VAV1	140	.	0			c.C1713A						.						141	140	140					19																	6833726		2203	4300	6503	SO:0001583	missense	7409	exon18			AGATTTCCCAGGA		CCDS12174.1, CCDS59341.1, CCDS59342.1	19p13.2	2013-02-14	2007-07-25			ENSG00000141968		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "SH2 domain containing"	12657	protein-coding gene	gene with protein product		164875	"vav 1 oncogene"	VAV		9438848	Standard	NM_005428		Approved		uc010xjh.2	P15498		ENST00000602142.1:c.1713C>A	chr19.hg19:g.6833726C>A	ENSP00000472929:p.Phe571Leu	36.0	0.0		28.0	15.0	NM_005428	B4DVK9|M0QXX6|Q15860	Missense_Mutation	SNP	ENST00000602142.1	hg19	CCDS12174.1	.	.	.	.	.	.	.	.	.	.	C	3.188	-0.166388	0.06461	.	.	ENSG00000141968	ENST00000304076;ENST00000539284	T;T	0.74209	0.16;-0.82	3.95	-0.242	0.13039	.	1.240100	0.05538	N	0.565122	T	0.50582	0.1624	N	0.08118	0	0.09310	N	0.999999	B;B;B;B	0.23249	0.082;0.002;0.049;0.0	B;B;B;B	0.18561	0.022;0.004;0.01;0.001	T	0.32107	-0.9919	10	0.11485	T	0.65	.	7.1926	0.25834	0.0:0.5028:0.0:0.4972	.	474;571;516;571	F5H5P4;B2R8B5;Q96D37;P15498	.;.;.;VAV_HUMAN	L	571;474	ENSP00000302269:F571L;ENSP00000443242:F474L	ENSP00000302269:F571L	F	+	3	2	VAV1	6784726	0.032000	0.19561	0.010000	0.14722	0.015000	0.08874	0.104000	0.15313	0.010000	0.14839	0.491000	0.48974	TTC	.	.		0.537	VAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458475.1			A	6833726	C	A	6833726	3	1	294	1	0	0	0	0	1	0	0	0	17146	854	30	3	1783	3	VAV1	19	6833726	Missense_Mutation	SNP	C	TCGA-G3-A7M9-01A-23D-A34Z-10		6833726	52295257	79	42851										
RYR1	6261	hgsc.bcm.edu	37	chr19	38960151	38960151	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	cccttgaacaccctcactatGaggtaaggactgagcccctc	8	15	1	3			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr19:38960151G>A	ENST00000359596.3	+	27	3763	c.3763G>A	c.(3763-3765)Gag>Aag	p.E1255K	RYR1_ENST00000360985.3_Missense_Mutation_p.E1255K|RYR1_ENST00000355481.4_Missense_Mutation_p.E1255K			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1255	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CCCTCACTATGAGGTAAGGAC	0.532																																					p.E1255K		Atlas-SNP	.											RYR1,right_lower_lobe,carcinoma,0,1	RYR1	708	.	0			c.G3763A						.						80	73	75					19																	38960151		2203	4300	6503	SO:0001583	missense	6261	exon27			CACTATGAGGTAA	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.3763G>A	chr19.hg19:g.38960151G>A	ENSP00000352608:p.Glu1255Lys	29.0	0.0		19.0	13.0	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	g	12.97	2.096627	0.36952	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.96885	-4.15;-4.16;-4.16	3.48	3.48	0.39840	.	0.000000	0.64402	U	0.000007	D	0.95414	0.8511	L	0.50333	1.59	0.51767	D	0.999937	D;P	0.59767	0.986;0.817	P;B	0.50405	0.64;0.164	D	0.94650	0.7838	10	0.39692	T	0.17	.	14.86	0.70372	0.0:0.0:1.0:0.0	.	1255;1255	P21817-2;P21817	.;RYR1_HUMAN	K	1255	ENSP00000352608:E1255K;ENSP00000347667:E1255K;ENSP00000354254:E1255K	ENSP00000347667:E1255K	E	+	1	0	RYR1	43651991	1.000000	0.71417	1.000000	0.80357	0.696000	0.40369	5.925000	0.70062	1.816000	0.52996	0.434000	0.28630	GAG	.	.		0.532	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			A	38960151	G	A	38960151	3	1	294	1	0	0	0	0	1	0	0	0	13783	1291	45	3	3869	3	RYR1	19	38960151	Missense_Mutation	SNP	G	TCGA-G3-A7M9-01A-23D-A34Z-10	32126425	38960151	20168832	80	42852										
RPL18	6141	hgsc.bcm.edu	37	chr19	49121059	49121059	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	cagcctcaccttgaccaacaGcctcaggtagatatcctggc	8	15	2	2			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr19:49121059G>T	ENST00000549920.1	-	2	471	c.79C>A	c.(79-81)Ctg>Atg	p.L27M	RPL18_ENST00000549273.1_Missense_Mutation_p.L27M|SPHK2_ENST00000340932.3_5'Flank|RPL18_ENST00000550645.1_Missense_Mutation_p.L27M|RPL18_ENST00000552588.1_Intron|SPHK2_ENST00000600537.1_5'Flank|FAM83E_ENST00000595110.1_5'Flank|AC022154.7_ENST00000598735.1_RNA|SPHK2_ENST00000601712.1_5'Flank|AC022154.7_ENST00000594850.1_RNA|AC022154.7_ENST00000600303.1_RNA|SPHK2_ENST00000245222.4_5'Flank|SPHK2_ENST00000598088.1_5'Flank	NM_000979.3	NP_000970.1	Q07020	RL18_HUMAN	ribosomal protein L18	27					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			cervix(1)|kidney(2)	3		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;9.89e-05)|all cancers(93;0.00011)|GBM - Glioblastoma multiforme(486;0.0061)|Epithelial(262;0.0154)		TTGACCAACAGCCTCAGGTAG	0.587																																					p.L27M		Atlas-SNP	.											.	RPL18	9	.	0			c.C79A						.						103	79	87					19																	49121059		2203	4300	6503	SO:0001583	missense	6141	exon2			CCAACAGCCTCAG	L11566	CCDS12726.1, CCDS58669.1	19q13	2011-04-06				ENSG00000063177		"L ribosomal proteins"	10310	protein-coding gene	gene with protein product	"60S ribosomal protein L18"	604179				8218404	Standard	NM_000979		Approved	L18	uc002pjq.2	Q07020	OTTHUMG00000169760	ENST00000549920.1:c.79C>A	chr19.hg19:g.49121059G>T	ENSP00000447001:p.Leu27Met	46.0	0.0		42.0	27.0	NM_000979	F8VWC5|Q8WTZ6	Missense_Mutation	SNP	ENST00000549920.1	hg19	CCDS12726.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.8|26.8	4.772589|4.772589	0.90108|0.90108	.|.	.|.	ENSG00000063177|ENSG00000063177	ENST00000084795|ENST00000549920;ENST00000550645;ENST00000549273;ENST00000450952	.|.	.|.	.|.	4.96|4.96	4.96|4.96	0.65561|0.65561	.|Ribosomal protein L18e/L15P (2);	.|0.070269	.|0.64402	.|D	.|0.000018	D|D	0.85292|0.85292	0.5663|0.5663	M|M	0.91561|0.91561	3.22|3.22	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;0.989	.|D;D	.|0.85130	.|0.997;0.918	D|D	0.87980|0.87980	0.2742|0.2742	5|9	.|0.62326	.|D	.|0.03	-18.4838|-18.4838	16.506|16.506	0.84272|0.84272	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|27;27	.|B4DDY5;Q07020	.|.;RL18_HUMAN	D|M	28|27	.|.	.|ENSP00000407348:L27M	A|L	-|-	2|1	0|2	RPL18|RPL18	53812871|53812871	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.991000|0.991000	0.79684|0.79684	6.673000|6.673000	0.74482|0.74482	2.690000|2.690000	0.91761|0.91761	0.655000|0.655000	0.94253|0.94253	GCT|CTG	.	.		0.587	RPL18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405732.2	NM_000979		T	49121059	G	T	49121059	3	4	294	1	0	0	0	0	1	0	0	0	13579	962	34	3	511	3	RPL18	19	49121059	Missense_Mutation	SNP	G	TCGA-G3-A7M9-01A-23D-A34Z-10	10160908	49121059	10007924	81	42853										
ZNF28	7576	hgsc.bcm.edu	37	chr19	53303883	53303883	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	ttgtatggtttctctccagtAtgaatcctcttatgtctttc	6	9	3	1			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr19:53303883A>G	ENST00000457749.2	-	4	1334	c.1215T>C	c.(1213-1215)caT>caC	p.H405H	ZNF28_ENST00000414252.2_Silent_p.H352H|ZNF28_ENST00000360272.4_Silent_p.H352H|ZNF28_ENST00000438150.2_Silent_p.H352H	NM_006969.3	NP_008900.3	P17035	ZNF28_HUMAN	zinc finger protein 28	405					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|liver(1)|lung(10)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(134;0.0386)|Lung(386;0.145)		TCTCTCCAGTATGAATCCTCT	0.373																																					p.H405H		Atlas-SNP	.											.	ZNF28	191	.	0			c.T1215C						.						105	112	110					19																	53303883		2203	4300	6503	SO:0001819	synonymous_variant	7576	exon4			TCCAGTATGAATC	X52355	CCDS33093.1, CCDS33093.2	19q13.41	2013-01-08	2006-05-10		ENSG00000198538	ENSG00000198538		"Zinc fingers, C2H2-type", "-"	13073	protein-coding gene	gene with protein product			"zinc finger protein 28 (KOX 24)"				Standard	NR_036599		Approved	KOX24, DKFZp781D0275	uc002qad.3	P17035	OTTHUMG00000154564	ENST00000457749.2:c.1215T>C	chr19.hg19:g.53303883A>G		52.0	0.0		46.0	30.0	NM_006969	A8KAK9|B4E3G0|B9EIK7|Q5H9V1|Q5HYM9|Q6ZML9|Q6ZN56	Silent	SNP	ENST00000457749.2	hg19	CCDS33093.2																																																																																			.	.		0.373	ZNF28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336038.2	NM_006969		G	53303883	A	G	53303883	2	3	294	1	0	0	0	0	0	0	0	1	17828	446	16	2		2	ZNF28	19	53303883	Silent	SNP	A	TCGA-G3-A7M9-01A-23D-A34Z-10	4182824	53303883	5825100	82	42854										
ZNF845	91664	hgsc.bcm.edu	37	chr19	53855612	53855612	+	Frame_Shift_Del	DEL	G	G	-													0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	agtgtggcaaagcctttcgtGggcagtcagcacttatttac							TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr19:53855612delG	ENST00000595091.1	+	5	1903	c.1684delG	c.(1684-1686)gggfs	p.G562fs	ZNF845_ENST00000458035.1_Frame_Shift_Del_p.G562fs			Q96IR2	ZN845_HUMAN	zinc finger protein 845	562					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						AGCCTTTCGTGGGCAGTCAGC	0.423																																					p.R561fs		Atlas-Indel,Pindel	.											.	ZNF845	101	.	0			c.1683delT						.			4,4240		1,2,2119	88	76	80			-1.5	0	19		79	12,8228		6,0,4114	no	frameshift	ZNF845	NM_138374.1		7,2,6233	A1A1,A1R,RR		0.1456,0.0943,0.1282			53855612	16,12468	692	1591	2283	SO:0001589	frameshift_variant	91664	exon4			.	BC007307	CCDS46170.1	19q13.42	2013-01-08			ENSG00000213799	ENSG00000213799		"Zinc fingers, C2H2-type", "-"	25112	protein-coding gene	gene with protein product							Standard	NM_138374		Approved		uc010ydv.1	Q96IR2		ENST00000595091.1:c.1684delG	chr19.hg19:g.53855612delG	ENSP00000470005:p.Gly562fs	52.0	0.0		45.0	25.0	NM_138374		Frame_Shift_Del	DEL	ENST00000595091.1	hg19	CCDS46170.1																																																																																			.	.		0.423	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908		-	53855612	G	-	53855612	7	5	294	1	0	1	0	1	0	0	0	0	18206	1348	47	0	1694	0	ZNF845	19	53855612	Frame_Shift_Del	DEL	G	TCGA-G3-A7M9-01A-23D-A34Z-10	551729	53855612	5273371	83	42855										
LENG8	114823	hgsc.bcm.edu	37	chr19	54966690	54966690	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	ctcaaggaggtgctgcaggcGcggctgcaggacggctcggc	18	12	1	0			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr19:54966690G>A	ENST00000326764.5	+	8	1448	c.969G>A	c.(967-969)gcG>gcA	p.A323A	LENG8_ENST00000376514.2_Intron	NM_052925.2	NP_443157.1	Q96PV6	LENG8_HUMAN	leukocyte receptor cluster (LRC) member 8	286										breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.139)		TGCTGCAGGCGCGGCTGCAGG	0.632																																					p.A323A		Atlas-SNP	.											.	LENG8	73	.	0			c.G969A						.						40	44	43					19																	54966690		2203	4300	6503	SO:0001819	synonymous_variant	114823	exon8			GCAGGCGCGGCTG	AF211975	CCDS12894.1	19q13.4	2008-02-05			ENSG00000167615	ENSG00000167615			15500	protein-coding gene	gene with protein product						10941842	Standard	XM_005278248		Approved	KIAA1932, MGC40108, pp13842	uc002qfw.2	Q96PV6	OTTHUMG00000065548	ENST00000326764.5:c.969G>A	chr19.hg19:g.54966690G>A		25.0	0.0		22.0	8.0	NM_052925	B0VJY9|Q8IZ27|Q8NCX6	Silent	SNP	ENST00000326764.5	hg19	CCDS12894.1																																																																																			.	.		0.632	LENG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140523.2	NM_052925		A	54966690	G	A	54966690	2	1	294	1	0	0	0	0	0	0	0	1	8733	1074	38	1		1	LENG8	19	54966690	Silent	SNP	G	TCGA-G3-A7M9-01A-23D-A34Z-10	1111078	54966690	4162293	84	42856										
ZSCAN5B	342933	hgsc.bcm.edu	37	chr19	56704398	56704398	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	cagggtcctccctgaccccaTgagagtgtccaatttgcagc	10	14	0	2			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr19:56704398T>A	ENST00000586855.2	-	2	337	c.24A>T	c.(22-24)tcA>tcT	p.S8S	ZSCAN5B_ENST00000358992.3_Silent_p.S8S			A6NJL1	ZSA5B_HUMAN	zinc finger and SCAN domain containing 5B	8					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|endometrium(5)|large_intestine(3)|lung(23)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						CCTGACCCCATGAGAGTGTCC	0.502																																					p.S8S		Atlas-SNP	.											.	ZSCAN5B	160	.	0			c.A24T						.						33	28	30					19																	56704398		692	1591	2283	SO:0001819	synonymous_variant	342933	exon1			ACCCCATGAGAGT		CCDS46203.1	19q13.42	2013-01-08			ENSG00000197213	ENSG00000197213		"-", "Zinc fingers, C2H2-type"	34246	protein-coding gene	gene with protein product							Standard	NM_001080456		Approved	ZNF495B, ZNF371	uc010ygh.2	A6NJL1		ENST00000586855.2:c.24A>T	chr19.hg19:g.56704398T>A		46.0	0.0		38.0	6.0	NM_001080456		Silent	SNP	ENST00000586855.2	hg19	CCDS46203.1																																																																																			.	.		0.502	ZSCAN5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457834.2	NM_001080456		A	56704398	T	A	56704398	2	1	294	1	0	0	0	0	0	0	0	1	18254	1451	51	4		4	ZSCAN5B	19	56704398	Silent	SNP	T	TCGA-G3-A7M9-01A-23D-A34Z-10	1737708	56704398	2424585	85	42857										
ZNF582	147948	hgsc.bcm.edu	37	chr19	56896171	56896171	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	gagccatatttaaaggccttCccacattccttacatttata	4	11	0	0			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr19:56896171C>T	ENST00000301310.4	-	5	773	c.615G>A	c.(613-615)ggG>ggA	p.G205G	ZNF582_ENST00000586929.1_Silent_p.G205G|AC006116.12_ENST00000589671.1_RNA	NM_144690.1	NP_653291.1	Q96NG8	ZN582_HUMAN	zinc finger protein 582	205					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0547)		TAAAGGCCTTCCCACATTCCT	0.338																																					p.G205G	Ovarian(183;1887 2032 4349 30507 51343)	Atlas-SNP	.											.	ZNF582	56	.	0			c.G615A						.						68	70	69					19																	56896171		2203	4300	6503	SO:0001819	synonymous_variant	147948	exon5			GGCCTTCCCACAT	AK055489	CCDS33121.1	19q13.43	2013-07-15			ENSG00000018869	ENSG00000018869		"Zinc fingers, C2H2-type", "-"	26421	protein-coding gene	gene with protein product		615600				12477932	Standard	NM_144690		Approved	FLJ30927	uc002qmz.1	Q96NG8	OTTHUMG00000181939	ENST00000301310.4:c.615G>A	chr19.hg19:g.56896171C>T		70.0	0.0		70.0	16.0	NM_144690	B4DQZ9|B7Z9R3|Q6PJT6	Silent	SNP	ENST00000301310.4	hg19	CCDS33121.1																																																																																			.	.		0.338	ZNF582-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458387.2	NM_144690		T	56896171	C	T	56896171	2	4	294	1	0	0	0	0	0	0	0	1	18029	842	30	3		3	ZNF582	19	56896171	Silent	SNP	C	TCGA-G3-A7M9-01A-23D-A34Z-10	191773	56896171	2232812	86	42858										
TTLL12	23170	hgsc.bcm.edu	37	chr22	43575637	43575637	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	6	1	1.48074841503015	1.19282511210762	1.55585884187951	0.102564102564103	0.617038875103394	0	ggctgcacctggtagtgctcGgcgggcggctcgggtgtgca	19	11	0	0			TCGA-G3-A7M9-01A-23D-A34Z-10	TCGA-G3-A7M9-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6df05259-d701-492f-ab3f-5fc66ecb1c34	546c2c7d-b949-4ef6-96c8-9f2479352bf3	g.chr22:43575637G>A	ENST00000216129.6	-	5	891	c.828C>T	c.(826-828)gcC>gcT	p.A276A		NM_015140.3	NP_055955.1	Q14166	TTL12_HUMAN	tubulin tyrosine ligase-like family, member 12	276					cellular protein modification process (GO:0006464)					central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)	13		Ovarian(80;0.221)|Glioma(61;0.222)				GGTAGTGCTCGGCGGGCGGCT	0.622																																					p.A276A		Atlas-SNP	.											.	TTLL12	50	.	0			c.C828T						.						54	58	57					22																	43575637		2203	4300	6503	SO:0001819	synonymous_variant	23170	exon5			GTGCTCGGCGGGC	D63487	CCDS14047.1	22q13.31	2013-02-14	2006-02-02		ENSG00000100304	ENSG00000100304		"Tubulin tyrosine ligase-like family"	28974	protein-coding gene	gene with protein product						15890843	Standard	NM_015140		Approved	KIAA0153	uc003bdp.3	Q14166	OTTHUMG00000150682	ENST00000216129.6:c.828C>T	chr22.hg19:g.43575637G>A		24.0	0.0		20.0	9.0	NM_015140	Q20WK5|Q9UGU3	Silent	SNP	ENST00000216129.6	hg19	CCDS14047.1																																																																																			.	.		0.622	TTLL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319611.1	NM_015140		A	43575637	G	A	43575637	2	1	294	1	0	0	0	0	0	0	0	1	16740	1103	39	1		1	TTLL12	22	43575637	Silent	SNP	G	TCGA-G3-A7M9-01A-23D-A34Z-10		43575637	7728929	87	42859										
TNFRSF4	7293	hgsc.bcm.edu	37	chr1	1148457	1148457	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	gtggccgtgcacagctgcttCcgctcactcccacttcctga	9	17	1	1			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr1:1148457C>G	ENST00000379236.3	-	3	289	c.285G>C	c.(283-285)cgG>cgC	p.R95R	TNFRSF4_ENST00000453580.1_5'UTR	NM_003327.3	NP_003318.1	P43489	TNR4_HUMAN	tumor necrosis factor receptor superfamily, member 4	95					cellular defense response (GO:0006968)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of immunoglobulin secretion (GO:0051024)|regulation of apoptotic process (GO:0042981)|regulation of protein kinase activity (GO:0045859)|T cell proliferation (GO:0042098)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	tumor necrosis factor-activated receptor activity (GO:0005031)			large_intestine(1)|lung(2)|urinary_tract(1)	4	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;3.73e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.01e-21)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		ACAGCTGCTTCCGCTCACTCC	0.677																																					p.R95R		Atlas-SNP	.											.	TNFRSF4	12	.	0			c.G285C						.						14	16	15					1																	1148457		2193	4289	6482	SO:0001819	synonymous_variant	7293	exon3			CTGCTTCCGCTCA	X75962	CCDS11.1	1p36	2008-02-05			ENSG00000186827	ENSG00000186827		"Tumor necrosis factor receptor superfamily", "CD molecules"	11918	protein-coding gene	gene with protein product		600315		TXGP1L		7510240, 2828930	Standard	NM_003327		Approved	ACT35, OX40, CD134	uc001ade.3	P43489	OTTHUMG00000001415	ENST00000379236.3:c.285G>C	chr1.hg19:g.1148457C>G		87.0	0.0		110.0	49.0	NM_003327	Q13663|Q2M312|Q5T7M0	Silent	SNP	ENST00000379236.3	hg19	CCDS11.1	.	.	.	.	.	.	.	.	.	.	c	0.024	-1.390492	0.01185	.	.	ENSG00000186827	ENST00000453580	.	.	.	3.69	0.631	0.17699	.	.	.	.	.	T	0.32133	0.0819	.	.	.	0.09310	N	0.999996	.	.	.	.	.	.	T	0.27297	-1.0078	4	.	.	.	-2.3683	7.4903	0.27458	0.1049:0.5304:0.3646:0.0	.	.	.	.	Q	41	.	.	E	-	1	0	TNFRSF4	1138320	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.663000	0.05299	0.040000	0.15660	-0.526000	0.04340	GAA	.	.		0.677	TNFRSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004086.1			G	1148457	C	G	1148457	2	3	295	1	0	0	0	0	0	0	0	1	16312	842	30	4		4	TNFRSF4	1	1148457	Silent	SNP	C	TCGA-G3-AAUZ-01A-11D-A382-10		1148457	248102164	1	42860										
AADACL3	126767	hgsc.bcm.edu	37	chr1	12785873	12785873	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	atggaggatggtttccatggAgtgctcaggaccattgacat	13	7	1	1			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr1:12785873A>G	ENST00000359318.5	+	4	1168	c.963A>G	c.(961-963)ggA>ggG	p.G321G	AADACL3_ENST00000332530.3_Silent_p.G251G	NM_001103170.1	NP_001096640.1	Q5VUY0	ADCL3_HUMAN	arylacetamide deacetylase-like 3	321							hydrolase activity (GO:0016787)			breast(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)	15	Ovarian(185;0.249)	Lung NSC(185;8.27e-05)|all_lung(284;9.47e-05)|Renal(390;0.000147)|Colorectal(325;0.000583)|Breast(348;0.000596)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00217)|KIRC - Kidney renal clear cell carcinoma(229;0.00579)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		GTTTCCATGGAGTGCTCAGGA	0.478																																					p.G321G		Atlas-SNP	.											.	AADACL3	84	.	0			c.A963G						.						75	73	73					1																	12785873		1973	4155	6128	SO:0001819	synonymous_variant	126767	exon4			CCATGGAGTGCTC		CCDS41253.1	1p36.21	2014-07-17			ENSG00000188984	ENSG00000188984			32037	protein-coding gene	gene with protein product							Standard	XM_006710337		Approved	OTTHUMG00000001887	uc009vnn.1	Q5VUY0	OTTHUMG00000001887	ENST00000359318.5:c.963A>G	chr1.hg19:g.12785873A>G		114.0	0.0		120.0	52.0	NM_001103170	B3KXR9|Q5VUY1	Silent	SNP	ENST00000359318.5	hg19	CCDS41253.1																																																																																			.	.		0.478	AADACL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005324.2	NM_001103170		G	12785873	A	G	12785873	2	3	295	1	0	0	0	0	0	0	0	1	12	291	11	2		2	AADACL3	1	12785873	Silent	SNP	A	TCGA-G3-AAUZ-01A-11D-A382-10	11637416	12785873	236464748	2	42861										
PRAMEF12	390999	hgsc.bcm.edu	37	chr1	12835197	12835197	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	tgcaggcctggcccttcaccTgccttcctctagggtccctg	10	17	2	0			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr1:12835197T>C	ENST00000357726.4	+	1	214	c.187T>C	c.(187-189)Tgc>Cgc	p.C63R		NM_001080830.1	NP_001074299.1	O95522	PRA12_HUMAN	PRAME family member 12	63					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					NS(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(9)|ovary(3)|skin(1)|urinary_tract(1)	23	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00818)|Colorectal(212;5.04e-06)|Kidney(185;4.99e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000198)|COAD - Colon adenocarcinoma(227;0.000245)|BRCA - Breast invasive adenocarcinoma(304;0.000295)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GCCCTTCACCTGCCTTCCTCT	0.577																																					p.C63R		Atlas-SNP	.											.	PRAMEF12	69	.	0			c.T187C						.						80	84	83					1																	12835197		2203	4300	6503	SO:0001583	missense	390999	exon1			TTCACCTGCCTTC		CCDS41254.1	1p36.21	2013-01-17			ENSG00000116726	ENSG00000116726		"-"	22125	protein-coding gene	gene with protein product							Standard	NM_001080830		Approved	OTTHUMG00000001927	uc001aui.3	O95522	OTTHUMG00000001927	ENST00000357726.4:c.187T>C	chr1.hg19:g.12835197T>C	ENSP00000350358:p.Cys63Arg	167.0	0.0		215.0	47.0	NM_001080830		Missense_Mutation	SNP	ENST00000357726.4	hg19	CCDS41254.1	.	.	.	.	.	.	.	.	.	.	.	1.284	-0.609441	0.03690	.	.	ENSG00000116726	ENST00000357726	T	0.13778	2.56	2.68	-1.2	0.09554	.	1.463560	0.03995	N	0.295465	T	0.06371	0.0164	N	0.05330	-0.07	0.09310	N	0.999993	B	0.02656	0.0	B	0.04013	0.001	T	0.34403	-0.9830	10	0.16896	T	0.51	.	4.5886	0.12295	0.0:0.1753:0.1834:0.6413	.	63	O95522	PRA12_HUMAN	R	63	ENSP00000350358:C63R	ENSP00000350358:C63R	C	+	1	0	PRAMEF12	12757784	0.000000	0.05858	0.005000	0.12908	0.312000	0.27988	-1.603000	0.02077	-0.268000	0.09312	0.164000	0.16699	TGC	.	.		0.577	PRAMEF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005457.1	XM_372760		C	12835197	T	C	12835197	3	2	295	1	0	0	0	0	1	0	0	0	12440	1580	55	2	189	2	PRAMEF12	1	12835197	Missense_Mutation	SNP	T	TCGA-G3-AAUZ-01A-11D-A382-10	49324	12835197	236415424	3	42862										
USP48	84196	hgsc.bcm.edu	37	chr1	22032230	22032230	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	aggaactcacagtttagaatCttctttggtcatggaagcaa	9	7	4	1			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr1:22032230C>T	ENST00000308271.9	-	19	3022	c.2374G>A	c.(2374-2376)Gat>Aat	p.D792N	USP48_ENST00000374732.3_Missense_Mutation_p.D330N|USP48_ENST00000400301.1_Missense_Mutation_p.D792N|USP48_ENST00000529637.1_Missense_Mutation_p.D804N	NM_032236.5	NP_115612.4	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 48	792	DUSP 3. {ECO:0000255|PROSITE- ProRule:PRU00613}.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			NS(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(14)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)		AGTTTAGAATCTTCTTTGGTC	0.378																																					p.D792N		Atlas-SNP	.											USP48,NS,carcinoma,0,1	USP48	91	.	0			c.G2374A						.						57	62	60					1																	22032230		2203	4300	6503	SO:0001583	missense	84196	exon19			TAGAATCTTCTTT	AF502942	CCDS30623.1, CCDS44084.1	1p36.12	2008-02-05	2005-08-08	2004-04-07	ENSG00000090686	ENSG00000090686		"Ubiquitin-specific peptidases"	18533	protein-coding gene	gene with protein product			"ubiquitin specific protease 31", "ubiquitin specific protease 48"	USP31		12838346	Standard	XM_005246009		Approved	FLJ23277, FLJ11328, FLJ20103, FLJ23054, MGC14879	uc001bfb.3	Q86UV5	OTTHUMG00000007798	ENST00000308271.9:c.2374G>A	chr1.hg19:g.22032230C>T	ENSP00000309262:p.Asp792Asn	402.0	2.0		492.0	110.0	NM_032236	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Missense_Mutation	SNP	ENST00000308271.9	hg19	CCDS30623.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.742447	0.89573	.	.	ENSG00000090686	ENST00000400301;ENST00000308271;ENST00000374732;ENST00000529637	T;T;T	0.06371	3.34;3.35;3.31	5.7	5.7	0.88788	Peptidase C19, ubiquitin-specific peptidase, DUSP domain (1);	0.000000	0.85682	D	0.000000	T	0.24198	0.0586	M	0.70595	2.14	0.80722	D	1	D;P;D;D;D	0.63880	0.993;0.867;0.976;0.958;0.993	P;B;P;P;D	0.63033	0.808;0.323;0.677;0.534;0.91	T	0.00049	-1.2202	10	0.59425	D	0.04	.	18.8179	0.92085	0.0:1.0:0.0:0.0	.	804;792;792;792;330	B7ZKS7;B7ZKS3;Q86UV5-2;Q86UV5;Q86UV5-5	.;.;.;UBP48_HUMAN;.	N	792;792;330;804	ENSP00000383157:D792N;ENSP00000309262:D792N;ENSP00000431949:D804N	ENSP00000309262:D792N	D	-	1	0	USP48	21904817	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	6.994000	0.76251	2.697000	0.92050	0.557000	0.71058	GAT	.	.		0.378	USP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021372.1	NM_032236		T	22032230	C	T	22032230	3	4	295	1	0	0	0	0	1	0	0	0	17094	913	32	3	769	3	USP48	1	22032230	Missense_Mutation	SNP	C	TCGA-G3-AAUZ-01A-11D-A382-10	9197033	22032230	227218391	4	42863										
EPHB2	2048	hgsc.bcm.edu	37	chr1	23232505	23232505	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	ccaggcatgaagatctacatCgatcctttcacctacgagga	8	12	2	2			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr1:23232505C>T	ENST00000400191.3	+	10	1809	c.1791C>T	c.(1789-1791)atC>atT	p.I597I	EPHB2_ENST00000374630.3_Silent_p.I597I|EPHB2_ENST00000374627.1_Silent_p.I592I|EPHB2_ENST00000374632.3_Silent_p.I598I	NM_004442.6|NM_017449.3	NP_004433.2|NP_059145.2	P29323	EPHB2_HUMAN	EPH receptor B2	597					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|camera-type eye morphogenesis (GO:0048593)|central nervous system projection neuron axonogenesis (GO:0021952)|commissural neuron axon guidance (GO:0071679)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|ephrin receptor signaling pathway (GO:0048013)|inner ear morphogenesis (GO:0042472)|learning (GO:0007612)|negative regulation of axonogenesis (GO:0050771)|nervous system development (GO:0007399)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse assembly (GO:0051965)|regulation of body fluid levels (GO:0050878)|retinal ganglion cell axon guidance (GO:0031290)|urogenital system development (GO:0001655)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|protein tyrosine kinase activity (GO:0004713)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(8)|stomach(1)|urinary_tract(1)	56		Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153)		AGATCTACATCGATCCTTTCA	0.522																																					p.I598I		Atlas-SNP	.											EPHB2_ENST00000374632,NS,carcinoma,0,2	EPHB2	257	.	0			c.C1794T						.						93	86	88					1																	23232505		2203	4300	6503	SO:0001819	synonymous_variant	2048	exon10			CTACATCGATCCT	AF025304	CCDS229.2, CCDS230.1	1p36.1-p35	2014-09-17	2004-10-28		ENSG00000133216	ENSG00000133216	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3393	protein-coding gene	gene with protein product		600997	"EphB2"	DRT, ERK, EPHT3		1648701	Standard	NM_017449		Approved	Hek5, Tyro5	uc001bge.3	P29323	OTTHUMG00000002881	ENST00000400191.3:c.1791C>T	chr1.hg19:g.23232505C>T		93.0	0.0		78.0	22.0	NM_004442	O43477|Q5T0U6|Q5T0U7|Q5T0U8	Silent	SNP	ENST00000400191.3	hg19																																																																																				.	.		0.522	EPHB2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000008060.2	NM_017449		T	23232505	C	T	23232505	2	4	295	1	0	0	0	0	0	0	0	1	5177	874	31	1		1	EPHB2	1	23232505	Silent	SNP	C	TCGA-G3-AAUZ-01A-11D-A382-10	1200275	23232505	226018116	5	42864										
THRAP3	9967	hgsc.bcm.edu	37	chr1	36755239	36755239	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	ctcatcacctcccccaagaaAgacctctgagagccgagaca	7	16	3	4			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr1:36755239A>G	ENST00000354618.5	+	5	1843	c.1619A>G	c.(1618-1620)aAg>aGg	p.K540R	THRAP3_ENST00000469141.2_Missense_Mutation_p.K540R	NM_005119.3	NP_005110.2	Q9Y2W1	TR150_HUMAN	thyroid hormone receptor associated protein 3	540	Required for mRNA decay activity.				androgen receptor signaling pathway (GO:0030521)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|mRNA processing (GO:0006397)|mRNA stabilization (GO:0048255)|nuclear-transcribed mRNA catabolic process (GO:0000956)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|phosphoprotein binding (GO:0051219)|poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(5)|stomach(1)	37		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				CCCCCAAGAAAGACCTCTGAG	0.512			T	USP6	aneurysmal bone cysts																																p.K540R	Pancreas(129;785 1795 20938 23278 32581)	Atlas-SNP	.		Dom	yes		1	1p34.3	9967	thyroid hormone receptor associated protein 3 (TRAP150)		M	.	THRAP3	93	.	0			c.A1619G						.						84	92	89					1																	36755239		2203	4300	6503	SO:0001583	missense	9967	exon5			CAAGAAAGACCTC	AF117756	CCDS405.1	1p34.3	2008-02-05			ENSG00000054118	ENSG00000054118			22964	protein-coding gene	gene with protein product		603809					Standard	NM_005119		Approved	TRAP150	uc001cae.4	Q9Y2W1	OTTHUMG00000007866	ENST00000354618.5:c.1619A>G	chr1.hg19:g.36755239A>G	ENSP00000346634:p.Lys540Arg	106.0	0.0		106.0	24.0	NM_005119	D3DPS5|Q5VTK6	Missense_Mutation	SNP	ENST00000354618.5	hg19	CCDS405.1	.	.	.	.	.	.	.	.	.	.	A	13.22	2.173270	0.38413	.	.	ENSG00000054118	ENST00000354618;ENST00000469141	T;T	0.16743	2.32;2.32	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.21022	0.0506	L	0.51422	1.61	0.42774	D	0.993849	B	0.26512	0.151	B	0.30716	0.119	T	0.02020	-1.1228	10	0.38643	T	0.18	-20.026	15.7905	0.78357	1.0:0.0:0.0:0.0	.	540	Q9Y2W1	TR150_HUMAN	R	540	ENSP00000346634:K540R;ENSP00000433825:K540R	ENSP00000346634:K540R	K	+	2	0	THRAP3	36527826	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	4.263000	0.58853	2.324000	0.78689	0.533000	0.62120	AAG	.	.		0.512	THRAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021688.2	NM_005119		G	36755239	A	G	36755239	3	3	295	1	0	0	0	0	1	0	0	0	15889	72	3	2	1629	2	THRAP3	1	36755239	Missense_Mutation	SNP	A	TCGA-G3-AAUZ-01A-11D-A382-10	13522734	36755239	212495382	6	42865										
COL9A2	1298	hgsc.bcm.edu	37	chr1	40770006	40770006	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	tggcaccttgtctcctttgaCgcctggcaagccttggggcc	12	14	1	1	rs148912050		TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr1:40770006C>T	ENST00000372748.3	-	24	1369	c.1273G>A	c.(1273-1275)Gtc>Atc	p.V425I	COL9A2_ENST00000466267.1_5'UTR	NM_001852.3	NP_001843.1	Q14055	CO9A2_HUMAN	collagen, type IX, alpha 2	425	Triple-helical region 3 (COL3).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(4)|stomach(2)|urinary_tract(2)	22	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;2.08e-17)			TCTCCTTTGACGCCTGGCAAG	0.612																																					p.V425I		Atlas-SNP	.											.	COL9A2	63	.	0			c.G1273A						.	C	ILE/VAL	0,4358		0,0,2179	26	26	26		1273	2	1	1	dbSNP_134	26	1,8535		0,1,4267	no	missense	COL9A2	NM_001852.3	29	0,1,6446	TT,TC,CC		0.0117,0.0,0.0078	benign	425/690	40770006	1,12893	2179	4268	6447	SO:0001583	missense	1298	exon24			CTTTGACGCCTGG	M95610	CCDS450.1	1p33-p32	2013-01-16			ENSG00000049089	ENSG00000049089		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2218	protein-coding gene	gene with protein product		120260		EDM2		8454052, 8528240, 1429648	Standard	NM_001852		Approved	MED	uc001cfh.1	Q14055	OTTHUMG00000005761	ENST00000372748.3:c.1273G>A	chr1.hg19:g.40770006C>T	ENSP00000361834:p.Val425Ile	80.0	0.0		108.0	33.0	NM_001852	B2RMP9	Missense_Mutation	SNP	ENST00000372748.3	hg19	CCDS450.1	.	.	.	.	.	.	.	.	.	.	C	4.579	0.107636	0.08780	0.0	1.17E-4	ENSG00000049089	ENST00000372748	D	0.93307	-3.2	5.49	1.97	0.26223	.	0.265492	0.43416	N	0.000568	T	0.78960	0.4366	N	0.05230	-0.09	0.19775	N	0.99996	P	0.39665	0.682	B	0.29716	0.106	T	0.72171	-0.4371	10	0.27785	T	0.31	.	6.9054	0.24305	0.0:0.3562:0.0:0.6438	.	425	Q14055	CO9A2_HUMAN	I	425	ENSP00000361834:V425I	ENSP00000361834:V425I	V	-	1	0	COL9A2	40542593	1.000000	0.71417	1.000000	0.80357	0.317000	0.28152	1.511000	0.35801	0.393000	0.25203	-0.340000	0.08031	GTC	.	C|1.000;G|0.000		0.612	COL9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015764.3	NM_001852		T	40770006	C	T	40770006	3	4	295	1	0	0	0	0	1	0	0	0	3710	536	19	1	832	1	COL9A2	1	40770006	Missense_Mutation	SNP	C	TCGA-G3-AAUZ-01A-11D-A382-10	4014767	40770006	208480615	7	42866										
NRD1	114883	hgsc.bcm.edu	37	chr1	52254955	52254955	+	IGR	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	aaggttgagtgttgttgtgaAagccctgatatcagtaatgg	13	4	1	3			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr1:52254955A>C	ENST00000428468.1	+	0	2893				NRD1_ENST00000352171.7_Missense_Mutation_p.F1137V|NRD1_ENST00000485608.1_5'UTR|NRD1_ENST00000539524.1_Missense_Mutation_p.F1073V|NRD1_ENST00000354831.7_Missense_Mutation_p.F1205V			Q96SU4	OSBL9_HUMAN	oxysterol binding protein-like 9						lipid transport (GO:0006869)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(3)|pancreas(1)|prostate(3)|skin(1)	18						GTTGTTGTGAAAGCCCTGATA	0.413																																					p.F1205V		Atlas-SNP	.											.	NRD1	89	.	0			c.T3613G						.						165	153	157					1																	52254955		2203	4300	6503	SO:0001628	intergenic_variant	4898	exon33			TTGTGAAAGCCCT	AF392445	CCDS558.1, CCDS41332.1, CCDS41333.1, CCDS41334.1, CCDS41332.2, CCDS41332.3, CCDS41333.2, CCDS44145.1, CCDS55598.1	1p32.3	2013-01-10			ENSG00000117859	ENSG00000117859		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16386	protein-coding gene	gene with protein product		606737					Standard	NM_148904		Approved		uc001csu.3	Q96SU4	OTTHUMG00000008234		chr1.hg19:g.52254955A>C		139.0	0.0		126.0	49.0	NM_002525	B1AKJ8|B3KPQ4|D3DQ31|Q5TFC0|Q6IA67|Q86YQ3|Q8NB17|Q8TAS8|Q96SK4|Q9H9X2	Missense_Mutation	SNP	ENST00000428468.1	hg19	CCDS41332.3	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	31|31	5.064047|5.064047	0.93898|0.93898	.|.	.|.	ENSG00000078618|ENSG00000078618	ENST00000440943|ENST00000352171;ENST00000354831;ENST00000539524;ENST00000371665	.|T;T;T	.|0.39229	.|1.09;1.14;1.12	5.75|5.75	5.75|5.75	0.90469|0.90469	.|.	0.146511|0.146511	0.64402|0.64402	D|D	0.000008|0.000008	T|T	0.66436|0.66436	0.2789|0.2789	M|M	0.85041|0.85041	2.73|2.73	0.80722|0.80722	D|D	1|1	.|D;D	.|0.71674	.|0.989;0.998	.|P;P	.|0.62813	.|0.744;0.907	T|T	0.72883|0.72883	-0.4157|-0.4157	6|10	.|0.87932	.|D	.|0	-9.4331|-9.4331	15.2446|15.2446	0.73497|0.73497	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|1136;1205	.|O43847;B1AKJ5	.|NRDC_HUMAN;.	C|V	523|1137;1205;1073;539	.|ENSP00000262679:F1137V;ENSP00000346890:F1205V;ENSP00000444416:F1073V	.|ENSP00000262679:F1137V	F|F	-|-	2|1	0|0	NRD1|NRD1	52027543|52027543	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	8.660000|8.660000	0.91121|0.91121	2.202000|2.202000	0.70862|0.70862	0.528000|0.528000	0.53228|0.53228	TTT|TTC	.	.		0.413	OSBPL9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000022584.4			C	52254955	A	C	52254955	1	2	295	0	1	0	0	0	0	0	0	0	10654	14	1	5		5	NRD1	1	52254955	IGR	SNP	A	TCGA-G3-AAUZ-01A-11D-A382-10	11484949	52254955	196995666	8	42867										
HOOK1	51361	hgsc.bcm.edu	37	chr1	60331564	60331564	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	tacaaaagatcaatgaacttGaagctgctcttcagaagaaa	7	7	3	5			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr1:60331564G>A	ENST00000371208.3	+	19	2022	c.1765G>A	c.(1765-1767)Gaa>Aaa	p.E589K	HOOK1_ENST00000465876.1_3'UTR|HOOK1_ENST00000395561.2_Missense_Mutation_p.E547K	NM_015888.4	NP_056972.1	Q9UJC3	HOOK1_HUMAN	hook microtubule-tethering protein 1	589					early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)|spermatid development (GO:0007286)	FHF complex (GO:0070695)|microtubule (GO:0005874)	identical protein binding (GO:0042802)			biliary_tract(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|urinary_tract(1)	29	all_cancers(7;0.000129)					CAATGAACTTGAAGCTGCTCT	0.294																																					p.E589K		Atlas-SNP	.											.	HOOK1	54	.	0			c.G1765A						.						60	68	65					1																	60331564		2203	4299	6502	SO:0001583	missense	51361	exon19			GAACTTGAAGCTG	AF044923	CCDS612.1	1p32.1	2013-08-21	2013-08-21		ENSG00000134709	ENSG00000134709			19884	protein-coding gene	gene with protein product		607820	"hook homolog 1 (Drosophila)"			9927460	Standard	XM_005270922		Approved	HK1	uc001czo.3	Q9UJC3	OTTHUMG00000008990	ENST00000371208.3:c.1765G>A	chr1.hg19:g.60331564G>A	ENSP00000360252:p.Glu589Lys	666.0	1.0		701.0	239.0	NM_015888	A8K8E9|A8MU44|B4DX15|O60561|Q5TG44	Missense_Mutation	SNP	ENST00000371208.3	hg19	CCDS612.1	.	.	.	.	.	.	.	.	.	.	G	17.66	3.444544	0.63178	.	.	ENSG00000134709	ENST00000371208;ENST00000395561	T;T	0.19250	2.16;2.16	5.56	5.56	0.83823	.	0.289394	0.42821	D	0.000658	T	0.21550	0.0519	L	0.33339	1.005	0.46749	D	0.999186	P	0.38395	0.629	B	0.39771	0.309	T	0.01500	-1.1339	10	0.27082	T	0.32	.	19.5309	0.95228	0.0:0.0:1.0:0.0	.	589	Q9UJC3	HOOK1_HUMAN	K	589;547	ENSP00000360252:E589K;ENSP00000378928:E547K	ENSP00000360252:E589K	E	+	1	0	HOOK1	60104152	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.884000	0.56175	2.636000	0.89361	0.650000	0.86243	GAA	.	.		0.294	HOOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024934.1	NM_015888		A	60331564	G	A	60331564	3	1	295	1	0	0	0	0	1	0	0	0	7291	1291	45	3	1839	3	HOOK1	1	60331564	Missense_Mutation	SNP	G	TCGA-G3-AAUZ-01A-11D-A382-10	8076609	60331564	188919057	9	42868										
RPF1	80135	hgsc.bcm.edu	37	chr1	84955365	84955365	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	tgcttcttacttcaacaaacAgacttctcccaagattctca	3	13	4	2			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr1:84955365A>T	ENST00000370654.5	+	4	431	c.416A>T	c.(415-417)cAg>cTg	p.Q139L		NM_025065.6	NP_079341.2	Q9H9Y2	RPF1_HUMAN	ribosome production factor 1 homolog (S. cerevisiae)	139					rRNA processing (GO:0006364)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)			breast(2)|endometrium(1)|kidney(3)|large_intestine(5)|lung(2)|prostate(1)	14						TTCAACAAACAGACTTCTCCC	0.338																																					p.Q139L		Atlas-SNP	.											.	RPF1	31	.	0			c.A416T						.						97	90	93					1																	84955365		2203	4300	6503	SO:0001583	missense	80135	exon4			ACAAACAGACTTC	AF322053	CCDS695.1	1p22.3	2009-09-25	2009-09-25	2009-09-25	ENSG00000117133	ENSG00000117133			30350	protein-coding gene	gene with protein product	"RNA processing factor 1", "ribosome production factor 1"		"brix domain containing 5"	BXDC5		11864606	Standard	NM_025065		Approved		uc001djv.4	Q9H9Y2	OTTHUMG00000009857	ENST00000370654.5:c.416A>T	chr1.hg19:g.84955365A>T	ENSP00000359688:p.Gln139Leu	101.0	0.0		93.0	29.0	NM_025065	Q5VSK7|Q6AHX1|Q8WXZ8	Missense_Mutation	SNP	ENST00000370654.5	hg19	CCDS695.1	.	.	.	.	.	.	.	.	.	.	A	14.22	2.469077	0.43839	.	.	ENSG00000117133	ENST00000370654	T	0.30714	1.52	5.96	5.96	0.96718	.	0.166320	0.53938	D	0.000049	T	0.09291	0.0229	N	0.10972	0.075	0.51012	D	0.999909	B	0.02656	0.0	B	0.04013	0.001	T	0.11494	-1.0585	10	0.27785	T	0.31	-4.8633	16.4484	0.83959	1.0:0.0:0.0:0.0	.	139	Q9H9Y2	RPF1_HUMAN	L	139	ENSP00000359688:Q139L	ENSP00000359688:Q139L	Q	+	2	0	RPF1	84727953	1.000000	0.71417	0.955000	0.39395	0.985000	0.73830	6.640000	0.74319	2.285000	0.76669	0.533000	0.62120	CAG	.	.		0.338	RPF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027238.1	NM_025065		T	84955365	A	T	84955365	3	4	295	1	0	0	0	0	1	0	0	0	13561	188	7	4	430	4	RPF1	1	84955365	Missense_Mutation	SNP	A	TCGA-G3-AAUZ-01A-11D-A382-10	24623801	84955365	164295256	10	42869										
POLR3C	10623	hgsc.bcm.edu	37	chr1	145608260	145608260	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	ctgccagtcgcacaaatgtgTttgatacttcagcatagtcc	8	11	1	1			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr1:145608260T>C	ENST00000334163.3	-	4	597	c.437A>G	c.(436-438)aAc>aGc	p.N146S	RNF115_ENST00000369291.5_5'Flank|POLR3C_ENST00000471254.1_5'UTR|POLR3C_ENST00000369294.1_Missense_Mutation_p.N146S	NM_006468.6	NP_006459.3	Q9BUI4	RPC3_HUMAN	polymerase (RNA) III (DNA directed) polypeptide C (62kD)	146					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			breast(2)|endometrium(4)|kidney(1)|large_intestine(3)|liver(1)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)		Epithelial(2;7.55e-13)			CACAAATGTGTTTGATACTTC	0.512																																					p.N146S		Atlas-SNP	.											.	POLR3C	41	.	0			c.A437G						.						186	165	172					1																	145608260		2203	4300	6503	SO:0001583	missense	10623	exon4			AATGTGTTTGATA	AJ238234	CCDS72864.1	1q21	2013-01-21			ENSG00000186141	ENSG00000186141		"RNA polymerase subunits"	30076	protein-coding gene	gene with protein product						9171375, 12391170	Standard	NM_006468		Approved	RPC62, RPC3	uc001eoh.3	Q9BUI4	OTTHUMG00000013753	ENST00000334163.3:c.437A>G	chr1.hg19:g.145608260T>C	ENSP00000334564:p.Asn146Ser	65.0	0.0		124.0	21.0	NM_006468	O15317|Q9Y3R6	Missense_Mutation	SNP	ENST00000334163.3	hg19	CCDS921.1	.	.	.	.	.	.	.	.	.	.	T	4.581	0.107977	0.08780	.	.	ENSG00000186141	ENST00000334163;ENST00000369294	T;T	0.39787	1.06;1.06	5.41	-1.27	0.09347	RNA polymerase III Rpc82, C -terminal (1);	0.652107	0.17151	N	0.185056	T	0.05227	0.0139	N	0.05031	-0.125	0.33947	D	0.643959	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.33828	-0.9853	10	0.08837	T	0.75	-13.0953	7.0262	0.24942	0.0:0.5191:0.1649:0.316	.	146;146;146	E9PHH9;Q9BUI4;Q53F76	.;RPC3_HUMAN;.	S	146	ENSP00000334564:N146S;ENSP00000358300:N146S	ENSP00000334564:N146S	N	-	2	0	POLR3C	144319617	0.188000	0.23250	0.973000	0.42090	0.426000	0.31534	0.158000	0.16422	-0.175000	0.10725	-0.290000	0.09829	AAC	.	.		0.512	POLR3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038542.1	NM_006468		C	145608260	T	C	145608260	3	2	295	1	0	0	0	0	1	0	0	0	12239	1725	60	2	1215	2	POLR3C	1	145608260	Missense_Mutation	SNP	T	TCGA-G3-AAUZ-01A-11D-A382-10	60652895	145608260	103642361	11	42870										
ASH1L	55870	hgsc.bcm.edu	37	chr1	155311812	155311812	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	caggatagcggttccggtggAtcttgtaaaacaggtgtgct	14	7	1	0			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr1:155311812A>C	ENST00000368346.3	-	25	9029	c.8390T>G	c.(8389-8391)aTc>aGc	p.I2797S	ASH1L_ENST00000392403.3_Missense_Mutation_p.I2792S			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	2797	BAH. {ECO:0000255|PROSITE- ProRule:PRU00370}.				cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			GTTCCGGTGGATCTTGTAAAA	0.478																																					p.I2792S		Atlas-SNP	.											.	ASH1L	279	.	0			c.T8375G						.						243	228	233					1																	155311812		2203	4300	6503	SO:0001583	missense	55870	exon25			CGGTGGATCTTGT	AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.8390T>G	chr1.hg19:g.155311812A>C	ENSP00000357330:p.Ile2797Ser	135.0	0.0		191.0	71.0	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	hg19		.	.	.	.	.	.	.	.	.	.	A	27.2	4.805699	0.90623	.	.	ENSG00000116539	ENST00000368346;ENST00000392403	D;D	0.91237	-2.81;-2.81	5.27	5.27	0.74061	Bromo adjacent homology (BAH) domain (2);	0.000000	0.85682	D	0.000000	D	0.93572	0.7948	M	0.68317	2.08	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.85130	0.997;0.994	D	0.94480	0.7692	10	0.87932	D	0	.	15.0168	0.71591	1.0:0.0:0.0:0.0	.	2797;2792	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	S	2797;2792	ENSP00000357330:I2797S;ENSP00000376204:I2792S	ENSP00000357330:I2797S	I	-	2	0	ASH1L	153578436	1.000000	0.71417	0.994000	0.49952	0.986000	0.74619	7.065000	0.76727	2.210000	0.71456	0.454000	0.30748	ATC	.	.		0.478	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		C	155311812	A	C	155311812	3	2	295	1	0	0	0	0	1	0	0	0	1041	333	12	5	535	5	ASH1L	1	155311812	Missense_Mutation	SNP	A	TCGA-G3-AAUZ-01A-11D-A382-10	9703552	155311812	93938809	12	42871										
KIRREL	55243	hgsc.bcm.edu	37	chr1	158046019	158046019	+	Frame_Shift_Del	DEL	G	G	-													0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	ttgtgcaatggaccaaggacGggctggccctgggcatgggc							TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr1:158046019delG	ENST00000359209.6	+	2	236	c.169delG	c.(169-171)gggfs	p.G57fs	KIRREL_ENST00000360089.4_5'UTR|KIRREL_ENST00000392272.2_Frame_Shift_Del_p.G57fs|KIRREL_ENST00000368173.3_Frame_Shift_Del_p.G57fs|KIRREL_ENST00000416935.2_Intron			Q96J84	KIRR1_HUMAN	kin of IRRE like (Drosophila)	57	Ig-like C2-type 1.				excretion (GO:0007588)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of actin filament polymerization (GO:0030838)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|dendritic shaft (GO:0043198)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	myosin binding (GO:0017022)			NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|prostate(5)|skin(3)|stomach(1)	38	all_hematologic(112;0.0378)					GACCAAGGACGGGCTGGCCCT	0.622																																					p.D56fs		Atlas-INDEL	.											.	KIRREL	346	.	0			c.168delC						.						102	103	102					1																	158046019		2203	4300	6503	SO:0001589	frameshift_variant	55243	exon2			.	AK001707	CCDS1172.2, CCDS72952.1	1q21-q25	2013-01-29			ENSG00000183853	ENSG00000183853		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15734	protein-coding gene	gene with protein product	"nephrin-like protein 1"	607428				12424224	Standard	NM_001286349		Approved	NEPH1	uc001frn.4	Q96J84	OTTHUMG00000022438	ENST00000359209.6:c.169delG	chr1.hg19:g.158046019delG	ENSP00000352138:p.Gly57fs	93.0	0.0		153.0	59.0	NM_018240	Q5W0F8|Q5XKC6|Q7Z696|Q7Z7N8|Q8TB15|Q9H9N1|Q9NVA5	Frame_Shift_Del	DEL	ENST00000359209.6	hg19	CCDS1172.2																																																																																			.	.		0.622	KIRREL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058342.3	NM_018240		-	158046019	G	-	158046019	7	5	295	1	0	1	0	1	0	0	0	0	8333	1116	39	0	175	0	KIRREL	1	158046019	Frame_Shift_Del	DEL	G	TCGA-G3-AAUZ-01A-11D-A382-10	2734207	158046019	91204602	13	42872										
WNT3A	89780	hgsc.bcm.edu	37	chr1	228246759	228246759	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	gctgcgaggtgaagacatgcTggtggtcgcaacccgacttc	14	11	0	2			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr1:228246759T>A	ENST00000284523.1	+	4	730	c.652T>A	c.(652-654)Tgg>Agg	p.W218R	WNT3A_ENST00000366753.2_Missense_Mutation_p.W218R	NM_033131.3	NP_149122.1	P56704	WNT3A_HUMAN	wingless-type MMTV integration site family, member 3A	218					axis elongation involved in somitogenesis (GO:0090245)|axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:0061317)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cellular response to retinoic acid (GO:0071300)|COP9 signalosome assembly (GO:0010387)|dorsal/ventral neural tube patterning (GO:0021904)|extracellular matrix organization (GO:0030198)|heart looping (GO:0001947)|hemopoiesis (GO:0030097)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|mammary gland development (GO:0030879)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron projection development (GO:0010977)|neuron differentiation (GO:0030182)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|paraxial mesodermal cell fate commitment (GO:0048343)|platelet aggregation (GO:0070527)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of canonical Wnt signaling pathway involved in controlling type B pancreatic cell proliferation (GO:2000081)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of collateral sprouting in absence of injury (GO:0048697)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of dermatome development (GO:0061184)|positive regulation of mesodermal cell fate specification (GO:0048337)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of receptor internalization (GO:0002092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-anal tail morphogenesis (GO:0036342)|regulation of microtubule cytoskeleton organization (GO:0070507)|skeletal muscle cell differentiation (GO:0035914)|spinal cord association neuron differentiation (GO:0021527)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|transcription coactivator activity (GO:0003713)			kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	12		Prostate(94;0.0405)				GAAGACATGCTGGTGGTCGCA	0.662																																					p.W218R		Atlas-SNP	.											.	WNT3A	40	.	0			c.T652A						.						52	53	52					1																	228246759		2203	4300	6503	SO:0001583	missense	89780	exon4			ACATGCTGGTGGT	AB060284	CCDS1564.1	1q42	2013-02-28			ENSG00000154342	ENSG00000154342		"Wingless-type MMTV integration sites", "Endogenous ligands"	15983	protein-coding gene	gene with protein product		606359				11414706	Standard	NM_033131		Approved		uc001hrq.2	P56704	OTTHUMG00000037593	ENST00000284523.1:c.652T>A	chr1.hg19:g.228246759T>A	ENSP00000284523:p.Trp218Arg	60.0	0.0		75.0	20.0	NM_033131	Q3SY79|Q3SY80|Q969P2	Missense_Mutation	SNP	ENST00000284523.1	hg19	CCDS1564.1	.	.	.	.	.	.	.	.	.	.	T	26.4	4.737611	0.89573	.	.	ENSG00000154342	ENST00000284523;ENST00000366753	T;T	0.81415	-1.49;-1.49	4.58	4.58	0.56647	.	0.000000	0.85682	D	0.000000	D	0.91274	0.7249	M	0.91920	3.255	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.967	D	0.93238	0.6623	10	0.87932	D	0	.	14.2315	0.65895	0.0:0.0:0.0:1.0	.	218;218	P56704;Q3SY79	WNT3A_HUMAN;.	R	218	ENSP00000284523:W218R;ENSP00000355715:W218R	ENSP00000284523:W218R	W	+	1	0	WNT3A	226313382	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.933000	0.87642	1.818000	0.53035	0.402000	0.26972	TGG	.	.		0.662	WNT3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091648.1	NM_033131		A	228246759	T	A	228246759	3	1	295	1	0	0	0	0	1	0	0	0	17404	1580	55	4	666	4	WNT3A	1	228246759	Missense_Mutation	SNP	T	TCGA-G3-AAUZ-01A-11D-A382-10	70200740	228246759	21003862	14	42873										
DISC1	27185	hgsc.bcm.edu	37	chr1	232144685	232144685	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	agggagctgctcctcctattCcccccaggctccactccgag	9	18	0	0			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr1:232144685C>A	ENST00000439617.2	+	11	2250	c.2197C>A	c.(2197-2199)Ccc>Acc	p.P733T	DISC1_ENST00000537876.1_3'UTR|DISC1_ENST00000366637.3_Missense_Mutation_p.P65T|DISC1_ENST00000427560.1_3'UTR|DISC1_ENST00000535983.1_3'UTR	NM_001164537.1|NM_001164540.1|NM_018662.2	NP_001158009.1|NP_001158012.1|NP_061132.2	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1	733	Interaction with ATF4 and ATF5.|Interaction with PAFAH1B1.|Necessary and sufficient for interaction with PCNT and localization at the centrosome.				canonical Wnt signaling pathway (GO:0060070)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cerebral cortex radially oriented cell migration (GO:0021799)|microtubule cytoskeleton organization (GO:0000226)|mitochondrial calcium ion homeostasis (GO:0051560)|neuron migration (GO:0001764)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neuron projection development (GO:0010975)|regulation of synapse maturation (GO:0090128)|TOR signaling (GO:0031929)	cell junction (GO:0030054)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|postsynaptic membrane (GO:0045211)				breast(1)|cervix(1)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	15		all_cancers(173;0.0208)|Prostate(94;0.0975)				TCCTCCTATTCCCCCCAGGCT	0.532																																					p.P765T		Atlas-SNP	.											.,1	DISC1	207	.	0			c.C2293A						.						67	66	66					1																	232144685		1920	4150	6070	SO:0001583	missense	27185	exon12			CCTATTCCCCCCA	AF222980	CCDS31055.1, CCDS31056.1, CCDS53482.1, CCDS53483.1, CCDS53484.1, CCDS59205.1, CCDS59206.1, CCDS59207.1	1q42.1	2008-02-05			ENSG00000162946	ENSG00000162946			2888	protein-coding gene	gene with protein product		605210				10814723	Standard	NM_001164550		Approved		uc010pxh.2	Q9NRI5	OTTHUMG00000037835	ENST00000439617.2:c.2197C>A	chr1.hg19:g.232144685C>A	ENSP00000403888:p.Pro733Thr	115.0	0.0		106.0	40.0	NM_001164537	A6NLH2|C4P091|C4P095|C4P0A1|C4P0A3|C4P0B3|C4P0B6|C4P0C1|C9J6D0|O75045|Q5VT44|Q5VT45|Q8IXJ0|Q8IXJ1|Q9BX19|Q9NRI3|Q9NRI4	Missense_Mutation	SNP	ENST00000439617.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	3.680|3.680	-0.065651|-0.065651	0.07273|0.07273	.|.	.|.	ENSG00000162946|ENSG00000162946	ENST00000422590|ENST00000439617;ENST00000366637;ENST00000366638;ENST00000532576;ENST00000427560	.|T	.|0.08634	.|3.07	4.46|4.46	-1.19|-1.19	0.09585|0.09585	.|.	.|1.195290	.|0.06147	.|N	.|0.673477	T|T	0.04048|0.04048	0.0113|0.0113	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	.|B;B;B;B;B;B;B	.|0.10296	.|0.001;0.001;0.003;0.001;0.0;0.001;0.003	.|B;B;B;B;B;B;B	.|0.12156	.|0.003;0.002;0.007;0.005;0.002;0.003;0.003	T|T	0.45205|0.45205	-0.9277|-0.9277	5|10	.|0.22706	.|T	.|0.39	0.2137|0.2137	0.5697|0.5697	0.00693|0.00693	0.1764:0.3345:0.1722:0.3169|0.1764:0.3345:0.1722:0.3169	.|.	.|765;611;765;733;611;733;733	.|C4P096;C4P094;E2QRA4;C4P098;F5H1F1;Q9NRI5-2;Q9NRI5	.|.;.;.;.;.;.;DISC1_HUMAN	L|T	135|733;733;765;611;65	.|ENSP00000403888:P733T	.|ENSP00000355597:P733T	F|P	+|+	3|1	2|0	DISC1|DISC1	230211308|230211308	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	0.551000|0.551000	0.23361|0.23361	-0.081000|-0.081000	0.12662|0.12662	-0.127000|-0.127000	0.14921|0.14921	TTC|CCC	.	.		0.532	DISC1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000092351.2	NM_018662		A	232144685	C	A	232144685	3	1	295	1	0	0	0	0	1	0	0	0	4540	855	30	3	2975	3	DISC1	1	232144685	Missense_Mutation	SNP	C	TCGA-G3-AAUZ-01A-11D-A382-10	3897926	232144685	17105936	15	42874										
MTIF2	4528	hgsc.bcm.edu	37	chr2	55470681	55470681	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	cagtagatggccatacttctCacgggctttctgatgtgctt	10	10	2	2			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr2:55470681C>A	ENST00000263629.4	-	12	1750	c.1435G>T	c.(1435-1437)Gag>Tag	p.E479*	MTIF2_ENST00000403721.1_Nonsense_Mutation_p.E479*|MTIF2_ENST00000394600.3_Nonsense_Mutation_p.E479*	NM_002453.2	NP_002444.2	P46199	IF2M_HUMAN	mitochondrial translational initiation factor 2	479					formation of translation initiation complex (GO:0001732)|regulation of translational initiation (GO:0006446)|ribosome disassembly (GO:0032790)	mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	24						CCATACTTCTCACGGGCTTTC	0.388																																					p.E479X		Atlas-SNP	.											.	MTIF2	64	.	0			c.G1435T						.						208	201	203					2																	55470681		2203	4300	6503	SO:0001587	stop_gained	4528	exon12			ACTTCTCACGGGC	L34600	CCDS1853.1	2p16.1	2008-02-05			ENSG00000085760	ENSG00000085760			7441	protein-coding gene	gene with protein product		603766				9925935, 7829522	Standard	XM_005264335		Approved	IF-2mt	uc002ryo.3	P46199	OTTHUMG00000129338	ENST00000263629.4:c.1435G>T	chr2.hg19:g.55470681C>A	ENSP00000263629:p.Glu479*	104.0	0.0		139.0	58.0	NM_002453	D6W5D0	Nonsense_Mutation	SNP	ENST00000263629.4	hg19	CCDS1853.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.711596	0.89112	.	.	ENSG00000085760	ENST00000403721;ENST00000263629;ENST00000394600;ENST00000418823	.	.	.	5.6	5.6	0.85130	.	0.220434	0.46145	D	0.000302	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	-6.8825	16.1438	0.81548	0.0:0.8575:0.1425:0.0	.	.	.	.	X	479;479;479;157	.	ENSP00000263629:E479X	E	-	1	0	MTIF2	55324185	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	5.087000	0.64480	2.645000	0.89757	0.655000	0.94253	GAG	.	.		0.388	MTIF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251486.4	NM_002453		A	55470681	C	A	55470681	4	1	295	1	0	0	0	0	0	1	0	0	9943	835	29	3	768	3	MTIF2	2	55470681	Nonsense_Mutation	SNP	C	TCGA-G3-AAUZ-01A-11D-A382-10		55470681	187728692	16	42875										
FAP	2191	hgsc.bcm.edu	37	chr2	163027578	163027578	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	gccggataagccgtggttctGgtcagagtaccactgaaaca	12	10	2	2			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr2:163027578G>T	ENST00000188790.4	-	26	2401	c.2194C>A	c.(2194-2196)Cag>Aag	p.Q732K	AC007750.5_ENST00000609668.1_RNA|FAP_ENST00000443424.1_Missense_Mutation_p.Q707K|AC007750.5_ENST00000418968.3_RNA	NM_004460.2	NP_004451.2			fibroblast activation protein, alpha											NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(34)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(4)	63						CCGTGGTTCTGGTCAGAGTAC	0.433																																					p.Q732K		Atlas-SNP	.											.	FAP	122	.	0			c.C2194A						.						128	125	126					2																	163027578		2203	4300	6503	SO:0001583	missense	2191	exon26			GGTTCTGGTCAGA	U09278	CCDS33311.1	2q23	2008-02-05			ENSG00000078098	ENSG00000078098			3590	protein-coding gene	gene with protein product	"seprase"	600403				9247085, 14707457	Standard	NM_004460		Approved	DPPIV	uc002ucd.3	Q12884	OTTHUMG00000153890	ENST00000188790.4:c.2194C>A	chr2.hg19:g.163027578G>T	ENSP00000188790:p.Gln732Lys	93.0	0.0		108.0	21.0	NM_004460		Missense_Mutation	SNP	ENST00000188790.4	hg19	CCDS33311.1	.	.	.	.	.	.	.	.	.	.	G	15.19	2.758770	0.49468	.	.	ENSG00000078098	ENST00000188790;ENST00000443424	T;T	0.28666	1.6;1.6	5.6	5.6	0.85130	Peptidase S9, prolyl oligopeptidase, catalytic domain (1);	0.057851	0.64402	D	0.000001	T	0.11410	0.0278	N	0.01424	-0.875	0.42777	D	0.993859	B;B;B	0.14438	0.004;0.001;0.01	B;B;B	0.18871	0.017;0.003;0.023	T	0.27706	-1.0066	10	0.15066	T	0.55	-19.1118	10.9947	0.47569	0.0:0.1392:0.7166:0.1442	.	707;211;732	B4DLR2;Q12884-2;Q12884	.;.;SEPR_HUMAN	K	732;707	ENSP00000188790:Q732K;ENSP00000411391:Q707K	ENSP00000188790:Q732K	Q	-	1	0	FAP	162735824	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	3.116000	0.50399	2.650000	0.89964	0.655000	0.94253	CAG	.	.		0.433	FAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332852.2			T	163027578	G	T	163027578	3	4	295	1	0	0	0	0	1	0	0	0	5681	1357	47	3	92	3	FAP	2	163027578	Missense_Mutation	SNP	G	TCGA-G3-AAUZ-01A-11D-A382-10	107556897	163027578	80171795	17	42876										
SPHKAP	80309	hgsc.bcm.edu	37	chr2	228996764	228996764	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	acagcctctgccctgctgcgGttccaaaacgtcatacatcc	7	16	2	0			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr2:228996764G>T	ENST00000392056.3	-	2	116	c.70C>A	c.(70-72)Ccg>Acg	p.P24T	SPHKAP_ENST00000344657.5_Missense_Mutation_p.P24T	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	24						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)			NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		CCCTGCTGCGGTTCCAAAACG	0.478																																					p.P24T		Atlas-SNP	.											.	SPHKAP	750	.	0			c.C70A						.						89	92	91					2																	228996764		2203	4300	6503	SO:0001583	missense	80309	exon2			GCTGCGGTTCCAA		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"A-kinase anchor proteins"	30619	protein-coding gene	gene with protein product	"sphingosine kinase type 1-interacting protein"	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.70C>A	chr2.hg19:g.228996764G>T	ENSP00000375909:p.Pro24Thr	76.0	0.0		73.0	32.0	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	hg19	CCDS46537.1	.	.	.	.	.	.	.	.	.	.	G	3.670	-0.067626	0.07273	.	.	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.55052	0.54;0.54	4.55	-9.09	0.00717	.	1.862920	0.02479	N	0.088282	T	0.29749	0.0743	N	0.14661	0.345	0.09310	N	1	B;B	0.10296	0.002;0.003	B;B	0.12156	0.003;0.007	T	0.18398	-1.0338	10	0.37606	T	0.19	.	5.3973	0.16276	0.1211:0.4938:0.1347:0.2504	.	24;24	Q2M3C7;Q2M3C7-2	SPKAP_HUMAN;.	T	24	ENSP00000375909:P24T;ENSP00000339886:P24T	ENSP00000339886:P24T	P	-	1	0	SPHKAP	228705008	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-1.352000	0.02619	-2.888000	0.00316	0.655000	0.94253	CCG	.	.		0.478	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623		T	228996764	G	T	228996764	3	4	295	1	0	0	0	0	1	0	0	0	15063	1261	44	3	5076	3	SPHKAP	2	228996764	Missense_Mutation	SNP	G	TCGA-G3-AAUZ-01A-11D-A382-10	65969186	228996764	14202609	18	42877										
CYP8B1	1582	hgsc.bcm.edu	37	chr3	42916016	42916016	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	gaaacgcccgaaccccagggCatggtgtagtggtggatctt	14	10	1	0			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr3:42916016C>A	ENST00000316161.4	-	1	1617	c.1293G>T	c.(1291-1293)atG>atT	p.M431I	KRBOX1_ENST00000426937.1_Intron|CYP8B1_ENST00000437102.1_Missense_Mutation_p.M431I|RP11-141M3.5_ENST00000471537.1_RNA	NM_004391.2	NP_004382.2	Q9UNU6	CP8B1_HUMAN	cytochrome P450, family 8, subfamily B, polypeptide 1	431					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	7alpha-hydroxycholest-4-en-3-one 12alpha-hydroxylase activity (GO:0033778)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|sterol 12-alpha-hydroxylase activity (GO:0008397)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(2)|prostate(2)|skin(5)	23				KIRC - Kidney renal clear cell carcinoma(284;0.213)|Kidney(284;0.249)		AACCCCAGGGCATGGTGTAGT	0.522																																					p.M431I		Atlas-SNP	.											.	CYP8B1	59	.	0			c.G1293T						.						117	112	114					3																	42916016		2203	4300	6503	SO:0001583	missense	1582	exon1			CCAGGGCATGGTG	AF090318	CCDS2707.1	3p22.1	2004-02-27	2003-01-14		ENSG00000180432	ENSG00000180432		"Cytochrome P450s"	2653	protein-coding gene	gene with protein product		602172	"cytochrome P450, subfamily VIIIB (sterol 12-alpha-hydroxylase), polypeptide 1"			10051404	Standard	NM_004391		Approved	CYP12	uc003cmh.3	Q9UNU6	OTTHUMG00000133047	ENST00000316161.4:c.1293G>T	chr3.hg19:g.42916016C>A	ENSP00000318867:p.Met431Ile	147.0	0.0		181.0	64.0	NM_004391	B2RCY3|O75958|Q6NWT2|Q6NWT3	Missense_Mutation	SNP	ENST00000316161.4	hg19	CCDS2707.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.841611	0.91197	.	.	ENSG00000180432	ENST00000437102;ENST00000316161	T;T	0.67523	-0.27;-0.27	5.39	5.39	0.77823	.	0.062837	0.64402	D	0.000018	T	0.74913	0.3779	L	0.42245	1.32	0.58432	D	0.999998	D;P	0.56287	0.975;0.949	P;P	0.60541	0.876;0.837	T	0.76041	-0.3104	10	0.56958	D	0.05	-26.4156	17.9083	0.88926	0.0:1.0:0.0:0.0	.	431;431	C9JFR9;Q9UNU6	.;CP8B1_HUMAN	I	431	ENSP00000404499:M431I;ENSP00000318867:M431I	ENSP00000318867:M431I	M	-	3	0	CYP8B1	42891020	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	7.728000	0.84847	2.526000	0.85167	0.462000	0.41574	ATG	.	.		0.522	CYP8B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256653.1	NM_004391		A	42916016	C	A	42916016	3	1	295	1	0	0	0	0	1	0	0	0	4200	710	25	3	216	3	CYP8B1	3	42916016	Missense_Mutation	SNP	C	TCGA-G3-AAUZ-01A-11D-A382-10		42916016	155106414	19	42878										
NR1I2	8856	hgsc.bcm.edu	37	chr3	119530469	119530469	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	ggacagggactcagccactgGgagtgcaggggctgacagag	18	9	1	2			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr3:119530469G>T	ENST00000337940.4	+	4	580	c.532G>T	c.(532-534)Gga>Tga	p.G178*	NR1I2_ENST00000393716.2_Nonsense_Mutation_p.G139*|NR1I2_ENST00000466380.1_Nonsense_Mutation_p.G139*	NM_022002.2	NP_071285.1	O75469	NR1I2_HUMAN	nuclear receptor subfamily 1, group I, member 2	139	Hinge.				drug export (GO:0046618)|exogenous drug catabolic process (GO:0042738)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|steroid metabolic process (GO:0008202)|transcription initiation from RNA polymerase II promoter (GO:0006367)|xenobiotic metabolic process (GO:0006805)|xenobiotic transport (GO:0042908)	nucleoplasm (GO:0005654)	drug binding (GO:0008144)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(2)|prostate(2)|skin(3)	23				GBM - Glioblastoma multiforme(114;0.175)	Docetaxel(DB01248)|Erlotinib(DB00530)|Estradiol(DB00783)|Ethinyl Estradiol(DB00977)|Paclitaxel(DB01229)|Rifampicin(DB01045)|Rifaximin(DB01220)|Rilpivirine(DB08864)|Vitamin E(DB00163)	TCAGCCACTGGGAGTGCAGGG	0.552																																					p.G178X		Atlas-SNP	.											.	NR1I2	44	.	0			c.G532T						.						106	100	102					3																	119530469		2203	4300	6503	SO:0001587	stop_gained	8856	exon4			CCACTGGGAGTGC	AF061056	CCDS2995.1, CCDS43136.1, CCDS54627.1	3q12-q13.3	2013-03-25			ENSG00000144852	ENSG00000144852		"Nuclear hormone receptors"	7968	protein-coding gene	gene with protein product	"pregnane X receptor", "orphan nuclear receptor PXR"	603065				9727070, 9770465	Standard	NM_003889		Approved	ONR1, PXR, BXR, SXR, PAR2	uc003edk.3	O75469	OTTHUMG00000159400	ENST00000337940.4:c.532G>T	chr3.hg19:g.119530469G>T	ENSP00000336528:p.Gly178*	133.0	0.0		131.0	8.0	NM_022002	Q006P5|Q008C8|Q96AC7|Q9UJ22|Q9UJ23|Q9UJ24|Q9UJ25|Q9UJ26|Q9UJ27|Q9UNW4	Nonsense_Mutation	SNP	ENST00000337940.4	hg19	CCDS2995.1	.	.	.	.	.	.	.	.	.	.	G	16.61	3.171214	0.57584	.	.	ENSG00000144852	ENST00000393716;ENST00000466380;ENST00000337940	.	.	.	4.91	4.04	0.47022	.	1.095510	0.06879	N	0.802090	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10902	T	0.67	.	11.0649	0.47970	0.0897:0.0:0.9103:0.0	.	.	.	.	X	139;139;178	.	ENSP00000336528:G178X	G	+	1	0	NR1I2	121013159	0.051000	0.20477	0.002000	0.10522	0.016000	0.09150	1.815000	0.38981	1.297000	0.44761	0.591000	0.81541	GGA	.	.		0.552	NR1I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355126.1			T	119530469	G	T	119530469	4	4	295	1	0	0	0	0	0	1	0	0	10629	1233	43	3	546	3	NR1I2	3	119530469	Nonsense_Mutation	SNP	G	TCGA-G3-AAUZ-01A-11D-A382-10	76614453	119530469	78491961	20	42879										
SLC2A2	6514	hgsc.bcm.edu	37	chr3	170732428	170732428	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	attgagtatgagattgtgggCagttcatctgtactgttgat	12	4	2	3			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr3:170732428C>G	ENST00000314251.3	-	3	280	c.201G>C	c.(199-201)ctG>ctC	p.L67L	SLC2A2_ENST00000382808.4_Intron	NM_000340.1	NP_000331.1	P11168	GTR2_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 2	67					carbohydrate metabolic process (GO:0005975)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transmembrane transport (GO:0035428)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	brush border (GO:0005903)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|hexose transmembrane transporter activity (GO:0015149)			central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)		Streptozocin(DB00428)	AGATTGTGGGCAGTTCATCTG	0.448																																					p.L67L		Atlas-SNP	.											.	SLC2A2	71	.	0			c.G201C						.						221	214	216					3																	170732428		2203	4300	6503	SO:0001819	synonymous_variant	6514	exon3			TGTGGGCAGTTCA	J03810	CCDS3215.1	3q26.2-q27	2013-05-22			ENSG00000163581	ENSG00000163581		"Solute carriers"	11006	protein-coding gene	gene with protein product		138160		GLUT2		1852621	Standard	NM_000340		Approved		uc003fhe.1	P11168	OTTHUMG00000158997	ENST00000314251.3:c.201G>C	chr3.hg19:g.170732428C>G		164.0	0.0		175.0	38.0	NM_000340	A8K481|B2R936|B7Z547|F8W8V8|Q9UCW9	Silent	SNP	ENST00000314251.3	hg19	CCDS3215.1																																																																																			.	.		0.448	SLC2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352834.1	NM_000340		G	170732428	C	G	170732428	2	3	295	1	0	0	0	0	0	0	0	1	14559	697	25	4		4	SLC2A2	3	170732428	Silent	SNP	C	TCGA-G3-AAUZ-01A-11D-A382-10	51201959	170732428	27290002	21	42880			1	50		2	2	28	N	GTT_C	7.326086e-05
SLC2A2	6514	hgsc.bcm.edu	37	chr3	170732455	170732457	+	In_Frame_Del	DEL	GTT	GTT	-													0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	tctgtactgttgataacataGttgttgatagcttttcggtc							TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	GTT	GTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr3:170732455_170732457delGTT	ENST00000314251.3	-	3	251_253	c.172_174delAAC	c.(172-174)aacdel	p.N58del	SLC2A2_ENST00000382808.4_Intron	NM_000340.1	NP_000331.1	P11168	GTR2_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 2	58					carbohydrate metabolic process (GO:0005975)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transmembrane transport (GO:0035428)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	brush border (GO:0005903)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|hexose transmembrane transporter activity (GO:0015149)			central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)		Streptozocin(DB00428)	TGATAACATAGTTGTTGATAGCT	0.404																																					p.58_59del		Atlas-INDEL	.											.	SLC2A2	71	.	0			c.173_175del						.																																			SO:0001651	inframe_deletion	6514	exon3			.	J03810	CCDS3215.1	3q26.2-q27	2013-05-22			ENSG00000163581	ENSG00000163581		"Solute carriers"	11006	protein-coding gene	gene with protein product		138160		GLUT2		1852621	Standard	NM_000340		Approved		uc003fhe.1	P11168	OTTHUMG00000158997	ENST00000314251.3:c.172_174delAAC	chr3.hg19:g.170732458_170732460delGTT	ENSP00000323568:p.Asn58del	141.0	0.0		161.0	41.0	NM_000340	A8K481|B2R936|B7Z547|F8W8V8|Q9UCW9	In_Frame_Del	DEL	ENST00000314251.3	hg19	CCDS3215.1																																																																																			.	.		0.404	SLC2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352834.1	NM_000340		-	170732457	GTT	-	170732455	7	5	295	1	0	1	0	1	0	0	0	0	14559	1020	36	0	1436	0	SLC2A2	3	170732455	In_Frame_Del	DEL	GTT	TCGA-G3-AAUZ-01A-11D-A382-10	27	170732455	27289975	22	42881			1	50		2	2	28	N	GTT_C	7.326086e-05
KIAA1211	57482	hgsc.bcm.edu	37	chr4	57164426	57164426	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	gggcattttcccatgacagtAtttttatccctgatggggga	11	8	0	2			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr4:57164426A>T	ENST00000504228.1	+	2	136	c.31A>T	c.(31-33)Att>Ttt	p.I11F	KIAA1211_ENST00000264229.6_Missense_Mutation_p.I11F|KIAA1211_ENST00000541073.1_5'UTR			Q6ZU35	K1211_HUMAN	KIAA1211	11										endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					CCATGACAGTATTTTTATCCC	0.418																																					p.I11F		Atlas-SNP	.											.	KIAA1211	178	.	0			c.A31T						.						86	82	83					4																	57164426		1828	4100	5928	SO:0001583	missense	57482	exon4			GACAGTATTTTTA	AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.31A>T	chr4.hg19:g.57164426A>T	ENSP00000423366:p.Ile11Phe	113.0	0.0		147.0	91.0	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Missense_Mutation	SNP	ENST00000504228.1	hg19	CCDS43230.1	.	.	.	.	.	.	.	.	.	.	A	18.02	3.529410	0.64860	.	.	ENSG00000109265	ENST00000264229;ENST00000504228	T;T	0.23348	1.91;1.91	5.18	5.18	0.71444	.	.	.	.	.	T	0.49847	0.1581	M	0.69358	2.11	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.52815	-0.8525	9	0.87932	D	0	-10.3488	15.1999	0.73126	1.0:0.0:0.0:0.0	.	11	Q6ZU35	K1211_HUMAN	F	11	ENSP00000264229:I11F;ENSP00000423366:I11F	ENSP00000264229:I11F	I	+	1	0	KIAA1211	56859183	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.899000	0.56288	2.186000	0.69663	0.533000	0.62120	ATT	.	.		0.418	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722		T	57164426	A	T	57164426	3	4	295	1	0	0	0	0	1	0	0	0	8224	449	16	4	33	4	KIAA1211	4	57164426	Missense_Mutation	SNP	A	TCGA-G3-AAUZ-01A-11D-A382-10		57164426	133989850	23	42882										
UBE2D3	7323	hgsc.bcm.edu	37	chr4	103720567	103720568	+	Frame_Shift_Del	DEL	TC	TC	-													0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	ctttttaacatacttacttaTctctgtctgttttatagatc							TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	TC	TC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr4:103720567_103720568delTC	ENST00000453744.2	-	7	907_908	c.394_395delGA	c.(394-396)gatfs	p.D132fs	UBE2D3_ENST00000343106.5_Frame_Shift_Del_p.D132fs|UBE2D3_ENST00000349311.8_Frame_Shift_Del_p.D132fs|UBE2D3_ENST00000394804.2_Frame_Shift_Del_p.D132fs|UBE2D3_ENST00000321805.7_Frame_Shift_Del_p.D132fs|UBE2D3_ENST00000357194.6_Frame_Shift_Del_p.D134fs|UBE2D3_ENST00000504211.1_Frame_Shift_Del_p.D103fs|UBE2D3_ENST00000394801.4_Frame_Shift_Del_p.D132fs|UBE2D3_ENST00000350435.7_Frame_Shift_Del_p.D126fs|UBE2D3_ENST00000507845.1_Frame_Shift_Del_p.D103fs|UBE2D3_ENST00000394803.5_Frame_Shift_Del_p.D132fs|UBE2D3_ENST00000505207.1_Frame_Shift_Del_p.D103fs|UBE2D3_ENST00000338145.3_Frame_Shift_Del_p.D132fs|UBE2D3_ENST00000502404.1_Frame_Shift_Del_p.D103fs	NM_181891.1	NP_871620.1	P61077	UB2D3_HUMAN	ubiquitin-conjugating enzyme E2D 3	132					apoptotic process (GO:0006915)|BMP signaling pathway (GO:0030509)|cellular protein modification process (GO:0006464)|cellular response to hypoxia (GO:0071456)|DNA repair (GO:0006281)|gene expression (GO:0010467)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of type I interferon production (GO:0032480)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K11-linked ubiquitination (GO:0070979)|protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			kidney(1)|lung(3)|skin(1)	5		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.13e-08)		TACTTACTTATCTCTGTCTGTT	0.351																																					p.134_134del		Atlas-INDEL	.											.	UBE2D3	25	.	0			c.401_402del						.																																			SO:0001589	frameshift_variant	7323	exon6			.	U39318	CCDS3659.1, CCDS3660.1, CCDS3661.1, CCDS75172.1	4q24	2011-05-19	2011-05-19		ENSG00000109332	ENSG00000109332		"Ubiquitin-conjugating enzymes E2"	12476	protein-coding gene	gene with protein product		602963	"ubiquitin-conjugating enzyme E2D 3 (homologous to yeast UBC4/5)", "ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast)"			8530467	Standard	NM_181886		Approved	UbcH5C	uc003hwl.3	P61077	OTTHUMG00000131119	ENST00000453744.2:c.394_395delGA	chr4.hg19:g.103720569_103720570delTC	ENSP00000396901:p.Asp132fs	307.0	0.0		472.0	242.0	NM_181893	A6NJ93|A6NJB1|A6NM99|P47986|Q6IB88|Q6NXS4|Q8N924	Frame_Shift_Del	DEL	ENST00000453744.2	hg19	CCDS3660.1																																																																																			.	.		0.351	UBE2D3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253791.2	NM_181893		-	103720568	TC	-	103720567	7	5	295	1	0	1	0	1	0	0	0	0	16865	1435	50	0	109	0	UBE2D3	4	103720567	Frame_Shift_Del	DEL	TC	TCGA-G3-AAUZ-01A-11D-A382-10	46556141	103720567	87433709	24	42883										
SYNPO2	171024	hgsc.bcm.edu	37	chr4	119947953	119947953	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	aagactgaagttcccctagcTgagaaccaaagaagtggtcc	10	10	0	4			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr4:119947953T>A	ENST00000429713.2	+	3	611	c.429T>A	c.(427-429)gcT>gcA	p.A143A	SYNPO2_ENST00000448416.2_Intron|SYNPO2_ENST00000434046.2_Silent_p.A143A|SYNPO2_ENST00000307142.4_Silent_p.A143A	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	143						actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|Z disc (GO:0030018)	14-3-3 protein binding (GO:0071889)|muscle alpha-actinin binding (GO:0051371)	p.A143A(2)		breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						TTCCCCTAGCTGAGAACCAAA	0.547																																					p.A143A		Atlas-SNP	.											SYNPO2_ENST00000307142,NS,carcinoma,0,2	SYNPO2	353	.	2	Substitution - coding silent(2)	kidney(2)	c.T429A						.						44	46	46					4																	119947953		2203	4300	6503	SO:0001819	synonymous_variant	171024	exon3			CCTAGCTGAGAAC	AJ010482	CCDS34054.1, CCDS47128.1, CCDS47129.1, CCDS75185.1, CCDS75186.1	4q26	2008-08-29			ENSG00000172403	ENSG00000172403			17732	protein-coding gene	gene with protein product						11673475, 17828378	Standard	NM_133477		Approved	MYOPODIN	uc010inb.3	Q9UMS6	OTTHUMG00000161165	ENST00000429713.2:c.429T>A	chr4.hg19:g.119947953T>A		188.0	0.0		274.0	67.0	NM_001128934	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Silent	SNP	ENST00000429713.2	hg19	CCDS47129.1	.	.	.	.	.	.	.	.	.	.	T	6.091	0.385118	0.11524	.	.	ENSG00000172403	ENST00000504178	.	.	.	5.29	-0.0133	0.13985	.	.	.	.	.	.	.	.	.	.	.	0.32797	N	0.500358	.	.	.	.	.	.	.	.	.	.	.	.	.	-4.2263	1.353	0.02177	0.1456:0.2677:0.133:0.4538	.	.	.	.	R	95	.	.	X	+	1	0	SYNPO2	120167401	0.933000	0.31639	0.792000	0.32020	0.495000	0.33615	0.117000	0.15583	0.355000	0.24131	0.455000	0.32223	TGA	.	.		0.547	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1			A	119947953	T	A	119947953	2	1	295	1	0	0	0	0	0	0	0	1	15472	1567	55	4		4	SYNPO2	4	119947953	Silent	SNP	T	TCGA-G3-AAUZ-01A-11D-A382-10	16227386	119947953	71206323	25	42884										
FAT4	79633	hgsc.bcm.edu	37	chr4	126237717	126237717	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	agccgcgccaggtgttccaaGtgctggaagagcaacctcca	12	13	0	1			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr4:126237717G>T	ENST00000394329.3	+	1	164	c.151G>T	c.(151-153)Gtg>Ttg	p.V51L		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	51	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						GGTGTTCCAAGTGCTGGAAGA	0.602											OREG0016317	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V51L		Atlas-SNP	.											.	FAT4	1752	.	0			c.G151T						.						58	69	65					4																	126237717		2002	4151	6153	SO:0001583	missense	79633	exon1			TTCCAAGTGCTGG	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.151G>T	chr4.hg19:g.126237717G>T	ENSP00000377862:p.Val51Leu	81.0	0.0	1548	95.0	50.0	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	hg19	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	20.2	3.954511	0.73902	.	.	ENSG00000196159	ENST00000394329	T	0.80909	-1.43	4.88	4.88	0.63580	Cadherin (2);Cadherin-like (1);	.	.	.	.	D	0.86744	0.6006	L	0.49699	1.58	0.80722	D	1	D	0.58970	0.984	D	0.70016	0.967	D	0.86096	0.1553	9	0.42905	T	0.14	.	17.846	0.88730	0.0:0.0:1.0:0.0	.	51	Q6V0I7	FAT4_HUMAN	L	51	ENSP00000377862:V51L	ENSP00000377862:V51L	V	+	1	0	FAT4	126457167	1.000000	0.71417	0.979000	0.43373	0.650000	0.38633	7.566000	0.82347	2.519000	0.84933	0.650000	0.86243	GTG	.	.		0.602	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		T	126237717	G	T	126237717	3	4	295	1	0	0	0	0	1	0	0	0	5700	1029	36	3	153	3	FAT4	4	126237717	Missense_Mutation	SNP	G	TCGA-G3-AAUZ-01A-11D-A382-10	6289764	126237717	64916559	26	42885										
TLL1	7092	hgsc.bcm.edu	37	chr4	166978381	166978381	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	ccgtggaggctgtgagcagcGatgtctgaacactctgggca	15	10	2	2			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr4:166978381G>A	ENST00000061240.2	+	14	2413	c.1766G>A	c.(1765-1767)cGa>cAa	p.R589Q	TLL1_ENST00000507499.1_Missense_Mutation_p.R612Q	NM_012464.4	NP_036596.3	O43897	TLL1_HUMAN	tolloid-like 1	589	EGF-like 1; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(21)|lung(26)|ovary(2)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		TGTGAGCAGCGATGTCTGAAC	0.478																																					p.R589Q		Atlas-SNP	.											.	TLL1	194	.	0			c.G1766A						.						181	171	174					4																	166978381		2203	4300	6503	SO:0001583	missense	7092	exon14			AGCAGCGATGTCT	AF282732	CCDS3811.1, CCDS56342.1	4q32-q33	2008-07-29			ENSG00000038295	ENSG00000038295			11843	protein-coding gene	gene with protein product		606742				10516436	Standard	NM_012464		Approved		uc003irh.2	O43897	OTTHUMG00000161112	ENST00000061240.2:c.1766G>A	chr4.hg19:g.166978381G>A	ENSP00000061240:p.Arg589Gln	119.0	0.0		148.0	97.0	NM_012464	B2RMU2|Q96AN3|Q9NQS4	Missense_Mutation	SNP	ENST00000061240.2	hg19	CCDS3811.1	.	.	.	.	.	.	.	.	.	.	G	17.56	3.420880	0.62622	.	.	ENSG00000038295	ENST00000061240;ENST00000507499	D;D	0.96265	-3.96;-3.96	5.85	4.12	0.48240	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.066004	0.56097	U	0.000023	D	0.94899	0.8351	L	0.37466	1.105	0.80722	D	1	D;P	0.54964	0.969;0.939	P;P	0.53360	0.583;0.724	D	0.93125	0.6528	10	0.26408	T	0.33	.	12.9648	0.58478	0.1331:0.0:0.8669:0.0	.	612;589	E9PD25;O43897	.;TLL1_HUMAN	Q	589;612	ENSP00000061240:R589Q;ENSP00000426082:R612Q	ENSP00000061240:R589Q	R	+	2	0	TLL1	167197831	1.000000	0.71417	0.852000	0.33557	0.151000	0.21798	4.843000	0.62838	1.479000	0.48272	0.650000	0.86243	CGA	.	.		0.478	TLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363821.1			A	166978381	G	A	166978381	3	1	295	1	0	0	0	0	1	0	0	0	15960	1058	37	1	1820	1	TLL1	4	166978381	Missense_Mutation	SNP	G	TCGA-G3-AAUZ-01A-11D-A382-10	40740664	166978381	24175895	27	42886										
MCC	4163	hgsc.bcm.edu	37	chr5	112823977	112823977	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	tccccgtcgccgtcgcacgtCtggaagaggcgccgcatcct	12	17	1	1			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr5:112823977C>G	ENST00000408903.3	-	1	550	c.135G>C	c.(133-135)caG>caC	p.Q45H		NM_001085377.1	NP_001078846	P23508	CRCM_HUMAN	mutated in colorectal cancers	0					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			endometrium(4)|kidney(3)|large_intestine(15)|liver(2)|lung(8)|ovary(2)|pancreas(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		CGTCGCACGTCTGGAAGAGGC	0.711																																					p.Q45H		Atlas-SNP	.											.	MCC	234	.	0			c.G135C						.						46	54	52					5																	112823977		2088	4206	6294	SO:0001583	missense	4163	exon1			GCACGTCTGGAAG		CCDS4111.1, CCDS43351.1	5q21-q22	2013-01-10			ENSG00000171444	ENSG00000171444		"EF-hand domain containing"	6935	protein-coding gene	gene with protein product		159350				1848370	Standard	NM_002387		Approved		uc003kql.4	P23508	OTTHUMG00000128804	ENST00000408903.3:c.135G>C	chr5.hg19:g.112823977C>G	ENSP00000386227:p.Gln45His	64.0	0.0		57.0	29.0	NM_001085377	D3DT05|Q6ZR04	Missense_Mutation	SNP	ENST00000408903.3	hg19	CCDS43351.1	.	.	.	.	.	.	.	.	.	.	C	16.34	3.094430	0.56075	.	.	ENSG00000171444	ENST00000408903	T	0.71817	-0.6	3.39	3.39	0.38822	.	.	.	.	.	D	0.82811	0.5118	.	.	.	0.37157	D	0.902417	D	0.54397	0.966	D	0.72338	0.977	D	0.87504	0.2435	8	0.87932	D	0	-10.8979	13.4127	0.60952	0.0:1.0:0.0:0.0	.	45	P23508-2	.	H	45	ENSP00000386227:Q45H	ENSP00000386227:Q45H	Q	-	3	2	MCC	112851876	1.000000	0.71417	1.000000	0.80357	0.015000	0.08874	5.043000	0.64208	1.826000	0.53198	0.491000	0.48974	CAG	.	.		0.711	MCC-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370839.1	NM_001085377		G	112823977	C	G	112823977	3	3	295	1	0	0	0	0	1	0	0	0	9382	912	32	4	3061	4	MCC	5	112823977	Missense_Mutation	SNP	C	TCGA-G3-AAUZ-01A-11D-A382-10		112823977	68091283	28	42887										
TGFBI	7045	hgsc.bcm.edu	37	chr5	135392457	135392457	+	Frame_Shift_Del	DEL	C	C	-													0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	atgaagccttccgagccctgCcaccaagagaacggagcaga							TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr5:135392457delC	ENST00000442011.2	+	12	1812	c.1651delC	c.(1651-1653)ccafs	p.P552fs	TGFBI_ENST00000508076.1_5'Flank|TGFBI_ENST00000305126.8_Frame_Shift_Del_p.P552fs	NM_000358.2	NP_000349.1	Q15582	BGH3_HUMAN	transforming growth factor, beta-induced, 68kDa	552	FAS1 4. {ECO:0000255|PROSITE- ProRule:PRU00082}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|chondrocyte differentiation (GO:0002062)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	collagen binding (GO:0005518)|extracellular matrix binding (GO:0050840)|integrin binding (GO:0005178)			breast(6)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CCGAGCCCTGCCACCAAGAGA	0.532																																					p.L550fs		Atlas-INDEL	.											.	TGFBI	76	.	0			c.1650delG						.						52	56	55					5																	135392457		1955	4138	6093	SO:0001589	frameshift_variant	7045	exon12			.	M77349	CCDS47266.1	5q31	2008-02-05	2002-08-29		ENSG00000120708	ENSG00000120708			11771	protein-coding gene	gene with protein product		601692	"transforming growth factor, beta-induced, 68kD"	CSD3, LCD1, CSD1, CSD2		9463327	Standard	NM_000358		Approved	BIGH3, CDB1, CDGG1	uc003lbf.4	Q15582	OTTHUMG00000163213	ENST00000442011.2:c.1651delC	chr5.hg19:g.135392457delC	ENSP00000416330:p.Pro552fs	297.0	0.0		225.0	38.0	NM_000358	D3DQB1|O14471|O14472|O14476|O43216|O43217|O43218|O43219|Q53XM1	Frame_Shift_Del	DEL	ENST00000442011.2	hg19	CCDS47266.1																																																																																			.	.		0.532	TGFBI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372108.1			-	135392457	C	-	135392457	7	5	295	1	0	1	0	1	0	0	0	0	15835	739	26	0	1697	0	TGFBI	5	135392457	Frame_Shift_Del	DEL	C	TCGA-G3-AAUZ-01A-11D-A382-10	22568480	135392457	45522803	29	42888	225	2								
TGFBI	7045	hgsc.bcm.edu	37	chr5	135392461	135392461	+	Missense_Mutation	SNP	C	C	T													0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	agccttccgagccctgccacCaagagaacggagcagactct							TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr5:135392461C>T	ENST00000442011.2	+	12	1816	c.1655C>T	c.(1654-1656)cCa>cTa	p.P552L	TGFBI_ENST00000508076.1_5'Flank|TGFBI_ENST00000305126.8_Missense_Mutation_p.P552L	NM_000358.2	NP_000349.1	Q15582	BGH3_HUMAN	transforming growth factor, beta-induced, 68kDa	552	FAS1 4. {ECO:0000255|PROSITE- ProRule:PRU00082}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|chondrocyte differentiation (GO:0002062)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	collagen binding (GO:0005518)|extracellular matrix binding (GO:0050840)|integrin binding (GO:0005178)			breast(6)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GCCCTGCCACCAAGAGAACGG	0.532																																					p.P552L		Atlas-SNP	.											.	TGFBI	76	.	0			c.C1655T						.						51	55	54					5																	135392461		1954	4141	6095	SO:0001583	missense	7045	exon12			TGCCACCAAGAGA	M77349	CCDS47266.1	5q31	2008-02-05	2002-08-29		ENSG00000120708	ENSG00000120708			11771	protein-coding gene	gene with protein product		601692	"transforming growth factor, beta-induced, 68kD"	CSD3, LCD1, CSD1, CSD2		9463327	Standard	NM_000358		Approved	BIGH3, CDB1, CDGG1	uc003lbf.4	Q15582	OTTHUMG00000163213	ENST00000442011.2:c.1655C>T	chr5.hg19:g.135392461C>T	ENSP00000416330:p.Pro552Leu	299.0	0.0		225.0	37.0	NM_000358	D3DQB1|O14471|O14472|O14476|O43216|O43217|O43218|O43219|Q53XM1	Missense_Mutation	SNP	ENST00000442011.2	hg19	CCDS47266.1	.	.	.	.	.	.	.	.	.	.	C	8.570	0.879751	0.17467	.	.	ENSG00000120708	ENST00000442011;ENST00000398813;ENST00000305126	D;D	0.91237	-2.81;-2.81	5.82	4.94	0.65067	FAS1 domain (5);	0.384151	0.30011	N	0.010630	D	0.89319	0.6681	M	0.81614	2.55	0.21627	N	0.999618	B;B	0.06786	0.001;0.001	B;B	0.12837	0.008;0.008	T	0.78727	-0.2091	10	0.29301	T	0.29	-14.3174	9.6118	0.39668	0.1819:0.581:0.2371:0.0	.	285;552	B9ZVW9;Q15582	.;BGH3_HUMAN	L	552;285;552	ENSP00000416330:P552L;ENSP00000306306:P552L	ENSP00000306306:P552L	P	+	2	0	TGFBI	135420360	0.000000	0.05858	0.248000	0.24265	0.413000	0.31143	0.165000	0.16564	1.456000	0.47831	0.655000	0.94253	CCA	.	.		0.532	TGFBI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372108.1			T	135392461	C	T	135392461	3	4	295	1	0	0	0	0	1	0	0	0	15835	594	21	3	1701	3	TGFBI	5	135392461	Missense_Mutation	SNP	C	TCGA-G3-AAUZ-01A-11D-A382-10	4	135392461	45522799	30	42889	225	2								
FAF2	23197	hgsc.bcm.edu	37	chr5	175923517	175923517	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	tttacgagagaacacctatcCattcctggccatgattatgc	7	11	0	2			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr5:175923517C>A	ENST00000261942.6	+	8	745	c.692C>A	c.(691-693)cCa>cAa	p.P231Q		NM_014613.2	NP_055428.1	Q96CS3	FAF2_HUMAN	Fas associated factor family member 2	231					lipid particle organization (GO:0034389)|negative regulation of catalytic activity (GO:0043086)|response to unfolded protein (GO:0006986)	Cdc48p-Npl4p-Ufd1p AAA ATPase complex (GO:0034098)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)	lipase binding (GO:0035473)|lipase inhibitor activity (GO:0055102)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	10						AACACCTATCCATTCCTGGCC	0.463																																					p.P231Q		Atlas-SNP	.											.	FAF2	38	.	0			c.C692A						.						164	148	154					5																	175923517		2203	4300	6503	SO:0001583	missense	23197	exon8			CCTATCCATTCCT	BC015791	CCDS34296.1	5q35.2	2011-06-28	2008-07-25	2008-07-25	ENSG00000113194	ENSG00000113194		"UBX domain containing"	24666	protein-coding gene	gene with protein product	"expressed in T cells and eosinophils in atopic dermatitis", "UBX domain protein 3B"		"UBX domain containing 8"	UBXD8		10048485, 12372427	Standard	NM_014613		Approved	ETEA, KIAA0887, UBXN3B	uc003mej.4	Q96CS3	OTTHUMG00000163228	ENST00000261942.6:c.692C>A	chr5.hg19:g.175923517C>A	ENSP00000261942:p.Pro231Gln	107.0	0.0		154.0	48.0	NM_014613	O94963|Q8IUF2|Q9BRP2|Q9BVM7	Missense_Mutation	SNP	ENST00000261942.6	hg19	CCDS34296.1	.	.	.	.	.	.	.	.	.	.	C	33	5.288098	0.95517	.	.	ENSG00000113194	ENST00000261942	D	0.87887	-2.31	6.03	6.03	0.97812	UAS (1);	0.044974	0.85682	D	0.000000	D	0.95175	0.8436	M	0.90019	3.08	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95035	0.8173	10	0.72032	D	0.01	-12.8976	20.5596	0.99324	0.0:1.0:0.0:0.0	.	231	Q96CS3	FAF2_HUMAN	Q	231	ENSP00000261942:P231Q	ENSP00000261942:P231Q	P	+	2	0	FAF2	175856123	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.380000	0.79704	2.868000	0.98415	0.555000	0.69702	CCA	.	.		0.463	FAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372194.1	NM_014613		A	175923517	C	A	175923517	3	1	295	1	0	0	0	0	1	0	0	0	5375	594	21	3	722	3	FAF2	5	175923517	Missense_Mutation	SNP	C	TCGA-G3-AAUZ-01A-11D-A382-10	40531056	175923517	4991743	31	42890										
ITPR3	3710	hgsc.bcm.edu	37	chr6	33638235	33638235	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	tgctgccctttgacctgcgcGcctccttctgccacctgatg	9	17	1	2			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr6:33638235G>T	ENST00000374316.5	+	20	3383	c.2323G>T	c.(2323-2325)Gcc>Tcc	p.A775S	ITPR3_ENST00000605930.1_Missense_Mutation_p.A775S			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	775					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	TGACCTGCGCGCCTCCTTCTG	0.627																																					p.A775S		Atlas-SNP	.											.	ITPR3	409	.	0			c.G2323T						.						126	108	114					6																	33638235		2203	4300	6503	SO:0001583	missense	3710	exon19			CTGCGCGCCTCCT	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"Ion channels / Inositol triphosphate receptors"	6182	protein-coding gene	gene with protein product		147267	"inositol 1,4,5-triphosphate receptor, type 3"			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.2323G>T	chr6.hg19:g.33638235G>T	ENSP00000363435:p.Ala775Ser	59.0	0.0		66.0	23.0	NM_002224	Q14649|Q5TAQ2	Missense_Mutation	SNP	ENST00000374316.5	hg19	CCDS4783.1	.	.	.	.	.	.	.	.	.	.	G	34	5.385389	0.95967	.	.	ENSG00000096433	ENST00000374316	D	0.94000	-3.33	4.81	4.81	0.61882	.	0.000000	0.85682	D	0.000000	D	0.96725	0.8931	M	0.85197	2.74	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.97509	1.0065	10	0.87932	D	0	-26.517	17.8678	0.88801	0.0:0.0:1.0:0.0	.	775	Q14573	ITPR3_HUMAN	S	775	ENSP00000363435:A775S	ENSP00000363435:A775S	A	+	1	0	ITPR3	33746213	1.000000	0.71417	0.997000	0.53966	0.981000	0.71138	9.720000	0.98763	2.209000	0.71365	0.563000	0.77884	GCC	.	.		0.627	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224		T	33638235	G	T	33638235	3	4	295	1	0	0	0	0	1	0	0	0	7931	1087	38	1	2397	1	ITPR3	6	33638235	Missense_Mutation	SNP	G	TCGA-G3-AAUZ-01A-11D-A382-10		33638235	137476832	32	42891										
CNPY3	10695	hgsc.bcm.edu	37	chr6	42905826	42905827	+	Splice_Site	DEL	AG	AG	-													0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	tatgaggtattatgattaacAgtgtgatgtgctggtggaag							TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr6:42905826_42905827delAG	ENST00000372836.4	+	5	866		c.e5-1		CNPY3_ENST00000394142.3_Splice_Site|RP3-475N16.1_ENST00000450671.1_RNA	NM_006586.3	NP_006577.2	Q9BT09	CNPY3_HUMAN	canopy FGF signaling regulator 3						innate immune response (GO:0045087)|toll-like receptor signaling pathway (GO:0002224)	endoplasmic reticulum lumen (GO:0005788)				central_nervous_system(1)|endometrium(1)|lung(3)|ovary(1)	6	Colorectal(47;0.196)		all cancers(41;0.000954)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|OV - Ovarian serous cystadenocarcinoma(102;0.0218)|Kidney(15;0.0388)			tatgattaACAGTGTGATGTGC	0.54																																					.		Atlas-INDEL	.											.	CNPY3	25	.	0			.						.																																			SO:0001630	splice_region_variant	10695	.			.	U80744	CCDS4875.1	6p21.1	2013-09-19	2013-07-23	2007-10-22	ENSG00000137161	ENSG00000137161		"Trinucleotide (CAG) repeat containing"	11968	protein-coding gene	gene with protein product		610774	"trinucleotide repeat containing 5", "canopy 3 homolog (zebrafish)"	TNRC5		9225980	Standard	NM_006586		Approved	CAG4A	uc003ota.4	Q9BT09	OTTHUMG00000014708	ENST00000372836.4:c.496-1AG>-	chr6.hg19:g.42905826_42905827delAG		156.0	0.0		178.0	41.0	.	O15412|Q0P6I2|Q8NF54|Q8WTU8|Q9P0F2	Splice_Site	DEL	ENST00000372836.4	hg19	CCDS4875.1																																																																																			.	.		0.54	CNPY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040564.1	NM_006586	Intron	-	42905827	AG	-	42905826	8	5	295	1	0	1	0	1	0	0	1	0	3631	202	7	0	512	0	CNPY3	6	42905826	Splice_Site	DEL	AG	TCGA-G3-AAUZ-01A-11D-A382-10	9267591	42905826	128209241	33	42892										
MICAL1	64780	hgsc.bcm.edu	37	chr6	109771627	109771627	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	cagagacatcaggctgcccaTgggcatcctgggcaaactct	11	13	2	1			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr6:109771627T>A	ENST00000358807.3	-	8	1378	c.1067A>T	c.(1066-1068)cAt>cTt	p.H356L	MICAL1_ENST00000483856.1_5'Flank|MICAL1_ENST00000358577.3_Intron|MICAL1_ENST00000368952.4_Missense_Mutation_p.H375L	NM_022765.3	NP_073602.3	Q8TDZ2	MICA1_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 1	356	Monooxygenase domain. {ECO:0000250}.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of protein phosphorylation (GO:0001933)|oxidation-reduction process (GO:0055114)|signal transduction (GO:0007165)|sulfur oxidation (GO:0019417)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|liver(1)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	40		all_cancers(87;0.000189)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00686)|Lung SC(18;0.0743)|Colorectal(196;0.101)|all_lung(197;0.149)		Epithelial(106;0.0142)|all cancers(137;0.0197)|OV - Ovarian serous cystadenocarcinoma(136;0.0233)|BRCA - Breast invasive adenocarcinoma(108;0.0574)		AGGCTGCCCATGGGCATCCTG	0.607																																					p.H356L		Atlas-SNP	.											.	MICAL1	79	.	0			c.A1067T						.						45	47	47					6																	109771627		2203	4300	6503	SO:0001583	missense	64780	exon8			TGCCCATGGGCAT	AB048948	CCDS5076.1, CCDS55047.1	6q21	2013-03-26	2013-03-26	2005-02-16	ENSG00000135596	ENSG00000135596			20619	protein-coding gene	gene with protein product		607129	"NEDD9 interacting protein with calponin homology and LIM domains"	NICAL		11827972	Standard	NM_022765		Approved	MICAL, FLJ11937, DKFZp434B1517, FLJ21739	uc003ptk.3	Q8TDZ2	OTTHUMG00000015350	ENST00000358807.3:c.1067A>T	chr6.hg19:g.109771627T>A	ENSP00000351664:p.His356Leu	150.0	0.0		172.0	65.0	NM_022765	B7Z3R5|E1P5F0|Q7Z633|Q8IVS9|Q96G47|Q9H6X6|Q9H7I0|Q9HAA1|Q9UFF7	Missense_Mutation	SNP	ENST00000358807.3	hg19	CCDS5076.1	.	.	.	.	.	.	.	.	.	.	T	5.314	0.243239	0.10077	.	.	ENSG00000135596	ENST00000358807;ENST00000368952	T;T	0.10763	2.84;2.84	4.5	-2.96	0.05547	.	1.530710	0.03256	N	0.182578	T	0.02727	0.0082	L	0.33485	1.01	0.09310	N	0.999999	B;B	0.06786	0.0;0.001	B;B	0.06405	0.002;0.001	T	0.44128	-0.9348	10	0.25751	T	0.34	.	11.1259	0.48317	0.0:0.5699:0.0:0.4301	.	375;356	B7Z3R5;Q8TDZ2	.;MICA1_HUMAN	L	356;375	ENSP00000351664:H356L;ENSP00000357948:H375L	ENSP00000351664:H356L	H	-	2	0	MICAL1	109878320	0.000000	0.05858	0.013000	0.15412	0.161000	0.22273	-2.004000	0.01461	-0.346000	0.08312	0.460000	0.39030	CAT	.	.		0.607	MICAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041759.2	NM_022765		A	109771627	T	A	109771627	3	1	295	1	0	0	0	0	1	0	0	0	9578	1464	51	4	2208	4	MICAL1	6	109771627	Missense_Mutation	SNP	T	TCGA-G3-AAUZ-01A-11D-A382-10	66865801	109771627	61343440	34	42893										
ZBTB24	9841	hgsc.bcm.edu	37	chr6	109803061	109803061	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	tgagaagtattcactactggCagcaagtaaggctttgtggg	13	6	1	1			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr6:109803061C>A	ENST00000230122.3	-	2	336	c.169G>T	c.(169-171)Gcc>Tcc	p.A57S		NM_001164313.1|NM_014797.2	NP_001157785.1|NP_055612.2	O43167	ZBT24_HUMAN	zinc finger and BTB domain containing 24	57	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				hematopoietic progenitor cell differentiation (GO:0002244)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	22		all_cancers(87;0.000189)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00686)|Lung SC(18;0.0743)|Colorectal(196;0.101)|all_lung(197;0.149)		Epithelial(106;0.0154)|all cancers(137;0.0216)|OV - Ovarian serous cystadenocarcinoma(136;0.0242)|BRCA - Breast invasive adenocarcinoma(108;0.059)		TCACTACTGGCAGCAAGTAAG	0.463																																					p.A57S		Atlas-SNP	.											.	ZBTB24	64	.	0			c.G169T						.						103	99	101					6																	109803061		2203	4300	6503	SO:0001583	missense	9841	exon2			TACTGGCAGCAAG	AB007901	CCDS34509.1	6q21	2014-09-17	2004-04-15	2004-04-16	ENSG00000112365	ENSG00000112365		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	21143	protein-coding gene	gene with protein product	"POZ (BTB) and AT hook containing zinc finger 2"	614064	"zinc finger protein 450"	ZNF450		9455477	Standard	NM_014797		Approved	KIAA0441, BIF1, PATZ2	uc003ptl.1	O43167	OTTHUMG00000015349	ENST00000230122.3:c.169G>T	chr6.hg19:g.109803061C>A	ENSP00000230122:p.Ala57Ser	144.0	0.0		172.0	59.0	NM_014797	Q17RC6|Q5TED5|Q8N455	Missense_Mutation	SNP	ENST00000230122.3	hg19	CCDS34509.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.536654	0.85812	.	.	ENSG00000112365	ENST00000230122	T	0.72725	-0.68	5.55	5.55	0.83447	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	T	0.75606	0.3872	L	0.43598	1.365	0.52501	D	0.999956	D;D	0.89917	1.0;0.978	D;P	0.79784	0.993;0.829	T	0.72659	-0.4226	9	.	.	.	-19.395	19.4993	0.95086	0.0:1.0:0.0:0.0	.	57;57	O43167-2;O43167	.;ZBT24_HUMAN	S	57	ENSP00000230122:A57S	.	A	-	1	0	ZBTB24	109909754	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.336000	0.79245	2.598000	0.87819	0.655000	0.94253	GCC	.	.		0.463	ZBTB24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041758.1	NM_014797		A	109803061	C	A	109803061	3	1	295	1	0	0	0	0	1	0	0	0	17546	710	25	3	1998	3	ZBTB24	6	109803061	Missense_Mutation	SNP	C	TCGA-G3-AAUZ-01A-11D-A382-10	31434	109803061	61312006	35	42894										
SERINC1	57515	hgsc.bcm.edu	37	chr6	122777722	122777722	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	tagccaaaccaaagcacaaaCgatatacagctttatagcca	5	11	0	0			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr6:122777722C>T	ENST00000339697.4	-	3	359	c.275G>A	c.(274-276)cGt>cAt	p.R92H		NM_020755.2	NP_065806.1	Q9NRX5	SERC1_HUMAN	serine incorporator 1	92					L-serine transport (GO:0015825)|phosphatidylserine metabolic process (GO:0006658)|phospholipid biosynthetic process (GO:0008654)|positive regulation of transferase activity (GO:0051347)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-serine transmembrane transporter activity (GO:0015194)			endometrium(2)|kidney(2)|large_intestine(4)|liver(1)|lung(2)|ovary(1)|skin(1)	13				GBM - Glioblastoma multiforme(226;0.126)		AAAGCACAAACGATATACAGC	0.378																																					p.R92H		Atlas-SNP	.											.	SERINC1	39	.	0			c.G275A						.						139	121	127					6																	122777722		2203	4300	6503	SO:0001583	missense	57515	exon3			CACAAACGATATA	AF087902	CCDS5125.1	6q22.32	2006-02-09	2005-10-14	2005-10-14	ENSG00000111897	ENSG00000111897			13464	protein-coding gene	gene with protein product		614548	"tumor differentially expressed 2"	TDE2		10637174	Standard	NM_020755		Approved	TMS-2, TDE1L, KIAA1253	uc003pyy.1	Q9NRX5	OTTHUMG00000015487	ENST00000339697.4:c.275G>A	chr6.hg19:g.122777722C>T	ENSP00000342962:p.Arg92His	151.0	0.0		180.0	24.0	NM_020755	B3KY69|E1P565|O75655|Q7Z2F5|Q8TAG1|Q9NTH8|Q9ULG7	Missense_Mutation	SNP	ENST00000339697.4	hg19	CCDS5125.1	.	.	.	.	.	.	.	.	.	.	C	35	5.566533	0.96540	.	.	ENSG00000111897	ENST00000339697;ENST00000368454	T;T	0.33438	1.41;1.41	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.63908	0.2551	M	0.93808	3.46	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.72802	-0.4183	10	0.72032	D	0.01	-15.0022	20.1551	0.98106	0.0:1.0:0.0:0.0	.	92	Q9NRX5	SERC1_HUMAN	H	92	ENSP00000342962:R92H;ENSP00000357439:R92H	ENSP00000342962:R92H	R	-	2	0	SERINC1	122819421	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.818000	0.86416	2.760000	0.94817	0.655000	0.94253	CGT	.	.		0.378	SERINC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042031.2	NM_020755		T	122777722	C	T	122777722	3	4	295	1	0	0	0	0	1	0	0	0	14094	536	19	1	1118	1	SERINC1	6	122777722	Missense_Mutation	SNP	C	TCGA-G3-AAUZ-01A-11D-A382-10	12974661	122777722	48337345	36	42895										
RMND1	55005	hgsc.bcm.edu	37	chr6	151748616	151748616	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	atttgatgaaaagttgcttaCtctatttttatgtagttaag	7	3	1	2			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr6:151748616C>T	ENST00000367303.4	-	6	953		c.e6+1		RMND1_ENST00000336451.3_Splice_Site	NM_017909.2	NP_060379.2	Q9NWS8	RMND1_HUMAN	required for meiotic nuclear division 1 homolog (S. cerevisiae)						translation (GO:0006412)	mitochondrion (GO:0005739)				central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.146)	OV - Ovarian serous cystadenocarcinoma(155;6.8e-11)		AAGTTGCTTACTCTATTTTTA	0.313																																					.		Atlas-SNP	.											.	RMND1	32	.	0			c.830+1G>A						.						90	87	88					6																	151748616		2201	4298	6499	SO:0001630	splice_region_variant	55005	exon7			TGCTTACTCTATT	AK000634	CCDS5232.1, CCDS75539.1	6q25.1	2008-02-05	2006-11-24	2006-11-24	ENSG00000155906	ENSG00000155906			21176	protein-coding gene	gene with protein product		614917	"chromosome 6 open reading frame 96"	C6orf96			Standard	NM_001271937		Approved	bA351K16.3, FLJ20627, RMD1	uc003qoi.3	Q9NWS8	OTTHUMG00000015837	ENST00000367303.4:c.830+1G>A	chr6.hg19:g.151748616C>T		66.0	0.0		88.0	23.0	NM_017909	A8K8H4|Q0VDG6|Q5SZ48|Q5SZ83|Q6NSC5|Q96EN7	Splice_Site	SNP	ENST00000367303.4	hg19	CCDS5232.1	.	.	.	.	.	.	.	.	.	.	C	15.58	2.877040	0.51801	.	.	ENSG00000155906	ENST00000336451;ENST00000367303;ENST00000444024	.	.	.	5.77	4.9	0.64082	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.226	0.65860	0.0:0.9278:0.0:0.0722	.	.	.	.	.	-1	.	.	.	-	.	.	RMND1	151790309	1.000000	0.71417	1.000000	0.80357	0.539000	0.34962	6.121000	0.71602	1.443000	0.47586	0.544000	0.68410	.	.	.		0.313	RMND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042718.2	NM_017909	Intron	T	151748616	C	T	151748616	5	4	295	1	0	0	0	0	0	0	1	0	13411	579	20	3	546	3	RMND1	6	151748616	Splice_Site	SNP	C	TCGA-G3-AAUZ-01A-11D-A382-10	28970894	151748616	19366451	37	42896										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152540223	152540223	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	gttgatccgattgaatagctGatgctgcggaagcatccact	11	9	0	3			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr6:152540223G>A	ENST00000367255.5	-	120	22560	c.21959C>T	c.(21958-21960)tCa>tTa	p.S7320L	SYNE1_ENST00000448038.1_Missense_Mutation_p.S7249L|SYNE1_ENST00000341594.5_Missense_Mutation_p.S6932L|SYNE1_ENST00000423061.1_Missense_Mutation_p.S7249L|SYNE1_ENST00000356820.4_Missense_Mutation_p.S1844L|SYNE1_ENST00000265368.4_Missense_Mutation_p.S7320L	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	7320					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TTGAATAGCTGATGCTGCGGA	0.478										HNSCC(10;0.0054)																											p.S7320L		Atlas-SNP	.											.	SYNE1	3227	.	0			c.C21959T						.						146	140	142					6																	152540223		2203	4300	6503	SO:0001583	missense	23345	exon120			ATAGCTGATGCTG	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.21959C>T	chr6.hg19:g.152540223G>A	ENSP00000356224:p.Ser7320Leu	69.0	0.0		96.0	30.0	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	G	8.359	0.832658	0.16820	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820;ENST00000367251	T;T;T;T;T;T;T	0.57595	0.48;0.52;0.39;0.52;0.62;2.52;1.59	5.79	3.95	0.45737	.	0.471003	0.18033	N	0.153877	T	0.28599	0.0708	L	0.40543	1.245	0.09310	N	1	B;B;B;B	0.28055	0.075;0.075;0.199;0.126	B;B;B;B	0.33620	0.08;0.08;0.167;0.08	T	0.22661	-1.0210	10	0.48119	T	0.1	.	12.4652	0.55753	0.0:0.1284:0.7379:0.1337	.	7320;7320;7249;7249	Q8NF91;E7EQI5;Q8NF91-4;E9PEL9	SYNE1_HUMAN;.;.;.	L	7320;7249;7320;7249;6932;1844;242	ENSP00000356224:S7320L;ENSP00000396024:S7249L;ENSP00000265368:S7320L;ENSP00000390975:S7249L;ENSP00000341887:S6932L;ENSP00000349276:S1844L;ENSP00000356220:S242L	ENSP00000265368:S7320L	S	-	2	0	SYNE1	152581916	0.998000	0.40836	0.002000	0.10522	0.075000	0.17131	6.179000	0.71974	0.740000	0.32651	0.650000	0.86243	TCA	.	.		0.478	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152540223	G	A	152540223	3	1	295	1	0	0	0	0	1	0	0	0	15460	1294	45	3	4615	3	SYNE1	6	152540223	Missense_Mutation	SNP	G	TCGA-G3-AAUZ-01A-11D-A382-10	791607	152540223	18574844	38	42897										
OPRM1	4988	hgsc.bcm.edu	37	chr6	154428655	154428655	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	aaagccttggccactgagctAcaatgcagggcagtctccat	10	12	1	1			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr6:154428655A>G	ENST00000330432.7	+	4	1401				OPRM1_ENST00000337049.4_Intron|OPRM1_ENST00000435918.2_Intron|OPRM1_ENST00000414028.2_Intron|OPRM1_ENST00000518759.1_Intron|OPRM1_ENST00000522555.1_Intron|OPRM1_ENST00000434900.2_Intron|OPRM1_ENST00000419506.2_Missense_Mutation_p.Y407C|OPRM1_ENST00000452687.2_Intron|OPRM1_ENST00000524163.1_Intron|OPRM1_ENST00000522236.1_Intron|OPRM1_ENST00000520708.1_Intron	NM_000914.3	NP_000905.3	P35372	OPRM_HUMAN	opioid receptor, mu 1						adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavioral response to ethanol (GO:0048149)|calcium ion transmembrane transport (GO:0070588)|cellular response to stress (GO:0033554)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|locomotory behavior (GO:0007626)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of Wnt protein secretion (GO:0061358)|neuropeptide signaling pathway (GO:0007218)|opioid receptor signaling pathway (GO:0038003)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neurogenesis (GO:0050769)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-endorphin receptor activity (GO:0004979)|G-protein alpha-subunit binding (GO:0001965)|G-protein coupled receptor activity (GO:0004930)|morphine receptor activity (GO:0038047)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(15)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	33		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;9.26e-11)|BRCA - Breast invasive adenocarcinoma(81;0.0154)	Alfentanil(DB00802)|Alvimopan(DB06274)|Amitriptyline(DB00321)|Anileridine(DB00913)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dezocine(DB01209)|Diphenoxylate(DB01081)|Ethylmorphine(DB01466)|Fentanyl(DB00813)|Heroin(DB01452)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levallorphan(DB00504)|Levomethadyl Acetate(DB01227)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Methadyl Acetate(DB01433)|Methylnaltrexone(DB06800)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Ondansetron(DB00904)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Pentazocine(DB00652)|Pethidine(DB00454)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	ccactgagctacaatgcaggg	0.418																																					p.Y407C		Atlas-SNP	.											.	OPRM1	241	.	0			c.A1220G						.						140	128	132					6																	154428655		692	1591	2283	SO:0001627	intron_variant	4988	exon4			TGAGCTACAATGC	L29301	CCDS43517.1, CCDS43518.1, CCDS47503.1, CCDS47504.1, CCDS47505.1, CCDS47506.1, CCDS47507.1, CCDS47508.1, CCDS55071.1, CCDS55068.1, CCDS55069.1, CCDS55070.1	6q24-q25	2012-08-08			ENSG00000112038	ENSG00000112038		"GPCR / Class A : Opioid receptors"	8156	protein-coding gene	gene with protein product		600018					Standard	NM_001145285		Approved	MOR1	uc003qpo.1	P35372	OTTHUMG00000015870	ENST00000330432.7:c.1165-11163A>G	chr6.hg19:g.154428655A>G		73.0	0.0		106.0	43.0	NM_001145286	B0FXJ1|B2R9S7|B8Q1L7|B8Q1L8|B8Q1L9|E7EWZ3|G8XRH6|G8XRH8|Q12930|Q4VWM1|Q4VWM2|Q4VWM3|Q4VWM4|Q4VWM6|Q4VWX6|Q5TDA1|Q6UPP1|Q6UQ80|Q7Z2D8|Q86V80|Q8IWW3|Q8IWW4|Q9UCZ4|Q9UN57	Missense_Mutation	SNP	ENST00000330432.7	hg19	CCDS55070.1	.	.	.	.	.	.	.	.	.	.	A	0.186	-1.057906	0.01965	.	.	ENSG00000112038	ENST00000419506	T	0.70282	-0.47	0.225	0.225	0.15325	.	.	.	.	.	T	0.43809	0.1264	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.39722	-0.9600	5	0.38643	T	0.18	.	.	.	.	.	407	P35372-9	.	C	407	ENSP00000403549:Y407C	ENSP00000403549:Y407C	Y	+	2	0	OPRM1	154470347	0.083000	0.21467	0.068000	0.19968	0.068000	0.16541	0.332000	0.19751	0.257000	0.21650	0.254000	0.18369	TAC	.	.		0.418	OPRM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042786.2	NM_000914		G	154428655	A	G	154428655	1	3	295	0	1	0	0	0	0	0	0	0	10896	391	14	2		2	OPRM1	6	154428655	Intron	SNP	A	TCGA-G3-AAUZ-01A-11D-A382-10	1888432	154428655	16686412	39	42898										
LFNG	3955	hgsc.bcm.edu	37	chr7	2564371	2564371	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	aagatgaggccctggccaggCacacgggtgagccctggact	15	12	0	3			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr7:2564371C>T	ENST00000222725.5	+	2	495	c.475C>T	c.(475-477)Cac>Tac	p.H159Y	LFNG_ENST00000338732.3_Missense_Mutation_p.H30Y|MIR4648_ENST00000580107.1_RNA|LFNG_ENST00000359574.3_Missense_Mutation_p.H159Y|LFNG_ENST00000402045.1_Missense_Mutation_p.H30Y|LFNG_ENST00000402506.1_Missense_Mutation_p.H88Y	NM_001040167.1	NP_001035257.1	Q8NES3	LFNG_HUMAN	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	159					compartment pattern specification (GO:0007386)|female meiotic division (GO:0007143)|metabolic process (GO:0008152)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|ovarian follicle development (GO:0001541)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of protein binding (GO:0032092)|regulation of Notch signaling pathway (GO:0008593)|regulation of somitogenesis (GO:0014807)|somitogenesis (GO:0001756)	extracellular region (GO:0005576)|integral component of Golgi membrane (GO:0030173)|vesicle (GO:0031982)	metal ion binding (GO:0046872)|O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity (GO:0033829)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)|urinary_tract(2)	6		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.54e-14)		CCTGGCCAGGCACACGGGTGA	0.667																																					p.H159Y		Atlas-SNP	.											.	LFNG	57	.	0			c.C475T						.						22	19	20					7																	2564371		2187	4290	6477	SO:0001583	missense	3955	exon2			GCCAGGCACACGG	BC014851	CCDS34586.1, CCDS34587.1, CCDS55081.1, CCDS55082.1	7p22.3	2013-02-19	2006-11-13		ENSG00000106003	ENSG00000106003	2.4.1.222	"Beta 3-glycosyltransferases"	6560	protein-coding gene	gene with protein product		602576	"lunatic fringe (Drosophila) homolog", "lunatic fringe homolog (Drosophila)"			9878264, 9187150	Standard	NM_001166355		Approved	SCDO3	uc003smf.3	Q8NES3	OTTHUMG00000152043	ENST00000222725.5:c.475C>T	chr7.hg19:g.2564371C>T	ENSP00000222725:p.His159Tyr	236.0	0.0		280.0	98.0	NM_001040167	B3KTY6|B5MCR5|O00589|Q96C39|Q9UJW5	Missense_Mutation	SNP	ENST00000222725.5	hg19	CCDS34587.1	.	.	.	.	.	.	.	.	.	.	C	11.56	1.675315	0.29783	.	.	ENSG00000106003	ENST00000402506;ENST00000402045;ENST00000338732;ENST00000222725;ENST00000359574	T;T;T;T;T	0.63096	0.97;-0.02;-0.02;-0.02;-0.02	4.83	4.83	0.62350	.	0.287035	0.37669	N	0.001982	T	0.53834	0.1821	L	0.36672	1.1	0.22266	N	0.999246	P;B	0.40681	0.727;0.134	B;B	0.41135	0.331;0.348	T	0.56001	-0.8051	10	0.66056	D	0.02	-15.7766	11.8814	0.52578	0.2998:0.7002:0.0:0.0	.	159;159	Q8NES3-3;Q8NES3	.;LFNG_HUMAN	Y	88;30;30;159;159	ENSP00000385764:H88Y;ENSP00000384786:H30Y;ENSP00000343095:H30Y;ENSP00000222725:H159Y;ENSP00000352579:H159Y	ENSP00000222725:H159Y	H	+	1	0	LFNG	2530897	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.060000	0.49955	2.378000	0.81104	0.655000	0.94253	CAC	.	.		0.667	LFNG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325021.1	NM_002304		T	2564371	C	T	2564371	3	4	295	1	0	0	0	0	1	0	0	0	8746	710	25	3	757	3	LFNG	7	2564371	Missense_Mutation	SNP	C	TCGA-G3-AAUZ-01A-11D-A382-10		2564371	156574292	40	42899										
SP8	221833	hgsc.bcm.edu	37	chr7	20824970	20824970	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	gccgcccccgccgccgccgcCgctgcccccggaaactccgg	12	24	0	0			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr7:20824970C>T	ENST00000361443.4	-	3	649	c.412G>A	c.(412-414)Ggc>Agc	p.G138S	SP8_ENST00000418710.2_Missense_Mutation_p.G156S	NM_198956.2	NP_945194.1	Q8IXZ3	SP8_HUMAN	Sp8 transcription factor	138					dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|proximal/distal pattern formation (GO:0009954)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	8						ccgccgccgccgctgcccccg	0.761																																					p.G156S		Atlas-SNP	.											.	SP8	43	.	0			c.G466A						.																																			SO:0001583	missense	221833	exon2			CGCCGCCGCTGCC		CCDS5372.1, CCDS43555.1	7p21.2	2013-01-08			ENSG00000164651	ENSG00000164651		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	19196	protein-coding gene	gene with protein product		608306					Standard	NM_182700		Approved		uc003suz.3	Q8IXZ3	OTTHUMG00000094788	ENST00000361443.4:c.412G>A	chr7.hg19:g.20824970C>T	ENSP00000354482:p.Gly138Ser	75.0	0.0		77.0	6.0	NM_182700	Q7Z615|Q7Z616|Q96MJ1	Missense_Mutation	SNP	ENST00000361443.4	hg19	CCDS5372.1	.	.	.	.	.	.	.	.	.	.	C	6.365	0.435495	0.12045	.	.	ENSG00000164651	ENST00000418710;ENST00000361443	D;D	0.81821	-1.54;-1.54	3.09	2.16	0.27623	.	0.366549	0.17990	U	0.155235	T	0.58308	0.2113	N	0.08118	0	0.31008	N	0.719562	D;D	0.55605	0.972;0.972	B;B	0.41860	0.368;0.368	T	0.60005	-0.7347	10	0.08837	T	0.75	.	10.7467	0.46185	0.1919:0.8081:0.0:0.0	.	138;138	Q7Z615;Q8IXZ3	.;SP8_HUMAN	S	156;138	ENSP00000408792:G156S;ENSP00000354482:G138S	ENSP00000354482:G138S	G	-	1	0	SP8	20791495	.	.	0.969000	0.41365	0.291000	0.27294	.	.	0.455000	0.26910	0.306000	0.20318	GGC	.	.		0.761	SP8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326904.2			T	20824970	C	T	20824970	3	4	295	1	0	0	0	0	1	0	0	0	14985	652	23	1	1064	1	SP8	7	20824970	Missense_Mutation	SNP	C	TCGA-G3-AAUZ-01A-11D-A382-10	18260599	20824970	138313693	41	42900										
ANLN	54443	hgsc.bcm.edu	37	chr7	36447554	36447554	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	atctcaatctaaagacaaatCtacgacaccaggttacgtat	5	10	3	1			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr7:36447554C>A	ENST00000265748.2	+	5	1306	c.1085C>A	c.(1084-1086)tCt>tAt	p.S362Y	ANLN_ENST00000396068.2_Missense_Mutation_p.S362Y|ANLN_ENST00000495714.1_3'UTR	NM_018685.2	NP_061155.2	Q9NQW6	ANLN_HUMAN	anillin, actin binding protein	362	Interaction with F-actin.				hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|regulation of exit from mitosis (GO:0007096)|septin ring assembly (GO:0000921)	actin cytoskeleton (GO:0015629)|actomyosin contractile ring (GO:0005826)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	actin binding (GO:0003779)			breast(2)|endometrium(5)|kidney(5)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(2)	45						AAAGACAAATCTACGACACCA	0.318																																					p.S362Y		Atlas-SNP	.											.	ANLN	101	.	0			c.C1085A						.						47	46	47					7																	36447554		2202	4299	6501	SO:0001583	missense	54443	exon5			ACAAATCTACGAC	AF273437	CCDS5447.1, CCDS64628.1	7p15-p14	2013-01-10	2006-08-22		ENSG00000011426	ENSG00000011426		"Pleckstrin homology (PH) domain containing"	14082	protein-coding gene	gene with protein product			"anillin (Drosophila Scraps homolog), actin binding protein", "anillin, actin binding protein (scraps homolog, Drosophila)"			10931866	Standard	NM_001284301		Approved	ANILLIN, Scraps, scra	uc003tff.3	Q9NQW6	OTTHUMG00000023143	ENST00000265748.2:c.1085C>A	chr7.hg19:g.36447554C>A	ENSP00000265748:p.Ser362Tyr	83.0	0.0		113.0	17.0	NM_018685	Q5CZ78|Q6NSK5|Q9H8Y4|Q9NVN9|Q9NVP0	Missense_Mutation	SNP	ENST00000265748.2	hg19	CCDS5447.1	.	.	.	.	.	.	.	.	.	.	C	3.727	-0.056405	0.07362	.	.	ENSG00000011426	ENST00000265748;ENST00000396068	T;T	0.12039	2.72;2.72	5.36	4.46	0.54185	.	0.924789	0.09407	N	0.806359	T	0.15262	0.0368	L	0.44542	1.39	0.30086	N	0.808731	B;B;B;B	0.14012	0.003;0.005;0.009;0.005	B;B;B;B	0.09377	0.002;0.002;0.004;0.002	T	0.06862	-1.0803	10	0.54805	T	0.06	-2.0518	12.2565	0.54627	0.0:0.9188:0.0:0.0812	.	239;362;362;362	B4DSL6;A8K5D9;Q9NQW6-2;Q9NQW6	.;.;.;ANLN_HUMAN	Y	362	ENSP00000265748:S362Y;ENSP00000379380:S362Y	ENSP00000265748:S362Y	S	+	2	0	ANLN	36414079	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	2.295000	0.43576	1.557000	0.49525	0.591000	0.81541	TCT	.	.		0.318	ANLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218582.3	NM_018685		A	36447554	C	A	36447554	3	1	295	1	0	0	0	0	1	0	0	0	694	913	32	3	1103	3	ANLN	7	36447554	Missense_Mutation	SNP	C	TCGA-G3-AAUZ-01A-11D-A382-10	15622584	36447554	122691109	42	42901										
WBSCR28	135886	hgsc.bcm.edu	37	chr7	73280168	73280168	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	cctcggactcagagtctggaAcagttttgccagagcaagaa	11	10	2	3			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr7:73280168A>G	ENST00000320531.2	+	3	799	c.763A>G	c.(763-765)Aca>Gca	p.T255A		NM_182504.3	NP_872310.2	Q6UE05	WBS28_HUMAN	Williams-Beuren syndrome chromosome region 28	255						integral component of membrane (GO:0016021)				breast(2)|kidney(2)|lung(6)|skin(1)	11		Lung NSC(55;0.159)				AGAGTCTGGAACAGTTTTGCC	0.572																																					p.T255A		Atlas-SNP	.											.	WBSCR28	24	.	0			c.A763G						.						105	114	112					7																	73280168		1979	4159	6138	SO:0001583	missense	135886	exon3			TCTGGAACAGTTT	BC030643	CCDS43597.1	7q11.23	2006-07-04			ENSG00000175877	ENSG00000175877			23018	protein-coding gene	gene with protein product		612547				8812460	Standard	NM_182504		Approved	MGC26719	uc003tzk.2	Q6UE05	OTTHUMG00000157243	ENST00000320531.2:c.763A>G	chr7.hg19:g.73280168A>G	ENSP00000316775:p.Thr255Ala	35.0	0.0		33.0	18.0	NM_182504	Q6UE04|Q8NHP4	Missense_Mutation	SNP	ENST00000320531.2	hg19	CCDS43597.1	.	.	.	.	.	.	.	.	.	.	a	8.344	0.829444	0.16749	.	.	ENSG00000175877	ENST00000320531	T	0.17054	2.3	3.75	-0.432	0.12291	.	1.335060	0.05287	N	0.520448	T	0.08133	0.0203	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33752	-0.9856	10	0.44086	T	0.13	-1.5	2.4764	0.04576	0.1789:0.3625:0.3474:0.1113	.	255	Q6UE05	WBS28_HUMAN	A	255	ENSP00000316775:T255A	ENSP00000316775:T255A	T	+	1	0	WBSCR28	72918104	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.108000	0.15396	-0.074000	0.12820	-0.142000	0.14014	ACA	.	.		0.572	WBSCR28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348130.1	NM_182504		G	73280168	A	G	73280168	3	3	295	1	0	0	0	0	1	0	0	0	17282	43	2	2	773	2	WBSCR28	7	73280168	Missense_Mutation	SNP	A	TCGA-G3-AAUZ-01A-11D-A382-10	36832614	73280168	85858495	43	42902										
TAF6	6878	hgsc.bcm.edu	37	chr7	99704953	99704953	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	gctggagggggactgtccccAgcctcctgcttccccccaca	11	18	0	0			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr7:99704953A>G	ENST00000344095.4	-	15	2475	c.1950T>C	c.(1948-1950)gcT>gcC	p.A650A	AP4M1_ENST00000421755.1_Intron|TAF6_ENST00000453269.2_Silent_p.A650A|TAF6_ENST00000452041.1_Silent_p.A650A|TAF6_ENST00000418432.2_Silent_p.A574A|TAF6_ENST00000472509.1_Silent_p.A707A|TAF6_ENST00000437822.2_Silent_p.A687A	NM_005641.3	NP_005632.1	P49848	TAF6_HUMAN	TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80kDa	650					DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(2)	26	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GACTGTCCCCAGCCTCCTGCT	0.672																																					p.A687A		Atlas-SNP	.											.	TAF6	55	.	0			c.T2061C						.						29	36	34					7																	99704953		2203	4298	6501	SO:0001819	synonymous_variant	6878	exon15			GTCCCCAGCCTCC		CCDS5686.1, CCDS55135.1	7q	2010-02-26	2002-08-29	2001-12-07	ENSG00000106290	ENSG00000106290			11540	protein-coding gene	gene with protein product	"TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80 kD", "transcription initiation factor TFIID 70 kD subunit"	602955	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, E, 70/85kD"	TAF2E		826207	Standard	NM_139315		Approved	TAFII70, TAFII80, MGC:8964, TAFII85	uc011kji.2	P49848	OTTHUMG00000154771	ENST00000344095.4:c.1950T>C	chr7.hg19:g.99704953A>G		35.0	0.0		49.0	27.0	NM_001190415	A4D2B2|A4D2B3|B4DT11|D6W5U2|Q6AI29	Silent	SNP	ENST00000344095.4	hg19	CCDS5686.1																																																																																			.	.		0.672	TAF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337024.2	NM_005641		G	99704953	A	G	99704953	2	3	295	1	0	0	0	0	0	0	0	1	15545	175	7	2		2	TAF6	7	99704953	Silent	SNP	A	TCGA-G3-AAUZ-01A-11D-A382-10	26424785	99704953	59433710	44	42903										
CALD1	800	hgsc.bcm.edu	37	chr7	134644750	134644750	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	aaaaagcgcaaaacctacaaAgccggcagcctcggatcttc	8	13	1	0			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr7:134644750A>C	ENST00000361675.2	+	12	2316	c.2087A>C	c.(2086-2088)aAg>aCg	p.K696T	CALD1_ENST00000422748.1_Missense_Mutation_p.K466T|CALD1_ENST00000495522.1_Missense_Mutation_p.K460T|CALD1_ENST00000424922.1_Missense_Mutation_p.K435T|CALD1_ENST00000393118.2_Missense_Mutation_p.K461T|CALD1_ENST00000543443.1_Missense_Mutation_p.K446T|CALD1_ENST00000417172.1_Missense_Mutation_p.K441T|CALD1_ENST00000361901.2_Missense_Mutation_p.K441T|CALD1_ENST00000361388.2_Missense_Mutation_p.K467T|CALD1_ENST00000466704.1_3'UTR			Q05682	CALD1_HUMAN	caldesmon 1	696					cellular component movement (GO:0006928)|muscle contraction (GO:0006936)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|calmodulin binding (GO:0005516)|tropomyosin binding (GO:0005523)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(15)|lung(10)	43						AAACCTACAAAGCCGGCAGCC	0.448																																					p.K696T		Atlas-SNP	.											.	CALD1	150	.	0			c.A2087C						.						87	81	83					7																	134644750		2203	4300	6503	SO:0001583	missense	800	exon12			CTACAAAGCCGGC	M64110	CCDS5834.1, CCDS5835.1, CCDS5836.1, CCDS47716.1, CCDS47717.1, CCDS5836.2	7q33	2007-04-23			ENSG00000122786	ENSG00000122786			1441	protein-coding gene	gene with protein product		114213				1885618	Standard	NM_004342		Approved	CDM, H-CAD, L-CAD	uc003vrz.3	Q05682	OTTHUMG00000155407	ENST00000361675.2:c.2087A>C	chr7.hg19:g.134644750A>C	ENSP00000354826:p.Lys696Thr	197.0	0.0		205.0	82.0	NM_033138	A8K0X1|Q13978|Q13979|Q14741|Q14742|Q9UD91	Missense_Mutation	SNP	ENST00000361675.2	hg19	CCDS5835.1	.	.	.	.	.	.	.	.	.	.	A	18.38	3.612287	0.66672	.	.	ENSG00000122786	ENST00000417172;ENST00000436461;ENST00000361388;ENST00000422748;ENST00000432646;ENST00000361675;ENST00000361901;ENST00000393118;ENST00000424922;ENST00000495522;ENST00000543443	T;T;T;T;T;T;T;T;T;T	0.55234	0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53	5.74	5.74	0.90152	.	0.000000	0.53938	D	0.000045	T	0.74442	0.3717	M	0.81682	2.555	0.48341	D	0.999635	D;D;D;D;D;D;D;D;D;D	0.89917	0.998;0.999;1.0;1.0;0.999;0.999;0.999;0.999;0.999;1.0	D;D;D;D;D;D;D;D;D;D	0.87578	0.978;0.981;0.989;0.989;0.981;0.981;0.962;0.981;0.989;0.998	T	0.78239	-0.2281	10	0.72032	D	0.01	-32.6572	16.0292	0.80564	1.0:0.0:0.0:0.0	.	390;446;466;460;435;461;441;467;696;441	B4DPW5;F5H1Z9;A8K0X1;E7EX44;Q05682-5;Q05682-3;Q05682-4;Q05682-2;Q05682;Q9NYG1	.;.;.;.;.;.;.;.;CALD1_HUMAN;.	T	441;441;467;466;74;696;441;461;435;460;446	ENSP00000398826:K441T;ENSP00000411476:K441T;ENSP00000355000:K467T;ENSP00000395710:K466T;ENSP00000354826:K696T;ENSP00000354513:K441T;ENSP00000376826:K461T;ENSP00000393621:K435T;ENSP00000419673:K460T;ENSP00000445641:K446T	ENSP00000355000:K467T	K	+	2	0	CALD1	134295290	1.000000	0.71417	0.983000	0.44433	0.234000	0.25298	4.742000	0.62103	2.187000	0.69744	0.533000	0.62120	AAG	.	.		0.448	CALD1-005	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339939.1	NM_033138		C	134644750	A	C	134644750	3	2	295	1	0	0	0	0	1	0	0	0	2583	72	3	5	2182	5	CALD1	7	134644750	Missense_Mutation	SNP	A	TCGA-G3-AAUZ-01A-11D-A382-10	34939797	134644750	24493913	45	42904										
MYOM2	9172	hgsc.bcm.edu	37	chr8	2054372	2054372	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	acggagtgtcctccagttttGttctggacccagaaggtaat	11	9	1	1			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr8:2054372G>T	ENST00000262113.4	+	23	3124	c.2983G>T	c.(2983-2985)Gtt>Ttt	p.V995F	MYOM2_ENST00000523438.1_Missense_Mutation_p.V420F	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	995	Ig-like C2-type 3.				muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		CTCCAGTTTTGTTCTGGACCC	0.408																																					p.V995F		Atlas-SNP	.											.	MYOM2	251	.	0			c.G2983T						.						82	80	81					8																	2054372		2203	4300	6503	SO:0001583	missense	9172	exon23			AGTTTTGTTCTGG		CCDS5957.1	8p23.3	2014-06-06	2012-10-17		ENSG00000036448	ENSG00000036448		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7614	protein-coding gene	gene with protein product		603509	"myomesin (M-protein) 2 (165kD)", "myomesin (M-protein) 2, 165kDa"				Standard	XM_006716237		Approved		uc003wpx.4	P54296	OTTHUMG00000129175	ENST00000262113.4:c.2983G>T	chr8.hg19:g.2054372G>T	ENSP00000262113:p.Val995Phe	148.0	0.0		81.0	56.0	NM_003970	Q7Z3Y2	Missense_Mutation	SNP	ENST00000262113.4	hg19	CCDS5957.1	.	.	.	.	.	.	.	.	.	.	G	7.702	0.693259	0.15039	.	.	ENSG00000036448	ENST00000262113;ENST00000523438	T;T	0.54071	0.59;0.76	5.33	4.45	0.53987	Immunoglobulin-like (1);	0.241386	0.42548	D	0.000687	T	0.47838	0.1467	M	0.63428	1.95	0.09310	N	0.999996	P	0.35208	0.49	B	0.32624	0.149	T	0.47959	-0.9076	10	0.52906	T	0.07	.	10.678	0.45797	0.2029:0.0:0.7971:0.0	.	995	P54296	MYOM2_HUMAN	F	995;420	ENSP00000262113:V995F;ENSP00000428396:V420F	ENSP00000262113:V995F	V	+	1	0	MYOM2	2041779	0.024000	0.19004	0.009000	0.14445	0.101000	0.19017	1.411000	0.34702	1.239000	0.43787	0.655000	0.94253	GTT	.	.		0.408	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970		T	2054372	G	T	2054372	3	4	295	1	0	0	0	0	1	0	0	0	10101	1377	48	3	3069	3	MYOM2	8	2054372	Missense_Mutation	SNP	G	TCGA-G3-AAUZ-01A-11D-A382-10		2054372	144309650	46	42905										
FNTA	2339	hgsc.bcm.edu	37	chr8	42938314	42938314	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	taatgaaagtgcatggaactAtttgaaagggtaagaggttg	13	2	0	3			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr8:42938314A>C	ENST00000302279.3	+	7	1030	c.836A>C	c.(835-837)tAt>tCt	p.Y279S	FNTA_ENST00000342116.4_Missense_Mutation_p.Y212S|FNTA_ENST00000529687.1_Missense_Mutation_p.Y128S	NM_002027.2	NP_002018.1	P49354	FNTA_HUMAN	farnesyltransferase, CAAX box, alpha	279					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|phototransduction, visible light (GO:0007603)|positive regulation of deacetylase activity (GO:0090045)|positive regulation of tubulin deacetylation (GO:0090044)|protein farnesylation (GO:0018343)|protein geranylgeranylation (GO:0018344)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|transforming growth factor beta receptor signaling pathway (GO:0007179)	CAAX-protein geranylgeranyltransferase complex (GO:0005953)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule associated complex (GO:0005875)|protein farnesyltransferase complex (GO:0005965)	alpha-tubulin binding (GO:0043014)|CAAX-protein geranylgeranyltransferase activity (GO:0004662)|microtubule binding (GO:0008017)|protein farnesyltransferase activity (GO:0004660)|protein geranylgeranyltransferase activity (GO:0004661)			cervix(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(8)|ovary(1)|prostate(1)|urinary_tract(1)	16	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)			GCATGGAACTATTTGAAAGGG	0.299																																					p.Y279S		Atlas-SNP	.											.	FNTA	34	.	0			c.A836C						.						81	93	89					8																	42938314		2203	4300	6503	SO:0001583	missense	2339	exon7			GGAACTATTTGAA	L10413	CCDS6140.1	8p11.21	2011-06-27			ENSG00000168522	ENSG00000168522		"Prenyltransferase alpha subunit repeat containing"	3782	protein-coding gene	gene with protein product	"protein prenyltransferase alpha subunit repeat containing 2"	134635				8276393	Standard	NR_033698		Approved	FPTA, PGGT1A, PTAR2	uc003xps.3	P49354	OTTHUMG00000165279	ENST00000302279.3:c.836A>C	chr8.hg19:g.42938314A>C	ENSP00000303423:p.Tyr279Ser	489.0	0.0		300.0	168.0	NM_002027	A6NJW0|Q53XJ9|Q9UDC1	Missense_Mutation	SNP	ENST00000302279.3	hg19	CCDS6140.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.970218	0.74246	.	.	ENSG00000168522	ENST00000302279;ENST00000342116;ENST00000533336	.	.	.	4.8	4.8	0.61643	Protein prenyltransferase (1);	0.000000	0.85682	D	0.000000	D	0.85243	0.5652	M	0.93808	3.46	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	D	0.88768	0.3262	9	0.87932	D	0	-16.0628	12.5844	0.56408	1.0:0.0:0.0:0.0	.	212;188;279	P49354-2;A8MVX8;P49354	.;.;FNTA_HUMAN	S	279;212;217	.	ENSP00000303423:Y279S	Y	+	2	0	FNTA	43057471	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.998000	0.93550	1.935000	0.56089	0.477000	0.44152	TAT	.	.		0.299	FNTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383178.1	NM_002027		C	42938314	A	C	42938314	3	2	295	1	0	0	0	0	1	0	0	0	5985	449	16	5	862	5	FNTA	8	42938314	Missense_Mutation	SNP	A	TCGA-G3-AAUZ-01A-11D-A382-10	40883942	42938314	103425708	47	42906										
FAM91A1	157769	hgsc.bcm.edu	37	chr8	124787447	124787447	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	actgctaaagtacagccgagAtcatctcatgctgtaccctt	7	12	2	1			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr8:124787447A>G	ENST00000334705.7	+	3	464	c.218A>G	c.(217-219)gAt>gGt	p.D73G	FAM91A1_ENST00000521166.1_Missense_Mutation_p.D73G	NM_144963.2	NP_659400	Q658Y4	F91A1_HUMAN	family with sequence similarity 91, member A1	73										breast(4)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28	Lung NSC(37;8.76e-13)|Ovarian(258;0.00744)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00192)			TACAGCCGAGATCATCTCATG	0.383																																					p.D73G		Atlas-SNP	.											.	FAM91A1	77	.	0			c.A218G						.						112	102	105					8																	124787447		1929	4138	6067	SO:0001583	missense	157769	exon3			GCCGAGATCATCT	AK074370	CCDS6346.2	8q24.13	2005-10-04			ENSG00000176853	ENSG00000176853			26306	protein-coding gene	gene with protein product						12477932	Standard	XM_005250806		Approved	FLJ23790	uc003yqv.3	Q658Y4	OTTHUMG00000133021	ENST00000334705.7:c.218A>G	chr8.hg19:g.124787447A>G	ENSP00000335082:p.Asp73Gly	112.0	0.0		218.0	20.0	NM_144963	B6YY23|Q658T5|Q8TE89	Missense_Mutation	SNP	ENST00000334705.7	hg19	CCDS6346.2	.	.	.	.	.	.	.	.	.	.	A	15.77	2.932100	0.52866	.	.	ENSG00000176853	ENST00000521166;ENST00000334705;ENST00000395537	T;T	0.44083	0.93;1.52	5.33	5.33	0.75918	.	0.120960	0.53938	U	0.000057	T	0.33789	0.0875	N	0.22421	0.69	0.80722	D	1	B;B	0.23185	0.081;0.081	B;B	0.28784	0.094;0.094	T	0.12889	-1.0530	10	0.48119	T	0.1	.	15.3017	0.73958	1.0:0.0:0.0:0.0	.	73;73	E7ER68;Q658Y4	.;F91A1_HUMAN	G	73	ENSP00000429491:D73G;ENSP00000335082:D73G	ENSP00000335082:D73G	D	+	2	0	FAM91A1	124856628	1.000000	0.71417	0.922000	0.36590	0.606000	0.37113	9.139000	0.94554	2.019000	0.59389	0.533000	0.62120	GAT	.	.		0.383	FAM91A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256607.1	NM_144963		G	124787447	A	G	124787447	3	3	295	1	0	0	0	0	1	0	0	0	5659	333	12	2	228	2	FAM91A1	8	124787447	Missense_Mutation	SNP	A	TCGA-G3-AAUZ-01A-11D-A382-10	81849133	124787447	21576575	48	42907										
SMARCA2	6595	hgsc.bcm.edu	37	chr9	2070419	2070419	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	cgacattgttgttttgcagaAggctgaggagaatgcagagg	15	5	0	4			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr9:2070419A>C	ENST00000382203.1	+	10	1903	c.1694A>C	c.(1693-1695)aAg>aCg	p.K565T	SMARCA2_ENST00000357248.2_Splice_Site_p.K565T|SMARCA2_ENST00000349721.2_Splice_Site_p.K565T|SMARCA2_ENST00000382194.1_Splice_Site_p.K565T			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	565					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|chromatin remodeling (GO:0006338)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		GTTTTGCAGAAGGCTGAGGAG	0.483																																					p.K565T		Atlas-SNP	.											.	SMARCA2	313	.	0			c.A1694C						.						179	151	161					9																	2070419		2203	4300	6503	SO:0001630	splice_region_variant	6595	exon10			TGCAGAAGGCTGA	D26155	CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1	9p24.3	2008-11-11	2006-11-09		ENSG00000080503	ENSG00000080503			11098	protein-coding gene	gene with protein product		600014		SNF2L2		8012116	Standard	NM_003070		Approved	BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2	uc003zhc.3	P51531	OTTHUMG00000019445	ENST00000382203.1:c.1693-1A>C	chr9.hg19:g.2070419A>C		141.0	0.0		127.0	52.0	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Missense_Mutation	SNP	ENST00000382203.1	hg19	CCDS34977.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.237751	0.79800	.	.	ENSG00000080503	ENST00000349721;ENST00000357248;ENST00000382203;ENST00000382194	D;D;D;D	0.88354	-2.36;-2.37;-2.36;-2.37	5.64	5.64	0.86602	.	0.126714	0.52532	D	0.000063	T	0.81814	0.4902	L	0.29908	0.895	0.80722	D	1	B;P;B	0.36535	0.14;0.557;0.421	B;B;B	0.33890	0.091;0.172;0.118	T	0.79815	-0.1644	10	0.15952	T	0.53	-38.2952	15.6824	0.77381	1.0:0.0:0.0:0.0	.	166;565;565	B4DK35;P51531-2;P51531	.;.;SMCA2_HUMAN	T	565	ENSP00000265773:K565T;ENSP00000349788:K565T;ENSP00000371638:K565T;ENSP00000371629:K565T	ENSP00000265773:K565T	K	+	2	0	SMARCA2	2060419	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.426000	0.73374	2.367000	0.80283	0.528000	0.53228	AAG	.	.		0.483	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070	Missense_Mutation	C	2070419	A	C	2070419	5	2	295	1	0	0	0	0	0	0	1	0	14784	86	3	5	1728	5	SMARCA2	9	2070419	Splice_Site	SNP	A	TCGA-G3-AAUZ-01A-11D-A382-10		2070419	139143012	49	42908										
BNC2	54796	hgsc.bcm.edu	37	chr9	16738420	16738420	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	atatgctggccagtcttgctCactaagcctgtcctctgatt	8	12	3	1			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr9:16738420C>A	ENST00000380672.4	-	2	124	c.67G>T	c.(67-69)Gag>Tag	p.E23*	BNC2_ENST00000380667.2_Nonsense_Mutation_p.E23*|BNC2_ENST00000380666.2_Nonsense_Mutation_p.E23*|BNC2_ENST00000545497.1_Intron	NM_017637.5	NP_060107.3			basonuclin 2											NS(2)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(16)|liver(1)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(50;9.01e-08)		CAGTCTTGCTCACTAAGCCTG	0.443																																					p.E23X		Atlas-SNP	.											.	BNC2	166	.	0			c.G67T						.						176	143	154					9																	16738420		2203	4300	6503	SO:0001587	stop_gained	54796	exon2			CTTGCTCACTAAG	AK092247	CCDS6482.2	9p22.2	2013-05-20			ENSG00000173068	ENSG00000173068		"Zinc fingers, C2H2-type"	30988	protein-coding gene	gene with protein product		608669				14702039	Standard	XM_006716784		Approved	BSN2, FLJ20043	uc003zml.3	Q6ZN30	OTTHUMG00000019593	ENST00000380672.4:c.67G>T	chr9.hg19:g.16738420C>A	ENSP00000370047:p.Glu23*	139.0	0.0		163.0	72.0	NM_017637		Nonsense_Mutation	SNP	ENST00000380672.4	hg19	CCDS6482.2	.	.	.	.	.	.	.	.	.	.	C	36	5.804736	0.96967	.	.	ENSG00000173068	ENST00000380672;ENST00000456672;ENST00000436939;ENST00000380667;ENST00000380666;ENST00000540340	.	.	.	3.75	2.86	0.33363	.	0.356329	0.20282	N	0.095439	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-1.5509	7.3435	0.26650	0.0:0.8803:0.0:0.1197	.	.	.	.	X	23	.	ENSP00000370041:E23X	E	-	1	0	BNC2	16728420	0.000000	0.05858	0.096000	0.21009	0.949000	0.60115	0.497000	0.22514	1.168000	0.42723	0.579000	0.79373	GAG	.	.		0.443	BNC2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216901.5	NM_017637		A	16738420	C	A	16738420	4	1	295	1	0	0	0	0	0	1	0	0	1475	835	29	3	3256	3	BNC2	9	16738420	Nonsense_Mutation	SNP	C	TCGA-G3-AAUZ-01A-11D-A382-10	14668001	16738420	124475011	50	42909										
AKAP2	11217	hgsc.bcm.edu	37	chr9	112900409	112900411	+	In_Frame_Del	DEL	CTC	CTC	-													0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	tgagccacctcaggtgtcttCtcctgttcaagagaaaaggg							TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr9:112900409_112900411delCTC	ENST00000259318.7	+	2	2099_2101	c.1892_1894delCTC	c.(1891-1896)tctcct>tct	p.P632del	AKAP2_ENST00000555236.1_In_Frame_Del_p.P863del|PALM2-AKAP2_ENST00000374530.3_In_Frame_Del_p.P863del|AKAP2_ENST00000434623.2_In_Frame_Del_p.P721del|AKAP2_ENST00000510514.5_In_Frame_Del_p.P863del|AKAP2_ENST00000374525.1_In_Frame_Del_p.P721del|PALM2-AKAP2_ENST00000302798.7_In_Frame_Del_p.P863del	NM_001136562.2	NP_001130034.1	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2	632										breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	33						CAGGTGTCTTCTCCTGTTCAAGA	0.567																																					p.862_862del		Atlas-INDEL	.											.	PALM2-AKAP2	117	.	0			c.2584_2586del						.																																			SO:0001651	inframe_deletion	445815	exon8			.	AB023137	CCDS43861.1, CCDS48003.1, CCDS56581.1	9q31.3	2009-10-16			ENSG00000241978	ENSG00000241978		"A-kinase anchor proteins"	372	protein-coding gene	gene with protein product	"protein kinase A2"	604582		PRKA2		10231032	Standard	NM_001136562		Approved	AKAP-KL, KIAA0920, DKFZp564L0716		Q9Y2D5	OTTHUMG00000156811	ENST00000259318.7:c.1892_1894delCTC	chr9.hg19:g.112900409_112900411delCTC	ENSP00000259318:p.Pro632del	57.0	0.0		65.0	11.0	NM_007203	B1ALX9|B2RTU4|B3KQ00|B4DTZ2|B7ZW07|B9EJB5|Q9UG26	In_Frame_Del	DEL	ENST00000259318.7	hg19	CCDS48003.1																																																																																			.	.		0.567	AKAP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346067.3	NM_001004065		-	112900411	CTC	-	112900409	7	5	295	1	0	1	0	1	0	0	0	0	451	913	32	0	2165	0	AKAP2	9	112900409	In_Frame_Del	DEL	CTC	TCGA-G3-AAUZ-01A-11D-A382-10	96161989	112900409	28313022	51	42910										
COL5A1	1289	hgsc.bcm.edu	37	chr9	137707833	137707833	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	tgatggtgaacccgggcagaCggtgagtccacaatctgggc	15	10	1	4	rs151115748		TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr9:137707833C>T	ENST00000371817.3	+	52	4535	c.4121C>T	c.(4120-4122)aCg>aTg	p.T1374M		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	1374	Triple-helical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		CCCGGGCAGACGGTGAGTCCA	0.552																																					p.T1374M		Atlas-SNP	.											.	COL5A1	323	.	0			c.C4121T						.	C	MET/THR	0,4406		0,0,2203	145	132	137		4121	5.2	1	9	dbSNP_134	137	3,8597	3.0+/-9.4	0,3,4297	yes	missense-near-splice	COL5A1	NM_000093.3	81	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	probably-damaging	1374/1839	137707833	3,13003	2203	4300	6503	SO:0001630	splice_region_variant	1289	exon52			GGCAGACGGTGAG	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"Collagens"	2209	protein-coding gene	gene with protein product	"alpha 1 type V collagen"	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.4122+1C>T	chr9.hg19:g.137707833C>T		181.0	0.0		210.0	75.0	NM_000093	Q15094|Q5SUX4	Missense_Mutation	SNP	ENST00000371817.3	hg19	CCDS6982.1	.	.	.	.	.	.	.	.	.	.	C	18.81	3.703132	0.68501	0.0	3.49E-4	ENSG00000130635	ENST00000371817	D	0.93763	-3.28	5.2	5.2	0.72013	.	0.141091	0.47852	U	0.000217	D	0.91099	0.7198	N	0.16602	0.42	0.49389	D	0.999785	D	0.67145	0.996	P	0.50490	0.642	D	0.92941	0.6372	10	0.87932	D	0	.	18.7294	0.91730	0.0:1.0:0.0:0.0	.	1374	P20908	CO5A1_HUMAN	M	1374	ENSP00000360882:T1374M	ENSP00000360882:T1374M	T	+	2	0	COL5A1	136847654	1.000000	0.71417	1.000000	0.80357	0.719000	0.41307	7.742000	0.85008	2.404000	0.81709	0.551000	0.68910	ACG	.	C|1.000;T|0.000		0.552	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	Missense_Mutation	T	137707833	C	T	137707833	5	4	295	1	0	0	0	0	0	0	1	0	3698	550	19	1	4327	1	COL5A1	9	137707833	Splice_Site	SNP	C	TCGA-G3-AAUZ-01A-11D-A382-10	24807424	137707833	3505598	52	42911										
AKR1C1	1645	hgsc.bcm.edu	37	chr10	5009211	5009211	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	gattatgttgacctctacctTattcattttccagtgtctgt	6	9	3	1			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr10:5009211T>G	ENST00000380872.4	+	3	537	c.345T>G	c.(343-345)ctT>ctG	p.L115L	AKR1C1_ENST00000434459.2_Silent_p.L115L|AKR1C1_ENST00000380859.1_Silent_p.L117L|AKR1C1_ENST00000477661.1_3'UTR	NM_001353.5	NP_001344.2	Q04828	AK1C1_HUMAN	aldo-keto reductase family 1, member C1	115					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|cellular response to jasmonic acid stimulus (GO:0071395)|cholesterol homeostasis (GO:0042632)|daunorubicin metabolic process (GO:0044597)|digestion (GO:0007586)|doxorubicin metabolic process (GO:0044598)|epithelial cell differentiation (GO:0030855)|intestinal cholesterol absorption (GO:0030299)|oxidation-reduction process (GO:0055114)|phototransduction, visible light (GO:0007603)|progesterone metabolic process (GO:0042448)|protein homooligomerization (GO:0051260)|response to organophosphorus (GO:0046683)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity (GO:0047006)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase (B-specific) activity (GO:0047042)|bile acid binding (GO:0032052)|carboxylic acid binding (GO:0031406)|indanol dehydrogenase activity (GO:0047718)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(2)|ovary(3)|prostate(1)	13					Acetylsalicylic acid(DB00945)|Salicylic acid(DB00936)	ACCTCTACCTTATTCATTTTC	0.383																																					p.L115L	Colon(130;2054 2316 13360 15380)	Atlas-SNP	.											.	AKR1C1	39	.	0			c.T345G						.						120	110	113					10																	5009211		2203	4300	6503	SO:0001819	synonymous_variant	1645	exon3			CTACCTTATTCAT	D26124	CCDS7061.1	10p15-p14	2012-12-04	2012-12-04		ENSG00000187134	ENSG00000187134	1.3.1.20, 1.1.1.149, 1.1.1.112	"Aldo-keto reductases"	384	protein-coding gene	gene with protein product	"dihydrodiol dehydrogenase 1; 20-alpha (3-alpha)-hydroxysteroid dehydrogenase"	600449	"aldo-keto reductase family 1, member C1 (dihydrodiol dehydrogenase 1; 20-alpha (3-alpha)-hydroxysteroid dehydrogenase)"	DDH1		8011662	Standard	NM_001353		Approved	DDH, MBAB, DD1, HAKRC		Q04828	OTTHUMG00000017580	ENST00000380872.4:c.345T>G	chr10.hg19:g.5009211T>G		198.0	0.0		168.0	16.0	NM_001353	P52896|Q5SR15|Q7M4N2|Q9UCX2	Silent	SNP	ENST00000380872.4	hg19	CCDS7061.1	.	.	.	.	.	.	.	.	.	.	T	3.872	-0.027723	0.07589	.	.	ENSG00000187134	ENST00000442997	.	.	.	2.95	0.525	0.17072	.	0.426776	0.20623	N	0.088733	.	.	.	.	.	.	0.58432	D	0.999996	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.4217	0.16403	0.0:0.2949:0.0:0.7051	.	.	.	.	X	82	.	ENSP00000416415:L82X	L	+	2	0	AKR1C1	4999211	0.974000	0.33945	0.027000	0.17364	0.019000	0.09904	-0.024000	0.12435	-0.002000	0.14469	0.254000	0.18369	TTA	.	.		0.383	AKR1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046523.2	NM_001353		G	5009211	T	G	5009211	2	3	295	1	0	0	0	0	0	0	0	1	469	1741	61	5		5	AKR1C1	10	5009211	Silent	SNP	T	TCGA-G3-AAUZ-01A-11D-A382-10		5009211	130525536	53	42912										
FZD8	8325	hgsc.bcm.edu	37	chr10	35930025	35930025	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	cagccggccttggcgcgctcGcacaccgagcggcagggcgg	17	16	0	0			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr10:35930025G>A	ENST00000374694.1	-	1	337	c.333C>T	c.(331-333)tgC>tgT	p.C111C	MIR4683_ENST00000579659.1_RNA	NM_031866.2	NP_114072.1	Q9H461	FZD8_HUMAN	frizzled class receptor 8	111	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|gonad development (GO:0008406)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|T cell differentiation in thymus (GO:0033077)|vasculature development (GO:0001944)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	11						TGGCGCGCTCGCACACCGAGC	0.682																																					p.C111C		Atlas-SNP	.											.	FZD8	41	.	0			c.C333T						.						23	26	25					10																	35930025		2200	4297	6497	SO:0001819	synonymous_variant	8325	exon1			GCGCTCGCACACC	AB043703	CCDS7192.1	10p11.2	2014-01-29	2014-01-29		ENSG00000177283	ENSG00000177283		"GPCR / Class F : Frizzled receptors"	4046	protein-coding gene	gene with protein product		606146	"frizzled (Drosophila) homolog 8", "frizzled homolog 8 (Drosophila)", "frizzled 8, seven transmembrane spanning receptor", "frizzled family receptor 8"			11295046	Standard	NM_031866		Approved		uc001iyz.1	Q9H461	OTTHUMG00000017956	ENST00000374694.1:c.333C>T	chr10.hg19:g.35930025G>A		38.0	0.0		63.0	14.0	NM_031866		Silent	SNP	ENST00000374694.1	hg19	CCDS7192.1																																																																																			.	.		0.682	FZD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047575.2	NM_031866		A	35930025	G	A	35930025	2	1	295	1	0	0	0	0	0	0	0	1	6144	1079	38	1		1	FZD8	10	35930025	Silent	SNP	G	TCGA-G3-AAUZ-01A-11D-A382-10	30920814	35930025	99604722	54	42913										
RBP3	5949	hgsc.bcm.edu	37	chr10	48388584	48388584	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	gctgttgccataccagccgcAccagctgtggccccacggcc	11	18	0	0			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr10:48388584A>G	ENST00000224600.4	-	1	2407	c.2294T>C	c.(2293-2295)gTg>gCg	p.V765A	AL731561.2_ENST00000581861.1_RNA	NM_002900.2	NP_002891.1	P10745	RET3_HUMAN	retinol binding protein 3, interstitial	765	4 X approximate tandem repeats.				lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transport (GO:0006810)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|interphotoreceptor matrix (GO:0033165)|vesicle (GO:0031982)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(30)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59					Vitamin A(DB00162)	TACCAGCCGCACCAGCTGTGG	0.647																																					p.V765A		Atlas-SNP	.											.	RBP3	152	.	0			c.T2294C						.						29	29	29					10																	48388584		2201	4299	6500	SO:0001583	missense	5949	exon1			AGCCGCACCAGCT	M22453	CCDS73119.1	10q11.2	2014-05-06	2001-11-28		ENSG00000107618	ENSG00000265203			9921	protein-coding gene	gene with protein product		180290	"retinol-binding protein 3, interstitial"				Standard	NM_002900		Approved	D10S64, D10S65, D10S66, RP66	uc001jez.3	P10745	OTTHUMG00000188321	ENST00000224600.4:c.2294T>C	chr10.hg19:g.48388584A>G	ENSP00000224600:p.Val765Ala	100.0	0.0		109.0	34.0	NM_002900	Q0QD34|Q5VSR0|Q8IXN0	Missense_Mutation	SNP	ENST00000224600.4	hg19	CCDS7218.1	.	.	.	.	.	.	.	.	.	.	A	11.50	1.658498	0.29425	.	.	ENSG00000107618	ENST00000224600	T	0.65916	-0.18	5.53	5.53	0.82687	Interphotoreceptor retinol-binding (2);	0.309269	0.28828	N	0.014018	T	0.59865	0.2225	L	0.48877	1.53	0.47949	D	0.999556	P	0.43938	0.822	B	0.42625	0.393	T	0.65504	-0.6152	10	0.87932	D	0	-20.2627	14.8399	0.70214	1.0:0.0:0.0:0.0	.	765	P10745	RET3_HUMAN	A	765	ENSP00000224600:V765A	ENSP00000224600:V765A	V	-	2	0	RBP3	48008590	0.569000	0.26643	0.954000	0.39281	0.020000	0.10135	5.629000	0.67798	2.109000	0.64355	0.533000	0.62120	GTG	.	.		0.647	RBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047888.1	NM_002900		G	48388584	A	G	48388584	3	3	295	1	0	0	0	0	1	0	0	0	13172	159	6	2	1465	2	RBP3	10	48388584	Missense_Mutation	SNP	A	TCGA-G3-AAUZ-01A-11D-A382-10	12458559	48388584	87146163	55	42914										
ZRANB1	54764	hgsc.bcm.edu	37	chr10	126655297	126655297	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	atgttggctatactcttgtaCacttggctatacgttttcag	8	8	2	0			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr10:126655297C>T	ENST00000359653.4	+	2	1320	c.949C>T	c.(949-951)Cac>Tac	p.H317Y		NM_017580.2	NP_060050.2	Q9UGI0	ZRAN1_HUMAN	zinc finger, RAN-binding domain containing 1	317					cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|positive regulation of Wnt signaling pathway (GO:0030177)|protein deubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0071947)|protein K29-linked deubiquitination (GO:0035523)|protein K33-linked deubiquitination (GO:1990168)|protein K63-linked deubiquitination (GO:0070536)|regulation of cell morphogenesis (GO:0022604)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	K63-linked polyubiquitin binding (GO:0070530)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(2)|lung(3)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	23		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.172)		Colorectal(40;0.113)|COAD - Colon adenocarcinoma(40;0.119)		TACTCTTGTACACTTGGCTAT	0.413																																					p.H317Y		Atlas-SNP	.											.	ZRANB1	60	.	0			c.C949T						.						262	193	217					10																	126655297		2203	4300	6503	SO:0001583	missense	54764	exon2			CTTGTACACTTGG	AJ252060	CCDS7642.1	10q26.12	2014-02-24			ENSG00000019995	ENSG00000019995		"Zinc fingers, RAN-binding domain containing", "OTU domain containing"	18224	protein-coding gene	gene with protein product		611749				11463333	Standard	NM_017580		Approved	TRABID	uc001lic.3	Q9UGI0	OTTHUMG00000019223	ENST00000359653.4:c.949C>T	chr10.hg19:g.126655297C>T	ENSP00000352676:p.His317Tyr	125.0	0.0		121.0	30.0	NM_017580	B4DZ98|D3DRF4|Q5SQP6|Q69YK3	Missense_Mutation	SNP	ENST00000359653.4	hg19	CCDS7642.1	.	.	.	.	.	.	.	.	.	.	C	33	5.261754	0.95368	.	.	ENSG00000019995	ENST00000359653	T	0.22539	1.95	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	T	0.50069	0.1594	M	0.73962	2.25	0.80722	D	1	D	0.63046	0.992	D	0.71656	0.974	T	0.47289	-0.9129	10	0.87932	D	0	-28.9487	20.2789	0.98501	0.0:1.0:0.0:0.0	.	317	Q9UGI0	ZRAN1_HUMAN	Y	317	ENSP00000352676:H317Y	ENSP00000352676:H317Y	H	+	1	0	ZRANB1	126645287	1.000000	0.71417	0.974000	0.42286	0.995000	0.86356	7.461000	0.80834	2.788000	0.95919	0.650000	0.86243	CAC	.	.		0.413	ZRANB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050898.1	NM_017580		T	126655297	C	T	126655297	3	4	295	1	0	0	0	0	1	0	0	0	18237	478	17	3	955	3	ZRANB1	10	126655297	Missense_Mutation	SNP	C	TCGA-G3-AAUZ-01A-11D-A382-10	78266713	126655297	8879450	56	42915										
C11orf41	25758	hgsc.bcm.edu	37	chr11	33628245	33628245	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	gacaactccagcaaggtggcCgctgaaccctttgacacatc	9	14	0	2			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr11:33628245C>A	ENST00000321505.4	+	13	4227	c.4047C>A	c.(4045-4047)gcC>gcA	p.A1349A	KIAA1549L_ENST00000389726.3_Silent_p.A1355A			Q6ZVL6	K154L_HUMAN	KIAA1549-like	1349						integral component of membrane (GO:0016021)											GCAAGGTGGCCGCTGAACCCT	0.542																																					p.A1349A		Atlas-SNP	.											.	.	.	.	0			c.C4047A						.						64	70	68					11																	33628245		2041	4195	6236	SO:0001819	synonymous_variant	25758	exon13			GGTGGCCGCTGAA	U10991	CCDS44565.1, CCDS44565.2	11p13	2012-08-09	2012-08-09	2012-08-09	ENSG00000110427	ENSG00000110427			24836	protein-coding gene	gene with protein product		612297	"chromosome 11 open reading frame 69", "chromosome 11 open reading frame 41"	C11orf69, C11orf41			Standard	NM_012194		Approved	G2, MGC34830	uc021qfs.1	Q6ZVL6	OTTHUMG00000150410	ENST00000321505.4:c.4047C>A	chr11.hg19:g.33628245C>A		125.0	0.0		136.0	58.0	NM_012194	B0QYU0	Silent	SNP	ENST00000321505.4	hg19	CCDS44565.2	.	.	.	.	.	.	.	.	.	.	C	2.219	-0.378866	0.05000	.	.	ENSG00000110427	ENST00000526400	.	.	.	5.43	-8.09	0.01090	.	.	.	.	.	T	0.17789	0.0427	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.28364	-1.0046	4	.	.	.	-3.1816	4.2001	0.10462	0.192:0.4617:0.154:0.1923	.	.	.	.	Q	747	.	.	P	+	2	0	C11orf41	33584821	0.000000	0.05858	0.019000	0.16419	0.288000	0.27193	-2.415000	0.01036	-0.899000	0.03901	-0.367000	0.07326	CCG	.	.		0.542	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194		A	33628245	C	A	33628245	2	1	295	1	0	0	0	0	0	0	0	1	1642	639	23	1		1	C11orf41	11	33628245	Silent	SNP	C	TCGA-G3-AAUZ-01A-11D-A382-10		33628245	101378271	57	42916										
PDGFD	80310	hgsc.bcm.edu	37	chr11	103780494	103780494	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	aactggatgtcaactagagcCatggtcttagctctacccct	8	12	3	1			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr11:103780494C>A	ENST00000393158.2	-	7	1220	c.1041G>T	c.(1039-1041)atG>atT	p.M347I	PDGFD_ENST00000302251.5_Missense_Mutation_p.M341I			Q9GZP0	PDGFD_HUMAN	platelet derived growth factor D	347					cellular response to amino acid stimulus (GO:0071230)|multicellular organismal development (GO:0007275)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell division (GO:0051781)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(8)|prostate(3)|upper_aerodigestive_tract(1)	23		Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Melanoma(852;0.0563)|all_neural(303;0.165)		BRCA - Breast invasive adenocarcinoma(274;0.00136)|Epithelial(105;0.111)		CAACTAGAGCCATGGTCTTAG	0.463																																					p.M347I		Atlas-SNP	.											.	PDGFD	125	.	0			c.G1041T						.						319	257	278					11																	103780494		2202	4299	6501	SO:0001583	missense	80310	exon7			TAGAGCCATGGTC	AF113216	CCDS8326.1, CCDS41703.1	11q22.3	2008-02-05			ENSG00000170962	ENSG00000170962			30620	protein-coding gene	gene with protein product	"spinal cord derived growth factor B"	609673				11162582, 11980634	Standard	NM_033135		Approved	SCDGF-B, MSTP036, IEGF	uc001phq.3	Q9GZP0	OTTHUMG00000165953	ENST00000393158.2:c.1041G>T	chr11.hg19:g.103780494C>A	ENSP00000376865:p.Met347Ile	123.0	0.0		122.0	42.0	NM_025208	A8K9T6|Q9BWV5	Missense_Mutation	SNP	ENST00000393158.2	hg19	CCDS41703.1	.	.	.	.	.	.	.	.	.	.	C	14.63	2.592965	0.46214	.	.	ENSG00000170962	ENST00000393158;ENST00000302251	T;T	0.25414	1.8;1.8	5.91	5.91	0.95273	Platelet-derived growth factor (PDGF) (3);	0.082351	0.85682	D	0.000000	T	0.49966	0.1588	L	0.57536	1.79	0.48830	D	0.999718	D;P	0.54964	0.969;0.885	D;B	0.70227	0.968;0.392	T	0.22034	-1.0228	10	0.42905	T	0.14	-33.239	20.3057	0.98631	0.0:1.0:0.0:0.0	.	347;341	Q9GZP0;Q9GZP0-2	PDGFD_HUMAN;.	I	347;341	ENSP00000376865:M347I;ENSP00000302193:M341I	ENSP00000302193:M341I	M	-	3	0	PDGFD	103285704	1.000000	0.71417	1.000000	0.80357	0.226000	0.24999	4.085000	0.57657	2.791000	0.96007	0.655000	0.94253	ATG	.	.		0.463	PDGFD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387231.2	NM_025208		A	103780494	C	A	103780494	3	1	295	1	0	0	0	0	1	0	0	0	11669	594	21	3	75	3	PDGFD	11	103780494	Missense_Mutation	SNP	C	TCGA-G3-AAUZ-01A-11D-A382-10	70152249	103780494	31226022	58	42917										
ZNF384	171017	hgsc.bcm.edu	37	chr12	6777081	6777081	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	ggtggctgttgctgctgctgCtgctgctgctgctgctgctg	16	11	0	0			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr12:6777081C>T	ENST00000396801.3	-	11	1740	c.1533G>A	c.(1531-1533)caG>caA	p.Q511Q	ZNF384_ENST00000361959.3_Silent_p.Q511Q|RP4-761J14.8_ENST00000586338.1_RNA|RP4-761J14.8_ENST00000589924.1_RNA|ZNF384_ENST00000355772.4_Silent_p.Q395Q|ZNF384_ENST00000319770.3_Silent_p.Q434Q|ZNF384_ENST00000396799.2_Silent_p.Q450Q|ZNF384_ENST00000396795.1_Silent_p.Q450Q	NM_001135734.2	NP_001129206.1	Q8TF68	ZN384_HUMAN	zinc finger protein 384	511	Gln-rich.				nucleocytoplasmic transport (GO:0006913)|positive regulation of protein secretion (GO:0050714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	focal adhesion (GO:0005925)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)		EWSR1/ZNF384(4)	breast(3)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(1)	18						gctgctgctgctgctgctgct	0.667			T	"EWSR1, TAF15 "	ALL																																p.Q511Q		Atlas-SNP	.		Dom	yes		12	12p13	171017	zinc finger protein 384 (CIZ/NMP4)		L	.,4	ZNF384	102	.	0			c.G1533A						.						15	19	18					12																	6777081		2200	4287	6487	SO:0001819	synonymous_variant	171017	exon11			CTGCTGCTGCTGC	U80738	CCDS8557.1, CCDS31732.1, CCDS44817.1	12p12	2013-01-08	2002-05-23	2002-05-24		ENSG00000126746		"Zinc fingers, C2H2-type"	11955	protein-coding gene	gene with protein product		609951	"trinucleotide repeat containing 1"	TNRC1		9225980, 11149472	Standard	NM_001135734		Approved	CAGH1A, CIZ, NMP4, NP	uc010sfh.2	Q8TF68		ENST00000396801.3:c.1533G>A	chr12.hg19:g.6777081C>T		33.0	0.0		47.0	8.0	NM_001135734	O15407|Q7Z722|Q8N938	Silent	SNP	ENST00000396801.3	hg19	CCDS44817.1																																																																																			.	.		0.667	ZNF384-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400712.1			T	6777081	C	T	6777081	2	4	295	1	0	0	0	0	0	0	0	1	17890	796	28	3		3	ZNF384	12	6777081	Silent	SNP	C	TCGA-G3-AAUZ-01A-11D-A382-10		6777081	127074814	59	42918										
CPNE8	144402	hgsc.bcm.edu	37	chr12	39242371	39242371	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	tagaacttacaagtcaaaacGaagattctctctttcttcaa	4	9	5	2			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr12:39242371G>A	ENST00000331366.5	-	4	376	c.280C>T	c.(280-282)Cgt>Tgt	p.R94C	CPNE8_ENST00000360449.3_Missense_Mutation_p.R82C	NM_153634.2	NP_705898.1	Q86YQ8	CPNE8_HUMAN	copine VIII	94	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.					extracellular vesicular exosome (GO:0070062)		p.R94C(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(6)|lung(6)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	21	Esophageal squamous(101;0.187)	Lung NSC(34;0.137)|Melanoma(24;0.152)|all_lung(34;0.157)				AAGTCAAAACGAAGATTCTCT	0.308																																					p.R94C		Atlas-SNP	.											CPNE8,caecum,carcinoma,0,1	CPNE8	66	.	1	Substitution - Missense(1)	large_intestine(1)	c.C280T						.						34	36	36					12																	39242371		2197	4285	6482	SO:0001583	missense	144402	exon4			CAAAACGAAGATT	AY177785	CCDS8733.1	12q12	2008-02-05				ENSG00000139117			23498	protein-coding gene	gene with protein product						12670487	Standard	NM_153634		Approved		uc001rls.1	Q86YQ8	OTTHUMG00000169396	ENST00000331366.5:c.280C>T	chr12.hg19:g.39242371G>A	ENSP00000329748:p.Arg94Cys	275.0	0.0		318.0	125.0	NM_153634	Q2TB41|Q86VY2	Missense_Mutation	SNP	ENST00000331366.5	hg19	CCDS8733.1	.	.	.	.	.	.	.	.	.	.	G	18.09	3.545615	0.65198	.	.	ENSG00000139117	ENST00000331366;ENST00000360449	T;T	0.70516	-0.49;-0.49	3.8	3.8	0.43715	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.64402	D	0.000003	D	0.84401	0.5464	M	0.89287	3.02	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	D	0.86708	0.1934	10	0.87932	D	0	-9.626	10.7166	0.46015	0.0:0.0:0.8086:0.1914	.	94	Q86YQ8	CPNE8_HUMAN	C	94;82	ENSP00000329748:R94C;ENSP00000353633:R82C	ENSP00000329748:R94C	R	-	1	0	CPNE8	37528638	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	4.160000	0.58164	2.045000	0.60652	0.484000	0.47621	CGT	.	.		0.308	CPNE8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403856.1	NM_153634		A	39242371	G	A	39242371	3	1	295	1	0	0	0	0	1	0	0	0	3820	1058	37	1	1482	1	CPNE8	12	39242371	Missense_Mutation	SNP	G	TCGA-G3-AAUZ-01A-11D-A382-10	32465290	39242371	94609524	60	42919										
GNPTAB	79158	hgsc.bcm.edu	37	chr12	102161840	102161840	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	caatccccaccatcccaatcGcaggctgaattattacaagc	5	15	0	1	rs377176041		TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr12:102161840G>T	ENST00000299314.7	-	11	1645	c.1383C>A	c.(1381-1383)tgC>tgA	p.C461*	GNPTAB_ENST00000549940.1_Nonsense_Mutation_p.C461*|RNU6-101P_ENST00000410323.1_RNA	NM_024312.4	NP_077288.2	Q3T906	GNPTA_HUMAN	N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits	461			C -> G (in MLIIIA). {ECO:0000269|PubMed:19634183}.		carbohydrate phosphorylation (GO:0046835)|cell differentiation (GO:0030154)|lysosome organization (GO:0007040)|protein secretion (GO:0009306)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity (GO:0003976)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(8)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	37						CATCCCAATCGCAGGCTGAAT	0.418																																					p.C461X		Atlas-SNP	.											.	GNPTAB	120	.	0			c.C1383A						.						99	90	93					12																	102161840		2203	4300	6503	SO:0001587	stop_gained	79158	exon11			CCAATCGCAGGCT	AY687932	CCDS9088.1	12q23.3	2013-01-10				ENSG00000111670		"EF-hand domain containing"	29670	protein-coding gene	gene with protein product		607840		GNPTA		10574462, 16116615	Standard	NM_024312		Approved	KIAA1208, MGC4170	uc001tit.3	Q3T906	OTTHUMG00000170444	ENST00000299314.7:c.1383C>A	chr12.hg19:g.102161840G>T	ENSP00000299314:p.Cys461*	130.0	0.0		119.0	5.0	NM_024312	A2RRQ9|Q3ZQK2|Q6IPW5|Q86TQ2|Q96N13|Q9ULL2	Nonsense_Mutation	SNP	ENST00000299314.7	hg19	CCDS9088.1	.	.	.	.	.	.	.	.	.	.	G	37	6.244113	0.97408	.	.	ENSG00000111670	ENST00000299314;ENST00000549940	.	.	.	5.71	0.637	0.17735	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-19.3477	9.7664	0.40563	0.7566:0.0:0.2434:0.0	.	.	.	.	X	461	.	ENSP00000299314:C461X	C	-	3	2	GNPTAB	100685971	1.000000	0.71417	0.997000	0.53966	0.873000	0.50193	1.385000	0.34408	-0.035000	0.13691	-1.000000	0.02509	TGC	.	.		0.418	GNPTAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409182.1			T	102161840	G	T	102161840	4	4	295	1	0	0	0	0	0	1	0	0	6553	1079	38	1	2431	1	GNPTAB	12	102161840	Nonsense_Mutation	SNP	G	TCGA-G3-AAUZ-01A-11D-A382-10	62919469	102161840	31690055	61	42920										
MYO1H	283446	hgsc.bcm.edu	37	chr12	109834356	109834356	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	gtcactacaaatagcccgtgAcagactgctgttctccaacc	7	14	2	2			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr12:109834356A>G	ENST00000431443.2	+	3	410	c.410A>G	c.(409-411)gAc>gGc	p.D137G	MYO1H_ENST00000310903.5_Missense_Mutation_p.D137G	NM_001101421.3	NP_001094891.3	Q8N1T3	MYO1H_HUMAN	myosin IH	137	Myosin motor.					myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(17)|prostate(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	47						ATAGCCCGTGACAGACTGCTG	0.522																																					p.D137G		Atlas-SNP	.											.	MYO1H	98	.	0			c.A410G						.						68	67	67					12																	109834356		1925	4142	6067	SO:0001583	missense	283446	exon3			CCCGTGACAGACT		CCDS53826.1	12q24.11	2011-09-27			ENSG00000174527	ENSG00000174527		"Myosins / Myosin superfamily : Class I"	13879	protein-coding gene	gene with protein product		614636					Standard	NM_001101421		Approved	FLJ37587	uc010sxn.1	Q8N1T3	OTTHUMG00000169252	ENST00000431443.2:c.410A>G	chr12.hg19:g.109834356A>G	ENSP00000444076:p.Asp137Gly	94.0	0.0		98.0	32.0	NM_001101421	F5H3C6	Missense_Mutation	SNP	ENST00000431443.2	hg19		.	.	.	.	.	.	.	.	.	.	A	23.6	4.430668	0.83776	.	.	ENSG00000174527	ENST00000310903;ENST00000431443	T;T	0.72505	-0.66;-0.66	4.8	4.8	0.61643	.	.	.	.	.	D	0.83797	0.5332	M	0.83223	2.63	0.53688	D	0.99997	D	0.76494	0.999	D	0.66716	0.946	D	0.86693	0.1924	9	0.87932	D	0	.	14.2704	0.66149	1.0:0.0:0.0:0.0	.	137	F5H3C6	.	G	137	ENSP00000439182:D137G;ENSP00000444076:D137G	ENSP00000439182:D137G	D	+	2	0	MYO1H	108318739	1.000000	0.71417	0.995000	0.50966	0.989000	0.77384	9.227000	0.95236	2.112000	0.64535	0.524000	0.50904	GAC	.	.		0.522	MYO1H-201	KNOWN	basic	protein_coding	protein_coding		NM_173597		G	109834356	A	G	109834356	3	3	295	1	0	0	0	0	1	0	0	0	10084	275	10	2	420	2	MYO1H	12	109834356	Missense_Mutation	SNP	A	TCGA-G3-AAUZ-01A-11D-A382-10	7672516	109834356	24017539	62	42921										
ATP2A2	488	hgsc.bcm.edu	37	chr12	110778716	110778716	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	agcgagacgcctgcctgaacGcccgctgttttgctcgagtt	12	13	0	2			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr12:110778716G>T	ENST00000539276.2	+	14	2123	c.2014G>T	c.(2014-2016)Gcc>Tcc	p.A672S	ATP2A2_ENST00000308664.6_Missense_Mutation_p.A672S|ATP2A2_ENST00000395494.2_Missense_Mutation_p.A645S			P16615	AT2A2_HUMAN	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	672					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|epidermis development (GO:0008544)|ER-nucleus signaling pathway (GO:0006984)|ion transmembrane transport (GO:0034220)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart rate (GO:0010460)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|calcium-transporting ATPase activity involved in regulation of cardiac muscle cell membrane potential (GO:0086039)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|S100 protein binding (GO:0044548)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(10)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	38						CTGCCTGAACGCCCGCTGTTT	0.512																																					p.A672S		Atlas-SNP	.											.	ATP2A2	78	.	0			c.G2014T						.						55	55	55					12																	110778716		2203	4300	6503	SO:0001583	missense	488	exon14			CTGAACGCCCGCT		CCDS9143.1, CCDS9144.1	12q24.11	2012-10-22			ENSG00000174437	ENSG00000174437	3.6.3.8	"ATPases / P-type"	812	protein-coding gene	gene with protein product	"sarcoplasmic/endoplasmic reticulum calcium ATPase 2", "calcium pump 2"	108740		ATP2B, DAR		10080178	Standard	NM_170665		Approved	SERCA2	uc001tqk.4	P16615	OTTHUMG00000169327	ENST00000539276.2:c.2014G>T	chr12.hg19:g.110778716G>T	ENSP00000440045:p.Ala672Ser	128.0	0.0		153.0	57.0	NM_001681	A6NDN7|B4DF05|P16614|Q86VJ2	Missense_Mutation	SNP	ENST00000539276.2	hg19	CCDS9144.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.8|21.8	4.195941|4.195941	0.78902|0.78902	.|.	.|.	ENSG00000174437|ENSG00000174437	ENST00000308664;ENST00000395494;ENST00000539276|ENST00000548169	D;D;D|.	0.96011|.	-3.88;-3.88;-3.88|.	5.81|5.81	5.81|5.81	0.92471|0.92471	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type,  transmembrane domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.71358|0.71358	0.3330|0.3330	L|L	0.49350|0.49350	1.555|1.555	0.80722|0.80722	D|D	1|1	B;B;B|.	0.20459|.	0.045;0.001;0.001|.	B;B;B|.	0.22152|.	0.038;0.012;0.02|.	T|T	0.65841|0.65841	-0.6070|-0.6070	10|5	0.48119|.	T|.	0.1|.	.|.	20.0784|20.0784	0.97758|0.97758	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	645;672;672|.	P16615-4;P16615-2;P16615|.	.;.;AT2A2_HUMAN|.	S|L	672;645;672|562	ENSP00000311186:A672S;ENSP00000378872:A645S;ENSP00000440045:A672S|.	ENSP00000311186:A672S|.	A|R	+|+	1|2	0|0	ATP2A2|ATP2A2	109263099|109263099	1.000000|1.000000	0.71417|0.71417	0.981000|0.981000	0.43875|0.43875	0.925000|0.925000	0.55904|0.55904	9.869000|9.869000	0.99810|0.99810	2.736000|2.736000	0.93811|0.93811	0.655000|0.655000	0.94253|0.94253	GCC|CGC	.	.		0.512	ATP2A2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403539.1	NM_001681		T	110778716	G	T	110778716	3	4	295	1	0	0	0	0	1	0	0	0	1137	1087	38	1	2068	1	ATP2A2	12	110778716	Missense_Mutation	SNP	G	TCGA-G3-AAUZ-01A-11D-A382-10	944360	110778716	23073179	63	42922										
CIT	11113	hgsc.bcm.edu	37	chr12	120271933	120271933	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	aacgctgtgaacagccaaaaTcagctcagctaggtaaaact	8	10	2	1			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr12:120271933T>C	ENST00000261833.7	-	6	668	c.616A>G	c.(616-618)Att>Gtt	p.I206V	CIT_ENST00000392521.2_Missense_Mutation_p.I206V	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	206	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		ACAGCCAAAATCAGCTCAGCT	0.443																																					p.I206V		Atlas-SNP	.											.	CIT	535	.	0			c.A616G						.						130	112	118					12																	120271933		2203	4300	6503	SO:0001583	missense	11113	exon6			CCAAAATCAGCTC	AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966			1985	protein-coding gene	gene with protein product	"serine/threonine kinase 21"	605629	"citron (rho-interacting, serine/threonine kinase 21)"			9792683	Standard	NM_001206999		Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000261833.7:c.616A>G	chr12.hg19:g.120271933T>C	ENSP00000261833:p.Ile206Val	152.0	0.0		110.0	38.0	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Missense_Mutation	SNP	ENST00000261833.7	hg19	CCDS9192.1	.	.	.	.	.	.	.	.	.	.	T	2.933	-0.220503	0.06061	.	.	ENSG00000122966	ENST00000392521;ENST00000261833	T;T	0.38240	1.15;1.15	5.45	4.32	0.51571	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.171581	0.37261	N	0.002161	T	0.09512	0.0234	N	0.01257	-0.925	0.41808	D	0.989958	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.28106	-1.0054	10	0.02654	T	1	.	5.1096	0.14802	0.0:0.2646:0.0:0.7354	.	206;206	Q2M5E1;O14578	.;CTRO_HUMAN	V	206	ENSP00000376306:I206V;ENSP00000261833:I206V	ENSP00000261833:I206V	I	-	1	0	CIT	118756316	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	2.199000	0.42715	2.086000	0.62901	0.379000	0.24179	ATT	.	.		0.443	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174		C	120271933	T	C	120271933	3	2	295	1	0	0	0	0	1	0	0	0	3440	1435	50	2	5635	2	CIT	12	120271933	Missense_Mutation	SNP	T	TCGA-G3-AAUZ-01A-11D-A382-10	9493217	120271933	13579962	64	42923										
SAP18	10284	hgsc.bcm.edu	37	chr13	21721331	21721331	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	tttctttcttacagagttaaGgagattggcagcaccatgtc	9	8	2	2			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr13:21721331G>A	ENST00000607003.1	+	4	344	c.312G>A	c.(310-312)aaG>aaA	p.K104K	SAP18_ENST00000382533.4_Silent_p.K123K			O00422	SAP18_HUMAN	Sin3A-associated protein, 18kDa	104	Involved in splicing regulation activity.				mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription corepressor activity (GO:0003714)			kidney(1)|large_intestine(1)|lung(4)	6		all_cancers(29;2.16e-20)|all_epithelial(30;2.97e-18)|all_lung(29;4.58e-16)|Lung SC(185;0.0262)|Breast(139;0.147)		all cancers(112;9.79e-05)|Epithelial(112;0.000292)|OV - Ovarian serous cystadenocarcinoma(117;0.00276)|Lung(94;0.0941)		ACAGAGTTAAGGAGATTGGCA	0.408																																					p.K123K		Atlas-SNP	.											.	SAP18	12	.	0			c.G369A						.						91	92	91					13																	21721331		2203	4300	6503	SO:0001819	synonymous_variant	10284	exon4			AGTTAAGGAGATT	U96915	CCDS9295.2	13q12.11	2008-02-05	2006-02-02		ENSG00000150459	ENSG00000150459			10530	protein-coding gene	gene with protein product		602949	"sin3A-associated protein, 18kDa"			9150135	Standard	NM_005870		Approved	SAP18p, 2HOR0202, MGC27131	uc001uns.3	O00422	OTTHUMG00000016535	ENST00000607003.1:c.312G>A	chr13.hg19:g.21721331G>A		283.0	0.0		341.0	72.0	NM_005870	B2R494|Q2TTR4|Q6IAW9|Q8N606|Q9UF14	Silent	SNP	ENST00000607003.1	hg19		.	.	.	.	.	.	.	.	.	.	G	8.608	0.888339	0.17540	.	.	ENSG00000150459	ENST00000450573	.	.	.	5.78	3.78	0.43462	.	.	.	.	.	T	0.62816	0.2459	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61628	-0.7024	4	.	.	.	-12.8462	11.9977	0.53212	0.1856:0.0:0.8144:0.0	.	.	.	.	R	118	.	.	G	+	1	0	SAP18	20619331	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	1.711000	0.37930	1.419000	0.47118	0.591000	0.81541	GGA	.	.		0.408	SAP18-009	PUTATIVE	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000470725.1	NM_005870		A	21721331	G	A	21721331	2	1	295	1	0	0	0	0	0	0	0	1	13847	991	35	3		3	SAP18	13	21721331	Silent	SNP	G	TCGA-G3-AAUZ-01A-11D-A382-10		21721331	93448547	65	42924										
SACS	26278	hgsc.bcm.edu	37	chr13	23907171	23907171	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	gcaatgtttctttggaccagTtttctgtattagccctcaca	7	10	3	0			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr13:23907171T>G	ENST00000382292.3	-	9	11117	c.10844A>C	c.(10843-10845)aAc>aCc	p.N3615T	SACS_ENST00000402364.1_Missense_Mutation_p.N2865T|SACS_ENST00000382298.3_Missense_Mutation_p.N3615T			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	3615					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		TTTGGACCAGTTTTCTGTATT	0.343																																					p.N3615T		Atlas-SNP	.											SACS_ENST00000382298,NS,adenocarcinoma,0,2	SACS	871	.	0			c.A10844C						.						62	65	64					13																	23907171		2203	4299	6502	SO:0001583	missense	26278	exon10			GACCAGTTTTCTG	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.10844A>C	chr13.hg19:g.23907171T>G	ENSP00000371729:p.Asn3615Thr	153.0	0.0		92.0	23.0	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	hg19	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	T	12.73	2.026858	0.35797	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.88124	-2.18;-2.34;-2.18	5.91	5.91	0.95273	.	0.147838	0.64402	D	0.000007	T	0.75925	0.3916	L	0.27053	0.805	0.27877	N	0.939824	P	0.35077	0.483	B	0.27887	0.084	T	0.67673	-0.5610	10	0.21540	T	0.41	.	10.6466	0.45623	0.0:0.0711:0.0:0.9289	.	3615	Q9NZJ4	SACS_HUMAN	T	3615;2865;3615	ENSP00000371729:N3615T;ENSP00000385844:N2865T;ENSP00000371735:N3615T	ENSP00000371729:N3615T	N	-	2	0	SACS	22805171	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.146000	0.58072	2.263000	0.75096	0.379000	0.24179	AAC	.	.		0.343	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		G	23907171	T	G	23907171	3	3	295	1	0	0	0	0	1	0	0	0	13819	1725	60	5	2899	5	SACS	13	23907171	Missense_Mutation	SNP	T	TCGA-G3-AAUZ-01A-11D-A382-10	2185840	23907171	91262707	66	42925										
FOXN3	1112	hgsc.bcm.edu	37	chr14	89878384	89878384	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	ttgcaaaatacggaaaatgtTccaagatccagttgtagata	8	6	0	2			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr14:89878384T>C	ENST00000345097.4	-	2	553	c.437A>G	c.(436-438)gAa>gGa	p.E146G	RP11-33N16.3_ENST00000555070.1_RNA|RP11-33N16.2_ENST00000556383.1_RNA|FOXN3_ENST00000557258.1_Missense_Mutation_p.E146G|FOXN3_ENST00000555353.1_Missense_Mutation_p.E146G|FOXN3_ENST00000261302.5_Missense_Mutation_p.E146G	NM_001085471.1	NP_001078940.1	O00409	FOXN3_HUMAN	forkhead box N3	146					mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|large_intestine(4)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						CGGAAAATGTTCCAAGATCCA	0.438																																					p.E146G		Atlas-SNP	.											.	FOXN3	78	.	0			c.A437G						.						82	84	83					14																	89878384		2203	4300	6503	SO:0001583	missense	1112	exon2			AAATGTTCCAAGA		CCDS32138.1, CCDS41977.1	14q32.11	2012-04-17	2007-05-02	2007-05-02	ENSG00000053254	ENSG00000053254		"Forkhead boxes"	1928	protein-coding gene	gene with protein product		602628	"chromosome 14 open reading frame 116", "checkpoint suppressor 1"	C14orf116, CHES1		9154802	Standard	NM_005197		Approved		uc001xxo.4	O00409	OTTHUMG00000170898	ENST00000345097.4:c.437A>G	chr14.hg19:g.89878384T>C	ENSP00000343288:p.Glu146Gly	164.0	0.0		160.0	32.0	NM_005197	Q96II7|Q9UIE7	Missense_Mutation	SNP	ENST00000345097.4	hg19	CCDS41977.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	22.0|22.0	4.231812|4.231812	0.79688|0.79688	.|.	.|.	ENSG00000053254|ENSG00000053254	ENST00000345097;ENST00000261302;ENST00000557258;ENST00000555353;ENST00000555855|ENST00000556916	D;D;D;D;D|.	0.95885|.	-3.84;-3.84;-3.84;-3.84;-3.84|.	4.99|4.99	4.99|4.99	0.66335|0.66335	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (4);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.70937|0.70937	0.3281|0.3281	M|M	0.64404|0.64404	1.975|1.975	0.80722|0.80722	D|D	1|1	B;P|.	0.39480|.	0.368;0.675|.	B;B|.	0.39379|.	0.219;0.298|.	T|T	0.70662|0.70662	-0.4810|-0.4810	10|5	0.66056|.	D|.	0.02|.	.|.	14.9853|14.9853	0.71342|0.71342	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	146;146|.	O00409;O00409-2|.	FOXN3_HUMAN;.|.	G|D	146|7	ENSP00000343288:E146G;ENSP00000261302:E146G;ENSP00000452005:E146G;ENSP00000452227:E146G;ENSP00000451135:E146G|.	ENSP00000261302:E146G|.	E|N	-|-	2|1	0|0	FOXN3|FOXN3	88948137|88948137	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	6.260000|6.260000	0.72502|0.72502	2.005000|2.005000	0.58758|0.58758	0.374000|0.374000	0.22700|0.22700	GAA|AAC	.	.		0.438	FOXN3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410902.2	NM_005197		C	89878384	T	C	89878384	3	2	295	1	0	0	0	0	1	0	0	0	6029	1783	62	2	1059	2	FOXN3	14	89878384	Missense_Mutation	SNP	T	TCGA-G3-AAUZ-01A-11D-A382-10		89878384	17471156	67	42926										
THBS1	7057	hgsc.bcm.edu	37	chr15	39874930	39874930	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	ccagactccgcatcgcaaagGggggcgtcaatgacaatttc	11	12	1	2			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr15:39874930G>T	ENST00000260356.5	+	3	769	c.604G>T	c.(604-606)Ggg>Tgg	p.G202W		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	202	Laminin G-like.				activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		CATCGCAAAGGGGGGCGTCAA	0.557																																					p.G202W		Atlas-SNP	.											.	THBS1	106	.	0			c.G604T						.						39	37	38					15																	39874930		2200	4297	6497	SO:0001583	missense	7057	exon3			GCAAAGGGGGGCG		CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"thrombospondin-1p180"	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.604G>T	chr15.hg19:g.39874930G>T	ENSP00000260356:p.Gly202Trp	16.0	0.0		41.0	15.0	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Missense_Mutation	SNP	ENST00000260356.5	hg19	CCDS32194.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.032978	0.93575	.	.	ENSG00000137801	ENST00000260356	T	0.02395	4.31	5.56	5.56	0.83823	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G, thrombospondin-type, N-terminal (1);	0.000000	0.35291	N	0.003319	T	0.16471	0.0396	M	0.76170	2.325	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.00007	-1.2504	10	0.87932	D	0	-13.6668	18.6764	0.91529	0.0:0.0:1.0:0.0	.	202	P07996	TSP1_HUMAN	W	202	ENSP00000260356:G202W	ENSP00000260356:G202W	G	+	1	0	THBS1	37662222	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.419000	0.97397	2.890000	0.99128	0.655000	0.94253	GGG	.	.		0.557	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246		T	39874930	G	T	39874930	3	4	295	1	0	0	0	0	1	0	0	0	15868	1232	43	3	610	3	THBS1	15	39874930	Missense_Mutation	SNP	G	TCGA-G3-AAUZ-01A-11D-A382-10		39874930	62656462	68	42927										
ONECUT1	3175	hgsc.bcm.edu	37	chr15	53081884	53081884	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	cggtggtggtggtggtaatcTccgccgccgctgccgccgtc	16	14	1	0			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr15:53081884T>G	ENST00000305901.5	-	1	325	c.198A>C	c.(196-198)ggA>ggC	p.G66G	ONECUT1_ENST00000561401.2_Intron	NM_004498.2	NP_004489.1	Q9UBC0	HNF6_HUMAN	one cut homeobox 1	66					B cell differentiation (GO:0030183)|cell fate commitment (GO:0045165)|cilium assembly (GO:0042384)|endocrine pancreas development (GO:0031018)|endoderm development (GO:0007492)|epithelial cell development (GO:0002064)|glucose metabolic process (GO:0006006)|liver development (GO:0001889)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell-matrix adhesion (GO:0001952)|regulation of transcription, DNA-templated (GO:0006355)|spleen development (GO:0048536)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|prostate(2)|skin(1)	17				all cancers(107;0.0708)		GGTGGTAATCTCCGCCGCCGC	0.736																																					p.G66G		Atlas-SNP	.											.	ONECUT1	48	.	0			c.A198C						.						13	14	13					15																	53081884		2187	4277	6464	SO:0001819	synonymous_variant	3175	exon1			GTAATCTCCGCCG	U77975	CCDS10150.1	15q21.3	2012-03-09	2007-07-16		ENSG00000169856	ENSG00000169856		"Homeoboxes / CUT class"	8138	protein-coding gene	gene with protein product		604164	"one cut domain, family member 1"	HNF6, HNF6A		8887657, 8790352	Standard	NM_004498		Approved	HNF-6	uc002aci.2	Q9UBC0	OTTHUMG00000131899	ENST00000305901.5:c.198A>C	chr15.hg19:g.53081884T>G		19.0	0.0		17.0	7.0	NM_004498	B2RTV4|Q99744|Q9UMR6	Silent	SNP	ENST00000305901.5	hg19	CCDS10150.1																																																																																			.	.		0.736	ONECUT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254849.2			G	53081884	T	G	53081884	2	3	295	1	0	0	0	0	0	0	0	1	10877	1538	54	5		5	ONECUT1	15	53081884	Silent	SNP	T	TCGA-G3-AAUZ-01A-11D-A382-10	13206954	53081884	49449508	69	42928										
ADAMTS7	11173	hgsc.bcm.edu	37	chr15	79067100	79067100	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	tgcagaggcggaagcgcttgCgctcacccacacagtatctg	12	13	2	1			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr15:79067100C>A	ENST00000388820.4	-	12	1952	c.1742G>T	c.(1741-1743)cGc>cTc	p.R581L	ADAMTS7_ENST00000566303.1_Intron	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	581	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						GAAGCGCTTGCGCTCACCCAC	0.647																																					p.R581L		Atlas-SNP	.											.	ADAMTS7	142	.	0			c.G1742T						.						69	79	76					15																	79067100		2196	4292	6488	SO:0001583	missense	11173	exon12			CGCTTGCGCTCAC	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"ADAM metallopeptidases with thrombospondin type 1 motif"	223	protein-coding gene	gene with protein product	"COMPase", "a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"	605009	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.1742G>T	chr15.hg19:g.79067100C>A	ENSP00000373472:p.Arg581Leu	28.0	0.0		35.0	6.0	NM_014272	Q14F51|Q6P7J9	Missense_Mutation	SNP	ENST00000388820.4	hg19	CCDS32303.1	.	.	.	.	.	.	.	.	.	.	C	16.48	3.135211	0.56828	.	.	ENSG00000136378	ENST00000388820	T	0.00441	7.41	3.51	3.51	0.40186	.	0.145279	0.42821	D	0.000653	T	0.00875	0.0029	L	0.55743	1.74	0.48762	D	0.999702	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.78516	-0.2174	10	0.87932	D	0	.	14.2729	0.66162	0.0:1.0:0.0:0.0	.	581;581	A8MQ00;Q9UKP4	.;ATS7_HUMAN	L	581	ENSP00000373472:R581L	ENSP00000373472:R581L	R	-	2	0	ADAMTS7	76854155	1.000000	0.71417	0.117000	0.21633	0.050000	0.14768	7.439000	0.80444	1.986000	0.57962	0.289000	0.19496	CGC	.	.		0.647	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272		A	79067100	C	A	79067100	3	1	295	1	0	0	0	0	1	0	0	0	271	768	27	1	3370	1	ADAMTS7	15	79067100	Missense_Mutation	SNP	C	TCGA-G3-AAUZ-01A-11D-A382-10	25985216	79067100	23464292	70	42929										
SMG1	23049	hgsc.bcm.edu	37	chr16	18841077	18841077	+	Splice_Site	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	gatcttcaagtgaacttgatCctacaaaaaggaaaaatttc	6	7	2	2			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr16:18841077C>A	ENST00000446231.2	-	54	9546	c.9134G>T	c.(9133-9135)gGa>gTa	p.G3045V	SMG1_ENST00000389467.3_Splice_Site_p.G3045V			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	3045					DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						TGAACTTGATCCTACAAAAAG	0.303																																					p.G3045V		Atlas-SNP	.											.	SMG1	401	.	0			c.G9134T						.						28	27	27					16																	18841077		1814	4078	5892	SO:0001630	splice_region_variant	23049	exon54			CTTGATCCTACAA	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase-related kinase"	607032	"smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.9134-1G>T	chr16.hg19:g.18841077C>A		59.0	0.0		81.0	28.0	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	ENST00000446231.2	hg19	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	C	17.02	3.280822	0.59758	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	T;T	0.01185	5.21;5.21	6.07	6.07	0.98685	.	0.000000	0.64402	D	0.000004	T	0.04452	0.0122	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.53739	-0.8396	10	0.87932	D	0	.	20.6525	0.99598	0.0:1.0:0.0:0.0	.	3045	Q96Q15	SMG1_HUMAN	V	3045	ENSP00000402515:G3045V;ENSP00000374118:G3045V	ENSP00000374118:G3045V	G	-	2	0	SMG1	18748578	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	6.644000	0.74338	2.890000	0.99128	0.585000	0.79938	GGA	.	.		0.303	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092	Missense_Mutation	A	18841077	C	A	18841077	5	1	295	1	0	0	0	0	0	0	1	0	14810	869	30	3	1891	3	SMG1	16	18841077	Splice_Site	SNP	C	TCGA-G3-AAUZ-01A-11D-A382-10		18841077	71513676	71	42930										
NCOR1	9611	hgsc.bcm.edu	37	chr17	16040642	16040642	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	cacctggtttctgcctctgcGtttcccataattccttctga	6	14	3	1			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr17:16040642G>A	ENST00000268712.3	-	14	1749	c.1492C>T	c.(1492-1494)Cgc>Tgc	p.R498C	NCOR1_ENST00000395848.1_Missense_Mutation_p.R389C|NCOR1_ENST00000395851.1_Missense_Mutation_p.R498C|RNU6-862P_ENST00000362804.1_RNA	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	498					CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		CTGCCTCTGCGTTTCCCATAA	0.373																																					p.R498C		Atlas-SNP	.											.	NCOR1	240	.	0			c.C1492T						.						74	69	71					17																	16040642		2203	4300	6503	SO:0001583	missense	9611	exon13			CTCTGCGTTTCCC	AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"thyroid hormone- and retinoic acid receptor-associated corepressor 1", "protein phosphatase 1, regulatory subunit 109"	600849	"nuclear receptor co-repressor 1"			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.1492C>T	chr17.hg19:g.16040642G>A	ENSP00000268712:p.Arg498Cys	99.0	0.0		70.0	49.0	NM_001190440	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Missense_Mutation	SNP	ENST00000268712.3	hg19	CCDS11175.1	.	.	.	.	.	.	.	.	.	.	G	12.16	1.854572	0.32791	.	.	ENSG00000141027	ENST00000268712;ENST00000395851;ENST00000395849;ENST00000458113;ENST00000395848;ENST00000411510;ENST00000436828	T;T;T;T;T	0.40225	1.04;1.04;1.04;1.04;1.04	5.09	4.12	0.48240	.	0.051934	0.85682	D	0.000000	T	0.62804	0.2458	M	0.83774	2.66	0.80722	D	1	D;D;D;D;D;B	0.89917	1.0;1.0;1.0;1.0;1.0;0.035	D;D;D;D;D;B	0.80764	0.972;0.972;0.972;0.973;0.994;0.016	T	0.65861	-0.6065	10	0.87932	D	0	-7.2267	7.8821	0.29629	0.0818:0.0:0.7586:0.1596	.	507;498;498;389;498;498	E7EU93;E7EV02;E7EW50;E9PGV6;O75376;O75376-2	.;.;.;.;NCOR1_HUMAN;.	C	498;498;389;507;389;498;507	ENSP00000268712:R498C;ENSP00000379192:R498C;ENSP00000379189:R389C;ENSP00000407998:R498C;ENSP00000387727:R507C	ENSP00000268712:R498C	R	-	1	0	NCOR1	15981367	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	6.117000	0.71577	1.269000	0.44280	0.563000	0.77884	CGC	.	.		0.373	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		A	16040642	G	A	16040642	3	1	295	1	0	0	0	0	1	0	0	0	10244	1145	40	1	5962	1	NCOR1	17	16040642	Missense_Mutation	SNP	G	TCGA-G3-AAUZ-01A-11D-A382-10		16040642	65154568	72	42931										
CYTSB	92521	hgsc.bcm.edu	37	chr17	20108414	20108414	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	ctccaccagtaacccctttaAgagttcaaagtgttctactg	6	12	2	1			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr17:20108414A>G	ENST00000261503.5	+	4	1103	c.1052A>G	c.(1051-1053)aAg>aGg	p.K351R	SPECC1_ENST00000395522.2_Missense_Mutation_p.K270R|SPECC1_ENST00000395529.3_Missense_Mutation_p.K351R|AC004702.2_ENST00000580225.1_lincRNA|SPECC1_ENST00000584527.1_5'Flank|SPECC1_ENST00000472876.1_Intron|SPECC1_ENST00000536879.1_Intron|SPECC1_ENST00000395530.2_Missense_Mutation_p.K270R|SPECC1_ENST00000395525.3_Missense_Mutation_p.K270R|SPECC1_ENST00000395527.4_Missense_Mutation_p.K351R	NM_001033553.2	NP_001028725.1	Q5M775	CYTSB_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1	351	Ser-rich.				cell adhesion (GO:0007155)	nucleus (GO:0005634)				breast(1)|large_intestine(3)|ovary(4)	8				KIRC - Kidney renal clear cell carcinoma(2;0.166)|Kidney(2;0.196)		AACCCCTTTAAGAGTTCAAAG	0.483																																					p.K351R		Atlas-SNP	.											.	SPECC1	100	.	0			c.A1052G						.						119	129	126					17																	20108414		2203	4300	6503	SO:0001583	missense	92521	exon4			CCTTTAAGAGTTC	AY816329, AB041533	CCDS32590.1, CCDS42280.1, CCDS42281.1, CCDS45628.1, CCDS58531.1	17p11.2	2012-11-19	2010-09-17	2010-09-17	ENSG00000128487	ENSG00000128487			30615	protein-coding gene	gene with protein product	"sperm antigen HCMOGT 1", "cytokinesis and spindle organization B", "cytospin B"	608793				15602574, 18763323, 15087372	Standard	NM_001033553		Approved	HCMOGT-1, FLJ36955, NSP, CYTSB	uc002gwq.3	Q5M775	OTTHUMG00000179808	ENST00000261503.5:c.1052A>G	chr17.hg19:g.20108414A>G	ENSP00000261503:p.Lys351Arg	128.0	0.0		182.0	13.0	NM_001033553	B4DHH0|B7WNS8|Q5IBP1|Q5IBP2|Q5IBP3|Q5IBP4|Q5M772|Q5M773|Q5M774|Q86XT8|Q8N4U4|Q8WU84|Q9HCQ3	Missense_Mutation	SNP	ENST00000261503.5	hg19	CCDS32590.1	.	.	.	.	.	.	.	.	.	.	A	4.500	0.092814	0.08632	.	.	ENSG00000128487	ENST00000395530;ENST00000261503;ENST00000395529;ENST00000395522;ENST00000395527;ENST00000395525	T;T;T;T	0.64991	-0.13;3.46;2.87;2.87	5.38	4.3	0.51218	.	0.271400	0.48286	N	0.000194	T	0.55689	0.1936	L	0.59436	1.845	0.80722	D	1	B;B;B;B;B	0.16603	0.001;0.018;0.018;0.018;0.003	B;B;B;B;B	0.17722	0.002;0.011;0.019;0.019;0.005	T	0.51156	-0.8741	10	0.34782	T	0.22	-34.3834	9.6345	0.39800	0.9167:0.0:0.0833:0.0	.	351;270;270;351;351	A8MV89;Q5M775-4;Q5M775-3;Q5M775-2;Q5M775	.;.;.;.;CYTSB_HUMAN	R	351;351;351;270;270;270	ENSP00000261503:K351R;ENSP00000378900:K351R;ENSP00000378893:K270R;ENSP00000378896:K270R	ENSP00000261503:K351R	K	+	2	0	SPECC1	20049006	1.000000	0.71417	0.992000	0.48379	0.115000	0.19883	3.056000	0.49923	0.997000	0.38969	0.533000	0.62120	AAG	.	.		0.483	SPECC1-018	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441206.1	NM_152904		G	20108414	A	G	20108414	3	3	295	1	0	0	0	0	1	0	0	0	4212	72	3	2	1106	2	CYTSB	17	20108414	Missense_Mutation	SNP	A	TCGA-G3-AAUZ-01A-11D-A382-10	4067772	20108414	61086796	73	42932										
NLK	51701	hgsc.bcm.edu	37	chr17	26495650	26495650	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	gcagaactactaggacgaagAatattgtttcaggcacagag	11	7	1	3			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr17:26495650A>T	ENST00000407008.3	+	6	1732	c.1014A>T	c.(1012-1014)agA>agT	p.R338S		NM_016231.4	NP_057315.3	Q9UBE8	NLK_HUMAN	nemo-like kinase	338	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|Sufficient for interaction with DAPK3.				intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of Wnt signaling pathway (GO:0030178)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|serine phosphorylation of STAT3 protein (GO:0033136)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase activity (GO:0004707)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|SH2 domain binding (GO:0042169)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(1)	14	all_lung(13;0.000343)|Lung NSC(42;0.00184)			UCEC - Uterine corpus endometrioid carcinoma (53;0.168)		TAGGACGAAGAATATTGTTTC	0.418																																					p.R338S		Atlas-SNP	.											.	NLK	88	.	0			c.A1014T						.						119	114	116					17																	26495650		2203	4300	6503	SO:0001583	missense	51701	exon6			ACGAAGAATATTG	AF197898	CCDS11224.2	17q11.2	2005-12-22	2005-12-22		ENSG00000087095	ENSG00000087095			29858	protein-coding gene	gene with protein product		609476	"nemo like kinase"			9448268, 10863097	Standard	NM_016231		Approved		uc010crj.3	Q9UBE8	OTTHUMG00000132451	ENST00000407008.3:c.1014A>T	chr17.hg19:g.26495650A>T	ENSP00000384625:p.Arg338Ser	86.0	0.0		123.0	9.0	NM_016231	B2RCX1|Q2PNI9|Q6P2A3	Missense_Mutation	SNP	ENST00000407008.3	hg19	CCDS11224.2	.	.	.	.	.	.	.	.	.	.	A	21.5	4.157440	0.78114	.	.	ENSG00000087095	ENST00000407008	T	0.66280	-0.2	6.08	4.98	0.66077	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.70298	0.3208	L	0.48260	1.515	0.80722	D	1	D	0.56746	0.977	D	0.65573	0.936	T	0.71586	-0.4548	10	0.72032	D	0.01	-6.235	10.3619	0.43998	0.8629:0.0:0.1371:0.0	.	338	Q9UBE8	NLK_HUMAN	S	338	ENSP00000384625:R338S	ENSP00000384625:R338S	R	+	3	2	NLK	23519777	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.644000	0.46613	1.079000	0.41038	0.533000	0.62120	AGA	.	.		0.418	NLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255607.3	NM_016231		T	26495650	A	T	26495650	3	4	295	1	0	0	0	0	1	0	0	0	10475	243	9	4	1036	4	NLK	17	26495650	Missense_Mutation	SNP	A	TCGA-G3-AAUZ-01A-11D-A382-10	6387236	26495650	54699560	74	42933										
DNAH17	8632	hgsc.bcm.edu	37	chr17	76481047	76481047	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	catgtcgtcgatgaagtagaCgagcttcttagtgcctggcg	13	9	1	2			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr17:76481047C>G	ENST00000585328.1	-	48	7661	c.7537G>C	c.(7537-7539)Gtc>Ctc	p.V2513L	DNAH17_ENST00000389840.5_Missense_Mutation_p.V2504L|RP11-559N14.5_ENST00000588565.1_RNA|DNAH17_ENST00000586052.1_5'UTR|RP11-559N14.5_ENST00000585969.1_RNA	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	2504	AAA 3. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			ATGAAGTAGACGAGCTTCTTA	0.622																																					p.V2518L		Atlas-SNP	.											.	DNAH17	347	.	0			c.G7552C						.						61	66	65					17																	76481047		2090	4219	6309	SO:0001583	missense	8632	exon48			AGTAGACGAGCTT	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"Axonemal dyneins"	2946	protein-coding gene	gene with protein product		610063	"dynein, axonemal, heavy polypeptide 17", "dynein, axonemal, heavy chain like 1", "dynein, axonemal, heavy like 1"	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.7537G>C	chr17.hg19:g.76481047C>G	ENSP00000465516:p.Val2513Leu	64.0	0.0		96.0	10.0	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Missense_Mutation	SNP	ENST00000585328.1	hg19		.	.	.	.	.	.	.	.	.	.	C	16.58	3.161819	0.57368	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.50277	0.75	4.96	3.88	0.44766	.	.	.	.	.	T	0.43344	0.1243	L	0.39147	1.195	0.25468	N	0.987857	.	.	.	.	.	.	T	0.33189	-0.9878	7	0.49607	T	0.09	.	7.9096	0.29782	0.0:0.1608:0.0:0.8392	.	.	.	.	L	2513;2504	ENSP00000374490:V2504L	ENSP00000300671:V2513L	V	-	1	0	DNAH17	73992642	0.974000	0.33945	0.999000	0.59377	0.939000	0.58152	1.813000	0.38962	0.742000	0.32697	-0.339000	0.08088	GTC	.	.		0.622	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		G	76481047	C	G	76481047	3	3	295	1	0	0	0	0	1	0	0	0	4603	536	19	4	5972	4	DNAH17	17	76481047	Missense_Mutation	SNP	C	TCGA-G3-AAUZ-01A-11D-A382-10	49985397	76481047	4714163	75	42934										
APCDD1	147495	hgsc.bcm.edu	37	chr18	10485748	10485748	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	ccgcggcgtcctctcgtccaGggtcatgggaggcaccgagt	15	14	2	0			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr18:10485748G>T	ENST00000355285.5	+	4	1418	c.1064G>T	c.(1063-1065)aGg>aTg	p.R355M	APCDD1_ENST00000578882.1_Splice_Site	NM_153000.4	NP_694545.1			adenomatosis polyposis coli down-regulated 1									p.R355M(1)		NS(1)|breast(1)|endometrium(3)|large_intestine(5)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22				READ - Rectum adenocarcinoma(15;0.08)		CTCTCGTCCAGGGTCATGGGA	0.582																																					p.R355M		Atlas-SNP	.											APCDD1,NS,carcinoma,0,1	APCDD1	57	.	1	Substitution - Missense(1)	endometrium(1)	c.G1064T						.						47	43	44					18																	10485748		2203	4300	6503	SO:0001583	missense	147495	exon4			CGTCCAGGGTCAT	AB056722	CCDS11849.1	18p11.21	2006-07-07			ENSG00000154856	ENSG00000154856			15718	protein-coding gene	gene with protein product		607479				12384519	Standard	NM_153000		Approved	B7323	uc002kom.4	Q8J025	OTTHUMG00000131635	ENST00000355285.5:c.1064G>T	chr18.hg19:g.10485748G>T	ENSP00000347433:p.Arg355Met	62.0	0.0		60.0	3.0	NM_153000		Missense_Mutation	SNP	ENST00000355285.5	hg19	CCDS11849.1	.	.	.	.	.	.	.	.	.	.	G	12.91	2.078007	0.36662	.	.	ENSG00000154856	ENST00000355285;ENST00000423585	T	0.16597	2.33	4.88	2.1	0.27182	.	0.206132	0.48286	D	0.000193	T	0.28928	0.0718	M	0.62723	1.935	0.80722	D	1	P	0.40032	0.699	P	0.54499	0.754	T	0.01617	-1.1311	10	0.62326	D	0.03	-21.8375	6.8657	0.24093	0.4703:0.0:0.5297:0.0	.	355	Q8J025	APCD1_HUMAN	M	355;406	ENSP00000347433:R355M	ENSP00000347433:R355M	R	+	2	0	APCDD1	10475748	0.351000	0.24887	0.943000	0.38184	0.640000	0.38277	1.560000	0.36331	0.260000	0.21731	0.561000	0.74099	AGG	.	.		0.582	APCDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254529.2	NM_153000		T	10485748	G	T	10485748	3	4	295	1	0	0	0	0	1	0	0	0	765	1000	35	3	1078	3	APCDD1	18	10485748	Missense_Mutation	SNP	G	TCGA-G3-AAUZ-01A-11D-A382-10		10485748	67591500	76	42935										
MUM1	84939	hgsc.bcm.edu	37	chr19	1360549	1360549	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	gtccagaatccaccacaaaaAttggactcttgcaagtaaga	7	10	1	2			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr19:1360549A>G	ENST00000415183.3	+	4	658	c.632A>G	c.(631-633)aAt>aGt	p.N211S	MUM1_ENST00000591806.1_Missense_Mutation_p.N211S|MUM1_ENST00000344663.3_Missense_Mutation_p.N211S|MUM1_ENST00000311401.5_Missense_Mutation_p.N142S			Q2TAK8	MUM1_HUMAN	melanoma associated antigen (mutated) 1	210					chromatin organization (GO:0006325)|DNA repair (GO:0006281)	nucleus (GO:0005634)	nucleosome binding (GO:0031491)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CACCACAAAAATTGGACTCTT	0.532											OREG0025088	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N211S		Atlas-SNP	.											.	MUM1	54	.	0			c.A632G						.						57	55	56					19																	1360549		2203	4300	6503	SO:0001583	missense	84939	exon5			ACAAAAATTGGAC	AK075241	CCDS12062.1	19p13.3	2008-02-05				ENSG00000160953			29641	protein-coding gene	gene with protein product						11042152, 7644523	Standard	NM_032853		Approved	MUM-1	uc002lrz.2	Q2TAK8		ENST00000415183.3:c.632A>G	chr19.hg19:g.1360549A>G	ENSP00000394925:p.Asn211Ser	149.0	0.0	595	175.0	50.0	NM_032853	A1L489|B5ME02|B7ZLY8|J3KQD6|Q13109|Q5XKB9|Q8N2I4|Q96A67	Missense_Mutation	SNP	ENST00000415183.3	hg19		.	.	.	.	.	.	.	.	.	.	A	0.026	-1.367576	0.01225	.	.	ENSG00000160953	ENST00000344663;ENST00000311401;ENST00000415183;ENST00000542512	T;T;T	0.35236	1.32;1.32;1.32	3.99	-7.97	0.01139	.	2.441580	0.01285	N	0.009850	T	0.15478	0.0373	N	0.08118	0	0.09310	N	1	B;B;B;B	0.12013	0.002;0.005;0.002;0.0	B;B;B;B	0.06405	0.001;0.001;0.002;0.0	T	0.21449	-1.0245	10	0.09084	T	0.74	.	8.9226	0.35621	0.1691:0.3778:0.4531:0.0	.	211;211;142;210	B7ZLY8;D6W5Y8;Q2TAK8-2;Q2TAK8	.;.;.;MUM1_HUMAN	S	211;142;211;140	ENSP00000345789:N211S;ENSP00000309135:N142S;ENSP00000394925:N211S	ENSP00000309135:N142S	N	+	2	0	MUM1	1311549	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.097000	0.11042	-1.614000	0.01575	-1.007000	0.02485	AAT	.	.		0.532	MUM1-016	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000449510.1	NM_032853		G	1360549	A	G	1360549	3	3	295	1	0	0	0	0	1	0	0	0	9994	101	4	2	646	2	MUM1	19	1360549	Missense_Mutation	SNP	A	TCGA-G3-AAUZ-01A-11D-A382-10		1360549	57768434	77	42936										
HNRNPM	4670	hgsc.bcm.edu	37	chr19	8550614	8550614	+	Frame_Shift_Del	DEL	C	C	-													0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	gatcgcgtgggctccgagatCgagcgcatgggcctggtcat					rs531035663		TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr19:8550614delC	ENST00000325495.4	+	14	1343	c.1302delC	c.(1300-1302)atcfs	p.I434fs	HNRNPM_ENST00000348943.3_Frame_Shift_Del_p.I395fs	NM_005968.4	NP_005959.2	P52272	HNRPM_HUMAN	heterogeneous nuclear ribonucleoprotein M	434	27 X 6 AA repeats of [GEVSTPAN]-[ILMV]- [DE]-[RH]-[MLVI]-[GAV].				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|RNA binding (GO:0003723)			endometrium(5)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)	25						GCTCCGAGATCGAGCGCATGG	0.706																																					p.I434fs		Atlas-INDEL	.											.	HNRNPM	61	.	0			c.1301delT						.						71	76	74					19																	8550614		2203	4298	6501	SO:0001589	frameshift_variant	4670	exon14			.	L03532	CCDS12203.1, CCDS12204.1	19p13.2	2013-06-12		2008-04-18	ENSG00000099783	ENSG00000099783		"RNA binding motif (RRM) containing"	5046	protein-coding gene	gene with protein product	"CEA receptor"	160994		NAGR1, HNRPM		8441656, 7558047	Standard	NM_005968		Approved	HTGR1, HNRNPM4, HNRPM4, CEAR	uc010dwe.3	P52272	OTTHUMG00000182383	ENST00000325495.4:c.1302delC	chr19.hg19:g.8550614delC	ENSP00000325376:p.Ile434fs	80.0	0.0		114.0	43.0	NM_005968	Q15584|Q8WZ44|Q96H56|Q9BWL9|Q9Y492	Frame_Shift_Del	DEL	ENST00000325495.4	hg19	CCDS12203.1																																																																																			.	.		0.706	HNRNPM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460894.1			-	8550614	C	-	8550614	7	5	295	1	0	1	0	1	0	0	0	0	7280	874	31	0	1356	0	HNRNPM	19	8550614	Frame_Shift_Del	DEL	C	TCGA-G3-AAUZ-01A-11D-A382-10	7190065	8550614	50578369	78	42937										
RYR1	6261	hgsc.bcm.edu	37	chr19	39025793	39025793	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	ccctccaggagagacaggtgCcatggtgtcctccaccctga	11	15	0	2			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr19:39025793C>A	ENST00000359596.3	+	80	11372	c.11372C>A	c.(11371-11373)gCc>gAc	p.A3791D	RYR1_ENST00000360985.3_Missense_Mutation_p.A3791D|RYR1_ENST00000355481.4_Missense_Mutation_p.A3786D|AC067969.2_ENST00000595853.1_RNA			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	3791					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GAGACAGGTGCCATGGTGTCC	0.552																																					p.A3791D		Atlas-SNP	.											.	RYR1	708	.	0			c.C11372A						.						77	56	63					19																	39025793		2203	4300	6503	SO:0001583	missense	6261	exon80			CAGGTGCCATGGT	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.11372C>A	chr19.hg19:g.39025793C>A	ENSP00000352608:p.Ala3791Asp	25.0	0.0		27.0	6.0	NM_000540	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	C	12.81	2.048735	0.36181	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.87650	-2.28;-2.28;-2.28	3.83	3.83	0.44106	.	0.601453	0.14238	U	0.332278	T	0.75413	0.3846	N	0.11313	0.125	0.38694	D	0.952844	B;B;B	0.30973	0.231;0.302;0.201	B;B;B	0.28232	0.087;0.079;0.036	T	0.73471	-0.3972	10	0.25106	T	0.35	.	15.0434	0.71807	0.0:1.0:0.0:0.0	.	3791;3786;3791	P21817-3;P21817-2;P21817	.;.;RYR1_HUMAN	D	3791;3786;3791	ENSP00000352608:A3791D;ENSP00000347667:A3786D;ENSP00000354254:A3791D	ENSP00000347667:A3786D	A	+	2	0	RYR1	43717633	0.557000	0.26546	0.980000	0.43619	0.988000	0.76386	0.728000	0.26013	2.146000	0.66826	0.561000	0.74099	GCC	.	.		0.552	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			A	39025793	C	A	39025793	3	1	295	1	0	0	0	0	1	0	0	0	13783	739	26	3	11690	3	RYR1	19	39025793	Missense_Mutation	SNP	C	TCGA-G3-AAUZ-01A-11D-A382-10	30475179	39025793	20103190	79	42938										
ZNF222	7673	hgsc.bcm.edu	37	chr19	44529605	44529605	+	5'UTR	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	cccaatgatcgattcaggagAaaagaagcctgggcggagag	14	8	1	4			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr19:44529605A>G	ENST00000187879.8	+	0	91				ZNF222_ENST00000590160.1_3'UTR|ZNF223_ENST00000591793.1_Missense_Mutation_p.E6G|ZNF222_ENST00000391960.3_Missense_Mutation_p.E6G|AC067968.3_ENST00000592583.1_lincRNA|ZNF222_ENST00000587846.1_Missense_Mutation_p.E6G	NM_013360.2	NP_037492.2	Q9UK12	ZN222_HUMAN	zinc finger protein 222						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(7)|lung(6)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	20		Prostate(69;0.0435)				GATTCAGGAGAAAAGAAGCCT	0.577																																					p.E6G		Atlas-SNP	.											.	ZNF222	90	.	0			c.A17G						.						21	22	22					19																	44529605		692	1591	2283	SO:0001623	5_prime_UTR_variant	7673	exon1			CAGGAGAAAAGAA	AF187988	CCDS33045.1, CCDS46098.1	19q13.2	2013-01-08				ENSG00000159885		"Zinc fingers, C2H2-type", "-"	13015	protein-coding gene	gene with protein product							Standard	NM_013360		Approved		uc002oye.3	Q9UK12		ENST00000187879.8:c.-72A>G	chr19.hg19:g.44529605A>G		63.0	0.0		76.0	30.0	NM_001129996	G5E9B9|Q8N6G7|Q9P1U5	Missense_Mutation	SNP	ENST00000187879.8	hg19	CCDS33045.1	.	.	.	.	.	.	.	.	.	.	A	13.37	2.216308	0.39201	.	.	ENSG00000159885	ENST00000391960	T	0.06371	3.31	1.3	0.145	0.14829	.	.	.	.	.	T	0.05181	0.0138	N	0.08118	0	0.09310	N	1	D	0.58620	0.983	P	0.53861	0.736	T	0.37753	-0.9692	9	0.36615	T	0.2	.	4.0037	0.09592	0.617:0.383:0.0:0.0	.	6	G5E9B9	.	G	6	ENSP00000375822:E6G	ENSP00000375822:E6G	E	+	2	0	ZNF222	49221445	0.019000	0.18553	0.003000	0.11579	0.004000	0.04260	0.157000	0.16402	-0.018000	0.14079	-0.805000	0.03199	GAA	.	.		0.577	ZNF222-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000460465.2			G	44529605	A	G	44529605	1	3	295	0	1	0	0	0	0	0	0	0	17791	246	9	2		2	ZNF222	19	44529605	5'UTR	SNP	A	TCGA-G3-AAUZ-01A-11D-A382-10	5503812	44529605	14599378	80	42939										
MARK4	57787	hgsc.bcm.edu	37	chr19	45797639	45797639	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	cctagcatgatgacccgcagAaacacctacgtttgcacaga	8	13	0	4			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr19:45797639A>G	ENST00000262891.4	+	14	1858	c.1527A>G	c.(1525-1527)agA>agG	p.R509R	MARK4_ENST00000300843.4_Silent_p.R509R	NM_001199867.1	NP_001186796.1	Q96L34	MARK4_HUMAN	MAP/microtubule affinity-regulating kinase 4	509					microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|nervous system development (GO:0007399)|positive regulation of programmed cell death (GO:0043068)|protein phosphorylation (GO:0006468)	centrosome (GO:0005813)|microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|gamma-tubulin binding (GO:0043015)|microtubule binding (GO:0008017)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)|ubiquitin binding (GO:0043130)			NS(1)|biliary_tract(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	31		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0102)		TGACCCGCAGAAACACCTACG	0.597																																					p.R509R		Atlas-SNP	.											.	MARK4	132	.	0			c.A1527G						.						77	57	64					19																	45797639		2203	4300	6503	SO:0001819	synonymous_variant	57787	exon14			CCGCAGAAACACC	AB049127	CCDS12658.1, CCDS56097.1	19q13.32	2014-04-07	2002-06-12	2002-06-14	ENSG00000007047	ENSG00000007047	2.7.11.1		13538	protein-coding gene	gene with protein product		606495	"MAP/microtubule affinity-regulating kinase like 1"	MARKL1		23400999, 11326310, 9108484	Standard	NM_001199867		Approved	Nbla00650, FLJ90097, KIAA1860, PAR-1D	uc002paz.2	Q96L34	OTTHUMG00000181769	ENST00000262891.4:c.1527A>G	chr19.hg19:g.45797639A>G		90.0	0.0		112.0	43.0	NM_001199867	Q8NG37|Q96JG7|Q96SQ2|Q9BYD8	Silent	SNP	ENST00000262891.4	hg19	CCDS56097.1																																																																																			.	.		0.597	MARK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457537.1	NM_031417		G	45797639	A	G	45797639	2	3	295	1	0	0	0	0	0	0	0	1	9324	243	9	2		2	MARK4	19	45797639	Silent	SNP	A	TCGA-G3-AAUZ-01A-11D-A382-10	1268034	45797639	13331344	81	42940										
ATF5	22809	hgsc.bcm.edu	37	chr19	50434173	50434173	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	ctcccagctagtgggctgggAtggctcgtagactatgggaa	15	9	0	1			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr19:50434173A>C	ENST00000423777.2	+	2	443	c.66A>C	c.(64-66)ggA>ggC	p.G22G	IL4I1_ENST00000341114.3_5'Flank|ATF5_ENST00000600336.1_Silent_p.G22G|NUP62_ENST00000597723.1_5'Flank|NUP62_ENST00000422090.2_5'Flank|ATF5_ENST00000595125.1_Silent_p.G22G|NUP62_ENST00000600583.1_5'Flank|IL4I1_ENST00000595948.1_5'Flank|NUP62_ENST00000596217.1_5'Flank|NUP62_ENST00000597029.1_5'Flank|CTC-326K19.6_ENST00000451973.1_Intron|NUP62_ENST00000413454.1_5'Flank|NUP62_ENST00000352066.3_5'Flank|MIR4751_ENST00000578027.1_RNA	NM_001193646.1	NP_001180575.1	Q9Y2D1	ATF5_HUMAN	activating transcription factor 5	22					multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of astrocyte differentiation (GO:0048712)|olfactory bulb interneuron development (GO:0021891)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|transcription corepressor activity (GO:0003714)			NS(1)|endometrium(2)|large_intestine(1)|skin(3)	7		all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17)		GBM - Glioblastoma multiforme(134;0.00221)|OV - Ovarian serous cystadenocarcinoma(262;0.017)	Pseudoephedrine(DB00852)	GTGGGCTGGGATGGCTCGTAG	0.677																																					p.G22G	GBM(48;768 989 9196 9511 26329)	Atlas-SNP	.											.	ATF5	27	.	0			c.A66C						.						22	22	22					19																	50434173		2203	4299	6502	SO:0001819	synonymous_variant	22809	exon3			GCTGGGATGGCTC	AF101388	CCDS12789.1	19q13.33	2013-09-20			ENSG00000169136	ENSG00000169136		"basic leucine zipper proteins"	790	protein-coding gene	gene with protein product		606398				10373550	Standard	NM_012068		Approved		uc002prd.3	Q9Y2D1	OTTHUMG00000183065	ENST00000423777.2:c.66A>C	chr19.hg19:g.50434173A>C		146.0	0.0		150.0	55.0	NM_012068	B3KND3|Q9BSA1|Q9UNQ3	Silent	SNP	ENST00000423777.2	hg19	CCDS12789.1																																																																																			.	.		0.677	ATF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464915.2			C	50434173	A	C	50434173	2	2	295	1	0	0	0	0	0	0	0	1	1083	320	12	5		5	ATF5	19	50434173	Silent	SNP	A	TCGA-G3-AAUZ-01A-11D-A382-10	4636534	50434173	8694810	82	42941										
SAMHD1	25939	hgsc.bcm.edu	37	chr20	35540887	35540887	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	gtatcaataatgttgccaacTttgtgttgataagctctacg	8	7	2	1			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr20:35540887T>G	ENST00000262878.4	-	10	1330	c.1131A>C	c.(1129-1131)aaA>aaC	p.K377N	SAMHD1_ENST00000373694.5_Missense_Mutation_p.K162N	NM_015474.3	NP_056289.2	Q9Y3Z3	SAMH1_HUMAN	SAM domain and HD domain 1	377					dATP catabolic process (GO:0046061)|defense response to virus (GO:0051607)|dGTP catabolic process (GO:0006203)|immune response (GO:0006955)|innate immune response (GO:0045087)|protein homotetramerization (GO:0051289)|regulation of innate immune response (GO:0045088)	intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dGTP binding (GO:0032567)|dGTPase activity (GO:0008832)|nucleic acid binding (GO:0003676)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(8)|urinary_tract(1)	20		Myeloproliferative disorder(115;0.00878)				TGTTGCCAACTTTGTGTTGAT	0.353																																					p.K377N		Atlas-SNP	.											.	SAMHD1	62	.	0			c.A1131C						.						114	107	110					20																	35540887		2203	4300	6503	SO:0001583	missense	25939	exon10			GCCAACTTTGTGT	AF228421	CCDS13288.1	20q11.23	2014-09-17			ENSG00000101347	ENSG00000101347		"Sterile alpha motif (SAM) domain containing"	15925	protein-coding gene	gene with protein product	"HD domain containing 1", "monocyte protein 5", "Aicardi-Goutieres syndrome 5"	606754				11064105, 11230166	Standard	NM_015474		Approved	SBBI88, Mg11, HDDC1, MOP-5, AGS5	uc002xgh.2	Q9Y3Z3	OTTHUMG00000032402	ENST00000262878.4:c.1131A>C	chr20.hg19:g.35540887T>G	ENSP00000262878:p.Lys377Asn	79.0	0.0		102.0	25.0	NM_015474	B4E2A5|E1P5V2|Q5JXG8|Q8N491|Q9H004|Q9H005|Q9H3U9	Missense_Mutation	SNP	ENST00000262878.4	hg19	CCDS13288.1	.	.	.	.	.	.	.	.	.	.	t	20.5	3.995882	0.74703	.	.	ENSG00000101347	ENST00000262878;ENST00000373694	D;D	0.95756	-3.8;-3.8	5.46	1.83	0.25207	HD domain (1);	0.140244	0.64402	D	0.000006	D	0.96463	0.8846	M	0.89785	3.06	0.50813	D	0.999896	P	0.49358	0.923	P	0.51615	0.675	D	0.94942	0.8092	10	0.62326	D	0.03	-19.3235	8.8773	0.35354	0.0:0.3191:0.0:0.6809	.	377	Q9Y3Z3	SAMH1_HUMAN	N	377;162	ENSP00000262878:K377N;ENSP00000362798:K162N	ENSP00000262878:K377N	K	-	3	2	SAMHD1	34974301	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.395000	0.34520	0.324000	0.23333	0.456000	0.33151	AAA	.	.		0.353	SAMHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079062.2	NM_015474		G	35540887	T	G	35540887	3	3	295	1	0	0	0	0	1	0	0	0	13843	1606	56	5	777	5	SAMHD1	20	35540887	Missense_Mutation	SNP	T	TCGA-G3-AAUZ-01A-11D-A382-10		35540887	27484633	83	42942										
TTC3	7267	hgsc.bcm.edu	37	chr21	38510935	38510935	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	gaggcatttttattgacagcAattgaacctggccatgatta	9	7	0	3			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr21:38510935A>G	ENST00000399017.2	+	19	4327	c.1580A>G	c.(1579-1581)cAa>cGa	p.Q527R	TTC3_ENST00000355666.1_Splice_Site_p.Q527R|TTC3_ENST00000354749.2_Splice_Site_p.Q527R|TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000540756.1_Splice_Site_p.Q217R	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	527					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				TATTGACAGCAATTGAACCTG	0.373																																					p.Q527R	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.A1580G						.						187	174	178					21																	38510935		2203	4300	6503	SO:0001630	splice_region_variant	7267	exon19			GACAGCAATTGAA	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"RING-type (C3HC4) zinc fingers", "Tetratricopeptide (TTC) repeat domain containing"	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.1579-1A>G	chr21.hg19:g.38510935A>G		131.0	0.0		207.0	27.0	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	hg19	CCDS13651.1	.	.	.	.	.	.	.	.	.	.	A	14.44	2.536054	0.45176	.	.	ENSG00000182670	ENST00000418766;ENST00000450533;ENST00000438055;ENST00000355666;ENST00000540756;ENST00000399017;ENST00000354749	T;T;T;T;T;T;T	0.48836	2.62;0.8;2.62;2.94;0.82;2.94;2.94	5.22	5.22	0.72569	Tetratricopeptide-like helical (1);	0.227351	0.31507	N	0.007523	T	0.48750	0.1517	N	0.17082	0.46	0.35037	D	0.759371	B;D	0.63880	0.141;0.993	B;D	0.70227	0.047;0.968	T	0.60172	-0.7315	10	0.44086	T	0.13	-17.0806	9.5896	0.39537	0.9199:0.0:0.0801:0.0	.	217;527	B4DSZ9;P53804	.;TTC3_HUMAN	R	527;527;509;527;217;527;527	ENSP00000403943:Q527R;ENSP00000408456:Q527R;ENSP00000391891:Q509R;ENSP00000347889:Q527R;ENSP00000442875:Q217R;ENSP00000381981:Q527R;ENSP00000346791:Q527R	ENSP00000346791:Q527R	Q	+	2	0	TTC3	37432805	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	4.926000	0.63433	2.103000	0.63969	0.460000	0.39030	CAA	.	.		0.373	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1		Missense_Mutation	G	38510935	A	G	38510935	5	3	295	1	0	0	0	0	0	0	1	0	16712	144	5	2	1650	2	TTC3	21	38510935	Splice_Site	SNP	A	TCGA-G3-AAUZ-01A-11D-A382-10		38510935	9618960	84	42943										
UMODL1	89766	hgsc.bcm.edu	37	chr21	43531035	43531035	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0476190476190476	4	1	1.36322125363221	1.49954337899543	1.32312651087832	0.559440559440559	1	0	tggactgtctgcggcaacagGggtaacggtcccaggtcttg	15	10	2	0			TCGA-G3-AAUZ-01A-11D-A382-10	TCGA-G3-AAUZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d883fcad-d1c0-4b14-9e2f-450d3c75f28e	8f178264-c9f3-4f66-9b51-f31d6244ba04	g.chr21:43531035G>C	ENST00000408910.2	+	11	1703	c.1703G>C	c.(1702-1704)gGg>gCg	p.G568A	C21orf128_ENST00000329015.2_5'Flank|UMODL1_ENST00000400427.1_Missense_Mutation_p.G496A|UMODL1_ENST00000400424.2_Missense_Mutation_p.G496A|UMODL1_ENST00000408989.2_Missense_Mutation_p.G568A	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	568					adipose tissue development (GO:0060612)|cellular response to gonadotropin-releasing hormone (GO:0097211)|multicellular organismal reproductive process (GO:0048609)|regulation of apoptotic process (GO:0042981)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|peptidase inhibitor activity (GO:0030414)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(22)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	47						GCGGCAACAGGGGTAACGGTC	0.632																																					p.G568A	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.G1703C						.						31	38	36					21																	43531035		2078	4211	6289	SO:0001583	missense	89766	exon11			CAACAGGGGTAAC		CCDS42935.1, CCDS42936.1, CCDS56214.1, CCDS56215.1	21q22.3	2008-07-04			ENSG00000177398	ENSG00000177398			12560	protein-coding gene	gene with protein product	"olfactorin"	613859				16026467	Standard	NM_173568		Approved		uc002zag.1	Q5DID0	OTTHUMG00000086788	ENST00000408910.2:c.1703G>C	chr21.hg19:g.43531035G>C	ENSP00000386147:p.Gly568Ala	211.0	0.0		311.0	156.0	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Missense_Mutation	SNP	ENST00000408910.2	hg19	CCDS42936.1	.	.	.	.	.	.	.	.	.	.	G	1.512	-0.549215	0.04024	.	.	ENSG00000177398	ENST00000400427;ENST00000400424;ENST00000408989;ENST00000408910	T;T;T;T	0.71579	-0.58;-0.56;-0.58;-0.55	3.61	-1.77	0.07982	.	0.797000	0.10786	N	0.634261	T	0.61899	0.2384	L	0.29908	0.895	0.09310	N	1	D;B	0.58970	0.984;0.329	P;B	0.56088	0.791;0.084	T	0.54214	-0.8327	10	0.14252	T	0.57	-7.7189	4.7456	0.13036	0.2949:0.2963:0.4087:0.0	.	568;568	Q5DID0-2;Q5DID0	.;UROL1_HUMAN	A	496;496;568;568	ENSP00000383279:G496A;ENSP00000383276:G496A;ENSP00000386126:G568A;ENSP00000386147:G568A	ENSP00000383276:G496A	G	+	2	0	UMODL1	42404104	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.020000	0.12525	-0.389000	0.07786	0.591000	0.81541	GGG	.	.		0.632	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2			C	43531035	G	C	43531035	3	2	295	1	0	0	0	0	1	0	0	0	16995	1232	43	4	1745	4	UMODL1	21	43531035	Missense_Mutation	SNP	G	TCGA-G3-AAUZ-01A-11D-A382-10	5020100	43531035	4598860	85	42944										
TPRG1L	127262	hgsc.bcm.edu	37	chr1	3542011	3542011	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ggcagcatcgagcaggcagtGgaggagatccgcgtggtggt	19	8	0	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:3542011G>A	ENST00000378344.2	+	2	296	c.225G>A	c.(223-225)gtG>gtA	p.V75V	RP11-46F15.2_ENST00000435049.1_RNA|TPRG1L_ENST00000344579.5_Silent_p.V75V	NM_182752.3	NP_877429.2	Q5T0D9	TPRGL_HUMAN	tumor protein p63 regulated 1-like	75						cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|synaptic vesicle (GO:0008021)				endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|prostate(1)	8	all_cancers(77;0.0119)|all_epithelial(69;0.00481)|Ovarian(185;0.0634)|Lung NSC(156;0.162)|all_lung(157;0.172)	all_epithelial(116;7.37e-22)|all_lung(118;8.23e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.41e-38)|OV - Ovarian serous cystadenocarcinoma(86;3.83e-22)|GBM - Glioblastoma multiforme(42;4.77e-14)|Colorectal(212;1.12e-05)|COAD - Colon adenocarcinoma(227;5.61e-05)|Kidney(185;0.000351)|BRCA - Breast invasive adenocarcinoma(365;0.000688)|KIRC - Kidney renal clear cell carcinoma(229;0.00553)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.201)		AGCAGGCAGTGGAGGAGATCC	0.716																																					p.V75V		Atlas-SNP	.											.	TPRG1L	24	.	0			c.G225A						.						28	33	31					1																	3542011		2198	4292	6490	SO:0001819	synonymous_variant	127262	exon2			GGCAGTGGAGGAG	BC019034	CCDS47.1	1p36.32	2008-02-05	2008-01-16	2008-01-16	ENSG00000158109	ENSG00000158109			27007	protein-coding gene	gene with protein product		611460	"family with sequence similarity 79, member A"	FAM79A		12477932	Standard	NM_182752		Approved	RP11-46F15.3, FLJ21811	uc001akm.3	Q5T0D9	OTTHUMG00000000609	ENST00000378344.2:c.225G>A	chr1.hg19:g.3542011G>A		202.0	0.0		173.0	73.0	NM_182752	A8K1K4|Q8WV04	Silent	SNP	ENST00000378344.2	hg19	CCDS47.1																																																																																			.	.		0.716	TPRG1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001466.1	NM_182752		A	3542011	G	A	3542011	2	1	296	1	0	0	0	0	0	0	0	1	16434	1335	47	3		3	TPRG1L	1	3542011	Silent	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10		3542011	245708610	1	42945										
CHD5	26038	hgsc.bcm.edu	37	chr1	6209325	6209325	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	cacagtgggggcagctccacTtgccctcgggagccttctcc	12	16	1	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:6209325T>G	ENST00000262450.3	-	8	1241	c.1142A>C	c.(1141-1143)aAg>aCg	p.K381T	CHD5_ENST00000378021.1_5'UTR	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5	0					tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		GCAGCTCCACTTGCCCTCGGG	0.677																																					p.K381T		Atlas-SNP	.											.	CHD5	267	.	0			c.A1142C						.						24	25	25					1																	6209325		2203	4299	6502	SO:0001583	missense	26038	exon8			CTCCACTTGCCCT	AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"Zinc fingers, PHD-type"	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.1142A>C	chr1.hg19:g.6209325T>G	ENSP00000262450:p.Lys381Thr	73.0	0.0		88.0	43.0	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Missense_Mutation	SNP	ENST00000262450.3	hg19	CCDS57.1	.	.	.	.	.	.	.	.	.	.	T	16.79	3.219164	0.58560	.	.	ENSG00000116254	ENST00000262450	D	0.85702	-2.02	4.03	4.03	0.46877	Zinc finger, PHD-finger (2);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);Zinc finger, RING-type (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.64402	U	0.000001	T	0.78142	0.4237	L	0.41415	1.275	0.80722	D	1	P	0.36909	0.573	B	0.33521	0.165	T	0.78979	-0.1990	10	0.49607	T	0.09	-28.7911	12.4529	0.55686	0.0:0.0:0.0:1.0	.	381	Q8TDI0	CHD5_HUMAN	T	381	ENSP00000262450:K381T	ENSP00000262450:K381T	K	-	2	0	CHD5	6131912	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	4.052000	0.57420	1.623000	0.50342	0.260000	0.18958	AAG	.	.		0.677	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557		G	6209325	T	G	6209325	3	3	296	1	0	0	0	0	1	0	0	0	3330	1609	56	5	4858	5	CHD5	1	6209325	Missense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	2667314	6209325	243041296	2	42946										
UBE4B	10277	hgsc.bcm.edu	37	chr1	10195205	10195205	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	atgatgagacgcgtgtgaatGcaacgatggaagatgtgaat	14	4	0	5			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:10195205G>C	ENST00000253251.8	+	15	2637	c.1798G>C	c.(1798-1800)Gca>Cca	p.A600P	UBE4B_ENST00000343090.6_Missense_Mutation_p.A729P|UBE4B_ENST00000377157.3_Missense_Mutation_p.A484P					ubiquitination factor E4B											NS(3)|breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(14)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	48		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		GCGTGTGAATGCAACGATGGA	0.438																																					p.A729P		Atlas-SNP	.											.	UBE4B	233	.	0			c.G2185C						.						142	121	128					1																	10195205		2203	4300	6503	SO:0001583	missense	10277	exon16			GTGAATGCAACGA	AF091093	CCDS110.1, CCDS41245.1	1p36.1	2013-01-28	2011-05-19		ENSG00000130939	ENSG00000130939		"U-box domain containing"	12500	protein-coding gene	gene with protein product		613565	"ubiquitination factor E4B (homologous to yeast UFD2)", "ubiquitination factor E4B (UFD2 homolog, yeast)"			9734811, 10089879	Standard	NM_006048		Approved	UBOX3, E4, UFD2, KIAA0684	uc001aqs.4	O95155	OTTHUMG00000001797	ENST00000253251.8:c.1798G>C	chr1.hg19:g.10195205G>C	ENSP00000253251:p.Ala600Pro	120.0	0.0		126.0	56.0	NM_001105562		Missense_Mutation	SNP	ENST00000253251.8	hg19	CCDS110.1	.	.	.	.	.	.	.	.	.	.	G	16.69	3.192376	0.58017	.	.	ENSG00000130939	ENST00000253251;ENST00000377157;ENST00000343090	T;T;T	0.48201	0.82;0.82;0.82	6.04	6.04	0.98038	Ubiquitin conjugation factor E4, core (1);	0.000000	0.85682	D	0.000000	T	0.72574	0.3477	M	0.83774	2.66	0.80722	D	1	D;D;D	0.76494	0.999;0.996;0.998	D;D;D	0.72338	0.977;0.915;0.962	T	0.69209	-0.5205	10	0.35671	T	0.21	-18.3443	20.5836	0.99426	0.0:0.0:1.0:0.0	.	600;729;600	A8K8S9;O95155;O95155-2	.;UBE4B_HUMAN;.	P	600;484;729	ENSP00000253251:A600P;ENSP00000366362:A484P;ENSP00000343001:A729P	ENSP00000253251:A600P	A	+	1	0	UBE4B	10117792	1.000000	0.71417	0.544000	0.28141	0.067000	0.16453	9.813000	0.99286	2.870000	0.98441	0.637000	0.83480	GCA	.	.		0.438	UBE4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005017.1	NM_006048		C	10195205	G	C	10195205	3	2	296	1	0	0	0	0	1	0	0	0	16898	1319	46	4	2247	4	UBE4B	1	10195205	Missense_Mutation	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10	3985880	10195205	239055416	3	42947										
EPHA8	2046	hgsc.bcm.edu	37	chr1	22902776	22902776	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	cgtaccaggtttgcaacgtcAtgagccccaaccagaacaac	8	14	1	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:22902776A>C	ENST00000166244.3	+	3	298	c.226A>C	c.(226-228)Atg>Ctg	p.M76L	EPHA8_ENST00000538803.1_Missense_Mutation_p.M76L|EPHA8_ENST00000374644.4_Missense_Mutation_p.M76L	NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8	76	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		TTGCAACGTCATGAGCCCCAA	0.602																																					p.M76L		Atlas-SNP	.											.	EPHA8	221	.	0			c.A226C						.						98	95	96					1																	22902776		2203	4300	6503	SO:0001583	missense	2046	exon3			AACGTCATGAGCC	BC038796	CCDS225.1, CCDS30626.1	1p36.12	2013-02-11	2004-10-28		ENSG00000070886	ENSG00000070886	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3391	protein-coding gene	gene with protein product		176945	"EphA8"	EEK		1648701	Standard	NM_001006943		Approved	Hek3	uc001bfx.1	P29322	OTTHUMG00000002892	ENST00000166244.3:c.226A>C	chr1.hg19:g.22902776A>C	ENSP00000166244:p.Met76Leu	262.0	0.0		275.0	109.0	NM_020526	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Missense_Mutation	SNP	ENST00000166244.3	hg19	CCDS225.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.073692	0.76415	.	.	ENSG00000070886	ENST00000166244;ENST00000374644;ENST00000538803	T;T;T	0.08984	3.03;3.03;3.03	4.47	4.47	0.54385	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	T	0.20210	0.0486	L	0.47078	1.49	0.58432	D	0.999996	P;D	0.61697	0.832;0.99	D;D	0.78314	0.921;0.991	T	0.00975	-1.1494	10	0.33940	T	0.23	.	12.7216	0.57146	1.0:0.0:0.0:0.0	.	76;76	P29322;P29322-2	EPHA8_HUMAN;.	L	76	ENSP00000166244:M76L;ENSP00000363775:M76L;ENSP00000440274:M76L	ENSP00000166244:M76L	M	+	1	0	EPHA8	22775363	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	5.937000	0.70162	1.877000	0.54381	0.363000	0.22086	ATG	.	.		0.602	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526		C	22902776	A	C	22902776	3	2	296	1	0	0	0	0	1	0	0	0	5175	217	8	5	236	5	EPHA8	1	22902776	Missense_Mutation	SNP	A	TCGA-G3-AAV0-01A-11D-A36X-10	12707571	22902776	226347845	4	42948										
EPHA8	2046	hgsc.bcm.edu	37	chr1	22902805	22902806	+	Frame_Shift_Del	DEL	CA	CA	-													0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	aaccagaacaactggctgcgCacgagctgggtcccccgaga							TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:22902805_22902806delCA	ENST00000166244.3	+	3	327_328	c.255_256delCA	c.(253-258)cgcacgfs	p.T86fs	EPHA8_ENST00000538803.1_Frame_Shift_Del_p.T86fs|EPHA8_ENST00000374644.4_Frame_Shift_Del_p.T86fs	NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8	86	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		ACTGGCTGCGCACGAGCTGGGT	0.614																																					p.85_85del		Atlas-Indel,Pindel	.											.	EPHA8	221	.	0			c.254_255del						.																																			SO:0001589	frameshift_variant	2046	exon3			.	BC038796	CCDS225.1, CCDS30626.1	1p36.12	2013-02-11	2004-10-28		ENSG00000070886	ENSG00000070886	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3391	protein-coding gene	gene with protein product		176945	"EphA8"	EEK		1648701	Standard	NM_001006943		Approved	Hek3	uc001bfx.1	P29322	OTTHUMG00000002892	ENST00000166244.3:c.255_256delCA	chr1.hg19:g.22902805_22902806delCA	ENSP00000166244:p.Thr86fs	248.0	0.0		249.0	96.0	NM_020526	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Frame_Shift_Del	DEL	ENST00000166244.3	hg19	CCDS225.1																																																																																			.	.		0.614	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526		-	22902806	CA	-	22902805	7	5	296	1	0	1	0	1	0	0	0	0	5175	697	25	0	265	0	EPHA8	1	22902805	Frame_Shift_Del	DEL	CA	TCGA-G3-AAV0-01A-11D-A36X-10	29	22902805	226347816	5	42949										
HMGCL	3155	hgsc.bcm.edu	37	chr1	24147006	24147006	+	Missense_Mutation	SNP	A	A	C													0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	atttccaactttaccttttcAttttgtagtccatctcgggg							TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:24147006A>C	ENST00000374490.3	-	2	181	c.138T>G	c.(136-138)aaT>aaG	p.N46K	HMGCL_ENST00000436439.2_Missense_Mutation_p.N46K|HMGCL_ENST00000374483.4_Missense_Mutation_p.N21K|HMGCL_ENST00000509389.1_5'UTR	NM_000191.2	NP_000182.2	P35914	HMGCL_HUMAN	3-hydroxymethyl-3-methylglutaryl-CoA lyase	46					acyl-CoA metabolic process (GO:0006637)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|ketone body biosynthetic process (GO:0046951)|leucine catabolic process (GO:0006552)|liver development (GO:0001889)|mitochondrion organization (GO:0007005)|protein tetramerization (GO:0051262)|response to fatty acid (GO:0070542)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)	carboxylic acid binding (GO:0031406)|fatty-acyl-CoA binding (GO:0000062)|hydroxymethylglutaryl-CoA lyase activity (GO:0004419)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	12		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.0044)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.38e-24)|Colorectal(126;5.58e-08)|COAD - Colon adenocarcinoma(152;3.12e-06)|GBM - Glioblastoma multiforme(114;4.9e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000982)|KIRC - Kidney renal clear cell carcinoma(1967;0.0034)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0856)|LUSC - Lung squamous cell carcinoma(448;0.188)		TTACCTTTTCATTTTGTAGTC	0.413																																					p.N46K		Atlas-SNP	.											.	HMGCL	22	.	0			c.T138G	GRCh37	CI952229	HMGCL	I		.						168	144	153					1																	24147006		2203	4300	6503	SO:0001583	missense	3155	exon2			CTTTTCATTTTGT	BC010570	CCDS243.1, CCDS53279.1	1p36.1-p35	2010-04-30	2010-04-30		ENSG00000117305	ENSG00000117305	4.1.3.4		5005	protein-coding gene	gene with protein product	"hydroxymethylglutaricaciduria"	613898	"3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase"			8102917, 8978493	Standard	NM_001166059		Approved	HL	uc001bib.3	P35914	OTTHUMG00000002963	ENST00000374490.3:c.138T>G	chr1.hg19:g.24147006A>C	ENSP00000363614:p.Asn46Lys	161.0	0.0		122.0	50.0	NM_000191	B4DUP4|B7UCC6|D3Y5K7|Q6IBC0|Q96FP8	Missense_Mutation	SNP	ENST00000374490.3	hg19	CCDS243.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.33|16.33	3.093907|3.093907	0.56075|0.56075	.|.	.|.	ENSG00000117305|ENSG00000117305	ENST00000235958|ENST00000374490;ENST00000436439;ENST00000374483;ENST00000543166	.|D;D;D	.|0.98264	.|-4.83;-4.65;-4.83	5.27|5.27	2.9|2.9	0.33743|0.33743	.|Aldolase-type TIM barrel (1);Pyruvate carboxyltransferase (2);	.|0.177290	.|0.64402	.|D	.|0.000009	D|D	0.98639|0.98639	0.9544|0.9544	H|H	0.98594|0.98594	4.275|4.275	0.53005|0.53005	D|D	0.999962|0.999962	.|B;B;B;B	.|0.33135	.|0.399;0.135;0.135;0.135	.|B;B;B;B	.|0.40782	.|0.34;0.217;0.275;0.217	D|D	0.99486|0.99486	1.0949|1.0949	5|10	.|0.72032	.|D	.|0.01	-5.5475|-5.5475	8.2613|8.2613	0.31786|0.31786	0.7729:0.0:0.2271:0.0|0.7729:0.0:0.2271:0.0	.|.	.|46;46;21;46	.|B4DUP4;Q6IBC0;B1AK13;P35914	.|.;.;.;HMGCL_HUMAN	R|K	42|46;46;21;21	.|ENSP00000363614:N46K;ENSP00000389281:N46K;ENSP00000363607:N21K	.|ENSP00000363607:N21K	M|N	-|-	2|3	0|2	HMGCL|HMGCL	24019593|24019593	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.984000|0.984000	0.73092|0.73092	3.196000|3.196000	0.51020|0.51020	1.026000|1.026000	0.39733|0.39733	0.456000|0.456000	0.33151|0.33151	ATG|AAT	.	.		0.413	HMGCL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008253.2	NM_000191		C	24147006	A	C	24147006	3	2	296	1	0	0	0	0	1	0	0	0	7238	214	8	5	871	5	HMGCL	1	24147006	Missense_Mutation	SNP	A	TCGA-G3-AAV0-01A-11D-A36X-10	1244201	24147006	225103615	6	42950	226	2								
HMGCL	3155	hgsc.bcm.edu	37	chr1	24147010	24147010	+	Missense_Mutation	SNP	T	T	A													0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ccaactttaccttttcatttTgtagtccatctcggggacca							TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:24147010T>A	ENST00000374490.3	-	2	177	c.134A>T	c.(133-135)cAa>cTa	p.Q45L	HMGCL_ENST00000436439.2_Missense_Mutation_p.Q45L|HMGCL_ENST00000374483.4_Missense_Mutation_p.Q20L|HMGCL_ENST00000509389.1_5'UTR	NM_000191.2	NP_000182.2	P35914	HMGCL_HUMAN	3-hydroxymethyl-3-methylglutaryl-CoA lyase	45					acyl-CoA metabolic process (GO:0006637)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|ketone body biosynthetic process (GO:0046951)|leucine catabolic process (GO:0006552)|liver development (GO:0001889)|mitochondrion organization (GO:0007005)|protein tetramerization (GO:0051262)|response to fatty acid (GO:0070542)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)	carboxylic acid binding (GO:0031406)|fatty-acyl-CoA binding (GO:0000062)|hydroxymethylglutaryl-CoA lyase activity (GO:0004419)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	12		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.0044)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.38e-24)|Colorectal(126;5.58e-08)|COAD - Colon adenocarcinoma(152;3.12e-06)|GBM - Glioblastoma multiforme(114;4.9e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000982)|KIRC - Kidney renal clear cell carcinoma(1967;0.0034)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0856)|LUSC - Lung squamous cell carcinoma(448;0.188)		CTTTTCATTTTGTAGTCCATC	0.408																																					p.Q45L		Atlas-SNP	.											.	HMGCL	22	.	0			c.A134T						.						164	142	149					1																	24147010		2203	4300	6503	SO:0001583	missense	3155	exon2			TCATTTTGTAGTC	BC010570	CCDS243.1, CCDS53279.1	1p36.1-p35	2010-04-30	2010-04-30		ENSG00000117305	ENSG00000117305	4.1.3.4		5005	protein-coding gene	gene with protein product	"hydroxymethylglutaricaciduria"	613898	"3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase"			8102917, 8978493	Standard	NM_001166059		Approved	HL	uc001bib.3	P35914	OTTHUMG00000002963	ENST00000374490.3:c.134A>T	chr1.hg19:g.24147010T>A	ENSP00000363614:p.Gln45Leu	159.0	0.0		123.0	12.0	NM_000191	B4DUP4|B7UCC6|D3Y5K7|Q6IBC0|Q96FP8	Missense_Mutation	SNP	ENST00000374490.3	hg19	CCDS243.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	32|32	5.114377|5.114377	0.94339|0.94339	.|.	.|.	ENSG00000117305|ENSG00000117305	ENST00000235958|ENST00000374490;ENST00000436439;ENST00000374483;ENST00000543166	.|D;D;D	.|0.99825	.|-6.6;-6.97;-6.6	5.27|5.27	5.27|5.27	0.74061|0.74061	.|Aldolase-type TIM barrel (1);Pyruvate carboxyltransferase (2);	.|0.047872	.|0.85682	.|D	.|0.000000	.|D	.|0.99910	.|0.9957	H|H	0.99391|0.99391	4.545|4.545	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.76494	.|0.999;0.987;0.987;0.987	.|D;D;D;D	.|0.79108	.|0.992;0.913;0.913;0.913	.|D	.|0.96097	.|0.9066	.|10	.|0.87932	.|D	.|0	-10.7394|-10.7394	14.3693|14.3693	0.66828|0.66828	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|45;45;20;45	.|B4DUP4;Q6IBC0;B1AK13;P35914	.|.;.;.;HMGCL_HUMAN	X|L	41|45;45;20;20	.|ENSP00000363614:Q45L;ENSP00000389281:Q45L;ENSP00000363607:Q20L	.|ENSP00000363607:Q20L	K|Q	-|-	1|2	0|0	HMGCL|HMGCL	24019597|24019597	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	7.271000|7.271000	0.78506|0.78506	2.227000|2.227000	0.72691|0.72691	0.456000|0.456000	0.33151|0.33151	AAA|CAA	.	.		0.408	HMGCL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008253.2	NM_000191		A	24147010	T	A	24147010	3	1	296	1	0	0	0	0	1	0	0	0	7238	1812	63	4	875	4	HMGCL	1	24147010	Missense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	4	24147010	225103611	7	42951	226	2								
AHDC1	27245	hgsc.bcm.edu	37	chr1	27874319	27874361	+	Frame_Shift_Del	DEL	GTGGCCCAGGCTGGCCCCCTGGAGTCCATGCTTGAGGGGCTCG	GTGGCCCAGGCTGGCCCCCTGGAGTCCATGCTTGAGGGGCTCG	-													0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tgggcctgggctgcagctgcGtggcccaggctggccccctg					rs566131872|rs368747937|rs527518359|rs375964883|rs372813656	byFrequency	TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	GTGGCCCAGGCTGGCCCCCTGGAGTCCATGCTTGAGGGGCTCG	GTGGCCCAGGCTGGCCCCCTGGAGTCCATGCTTGAGGGGCTCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:27874319_27874361delGTGGCCCAGGCTGGCCCCCTGGAGTCCATGCTTGAGGGGCTCG	ENST00000247087.5	-	5	4862_4904	c.4266_4308delCGAGCCCCTCAAGCATGGACTCCAGGGGGCCAGCCTGGGCCAC	c.(4264-4308)tgcgagcccctcaagcatggactccagggggccagcctgggccacfs	p.CEPLKHGLQGASLGH1422fs	AHDC1_ENST00000374011.2_Frame_Shift_Del_p.CEPLKHGLQGASLGH1422fs			Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	1422							DNA binding (GO:0003677)	p.L1429R(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)		CTGCAGCTGCGTGGCCCAGGCTGGCCCCCTGGAGTCCATGCTTGAGGGGCTCGCAGGCAGCCA	0.675																																					p.1423_1437del		Atlas-Indel,Pindel	.											.	AHDC1	98	.	1	Substitution - Missense(1)	prostate(1)	c.4267_4309del						.																																			SO:0001589	frameshift_variant	27245	exon6			.	AK125431	CCDS30652.1	1p36.13	2008-02-05			ENSG00000126705	ENSG00000126705			25230	protein-coding gene	gene with protein product		615790				8619474, 9110174	Standard	XM_005245848		Approved	DJ159A19.3, RP1-159A19.1	uc009vsy.3	Q5TGY3	OTTHUMG00000003398	ENST00000247087.5:c.4266_4308delCGAGCCCCTCAAGCATGGACTCCAGGGGGCCAGCCTGGGCCAC	chr1.hg19:g.27874319_27874361delGTGGCCCAGGCTGGCCCCCTGGAGTCCATGCTTGAGGGGCTCG	ENSP00000247087:p.Cys1422fs	86.0	0.0		52.0	16.0	NM_001029882	Q5TGY4|Q6PJK1|Q6ZUQ6|Q99769|Q9NUF5	Frame_Shift_Del	DEL	ENST00000247087.5	hg19	CCDS30652.1																																																																																			.	.		0.675	AHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009523.3			-	27874361	GTGGCCCAGGCTGGCCCCCTGGAGTCCATGCTTGAGGGGCTCG	-	27874319	7	5	296	1	0	1	0	1	0	0	0	0	412	1136	40	0	507	0	AHDC1	1	27874319	Frame_Shift_Del	DEL	GTGGCCCAGGCTGGCCCCCTGGAGTCCATGCTTGAGGGGCTCG	TCGA-G3-AAV0-01A-11D-A36X-10	3727309	27874319	221376302	8	42952										
RNF19B	127544	hgsc.bcm.edu	37	chr1	33430200	33430200	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tgcaaggtgaggcgccggcgCcggccgccgctgcggcactt	17	15	0	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:33430200C>T	ENST00000373456.7	-	1	86	c.87G>A	c.(85-87)cgG>cgA	p.R29R	RNF19B_ENST00000356990.5_Silent_p.R29R|RNF19B_ENST00000235150.4_Silent_p.R29R	NM_153341.2	NP_699172.2	Q6ZMZ0	RN19B_HUMAN	ring finger protein 19B	29	Poly-Arg.				interferon-gamma secretion (GO:0072643)|natural killer cell mediated cytotoxicity (GO:0042267)|protein ubiquitination (GO:0016567)	cytolytic granule (GO:0044194)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(2)|large_intestine(3)|lung(4)	13		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				ggcgccggcgccggccgccgc	0.776																																					p.R29R		Atlas-SNP	.											.	RNF19B	43	.	0			c.G87A						.						1	2	2					1																	33430200		240	871	1111	SO:0001819	synonymous_variant	127544	exon1			CCGGCGCCGGCCG	AK074486	CCDS372.2, CCDS44107.1, CCDS72754.1	1p35.1	2010-05-11	2007-08-20	2007-08-20	ENSG00000116514	ENSG00000116514		"RING-type (C3HC4) zinc fingers"	26886	protein-coding gene	gene with protein product		610872	"IBR domain containing 3"	IBRDC3		12477932	Standard	XM_006710356		Approved	FLJ90005	uc010oho.2	Q6ZMZ0	OTTHUMG00000004013	ENST00000373456.7:c.87G>A	chr1.hg19:g.33430200C>T		27.0	0.0		41.0	21.0	NM_001127361	B7ZLB2|E9PAW6|G3XA82|Q0VG77|Q5TH44|Q5TH45|Q6P6A4|Q8N2S8|Q8WUF3	Silent	SNP	ENST00000373456.7	hg19	CCDS372.2																																																																																			.	.		0.776	RNF19B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011465.3	NM_153341		T	33430200	C	T	33430200	2	4	296	1	0	0	0	0	0	0	0	1	13486	726	26	3		3	RNF19B	1	33430200	Silent	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	5555881	33430200	215820421	9	42953										
GJB5	2709	hgsc.bcm.edu	37	chr1	35223441	35223441	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tgccacgcagatccatgtccCaatatagtggactgcttcat	8	12	1	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:35223441C>G	ENST00000338513.1	+	2	683	c.510C>G	c.(508-510)ccC>ccG	p.P170P	GJB4_ENST00000339480.1_5'Flank	NM_005268.3	NP_005259.1	O95377	CXB5_HUMAN	gap junction protein, beta 5, 31.1kDa	170					cell communication (GO:0007154)|epidermis development (GO:0008544)|labyrinthine layer morphogenesis (GO:0060713)|spongiotrophoblast differentiation (GO:0060708)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|stomach(1)	10		Myeloproliferative disorder(586;0.0393)				ATCCATGTCCCAATATAGTGG	0.517																																					p.P170P		Atlas-SNP	.											.	GJB5	35	.	0			c.C510G						.						103	91	95					1																	35223441		2203	4300	6503	SO:0001819	synonymous_variant	2709	exon2			ATGTCCCAATATA	BC004379	CCDS382.1	1p34.3	2008-05-14	2007-11-06		ENSG00000189280	ENSG00000189280		"Ion channels / Gap junction proteins (connexins)"	4287	protein-coding gene	gene with protein product	"connexin 31.1"	604493	"gap junction protein, beta 5 (connexin 31.1)", "gap junction protein, beta 5"			9843209	Standard	NM_005268		Approved	CX31.1	uc001bxu.4	O95377	OTTHUMG00000004053	ENST00000338513.1:c.510C>G	chr1.hg19:g.35223441C>G		86.0	0.0		58.0	22.0	NM_005268	Q9UPA3	Silent	SNP	ENST00000338513.1	hg19	CCDS382.1																																																																																			.	.		0.517	GJB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011561.1	NM_005268		G	35223441	C	G	35223441	2	3	296	1	0	0	0	0	0	0	0	1	6419	581	21	4		4	GJB5	1	35223441	Silent	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	1793241	35223441	214027180	10	42954										
HIVEP3	59269	hgsc.bcm.edu	37	chr1	41976245	41976245	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gagaggttcctcgtccgggcTgggaagcgggcagaggcctc	18	11	0	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:41976245T>A	ENST00000372583.1	-	9	7983	c.7098A>T	c.(7096-7098)ccA>ccT	p.P2366P	HIVEP3_ENST00000247584.5_Silent_p.P2366P|HIVEP3_ENST00000429157.2_Silent_p.P2365P|HIVEP3_ENST00000460604.1_5'UTR|HIVEP3_ENST00000372584.1_Silent_p.P2365P	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	2366					positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				TCGTCCGGGCTGGGAAGCGGG	0.701																																					p.P2366P		Atlas-SNP	.											.	HIVEP3	235	.	0			c.A7098T						.						14	14	14					1																	41976245		2165	4253	6418	SO:0001819	synonymous_variant	59269	exon9			CCGGGCTGGGAAG	AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"Zinc fingers, C2H2-type"	13561	protein-coding gene	gene with protein product	"kappabinding protein-1"	606649	"human immunodeficiency virus type I enhancer-binding protein 3"			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.7098A>T	chr1.hg19:g.41976245T>A		119.0	0.0		79.0	23.0	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Silent	SNP	ENST00000372583.1	hg19	CCDS463.1																																																																																			.	.		0.701	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503		A	41976245	T	A	41976245	2	1	296	1	0	0	0	0	0	0	0	1	7197	1567	55	4		4	HIVEP3	1	41976245	Silent	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	6752804	41976245	207274376	11	42955										
MAST2	23139	hgsc.bcm.edu	37	chr1	46269721	46269721	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tggaggagcggacgggccccGcggggcccgagggcaaggag	22	11	0	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:46269721G>A	ENST00000361297.2	+	1	437	c.154G>A	c.(154-156)Gcg>Acg	p.A52T	MAST2_ENST00000372009.2_Missense_Mutation_p.A52T	NM_015112.2	NP_055927.2			microtubule associated serine/threonine kinase 2											breast(1)|lung(3)|ovary(5)|stomach(2)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					GACGGGCCCCGCGGGGCCCGA	0.736																																					p.A52T		Atlas-SNP	.											.	MAST2	136	.	0			c.G154A						.						2	3	3					1																	46269721		741	1926	2667	SO:0001583	missense	23139	exon1			GGCCCCGCGGGGC	AB047005	CCDS41326.1	1p34.1	2008-02-05			ENSG00000086015	ENSG00000086015			19035	protein-coding gene	gene with protein product		612257					Standard	NM_015112		Approved	MAST205, KIAA0807	uc001cov.3	Q6P0Q8	OTTHUMG00000008007	ENST00000361297.2:c.154G>A	chr1.hg19:g.46269721G>A	ENSP00000354671:p.Ala52Thr	166.0	0.0		222.0	78.0	NM_015112		Missense_Mutation	SNP	ENST00000361297.2	hg19	CCDS41326.1	.	.	.	.	.	.	.	.	.	.	G	5.516	0.280175	0.10458	.	.	ENSG00000086015	ENST00000361297;ENST00000372009	T;T	0.63913	-0.0;-0.07	2.79	-5.58	0.02512	.	.	.	.	.	T	0.29355	0.0731	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.12400	-1.0549	9	0.23891	T	0.37	2.0859	0.4333	0.00475	0.2152:0.2892:0.2032:0.2925	.	52;52	E7ERL6;Q6P0Q8	.;MAST2_HUMAN	T	52	ENSP00000354671:A52T;ENSP00000361079:A52T	ENSP00000354671:A52T	A	+	1	0	MAST2	46042308	0.001000	0.12720	0.001000	0.08648	0.196000	0.23810	-1.625000	0.02036	-1.437000	0.01967	-1.283000	0.01379	GCG	.	.		0.736	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112		A	46269721	G	A	46269721	3	1	296	1	0	0	0	0	1	0	0	0	9334	1087	38	1	156	1	MAST2	1	46269721	Missense_Mutation	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10	4293476	46269721	202980900	12	42956										
ZFYVE9	9372	hgsc.bcm.edu	37	chr1	52705044	52705044	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tggggaacatttagaaagttAtgaggctgagatctccacta	11	6	1	3			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:52705044A>T	ENST00000371591.1	+	3	2086	c.1955A>T	c.(1954-1956)tAt>tTt	p.Y652F	ZFYVE9_ENST00000287727.3_Missense_Mutation_p.Y652F|ZFYVE9_ENST00000357206.2_Missense_Mutation_p.Y652F	NM_004799.2|NM_007324.2	NP_004790.2|NP_015563.2	O95405	ZFYV9_HUMAN	zinc finger, FYVE domain containing 9	652					endocytosis (GO:0006897)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|SMAD protein complex assembly (GO:0007183)|SMAD protein import into nucleus (GO:0007184)|transforming growth factor beta receptor signaling pathway (GO:0007179)	early endosome (GO:0005769)|early endosome membrane (GO:0031901)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|serine-type peptidase activity (GO:0008236)			breast(1)|central_nervous_system(4)|endometrium(3)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	53						TTAGAAAGTTATGAGGCTGAG	0.433																																					p.Y652F		Atlas-SNP	.											.	ZFYVE9	131	.	0			c.A1955T						.						109	107	108					1																	52705044		2203	4300	6503	SO:0001583	missense	9372	exon4			AAAGTTATGAGGC	AF104304	CCDS563.1, CCDS564.1	1p32.3	2014-06-13	2004-05-21	2004-05-26	ENSG00000157077	ENSG00000157077		"Zinc fingers, FYVE domain containing"	6775	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 173"	603755	"MAD, mothers against decapentaplegic homolog (Drosophila) interacting protein, receptor activation anchor"	MADHIP		9865696	Standard	NM_007324		Approved	SMADIP, SARA, PPP1R173	uc001cto.4	O95405	OTTHUMG00000008061	ENST00000371591.1:c.1955A>T	chr1.hg19:g.52705044A>T	ENSP00000360647:p.Tyr652Phe	141.0	0.0		175.0	67.0	NM_007323	Q5T0F6|Q5T0F7|Q9UNE1|Q9Y5R7	Missense_Mutation	SNP	ENST00000371591.1	hg19	CCDS563.1	.	.	.	.	.	.	.	.	.	.	A	6.680	0.494102	0.12702	.	.	ENSG00000157077	ENST00000357206;ENST00000361625;ENST00000287727;ENST00000371591	T;T;T;T	0.54279	1.05;0.58;1.07;1.07	4.94	3.79	0.43588	.	0.000000	0.49305	D	0.000157	T	0.28764	0.0713	N	0.12182	0.205	0.28834	N	0.896984	B;B;B	0.14438	0.001;0.001;0.01	B;B;B	0.11329	0.004;0.002;0.006	T	0.15838	-1.0423	10	0.15952	T	0.53	.	7.1007	0.25336	0.7017:0.1524:0.0:0.1459	.	652;652;652	O95405-2;O95405;O95405-3	.;ZFYV9_HUMAN;.	F	652	ENSP00000349737:Y652F;ENSP00000355358:Y652F;ENSP00000287727:Y652F;ENSP00000360647:Y652F	ENSP00000287727:Y652F	Y	+	2	0	ZFYVE9	52477632	1.000000	0.71417	1.000000	0.80357	0.724000	0.41520	3.057000	0.49931	0.983000	0.38602	0.459000	0.35465	TAT	.	.		0.433	ZFYVE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022083.1	NM_007324		T	52705044	A	T	52705044	3	4	296	1	0	0	0	0	1	0	0	0	17686	449	16	4	1961	4	ZFYVE9	1	52705044	Missense_Mutation	SNP	A	TCGA-G3-AAV0-01A-11D-A36X-10	6435323	52705044	196545577	13	42957										
GLIS1	148979	hgsc.bcm.edu	37	chr1	53995579	53995579	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ccgtgtggctcctcaggtggAtcttgaggttctccagccgt	13	12	3	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:53995579A>C	ENST00000312233.2	-	4	1408	c.842T>G	c.(841-843)aTc>aGc	p.I281S		NM_147193.2	NP_671726.2			GLIS family zinc finger 1											endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|skin(3)|urinary_tract(4)	24						CCTCAGGTGGATCTTGAGGTT	0.652																																					p.I281S		Atlas-SNP	.											.	GLIS1	52	.	0			c.T842G						.						55	59	58					1																	53995579		2203	4300	6503	SO:0001583	missense	148979	exon4			AGGTGGATCTTGA	AK093474	CCDS582.1	1p32.3	2008-02-05			ENSG00000174332	ENSG00000174332		"Zinc fingers, C2H2-type"	29525	protein-coding gene	gene with protein product		610378				12042312, 14500813	Standard	NM_147193		Approved	FLJ36155	uc001cvr.1	Q8NBF1	OTTHUMG00000008079	ENST00000312233.2:c.842T>G	chr1.hg19:g.53995579A>C	ENSP00000309653:p.Ile281Ser	63.0	0.0		49.0	20.0	NM_147193		Missense_Mutation	SNP	ENST00000312233.2	hg19	CCDS582.1	.	.	.	.	.	.	.	.	.	.	A	18.32	3.598955	0.66332	.	.	ENSG00000174332	ENST00000312233	T	0.17213	2.29	4.58	4.58	0.56647	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.48286	D	0.000184	T	0.26991	0.0661	N	0.17872	0.535	0.58432	D	0.999994	D	0.89917	1.0	D	0.85130	0.997	T	0.07635	-1.0762	10	0.56958	D	0.05	.	14.2651	0.66113	1.0:0.0:0.0:0.0	.	281	Q8NBF1	GLIS1_HUMAN	S	281	ENSP00000309653:I281S	ENSP00000309653:I281S	I	-	2	0	GLIS1	53768167	1.000000	0.71417	1.000000	0.80357	0.716000	0.41182	9.287000	0.95975	1.842000	0.53543	0.402000	0.26972	ATC	.	.		0.652	GLIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022109.1	NM_147193		C	53995579	A	C	53995579	3	2	296	1	0	0	0	0	1	0	0	0	6453	333	12	5	1048	5	GLIS1	1	53995579	Missense_Mutation	SNP	A	TCGA-G3-AAV0-01A-11D-A36X-10	1290535	53995579	195255042	14	42958										
SLC35D1	23169	hgsc.bcm.edu	37	chr1	67518480	67518480	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	aggtacatttctgtcaaggtCaggaaacttgactactctga	9	8	4	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:67518480C>T	ENST00000235345.5	-	3	383	c.298G>A	c.(298-300)Gac>Aac	p.D100N	SLC35D1_ENST00000506472.2_Missense_Mutation_p.D21N	NM_015139.2	NP_055954.1	Q9NTN3	S35D1_HUMAN	solute carrier family 35 (UDP-GlcA/UDP-GalNAc transporter), member D1	100					carbohydrate transport (GO:0008643)|cellular glucuronidation (GO:0052695)|chondroitin sulfate biosynthetic process (GO:0030206)|embryonic skeletal system development (GO:0048706)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|UDP-glucuronate biosynthetic process (GO:0006065)|UDP-glucuronic acid transport (GO:0015787)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	UDP-glucuronic acid transmembrane transporter activity (GO:0005461)			endometrium(2)|kidney(1)|large_intestine(3)|lung(4)	10						CTGTCAAGGTCAGGAAACTTG	0.398																																					p.D100N		Atlas-SNP	.											.	SLC35D1	22	.	0			c.G298A						.						114	113	113					1																	67518480		2203	4300	6503	SO:0001583	missense	23169	exon3			CAAGGTCAGGAAA	AB044343	CCDS636.1	1p32-p31	2013-07-17	2013-07-17		ENSG00000116704	ENSG00000116704		"Solute carriers"	20800	protein-coding gene	gene with protein product		610804	"solute carrier family 35 (UDP-glucuronic acid/UDP-N-acetylgalactosamine dual transporter), member D1"			11322953	Standard	NM_015139		Approved	UGTREL7, KIAA0260	uc001ddk.2	Q9NTN3	OTTHUMG00000009360	ENST00000235345.5:c.298G>A	chr1.hg19:g.67518480C>T	ENSP00000235345:p.Asp100Asn	129.0	0.0		144.0	58.0	NM_015139	A8K185|B7Z3X2|Q52LU5|Q92548	Missense_Mutation	SNP	ENST00000235345.5	hg19	CCDS636.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.944537	0.73672	.	.	ENSG00000116704	ENST00000235345;ENST00000506472	T;T	0.64991	-0.13;0.3	5.18	5.18	0.71444	.	0.045850	0.85682	D	0.000000	T	0.45418	0.1341	L	0.60957	1.885	0.80722	D	1	B;B	0.23442	0.085;0.038	B;B	0.21151	0.033;0.033	T	0.44467	-0.9326	10	0.21540	T	0.41	-30.0873	17.4611	0.87620	0.0:1.0:0.0:0.0	.	21;100	B7Z3X2;Q9NTN3	.;S35D1_HUMAN	N	100;21	ENSP00000235345:D100N;ENSP00000445189:D21N	ENSP00000235345:D100N	D	-	1	0	SLC35D1	67291068	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.390000	0.79816	2.412000	0.81896	0.655000	0.94253	GAC	.	.		0.398	SLC35D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025948.1	NM_015139		T	67518480	C	T	67518480	3	4	296	1	0	0	0	0	1	0	0	0	14596	826	29	3	809	3	SLC35D1	1	67518480	Missense_Mutation	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	13522901	67518480	181732141	15	42959										
ACADM	34	hgsc.bcm.edu	37	chr1	76216231	76216231	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ttcggaaagctacttgtagaGgtaattttaatactgcttgc	9	6	0	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:76216231G>C	ENST00000370841.4	+	10	1382	c.945G>C	c.(943-945)gaG>gaC	p.E315D	ACADM_ENST00000420607.2_Splice_Site_p.E319D|ACADM_ENST00000370834.5_Splice_Site_p.E348D|ACADM_ENST00000543667.1_Splice_Site_p.E126D|ACADM_ENST00000481374.1_3'UTR|ACADM_ENST00000541113.1_Splice_Site_p.E279D	NM_000016.4|NM_001127328.1	NP_000007.1|NP_001120800.1	P11310	ACADM_HUMAN	acyl-CoA dehydrogenase, C-4 to C-12 straight chain	315					cardiac muscle cell differentiation (GO:0055007)|carnitine biosynthetic process (GO:0045329)|carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|glycogen biosynthetic process (GO:0005978)|liver development (GO:0001889)|medium-chain fatty acid catabolic process (GO:0051793)|medium-chain fatty acid metabolic process (GO:0051791)|oxidation-reduction process (GO:0055114)|post-embryonic development (GO:0009791)|regulation of gluconeogenesis (GO:0006111)|response to cold (GO:0009409)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	axon (GO:0030424)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|identical protein binding (GO:0042802)|medium-chain-acyl-CoA dehydrogenase activity (GO:0070991)			breast(3)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|skin(1)	18					Flavin adenine dinucleotide(DB03147)	TACTTGTAGAGGTAATTTTAA	0.343																																					p.E319D		Atlas-SNP	.											.	ACADM	50	.	0			c.G957C						.						65	71	69					1																	76216231		2203	4299	6502	SO:0001630	splice_region_variant	34	exon10			TGTAGAGGTAATT	M16827	CCDS668.1, CCDS44165.1, CCDS65562.1, CCDS72807.1	1p31	2014-09-17	2010-04-30		ENSG00000117054	ENSG00000117054	1.3.99.3		89	protein-coding gene	gene with protein product		607008	"acyl-Coenzyme A dehydrogenase, C-4 to C-12 straight chain"			3035565	Standard	NM_000016		Approved	MCAD, MCADH, ACAD1	uc009wbp.3	P11310	OTTHUMG00000009784	ENST00000370841.4:c.945+1G>C	chr1.hg19:g.76216231G>C		94.0	0.0		131.0	14.0	NM_001127328	Q5T4U4|Q9NYF1	Missense_Mutation	SNP	ENST00000370841.4	hg19	CCDS668.1	.	.	.	.	.	.	.	.	.	.	G	10.91	1.485317	0.26598	.	.	ENSG00000117054	ENST00000370841;ENST00000370834;ENST00000541113;ENST00000543667;ENST00000420607	D;D;D;D;D	0.95821	-3.82;-3.82;-3.82;-3.82;-3.82	5.58	5.58	0.84498	Acyl-CoA dehydrogenase/oxidase C-terminal (2);Acyl-CoA oxidase/dehydrogenase, type 1 (1);	0.000000	0.85682	D	0.000000	D	0.86234	0.5884	N	0.12920	0.275	0.80722	D	1	B;B;B;B;B	0.12013	0.0;0.0;0.005;0.0;0.0	B;B;B;B;B	0.21360	0.001;0.001;0.034;0.0;0.0	T	0.82627	-0.0364	10	0.40728	T	0.16	.	13.8243	0.63342	0.0753:0.0:0.9247:0.0	.	279;229;348;319;315	B7Z9I1;B4DVE0;Q5T4U5;P11310-2;P11310	.;.;.;.;ACADM_HUMAN	D	315;348;279;126;319	ENSP00000359878:E315D;ENSP00000359871:E348D;ENSP00000442324:E279D;ENSP00000446176:E126D;ENSP00000409612:E319D	ENSP00000359871:E348D	E	+	3	2	ACADM	75988819	1.000000	0.71417	1.000000	0.80357	0.078000	0.17371	5.052000	0.64263	2.622000	0.88805	0.585000	0.79938	GAG	.	.		0.343	ACADM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026967.1		Missense_Mutation	C	76216231	G	C	76216231	5	2	296	1	0	0	0	0	0	0	1	0	113	1014	35	4	995	4	ACADM	1	76216231	Splice_Site	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10	8697751	76216231	173034390	16	42960										
CELSR2	1952	hgsc.bcm.edu	37	chr1	109793071	109793072	+	Frame_Shift_Ins	INS	-	-	C													0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gggcattggaggccacctttINSccccacagggcaagctcaca					rs140803839		TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:109793071_109793072insC	ENST00000271332.3	+	1	431_432	c.370_371insC	c.(370-372)tccfs	p.S124fs		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	124					cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		AGGCCACCTTTCCCCACAGGGC	0.644																																					p.S124fs	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-Indel,Pindel	.											.	CELSR2	228	.	0			c.370_371insC						.																																			SO:0001589	frameshift_variant	1952	exon1			.	D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3231	protein-coding gene	gene with protein product		604265	"cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.374dupC	chr1.hg19:g.109793075_109793075dupC	ENSP00000271332:p.Ser124fs	116.0	0.0		132.0	52.0	NM_001408	Q5T2Y7|Q92566	Frame_Shift_Ins	INS	ENST00000271332.3	hg19	CCDS796.1																																																																																			.	.		0.644	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408		C	109793072	-	C	109793071	7	5	296	1	0	1	1	0	0	0	0	0	3224	1783	62	0	372	0	CELSR2	1	109793071	Frame_Shift_Ins	INS	-	TCGA-G3-AAV0-01A-11D-A36X-10	33576840	109793071	139457550	17	42961										
CSDE1	7812	hgsc.bcm.edu	37	chr1	115262274	115262275	+	Frame_Shift_Ins	INS	-	-	G													0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ctgagaactccacctcatctINScctgcctgtagctcaatgcc							TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:115262274_115262275insG	ENST00000358528.4	-	18	2567_2568	c.2141_2142insC	c.(2140-2142)ggafs	p.G714fs	CSDE1_ENST00000483407.1_5'Flank|CSDE1_ENST00000438362.2_Frame_Shift_Ins_p.G760fs|CSDE1_ENST00000339438.6_Frame_Shift_Ins_p.G683fs|CSDE1_ENST00000534699.1_Frame_Shift_Ins_p.G714fs|CSDE1_ENST00000369530.1_Frame_Shift_Ins_p.G729fs|CSDE1_ENST00000261443.5_Frame_Shift_Ins_p.G683fs|NRAS_ENST00000369535.4_5'Flank|CSDE1_ENST00000530886.1_Frame_Shift_Ins_p.G584fs	NM_001007553.2	NP_001007554.1	O75534	CSDE1_HUMAN	cold shock domain containing E1, RNA-binding	714	CSD 9.				male gonad development (GO:0008584)|nuclear-transcribed mRNA catabolic process, no-go decay (GO:0070966)|regulation of transcription, DNA-templated (GO:0006355)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.G714V(1)		NS(1)|breast(4)|endometrium(11)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	51	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		CCACCTCATCTCCTGCCTGTAG	0.426																																					p.G760fs		Atlas-Indel,Pindel	.											.	CSDE1	145	.	1	Substitution - Missense(1)	lung(1)	c.2280_2281insC						.																																			SO:0001589	frameshift_variant	7812	exon19			.		CCDS30811.1, CCDS30812.1, CCDS44197.1, CCDS55626.1	1p13.2	2011-11-02			ENSG00000009307	ENSG00000009307			29905	protein-coding gene	gene with protein product	"upstream of NRAS"	191510				2204029, 10048485	Standard	NM_007158		Approved	D1S155E, UNR	uc001efi.3	O75534	OTTHUMG00000012060	ENST00000358528.4:c.2141_2142insC	chr1.hg19:g.115262274_115262275insG	ENSP00000351329:p.Gly714fs	93.0	0.0		107.0	37.0	NM_001242891	A8K281|E9PGZ0|G5E9Q2|O94961|Q5TF04|Q5TF05|Q68DF1|Q68DI9|Q9Y2S4	Frame_Shift_Ins	INS	ENST00000358528.4	hg19	CCDS30812.1																																																																																			.	.		0.426	CSDE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033397.1	NM_007158		G	115262275	-	G	115262274	7	5	296	1	0	1	1	0	0	0	0	0	3931	1538	54	0	266	0	CSDE1	1	115262274	Frame_Shift_Ins	INS	-	TCGA-G3-AAV0-01A-11D-A36X-10	5469203	115262274	133988347	18	42962										
ADAM30	11085	hgsc.bcm.edu	37	chr1	120436684	120436684	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tttttgctttagattcttccTgtccagtttttgcttcagat	6	8	2	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:120436684T>C	ENST00000369400.1	-	1	2434	c.2276A>G	c.(2275-2277)cAg>cGg	p.Q759R		NM_021794.3	NP_068566.2	Q9UKF2	ADA30_HUMAN	ADAM metallopeptidase domain 30	759	5 X 9 AA approximate repeats.				binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(16)|ovary(2)|skin(2)	38	all_cancers(5;7.07e-10)|all_epithelial(5;1.62e-10)|all_neural(166;0.153)|Breast(55;0.234)	all_lung(203;1.55e-06)|Lung NSC(69;1.04e-05)|all_epithelial(167;0.00138)		Lung(183;0.0204)|LUSC - Lung squamous cell carcinoma(189;0.117)		AGATTCTTCCTGTCCAGTTTT	0.353																																					p.Q759R		Atlas-SNP	.											.	ADAM30	88	.	0			c.A2276G						.						280	293	288					1																	120436684		2203	4300	6503	SO:0001583	missense	11085	exon1			TCTTCCTGTCCAG	AF171932	CCDS907.1	1p12	2012-05-16	2005-08-18		ENSG00000134249	ENSG00000134249		"ADAM metallopeptidase domain containing"	208	protein-coding gene	gene with protein product		604779	"a disintegrin and metalloproteinase domain 30"				Standard	NM_021794		Approved	svph4	uc001eij.3	Q9UKF2	OTTHUMG00000012176	ENST00000369400.1:c.2276A>G	chr1.hg19:g.120436684T>C	ENSP00000358407:p.Gln759Arg	171.0	0.0		162.0	72.0	NM_021794	A8K8W8|Q5T3X6|Q9UKF1	Missense_Mutation	SNP	ENST00000369400.1	hg19	CCDS907.1	.	.	.	.	.	.	.	.	.	.	T	7.085	0.571068	0.13623	.	.	ENSG00000134249	ENST00000369400;ENST00000543066	T	0.01145	5.27	2.47	-1.66	0.08265	.	.	.	.	.	T	0.00241	0.0007	N	0.19112	0.55	0.09310	N	1	B	0.16802	0.019	B	0.04013	0.001	T	0.35724	-0.9777	9	0.09843	T	0.71	.	3.5289	0.07769	0.0:0.2834:0.2063:0.5103	.	759	Q9UKF2	ADA30_HUMAN	R	759	ENSP00000358407:Q759R	ENSP00000358407:Q759R	Q	-	2	0	ADAM30	120238207	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.167000	0.03126	-0.189000	0.10482	-0.619000	0.04042	CAG	.	.		0.353	ADAM30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033678.1	NM_021794		C	120436684	T	C	120436684	3	2	296	1	0	0	0	0	1	0	0	0	248	1580	55	2	100	2	ADAM30	1	120436684	Missense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	5174410	120436684	128813937	19	42963										
PGLYRP4	57115	hgsc.bcm.edu	37	chr1	153315636	153315636	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tgggtgtgcactccttggatAttccagccaacaccttcata	8	12	1	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:153315636A>T	ENST00000359650.5	-	5	466	c.402T>A	c.(400-402)aaT>aaA	p.N134K	PGLYRP4_ENST00000490266.1_5'Flank|PGLYRP4_ENST00000368739.3_Missense_Mutation_p.N130K	NM_020393.2	NP_065126.2	Q96LB8	PGRP4_HUMAN	peptidoglycan recognition protein 4	134					defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|skin(1)|stomach(1)	23	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.171)			CTCCTTGGATATTCCAGCCAA	0.488																																					p.N134K		Atlas-SNP	.											.	PGLYRP4	45	.	0			c.T402A						.						219	166	184					1																	153315636		2203	4300	6503	SO:0001583	missense	57115	exon5			TTGGATATTCCAG	AF242518	CCDS30871.1	1q21	2008-02-05			ENSG00000163218	ENSG00000163218			30015	protein-coding gene	gene with protein product	"peptidoglycan recognition protein I beta precursor"	608198				11461926	Standard	XR_241090		Approved	SBBI67, PGRPIB, PGLYRPIbeta, PGRP-Ibeta	uc001fbo.3	Q96LB8	OTTHUMG00000037057	ENST00000359650.5:c.402T>A	chr1.hg19:g.153315636A>T	ENSP00000352672:p.Asn134Lys	183.0	0.0		250.0	69.0	NM_020393	A8K838|Q3B822|Q3B823|Q5SY63|Q5SY64|Q9HD75	Missense_Mutation	SNP	ENST00000359650.5	hg19	CCDS30871.1	.	.	.	.	.	.	.	.	.	.	A	9.868	1.198211	0.22037	.	.	ENSG00000163218	ENST00000368739;ENST00000359650	T;T	0.24723	1.84;1.84	4.71	-8.85	0.00799	Peptidoglycan recognition protein family domain, metazoa/bacteria (1);N-acetylmuramoyl-L-alanine amidase domain (4);	0.680921	0.13774	N	0.363694	T	0.08447	0.0210	M	0.62154	1.92	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.17979	0.011;0.02	T	0.26018	-1.0115	10	0.66056	D	0.02	-21.3531	10.1063	0.42535	0.7094:0.0:0.1863:0.1043	.	130;134	Q96LB8-2;Q96LB8	.;PGRP4_HUMAN	K	130;134	ENSP00000357728:N130K;ENSP00000352672:N134K	ENSP00000352672:N134K	N	-	3	2	PGLYRP4	151582260	0.000000	0.05858	0.000000	0.03702	0.598000	0.36846	-2.644000	0.00862	-2.005000	0.00959	-1.179000	0.01719	AAT	.	.		0.488	PGLYRP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000089978.1	NM_020393		T	153315636	A	T	153315636	3	4	296	1	0	0	0	0	1	0	0	0	11805	446	16	4	739	4	PGLYRP4	1	153315636	Missense_Mutation	SNP	A	TCGA-G3-AAV0-01A-11D-A36X-10	32878952	153315636	95934985	20	42964										
ASH1L	55870	hgsc.bcm.edu	37	chr1	155451459	155451459	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gtttctttccaatgtccttaTtaaccaatcccattgctgaa	4	11	1	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:155451459T>A	ENST00000368346.3	-	3	1841	c.1202A>T	c.(1201-1203)aAt>aTt	p.N401I	ASH1L_ENST00000392403.3_Missense_Mutation_p.N401I|ASH1L_ENST00000548830.1_3'UTR			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	401					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			AATGTCCTTATTAACCAATCC	0.423																																					p.N401I		Atlas-SNP	.											.	ASH1L	279	.	0			c.A1202T						.						140	136	137					1																	155451459		2203	4300	6503	SO:0001583	missense	55870	exon3			TCCTTATTAACCA	AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.1202A>T	chr1.hg19:g.155451459T>A	ENSP00000357330:p.Asn401Ile	70.0	0.0		104.0	31.0	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	hg19		.	.	.	.	.	.	.	.	.	.	T	11.84	1.757434	0.31137	.	.	ENSG00000116539	ENST00000368346;ENST00000392403	D;D	0.89123	-2.47;-2.47	4.64	-1.93	0.07594	.	0.303702	0.27936	N	0.017252	T	0.59280	0.2182	N	0.08118	0	0.80722	D	1	B;B	0.27791	0.119;0.189	B;B	0.30179	0.052;0.112	T	0.51403	-0.8710	10	0.72032	D	0.01	.	4.7871	0.13230	0.0:0.3613:0.3509:0.2878	.	401;401	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	I	401	ENSP00000357330:N401I;ENSP00000376204:N401I	ENSP00000357330:N401I	N	-	2	0	ASH1L	153718083	0.991000	0.36638	0.992000	0.48379	0.995000	0.86356	0.004000	0.13106	-0.203000	0.10251	0.460000	0.39030	AAT	.	.		0.423	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		A	155451459	T	A	155451459	3	1	296	1	0	0	0	0	1	0	0	0	1041	1493	52	4	7796	4	ASH1L	1	155451459	Missense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	2135823	155451459	93799162	21	42965										
C1orf156	92342	hgsc.bcm.edu	37	chr1	169762137	169762137	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ttcatcttccaaagtggagtTagctactacattaggtaagg	9	7	2	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:169762137T>A	ENST00000310392.4	-	2	1053	c.700A>T	c.(700-702)Aac>Tac	p.N234Y	METTL18_ENST00000303469.2_Missense_Mutation_p.N234Y|C1orf112_ENST00000498289.1_Intron|C1orf112_ENST00000413811.2_5'Flank|C1orf112_ENST00000456684.1_5'Flank|C1orf112_ENST00000359326.4_5'Flank|C1orf112_ENST00000286031.6_5'Flank	NM_033418.2	NP_219486.1	O95568	MET18_HUMAN	methyltransferase like 18	234						cytoplasm (GO:0005737)	protein methyltransferase activity (GO:0008276)			kidney(1)|large_intestine(3)|lung(4)	8						AAAGTGGAGTTAGCTACTACA	0.348																																					p.N234Y		Atlas-SNP	.											.	METTL18	23	.	0			c.A700T						.						131	140	137					1																	169762137		2202	4299	6501	SO:0001583	missense	92342	exon2			TGGAGTTAGCTAC	AL035369	CCDS1284.1	1q24.2	2013-10-11	2011-03-02	2011-03-02	ENSG00000171806	ENSG00000171806			28793	protein-coding gene	gene with protein product	"histidine protein methyltransferase 1"	615255	"chromosome 1 open reading frame 156"	C1orf156		20864530	Standard	NM_033418		Approved	MGC9084, AsTP2, HPM1	uc001ggn.4	O95568	OTTHUMG00000035813	ENST00000310392.4:c.700A>T	chr1.hg19:g.169762137T>A	ENSP00000307975:p.Asn234Tyr	160.0	0.0		279.0	85.0	NM_033418	B2R9T5	Missense_Mutation	SNP	ENST00000310392.4	hg19	CCDS1284.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.304733	0.81247	.	.	ENSG00000171806	ENST00000310392;ENST00000303469	D;D	0.89415	-2.51;-2.51	6.06	6.06	0.98353	.	0.052808	0.64402	D	0.000001	D	0.94182	0.8133	M	0.85542	2.76	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.94930	0.8081	10	0.72032	D	0.01	-53.9551	15.4394	0.75171	0.0:0.0:0.0:1.0	.	234	O95568	MET18_HUMAN	Y	234	ENSP00000307975:N234Y;ENSP00000307077:N234Y	ENSP00000307077:N234Y	N	-	1	0	METTL18	168028761	1.000000	0.71417	0.714000	0.30535	0.987000	0.75469	7.470000	0.80973	2.315000	0.78130	0.533000	0.62120	AAC	.	.		0.348	METTL18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087109.1	NM_033418		A	169762137	T	A	169762137	3	1	296	1	0	0	0	0	1	0	0	0	2008	1754	61	4	422	4	C1orf156	1	169762137	Missense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	14310678	169762137	79488484	22	42966										
BAT2L2	23215	hgsc.bcm.edu	37	chr1	171511016	171511016	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ataatgtggctcaagaaccaGttaatactcttggggatatt	9	6	2	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:171511016G>A	ENST00000338920.4	+	16	4642	c.4405G>A	c.(4405-4407)Gtt>Att	p.V1469I	PRRC2C_ENST00000367742.3_Missense_Mutation_p.V1471I|PRRC2C_ENST00000426496.2_Missense_Mutation_p.V1469I|PRRC2C_ENST00000392078.3_Missense_Mutation_p.V1471I	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	1469					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										TCAAGAACCAGTTAATACTCT	0.423																																					p.V1469I		Atlas-SNP	.											.	.	.	.	0			c.G4405A						.						64	65	65					1																	171511016		2203	4300	6503	SO:0001583	missense	23215	exon16			GAACCAGTTAATA	AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"BAT2 domain containing 1", "HLA-B associated transcript 2-like 2"	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.4405G>A	chr1.hg19:g.171511016G>A	ENSP00000343629:p.Val1469Ile	190.0	0.0		247.0	79.0	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Missense_Mutation	SNP	ENST00000338920.4	hg19	CCDS1296.2	.	.	.	.	.	.	.	.	.	.	G	3.787	-0.044463	0.07452	.	.	ENSG00000117523	ENST00000392078;ENST00000451306;ENST00000426496;ENST00000367742;ENST00000338920;ENST00000392080	T;T;T;T	0.01947	4.54;4.54;4.54;4.54	5.65	3.78	0.43462	.	0.344565	0.20672	N	0.087809	T	0.00784	0.0026	L	0.46157	1.445	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.49447	-0.8939	10	0.54805	T	0.06	.	3.1049	0.06339	0.1466:0.2159:0.5056:0.1319	.	1469	Q9Y520-4	.	I	1471;1470;1469;1471;1469;1226	ENSP00000375928:V1471I;ENSP00000410219:V1469I;ENSP00000356716:V1471I;ENSP00000343629:V1469I	ENSP00000343629:V1469I	V	+	1	0	PRRC2C	169777640	0.942000	0.31987	0.700000	0.30305	0.782000	0.44232	1.683000	0.37638	0.747000	0.32809	-0.156000	0.13503	GTT	.	.		0.423	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172		A	171511016	G	A	171511016	3	1	296	1	0	0	0	0	1	0	0	0	1321	1029	36	3	4463	3	BAT2L2	1	171511016	Missense_Mutation	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10	1748879	171511016	77739605	23	42967										
RASAL2	9462	hgsc.bcm.edu	37	chr1	178408712	178408712	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	acaagacttctgctttgaggTaaaaataaagtgtagaaaaa	8	4	1	3			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:178408712T>C	ENST00000462775.1	+	4	509		c.e4+2		RASAL2_ENST00000367649.3_Splice_Site|RASAL2_ENST00000448150.3_Splice_Site	NM_004841.3	NP_004832.1	Q9UJF2	NGAP_HUMAN	RAS protein activator like 2						negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Ras GTPase activator activity (GO:0005099)			biliary_tract(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(2)|lung(25)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54						TGCTTTGAGGTAAAAATAAAG	0.373																																					.		Atlas-SNP	.											.	RASAL2	334	.	0			c.828+2T>C						.						80	78	79					1																	178408712		2203	4300	6503	SO:0001630	splice_region_variant	9462	exon6			TTGAGGTAAAAAT	AF047711	CCDS1321.1, CCDS1322.1, CCDS1321.2	1q25	2013-01-10			ENSG00000075391	ENSG00000075391		"Pleckstrin homology (PH) domain containing"	9874	protein-coding gene	gene with protein product	"Ras GTPase activating protein-like", "Ras protein activator like 1"	606136				9877179	Standard	NM_004841		Approved	nGAP	uc001glq.3	Q9UJF2	OTTHUMG00000035022	ENST00000462775.1:c.384+2T>C	chr1.hg19:g.178408712T>C		85.0	0.0		154.0	39.0	NM_170692	F8W755|O95174|Q2TB22|Q5TFU9	Splice_Site	SNP	ENST00000462775.1	hg19	CCDS1322.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.151339	0.78001	.	.	ENSG00000075391	ENST00000448150;ENST00000367649;ENST00000462775	.	.	.	6.02	4.89	0.63831	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.9635	0.53021	0.0:0.0674:0.0:0.9326	.	.	.	.	.	-1	.	.	.	+	.	.	RASAL2	176675335	1.000000	0.71417	0.997000	0.53966	0.921000	0.55340	5.869000	0.69613	1.099000	0.41499	0.533000	0.62120	.	.	.		0.373	RASAL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000084758.3	NM_170692	Intron	C	178408712	T	C	178408712	5	2	296	1	0	0	0	0	0	0	1	0	13079	1652	57	2	869	2	RASAL2	1	178408712	Splice_Site	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	6897696	178408712	70841909	24	42968										
ABL2	27	hgsc.bcm.edu	37	chr1	179112161	179112161	+	Intron	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ataactattaggtggaaggaGaactgtcccaaggaccatac	10	8	0	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:179112161G>T	ENST00000502732.1	-	2	361				ABL2_ENST00000392043.3_Intron|ABL2_ENST00000344730.3_Missense_Mutation_p.L7I|ABL2_ENST00000408940.3_Missense_Mutation_p.L7I|ABL2_ENST00000504405.1_Missense_Mutation_p.L7I|ABL2_ENST00000507173.1_Intron|ABL2_ENST00000512653.1_Missense_Mutation_p.L7I|ABL2_ENST00000367623.4_Intron|ABL2_ENST00000511413.1_Intron	NM_001168236.1|NM_001168237.1|NM_001168238.1|NM_007314.3	NP_001161708.1|NP_001161709.1|NP_001161710.1|NP_009298.1	P42684	ABL2_HUMAN	ABL proto-oncogene 2, non-receptor tyrosine kinase						actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular protein modification process (GO:0006464)|cellular response to retinoic acid (GO:0071300)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of neuron projection development (GO:0010976)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phospholipase C activity (GO:0010863)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)			breast(8)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	65					Adenosine triphosphate(DB00171)|Dasatinib(DB01254)	GGTGGAAGGAGAACTGTCCCA	0.458			T	ETV6	AML																																p.L7I		Atlas-SNP	.		Dom	yes		1	1q24-q25	27	v-abl Abelson murine leukemia viral oncogene homolog 2		L	.	ABL2	307	.	0			c.C19A						.						101	98	99					1																	179112161		1950	4141	6091	SO:0001627	intron_variant	27	exon1			GAAGGAGAACTGT	M14904	CCDS30947.1, CCDS41441.1, CCDS44282.1, CCDS44283.1, CCDS41441.2, CCDS53435.1, CCDS53436.1, CCDS53437.1, CCDS53438.1	1q25.2	2014-06-26	2014-06-26		ENSG00000143322	ENSG00000143322		"SH2 domain containing"	77	protein-coding gene	gene with protein product	"Abelson-related gene"	164690	"v-abl Abelson murine leukemia viral oncogene homolog 2 (arg, Abelson-related gene)", "v-abl Abelson murine leukemia viral oncogene homolog 2", "c-abl oncogene 2, non-receptor tyrosine kinase"	ABLL		3787260	Standard	NM_001136001		Approved	ARG	uc001gmi.4	P42684	OTTHUMG00000035199	ENST00000502732.1:c.158-9652C>A	chr1.hg19:g.179112161G>T		126.0	0.0		170.0	44.0	NM_001136000	A0M8X0|B7UEF2|B7UEF3|B7UEF4|B7UEF5|Q5T0X6|Q5W0C5|Q6NZY6|Q7Z301	Missense_Mutation	SNP	ENST00000502732.1	hg19	CCDS30947.1	.	.	.	.	.	.	.	.	.	.	G	11.71	1.718852	0.30503	.	.	ENSG00000143322	ENST00000408940;ENST00000344730;ENST00000512653;ENST00000504405	T;T;T;T	0.76186	-0.98;-0.91;-0.92;-1.0	5.62	2.73	0.32206	.	.	.	.	.	T	0.59783	0.2219	.	.	.	0.21220	N	0.999756	B;B;B;B;B;B	0.32968	0.003;0.392;0.392;0.01;0.006;0.003	B;B;B;B;B;B	0.25140	0.007;0.058;0.058;0.007;0.003;0.007	T	0.53344	-0.8452	8	0.66056	D	0.02	.	6.3642	0.21445	0.1635:0.1524:0.6841:0.0	.	7;7;7;7;7;7	P42684-4;P42684-9;P42684-2;P42684-3;D1MPS6;P42684-10	.;.;.;.;.;.	I	7	ENSP00000386152:L7I;ENSP00000339209:L7I;ENSP00000423578:L7I;ENSP00000426831:L7I	ENSP00000339209:L7I	L	-	1	0	ABL2	177378784	1.000000	0.71417	0.897000	0.35233	0.399000	0.30720	2.343000	0.44001	0.726000	0.32339	-0.136000	0.14681	CTC	.	.		0.458	ABL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085174.3	NM_005158		T	179112161	G	T	179112161	1	4	296	0	1	0	0	0	0	0	0	0	93	942	33	3		3	ABL2	1	179112161	Intron	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10	703449	179112161	70138460	25	42969										
CAMSAP1L1	23271	hgsc.bcm.edu	37	chr1	200819254	200819254	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	attgaagtttccctctcagaTttgaaaccccctgaaaaggc	7	11	1	4			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:200819254T>C	ENST00000236925.4	+	12	3439	c.3390T>C	c.(3388-3390)gaT>gaC	p.D1130D	CAMSAP2_ENST00000413307.2_Silent_p.D1103D|CAMSAP2_ENST00000358823.2_Silent_p.D1119D			Q08AD1	CAMP2_HUMAN	calmodulin regulated spectrin-associated protein family, member 2	1130					microtubule cytoskeleton organization (GO:0000226)|regulation of organelle organization (GO:0033043)	cytoplasm (GO:0005737)|microtubule minus-end (GO:0036449)	microtubule minus-end binding (GO:0051011)										CCCTCTCAGATTTGAAACCCC	0.408																																					p.D1119D		Atlas-SNP	.											.	.	.	.	0			c.T3357C						.						109	121	117					1																	200819254		2203	4300	6503	SO:0001819	synonymous_variant	23271	exon11			CTCAGATTTGAAA	AB029001	CCDS1404.1, CCDS72998.1, CCDS72999.1	1q32	2011-08-18	2011-08-18	2011-08-18	ENSG00000118200	ENSG00000118200			29188	protein-coding gene	gene with protein product		613775	"calmodulin regulated spectrin-associated protein 1-like 1"	CAMSAP1L1		15897902, 19508979	Standard	XM_005245040		Approved	KIAA1078	uc001gvk.3	Q08AD1	OTTHUMG00000035740	ENST00000236925.4:c.3390T>C	chr1.hg19:g.200819254T>C		211.0	0.0		300.0	163.0	NM_203459	B1APG6|Q08AD2|Q6PGN8|Q96FB3|Q9UG20|Q9UPS4	Silent	SNP	ENST00000236925.4	hg19																																																																																				.	.		0.408	CAMSAP2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086956.2	NM_203459		C	200819254	T	C	200819254	2	2	296	1	0	0	0	0	0	0	0	1	2614	1490	52	2		2	CAMSAP1L1	1	200819254	Silent	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	21707093	200819254	48431367	26	42970										
PTPN7	5778	hgsc.bcm.edu	37	chr1	202119444	202119444	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	cacccacagacccacctgtcTagccgcagttggcacacaat	7	17	1	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:202119444T>G	ENST00000308986.5	-	9	1114	c.984A>C	c.(982-984)ctA>ctC	p.L328L	PTPN7_ENST00000543735.1_Silent_p.L157L|PTPN7_ENST00000492977.1_5'UTR|PTPN7_ENST00000367279.4_Silent_p.L367L|PTPN7_ENST00000544762.1_Silent_p.L104L|PTPN7_ENST00000309017.3_Silent_p.L433L			P35236	PTN7_HUMAN	protein tyrosine phosphatase, non-receptor type 7	328	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)|soft_tissue(1)|urinary_tract(1)	13						CCCACCTGTCTAGCCGCAGTT	0.567																																					p.L433L		Atlas-SNP	.											.	PTPN7	31	.	0			c.A1299C						.						76	59	65					1																	202119444		2203	4300	6503	SO:0001819	synonymous_variant	5778	exon9			CCTGTCTAGCCGC	BC001746	CCDS1422.1, CCDS1423.1, CCDS1423.2	1q32.1	2011-06-09			ENSG00000143851	ENSG00000143851		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9659	protein-coding gene	gene with protein product		176889				1510684	Standard	NM_002832		Approved	HEPTP, LC-PTP	uc010ppx.2	P35236	OTTHUMG00000035931	ENST00000308986.5:c.984A>C	chr1.hg19:g.202119444T>G		114.0	0.0		105.0	30.0	NM_002832	B3KXE1|Q53XK4|Q5SXQ0|Q5SXQ1|Q9BV05	Silent	SNP	ENST00000308986.5	hg19																																																																																				.	.		0.567	PTPN7-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_002832		G	202119444	T	G	202119444	2	3	296	1	0	0	0	0	0	0	0	1	12808	1509	53	5		5	PTPN7	1	202119444	Silent	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	1300190	202119444	47131177	27	42971										
LGR6	59352	hgsc.bcm.edu	37	chr1	202163198	202163198	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	agggccggcggcgccccccaGcccggcccggggcccaccgc	16	22	0	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:202163198G>T	ENST00000367278.3	+	1	170	c.81G>T	c.(79-81)caG>caT	p.Q27H		NM_001017403.1	NP_001017403.1	Q9HBX8	LGR6_HUMAN	leucine-rich repeat containing G protein-coupled receptor 6	27	LRRNT.				G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of Wnt signaling pathway (GO:0030177)|Wnt signaling pathway (GO:0016055)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	36						gcgccccccagcccggcccgg	0.771																																					p.Q27H		Atlas-SNP	.											.	LGR6	102	.	0			c.G81T						.						3	3	3					1																	202163198		1342	2962	4304	SO:0001583	missense	59352	exon1			CCCCCAGCCCGGC	AF190501	CCDS1424.1, CCDS30971.1, CCDS30972.1	1q32.1	2012-08-21	2011-01-25		ENSG00000133067	ENSG00000133067		"GPCR / Class A : Orphans"	19719	protein-coding gene	gene with protein product		606653	"leucine-rich repeat-containing G protein-coupled receptor 6"			10935549	Standard	XM_005245404		Approved	FLJ14471	uc001gxu.3	Q9HBX8	OTTHUMG00000041383	ENST00000367278.3:c.81G>T	chr1.hg19:g.202163198G>T	ENSP00000356247:p.Gln27His	15.0	0.0		28.0	9.0	NM_001017403	Q5T509|Q5T512|Q6UY15|Q86VU0|Q96K69|Q9BYD7	Missense_Mutation	SNP	ENST00000367278.3	hg19	CCDS30971.1	.	.	.	.	.	.	.	.	.	.	G	9.610	1.130892	0.21041	.	.	ENSG00000133067	ENST00000367278	T	0.60920	0.15	3.74	3.74	0.42951	.	1.063570	0.07431	U	0.895695	T	0.45438	0.1342	L	0.36672	1.1	0.80722	D	1	P	0.36438	0.553	B	0.28849	0.095	T	0.39840	-0.9594	10	0.45353	T	0.12	.	9.0658	0.36462	0.1066:0.0:0.8934:0.0	.	27	Q9HBX8	LGR6_HUMAN	H	27	ENSP00000356247:Q27H	ENSP00000356247:Q27H	Q	+	3	2	LGR6	200429821	0.991000	0.36638	0.528000	0.27938	0.105000	0.19272	2.672000	0.46850	1.777000	0.52277	0.305000	0.20034	CAG	.	.		0.771	LGR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099143.1	NM_021636		T	202163198	G	T	202163198	3	4	296	1	0	0	0	0	1	0	0	0	8767	962	34	3	83	3	LGR6	1	202163198	Missense_Mutation	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10	43754	202163198	47087423	28	42972										
HSD11B1	3290	hgsc.bcm.edu	37	chr1	209879238	209879239	+	Frame_Shift_Ins	INS	-	-	GGAGCCCATGTGGT													0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	cttatcatctggcgaagatgINSggagcccatgtggtggtgac							TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:209879238_209879239insGGAGCCCATGTGGT	ENST00000367028.2	+	3	340_341	c.171_172insGGAGCCCATGTGGT	c.(172-174)ggafs	p.-62fs	RP1-28O10.1_ENST00000441672.1_RNA|HSD11B1_ENST00000261465.1_Frame_Shift_Ins_p.-62fs|HSD11B1_ENST00000367027.3_Frame_Shift_Ins_p.-62fs	NM_001206741.1	NP_001193670.1	P28845	DHI1_HUMAN	hydroxysteroid (11-beta) dehydrogenase 1						glucocorticoid biosynthetic process (GO:0006704)|lung development (GO:0030324)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	11-beta-hydroxysteroid dehydrogenase (NADP+) activity (GO:0070524)|11-beta-hydroxysteroid dehydrogenase [NAD(P)] activity (GO:0003845)			breast(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(9)	16				OV - Ovarian serous cystadenocarcinoma(81;1.04e-55)|Epithelial(68;1.57e-52)|all cancers(67;1.83e-46)|Colorectal(1306;0.115)	Prednisone(DB00635)	TGGCGAAGATGGGAGCCCATGT	0.51																																					p.M57fs		Atlas-Indel,Pindel	.											.	HSD11B1	35	.	0			c.171_172insGGAGCCCATGTGGT						.																																			SO:0001589	frameshift_variant	3290	exon2			.	BC012593	CCDS1489.1	1q32-q41	2011-09-20			ENSG00000117594	ENSG00000117594	1.1.1.146	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	5208	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 26C, member 1"	600713		HSD11B, HSD11		1885595, 19027726	Standard	NM_005525		Approved	SDR26C1	uc001hhk.3	P28845	OTTHUMG00000036481	ENST00000367028.2:c.172_185dupGGAGCCCATGTGGT	chr1.hg19:g.209879238_209879239insGGAGCCCATGTGGT	ENSP00000355995:p.Val62fs	132.0	0.0		136.0	16.0	NM_005525	B2R9Z1|D3DT89	Frame_Shift_Ins	INS	ENST00000367028.2	hg19	CCDS1489.1																																																																																			.	.		0.51	HSD11B1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088743.2	NM_005525		GGAGCCCATGTGGT	209879239	-	GGAGCCCATGTGGT	209879238	7	5	296	1	0	1	1	0	0	0	0	0	7384	1348	47	0	177	0	HSD11B1	1	209879238	Frame_Shift_Ins	INS	-	TCGA-G3-AAV0-01A-11D-A36X-10	7716040	209879238	39371383	29	42973										
SYT14	255928	hgsc.bcm.edu	37	chr1	210334239	210334239	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	actcatactgtctgtgtataAcaaacgcagcatgaaaagaa	7	8	2	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:210334239A>G	ENST00000472886.1	+	8	1534	c.1520A>G	c.(1519-1521)aAc>aGc	p.N507S	SYT14_ENST00000422431.1_Missense_Mutation_p.N571S|SYT14_ENST00000271745.7_3'UTR|SYT14_ENST00000399639.2_3'UTR|SYT14_ENST00000537238.1_Missense_Mutation_p.N469S|SYT14_ENST00000367019.1_Missense_Mutation_p.N526S|SYT14_ENST00000367015.1_Missense_Mutation_p.N469S|SYT14_ENST00000534859.1_Missense_Mutation_p.N533S			Q8NB59	SYT14_HUMAN	synaptotagmin XIV	507	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				cell death (GO:0008219)	integral component of membrane (GO:0016021)	phospholipid binding (GO:0005543)			endometrium(4)|large_intestine(11)|lung(17)|ovary(1)|prostate(1)|skin(3)	37				OV - Ovarian serous cystadenocarcinoma(81;0.085)		TCTGTGTATAACAAACGCAGC	0.413																																					p.N571S		Atlas-SNP	.											.	SYT14	89	.	0			c.A1712G						.						146	143	144					1																	210334239		2203	4299	6502	SO:0001583	missense	255928	exon10			TGTATAACAAACG	AK091517	CCDS31014.1, CCDS53470.1, CCDS58058.1	1q32.2	2013-01-21			ENSG00000143469	ENSG00000143469		"Synaptotagmins"	23143	protein-coding gene	gene with protein product		610949					Standard	NM_001256006		Approved	sytXIV, FLJ34198	uc001hhs.5	Q8NB59	OTTHUMG00000036652	ENST00000472886.1:c.1520A>G	chr1.hg19:g.210334239A>G	ENSP00000418901:p.Asn507Ser	159.0	0.0		181.0	49.0	NM_001146261	B1AJU0|B1AJU1|F5H426|Q5THX7|Q707N3|Q707N4|Q707N5|Q707N6|Q707N7	Missense_Mutation	SNP	ENST00000472886.1	hg19	CCDS31014.1	.	.	.	.	.	.	.	.	.	.	A	8.561	0.877760	0.17395	.	.	ENSG00000143469	ENST00000422431;ENST00000534859;ENST00000537238;ENST00000367019;ENST00000472886;ENST00000367015	T;T;T;T;T;T	0.72167	-0.63;-0.63;-0.63;-0.63;-0.63;-0.63	5.54	4.39	0.52855	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.145255	0.64402	D	0.000012	T	0.59742	0.2216	N	0.26162	0.8	0.50039	D	0.999846	B;B;B;B	0.32338	0.198;0.08;0.15;0.365	B;B;B;B	0.35607	0.206;0.05;0.082;0.131	T	0.57562	-0.7790	10	0.41790	T	0.15	-6.2841	12.4631	0.55743	0.8287:0.1713:0.0:0.0	.	554;507;526;571	A1L3Y1;Q8NB59;Q8NB59-6;F5H426	.;SYT14_HUMAN;.;.	S	571;533;469;526;507;469	ENSP00000389039:N571S;ENSP00000442891:N533S;ENSP00000437423:N469S;ENSP00000355986:N526S;ENSP00000418901:N507S;ENSP00000355982:N469S	ENSP00000355982:N469S	N	+	2	0	SYT14	208400862	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.302000	0.51849	0.963000	0.38082	0.477000	0.44152	AAC	.	.		0.413	SYT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089124.1	NM_153262		G	210334239	A	G	210334239	3	3	296	1	0	0	0	0	1	0	0	0	15485	43	2	2	1750	2	SYT14	1	210334239	Missense_Mutation	SNP	A	TCGA-G3-AAV0-01A-11D-A36X-10	455001	210334239	38916382	30	42974										
SPATA17	128153	hgsc.bcm.edu	37	chr1	217822303	217822303	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ttcgaggatgtcaagttcggGcatatatcaggtatattgct	11	6	2	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:217822303G>A	ENST00000366933.4	+	2	203	c.148G>A	c.(148-150)Gca>Aca	p.A50T		NM_138796.2	NP_620151.1	Q96L03	SPT17_HUMAN	spermatogenesis associated 17	50	IQ 1. {ECO:0000255|PROSITE- ProRule:PRU00116}.					cytoplasm (GO:0005737)				endometrium(1)|kidney(1)|large_intestine(9)|lung(6)|pancreas(2)|prostate(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(81;0.0516)|all cancers(67;0.0891)|GBM - Glioblastoma multiforme(131;0.117)		TCAAGTTCGGGCATATATCAG	0.299																																					p.A50T		Atlas-SNP	.											.	SPATA17	59	.	0			c.G148A						.						116	114	115					1																	217822303		2203	4299	6502	SO:0001583	missense	128153	exon2			GTTCGGGCATATA	AK098591	CCDS1519.1	1q41	2008-02-05			ENSG00000162814	ENSG00000162814			25184	protein-coding gene	gene with protein product	"IQ motif containing H"	611032				16395525	Standard	NM_138796		Approved	IQCH	uc001hlh.1	Q96L03	OTTHUMG00000037875	ENST00000366933.4:c.148G>A	chr1.hg19:g.217822303G>A	ENSP00000355900:p.Ala50Thr	90.0	0.0		168.0	93.0	NM_138796	A5D6N2	Missense_Mutation	SNP	ENST00000366933.4	hg19	CCDS1519.1	.	.	.	.	.	.	.	.	.	.	G	16.73	3.205169	0.58234	.	.	ENSG00000162814	ENST00000366933	T	0.25085	1.82	5.33	5.33	0.75918	.	0.059144	0.64402	D	0.000003	T	0.34687	0.0906	M	0.79475	2.455	0.42444	D	0.992727	P	0.37083	0.581	B	0.39258	0.295	T	0.14309	-1.0477	10	0.38643	T	0.18	-15.578	14.8927	0.70620	0.0:0.0:1.0:0.0	.	50	Q96L03	SPT17_HUMAN	T	50	ENSP00000355900:A50T	ENSP00000355900:A50T	A	+	1	0	SPATA17	215888926	1.000000	0.71417	0.974000	0.42286	0.947000	0.59692	3.078000	0.50096	2.655000	0.90218	0.650000	0.86243	GCA	.	.		0.299	SPATA17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092433.2	NM_138796		A	217822303	G	A	217822303	3	1	296	1	0	0	0	0	1	0	0	0	15017	1203	42	3	154	3	SPATA17	1	217822303	Missense_Mutation	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10	7488064	217822303	31428318	31	42975										
AHCTF1	25909	hgsc.bcm.edu	37	chr1	247027263	247027263	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tttcaagcaaatgtaattctGaagccctggagatggcctga	10	8	2	3			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:247027263G>T	ENST00000391829.2	-	27	3626	c.3503C>A	c.(3502-3504)tCa>tAa	p.S1168*	AHCTF1_ENST00000326225.3_Nonsense_Mutation_p.S1177*|AHCTF1_ENST00000366508.1_Nonsense_Mutation_p.S1203*|AHCTF1_ENST00000470300.1_5'UTR			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	1168	Disordered. {ECO:0000250}.|Necessary for nuclear localization. {ECO:0000250}.				cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(6)|cervix(3)|endometrium(8)|kidney(6)|large_intestine(12)|liver(2)|lung(21)|ovary(5)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	74	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			ATGTAATTCTGAAGCCCTGGA	0.418																																					p.S1177X	Colon(145;197 1800 4745 15099 26333)	Atlas-SNP	.											.	AHCTF1	187	.	0			c.C3530A						.						87	93	91					1																	247027263		2203	4300	6503	SO:0001587	stop_gained	25909	exon27			AATTCTGAAGCCC		CCDS1629.1, CCDS1629.2	1q44	2008-09-09			ENSG00000153207	ENSG00000153207			24618	protein-coding gene	gene with protein product	"ELYS transcription factor like protein TMBS62"	610853				11952839	Standard	NM_015446		Approved	ELYS	uc001ibv.2	Q8WYP5	OTTHUMG00000040706	ENST00000391829.2:c.3503C>A	chr1.hg19:g.247027263G>T	ENSP00000375705:p.Ser1168*	198.0	0.0		318.0	28.0	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Nonsense_Mutation	SNP	ENST00000391829.2	hg19		.	.	.	.	.	.	.	.	.	.	G	41	8.802195	0.98960	.	.	ENSG00000153207	ENST00000366508;ENST00000326225;ENST00000391829	.	.	.	5.82	4.92	0.64577	.	0.327598	0.30020	N	0.010613	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.6241	13.1694	0.59589	0.0733:0.0:0.9267:0.0	.	.	.	.	X	1203;1177;1168	.	ENSP00000355465:S1177X	S	-	2	0	AHCTF1	245093886	1.000000	0.71417	0.988000	0.46212	0.175000	0.22909	3.486000	0.53215	1.483000	0.48342	0.650000	0.86243	TCA	.	.		0.418	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446		T	247027263	G	T	247027263	4	4	296	1	0	0	0	0	0	1	0	0	408	1294	45	3	3337	3	AHCTF1	1	247027263	Nonsense_Mutation	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10	29204960	247027263	2223358	32	42976										
OR2G2	81470	hgsc.bcm.edu	37	chr1	247751681	247751681	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tatggggatggtgagacataCcaatgagagcaacctagcag	13	7	0	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:247751681C>A	ENST00000320065.1	+	1	20	c.20C>A	c.(19-21)aCc>aAc	p.T7N	RP11-978I15.10_ENST00000446347.1_RNA|RP11-978I15.10_ENST00000435333.1_RNA	NM_001001915.1	NP_001001915.1	Q8NGZ5	OR2G2_HUMAN	olfactory receptor, family 2, subfamily G, member 2	7						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(4)|large_intestine(3)|lung(30)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			GTGAGACATACCAATGAGAGC	0.398																																					p.T7N		Atlas-SNP	.											.	OR2G2	88	.	0			c.C20A						.						159	147	151					1																	247751681		2203	4300	6503	SO:0001583	missense	81470	exon1			GACATACCAATGA	BK004472	CCDS31092.1	1q44	2012-08-09	2008-05-23		ENSG00000177489	ENSG00000177489		"GPCR / Class A : Olfactory receptors"	15007	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily G, member 2", "olfactory receptor, family 2, subfamily G, member 2 pseudogene"				Standard	NM_001001915		Approved		uc010pyy.2	Q8NGZ5	OTTHUMG00000040575	ENST00000320065.1:c.20C>A	chr1.hg19:g.247751681C>A	ENSP00000326349:p.Thr7Asn	113.0	0.0		171.0	51.0	NM_001001915	Q5JQT2|Q6IEZ0	Missense_Mutation	SNP	ENST00000320065.1	hg19	CCDS31092.1	.	.	.	.	.	.	.	.	.	.	C	4.228	0.041136	0.08196	.	.	ENSG00000177489	ENST00000320065	T	0.00265	8.39	3.57	-0.81	0.10860	.	0.600527	0.12505	U	0.463024	T	0.00073	0.0002	N	0.11023	0.085	0.09310	N	1	B	0.18741	0.03	B	0.09377	0.004	T	0.03840	-1.0999	10	0.13108	T	0.6	.	2.94	0.05826	0.1969:0.4596:0.0:0.3435	.	7	Q8NGZ5	OR2G2_HUMAN	N	7	ENSP00000326349:T7N	ENSP00000326349:T7N	T	+	2	0	OR2G2	245818304	0.145000	0.22656	0.000000	0.03702	0.018000	0.09664	0.300000	0.19156	-0.287000	0.09064	0.591000	0.81541	ACC	.	.		0.398	OR2G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097623.1			A	247751681	C	A	247751681	3	1	296	1	0	0	0	0	1	0	0	0	11007	507	18	3	22	3	OR2G2	1	247751681	Missense_Mutation	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	724418	247751681	1498940	33	42977										
OR2T3	343173	hgsc.bcm.edu	37	chr1	248637531	248637531	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ctcctgtgctgaaccccctcAtttacagtctccgcaacaaa	5	16	2	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr1:248637531A>T	ENST00000359594.2	+	1	905	c.880A>T	c.(880-882)Att>Ttt	p.I294F		NM_001005495.1	NP_001005495.1	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T, member 3	294						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(5)|lung(19)|ovary(1)|prostate(1)|skin(3)	31	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GAACCCCCTCATTTACAGTCT	0.498																																					p.I294F		Atlas-SNP	.											.	OR2T3	79	.	0			c.A880T						.						126	128	128					1																	248637531		2201	4277	6478	SO:0001583	missense	343173	exon1			CCCCTCATTTACA		CCDS31117.1	1q44	2012-08-09			ENSG00000196539	ENSG00000196539		"GPCR / Class A : Olfactory receptors"	14727	protein-coding gene	gene with protein product							Standard	NM_001005495		Approved		uc001iel.1	Q8NH03	OTTHUMG00000040452	ENST00000359594.2:c.880A>T	chr1.hg19:g.248637531A>T	ENSP00000352604:p.Ile294Phe	912.0	0.0		1255.0	159.0	NM_001005495	B2RNJ1	Missense_Mutation	SNP	ENST00000359594.2	hg19	CCDS31117.1	.	.	.	.	.	.	.	.	.	.	a	11.32	1.602647	0.28534	.	.	ENSG00000196539	ENST00000359594	T	0.57107	0.42	2.37	-0.371	0.12525	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.62684	0.2448	M	0.84219	2.685	0.09310	N	1	P	0.49862	0.929	P	0.53689	0.732	T	0.55321	-0.8159	9	0.87932	D	0	.	6.2504	0.20842	0.7015:0.0:0.2985:0.0	.	294	Q8NH03	OR2T3_HUMAN	F	294	ENSP00000352604:I294F	ENSP00000352604:I294F	I	+	1	0	OR2T3	246704154	0.619000	0.27059	0.003000	0.11579	0.069000	0.16628	1.324000	0.33712	-0.459000	0.07013	-1.388000	0.01159	ATT	.	.		0.498	OR2T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097348.1	NM_001005495		T	248637531	A	T	248637531	3	4	296	1	0	0	0	0	1	0	0	0	11032	217	8	4	882	4	OR2T3	1	248637531	Missense_Mutation	SNP	A	TCGA-G3-AAV0-01A-11D-A36X-10	885850	248637531	613090	34	42978										
RSAD2	91543	hgsc.bcm.edu	37	chr2	7017965	7017965	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	cacctgctgcttttgctgggAagctcttgagtgtgttcagg	13	9	2	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr2:7017965A>T	ENST00000382040.3	+	1	170	c.34A>T	c.(34-36)Aag>Tag	p.K12*	RSAD2_ENST00000541728.1_5'Flank	NM_080657.4	NP_542388.2			radical S-adenosyl methionine domain containing 2											endometrium(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(1)	20	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			OV - Ovarian serous cystadenocarcinoma(76;0.191)		TTTTGCTGGGAAGCTCTTGAG	0.542																																					p.K12X		Atlas-SNP	.											.	RSAD2	38	.	0			c.A34T						.						76	71	73					2																	7017965		2203	4300	6503	SO:0001587	stop_gained	91543	exon1			GCTGGGAAGCTCT	AF442151	CCDS1656.1	2p25.2	2008-02-05			ENSG00000134321	ENSG00000134321			30908	protein-coding gene	gene with protein product		607810				11752458	Standard	NM_080657		Approved	cig5, viperin, vig1	uc002qyp.1	Q8WXG1	OTTHUMG00000090352	ENST00000382040.3:c.34A>T	chr2.hg19:g.7017965A>T	ENSP00000371471:p.Lys12*	72.0	0.0		131.0	40.0	NM_080657		Nonsense_Mutation	SNP	ENST00000382040.3	hg19	CCDS1656.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.389101	0.82902	.	.	ENSG00000134321	ENST00000382040	.	.	.	5.31	1.47	0.22746	.	0.910843	0.09520	N	0.791097	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.05351	T	0.99	-12.0684	5.7876	0.18343	0.6063:0.2397:0.154:0.0	.	.	.	.	X	12	.	ENSP00000371471:K12X	K	+	1	0	RSAD2	6935416	0.001000	0.12720	0.000000	0.03702	0.009000	0.06853	0.068000	0.14531	0.075000	0.16796	0.460000	0.39030	AAG	.	.		0.542	RSAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206724.2	NM_080657		T	7017965	A	T	7017965	4	4	296	1	0	0	0	0	0	1	0	0	13710	247	9	4	36	4	RSAD2	2	7017965	Nonsense_Mutation	SNP	A	TCGA-G3-AAV0-01A-11D-A36X-10		7017965	236181408	35	42979										
PDIA6	10130	hgsc.bcm.edu	37	chr2	10937247	10937247	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tttttgttggatccaaaaatCttaatggtaggaaatccctg	8	6	1	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr2:10937247C>A	ENST00000272227.3	-	4	453	c.306G>T	c.(304-306)aaG>aaT	p.K102N	PDIA6_ENST00000404371.2_Missense_Mutation_p.K154N|PDIA6_ENST00000404824.2_Missense_Mutation_p.K150N|PDIA6_ENST00000381611.4_Missense_Mutation_p.K107N|PDIA6_ENST00000489662.1_5'UTR|PDIA6_ENST00000540494.1_Missense_Mutation_p.K99N	NM_001282707.1|NM_005742.2	NP_001269636.1|NP_005733.1	Q15084	PDIA6_HUMAN	protein disulfide isomerase family A, member 6	102	Thioredoxin 1. {ECO:0000255|PROSITE- ProRule:PRU00691}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic cell clearance (GO:0043277)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	protein disulfide isomerase activity (GO:0003756)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|prostate(2)	18	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.149)|OV - Ovarian serous cystadenocarcinoma(76;0.15)		ATCCAAAAATCTTAATGGTAG	0.408																																					p.K102N	GBM(73;509 1219 34219 41343 41551)	Atlas-SNP	.											.	PDIA6	31	.	0			c.G306T						.						176	173	174					2																	10937247		2203	4300	6503	SO:0001583	missense	10130	exon4			AAAAATCTTAATG	BC001312	CCDS1675.1, CCDS62852.1, CCDS62853.1, CCDS62854.1, CCDS62855.1	2p25.1	2009-11-20	2005-06-29	2005-03-03	ENSG00000143870	ENSG00000143870	5.3.4.1	"Protein disulfide isomerases"	30168	protein-coding gene	gene with protein product	"protein disulfide isomerase-related protein"	611099	"thioredoxin domain containing 7 (protein disulfide isomerase)", "protein disulfide isomerase-associated 6"	TXNDC7		7590364, 12204115	Standard	XM_005246145		Approved	P5, ERp5	uc002rau.3	Q15084	OTTHUMG00000090479	ENST00000272227.3:c.306G>T	chr2.hg19:g.10937247C>A	ENSP00000272227:p.Lys102Asn	119.0	0.0		163.0	46.0	NM_005742	B3KY95|B5MCQ5|B7Z254|B7Z4M8|F8WA83|Q53RC7|Q6ZSH5|Q99778	Missense_Mutation	SNP	ENST00000272227.3	hg19	CCDS1675.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.969369	0.92855	.	.	ENSG00000143870	ENST00000272227;ENST00000404371;ENST00000404824;ENST00000540494;ENST00000381611	T;T;T;T;T	0.41400	1.0;1.0;1.0;1.0;1.0	5.86	5.86	0.93980	Thioredoxin domain (1);Thioredoxin-like fold (3);Disulphide isomerase (1);	0.040380	0.85682	D	0.000000	T	0.74824	0.3767	H	0.96175	3.78	0.80722	D	1	B;D;D;P	0.89917	0.246;1.0;1.0;0.823	P;D;D;P	0.97110	0.514;1.0;0.999;0.818	T	0.81714	-0.0807	10	0.87932	D	0	.	13.7319	0.62792	0.0:0.9298:0.0:0.0702	.	99;150;154;102	B7Z254;B5MCQ5;Q15084-2;Q15084	.;.;.;PDIA6_HUMAN	N	102;154;150;99;107	ENSP00000272227:K102N;ENSP00000385385:K154N;ENSP00000384459:K150N;ENSP00000438778:K99N;ENSP00000371024:K107N	ENSP00000272227:K102N	K	-	3	2	PDIA6	10854698	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.992000	0.56980	2.937000	0.99478	0.650000	0.86243	AAG	.	.		0.408	PDIA6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206933.1	NM_005742		A	10937247	C	A	10937247	3	1	296	1	0	0	0	0	1	0	0	0	11681	912	32	3	1056	3	PDIA6	2	10937247	Missense_Mutation	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	3919282	10937247	232262126	36	42980										
UBXN2A	165324	hgsc.bcm.edu	37	chr2	24199886	24199886	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	aacggattcaccgtcaacgaCgatttcagaagttattccga	8	10	3	1	rs538162030	byFrequency	TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr2:24199886C>G	ENST00000309033.4	+	4	472	c.228C>G	c.(226-228)gaC>gaG	p.D76E	UBXN2A_ENST00000446425.2_3'UTR|UBXN2A_ENST00000535786.1_Missense_Mutation_p.D76E|UBXN2A_ENST00000404924.1_Missense_Mutation_p.D76E	NM_181713.3	NP_859064.2	P68543	UBX2A_HUMAN	UBX domain protein 2A	76	SEP. {ECO:0000255|PROSITE- ProRule:PRU00732}.				regulation of gene expression (GO:0010468)|regulation of protein catabolic process (GO:0042176)|regulation of protein ubiquitination (GO:0031396)	cis-Golgi network (GO:0005801)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)				endometrium(1)|large_intestine(3)|liver(1)|lung(6)	11						CCGTCAACGACGATTTCAGAA	0.393																																					p.D76E		Atlas-SNP	.											.	UBXN2A	20	.	0			c.C228G						.						80	77	78					2																	24199886		2203	4300	6503	SO:0001583	missense	165324	exon4			CAACGACGATTTC	BC037901	CCDS1704.1	2p24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000173960	ENSG00000173960		"UBX domain containing"	27265	protein-coding gene	gene with protein product			"UBX domain containing 4"	UBXD4		12477932	Standard	NM_181713		Approved		uc002ren.3	P68543	OTTHUMG00000125497	ENST00000309033.4:c.228C>G	chr2.hg19:g.24199886C>G	ENSP00000312107:p.Asp76Glu	48.0	0.0		110.0	22.0	NM_181713	A8K577|B7ZKP8|Q569G8	Missense_Mutation	SNP	ENST00000309033.4	hg19	CCDS1704.1	.	.	.	.	.	.	.	.	.	.	C	15.53	2.859909	0.51482	.	.	ENSG00000173960	ENST00000404924;ENST00000309033;ENST00000535786	T;T;T	0.68025	-0.07;-0.07;-0.3	4.81	2.39	0.29439	SEP domain (4);	0.145094	0.64402	D	0.000013	T	0.74313	0.3700	M	0.74258	2.255	0.29087	N	0.882318	D;P	0.62365	0.991;0.925	P;P	0.59546	0.859;0.619	T	0.68625	-0.5359	10	0.56958	D	0.05	5.3368	7.6482	0.28334	0.0:0.2538:0.0:0.7462	.	76;76	B7ZKP8;P68543	.;UBX2A_HUMAN	E	76	ENSP00000385525:D76E;ENSP00000312107:D76E;ENSP00000440533:D76E	ENSP00000312107:D76E	D	+	3	2	UBXN2A	24053390	0.994000	0.37717	0.999000	0.59377	0.390000	0.30446	0.065000	0.14466	0.397000	0.25310	-0.340000	0.08031	GAC	.	.		0.393	UBXN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246824.2	NM_181713		G	24199886	C	G	24199886	3	3	296	1	0	0	0	0	1	0	0	0	16929	535	19	4	238	4	UBXN2A	2	24199886	Missense_Mutation	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	13262639	24199886	218999487	37	42981										
NCOA1	8648	hgsc.bcm.edu	37	chr2	24929659	24929659	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tctagcaacagccaaggaagTttcggatgctcacccggaag	11	11	2	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr2:24929659T>C	ENST00000406961.1	+	13	1972	c.1320T>C	c.(1318-1320)agT>agC	p.S440S	NCOA1_ENST00000288599.5_Silent_p.S440S|NCOA1_ENST00000395856.3_Silent_p.S440S|NCOA1_ENST00000538539.1_Silent_p.S440S|NCOA1_ENST00000405141.1_Silent_p.S440S|NCOA1_ENST00000348332.3_Silent_p.S440S|NCOA1_ENST00000407230.1_Silent_p.S289S			Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1	440	Interaction with STAT3.|Ser-rich.				androgen receptor signaling pathway (GO:0030521)|cellular lipid metabolic process (GO:0044255)|cellular response to hormone stimulus (GO:0032870)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|estrous cycle phase (GO:0060206)|hippocampus development (GO:0021766)|histone H4 acetylation (GO:0043967)|hypothalamus development (GO:0021854)|labyrinthine layer morphogenesis (GO:0060713)|lactation (GO:0007595)|male gonad development (GO:0008584)|male mating behavior (GO:0060179)|ovulation cycle (GO:0042698)|positive regulation of apoptotic process (GO:0043065)|positive regulation of female receptivity (GO:0045925)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by galactose (GO:0000435)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular response to drug (GO:2001038)|response to estradiol (GO:0032355)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region DNA binding (GO:0001012)|RNA polymerase II transcription coactivator activity (GO:0001105)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)		PAX3/NCOA1(8)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(26)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	53	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCCAAGGAAGTTTCGGATGCT	0.463			T	PAX3	alveolar rhadomyosarcoma																																p.S440S		Atlas-SNP	.		Dom	yes		2	2p23	8648	nuclear receptor coactivator 1		M	.	NCOA1	210	.	0			c.T1320C						.						94	92	93					2																	24929659		2203	4300	6503	SO:0001819	synonymous_variant	8648	exon11			AGGAAGTTTCGGA	U40396	CCDS1712.1, CCDS1713.1, CCDS42660.1	2p23	2011-07-01			ENSG00000084676	ENSG00000084676		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7668	protein-coding gene	gene with protein product		602691				7481822, 9575154	Standard	XM_005264625		Approved	SRC1, F-SRC-1, NCoA-1, KAT13A, RIP160, bHLHe74	uc002rfk.3	Q15788	OTTHUMG00000125523	ENST00000406961.1:c.1320T>C	chr2.hg19:g.24929659T>C		148.0	0.0		180.0	47.0	NM_147223	O00150|O43792|O43793|Q13071|Q13420|Q2T9G5|Q53SX3|Q6GVI5|Q7KYV3	Silent	SNP	ENST00000406961.1	hg19	CCDS1712.1																																																																																			.	.		0.463	NCOA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246852.3	NM_147223		C	24929659	T	C	24929659	2	2	296	1	0	0	0	0	0	0	0	1	10237	1722	60	2		2	NCOA1	2	24929659	Silent	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	729773	24929659	218269714	38	42982										
SNX17	9784	hgsc.bcm.edu	37	chr2	27598432	27598432	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ttgcgctttgatgcctgtgtGgctgacttcccagaaaagga	12	9	0	3			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr2:27598432G>A	ENST00000233575.2	+	10	1056	c.834G>A	c.(832-834)gtG>gtA	p.V278V	SNX17_ENST00000543024.1_Silent_p.V64V|SNX17_ENST00000542478.1_Silent_p.V64V|ZNF513_ENST00000491924.1_5'Flank|SNX17_ENST00000537606.1_Silent_p.V253V	NM_001267059.1|NM_001267061.1|NM_014748.3	NP_001253988.1|NP_001253990.1|NP_055563.1	Q15036	SNX17_HUMAN	sorting nexin 17	278	FERM-like.|PTB-like F3 module.				cholesterol catabolic process (GO:0006707)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|receptor-mediated endocytosis (GO:0006898)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|protein complex (GO:0043234)	low-density lipoprotein particle receptor binding (GO:0050750)|phosphatidylinositol binding (GO:0035091)|protein C-terminus binding (GO:0008022)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)	14	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ATGCCTGTGTGGCTGACTTCC	0.582																																					p.V278V		Atlas-SNP	.											.	SNX17	40	.	0			c.G834A						.						91	83	86					2																	27598432		2203	4300	6503	SO:0001819	synonymous_variant	9784	exon10			CTGTGTGGCTGAC	D31764	CCDS1750.1, CCDS58704.1	2p23-p22	2008-05-21			ENSG00000115234	ENSG00000115234		"Sorting nexins"	14979	protein-coding gene	gene with protein product		605963				12169628, 15769472	Standard	NM_014748		Approved	KIAA0064	uc002rkg.2	Q15036	OTTHUMG00000097781	ENST00000233575.2:c.834G>A	chr2.hg19:g.27598432G>A		68.0	0.0		111.0	26.0	NM_014748	B4DQM7|Q53HN7|Q6IAS3	Silent	SNP	ENST00000233575.2	hg19	CCDS1750.1																																																																																			.	.		0.582	SNX17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215024.1	NM_014748		A	27598432	G	A	27598432	2	1	296	1	0	0	0	0	0	0	0	1	14903	1335	47	3		3	SNX17	2	27598432	Silent	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10	2668773	27598432	215600941	39	42983										
LTBP1	4052	hgsc.bcm.edu	37	chr2	33498742	33498742	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gaaatcaatgaatgtactgtGaaccctgatatctgtggagc	10	7	2	3			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr2:33498742G>A	ENST00000404816.2	+	16	2990	c.2637G>A	c.(2635-2637)gtG>gtA	p.V879V	LTBP1_ENST00000390003.4_Silent_p.V554V|LTBP1_ENST00000354476.3_Silent_p.V880V|LTBP1_ENST00000418533.2_Silent_p.V553V|LTBP1_ENST00000407925.1_Silent_p.V553V|LTBP1_ENST00000404525.1_Silent_p.V500V|LTBP1_ENST00000402934.1_Silent_p.V500V			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	879	EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				AATGTACTGTGAACCCTGATA	0.368																																					p.V879V		Atlas-SNP	.											.	LTBP1	317	.	0			c.G2637A						.						70	68	69					2																	33498742		2203	4300	6503	SO:0001819	synonymous_variant	4052	exon16			TACTGTGAACCCT		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"Latent transforming growth factor, beta binding proteins"	6714	protein-coding gene	gene with protein product	"TGF-beta1-BP-1"	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.2637G>A	chr2.hg19:g.33498742G>A		106.0	0.0		105.0	36.0	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Silent	SNP	ENST00000404816.2	hg19	CCDS33177.2																																																																																			.	.		0.368	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943		A	33498742	G	A	33498742	2	1	296	1	0	0	0	0	0	0	0	1	9082	1277	45	3		3	LTBP1	2	33498742	Silent	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10	5900310	33498742	209700631	40	42984										
VPS54	51542	hgsc.bcm.edu	37	chr2	64126619	64126619	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	acttctcacctgtgtttgttCttctggaaggagatcaaata	8	8	4	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr2:64126619C>T	ENST00000272322.4	-	21	2876	c.2722G>A	c.(2722-2724)Gaa>Aaa	p.E908K	VPS54_ENST00000354504.3_Missense_Mutation_p.E755K|VPS54_ENST00000409558.4_Missense_Mutation_p.E896K			Q9P1Q0	VPS54_HUMAN	vacuolar protein sorting 54 homolog (S. cerevisiae)	908					growth (GO:0040007)|homeostasis of number of cells within a tissue (GO:0048873)|musculoskeletal movement (GO:0050881)|neurofilament cytoskeleton organization (GO:0060052)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	GARP complex (GO:0000938)				endometrium(3)|kidney(4)|large_intestine(8)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	27						TGTGTTTGTTCTTCTGGAAGG	0.358																																					p.E908K		Atlas-SNP	.											VPS54,colon,carcinoma,0,1	VPS54	57	.	0			c.G2722A						.						116	115	115					2																	64126619		2203	4300	6503	SO:0001583	missense	51542	exon21			TTTGTTCTTCTGG	AF102177	CCDS33208.1, CCDS46302.1	2p15-p14	2014-06-13	2006-12-19		ENSG00000143952	ENSG00000143952			18652	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 164"	614633	"vacuolar protein sorting 54 (yeast)"			12039048	Standard	NM_016516		Approved	HCC8, PPP1R164	uc002scq.3	Q9P1Q0	OTTHUMG00000152627	ENST00000272322.4:c.2722G>A	chr2.hg19:g.64126619C>T	ENSP00000272322:p.Glu908Lys	58.0	0.0		66.0	25.0	NM_016516	Q5VIR5|Q86YF7|Q8N6G3|Q9NPV0|Q9NT07|Q9NUJ0	Missense_Mutation	SNP	ENST00000272322.4	hg19	CCDS33208.1	.	.	.	.	.	.	.	.	.	.	C	16.15	3.041656	0.55003	.	.	ENSG00000143952	ENST00000354504;ENST00000272322;ENST00000409558;ENST00000483277;ENST00000394400	T;T;T	0.33438	1.41;1.42;1.42	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.23133	0.0559	L	0.41710	1.295	0.80722	D	1	P;B;B	0.36768	0.569;0.043;0.072	B;B;B	0.26770	0.073;0.012;0.026	T	0.07731	-1.0757	10	0.08381	T	0.77	.	19.9348	0.97133	0.0:1.0:0.0:0.0	.	755;908;896	Q9P1Q0-3;Q9P1Q0;Q9P1Q0-4	.;VPS54_HUMAN;.	K	755;908;896;896;908	ENSP00000346499:E755K;ENSP00000272322:E908K;ENSP00000386980:E896K	ENSP00000272322:E908K	E	-	1	0	VPS54	63980123	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.189000	0.77747	2.789000	0.95967	0.591000	0.81541	GAA	.	.		0.358	VPS54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327062.2	NM_016516		T	64126619	C	T	64126619	3	4	296	1	0	0	0	0	1	0	0	0	17231	922	32	3	223	3	VPS54	2	64126619	Missense_Mutation	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	30627877	64126619	179072754	41	42985										
IMMT	10989	hgsc.bcm.edu	37	chr2	86385747	86385747	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	acccaggaaggacttctggaGtaatactgtccagctctcgt	10	11	2	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr2:86385747G>T	ENST00000410111.3	-	10	1517	c.1130C>A	c.(1129-1131)aCt>aAt	p.T377N	IMMT_ENST00000442664.2_Missense_Mutation_p.T376N|IMMT_ENST00000409051.2_Missense_Mutation_p.T330N|IMMT_ENST00000449247.2_Missense_Mutation_p.T366N|IMMT_ENST00000254636.5_Missense_Mutation_p.T278N|Y_RNA_ENST00000363371.1_RNA|IMMT_ENST00000490238.1_5'UTR	NM_001100169.1|NM_001100170.1|NM_006839.2	NP_001093639.1|NP_001093640.1|NP_006830.2	Q16891	MIC60_HUMAN	inner membrane protein, mitochondrial	377					mitochondrial calcium ion homeostasis (GO:0051560)|response to cold (GO:0009409)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						GACTTCTGGAGTAATACTGTC	0.423																																					p.T377N		Atlas-SNP	.											.	IMMT	65	.	0			c.C1130A						.						82	74	77					2																	86385747		1881	4113	5994	SO:0001583	missense	10989	exon10			TCTGGAGTAATAC	D21094	CCDS46355.1, CCDS46356.1, CCDS46357.1	2p11.2	2011-10-04	2010-04-29		ENSG00000132305	ENSG00000132305			6047	protein-coding gene	gene with protein product	"mitofilin", "mitochondrial inner membrane organizing system 2"	600378	"inner membrane protein, mitochondrial (mitofilin)"			9168817, 8039717	Standard	NM_001100169		Approved	P87, P89, HMP, MINOS2	uc002sqz.4	Q16891	OTTHUMG00000153170	ENST00000410111.3:c.1130C>A	chr2.hg19:g.86385747G>T	ENSP00000387262:p.Thr377Asn	125.0	0.0		123.0	46.0	NM_006839	B1H0U5|B2R5N6|Q14539|Q15092|Q68D41|Q69HW5|Q6IBL0|Q7Z3X1|Q8TAJ5|Q9P0V2	Missense_Mutation	SNP	ENST00000410111.3	hg19	CCDS46355.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	32|32	5.145014|5.145014	0.94603|0.94603	.|.	.|.	ENSG00000132305|ENSG00000132305	ENST00000254636;ENST00000449247;ENST00000410111;ENST00000442664;ENST00000409051;ENST00000545283;ENST00000377310;ENST00000409715|ENST00000419070	T;T;T;T;T|.	0.32272|.	1.46;1.46;1.46;1.46;1.46|.	5.95|5.95	5.95|5.95	0.96441|0.96441	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.77260|.	0.4104|.	M|M	0.72118|0.72118	2.19|2.19	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D|.	0.67145|.	0.993;0.996;0.995;0.996;0.995;0.995;0.996|.	D;D;D;D;P;D;D|.	0.67900|.	0.937;0.937;0.923;0.954;0.897;0.948;0.937|.	T|.	0.74383|.	-0.3683|.	10|.	0.16420|.	T|.	0.52|.	-20.7377|-20.7377	20.4024|20.4024	0.99000|0.99000	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	330;365;345;279;366;345;377|.	B9A067;B4DKR1;F8W9I1;B4DS66;Q16891-2;Q16891-3;Q16891|.	.;.;.;.;.;.;IMMT_HUMAN|.	N|X	278;366;377;376;330;366;345;278|231	ENSP00000254636:T278N;ENSP00000396899:T366N;ENSP00000387262:T377N;ENSP00000407788:T376N;ENSP00000387227:T330N|.	ENSP00000254636:T278N|.	T|Y	-|-	2|3	0|2	IMMT|IMMT	86239258|86239258	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	9.246000|9.246000	0.95438|0.95438	2.827000|2.827000	0.97445|0.97445	0.650000|0.650000	0.86243|0.86243	ACT|TAC	.	.		0.423	IMMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329909.2	NM_006839		T	86385747	G	T	86385747	3	4	296	1	0	0	0	0	1	0	0	0	7727	1029	36	3	1170	3	IMMT	2	86385747	Missense_Mutation	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10	22259128	86385747	156813626	42	42986										
MRPL35	51318	hgsc.bcm.edu	37	chr2	86434440	86434440	+	Frame_Shift_Del	DEL	T	T	-													0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	acttcattgtggcctttgggTgaggagaaaggtgagtcttc							TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr2:86434440delT	ENST00000337109.4	+	3	402	c.368delT	c.(367-369)gtgfs	p.V123fs	MRPL35_ENST00000409180.1_Frame_Shift_Del_p.V123fs|MRPL35_ENST00000605125.1_Intron|MRPL35_ENST00000254644.8_Frame_Shift_Del_p.V123fs	NM_016622.3	NP_057706.2	Q9NZE8	RM35_HUMAN	mitochondrial ribosomal protein L35	123					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)	structural constituent of ribosome (GO:0003735)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(4)|skin(1)|stomach(1)|urinary_tract(2)	14						GGCCTTTGGGTGAGGAGAAAG	0.483																																					p.V123X		Atlas-Indel,Pindel	.											MRPL35,NS,carcinoma,0,1	MRPL35	23	.	0			c.367delG						.						98	93	95					2																	86434440		2203	4300	6503	SO:0001589	frameshift_variant	51318	exon3			.	AF208849	CCDS1987.1, CCDS1988.1	2p11.2	2012-09-13			ENSG00000132313	ENSG00000132313		"Mitochondrial ribosomal proteins / large subunits"	14489	protein-coding gene	gene with protein product		611841				11042152, 11551941	Standard	NM_016622		Approved		uc002srg.4	Q9NZE8	OTTHUMG00000037385	ENST00000337109.4:c.368delT	chr2.hg19:g.86434440delT	ENSP00000338389:p.Val123fs	145.0	0.0		153.0	59.0	NM_145644	A6NKV6|B2RB93|Q658U7|Q8WWA2	Frame_Shift_Del	DEL	ENST00000337109.4	hg19	CCDS1988.1																																																																																			.	.		0.483	MRPL35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091002.2	NM_016622		-	86434440	T	-	86434440	7	5	296	1	0	1	0	1	0	0	0	0	9807	1696	59	0	378	0	MRPL35	2	86434440	Frame_Shift_Del	DEL	T	TCGA-G3-AAV0-01A-11D-A36X-10	48693	86434440	156764933	43	42987										
RGPD1	729857	hgsc.bcm.edu	37	chr2	88095295	88095295	+	Frame_Shift_Del	DEL	G	G	-													0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	attttcggattccaggtaaaGcaggcaatgaattccactgt							TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr2:88095295delG	ENST00000398146.3	-	10	1568	c.1346delC	c.(1345-1347)gctfs	p.A449fs	RGPD2_ENST00000327544.6_5'UTR|RGPD2_ENST00000420840.2_Frame_Shift_Del_p.A441fs			P0DJD1	RGPD2_HUMAN	RANBP2-like and GRIP domain containing 2	449					protein targeting to Golgi (GO:0000042)					breast(1)|pancreas(1)	2						TCCAGGTAAAGCAGGCAATGA	0.378																																					p.A449fs		Atlas-INDEL	.											.	RGPD2	14	.	0			c.1347delT						.						1	1	1					2																	88095295		23	63	86	SO:0001589	frameshift_variant	729857	exon10			.		CCDS42710.1, CCDS42710.2	2p11.2	2013-01-10			ENSG00000185304	ENSG00000185304		"Tetratricopeptide (TTC) repeat domain containing"	32415	protein-coding gene	gene with protein product		612705				15710750, 15815621	Standard	NM_001078170		Approved	RGP2, RANBP2L2		P0DJD1	OTTHUMG00000153276	ENST00000398146.3:c.1346delC	chr2.hg19:g.88095295delG	ENSP00000381214:p.Ala449fs	927.0	0.0		1040.0	71.0	NM_001078170	P0C839|Q68DN6|Q6V1X0	Frame_Shift_Del	DEL	ENST00000398146.3	hg19	CCDS42710.2																																																																																			.	.		0.378	RGPD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330534.2	NM_001078170		-	88095295	G	-	88095295	7	5	296	1	0	1	0	1	0	0	0	0	13300	971	34	0	9319	0	RGPD1	2	88095295	Frame_Shift_Del	DEL	G	TCGA-G3-AAV0-01A-11D-A36X-10	1660855	88095295	155104078	44	42988										
RGPD3	653489	hgsc.bcm.edu	37	chr2	107053238	107053238	+	Frame_Shift_Del	DEL	G	G	-													0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	attttcggattccaggtaaaGcaggcaatgaattccactgt							TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr2:107053238delG	ENST00000409886.3	-	10	1436	c.1349delC	c.(1348-1350)gctfs	p.A450fs	RGPD3_ENST00000304514.7_Frame_Shift_Del_p.A450fs	NM_001144013.1	NP_001137485.1	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	450					protein targeting to Golgi (GO:0000042)					breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						TCCAGGTAAAGCAGGCAATGA	0.383																																					p.A450fs		Atlas-INDEL	.											.	RGPD3	316	.	0			c.1350delT						.																																			SO:0001589	frameshift_variant	653489	exon10			.		CCDS46379.1	2q12.2	2013-01-10			ENSG00000153165	ENSG00000153165		"Tetratricopeptide (TTC) repeat domain containing"	32416	protein-coding gene	gene with protein product		612706				15710750, 15815621	Standard	NM_001144013		Approved	RGP3	uc010ywi.1	A6NKT7	OTTHUMG00000153182	ENST00000409886.3:c.1349delC	chr2.hg19:g.107053238delG	ENSP00000386588:p.Ala450fs	1114.0	0.0		1291.0	193.0	NM_001144013	B8ZZM4	Frame_Shift_Del	DEL	ENST00000409886.3	hg19	CCDS46379.1																																																																																			.	.		0.383	RGPD3-002	KNOWN	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329975.1	XM_929931		-	107053238	G	-	107053238	7	5	296	1	0	1	0	1	0	0	0	0	13302	971	34	0	3983	0	RGPD3	2	107053238	Frame_Shift_Del	DEL	G	TCGA-G3-AAV0-01A-11D-A36X-10	18957943	107053238	136146135	45	42989										
RGPD4	285190	hgsc.bcm.edu	37	chr2	108475642	108475642	+	Frame_Shift_Del	DEL	C	C	-													0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	acagtggaattcattgcctgCtttacctggaatccgaaaat							TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr2:108475642delC	ENST00000408999.3	+	10	1426	c.1349delC	c.(1348-1350)gctfs	p.A450fs	RGPD4_ENST00000354986.4_Frame_Shift_Del_p.A450fs	NM_182588.2	NP_872394.2	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4	450					protein targeting to Golgi (GO:0000042)					breast(1)|endometrium(7)|kidney(4)|lung(23)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(3)	43						TCATTGCCTGCTTTACCTGGA	0.383																																					p.A450fs		Atlas-INDEL	.											.	RGPD4	112	.	0			c.1348delG						.						1	1	1					2																	108475642		2	4	6	SO:0001589	frameshift_variant	285190	exon10			.	BX537861	CCDS46381.1	2q12.3	2013-01-10			ENSG00000196862	ENSG00000196862		"Tetratricopeptide (TTC) repeat domain containing"	32417	protein-coding gene	gene with protein product		612707				15710750, 15815621	Standard	NM_182588		Approved	RGP4, DKFZp686P0288	uc010ywk.2	Q7Z3J3	OTTHUMG00000153208	ENST00000408999.3:c.1349delC	chr2.hg19:g.108475642delC	ENSP00000386810:p.Ala450fs	1028.0	0.0		1263.0	228.0	NM_182588	B9A029	Frame_Shift_Del	DEL	ENST00000408999.3	hg19	CCDS46381.1																																																																																			.	.		0.383	RGPD4-001	NOVEL	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330096.2	XM_496581		-	108475642	C	-	108475642	7	5	296	1	0	1	0	1	0	0	0	0	13303	797	28	0	1387	0	RGPD4	2	108475642	Frame_Shift_Del	DEL	C	TCGA-G3-AAV0-01A-11D-A36X-10	1422404	108475642	134723731	46	42990										
POTEE	445582	hgsc.bcm.edu	37	chr2	131984418	131984418	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tggcctcacaccactgttacTtggtgtacatgagcaaaaac	8	11	1	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr2:131984418T>G	ENST00000356920.5	+	4	927	c.833T>G	c.(832-834)cTt>cGt	p.L278R	POTEE_ENST00000358087.5_Missense_Mutation_p.L288R|PLEKHB2_ENST00000404460.1_Intron|PLEKHB2_ENST00000303908.3_Intron|RNU6-127P_ENST00000390897.1_RNA	NM_001083538.1	NP_001077007.1	Q6S8J3	POTEE_HUMAN	POTE ankyrin domain family, member E	278					retina homeostasis (GO:0001895)|substantia nigra development (GO:0021762)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)											CCACTGTTACTTGGTGTACAT	0.323																																					p.L278R		Atlas-SNP	.											.	.	.	.	0			c.T833G						.						78	92	87					2																	131984418		1497	2701	4198	SO:0001583	missense	445582	exon4			TGTTACTTGGTGT	AY462868	CCDS46414.1	2q21.1	2014-04-10	2008-11-26	2008-11-26	ENSG00000188219	ENSG00000188219		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	33895	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 2"	608914	"ANKRD26-like family C, member 1A"	A26C1A			Standard	NM_001083538		Approved	POTE2, POTE-2, A26C1, POTE2gamma, CT104.2	uc002tsn.2	Q6S8J3	OTTHUMG00000186974	ENST00000356920.5:c.833T>G	chr2.hg19:g.131984418T>G	ENSP00000439189:p.Leu278Arg	321.0	0.0		384.0	112.0	NM_001083538	Q6S8J4|Q6S8J5|Q6S8J8	Missense_Mutation	SNP	ENST00000356920.5	hg19	CCDS46414.1	.	.	.	.	.	.	.	.	.	.	.	10.60	1.395571	0.25205	.	.	ENSG00000188219	ENST00000356920;ENST00000358087	T;T	0.68624	0.47;-0.34	1.16	1.16	0.20824	Ankyrin repeat-containing domain (4);	0.279276	0.18784	U	0.131260	T	0.68311	0.2987	L	0.55990	1.75	0.09310	N	1	D	0.67145	0.996	P	0.58970	0.849	T	0.56950	-0.7894	10	0.87932	D	0	.	4.5417	0.12061	0.0:0.0:0.0:1.0	.	278	Q6S8J3	POTEE_HUMAN	R	278;288	ENSP00000439189:L278R;ENSP00000443049:L288R	ENSP00000439189:L278R	L	+	2	0	AC131180.1	131700888	0.697000	0.27767	0.043000	0.18650	0.028000	0.11728	1.583000	0.36579	0.784000	0.33661	0.136000	0.15936	CTT	.	.		0.323	POTEE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001083538		G	131984418	T	G	131984418	3	3	296	1	0	0	0	0	1	0	0	0	12273	1609	56	5	847	5	POTEE	2	131984418	Missense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	23508776	131984418	111214955	47	42991										
FMNL2	114793	hgsc.bcm.edu	37	chr2	153192209	153192209	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gatgccagagccaggtgaacTggaggagcgatttgccatcg	15	9	0	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr2:153192209T>A	ENST00000288670.9	+	1	459	c.92T>A	c.(91-93)cTg>cAg	p.L31Q		NM_052905.3	NP_443137.2	Q96PY5	FMNL2_HUMAN	formin-like 2	31	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				cortical actin cytoskeleton organization (GO:0030866)|cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)				central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(2)|lung(3)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	23						CCAGGTGAACTGGAGGAGCGA	0.706																																					p.L31Q		Atlas-SNP	.											.	FMNL2	75	.	0			c.T92A						.						53	58	56					2																	153192209		2032	4192	6224	SO:0001583	missense	114793	exon1			GTGAACTGGAGGA	AB067489	CCDS46429.1	2q23.3	2008-02-05	2003-12-02	2003-12-03	ENSG00000157827	ENSG00000157827			18267	protein-coding gene	gene with protein product			"formin homology 2 domain containing 2"	FHOD2			Standard	XM_005246263		Approved	KIAA1902	uc002tye.3	Q96PY5	OTTHUMG00000154035	ENST00000288670.9:c.92T>A	chr2.hg19:g.153192209T>A	ENSP00000288670:p.Leu31Gln	299.0	0.0		333.0	153.0	NM_052905	B2RZH5|Q14CC9|Q4ZG52|Q8N3E0	Missense_Mutation	SNP	ENST00000288670.9	hg19	CCDS46429.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.284392	0.80803	.	.	ENSG00000157827	ENST00000288670	D	0.89681	-2.55	4.83	4.83	0.62350	.	0.000000	0.53938	D	0.000044	D	0.94798	0.8320	M	0.86953	2.85	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.95606	0.8667	10	0.87932	D	0	.	14.2262	0.65860	0.0:0.0:0.0:1.0	.	31	Q96PY5-3	.	Q	31	ENSP00000288670:L31Q	ENSP00000288670:L31Q	L	+	2	0	FMNL2	152900455	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.287000	0.78681	2.028000	0.59812	0.533000	0.62120	CTG	.	.		0.706	FMNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333582.2	NM_052905		A	153192209	T	A	153192209	3	1	296	1	0	0	0	0	1	0	0	0	5960	1580	55	4	94	4	FMNL2	2	153192209	Missense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	21207791	153192209	90007164	48	42992										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168100314	168100315	+	Missense_Mutation	DNP	GG	GG	TT													0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gaagaaaatgtcaaaggtggGgtgagtaaggcaaagtggtt					rs530786380		TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr2:168100314_168100315GG>TT	ENST00000409195.1	+	9	2501_2502	c.2412_2413GG>TT	c.(2410-2415)ggGGtg>ggTTtg	p.V805L	XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.V805L|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.V583L|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	630					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TCAAAGGTGGGGTGAGTAAGGC	0.376																																					p.G804G|p.V805L		Atlas-SNP	.											.	XIRP2	914	.	0			c.G2412T|c.G2413T						.																																			SO:0001583	missense	129446	exon9			AGGTGGGGTGAGT|GGTGGGGTGAGTA	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	Exception_encountered	chr2.hg19:g.168100314_168100315delinsTT	ENSP00000386840:p.Val805Leu	403.0|400.0	0.0|1.0		409.0|405.0	187.0|186.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent|Missense_Mutation	SNP	ENST00000409195.1	hg19	CCDS42769.1																																																																																			.	.		0.376	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		TT	168100315	GG	TT	168100314	3	4	296	1	0	0	0	0	1	0	0	0	17445	1219	43	3	2442	3	XIRP2	2	168100314	Missense_Mutation	DNP	GG	TCGA-G3-AAV0-01A-11D-A36X-10	14908105	168100314	75099059	49	42993										
TTN	7273	hgsc.bcm.edu	37	chr2	179638708	179638708	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tgtgaaccctgtcactgggcTgcacttcttggccgtctttc	10	13	3	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr2:179638708T>A	ENST00000591111.1	-	31	7411	c.7187A>T	c.(7186-7188)cAg>cTg	p.Q2396L	TTN_ENST00000360870.5_Missense_Mutation_p.Q2396L|TTN_ENST00000589042.1_Missense_Mutation_p.Q2396L|TTN_ENST00000342992.6_Missense_Mutation_p.Q2396L|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000584485.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.Q2350L|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.Q2350L|RP11-88L24.4_ENST00000582038.2_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.Q2350L			Q8WZ42	TITIN_HUMAN	titin	12718	Ig-like 13.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTCACTGGGCTGCACTTCTTG	0.438																																					p.Q2396L		Atlas-SNP	.											.	TTN	18412	.	0			c.A7187T						.						142	126	131					2																	179638708		2203	4300	6503	SO:0001583	missense	7273	exon31			CTGGGCTGCACTT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.7187A>T	chr2.hg19:g.179638708T>A	ENSP00000465570:p.Gln2396Leu	103.0	0.0		112.0	45.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	11.91	1.780606	0.31502	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29;-0.29	5.82	4.66	0.58398	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.65417	0.2689	L	0.42529	1.33	0.24873	N	0.992273	B;B;B;B;P	0.41848	0.175;0.175;0.175;0.175;0.763	B;B;B;B;P	0.44897	0.174;0.174;0.174;0.174;0.463	T	0.59300	-0.7480	9	0.87932	D	0	.	13.2513	0.60053	0.0:0.0:0.1325:0.8675	.	2350;2350;2350;2396;2396	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	L	2396;2350;2350;2350;2350;2396	ENSP00000343764:Q2396L;ENSP00000434586:Q2350L;ENSP00000340554:Q2350L;ENSP00000352154:Q2350L;ENSP00000354117:Q2396L	ENSP00000340554:Q2350L	Q	-	2	0	TTN	179346953	1.000000	0.71417	0.647000	0.29507	0.982000	0.71751	4.352000	0.59404	1.021000	0.39600	0.528000	0.53228	CAG	.	.		0.438	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179638708	T	A	179638708	3	1	296	1	0	0	0	0	1	0	0	0	16750	1580	55	4	104129	4	TTN	2	179638708	Missense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	11538394	179638708	63560665	50	42994										
FN1	2335	hgsc.bcm.edu	37	chr2	216243896	216243896	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	atgagctgtcaggagcaaggTtgatttctttcattggtccg	12	7	3	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr2:216243896T>A	ENST00000359671.1	-	33	5571	c.5306A>T	c.(5305-5307)aAc>aTc	p.N1769I	FN1_ENST00000443816.1_Missense_Mutation_p.N1679I|FN1_ENST00000432072.2_Missense_Mutation_p.N1770I|FN1_ENST00000490833.1_5'Flank|FN1_ENST00000346544.3_Missense_Mutation_p.N1769I|FN1_ENST00000336916.4_Missense_Mutation_p.N1769I|FN1_ENST00000323926.6_Missense_Mutation_p.N1860I|FN1_ENST00000356005.4_Missense_Mutation_p.N1679I|FN1_ENST00000421182.1_Missense_Mutation_p.N1679I|FN1_ENST00000354785.4_Missense_Mutation_p.N1860I|FN1_ENST00000357867.4_Missense_Mutation_p.N1679I|FN1_ENST00000345488.5_Missense_Mutation_p.N1769I|FN1_ENST00000357009.2_Missense_Mutation_p.N1769I|FN1_ENST00000446046.1_Missense_Mutation_p.N1769I			P02751	FINC_HUMAN	fibronectin 1	1769	Fibronectin type-III 13. {ECO:0000255|PROSITE-ProRule:PRU00316}.|Heparin-binding 2.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	AGGAGCAAGGTTGATTTCTTT	0.488																																					p.N1860I		Atlas-SNP	.											.	FN1	521	.	0			c.A5579T						.						148	136	140					2																	216243896		2203	4300	6503	SO:0001583	missense	2335	exon34			GCAAGGTTGATTT		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"Fibronectin type III domain containing", "Endogenous ligands"	3778	protein-coding gene	gene with protein product	"migration-stimulating factor", "cold-insoluble globulin"	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.5306A>T	chr2.hg19:g.216243896T>A	ENSP00000352696:p.Asn1769Ile	159.0	0.0		195.0	30.0	NM_212482	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Missense_Mutation	SNP	ENST00000359671.1	hg19		.	.	.	.	.	.	.	.	.	.	T	15.35	2.808682	0.50421	.	.	ENSG00000115414	ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000265313;ENST00000359671;ENST00000346544;ENST00000345488;ENST00000357009;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005;ENST00000456923	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.58506	0.33;0.33;0.33;0.33;0.33;0.33;0.33;0.33;0.33;0.33;0.33;0.33;0.33;0.33	6.17	6.17	0.99709	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.139910	0.49916	D	0.000121	T	0.73783	0.3631	M	0.74546	2.27	0.22034	N	0.999406	D;D;P;D;D;D;D;D;D;D;D;D	0.76494	0.993;0.997;0.887;0.996;0.999;0.997;0.957;0.999;0.996;0.996;0.997;0.993	D;D;D;D;D;D;D;D;D;D;D;D	0.97110	0.999;0.987;0.933;0.987;0.999;0.992;0.961;1.0;0.999;0.999;0.999;0.992	T	0.68911	-0.5284	10	0.51188	T	0.08	.	11.0511	0.47889	0.0:0.0685:0.0:0.9315	.	1769;1770;1860;1679;1679;1769;1769;1770;1679;1679;1860;1769	F8W7G7;P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;E7ERA1;P02751-9;P02751-14;P02751-15;P02751	.;.;.;.;.;.;.;.;.;.;.;FINC_HUMAN	I	1679;1860;1769;1679;1860;1770;1769;1769;1769;1769;1769;1679;1770;1679;486	ENSP00000394423:N1679I;ENSP00000323534:N1860I;ENSP00000338200:N1769I;ENSP00000350534:N1679I;ENSP00000346839:N1860I;ENSP00000352696:N1769I;ENSP00000265312:N1769I;ENSP00000273049:N1769I;ENSP00000349509:N1769I;ENSP00000410422:N1769I;ENSP00000415018:N1679I;ENSP00000399538:N1770I;ENSP00000348285:N1679I;ENSP00000416139:N486I	ENSP00000265313:N1770I	N	-	2	0	FN1	215952141	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.153000	0.50685	2.371000	0.80710	0.533000	0.62120	AAC	.	.		0.488	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		A	216243896	T	A	216243896	3	1	296	1	0	0	0	0	1	0	0	0	5970	1725	60	4	1906	4	FN1	2	216243896	Missense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	36605188	216243896	26955477	51	42995										
HRH1	3269	hgsc.bcm.edu	37	chr3	11300884	11300884	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ggtgctgtatgccgtacggaGtgagcggaagctccacactg	15	10	0	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr3:11300884G>T	ENST00000397056.1	+	3	352	c.161G>T	c.(160-162)aGt>aTt	p.S54I	HRH1_ENST00000431010.2_Missense_Mutation_p.S54I|HRH1_ENST00000438284.2_Missense_Mutation_p.S54I	NM_000861.3|NM_001098211.1	NP_000852.1|NP_001091681.1	P35367	HRH1_HUMAN	histamine receptor H1	54					cellular response to histamine (GO:0071420)|eosinophil chemotaxis (GO:0048245)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|inositol phosphate-mediated signaling (GO:0048016)|memory (GO:0007613)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of vasoconstriction (GO:0045907)|regulation of synaptic plasticity (GO:0048167)|regulation of vascular permeability (GO:0043114)|visual learning (GO:0008542)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|histamine receptor activity (GO:0004969)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25					Aceprometazine(DB01615)|Alcaftadine(DB06766)|Alimemazine(DB01246)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Antazoline(DB08799)|Aripiprazole(DB01238)|Asenapine(DB06216)|Astemizole(DB00637)|Azatadine(DB00719)|Azelastine(DB00972)|Benzatropine(DB00245)|Bepotastine(DB04890)|Betahistine(DB06698)|Bromodiphenhydramine(DB01237)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbinoxamine(DB00748)|Cetirizine(DB00341)|Chlorcyclizine(DB08936)|Chloropyramine(DB08800)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Citalopram(DB00215)|Clemastine(DB00283)|Clofedanol(DB04837)|Clozapine(DB00363)|Cyclizine(DB01176)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexbrompheniramine(DB00405)|Dimenhydrinate(DB00985)|Dimetindene(DB08801)|Diphenhydramine(DB01075)|Diphenylpyraline(DB01146)|Doxepin(DB01142)|Doxylamine(DB00366)|Emedastine(DB01084)|Epinastine(DB00751)|Escitalopram(DB01175)|Fexofenadine(DB00950)|Flunarizine(DB04841)|Histamine Phosphate(DB00667)|Hydroxyzine(DB00557)|Iloperidone(DB04946)|Imipramine(DB00458)|Isothipendyl(DB08802)|Ketotifen(DB00920)|Levocabastine(DB01106)|Loratadine(DB00455)|Loxapine(DB00408)|Maprotiline(DB00934)|Meclizine(DB00737)|Mepyramine(DB06691)|Mequitazine(DB01071)|Methdilazine(DB00902)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Olopatadine(DB00768)|Orphenadrine(DB01173)|Paliperidone(DB01267)|Phenindamine(DB01619)|Pheniramine(DB01620)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Tolazoline(DB00797)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Ziprasidone(DB00246)	GCCGTACGGAGTGAGCGGAAG	0.592																																					p.S54I		Atlas-SNP	.											.	HRH1	58	.	0			c.G161T						.						128	101	110					3																	11300884		2203	4300	6503	SO:0001583	missense	3269	exon3			TACGGAGTGAGCG		CCDS2604.1	3p25	2012-11-12			ENSG00000196639	ENSG00000196639		"GPCR / Class A : Histamine receptors"	5182	protein-coding gene	gene with protein product		600167				8003029	Standard	NM_001098211		Approved		uc010hds.3	P35367	OTTHUMG00000129719	ENST00000397056.1:c.161G>T	chr3.hg19:g.11300884G>T	ENSP00000380247:p.Ser54Ile	136.0	0.0		149.0	66.0	NM_000861	A8K047|Q6P9E5	Missense_Mutation	SNP	ENST00000397056.1	hg19	CCDS2604.1	.	.	.	.	.	.	.	.	.	.	G	7.694	0.691604	0.15039	.	.	ENSG00000196639	ENST00000438284;ENST00000431010;ENST00000397056	T;T;T	0.37235	1.21;1.21;1.21	5.98	-2.52	0.06346	GPCR, rhodopsin-like superfamily (1);	0.328255	0.33959	N	0.004384	T	0.16642	0.0400	N	0.21508	0.67	0.09310	N	1	B	0.31503	0.326	B	0.34536	0.185	T	0.12477	-1.0546	10	0.23302	T	0.38	-0.2436	2.1031	0.03684	0.1386:0.3575:0.1771:0.3268	.	54	P35367	HRH1_HUMAN	I	54	ENSP00000406705:S54I;ENSP00000397028:S54I;ENSP00000380247:S54I	ENSP00000380247:S54I	S	+	2	0	HRH1	11275884	0.000000	0.05858	0.000000	0.03702	0.115000	0.19883	-0.037000	0.12164	-0.393000	0.07739	-0.169000	0.13324	AGT	.	.		0.592	HRH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251928.2			T	11300884	G	T	11300884	3	4	296	1	0	0	0	0	1	0	0	0	7364	1029	36	3	163	3	HRH1	3	11300884	Missense_Mutation	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10		11300884	186721546	52	42996										
NKTR	4820	hgsc.bcm.edu	37	chr3	42678871	42678871	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gatctagttccaagtctgggCaccgaaagagagcatcaaaa	10	9	3	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr3:42678871C>A	ENST00000232978.8	+	13	1863	c.1675C>A	c.(1675-1677)Cac>Aac	p.H559N	RP4-613B23.1_ENST00000445452.1_RNA|RP4-613B23.1_ENST00000434363.1_RNA|RP4-613B23.1_ENST00000438017.1_RNA	NM_005385.3	NP_005376.2	P30414	NKTR_HUMAN	natural killer cell triggering receptor	559	Arg/Ser-rich.				protein folding (GO:0006457)	membrane (GO:0016020)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	41				KIRC - Kidney renal clear cell carcinoma(284;0.24)		CAAGTCTGGGCACCGAAAGAG	0.403																																					p.H559N		Atlas-SNP	.											.	NKTR	116	.	0			c.C1675A						.						82	88	86					3																	42678871		2203	4300	6503	SO:0001583	missense	4820	exon13			TCTGGGCACCGAA		CCDS2702.1	3p22.1	2014-01-20	2014-01-20		ENSG00000114857	ENSG00000114857			7833	protein-coding gene	gene with protein product	"NK-tumor recognition protein", "natural-killer cells cyclophilin-related protein", "NK-TR protein"	161565	"natural killer-tumor recognition sequence"			8314596, 8144875	Standard	XM_005265173		Approved	p104	uc003clo.3	P30414	OTTHUMG00000133037	ENST00000232978.8:c.1675C>A	chr3.hg19:g.42678871C>A	ENSP00000232978:p.His559Asn	264.0	0.0		319.0	143.0	NM_005385		Missense_Mutation	SNP	ENST00000232978.8	hg19	CCDS2702.1	.	.	.	.	.	.	.	.	.	.	C	1.288	-0.608404	0.03717	.	.	ENSG00000114857	ENST00000232978	T	0.11712	2.75	5.65	4.59	0.56863	.	0.724193	0.14537	N	0.313484	T	0.10508	0.0257	L	0.40543	1.245	0.27381	N	0.955405	B;B	0.30973	0.302;0.09	B;B	0.32465	0.146;0.069	T	0.17684	-1.0361	10	0.08179	T	0.78	-0.9586	15.4557	0.75311	0.0:0.9221:0.0:0.0779	.	259;559	Q6M1B8;P30414	.;NKTR_HUMAN	N	559	ENSP00000232978:H559N	ENSP00000232978:H559N	H	+	1	0	NKTR	42653875	0.906000	0.30813	0.879000	0.34478	0.330000	0.28571	2.371000	0.44248	2.664000	0.90586	0.491000	0.48974	CAC	.	.		0.403	NKTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256642.2	NM_005385		A	42678871	C	A	42678871	3	1	296	1	0	0	0	0	1	0	0	0	10457	710	25	3	1721	3	NKTR	3	42678871	Missense_Mutation	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	31377987	42678871	155343559	53	42997										
LAMB2	3913	hgsc.bcm.edu	37	chr3	49166162	49166162	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	agaggccaccaggaactccaGggtctgaccttcctgtagcc	11	14	1	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr3:49166162G>A	ENST00000418109.1	-	15	1986	c.1822C>T	c.(1822-1824)Ctg>Ttg	p.L608L	LAMB2_ENST00000305544.4_Silent_p.L608L	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	608	Laminin IV type B. {ECO:0000255|PROSITE- ProRule:PRU00462}.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		AGGAACTCCAGGGTCTGACCT	0.597																																					p.L608L		Atlas-SNP	.											.	LAMB2	156	.	0			c.C1822T						.						73	77	76					3																	49166162		2203	4300	6503	SO:0001819	synonymous_variant	3913	exon14			ACTCCAGGGTCTG		CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"Laminins"	6487	protein-coding gene	gene with protein product	"laminin S"	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.1822C>T	chr3.hg19:g.49166162G>A		74.0	0.0		96.0	46.0	NM_002292	Q16321	Silent	SNP	ENST00000418109.1	hg19	CCDS2789.1																																																																																			.	.		0.597	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292		A	49166162	G	A	49166162	2	1	296	1	0	0	0	0	0	0	0	1	8620	991	35	3		3	LAMB2	3	49166162	Silent	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10	6487291	49166162	148856268	54	42998										
BSN	8927	hgsc.bcm.edu	37	chr3	49694957	49694957	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tcatcatccagtgctgctgcCactgtgagggccatgagcag	12	12	2	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr3:49694957C>A	ENST00000296452.4	+	5	8082	c.7968C>A	c.(7966-7968)gcC>gcA	p.A2656A		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	2656					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)	p.A2656A(1)		breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		GTGCTGCTGCCACTGTGAGGG	0.637																																					p.A2656A		Atlas-SNP	.											BSN,NS,carcinoma,0,1	BSN	272	.	1	Substitution - coding silent(1)	lung(1)	c.C7968A						.						44	46	46					3																	49694957		2203	4298	6501	SO:0001819	synonymous_variant	8927	exon5			TGCTGCCACTGTG	AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"zinc finger protein 231", "neuronal double zinc finger protein"	604020	"bassoon (presynaptic cytomatrix protein)"	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.7968C>A	chr3.hg19:g.49694957C>A		141.0	0.0		157.0	63.0	NM_003458	O43161|Q7LGH3	Silent	SNP	ENST00000296452.4	hg19	CCDS2800.1																																																																																			.	.		0.637	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458		A	49694957	C	A	49694957	2	1	296	1	0	0	0	0	0	0	0	1	1532	581	21	3		3	BSN	3	49694957	Silent	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	528795	49694957	148327473	55	42999										
RG9MTD1	54931	hgsc.bcm.edu	37	chr3	101284684	101284684	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ggtaacaaaaatctcaccttAgatcaaatgatacgtatttt	5	7	2	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr3:101284684A>G	ENST00000309922.6	+	2	1213	c.1059A>G	c.(1057-1059)ttA>ttG	p.L353L		NM_017819.2	NP_060289.2	Q7L0Y3	MRRP1_HUMAN	tRNA methyltransferase 10 homolog C (S. cerevisiae)	353	SAM-dependent MTase TRM10-type. {ECO:0000255|PROSITE-ProRule:PRU01012}.				mitochondrial RNA 5'-end processing (GO:0000964)|tRNA processing (GO:0008033)	mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)										ATCTCACCTTAGATCAAATGA	0.388																																					p.L353L		Atlas-SNP	.											.	.	.	.	0			c.A1059G						.						49	49	49					3																	101284684		1828	4072	5900	SO:0001819	synonymous_variant	54931	exon2			CACCTTAGATCAA	AK000439	CCDS43122.1	3q12.3	2012-06-28	2012-06-28	2012-06-28	ENSG00000174173	ENSG00000174173			26022	protein-coding gene	gene with protein product	"mitochondrial RNase P subunit 1"	615423	"RNA (guanine-9-) methyltransferase domain containing 1"	RG9MTD1		18984158	Standard	NM_017819		Approved	FLJ20432, MRPP1	uc003duz.4	Q7L0Y3	OTTHUMG00000159114	ENST00000309922.6:c.1059A>G	chr3.hg19:g.101284684A>G		119.0	0.0		133.0	54.0	NM_017819	Q9NRG5|Q9NX54|Q9Y596	Silent	SNP	ENST00000309922.6	hg19	CCDS43122.1																																																																																			.	.		0.388	TRMT10C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353400.2	NM_017819		G	101284684	A	G	101284684	2	3	296	1	0	0	0	0	0	0	0	1	13286	417	15	2		2	RG9MTD1	3	101284684	Silent	SNP	A	TCGA-G3-AAV0-01A-11D-A36X-10	51589727	101284684	96737746	56	43000										
GOLGB1	2804	hgsc.bcm.edu	37	chr3	121409566	121409566	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	acatagctttttttaaactcTgtacttcagctgggctggtg	9	8	2	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr3:121409566T>A	ENST00000340645.5	-	14	8755	c.8630A>T	c.(8629-8631)cAg>cTg	p.Q2877L	GOLGB1_ENST00000393667.3_Missense_Mutation_p.Q2882L	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	2877					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		TTTTAAACTCTGTACTTCAGC	0.433																																					p.Q2882L		Atlas-SNP	.											.	GOLGB1	319	.	0			c.A8645T						.						51	51	51					3																	121409566		2203	4300	6503	SO:0001583	missense	2804	exon14			AAACTCTGTACTT	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"macrogolgin", "golgi integral membrane protein 1"	602500	"golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1", "golgin B1, golgi integral membrane protein"			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.8630A>T	chr3.hg19:g.121409566T>A	ENSP00000341848:p.Gln2877Leu	65.0	0.0		63.0	23.0	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	hg19	CCDS3004.1	.	.	.	.	.	.	.	.	.	.	T	9.079	0.998930	0.19121	.	.	ENSG00000173230	ENST00000340645;ENST00000393667	T;T	0.15139	2.45;2.45	5.3	5.3	0.74995	.	0.220504	0.32533	N	0.005966	T	0.12050	0.0293	N	0.14661	0.345	0.39773	D	0.972197	P;P;B	0.39480	0.493;0.675;0.152	B;B;B	0.41988	0.157;0.372;0.074	T	0.22626	-1.0211	10	0.28530	T	0.3	.	11.5637	0.50792	0.0:0.0:0.0:1.0	.	2882;2882;2877	E7EP74;B2ZZ91;Q14789	.;.;GOGB1_HUMAN	L	2877;2882	ENSP00000341848:Q2877L;ENSP00000377275:Q2882L	ENSP00000341848:Q2877L	Q	-	2	0	GOLGB1	122892256	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	2.182000	0.42556	2.225000	0.72522	0.533000	0.62120	CAG	.	.		0.433	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		A	121409566	T	A	121409566	3	1	296	1	0	0	0	0	1	0	0	0	6573	1580	55	4	1185	4	GOLGB1	3	121409566	Missense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	20124882	121409566	76612864	57	43001										
UROC1	131669	hgsc.bcm.edu	37	chr3	126236538	126236538	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gggccgcaggggcaggccagAgcacagcgcctggaggctag	19	12	0	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr3:126236538A>C	ENST00000290868.2	-	1	78	c.25T>G	c.(25-27)Tct>Gct	p.S9A	UROC1_ENST00000383579.3_Missense_Mutation_p.S9A	NM_144639.2	NP_653240.1	Q96N76	HUTU_HUMAN	urocanate hydratase 1	9					cellular nitrogen compound metabolic process (GO:0034641)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	urocanate hydratase activity (GO:0016153)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(1)|skin(1)	39				GBM - Glioblastoma multiforme(114;0.17)		GGCAGGCCAGAGCACAGCGCC	0.672																																					p.S9A		Atlas-SNP	.											.	UROC1	150	.	0			c.T25G						.						16	19	18					3																	126236538		2168	4274	6442	SO:0001583	missense	131669	exon1			GGCCAGAGCACAG	AK055862	CCDS3038.1, CCDS54636.1	3q21.2	2012-08-21	2012-08-21		ENSG00000159650	ENSG00000159650	4.2.1.49		26444	protein-coding gene	gene with protein product	"urocanase 1"	613012	"urocanase domain containing 1"			19304569	Standard	NM_144639		Approved	FLJ31300, HMFN0320	uc010hsi.2	Q96N76	OTTHUMG00000162753	ENST00000290868.2:c.25T>G	chr3.hg19:g.126236538A>C	ENSP00000290868:p.Ser9Ala	208.0	0.0		214.0	104.0	NM_001165974	E9PE13|Q14C64|Q68CJ7	Missense_Mutation	SNP	ENST00000290868.2	hg19	CCDS3038.1	.	.	.	.	.	.	.	.	.	.	A	5.808	0.333380	0.11013	.	.	ENSG00000159650	ENST00000290868;ENST00000383579	T;T	0.57436	0.41;0.4	4.64	0.886	0.19194	.	0.659026	0.15719	N	0.248014	T	0.20210	0.0486	N	0.05441	-0.05	0.26651	N	0.972101	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.003	T	0.23297	-1.0192	10	0.06757	T	0.87	-2.6157	0.9693	0.01412	0.4991:0.1985:0.1113:0.1911	.	9;9	E9PE13;Q96N76	.;HUTU_HUMAN	A	9	ENSP00000290868:S9A;ENSP00000373073:S9A	ENSP00000290868:S9A	S	-	1	0	UROC1	127719228	0.886000	0.30341	1.000000	0.80357	0.606000	0.37113	0.690000	0.25451	1.727000	0.51537	0.402000	0.26972	TCT	.	.		0.672	UROC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370325.2	NM_144639		C	126236538	A	C	126236538	3	2	296	1	0	0	0	0	1	0	0	0	17043	304	11	5	2269	5	UROC1	3	126236538	Missense_Mutation	SNP	A	TCGA-G3-AAV0-01A-11D-A36X-10	4826972	126236538	71785892	58	43002										
PODXL2	50512	hgsc.bcm.edu	37	chr3	127391218	127391218	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	caggagaagcaccccagcctGaacggcggcggggccctcaa	14	15	1	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr3:127391218G>T	ENST00000342480.6	+	8	1752	c.1713G>T	c.(1711-1713)ctG>ctT	p.L571L	ABTB1_ENST00000468137.1_5'Flank|ABTB1_ENST00000393363.3_5'Flank|ABTB1_ENST00000232744.8_5'Flank|ABTB1_ENST00000453791.2_5'Flank	NM_015720.2	NP_056535.1	Q9NZ53	PDXL2_HUMAN	podocalyxin-like 2	571					leukocyte tethering or rolling (GO:0050901)	integral component of plasma membrane (GO:0005887)	glycosaminoglycan binding (GO:0005539)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	26						ACCCCAGCCTGAACGGCGGCG	0.711																																					p.L571L		Atlas-SNP	.											.	PODXL2	53	.	0			c.G1713T						.						5	6	6					3																	127391218		2019	4017	6036	SO:0001819	synonymous_variant	50512	exon8			CAGCCTGAACGGC	AF219137	CCDS3044.1	3q21.3	2005-02-18			ENSG00000114631	ENSG00000114631			17936	protein-coding gene	gene with protein product	"endoglycan"					10722749	Standard	NM_015720		Approved	PODLX2, endoglycan	uc003ejq.3	Q9NZ53	OTTHUMG00000159642	ENST00000342480.6:c.1713G>T	chr3.hg19:g.127391218G>T		90.0	0.0		84.0	32.0	NM_015720	Q6UVY4|Q8WUV6	Silent	SNP	ENST00000342480.6	hg19	CCDS3044.1																																																																																			.	.		0.711	PODXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356638.1	NM_015720		T	127391218	G	T	127391218	2	4	296	1	0	0	0	0	0	0	0	1	12190	1277	45	3		3	PODXL2	3	127391218	Silent	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10	1154680	127391218	70631212	59	43003										
PPP2R3A	5523	hgsc.bcm.edu	37	chr3	135721279	135721279	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ttaacagaactgatcagtaaTatgcctagcttacaactgac	6	9	1	3	rs35214119	byFrequency	TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr3:135721279T>C	ENST00000264977.3	+	2	1556	c.939T>C	c.(937-939)aaT>aaC	p.N313N	PPP2R3A_ENST00000490467.1_Intron	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	313					eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein catabolic process (GO:0045732)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|somite development (GO:0061053)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						TGATCAGTAATATGCCTAGCT	0.423																																					p.N313N		Atlas-SNP	.											.	PPP2R3A	114	.	0			c.T939C						.						120	113	115					3																	135721279		2203	4300	6503	SO:0001819	synonymous_variant	5523	exon2			CAGTAATATGCCT	L12146	CCDS3087.1, CCDS3088.1, CCDS54642.1	3q22.2-q22.3	2013-01-10	2010-06-18	2002-04-26	ENSG00000073711	ENSG00000073711	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "EF-hand domain containing"	9307	protein-coding gene	gene with protein product		604944	"protein phosphatase 2 (formerly 2A), regulatory subunit B'' (PR 72), alpha isoform and (PR 130), beta isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha"	PPP2R3		8392071	Standard	NM_002718		Approved		uc003eqv.2	Q06190	OTTHUMG00000159766	ENST00000264977.3:c.939T>C	chr3.hg19:g.135721279T>C		117.0	0.0		154.0	60.0	NM_002718	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Silent	SNP	ENST00000264977.3	hg19	CCDS3087.1																																																																																			.	T|1.000;G|0.000		0.423	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718		C	135721279	T	C	135721279	2	2	296	1	0	0	0	0	0	0	0	1	12400	1403	49	2		2	PPP2R3A	3	135721279	Silent	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	8330061	135721279	62301151	60	43004										
TBL1XR1	79718	hgsc.bcm.edu	37	chr3	176750884	176750884	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ggtatggatgcatatccctcGgtctacatcccataacctaa	7	12	1	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr3:176750884G>A	ENST00000430069.1	-	14	1550	c.1291C>T	c.(1291-1293)Cga>Tga	p.R431*	TBL1XR1_ENST00000457928.2_Nonsense_Mutation_p.R431*			Q9BZK7	TBL1R_HUMAN	transducin (beta)-like 1 X-linked receptor 1	431					canonical Wnt signaling pathway (GO:0060070)|cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|histone binding (GO:0042393)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(7)|liver(1)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	31	all_cancers(143;1.44e-17)|Ovarian(172;0.00163)|Breast(254;0.214)	Acute lymphoblastic leukemia(1;0.00599)|all_hematologic(1;0.0632)|Prostate(884;0.215)	OV - Ovarian serous cystadenocarcinoma(80;9.83e-31)			CATATCCCTCGGTCTACATCC	0.423																																					p.R431X		Atlas-SNP	.											.	TBL1XR1	87	.	0			c.C1291T						.						116	112	113					3																	176750884		1916	4154	6070	SO:0001587	stop_gained	79718	exon14			TCCCTCGGTCTAC	AK022956	CCDS46961.1	3q26.33	2013-01-10	2008-01-17		ENSG00000177565	ENSG00000177565		"WD repeat domain containing"	29529	protein-coding gene	gene with protein product		608628	"transducin (beta)-like 1X-linked receptor 1"			11063877, 11931768	Standard	NM_024665		Approved	IRA1, FLJ12894, TBLR1, C21, DC42	uc003fix.4	Q9BZK7	OTTHUMG00000157140	ENST00000430069.1:c.1291C>T	chr3.hg19:g.176750884G>A	ENSP00000405574:p.Arg431*	283.0	0.0		294.0	117.0	NM_024665	D3DNQ9|Q14DC3|Q9H2I1|Q9H9A1	Nonsense_Mutation	SNP	ENST00000430069.1	hg19	CCDS46961.1	.	.	.	.	.	.	.	.	.	.	G	40	8.405543	0.98796	.	.	ENSG00000177565	ENST00000430069;ENST00000457928;ENST00000536758	.	.	.	5.87	-0.529	0.11901	.	0.072293	0.53938	D	0.000043	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10111	T	0.7	-4.6556	12.7824	0.57485	0.0621:0.0:0.226:0.7119	.	.	.	.	X	431;431;293	.	ENSP00000405574:R431X	R	-	1	2	TBL1XR1	178233578	1.000000	0.71417	0.984000	0.44739	0.993000	0.82548	1.640000	0.37186	-0.421000	0.07416	0.655000	0.94253	CGA	.	.		0.423	TBL1XR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347587.3	NM_024665		A	176750884	G	A	176750884	4	1	296	1	0	0	0	0	0	1	0	0	15655	1124	39	1	265	1	TBL1XR1	3	176750884	Nonsense_Mutation	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10	41029605	176750884	21271546	61	43005										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178952085	178952085	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gaaacaaatgaatgatgcacAtcatggtggctggacaacaa	10	7	1	2	rs121913279		TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr3:178952085A>T	ENST00000263967.3	+	21	3297	c.3140A>T	c.(3139-3141)cAt>cTt	p.H1047L	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1047	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		H -> L (in BC; unknown pathological significance). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16353168}.|H -> R (in CLOVE, KERSEB, CRC, BC and OC; also found in an endometrial carcinoma sample; shows an increase in lipid kinase activity; oncogenic in vivo; requires binding to p85 regulatory subunit to induce cellular transformation but not interaction with RAS; may mimic the conformatitonal change triggered by the interaction with RAS; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells; increases lipid kinase activity; may alter the interaction of the PI3K/ PI4K kinase domain with the cell membrane). {ECO:0000269|PubMed:15016963, ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16114017, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|H -> Y (in MCAP; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.H1047R(1387)|p.H1047L(194)|p.H1047P(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AATGATGCACATCATGGTGGC	0.378	H1047L(EFM19_BREAST)|H1047R(BT20_BREAST)|H1047R(CAL29_URINARY_TRACT)|H1047R(CAL33_UPPER_AERODIGESTIVE_TRACT)|H1047R(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|H1047R(HCC1954_BREAST)|H1047R(HCT116_LARGE_INTESTINE)|H1047R(HSC2_UPPER_AERODIGESTIVE_TRACT)|H1047R(LS180_LARGE_INTESTINE)|H1047R(MCAS_OVARY)|H1047R(MDAMB453_BREAST)|H1047R(NCIH1048_LUNG)|H1047R(RKO_LARGE_INTESTINE)|H1047R(SKOV3_OVARY)|H1047R(T47D_BREAST)	57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											p.H1047L	Colon(199;1504 1750 3362 26421 31210 32040)	Atlas-SNP	.		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	PIK3CA_ENST00000263967,NS,adenocarcinoma,0,2044	PIK3CA	8460	.	1582	Substitution - Missense(1582)	breast(961)|large_intestine(245)|endometrium(114)|ovary(77)|urinary_tract(36)|upper_aerodigestive_tract(26)|lung(19)|central_nervous_system(19)|stomach(19)|haematopoietic_and_lymphoid_tissue(11)|thyroid(10)|NS(9)|liver(7)|kidney(6)|soft_tissue(6)|skin(4)|prostate(4)|pituitary(3)|pancreas(3)|meninges(1)|cervix(1)|bone(1)	c.A3140T						.						99	89	92					3																	178952085		1912	4130	6042	SO:0001583	missense	5290	exon21			ATGCACATCATGG		CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3140A>T	chr3.hg19:g.178952085A>T	ENSP00000263967:p.His1047Leu	182.0	0.0		178.0	77.0	NM_006218	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	hg19	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	4.518	0.096038	0.08681	.	.	ENSG00000121879	ENST00000263967	T	0.78126	-1.15	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	T	0.47002	0.1422	N	0.00611	-1.325	0.80722	D	1	B	0.14438	0.01	B	0.12156	0.007	T	0.58053	-0.7704	10	0.02654	T	1	-21.2893	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1047	P42336	PK3CA_HUMAN	L	1047	ENSP00000263967:H1047L	ENSP00000263967:H1047L	H	+	2	0	PIK3CA	180434779	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	8.859000	0.92264	2.333000	0.79357	0.482000	0.46254	CAT	.	.		0.378	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			T	178952085	A	T	178952085	3	4	296	1	0	0	0	0	1	0	0	0	11922	217	8	4	3218	4	PIK3CA	3	178952085	Missense_Mutation	SNP	A	TCGA-G3-AAV0-01A-11D-A36X-10	2201201	178952085	19070345	62	43006										
HRG	3273	hgsc.bcm.edu	37	chr3	186395095	186395095	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tcaacatgccacttttggcaCaaatggggcccaaagacatt	8	11	1	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr3:186395095C>T	ENST00000232003.4	+	7	1081	c.1001C>T	c.(1000-1002)aCa>aTa	p.T334I		NM_000412.2	NP_000403.1	P04196	HRG_HUMAN	histidine-rich glycoprotein	334					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|defense response to fungus (GO:0050832)|fibrinolysis (GO:0042730)|heme export (GO:0097037)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel remodeling (GO:2000504)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of immune response to tumor cell (GO:0002839)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet activation (GO:0010543)|regulation of protein complex assembly (GO:0043254)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|response to organic cyclic compound (GO:0014070)	blood microparticle (GO:0072562)|endolysosome (GO:0036019)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|phagolysosome membrane (GO:0061474)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heme binding (GO:0020037)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|immunoglobulin binding (GO:0019865)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(12)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0683)		ACTTTTGGCACAAATGGGGCC	0.493																																					p.T334I		Atlas-SNP	.											.	HRG	81	.	0			c.C1001T						.						147	137	140					3																	186395095		2203	4300	6503	SO:0001583	missense	3273	exon7			TTGGCACAAATGG		CCDS3280.1	3q27	2008-07-18			ENSG00000113905	ENSG00000113905			5181	protein-coding gene	gene with protein product	"histidine-proline rich glycoprotein", "thrombophilia due to elevated HRG"	142640				1678514	Standard	NM_000412		Approved	HRGP, HPRG	uc003fqq.3	P04196	OTTHUMG00000156578	ENST00000232003.4:c.1001C>T	chr3.hg19:g.186395095C>T	ENSP00000232003:p.Thr334Ile	160.0	0.0		164.0	76.0	NM_000412	B9EK35|D3DNU7	Missense_Mutation	SNP	ENST00000232003.4	hg19	CCDS3280.1	.	.	.	.	.	.	.	.	.	.	C	12.16	1.854561	0.32791	.	.	ENSG00000113905	ENST00000232003	T	0.12984	2.63	4.37	-4.63	0.03359	.	1.713730	0.02938	N	0.140060	T	0.11281	0.0275	L	0.51422	1.61	0.09310	N	1	B	0.12013	0.005	B	0.08055	0.003	T	0.28299	-1.0048	10	0.34782	T	0.22	6.2402	2.4691	0.04560	0.1364:0.209:0.1342:0.5204	.	334	P04196	HRG_HUMAN	I	334	ENSP00000232003:T334I	ENSP00000232003:T334I	T	+	2	0	HRG	187877789	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.189000	0.09629	-0.779000	0.04560	-0.300000	0.09419	ACA	.	.		0.493	HRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344655.1	NM_000412		T	186395095	C	T	186395095	3	4	296	1	0	0	0	0	1	0	0	0	7363	478	17	3	1027	3	HRG	3	186395095	Missense_Mutation	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	7443010	186395095	11627335	63	43007										
LCORL	254251	hgsc.bcm.edu	37	chr4	17885695	17885695	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ttttagaattaagacacaaaGgagagaggtccccatgtaga	10	6	0	4			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr4:17885695G>C	ENST00000382226.5	-	7	1565	c.1457C>G	c.(1456-1458)cCt>cGt	p.P486R	LCORL_ENST00000326877.4_Intron|LCORL_ENST00000539056.1_Intron|LCORL_ENST00000382224.1_Missense_Mutation_p.P402R	NM_001166139.1	NP_001159611.1	Q8N3X6	LCORL_HUMAN	ligand dependent nuclear receptor corepressor-like	486					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)			kidney(1)|large_intestine(1)|lung(1)|prostate(1)	4						AAGACACAAAGGAGAGAGGTC	0.378																																					p.P486R		Atlas-SNP	.											.	LCORL	60	.	0			c.C1457G						.						36	27	30					4																	17885695		692	1590	2282	SO:0001583	missense	254251	exon7			CACAAAGGAGAGA		CCDS3425.1, CCDS54749.1	4p15.32	2006-06-14			ENSG00000178177	ENSG00000178177			30776	protein-coding gene	gene with protein product		611799				12560079	Standard	NM_153686		Approved	MLR1, FLJ30696	uc021xmr.1	Q8N3X6	OTTHUMG00000128538	ENST00000382226.5:c.1457C>G	chr4.hg19:g.17885695G>C	ENSP00000371661:p.Pro486Arg	202.0	0.0		240.0	99.0	NM_001166139	Q96NK1	Missense_Mutation	SNP	ENST00000382226.5	hg19	CCDS54749.1	.	.	.	.	.	.	.	.	.	.	G	13.02	2.111331	0.37242	.	.	ENSG00000178177	ENST00000382224;ENST00000382226	.	.	.	5.19	5.19	0.71726	.	0.200177	0.45126	D	0.000381	T	0.50684	0.1630	N	0.08118	0	0.58432	D	0.999999	.	.	.	.	.	.	T	0.58983	-0.7539	7	0.54805	T	0.06	.	19.0837	0.93194	0.0:0.0:1.0:0.0	.	.	.	.	R	402;486	.	ENSP00000371659:P402R	P	-	2	0	LCORL	17494793	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.851000	0.69481	2.577000	0.86979	0.655000	0.94253	CCT	.	.		0.378	LCORL-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_153686		C	17885695	G	C	17885695	3	2	296	1	0	0	0	0	1	0	0	0	8699	1000	35	4	540	4	LCORL	4	17885695	Missense_Mutation	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10		17885695	173268581	64	43008										
RFC1	5981	hgsc.bcm.edu	37	chr4	39344053	39344054	+	Frame_Shift_Ins	INS	-	-	T													0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tttctggtggctttttggcaINSttttttacctgcaacgtctc							TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr4:39344053_39344054insT	ENST00000381897.1	-	4	375_376	c.242_243insA	c.(241-243)aatfs	p.N81fs	RFC1_ENST00000349703.2_Frame_Shift_Ins_p.N81fs|RFC1_ENST00000418436.1_5'UTR	NM_001204747.1|NM_002913.4	NP_001191676.1|NP_002904.3	P35251	RFC1_HUMAN	replication factor C (activator 1) 1, 145kDa	81					DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription, DNA-templated (GO:0045893)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|telomere maintenance via telomerase (GO:0007004)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	cell junction (GO:0030054)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA clamp loader activity (GO:0003689)|double-stranded DNA binding (GO:0003690)|enzyme activator activity (GO:0008047)|sequence-specific DNA binding (GO:0043565)	p.N81fs*61(1)		haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16						GCTTTTTGGCATTTTTTACCTG	0.351																																					p.N81fs	Colon(109;59 1555 12203 17579 39824)|Esophageal Squamous(18;360 542 16186 28570 51157)	Atlas-Indel,Pindel	.											.	RFC1	114	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.243_244insA						.																																			SO:0001589	frameshift_variant	5981	exon4			.	L23320	CCDS3450.1, CCDS56329.1	4p14-p13	2010-04-21	2002-08-29		ENSG00000035928	ENSG00000035928		"ATPases / AAA-type"	9969	protein-coding gene	gene with protein product		102579	"replication factor C (activator 1) 1 (145kD)"			8114700	Standard	NM_002913		Approved	A1, PO-GA, RFC140, MHCBFB	uc003gty.2	P35251	OTTHUMG00000099363	ENST00000381897.1:c.243dupA	chr4.hg19:g.39344059_39344059dupT	ENSP00000371321:p.Asn81fs	110.0	0.0		116.0	12.0	NM_002913	A8K6E7|Q5XKF5|Q6PKU0|Q86V41|Q86V46	Frame_Shift_Ins	INS	ENST00000381897.1	hg19	CCDS56329.1																																																																																			.	.		0.351	RFC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216808.1	NM_002913		T	39344054	-	T	39344053	7	5	296	1	0	1	1	0	0	0	0	0	13259	214	8	0	3288	0	RFC1	4	39344053	Frame_Shift_Ins	INS	-	TCGA-G3-AAV0-01A-11D-A36X-10	21458358	39344053	151810223	65	43009										
GABRA2	2555	hgsc.bcm.edu	37	chr4	46305505	46305505	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gttcttgcaggcacagattcTctgttaagccagaatgaaac	9	9	2	3			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr4:46305505T>A	ENST00000510861.1	-	8	1001	c.828A>T	c.(826-828)agA>agT	p.R276S	GABRA2_ENST00000381620.4_Missense_Mutation_p.R276S|GABRA2_ENST00000514090.1_Missense_Mutation_p.R276S|GABRA2_ENST00000540012.1_Missense_Mutation_p.R221S|GABRA2_ENST00000507069.1_Missense_Mutation_p.R276S|GABRA2_ENST00000515082.1_Missense_Mutation_p.R276S|GABRA2_ENST00000356504.1_Missense_Mutation_p.R276S			P47869	GBRA2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 2	276					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|neurotransmitter transport (GO:0006836)|regulation of neurotransmitter levels (GO:0001505)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of synaptic vesicle membrane (GO:0030285)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(9)|lung(33)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	56					Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zolpidem(DB00425)|Zopiclone(DB01198)	GCACAGATTCTCTGTTAAGCC	0.373																																					p.R276S		Atlas-SNP	.											.	GABRA2	134	.	0			c.A828T						.						120	116	118					4																	46305505		2203	4300	6503	SO:0001583	missense	2555	exon8			AGATTCTCTGTTA		CCDS3471.1	4p12	2012-06-22			ENSG00000151834	ENSG00000151834		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4076	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 2"	137140					Standard	NM_000807		Approved		uc010igc.2	P47869	OTTHUMG00000044266	ENST00000510861.1:c.828A>T	chr4.hg19:g.46305505T>A	ENSP00000421828:p.Arg276Ser	273.0	1.0		315.0	144.0	NM_000807	A8K0U7|B7Z1H8|Q59G14	Missense_Mutation	SNP	ENST00000510861.1	hg19	CCDS3471.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.305102	0.81247	.	.	ENSG00000151834	ENST00000510861;ENST00000514090;ENST00000381620;ENST00000356504;ENST00000540012;ENST00000507069;ENST00000515082	D;D;D;D;D;D;D	0.84660	-1.88;-1.88;-1.88;-1.88;-1.88;-1.88;-1.88	5.17	2.76	0.32466	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.85522	0.5716	L	0.28740	0.885	0.54753	D	0.999987	D;D;D	0.89917	1.0;0.993;1.0	D;P;D	0.91635	0.987;0.898;0.999	D	0.83985	0.0334	10	0.52906	T	0.07	.	8.4705	0.32982	0.0:0.1592:0.0:0.8408	.	221;276;276	B7Z1H8;G5E9Z6;P47869	.;.;GBRA2_HUMAN	S	276;276;276;276;221;276;276	ENSP00000421828:R276S;ENSP00000421300:R276S;ENSP00000371033:R276S;ENSP00000348897:R276S;ENSP00000444409:R221S;ENSP00000427603:R276S;ENSP00000423840:R276S	ENSP00000348897:R276S	R	-	3	2	GABRA2	46000262	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.032000	0.30178	0.928000	0.37168	0.533000	0.62120	AGA	.	.		0.373	GABRA2-005	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360848.2			A	46305505	T	A	46305505	3	1	296	1	0	0	0	0	1	0	0	0	6169	1548	54	4	539	4	GABRA2	4	46305505	Missense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	6961452	46305505	144848771	66	43010										
KIAA1211	57482	hgsc.bcm.edu	37	chr4	57181349	57181349	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	acctgagccccgtgacgcccGcaaaggacacggggctcacc	12	17	1	2	rs370638037		TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr4:57181349G>A	ENST00000504228.1	+	6	1786	c.1681G>A	c.(1681-1683)Gca>Aca	p.A561T	KIAA1211_ENST00000264229.6_Missense_Mutation_p.A561T|KIAA1211_ENST00000541073.1_Missense_Mutation_p.A554T			Q6ZU35	K1211_HUMAN	KIAA1211	561										endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					CGTGACGCCCGCAAAGGACAC	0.647																																					p.A561T		Atlas-SNP	.											.	KIAA1211	178	.	0			c.G1681A						.						12	18	16					4																	57181349		1973	4130	6103	SO:0001583	missense	57482	exon8			ACGCCCGCAAAGG	AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.1681G>A	chr4.hg19:g.57181349G>A	ENSP00000423366:p.Ala561Thr	144.0	0.0		155.0	59.0	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Missense_Mutation	SNP	ENST00000504228.1	hg19	CCDS43230.1	.	.	.	.	.	.	.	.	.	.	G	8.498	0.863525	0.17250	.	.	ENSG00000109265	ENST00000264229;ENST00000504228;ENST00000541073;ENST00000546221	T;T;T	0.02216	4.39;4.39;4.39	4.48	-2.49	0.06403	.	.	.	.	.	T	0.01489	0.0048	L	0.38175	1.15	0.09310	N	1	P;P;P	0.43314	0.803;0.803;0.645	B;B;B	0.33454	0.164;0.164;0.071	T	0.38585	-0.9654	9	0.62326	D	0.03	-1.8037	1.1214	0.01725	0.2132:0.3164:0.2556:0.2147	.	554;554;561	B7ZVZ4;F5H1N7;Q6ZU35	.;.;K1211_HUMAN	T	561;561;554;471	ENSP00000264229:A561T;ENSP00000423366:A561T;ENSP00000444006:A554T	ENSP00000264229:A561T	A	+	1	0	KIAA1211	56876106	0.000000	0.05858	0.000000	0.03702	0.185000	0.23345	0.028000	0.13644	-0.927000	0.03766	-0.314000	0.08810	GCA	.	.		0.647	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722		A	57181349	G	A	57181349	3	1	296	1	0	0	0	0	1	0	0	0	8224	1087	38	1	1699	1	KIAA1211	4	57181349	Missense_Mutation	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10	10875844	57181349	133972927	67	43011										
ALB	213	hgsc.bcm.edu	37	chr4	74285253	74285253	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tgagctcgtgaaacacaagcCcaaggcaacaaaagagcaac	9	11	0	3			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr4:74285253C>G	ENST00000503124.1	+	11	1439	c.1232C>G	c.(1231-1233)cCc>cGc	p.P411R	ALB_ENST00000295897.4_Missense_Mutation_p.P561R|ALB_ENST00000509063.1_Missense_Mutation_p.P561R|ALB_ENST00000505649.1_3'UTR|ALB_ENST00000415165.2_Missense_Mutation_p.P369R|ALB_ENST00000401494.3_Missense_Mutation_p.P446R			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			AAACACAAGCCCAAGGCAACA	0.408																																					p.P561R		Atlas-SNP	.											.	ALB	132	.	0			c.C1682G						.						88	83	84					4																	74285253		2203	4300	6503	SO:0001583	missense	213	exon13			ACAAGCCCAAGGC	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.1232C>G	chr4.hg19:g.74285253C>G	ENSP00000421027:p.Pro411Arg	116.0	0.0		104.0	34.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000503124.1	hg19		.	.	.	.	.	.	.	.	.	.	C	22.4	4.285424	0.80803	.	.	ENSG00000163631	ENST00000295897;ENST00000415165;ENST00000329326;ENST00000503124;ENST00000509063;ENST00000401494;ENST00000430202	T;T;T;T;T	0.71222	-0.55;-0.55;-0.55;-0.55;-0.55	6.17	6.17	0.99709	Serum albumin-like (1);Serum albumin, N-terminal (3);	0.000000	0.85682	D	0.000000	D	0.88299	0.6399	M	0.91406	3.205	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	D	0.89512	0.3772	10	0.87932	D	0	-24.0555	19.4432	0.94831	0.0:1.0:0.0:0.0	.	446;369;411;561;561	B7WNR0;C9JKR2;D6RHD5;A6NBZ8;P02768	.;.;.;.;ALBU_HUMAN	R	561;369;348;411;561;446;570	ENSP00000295897:P561R;ENSP00000401820:P369R;ENSP00000421027:P411R;ENSP00000422784:P561R;ENSP00000384695:P446R	ENSP00000295897:P561R	P	+	2	0	ALB	74504117	1.000000	0.71417	0.999000	0.59377	0.834000	0.47266	3.206000	0.51098	2.941000	0.99782	0.655000	0.94253	CCC	.	.		0.408	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		G	74285253	C	G	74285253	3	3	296	1	0	0	0	0	1	0	0	0	486	623	22	4	1732	4	ALB	4	74285253	Missense_Mutation	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	17103904	74285253	116869023	68	43012										
CDS1	1040	hgsc.bcm.edu	37	chr4	85569727	85569727	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	taggggcccaaatcccagcaAagtgctacagcagttgttgg	12	10	0	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr4:85569727A>C	ENST00000295887.5	+	13	1697	c.1274A>C	c.(1273-1275)aAa>aCa	p.K425T		NM_001263.3	NP_001254.2	O96017	CHK2_HUMAN	CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 1	0	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|liver(2)|lung(5)|ovary(1)	20		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.00101)		AATCCCAGCAAAGTGCTACAG	0.393																																					p.K425T		Atlas-SNP	.											.	CDS1	58	.	0			c.A1274C						.						66	65	65					4																	85569727		2203	4300	6503	SO:0001583	missense	1040	exon13			CCAGCAAAGTGCT	U65887	CCDS3608.1	4q21	2008-02-05			ENSG00000163624	ENSG00000163624	2.7.7.41		1800	protein-coding gene	gene with protein product		603548				9806839, 9115637	Standard	NM_001263		Approved		uc011ccv.2	Q92903	OTTHUMG00000130428	ENST00000295887.5:c.1274A>C	chr4.hg19:g.85569727A>C	ENSP00000295887:p.Lys425Thr	277.0	0.0		147.0	107.0	NM_001263	A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Missense_Mutation	SNP	ENST00000295887.5	hg19	CCDS3608.1	.	.	.	.	.	.	.	.	.	.	A	14.88	2.666965	0.47677	.	.	ENSG00000163624	ENST00000295887	T	0.45276	0.9	5.66	2.0	0.26442	.	0.131525	0.64402	D	0.000003	T	0.39517	0.1081	M	0.69823	2.125	0.58432	D	0.999999	P	0.42357	0.777	B	0.42030	0.373	T	0.14559	-1.0468	10	0.24483	T	0.36	-5.9792	8.3155	0.32097	0.7621:0.0:0.2379:0.0	.	425	Q92903	CDS1_HUMAN	T	425	ENSP00000295887:K425T	ENSP00000295887:K425T	K	+	2	0	CDS1	85788751	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.630000	0.61297	0.418000	0.25898	0.528000	0.53228	AAA	.	.		0.393	CDS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252817.2			C	85569727	A	C	85569727	3	2	296	1	0	0	0	0	1	0	0	0	3179	14	1	5	1324	5	CDS1	4	85569727	Missense_Mutation	SNP	A	TCGA-G3-AAV0-01A-11D-A36X-10	11284474	85569727	105584549	69	43013										
C4orf21	55345	hgsc.bcm.edu	37	chr4	113538660	113538660	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tgaaagacagtatttttcttTttcaatatttccaagctgtc	5	7	2	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr4:113538660T>A	ENST00000505019.1	-	6	2663	c.2538A>T	c.(2536-2538)aaA>aaT	p.K846N	C4orf21_ENST00000309071.5_Missense_Mutation_p.K846N|C4orf21_ENST00000445203.2_Missense_Mutation_p.K815N	NM_018392.4	NP_060862.3	Q86YA3	ZGRF1_HUMAN		846						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(6)|lung(21)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)		TATTTTTCTTTTTCAATATTT	0.348																																					p.K846N		Atlas-SNP	.											.	C4orf21	223	.	0			c.A2538T						.						121	118	119					4																	113538660		2203	4300	6503	SO:0001583	missense	55345	exon6			TTTCTTTTTCAAT																												ENST00000505019.1:c.2538A>T	chr4.hg19:g.113538660T>A	ENSP00000424737:p.Lys846Asn	213.0	0.0		254.0	108.0	NM_018392	B3KQX2|B4DSN6|B4DYU8|E9PDE1|G5EA02|Q6ZU11|Q9NSW3|Q9NUJ4	Missense_Mutation	SNP	ENST00000505019.1	hg19		.	.	.	.	.	.	.	.	.	.	T	14.42	2.528647	0.44969	.	.	ENSG00000138658	ENST00000505019;ENST00000309071;ENST00000445203	D;T;T	0.91740	-2.9;0.7;0.25	5.98	0.805	0.18703	.	0.517073	0.18868	N	0.128941	D	0.88433	0.6435	M	0.68952	2.095	0.09310	N	1	B;B	0.31227	0.314;0.096	B;B	0.31686	0.134;0.134	T	0.81113	-0.1080	10	0.72032	D	0.01	-4.388	5.6126	0.17414	0.1305:0.377:0.0:0.4925	.	846;846	Q86YA3;G5EA02	CD021_HUMAN;.	N	846;846;815	ENSP00000424737:K846N;ENSP00000309095:K846N;ENSP00000390505:K815N	ENSP00000309095:K846N	K	-	3	2	C4orf21	113758109	0.000000	0.05858	0.001000	0.08648	0.071000	0.16799	-0.002000	0.12924	0.169000	0.19679	0.533000	0.62120	AAA	.	.		0.348	C4orf21-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000256413.1			A	113538660	T	A	113538660	3	1	296	1	0	0	0	0	1	0	0	0	2256	1838	64	4	3868	4	C4orf21	4	113538660	Missense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	27968933	113538660	77615616	70	43014										
SPATA5	166378	hgsc.bcm.edu	37	chr4	123868516	123868516	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gttcccaatgctcaggaccgGctagatattctccagaaact	8	12	2	2	rs140187138		TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr4:123868516G>A	ENST00000274008.4	+	9	1656	c.1587G>A	c.(1585-1587)cgG>cgA	p.R529R	SPATA5_ENST00000422835.2_3'UTR	NM_145207.2	NP_660208.2	Q8NB90	SPAT5_HUMAN	spermatogenesis associated 5	529					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24						CTCAGGACCGGCTAGATATTC	0.522																																					p.R529R		Atlas-SNP	.											.	SPATA5	62	.	0			c.G1587A						.						91	90	90					4																	123868516		2203	4300	6503	SO:0001819	synonymous_variant	166378	exon9			GGACCGGCTAGAT	AF361489	CCDS3730.1	4q28.1	2010-04-21			ENSG00000145375	ENSG00000145375		"ATPases / AAA-type"	18119	protein-coding gene	gene with protein product	"ATPase family gene 2 homolog (S. cerevisiae)"	613940				16465403	Standard	NM_145207		Approved	SPAF, AFG2	uc003iez.4	Q8NB90	OTTHUMG00000133074	ENST00000274008.4:c.1587G>A	chr4.hg19:g.123868516G>A		101.0	0.0		107.0	40.0	NM_145207	C9JT97|Q86XW1|Q8NI20|Q8TDL7	Silent	SNP	ENST00000274008.4	hg19	CCDS3730.1																																																																																			.	G|1.000;T|0.000		0.522	SPATA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256714.2	NM_145207		A	123868516	G	A	123868516	2	1	296	1	0	0	0	0	0	0	0	1	15026	1190	42	3		3	SPATA5	4	123868516	Silent	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10	10329856	123868516	67285760	71	43015										
PHF17	79960	hgsc.bcm.edu	37	chr4	129782877	129782877	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	agtgctctgtgaagaactgcCgcacagccttccatgtgacc	10	13	1	3	rs369651997		TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr4:129782877C>T	ENST00000226319.6	+	9	1280	c.1000C>T	c.(1000-1002)Cgc>Tgc	p.R334C	PHF17_ENST00000512960.1_Missense_Mutation_p.R334C|PHF17_ENST00000413543.2_Missense_Mutation_p.R334C|PHF17_ENST00000511647.1_Missense_Mutation_p.R334C|PHF17_ENST00000452328.2_Missense_Mutation_p.R322C	NM_199320.2	NP_955352.1														NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						GAAGAACTGCCGCACAGCCTT	0.483																																					p.R334C		Atlas-SNP	.											.	PHF17	63	.	0			c.C1000T						.	C	CYS/ARG,CYS/ARG	0,4406		0,0,2203	83	86	85		1000,1000	5.1	1	4		85	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	PHF17	NM_024900.3,NM_199320.2	180,180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	334/510,334/843	129782877	1,13005	2203	4300	6503	SO:0001583	missense	79960	exon9			AACTGCCGCACAG																												ENST00000226319.6:c.1000C>T	chr4.hg19:g.129782877C>T	ENSP00000226319:p.Arg334Cys	115.0	0.0		138.0	59.0	NM_199320		Missense_Mutation	SNP	ENST00000226319.6	hg19	CCDS34062.1	.	.	.	.	.	.	.	.	.	.	C	19.76	3.887780	0.72410	0.0	1.16E-4	ENSG00000077684	ENST00000226319;ENST00000511647;ENST00000452328;ENST00000512960;ENST00000535321;ENST00000413543	T;T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07;-0.07	5.08	5.08	0.68730	Zinc finger, PHD-type (1);	0.000000	0.85682	D	0.000000	T	0.73583	0.3605	L	0.56199	1.76	0.80722	D	1	D;D;D	0.89917	0.998;1.0;0.996	D;D;P	0.75020	0.94;0.985;0.894	T	0.72161	-0.4374	9	.	.	.	.	14.5181	0.67833	0.1557:0.8443:0.0:0.0	.	322;334;334	Q6IE81-2;Q6IE81;Q6IE81-3	.;JADE1_HUMAN;.	C	334;334;322;334;334;334	ENSP00000226319:R334C;ENSP00000423737:R334C;ENSP00000388015:R322C;ENSP00000425730:R334C;ENSP00000404211:R334C	.	R	+	1	0	PHF17	130002327	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	3.337000	0.52120	2.640000	0.89533	0.655000	0.94253	CGC	.	.		0.483	PHF17-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364280.1			T	129782877	C	T	129782877	3	4	296	1	0	0	0	0	1	0	0	0	11837	652	23	1	1030	1	PHF17	4	129782877	Missense_Mutation	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	5914361	129782877	61371399	72	43016										
TBC1D9	23158	hgsc.bcm.edu	37	chr4	141600769	141600769	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tgaaattttagatgacttacCttcccttcccataagaaaag	5	9	0	4			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr4:141600769C>T	ENST00000442267.2	-	4	663	c.589G>A	c.(589-591)Gcg>Acg	p.A197T		NM_015130.2	NP_055945.2	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)	197	GRAM 1.						calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	31	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				GATGACTTACCTTCCCTTCCC	0.398																																					p.A197T		Atlas-SNP	.											.	TBC1D9	198	.	0			c.G589A						.						38	37	37					4																	141600769		1815	4080	5895	SO:0001630	splice_region_variant	23158	exon4			ACTTACCTTCCCT	AB020689	CCDS47136.1	4q31.1	2013-01-10	2006-07-12		ENSG00000109436	ENSG00000109436		"EF-hand domain containing"	21710	protein-coding gene	gene with protein product			"TBC1 domain family, member 9"			12970790	Standard	NM_015130		Approved	KIAA0882, MDR1	uc010ioj.3	Q6ZT07	OTTHUMG00000161405	ENST00000442267.2:c.589+1G>A	chr4.hg19:g.141600769C>T		127.0	0.0		168.0	69.0	NM_015130	A6H8U8|D3DNZ1|O94958	Missense_Mutation	SNP	ENST00000442267.2	hg19	CCDS47136.1	.	.	.	.	.	.	.	.	.	.	C	16.09	3.024541	0.54683	.	.	ENSG00000109436	ENST00000442267	D	0.87029	-2.2	5.41	5.41	0.78517	GRAM (2);	0.107851	0.64402	D	0.000006	T	0.68915	0.3053	N	0.01096	-1.015	0.80722	D	1	B	0.15141	0.012	B	0.15052	0.012	T	0.66976	-0.5787	9	.	.	.	.	19.2074	0.93736	0.0:1.0:0.0:0.0	.	197	Q6ZT07	TBCD9_HUMAN	T	197	ENSP00000411197:A197T	.	A	-	1	0	TBC1D9	141820219	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.572000	0.82409	2.548000	0.85928	0.655000	0.94253	GCG	.	.		0.398	TBC1D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364806.1	NM_015130	Missense_Mutation	T	141600769	C	T	141600769	5	4	296	1	0	0	0	0	0	0	1	0	15642	695	24	3	3283	3	TBC1D9	4	141600769	Splice_Site	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	11817892	141600769	49553507	73	43017										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155163890	155163890	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tacagtcgtattagaaagccTgggcatccctttatctgtgg	10	9	1	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr4:155163890T>A	ENST00000357232.4	-	22	5610	c.5611A>T	c.(5611-5613)Agg>Tgg	p.R1871W		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1871	Cadherin 16. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		TTAGAAAGCCTGGGCATCCCT	0.388																																					p.R1871W		Atlas-SNP	.											.	DCHS2	594	.	0			c.A5611T						.						115	109	111					4																	155163890		2203	4300	6503	SO:0001583	missense	54798	exon22			AAAGCCTGGGCAT	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.5611A>T	chr4.hg19:g.155163890T>A	ENSP00000349768:p.Arg1871Trp	65.0	0.0		58.0	30.0	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	hg19	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	T	18.13	3.555579	0.65425	.	.	ENSG00000197410	ENST00000357232	T	0.53206	0.63	5.24	2.69	0.31865	Cadherin (4);Cadherin-like (1);	0.392907	0.22924	N	0.053987	T	0.60753	0.2293	L	0.54323	1.7	0.80722	D	1	D	0.76494	0.999	D	0.70487	0.969	T	0.60352	-0.7280	10	0.72032	D	0.01	.	11.9721	0.53069	0.0:0.0:0.3225:0.6775	.	1871	Q6V1P9	PCD23_HUMAN	W	1871	ENSP00000349768:R1871W	ENSP00000349768:R1871W	R	-	1	2	DCHS2	155383340	1.000000	0.71417	0.273000	0.24645	0.830000	0.47004	2.930000	0.48924	0.326000	0.23384	0.533000	0.62120	AGG	.	.		0.388	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		A	155163890	T	A	155163890	3	1	296	1	0	0	0	0	1	0	0	0	4290	1579	55	4	3155	4	DCHS2	4	155163890	Missense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	13563121	155163890	35990386	74	43018										
TRIML1	339976	hgsc.bcm.edu	37	chr4	189068011	189068011	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	acccagccacagctaatgccTatctcgtgttgtcggaggat	10	12	1	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr4:189068011T>A	ENST00000332517.3	+	6	1032	c.892T>A	c.(892-894)Tat>Aat	p.Y298N	TRIML1_ENST00000507581.1_3'UTR	NM_178556.3	NP_848651.2	Q8N9V2	TRIML_HUMAN	tripartite motif family-like 1	298	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				multicellular organismal development (GO:0007275)|protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	60		all_cancers(14;1.33e-43)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)|all_hematologic(60;0.062)		OV - Ovarian serous cystadenocarcinoma(60;1.52e-11)|BRCA - Breast invasive adenocarcinoma(30;4.19e-06)|GBM - Glioblastoma multiforme(59;0.000232)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.156)		AGCTAATGCCTATCTCGTGTT	0.507																																					p.Y298N	Melanoma(31;213 1036 16579 23968 32372)	Atlas-SNP	.											.	TRIML1	126	.	0			c.T892A						.						155	156	156					4																	189068011		2203	4300	6503	SO:0001583	missense	339976	exon6			AATGCCTATCTCG	AK093499	CCDS3851.1	4q35.2	2013-01-09			ENSG00000184108	ENSG00000184108		"RING-type (C3HC4) zinc fingers"	26698	protein-coding gene	gene with protein product						12477932	Standard	NM_178556		Approved	FLJ36180, RNF209	uc003izm.1	Q8N9V2	OTTHUMG00000160237	ENST00000332517.3:c.892T>A	chr4.hg19:g.189068011T>A	ENSP00000327738:p.Tyr298Asn	168.0	0.0		182.0	69.0	NM_178556	Q96BE5	Missense_Mutation	SNP	ENST00000332517.3	hg19	CCDS3851.1	.	.	.	.	.	.	.	.	.	.	t	9.157	1.017748	0.19355	.	.	ENSG00000184108	ENST00000332517	T	0.13420	2.59	4.92	3.74	0.42951	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	0.140133	0.33631	N	0.004715	T	0.07593	0.0191	N	0.20986	0.625	0.22171	N	0.999317	B	0.17268	0.021	B	0.19666	0.026	T	0.34403	-0.9830	10	0.19147	T	0.46	-11.4335	4.3025	0.10932	0.1757:0.0929:0.0:0.7315	.	298	Q8N9V2	TRIML_HUMAN	N	298	ENSP00000327738:Y298N	ENSP00000327738:Y298N	Y	+	1	0	TRIML1	189305005	0.000000	0.05858	0.740000	0.30986	0.021000	0.10359	-1.860000	0.01656	1.036000	0.39998	0.449000	0.29647	TAT	.	.		0.507	TRIML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359813.1	NM_178556		A	189068011	T	A	189068011	3	1	296	1	0	0	0	0	1	0	0	0	16565	1522	53	4	914	4	TRIML1	4	189068011	Missense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	33904121	189068011	2086265	75	43019										
TRIO	7204	hgsc.bcm.edu	37	chr5	14394211	14394211	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ccttattaaaccagttcagcGaataacgaagtatcagctcc	6	11	2	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr5:14394211G>A	ENST00000344204.4	+	28	4307	c.4283G>A	c.(4282-4284)cGa>cAa	p.R1428Q	TRIO_ENST00000537187.1_Missense_Mutation_p.R1428Q|TRIO_ENST00000509967.2_Missense_Mutation_p.R1379Q	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	1428	DH 1. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118	Lung NSC(4;0.000742)					CCAGTTCAGCGAATAACGAAG	0.313																																					p.R1428Q		Atlas-SNP	.											.	TRIO	305	.	0			c.G4283A						.						118	115	116					5																	14394211		2203	4300	6503	SO:0001583	missense	7204	exon28			TTCAGCGAATAAC	AF091395	CCDS3883.1	5p14-p15.1	2013-01-11	2012-07-12		ENSG00000038382	ENSG00000038382		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing"	12303	protein-coding gene	gene with protein product		601893	"triple functional domain (PTPRF interacting)"			8643598	Standard	NM_007118		Approved	ARHGEF23	uc003jff.3	O75962	OTTHUMG00000131057	ENST00000344204.4:c.4283G>A	chr5.hg19:g.14394211G>A	ENSP00000339299:p.Arg1428Gln	160.0	0.0		188.0	73.0	NM_007118	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Missense_Mutation	SNP	ENST00000344204.4	hg19	CCDS3883.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.683643	0.88639	.	.	ENSG00000038382	ENST00000344204;ENST00000537187;ENST00000509967;ENST00000513206	T;T;T	0.67698	-0.28;-0.28;-0.28	5.1	5.1	0.69264	Dbl homology (DH) domain (5);	0.000000	0.85682	D	0.000000	D	0.87744	0.6254	H	0.95504	3.68	0.80722	D	1	D;D;D	0.89917	1.0;0.993;1.0	D;B;D	0.87578	0.998;0.392;0.996	D	0.91409	0.5149	10	0.87932	D	0	.	18.8837	0.92367	0.0:0.0:1.0:0.0	.	1379;1428;1428	F5H228;O75962-5;O75962	.;.;TRIO_HUMAN	Q	1428;1428;1379;1115	ENSP00000339299:R1428Q;ENSP00000446348:R1428Q;ENSP00000445592:R1379Q	ENSP00000339299:R1428Q	R	+	2	0	TRIO	14447211	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	9.813000	0.99286	2.520000	0.84964	0.655000	0.94253	CGA	.	.		0.313	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118		A	14394211	G	A	14394211	3	1	296	1	0	0	0	0	1	0	0	0	16567	1058	37	1	4393	1	TRIO	5	14394211	Missense_Mutation	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10		14394211	166521049	76	43020										
ITGA2	3673	hgsc.bcm.edu	37	chr5	52376395	52376395	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ctgtaatcatccacatccctCagtataccaaagaaaagaac	4	12	2	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr5:52376395C>T	ENST00000296585.5	+	25	3126	c.2983C>T	c.(2983-2985)Cag>Tag	p.Q995*		NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	995					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular response to hormone stimulus (GO:0032870)|collagen-activated signaling pathway (GO:0038065)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|hepatocyte differentiation (GO:0070365)|hypotonic response (GO:0006971)|integrin-mediated signaling pathway (GO:0007229)|mammary gland development (GO:0030879)|mesodermal cell differentiation (GO:0048333)|organ morphogenesis (GO:0009887)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell projection organization (GO:0031346)|positive regulation of collagen binding (GO:0033343)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA binding (GO:0043388)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|response to amine (GO:0014075)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to muscle activity (GO:0014850)|response to organic cyclic compound (GO:0014070)|skin morphogenesis (GO:0043589)|substrate-dependent cell migration (GO:0006929)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	axon terminus (GO:0043679)|basal part of cell (GO:0045178)|cell outer membrane (GO:0009279)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin alpha2-beta1 complex (GO:0034666)|integrin complex (GO:0008305)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)			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)				CCACATCCCTCAGTATACCAA	0.388																																					p.Q995X		Atlas-SNP	.											.	ITGA2	211	.	0			c.C2983T						.						173	163	167					5																	52376395		2203	4300	6503	SO:0001587	stop_gained	3673	exon25			ATCCCTCAGTATA		CCDS3957.1	5q11.2	2010-03-23			ENSG00000164171	ENSG00000164171		"CD molecules", "Integrins"	6137	protein-coding gene	gene with protein product		192974		CD49B			Standard	NM_002203		Approved	CD49b	uc003joy.3	P17301	OTTHUMG00000131165	ENST00000296585.5:c.2983C>T	chr5.hg19:g.52376395C>T	ENSP00000296585:p.Gln995*	159.0	0.0		136.0	55.0	NM_002203	Q14595	Nonsense_Mutation	SNP	ENST00000296585.5	hg19	CCDS3957.1	.	.	.	.	.	.	.	.	.	.	C	40	8.334747	0.98764	.	.	ENSG00000164171	ENST00000296585	.	.	.	5.1	5.1	0.69264	.	0.632453	0.17193	N	0.183421	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05721	T	0.95	.	10.9753	0.47463	0.1419:0.7205:0.1376:0.0	.	.	.	.	X	995	.	ENSP00000296585:Q995X	Q	+	1	0	ITGA2	52412152	0.602000	0.26916	0.991000	0.47740	0.951000	0.60555	1.096000	0.30976	2.814000	0.96858	0.655000	0.94253	CAG	.	.		0.388	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203		T	52376395	C	T	52376395	4	4	296	1	0	0	0	0	0	1	0	0	7884	827	29	3	3081	3	ITGA2	5	52376395	Nonsense_Mutation	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	37982184	52376395	128538865	77	43021										
FST	10468	hgsc.bcm.edu	37	chr5	52776658	52776658	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	accagccgggtgggctttgcCtcctgctgctgctgctctgc	13	15	1	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr5:52776658C>G	ENST00000256759.3	+	1	420	c.37C>G	c.(37-39)Ctc>Gtc	p.L13V	FST_ENST00000396947.3_Missense_Mutation_p.L13V	NM_013409.2	NP_037541.1	P19883	FST_HUMAN	follistatin	13					BMP signaling pathway (GO:0030509)|female gonad development (GO:0008585)|gamete generation (GO:0007276)|hair follicle morphogenesis (GO:0031069)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinocyte proliferation (GO:0043616)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|pattern specification process (GO:0007389)|positive regulation of hair follicle development (GO:0051798)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleus (GO:0005634)	activin binding (GO:0048185)|signal transducer activity (GO:0004871)			breast(1)|endometrium(1)|large_intestine(4)|lung(7)|prostate(1)|urinary_tract(1)	15		Ovarian(174;1.78e-06)|Lung NSC(810;3.55e-06)|Breast(144;4.08e-05)				TGGGCTTTGCCTCCTGCTGCT	0.741																																					p.L13V		Atlas-SNP	.											.	FST	42	.	0			c.C37G						.						20	15	17					5																	52776658		1986	3815	5801	SO:0001583	missense	10468	exon1			CTTTGCCTCCTGC	M19481	CCDS3959.1, CCDS43315.1	5q11.2	2008-02-05			ENSG00000134363	ENSG00000134363			3971	protein-coding gene	gene with protein product		136470				10411917, 3380788	Standard	NM_006350		Approved	FS	uc003jpd.3	P19883	OTTHUMG00000131183	ENST00000256759.3:c.37C>G	chr5.hg19:g.52776658C>G	ENSP00000256759:p.Leu13Val	65.0	0.0		83.0	40.0	NM_013409	B5BU94|Q9BTH0	Missense_Mutation	SNP	ENST00000256759.3	hg19	CCDS3959.1	.	.	.	.	.	.	.	.	.	.	C	11.90	1.776810	0.31411	.	.	ENSG00000134363	ENST00000256759;ENST00000511025;ENST00000396947	T;T	0.36340	1.26;1.53	3.97	3.1	0.35709	.	0.072035	0.51477	D	0.000096	T	0.23210	0.0561	L	0.31664	0.95	0.44728	D	0.997725	B	0.06786	0.001	B	0.06405	0.002	T	0.05053	-1.0909	10	0.30078	T	0.28	-8.9785	7.7763	0.29039	0.1712:0.7379:0.0:0.0908	.	13	P19883	FST_HUMAN	V	13	ENSP00000256759:L13V;ENSP00000380151:L13V	ENSP00000256759:L13V	L	+	1	0	FST	52812415	1.000000	0.71417	0.999000	0.59377	0.718000	0.41266	1.512000	0.35812	0.885000	0.36088	-0.339000	0.08088	CTC	.	.		0.741	FST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253906.1	NM_013409		G	52776658	C	G	52776658	3	3	296	1	0	0	0	0	1	0	0	0	6084	681	24	4	39	4	FST	5	52776658	Missense_Mutation	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	400263	52776658	128138602	78	43022										
BHMT2	23743	hgsc.bcm.edu	37	chr5	78379661	78379661	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tggtttggacatgcacaccaAaccctggattagagcaaggt	11	9	0	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr5:78379661A>C	ENST00000255192.3	+	7	1058	c.992A>C	c.(991-993)aAa>aCa	p.K331T	BHMT2_ENST00000521567.1_Missense_Mutation_p.K267T|DMGDH_ENST00000520388.1_Intron	NM_017614.4	NP_060084.2	Q9H2M3	BHMT2_HUMAN	betaine--homocysteine S-methyltransferase 2	331					L-methionine salvage (GO:0071267)|S-adenosylmethionine metabolic process (GO:0046500)|S-methylmethionine metabolic process (GO:0033477)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|S-methylmethionine-homocysteine S-methyltransferase activity (GO:0061627)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(8)|lung(2)|ovary(1)|skin(1)|urinary_tract(1)	15		all_lung(232;0.00063)|Lung NSC(167;0.00171)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;2.09e-45)|Epithelial(54;9.3e-41)|all cancers(79;4.09e-36)	L-Methionine(DB00134)	ATGCACACCAAACCCTGGATT	0.413																																					p.K331T		Atlas-SNP	.											.	BHMT2	44	.	0			c.A992C						.						31	33	32					5																	78379661		2203	4300	6503	SO:0001583	missense	23743	exon7			ACACCAAACCCTG		CCDS4045.1, CCDS54871.1	5q13	2010-04-28	2010-04-28		ENSG00000132840	ENSG00000132840	2.1.1.5		1048	protein-coding gene	gene with protein product		605932				11087663, 18230605	Standard	NM_017614		Approved		uc003kft.3	Q9H2M3	OTTHUMG00000108158	ENST00000255192.3:c.992A>C	chr5.hg19:g.78379661A>C	ENSP00000255192:p.Lys331Thr	293.0	0.0		308.0	109.0	NM_017614	B7Z516|Q9NXX7	Missense_Mutation	SNP	ENST00000255192.3	hg19	CCDS4045.1	.	.	.	.	.	.	.	.	.	.	A	15.46	2.840213	0.51057	.	.	ENSG00000132840	ENST00000255192;ENST00000521567	T;T	0.30981	1.51;1.51	5.44	5.44	0.79542	Homocysteine S-methyltransferase (2);	0.091397	0.64402	D	0.000001	T	0.57888	0.2084	M	0.85859	2.78	0.80722	D	1	D;D	0.71674	0.998;0.968	D;P	0.71870	0.975;0.63	T	0.59606	-0.7423	10	0.26408	T	0.33	-22.597	15.4981	0.75673	1.0:0.0:0.0:0.0	.	267;331	B7Z516;Q9H2M3	.;BHMT2_HUMAN	T	331;267	ENSP00000255192:K331T;ENSP00000430278:K267T	ENSP00000255192:K331T	K	+	2	0	BHMT2	78415417	1.000000	0.71417	1.000000	0.80357	0.017000	0.09413	9.086000	0.94088	2.061000	0.61500	0.533000	0.62120	AAA	.	.		0.413	BHMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226962.2	NM_017614		C	78379661	A	C	78379661	3	2	296	1	0	0	0	0	1	0	0	0	1426	14	1	5	1018	5	BHMT2	5	78379661	Missense_Mutation	SNP	A	TCGA-G3-AAV0-01A-11D-A36X-10	25603003	78379661	102535599	79	43023										
GPR98	84059	hgsc.bcm.edu	37	chr5	90079735	90079735	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gcgccacctagtgagcagaaTcataatagctaagagtgact	10	9	1	4			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr5:90079735T>C	ENST00000405460.2	+	67	13610	c.13514T>C	c.(13513-13515)aTc>aCc	p.I4505T	GPR98_ENST00000425867.2_Missense_Mutation_p.I166T	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	4505					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		GTGAGCAGAATCATAATAGCT	0.433																																					p.I4505T		Atlas-SNP	.											.	GPR98	605	.	0			c.T13514C						.						62	60	61					5																	90079735		1839	4086	5925	SO:0001583	missense	84059	exon67			GCAGAATCATAAT	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.13514T>C	chr5.hg19:g.90079735T>C	ENSP00000384582:p.Ile4505Thr	117.0	0.0		127.0	53.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	T	12.85	2.062368	0.36373	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.32272	1.46;1.46	5.97	5.97	0.96955	.	0.260709	0.43110	D	0.000606	T	0.40145	0.1105	M	0.79475	2.455	0.39623	D	0.970056	P;B;P	0.46512	0.546;0.361;0.879	B;B;B	0.40940	0.1;0.054;0.344	T	0.51624	-0.8682	10	0.87932	D	0	.	16.4454	0.83928	0.0:0.0:0.0:1.0	.	166;4505;166	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	T	4505;4505;166	ENSP00000384582:I4505T;ENSP00000392618:I166T	ENSP00000296619:I4505T	I	+	2	0	GPR98	90115491	1.000000	0.71417	0.647000	0.29507	0.239000	0.25481	7.756000	0.85195	2.275000	0.75901	0.533000	0.62120	ATC	.	.		0.433	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		C	90079735	T	C	90079735	3	2	296	1	0	0	0	0	1	0	0	0	6730	1435	50	2	13780	2	GPR98	5	90079735	Missense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	11700074	90079735	90835525	80	43024										
VDAC1	7416	hgsc.bcm.edu	37	chr5	133326695	133326695	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tttcacagcagccattacctGatcttccacagtaatctcgg	6	13	3	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr5:133326695G>A	ENST00000265333.3	-	4	512	c.268C>T	c.(268-270)Cag>Tag	p.Q90*	VDAC1_ENST00000395047.2_Nonsense_Mutation_p.Q90*|VDAC1_ENST00000466080.1_5'UTR|VDAC1_ENST00000395044.3_Nonsense_Mutation_p.Q90*	NM_003374.2	NP_003365.1	P21796	VDAC1_HUMAN	voltage-dependent anion channel 1	90					anion transport (GO:0006820)|apoptotic process (GO:0006915)|behavioral fear response (GO:0001662)|epithelial cell differentiation (GO:0030855)|learning (GO:0007612)|neuron-neuron synaptic transmission (GO:0007270)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|pore complex (GO:0046930)	porin activity (GO:0015288)|protein kinase binding (GO:0019901)|voltage-gated anion channel activity (GO:0008308)			endometrium(1)|large_intestine(1)|lung(1)|skin(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00806)|Kidney(363;0.02)		Dihydroxyaluminium(DB01375)	GCCATTACCTGATCTTCCACA	0.438																																					p.Q90X	NSCLC(127;1776 1806 35523 41489 48154)	Atlas-SNP	.											.	VDAC1	17	.	0			c.C268T						.						233	219	224					5																	133326695		2203	4300	6503	SO:0001587	stop_gained	7416	exon4			TTACCTGATCTTC		CCDS4168.1	5q31	2011-11-15			ENSG00000213585	ENSG00000213585		"Voltage-dependent anion channels"	12669	protein-coding gene	gene with protein product		604492				7517385	Standard	NM_003374		Approved	MGC111064, PORIN	uc003kyr.2	P21796	OTTHUMG00000129118	ENST00000265333.3:c.268C>T	chr5.hg19:g.133326695G>A	ENSP00000265333:p.Gln90*	100.0	0.0		96.0	41.0	NM_003374	B3KVK4|D3DQ93|Q5FVE7|Q9UIQ5|Q9UPL0	Nonsense_Mutation	SNP	ENST00000265333.3	hg19	CCDS4168.1	.	.	.	.	.	.	.	.	.	.	G	36	5.735651	0.96865	.	.	ENSG00000213585	ENST00000265333;ENST00000395044;ENST00000395047;ENST00000425992	.	.	.	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09843	T	0.71	.	20.2985	0.98592	0.0:0.0:1.0:0.0	.	.	.	.	X	90	.	ENSP00000265333:Q90X	Q	-	1	0	VDAC1	133354594	1.000000	0.71417	0.997000	0.53966	0.363000	0.29612	7.968000	0.87980	2.793000	0.96121	0.655000	0.94253	CAG	.	.		0.438	VDAC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259208.1			A	133326695	G	A	133326695	4	1	296	1	0	0	0	0	0	1	0	0	17161	1299	45	3	607	3	VDAC1	5	133326695	Nonsense_Mutation	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10	43246960	133326695	47588565	81	43025										
TGFBI	7045	hgsc.bcm.edu	37	chr5	135389646	135389646	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ttgtagccaagacactatttGaattggctgcagagtctgat	10	7	1	4			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr5:135389646G>A	ENST00000442011.2	+	9	1302	c.1141G>A	c.(1141-1143)Gaa>Aaa	p.E381K	TGFBI_ENST00000305126.8_Missense_Mutation_p.E381K	NM_000358.2	NP_000349.1	Q15582	BGH3_HUMAN	transforming growth factor, beta-induced, 68kDa	381	FAS1 3. {ECO:0000255|PROSITE- ProRule:PRU00082}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|chondrocyte differentiation (GO:0002062)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	collagen binding (GO:0005518)|extracellular matrix binding (GO:0050840)|integrin binding (GO:0005178)			breast(6)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GACACTATTTGAATTGGCTGC	0.488																																					p.E381K		Atlas-SNP	.											.	TGFBI	76	.	0			c.G1141A						.						77	79	78					5																	135389646		1914	4148	6062	SO:0001583	missense	7045	exon9			CTATTTGAATTGG	M77349	CCDS47266.1	5q31	2008-02-05	2002-08-29		ENSG00000120708	ENSG00000120708			11771	protein-coding gene	gene with protein product		601692	"transforming growth factor, beta-induced, 68kD"	CSD3, LCD1, CSD1, CSD2		9463327	Standard	NM_000358		Approved	BIGH3, CDB1, CDGG1	uc003lbf.4	Q15582	OTTHUMG00000163213	ENST00000442011.2:c.1141G>A	chr5.hg19:g.135389646G>A	ENSP00000416330:p.Glu381Lys	80.0	0.0		98.0	35.0	NM_000358	D3DQB1|O14471|O14472|O14476|O43216|O43217|O43218|O43219|Q53XM1	Missense_Mutation	SNP	ENST00000442011.2	hg19	CCDS47266.1	.	.	.	.	.	.	.	.	.	.	G	34	5.379424	0.95945	.	.	ENSG00000120708	ENST00000442011;ENST00000398813;ENST00000305126	T;T	0.74002	-0.8;-0.8	5.87	5.87	0.94306	FAS1 domain (2);	0.000000	0.85682	D	0.000000	D	0.87716	0.6247	M	0.82056	2.57	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.993	D	0.88088	0.2811	10	0.72032	D	0.01	-19.453	19.8011	0.96507	0.0:0.0:1.0:0.0	.	114;381	B9ZVW9;Q15582	.;BGH3_HUMAN	K	381;114;381	ENSP00000416330:E381K;ENSP00000306306:E381K	ENSP00000306306:E381K	E	+	1	0	TGFBI	135417545	1.000000	0.71417	0.995000	0.50966	0.772000	0.43724	9.690000	0.98676	2.785000	0.95823	0.655000	0.94253	GAA	.	.		0.488	TGFBI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372108.1			A	135389646	G	A	135389646	3	1	296	1	0	0	0	0	1	0	0	0	15835	1291	45	3	1175	3	TGFBI	5	135389646	Missense_Mutation	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10	2062951	135389646	45525614	82	43026										
KDM3B	51780	hgsc.bcm.edu	37	chr5	137708413	137708413	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	aagcaacactcctgggtaaaAgttcatgctgaggaagttat	10	7	1	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr5:137708413A>G	ENST00000314358.5	+	2	443	c.243A>G	c.(241-243)aaA>aaG	p.K81K		NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	81					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(15)|liver(2)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	65						CCTGGGTAAAAGTTCATGCTG	0.473																																					p.K81K		Atlas-SNP	.											.	KDM3B	177	.	0			c.A243G						.						110	105	107					5																	137708413		2203	4300	6503	SO:0001819	synonymous_variant	51780	exon2			GGTAAAAGTTCAT	AF251039	CCDS34242.1	5q31	2011-07-01	2009-04-06	2009-04-06	ENSG00000120733	ENSG00000120733		"Chromatin-modifying enzymes / K-demethylases"	1337	protein-coding gene	gene with protein product		609373	"chromosome 5 open reading frame 7", "jumonji domain containing 1B"	C5orf7, JMJD1B		15138608	Standard	NM_016604		Approved	KIAA1082, NET22	uc003lcy.1	Q7LBC6	OTTHUMG00000163469	ENST00000314358.5:c.243A>G	chr5.hg19:g.137708413A>G		128.0	0.0		135.0	61.0	NM_016604	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	Silent	SNP	ENST00000314358.5	hg19	CCDS34242.1																																																																																			.	.		0.473	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373597.1	NM_016604		G	137708413	A	G	137708413	2	3	296	1	0	0	0	0	0	0	0	1	8136	69	3	2		2	KDM3B	5	137708413	Silent	SNP	A	TCGA-G3-AAV0-01A-11D-A36X-10	2318767	137708413	43206847	83	43027										
LCP2	3937	hgsc.bcm.edu	37	chr5	169693828	169693828	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ccacctagtgtgaagggttcTctatcaaacggagctaatga	10	9	2	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr5:169693828T>G	ENST00000046794.5	-	10	1371	c.756A>C	c.(754-756)agA>agC	p.R252S	LCP2_ENST00000521416.1_Missense_Mutation_p.R47S	NM_005565.3	NP_005556.1	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte protein of 76kDa)	252					blood coagulation (GO:0007596)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|innate immune response (GO:0045087)|mast cell activation (GO:0045576)|platelet activation (GO:0030168)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)				cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	23	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.247)		TGAAGGGTTCTCTATCAAACG	0.413																																					p.R252S		Atlas-SNP	.											.	LCP2	133	.	0			c.A756C						.						220	216	217					5																	169693828		1899	4110	6009	SO:0001583	missense	3937	exon10			GGGTTCTCTATCA		CCDS47339.1	5q35.1	2013-02-14	2002-08-29		ENSG00000043462	ENSG00000043462		"SH2 domain containing"	6529	protein-coding gene	gene with protein product	"76 kDa tyrosine phosphoprotein", "SH2 domain-containing leukocyte protein of 76kD"	601603	"lymphocyte cytosolic protein 2 (SH2 domain-containing leukocyte protein of 76kD)"	SLP76		7706237	Standard	NM_005565		Approved	SLP-76	uc003man.1	Q13094	OTTHUMG00000163121	ENST00000046794.5:c.756A>C	chr5.hg19:g.169693828T>G	ENSP00000046794:p.Arg252Ser	153.0	0.0		177.0	65.0	NM_005565	A8KA25|Q53XV4	Missense_Mutation	SNP	ENST00000046794.5	hg19	CCDS47339.1	.	.	.	.	.	.	.	.	.	.	T	17.87	3.496044	0.64186	.	.	ENSG00000043462	ENST00000046794;ENST00000521416	T;T	0.52983	0.85;0.64	5.46	0.604	0.17547	.	0.000000	0.48286	D	0.000200	T	0.57917	0.2086	M	0.64997	1.995	0.42249	D	0.991967	D;D;D	0.89917	1.0;0.999;0.994	D;D;P	0.80764	0.943;0.994;0.873	T	0.53725	-0.8398	9	.	.	.	-18.2395	7.0587	0.25113	0.0:0.3763:0.0:0.6237	.	47;252;252	E7ESF6;A8KA25;Q13094	.;.;LCP2_HUMAN	S	252;47	ENSP00000046794:R252S;ENSP00000428871:R47S	.	R	-	3	2	LCP2	169626406	1.000000	0.71417	0.999000	0.59377	0.901000	0.52897	1.401000	0.34589	0.089000	0.17243	0.533000	0.62120	AGA	.	.		0.413	LCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371727.1	NM_005565		G	169693828	T	G	169693828	3	3	296	1	0	0	0	0	1	0	0	0	8701	1548	54	5	893	5	LCP2	5	169693828	Missense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	31985415	169693828	11221432	84	43028										
HNRNPH1	3187	hgsc.bcm.edu	37	chr5	179046347	179046347	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gcaaactgcacgaaggcctcCcccgtactcctcccctggaa	8	18	0	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr5:179046347C>T	ENST00000356731.5	-	4	1994	c.459G>A	c.(457-459)ggG>ggA	p.G153G	HNRNPH1_ENST00000329433.6_Silent_p.G153G|HNRNPH1_ENST00000393432.4_Silent_p.G153G|HNRNPH1_ENST00000524180.1_5'Flank|HNRNPH1_ENST00000442819.2_Silent_p.G153G|HNRNPH1_ENST00000511300.2_5'Flank|HNRNPH1_ENST00000510411.1_Silent_p.G153G			P31943	HNRH1_HUMAN	heterogeneous nuclear ribonucleoprotein H1 (H)	153	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA splicing (GO:0043484)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(4)|skin(1)	14						CGAAGGCCTCCCCCGTACTCC	0.512																																					p.G153G		Atlas-SNP	.											.	HNRNPH1	62	.	0			c.G459A						.						172	165	168					5																	179046347		2203	4300	6503	SO:0001819	synonymous_variant	3187	exon5			GGCCTCCCCCGTA	BC001348	CCDS4446.1	5q35.3	2013-02-12		2008-04-18	ENSG00000169045	ENSG00000169045		"RNA binding motif (RRM) containing"	5041	protein-coding gene	gene with protein product		601035		HNRPH1		7499401	Standard	NM_005520		Approved	hnRNPH	uc003mkf.5	P31943	OTTHUMG00000130908	ENST00000356731.5:c.459G>A	chr5.hg19:g.179046347C>T		154.0	0.0		196.0	80.0	NM_001257293	B3KW86|D3DWQ2|Q6IBM4	Silent	SNP	ENST00000356731.5	hg19	CCDS4446.1	.	.	.	.	.	.	.	.	.	.	c	5.226	0.227111	0.09916	.	.	ENSG00000169045	ENST00000521173	T	0.52983	0.64	5.77	5.77	0.91146	.	0.045398	0.85682	N	0.000000	T	0.69593	0.3128	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.72235	-0.4352	7	0.87932	D	0	-5.6286	19.9855	0.97347	0.0:1.0:0.0:0.0	.	.	.	.	E	28	ENSP00000428620:G28E	ENSP00000428620:G28E	G	-	2	0	HNRNPH1	178978953	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	7.818000	0.86416	2.715000	0.92844	0.655000	0.94253	GGG	.	.		0.512	HNRNPH1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253497.3	NM_005520		T	179046347	C	T	179046347	2	4	296	1	0	0	0	0	0	0	0	1	7275	610	22	3		3	HNRNPH1	5	179046347	Silent	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	9352519	179046347	1868913	85	43029										
NEDD9	4739	hgsc.bcm.edu	37	chr6	11213881	11213881	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ctgtgttctgctctatgacgGtcaggatgtctcccttgcga	11	11	4	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr6:11213881G>A	ENST00000379446.5	-	2	258	c.92C>T	c.(91-93)aCc>aTc	p.T31I	RP3-510L9.1_ENST00000500636.2_RNA|NEDD9_ENST00000504387.1_Missense_Mutation_p.T31I|NEDD9_ENST00000379433.5_Missense_Mutation_p.T31I	NM_001271033.1|NM_006403.3	NP_001257962.1|NP_006394.1	Q14511	CASL_HUMAN	neural precursor cell expressed, developmentally down-regulated 9	31	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin filament bundle assembly (GO:0051017)|cell adhesion (GO:0007155)|cytoskeleton organization (GO:0007010)|integrin-mediated signaling pathway (GO:0007229)|mitotic nuclear division (GO:0007067)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle pole (GO:0000922)				endometrium(3)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	Breast(50;0.0768)|Ovarian(93;0.152)	all_hematologic(90;0.135)	Epithelial(50;0.0647)|all cancers(50;0.179)			CTCTATGACGGTCAGGATGTC	0.537																																					p.T31I		Atlas-SNP	.											.	NEDD9	191	.	0			c.C92T						.						127	110	116					6																	11213881		2203	4300	6503	SO:0001583	missense	4739	exon2			ATGACGGTCAGGA	L43821	CCDS4520.1, CCDS34340.1, CCDS47373.1, CCDS75400.1	6p25-p24	2011-04-13			ENSG00000111859	ENSG00000111859		"Cas scaffolding proteins"	7733	protein-coding gene	gene with protein product	"Cas scaffolding protein family member 2", "Cas-like"	602265					Standard	NM_182966		Approved	HEF1, CAS-L, CASS2	uc003mzv.2	Q14511	OTTHUMG00000014255	ENST00000379446.5:c.92C>T	chr6.hg19:g.11213881G>A	ENSP00000368759:p.Thr31Ile	102.0	0.0		100.0	41.0	NM_182966	A8K9G7|A8MSJ9|G5E9Y9|Q5T9R4|Q5XKI0	Missense_Mutation	SNP	ENST00000379446.5	hg19	CCDS4520.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.014436	0.75161	.	.	ENSG00000111859	ENST00000379446;ENST00000504387;ENST00000379433;ENST00000513989;ENST00000397378	T;T;T;T;T	0.63417	-0.04;-0.04;-0.04;0.62;1.92	6.17	6.17	0.99709	Src homology-3 domain (4);	0.000000	0.85682	D	0.000000	T	0.68659	0.3025	L	0.33093	0.98	0.80722	D	1	D;D;D	0.89917	0.996;1.0;0.999	D;D;D	0.87578	0.976;0.998;0.995	T	0.68462	-0.5402	10	0.59425	D	0.04	-24.8521	20.8794	0.99867	0.0:0.0:1.0:0.0	.	31;31;31	G5E9Y9;Q5XKI0;Q14511	.;.;CASL_HUMAN	I	31;31;31;25;31	ENSP00000368759:T31I;ENSP00000422871:T31I;ENSP00000368745:T31I;ENSP00000421282:T25I;ENSP00000380534:T31I	ENSP00000368745:T31I	T	-	2	0	NEDD9	11321867	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	9.441000	0.97557	2.941000	0.99782	0.655000	0.94253	ACC	.	.		0.537	NEDD9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039853.2	NM_006403		A	11213881	G	A	11213881	3	1	296	1	0	0	0	0	1	0	0	0	10322	1261	44	3	2506	3	NEDD9	6	11213881	Missense_Mutation	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10		11213881	159901186	86	43030										
OR2J3	442186	hgsc.bcm.edu	37	chr6	29079911	29079911	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gctacaccaccagctctatcCctcagttgctggtcaatctc	6	16	4	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr6:29079911C>T	ENST00000377169.1	+	1	244	c.244C>T	c.(244-246)Cct>Tct	p.P82S		NM_001005216.2	NP_001005216.2	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J, member 3	82						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(5)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	24						CAGCTCTATCCCTCAGTTGCT	0.483																																					p.P82S		Atlas-SNP	.											.	OR2J3	53	.	0			c.C244T						.						199	204	202					6																	29079911		1276	2597	3873	SO:0001583	missense	442186	exon1			TCTATCCCTCAGT		CCDS43433.1	6p22.2-p21.31	2012-08-09			ENSG00000204701	ENSG00000204701		"GPCR / Class A : Olfactory receptors"	8261	protein-coding gene	gene with protein product		615016					Standard	NM_001005216		Approved	OR6-6	uc011dll.2	O76001	OTTHUMG00000031092	ENST00000377169.1:c.244C>T	chr6.hg19:g.29079911C>T	ENSP00000366374:p.Pro82Ser	132.0	0.0		148.0	66.0	NM_001005216	B0UY52|B9EH11|Q5SUJ7|Q6IF25|Q96R15|Q9GZK5|Q9GZL4|Q9GZL5	Missense_Mutation	SNP	ENST00000377169.1	hg19	CCDS43433.1	.	.	.	.	.	.	.	.	.	.	C	13.45	2.239944	0.39598	.	.	ENSG00000204701	ENST00000377169	T	0.01854	4.6	2.78	2.78	0.32641	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.13372	0.0324	H	0.97186	3.955	0.42398	D	0.992556	D	0.89917	1.0	D	0.97110	1.0	T	0.17198	-1.0377	9	0.87932	D	0	.	13.5409	0.61672	0.0:1.0:0.0:0.0	.	82	O76001	OR2J3_HUMAN	S	82	ENSP00000366374:P82S	ENSP00000366374:P82S	P	+	1	0	OR2J3	29187890	0.980000	0.34600	0.833000	0.33012	0.252000	0.25951	4.241000	0.58707	1.549000	0.49425	0.436000	0.28706	CCT	.	.		0.483	OR2J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076132.2			T	29079911	C	T	29079911	3	4	296	1	0	0	0	0	1	0	0	0	11013	623	22	3	246	3	OR2J3	6	29079911	Missense_Mutation	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	17866030	29079911	142035156	87	43031										
MUC21	394263	hgsc.bcm.edu	37	chr6	30955326	30955326	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ctgactggaatgcacacaacTtcccatagtgcatctactgc	7	13	1	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr6:30955326T>G	ENST00000376296.3	+	2	1615	c.1374T>G	c.(1372-1374)acT>acG	p.T458T	MUC21_ENST00000486149.2_Silent_p.T4T	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	458					cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						TGCACACAACTTCCCATAGTG	0.597																																					p.T458T		Atlas-SNP	.											MUC21,NS,malignant_melanoma,0,2	MUC21	98	.	0			c.T1374G						.						121	115	117					6																	30955326		2203	4300	6503	SO:0001819	synonymous_variant	394263	exon2			CACAACTTCCCAT	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"Mucins"	21661	protein-coding gene	gene with protein product	"epiglycanin"		"chromosome 6 open reading frame 205"	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.1374T>G	chr6.hg19:g.30955326T>G		136.0	0.0		149.0	65.0	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Silent	SNP	ENST00000376296.3	hg19	CCDS34388.1																																																																																			.	.		0.597	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909		G	30955326	T	G	30955326	2	3	296	1	0	0	0	0	0	0	0	1	9986	1596	56	5		5	MUC21	6	30955326	Silent	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	1875415	30955326	140159741	88	43032										
HLA-C	3107	hgsc.bcm.edu	37	chr6	31238146	31238146	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ggtgtcctgggtctggtcctCcccatcccgctgccaggtca	12	16	2	0	rs281860561		TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr6:31238146C>T	ENST00000376228.5	-	4	750	c.736G>A	c.(736-738)Gag>Aag	p.E246K	HLA-C_ENST00000383329.3_Missense_Mutation_p.E246K	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	246	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						GTCTGGTCCTCCCCATCCCGC	0.637																																					p.E246K		Atlas-SNP	.											.	HLA-C	92	.	0			c.G736A						.						40	36	37					6																	31238146		2195	4276	6471	SO:0001583	missense	3107	exon4			GGTCCTCCCCATC	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4933	protein-coding gene	gene with protein product		142840	"psoriasis susceptibility 1"	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.736G>A	chr6.hg19:g.31238146C>T	ENSP00000365402:p.Glu246Lys	84.0	0.0		87.0	35.0	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	hg19	CCDS34393.1	.	.	.	.	.	.	.	.	.	.	.	5.901	0.350405	0.11182	.	.	ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	T;T	0.02682	4.2;4.2	2.67	1.74	0.24563	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.716864	0.11456	U	0.562222	T	0.01421	0.0046	L	0.53780	1.695	0.30207	N	0.79809	B;B;B;B	0.15141	0.012;0.001;0.001;0.006	B;B;B;B	0.23852	0.049;0.013;0.021;0.023	T	0.36504	-0.9745	10	0.87932	D	0	.	7.2957	0.26391	0.0:0.724:0.276:0.0	.	246;246;246;246	A2AEA4;A6H578;A2AEA2;P10321	.;.;.;1C07_HUMAN	K	246;246;246;283	ENSP00000365402:E246K;ENSP00000372819:E246K	ENSP00000365402:E246K	E	-	1	0	HLA-C	31346125	0.000000	0.05858	1.000000	0.80357	0.326000	0.28443	0.060000	0.14342	0.656000	0.30886	0.298000	0.19748	GAG	.	.		0.637	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117		T	31238146	C	T	31238146	3	4	296	1	0	0	0	0	1	0	0	0	7206	864	30	3	384	3	HLA-C	6	31238146	Missense_Mutation	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	282820	31238146	139876921	89	43033										
C2	717	hgsc.bcm.edu	37	chr6	31903820	31903820	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ctgaggtgatcagcagcctgGaaaatgccaactataaaggt	11	8	1	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr6:31903820G>A	ENST00000299367.5	+	7	1246	c.970G>A	c.(970-972)Gaa>Aaa	p.E324K	CFB_ENST00000456570.1_Intron|C2_ENST00000469372.1_Missense_Mutation_p.E78K|CFB_ENST00000477310.1_Intron|C2_ENST00000452323.2_Intron|C2_ENST00000442278.2_Missense_Mutation_p.E192K|CFB_ENST00000556679.1_Intron	NM_000063.4	NP_000054.2	P06681	CO2_HUMAN	complement component 2	324	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|positive regulation of apoptotic cell clearance (GO:2000427)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)|skin(2)|urinary_tract(2)	27		Ovarian(999;0.00965)		LUAD - Lung adenocarcinoma(999;0.247)		CAGCAGCCTGGAAAATGCCAA	0.498																																					p.E324K		Atlas-SNP	.											.	C2	50	.	0			c.G970A						.						68	61	64					6																	31903820		1511	2709	4220	SO:0001583	missense	717	exon7			AGCCTGGAAAATG		CCDS4728.1, CCDS54991.1, CCDS56416.1, CCDS75427.1, CCDS75428.1	6p21.3	2014-09-17			ENSG00000166278	ENSG00000166278		"Complement system"	1248	protein-coding gene	gene with protein product		613927					Standard	NM_001145903		Approved		uc011hbs.1	P06681	OTTHUMG00000031190	ENST00000299367.5:c.970G>A	chr6.hg19:g.31903820G>A	ENSP00000299367:p.Glu324Lys	103.0	0.0		117.0	38.0	NM_000063	B4DPF3|B4DV20|E9PFN7|O19694|Q13904	Missense_Mutation	SNP	ENST00000299367.5	hg19	CCDS4728.1	.	.	.	.	.	.	.	.	.	.	G	11.48	1.652514	0.29336	.	.	ENSG00000166278	ENST00000469372;ENST00000497706;ENST00000432397;ENST00000299367;ENST00000375493;ENST00000442278	T;T;T;T	0.76839	-1.05;-1.05;-1.05;-1.05	5.51	0.249	0.15531	von Willebrand factor, type A (3);	1.434070	0.04871	N	0.445996	T	0.39145	0.1067	.	.	.	0.49582	D	0.999807	B;B;B;B;B	0.28783	0.222;0.024;0.017;0.022;0.024	B;B;B;B;B	0.22880	0.032;0.014;0.013;0.042;0.023	T	0.40813	-0.9543	9	0.16420	T	0.52	-4.1617	5.789	0.18349	0.2369:0.4129:0.3502:0.0	.	295;78;192;324;111	B4DV48;B4DQI1;E9PFN7;P06681;E9PDZ0	.;.;.;CO2_HUMAN;.	K	78;111;111;324;9;192	ENSP00000418923:E78K;ENSP00000417482:E111K;ENSP00000299367:E324K;ENSP00000395683:E192K	ENSP00000299367:E324K	E	+	1	0	C2	32011799	0.998000	0.40836	0.082000	0.20525	0.019000	0.09904	0.916000	0.28651	0.027000	0.15297	0.461000	0.40582	GAA	.	.		0.498	C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076379.9			A	31903820	G	A	31903820	3	1	296	1	0	0	0	0	1	0	0	0	2076	1175	41	3	1073	3	C2	6	31903820	Missense_Mutation	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10	665674	31903820	139211247	90	43034										
SKIV2L	6499	hgsc.bcm.edu	37	chr6	31933608	31933608	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tgggagtaaacatgcctgctCgtacagtagtgtttgactcc	11	9	0	1	rs565924623		TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr6:31933608C>G	ENST00000375394.2	+	18	2133	c.2020C>G	c.(2020-2022)Cgt>Ggt	p.R674G	SKIV2L_ENST00000544581.1_Missense_Mutation_p.R481G	NM_006929.4	NP_008860.4	Q15477	SKIV2_HUMAN	superkiller viralicidic activity 2-like (S. cerevisiae)	674	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)	nucleus (GO:0005634)|Ski complex (GO:0055087)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|large_intestine(1)|ovary(1)	4						CATGCCTGCTCGTACAGTAGT	0.562																																					p.R674G		Atlas-SNP	.											.	SKIV2L	97	.	0			c.C2020G						.						149	112	125					6																	31933608		1511	2709	4220	SO:0001583	missense	6499	exon18			CCTGCTCGTACAG		CCDS4731.1	6p21	2010-02-17	2001-11-28		ENSG00000204351	ENSG00000204351			10898	protein-coding gene	gene with protein product		600478	"superkiller viralicidic activity 2 (S. cerevisiae homolog)-like"	SKIV2		7759100, 9799600	Standard	XM_006715168		Approved	HLP, DDX13, SKI2W, 170A	uc003nyn.1	Q15477	OTTHUMG00000031146	ENST00000375394.2:c.2020C>G	chr6.hg19:g.31933608C>G	ENSP00000364543:p.Arg674Gly	157.0	0.0		161.0	48.0	NM_006929	O15005|Q12902|Q15476|Q5ST66	Missense_Mutation	SNP	ENST00000375394.2	hg19	CCDS4731.1	.	.	.	.	.	.	.	.	.	.	C	16.41	3.114822	0.56505	.	.	ENSG00000204351	ENST00000375394;ENST00000433155;ENST00000544581	T;T	0.75050	-0.9;-0.9	5.48	3.58	0.41010	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.84437	0.5472	M	0.88640	2.97	0.58432	D	0.999997	D	0.89917	1.0	D	0.85130	0.997	D	0.87690	0.2553	10	0.87932	D	0	-12.3974	12.9788	0.58552	0.4201:0.5799:0.0:0.0	.	674	Q15477	SKIV2_HUMAN	G	674;516;481	ENSP00000364543:R674G;ENSP00000442645:R481G	ENSP00000364543:R674G	R	+	1	0	SKIV2L	32041587	0.514000	0.26202	0.463000	0.27130	0.840000	0.47671	1.048000	0.30379	1.256000	0.44068	0.655000	0.94253	CGT	.	.		0.562	SKIV2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076264.3			G	31933608	C	G	31933608	3	3	296	1	0	0	0	0	1	0	0	0	14374	884	31	4	2090	4	SKIV2L	6	31933608	Missense_Mutation	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	29788	31933608	139181459	91	43035										
RGL2	5863	hgsc.bcm.edu	37	chr6	33264534	33264534	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ctcggagccgtcgggaggaaCgtgggggaggcatagggacc	20	9	0	0	rs562018570		TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr6:33264534C>T	ENST00000497454.1	-	4	755	c.260G>A	c.(259-261)cGt>cAt	p.R87H	RGL2_ENST00000444031.2_Missense_Mutation_p.R5H|RGL2_ENST00000437840.2_5'UTR|PFDN6_ENST00000463584.1_Intron	NM_001243738.1|NM_004761.4	NP_001230667.1|NP_004752.1	O15211	RGL2_HUMAN	ral guanine nucleotide dissociation stimulator-like 2	87					positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)	intracellular (GO:0005622)	Ras guanyl-nucleotide exchange factor activity (GO:0005088)			breast(2)|cervix(2)|endometrium(7)|kidney(2)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	34						TCGGGAGGAACGTGGGGGAGG	0.577													C|||	1	0.000199681	0	0	5008	,	,		18926	0		0.001	False		,,,				2504	0				p.R87H		Atlas-SNP	.											.	RGL2	58	.	0			c.G260A						.						51	56	54					6																	33264534		2203	4300	6503	SO:0001583	missense	5863	exon4			GAGGAACGTGGGG		CCDS4774.1	6p21.3	2010-02-17	2004-06-11	2004-06-16	ENSG00000237441	ENSG00000237441			9769	protein-coding gene	gene with protein product		602306	"RAB2, member RAS oncogene family-like"	RAB2L		8976381	Standard	NM_001243738		Approved	KE1.5, HKE1.5	uc003odv.3	O15211	OTTHUMG00000031072	ENST00000497454.1:c.260G>A	chr6.hg19:g.33264534C>T	ENSP00000420211:p.Arg87His	153.0	0.0		170.0	63.0	NM_004761	B4DG72|Q5STK0|Q9Y3F3	Missense_Mutation	SNP	ENST00000497454.1	hg19	CCDS4774.1	.	.	.	.	.	.	.	.	.	.	C	13.81	2.348003	0.41599	.	.	ENSG00000237441	ENST00000497454;ENST00000444031;ENST00000425946	T;T;T	0.31247	1.5;1.5;1.5	4.22	4.22	0.49857	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (1);	0.522151	0.19201	N	0.120193	T	0.33089	0.0851	L	0.44542	1.39	0.37229	D	0.905586	D;D	0.76494	0.999;0.998	P;D	0.69479	0.869;0.964	T	0.05007	-1.0912	10	0.40728	T	0.16	.	11.9785	0.53107	0.0:1.0:0.0:0.0	.	5;87	B4DG72;O15211	.;RGL2_HUMAN	H	87;5;87	ENSP00000420211:R87H;ENSP00000403070:R5H;ENSP00000392918:R87H	ENSP00000392918:R87H	R	-	2	0	RGL2	33372512	0.917000	0.31117	0.652000	0.29579	0.710000	0.40934	2.303000	0.43646	2.177000	0.69029	0.643000	0.83706	CGT	.	.		0.577	RGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076098.2			T	33264534	C	T	33264534	3	4	296	1	0	0	0	0	1	0	0	0	13292	536	19	1	2133	1	RGL2	6	33264534	Missense_Mutation	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	1330926	33264534	137850533	92	43036										
DNAH8	1769	hgsc.bcm.edu	37	chr6	38758095	38758095	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tgttgaggcaaggactcacaGtgttaacatggtcgtcttta	11	7	2	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr6:38758095G>A	ENST00000359357.3	+	18	2298	c.2044G>A	c.(2044-2046)Gtg>Atg	p.V682M	DNAH8_ENST00000441566.1_Missense_Mutation_p.V682M|DNAH8_ENST00000449981.2_Missense_Mutation_p.V899M			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	682					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						AGGACTCACAGTGTTAACATG	0.363																																					p.V899M		Atlas-SNP	.											.	DNAH8	1239	.	0			c.G2695A						.						172	165	168					6																	38758095		2203	4300	6503	SO:0001583	missense	1769	exon20			CTCACAGTGTTAA	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.2044G>A	chr6.hg19:g.38758095G>A	ENSP00000352312:p.Val682Met	132.0	0.0		155.0	63.0	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	hg19		.	.	.	.	.	.	.	.	.	.	G	3.405	-0.121364	0.06838	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.55588	0.51;0.51;0.51	5.2	2.38	0.29361	Dynein heavy chain, domain-1 (1);	0.341577	0.26086	N	0.026430	T	0.10852	0.0265	N	0.05351	-0.065	0.27704	N	0.945672	B	0.10296	0.003	B	0.16722	0.016	T	0.21484	-1.0244	10	0.41790	T	0.15	.	3.9524	0.09375	0.637:0.0:0.2153:0.1477	.	682	Q96JB1	DYH8_HUMAN	M	887;887;682;682	ENSP00000333363:V887M;ENSP00000352312:V682M;ENSP00000402294:V682M	ENSP00000333363:V887M	V	+	1	0	DNAH8	38866073	0.065000	0.20965	0.930000	0.37139	0.007000	0.05969	0.423000	0.21313	0.244000	0.21351	-0.312000	0.09012	GTG	.	.		0.363	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		A	38758095	G	A	38758095	3	1	296	1	0	0	0	0	1	0	0	0	4609	1029	36	3	2106	3	DNAH8	6	38758095	Missense_Mutation	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10	5493561	38758095	132356972	93	43037										
MCM3	4172	hgsc.bcm.edu	37	chr6	52132768	52132768	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tcttctccttctccagaaccTaagaccaaggcaagtgtggc	8	13	3	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr6:52132768T>A	ENST00000229854.7	-	14	2045		c.e14-2		MCM3_ENST00000419835.2_Splice_Site|MCM3_ENST00000596288.1_Splice_Site			P25205	MCM3_HUMAN	minichromosome maintenance complex component 3						DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	alpha DNA polymerase:primase complex (GO:0005658)|centrosome (GO:0005813)|intracellular membrane-bounded organelle (GO:0043231)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			endometrium(4)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	20	Lung NSC(77;0.0931)					ctccAGAACCTAAGACCAAGG	0.502																																					.		Atlas-SNP	.											.	MCM3	63	.	0			c.1999-2A>T						.						163	135	145					6																	52132768		2203	4300	6503	SO:0001630	splice_region_variant	4172	exon14			AGAACCTAAGACC	X62153	CCDS4940.1, CCDS4940.2, CCDS75468.1	6p12	2008-02-05	2007-04-04		ENSG00000112118	ENSG00000112118			6945	protein-coding gene	gene with protein product		602693	"minichromosome maintenance deficient (S. cerevisiae) 3", "MCM3 minichromosome maintenance deficient 3 (S. cerevisiae)"			1549468	Standard	NM_002388		Approved		uc011dwu.2	P25205	OTTHUMG00000014844	ENST00000229854.7:c.1969-2A>T	chr6.hg19:g.52132768T>A		91.0	0.0		111.0	43.0	NM_001270472	B4DWW4|Q92660|Q9BTR3|Q9NUE7	Splice_Site	SNP	ENST00000229854.7	hg19		.	.	.	.	.	.	.	.	.	.	T	16.96	3.266946	0.59540	.	.	ENSG00000112118	ENST00000229854;ENST00000340349;ENST00000419835;ENST00000421471	.	.	.	4.59	4.59	0.56863	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.6461	0.45621	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	MCM3	52240727	1.000000	0.71417	0.997000	0.53966	0.874000	0.50279	3.003000	0.49505	2.288000	0.76882	0.533000	0.62120	.	.	.		0.502	MCM3-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470784.1		Intron	A	52132768	T	A	52132768	5	1	296	1	0	0	0	0	0	0	1	0	9396	1536	53	4	475	4	MCM3	6	52132768	Splice_Site	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	13374673	52132768	118982299	94	43038										
RIMS1	22999	hgsc.bcm.edu	37	chr6	73017046	73017046	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	acagggtctggttctagtcaAgaacttgatcgcgagcaata	11	8	3	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr6:73017046A>G	ENST00000521978.1	+	27	3936	c.3936A>G	c.(3934-3936)caA>caG	p.Q1312Q	RIMS1_ENST00000401910.3_Silent_p.Q632Q|RIMS1_ENST00000517960.1_Silent_p.Q1104Q|RIMS1_ENST00000517827.1_Intron|RIMS1_ENST00000538414.1_Silent_p.Q118Q|RIMS1_ENST00000348717.5_Silent_p.Q1104Q|RIMS1_ENST00000518273.1_Intron|RIMS1_ENST00000520567.1_Intron|RIMS1_ENST00000264839.7_Silent_p.Q1161Q|RIMS1_ENST00000522291.1_Intron|RIMS1_ENST00000523963.1_Intron|RIMS1_ENST00000491071.2_Silent_p.Q1135Q|RIMS1_ENST00000425662.2_Intron	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	1312					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				GTTCTAGTCAAGAACTTGATC	0.388																																					p.Q1312Q		Atlas-SNP	.											.	RIMS1	278	.	0			c.A3936G						.						71	67	69					6																	73017046		1874	4111	5985	SO:0001819	synonymous_variant	22999	exon27			TAGTCAAGAACTT	AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"Rab3-interacting molecule"	606629	"RAB3 interacting protein 2"	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.3936A>G	chr6.hg19:g.73017046A>G		106.0	0.0		114.0	43.0	NM_014989	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Silent	SNP	ENST00000521978.1	hg19	CCDS47449.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	8.893|8.893	0.954576|0.954576	0.18431|0.18431	.|.	.|.	ENSG00000079841|ENSG00000079841	ENST00000522211|ENST00000517433	.|.	.|.	.|.	5.65|5.65	5.65|5.65	0.86999|0.86999	.|.	.|.	.|.	.|.	.|.	T|T	0.64516|0.64516	0.2605|0.2605	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.64846|0.64846	-0.6311|-0.6311	4|4	.|.	.|.	.|.	-14.1812|-14.1812	15.8645|15.8645	0.79055|0.79055	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|.	.|.	.|.	R|G	230|658	.|.	.|.	K|R	+|+	2|1	0|2	RIMS1|RIMS1	73073767|73073767	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	6.159000|6.159000	0.71856|0.71856	2.147000|2.147000	0.66899|0.66899	0.528000|0.528000	0.53228|0.53228	AAG|AGA	.	.		0.388	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1			G	73017046	A	G	73017046	2	3	296	1	0	0	0	0	0	0	0	1	13382	69	3	2		2	RIMS1	6	73017046	Silent	SNP	A	TCGA-G3-AAV0-01A-11D-A36X-10	20884278	73017046	98098021	95	43039										
C6orf186	728464	hgsc.bcm.edu	37	chr6	110620219	110620219	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ctggatggggatcccgccagTcaatggacaagcggtgatac	14	10	1	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr6:110620219T>C	ENST00000338882.4	-	4	691	c.692A>G	c.(691-693)gAc>gGc	p.D231G		NM_001123364.1	NP_001116836.1	Q5JXM2	MET24_HUMAN	methyltransferase like 24	231						extracellular region (GO:0005576)	methyltransferase activity (GO:0008168)										ATCCCGCCAGTCAATGGACAA	0.483																																					p.D231G		Atlas-SNP	.											.	.	.	.	0			c.A692G						.						98	87	90					6																	110620219		1568	3582	5150	SO:0001583	missense	728464	exon4			CGCCAGTCAATGG		CCDS43489.1	6q21	2012-03-08	2012-02-21	2012-02-21	ENSG00000053328	ENSG00000053328			21566	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 186"	C6orf186			Standard	NM_001123364		Approved	dJ71D21.2	uc010kdu.1	Q5JXM2	OTTHUMG00000015359	ENST00000338882.4:c.692A>G	chr6.hg19:g.110620219T>C	ENSP00000344071:p.Asp231Gly	51.0	0.0		50.0	20.0	NM_001123364	Q6ZSU5	Missense_Mutation	SNP	ENST00000338882.4	hg19	CCDS43489.1	.	.	.	.	.	.	.	.	.	.	T	13.46	2.243430	0.39697	.	.	ENSG00000053328	ENST00000338882	T	0.33438	1.41	5.56	4.37	0.52481	.	0.096695	0.64402	D	0.000002	T	0.10594	0.0259	L	0.38175	1.15	0.54753	D	0.999984	B	0.25312	0.123	B	0.30943	0.122	T	0.05616	-1.0874	10	0.09338	T	0.73	-10.2894	12.6085	0.56538	0.0:0.0:0.1387:0.8613	.	231	Q5JXM2	CF186_HUMAN	G	231	ENSP00000344071:D231G	ENSP00000344071:D231G	D	-	2	0	C6orf186	110726912	1.000000	0.71417	0.460000	0.27093	0.967000	0.64934	5.473000	0.66774	0.905000	0.36596	0.533000	0.62120	GAC	.	.		0.483	METTL24-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000041794.1	NM_001123364		C	110620219	T	C	110620219	3	2	296	1	0	0	0	0	1	0	0	0	2349	1667	58	2	416	2	C6orf186	6	110620219	Missense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	37603173	110620219	60494848	96	43040										
REV3L	5980	hgsc.bcm.edu	37	chr6	111695854	111695854	+	Frame_Shift_Del	DEL	G	G	-													0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	caaacttaacctcagcaccaGactgagattttattttttca							TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr6:111695854delG	ENST00000358835.3	-	14	4158	c.3704delC	c.(3703-3705)tctfs	p.S1235fs	REV3L_ENST00000435970.1_Frame_Shift_Del_p.S1157fs|REV3L_ENST00000368805.1_Frame_Shift_Del_p.S1235fs|REV3L_ENST00000368802.3_Frame_Shift_Del_p.S1235fs			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	1235					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		CTCAGCACCAGACTGAGATTT	0.353								DNA polymerases (catalytic subunits)																													p.S1235fs		Atlas-Indel,Pindel	.											.	REV3L	386	.	0			c.3705delT						.						83	84	84					6																	111695854		2202	4298	6500	SO:0001589	frameshift_variant	5980	exon13			.	AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"DNA polymerases"	9968	protein-coding gene	gene with protein product	"polymerase, DNA, zeta"	602776	"REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta", "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.3704delC	chr6.hg19:g.111695854delG	ENSP00000351697:p.Ser1235fs	61.0	0.0		76.0	30.0	NM_002912	O43214|Q5TC33	Frame_Shift_Del	DEL	ENST00000358835.3	hg19	CCDS5091.2																																																																																			.	.		0.353	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		-	111695854	G	-	111695854	7	5	296	1	0	1	0	1	0	0	0	0	13255	942	33	0	5768	0	REV3L	6	111695854	Frame_Shift_Del	DEL	G	TCGA-G3-AAV0-01A-11D-A36X-10	1075635	111695854	59419213	97	43041										
C6orf170	221322	hgsc.bcm.edu	37	chr6	121624863	121624863	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	catggctttgattatgtttaActgttaacaaggacaaagta	8	5	0	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr6:121624863A>C	ENST00000398212.2	-	9	1029	c.980T>G	c.(979-981)gTt>gGt	p.V327G	TBC1D32_ENST00000275159.6_Missense_Mutation_p.V327G	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	327					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)										ATTATGTTTAACTGTTAACAA	0.338																																					p.V327G		Atlas-SNP	.											.	C6orf170	146	.	0			c.T980G						.						109	99	102					6																	121624863		1815	4079	5894	SO:0001583	missense	221322	exon9			TGTTTAACTGTTA	AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"broad-minded homolog"	615867	"chromosome 6 open reading frame 171", "chromosome 6 open reading frame 170"	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.980T>G	chr6.hg19:g.121624863A>C	ENSP00000381270:p.Val327Gly	168.0	0.0		179.0	11.0	NM_152730	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Missense_Mutation	SNP	ENST00000398212.2	hg19	CCDS43501.1	.	.	.	.	.	.	.	.	.	.	A	13.31	2.199180	0.38806	.	.	ENSG00000146350	ENST00000275159;ENST00000398212	T;T	0.21932	1.98;1.98	5.19	4.04	0.47022	.	0.501604	0.20236	N	0.096390	T	0.10937	0.0267	L	0.56769	1.78	0.58432	D	0.999994	B	0.32573	0.376	B	0.29942	0.109	T	0.02766	-1.1113	10	0.72032	D	0.01	-19.3815	10.9913	0.47551	0.9261:0.0:0.0739:0.0	.	327	Q96NH3	BROMI_HUMAN	G	327	ENSP00000275159:V327G;ENSP00000381270:V327G	ENSP00000275159:V327G	V	-	2	0	C6orf170	121666562	1.000000	0.71417	0.990000	0.47175	0.555000	0.35460	3.511000	0.53400	0.918000	0.36919	-0.334000	0.08254	GTT	.	.		0.338	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730		C	121624863	A	C	121624863	3	2	296	1	0	0	0	0	1	0	0	0	2346	43	2	5	2889	5	C6orf170	6	121624863	Missense_Mutation	SNP	A	TCGA-G3-AAV0-01A-11D-A36X-10	9929009	121624863	49490204	98	43042										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152671436	152671436	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	cactgttgtagtcttcatggTctttgactttcgcctccaga	8	11	3	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr6:152671436T>C	ENST00000367255.5	-	72	12369	c.11768A>G	c.(11767-11769)gAc>gGc	p.D3923G	SYNE1_ENST00000448038.1_Intron|SYNE1_ENST00000341594.5_Missense_Mutation_p.D3847G|SYNE1_ENST00000265368.4_Missense_Mutation_p.D3923G|SYNE1_ENST00000423061.1_Intron	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	3923					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GTCTTCATGGTCTTTGACTTT	0.488										HNSCC(10;0.0054)																											p.D3923G		Atlas-SNP	.											SYNE1_ENST00000265368,NS,carcinoma,0,2	SYNE1	3227	.	0			c.A11768G						.						110	100	104					6																	152671436		2203	4300	6503	SO:0001583	missense	23345	exon72			TCATGGTCTTTGA	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.11768A>G	chr6.hg19:g.152671436T>C	ENSP00000356224:p.Asp3923Gly	61.0	0.0		54.0	21.0	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	T	15.88	2.964310	0.53507	.	.	ENSG00000131018	ENST00000367255;ENST00000265368;ENST00000341594	T;T;T	0.35789	1.29;1.29;1.29	5.93	5.93	0.95920	.	0.090393	0.47455	D	0.000234	T	0.16854	0.0405	N	0.22421	0.69	0.80722	D	1	B;B;B	0.27823	0.19;0.19;0.19	B;B;B	0.29785	0.107;0.107;0.107	T	0.05053	-1.0909	10	0.42905	T	0.14	.	16.3943	0.83563	0.0:0.0:0.0:1.0	.	3923;3923;3923	B7ZBC3;Q8NF91;E7EQI5	.;SYNE1_HUMAN;.	G	3923;3923;3847	ENSP00000356224:D3923G;ENSP00000265368:D3923G;ENSP00000341887:D3847G	ENSP00000265368:D3923G	D	-	2	0	SYNE1	152713129	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.676000	0.84012	2.281000	0.76405	0.533000	0.62120	GAC	.	.		0.488	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		C	152671436	T	C	152671436	3	2	296	1	0	0	0	0	1	0	0	0	15460	1667	58	2	14998	2	SYNE1	6	152671436	Missense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	31046573	152671436	18443631	99	43043										
GPR146	115330	hgsc.bcm.edu	37	chr7	1097405	1097405	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	cctggcccctgtgcacctgcTcggccccccgagctcccggt	11	21	0	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr7:1097405T>G	ENST00000397095.1	+	2	477	c.254T>G	c.(253-255)cTc>cGc	p.L85R	C7orf50_ENST00000357429.6_Intron|RP11-449P15.1_ENST00000549241.1_RNA|C7orf50_ENST00000397100.2_Intron|C7orf50_ENST00000488073.1_Intron|C7orf50_ENST00000397098.3_Intron|GPR146_ENST00000297468.3_Missense_Mutation_p.L85R			Q96CH1	GP146_HUMAN	G protein-coupled receptor 146	85						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|ovary(1)|skin(1)	8		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;1.74e-15)		GTGCACCTGCTCGGCCCCCCG	0.642																																					p.L85R		Atlas-SNP	.											.	GPR146	20	.	0			c.T254G						.						31	30	31					7																	1097405		2200	4299	6499	SO:0001583	missense	115330	exon1			ACCTGCTCGGCCC	BC014241	CCDS5321.1	7p22.3	2012-08-21			ENSG00000164849	ENSG00000164849		"GPCR / Class A : Orphans"	21718	protein-coding gene	gene with protein product							Standard	NM_138445		Approved	PGR8	uc003sjy.1	Q96CH1	OTTHUMG00000023934	ENST00000397095.1:c.254T>G	chr7.hg19:g.1097405T>G	ENSP00000380283:p.Leu85Arg	56.0	0.0		83.0	27.0	NM_138445	Q86SP5	Missense_Mutation	SNP	ENST00000397095.1	hg19	CCDS5321.1	.	.	.	.	.	.	.	.	.	.	T	14.67	2.605579	0.46527	.	.	ENSG00000164849	ENST00000444847;ENST00000397095;ENST00000500070;ENST00000297468	T;T;T	0.49720	0.77;0.77;0.77	5.09	3.91	0.45181	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000001	T	0.55878	0.1948	L	0.36672	1.1	0.52099	D	0.999947	D	0.89917	1.0	D	0.76071	0.987	T	0.55573	-0.8120	10	0.62326	D	0.03	-17.8684	10.4615	0.44583	0.1459:0.0:0.0:0.8541	.	85	Q96CH1	GP146_HUMAN	R	85;85;3;85	ENSP00000410743:L85R;ENSP00000380283:L85R;ENSP00000297468:L85R	ENSP00000297468:L85R	L	+	2	0	GPR146	1063931	1.000000	0.71417	0.503000	0.27626	0.014000	0.08584	7.422000	0.80217	0.762000	0.33152	0.459000	0.35465	CTC	.	.		0.642	GPR146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206855.1	NM_138445		G	1097405	T	G	1097405	3	3	296	1	0	0	0	0	1	0	0	0	6660	1551	54	5	256	5	GPR146	7	1097405	Missense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10		1097405	158041258	100	43044										
AOAH	313	hgsc.bcm.edu	37	chr7	36570105	36570124	+	Splice_Site	DEL	AGAGTTGCTCTGCTCTCTGA	AGAGTTGCTCTGCTCTCTGA	-													0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	aatttttttcagtgtgttggAgagttgctctgctctctgaa					rs143459033	byFrequency	TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	AGAGTTGCTCTGCTCTCTGA	AGAGTTGCTCTGCTCTCTGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr7:36570105_36570124delAGAGTTGCTCTGCTCTCTGA	ENST00000258749.5	-	19	1825_1840	c.1426_1441delTCAGAGAGCAGAGCAACTCT	c.(1426-1443)tcagagagcagagcaact>ct	p.SESRAT476fs	AOAH_ENST00000491444.1_5'UTR|AOAH_ENST00000538464.1_Splice_Site_p.SESRAT198fs|AOAH_ENST00000431169.1_Splice_Site_p.SESRAT476fs|AOAH_ENST00000535891.1_Splice_Site_p.SESRAT444fs	NM_001637.3	NP_001628.1	P28039	AOAH_HUMAN	acyloxyacyl hydrolase (neutrophil)	476					inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|lipopolysaccharide metabolic process (GO:0008653)|negative regulation of inflammatory response (GO:0050728)	extracellular region (GO:0005576)	acyloxyacyl hydrolase activity (GO:0050528)|catalytic activity (GO:0003824)|lipoprotein lipase activity (GO:0004465)	p.E478E(1)		NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(21)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	41						AGTGTGTTGGAGAGTTGCTCTGCTCTCTGAAGAGAGAGGA	0.395																																					p.476_481del		Atlas-Indel,Pindel	.											.	AOAH	79	.	1	Substitution - coding silent(1)	large_intestine(1)	c.1426_1442del						.																																			SO:0001630	splice_region_variant	313	exon19			.	BC025698	CCDS5448.1, CCDS55102.1, CCDS75584.1	7p14-p12	2014-03-14			ENSG00000136250	ENSG00000136250	3.1.1.77		548	protein-coding gene	gene with protein product		102593				1883828	Standard	NM_001637		Approved		uc022abu.1	P28039	OTTHUMG00000023566	ENST00000258749.5:c.1426-1TCAGAGAGCAGAGCAACTCT>-	chr7.hg19:g.36570105_36570124delAGAGTTGCTCTGCTCTCTGA		93.0	0.0		82.0	14.0	NM_001637	A4D1Y5|B7Z490|Q53F13	Frame_Shift_Del	DEL	ENST00000258749.5	hg19	CCDS5448.1																																																																																			.	.		0.395	AOAH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219829.2	NM_001637	Frame_Shift_Del	-	36570124	AGAGTTGCTCTGCTCTCTGA	-	36570105	8	5	296	1	0	1	0	1	0	0	1	0	726	304	11	0	639	0	AOAH	7	36570105	Splice_Site	DEL	AGAGTTGCTCTGCTCTCTGA	TCGA-G3-AAV0-01A-11D-A36X-10	35472700	36570105	122568558	101	43045										
SFRP4	6424	hgsc.bcm.edu	37	chr7	37955894	37955894	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	aactccagggtgcaaatgggCgcgtacatggcacagaggaa	14	9	0	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr7:37955894C>T	ENST00000436072.2	-	1	623	c.246G>A	c.(244-246)gcG>gcA	p.A82A	EPDR1_ENST00000476620.1_Intron	NM_003014.3	NP_003005.2	Q6FHJ7	SFRP4_HUMAN	secreted frizzled-related protein 4	82	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				brain development (GO:0007420)|cell differentiation (GO:0030154)|decidualization (GO:0046697)|epithelium development (GO:0060429)|gonad development (GO:0008406)|mammary gland involution (GO:0060056)|menstrual cycle phase (GO:0022601)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of JNK cascade (GO:0046329)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of sodium-dependent phosphate transport (GO:2000119)|phosphate ion homeostasis (GO:0055062)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of epidermal cell differentiation (GO:0045606)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte apoptotic process (GO:1902174)|positive regulation of receptor internalization (GO:0002092)|response to hormone (GO:0009725)|vasculature development (GO:0001944)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)	PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	29						TGCAAATGGGCGCGTACATGG	0.622																																					p.A82A		Atlas-SNP	.											.	SFRP4	66	.	0			c.G246A						.						113	91	99					7																	37955894		2203	4300	6503	SO:0001819	synonymous_variant	6424	exon1			AATGGGCGCGTAC	AF026692	CCDS5453.1	7p14.1	2008-07-18			ENSG00000106483	ENSG00000106483		"Secreted frizzled-related proteins"	10778	protein-coding gene	gene with protein product		606570				10211996	Standard	NM_003014		Approved	frpHE, FRP-4, FRPHE	uc003tfo.4	Q6FHJ7	OTTHUMG00000023026	ENST00000436072.2:c.246G>A	chr7.hg19:g.37955894C>T		96.0	0.0		95.0	37.0	NM_003014	B4DYC1|O14877|Q05BG7|Q1ZYW2|Q4G124|Q6FHM0|Q6PD64	Silent	SNP	ENST00000436072.2	hg19	CCDS5453.1																																																																																			.	.		0.622	SFRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220017.2	NM_003014		T	37955894	C	T	37955894	2	4	296	1	0	0	0	0	0	0	0	1	14178	755	27	1		1	SFRP4	7	37955894	Silent	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	1385789	37955894	121182769	102	43046										
PCLO	27445	hgsc.bcm.edu	37	chr7	82545938	82545938	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tcaatctccttttcttcttcAtcaagctctgcttgtttctt	3	12	8	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr7:82545938A>T	ENST00000333891.9	-	7	11701	c.11364T>A	c.(11362-11364)gaT>gaA	p.D3788E	PCLO_ENST00000423517.2_Missense_Mutation_p.D3788E|PCLO_ENST00000437081.1_Missense_Mutation_p.D508E	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TTTCTTCTTCATCAAGCTCTG	0.438																																					p.D3788E		Atlas-SNP	.											.	PCLO	1506	.	0			c.T11364A						.						144	128	133					7																	82545938		1903	4131	6034	SO:0001583	missense	27445	exon7			TTCTTCATCAAGC	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.11364T>A	chr7.hg19:g.82545938A>T	ENSP00000334319:p.Asp3788Glu	114.0	0.0		106.0	40.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	A	14.26	2.483676	0.44147	.	.	ENSG00000186472	ENST00000333891;ENST00000423517;ENST00000437081	T;T	0.19250	2.17;2.16	5.8	4.66	0.58398	.	.	.	.	.	T	0.36082	0.0954	L	0.41236	1.265	0.51233	D	0.99991	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.91635	0.991;0.999;0.999	T	0.08680	-1.0710	9	0.87932	D	0	.	11.5677	0.50815	0.9308:0.0:0.0692:0.0	.	3719;3788;3788	Q9Y6V0;Q9Y6V0-5;Q9Y6V0-6	PCLO_HUMAN;.;.	E	3788;3788;508	ENSP00000334319:D3788E;ENSP00000388393:D3788E	ENSP00000334319:D3788E	D	-	3	2	PCLO	82383874	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.416000	0.66417	1.047000	0.40274	0.460000	0.39030	GAT	.	.		0.438	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		T	82545938	A	T	82545938	3	4	296	1	0	0	0	0	1	0	0	0	11592	214	8	4	4157	4	PCLO	7	82545938	Missense_Mutation	SNP	A	TCGA-G3-AAV0-01A-11D-A36X-10	44590044	82545938	76592725	103	43047										
ABCB4	5244	hgsc.bcm.edu	37	chr7	87047881	87047881	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	cttgggcagcatctgtggcaAgtcttgtagaaagtgcacca	12	9	2	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr7:87047881A>T	ENST00000265723.4	-	20	2561	c.2450T>A	c.(2449-2451)cTt>cAt	p.L817H	ABCB4_ENST00000359206.3_Missense_Mutation_p.L817H|ABCB4_ENST00000453593.1_Missense_Mutation_p.L817H|ABCB4_ENST00000545634.1_Missense_Mutation_p.L817H|ABCB4_ENST00000358400.3_Missense_Mutation_p.L817H	NM_000443.3|NM_018849.2	NP_000434.1|NP_061337.1	P21439	MDR3_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 4	817	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular lipid metabolic process (GO:0044255)|lipid metabolic process (GO:0006629)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|xenobiotic-transporting ATPase activity (GO:0008559)			breast(5)|endometrium(7)|kidney(2)|large_intestine(15)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				Colchicine(DB01394)|Etravirine(DB06414)|Silodosin(DB06207)	ATCTGTGGCAAGTCTTGTAGA	0.383																																					p.L817H		Atlas-SNP	.											.	ABCB4	177	.	0			c.T2450A						.						136	111	119					7																	87047881		2203	4300	6503	SO:0001583	missense	5244	exon20			GTGGCAAGTCTTG	M23234	CCDS5605.1, CCDS5606.1, CCDS5607.1	7q21	2012-03-14			ENSG00000005471	ENSG00000005471		"ATP binding cassette transporters / subfamily B"	45	protein-coding gene	gene with protein product		171060		PGY3, MDR3		2892668, 11313316	Standard	NM_018850		Approved	MDR2, PFIC-3, GBD1	uc003uiv.1	P21439	OTTHUMG00000023396	ENST00000265723.4:c.2450T>A	chr7.hg19:g.87047881A>T	ENSP00000265723:p.Leu817His	81.0	0.0		103.0	41.0	NM_018850	A0A2V7|A4D1D3|A4D1D4|A4D1D5|D6W5P3|D6W5P4|Q14813	Missense_Mutation	SNP	ENST00000265723.4	hg19	CCDS5606.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.492753	0.84962	.	.	ENSG00000005471	ENST00000359206;ENST00000358400;ENST00000265723;ENST00000453593;ENST00000545634	D;D;D;D;D	0.92911	-3.13;-3.13;-3.13;-3.13;-3.13	5.58	5.58	0.84498	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.97601	0.9214	H	0.97214	3.96	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.99094	1.0841	10	0.87932	D	0	-15.9331	15.7496	0.77972	1.0:0.0:0.0:0.0	.	817;817;817	A4D1D5;P21439-2;P21439	.;.;MDR3_HUMAN	H	817	ENSP00000352135:L817H;ENSP00000351172:L817H;ENSP00000265723:L817H;ENSP00000392983:L817H;ENSP00000437465:L817H	ENSP00000265723:L817H	L	-	2	0	ABCB4	86885817	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.933000	0.87642	2.117000	0.64856	0.528000	0.53228	CTT	.	.		0.383	ABCB4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000336083.1	NM_000443		T	87047881	A	T	87047881	3	4	296	1	0	0	0	0	1	0	0	0	43	72	3	4	1446	4	ABCB4	7	87047881	Missense_Mutation	SNP	A	TCGA-G3-AAV0-01A-11D-A36X-10	4501943	87047881	72090782	104	43048										
RELN	5649	hgsc.bcm.edu	37	chr7	103185629	103185629	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	cttattttacaggttggaccTgagtagccagggtcacatat	10	8	1	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr7:103185629T>C	ENST00000428762.1	-	42	6624	c.6465A>G	c.(6463-6465)tcA>tcG	p.S2155S	RELN_ENST00000424685.2_Silent_p.S2155S|RELN_ENST00000343529.5_Silent_p.S2155S	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	2155	EGF-like 5. {ECO:0000255|PROSITE- ProRule:PRU00076}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		AGGTTGGACCTGAGTAGCCAG	0.403																																					p.S2155S	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.A6465G						.						127	124	125					7																	103185629		2203	4300	6503	SO:0001819	synonymous_variant	5649	exon42			TGGACCTGAGTAG		CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.6465A>G	chr7.hg19:g.103185629T>C		155.0	0.0		198.0	9.0	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Silent	SNP	ENST00000428762.1	hg19	CCDS47680.1																																																																																			.	.		0.403	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		C	103185629	T	C	103185629	2	2	296	1	0	0	0	0	0	0	0	1	13235	1567	55	2		2	RELN	7	103185629	Silent	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	16137748	103185629	55953034	105	43049										
KCND2	3751	hgsc.bcm.edu	37	chr7	120381672	120381672	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	aacggaatggtttactcagtAatcagctgcaggtacaatca	9	8	3	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr7:120381672A>G	ENST00000331113.4	+	3	2328	c.1363A>G	c.(1363-1365)Aat>Gat	p.N455D		NM_012281.2	NP_036413.1	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 2	455					action potential (GO:0001508)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)			NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(35)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	75	all_neural(327;0.117)				Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458)	TTTACTCAGTAATCAGCTGCA	0.363																																					p.N455D		Atlas-SNP	.											.	KCND2	194	.	0			c.A1363G						.						88	93	91					7																	120381672		2203	4300	6503	SO:0001583	missense	3751	exon3			CTCAGTAATCAGC	AJ010969	CCDS5776.1	7q31	2012-07-05			ENSG00000184408	ENSG00000184408		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6238	protein-coding gene	gene with protein product		605410				10551270, 16382104	Standard	NM_012281		Approved	Kv4.2, RK5, KIAA1044	uc003vjj.1	Q9NZV8	OTTHUMG00000156989	ENST00000331113.4:c.1363A>G	chr7.hg19:g.120381672A>G	ENSP00000333496:p.Asn455Asp	271.0	0.0		333.0	137.0	NM_012281	O95012|O95021|Q2TBD3|Q9UBY7|Q9UN98|Q9UNH9	Missense_Mutation	SNP	ENST00000331113.4	hg19	CCDS5776.1	.	.	.	.	.	.	.	.	.	.	A	4.242	0.043940	0.08196	.	.	ENSG00000184408	ENST00000331113	D	0.81739	-1.53	5.11	5.11	0.69529	Potassium channel, voltage dependent, Kv4, C-terminal (1);	0.060294	0.64402	D	0.000005	T	0.50582	0.1624	N	0.01297	-0.9	0.30045	N	0.812238	B	0.02656	0.0	B	0.01281	0.0	T	0.48115	-0.9063	9	.	.	.	.	7.6847	0.28534	0.8408:0.0:0.1592:0.0	.	455	Q9NZV8	KCND2_HUMAN	D	455	ENSP00000333496:N455D	.	N	+	1	0	KCND2	120168908	1.000000	0.71417	0.930000	0.37139	0.992000	0.81027	4.775000	0.62346	1.938000	0.56188	0.528000	0.53228	AAT	.	.		0.363	KCND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346996.1	NM_012281		G	120381672	A	G	120381672	3	3	296	1	0	0	0	0	1	0	0	0	8028	362	13	2	1373	2	KCND2	7	120381672	Missense_Mutation	SNP	A	TCGA-G3-AAV0-01A-11D-A36X-10	17196043	120381672	38756991	106	43050										
SND1	27044	hgsc.bcm.edu	37	chr7	127729698	127729698	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gctgggcttggtgaaggaagGgctggtcatggtggaggtgc	21	5	1	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr7:127729698G>A	ENST00000354725.3	+	22	2770	c.2576G>A	c.(2575-2577)gGg>gAg	p.G859E		NM_014390.2	NP_055205.2	Q7KZF4	SND1_HUMAN	staphylococcal nuclease and tudor domain containing 1	859					gene silencing by RNA (GO:0031047)|osteoblast differentiation (GO:0001649)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|dense body (GO:0097433)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|RISC complex (GO:0016442)	nuclease activity (GO:0004518)|poly(A) RNA binding (GO:0044822)|transcription cofactor activity (GO:0003712)			central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	41						GTGAAGGAAGGGCTGGTCATG	0.592																																					p.G859E		Atlas-SNP	.											.	SND1	104	.	0			c.G2576A						.						147	140	142					7																	127729698		2203	4300	6503	SO:0001583	missense	27044	exon22			AGGAAGGGCTGGT		CCDS34747.1	7q31.3	2014-03-24			ENSG00000197157	ENSG00000197157		"Tudor domain containing"	30646	protein-coding gene	gene with protein product	"p100 EBNA2 co-activator", "Tudor-SN"	602181				7651391, 9003410, 12819296	Standard	NM_014390		Approved	TDRD11, p100	uc003vmi.3	Q7KZF4	OTTHUMG00000157560	ENST00000354725.3:c.2576G>A	chr7.hg19:g.127729698G>A	ENSP00000346762:p.Gly859Glu	116.0	0.0		146.0	73.0	NM_014390	Q13122|Q96AG0	Missense_Mutation	SNP	ENST00000354725.3	hg19	CCDS34747.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.767568	0.90020	.	.	ENSG00000197157	ENST00000354725;ENST00000438400	D	0.85484	-1.99	5.02	5.02	0.67125	Staphylococcal nuclease (SNase-like) (2);Staphylococcal nuclease (SNase-like), OB-fold (1);	0.049893	0.85682	N	0.000000	D	0.93556	0.7943	M	0.89904	3.07	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94802	0.7971	10	0.87932	D	0	-18.6366	15.8344	0.78787	0.0:0.0:1.0:0.0	.	859	Q7KZF4	SND1_HUMAN	E	859;849	ENSP00000346762:G859E	ENSP00000346762:G859E	G	+	2	0	SND1	127516934	1.000000	0.71417	0.950000	0.38849	0.990000	0.78478	9.162000	0.94745	2.346000	0.79739	0.549000	0.68633	GGG	.	.		0.592	SND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349148.1	NM_014390		A	127729698	G	A	127729698	3	1	296	1	0	0	0	0	1	0	0	0	14859	1232	43	3	2662	3	SND1	7	127729698	Missense_Mutation	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10	7348026	127729698	31408965	107	43051										
NOM1	64434	hgsc.bcm.edu	37	chr7	156743034	156743034	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ttgaacaagcgcaaaaagaaGgacggcagcagctccgtgcc	12	11	0	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr7:156743034G>A	ENST00000275820.3	+	1	618	c.603G>A	c.(601-603)aaG>aaA	p.K201K		NM_138400.1	NP_612409.1	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	201	Necessary for nucleolar localization and for targeting PPP1CA to the nucleolus.					nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(4)|large_intestine(9)|lung(7)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	31	Ovarian(565;0.218)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)		GCAAAAAGAAGGACGGCAGCA	0.587																																					p.K201K		Atlas-SNP	.											.	NOM1	73	.	0			c.G603A						.						91	103	99					7																	156743034		2203	4300	6503	SO:0001819	synonymous_variant	64434	exon1			AAAGAAGGACGGC	AF107455	CCDS34787.1	7q36.3	2014-06-13	2005-03-30	2005-03-30	ENSG00000146909	ENSG00000146909			13244	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 113"	611269	"chromosome 7 open reading frame 3"	C7orf3		10329000	Standard	XM_005249560		Approved	SGD1, PPP1R113	uc003wmy.3	Q5C9Z4	OTTHUMG00000152639	ENST00000275820.3:c.603G>A	chr7.hg19:g.156743034G>A		144.0	0.0		128.0	60.0	NM_138400	Q96I08	Silent	SNP	ENST00000275820.3	hg19	CCDS34787.1																																																																																			.	.		0.587	NOM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327098.1	NM_138400		A	156743034	G	A	156743034	2	1	296	1	0	0	0	0	0	0	0	1	10539	991	35	3		3	NOM1	7	156743034	Silent	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10	29013336	156743034	2395629	108	43052										
LOXL2	4017	hgsc.bcm.edu	37	chr8	23217767	23217767	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	agtacagtggagattgtctaAccagatgggccctgaaggag	14	7	1	3			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr8:23217767A>C	ENST00000389131.3	-	3	736	c.367T>G	c.(367-369)Tta>Gta	p.L123V	RP11-177H13.2_ENST00000519692.1_RNA	NM_002318.2	NP_002309.1	Q9Y4K0	LOXL2_HUMAN	lysyl oxidase-like 2	123	SRCR 1. {ECO:0000255|PROSITE- ProRule:PRU00196}.				aging (GO:0007568)|cell adhesion (GO:0007155)|cellular protein modification process (GO:0006464)|collagen fibril organization (GO:0030199)|endothelial cell migration (GO:0043542)|endothelial cell proliferation (GO:0001935)|epithelial to mesenchymal transition (GO:0001837)|histone modification (GO:0016570)|negative regulation of transcription, DNA-templated (GO:0045892)|oxidation-reduction process (GO:0055114)|positive regulation of chondrocyte differentiation (GO:0032332)|protein deamination (GO:0018277)|response to copper ion (GO:0046688)|response to hypoxia (GO:0001666)|sprouting angiogenesis (GO:0002040)|transcription, DNA-templated (GO:0006351)	basement membrane (GO:0005604)|chromosome (GO:0005694)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|electron carrier activity (GO:0009055)|methylated histone binding (GO:0035064)|oligosaccharide binding (GO:0070492)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)|transcription corepressor activity (GO:0003714)			breast(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(5)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(55;0.0453)|Breast(100;0.143)		Colorectal(74;0.0288)|COAD - Colon adenocarcinoma(73;0.096)		AGATTGTCTAACCAGATGGGC	0.567																																					p.L123V		Atlas-SNP	.											.	LOXL2	97	.	0			c.T367G						.						52	40	44					8																	23217767		2203	4300	6503	SO:0001583	missense	4017	exon3			TGTCTAACCAGAT	U89942	CCDS34864.1	8p21.3	2008-05-15				ENSG00000134013			6666	protein-coding gene	gene with protein product		606663				9722957	Standard	NM_002318		Approved	WS9-14	uc003xdh.1	Q9Y4K0		ENST00000389131.3:c.367T>G	chr8.hg19:g.23217767A>C	ENSP00000373783:p.Leu123Val	86.0	0.0		31.0	14.0	NM_002318	B2R5Q0|Q53HV3|Q9BW70|Q9Y5Y8	Missense_Mutation	SNP	ENST00000389131.3	hg19	CCDS34864.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.171023	0.78452	.	.	ENSG00000134013	ENST00000389131;ENST00000524144;ENST00000520871;ENST00000518083;ENST00000524168	T;T;T;T;T	0.64803	-0.12;-0.12;-0.12;1.17;1.17	5.53	-4.55	0.03441	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.225756	0.45126	D	0.000384	T	0.71022	0.3291	M	0.85099	2.735	0.43439	D	0.995612	D	0.58970	0.984	P	0.61874	0.895	T	0.72246	-0.4349	10	0.87932	D	0	.	6.9493	0.24536	0.3951:0.0:0.4516:0.1532	.	123	Q9Y4K0	LOXL2_HUMAN	V	123;204;164;123;123	ENSP00000373783:L123V;ENSP00000427883:L204V;ENSP00000429778:L164V;ENSP00000430519:L123V;ENSP00000428497:L123V	ENSP00000373783:L123V	L	-	1	2	LOXL2	23273712	0.007000	0.16637	0.991000	0.47740	0.947000	0.59692	-1.028000	0.03589	-0.381000	0.07882	-0.256000	0.11100	TTA	.	.		0.567	LOXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375603.1			C	23217767	A	C	23217767	3	2	296	1	0	0	0	0	1	0	0	0	8909	40	2	5	2005	5	LOXL2	8	23217767	Missense_Mutation	SNP	A	TCGA-G3-AAV0-01A-11D-A36X-10		23217767	123146255	109	43053										
PLAT	5327	hgsc.bcm.edu	37	chr8	42037780	42037780	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	caatgtcattgtcgtaagtgTcatcatcgaattccttatgg	8	8	3	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr8:42037780T>C	ENST00000220809.4	-	11	1458	c.1202A>G	c.(1201-1203)gAc>gGc	p.D401G	PLAT_ENST00000429089.2_Missense_Mutation_p.D401G|PLAT_ENST00000429710.2_Missense_Mutation_p.D275G|PLAT_ENST00000270189.6_Intron|PLAT_ENST00000352041.3_Missense_Mutation_p.D355G|PLAT_ENST00000524009.1_Missense_Mutation_p.D312G|PLAT_ENST00000519510.1_Missense_Mutation_p.D338G	NM_000930.3	NP_000921.1	P00750	TPA_HUMAN	plasminogen activator, tissue	401	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|cellular protein modification process (GO:0006464)|fibrinolysis (GO:0042730)|negative regulation of proteolysis (GO:0045861)|plasminogen activation (GO:0031639)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of ovulation (GO:0060279)|proteolysis (GO:0006508)|regulation of synaptic plasticity (GO:0048167)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|smooth muscle cell migration (GO:0014909)|synaptic transmission, glutamatergic (GO:0035249)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|secretory granule (GO:0030141)|synapse (GO:0045202)	serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(10)|skin(1)|soft_tissue(1)|urinary_tract(1)	27	all_cancers(6;3.84e-26)|all_epithelial(6;9.61e-28)|all_lung(13;7.2e-13)|Lung NSC(13;1.18e-11)|Ovarian(28;0.00438)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000378)|Lung NSC(58;0.00145)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;5.23e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00135)|Colorectal(10;0.00165)|Lung(22;0.00467)|COAD - Colon adenocarcinoma(11;0.0171)|LUSC - Lung squamous cell carcinoma(45;0.024)		Aminocaproic Acid(DB00513)|Ibuprofen(DB01050)|Iloprost(DB01088)|Urokinase(DB00013)	GTCGTAAGTGTCATCATCGAA	0.473																																					p.D401G		Atlas-SNP	.											.	PLAT	62	.	0			c.A1202G						.						170	171	171					8																	42037780		2203	4300	6503	SO:0001583	missense	5327	exon11			TAAGTGTCATCAT		CCDS6126.1, CCDS6127.1	8p11.21	2012-10-02			ENSG00000104368	ENSG00000104368			9051	protein-coding gene	gene with protein product		173370					Standard	NM_033011		Approved		uc003xos.2	P00750	OTTHUMG00000164072	ENST00000220809.4:c.1202A>G	chr8.hg19:g.42037780T>C	ENSP00000220809:p.Asp401Gly	81.0	0.0		95.0	41.0	NM_000930	A8K022|B2R8E8|Q15103|Q503B0|Q6PJA5|Q7Z7N2|Q86YK8|Q9BU99|Q9BZW1	Missense_Mutation	SNP	ENST00000220809.4	hg19	CCDS6126.1	.	.	.	.	.	.	.	.	.	.	T	11.18	1.562750	0.27915	.	.	ENSG00000104368	ENST00000429089;ENST00000220809;ENST00000352041;ENST00000519510;ENST00000429710;ENST00000524009	D;D;D;D;D;D	0.89123	-2.47;-2.47;-2.47;-2.47;-2.47;-2.47	5.39	2.78	0.32641	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.343467	0.37178	N	0.002210	T	0.80994	0.4731	L	0.29908	0.895	0.80722	D	1	B;B;B;B;B;B	0.11235	0.004;0.004;0.002;0.002;0.002;0.001	B;B;B;B;B;B	0.17979	0.02;0.02;0.017;0.014;0.008;0.011	T	0.75139	-0.3423	10	0.51188	T	0.08	.	8.3543	0.32321	0.0:0.0696:0.2237:0.7067	.	275;312;338;401;355;401	B4DNJ1;B4DN26;B4DV92;B8ZX62;P00750-3;P00750	.;.;.;.;.;TPA_HUMAN	G	401;401;355;338;275;312	ENSP00000392045:D401G;ENSP00000220809:D401G;ENSP00000270188:D355G;ENSP00000428886:D338G;ENSP00000407861:D275G;ENSP00000429401:D312G	ENSP00000220809:D401G	D	-	2	0	PLAT	42156937	1.000000	0.71417	0.168000	0.22838	0.482000	0.33219	3.754000	0.55189	0.952000	0.37798	0.533000	0.62120	GAC	.	.		0.473	PLAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377100.1	NM_000930		C	42037780	T	C	42037780	3	2	296	1	0	0	0	0	1	0	0	0	12030	1667	58	2	502	2	PLAT	8	42037780	Missense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	18820013	42037780	104326242	110	43054										
TRPA1	8989	hgsc.bcm.edu	37	chr8	72958795	72958795	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	aacatcctgtgtaggtgtttTtttggtgaattctaatggac	10	5	1	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr8:72958795T>G	ENST00000262209.4	-	17	2221	c.2014A>C	c.(2014-2016)Aaa>Caa	p.K672Q	RP11-383H13.1_ENST00000457356.4_Intron|RP11-383H13.1_ENST00000537896.1_Intron|RP11-383H13.1_ENST00000524152.1_Intron	NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	672					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	GTAGGTGTTTTTTTGGTGAAT	0.274																																					p.K672Q		Atlas-SNP	.											.	TRPA1	256	.	0			c.A2014C						.						138	153	148					8																	72958795		2203	4299	6502	SO:0001583	missense	8989	exon17			GTGTTTTTTTGGT	Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	497	protein-coding gene	gene with protein product		604775	"ankyrin-like with transmembrane domains 1"	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.2014A>C	chr8.hg19:g.72958795T>G	ENSP00000262209:p.Lys672Gln	62.0	0.0		61.0	30.0	NM_007332	A6NIN6	Missense_Mutation	SNP	ENST00000262209.4	hg19	CCDS34908.1	.	.	.	.	.	.	.	.	.	.	T	5.274	0.235932	0.10023	.	.	ENSG00000104321	ENST00000523582;ENST00000262209	T;T	0.79033	-1.23;-1.23	4.89	3.72	0.42706	.	0.658545	0.15998	N	0.234499	T	0.68531	0.3011	L	0.57536	1.79	0.21841	N	0.999511	B	0.26975	0.165	B	0.24701	0.055	T	0.53099	-0.8486	10	0.16420	T	0.52	-14.2475	6.2149	0.20649	0.0:0.0838:0.1607:0.7555	.	672	O75762	TRPA1_HUMAN	Q	524;672	ENSP00000428151:K524Q;ENSP00000262209:K672Q	ENSP00000262209:K672Q	K	-	1	0	TRPA1	73121349	0.546000	0.26457	0.111000	0.21465	0.033000	0.12548	0.393000	0.20817	0.803000	0.34113	0.454000	0.30748	AAA	.	.		0.274	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332		G	72958795	T	G	72958795	3	3	296	1	0	0	0	0	1	0	0	0	16592	1850	64	5	1389	5	TRPA1	8	72958795	Missense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	30921015	72958795	73405227	111	43055										
KCNQ3	3786	hgsc.bcm.edu	37	chr8	133492604	133492604	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tcccgtctttgtcggctccgGccccgagcgccaaggtgact	12	16	1	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr8:133492604G>T	ENST00000388996.4	-	1	596	c.176C>A	c.(175-177)gCc>gAc	p.A59D	KCNQ3_ENST00000519445.1_Missense_Mutation_p.A59D	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	59					axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	70	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	GTCGGCTCCGGCCCCGAGCGC	0.761																																					p.A59D		Atlas-SNP	.											.	KCNQ3	164	.	0			c.C176A						.						9	11	11					8																	133492604		2164	4191	6355	SO:0001583	missense	3786	exon1			GCTCCGGCCCCGA	AB208890	CCDS34943.1, CCDS56554.1	8q24	2012-07-05			ENSG00000184156	ENSG00000184156		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6297	protein-coding gene	gene with protein product		602232		EBN2		9425900, 16382104	Standard	NM_004519		Approved	Kv7.3	uc003ytj.3	O43525	OTTHUMG00000137472	ENST00000388996.4:c.176C>A	chr8.hg19:g.133492604G>T	ENSP00000373648:p.Ala59Asp	326.0	1.0		353.0	131.0	NM_004519	A2VCT8|B4DJY4|E7EQ89	Missense_Mutation	SNP	ENST00000388996.4	hg19	CCDS34943.1	.	.	.	.	.	.	.	.	.	.	G	11.47	1.647114	0.29246	.	.	ENSG00000184156	ENST00000388996;ENST00000519445;ENST00000542679	D;D	0.99167	-5.49;-5.51	4.1	4.1	0.47936	.	0.490062	0.15630	N	0.252412	D	0.96125	0.8737	N	0.14661	0.345	0.29963	N	0.819181	B;B	0.26400	0.148;0.148	B;B	0.19946	0.027;0.027	D	0.94511	0.7718	10	0.52906	T	0.07	-3.6727	15.0561	0.71915	0.0:0.0:1.0:0.0	.	59;59	E7ET42;O43525	.;KCNQ3_HUMAN	D	59;59;48	ENSP00000373648:A59D;ENSP00000428790:A59D	ENSP00000373648:A59D	A	-	2	0	KCNQ3	133561786	1.000000	0.71417	0.546000	0.28166	0.135000	0.20990	3.603000	0.54074	2.113000	0.64589	0.557000	0.71058	GCC	.	.		0.761	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519		T	133492604	G	T	133492604	3	4	296	1	0	0	0	0	1	0	0	0	8093	1203	42	3	2502	3	KCNQ3	8	133492604	Missense_Mutation	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10	60533809	133492604	12871418	112	43056										
RECQL4	113655	hgsc.bcm.edu	37	chr8	145737311	145737311	+	IGR	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	cactctggcctgccctggctCggggccctgtgcgtcctcca	12	18	1	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr8:145737311C>T	ENST00000301327.4	+	0	1548				CTD-2517M22.17_ENST00000580385.1_RNA|RECQL4_ENST00000428558.2_Missense_Mutation_p.E1126K|RECQL4_ENST00000532237.1_5'UTR	NM_138431.1	NP_612440.1	Q96ES6	MFSD3_HUMAN	major facilitator superfamily domain containing 3						transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(1)|kidney(1)|lung(4)	8	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			TGCCCTGGCTCGGGGCCCTGT	0.657																																					p.E1126K		Atlas-SNP	.											.	RECQL4	75	.	0			c.G3376A						.						25	28	27					8																	145737311		2149	4250	6399	SO:0001628	intergenic_variant	9401	exon20			CTGGCTCGGGGCC		CCDS6431.1	8q24.3	2005-11-17			ENSG00000167700	ENSG00000167700			25157	protein-coding gene	gene with protein product							Standard	NM_138431		Approved		uc003zdi.1	Q96ES6	OTTHUMG00000165177		chr8.hg19:g.145737311C>T		55.0	0.0		87.0	11.0	NM_004260		Missense_Mutation	SNP	ENST00000301327.4	hg19	CCDS6431.1																																																																																			.	.		0.657	MFSD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382478.2	NM_138431		T	145737311	C	T	145737311	1	4	296	0	1	0	0	0	0	0	0	0	13217	893	31	1		1	RECQL4	8	145737311	IGR	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	12244707	145737311	626711	113	43057										
CDKN2A	1029	hgsc.bcm.edu	37	chr9	21971036	21971036	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gggcagacggccccaggcatCgcgcacgtccagccgcgccc	14	19	0	1	rs121913381		TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr9:21971036C>A	ENST00000304494.5	-	2	592	c.322G>T	c.(322-324)Gat>Tat	p.D108Y	CDKN2A_ENST00000579122.1_Missense_Mutation_p.D108Y|CDKN2A_ENST00000579755.1_Missense_Mutation_p.R122L|CDKN2A_ENST00000498628.2_Missense_Mutation_p.D57Y|CDKN2A_ENST00000578845.2_Missense_Mutation_p.D57Y|CDKN2A_ENST00000479692.2_Missense_Mutation_p.D57Y|CDKN2A_ENST00000498124.1_Missense_Mutation_p.D108Y|CDKN2A_ENST00000494262.1_Missense_Mutation_p.D57Y|CDKN2A_ENST00000530628.2_Missense_Mutation_p.R122L|CDKN2A_ENST00000446177.1_Missense_Mutation_p.D108Y|CDKN2A_ENST00000361570.3_Missense_Mutation_p.R163L|CDKN2A_ENST00000497750.1_Missense_Mutation_p.D57Y|RP11-145E5.5_ENST00000404796.2_Intron	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	108			D -> H (in a bladder tumor).|D -> Y (in a head and neck tumor).		cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular senescence (GO:2000774)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|Ras protein signal transduction (GO:0007265)|replicative senescence (GO:0090399)|senescence-associated heterochromatin focus assembly (GO:0035986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|senescence-associated heterochromatin focus (GO:0035985)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.0?(1315)|p.?(44)|p.D108Y(18)|p.D108N(7)|p.D108H(7)|p.R163L(3)|p.H83fs*2(2)|p.D105fs*8(1)|p.0(1)|p.R163Q(1)|p.A68fs*3(1)|p.R107fs*33(1)		NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		CCCCAGGCATCGCGCACGTCC	0.741		17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)																											p.R122L		Atlas-SNP	.											CDKN2A_ENST00000498124,bladder,carcinoma,0,3	CDKN2A	4810	.	1401	Whole gene deletion(1316)|Unknown(44)|Substitution - Missense(36)|Deletion - Frameshift(5)	haematopoietic_and_lymphoid_tissue(283)|skin(174)|central_nervous_system(167)|lung(160)|urinary_tract(97)|bone(74)|upper_aerodigestive_tract(62)|soft_tissue(57)|pleura(51)|oesophagus(51)|ovary(36)|kidney(32)|pancreas(32)|breast(32)|thyroid(14)|biliary_tract(13)|NS(12)|stomach(12)|autonomic_ganglia(9)|meninges(7)|large_intestine(6)|liver(6)|salivary_gland(4)|thymus(4)|vulva(2)|endometrium(2)|prostate(2)	c.G365T	GRCh37	CM071585|CM973278	CDKN2A	M	rs121913381	.						16	19	18					9																	21971036		2198	4292	6490	SO:0001583	missense	1029	exon2			AGGCATCGCGCAC	L27211	CCDS6510.1, CCDS6511.1, CCDS6511.2, CCDS56565.1	9p21	2014-09-17	2012-03-08		ENSG00000147889	ENSG00000147889			1787	protein-coding gene	gene with protein product		600160	"cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)"	CDKN2, MLM		8152487, 7606716	Standard	NM_058195		Approved	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf	uc003zpk.3	P42771	OTTHUMG00000019686	ENST00000304494.5:c.322G>T	chr9.hg19:g.21971036C>A	ENSP00000307101:p.Asp108Tyr	120.0	0.0		133.0	54.0	NM_058195	A5X2G7|D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	Missense_Mutation	SNP	ENST00000304494.5	hg19	CCDS6510.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.6|22.6	4.308521|4.308521	0.81247|0.81247	.|.	.|.	ENSG00000147889|ENSG00000147889	ENST00000304494;ENST00000446177|ENST00000361570;ENST00000530628	D;D|T;T	0.94232|0.79845	-3.38;-3.38|-1.31;-1.25	5.93|5.93	5.93|5.93	0.95920|0.95920	Ankyrin repeat-containing domain (4);|.	.|0.000000	.|0.30428	.|N	.|0.009646	D|D	0.84678|0.84678	0.5525|0.5525	L|L	0.29908|0.29908	0.895|0.895	0.47308|0.47308	D|D	0.999383|0.999383	D|D	0.89917|0.89917	1.0|1.0	D|D	0.97110|0.67548	1.0|0.952	D|D	0.85416|0.85416	0.1140|0.1140	9|10	0.87932|0.62326	D|D	0|0.03	-14.8146|-14.8146	19.1221|19.1221	0.93367|0.93367	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	108|163	P42771|Q8N726	CD2A1_HUMAN|CD2A2_HUMAN	Y|L	108|163;122	ENSP00000307101:D108Y;ENSP00000394932:D108Y|ENSP00000355153:R163L;ENSP00000432664:R122L	ENSP00000307101:D108Y|ENSP00000355153:R163L	D|R	-|-	1|2	0|0	CDKN2A|CDKN2A	21961036|21961036	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.627000|0.627000	0.37826|0.37826	5.136000|5.136000	0.64783|0.64783	2.808000|2.808000	0.96608|0.96608	0.655000|0.655000	0.94253|0.94253	GAT|CGA	.	.		0.741	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	NM_000077		A	21971036	C	A	21971036	3	1	296	1	0	0	0	0	1	0	0	0	3163	884	31	1	156	1	CDKN2A	9	21971036	Missense_Mutation	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10		21971036	119242395	114	43058										
AQP3	360	hgsc.bcm.edu	37	chr9	33442436	33442436	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	accaggcccacggtgaaggcCtccaggcctcgggggacggg	17	14	0	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr9:33442436C>T	ENST00000297991.4	-	5	653	c.573G>A	c.(571-573)gaG>gaA	p.E191E	AQP3_ENST00000493581.1_5'UTR	NM_004925.4	NP_004916.1	Q92482	AQP3_HUMAN	aquaporin 3 (Gill blood group)	191					excretion (GO:0007588)|odontogenesis (GO:0042476)|positive regulation of immune system process (GO:0002684)|regulation of keratinocyte differentiation (GO:0045616)|renal water absorption (GO:0070295)|response to calcium ion (GO:0051592)|response to retinoic acid (GO:0032526)|response to vitamin D (GO:0033280)|transmembrane transport (GO:0055085)|transport (GO:0006810)|urea transport (GO:0015840)|water transport (GO:0006833)	basolateral plasma membrane (GO:0016323)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycerol channel activity (GO:0015254)|transporter activity (GO:0005215)|water channel activity (GO:0015250)			endometrium(2)|large_intestine(3)|lung(2)|ovary(1)	8			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.0899)		CGGTGAAGGCCTCCAGGCCTC	0.627																																					p.E191E		Atlas-SNP	.											.	AQP3	18	.	0			c.G573A						.						37	44	41					9																	33442436		2203	4300	6503	SO:0001819	synonymous_variant	360	exon5			GAAGGCCTCCAGG		CCDS6542.1	9p13	2014-07-18	2006-02-23		ENSG00000165272	ENSG00000165272		"Ion channels / Aquaporins", "Blood group antigens"	636	protein-coding gene	gene with protein product	"Gill blood group"	600170	"aquaporin 3", "aquaporin 3 (GIL blood group)"			7558005	Standard	NM_004925		Approved	GIL	uc003zsx.3	Q92482	OTTHUMG00000019769	ENST00000297991.4:c.573G>A	chr9.hg19:g.33442436C>T		226.0	0.0		197.0	70.0	NM_004925	A8K843|B2RE16|D3DRL3|O00108|Q6FGT2|Q6FGW6	Silent	SNP	ENST00000297991.4	hg19	CCDS6542.1																																																																																			.	.		0.627	AQP3-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052055.1	NM_004925		T	33442436	C	T	33442436	2	4	296	1	0	0	0	0	0	0	0	1	827	680	24	3		3	AQP3	9	33442436	Silent	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	11471400	33442436	107770995	115	43059										
SLC46A2	57864	hgsc.bcm.edu	37	chr9	115652684	115652684	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tgagccatcccagcccgtagGcggacagcaggggggacagg	17	12	0	1	rs376774946		TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr9:115652684G>C	ENST00000374228.4	-	1	509	c.278C>G	c.(277-279)gCc>gGc	p.A93G		NM_033051.3	NP_149040.3	Q9BY10	TSCOT_HUMAN	solute carrier family 46, member 2	93					negative regulation of T cell apoptotic process (GO:0070233)|regulation of T cell differentiation (GO:0045580)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(11)|pancreas(1)|skin(1)	18						CAGCCCGTAGGCGGACAGCAG	0.617																																					p.A93G		Atlas-SNP	.											.	SLC46A2	30	.	0			c.C278G						.						91	93	92					9																	115652684		2203	4300	6503	SO:0001583	missense	57864	exon1			CCGTAGGCGGACA	AF242557	CCDS6786.1	9q32	2013-05-22	2007-03-29	2007-03-29	ENSG00000119457	ENSG00000119457		"Solute carriers"	16055	protein-coding gene	gene with protein product		608956	"thymic stromal co-transporter"	TSCOT		10978518, 12826694	Standard	NM_033051		Approved	Ly110	uc004bgk.3	Q9BY10	OTTHUMG00000020513	ENST00000374228.4:c.278C>G	chr9.hg19:g.115652684G>C	ENSP00000363345:p.Ala93Gly	132.0	0.0		151.0	62.0	NM_033051	B1ALK1|Q86VT0|Q96NE2	Missense_Mutation	SNP	ENST00000374228.4	hg19	CCDS6786.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.285827	0.80803	.	.	ENSG00000119457	ENST00000374228	T	0.58797	0.31	5.56	5.56	0.83823	Major facilitator superfamily domain, general substrate transporter (1);	0.157498	0.56097	D	0.000028	T	0.72938	0.3523	L	0.59436	1.845	0.58432	D	0.999998	D	0.71674	0.998	D	0.72982	0.979	T	0.68550	-0.5379	10	0.31617	T	0.26	-25.0855	19.1663	0.93559	0.0:0.0:1.0:0.0	.	93	Q9BY10	TSCOT_HUMAN	G	93	ENSP00000363345:A93G	ENSP00000363345:A93G	A	-	2	0	SLC46A2	114692505	1.000000	0.71417	0.938000	0.37757	0.964000	0.63967	7.771000	0.85420	2.623000	0.88846	0.650000	0.86243	GCC	.	.		0.617	SLC46A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053702.1	NM_033051		C	115652684	G	C	115652684	3	2	296	1	0	0	0	0	1	0	0	0	14660	1203	42	4	1165	4	SLC46A2	9	115652684	Missense_Mutation	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10	82210248	115652684	25560747	116	43060										
EHMT1	79813	hgsc.bcm.edu	37	chr9	140671290	140671290	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gggcagggccgacaccacaaCgggcaggtacctggcacagg	16	13	0	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr9:140671290C>T	ENST00000460843.1	+	12	2039	c.2012C>T	c.(2011-2013)aCg>aTg	p.T671M	EHMT1_ENST00000462484.1_Missense_Mutation_p.T671M|EHMT1_ENST00000371394.2_3'UTR|EHMT1_ENST00000334856.6_Missense_Mutation_p.T640M	NM_024757.4	NP_079033.4	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	671					chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|embryo development (GO:0009790)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|methyltransferase activity (GO:0008168)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		GACACCACAACGGGCAGGTAC	0.572																																					p.T671M		Atlas-SNP	.											.	EHMT1	196	.	0			c.C2012T						.						43	40	41					9																	140671290		2203	4300	6503	SO:0001583	missense	79813	exon12			CCACAACGGGCAG	AY083210	CCDS7050.1, CCDS7050.2, CCDS56595.1	9q34.3	2013-09-20			ENSG00000181090	ENSG00000181090	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases", "Ankyrin repeat domain containing"	24650	protein-coding gene	gene with protein product		607001	"euchromatic histone methyltransferase 1"			11347906, 12004135	Standard	NM_024757		Approved	Eu-HMTase1, FLJ12879, KIAA1876, bA188C12.1, KMT1D	uc011mfc.2	Q9H9B1	OTTHUMG00000020995	ENST00000460843.1:c.2012C>T	chr9.hg19:g.140671290C>T	ENSP00000417980:p.Thr671Met	127.0	0.0		118.0	9.0	NM_001145527	B1AQ58|B1AQ59|Q86X08|Q8TCN7|Q96F53|Q96JF1|Q96KH4	Missense_Mutation	SNP	ENST00000460843.1	hg19	CCDS7050.2	.	.	.	.	.	.	.	.	.	.	C	25.0	4.588333	0.86851	.	.	ENSG00000181090	ENST00000334856;ENST00000371400;ENST00000462484;ENST00000460843	T;T;T	0.71817	1.44;0.67;-0.6	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	D	0.82949	0.5148	M	0.69823	2.125	0.58432	D	0.999999	P;D;D	0.76494	0.607;0.998;0.999	B;P;D	0.66084	0.107;0.849;0.941	D	0.83742	0.0204	10	0.52906	T	0.07	.	18.6174	0.91308	0.0:1.0:0.0:0.0	.	671;640;671	Q9H9B1;Q9H9B1-2;Q9H9B1-4	EHMT1_HUMAN;.;.	M	640;640;671;671	ENSP00000334476:T640M;ENSP00000417328:T671M;ENSP00000417980:T671M	ENSP00000334476:T640M	T	+	2	0	EHMT1	139791111	1.000000	0.71417	0.982000	0.44146	0.959000	0.62525	7.578000	0.82498	2.477000	0.83638	0.561000	0.74099	ACG	.	.		0.572	EHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055371.2	NM_024757		T	140671290	C	T	140671290	3	4	296	1	0	0	0	0	1	0	0	0	4985	536	19	1	2058	1	EHMT1	9	140671290	Missense_Mutation	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	25018606	140671290	542141	117	43061										
WAPAL	23063	hgsc.bcm.edu	37	chr10	88231999	88232010	+	In_Frame_Del	DEL	TTAAGCCACTTA	TTAAGCCACTTA	-													0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gtttagaggctgagtgctctTtaagccacttaacaagtact							TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	TTAAGCCACTTA	TTAAGCCACTTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr10:88231999_88232010delTTAAGCCACTTA	ENST00000298767.5	-	7	2457_2468	c.1985_1996delTAAGTGGCTTAA	c.(1984-1998)ttaagtggcttaaag>tag	p.662_666LSGLK>*	WAPAL_ENST00000263070.7_5'Flank	NM_015045.2	NP_055860.1	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog (Drosophila)	662	WAPL. {ECO:0000255|PROSITE- ProRule:PRU00603}.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA replication (GO:0008156)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of fibroblast proliferation (GO:0048146)|protein localization to chromatin (GO:0071168)|regulation of chromosome condensation (GO:0060623)|regulation of cohesin localization to chromatin (GO:0071922)|response to toxic substance (GO:0009636)|viral process (GO:0016032)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)				breast(2)|endometrium(2)|kidney(5)|large_intestine(6)|lung(13)|ovary(2)|stomach(1)	31						TGAGTGCTCTTTAAGCCACTTAACAAGTACTC	0.349																																					p.662_666del		Atlas-Indel,Pindel	.											WAPAL,NS,carcinoma,0,1	WAPAL	81	.	0			c.1986_1997del						.																																			SO:0001651	inframe_deletion	23063	exon7			.	AB065003	CCDS7375.1	10q23.31	2006-12-08	2006-03-16	2006-03-16	ENSG00000062650	ENSG00000062650			23293	protein-coding gene	gene with protein product	"friend of EBNA2"	610754	"KIAA0261"	KIAA0261		9039502, 17112726	Standard	XM_006717726		Approved	FOE, WAPL	uc001kdo.3	Q7Z5K2	OTTHUMG00000018651	ENST00000298767.5:c.1985_1996delTAAGTGGCTTAA	chr10.hg19:g.88231999_88232010delTTAAGCCACTTA	ENSP00000298767:p.Leu662_Lys666delins*	335.0	0.0		343.0	100.0	NM_015045	A7E2B5|Q5VSK5|Q8IX10|Q92549	In_Frame_Del	DEL	ENST00000298767.5	hg19	CCDS7375.1																																																																																			.	.		0.349	WAPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049151.2	NM_015045		-	88232010	TTAAGCCACTTA	-	88231999	7	5	296	1	0	1	0	1	0	0	0	0	17263	1850	64	0	1628	0	WAPAL	10	88231999	In_Frame_Del	DEL	TTAAGCCACTTA	TCGA-G3-AAV0-01A-11D-A36X-10		88231999	47302748	118	43062										
EXOC6	54536	hgsc.bcm.edu	37	chr10	94669328	94669328	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	atctccatgtctgatctcaaAgactttttggaaagtattcg	7	8	3	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr10:94669328A>C	ENST00000260762.6	+	6	617	c.603A>C	c.(601-603)aaA>aaC	p.K201N	EXOC6_ENST00000443748.2_Missense_Mutation_p.K201N|EXOC6_ENST00000371547.4_Missense_Mutation_p.K217N|EXOC6_ENST00000497262.1_3'UTR|EXOC6_ENST00000371552.4_Missense_Mutation_p.K196N	NM_019053.4	NP_061926.3	Q8TAG9	EXOC6_HUMAN	exocyst complex component 6	201					cellular protein metabolic process (GO:0044267)|erythrocyte differentiation (GO:0030218)|membrane organization (GO:0061024)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	exocyst (GO:0000145)|plasma membrane (GO:0005886)				cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	26		Colorectal(252;0.123)				CTGATCTCAAAGACTTTTTGG	0.323																																					p.K201N		Atlas-SNP	.											.	EXOC6	147	.	0			c.A603C						.						73	73	73					10																	94669328		2203	4300	6503	SO:0001583	missense	54536	exon6			TCTCAAAGACTTT	BC028395	CCDS7424.2, CCDS31247.1	10q23.33	2013-01-22	2006-11-07	2006-11-07	ENSG00000138190	ENSG00000138190			23196	protein-coding gene	gene with protein product		609672	"SEC15-like 1 (S. cerevisiae)"	SEC15L1		8889548	Standard	NM_001013848		Approved	SEC15L, FLJ1125, DKFZp761I2124, MGC33397, Sec15p, EXOC6A	uc001kig.3	Q8TAG9	OTTHUMG00000018767	ENST00000260762.6:c.603A>C	chr10.hg19:g.94669328A>C	ENSP00000260762:p.Lys201Asn	235.0	0.0		237.0	91.0	NM_019053	E9PHI3|Q5VXH8|Q9NZ24	Missense_Mutation	SNP	ENST00000260762.6	hg19	CCDS7424.2	.	.	.	.	.	.	.	.	.	.	A	15.67	2.903345	0.52333	.	.	ENSG00000138190	ENST00000371547;ENST00000371552;ENST00000443748;ENST00000260762	T;T;T;T	0.29655	1.56;1.56;1.56;1.56	5.69	2.17	0.27698	.	0.000000	0.85682	D	0.000000	T	0.32406	0.0828	M	0.82056	2.57	0.30859	N	0.733747	B;B;B;B;B	0.32071	0.149;0.355;0.128;0.031;0.031	B;B;B;B;B	0.32393	0.145;0.057;0.06;0.017;0.028	T	0.34576	-0.9823	10	0.54805	T	0.06	-20.5353	6.8684	0.24106	0.5099:0.0:0.4901:0.0	.	217;201;193;201;196	F2Z2Q3;E7EW84;B4DEZ1;Q8TAG9;E9PHI3	.;.;.;EXOC6_HUMAN;.	N	217;196;201;201	ENSP00000360602:K217N;ENSP00000360607:K196N;ENSP00000396206:K201N;ENSP00000260762:K201N	ENSP00000260762:K201N	K	+	3	2	EXOC6	94659308	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.552000	0.36244	0.451000	0.26802	0.528000	0.53228	AAA	.	.		0.323	EXOC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049410.2	NM_019053		C	94669328	A	C	94669328	3	2	296	1	0	0	0	0	1	0	0	0	5310	69	3	5	715	5	EXOC6	10	94669328	Missense_Mutation	SNP	A	TCGA-G3-AAV0-01A-11D-A36X-10	6437329	94669328	40865419	119	43063										
CYP2C9	1559	hgsc.bcm.edu	37	chr10	96745877	96745877	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tgtttgaccctcatcactttCtggatgaaggtggcaatttt	9	8	3	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr10:96745877C>A	ENST00000260682.6	+	8	1249	c.1237C>A	c.(1237-1239)Ctg>Atg	p.L413M		NM_000771.3	NP_000762.2	P11712	CP2C9_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 9	413			L -> P (in dbSNP:rs28371687). {ECO:0000269|PubMed:15469410}.		arachidonic acid metabolic process (GO:0019369)|cellular amide metabolic process (GO:0043603)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|monocarboxylic acid metabolic process (GO:0032787)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|urea metabolic process (GO:0019627)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	(R)-limonene 6-monooxygenase activity (GO:0052741)|(S)-limonene 6-monooxygenase activity (GO:0018675)|(S)-limonene 7-monooxygenase activity (GO:0018676)|caffeine oxidase activity (GO:0034875)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|steroid hydroxylase activity (GO:0008395)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	34		Colorectal(252;0.0902)		all cancers(201;6.93e-05)	Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Agomelatine(DB06594)|Alosetron(DB00969)|Alprazolam(DB00404)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amprenavir(DB00701)|Anastrozole(DB01217)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Arformoterol(DB01274)|Artemether(DB06697)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Atovaquone(DB01117)|Azelastine(DB00972)|Bexarotene(DB00307)|Bicalutamide(DB01128)|Bortezomib(DB00188)|Bosentan(DB00559)|Brompheniramine(DB00835)|Buprenorphine(DB00921)|Bupropion(DB01156)|Cabozantinib(DB08875)|Caffeine(DB00201)|Candesartan(DB00796)|Capecitabine(DB01101)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Carvedilol(DB01136)|Celecoxib(DB00482)|Chloramphenicol(DB00446)|Chlorpropamide(DB00672)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Cinnarizine(DB00568)|Cisapride(DB00604)|Cisplatin(DB00515)|Clevidipine(DB04920)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Colchicine(DB01394)|Cyclizine(DB01176)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Dapsone(DB00250)|Delavirdine(DB00705)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Diclofenamide(DB01144)|Dicoumarol(DB00266)|Diethylstilbestrol(DB00255)|Diltiazem(DB00343)|Diphenhydramine(DB01075)|Disulfiram(DB00822)|Dolasetron(DB00757)|Donepezil(DB00843)|Dopamine(DB00988)|Dorzolamide(DB00869)|Doxepin(DB01142)|Dronabinol(DB00470)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enzalutamide(DB08899)|Epinephrine(DB00668)|Epoprostenol(DB01240)|Eprosartan(DB00876)|Estradiol(DB00783)|Estrone(DB00655)|Estropipate(DB04574)|Eszopiclone(DB00402)|Ethanol(DB00898)|Etodolac(DB00749)|Etoricoxib(DB01628)|Etravirine(DB06414)|Felodipine(DB01023)|Fenofibrate(DB01039)|Flecainide(DB01195)|Fluconazole(DB00196)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Fluoxetine(DB00472)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Fosphenytoin(DB01320)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Ginkgo biloba(DB01381)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Glyburide(DB01016)|Guanfacine(DB01018)|Haloperidol(DB00502)|Halothane(DB01159)|Hexobarbital(DB01355)|Histamine Phosphate(DB00667)|Human Serum Albumin(DB00062)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Ifosfamide(DB01181)|Imatinib(DB00619)|Indinavir(DB00224)|Indomethacin(DB00328)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Lidocaine(DB00281)|Lopinavir(DB01601)|Loratadine(DB00455)|Lornoxicam(DB06725)|Losartan(DB00678)|Lovastatin(DB00227)|Lumiracoxib(DB01283)|Medroxyprogesterone Acetate(DB00603)|Mefenamic acid(DB00784)|Melatonin(DB01065)|Meloxicam(DB00814)|Mestranol(DB01357)|Methadone(DB00333)|Methazolamide(DB00703)|Methimazole(DB00763)|Methoxyflurane(DB01028)|Metronidazole(DB00916)|Miconazole(DB01110)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Modafinil(DB00745)|Montelukast(DB00471)|Naproxen(DB00788)|Nateglinide(DB00731)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Niclosamide(DB06803)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Ospemifene(DB04938)|Oxaprozin(DB00991)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paramethadione(DB00617)|Paroxetine(DB00715)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phenprocoumon(DB00946)|Phentermine(DB00191)|Phenylbutazone(DB00812)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Prasugrel(DB06209)|Pravastatin(DB00175)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Pyrimethamine(DB00205)|Quazepam(DB01589)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rifapentine(DB01201)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Secobarbital(DB00418)|Selegiline(DB01037)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sitaxentan(DB06268)|Sorafenib(DB00398)|Sulfadiazine(DB00359)|Sulfadimethoxine(DB06150)|Sulfamethizole(DB00576)|Sulfamethoxazole(DB01015)|Sulfamoxole(DB08798)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Sulfapyridine(DB00891)|Sulfinpyrazone(DB01138)|Sulfisoxazole(DB00263)|Suprofen(DB00870)|Tamoxifen(DB00675)|Tapentadol(DB06204)|Temazepam(DB00231)|Teniposide(DB00444)|Tenoxicam(DB00469)|Terbinafine(DB00857)|Testosterone(DB00624)|Thalidomide(DB01041)|Theophylline(DB00277)|Thiamylal(DB01154)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tolbutamide(DB01124)|Tolcapone(DB00323)|Tolterodine(DB01036)|Torasemide(DB00214)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Treprostinil(DB00374)|Tretinoin(DB00755)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Valsartan(DB00177)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vismodegib(DB08828)|Voriconazole(DB00582)|Warfarin(DB00682)|Ximelagatran(DB04898)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Zidovudine(DB00495)|Zileuton(DB00744)|Zolpidem(DB00425)|Zopiclone(DB01198)	TCATCACTTTCTGGATGAAGG	0.368																																					p.L413M	Ovarian(54;1266 1406 16072 35076)	Atlas-SNP	.											.	CYP2C9	82	.	0			c.C1237A						.						120	117	118					10																	96745877		2203	4300	6503	SO:0001583	missense	1559	exon8			CACTTTCTGGATG	M61855	CCDS7437.1	10q24.1	2007-12-14	2003-01-14		ENSG00000138109	ENSG00000138109		"Cytochrome P450s"	2623	protein-coding gene	gene with protein product		601130	"cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 9"	CYP2C10		2009263, 7841444	Standard	NM_000771		Approved	P450IIC9	uc001kka.4	P11712	OTTHUMG00000018805	ENST00000260682.6:c.1237C>A	chr10.hg19:g.96745877C>A	ENSP00000260682:p.Leu413Met	121.0	0.0		138.0	50.0	NM_000771	P11713|Q16756|Q16872|Q5VX92|Q6IRV8|Q8WW80	Missense_Mutation	SNP	ENST00000260682.6	hg19	CCDS7437.1	.	.	.	.	.	.	.	.	.	.	.	12.84	2.059761	0.36373	.	.	ENSG00000138109	ENST00000545448;ENST00000260682	T	0.74106	-0.81	3.57	2.63	0.31362	.	0.000000	0.53938	U	0.000057	D	0.86397	0.5923	M	0.93062	3.375	0.30354	N	0.784481	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.82172	-0.0589	10	0.87932	D	0	.	6.1827	0.20480	0.0:0.7582:0.0:0.2418	.	413;413	Q5VX92;P11712	.;CP2C9_HUMAN	M	413	ENSP00000260682:L413M	ENSP00000260682:L413M	L	+	1	2	CYP2C9	96735867	0.999000	0.42202	0.945000	0.38365	0.384000	0.30261	1.294000	0.33365	0.813000	0.34350	0.446000	0.29264	CTG	.	.		0.368	CYP2C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049501.1	NM_000771		A	96745877	C	A	96745877	3	1	296	1	0	0	0	0	1	0	0	0	4170	912	32	3	1267	3	CYP2C9	10	96745877	Missense_Mutation	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	2076549	96745877	38788870	120	43064										
COX15	1355	hgsc.bcm.edu	37	chr10	101476153	101476153	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	actgctgccatcttggtcctTctaggaaggggaattctccg	11	11	3	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr10:101476153T>C	ENST00000016171.5	-	8	1103	c.1053A>G	c.(1051-1053)agA>agG	p.R351R	CUTC_ENST00000493385.1_Intron|COX15_ENST00000497381.1_5'UTR|COX15_ENST00000370483.5_Silent_p.R351R			Q7KZN9	COX15_HUMAN	cytochrome c oxidase assembly homolog 15 (yeast)	351					cellular respiration (GO:0045333)|heme a biosynthetic process (GO:0006784)|heme biosynthetic process (GO:0006783)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound metabolic process (GO:0006778)|respiratory chain complex IV assembly (GO:0008535)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	cytochrome-c oxidase activity (GO:0004129)|oxidoreductase activity, acting on the CH-CH group of donors (GO:0016627)			endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	13		Colorectal(252;0.234)		Epithelial(162;3.08e-10)|all cancers(201;2.43e-08)		TCTTGGTCCTTCTAGGAAGGG	0.438																																					p.R351R		Atlas-SNP	.											.	COX15	25	.	0			c.A1053G						.						132	133	133					10																	101476153		2203	4300	6503	SO:0001819	synonymous_variant	1355	exon8			GGTCCTTCTAGGA	AF044323	CCDS7481.1, CCDS7482.1	10q24	2014-09-17	2012-10-15		ENSG00000014919	ENSG00000014919		"Mitochondrial respiratory chain complex assembly factors"	2263	protein-coding gene	gene with protein product		603646	"COX15 (yeast) homolog, cytochrome c oxidase assembly protein", "COX15 homolog, cytochrome c oxidase assembly protein (yeast)"			9878253	Standard	NM_078470		Approved		uc001kqb.4	Q7KZN9	OTTHUMG00000018893	ENST00000016171.5:c.1053A>G	chr10.hg19:g.101476153T>C		90.0	0.0		86.0	29.0	NM_078470	A8K6I9|O60556|O75878|Q5TD00|Q5TD01|Q7Z3Q3|Q9NTN0	Silent	SNP	ENST00000016171.5	hg19	CCDS7482.1																																																																																			.	.		0.438	COX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049818.1	NP_510870		C	101476153	T	C	101476153	2	2	296	1	0	0	0	0	0	0	0	1	3766	1780	62	2		2	COX15	10	101476153	Silent	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	4730276	101476153	34058594	121	43065										
ADRA2A	150	hgsc.bcm.edu	37	chr10	112838915	112838915	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	cagaaccgcgagaagcgcttCacgttcgtgctggccgtggt	14	12	1	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr10:112838915C>T	ENST00000280155.2	+	1	2126	c.1161C>T	c.(1159-1161)ttC>ttT	p.F387F		NM_000681.3	NP_000672.3	P08913	ADA2A_HUMAN	adrenoceptor alpha 2A	372					actin cytoskeleton organization (GO:0030036)|activation of MAPK activity by adrenergic receptor signaling pathway (GO:0071883)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|acute inflammatory response (GO:0002526)|adenylate cyclase-inhibiting adrenergic receptor signaling pathway (GO:0071881)|blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|cellular response to hormone stimulus (GO:0032870)|DNA replication (GO:0006260)|energy reserve metabolic process (GO:0006112)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|fear response (GO:0042596)|female pregnancy (GO:0007565)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|intestinal absorption (GO:0050892)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of adrenergic receptor signaling pathway (GO:0071878)|negative regulation of calcium ion transmembrane transporter activity (GO:1901020)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of insulin secretion (GO:0046676)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of norepinephrine secretion (GO:0010700)|negative regulation of uterine smooth muscle contraction (GO:0070473)|phospholipase C-activating adrenergic receptor signaling pathway (GO:0071882)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokine production (GO:0001819)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of potassium ion transport (GO:0043268)|positive regulation of vasodilation (GO:0045909)|positive regulation of wound healing (GO:0090303)|Ras protein signal transduction (GO:0007265)|regulation of insulin secretion (GO:0050796)|regulation of vasoconstriction (GO:0019229)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|thermoception (GO:0050955)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	alpha-1B adrenergic receptor binding (GO:0031692)|alpha-2C adrenergic receptor binding (GO:0031696)|alpha2-adrenergic receptor activity (GO:0004938)|epinephrine binding (GO:0051379)|heterotrimeric G-protein binding (GO:0032795)|norepinephrine binding (GO:0051380)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|thioesterase binding (GO:0031996)			breast(1)|cervix(3)|endometrium(6)|large_intestine(3)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(234;0.0735)|Lung NSC(174;0.238)		Epithelial(162;0.000316)|all cancers(201;0.00501)|BRCA - Breast invasive adenocarcinoma(275;0.118)	Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Apraclonidine(DB00964)|Aripiprazole(DB01238)|Asenapine(DB06216)|Benzphetamine(DB00865)|Bethanidine(DB00217)|Brimonidine(DB00484)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Clozapine(DB00363)|Desipramine(DB01151)|Dexmedetomidine(DB00633)|Dihydroergotamine(DB00320)|Dipivefrin(DB00449)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinastine(DB00751)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Flupirtine(DB06623)|Guanabenz(DB00629)|Guanfacine(DB01018)|Lisuride(DB00589)|Lofexidine(DB04948)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methamphetamine(DB01577)|Methotrimeprazine(DB01403)|Methyldopa(DB00968)|Mianserin(DB06148)|Mirtazapine(DB00370)|Naphazoline(DB06711)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxymetazoline(DB00935)|Paliperidone(DB01267)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Phentolamine(DB00692)|Phenylpropanolamine(DB00397)|Pramipexole(DB00413)|Prazosin(DB00457)|Propericiazine(DB01608)|Pseudoephedrine(DB00852)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Tizanidine(DB00697)|Tolazoline(DB00797)|Trazodone(DB00656)|Trimipramine(DB00726)|Xylometazoline(DB06694)|Yohimbine(DB01392)|Ziprasidone(DB00246)	AGAAGCGCTTCACGTTCGTGC	0.706																																					p.F387F	Esophageal Squamous(173;605 2658 7278 49362)	Atlas-SNP	.											.	ADRA2A	38	.	0			c.C1161T						.						110	89	96					10																	112838915		2203	4300	6503	SO:0001819	synonymous_variant	150	exon1			GCGCTTCACGTTC	AF284095	CCDS7569.2	10q25.2	2012-08-08	2012-05-09		ENSG00000150594	ENSG00000150594		"GPCR / Class A : Adrenoceptors : alpha"	281	protein-coding gene	gene with protein product	"alpha-2AAR subtype C10", " alpha-2A-adrenergic receptor"	104210	"adrenergic, alpha-2A-, receptor"	ADRA2, ADRA2R			Standard	NM_000681		Approved	ADRAR	uc001kzo.3	P08913	OTTHUMG00000019050	ENST00000280155.2:c.1161C>T	chr10.hg19:g.112838915C>T		48.0	0.0		38.0	12.0	NM_000681	B0LPF6|Q2I8G2|Q2XN99|Q86TH8|Q9BZK1	Silent	SNP	ENST00000280155.2	hg19	CCDS7569.2																																																																																			.	.		0.706	ADRA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050372.2	NM_000681		T	112838915	C	T	112838915	2	4	296	1	0	0	0	0	0	0	0	1	337	825	29	3		3	ADRA2A	10	112838915	Silent	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	11362762	112838915	22695832	122	43066										
SFXN4	119559	hgsc.bcm.edu	37	chr10	120917178	120917237	+	Splice_Site	DEL	ATTTGACAGATTCTAAAAATACCTACTCCTAAGAAAGTTGAAGAAGCAACGGCTCCCGCC	ATTTGACAGATTCTAAAAATACCTACTCCTAAGAAAGTTGAAGAAGCAACGGCTCCCGCC	-													0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gacagattctaaaaatacctActcctaagaaagttgaagaa					rs543162504|rs202129977|rs370994281|rs368279951|rs374603053	byFrequency	TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	ATTTGACAGATTCTAAAAATACCTACTCCTAAGAAAGTTGAAGAAGCAACGGCTCCCGCC	ATTTGACAGATTCTAAAAATACCTACTCCTAAGAAAGTTGAAGAAGCAACGGCTCCCGCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr10:120917178_120917237delATTTGACAGATTCTAAAAATACCTACTCCTAAGAAAGTTGAAGAAGCAACGGCTCCCGCC	ENST00000355697.2	-	9	499_557	c.480_538delGGCGGGAGCCGTTGCTTCTTCAACTTTCTTAGGAGTAGGTATTTTTAGAATCTGTCAAAT	c.(478-540)aaggcgggagccgttgcttcttcaactttcttaggagtaggtatttttagaatctgtcaaatt>aatt	p.160_180KAGAVASSTFLGVGIFRICQI>N	SFXN4_ENST00000461438.1_5'UTR|SFXN4_ENST00000330036.6_Splice_Site_p.151_171KAGAVASSTFLGVGIFRICQI>N	NM_213649.1	NP_998814.1	Q6P4A7	SFXN4_HUMAN	sideroflexin 4	160					iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)			central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	11		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0261)		AAAAATACCTACTCCTAAGAAAGTTGAAGAAGCAACGGCTCCCGCCATTAGTAATGATCTTTCTAGTGGCTTACAAGTCT	0.304																																					p.169_179del		Pindel	.											.	SFXN4	24	.	0			c.505_537del						.																																			SO:0001630	splice_region_variant	119559	exon9			.		CCDS7610.1	10q26.11	2006-03-13			ENSG00000183605	ENSG00000183605		"Sideroflexins"	16088	protein-coding gene	gene with protein product		615564				14756423	Standard	NM_213649		Approved		uc001leb.3	Q6P4A7	OTTHUMG00000019147	ENST00000355697.2:c.537+1GGCGGGAGCCGTTGCTTCTTCAACTTTCTTAGGAGTAGGTATTTTTAGAATCTGTCAAAT>-	chr10.hg19:g.120917178_120917237delATTTGACAGATTCTAAAAATACCTACTCCTAAGAAAGTTGAAGAAGCAACGGCTCCCGCC		431.0	0.0		324.0	58.0	NM_213649	Q6WSU4|Q86TD9	In_Frame_Del	DEL	ENST00000355697.2	hg19	CCDS7610.1																																																																																			.	.		0.304	SFXN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050642.3	XM_058406	In_Frame_Del	-	120917237	ATTTGACAGATTCTAAAAATACCTACTCCTAAGAAAGTTGAAGAAGCAACGGCTCCCGCC	-	120917178	8	5	296	1	0	1	0	1	0	0	1	0	14212	405	14	0	498	0	SFXN4	10	120917178	Splice_Site	DEL	ATTTGACAGATTCTAAAAATACCTACTCCTAAGAAAGTTGAAGAAGCAACGGCTCCCGCC	TCGA-G3-AAV0-01A-11D-A36X-10	8078263	120917178	14617569	123	43067										
C11orf41	25758	hgsc.bcm.edu	37	chr11	33565296	33565296	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gatttaaatggacacacaatTagcaccacaagttgggaaac	8	8	0	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr11:33565296T>A	ENST00000321505.4	+	1	1476	c.1296T>A	c.(1294-1296)atT>atA	p.I432I	KIAA1549L_ENST00000265654.5_Silent_p.I432I|KIAA1549L_ENST00000389726.3_Silent_p.I432I			Q6ZVL6	K154L_HUMAN	KIAA1549-like	432						integral component of membrane (GO:0016021)											GACACACAATTAGCACCACAA	0.403											OREG0020868	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I432I		Atlas-SNP	.											.	.	.	.	0			c.T1296A						.						91	88	89					11																	33565296		1869	4096	5965	SO:0001819	synonymous_variant	25758	exon1			CACAATTAGCACC	U10991	CCDS44565.1, CCDS44565.2	11p13	2012-08-09	2012-08-09	2012-08-09	ENSG00000110427	ENSG00000110427			24836	protein-coding gene	gene with protein product		612297	"chromosome 11 open reading frame 69", "chromosome 11 open reading frame 41"	C11orf69, C11orf41			Standard	NM_012194		Approved	G2, MGC34830	uc021qfs.1	Q6ZVL6	OTTHUMG00000150410	ENST00000321505.4:c.1296T>A	chr11.hg19:g.33565296T>A		88.0	0.0	841	81.0	28.0	NM_012194	B0QYU0	Silent	SNP	ENST00000321505.4	hg19	CCDS44565.2																																																																																			.	.		0.403	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194		A	33565296	T	A	33565296	2	1	296	1	0	0	0	0	0	0	0	1	1642	1742	61	4		4	C11orf41	11	33565296	Silent	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10		33565296	101441220	124	43068										
AMBRA1	55626	hgsc.bcm.edu	37	chr11	46567302	46567302	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ggcaatggcattgttgctatCtgtgaaccagctttcactgc	10	10	2	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr11:46567302C>A	ENST00000458649.2	-	5	821	c.403G>T	c.(403-405)Gat>Tat	p.D135Y	AMBRA1_ENST00000426438.1_Missense_Mutation_p.D135Y|AMBRA1_ENST00000314845.3_Missense_Mutation_p.D135Y|AMBRA1_ENST00000533727.1_Missense_Mutation_p.D135Y|AMBRA1_ENST00000528950.1_Missense_Mutation_p.D135Y|AMBRA1_ENST00000298834.3_Missense_Mutation_p.D135Y|AMBRA1_ENST00000534300.1_Missense_Mutation_p.D135Y			Q9C0C7	AMRA1_HUMAN	autophagy/beclin-1 regulator 1	135					autophagy (GO:0006914)|cell differentiation (GO:0030154)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neural tube development (GO:0021915)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|phagocytic vesicle (GO:0045335)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	39				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)		TTGTTGCTATCTGTGAACCAG	0.507																																					p.D135Y		Atlas-SNP	.											.	AMBRA1	201	.	0			c.G403T						.						90	78	82					11																	46567302		2201	4299	6500	SO:0001583	missense	55626	exon5			TGCTATCTGTGAA	AB051523	CCDS31475.1, CCDS58132.1, CCDS73281.1	11p11.2	2013-01-09			ENSG00000110497	ENSG00000110497		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	25990	protein-coding gene	gene with protein product	"WD repeat domain 94", "DDB1 and CUL4 associated factor 3"	611359				17622796, 17603510, 17589504	Standard	NM_001267782		Approved	FLJ20294, KIAA1736, WDR94, DCAF3	uc001ncv.3	Q9C0C7	OTTHUMG00000166500	ENST00000458649.2:c.403G>T	chr11.hg19:g.46567302C>A	ENSP00000415327:p.Asp135Tyr	105.0	0.0		133.0	54.0	NM_001267783	A6XN33|D3DQP8|G3V193|Q86XD6|Q9H8Z0|Q9NXE7	Missense_Mutation	SNP	ENST00000458649.2	hg19		.	.	.	.	.	.	.	.	.	.	C	22.1	4.240509	0.79912	.	.	ENSG00000110497	ENST00000314845;ENST00000533727;ENST00000534300;ENST00000426438;ENST00000298834;ENST00000314823;ENST00000458649;ENST00000528950	T;T;T;T;T;T;T	0.30714	1.52;1.52;1.52;1.52;1.52;1.52;1.52	5.75	5.75	0.90469	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.045696	0.85682	D	0.000000	T	0.39860	0.1094	N	0.14661	0.345	0.80722	D	1	D;D;D;D;D;D	0.71674	0.996;0.998;0.998;0.994;0.998;0.994	P;D;D;P;D;P	0.63381	0.823;0.914;0.914;0.878;0.914;0.878	T	0.42682	-0.9437	10	0.87932	D	0	.	19.9478	0.97189	0.0:1.0:0.0:0.0	.	135;135;135;135;135;135	Q9C0C7;Q9C0C7-3;Q9C0C7-2;G3V193;Q9C0C7-5;Q9C0C7-4	AMRA1_HUMAN;.;.;.;.;.	Y	135	ENSP00000318313:D135Y;ENSP00000433372:D135Y;ENSP00000431926:D135Y;ENSP00000410899:D135Y;ENSP00000298834:D135Y;ENSP00000415327:D135Y;ENSP00000433945:D135Y	ENSP00000298834:D135Y	D	-	1	0	AMBRA1	46523878	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.696000	0.84270	2.712000	0.92718	0.591000	0.81541	GAT	.	.		0.507	AMBRA1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000390103.1	NM_017749		A	46567302	C	A	46567302	3	1	296	1	0	0	0	0	1	0	0	0	565	913	32	3	3283	3	AMBRA1	11	46567302	Missense_Mutation	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	13002006	46567302	88439214	125	43069										
OR5L1	219437	hgsc.bcm.edu	37	chr11	55579061	55579061	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	catctatggagtcacgttgtTagccaacctgggcatgattg	11	9	2	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr11:55579061T>A	ENST00000333973.2	+	1	208	c.119T>A	c.(118-120)tTa>tAa	p.L40*		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, member 1	40						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(4)|liver(4)|lung(36)|ovary(2)|pancreas(1)|prostate(5)|skin(9)|stomach(4)|upper_aerodigestive_tract(3)	78		all_epithelial(135;0.208)				GTCACGTTGTTAGCCAACCTG	0.502																																					p.L40X		Atlas-SNP	.											.	OR5L1	145	.	0			c.T119A						.						313	275	288					11																	55579061		2200	4296	6496	SO:0001587	stop_gained	219437	exon1			CGTTGTTAGCCAA	AB065780	CCDS31509.1	11q11	2012-08-09			ENSG00000186117	ENSG00000186117		"GPCR / Class A : Olfactory receptors"	8350	protein-coding gene	gene with protein product							Standard	NM_001004738		Approved	OST262	uc001nhw.1	Q8NGL2	OTTHUMG00000166810	ENST00000333973.2:c.119T>A	chr11.hg19:g.55579061T>A	ENSP00000335529:p.Leu40*	100.0	0.0		95.0	36.0	NM_001004738	B2RNK6|Q6IFD0	Nonsense_Mutation	SNP	ENST00000333973.2	hg19	CCDS31509.1	.	.	.	.	.	.	.	.	.	.	t	14.22	2.469113	0.43839	.	.	ENSG00000186117	ENST00000333973	.	.	.	4.32	1.74	0.24563	.	1.310130	0.05498	N	0.557829	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.14656	T	0.56	-8.9498	5.9005	0.18964	0.0:0.0897:0.3188:0.5915	.	.	.	.	X	40	.	ENSP00000335529:L40X	L	+	2	0	OR5L1	55335637	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.795000	0.26972	0.517000	0.28361	0.358000	0.22013	TTA	.	.		0.502	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738		A	55579061	T	A	55579061	4	1	296	1	0	0	0	0	0	1	0	0	11179	1764	61	4	121	4	OR5L1	11	55579061	Nonsense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	9011759	55579061	79427455	126	43070										
VEGFB	7423	hgsc.bcm.edu	37	chr11	64005084	64005084	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gccgacgccgcagcttcctcCgttgccaagggcggggctta	14	15	0	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr11:64005084C>G	ENST00000309422.2	+	6	899	c.603C>G	c.(601-603)tcC>tcG	p.S201S	VEGFB_ENST00000426086.2_Missense_Mutation_p.R168G	NM_001243733.1|NM_003377.4	NP_001230662.1|NP_003368.1	P49765	VEGFB_HUMAN	vascular endothelial growth factor B	201					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|coronary vasculature development (GO:0060976)|induction of positive chemotaxis (GO:0050930)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|negative regulation of neuron apoptotic process (GO:0043524)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of cell division (GO:0051781)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of mast cell chemotaxis (GO:0060754)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation of vascular wound healing (GO:0035470)|protein O-linked glycosylation (GO:0006493)|response to drug (GO:0042493)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	chemoattractant activity (GO:0042056)|heparin binding (GO:0008201)|vascular endothelial growth factor receptor 1 binding (GO:0043183)			endometrium(2)|large_intestine(2)|prostate(1)|stomach(1)	6					Aflibercept(DB08885)	CAGCTTCCTCCGTTGCCAAGG	0.692																																					p.R168G		Atlas-SNP	.											.	VEGFB	18	.	0			c.C502G						.						6	7	7					11																	64005084		2088	4112	6200	SO:0001819	synonymous_variant	7423	exon6			TTCCTCCGTTGCC	BC008818	CCDS8062.1, CCDS58144.1	11q13	2005-09-29				ENSG00000173511			12681	protein-coding gene	gene with protein product		601398		VRF		8637916, 8919691	Standard	NM_001243733		Approved	VEGFL	uc001nyw.3	P49765		ENST00000309422.2:c.603C>G	chr11.hg19:g.64005084C>G		37.0	0.0		59.0	18.0	NM_001243733	Q16528	Missense_Mutation	SNP	ENST00000309422.2	hg19	CCDS8062.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.44|16.44	3.124247|3.124247	0.56613|0.56613	.|.	.|.	ENSG00000173511|ENSG00000173511	ENST00000541681|ENST00000426086	.|.	.|.	.|.	4.86|4.86	4.86|4.86	0.63082|0.63082	.|.	.|.	.|.	.|.	.|.	T|T	0.43500|0.43500	0.1250|0.1250	.|.	.|.	.|.	0.29978|0.29978	N|N	0.817926|0.817926	.|B	.|0.30281	.|0.275	.|B	.|0.31614	.|0.133	T|T	0.51044|0.51044	-0.8755|-0.8755	4|7	.|0.72032	.|D	.|0.01	-5.9925|-5.9925	15.2806|15.2806	0.73781|0.73781	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|168	.|P49765-2	.|.	R|G	26|168	.|.	.|ENSP00000401550:R168G	P|R	+|+	2|1	0|0	VEGFB|VEGFB	63761660|63761660	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	2.775000|2.775000	0.47702|0.47702	2.437000|2.437000	0.82529|0.82529	0.561000|0.561000	0.74099|0.74099	CCG|CGT	.	.		0.692	VEGFB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396393.2	NM_003377		G	64005084	C	G	64005084	2	3	296	1	0	0	0	0	0	0	0	1	17166	639	23	4		4	VEGFB	11	64005084	Silent	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	8426023	64005084	71001432	127	43071										
RPS6KB2	6199	hgsc.bcm.edu	37	chr11	67200122	67200122	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gggcatcttcctggaagataCggcctggtgggtgttaatcc	14	9	1	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr11:67200122C>A	ENST00000312629.5	+	6	554	c.509C>A	c.(508-510)aCg>aAg	p.T170K	RPS6KB2_ENST00000539188.1_3'UTR|AP003419.16_ENST00000535922.1_RNA|RPS6KB2_ENST00000524814.1_3'UTR	NM_003952.2	NP_003943.2	Q9UBS0	KS6B2_HUMAN	ribosomal protein S6 kinase, 70kDa, polypeptide 2	170	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of translational initiation (GO:0045948)|protein kinase B signaling (GO:0043491)|signal transduction (GO:0007165)|translation (GO:0006412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|peptide binding (GO:0042277)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ribosomal protein S6 kinase activity (GO:0004711)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|prostate(3)|salivary_gland(1)|stomach(2)	25			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)			CTGGAAGATACGGCCTGGTGG	0.592																																					p.T170K		Atlas-SNP	.											.	RPS6KB2	92	.	0			c.C509A						.						134	152	146					11																	67200122		2178	4267	6445	SO:0001583	missense	6199	exon6			AAGATACGGCCTG	AB019245	CCDS41677.1	11q13.1	2011-04-05	2002-08-29		ENSG00000175634	ENSG00000175634			10437	protein-coding gene	gene with protein product		608939	"ribosomal protein S6 kinase, 70kD, polypeptide 2"			9878560, 9804755	Standard	XM_005274164		Approved	p70S6Kb, P70-BETA, STK14B, KLS	uc001old.3	Q9UBS0	OTTHUMG00000167673	ENST00000312629.5:c.509C>A	chr11.hg19:g.67200122C>A	ENSP00000308413:p.Thr170Lys	91.0	0.0		135.0	46.0	NM_003952	B2RMZ9|B4DML8|O94809|Q9UEC1	Missense_Mutation	SNP	ENST00000312629.5	hg19	CCDS41677.1	.	.	.	.	.	.	.	.	.	.	C	17.57	3.421834	0.62622	.	.	ENSG00000175634	ENST00000312629	T	0.64438	-0.1	5.43	5.43	0.79202	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.64091	0.2567	N	0.13198	0.31	0.80722	D	1	D;D	0.56746	0.965;0.977	P;P	0.59703	0.77;0.862	T	0.70132	-0.4956	10	0.66056	D	0.02	.	18.8483	0.92217	0.0:1.0:0.0:0.0	.	170;170	Q9BRS0;Q9UBS0	.;KS6B2_HUMAN	K	170	ENSP00000308413:T170K	ENSP00000308413:T170K	T	+	2	0	RPS6KB2	66956698	1.000000	0.71417	0.992000	0.48379	0.131000	0.20780	5.601000	0.67606	2.542000	0.85734	0.561000	0.74099	ACG	.	.		0.592	RPS6KB2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395508.1	NM_003952		A	67200122	C	A	67200122	3	1	296	1	0	0	0	0	1	0	0	0	13672	536	19	1	531	1	RPS6KB2	11	67200122	Missense_Mutation	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	3195038	67200122	67806394	128	43072										
MYO7A	4647	hgsc.bcm.edu	37	chr11	76890167	76890167	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gtcacaactgtaggaagaacTacgggctggtgagcctcccc	12	12	1	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr11:76890167T>C	ENST00000409709.3	+	20	2631	c.2359T>C	c.(2359-2361)Tac>Cac	p.Y787H	MYO7A_ENST00000409893.1_Missense_Mutation_p.Y787H|MYO7A_ENST00000409619.2_Missense_Mutation_p.Y776H|MYO7A_ENST00000458637.2_Missense_Mutation_p.Y787H	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	787	IQ 2. {ECO:0000255|PROSITE- ProRule:PRU00116}.				actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						TAGGAAGAACTACGGGCTGGT	0.597																																					p.Y787H		Atlas-SNP	.											.	MYO7A	164	.	0			c.T2359C						.						34	39	38					11																	76890167		2059	4192	6251	SO:0001583	missense	4647	exon20			AAGAACTACGGGC	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"A-kinase anchor proteins", "Myosins / Myosin superfamily : Class VII"	7606	protein-coding gene	gene with protein product		276903	"myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.2359T>C	chr11.hg19:g.76890167T>C	ENSP00000386331:p.Tyr787His	79.0	0.0		97.0	53.0	NM_001127179	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Missense_Mutation	SNP	ENST00000409709.3	hg19	CCDS53683.1	.	.	.	.	.	.	.	.	.	.	T	17.30	3.354888	0.61293	.	.	ENSG00000137474	ENST00000409709;ENST00000409893;ENST00000458637;ENST00000409619;ENST00000358342;ENST00000343356;ENST00000341717;ENST00000343419	T;T;T;T	0.36157	1.27;1.27;1.27;1.27	4.87	4.87	0.63330	.	0.000000	0.64402	D	0.000001	T	0.61451	0.2348	M	0.80746	2.51	0.80722	D	1	D;B;D	0.89917	1.0;0.154;0.996	D;B;D	0.83275	0.996;0.152;0.975	T	0.66500	-0.5908	10	0.59425	D	0.04	.	13.6853	0.62513	0.0:0.0:0.0:1.0	.	787;787;787	B9A012;F8VUN5;Q13402	.;.;MYO7A_HUMAN	H	787;787;787;776;786;786;663;786	ENSP00000386331:Y787H;ENSP00000386689:Y787H;ENSP00000392185:Y787H;ENSP00000386635:Y776H	ENSP00000345075:Y663H	Y	+	1	0	MYO7A	76567815	1.000000	0.71417	0.969000	0.41365	0.417000	0.31264	7.979000	0.88103	1.843000	0.53566	0.240000	0.17902	TAC	.	.		0.597	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260		C	76890167	T	C	76890167	3	2	296	1	0	0	0	0	1	0	0	0	10091	1522	53	2	2433	2	MYO7A	11	76890167	Missense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	9690045	76890167	58116349	129	43073										
INTS4	92105	hgsc.bcm.edu	37	chr11	77669833	77669833	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	acgacccagataagctggacTgcagcactgcgcacttgttc	10	13	0	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr11:77669833T>A	ENST00000534064.1	-	7	790	c.756A>T	c.(754-756)gcA>gcT	p.A252A	INTS4_ENST00000529807.1_Silent_p.A252A	NM_033547.3	NP_291025.3	Q96HW7	INT4_HUMAN	integrator complex subunit 4	252					snRNA processing (GO:0016180)	integrator complex (GO:0032039)			INTS4/GAB2(2)	NS(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(5)|upper_aerodigestive_tract(1)	32	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)			TAAGCTGGACTGCAGCACTGC	0.463																																					p.A252A		Atlas-SNP	.											.	INTS4	89	.	0			c.A756T						.						56	47	50					11																	77669833		2200	4292	6492	SO:0001819	synonymous_variant	92105	exon7			CTGGACTGCAGCA	BC015664	CCDS31644.1	11q14.1	2006-04-26			ENSG00000149262	ENSG00000149262			25048	protein-coding gene	gene with protein product		611348				16239144	Standard	NM_033547		Approved	INT4, MGC16733, MST093	uc001oys.3	Q96HW7	OTTHUMG00000166629	ENST00000534064.1:c.756A>T	chr11.hg19:g.77669833T>A		436.0	0.0		702.0	402.0	NM_033547	Q2YD62|Q6PJG4|Q7Z4E7|Q96G32|Q96GA1|Q9BRC0	Silent	SNP	ENST00000534064.1	hg19	CCDS31644.1																																																																																			.	.		0.463	INTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390927.1	NM_033547		A	77669833	T	A	77669833	2	1	296	1	0	0	0	0	0	0	0	1	7789	1567	55	4		4	INTS4	11	77669833	Silent	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	779666	77669833	57336683	130	43074										
FAM181B	220382	hgsc.bcm.edu	37	chr11	82443621	82443621	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	cctgatggggcggcggcggcGggggcagggcgcagtctgga	23	10	1	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr11:82443621G>A	ENST00000329203.3	-	1	1285	c.1151C>T	c.(1150-1152)cCg>cTg	p.P384L		NM_175885.3	NP_787081.2	A6NEQ2	F181B_HUMAN	family with sequence similarity 181, member B	384	Pro-rich.									large_intestine(1)|lung(2)|prostate(1)	4						CGGCGGCGGCGGGGGCAGGGC	0.697																																					p.P384L		Atlas-SNP	.											.	FAM181B	14	.	0			c.C1151T						.						5	6	6					11																	82443621		1835	3917	5752	SO:0001583	missense	220382	exon1			GGCGGCGGGGGCA	AK095054, BC039262	CCDS31648.1	11q14.1	2011-11-30			ENSG00000182103	ENSG00000182103			28512	protein-coding gene	gene with protein product						12477932	Standard	NM_175885		Approved	LOC220382, MGC33846	uc001ozp.3	A6NEQ2	OTTHUMG00000166869	ENST00000329203.3:c.1151C>T	chr11.hg19:g.82443621G>A	ENSP00000365295:p.Pro384Leu	144.0	0.0		197.0	14.0	NM_175885	B2RWP1	Missense_Mutation	SNP	ENST00000329203.3	hg19	CCDS31648.1	.	.	.	.	.	.	.	.	.	.	G	15.46	2.841559	0.51057	.	.	ENSG00000182103	ENST00000329203	T	0.34859	1.34	5.08	4.16	0.48862	.	.	.	.	.	T	0.27384	0.0672	N	0.24115	0.695	0.43255	D	0.995188	D	0.57899	0.981	P	0.45406	0.479	T	0.02087	-1.1216	8	.	.	.	.	11.6849	0.51481	0.0:0.0:0.6785:0.3215	.	384	A6NEQ2	F181B_HUMAN	L	384	ENSP00000365295:P384L	.	P	-	2	0	FAM181B	82121269	1.000000	0.71417	0.999000	0.59377	0.984000	0.73092	0.991000	0.29654	1.331000	0.45412	0.655000	0.94253	CCG	.	.		0.697	FAM181B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391626.1	NM_175885		A	82443621	G	A	82443621	3	1	296	1	0	0	0	0	1	0	0	0	5514	1116	39	1	133	1	FAM181B	11	82443621	Missense_Mutation	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10	4773788	82443621	52562895	131	43075										
PCF11	51585	hgsc.bcm.edu	37	chr11	82877710	82877710	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	atgtagaaaactggcaaagtTccaagtctgccaaaagatgg	10	7	1	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr11:82877710T>C	ENST00000298281.4	+	5	2223	c.1771T>C	c.(1771-1773)Tcc>Ccc	p.S591P		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	591					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						CTGGCAAAGTTCCAAGTCTGC	0.358																																					p.S591P		Atlas-SNP	.											.	PCF11	220	.	0			c.T1771C						.						70	70	70					11																	82877710		1795	3967	5762	SO:0001583	missense	51585	exon5			CAAAGTTCCAAGT	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)", "PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.1771T>C	chr11.hg19:g.82877710T>C	ENSP00000298281:p.Ser591Pro	375.0	0.0		457.0	143.0	NM_015885	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	hg19	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	T	10.60	1.394882	0.25205	.	.	ENSG00000165494	ENST00000298281;ENST00000530660;ENST00000530304	T;T;T	0.48836	1.79;0.83;0.8	6.07	6.07	0.98685	.	0.000000	0.64402	D	0.000015	T	0.30135	0.0755	N	0.17082	0.46	0.37024	D	0.896341	B;B	0.19073	0.033;0.027	B;B	0.15484	0.013;0.012	T	0.30238	-0.9985	9	.	.	.	.	10.8996	0.47043	0.0:0.0695:0.0:0.9305	.	591;591	E9PQ01;O94913	.;PCF11_HUMAN	P	591	ENSP00000298281:S591P;ENSP00000434540:S591P;ENSP00000431567:S591P	.	S	+	1	0	PCF11	82555358	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.091000	0.41691	2.326000	0.78906	0.533000	0.62120	TCC	.	.		0.358	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		C	82877710	T	C	82877710	3	2	296	1	0	0	0	0	1	0	0	0	11582	1783	62	2	1789	2	PCF11	11	82877710	Missense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	434089	82877710	52128806	132	43076										
PCF11	51585	hgsc.bcm.edu	37	chr11	82877748	82877749	+	In_Frame_Ins	INS	-	-	AAT													0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ggaaatctggttgggaagaaINSaataaaaggtatgatgttaa							TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr11:82877748_82877749insAAT	ENST00000298281.4	+	5	2261_2262	c.1809_1810insAAT	c.(1810-1812)aat>AATaat	p.604_604N>NN		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	604					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						GTTGGGAAGAAAATAAAAGGTA	0.327																																					p.E603delinsEN		Atlas-Indel,Pindel	.											.	PCF11	220	.	0			c.1809_1810insAAT						.																																			SO:0001652	inframe_insertion	51585	exon5			.	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)", "PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.1810_1812dupAAT	chr11.hg19:g.82877749_82877751dupAAT	ENSP00000298281:p.Asn604dup	353.0	0.0		428.0	91.0	NM_015885	A6H8W7|O43671|Q6P0X8	In_Frame_Ins	INS	ENST00000298281.4	hg19	CCDS44689.1																																																																																			.	.		0.327	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		AAT	82877749	-	AAT	82877748	7	5	296	1	0	1	1	0	0	0	0	0	11582	11	1	0	1827	0	PCF11	11	82877748	In_Frame_Ins	INS	-	TCGA-G3-AAV0-01A-11D-A36X-10	38	82877748	52128768	133	43077										
RBM7	10179	hgsc.bcm.edu	37	chr11	114271428	114271428	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ggcggaagcggatcgcactcTctttgtgggcaaccttgaaa	13	10	1	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr11:114271428T>C	ENST00000540163.1	+	1	677	c.35T>C	c.(34-36)cTc>cCc	p.L12P	RP11-212D19.4_ENST00000544347.1_Missense_Mutation_p.S9P|C11orf71_ENST00000325636.4_5'Flank|RBM7_ENST00000375490.5_Missense_Mutation_p.L12P|RBM7_ENST00000545678.1_5'UTR|RBM7_ENST00000544582.1_Missense_Mutation_p.L12P|RBM7_ENST00000541475.1_Missense_Mutation_p.L12P			Q9Y580	RBM7_HUMAN	RNA binding motif protein 7	12	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				meiotic nuclear division (GO:0007126)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17		all_cancers(61;5.06e-12)|all_epithelial(67;5.3e-06)|all_hematologic(158;7.68e-05)|Acute lymphoblastic leukemia(157;0.000966)|Melanoma(852;0.00153)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Breast(348;0.0818)|Prostate(24;0.104)		BRCA - Breast invasive adenocarcinoma(274;2.56e-06)|Epithelial(105;4.17e-05)|all cancers(92;0.000348)		GATCGCACTCTCTTTGTGGGC	0.617																																					p.L12P		Atlas-SNP	.											.	RBM7	33	.	0			c.T35C						.						55	60	58					11																	114271428		2201	4296	6497	SO:0001583	missense	10179	exon1			GCACTCTCTTTGT	AF156098	CCDS8370.1, CCDS66233.1, CCDS73395.1	11q23.1-q23.2	2013-02-12			ENSG00000076053	ENSG00000076053		"RNA binding motif (RRM) containing"	9904	protein-coding gene	gene with protein product		612413				12477932	Standard	NM_001286045		Approved		uc001pov.3	Q9Y580		ENST00000540163.1:c.35T>C	chr11.hg19:g.114271428T>C	ENSP00000439918:p.Leu12Pro	163.0	0.0		75.0	10.0	NM_016090	B2R6K8|Q9NUT4	Missense_Mutation	SNP	ENST00000540163.1	hg19	CCDS8370.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.215709	0.79352	.	.	ENSG00000076053	ENST00000540163;ENST00000375490;ENST00000541475;ENST00000544582	D;D;D;D	0.82526	-1.62;-1.62;-1.62;-1.62	5.4	4.28	0.50868	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.057265	0.64402	N	0.000001	D	0.93324	0.7872	H	0.97131	3.945	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.93462	0.6811	10	0.87932	D	0	-6.8725	10.1373	0.42715	0.0:0.0792:0.0:0.9208	.	12;12	Q6IRX3;Q9Y580	.;RBM7_HUMAN	P	12	ENSP00000439918:L12P;ENSP00000364639:L12P;ENSP00000440949:L12P;ENSP00000440923:L12P	ENSP00000364639:L12P	L	+	2	0	RBM7	113776638	1.000000	0.71417	0.971000	0.41717	0.740000	0.42216	7.030000	0.76484	0.898000	0.36418	0.460000	0.39030	CTC	.	.		0.617	RBM7-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399010.1	NM_016090		C	114271428	T	C	114271428	3	2	296	1	0	0	0	0	1	0	0	0	13160	1551	54	2	37	2	RBM7	11	114271428	Missense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	31393680	114271428	20735088	134	43078										
CD163L1	283316	hgsc.bcm.edu	37	chr12	7551140	7551140	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tccaatctcccataacagggGctatgagccccgacaagcct	8	15	1	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr12:7551140G>T	ENST00000313599.3	-	7	1506	c.1449C>A	c.(1447-1449)agC>agA	p.S483R	CD163L1_ENST00000416109.2_Missense_Mutation_p.S493R|CD163L1_ENST00000396630.1_Missense_Mutation_p.S483R			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	483	SRCR 5. {ECO:0000255|PROSITE- ProRule:PRU00196}.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						CATAACAGGGGCTATGAGCCC	0.458																																					p.S483R		Atlas-SNP	.											.	CD163L1	238	.	0			c.C1449A						.						77	67	71					12																	7551140		2203	4300	6503	SO:0001583	missense	283316	exon7			ACAGGGGCTATGA	AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"CD163 antigen-like 1"			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.1449C>A	chr12.hg19:g.7551140G>T	ENSP00000315945:p.Ser483Arg	104.0	0.0		149.0	53.0	NM_174941	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Missense_Mutation	SNP	ENST00000313599.3	hg19	CCDS8577.1	.	.	.	.	.	.	.	.	.	.	G	10.22	1.288910	0.23478	.	.	ENSG00000177675	ENST00000313599;ENST00000416109;ENST00000396630	T;T;T	0.33654	1.4;1.4;1.4	1.88	-1.28	0.09318	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.534254	0.14164	U	0.337200	T	0.34861	0.0912	L	0.52759	1.655	0.09310	N	1	P;P	0.45078	0.85;0.85	P;P	0.48524	0.58;0.58	T	0.21415	-1.0246	10	0.51188	T	0.08	.	6.3128	0.21174	0.6182:0.0:0.3818:0.0	.	493;483	E7EVK4;Q9NR16	.;C163B_HUMAN	R	483;493;483	ENSP00000315945:S483R;ENSP00000393474:S493R;ENSP00000379871:S483R	ENSP00000315945:S483R	S	-	3	2	CD163L1	7442407	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.571000	0.05889	-0.402000	0.07633	-0.459000	0.05422	AGC	.	.		0.458	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941		T	7551140	G	T	7551140	3	4	296	1	0	0	0	0	1	0	0	0	2970	1194	42	3	2964	3	CD163L1	12	7551140	Missense_Mutation	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10		7551140	126300755	135	43079										
LRRK2	120892	hgsc.bcm.edu	37	chr12	40668428	40668428	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gaaatgtggattaaaagtaaTttcttctattgtacattttc	6	4	2	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr12:40668428T>C	ENST00000298910.7	+	15	1758	c.1700T>C	c.(1699-1701)aTt>aCt	p.I567T	LRRK2_ENST00000343742.2_Missense_Mutation_p.I567T	NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	567					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				TTAAAAGTAATTTCTTCTATT	0.348																																					p.I567T		Atlas-SNP	.											.	LRRK2	763	.	0			c.T1700C						.						145	147	146					12																	40668428		2203	4300	6503	SO:0001583	missense	120892	exon15			AAGTAATTTCTTC	AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"Parkinson disease"	18618	protein-coding gene	gene with protein product		609007	"Parkinson disease (autosomal dominant) 8"	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.1700T>C	chr12.hg19:g.40668428T>C	ENSP00000298910:p.Ile567Thr	83.0	0.0		80.0	27.0	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	hg19	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	T	11.93	1.785895	0.31593	.	.	ENSG00000188906	ENST00000416796;ENST00000343742;ENST00000298910	T;T;T	0.68624	-0.34;1.12;1.12	6.07	6.07	0.98685	Armadillo-like helical (1);Armadillo-type fold (1);	0.264252	0.38548	N	0.001644	T	0.58221	0.2107	L	0.43152	1.355	0.31900	N	0.61603	B;P	0.37914	0.03;0.611	B;B	0.29524	0.033;0.103	T	0.70457	-0.4866	10	0.72032	D	0.01	.	16.6407	0.85098	0.0:0.0:0.0:1.0	.	567;567	E9PC85;Q5S007	.;LRRK2_HUMAN	T	315;567;567	ENSP00000398726:I315T;ENSP00000341930:I567T;ENSP00000298910:I567T	ENSP00000298910:I567T	I	+	2	0	LRRK2	38954695	0.999000	0.42202	0.260000	0.24451	0.226000	0.24999	6.609000	0.74173	2.326000	0.78906	0.533000	0.62120	ATT	.	.		0.348	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		C	40668428	T	C	40668428	3	2	296	1	0	0	0	0	1	0	0	0	9042	1493	52	2	1758	2	LRRK2	12	40668428	Missense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	33117288	40668428	93183467	136	43080										
MLL2	8085	hgsc.bcm.edu	37	chr12	49431855	49431855	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ggggagggcgctcctcagggCccaagggtcctggctccacc	16	15	1	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr12:49431855C>T	ENST00000301067.7	-	34	9283	c.9284G>A	c.(9283-9285)gGc>gAc	p.G3095D	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3095					chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										CTCCTCAGGGCCCAAGGGTCC	0.632																																					p.G3095D		Atlas-SNP	.											.	MLL2	1173	.	0			c.G9284A						.						33	32	33					12																	49431855		1959	4144	6103	SO:0001583	missense	8085	exon34			TCAGGGCCCAAGG	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.9284G>A	chr12.hg19:g.49431855C>T	ENSP00000301067:p.Gly3095Asp	94.0	0.0		81.0	33.0	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	hg19	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	C	9.243	1.038899	0.19669	.	.	ENSG00000167548	ENST00000301067	T	0.79141	-1.24	5.2	3.19	0.36642	.	0.199359	0.25208	N	0.032327	T	0.60170	0.2248	N	0.14661	0.345	0.27352	N	0.956227	P	0.43477	0.808	B	0.39419	0.299	T	0.58945	-0.7546	10	0.87932	D	0	.	9.3404	0.38076	0.1625:0.6803:0.1572:0.0	.	3095	O14686	MLL2_HUMAN	D	3095	ENSP00000301067:G3095D	ENSP00000301067:G3095D	G	-	2	0	MLL2	47718122	0.001000	0.12720	0.997000	0.53966	0.991000	0.79684	-0.060000	0.11712	1.289000	0.44618	0.655000	0.94253	GGC	.	.		0.632	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			T	49431855	C	T	49431855	3	4	296	1	0	0	0	0	1	0	0	0	9630	739	26	3	7413	3	MLL2	12	49431855	Missense_Mutation	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	8763427	49431855	84420040	137	43081										
KRT85	3891	hgsc.bcm.edu	37	chr12	52757067	52757067	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	actcagcctcggcccggctgCggctggcaacatcgtcatac	11	16	2	0	rs529513894		TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr12:52757067C>A	ENST00000257901.3	-	5	989	c.914G>T	c.(913-915)cGc>cTc	p.R305L	KRT85_ENST00000544265.1_Missense_Mutation_p.R93L	NM_002283.3	NP_002274.1	P78386	KRT85_HUMAN	keratin 85	305	Coil 2.|Rod.				epidermis development (GO:0008544)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(6)|kidney(1)|large_intestine(7)|liver(1)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	36	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		GGCCCGGCTGCGGCTGGCAAC	0.557																																					p.R305L		Atlas-SNP	.											.	KRT85	78	.	0			c.G914T						.						89	68	75					12																	52757067		2203	4300	6503	SO:0001583	missense	3891	exon5			CGGCTGCGGCTGG	X99140	CCDS8824.1, CCDS73472.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000135443	ENSG00000135443		"-", "Intermediate filaments type II, keratins (basic)"	6462	protein-coding gene	gene with protein product	"hard keratin type II"	602767	"keratin, hair, basic, 5"	KRTHB5		9084137, 16831889	Standard	NM_002283		Approved	Hb-5	uc001sag.3	P78386	OTTHUMG00000169633	ENST00000257901.3:c.914G>T	chr12.hg19:g.52757067C>A	ENSP00000257901:p.Arg305Leu	79.0	0.0		85.0	7.0	NM_002283	Q9NSB1	Missense_Mutation	SNP	ENST00000257901.3	hg19	CCDS8824.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.416862	0.83449	.	.	ENSG00000135443	ENST00000257901;ENST00000544265	D;T	0.89050	-2.46;-1.13	4.87	4.87	0.63330	Filament (1);	0.000000	0.64402	D	0.000015	D	0.94847	0.8335	H	0.94886	3.595	0.27837	N	0.941246	D	0.54601	0.967	P	0.60345	0.873	D	0.90562	0.4516	10	0.66056	D	0.02	.	11.1722	0.48577	0.0:0.8637:0.0:0.1363	.	305	P78386	KRT85_HUMAN	L	305;93	ENSP00000257901:R305L;ENSP00000440240:R93L	ENSP00000257901:R305L	R	-	2	0	KRT85	51043334	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.336000	0.33850	2.243000	0.73865	0.561000	0.74099	CGC	.	.		0.557	KRT85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405184.1	NM_002283		A	52757067	C	A	52757067	3	1	296	1	0	0	0	0	1	0	0	0	8508	768	27	1	629	1	KRT85	12	52757067	Missense_Mutation	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	3325212	52757067	81094828	138	43082										
KRT75	9119	hgsc.bcm.edu	37	chr12	52826861	52826861	+	Frame_Shift_Del	DEL	A	A	-													0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	caacatcctgcatgttcctcAgttcagcttcaagcctgccc							TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr12:52826861delA	ENST00000252245.5	-	2	894	c.674delT	c.(673-675)ctgfs	p.L225fs		NM_004693.2	NP_004684.2	O95678	K2C75_HUMAN	keratin 75	225	Coil 1B.|Rod.				hematopoietic progenitor cell differentiation (GO:0002244)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(10)|prostate(1)|skin(1)	28				BRCA - Breast invasive adenocarcinoma(357;0.192)		CATGTTCCTCAGTTCAGCTTC	0.537																																					p.L225fs		Atlas-Indel,Pindel	.											.	KRT75	75	.	0			c.675delG						.						121	108	112					12																	52826861		2203	4300	6503	SO:0001589	frameshift_variant	9119	exon2			.	Y19212	CCDS8827.1	12q13.13	2013-06-25			ENSG00000170454	ENSG00000170454		"-", "Intermediate filaments type II, keratins (basic)"	24431	protein-coding gene	gene with protein product		609025				9856802, 10692104, 16831889	Standard	NM_004693		Approved	K6HF	uc001saj.2	O95678	OTTHUMG00000169592	ENST00000252245.5:c.674delT	chr12.hg19:g.52826861delA	ENSP00000252245:p.Leu225fs	129.0	0.0		116.0	51.0	NM_004693	B4DQU4|Q9NSA9	Frame_Shift_Del	DEL	ENST00000252245.5	hg19	CCDS8827.1																																																																																			.	.		0.537	KRT75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404968.1	NM_004693		-	52826861	A	-	52826861	7	5	296	1	0	1	0	1	0	0	0	0	8497	188	7	0	1013	0	KRT75	12	52826861	Frame_Shift_Del	DEL	A	TCGA-G3-AAV0-01A-11D-A36X-10	69794	52826861	81025034	139	43083										
TIMELESS	8914	hgsc.bcm.edu	37	chr12	56817448	56817448	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tcctcttcctcctcctcctcCtcttcttcttcctctgcccc	1	23	5	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr12:56817448C>T	ENST00000553532.1	-	17	2160	c.2010G>A	c.(2008-2010)gaG>gaA	p.E670E	TIMELESS_ENST00000554616.1_Intron|TIMELESS_ENST00000229201.4_Silent_p.E669E					timeless circadian clock									p.E670E(1)		NS(1)|breast(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(8)|lung(14)|ovary(7)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	49						cctcctcctcctcttcttctt	0.527																																					p.E670E		Atlas-SNP	.											TIMELESS,NS,carcinoma,0,1	TIMELESS	107	.	1	Substitution - coding silent(1)	kidney(1)	c.G2010A						.						51	49	50					12																	56817448		2203	4300	6503	SO:0001819	synonymous_variant	8914	exon17			CTCCTCCTCTTCT	AF098162	CCDS8918.1	12q13.3	2012-12-14	2012-12-14		ENSG00000111602	ENSG00000111602			11813	protein-coding gene	gene with protein product	"Tof1 homolog (S. cerevisiae)", "timeless circadian clock 1"	603887	"timeless (Drosophila) homolog", "timeless homolog (Drosophila)"			9856465	Standard	NM_003920		Approved	hTIM, TIM, TIM1	uc001slf.2	Q9UNS1	OTTHUMG00000170600	ENST00000553532.1:c.2010G>A	chr12.hg19:g.56817448C>T		52.0	0.0		63.0	4.0	NM_003920		Silent	SNP	ENST00000553532.1	hg19	CCDS8918.1																																																																																			.	.		0.527	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920		T	56817448	C	T	56817448	2	4	296	1	0	0	0	0	0	0	0	1	15919	680	24	3		3	TIMELESS	12	56817448	Silent	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	3990587	56817448	77034447	140	43084										
PRIM1	5557	hgsc.bcm.edu	37	chr12	57136845	57136845	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	cttgattaaccaaggcatatTcttcaaagtatttttttatt	4	6	2	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr12:57136845T>A	ENST00000338193.6	-	7	710	c.674A>T	c.(673-675)gAa>gTa	p.E225V		NM_000946.2	NP_000937.1	P49642	PRI1_HUMAN	primase, DNA, polypeptide 1 (49kDa)	225					DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	membrane (GO:0016020)|nucleoplasm (GO:0005654)|primosome complex (GO:1990077)	DNA primase activity (GO:0003896)|metal ion binding (GO:0046872)			kidney(1)|lung(6)|prostate(1)	8						CAAGGCATATTCTTCAAAGTA	0.318																																					p.E225V		Atlas-SNP	.											.	PRIM1	22	.	0			c.A674T						.						42	34	37					12																	57136845		1763	4032	5795	SO:0001583	missense	5557	exon7			GCATATTCTTCAA	BC005266	CCDS44926.1	12q13.3	2007-06-19	2007-06-19			ENSG00000198056			9369	protein-coding gene	gene with protein product		176635				8530050	Standard	NM_000946		Approved		uc001smd.3	P49642	OTTHUMG00000170034	ENST00000338193.6:c.674A>T	chr12.hg19:g.57136845T>A	ENSP00000350491:p.Glu225Val	60.0	0.0		62.0	26.0	NM_000946		Missense_Mutation	SNP	ENST00000338193.6	hg19	CCDS44926.1	.	.	.	.	.	.	.	.	.	.	T	13.82	2.352023	0.41700	.	.	ENSG00000198056	ENST00000537418;ENST00000338193;ENST00000549549;ENST00000550770	T;T;T	0.46819	0.86;0.86;0.86	5.12	2.76	0.32466	.	0.670556	0.15662	N	0.250865	T	0.47060	0.1425	L	0.56769	1.78	0.37668	D	0.923021	P	0.36222	0.544	B	0.41299	0.353	T	0.49634	-0.8919	10	0.52906	T	0.07	-1.3865	9.2186	0.37362	0.0:0.1544:0.0:0.8456	.	225	P49642	PRI1_HUMAN	V	226;225;13;228	ENSP00000350491:E225V;ENSP00000449806:E13V;ENSP00000450185:E228V	ENSP00000350491:E225V	E	-	2	0	PRIM1	55423112	0.807000	0.29009	0.992000	0.48379	0.802000	0.45316	1.296000	0.33389	0.491000	0.27793	0.402000	0.26972	GAA	.	.		0.318	PRIM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406956.1	NM_000946		A	57136845	T	A	57136845	3	1	296	1	0	0	0	0	1	0	0	0	12502	1783	62	4	616	4	PRIM1	12	57136845	Missense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	319397	57136845	76715050	141	43085										
PAH	5053	hgsc.bcm.edu	37	chr12	103310862	103310862	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ggctcacctgtccaaagtcaGagagtttcctgcccaagcct	9	14	2	1	rs62642906		TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr12:103310862G>A	ENST00000553106.1	-	1	519	c.47C>T	c.(46-48)tCt>tTt	p.S16F	PAH_ENST00000307000.2_5'UTR|PAH_ENST00000551988.1_5'UTR	NM_000277.1	NP_000268.1	P00439	PH4H_HUMAN	phenylalanine hydroxylase	16			S -> P (in PKU).		catecholamine biosynthetic process (GO:0042423)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|neurotransmitter biosynthetic process (GO:0042136)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|phenylalanine 4-monooxygenase activity (GO:0004505)			endometrium(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(5)|skin(2)|urinary_tract(1)	27					Droxidopa(DB06262)|Epinephrine(DB00668)|L-Phenylalanine(DB00120)|Norepinephrine(DB00368)|Tetrahydrobiopterin(DB00360)	TCCAAAGTCAGAGAGTTTCCT	0.577																																					p.S16F		Atlas-SNP	.											.	PAH	77	.	0			c.C47T						.						86	82	83					12																	103310862		2203	4300	6503	SO:0001583	missense	5053	exon1			AAGTCAGAGAGTT	U49897	CCDS9092.1	12q22-q24.2	2010-04-27				ENSG00000171759	1.14.16.1		8582	protein-coding gene	gene with protein product	"phenylalanine 4-monooxygenase"	612349				2063869	Standard	NM_000277		Approved	PH	uc001tjq.1	P00439		ENST00000553106.1:c.47C>T	chr12.hg19:g.103310862G>A	ENSP00000448059:p.Ser16Phe	88.0	0.0		87.0	32.0	NM_000277	Q16717|Q8TC14	Missense_Mutation	SNP	ENST00000553106.1	hg19	CCDS9092.1	.	.	.	.	.	.	.	.	.	.	G	9.961	1.222897	0.22457	.	.	ENSG00000171759	ENST00000553106;ENST00000551337;ENST00000546844	D;D;D	0.99405	-5.84;-4.63;-5.07	5.2	3.36	0.38483	.	0.377447	0.28156	N	0.016381	D	0.96331	0.8803	N	0.08118	0	0.26233	N	0.978983	B;B	0.09022	0.002;0.0	B;B	0.04013	0.001;0.0	D	0.93323	0.6694	10	0.49607	T	0.09	-9.4426	8.416	0.32672	0.0:0.183:0.6515:0.1655	.	16;16	B4DPN2;P00439	.;PH4H_HUMAN	F	16	ENSP00000448059:S16F;ENSP00000447620:S16F;ENSP00000446658:S16F	ENSP00000446658:S16F	S	-	2	0	PAH	101834992	0.943000	0.32029	0.010000	0.14722	0.008000	0.06430	1.681000	0.37618	0.867000	0.35654	0.655000	0.94253	TCT	.	.		0.577	PAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406692.1			A	103310862	G	A	103310862	3	1	296	1	0	0	0	0	1	0	0	0	11403	942	33	3	1363	3	PAH	12	103310862	Missense_Mutation	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10	46174017	103310862	30541033	142	43086										
ATP6V0A2	23545	hgsc.bcm.edu	37	chr12	124242532	124242532	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ccaaatttgttcctttctcaTtcagtctactttcatcaaag	3	11	5	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr12:124242532T>G	ENST00000330342.3	+	20	2772	c.2524T>G	c.(2524-2526)Ttc>Gtc	p.F842V	ATP6V0A2_ENST00000543687.1_3'UTR|ATP6V0A2_ENST00000544833.1_Missense_Mutation_p.F124V	NM_012463.3	NP_036595.2	Q9Y487	VPP2_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a2	842					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|immune response (GO:0006955)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	hydrogen ion transmembrane transporter activity (GO:0015078)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.000625)|all cancers(50;0.00775)		TCCTTTCTCATTCAGTCTACT	0.343																																					p.F842V		Atlas-SNP	.											.	ATP6V0A2	68	.	0			c.T2524G						.						126	113	117					12																	124242532		2203	4300	6503	SO:0001583	missense	23545	exon20			TTCTCATTCAGTC	AF112972	CCDS9254.1	12q24.31	2010-04-21	2006-01-20		ENSG00000185344	ENSG00000185344		"ATPases / V-type"	18481	protein-coding gene	gene with protein product	"infantile malignant osteopetrosis"	611716	"infantile malignant osteopetrosis", "ATPase, H+ transporting, lysosomal V0 subunit a isoform 2", "ATPase, H+ transporting, lysosomal V0 subunit A2"			2247090, 18157129	Standard	NM_012463		Approved	TJ6, a2, TJ6s, TJ6M, ATP6a2, J6B7, ATP6N1D, Vph1, Stv1	uc001ufr.3	Q9Y487	OTTHUMG00000168723	ENST00000330342.3:c.2524T>G	chr12.hg19:g.124242532T>G	ENSP00000332247:p.Phe842Val	64.0	0.0		71.0	19.0	NM_012463	A8K026|Q6NUM0	Missense_Mutation	SNP	ENST00000330342.3	hg19	CCDS9254.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.134365	0.77662	.	.	ENSG00000185344	ENST00000330342;ENST00000534943;ENST00000544833	D;D;D	0.87029	-2.2;-2.2;-2.2	5.71	4.56	0.56223	.	0.000000	0.85682	D	0.000000	D	0.89942	0.6861	M	0.90019	3.08	0.80722	D	1	P	0.40000	0.698	B	0.41946	0.371	D	0.89950	0.4079	10	0.87932	D	0	-19.7366	11.829	0.52283	0.0:0.0685:0.0:0.9315	.	842	Q9Y487	VPP2_HUMAN	V	842;122;124	ENSP00000332247:F842V;ENSP00000443726:F122V;ENSP00000441143:F124V	ENSP00000332247:F842V	F	+	1	0	ATP6V0A2	122808485	1.000000	0.71417	0.918000	0.36340	0.671000	0.39405	6.235000	0.72332	0.982000	0.38575	0.533000	0.62120	TTC	.	.		0.343	ATP6V0A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400765.2	NM_012463		G	124242532	T	G	124242532	3	3	296	1	0	0	0	0	1	0	0	0	1169	1493	52	5	2602	5	ATP6V0A2	12	124242532	Missense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	20931670	124242532	9609363	143	43087										
ATP12A	479	hgsc.bcm.edu	37	chr13	25265114	25265114	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gaataaagcatctacttcccCtgtaggcactgtcaccggca	8	13	2	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr13:25265114C>T	ENST00000381946.3	+	8	966				ATP12A_ENST00000218548.6_Missense_Mutation_p.P271L			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide						ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		TCTACTTCCCCTGTAGGCACT	0.572																																					p.P271L	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-SNP	.											.	ATP12A	172	.	0			c.C812T						.						132	125	128					13																	25265114		2203	4300	6503	SO:0001627	intron_variant	479	exon8			CTTCCCCTGTAGG	L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"ATPases / P-type"	13816	protein-coding gene	gene with protein product	"ATPase, Na+K+ transporting, alpha-1 polypeptide-like", "potassium-transporting ATPase alpha chain 2", "proton pump", "non-gastric H(+)/K(+) ATPase alpha subunit", "sodium/potassium ATPase, alpha polypeptide-like"	182360	"ATPase, Na+/K+ transporting, alpha polypeptide-like 1"	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.800-6C>T	chr13.hg19:g.25265114C>T		91.0	0.0		76.0	29.0	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Missense_Mutation	SNP	ENST00000381946.3	hg19	CCDS31948.1	.	.	.	.	.	.	.	.	.	.	C	4.251	0.045541	0.08196	.	.	ENSG00000075673	ENST00000218548	D	0.92911	-3.13	5.02	4.09	0.47781	.	0.466770	0.15887	U	0.239723	D	0.86146	0.5863	.	.	.	0.33231	D	0.555972	B	0.06786	0.001	B	0.08055	0.003	D	0.84299	0.0504	9	0.45353	T	0.12	.	7.5117	0.27577	0.0:0.8826:0.0:0.1174	.	271	P54707-2	.	L	271	ENSP00000218548:P271L	ENSP00000218548:P271L	P	+	2	0	ATP12A	24163114	0.002000	0.14202	0.066000	0.19879	0.004000	0.04260	0.619000	0.24388	2.600000	0.87896	0.462000	0.41574	CCT	.	.		0.572	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676		T	25265114	C	T	25265114	1	4	296	0	1	0	0	0	0	0	0	0	1122	681	24	3		3	ATP12A	13	25265114	Intron	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10		25265114	89904764	144	43088										
TM9SF2	9375	hgsc.bcm.edu	37	chr13	100206556	100206556	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ttccttcctttttttactgaAggccattgaacacccagttc	5	12	0	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr13:100206556A>T	ENST00000376387.4	+	14	1678		c.e14-1			NM_004800.1	NP_004791.1	Q99805	TM9S2_HUMAN	transmembrane 9 superfamily member 2						transport (GO:0006810)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)	17	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.218)					TTTTTACTGAAGGCCATTGAA	0.403																																					.		Atlas-SNP	.											.	TM9SF2	52	.	0			c.1489-2A>T						.						132	126	128					13																	100206556		2203	4300	6503	SO:0001630	splice_region_variant	9375	exon14			TACTGAAGGCCAT	U81006	CCDS9493.1	13q32.2	2011-03-28			ENSG00000125304	ENSG00000125304			11865	protein-coding gene	gene with protein product		604678				9729438	Standard	NM_004800		Approved	P76	uc001voj.2	Q99805	OTTHUMG00000017272	ENST00000376387.4:c.1489-1A>T	chr13.hg19:g.100206556A>T		70.0	0.0		76.0	25.0	NM_004800	A8K399|Q2TAY5	Splice_Site	SNP	ENST00000376387.4	hg19	CCDS9493.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.086358	0.76642	.	.	ENSG00000125304	ENST00000376387	.	.	.	5.93	5.93	0.95920	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3943	0.83563	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TM9SF2	99004557	1.000000	0.71417	0.939000	0.37840	0.726000	0.41606	9.098000	0.94202	2.281000	0.76405	0.533000	0.62120	.	.	.		0.403	TM9SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045602.3		Intron	T	100206556	A	T	100206556	5	4	296	1	0	0	0	0	0	0	1	0	15993	86	3	4	1541	4	TM9SF2	13	100206556	Splice_Site	SNP	A	TCGA-G3-AAV0-01A-11D-A36X-10	74941442	100206556	14963322	145	43089										
IRS2	8660	hgsc.bcm.edu	37	chr13	110434682	110434682	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	agccggcagaggtctctctgCgcatgggcgatccaccgctc	13	15	2	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr13:110434682C>T	ENST00000375856.3	-	1	4233	c.3719G>A	c.(3718-3720)cGc>cAc	p.R1240H		NM_003749.2	NP_003740.2	Q9Y4H2	IRS2_HUMAN	insulin receptor substrate 2	1240					brain development (GO:0007420)|cell proliferation (GO:0008283)|cellular response to glucose stimulus (GO:0071333)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid homeostasis (GO:0055088)|mammary gland development (GO:0030879)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of kinase activity (GO:0033673)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin secretion (GO:0032024)|positive regulation of mesenchymal cell proliferation (GO:0002053)|regulation of lipid metabolic process (GO:0019216)|response to glucose (GO:0009749)|signal transduction (GO:0007165)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	19	all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155)	Breast(118;0.159)	all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147)			GGTCTCTCTGCGCATGGGCGA	0.721																																					p.R1240H	Melanoma(100;613 2409 40847)	Atlas-SNP	.											.	IRS2	44	.	0			c.G3719A						.						15	16	15					13																	110434682		2082	4127	6209	SO:0001583	missense	8660	exon1			TCTCTGCGCATGG	AB000732	CCDS9510.1	13q34	2013-01-10			ENSG00000185950	ENSG00000185950		"Pleckstrin homology (PH) domain containing"	6126	protein-coding gene	gene with protein product		600797				9312143	Standard	NM_003749		Approved		uc001vqv.3	Q9Y4H2	OTTHUMG00000017338	ENST00000375856.3:c.3719G>A	chr13.hg19:g.110434682C>T	ENSP00000365016:p.Arg1240His	137.0	0.0		136.0	55.0	NM_003749	Q96RR2|Q9BZG0|Q9Y6I5	Missense_Mutation	SNP	ENST00000375856.3	hg19	CCDS9510.1	.	.	.	.	.	.	.	.	.	.	C	13.74	2.326636	0.41197	.	.	ENSG00000185950	ENST00000375856	T	0.49432	0.78	3.85	3.0	0.34707	.	0.117336	0.64402	N	0.000014	T	0.40694	0.1127	L	0.44542	1.39	0.28707	N	0.903781	D	0.61697	0.99	P	0.45099	0.469	T	0.37174	-0.9717	10	0.54805	T	0.06	-20.5501	9.4461	0.38699	0.0:0.8998:0.0:0.1002	.	1240	Q9Y4H2	IRS2_HUMAN	H	1240	ENSP00000365016:R1240H	ENSP00000365016:R1240H	R	-	2	0	IRS2	109232683	1.000000	0.71417	0.968000	0.41197	0.678000	0.39670	3.797000	0.55514	0.819000	0.34492	0.462000	0.41574	CGC	.	.		0.721	IRS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045755.1	NM_003749		T	110434682	C	T	110434682	3	4	296	1	0	0	0	0	1	0	0	0	7850	768	27	1	305	1	IRS2	13	110434682	Missense_Mutation	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	10228126	110434682	4735196	146	43090										
MCF2L	23263	hgsc.bcm.edu	37	chr13	113750772	113750772	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gcggggacgtggtggagctgGtgcaggagggcgacgagggc	24	7	0	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr13:113750772G>A	ENST00000375608.3	+	29	3311	c.3253G>A	c.(3253-3255)Gtg>Atg	p.V1085M	MCF2L_ENST00000423482.2_Missense_Mutation_p.V1053M|MCF2L_ENST00000375604.2_Missense_Mutation_p.V1112M|MCF2L_ENST00000434480.2_Missense_Mutation_p.V1061M|MCF2L_ENST00000535094.2_Missense_Mutation_p.V1055M|MCF2L_ENST00000397030.1_Missense_Mutation_p.V1088M|MCF2L_ENST00000375601.3_Missense_Mutation_p.V1059M|MCF2L_ENST00000442652.2_Missense_Mutation_p.V1085M|MCF2L_ENST00000421756.1_Missense_Mutation_p.V1059M			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	1085	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular space (GO:0005615)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			kidney(1)|large_intestine(5)|ovary(1)|stomach(1)	8	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)				GGTGGAGCTGGTGCAGGAGGG	0.697																																					p.V1055M		Atlas-SNP	.											.	MCF2L	182	.	0			c.G3163A						.						23	35	31					13																	113750772		1553	3571	5124	SO:0001583	missense	23263	exon28			GAGCTGGTGCAGG	AB002360	CCDS9527.2, CCDS45070.1, CCDS9527.3, CCDS45070.2	13q34	2013-01-10			ENSG00000126217	ENSG00000126217		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	14576	protein-coding gene	gene with protein product		609499				9205841	Standard	NM_001112732		Approved	KIAA0362, DBS, OST, ARHGEF14	uc010tjr.2	O15068	OTTHUMG00000017377	ENST00000375608.3:c.3253G>A	chr13.hg19:g.113750772G>A	ENSP00000364758:p.Val1085Met	194.0	0.0		189.0	91.0	NM_001112732	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Missense_Mutation	SNP	ENST00000375608.3	hg19		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	14.08|14.08|14.08	2.428920|2.428920|2.428920	0.43122|0.43122|0.43122	.|.|.	.|.|.	ENSG00000126217|ENSG00000126217|ENSG00000126217	ENST00000397017;ENST00000453297|ENST00000375608;ENST00000442652;ENST00000375604;ENST00000397030;ENST00000535094;ENST00000421756;ENST00000375601;ENST00000434480;ENST00000423482;ENST00000440749|ENST00000261963;ENST00000420013	.|T;T;T;T;T;T;T;T;T|.	.|0.36520|.	.|3.06;3.06;3.06;1.25;3.06;1.25;3.06;3.06;3.06|.	5.14|5.14|5.14	-3.77|-3.77|-3.77	0.04346|0.04346|0.04346	.|Src homology-3 domain (3);Variant SH3 (1);|.	.|0.488214|.	.|0.20551|.	.|N|.	.|0.090106|.	T|T|.	0.50086|0.50086|.	0.1595|0.1595|.	M|M|M	0.69248|0.69248|0.69248	2.105|2.105|2.105	0.33741|0.33741|0.33741	D|D|D	0.619422|0.619422|0.619422	.|P;P;P;P|.	.|0.42620|.	.|0.534;0.534;0.745;0.785|.	.|P;P;P;P|.	.|0.52710|.	.|0.459;0.459;0.583;0.707|.	T|T|.	0.58713|0.58713|.	-0.7588|-0.7588|.	5|10|.	.|0.48119|.	.|T|.	.|0.1|.	.|.|.	3.9769|3.9769|3.9769	0.09478|0.09478|0.09478	0.2268:0.5102:0.1459:0.1171|0.2268:0.5102:0.1459:0.1171|0.2268:0.5102:0.1459:0.1171	.|.|.	.|1053;1055;1112;1085|.	.|E9PDN8;O15068-9;G5E9A1;O15068|.	.|.;.;.;MCF2L_HUMAN|.	D|M|X	740;265|1085;1085;1112;1088;1055;1059;1059;1061;1053;896|225;126	.|ENSP00000364758:V1085M;ENSP00000401422:V1085M;ENSP00000364754:V1112M;ENSP00000380225:V1088M;ENSP00000440374:V1055M;ENSP00000397285:V1059M;ENSP00000364751:V1059M;ENSP00000407722:V1061M;ENSP00000405639:V1053M|.	.|ENSP00000364751:V1059M|.	G|V|W	+|+|+	2|1|3	0|0|0	MCF2L|MCF2L|MCF2L	112798773|112798773|112798773	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.198000|0.198000|0.198000	0.23420|0.23420|0.23420	0.043000|0.043000|0.043000	0.13939|0.13939|0.13939	1.334000|1.334000|1.334000	0.33827|0.33827|0.33827	-0.395000|-0.395000|-0.395000	0.07715|0.07715|0.07715	-0.302000|-0.302000|-0.302000	0.09304|0.09304|0.09304	GGT|GTG|TGG	.	.		0.697	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4			A	113750772	G	A	113750772	3	1	296	1	0	0	0	0	1	0	0	0	9388	1261	44	3	3539	3	MCF2L	13	113750772	Missense_Mutation	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10	3316090	113750772	1419106	147	43091										
OR4Q3	441669	hgsc.bcm.edu	37	chr14	20216431	20216431	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ttacacagtgattacacctaTgttgaaccccctcatctaca	4	13	2	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr14:20216431T>C	ENST00000331723.1	+	1	845	c.845T>C	c.(844-846)aTg>aCg	p.M282T		NM_172194.1	NP_751944.1	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q, member 3	282						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(4)|endometrium(3)|kidney(2)|large_intestine(1)|lung(28)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	47	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		ATTACACCTATGTTGAACCCC	0.418																																					p.M282T		Atlas-SNP	.											.	OR4Q3	117	.	0			c.T845C						.						124	125	125					14																	20216431		2203	4300	6503	SO:0001583	missense	441669	exon1			CACCTATGTTGAA	AF179768	CCDS32020.1	14p13	2012-08-09				ENSG00000182652		"GPCR / Class A : Olfactory receptors"	15426	protein-coding gene	gene with protein product				OR4Q4			Standard	NM_172194		Approved	C14orf13	uc010tkt.2	Q8NH05		ENST00000331723.1:c.845T>C	chr14.hg19:g.20216431T>C	ENSP00000330049:p.Met282Thr	117.0	0.0		101.0	18.0	NM_172194	Q6IEX4	Missense_Mutation	SNP	ENST00000331723.1	hg19	CCDS32020.1	.	.	.	.	.	.	.	.	.	.	.	10.74	1.434411	0.25813	.	.	ENSG00000182652	ENST00000331723	T	0.37411	1.2	4.35	4.35	0.52113	GPCR, rhodopsin-like superfamily (1);	0.312743	0.22513	U	0.059065	T	0.33962	0.0881	L	0.28054	0.825	0.28647	N	0.906885	P	0.52842	0.956	P	0.49829	0.623	T	0.19484	-1.0304	10	0.87932	D	0	.	11.5383	0.50651	0.0:0.0:0.0:1.0	.	282	Q8NH05	OR4Q3_HUMAN	T	282	ENSP00000330049:M282T	ENSP00000330049:M282T	M	+	2	0	OR4Q3	19286271	0.111000	0.22076	1.000000	0.80357	0.959000	0.62525	2.433000	0.44793	1.827000	0.53221	0.411000	0.27672	ATG	.	.		0.418	OR4Q3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409818.2			C	20216431	T	C	20216431	3	2	296	1	0	0	0	0	1	0	0	0	11090	1464	51	2	847	2	OR4Q3	14	20216431	Missense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10		20216431	87133109	148	43092										
MGA	23269	hgsc.bcm.edu	37	chr15	41988768	41988768	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	aattccaatgagactgccttCtgcttaggcaaggaatcaga	9	9	2	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr15:41988768C>T	ENST00000570161.1	+	2	1560	c.1560C>T	c.(1558-1560)ttC>ttT	p.F520F	MGA_ENST00000568630.1_3'UTR|MGA_ENST00000545763.1_Silent_p.F520F|MGA_ENST00000219905.7_Silent_p.F520F|MGA_ENST00000566586.1_Silent_p.F520F|MGA_ENST00000389936.4_Silent_p.F520F			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	Maltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	AGACTGCCTTCTGCTTAGGCA	0.383																																					p.F520F		Atlas-SNP	.											.	MGA	264	.	0			c.C1560T						.						69	63	65					15																	41988768		1845	4098	5943	SO:0001819	synonymous_variant	23269	exon3			TGCCTTCTGCTTA	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.1560C>T	chr15.hg19:g.41988768C>T		135.0	0.0		166.0	62.0	NM_001080541	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000570161.1	hg19	CCDS55959.1																																																																																			.	.		0.383	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		T	41988768	C	T	41988768	2	4	296	1	0	0	0	0	0	0	0	1	9549	912	32	3		3	MGA	15	41988768	Silent	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10		41988768	60542624	149	43093										
LRRC57	255252	hgsc.bcm.edu	37	chr15	42839593	42839593	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ttggggaggtaatgctcccaGttggttcccagagaggctca	14	9	1	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr15:42839593G>C	ENST00000323443.2	-	3	725	c.358C>G	c.(358-360)Ctg>Gtg	p.L120V	LRRC57_ENST00000397130.3_Missense_Mutation_p.L120V|HAUS2_ENST00000568876.1_5'Flank|HAUS2_ENST00000568846.2_5'Flank|LRRC57_ENST00000563454.1_Missense_Mutation_p.L120V|HAUS2_ENST00000260372.3_5'Flank			Q8N9N7	LRC57_HUMAN	leucine rich repeat containing 57	120						extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|lung(5)|prostate(1)	8		all_cancers(109;1.99e-12)|all_epithelial(112;5.11e-11)|Lung NSC(122;4.53e-07)|all_lung(180;1.64e-06)|Melanoma(134;0.0262)		GBM - Glioblastoma multiforme(94;6.87e-07)		AATGCTCCCAGTTGGTTCCCA	0.512																																					p.L120V		Atlas-SNP	.											.	LRRC57	20	.	0			c.C358G						.						91	79	83					15																	42839593		2203	4299	6502	SO:0001583	missense	255252	exon4			CTCCCAGTTGGTT	AK094891	CCDS10089.1	15q15.1	2006-02-13			ENSG00000180979	ENSG00000180979			26719	protein-coding gene	gene with protein product							Standard	NM_153260		Approved	FLJ36812	uc001zqc.3	Q8N9N7	OTTHUMG00000130679	ENST00000323443.2:c.358C>G	chr15.hg19:g.42839593G>C	ENSP00000326817:p.Leu120Val	122.0	0.0		131.0	53.0	NM_153260	Q7Z2Z6|Q8N1T6	Missense_Mutation	SNP	ENST00000323443.2	hg19	CCDS10089.1	.	.	.	.	.	.	.	.	.	.	G	13.66	2.302679	0.40795	.	.	ENSG00000180979	ENST00000323443;ENST00000397130	T;T	0.64438	-0.1;-0.1	5.41	4.5	0.54988	.	0.121671	0.56097	D	0.000030	T	0.66733	0.2819	M	0.84082	2.675	0.46298	D	0.998978	B	0.31413	0.322	B	0.32980	0.156	T	0.70128	-0.4957	10	0.56958	D	0.05	.	14.2328	0.65906	0.0716:0.0:0.9284:0.0	.	120	Q8N9N7	LRC57_HUMAN	V	120	ENSP00000326817:L120V;ENSP00000380319:L120V	ENSP00000326817:L120V	L	-	1	2	LRRC57	40626885	1.000000	0.71417	0.945000	0.38365	0.949000	0.60115	3.210000	0.51129	1.433000	0.47394	0.655000	0.94253	CTG	.	.		0.512	LRRC57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253174.1	NM_153260		C	42839593	G	C	42839593	3	2	296	1	0	0	0	0	1	0	0	0	9022	1020	36	4	373	4	LRRC57	15	42839593	Missense_Mutation	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10	850825	42839593	59691799	150	43094										
PRTG	283659	hgsc.bcm.edu	37	chr15	55972370	55972370	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gatatcatgagattaccattTccaagtacccgagtattaaa	6	8	1	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr15:55972370T>G	ENST00000389286.4	-	6	902	c.855A>C	c.(853-855)ggA>ggC	p.G285G	RP11-420M1.2_ENST00000561155.1_RNA	NM_173814.4	NP_776175.2			protogenin											breast(1)|endometrium(6)|kidney(4)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)		GATTACCATTTCCAAGTACCC	0.378																																					p.G285G		Atlas-SNP	.											.	PRTG	110	.	0			c.A855C						.						70	66	68					15																	55972370		1880	4112	5992	SO:0001819	synonymous_variant	283659	exon6			ACCATTTCCAAGT	AK098622	CCDS42040.1	15q21.3	2013-02-11	2010-06-24		ENSG00000166450	ENSG00000166450		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	26373	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 5"	613261	"protogenin homolog (Gallus gallus)"				Standard	NM_173814		Approved	FLJ25756, IGDCC5	uc002adg.3	Q2VWP7		ENST00000389286.4:c.855A>C	chr15.hg19:g.55972370T>G		202.0	0.0		213.0	87.0	NM_173814		Silent	SNP	ENST00000389286.4	hg19	CCDS42040.1																																																																																			.	.		0.378	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814		G	55972370	T	G	55972370	2	3	296	1	0	0	0	0	0	0	0	1	12650	1770	62	5		5	PRTG	15	55972370	Silent	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	13132777	55972370	46559022	151	43095										
IGDCC4	57722	hgsc.bcm.edu	37	chr15	65693281	65693281	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gccccctggtggacgccaggGaccctggcgagaagacagac	15	14	0	3			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr15:65693281G>A	ENST00000352385.2	-	5	913	c.704C>T	c.(703-705)tCc>tTc	p.S235F		NM_020962.1	NP_066013.1	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member 4	235						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	44						GGACGCCAGGGACCCTGGCGA	0.592											OREG0023196	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S235F		Atlas-SNP	.											IGDCC4,NS,lymphoid_neoplasm,0,2	IGDCC4	95	.	0			c.C704T						.						91	81	84					15																	65693281		2201	4299	6500	SO:0001583	missense	57722	exon5			GCCAGGGACCCTG		CCDS10206.1	15q22.31	2013-02-11			ENSG00000103742	ENSG00000103742		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	13770	protein-coding gene	gene with protein product	"likely ortholog of mouse neighbor of Punc E11"						Standard	NM_020962		Approved	NOPE, LOC57722	uc002aou.1	Q8TDY8	OTTHUMG00000133136	ENST00000352385.2:c.704C>T	chr15.hg19:g.65693281G>A	ENSP00000319623:p.Ser235Phe	63.0	0.0	1086	88.0	9.0	NM_020962	Q9HCE4	Missense_Mutation	SNP	ENST00000352385.2	hg19	CCDS10206.1	.	.	.	.	.	.	.	.	.	.	G	19.94	3.919954	0.73098	.	.	ENSG00000103742	ENST00000352385	T	0.61392	0.11	5.15	5.15	0.70609	.	0.750986	0.12048	N	0.504402	T	0.69287	0.3094	L	0.60455	1.87	0.47374	D	0.999409	D	0.54397	0.966	P	0.53593	0.73	T	0.69837	-0.5037	10	0.56958	D	0.05	-24.9329	18.6484	0.91419	0.0:0.0:1.0:0.0	.	235	Q8TDY8	IGDC4_HUMAN	F	235	ENSP00000319623:S235F	ENSP00000319623:S235F	S	-	2	0	IGDCC4	63480334	1.000000	0.71417	1.000000	0.80357	0.402000	0.30811	4.742000	0.62103	2.409000	0.81822	0.561000	0.74099	TCC	.	.		0.592	IGDCC4-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256825.2	NM_020962		A	65693281	G	A	65693281	3	1	296	1	0	0	0	0	1	0	0	0	7578	1174	41	3	3112	3	IGDCC4	15	65693281	Missense_Mutation	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10	9720911	65693281	36838111	152	43096										
DNAJA4	55466	hgsc.bcm.edu	37	chr15	78556708	78556709	+	5'Flank	INS	-	-	AAAGG													0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ggggaatcagacgggcagccINSaaaggagcagacgcccgaga							TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr15:78556708_78556709insAAAGG	ENST00000394852.3	+	0	0				DNAJA4_ENST00000394855.3_Frame_Shift_Ins_p.-20fs|DNAJA4_ENST00000343789.3_5'Flank|RP11-762H8.3_ENST00000558971.1_RNA|DNAJA4_ENST00000489435.2_Frame_Shift_Ins_p.-20fs|DNAJA4_ENST00000446172.2_5'Flank|RP11-762H8.3_ENST00000559954.1_RNA	NM_001130182.1	NP_001123654.1	Q8WW22	DNJA4_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 4						negative regulation of inclusion body assembly (GO:0090084)|protein refolding (GO:0042026)|response to heat (GO:0009408)	cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|unfolded protein binding (GO:0051082)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	8						GACGGGCAGCCAAAGGAGCAGA	0.767																																					p.P18fs		Atlas-Indel,Pindel	.											.	DNAJA4	63	.	0			c.53_54insAAAGG						.																																			SO:0001631	upstream_gene_variant	55466	exon1			.	AF116663	CCDS10299.2, CCDS45316.1, CCDS45317.1	15q24.1	2011-09-02			ENSG00000140403	ENSG00000140403		"Heat shock proteins / DNAJ (HSP40)"	14885	protein-coding gene	gene with protein product						11147971	Standard	NM_018602		Approved	PRO1472	uc002bdi.3	Q8WW22	OTTHUMG00000143733		chr15.hg19:g.78556709_78556713dupAAAGG	Exception_encountered	26.0	0.0		20.0	10.0	NM_018602	E9PDM9|Q6AW87|Q8N5Z4|Q8N7P2	Frame_Shift_Ins	INS	ENST00000394852.3	hg19	CCDS45316.1																																																																																			.	.		0.767	DNAJA4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289801.1	NM_018602		AAAGG	78556709	-	AAAGG	78556708	6	5	296	0	1	1	1	0	0	0	0	0	4616	594	21	0		0	DNAJA4	15	78556708	5'Flank	INS	-	TCGA-G3-AAV0-01A-11D-A36X-10	12863427	78556708	23974684	153	43097										
AKAP13	11214	hgsc.bcm.edu	37	chr15	86124904	86124904	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ccccacagacatggagctctCagcccatgatgatggggccc	11	15	1	3			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr15:86124904C>G	ENST00000394518.2	+	7	3700	c.3605C>G	c.(3604-3606)tCa>tGa	p.S1202*	RP11-815J21.2_ENST00000561409.1_RNA|AKAP13_ENST00000361243.2_Nonsense_Mutation_p.S1202*	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	1202					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						ATGGAGCTCTCAGCCCATGAT	0.582																																					p.S1202X	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.C3605G						.						55	53	53					15																	86124904		2202	4299	6501	SO:0001587	stop_gained	11214	exon7			AGCTCTCAGCCCA	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"A-kinase anchor proteins", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	371	protein-coding gene	gene with protein product		604686	"lymphoid blast crisis oncogene"	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.3605C>G	chr15.hg19:g.86124904C>G	ENSP00000378026:p.Ser1202*	58.0	0.0		56.0	11.0	NM_007200	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Nonsense_Mutation	SNP	ENST00000394518.2	hg19	CCDS32319.1	.	.	.	.	.	.	.	.	.	.	C	41	9.005782	0.99033	.	.	ENSG00000170776	ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540	.	.	.	5.29	-1.9	0.07665	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	4.9398	0.13960	0.0:0.371:0.1569:0.4721	.	.	.	.	X	1202;1202;1201;1201	.	ENSP00000354718:S1202X	S	+	2	0	AKAP13	83925908	0.000000	0.05858	0.000000	0.03702	0.050000	0.14768	-0.327000	0.07955	-0.011000	0.14247	0.650000	0.86243	TCA	.	.		0.582	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200		G	86124904	C	G	86124904	4	3	296	1	0	0	0	0	0	1	0	0	449	838	29	4	3627	4	AKAP13	15	86124904	Nonsense_Mutation	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	7568196	86124904	16406488	154	43098										
AGBL1	123624	hgsc.bcm.edu	37	chr15	86814917	86814917	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	cccacctggataaggacaggCcatgaaatatgttattacaa	8	9	0	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr15:86814917C>T	ENST00000441037.2	+	14	2012	c.1917C>T	c.(1915-1917)ggC>ggT	p.G639G	AGBL1_ENST00000421325.2_Silent_p.G639G|AGBL1_ENST00000389298.3_Silent_p.G370G	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	639					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						TAAGGACAGGCCATGAAATAT	0.403																																					p.G639G		Atlas-SNP	.											.	AGBL1	151	.	0			c.C1917T						.						162	161	161					15																	86814917		1867	4096	5963	SO:0001819	synonymous_variant	123624	exon14			GACAGGCCATGAA	AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 4"	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.1917C>T	chr15.hg19:g.86814917C>T		97.0	0.0		105.0	35.0	NM_152336	A1A4X5|A6NJH6|C9JHL5	Silent	SNP	ENST00000441037.2	hg19	CCDS58398.1																																																																																			.	.		0.403	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336		T	86814917	C	T	86814917	2	4	296	1	0	0	0	0	0	0	0	1	375	726	26	3		3	AGBL1	15	86814917	Silent	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	690013	86814917	15716475	155	43099										
NTAN1	123803	hgsc.bcm.edu	37	chr16	15131989	15131990	+	Frame_Shift_Ins	INS	-	-	T													0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gtgtgagctggagatgggtgINStttttttaaaaacatcaagg							TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr16:15131989_15131990insT	ENST00000287706.3	-	10	923_924	c.831_832insA	c.(829-834)aaacacfs	p.H278fs	PDXDC1_ENST00000535621.2_Intron	NM_001270766.1|NM_173474.3	NP_001257695.1|NP_775745.1	Q96AB6	NTAN1_HUMAN	N-terminal asparagine amidase	278					adult locomotory behavior (GO:0008344)|memory (GO:0007613)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein-N-terminal asparagine amidohydrolase activity (GO:0008418)	p.K277fs*>34(2)		endometrium(1)|large_intestine(4)|lung(3)	8						GGAGATGGGTGTTTTTTTAAAA	0.411																																					p.H278fs		Atlas-Indel,Pindel	.											.,1	NTAN1	21	.	2	Deletion - Frameshift(2)	large_intestine(1)|lung(1)	c.832_833insA						.																																			SO:0001589	frameshift_variant	123803	exon10			.	AF092440	CCDS10558.1, CCDS73832.1	16p13	2008-02-05			ENSG00000157045	ENSG00000157045			29909	protein-coding gene	gene with protein product		615367				8910481	Standard	NM_173474		Approved		uc002ddd.4	Q96AB6	OTTHUMG00000129849	ENST00000287706.3:c.832dupA	chr16.hg19:g.15131996_15131996dupT	ENSP00000287706:p.His278fs	142.0	0.0		165.0	65.0	NM_173474	Q7Z4Z0	Frame_Shift_Ins	INS	ENST00000287706.3	hg19	CCDS10558.1																																																																																			.	.		0.411	NTAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252089.1	NM_173474		T	15131990	-	T	15131989	7	5	296	1	0	1	1	0	0	0	0	0	10704	1377	48	0	104	0	NTAN1	16	15131989	Frame_Shift_Ins	INS	-	TCGA-G3-AAV0-01A-11D-A36X-10		15131989	75222764	156	43100										
LONP2	83752	hgsc.bcm.edu	37	chr16	48385598	48385598	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tgagggaatcccaggcaacgTacgacaggatttaagttttg	12	7	0	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr16:48385598T>C	ENST00000285737.4	+	15	2537	c.2444T>C	c.(2443-2445)gTa>gCa	p.V815A	LONP2_ENST00000564259.1_3'UTR|LONP2_ENST00000535754.1_Missense_Mutation_p.V771A	NM_031490.2	NP_113678.2			lon peptidase 2, peroxisomal											breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						CCAGGCAACGTACGACAGGAT	0.468																																					p.V815A		Atlas-SNP	.											.	LONP2	63	.	0			c.T2444C						.						91	88	89					16																	48385598		2200	4300	6500	SO:0001583	missense	83752	exon15			GCAACGTACGACA	AJ548761	CCDS10734.1, CCDS73880.1	16q12.1	2010-04-21			ENSG00000102910	ENSG00000102910		"ATPases / AAA-type"	20598	protein-coding gene	gene with protein product						14561759	Standard	XM_005256191		Approved	MGC4840, LONP, LONPL	uc002efi.1	Q86WA8	OTTHUMG00000133144	ENST00000285737.4:c.2444T>C	chr16.hg19:g.48385598T>C	ENSP00000285737:p.Val815Ala	75.0	0.0		87.0	26.0	NM_031490		Missense_Mutation	SNP	ENST00000285737.4	hg19	CCDS10734.1	.	.	.	.	.	.	.	.	.	.	T	16.20	3.056363	0.55325	.	.	ENSG00000102910	ENST00000285737;ENST00000544734;ENST00000535754	T;T	0.35973	1.28;1.28	6.04	6.04	0.98038	Ribosomal protein S5 domain 2-type fold (1);Peptidase S16, Lon C-terminal (1);	0.163209	0.53938	D	0.000051	T	0.52008	0.1708	M	0.71871	2.18	0.80722	D	1	D;D	0.53151	0.958;0.958	P;P	0.51833	0.681;0.681	T	0.56432	-0.7980	10	0.87932	D	0	-18.691	16.6349	0.85050	0.0:0.0:0.0:1.0	.	771;815	B7ZKL7;Q86WA8	.;LONP2_HUMAN	A	815;544;771	ENSP00000285737:V815A;ENSP00000445426:V771A	ENSP00000285737:V815A	V	+	2	0	LONP2	46943099	1.000000	0.71417	0.045000	0.18777	0.397000	0.30659	8.008000	0.88588	2.330000	0.79161	0.477000	0.44152	GTA	.	.		0.468	LONP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256839.2	NM_031490		C	48385598	T	C	48385598	3	2	296	1	0	0	0	0	1	0	0	0	8902	1638	57	2	2502	2	LONP2	16	48385598	Missense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	33253609	48385598	41969155	157	43101										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11650915	11650915	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tggctgtgcggcactctgtaTttgtggtgggtggcgctggt	18	7	1	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr17:11650915T>C	ENST00000262442.4	+	32	6510	c.6442T>C	c.(6442-6444)Ttt>Ctt	p.F2148L	DNAH9_ENST00000454412.2_Missense_Mutation_p.F2148L	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2148	AAA 2. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		GCACTCTGTATTTGTGGTGGG	0.592																																					p.F2148L		Atlas-SNP	.											.	DNAH9	695	.	0			c.T6442C						.						69	65	66					17																	11650915		2203	4300	6503	SO:0001583	missense	1770	exon32			TCTGTATTTGTGG	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.6442T>C	chr17.hg19:g.11650915T>C	ENSP00000262442:p.Phe2148Leu	51.0	0.0		83.0	29.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	hg19	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	T	18.27	3.585991	0.66105	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.21361	2.01;2.01	4.5	4.5	0.54988	ATPase, AAA+ type, core (1);ATPase, dynein-related, AAA domain (1);	0.000000	0.85682	D	0.000000	T	0.49201	0.1543	M	0.83953	2.67	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.56860	-0.7909	10	0.72032	D	0.01	.	13.9979	0.64414	0.0:0.0:0.0:1.0	.	2148	Q9NYC9	DYH9_HUMAN	L	2148;2148;730	ENSP00000262442:F2148L;ENSP00000414874:F2148L	ENSP00000262442:F2148L	F	+	1	0	DNAH9	11591640	1.000000	0.71417	0.994000	0.49952	0.122000	0.20287	7.697000	0.84279	1.902000	0.55061	0.455000	0.32223	TTT	.	.		0.592	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		C	11650915	T	C	11650915	3	2	296	1	0	0	0	0	1	0	0	0	4610	1493	52	2	6568	2	DNAH9	17	11650915	Missense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10		11650915	69544295	158	43102										
CRLF3	51379	hgsc.bcm.edu	37	chr17	29123225	29123225	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	aggtttctctattagttcttCtatctgtactggtgggcgag	11	7	4	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr17:29123225C>T	ENST00000324238.6	-	4	680	c.556G>A	c.(556-558)Gaa>Aaa	p.E186K	CRLF3_ENST00000544695.1_Missense_Mutation_p.E70K|CRLF3_ENST00000577725.1_Intron	NM_015986.3	NP_057070.3	Q8IUI8	CRLF3_HUMAN	cytokine receptor-like factor 3	186	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of cell growth (GO:0030308)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	17		all_hematologic(16;0.014)|Acute lymphoblastic leukemia(14;0.0236)|Myeloproliferative disorder(56;0.0255)				ATTAGTTCTTCTATCTGTACT	0.393																																					p.E186K	Pancreas(30;346 881 29244 33464 41299)	Atlas-SNP	.											.	CRLF3	36	.	0			c.G556A						.						123	107	113					17																	29123225		2203	4300	6503	SO:0001583	missense	51379	exon4			GTTCTTCTATCTG	AF120151	CCDS32607.1	17q11.2	2008-05-02				ENSG00000176390			17177	protein-coding gene	gene with protein product		614853					Standard	NM_015986		Approved	CREME9, CYTOR4	uc002hfr.4	Q8IUI8		ENST00000324238.6:c.556G>A	chr17.hg19:g.29123225C>T	ENSP00000318804:p.Glu186Lys	105.0	0.0		121.0	10.0	NM_015986	A6NJF3|B2R8C3|Q2MLY7|Q9UNI3|Q9Y6M8	Missense_Mutation	SNP	ENST00000324238.6	hg19	CCDS32607.1	.	.	.	.	.	.	.	.	.	.	C	32	5.109650	0.94292	.	.	ENSG00000176390	ENST00000324238;ENST00000544695	T;T	0.27557	1.66;1.66	5.24	5.24	0.73138	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.045060	0.85682	D	0.000000	T	0.54791	0.1880	M	0.65498	2.005	0.80722	D	1	D	0.69078	0.997	D	0.68765	0.96	T	0.54925	-0.8220	10	0.51188	T	0.08	-24.7215	18.8146	0.92072	0.0:1.0:0.0:0.0	.	186	Q8IUI8	CRLF3_HUMAN	K	186;70	ENSP00000318804:E186K;ENSP00000444188:E70K	ENSP00000318804:E186K	E	-	1	0	CRLF3	26147351	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	7.059000	0.76684	2.457000	0.83068	0.313000	0.20887	GAA	.	.		0.393	CRLF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444354.1			T	29123225	C	T	29123225	3	4	296	1	0	0	0	0	1	0	0	0	3890	922	32	3	792	3	CRLF3	17	29123225	Missense_Mutation	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	17472310	29123225	52071985	159	43103										
AP2B1	163	hgsc.bcm.edu	37	chr17	33968894	33968894	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	atcacaaattatgtctgtttAggtgcagctcactctgctta	7	9	4	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr17:33968894A>T	ENST00000262325.7	+	12	1990		c.e12-1		AP2B1_ENST00000537622.2_Splice_Site|AP2B1_ENST00000545922.2_Splice_Site|AP2B1_ENST00000538556.1_Splice_Site|AP2B1_ENST00000589344.1_Splice_Site|AP2B1_ENST00000312678.8_Splice_Site|AP2B1_ENST00000592545.1_Splice_Site	NM_001282.2	NP_001273.1	P63010	AP2B1_HUMAN	adaptor-related protein complex 2, beta 1 subunit						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	clathrin binding (GO:0030276)|protein transporter activity (GO:0008565)			NS(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)		ATGTCTGTTTAGGTGCAGCTC	0.443																																					.		Atlas-SNP	.											.	AP2B1	70	.	0			c.1438-2A>T						.						69	64	66					17																	33968894		2203	4300	6503	SO:0001630	splice_region_variant	163	exon12			CTGTTTAGGTGCA	M34175	CCDS32621.1, CCDS32622.1	17q11.2-q12	2010-06-18			ENSG00000006125	ENSG00000006125			563	protein-coding gene	gene with protein product		601025		ADTB2, CLAPB1		8262066, 8595912	Standard	XM_005257937		Approved		uc002hjq.3	P63010		ENST00000262325.7:c.1438-1A>T	chr17.hg19:g.33968894A>T		60.0	0.0		62.0	22.0	NM_001282	A6NJP3|P21851|Q7Z451|Q96J19	Splice_Site	SNP	ENST00000262325.7	hg19	CCDS32622.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.517642	0.85495	.	.	ENSG00000006125	ENST00000262325;ENST00000312678;ENST00000538556;ENST00000537622;ENST00000545922	.	.	.	5.52	5.52	0.82312	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1167	0.72407	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	AP2B1	30993007	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	9.069000	0.93967	2.222000	0.72286	0.528000	0.53228	.	.	.		0.443	AP2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448969.1		Intron	T	33968894	A	T	33968894	5	4	296	1	0	0	0	0	0	0	1	0	741	434	15	4	1478	4	AP2B1	17	33968894	Splice_Site	SNP	A	TCGA-G3-AAV0-01A-11D-A36X-10	4845669	33968894	47226316	160	43104										
HDAC5	10014	hgsc.bcm.edu	37	chr17	42171077	42171078	+	Missense_Mutation	DNP	GC	GC	TT													0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gagctcctgctgcagttgctGctcccgcagtgtggggtcca							TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr17:42171077_42171078GC>TT	ENST00000393622.2	-	4	550_551	c.219_220GC>AA	c.(217-222)gaGCag>gaAAag	p.Q74K	HDAC5_ENST00000586802.1_Missense_Mutation_p.Q74K|HDAC5_ENST00000336057.5_Missense_Mutation_p.Q74K|HDAC5_ENST00000225983.6_Missense_Mutation_p.Q75K	NM_001015053.1|NM_005474.4	NP_001015053.1|NP_005465.2	Q9UQL6	HDAC5_HUMAN	histone deacetylase 5	74					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|chromatin silencing (GO:0006342)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|inflammatory response (GO:0006954)|multicellular organismal response to stress (GO:0033555)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|osteoblast development (GO:0002076)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression, epigenetic (GO:0040029)|regulation of myotube differentiation (GO:0010830)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|histone deacetylase complex (GO:0000118)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	21		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.118)		tgcagttgctgctcccgcAGTG	0.649																																					p.Q75K|p.E74E		Atlas-SNP	.											.	HDAC5	67	.	0			c.C223A|c.G222A						.																																			SO:0001583	missense	10014	exon4			GTTGCTGCTCCCG|TTGCTGCTCCCGC	AF249731	CCDS32663.1, CCDS45696.1	17q21	2008-07-18					3.5.1.98		14068	protein-coding gene	gene with protein product		605315				10220385, 9610721	Standard	XM_005256905		Approved	KIAA0600, NY-CO-9, FLJ90614	uc002iff.1	Q9UQL6		ENST00000393622.2:c.219_220delinsTT	chr17.hg19:g.42171077_42171078delinsTT	ENSP00000377244:p.Gln74Lys	80.0	0.0		121.0|119.0	53.0|52.0	NM_001015053	C9JFV9|O60340|O60528|Q96DY4	Missense_Mutation|Silent	SNP	ENST00000393622.2	hg19	CCDS45696.1																																																																																			.	.		0.649	HDAC5-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457686.1	NM_001015053		TT	42171078	GC	TT	42171077	3	4	296	1	0	0	0	0	1	0	0	0	7019	1328	46	3	3244	3	HDAC5	17	42171077	Missense_Mutation	DNP	GC	TCGA-G3-AAV0-01A-11D-A36X-10	8202183	42171077	39024133	161	43105										
ITGA2B	3674	hgsc.bcm.edu	37	chr17	42452979	42452979	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tacgagaactggatcctgaaGcctcgagggctgctcgggct	14	11	0	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr17:42452979G>T	ENST00000262407.5	-	26	2738	c.2707C>A	c.(2707-2709)Ctt>Att	p.L903I	ITGA2B_ENST00000353281.4_Missense_Mutation_p.L903I	NM_000419.3	NP_000410.2	P08514	ITA2B_HUMAN	integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41)	903					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of leukocyte migration (GO:0002687)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)	extracellular matrix binding (GO:0050840)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			biliary_tract(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.191)	Abciximab(DB00054)|Tirofiban(DB00775)	GGATCCTGAAGCCTCGAGGGC	0.687																																					p.L903I		Atlas-SNP	.											.	ITGA2B	88	.	0			c.C2707A						.						42	42	42					17																	42452979		2203	4300	6503	SO:0001583	missense	3674	exon26			CCTGAAGCCTCGA		CCDS32665.1	17q21.32	2014-09-17	2006-02-22			ENSG00000005961		"CD molecules", "Integrins"	6138	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 93"	607759	"integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41B)"	GP2B			Standard	NM_000419		Approved	CD41B, CD41, PPP1R93	uc002igt.1	P08514		ENST00000262407.5:c.2707C>A	chr17.hg19:g.42452979G>T	ENSP00000262407:p.Leu903Ile	99.0	0.0		100.0	40.0	NM_000419	B2RCY8|O95366|Q14443|Q17R67	Missense_Mutation	SNP	ENST00000262407.5	hg19	CCDS32665.1	.	.	.	.	.	.	.	.	.	.	G	13.50	2.257087	0.39896	.	.	ENSG00000005961	ENST00000262407;ENST00000353281	T;T	0.57436	0.4;0.4	3.66	1.54	0.23209	Integrin alpha-2 (1);	0.374925	0.16034	U	0.232720	T	0.54111	0.1838	M	0.61703	1.905	0.09310	N	1	P;P	0.47191	0.891;0.822	P;P	0.48952	0.596;0.471	T	0.43278	-0.9401	10	0.33141	T	0.24	.	9.7263	0.40333	0.0:0.4075:0.5925:0.0	.	501;903	Q59FA8;P08514	.;ITA2B_HUMAN	I	903	ENSP00000262407:L903I;ENSP00000340536:L903I	ENSP00000262407:L903I	L	-	1	0	ITGA2B	39808505	0.004000	0.15560	0.001000	0.08648	0.352000	0.29268	1.498000	0.35660	0.475000	0.27415	0.491000	0.48974	CTT	.	.		0.687	ITGA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439823.1			T	42452979	G	T	42452979	3	4	296	1	0	0	0	0	1	0	0	0	7885	971	34	3	432	3	ITGA2B	17	42452979	Missense_Mutation	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10	281902	42452979	38742231	162	43106										
OR4D2	124538	hgsc.bcm.edu	37	chr17	56247048	56247048	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gaacctcacgtgggtatcagActttgtcttcctggggctct	11	11	4	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr17:56247048A>T	ENST00000545221.1	+	1	32	c.32A>T	c.(31-33)gAc>gTc	p.D11V		NM_001004707.3	NP_001004707.1	P58180	OR4D2_HUMAN	olfactory receptor, family 4, subfamily D, member 2	11						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(1)|large_intestine(1)|lung(19)|ovary(1)|skin(2)|stomach(1)	26						TGGGTATCAGACTTTGTCTTC	0.463																																					p.D11V		Atlas-SNP	.											.	OR4D2	48	.	0			c.A32T						.						116	108	111					17																	56247048		2203	4300	6503	SO:0001583	missense	124538	exon1			TATCAGACTTTGT		CCDS32688.1	17q22	2013-09-23			ENSG00000255713	ENSG00000255713		"GPCR / Class A : Olfactory receptors"	8294	protein-coding gene	gene with protein product							Standard	NM_001004707		Approved		uc010wnp.2	P58180	OTTHUMG00000178801	ENST00000545221.1:c.32A>T	chr17.hg19:g.56247048A>T	ENSP00000441354:p.Asp11Val	141.0	0.0		111.0	45.0	NM_001004707	Q6IFN8|Q96R75	Missense_Mutation	SNP	ENST00000545221.1	hg19	CCDS32688.1	.	.	.	.	.	.	.	.	.	.	A	8.969	0.972496	0.18736	.	.	ENSG00000255713	ENST00000545221	T	0.02944	4.1	5.4	5.4	0.78164	.	0.511199	0.17605	N	0.168286	T	0.02848	0.0085	N	0.13140	0.3	0.45899	D	0.998745	B	0.18013	0.025	B	0.23275	0.045	T	0.54002	-0.8358	10	0.87932	D	0	-1.0221	13.6574	0.62346	1.0:0.0:0.0:0.0	.	11	P58180	OR4D2_HUMAN	V	11	ENSP00000441354:D11V	ENSP00000441354:D11V	D	+	2	0	OR4D2	53602047	1.000000	0.71417	0.996000	0.52242	0.068000	0.16541	6.389000	0.73199	2.178000	0.69098	0.496000	0.49642	GAC	.	.		0.463	OR4D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443366.1			T	56247048	A	T	56247048	3	4	296	1	0	0	0	0	1	0	0	0	11065	275	10	4	34	4	OR4D2	17	56247048	Missense_Mutation	SNP	A	TCGA-G3-AAV0-01A-11D-A36X-10	13794069	56247048	24948162	163	43107										
SECTM1	6398	hgsc.bcm.edu	37	chr17	80280192	80280192	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tctgctcaggccctgctgggCtcccgctctgagggctgcga	14	15	3	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr17:80280192C>T	ENST00000269389.3	-	5	942	c.592G>A	c.(592-594)Gcc>Acc	p.A198T	SECTM1_ENST00000580437.1_3'UTR	NM_003004.2	NP_002995.1	Q8WVN6	SCTM1_HUMAN	secreted and transmembrane 1	198					immune response (GO:0006955)|mesoderm development (GO:0007498)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cytokine activity (GO:0005125)|signal transducer activity (GO:0004871)			endometrium(1)|large_intestine(2)|lung(1)	4	Breast(20;0.000675)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.249)		OV - Ovarian serous cystadenocarcinoma(97;0.00928)|BRCA - Breast invasive adenocarcinoma(99;0.0833)			CCCTGCTGGGCTCCCGCTCTG	0.652																																					p.A198T		Atlas-SNP	.											.	SECTM1	14	.	0			c.G592A						.						60	65	63					17																	80280192		2203	4300	6503	SO:0001583	missense	6398	exon5			GCTGGGCTCCCGC	U77643	CCDS11808.1	17q25	2008-07-18				ENSG00000141574			10707	protein-coding gene	gene with protein product	"K12 protein", "type 1a transmembrane protein"	602602				9480746	Standard	NM_003004		Approved	K12	uc002keo.3	Q8WVN6		ENST00000269389.3:c.592G>A	chr17.hg19:g.80280192C>T	ENSP00000269389:p.Ala198Thr	90.0	0.0		80.0	34.0	NM_003004	B2R7H0|O00466	Missense_Mutation	SNP	ENST00000269389.3	hg19	CCDS11808.1	.	.	.	.	.	.	.	.	.	.	C	0.010	-1.747134	0.00669	.	.	ENSG00000141574	ENST00000269389	.	.	.	0.775	-0.253	0.12996	.	.	.	.	.	T	0.14527	0.0351	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.26780	-1.0093	8	0.20046	T	0.44	.	3.2483	0.06804	0.0:0.6765:0.0:0.3235	.	198;198	Q8WVN6;A8K3U3	SCTM1_HUMAN;.	T	198	.	ENSP00000269389:A198T	A	-	1	0	SECTM1	77873481	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.811000	0.01728	-0.085000	0.12573	-0.444000	0.05651	GCC	.	.		0.652	SECTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442856.1	NM_003004		T	80280192	C	T	80280192	3	4	296	1	0	0	0	0	1	0	0	0	14023	797	28	3	158	3	SECTM1	17	80280192	Missense_Mutation	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	24033144	80280192	915018	164	43108										
FN3KRP	79672	hgsc.bcm.edu	37	chr17	80684867	80684867	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tatgagctggcaatagctggCatgtttgggggctttagcag	15	6	0	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr17:80684867C>T	ENST00000269373.6	+	6	823	c.750C>T	c.(748-750)ggC>ggT	p.G250G	RP11-388C12.5_ENST00000570919.1_lincRNA|FN3KRP_ENST00000535965.1_Silent_p.G200G	NM_024619.3	NP_078895.2	Q9HA64	KT3K_HUMAN	fructosamine 3 kinase related protein	250							kinase activity (GO:0016301)			breast(1)|large_intestine(2)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	7	Breast(20;0.000523)|all_neural(118;0.0952)		BRCA - Breast invasive adenocarcinoma(99;0.0344)|OV - Ovarian serous cystadenocarcinoma(97;0.061)			CAATAGCTGGCATGTTTGGGG	0.537																																					p.G250G		Atlas-SNP	.											.	FN3KRP	31	.	0			c.C750T						.						61	65	64					17																	80684867		2203	4300	6503	SO:0001819	synonymous_variant	79672	exon6			AGCTGGCATGTTT	AY360465	CCDS11817.1	17q25.3	2014-08-12			ENSG00000141560	ENSG00000141560			25700	protein-coding gene	gene with protein product		611683				14633848	Standard	NM_024619		Approved	FLJ12171, FN3KL	uc002kfu.3	Q9HA64	OTTHUMG00000177846	ENST00000269373.6:c.750C>T	chr17.hg19:g.80684867C>T		101.0	0.0		109.0	41.0	NM_024619	Q969F4|Q9H0U7	Silent	SNP	ENST00000269373.6	hg19	CCDS11817.1																																																																																			.	.		0.537	FN3KRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439219.1	NM_024619		T	80684867	C	T	80684867	2	4	296	1	0	0	0	0	0	0	0	1	5972	697	25	3		3	FN3KRP	17	80684867	Silent	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	404675	80684867	510343	165	43109										
LAMA3	3909	hgsc.bcm.edu	37	chr18	21343451	21343451	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gcaagcttgaatacccagggCatctatgctggtggaggggt	15	8	1	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr18:21343451C>T	ENST00000313654.9	+	8	1387	c.1146C>T	c.(1144-1146)ggC>ggT	p.G382G	LAMA3_ENST00000399516.3_Silent_p.G382G	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	382	Domain V.|Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					ATACCCAGGGCATCTATGCTG	0.468																																					p.G382G		Atlas-SNP	.											.	LAMA3	397	.	0			c.C1146T						.						126	128	128					18																	21343451		2024	4183	6207	SO:0001819	synonymous_variant	3909	exon8			CCAGGGCATCTAT	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"Laminins"	6483	protein-coding gene	gene with protein product		600805	"laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.1146C>T	chr18.hg19:g.21343451C>T		106.0	0.0		105.0	40.0	NM_001127717	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Silent	SNP	ENST00000313654.9	hg19	CCDS42419.1																																																																																			.	.		0.468	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		T	21343451	C	T	21343451	2	4	296	1	0	0	0	0	0	0	0	1	8616	697	25	3		3	LAMA3	18	21343451	Silent	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10		21343451	56733797	166	43110										
TTC39C	125488	hgsc.bcm.edu	37	chr18	21649143	21649143	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tgatgtccgaaaatccgcccCctctatggttgatcggcttc	9	13	1	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr18:21649143C>T	ENST00000317571.3	+	4	604	c.368C>T	c.(367-369)cCc>cTc	p.P123L	TTC39C_ENST00000578150.1_Intron|TTC39C_ENST00000304621.6_Missense_Mutation_p.P62L	NM_001135993.1	NP_001129465.1	Q8N584	TT39C_HUMAN	tetratricopeptide repeat domain 39C	123										breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)	19						AAATCCGCCCCCTCTATGGTT	0.443																																					p.P123L		Atlas-SNP	.											.	TTC39C	83	.	0			c.C368T						.						105	93	97					18																	21649143		2203	4300	6503	SO:0001583	missense	125488	exon4			CCGCCCCCTCTAT	AK091080	CCDS32804.1, CCDS45839.1, CCDS58616.1	18q11.2	2014-02-07	2008-06-23	2008-06-23	ENSG00000168234	ENSG00000168234		"Tetratricopeptide (TTC) repeat domain containing"	26595	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 17"	C18orf17		14702039	Standard	NM_153211		Approved	FLJ33761, HsT2697	uc002kuw.3	Q8N584	OTTHUMG00000179403	ENST00000317571.3:c.368C>T	chr18.hg19:g.21649143C>T	ENSP00000323645:p.Pro123Leu	104.0	0.0		127.0	55.0	NM_001135993	B7WP63|J3QRR1|Q0VAJ2|Q8N284	Missense_Mutation	SNP	ENST00000317571.3	hg19	CCDS45839.1	.	.	.	.	.	.	.	.	.	.	C	8.770	0.925719	0.18056	.	.	ENSG00000168234	ENST00000304621;ENST00000317571	T;T	0.40756	1.02;1.02	5.54	4.68	0.58851	.	0.481843	0.24089	N	0.041644	T	0.21962	0.0529	N	0.12182	0.205	0.21147	N	0.99977	B	0.02656	0.0	B	0.01281	0.0	T	0.11616	-1.0580	10	0.27785	T	0.31	0.2152	6.344	0.21339	0.1488:0.6893:0.0:0.1619	.	123	Q8N584	TT39C_HUMAN	L	62;123	ENSP00000306598:P62L;ENSP00000323645:P123L	ENSP00000306598:P62L	P	+	2	0	TTC39C	19903141	0.003000	0.15002	0.995000	0.50966	0.774000	0.43823	0.509000	0.22707	1.359000	0.45940	0.655000	0.94253	CCC	.	.		0.443	TTC39C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446107.1	NM_153211		T	21649143	C	T	21649143	3	4	296	1	0	0	0	0	1	0	0	0	16724	623	22	3	382	3	TTC39C	18	21649143	Missense_Mutation	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	305692	21649143	56428105	167	43111										
TAF4B	6875	hgsc.bcm.edu	37	chr18	23937719	23937719	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ctcacagctcttgcagctatTggaccaaggaagaagagacc	10	11	2	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr18:23937719T>A	ENST00000269142.5	+	14	3380	c.2382T>A	c.(2380-2382)atT>atA	p.I794I	TAF4B_ENST00000578121.1_Silent_p.I799I	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	794					gene expression (GO:0010467)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|NF-kappaB binding (GO:0051059)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|prostate(1)|skin(1)	29	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			TTGCAGCTATTGGACCAAGGA	0.343																																					p.I794I		Atlas-SNP	.											.	TAF4B	71	.	0			c.T2382A						.						98	85	89					18																	23937719		1836	4088	5924	SO:0001819	synonymous_variant	6875	exon14			AGCTATTGGACCA	Y09321	CCDS42421.1	18q11.1	2008-08-01	2002-08-29	2001-12-07		ENSG00000141384			11538	protein-coding gene	gene with protein product	"TATA box binding protein (TBP)-associated factor 4B"	601689	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, C2, 105kD"	TAF2C2		8858156, 10849440	Standard	XM_005258339		Approved	TAFII105	uc002kvu.4	Q92750		ENST00000269142.5:c.2382T>A	chr18.hg19:g.23937719T>A		419.0	1.0		560.0	219.0	NM_005640	Q29YA4|Q29YA5	Silent	SNP	ENST00000269142.5	hg19	CCDS42421.1																																																																																			.	.		0.343	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000446260.3	NM_005640		A	23937719	T	A	23937719	2	1	296	1	0	0	0	0	0	0	0	1	15542	1800	63	4		4	TAF4B	18	23937719	Silent	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	2288576	23937719	54139529	168	43112										
SAFB	6294	hgsc.bcm.edu	37	chr19	5645350	5645350	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tctccatttattttacagatAgaggacaaagaaactataaa	5	6	1	3			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr19:5645350A>G	ENST00000292123.5	+	5	656	c.549A>G	c.(547-549)atA>atG	p.I183M	SAFB_ENST00000586934.1_3'UTR|SAFB_ENST00000454510.1_Missense_Mutation_p.I114M|SAFB_ENST00000433404.1_Missense_Mutation_p.I13M|SAFB_ENST00000592224.1_Missense_Mutation_p.I183M|SAFB_ENST00000588852.1_Missense_Mutation_p.I183M|SAFB_ENST00000538656.1_Missense_Mutation_p.I26M	NM_001201338.1|NM_001201339.1|NM_002967.3	NP_001188267.1|NP_001188268.1|NP_002958.2	Q15424	SAFB1_HUMAN	scaffold attachment factor B	183					chromatin organization (GO:0006325)|growth (GO:0040007)|hormone metabolic process (GO:0042445)|intracellular estrogen receptor signaling pathway (GO:0030520)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|liver(1)|lung(6)|ovary(2)|skin(1)	23				UCEC - Uterine corpus endometrioid carcinoma (162;0.000222)		TTTTACAGATAGAGGACAAAG	0.299																																					p.I183M	Colon(88;338 1345 6184 8214 20897)	Atlas-SNP	.											.	SAFB	74	.	0			c.A549G						.						94	87	89					19																	5645350		2198	4297	6495	SO:0001583	missense	6294	exon5			ACAGATAGAGGAC	L43631	CCDS12142.1, CCDS56077.1, CCDS59339.1, CCDS59340.1	19p13.3-p13.2	2013-02-12				ENSG00000160633		"RNA binding motif (RRM) containing"	10520	protein-coding gene	gene with protein product	"Hsp27 ERE-TATA binding protein"	602895				9605873, 8600450	Standard	NM_002967		Approved	HET, SAFB1	uc002mcg.3	Q15424		ENST00000292123.5:c.549A>G	chr19.hg19:g.5645350A>G	ENSP00000292123:p.Ile183Met	76.0	0.0		137.0	36.0	NM_002967	A0AV56|B7Z5B6|B7ZLP6|F5H0H3|O60406|Q59HH8	Missense_Mutation	SNP	ENST00000292123.5	hg19	CCDS12142.1	.	.	.	.	.	.	.	.	.	.	A	11.37	1.618922	0.28801	.	.	ENSG00000160633	ENST00000454510;ENST00000433404;ENST00000292123;ENST00000538656	T;T;T;T	0.11063	2.9;3.06;2.93;2.81	5.31	-5.78	0.02362	.	1.274100	0.05472	N	0.553294	T	0.03390	0.0098	N	0.03115	-0.41	0.09310	N	0.999991	B;P;B;B;B;B;B	0.45176	0.113;0.852;0.08;0.0;0.08;0.08;0.08	B;B;B;B;B;B;B	0.29663	0.04;0.105;0.029;0.0;0.029;0.029;0.029	T	0.42832	-0.9428	10	0.38643	T	0.18	-3.8438	10.8267	0.46635	0.3023:0.0:0.5854:0.1123	.	26;114;183;183;183;183;183	B7Z2F6;F5H0H3;B7ZLP5;B7Z2H3;A0AV56;Q15424;B7ZLP6	.;.;.;.;.;SAFB1_HUMAN;.	M	114;13;183;26	ENSP00000415895:I114M;ENSP00000404545:I13M;ENSP00000292123:I183M;ENSP00000438880:I26M	ENSP00000292123:I183M	I	+	3	3	SAFB	5596350	0.000000	0.05858	0.183000	0.23137	0.856000	0.48823	-1.525000	0.02231	-1.165000	0.02786	-0.400000	0.06385	ATA	.	.		0.299	SAFB-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000451641.2			G	5645350	A	G	5645350	3	3	296	1	0	0	0	0	1	0	0	0	13821	410	15	2	567	2	SAFB	19	5645350	Missense_Mutation	SNP	A	TCGA-G3-AAV0-01A-11D-A36X-10		5645350	53483633	169	43113										
FBN3	84467	hgsc.bcm.edu	37	chr19	8191482	8191482	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ttcagccagcaggtgcccttGgtgctgtctggggagaagag	16	9	2	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr19:8191482G>A	ENST00000600128.1	-	20	2838	c.2424C>T	c.(2422-2424)acC>acT	p.T808T	FBN3_ENST00000601739.1_Silent_p.T808T|FBN3_ENST00000270509.2_Silent_p.T808T			Q75N90	FBN3_HUMAN	fibrillin 3	808						proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						AGGTGCCCTTGGTGCTGTCTG	0.667																																					p.T808T		Atlas-SNP	.											.	FBN3	300	.	0			c.C2424T						.						37	34	35					19																	8191482		2203	4300	6503	SO:0001819	synonymous_variant	84467	exon19			GCCCTTGGTGCTG		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.2424C>T	chr19.hg19:g.8191482G>A		44.0	0.0		72.0	13.0	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	hg19	CCDS12196.1																																																																																			.	.		0.667	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447		A	8191482	G	A	8191482	2	1	296	1	0	0	0	0	0	0	0	1	5712	1335	47	3		3	FBN3	19	8191482	Silent	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10	2546132	8191482	50937501	170	43114										
TMED1	11018	hgsc.bcm.edu	37	chr19	10943778	10943791	+	Frame_Shift_Del	DEL	CCCGCTCCAAGTTG	CCCGCTCCAAGTTG	-													0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gacagctgaccagaagttgaCccgctccaagttgccctctt					rs139968960		TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	CCCGCTCCAAGTTG	CCCGCTCCAAGTTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr19:10943778_10943791delCCCGCTCCAAGTTG	ENST00000214869.2	-	4	662_675	c.564_577delCAACTTGGAGCGGG	c.(562-579)ggcaacttggagcgggtcfs	p.NLERV189fs	TMED1_ENST00000591695.1_Frame_Shift_Del_p.ATWSG127fs|TMED1_ENST00000588289.1_Frame_Shift_Del_p.NLERV44fs	NM_006858.2	NP_006849.1	Q13445	TMED1_HUMAN	transmembrane emp24 protein transport domain containing 1	189					cell-cell signaling (GO:0007267)|protein transport (GO:0015031)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(1)|central_nervous_system(2)|lung(2)|ovary(3)|prostate(1)|skin(1)	10						CAGAAGTTGACCCGCTCCAAGTTGCCCTCTTGCA	0.636																																					p.189_193del		Atlas-Indel,Pindel	.											.	TMED1	22	.	0			c.565_578del						.																																			SO:0001589	frameshift_variant	11018	exon4			.	U41804	CCDS12249.1	19p13.2	2008-02-05	2005-08-26			ENSG00000099203			17291	protein-coding gene	gene with protein product		605395	"transmembrane emp24 domain containing 1"			11466339, 8621446	Standard	NM_006858		Approved	ST2L, MGC1270, IL1RL1LG, Il1rl1l	uc002mpy.3	Q13445		ENST00000214869.2:c.564_577delCAACTTGGAGCGGG	chr19.hg19:g.10943778_10943791delCCCGCTCCAAGTTG	ENSP00000214869:p.Asn189fs	106.0	0.0		119.0	33.0	NM_006858		Frame_Shift_Del	DEL	ENST00000214869.2	hg19	CCDS12249.1																																																																																			.	.		0.636	TMED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452614.1	NM_006858		-	10943791	CCCGCTCCAAGTTG	-	10943778	7	5	296	1	0	1	0	1	0	0	0	0	16017	507	18	0	110	0	TMED1	19	10943778	Frame_Shift_Del	DEL	CCCGCTCCAAGTTG	TCGA-G3-AAV0-01A-11D-A36X-10	2752296	10943778	48185205	171	43115										
DOCK6	57572	hgsc.bcm.edu	37	chr19	11339658	11339658	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gcgtgctggaggatggcctcGcgtacggcactgctgctgac	16	12	0	1	rs201482446	byFrequency	TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr19:11339658G>A	ENST00000294618.7	-	23	2783	c.2772C>T	c.(2770-2772)cgC>cgT	p.R924R	DOCK6_ENST00000319867.7_Silent_p.R263R	NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	924					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(8)|liver(2)|lung(9)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	39						GGATGGCCTCGCGTACGGCAC	0.647																																					p.R924R		Atlas-SNP	.											.	DOCK6	104	.	0			c.C2772T						.						38	43	41					19																	11339658		2150	4248	6398	SO:0001819	synonymous_variant	57572	exon23			GGCCTCGCGTACG		CCDS45975.1	19p13.2	2011-08-04			ENSG00000130158	ENSG00000130158			19189	protein-coding gene	gene with protein product		614194				12432077	Standard	NM_020812		Approved	KIAA1395, ZIR1	uc002mqs.5	Q96HP0		ENST00000294618.7:c.2772C>T	chr19.hg19:g.11339658G>A		129.0	0.0		163.0	47.0	NM_020812	A6H8X5|Q7Z7P4|Q9P2F2	Silent	SNP	ENST00000294618.7	hg19	CCDS45975.1																																																																																			.	G|0.998;C|0.002		0.647	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812		A	11339658	G	A	11339658	2	1	296	1	0	0	0	0	0	0	0	1	4693	1074	38	1		1	DOCK6	19	11339658	Silent	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10	395880	11339658	47789325	172	43116										
ZNF20	7568	hgsc.bcm.edu	37	chr19	12244794	12244794	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ctttcacagagtttctctctCataagacttcagtgaaaaat	5	9	4	3			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr19:12244794C>T	ENST00000334213.5	-	4	431	c.207G>A	c.(205-207)atG>atA	p.M69I	ZNF20_ENST00000485451.1_5'UTR|ZNF625-ZNF20_ENST00000430024.1_3'UTR|ZNF20_ENST00000600335.1_Intron	NM_001203250.1|NM_021143.3	NP_001190179.1|NP_066966.2	P17024	ZNF20_HUMAN	zinc finger protein 20	69	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|lung(6)	8						GTTTCTCTCTCATAAGACTTC	0.413																																					p.M69I		Atlas-SNP	.											.	ZNF20	86	.	0			c.G207A						.						66	60	62					19																	12244794		1879	4107	5986	SO:0001583	missense	7568	exon4			CTCTCTCATAAGA	X52344	CCDS45986.1	19p13.2	2013-01-08	2006-05-10		ENSG00000132010	ENSG00000132010		"Zinc fingers, C2H2-type", "-"	12992	protein-coding gene	gene with protein product		194557	"zinc finger protein 20 (KOX 13)"				Standard	NM_021143		Approved	KOX13	uc002mtf.2	P17024	OTTHUMG00000156409	ENST00000334213.5:c.207G>A	chr19.hg19:g.12244794C>T	ENSP00000335437:p.Met69Ile	27.0	0.0		71.0	22.0	NM_021143	Q8N457|Q9UG41	Missense_Mutation	SNP	ENST00000334213.5	hg19	CCDS45986.1	.	.	.	.	.	.	.	.	.	.	C	0.731	-0.779892	0.02929	.	.	ENSG00000132010	ENST00000334213;ENST00000292241;ENST00000418866	T;T	0.05447	3.44;6.81	0.94	-1.88	0.07713	Krueppel-associated box (1);	.	.	.	.	T	0.03178	0.0093	N	0.16478	0.41	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.43212	-0.9405	9	0.31617	T	0.26	.	2.0414	0.03551	0.257:0.3425:0.0:0.4005	.	69	P17024	ZNF20_HUMAN	I	69;69;66	ENSP00000335437:M69I;ENSP00000390115:M66I	ENSP00000292241:M69I	M	-	3	0	ZNF20	12105794	0.000000	0.05858	0.000000	0.03702	0.138000	0.21146	-1.142000	0.03203	-1.394000	0.02077	-0.823000	0.03104	ATG	.	.		0.413	ZNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344101.1	NM_021143		T	12244794	C	T	12244794	3	4	296	1	0	0	0	0	1	0	0	0	17776	826	29	3	1395	3	ZNF20	19	12244794	Missense_Mutation	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	905136	12244794	46884189	173	43117										
FAM125A	93343	hgsc.bcm.edu	37	chr19	17534830	17534830	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ttcagccatggatggggttcCcttcacactccacccacgat	8	15	2	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr19:17534830C>T	ENST00000317040.7	+	7	1711	c.656C>T	c.(655-657)cCc>cTc	p.P219L	MVB12A_ENST00000528515.1_Missense_Mutation_p.P177S|MVB12A_ENST00000392702.2_Missense_Mutation_p.P179L|MVB12A_ENST00000529939.1_Missense_Mutation_p.P219L|MVB12A_ENST00000543795.1_Missense_Mutation_p.P219L|CTD-2521M24.6_ENST00000593957.1_RNA			Q96EY5	MB12A_HUMAN	multivesicular body subunit 12A	219	Interaction with TSG101, VPS37B and VPS28.|UMA. {ECO:0000255|PROSITE- ProRule:PRU00830}.				protein transport (GO:0015031)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|vesicle (GO:0031982)	lipid binding (GO:0008289)|ubiquitin binding (GO:0043130)										GATGGGGTTCCCTTCACACTC	0.637																																					p.P219L		Atlas-SNP	.											.	.	.	.	0			c.C656T						.						91	76	81					19																	17534830		2203	4300	6503	SO:0001583	missense	93343	exon7			GGGTTCCCTTCAC	BC011840	CCDS12359.1	19p13.11	2013-10-11	2012-12-03	2012-12-03	ENSG00000141971	ENSG00000141971			25153	protein-coding gene	gene with protein product			"family with sequence similarity 125, member A"	FAM125A		18005716, 20654576, 22232651	Standard	NM_138401		Approved	FLJ32495	uc002ngo.1	Q96EY5	OTTHUMG00000166252	ENST00000317040.7:c.656C>T	chr19.hg19:g.17534830C>T	ENSP00000324810:p.Pro219Leu	25.0	0.0		42.0	14.0	NM_138401	Q96I18	Missense_Mutation	SNP	ENST00000317040.7	hg19	CCDS12359.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	21.2|21.2	4.117011|4.117011	0.77323|0.77323	.|.	.|.	ENSG00000141971|ENSG00000141971	ENST00000528604;ENST00000317040;ENST00000392702;ENST00000529939;ENST00000543795|ENST00000528515	T;T;T;T;T|.	0.63744|.	-0.06;-0.06;-0.06;-0.06;-0.06|.	4.97|4.97	4.97|4.97	0.65823|0.65823	UMA domain (1);|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.73329|0.73329	0.3573|0.3573	M|M	0.71581|0.71581	2.175|2.175	0.58432|0.58432	D|D	0.999994|0.999994	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	T|T	0.76506|0.76506	-0.2934|-0.2934	10|7	0.87932|0.66056	D|D	0|0.02	7.0E-4|7.0E-4	13.7604|13.7604	0.62961|0.62961	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	219|.	Q96EY5|.	F125A_HUMAN|.	L|S	80;219;179;219;219|177	ENSP00000435052:P80L;ENSP00000324810:P219L;ENSP00000376466:P179L;ENSP00000432526:P219L;ENSP00000444653:P219L|.	ENSP00000324810:P219L|ENSP00000433677:P177S	P|P	+|+	2|1	0|0	FAM125A|FAM125A	17395830|17395830	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.922000|0.922000	0.55478|0.55478	5.053000|5.053000	0.64269|0.64269	2.315000|2.315000	0.78130|0.78130	0.558000|0.558000	0.71614|0.71614	CCC|CCT	.	.		0.637	MVB12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388723.2	NM_138401		T	17534830	C	T	17534830	3	4	296	1	0	0	0	0	1	0	0	0	5432	623	22	3	682	3	FAM125A	19	17534830	Missense_Mutation	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	5290036	17534830	41594153	174	43118										
LPAR2	9170	hgsc.bcm.edu	37	chr19	19737371	19737371	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	cccaggatgatgacaacagtCttgaccaggctgagcgtggt	13	10	1	4			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr19:19737371C>T	ENST00000542587.1	-	5	1625	c.723G>A	c.(721-723)aaG>aaA	p.K241K	LPAR2_ENST00000586703.1_Silent_p.K241K|LPAR2_ENST00000407877.3_Silent_p.K241K|LPAR2_ENST00000589311.1_5'Flank			Q9HBW0	LPAR2_HUMAN	lysophosphatidic acid receptor 2	241					activation of MAPK activity (GO:0000187)|activation of phospholipase C activity (GO:0007202)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of Rho protein signal transduction (GO:0035025)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)|lysophosphatidic acid receptor activity (GO:0070915)			breast(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|urinary_tract(1)	10						TGACAACAGTCTTGACCAGGC	0.597																																					p.K241K		Atlas-SNP	.											.	LPAR2	28	.	0			c.G723A						.						83	94	90					19																	19737371		2194	4292	6486	SO:0001819	synonymous_variant	9170	exon2			AACAGTCTTGACC	AF011466	CCDS12407.1	19p12	2012-08-08	2008-04-11	2008-04-11		ENSG00000064547		"GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"	3168	protein-coding gene	gene with protein product		605110	"endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 4"	EDG4		9525886, 9804623	Standard	NM_004720		Approved	EDG-4, LPA2	uc002nnb.4	Q9HBW0		ENST00000542587.1:c.723G>A	chr19.hg19:g.19737371C>T		152.0	0.0		221.0	57.0	NM_004720	O00543|O43431	Silent	SNP	ENST00000542587.1	hg19	CCDS12407.1																																																																																			.	.		0.597	LPAR2-003	KNOWN	alternative_5_UTR|non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460544.1	NM_004720		T	19737371	C	T	19737371	2	4	296	1	0	0	0	0	0	0	0	1	8914	912	32	3		3	LPAR2	19	19737371	Silent	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	2202541	19737371	39391612	175	43119										
ZNF14	7561	hgsc.bcm.edu	37	chr19	19823467	19823467	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gtttttgaaaagactggtaaTatataaaggtttttccacat	7	4	0	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr19:19823467T>C	ENST00000344099.3	-	4	761	c.623A>G	c.(622-624)tAt>tGt	p.Y208C		NM_021030.2	NP_066358.2	P17017	ZNF14_HUMAN	zinc finger protein 14	208					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(2)|endometrium(1)|large_intestine(9)|lung(8)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	32		Renal(1328;0.0474)				AGACTGGTAATATATAAAGGT	0.358																																					p.Y208C		Atlas-SNP	.											.	ZNF14	89	.	0			c.A623G						.						63	64	64					19																	19823467		2203	4300	6503	SO:0001583	missense	7561	exon4			TGGTAATATATAA	AA286756	CCDS12409.1	19p13.11	2013-01-08	2006-05-10					"Zinc fingers, C2H2-type", "-"	12924	protein-coding gene	gene with protein product		194556	"zinc finger protein 14 (KOX 6)"				Standard	NM_021030		Approved	KOX6, GIOT-4	uc002nnk.1	P17017		ENST00000344099.3:c.623A>G	chr19.hg19:g.19823467T>C	ENSP00000340514:p.Tyr208Cys	114.0	0.0		179.0	45.0	NM_021030	B9EGA4|Q9ULZ5	Missense_Mutation	SNP	ENST00000344099.3	hg19	CCDS12409.1	.	.	.	.	.	.	.	.	.	.	T	9.599	1.128182	0.20959	.	.	ENSG00000105708	ENST00000344099	T	0.08546	3.08	1.86	-0.936	0.10419	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04588	0.0125	N	0.17838	0.53	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.41179	-0.9523	9	0.37606	T	0.19	.	3.164	0.06529	0.0:0.1663:0.2438:0.5899	.	208	P17017	ZNF14_HUMAN	C	208	ENSP00000340514:Y208C	ENSP00000340514:Y208C	Y	-	2	0	ZNF14	19684467	0.000000	0.05858	0.000000	0.03702	0.859000	0.49053	0.146000	0.16180	-0.498000	0.06632	0.383000	0.25322	TAT	.	.		0.358	ZNF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460775.1	NM_021030		C	19823467	T	C	19823467	3	2	296	1	0	0	0	0	1	0	0	0	17743	1406	49	2	1309	2	ZNF14	19	19823467	Missense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	86096	19823467	39305516	176	43120										
RYR1	6261	hgsc.bcm.edu	37	chr19	39068789	39068789	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	cccccgcccccacaggctcaTgtccatcgatgtcaagtacc	7	19	2	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr19:39068789T>A	ENST00000359596.3	+	99	14309	c.14309T>A	c.(14308-14310)aTg>aAg	p.M4770K	RYR1_ENST00000360985.3_Missense_Mutation_p.M4765K|RYR1_ENST00000355481.4_Missense_Mutation_p.M4765K			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	4770					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CACAGGCTCATGTCCATCGAT	0.627																																					p.M4770K		Atlas-SNP	.											.	RYR1	708	.	0			c.T14309A						.						52	48	49					19																	39068789		2203	4300	6503	SO:0001583	missense	6261	exon99			GGCTCATGTCCAT	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.14309T>A	chr19.hg19:g.39068789T>A	ENSP00000352608:p.Met4770Lys	81.0	0.0		111.0	34.0	NM_000540	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	T	11.45	1.641536	0.29157	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.96427	-4.01;-4.01;-4.01	4.93	4.93	0.64822	.	0.152050	0.41001	U	0.000979	D	0.91123	0.7205	L	0.36672	1.1	0.34127	D	0.664818	B;B	0.26775	0.131;0.159	B;B	0.27262	0.046;0.078	D	0.87234	0.2262	10	0.19590	T	0.45	.	3.9929	0.09545	0.0:0.167:0.1869:0.6461	.	4765;4770	P21817-2;P21817	.;RYR1_HUMAN	K	4770;4765;4765	ENSP00000352608:M4770K;ENSP00000347667:M4765K;ENSP00000354254:M4765K	ENSP00000347667:M4765K	M	+	2	0	RYR1	43760629	0.947000	0.32204	1.000000	0.80357	0.985000	0.73830	0.534000	0.23098	2.077000	0.62373	0.454000	0.30748	ATG	.	.		0.627	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			A	39068789	T	A	39068789	3	1	296	1	0	0	0	0	1	0	0	0	13783	1464	51	4	14703	4	RYR1	19	39068789	Missense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	19245322	39068789	20060194	177	43121										
TIMM50	92609	hgsc.bcm.edu	37	chr19	39971479	39971479	+	5'UTR	DEL	T	T	-													0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	agcgagtgggcggggccgcgTggcgtcagcgcaagatggcg							TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr19:39971479delT	ENST00000607714.1	+	0	8				TIMM50_ENST00000314349.4_Frame_Shift_Del_p.W99fs|TIMM50_ENST00000544017.1_5'Flank|TIMM50_ENST00000599794.1_5'Flank			Q3ZCQ8	TIM50_HUMAN	translocase of inner mitochondrial membrane 50 homolog (S. cerevisiae)						cellular protein metabolic process (GO:0044267)|mitochondrial membrane organization (GO:0007006)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein targeting to mitochondrion (GO:0006626)|release of cytochrome c from mitochondria (GO:0001836)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial inner membrane presequence translocase complex (GO:0005744)|mitochondrion (GO:0005739)|nuclear speck (GO:0016607)	interleukin-2 receptor binding (GO:0005134)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|ribonucleoprotein complex binding (GO:0043021)|RNA binding (GO:0003723)			NS(1)|endometrium(3)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)	14	all_cancers(60;4.04e-06)|all_lung(34;1.77e-07)|Lung NSC(34;2.09e-07)|all_epithelial(25;1.13e-05)|Ovarian(47;0.159)		Epithelial(26;5.89e-26)|all cancers(26;1.96e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			CGGGGCCGCGTGGCGTCAGCG	0.736																																					p.A98fs		Atlas-Indel,Pindel	.											.	TIMM50	37	.	0			c.294delG						.						9	11	10					19																	39971479		2156	4181	6337	SO:0001623	5_prime_UTR_variant	92609	exon1			.	BC009072	CCDS33023.1	19q13.2	2010-06-21	2006-04-04		ENSG00000105197	ENSG00000105197		"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	23656	protein-coding gene	gene with protein product		607381	"translocase of inner mitochondrial membrane 50 homolog (yeast)"			12437925	Standard	NM_001001563		Approved	TIM50L	uc002olu.1	Q3ZCQ8		ENST00000607714.1:c.-15T>-	chr19.hg19:g.39971479delT		49.0	0.0		85.0	21.0	NM_001001563	Q330K1|Q6QA00|Q96FJ5|Q96GY2|Q9H370	Frame_Shift_Del	DEL	ENST00000607714.1	hg19																																																																																				.	.		0.736	TIMM50-021	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470728.1	NM_001001563		-	39971479	T	-	39971479	6	5	296	0	1	1	0	1	0	0	0	0	15928	1696	59	0		0	TIMM50	19	39971479	5'UTR	DEL	T	TCGA-G3-AAV0-01A-11D-A36X-10	902690	39971479	19157504	178	43122										
FCGBP	8857	hgsc.bcm.edu	37	chr19	40366455	40366455	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	cgcaggcgcacgaagctgtcCccatcgaaagccagcgagag	13	14	0	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr19:40366455C>T	ENST00000221347.6	-	30	13786	c.13779G>A	c.(13777-13779)ggG>ggA	p.G4593G		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4593	VWFD 11. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			CGAAGCTGTCCCCATCGAAAG	0.662																																					p.G4593G		Atlas-SNP	.											.	FCGBP	416	.	0			c.G13779A						.						34	40	38					19																	40366455		2199	4298	6497	SO:0001819	synonymous_variant	8857	exon30			GCTGTCCCCATCG	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.13779G>A	chr19.hg19:g.40366455C>T		147.0	0.0		260.0	56.0	NM_003890	O95784	Silent	SNP	ENST00000221347.6	hg19	CCDS12546.1																																																																																			.	.		0.662	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		T	40366455	C	T	40366455	2	4	296	1	0	0	0	0	0	0	0	1	5786	610	22	3		3	FCGBP	19	40366455	Silent	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	394976	40366455	18762528	179	43123										
HNRNPUL1	11100	hgsc.bcm.edu	37	chr19	41787180	41787180	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gatgtgattggctgctttgcGgtgagtgctagcagcctgtg	16	7	0	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr19:41787180G>T	ENST00000392006.3	+	7	1172	c.999G>T	c.(997-999)gcG>gcT	p.A333A	HNRNPUL1_ENST00000595018.1_Splice_Site_p.A233A|HNRNPUL1_ENST00000352456.3_Splice_Site_p.A233A|HNRNPUL1_ENST00000263367.3_Splice_Site_p.A244A|HNRNPUL1_ENST00000378215.4_Intron|HNRNPUL1_ENST00000602130.1_Splice_Site_p.A333A|HNRNPUL1_ENST00000593587.1_Splice_Site_p.A233A	NM_007040.3	NP_008971.2	Q9BUJ2	HNRL1_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 1	333	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.|Necessary for interaction with TP53.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	29						GCTGCTTTGCGGTGAGTGCTA	0.502																																					p.A333A		Atlas-SNP	.											.	HNRNPUL1	73	.	0			c.G999T						.						68	50	56					19																	41787180		2203	4300	6503	SO:0001630	splice_region_variant	11100	exon7			CTTTGCGGTGAGT	AJ007509	CCDS12576.1, CCDS12577.1	19q13.2	2013-06-12		2008-04-18	ENSG00000105323	ENSG00000105323			17011	protein-coding gene	gene with protein product	"E1B 55kDa associated protein 5"	605800		HNRPUL1		9733834, 12489984	Standard	XM_005258459		Approved	E1B-AP5, E1BAP5, FLJ12944	uc002oqb.4	Q9BUJ2	OTTHUMG00000182740	ENST00000392006.3:c.999+1G>T	chr19.hg19:g.41787180G>T		87.0	0.0		203.0	46.0	NM_007040	B3KMW7|O76022|Q6ZSZ0|Q7L8P4|Q8N6Z4|Q96G37|Q9HAL3|Q9UG75	Silent	SNP	ENST00000392006.3	hg19	CCDS12576.1																																																																																			.	.		0.502	HNRNPUL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463406.1	NM_144732, NM_007040	Silent	T	41787180	G	T	41787180	5	4	296	1	0	0	0	0	0	0	1	0	7283	1130	39	1	1025	1	HNRNPUL1	19	41787180	Splice_Site	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10	1420725	41787180	17341803	180	43124										
IRGC	56269	hgsc.bcm.edu	37	chr19	44223843	44223843	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ggtggctggcggcatcagctTtggcgctgtctacaccatgc	14	12	2	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr19:44223843T>G	ENST00000244314.5	+	2	1332	c.1133T>G	c.(1132-1134)tTt>tGt	p.F378C		NM_019612.3	NP_062558.1	Q6NXR0	IIGP5_HUMAN	immunity-related GTPase family, cinema	378						membrane (GO:0016020)	GTP binding (GO:0005525)|hydrolase activity, acting on acid anhydrides (GO:0016817)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|skin(2)	25		Prostate(69;0.0435)				GGCATCAGCTTTGGCGCTGTC	0.667																																					p.F378C	Colon(189;350 2037 11447 13433 38914)	Atlas-SNP	.											.	IRGC	67	.	0			c.T1133G						.						33	29	30					19																	44223843		2203	4300	6503	SO:0001583	missense	56269	exon2			TCAGCTTTGGCGC	BC066939	CCDS12629.1	19q13.32	2008-02-05	2005-10-31	2005-10-31	ENSG00000124449	ENSG00000124449			28835	protein-coding gene	gene with protein product			"immunity-related GTPase family, cinema 1"	IRGC1		12477932	Standard	NM_019612		Approved	Iigp5, CINEMA	uc002oxh.3	Q6NXR0	OTTHUMG00000154587	ENST00000244314.5:c.1133T>G	chr19.hg19:g.44223843T>G	ENSP00000244314:p.Phe378Cys	69.0	0.0		113.0	29.0	NM_019612	Q05BR8	Missense_Mutation	SNP	ENST00000244314.5	hg19	CCDS12629.1	.	.	.	.	.	.	.	.	.	.	T	13.14	2.149132	0.37923	.	.	ENSG00000124449	ENST00000244314	T	0.28255	1.62	4.78	4.78	0.61160	.	0.074705	0.56097	D	0.000034	T	0.48187	0.1486	L	0.50333	1.59	0.32833	D	0.504261	D	0.89917	1.0	D	0.83275	0.996	T	0.61113	-0.7128	10	0.62326	D	0.03	.	12.2724	0.54714	0.0:0.0:0.0:1.0	.	378	Q6NXR0	IIGP5_HUMAN	C	378	ENSP00000244314:F378C	ENSP00000244314:F378C	F	+	2	0	IRGC	48915683	0.995000	0.38212	1.000000	0.80357	0.537000	0.34900	2.486000	0.45259	1.804000	0.52760	0.533000	0.62120	TTT	.	.		0.667	IRGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336191.1	NM_019612		G	44223843	T	G	44223843	3	3	296	1	0	0	0	0	1	0	0	0	7847	1841	64	5	1135	5	IRGC	19	44223843	Missense_Mutation	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	2436663	44223843	14905140	181	43125										
DKKL1	27120	hgsc.bcm.edu	37	chr19	49868878	49868879	+	In_Frame_Ins	INS	-	-	CCTCTCCAG													0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	caccagctggggaacaacacINScctctccagccacctccaga							TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr19:49868878_49868879insCCTCTCCAG	ENST00000221498.2	+	3	701_702	c.296_297insCCTCTCCAG	c.(295-300)accctc>acCCTCTCCAGcctc	p.100_101insSSL	DKKL1_ENST00000594268.1_Intron	NM_014419.3	NP_055234.1	Q9UK85	DKKL1_HUMAN	dickkopf-like 1	100					anatomical structure morphogenesis (GO:0009653)|positive regulation of fat cell differentiation (GO:0045600)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	signal transducer activity (GO:0004871)			large_intestine(2)|upper_aerodigestive_tract(1)	3		all_lung(116;1.66e-06)|Lung NSC(112;5.89e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0456)		GGGAACAACACCCTCTCCAGCC	0.604																																					p.T99delinsTLSS		Atlas-Indel,Pindel	.											.	DKKL1	23	.	0			c.296_297insCCTCTCCAG						.																																			SO:0001652	inframe_insertion	27120	exon3			.	AB047816	CCDS12762.1	19q13.3	2010-10-12	2010-10-12		ENSG00000104901	ENSG00000104901			16528	protein-coding gene	gene with protein product	"cancer/testis antigen 34", "soggy"	605418	"dickkopf-like 1 (soggy)"			10570958	Standard	NM_001197301		Approved	SGY-1, CT34	uc002pnk.3	Q9UK85		ENST00000221498.2:c.297_305dupCCTCTCCAG	chr19.hg19:g.49868879_49868887dupCCTCTCCAG	ENSP00000221498:p.Leu100_Ser101insSerSerLeu	80.0	0.0		142.0	15.0	NM_014419		In_Frame_Ins	INS	ENST00000221498.2	hg19	CCDS12762.1																																																																																			.	.		0.604	DKKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465454.2	NM_014419		CCTCTCCAG	49868879	-	CCTCTCCAG	49868878	7	5	296	1	0	1	1	0	0	0	0	0	4550	507	18	0	306	0	DKKL1	19	49868878	In_Frame_Ins	INS	-	TCGA-G3-AAV0-01A-11D-A36X-10	5645035	49868878	9260105	182	43126										
SLC17A7	57030	hgsc.bcm.edu	37	chr19	49937289	49937289	+	Frame_Shift_Del	DEL	C	C	-													0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gaggggcatcgcgaccaccgCcccagcataggaacctaagg							TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr19:49937289delC	ENST00000221485.3	-	6	823	c.652delG	c.(652-654)gcgfs	p.A218fs	SLC17A7_ENST00000600601.1_Frame_Shift_Del_p.A151fs|SLC17A7_ENST00000543531.1_Frame_Shift_Del_p.A206fs	NM_020309.3	NP_064705.1	Q9P2U7	VGLU1_HUMAN	solute carrier family 17 (vesicular glutamate transporter), member 7	218					glutamate secretion (GO:0014047)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|long-term memory (GO:0007616)|neurotransmitter secretion (GO:0007269)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|sequestering of neurotransmitter (GO:0042137)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|cerebellar mossy fiber (GO:0044300)|clathrin-sculpted glutamate transport vesicle membrane (GO:0060203)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|synaptic vesicle membrane (GO:0030672)	inorganic phosphate transmembrane transporter activity (GO:0005315)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|sodium:inorganic phosphate symporter activity (GO:0015319)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(7)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	26		all_lung(116;1.62e-07)|Lung NSC(112;8.47e-07)|all_neural(266;0.0381)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(486;0.0245)		GCGACCACCGCCCCAGCATAG	0.632																																					p.A218fs		Atlas-Indel,Pindel	.											SLC17A7,colon,carcinoma,0,1	SLC17A7	57	.	0			c.653delC						.						31	32	32					19																	49937289		2203	4299	6502	SO:0001589	frameshift_variant	57030	exon6			.	AB032436	CCDS12764.1	19q13.33	2013-07-18	2013-07-18		ENSG00000104888	ENSG00000104888		"Solute carriers"	16704	protein-coding gene	gene with protein product	"vesicular glutamate transporter 1"	605208	"solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 7"			8632143, 10820226	Standard	NM_020309		Approved	BNPI, VGLUT1	uc002pnp.3	Q9P2U7		ENST00000221485.3:c.652delG	chr19.hg19:g.49937289delC	ENSP00000221485:p.Ala218fs	201.0	0.0		437.0	81.0	NM_020309	B4DFR9|B4DG46|Q6PCD0	Frame_Shift_Del	DEL	ENST00000221485.3	hg19	CCDS12764.1																																																																																			.	.		0.632	SLC17A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465367.2			-	49937289	C	-	49937289	7	5	296	1	0	1	0	1	0	0	0	0	14437	739	26	0	1058	0	SLC17A7	19	49937289	Frame_Shift_Del	DEL	C	TCGA-G3-AAV0-01A-11D-A36X-10	68411	49937289	9191694	183	43127										
SHANK1	50944	hgsc.bcm.edu	37	chr19	51170365	51170365	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	caggctggatgcggtggagtCcagggtgggaggggctgcgg	23	7	0	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr19:51170365C>A	ENST00000293441.1	-	22	4870	c.4852G>T	c.(4852-4854)Gac>Tac	p.D1618Y	SHANK1_ENST00000391813.1_Missense_Mutation_p.D1005Y|SHANK1_ENST00000391814.1_Missense_Mutation_p.D1626Y|SYT3_ENST00000544769.1_Intron|SHANK1_ENST00000359082.3_Missense_Mutation_p.D1609Y	NM_016148.2	NP_057232.2	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	1618					adult behavior (GO:0030534)|associative learning (GO:0008306)|cytoskeletal anchoring at plasma membrane (GO:0007016)|dendritic spine morphogenesis (GO:0060997)|determination of affect (GO:0050894)|habituation (GO:0046959)|long-term memory (GO:0007616)|negative regulation of actin filament bundle assembly (GO:0032232)|neuromuscular process controlling balance (GO:0050885)|olfactory behavior (GO:0042048)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|protein complex assembly (GO:0006461)|protein localization to synapse (GO:0035418)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|righting reflex (GO:0060013)|social behavior (GO:0035176)|synapse maturation (GO:0060074)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|excitatory synapse (GO:0060076)|intracellular (GO:0005622)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ankyrin repeat binding (GO:0071532)|GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|somatostatin receptor binding (GO:0031877)			breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	64		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)		GCGGTGGAGTCCAGGGTGGGA	0.741																																					p.D1618Y		Atlas-SNP	.											.	SHANK1	210	.	0			c.G4852T						.						6	7	6					19																	51170365		2103	4139	6242	SO:0001583	missense	50944	exon22			TGGAGTCCAGGGT	AF163302	CCDS12799.1	19q13.3	2013-01-10			ENSG00000161681	ENSG00000161681		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	15474	protein-coding gene	gene with protein product	"somatostatin receptor-interacting protein"	604999				10551867	Standard	NM_016148		Approved	SSTRIP, SPANK-1, synamon	uc002psx.1	Q9Y566	OTTHUMG00000137380	ENST00000293441.1:c.4852G>T	chr19.hg19:g.51170365C>A	ENSP00000293441:p.Asp1618Tyr	48.0	0.0		110.0	30.0	NM_016148	A8MXP5|B7WNY6|Q9NYW9	Missense_Mutation	SNP	ENST00000293441.1	hg19	CCDS12799.1	.	.	.	.	.	.	.	.	.	.	C	9.919	1.211589	0.22289	.	.	ENSG00000161681	ENST00000293441;ENST00000391813;ENST00000359082;ENST00000391814	T;T;T;T	0.50277	0.83;1.37;0.81;0.75	2.39	2.39	0.29439	.	0.373786	0.24703	U	0.036292	T	0.58666	0.2138	L	0.46157	1.445	0.53005	D	0.999969	D;D	0.89917	1.0;1.0	D;D	0.79108	0.981;0.992	T	0.61302	-0.7090	10	0.72032	D	0.01	.	11.7292	0.51726	0.0:1.0:0.0:0.0	.	1618;1005	Q9Y566;Q9Y566-2	SHAN1_HUMAN;.	Y	1618;1005;1609;1626	ENSP00000293441:D1618Y;ENSP00000375689:D1005Y;ENSP00000351984:D1609Y;ENSP00000375690:D1626Y	ENSP00000293441:D1618Y	D	-	1	0	SHANK1	55862177	1.000000	0.71417	1.000000	0.80357	0.865000	0.49528	5.427000	0.66483	1.043000	0.40175	0.205000	0.17691	GAC	.	.		0.741	SHANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268071.1	NM_016148		A	51170365	C	A	51170365	3	1	296	1	0	0	0	0	1	0	0	0	14279	855	30	3	1641	3	SHANK1	19	51170365	Missense_Mutation	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	1233076	51170365	7958618	184	43128										
KLK6	5653	hgsc.bcm.edu	37	chr19	51462563	51462563	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tccacataccagcggaccccCagaatcaccctgcaggaaag	8	16	1	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr19:51462563C>A	ENST00000376851.3	-	6	1031	c.592G>T	c.(592-594)Ggg>Tgg	p.G198W	KLK6_ENST00000456750.2_Missense_Mutation_p.G91W|KLK6_ENST00000594641.1_Missense_Mutation_p.G198W|KLK6_ENST00000376853.4_Silent_p.L69L|CTB-147C22.8_ENST00000594939.1_RNA|KLK6_ENST00000310157.2_Missense_Mutation_p.G198W|KLK6_ENST00000391808.1_Missense_Mutation_p.G91W|CTB-147C22.8_ENST00000601506.1_RNA	NM_001012964.1	NP_001012982.1	Q92876	KLK6_HUMAN	kallikrein-related peptidase 6	198	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				amyloid precursor protein metabolic process (GO:0042982)|central nervous system development (GO:0007417)|collagen catabolic process (GO:0030574)|hormone metabolic process (GO:0042445)|myelination (GO:0042552)|neuron death (GO:0070997)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|protein autoprocessing (GO:0016540)|regulation of cell differentiation (GO:0045595)|regulation of neuron projection development (GO:0010975)|response to wounding (GO:0009611)|tissue regeneration (GO:0042246)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|skin(4)	13		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00372)|GBM - Glioblastoma multiforme(134;0.00871)		AGCGGACCCCCAGAATCACCC	0.532																																					p.G198W		Atlas-SNP	.											.	KLK6	35	.	0			c.G592T						.						113	105	108					19																	51462563		2203	4300	6503	SO:0001583	missense	5653	exon6			GACCCCCAGAATC	U62801	CCDS12811.1, CCDS42599.1	19q13.3	2011-09-07	2006-10-27			ENSG00000167755		"Kallikreins", "Serine peptidases / Serine peptidases"	6367	protein-coding gene	gene with protein product		602652	"protease, serine, 18", "kallikrein 6 (neurosin, zyme)"	PRSS9, PRSS18		9003450, 16800724, 16800723	Standard	NM_002774		Approved	Bssp, Klk7, neurosin	uc002pui.3	Q92876		ENST00000376851.3:c.592G>T	chr19.hg19:g.51462563C>A	ENSP00000366047:p.Gly198Trp	126.0	0.0		193.0	42.0	NM_001012964	A6NJA1|A8MW09|Q6H301	Missense_Mutation	SNP	ENST00000376851.3	hg19	CCDS12811.1	.	.	.	.	.	.	.	.	.	.	N	13.69	2.312081	0.40895	.	.	ENSG00000167755	ENST00000310157;ENST00000376851;ENST00000391808;ENST00000456750	D;D;D;D	0.99871	-7.35;-7.35;-7.35;-7.35	3.89	3.89	0.44902	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	D	0.99919	0.9962	H	0.99464	4.58	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95920	0.8930	9	0.87932	D	0	.	13.7773	0.63062	0.0:1.0:0.0:0.0	.	198;91	Q92876;Q92876-2	KLK6_HUMAN;.	W	198;198;91;91	ENSP00000309148:G198W;ENSP00000366047:G198W;ENSP00000375684:G91W;ENSP00000409241:G91W	ENSP00000309148:G198W	G	-	1	0	KLK6	56154375	1.000000	0.71417	0.505000	0.27651	0.043000	0.13939	6.767000	0.74975	2.156000	0.67533	0.645000	0.84053	GGG	.	.		0.532	KLK6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465060.1	NM_002774		A	51462563	C	A	51462563	3	1	296	1	0	0	0	0	1	0	0	0	8417	594	21	3	146	3	KLK6	19	51462563	Missense_Mutation	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	292198	51462563	7666420	185	43129										
CD33	945	hgsc.bcm.edu	37	chr19	51729149	51729149	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ctctgtgtcctgggcctgtgAgcagggaacacccccgatct	12	14	2	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr19:51729149A>G	ENST00000262262.4	+	3	530	c.509A>G	c.(508-510)gAg>gGg	p.E170G	CD33_ENST00000391796.3_Missense_Mutation_p.E170G|CD33_ENST00000436584.2_Missense_Mutation_p.E43G|CD33_ENST00000421133.2_Missense_Mutation_p.E43G	NM_001772.3	NP_001763.3	P20138	CD33_HUMAN	CD33 molecule	170	Ig-like C2-type.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|negative regulation of cell proliferation (GO:0008285)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(15)|skin(1)|stomach(1)	24		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000224)|OV - Ovarian serous cystadenocarcinoma(262;0.00468)	Gemtuzumab ozogamicin(DB00056)	TGGGCCTGTGAGCAGGGAACA	0.607																																					p.E170G		Atlas-SNP	.											.	CD33	55	.	0			c.A509G						.						89	87	88					19																	51729149		2203	4300	6503	SO:0001583	missense	945	exon3			CCTGTGAGCAGGG	M23197	CCDS33084.1, CCDS46157.1, CCDS54299.1	19q13.3	2013-01-29	2006-03-28		ENSG00000105383	ENSG00000105383		"CD molecules", "Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1659	protein-coding gene	gene with protein product	"sialic acid binding Ig-like lectin 3"	159590	"CD33 antigen (gp67)"			3139766, 9465907	Standard	NM_001772		Approved	SIGLEC3, SIGLEC-3, p67, FLJ00391	uc002pwa.2	P20138		ENST00000262262.4:c.509A>G	chr19.hg19:g.51729149A>G	ENSP00000262262:p.Glu170Gly	52.0	0.0		97.0	19.0	NM_001772	B4E3P8|C9JEN7|F8WAL2|Q8TD24	Missense_Mutation	SNP	ENST00000262262.4	hg19	CCDS33084.1	.	.	.	.	.	.	.	.	.	.	.	13.82	2.350121	0.41599	.	.	ENSG00000105383	ENST00000436584;ENST00000262262;ENST00000421133;ENST00000391796	T;T;T;T	0.03386	3.95;3.95;3.95;3.95	3.07	2.04	0.26737	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.496120	0.14910	N	0.291331	T	0.09202	0.0227	M	0.83483	2.645	0.09310	N	1	B;B;B	0.32302	0.363;0.073;0.046	B;B;B	0.42692	0.395;0.14;0.033	T	0.13980	-1.0489	10	0.62326	D	0.03	.	4.344	0.11124	0.8389:0.0:0.1611:0.0	.	43;170;170	C9JEN7;F8WAL2;P20138	.;.;CD33_HUMAN	G	43;170;43;170	ENSP00000403331:E43G;ENSP00000262262:E170G;ENSP00000410126:E43G;ENSP00000375673:E170G	ENSP00000262262:E170G	E	+	2	0	CD33	56420961	0.364000	0.24997	0.364000	0.25888	0.606000	0.37113	2.064000	0.41432	1.409000	0.46915	0.374000	0.22700	GAG	.	.		0.607	CD33-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464199.2	NM_001772		G	51729149	A	G	51729149	3	3	296	1	0	0	0	0	1	0	0	0	3007	304	11	2	519	2	CD33	19	51729149	Missense_Mutation	SNP	A	TCGA-G3-AAV0-01A-11D-A36X-10	266586	51729149	7399834	186	43130										
ZNF845	91664	hgsc.bcm.edu	37	chr19	53855788	53855788	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	aaatttttcagacatcgttcAtaccttgcagttcattggcg	7	9	3	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr19:53855788A>G	ENST00000595091.1	+	5	2079	c.1860A>G	c.(1858-1860)tcA>tcG	p.S620S	ZNF845_ENST00000458035.1_Silent_p.S620S			Q96IR2	ZN845_HUMAN	zinc finger protein 845	620					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						GACATCGTTCATACCTTGCAG	0.358																																					p.S620S		Atlas-SNP	.											.	ZNF845	101	.	0			c.A1860G						.						30	25	27					19																	53855788		692	1590	2282	SO:0001819	synonymous_variant	91664	exon4			TCGTTCATACCTT	BC007307	CCDS46170.1	19q13.42	2013-01-08			ENSG00000213799	ENSG00000213799		"Zinc fingers, C2H2-type", "-"	25112	protein-coding gene	gene with protein product							Standard	NM_138374		Approved		uc010ydv.1	Q96IR2		ENST00000595091.1:c.1860A>G	chr19.hg19:g.53855788A>G		89.0	0.0		136.0	61.0	NM_138374		Silent	SNP	ENST00000595091.1	hg19	CCDS46170.1																																																																																			.	.		0.358	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908		G	53855788	A	G	53855788	2	3	296	1	0	0	0	0	0	0	0	1	18206	204	8	2		2	ZNF845	19	53855788	Silent	SNP	A	TCGA-G3-AAV0-01A-11D-A36X-10	2126639	53855788	5273195	187	43131										
SAPS1	22870	hgsc.bcm.edu	37	chr19	55756527	55756527	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tggatctgctcaatcagccgCtggacgatcttctcctcgtt	9	13	5	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr19:55756527C>T	ENST00000412770.2	-	5	1145	c.579G>A	c.(577-579)caG>caA	p.Q193Q	PPP6R1_ENST00000587283.1_Silent_p.Q193Q	NM_014931.3	NP_055746.3	Q9UPN7	PP6R1_HUMAN	protein phosphatase 6, regulatory subunit 1	193	Interaction with PPP6C.				regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)	protein phosphatase binding (GO:0019903)			breast(1)	1						CAATCAGCCGCTGGACGATCT	0.632																																					p.Q193Q		Atlas-SNP	.											.	PPP6R1	63	.	0			c.G579A						.						58	71	67					19																	55756527		2123	4241	6364	SO:0001819	synonymous_variant	22870	exon5			CAGCCGCTGGACG	AB029038	CCDS46186.1	19q13.42	2012-04-17	2010-06-28	2010-06-28	ENSG00000105063	ENSG00000105063		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"	29195	protein-coding gene	gene with protein product		610875	"KIAA1115", "SAPS domain family, member 1"	KIAA1115, SAPS1		16769727	Standard	NM_014931		Approved	SAP190	uc002qjw.4	Q9UPN7		ENST00000412770.2:c.579G>A	chr19.hg19:g.55756527C>T		60.0	0.0		128.0	23.0	NM_014931	Q2M2H3|Q504V2|Q6NVJ6|Q9BU97	Silent	SNP	ENST00000412770.2	hg19	CCDS46186.1																																																																																			.	.		0.632	PPP6R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452663.1	NM_014931		T	55756527	C	T	55756527	2	4	296	1	0	0	0	0	0	0	0	1	13851	796	28	3		3	SAPS1	19	55756527	Silent	SNP	C	TCGA-G3-AAV0-01A-11D-A36X-10	1900739	55756527	3372456	188	43132										
C20orf186	149954	hgsc.bcm.edu	37	chr20	31671301	31671301	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	acgacaacactgctcagctgGggggcaaataccgatatggt	12	10	1	0			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr20:31671301G>T	ENST00000375483.3	+	3	298	c.298G>T	c.(298-300)Ggg>Tgg	p.G100W		NM_182519.2	NP_872325.2	P59827	BPIB4_HUMAN	BPI fold containing family B, member 4	100						cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										TGCTCAGCTGGGGGGCAAATA	0.522																																					p.G100W		Atlas-SNP	.											.	.	.	.	0			c.G298T						.						83	75	78					20																	31671301		2203	4300	6503	SO:0001583	missense	149954	exon3			CAGCTGGGGGGCA	AF549190	CCDS13213.2	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186191	ENSG00000186191		"BPI fold containing"	16179	protein-coding gene	gene with protein product		615718	"chromosome 20 open reading frame 186"	C20orf186		11971875, 21787333	Standard	NM_182519		Approved	dJ726C3.5, LPLUNC4	uc010zue.2	P59827	OTTHUMG00000032235	ENST00000375483.3:c.298G>T	chr20.hg19:g.31671301G>T	ENSP00000364632:p.Gly100Trp	116.0	0.0		124.0	55.0	NM_182519	Q5TDX6	Missense_Mutation	SNP	ENST00000375483.3	hg19	CCDS13213.2	.	.	.	.	.	.	.	.	.	.	G	12.42	1.931534	0.34096	.	.	ENSG00000186191	ENST00000375483	T	0.02103	4.45	3.28	3.28	0.37604	.	0.291835	0.22981	N	0.053309	T	0.06234	0.0161	L	0.32530	0.975	0.35533	D	0.802407	D	0.89917	1.0	D	0.83275	0.996	T	0.36768	-0.9734	10	0.87932	D	0	-14.8948	10.1994	0.43073	0.0:0.0:1.0:0.0	.	100	P59827	BPIB4_HUMAN	W	100	ENSP00000364632:G100W	ENSP00000364632:G100W	G	+	1	0	BPIFB4	31134962	1.000000	0.71417	1.000000	0.80357	0.307000	0.27823	2.936000	0.48971	1.827000	0.53221	0.462000	0.41574	GGG	.	.		0.522	BPIFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078655.5	NM_182519		T	31671301	G	T	31671301	3	4	296	1	0	0	0	0	1	0	0	0	2100	1232	43	3	308	3	C20orf186	20	31671301	Missense_Mutation	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10		31671301	31354219	189	43133										
CHD6	84181	hgsc.bcm.edu	37	chr20	40127986	40127986	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	tcaatgatgtttgcatcatcTtctggaggctcctggggaca	11	9	4	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr20:40127986T>C	ENST00000373233.3	-	6	1041	c.864A>G	c.(862-864)gaA>gaG	p.E288E	CHD6_ENST00000373222.3_Silent_p.E323E|CHD6_ENST00000309279.7_Silent_p.E288E	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	288	Required for DNA-dependent ATPase activity.				ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				TTGCATCATCTTCTGGAGGCT	0.388																																					p.E288E		Atlas-SNP	.											.	CHD6	312	.	0			c.A864G						.						58	48	51					20																	40127986		2203	4300	6503	SO:0001819	synonymous_variant	84181	exon6			ATCATCTTCTGGA	AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.864A>G	chr20.hg19:g.40127986T>C		77.0	0.0		64.0	31.0	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Silent	SNP	ENST00000373233.3	hg19	CCDS13317.1																																																																																			.	.		0.388	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			C	40127986	T	C	40127986	2	2	296	1	0	0	0	0	0	0	0	1	3331	1606	56	2		2	CHD6	20	40127986	Silent	SNP	T	TCGA-G3-AAV0-01A-11D-A36X-10	8456685	40127986	22897534	190	43134										
PCK1	5105	hgsc.bcm.edu	37	chr20	56140173	56140177	+	Frame_Shift_Del	DEL	GCGGC	GCGGC	-													0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ccatgagatcagaggccacaGcggctgcagaacataaaggt					rs548285338		TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	GCGGC	GCGGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr20:56140173_56140177delGCGGC	ENST00000319441.4	+	9	1560_1564	c.1396_1400delGCGGC	c.(1396-1401)gcggctfs	p.AA466fs	PCK1_ENST00000543666.1_Frame_Shift_Del_p.AA149fs|PCK1_ENST00000535860.1_3'UTR	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	466					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			AGAGGCCACAGCGGCTGCAGAACAT	0.473																																					p.465_467del		Atlas-INDEL	.											.	PCK1	95	.	0			c.1395_1399del						.																																			SO:0001589	frameshift_variant	5105	exon9			.		CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.1396_1400delGCGGC	chr20.hg19:g.56140173_56140177delGCGGC	ENSP00000319814:p.Ala466fs	222.0	0.0		156.0	23.0	NM_002591	A8K437|B4DT64|Q8TCA3|Q9UJD2	Frame_Shift_Del	DEL	ENST00000319441.4	hg19	CCDS13460.1																																																																																			.	.		0.473	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2			-	56140177	GCGGC	-	56140173	7	5	296	1	0	1	0	1	0	0	0	0	11590	971	34	0	1426	0	PCK1	20	56140173	Frame_Shift_Del	DEL	GCGGC	TCGA-G3-AAV0-01A-11D-A36X-10	16012187	56140173	6885347	191	43135	227	2								
PCK1	5105	hgsc.bcm.edu	37	chr20	56140179	56140191	+	Splice_Site	DEL	GCAGAACATAAAG	GCAGAACATAAAG	-													0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	gatcagaggccacagcggctGcagaacataaaggtaaatca					rs373827777		TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	GCAGAACATAAAG	GCAGAACATAAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr20:56140179_56140191delGCAGAACATAAAG	ENST00000319441.4	+	9	1566_1578	c.1402_1414delGCAGAACATAAAG	c.(1402-1416)gcagaacataaaggc>gc	p.AEHKG468fs	PCK1_ENST00000543666.1_Splice_Site_p.AEHKG151fs|PCK1_ENST00000535860.1_3'UTR	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	468					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			CACAGCGGCTGCAGAACATAAAGGTAAATCAAA	0.484																																					p.467_471del		Atlas-INDEL	.											.	PCK1	95	.	0			c.1401_1413del						.																																			SO:0001630	splice_region_variant	5105	exon9			.		CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.1414+1GCAGAACATAAAG>-	chr20.hg19:g.56140179_56140191delGCAGAACATAAAG		213.0	0.0		149.0	23.0	NM_002591	A8K437|B4DT64|Q8TCA3|Q9UJD2	Frame_Shift_Del	DEL	ENST00000319441.4	hg19	CCDS13460.1																																																																																			.	.		0.484	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2		Frame_Shift_Del	-	56140191	GCAGAACATAAAG	-	56140179	8	5	296	1	0	1	0	1	0	0	1	0	11590	1319	46	0	1432	0	PCK1	20	56140179	Splice_Site	DEL	GCAGAACATAAAG	TCGA-G3-AAV0-01A-11D-A36X-10	6	56140179	6885341	192	43136	227	2								
DIP2A	23181	hgsc.bcm.edu	37	chr21	47983839	47983839	+	Frame_Shift_Del	DEL	G	G	-													0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	cccttgggagactcacacctGggagaggtgagcaggggccc							TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr21:47983839delG	ENST00000417564.2	+	35	4179	c.4158delG	c.(4156-4158)ctgfs	p.L1386fs	DIP2A_ENST00000400274.1_Frame_Shift_Del_p.L1382fs|DIP2A_ENST00000479654.1_3'UTR|DIP2A_ENST00000318711.7_Frame_Shift_Del_p.L1387fs			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	1386					multicellular organismal development (GO:0007275)|negative regulation of gene expression (GO:0010629)|regulation of apoptotic process (GO:0042981)	cell surface (GO:0009986)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(22)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		ACTCACACCTGGGAGAGGTGA	0.542																																					p.L1386fs		Atlas-Indel,Pindel	.											.	DIP2A	332	.	0			c.4157delT						.						44	46	45					21																	47983839		1911	4136	6047	SO:0001589	frameshift_variant	23181	exon35			.	AF490768	CCDS46655.1, CCDS46656.1, CCDS46657.1, CCDS54490.1, CCDS54491.1	21q22.3	2010-08-20	2006-01-13	2006-01-13	ENSG00000160305	ENSG00000160305			17217	protein-coding gene	gene with protein product		607711	"chromosome 21 open reading frame 106"	C21orf106			Standard	NM_015151		Approved	Dip2, KIAA0184	uc002zjo.2	Q14689	OTTHUMG00000090717	ENST00000417564.2:c.4158delG	chr21.hg19:g.47983839delG	ENSP00000392066:p.Leu1386fs	98.0	0.0		76.0	33.0	NM_015151	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Frame_Shift_Del	DEL	ENST00000417564.2	hg19	CCDS46655.1																																																																																			.	.		0.542	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151		-	47983839	G	-	47983839	7	5	296	1	0	1	0	1	0	0	0	0	4529	1335	47	0	4409	0	DIP2A	21	47983839	Frame_Shift_Del	DEL	G	TCGA-G3-AAV0-01A-11D-A36X-10		47983839	146056	193	43137										
ST13	6767	hgsc.bcm.edu	37	chr22	41252470	41252470	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ctcaggaagcgcatttcctcGgtgtgcagaacgctcggatc	12	12	1	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chr22:41252470G>C	ENST00000216218.3	-	1	556	c.75C>G	c.(73-75)acC>acG	p.T25T	XPNPEP3_ENST00000357137.4_5'Flank|XPNPEP3_ENST00000414396.1_5'Flank|XPNPEP3_ENST00000541156.1_5'Flank	NM_003932.3	NP_003923.2	P50502	F10A1_HUMAN	suppression of tumorigenicity 13 (colon carcinoma) (Hsp70 interacting protein)	25					chaperone cofactor-dependent protein refolding (GO:0070389)|negative regulation of protein refolding (GO:0061084)|protein folding (GO:0006457)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	dATP binding (GO:0032564)|protein binding, bridging (GO:0030674)			cervix(1)|large_intestine(1)|lung(3)|skin(1)	6						GCATTTCCTCGGTGTGCAGAA	0.637																																					p.T25T		Atlas-SNP	.											.	ST13	16	.	0			c.C75G						.						60	64	62					22																	41252470		2203	4300	6503	SO:0001819	synonymous_variant	6767	exon1			TTCCTCGGTGTGC		CCDS14006.1	22q13.2	2013-01-10	2001-11-29		ENSG00000100380	ENSG00000100380		"Tetratricopeptide (TTC) repeat domain containing"	11343	protein-coding gene	gene with protein product	"progesterone receptor-associated p48 protein"	606796	"suppression of tumorigenicity 13 (colon carcinoma) (Hsp70-interacting protein)"			9925927, 8721986	Standard	NM_003932		Approved	SNC6, HSPABP1, HIP, P48, FAM10A1	uc003aze.3	P50502	OTTHUMG00000151201	ENST00000216218.3:c.75C>G	chr22.hg19:g.41252470G>C		399.0	0.0		482.0	27.0	NM_003932	O14999|Q2TU77	Silent	SNP	ENST00000216218.3	hg19	CCDS14006.1																																																																																			.	.		0.637	ST13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321759.1	NM_003932		C	41252470	G	C	41252470	2	2	296	1	0	0	0	0	0	0	0	1	15225	1103	39	4		4	ST13	22	41252470	Silent	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10		41252470	10052096	194	43138										
CAPN6	827	hgsc.bcm.edu	37	chrX	110490682	110490682	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	aactgtattcttctggacagGagaacggacttcctcctttc	8	11	2	1			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chrX:110490682G>T	ENST00000324068.1	-	12	1824	c.1657C>A	c.(1657-1659)Cct>Act	p.P553T	CAPN6_ENST00000541758.1_Missense_Mutation_p.P298T	NM_014289.3	NP_055104.2	Q9Y6Q1	CAN6_HUMAN	calpain 6	553	C2.				microtubule bundle formation (GO:0001578)|proteolysis (GO:0006508)|regulation of cytoskeleton organization (GO:0051493)	perinuclear region of cytoplasm (GO:0048471)|spindle microtubule (GO:0005876)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|microtubule binding (GO:0008017)			cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(25)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	47						TTCTGGACAGGAGAACGGACT	0.398																																					p.P553T		Atlas-SNP	.											.	CAPN6	120	.	0			c.C1657A						.						153	130	138					X																	110490682		2203	4300	6503	SO:0001583	missense	827	exon12			GGACAGGAGAACG	AF029232	CCDS14555.1	Xq23	2008-07-29			ENSG00000077274	ENSG00000077274			1483	protein-coding gene	gene with protein product		300146				9503024, 9339374	Standard	NM_014289		Approved	CAPNX, CalpM, CANPX	uc004epc.2	Q9Y6Q1	OTTHUMG00000022203	ENST00000324068.1:c.1657C>A	chrX.hg19:g.110490682G>T	ENSP00000317214:p.Pro553Thr	160.0	0.0		137.0	16.0	NM_014289	D3DUY7|Q9UEQ1|Q9UJA8	Missense_Mutation	SNP	ENST00000324068.1	hg19	CCDS14555.1	.	.	.	.	.	.	.	.	.	.	G	10.78	1.448025	0.26074	.	.	ENSG00000077274	ENST00000324068;ENST00000541758	T;T	0.68181	-0.31;-0.31	4.99	4.99	0.66335	C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	1.323950	0.04588	N	0.396165	T	0.58061	0.2096	N	0.24115	0.695	0.32655	N	0.518917	B	0.33777	0.425	B	0.36378	0.223	T	0.53479	-0.8433	10	0.37606	T	0.19	.	9.7844	0.40666	0.0974:0.0:0.9026:0.0	.	553	Q9Y6Q1	CAN6_HUMAN	T	553;298	ENSP00000317214:P553T;ENSP00000441736:P298T	ENSP00000317214:P553T	P	-	1	0	CAPN6	110377338	0.325000	0.24660	1.000000	0.80357	0.989000	0.77384	0.534000	0.23098	2.308000	0.77769	0.517000	0.50305	CCT	.	.		0.398	CAPN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057922.1			T	110490682	G	T	110490682	3	4	296	1	0	0	0	0	1	0	0	0	2632	1174	41	3	276	3	CAPN6	23	110490682	Missense_Mutation	SNP	G	TCGA-G3-AAV0-01A-11D-A36X-10		110490682	44779878	195	43139										
GRIA3	2892	hgsc.bcm.edu	37	chrX	122551286	122551286	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0670103092783505	13	1	1.48265358471207	0.605343771272975	1.68631479140329	0.00036362439032072	0.0150702108432921	0	ctgttgctccactcactataAcattggtccgtgaagaagtc	8	11	1	2			TCGA-G3-AAV0-01A-11D-A36X-10	TCGA-G3-AAV0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf7c19ad-4570-4952-9604-41305e544984	60d8b369-5133-44f7-9021-71ffb112a0ce	g.chrX:122551286A>C	ENST00000371251.1	+	11	1586	c.1534A>C	c.(1534-1536)Aca>Cca	p.T512P	GRIA3_ENST00000542149.1_Missense_Mutation_p.T512P|GRIA3_ENST00000264357.5_Missense_Mutation_p.T512P|GRIA3_ENST00000541091.1_Missense_Mutation_p.T496P|GRIA3_ENST00000371256.5_Missense_Mutation_p.T512P			P42263	GRIA3_HUMAN	glutamate receptor, ionotropic, AMPA 3	512					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)			breast(2)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|pancreas(2)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	57					Lithium(DB01356)	ACTCACTATAACATTGGTCCG	0.358																																					p.T512P		Atlas-SNP	.											.	GRIA3	386	.	0			c.A1534C						.						120	122	121					X																	122551286		2203	4300	6503	SO:0001583	missense	2892	exon11			ACTATAACATTGG	U10301	CCDS14604.1, CCDS14605.1, CCDS76017.1	Xq25	2012-08-29	2012-02-03		ENSG00000125675	ENSG00000125675		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4573	protein-coding gene	gene with protein product		305915	"glutamate receptor, ionotrophic, AMPA 3"	GLUR3		1319477, 10644433	Standard	NM_007325		Approved	GluA3, GLURC, MRX94	uc004etr.4	P42263	OTTHUMG00000022685	ENST00000371251.1:c.1534A>C	chrX.hg19:g.122551286A>C	ENSP00000360297:p.Thr512Pro	145.0	0.0		299.0	129.0	NM_000828	D3DTF1|Q4VXD5|Q4VXD6|Q9HDA0|Q9HDA1|Q9HDA2|Q9P0H1	Missense_Mutation	SNP	ENST00000371251.1	hg19	CCDS14604.1	.	.	.	.	.	.	.	.	.	.	A	19.62	3.862388	0.71949	.	.	ENSG00000125675	ENST00000264357;ENST00000542149;ENST00000371256;ENST00000371251;ENST00000541091	T;T;T;T;T	0.62105	0.69;0.69;0.69;0.69;0.05	5.84	5.84	0.93424	Ionotropic glutamate receptor (1);	0.000000	0.85682	D	0.000000	D	0.87398	0.6167	H	0.98769	4.325	0.80722	D	1	D;D;D	0.89917	1.0;0.998;0.999	D;D;D	0.80764	0.993;0.986;0.994	D	0.92172	0.5744	10	0.87932	D	0	.	14.2236	0.65843	1.0:0.0:0.0:0.0	.	496;512;512	B7Z4C0;P42263;P42263-2	.;GRIA3_HUMAN;.	P	512;512;512;512;496	ENSP00000264357:T512P;ENSP00000446146:T512P;ENSP00000360302:T512P;ENSP00000360297:T512P;ENSP00000446440:T496P	ENSP00000264357:T512P	T	+	1	0	GRIA3	122378967	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.327000	0.79147	1.957000	0.56846	0.486000	0.48141	ACA	.	.		0.358	GRIA3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058854.1	NM_000828		C	122551286	A	C	122551286	3	2	296	1	0	0	0	0	1	0	0	0	6778	43	2	5	1576	5	GRIA3	23	122551286	Missense_Mutation	SNP	A	TCGA-G3-AAV0-01A-11D-A36X-10	12060604	122551286	32719274	196	43140										
RHBDL2	54933	hgsc.bcm.edu	37	chr1	39352191	39352191	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	gcaggtcagtttgctggagaTaggaaaatgttgaaaaacac	12	5	1	2			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr1:39352191T>C	ENST00000289248.2	-	8	1905	c.897A>G	c.(895-897)ctA>ctG	p.L299L	RHBDL2_ENST00000372985.3_Silent_p.L379L|RHBDL2_ENST00000538156.1_Silent_p.L366L|RP5-864K19.4_ENST00000433671.2_RNA|RHBDL2_ENST00000372990.1_Silent_p.L299L			Q9NX52	RHBL2_HUMAN	rhomboid, veinlet-like 2 (Drosophila)	299						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)	8	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;8.23e-17)			TTGCTGGAGATAGGAAAATGT	0.363																																					p.L299L		Atlas-SNP	.											.	RHBDL2	28	.	0			c.A897G						.						77	71	73					1																	39352191		2203	4300	6503	SO:0001819	synonymous_variant	54933	exon8			TGGAGATAGGAAA	AK000442	CCDS30680.1	1p35.1	2014-01-28	2001-11-28		ENSG00000158315	ENSG00000158315			16083	protein-coding gene	gene with protein product		608962	"rhomboid (veinlet, Drosophila)-like 2"				Standard	NM_017821		Approved	FLJ20435	uc001ccu.1	Q9NX52	OTTHUMG00000000487	ENST00000289248.2:c.897A>G	chr1.hg19:g.39352191T>C		76.0	0.0		66.0	38.0	NM_017821	B2RNT3|B9EH75|Q6P175|Q8NER8|Q96E02	Silent	SNP	ENST00000289248.2	hg19	CCDS30680.1																																																																																			.	.		0.363	RHBDL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001216.1	NM_017821		C	39352191	T	C	39352191	2	2	297	1	0	0	0	0	0	0	0	1	13337	1393	49	2		2	RHBDL2	1	39352191	Silent	SNP	T	TCGA-G3-AAV1-01A-11D-A382-10		39352191	209898430	1	43141										
NASP	4678	hgsc.bcm.edu	37	chr1	46080777	46080777	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	accgtctccttgcagagaccCactaccagctgggcttggct	10	15	1	1			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr1:46080777C>T	ENST00000350030.3	+	10	1846	c.1759C>T	c.(1759-1761)Cac>Tac	p.H587Y	NASP_ENST00000530073.1_3'UTR|NASP_ENST00000351223.3_Missense_Mutation_p.H248Y|NASP_ENST00000372052.4_Missense_Mutation_p.H221Y|NASP_ENST00000537798.1_Missense_Mutation_p.H523Y|NASP_ENST00000402363.3_Missense_Mutation_p.H589Y	NM_002482.3	NP_002473.2	P49321	NASP_HUMAN	nuclear autoantigenic sperm protein (histone-binding)	587	Glu-rich (acidic).				blastocyst development (GO:0001824)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone exchange (GO:0043486)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	Hsp90 protein binding (GO:0051879)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	17	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.211)					TGCAGAGACCCACTACCAGCT	0.493																																					p.H587Y		Atlas-SNP	.											.	NASP	77	.	0			c.C1759T						.						84	79	81					1																	46080777		2203	4300	6503	SO:0001583	missense	4678	exon10			GAGACCCACTACC	M97856	CCDS524.1, CCDS525.1, CCDS55597.1	1p34.1	2013-01-10			ENSG00000132780	ENSG00000132780		"Tetratricopeptide (TTC) repeat domain containing"	7644	protein-coding gene	gene with protein product		603185				1426632	Standard	NM_002482		Approved	FLB7527, FLJ31599, FLJ35510, MGC19722, MGC20372, MGC2297, DKFZp547F162, PRO1999	uc001coi.2	P49321	OTTHUMG00000007826	ENST00000350030.3:c.1759C>T	chr1.hg19:g.46080777C>T	ENSP00000255120:p.His587Tyr	138.0	0.0		159.0	74.0	NM_002482	A8K6H2|B4DQP3|D3DQ07|F5H3J2|Q53GW5|Q5T622|Q5T625|Q96A69|Q9BTW2	Missense_Mutation	SNP	ENST00000350030.3	hg19	CCDS524.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.6|24.6	4.551819|4.551819	0.86127|0.86127	.|.	.|.	ENSG00000132780|ENSG00000132780	ENST00000437901;ENST00000537798;ENST00000402363;ENST00000341288;ENST00000528238;ENST00000350030;ENST00000372052;ENST00000351223|ENST00000534450	T;T;T;T;T;T;T|.	0.71461|.	-0.57;0.29;0.29;0.29;0.29;0.29;0.29|.	5.3|5.3	5.3|5.3	0.74995|0.74995	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);|.	0.042533|.	0.85682|.	D|.	0.000000|.	T|T	0.63283|0.63283	0.2498|0.2498	L|L	0.52126|0.52126	1.63|1.63	0.58432|0.58432	D|D	0.999998|0.999998	D;D;B;B|.	0.76494|.	0.958;0.999;0.268;0.006|.	P;D;P;B|.	0.67548|.	0.781;0.952;0.488;0.03|.	T|T	0.59847|0.59847	-0.7377|-0.7377	10|5	0.87932|.	D|.	0|.	-5.2361|-5.2361	14.1917|14.1917	0.65641|0.65641	0.1495:0.8504:0.0:0.0|0.1495:0.8504:0.0:0.0	.|.	523;248;587;589|.	F5H3J2;Q5T626;P49321;P49321-3|.	.;.;NASP_HUMAN;.|.	Y|L	248;523;589;487;184;587;221;248|16	ENSP00000400792:H248Y;ENSP00000438871:H523Y;ENSP00000384529:H589Y;ENSP00000432289:H184Y;ENSP00000255120:H587Y;ENSP00000361122:H221Y;ENSP00000255121:H248Y|.	ENSP00000345532:H487Y|.	H|P	+|+	1|2	0|0	NASP|NASP	45853364|45853364	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.377000|5.377000	0.66184|0.66184	2.635000|2.635000	0.89317|0.89317	0.655000|0.655000	0.94253|0.94253	CAC|CCA	.	.		0.493	NASP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021533.2	NM_002482		T	46080777	C	T	46080777	3	4	297	1	0	0	0	0	1	0	0	0	10181	594	21	3	1874	3	NASP	1	46080777	Missense_Mutation	SNP	C	TCGA-G3-AAV1-01A-11D-A382-10	6728586	46080777	203169844	2	43142										
CCDC18	343099	hgsc.bcm.edu	37	chr1	93649646	93649646	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	ttgaattattcaccttatgaAaacgtctgtaaaatatctgg	6	6	3	2			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr1:93649646A>G	ENST00000343253.7	+	3	748	c.246A>G	c.(244-246)gaA>gaG	p.E82E	CCDC18_ENST00000557479.1_Silent_p.E200E|CCDC18_ENST00000401026.3_Silent_p.E82E|CCDC18_ENST00000338949.4_5'UTR|CCDC18_ENST00000334652.5_5'UTR			Q5T9S5	CCD18_HUMAN	coiled-coil domain containing 18	82										breast(5)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)		CACCTTATGAAAACGTCTGTA	0.348																																					p.E82E		Atlas-SNP	.											.	CCDC18	93	.	0			c.A246G						.						85	77	80					1																	93649646		1808	4075	5883	SO:0001819	synonymous_variant	343099	exon3			TTATGAAAACGTC			1p22.1	2008-02-05			ENSG00000122483	ENSG00000122483			30370	protein-coding gene	gene with protein product						12601173	Standard	XM_006710609		Approved	NY-SAR-41	uc021opx.1	Q5T9S5	OTTHUMG00000010598	ENST00000343253.7:c.246A>G	chr1.hg19:g.93649646A>G		89.0	0.0		118.0	48.0	NM_206886	Q6ZU17	Silent	SNP	ENST00000343253.7	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	2.242|2.242	-0.373521|-0.373521	0.05034|0.05034	.|.	.|.	ENSG00000122483|ENSG00000122483	ENST00000448243|ENST00000370276	.|.	.|.	.|.	5.75|5.75	0.14|0.14	0.14804|0.14804	.|.	.|.	.|.	.|.	.|.	T|T	0.34077|0.34077	0.0885|0.0885	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.22277|0.22277	-1.0221|-1.0221	4|4	.|.	.|.	.|.	.|.	4.5408|4.5408	0.12056|0.12056	0.4817:0.3081:0.2102:0.0|0.4817:0.3081:0.2102:0.0	.|.	.|.	.|.	.|.	E|R	129|136	.|.	.|.	K|K	+|+	1|2	0|0	CCDC18|CCDC18	93422234|93422234	0.999000|0.999000	0.42202|0.42202	0.848000|0.848000	0.33437|0.33437	0.332000|0.332000	0.28634|0.28634	0.495000|0.495000	0.22483|0.22483	-0.001000|-0.001000	0.14495|0.14495	0.482000|0.482000	0.46254|0.46254	AAA|AAA	.	.		0.348	CCDC18-008	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000382327.1	NM_206886		G	93649646	A	G	93649646	2	3	297	1	0	0	0	0	0	0	0	1	2796	11	1	2		2	CCDC18	1	93649646	Silent	SNP	A	TCGA-G3-AAV1-01A-11D-A382-10	47568869	93649646	155600975	3	43143										
VCAM1	7412	hgsc.bcm.edu	37	chr1	101194785	101194785	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	ctttctcctggagaacccagAtagacagccctctgagcggg	11	13	2	4			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr1:101194785A>G	ENST00000294728.2	+	5	1152	c.1051A>G	c.(1051-1053)Ata>Gta	p.I351V	VCAM1_ENST00000370115.1_Intron|VCAM1_ENST00000370119.4_Missense_Mutation_p.I289V|VCAM1_ENST00000347652.2_Intron	NM_001078.3	NP_001069.1	P19320	VCAM1_HUMAN	vascular cell adhesion molecule 1	351	Ig-like C2-type 4.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|amine metabolic process (GO:0009308)|B cell differentiation (GO:0030183)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-matrix adhesion (GO:0007160)|cellular response to glucose stimulus (GO:0071333)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|chorio-allantoic fusion (GO:0060710)|chronic inflammatory response (GO:0002544)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|oxidation-reduction process (GO:0055114)|positive regulation of T cell proliferation (GO:0042102)|regulation of immune response (GO:0050776)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|response to lipopolysaccharide (GO:0032496)|response to nicotine (GO:0035094)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|viral process (GO:0016032)	alpha9-beta1 integrin-vascular cell adhesion molecule-1 complex (GO:0071065)|apical part of cell (GO:0045177)|cell surface (GO:0009986)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|podosome (GO:0002102)|sarcolemma (GO:0042383)	cell adhesion molecule binding (GO:0050839)|integrin binding (GO:0005178)|primary amine oxidase activity (GO:0008131)			central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(27)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_epithelial(167;3.83e-06)|all_lung(203;0.000485)|Lung NSC(277;0.0011)		Epithelial(280;0.0227)|all cancers(265;0.0276)|COAD - Colon adenocarcinoma(174;0.149)|Colorectal(144;0.169)|Lung(183;0.196)	Carvedilol(DB01136)	GAGAACCCAGATAGACAGCCC	0.542																																					p.I351V		Atlas-SNP	.											.	VCAM1	111	.	0			c.A1051G						.						107	109	108					1																	101194785		2203	4300	6503	SO:0001583	missense	7412	exon5			ACCCAGATAGACA	M60335	CCDS773.1, CCDS774.1, CCDS55617.1	1p32-p31	2014-01-30			ENSG00000162692	ENSG00000162692		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Endogenous ligands"	12663	protein-coding gene	gene with protein product		192225					Standard	NM_080682		Approved	CD106	uc001dti.3	P19320	OTTHUMG00000010982	ENST00000294728.2:c.1051A>G	chr1.hg19:g.101194785A>G	ENSP00000294728:p.Ile351Val	163.0	0.0		198.0	73.0	NM_001078	A8K6R7|B4DKS4|E9PDD1|Q6NUP8	Missense_Mutation	SNP	ENST00000294728.2	hg19	CCDS773.1	.	.	.	.	.	.	.	.	.	.	A	6.714	0.500487	0.12822	.	.	ENSG00000162692	ENST00000370119;ENST00000294728	T;T	0.53423	0.62;2.96	5.41	3.07	0.35406	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.864402	0.10744	N	0.639117	T	0.27594	0.0678	M	0.81341	2.54	0.80722	D	1	B;B	0.22414	0.032;0.069	B;B	0.25614	0.062;0.062	T	0.19976	-1.0289	10	0.22706	T	0.39	-4.5994	4.2123	0.10517	0.677:0.1302:0.0681:0.1247	.	289;351	E9PDD1;P19320	.;VCAM1_HUMAN	V	289;351	ENSP00000359137:I289V;ENSP00000294728:I351V	ENSP00000294728:I351V	I	+	1	0	VCAM1	100967373	0.997000	0.39634	0.839000	0.33178	0.249000	0.25844	0.929000	0.28844	0.489000	0.27749	0.533000	0.62120	ATA	.	.		0.542	VCAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030213.1	NM_001078		G	101194785	A	G	101194785	3	3	297	1	0	0	0	0	1	0	0	0	17152	333	12	2	1069	2	VCAM1	1	101194785	Missense_Mutation	SNP	A	TCGA-G3-AAV1-01A-11D-A382-10	7545139	101194785	148055836	4	43144										
SPAG17	200162	hgsc.bcm.edu	37	chr1	118584651	118584651	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	tcttctgctaatcgatgttgCtcttctttccatgcctgtaa	6	11	4	0			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr1:118584651C>T	ENST00000336338.5	-	21	2894	c.2829G>A	c.(2827-2829)gaG>gaA	p.E943E		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	943						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		ATCGATGTTGCTCTTCTTTCC	0.358																																					p.E943E		Atlas-SNP	.											.	SPAG17	263	.	0			c.G2829A						.						169	162	164					1																	118584651		2203	4300	6503	SO:0001819	synonymous_variant	200162	exon21			ATGTTGCTCTTCT		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.2829G>A	chr1.hg19:g.118584651C>T		82.0	0.0		97.0	28.0	NM_206996	Q8NAZ1|Q9NT21	Silent	SNP	ENST00000336338.5	hg19	CCDS899.1																																																																																			.	.		0.358	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		T	118584651	C	T	118584651	2	4	297	1	0	0	0	0	0	0	0	1	14994	796	28	3		3	SPAG17	1	118584651	Silent	SNP	C	TCGA-G3-AAV1-01A-11D-A382-10	17389866	118584651	130665970	5	43145										
ATF3	467	hgsc.bcm.edu	37	chr1	212792748	212792748	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	ctgaactgaaggctcagattGaggagctcaagaacgagaag	13	7	2	6			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr1:212792748G>A	ENST00000341491.4	+	4	662	c.397G>A	c.(397-399)Gag>Aag	p.E133K	ATF3_ENST00000492118.1_3'UTR|ATF3_ENST00000366987.2_Missense_Mutation_p.E133K|ATF3_ENST00000366985.1_Missense_Mutation_p.E76K|ATF3_ENST00000366983.1_3'UTR	NM_001040619.2|NM_001206488.2|NM_001674.3	NP_001035709.1|NP_001193417.2|NP_001665.1	P18847	ATF3_HUMAN	activating transcription factor 3	133	Leucine-zipper. {ECO:0000255|PROSITE- ProRule:PRU00978}.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|gluconeogenesis (GO:0006094)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	6				OV - Ovarian serous cystadenocarcinoma(81;0.00628)|all cancers(67;0.0097)|GBM - Glioblastoma multiforme(131;0.0388)|Epithelial(68;0.0933)	Pseudoephedrine(DB00852)	GGCTCAGATTGAGGAGCTCAA	0.517																																					p.E133K		Atlas-SNP	.											.	ATF3	22	.	0			c.G397A						.						114	100	105					1																	212792748		2203	4300	6503	SO:0001583	missense	467	exon4			CAGATTGAGGAGC	L19871	CCDS1506.1, CCDS41464.1, CCDS55688.1, CCDS58059.1	1q32.3	2013-01-10			ENSG00000162772	ENSG00000162772		"basic leucine zipper proteins"	785	protein-coding gene	gene with protein product		603148				7515060	Standard	NM_001674		Approved		uc021pit.1	P18847	OTTHUMG00000036747	ENST00000341491.4:c.397G>A	chr1.hg19:g.212792748G>A	ENSP00000344352:p.Glu133Lys	79.0	0.0		124.0	41.0	NM_001674	Q5VTZ2|Q6ICQ9|Q7Z566|Q8WYM6	Missense_Mutation	SNP	ENST00000341491.4	hg19	CCDS1506.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.948807	0.92660	.	.	ENSG00000162772	ENST00000366981;ENST00000366987;ENST00000341491;ENST00000366985	T;T;T;T	0.55588	0.51;0.51;0.51;0.51	6.17	5.26	0.73747	Basic-leucine zipper (bZIP) transcription factor (2);bZIP transcription factor, bZIP-1 (1);	0.042570	0.85682	D	0.000000	T	0.55162	0.1903	L	0.49513	1.565	0.80722	D	1	P	0.35328	0.495	B	0.42555	0.391	T	0.50224	-0.8853	10	0.23891	T	0.37	-0.2071	17.6945	0.88277	0.0:0.1227:0.8773:0.0	.	133	P18847	ATF3_HUMAN	K	133;133;133;76	ENSP00000355948:E133K;ENSP00000355954:E133K;ENSP00000344352:E133K;ENSP00000355952:E76K	ENSP00000344352:E133K	E	+	1	0	ATF3	210859371	1.000000	0.71417	0.959000	0.39883	0.954000	0.61252	6.532000	0.73825	1.611000	0.50210	0.655000	0.94253	GAG	.	.		0.517	ATF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089296.1	NM_001674		A	212792748	G	A	212792748	3	1	297	1	0	0	0	0	1	0	0	0	1081	1291	45	3	471	3	ATF3	1	212792748	Missense_Mutation	SNP	G	TCGA-G3-AAV1-01A-11D-A382-10	94208097	212792748	36457873	6	43146										
DISP1	84976	hgsc.bcm.edu	37	chr1	223116176	223116176	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	aaattggagcatggctatgaGcaatggaaacaatgattttg	11	4	0	2			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr1:223116176G>A	ENST00000284476.6	+	2	175	c.11G>A	c.(10-12)aGc>aAc	p.S4N	DISP1_ENST00000495684.1_Intron|DISP1_ENST00000360254.2_Missense_Mutation_p.S4N	NM_032890.3	NP_116279.2	Q96F81	DISP1_HUMAN	dispatched homolog 1 (Drosophila)	4					determination of left/right symmetry (GO:0007368)|diaphragm development (GO:0060539)|dorsal/ventral pattern formation (GO:0009953)|embryonic pattern specification (GO:0009880)|patched ligand maturation (GO:0007225)|peptide transport (GO:0015833)|protein homotrimerization (GO:0070207)|regulation of protein secretion (GO:0050708)|smoothened signaling pathway (GO:0007224)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)|peptide transporter activity (GO:0015197)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(20)|lung(25)|prostate(4)|skin(1)|stomach(1)|urinary_tract(5)	69				GBM - Glioblastoma multiforme(131;0.102)		ATGGCTATGAGCAATGGAAAC	0.458																																					p.S4N		Atlas-SNP	.											.	DISP1	145	.	0			c.G11A						.						94	88	90					1																	223116176		2203	4300	6503	SO:0001583	missense	84976	exon4			CTATGAGCAATGG	AK056569	CCDS1536.1	1q42.12	2008-02-05			ENSG00000154309	ENSG00000154309			19711	protein-coding gene	gene with protein product		607502				10619433	Standard	NM_032890		Approved	DISPA, MGC13130, DKFZP434I0428, MGC16796	uc001hnu.2	Q96F81	OTTHUMG00000037893	ENST00000284476.6:c.11G>A	chr1.hg19:g.223116176G>A	ENSP00000284476:p.Ser4Asn	111.0	0.0		153.0	7.0	NM_032890	Q8N7C2|Q96I92|Q9H698|Q9H8H9|Q9UFA2	Missense_Mutation	SNP	ENST00000284476.6	hg19	CCDS1536.1	.	.	.	.	.	.	.	.	.	.	G	14.54	2.567095	0.45694	.	.	ENSG00000154309	ENST00000360254;ENST00000284476	T;D	0.93426	0.63;-3.22	5.77	3.86	0.44501	.	0.152863	0.56097	D	0.000032	D	0.88897	0.6562	L	0.46157	1.445	0.27661	N	0.947087	B	0.11235	0.004	B	0.11329	0.006	T	0.80054	-0.1543	10	0.44086	T	0.13	-17.7172	7.1702	0.25715	0.1408:0.0:0.7165:0.1427	.	4	Q96F81	DISP1_HUMAN	N	4	ENSP00000355848:S4N;ENSP00000284476:S4N	ENSP00000284476:S4N	S	+	2	0	DISP1	221182799	0.995000	0.38212	0.994000	0.49952	0.997000	0.91878	2.180000	0.42537	0.743000	0.32719	0.650000	0.86243	AGC	.	.		0.458	DISP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092512.1	NM_032890		A	223116176	G	A	223116176	3	1	297	1	0	0	0	0	1	0	0	0	4541	971	34	3	13	3	DISP1	1	223116176	Missense_Mutation	SNP	G	TCGA-G3-AAV1-01A-11D-A382-10	10323428	223116176	26134445	7	43147										
OTOF	9381	hgsc.bcm.edu	37	chr2	26681020	26681020	+	3'UTR	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	tgatgatgagccacttgtacCgggtgcagatgaggtacttg	14	7	0	5			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr2:26681020C>A	ENST00000272371.2	-	0	6206				OTOF_ENST00000339598.3_Missense_Mutation_p.R1194L|OTOF_ENST00000403946.3_Missense_Mutation_p.R1961L|OTOF_ENST00000338581.6_3'UTR|OTOF_ENST00000402415.3_3'UTR	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin						membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			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)					CCACTTGTACCGGGTGCAGAT	0.582																																					p.R1194L	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											.	OTOF	524	.	0			c.G3581T						.						92	79	84					2																	26681020		2203	4300	6503	SO:0001624	3_prime_UTR_variant	9381	exon29			TTGTACCGGGTGC	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"fer-1-like family member 2"	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.*86G>T	chr2.hg19:g.26681020C>A		135.0	0.0		163.0	67.0	NM_194323	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Missense_Mutation	SNP	ENST00000272371.2	hg19	CCDS1725.1	.	.	.	.	.	.	.	.	.	.	C	17.61	3.431724	0.62844	.	.	ENSG00000115155	ENST00000339598;ENST00000403946;ENST00000361394	T;T	0.81247	-1.2;-1.47	4.93	4.06	0.47325	.	.	.	.	.	T	0.73984	0.3657	.	.	.	0.31931	N	0.612168	B	0.26120	0.142	B	0.26310	0.068	T	0.74253	-0.3725	8	0.44086	T	0.13	.	13.0503	0.58950	0.0:0.9207:0.0:0.0793	.	1194	Q9HC10-2	.	L	1194;1961;44	ENSP00000344521:R1194L;ENSP00000385255:R1961L	ENSP00000344521:R1194L	R	-	2	0	OTOF	26534524	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	4.909000	0.63314	1.069000	0.40788	0.551000	0.68910	CGG	.	.		0.582	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3			A	26681020	C	A	26681020	1	1	297	0	1	0	0	0	0	0	0	0	11312	652	23	1		1	OTOF	2	26681020	3'UTR	SNP	C	TCGA-G3-AAV1-01A-11D-A382-10		26681020	216518353	8	43148										
MRPL35	51318	hgsc.bcm.edu	37	chr2	86433255	86433255	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	tacggcccctgaatattttgGcatcttcaacctaccgcaac	6	14	2	1	rs17851803		TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr2:86433255G>T	ENST00000337109.4	+	2	104	c.70G>T	c.(70-72)Gca>Tca	p.A24S	MRPL35_ENST00000409180.1_Missense_Mutation_p.A24S|MRPL35_ENST00000605125.1_Missense_Mutation_p.A24S|MRPL35_ENST00000254644.8_Missense_Mutation_p.A24S	NM_016622.3	NP_057706.2	Q9NZE8	RM35_HUMAN	mitochondrial ribosomal protein L35	24			A -> T (in dbSNP:rs17851803). {ECO:0000269|PubMed:15489334}.		translation (GO:0006412)	mitochondrial ribosome (GO:0005761)	structural constituent of ribosome (GO:0003735)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(4)|skin(1)|stomach(1)|urinary_tract(2)	14						GAATATTTTGGCATCTTCAAC	0.378																																					p.A24S		Atlas-SNP	.											.	MRPL35	23	.	0			c.G70T						.						158	155	156					2																	86433255		2203	4300	6503	SO:0001583	missense	51318	exon2			ATTTTGGCATCTT	AF208849	CCDS1987.1, CCDS1988.1	2p11.2	2012-09-13			ENSG00000132313	ENSG00000132313		"Mitochondrial ribosomal proteins / large subunits"	14489	protein-coding gene	gene with protein product		611841				11042152, 11551941	Standard	NM_016622		Approved		uc002srg.4	Q9NZE8	OTTHUMG00000037385	ENST00000337109.4:c.70G>T	chr2.hg19:g.86433255G>T	ENSP00000338389:p.Ala24Ser	352.0	1.0		426.0	167.0	NM_016622	A6NKV6|B2RB93|Q658U7|Q8WWA2	Missense_Mutation	SNP	ENST00000337109.4	hg19	CCDS1988.1	.	.	.	.	.	.	.	.	.	.	G	17.36	3.370309	0.61624	.	.	ENSG00000132313	ENST00000254644;ENST00000337109;ENST00000409180	T;T;T	0.15139	2.48;2.71;2.45	5.62	5.62	0.85841	.	0.594515	0.18878	N	0.128652	T	0.20088	0.0483	L	0.60455	1.87	0.29229	N	0.873397	B	0.31318	0.319	B	0.30105	0.111	T	0.05649	-1.0872	10	0.30078	T	0.28	-1.2034	15.5672	0.76303	0.0:0.0:1.0:0.0	.	24	Q9NZE8	RM35_HUMAN	S	24	ENSP00000254644:A24S;ENSP00000338389:A24S;ENSP00000386255:A24S	ENSP00000254644:A24S	A	+	1	0	MRPL35	86286766	0.998000	0.40836	0.581000	0.28614	0.971000	0.66376	3.301000	0.51842	2.820000	0.97059	0.650000	0.86243	GCA	.	G|1.000;|0.000		0.378	MRPL35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091002.2	NM_016622		T	86433255	G	T	86433255	3	4	297	1	0	0	0	0	1	0	0	0	9807	1203	42	3	76	3	MRPL35	2	86433255	Missense_Mutation	SNP	G	TCGA-G3-AAV1-01A-11D-A382-10	59752235	86433255	156766118	9	43149										
IL1F8	27177	hgsc.bcm.edu	37	chr2	113785625	113785635	+	Intron	DEL	TTATTGTGGAA	TTATTGTGGAA	-													0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	agacagaagtggagccttctTtattgtggaaaaagagaaag							TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	TTATTGTGGAA	TTATTGTGGAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr2:113785625_113785635delTTATTGTGGAA	ENST00000259213.4	-	4	369				IL36B_ENST00000327407.2_Frame_Shift_Del_p.FHNK107fs	NM_014438.3	NP_055253.2	Q9NZH7	IL36B_HUMAN	interleukin 36, beta						immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of T cell differentiation (GO:0045582)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	interleukin-1 receptor binding (GO:0005149)	p.N109N(1)		kidney(1)|ovary(1)|pancreas(1)	3						GGAGCCTTCTTTATTGTGGAAAAAGAGAAAG	0.474																																					p.107_110del		Atlas-INDEL	.											.	IL36B	69	.	1	Substitution - coding silent(1)	lung(1)	c.320_330del						.																																			SO:0001627	intron_variant	27177	exon5			.	AF201833	CCDS2109.1, CCDS2110.1	2q14	2011-07-14	2011-06-06	2011-06-06	ENSG00000136696	ENSG00000136696		"Interleukins and interleukin receptors"	15564	protein-coding gene	gene with protein product		605508	"interleukin 1 family, member 8 (eta)"	IL1F8		10625660, 10512743, 16646978	Standard	NM_173178		Approved	FIL1, IL-1H2, IL-1F8, FILI-(ETA), IL1-ETA, IL1H2, MGC126880, MGC126882	uc002tiq.1	Q9NZH7	OTTHUMG00000131338	ENST00000259213.4:c.261+880TTCCACAATAA>-	chr2.hg19:g.113785625_113785635delTTATTGTGGAA		73.0	0.0		104.0	26.0	NM_173178	Q3MIH0|Q53SR6|Q7RTZ7|Q9UHA5	Frame_Shift_Del	DEL	ENST00000259213.4	hg19	CCDS2109.1																																																																																			.	.		0.474	IL36B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254110.1	NM_014438		-	113785635	TTATTGTGGAA	-	113785625	6	5	297	0	1	1	0	1	0	0	0	0	7665	1841	64	0		0	IL1F8	2	113785625	Intron	DEL	TTATTGTGGAA	TCGA-G3-AAV1-01A-11D-A382-10	27352370	113785625	129413748	10	43150										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196799358	196799358	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	ctctctctaattcaaccaacCacttctccacttgacctctg	2	17	5	1			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr2:196799358C>A	ENST00000312428.6	-	21	3528	c.3428G>T	c.(3427-3429)tGg>tTg	p.W1143L		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	1143	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						TTCAACCAACCACTTCTCCAC	0.373																																					p.W1143L		Atlas-SNP	.											.	DNAH7	512	.	0			c.G3428T						.						185	179	181					2																	196799358		1856	4112	5968	SO:0001583	missense	56171	exon21			ACCAACCACTTCT	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.3428G>T	chr2.hg19:g.196799358C>A	ENSP00000311273:p.Trp1143Leu	193.0	0.0		201.0	77.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	hg19	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	C	32	5.116190	0.94339	.	.	ENSG00000118997	ENST00000312428	T	0.71341	-0.56	5.72	5.72	0.89469	Dynein heavy chain, domain-2 (1);	0.000000	0.85682	D	0.000000	D	0.91942	0.7448	H	0.99545	4.62	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95125	0.8250	10	0.87932	D	0	.	19.474	0.94979	0.0:1.0:0.0:0.0	.	1143	Q8WXX0	DYH7_HUMAN	L	1143	ENSP00000311273:W1143L	ENSP00000311273:W1143L	W	-	2	0	DNAH7	196507603	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.661000	0.83786	2.695000	0.91970	0.655000	0.94253	TGG	.	.		0.373	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		A	196799358	C	A	196799358	3	1	297	1	0	0	0	0	1	0	0	0	4608	595	21	3	8826	3	DNAH7	2	196799358	Missense_Mutation	SNP	C	TCGA-G3-AAV1-01A-11D-A382-10	83013733	196799358	46400015	11	43151										
SF3B1	23451	hgsc.bcm.edu	37	chr2	198274569	198274569	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	gcctccatggcctggtgtcgCatggcctggtgtatcacctc	12	14	1	0			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr2:198274569C>A	ENST00000335508.6	-	7	920	c.829G>T	c.(829-831)Gcg>Tcg	p.A277S		NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	277	Interaction with PPP1R8.|U2AF homology region; mediates interaction with RMB39.				anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)			NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			CCTGGTGTCGCATGGCCTGGT	0.547			Mis		myelodysplastic syndrome																																p.A277S		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	.	SF3B1	1038	.	0			c.G829T						.						222	220	221					2																	198274569		2203	4300	6503	SO:0001583	missense	23451	exon7			GTGTCGCATGGCC	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"splicing factor 3b, subunit 1, 155kD"			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.829G>T	chr2.hg19:g.198274569C>A	ENSP00000335321:p.Ala277Ser	142.0	0.0		155.0	60.0	NM_012433	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	hg19	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	C	14.13	2.442572	0.43326	.	.	ENSG00000115524	ENST00000335508	.	.	.	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.57140	0.2033	N	0.22421	0.69	0.80722	D	1	P	0.44690	0.841	P	0.54210	0.745	T	0.48115	-0.9063	9	0.11485	T	0.65	.	19.0839	0.93194	0.0:1.0:0.0:0.0	.	277	O75533	SF3B1_HUMAN	S	277	.	ENSP00000335321:A277S	A	-	1	0	SF3B1	197982814	1.000000	0.71417	0.731000	0.30826	0.485000	0.33311	7.729000	0.84864	2.502000	0.84385	0.655000	0.94253	GCG	.	.		0.547	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			A	198274569	C	A	198274569	3	1	297	1	0	0	0	0	1	0	0	0	14164	710	25	3	3161	3	SF3B1	2	198274569	Missense_Mutation	SNP	C	TCGA-G3-AAV1-01A-11D-A382-10	1475211	198274569	44924804	12	43152										
ABCA12	26154	hgsc.bcm.edu	37	chr2	215848388	215848388	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	tgcctttttacttcctcgtgGagctgctttttagtccagtg	9	10	0	0			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr2:215848388G>A	ENST00000272895.7	-	29	4584	c.4365C>T	c.(4363-4365)ctC>ctT	p.L1455L	ABCA12_ENST00000389661.4_Silent_p.L1137L	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1455	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		CTTCCTCGTGGAGCTGCTTTT	0.433																																					p.L1455L	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											.	ABCA12	368	.	0			c.C4365T						.						171	155	161					2																	215848388		2203	4300	6503	SO:0001819	synonymous_variant	26154	exon29			CTCGTGGAGCTGC	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.4365C>T	chr2.hg19:g.215848388G>A		121.0	0.0		130.0	56.0	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Silent	SNP	ENST00000272895.7	hg19	CCDS33372.1																																																																																			.	.		0.433	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		A	215848388	G	A	215848388	2	1	297	1	0	0	0	0	0	0	0	1	30	1161	41	3		3	ABCA12	2	215848388	Silent	SNP	G	TCGA-G3-AAV1-01A-11D-A382-10	17573819	215848388	27350985	13	43153										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266098	41266098	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	gcagcaacagtcttacctggActctggaatccattctggtg	10	11	3	0	rs121913396|rs121913416		TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr3:41266098A>G	ENST00000349496.5	+	3	375	c.95A>G	c.(94-96)gAc>gGc	p.D32G	CTNNB1_ENST00000396185.3_Missense_Mutation_p.D32G|CTNNB1_ENST00000405570.1_Missense_Mutation_p.D32G|CTNNB1_ENST00000396183.3_Missense_Mutation_p.D32G|CTNNB1_ENST00000453024.1_Missense_Mutation_p.D25G	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	32			D -> A (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|D -> G (in PTR and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629}.|D -> Y (in PTR, hepatoblastoma and hepatocellular carcinoma; dbSNP:rs28931588). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:11703283, ECO:0000269|PubMed:9927029}.|Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.D32G(65)|p.A5_A80del(53)|p.D32V(33)|p.D32A(16)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.WQQQSYLD25?(5)|p.W25_D32del(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.S29_H36del(1)|p.D32del(1)|p.M14_S45del(1)|p.Q28_D32>H(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.D32fs*9(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TCTTACCTGGACTCTGGAATC	0.483	D32V(HEC265_ENDOMETRIUM)|D32V(HEC6_ENDOMETRIUM)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.D32G	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,+1,128	CTNNB1	4904	.	260	Deletion - In frame(120)|Substitution - Missense(114)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(154)|large_intestine(24)|pancreas(19)|central_nervous_system(16)|stomach(14)|endometrium(7)|skin(7)|ovary(4)|prostate(3)|pituitary(3)|small_intestine(2)|NS(2)|adrenal_gland(1)|soft_tissue(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)	c.A95G						.						92	77	82					3																	41266098		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	ACCTGGACTCTGG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.95A>G	chr3.hg19:g.41266098A>G	ENSP00000344456:p.Asp32Gly	161.0	0.0		258.0	84.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.308122	0.81247	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.50001	0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.69788	0.3150	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.74137	-0.3762	10	0.87932	D	0	0.3843	16.0676	0.80897	1.0:0.0:0.0:0.0	.	32	P35222	CTNB1_HUMAN	G	25;32;32;32;32;25;32;32;32	ENSP00000400508:D25G;ENSP00000385604:D32G;ENSP00000412219:D32G;ENSP00000379486:D32G;ENSP00000344456:D32G;ENSP00000411226:D25G;ENSP00000379488:D32G;ENSP00000409302:D32G;ENSP00000401599:D32G	ENSP00000344456:D32G	D	+	2	0	CTNNB1	41241102	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.201000	0.70794	0.533000	0.62120	GAC	.	.		0.483	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266098	A	G	41266098	3	3	297	1	0	0	0	0	1	0	0	0	4018	275	10	2	101	2	CTNNB1	3	41266098	Missense_Mutation	SNP	A	TCGA-G3-AAV1-01A-11D-A382-10		41266098	156756332	14	43154										
CACNA2D2	9254	hgsc.bcm.edu	37	chr3	50404287	50404287	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	gaggctggtcttggtgggtaCggttgctggctagcaccttg	17	8	1	0			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr3:50404287C>T	ENST00000479441.1	-	30	2584	c.2585G>A	c.(2584-2586)cGt>cAt	p.R862H	CACNA2D2_ENST00000424201.2_Missense_Mutation_p.R855H|CACNA2D2_ENST00000266039.3_Missense_Mutation_p.R855H|XXcos-LUCA11.4_ENST00000606259.1_RNA|CACNA2D2_ENST00000423994.2_Missense_Mutation_p.R862H|CACNA2D2_ENST00000395083.1_Missense_Mutation_p.R855H|CACNA2D2_ENST00000429770.1_Missense_Mutation_p.R855H|CACNA2D2_ENST00000435965.1_Missense_Mutation_p.R862H|XXcos-LUCA11.4_ENST00000607583.1_RNA|CACNA2D2_ENST00000360963.3_Missense_Mutation_p.R786H|XXcos-LUCA11.4_ENST00000607088.1_RNA|XXcos-LUCA11.4_ENST00000607362.1_RNA|XXcos-LUCA11.5_ENST00000606589.1_Intron|XXcos-LUCA11.4_ENST00000606665.1_RNA|XXcos-LUCA11.4_ENST00000607121.1_RNA			Q9NY47	CA2D2_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 2	862					energy reserve metabolic process (GO:0006112)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|positive regulation of organ growth (GO:0046622)|regulation of insulin secretion (GO:0050796)|regulation of multicellular organism growth (GO:0040014)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|cervix(1)|endometrium(4)|large_intestine(4)|lung(8)|ovary(2)|prostate(4)|skin(4)|urinary_tract(1)	31				BRCA - Breast invasive adenocarcinoma(193;0.000365)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)	Amiodarone(DB01118)|Bepridil(DB01244)|Felodipine(DB01023)|Gabapentin(DB00996)|Isradipine(DB00270)|Nitrendipine(DB01054)|Spironolactone(DB00421)	TTGGTGGGTACGGTTGCTGGC	0.617																																					p.R862H		Atlas-SNP	.											.	CACNA2D2	82	.	0			c.G2585A						.						64	54	57					3																	50404287		2202	4299	6501	SO:0001583	missense	9254	exon30			TGGGTACGGTTGC	AF040709	CCDS33763.1, CCDS54588.1, CCDS63647.1	3p21.3	2004-02-27			ENSG00000007402	ENSG00000007402		"Calcium channel subunits"	1400	protein-coding gene	gene with protein product	"gene 26"	607082					Standard	XM_005265581		Approved	KIAA0558	uc003daq.3	Q9NY47	OTTHUMG00000156887	ENST00000479441.1:c.2585G>A	chr3.hg19:g.50404287C>T	ENSP00000418081:p.Arg862His	46.0	0.0		52.0	6.0	NM_001174051	A7MD15|Q9NY48|Q9UEW0|Q9Y268	Missense_Mutation	SNP	ENST00000479441.1	hg19	CCDS54588.1	.	.	.	.	.	.	.	.	.	.	C	11.61	1.689400	0.29962	.	.	ENSG00000007402	ENST00000423994;ENST00000429770;ENST00000266039;ENST00000360963;ENST00000435965;ENST00000395083;ENST00000424201;ENST00000479441	T;T;T;T;T;T;T;T	0.74209	-0.82;-0.82;-0.82;-0.82;-0.82;-0.82;-0.82;-0.82	5.22	5.22	0.72569	.	0.946890	0.08901	N	0.877207	T	0.58793	0.2147	N	0.08118	0	0.35394	D	0.790977	B;B	0.15930	0.011;0.015	B;B	0.08055	0.002;0.003	T	0.50406	-0.8832	10	0.13853	T	0.58	-6.9204	17.359	0.87345	0.0:1.0:0.0:0.0	.	862;855	Q9NY47;Q9NY47-2	CA2D2_HUMAN;.	H	862;855;855;786;862;855;855;862	ENSP00000407393:R862H;ENSP00000404631:R855H;ENSP00000266039:R855H;ENSP00000354228:R786H;ENSP00000390526:R862H;ENSP00000378519:R855H;ENSP00000390329:R855H;ENSP00000418081:R862H	ENSP00000266039:R855H	R	-	2	0	CACNA2D2	50379291	0.995000	0.38212	1.000000	0.80357	0.995000	0.86356	3.024000	0.49674	2.436000	0.82500	0.655000	0.94253	CGT	.	.		0.617	CACNA2D2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346457.1	NM_006030		T	50404287	C	T	50404287	3	4	297	1	0	0	0	0	1	0	0	0	2551	536	19	1	913	1	CACNA2D2	3	50404287	Missense_Mutation	SNP	C	TCGA-G3-AAV1-01A-11D-A382-10	9138189	50404287	147618143	15	43155										
CADPS	8618	hgsc.bcm.edu	37	chr3	62648033	62648033	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	tagacgtccatccagctctcGtctgatctgggctgcttgct	10	13	3	2			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr3:62648033G>T	ENST00000383710.4	-	4	1274	c.925C>A	c.(925-927)Cga>Aga	p.R309R	CADPS_ENST00000283269.9_Silent_p.R309R|CADPS_ENST00000490353.2_Silent_p.R309R|CADPS_ENST00000357948.3_Silent_p.R309R	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	309					catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		TCCAGCTCTCGTCTGATCTGG	0.493																																					p.R309R		Atlas-SNP	.											.	CADPS	387	.	0			c.C925A						.						165	136	146					3																	62648033		2203	4300	6503	SO:0001819	synonymous_variant	8618	exon4			GCTCTCGTCTGAT	U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"Pleckstrin homology (PH) domain containing"	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.925C>A	chr3.hg19:g.62648033G>T		67.0	0.0		42.0	24.0	NM_003716	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Silent	SNP	ENST00000383710.4	hg19	CCDS46858.1																																																																																			.	.		0.493	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394		T	62648033	G	T	62648033	2	4	297	1	0	0	0	0	0	0	0	1	2572	1153	40	1		1	CADPS	3	62648033	Silent	SNP	G	TCGA-G3-AAV1-01A-11D-A382-10	12243746	62648033	135374397	16	43156										
LRIG1	26018	hgsc.bcm.edu	37	chr3	66430695	66430695	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	ggtagacaaaacctagctttTtggtgccaacagcagtggca	11	9	0	1	rs199537042		TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr3:66430695T>G	ENST00000273261.3	-	19	3798	c.3274A>C	c.(3274-3276)Aaa>Caa	p.K1092Q	LRIG1_ENST00000383703.3_Missense_Mutation_p.K1069Q|LRIG1_ENST00000496559.2_5'UTR|SLC25A26_ENST00000536651.1_3'UTR	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	1092					innervation (GO:0060384)|otolith morphogenesis (GO:0032474)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)				NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		ACCTAGCTTTTTGGTGCCAAC	0.552																																					p.K1092Q		Atlas-SNP	.											.	LRIG1	138	.	0			c.A3274C						.						58	55	56					3																	66430695		2203	4300	6503	SO:0001583	missense	26018	exon19			AGCTTTTTGGTGC	AB050468	CCDS33783.1	3p14	2013-01-14			ENSG00000144749	ENSG00000144749		"Immunoglobulin superfamily / I-set domain containing"	17360	protein-coding gene	gene with protein product	"ortholog of mouse integral membrane glycoprotein LIG-1", "leucine-rich repeat protein LRIG1"	608868				11414704, 12234026	Standard	NM_015541		Approved	LIG-1, DKFZP586O1624, LIG1	uc003dmx.3	Q96JA1	OTTHUMG00000158727	ENST00000273261.3:c.3274A>C	chr3.hg19:g.66430695T>G	ENSP00000273261:p.Lys1092Gln	81.0	0.0		74.0	26.0	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Missense_Mutation	SNP	ENST00000273261.3	hg19	CCDS33783.1	.	.	.	.	.	.	.	.	.	.	T	10.68	1.418757	0.25552	.	.	ENSG00000144749	ENST00000273261;ENST00000383703;ENST00000383702	T;T	0.64260	-0.09;-0.04	5.27	2.8	0.32819	.	0.480260	0.19445	N	0.114081	T	0.47783	0.1464	N	0.24115	0.695	0.21841	N	0.999518	B;B;B	0.14438	0.01;0.005;0.003	B;B;B	0.18561	0.022;0.003;0.007	T	0.40175	-0.9577	10	0.51188	T	0.08	.	12.1617	0.54107	0.0:0.0:0.2707:0.7292	.	1069;1092;1092	Q96JA1-2;Q5XWD3;Q96JA1	.;.;LRIG1_HUMAN	Q	1092;1069;995	ENSP00000273261:K1092Q;ENSP00000373208:K1069Q	ENSP00000273261:K1092Q	K	-	1	0	LRIG1	66513385	0.437000	0.25593	0.729000	0.30791	0.078000	0.17371	2.453000	0.44970	0.290000	0.22444	-0.313000	0.08912	AAA	.	.		0.552	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541		G	66430695	T	G	66430695	3	3	297	1	0	0	0	0	1	0	0	0	8953	1850	64	5	11	5	LRIG1	3	66430695	Missense_Mutation	SNP	T	TCGA-G3-AAV1-01A-11D-A382-10	3782662	66430695	131591735	17	43157										
EPHA3	2042	hgsc.bcm.edu	37	chr3	89259351	89259351	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	gaccgtattctgaagctcaaCactgagattagagaagtagg	11	7	2	3			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr3:89259351C>T	ENST00000336596.2	+	3	720	c.495C>T	c.(493-495)aaC>aaT	p.N165N	EPHA3_ENST00000452448.2_Silent_p.N165N|EPHA3_ENST00000494014.1_Silent_p.N165N	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	165	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		TGAAGCTCAACACTGAGATTA	0.418										TSP Lung(6;0.00050)																											p.N165N		Atlas-SNP	.											.	EPHA3	501	.	0			c.C495T						.						157	136	143					3																	89259351		2203	4300	6503	SO:0001819	synonymous_variant	2042	exon3			GCTCAACACTGAG	M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3387	protein-coding gene	gene with protein product		179611	"EphA3"	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.495C>T	chr3.hg19:g.89259351C>T		117.0	0.0		106.0	45.0	NM_005233	Q9H2V3|Q9H2V4	Silent	SNP	ENST00000336596.2	hg19	CCDS2922.1																																																																																			.	.		0.418	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		T	89259351	C	T	89259351	2	4	297	1	0	0	0	0	0	0	0	1	5170	477	17	3		3	EPHA3	3	89259351	Silent	SNP	C	TCGA-G3-AAV1-01A-11D-A382-10	22828656	89259351	108763079	18	43158										
IFT122	55764	hgsc.bcm.edu	37	chr3	129239078	129239078	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	catggctgctgcccctactgCcgcaggtgcaaggatgaccc	12	15	0	1			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr3:129239078C>G	ENST00000348417.2	+	30	3773	c.3696C>G	c.(3694-3696)tgC>tgG	p.C1232W	IFT122_ENST00000504021.1_Missense_Mutation_p.C1109W|IFT122_ENST00000347300.2_Missense_Mutation_p.C1173W|IFT122_ENST00000507564.1_Missense_Mutation_p.C1225W|IFT122_ENST00000296266.3_Missense_Mutation_p.C1283W|IFT122_ENST00000440957.2_Missense_Mutation_p.C1023W|IFT122_ENST00000431818.2_Missense_Mutation_p.C1082W|IFT122_ENST00000349441.2_Missense_Mutation_p.C1122W	NM_052989.1	NP_443715.1	Q9HBG6	IF122_HUMAN	intraflagellar transport 122	1232					camera-type eye morphogenesis (GO:0048593)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|establishment of protein localization to organelle (GO:0072594)|intraciliary anterograde transport (GO:0035720)|intraciliary retrograde transport (GO:0035721)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|protein localization to cilium (GO:0061512)|signal transduction downstream of smoothened (GO:0007227)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|intraciliary transport particle A (GO:0030991)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)				breast(3)|cervix(1)|endometrium(9)|large_intestine(10)|lung(21)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	52						GCCCCTACTGCCGCAGGTGCA	0.587																																					p.C1283W		Atlas-SNP	.											.	IFT122	117	.	0			c.C3849G						.						78	64	68					3																	129239078		2203	4300	6503	SO:0001583	missense	55764	exon31			CTACTGCCGCAGG	AF244930	CCDS3059.1, CCDS3060.1, CCDS3061.1, CCDS3062.1, CCDS63770.1, CCDS63772.1, CCDS63773.1	3q21	2014-07-03	2014-07-03	2005-11-02	ENSG00000163913	ENSG00000163913		"WD repeat domain containing", "Intraflagellar transport homologs"	13556	protein-coding gene	gene with protein product		606045	"WD repeat domain 10", "intraflagellar transport 122 homolog (Chlamydomonas)"	WDR10		11242542	Standard	NM_052985		Approved	WDR140, WDR10p, SPG	uc003emm.3	Q9HBG6	OTTHUMG00000159516	ENST00000348417.2:c.3696C>G	chr3.hg19:g.129239078C>G	ENSP00000324005:p.Cys1232Trp	24.0	0.0		31.0	5.0	NM_052985	B3KW53|B4DEY9|B4DPW7|E7EQF4|E9PDG2|E9PDX2|G3XAB1|H7C3C0|Q53G36|Q8TC06|Q9BTB9|Q9BTY4|Q9HAT9|Q9HBG5|Q9NV68|Q9UF80	Missense_Mutation	SNP	ENST00000348417.2	hg19	CCDS3061.1	.	.	.	.	.	.	.	.	.	.	C	16.91	3.251713	0.59212	.	.	ENSG00000163913	ENST00000347300;ENST00000296266;ENST00000507564;ENST00000431818;ENST00000504021;ENST00000349441;ENST00000348417;ENST00000446384;ENST00000440957	T;T;T;T;T;T;T;T	0.74526	-0.18;-0.85;-0.69;-0.65;-0.01;-0.02;-0.22;-0.6	5.69	2.84	0.33178	.	0.000000	0.85682	D	0.000000	D	0.85261	0.5656	M	0.85777	2.775	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;0.998;1.0;1.0;1.0;1.0;1.0;0.999;1.0	D;D;D;D;D;D;D;D;D;D	0.97110	0.997;1.0;0.987;1.0;0.999;0.999;0.999;1.0;0.993;0.997	D	0.85357	0.1105	10	0.87932	D	0	-25.7075	9.606	0.39634	0.0:0.5836:0.0:0.4164	.	1023;558;1225;620;1109;1074;1122;1173;1232;1283	E9PDG2;B3KUD1;E7EQF4;B3KT43;B4DEY9;B4DPW7;Q9BTY4;Q9HBG6-3;Q9HBG6;G3XAB1	.;.;.;.;.;.;.;.;IF122_HUMAN;.	W	1173;1283;1225;1082;1109;1122;1232;1074;1023	ENSP00000323973:C1173W;ENSP00000296266:C1283W;ENSP00000425536:C1225W;ENSP00000410946:C1082W;ENSP00000422179:C1109W;ENSP00000324165:C1122W;ENSP00000324005:C1232W;ENSP00000401569:C1023W	ENSP00000296266:C1283W	C	+	3	2	IFT122	130721768	0.997000	0.39634	1.000000	0.80357	0.941000	0.58515	0.541000	0.23207	0.714000	0.32081	0.563000	0.77884	TGC	.	.		0.587	IFT122-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355852.1	NM_018262		G	129239078	C	G	129239078	3	3	297	1	0	0	0	0	1	0	0	0	7564	747	26	4	3974	4	IFT122	3	129239078	Missense_Mutation	SNP	C	TCGA-G3-AAV1-01A-11D-A382-10	39979727	129239078	68783352	19	43159										
TMEM175	84286	hgsc.bcm.edu	37	chr4	944244	944244	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	gtacagaggcttctggcaacAcggattgccgtctacctgat	11	11	2	2			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr4:944244A>T	ENST00000264771.4	+	4	413	c.228A>T	c.(226-228)acA>acT	p.T76T	TMEM175_ENST00000504180.1_3'UTR|TMEM175_ENST00000508204.1_De_novo_Start_OutOfFrame|TMEM175_ENST00000515740.1_De_novo_Start_OutOfFrame	NM_032326.2	NP_115702.1	Q9BSA9	TM175_HUMAN	transmembrane protein 175	76						integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)				NS(1)|endometrium(1)|large_intestine(2)|lung(6)|pancreas(1)|upper_aerodigestive_tract(3)	14			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			TTCTGGCAACACGGATTGCCG	0.577																																					p.T76T		Atlas-SNP	.											.	TMEM175	44	.	0			c.A228T						.						131	114	120					4																	944244		2203	4300	6503	SO:0001819	synonymous_variant	84286	exon4			GGCAACACGGATT	BC005158	CCDS3341.1, CCDS75087.1, CCDS75088.1	4p16.3	2008-02-05			ENSG00000127419	ENSG00000127419			28709	protein-coding gene	gene with protein product						12477932	Standard	XM_005272301		Approved	MGC4618	uc003gbq.3	Q9BSA9	OTTHUMG00000118996	ENST00000264771.4:c.228A>T	chr4.hg19:g.944244A>T		149.0	0.0		177.0	83.0	NM_032326	D3DVN4|Q8ND13	Silent	SNP	ENST00000264771.4	hg19	CCDS3341.1																																																																																			.	.		0.577	TMEM175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239193.2	NM_032326		T	944244	A	T	944244	2	4	297	1	0	0	0	0	0	0	0	1	16106	146	6	4		4	TMEM175	4	944244	Silent	SNP	A	TCGA-G3-AAV1-01A-11D-A382-10		944244	190210032	20	43160										
EVC2	132884	hgsc.bcm.edu	37	chr4	5620343	5620343	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	tccatctgagcaaagcagccAtggacctcctgcctcatcct	7	16	2	1			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr4:5620343A>T	ENST00000344408.5	-	15	2621	c.2568T>A	c.(2566-2568)caT>caA	p.H856Q	EVC2_ENST00000344938.1_Missense_Mutation_p.H856Q|EVC2_ENST00000310917.2_Missense_Mutation_p.H776Q	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	856					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						CAAAGCAGCCATGGACCTCCT	0.567																																					p.H856Q		Atlas-SNP	.											.	EVC2	202	.	0			c.T2568A						.						36	33	34					4																	5620343		2203	4300	6503	SO:0001583	missense	132884	exon15			GCAGCCATGGACC	AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.2568T>A	chr4.hg19:g.5620343A>T	ENSP00000342144:p.His856Gln	147.0	0.0		159.0	83.0	NM_147127	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	hg19	CCDS3382.2	.	.	.	.	.	.	.	.	.	.	A	3.921	-0.018201	0.07681	.	.	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	T;T;T	0.73363	-0.74;-0.72;-0.73	5.3	-7.38	0.01407	.	0.000000	0.85682	D	0.000000	T	0.48223	0.1488	N	0.20986	0.625	0.09310	N	0.999993	B	0.17465	0.022	B	0.14023	0.01	T	0.44922	-0.9296	10	0.11485	T	0.65	-10.0435	9.8688	0.41162	0.3791:0.4641:0.1568:0.0	.	856	Q86UK5	LBN_HUMAN	Q	856;776;856	ENSP00000339954:H856Q;ENSP00000311683:H776Q;ENSP00000342144:H856Q	ENSP00000311683:H776Q	H	-	3	2	EVC2	5671244	0.330000	0.24705	0.069000	0.20011	0.711000	0.40976	-0.495000	0.06443	-1.498000	0.01824	-1.148000	0.01847	CAT	.	.		0.567	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127		T	5620343	A	T	5620343	3	4	297	1	0	0	0	0	1	0	0	0	5288	214	8	4	1390	4	EVC2	4	5620343	Missense_Mutation	SNP	A	TCGA-G3-AAV1-01A-11D-A382-10	4676099	5620343	185533933	21	43161										
PLRG1	5356	hgsc.bcm.edu	37	chr4	155457860	155457860	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	aaatctctttctcttgataaTttctggtttccagctgactg	6	9	3	2			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr4:155457860T>G	ENST00000499023.2	-	15	1648	c.1522A>C	c.(1522-1524)Att>Ctt	p.I508L	PLRG1_ENST00000302078.5_Missense_Mutation_p.I499L|PLRG1_ENST00000393905.2_Missense_Mutation_p.I508L	NM_001201564.1|NM_002669.3	NP_001188493.1|NP_002660.1	O43660	PLRG1_HUMAN	pleiotropic regulator 1	508					mRNA splicing, via spliceosome (GO:0000398)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|protein localization to nucleus (GO:0034504)|regulation of RNA biosynthetic process (GO:2001141)|signal transduction (GO:0007165)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|skin(1)|urinary_tract(1)	22	all_hematologic(180;0.215)	Renal(120;0.0854)				CTCTTGATAATTTCTGGTTTC	0.289																																					p.I508L		Atlas-SNP	.											.	PLRG1	43	.	0			c.A1522C						.						49	53	52					4																	155457860		2198	4283	6481	SO:0001583	missense	5356	exon15			TGATAATTTCTGG	AF044333	CCDS34083.1, CCDS56341.1	4q31.2-q32.1	2013-01-10	2011-05-19		ENSG00000171566	ENSG00000171566		"WD repeat domain containing"	9089	protein-coding gene	gene with protein product	"transport and golgi organization 4 homolog (Drosophila)"	605961	"pleiotropic regulator 1 (PRL1, Arabidopsis homolog)", "pleiotropic regulator 1 (PRL1 homolog, Arabidopsis)"				Standard	NM_002669		Approved	PRL1, Prp46, PRPF46, Cwc1, TANGO4	uc003iny.3	O43660	OTTHUMG00000161411	ENST00000499023.2:c.1522A>C	chr4.hg19:g.155457860T>G	ENSP00000424417:p.Ile508Leu	201.0	0.0		215.0	94.0	NM_002669	B3KMK4|Q3KQY5|Q8WUD8	Missense_Mutation	SNP	ENST00000499023.2	hg19	CCDS34083.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.825|9.825	1.186766|1.186766	0.21870|0.21870	.|.	.|.	ENSG00000171566|ENSG00000171566	ENST00000499023;ENST00000393905;ENST00000302078|ENST00000503251	T;T;T|T	0.61158|0.63096	0.13;0.13;0.17|-0.02	5.4|5.4	4.2|4.2	0.49525|0.49525	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.48187|0.48187	0.1486|0.1486	L|L	0.31752|0.31752	0.955|0.955	0.58432|0.58432	D|D	0.999999|0.999999	B;B|.	0.09022|.	0.002;0.0|.	B;B|.	0.06405|.	0.002;0.001|.	T|T	0.40156|0.40156	-0.9578|-0.9578	10|7	0.11485|0.02654	T|T	0.65|1	-22.8578|-22.8578	11.226|11.226	0.48884|0.48884	0.0:0.0745:0.0:0.9255|0.0:0.0745:0.0:0.9255	.|.	499;508|.	O43660-2;O43660|.	.;PLRG1_HUMAN|.	L|T	508;508;499|86	ENSP00000424417:I508L;ENSP00000377483:I508L;ENSP00000303191:I499L|ENSP00000426497:N86T	ENSP00000303191:I499L|ENSP00000426497:N86T	I|N	-|-	1|2	0|0	PLRG1|PLRG1	155677310|155677310	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.696000|5.696000	0.68287|0.68287	2.046000|2.046000	0.60703|0.60703	0.482000|0.482000	0.46254|0.46254	ATT|AAT	.	.		0.289	PLRG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364824.1	NM_002669		G	155457860	T	G	155457860	3	3	297	1	0	0	0	0	1	0	0	0	12115	1493	52	5	26	5	PLRG1	4	155457860	Missense_Mutation	SNP	T	TCGA-G3-AAV1-01A-11D-A382-10	149837517	155457860	35696416	22	43162										
PLRG1	5356	hgsc.bcm.edu	37	chr4	155460301	155460301	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	ctaactgattttttgtgattTgttaatgtcactcttgtttt	6	5	2	2			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr4:155460301T>C	ENST00000499023.2	-	12	1233	c.1107A>G	c.(1105-1107)acA>acG	p.T369T	PLRG1_ENST00000302078.5_Silent_p.T360T|PLRG1_ENST00000393905.2_Silent_p.T369T	NM_001201564.1|NM_002669.3	NP_001188493.1|NP_002660.1	O43660	PLRG1_HUMAN	pleiotropic regulator 1	369					mRNA splicing, via spliceosome (GO:0000398)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|protein localization to nucleus (GO:0034504)|regulation of RNA biosynthetic process (GO:2001141)|signal transduction (GO:0007165)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|skin(1)|urinary_tract(1)	22	all_hematologic(180;0.215)	Renal(120;0.0854)				TTTTGTGATTTGTTAATGTCA	0.348																																					p.T369T		Atlas-SNP	.											.	PLRG1	43	.	0			c.A1107G						.						237	220	225					4																	155460301		2203	4300	6503	SO:0001819	synonymous_variant	5356	exon12			GTGATTTGTTAAT	AF044333	CCDS34083.1, CCDS56341.1	4q31.2-q32.1	2013-01-10	2011-05-19		ENSG00000171566	ENSG00000171566		"WD repeat domain containing"	9089	protein-coding gene	gene with protein product	"transport and golgi organization 4 homolog (Drosophila)"	605961	"pleiotropic regulator 1 (PRL1, Arabidopsis homolog)", "pleiotropic regulator 1 (PRL1 homolog, Arabidopsis)"				Standard	NM_002669		Approved	PRL1, Prp46, PRPF46, Cwc1, TANGO4	uc003iny.3	O43660	OTTHUMG00000161411	ENST00000499023.2:c.1107A>G	chr4.hg19:g.155460301T>C		126.0	0.0		135.0	65.0	NM_002669	B3KMK4|Q3KQY5|Q8WUD8	Silent	SNP	ENST00000499023.2	hg19	CCDS34083.1																																																																																			.	.		0.348	PLRG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364824.1	NM_002669		C	155460301	T	C	155460301	2	2	297	1	0	0	0	0	0	0	0	1	12115	1799	63	2		2	PLRG1	4	155460301	Silent	SNP	T	TCGA-G3-AAV1-01A-11D-A382-10	2441	155460301	35693975	23	43163										
C5orf36	285600	hgsc.bcm.edu	37	chr5	93798152	93798152	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	ttgtaaacagattattacaaTgagtgtgaattttaaaaatt	6	2	0	3			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr5:93798152T>C	ENST00000513200.3	-	11	2258	c.2186A>G	c.(2185-2187)cAt>cGt	p.H729R	KIAA0825_ENST00000312498.7_Missense_Mutation_p.H729R|KIAA0825_ENST00000427991.2_Missense_Mutation_p.H729R	NM_001145678.1	NP_001139150.1	Q8IV33	K0825_HUMAN	KIAA0825	729										breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|pancreas(1)|prostate(1)|skin(1)	13						ATTATTACAATGAGTGTGAAT	0.274																																					p.H729R		Atlas-SNP	.											.	KIAA0825	172	.	0			c.A2186G						.						81	73	76					5																	93798152		692	1585	2277	SO:0001583	missense	285600	exon12			TTACAATGAGTGT	BX648338	CCDS4070.1	5q15	2011-02-23	2011-02-23	2011-02-23	ENSG00000185261	ENSG00000185261			28532	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 36"	C5orf36		12477932	Standard	NM_173665		Approved	DKFZp686F0372, MGC34713	uc011cuk.2	Q8IV33	OTTHUMG00000131331	ENST00000513200.3:c.2186A>G	chr5.hg19:g.93798152T>C	ENSP00000424618:p.His729Arg	314.0	0.0		558.0	332.0	NM_001145678	O94914|Q6ZNN2	Missense_Mutation	SNP	ENST00000513200.3	hg19		.	.	.	.	.	.	.	.	.	.	T	6.930	0.541368	0.13250	.	.	ENSG00000185261	ENST00000513200;ENST00000427991;ENST00000312498	T;T;T	0.46063	0.88;0.88;0.88	5.51	4.35	0.52113	.	0.193223	0.34025	N	0.004321	T	0.41581	0.1165	M	0.66939	2.045	0.31999	N	0.60364	B	0.18166	0.026	B	0.18561	0.022	T	0.50285	-0.8846	10	0.48119	T	0.1	.	11.3381	0.49516	0.0:0.0713:0.0:0.9287	.	729	Q8IV33	K0825_HUMAN	R	729	ENSP00000424618:H729R;ENSP00000400288:H729R;ENSP00000312205:H729R	ENSP00000312205:H729R	H	-	2	0	KIAA0825	93823908	1.000000	0.71417	0.974000	0.42286	0.632000	0.37999	5.433000	0.66520	1.032000	0.39892	0.533000	0.62120	CAT	.	.		0.274	KIAA0825-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000254102.5	NM_173665		C	93798152	T	C	93798152	3	2	297	1	0	0	0	0	1	0	0	0	2297	1464	51	2	1681	2	C5orf36	5	93798152	Missense_Mutation	SNP	T	TCGA-G3-AAV1-01A-11D-A382-10		93798152	87117108	24	43164										
PCDH12	51294	hgsc.bcm.edu	37	chr5	141324975	141324976	+	Missense_Mutation	DNP	CT	CT	TG													0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	cctgctgctgctgctgctgcCtctgctcttgccctcagtcc					rs13188049|rs3833449		TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C|T	C|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr5:141324975_141324976CT>TG	ENST00000231484.3	-	4	4735_4736	c.3525_3526AG>CA	c.(3523-3528)agAGgc>agCAgc	p.1175_1176RG>SS		NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	1175					calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ctgctgctgcctctgctCTTGC	0.584																																					p.G1176S|p.R1175S		Atlas-SNP	.											.	PCDH12	133	.	0			c.G3526A|c.A3525C						.																																			SO:0001583	missense	51294	exon4			TGCTGCCTCTGCT|GCTGCCTCTGCTC	AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"Cadherins / Protocadherins : Non-clustered"	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.3525_3526delinsTG	chr5.hg19:g.141324975_141324976delinsTG	ENSP00000231484:p.R1175_G1176delinsSS	43.0|44.0	0.0		125.0	14.0|12.0	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	hg19	CCDS4269.1																																																																																			.	.		0.584	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580		TG	141324976	CT	TG	141324975	3	4	297	1	0	0	0	0	1	0	0	0	11519	681	24	3	32	3	PCDH12	5	141324975	Missense_Mutation	DNP	CT	TCGA-G3-AAV1-01A-11D-A382-10	47526823	141324975	39590285	25	43165										
GABRA1	2554	hgsc.bcm.edu	37	chr5	161317904	161317904	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	ttgtgtgttttacttctcagGagaatatgttgttatgacca	9	5	1	2			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr5:161317904G>C	ENST00000428797.2	+	9	1059	c.704G>C	c.(703-705)gGa>gCa	p.G235A	GABRA1_ENST00000420560.1_Splice_Site_p.G235A|GABRA1_ENST00000444819.1_Splice_Site_p.G235A|GABRA1_ENST00000023897.6_Splice_Site_p.G235A|GABRA1_ENST00000393943.4_Splice_Site_p.G235A|GABRA1_ENST00000437025.2_Splice_Site_p.G235A	NM_001127643.1	NP_001121115.1	P14867	GBRA1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 1	235					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|drug binding (GO:0008144)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|endometrium(2)|kidney(3)|large_intestine(4)|liver(1)|lung(22)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(1)	42	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.228)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethanol(DB00898)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methohexital(DB00474)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Prazepam(DB01588)|Primidone(DB00794)|Progabide(DB00837)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiamylal(DB01154)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zaleplon(DB00962)|Zolpidem(DB00425)|Zopiclone(DB01198)	TACTTCTCAGGAGAATATGTT	0.363																																					p.G235A		Atlas-SNP	.											.	GABRA1	132	.	0			c.G704C						.						121	115	117					5																	161317904		2203	4300	6503	SO:0001630	splice_region_variant	2554	exon9			TCTCAGGAGAATA		CCDS4357.1	5q34	2012-06-22			ENSG00000022355	ENSG00000022355		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4075	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 1"	137160				1330891	Standard	NM_000806		Approved	EJM5	uc003lyx.4	P14867	OTTHUMG00000163586	ENST00000428797.2:c.704-1G>C	chr5.hg19:g.161317904G>C		69.0	0.0		110.0	67.0	NM_001127643	D3DQK6|Q8N629	Missense_Mutation	SNP	ENST00000428797.2	hg19	CCDS4357.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.424680	0.83667	.	.	ENSG00000022355	ENST00000023897;ENST00000428797;ENST00000393943;ENST00000437025;ENST00000420560;ENST00000444819	T;T;T;T;T;T	0.80738	-1.41;-1.41;-1.41;-1.41;-1.41;-1.41	5.52	5.52	0.82312	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	D	0.92766	0.7700	M	0.93638	3.44	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94197	0.7446	9	.	.	.	.	19.4464	0.94849	0.0:0.0:1.0:0.0	.	235	P14867	GBRA1_HUMAN	A	235	ENSP00000023897:G235A;ENSP00000393097:G235A;ENSP00000377517:G235A;ENSP00000415441:G235A;ENSP00000408041:G235A;ENSP00000414232:G235A	.	G	+	2	0	GABRA1	161250482	1.000000	0.71417	1.000000	0.80357	0.732000	0.41865	9.695000	0.98691	2.603000	0.88011	0.650000	0.86243	GGA	.	.		0.363	GABRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252702.2	NM_000806.5	Missense_Mutation	C	161317904	G	C	161317904	5	2	297	1	0	0	0	0	0	0	1	0	6168	1188	41	4	730	4	GABRA1	5	161317904	Splice_Site	SNP	G	TCGA-G3-AAV1-01A-11D-A382-10	19992929	161317904	19597356	26	43166										
DRD1	1812	hgsc.bcm.edu	37	chr5	174869355	174869355	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	cggttgagaacattcgacagGctttccattacctgtggtgg	12	9	0	1	rs200037245	byFrequency	TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr5:174869355G>A	ENST00000393752.2	-	2	1740	c.748C>T	c.(748-750)Cct>Tct	p.P250S		NM_000794.3	NP_000785.1	P21728	DRD1_HUMAN	dopamine receptor D1	250					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adult walking behavior (GO:0007628)|astrocyte development (GO:0014002)|behavioral fear response (GO:0001662)|behavioral response to cocaine (GO:0048148)|cellular response to catecholamine stimulus (GO:0071870)|cerebral cortex GABAergic interneuron migration (GO:0021853)|conditioned taste aversion (GO:0001661)|dentate gyrus development (GO:0021542)|dopamine metabolic process (GO:0042417)|dopamine transport (GO:0015872)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose import (GO:0046323)|grooming behavior (GO:0007625)|habituation (GO:0046959)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|maternal behavior (GO:0042711)|mating behavior (GO:0007617)|memory (GO:0007613)|neuronal action potential (GO:0019228)|operant conditioning (GO:0035106)|peristalsis (GO:0030432)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell migration (GO:0030335)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of potassium ion transport (GO:0043268)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|prepulse inhibition (GO:0060134)|protein import into nucleus (GO:0006606)|regulation of dopamine metabolic process (GO:0042053)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|sensitization (GO:0046960)|striatum development (GO:0021756)|synapse assembly (GO:0007416)|synaptic transmission, dopaminergic (GO:0001963)|temperature homeostasis (GO:0001659)|transmission of nerve impulse (GO:0019226)|vasodilation (GO:0042311)|visual learning (GO:0008542)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity (GO:0004952)|dopamine neurotransmitter receptor activity, coupled via Gs (GO:0001588)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	23	all_cancers(89;0.00895)|Renal(175;0.000159)|Lung NSC(126;0.00625)|all_lung(126;0.0104)	Medulloblastoma(196;0.0208)|all_neural(177;0.0277)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)		Acepromazine(DB01614)|Acetophenazine(DB01063)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Dopamine(DB00988)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Haloperidol(DB00502)|Iloperidone(DB04946)|Imipramine(DB00458)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Methylergometrine(DB00353)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Perphenazine(DB00850)|Phenylpropanolamine(DB00397)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Promazine(DB00420)|Propericiazine(DB01608)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Thiothixene(DB01623)|Triflupromazine(DB00508)|Trimipramine(DB00726)|Ziprasidone(DB00246)	CATTCGACAGGCTTTCCATTA	0.478													G|||	2	0.000399361	0	0	5008	,	,		20953	0		0	False		,,,				2504	0.002				p.P250S		Atlas-SNP	.											.	DRD1	56	.	0			c.C748T						.						101	105	103					5																	174869355		2203	4300	6503	SO:0001583	missense	1812	exon2			CGACAGGCTTTCC	X55760	CCDS4393.1	5q34-q35	2012-08-08			ENSG00000184845	ENSG00000184845		"GPCR / Class A : Dopamine receptors"	3020	protein-coding gene	gene with protein product		126449					Standard	NM_000794		Approved		uc003mcz.3	P21728	OTTHUMG00000130557	ENST00000393752.2:c.748C>T	chr5.hg19:g.174869355G>A	ENSP00000377353:p.Pro250Ser	65.0	0.0		122.0	31.0	NM_000794	B2RA44|Q4QRJ0	Missense_Mutation	SNP	ENST00000393752.2	hg19	CCDS4393.1	.	.	.	.	.	.	.	.	.	.	G	2.740	-0.262460	0.05791	.	.	ENSG00000184845	ENST00000393752;ENST00000329144	T	0.69435	-0.4	5.2	3.05	0.35203	GPCR, rhodopsin-like superfamily (1);	0.351936	0.34110	N	0.004243	T	0.27697	0.0681	N	0.01009	-1.055	0.22479	N	0.999064	B	0.02656	0.0	B	0.09377	0.004	T	0.34004	-0.9846	10	0.02654	T	1	.	7.3006	0.26418	0.0:0.1267:0.5002:0.3731	.	250	P21728	DRD1_HUMAN	S	250	ENSP00000377353:P250S	ENSP00000327652:P250S	P	-	1	0	DRD1	174801961	1.000000	0.71417	0.195000	0.23364	0.521000	0.34408	3.417000	0.52714	1.281000	0.44480	0.650000	0.86243	CCT	.	G|0.999;A|0.001		0.478	DRD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252982.2	NM_000794		A	174869355	G	A	174869355	3	1	297	1	0	0	0	0	1	0	0	0	4758	1203	42	3	596	3	DRD1	5	174869355	Missense_Mutation	SNP	G	TCGA-G3-AAV1-01A-11D-A382-10	13551451	174869355	6045905	27	43167										
BPHL	670	hgsc.bcm.edu	37	chr6	3140642	3140660	+	Frame_Shift_Del	DEL	GCCCCGGGTCCAGTGCCCC	GCCCCGGGTCCAGTGCCCC	-													0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	aacatctgccggcacctgctGccccgggtccagtgccccgc					rs200713081		TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	GCCCCGGGTCCAGTGCCCC	GCCCCGGGTCCAGTGCCCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr6:3140642_3140660delGCCCCGGGTCCAGTGCCCC	ENST00000380379.5	+	6	736_754	c.687_705delGCCCCGGGTCCAGTGCCCC	c.(685-705)ctgccccgggtccagtgccccfs	p.LPRVQCP229fs	RP1-40E16.11_ENST00000447644.1_RNA|BPHL_ENST00000380368.2_3'UTR|BPHL_ENST00000380375.3_Frame_Shift_Del_p.LPRVQCP212fs|BPHL_ENST00000434640.1_Frame_Shift_Del_p.LPRVQCP212fs	NM_004332.2	NP_004323.2	Q86WA6	BPHL_HUMAN	biphenyl hydrolase-like (serine hydrolase)	229					cellular amino acid metabolic process (GO:0006520)|response to toxic substance (GO:0009636)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)	p.R214L(1)		endometrium(4)|kidney(1)|large_intestine(2)|lung(6)	13	Ovarian(93;0.0386)	all_hematologic(90;0.108)				GGCACCTGCTGCCCCGGGTCCAGTGCCCCGCCTTGATTG	0.58																																					p.229_235del		Atlas-INDEL	.											.	BPHL	32	.	1	Substitution - Missense(1)	lung(1)	c.686_704del						.																																			SO:0001589	frameshift_variant	670	exon6			.	X81372	CCDS4483.2	6p25	2008-08-29	2008-08-29		ENSG00000137274	ENSG00000137274			1094	protein-coding gene	gene with protein product	"breast epithelial mucin-associated antigen"	603156		MCNAA		7759552, 9721218, 15832508	Standard	NM_004332		Approved	Bph-rp	uc003mva.3	Q86WA6	OTTHUMG00000014140	ENST00000380379.5:c.687_705delGCCCCGGGTCCAGTGCCCC	chr6.hg19:g.3140642_3140660delGCCCCGGGTCCAGTGCCCC	ENSP00000369739:p.Leu229fs	99.0	0.0		91.0	20.0	NM_004332	Q00306|Q13855|Q3KP51	Frame_Shift_Del	DEL	ENST00000380379.5	hg19	CCDS4483.2																																																																																			.	.		0.58	BPHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039670.5			-	3140660	GCCCCGGGTCCAGTGCCCC	-	3140642	7	5	297	1	0	1	0	1	0	0	0	0	1491	1306	46	0	709	0	BPHL	6	3140642	Frame_Shift_Del	DEL	GCCCCGGGTCCAGTGCCCC	TCGA-G3-AAV1-01A-11D-A382-10		3140642	167974425	28	43168										
DPCR1	135656	hgsc.bcm.edu	37	chr6	30918818	30918818	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	accacaccattcccagcagaGcctacagaaaatagagaatg	7	12	0	3			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr6:30918818G>A	ENST00000462446.1	+	2	2605	c.2577G>A	c.(2575-2577)gaG>gaA	p.E859E	DPCR1_ENST00000304311.2_5'UTR|HCG21_ENST00000419481.1_RNA			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	303						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						TCCCAGCAGAGCCTACAGAAA	0.473																																					p.E859E		Atlas-SNP	.											.	DPCR1	99	.	0			c.G2577A						.						79	70	73					6																	30918818		692	1591	2283	SO:0001819	synonymous_variant	135656	exon2			AGCAGAGCCTACA	AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.2577G>A	chr6.hg19:g.30918818G>A		70.0	0.0		88.0	44.0	NM_080870	C9IZC0|Q658M7|Q8WYN2	Silent	SNP	ENST00000462446.1	hg19	CCDS4692.2																																																																																			.	.		0.473	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870		A	30918818	G	A	30918818	2	1	297	1	0	0	0	0	0	0	0	1	4714	962	34	3		3	DPCR1	6	30918818	Silent	SNP	G	TCGA-G3-AAV1-01A-11D-A382-10	27778176	30918818	140196249	29	43169										
BAT1	7919	hgsc.bcm.edu	37	chr6	31500561	31500561	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	tggacgtctaactgacctggTtgaactcaaggacatccaga	10	10	2	3			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr6:31500561T>C	ENST00000396172.1	-	7	1493	c.863A>G	c.(862-864)aAc>aGc	p.N288S	DDX39B_ENST00000376177.2_Missense_Mutation_p.N288S|DDX39B_ENST00000415382.2_Missense_Mutation_p.N210S|DDX39B_ENST00000462421.1_5'Flank|DDX39B_ENST00000458640.1_Missense_Mutation_p.N288S|ATP6V1G2-DDX39B_ENST00000376185.1_3'UTR|DDX39B_ENST00000417556.2_Missense_Mutation_p.N303S	NM_004640.6	NP_004631.1	Q13838	DX39B_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B	288	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of DNA damage checkpoint (GO:2000002)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|RNA secondary structure unwinding (GO:0010501)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|transcription export complex (GO:0000346)	ATP binding (GO:0005524)|ATP-dependent protein binding (GO:0043008)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)|RNA-dependent ATPase activity (GO:0008186)|U4 snRNA binding (GO:0030621)|U6 snRNA binding (GO:0017070)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19						ACTGACCTGGTTGAACTCAAG	0.473																																					p.N288S		Atlas-SNP	.											DDX39B,NS,carcinoma,0,1	DDX39B	38	.	0			c.A863G						.						129	105	114					6																	31500561		1511	2709	4220	SO:0001583	missense	7919	exon7			ACCTGGTTGAACT	Z37166	CCDS4697.1	6p21.33	2011-02-09	2011-02-08	2011-02-08	ENSG00000198563	ENSG00000198563		"DEAD-boxes"	13917	protein-coding gene	gene with protein product	"U2AF65-associated protein 56"	142560	"HLA-B associated transcript 1"	BAT1		7601445, 2813433	Standard	NM_004640		Approved	D6S81E, UAP56	uc003ntu.3	Q13838	OTTHUMG00000031165	ENST00000396172.1:c.863A>G	chr6.hg19:g.31500561T>C	ENSP00000379475:p.Asn288Ser	101.0	0.0		142.0	65.0	NM_004640	B0S8C0|O43496|Q0EFA1|Q2L6F9|Q53GL9|Q5RJ64|Q5RJ66|Q5ST94|Q5STB4|Q5STB5|Q5STB7|Q5STB8|Q5STU4|Q5STU5|Q5STU6|Q5STU8|Q71V76	Missense_Mutation	SNP	ENST00000396172.1	hg19	CCDS4697.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.3|20.3	3.965361|3.965361	0.74131|0.74131	.|.	.|.	ENSG00000198563|ENSG00000198563	ENST00000376177;ENST00000458640;ENST00000396172;ENST00000417556;ENST00000415382;ENST00000431908;ENST00000427214|ENST00000417023	D;T;T;T;T;T;T|.	0.92099|.	-2.97;3.61;3.61;3.61;3.61;3.61;3.37|.	5.28|5.28	5.28|5.28	0.74379|0.74379	Helicase, C-terminal (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.45895|0.45895	0.1365|0.1365	L|L	0.41236|0.41236	1.265|1.265	0.80722|0.80722	D|D	1|1	D;D;D;P|.	0.89917|.	0.967;1.0;0.984;0.806|.	P;D;P;P|.	0.77004|.	0.561;0.989;0.703;0.796|.	T|T	0.44847|0.44847	-0.9301|-0.9301	10|5	0.72032|.	D|.	0.01|.	-18.6328|-18.6328	13.1727|13.1727	0.59609|0.59609	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	210;288;288;303|.	B4DP52;Q13838;Q5STU3;F8VQ10|.	.;DX39B_HUMAN;.;.|.	S|A	288;288;288;303;210;210;288|52	ENSP00000365347:N288S;ENSP00000416269:N288S;ENSP00000379475:N288S;ENSP00000412582:N303S;ENSP00000392669:N210S;ENSP00000408000:N210S;ENSP00000399371:N288S|.	ENSP00000365347:N288S|.	N|T	-|-	2|1	0|0	DDX39B|DDX39B	31608540|31608540	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.673000|7.673000	0.83973|0.83973	2.000000|2.000000	0.58554|0.58554	0.533000|0.533000	0.62120|0.62120	AAC|ACC	.	.		0.473	DDX39B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259083.1	NM_004640		C	31500561	T	C	31500561	3	2	297	1	0	0	0	0	1	0	0	0	1318	1725	60	2	443	2	BAT1	6	31500561	Missense_Mutation	SNP	T	TCGA-G3-AAV1-01A-11D-A382-10	581743	31500561	139614506	30	43170										
LMTK2	22853	hgsc.bcm.edu	37	chr7	97822810	97822814	+	Frame_Shift_Del	DEL	CTCTT	CTCTT	-													0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	gtccacgaagcgctactggaCtctttaggatctcacactcc							TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	CTCTT	CTCTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr7:97822810_97822814delCTCTT	ENST00000297293.5	+	11	3326_3330	c.3033_3037delCTCTT	c.(3031-3039)gactctttafs	p.SL1012fs		NM_014916.3	NP_055731.2	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2	1012					early endosome to late endosome transport (GO:0045022)|endocytic recycling (GO:0032456)|negative regulation of catalytic activity (GO:0043086)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor recycling (GO:0001881)|transferrin transport (GO:0033572)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|myosin VI binding (GO:0070853)|protein phosphatase inhibitor activity (GO:0004864)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|pancreas(2)|skin(2)|stomach(3)	59	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)					CGCTACTGGACTCTTTAGGATCTCA	0.58																																					p.1011_1012del		Atlas-INDEL	.											.	LMTK2	228	.	0			c.3032_3036del						.																																			SO:0001589	frameshift_variant	22853	exon11			.	AB029002	CCDS5654.1	7q22.1	2014-06-12			ENSG00000164715	ENSG00000164715			17880	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 100"	610989				15005709	Standard	NM_014916		Approved	KIAA1079, KPI2, KPI-2, cprk, LMR2, BREK, AATYK2, PPP1R100	uc003upd.2	Q8IWU2	OTTHUMG00000154256	ENST00000297293.5:c.3033_3037delCTCTT	chr7.hg19:g.97822810_97822814delCTCTT	ENSP00000297293:p.Ser1012fs	57.0	0.0		73.0	27.0	NM_014916	A4D272|Q75MG7|Q9UPS3	Frame_Shift_Del	DEL	ENST00000297293.5	hg19	CCDS5654.1																																																																																			.	.		0.58	LMTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334560.1	NM_014916		-	97822814	CTCTT	-	97822810	7	5	297	1	0	1	0	1	0	0	0	0	8868	564	20	0	3075	0	LMTK2	7	97822810	Frame_Shift_Del	DEL	CTCTT	TCGA-G3-AAV1-01A-11D-A382-10		97822810	61315853	31	43171										
TAS2R39	259285	hgsc.bcm.edu	37	chr7	142880762	142880762	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	tttcctgagtgtatccagaaTagctctccaaagcctcatga	7	11	2	3			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr7:142880762T>C	ENST00000446620.1	+	1	251	c.251T>C	c.(250-252)aTa>aCa	p.I84T		NM_176881.2	NP_795362.2	P59534	T2R39_HUMAN	taste receptor, type 2, member 39	84					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20	Melanoma(164;0.059)					GTATCCAGAATAGCTCTCCAA	0.393																																					p.I84T		Atlas-SNP	.											.	TAS2R39	42	.	0			c.T251C						.						115	109	111					7																	142880762		1871	4113	5984	SO:0001583	missense	259285	exon1			CCAGAATAGCTCT	AF494230	CCDS47729.1	7q34	2012-08-22			ENSG00000236398	ENSG00000236398		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	18886	protein-coding gene	gene with protein product						12379855	Standard	NM_176881		Approved		uc011ksw.2	P59534	OTTHUMG00000152636	ENST00000446620.1:c.251T>C	chr7.hg19:g.142880762T>C	ENSP00000405095:p.Ile84Thr	54.0	0.0		78.0	34.0	NM_176881	A4FUI7|Q3ZCN6|Q645W4	Missense_Mutation	SNP	ENST00000446620.1	hg19	CCDS47729.1	.	.	.	.	.	.	.	.	.	.	T	17.02	3.282503	0.59867	.	.	ENSG00000236398	ENST00000446620	T	0.01192	5.2	4.76	2.35	0.29111	.	.	.	.	.	T	0.05318	0.0141	M	0.86864	2.845	0.22317	N	0.999204	D	0.58970	0.984	P	0.57960	0.83	T	0.17289	-1.0374	9	0.87932	D	0	.	7.1654	0.25687	0.0:0.0776:0.147:0.7754	.	84	P59534	T2R39_HUMAN	T	84	ENSP00000405095:I84T	ENSP00000405095:I84T	I	+	2	0	TAS2R39	142590884	0.581000	0.26741	0.306000	0.25113	0.937000	0.57800	1.411000	0.34702	0.398000	0.25338	0.528000	0.53228	ATA	.	.		0.393	TAS2R39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327090.2	NM_176881		C	142880762	T	C	142880762	3	2	297	1	0	0	0	0	1	0	0	0	15591	1406	49	2	253	2	TAS2R39	7	142880762	Missense_Mutation	SNP	T	TCGA-G3-AAV1-01A-11D-A382-10	45057952	142880762	16257901	32	43172										
SH2D4A	63898	hgsc.bcm.edu	37	chr8	19192209	19192209	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	ctcttcagaaaaactcactcTgaagaattcaccaatagctt	4	11	5	3			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr8:19192209T>A	ENST00000265807.3	+	4	765	c.354T>A	c.(352-354)tcT>tcA	p.S118S	SH2D4A_ENST00000519207.1_Silent_p.S118S|SH2D4A_ENST00000518040.1_Silent_p.S73S	NM_001174160.1|NM_022071.3	NP_001167631.1|NP_071354.2	Q9H788	SH24A_HUMAN	SH2 domain containing 4A	118					negative regulation of phosphatase activity (GO:0010923)	cytoplasm (GO:0005737)	phosphatase binding (GO:0019902)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|stomach(1)	16				Colorectal(111;0.0732)		AAACTCACTCTGAAGAATTCA	0.388																																					p.S118S		Atlas-SNP	.											.	SH2D4A	49	.	0			c.T354A						.						62	63	63					8																	19192209		2203	4300	6503	SO:0001819	synonymous_variant	63898	exon4			TCACTCTGAAGAA	AY190323	CCDS6009.1, CCDS55206.1	8p21	2013-02-14			ENSG00000104611	ENSG00000104611		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "SH2 domain containing"	26102	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 38"	614968					Standard	NM_022071		Approved	FLJ20967, SH2A, PPP1R38	uc003wzc.3	Q9H788	OTTHUMG00000097005	ENST00000265807.3:c.354T>A	chr8.hg19:g.19192209T>A		98.0	0.0		126.0	62.0	NM_022071	B4DDR1|Q5XKC1|Q6NXE9|Q86YM2|Q96C88|Q9H7F7	Silent	SNP	ENST00000265807.3	hg19	CCDS6009.1																																																																																			.	.		0.388	SH2D4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214094.1	NM_022071		A	19192209	T	A	19192209	2	1	297	1	0	0	0	0	0	0	0	1	14250	1567	55	4		4	SH2D4A	8	19192209	Silent	SNP	T	TCGA-G3-AAV1-01A-11D-A382-10		19192209	127171813	33	43173										
NRG1	3084	hgsc.bcm.edu	37	chr8	32505644	32505644	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	gcctcagctgtgtgggtgtcGtctgaggcatacacttcacc	12	12	3	1	rs192228210		TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr8:32505644G>A	ENST00000405005.3	+	5	502				NRG1_ENST00000520502.2_Silent_p.S136S|NRG1_ENST00000521670.1_Intron|NRG1_ENST00000523079.1_Intron|NRG1_ENST00000341377.5_Intron|NRG1_ENST00000338921.4_Intron|NRG1_ENST00000287842.3_Intron|NRG1_ENST00000287845.5_Intron|NRG1_ENST00000519301.1_Intron|NRG1_ENST00000356819.4_Intron|NRG1_ENST00000520407.1_Intron			Q02297	NRG1_HUMAN	neuregulin 1						activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell myoblast differentiation (GO:0060379)|cell communication (GO:0007154)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cellular protein complex disassembly (GO:0043624)|embryo development (GO:0009790)|endocardial cell differentiation (GO:0060956)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell fate commitment (GO:0021781)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|mammary gland development (GO:0030879)|MAPK cascade (GO:0000165)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of secretion (GO:0051048)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|neural crest cell development (GO:0014032)|neuron fate commitment (GO:0048663)|neurotransmitter receptor metabolic process (GO:0045213)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|synapse assembly (GO:0007416)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular trabecula myocardium morphogenesis (GO:0003222)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|ErbB-3 class receptor binding (GO:0043125)|growth factor activity (GO:0008083)|protein tyrosine kinase activator activity (GO:0030296)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(1)|skin(1)	39		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		TGTGGGTGTCGTCTGAGGCAT	0.502																																					p.S136S		Atlas-SNP	.											.	NRG1	260	.	0			c.G408A						.						147	128	134					8																	32505644		2203	4300	6503	SO:0001627	intron_variant	3084	exon1			GGTGTCGTCTGAG	L12261	CCDS6084.1, CCDS6085.1, CCDS6086.1, CCDS6087.1, CCDS47836.1, CCDS55218.1, CCDS55219.1, CCDS75727.1	8p21-p12	2014-06-23			ENSG00000157168	ENSG00000157168		"Immunoglobulin superfamily / I-set domain containing"	7997	protein-coding gene	gene with protein product		142445	"NRG1 intronic transcript 2 (non-protein coding)"	HGL, NRG1-IT2		1350381, 8095334	Standard	NM_013962		Approved	HRG, NDF, GGF	uc003xiu.2	Q02297	OTTHUMG00000163918	ENST00000405005.3:c.502+31241G>A	chr8.hg19:g.32505644G>A		93.0	0.0		110.0	19.0	NM_013959	A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	Silent	SNP	ENST00000405005.3	hg19	CCDS6085.1																																																																																			.	G|1.000;T|0.000		0.502	NRG1-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472504.1			A	32505644	G	A	32505644	1	1	297	0	1	0	0	0	0	0	0	0	10656	1132	40	1		1	NRG1	8	32505644	Intron	SNP	G	TCGA-G3-AAV1-01A-11D-A382-10	13313435	32505644	113858378	34	43174										
C9orf93	203238	hgsc.bcm.edu	37	chr9	15778979	15778980	+	Missense_Mutation	DNP	CG	CG	AC													0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	acaacagaaaagcacagcatCgttgcagaagcaaatacttg					rs375214888		TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C|G	C|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr9:15778979_15778980CG>AC	ENST00000380701.3	+	20	3240_3241	c.2912_2913CG>AC	c.(2911-2913)tCG>tAC	p.S971Y	RNU6-14P_ENST00000384630.1_RNA|CCDC171_ENST00000297641.3_Missense_Mutation_p.S971Y	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	971																	AGCACAGCATCGTTGCAGAAGC	0.366																																					p.S971X|p.S971S		Atlas-SNP	.											.	.	.	.	0			c.C2912A|c.G2913C						.																																			SO:0001583	missense	203238	exon20			CAGCATCGTTGCA|AGCATCGTTGCAG	AY422473	CCDS6481.1	9p22.2	2012-03-26	2012-03-26	2012-03-26	ENSG00000164989	ENSG00000164989			29828	protein-coding gene	gene with protein product	"myosin tail domain containing protein"		"chromosome 9 open reading frame 93"	C9orf93		14702039	Standard	NM_173550		Approved	FLJ39267, FLJ46740, Em:AL513423.1, bA778P13.1, bA536D16.1	uc003zmd.3	Q6TFL3	OTTHUMG00000019584	Exception_encountered	chr9.hg19:g.15778979_15778980delinsAC	ENSP00000370077:p.Ser971Tyr	111.0|110.0	0.0		41.0	24.0	NM_173550	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	Nonsense_Mutation|Silent	SNP	ENST00000380701.3	hg19	CCDS6481.1																																																																																			.	.		0.366	CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051768.4	NM_173550		AC	15778980	CG	AC	15778979	3	1	297	1	0	0	0	0	1	0	0	0	2508	893	31	1	2986	1	C9orf93	9	15778979	Missense_Mutation	DNP	CG	TCGA-G3-AAV1-01A-11D-A382-10		15778979	125434452	35	43175										
FRMPD1	22844	hgsc.bcm.edu	37	chr9	37707441	37707441	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	ttgctgcagctgatgggcccGccaggaacccaactcagacc	11	15	1	2	rs2296556	byFrequency	TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr9:37707441G>T	ENST00000539465.1	+	3	723	c.130G>T	c.(130-132)Gcc>Tcc	p.A44S	FRMPD1_ENST00000377765.3_Missense_Mutation_p.A44S|RP11-613M10.9_ENST00000540557.1_Intron			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	44			A -> T (in dbSNP:rs2296556).			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		TGATGGGCCCGCCAGGAACCC	0.498																																					p.A44S		Atlas-SNP	.											.	FRMPD1	237	.	0			c.G130T						.						91	94	93					9																	37707441		2203	4300	6503	SO:0001583	missense	22844	exon3			GGGCCCGCCAGGA	AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.130G>T	chr9.hg19:g.37707441G>T	ENSP00000444411:p.Ala44Ser	93.0	0.0		104.0	23.0	NM_014907	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	hg19	CCDS6612.1	.	.	.	.	.	.	.	.	.	.	G	6.373	0.437009	0.12104	.	.	ENSG00000070601	ENST00000377765;ENST00000539465;ENST00000359927	T;T;T	0.37752	1.18;1.18;1.84	5.66	-3.77	0.04346	PDZ/DHR/GLGF (1);	0.757438	0.12731	N	0.443880	T	0.14356	0.0347	N	0.14661	0.345	0.54753	P	1.0999999999983245E-5	B	0.06786	0.001	B	0.04013	0.001	T	0.27088	-1.0084	9	0.16896	T	0.51	-2.5959	3.8898	0.09114	0.1038:0.285:0.4164:0.1948	.	44	Q5SYB0	FRPD1_HUMAN	S	44	ENSP00000366995:A44S;ENSP00000444411:A44S;ENSP00000439868:A44S	ENSP00000439868:A44S	A	+	1	0	FRMPD1	37697441	0.000000	0.05858	0.006000	0.13384	0.922000	0.55478	-0.656000	0.05342	-0.631000	0.05560	-0.798000	0.03219	GCC	.	G|0.935;A|0.065		0.498	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907		T	37707441	G	T	37707441	3	4	297	1	0	0	0	0	1	0	0	0	6065	1087	38	1	136	1	FRMPD1	9	37707441	Missense_Mutation	SNP	G	TCGA-G3-AAV1-01A-11D-A382-10	21928462	37707441	103505990	36	43176										
FANCC	2176	hgsc.bcm.edu	37	chr9	98011462	98011462	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	gaactcctggaactgagccaCgtgaagacaggtgtcttgct	12	10	1	3			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr9:98011462C>A	ENST00000289081.3	-	2	366	c.112G>T	c.(112-114)Gtg>Ttg	p.V38L	FANCC_ENST00000375305.1_Missense_Mutation_p.V38L	NM_000136.2	NP_000127.2	Q00597	FANCC_HUMAN	Fanconi anemia, complementation group C	38					DNA repair (GO:0006281)|germ cell development (GO:0007281)|myeloid cell homeostasis (GO:0002262)|nucleotide-excision repair (GO:0006289)|protein complex assembly (GO:0006461)|removal of superoxide radicals (GO:0019430)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				kidney(1)|skin(1)|upper_aerodigestive_tract(1)	3		Acute lymphoblastic leukemia(62;0.138)				AACTGAGCCACGTGAAGACAG	0.423			"D, Mis, N, F, S"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.V38L		Atlas-SNP	.	yes	Rec		Fanconi anaemia C	9	9q22.3	2176	"Fanconi anemia, complementation group C"		L	FANCC_ENST00000289081,caecum,carcinoma,0,1	FANCC	53	.	0			c.G112T						.						117	109	112					9																	98011462		2203	4300	6503	SO:0001583	missense	2176	exon2	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GAGCCACGTGAAG	BC006303	CCDS35071.1, CCDS75861.1	9q22.3	2014-09-17			ENSG00000158169	ENSG00000158169		"Fanconi anemia, complementation groups"	3584	protein-coding gene	gene with protein product		613899		FACC		1303234	Standard	NM_001243743		Approved	FAC, FA3	uc004avh.3	Q00597	OTTHUMG00000020279	ENST00000289081.3:c.112G>T	chr9.hg19:g.98011462C>A	ENSP00000289081:p.Val38Leu	82.0	0.0		83.0	44.0	NM_001243743	B1ALR8	Missense_Mutation	SNP	ENST00000289081.3	hg19	CCDS35071.1	.	.	.	.	.	.	.	.	.	.	G	0.005	-2.128330	0.00342	.	.	ENSG00000158169	ENST00000289081;ENST00000375305;ENST00000433829	T;T;T	0.35421	1.31;1.31;1.31	5.13	3.27	0.37495	.	0.000000	0.64402	N	0.000001	T	0.05960	0.0155	N	0.00142	-2.005	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37314	-0.9711	10	0.02654	T	1	-3.5558	3.8829	0.09086	0.3822:0.1751:0.4427:0.0	.	38;38	B1ALR7;Q00597	.;FANCC_HUMAN	L	38	ENSP00000289081:V38L;ENSP00000364454:V38L;ENSP00000406908:V38L	ENSP00000289081:V38L	V	-	1	0	FANCC	97051283	0.992000	0.36948	0.709000	0.30452	0.913000	0.54294	0.145000	0.16157	0.421000	0.25980	-0.127000	0.14921	GTG	.	.		0.423	FANCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053219.1	NM_000136		A	98011462	C	A	98011462	3	1	297	1	0	0	0	0	1	0	0	0	5672	536	19	1	1620	1	FANCC	9	98011462	Missense_Mutation	SNP	C	TCGA-G3-AAV1-01A-11D-A382-10	60304021	98011462	43201969	37	43177										
TMEM26	219623	hgsc.bcm.edu	37	chr10	63170436	63170436	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	gatgttccacagatcggcacTgtactggcaaaagaacaggc	11	10	0	2			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr10:63170436T>G	ENST00000399298.3	-	6	1119	c.751A>C	c.(751-753)Agt>Cgt	p.S251R	TMEM26_ENST00000507507.1_5'UTR	NM_178505.6	NP_848600.2	Q6ZUK4	TMM26_HUMAN	transmembrane protein 26	251						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	18	Prostate(12;0.0112)					AGATCGGCACTGTACTGGCAA	0.473																																					p.S251R		Atlas-SNP	.											.	TMEM26	47	.	0			c.A751C						.						55	59	57					10																	63170436		2073	4225	6298	SO:0001583	missense	219623	exon6			CGGCACTGTACTG	BC042872	CCDS41530.1	10q21.3	2008-10-20			ENSG00000196932	ENSG00000196932			28550	protein-coding gene	gene with protein product						12477932	Standard	NM_178505		Approved	MGC35010, Em:AC068892.1	uc001jlo.2	Q6ZUK4	OTTHUMG00000018293	ENST00000399298.3:c.751A>C	chr10.hg19:g.63170436T>G	ENSP00000382237:p.Ser251Arg	203.0	0.0		264.0	126.0	NM_178505	Q6ZVM0|Q8IVN9	Missense_Mutation	SNP	ENST00000399298.3	hg19	CCDS41530.1	.	.	.	.	.	.	.	.	.	.	T	18.72	3.683708	0.68157	.	.	ENSG00000196932	ENST00000399298	.	.	.	6.17	6.17	0.99709	.	0.079457	0.85682	D	0.000000	T	0.78830	0.4345	M	0.70275	2.135	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.78959	-0.1998	9	0.49607	T	0.09	0.0227	16.8222	0.85835	0.0:0.0:0.0:1.0	.	251	Q6ZUK4	TMM26_HUMAN	R	251	.	ENSP00000382237:S251R	S	-	1	0	TMEM26	62840442	1.000000	0.71417	1.000000	0.80357	0.115000	0.19883	5.974000	0.70465	2.371000	0.80710	0.533000	0.62120	AGT	.	.		0.473	TMEM26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359121.1	NM_178505		G	63170436	T	G	63170436	3	3	297	1	0	0	0	0	1	0	0	0	16166	1580	55	5	359	5	TMEM26	10	63170436	Missense_Mutation	SNP	T	TCGA-G3-AAV1-01A-11D-A382-10		63170436	72364311	38	43178										
GRID1	2894	hgsc.bcm.edu	37	chr10	87489367	87489367	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	ccttctctgagtcccatgtcGccaactgtgaaggaaaaata	8	11	1	2			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr10:87489367G>A	ENST00000327946.7	-	9	1323	c.1238C>T	c.(1237-1239)gCg>gTg	p.A413V	GRID1_ENST00000536331.1_5'UTR	NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	413					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|social behavior (GO:0035176)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|ionotropic glutamate receptor complex (GO:0008328)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(46)|ovary(5)|prostate(4)|skin(5)|stomach(4)|upper_aerodigestive_tract(5)	106						GTCCCATGTCGCCAACTGTGA	0.527										Multiple Myeloma(13;0.14)																											p.A413V		Atlas-SNP	.											.	GRID1	204	.	0			c.C1238T						.						64	58	60					10																	87489367		2203	4300	6503	SO:0001583	missense	2894	exon9			CATGTCGCCAACT	AB033046	CCDS31236.1	10q22	2012-08-29			ENSG00000182771	ENSG00000182771		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4575	protein-coding gene	gene with protein product		610659					Standard	NM_017551		Approved	GluD1, KIAA1220	uc001kdl.1	Q9ULK0	OTTHUMG00000018650	ENST00000327946.7:c.1238C>T	chr10.hg19:g.87489367G>A	ENSP00000330148:p.Ala413Val	89.0	0.0		101.0	6.0	NM_017551	B3KXD5|B7Z7L0|Q8IXT3	Missense_Mutation	SNP	ENST00000327946.7	hg19	CCDS31236.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.691298	0.88735	.	.	ENSG00000182771	ENST00000327946	D	0.87491	-2.26	5.54	5.54	0.83059	.	0.051892	0.85682	D	0.000000	D	0.90338	0.6977	L	0.32530	0.975	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	D	0.91409	0.5149	10	0.87932	D	0	.	18.4481	0.90693	0.0:0.0:1.0:0.0	.	413	Q9ULK0	GRID1_HUMAN	V	413	ENSP00000330148:A413V	ENSP00000330148:A413V	A	-	2	0	GRID1	87479347	1.000000	0.71417	0.954000	0.39281	0.599000	0.36880	9.476000	0.97823	2.593000	0.87608	0.655000	0.94253	GCG	.	.		0.527	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3	XM_043613		A	87489367	G	A	87489367	3	1	297	1	0	0	0	0	1	0	0	0	6780	1087	38	1	1823	1	GRID1	10	87489367	Missense_Mutation	SNP	G	TCGA-G3-AAV1-01A-11D-A382-10	24318931	87489367	48045380	39	43179										
MUC5B	727897	hgsc.bcm.edu	37	chr11	1279360	1279376	+	Frame_Shift_Del	DEL	GCCTGTGTGCCCGCCAG	GCCTGTGTGCCCGCCAG	-													0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	accacctgcccccagagcctGcctgtgtgcccgccagggca							TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	GCCTGTGTGCCCGCCAG	GCCTGTGTGCCCGCCAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr11:1279360_1279376delGCCTGTGTGCCCGCCAG	ENST00000529681.1	+	42	16540_16556	c.16482_16498delGCCTGTGTGCCCGCCAG	c.(16480-16500)ctgcctgtgtgcccgccagggfs	p.PVCPPG5495fs	MUC5B_ENST00000447027.1_Frame_Shift_Del_p.PVCPPG5498fs	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	5495					cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CCCAGAGCCTGCCTGTGTGCCCGCCAGGGCAGGAGTC	0.677																																					p.5494_5499del		Atlas-INDEL	.											.	MUC5B	473	.	0			c.16481_16497del						.																																			SO:0001589	frameshift_variant	727897	exon42			.	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.16482_16498delGCCTGTGTGCCCGCCAG	chr11.hg19:g.1279360_1279376delGCCTGTGTGCCCGCCAG	ENSP00000436812:p.Pro5495fs	187.0	0.0		124.0	41.0	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Frame_Shift_Del	DEL	ENST00000529681.1	hg19	CCDS44515.2																																																																																			.	.		0.677	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		-	1279376	GCCTGTGTGCCCGCCAG	-	1279360	7	5	297	1	0	1	0	1	0	0	0	0	9988	1306	46	0	16657	0	MUC5B	11	1279360	Frame_Shift_Del	DEL	GCCTGTGTGCCCGCCAG	TCGA-G3-AAV1-01A-11D-A382-10		1279360	133727156	40	43180			1	51		2	2	22	N	GCCTGTGTGCCCGCCAG_G	4.070113e-05
MUC5B	727897	hgsc.bcm.edu	37	chr11	1279381	1279381	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	cctgtgtgcccgccagggcaGgagtccatctgcacccagga	13	15	1	0			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr11:1279381G>A	ENST00000529681.1	+	42	16561	c.16503G>A	c.(16501-16503)caG>caA	p.Q5501Q	MUC5B_ENST00000447027.1_Silent_p.Q5504Q	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	5501					cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CGCCAGGGCAGGAGTCCATCT	0.697																																					p.Q5501Q		Atlas-SNP	.											.	MUC5B	473	.	0			c.G16503A						.						9	12	11					11																	1279381		1956	4096	6052	SO:0001819	synonymous_variant	727897	exon42			AGGGCAGGAGTCC	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.16503G>A	chr11.hg19:g.1279381G>A		160.0	0.0		117.0	47.0	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	hg19	CCDS44515.2																																																																																			.	.		0.697	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		A	1279381	G	A	1279381	2	1	297	1	0	0	0	0	0	0	0	1	9988	991	35	3		3	MUC5B	11	1279381	Silent	SNP	G	TCGA-G3-AAV1-01A-11D-A382-10	21	1279381	133727135	41	43181			1	51		2	2	22	N	GCCTGTGTGCCCGCCAG_G	4.070113e-05
APLNR	187	hgsc.bcm.edu	37	chr11	57004140	57004140	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	aggcagaagacgctggcgtaCatgttgacgaagatgaggta	15	6	0	5			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr11:57004140C>T	ENST00000606794.1	-	1	535	c.339G>A	c.(337-339)atG>atA	p.M113I		NM_005161.4	NP_005152.1	P35414	APJ_HUMAN	apelin receptor	113					G-protein coupled receptor signaling pathway (GO:0007186)|gastrulation (GO:0007369)|heart development (GO:0007507)|regulation of body fluid levels (GO:0050878)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32						CGCTGGCGTACATGTTGACGA	0.622																																					p.M113I		Atlas-SNP	.											.	APLNR	62	.	0			c.G339A						.						62	45	51					11																	57004140		2201	4296	6497	SO:0001583	missense	187	exon1			GGCGTACATGTTG	U03642	CCDS7950.1	11q12.1	2012-08-08	2008-05-12	2008-05-12	ENSG00000134817	ENSG00000134817			339	protein-coding gene	gene with protein product	"APJ (apelin) receptor"	600052	"angiotensin II receptor-like 1"	AGTRL1		8294032, 14622440	Standard	NM_005161		Approved	FLJ90771, APJ, APJR	uc001njo.3	P35414	OTTHUMG00000167021	ENST00000606794.1:c.339G>A	chr11.hg19:g.57004140C>T	ENSP00000475344:p.Met113Ile	40.0	0.0		49.0	20.0	NM_005161		Missense_Mutation	SNP	ENST00000606794.1	hg19	CCDS7950.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.584923	0.86748	.	.	ENSG00000134817	ENST00000257254;ENST00000444275	T	0.71934	-0.61	5.46	5.46	0.80206	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.85066	0.5612	M	0.76938	2.355	0.58432	D	0.999997	D	0.89917	1.0	D	0.87578	0.998	D	0.86448	0.1771	10	0.72032	D	0.01	-35.4311	18.9023	0.92448	0.0:1.0:0.0:0.0	.	113	P35414	APJ_HUMAN	I	113;78	ENSP00000257254:M113I	ENSP00000257254:M113I	M	-	3	0	APLNR	56760716	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	4.923000	0.63412	2.558000	0.86282	0.555000	0.69702	ATG	.	.		0.622	APLNR-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000470575.1	NM_005161		T	57004140	C	T	57004140	3	4	297	1	0	0	0	0	1	0	0	0	777	478	17	3	807	3	APLNR	11	57004140	Missense_Mutation	SNP	C	TCGA-G3-AAV1-01A-11D-A382-10	55724759	57004140	78002376	42	43182										
FZD4	8322	hgsc.bcm.edu	37	chr11	86665880	86665881	+	Frame_Shift_Ins	INS	-	-	T													0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	gccgtactggatgagcggtgINStgaaagttgtcagctgcagc					rs80358283		TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr11:86665880_86665881insT	ENST00000531380.1	-	1	552_553	c.247_248insA	c.(247-249)acafs	p.T83fs	RP11-736K20.6_ENST00000499504.3_lincRNA	NM_012193.3	NP_036325.2	Q9ULV1	FZD4_HUMAN	frizzled class receptor 4	83	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|cerebellum vasculature morphogenesis (GO:0061301)|extracellular matrix-cell signaling (GO:0035426)|locomotion involved in locomotory behavior (GO:0031987)|negative regulation of cell-substrate adhesion (GO:0010812)|neuron differentiation (GO:0030182)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone secretion (GO:0042701)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal blood vessel morphogenesis (GO:0061304)|sensory perception of sound (GO:0007605)|substrate adhesion-dependent cell spreading (GO:0034446)|vasculogenesis (GO:0001570)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine binding (GO:0019955)|G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(1)|kidney(1)|large_intestine(3)|lung(9)|prostate(6)|skin(1)	21		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				GATGAGCGGTGTGAAAGTTGTC	0.634																																					p.T83fs		Atlas-INDEL	.											.	FZD4	52	.	0			c.248_249insA						.																																			SO:0001589	frameshift_variant	8322	exon1			.	AB032417	CCDS8279.1	11q14-q21	2014-01-29	2014-01-29			ENSG00000174804		"GPCR / Class F : Frizzled receptors", "CD molecules"	4042	protein-coding gene	gene with protein product		604579	"frizzled (Drosophila) homolog 4", "exudative vitreoretinopathy 1", "frizzled homolog 4 (Drosophila)", "frizzled 4, seven transmembrane spanning receptor", "frizzled family receptor 4"	EVR1		10544037, 15024691	Standard	NM_012193		Approved	CD344	uc001pce.3	Q9ULV1		ENST00000531380.1:c.248dupA	chr11.hg19:g.86665881_86665881dupT	ENSP00000434034:p.Thr83fs	140.0	0.0		124.0	29.0	NM_012193	A8K9Q3|Q14C97|Q6S9E4	Frame_Shift_Ins	INS	ENST00000531380.1	hg19	CCDS8279.1																																																																																			.	.		0.634	FZD4-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393818.2	NM_012193		T	86665881	-	T	86665880	7	5	297	1	0	1	1	0	0	0	0	0	6140	1377	48	0	1373	0	FZD4	11	86665880	Frame_Shift_Ins	INS	-	TCGA-G3-AAV1-01A-11D-A382-10	29661740	86665880	48340636	43	43183										
GUCY1A2	2977	hgsc.bcm.edu	37	chr11	106888708	106888708	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	acagggggcactccccctccTcctccgggctggtctccagg	12	18	1	0			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr11:106888708T>A	ENST00000526355.2	-	1	542	c.74A>T	c.(73-75)gAg>gTg	p.E25V	GUCY1A2_ENST00000347596.2_Missense_Mutation_p.E25V|GUCY1A2_ENST00000282249.2_Missense_Mutation_p.E25V	NM_000855.2	NP_000846.1	P33402	GCYA2_HUMAN	guanylate cyclase 1, soluble, alpha 2	25					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|positive regulation of cGMP biosynthetic process (GO:0030828)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)			breast(5)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(18)|liver(1)|lung(32)|ovary(1)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	74		all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068)		BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476)	Isosorbide Mononitrate(DB01020)|Nitric Oxide(DB00435)	CTCCCCCTCCTCCTCCGGGCT	0.721																																					p.E25V		Atlas-SNP	.											.	GUCY1A2	180	.	0			c.A74T						.						12	14	13					11																	106888708		2162	4244	6406	SO:0001583	missense	2977	exon1			CCCTCCTCCTCCG	X63282	CCDS8335.1, CCDS58170.1	11q21-q22	2008-03-18			ENSG00000152402	ENSG00000152402	4.6.1.2		4684	protein-coding gene	gene with protein product		601244		GUC1A2		1683630	Standard	NM_000855		Approved	GC-SA2	uc001pjg.2	P33402	OTTHUMG00000166296	ENST00000526355.2:c.74A>T	chr11.hg19:g.106888708T>A	ENSP00000431245:p.Glu25Val	52.0	0.0		74.0	18.0	NM_000855	A1L4C4|B7ZLT5	Missense_Mutation	SNP	ENST00000526355.2	hg19	CCDS8335.1	.	.	.	.	.	.	.	.	.	.	T	17.47	3.397752	0.62177	.	.	ENSG00000152402	ENST00000526355;ENST00000282249;ENST00000347596	D;D;D	0.87571	-1.95;-2.27;-1.95	3.34	3.34	0.38264	.	.	.	.	.	T	0.80639	0.4661	L	0.36672	1.1	0.42502	D	0.992939	B;P;B	0.35656	0.145;0.514;0.38	B;B;B	0.34242	0.086;0.178;0.086	T	0.81411	-0.0945	9	0.72032	D	0.01	.	11.0229	0.47728	0.0:0.0:0.0:1.0	.	25;25;25	B7ZLT5;P33402-2;P33402	.;.;GCYA2_HUMAN	V	25	ENSP00000431245:E25V;ENSP00000282249:E25V;ENSP00000344874:E25V	ENSP00000282249:E25V	E	-	2	0	GUCY1A2	106393918	1.000000	0.71417	0.961000	0.40146	0.662000	0.39071	2.441000	0.44864	1.370000	0.46153	0.334000	0.21626	GAG	.	.		0.721	GUCY1A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389003.2			A	106888708	T	A	106888708	3	1	297	1	0	0	0	0	1	0	0	0	6902	1551	54	4	2156	4	GUCY1A2	11	106888708	Missense_Mutation	SNP	T	TCGA-G3-AAV1-01A-11D-A382-10	20222828	106888708	28117808	44	43184										
EXPH5	23086	hgsc.bcm.edu	37	chr11	108382004	108382004	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	atggattgttgacaattttcAgatttttcttcggatacatt	7	5	2	2	rs369244769		TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr11:108382004A>C	ENST00000265843.4	-	6	4340	c.4230T>G	c.(4228-4230)tcT>tcG	p.S1410S	EXPH5_ENST00000443411.1_Silent_p.S1222S|EXPH5_ENST00000428840.1_Silent_p.S1334S|EXPH5_ENST00000525344.1_Silent_p.S1403S|EXPH5_ENST00000524840.1_5'Flank	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	1410					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		GACAATTTTCAGATTTTTCTT	0.353																																					p.S1410S		Atlas-SNP	.											.	EXPH5	193	.	0			c.T4230G						.						95	97	96					11																	108382004		2200	4298	6498	SO:0001819	synonymous_variant	23086	exon6			ATTTTCAGATTTT		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"synaptotagmin-like homologue lacking C2 domains b"	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.4230T>G	chr11.hg19:g.108382004A>C		142.0	0.0		108.0	50.0	NM_015065	Q2KHM1|Q9Y4D6	Silent	SNP	ENST00000265843.4	hg19	CCDS8341.1																																																																																			.	.		0.353	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065		C	108382004	A	C	108382004	2	2	297	1	0	0	0	0	0	0	0	1	5324	175	7	5		5	EXPH5	11	108382004	Silent	SNP	A	TCGA-G3-AAV1-01A-11D-A382-10	1493296	108382004	26624512	45	43185										
C13orf33	84935	hgsc.bcm.edu	37	chr13	31495898	31495898	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	agtccagaaaagaaggagacGattaagttatttctggaaaa	10	4	1	3	rs375543579		TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr13:31495898G>A	ENST00000380482.4	+	4	1027	c.702G>A	c.(700-702)acG>acA	p.T234T	TEX26-AS1_ENST00000588425.1_RNA|TEX26-AS1_ENST00000590344.1_RNA|TEX26-AS1_ENST00000586464.1_RNA|TEX26-AS1_ENST00000588726.1_RNA|TEX26-AS1_ENST00000451495.2_RNA|TEX26-AS1_ENST00000585870.1_RNA|TEX26-AS1_ENST00000590721.1_RNA|TEX26-AS1_ENST00000593246.1_RNA|TEX26-AS1_ENST00000586973.1_RNA|TEX26-AS1_ENST00000592950.1_RNA	NM_032849.3	NP_116238	Q5VYS4	MEDAG_HUMAN	mesenteric estrogen-dependent adipogenesis	234					positive regulation of fat cell differentiation (GO:0045600)	cytoplasm (GO:0005737)											AGAAGGAGACGATTAAGTTAT	0.353																																					p.T234T		Atlas-SNP	.											C13orf33,caecum,carcinoma,0,1	.	.	.	0			c.G702A						.						59	60	60					13																	31495898		2203	4300	6503	SO:0001819	synonymous_variant	84935	exon4			GGAGACGATTAAG	AB055407	CCDS9338.1	13q12.3	2013-10-11	2012-09-26	2012-09-26	ENSG00000102802	ENSG00000102802			25926	protein-coding gene	gene with protein product	"mesenteric estrogen-dependent adipose 4", "activated in W/Wv mouse stomach 3 homolog"		"chromosome 13 open reading frame 33"	C13orf33		22510272	Standard	NM_032849		Approved	FLJ14834, AWMS3, MEDA-4	uc001uth.4	Q5VYS4	OTTHUMG00000016679	ENST00000380482.4:c.702G>A	chr13.hg19:g.31495898G>A		181.0	0.0		200.0	76.0	NM_032849	Q8IXF1|Q96K26|Q96NC8	Silent	SNP	ENST00000380482.4	hg19	CCDS9338.1																																																																																			.	.		0.353	MEDAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044375.1	NM_032849		A	31495898	G	A	31495898	2	1	297	1	0	0	0	0	0	0	0	1	1729	1045	37	1		1	C13orf33	13	31495898	Silent	SNP	G	TCGA-G3-AAV1-01A-11D-A382-10		31495898	83673980	46	43186										
MCF2L	23263	hgsc.bcm.edu	37	chr13	113731386	113731386	+	Frame_Shift_Del	DEL	C	C	-													0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	gagcacgtgcgaaaggtcttCcagaagcaggcaagcatgga							TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr13:113731386delC	ENST00000375608.3	+	14	1669	c.1611delC	c.(1609-1611)ttcfs	p.F537fs	MCF2L_ENST00000421756.1_Frame_Shift_Del_p.F511fs|MCF2L_ENST00000375597.4_Frame_Shift_Del_p.F505fs|MCF2L_ENST00000375601.3_Frame_Shift_Del_p.F511fs|MCF2L_ENST00000423482.2_Frame_Shift_Del_p.F505fs|MCF2L_ENST00000535094.2_Frame_Shift_Del_p.F507fs|MCF2L_ENST00000375604.2_Frame_Shift_Del_p.F564fs|MCF2L_ENST00000397030.1_Frame_Shift_Del_p.F540fs|MCF2L_ENST00000442652.2_Frame_Shift_Del_p.F537fs|MCF2L_ENST00000434480.2_Frame_Shift_Del_p.F513fs			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	537					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular space (GO:0005615)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			kidney(1)|large_intestine(5)|ovary(1)|stomach(1)	8	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)				GAAAGGTCTTCCAGAAGCAGG	0.607																																					p.F507fs		Atlas-INDEL	.											.	MCF2L	182	.	0			c.1520delT						.						75	60	65					13																	113731386		2203	4300	6503	SO:0001589	frameshift_variant	23263	exon13			.	AB002360	CCDS9527.2, CCDS45070.1, CCDS9527.3, CCDS45070.2	13q34	2013-01-10			ENSG00000126217	ENSG00000126217		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	14576	protein-coding gene	gene with protein product		609499				9205841	Standard	NM_001112732		Approved	KIAA0362, DBS, OST, ARHGEF14	uc010tjr.2	O15068	OTTHUMG00000017377	ENST00000375608.3:c.1611delC	chr13.hg19:g.113731386delC	ENSP00000364758:p.Phe537fs	312.0	0.0		411.0	165.0	NM_001112732	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Frame_Shift_Del	DEL	ENST00000375608.3	hg19																																																																																				.	.		0.607	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4			-	113731386	C	-	113731386	7	5	297	1	0	1	0	1	0	0	0	0	9388	854	30	0	1837	0	MCF2L	13	113731386	Frame_Shift_Del	DEL	C	TCGA-G3-AAV1-01A-11D-A382-10	82235488	113731386	1438492	47	43187										
REM2	161253	hgsc.bcm.edu	37	chr14	23355255	23355255	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	ggatgcaggagggtggctgcGggaccactgccttcagaccg	17	11	1	1			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr14:23355255G>A	ENST00000267396.4	+	4	665	c.542G>A	c.(541-543)cGg>cAg	p.R181Q	REM2_ENST00000536884.1_Silent_p.A156A	NM_173527.2	NP_775798.2	Q8IYK8	REM2_HUMAN	RAS (RAD and GEM)-like GTP binding 2	181					small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|central_nervous_system(1)|large_intestine(2)|ovary(1)	5	all_cancers(95;4.69e-05)			GBM - Glioblastoma multiforme(265;0.012)		GGGTGGCTGCGGGACCACTGC	0.597																																					p.R181Q		Atlas-SNP	.											.	REM2	21	.	0			c.G542A						.						53	59	57					14																	23355255		2039	4173	6212	SO:0001583	missense	161253	exon4			GGCTGCGGGACCA		CCDS45082.1	14q11.2	2014-05-09	2006-12-14		ENSG00000139890	ENSG00000139890			20248	protein-coding gene	gene with protein product			"RAS (RAD and GEM) like GTP binding 2"			10727423	Standard	NM_173527		Approved	FLJ38964	uc001whf.1	Q8IYK8	OTTHUMG00000170277	ENST00000267396.4:c.542G>A	chr14.hg19:g.23355255G>A	ENSP00000267396:p.Arg181Gln	58.0	0.0		108.0	48.0	NM_173527	B7Z5P1|Q8N8R8	Missense_Mutation	SNP	ENST00000267396.4	hg19	CCDS45082.1	.	.	.	.	.	.	.	.	.	.	G	8.539	0.872759	0.17322	.	.	ENSG00000139890	ENST00000267396	T	0.80994	-1.44	5.48	-2.23	0.06930	.	0.644098	0.16252	N	0.222680	T	0.61248	0.2332	N	0.25201	0.72	0.80722	D	1	B	0.06786	0.001	B	0.01281	0.0	T	0.32771	-0.9894	10	0.16896	T	0.51	.	8.0204	0.30406	0.5986:0.1207:0.2807:0.0	.	181	Q8IYK8	REM2_HUMAN	Q	181	ENSP00000267396:R181Q	ENSP00000267396:R181Q	R	+	2	0	REM2	22425095	1.000000	0.71417	0.970000	0.41538	0.993000	0.82548	1.149000	0.31626	-0.624000	0.05611	0.563000	0.77884	CGG	.	.		0.597	REM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408290.1	NM_173527		A	23355255	G	A	23355255	3	1	297	1	0	0	0	0	1	0	0	0	13238	1116	39	1	556	1	REM2	14	23355255	Missense_Mutation	SNP	G	TCGA-G3-AAV1-01A-11D-A382-10		23355255	83994285	48	43188										
NOVA1	4857	hgsc.bcm.edu	37	chr14	26949340	26949340	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	cctggatcaagcacactcgcTcagtagtacctgtggataaa	9	11	2	0			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr14:26949340T>A	ENST00000344429.5	-	3	293	c.290A>T	c.(289-291)gAg>gTg	p.E97V	NOVA1_ENST00000547619.1_Missense_Mutation_p.E97V|NOVA1_ENST00000267422.7_5'UTR|NOVA1_ENST00000539517.2_Missense_Mutation_p.E97V|NOVA1_ENST00000465357.2_Missense_Mutation_p.E97V|NOVA1_ENST00000574031.1_Missense_Mutation_p.E97V	NM_006491.2	NP_006482.1	P51513	NOVA1_HUMAN	neuro-oncological ventral antigen 1	100	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.				locomotory behavior (GO:0007626)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA metabolic process (GO:0051252)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(265;0.0135)		GCACACTCGCTCAGTAGTACC	0.368																																					p.E97V		Atlas-SNP	.											.	NOVA1	146	.	0			c.A290T						.						78	68	72					14																	26949340		2203	4300	6503	SO:0001583	missense	4857	exon3			ACTCGCTCAGTAG	U04840	CCDS9635.1, CCDS32060.1, CCDS32061.1	14q12	2006-06-09			ENSG00000139910	ENSG00000139910			7886	protein-coding gene	gene with protein product		602157				8558240	Standard	NM_006489		Approved		uc001wpy.3	P51513	OTTHUMG00000029385	ENST00000344429.5:c.290A>T	chr14.hg19:g.26949340T>A	ENSP00000342387:p.Glu97Val	54.0	0.0		77.0	26.0	NM_006489	A8K0S4|A8K4Q7|D3DS81|D3DS82|Q6B004	Missense_Mutation	SNP	ENST00000344429.5	hg19	CCDS9635.1	.	.	.	.	.	.	.	.	.	.	T	18.94	3.730730	0.69074	.	.	ENSG00000139910	ENST00000465357;ENST00000539517;ENST00000449198;ENST00000549571;ENST00000344429;ENST00000547619	T;T;T;T;T;T	0.35973	1.28;1.28;1.28;1.28;1.28;1.28	5.26	5.26	0.73747	.	0.839868	0.10332	N	0.687495	T	0.67711	0.2922	M	0.86953	2.85	0.80722	D	1	D;D;D	0.89917	1.0;0.991;0.989	D;D;D	0.85130	0.997;0.987;0.978	T	0.67448	-0.5668	10	0.87932	D	0	-6.5518	15.1667	0.72833	0.0:0.0:0.0:1.0	.	97;97;97	P51513-2;D3DS81;P51513-4	.;.;.	V	97;97;56;60;97;97	ENSP00000447391:E97V;ENSP00000438875:E97V;ENSP00000408914:E56V;ENSP00000449185:E60V;ENSP00000342387:E97V;ENSP00000448157:E97V	ENSP00000342387:E97V	E	-	2	0	NOVA1	26019180	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.013000	0.88655	2.002000	0.58637	0.477000	0.44152	GAG	.	.		0.368	NOVA1-001	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276557.1	NM_006491		A	26949340	T	A	26949340	3	1	297	1	0	0	0	0	1	0	0	0	10563	1551	54	4	1276	4	NOVA1	14	26949340	Missense_Mutation	SNP	T	TCGA-G3-AAV1-01A-11D-A382-10	3594085	26949340	80400200	49	43189										
GABRA5	2558	hgsc.bcm.edu	37	chr15	27126102	27126102	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	gctacgacaacagacttcggCccgggctgggaggtgagtgt	16	10	0	2			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr15:27126102C>A	ENST00000335625.5	+	4	1084	c.196C>A	c.(196-198)Ccc>Acc	p.P66T	GABRB3_ENST00000541819.2_Intron|GABRA5_ENST00000557449.1_3'UTR|GABRA5_ENST00000355395.5_Missense_Mutation_p.P66T|GABRA5_ENST00000400081.3_Missense_Mutation_p.P66T	NM_000810.3	NP_000801.1	P31644	GBRA5_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 5	66					associative learning (GO:0008306)|behavioral fear response (GO:0001662)|brain development (GO:0007420)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|receptor activity (GO:0004872)|transporter activity (GO:0005215)	p.P66T(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(1)|upper_aerodigestive_tract(1)	49		all_lung(180;4.59e-13)|Breast(32;0.000563)|Colorectal(260;0.227)		all cancers(64;1.45e-08)|Epithelial(43;4.96e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0232)|Lung(196;0.182)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zopiclone(DB01198)	CAGACTTCGGCCCGGGCTGGG	0.517																																					p.P66T		Atlas-SNP	.											GABRA5,rectum,carcinoma,-1,1	GABRA5	127	.	1	Substitution - Missense(1)	kidney(1)	c.C196A						.						70	71	70					15																	27126102		2003	4172	6175	SO:0001583	missense	2558	exon4			CTTCGGCCCGGGC		CCDS45194.1	15q12	2012-06-22			ENSG00000186297	ENSG00000186297		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4079	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 5"	137142				1321750	Standard	NM_000810		Approved		uc021sgi.1	P31644	OTTHUMG00000171824	ENST00000335625.5:c.196C>A	chr15.hg19:g.27126102C>A	ENSP00000335592:p.Pro66Thr	108.0	0.0		82.0	37.0	NM_001165037	A8K338|Q14DC2|Q53XL6|Q9NYT3|Q9NYT4|Q9NYT5	Missense_Mutation	SNP	ENST00000335625.5	hg19	CCDS45194.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.530918	0.85706	.	.	ENSG00000186297	ENST00000335625;ENST00000355395;ENST00000555182;ENST00000400081;ENST00000554038;ENST00000554596;ENST00000554599;ENST00000554083	D;D;D;D;D;D;D;D	0.94966	-3.57;-3.57;-3.57;-3.57;-3.57;-3.57;-3.57;-3.57	5.22	5.22	0.72569	Neurotransmitter-gated ion-channel ligand-binding (3);	0.105687	0.64402	D	0.000003	D	0.98153	0.9390	H	0.95079	3.62	0.80722	D	1	D	0.76494	0.999	D	0.77004	0.989	D	0.99501	1.0953	10	0.87932	D	0	.	17.756	0.88449	0.0:1.0:0.0:0.0	.	66	P31644	GBRA5_HUMAN	T	66;66;34;66;66;66;66;34	ENSP00000335592:P66T;ENSP00000347557:P66T;ENSP00000450653:P34T;ENSP00000382953:P66T;ENSP00000451527:P66T;ENSP00000450806:P66T;ENSP00000450717:P66T;ENSP00000450529:P34T	ENSP00000335592:P66T	P	+	1	0	GABRA5	24677195	1.000000	0.71417	0.991000	0.47740	0.856000	0.48823	7.617000	0.83032	2.441000	0.82636	0.561000	0.74099	CCC	.	.		0.517	GABRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415234.1			A	27126102	C	A	27126102	3	1	297	1	0	0	0	0	1	0	0	0	6172	739	26	3	202	3	GABRA5	15	27126102	Missense_Mutation	SNP	C	TCGA-G3-AAV1-01A-11D-A382-10		27126102	75405290	50	43190										
CHRNA7	1139	hgsc.bcm.edu	37	chr15	32455518	32455518	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	caccaccacgaccccgacggGggcaagatgcccaagtgggt	13	15	0	1			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr15:32455518G>A	ENST00000306901.3	+	9	1069	c.972G>A	c.(970-972)ggG>ggA	p.G324G	CHRNA7_ENST00000454250.3_Silent_p.G353G|CHRNA7_ENST00000455693.2_Silent_p.G143G	NM_000746.5	NP_000737.1	P36544	ACHA7_HUMAN	cholinergic receptor, nicotinic, alpha 7 (neuronal)	324					activation of MAPK activity (GO:0000187)|associative learning (GO:0008306)|B cell activation (GO:0042113)|behavioral response to ethanol (GO:0048149)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cellular calcium ion homeostasis (GO:0006874)|cognition (GO:0050890)|dopamine biosynthetic process (GO:0042416)|endocytosis (GO:0006897)|generation of ovulation cycle rhythm (GO:0060112)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|memory (GO:0007613)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of tumor necrosis factor production (GO:0032720)|neuronal action potential (GO:0019228)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of heart rate involved in baroreceptor response to decreased systemic arterial blood pressure (GO:0001988)|regulation of norepinephrine secretion (GO:0014061)|regulation of synaptic transmission, dopaminergic (GO:0032225)|response to food (GO:0032094)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|signal transduction (GO:0007165)|sperm motility (GO:0030317)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|T cell activation (GO:0042110)	acetylcholine-gated channel complex (GO:0005892)|apical plasma membrane (GO:0016324)|asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|external side of plasma membrane (GO:0009897)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|acetylcholine-gated cation channel activity (GO:0022848)|beta-amyloid binding (GO:0001540)|chloride channel regulator activity (GO:0017081)|drug binding (GO:0008144)|protein homodimerization activity (GO:0042803)|toxic substance binding (GO:0015643)			endometrium(3)|large_intestine(1)|lung(6)|ovary(2)	12		all_lung(180;6.35e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273)	ACCCCGACGGGGGCAAGATGC	0.582																																					p.G353G	Esophageal Squamous(193;529 2900 40232 43193)	Atlas-SNP	.											.	CHRNA7	57	.	0			c.G1059A						.						16	17	16					15																	32455518		1244	2181	3425	SO:0001819	synonymous_variant	1139	exon9			CGACGGGGGCAAG	Z23141	CCDS10027.1, CCDS53924.1	15q13.3	2012-02-11	2012-02-07		ENSG00000175344	ENSG00000175344		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1960	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 7 (neuronal)"	118511	"cholinergic receptor, nicotinic, alpha polypeptide 7"			8188270	Standard	NM_001190455		Approved		uc021sic.2	P36544	OTTHUMG00000129285	ENST00000306901.3:c.972G>A	chr15.hg19:g.32455518G>A		411.0	0.0		428.0	220.0	NM_001190455	A8K7Q4|B4DFS0|Q15826|Q8IUZ4|Q96RH2|Q99555|Q9BXH0	Silent	SNP	ENST00000306901.3	hg19	CCDS10027.1																																																																																			.	.		0.582	CHRNA7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251410.2			A	32455518	G	A	32455518	2	1	297	1	0	0	0	0	0	0	0	1	3390	1219	43	3		3	CHRNA7	15	32455518	Silent	SNP	G	TCGA-G3-AAV1-01A-11D-A382-10	5329416	32455518	70075874	51	43191										
HERC1	8925	hgsc.bcm.edu	37	chr15	63922816	63922816	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	gattgcgagcacgcccctctGgcaagcctatcaggcgatct	11	14	3	0			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr15:63922816G>T	ENST00000443617.2	-	69	12902	c.12815C>A	c.(12814-12816)cCa>cAa	p.P4272Q		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	4272					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						ACGCCCCTCTGGCAAGCCTAT	0.438																																					p.P4272Q		Atlas-SNP	.											.	HERC1	624	.	0			c.C12815A						.						87	87	87					15																	63922816		1929	4132	6061	SO:0001583	missense	8925	exon69			CCCTCTGGCAAGC	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.12815C>A	chr15.hg19:g.63922816G>T	ENSP00000390158:p.Pro4272Gln	91.0	0.0		110.0	5.0	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	hg19	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	G	30	5.050103	0.93740	.	.	ENSG00000103657	ENST00000443617	D	0.84730	-1.89	5.77	5.77	0.91146	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.85682	D	0.000000	D	0.92051	0.7481	M	0.67953	2.075	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.91129	0.4936	10	0.52906	T	0.07	.	20.3473	0.98799	0.0:0.0:1.0:0.0	.	4272	Q15751	HERC1_HUMAN	Q	4272	ENSP00000390158:P4272Q	ENSP00000390158:P4272Q	P	-	2	0	HERC1	61709869	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.813000	0.99286	2.884000	0.98904	0.655000	0.94253	CCA	.	.		0.438	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		T	63922816	G	T	63922816	3	4	297	1	0	0	0	0	1	0	0	0	7066	1348	47	3	1810	3	HERC1	15	63922816	Missense_Mutation	SNP	G	TCGA-G3-AAV1-01A-11D-A382-10	31467298	63922816	38608576	52	43192										
INTS2	57508	hgsc.bcm.edu	37	chr17	59958425	59958425	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	attagtcaggagcattcgccGtagcagggcatcagtccctg	12	11	2	0	rs201173583		TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr17:59958425G>A	ENST00000444766.3	-	17	2296	c.2221C>T	c.(2221-2223)Cgg>Tgg	p.R741W	INTS2_ENST00000251334.6_Missense_Mutation_p.R733W	NM_020748.2	NP_065799	Q9H0H0	INT2_HUMAN	integrator complex subunit 2	741					snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|intracellular (GO:0005622)|membrane (GO:0016020)				NS(1)|breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	38						AGCATTCGCCGTAGCAGGGCA	0.393																																					p.R741W		Atlas-SNP	.											.	INTS2	89	.	0			c.C2221T						.						118	111	113					17																	59958425		1897	4111	6008	SO:0001583	missense	57508	exon17			TTCGCCGTAGCAG	AB033113	CCDS45750.1	17q23.2	2006-04-26	2006-03-15	2006-03-15		ENSG00000108506			29241	protein-coding gene	gene with protein product		611346	"KIAA1287"	KIAA1287		16239144	Standard	NR_026641		Approved	INT2	uc002izn.3	Q9H0H0		ENST00000444766.3:c.2221C>T	chr17.hg19:g.59958425G>A	ENSP00000414237:p.Arg741Trp	81.0	0.0		192.0	59.0	NM_020748	Q9ULD3	Missense_Mutation	SNP	ENST00000444766.3	hg19	CCDS45750.1	.	.	.	.	.	.	.	.	.	.	G	19.00	3.741282	0.69304	.	.	ENSG00000108506	ENST00000444766;ENST00000251334	T	0.48201	0.82	5.74	0.689	0.18033	.	0.000000	0.85682	D	0.000000	T	0.58764	0.2145	L	0.47716	1.5	0.58432	D	0.999998	D	0.89917	1.0	D	0.79108	0.992	T	0.55711	-0.8098	9	.	.	.	-12.666	15.4887	0.75587	0.0:0.0:0.5122:0.4878	.	741	Q9H0H0	INT2_HUMAN	W	741;740	ENSP00000414237:R741W	.	R	-	1	2	INTS2	57313207	0.976000	0.34144	0.997000	0.53966	0.980000	0.70556	0.245000	0.18142	0.086000	0.17137	-0.474000	0.04947	CGG	.	.		0.393	INTS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000445368.1	NM_020748		A	59958425	G	A	59958425	3	1	297	1	0	0	0	0	1	0	0	0	7787	1144	40	1	1429	1	INTS2	17	59958425	Missense_Mutation	SNP	G	TCGA-G3-AAV1-01A-11D-A382-10		59958425	21236785	53	43193										
MYOM1	8736	hgsc.bcm.edu	37	chr18	3100192	3100192	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	catggctgagagcaagtaaaCgtttcaattctgtaggggga	13	6	2	1			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr18:3100192C>T	ENST00000356443.4	-	25	4025	c.3692G>A	c.(3691-3693)cGt>cAt	p.R1231H	MYOM1_ENST00000261606.7_Missense_Mutation_p.R1135H|MYOM1_ENST00000400569.3_Missense_Mutation_p.R1231H	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	1231					muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						AGCAAGTAAACGTTTCAATTC	0.363																																					p.R1231H		Atlas-SNP	.											.	MYOM1	192	.	0			c.G3692A						.						117	112	114					18																	3100192		1851	4094	5945	SO:0001583	missense	8736	exon25			AGTAAACGTTTCA	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7613	protein-coding gene	gene with protein product	"skelemin"	603508	"myomesin 1 (skelemin) (185kD)", "myomesin 1 (skelemin) 185kDa", "myomesin 1, 185kDa"			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.3692G>A	chr18.hg19:g.3100192C>T	ENSP00000348821:p.Arg1231His	144.0	0.0		184.0	49.0	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	hg19	CCDS45824.1	.	.	.	.	.	.	.	.	.	.	C	17.54	3.415621	0.62511	.	.	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.50277	0.89;0.9;0.75	5.38	5.38	0.77491	.	0.145720	0.53938	D	0.000060	T	0.70945	0.3282	M	0.77103	2.36	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.72338	0.977;0.963	T	0.73388	-0.3998	10	0.72032	D	0.01	.	19.317	0.94218	0.0:1.0:0.0:0.0	.	1135;1231	P52179-2;P52179	.;MYOM1_HUMAN	H	1231;1231;1135	ENSP00000348821:R1231H;ENSP00000383413:R1231H;ENSP00000261606:R1135H	ENSP00000261606:R1135H	R	-	2	0	MYOM1	3090192	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.565000	0.60836	2.806000	0.96561	0.655000	0.94253	CGT	.	.		0.363	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803		T	3100192	C	T	3100192	3	4	297	1	0	0	0	0	1	0	0	0	10100	536	19	1	1421	1	MYOM1	18	3100192	Missense_Mutation	SNP	C	TCGA-G3-AAV1-01A-11D-A382-10		3100192	74977056	54	43194										
CHAF1A	10036	hgsc.bcm.edu	37	chr19	4428721	4428721	+	Missense_Mutation	SNP	G	G	T													0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	ttaaagagcacatggtcctgGcccctcggcgtcggaccgct							TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr19:4428721G>T	ENST00000301280.5	+	8	1539	c.1438G>T	c.(1438-1440)Gcc>Tcc	p.A480S	CTB-50L17.5_ENST00000590159.1_RNA	NM_005483.2	NP_005474	Q13111	CAF1A_HUMAN	chromatin assembly factor 1, subunit A (p150)	480					cell cycle (GO:0007049)|chromatin assembly (GO:0031497)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|protein complex assembly (GO:0006461)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	CAF-1 complex (GO:0033186)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|identical protein binding (GO:0042802)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	27		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)		CATGGTCCTGGCCCCTCGGCG	0.572								Chromatin Structure																													p.A480S		Atlas-SNP	.											.	CHAF1A	69	.	0			c.G1438T						.						62	67	65					19																	4428721		2203	4300	6503	SO:0001583	missense	10036	exon8			GTCCTGGCCCCTC	U20979	CCDS32875.1	19p13.3	2008-07-16				ENSG00000167670			1910	protein-coding gene	gene with protein product	"chromatin assembly factor I (150 kDa)"	601246				7600578	Standard	NM_005483		Approved	CAF1P150, CAF1B, CAF-1, CAF1, P150, MGC71229	uc002mal.3	Q13111		ENST00000301280.5:c.1438G>T	chr19.hg19:g.4428721G>T	ENSP00000301280:p.Ala480Ser	73.0	0.0		69.0	38.0	NM_005483	Q6NXG5|Q7Z7K3|Q9UJY8	Missense_Mutation	SNP	ENST00000301280.5	hg19	CCDS32875.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.555584	0.86231	.	.	ENSG00000167670	ENST00000344143;ENST00000535117;ENST00000301280	T	0.25912	1.77	5.4	5.4	0.78164	.	.	.	.	.	T	0.51686	0.1689	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.53337	-0.8453	9	0.87932	D	0	-38.3682	18.1396	0.89634	0.0:0.0:1.0:0.0	.	480	Q13111	CAF1A_HUMAN	S	480	ENSP00000301280:A480S	ENSP00000301280:A480S	A	+	1	0	CHAF1A	4379721	1.000000	0.71417	0.888000	0.34837	0.399000	0.30720	9.622000	0.98378	2.518000	0.84900	0.455000	0.32223	GCC	.	.		0.572	CHAF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458310.2	NM_005483		T	4428721	G	T	4428721	3	4	297	1	0	0	0	0	1	0	0	0	3313	1203	42	3	1468	3	CHAF1A	19	4428721	Missense_Mutation	SNP	G	TCGA-G3-AAV1-01A-11D-A382-10		4428721	54700262	55	43195	228	2								
CHAF1A	10036	hgsc.bcm.edu	37	chr19	4428728	4428728	+	Missense_Mutation	SNP	G	G	T													0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	gcacatggtcctggcccctcGgcgtcggaccgctttccatc					rs373148905		TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr19:4428728G>T	ENST00000301280.5	+	8	1546	c.1445G>T	c.(1444-1446)cGg>cTg	p.R482L	CTB-50L17.5_ENST00000590159.1_RNA	NM_005483.2	NP_005474	Q13111	CAF1A_HUMAN	chromatin assembly factor 1, subunit A (p150)	482					cell cycle (GO:0007049)|chromatin assembly (GO:0031497)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|protein complex assembly (GO:0006461)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	CAF-1 complex (GO:0033186)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|identical protein binding (GO:0042802)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	27		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)		CTGGCCCCTCGGCGTCGGACC	0.587								Chromatin Structure																													p.R482L		Atlas-SNP	.											CHAF1A,NS,carcinoma,0,1	CHAF1A	69	.	0			c.G1445T						.						62	66	64					19																	4428728		2203	4300	6503	SO:0001583	missense	10036	exon8			CCCCTCGGCGTCG	U20979	CCDS32875.1	19p13.3	2008-07-16				ENSG00000167670			1910	protein-coding gene	gene with protein product	"chromatin assembly factor I (150 kDa)"	601246				7600578	Standard	NM_005483		Approved	CAF1P150, CAF1B, CAF-1, CAF1, P150, MGC71229	uc002mal.3	Q13111		ENST00000301280.5:c.1445G>T	chr19.hg19:g.4428728G>T	ENSP00000301280:p.Arg482Leu	69.0	0.0		66.0	39.0	NM_005483	Q6NXG5|Q7Z7K3|Q9UJY8	Missense_Mutation	SNP	ENST00000301280.5	hg19	CCDS32875.1	.	.	.	.	.	.	.	.	.	.	G	3.511	-0.099825	0.07010	.	.	ENSG00000167670	ENST00000344143;ENST00000535117;ENST00000301280	T	0.11821	2.74	5.52	-1.97	0.07503	.	.	.	.	.	T	0.05593	0.0147	N	0.04636	-0.2	0.09310	N	1	B	0.21753	0.06	B	0.09377	0.004	T	0.34625	-0.9821	9	0.87932	D	0	-8.6972	6.6881	0.23156	0.2506:0.0:0.1606:0.5888	.	482	Q13111	CAF1A_HUMAN	L	482	ENSP00000301280:R482L	ENSP00000301280:R482L	R	+	2	0	CHAF1A	4379728	0.738000	0.28186	0.000000	0.03702	0.197000	0.23852	2.058000	0.41374	-0.587000	0.05890	-0.263000	0.10527	CGG	.	.		0.587	CHAF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458310.2	NM_005483		T	4428728	G	T	4428728	3	4	297	1	0	0	0	0	1	0	0	0	3313	1116	39	1	1475	1	CHAF1A	19	4428728	Missense_Mutation	SNP	G	TCGA-G3-AAV1-01A-11D-A382-10	7	4428728	54700255	56	43196	228	2								
LOC55908	55908	hgsc.bcm.edu	37	chr19	11350522	11350522	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	caggaacagcctgggtctctAtggccgcacaatagaactcc	10	13	1	1			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr19:11350522A>G	ENST00000252453.8	+	1	228	c.209A>G	c.(208-210)tAt>tGt	p.Y70C	DOCK6_ENST00000294618.7_Intron|DOCK6_ENST00000319867.7_5'Flank|C19orf80_ENST00000591200.1_Intron	NM_018687.6	NP_061157.3	Q6UXH0	BETAT_HUMAN	chromosome 19 open reading frame 80	70					cellular lipid metabolic process (GO:0044255)|glucose metabolic process (GO:0006006)|positive regulation of protein processing (GO:0010954)|regulation of lipoprotein metabolic process (GO:0050746)|triglyceride homeostasis (GO:0070328)|type B pancreatic cell proliferation (GO:0044342)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(1)|breast(1)|endometrium(2)	4						CTGGGTCTCTATGGCCGCACA	0.642																																					p.Y70C		Atlas-SNP	.											.	C19orf80	8	.	0			c.A209G						.						20	24	23					19																	11350522		1967	4138	6105	SO:0001583	missense	55908	exon1			GTCTCTATGGCCG		CCDS54220.1	19p13.2	2014-02-13			ENSG00000130173	ENSG00000130173			24933	protein-coding gene	gene with protein product	"lipasin", "betatrophin"					22809513, 23150577, 24262987	Standard	NM_018687		Approved	TD26, RIFL, ANGPTL8	uc021upg.1	Q6UXH0		ENST00000252453.8:c.209A>G	chr19.hg19:g.11350522A>G	ENSP00000252453:p.Tyr70Cys	144.0	0.0		134.0	71.0	NM_018687	Q9NQZ1	Missense_Mutation	SNP	ENST00000252453.8	hg19	CCDS54220.1	.	.	.	.	.	.	.	.	.	.	A	12.59	1.982465	0.34942	.	.	ENSG00000130173	ENST00000252453	T	0.53857	0.6	4.62	2.29	0.28610	.	0.153884	0.30347	N	0.009822	T	0.60444	0.2269	L	0.52573	1.65	0.28431	N	0.917275	D	0.76494	0.999	D	0.66351	0.943	T	0.55780	-0.8087	10	0.87932	D	0	-14.8018	8.0808	0.30744	0.7517:0.0:0.0:0.2483	.	70	Q6UXH0	TD26_HUMAN	C	70	ENSP00000252453:Y70C	ENSP00000252453:Y70C	Y	+	2	0	C19orf80	11211522	0.035000	0.19736	0.192000	0.23308	0.134000	0.20937	0.351000	0.20096	0.032000	0.15435	0.379000	0.24179	TAT	.	.		0.642	C19orf80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453175.1	NM_018687		G	11350522	A	G	11350522	3	3	297	1	0	0	0	0	1	0	0	0	8890	449	16	2	211	2	LOC55908	19	11350522	Missense_Mutation	SNP	A	TCGA-G3-AAV1-01A-11D-A382-10	6921794	11350522	47778461	57	43197										
GIPC1	10755	hgsc.bcm.edu	37	chr19	14591536	14591536	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	gtcctccagcccgatctggcCccccaggagcttgtccatgt	10	17	1	0			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr19:14591536C>T	ENST00000393033.4	-	5	612	c.343G>A	c.(343-345)Ggc>Agc	p.G115S	GIPC1_ENST00000591349.1_Missense_Mutation_p.G18S|GIPC1_ENST00000586027.1_Missense_Mutation_p.G115S|GIPC1_ENST00000393029.3_Missense_Mutation_p.G18S|GIPC1_ENST00000345425.2_Missense_Mutation_p.G115S|GIPC1_ENST00000393028.1_Missense_Mutation_p.G18S	NM_005716.3	NP_005707.1	O14908	GIPC1_HUMAN	GIPC PDZ domain containing family, member 1	115					endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|glutamate secretion (GO:0014047)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of cytokinesis (GO:0032467)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein targeting (GO:0006605)|regulation of protein stability (GO:0031647)|regulation of synaptic plasticity (GO:0048167)|synaptic transmission (GO:0007268)	brush border (GO:0005903)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|myosin binding (GO:0017022)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			endometrium(1)|lung(4)|upper_aerodigestive_tract(1)	6						CCGATCTGGCCCCCCAGGAGC	0.617											OREG0025316	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G115S	Pancreas(33;78 923 2910 41023 52850)	Atlas-SNP	.											.	GIPC1	21	.	0			c.G343A						.						126	106	113					19																	14591536		2203	4300	6503	SO:0001583	missense	10755	exon4			TCTGGCCCCCCAG	AF089816	CCDS12310.1, CCDS12311.1	19p13.1	2009-09-22	2005-06-28	2005-06-28					1226	protein-coding gene	gene with protein product		605072	"chromosome 19 open reading frame 3", "regulator of G-protein signalling 19 interacting protein 1"	C19orf3, RGS19IP1		9770488, 9482110	Standard	NM_005716		Approved	TIP-2, Hs.6454, GIPC, SEMCAP, GLUT1CBP, SYNECTIN, NIP	uc002myx.4	O14908		ENST00000393033.4:c.343G>A	chr19.hg19:g.14591536C>T	ENSP00000376753:p.Gly115Ser	80.0	0.0	696	98.0	31.0	NM_202468	A8K4I3|A8MZG3|Q9BTC9	Missense_Mutation	SNP	ENST00000393033.4	hg19	CCDS12310.1	.	.	.	.	.	.	.	.	.	.	C	17.10	3.303551	0.60195	.	.	ENSG00000123159	ENST00000393033;ENST00000345425;ENST00000393029;ENST00000393028;ENST00000351277	T;T;T;T	0.37915	1.17;1.17;1.17;1.17	4.22	4.22	0.49857	PDZ/DHR/GLGF (1);	0.000000	0.85682	D	0.000000	T	0.37019	0.0988	M	0.64567	1.98	0.80722	D	1	P	0.37864	0.61	B	0.37267	0.245	T	0.32322	-0.9911	10	0.40728	T	0.16	-9.9044	14.4052	0.67079	0.0:1.0:0.0:0.0	.	115	O14908	GIPC1_HUMAN	S	115;115;18;18;115	ENSP00000376753:G115S;ENSP00000340698:G115S;ENSP00000376749:G18S;ENSP00000376748:G18S	ENSP00000340698:G115S	G	-	1	0	GIPC1	14452536	0.996000	0.38824	0.995000	0.50966	0.737000	0.42083	7.195000	0.77798	2.079000	0.62486	0.561000	0.74099	GGC	.	.		0.617	GIPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460239.2			T	14591536	C	T	14591536	3	4	297	1	0	0	0	0	1	0	0	0	6400	623	22	3	678	3	GIPC1	19	14591536	Missense_Mutation	SNP	C	TCGA-G3-AAV1-01A-11D-A382-10	3241014	14591536	44537447	58	43198										
TUBB1	81027	hgsc.bcm.edu	37	chr20	57594619	57594619	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	cagattggccagtgtggcaaCcagatcggagccaaggtaag	14	9	0	2			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr20:57594619C>A	ENST00000217133.1	+	1	311	c.42C>A	c.(40-42)aaC>aaA	p.N14K		NM_030773.3	NP_110400.1	Q9H4B7	TBB1_HUMAN	tubulin, beta 1 class VI	14					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|protein polymerization (GO:0051258)|spindle assembly (GO:0051225)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|skin(2)	16	all_lung(29;0.00711)		Colorectal(105;0.109)		Cabazitaxel(DB06772)|Colchicine(DB01394)|Docetaxel(DB01248)|Paclitaxel(DB01229)|Vindesine(DB00309)	AGTGTGGCAACCAGATCGGAG	0.463																																					p.N14K		Atlas-SNP	.											.	TUBB1	42	.	0			c.C42A						.						156	137	144					20																	57594619		2203	4300	6503	SO:0001583	missense	81027	exon1			TGGCAACCAGATC	AJ292757	CCDS13475.1	20q13.32	2014-09-17	2011-10-10		ENSG00000101162	ENSG00000101162		"Tubulins"	16257	protein-coding gene	gene with protein product	"class VI beta-tubulin"	612901	"tubulin, beta 1"				Standard	NM_030773		Approved	dJ543J19.4	uc002yak.3	Q9H4B7	OTTHUMG00000032860	ENST00000217133.1:c.42C>A	chr20.hg19:g.57594619C>A	ENSP00000217133:p.Asn14Lys	74.0	0.0		105.0	35.0	NM_030773		Missense_Mutation	SNP	ENST00000217133.1	hg19	CCDS13475.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.220782	0.79464	.	.	ENSG00000101162	ENST00000217133	T	0.74947	-0.89	5.51	3.55	0.40652	Tubulin/FtsZ, GTPase domain (3);	0.091425	0.64402	D	0.000001	D	0.89389	0.6701	H	0.98370	4.215	0.53688	D	0.999974	D	0.71674	0.998	P	0.61070	0.883	D	0.92012	0.5619	10	0.87932	D	0	.	11.8023	0.52135	0.0:0.8713:0.0:0.1287	.	14	Q9H4B7	TBB1_HUMAN	K	14	ENSP00000217133:N14K	ENSP00000217133:N14K	N	+	3	2	TUBB1	57028014	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.639000	0.37176	2.592000	0.87571	0.563000	0.77884	AAC	.	.		0.463	TUBB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079903.1	NM_030773		A	57594619	C	A	57594619	3	1	297	1	0	0	0	0	1	0	0	0	16768	506	18	3	44	3	TUBB1	20	57594619	Missense_Mutation	SNP	C	TCGA-G3-AAV1-01A-11D-A382-10		57594619	5430901	59	43199										
ZNF831	128611	hgsc.bcm.edu	37	chr20	57767039	57767039	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	gcagcggcagcaggcgacggCagcggagaagccctgggatg	19	11	0	1			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr20:57767039C>T	ENST00000371030.2	+	1	965	c.965C>T	c.(964-966)gCa>gTa	p.A322V		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	322							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					CAGGCGACGGCAGCGGAGAAG	0.716																																					p.A322V		Atlas-SNP	.											.	ZNF831	287	.	0			c.C965T						.						11	14	14					20																	57767039		1640	3881	5521	SO:0001583	missense	128611	exon1			CGACGGCAGCGGA	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 174"	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.965C>T	chr20.hg19:g.57767039C>T	ENSP00000360069:p.Ala322Val	130.0	0.0		266.0	141.0	NM_178457	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	hg19	CCDS42894.1	.	.	.	.	.	.	.	.	.	.	C	1.145	-0.648369	0.03506	.	.	ENSG00000124203	ENST00000371030	T	0.04275	3.66	5.29	1.93	0.25924	.	.	.	.	.	T	0.01976	0.0062	N	0.08118	0	0.09310	N	1	B	0.29716	0.255	B	0.19148	0.024	T	0.45877	-0.9231	9	0.18710	T	0.47	-1.8223	3.0916	0.06296	0.1565:0.5426:0.1428:0.1581	.	322	Q5JPB2	ZN831_HUMAN	V	322	ENSP00000360069:A322V	ENSP00000360069:A322V	A	+	2	0	ZNF831	57200434	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	0.639000	0.24690	1.192000	0.43071	0.655000	0.94253	GCA	.	.		0.716	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		T	57767039	C	T	57767039	3	4	297	1	0	0	0	0	1	0	0	0	18200	710	25	3	967	3	ZNF831	20	57767039	Missense_Mutation	SNP	C	TCGA-G3-AAV1-01A-11D-A382-10	172420	57767039	5258481	60	43200										
KCNQ2	3785	hgsc.bcm.edu	37	chr20	62045484	62045484	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0166666666666667	1	1	0.30674671240709	0	0.337421383647799	1	1	0	gaggcccggggtcaggtcctCggtcacaaactcgcaggggc	16	13	2	0			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr20:62045484C>A	ENST00000359125.2	-	14	1762	c.1588G>T	c.(1588-1590)Gag>Tag	p.E530*	KCNQ2_ENST00000344462.4_Nonsense_Mutation_p.E499*|KCNQ2_ENST00000357249.2_Nonsense_Mutation_p.E512*|KCNQ2_ENST00000360480.3_Nonsense_Mutation_p.E502*|KCNQ2_ENST00000359689.1_Nonsense_Mutation_p.E530*|KCNQ2_ENST00000354587.3_Nonsense_Mutation_p.E502*|KCNQ2_ENST00000370224.1_Nonsense_Mutation_p.E502*	NM_172107.2	NP_742105.1	O43526	KCNQ2_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 2	530					axon guidance (GO:0007411)|nervous system development (GO:0007399)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ankyrin binding (GO:0030506)|delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|liver(1)|lung(30)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	GTCAGGTCCTCGGTCACAAAC	0.682																																					p.E530X		Atlas-SNP	.											.	KCNQ2	201	.	0			c.G1588T						.						55	60	58					20																	62045484		2203	4300	6503	SO:0001587	stop_gained	3785	exon14			GGTCCTCGGTCAC	AF033348	CCDS13518.1, CCDS13519.1, CCDS13520.1, CCDS13521.1, CCDS46629.1	20q13.33	2012-07-05			ENSG00000075043	ENSG00000075043		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6296	protein-coding gene	gene with protein product		602235		EBN, EBN1		9425895, 16382104	Standard	NM_172107		Approved	Kv7.2, ENB1, BFNC, KCNA11, HNSPC	uc002yex.3	O43526	OTTHUMG00000033049	ENST00000359125.2:c.1588G>T	chr20.hg19:g.62045484C>A	ENSP00000352035:p.Glu530*	140.0	0.0		210.0	97.0	NM_172107	O43796|O75580|O95845|Q4VXP4|Q4VXR6|Q5VYT8|Q96J59|Q99454	Nonsense_Mutation	SNP	ENST00000359125.2	hg19	CCDS13520.1	.	.	.	.	.	.	.	.	.	.	C	38	7.049044	0.98029	.	.	ENSG00000075043	ENST00000357249;ENST00000359125;ENST00000370226;ENST00000354587;ENST00000359689;ENST00000430658;ENST00000360480;ENST00000344462;ENST00000370224;ENST00000370222	.	.	.	5.37	5.37	0.77165	.	0.064931	0.64402	D	0.000008	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-3.0508	19.1082	0.93305	0.0:1.0:0.0:0.0	.	.	.	.	X	512;530;500;502;530;499;502;490;502;502	.	ENSP00000339611:E490X	E	-	1	0	KCNQ2	61515928	1.000000	0.71417	0.938000	0.37757	0.666000	0.39218	5.745000	0.68672	2.519000	0.84933	0.563000	0.77884	GAG	.	.		0.682	KCNQ2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080353.1	NM_172109		A	62045484	C	A	62045484	4	1	297	1	0	0	0	0	0	1	0	0	8092	893	31	1	1046	1	KCNQ2	20	62045484	Nonsense_Mutation	SNP	C	TCGA-G3-AAV1-01A-11D-A382-10	4278445	62045484	980036	61	43201										
TAS1R3	83756	hgsc.bcm.edu	37	chr1	1266805	1266805	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	ggccccattgtgcctgtcacAgcaacttaggatgaaggggg	14	10	1	1			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr1:1266805A>C	ENST00000339381.5	+	1	112	c.80A>C	c.(79-81)cAg>cCg	p.Q27P		NM_152228.1	NP_689414	Q7RTX0	TS1R3_HUMAN	taste receptor, type 1, member 3	27					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			kidney(2)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.88e-21)|Colorectal(212;0.000157)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00251)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.146)		TGCCTGTCACAGCAACTTAGG	0.687																																					p.Q27P		Atlas-SNP	.											.	TAS1R3	39	.	0			c.A80C						.						19	20	20					1																	1266805		2190	4280	6470	SO:0001583	missense	83756	exon1			TGTCACAGCAACT	AC026283	CCDS30556.1	1p36	2012-08-22			ENSG00000169962	ENSG00000169962		"Taste receptors / Type 1", "GPCR / Unclassified : Taste receptors"	15661	protein-coding gene	gene with protein product		605865				11319557	Standard	XM_006710939		Approved	T1R3	uc010nyk.2	Q7RTX0	OTTHUMG00000003071	ENST00000339381.5:c.80A>C	chr1.hg19:g.1266805A>C	ENSP00000344411:p.Gln27Pro	170.0	0.0		137.0	51.0	NM_152228	Q5TA49|Q8NGW9	Missense_Mutation	SNP	ENST00000339381.5	hg19	CCDS30556.1	.	.	.	.	.	.	.	.	.	.	A	6.424	0.446438	0.12223	.	.	ENSG00000169962	ENST00000339381	D	0.89270	-2.49	4.18	-4.54	0.03452	.	1.163060	0.06289	N	0.698755	T	0.72407	0.3456	N	0.08118	0	0.09310	N	1	P	0.34934	0.476	B	0.28553	0.091	T	0.62723	-0.6794	10	0.33940	T	0.23	.	7.7272	0.28767	0.6168:0.1568:0.2264:0.0	.	27	Q7RTX0	TS1R3_HUMAN	P	27	ENSP00000344411:Q27P	ENSP00000344411:Q27P	Q	+	2	0	TAS1R3	1256668	0.000000	0.05858	0.006000	0.13384	0.247000	0.25773	-0.804000	0.04535	-1.207000	0.02637	-0.736000	0.03550	CAG	.	.		0.687	TAS1R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008493.1			C	1266805	A	C	1266805	3	2	298	1	0	0	0	0	1	0	0	0	15579	188	7	5	82	5	TAS1R3	1	1266805	Missense_Mutation	SNP	A	TCGA-G3-AAV2-01A-11D-A36X-10		1266805	247983816	1	43202										
CTRC	11330	hgsc.bcm.edu	37	chr1	15772242	15772242	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	cctacatcgactggatcaacGaggtgggtgctgcctccaca	11	13	1	0			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr1:15772242G>T	ENST00000375949.4	+	7	816	c.790G>T	c.(790-792)Gag>Tag	p.E264*	CTRC_ENST00000375943.2_3'UTR|CTRC_ENST00000483406.1_3'UTR	NM_007272.2	NP_009203.2	Q99895	CTRC_HUMAN	chymotrypsin C (caldecrin)	264	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				proteolysis (GO:0006508)		peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)	13		Breast(348;0.000207)|all_lung(284;0.00021)|Colorectal(325;0.000257)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)|Hepatocellular(190;0.0634)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.56e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CTGGATCAACGAGGTGGGTGC	0.597																																					p.E264X		Atlas-SNP	.											CTRC,NS,malignant_melanoma,0,1	CTRC	28	.	0			c.G790T						.						78	77	77					1																	15772242		2203	4300	6503	SO:0001587	stop_gained	11330	exon7			ATCAACGAGGTGG	BC015118	CCDS156.1	1p36.21	2009-02-18			ENSG00000162438	ENSG00000162438	3.4.21.2		2523	protein-coding gene	gene with protein product	"elastase 4"	601405				8635596	Standard	NM_007272		Approved	CLCR, ELA4	uc001awi.1	Q99895	OTTHUMG00000002255	ENST00000375949.4:c.790G>T	chr1.hg19:g.15772242G>T	ENSP00000365116:p.Glu264*	72.0	0.0		52.0	26.0	NM_007272	A8K082|O00765|Q9NUH5	Nonsense_Mutation	SNP	ENST00000375949.4	hg19	CCDS156.1	.	.	.	.	.	.	.	.	.	.	G	13.55	2.271338	0.40194	.	.	ENSG00000162438	ENST00000375949	.	.	.	4.68	-9.36	0.00629	.	0.945603	0.08885	N	0.879394	.	.	.	.	.	.	0.34632	D	0.71971	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	-12.9763	13.4365	0.61086	0.1769:0.6167:0.2064:0.0	.	.	.	.	X	264	.	ENSP00000365116:E264X	E	+	1	0	CTRC	15644829	0.000000	0.05858	0.001000	0.08648	0.610000	0.37248	-1.418000	0.02462	-2.565000	0.00471	-0.835000	0.03068	GAG	.	.		0.597	CTRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006435.1	NM_007272		T	15772242	G	T	15772242	4	4	298	1	0	0	0	0	0	1	0	0	4029	1059	37	1	816	1	CTRC	1	15772242	Nonsense_Mutation	SNP	G	TCGA-G3-AAV2-01A-11D-A36X-10	14505437	15772242	233478379	2	43203										
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144867973	144867973	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	gagcctgaggataggtccccAgatacactccctttctgagg	11	12	1	3			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr1:144867973A>T	ENST00000369354.3	-	33	5655	c.5466T>A	c.(5464-5466)tcT>tcA	p.S1822S	PDE4DIP_ENST00000369359.4_Silent_p.S1958S|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000530740.1_Silent_p.S1907S|PDE4DIP_ENST00000313382.9_Silent_p.S1716S|PDE4DIP_ENST00000369356.4_Silent_p.S1822S|RP4-791M13.4_ENST00000532137.1_RNA			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1822					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		ATAGGTCCCCAGATACACTCC	0.522			T	PDGFRB	MPD																																p.S1822S		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.T5466A						.						290	295	293					1																	144867973		2203	4296	6499	SO:0001819	synonymous_variant	9659	exon33			GTCCCCAGATACA	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"myomegalin"	608117	"cardiomyopathy associated 2"	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.5466T>A	chr1.hg19:g.144867973A>T		183.0	0.0		158.0	29.0	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Silent	SNP	ENST00000369354.3	hg19	CCDS30824.1																																																																																			.	.		0.522	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		T	144867973	A	T	144867973	2	4	298	1	0	0	0	0	0	0	0	1	11652	175	7	4		4	PDE4DIP	1	144867973	Silent	SNP	A	TCGA-G3-AAV2-01A-11D-A36X-10	129095731	144867973	104382648	3	43204										
VSIG8	391123	hgsc.bcm.edu	37	chr1	159826324	159826324	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	ctgcacctacctgagaccttCacctccaccacacaaacact	3	19	1	1			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr1:159826324C>G	ENST00000368100.1	-	5	897	c.762G>C	c.(760-762)gtG>gtC	p.V254V	C1orf204_ENST00000491974.1_5'Flank|C1orf204_ENST00000368102.1_5'Flank	NM_001013661.1	NP_001013683.1	Q5VU13	VSIG8_HUMAN	V-set and immunoglobulin domain containing 8	254	Ig-like V-type 2.					integral component of membrane (GO:0016021)|intracellular (GO:0005622)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	8	all_hematologic(112;0.0597)					CTGAGACCTTCACCTCCACCA	0.567																																					p.V254V		Atlas-SNP	.											.	VSIG8	24	.	0			c.G762C						.						318	246	270					1																	159826324		2203	4300	6503	SO:0001819	synonymous_variant	391123	exon5			GACCTTCACCTCC		CCDS30913.1	1q23.2	2013-01-11			ENSG00000243284	ENSG00000243284		"Immunoglobulin superfamily / V-set domain containing"	32063	protein-coding gene	gene with protein product							Standard	NM_001013661		Approved		uc001fuh.3	Q5VU13	OTTHUMG00000168834	ENST00000368100.1:c.762G>C	chr1.hg19:g.159826324C>G		92.0	0.0		153.0	113.0	NM_001013661	Q5VU14	Silent	SNP	ENST00000368100.1	hg19	CCDS30913.1																																																																																			.	.		0.567	VSIG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085978.8	NM_001013661		G	159826324	C	G	159826324	2	3	298	1	0	0	0	0	0	0	0	1	17241	813	29	4		4	VSIG8	1	159826324	Silent	SNP	C	TCGA-G3-AAV2-01A-11D-A36X-10	14958351	159826324	89424297	4	43205										
FLVCR1	28982	hgsc.bcm.edu	37	chr1	213031877	213031877	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	atacctcccgttgccgagggGcgcgcccgttgggaaggaga	16	12	0	1			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr1:213031877G>A	ENST00000366971.4	+	1	281	c.83G>A	c.(82-84)gGc>gAc	p.G28D	FLVCR1-AS1_ENST00000356684.3_lincRNA	NM_014053.3	NP_054772.1	Q9Y5Y0	FLVC1_HUMAN	feline leukemia virus subgroup C cellular receptor 1	28					blood vessel development (GO:0001568)|cell death (GO:0008219)|cellular iron ion homeostasis (GO:0006879)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|erythrocyte differentiation (GO:0030218)|erythrocyte maturation (GO:0043249)|head morphogenesis (GO:0060323)|heme export (GO:0097037)|heme transport (GO:0015886)|in utero embryonic development (GO:0001701)|mitochondrial transport (GO:0006839)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|regulation of organ growth (GO:0046620)|spleen development (GO:0048536)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	heme transporter activity (GO:0015232)|transporter activity (GO:0005215)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(2)	12				OV - Ovarian serous cystadenocarcinoma(81;0.00733)|all cancers(67;0.013)|GBM - Glioblastoma multiforme(131;0.0845)|Epithelial(68;0.11)		TTGCCGAGGGGCGCGCCCGTT	0.736																																					p.G28D	Esophageal Squamous(199;2235 2952 19233 26256)	Atlas-SNP	.											.	FLVCR1	31	.	0			c.G83A						.						4	6	5					1																	213031877		1933	3871	5804	SO:0001583	missense	28982	exon1			CGAGGGGCGCGCC	AF118637	CCDS1510.1	1q32.3	2014-05-30			ENSG00000162769	ENSG00000162769		"Solute carriers"	24682	protein-coding gene	gene with protein product		609144	"ataxia, posterior column 1, with retinitis pigmentosa"	AXPC1		10400745, 10648427, 21070897	Standard	NM_014053		Approved	FLVCR, MFSD7B, PCA	uc001hjt.3	Q9Y5Y0	OTTHUMG00000036924	ENST00000366971.4:c.83G>A	chr1.hg19:g.213031877G>A	ENSP00000355938:p.Gly28Asp	75.0	0.0		117.0	58.0	NM_014053	Q1HE16|Q86XY9|Q9NVR9	Missense_Mutation	SNP	ENST00000366971.4	hg19	CCDS1510.1	.	.	.	.	.	.	.	.	.	.	G	13.39	2.222810	0.39300	.	.	ENSG00000162769	ENST00000366971	D	0.81739	-1.53	4.74	-9.48	0.00591	.	1.441100	0.04630	N	0.403573	T	0.51991	0.1707	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.44174	-0.9345	10	0.10636	T	0.68	-10.7686	4.3548	0.11172	0.1266:0.217:0.5344:0.122	.	28	Q9Y5Y0	FLVC1_HUMAN	D	28	ENSP00000355938:G28D	ENSP00000355938:G28D	G	+	2	0	FLVCR1	211098500	0.000000	0.05858	0.000000	0.03702	0.603000	0.37013	-0.361000	0.07612	-1.710000	0.01397	0.563000	0.77884	GGC	.	.		0.736	FLVCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089678.2	NM_014053		A	213031877	G	A	213031877	3	1	298	1	0	0	0	0	1	0	0	0	5953	1203	42	3	85	3	FLVCR1	1	213031877	Missense_Mutation	SNP	G	TCGA-G3-AAV2-01A-11D-A36X-10	53205553	213031877	36218744	5	43206										
CNST	163882	hgsc.bcm.edu	37	chr1	246811256	246811256	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	atctctctcctgaagaagcaTcctatagtctccaggagaat	7	11	3	3			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr1:246811256T>A	ENST00000366513.4	+	9	2022	c.1753T>A	c.(1753-1755)Tcc>Acc	p.S585T	CNST_ENST00000366512.3_Missense_Mutation_p.S585T|CNST_ENST00000483271.1_3'UTR	NM_152609.2	NP_689822.2	Q6PJW8	CNST_HUMAN	consortin, connexin sorting protein	585					negative regulation of phosphatase activity (GO:0010923)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)	connexin binding (GO:0071253)|phosphatase binding (GO:0019902)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|prostate(1)|urinary_tract(2)	28						TGAAGAAGCATCCTATAGTCT	0.413																																					p.S585T		Atlas-SNP	.											.	CNST	73	.	0			c.T1753A						.						103	108	106					1																	246811256		2203	4300	6503	SO:0001583	missense	163882	exon9			GAAGCATCCTATA	AK056563	CCDS1628.1, CCDS44343.1	1q44	2012-04-17	2009-11-03	2009-11-03	ENSG00000162852	ENSG00000162852		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	26486	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 64"	613439	"chromosome 1 open reading frame 71"	C1orf71		19864490	Standard	NM_152609		Approved	FLJ32001, PPP1R64	uc001ibp.3	Q6PJW8	OTTHUMG00000040090	ENST00000366513.4:c.1753T>A	chr1.hg19:g.246811256T>A	ENSP00000355470:p.Ser585Thr	186.0	0.0		277.0	56.0	NM_152609	Q5VSY9|Q5VTM7|Q8IYA9|Q8N3L5|Q8NB09|Q8TEI2|Q96MR5	Missense_Mutation	SNP	ENST00000366513.4	hg19	CCDS1628.1	.	.	.	.	.	.	.	.	.	.	T	19.56	3.851342	0.71719	.	.	ENSG00000162852	ENST00000366513;ENST00000366512	T;T	0.30182	1.95;1.54	5.5	5.5	0.81552	.	0.000000	0.64402	D	0.000002	T	0.54631	0.1870	M	0.78049	2.395	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.81914	0.98;0.995	T	0.59500	-0.7443	10	0.87932	D	0	-10.1401	11.0358	0.47799	0.0:0.0727:0.0:0.9273	.	585;585	Q6PJW8;Q6PJW8-2	CNST_HUMAN;.	T	585	ENSP00000355470:S585T;ENSP00000355469:S585T	ENSP00000355469:S585T	S	+	1	0	CNST	244877879	0.998000	0.40836	0.944000	0.38274	0.578000	0.36192	3.528000	0.53524	2.220000	0.72140	0.383000	0.25322	TCC	.	.		0.413	CNST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096780.1	NM_152609		A	246811256	T	A	246811256	3	1	298	1	0	0	0	0	1	0	0	0	3636	1435	50	4	1783	4	CNST	1	246811256	Missense_Mutation	SNP	T	TCGA-G3-AAV2-01A-11D-A36X-10	33779379	246811256	2439365	6	43207										
TTN	7273	hgsc.bcm.edu	37	chr2	179413257	179413257	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	gcatcccacatcaatgtagcAgatccccgggtcacatcttt	7	14	3	1			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr2:179413257A>G	ENST00000591111.1	-	289	88397	c.88173T>C	c.(88171-88173)tcT>tcC	p.S29391S	TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Silent_p.S28464S|TTN_ENST00000342175.6_Silent_p.S22159S|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590807.1_RNA|RP11-65L3.2_ENST00000603415.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000359218.5_Silent_p.S22092S|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000460472.2_Silent_p.S21967S|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000589042.1_Silent_p.S31032S|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586707.1_RNA			Q8WZ42	TITIN_HUMAN	titin	29391	Fibronectin type-III 114. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCAATGTAGCAGATCCCCGGG	0.502																																					p.S31032S		Atlas-SNP	.											.	TTN	18412	.	0			c.T93096C						.						175	172	173					2																	179413257		1945	4155	6100	SO:0001819	synonymous_variant	7273	exon339			TGTAGCAGATCCC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.88173T>C	chr2.hg19:g.179413257A>G		113.0	0.0		135.0	50.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.502	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179413257	A	G	179413257	2	3	298	1	0	0	0	0	0	0	0	1	16750	175	7	2		2	TTN	2	179413257	Silent	SNP	A	TCGA-G3-AAV2-01A-11D-A36X-10		179413257	63786116	7	43208										
TTN	7273	hgsc.bcm.edu	37	chr2	179523961	179523962	+	Intron	INS	-	-	CTT													0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	cactttcttttcaggaacaaINScttctttgggagcctcaggc							TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr2:179523961_179523962insCTT	ENST00000591111.1	-	154	34489				TTN_ENST00000342992.6_In_Frame_Ins_p.10531_10532insE|TTN_ENST00000342175.6_Intron|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000589042.1_In_Frame_Ins_p.12435_12436insE|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000431752.1_RNA			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTCAGGAACAACTTCTTTGGGA	0.406																																					p.V12436delinsEV		Atlas-INDEL	.											.	TTN	18412	.	0			c.37307_37308insAAG						.																																			SO:0001627	intron_variant	7273	exon181			.	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.34265-440->AAG	chr2.hg19:g.179523965_179523967dupCTT		278.0	0.0		230.0	32.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	In_Frame_Ins	INS	ENST00000591111.1	hg19																																																																																				.	.		0.406	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		CTT	179523962	-	CTT	179523961	6	5	298	0	1	1	1	0	0	0	0	0	16750	43	2	0		0	TTN	2	179523961	Intron	INS	-	TCGA-G3-AAV2-01A-11D-A36X-10	110704	179523961	63675412	8	43209										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266136	41266136	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	gtgccactaccacagctcctTctctgagtggtaaaggcaat	9	12	1	1	rs121913407		TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr3:41266136T>C	ENST00000349496.5	+	3	413	c.133T>C	c.(133-135)Tct>Cct	p.S45P	CTNNB1_ENST00000396185.3_Missense_Mutation_p.S45P|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S45P|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S45P|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S38P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	45			Missing (in colorectal cancer). {ECO:0000269|PubMed:9065402}.|S -> F (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> P (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S45P(168)|p.A5_A80del(53)|p.S45del(50)|p.S45A(11)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.S45_G48del(1)|p.Q28_Q61del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.S45_L46del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.P44_N51del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.T40_L46del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.S45E(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.S45T(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.T42_K49>Q(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CACAGCTCCTTCTCTGAGTGG	0.502		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S45P	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,carcinoma,0,1	CTNNB1	4904	.	355	Substitution - Missense(181)|Deletion - In frame(149)|Complex - deletion inframe(18)|Unknown(7)	liver(151)|kidney(53)|soft_tissue(47)|large_intestine(37)|adrenal_gland(28)|endometrium(9)|stomach(7)|skin(6)|pituitary(3)|prostate(3)|thyroid(2)|small_intestine(2)|bone(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)	c.T133C						.						84	74	78					3																	41266136		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	GCTCCTTCTCTGA	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.133T>C	chr3.hg19:g.41266136T>C	ENSP00000344456:p.Ser45Pro	146.0	1.0		189.0	109.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.440246	0.83993	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.65903	0.2736	M	0.65677	2.01	0.80722	D	1	D	0.60575	0.988	P	0.62649	0.905	T	0.69083	-0.5239	10	0.87932	D	0	-13.6823	16.3453	0.83126	0.0:0.0:0.0:1.0	.	45	P35222	CTNB1_HUMAN	P	38;45;45;45;45;38;45;45;45	ENSP00000400508:S38P;ENSP00000385604:S45P;ENSP00000412219:S45P;ENSP00000379486:S45P;ENSP00000344456:S45P;ENSP00000411226:S38P;ENSP00000379488:S45P;ENSP00000409302:S45P;ENSP00000401599:S45P	ENSP00000344456:S45P	S	+	1	0	CTNNB1	41241140	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.261000	0.74972	0.533000	0.62120	TCT	.	.		0.502	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266136	T	C	41266136	3	2	298	1	0	0	0	0	1	0	0	0	4018	1783	62	2	139	2	CTNNB1	3	41266136	Missense_Mutation	SNP	T	TCGA-G3-AAV2-01A-11D-A36X-10		41266136	156756294	9	43210										
CISH	1154	hgsc.bcm.edu	37	chr3	50645253	50645253	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	gtcactaggcgcatcctcctTaggcataggcagggccgggg	15	12	1	0			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr3:50645253T>C	ENST00000348721.3	-	3	742	c.562A>G	c.(562-564)Aag>Gag	p.K188E	CISH_ENST00000443053.2_Missense_Mutation_p.K205E	NM_145071.2	NP_659508.1	Q9NSE2	CISH_HUMAN	cytokine inducible SH2-containing protein	188					intracellular signal transduction (GO:0035556)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of signal transduction (GO:0009968)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein ubiquitination (GO:0016567)|regulation of cell growth (GO:0001558)	cytosol (GO:0005829)|plasma membrane (GO:0005886)				breast(2)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)		GCATCCTCCTTAGGCATAGGC	0.617																																					p.K205E		Atlas-SNP	.											.	CISH	27	.	0			c.A613G						.						64	63	63					3																	50645253		2203	4300	6503	SO:0001583	missense	1154	exon4			CCTCCTTAGGCAT	Z77852	CCDS2831.1, CCDS46834.1	3p21.3	2013-02-14			ENSG00000114737	ENSG00000114737		"Suppressors of cytokine signaling", "SH2 domain containing"	1984	protein-coding gene	gene with protein product		602441				9465889, 7796808	Standard	NM_013324		Approved	CIS, G18, CIS-1, SOCS	uc003dax.3	Q9NSE2	OTTHUMG00000156853	ENST00000348721.3:c.562A>G	chr3.hg19:g.50645253T>C	ENSP00000294173:p.Lys188Glu	86.0	0.0		113.0	41.0	NM_013324	B2R9N1|G5E9R1|Q9NS38|Q9Y5R1	Missense_Mutation	SNP	ENST00000348721.3	hg19	CCDS2831.1	.	.	.	.	.	.	.	.	.	.	T	8.738	0.918390	0.17982	.	.	ENSG00000114737	ENST00000443053;ENST00000348721	T;T	0.44482	0.92;0.95	5.38	5.38	0.77491	SH2 motif (1);	0.527887	0.22366	N	0.061006	T	0.40247	0.1109	L	0.59436	1.845	0.39548	D	0.968932	P;P	0.48230	0.907;0.85	P;B	0.45099	0.469;0.214	T	0.28106	-1.0054	10	0.10377	T	0.69	-12.4336	11.5189	0.50539	0.0:0.0:0.1902:0.8098	.	205;188	G5E9R1;Q9NSE2	.;CISH_HUMAN	E	205;188	ENSP00000409346:K205E;ENSP00000294173:K188E	ENSP00000294173:K188E	K	-	1	0	CISH	50620257	0.655000	0.27376	0.915000	0.36163	0.112000	0.19704	2.494000	0.45329	2.248000	0.74166	0.460000	0.39030	AAG	.	.		0.617	CISH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346245.1	NM_145071		C	50645253	T	C	50645253	3	2	298	1	0	0	0	0	1	0	0	0	3439	1763	61	2	218	2	CISH	3	50645253	Missense_Mutation	SNP	T	TCGA-G3-AAV2-01A-11D-A36X-10	9379117	50645253	147377177	10	43211										
CACNA2D3	55799	hgsc.bcm.edu	37	chr3	54930804	54930804	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	tgaaagctggcgacaaggagAacatttttaacgcagaccat	10	8	0	3			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr3:54930804A>T	ENST00000474759.1	+	26	2323	c.2275A>T	c.(2275-2277)Aac>Tac	p.N759Y	CACNA2D3_ENST00000288197.5_Missense_Mutation_p.N759Y|CACNA2D3_ENST00000415676.2_Missense_Mutation_p.N759Y|CACNA2D3-AS1_ENST00000471265.1_RNA|CACNA2D3_ENST00000490478.1_Missense_Mutation_p.N665Y	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3	759						integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(3)	59				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)	Amlodipine(DB00381)|Nilvadipine(DB06712)|Spironolactone(DB00421)	CGACAAGGAGAACATTTTTAA	0.522																																					p.N759Y		Atlas-SNP	.											.	CACNA2D3	159	.	0			c.A2275T						.						136	138	137					3																	54930804		1991	4154	6145	SO:0001583	missense	55799	exon26			AAGGAGAACATTT	AJ272268	CCDS54598.1	3p21.1	2010-10-05	2008-02-26		ENSG00000157445	ENSG00000157445		"Calcium channel subunits"	15460	protein-coding gene	gene with protein product		606399				11245980	Standard	XM_005265318		Approved	HSA272268	uc003dhf.3	Q8IZS8	OTTHUMG00000158580	ENST00000474759.1:c.2275A>T	chr3.hg19:g.54930804A>T	ENSP00000419101:p.Asn759Tyr	113.0	0.0		142.0	38.0	NM_018398	B2RPL6|Q9NY16|Q9NY18	Missense_Mutation	SNP	ENST00000474759.1	hg19	CCDS54598.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.243099	0.79912	.	.	ENSG00000157445	ENST00000415676;ENST00000474759;ENST00000288197;ENST00000490478;ENST00000398624	T;T;T;T	0.30182	1.54;1.54;1.54;1.54	5.69	5.69	0.88448	.	0.288637	0.41194	D	0.000921	T	0.31765	0.0807	L	0.27053	0.805	0.44523	D	0.997479	D	0.54397	0.966	P	0.49708	0.62	T	0.05903	-1.0857	10	0.59425	D	0.04	.	14.4892	0.67639	1.0:0.0:0.0:0.0	.	759	Q8IZS8	CA2D3_HUMAN	Y	759;759;759;665;665	ENSP00000389506:N759Y;ENSP00000419101:N759Y;ENSP00000288197:N759Y;ENSP00000417279:N665Y	ENSP00000288197:N759Y	N	+	1	0	CACNA2D3	54905844	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	6.847000	0.75404	2.291000	0.77112	0.533000	0.62120	AAC	.	.		0.522	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351402.1			T	54930804	A	T	54930804	3	4	298	1	0	0	0	0	1	0	0	0	2552	246	9	4	2377	4	CACNA2D3	3	54930804	Missense_Mutation	SNP	A	TCGA-G3-AAV2-01A-11D-A36X-10	4285551	54930804	143091626	11	43212										
OR5H1	26341	hgsc.bcm.edu	37	chr3	97851822	97851822	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	taagagtaagatgatatctcTctctgaatgcaagatacagt	8	6	2	5			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr3:97851822T>A	ENST00000354565.2	+	1	281	c.281T>A	c.(280-282)cTc>cAc	p.L94H	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005338.1	NP_001005338.1	A6NKK0	OR5H1_HUMAN	olfactory receptor, family 5, subfamily H, member 1	94						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(7)|kidney(8)|large_intestine(3)|lung(13)|ovary(1)|skin(1)	34						ATGATATCTCTCTCTGAATGC	0.398																																					p.L94H		Atlas-SNP	.											.	OR5H1	71	.	0			c.T281A						.						160	158	159					3																	97851822		2203	4299	6502	SO:0001583	missense	26341	exon1			TATCTCTCTCTGA	X64988	CCDS33797.1	3q12.1	2012-08-09			ENSG00000231192	ENSG00000231192		"GPCR / Class A : Olfactory receptors"	8346	protein-coding gene	gene with protein product						1370859	Standard	NM_001005338		Approved	HTPCRX14, HSHTPCRX14	uc011bgt.2	A6NKK0	OTTHUMG00000160070	ENST00000354565.2:c.281T>A	chr3.hg19:g.97851822T>A	ENSP00000346575:p.Leu94His	372.0	0.0		277.0	106.0	NM_001005338		Missense_Mutation	SNP	ENST00000354565.2	hg19	CCDS33797.1	.	.	.	.	.	.	.	.	.	.	T	8.713	0.912557	0.17907	.	.	ENSG00000231192	ENST00000354565	T	0.00488	7.04	3.57	2.36	0.29203	GPCR, rhodopsin-like superfamily (1);	1.009930	0.07969	N	0.983766	T	0.00754	0.0025	L	0.58969	1.84	0.09310	N	1	D	0.53745	0.962	P	0.52823	0.71	T	0.55042	-0.8202	10	0.59425	D	0.04	.	7.1495	0.25601	0.2006:0.0:0.0:0.7994	.	94	A6NKK0	OR5H1_HUMAN	H	94	ENSP00000346575:L94H	ENSP00000346575:L94H	L	+	2	0	OR5H1	99334512	0.000000	0.05858	0.059000	0.19551	0.036000	0.12997	0.779000	0.26746	0.415000	0.25817	0.164000	0.16699	CTC	.	.		0.398	OR5H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359100.2	NM_001005338		A	97851822	T	A	97851822	3	1	298	1	0	0	0	0	1	0	0	0	11168	1551	54	4	283	4	OR5H1	3	97851822	Missense_Mutation	SNP	T	TCGA-G3-AAV2-01A-11D-A36X-10	42921018	97851822	100170608	12	43213										
ACAP2	23527	hgsc.bcm.edu	37	chr3	195017930	195017930	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	aaatagtacctttgtcctggTtggggtttctttattcccat	8	8	1	0			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr3:195017930T>A	ENST00000326793.6	-	16	1706	c.1476A>T	c.(1474-1476)caA>caT	p.Q492H		NM_012287.5	NP_036419.3	Q15057	ACAP2_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	492	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				cellular response to nerve growth factor stimulus (GO:1990090)|protein localization to endosome (GO:0036010)|regulation of ARF GTPase activity (GO:0032312)	endosome membrane (GO:0010008)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	27						TTTGTCCTGGTTGGGGTTTCT	0.313																																					p.Q492H		Atlas-SNP	.											.	ACAP2	72	.	0			c.A1476T						.						159	160	160					3																	195017930		2203	4296	6499	SO:0001583	missense	23527	exon16			TCCTGGTTGGGGT		CCDS33924.1	3q29	2013-01-10	2008-09-22	2008-09-22	ENSG00000114331	ENSG00000114331		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16469	protein-coding gene	gene with protein product		607766	"centaurin, beta 2"	CENTB2		11050434, 11062263	Standard	NM_012287		Approved	KIAA0041, CNT-B2	uc003fun.4	Q15057	OTTHUMG00000155885	ENST00000326793.6:c.1476A>T	chr3.hg19:g.195017930T>A	ENSP00000324287:p.Gln492His	66.0	0.0		46.0	14.0	NM_012287	A8K2V4|Q8N5Z8|Q9UQR3	Missense_Mutation	SNP	ENST00000326793.6	hg19	CCDS33924.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.89|12.89	2.073147|2.073147	0.36566|0.36566	.|.	.|.	ENSG00000114331|ENSG00000114331	ENST00000326793|ENST00000450200	T|.	0.43688|.	0.94|.	5.29|5.29	-1.05|-1.05	0.10036|0.10036	.|.	0.155495|.	0.64402|.	N|.	0.000015|.	T|T	0.38665|0.38665	0.1049|0.1049	L|L	0.35542|0.35542	1.07|1.07	0.43782|0.43782	D|D	0.996315|0.996315	P|.	0.45715|.	0.865|.	P|.	0.53954|.	0.738|.	T|T	0.16305|0.16305	-1.0407|-1.0407	10|5	0.36615|.	T|.	0.2|.	.|.	3.5872|3.5872	0.07975|0.07975	0.2846:0.362:0.0:0.3534|0.2846:0.362:0.0:0.3534	.|.	492|.	Q15057|.	ACAP2_HUMAN|.	H|S	492|51	ENSP00000324287:Q492H|.	ENSP00000324287:Q492H|.	Q|T	-|-	3|1	2|0	ACAP2|ACAP2	196499219|196499219	0.918000|0.918000	0.31147|0.31147	0.998000|0.998000	0.56505|0.56505	0.992000|0.992000	0.81027|0.81027	-0.002000|-0.002000	0.12924|0.12924	-0.014000|-0.014000	0.14175|0.14175	-0.309000|-0.309000	0.09137|0.09137	CAA|ACC	.	.		0.313	ACAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342126.2	NM_012287		A	195017930	T	A	195017930	3	1	298	1	0	0	0	0	1	0	0	0	119	1722	60	4	892	4	ACAP2	3	195017930	Missense_Mutation	SNP	T	TCGA-G3-AAV2-01A-11D-A36X-10	97166108	195017930	3004500	13	43214										
CYP2U1	113612	hgsc.bcm.edu	37	chr4	108866371	108866371	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	agcgctttgattacactaatAgtgagttcaagaaaatgctt	8	6	1	3			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr4:108866371A>G	ENST00000332884.6	+	2	1011	c.736A>G	c.(736-738)Agt>Ggt	p.S246G	RP11-286E11.1_ENST00000513071.1_RNA|CYP2U1_ENST00000508453.1_Missense_Mutation_p.S37G	NM_183075.2	NP_898898.1	Q7Z449	CP2U1_HUMAN	cytochrome P450, family 2, subfamily U, polypeptide 1	246					arachidonic acid metabolic process (GO:0019369)|cell death (GO:0008219)|omega-hydroxylase P450 pathway (GO:0097267)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(1)|large_intestine(2)|lung(4)|skin(2)|urinary_tract(1)	10		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000128)		TTACACTAATAGTGAGTTCAA	0.458																																					p.S246G		Atlas-SNP	.											.	CYP2U1	20	.	0			c.A736G						.						129	128	128					4																	108866371		2203	4300	6503	SO:0001583	missense	113612	exon2			ACTAATAGTGAGT	BC012027	CCDS34047.1	4q25	2012-11-23			ENSG00000155016	ENSG00000155016		"Cytochrome P450s"	20582	protein-coding gene	gene with protein product	"spastic paraplegia 49"	610670				14975754, 14660610	Standard	XM_005262717		Approved	SPG49	uc003hyp.3	Q7Z449	OTTHUMG00000161084	ENST00000332884.6:c.736A>G	chr4.hg19:g.108866371A>G	ENSP00000333212:p.Ser246Gly	152.0	0.0		115.0	54.0	NM_183075	B2RMV7|Q96EQ6	Missense_Mutation	SNP	ENST00000332884.6	hg19	CCDS34047.1	.	.	.	.	.	.	.	.	.	.	A	11.44	1.640345	0.29157	.	.	ENSG00000155016	ENST00000332884;ENST00000424249;ENST00000508453	T;T	0.78924	-1.22;-1.22	5.63	3.26	0.37387	.	0.767472	0.13384	N	0.391874	T	0.61540	0.2355	N	0.17564	0.495	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.51663	-0.8677	10	0.41790	T	0.15	.	8.5967	0.33721	0.786:0.0:0.214:0.0	.	246	Q7Z449	CP2U1_HUMAN	G	246;203;37	ENSP00000333212:S246G;ENSP00000423667:S37G	ENSP00000333212:S246G	S	+	1	0	CYP2U1	109085820	0.000000	0.05858	0.606000	0.28943	0.943000	0.58893	0.395000	0.20850	0.975000	0.38392	0.533000	0.62120	AGT	.	.		0.458	CYP2U1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363691.2	NM_183075		G	108866371	A	G	108866371	3	3	298	1	0	0	0	0	1	0	0	0	4177	420	15	2	742	2	CYP2U1	4	108866371	Missense_Mutation	SNP	A	TCGA-G3-AAV2-01A-11D-A36X-10		108866371	82287905	14	43215			1	52		2	2	14	A		2.183668e-05
CYP2U1	113612	hgsc.bcm.edu	37	chr4	108866384	108866384	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	cactaatagtgagttcaagaAaatgcttggttttatgtcac	8	6	2	2	rs200772412		TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr4:108866384A>C	ENST00000332884.6	+	2	1024	c.749A>C	c.(748-750)aAa>aCa	p.K250T	RP11-286E11.1_ENST00000513071.1_RNA|CYP2U1_ENST00000508453.1_Missense_Mutation_p.K41T	NM_183075.2	NP_898898.1	Q7Z449	CP2U1_HUMAN	cytochrome P450, family 2, subfamily U, polypeptide 1	250					arachidonic acid metabolic process (GO:0019369)|cell death (GO:0008219)|omega-hydroxylase P450 pathway (GO:0097267)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(1)|large_intestine(2)|lung(4)|skin(2)|urinary_tract(1)	10		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000128)		GAGTTCAAGAAAATGCTTGGT	0.453																																					p.K250T		Atlas-SNP	.											.	CYP2U1	20	.	0			c.A749C						.						127	126	127					4																	108866384		2203	4300	6503	SO:0001583	missense	113612	exon2			TCAAGAAAATGCT	BC012027	CCDS34047.1	4q25	2012-11-23			ENSG00000155016	ENSG00000155016		"Cytochrome P450s"	20582	protein-coding gene	gene with protein product	"spastic paraplegia 49"	610670				14975754, 14660610	Standard	XM_005262717		Approved	SPG49	uc003hyp.3	Q7Z449	OTTHUMG00000161084	ENST00000332884.6:c.749A>C	chr4.hg19:g.108866384A>C	ENSP00000333212:p.Lys250Thr	162.0	0.0		122.0	55.0	NM_183075	B2RMV7|Q96EQ6	Missense_Mutation	SNP	ENST00000332884.6	hg19	CCDS34047.1	.	.	.	.	.	.	.	.	.	.	A	8.895	0.955024	0.18507	.	.	ENSG00000155016	ENST00000332884;ENST00000424249;ENST00000508453	T;T	0.68765	-0.35;-0.35	5.63	3.15	0.36227	.	0.562750	0.21143	N	0.079450	T	0.42040	0.1185	N	0.16790	0.44	0.30712	N	0.749181	B	0.06786	0.001	B	0.16722	0.016	T	0.34129	-0.9841	10	0.07030	T	0.85	.	6.0234	0.19642	0.6052:0.2407:0.154:0.0	.	250	Q7Z449	CP2U1_HUMAN	T	250;207;41	ENSP00000333212:K250T;ENSP00000423667:K41T	ENSP00000333212:K250T	K	+	2	0	CYP2U1	109085833	0.011000	0.17503	0.941000	0.38009	0.654000	0.38779	0.206000	0.17375	0.404000	0.25506	0.533000	0.62120	AAA	.	.		0.453	CYP2U1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363691.2	NM_183075		C	108866384	A	C	108866384	3	2	298	1	0	0	0	0	1	0	0	0	4177	14	1	5	755	5	CYP2U1	4	108866384	Missense_Mutation	SNP	A	TCGA-G3-AAV2-01A-11D-A36X-10	13	108866384	82287892	15	43216			1	52		2	2	14	A		2.183668e-05
MCC	4163	hgsc.bcm.edu	37	chr5	112720863	112720863	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	ctggttcatgatctcagccaCagactcttccatattcagct	6	13	4	2			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr5:112720863C>A	ENST00000408903.3	-	2	632	c.217G>T	c.(217-219)Gtg>Ttg	p.V73L	CTD-2201G3.1_ENST00000416046.2_RNA	NM_001085377.1	NP_001078846	P23508	CRCM_HUMAN	mutated in colorectal cancers	0					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			endometrium(4)|kidney(3)|large_intestine(15)|liver(2)|lung(8)|ovary(2)|pancreas(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		ATCTCAGCCACAGACTCTTCC	0.428																																					p.V73L		Atlas-SNP	.											.	MCC	234	.	0			c.G217T						.						126	115	118					5																	112720863		1902	4119	6021	SO:0001583	missense	4163	exon2			CAGCCACAGACTC		CCDS4111.1, CCDS43351.1	5q21-q22	2013-01-10			ENSG00000171444	ENSG00000171444		"EF-hand domain containing"	6935	protein-coding gene	gene with protein product		159350				1848370	Standard	NM_002387		Approved		uc003kql.4	P23508	OTTHUMG00000128804	ENST00000408903.3:c.217G>T	chr5.hg19:g.112720863C>A	ENSP00000386227:p.Val73Leu	159.0	0.0		138.0	44.0	NM_001085377	D3DT05|Q6ZR04	Missense_Mutation	SNP	ENST00000408903.3	hg19	CCDS43351.1	.	.	.	.	.	.	.	.	.	.	C	12.56	1.974349	0.34848	.	.	ENSG00000171444	ENST00000408903	T	0.68765	-0.35	4.7	3.81	0.43845	.	0.128024	0.31809	N	0.007034	T	0.53769	0.1817	.	.	.	0.33285	D	0.562819	B	0.23128	0.08	B	0.18561	0.022	T	0.59716	-0.7402	9	0.27082	T	0.32	-3.3795	13.646	0.62281	0.1565:0.8435:0.0:0.0	.	73	P23508-2	.	L	73	ENSP00000386227:V73L	ENSP00000386227:V73L	V	-	1	0	MCC	112748762	1.000000	0.71417	0.993000	0.49108	0.818000	0.46254	5.417000	0.66423	1.267000	0.44247	-0.188000	0.12872	GTG	.	.		0.428	MCC-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370839.1	NM_001085377		A	112720863	C	A	112720863	3	1	298	1	0	0	0	0	1	0	0	0	9382	478	17	3	2975	3	MCC	5	112720863	Missense_Mutation	SNP	C	TCGA-G3-AAV2-01A-11D-A36X-10		112720863	68194397	16	43217										
CDHR2	54825	hgsc.bcm.edu	37	chr5	176002561	176002561	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	gcgacaaaggcatcaatgacCctgtgatctacagcatctcc	8	13	3	2			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr5:176002561C>T	ENST00000510636.1	+	10	1097	c.823C>T	c.(823-825)Cct>Tct	p.P275S	CDHR2_ENST00000506348.1_Missense_Mutation_p.P275S|CDHR2_ENST00000261944.5_Missense_Mutation_p.P275S	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	275	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|liver(1)|lung(23)|ovary(3)|prostate(5)|skin(4)|urinary_tract(1)	56						CATCAATGACCCTGTGATCTA	0.647																																					p.P275S		Atlas-SNP	.											.	CDHR2	152	.	0			c.C823T						.						98	102	100					5																	176002561		2203	4300	6503	SO:0001583	missense	54825	exon10			AATGACCCTGTGA	AB047004	CCDS34297.1	5q35.2	2011-07-01	2010-01-25	2010-01-25		ENSG00000074276		"Cadherins / Cadherin-related"	18231	protein-coding gene	gene with protein product	"protocadherin LKC"		"protocadherin 24"	PCDH24		11082270, 12117771	Standard	NM_001171976		Approved	PC-LKC, FLJ20124, FLJ20383, PCLKC	uc003mem.2	Q9BYE9		ENST00000510636.1:c.823C>T	chr5.hg19:g.176002561C>T	ENSP00000424565:p.Pro275Ser	103.0	0.0		75.0	35.0	NM_017675	A1L3U4|A6NC80|Q9NXP8	Missense_Mutation	SNP	ENST00000510636.1	hg19	CCDS34297.1	.	.	.	.	.	.	.	.	.	.	C	0.010	-1.795427	0.00617	.	.	ENSG00000074276	ENST00000510636;ENST00000261944;ENST00000506348	T;T;T	0.47528	0.84;0.84;0.84	4.27	0.0758	0.14400	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.29158	0.0725	N	0.25426	0.745	0.09310	N	1	B	0.18968	0.032	B	0.24394	0.053	T	0.31081	-0.9956	9	0.09338	T	0.73	6.0787	7.7866	0.29095	0.3596:0.2647:0.3757:0.0	.	275	Q9BYE9	CDHR2_HUMAN	S	275	ENSP00000424565:P275S;ENSP00000261944:P275S;ENSP00000421078:P275S	ENSP00000261944:P275S	P	+	1	0	CDHR2	175935167	0.000000	0.05858	0.007000	0.13788	0.081000	0.17604	-0.690000	0.05138	-0.209000	0.10156	-1.396000	0.01147	CCT	.	.		0.647	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675		T	176002561	C	T	176002561	3	4	298	1	0	0	0	0	1	0	0	0	3121	623	22	3	857	3	CDHR2	5	176002561	Missense_Mutation	SNP	C	TCGA-G3-AAV2-01A-11D-A36X-10	63281698	176002561	4912699	17	43218										
OR2B3	442184	hgsc.bcm.edu	37	chr6	29054623	29054623	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	gcagaaccaataattcatgaTgactacatagtggaggggtc	11	7	1	3			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr6:29054623T>C	ENST00000377173.2	-	1	467	c.403A>G	c.(403-405)Atc>Gtc	p.I135V		NM_001005226.2	NP_001005226.1	O76000	OR2B3_HUMAN	olfactory receptor, family 2, subfamily B, member 3	135						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|kidney(2)|lung(17)|prostate(1)|skin(2)	24						TAATTCATGATGACTACATAG	0.488																																					p.I135V		Atlas-SNP	.											.	OR2B3	44	.	0			c.A403G						.						72	70	70					6																	29054623		2203	4300	6503	SO:0001583	missense	442184	exon1			TCATGATGACTAC		CCDS34358.1	6p22.2-p21.31	2012-08-09	2008-10-22	2008-10-22	ENSG00000204703	ENSG00000204703		"GPCR / Class A : Olfactory receptors"	8238	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily B, member 3 pseudogene"	OR2B3P			Standard	NM_001005226		Approved	OR6-4	uc003nlx.3	O76000	OTTHUMG00000031226	ENST00000377173.2:c.403A>G	chr6.hg19:g.29054623T>C	ENSP00000366378:p.Ile135Val	109.0	0.0		106.0	41.0	NM_001005226	B0UYQ1|Q5ST41|Q96R13	Missense_Mutation	SNP	ENST00000377173.2	hg19	CCDS34358.1	.	.	.	.	.	.	.	.	.	.	T	11.27	1.589048	0.28357	.	.	ENSG00000204703	ENST00000377173	T	0.19669	2.13	3.9	3.9	0.45041	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41001	U	0.000980	T	0.06872	0.0175	L	0.41824	1.3	0.22305	N	0.99921	B	0.12630	0.006	B	0.14578	0.011	T	0.19224	-1.0312	10	0.46703	T	0.11	.	8.9749	0.35930	0.0:0.0:0.3722:0.6278	.	135	O76000	OR2B3_HUMAN	V	135	ENSP00000366378:I135V	ENSP00000366378:I135V	I	-	1	0	OR2B3	29162602	0.000000	0.05858	1.000000	0.80357	0.955000	0.61496	-0.042000	0.12063	1.385000	0.46445	0.472000	0.43445	ATC	.	.		0.488	OR2B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076469.2			C	29054623	T	C	29054623	3	2	298	1	0	0	0	0	1	0	0	0	10999	1464	51	2	542	2	OR2B3	6	29054623	Missense_Mutation	SNP	T	TCGA-G3-AAV2-01A-11D-A36X-10		29054623	142060444	18	43219										
PPP1R10	5514	hgsc.bcm.edu	37	chr6	30573978	30573980	+	In_Frame_Del	DEL	TTC	TTC	-													0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	aaaccaccactgtgctggcaTtcttcttcacaggcaccaag							TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr6:30573978_30573980delTTC	ENST00000376511.2	-	9	1227_1229	c.675_677delGAA	c.(673-678)aagaat>aat	p.K225del		NM_002714.3	NP_002705.2	Q96QC0	PP1RA_HUMAN	protein phosphatase 1, regulatory subunit 10	225	Interaction with TOX4. {ECO:0000250}.			K -> E (in Ref. 1; CAA73697). {ECO:0000305}.	protein import into nucleus (GO:0006606)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|nucleus (GO:0005634)|PTW/PP1 phosphatase complex (GO:0072357)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein phosphatase inhibitor activity (GO:0004864)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(3)|skin(1)	25						TGTGCTGGCATTCTTCTTCACAG	0.522																																					p.226_226del		Atlas-INDEL	.											.	PPP1R10	60	.	0			c.676_678del						.																																			SO:0001651	inframe_deletion	5514	exon9			.	Y13247	CCDS4681.1	6p21.3	2012-04-17	2011-10-04		ENSG00000204569	ENSG00000204569		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9284	protein-coding gene	gene with protein product	"phosphatase 1 nuclear targeting subunit", "HLA-C associated transcript 53"	603771	"protein phosphatase 1, regulatory (inhibitor) subunit 10"			9461602, 9784381	Standard	NM_002714		Approved	PNUTS, FB19, CAT53, p99	uc003nqn.2	Q96QC0	OTTHUMG00000031259	ENST00000376511.2:c.675_677delGAA	chr6.hg19:g.30573984_30573986delTTC	ENSP00000365694:p.Lys225del	39.0	0.0		46.0	13.0	NM_002714	O00405	In_Frame_Del	DEL	ENST00000376511.2	hg19	CCDS4681.1																																																																																			.	.		0.522	PPP1R10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076556.2	NM_002714		-	30573980	TTC	-	30573978	7	5	298	1	0	1	0	1	0	0	0	0	12364	1493	52	0	2193	0	PPP1R10	6	30573978	In_Frame_Del	DEL	TTC	TCGA-G3-AAV2-01A-11D-A36X-10	1519355	30573978	140541089	19	43220										
STK19	8859	hgsc.bcm.edu	37	chr6	31948260	31948260	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	tgctggagtcctcaccgtccGagatgctgggagctggtggc	16	11	1	1	rs534517982		TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr6:31948260G>T	ENST00000375333.2	+	6	901	c.848G>T	c.(847-849)cGa>cTa	p.R283L	C4A_ENST00000498271.1_5'Flank|C4A_ENST00000428956.2_5'Flank|STK19_ENST00000375331.2_Missense_Mutation_p.R279L|C4A_ENST00000537134.1_5'Flank	NM_032454.1	NP_115830.1	P49842	STK19_HUMAN	serine/threonine kinase 19	283					protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			skin(5)|upper_aerodigestive_tract(2)	7						CTCACCGTCCGAGATGCTGGG	0.567																																					p.R283L		Atlas-SNP	.											STK19_ENST00000375333,right_upper_lobe,carcinoma,0,1	STK19	33	.	0			c.G848T						.						71	62	65					6																	31948260		1511	2709	4220	SO:0001583	missense	8859	exon6			CCGTCCGAGATGC	X77474	CCDS4733.1, CCDS34417.1	6p21.33	2011-09-15			ENSG00000204344	ENSG00000204344			11398	protein-coding gene	gene with protein product		604977				8012361, 9812991	Standard	NM_032454		Approved	D6S60, G11, RP1	uc003nyv.3	P49842	OTTHUMG00000166424	ENST00000375333.2:c.848G>T	chr6.hg19:g.31948260G>T	ENSP00000364482:p.Arg283Leu	108.0	0.0		64.0	3.0	NM_032454	A6NF95|A6NFW8|B0QZR5|Q13159|Q31617|Q5JP77|Q5ST72|Q5ST75	Missense_Mutation	SNP	ENST00000375333.2	hg19	CCDS4733.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.946040	0.92593	.	.	ENSG00000204344	ENST00000375331;ENST00000375333	T;T	0.30448	1.53;1.53	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	T	0.42653	0.1212	L	0.59436	1.845	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;0.998	D;D;D;D	0.91635	0.999;0.965;0.999;0.97	T	0.12142	-1.0559	10	0.30078	T	0.28	-10.3514	17.2166	0.86946	0.0:0.0:1.0:0.0	.	236;279;283;236	C9IZ87;P49842-2;P49842;B7ZLI8	.;.;STK19_HUMAN;.	L	279;283	ENSP00000364480:R279L;ENSP00000364482:R283L	ENSP00000364480:R279L	R	+	2	0	STK19	32056239	1.000000	0.71417	0.990000	0.47175	0.926000	0.56050	8.148000	0.89630	2.364000	0.80123	0.555000	0.69702	CGA	.	.		0.567	STK19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076484.3			T	31948260	G	T	31948260	3	4	298	1	0	0	0	0	1	0	0	0	15307	1058	37	1	870	1	STK19	6	31948260	Missense_Mutation	SNP	G	TCGA-G3-AAV2-01A-11D-A36X-10	1374282	31948260	139166807	20	43221										
HS3ST5	222537	hgsc.bcm.edu	37	chr6	114378489	114378489	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	aaaaggatgaaagaatttgcGcaatttagtaatgacagagg	11	3	0	4	rs374141405		TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr6:114378489G>A	ENST00000312719.5	-	5	2161	c.973C>T	c.(973-975)Cgc>Tgc	p.R325C	RP3-399L15.3_ENST00000519104.1_RNA|RP3-399L15.3_ENST00000519270.1_RNA|RP3-399L15.3_ENST00000523087.1_RNA|HS3ST5_ENST00000411826.1_Missense_Mutation_p.R325C			Q8IZT8	HS3S5_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	325					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|negative regulation of coagulation (GO:0050819)|protein sulfation (GO:0006477)|regulation of viral entry into host cell (GO:0046596)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)			breast(4)|endometrium(2)|kidney(1)|large_intestine(7)|lung(17)|ovary(1)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	41		all_cancers(87;0.0587)|Colorectal(196;0.0676)|all_epithelial(87;0.154)		OV - Ovarian serous cystadenocarcinoma(136;0.00937)|all cancers(137;0.0117)|Epithelial(106;0.0274)|GBM - Glioblastoma multiforme(226;0.143)		AAGAATTTGCGCAATTTAGTA	0.408																																					p.R325C		Atlas-SNP	.											HS3ST5,NS,carcinoma,0,2	HS3ST5	80	.	0			c.C973T						.	G	CYS/ARG	1,4405	4.2+/-10.8	0,1,2202	64	68	66		973	6	1	6		66	1,8597	1.2+/-3.3	0,1,4298	no	missense	HS3ST5	NM_153612.3	180	0,2,6500	AA,AG,GG		0.0116,0.0227,0.0154	benign	325/347	114378489	2,13002	2203	4299	6502	SO:0001583	missense	222537	exon2			ATTTGCGCAATTT	AF503292	CCDS34517.1	6q21	2011-11-16			ENSG00000249853	ENSG00000249853		"Sulfotransferases, membrane-bound"	19419	protein-coding gene	gene with protein product		609407				12138164	Standard	NM_153612		Approved	3-OST-5	uc003pwg.4	Q8IZT8	OTTHUMG00000015412	ENST00000312719.5:c.973C>T	chr6.hg19:g.114378489G>A	ENSP00000427888:p.Arg325Cys	136.0	0.0		99.0	41.0	NM_153612	A8K1J2|Q52LI2|Q8N285	Missense_Mutation	SNP	ENST00000312719.5	hg19	CCDS34517.1	.	.	.	.	.	.	.	.	.	.	G	15.06	2.722416	0.48728	2.27E-4	1.16E-4	ENSG00000249853	ENST00000312719;ENST00000411826	D;D	0.82803	-1.65;-1.65	6.02	6.02	0.97574	Sulfotransferase domain (1);	0.108901	0.64402	D	0.000004	D	0.83031	0.5166	M	0.63208	1.945	0.80722	D	1	D	0.69078	0.997	P	0.49252	0.604	T	0.81752	-0.0789	10	0.41790	T	0.15	.	20.5407	0.99260	0.0:0.0:1.0:0.0	.	325	Q8IZT8	HS3S5_HUMAN	C	325	ENSP00000427888:R325C;ENSP00000440332:R325C	ENSP00000427888:R325C	R	-	1	0	HS3ST5	114485182	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.618000	0.83043	2.865000	0.98341	0.655000	0.94253	CGC	.	.		0.408	HS3ST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041911.2	NM_153612		A	114378489	G	A	114378489	3	1	298	1	0	0	0	0	1	0	0	0	7377	1087	38	1	71	1	HS3ST5	6	114378489	Missense_Mutation	SNP	G	TCGA-G3-AAV2-01A-11D-A36X-10	82430229	114378489	56736578	21	43222										
LAMA2	3908	hgsc.bcm.edu	37	chr6	129663536	129663536	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	tctgtgaacgatgtgctcttGgatactatggaattgtcaag	11	6	3	1			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr6:129663536G>C	ENST00000421865.2	+	30	4409	c.4360G>C	c.(4360-4362)Gga>Cga	p.G1454R		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	1454	Laminin EGF-like 15. {ECO:0000255|PROSITE-ProRule:PRU00460}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		ATGTGCTCTTGGATACTATGG	0.378																																					p.G1454R		Atlas-SNP	.											.	LAMA2	481	.	0			c.G4360C						.						163	151	155					6																	129663536		2203	4300	6503	SO:0001583	missense	3908	exon30			GCTCTTGGATACT	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"Laminins"	6482	protein-coding gene	gene with protein product	"merosin", "congenital muscular dystrophy"	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.4360G>C	chr6.hg19:g.129663536G>C	ENSP00000400365:p.Gly1454Arg	103.0	0.0		90.0	36.0	NM_000426	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	hg19	CCDS5138.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.799841	0.90538	.	.	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865	T	0.66638	-0.22	5.57	5.57	0.84162	EGF-like, laminin (4);	0.000000	0.85682	D	0.000000	D	0.87888	0.6291	H	0.97365	3.99	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.993	D	0.91403	0.5145	10	0.87932	D	0	.	18.6919	0.91586	0.0:0.0:1.0:0.0	.	1454;1454	A6NF00;P24043	.;LAMA2_HUMAN	R	1454	ENSP00000400365:G1454R	ENSP00000346769:G1454R	G	+	1	0	LAMA2	129705229	1.000000	0.71417	0.976000	0.42696	0.999000	0.98932	8.479000	0.90431	2.785000	0.95823	0.655000	0.94253	GGA	.	.		0.378	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			C	129663536	G	C	129663536	3	2	298	1	0	0	0	0	1	0	0	0	8615	1349	47	4	4478	4	LAMA2	6	129663536	Missense_Mutation	SNP	G	TCGA-G3-AAV2-01A-11D-A36X-10	15285047	129663536	41451531	22	43223										
FAM126A	84668	hgsc.bcm.edu	37	chr7	22985753	22985753	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	aacttcagatatctccatcaGttcttcttgacctgttaatt	4	10	5	2			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr7:22985753G>C	ENST00000432176.2	-	11	1253	c.1021C>G	c.(1021-1023)Ctg>Gtg	p.L341V	FAM126A_ENST00000409923.1_3'UTR|FAM126A_ENST00000498833.1_5'UTR	NM_032581.3	NP_115970.2	Q9BYI3	HYCCI_HUMAN	family with sequence similarity 126, member A	341					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(8)|urinary_tract(2)	23						ATCTCCATCAGTTCTTCTTGA	0.338																																					p.L341V		Atlas-SNP	.											.	FAM126A	53	.	0			c.C1021G						.						50	52	51					7																	22985753		2203	4295	6498	SO:0001583	missense	84668	exon11			CCATCAGTTCTTC	BC018710	CCDS5377.1	7p15.3	2008-10-02			ENSG00000122591	ENSG00000122591			24587	protein-coding gene	gene with protein product	"down regulated by Ctnnb1, a"	610531				10910037, 16951682	Standard	NM_032581		Approved	DRCTNNB1A, HCC, HYCC1, hyccin	uc003svm.4	Q9BYI3	OTTHUMG00000128435	ENST00000432176.2:c.1021C>G	chr7.hg19:g.22985753G>C	ENSP00000403396:p.Leu341Val	84.0	0.0		76.0	4.0	NM_032581	A4D145|Q6N010|Q75MR4|Q7LDZ4|Q96MX1|Q96NQ6	Missense_Mutation	SNP	ENST00000432176.2	hg19	CCDS5377.1	.	.	.	.	.	.	.	.	.	.	G	0.323	-0.960826	0.02249	.	.	ENSG00000122591	ENST00000432176	T	0.78364	-1.17	6.17	4.39	0.52855	.	0.000000	0.85682	D	0.000000	T	0.69477	0.3115	L	0.59436	1.845	0.80722	D	1	B	0.21606	0.058	B	0.20184	0.028	T	0.59867	-0.7373	10	0.12103	T	0.63	-1.4832	9.1636	0.37038	0.1303:0.1215:0.7482:0.0	.	341	Q9BYI3	HYCCI_HUMAN	V	341	ENSP00000403396:L341V	ENSP00000403396:L341V	L	-	1	2	FAM126A	22952278	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.730000	0.55006	0.955000	0.37878	0.655000	0.94253	CTG	.	.		0.338	FAM126A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250230.1	NM_032581		C	22985753	G	C	22985753	3	2	298	1	0	0	0	0	1	0	0	0	5434	1020	36	4	548	4	FAM126A	7	22985753	Missense_Mutation	SNP	G	TCGA-G3-AAV2-01A-11D-A36X-10		22985753	136152910	23	43224										
PLXNA4	91584	hgsc.bcm.edu	37	chr7	132192343	132192343	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	ccccggtaacaagactgcagCcgctccttaatgcggtcatt	9	14	1	1			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr7:132192343C>A	ENST00000359827.3	-	2	2072	c.1110G>T	c.(1108-1110)cgG>cgT	p.R370R	PLXNA4_ENST00000423507.2_Silent_p.R370R|PLXNA4_ENST00000378539.5_Silent_p.R370R|PLXNA4_ENST00000321063.4_Silent_p.R370R			Q9HCM2	PLXA4_HUMAN	plexin A4	370	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						AAGACTGCAGCCGCTCCTTAA	0.587																																					p.R370R		Atlas-SNP	.											.	PLXNA4	873	.	0			c.G1110T						.						65	57	60					7																	132192343		2203	4300	6503	SO:0001819	synonymous_variant	91584	exon2			CTGCAGCCGCTCC	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"Plexins"	9102	protein-coding gene	gene with protein product		604280	"plexin A4, A", "plexin A4, B"	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.1110G>T	chr7.hg19:g.132192343C>A		80.0	0.0		62.0	19.0	NM_001105543	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Silent	SNP	ENST00000359827.3	hg19	CCDS43646.1																																																																																			.	.		0.587	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		A	132192343	C	A	132192343	2	1	298	1	0	0	0	0	0	0	0	1	12131	726	26	3		3	PLXNA4	7	132192343	Silent	SNP	C	TCGA-G3-AAV2-01A-11D-A36X-10	109206590	132192343	26946320	24	43225										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113331084	113331084	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	accttgacaaactggaggtgCtccatccatctgcagtcgtt	9	12	1	1			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr8:113331084C>A	ENST00000297405.5	-	47	7586	c.7342G>T	c.(7342-7344)Gca>Tca	p.A2448S	CSMD3_ENST00000343508.3_Missense_Mutation_p.A2408S|CSMD3_ENST00000352409.3_Missense_Mutation_p.A2378S|CSMD3_ENST00000455883.2_Missense_Mutation_p.A2344S	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2448	Sushi 13. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						ACTGGAGGTGCTCCATCCATC	0.333										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.A2448S		Atlas-SNP	.											.	CSMD3	2325	.	0			c.G7342T						.						105	95	98					8																	113331084		2203	4300	6503	SO:0001583	missense	114788	exon47			GAGGTGCTCCATC	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.7342G>T	chr8.hg19:g.113331084C>A	ENSP00000297405:p.Ala2448Ser	44.0	0.0		61.0	12.0	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	12.59	1.982361	0.34942	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.63255	-0.03;-0.03;-0.03;-0.03;-0.03	5.82	4.94	0.65067	Complement control module (2);Sushi/SCR/CCP (3);	0.165679	0.40818	N	0.001003	T	0.27967	0.0689	N	0.01003	-1.06	0.30476	N	0.772834	B;B;B	0.14012	0.009;0.005;0.005	B;B;B	0.16289	0.013;0.014;0.015	T	0.21655	-1.0239	10	0.05721	T	0.95	.	11.9201	0.52787	0.1373:0.7306:0.132:0.0	.	2344;2448;2408	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	S	2408;2448;1718;2344;2378	ENSP00000345799:A2408S;ENSP00000297405:A2448S;ENSP00000341558:A1718S;ENSP00000412263:A2344S;ENSP00000343124:A2378S	ENSP00000297405:A2448S	A	-	1	0	CSMD3	113400260	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.851000	0.48302	1.464000	0.47987	0.579000	0.79373	GCA	.	.		0.333	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	113331084	C	A	113331084	3	1	298	1	0	0	0	0	1	0	0	0	3948	797	28	3	3881	3	CSMD3	8	113331084	Missense_Mutation	SNP	C	TCGA-G3-AAV2-01A-11D-A36X-10		113331084	33032938	25	43226			2	53		2	2	35	C		5.711031e-05
CSMD3	114788	hgsc.bcm.edu	37	chr8	113331118	113331118	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	agtcgttctcctaatctgcaCgtcagaattgcattaccaac	6	12	3	1	rs371684642		TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr8:113331118C>A	ENST00000297405.5	-	47	7552	c.7308G>T	c.(7306-7308)acG>acT	p.T2436T	CSMD3_ENST00000343508.3_Silent_p.T2396T|CSMD3_ENST00000352409.3_Silent_p.T2366T|CSMD3_ENST00000455883.2_Silent_p.T2332T	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2436	Sushi 13. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.T2436T(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						CTAATCTGCACGTCAGAATTG	0.353										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.T2436T		Atlas-SNP	.											CSMD3,rectum,carcinoma,0,1	CSMD3	2325	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G7308T						.						108	100	103					8																	113331118		2203	4300	6503	SO:0001819	synonymous_variant	114788	exon47			TCTGCACGTCAGA	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.7308G>T	chr8.hg19:g.113331118C>A		54.0	0.0		68.0	15.0	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	hg19	CCDS6315.1																																																																																			.	.		0.353	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	113331118	C	A	113331118	2	1	298	1	0	0	0	0	0	0	0	1	3948	523	19	1		1	CSMD3	8	113331118	Silent	SNP	C	TCGA-G3-AAV2-01A-11D-A36X-10	34	113331118	33032904	26	43227			2	53		2	2	35	C		5.711031e-05
ACTL7A	10881	hgsc.bcm.edu	37	chr9	111625852	111625852	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	gggtttccaaccattgtgggTccaccgctttgagtacgagg	13	10	0	1			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr9:111625852T>A	ENST00000333999.3	+	1	1250	c.1250T>A	c.(1249-1251)gTc>gAc	p.V417D		NM_006687.2	NP_006678.1	Q9Y615	ACL7A_HUMAN	actin-like 7A	417						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|male germ cell nucleus (GO:0001673)|motile cilium (GO:0031514)|nucleus (GO:0005634)|protein complex (GO:0043234)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(2)|large_intestine(4)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						CCATTGTGGGTCCACCGCTTT	0.572																																					p.V417D	Esophageal Squamous(177;1480 3591 17554)	Atlas-SNP	.											.	ACTL7A	34	.	0			c.T1250A						.						85	74	78					9																	111625852		2203	4300	6503	SO:0001583	missense	10881	exon1			TGTGGGTCCACCG	BC014610	CCDS6772.1	9q31	2008-02-05			ENSG00000187003	ENSG00000187003			161	protein-coding gene	gene with protein product		604303				10373328	Standard	NM_006687		Approved		uc004bdj.1	Q9Y615	OTTHUMG00000020461	ENST00000333999.3:c.1250T>A	chr9.hg19:g.111625852T>A	ENSP00000334300:p.Val417Asp	127.0	0.0		101.0	40.0	NM_006687	B2RC83|Q5JSV0	Missense_Mutation	SNP	ENST00000333999.3	hg19	CCDS6772.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.185182	0.78677	.	.	ENSG00000187003	ENST00000333999	D	0.96136	-3.92	5.44	5.44	0.79542	.	0.000000	0.41938	D	0.000782	D	0.98194	0.9403	M	0.93197	3.39	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99264	1.0891	10	0.87932	D	0	.	13.7503	0.62904	0.0:0.0:0.0:1.0	.	417	Q9Y615	ACL7A_HUMAN	D	417	ENSP00000334300:V417D	ENSP00000334300:V417D	V	+	2	0	ACTL7A	110665673	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.018000	0.88722	2.193000	0.70182	0.533000	0.62120	GTC	.	.		0.572	ACTL7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053570.1	NM_006687		A	111625852	T	A	111625852	3	1	298	1	0	0	0	0	1	0	0	0	200	1667	58	4	1252	4	ACTL7A	9	111625852	Missense_Mutation	SNP	T	TCGA-G3-AAV2-01A-11D-A36X-10		111625852	29587579	27	43228										
CHST3	9469	hgsc.bcm.edu	37	chr10	73767947	73767947	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	cagaaggcccgcgagatgtaCcgcttcgccggcatccccct	11	17	0	2			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr10:73767947C>T	ENST00000373115.4	+	3	1595	c.1158C>T	c.(1156-1158)taC>taT	p.Y386Y		NM_004273.4	NP_004264.2	Q7LGC8	CHST3_HUMAN	carbohydrate (chondroitin 6) sulfotransferase 3	386					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)|T cell homeostasis (GO:0043029)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin 6-sulfotransferase activity (GO:0008459)|proteoglycan sulfotransferase activity (GO:0050698)|sulfotransferase activity (GO:0008146)			endometrium(1)|lung(5)	6						GCGAGATGTACCGCTTCGCCG	0.692																																					p.Y386Y		Atlas-SNP	.											.	CHST3	36	.	0			c.C1158T						.						10	11	10					10																	73767947		2087	4085	6172	SO:0001819	synonymous_variant	9469	exon3			GATGTACCGCTTC	AB017915	CCDS7312.1	10q22.1	2007-03-14			ENSG00000122863	ENSG00000122863		"Sulfotransferases, membrane-bound"	1971	protein-coding gene	gene with protein product		603799				9883891, 9714738	Standard	NM_004273		Approved	C6ST, C6ST1	uc001jsn.3	Q7LGC8	OTTHUMG00000018431	ENST00000373115.4:c.1158C>T	chr10.hg19:g.73767947C>T		168.0	0.0		117.0	48.0	NM_004273	O75099|Q52M30	Silent	SNP	ENST00000373115.4	hg19	CCDS7312.1																																																																																			.	.		0.692	CHST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048563.1	NM_004273		T	73767947	C	T	73767947	2	4	298	1	0	0	0	0	0	0	0	1	3407	518	18	3		3	CHST3	10	73767947	Silent	SNP	C	TCGA-G3-AAV2-01A-11D-A36X-10		73767947	61766800	28	43229										
ABCC2	1244	hgsc.bcm.edu	37	chr10	101601846	101601846	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	ctttgttctgtccaatgcacTcaatgtgagtttgaaggttg	10	7	2	2			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr10:101601846T>A	ENST00000370449.4	+	26	3850	c.3737T>A	c.(3736-3738)cTc>cAc	p.L1246H		NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	1246	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular chloride ion homeostasis (GO:0030644)|drug transmembrane transport (GO:0006855)|prostaglandin transport (GO:0015732)|response to arsenic-containing substance (GO:0046685)|response to estrogen (GO:0043627)|response to heat (GO:0009408)|response to methotrexate (GO:0031427)|response to oxidative stress (GO:0006979)|thyroid hormone transport (GO:0070327)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(5)|endometrium(9)|kidney(2)|large_intestine(20)|liver(1)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	67		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Aminohippurate(DB00345)|Arsenic trioxide(DB01169)|Atorvastatin(DB01076)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carboplatin(DB00958)|Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Eprosartan(DB00876)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Ezetimibe(DB00973)|Furosemide(DB00695)|Fusidic Acid(DB02703)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Leucovorin(DB00650)|Levetiracetam(DB01202)|Lomefloxacin(DB00978)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nifedipine(DB01115)|Norgestimate(DB00957)|Ofloxacin(DB01165)|Olmesartan(DB00275)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Ritonavir(DB00503)|Saquinavir(DB01232)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Sulfasalazine(DB00795)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Tenofovir(DB00300)|Tetrahydrofolic acid(DB00116)|Ursodeoxycholic acid(DB01586)|Vasopressin(DB00067)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	TCCAATGCACTCAATGTGAGT	0.418																																					p.L1246H		Atlas-SNP	.											.	ABCC2	160	.	0			c.T3737A						.						235	220	225					10																	101601846		2203	4300	6503	SO:0001583	missense	1244	exon26			ATGCACTCAATGT	U63970	CCDS7484.1	10q24	2012-03-14			ENSG00000023839	ENSG00000023839		"ATP binding cassette transporters / subfamily C"	53	protein-coding gene	gene with protein product		601107	"canalicular multispecific organic anion transporter 1"	CMOAT		8797578, 9284939	Standard	XM_006717630		Approved	DJS, MRP2, cMRP	uc001kqf.2	Q92887	OTTHUMG00000018895	ENST00000370449.4:c.3737T>A	chr10.hg19:g.101601846T>A	ENSP00000359478:p.Leu1246His	76.0	0.0		63.0	28.0	NM_000392	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Missense_Mutation	SNP	ENST00000370449.4	hg19	CCDS7484.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.410000	0.83340	.	.	ENSG00000023839	ENST00000370449	D	0.90444	-2.67	6.16	5.03	0.67393	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.241597	0.41294	D	0.000910	D	0.97222	0.9092	H	0.98965	4.385	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97485	1.0050	10	0.87932	D	0	-16.1753	12.1862	0.54241	0.0:0.0661:0.0:0.9339	.	1246	Q92887	MRP2_HUMAN	H	1246	ENSP00000359478:L1246H	ENSP00000359478:L1246H	L	+	2	0	ABCC2	101591836	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	7.684000	0.84104	1.146000	0.42352	0.528000	0.53228	CTC	.	.		0.418	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392		A	101601846	T	A	101601846	3	1	298	1	0	0	0	0	1	0	0	0	53	1551	54	4	3839	4	ABCC2	10	101601846	Missense_Mutation	SNP	T	TCGA-G3-AAV2-01A-11D-A36X-10	27833899	101601846	33932901	29	43230										
KCNA4	3739	hgsc.bcm.edu	37	chr11	30033717	30033717	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	gttcacaacagtcactgtagCggactgaactgtagccgcca	10	12	2	1			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr11:30033717C>T	ENST00000328224.6	-	2	1742	c.509G>A	c.(508-510)cGc>cAc	p.R170H	KCNA4_ENST00000526518.1_5'Flank	NM_002233.3	NP_002224.1	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 4	170					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	potassium ion binding (GO:0030955)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(39)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	78					Dalfampridine(DB06637)	GTCACTGTAGCGGACTGAACT	0.502																																					p.R170H		Atlas-SNP	.											KCNA4,NS,carcinoma,0,1	KCNA4	158	.	0			c.G509A						.						65	65	65					11																	30033717		2153	4253	6406	SO:0001583	missense	3739	exon2			CTGTAGCGGACTG	M55514	CCDS41629.1	11p14	2012-07-05	2002-07-10			ENSG00000182255		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6222	protein-coding gene	gene with protein product		176266	"potassium voltage-gated channel, shaker-related subfamily, member 4-like"	KCNA4L		2263489, 16382104	Standard	NM_002233		Approved	Kv1.4, HK1, HPCN2	uc001msk.3	P22459		ENST00000328224.6:c.509G>A	chr11.hg19:g.30033717C>T	ENSP00000328511:p.Arg170His	67.0	1.0		66.0	26.0	NM_002233		Missense_Mutation	SNP	ENST00000328224.6	hg19	CCDS41629.1	.	.	.	.	.	.	.	.	.	.	C	18.14	3.557223	0.65425	.	.	ENSG00000182255	ENST00000328224	D	0.96940	-4.18	4.66	4.66	0.58398	.	0.133902	0.45126	U	0.000393	D	0.92724	0.7687	N	0.14661	0.345	0.45747	D	0.998647	D	0.60575	0.988	P	0.49799	0.622	D	0.91051	0.4878	10	0.13108	T	0.6	.	15.7518	0.77992	0.0:1.0:0.0:0.0	.	170	P22459	KCNA4_HUMAN	H	170	ENSP00000328511:R170H	ENSP00000328511:R170H	R	-	2	0	KCNA4	29990293	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	4.447000	0.60020	2.145000	0.66743	0.561000	0.74099	CGC	.	.		0.502	KCNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388074.2	NM_002233		T	30033717	C	T	30033717	3	4	298	1	0	0	0	0	1	0	0	0	8014	768	27	1	1456	1	KCNA4	11	30033717	Missense_Mutation	SNP	C	TCGA-G3-AAV2-01A-11D-A36X-10		30033717	104972799	30	43231										
DAK	26007	hgsc.bcm.edu	37	chr11	61110239	61110241	+	In_Frame_Del	DEL	TGA	TGA	-													0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	acccgcaggctcctcagttgTgatgatggtcaacaacctgg							TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	TGA	TGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr11:61110239_61110241delTGA	ENST00000394900.3	+	10	1017_1019	c.788_790delTGA	c.(787-792)gtgatg>gtg	p.M265del		NM_015533.3	NP_056348.2	Q3LXA3	DHAK_HUMAN	dihydroxyacetone kinase 2 homolog (S. cerevisiae)	265	DhaK. {ECO:0000255|PROSITE- ProRule:PRU00814}.				carbohydrate phosphorylation (GO:0046835)|cellular carbohydrate metabolic process (GO:0044262)|glycerol metabolic process (GO:0006071)|innate immune response (GO:0045087)|regulation of innate immune response (GO:0045088)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|FAD-AMP lyase (cyclizing) activity (GO:0034012)|glycerone kinase activity (GO:0004371)|metal ion binding (GO:0046872)|triokinase activity (GO:0050354)			NS(1)|breast(3)|endometrium(3)|large_intestine(5)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	23						TCCTCAGTTGTGATGATGGTCAA	0.621																																					p.263_263del		Atlas-INDEL	.											.	DAK	52	.	0			c.787_789del						.																																			SO:0001651	inframe_deletion	26007	exon10			.		CCDS8003.1	11q12.2	2009-11-06	2006-04-04		ENSG00000149476	ENSG00000149476			24552	protein-coding gene	gene with protein product		615844	"dihydroxyacetone kinase 2 homolog (yeast)"				Standard	XM_005273898		Approved	DKFZP586B1621, NET45	uc001nre.3	Q3LXA3	OTTHUMG00000168076	ENST00000394900.3:c.788_790delTGA	chr11.hg19:g.61110242_61110244delTGA	ENSP00000378360:p.Met265del	109.0	0.0		86.0	30.0	NM_015533	Q2L9C1|Q53EQ9|Q9BVA7|Q9H895	In_Frame_Del	DEL	ENST00000394900.3	hg19	CCDS8003.1																																																																																			.	.		0.621	DAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394425.4	NM_015533		-	61110241	TGA	-	61110239	7	5	298	1	0	1	0	1	0	0	0	0	4230	1696	59	0	822	0	DAK	11	61110239	In_Frame_Del	DEL	TGA	TCGA-G3-AAV2-01A-11D-A36X-10	31076522	61110239	73896277	31	43232										
AHNAK	79026	hgsc.bcm.edu	37	chr11	62291321	62291321	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	tgggacctttcaagcctcccTccggaccttccacattgaga	8	15	1	1			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr11:62291321T>A	ENST00000378024.4	-	5	10842	c.10568A>T	c.(10567-10569)gAg>gTg	p.E3523V	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	3523					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				CAAGCCTCCCTCCGGACCTTC	0.483																																					p.E3523V		Atlas-SNP	.											.	AHNAK	532	.	0			c.A10568T						.						107	114	111					11																	62291321		2202	4299	6501	SO:0001583	missense	79026	exon5			CCTCCCTCCGGAC	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.10568A>T	chr11.hg19:g.62291321T>A	ENSP00000367263:p.Glu3523Val	79.0	0.0		75.0	27.0	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	hg19	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	-	19.65	3.866916	0.72065	.	.	ENSG00000124942	ENST00000378024	T	0.01133	5.29	4.65	4.65	0.58169	.	0.328463	0.31177	N	0.008104	T	0.04724	0.0128	M	0.81497	2.545	0.43632	D	0.996028	D	0.57571	0.98	P	0.53649	0.731	T	0.29243	-1.0018	10	0.54805	T	0.06	.	13.765	0.62990	0.0:0.0:0.0:1.0	.	3523	Q09666	AHNK_HUMAN	V	3523	ENSP00000367263:E3523V	ENSP00000367263:E3523V	E	-	2	0	AHNAK	62047897	0.750000	0.28316	0.828000	0.32881	0.843000	0.47879	1.933000	0.40153	1.744000	0.51775	0.372000	0.22366	GAG	.	.		0.483	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		A	62291321	T	A	62291321	3	1	298	1	0	0	0	0	1	0	0	0	414	1551	54	4	7224	4	AHNAK	11	62291321	Missense_Mutation	SNP	T	TCGA-G3-AAV2-01A-11D-A36X-10	1181082	62291321	72715195	32	43233										
ADAMTS20	80070	hgsc.bcm.edu	37	chr12	43821122	43821122	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	atgacttacttctccccaatTtccgtagttccactgtggac	6	13	1	1			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr12:43821122T>A	ENST00000389420.3	-	27	4095	c.4096A>T	c.(4096-4098)Aat>Tat	p.N1366Y	ADAMTS20_ENST00000395541.2_Missense_Mutation_p.N484Y|ADAMTS20_ENST00000553158.1_Missense_Mutation_p.N1366Y	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	1366	TSP type-1 10. {ECO:0000255|PROSITE- ProRule:PRU00210}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		TCTCCCCAATTTCCGTAGTTC	0.403																																					p.N1366Y		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.A4096T						.						86	75	79					12																	43821122		2203	4300	6503	SO:0001583	missense	80070	exon27			CCCAATTTCCGTA	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.4096A>T	chr12.hg19:g.43821122T>A	ENSP00000374071:p.Asn1366Tyr	122.0	0.0		105.0	26.0	NM_025003	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	hg19	CCDS31778.2	.	.	.	.	.	.	.	.	.	.	T	13.22	2.173541	0.38413	.	.	ENSG00000173157	ENST00000389420;ENST00000549670;ENST00000395541;ENST00000553158;ENST00000389417	T;T;T;T	0.53423	0.62;0.62;0.62;0.62	4.94	2.57	0.30868	.	0.521883	0.18557	N	0.137744	T	0.63474	0.2514	M	0.88704	2.975	0.19945	N	0.999944	P;P	0.48640	0.46;0.913	B;P	0.53266	0.436;0.722	T	0.57528	-0.7796	10	0.66056	D	0.02	.	9.3942	0.38392	0.0:0.1483:0.0:0.8517	.	1366;484	P59510;E9PBD5	ATS20_HUMAN;.	Y	1366;496;484;1366;1366	ENSP00000374071:N1366Y;ENSP00000447427:N496Y;ENSP00000378911:N484Y;ENSP00000448341:N1366Y	ENSP00000374068:N1366Y	N	-	1	0	ADAMTS20	42107389	0.696000	0.27757	0.091000	0.20842	0.523000	0.34469	3.801000	0.55545	0.438000	0.26450	0.528000	0.53228	AAT	.	.		0.403	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		A	43821122	T	A	43821122	3	1	298	1	0	0	0	0	1	0	0	0	266	1841	64	4	1687	4	ADAMTS20	12	43821122	Missense_Mutation	SNP	T	TCGA-G3-AAV2-01A-11D-A36X-10		43821122	90030773	33	43234										
MED13L	23389	hgsc.bcm.edu	37	chr12	116443800	116443800	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	gcattatcctgccggacatcTgtaggaaaggaggcaaaaga	12	8	1	1			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr12:116443800T>C	ENST00000281928.3	-	13	2551		c.e13-2			NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like							mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		GCCGGACATCTGTAGGAAAGG	0.493																																					.		Atlas-SNP	.											.	MED13L	193	.	0			c.2345-2A>G						.						69	70	70					12																	116443800		2203	4300	6503	SO:0001630	splice_region_variant	23389	exon14			GACATCTGTAGGA	AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"thyroid hormone receptor associated protein 2"	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.2345-2A>G	chr12.hg19:g.116443800T>C		82.0	0.0		84.0	35.0	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Splice_Site	SNP	ENST00000281928.3	hg19	CCDS9177.1	.	.	.	.	.	.	.	.	.	.	T	18.32	3.598135	0.66332	.	.	ENSG00000123066	ENST00000281928	.	.	.	6.02	6.02	0.97574	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5446	0.84426	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	MED13L	114928183	1.000000	0.71417	0.990000	0.47175	0.944000	0.59088	6.824000	0.75288	2.311000	0.77944	0.533000	0.62120	.	.	.		0.493	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3		Intron	C	116443800	T	C	116443800	5	2	298	1	0	0	0	0	0	0	1	0	9440	1594	55	2	4365	2	MED13L	12	116443800	Splice_Site	SNP	T	TCGA-G3-AAV2-01A-11D-A36X-10	72622678	116443800	17408095	34	43235										
C13orf39	196541	hgsc.bcm.edu	37	chr13	103346826	103346826	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	cccggcgcccaggctgctgcGcggagctcagacacacgtcc	13	18	1	1			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr13:103346826G>A	ENST00000267273.6	-	1	28	c.23C>T	c.(22-24)gCg>gTg	p.A8V		NM_001010977.1	NP_001010977.1	Q5VZV1	MT21C_HUMAN	methyltransferase like 21C	8					peptidyl-lysine methylation (GO:0018022)|protein methylation (GO:0006479)	nucleus (GO:0005634)	protein-lysine N-methyltransferase activity (GO:0016279)			breast(1)|large_intestine(3)|lung(2)|skin(1)	7						AGGCTGCTGCGCGGAGCTCAG	0.577																																					p.A8V		Atlas-SNP	.											.	METTL21C	23	.	0			c.C23T						.						15	17	16					13																	103346826		2201	4299	6500	SO:0001583	missense	196541	exon1			TGCTGCGCGGAGC		CCDS32003.1	13q33.1	2011-03-03	2011-03-03	2011-03-03	ENSG00000139780	ENSG00000139780			33717	protein-coding gene	gene with protein product		615259	"chromosome 13 open reading frame 39"	C13orf39			Standard	NM_001010977		Approved	LOC196541	uc001vpj.4	Q5VZV1	OTTHUMG00000017304	ENST00000267273.6:c.23C>T	chr13.hg19:g.103346826G>A	ENSP00000267273:p.Ala8Val	42.0	0.0		36.0	13.0	NM_001010977		Missense_Mutation	SNP	ENST00000267273.6	hg19	CCDS32003.1	.	.	.	.	.	.	.	.	.	.	G	10.44	1.351210	0.24512	.	.	ENSG00000139780	ENST00000267273	T	0.14893	2.47	3.79	-1.74	0.08056	.	1.133920	0.06768	N	0.783024	T	0.05960	0.0155	N	0.03608	-0.345	0.21740	N	0.999562	B	0.09022	0.002	B	0.04013	0.001	T	0.35822	-0.9773	10	0.30854	T	0.27	0.5169	1.38	0.02228	0.1602:0.1387:0.4585:0.2427	.	8	Q5VZV1	MT21C_HUMAN	V	8	ENSP00000267273:A8V	ENSP00000267273:A8V	A	-	2	0	METTL21C	102144827	0.000000	0.05858	0.722000	0.30670	0.875000	0.50365	-0.483000	0.06536	-0.257000	0.09459	-0.300000	0.09419	GCG	.	.		0.577	METTL21C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045682.2	NM_001010977		A	103346826	G	A	103346826	3	1	298	1	0	0	0	0	1	0	0	0	1734	1087	38	1	787	1	C13orf39	13	103346826	Missense_Mutation	SNP	G	TCGA-G3-AAV2-01A-11D-A36X-10		103346826	11823052	35	43236										
PSMB11	122706	hgsc.bcm.edu	37	chr14	23511534	23511534	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	gggctgtgccccggggttgtGaccctcaaaccttcctgcag	13	14	1	1			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr14:23511534G>T	ENST00000408907.2	+	1	159	c.100G>T	c.(100-102)Gac>Tac	p.D34Y		NM_001099780.1	NP_001093250.1	A5LHX3	PSB11_HUMAN	proteasome (prosome, macropain) subunit, beta type, 11	34					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)			endometrium(1)|kidney(2)|lung(4)	7	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.00643)		CCGGGGTTGTGACCCTCAAAC	0.642																																					p.D34Y		Atlas-SNP	.											.	PSMB11	40	.	0			c.G100T						.						59	70	66					14																	23511534		2129	4223	6352	SO:0001583	missense	122706	exon1			GGTTGTGACCCTC		CCDS41923.1	14q11.2	2008-01-31				ENSG00000222028			31963	protein-coding gene	gene with protein product		611137				17540904	Standard	NM_001099780		Approved	beta5t	uc010ake.1	A5LHX3		ENST00000408907.2:c.100G>T	chr14.hg19:g.23511534G>T	ENSP00000386212:p.Asp34Tyr	49.0	0.0		39.0	10.0	NM_001099780		Missense_Mutation	SNP	ENST00000408907.2	hg19	CCDS41923.1	.	.	.	.	.	.	.	.	.	.	G	18.38	3.611342	0.66558	.	.	ENSG00000222028	ENST00000408907	T	0.32988	1.43	5.4	4.49	0.54785	.	0.300277	0.26103	N	0.026327	T	0.33118	0.0852	M	0.62723	1.935	0.35678	D	0.813873	B	0.17038	0.02	B	0.17433	0.018	T	0.41324	-0.9515	10	0.87932	D	0	0.4639	12.6451	0.56729	0.0:0.0:0.8343:0.1657	.	34	A5LHX3	PSB11_HUMAN	Y	34	ENSP00000386212:D34Y	ENSP00000386212:D34Y	D	+	1	0	PSMB11	22581374	0.965000	0.33210	0.840000	0.33206	0.983000	0.72400	3.744000	0.55112	1.240000	0.43803	0.563000	0.77884	GAC	.	.		0.642	PSMB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408294.1	NM_001099780		T	23511534	G	T	23511534	3	4	298	1	0	0	0	0	1	0	0	0	12688	1290	45	3	102	3	PSMB11	14	23511534	Missense_Mutation	SNP	G	TCGA-G3-AAV2-01A-11D-A36X-10		23511534	83838006	36	43237										
NDN	4692	hgsc.bcm.edu	37	chr15	23931514	23931514	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	gccaggcctgggggtctttcTtaaagaccctggccaggaac	13	12	2	1			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr15:23931514T>C	ENST00000331837.4	-	1	936	c.851A>G	c.(850-852)aAg>aGg	p.K284R		NM_002487.2	NP_002478.1	Q99608	NECD_HUMAN	necdin, melanoma antigen (MAGE) family member	284	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				axon extension (GO:0048675)|axonal fasciculation (GO:0007413)|central nervous system development (GO:0007417)|genetic imprinting (GO:0071514)|glial cell migration (GO:0008347)|multicellular organismal homeostasis (GO:0048871)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|post-embryonic development (GO:0009791)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|respiratory system process (GO:0003016)|sensory perception of pain (GO:0019233)|transcription, DNA-templated (GO:0006351)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|skin(1)	39		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;8.37e-11)|Epithelial(43;9.29e-10)|BRCA - Breast invasive adenocarcinoma(123;0.00179)|GBM - Glioblastoma multiforme(186;0.018)|Lung(196;0.153)		GGGGTCTTTCTTAAAGACCCT	0.602									Prader-Willi syndrome																												p.K284R		Atlas-SNP	.											NDN,NS,carcinoma,0,2	NDN	79	.	0			c.A851G						.						27	31	30					15																	23931514		2201	4299	6500	SO:0001583	missense	4692	exon1	Familial Cancer Database	Prader-Labhart-Willi syndrome	TCTTTCTTAAAGA	U35139	CCDS10014.1	15q11-q12	2012-12-07	2012-12-07		ENSG00000182636	ENSG00000182636			7675	protein-coding gene	gene with protein product	"Prader-Willi syndrome chromosome region"	602117	"necdin (mouse) homolog", "necdin homolog (mouse)"			9302265	Standard	NM_002487		Approved	HsT16328, PWCR	uc001ywk.3	Q99608	OTTHUMG00000129161	ENST00000331837.4:c.851A>G	chr15.hg19:g.23931514T>C	ENSP00000332643:p.Lys284Arg	71.0	0.0		49.0	21.0	NM_002487	B2R6Z5	Missense_Mutation	SNP	ENST00000331837.4	hg19	CCDS10014.1	.	.	.	.	.	.	.	.	.	.	T	15.42	2.827791	0.50845	.	.	ENSG00000182636	ENST00000331837	T	0.02301	4.35	3.64	3.64	0.41730	.	0.401321	0.27143	N	0.020721	T	0.02767	0.0083	L	0.41027	1.25	0.27508	N	0.951775	B	0.33345	0.409	B	0.37550	0.253	T	0.36720	-0.9736	10	0.34782	T	0.22	.	8.9497	0.35781	0.0:0.0:0.0:1.0	.	284	Q99608	NECD_HUMAN	R	284	ENSP00000332643:K284R	ENSP00000332643:K284R	K	-	2	0	NDN	21482607	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	3.282000	0.51693	1.888000	0.54679	0.533000	0.62120	AAG	.	.		0.602	NDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251226.2	NM_002487		C	23931514	T	C	23931514	3	2	298	1	0	0	0	0	1	0	0	0	10256	1609	56	2	118	2	NDN	15	23931514	Missense_Mutation	SNP	T	TCGA-G3-AAV2-01A-11D-A36X-10		23931514	78599878	37	43238										
NTN3	4917	hgsc.bcm.edu	37	chr16	2522557	2522557	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	ggcaccgagggccctgactgCggccgctgcaagcccttcta	13	16	1	1			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr16:2522557C>T	ENST00000293973.1	+	1	1058	c.855C>T	c.(853-855)tgC>tgT	p.C285C	TBC1D24_ENST00000567020.1_5'Flank|TBC1D24_ENST00000293970.5_5'Flank	NM_006181.2	NP_006172.1	O00634	NET3_HUMAN	netrin 3	285	Laminin EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)	Golgi apparatus (GO:0005794)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|central_nervous_system(2)|lung(3)|prostate(1)	7						GCCCTGACTGCGGCCGCTGCA	0.687																																					p.C285C		Atlas-SNP	.											.	NTN3	28	.	0			c.C855T						.						22	25	24					16																	2522557		2177	4249	6426	SO:0001819	synonymous_variant	4917	exon1			TGACTGCGGCCGC	U86759	CCDS10469.1	16p13.3	2013-03-01	2008-10-29	2008-10-29	ENSG00000162068	ENSG00000162068		"Netrins"	8030	protein-coding gene	gene with protein product	"Netrin-3"	602349	"netrin 2 (chicken)-like", "netrin 2-like (chicken)"	NTN2L		9143507, 10366627	Standard	NM_006181		Approved		uc002cqj.3	O00634	OTTHUMG00000128867	ENST00000293973.1:c.855C>T	chr16.hg19:g.2522557C>T		83.0	0.0		71.0	31.0	NM_006181		Silent	SNP	ENST00000293973.1	hg19	CCDS10469.1																																																																																			.	.		0.687	NTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250812.1	NM_006181		T	2522557	C	T	2522557	2	4	298	1	0	0	0	0	0	0	0	1	10710	776	27	1		1	NTN3	16	2522557	Silent	SNP	C	TCGA-G3-AAV2-01A-11D-A36X-10		2522557	87832196	38	43239										
ASPHD1	253982	hgsc.bcm.edu	37	chr16	29913162	29913162	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	gccaacaccttcggcaatgcCggcttttccgttctcctgcc	8	17	1	0	rs374797206		TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr16:29913162C>T	ENST00000308748.5	+	1	1122	c.870C>T	c.(868-870)gcC>gcT	p.A290A	SEZ6L2_ENST00000350527.3_5'Flank|SEZ6L2_ENST00000537485.1_5'Flank|SEZ6L2_ENST00000346932.5_5'Flank|ASPHD1_ENST00000483405.1_Silent_p.A9A|SEZ6L2_ENST00000308713.5_5'Flank	NM_181718.3	NP_859069.2	Q5U4P2	ASPH1_HUMAN	aspartate beta-hydroxylase domain containing 1	290					peptidyl-amino acid modification (GO:0018193)	integral component of membrane (GO:0016021)	dioxygenase activity (GO:0051213)			endometrium(4)|large_intestine(2)|lung(1)|prostate(1)	8						TCGGCAATGCCGGCTTTTCCG	0.667																																					p.A290A		Atlas-SNP	.											.	ASPHD1	28	.	0			c.C870T						.	C		1,4311		0,1,2155	22	22	22		870	2.2	1	16		22	0,8442		0,0,4221	no	coding-synonymous	ASPHD1	NM_181718.3		0,1,6376	TT,TC,CC		0.0,0.0232,0.0078		290/391	29913162	1,12753	2156	4221	6377	SO:0001819	synonymous_variant	253982	exon1			CAATGCCGGCTTT	AF070642	CCDS10660.1	16p11.2	2008-02-05			ENSG00000174939	ENSG00000174939			27380	protein-coding gene	gene with protein product							Standard	NM_181718		Approved		uc002dut.3	Q5U4P2	OTTHUMG00000132121	ENST00000308748.5:c.870C>T	chr16.hg19:g.29913162C>T		63.0	0.0		70.0	30.0	NM_181718	A0AVE3|B7ZLZ3|Q8IW63|Q8N316|Q96H00	Silent	SNP	ENST00000308748.5	hg19	CCDS10660.1																																																																																			.	.		0.667	ASPHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255163.2	NM_181718		T	29913162	C	T	29913162	2	4	298	1	0	0	0	0	0	0	0	1	1054	639	23	1		1	ASPHD1	16	29913162	Silent	SNP	C	TCGA-G3-AAV2-01A-11D-A36X-10	27390605	29913162	60441591	39	43240										
LONP2	83752	hgsc.bcm.edu	37	chr16	48385505	48385505	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	cttacaggtgggtggaattaAagacaaagtgctggcggcac	14	7	0	1			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr16:48385505A>C	ENST00000285737.4	+	15	2444	c.2351A>C	c.(2350-2352)aAa>aCa	p.K784T	LONP2_ENST00000535754.1_Missense_Mutation_p.K740T|LONP2_ENST00000564259.1_3'UTR	NM_031490.2	NP_113678.2			lon peptidase 2, peroxisomal											breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						GGTGGAATTAAAGACAAAGTG	0.448																																					p.K784T		Atlas-SNP	.											.	LONP2	63	.	0			c.A2351C						.						54	57	56					16																	48385505		2200	4300	6500	SO:0001583	missense	83752	exon15			GAATTAAAGACAA	AJ548761	CCDS10734.1, CCDS73880.1	16q12.1	2010-04-21			ENSG00000102910	ENSG00000102910		"ATPases / AAA-type"	20598	protein-coding gene	gene with protein product						14561759	Standard	XM_005256191		Approved	MGC4840, LONP, LONPL	uc002efi.1	Q86WA8	OTTHUMG00000133144	ENST00000285737.4:c.2351A>C	chr16.hg19:g.48385505A>C	ENSP00000285737:p.Lys784Thr	74.0	0.0		50.0	21.0	NM_031490		Missense_Mutation	SNP	ENST00000285737.4	hg19	CCDS10734.1	.	.	.	.	.	.	.	.	.	.	A	28.2	4.897938	0.91962	.	.	ENSG00000102910	ENST00000285737;ENST00000544734;ENST00000535754	T;T	0.41758	0.99;0.99	5.93	5.93	0.95920	Ribosomal protein S5 domain 2-type fold (1);Peptidase S16, Lon C-terminal (1);	0.173319	0.64402	D	0.000008	T	0.68540	0.3012	M	0.83692	2.655	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.73531	-0.3953	10	0.87932	D	0	-24.883	16.422	0.83766	1.0:0.0:0.0:0.0	.	740;784	B7ZKL7;Q86WA8	.;LONP2_HUMAN	T	784;513;740	ENSP00000285737:K784T;ENSP00000445426:K740T	ENSP00000285737:K784T	K	+	2	0	LONP2	46943006	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	9.300000	0.96151	2.283000	0.76528	0.477000	0.44152	AAA	.	.		0.448	LONP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256839.2	NM_031490		C	48385505	A	C	48385505	3	2	298	1	0	0	0	0	1	0	0	0	8902	14	1	5	2409	5	LONP2	16	48385505	Missense_Mutation	SNP	A	TCGA-G3-AAV2-01A-11D-A36X-10	18472343	48385505	41969248	40	43241										
ROCK1	6093	hgsc.bcm.edu	37	chr18	18625364	18625364	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	tgctcattaagtttacaagaTctccaccaggcatgtattcc	6	11	2	1			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr18:18625364T>C	ENST00000399799.2	-	5	1419	c.479A>G	c.(478-480)gAt>gGt	p.D160G		NM_005406.2	NP_005397.1	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein kinase 1	160	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|apical constriction (GO:0003383)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|bleb assembly (GO:0032060)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of focal adhesion assembly (GO:0051894)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(4)|central_nervous_system(1)|large_intestine(8)|lung(2)	16	Melanoma(1;0.165)					GTTTACAAGATCTCCACCAGG	0.368																																					p.D160G		Atlas-SNP	.											.	ROCK1	162	.	0			c.A479G						.						126	114	118					18																	18625364		2203	4300	6503	SO:0001583	missense	6093	exon5			ACAAGATCTCCAC		CCDS11870.2	18q11.2	2013-01-10			ENSG00000067900	ENSG00000067900	2.7.11.1	"Pleckstrin homology (PH) domain containing"	10251	protein-coding gene	gene with protein product		601702				8617235	Standard	NM_005406		Approved	p160ROCK	uc002kte.3	Q13464	OTTHUMG00000131723	ENST00000399799.2:c.479A>G	chr18.hg19:g.18625364T>C	ENSP00000382697:p.Asp160Gly	61.0	0.0		55.0	20.0	NM_005406	B0YJ91|Q2KHM4|Q59GZ4	Missense_Mutation	SNP	ENST00000399799.2	hg19	CCDS11870.2	.	.	.	.	.	.	.	.	.	.	T	29.2	4.982065	0.93044	.	.	ENSG00000067900	ENST00000399799	T	0.28454	1.61	5.36	5.36	0.76844	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.66147	0.2760	M	0.93678	3.445	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.76323	-0.3001	10	0.87932	D	0	.	15.5304	0.75956	0.0:0.0:0.0:1.0	.	160	Q13464	ROCK1_HUMAN	G	160	ENSP00000382697:D160G	ENSP00000382697:D160G	D	-	2	0	ROCK1	16879362	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.773000	0.85462	2.246000	0.74042	0.533000	0.62120	GAT	.	.		0.368	ROCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254641.2	NM_005406		C	18625364	T	C	18625364	3	2	298	1	0	0	0	0	1	0	0	0	13532	1435	50	2	3701	2	ROCK1	18	18625364	Missense_Mutation	SNP	T	TCGA-G3-AAV2-01A-11D-A36X-10		18625364	59451884	41	43242										
MKNK2	2872	hgsc.bcm.edu	37	chr19	2042023	2042024	+	Missense_Mutation	DNP	GC	GC	AT													0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	cctccggggccatgtactccGccgagccgcactgcgggcgg							TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr19:2042023_2042024GC>AT	ENST00000591601.1	-	10	795_796	c.760_761GC>AT	c.(760-762)GCg>ATg	p.A254M	MKNK2_ENST00000591588.1_De_novo_Start_InFrame|MKNK2_ENST00000309340.7_Missense_Mutation_p.A254M|MKNK2_ENST00000541165.1_Missense_Mutation_p.A123M|MKNK2_ENST00000591142.1_De_novo_Start_InFrame|MKNK2_ENST00000588014.1_De_novo_Start_InFrame|MKNK2_ENST00000250896.3_Missense_Mutation_p.A254M			Q9HBH9	MKNK2_HUMAN	MAP kinase interacting serine/threonine kinase 2	254	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell surface receptor signaling pathway (GO:0007166)|cellular response to arsenic-containing substance (GO:0071243)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|hemopoiesis (GO:0030097)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of translation (GO:0006417)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|kidney(3)|large_intestine(3)|lung(3)	10		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CATGTACTCCGCCGAGCCGCAC	0.673																																					p.A254V|p.A254T		Atlas-SNP	.											.	MKNK2	56	.	0			c.C761T|c.G760A						.																																			SO:0001583	missense	2872	exon11			TACTCCGCCGAGC|ACTCCGCCGAGCC	AF125532	CCDS12079.1, CCDS12080.1	19p13.3	2012-12-20			ENSG00000099875	ENSG00000099875			7111	protein-coding gene	gene with protein product	"Putative map kinase interacting kinase"	605069	"G protein-coupled receptor kinase 7"	GPRK7		11013076	Standard	NM_199054		Approved	MNK2	uc002lus.2	Q9HBH9	OTTHUMG00000180020	ENST00000591601.1:c.760_761delinsAT	chr19.hg19:g.2042023_2042024delinsAT	ENSP00000467811:p.Ala254Met	61.0|59.0	0.0		70.0|69.0	18.0|16.0	NM_017572	Q6GPI3|Q9HBH8|Q9UHR0|Q9Y2N6	Missense_Mutation	SNP	ENST00000591601.1	hg19	CCDS12080.1																																																																																			.	.		0.673	MKNK2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449312.1	NM_199054		AT	2042024	GC	AT	2042023	3	1	298	1	0	0	0	0	1	0	0	0	9614	1087	38	1	747	1	MKNK2	19	2042023	Missense_Mutation	DNP	GC	TCGA-G3-AAV2-01A-11D-A36X-10		2042023	57086960	42	43243										
C3	718	hgsc.bcm.edu	37	chr19	6707900	6707900	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	cgtaatccttcccactgcccGgggtgcagccgatgtctgcc	11	16	1	0			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr19:6707900G>A	ENST00000245907.6	-	15	1978	c.1886C>T	c.(1885-1887)cCg>cTg	p.P629L		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	629					complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	CCCACTGCCCGGGGTGCAGCC	0.677																																					p.P629L		Atlas-SNP	.											.	C3	192	.	0			c.C1886T						.						57	51	53					19																	6707900		2203	4300	6503	SO:0001583	missense	718	exon15			CTGCCCGGGGTGC	J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"Complement system", "Endogenous ligands"	1318	protein-coding gene	gene with protein product	"C3a anaphylatoxin", "complement component C3a", "complement component C3b", "prepro-C3"	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.1886C>T	chr19.hg19:g.6707900G>A	ENSP00000245907:p.Pro629Leu	90.0	0.0		83.0	33.0	NM_000064	A7E236	Missense_Mutation	SNP	ENST00000245907.6	hg19	CCDS32883.1	.	.	.	.	.	.	.	.	.	.	G	13.21	2.169803	0.38315	.	.	ENSG00000125730	ENST00000245907	T	0.34472	1.36	4.83	3.79	0.43588	.	0.222891	0.46758	D	0.000261	T	0.43743	0.1261	M	0.88241	2.94	0.36280	D	0.855692	P	0.48162	0.906	B	0.42282	0.382	T	0.58418	-0.7640	10	0.19147	T	0.46	.	11.9609	0.53007	0.0869:0.0:0.9131:0.0	.	629	P01024	CO3_HUMAN	L	629	ENSP00000245907:P629L	ENSP00000245907:P629L	P	-	2	0	C3	6658900	0.957000	0.32711	0.215000	0.23724	0.189000	0.23516	5.614000	0.67695	1.043000	0.40175	-0.192000	0.12808	CCG	.	.		0.677	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064		A	6707900	G	A	6707900	3	1	298	1	0	0	0	0	1	0	0	0	2206	1116	39	1	3213	1	C3	19	6707900	Missense_Mutation	SNP	G	TCGA-G3-AAV2-01A-11D-A36X-10	4665877	6707900	52421083	43	43244										
RLN3	117579	hgsc.bcm.edu	37	chr19	14139180	14139180	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	gggctcccggtggagacgatCagacatcctggcccacgagg	15	13	1	2			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr19:14139180C>A	ENST00000431365.2	+	1	221	c.164C>A	c.(163-165)tCa>tAa	p.S55*	RLN3_ENST00000585987.1_Nonsense_Mutation_p.S55*|CTB-55O6.4_ENST00000590528.1_RNA	NM_080864.2	NP_543140.1	Q8WXF3	REL3_HUMAN	relaxin 3	55						extracellular region (GO:0005576)				endometrium(1)|lung(4)	5						TGGAGACGATCAGACATCCTG	0.627																																					p.S55X		Atlas-SNP	.											.	RLN3	10	.	0			c.C164A						.						45	48	47					19																	14139180		2203	4300	6503	SO:0001587	stop_gained	117579	exon1			GACGATCAGACAT	AF447451	CCDS12302.1	19p13.2	2013-02-26	2004-11-15					"Endogenous ligands"	17135	protein-coding gene	gene with protein product	"prorelaxin H3"	606855	"relaxin 3 (H3)"				Standard	NM_080864		Approved	ZINS4, RXN3, H3	uc002mxw.1	Q8WXF3		ENST00000431365.2:c.164C>A	chr19.hg19:g.14139180C>A	ENSP00000397415:p.Ser55*	152.0	0.0		137.0	60.0	NM_080864	Q6UXW5	Nonsense_Mutation	SNP	ENST00000431365.2	hg19	CCDS12302.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.401240	0.83120	.	.	ENSG00000171136	ENST00000431365	.	.	.	4.13	1.88	0.25563	.	2.180380	0.01897	N	0.038922	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.6451	6.6943	0.23191	0.0:0.7172:0.1805:0.1023	.	.	.	.	X	55	.	ENSP00000397415:S55X	S	+	2	0	RLN3	14000180	0.888000	0.30383	0.002000	0.10522	0.223000	0.24884	2.573000	0.46007	0.296000	0.22592	0.491000	0.48974	TCA	.	.		0.627	RLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458529.1			A	14139180	C	A	14139180	4	1	298	1	0	0	0	0	0	1	0	0	13408	838	29	3	166	3	RLN3	19	14139180	Nonsense_Mutation	SNP	C	TCGA-G3-AAV2-01A-11D-A36X-10	7431280	14139180	44989803	44	43245										
PRR12	57479	hgsc.bcm.edu	37	chr19	50100111	50100111	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	ccagccacctccaccgccacCcccgcctccaccacccatgc	4	27	0	0			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr19:50100111C>T	ENST00000418929.2	+	4	2531	c.2519C>T	c.(2518-2520)cCc>cTc	p.P840L		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	0							DNA binding (GO:0003677)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)|prostate(2)	11		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		CCACCGCCACCCCCGCCTCCA	0.746																																					p.P840L		Atlas-SNP	.											.	PRR12	157	.	0			c.C2519T						.						4	5	4					19																	50100111		1580	3492	5072	SO:0001583	missense	57479	exon4			CGCCACCCCCGCC	AB033031	CCDS46143.1	19q13.33	2008-07-02	2006-02-06	2006-02-06		ENSG00000126464			29217	protein-coding gene	gene with protein product			"KIAA1205"	KIAA1205		10574462	Standard	NM_020719		Approved		uc002poo.4	Q9ULL5		ENST00000418929.2:c.2519C>T	chr19.hg19:g.50100111C>T	ENSP00000394510:p.Pro840Leu	30.0	0.0		43.0	21.0	NM_020719	E9PB06|Q8N4J6	Missense_Mutation	SNP	ENST00000418929.2	hg19	CCDS46143.1	.	.	.	.	.	.	.	.	.	.	C	9.793	1.178479	0.21787	.	.	ENSG00000126464	ENST00000418929	.	.	.	3.92	3.92	0.45320	.	.	.	.	.	T	0.48624	0.1510	.	.	.	0.38061	D	0.936074	P	0.36909	0.573	B	0.39217	0.294	T	0.50004	-0.8878	7	0.25751	T	0.34	-8.8078	13.8501	0.63492	0.0:1.0:0.0:0.0	.	840	Q9ULL5-3	.	L	840	.	ENSP00000394510:P840L	P	+	2	0	PRR12	54791923	0.001000	0.12720	0.806000	0.32338	0.633000	0.38033	0.248000	0.18198	2.470000	0.83445	0.313000	0.20887	CCC	.	.		0.746	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719		T	50100111	C	T	50100111	3	4	298	1	0	0	0	0	1	0	0	0	12596	623	22	3	2533	3	PRR12	19	50100111	Missense_Mutation	SNP	C	TCGA-G3-AAV2-01A-11D-A36X-10	35960931	50100111	9028872	45	43246										
USP29	57663	hgsc.bcm.edu	37	chr19	57641581	57641581	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	ccttatcattcatctgaaacGctatagcttcaacaatgctt	4	11	4	1	rs148182755		TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr19:57641581G>T	ENST00000254181.4	+	4	1992	c.1538G>T	c.(1537-1539)cGc>cTc	p.R513L	USP29_ENST00000598197.1_Missense_Mutation_p.R513L	NM_020903.2	NP_065954.1	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	513	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			breast(3)|endometrium(4)|kidney(3)|large_intestine(15)|lung(47)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		CATCTGAAACGCTATAGCTTC	0.378																																					p.R513L		Atlas-SNP	.											.	USP29	186	.	0			c.G1538T						.						114	117	116					19																	57641581		2203	4300	6503	SO:0001583	missense	57663	exon4			TGAAACGCTATAG		CCDS33124.1	19q13.4	2008-06-23	2005-08-08			ENSG00000131864		"Ubiquitin-specific peptidases"	18563	protein-coding gene	gene with protein product		609546	"ubiquitin specific protease 29"			12838346	Standard	NM_020903		Approved		uc002qny.3	Q9HBJ7		ENST00000254181.4:c.1538G>T	chr19.hg19:g.57641581G>T	ENSP00000254181:p.Arg513Leu	95.0	0.0		75.0	38.0	NM_020903		Missense_Mutation	SNP	ENST00000254181.4	hg19	CCDS33124.1	.	.	.	.	.	.	.	.	.	.	G	14.30	2.492932	0.44352	.	.	ENSG00000131864	ENST00000254181	D	0.91843	-2.92	2.69	1.58	0.23477	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.47093	U	0.000259	D	0.95191	0.8441	M	0.85041	2.73	0.30436	N	0.776635	D	0.89917	1.0	D	0.76575	0.988	D	0.91418	0.5156	10	0.87932	D	0	0.0014	8.6437	0.33991	0.0:0.0:0.7699:0.23	.	513	Q9HBJ7	UBP29_HUMAN	L	513	ENSP00000254181:R513L	ENSP00000254181:R513L	R	+	2	0	USP29	62333393	1.000000	0.71417	0.941000	0.38009	0.318000	0.28184	3.914000	0.56401	0.614000	0.30107	0.591000	0.81541	CGC	.	G|1.000;A|0.000		0.378	USP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465075.1			T	57641581	G	T	57641581	3	4	298	1	0	0	0	0	1	0	0	0	17074	1087	38	1	1540	1	USP29	19	57641581	Missense_Mutation	SNP	G	TCGA-G3-AAV2-01A-11D-A36X-10	7541470	57641581	1487402	46	43247										
ARFGEF2	10564	hgsc.bcm.edu	37	chr20	47592685	47592685	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	tgttcaggatgaccctgagcAatttgaggtcatcaagcaac	10	9	3	3			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr20:47592685A>G	ENST00000371917.4	+	14	1907	c.1907A>G	c.(1906-1908)cAa>cGa	p.Q636R		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	636					endomembrane system organization (GO:0010256)|endosome organization (GO:0007032)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of tumor necrosis factor production (GO:0032760)|protein transport (GO:0015031)|receptor recycling (GO:0001881)|regulation of ARF protein signal transduction (GO:0032012)|vesicle-mediated transport (GO:0016192)	asymmetric synapse (GO:0032279)|axonemal microtubule (GO:0005879)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|recycling endosome (GO:0055037)|symmetric synapse (GO:0032280)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|GABA receptor binding (GO:0050811)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase A regulatory subunit binding (GO:0034237)			breast(7)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	63			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			GACCCTGAGCAATTTGAGGTC	0.502																																					p.Q636R	Esophageal Squamous(176;1738 1974 26285 33069 35354)	Atlas-SNP	.											.	ARFGEF2	160	.	0			c.A1907G						.						106	79	88					20																	47592685		2203	4300	6503	SO:0001583	missense	10564	exon14			CTGAGCAATTTGA	AF084521	CCDS13411.1	20q13.13	2010-08-20			ENSG00000124198	ENSG00000124198		"A-kinase anchor proteins"	15853	protein-coding gene	gene with protein product	"Brefeldin A-inhibited guanine nucleotide-exchange protein 2"	605371				10212200	Standard	NM_006420		Approved	BIG2	uc002xtx.4	Q9Y6D5	OTTHUMG00000032687	ENST00000371917.4:c.1907A>G	chr20.hg19:g.47592685A>G	ENSP00000360985:p.Gln636Arg	261.0	0.0		206.0	89.0	NM_006420	Q5TFT9|Q9NTS1	Missense_Mutation	SNP	ENST00000371917.4	hg19	CCDS13411.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.468387	0.84533	.	.	ENSG00000124198	ENST00000538445;ENST00000371917	T	0.76578	-1.03	5.79	5.79	0.91817	Armadillo-type fold (1);SEC7-like (2);	0.113718	0.64402	D	0.000008	D	0.85630	0.5741	M	0.81341	2.54	0.80722	D	1	D	0.54772	0.968	P	0.54664	0.758	D	0.86798	0.1990	10	0.51188	T	0.08	.	16.1354	0.81481	1.0:0.0:0.0:0.0	.	636	Q9Y6D5	BIG2_HUMAN	R	636	ENSP00000360985:Q636R	ENSP00000360985:Q636R	Q	+	2	0	ARFGEF2	47026092	1.000000	0.71417	1.000000	0.80357	0.725000	0.41563	9.310000	0.96267	2.207000	0.71202	0.533000	0.62120	CAA	.	.		0.502	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1	NM_006420		G	47592685	A	G	47592685	3	3	298	1	0	0	0	0	1	0	0	0	853	130	5	2	1961	2	ARFGEF2	20	47592685	Missense_Mutation	SNP	A	TCGA-G3-AAV2-01A-11D-A36X-10		47592685	15432835	47	43248										
NDUFV3	4731	hgsc.bcm.edu	37	chr21	44324122	44324122	+	Intron	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	ctggggcggcagaggggcatCtggaaaaacccgtgccagag	17	10	1	2			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr21:44324122C>T	ENST00000340344.4	+	3	235				NDUFV3_ENST00000354250.2_Silent_p.L334L|NDUFV3_ENST00000460259.1_3'UTR	NM_001001503.1	NP_001001503.1	P56181	NDUV3_HUMAN	NADH dehydrogenase (ubiquinone) flavoprotein 3, 10kDa						cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(2)|skin(1)	10				STAD - Stomach adenocarcinoma(101;0.0606)		AGAGGGGCATCTGGAAAAACC	0.667																																					p.L334L		Atlas-SNP	.											.	NDUFV3	23	.	0			c.C1000T						.						28	33	32					21																	44324122		2203	4300	6503	SO:0001627	intron_variant	4731	exon3			GGGCATCTGGAAA		CCDS33572.1, CCDS33573.1	21q22.3	2011-07-04	2002-08-29		ENSG00000160194	ENSG00000160194	1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7719	protein-coding gene	gene with protein product	"complex I 10kDa subunit"	602184	"NADH dehydrogenase (ubiquinone) flavoprotein 3 (10kD)"			9344673	Standard	NM_021075		Approved	CI-10k	uc002zcm.3	P56181	OTTHUMG00000086823	ENST00000340344.4:c.170-4852C>T	chr21.hg19:g.44324122C>T		130.0	0.0		68.0	50.0	NM_021075	A8K0M1|J3KNX7|Q6FGD3|Q8WU60|Q9HCR5	Silent	SNP	ENST00000340344.4	hg19	CCDS33573.1																																																																																			.	.		0.667	NDUFV3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195448.2			T	44324122	C	T	44324122	1	4	298	0	1	0	0	0	0	0	0	0	10310	912	32	3		3	NDUFV3	21	44324122	Intron	SNP	C	TCGA-G3-AAV2-01A-11D-A36X-10		44324122	3805773	48	43249										
EP300	2033	hgsc.bcm.edu	37	chr22	41568575	41568575	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	cttatttcgagggtgatttcTggcccaatgttctggaagaa	11	7	2	2			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr22:41568575T>A	ENST00000263253.7	+	28	5744	c.4525T>A	c.(4525-4527)Tgg>Agg	p.W1509R	RP1-85F18.5_ENST00000420537.1_RNA|RP1-85F18.6_ENST00000415054.1_RNA	NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	1509	CBP/p300-type HAT. {ECO:0000255|PROSITE- ProRule:PRU01065}.				apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						GGGTGATTTCTGGCCCAATGT	0.398			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																												p.W1509R		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	.	EP300	367	.	0			c.T4525A						.						109	105	107					22																	41568575		2203	4300	6503	SO:0001583	missense	2033	exon28	Familial Cancer Database	Broad Thumb-Hallux syndrome	GATTTCTGGCCCA	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.4525T>A	chr22.hg19:g.41568575T>A	ENSP00000263253:p.Trp1509Arg	181.0	0.0		141.0	71.0	NM_001429	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	hg19	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.134333	0.77662	.	.	ENSG00000100393	ENST00000263253	D	0.94000	-3.33	5.96	5.96	0.96718	.	0.000000	0.46145	D	0.000307	D	0.97882	0.9304	H	0.96269	3.795	0.58432	D	0.999998	D	0.89917	1.0	D	0.91635	0.999	D	0.99133	1.0853	10	0.87932	D	0	-5.3558	16.4484	0.83959	0.0:0.0:0.0:1.0	.	1509	Q09472	EP300_HUMAN	R	1509	ENSP00000263253:W1509R	ENSP00000263253:W1509R	W	+	1	0	EP300	39898521	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.953000	0.87836	2.285000	0.76669	0.533000	0.62120	TGG	.	.		0.398	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		A	41568575	T	A	41568575	3	1	298	1	0	0	0	0	1	0	0	0	5150	1580	55	4	4635	4	EP300	22	41568575	Missense_Mutation	SNP	T	TCGA-G3-AAV2-01A-11D-A36X-10		41568575	9735991	49	43250										
EFCAB6	64800	hgsc.bcm.edu	37	chr22	43976358	43976358	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	tcataccgtggacaaagccaGctgggaggactcaactactt	10	11	2	0			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr22:43976358G>A	ENST00000262726.7	-	25	3467	c.3214C>T	c.(3214-3216)Ctg>Ttg	p.L1072L	EFCAB6_ENST00000396231.2_Silent_p.L920L	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	1072	EF-hand 12. {ECO:0000255|PROSITE- ProRule:PRU00448}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				GACAAAGCCAGCTGGGAGGAC	0.493																																					p.L1072L		Atlas-SNP	.											.	EFCAB6	177	.	0			c.C3214T						.						204	177	186					22																	43976358		2203	4300	6503	SO:0001819	synonymous_variant	64800	exon25			AAGCCAGCTGGGA	Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"EF-hand domain containing"	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.3214C>T	chr22.hg19:g.43976358G>A		96.0	0.0		96.0	34.0	NM_022785	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Silent	SNP	ENST00000262726.7	hg19	CCDS14049.1																																																																																			.	.		0.493	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785		A	43976358	G	A	43976358	2	1	298	1	0	0	0	0	0	0	0	1	4941	962	34	3		3	EFCAB6	22	43976358	Silent	SNP	G	TCGA-G3-AAV2-01A-11D-A36X-10	2407783	43976358	7328208	50	43251										
CELSR1	9620	hgsc.bcm.edu	37	chr22	46792558	46792558	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	cactcgcacacgtagccctgCggggagccgggggagcgcac	16	15	0	0			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chr22:46792558C>T	ENST00000262738.3	-	13	5786	c.5787G>A	c.(5785-5787)ccG>ccA	p.P1929P		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	1929	EGF-like 6; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		CGTAGCCCTGCGGGGAGCCGG	0.622																																					p.P1929P		Atlas-SNP	.											.	CELSR1	242	.	0			c.G5787A						.						38	34	36					22																	46792558		2203	4300	6503	SO:0001819	synonymous_variant	9620	exon13			GCCCTGCGGGGAG	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	1850	protein-coding gene	gene with protein product	"flamingo homolog 2 (Drosophila)"	604523	"cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.5787G>A	chr22.hg19:g.46792558C>T		92.0	0.0		80.0	5.0	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Silent	SNP	ENST00000262738.3	hg19	CCDS14076.1																																																																																			.	.		0.622	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		T	46792558	C	T	46792558	2	4	298	1	0	0	0	0	0	0	0	1	3223	755	27	1		1	CELSR1	22	46792558	Silent	SNP	C	TCGA-G3-AAV2-01A-11D-A36X-10	2816200	46792558	4512008	51	43252										
ZMAT1	84460	hgsc.bcm.edu	37	chrX	101139682	101139682	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0576923076923077	3	1	1.29246064623032	2.44131455399061	1.04627766599598	1	1	0	tccatctttctgaaacaagtCttggcctctagtcctctggc	7	13	5	1			TCGA-G3-AAV2-01A-11D-A36X-10	TCGA-G3-AAV2-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cef171de-1b26-42a6-b2c3-6b4123a54ee4	9800974a-91e2-4674-9dfb-f809efce470b	g.chrX:101139682C>T	ENST00000372782.3	-	7	764	c.717G>A	c.(715-717)aaG>aaA	p.K239K	ZMAT1_ENST00000540921.1_Silent_p.K239K|ZMAT1_ENST00000458570.1_Silent_p.K68K|ZMAT1_ENST00000494068.1_5'UTR	NM_001011657.3	NP_001011657	Q5H9K5	ZMAT1_HUMAN	zinc finger, matrin-type 1	239						nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	22						TGAAACAAGTCTTGGCCTCTA	0.413																																					p.K239K		Atlas-SNP	.											.	ZMAT1	143	.	0			c.G717A						.						204	179	187					X																	101139682		2203	4300	6503	SO:0001819	synonymous_variant	84460	exon7			ACAAGTCTTGGCC	Z69304	CCDS35348.1	Xq21	2012-10-05	2010-09-15		ENSG00000166432	ENSG00000166432		"Zinc fingers, matrin-type"	29377	protein-coding gene	gene with protein product							Standard	NM_001011657		Approved	KIAA1789	uc011mrl.2	Q5H9K5	OTTHUMG00000022044	ENST00000372782.3:c.717G>A	chrX.hg19:g.101139682C>T		66.0	0.0		111.0	52.0	NM_001011657	Q8NDS3|Q96JN6	Silent	SNP	ENST00000372782.3	hg19	CCDS35348.1																																																																																			.	.		0.413	ZMAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057598.1			T	101139682	C	T	101139682	2	4	298	1	0	0	0	0	0	0	0	1	17706	912	32	3		3	ZMAT1	23	101139682	Silent	SNP	C	TCGA-G3-AAV2-01A-11D-A36X-10		101139682	54130878	52	43253										
GABPB2	126626	hgsc.bcm.edu	37	chr1	151079530	151079530	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	tagccaatacagaggaaattAtagaaggaaattccgttgac	9	6	0	3			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr1:151079530A>G	ENST00000368918.3	+	7	1085	c.754A>G	c.(754-756)Ata>Gta	p.I252V	GABPB2_ENST00000467551.1_3'UTR|GABPB2_ENST00000368916.1_Missense_Mutation_p.I214V|GABPB2_ENST00000368917.1_Missense_Mutation_p.I214V	NM_144618.2	NP_653219.1	Q8TAK5	GABP2_HUMAN	GA binding protein transcription factor, beta subunit 2	252					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(2)|large_intestine(3)|liver(2)|lung(7)	15				all cancers(107;7.17e-05)|GBM - Glioblastoma multiforme(94;0.000662)		AGAGGAAATTATAGAAGGAAA	0.398																																					p.I252V		Atlas-SNP	.											.	GABPB2	41	.	0			c.A754G						.						56	58	57					1																	151079530		2203	4300	6503	SO:0001583	missense	126626	exon7			GAAATTATAGAAG		CCDS983.1	1q21.2	2013-01-10			ENSG00000143458	ENSG00000143458		"Ankyrin repeat domain containing"	28441	protein-coding gene	gene with protein product						7958862	Standard	NM_144618		Approved	MGC29891	uc001ewr.2	Q8TAK5	OTTHUMG00000012193	ENST00000368918.3:c.754A>G	chr1.hg19:g.151079530A>G	ENSP00000357914:p.Ile252Val	61.0	0.0		103.0	16.0	NM_144618	B1AVJ8|D3DV14|Q8NAR5	Missense_Mutation	SNP	ENST00000368918.3	hg19	CCDS983.1	.	.	.	.	.	.	.	.	.	.	A	0.009	-1.846529	0.00568	.	.	ENSG00000143458	ENST00000368918;ENST00000368917;ENST00000368916	T;T;T	0.55234	0.57;0.53;0.53	5.41	-2.48	0.06423	.	0.560322	0.20442	N	0.092264	T	0.06371	0.0164	N	0.10916	0.065	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.29882	-0.9997	10	0.07030	T	0.85	-4.0734	2.6748	0.05078	0.2388:0.2474:0.3931:0.1208	.	214;252;252	Q5SZG2;B2R924;Q8TAK5	.;.;GABP2_HUMAN	V	252;214;214	ENSP00000357914:I252V;ENSP00000357913:I214V;ENSP00000357912:I214V	ENSP00000357912:I214V	I	+	1	0	GABPB2	149346154	0.004000	0.15560	0.049000	0.19019	0.344000	0.29017	0.023000	0.13533	-0.623000	0.05618	0.455000	0.32223	ATA	.	.		0.398	GABPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033700.2	NM_144618		G	151079530	A	G	151079530	3	3	299	1	0	0	0	0	1	0	0	0	6167	449	16	2	776	2	GABPB2	1	151079530	Missense_Mutation	SNP	A	TCGA-G3-AAV3-01A-11D-A36X-10		151079530	98171091	1	43254										
PIGM	93183	hgsc.bcm.edu	37	chr1	160000854	160000854	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	tgctacaaacagcagcacagCccgattacacagccttttca	6	14	1	0			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr1:160000854C>A	ENST00000368090.2	-	1	929	c.676G>T	c.(676-678)Gct>Tct	p.A226S		NM_145167.2	NP_660150.1	Q9H3S5	PIGM_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class M	226					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	mannosyltransferase activity (GO:0000030)			kidney(1)|large_intestine(4)|lung(9)|ovary(2)|skin(1)	17	all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			AGCAGCACAGCCCGATTACAC	0.483																																					p.A226S		Atlas-SNP	.											.	PIGM	27	.	0			c.G676T						.						96	101	99					1																	160000854		2203	4300	6503	SO:0001583	missense	93183	exon1			GCACAGCCCGATT	AB028127	CCDS1192.1	1q23.2	2013-02-26	2006-06-28		ENSG00000143315	ENSG00000143315		"Dolichyl D-mannosyl phosphate dependent mannosyltransferases", "Phosphatidylinositol glycan anchor biosynthesis"	18858	protein-coding gene	gene with protein product	"GPI mannosyltransferase 1", "DPM:GlcN-(acyl-)PI mannosyltransferase", "dol-P-Man dependent GPI mannosyltransferase"	610273	"phosphatidylinositol glycan, class M"			11226175	Standard	NM_145167		Approved	GPI-MT-I	uc001fuv.1	Q9H3S5	OTTHUMG00000024081	ENST00000368090.2:c.676G>T	chr1.hg19:g.160000854C>A	ENSP00000357069:p.Ala226Ser	92.0	0.0		200.0	28.0	NM_145167		Missense_Mutation	SNP	ENST00000368090.2	hg19	CCDS1192.1	.	.	.	.	.	.	.	.	.	.	C	0.677	-0.799710	0.02841	.	.	ENSG00000143315	ENST00000368090	T	0.45276	0.9	5.16	4.25	0.50352	.	0.742461	0.12881	N	0.431423	T	0.11452	0.0279	N	0.13098	0.295	0.09310	N	0.999999	B	0.02656	0.0	B	0.12156	0.007	T	0.23013	-1.0200	9	.	.	.	-14.9299	13.6165	0.62110	0.0:0.8438:0.1562:0.0	.	226	Q9H3S5	PIGM_HUMAN	S	226	ENSP00000357069:A226S	.	A	-	1	0	PIGM	158267478	0.000000	0.05858	0.059000	0.19551	0.051000	0.14879	0.048000	0.14078	1.401000	0.46761	0.462000	0.41574	GCT	.	.		0.483	PIGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060643.2	NM_145167		A	160000854	C	A	160000854	3	1	299	1	0	0	0	0	1	0	0	0	11901	739	26	3	599	3	PIGM	1	160000854	Missense_Mutation	SNP	C	TCGA-G3-AAV3-01A-11D-A36X-10	8921324	160000854	89249767	2	43255										
TROVE2	6738	hgsc.bcm.edu	37	chr1	193045716	193045716	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	tgctaattcagtacttgaacCaggaaattcagaagtatctt	7	7	3	2			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr1:193045716C>T	ENST00000367446.3	+	4	1097	c.887C>T	c.(886-888)cCa>cTa	p.P296L	TROVE2_ENST00000367443.1_Missense_Mutation_p.P296L|TROVE2_ENST00000367445.3_Missense_Mutation_p.P296L|TROVE2_ENST00000400968.2_Missense_Mutation_p.P296L|TROVE2_ENST00000432079.1_Missense_Mutation_p.P21L|TROVE2_ENST00000367444.3_Missense_Mutation_p.P296L|TROVE2_ENST00000367441.1_Missense_Mutation_p.P296L|TROVE2_ENST00000460715.2_3'UTR|TROVE2_ENST00000416058.2_Missense_Mutation_p.P21L	NM_004600.5	NP_004591.2	P10155	RO60_HUMAN	TROVE domain family, member 2	296	TROVE. {ECO:0000255|PROSITE- ProRule:PRU00343}.				cilium morphogenesis (GO:0060271)|immune system development (GO:0002520)|response to UV (GO:0009411)|smoothened signaling pathway (GO:0007224)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	metal ion binding (GO:0046872)|RNA binding (GO:0003723)|U2 snRNA binding (GO:0030620)			biliary_tract(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|urinary_tract(1)	21						GTACTTGAACCAGGAAATTCA	0.318																																					p.P296L		Atlas-SNP	.											.	TROVE2	50	.	0			c.C887T						.						111	106	107					1																	193045716		1818	4078	5896	SO:0001583	missense	6738	exon4			TTGAACCAGGAAA	BC036658	CCDS41449.1, CCDS1379.1, CCDS41450.1, CCDS41450.2, CCDS53451.1	1q31	2014-08-06	2005-06-14	2005-06-14	ENSG00000116747	ENSG00000116747			11313	protein-coding gene	gene with protein product		600063	"Sjogren syndrome antigen A2 (60kDa, ribonucleoprotein autoantigen SS-A/Ro)"	SSA2		8188321	Standard	NM_001042369		Approved	Ro60	uc001gss.3	P10155	OTTHUMG00000035675	ENST00000367446.3:c.887C>T	chr1.hg19:g.193045716C>T	ENSP00000356416:p.Pro296Leu	250.0	0.0		419.0	84.0	NM_004600	B2RBB9|Q5LJ98|Q5LJ99|Q5LJA0|Q86WL3|Q86WL4|Q92787|Q9H1W6	Missense_Mutation	SNP	ENST00000367446.3	hg19	CCDS1379.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.920793	0.92249	.	.	ENSG00000116747	ENST00000400968;ENST00000416058;ENST00000367446;ENST00000367443;ENST00000367445;ENST00000367444;ENST00000367441	T;T;T;T;T;T;T	0.15952	2.38;2.38;2.38;2.38;2.38;2.38;2.38	5.38	5.38	0.77491	TROVE (2);	0.049749	0.85682	D	0.000000	T	0.48589	0.1508	M	0.84433	2.695	0.80722	D	1	P;P;D;D	0.76494	0.951;0.951;0.99;0.999	D;D;D;D	0.79108	0.94;0.94;0.936;0.992	T	0.47711	-0.9096	10	0.44086	T	0.13	-31.9485	19.5625	0.95378	0.0:1.0:0.0:0.0	.	296;296;296;296	Q5LJ99;Q5LJ98;Q5LJA0;P10155	.;.;.;RO60_HUMAN	L	296;21;296;296;296;296;296	ENSP00000383752:P296L;ENSP00000411421:P21L;ENSP00000356416:P296L;ENSP00000356413:P296L;ENSP00000356415:P296L;ENSP00000356414:P296L;ENSP00000356411:P296L	ENSP00000356411:P296L	P	+	2	0	TROVE2	191312339	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.290000	0.59019	2.700000	0.92200	0.558000	0.71614	CCA	.	.		0.318	TROVE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086688.1	NM_004600		T	193045716	C	T	193045716	3	4	299	1	0	0	0	0	1	0	0	0	16591	594	21	3	897	3	TROVE2	1	193045716	Missense_Mutation	SNP	C	TCGA-G3-AAV3-01A-11D-A36X-10	33044862	193045716	56204905	3	43256										
HHAT	55733	hgsc.bcm.edu	37	chr1	210637884	210637884	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	cccaggtgctctttttctacGtgaagtacttggtgctcttt	9	10	3	1			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr1:210637884G>T	ENST00000367010.1	+	8	1119	c.892G>T	c.(892-894)Gtg>Ttg	p.V298L	HHAT_ENST00000367009.1_5'UTR|HHAT_ENST00000413764.2_Missense_Mutation_p.V298L|HHAT_ENST00000261458.3_Missense_Mutation_p.V298L|HHAT_ENST00000391905.3_Missense_Mutation_p.V298L|HHAT_ENST00000545154.1_Missense_Mutation_p.V299L|HHAT_ENST00000541565.1_Missense_Mutation_p.V161L|HHAT_ENST00000545781.1_Missense_Mutation_p.V235L|HHAT_ENST00000537898.1_Missense_Mutation_p.V233L|HHAT_ENST00000308852.6_Missense_Mutation_p.V253L	NM_001170580.1	NP_001164051.1	Q5VTY9	HHAT_HUMAN	hedgehog acyltransferase	298					multicellular organismal development (GO:0007275)|protein palmitoylation (GO:0018345)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|palmitoyltransferase activity (GO:0016409)			breast(3)|central_nervous_system(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	27				OV - Ovarian serous cystadenocarcinoma(81;0.0136)|all cancers(67;0.161)|KIRC - Kidney renal clear cell carcinoma(1967;0.215)		CTTTTTCTACGTGAAGTACTT	0.557																																					p.V299L		Atlas-SNP	.											.	HHAT	66	.	0			c.G895T						.						219	214	215					1																	210637884		2203	4300	6503	SO:0001583	missense	55733	exon7			TTCTACGTGAAGT	AK001586	CCDS1495.1, CCDS53471.1, CCDS53472.1, CCDS53473.1	1q32	2008-02-05			ENSG00000054392	ENSG00000054392			18270	protein-coding gene	gene with protein product		605743				11160356	Standard	NM_001170587		Approved	FLJ10724, MART-2, MART2, Skn, ski, rasp, sit, GUP2	uc009xcx.3	Q5VTY9	OTTHUMG00000036447	ENST00000367010.1:c.892G>T	chr1.hg19:g.210637884G>T	ENSP00000355977:p.Val298Leu	55.0	0.0		92.0	15.0	NM_001170587	B7Z4D5|B7Z5I1|B7Z868|B7ZA75|D3DT91|F5H444|Q17RZ7|Q4G0K3|Q5CZ95|Q5TGI2|Q9NVH9|Q9Y3N8	Missense_Mutation	SNP	ENST00000367010.1	hg19	CCDS1495.1	.	.	.	.	.	.	.	.	.	.	G	16.28	3.077886	0.55753	.	.	ENSG00000054392	ENST00000413764;ENST00000541565;ENST00000545154;ENST00000537898;ENST00000391905;ENST00000545781;ENST00000261458;ENST00000308852;ENST00000367010;ENST00000426968	T;T;T;T;T;T;T;T;T;T	0.71341	-0.56;-0.56;-0.56;-0.56;-0.56;-0.56;-0.56;-0.56;-0.56;-0.56	5.42	4.5	0.54988	.	0.128145	0.51477	N	0.000087	T	0.60077	0.2241	L	0.31207	0.915	0.40205	D	0.977564	B;B;B;B;B	0.31680	0.188;0.256;0.115;0.221;0.335	B;B;B;B;B	0.39379	0.18;0.133;0.14;0.237;0.298	T	0.55418	-0.8144	10	0.02654	T	1	-20.7441	14.9169	0.70805	0.0:0.1533:0.8467:0.0	.	253;299;161;233;298	B7Z2U8;F5H444;B7Z4D5;B7Z5I1;Q5VTY9	.;.;.;.;HHAT_HUMAN	L	298;161;299;233;298;235;298;253;298;170	ENSP00000416845:V298L;ENSP00000444995:V161L;ENSP00000438468:V299L;ENSP00000442625:V233L;ENSP00000375773:V298L;ENSP00000439229:V235L;ENSP00000261458:V298L;ENSP00000308628:V253L;ENSP00000355977:V298L;ENSP00000413399:V170L	ENSP00000261458:V298L	V	+	1	0	HHAT	208704507	1.000000	0.71417	0.993000	0.49108	0.944000	0.59088	5.922000	0.70036	1.263000	0.44181	0.555000	0.69702	GTG	.	.		0.557	HHAT-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088662.1	NM_018194		T	210637884	G	T	210637884	3	4	299	1	0	0	0	0	1	0	0	0	7098	1145	40	1	1016	1	HHAT	1	210637884	Missense_Mutation	SNP	G	TCGA-G3-AAV3-01A-11D-A36X-10	17592168	210637884	38612737	4	43257										
EPHX1	2052	hgsc.bcm.edu	37	chr1	226027596	226027596	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	ttctctaccctgaccctcctCctgggacagcgtttcgggag	10	15	1	1			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr1:226027596C>T	ENST00000366837.4	+	6	985	c.789C>T	c.(787-789)ctC>ctT	p.L263L	RP11-285F7.2_ENST00000424332.1_RNA|EPHX1_ENST00000272167.5_Silent_p.L263L	NM_000120.3	NP_000111.1	P07099	HYEP_HUMAN	epoxide hydrolase 1, microsomal (xenobiotic)	263					aromatic compound catabolic process (GO:0019439)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cis-stilbene-oxide hydrolase activity (GO:0033961)|epoxide hydrolase activity (GO:0004301)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(7)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	28	Breast(184;0.197)					TGACCCTCCTCCTGGGACAGC	0.567																																					p.L263L		Atlas-SNP	.											.	EPHX1	57	.	0			c.C789T						.						198	184	189					1																	226027596		2203	4300	6503	SO:0001819	synonymous_variant	2052	exon6			CCTCCTCCTGGGA	J03518	CCDS1547.1	1q42.1	2009-07-10			ENSG00000143819	ENSG00000143819	3.3.2.9		3401	protein-coding gene	gene with protein product		132810		EPHX		9925921	Standard	NM_000120		Approved		uc001hpk.3	P07099	OTTHUMG00000037743	ENST00000366837.4:c.789C>T	chr1.hg19:g.226027596C>T		92.0	0.0		173.0	68.0	NM_001136018	B2R8N0|Q5VTJ6|Q9NP75|Q9NPE7|Q9NQU6|Q9NQU7|Q9NQU8|Q9NQU9|Q9NQV0|Q9NQV1|Q9NQV2	Silent	SNP	ENST00000366837.4	hg19	CCDS1547.1																																																																																			.	.		0.567	EPHX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092064.1	NM_000120		T	226027596	C	T	226027596	2	4	299	1	0	0	0	0	0	0	0	1	5181	842	30	3		3	EPHX1	1	226027596	Silent	SNP	C	TCGA-G3-AAV3-01A-11D-A36X-10	15389712	226027596	23223025	5	43258										
OR2T4	127074	hgsc.bcm.edu	37	chr1	248525799	248525799	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	ccctgagaaggacatgatggTatctgtcttctataccatcc	8	11	3	2			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr1:248525799T>C	ENST00000366475.1	+	1	917	c.917T>C	c.(916-918)gTa>gCa	p.V306A		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	306						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GACATGATGGTATCTGTCTTC	0.488																																					p.V306A		Atlas-SNP	.											.	OR2T4	126	.	0			c.T917C						.						146	144	144					1																	248525799		2203	4300	6503	SO:0001583	missense	127074	exon1			TGATGGTATCTGT	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"GPCR / Class A : Olfactory receptors"	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.917T>C	chr1.hg19:g.248525799T>C	ENSP00000355431:p.Val306Ala	496.0	0.0		736.0	154.0	NM_001004696	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	hg19	CCDS31113.1	.	.	.	.	.	.	.	.	.	.	T	9.787	1.176907	0.21787	.	.	ENSG00000196944	ENST00000366475	T	0.39406	1.08	3.0	0.497	0.16902	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42294	D	0.000722	T	0.30541	0.0768	L	0.35341	1.055	0.09310	N	1	B	0.24618	0.107	B	0.32724	0.151	T	0.29058	-1.0024	10	0.59425	D	0.04	.	7.1922	0.25832	0.0:0.2085:0.0:0.7914	.	306	Q8NH00	OR2T4_HUMAN	A	306	ENSP00000355431:V306A	ENSP00000355431:V306A	V	+	2	0	OR2T4	246592422	0.000000	0.05858	0.997000	0.53966	0.727000	0.41649	-0.087000	0.11215	0.265000	0.21872	0.477000	0.44152	GTA	.	.		0.488	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696		C	248525799	T	C	248525799	3	2	299	1	0	0	0	0	1	0	0	0	11036	1638	57	2	919	2	OR2T4	1	248525799	Missense_Mutation	SNP	T	TCGA-G3-AAV3-01A-11D-A36X-10	22498203	248525799	724822	6	43259										
PGBD2	267002	hgsc.bcm.edu	37	chr1	249212344	249212344	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	ttgccttccggagatacattGcctgtgtgtatctggagagc	12	9	1	2			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr1:249212344G>T	ENST00000329291.5	+	3	1708	c.1561G>T	c.(1561-1563)Gcc>Tcc	p.A521S	PGBD2_ENST00000539153.1_Missense_Mutation_p.A518S|PGBD2_ENST00000355360.4_Missense_Mutation_p.A270S	NM_170725.2	NP_733843.1	Q6P3X8	PGBD2_HUMAN	piggyBac transposable element derived 2	521										NS(1)|endometrium(3)|lung(6)|ovary(1)|skin(3)	14	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.012)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			GAGATACATTGCCTGTGTGTA	0.532																																					p.A521S		Atlas-SNP	.											.	PGBD2	103	.	0			c.G1561T						.						112	97	102					1																	249212344		2203	4300	6503	SO:0001583	missense	267002	exon3			TACATTGCCTGTG	AF229602	CCDS31128.1, CCDS31129.1	1q	2008-02-05			ENSG00000185220	ENSG00000185220			19399	protein-coding gene	gene with protein product							Standard	XM_005270333		Approved		uc001ifh.3	Q6P3X8	OTTHUMG00000040424	ENST00000329291.5:c.1561G>T	chr1.hg19:g.249212344G>T	ENSP00000331643:p.Ala521Ser	57.0	0.0		78.0	14.0	NM_170725	B3KVR8|Q6MZF8	Missense_Mutation	SNP	ENST00000329291.5	hg19	CCDS31128.1	.	.	.	.	.	.	.	.	.	.	.	12.34	1.907149	0.33628	.	.	ENSG00000185220	ENST00000355360;ENST00000329291;ENST00000539153	T;T;T	0.15139	2.45;2.61;2.61	3.05	3.05	0.35203	.	0.122356	0.33650	N	0.004692	T	0.18045	0.0433	N	0.11201	0.11	0.28769	N	0.900468	D;D	0.76494	0.998;0.999	D;D	0.78314	0.954;0.991	T	0.06716	-1.0811	10	0.21014	T	0.42	.	9.8324	0.40950	0.0:0.0:1.0:0.0	.	518;521	F5H4U7;Q6P3X8	.;PGBD2_HUMAN	S	270;521;518	ENSP00000355424:A270S;ENSP00000331643:A521S;ENSP00000439950:A518S	ENSP00000331643:A521S	A	+	1	0	PGBD2	247178967	0.991000	0.36638	0.858000	0.33744	0.037000	0.13140	3.764000	0.55264	1.999000	0.58509	0.467000	0.42956	GCC	.	.		0.532	PGBD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000097318.1			T	249212344	G	T	249212344	3	4	299	1	0	0	0	0	1	0	0	0	11790	1319	46	3	1567	3	PGBD2	1	249212344	Missense_Mutation	SNP	G	TCGA-G3-AAV3-01A-11D-A36X-10	686545	249212344	38277	7	43260										
TPO	7173	hgsc.bcm.edu	37	chr2	1459869	1459869	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	tccgggaggtgacaagacatGtcattcaagtttcaaatgag	11	7	3	3			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr2:1459869G>T	ENST00000345913.4	+	7	725	c.634G>T	c.(634-636)Gtc>Ttc	p.V212F	TPO_ENST00000346956.3_Missense_Mutation_p.V212F|TPO_ENST00000329066.4_Missense_Mutation_p.V212F|TPO_ENST00000382201.3_Missense_Mutation_p.V212F|TPO_ENST00000497517.2_Intron|TPO_ENST00000382198.1_Missense_Mutation_p.V212F|TPO_ENST00000337415.3_Missense_Mutation_p.V212F|TPO_ENST00000349624.3_Missense_Mutation_p.V212F	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	212					cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	GACAAGACATGTCATTCAAGT	0.507																																					p.V212F		Atlas-SNP	.											.	TPO	224	.	0			c.G634T						.						108	77	87					2																	1459869		2203	4300	6503	SO:0001583	missense	7173	exon7			AGACATGTCATTC		CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.634G>T	chr2.hg19:g.1459869G>T	ENSP00000318820:p.Val212Phe	123.0	0.0		174.0	35.0	NM_175719	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	hg19	CCDS1643.1	.	.	.	.	.	.	.	.	.	.	G	11.46	1.643946	0.29246	.	.	ENSG00000115705	ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000329066;ENST00000382201;ENST00000382198;ENST00000422464	T;T;T;T;T;T;T;T	0.70045	-0.45;-0.45;-0.45;-0.45;-0.45;-0.45;-0.45;-0.45	5.04	-2.11	0.07187	.	0.195535	0.50627	D	0.000120	T	0.62109	0.2401	L	0.53729	1.69	0.35091	D	0.76429	P;B;P;D	0.52996	0.946;0.112;0.946;0.957	P;B;P;P	0.50490	0.509;0.029;0.509;0.642	T	0.67078	-0.5761	10	0.72032	D	0.01	-15.945	6.9462	0.24520	0.6615:0.1569:0.1816:0.0	.	212;212;212;212	P07202-4;P07202-5;P07202-2;P07202	.;.;.;PERT_HUMAN	F	212;212;212;212;212;212;212;141	ENSP00000337263:V212F;ENSP00000318820:V212F;ENSP00000263886:V212F;ENSP00000332044:V212F;ENSP00000329869:V212F;ENSP00000371636:V212F;ENSP00000371633:V212F;ENSP00000405788:V141F	ENSP00000329869:V212F	V	+	1	0	TPO	1438876	0.769000	0.28531	0.000000	0.03702	0.036000	0.12997	1.078000	0.30754	-0.249000	0.09569	0.563000	0.77884	GTC	.	.		0.507	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547		T	1459869	G	T	1459869	3	4	299	1	0	0	0	0	1	0	0	0	16425	1377	48	3	656	3	TPO	2	1459869	Missense_Mutation	SNP	G	TCGA-G3-AAV3-01A-11D-A36X-10		1459869	241739504	8	43261										
HADHB	3032	hgsc.bcm.edu	37	chr2	26502123	26502123	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	atgcactgcgctctcacagtCtagccaagaaggcacaggat	10	12	2	1			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr2:26502123C>G	ENST00000317799.5	+	9	855	c.751C>G	c.(751-753)Cta>Gta	p.L251V	HADHB_ENST00000405867.3_Intron|HADHB_ENST00000545822.1_Missense_Mutation_p.L229V|HADHB_ENST00000494615.1_3'UTR|HADHB_ENST00000537713.1_Missense_Mutation_p.L236V	NM_000183.2	NP_000174.1	P55084	ECHB_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), beta subunit	251					cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrial envelope (GO:0005740)|mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acyltransferase activity (GO:0003988)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTCTCACAGTCTAGCCAAGAA	0.512																																					p.L251V		Atlas-SNP	.											.	HADHB	50	.	0			c.C751G						.						108	99	102					2																	26502123		2203	4300	6503	SO:0001583	missense	3032	exon9			CACAGTCTAGCCA		CCDS1722.1, CCDS62871.1, CCDS62872.1	2p23	2010-04-30	2010-04-30		ENSG00000138029	ENSG00000138029	2.3.1.16		4803	protein-coding gene	gene with protein product	"mitochondrial trifunctional protein, beta subunit"	143450	"hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), beta subunit"			9605857	Standard	NM_000183		Approved	MTPB	uc002rgz.3	P55084	OTTHUMG00000096978	ENST00000317799.5:c.751C>G	chr2.hg19:g.26502123C>G	ENSP00000325136:p.Leu251Val	54.0	0.0		78.0	16.0	NM_000183	B2RB16|B4E2W0|O14969|Q53TA6|Q96C77|Q9H3F5|Q9T2V8	Missense_Mutation	SNP	ENST00000317799.5	hg19	CCDS1722.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.573593	0.86542	.	.	ENSG00000138029	ENST00000317799;ENST00000537713;ENST00000545822	D;D;D	0.87966	-2.32;-2.32;-2.32	5.2	5.2	0.72013	Thiolase-like, subgroup (1);Thiolase, N-terminal (1);Thiolase-like (1);	0.000000	0.85682	D	0.000000	D	0.95541	0.8551	H	0.96208	3.785	0.80722	D	1	P;P;D	0.63046	0.94;0.873;0.992	P;P;D	0.66351	0.755;0.752;0.943	D	0.96412	0.9305	10	0.66056	D	0.02	-12.5094	18.179	0.89771	0.0:1.0:0.0:0.0	.	236;229;251	F5GZQ3;B4E2W0;P55084	.;.;ECHB_HUMAN	V	251;236;229	ENSP00000325136:L251V;ENSP00000444295:L236V;ENSP00000442665:L229V	ENSP00000325136:L251V	L	+	1	2	HADHB	26355627	0.974000	0.33945	1.000000	0.80357	0.998000	0.95712	2.417000	0.44653	2.805000	0.96524	0.655000	0.94253	CTA	.	.		0.512	HADHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214050.2	NM_000183		G	26502123	C	G	26502123	3	3	299	1	0	0	0	0	1	0	0	0	6953	912	32	4	781	4	HADHB	2	26502123	Missense_Mutation	SNP	C	TCGA-G3-AAV3-01A-11D-A36X-10	25042254	26502123	216697250	9	43262										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141625228	141625228	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	actggttttctgaatcacacTgacattctgccctgtccact	6	13	3	2			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr2:141625228T>C	ENST00000389484.3	-	27	5481	c.4510A>G	c.(4510-4512)Agt>Ggt	p.S1504G		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1504					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TGAATCACACTGACATTCTGC	0.478										TSP Lung(27;0.18)																											p.S1504G	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.A4510G						.						209	182	191					2																	141625228		2203	4300	6503	SO:0001583	missense	53353	exon27			TCACACTGACATT	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.4510A>G	chr2.hg19:g.141625228T>C	ENSP00000374135:p.Ser1504Gly	126.0	0.0		131.0	26.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	T	19.30	3.801275	0.70567	.	.	ENSG00000168702	ENST00000389484;ENST00000544579;ENST00000434794	D;D	0.90788	-2.73;-2.73	5.42	5.42	0.78866	Six-bladed beta-propeller, TolB-like (1);	0.061302	0.64402	D	0.000004	D	0.86322	0.5905	L	0.49778	1.585	0.43662	D	0.996089	B;P	0.43094	0.227;0.799	B;B	0.35182	0.179;0.197	D	0.85354	0.1103	10	0.26408	T	0.33	.	15.4528	0.75285	0.0:0.0:0.0:1.0	.	687;1504	Q96NT6;Q9NZR2	.;LRP1B_HUMAN	G	1504;1442;649	ENSP00000374135:S1504G;ENSP00000413239:S649G	ENSP00000374135:S1504G	S	-	1	0	LRP1B	141341698	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.986000	0.88173	2.060000	0.61445	0.533000	0.62120	AGT	.	.		0.478	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		C	141625228	T	C	141625228	3	2	299	1	0	0	0	0	1	0	0	0	8964	1580	55	2	9549	2	LRP1B	2	141625228	Missense_Mutation	SNP	T	TCGA-G3-AAV3-01A-11D-A36X-10	115123105	141625228	101574145	10	43263										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168107938	168107938	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	aatttgagcatggcccagttTctgaagcaaagtcaaataga	9	7	2	3			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr2:168107938T>A	ENST00000409195.1	+	9	10125	c.10036T>A	c.(10036-10038)Tct>Act	p.S3346T	XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.S3346T|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.S3124T|XIRP2_ENST00000409756.2_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	3171					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TGGCCCAGTTTCTGAAGCAAA	0.383																																					p.S3346T		Atlas-SNP	.											.	XIRP2	914	.	0			c.T10036A						.						98	94	95					2																	168107938		1862	4107	5969	SO:0001583	missense	129446	exon9			CCAGTTTCTGAAG	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.10036T>A	chr2.hg19:g.168107938T>A	ENSP00000386840:p.Ser3346Thr	107.0	0.0		193.0	40.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	hg19	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	T	12.52	1.962708	0.34659	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273;ENST00000413534	T;T;T	0.02369	4.32;4.32;4.32	6.07	6.07	0.98685	.	0.300219	0.38111	N	0.001808	T	0.02929	0.0087	N	0.22421	0.69	0.20196	N	0.999922	B;B;B	0.12013	0.003;0.005;0.001	B;B;B	0.12837	0.003;0.008;0.002	T	0.39231	-0.9624	10	0.72032	D	0.01	-11.3709	11.2379	0.48951	0.1371:0.0:0.0:0.8629	.	3171;3171;3124	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	T	3346;3346;3124;760	ENSP00000386840:S3346T;ENSP00000295237:S3346T;ENSP00000387255:S3124T	ENSP00000295237:S3346T	S	+	1	0	XIRP2	167816184	0.994000	0.37717	0.991000	0.47740	0.979000	0.70002	3.091000	0.50199	2.330000	0.79161	0.477000	0.44152	TCT	.	.		0.383	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		A	168107938	T	A	168107938	3	1	299	1	0	0	0	0	1	0	0	0	17445	1783	62	4	10066	4	XIRP2	2	168107938	Missense_Mutation	SNP	T	TCGA-G3-AAV3-01A-11D-A36X-10	26482710	168107938	75091435	11	43264										
NFE2L2	4780	hgsc.bcm.edu	37	chr2	178098803	178098803	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	gctgaattgggagaaattcaCctgtctcttcatctagttgt	9	8	4	2			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr2:178098803C>G	ENST00000397062.3	-	2	796	c.242G>C	c.(241-243)gGt>gCt	p.G81A	NFE2L2_ENST00000423513.1_Missense_Mutation_p.G65A|NFE2L2_ENST00000446151.2_Missense_Mutation_p.G65A|NFE2L2_ENST00000464747.1_Missense_Mutation_p.G65A|NFE2L2_ENST00000397063.4_Missense_Mutation_p.G65A	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	81					cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G81D(5)|p.G81V(4)|p.G81_F83delGEF(1)		central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			GAGAAATTCACCTGTCTCTTC	0.433			Mis		"NSCLC, HNSCC"					HNSCC(56;0.16)																											p.G81A		Atlas-SNP	.		Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	NFE2L2,NS,carcinoma,-1,11	NFE2L2	225	.	10	Substitution - Missense(9)|Deletion - In frame(1)	lung(4)|oesophagus(2)|liver(2)|endometrium(1)|kidney(1)	c.G242C						.						143	142	142					2																	178098803		1901	4105	6006	SO:0001583	missense	4780	exon2			AATTCACCTGTCT		CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"basic leucine zipper proteins"	7782	protein-coding gene	gene with protein product	"NF-E2-related factor 2"	600492	"nuclear factor (erythroid-derived 2)-like 2"			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.242G>C	chr2.hg19:g.178098803C>G	ENSP00000380252:p.Gly81Ala	48.0	0.0		69.0	17.0	NM_006164	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	Missense_Mutation	SNP	ENST00000397062.3	hg19	CCDS42782.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	27.3|27.3	4.820816|4.820816	0.90873|0.90873	.|.	.|.	ENSG00000116044|ENSG00000116044	ENST00000449627|ENST00000397063;ENST00000397062;ENST00000446151;ENST00000448782;ENST00000421929;ENST00000423513	.|T;T;T;T;T;T	.|0.51574	.|1.23;1.23;1.23;0.7;0.7;1.23	5.78|5.78	5.78|5.78	0.91487|0.91487	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	.|T	.|0.74749	.|0.3757	M|M	0.87180|0.87180	2.865|2.865	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;0.999;1.0;1.0	.|D;D;D;D	.|0.91635	.|0.998;0.997;0.999;0.998	.|T	.|0.76350	.|-0.2991	.|10	.|0.51188	.|T	.|0.08	.|.	19.9976|19.9976	0.97389|0.97389	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|65;65;65;81	.|E9PGJ7;B4DNB0;C9JFL6;Q16236	.|.;.;.;NF2L2_HUMAN	.|A	-1|65;81;65;65;65;65	.|ENSP00000380253:G65A;ENSP00000380252:G81A;ENSP00000411575:G65A;ENSP00000400073:G65A;ENSP00000412191:G65A;ENSP00000410015:G65A	.|ENSP00000380252:G81A	.|G	-|-	.|2	.|0	NFE2L2|NFE2L2	177807049|177807049	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.993000|0.993000	0.82548|0.82548	7.298000|7.298000	0.78815|0.78815	2.737000|2.737000	0.93849|0.93849	0.563000|0.563000	0.77884|0.77884	.|GGT	.	.		0.433	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4	NM_006164		G	178098803	C	G	178098803	3	3	299	1	0	0	0	0	1	0	0	0	10377	507	18	4	1591	4	NFE2L2	2	178098803	Missense_Mutation	SNP	C	TCGA-G3-AAV3-01A-11D-A36X-10	9990865	178098803	65100570	12	43265										
ATIC	471	hgsc.bcm.edu	37	chr2	216198147	216198147	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	atgatctctataaaaccctcAcacccatctcagcggcatat	4	14	3	1			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr2:216198147A>T	ENST00000236959.9	+	9	1215	c.889A>T	c.(889-891)Aca>Tca	p.T297S	ATIC_ENST00000540518.1_Missense_Mutation_p.T238S|ATIC_ENST00000435675.1_Missense_Mutation_p.T296S	NM_004044.6	NP_004035.2	P31939	PUR9_HUMAN	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	297					'de novo' IMP biosynthetic process (GO:0006189)|brainstem development (GO:0003360)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|dihydrofolate metabolic process (GO:0046452)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|organ regeneration (GO:0031100)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to inorganic substance (GO:0010035)|small molecule metabolic process (GO:0044281)|tetrahydrofolate biosynthetic process (GO:0046654)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	IMP cyclohydrolase activity (GO:0003937)|phosphoribosylaminoimidazolecarboxamide formyltransferase activity (GO:0004643)|protein homodimerization activity (GO:0042803)		ATIC/ALK(24)	large_intestine(2)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	8		Renal(323;0.229)		Epithelial(149;2.02e-06)|all cancers(144;0.000316)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.0097)	Methotrexate(DB00563)|Pemetrexed(DB00642)|Tetrahydrofolic acid(DB00116)	TAAAACCCTCACACCCATCTC	0.393			T	ALK	ALCL																																p.T297S		Atlas-SNP	.		Dom	yes		2	2q35	471	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase		L	.	ATIC	84	.	0			c.A889T						.						109	104	106					2																	216198147		2203	4300	6503	SO:0001583	missense	471	exon9			ACCCTCACACCCA		CCDS2398.1	2q35	2010-04-27			ENSG00000138363	ENSG00000138363	2.1.2.3, 3.5.4.10		794	protein-coding gene	gene with protein product	"phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase"	601731				8567683, 9378707	Standard	NM_004044		Approved	PURH, AICARFT, IMPCHASE	uc002vex.4	P31939	OTTHUMG00000133023	ENST00000236959.9:c.889A>T	chr2.hg19:g.216198147A>T	ENSP00000236959:p.Thr297Ser	129.0	0.0		171.0	31.0	NM_004044	A8K202|E9PBU3|Q13856|Q53S28	Missense_Mutation	SNP	ENST00000236959.9	hg19	CCDS2398.1	.	.	.	.	.	.	.	.	.	.	A	9.052	0.992251	0.18966	.	.	ENSG00000138363	ENST00000236959;ENST00000540518;ENST00000435675	T;T;T	0.75704	-0.96;-0.96;-0.96	6.07	6.07	0.98685	AICAR transformylase domain (1);Cytidine deaminase-like (1);	0.044591	0.85682	D	0.000000	T	0.54062	0.1835	N	0.04787	-0.16	0.80722	D	1	B;B	0.12630	0.004;0.006	B;B	0.11329	0.006;0.004	T	0.53968	-0.8363	10	0.10636	T	0.68	-25.2601	16.2891	0.82738	1.0:0.0:0.0:0.0	.	296;297	E9PBU3;P31939	.;PUR9_HUMAN	S	297;238;296	ENSP00000236959:T297S;ENSP00000440523:T238S;ENSP00000415935:T296S	ENSP00000236959:T297S	T	+	1	0	ATIC	215906392	1.000000	0.71417	0.165000	0.22776	0.015000	0.08874	7.349000	0.79376	2.330000	0.79161	0.528000	0.53228	ACA	.	.		0.393	ATIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256610.1	NM_004044		T	216198147	A	T	216198147	3	4	299	1	0	0	0	0	1	0	0	0	1105	159	6	4	923	4	ATIC	2	216198147	Missense_Mutation	SNP	A	TCGA-G3-AAV3-01A-11D-A36X-10	38099344	216198147	27001226	13	43266										
IGFBP5	3488	hgsc.bcm.edu	37	chr2	217542908	217542908	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	ggggcaccatgcgtgggctgGctttgagctcctgcagggaa	17	10	0	1			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr2:217542908G>A	ENST00000233813.4	-	3	1363	c.614C>T	c.(613-615)gCc>gTc	p.A205V		NM_000599.3	NP_000590.1	P24593	IBP5_HUMAN	insulin-like growth factor binding protein 5	205	Thyroglobulin type-1. {ECO:0000255|PROSITE-ProRule:PRU00500}.				cellular protein metabolic process (GO:0044267)|cellular response to cAMP (GO:0071320)|cellular response to organic cyclic compound (GO:0071407)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|hair follicle morphogenesis (GO:0031069)|intracellular signal transduction (GO:0035556)|mammary gland involution (GO:0060056)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of translation (GO:0017148)|osteoblast differentiation (GO:0001649)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell growth (GO:0001558)|regulation of glucose metabolic process (GO:0010906)|signal transduction (GO:0007165)|skeletal muscle tissue growth (GO:0048630)|striated muscle cell differentiation (GO:0051146)|type B pancreatic cell proliferation (GO:0044342)	extracellular region (GO:0005576)|insulin-like growth factor binding protein complex (GO:0016942)	insulin-like growth factor I binding (GO:0031994)			endometrium(1)|large_intestine(3)|lung(1)	5		Renal(323;0.0822)		Epithelial(149;2.1e-06)|all cancers(144;0.000165)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GCGTGGGCTGGCTTTGAGCTC	0.622																																					p.A205V		Atlas-SNP	.											.	IGFBP5	13	.	0			c.C614T						.						80	75	76					2																	217542908		2203	4300	6503	SO:0001583	missense	3488	exon3			GGGCTGGCTTTGA		CCDS2405.1	2q35	2014-09-16			ENSG00000115461	ENSG00000115461			5474	protein-coding gene	gene with protein product		146734				7511611	Standard	NM_000599		Approved		uc002vgj.4	P24593	OTTHUMG00000133058	ENST00000233813.4:c.614C>T	chr2.hg19:g.217542908G>A	ENSP00000233813:p.Ala205Val	166.0	0.0		236.0	48.0	NM_000599	Q5U0A3	Missense_Mutation	SNP	ENST00000233813.4	hg19	CCDS2405.1	.	.	.	.	.	.	.	.	.	.	G	12.03	1.816648	0.32145	.	.	ENSG00000115461	ENST00000233813	T	0.63744	-0.06	4.75	3.87	0.44632	Thyroglobulin type-1 (4);	0.448714	0.25590	N	0.029636	T	0.44008	0.1273	N	0.14661	0.345	0.28199	N	0.927433	B	0.23442	0.085	B	0.25759	0.063	T	0.27365	-1.0076	10	0.20519	T	0.43	-16.0966	13.5892	0.61951	0.0:0.3177:0.6823:0.0	.	205	P24593	IBP5_HUMAN	V	205	ENSP00000233813:A205V	ENSP00000233813:A205V	A	-	2	0	IGFBP5	217251153	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	3.973000	0.56845	1.195000	0.43115	0.561000	0.74099	GCC	.	.		0.622	IGFBP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256674.2	NM_000599		A	217542908	G	A	217542908	3	1	299	1	0	0	0	0	1	0	0	0	7591	1203	42	3	212	3	IGFBP5	2	217542908	Missense_Mutation	SNP	G	TCGA-G3-AAV3-01A-11D-A36X-10	1344761	217542908	25656465	14	43267										
STK11IP	114790	hgsc.bcm.edu	37	chr2	220466724	220466724	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	tcccagctccgaggtgttccCctccactgtctgcatggcct	9	17	1	0			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr2:220466724C>T	ENST00000456909.1	+	5	447	c.357C>T	c.(355-357)ccC>ccT	p.P119P	STK11IP_ENST00000295641.10_Silent_p.P130P|STK11IP_ENST00000459692.1_3'UTR			Q8N1F8	S11IP_HUMAN	serine/threonine kinase 11 interacting protein	130					protein localization (GO:0008104)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)	protein kinase binding (GO:0019901)			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)		GAGGTGTTCCCCTCCACTGTC	0.587																																					p.P130P		Atlas-SNP	.											.	STK11IP	152	.	0			c.C390T						.						44	43	43					2																	220466724		1979	4152	6131	SO:0001819	synonymous_variant	114790	exon5			TGTTCCCCTCCAC	AF450267	CCDS46521.1	2q35	2008-06-03			ENSG00000144589	ENSG00000144589			19184	protein-coding gene	gene with protein product	"LKB1 interacting protein"	607172				11741830	Standard	NM_052902		Approved	LIP1, KIAA1898, LKB1IP, STK11IP1	uc002vml.3	Q8N1F8	OTTHUMG00000059239	ENST00000456909.1:c.357C>T	chr2.hg19:g.220466724C>T		28.0	0.0		59.0	16.0	NM_052902	Q8NAW9|Q8WXE4|Q96CN3|Q96PY9	Silent	SNP	ENST00000456909.1	hg19																																																																																				.	.		0.587	STK11IP-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000131432.1	NM_052902		T	220466724	C	T	220466724	2	4	299	1	0	0	0	0	0	0	0	1	15303	610	22	3		3	STK11IP	2	220466724	Silent	SNP	C	TCGA-G3-AAV3-01A-11D-A36X-10	2923816	220466724	22732649	15	43268										
PER2	8864	hgsc.bcm.edu	37	chr2	239184515	239184515	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	ttatcagttctttgtgtgtgTccactttcgaagactggtcg	10	8	2	1			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr2:239184515T>A	ENST00000254657.3	-	4	596	c.317A>T	c.(316-318)gAc>gTc	p.D106V	PER2_ENST00000254658.3_Missense_Mutation_p.D106V|PER2_ENST00000440245.1_Missense_Mutation_p.D106V|PER2_ENST00000355768.2_Missense_Mutation_p.D106V	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN	period circadian clock 2	106					circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|fatty acid metabolic process (GO:0006631)|gluconeogenesis (GO:0006094)|glycogen biosynthetic process (GO:0005978)|histone H3 deacetylation (GO:0070932)|lactate biosynthetic process (GO:0019249)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of DNA-templated transcription, termination (GO:0060567)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of glutamate uptake involved in transmission of nerve impulse (GO:0051946)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of vasoconstriction (GO:0019229)|response to ischemia (GO:0002931)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	pre-mRNA binding (GO:0036002)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|ubiquitin binding (GO:0043130)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)		TTTGTGTGTGTCCACTTTCGA	0.507																																					p.D106V		Atlas-SNP	.											.	PER2	85	.	0			c.A317T						.						205	197	200					2																	239184515		2203	4300	6503	SO:0001583	missense	8864	exon4			TGTGTGTCCACTT	AB002345	CCDS2528.1	2q37.3	2012-12-13	2012-12-13		ENSG00000132326	ENSG00000132326			8846	protein-coding gene	gene with protein product		603426	"period (Drosophila) homolog 2", "period homolog 2 (Drosophila)"			9427249, 17218255	Standard	NM_022817		Approved	KIAA0347	uc002vyc.3	O15055	OTTHUMG00000152884	ENST00000254657.3:c.317A>T	chr2.hg19:g.239184515T>A	ENSP00000254657:p.Asp106Val	69.0	0.0		98.0	20.0	NM_022817	A2I2P7|Q4ZG49|Q6DT41|Q9UQ45	Missense_Mutation	SNP	ENST00000254657.3	hg19	CCDS2528.1	.	.	.	.	.	.	.	.	.	.	T	13.03	2.115550	0.37339	.	.	ENSG00000132326	ENST00000254657;ENST00000254658;ENST00000440245;ENST00000355768;ENST00000431832	T;T;T;T;T	0.47869	2.85;0.9;1.92;0.9;0.83	4.43	4.43	0.53597	.	0.206996	0.48767	D	0.000175	T	0.58352	0.2116	M	0.65975	2.015	0.32947	D	0.519221	P;D;P;B	0.63880	0.951;0.993;0.713;0.437	P;P;P;B	0.55161	0.576;0.77;0.69;0.397	T	0.72516	-0.4269	10	0.72032	D	0.01	-24.5296	11.971	0.53063	0.0:0.0:0.0:1.0	.	106;106;106;106	F5GYD5;B4DH14;O15055-2;O15055	.;.;.;PER2_HUMAN	V	106	ENSP00000254657:D106V;ENSP00000254658:D106V;ENSP00000397516:D106V;ENSP00000348013:D106V;ENSP00000405891:D106V	ENSP00000254657:D106V	D	-	2	0	PER2	238849254	1.000000	0.71417	0.003000	0.11579	0.001000	0.01503	6.016000	0.70798	1.782000	0.52362	0.533000	0.62120	GAC	.	.		0.507	PER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257167.1	NM_022817		A	239184515	T	A	239184515	3	1	299	1	0	0	0	0	1	0	0	0	11739	1667	58	4	3530	4	PER2	2	239184515	Missense_Mutation	SNP	T	TCGA-G3-AAV3-01A-11D-A36X-10	18717791	239184515	4014858	16	43269										
LRRN1	57633	hgsc.bcm.edu	37	chr3	3887129	3887129	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	gttccaaatttgaaattcttAgacctcaacaaaaaccccat	3	11	2	2			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr3:3887129A>C	ENST00000319331.3	+	2	1565	c.804A>C	c.(802-804)ttA>ttC	p.L268F	SUMF1_ENST00000534863.1_Intron	NM_020873.5	NP_065924.3	Q6UXK5	LRRN1_HUMAN	leucine rich repeat neuronal 1	268						integral component of membrane (GO:0016021)				NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|skin(1)|urinary_tract(2)	26				Epithelial(13;0.000886)|all cancers(10;0.0032)|OV - Ovarian serous cystadenocarcinoma(96;0.00608)|STAD - Stomach adenocarcinoma(44;0.0617)		TGAAATTCTTAGACCTCAACA	0.403																																					p.L268F		Atlas-SNP	.											.	LRRN1	82	.	0			c.A804C						.						69	77	74					3																	3887129		2203	4297	6500	SO:0001583	missense	57633	exon2			ATTCTTAGACCTC	AB040930	CCDS33685.1	3p26.2	2013-01-11			ENSG00000175928	ENSG00000175928		"Immunoglobulin superfamily / I-set domain containing"	20980	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 3"					10819331	Standard	NM_020873		Approved	FIGLER3	uc003bpt.4	Q6UXK5	OTTHUMG00000154934	ENST00000319331.3:c.804A>C	chr3.hg19:g.3887129A>C	ENSP00000314901:p.Leu268Phe	118.0	0.0		150.0	21.0	NM_020873	Q3LID5|Q8IYV5|Q9H8V1|Q9P231	Missense_Mutation	SNP	ENST00000319331.3	hg19	CCDS33685.1	.	.	.	.	.	.	.	.	.	.	A	19.24	3.789643	0.70337	.	.	ENSG00000175928	ENST00000319331	D	0.81499	-1.5	5.55	4.38	0.52667	.	0.000000	0.64402	D	0.000001	D	0.90205	0.6938	H	0.94847	3.59	0.54753	D	0.99998	D	0.89917	1.0	D	0.79784	0.993	D	0.88501	0.3082	10	0.87932	D	0	.	3.8344	0.08888	0.6225:0.1963:0.1812:0.0	.	268	Q6UXK5	LRRN1_HUMAN	F	268	ENSP00000314901:L268F	ENSP00000314901:L268F	L	+	3	2	LRRN1	3862129	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.344000	0.33941	0.906000	0.36621	0.528000	0.53228	TTA	.	.		0.403	LRRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337704.2	NM_020873		C	3887129	A	C	3887129	3	2	299	1	0	0	0	0	1	0	0	0	9043	417	15	5	806	5	LRRN1	3	3887129	Missense_Mutation	SNP	A	TCGA-G3-AAV3-01A-11D-A36X-10		3887129	194135301	17	43270										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266097	41266097	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	ggcagcaacagtcttacctgGactctggaatccattctggt	10	11	3	0	rs28931588|rs121913416|rs121913417		TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr3:41266097G>T	ENST00000349496.5	+	3	374	c.94G>T	c.(94-96)Gac>Tac	p.D32Y	CTNNB1_ENST00000405570.1_Missense_Mutation_p.D32Y|CTNNB1_ENST00000453024.1_Missense_Mutation_p.D25Y|CTNNB1_ENST00000396183.3_Missense_Mutation_p.D32Y|CTNNB1_ENST00000396185.3_Missense_Mutation_p.D32Y	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	32			D -> A (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|D -> G (in PTR and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629}.|D -> Y (in PTR, hepatoblastoma and hepatocellular carcinoma; dbSNP:rs28931588). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:11703283, ECO:0000269|PubMed:9927029}.|Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.D32Y(128)|p.D32N(82)|p.A5_A80del(53)|p.D32H(40)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.WQQQSYLD25?(5)|p.W25_D32del(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.S29_H36del(1)|p.D32del(1)|p.M14_S45del(1)|p.Q28_D32>H(1)|p.Q28fs*20(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.D32fs*9(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GTCTTACCTGGACTCTGGAAT	0.478	D32N(KE39_STOMACH)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.D32Y	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,0,2	CTNNB1	4904	.	397	Substitution - Missense(250)|Deletion - In frame(120)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)|Complex - frameshift(1)	liver(155)|central_nervous_system(55)|endometrium(40)|stomach(36)|pancreas(28)|large_intestine(22)|pituitary(22)|skin(11)|ovary(9)|soft_tissue(4)|prostate(4)|small_intestine(2)|haematopoietic_and_lymphoid_tissue(2)|bone(2)|adrenal_gland(1)|biliary_tract(1)|urinary_tract(1)|lung(1)|NS(1)	c.G94T						.						92	77	82					3																	41266097		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	TACCTGGACTCTG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.94G>T	chr3.hg19:g.41266097G>T	ENSP00000344456:p.Asp32Tyr	151.0	0.0		152.0	45.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.337485	0.81911	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92;0.92;0.92;0.92;0.92	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.68210	0.2976	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.70498	-0.4855	10	0.87932	D	0	0.3843	19.9596	0.97236	0.0:0.0:1.0:0.0	rs28931588	32	P35222	CTNB1_HUMAN	Y	25;32;32;32;32;25;32;32;32	ENSP00000400508:D25Y;ENSP00000385604:D32Y;ENSP00000412219:D32Y;ENSP00000379486:D32Y;ENSP00000344456:D32Y;ENSP00000411226:D25Y;ENSP00000379488:D32Y;ENSP00000409302:D32Y;ENSP00000401599:D32Y	ENSP00000344456:D32Y	D	+	1	0	CTNNB1	41241101	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.726000	0.93360	0.655000	0.94253	GAC	.	.		0.478	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41266097	G	T	41266097	3	4	299	1	0	0	0	0	1	0	0	0	4018	1174	41	3	100	3	CTNNB1	3	41266097	Missense_Mutation	SNP	G	TCGA-G3-AAV3-01A-11D-A36X-10	37378968	41266097	156756333	18	43271										
LAMB2	3913	hgsc.bcm.edu	37	chr3	49162791	49162814	+	In_Frame_Del	DEL	GGGAATCCCCACTGGCCACGCTGG	GGGAATCCCCACTGGCCACGCTGG	-													0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	agacacatggccggcagctaGggaatccccactggccacgc							TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	GGGAATCCCCACTGGCCACGCTGG	GGGAATCCCCACTGGCCACGCTGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr3:49162791_49162814delGGGAATCCCCACTGGCCACGCTGG	ENST00000418109.1	-	20	2756_2779	c.2592_2615delCCAGCGTGGCCAGTGGGGATTCCC	c.(2590-2616)tgccagcgtggccagtggggattccct>tgt	p.QRGQWGFP865del	LAMB2_ENST00000305544.4_In_Frame_Del_p.QRGQWGFP865del|LAMB2_ENST00000464891.1_5'UTR	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	865	Laminin EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00460}.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		CCGGCAGCTAGGGAATCCCCACTGGCCACGCTGGCAGCGGTCAC	0.616																																					p.865_872del		Atlas-INDEL	.											.	LAMB2	156	.	0			c.2593_2616del	GRCh37	CM085509	LAMB2	M		.																																			SO:0001651	inframe_deletion	3913	exon19			.		CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"Laminins"	6487	protein-coding gene	gene with protein product	"laminin S"	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.2592_2615delCCAGCGTGGCCAGTGGGGATTCCC	chr3.hg19:g.49162791_49162814delGGGAATCCCCACTGGCCACGCTGG	ENSP00000388325:p.Gln865_Pro872del	125.0	0.0		164.0	17.0	NM_002292	Q16321	In_Frame_Del	DEL	ENST00000418109.1	hg19	CCDS2789.1																																																																																			.	.		0.616	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292		-	49162814	GGGAATCCCCACTGGCCACGCTGG	-	49162791	7	5	299	1	0	1	0	1	0	0	0	0	8620	1000	35	0	2837	0	LAMB2	3	49162791	In_Frame_Del	DEL	GGGAATCCCCACTGGCCACGCTGG	TCGA-G3-AAV3-01A-11D-A36X-10	7896694	49162791	148859639	19	43272										
C3orf63	23272	hgsc.bcm.edu	37	chr3	56705673	56705673	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	gcataggattctgaaagttcCttatctaaacgaccatcaaa	6	9	3	1			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr3:56705673C>A	ENST00000493960.2	-	3	535	c.525G>T	c.(523-525)aaG>aaT	p.K175N	FAM208A_ENST00000355628.5_Missense_Mutation_p.K175N	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	175							poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(11)|prostate(3)|skin(1)	32						CTGAAAGTTCCTTATCTAAAC	0.318																																					p.K175N		Atlas-SNP	.											.	FAM208A	113	.	0			c.G525T						.						225	202	209					3																	56705673		692	1591	2283	SO:0001583	missense	23272	exon3			AAGTTCCTTATCT	AF180425	CCDS2877.1, CCDS46853.1	3p14.3	2011-09-14	2011-09-14	2011-09-14	ENSG00000163946	ENSG00000163946			30314	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 63"	C3orf63		10470851, 11149944	Standard	NM_015224		Approved	se89-1, RAP140, KIAA1105	uc003die.4	Q9UK61	OTTHUMG00000158827	ENST00000493960.2:c.525G>T	chr3.hg19:g.56705673C>A	ENSP00000417509:p.Lys175Asn	54.0	0.0		116.0	29.0	NM_001112736	A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Missense_Mutation	SNP	ENST00000493960.2	hg19	CCDS46853.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.979118	0.74360	.	.	ENSG00000163946	ENST00000493960;ENST00000355628	T;T	0.48522	0.81;0.81	5.85	3.65	0.41850	.	.	.	.	.	T	0.54447	0.1859	L	0.42245	1.32	0.42229	D	0.991883	D;D	0.76494	0.999;0.999	D;D	0.71656	0.953;0.974	T	0.55964	-0.8057	9	0.66056	D	0.02	-5.0504	6.2185	0.20667	0.0:0.3753:0.0:0.6247	.	175;175	Q9UK61-3;Q9UK61-4	.;.	N	175	ENSP00000417509:K175N;ENSP00000347845:K175N	ENSP00000347845:K175N	K	-	3	2	C3orf63	56680713	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.853000	0.27777	1.310000	0.45006	0.655000	0.94253	AAG	.	.		0.318	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352352.2	NM_015224		A	56705673	C	A	56705673	3	1	299	1	0	0	0	0	1	0	0	0	2241	680	24	3	4635	3	C3orf63	3	56705673	Missense_Mutation	SNP	C	TCGA-G3-AAV3-01A-11D-A36X-10	7542882	56705673	141316757	20	43273										
PLA1A	51365	hgsc.bcm.edu	37	chr3	119328406	119328406	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	gggacagctcttcggaggccAgctgggacagatcacaggta	15	10	2	1			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr3:119328406A>T	ENST00000273371.4	+	4	617	c.545A>T	c.(544-546)cAg>cTg	p.Q182L	PLA1A_ENST00000495992.1_Missense_Mutation_p.Q166L|PLA1A_ENST00000494440.1_Missense_Mutation_p.Q166L|PLA1A_ENST00000488919.1_Missense_Mutation_p.Q9L	NM_015900.3	NP_056984.1	Q53H76	PLA1A_HUMAN	phospholipase A1 member A	182					lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)|phosphatidylserine metabolic process (GO:0006658)	extracellular vesicular exosome (GO:0070062)	phosphatidylcholine 1-acylhydrolase activity (GO:0008970)			NS(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						TTCGGAGGCCAGCTGGGACAG	0.537																																					p.Q182L		Atlas-SNP	.											.	PLA1A	65	.	0			c.A545T						.						102	100	100					3																	119328406		2203	4300	6503	SO:0001583	missense	51365	exon4			GAGGCCAGCTGGG	AF035268	CCDS2991.1, CCDS56268.1, CCDS56269.1	3q13.13-q13.2	2002-11-28			ENSG00000144837	ENSG00000144837			17661	protein-coding gene	gene with protein product		607460				10196188	Standard	NM_015900		Approved	ps-PLA1	uc003ecu.3	Q53H76	OTTHUMG00000159425	ENST00000273371.4:c.545A>T	chr3.hg19:g.119328406A>T	ENSP00000273371:p.Gln182Leu	73.0	0.0		90.0	19.0	NM_015900	B2R8V2|B4DXA2|O95991|Q86WX6|Q9UPD2	Missense_Mutation	SNP	ENST00000273371.4	hg19	CCDS2991.1	.	.	.	.	.	.	.	.	.	.	A	15.88	2.962976	0.53507	.	.	ENSG00000144837	ENST00000273371;ENST00000488919;ENST00000495992;ENST00000494440;ENST00000475963	D;D;D;D;D	0.91011	-2.77;-2.77;-2.77;-2.77;-2.77	5.31	5.31	0.75309	Lipase, N-terminal (1);	0.226040	0.36482	U	0.002561	D	0.87148	0.6105	L	0.55481	1.735	0.49389	D	0.999785	P;P	0.40230	0.708;0.574	B;B	0.37650	0.165;0.255	D	0.87338	0.2329	10	0.59425	D	0.04	-14.8871	9.8108	0.40822	0.8468:0.0:0.0:0.1531	.	166;182	Q53H76-3;Q53H76	.;PLA1A_HUMAN	L	182;9;166;166;48	ENSP00000273371:Q182L;ENSP00000420625:Q9L;ENSP00000417326:Q166L;ENSP00000418793:Q166L;ENSP00000417295:Q48L	ENSP00000273371:Q182L	Q	+	2	0	PLA1A	120811096	0.964000	0.33143	1.000000	0.80357	0.922000	0.55478	2.130000	0.42064	2.123000	0.65237	0.459000	0.35465	CAG	.	.		0.537	PLA1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355252.2			T	119328406	A	T	119328406	3	4	299	1	0	0	0	0	1	0	0	0	11997	188	7	4	559	4	PLA1A	3	119328406	Missense_Mutation	SNP	A	TCGA-G3-AAV3-01A-11D-A36X-10	62622733	119328406	78694024	21	43274										
SLC2A2	6514	hgsc.bcm.edu	37	chr3	170732356	170732356	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	gaccagagcatggtgattagTtgagcagctgccacagtctc	12	10	1	3			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr3:170732356T>C	ENST00000314251.3	-	3	352	c.273A>G	c.(271-273)caA>caG	p.Q91Q	SLC2A2_ENST00000382808.4_Intron	NM_000340.1	NP_000331.1	P11168	GTR2_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 2	91					carbohydrate metabolic process (GO:0005975)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transmembrane transport (GO:0035428)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	brush border (GO:0005903)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|hexose transmembrane transporter activity (GO:0015149)			central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)		Streptozocin(DB00428)	TGGTGATTAGTTGAGCAGCTG	0.488																																					p.Q91Q		Atlas-SNP	.											.	SLC2A2	71	.	0			c.A273G						.						217	198	205					3																	170732356		2203	4300	6503	SO:0001819	synonymous_variant	6514	exon3			GATTAGTTGAGCA	J03810	CCDS3215.1	3q26.2-q27	2013-05-22			ENSG00000163581	ENSG00000163581		"Solute carriers"	11006	protein-coding gene	gene with protein product		138160		GLUT2		1852621	Standard	NM_000340		Approved		uc003fhe.1	P11168	OTTHUMG00000158997	ENST00000314251.3:c.273A>G	chr3.hg19:g.170732356T>C		100.0	0.0		117.0	29.0	NM_000340	A8K481|B2R936|B7Z547|F8W8V8|Q9UCW9	Silent	SNP	ENST00000314251.3	hg19	CCDS3215.1																																																																																			.	.		0.488	SLC2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352834.1	NM_000340		C	170732356	T	C	170732356	2	2	299	1	0	0	0	0	0	0	0	1	14559	1722	60	2		2	SLC2A2	3	170732356	Silent	SNP	T	TCGA-G3-AAV3-01A-11D-A36X-10	51403950	170732356	27290074	22	43275										
CPZ	8532	hgsc.bcm.edu	37	chr4	8605798	8605798	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	cccagatggtgcgtgtgctgAggcggacggcctcccgctgc	16	14	0	2			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr4:8605798A>T	ENST00000360986.4	+	4	766	c.592A>T	c.(592-594)Agg>Tgg	p.R198W	CPZ_ENST00000315782.6_Missense_Mutation_p.R187W|CPZ_ENST00000429646.2_De_novo_Start_OutOfFrame|CPZ_ENST00000382480.2_Missense_Mutation_p.R61W	NM_001014447.2	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z	198					proteolysis (GO:0006508)|Wnt signaling pathway (GO:0016055)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(23)|ovary(3)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						GCGTGTGCTGAGGCGGACGGC	0.697																																					p.R198W		Atlas-SNP	.											.	CPZ	95	.	0			c.A592T						.						21	18	19					4																	8605798		2173	4259	6432	SO:0001583	missense	8532	exon4			GTGCTGAGGCGGA	U83411	CCDS3404.1, CCDS33953.1, CCDS43212.1	4p16.1	2012-02-10			ENSG00000109625	ENSG00000109625			2333	protein-coding gene	gene with protein product	"metallocarboxypeptidase Z"	603105				9099699	Standard	NM_001014447		Approved		uc003glm.3	Q66K79	OTTHUMG00000090513	ENST00000360986.4:c.592A>T	chr4.hg19:g.8605798A>T	ENSP00000354255:p.Arg198Trp	45.0	0.0		78.0	19.0	NM_001014447	O00520|Q96MX2	Missense_Mutation	SNP	ENST00000360986.4	hg19	CCDS33953.1	.	.	.	.	.	.	.	.	.	.	A	16.12	3.032501	0.54790	.	.	ENSG00000109625	ENST00000360986;ENST00000382480;ENST00000315782	T;T;T	0.11821	2.74;2.74;2.74	3.86	1.07	0.20283	Peptidase M14, carboxypeptidase A (1);	0.303434	0.33217	N	0.005152	T	0.31827	0.0809	M	0.83012	2.62	0.80722	D	1	D;D	0.64830	0.994;0.992	P;P	0.59948	0.835;0.866	T	0.06127	-1.0844	10	0.66056	D	0.02	-12.9779	9.9057	0.41375	0.6698:0.3301:0.0:0.0	.	187;198	Q66K79-2;Q66K79	.;CBPZ_HUMAN	W	198;61;187	ENSP00000354255:R198W;ENSP00000371920:R61W;ENSP00000315074:R187W	ENSP00000315074:R187W	R	+	1	2	CPZ	8656698	1.000000	0.71417	0.802000	0.32245	0.340000	0.28889	1.936000	0.40183	0.039000	0.15632	0.454000	0.30748	AGG	.	.		0.697	CPZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207001.4	NM_003652		T	8605798	A	T	8605798	3	4	299	1	0	0	0	0	1	0	0	0	3841	295	11	4	606	4	CPZ	4	8605798	Missense_Mutation	SNP	A	TCGA-G3-AAV3-01A-11D-A36X-10		8605798	182548478	23	43276										
PRKG2	5593	hgsc.bcm.edu	37	chr4	82073196	82073196	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	atcatggccttctgtgctctGtgttacttttacctaaacaa	6	10	3	0			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr4:82073196G>A	ENST00000395578.1	-	8	1119	c.1003C>T	c.(1003-1005)Cag>Tag	p.Q335*	PRKG2_ENST00000418486.2_Nonsense_Mutation_p.Q335*|PRKG2_ENST00000545647.1_5'UTR|PRKG2_ENST00000264399.1_Nonsense_Mutation_p.Q335*|PRKG2_ENST00000509169.1_5'UTR			Q13237	KGP2_HUMAN	protein kinase, cGMP-dependent, type II	335					blood coagulation (GO:0007596)|circadian regulation of gene expression (GO:0032922)|nitric oxide metabolic process (GO:0046209)|protein phosphorylation (GO:0006468)|regulation of nitric-oxide synthase activity (GO:0050999)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)|protein kinase activity (GO:0004672)			NS(1)|breast(4)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	37						TCTGTGCTCTGTGTTACTTTT	0.368																																					p.Q335X		Atlas-SNP	.											.	PRKG2	195	.	0			c.C1003T						.						233	225	228					4																	82073196		2203	4300	6503	SO:0001587	stop_gained	5593	exon7			TGCTCTGTGTTAC	X94612	CCDS3589.1, CCDS75150.1	4q13.1-q21.1	2009-07-10			ENSG00000138669	ENSG00000138669	2.7.11.1		9416	protein-coding gene	gene with protein product		601591				7498513	Standard	XM_005263126		Approved	cGKII, PRKGR2	uc003hmh.2	Q13237	OTTHUMG00000130296	ENST00000395578.1:c.1003C>T	chr4.hg19:g.82073196G>A	ENSP00000378945:p.Gln335*	62.0	0.0		81.0	24.0	NM_006259	B4DMX3|E7EPE6|O00125|O60916	Nonsense_Mutation	SNP	ENST00000395578.1	hg19	CCDS3589.1	.	.	.	.	.	.	.	.	.	.	G	39	7.639657	0.98406	.	.	ENSG00000138669	ENST00000395578;ENST00000264399;ENST00000418486	.	.	.	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-24.687	18.7444	0.91787	0.0:0.0:1.0:0.0	.	.	.	.	X	335	.	ENSP00000264399:Q335X	Q	-	1	0	PRKG2	82292220	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	8.344000	0.90055	2.729000	0.93468	0.591000	0.81541	CAG	.	.		0.368	PRKG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252639.1	NM_006259		A	82073196	G	A	82073196	4	1	299	1	0	0	0	0	0	1	0	0	12535	1386	48	3	1333	3	PRKG2	4	82073196	Nonsense_Mutation	SNP	G	TCGA-G3-AAV3-01A-11D-A36X-10	73467398	82073196	109081080	24	43277										
ESM1	11082	hgsc.bcm.edu	37	chr5	54281052	54281052	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	ggtcactctttacctttgcaGataccaaactcttcaccaaa	4	13	4	1			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr5:54281052G>T	ENST00000381405.4	-	1	439	c.294C>A	c.(292-294)atC>atA	p.I98I	ESM1_ENST00000381403.4_Silent_p.I98I|ESM1_ENST00000598310.1_Intron	NM_007036.4	NP_008967.1	Q9NQ30	ESM1_HUMAN	endothelial cell-specific molecule 1	98	IGFBP N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00653}.				angiogenesis (GO:0001525)|positive regulation of cell proliferation (GO:0008284)|positive regulation of hepatocyte growth factor receptor signaling pathway (GO:1902204)|regulation of cell growth (GO:0001558)|sprouting angiogenesis (GO:0002040)	extracellular region (GO:0005576)	hepatocyte growth factor receptor binding (GO:0005171)|integrin binding (GO:0005178)			breast(1)|kidney(1)|large_intestine(4)|lung(4)	10		Lung NSC(810;4.08e-05)|Breast(144;0.0433)|Prostate(74;0.116)	Lung(15;0.23)			TACCTTTGCAGATACCAAACT	0.552																																					p.I98I		Atlas-SNP	.											.	ESM1	27	.	0			c.C294A						.						102	104	104					5																	54281052		2203	4300	6503	SO:0001819	synonymous_variant	11082	exon1			TTTGCAGATACCA	X89426	CCDS3963.1, CCDS47206.1	5q11	2008-02-05			ENSG00000164283	ENSG00000164283			3466	protein-coding gene	gene with protein product		601521				8702785	Standard	NM_001135604		Approved		uc003jpk.3	Q9NQ30	OTTHUMG00000097010	ENST00000381405.4:c.294C>A	chr5.hg19:g.54281052G>T		59.0	0.0		97.0	5.0	NM_001135604	B2R4G3|Q15330|Q3V4E3|Q96ES3	Silent	SNP	ENST00000381405.4	hg19	CCDS3963.1																																																																																			.	.		0.552	ESM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214099.2	NM_007036		T	54281052	G	T	54281052	2	4	299	1	0	0	0	0	0	0	0	1	5254	932	33	3		3	ESM1	5	54281052	Silent	SNP	G	TCGA-G3-AAV3-01A-11D-A36X-10		54281052	126634208	25	43278										
BDP1	55814	hgsc.bcm.edu	37	chr5	70805742	70805742	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	agagaaatatccccacagaaAaatggcccagaggaggttaa	10	8	0	3			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr5:70805742A>T	ENST00000358731.4	+	17	3086	c.2823A>T	c.(2821-2823)aaA>aaT	p.K941N	BDP1_ENST00000380675.2_5'UTR	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	941	9 X 55 AA repeats of G-R-R-X-I-S-P-X-E-N- G-X-E-E-V-K-P-X-X-E-M-E-T-D-L-K-X-T-G-R- E-X-X-X-R-E-K-T-X-E-X-X-D-A-X-E-E-I-D-X- D-L-E-E-T.				gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(34)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		CCCCACAGAAAAATGGCCCAG	0.463																																					p.K941N		Atlas-SNP	.											.	BDP1	204	.	0			c.A2823T						.						72	73	73					5																	70805742		1850	4092	5942	SO:0001583	missense	55814	exon17			ACAGAAAAATGGC	AF298151	CCDS43328.1	5q12-q13	2008-02-05	2001-11-29	2001-11-30	ENSG00000145734	ENSG00000145734			13652	protein-coding gene	gene with protein product		607012	"TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 1"	TFNR, TAF3B1		11214970, 11040218	Standard	NM_018429		Approved	TFIIIB150, TFC5, TFIIIB90, KIAA1689, HSA238520, KIAA1241	uc003kbp.1	A6H8Y1	OTTHUMG00000162506	ENST00000358731.4:c.2823A>T	chr5.hg19:g.70805742A>T	ENSP00000351575:p.Lys941Asn	168.0	0.0		206.0	38.0	NM_018429	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Missense_Mutation	SNP	ENST00000358731.4	hg19	CCDS43328.1	.	.	.	.	.	.	.	.	.	.	A	6.480	0.456828	0.12283	.	.	ENSG00000145734	ENST00000358731;ENST00000451951	T	0.11277	2.79	2.76	-1.47	0.08772	.	.	.	.	.	T	0.04227	0.0117	N	0.08118	0	0.09310	N	0.999999	B;B;B	0.18310	0.0;0.0;0.027	B;B;B	0.19391	0.0;0.0;0.025	T	0.44081	-0.9351	9	0.23891	T	0.37	.	3.1392	0.06450	0.5072:0.2223:0.2705:0.0	.	941;941;941	A6H8Y1;A6H8Y1-2;A6H8Y1-4	BDP1_HUMAN;.;.	N	941;521	ENSP00000351575:K941N	ENSP00000351575:K941N	K	+	3	2	BDP1	70841498	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.586000	0.05787	-0.283000	0.09115	0.260000	0.18958	AAA	.	.		0.463	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429		T	70805742	A	T	70805742	3	4	299	1	0	0	0	0	1	0	0	0	1395	11	1	4	2889	4	BDP1	5	70805742	Missense_Mutation	SNP	A	TCGA-G3-AAV3-01A-11D-A36X-10	16524690	70805742	110109518	26	43279										
PCDHA13	56136	hgsc.bcm.edu	37	chr5	140263516	140263516	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	acgtgacgctgcaggtgttcGtgctggacgagaacgacaac	14	10	0	2			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr5:140263516G>A	ENST00000289272.2	+	1	1663	c.1663G>A	c.(1663-1665)Gtg>Atg	p.V555M	PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA13_ENST00000409494.1_Missense_Mutation_p.V555M|PCDHA12_ENST00000398631.2_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA9_ENST00000532602.1_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	555	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|biliary_tract(2)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(18)|liver(3)|lung(23)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCAGGTGTTCGTGCTGGACGA	0.697																																					p.V555M	Melanoma(147;1739 1852 5500 27947 37288)	Atlas-SNP	.											.	PCDHA13	213	.	0			c.G1663A						.						67	73	71					5																	140263516		2203	4297	6500	SO:0001583	missense	56136	exon1			GTGTTCGTGCTGG	AF152478	CCDS4240.1	5q31	2010-11-26			ENSG00000239389	ENSG00000239389		"Cadherins / Protocadherins : Clustered"	8667	other	complex locus constituent	"KIAA0345-like 1", "ortholog of mouse CNR5"	606319		CNRS5		10380929, 10662547	Standard	NM_018904		Approved	CNR5, CRNR5, CNRN5, PCDH-ALPHA13		Q9Y5I0	OTTHUMG00000129614	ENST00000289272.2:c.1663G>A	chr5.hg19:g.140263516G>A	ENSP00000289272:p.Val555Met	39.0	0.0		82.0	21.0	NM_031865	O75277	Missense_Mutation	SNP	ENST00000289272.2	hg19	CCDS4240.1	.	.	.	.	.	.	.	.	.	.	G	15.74	2.922816	0.52653	.	.	ENSG00000239389	ENST00000409494;ENST00000289272	T;T	0.68181	-0.31;-0.31	4.08	4.08	0.47627	Cadherin (5);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	D	0.83271	0.5218	M	0.90650	3.135	0.24944	N	0.991835	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	T	0.73550	-0.3947	9	0.87932	D	0	.	9.8562	0.41088	0.0957:0.0:0.9043:0.0	.	555;555;555	Q9Y5I0;C9JA99;Q9Y5I0-2	PCDAD_HUMAN;.;.	M	555	ENSP00000386821:V555M;ENSP00000289272:V555M	ENSP00000289272:V555M	V	+	1	0	PCDHA13	140243700	0.995000	0.38212	1.000000	0.80357	0.906000	0.53458	2.470000	0.45119	2.073000	0.62155	0.561000	0.74099	GTG	.	.		0.697	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904		A	140263516	G	A	140263516	3	1	299	1	0	0	0	0	1	0	0	0	11532	1145	40	1	1665	1	PCDHA13	5	140263516	Missense_Mutation	SNP	G	TCGA-G3-AAV3-01A-11D-A36X-10	69457774	140263516	40651744	27	43280										
LRRC16A	55604	hgsc.bcm.edu	37	chr6	25420378	25420378	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	gagccttccttgtaacagcgCgaatccccaccaaggtaagt	9	13	0	0	rs79463028	byFrequency	TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr6:25420378C>T	ENST00000329474.6	+	3	543	c.175C>T	c.(175-177)Cga>Tga	p.R59*	LRRC16A_ENST00000377969.3_5'UTR	NM_001173977.1|NM_017640.5	NP_001167448.1|NP_060110.4	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	59					actin filament organization (GO:0007015)|barbed-end actin filament uncapping (GO:0051638)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|lamellipodium assembly (GO:0030032)|negative regulation of barbed-end actin filament capping (GO:2000813)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of lamellipodium organization (GO:1902745)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|ruffle organization (GO:0031529)|urate metabolic process (GO:0046415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|lamellipodium (GO:0030027)|nucleus (GO:0005634)	protein complex binding (GO:0032403)	p.R59R(1)		breast(4)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	50						TGTAACAGCGCGAATCCCCAC	0.488																																					p.R59X		Atlas-SNP	.											LRRC16A,NS,carcinoma,0,1	LRRC16A	168	.	1	Substitution - coding silent(1)	stomach(1)	c.C175T						.	C	stop/ARG,stop/ARG	1,4109		0,1,2054	188	176	180		175,175	4.4	1	6	dbSNP_131	180	0,8410		0,0,4205	no	stop-gained,stop-gained	LRRC16A	NM_001173977.1,NM_017640.5	,	0,1,6259	TT,TC,CC		0.0,0.0243,0.0080	,	59/1366,59/1372	25420378	1,12519	2055	4205	6260	SO:0001587	stop_gained	55604	exon3			ACAGCGCGAATCC	AK000055	CCDS54973.1	6p22.1	2010-09-10	2008-02-12	2008-02-12	ENSG00000079691	ENSG00000079691			21581	protein-coding gene	gene with protein product	"capping protein, Arp2/3, and Myosin-I Linker homolog 1 (Dictyostelium)"	609593	"leucine rich repeat containing 16"	LRRC16		19846667	Standard	NM_017640		Approved	dJ501N12.1, FLJ20048, CARMIL, CARMIL1	uc011djw.2	Q5VZK9	OTTHUMG00000014393	ENST00000329474.6:c.175C>T	chr6.hg19:g.25420378C>T	ENSP00000331983:p.Arg59*	74.0	0.0		104.0	15.0	NM_001173977	B8X1J0|Q6ZUH5|Q6ZW07|Q9NXU7	Nonsense_Mutation	SNP	ENST00000329474.6	hg19	CCDS54973.1	.	.	.	.	.	.	.	.	.	.	C	39	7.581949	0.98371	2.43E-4	0.0	ENSG00000079691	ENST00000329474;ENST00000399313	.	.	.	4.38	4.38	0.52667	.	0.000000	0.64402	D	0.000012	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.18710	T	0.47	.	12.3158	0.54955	0.0:1.0:0.0:0.0	.	.	.	.	X	59	.	ENSP00000331983:R59X	R	+	1	2	LRRC16A	25528357	0.997000	0.39634	0.969000	0.41365	0.954000	0.61252	3.801000	0.55545	2.246000	0.74042	0.655000	0.94253	CGA	.	.		0.488	LRRC16A-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040045.2	NM_017640		T	25420378	C	T	25420378	4	4	299	1	0	0	0	0	0	1	0	0	8980	760	27	1	185	1	LRRC16A	6	25420378	Nonsense_Mutation	SNP	C	TCGA-G3-AAV3-01A-11D-A36X-10		25420378	145694689	28	43281										
HIST1H3I	8354	hgsc.bcm.edu	37	chr6	27839711	27839711	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	tctcccctcggatgcggcgcGcaagctggatgtctttaggc	13	13	2	0			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr6:27839711G>A	ENST00000328488.2	-	1	388	c.383C>T	c.(382-384)gCg>gTg	p.A128V		NM_003533.2	NP_003524.1	P68431	H31_HUMAN	histone cluster 1, H3i	128					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			endometrium(2)|kidney(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						GATGCGGCGCGCAAGCTGGAT	0.532																																					p.A128V		Atlas-SNP	.											.	HIST1H3I	28	.	0			c.C383T						.						140	154	149					6																	27839711		2203	4300	6503	SO:0001583	missense	8354	exon1			CGGCGCGCAAGCT	X83550	CCDS4636.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000182572	ENSG00000275379		"Histones / Replication-dependent"	4771	protein-coding gene	gene with protein product		602814	"H3 histone family, member F", "histone 1, H3i"	H3FF		9031620, 9439656, 12408966	Standard	NM_003533		Approved	H3/f, H3.f	uc003njy.3	P68431	OTTHUMG00000016184	ENST00000328488.2:c.383C>T	chr6.hg19:g.27839711G>A	ENSP00000329554:p.Ala128Val	88.0	0.0		144.0	29.0	NM_003533	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Missense_Mutation	SNP	ENST00000328488.2	hg19	CCDS4636.1	.	.	.	.	.	.	.	.	.	.	G	16.16	3.044211	0.55110	.	.	ENSG00000182572	ENST00000328488	T	0.78816	-1.21	4.12	4.12	0.48240	.	.	.	.	.	D	0.83367	0.5239	.	.	.	0.46725	D	0.999173	.	.	.	.	.	.	D	0.85408	0.1135	6	0.72032	D	0.01	.	16.6345	0.85043	0.0:0.0:1.0:0.0	.	.	.	.	V	128	ENSP00000329554:A128V	ENSP00000329554:A128V	A	-	2	0	HIST1H3I	27947690	1.000000	0.71417	0.741000	0.31004	0.983000	0.72400	9.288000	0.96055	2.580000	0.87095	0.650000	0.86243	GCG	.	.		0.532	HIST1H3I-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043452.1	NM_003533		A	27839711	G	A	27839711	3	1	299	1	0	0	0	0	1	0	0	0	7172	1087	38	1	31	1	HIST1H3I	6	27839711	Missense_Mutation	SNP	G	TCGA-G3-AAV3-01A-11D-A36X-10	2419333	27839711	143275356	29	43282										
FTSJD2	23070	hgsc.bcm.edu	37	chr6	37414111	37414111	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	gaaggattgggtaaatacagCcagggtcggaaggacatcgt	15	6	0	0			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr6:37414111C>A	ENST00000373451.4	+	4	494	c.330C>A	c.(328-330)agC>agA	p.S110R		NM_015050.2	NP_055865.1	Q8N1G2	CMTR1_HUMAN	cap methyltransferase 1	110	G-patch. {ECO:0000255|PROSITE- ProRule:PRU00092}.				7-methylguanosine mRNA capping (GO:0006370)|cap1 mRNA methylation (GO:0097309)|mRNA methylation (GO:0080009)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)|nucleic acid binding (GO:0003676)										GTAAATACAGCCAGGGTCGGA	0.498																																					p.S110R		Atlas-SNP	.											.	FTSJD2	64	.	0			c.C330A						.						186	180	182					6																	37414111		2203	4300	6503	SO:0001583	missense	23070	exon4			ATACAGCCAGGGT	BC031890	CCDS4835.1	6p21.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000137200	ENSG00000137200	2.1.1.57	"G patch domain containing"	21077	protein-coding gene	gene with protein product			"KIAA0082", "FtsJ methyltransferase domain containing 2"	KIAA0082, FTSJD2		20713356	Standard	NM_015050		Approved	MTr1, ISG95	uc003ons.3	Q8N1G2	OTTHUMG00000014624	ENST00000373451.4:c.330C>A	chr6.hg19:g.37414111C>A	ENSP00000362550:p.Ser110Arg	114.0	0.0		226.0	40.0	NM_015050	A8K949|Q14670|Q96FJ9	Missense_Mutation	SNP	ENST00000373451.4	hg19	CCDS4835.1	.	.	.	.	.	.	.	.	.	.	C	14.82	2.648571	0.47258	.	.	ENSG00000137200	ENST00000373451;ENST00000455891;ENST00000373427	T;T	0.30182	1.54;1.54	5.44	3.68	0.42216	D111/G-patch (3);	0.049764	0.85682	D	0.000000	T	0.08403	0.0209	N	0.16790	0.44	0.39936	D	0.974359	P;B	0.36909	0.573;0.093	B;B	0.37833	0.259;0.124	T	0.09975	-1.0650	10	0.46703	T	0.11	-13.3449	6.9995	0.24801	0.0:0.7068:0.1408:0.1524	.	110;110	Q5T7F5;Q8N1G2	.;MTR1_HUMAN	R	110	ENSP00000362550:S110R;ENSP00000414233:S110R	ENSP00000362526:S110R	S	+	3	2	FTSJD2	37522089	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.996000	0.40776	0.680000	0.31366	0.655000	0.94253	AGC	.	.		0.498	CMTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040408.1	NM_015050		A	37414111	C	A	37414111	3	1	299	1	0	0	0	0	1	0	0	0	6099	738	26	3	340	3	FTSJD2	6	37414111	Missense_Mutation	SNP	C	TCGA-G3-AAV3-01A-11D-A36X-10	9574400	37414111	133700956	30	43283										
LAMA4	3910	hgsc.bcm.edu	37	chr6	112430681	112430681	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	gatgcttacggcgccgctgaCcagggctgctttactgaagc	13	12	0	2			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr6:112430681C>T	ENST00000230538.7	-	39	5828	c.5431G>A	c.(5431-5433)Gtc>Atc	p.V1811I	LAMA4_ENST00000522006.1_Missense_Mutation_p.V1804I|LAMA4_ENST00000389463.4_Missense_Mutation_p.V1804I|LAMA4_ENST00000424408.2_Missense_Mutation_p.V1804I	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	1811	Laminin G-like 5. {ECO:0000255|PROSITE- ProRule:PRU00122}.				blood vessel development (GO:0001568)|brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(42)|ovary(4)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(8)	100		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		GCGCCGCTGACCAGGGCTGCT	0.522																																					p.V1811I		Atlas-SNP	.											.	LAMA4	227	.	0			c.G5431A						.						83	76	78					6																	112430681		2203	4300	6503	SO:0001583	missense	3910	exon39			CGCTGACCAGGGC		CCDS34514.1, CCDS43491.1, CCDS43492.1	6q21	2014-09-17			ENSG00000112769	ENSG00000112769		"Laminins"	6484	protein-coding gene	gene with protein product		600133				7959779	Standard	NM_001105206		Approved	LAMA3	uc003pvu.3	Q16363	OTTHUMG00000015386	ENST00000230538.7:c.5431G>A	chr6.hg19:g.112430681C>T	ENSP00000230538:p.Val1811Ile	71.0	0.0		85.0	30.0	NM_001105206	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Missense_Mutation	SNP	ENST00000230538.7	hg19	CCDS43491.1	.	.	.	.	.	.	.	.	.	.	C	34	5.401689	0.96030	.	.	ENSG00000112769	ENST00000230538;ENST00000522006;ENST00000389463;ENST00000424408	T;T;T;T	0.79554	-1.28;-1.28;-1.28;-1.28	6.17	6.17	0.99709	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	0.060035	0.64402	D	0.000003	D	0.84129	0.5404	L	0.51422	1.61	0.80722	D	1	D;D	0.64830	0.991;0.994	P;P	0.60473	0.754;0.875	T	0.80736	-0.1249	10	0.39692	T	0.17	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	1811;1804	Q16363;Q16363-2	LAMA4_HUMAN;.	I	1811;1804;1804;1804	ENSP00000230538:V1811I;ENSP00000429488:V1804I;ENSP00000374114:V1804I;ENSP00000416470:V1804I	ENSP00000230538:V1811I	V	-	1	0	LAMA4	112537374	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.848000	0.75409	2.941000	0.99782	0.655000	0.94253	GTC	.	.		0.522	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206		T	112430681	C	T	112430681	3	4	299	1	0	0	0	0	1	0	0	0	8617	507	18	3	44	3	LAMA4	6	112430681	Missense_Mutation	SNP	C	TCGA-G3-AAV3-01A-11D-A36X-10	75016570	112430681	58684386	31	43284										
PLEKHG1	57480	hgsc.bcm.edu	37	chr6	151130378	151130378	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	ttcgacaagctgctgctcatCacgaagaagagagatgacac	10	10	2	4			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr6:151130378C>G	ENST00000358517.2	+	8	1261	c.1050C>G	c.(1048-1050)atC>atG	p.I350M	PLEKHG1_ENST00000367328.1_Missense_Mutation_p.I350M			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	350	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(19)|ovary(5)|prostate(4)|stomach(1)|urinary_tract(3)	53			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		TGCTGCTCATCACGAAGAAGA	0.557																																					p.I350M		Atlas-SNP	.											.	PLEKHG1	97	.	0			c.C1050G						.						113	107	109					6																	151130378		2203	4300	6503	SO:0001583	missense	57480	exon9			GCTCATCACGAAG	AB033035	CCDS34552.1	6q25.1	2013-01-11			ENSG00000120278	ENSG00000120278		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	20884	protein-coding gene	gene with protein product						10574462	Standard	XM_005267064		Approved	KIAA1209, ARHGEF41	uc003qny.1	Q9ULL1	OTTHUMG00000015824	ENST00000358517.2:c.1050C>G	chr6.hg19:g.151130378C>G	ENSP00000351318:p.Ile350Met	62.0	0.0		63.0	13.0	NM_001029884	Q5T1F2	Missense_Mutation	SNP	ENST00000358517.2	hg19	CCDS34552.1	.	.	.	.	.	.	.	.	.	.	C	14.71	2.618051	0.46736	.	.	ENSG00000120278	ENST00000367328;ENST00000535018;ENST00000358517	D;D	0.88586	-2.4;-2.4	5.63	4.76	0.60689	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.045865	0.85682	D	0.000000	D	0.91751	0.7391	M	0.74881	2.28	0.53688	D	0.999973	D;D;D	0.76494	0.973;0.999;0.999	P;D;D	0.75484	0.827;0.986;0.986	D	0.92648	0.6130	10	0.72032	D	0.01	.	10.9189	0.47152	0.0:0.8029:0.0:0.1971	.	157;350;350	Q5EBL9;Q5JYA6;Q9ULL1	.;.;PKHG1_HUMAN	M	350	ENSP00000356297:I350M;ENSP00000351318:I350M	ENSP00000351318:I350M	I	+	3	3	PLEKHG1	151172071	1.000000	0.71417	0.998000	0.56505	0.425000	0.31504	0.827000	0.27421	1.374000	0.46228	0.650000	0.86243	ATC	.	.		0.557	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042691.1			G	151130378	C	G	151130378	3	3	299	1	0	0	0	0	1	0	0	0	12077	816	29	4	1076	4	PLEKHG1	6	151130378	Missense_Mutation	SNP	C	TCGA-G3-AAV3-01A-11D-A36X-10	38699697	151130378	19984689	32	43285										
C6orf97	80129	hgsc.bcm.edu	37	chr6	151907029	151907029	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	tttctttgtttccagatggtCtcccagcttgaagcccaaat	7	11	2	2			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr6:151907029C>A	ENST00000239374.7	+	7	1197	c.1098C>A	c.(1096-1098)gtC>gtA	p.V366V	CCDC170_ENST00000367290.5_Silent_p.V366V	NM_025059.3	NP_079335.2	Q8IYT3	CC170_HUMAN	coiled-coil domain containing 170	366																	TCCAGATGGTCTCCCAGCTTG	0.448																																					p.V366V		Atlas-SNP	.											.	.	.	.	0			c.C1098A						.						69	62	64					6																	151907029		1905	4125	6030	SO:0001819	synonymous_variant	80129	exon7			GATGGTCTCCCAG	AK026958	CCDS43515.1	6q25.1	2012-03-26	2012-03-26	2012-03-26	ENSG00000120262	ENSG00000120262			21177	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 97"	C6orf97			Standard	NM_025059		Approved	FLJ23305, bA282P11.1	uc003qol.3	Q8IYT3	OTTHUMG00000015839	ENST00000239374.7:c.1098C>A	chr6.hg19:g.151907029C>A		85.0	0.0		71.0	14.0	NM_025059	Q5VXB7|Q6P9E4|Q96KA9|Q9H5M3	Silent	SNP	ENST00000239374.7	hg19	CCDS43515.1																																																																																			.	.		0.448	CCDC170-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042727.2	NM_025059		A	151907029	C	A	151907029	2	1	299	1	0	0	0	0	0	0	0	1	2376	900	32	3		3	C6orf97	6	151907029	Silent	SNP	C	TCGA-G3-AAV3-01A-11D-A36X-10	776651	151907029	19208038	33	43286										
AMPH	273	hgsc.bcm.edu	37	chr7	38500941	38500941	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	tgtcctcaaagaaactgatgAtgttctcctgctgcagttcc	8	11	2	3			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr7:38500941A>T	ENST00000356264.2	-	11	1174	c.959T>A	c.(958-960)aTc>aAc	p.I320N	AMPH_ENST00000428293.2_Missense_Mutation_p.I320N|AMPH_ENST00000325590.5_Missense_Mutation_p.I320N	NM_001635.3	NP_001626.1	P49418	AMPH_HUMAN	amphiphysin	320					endocytosis (GO:0006897)|learning (GO:0007612)|synaptic transmission (GO:0007268)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|leading edge membrane (GO:0031256)|synaptic vesicle (GO:0008021)	phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|kidney(3)|large_intestine(12)|liver(3)|lung(27)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)	62						GAAACTGATGATGTTCTCCTG	0.468																																					p.I320N		Atlas-SNP	.											.	AMPH	157	.	0			c.T959A						.						197	194	195					7																	38500941		2203	4300	6503	SO:0001583	missense	273	exon11			CTGATGATGTTCT		CCDS5456.1, CCDS47574.1	7p14-p13	2007-06-19	2007-06-19		ENSG00000078053	ENSG00000078053			471	protein-coding gene	gene with protein product		600418	"amphiphysin (Stiff-Mann syndrome with breast cancer 128kD autoantigen)", "amphiphysin (Stiff-Man syndrome with breast cancer 128kDa autoantigen)"			8245793	Standard	NM_139316		Approved		uc003tgu.3	P49418	OTTHUMG00000023725	ENST00000356264.2:c.959T>A	chr7.hg19:g.38500941A>T	ENSP00000348602:p.Ile320Asn	109.0	0.0		129.0	12.0	NM_139316	A4D1X8|A4D1X9|O43538|Q75MJ8|Q75MK5|Q75MM3|Q8N4G0	Missense_Mutation	SNP	ENST00000356264.2	hg19	CCDS5456.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	23.6|23.6	4.432527|4.432527	0.83776|0.83776	.|.	.|.	ENSG00000078053|ENSG00000078053	ENST00000441628|ENST00000325590;ENST00000356264;ENST00000428293;ENST00000353242;ENST00000544070	.|T;T;T	.|0.53206	.|0.63;0.63;0.63	5.77|5.77	5.77|5.77	0.91146|0.91146	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.68458|0.68458	0.3003|0.3003	M|M	0.73962|0.73962	2.25|2.25	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.91635	.|0.999;0.999;0.998	T|T	0.67662|0.67662	-0.5613|-0.5613	5|10	.|0.35671	.|T	.|0.21	-19.4544|-19.4544	16.0937|16.0937	0.81106|0.81106	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|320;320;76	.|P49418-2;P49418;Q8NFL4	.|.;AMPH_HUMAN;.	Q|N	70|320;320;320;90;323	.|ENSP00000317441:I320N;ENSP00000348602:I320N;ENSP00000390734:I320N	.|ENSP00000317441:I320N	H|I	-|-	3|2	2|0	AMPH|AMPH	38467466|38467466	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.481000|7.481000	0.81124|0.81124	2.211000|2.211000	0.71520|0.71520	0.455000|0.455000	0.32223|0.32223	CAT|ATC	.	.		0.468	AMPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226953.2	NM_001635		T	38500941	A	T	38500941	3	4	299	1	0	0	0	0	1	0	0	0	588	333	12	4	1172	4	AMPH	7	38500941	Missense_Mutation	SNP	A	TCGA-G3-AAV3-01A-11D-A36X-10		38500941	120637722	34	43287										
TNS3	64759	hgsc.bcm.edu	37	chr7	47451383	47451383	+	Frame_Shift_Del	DEL	T	T	-													0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	cgatgcagatcctgctggggTtttctgggccaacgttgctt							TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr7:47451383delT	ENST00000398879.1	-	13	1031	c.665delA	c.(664-666)aacfs	p.N222fs	TNS3_ENST00000442536.2_Frame_Shift_Del_p.N222fs|TNS3_ENST00000311160.9_Frame_Shift_Del_p.N222fs|TNS3_ENST00000355730.3_Frame_Shift_Del_p.N222fs|TNS3_ENST00000458317.2_Frame_Shift_Del_p.N222fs			Q68CZ2	TENS3_HUMAN	tensin 3	222	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				cell migration (GO:0016477)|lung alveolus development (GO:0048286)|positive regulation of cell proliferation (GO:0008284)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(17)|endometrium(5)|kidney(4)|large_intestine(7)|liver(1)|lung(16)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	64						CCTGCTGGGGTTTTCTGGGCC	0.512																																					p.N222fs		Atlas-INDEL	.											.	TNS3	140	.	0			c.666delC						.						78	82	81					7																	47451383		1995	4175	6170	SO:0001589	frameshift_variant	64759	exon13			.	AF378756	CCDS5506.2	7p12.3	2013-02-14	2005-05-13	2005-05-13	ENSG00000136205	ENSG00000136205		"SH2 domain containing"	21616	protein-coding gene	gene with protein product	"tumor endothelial marker 6"	606825	"tensin-like SH2 domain-containing 1"	TENS1		11559528	Standard	NM_022748		Approved	TEM6, H_NH0549I23.2, FLJ13732	uc003tnw.3	Q68CZ2	OTTHUMG00000074075	ENST00000398879.1:c.665delA	chr7.hg19:g.47451383delT	ENSP00000381854:p.Asn222fs	100.0	0.0		123.0	23.0	NM_022748	B2RNV1|Q6IPQ2|Q8IZW7|Q8NAD0|Q96PE0|Q96S48	Frame_Shift_Del	DEL	ENST00000398879.1	hg19	CCDS5506.2																																																																																			.	.		0.512	TNS3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157253.1	NM_022748		-	47451383	T	-	47451383	7	5	299	1	0	1	0	1	0	0	0	0	16359	1725	60	0	3748	0	TNS3	7	47451383	Frame_Shift_Del	DEL	T	TCGA-G3-AAV3-01A-11D-A36X-10	8950442	47451383	111687280	35	43288										
SAMD9	54809	hgsc.bcm.edu	37	chr7	92735147	92735147	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	gcatttttactgggctttccCatcttagatgtctgaatcga	8	9	2	2			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr7:92735147C>A	ENST00000379958.2	-	3	533	c.264G>T	c.(262-264)atG>atT	p.M88I		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	88						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			TGGGCTTTCCCATCTTAGATG	0.383																																					p.M88I		Atlas-SNP	.											.	SAMD9	239	.	0			c.G264T						.						175	173	173					7																	92735147		2203	4300	6503	SO:0001583	missense	54809	exon2			CTTTCCCATCTTA	AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"Sterile alpha motif (SAM) domain containing"	1348	protein-coding gene	gene with protein product		610456	"chromosome 7 open reading frame 5"	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.264G>T	chr7.hg19:g.92735147C>A	ENSP00000369292:p.Met88Ile	100.0	0.0		146.0	35.0	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Missense_Mutation	SNP	ENST00000379958.2	hg19	CCDS34680.1	.	.	.	.	.	.	.	.	.	.	C	9.175	1.022214	0.19433	.	.	ENSG00000205413	ENST00000379958;ENST00000446617	T;T	0.21543	2.0;2.81	4.6	-2.09	0.07232	.	2.447570	0.01856	N	0.036287	T	0.09598	0.0236	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.19192	-1.0313	10	0.38643	T	0.18	.	0.5965	0.00737	0.4235:0.1949:0.1414:0.2402	.	88	Q5K651	SAMD9_HUMAN	I	88	ENSP00000369292:M88I;ENSP00000414529:M88I	ENSP00000369292:M88I	M	-	3	0	SAMD9	92573083	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.094000	0.15107	-0.257000	0.09459	0.603000	0.83216	ATG	.	.		0.383	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654		A	92735147	C	A	92735147	3	1	299	1	0	0	0	0	1	0	0	0	13841	594	21	3	4509	3	SAMD9	7	92735147	Missense_Mutation	SNP	C	TCGA-G3-AAV3-01A-11D-A36X-10	45283764	92735147	66403516	36	43289										
NRCAM	4897	hgsc.bcm.edu	37	chr7	107875094	107875094	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	ccgagggtcaataatgtaatCttttggagactgttgggtga	13	5	2	2			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr7:107875094C>G	ENST00000425651.2	-	3	162	c.163G>C	c.(163-165)Gat>Cat	p.D55H	NRCAM_ENST00000379024.4_Missense_Mutation_p.D55H|NRCAM_ENST00000351718.4_Missense_Mutation_p.D49H|NRCAM_ENST00000413765.2_Missense_Mutation_p.D55H|NRCAM_ENST00000379022.4_Missense_Mutation_p.D55H|NRCAM_ENST00000379028.3_Missense_Mutation_p.D55H	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	55	Ig-like 1.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						ATAATGTAATCTTTTGGAGAC	0.368																																					p.D55H		Atlas-SNP	.											.	NRCAM	267	.	0			c.G163C						.						108	116	113					7																	107875094		2203	4300	6503	SO:0001583	missense	4897	exon3			TGTAATCTTTTGG		CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7994	protein-coding gene	gene with protein product	"NgCAM-related cell adhesion molecule"	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.163G>C	chr7.hg19:g.107875094C>G	ENSP00000401244:p.Asp55His	70.0	0.0		110.0	25.0	NM_001037132	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Missense_Mutation	SNP	ENST00000425651.2	hg19	CCDS47686.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.490125	0.84962	.	.	ENSG00000091129	ENST00000379032;ENST00000379028;ENST00000413765;ENST00000537765;ENST00000351718;ENST00000379024;ENST00000425651;ENST00000379022;ENST00000445979;ENST00000417701;ENST00000442580;ENST00000419936;ENST00000456431;ENST00000418239	T;T;T;T;T;T;T;T;T;T	0.72282	0.0;0.3;0.02;0.09;0.0;0.04;-0.64;-0.42;-0.42;-0.42	5.61	5.61	0.85477	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.044905	0.85682	D	0.000000	D	0.84547	0.5496	M	0.85041	2.73	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.999;0.999;0.999;0.994	D;D;D;D;D	0.75020	0.981;0.981;0.985;0.965;0.954	D	0.86170	0.1599	10	0.72032	D	0.01	.	13.2433	0.60010	0.0:0.9272:0.0:0.0728	.	55;55;55;49;55	Q92823-5;Q92823-3;E9PDA4;Q92823-4;Q92823	.;.;.;.;NRCAM_HUMAN	H	55;55;55;55;49;55;55;55;49;49;55;49;49;55	ENSP00000368314:D55H;ENSP00000407858:D55H;ENSP00000325269:D49H;ENSP00000368310:D55H;ENSP00000401244:D55H;ENSP00000368308:D55H;ENSP00000390421:D49H;ENSP00000390868:D55H;ENSP00000397544:D49H;ENSP00000408203:D49H	ENSP00000325269:D49H	D	-	1	0	NRCAM	107662330	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.066000	0.57520	2.813000	0.96785	0.655000	0.94253	GAT	.	.		0.368	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132		G	107875094	C	G	107875094	3	3	299	1	0	0	0	0	1	0	0	0	10653	913	32	4	3893	4	NRCAM	7	107875094	Missense_Mutation	SNP	C	TCGA-G3-AAV3-01A-11D-A36X-10	15139947	107875094	51263569	37	43290										
DENND4C	55667	hgsc.bcm.edu	37	chr9	19316642	19316642	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	accaaaaaactcaagaaggcTcagcgattgacatgactcca	7	11	2	3			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr9:19316642T>G	ENST00000380432.2	+	8	937	c.904T>G	c.(904-906)Tca>Gca	p.S302A	DENND4C_ENST00000434457.2_Missense_Mutation_p.S538A|DENND4C_ENST00000602925.1_Missense_Mutation_p.S538A			Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	302					cellular response to insulin stimulus (GO:0032869)|positive regulation of Rab GTPase activity (GO:0032851)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)	cytosol (GO:0005829)|insulin-responsive compartment (GO:0032593)|plasma membrane (GO:0005886)|retromer complex (GO:0030904)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(8)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						TCAAGAAGGCTCAGCGATTGA	0.348																																					p.S538A		Atlas-SNP	.											.	DENND4C	120	.	0			c.T1612G						.						88	95	93					9																	19316642		2202	4300	6502	SO:0001583	missense	55667	exon12			GAAGGCTCAGCGA	AK000693	CCDS6491.2, CCDS6491.3	9p22.1	2012-10-03	2006-01-27	2006-01-27	ENSG00000137145	ENSG00000137145		"DENN/MADD domain containing"	26079	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 55B", "chromosome 9 open reading frame 55"	C9orf55B, C9orf55		12906859	Standard	NM_017925		Approved	FLJ20686, bA513M16.3	uc031tcw.1	Q5VZ89	OTTHUMG00000019627	ENST00000380432.2:c.904T>G	chr9.hg19:g.19316642T>G	ENSP00000369797:p.Ser302Ala	125.0	0.0		161.0	28.0	NM_017925	A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	Missense_Mutation	SNP	ENST00000380432.2	hg19		.	.	.	.	.	.	.	.	.	.	T	7.755	0.704263	0.15172	.	.	ENSG00000137145	ENST00000380437	.	.	.	5.15	5.15	0.70609	.	0.240505	0.43919	D	0.000504	T	0.45155	0.1328	L	0.39898	1.24	0.80722	D	1	B	0.30937	0.301	B	0.27170	0.077	T	0.38373	-0.9664	9	0.07990	T	0.79	-15.7034	15.1295	0.72511	0.0:0.0:0.0:1.0	.	302	Q5VZ89	DEN4C_HUMAN	A	302	.	ENSP00000369802:S302A	S	+	1	0	DENND4C	19306642	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	4.576000	0.60915	2.162000	0.67917	0.477000	0.44152	TCA	.	.		0.348	DENND4C-201	KNOWN	basic	protein_coding	protein_coding		NM_017925		G	19316642	T	G	19316642	3	3	299	1	0	0	0	0	1	0	0	0	4437	1551	54	5	934	5	DENND4C	9	19316642	Missense_Mutation	SNP	T	TCGA-G3-AAV3-01A-11D-A36X-10		19316642	121896789	38	43291										
FAM22F	54754	hgsc.bcm.edu	37	chr9	97084601	97084601	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	cttccgccgggccagggatcGgagaactgggctgtaaacca	14	12	0	1	rs376058940		TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr9:97084601G>A	ENST00000253262.4	-	3	744	c.724C>T	c.(724-726)Cga>Tga	p.R242*	NUTM2F_ENST00000335456.7_Nonsense_Mutation_p.R242*|NUTM2F_ENST00000341207.4_Nonsense_Mutation_p.R242*	NM_017561.1	NP_060031.1	A1L443	NTM2F_HUMAN	NUT family member 2F	242																	GCCAGGGATCGGAGAACTGGG	0.632																																					p.R242X		Atlas-SNP	.											.	FAM22F	72	.	0			c.C724T						.	G	stop/ARG	0,2600		0,0,1300	38	42	41		724	0.2	0.4	9		41	1,5173		0,1,2586	no	stop-gained	FAM22F	NM_017561.1		0,1,3886	AA,AG,GG		0.0193,0.0,0.0129		242/757	97084601	1,7773	1300	2587	3887	SO:0001587	stop_gained	54754	exon3			GGGATCGGAGAAC		CCDS47994.1	9q22.32	2013-05-02	2013-03-14	2013-05-02	ENSG00000130950	ENSG00000130950			23450	protein-coding gene	gene with protein product			"family with sequence similarity 22, member F"	FAM22F			Standard	NM_017561		Approved	DKFZp434I1117		A1L443	OTTHUMG00000020260	ENST00000253262.4:c.724C>T	chr9.hg19:g.97084601G>A	ENSP00000253262:p.Arg242*	243.0	0.0		392.0	77.0	NM_017561	B6ZDF0|Q5SR58|Q5SR59|Q9UFB1	Nonsense_Mutation	SNP	ENST00000253262.4	hg19	CCDS47994.1	.	.	.	.	.	.	.	.	.	.	.	16.25	3.070437	0.55539	0.0	1.93E-4	ENSG00000130950	ENST00000335456;ENST00000253262;ENST00000341207	.	.	.	1.2	0.228	0.15364	.	0.141745	0.32736	N	0.005705	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.5239	0.11973	0.0:0.0:0.6224:0.3776	.	.	.	.	X	242	.	ENSP00000253262:R242X	R	-	1	2	FAM22F	96124422	0.081000	0.21417	0.428000	0.26697	0.206000	0.24218	1.143000	0.31553	0.087000	0.17167	-0.496000	0.04628	CGA	.	.		0.632	NUTM2F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053173.2	NM_017561		A	97084601	G	A	97084601	4	1	299	1	0	0	0	0	0	1	0	0	5550	1124	39	1	1566	1	FAM22F	9	97084601	Nonsense_Mutation	SNP	G	TCGA-G3-AAV3-01A-11D-A36X-10	77767959	97084601	44128830	39	43292										
PRKCQ	5588	hgsc.bcm.edu	37	chr10	6504265	6504265	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	ttccacaaagcaaaatttacCtgtagactattcctttggaa	5	9	0	1			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr10:6504265C>A	ENST00000263125.5	-	14	1607	c.1508G>T	c.(1507-1509)aGg>aTg	p.R503M	PRKCQ_ENST00000397176.2_Splice_Site_p.R503M|PRKCQ_ENST00000539722.1_Splice_Site_p.R378M	NM_001282644.1|NM_006257.3	NP_001269573.1|NP_006248.1	Q04759	KPCT_HUMAN	protein kinase C, theta	503	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of T cell apoptotic process (GO:0070233)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of T-helper 2 cell activation (GO:2000570)|protein ubiquitination (GO:0016567)|regulation of cell growth (GO:0001558)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of transcription, DNA-templated (GO:0006355)|rhodopsin mediated signaling pathway (GO:0016056)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(2)	45					Tamoxifen(DB00675)	CAAAATTTACCTGTAGACTAT	0.413																																					p.R503M	Ovarian(50;572 1126 10530 25349 30594)	Atlas-SNP	.											.	PRKCQ	113	.	0			c.G1508T						.						115	118	117					10																	6504265		2203	4300	6503	SO:0001630	splice_region_variant	5588	exon14			ATTTACCTGTAGA	L07032	CCDS7079.1, CCDS55701.1, CCDS60482.1	10p15	2009-07-10			ENSG00000065675	ENSG00000065675	2.7.11.1		9410	protein-coding gene	gene with protein product		600448				8444877	Standard	NM_001282645		Approved		uc001ijj.2	Q04759	OTTHUMG00000017623	ENST00000263125.5:c.1508+1G>T	chr10.hg19:g.6504265C>A		66.0	0.0		74.0	17.0	NM_006257	B4DF52|Q14DH6|Q3MJF1|Q64FY5|Q9H508|Q9H549	Missense_Mutation	SNP	ENST00000263125.5	hg19	CCDS7079.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.36|17.36	3.368760|3.368760	0.61624|0.61624	.|.	.|.	ENSG00000065675|ENSG00000065675	ENST00000397178|ENST00000263125;ENST00000397176;ENST00000539722	.|T;T;T	.|0.74632	.|-0.86;-0.86;-0.86	5.45|5.45	5.45|5.45	0.79879|0.79879	.|Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.93223|0.93223	0.7841|0.7841	H|H	0.99626|0.99626	4.665|4.665	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0	.|D;D;D;D	.|0.97110	.|1.0;0.999;0.997;0.999	D|D	0.96302|0.96302	0.9222|0.9222	5|9	.|.	.|.	.|.	.|.	19.2789|19.2789	0.94044|0.94044	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|378;275;503;503	.|B4DF52;Q5JUN8;Q04759-2;Q04759	.|.;.;.;KPCT_HUMAN	W|M	276|503;503;378	.|ENSP00000263125:R503M;ENSP00000380361:R503M;ENSP00000441752:R378M	.|.	G|R	-|-	1|2	0|0	PRKCQ|PRKCQ	6544271|6544271	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.013000|0.013000	0.08279|0.08279	7.513000|7.513000	0.81739|0.81739	2.542000|2.542000	0.85734|0.85734	0.563000|0.563000	0.77884|0.77884	GGG|AGG	.	.		0.413	PRKCQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046665.1	NM_006257	Missense_Mutation	A	6504265	C	A	6504265	5	1	299	1	0	0	0	0	0	0	1	0	12527	695	24	3	632	3	PRKCQ	10	6504265	Splice_Site	SNP	C	TCGA-G3-AAV3-01A-11D-A36X-10		6504265	129030482	40	43293										
BEND7	222389	hgsc.bcm.edu	37	chr10	13523008	13523008	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	aaagtcttgtcatcaaaaaaCgcacacaccagttttctaaa	4	10	4	0			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr10:13523008C>T	ENST00000396900.2	-	6	953	c.954G>A	c.(952-954)gcG>gcA	p.A318A	BEND7_ENST00000341083.3_Silent_p.A266A|BEND7_ENST00000378605.3_Silent_p.A279A|BEND7_ENST00000396898.2_Silent_p.A331A			Q8N7W2	BEND7_HUMAN	BEN domain containing 7	318	BEN. {ECO:0000255|PROSITE- ProRule:PRU00784}.					extracellular vesicular exosome (GO:0070062)				breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|stomach(1)	17						CATCAAAAAACGCACACACCA	0.433																																					p.A279A		Atlas-SNP	.											.	BEND7	85	.	0			c.G837A						.						162	156	158					10																	13523008		2203	4300	6503	SO:0001819	synonymous_variant	222389	exon5			AAAAAACGCACAC	BC031618	CCDS7099.1, CCDS41490.1	10p14	2012-11-22	2008-10-03	2008-10-03	ENSG00000165626	ENSG00000165626		"BEN domain containing"	23514	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 30"	C10orf30			Standard	NM_152751		Approved	FLJ40283	uc001imm.2	Q8N7W2	OTTHUMG00000017699	ENST00000396900.2:c.954G>A	chr10.hg19:g.13523008C>T		86.0	0.0		115.0	5.0	NM_001100912	Q5SYY7|Q5SYY8|Q5SYY9|Q8N5T7	Silent	SNP	ENST00000396900.2	hg19																																																																																				.	.		0.433	BEND7-202	KNOWN	basic	protein_coding	protein_coding		NM_152751		T	13523008	C	T	13523008	2	4	299	1	0	0	0	0	0	0	0	1	1403	523	19	1		1	BEND7	10	13523008	Silent	SNP	C	TCGA-G3-AAV3-01A-11D-A36X-10	7018743	13523008	122011739	41	43294										
CCDC7	79741	hgsc.bcm.edu	37	chr10	32740800	32740801	+	Frame_Shift_Ins	INS	-	-	A													0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	tcgagtaagacaaagaacttINSactaccagaagatgaaatga							TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr10:32740800_32740801insA	ENST00000362006.5	+	2	773_774	c.230_231insA	c.(229-234)ttactafs	p.L78fs	CCDC7_ENST00000537047.1_Frame_Shift_Ins_p.L78fs|CCDC7_ENST00000277657.6_Frame_Shift_Ins_p.L78fs|CCDC7_ENST00000535327.1_Frame_Shift_Ins_p.L78fs|CCDC7_ENST00000539197.1_Frame_Shift_Ins_p.L78fs|CCDC7_ENST00000545067.1_Frame_Shift_Ins_p.L78fs	NM_145023.4	NP_659460.3	Q96M83	CCDC7_HUMAN	coiled-coil domain containing 7	78										NS(1)|breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(2)	14		Breast(68;0.000207)|Prostate(175;0.0107)				ACAAAGAACTTACTACCAGAAG	0.411																																					p.L77fs		Atlas-INDEL	.											.,6	CCDC7	47	.	0			c.230_231insA						.																																			SO:0001589	frameshift_variant	221016	exon2			.	BC022020	CCDS7173.1	10p11.23	2013-12-13			ENSG00000216937	ENSG00000216937			26533	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 68"	C10orf68		12477932	Standard	NM_024688		Approved	FLJ32762, FLJ13031	uc001iwk.3	Q96M83	OTTHUMG00000150517	ENST00000362006.5:c.231dupA	chr10.hg19:g.32740801_32740801dupA	ENSP00000355078:p.Leu78fs	150.0	0.0		181.0	48.0	NM_145023	Q5VW55|Q8IVQ0|Q8NEQ0	Frame_Shift_Ins	INS	ENST00000362006.5	hg19	CCDS7173.1																																																																																			.	.		0.411	CCDC7-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047490.1	NM_145023		A	32740801	-	A	32740800	7	5	299	1	0	1	1	0	0	0	0	0	2844	1764	61	0	232	0	CCDC7	10	32740800	Frame_Shift_Ins	INS	-	TCGA-G3-AAV3-01A-11D-A36X-10	19217792	32740800	102793947	42	43295										
BMS1	9790	hgsc.bcm.edu	37	chr10	43292088	43292088	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	gctctagtgatgaggaagcaGaagaggaggaaaatgctgag	16	4	1	5			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr10:43292088G>A	ENST00000374518.5	+	10	1459	c.1396G>A	c.(1396-1398)Gaa>Aaa	p.E466K		NM_014753.3	NP_055568.3	Q14692	BMS1_HUMAN	BMS1 ribosome biogenesis factor	466					ribosome assembly (GO:0042255)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(23)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						TGAGGAAGCAGAAGAGGAGGA	0.428																																					p.E466K		Atlas-SNP	.											.	BMS1	132	.	0			c.G1396A						.						226	206	213					10																	43292088		2203	4300	6503	SO:0001583	missense	9790	exon10			GAAGCAGAAGAGG	BC043345	CCDS7199.1	10q11.21	2013-05-01	2013-05-01	2007-03-20	ENSG00000165733	ENSG00000165733			23505	protein-coding gene	gene with protein product		611448	"BMS1-like, ribosome assembly protein (yeast)", "BMS1 homolog, ribosome assembly protein (yeast)"	BMS1L		11779832	Standard	NM_014753		Approved	KIAA0187	uc001jaj.3	Q14692	OTTHUMG00000018020	ENST00000374518.5:c.1396G>A	chr10.hg19:g.43292088G>A	ENSP00000363642:p.Glu466Lys	135.0	0.0		191.0	37.0	NM_014753	Q5QPT5|Q86XJ9	Missense_Mutation	SNP	ENST00000374518.5	hg19	CCDS7199.1	.	.	.	.	.	.	.	.	.	.	g	12.24	1.879737	0.33162	.	.	ENSG00000165733	ENST00000374518	T	0.24723	1.84	4.77	2.87	0.33458	.	0.615955	0.15639	N	0.251992	T	0.23611	0.0571	L	0.51422	1.61	0.33279	D	0.562071	B	0.20671	0.047	B	0.15870	0.014	T	0.23048	-1.0199	10	0.36615	T	0.2	.	11.7482	0.51832	0.1536:0.0:0.8464:0.0	.	466	Q14692	BMS1_HUMAN	K	466	ENSP00000363642:E466K	ENSP00000363642:E466K	E	+	1	0	BMS1	42612094	0.963000	0.33076	0.791000	0.31998	0.263000	0.26337	4.236000	0.58675	1.135000	0.42183	0.580000	0.79431	GAA	.	.		0.428	BMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047690.2	NM_014753		A	43292088	G	A	43292088	3	1	299	1	0	0	0	0	1	0	0	0	1472	943	33	3	1430	3	BMS1	10	43292088	Missense_Mutation	SNP	G	TCGA-G3-AAV3-01A-11D-A36X-10	10551288	43292088	92242659	43	43296										
TNKS2	80351	hgsc.bcm.edu	37	chr10	93558604	93558604	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	ctgagaaggtgaacagccgcGacacggcgggcaggaaatcc	15	11	0	2			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr10:93558604G>T	ENST00000371627.4	+	1	536	c.157G>T	c.(157-159)Gac>Tac	p.D53Y	TNKS2-AS1_ENST00000432246.1_RNA|TNKS2-AS1_ENST00000432938.1_RNA	NM_025235.3	NP_079511.1	Q9H2K2	TNKS2_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2	53					multicellular organism growth (GO:0035264)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein polyubiquitination (GO:0000209)|regulation of multicellular organism growth (GO:0040014)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			biliary_tract(1)|breast(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	48		Colorectal(252;0.162)				GAACAGCCGCGACACGGCGGG	0.716																																					p.D53Y		Atlas-SNP	.											.	TNKS2	103	.	0			c.G157T						.						10	12	12					10																	93558604		2143	4233	6376	SO:0001583	missense	80351	exon1			AGCCGCGACACGG	AF342982	CCDS7417.1	10q23.3	2013-01-10			ENSG00000107854	ENSG00000107854		"Poly (ADP-ribose) polymerases", "Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	15677	protein-coding gene	gene with protein product		607128					Standard	NM_025235		Approved	TNKL, TANK2, PARP-5b, PARP-5c, PARP5B, PARP5C, pART6	uc001khp.3	Q9H2K2	OTTHUMG00000018747	ENST00000371627.4:c.157G>T	chr10.hg19:g.93558604G>T	ENSP00000360689:p.Asp53Tyr	74.0	0.0		93.0	27.0	NM_025235	B2RBD3|Q9H8F2|Q9HAS4	Missense_Mutation	SNP	ENST00000371627.4	hg19	CCDS7417.1	.	.	.	.	.	.	.	.	.	.	G	35	5.595741	0.96602	.	.	ENSG00000107854	ENST00000371627	T	0.68903	-0.36	4.85	4.85	0.62838	Ankyrin repeat-containing domain (4);	0.000000	0.56097	D	0.000029	D	0.84800	0.5552	M	0.89478	3.035	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87967	0.2734	10	0.87932	D	0	.	17.7371	0.88396	0.0:0.0:1.0:0.0	.	53	Q9H2K2	TNKS2_HUMAN	Y	53	ENSP00000360689:D53Y	ENSP00000360689:D53Y	D	+	1	0	TNKS2	93548584	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.046000	0.93817	2.513000	0.84729	0.561000	0.74099	GAC	.	.		0.716	TNKS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049374.1	NM_025235		T	93558604	G	T	93558604	3	4	299	1	0	0	0	0	1	0	0	0	16336	1058	37	1	159	1	TNKS2	10	93558604	Missense_Mutation	SNP	G	TCGA-G3-AAV3-01A-11D-A36X-10	50266516	93558604	41976143	44	43297										
PAX2	5076	hgsc.bcm.edu	37	chr10	102587329	102587330	+	Frame_Shift_Ins	INS	-	-	GG													0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	ttattatagtgccgccccccINSggggctccgcccctgccgct					rs576371733		TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr10:102587329_102587330insGG	ENST00000428433.1	+	11	1757_1758	c.1207_1208insGG	c.(1207-1209)cggfs	p.R403fs	PAX2_ENST00000556085.1_Frame_Shift_Ins_p.R379fs|PAX2_ENST00000370296.2_3'UTR|PAX2_ENST00000361791.3_3'UTR|PAX2_ENST00000355243.3_Frame_Shift_Ins_p.R380fs	NM_003987.3|NM_003990.3	NP_003978|NP_003981.2	Q02962	PAX2_HUMAN	paired box 2	403					aging (GO:0007568)|axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye development (GO:0043010)|cell fate determination (GO:0001709)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucose stimulus (GO:0071333)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cochlea development (GO:0090102)|cochlea morphogenesis (GO:0090103)|glial cell differentiation (GO:0010001)|inner ear morphogenesis (GO:0042472)|mesenchymal to epithelial transition (GO:0060231)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|mesodermal cell fate specification (GO:0007501)|mesonephric duct development (GO:0072177)|mesonephric tubule formation (GO:0072172)|mesonephros development (GO:0001823)|metanephric collecting duct development (GO:0072205)|metanephric distal convoluted tubule development (GO:0072221)|metanephric epithelium development (GO:0072207)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchyme development (GO:0072075)|metanephric nephron tubule formation (GO:0072289)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic process involved in metanephric collecting duct development (GO:1900215)|negative regulation of apoptotic process involved in metanephric nephron tubule development (GO:1900218)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of cytolysis (GO:0045918)|negative regulation of mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis (GO:0072305)|negative regulation of mesenchymal cell apoptotic process involved in metanephros development (GO:1900212)|negative regulation of programmed cell death (GO:0043069)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct formation (GO:0072179)|neural tube closure (GO:0001843)|optic chiasma development (GO:0061360)|optic cup morphogenesis involved in camera-type eye development (GO:0002072)|optic nerve development (GO:0021554)|optic nerve morphogenesis (GO:0021631)|optic nerve structural organization (GO:0021633)|pancreas development (GO:0031016)|paramesonephric duct development (GO:0061205)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0072108)|positive regulation of metanephric DCT cell differentiation (GO:2000594)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of optic nerve formation (GO:2000597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephric field specification (GO:0039003)|pronephros development (GO:0048793)|protein kinase B signaling (GO:0043491)|reactive oxygen species metabolic process (GO:0072593)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of metanephros size (GO:0035566)|response to nutrient levels (GO:0031667)|retinal pigment epithelium development (GO:0003406)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|ureter development (GO:0072189)|ureter maturation (GO:0035799)|ureter morphogenesis (GO:0072197)|urogenital system development (GO:0001655)|vestibulocochlear nerve formation (GO:0021650)|visual perception (GO:0007601)	centriolar satellite (GO:0034451)|lysosome (GO:0005764)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|protein complex (GO:0043234)|protein-DNA complex (GO:0032993)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|superoxide-generating NADPH oxidase activity (GO:0016175)|transcription regulatory region DNA binding (GO:0044212)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	18		Colorectal(252;0.234)		Epithelial(162;1.32e-08)|all cancers(201;7.32e-07)		TGCCGCCCCCCGGGGCTCCGCC	0.569																																					p.R403fs		Atlas-INDEL	.											PAX2_ENST00000428433,colon,carcinoma,0,2	PAX2	83	.	0			c.1207_1208insGG						.																																			SO:0001589	frameshift_variant	5076	exon11			.		CCDS7499.1, CCDS41561.1	10q24.31	2011-06-20	2007-07-12		ENSG00000075891	ENSG00000075891		"Paired boxes", "Homeoboxes / PRD class"	8616	protein-coding gene	gene with protein product		167409	"paired box gene 2"			8431641, 7981748	Standard	NM_003990		Approved		uc001krk.4	Q02962	OTTHUMG00000018913	ENST00000428433.1:c.1210_1211dupGG	chr10.hg19:g.102587332_102587333dupGG	ENSP00000396259:p.Arg403fs	84.0	0.0		135.0	10.0	NM_003987	Q15105|Q15110|Q15837|Q5SZP2|Q5SZP3	Frame_Shift_Ins	INS	ENST00000428433.1	hg19	CCDS53569.1																																																																																			.	.		0.569	PAX2-202	KNOWN	basic|CCDS	protein_coding	protein_coding				GG	102587330	-	GG	102587329	7	5	299	1	0	1	1	0	0	0	0	0	11488	643	23	0	1336	0	PAX2	10	102587329	Frame_Shift_Ins	INS	-	TCGA-G3-AAV3-01A-11D-A36X-10	9028725	102587329	32947418	45	43298										
PKP3	11187	hgsc.bcm.edu	37	chr11	404567	404567	+	Nonstop_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	aggaggacttcctgggcccaTaggtgaagccttctggagga	15	9	1	1			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr11:404567T>A	ENST00000331563.2	+	13	2468	c.2392T>A	c.(2392-2394)Tag>Aag	p.*798K	SIGIRR_ENST00000529486.1_5'Flank	NM_007183.2	NP_009114.1	Q9Y446	PKP3_HUMAN	plakophilin 3	0					desmosome assembly (GO:0002159)|establishment of protein localization to plasma membrane (GO:0090002)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|desmosome (GO:0030057)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)			breast(1)|central_nervous_system(1)|endometrium(3)|lung(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_cancers(49;3.02e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CCTGGGCCCATAGGTGAAGCC	0.617																																					p.X798K		Atlas-SNP	.											.	PKP3	36	.	0			c.T2392A						.						89	77	81					11																	404567		2193	4287	6480	SO:0001578	stop_lost	11187	exon13			GGCCCATAGGTGA	Z98265	CCDS7695.1	11p15	2013-02-14			ENSG00000184363	ENSG00000184363		"Armadillo repeat containing"	9025	protein-coding gene	gene with protein product		605561				10374265	Standard	XM_005252760		Approved		uc001lpc.3	Q9Y446	OTTHUMG00000119068	ENST00000331563.2:c.2392T>A	chr11.hg19:g.404567T>A	ENSP00000331678:p.*798Lysext*?	73.0	0.0		138.0	28.0	NM_007183	F8J390|Q53EX8	Missense_Mutation	SNP	ENST00000331563.2	hg19	CCDS7695.1	.	.	.	.	.	.	.	.	.	.	t	17.38	3.376069	0.61735	.	.	ENSG00000184363	ENST00000331563	.	.	.	4.39	4.39	0.52855	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.918	0.63914	0.0:0.0:0.0:1.0	.	.	.	.	K	798	.	.	X	+	1	0	PKP3	394567	0.404000	0.25328	0.114000	0.21550	0.596000	0.36781	2.645000	0.46621	1.761000	0.52028	0.402000	0.26972	TAG	.	.		0.617	PKP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239281.1	NM_007183		A	404567	T	A	404567	4	1	299	1	0	0	0	0	0	0	0	0	11995	1419	49	4	2442	4	PKP3	11	404567	Nonstop_Mutation	SNP	T	TCGA-G3-AAV3-01A-11D-A36X-10		404567	134601949	46	43299										
UBQLNL	143630	hgsc.bcm.edu	37	chr11	5537290	5537290	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	tctgctgctgtttcctttggTgtttctgtcccggtggcagg	13	10	2	0			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr11:5537290T>A	ENST00000380184.1	-	1	645	c.382A>T	c.(382-384)Acc>Tcc	p.T128S	HBG2_ENST00000380259.2_Intron	NM_145053.4	NP_659490.4	Q8IYU4	UBQLN_HUMAN	ubiquilin-like	128										endometrium(1)|kidney(3)|large_intestine(9)|lung(13)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.136)		TTTCCTTTGGTGTTTCTGTCC	0.537																																					p.T128S		Atlas-SNP	.											.	UBQLNL	74	.	0			c.A382T						.						214	209	211					11																	5537290		2201	4297	6498	SO:0001583	missense	143630	exon1			CTTTGGTGTTTCT	AK127987	CCDS31385.1	11p15.4	2014-02-12			ENSG00000175518	ENSG00000175518		"Ubiquilin family"	28294	protein-coding gene	gene with protein product							Standard	NM_145053		Approved	MGC20470, MGC26958	uc001maz.4	Q8IYU4	OTTHUMG00000066903	ENST00000380184.1:c.382A>T	chr11.hg19:g.5537290T>A	ENSP00000369531:p.Thr128Ser	63.0	0.0		84.0	27.0	NM_145053	Q6ZRU1|Q96EK3|Q96MB0	Missense_Mutation	SNP	ENST00000380184.1	hg19	CCDS31385.1	.	.	.	.	.	.	.	.	.	.	T	3.622	-0.077334	0.07184	.	.	ENSG00000175518	ENST00000380184;ENST00000538889	T	0.51325	0.71	4.87	2.44	0.29823	.	1.212050	0.06116	N	0.668049	T	0.35307	0.0927	L	0.44542	1.39	0.09310	N	1	P	0.41673	0.759	B	0.35413	0.202	T	0.22417	-1.0217	10	0.27785	T	0.31	0.0681	4.8692	0.13624	0.0:0.1013:0.1989:0.6998	.	128	Q8IYU4	UBQLN_HUMAN	S	128	ENSP00000369531:T128S	ENSP00000369531:T128S	T	-	1	0	UBQLNL	5493866	0.006000	0.16342	0.472000	0.27241	0.382000	0.30200	0.385000	0.20685	0.848000	0.35191	0.533000	0.62120	ACC	.	.		0.537	UBQLNL-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143386.1	NM_145053		A	5537290	T	A	5537290	3	1	299	1	0	0	0	0	1	0	0	0	16915	1696	59	4	1049	4	UBQLNL	11	5537290	Missense_Mutation	SNP	T	TCGA-G3-AAV3-01A-11D-A36X-10	5132723	5537290	129469226	47	43300										
USH1C	10083	hgsc.bcm.edu	37	chr11	17527406	17527406	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	agatttcacagctggcctgtAgatgaaattgggctcctggt	12	8	1	3			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr11:17527406A>G	ENST00000318024.4	-	16	1393				USH1C_ENST00000005226.7_Missense_Mutation_p.Y702H|USH1C_ENST00000527720.1_Intron|USH1C_ENST00000527020.1_Intron|USH1C_ENST00000529563.1_Intron	NM_005709.3	NP_005700.2	Q9Y6N9	USH1C_HUMAN	Usher syndrome 1C (autosomal recessive, severe)						auditory receptor cell differentiation (GO:0042491)|equilibrioception (GO:0050957)|G2/M transition of mitotic cell cycle (GO:0000086)|inner ear morphogenesis (GO:0042472)|parallel actin filament bundle assembly (GO:0030046)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	spectrin binding (GO:0030507)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	48						GCTGGCCTGTAGATGAAATTG	0.572																																					p.Y702H		Atlas-SNP	.											.	USH1C	157	.	0			c.T2104C						.						70	67	68					11																	17527406		2200	4293	6493	SO:0001627	intron_variant	10083	exon19			GCCTGTAGATGAA	AB006955	CCDS7825.1, CCDS31438.1, CCDS73265.1	11p14.3	2013-06-19	2004-05-19		ENSG00000006611	ENSG00000006611			12597	protein-coding gene	gene with protein product	"harmonin"	605242	"deafness, autosomal recessive 18"	DFNB18		10973247, 12107438	Standard	NM_005709		Approved	PDZ73, harmonin, NY-CO-37, NY-CO-38, PDZ-73, AIE-75, PDZD7C	uc001mne.3	Q9Y6N9	OTTHUMG00000166323	ENST00000318024.4:c.1285-3879T>C	chr11.hg19:g.17527406A>G		99.0	0.0		121.0	28.0	NM_153676	A8K423|Q7RTU8|Q96B29|Q9UM04|Q9UM17|Q9UPC3	Missense_Mutation	SNP	ENST00000318024.4	hg19	CCDS31438.1	.	.	.	.	.	.	.	.	.	.	A	11.74	1.728801	0.30593	.	.	ENSG00000006611	ENST00000005226	T	0.23147	1.92	5.22	2.88	0.33553	.	0.726301	0.12886	N	0.431048	T	0.10508	0.0257	.	.	.	0.24802	N	0.992694	B	0.02656	0.0	B	0.01281	0.0	T	0.28364	-1.0046	9	0.15066	T	0.55	.	1.752	0.02974	0.5025:0.2556:0.098:0.1439	.	702	Q7RTU8	.	H	702	ENSP00000005226:Y702H	ENSP00000005226:Y702H	Y	-	1	0	USH1C	17483982	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.943000	0.40253	1.961000	0.56991	0.459000	0.35465	TAC	.	.		0.572	USH1C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389146.1	NM_005709		G	17527406	A	G	17527406	1	3	299	0	1	0	0	0	0	0	0	0	17049	420	15	2		2	USH1C	11	17527406	Intron	SNP	A	TCGA-G3-AAV3-01A-11D-A36X-10	11990116	17527406	117479110	48	43301										
NR1H3	10062	hgsc.bcm.edu	37	chr11	47281483	47281483	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	ggtggggctggaggctgcagAgcccacagccctgctcacca	15	14	1	1			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr11:47281483A>T	ENST00000467728.1	+	2	1423	c.185A>T	c.(184-186)gAg>gTg	p.E62V	NR1H3_ENST00000527949.1_5'Flank|NR1H3_ENST00000481889.2_Missense_Mutation_p.E17V|NR1H3_ENST00000441012.2_Missense_Mutation_p.E62V|NR1H3_ENST00000395397.3_Missense_Mutation_p.E17V|NR1H3_ENST00000405576.1_Missense_Mutation_p.E17V|NR1H3_ENST00000529540.1_3'UTR|NR1H3_ENST00000407404.1_Missense_Mutation_p.E62V|NR1H3_ENST00000405853.3_Missense_Mutation_p.E62V			Q13133	NR1H3_HUMAN	nuclear receptor subfamily 1, group H, member 3	62					apoptotic cell clearance (GO:0043277)|cellular lipid metabolic process (GO:0044255)|cellular response to lipopolysaccharide (GO:0071222)|cholesterol homeostasis (GO:0042632)|gene expression (GO:0010467)|lipid homeostasis (GO:0055088)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of lipid transport (GO:0032369)|negative regulation of macrophage activation (GO:0043031)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of pinocytosis (GO:0048550)|negative regulation of proteolysis (GO:0045861)|negative regulation of secretion of lysosomal enzymes (GO:0090341)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of cholesterol transport (GO:0032376)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cholesterol homeostasis (GO:2000188)|regulation of circadian rhythm (GO:0042752)|response to progesterone (GO:0032570)|sterol homeostasis (GO:0055092)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cholesterol binding (GO:0015485)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|steroid hormone receptor activity (GO:0003707)|sterol response element binding (GO:0032810)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|ovary(5)	20						GAGGCTGCAGAGCCCACAGCC	0.652											OREG0020956	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E68V		Atlas-SNP	.											.	NR1H3	52	.	0			c.A203T						.						13	14	14					11																	47281483		2197	4292	6489	SO:0001583	missense	10062	exon3			CTGCAGAGCCCAC	U22662	CCDS7929.1, CCDS44584.1, CCDS44585.1, CCDS73285.1	11p11.2	2013-01-16			ENSG00000025434	ENSG00000025434		"Nuclear hormone receptors"	7966	protein-coding gene	gene with protein product	"liver X receptor-alpha"	602423				8621574, 7744246	Standard	NM_005693		Approved	LXR-a, RLD-1	uc009ylm.3	Q13133	OTTHUMG00000150628	ENST00000467728.1:c.185A>T	chr11.hg19:g.47281483A>T	ENSP00000420656:p.Glu62Val	180.0	0.0	945	238.0	55.0	NM_001251934	A8K3J9|D3DQR1|Q8IW13|Q96H87	Missense_Mutation	SNP	ENST00000467728.1	hg19	CCDS7929.1	.	.	.	.	.	.	.	.	.	.	A	10.94	1.493085	0.26774	.	.	ENSG00000025434	ENST00000395397;ENST00000405576;ENST00000481889;ENST00000436778;ENST00000531660;ENST00000407404;ENST00000444396;ENST00000457932;ENST00000412937;ENST00000449369;ENST00000441012;ENST00000437276;ENST00000436029;ENST00000467728;ENST00000405853	D;D;D;T;T;T;T;T;D;T;T;T;T;T;T	0.93133	-2.89;-3.17;-3.04;0.84;0.52;0.84;0.84;0.84;-2.63;0.84;0.84;0.84;0.84;0.84;0.84	5.56	2.91	0.33838	.	1.108690	0.06616	N	0.756596	D	0.88381	0.6421	L	0.29908	0.895	0.31069	N	0.713248	B;B;B;B	0.20671	0.0;0.0;0.047;0.0	B;B;B;B	0.13407	0.001;0.001;0.009;0.002	T	0.81616	-0.0852	10	0.48119	T	0.1	.	7.0506	0.25071	0.7929:0.0:0.2071:0.0	.	68;62;17;62	B4DXU5;Q13133;E9PLL4;Q13133-2	.;NR1H3_HUMAN;.;.	V	17;17;17;62;17;62;62;62;17;62;62;62;62;62;62	ENSP00000378793:E17V;ENSP00000385073:E17V;ENSP00000433271:E17V;ENSP00000403798:E62V;ENSP00000434650:E17V;ENSP00000385801:E62V;ENSP00000391005:E62V;ENSP00000413095:E62V;ENSP00000412636:E17V;ENSP00000415591:E62V;ENSP00000387946:E62V;ENSP00000396132:E62V;ENSP00000403696:E62V;ENSP00000420656:E62V;ENSP00000384745:E62V	ENSP00000378793:E17V	E	+	2	0	NR1H3	47238059	0.701000	0.27806	0.924000	0.36721	0.469000	0.32828	1.484000	0.35508	0.950000	0.37743	0.379000	0.24179	GAG	.	.		0.652	NR1H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319214.3			T	47281483	A	T	47281483	3	4	299	1	0	0	0	0	1	0	0	0	10627	304	11	4	191	4	NR1H3	11	47281483	Missense_Mutation	SNP	A	TCGA-G3-AAV3-01A-11D-A36X-10	29754077	47281483	87725033	49	43302										
KBTBD4	55709	hgsc.bcm.edu	37	chr11	47594682	47594682	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	ggcctcaggaaggcaaagccGggtgaagctgtctagcaagg	16	9	2	1	rs573433525		TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr11:47594682G>T	ENST00000526005.1	-	4	1510	c.1357C>A	c.(1357-1359)Cgg>Agg	p.R453R	KBTBD4_ENST00000430070.2_Silent_p.R469R|PTPMT1_ENST00000527079.2_3'UTR|KBTBD4_ENST00000533290.1_Silent_p.R478R|NDUFS3_ENST00000533507.1_Intron|KBTBD4_ENST00000395288.2_Silent_p.R453R			Q9NVX7	KBTB4_HUMAN	kelch repeat and BTB (POZ) domain containing 4	453										NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	24						AGGCAAAGCCGGGTGAAGCTG	0.562																																					p.R469R		Atlas-SNP	.											.	KBTBD4	55	.	0			c.C1405A						.						58	56	57					11																	47594682		2201	4298	6499	SO:0001819	synonymous_variant	55709	exon4			AAAGCCGGGTGAA	AF151086	CCDS7940.1, CCDS44594.1	11p11.2	2013-01-08	2003-12-12	2003-12-17	ENSG00000123444	ENSG00000123444		"BTB/POZ domain containing"	23761	protein-coding gene	gene with protein product			"BTB and kelch domain containing 4"	BKLHD4		11042152	Standard	NM_018095		Approved	FLJ10450, HSPC252	uc001nfz.3	Q9NVX7	OTTHUMG00000166894	ENST00000526005.1:c.1357C>A	chr11.hg19:g.47594682G>T		87.0	0.0		137.0	6.0	NM_018095	D3DQS1|D3DQS2|Q6IA85|Q9BUC3|Q9NV76	Silent	SNP	ENST00000526005.1	hg19	CCDS7940.1																																																																																			.	.		0.562	KBTBD4-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000391763.1	NM_016506		T	47594682	G	T	47594682	2	4	299	1	0	0	0	0	0	0	0	1	8004	1115	39	1		1	KBTBD4	11	47594682	Silent	SNP	G	TCGA-G3-AAV3-01A-11D-A36X-10	313199	47594682	87411834	50	43303										
ACAD8	27034	hgsc.bcm.edu	37	chr11	134131244	134131244	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	caatgtccggaagcagtttgGagagcctctggccagtaacc	12	11	1	1			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr11:134131244G>C	ENST00000281182.4	+	8	1023	c.917G>C	c.(916-918)gGa>gCa	p.G306A	ACAD8_ENST00000543332.1_Missense_Mutation_p.G208A|ACAD8_ENST00000374752.4_Missense_Mutation_p.G179A|ACAD8_ENST00000537423.1_Missense_Mutation_p.G229A|ACAD8_ENST00000524547.1_3'UTR	NM_014384.2	NP_055199.1	Q9UKU7	ACAD8_HUMAN	acyl-CoA dehydrogenase family, member 8	306					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|lipid metabolic process (GO:0006629)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|valine catabolic process (GO:0006574)	mitochondrial matrix (GO:0005759)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)			endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	14	all_hematologic(175;0.127)	all_cancers(12;8e-23)|all_epithelial(12;2.59e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|all_neural(223;0.0189)|Medulloblastoma(222;0.0245)|Esophageal squamous(93;0.0559)		Epithelial(10;1.92e-10)|all cancers(11;2.26e-09)|BRCA - Breast invasive adenocarcinoma(10;8.73e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00154)|Lung(977;0.21)	Flavin adenine dinucleotide(DB03147)	AAGCAGTTTGGAGAGCCTCTG	0.607																																					p.G306A	GBM(65;238 1125 33403 41853 48889)	Atlas-SNP	.											.	ACAD8	33	.	0			c.G917C						.						88	88	88					11																	134131244		2201	4297	6498	SO:0001583	missense	27034	exon8			AGTTTGGAGAGCC	AF126245	CCDS8498.1	11q25	2014-09-17	2010-04-30		ENSG00000151498	ENSG00000151498			87	protein-coding gene	gene with protein product		604773	"acyl-Coenzyme A dehydrogenase family, member 8"			10524212	Standard	NM_014384		Approved		uc001qhk.3	Q9UKU7	OTTHUMG00000167177	ENST00000281182.4:c.917G>C	chr11.hg19:g.134131244G>C	ENSP00000281182:p.Gly306Ala	98.0	0.0		114.0	27.0	NM_014384	B7Z5W4|Q6ZWP6|Q9BUS8	Missense_Mutation	SNP	ENST00000281182.4	hg19	CCDS8498.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	28.4|28.4	4.915777|4.915777	0.92178|0.92178	.|.	.|.	ENSG00000151498|ENSG00000151498	ENST00000281182;ENST00000537423;ENST00000543332;ENST00000374752|ENST00000537915	D;D;D;D|.	0.98090|.	-4.71;-4.71;-4.44;-4.71|.	5.35|5.35	5.35|5.35	0.76521|0.76521	Acyl-CoA dehydrogenase/oxidase C-terminal (2);Acyl-CoA oxidase/dehydrogenase, type 1 (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.91147|0.91147	0.7212|0.7212	H|H	0.99011|0.99011	4.4|4.4	0.80722|0.80722	D|D	1|1	B;P;B|.	0.42456|.	0.346;0.78;0.346|.	P;P;B|.	0.49953|.	0.489;0.627;0.356|.	D|D	0.94129|0.94129	0.7386|0.7386	10|6	0.87932|0.54805	D|T	0|0.06	.|.	19.0341|19.0341	0.92970|0.92970	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	229;179;306|.	B7Z5W4;Q6ZWP6;Q9UKU7|.	.;.;ACAD8_HUMAN|.	A|C	306;229;208;179|267	ENSP00000281182:G306A;ENSP00000443763:G229A;ENSP00000438302:G208A;ENSP00000363884:G179A|.	ENSP00000281182:G306A|ENSP00000445511:W267C	G|W	+|+	2|3	0|0	ACAD8|ACAD8	133636454|133636454	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.982000|0.982000	0.71751|0.71751	9.247000|9.247000	0.95444|0.95444	2.513000|2.513000	0.84729|0.84729	0.561000|0.561000	0.74099|0.74099	GGA|TGG	.	.		0.607	ACAD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393607.1	NM_014384		C	134131244	G	C	134131244	3	2	299	1	0	0	0	0	1	0	0	0	110	1174	41	4	947	4	ACAD8	11	134131244	Missense_Mutation	SNP	G	TCGA-G3-AAV3-01A-11D-A36X-10	86536562	134131244	875272	51	43304										
WNK1	65125	hgsc.bcm.edu	37	chr12	922935	922935	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	cacagtaaaaggaaagaagtGcattgttttggtgactgaac	11	5	0	3			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr12:922935G>A	ENST00000315939.6	+	2	1530	c.887G>A	c.(886-888)tGc>tAc	p.C296Y	WNK1_ENST00000530271.2_Missense_Mutation_p.C296Y|WNK1_ENST00000535572.1_Missense_Mutation_p.C296Y|WNK1_ENST00000447667.2_Missense_Mutation_p.C296Y|WNK1_ENST00000537687.1_Missense_Mutation_p.C296Y	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	296	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			GGAAAGAAGTGCATTGTTTTG	0.343																																					p.C296Y	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.G887A						.						112	106	108					12																	922935		2203	4300	6503	SO:0001583	missense	65125	exon2			AGAAGTGCATTGT	AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 167"	605232	"protein kinase, lysine deficient 1", "hereditary sensory neuropathy, type II"	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.887G>A	chr12.hg19:g.922935G>A	ENSP00000313059:p.Cys296Tyr	87.0	0.0		110.0	18.0	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	hg19	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.457240	0.84317	.	.	ENSG00000060237	ENST00000535572;ENST00000315939;ENST00000537687;ENST00000447667;ENST00000530271	T;T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07;-0.07	5.83	5.83	0.93111	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000001	T	0.62612	0.2442	N	0.16602	0.42	0.80722	D	1	P;P;B	0.51147	0.866;0.942;0.118	P;P;B	0.54460	0.638;0.753;0.179	T	0.63171	-0.6697	10	0.42905	T	0.14	-8.5053	20.1212	0.97961	0.0:0.0:1.0:0.0	.	296;296;296	F5GWT4;Q9H4A3;F6UYG0	.;WNK1_HUMAN;.	Y	296	ENSP00000441972:C296Y;ENSP00000313059:C296Y;ENSP00000444465:C296Y;ENSP00000392542:C296Y;ENSP00000433548:C296Y	ENSP00000313059:C296Y	C	+	2	0	WNK1	793196	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.942000	0.87708	2.751000	0.94390	0.561000	0.74099	TGC	.	.		0.343	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979		A	922935	G	A	922935	3	1	299	1	0	0	0	0	1	0	0	0	17392	1319	46	3	893	3	WNK1	12	922935	Missense_Mutation	SNP	G	TCGA-G3-AAV3-01A-11D-A36X-10		922935	132928960	52	43305										
ART4	420	hgsc.bcm.edu	37	chr12	14995920	14995920	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	ctacctcagaaccctctgtgGgtctctgcaggccagagagg	12	13	3	2			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr12:14995920G>A	ENST00000228936.4	-	1	509	c.128C>T	c.(127-129)cCc>cTc	p.P43L	C12orf60_ENST00000527783.1_Intron|RP11-233G1.4_ENST00000444324.2_RNA	NM_021071.2	NP_066549.2	Q93070	NAR4_HUMAN	ADP-ribosyltransferase 4 (Dombrock blood group)	43					arginine metabolic process (GO:0006525)|protein ADP-ribosylation (GO:0006471)	anchored component of membrane (GO:0031225)|membrane (GO:0016020)|plasma membrane (GO:0005886)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)			large_intestine(5)|liver(1)|lung(3)|prostate(1)|skin(2)|stomach(3)	15						ACCCTCTGTGGGTCTCTGCAG	0.542																																					p.P43L		Atlas-SNP	.											.	ART4	27	.	0			c.C128T						.						56	55	55					12																	14995920		2203	4300	6503	SO:0001583	missense	420	exon1			TCTGTGGGTCTCT	X95826	CCDS8668.1	12q13.2-q13.3	2014-07-18	2014-01-02	2006-01-12	ENSG00000111339	ENSG00000111339		"CD molecules", "Blood group antigens"	726	protein-coding gene	gene with protein product		110600	"Dombrock blood group", "ADP-ribosyltransferase 4 (DO blood group)", "ADP-ribosyltransferase 4"	DO		9119374	Standard	NM_021071		Approved	DOK1, CD297	uc001rcl.1	Q93070	OTTHUMG00000168738	ENST00000228936.4:c.128C>T	chr12.hg19:g.14995920G>A	ENSP00000228936:p.Pro43Leu	82.0	0.0		95.0	4.0	NM_021071	Q9BZ50|Q9BZ51|Q9HB06	Missense_Mutation	SNP	ENST00000228936.4	hg19	CCDS8668.1	.	.	.	.	.	.	.	.	.	.	G	15.23	2.770843	0.49680	.	.	ENSG00000111339	ENST00000228936;ENST00000430826;ENST00000544616;ENST00000430129;ENST00000420600	T;T	0.08282	3.27;3.11	4.51	1.56	0.23342	.	0.812904	0.11194	N	0.589536	T	0.10165	0.0249	L	0.34521	1.04	0.09310	N	0.999998	D;D	0.53619	0.961;0.961	P;P	0.49637	0.617;0.617	T	0.25882	-1.0119	10	0.87932	D	0	-12.987	7.1465	0.25585	0.0:0.1701:0.4784:0.3514	.	43;43	A8K6J7;Q93070	.;NAR4_HUMAN	L	43;43;26;26;26	ENSP00000228936:P43L;ENSP00000405689:P26L	ENSP00000228936:P43L	P	-	2	0	ART4	14887187	0.881000	0.30235	0.081000	0.20488	0.090000	0.18270	1.569000	0.36428	0.351000	0.24027	-0.188000	0.12872	CCC	.	.		0.542	ART4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400859.1	NM_021071		A	14995920	G	A	14995920	3	1	299	1	0	0	0	0	1	0	0	0	999	1232	43	3	828	3	ART4	12	14995920	Missense_Mutation	SNP	G	TCGA-G3-AAV3-01A-11D-A36X-10	14072985	14995920	118855975	53	43306										
LIMA1	51474	hgsc.bcm.edu	37	chr12	50575756	50575756	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	cctgctggttggccaagagaCgctccattggatagactgtc	12	11	0	2	rs200141288		TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr12:50575756C>A	ENST00000341247.4	-	10	1354	c.1205G>T	c.(1204-1206)cGt>cTt	p.R402L	LIMA1_ENST00000552491.1_Missense_Mutation_p.R99L|LIMA1_ENST00000552909.1_Missense_Mutation_p.R241L|LIMA1_ENST00000552783.1_Missense_Mutation_p.R243L|LIMA1_ENST00000552823.1_Missense_Mutation_p.R242L|LIMA1_ENST00000394943.3_Missense_Mutation_p.R403L|LIMA1_ENST00000547825.1_Missense_Mutation_p.R100L	NM_001113546.1|NM_016357.4	NP_001107018.1|NP_057441.1	Q9UHB6	LIMA1_HUMAN	LIM domain and actin binding 1	402	LIM zinc-binding. {ECO:0000255|PROSITE- ProRule:PRU00125}.				actin filament bundle assembly (GO:0051017)|negative regulation of actin filament depolymerization (GO:0030835)|ruffle organization (GO:0031529)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(2)	44						GGCCAAGAGACGCTCCATTGG	0.473																																					p.R403L		Atlas-SNP	.											.	LIMA1	67	.	0			c.G1208T						.						109	99	102					12																	50575756		2203	4300	6503	SO:0001583	missense	51474	exon10			AAGAGACGCTCCA	AF198454	CCDS8802.1, CCDS44877.1, CCDS55826.1, CCDS58230.1	12q13.12	2006-04-12				ENSG00000050405			24636	protein-coding gene	gene with protein product	"epithelial protein lost in neoplasm beta"	608364				10806352, 10618726, 12566430	Standard	NM_016357		Approved	EPLIN	uc001rwk.4	Q9UHB6		ENST00000341247.4:c.1205G>T	chr12.hg19:g.50575756C>A	ENSP00000340184:p.Arg402Leu	78.0	0.0		112.0	24.0	NM_001113546	B2RB09|Q2TAN7|Q59FE8|Q9BVF2|Q9H8J1|Q9HBN5|Q9NX96|Q9NXC3|Q9NXU6|Q9P0H8|Q9UHB5	Missense_Mutation	SNP	ENST00000341247.4	hg19	CCDS8802.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.813060	0.90707	.	.	ENSG00000050405	ENST00000552491;ENST00000547825;ENST00000552823;ENST00000394943;ENST00000341247;ENST00000552783;ENST00000552909;ENST00000420992	D;D;D;D;D;D;D	0.86230	-2.09;-2.09;-2.09;-2.09;-2.09;-2.09;-2.09	5.49	5.49	0.81192	Zinc finger, LIM-type (5);	0.099034	0.64402	D	0.000002	D	0.91270	0.7248	L	0.39566	1.225	0.50171	D	0.999852	P;D;P	0.89917	0.945;1.0;0.937	P;D;P	0.91635	0.878;0.999;0.884	D	0.91466	0.5193	10	0.62326	D	0.03	.	19.7347	0.96198	0.0:1.0:0.0:0.0	.	412;402;241	Q59FE8;Q9UHB6;F8VQE1	.;LIMA1_HUMAN;.	L	99;100;242;403;402;243;241;321	ENSP00000448463:R99L;ENSP00000448706:R100L;ENSP00000450266:R242L;ENSP00000378400:R403L;ENSP00000340184:R402L;ENSP00000448779:R243L;ENSP00000450087:R241L	ENSP00000340184:R402L	R	-	2	0	LIMA1	48862023	0.998000	0.40836	1.000000	0.80357	0.996000	0.88848	3.716000	0.54904	2.746000	0.94184	0.655000	0.94253	CGT	.	.		0.473	LIMA1-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406235.2	NM_016357		A	50575756	C	A	50575756	3	1	299	1	0	0	0	0	1	0	0	0	8805	536	19	1	1082	1	LIMA1	12	50575756	Missense_Mutation	SNP	C	TCGA-G3-AAV3-01A-11D-A36X-10	35579836	50575756	83276139	54	43307										
TMEM5	10329	hgsc.bcm.edu	37	chr12	64202488	64202488	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	gaaacaaatgaaagtcttaaGaattaccaagatgccttgct	7	7	1	3			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr12:64202488G>A	ENST00000261234.6	+	6	1106	c.948G>A	c.(946-948)aaG>aaA	p.K316K	TMEM5-AS1_ENST00000546214.1_RNA|TMEM5_ENST00000537373.1_Silent_p.K56K	NM_014254.1	NP_055069.1	Q9Y2B1	TMEM5_HUMAN	transmembrane protein 5	316						integral component of plasma membrane (GO:0005887)				breast(1)|large_intestine(3)|liver(2)|lung(7)|prostate(1)|skin(1)	15		Myeloproliferative disorder(1001;0.0255)	BRCA - Breast invasive adenocarcinoma(9;0.0985)	GBM - Glioblastoma multiforme(28;9e-08)|BRCA - Breast invasive adenocarcinoma(357;0.000175)		AAAGTCTTAAGAATTACCAAG	0.398																																					p.K316K		Atlas-SNP	.											.	TMEM5	35	.	0			c.G948A						.						100	95	96					12																	64202488		2203	4300	6503	SO:0001819	synonymous_variant	10329	exon6			TCTTAAGAATTAC	AB015633	CCDS8966.1, CCDS61179.1	12q14.1	2013-05-07			ENSG00000118600	ENSG00000118600			13530	protein-coding gene	gene with protein product		605862				10072769, 23217329	Standard	NM_014254		Approved	HP10481	uc001srq.2	Q9Y2B1	OTTHUMG00000168730	ENST00000261234.6:c.948G>A	chr12.hg19:g.64202488G>A		66.0	0.0		101.0	29.0	NM_014254	A8K017|Q6PKD6	Silent	SNP	ENST00000261234.6	hg19	CCDS8966.1																																																																																			.	.		0.398	TMEM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400821.1	NM_014254		A	64202488	G	A	64202488	2	1	299	1	0	0	0	0	0	0	0	1	16189	933	33	3		3	TMEM5	12	64202488	Silent	SNP	G	TCGA-G3-AAV3-01A-11D-A36X-10	13626732	64202488	69649407	55	43308										
TCTN1	79600	hgsc.bcm.edu	37	chr12	111066708	111066708	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	accaaactggatattcctacTgctgctaaatatgaggtgag	9	8	0	2			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr12:111066708T>C	ENST00000551590.1	+	4	765	c.609T>C	c.(607-609)acT>acC	p.T203T	TCTN1_ENST00000377654.3_Silent_p.T25T|TCTN1_ENST00000551555.2_3'UTR|TCTN1_ENST00000397659.4_Silent_p.T203T|TCTN1_ENST00000550703.2_Silent_p.T203T|HVCN1_ENST00000548312.1_Intron|RN7SL387P_ENST00000581015.1_RNA|TCTN1_ENST00000397655.3_Silent_p.T203T			Q2MV58	TECT1_HUMAN	tectonic family member 1	203					central nervous system interneuron axonogenesis (GO:0021956)|cilium morphogenesis (GO:0060271)|dorsal/ventral neural tube patterning (GO:0021904)|in utero embryonic development (GO:0001701)|neural tube formation (GO:0001841)|regulation of smoothened signaling pathway (GO:0008589)|somatic motor neuron differentiation (GO:0021523)|telencephalon development (GO:0021537)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|membrane (GO:0016020)|TCTN-B9D complex (GO:0036038)				NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(9)|urinary_tract(1)	15						ATATTCCTACTGCTGCTAAAT	0.338																																					p.T203T		Atlas-SNP	.											.	TCTN1	37	.	0			c.T609C						.						137	141	140					12																	111066708		1870	4106	5976	SO:0001819	synonymous_variant	79600	exon4			TCCTACTGCTGCT	AK055891	CCDS41833.1, CCDS41834.1, CCDS41835.1	12q24.11	2011-09-07			ENSG00000204852	ENSG00000204852		"Tectonic proteins"	26113	protein-coding gene	gene with protein product		609863				16357211	Standard	NM_001082537		Approved	FLJ21127, TECT1, JBTS13	uc001trn.4	Q2MV58	OTTHUMG00000150051	ENST00000551590.1:c.609T>C	chr12.hg19:g.111066708T>C		63.0	0.0		47.0	15.0	NM_024549	A8MX11|Q49A60|Q6P5X1|Q6UXW2|Q8NAE9|Q96N72|Q9H798	Silent	SNP	ENST00000551590.1	hg19	CCDS41835.1																																																																																			.	.		0.338	TCTN1-001	KNOWN	non_canonical_TEC|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316016.2	NM_024549		C	111066708	T	C	111066708	2	2	299	1	0	0	0	0	0	0	0	1	15737	1567	55	2		2	TCTN1	12	111066708	Silent	SNP	T	TCGA-G3-AAV3-01A-11D-A36X-10	46864220	111066708	22785187	56	43309										
RPH3A	22895	hgsc.bcm.edu	37	chr12	113306371	113306371	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	tgaacagcctgctcctgagcCcaagcaccctgcccgggctc	10	18	0	2			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr12:113306371C>A	ENST00000389385.4	+	8	1078	c.581C>A	c.(580-582)cCc>cAc	p.P194H	RPH3A_ENST00000543106.2_Missense_Mutation_p.P194H|RPH3A_ENST00000551052.1_Missense_Mutation_p.P190H|RPH3A_ENST00000415485.3_Missense_Mutation_p.P194H|RPH3A_ENST00000548866.1_Missense_Mutation_p.P145H|RPH3A_ENST00000420983.2_Missense_Mutation_p.P194H|RPH3A_ENST00000447659.2_Missense_Mutation_p.P145H|RPH3A_ENST00000549913.2_3'UTR	NM_001143854.1|NM_014954.3	NP_001137326.1|NP_055769.2	Q9Y2J0	RP3A_HUMAN	rabphilin 3A	194	Pro-rich.				intracellular protein transport (GO:0006886)	cell junction (GO:0030054)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylinositol phosphate binding (GO:1901981)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)|ovary(3)|prostate(4)|skin(6)|urinary_tract(1)	47				BRCA - Breast invasive adenocarcinoma(302;0.00453)		GCTCCTGAGCCCAAGCACCCT	0.582																																					p.P194H		Atlas-SNP	.											.	RPH3A	98	.	0			c.C581A						.						42	42	42					12																	113306371		2203	4300	6503	SO:0001583	missense	22895	exon8			CTGAGCCCAAGCA	AB023202	CCDS31904.1, CCDS44979.1	12q24.13	2014-07-02	2014-07-02		ENSG00000089169	ENSG00000089169		"Synaptotagmins"	17056	protein-coding gene	gene with protein product		612159	"rabphilin 3A homolog (mouse)"			10231032, 7822236	Standard	NM_014954		Approved	KIAA0985, rabphilin, exophilin-1	uc001ttz.3	Q9Y2J0	OTTHUMG00000169713	ENST00000389385.4:c.581C>A	chr12.hg19:g.113306371C>A	ENSP00000374036:p.Pro194His	50.0	0.0		66.0	20.0	NM_001143854	B7Z3C3|Q96AE0	Missense_Mutation	SNP	ENST00000389385.4	hg19	CCDS44979.1	.	.	.	.	.	.	.	.	.	.	C	11.60	1.687526	0.29962	.	.	ENSG00000089169	ENST00000543106;ENST00000389385;ENST00000447659;ENST00000551052;ENST00000415485;ENST00000548866;ENST00000420983	T;T;T;T;T;T;T	0.62941	0.01;0.01;-0.01;0.01;0.01;-0.01;0.01	5.05	4.14	0.48551	.	0.208215	0.33670	N	0.004663	T	0.64929	0.2643	L	0.50333	1.59	0.31229	N	0.696588	B;D;D;D	0.58268	0.007;0.97;0.97;0.982	B;P;P;P	0.52267	0.01;0.498;0.498;0.694	T	0.70651	-0.4813	10	0.72032	D	0.01	.	11.6809	0.51457	0.3219:0.6781:0.0:0.0	.	145;194;194;190	F8VP47;B7Z9Z7;Q9Y2J0;Q9Y2J0-2	.;.;RP3A_HUMAN;.	H	194;194;145;190;194;145;194	ENSP00000440384:P194H;ENSP00000374036:P194H;ENSP00000413254:P145H;ENSP00000448297:P190H;ENSP00000405357:P194H;ENSP00000450347:P145H;ENSP00000408889:P194H	ENSP00000374036:P194H	P	+	2	0	RPH3A	111790754	1.000000	0.71417	0.942000	0.38095	0.284000	0.27059	1.371000	0.34250	1.113000	0.41760	-0.181000	0.13052	CCC	.	.		0.582	RPH3A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405561.1	NM_014954		A	113306371	C	A	113306371	3	1	299	1	0	0	0	0	1	0	0	0	13566	623	22	3	603	3	RPH3A	12	113306371	Missense_Mutation	SNP	C	TCGA-G3-AAV3-01A-11D-A36X-10	2239663	113306371	20545524	57	43310										
MED13L	23389	hgsc.bcm.edu	37	chr12	116446438	116446438	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	gacagttctgtcatccagagTagacaactgctggagttcta	10	9	3	2			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr12:116446438T>A	ENST00000281928.3	-	10	1986	c.1780A>T	c.(1780-1782)Act>Tct	p.T594S		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	594						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		TCATCCAGAGTAGACAACTGC	0.537																																					p.T594S		Atlas-SNP	.											.	MED13L	193	.	0			c.A1780T						.						64	56	58					12																	116446438		2203	4300	6503	SO:0001583	missense	23389	exon10			CCAGAGTAGACAA	AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"thyroid hormone receptor associated protein 2"	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.1780A>T	chr12.hg19:g.116446438T>A	ENSP00000281928:p.Thr594Ser	55.0	0.0		77.0	23.0	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Missense_Mutation	SNP	ENST00000281928.3	hg19	CCDS9177.1	.	.	.	.	.	.	.	.	.	.	T	4.350	0.064337	0.08388	.	.	ENSG00000123066	ENST00000281928	T	0.71817	-0.6	5.91	-0.653	0.11447	.	0.691028	0.15575	N	0.255243	T	0.38558	0.1045	N	0.03608	-0.345	0.20307	N	0.999913	B	0.02656	0.0	B	0.01281	0.0	T	0.19877	-1.0292	10	0.20046	T	0.44	.	5.0638	0.14572	0.1223:0.2721:0.0:0.6056	.	594	Q71F56	MD13L_HUMAN	S	594	ENSP00000281928:T594S	ENSP00000281928:T594S	T	-	1	0	MED13L	114930821	0.934000	0.31675	0.907000	0.35723	0.996000	0.88848	0.683000	0.25349	-0.105000	0.12132	0.533000	0.62120	ACT	.	.		0.537	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3			A	116446438	T	A	116446438	3	1	299	1	0	0	0	0	1	0	0	0	9440	1638	57	4	4940	4	MED13L	12	116446438	Missense_Mutation	SNP	T	TCGA-G3-AAV3-01A-11D-A36X-10	3140067	116446438	17405457	58	43311										
VPS33A	65082	hgsc.bcm.edu	37	chr12	122734446	122734446	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	atgccataaatttcatcaatGagtccttcatatgtcagctg	6	9	4	1			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr12:122734446G>C	ENST00000267199.4	-	6	859	c.747C>G	c.(745-747)ctC>ctG	p.L249L	RP11-512M8.5_ENST00000535844.1_Silent_p.L210L|VPS33A_ENST00000542310.1_5'Flank	NM_022916.4	NP_075067.2	Q96AX1	VP33A_HUMAN	vacuolar protein sorting 33 homolog A (S. cerevisiae)	249					lysosome localization (GO:0032418)|melanosome localization (GO:0032400)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of developmental pigmentation (GO:0048070)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	early endosome (GO:0005769)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)				NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(13)|ovary(1)|skin(2)	28	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000336)|Epithelial(86;0.000606)|BRCA - Breast invasive adenocarcinoma(302;0.23)		TTTCATCAATGAGTCCTTCAT	0.358																																					p.L249L		Atlas-SNP	.											.	VPS33A	61	.	0			c.C747G						.						145	140	142					12																	122734446		2203	4300	6503	SO:0001819	synonymous_variant	65082	exon6			ATCAATGAGTCCT	AK026048	CCDS9231.1	12q24.31	2008-06-23	2006-04-04		ENSG00000139719	ENSG00000139719			18179	protein-coding gene	gene with protein product		610034	"vacuolar protein sorting 33A (yeast)"			11250079	Standard	NM_022916		Approved		uc001ucd.3	Q96AX1	OTTHUMG00000168920	ENST00000267199.4:c.747C>G	chr12.hg19:g.122734446G>C		98.0	0.0		130.0	22.0	NM_022916	Q547V4|Q9H5Q0	Silent	SNP	ENST00000267199.4	hg19	CCDS9231.1																																																																																			.	.		0.358	VPS33A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401607.2			C	122734446	G	C	122734446	2	2	299	1	0	0	0	0	0	0	0	1	17216	1277	45	4		4	VPS33A	12	122734446	Silent	SNP	G	TCGA-G3-AAV3-01A-11D-A36X-10	6288008	122734446	11117449	59	43312										
ZCCHC8	55596	hgsc.bcm.edu	37	chr12	122983386	122983387	+	Frame_Shift_Del	DEL	AG	AG	-													0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	tctcatacctcggtcgagtcAgaatgttcaattttcgttta							TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr12:122983386_122983387delAG	ENST00000336229.4	-	2	359_360	c.229_230delCT	c.(229-231)ctgfs	p.L77fs	ZCCHC8_ENST00000543897.1_5'UTR|ZCCHC8_ENST00000536306.1_5'UTR	NM_017612.3	NP_060082.2	Q6NZY4	ZCHC8_HUMAN	zinc finger, CCHC domain containing 8	77					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(2)|large_intestine(8)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.25e-05)|Epithelial(86;0.000113)|BRCA - Breast invasive adenocarcinoma(302;0.202)		CGGTCGAGTCAGAATGTTCAAT	0.287																																					p.77_77del		Atlas-INDEL	.											.	ZCCHC8	56	.	0			c.230_231del						.																																			SO:0001589	frameshift_variant	55596	exon2			.	BC017704		12q24.31	2014-04-14				ENSG00000033030		"Zinc fingers, CCHC domain containing"	25265	protein-coding gene	gene with protein product						12477932	Standard	XM_005253581		Approved	DKFZp434E2220	uc001ucn.3	Q6NZY4		ENST00000336229.4:c.229_230delCT	chr12.hg19:g.122983386_122983387delAG	ENSP00000337313:p.Leu77fs	74.0	0.0		111.0	24.0	NM_017612	Q7L2P6|Q8N2K5|Q96SK7|Q9NSS2|Q9NSS3	Frame_Shift_Del	DEL	ENST00000336229.4	hg19																																																																																				.	.		0.287	ZCCHC8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017612		-	122983387	AG	-	122983386	7	5	299	1	0	1	0	1	0	0	0	0	17609	188	7	0	1945	0	ZCCHC8	12	122983386	Frame_Shift_Del	DEL	AG	TCGA-G3-AAV3-01A-11D-A36X-10	248940	122983386	10868509	60	43313										
DNAH10	196385	hgsc.bcm.edu	37	chr12	124360035	124360035	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	tccatcctgaaaggccacacCtcggtaacttgattttaact	6	12	0	2			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr12:124360035C>A	ENST00000409039.3	+	46	7867	c.7842C>A	c.(7840-7842)acC>acA	p.T2614T		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2614	AAA 3. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		AAGGCCACACCTCGGTAACTT	0.438																																					p.T2614T		Atlas-SNP	.											.	DNAH10	888	.	0			c.C7842A						.						105	97	99					12																	124360035		1862	4096	5958	SO:0001819	synonymous_variant	196385	exon46			CCACACCTCGGTA	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.7842C>A	chr12.hg19:g.124360035C>A		78.0	0.0		73.0	15.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	hg19	CCDS9255.2																																																																																			.	.		0.438	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			A	124360035	C	A	124360035	2	1	299	1	0	0	0	0	0	0	0	1	4600	668	24	3		3	DNAH10	12	124360035	Silent	SNP	C	TCGA-G3-AAV3-01A-11D-A36X-10	1376649	124360035	9491860	61	43314										
SLC25A21	89874	hgsc.bcm.edu	37	chr14	37641486	37641486	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	gcagggcgggctgtccttacCtgcagaaccaccggccacga	13	15	0	1			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr14:37641486C>T	ENST00000331299.5	-	1	585	c.70G>A	c.(70-72)Ggt>Agt	p.G24S	SLC25A21-AS1_ENST00000556667.1_5'UTR|SLC25A21_ENST00000555449.1_Splice_Site_p.G24S|SLC25A21_ENST00000557611.1_5'UTR	NM_030631.3	NP_085134.1	Q9BQT8	ODC_HUMAN	solute carrier family 25 (mitochondrial oxoadipate carrier), member 21	24					cellular nitrogen compound metabolic process (GO:0034641)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|pancreas(1)|prostate(1)|skin(1)	9	Esophageal squamous(585;0.164)|Breast(36;0.179)|Hepatocellular(127;0.213)		Lung(8;2.16e-08)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.0112)|all cancers(34;0.0274)|LUSC - Lung squamous cell carcinoma(13;0.149)	GBM - Glioblastoma multiforme(112;0.00204)		CTGTCCTTACCTGCAGAACCA	0.642																																					p.G24S		Atlas-SNP	.											.	SLC25A21	24	.	0			c.G70A						.						30	24	26					14																	37641486		2199	4292	6491	SO:0001630	splice_region_variant	89874	exon1			CCTTACCTGCAGA	AJ278148	CCDS9663.1, CCDS55913.1	14q13.3	2014-01-28	2012-03-29		ENSG00000183032	ENSG00000183032		"Solute carriers"	14411	protein-coding gene	gene with protein product		607571	"solute carrier family 25 (mitochondrial oxodicarboxylate carrier), member 21"			11083877	Standard	NM_030631		Approved	ODC1, ODC	uc001wtz.2	Q9BQT8	OTTHUMG00000140250	ENST00000331299.5:c.70+1G>A	chr14.hg19:g.37641486C>T		181.0	0.0		283.0	58.0	NM_030631	A8K0L0|G3V4L5|Q3MJ99	Missense_Mutation	SNP	ENST00000331299.5	hg19	CCDS9663.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.072178	0.76415	.	.	ENSG00000183032	ENST00000555449;ENST00000331299	D;D	0.85171	-1.95;-1.95	3.4	3.4	0.38934	Mitochondrial carrier domain (2);	0.175102	0.37623	U	0.002012	D	0.90380	0.6989	M	0.79693	2.465	0.58432	D	0.999999	D	0.59357	0.985	D	0.63597	0.916	D	0.90289	0.4321	9	.	.	.	-4.6058	10.4757	0.44663	0.0:1.0:0.0:0.0	.	24	Q9BQT8	ODC_HUMAN	S	24	ENSP00000451873:G24S;ENSP00000329452:G24S	.	G	-	1	0	SLC25A21	36711237	0.993000	0.37304	0.993000	0.49108	0.471000	0.32888	3.035000	0.49759	1.868000	0.54150	0.557000	0.71058	GGT	.	.		0.642	SLC25A21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276732.2	NM_030631	Missense_Mutation	T	37641486	C	T	37641486	5	4	299	1	0	0	0	0	0	0	1	0	14499	695	24	3	874	3	SLC25A21	14	37641486	Splice_Site	SNP	C	TCGA-G3-AAV3-01A-11D-A36X-10		37641486	69708054	62	43315										
BCL11B	64919	hgsc.bcm.edu	37	chr14	99641568	99641568	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	tcctcctcctcctcctcctcCtcgtcctcctcctccggctc	3	25	0	0			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr14:99641568C>G	ENST00000357195.3	-	4	1614	c.1605G>C	c.(1603-1605)gaG>gaC	p.E535D	BCL11B_ENST00000443726.2_Missense_Mutation_p.E341D|BCL11B_ENST00000345514.2_Missense_Mutation_p.E464D	NM_001282237.1|NM_138576.2	NP_001269166.1|NP_612808.1	Q9C0K0	BC11B_HUMAN	B-cell CLL/lymphoma 11B (zinc finger protein)	535	Glu-rich.				alpha-beta T cell differentiation (GO:0046632)|epithelial cell morphogenesis (GO:0003382)|keratinocyte development (GO:0003334)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|odontogenesis of dentin-containing tooth (GO:0042475)|olfactory bulb axon guidance (GO:0071678)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive T cell selection (GO:0043368)|post-embryonic camera-type eye development (GO:0031077)|regulation of keratinocyte proliferation (GO:0010837)|regulation of lipid metabolic process (GO:0019216)|regulation of neuron differentiation (GO:0045664)|striatal medium spiny neuron differentiation (GO:0021773)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|thymus development (GO:0048538)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.E535_E536delEE(1)		NS(3)|breast(1)|central_nervous_system(9)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(9)|prostate(2)|skin(2)	34		Melanoma(154;0.0866)|all_epithelial(191;0.241)		COAD - Colon adenocarcinoma(157;0.103)		cctcctcctcctcgtcctcct	0.697			T	TLX3	T-ALL																																p.E535D		Atlas-SNP	.		Dom	yes		14	14q32.1	64919	B-cell CLL/lymphoma 11B  (CTIP2)		L	BCL11B,colon,carcinoma,0,1	BCL11B	108	.	1	Deletion - In frame(1)	prostate(1)	c.G1605C						.						5	5	5					14																	99641568		2084	4070	6154	SO:0001583	missense	64919	exon4			CTCCTCCTCGTCC	AJ404614	CCDS9949.1, CCDS9950.1	14q32	2013-01-08			ENSG00000127152	ENSG00000127152		"Zinc fingers, C2H2-type"	13222	protein-coding gene	gene with protein product		606558		ZNF856B		11719382, 16950772	Standard	NM_138576		Approved	CTIP-2, CTIP2, hRIT1-alpha	uc001yga.3	Q9C0K0	OTTHUMG00000028967	ENST00000357195.3:c.1605G>C	chr14.hg19:g.99641568C>G	ENSP00000349723:p.Glu535Asp	19.0	0.0		32.0	2.0	NM_138576	Q9H162	Missense_Mutation	SNP	ENST00000357195.3	hg19	CCDS9950.1	.	.	.	.	.	.	.	.	.	.	C	13.20	2.167616	0.38315	.	.	ENSG00000127152	ENST00000357195;ENST00000345514;ENST00000443726	T;T;T	0.13657	2.57;2.6;2.57	3.81	0.863	0.19062	.	0.158674	0.40144	N	0.001176	T	0.07324	0.0185	N	0.22421	0.69	0.40982	D	0.984788	B;B	0.31413	0.322;0.185	B;B	0.31390	0.129;0.048	T	0.38394	-0.9663	10	0.30854	T	0.27	-8.4478	4.8239	0.13407	0.0:0.4986:0.1502:0.3512	.	464;535	Q9C0K0-2;Q9C0K0	.;BC11B_HUMAN	D	535;464;341	ENSP00000349723:E535D;ENSP00000280435:E464D;ENSP00000387419:E341D	ENSP00000280435:E464D	E	-	3	2	BCL11B	98711321	0.591000	0.26824	0.998000	0.56505	0.990000	0.78478	-0.193000	0.09573	-0.059000	0.13154	0.561000	0.74099	GAG	.	.		0.697	BCL11B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000072332.2	NM_138576		G	99641568	C	G	99641568	3	3	299	1	0	0	0	0	1	0	0	0	1364	680	24	4	1083	4	BCL11B	14	99641568	Missense_Mutation	SNP	C	TCGA-G3-AAV3-01A-11D-A36X-10	62000082	99641568	7707972	63	43316										
GNB5	10681	hgsc.bcm.edu	37	chr15	52416719	52416719	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	agaaagcagtcccatcggggGaaactcgtagagtgctaacg	13	9	0	2			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr15:52416719G>A	ENST00000261837.7	-	12	1192	c.1127C>T	c.(1126-1128)tCc>tTc	p.S376F	CTD-2184D3.7_ENST00000557898.1_RNA|GNB5_ENST00000396335.4_Missense_Mutation_p.S264F|GNB5_ENST00000358784.7_Missense_Mutation_p.S334F|GNB5_ENST00000559348.1_5'UTR|CTD-2184D3.6_ENST00000559825.1_lincRNA	NM_016194.3	NP_057278.2	O14775	GBB5_HUMAN	guanine nucleotide binding protein (G protein), beta 5	376					GTP catabolic process (GO:0006184)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	chaperone binding (GO:0051087)|G-protein gamma-subunit binding (GO:0031682)|GTPase activity (GO:0003924)|signal transducer activity (GO:0004871)			large_intestine(1)|lung(1)	2				all cancers(107;0.0163)		CCCATCGGGGGAAACTCGTAG	0.498																																					p.S376F		Atlas-SNP	.											.	GNB5	28	.	0			c.C1127T						.						104	104	104					15																	52416719		2195	4293	6488	SO:0001583	missense	10681	exon12			TCGGGGGAAACTC	AF017656	CCDS10149.1, CCDS45261.1	15q21.1	2013-01-10			ENSG00000069966	ENSG00000069966		"WD repeat domain containing"	4401	protein-coding gene	gene with protein product		604447				9606987	Standard	NM_016194		Approved	GB5	uc031qrz.1	O14775	OTTHUMG00000131892	ENST00000261837.7:c.1127C>T	chr15.hg19:g.52416719G>A	ENSP00000261837:p.Ser376Phe	101.0	0.0		132.0	25.0	NM_016194	B2RBR5|Q9HAU9|Q9UFT3	Missense_Mutation	SNP	ENST00000261837.7	hg19	CCDS10149.1	.	.	.	.	.	.	.	.	.	.	G	19.75	3.885268	0.72410	.	.	ENSG00000069966	ENST00000261837;ENST00000396335;ENST00000544480;ENST00000358784	T	0.66460	-0.21	5.98	5.06	0.68205	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.86096	0.5851	M	0.93062	3.375	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.994;0.996	D	0.89930	0.4065	10	0.87932	D	0	-28.054	16.7076	0.85376	0.0:0.0:0.8694:0.1306	.	376;264	O14775;O14775-3	GBB5_HUMAN;.	F	376;334;174;264	ENSP00000261837:S376F	ENSP00000261837:S376F	S	-	2	0	GNB5	50204011	1.000000	0.71417	0.303000	0.25071	0.387000	0.30353	9.648000	0.98483	1.537000	0.49254	0.644000	0.83932	TCC	.	.		0.498	GNB5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254842.1			A	52416719	G	A	52416719	3	1	299	1	0	0	0	0	1	0	0	0	6529	1174	41	3	68	3	GNB5	15	52416719	Missense_Mutation	SNP	G	TCGA-G3-AAV3-01A-11D-A36X-10		52416719	50114673	64	43317										
NTRK3	4916	hgsc.bcm.edu	37	chr15	88678582	88678582	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	accacaaactcgatgcagtgCtccaggcgcagctcaggctc	10	15	1	0			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr15:88678582C>A	ENST00000360948.2	-	9	1115	c.954G>T	c.(952-954)gaG>gaT	p.E318D	NTRK3_ENST00000557856.1_Missense_Mutation_p.E318D|NTRK3_ENST00000558676.1_Missense_Mutation_p.E318D|NTRK3_ENST00000317501.3_Missense_Mutation_p.E318D|NTRK3_ENST00000542733.2_Missense_Mutation_p.E220D|NTRK3_ENST00000355254.2_Missense_Mutation_p.E318D|NTRK3_ENST00000357724.2_Missense_Mutation_p.E318D|NTRK3_ENST00000394480.2_Missense_Mutation_p.E318D|NTRK3_ENST00000540489.2_Missense_Mutation_p.E318D	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	318	Ig-like C2-type 2.				activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|cochlea development (GO:0090102)|lens fiber cell differentiation (GO:0070306)|mechanoreceptor differentiation (GO:0042490)|modulation by virus of host transcription (GO:0019056)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell death (GO:0060548)|negative regulation of protein phosphorylation (GO:0001933)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|neurotrophin signaling pathway (GO:0038179)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of axon extension involved in regeneration (GO:0048691)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of positive chemotaxis (GO:0050927)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|neurotrophin binding (GO:0043121)|neurotrophin receptor activity (GO:0005030)|p53 binding (GO:0002039)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ETV6/NTRK3(238)	breast(3)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(22)|lung(63)|ovary(6)|pancreas(3)|prostate(1)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)	119			BRCA - Breast invasive adenocarcinoma(143;0.211)			CGATGCAGTGCTCCAGGCGCA	0.602			T	ETV6	"congenital fibrosarcoma, Secretory breast "					TSP Lung(13;0.10)																											p.E318D		Atlas-SNP	.		Dom	yes		15	15q25	4916	"neurotrophic tyrosine kinase, receptor, type 3"		"E, M"	.	NTRK3	587	.	0			c.G954T						.						49	50	50					15																	88678582		2201	4299	6500	SO:0001583	missense	4916	exon10			GCAGTGCTCCAGG	U05012	CCDS10340.1, CCDS32322.1, CCDS32323.1, CCDS58399.1	15q24-q25	2013-01-11			ENSG00000140538	ENSG00000140538	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing"	8033	protein-coding gene	gene with protein product		191316				7806211	Standard	NM_001012338		Approved	TRKC	uc002bme.2	Q16288	OTTHUMG00000148677	ENST00000360948.2:c.954G>T	chr15.hg19:g.88678582C>A	ENSP00000354207:p.Glu318Asp	43.0	0.0		72.0	17.0	NM_001243101	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Missense_Mutation	SNP	ENST00000360948.2	hg19	CCDS32322.1	.	.	.	.	.	.	.	.	.	.	C	13.13	2.145219	0.37825	.	.	ENSG00000140538	ENST00000394480;ENST00000360948;ENST00000357724;ENST00000355254;ENST00000542733;ENST00000540489;ENST00000317501	T;T;T;T;T;T;T	0.74209	-0.82;-0.77;-0.76;-0.82;-0.7;0.08;0.08	5.28	2.33	0.28932	.	0.047530	0.85682	D	0.000000	T	0.51805	0.1696	N	0.12746	0.255	0.38505	D	0.948321	B;B;B;B;B;B	0.09022	0.0;0.002;0.0;0.001;0.002;0.0	B;B;B;B;B;B	0.11329	0.002;0.005;0.006;0.005;0.004;0.006	T	0.33292	-0.9874	10	0.32370	T	0.25	.	6.8304	0.23907	0.0:0.6494:0.1259:0.2247	.	220;318;318;318;318;318	B7Z7U4;E9PG56;B7Z4C5;Q96CY4;Q16288-3;Q16288	.;.;.;.;.;NTRK3_HUMAN	D	318;318;318;318;220;318;318	ENSP00000377990:E318D;ENSP00000354207:E318D;ENSP00000350356:E318D;ENSP00000347397:E318D;ENSP00000437773:E220D;ENSP00000444673:E318D;ENSP00000318328:E318D	ENSP00000318328:E318D	E	-	3	2	NTRK3	86479586	0.999000	0.42202	1.000000	0.80357	0.965000	0.64279	0.418000	0.21230	0.206000	0.20587	0.563000	0.77884	GAG	.	.		0.602	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding				A	88678582	C	A	88678582	3	1	299	1	0	0	0	0	1	0	0	0	10717	796	28	3	1871	3	NTRK3	15	88678582	Missense_Mutation	SNP	C	TCGA-G3-AAV3-01A-11D-A36X-10	36261863	88678582	13852810	65	43318										
SV2B	9899	hgsc.bcm.edu	37	chr15	91832791	91832792	+	Frame_Shift_Ins	INS	-	-	T													0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	cagtctgctgcttcttcctgINSttttttggcaacagtgagtc							TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr15:91832791_91832792insT	ENST00000394232.1	+	12	2219_2220	c.1749_1750insT	c.(1750-1752)tttfs	p.F584fs	SV2B_ENST00000330276.4_Frame_Shift_Ins_p.F584fs|SV2B_ENST00000545111.2_Frame_Shift_Ins_p.F433fs	NM_014848.4	NP_055663.1	Q7L1I2	SV2B_HUMAN	synaptic vesicle glycoprotein 2B	584					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)			NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(17)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)			GCTTCTTCCTGTTTTTTGGCAA	0.52																																					p.L583fs		Atlas-INDEL	.											.,2	SV2B	98	.	0			c.1749_1750insT						.																																			SO:0001589	frameshift_variant	9899	exon13			.	AB018278	CCDS10370.1, CCDS53972.1	15q26.1	2005-01-10			ENSG00000185518	ENSG00000185518			16874	protein-coding gene	gene with protein product		185861				9872452, 7681585	Standard	NM_014848		Approved	KIAA0735, HsT19680	uc002bqv.3	Q7L1I2	OTTHUMG00000149833	ENST00000394232.1:c.1755dupT	chr15.hg19:g.91832797_91832797dupT	ENSP00000377779:p.Phe584fs	56.0	0.0		66.0	11.0	NM_014848	B4DH30|C6G489|O94840|Q6IAR8	Frame_Shift_Ins	INS	ENST00000394232.1	hg19	CCDS10370.1																																																																																			.	.		0.52	SV2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313494.3	NM_014848		T	91832792	-	T	91832791	7	5	299	1	0	1	1	0	0	0	0	0	15433	1364	48	0	1791	0	SV2B	15	91832791	Frame_Shift_Ins	INS	-	TCGA-G3-AAV3-01A-11D-A36X-10	3154209	91832791	10698601	66	43319										
HAGHL	84264	hgsc.bcm.edu	37	chr16	777615	777615	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	acgtggctgtgcccaagaggGtgagggcaggccgcgggccg	20	11	0	2			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr16:777615G>T	ENST00000341413.4	+	2	386		c.e2+1		HAGHL_ENST00000564537.1_Splice_Site|HAGHL_ENST00000561546.1_Splice_Site|CCDC78_ENST00000293889.6_5'Flank|HAGHL_ENST00000549114.1_Splice_Site|NARFL_ENST00000562862.1_5'Flank|HAGHL_ENST00000564545.1_Splice_Site|HAGHL_ENST00000389703.3_Splice_Site			Q6PII5	HAGHL_HUMAN	hydroxyacylglutathione hydrolase-like								hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			lung(3)	3		Hepatocellular(780;0.00335)				GCCCAAGAGGGTGAGGGCAGG	0.701																																					.	Pancreas(46;538 1326 12403 32360)	Atlas-SNP	.											.	HAGHL	18	.	0			c.105+1G>T						.						39	29	33					16																	777615		2180	4284	6464	SO:0001630	splice_region_variant	84264	exon1			AAGAGGGTGAGGG	AK054841	CCDS32354.1	16p13.3	2008-02-05	2003-11-04						14177	protein-coding gene	gene with protein product			"hydroxyacyl glutathione hydrolase-like"			12477932	Standard	XM_005255629		Approved	MGC2605	uc002cjo.1	Q6PII5		ENST00000341413.4:c.105+1G>T	chr16.hg19:g.777615G>T		82.0	0.0		106.0	29.0	NM_032304	A6NCC4|D3DU64|Q59FX8|Q96BZ3|Q96NR5|Q96S11|Q9BT45	Splice_Site	SNP	ENST00000341413.4	hg19		.	.	.	.	.	.	.	.	.	.	G	13.65	2.299137	0.40694	.	.	ENSG00000103253	ENST00000549114;ENST00000341413;ENST00000389701;ENST00000389703	.	.	.	3.43	0.29	0.15728	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.7686	0.13144	0.1973:0.0:0.6325:0.1702	.	.	.	.	.	-1	.	.	.	+	.	.	HAGHL	717616	0.991000	0.36638	0.180000	0.23079	0.749000	0.42624	-0.007000	0.12810	-0.099000	0.12263	-0.258000	0.10820	.	.	.		0.701	HAGHL-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409607.1	NM_032304	Intron	T	777615	G	T	777615	5	4	299	1	0	0	0	0	0	0	1	0	6955	1275	44	3	108	3	HAGHL	16	777615	Splice_Site	SNP	G	TCGA-G3-AAV3-01A-11D-A36X-10		777615	89577138	67	43320										
BRD7	29117	hgsc.bcm.edu	37	chr16	50357604	50357604	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	ggcacgtggccaaaaactcaTggatgctgcaagagacagtt	12	9	1	1	rs539023856		TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr16:50357604T>C	ENST00000394688.3	-	12	1496	c.1337A>G	c.(1336-1338)cAt>cGt	p.H446R	BRD7_ENST00000394689.2_Missense_Mutation_p.H446R			Q9NPI1	BRD7_HUMAN	bromodomain containing 7	446					cell cycle (GO:0007049)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|prostate(2)|urinary_tract(2)	22		all_cancers(37;0.0127)				CAAAAACTCATGGATGCTGCA	0.453																																					p.H446R		Atlas-SNP	.											.	BRD7	61	.	0			c.A1337G						.						84	72	76					16																	50357604		2198	4300	6498	SO:0001583	missense	29117	exon12			AACTCATGGATGC	AF213969	CCDS10742.1, CCDS54007.1	16q12.1	2008-11-18	2002-01-14		ENSG00000166164	ENSG00000166164			14310	protein-coding gene	gene with protein product			"bromodomain-containing 7"			10526152, 18809673	Standard	NM_013263		Approved	CELTIX1, BP75	uc002ege.2	Q9NPI1	OTTHUMG00000133170	ENST00000394688.3:c.1337A>G	chr16.hg19:g.50357604T>C	ENSP00000378180:p.His446Arg	63.0	0.0		74.0	18.0	NM_013263	Q4VC09|Q8N2L9|Q96KA4|Q9BV48|Q9UH59	Missense_Mutation	SNP	ENST00000394688.3	hg19	CCDS10742.1	.	.	.	.	.	.	.	.	.	.	T	9.394	1.076271	0.20227	.	.	ENSG00000166164	ENST00000394688;ENST00000394689	T;T	0.40225	1.04;1.04	5.53	4.41	0.53225	.	0.429674	0.28057	N	0.016762	T	0.25606	0.0623	N	0.19112	0.55	0.28177	N	0.928349	B;B	0.22909	0.077;0.063	B;B	0.24394	0.053;0.031	T	0.17561	-1.0365	10	0.07325	T	0.83	-27.1784	12.4257	0.55544	0.0:0.0:0.1455:0.8545	.	446;446	Q9NPI1;Q9NPI1-2	BRD7_HUMAN;.	R	446	ENSP00000378180:H446R;ENSP00000378181:H446R	ENSP00000378180:H446R	H	-	2	0	BRD7	48915105	1.000000	0.71417	0.999000	0.59377	0.977000	0.68977	4.725000	0.61979	0.906000	0.36621	0.533000	0.62120	CAT	.	.		0.453	BRD7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256874.3	NM_013263		C	50357604	T	C	50357604	3	2	299	1	0	0	0	0	1	0	0	0	1507	1464	51	2	645	2	BRD7	16	50357604	Missense_Mutation	SNP	T	TCGA-G3-AAV3-01A-11D-A36X-10	49579989	50357604	39997149	68	43321										
CNOT1	23019	hgsc.bcm.edu	37	chr16	58559196	58559196	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	ggatgtgcgcaatggcctgaGtcccgacatagagcaccagt	13	11	0	2			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr16:58559196G>T	ENST00000317147.5	-	46	7003	c.6671C>A	c.(6670-6672)aCt>aAt	p.T2224N	CNOT1_ENST00000569240.1_Missense_Mutation_p.T2219N|CNOT1_ENST00000245138.4_Missense_Mutation_p.T1075N	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	2224					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		AATGGCCTGAGTCCCGACATA	0.483																																					p.T2224N		Atlas-SNP	.											.	CNOT1	359	.	0			c.C6671A						.						222	162	182					16																	58559196		2198	4300	6498	SO:0001583	missense	23019	exon46			GCCTGAGTCCCGA	AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.6671C>A	chr16.hg19:g.58559196G>T	ENSP00000320949:p.Thr2224Asn	41.0	0.0		89.0	21.0	NM_016284	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Missense_Mutation	SNP	ENST00000317147.5	hg19	CCDS10799.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.042376	0.93685	.	.	ENSG00000125107	ENST00000317147;ENST00000422872;ENST00000546037;ENST00000245138	T	0.47528	0.84	5.98	5.98	0.97165	CCR4-Not complex component, Not1, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.60830	0.2299	L	0.60455	1.87	0.80722	D	1	D;D;P	0.56287	0.975;0.958;0.954	P;P;P	0.56700	0.729;0.77;0.804	T	0.50841	-0.8780	10	0.24483	T	0.36	-17.3407	19.4402	0.94817	0.0:0.0:1.0:0.0	.	1075;2224;2219	B5MDN3;A5YKK6;A5YKK6-2	.;CNOT1_HUMAN;.	N	2224;918;229;1075	ENSP00000320949:T2224N	ENSP00000245138:T1075N	T	-	2	0	CNOT1	57116697	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.572000	0.98179	2.838000	0.97847	0.591000	0.81541	ACT	.	.		0.483	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284		T	58559196	G	T	58559196	3	4	299	1	0	0	0	0	1	0	0	0	3619	1029	36	3	475	3	CNOT1	16	58559196	Missense_Mutation	SNP	G	TCGA-G3-AAV3-01A-11D-A36X-10	8201592	58559196	31795557	69	43322										
FTSJD1	55783	hgsc.bcm.edu	37	chr16	71318721	71318721	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	tagtctctagctgatatttaTgaaagaacacacaacattct	5	8	2	3			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr16:71318721T>C	ENST00000338099.5	-	3	1439	c.1103A>G	c.(1102-1104)cAt>cGt	p.H368R	CMTR2_ENST00000434935.2_Missense_Mutation_p.H368R			Q8IYT2	CMTR2_HUMAN	cap methyltransferase 2	368					7-methylguanosine mRNA capping (GO:0006370)|cap2 mRNA methylation (GO:0097310)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)										CTGATATTTATGAAAGAACAC	0.353																																					p.H368R		Atlas-SNP	.											.	FTSJD1	70	.	0			c.A1103G						.						42	45	44					16																	71318721		2197	4299	6496	SO:0001583	missense	55783	exon3			TATTTATGAAAGA	BC035005	CCDS10898.1	16q22.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000180917	ENSG00000180917			25635	protein-coding gene	gene with protein product	"adrift homolog (Drosophila)"		"FtsJ methyltransferase domain containing 1"	FTSJD1		21310715	Standard	NM_018348		Approved	FLJ11171, AFT, MTr2	uc010cga.3	Q8IYT2	OTTHUMG00000137587	ENST00000338099.5:c.1103A>G	chr16.hg19:g.71318721T>C	ENSP00000337512:p.His368Arg	133.0	0.0		142.0	41.0	NM_018348	B2RCD5|D3DWS1|Q8NE77|Q8NFR5|Q9H8Z4|Q9NUS3|Q9NXF5	Missense_Mutation	SNP	ENST00000338099.5	hg19	CCDS10898.1	.	.	.	.	.	.	.	.	.	.	T	12.05	1.821505	0.32237	.	.	ENSG00000180917	ENST00000338099;ENST00000434935	T;T	0.14516	2.5;2.5	5.95	5.95	0.96441	.	0.108387	0.64402	D	0.000005	T	0.28632	0.0709	L	0.60455	1.87	0.54753	D	0.999987	D	0.63880	0.993	P	0.58520	0.84	T	0.01140	-1.1439	10	0.25751	T	0.34	-8.5113	15.5864	0.76485	0.0:0.0:0.0:1.0	.	368	Q8IYT2	FTSJ1_HUMAN	R	368	ENSP00000337512:H368R;ENSP00000411148:H368R	ENSP00000337512:H368R	H	-	2	0	FTSJD1	69876222	1.000000	0.71417	1.000000	0.80357	0.874000	0.50279	7.698000	0.84413	2.279000	0.76181	0.402000	0.26972	CAT	.	.		0.353	CMTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268984.2	NM_018348		C	71318721	T	C	71318721	3	2	299	1	0	0	0	0	1	0	0	0	6098	1464	51	2	1213	2	FTSJD1	16	71318721	Missense_Mutation	SNP	T	TCGA-G3-AAV3-01A-11D-A36X-10	12759525	71318721	19036032	70	43323										
KIAA0664	23277	hgsc.bcm.edu	37	chr17	2604933	2604933	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	gtcacggttttggggctgcaGgggacacagtggccgctccc	16	12	1	0			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr17:2604933G>A	ENST00000570628.2	-	5	709	c.604C>T	c.(604-606)Ctg>Ttg	p.L202L	CLUH_ENST00000435359.1_Silent_p.L202L|CLUH_ENST00000538975.1_Silent_p.L202L			O75153	CLU_HUMAN	clustered mitochondria (cluA/CLU1) homolog	202					intracellular distribution of mitochondria (GO:0048312)	cytoplasm (GO:0005737)											TGGGGCTGCAGGGGACACAGT	0.667																																					p.L202L		Atlas-SNP	.											.	.	.	.	0			c.C604T						.						29	39	36					17																	2604933		2016	4161	6177	SO:0001819	synonymous_variant	23277	exon5			GCTGCAGGGGACA	AB014564	CCDS45572.1	17p13.3	2012-12-18	2012-11-30	2012-11-30	ENSG00000132361	ENSG00000132361			29094	protein-coding gene	gene with protein product			"KIAA0664"	KIAA0664			Standard	XM_005256567		Approved	CLU1	uc002fuy.1	O75153	OTTHUMG00000177575	ENST00000570628.2:c.604C>T	chr17.hg19:g.2604933G>A		39.0	0.0		60.0	9.0	NM_015229	Q6AHY2|Q6P3X7|Q6ZUG8|Q8N4U7|Q9BTA3|Q9H979	Silent	SNP	ENST00000570628.2	hg19	CCDS45572.1																																																																																			.	.		0.667	CLUH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437807.2	NM_015229		A	2604933	G	A	2604933	2	1	299	1	0	0	0	0	0	0	0	1	8198	991	35	3		3	KIAA0664	17	2604933	Silent	SNP	G	TCGA-G3-AAV3-01A-11D-A36X-10		2604933	78590277	71	43324										
ENO3	2027	hgsc.bcm.edu	37	chr17	4859417	4859417	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	gaaggtcaaccagatcggctCggtgaccgaatcgatccagg	13	11	1	2			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr17:4859417C>A	ENST00000323997.6	+	9	1178	c.1046C>A	c.(1045-1047)tCg>tAg	p.S349*	ENO3_ENST00000519584.1_Nonsense_Mutation_p.S306*|ENO3_ENST00000518175.1_Nonsense_Mutation_p.S349*	NM_001976.4|NM_053013.3	NP_001967.3|NP_443739.3	P13929	ENOB_HUMAN	enolase 3 (beta, muscle)	349					aging (GO:0007568)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|response to drug (GO:0042493)|skeletal muscle tissue regeneration (GO:0043403)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|phosphopyruvate hydratase complex (GO:0000015)|plasma membrane (GO:0005886)	magnesium ion binding (GO:0000287)|phosphopyruvate hydratase activity (GO:0004634)			cervix(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)	15						CAGATCGGCTCGGTGACCGAA	0.597																																					p.S349X		Atlas-SNP	.											.	ENO3	36	.	0			c.C1046A						.						82	62	69					17																	4859417		2203	4300	6503	SO:0001587	stop_gained	2027	exon9			TCGGCTCGGTGAC	X16504	CCDS11062.1, CCDS54070.1	17p13.2	2013-09-19	2004-11-22		ENSG00000108515	ENSG00000108515	4.2.1.11		3354	protein-coding gene	gene with protein product		131370	"enolase 3, (beta, muscle)"				Standard	NM_001976		Approved		uc002gab.4	P13929	OTTHUMG00000099394	ENST00000323997.6:c.1046C>A	chr17.hg19:g.4859417C>A	ENSP00000324105:p.Ser349*	46.0	0.0		72.0	11.0	NM_001976	B4DUI6|B4DUM6|D3DTL2|E7ENK8|Q96AE2	Nonsense_Mutation	SNP	ENST00000323997.6	hg19	CCDS11062.1	.	.	.	.	.	.	.	.	.	.	C	33	5.273062	0.95429	.	.	ENSG00000108515	ENST00000323997;ENST00000519584;ENST00000518175	.	.	.	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.1514	17.0153	0.86416	0.0:1.0:0.0:0.0	.	.	.	.	X	349;306;349	.	ENSP00000324105:S349X	S	+	2	0	ENO3	4800141	1.000000	0.71417	0.953000	0.39169	0.633000	0.38033	5.982000	0.70532	2.620000	0.88729	0.460000	0.39030	TCG	.	.		0.597	ENO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216851.2			A	4859417	C	A	4859417	4	1	299	1	0	0	0	0	0	1	0	0	5125	893	31	1	1076	1	ENO3	17	4859417	Nonsense_Mutation	SNP	C	TCGA-G3-AAV3-01A-11D-A36X-10	2254484	4859417	76335793	72	43325										
ZNF207	7756	hgsc.bcm.edu	37	chr17	30687931	30687931	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	gcatacctccattaatgccaGgtgttcctcctctgatgcca	7	14	1	1			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr17:30687931G>A	ENST00000321233.6	+	5	650	c.496G>A	c.(496-498)Ggt>Agt	p.G166S	ZNF207_ENST00000341711.6_Missense_Mutation_p.G67S|ZNF207_ENST00000394670.4_Missense_Mutation_p.G166S|RP11-227G15.3_ENST00000581915.1_RNA|ZNF207_ENST00000394673.2_Missense_Mutation_p.G166S|ZNF207_ENST00000342555.6_Missense_Mutation_p.G169S|ZNF207_ENST00000577908.1_Missense_Mutation_p.G166S	NM_003457.3	NP_003448.1	O43670	ZN207_HUMAN	zinc finger protein 207	166					attachment of spindle microtubules to kinetochore (GO:0008608)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|protein stabilization (GO:0050821)|regulation of chromosome segregation (GO:0051983)|regulation of transcription, DNA-templated (GO:0006355)	kinetochore (GO:0000776)|microtubule (GO:0005874)|nucleus (GO:0005634)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|lung(3)|urinary_tract(2)	10		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)			ATTAATGCCAGGTGTTCCTCC	0.393																																					p.G166S		Atlas-SNP	.											.	ZNF207	32	.	0			c.G496A						.						46	45	45					17																	30687931		2203	4300	6503	SO:0001583	missense	7756	exon5			ATGCCAGGTGTTC	AF046001	CCDS11271.1, CCDS32614.1, CCDS42294.1	17q11.2	2008-07-10			ENSG00000010244	ENSG00000010244		"Zinc fingers, C2H2-type"	12998	protein-coding gene	gene with protein product		603428				9799612	Standard	NM_001098507		Approved		uc002hhj.4	O43670	OTTHUMG00000132810	ENST00000321233.6:c.496G>A	chr17.hg19:g.30687931G>A	ENSP00000322777:p.Gly166Ser	85.0	0.0		105.0	22.0	NM_003457	A8K6Y6|E1P660|E1P661|E1P662|Q53XS9|Q96HW5|Q9BUQ7	Missense_Mutation	SNP	ENST00000321233.6	hg19	CCDS11271.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.294142	0.81025	.	.	ENSG00000010244	ENST00000394670;ENST00000394673;ENST00000394679;ENST00000321233;ENST00000341711;ENST00000342555	T;T;T;T	0.58506	0.76;0.71;0.81;0.33	5.55	5.55	0.83447	.	0.047908	0.85682	D	0.000000	T	0.65688	0.2715	M	0.76574	2.34	0.80722	D	1	P;P;P;P;P	0.45957	0.869;0.869;0.869;0.869;0.869	P;P;P;P;B	0.47015	0.534;0.534;0.534;0.534;0.437	T	0.62676	-0.6804	10	0.20519	T	0.43	.	19.5027	0.95103	0.0:0.0:1.0:0.0	.	166;169;166;166;166	A8MTG3;Q59G94;E1P660;O43670-2;O43670	.;.;.;.;ZN207_HUMAN	S	166;166;169;166;67;166	ENSP00000378165:G166S;ENSP00000378168:G166S;ENSP00000322777:G166S;ENSP00000344913:G67S	ENSP00000322777:G166S	G	+	1	0	ZNF207	27712044	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.805000	0.99149	2.610000	0.88304	0.655000	0.94253	GGT	.	.		0.393	ZNF207-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256251.2			A	30687931	G	A	30687931	3	1	299	1	0	0	0	0	1	0	0	0	17780	1000	35	3	514	3	ZNF207	17	30687931	Missense_Mutation	SNP	G	TCGA-G3-AAV3-01A-11D-A36X-10	25828514	30687931	50507279	73	43326										
AP2B1	163	hgsc.bcm.edu	37	chr17	34001338	34001338	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	gcaatccagtttaacaaaaaTaggtaagcaatctgggtccc	8	9	1	0			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr17:34001338T>A	ENST00000262325.7	+	16	2833	c.2280T>A	c.(2278-2280)aaT>aaA	p.N760K	AP2B1_ENST00000545922.2_3'UTR|AP2B1_ENST00000537622.2_Missense_Mutation_p.N774K|AP2B1_ENST00000312678.8_Missense_Mutation_p.N774K|AP2B1_ENST00000592545.1_Missense_Mutation_p.N736K|AP2B1_ENST00000538556.1_Missense_Mutation_p.N703K|AP2B1_ENST00000589344.1_Missense_Mutation_p.N774K	NM_001282.2	NP_001273.1	P63010	AP2B1_HUMAN	adaptor-related protein complex 2, beta 1 subunit	760					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	clathrin binding (GO:0030276)|protein transporter activity (GO:0008565)			NS(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)		TTAACAAAAATAGGTAAGCAA	0.393																																					p.N774K		Atlas-SNP	.											.	AP2B1	70	.	0			c.T2322A						.						100	96	97					17																	34001338		2203	4300	6503	SO:0001583	missense	163	exon17			CAAAAATAGGTAA	M34175	CCDS32621.1, CCDS32622.1	17q11.2-q12	2010-06-18			ENSG00000006125	ENSG00000006125			563	protein-coding gene	gene with protein product		601025		ADTB2, CLAPB1		8262066, 8595912	Standard	XM_005257937		Approved		uc002hjq.3	P63010		ENST00000262325.7:c.2280T>A	chr17.hg19:g.34001338T>A	ENSP00000262325:p.Asn760Lys	36.0	0.0		54.0	11.0	NM_001030006	A6NJP3|P21851|Q7Z451|Q96J19	Missense_Mutation	SNP	ENST00000262325.7	hg19	CCDS32622.1	.	.	.	.	.	.	.	.	.	.	T	18.42	3.619059	0.66787	.	.	ENSG00000006125	ENST00000262325;ENST00000312678;ENST00000538556;ENST00000537622;ENST00000545922	D;D;D;D	0.90955	-2.76;-2.76;-2.76;-2.76	5.1	1.64	0.23874	Coatomer/clathrin adaptor appendage, Ig-like subdomain (1);Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain (2);Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain (1);	0.000000	0.85682	D	0.000000	D	0.95601	0.8570	M	0.93720	3.45	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.94330	0.7561	10	0.87932	D	0	-14.7963	9.1692	0.37069	0.0:0.3931:0.0:0.6069	.	511;736;760;774	F5GYG9;B4DWG4;P63010;P63010-2	.;.;AP2B1_HUMAN;.	K	760;774;703;774;511	ENSP00000262325:N760K;ENSP00000314414:N774K;ENSP00000440563:N703K;ENSP00000437413:N774K	ENSP00000262325:N760K	N	+	3	2	AP2B1	31025451	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	1.102000	0.31050	0.306000	0.22856	0.460000	0.39030	AAT	.	.		0.393	AP2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448969.1			A	34001338	T	A	34001338	3	1	299	1	0	0	0	0	1	0	0	0	741	1403	49	4	2384	4	AP2B1	17	34001338	Missense_Mutation	SNP	T	TCGA-G3-AAV3-01A-11D-A36X-10	3313407	34001338	47193872	74	43327										
FASN	2194	hgsc.bcm.edu	37	chr17	80043185	80043185	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	ggggctgtcctgcggggtggGccggcggcacaggaagagcg	22	10	0	1			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr17:80043185G>A	ENST00000306749.2	-	24	4434	c.4216C>T	c.(4216-4218)Ccc>Tcc	p.P1406S	FASN_ENST00000579758.1_5'Flank	NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	1406					acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	TGCGGGGTGGGCCGGCGGCAC	0.677																																					p.P1406S	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.C4216T						.						16	21	20					17																	80043185		2180	4274	6454	SO:0001583	missense	2194	exon24			GGGTGGGCCGGCG	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.4216C>T	chr17.hg19:g.80043185G>A	ENSP00000304592:p.Pro1406Ser	132.0	0.0		182.0	54.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	hg19	CCDS11801.1	.	.	.	.	.	.	.	.	.	.	G	1.387	-0.581722	0.03854	.	.	ENSG00000169710	ENST00000306749;ENST00000545909	T	0.25085	1.82	4.49	3.48	0.39840	.	0.673781	0.14699	N	0.303703	T	0.17195	0.0413	N	0.22421	0.69	0.23309	N	0.997937	B	0.21688	0.059	B	0.21546	0.035	T	0.18840	-1.0324	10	0.09338	T	0.73	-5.3865	14.3699	0.66833	0.0:0.1497:0.8503:0.0	.	1406	P49327	FAS_HUMAN	S	1406;371	ENSP00000304592:P1406S	ENSP00000304592:P1406S	P	-	1	0	FASN	77636474	0.816000	0.29132	0.615000	0.29064	0.126000	0.20510	2.536000	0.45693	0.933000	0.37291	0.462000	0.41574	CCC	.	.		0.677	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		A	80043185	G	A	80043185	3	1	299	1	0	0	0	0	1	0	0	0	5691	1203	42	3	3399	3	FASN	17	80043185	Missense_Mutation	SNP	G	TCGA-G3-AAV3-01A-11D-A36X-10	46041847	80043185	1152025	75	43328										
SMCHD1	23347	hgsc.bcm.edu	37	chr18	2747624	2747624	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	caacatgttaaaataagtctTacaaaagctagcaatttaaa	4	6	1	0			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr18:2747624T>A	ENST00000320876.6	+	30	4244	c.3906T>A	c.(3904-3906)ctT>ctA	p.L1302L	SMCHD1_ENST00000261598.8_Silent_p.L1302L|RP11-703M24.5_ENST00000583546.1_RNA	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	1302					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						AAATAAGTCTTACAAAAGCTA	0.313																																					p.L1302L		Atlas-SNP	.											.	SMCHD1	88	.	0			c.T3906A						.						60	55	57					18																	2747624		1800	4060	5860	SO:0001819	synonymous_variant	23347	exon30			AAGTCTTACAAAA	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.3906T>A	chr18.hg19:g.2747624T>A		193.0	0.0		265.0	54.0	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Silent	SNP	ENST00000320876.6	hg19	CCDS45822.1																																																																																			.	.		0.313	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			A	2747624	T	A	2747624	2	1	299	1	0	0	0	0	0	0	0	1	14803	1741	61	4		4	SMCHD1	18	2747624	Silent	SNP	T	TCGA-G3-AAV3-01A-11D-A36X-10		2747624	75329624	76	43329										
OSBPL1A	114876	hgsc.bcm.edu	37	chr18	21860862	21860862	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	caaagctacacaagtttctcTagaagcttctgagacaactt	6	10	2	2			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr18:21860862T>A	ENST00000319481.3	-	15	1431	c.1225A>T	c.(1225-1227)Aga>Tga	p.R409*	OSBPL1A_ENST00000357041.4_Nonsense_Mutation_p.R27*	NM_080597.3	NP_542164.2	Q9BXW6	OSBL1_HUMAN	oxysterol binding protein-like 1A	409					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	cholesterol binding (GO:0015485)|phospholipid binding (GO:0005543)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)					CAAGTTTCTCTAGAAGCTTCT	0.328																																					p.R409X		Atlas-SNP	.											.	OSBPL1A	94	.	0			c.A1225T						.						78	78	78					18																	21860862		2203	4300	6503	SO:0001587	stop_gained	114876	exon15			TTTCTCTAGAAGC	AF392449, AF274714	CCDS11884.1, CCDS11885.1, CCDS56056.1	18q11.2	2014-06-03	2014-06-03	2014-06-03	ENSG00000141447	ENSG00000141447		"Oxysterol binding proteins", "Ankyrin repeat domain containing"	16398	protein-coding gene	gene with protein product		606730	"oxysterol binding protein-like 1B"	OSBPL1B		11279184, 10588946	Standard	NM_080597		Approved	ORP-1, ORP1	uc002kve.3	Q9BXW6	OTTHUMG00000131944	ENST00000319481.3:c.1225A>T	chr18.hg19:g.21860862T>A	ENSP00000320291:p.Arg409*	35.0	0.0		38.0	6.0	NM_080597	B7Z7D3|Q9BZF5|Q9NW87	Nonsense_Mutation	SNP	ENST00000319481.3	hg19	CCDS11884.1	.	.	.	.	.	.	.	.	.	.	T	37	6.590701	0.97688	.	.	ENSG00000141447	ENST00000319481;ENST00000357041	.	.	.	5.71	1.39	0.22231	.	0.263488	0.43110	D	0.000619	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.7353	6.906	0.24309	0.0:0.0856:0.2807:0.6337	.	.	.	.	X	409;27	.	ENSP00000320291:R409X	R	-	1	2	OSBPL1A	20114860	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	0.995000	0.29706	0.382000	0.24878	0.402000	0.26972	AGA	.	.		0.328	OSBPL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254902.1	NM_080597		A	21860862	T	A	21860862	4	1	299	1	0	0	0	0	0	1	0	0	11286	1530	53	4	1683	4	OSBPL1A	18	21860862	Nonsense_Mutation	SNP	T	TCGA-G3-AAV3-01A-11D-A36X-10	19113238	21860862	56216386	77	43330										
CREB3L3	84699	hgsc.bcm.edu	37	chr19	4171378	4171378	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	actctgccgctgtctccaccAggtcctgttgctgtcctttg	9	15	2	0			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr19:4171378A>T	ENST00000078445.2	+	9	1122		c.e9-1		CREB3L3_ENST00000252587.3_Splice_Site|CREB3L3_ENST00000602257.1_Splice_Site|CREB3L3_ENST00000595923.1_Splice_Site|CREB3L3_ENST00000602147.1_Splice_Site	NM_001271995.1|NM_001271996.1|NM_032607.1	NP_001258924.1|NP_001258925.1|NP_115996.1	Q68CJ9	CR3L3_HUMAN	cAMP responsive element binding protein 3-like 3						positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|urinary_tract(3)	24				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0232)|STAD - Stomach adenocarcinoma(1328;0.18)		TGTCTCCACCAGGTCCTGTTG	0.607																																					.		Atlas-SNP	.											.	CREB3L3	53	.	0			c.973-2A>T						.						91	79	83					19																	4171378		2203	4300	6503	SO:0001630	splice_region_variant	84699	exon9			TCCACCAGGTCCT		CCDS12121.1, CCDS62498.1, CCDS62499.1, CCDS62500.1	19p13.3	2013-01-10				ENSG00000060566		"basic leucine zipper proteins"	18855	protein-coding gene	gene with protein product		611998				11353085	Standard	NM_032607		Approved	CREB-H	uc002lzl.4	Q68CJ9		ENST00000078445.2:c.976-1A>T	chr19.hg19:g.4171378A>T		34.0	0.0		76.0	27.0	NM_001271995	B2R7S6|B7ZL69|M0QYW7|Q6ZMC5|Q96TB9	Splice_Site	SNP	ENST00000078445.2	hg19	CCDS12121.1	.	.	.	.	.	.	.	.	.	.	A	13.77	2.335768	0.41398	.	.	ENSG00000060566	ENST00000078445;ENST00000381943;ENST00000252587	.	.	.	4.58	4.58	0.56647	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.8958	0.52656	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CREB3L3	4122378	1.000000	0.71417	0.988000	0.46212	0.273000	0.26683	6.155000	0.71833	1.700000	0.51204	0.459000	0.35465	.	.	.		0.607	CREB3L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457922.1	NM_032607	Intron	T	4171378	A	T	4171378	5	4	299	1	0	0	0	0	0	0	1	0	3860	202	7	4	1008	4	CREB3L3	19	4171378	Splice_Site	SNP	A	TCGA-G3-AAV3-01A-11D-A36X-10		4171378	54957605	78	43331										
TUBB4	10382	hgsc.bcm.edu	37	chr19	6496156	6496156	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	tcggcctccttccggactacGtccaggacagcgtccaccag	10	17	0	0			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr19:6496156G>A	ENST00000264071.2	-	4	725	c.354C>T	c.(352-354)gaC>gaT	p.D118D	TUBB4A_ENST00000540257.1_Silent_p.D118D|TUBB4A_ENST00000601152.1_Missense_Mutation_p.T93M|CTD-2396E7.10_ENST00000596027.1_RNA|TUBB4A_ENST00000598006.1_Missense_Mutation_p.T104M|CTD-2396E7.9_ENST00000599292.1_RNA|TUBB4A_ENST00000596926.1_3'UTR			P04350	TBB4A_HUMAN	tubulin, beta 4A class IVa	118					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|internode region of axon (GO:0033269)|microtubule (GO:0005874)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)										TCCGGACTACGTCCAGGACAG	0.667																																					p.D118D		Atlas-SNP	.											TUBB4,NS,carcinoma,0,1	.	.	.	0			c.C354T						.						73	67	69					19																	6496156		2203	4300	6503	SO:0001819	synonymous_variant	10382	exon4			GACTACGTCCAGG	AK075307	CCDS12168.1	19p13.3	2014-02-05	2011-10-11	2011-10-10	ENSG00000104833	ENSG00000104833		"Tubulins"	20774	protein-coding gene	gene with protein product	"class IVa beta-tubulin"	602662	"tubulin, beta 4", "tubulin, beta 4 class IVa", "dystonia 4, torsion (autosomal dominant)"	TUBB4, DYT4		6865944, 6462917, 23595291	Standard	NM_001289123		Approved	beta-5	uc002mfg.1	P04350		ENST00000264071.2:c.354C>T	chr19.hg19:g.6496156G>A		52.0	0.0		72.0	15.0	NM_006087	B3KQP4|Q969E5	Silent	SNP	ENST00000264071.2	hg19	CCDS12168.1																																																																																			.	.		0.667	TUBB4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457841.1	NM_006087		A	6496156	G	A	6496156	2	1	299	1	0	0	0	0	0	0	0	1	16773	1136	40	1		1	TUBB4	19	6496156	Silent	SNP	G	TCGA-G3-AAV3-01A-11D-A36X-10	2324778	6496156	52632827	79	43332										
NDUFA7	4701	hgsc.bcm.edu	37	chr19	8386229	8386229	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	gcagccgctggatgagacggGtggcggacgccatcttccgt	16	12	1	1			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr19:8386229G>A	ENST00000301457.2	-	1	51	c.14C>T	c.(13-15)aCc>aTc	p.T5I	RPS28_ENST00000600659.2_5'Flank|NDUFA7_ENST00000598884.1_Missense_Mutation_p.T5I	NM_005001.3	NP_004992.2	O95182	NDUA7_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 7, 14.5kDa	5					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			NS(1)|central_nervous_system(1)|lung(2)|ovary(1)	5						GATGAGACGGGTGGCGGACGC	0.716																																					p.T5I		Atlas-SNP	.											.	NDUFA7	11	.	0			c.C14T						.						6	10	9					19																	8386229		1896	4050	5946	SO:0001583	missense	4701	exon1			AGACGGGTGGCGG	AF050637	CCDS42492.1	19p13.2	2013-05-14	2002-08-29		ENSG00000267855	ENSG00000267855		"Mitochondrial respiratory chain complex / Complex I"	7691	protein-coding gene	gene with protein product	"complex I B14.5a subunit"	602139	"NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 7 (14.5kD, B14.5a)"			9763676	Standard	NM_005001		Approved	B14.5a	uc002mjm.2	O95182	OTTHUMG00000182459	ENST00000301457.2:c.14C>T	chr19.hg19:g.8386229G>A	ENSP00000301457:p.Thr5Ile	58.0	0.0		90.0	16.0	NM_005001		Missense_Mutation	SNP	ENST00000301457.2	hg19	CCDS42492.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.421119	0.83559	.	.	ENSG00000167774	ENST00000301457	T	0.52295	0.67	5.54	4.51	0.55191	.	0.000000	0.85682	D	0.000000	T	0.68146	0.2969	M	0.79258	2.445	0.52099	D	0.999945	D	0.89917	1.0	D	0.83275	0.996	T	0.72833	-0.4173	10	0.72032	D	0.01	-19.0894	13.0983	0.59206	0.0768:0.0:0.9231:0.0	.	5	O95182	NDUA7_HUMAN	I	5	ENSP00000301457:T5I	ENSP00000301457:T5I	T	-	2	0	NDUFA7	8292229	1.000000	0.71417	0.101000	0.21167	0.724000	0.41520	7.476000	0.81055	1.584000	0.49913	0.655000	0.94253	ACC	.	.		0.716	NDUFA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461373.1	NM_005001		A	8386229	G	A	8386229	3	1	299	1	0	0	0	0	1	0	0	0	10279	1261	44	3	343	3	NDUFA7	19	8386229	Missense_Mutation	SNP	G	TCGA-G3-AAV3-01A-11D-A36X-10	1890073	8386229	50742754	80	43333										
CEACAM18	729767	hgsc.bcm.edu	37	chr19	51983676	51983676	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	agggatatcggactgtcgtgGccctggataaggtccctgag	15	9	0	1			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr19:51983676G>A	ENST00000396477.4	+	2	163	c.142G>A	c.(142-144)Gcc>Acc	p.A48T	CEACAM18_ENST00000451626.1_Missense_Mutation_p.A109T	NM_001278392.1	NP_001265321.1	A8MTB9	CEA18_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 18	48										breast(1)|endometrium(4)|large_intestine(3)|lung(8)|skin(1)	17		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		GACTGTCGTGGCCCTGGATAA	0.557																																					p.A109T		Atlas-SNP	.											CEACAM18_ENST00000451626,NS,carcinoma,0,2	CEACAM18	96	.	0			c.G325A						.						54	52	52					19																	51983676		2002	4156	6158	SO:0001583	missense	729767	exon3			GTCGTGGCCCTGG			19q13.41	2013-01-29				ENSG00000213822		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	31949	protein-coding gene	gene with protein product							Standard	NM_001278392		Approved		uc002pwv.1	A8MTB9		ENST00000396477.4:c.142G>A	chr19.hg19:g.51983676G>A	ENSP00000379738:p.Ala48Thr	103.0	0.0		126.0	20.0	NM_001080405	C9JN24	Missense_Mutation	SNP	ENST00000396477.4	hg19		.	.	.	.	.	.	.	.	.	.	.	4.535	0.099356	0.08681	.	.	ENSG00000213822	ENST00000451626;ENST00000451086;ENST00000396477	T	0.04654	3.58	2.79	-3.67	0.04476	.	.	.	.	.	T	0.02012	0.0063	N	0.05383	-0.06	0.09310	N	1	B	0.20988	0.05	B	0.18871	0.023	T	0.48127	-0.9062	9	0.18276	T	0.48	-0.8791	4.452	0.11624	0.5625:0.1896:0.2479:0.0	.	109	A8MTB9	CEA18_HUMAN	T	109;48;48	ENSP00000402203:A109T	ENSP00000379738:A48T	A	+	1	0	CEACAM18	56675488	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.692000	0.05127	-0.752000	0.04728	0.650000	0.86243	GCC	.	.		0.557	CEACAM18-001	PUTATIVE	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000323114.2			A	51983676	G	A	51983676	3	1	299	1	0	0	0	0	1	0	0	0	3191	1203	42	3	335	3	CEACAM18	19	51983676	Missense_Mutation	SNP	G	TCGA-G3-AAV3-01A-11D-A36X-10	43597447	51983676	7145307	81	43334										
NPEPL1	79716	hgsc.bcm.edu	37	chr20	57289000	57289000	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	ccacagggaagtaccacgccGcggtgctcaccaacagcgct	11	16	1	0			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr20:57289000G>A	ENST00000356091.6	+	10	1441	c.1153G>A	c.(1153-1155)Gcg>Acg	p.A385T	STX16-NPEPL1_ENST00000530122.1_3'UTR|RP11-261P9.4_ENST00000530479.1_RNA|NPEPL1_ENST00000525967.1_Missense_Mutation_p.A357T|NPEPL1_ENST00000525817.1_Missense_Mutation_p.A337T	NM_024663.3	NP_078939.3	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	385						cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)	14	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;2.88e-09)|Colorectal(105;0.109)			GTACCACGCCGCGGTGCTCAC	0.667																																					p.A385T		Atlas-SNP	.											.	NPEPL1	36	.	0			c.G1153A						.						14	19	18					20																	57289000		1801	3715	5516	SO:0001583	missense	79716	exon10			CACGCCGCGGTGC	AK021645	CCDS46621.1, CCDS56200.1, CCDS56201.1	20q13.32	2008-07-02			ENSG00000215440	ENSG00000215440			16244	protein-coding gene	gene with protein product						14702039	Standard	NM_001204872		Approved	FLJ11583, bA261P9.2	uc010zzs.1	Q8NDH3	OTTHUMG00000033060	ENST00000356091.6:c.1153G>A	chr20.hg19:g.57289000G>A	ENSP00000348395:p.Ala385Thr	42.0	0.0		48.0	10.0	NM_024663	A6NGZ0|B4DMW7|B7ZBN0|E9PN47|G5EA34|Q53G37|Q5W083|Q8TF28|Q8WUI2|Q9H1T6|Q9HAI5	Missense_Mutation	SNP	ENST00000356091.6	hg19	CCDS46621.1	.	.	.	.	.	.	.	.	.	.	G	34	5.410985	0.96072	.	.	ENSG00000215440	ENST00000525967;ENST00000525817;ENST00000356091	T;T;T	0.50001	0.76;0.76;0.76	5.67	5.67	0.87782	Peptidase M17, leucyl aminopeptidase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.78444	0.4284	H	0.95816	3.725	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79784	0.993;0.983;0.989	D	0.84747	0.0754	10	0.87932	D	0	-26.7612	16.9188	0.86158	0.0:0.0:1.0:0.0	.	385;337;357	Q8NDH3;G5EA34;E9PN47	PEPL1_HUMAN;.;.	T	357;337;385	ENSP00000434810:A357T;ENSP00000437112:A337T;ENSP00000348395:A385T	ENSP00000348395:A385T	A	+	1	0	NPEPL1	56722407	1.000000	0.71417	0.136000	0.22124	0.983000	0.72400	8.981000	0.93465	2.666000	0.90696	0.561000	0.74099	GCG	.	.		0.667	NPEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080402.6	NM_024663		A	57289000	G	A	57289000	3	1	299	1	0	0	0	0	1	0	0	0	10583	1087	38	1	1037	1	NPEPL1	20	57289000	Missense_Mutation	SNP	G	TCGA-G3-AAV3-01A-11D-A36X-10		57289000	5736520	82	43335										
COL20A1	57642	hgsc.bcm.edu	37	chr20	61945549	61945549	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	gctgtgtctgccacgggccaGacaggtgagtgggcaccaag	16	11	1	2			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr20:61945549G>T	ENST00000358894.6	+	19	2584	c.2484G>T	c.(2482-2484)caG>caT	p.Q828H	COL20A1_ENST00000326996.6_Missense_Mutation_p.Q828H|COL20A1_ENST00000435874.1_Missense_Mutation_p.Q835H|COL20A1_ENST00000422202.1_Missense_Mutation_p.Q835H	NM_020882.2	NP_065933.2	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1	828	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)				NS(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(21)|ovary(1)|prostate(3)|urinary_tract(2)	36	all_cancers(38;1.39e-10)					CCACGGGCCAGACAGGTGAGT	0.642																																					p.Q828H		Atlas-SNP	.											.	COL20A1	137	.	0			c.G2484T						.						34	41	38					20																	61945549		2068	4175	6243	SO:0001583	missense	57642	exon19			GGGCCAGACAGGT	BC043183	CCDS46628.1	20q13.33	2014-02-12			ENSG00000101203	ENSG00000101203		"Collagens", "Fibronectin type III domain containing"	14670	protein-coding gene	gene with protein product						10819331	Standard	NM_020882		Approved	KIAA1510	uc011aau.2	Q9P218	OTTHUMG00000032964	ENST00000358894.6:c.2484G>T	chr20.hg19:g.61945549G>T	ENSP00000351767:p.Gln828His	114.0	0.0		180.0	12.0	NM_020882	Q4VXQ4|Q6PI59|Q8WUT2|Q96CY9|Q9BQU6|Q9BQU7	Missense_Mutation	SNP	ENST00000358894.6	hg19	CCDS46628.1	.	.	.	.	.	.	.	.	.	.	G	4.320	0.058639	0.08339	.	.	ENSG00000101203	ENST00000358894;ENST00000326996;ENST00000435874;ENST00000422202	D;D;D;D	0.87334	-2.23;-2.24;-2.21;-2.21	3.57	0.261	0.15592	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.456078	0.20612	U	0.088942	T	0.72526	0.3471	N	0.19112	0.55	0.09310	N	1	B;B	0.15473	0.013;0.008	B;B	0.13407	0.009;0.004	T	0.58612	-0.7606	10	0.41790	T	0.15	.	3.8302	0.08871	0.2514:0.2142:0.5344:0.0	.	835;828	Q9P218-2;Q9P218	.;COKA1_HUMAN	H	828;828;835;835	ENSP00000351767:Q828H;ENSP00000323077:Q828H;ENSP00000408690:Q835H;ENSP00000414753:Q835H	ENSP00000323077:Q828H	Q	+	3	2	COL20A1	61415994	0.039000	0.19947	0.010000	0.14722	0.138000	0.21146	0.169000	0.16641	-0.130000	0.11599	0.306000	0.20318	CAG	.	.		0.642	COL20A1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000144595.2	NM_020882		T	61945549	G	T	61945549	3	4	299	1	0	0	0	0	1	0	0	0	3681	933	33	3	2554	3	COL20A1	20	61945549	Missense_Mutation	SNP	G	TCGA-G3-AAV3-01A-11D-A36X-10	4656549	61945549	1079971	83	43336										
BACH1	571	hgsc.bcm.edu	37	chr21	30699119	30699119	+	Frame_Shift_Del	DEL	T	T	-													0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	tggactttattctttgtctcTtttacacacatatgaccaat							TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chr21:30699119delT	ENST00000399921.1	+	3	1217	c.974delT	c.(973-975)cttfs	p.L326fs	BACH1_ENST00000286800.3_Frame_Shift_Del_p.L326fs	NM_206866.1	NP_996749.1	Q9BX63	FANCJ_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 1	320	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				DNA damage checkpoint (GO:0000077)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|urinary_tract(2)	27						TCTTTGTCTCTTTTACACACA	0.403																																					p.L325fs		Atlas-INDEL	.											.	BACH1	66	.	0			c.973delC						.						119	123	121					21																	30699119		2203	4300	6503	SO:0001589	frameshift_variant	571	exon3			.	AF026200	CCDS13585.1	21q22.1	2013-01-10			ENSG00000156273	ENSG00000156273		"BTB/POZ domain containing", "basic leucine zipper proteins"	935	protein-coding gene	gene with protein product		602751				9544839, 9479503	Standard	NR_027655		Approved	BACH-1, BTBD24	uc002ynj.3	O14867	OTTHUMG00000078878	ENST00000399921.1:c.974delT	chr21.hg19:g.30699119delT	ENSP00000382805:p.Leu326fs	70.0	0.0		65.0	22.0	NM_206866	Q3MJE2|Q8NCI5	Frame_Shift_Del	DEL	ENST00000399921.1	hg19	CCDS13585.1																																																																																			.	.		0.403	BACH1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171974.1	NM_206866		-	30699119	T	-	30699119	7	5	299	1	0	1	0	1	0	0	0	0	1283	1609	56	0	980	0	BACH1	21	30699119	Frame_Shift_Del	DEL	T	TCGA-G3-AAV3-01A-11D-A36X-10		30699119	17430776	84	43337										
MAGEE1	57692	hgsc.bcm.edu	37	chrX	75649655	75649655	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	gtaaccaaggcctccgtggaCtcagattctgagggtcctaa	11	11	2	2			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chrX:75649655C>A	ENST00000361470.2	+	1	1610	c.1332C>A	c.(1330-1332)gaC>gaA	p.D444E		NM_020932.2	NP_065983.1	Q9HCI5	MAGE1_HUMAN	melanoma antigen family E, 1	444						dendrite (GO:0030425)|dystrophin-associated glycoprotein complex (GO:0016010)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	51						CCTCCGTGGACTCAGATTCTG	0.527																																					p.D444E		Atlas-SNP	.											.	MAGEE1	236	.	0			c.C1332A						.						39	34	36					X																	75649655		2203	4300	6503	SO:0001583	missense	57692	exon1			CGTGGACTCAGAT	AF490507	CCDS14433.1	Xq13	2008-02-05			ENSG00000198934	ENSG00000198934			24934	protein-coding gene	gene with protein product		300759				14623885	Standard	NM_020932		Approved	KIAA1587, DAMAGE	uc004ecm.2	Q9HCI5	OTTHUMG00000021879	ENST00000361470.2:c.1332C>A	chrX.hg19:g.75649655C>A	ENSP00000354912:p.Asp444Glu	61.0	0.0		79.0	21.0	NM_020932	Q5JXC7|Q86TG0|Q8TD92|Q9H216	Missense_Mutation	SNP	ENST00000361470.2	hg19	CCDS14433.1	.	.	.	.	.	.	.	.	.	.	C	7.881	0.730176	0.15507	.	.	ENSG00000198934	ENST00000361470	T	0.03124	4.04	1.5	1.5	0.22942	.	.	.	.	.	T	0.02083	0.0065	N	0.14661	0.345	0.09310	N	1	B	0.23854	0.092	B	0.10450	0.005	T	0.48843	-0.8999	9	0.13108	T	0.6	.	6.6181	0.22788	0.0:1.0:0.0:0.0	.	444	Q9HCI5	MAGE1_HUMAN	E	444	ENSP00000354912:D444E	ENSP00000354912:D444E	D	+	3	2	MAGEE1	75566059	0.000000	0.05858	0.024000	0.17045	0.053000	0.15095	0.022000	0.13511	0.651000	0.30788	0.538000	0.68166	GAC	.	.		0.527	MAGEE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057298.1	NM_020932		A	75649655	C	A	75649655	3	1	299	1	0	0	0	0	1	0	0	0	9194	564	20	3	1334	3	MAGEE1	23	75649655	Missense_Mutation	SNP	C	TCGA-G3-AAV3-01A-11D-A36X-10		75649655	79620905	85	43338										
GRIA3	2892	hgsc.bcm.edu	37	chrX	122387320	122387320	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0813953488372093	7	1	1.6199063876652	4.23159219634991	0.88863436123348	1	1	0	atccagatgcgcccagccttGaagggcgctattctgagtct	11	12	2	3			TCGA-G3-AAV3-01A-11D-A36X-10	TCGA-G3-AAV3-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f5dc334-4cc1-4093-8189-205203b4b459	5594728a-7cd4-4fd6-862e-6701512130e3	g.chrX:122387320G>A	ENST00000371251.1	+	3	487	c.435G>A	c.(433-435)ttG>ttA	p.L145L	GRIA3_ENST00000479118.1_3'UTR|GRIA3_ENST00000264357.5_Silent_p.L145L|GRIA3_ENST00000541091.1_Silent_p.L129L|GRIA3_ENST00000371256.5_Silent_p.L145L|GRIA3_ENST00000542149.1_Silent_p.L145L			P42263	GRIA3_HUMAN	glutamate receptor, ionotropic, AMPA 3	145					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)			breast(2)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|pancreas(2)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	57					Lithium(DB01356)	GCCCAGCCTTGAAGGGCGCTA	0.532																																					p.L145L		Atlas-SNP	.											.	GRIA3	386	.	0			c.G435A						.						107	91	96					X																	122387320		2203	4300	6503	SO:0001819	synonymous_variant	2892	exon3			AGCCTTGAAGGGC	U10301	CCDS14604.1, CCDS14605.1, CCDS76017.1	Xq25	2012-08-29	2012-02-03		ENSG00000125675	ENSG00000125675		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4573	protein-coding gene	gene with protein product		305915	"glutamate receptor, ionotrophic, AMPA 3"	GLUR3		1319477, 10644433	Standard	NM_007325		Approved	GluA3, GLURC, MRX94	uc004etr.4	P42263	OTTHUMG00000022685	ENST00000371251.1:c.435G>A	chrX.hg19:g.122387320G>A		65.0	0.0		65.0	21.0	NM_000828	D3DTF1|Q4VXD5|Q4VXD6|Q9HDA0|Q9HDA1|Q9HDA2|Q9P0H1	Silent	SNP	ENST00000371251.1	hg19	CCDS14604.1																																																																																			.	.		0.532	GRIA3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058854.1	NM_000828		A	122387320	G	A	122387320	2	1	299	1	0	0	0	0	0	0	0	1	6778	1281	45	3		3	GRIA3	23	122387320	Silent	SNP	G	TCGA-G3-AAV3-01A-11D-A36X-10	46737665	122387320	32883240	86	43339										
EXTL1	2134	hgsc.bcm.edu	37	chr1	26349593	26349593	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	tgcagctcaatgcctctgcaAtggaacaggggcaggaacca	12	11	2	0			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr1:26349593A>G	ENST00000374280.3	+	1	1323	c.456A>G	c.(454-456)caA>caG	p.Q152Q		NM_004455.2	NP_004446.2	Q92935	EXTL1_HUMAN	exostosin-like glycosyltransferase 1	152					protein glycosylation (GO:0006486)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|stomach(1)|urinary_tract(1)	23		Colorectal(325;3.46e-05)|Lung NSC(340;6.18e-05)|all_lung(284;9.43e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00594)|READ - Rectum adenocarcinoma(331;0.0649)		TGCCTCTGCAATGGAACAGGG	0.647																																					p.Q152Q		Atlas-SNP	.											.	EXTL1	61	.	0			c.A456G						.						55	54	54					1																	26349593		2203	4300	6503	SO:0001819	synonymous_variant	2134	exon1			TCTGCAATGGAAC	U67191	CCDS271.1	1p36.1	2013-03-01	2013-03-01		ENSG00000158008	ENSG00000158008	2.4.1.224	"Exostosin glycosyltransferase family"	3515	protein-coding gene	gene with protein product	"glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase", "alpha-N-acetylglucosaminyltransferase II", "glucuronyl-N-acetylglucosaminylproteoglycan alpha-1,4-N- acetylglucosaminyltransferase", "exostosin-L"	601738	"exostoses (multiple)-like 1"			9037597	Standard	NM_004455		Approved	EXTL, MGC70794	uc001blf.3	Q92935	OTTHUMG00000007509	ENST00000374280.3:c.456A>G	chr1.hg19:g.26349593A>G		132.0	0.0		94.0	36.0	NM_004455	Q6GSC1	Silent	SNP	ENST00000374280.3	hg19	CCDS271.1																																																																																			.	.		0.647	EXTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019749.1	NM_004455		G	26349593	A	G	26349593	2	3	300	1	0	0	0	0	0	0	0	1	5327	98	4	2		2	EXTL1	1	26349593	Silent	SNP	A	TCGA-G3-AAV4-01A-11D-A382-10		26349593	222901028	1	43340										
HECTD3	79654	hgsc.bcm.edu	37	chr1	45469948	45469948	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	cgcagagcatccacagtgacCtctggatccccacacacttt	7	16	1	2			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr1:45469948C>T	ENST00000372172.4	-	17	2315	c.2244G>A	c.(2242-2244)gaG>gaA	p.E748E	HECTD3_ENST00000486132.1_5'UTR|HECTD3_ENST00000372168.3_Silent_p.E358E	NM_024602.5	NP_078878.3	Q5T447	HECD3_HUMAN	HECT domain containing E3 ubiquitin protein ligase 3	748	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|stomach(1)	28	Acute lymphoblastic leukemia(166;0.155)					CCACAGTGACCTCTGGATCCC	0.602																																					p.E748E		Atlas-SNP	.											.	HECTD3	158	.	0			c.G2244A						.						96	99	98					1																	45469948		2128	4262	6390	SO:0001819	synonymous_variant	79654	exon17			AGTGACCTCTGGA	BC019105	CCDS41318.1	1p34.1	2012-02-23	2012-02-23		ENSG00000126107	ENSG00000126107			26117	protein-coding gene	gene with protein product			"HECT domain containing 3"			12477932	Standard	NM_024602		Approved	FLJ21156	uc009vxk.3	Q5T447	OTTHUMG00000008587	ENST00000372172.4:c.2244G>A	chr1.hg19:g.45469948C>T		103.0	0.0		79.0	37.0	NM_024602	B3KPV7|B3KRH4|Q5T448|Q9H783	Silent	SNP	ENST00000372172.4	hg19	CCDS41318.1																																																																																			.	.		0.602	HECTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023734.1	NM_024602		T	45469948	C	T	45469948	2	4	300	1	0	0	0	0	0	0	0	1	7050	680	24	3		3	HECTD3	1	45469948	Silent	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	19120355	45469948	203780673	2	43341										
TMEM48	55706	hgsc.bcm.edu	37	chr1	54238115	54238115	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	acaaggcttcctgaaatccgGggtggtttactggaagcatg	13	8	0	1			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr1:54238115G>A	ENST00000371429.3	-	17	2446	c.1848C>T	c.(1846-1848)ccC>ccT	p.P616P	NDC1_ENST00000540001.1_3'UTR|NDC1_ENST00000234725.8_Silent_p.P501P|NDC1_ENST00000537333.1_Silent_p.P281P|SNORA58_ENST00000364133.1_RNA	NM_001168551.1|NM_018087.4	NP_001162023.1|NP_060557.3	Q9BTX1	NDC1_HUMAN	NDC1 transmembrane nucleoporin	616					mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore distribution (GO:0031081)|protein transport (GO:0015031)|spermatogenesis (GO:0007283)|synapsis (GO:0007129)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)										CTGAAATCCGGGGTGGTTTAC	0.388																																					p.P616P		Atlas-SNP	.											.	TMEM48	47	.	0			c.C1848T						.						116	115	116					1																	54238115		2203	4300	6503	SO:0001819	synonymous_variant	55706	exon17			AATCCGGGGTGGT	AL354613	CCDS583.1	1p32.3	2014-01-28	2013-05-23	2013-05-23	ENSG00000058804	ENSG00000058804			25525	protein-coding gene	gene with protein product	"nuclear division cycle 1 homolog (S. cerevisiae)"	610115	"transmembrane protein 48"	TMEM48		16779818, 12958361	Standard	NR_033142		Approved	FLJ10407, NET3		Q9BTX1	OTTHUMG00000008073	ENST00000371429.3:c.1848C>T	chr1.hg19:g.54238115G>A		157.0	0.0		155.0	58.0	NM_018087	B4DHA3|B4DQQ5|G3XA81|Q8NB76|Q9H9T6|Q9NSG3|Q9NSG4|Q9NVZ7	Silent	SNP	ENST00000371429.3	hg19	CCDS583.1																																																																																			.	.		0.388	NDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022101.1	NM_018087		A	54238115	G	A	54238115	2	1	300	1	0	0	0	0	0	0	0	1	16187	1219	43	3		3	TMEM48	1	54238115	Silent	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10	8768167	54238115	195012506	3	43342										
PKN2	5586	hgsc.bcm.edu	37	chr1	89251817	89251817	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	tgctgttttgaagctcgataAtactgtggttggccaaacta	10	7	0	1			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr1:89251817A>G	ENST00000370521.3	+	8	1561	c.1202A>G	c.(1201-1203)aAt>aGt	p.N401S	PKN2_ENST00000370505.3_Missense_Mutation_p.N244S|PKN2_ENST00000370513.5_Missense_Mutation_p.N401S|PKN2_ENST00000316005.7_Missense_Mutation_p.N401S|PKN2_ENST00000544045.1_Missense_Mutation_p.N75S	NM_006256.2	NP_006247.1	Q16513	PKN2_HUMAN	protein kinase N2	401	C2.|Necessary to rescue apical junction formation. {ECO:0000250}.				apical junction assembly (GO:0043297)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|epithelial cell migration (GO:0010631)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic cell cycle (GO:0045931)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	apical junction complex (GO:0043296)|centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium (GO:0030027)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(3)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(1)	33		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)		AAGCTCGATAATACTGTGGTT	0.368																																					p.N401S		Atlas-SNP	.											.	PKN2	109	.	0			c.A1202G						.						100	94	96					1																	89251817		1843	4094	5937	SO:0001583	missense	5586	exon8			TCGATAATACTGT	U33052	CCDS714.1	1p22	2014-04-23	2004-07-01	2004-07-01	ENSG00000065243	ENSG00000065243			9406	protein-coding gene	gene with protein product	"cardiolipin-activated protein kinase Pak2"	602549	"protein kinase C-like 2"	PRKCL2		7988719, 7851406	Standard	NM_006256		Approved	PRK2, Pak-2, STK7	uc001dmn.3	Q16513	OTTHUMG00000010074	ENST00000370521.3:c.1202A>G	chr1.hg19:g.89251817A>G	ENSP00000359552:p.Asn401Ser	126.0	0.0		132.0	51.0	NM_006256	B4DQ21|B4DTP5|B4DVG1|D3DT24|Q08AF4|Q9H1W4	Missense_Mutation	SNP	ENST00000370521.3	hg19	CCDS714.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.340161	0.81911	.	.	ENSG00000065243	ENST00000370521;ENST00000316005;ENST00000370505;ENST00000370513;ENST00000544045	T;T;T;T;T	0.21932	2.93;2.93;2.93;1.98;2.93	5.48	5.48	0.80851	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.47852	U	0.000210	T	0.40670	0.1126	M	0.80028	2.48	0.58432	D	0.999999	P;P;D;D	0.76494	0.952;0.952;0.997;0.999	P;P;D;P	0.75020	0.831;0.831;0.985;0.867	T	0.44314	-0.9336	10	0.66056	D	0.02	.	15.5726	0.76352	1.0:0.0:0.0:0.0	.	385;401;401;401	B4DTP5;E7ESL7;Q16513;B1AL79	.;.;PKN2_HUMAN;.	S	401;401;244;401;75	ENSP00000359552:N401S;ENSP00000317851:N401S;ENSP00000359536:N244S;ENSP00000359544:N401S;ENSP00000439643:N75S	ENSP00000317851:N401S	N	+	2	0	PKN2	89024405	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	8.962000	0.93254	2.080000	0.62538	0.455000	0.32223	AAT	.	.		0.368	PKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027828.3	NM_006256		G	89251817	A	G	89251817	3	3	300	1	0	0	0	0	1	0	0	0	11989	101	4	2	1232	2	PKN2	1	89251817	Missense_Mutation	SNP	A	TCGA-G3-AAV4-01A-11D-A382-10	35013702	89251817	159998804	4	43343										
SETDB1	9869	hgsc.bcm.edu	37	chr1	150936503	150936503	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	cccaacctgtttgtccagaaTgtcttcgtggatacccatga	8	12	1	2			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr1:150936503T>G	ENST00000271640.5	+	21	3892	c.3702T>G	c.(3700-3702)aaT>aaG	p.N1234K	RP11-316M1.12_ENST00000560481.1_RNA|CERS2_ENST00000561294.1_3'UTR|RP11-316M1.12_ENST00000561111.1_RNA|SETDB1_ENST00000368969.4_Missense_Mutation_p.N1234K|CERS2_ENST00000345896.4_5'Flank	NM_001145415.1|NM_012432.3	NP_001138887.1|NP_036564.3	Q15047	SETB1_HUMAN	SET domain, bifurcated 1	1234	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				bone development (GO:0060348)|histone H3-K9 trimethylation (GO:0036124)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|BRCA - Breast invasive adenocarcinoma(12;0.0152)|LUSC - Lung squamous cell carcinoma(543;0.211)			TTGTCCAGAATGTCTTCGTGG	0.527																																					p.N1234K		Atlas-SNP	.											.	SETDB1	204	.	0			c.T3702G						.						143	128	133					1																	150936503		2203	4300	6503	SO:0001583	missense	9869	exon21			CCAGAATGTCTTC	D31891	CCDS972.1, CCDS44217.1, CCDS58026.1	1q21	2013-01-23			ENSG00000143379	ENSG00000143379		"Chromatin-modifying enzymes / K-methyltransferases", "Tudor domain containing"	10761	protein-coding gene	gene with protein product	"tudor domain containing 21"	604396				10343109	Standard	NM_001145415		Approved	KG1T, KIAA0067, ESET, KMT1E, TDRD21	uc001evu.2	Q15047	OTTHUMG00000035003	ENST00000271640.5:c.3702T>G	chr1.hg19:g.150936503T>G	ENSP00000271640:p.Asn1234Lys	154.0	0.0		129.0	54.0	NM_012432	A6NEW2|Q5SZD8|Q5SZD9|Q5SZE0|Q5SZE7|Q96GM9	Missense_Mutation	SNP	ENST00000271640.5	hg19	CCDS44217.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.238181	0.79800	.	.	ENSG00000143379	ENST00000271640;ENST00000368969	D;D	0.81579	-1.51;-1.51	5.65	2.08	0.27032	SET domain (3);	0.000000	0.85682	D	0.000000	T	0.63105	0.2483	N	0.02266	-0.62	0.80722	D	1	D;D	0.76494	0.995;0.999	D;D	0.87578	0.972;0.998	T	0.72656	-0.4227	10	0.87932	D	0	.	7.8288	0.29330	0.0:0.2964:0.0:0.7036	.	1234;1234	Q15047-3;Q15047	.;SETB1_HUMAN	K	1234	ENSP00000271640:N1234K;ENSP00000357965:N1234K	ENSP00000271640:N1234K	N	+	3	2	SETDB1	149203127	0.886000	0.30341	1.000000	0.80357	0.992000	0.81027	-0.081000	0.11321	0.934000	0.37316	0.379000	0.24179	AAT	.	.		0.527	SETDB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084717.2			G	150936503	T	G	150936503	3	3	300	1	0	0	0	0	1	0	0	0	14153	1461	51	5	3780	5	SETDB1	1	150936503	Missense_Mutation	SNP	T	TCGA-G3-AAV4-01A-11D-A382-10	61684686	150936503	98314118	5	43344										
FLG	2312	hgsc.bcm.edu	37	chr1	152285059	152285059	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	ggctctgctgatggtgaccaGcctgtccatggcctgacact	12	13	1	3			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr1:152285059G>T	ENST00000368799.1	-	3	2338	c.2303C>A	c.(2302-2304)gCt>gAt	p.A768D	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	768	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ATGGTGACCAGCCTGTCCATG	0.562									Ichthyosis																												p.A768D		Atlas-SNP	.											.	FLG	900	.	0			c.C2303A						.						361	339	347					1																	152285059		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGACCAGCCTGTC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.2303C>A	chr1.hg19:g.152285059G>T	ENSP00000357789:p.Ala768Asp	124.0	0.0		137.0	67.0	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	hg19	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	-	7.512	0.654832	0.14580	.	.	ENSG00000143631	ENST00000368799	T	0.01767	4.65	2.81	2.81	0.32909	.	.	.	.	.	T	0.00875	0.0029	M	0.78223	2.4	0.09310	N	1	P	0.41232	0.743	B	0.31442	0.13	T	0.46317	-0.9200	9	0.19590	T	0.45	.	8.9131	0.35565	0.0:0.0:1.0:0.0	.	768	P20930	FILA_HUMAN	D	768	ENSP00000357789:A768D	ENSP00000357789:A768D	A	-	2	0	FLG	150551683	0.010000	0.17322	0.002000	0.10522	0.012000	0.07955	1.677000	0.37576	1.418000	0.47098	0.479000	0.44913	GCT	.	.		0.562	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		T	152285059	G	T	152285059	3	4	300	1	0	0	0	0	1	0	0	0	5930	971	34	3	9886	3	FLG	1	152285059	Missense_Mutation	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10	1348556	152285059	96965562	6	43345										
PIK3C2B	5287	hgsc.bcm.edu	37	chr1	204438438	204438438	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	caggggaggggtatcccagaTagaagctcggggaggcagag	19	7	0	3			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr1:204438438T>C	ENST00000367187.3	-	3	1049	c.493A>G	c.(493-495)Atc>Gtc	p.I165V	PIK3C2B_ENST00000424712.2_Missense_Mutation_p.I165V	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	165	Interaction with GRB2.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			GTATCCCAGATAGAAGCTCGG	0.562																																					p.I165V		Atlas-SNP	.											.	PIK3C2B	142	.	0			c.A493G						.						55	65	62					1																	204438438		2203	4300	6503	SO:0001583	missense	5287	exon3			CCCAGATAGAAGC	Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"phosphoinositide-3-kinase, class 2, beta polypeptide"			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.493A>G	chr1.hg19:g.204438438T>C	ENSP00000356155:p.Ile165Val	74.0	0.0		77.0	25.0	NM_002646	O95666|Q5SW99	Missense_Mutation	SNP	ENST00000367187.3	hg19	CCDS1446.1	.	.	.	.	.	.	.	.	.	.	T	14.55	2.570129	0.45798	.	.	ENSG00000133056	ENST00000367187;ENST00000424712	T;T	0.61392	0.11;0.15	5.14	5.14	0.70334	.	0.928229	0.09093	N	0.849583	T	0.51261	0.1664	L	0.29908	0.895	0.27710	N	0.945509	P;P	0.45078	0.85;0.766	P;B	0.46320	0.512;0.314	T	0.23904	-1.0175	10	0.10111	T	0.7	.	13.2033	0.59780	0.0:0.0:0.0:1.0	.	165;165	F5GWN5;O00750	.;P3C2B_HUMAN	V	165	ENSP00000356155:I165V;ENSP00000400561:I165V	ENSP00000356155:I165V	I	-	1	0	PIK3C2B	202705061	1.000000	0.71417	1.000000	0.80357	0.781000	0.44180	0.748000	0.26305	1.932000	0.55993	0.379000	0.24179	ATC	.	.		0.562	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646		C	204438438	T	C	204438438	3	2	300	1	0	0	0	0	1	0	0	0	11919	1406	49	2	4539	2	PIK3C2B	1	204438438	Missense_Mutation	SNP	T	TCGA-G3-AAV4-01A-11D-A382-10	52153379	204438438	44812183	7	43346										
INTS7	25896	hgsc.bcm.edu	37	chr1	212193463	212193463	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	ttattataatacggtatataCcggagggtgatggctcttgc	11	6	1	1			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr1:212193463C>T	ENST00000366994.3	-	3	476		c.e3+1		INTS7_ENST00000440600.2_Intron|INTS7_ENST00000366993.3_Splice_Site|INTS7_ENST00000366992.3_Splice_Site|INTS7_ENST00000469606.1_Splice_Site	NM_001199811.1|NM_001199812.1|NM_015434.3	NP_001186740.1|NP_001186741.1|NP_056249.1	Q9NVH2	INT7_HUMAN	integrator complex subunit 7						cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|snRNA processing (GO:0016180)	chromosome (GO:0005694)|integrator complex (GO:0032039)				NS(1)|breast(1)|kidney(1)|large_intestine(8)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20				OV - Ovarian serous cystadenocarcinoma(81;0.00584)|all cancers(67;0.0318)|Epithelial(68;0.0852)		ACGGTATATACCGGAGGGTGA	0.313																																					.		Atlas-SNP	.											.	INTS7	68	.	0			c.371+1G>A						.						54	54	54					1																	212193463		2203	4298	6501	SO:0001630	splice_region_variant	25896	exon4			TATATACCGGAGG	AK022509	CCDS1501.1, CCDS55684.1, CCDS55683.1, CCDS55685.1	1q32.3	2008-02-05	2006-03-15	2006-03-15	ENSG00000143493	ENSG00000143493			24484	protein-coding gene	gene with protein product		611350	"chromosome 1 open reading frame 73"	C1orf73		16239144	Standard	NM_015434		Approved	DKFZP434B168, INT7	uc001hiw.2	Q9NVH2	OTTHUMG00000037119	ENST00000366994.3:c.371+1G>A	chr1.hg19:g.212193463C>T		154.0	0.0		216.0	112.0	NM_001199811	B4DLZ6|B7WNP6|B7WPB6|Q8N4K7|Q8WUH5|Q9H9V3|Q9NVU5|Q9UFC6|Q9UFM3	Splice_Site	SNP	ENST00000366994.3	hg19	CCDS1501.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.642815	0.87859	.	.	ENSG00000143493	ENST00000366994;ENST00000366993;ENST00000366992	.	.	.	5.21	5.21	0.72293	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.7919	0.91976	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	INTS7	210260086	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	7.459000	0.80802	2.431000	0.82371	0.650000	0.86243	.	.	.		0.313	INTS7-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090142.1	NM_015434	Intron	T	212193463	C	T	212193463	5	4	300	1	0	0	0	0	0	0	1	0	7792	521	18	3	2588	3	INTS7	1	212193463	Splice_Site	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	7755025	212193463	37057158	8	43347										
FLVCR1	28982	hgsc.bcm.edu	37	chr1	213046020	213046020	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	cttttcgtgtatattctcagCcttcaaagaaaaacctcggt	6	10	2	1	rs138069386		TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr1:213046020C>T	ENST00000366971.4	+	3	1082	c.884C>T	c.(883-885)gCc>gTc	p.A295V		NM_014053.3	NP_054772.1	Q9Y5Y0	FLVC1_HUMAN	feline leukemia virus subgroup C cellular receptor 1	295					blood vessel development (GO:0001568)|cell death (GO:0008219)|cellular iron ion homeostasis (GO:0006879)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|erythrocyte differentiation (GO:0030218)|erythrocyte maturation (GO:0043249)|head morphogenesis (GO:0060323)|heme export (GO:0097037)|heme transport (GO:0015886)|in utero embryonic development (GO:0001701)|mitochondrial transport (GO:0006839)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|regulation of organ growth (GO:0046620)|spleen development (GO:0048536)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	heme transporter activity (GO:0015232)|transporter activity (GO:0005215)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(2)	12				OV - Ovarian serous cystadenocarcinoma(81;0.00733)|all cancers(67;0.013)|GBM - Glioblastoma multiforme(131;0.0845)|Epithelial(68;0.11)		ATATTCTCAGCCTTCAAAGAA	0.333																																					p.A295V	Esophageal Squamous(199;2235 2952 19233 26256)	Atlas-SNP	.											.	FLVCR1	31	.	0			c.C884T						.						46	49	48					1																	213046020		2203	4300	6503	SO:0001630	splice_region_variant	28982	exon3			TCTCAGCCTTCAA	AF118637	CCDS1510.1	1q32.3	2014-05-30			ENSG00000162769	ENSG00000162769		"Solute carriers"	24682	protein-coding gene	gene with protein product		609144	"ataxia, posterior column 1, with retinitis pigmentosa"	AXPC1		10400745, 10648427, 21070897	Standard	NM_014053		Approved	FLVCR, MFSD7B, PCA	uc001hjt.3	Q9Y5Y0	OTTHUMG00000036924	ENST00000366971.4:c.884-1C>T	chr1.hg19:g.213046020C>T		449.0	1.0		481.0	229.0	NM_014053	Q1HE16|Q86XY9|Q9NVR9	Missense_Mutation	SNP	ENST00000366971.4	hg19	CCDS1510.1	.	.	.	.	.	.	.	.	.	.	C	2.446	-0.327410	0.05350	.	.	ENSG00000162769	ENST00000366971	T	0.56776	0.44	5.43	4.52	0.55395	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.055946	0.64402	D	0.000001	T	0.13415	0.0325	N	0.00226	-1.805	0.42382	D	0.992497	B	0.10296	0.003	B	0.14023	0.01	T	0.29852	-0.9998	9	.	.	.	.	5.4954	0.16799	0.0:0.7235:0.0:0.2765	.	295	Q9Y5Y0	FLVC1_HUMAN	V	295	ENSP00000355938:A295V	.	A	+	2	0	FLVCR1	211112643	1.000000	0.71417	0.998000	0.56505	0.351000	0.29236	2.007000	0.40883	2.559000	0.86315	0.655000	0.94253	GCC	.	C|1.000;G|0.000		0.333	FLVCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089678.2	NM_014053	Missense_Mutation	T	213046020	C	T	213046020	5	4	300	1	0	0	0	0	0	0	1	0	5953	753	26	3	894	3	FLVCR1	1	213046020	Splice_Site	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	852557	213046020	36204601	9	43348										
NUP133	55746	hgsc.bcm.edu	37	chr1	229641905	229641905	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	aacattcgtgttggtgttccCctaaagaaaagagtctatat	8	7	1	2			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr1:229641905C>T	ENST00000261396.3	-	2	274	c.183G>A	c.(181-183)cgG>cgA	p.R61R	NUP133_ENST00000366678.3_Splice_Site_p.R61R|RP4-613A2.1_ENST00000417605.1_RNA|NUP133_ENST00000537506.1_Splice_Site_p.R45R	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	61				R -> G (in Ref. 1; BAA91829). {ECO:0000305}.	carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore organization (GO:0006999)|paraxial mesoderm development (GO:0048339)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)			NS(1)|breast(7)|endometrium(1)|kidney(6)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(4)	56	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				TTGGTGTTCCCCTAAAGAAAA	0.338																																					p.R61R		Atlas-SNP	.											.	NUP133	111	.	0			c.G183A						.						152	145	147					1																	229641905		2203	4300	6503	SO:0001630	splice_region_variant	55746	exon2			TGTTCCCCTAAAG		CCDS1579.1	1q42.13	2008-02-05	2002-08-29		ENSG00000069248	ENSG00000069248			18016	protein-coding gene	gene with protein product		607613	"nucleoporin 133kD"			11684705	Standard	NM_018230		Approved	FLJ10814	uc001htn.3	Q8WUM0	OTTHUMG00000039462	ENST00000261396.3:c.183-1G>A	chr1.hg19:g.229641905C>T		77.0	0.0		122.0	45.0	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Silent	SNP	ENST00000261396.3	hg19	CCDS1579.1																																																																																			.	.		0.338	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230	Silent	T	229641905	C	T	229641905	5	4	300	1	0	0	0	0	0	0	1	0	10763	637	22	3	3387	3	NUP133	1	229641905	Splice_Site	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	16595885	229641905	19608716	10	43349										
CMPK2	129607	hgsc.bcm.edu	37	chr2	6990084	6990084	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	ggcagccaggattctccatcCgctggtaggacatttctacc	10	13	2	0			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:6990084C>T	ENST00000256722.5	-	5	1246	c.1247G>A	c.(1246-1248)cGg>cAg	p.R416Q	CMPK2_ENST00000478738.1_5'UTR|CMPK2_ENST00000458098.1_Intron	NM_207315.3	NP_997198.2	Q5EBM0	CMPK2_HUMAN	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	416					cellular response to lipopolysaccharide (GO:0071222)|dTDP biosynthetic process (GO:0006233)|dUDP biosynthetic process (GO:0006227)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)|thymidylate kinase activity (GO:0004798)|UMP kinase activity (GO:0033862)			large_intestine(1)|lung(13)|prostate(1)|upper_aerodigestive_tract(1)	16	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					ATTCTCCATCCGCTGGTAGGA	0.458																																					p.R416Q		Atlas-SNP	.											CMPK2,NS,carcinoma,0,1	CMPK2	30	.	0			c.G1247A						.						70	70	70					2																	6990084		1898	4104	6002	SO:0001583	missense	129607	exon5			TCCATCCGCTGGT		CCDS42648.1, CCDS58695.1, CCDS58696.1	2p25.2	2008-01-25			ENSG00000134326	ENSG00000134326	2.7.4.14		27015	protein-coding gene	gene with protein product	"cytidylate kinase 2"	611787				17999954	Standard	NM_207315		Approved	TYKi, UMP-CMPK2	uc002qyo.4	Q5EBM0	OTTHUMG00000151629	ENST00000256722.5:c.1247G>A	chr2.hg19:g.6990084C>T	ENSP00000256722:p.Arg416Gln	85.0	0.0		134.0	44.0	NM_207315	A2RUB0|A5D8T2|B7ZM18|Q6ZRU2|Q96AL8	Missense_Mutation	SNP	ENST00000256722.5	hg19	CCDS42648.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.852651	0.91355	.	.	ENSG00000134326	ENST00000256722	T	0.41400	1.0	5.69	3.86	0.44501	.	0.000000	0.85682	D	0.000000	T	0.42359	0.1199	L	0.55990	1.75	0.80722	D	1	P	0.51653	0.947	P	0.45998	0.5	T	0.36792	-0.9733	10	0.62326	D	0.03	-23.9803	10.7854	0.46403	0.1319:0.8005:0.0:0.0676	.	416	Q5EBM0	CMPK2_HUMAN	Q	416	ENSP00000256722:R416Q	ENSP00000256722:R416Q	R	-	2	0	CMPK2	6907535	1.000000	0.71417	0.985000	0.45067	0.804000	0.45430	5.144000	0.64832	0.839000	0.34971	0.655000	0.94253	CGG	.	.		0.458	CMPK2-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323339.2	NM_207315		T	6990084	C	T	6990084	3	4	300	1	0	0	0	0	1	0	0	0	3583	652	23	1	106	1	CMPK2	2	6990084	Missense_Mutation	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10		6990084	236209289	11	43350										
APOB	338	hgsc.bcm.edu	37	chr2	21231070	21231070	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	ttggggatgttcaatttgtgGaagtatttagtgttgctatc	12	3	1	0			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:21231070G>T	ENST00000233242.1	-	26	8797	c.8670C>A	c.(8668-8670)ttC>ttA	p.F2890L		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	2890					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCAATTTGTGGAAGTATTTAG	0.423																																					p.F2890L		Atlas-SNP	.											APOB,NS,carcinoma,0,1	APOB	761	.	0			c.C8670A						.						180	177	178					2																	21231070		2203	4299	6502	SO:0001583	missense	338	exon26			TTTGTGGAAGTAT	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.8670C>A	chr2.hg19:g.21231070G>T	ENSP00000233242:p.Phe2890Leu	137.0	0.0		143.0	50.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	G	11.36	1.614336	0.28712	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.00686	5.85	5.51	1.68	0.24146	.	0.727572	0.12466	N	0.466471	T	0.01156	0.0038	M	0.72479	2.2	0.80722	D	1	B	0.26318	0.146	B	0.19148	0.024	T	0.52931	-0.8509	10	0.52906	T	0.07	.	5.2808	0.15674	0.4271:0.0:0.4419:0.131	.	2890	P04114	APOB_HUMAN	L	2890	ENSP00000233242:F2890L	ENSP00000233242:F2890L	F	-	3	2	APOB	21084575	0.184000	0.23200	0.953000	0.39169	0.951000	0.60555	-0.299000	0.08254	0.301000	0.22738	-0.266000	0.10368	TTC	.	.		0.423	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			T	21231070	G	T	21231070	3	4	300	1	0	0	0	0	1	0	0	0	785	1165	41	3	5037	3	APOB	2	21231070	Missense_Mutation	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10	14240986	21231070	221968303	12	43351										
ABCG5	64240	hgsc.bcm.edu	37	chr2	44051474	44051474	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	ttcttcaaagttttatgacaAattgctgatttcttgtaggc	7	6	3	2			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:44051474A>C	ENST00000260645.1	-	8	1141	c.1002T>G	c.(1000-1002)atT>atG	p.I334M	ABCG5_ENST00000543989.1_Intron|ABCG5_ENST00000405322.1_Missense_Mutation_p.I163M	NM_022436.2	NP_071881.1	Q9H222	ABCG5_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 5	334					ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|excretion (GO:0007588)|intestinal cholesterol absorption (GO:0030299)|negative regulation of intestinal cholesterol absorption (GO:0045796)|negative regulation of intestinal phytosterol absorption (GO:0010949)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cholesterol transporter activity (GO:0017127)|protein heterodimerization activity (GO:0046982)			breast(1)|kidney(2)|large_intestine(4)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	33		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)			Ezetimibe(DB00973)	TTTTATGACAAATTGCTGATT	0.388																																					p.I334M		Atlas-SNP	.											.	ABCG5	72	.	0			c.T1002G						.						126	134	131					2																	44051474		2203	4300	6503	SO:0001583	missense	64240	exon8			ATGACAAATTGCT	T93792	CCDS1814.1	2p21	2012-03-14	2008-07-31		ENSG00000138075	ENSG00000138075		"ATP binding cassette transporters / subfamily G"	13886	protein-coding gene	gene with protein product	"sterolin 1"	605459				11099417, 11452359	Standard	NM_022436		Approved	STSL	uc002rtn.3	Q9H222	OTTHUMG00000128758	ENST00000260645.1:c.1002T>G	chr2.hg19:g.44051474A>C	ENSP00000260645:p.Ile334Met	140.0	0.0		174.0	104.0	NM_022436	Q2T9G2|Q96QZ2|Q96QZ3	Missense_Mutation	SNP	ENST00000260645.1	hg19	CCDS1814.1	.	.	.	.	.	.	.	.	.	.	A	10.96	1.499787	0.26861	.	.	ENSG00000138075	ENST00000260645;ENST00000405322	T;T	0.80653	1.79;-1.4	5.45	1.91	0.25777	.	0.867855	0.10025	N	0.725453	T	0.62588	0.2440	N	0.19112	0.55	0.80722	D	1	B;B	0.31485	0.325;0.132	B;B	0.23716	0.037;0.048	T	0.50215	-0.8854	10	0.34782	T	0.22	.	4.9726	0.14123	0.5604:0.16:0.2796:0.0	.	163;334	E7EX35;Q9H222	.;ABCG5_HUMAN	M	334;163	ENSP00000260645:I334M;ENSP00000384513:I163M	ENSP00000260645:I334M	I	-	3	3	ABCG5	43904978	1.000000	0.71417	0.083000	0.20561	0.678000	0.39670	1.711000	0.37930	0.152000	0.19188	0.533000	0.62120	ATT	.	.		0.388	ABCG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250675.1	NM_022436		C	44051474	A	C	44051474	3	2	300	1	0	0	0	0	1	0	0	0	71	10	1	5	977	5	ABCG5	2	44051474	Missense_Mutation	SNP	A	TCGA-G3-AAV4-01A-11D-A382-10	22820404	44051474	199147899	13	43352										
STON1	11037	hgsc.bcm.edu	37	chr2	48809181	48809181	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	gccgaagcgagatgaatcctAttatgagaaggactcagaaa	11	7	1	4			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:48809181A>G	ENST00000406226.1	+	3	1604	c.1409A>G	c.(1408-1410)tAt>tGt	p.Y470C	STON1_ENST00000309835.3_Missense_Mutation_p.Y470C|STON1-GTF2A1L_ENST00000402114.2_Missense_Mutation_p.Y470C|STON1-GTF2A1L_ENST00000309827.2_Missense_Mutation_p.Y470C|STON1_ENST00000404752.1_Missense_Mutation_p.Y470C|STON1-GTF2A1L_ENST00000394754.1_Missense_Mutation_p.Y470C|STON1-GTF2A1L_ENST00000405008.1_Missense_Mutation_p.Y470C|STON1-GTF2A1L_ENST00000394751.3_Missense_Mutation_p.Y470C	NM_001198595.1	NP_001185524.1	Q9Y6Q2	STON1_HUMAN	stonin 1	470	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)	clathrin adaptor complex (GO:0030131)				NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(19)|prostate(3)|skin(2)	37		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GATGAATCCTATTATGAGAAG	0.368																																					p.Y470C		Atlas-SNP	.											.	STON1	100	.	0			c.A1409G						.						113	118	116					2																	48809181		2203	4300	6503	SO:0001583	missense	11037	exon3			AATCCTATTATGA	AF026169	CCDS1841.1	2p16.3	2008-02-05			ENSG00000243244	ENSG00000243244			17003	protein-coding gene	gene with protein product	"stoned B homolog 1 (Drosophila)"	605357				14504226, 10364255	Standard	NM_001198595		Approved	SBLF, stoned-b1		Q9Y6Q2	OTTHUMG00000129169	ENST00000406226.1:c.1409A>G	chr2.hg19:g.48809181A>G	ENSP00000384615:p.Tyr470Cys	129.0	0.0		152.0	79.0	NM_001198595	A8MXJ1|B5MCF5|B7ZL16|Q96JE3|Q9BYX3	Missense_Mutation	SNP	ENST00000406226.1	hg19	CCDS1841.1	.	.	.	.	.	.	.	.	.	.	A	3.981	-0.006517	0.07773	.	.	ENSG00000243244;ENSG00000243244;ENSG00000243244;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781	ENST00000404752;ENST00000406226;ENST00000309835;ENST00000405008;ENST00000402114;ENST00000394754;ENST00000309827;ENST00000394751	T;T;T;T;T;T;T;T	0.20069	2.1;2.1;2.1;2.1;2.1;2.1;2.1;2.1	5.3	2.74	0.32292	Clathrin adaptor, mu subunit, C-terminal (3);	0.182483	0.49916	N	0.000127	T	0.24084	0.0583	M	0.65975	2.015	0.35933	D	0.832659	B;B;B	0.25390	0.003;0.125;0.052	B;B;B	0.27500	0.009;0.073;0.08	T	0.18209	-1.0344	10	0.72032	D	0.01	.	10.6345	0.45556	0.9092:0.0:0.0908:0.0	.	470;470;470	A8MXJ1;Q53S48;Q9Y6Q2	.;.;STON1_HUMAN	C	470	ENSP00000385273:Y470C;ENSP00000384615:Y470C;ENSP00000310969:Y470C;ENSP00000385499:Y470C;ENSP00000385701:Y470C;ENSP00000378236:Y470C;ENSP00000311493:Y470C;ENSP00000378234:Y470C	ENSP00000310969:Y470C	Y	+	2	0	STON1-GTF2A1L;STON1	48662685	1.000000	0.71417	0.228000	0.23943	0.136000	0.21042	4.173000	0.58249	0.387000	0.25024	0.533000	0.62120	TAT	.	.		0.368	STON1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323848.2	NM_006873		G	48809181	A	G	48809181	3	3	300	1	0	0	0	0	1	0	0	0	15331	449	16	2	1411	2	STON1	2	48809181	Missense_Mutation	SNP	A	TCGA-G3-AAV4-01A-11D-A382-10	4757707	48809181	194390192	14	43353										
C2orf42	54980	hgsc.bcm.edu	37	chr2	70392230	70392230	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	aaataaactctcacctctggGgtatctaagatttgtttaac	6	8	3	1			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:70392230G>A	ENST00000264434.2	-	8	1726	c.1347C>T	c.(1345-1347)acC>acT	p.T449T	C2orf42_ENST00000420306.1_Silent_p.T449T	NM_017880.1	NP_060350.1	Q9NWW7	CB042_HUMAN	chromosome 2 open reading frame 42	449										endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|urinary_tract(1)	12						TCACCTCTGGGGTATCTAAGA	0.423																																					p.T449T		Atlas-SNP	.											.	C2orf42	30	.	0			c.C1347T						.						108	116	113					2																	70392230		2203	4300	6503	SO:0001819	synonymous_variant	54980	exon8			CTCTGGGGTATCT	AK000565	CCDS1899.1	2p14	2011-03-08			ENSG00000115998	ENSG00000115998			26056	protein-coding gene	gene with protein product						12477932	Standard	XM_005264389		Approved	FLJ20558	uc002sgh.3	Q9NWW7	OTTHUMG00000129642	ENST00000264434.2:c.1347C>T	chr2.hg19:g.70392230G>A		133.0	0.0		120.0	46.0	NM_017880	D6W5G3|Q9H629	Silent	SNP	ENST00000264434.2	hg19	CCDS1899.1																																																																																			.	.		0.423	C2orf42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251840.1	NM_017880		A	70392230	G	A	70392230	2	1	300	1	0	0	0	0	0	0	0	1	2168	1219	43	3		3	C2orf42	2	70392230	Silent	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10	21583049	70392230	172807143	15	43354										
LRRTM1	347730	hgsc.bcm.edu	37	chr2	80529936	80529936	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	ggcgcactgcaagttgccatCgtagcgcccctggaagttgt	13	12	0	0			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:80529936C>T	ENST00000295057.3	-	2	1665	c.1009G>A	c.(1009-1011)Gat>Aat	p.D337N	CTNNA2_ENST00000540488.1_Intron|LRRTM1_ENST00000409148.1_Missense_Mutation_p.D337N|CTNNA2_ENST00000402739.4_Intron|CTNNA2_ENST00000541047.1_Intron|CTNNA2_ENST00000496558.1_Intron|CTNNA2_ENST00000361291.4_Intron|CTNNA2_ENST00000466387.1_Intron	NM_178839.4	NP_849161.2	Q86UE6	LRRT1_HUMAN	leucine rich repeat transmembrane neuronal 1	337	LRRCT.				exploration behavior (GO:0035640)|locomotory behavior (GO:0007626)|long-term synaptic potentiation (GO:0060291)|negative regulation of receptor internalization (GO:0002091)|protein localization to synapse (GO:0035418)|synapse organization (GO:0050808)	axon (GO:0030424)|cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				NS(1)|breast(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(33)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	63						AAGTTGCCATCGTAGCGCCCC	0.657										HNSCC(69;0.2)																											p.D337N		Atlas-SNP	.											.	LRRTM1	251	.	0			c.G1009A						.						29	27	27					2																	80529936		2203	4300	6503	SO:0001583	missense	347730	exon2			TGCCATCGTAGCG	AY358310	CCDS1966.1	2p12	2004-06-22			ENSG00000162951	ENSG00000162951			19408	protein-coding gene	gene with protein product		610867				12676565	Standard	XR_244930		Approved	FLJ32082	uc002sok.1	Q86UE6	OTTHUMG00000130021	ENST00000295057.3:c.1009G>A	chr2.hg19:g.80529936C>T	ENSP00000295057:p.Asp337Asn	233.0	0.0		222.0	112.0	NM_178839	A8K397|D6W5K1|Q96DN1	Missense_Mutation	SNP	ENST00000295057.3	hg19	CCDS1966.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.789431	0.90367	.	.	ENSG00000162951	ENST00000295057;ENST00000409148	T;T	0.42900	0.96;0.96	5.32	5.32	0.75619	.	0.000000	0.85682	U	0.000000	T	0.58694	0.2140	L	0.58428	1.81	0.80722	D	1	D	0.71674	0.998	P	0.60012	0.867	T	0.56165	-0.8024	9	.	.	.	.	18.995	0.92809	0.0:1.0:0.0:0.0	.	337	Q86UE6	LRRT1_HUMAN	N	337	ENSP00000295057:D337N;ENSP00000386646:D337N	.	D	-	1	0	LRRTM1	80383447	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.808000	0.86044	2.452000	0.82932	0.655000	0.94253	GAT	.	.		0.657	LRRTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313614.1	NM_178839		T	80529936	C	T	80529936	3	4	300	1	0	0	0	0	1	0	0	0	9048	884	31	1	563	1	LRRTM1	2	80529936	Missense_Mutation	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	10137706	80529936	162669437	16	43355										
CNNM4	26504	hgsc.bcm.edu	37	chr2	97426789	97426789	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	cggcggaccggcccgcgggcGcctcctcctggcggcgccgg	18	19	0	0			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:97426789G>T	ENST00000377075.2	+	1	151	c.53G>T	c.(52-54)cGc>cTc	p.R18L		NM_020184.3	NP_064569.3	Q6P4Q7	CNNM4_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 4	18					biomineral tissue development (GO:0031214)|ion transport (GO:0006811)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)			breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)	20						gcccgcgggcgccTCCTCCTG	0.821																																					p.R18L		Atlas-SNP	.											.	CNNM4	48	.	0			c.G53T						.						3	4	4					2																	97426789		1705	3177	4882	SO:0001583	missense	26504	exon1			GCGGGCGCCTCCT	AB046812	CCDS2024.2	2q11.2	2014-08-08	2014-08-07		ENSG00000158158	ENSG00000158158			105	protein-coding gene	gene with protein product		607805	"cyclin M4"	ACDP4		21393841, 24194943	Standard	XM_005263914		Approved	KIAA1592	uc002swx.3	Q6P4Q7	OTTHUMG00000130532	ENST00000377075.2:c.53G>T	chr2.hg19:g.97426789G>T	ENSP00000366275:p.Arg18Leu	397.0	0.0		378.0	184.0	NM_020184	B7Z1U0|C7SQM3|C7SQM4|C7SQM5|Q53RE5|Q9H9G3|Q9HCI0|Q9NRN1	Missense_Mutation	SNP	ENST00000377075.2	hg19	CCDS2024.2	.	.	.	.	.	.	.	.	.	.	G	10.47	1.359159	0.24598	.	.	ENSG00000158158	ENST00000377075	T	0.73152	-0.72	3.54	2.62	0.31277	.	4.504510	0.01309	U	0.010559	T	0.63379	0.2506	L	0.34521	1.04	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.52859	-0.8519	10	0.72032	D	0.01	-18.0963	7.3926	0.26919	0.0:0.1855:0.6235:0.1909	.	18	Q6P4Q7	CNNM4_HUMAN	L	18	ENSP00000366275:R18L	ENSP00000366275:R18L	R	+	2	0	CNNM4	96790516	0.998000	0.40836	0.989000	0.46669	0.034000	0.12701	2.038000	0.41184	0.776000	0.33473	0.462000	0.41574	CGC	.	.		0.821	CNNM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252954.1	NM_020184		T	97426789	G	T	97426789	3	4	300	1	0	0	0	0	1	0	0	0	3617	1087	38	1	55	1	CNNM4	2	97426789	Missense_Mutation	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10	16896853	97426789	145772584	17	43356										
CNGA3	1261	hgsc.bcm.edu	37	chr2	98999859	98999859	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	accttcccgcagcgcctggcCcctggccaaatgcaacacta	8	18	0	0			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:98999859C>T	ENST00000272602.2	+	4	443	c.404C>T	c.(403-405)cCc>cTc	p.P135L	CNGA3_ENST00000436404.2_Intron|CNGA3_ENST00000393504.1_Missense_Mutation_p.P135L|CNGA3_ENST00000409937.1_Missense_Mutation_p.P139L			Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3	135					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to magnesium ion (GO:0032026)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|photoreceptor outer segment membrane (GO:0042622)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(17)|ovary(5)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	49						AGCGCCTGGCCCCTGGCCAAA	0.597																																					p.P135L		Atlas-SNP	.											CNGA3,colon,carcinoma,0,1	CNGA3	118	.	0			c.C404T						.						107	95	99					2																	98999859		2203	4300	6503	SO:0001583	missense	1261	exon5			CCTGGCCCCTGGC	S76069	CCDS2034.1, CCDS42719.1	2q11.2	2013-01-08			ENSG00000144191	ENSG00000144191		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2150	protein-coding gene	gene with protein product		600053		CNCG3, ACHM2		7532814, 9517456, 16382102	Standard	NM_001298		Approved	CCNC1, CCNCa, CNG3	uc002syt.3	Q16281	OTTHUMG00000130561	ENST00000272602.2:c.404C>T	chr2.hg19:g.98999859C>T	ENSP00000272602:p.Pro135Leu	107.0	0.0		106.0	43.0	NM_001298	E9PF93|Q4VAP7|Q53RD2|Q6ZNA7|Q9UP64	Missense_Mutation	SNP	ENST00000272602.2	hg19	CCDS2034.1	.	.	.	.	.	.	.	.	.	.	C	16.00	2.999736	0.54147	.	.	ENSG00000144191	ENST00000393504;ENST00000272602;ENST00000409937	D;D;D	0.97620	-4.39;-4.39;-4.46	4.76	4.76	0.60689	.	0.450627	0.22121	N	0.064324	D	0.95268	0.8465	L	0.47716	1.5	0.44523	D	0.997477	D;B	0.54047	0.964;0.001	P;B	0.45310	0.476;0.001	D	0.94006	0.7280	10	0.29301	T	0.29	.	14.7937	0.69863	0.0:1.0:0.0:0.0	.	139;135	E9PF93;Q16281	.;CNGA3_HUMAN	L	135;135;139	ENSP00000377140:P135L;ENSP00000272602:P135L;ENSP00000386761:P139L	ENSP00000272602:P135L	P	+	2	0	CNGA3	98366291	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	5.449000	0.66619	2.483000	0.83821	0.561000	0.74099	CCC	.	.		0.597	CNGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252986.1	NM_001298		T	98999859	C	T	98999859	3	4	300	1	0	0	0	0	1	0	0	0	3600	623	22	3	418	3	CNGA3	2	98999859	Missense_Mutation	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	1573070	98999859	144199514	18	43357										
SMPD4	55627	hgsc.bcm.edu	37	chr2	130914822	130914851	+	Splice_Site	DEL	CCGCAAGGGCCACCCACCGTTTGAACTCCT	CCGCAAGGGCCACCCACCGTTTGAACTCCT	-													0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	ggaagccgcaagggccacccAccgtttgaactcctccaggg					rs541644496		TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	CCGCAAGGGCCACCCACCGTTTGAACTCCT	CCGCAAGGGCCACCCACCGTTTGAACTCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:130914822_130914851delCCGCAAGGGCCACCCACCGTTTGAACTCCT	ENST00000409031.1	-	12	2335_2363	c.1187_1215delAGGAGTTCAAACGGTGGGTGGCCCTTGCGG	c.(1186-1215)gaggagttcaaacggtgggtggcccttgcg>g	p.EEFKRWVALA396del	SMPD4_ENST00000452225.2_Splice_Site_p.EEFKRWVALA137del|SMPD4_ENST00000351288.6_Splice_Site_p.EEFKRWVALA367del|SMPD4_ENST00000339679.7_Splice_Site_p.EEFKRWVALA254del|SMPD4_ENST00000426662.2_Intron|SMPD4_ENST00000443958.2_Splice_Site_p.EEFKRWVALA60del|SMPD4_ENST00000473720.1_Intron|SMPD4_ENST00000431183.2_Splice_Site_p.EEFKRWVALA294del|SMPD4_ENST00000453750.1_Splice_Site_p.EEFKRWVALA145del	NM_017951.4	NP_060421.2	Q9NXE4	NSMA3_HUMAN	sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3)	357					cellular response to tumor necrosis factor (GO:0071356)|ceramide biosynthetic process (GO:0046513)|glycerophospholipid catabolic process (GO:0046475)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)|sphingomyelin phosphodiesterase D activity (GO:0050290)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(17)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29	Colorectal(110;0.1)				Phosphatidylserine(DB00144)	AGGGCCACCCACCGTTTGAACTCCTCCAGGGGGCTGGTGGCGTGGGAGTG	0.665																																					p.401_405del		Pindel	.											.	SMPD4	67	.	0			c.1203_1214del						.																																			SO:0001630	splice_region_variant	55627	exon12			.	AF052134	CCDS2156.2, CCDS42751.1, CCDS54398.1	2q21.1	2009-11-06			ENSG00000136699	ENSG00000136699			32949	protein-coding gene	gene with protein product		610457				16517606	Standard	NM_001171083		Approved	FLJ20297, FLJ20756, nSMase-3, KIAA1418, NSMASE3, NET13	uc002tqr.2	Q9NXE4	OTTHUMG00000131624	ENST00000409031.1:c.1214+1AGGAGTTCAAACGGTGGGTGGCCCTTGCGG>-	chr2.hg19:g.130914822_130914851delCCGCAAGGGCCACCCACCGTTTGAACTCCT		236.0	0.0		148.0	11.0	NM_017951	B4DM23|B4DQ31|B4DRB8|B4DWK7|B4E0L6|E7ESA2|E9PCE6|Q6FI76|Q6P1P7|Q6ZT43|Q9H0M2|Q9NW20|Q9NWL2|Q9P2C9	In_Frame_Del	DEL	ENST00000409031.1	hg19	CCDS42751.1																																																																																			.	.		0.665	SMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254516.3	NM_017751	In_Frame_Del	-	130914851	CCGCAAGGGCCACCCACCGTTTGAACTCCT	-	130914822	8	5	300	1	0	1	0	1	0	0	1	0	14822	173	6	0	1420	0	SMPD4	2	130914822	Splice_Site	DEL	CCGCAAGGGCCACCCACCGTTTGAACTCCT	TCGA-G3-AAV4-01A-11D-A382-10	31914963	130914822	112284551	19	43358										
ARHGEF4	50649	hgsc.bcm.edu	37	chr2	131801932	131801932	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	tggacatggacggcctggagGtggtggacctggaggacggg	21	7	0	0			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:131801932G>A	ENST00000326016.5	+	12	2179	c.1660G>A	c.(1660-1662)Gtg>Atg	p.V554M	ARHGEF4_ENST00000409303.1_Missense_Mutation_p.V494M|ARHGEF4_ENST00000355771.3_Missense_Mutation_p.V483M|ARHGEF4_ENST00000392953.3_Missense_Mutation_p.V554M|ARHGEF4_ENST00000525839.1_Missense_Mutation_p.V554M|ARHGEF4_ENST00000428230.2_Intron	NM_015320.2	NP_056135.2	Q9NR80	ARHG4_HUMAN	Rho guanine nucleotide exchange factor (GEF) 4	554	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein domain specific binding (GO:0019904)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(4)	29		Prostate(154;0.055)		BRCA - Breast invasive adenocarcinoma(221;0.097)		CGGCCTGGAGGTGGTGGACCT	0.657																																					p.V554M		Atlas-SNP	.											.	ARHGEF4	89	.	0			c.G1660A						.						67	52	57					2																	131801932		2197	4300	6497	SO:0001583	missense	50649	exon12			CTGGAGGTGGTGG	AL137289	CCDS2165.1, CCDS42754.1	2q22	2013-01-10			ENSG00000136002	ENSG00000136002		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	684	protein-coding gene	gene with protein product	"APC-stimulated guanine nucleotide exchange factor"	605216				10873612	Standard	NM_015320		Approved	STM6, KIAA1112, ASEF	uc002tsa.1	Q9NR80	OTTHUMG00000131657	ENST00000326016.5:c.1660G>A	chr2.hg19:g.131801932G>A	ENSP00000316845:p.Val554Met	287.0	0.0		233.0	13.0	NM_032995	Q9HDC6|Q9UPP0	Missense_Mutation	SNP	ENST00000326016.5	hg19	CCDS2165.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.69|17.69	3.452100|3.452100	0.63290|0.63290	.|.	.|.	ENSG00000136002|ENSG00000136002	ENST00000532720|ENST00000326016;ENST00000392953;ENST00000525839;ENST00000409303;ENST00000355771	.|D;D;D;D;D	.|0.91068	.|-2.78;-2.78;-2.78;-2.78;-2.78	5.2|5.2	0.445|0.445	0.16597|0.16597	.|Pleckstrin homology-type (1);Pleckstrin homology domain (3);	.|0.254015	.|0.33180	.|N	.|0.005191	D|D	0.91938|0.91938	0.7447|0.7447	M|M	0.80982|0.80982	2.52|2.52	0.43304|0.43304	D|D	0.995301|0.995301	.|P;P;P	.|0.51653	.|0.943;0.947;0.943	.|P;P;P	.|0.58172	.|0.834;0.732;0.834	D|D	0.88392|0.88392	0.3009|0.3009	5|10	.|0.87932	.|D	.|0	.|.	3.3375|3.3375	0.07106|0.07106	0.1082:0.3074:0.4285:0.156|0.1082:0.3074:0.4285:0.156	.|.	.|494;554;554	.|E9PEM0;Q9NR80-4;Q9NR80	.|.;.;ARHG4_HUMAN	D|M	170|554;554;554;494;483	.|ENSP00000316845:V554M;ENSP00000376680:V554M;ENSP00000432267:V554M;ENSP00000387285:V494M;ENSP00000348017:V483M	.|ENSP00000316845:V554M	G|V	+|+	2|1	0|0	ARHGEF4|ARHGEF4	131518402|131518402	1.000000|1.000000	0.71417|0.71417	0.004000|0.004000	0.12327|0.12327	0.829000|0.829000	0.46940|0.46940	2.639000|2.639000	0.46570|0.46570	0.164000|0.164000	0.19529|0.19529	0.561000|0.561000	0.74099|0.74099	GGT|GTG	.	.		0.657	ARHGEF4-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254554.4			A	131801932	G	A	131801932	3	1	300	1	0	0	0	0	1	0	0	0	908	1261	44	3	1698	3	ARHGEF4	2	131801932	Missense_Mutation	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10	887110	131801932	111397441	20	43359										
YSK4	80122	hgsc.bcm.edu	37	chr2	135741259	135741259	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	aacttactgtgccgtaggctCcctttccaagaatctcaccc	6	15	1	1			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:135741259C>A	ENST00000375845.3	-	8	3239	c.3209G>T	c.(3208-3210)gGa>gTa	p.G1070V	MAP3K19_ENST00000392918.3_Intron|MAP3K19_ENST00000392915.1_Missense_Mutation_p.G1087V|MAP3K19_ENST00000315513.3_5'UTR|MAP3K19_ENST00000375844.3_Missense_Mutation_p.G252V|MAP3K19_ENST00000392917.3_Intron|MAP3K19_ENST00000358371.4_Missense_Mutation_p.G957V	NM_001018044.2|NM_025052.3	NP_001018054.1|NP_079328.3	Q56UN5	M3K19_HUMAN	mitogen-activated protein kinase kinase kinase 19	1070	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)										GCCGTAGGCTCCCTTTCCAAG	0.468																																					p.G1070V		Atlas-SNP	.											.	.	.	.	0			c.G3209T						.						91	95	94					2																	135741259		2203	4300	6503	SO:0001583	missense	80122	exon8			TAGGCTCCCTTTC	AK026727	CCDS2176.2, CCDS33293.1, CCDS63021.1, CCDS63020.1, CCDS63022.1	2q21.3	2012-10-16	2012-10-16	2012-10-16	ENSG00000176601	ENSG00000176601		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	26249	protein-coding gene	gene with protein product			"Yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)", "yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)", "YSK4 Sps1/Ste20-related kinase homolog (S. cerevisiae)"	YSK4		12477932	Standard	NM_001282883		Approved	FLJ23074	uc002tue.1	Q56UN5	OTTHUMG00000074083	ENST00000375845.3:c.3209G>T	chr2.hg19:g.135741259C>A	ENSP00000365005:p.Gly1070Val	182.0	0.0		222.0	37.0	NM_025052	B2RP57|B7ZMH9|E2QRE3|Q56UN1|Q56UN2|Q56UN3|Q56UN4|Q8N4E9|Q9H5T2	Missense_Mutation	SNP	ENST00000375845.3	hg19	CCDS2176.2	.	.	.	.	.	.	.	.	.	.	C	25.9	4.689516	0.88735	.	.	ENSG00000176601	ENST00000375845;ENST00000358371;ENST00000375844;ENST00000392915;ENST00000437365	D;D;D;T;D	0.85339	-1.97;-1.97;-1.97;-0.05;-1.97	5.91	5.91	0.95273	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.48767	D	0.000172	D	0.96334	0.8804	H	0.99357	4.53	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.97543	1.0087	10	0.87932	D	0	.	20.303	0.98618	0.0:1.0:0.0:0.0	.	957;1087;252;1070	Q56UN5-3;A8MWG7;Q56UN5-5;Q56UN5	.;.;.;YSK4_HUMAN	V	1070;957;252;1087;460	ENSP00000365005:G1070V;ENSP00000351140:G957V;ENSP00000365004:G252V;ENSP00000376647:G1087V;ENSP00000392827:G460V	ENSP00000351140:G957V	G	-	2	0	YSK4	135457729	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.101000	0.76997	2.806000	0.96561	0.549000	0.68633	GGA	.	.		0.468	MAP3K19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000158244.1	NM_025052		A	135741259	C	A	135741259	3	1	300	1	0	0	0	0	1	0	0	0	17510	855	30	3	789	3	YSK4	2	135741259	Missense_Mutation	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	3939327	135741259	107458114	21	43360										
YSK4	80122	hgsc.bcm.edu	37	chr2	135741322	135741322	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	cagactttaaactattttcaGaaaatatcttcttttcattt	2	7	4	2			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:135741322G>C	ENST00000375845.3	-	8	3176	c.3146C>G	c.(3145-3147)tCt>tGt	p.S1049C	MAP3K19_ENST00000392918.3_Missense_Mutation_p.S231C|MAP3K19_ENST00000392915.1_Missense_Mutation_p.S1066C|MAP3K19_ENST00000315513.3_5'UTR|MAP3K19_ENST00000375844.3_Missense_Mutation_p.S231C|MAP3K19_ENST00000392917.3_Intron|MAP3K19_ENST00000358371.4_Missense_Mutation_p.S936C	NM_001018044.2|NM_025052.3	NP_001018054.1|NP_079328.3	Q56UN5	M3K19_HUMAN	mitogen-activated protein kinase kinase kinase 19	1049							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)										ACTATTTTCAGAAAATATCTT	0.388																																					p.S1049C		Atlas-SNP	.											YSK4_ENST00000375845,colon,carcinoma,0,2	.	.	.	0			c.C3146G						.						96	98	97					2																	135741322		2203	4300	6503	SO:0001583	missense	80122	exon8			TTTTCAGAAAATA	AK026727	CCDS2176.2, CCDS33293.1, CCDS63021.1, CCDS63020.1, CCDS63022.1	2q21.3	2012-10-16	2012-10-16	2012-10-16	ENSG00000176601	ENSG00000176601		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	26249	protein-coding gene	gene with protein product			"Yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)", "yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)", "YSK4 Sps1/Ste20-related kinase homolog (S. cerevisiae)"	YSK4		12477932	Standard	NM_001282883		Approved	FLJ23074	uc002tue.1	Q56UN5	OTTHUMG00000074083	ENST00000375845.3:c.3146C>G	chr2.hg19:g.135741322G>C	ENSP00000365005:p.Ser1049Cys	168.0	0.0		210.0	39.0	NM_025052	B2RP57|B7ZMH9|E2QRE3|Q56UN1|Q56UN2|Q56UN3|Q56UN4|Q8N4E9|Q9H5T2	Missense_Mutation	SNP	ENST00000375845.3	hg19	CCDS2176.2	.	.	.	.	.	.	.	.	.	.	G	12.91	2.080809	0.36758	.	.	ENSG00000176601	ENST00000375845;ENST00000358371;ENST00000375844;ENST00000392918;ENST00000392915;ENST00000437365	T;T;T;T;T;T	0.74632	-0.75;-0.74;-0.63;-0.24;0.89;-0.86	5.91	5.04	0.67666	Protein kinase-like domain (1);	0.136119	0.34223	N	0.004151	D	0.83723	0.5316	M	0.68952	2.095	0.80722	D	1	D;D;D;P;D	0.89917	0.996;0.969;1.0;0.933;0.988	P;P;D;P;P	0.66497	0.855;0.708;0.944;0.614;0.635	D	0.85364	0.1109	10	0.62326	D	0.03	.	14.9815	0.71313	0.0:0.0:0.8574:0.1426	.	936;231;1066;231;1049	Q56UN5-3;Q56UN5-4;A8MWG7;Q56UN5-5;Q56UN5	.;.;.;.;YSK4_HUMAN	C	1049;936;231;231;1066;439	ENSP00000365005:S1049C;ENSP00000351140:S936C;ENSP00000365004:S231C;ENSP00000376650:S231C;ENSP00000376647:S1066C;ENSP00000392827:S439C	ENSP00000351140:S936C	S	-	2	0	YSK4	135457792	1.000000	0.71417	1.000000	0.80357	0.120000	0.20174	3.272000	0.51616	1.507000	0.48752	-0.287000	0.09952	TCT	.	.		0.388	MAP3K19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000158244.1	NM_025052		C	135741322	G	C	135741322	3	2	300	1	0	0	0	0	1	0	0	0	17510	942	33	4	852	4	YSK4	2	135741322	Missense_Mutation	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10	63	135741322	107458051	22	43361										
KIF5C	3800	hgsc.bcm.edu	37	chr2	149864490	149864490	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	aatgcagagtgtggagttggAcaacgatgatggagggggca	18	4	0	2			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:149864490A>G	ENST00000435030.1	+	23	2827	c.2459A>G	c.(2458-2460)gAc>gGc	p.D820G	KIF5C_ENST00000414838.2_Missense_Mutation_p.D725G|KIF5C_ENST00000397413.1_Missense_Mutation_p.D588G|KIF5C_ENST00000464066.1_3'UTR			O60282	KIF5C_HUMAN	kinesin family member 5C	820					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mRNA transport (GO:0051028)|organelle organization (GO:0006996)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(221;0.108)		GTGGAGTTGGACAACGATGAT	0.527																																					p.D820G		Atlas-SNP	.											.	KIF5C	166	.	0			c.A2459G						.						70	75	74					2																	149864490		1941	4156	6097	SO:0001583	missense	3800	exon23			AGTTGGACAACGA	AB011103	CCDS74586.1	2q23	2008-02-05			ENSG00000168280	ENSG00000168280		"Kinesins"	6325	protein-coding gene	gene with protein product		604593				7514426	Standard	NM_004522		Approved		uc010zbu.2	O60282	OTTHUMG00000153779	ENST00000435030.1:c.2459A>G	chr2.hg19:g.149864490A>G	ENSP00000393379:p.Asp820Gly	78.0	0.0		75.0	36.0	NM_004522	O95079|Q2YDC5	Missense_Mutation	SNP	ENST00000435030.1	hg19		.	.	.	.	.	.	.	.	.	.	A	21.3	4.124208	0.77436	.	.	ENSG00000168280	ENST00000435030;ENST00000414838;ENST00000334436;ENST00000397413	D;D;D	0.86865	-2.18;-2.18;-2.18	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.81513	0.4838	.	.	.	0.58432	D	0.999998	B;B	0.20368	0.044;0.022	B;B	0.22386	0.039;0.03	T	0.76236	-0.3033	8	.	.	.	.	15.7543	0.78013	1.0:0.0:0.0:0.0	.	820;128	O60282;Q59GB8	KIF5C_HUMAN;.	G	820;725;723;588	ENSP00000393379:D820G;ENSP00000410115:D725G;ENSP00000380560:D588G	.	D	+	2	0	KIF5C	149572736	1.000000	0.71417	1.000000	0.80357	0.657000	0.38888	9.339000	0.96797	2.134000	0.65973	0.460000	0.39030	GAC	.	.		0.527	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000332562.3	NM_004522		G	149864490	A	G	149864490	3	3	300	1	0	0	0	0	1	0	0	0	8316	275	10	2	2471	2	KIF5C	2	149864490	Missense_Mutation	SNP	A	TCGA-G3-AAV4-01A-11D-A382-10	14123168	149864490	93334883	23	43362										
LY75	4065	hgsc.bcm.edu	37	chr2	160755561	160755561	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	ttccatggacgatggtgaagGggtcattagctgagtcaaat	13	6	2	2			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:160755561G>T	ENST00000263636.4	-	2	131	c.104C>A	c.(103-105)cCc>cAc	p.P35H	LY75_ENST00000554112.1_Missense_Mutation_p.P35H|LY75-CD302_ENST00000505052.1_Missense_Mutation_p.P35H|LY75_ENST00000553424.1_Missense_Mutation_p.P35H|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.P35H	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	35	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		GATGGTGAAGGGGTCATTAGC	0.493																																					p.P35H		Atlas-SNP	.											.	LY75	151	.	0			c.C104A						.						155	150	152					2																	160755561		2203	4300	6503	SO:0001583	missense	4065	exon2			GTGAAGGGGTCAT	AF011333	CCDS2211.1	2q24	2011-08-30			ENSG00000054219	ENSG00000054219		"CD molecules", "C-type lectin domain containing"	6729	protein-coding gene	gene with protein product		604524				9553150	Standard	NM_002349		Approved	DEC-205, CLEC13B, CD205		O60449	OTTHUMG00000132025	ENST00000263636.4:c.104C>A	chr2.hg19:g.160755561G>T	ENSP00000263636:p.Pro35His	61.0	0.0		46.0	31.0	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	hg19	CCDS2211.1	.	.	.	.	.	.	.	.	.	.	G	19.98	3.927402	0.73327	.	.	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98	6.02	6.02	0.97574	Ricin B-related lectin (1);Ricin B lectin (2);	0.000000	0.34959	N	0.003556	T	0.63058	0.2479	M	0.72479	2.2	0.33698	D	0.61414	D;D;D	0.69078	0.997;0.991;0.997	P;P;P	0.58970	0.849;0.621;0.847	T	0.70249	-0.4924	10	0.62326	D	0.03	-2.3155	20.5407	0.99260	0.0:0.0:1.0:0.0	.	35;35;35	O60449-3;O60449;O60449-2	.;LY75_HUMAN;.	H	35	ENSP00000451511:P35H;ENSP00000451446:P35H;ENSP00000263636:P35H;ENSP00000423463:P35H;ENSP00000421035:P35H	ENSP00000423463:P35H	P	-	2	0	LY75;LY75-CD302	160463807	0.671000	0.27521	0.999000	0.59377	0.679000	0.39708	3.447000	0.52936	2.865000	0.98341	0.655000	0.94253	CCC	.	.		0.493	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1			T	160755561	G	T	160755561	3	4	300	1	0	0	0	0	1	0	0	0	9108	1232	43	3	5200	3	LY75	2	160755561	Missense_Mutation	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10	10891071	160755561	82443812	24	43363										
FRZB	2487	hgsc.bcm.edu	37	chr2	183731006	183731006	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	caatggtgcagatgggcgcgTacatggcacagaggaagaag	16	7	0	3			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:183731006T>C	ENST00000295113.4	-	1	884	c.275A>G	c.(274-276)tAc>tGc	p.Y92C		NM_001463.3	NP_001454.2	Q92765	SFRP3_HUMAN	frizzled-related protein	92	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				brain development (GO:0007420)|cochlea morphogenesis (GO:0090103)|convergent extension involved in organogenesis (GO:0060029)|epithelium development (GO:0060429)|gonad development (GO:0008406)|mammary gland involution (GO:0060056)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell development (GO:0010721)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of hepatocyte differentiation (GO:0070367)|negative regulation of Wnt signaling pathway (GO:0030178)|neural crest cell differentiation (GO:0014033)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fat cell differentiation (GO:0045600)|skeletal system development (GO:0001501)|somite development (GO:0061053)|vasculature development (GO:0001944)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)	PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)	21			OV - Ovarian serous cystadenocarcinoma(117;0.109)|Epithelial(96;0.231)			GATGGGCGCGTACATGGCACA	0.612																																					p.Y92C		Atlas-SNP	.											.	FRZB	42	.	0			c.A275G						.						91	80	84					2																	183731006		2203	4300	6503	SO:0001583	missense	2487	exon1			GGCGCGTACATGG	U24163	CCDS2286.1	2q32.1	2013-09-19			ENSG00000162998	ENSG00000162998		"Secreted frizzled-related proteins"	3959	protein-coding gene	gene with protein product		605083				8824257, 9118218	Standard	NM_001463		Approved	FRZB-PEN, FRZB1, SRFP3, FRP-3, SFRP3, FRE, FRITZ, FRZB-1, FZRB, hFIZ	uc002upa.2	Q92765	OTTHUMG00000132597	ENST00000295113.4:c.275A>G	chr2.hg19:g.183731006T>C	ENSP00000295113:p.Tyr92Cys	91.0	0.0		90.0	44.0	NM_001463	O00181|Q99686	Missense_Mutation	SNP	ENST00000295113.4	hg19	CCDS2286.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.332653	0.81801	.	.	ENSG00000162998	ENST00000295113	T	0.76968	-1.06	4.78	4.78	0.61160	Frizzled domain (5);	0.000000	0.85682	D	0.000000	D	0.90913	0.7144	H	0.94771	3.58	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93403	0.6762	10	0.87932	D	0	.	14.463	0.67465	0.0:0.0:0.0:1.0	.	92	Q92765	SFRP3_HUMAN	C	92	ENSP00000295113:Y92C	ENSP00000295113:Y92C	Y	-	2	0	FRZB	183439251	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.726000	0.84824	1.992000	0.58205	0.379000	0.24179	TAC	.	.		0.612	FRZB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255808.1	NM_001463		C	183731006	T	C	183731006	3	2	300	1	0	0	0	0	1	0	0	0	6073	1638	57	2	726	2	FRZB	2	183731006	Missense_Mutation	SNP	T	TCGA-G3-AAV4-01A-11D-A382-10	22975445	183731006	59468367	25	43364										
PGAP1	80055	hgsc.bcm.edu	37	chr2	197761869	197761869	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	acatacttgtttagtatcagCatcaataagatcaaagaatg	6	6	3	2			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:197761869C>A	ENST00000354764.4	-	7	1027	c.913G>T	c.(913-915)Gct>Tct	p.A305S	PGAP1_ENST00000409475.1_Missense_Mutation_p.A305S|PGAP1_ENST00000485830.1_5'UTR|PGAP1_ENST00000409188.1_Missense_Mutation_p.A263S	NM_024989.3	NP_079265.2	Q75T13	PGAP1_HUMAN	post-GPI attachment to proteins 1	305					anterior/posterior axis specification (GO:0009948)|attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|embryonic pattern specification (GO:0009880)|forebrain regionalization (GO:0021871)|head development (GO:0060322)|intracellular protein transport (GO:0006886)|myo-inositol transport (GO:0015798)|post-translational protein modification (GO:0043687)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	nuclease activity (GO:0004518)|phosphoric ester hydrolase activity (GO:0042578)			breast(4)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|ovary(6)|stomach(1)|urinary_tract(1)	40						TTAGTATCAGCATCAATAAGA	0.249																																					p.A305S		Atlas-SNP	.											.	PGAP1	84	.	0			c.G913T						.						34	33	33					2																	197761869		2190	4279	6469	SO:0001583	missense	80055	exon7			TATCAGCATCAAT		CCDS2318.1	2q33.1	2014-03-03			ENSG00000197121	ENSG00000197121			25712	protein-coding gene	gene with protein product	"GPI inositol-deacylase"	611655				14734546, 17711852, 24482476	Standard	XM_005246866		Approved	FLJ12377, Bst1, SPG67	uc002utw.3	Q75T13	OTTHUMG00000132743	ENST00000354764.4:c.913G>T	chr2.hg19:g.197761869C>A	ENSP00000346809:p.Ala305Ser	834.0	0.0		862.0	384.0	NM_024989	Q4G0R8|Q4ZG47|Q53SM0|Q6AW92|Q6UWV4|Q9HA24	Missense_Mutation	SNP	ENST00000354764.4	hg19	CCDS2318.1	.	.	.	.	.	.	.	.	.	.	C	12.57	1.976249	0.34848	.	.	ENSG00000197121	ENST00000422382;ENST00000354764;ENST00000409475;ENST00000409188;ENST00000374738	.	.	.	4.65	4.65	0.58169	.	0.270973	0.38436	N	0.001687	T	0.17619	0.0423	N	0.08118	0	0.27349	N	0.9563	B;B;B	0.32467	0.255;0.372;0.118	B;B;B	0.27796	0.016;0.083;0.054	T	0.07366	-1.0776	9	0.09338	T	0.73	-16.2658	15.8224	0.78667	0.0:1.0:0.0:0.0	.	263;305;305	B4DYY6;Q75T13-3;Q75T13	.;.;PGAP1_HUMAN	S	85;305;305;263;85	.	ENSP00000346809:A305S	A	-	1	0	PGAP1	197470114	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.411000	0.44600	2.576000	0.86940	0.563000	0.77884	GCT	.	.		0.249	PGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256103.5	NM_024989		A	197761869	C	A	197761869	3	1	300	1	0	0	0	0	1	0	0	0	11786	710	25	3	1939	3	PGAP1	2	197761869	Missense_Mutation	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	14030863	197761869	45437504	26	43365										
DNER	92737	hgsc.bcm.edu	37	chr2	230312120	230312120	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	gcacagaagtcaataagctgGgcacaggtcggccctgtgaa	13	10	1	2			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:230312120G>A	ENST00000341772.4	-	8	1532	c.1398C>T	c.(1396-1398)gcC>gcT	p.A466A		NM_139072.3	NP_620711.3	Q8NFT8	DNER_HUMAN	delta/notch-like EGF repeat containing	466	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				central nervous system development (GO:0007417)|endocytosis (GO:0006897)|glial cell differentiation (GO:0010001)|neuron migration (GO:0001764)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|skeletal muscle fiber development (GO:0048741)|synapse assembly (GO:0007416)	dendrite (GO:0030425)|early endosome (GO:0005769)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|clathrin binding (GO:0030276)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	63		all_lung(227;0.00413)|Renal(207;0.0113)|Lung NSC(271;0.0211)|all_hematologic(139;0.105)|Acute lymphoblastic leukemia(138;0.175)		Epithelial(121;1.4e-11)|all cancers(144;7.7e-09)|LUSC - Lung squamous cell carcinoma(224;0.034)|Lung(119;0.0375)		CAATAAGCTGGGCACAGGTCG	0.627																																					p.A466A		Atlas-SNP	.											.	DNER	129	.	0			c.C1398T						.						51	47	48					2																	230312120		2203	4300	6503	SO:0001819	synonymous_variant	92737	exon8			AAGCTGGGCACAG	AY358891	CCDS33390.1	2q36.3	2006-10-26			ENSG00000187957	ENSG00000187957			24456	protein-coding gene	gene with protein product		607299				11950833, 11997712	Standard	NM_139072		Approved	UNQ26, bet	uc002vpv.3	Q8NFT8	OTTHUMG00000153637	ENST00000341772.4:c.1398C>T	chr2.hg19:g.230312120G>A		394.0	0.0		372.0	166.0	NM_139072	A6NP39|Q53R88|Q53TP7|Q53TQ5|Q8IYT0|Q8TB42|Q9NTF1|Q9UDM2	Silent	SNP	ENST00000341772.4	hg19	CCDS33390.1																																																																																			.	.		0.627	DNER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331902.1	NM_139072		A	230312120	G	A	230312120	2	1	300	1	0	0	0	0	0	0	0	1	4669	1219	43	3		3	DNER	2	230312120	Silent	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10	32550251	230312120	12887253	27	43366										
TRPM8	79054	hgsc.bcm.edu	37	chr2	234846104	234846104	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	acacaccaaggaatttcctaCcgacgcctttggggatattc	8	12	0	0			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:234846104C>A	ENST00000324695.4	+	4	339	c.299C>A	c.(298-300)aCc>aAc	p.T100N	TRPM8_ENST00000409625.1_Missense_Mutation_p.T23N|TRPM8_ENST00000433712.2_5'UTR|TRPM8_ENST00000355722.4_Missense_Mutation_p.T50N	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8	100					calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|protein homotetramerization (GO:0051289)|protein homotrimerization (GO:0070207)|response to cold (GO:0009409)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(2)|lung(27)|prostate(2)|skin(7)|stomach(2)	66		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)	GAATTTCCTACCGACGCCTTT	0.473																																					p.T100N		Atlas-SNP	.											.	TRPM8	146	.	0			c.C299A						.						154	150	151					2																	234846104		2203	4300	6503	SO:0001583	missense	79054	exon4			TTCCTACCGACGC	AC005538	CCDS33407.1	2q37	2011-12-14			ENSG00000144481	ENSG00000144481		"Voltage-gated ion channels / Transient receptor potential cation channels"	17961	protein-coding gene	gene with protein product		606678				16382100	Standard	NM_024080		Approved		uc002vvh.3	Q7Z2W7	OTTHUMG00000059129	ENST00000324695.4:c.299C>A	chr2.hg19:g.234846104C>A	ENSP00000323926:p.Thr100Asn	152.0	0.0		163.0	73.0	NM_024080	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Missense_Mutation	SNP	ENST00000324695.4	hg19	CCDS33407.1	.	.	.	.	.	.	.	.	.	.	C	19.53	3.844452	0.71488	.	.	ENSG00000144481	ENST00000324695;ENST00000355722;ENST00000409625	T;T;T	0.70164	-0.46;-0.46;-0.46	5.68	5.68	0.88126	.	0.145975	0.47093	D	0.000247	D	0.86414	0.5927	M	0.92784	3.345	0.80722	D	1	D;D	0.76494	0.987;0.999	D;D	0.80764	0.96;0.994	D	0.89215	0.3567	10	0.87932	D	0	-23.5913	18.3402	0.90303	0.0:1.0:0.0:0.0	.	50;100	Q7Z2W7-2;Q7Z2W7	.;TRPM8_HUMAN	N	100;50;23	ENSP00000323926:T100N;ENSP00000347956:T50N;ENSP00000386771:T23N	ENSP00000323926:T100N	T	+	2	0	TRPM8	234510843	1.000000	0.71417	0.623000	0.29173	0.371000	0.29859	6.749000	0.74883	2.676000	0.91093	0.591000	0.81541	ACC	.	.		0.473	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080		A	234846104	C	A	234846104	3	1	300	1	0	0	0	0	1	0	0	0	16607	507	18	3	309	3	TRPM8	2	234846104	Missense_Mutation	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	4533984	234846104	8353269	28	43367										
CAPN7	23473	hgsc.bcm.edu	37	chr3	15262371	15262371	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	gccaaagccacctccagtgaGagcacattttccactgggcg	10	14	0	1			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr3:15262371G>C	ENST00000253693.2	+	5	774	c.521G>C	c.(520-522)aGa>aCa	p.R174T		NM_014296.2	NP_055111.1	Q9Y6W3	CAN7_HUMAN	calpain 7	174					positive regulation of epithelial cell migration (GO:0010634)|self proteolysis (GO:0097264)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|endopeptidase activity (GO:0004175)|MIT domain binding (GO:0090541)			breast(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|skin(2)	22						CCTCCAGTGAGAGCACATTTT	0.468																																					p.R174T		Atlas-SNP	.											.	CAPN7	63	.	0			c.G521C						.						102	94	97					3																	15262371		2203	4300	6503	SO:0001583	missense	23473	exon5			CAGTGAGAGCACA	AB028639	CCDS2624.1	3p24	2008-07-18			ENSG00000131375	ENSG00000131375			1484	protein-coding gene	gene with protein product	"calpain like protease", "homolog of Aspergillus Nidulans PALB"	606400				8163008, 10051333	Standard	NM_014296		Approved	PalBH	uc003bzn.3	Q9Y6W3	OTTHUMG00000129863	ENST00000253693.2:c.521G>C	chr3.hg19:g.15262371G>C	ENSP00000253693:p.Arg174Thr	317.0	0.0		320.0	72.0	NM_014296		Missense_Mutation	SNP	ENST00000253693.2	hg19	CCDS2624.1	.	.	.	.	.	.	.	.	.	.	G	4.322	0.059138	0.08339	.	.	ENSG00000131375	ENST00000253693	D	0.85955	-2.05	5.79	3.95	0.45737	.	0.526289	0.21304	N	0.076748	T	0.80808	0.4694	M	0.72118	2.19	0.46078	D	0.99885	B	0.13594	0.008	B	0.06405	0.002	T	0.72064	-0.4403	10	0.10636	T	0.68	-17.5957	9.775	0.40614	0.0744:0.1392:0.7864:0.0	.	174	Q9Y6W3	CAN7_HUMAN	T	174	ENSP00000253693:R174T	ENSP00000253693:R174T	R	+	2	0	CAPN7	15237375	1.000000	0.71417	0.755000	0.31263	0.065000	0.16274	3.187000	0.50950	1.470000	0.48102	0.555000	0.69702	AGA	.	.		0.468	CAPN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252105.2	NM_014296		C	15262371	G	C	15262371	3	2	300	1	0	0	0	0	1	0	0	0	2633	942	33	4	539	4	CAPN7	3	15262371	Missense_Mutation	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10		15262371	182760059	29	43368										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266101	41266101	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	gcaacagtcttacctggactCtggaatccattctggtgcca	9	12	3	0	rs121913416|rs121913400		TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr3:41266101C>G	ENST00000349496.5	+	3	378	c.98C>G	c.(97-99)tCt>tGt	p.S33C	CTNNB1_ENST00000453024.1_Missense_Mutation_p.S26C|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S33C|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S33C|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S33C	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	33			Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> F (in PTR, MDB and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10666372}.|S -> L (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> Y (in colorectal cancer and PTR; enhances transactivation of target genes). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:9065402}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S33C(168)|p.S33F(97)|p.S33Y(60)|p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.S33L(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S33N(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.D32fs*9(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.S29_H36del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.D32_H36>D(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TACCTGGACTCTGGAATCCAT	0.488	S33C(SKMEL1_SKIN)|S33F(SW1573_LUNG)|S33Y(SW48_LARGE_INTESTINE)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S33C	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,0,359	CTNNB1	4904	.	468	Substitution - Missense(331)|Deletion - In frame(111)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(165)|central_nervous_system(82)|large_intestine(40)|endometrium(37)|stomach(32)|skin(21)|ovary(20)|pituitary(19)|pancreas(12)|lung(7)|biliary_tract(6)|soft_tissue(4)|bone(4)|breast(3)|prostate(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|parathyroid(2)|small_intestine(2)|thyroid(1)|NS(1)|urinary_tract(1)|adrenal_gland(1)	c.C98G						.						92	77	82					3																	41266101		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	TGGACTCTGGAAT	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.98C>G	chr3.hg19:g.41266101C>G	ENSP00000344456:p.Ser33Cys	160.0	0.0		148.0	71.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.381716	0.82792	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.51071	0.72;0.72;0.72;0.72;0.72;0.72;0.72;0.72;0.72	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.72053	0.3413	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74188	-0.3746	10	0.87932	D	0	-10.7796	19.9596	0.97236	0.0:1.0:0.0:0.0	.	33	P35222	CTNB1_HUMAN	C	26;33;33;33;33;26;33;33;33	ENSP00000400508:S26C;ENSP00000385604:S33C;ENSP00000412219:S33C;ENSP00000379486:S33C;ENSP00000344456:S33C;ENSP00000411226:S26C;ENSP00000379488:S33C;ENSP00000409302:S33C;ENSP00000401599:S33C	ENSP00000344456:S33C	S	+	2	0	CTNNB1	41241105	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.726000	0.93360	0.655000	0.94253	TCT	.	.		0.488	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266101	C	G	41266101	3	3	300	1	0	0	0	0	1	0	0	0	4018	913	32	4	104	4	CTNNB1	3	41266101	Missense_Mutation	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	26003730	41266101	156756329	30	43369										
ROBO1	6091	hgsc.bcm.edu	37	chr3	78701014	78701014	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	tatgaaggccggctgcttcaCcacatctgaaatctgctgag	10	11	3	3			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr3:78701014C>T	ENST00000464233.1	-	19	2793	c.2680G>A	c.(2680-2682)Gtg>Atg	p.V894M	ROBO1_ENST00000467549.1_Missense_Mutation_p.V858M|ROBO1_ENST00000495273.1_Missense_Mutation_p.V858M|ROBO1_ENST00000436010.2_Missense_Mutation_p.V855M	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	894					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		GGCTGCTTCACCACATCTGAA	0.502																																					p.V894M		Atlas-SNP	.											.	ROBO1	833	.	0			c.G2680A						.						132	132	132					3																	78701014		2044	4192	6236	SO:0001583	missense	6091	exon19			GCTTCACCACATC	AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.2680G>A	chr3.hg19:g.78701014C>T	ENSP00000420321:p.Val894Met	130.0	0.0		122.0	47.0	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Missense_Mutation	SNP	ENST00000464233.1	hg19	CCDS54611.1	.	.	.	.	.	.	.	.	.	.	C	18.57	3.652506	0.67472	.	.	ENSG00000169855	ENST00000436010;ENST00000398412;ENST00000464233;ENST00000495273;ENST00000467549;ENST00000398414	T;T;T;T	0.63417	-0.02;-0.04;-0.04;0.03	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	T	0.79873	0.4521	M	0.71036	2.16	0.80722	D	1	D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0	D;D;D;D;D	0.83275	0.996;0.993;0.979;0.993;0.996	T	0.77183	-0.2681	9	.	.	.	.	20.4434	0.99119	0.0:1.0:0.0:0.0	.	858;894;858;858;855	Q9Y6N7-3;Q9Y6N7;B2RXI1;E9PD49;Q9Y6N7-4	.;ROBO1_HUMAN;.;.;.	M	855;858;894;858;858;898	ENSP00000406043:V855M;ENSP00000420321:V894M;ENSP00000420637:V858M;ENSP00000417992:V858M	.	V	-	1	0	ROBO1	78783704	1.000000	0.71417	0.969000	0.41365	0.004000	0.04260	7.818000	0.86416	2.838000	0.97847	0.655000	0.94253	GTG	.	.		0.502	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		T	78701014	C	T	78701014	3	4	300	1	0	0	0	0	1	0	0	0	13528	507	18	3	2327	3	ROBO1	3	78701014	Missense_Mutation	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	37434913	78701014	119321416	31	43370										
MYH15	22989	hgsc.bcm.edu	37	chr3	108140007	108140007	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	agtcaccttatctagctttgCagttgcttcatgcaagcgct	8	11	3	0			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr3:108140007C>T	ENST00000273353.3	-	29	3873	c.3817G>A	c.(3817-3819)Gca>Aca	p.A1273T		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	1273						cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						TCTAGCTTTGCAGTTGCTTCA	0.453																																					p.A1273T		Atlas-SNP	.											.	MYH15	223	.	0			c.G3817A						.						232	213	219					3																	108140007		1942	4146	6088	SO:0001583	missense	22989	exon29			GCTTTGCAGTTGC	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"Myosins / Myosin superfamily : Class II"	31073	protein-coding gene	gene with protein product		609929	"myosin, heavy polypeptide 15"			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.3817G>A	chr3.hg19:g.108140007C>T	ENSP00000273353:p.Ala1273Thr	39.0	0.0		51.0	23.0	NM_014981		Missense_Mutation	SNP	ENST00000273353.3	hg19	CCDS43127.1	.	.	.	.	.	.	.	.	.	.	C	0.707	-0.788757	0.02884	.	.	ENSG00000144821	ENST00000273353	T	0.77750	-1.12	4.72	1.89	0.25635	Myosin tail (1);	.	.	.	.	T	0.54208	0.1844	N	0.10972	0.075	0.20489	N	0.999891	B	0.06786	0.001	B	0.14023	0.01	T	0.35400	-0.9790	9	0.08599	T	0.76	.	8.0084	0.30338	0.0:0.6028:0.0:0.3972	.	1273	Q9Y2K3	MYH15_HUMAN	T	1273	ENSP00000273353:A1273T	ENSP00000273353:A1273T	A	-	1	0	MYH15	109622697	0.000000	0.05858	0.985000	0.45067	0.612000	0.37316	-0.324000	0.07986	0.609000	0.30018	0.655000	0.94253	GCA	.	.		0.453	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988		T	108140007	C	T	108140007	3	4	300	1	0	0	0	0	1	0	0	0	10043	710	25	3	2079	3	MYH15	3	108140007	Missense_Mutation	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	29438993	108140007	89882423	32	43371										
AMOTL2	51421	hgsc.bcm.edu	37	chr3	134080568	134080568	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	cctgctccagcagctcggcaCgccgccgctggtcctcgatg	12	18	0	0	rs543579880		TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr3:134080568C>A	ENST00000422605.2	-	6	1527	c.1361G>T	c.(1360-1362)cGt>cTt	p.R454L	AMOTL2_ENST00000249883.5_Missense_Mutation_p.R454L|AMOTL2_ENST00000513145.1_Missense_Mutation_p.R454L|AMOTL2_ENST00000514516.1_Missense_Mutation_p.R512L			Q9Y2J4	AMOL2_HUMAN	angiomotin like 2	454					hippo signaling (GO:0035329)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|tight junction (GO:0005923)				endometrium(8)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	19						CAGCTCGGCACGCCGCCGCTG	0.647																																					p.R454L		Atlas-SNP	.											.	AMOTL2	52	.	0			c.G1361T						.						11	12	12					3																	134080568		2197	4283	6480	SO:0001583	missense	51421	exon6			TCGGCACGCCGCC	AF175966	CCDS33860.1, CCDS63783.1, CCDS63784.1	3q21-q22	2008-07-18			ENSG00000114019	ENSG00000114019			17812	protein-coding gene	gene with protein product	"Leman coiled-coil protein", "angiomotin-like protein 2"	614658					Standard	NM_016201		Approved	LCCP	uc003eqg.1	Q9Y2J4	OTTHUMG00000159777	ENST00000422605.2:c.1361G>T	chr3.hg19:g.134080568C>A	ENSP00000409999:p.Arg454Leu	68.0	0.0		55.0	27.0	NM_016201	A8K6F1|B7Z5Q1|E9PHW3|Q53EP1|Q96F99|Q9UKB4	Missense_Mutation	SNP	ENST00000422605.2	hg19		.	.	.	.	.	.	.	.	.	.	C	19.79	3.892906	0.72524	.	.	ENSG00000114019	ENST00000249883;ENST00000422605;ENST00000514516;ENST00000513145	T;T;T;T	0.24151	1.87;1.87;1.87;1.87	5.32	4.43	0.53597	.	0.053091	0.85682	D	0.000000	T	0.29749	0.0743	L	0.53249	1.67	0.58432	D	0.99999	P;P;P	0.44690	0.841;0.841;0.753	B;B;B	0.42882	0.401;0.401;0.325	T	0.11372	-1.0590	10	0.66056	D	0.02	-15.3774	14.5284	0.67905	0.0:0.9287:0.0:0.0713	.	454;454;512	Q9Y2J4-3;Q9Y2J4-2;E9PHW3	.;.;.	L	454;454;512;454	ENSP00000249883:R454L;ENSP00000409999:R454L;ENSP00000424765:R512L;ENSP00000425475:R454L	ENSP00000249883:R454L	R	-	2	0	AMOTL2	135563258	0.920000	0.31207	0.854000	0.33618	0.991000	0.79684	1.947000	0.40293	1.447000	0.47661	0.563000	0.77884	CGT	.	.		0.647	AMOTL2-014	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000358149.1	NM_016201		A	134080568	C	A	134080568	3	1	300	1	0	0	0	0	1	0	0	0	584	536	19	1	1001	1	AMOTL2	3	134080568	Missense_Mutation	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	25940561	134080568	63941862	33	43372										
LSG1	55341	hgsc.bcm.edu	37	chr3	194369508	194369508	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	tgccataggtagcttctaaaAcatgtcttggaatattctgg	9	7	3	0			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr3:194369508A>C	ENST00000265245.5	-	11	1759	c.1445T>G	c.(1444-1446)gTt>gGt	p.V482G	AC046143.2_ENST00000582474.1_RNA	NM_018385.2	NP_060855.2	Q9H089	LSG1_HUMAN	large 60S subunit nuclear export GTPase 1	482					GTP catabolic process (GO:0006184)|nuclear export (GO:0051168)|protein transport (GO:0015031)|ribosome biogenesis (GO:0042254)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(3)|large_intestine(2)|lung(9)	16	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;4.34e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;7.55e-06)		AGCTTCTAAAACATGTCTTGG	0.463																																					p.V482G		Atlas-SNP	.											.	LSG1	38	.	0			c.T1445G						.						161	144	149					3																	194369508		2203	4300	6503	SO:0001583	missense	55341	exon11			TCTAAAACATGTC		CCDS33922.1	3q29	2013-08-21	2013-08-21		ENSG00000041802	ENSG00000041802			25652	protein-coding gene	gene with protein product		610780	"large subunit GTPase 1 homolog (S. cerevisiae)"			11230166	Standard	NM_018385		Approved	FLJ11301	uc003fui.3	Q9H089	OTTHUMG00000156021	ENST00000265245.5:c.1445T>G	chr3.hg19:g.194369508A>C	ENSP00000265245:p.Val482Gly	109.0	0.0		98.0	38.0	NM_018385	A0JLT4|A0PJK3|A6NI18|Q7L9H8|Q9NUK8	Missense_Mutation	SNP	ENST00000265245.5	hg19	CCDS33922.1	.	.	.	.	.	.	.	.	.	.	A	26.8	4.767811	0.90020	.	.	ENSG00000041802	ENST00000265245	T	0.16897	2.31	5.79	5.79	0.91817	.	0.122706	0.53938	D	0.000044	T	0.42562	0.1208	M	0.85462	2.755	0.80722	D	1	D	0.59357	0.985	D	0.65323	0.934	T	0.44559	-0.9320	10	0.66056	D	0.02	.	10.4659	0.44607	0.9278:0.0:0.0722:0.0	.	482	Q9H089	LSG1_HUMAN	G	482	ENSP00000265245:V482G	ENSP00000265245:V482G	V	-	2	0	LSG1	195850797	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.574000	0.82434	2.215000	0.71742	0.528000	0.53228	GTT	.	.		0.463	LSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342740.1	NM_018385		C	194369508	A	C	194369508	3	2	300	1	0	0	0	0	1	0	0	0	9058	43	2	5	547	5	LSG1	3	194369508	Missense_Mutation	SNP	A	TCGA-G3-AAV4-01A-11D-A382-10	60288940	194369508	3652922	34	43373										
DLG1	1739	hgsc.bcm.edu	37	chr3	196867115	196867115	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	tccgtacctcctgcaatgctGaaaccaagccctgaatttcc	6	15	0	2			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr3:196867115G>T	ENST00000419354.1	-	9	994	c.708C>A	c.(706-708)ttC>ttA	p.F236L	DLG1_ENST00000452595.1_Missense_Mutation_p.F120L|DLG1_ENST00000448528.2_Missense_Mutation_p.F236L|DLG1_ENST00000357674.4_Missense_Mutation_p.F203L|DLG1_ENST00000443183.1_Missense_Mutation_p.F120L|DLG1_ENST00000346964.2_Missense_Mutation_p.F236L|DLG1_ENST00000314062.3_Missense_Mutation_p.F185L|DLG1_ENST00000422288.1_Missense_Mutation_p.F185L|DLG1_ENST00000450955.1_Missense_Mutation_p.F203L|DLG1_ENST00000392382.2_Missense_Mutation_p.F203L			Q12959	DLG1_HUMAN	discs, large homolog 1 (Drosophila)	236	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				actin filament organization (GO:0007015)|activation of protein kinase activity (GO:0032147)|amyloid precursor protein metabolic process (GO:0042982)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|cortical actin cytoskeleton organization (GO:0030866)|dephosphorylation (GO:0016311)|embryonic skeletal system morphogenesis (GO:0048704)|endothelial cell proliferation (GO:0001935)|establishment or maintenance of cell polarity (GO:0007163)|hard palate development (GO:0060022)|immunological synapse formation (GO:0001771)|lens development in camera-type eye (GO:0002088)|membrane raft organization (GO:0031579)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell proliferation (GO:0042130)|nucleotide phosphorylation (GO:0046939)|peristalsis (GO:0030432)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell proliferation (GO:0008284)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|protein localization to plasma membrane (GO:0072659)|regulation of membrane potential (GO:0042391)|regulation of myelination (GO:0031641)|regulation of sodium ion transmembrane transport (GO:1902305)|reproductive structure development (GO:0048608)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|synaptic transmission (GO:0007268)|T cell activation (GO:0042110)|T cell cytokine production (GO:0002369)|tight junction assembly (GO:0070830)|viral process (GO:0016032)	basal lamina (GO:0005605)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell projection membrane (GO:0031253)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|immunological synapse (GO:0001772)|intercalated disc (GO:0014704)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|membrane raft (GO:0045121)|microtubule (GO:0005874)|MPP7-DLG1-LIN7 complex (GO:0097025)|myelin sheath abaxonal region (GO:0035748)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	cytoskeletal protein binding (GO:0008092)|guanylate kinase activity (GO:0004385)|ion channel binding (GO:0044325)|L27 domain binding (GO:0097016)|mitogen-activated protein kinase kinase binding (GO:0031434)|phosphatase binding (GO:0019902)|phosphoprotein phosphatase activity (GO:0004721)|potassium channel regulator activity (GO:0015459)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	26	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)		CTGCAATGCTGAAACCAAGCC	0.418																																					p.F236L		Atlas-SNP	.											.	DLG1	120	.	0			c.C708A						.						133	129	130					3																	196867115		2203	4300	6503	SO:0001583	missense	1739	exon9			AATGCTGAAACCA	U13897	CCDS3327.1, CCDS43194.1, CCDS56300.1, CCDS56301.1, CCDS75072.1	3q29	2008-12-15	2001-11-28		ENSG00000075711	ENSG00000075711			2900	protein-coding gene	gene with protein product	"discs large homolog 1", "presynaptic protein SAP97", "synapse-associated protein 97"	601014	"discs, large (Drosophila) homolog 1"			7937897, 8825652	Standard	NM_004087		Approved	SAP97, SAP-97, hdlg, DLGH1, dJ1061C18.1.1	uc003fxn.4	Q12959	OTTHUMG00000047972	ENST00000419354.1:c.708C>A	chr3.hg19:g.196867115G>T	ENSP00000407531:p.Phe236Leu	114.0	0.0		127.0	57.0	NM_001098424	A5YKK7|B4DGU1|B4DGZ8|B7ZMM0|B9EIQ5|D3DXB8|D3DXB9|E7EWL7|E9PG21|Q12958	Missense_Mutation	SNP	ENST00000419354.1	hg19	CCDS43194.1	.	.	.	.	.	.	.	.	.	.	G	19.86	3.904979	0.72868	.	.	ENSG00000075711	ENST00000346964;ENST00000359922;ENST00000357674;ENST00000381807;ENST00000314062;ENST00000419354;ENST00000452595;ENST00000422288;ENST00000448528;ENST00000443183;ENST00000392382;ENST00000450955;ENST00000447466;ENST00000453607	T;T;T;T;T;T;T;T;T;T;T;T	0.18502	2.21;2.21;2.21;2.21;2.21;2.21;2.21;2.21;2.21;2.21;2.21;2.21	5.67	2.47	0.30058	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.33147	0.0853	M	0.67625	2.065	0.53688	D	0.99997	D;D;D;D;D;D;D	0.89917	0.987;1.0;1.0;1.0;1.0;0.999;1.0	P;D;D;D;D;D;D	0.91635	0.895;0.991;0.999;0.999;0.999;0.992;0.999	T	0.04413	-1.0953	10	0.66056	D	0.02	.	5.6317	0.17514	0.4577:0.0:0.5423:0.0	.	203;120;120;120;203;236;236	Q12959-4;E9PG21;E7EWL7;B4DGU1;Q12959-3;Q12959;Q12959-2	.;.;.;.;.;DLG1_HUMAN;.	L	236;236;203;236;185;236;120;185;236;120;203;203;45;89	ENSP00000345731:F236L;ENSP00000350303:F203L;ENSP00000321087:F185L;ENSP00000407531:F236L;ENSP00000398939:F120L;ENSP00000413238:F185L;ENSP00000391732:F236L;ENSP00000396658:F120L;ENSP00000376187:F203L;ENSP00000411278:F203L;ENSP00000398702:F45L;ENSP00000412579:F89L	ENSP00000321087:F185L	F	-	3	2	DLG1	198351512	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	0.789000	0.26886	0.878000	0.35920	-0.942000	0.02676	TTC	.	.		0.418	DLG1-008	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000258170.2	NM_004087		T	196867115	G	T	196867115	3	4	300	1	0	0	0	0	1	0	0	0	4556	1281	45	3	2182	3	DLG1	3	196867115	Missense_Mutation	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10	2497607	196867115	1155315	35	43374										
FGFRL1	53834	hgsc.bcm.edu	37	chr4	1017449	1017449	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	atgacattagcccagggaagGagagcctggggcccgacagc	15	11	0	2			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr4:1017449G>T	ENST00000398484.2	+	5	953	c.373G>T	c.(373-375)Gag>Tag	p.E125*	FGFRL1_ENST00000510644.1_Nonsense_Mutation_p.E125*|FGFRL1_ENST00000264748.6_Nonsense_Mutation_p.E125*|FGFRL1_ENST00000504138.1_Nonsense_Mutation_p.E125*			Q8N441	FGRL1_HUMAN	fibroblast growth factor receptor-like 1	125					diaphragm development (GO:0060539)|heart valve morphogenesis (GO:0003179)|negative regulation of cell proliferation (GO:0008285)|skeletal system development (GO:0001501)|ventricular septum morphogenesis (GO:0060412)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)			endometrium(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	13			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			CCCAGGGAAGGAGAGCCTGGG	0.697																																					p.E125X		Atlas-SNP	.											.	FGFRL1	77	.	0			c.G373T						.						11	13	12					4																	1017449		2191	4291	6482	SO:0001587	stop_gained	53834	exon4			GGGAAGGAGAGCC		CCDS3344.1	4p16	2013-01-11			ENSG00000127418	ENSG00000127418		"Immunoglobulin superfamily / I-set domain containing"	3693	protein-coding gene	gene with protein product		605830					Standard	NM_021923		Approved		uc003gcg.3	Q8N441	OTTHUMG00000118998	ENST00000398484.2:c.373G>T	chr4.hg19:g.1017449G>T	ENSP00000381498:p.Glu125*	182.0	0.0		114.0	68.0	NM_001004356	B2RAU9|Q6PJN1|Q9BXN7|Q9H4D7	Nonsense_Mutation	SNP	ENST00000398484.2	hg19	CCDS3344.1	.	.	.	.	.	.	.	.	.	.	g	15.25	2.776659	0.49786	.	.	ENSG00000127418	ENST00000398484;ENST00000542622;ENST00000510644;ENST00000504138;ENST00000507339;ENST00000264748	.	.	.	4.24	2.44	0.29823	.	1.293420	0.05166	N	0.498823	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-17.007	4.7739	0.13169	0.2713:0.1616:0.5672:0.0	.	.	.	.	X	125;95;125;125;125;125	.	ENSP00000264748:E125X	E	+	1	0	FGFRL1	1007449	0.476000	0.25901	0.136000	0.22124	0.580000	0.36256	2.004000	0.40854	0.229000	0.21039	0.436000	0.28706	GAG	.	.		0.697	FGFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239195.2	NM_021923		T	1017449	G	T	1017449	4	4	300	1	0	0	0	0	0	1	0	0	5877	1175	41	3	383	3	FGFRL1	4	1017449	Nonsense_Mutation	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10		1017449	190136827	36	43375										
PRDM8	56978	hgsc.bcm.edu	37	chr4	81123578	81123578	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	gaaattcccggaggaggcggCggagggcggcggtggcgctg	22	9	0	0			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr4:81123578C>T	ENST00000504452.1	+	8	1801	c.962C>T	c.(961-963)gCg>gTg	p.A321V	PRDM8_ENST00000339711.4_Missense_Mutation_p.A321V|PRDM8_ENST00000415738.2_Missense_Mutation_p.A321V			Q9NQV8	PRDM8_HUMAN	PR domain containing 8	321	Gly-rich.				corpus callosum morphogenesis (GO:0021540)|corticospinal tract morphogenesis (GO:0021957)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(2)	10						GAGGAGGCGGCGGAGGGCGGC	0.741																																					p.A321V		Atlas-SNP	.											.	PRDM8	44	.	0			c.C962T						.						2	3	3					4																	81123578		1143	2876	4019	SO:0001583	missense	56978	exon4			AGGCGGCGGAGGG	AF275815	CCDS43243.1	4q21	2008-08-21				ENSG00000152784			13993	protein-coding gene	gene with protein product							Standard	NM_020226		Approved		uc003hmc.4	Q9NQV8		ENST00000504452.1:c.962C>T	chr4.hg19:g.81123578C>T	ENSP00000423985:p.Ala321Val	119.0	0.0		82.0	47.0	NM_001099403	A8K7X2|Q6IQ36	Missense_Mutation	SNP	ENST00000504452.1	hg19	CCDS43243.1	.	.	.	.	.	.	.	.	.	.	C	8.401	0.842005	0.16963	.	.	ENSG00000152784	ENST00000504452;ENST00000515013;ENST00000339711;ENST00000415738	T;T;T;T	0.65549	-0.16;0.37;-0.16;-0.16	4.11	-1.67	0.08238	.	0.809757	0.10439	N	0.674507	T	0.37210	0.0995	N	0.19112	0.55	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.14980	-1.0453	10	0.27785	T	0.31	.	1.8168	0.03102	0.1481:0.4421:0.132:0.2777	.	321	Q9NQV8	PRDM8_HUMAN	V	321	ENSP00000423985:A321V;ENSP00000425149:A321V;ENSP00000339764:A321V;ENSP00000406998:A321V	ENSP00000339764:A321V	A	+	2	0	PRDM8	81342602	0.028000	0.19301	0.006000	0.13384	0.327000	0.28475	0.389000	0.20751	-0.184000	0.10567	0.313000	0.20887	GCG	.	.		0.741	PRDM8-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362793.1			T	81123578	C	T	81123578	3	4	300	1	0	0	0	0	1	0	0	0	12474	768	27	1	972	1	PRDM8	4	81123578	Missense_Mutation	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	80106129	81123578	110030698	37	43376										
SPARCL1	8404	hgsc.bcm.edu	37	chr4	88411474	88411474	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	agttgatgcccctttttggtCccctccagtctgcatttagt	8	12	1	1			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr4:88411474C>A	ENST00000282470.6	-	7	1952	c.1482G>T	c.(1480-1482)ggG>ggT	p.G494G	SPARCL1_ENST00000418378.1_Silent_p.G494G|SPARCL1_ENST00000503414.1_Silent_p.G369G	NM_004684.4	NP_004675.3	Q14515	SPRL1_HUMAN	SPARC-like 1 (hevin)	494	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(2)	21				OV - Ovarian serous cystadenocarcinoma(123;0.00118)		CCTTTTTGGTCCCCTCCAGTC	0.458																																					p.G494G		Atlas-SNP	.											.	SPARCL1	59	.	0			c.G1482T						.						257	265	262					4																	88411474		2203	4300	6503	SO:0001819	synonymous_variant	8404	exon7			TTTGGTCCCCTCC	X86693	CCDS3622.1	4q22-q25	2013-01-10	2008-08-29		ENSG00000152583	ENSG00000152583		"EF-hand domain containing"	11220	protein-coding gene	gene with protein product		606041	"SPARC-like 1 (mast9, hevin)"			8488563, 7600298, 16844696	Standard	NM_001128310		Approved	MAST9	uc003hqs.4	Q14515	OTTHUMG00000130605	ENST00000282470.6:c.1482G>T	chr4.hg19:g.88411474C>A		80.0	0.0		57.0	28.0	NM_004684	B4E2Z0|E7ESU2|Q14800	Silent	SNP	ENST00000282470.6	hg19	CCDS3622.1																																																																																			.	.		0.458	SPARCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253059.2			A	88411474	C	A	88411474	2	1	300	1	0	0	0	0	0	0	0	1	15011	842	30	3		3	SPARCL1	4	88411474	Silent	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	7287896	88411474	102742802	38	43377										
PLRG1	5356	hgsc.bcm.edu	37	chr4	155460255	155460255	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	ctaattaggaaaatacacttActgtcttggatgtaaaacca	6	7	1	0			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr4:155460255A>G	ENST00000499023.2	-	12	1278		c.e12+1		PLRG1_ENST00000393905.2_Splice_Site|PLRG1_ENST00000302078.5_Splice_Site	NM_001201564.1|NM_002669.3	NP_001188493.1|NP_002660.1	O43660	PLRG1_HUMAN	pleiotropic regulator 1						mRNA splicing, via spliceosome (GO:0000398)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|protein localization to nucleus (GO:0034504)|regulation of RNA biosynthetic process (GO:2001141)|signal transduction (GO:0007165)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|skin(1)|urinary_tract(1)	22	all_hematologic(180;0.215)	Renal(120;0.0854)				AAATACACTTACTGTCTTGGA	0.368																																					.		Atlas-SNP	.											.	PLRG1	43	.	0			c.1151+2T>C						.						192	178	183					4																	155460255		2202	4300	6502	SO:0001630	splice_region_variant	5356	exon13			ACACTTACTGTCT	AF044333	CCDS34083.1, CCDS56341.1	4q31.2-q32.1	2013-01-10	2011-05-19		ENSG00000171566	ENSG00000171566		"WD repeat domain containing"	9089	protein-coding gene	gene with protein product	"transport and golgi organization 4 homolog (Drosophila)"	605961	"pleiotropic regulator 1 (PRL1, Arabidopsis homolog)", "pleiotropic regulator 1 (PRL1 homolog, Arabidopsis)"				Standard	NM_002669		Approved	PRL1, Prp46, PRPF46, Cwc1, TANGO4	uc003iny.3	O43660	OTTHUMG00000161411	ENST00000499023.2:c.1151+1T>C	chr4.hg19:g.155460255A>G		80.0	0.0		90.0	53.0	NM_002669	B3KMK4|Q3KQY5|Q8WUD8	Splice_Site	SNP	ENST00000499023.2	hg19	CCDS34083.1	.	.	.	.	.	.	.	.	.	.	A	20.0	3.931131	0.73327	.	.	ENSG00000171566	ENST00000499023;ENST00000393905;ENST00000503251;ENST00000302078	.	.	.	5.83	5.83	0.93111	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.2127	0.82178	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PLRG1	155679705	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	8.730000	0.91510	2.236000	0.73375	0.533000	0.62120	.	.	.		0.368	PLRG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364824.1	NM_002669	Intron	G	155460255	A	G	155460255	5	3	300	1	0	0	0	0	0	0	1	0	12115	405	14	2	407	2	PLRG1	4	155460255	Splice_Site	SNP	A	TCGA-G3-AAV4-01A-11D-A382-10	67048781	155460255	35694021	39	43378										
ANP32C	55016	hgsc.bcm.edu	37	chr4	165118847	165118847	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	tccgcagctctgaatgaatcCgtctgcccatctccatctct	6	16	4	2			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr4:165118847C>T	ENST00000503008.1	-	2	864				MARCH1_ENST00000508725.1_Intron|MARCH1_ENST00000514618.1_Intron	NM_001166373.1	NP_001159845.1	Q8TCQ1	MARH1_HUMAN	membrane-associated ring finger (C3HC4) 1, E3 ubiquitin protein ligase						antigen processing and presentation of peptide antigen via MHC class II (GO:0002495)|immune response (GO:0006955)|protein polyubiquitination (GO:0000209)	cytoplasmic vesicle (GO:0031410)|early endosome membrane (GO:0031901)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	ligase activity (GO:0016874)|MHC protein binding (GO:0042287)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|lung(20)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	36	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				TGAATGAATCCGTCTGCCCAT	0.547																																					p.R6Q		Atlas-SNP	.											.	ANP32C	59	.	0			c.G17A						.						99	102	101					4																	165118847		2203	4300	6503	SO:0001627	intron_variant	23520	exon1			TGAATCCGTCTGC	AK000675	CCDS3806.1, CCDS54814.1	4q32.2	2013-01-09	2012-02-23			ENSG00000145416		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	26077	protein-coding gene	gene with protein product		613331	"membrane-associated ring finger (C3HC4) 1"			14722266	Standard	NM_017923		Approved	FLJ20668, MARCH-I, RNF171	uc003iqs.2	Q8TCQ1		ENST00000503008.1:c.113-86033G>A	chr4.hg19:g.165118847C>T		86.0	0.0		67.0	17.0	NM_012403	D3DP29|Q9NWR0	Missense_Mutation	SNP	ENST00000503008.1	hg19	CCDS54814.1																																																																																			.	.		0.547	MARCH1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364493.2	NM_017923		T	165118847	C	T	165118847	1	4	300	0	1	0	0	0	0	0	0	0	707	652	23	1		1	ANP32C	4	165118847	Intron	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	9658592	165118847	26035429	40	43379										
FBN2	2201	hgsc.bcm.edu	37	chr5	127595357	127595357	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	ctttggtggatgcggaagacGctgtcatcgttcccttgaga	13	9	1	2	rs140437100		TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr5:127595357G>A	ENST00000508053.1	-	71	9503	c.8529C>T	c.(8527-8529)agC>agT	p.S2843S	FBN2_ENST00000262464.4_Silent_p.S2843S			P35556	FBN2_HUMAN	fibrillin 2	2843					anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.S2843S(2)		NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		TGCGGAAGACGCTGTCATCGT	0.552																																					p.S2843S		Atlas-SNP	.											FBN2_ENST00000508053,NS,carcinoma,0,1	FBN2	858	.	2	Substitution - coding silent(2)	endometrium(2)	c.C8529T						.	G		1,4405	2.1+/-5.4	0,1,2202	209	181	190		8529	-0.6	0	5	dbSNP_134	190	0,8600		0,0,4300	no	coding-synonymous	FBN2	NM_001999.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		2843/2913	127595357	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	2201	exon65			GAAGACGCTGTCA	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.8529C>T	chr5.hg19:g.127595357G>A		134.0	0.0		143.0	69.0	NM_001999	B4DU01|Q59ES6	Silent	SNP	ENST00000508053.1	hg19	CCDS34222.1																																																																																			.	G|1.000;A|0.000		0.552	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		A	127595357	G	A	127595357	2	1	300	1	0	0	0	0	0	0	0	1	5711	1078	38	1		1	FBN2	5	127595357	Silent	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10		127595357	53319903	41	43380										
PCDHGA4	56111	hgsc.bcm.edu	37	chr5	140736155	140736155	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	ctactctgcttacattcctgAaaacaaccccagaggagcct	6	14	1	2			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr5:140736155A>C	ENST00000571252.1	+	1	1388	c.1388A>C	c.(1387-1389)gAa>gCa	p.E463A	PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018917.2	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4	463	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TACATTCCTGAAAACAACCCC	0.488																																					p.E463A		Atlas-SNP	.											.	PCDHGA4	150	.	0			c.A1388C						.						106	110	109					5																	140736155		2063	4247	6310	SO:0001583	missense	56111	exon1			TTCCTGAAAACAA	AF152511	CCDS58979.1, CCDS58979.2, CCDS75331.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8702	other	protocadherin		606291				10380929	Standard	NM_018917		Approved	PCDH-GAMMA-A4		Q9Y5G9		ENST00000571252.1:c.1388A>C	chr5.hg19:g.140736155A>C	ENSP00000458570:p.Glu463Ala	107.0	0.0		126.0	58.0	NM_018917	Q9Y5D3	Missense_Mutation	SNP	ENST00000571252.1	hg19	CCDS58979.1																																																																																			.	.		0.488	PCDHGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437959.1	NM_018917		C	140736155	A	C	140736155	3	2	300	1	0	0	0	0	1	0	0	0	11565	246	9	5	1390	5	PCDHGA4	5	140736155	Missense_Mutation	SNP	A	TCGA-G3-AAV4-01A-11D-A382-10	13140798	140736155	40179105	42	43381										
DIAPH1	1729	hgsc.bcm.edu	37	chr5	140908429	140908429	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	cagacacaatctctggcttgAtattctccacttgctcgctg	7	13	2	2			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr5:140908429A>C	ENST00000398557.4	-	22	2998	c.2858T>G	c.(2857-2859)aTc>aGc	p.I953S	DIAPH1_ENST00000389057.5_Missense_Mutation_p.I944S|DIAPH1_ENST00000494967.1_5'UTR|DIAPH1_ENST00000520569.1_Missense_Mutation_p.I896S|DIAPH1_ENST00000389054.3_Missense_Mutation_p.I950S|DIAPH1_ENST00000398562.2_Missense_Mutation_p.I929S|DIAPH1_ENST00000518047.1_Missense_Mutation_p.I941S|DIAPH1_ENST00000253811.6_Missense_Mutation_p.I954S|DIAPH1_ENST00000398566.3_Missense_Mutation_p.I945S	NM_005219.4	NP_005210.3	O60610	DIAP1_HUMAN	diaphanous-related formin 1	953	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin filament polymerization (GO:0030041)|cellular response to histamine (GO:0071420)|cytoskeleton organization (GO:0007010)|positive regulation of cell migration (GO:0030335)|protein localization to microtubule (GO:0035372)|regulation of cell shape (GO:0008360)|regulation of microtubule-based process (GO:0032886)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|mitotic spindle (GO:0072686)|ruffle membrane (GO:0032587)	ion channel binding (GO:0044325)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(12)|pancreas(1)|skin(2)|stomach(2)	23			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCTGGCTTGATATTCTCCAC	0.473																																					p.I953S		Atlas-SNP	.											.	DIAPH1	64	.	0			c.T2858G						.						80	75	77					5																	140908429		2046	4201	6247	SO:0001583	missense	1729	exon22			GGCTTGATATTCT	BC007411		5q31	2013-05-24	2013-05-24		ENSG00000131504	ENSG00000131504			2876	protein-coding gene	gene with protein product		602121	"diaphanous (Drosophila, homolog) 1", "diaphanous homolog 1 (Drosophila)"	DFNA1		9360932, 1350680	Standard	NM_005219		Approved	hDIA1, LFHL1	uc003llb.4	O60610	OTTHUMG00000149893	ENST00000398557.4:c.2858T>G	chr5.hg19:g.140908429A>C	ENSP00000381565:p.Ile953Ser	98.0	0.0		85.0	37.0	NM_005219	A6NF18|B7ZKW2|E9PEZ2|Q17RN4|Q59FH8|Q9UC76	Missense_Mutation	SNP	ENST00000398557.4	hg19	CCDS43374.1	.	.	.	.	.	.	.	.	.	.	A	18.81	3.702334	0.68501	.	.	ENSG00000131504	ENST00000389054;ENST00000520569;ENST00000398562;ENST00000389057;ENST00000398566;ENST00000398557;ENST00000253811;ENST00000518047	T;T;T;T;T;T;T;T	0.19669	2.13;2.13;2.13;2.13;2.13;2.13;2.13;2.13	5.27	5.27	0.74061	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.202993	0.40469	N	0.001098	T	0.47985	0.1475	M	0.79123	2.44	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.986;0.986	T	0.52675	-0.8544	10	0.87932	D	0	.	14.1712	0.65510	1.0:0.0:0.0:0.0	.	896;944;953	E7ERW8;E9PEZ2;O60610	.;.;DIAP1_HUMAN	S	950;896;929;944;945;953;954;941	ENSP00000373706:I950S;ENSP00000429282:I896S;ENSP00000381570:I929S;ENSP00000373709:I944S;ENSP00000381572:I945S;ENSP00000381565:I953S;ENSP00000253811:I954S;ENSP00000428268:I941S	ENSP00000253811:I954S	I	-	2	0	DIAPH1	140888613	1.000000	0.71417	0.996000	0.52242	0.951000	0.60555	9.339000	0.96797	1.975000	0.57531	0.455000	0.32223	ATC	.	.		0.473	DIAPH1-203	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_005219		C	140908429	A	C	140908429	3	2	300	1	0	0	0	0	1	0	0	0	4520	333	12	5	988	5	DIAPH1	5	140908429	Missense_Mutation	SNP	A	TCGA-G3-AAV4-01A-11D-A382-10	172274	140908429	40006831	43	43382										
ATOX1	475	hgsc.bcm.edu	37	chr5	151138108	151138108	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	ggacggcgcaaccactcaccGgcatgactgaggcagcggcg	15	14	1	2			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr5:151138108G>A	ENST00000524142.1	-	2	362	c.5C>T	c.(4-6)cCg>cTg	p.P2L	ATOX1_ENST00000313115.6_Splice_Site_p.P2L|ATOX1_ENST00000522710.1_Splice_Site_p.P2L|CTB-113P19.3_ENST00000518182.1_RNA			O00244	ATOX1_HUMAN	antioxidant 1 copper chaperone	2	HMA. {ECO:0000255|PROSITE- ProRule:PRU00280}.				cellular copper ion homeostasis (GO:0006878)|copper ion transport (GO:0006825)|response to oxidative stress (GO:0006979)	cytosol (GO:0005829)	copper chaperone activity (GO:0016531)|copper ion binding (GO:0005507)|copper-dependent protein binding (GO:0032767)|metallochaperone activity (GO:0016530)						Medulloblastoma(196;0.091)|all_hematologic(541;0.103)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)			ACCACTCACCGGCATGACTGA	0.682																																					p.P2L		Atlas-SNP	.											.	ATOX1	4	.	0			c.C5T						.						10	15	13					5																	151138108		2010	4146	6156	SO:0001630	splice_region_variant	475	exon1			CTCACCGGCATGA	U70660	CCDS47317.1	5q32	2013-05-01	2013-05-01			ENSG00000177556			798	protein-coding gene	gene with protein product		602270	"ATX1 (antioxidant protein 1, yeast) homolog 1", "ATX1 antioxidant protein 1 homolog (yeast)"			9083055	Standard	NM_004045		Approved	HAH1	uc003luk.3	O00244		ENST00000524142.1:c.6+1C>T	chr5.hg19:g.151138108G>A		404.0	0.0		426.0	59.0	NM_004045	A8KAJ8|D3DQI2|Q2M1R6|Q56AP3	Missense_Mutation	SNP	ENST00000524142.1	hg19	CCDS47317.1	.	.	.	.	.	.	.	.	.	.	G	13.26	2.185572	0.38609	.	.	ENSG00000177556	ENST00000524142;ENST00000313115;ENST00000522710	.	.	.	3.81	3.81	0.43845	Heavy metal-associated domain, HMA (1);	0.424673	0.23738	N	0.045058	T	0.44138	0.1279	.	.	.	0.44736	D	0.997738	B	0.02656	0.0	B	0.01281	0.0	T	0.33854	-0.9852	8	0.31617	T	0.26	-2.2352	11.5135	0.50507	0.0:0.0:1.0:0.0	.	2	O00244	ATOX1_HUMAN	L	2	.	ENSP00000316854:P2L	P	-	2	0	ATOX1	151118301	1.000000	0.71417	1.000000	0.80357	0.079000	0.17450	3.513000	0.53414	2.425000	0.82216	0.491000	0.48974	CCG	.	.		0.682	ATOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373823.2	NM_004045	Missense_Mutation	A	151138108	G	A	151138108	5	1	300	1	0	0	0	0	0	0	1	0	1115	1130	39	1	213	1	ATOX1	5	151138108	Splice_Site	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10	10229679	151138108	29777152	44	43383										
DOCK2	1794	hgsc.bcm.edu	37	chr5	169111291	169111291	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	tgtgagaaactttgtgtgcaGaattggggaagatgctgagc	15	4	0	4			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr5:169111291G>T	ENST00000256935.8	+	8	778	c.698G>T	c.(697-699)aGa>aTa	p.R233I		NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	233					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TTTGTGTGCAGAATTGGGGAA	0.483																																					p.R233I		Atlas-SNP	.											.	DOCK2	389	.	0			c.G698T						.						193	175	181					5																	169111291		2203	4300	6503	SO:0001583	missense	1794	exon8			TGTGCAGAATTGG	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.698G>T	chr5.hg19:g.169111291G>T	ENSP00000256935:p.Arg233Ile	119.0	0.0		86.0	36.0	NM_004946	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	hg19	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.761599	0.89932	.	.	ENSG00000134516	ENST00000256935	T	0.51071	0.72	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.70037	0.3178	M	0.74258	2.255	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.70464	-0.4864	10	0.48119	T	0.1	.	19.2567	0.93948	0.0:0.0:1.0:0.0	.	233	Q92608	DOCK2_HUMAN	I	233	ENSP00000256935:R233I	ENSP00000256935:R233I	R	+	2	0	DOCK2	169043869	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.372000	0.73123	2.544000	0.85801	0.655000	0.94253	AGA	.	.		0.483	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		T	169111291	G	T	169111291	3	4	300	1	0	0	0	0	1	0	0	0	4689	942	33	3	728	3	DOCK2	5	169111291	Missense_Mutation	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10	17973183	169111291	11803969	45	43384										
DOCK2	1794	hgsc.bcm.edu	37	chr5	169494540	169494540	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	attagtcctctggagaatgcCatagaaaccatgtccacggc	9	11	1	2			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr5:169494540C>T	ENST00000256935.8	+	45	4574	c.4494C>T	c.(4492-4494)gcC>gcT	p.A1498A	DOCK2_ENST00000540750.1_Silent_p.A559A|DOCK2_ENST00000520908.1_Silent_p.A990A|DOCK2_ENST00000523351.1_3'UTR	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1498	DHR-2.				actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TGGAGAATGCCATAGAAACCA	0.428																																					p.A1498A		Atlas-SNP	.											.	DOCK2	389	.	0			c.C4494T						.						149	136	141					5																	169494540		2203	4300	6503	SO:0001819	synonymous_variant	1794	exon45			GAATGCCATAGAA	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.4494C>T	chr5.hg19:g.169494540C>T		149.0	0.0		119.0	48.0	NM_004946	Q2M3I0|Q96AK7	Silent	SNP	ENST00000256935.8	hg19	CCDS4371.1																																																																																			.	.		0.428	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		T	169494540	C	T	169494540	2	4	300	1	0	0	0	0	0	0	0	1	4689	581	21	3		3	DOCK2	5	169494540	Silent	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	383249	169494540	11420720	46	43385										
BTN1A1	696	hgsc.bcm.edu	37	chr6	26508287	26508307	+	Splice_Site	DEL	ATCTTTCTCTTTTGTTGCAGA	ATCTTTCTCTTTTGTTGCAGA	-													0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	ctatctttctcttttgttgcAgaatggaaaaaggctacctt					rs41267931	byFrequency	TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	ATCTTTCTCTTTTGTTGCAGA	ATCTTTCTCTTTTGTTGCAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr6:26508287_26508307delATCTTTCTCTTTTGTTGCAGA	ENST00000244513.6	+	6	946_965	c.880_899delATCTTTCTCTTTTGTTGCAGA	c.(880-900)atctttctcttttgttgcaga>a	p.IFLFCCR294del		NM_001732.2	NP_001723.2	Q13410	BT1A1_HUMAN	butyrophilin, subfamily 1, member A1	294	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(1)	26						CTTTTGTTGCAGAATGGAAAAAGGCTACCTTGCATGCAGGT	0.398																																					.		Atlas-Indel,Pindel	.											.	BTN1A1	68	.	0			.						.																																			SO:0001630	splice_region_variant	696	.			.	U39576	CCDS4614.1	6p22.1	2014-01-14			ENSG00000124557	ENSG00000124557		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Butyrophilins"	1135	protein-coding gene	gene with protein product		601610		BTN		8114113, 9382921	Standard	NM_001732		Approved	BT, BTN1	uc003nif.4	Q13410	OTTHUMG00000016358	ENST00000244513.6:c.881-1ATCTTTCTCTTTTGTTGCAGA>-	chr6.hg19:g.26508287_26508307delATCTTTCTCTTTTGTTGCAGA		111.0	0.0		103.0	30.0	.	Q4VAN3|Q4VAN4|Q9H458	Splice_Site	DEL	ENST00000244513.6	hg19	CCDS4614.1																																																																																			.	.		0.398	BTN1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043776.1	NM_001732	In_Frame_Del	-	26508307	ATCTTTCTCTTTTGTTGCAGA	-	26508287	8	5	300	1	0	1	0	1	0	0	1	0	1561	202	7	0	901	0	BTN1A1	6	26508287	Splice_Site	DEL	ATCTTTCTCTTTTGTTGCAGA	TCGA-G3-AAV4-01A-11D-A382-10		26508287	144606780	47	43386	229	2								
BTN1A1	696	hgsc.bcm.edu	37	chr6	26508294	26508294	+	Missense_Mutation	SNP	A	A	G													0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	tctcttttgttgcagaatggAaaaaggctaccttgcatgca							TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr6:26508294A>G	ENST00000244513.6	+	6	952	c.886A>G	c.(886-888)Aaa>Gaa	p.K296E		NM_001732.2	NP_001723.2	Q13410	BT1A1_HUMAN	butyrophilin, subfamily 1, member A1	296	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(1)	26						TGCAGAATGGAAAAAGGCTAC	0.403																																					p.K296E		Atlas-SNP	.											.	BTN1A1	68	.	0			c.A886G						.						170	169	169					6																	26508294		2203	4300	6503	SO:0001583	missense	696	exon6			GAATGGAAAAAGG	U39576	CCDS4614.1	6p22.1	2014-01-14			ENSG00000124557	ENSG00000124557		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Butyrophilins"	1135	protein-coding gene	gene with protein product		601610		BTN		8114113, 9382921	Standard	NM_001732		Approved	BT, BTN1	uc003nif.4	Q13410	OTTHUMG00000016358	ENST00000244513.6:c.886A>G	chr6.hg19:g.26508294A>G	ENSP00000244513:p.Lys296Glu	102.0	0.0		111.0	45.0	NM_001732	Q4VAN3|Q4VAN4|Q9H458	Missense_Mutation	SNP	ENST00000244513.6	hg19	CCDS4614.1	.	.	.	.	.	.	.	.	.	.	A	16.80	3.223381	0.58668	.	.	ENSG00000124557	ENST00000244513;ENST00000377586	T	0.59502	0.26	5.68	5.68	0.88126	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);	0.106321	0.42420	D	0.000720	T	0.31979	0.0814	L	0.31065	0.9	0.37965	D	0.933099	B	0.17038	0.02	B	0.12837	0.008	T	0.33675	-0.9859	10	0.72032	D	0.01	.	12.5848	0.56410	1.0:0.0:0.0:0.0	.	296	Q13410	BT1A1_HUMAN	E	296	ENSP00000244513:K296E	ENSP00000244513:K296E	K	+	1	0	BTN1A1	26616273	1.000000	0.71417	0.998000	0.56505	0.846000	0.48090	5.352000	0.66028	2.284000	0.76573	0.533000	0.62120	AAA	.	.		0.403	BTN1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043776.1	NM_001732		G	26508294	A	G	26508294	3	3	300	1	0	0	0	0	1	0	0	0	1561	247	9	2	908	2	BTN1A1	6	26508294	Missense_Mutation	SNP	A	TCGA-G3-AAV4-01A-11D-A382-10	7	26508294	144606773	48	43387	229	2								
MDC1	9656	hgsc.bcm.edu	37	chr6	30668320	30668320	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	ttcagcactccagtcagcagGaactcaggcgagaggagggg	15	10	3	1			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr6:30668320G>A	ENST00000376406.3	-	15	6839	c.6192C>T	c.(6190-6192)ttC>ttT	p.F2064F	MDC1_ENST00000376405.2_Silent_p.F1800F|MDC1-AS1_ENST00000442150.1_RNA	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	2064	BRCT 2. {ECO:0000255|PROSITE- ProRule:PRU00033}.|Required for nuclear localization (NLS2).				DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intra-S DNA damage checkpoint (GO:0031573)	chromosome (GO:0005694)|focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	FHA domain binding (GO:0070975)|protein C-terminus binding (GO:0008022)			breast(2)|kidney(1)|ovary(1)	4						CAGTCAGCAGGAACTCAGGCG	0.567								Other conserved DNA damage response genes																													p.F2064F		Atlas-SNP	.											.	MDC1	218	.	0			c.C6192T						.						133	125	128					6																	30668320		1511	2709	4220	SO:0001819	synonymous_variant	9656	exon15			CAGCAGGAACTCA	D79992	CCDS34384.1	6p21.3	2010-02-17	2009-06-12		ENSG00000137337	ENSG00000137337			21163	protein-coding gene	gene with protein product		607593				10975465, 12607005	Standard	NM_014641		Approved	NFBD1, KIAA0170, Em:AB023051.5	uc003nrg.4	Q14676	OTTHUMG00000031075	ENST00000376406.3:c.6192C>T	chr6.hg19:g.30668320G>A		197.0	0.0		235.0	63.0	NM_014641	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Silent	SNP	ENST00000376406.3	hg19	CCDS34384.1																																																																																			.	.		0.567	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641		A	30668320	G	A	30668320	2	1	300	1	0	0	0	0	0	0	0	1	9412	1165	41	3		3	MDC1	6	30668320	Silent	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10	4160026	30668320	140446747	49	43388										
DNAH8	1769	hgsc.bcm.edu	37	chr6	38941510	38941510	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	attactagagacgctaattaCcactgaagccagtgatgatt	8	8	0	4			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr6:38941510C>T	ENST00000359357.3	+	82	12202	c.11948C>T	c.(11947-11949)aCc>aTc	p.T3983I	DNAH8_ENST00000441566.1_Missense_Mutation_p.T3947I			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	3983	AAA 6. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						ACGCTAATTACCACTGAAGCC	0.388																																					p.T4200I		Atlas-SNP	.											.	DNAH8	1239	.	0			c.C12599T						.						96	96	96					6																	38941510		2203	4300	6503	SO:0001583	missense	1769	exon84			TAATTACCACTGA	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.11948C>T	chr6.hg19:g.38941510C>T	ENSP00000352312:p.Thr3983Ile	97.0	0.0		144.0	40.0	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	hg19		.	.	.	.	.	.	.	.	.	.	C	7.928	0.740127	0.15642	.	.	ENSG00000124721	ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.08634	3.07;3.07;3.07	5.99	-0.037	0.13886	Dynein heavy chain (1);	0.488542	0.22998	N	0.053120	T	0.04272	0.0118	M	0.86028	2.79	0.09310	N	1	B;B	0.16166	0.013;0.016	B;B	0.26969	0.045;0.075	T	0.31308	-0.9948	10	0.51188	T	0.08	.	4.1261	0.10128	0.3571:0.3827:0.0:0.2602	.	3947;3983	Q96JB1-2;Q96JB1	.;DYH8_HUMAN	I	4188;3983;3947	ENSP00000333363:T4188I;ENSP00000352312:T3983I;ENSP00000402294:T3947I	ENSP00000333363:T4188I	T	+	2	0	DNAH8	39049488	0.000000	0.05858	0.000000	0.03702	0.074000	0.17049	-0.242000	0.08928	-0.318000	0.08665	0.655000	0.94253	ACC	.	.		0.388	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		T	38941510	C	T	38941510	3	4	300	1	0	0	0	0	1	0	0	0	4609	507	18	3	12266	3	DNAH8	6	38941510	Missense_Mutation	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	8273190	38941510	132173557	50	43389										
DST	667	hgsc.bcm.edu	37	chr6	56504967	56504967	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	ctcatcaacccaattcaaaaGatcctgaacaaatttcatat	2	11	4	2			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr6:56504967G>T	ENST00000361203.3	-	14	1838	c.1831C>A	c.(1831-1833)Ctt>Att	p.L611I	DST_ENST00000518935.1_Missense_Mutation_p.L285I|DST_ENST00000446842.2_Missense_Mutation_p.L285I|DST_ENST00000370769.4_Missense_Mutation_p.L611I|DST_ENST00000370765.6_Missense_Mutation_p.L285I|DST_ENST00000312431.6_Missense_Mutation_p.L611I|DST_ENST00000370754.5_Missense_Mutation_p.L789I|DST_ENST00000370788.2_Missense_Mutation_p.L611I|DST_ENST00000244364.6_Missense_Mutation_p.L285I|DST_ENST00000421834.2_Missense_Mutation_p.L611I			Q03001	DYST_HUMAN	dystonin	611					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			CAATTCAAAAGATCCTGAACA	0.299																																					p.L285I		Atlas-SNP	.											.	DST	1427	.	0			c.C853A						.						36	39	38					6																	56504967		2202	4298	6500	SO:0001583	missense	667	exon4			TCAAAAGATCCTG	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.1831C>A	chr6.hg19:g.56504967G>T	ENSP00000354508:p.Leu611Ile	83.0	0.0		138.0	52.0	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	hg19		.	.	.	.	.	.	.	.	.	.	G	24.0	4.480621	0.84747	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000312431;ENST00000370788;ENST00000361203;ENST00000439203;ENST00000520645;ENST00000370765;ENST00000518935	D;D;D;D;D;D;D;D;D;D;D;D	0.94417	-3.42;-3.42;-3.42;-3.42;-3.42;-3.42;-3.42;-3.42;-3.42;-3.42;-3.42;-3.42	4.99	4.99	0.66335	.	0.000000	0.41194	D	0.000933	D	0.96691	0.8920	M	0.78456	2.415	0.29535	N	0.852531	D;D;D;D;D;P;D;D;D;P	0.65815	0.967;0.967;0.967;0.967;0.981;0.71;0.982;0.995;0.967;0.937	D;D;D;D;D;P;D;D;D;D	0.91635	0.979;0.992;0.979;0.992;0.991;0.769;0.991;0.999;0.992;0.96	D	0.95214	0.8328	9	0.32370	T	0.25	.	18.4618	0.90741	0.0:0.0:1.0:0.0	.	640;611;611;789;727;285;285;285;611;285	B4DGY0;Q5TBT1;E7ERU2;E9PEB9;Q03001-13;Q6P0N6;Q03001-3;Q03001-9;Q03001;Q03001-8	.;.;.;.;.;.;.;.;DYST_HUMAN;.	I	285;789;611;611;285;611;611;611;285;651;285;285	ENSP00000244364:L285I;ENSP00000359790:L789I;ENSP00000359805:L611I;ENSP00000400883:L611I;ENSP00000393645:L285I;ENSP00000307959:L611I;ENSP00000359824:L611I;ENSP00000354508:L611I;ENSP00000404924:L285I;ENSP00000431030:L651I;ENSP00000359801:L285I;ENSP00000431003:L285I	ENSP00000244364:L285I	L	-	1	0	DST	56612926	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	6.155000	0.71833	2.603000	0.88011	0.655000	0.94253	CTT	.	.		0.299	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		T	56504967	G	T	56504967	3	4	300	1	0	0	0	0	1	0	0	0	4785	942	33	3	19626	3	DST	6	56504967	Missense_Mutation	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10	17563457	56504967	114610100	51	43390										
C6orf167	253714	hgsc.bcm.edu	37	chr6	97610000	97610000	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	aggccagaatggatgctaagCgaggaggaggtgaggacccc	17	8	0	2	rs149054595	byFrequency	TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr6:97610000C>A	ENST00000275053.4	-	22	3528	c.3263G>T	c.(3262-3264)cGc>cTc	p.R1088L	MMS22L_ENST00000369251.2_Missense_Mutation_p.R1048L	NM_198468.2	NP_940870.2	Q6ZRQ5	MMS22_HUMAN	MMS22-like, DNA repair protein	1088					double-strand break repair via homologous recombination (GO:0000724)|replication fork processing (GO:0031297)	nuclear replication fork (GO:0043596)		p.R1088H(2)		breast(1)|endometrium(9)|kidney(2)|large_intestine(12)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	50						GGATGCTAAGCGAGGAGGAGG	0.408																																					p.R1088L		Atlas-SNP	.											MMS22L,colon,carcinoma,0,2	MMS22L	102	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G3263T						.						120	115	117					6																	97610000		2203	4300	6503	SO:0001583	missense	253714	exon22			GCTAAGCGAGGAG		CCDS5039.1	6q16.3	2010-11-11	2010-11-11	2010-11-11	ENSG00000146263	ENSG00000146263			21475	protein-coding gene	gene with protein product		615614	"chromosome 6 open reading frame 167"	C6orf167		21055983, 21055984	Standard	NM_198468		Approved	dJ39B17.2	uc003ppb.3	Q6ZRQ5	OTTHUMG00000015248	ENST00000275053.4:c.3263G>T	chr6.hg19:g.97610000C>A	ENSP00000275053:p.Arg1088Leu	77.0	0.0		48.0	40.0	NM_198468	D6R9Y8|D6RBQ4|E1P529|Q5THT2|Q68CQ6|Q68D32	Missense_Mutation	SNP	ENST00000275053.4	hg19	CCDS5039.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.238564	0.79800	.	.	ENSG00000146263	ENST00000275053;ENST00000369251	T;T	0.33654	1.4;1.4	5.68	4.81	0.61882	.	0.052393	0.85682	D	0.000000	T	0.44138	0.1279	M	0.69823	2.125	0.51233	D	0.999916	D;D	0.71674	0.998;0.979	D;P	0.63033	0.91;0.736	T	0.47824	-0.9087	10	0.52906	T	0.07	-19.3496	11.5924	0.50953	0.0:0.8568:0.0:0.1432	.	1048;1088	E2QRD4;Q6ZRQ5	.;MMS22_HUMAN	L	1088;1048	ENSP00000275053:R1088L;ENSP00000358254:R1048L	ENSP00000275053:R1088L	R	-	2	0	MMS22L	97716721	1.000000	0.71417	0.971000	0.41717	0.952000	0.60782	2.641000	0.46587	1.395000	0.46643	0.650000	0.86243	CGC	.	C|1.000;T|0.000		0.408	MMS22L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041573.3	NM_198468		A	97610000	C	A	97610000	3	1	300	1	0	0	0	0	1	0	0	0	2344	768	27	1	484	1	C6orf167	6	97610000	Missense_Mutation	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	41105033	97610000	73505067	52	43391										
TBP	6908	hgsc.bcm.edu	37	chr6	170871073	170871074	+	In_Frame_Ins	INS	-	-	CAA													0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	agcagcagcagcagcagcagINScagcagcagcagcagcagca					rs551889211	byFrequency	TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr6:170871073_170871074insCAA	ENST00000392092.2	+	3	528_529	c.249_250insCAA	c.(250-252)cag>CAAcag	p.84_84Q>QQ	TBP_ENST00000230354.6_In_Frame_Ins_p.84_84Q>QQ|TBP_ENST00000540980.1_In_Frame_Ins_p.64_64Q>QQ	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	84	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.Q83Q(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		agcagcagcagcagcagcagca	0.594																																					p.Q83delinsQQ		Atlas-INDEL	.											TBP,NS,carcinoma,0,1	TBP	58	.	1	Substitution - coding silent(1)	lung(1)	c.249_250insCAA						.																																			SO:0001652	inframe_insertion	6908	exon3			.	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"General transcription factors"	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	Exception_encountered	chr6.hg19:g.170871073_170871074insCAA	ENSP00000375942:p.Gln95dup	74.0	0.0		27.0	17.0	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	In_Frame_Ins	INS	ENST00000392092.2	hg19	CCDS5315.1																																																																																			.	-|0.138;CAG|0.862		0.594	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194		CAA	170871074	-	CAA	170871073	7	5	300	1	0	1	1	0	0	0	0	0	15659	962	34	0	255	0	TBP	6	170871073	In_Frame_Ins	INS	-	TCGA-G3-AAV4-01A-11D-A382-10	73261073	170871073	243994	53	43392										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48315020	48315020	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	cttgtgaaaactgtgcagaaAttttggcataagatattacc	8	6	0	3			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr7:48315020A>G	ENST00000435803.1	+	17	5781	c.5757A>G	c.(5755-5757)aaA>aaG	p.K1919K		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1919					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						CTGTGCAGAAATTTTGGCATA	0.383																																					p.K1919K		Atlas-SNP	.											.	ABCA13	1192	.	0			c.A5757G						.						121	123	123					7																	48315020		1827	4083	5910	SO:0001819	synonymous_variant	154664	exon17			GCAGAAATTTTGG	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.5757A>G	chr7.hg19:g.48315020A>G		180.0	0.0		193.0	97.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	hg19	CCDS47584.1																																																																																			.	.		0.383	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		G	48315020	A	G	48315020	2	3	300	1	0	0	0	0	0	0	0	1	31	98	4	2		2	ABCA13	7	48315020	Silent	SNP	A	TCGA-G3-AAV4-01A-11D-A382-10		48315020	110823643	54	43393										
ZPBP	11055	hgsc.bcm.edu	37	chr7	50121482	50121482	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	ggactcttttgatggagcatGacatacgctttcactgaaaa	9	8	2	3			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr7:50121482G>A	ENST00000046087.2	-	3	291	c.222C>T	c.(220-222)gtC>gtT	p.V74V	ZPBP_ENST00000419417.1_Silent_p.V74V	NM_001159878.1|NM_007009.2	NP_001153350.1|NP_008940.2	Q9BS86	ZPBP1_HUMAN	zona pellucida binding protein	74					acrosome assembly (GO:0001675)|binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|extracellular region (GO:0005576)|nucleus (GO:0005634)|zona pellucida receptor complex (GO:0002199)				NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(3)	29	Glioma(55;0.08)|all_neural(89;0.245)					GATGGAGCATGACATACGCTT	0.353																																					p.V74V		Atlas-SNP	.											.	ZPBP	65	.	0			c.C222T						.						126	115	119					7																	50121482		2202	4300	6502	SO:0001819	synonymous_variant	11055	exon3			GAGCATGACATAC	D17570	CCDS5509.1, CCDS55110.1	7p14.3	2013-01-11			ENSG00000042813	ENSG00000042813		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15662	protein-coding gene	gene with protein product		608498				9378618	Standard	NM_007009		Approved	SP38, ZPBP1	uc003tou.3	Q9BS86	OTTHUMG00000023528	ENST00000046087.2:c.222C>T	chr7.hg19:g.50121482G>A		32.0	0.0		81.0	37.0	NM_007009	A4D253|C9JPU1|Q15941|Q75KX9|Q75MI3	Silent	SNP	ENST00000046087.2	hg19	CCDS5509.1																																																																																			.	.		0.353	ZPBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251374.1	NM_007009		A	50121482	G	A	50121482	2	1	300	1	0	0	0	0	0	0	0	1	18234	1277	45	3		3	ZPBP	7	50121482	Silent	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10	1806462	50121482	109017181	55	43394										
ABHD11	83451	hgsc.bcm.edu	37	chr7	73152683	73152692	+	Frame_Shift_Del	DEL	ATCTTGGCGA	ATCTTGGCGA	-													0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	ggcctgtctgctgggccaagAtcttggcgatggagttgaag							TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	ATCTTGGCGA	ATCTTGGCGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr7:73152683_73152692delATCTTGGCGA	ENST00000222800.3	-	2	323_332	c.254_263delTCGCCAAGAT	c.(253-264)atcgccaagatcfs	p.IAKI85fs	LINC00035_ENST00000427153.1_RNA|ABHD11_ENST00000395147.4_Frame_Shift_Del_p.IAKI85fs|ABHD11_ENST00000437775.2_Frame_Shift_Del_p.IAKI78fs|ABHD11_ENST00000468998.1_5'UTR|ABHD11_ENST00000458339.1_Frame_Shift_Del_p.IAKI85fs	NM_148912.2	NP_683710.1	Q8NFV4	ABHDB_HUMAN	abhydrolase domain containing 11	85						mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)			breast(1)|endometrium(1)|large_intestine(1)|lung(1)	4		Lung NSC(55;0.0908)|all_lung(88;0.198)				CTGGGCCAAGATCTTGGCGATGGAGTTGAA	0.657																																					p.85_88del		Atlas-Indel,Pindel	.											.	ABHD11	11	.	0			c.255_264del						.																																			SO:0001589	frameshift_variant	83451	exon2			.	AF217971	CCDS5558.1, CCDS47607.1, CCDS47608.1, CCDS75615.1	7q11.23	2010-08-05	2005-01-24	2005-01-27	ENSG00000106077	ENSG00000106077		"Abhydrolase domain containing"	16407	protein-coding gene	gene with protein product			"Williams Beuren syndrome chromosome region 21"	WBSCR21		12073013	Standard	NR_026910		Approved	PP1226	uc003tzb.3	Q8NFV4	OTTHUMG00000130029	ENST00000222800.3:c.254_263delTCGCCAAGAT	chr7.hg19:g.73152683_73152692delATCTTGGCGA	ENSP00000222800:p.Ile85fs	222.0	0.0		123.0	42.0	NM_001145364	H7BYM8|Q6PJU0|Q8N722|Q8N723|Q8NFV2|Q8NFV3|Q9HBS8	Frame_Shift_Del	DEL	ENST00000222800.3	hg19	CCDS5558.1																																																																																			.	.		0.657	ABHD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252306.1			-	73152692	ATCTTGGCGA	-	73152683	7	5	300	1	0	1	0	1	0	0	0	0	75	333	12	0	975	0	ABHD11	7	73152683	Frame_Shift_Del	DEL	ATCTTGGCGA	TCGA-G3-AAV4-01A-11D-A382-10	23031201	73152683	85985980	56	43395										
SEMA3C	10512	hgsc.bcm.edu	37	chr7	80374265	80374265	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	ttttccgactattgatgaggGcctttaacttgccatagtcc	8	10	0	2			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr7:80374265G>A	ENST00000265361.3	-	18	2762	c.2201C>T	c.(2200-2202)gCc>gTc	p.A734V	SEMA3C_ENST00000419255.2_Missense_Mutation_p.A734V|SEMA3C_ENST00000544525.1_Missense_Mutation_p.A752V	NM_006379.3	NP_006370.1	Q99985	SEM3C_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	734	Arg/Lys-rich (basic).				axon guidance (GO:0007411)|blood vessel remodeling (GO:0001974)|cardiac right ventricle morphogenesis (GO:0003215)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|immune response (GO:0006955)|limb bud formation (GO:0060174)|neural crest cell migration (GO:0001755)|neural tube development (GO:0021915)|outflow tract morphogenesis (GO:0003151)|post-embryonic development (GO:0009791)|pulmonary myocardium development (GO:0003350)|response to drug (GO:0042493)|somitogenesis (GO:0001756)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						ATTGATGAGGGCCTTTAACTT	0.408																																					p.A734V		Atlas-SNP	.											.	SEMA3C	106	.	0			c.C2201T						.						149	141	144					7																	80374265		2203	4300	6503	SO:0001583	missense	10512	exon18			ATGAGGGCCTTTA	AB000220	CCDS5596.1	7q21-q31	2013-01-11			ENSG00000075223	ENSG00000075223		"Semaphorins", "Immunoglobulin superfamily / I-set domain containing"	10725	protein-coding gene	gene with protein product		602645		SEMAE		7748561, 9168980	Standard	NM_006379		Approved	SemE	uc003uhj.3	Q99985	OTTHUMG00000023447	ENST00000265361.3:c.2201C>T	chr7.hg19:g.80374265G>A	ENSP00000265361:p.Ala734Val	98.0	0.0		113.0	49.0	NM_006379	B4DRL8	Missense_Mutation	SNP	ENST00000265361.3	hg19	CCDS5596.1	.	.	.	.	.	.	.	.	.	.	G	13.09	2.132115	0.37630	.	.	ENSG00000075223	ENST00000265361;ENST00000419255;ENST00000544525	T;T;T	0.26067	1.77;1.77;1.76	5.56	5.56	0.83823	.	0.105207	0.64402	D	0.000004	T	0.13756	0.0333	N	0.08118	0	0.80722	D	1	B;B	0.09022	0.002;0.001	B;B	0.12837	0.008;0.003	T	0.14727	-1.0462	10	0.22706	T	0.39	.	12.8104	0.57637	0.075:0.0:0.9249:0.0	.	752;734	F5H1Z7;Q99985	.;SEM3C_HUMAN	V	734;734;752	ENSP00000265361:A734V;ENSP00000411193:A734V;ENSP00000445649:A752V	ENSP00000265361:A734V	A	-	2	0	SEMA3C	80212201	1.000000	0.71417	0.995000	0.50966	0.992000	0.81027	7.610000	0.82949	2.606000	0.88127	0.557000	0.71058	GCC	.	.		0.408	SEMA3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253279.1	NM_006379		A	80374265	G	A	80374265	3	1	300	1	0	0	0	0	1	0	0	0	14041	1203	42	3	58	3	SEMA3C	7	80374265	Missense_Mutation	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10	7221582	80374265	78764398	57	43396										
MCM7	4176	hgsc.bcm.edu	37	chr7	99697718	99697718	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	aagaacttcttaaccttttcTgtaacatgaaatgtaaaacc	4	8	2	2			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr7:99697718T>C	ENST00000303887.5	-	2	677		c.e2-2		AP4M1_ENST00000359593.4_5'Flank|MCM7_ENST00000343023.6_Splice_Site|AP4M1_ENST00000421755.1_5'Flank|AP4M1_ENST00000429084.1_5'Flank|MCM7_ENST00000354230.3_Splice_Site|AP4M1_ENST00000422582.1_5'Flank	NM_005916.3	NP_005907.3	P33993	MCM7_HUMAN	minichromosome maintenance complex component 7						cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to epidermal growth factor stimulus (GO:0071364)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of phosphorylation (GO:0042325)|response to drug (GO:0042493)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|single-stranded DNA binding (GO:0003697)			endometrium(1)|kidney(5)|large_intestine(5)|lung(4)|ovary(1)|stomach(1)	17	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TAACCTTTTCTGTAACATGAA	0.353																																					.		Atlas-SNP	.											.	MCM7	136	.	0			c.32-2A>G						.						71	66	68					7																	99697718		2203	4300	6503	SO:0001630	splice_region_variant	4176	exon3			CTTTTCTGTAACA		CCDS5683.1, CCDS5684.1	7q21.3-q22.1	2014-06-12	2007-04-04		ENSG00000166508	ENSG00000166508			6950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 104"	600592	"minichromosome maintenance deficient (S. cerevisiae) 7", "MCM7 minichromosome maintenance deficient 7 (S. cerevisiae)"	MCM2		7842741	Standard	NM_005916		Approved	CDC47, PPP1R104	uc003usw.1	P33993	OTTHUMG00000154671	ENST00000303887.5:c.32-2A>G	chr7.hg19:g.99697718T>C		121.0	0.0		158.0	67.0	NM_005916	A4D2A1|A4D2A2|E9PGN9|Q15076|Q96D34|Q96GL1	Splice_Site	SNP	ENST00000303887.5	hg19	CCDS5683.1	.	.	.	.	.	.	.	.	.	.	T	9.841	1.190978	0.21954	.	.	ENSG00000166508	ENST00000343023;ENST00000303887	.	.	.	4.0	2.79	0.32731	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.5406	0.22378	0.0:0.1101:0.0:0.8899	.	.	.	.	.	-1	.	.	.	-	.	.	MCM7	99535654	1.000000	0.71417	0.730000	0.30809	0.418000	0.31294	6.639000	0.74314	0.830000	0.34757	0.533000	0.62120	.	.	.		0.353	MCM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336534.3		Intron	C	99697718	T	C	99697718	5	2	300	1	0	0	0	0	0	0	1	0	9401	1594	55	2	2185	2	MCM7	7	99697718	Splice_Site	SNP	T	TCGA-G3-AAV4-01A-11D-A382-10	19323453	99697718	59440945	58	43397										
MUC17	140453	hgsc.bcm.edu	37	chr7	100682982	100682982	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	tatacttgtcagcaccctgcCagtggccagttctgaggcta	10	12	2	1			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr7:100682982C>A	ENST00000306151.4	+	3	8349	c.8285C>A	c.(8284-8286)cCa>cAa	p.P2762Q		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2762	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					AGCACCCTGCCAGTGGCCAGT	0.493																																					p.P2762Q		Atlas-SNP	.											.	MUC17	804	.	0			c.C8285A						.						252	247	248					7																	100682982		2203	4300	6503	SO:0001583	missense	140453	exon3			CCCTGCCAGTGGC	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.8285C>A	chr7.hg19:g.100682982C>A	ENSP00000302716:p.Pro2762Gln	100.0	0.0		112.0	22.0	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	5.606	0.296472	0.10622	.	.	ENSG00000169876	ENST00000306151	T	0.01548	4.78	0.778	-0.297	0.12820	.	.	.	.	.	T	0.03136	0.0092	L	0.32530	0.975	0.09310	N	1	D	0.64830	0.994	D	0.65684	0.937	T	0.44065	-0.9352	9	0.12766	T	0.61	.	5.2309	0.15422	0.0:0.7573:0.0:0.2427	.	2762	Q685J3	MUC17_HUMAN	Q	2762	ENSP00000302716:P2762Q	ENSP00000302716:P2762Q	P	+	2	0	MUC17	100469702	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.135000	0.15952	-0.104000	0.12154	0.134000	0.15878	CCA	.	.		0.493	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		A	100682982	C	A	100682982	3	1	300	1	0	0	0	0	1	0	0	0	9983	594	21	3	8295	3	MUC17	7	100682982	Missense_Mutation	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	985264	100682982	58455681	59	43398										
GRM8	2918	hgsc.bcm.edu	37	chr7	126746765	126746765	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	atgcatagctgatttgaggtAtctgcaaaacaaatgatggg	11	5	1	3			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr7:126746765A>G	ENST00000339582.2	-	3	1320	c.512T>C	c.(511-513)aTa>aCa	p.I171T	GRM8_ENST00000444921.2_Splice_Site_p.I171T|GRM8_ENST00000405249.1_Splice_Site_p.I171T|GRM8_ENST00000480995.1_5'UTR|GRM8_ENST00000358373.3_Splice_Site_p.I171T			O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8	171					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of cAMP biosynthetic process (GO:0030818)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(16)|lung(62)|ovary(5)|pancreas(1)|prostate(1)|skin(14)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(4)	125		Prostate(267;0.186)				GATTTGAGGTATCTGCAAAAC	0.448										HNSCC(24;0.065)																											p.I171T		Atlas-SNP	.											.	GRM8	377	.	0			c.T512C						.						101	103	102					7																	126746765		2203	4300	6503	SO:0001630	splice_region_variant	2918	exon2			TGAGGTATCTGCA		CCDS5794.1, CCDS47696.1	7q31.3-q32.1	2012-08-29			ENSG00000179603	ENSG00000179603		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4600	protein-coding gene	gene with protein product		601116				8824806	Standard	NM_000845		Approved	GLUR8, GPRC1H, mGlu8, MGLUR8	uc003vlr.2	O00222	OTTHUMG00000022888	ENST00000339582.2:c.511-1T>C	chr7.hg19:g.126746765A>G		119.0	0.0		115.0	58.0	NM_000845	A4D0Y3|B0FZ74|B0M0L0|O15493|O95945|O95946|Q3MIV9|Q52M02|Q6J165	Missense_Mutation	SNP	ENST00000339582.2	hg19	CCDS5794.1	.	.	.	.	.	.	.	.	.	.	A	19.69	3.875587	0.72180	.	.	ENSG00000179603	ENST00000339582;ENST00000444921;ENST00000358373;ENST00000405249;ENST00000457830	D;D;D;D;D	0.86694	-2.16;-2.16;-2.16;-2.16;-2.16	4.91	4.91	0.64330	GPCR, family 3, conserved site (1);Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.93946	0.8062	M	0.92317	3.295	0.80722	D	1	D;D	0.61697	0.99;0.972	P;P	0.60682	0.878;0.877	D	0.95218	0.8331	10	0.87932	D	0	.	13.764	0.62983	1.0:0.0:0.0:0.0	.	171;171	O00222-2;O00222	.;GRM8_HUMAN	T	171	ENSP00000344173:I171T;ENSP00000409790:I171T;ENSP00000351142:I171T;ENSP00000385731:I171T;ENSP00000415522:I171T	ENSP00000344173:I171T	I	-	2	0	GRM8	126534001	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.339000	0.96797	1.850000	0.53721	0.460000	0.39030	ATA	.	.		0.448	GRM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059209.4		Missense_Mutation	G	126746765	A	G	126746765	5	3	300	1	0	0	0	0	0	0	1	0	6812	463	16	2	2300	2	GRM8	7	126746765	Splice_Site	SNP	A	TCGA-G3-AAV4-01A-11D-A382-10	26063783	126746765	32391898	60	43399										
FLNC	2318	hgsc.bcm.edu	37	chr7	128485212	128485212	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	accattaccatcaagtatggCgggcatcccgtgcccaaatt	8	13	1	0			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr7:128485212C>T	ENST00000325888.8	+	21	3954	c.3693C>T	c.(3691-3693)ggC>ggT	p.G1231G	FLNC_ENST00000346177.6_Silent_p.G1231G	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	1231					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						TCAAGTATGGCGGGCATCCCG	0.602																																					p.G1231G		Atlas-SNP	.											FLNC,NS,carcinoma,0,1	FLNC	339	.	0			c.C3693T						.						60	70	67					7																	128485212		2180	4261	6441	SO:0001819	synonymous_variant	2318	exon21			GTATGGCGGGCAT	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"actin binding protein 280"	102565	"filamin C, gamma (actin binding protein 280)"	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.3693C>T	chr7.hg19:g.128485212C>T		173.0	0.0		112.0	47.0	NM_001127487	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Silent	SNP	ENST00000325888.8	hg19	CCDS43644.1																																																																																			.	.		0.602	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3			T	128485212	C	T	128485212	2	4	300	1	0	0	0	0	0	0	0	1	5943	755	27	1		1	FLNC	7	128485212	Silent	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	1738447	128485212	30653451	61	43400										
PPP2R2A	5520	hgsc.bcm.edu	37	chr8	26220351	26220351	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	agggcatctgccctctgtgaTagacattctaaatgtaagtt	9	8	3	2			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr8:26220351T>C	ENST00000380737.3	+	7	1118	c.789T>C	c.(787-789)gaT>gaC	p.D263D	PPP2R2A_ENST00000315985.7_Silent_p.D273D	NM_002717.3	NP_002708.1	P63151	2ABA_HUMAN	protein phosphatase 2, regulatory subunit B, alpha	263					G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope reassembly (GO:0007084)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|response to morphine (GO:0043278)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			kidney(1)|large_intestine(2)|ovary(1)	4		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)		CCCTCTGTGATAGACATTCTA	0.368																																					p.D273D		Atlas-SNP	.											.	PPP2R2A	44	.	0			c.T819C						.						70	64	66					8																	26220351		2203	4300	6503	SO:0001819	synonymous_variant	5520	exon7			CTGTGATAGACAT	M64929	CCDS34867.1, CCDS55213.1	8p21.2	2013-01-10	2010-04-14		ENSG00000221914	ENSG00000221914	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "WD repeat domain containing"	9304	protein-coding gene	gene with protein product	"PP2A subunit B isoform alpha"	604941	"protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), alpha isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B, alpha isoform"			1849734	Standard	NM_001177591		Approved	PR52A, PR55A, B55A		P63151	OTTHUMG00000163850	ENST00000380737.3:c.789T>C	chr8.hg19:g.26220351T>C		82.0	0.0		82.0	27.0	NM_001177591	B2RBU8|B4E1T7|P50409|Q00007	Silent	SNP	ENST00000380737.3	hg19	CCDS34867.1																																																																																			.	.		0.368	PPP2R2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375954.2	NM_002717		C	26220351	T	C	26220351	2	2	300	1	0	0	0	0	0	0	0	1	12396	1403	49	2		2	PPP2R2A	8	26220351	Silent	SNP	T	TCGA-G3-AAV4-01A-11D-A382-10		26220351	120143671	62	43401										
DMRT3	58524	hgsc.bcm.edu	37	chr9	990709	990709	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	acccgctgatgctgaggaatActttggcgagaagccagtcg	13	10	0	3			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr9:990709A>G	ENST00000190165.2	+	2	1161	c.1123A>G	c.(1123-1125)Act>Gct	p.T375A		NM_021240.2	NP_067063.1	Q9NQL9	DMRT3_HUMAN	doublesex and mab-3 related transcription factor 3	375					adult walking behavior (GO:0007628)|male sex differentiation (GO:0046661)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|sex differentiation (GO:0007548)|transcription, DNA-templated (GO:0006351)|transmission of nerve impulse (GO:0019226)|ventral spinal cord interneuron specification (GO:0021521)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	26		all_lung(10;1.39e-08)|Lung NSC(10;1.42e-08)		Lung(218;0.0196)		GCTGAGGAATACTTTGGCGAG	0.587																																					p.T375A		Atlas-SNP	.											.	DMRT3	83	.	0			c.A1123G						.						44	43	44					9																	990709		2203	4300	6503	SO:0001583	missense	58524	exon2			AGGAATACTTTGG	AJ301581	CCDS6443.1	9p24.3	2008-07-21	2001-12-17	2001-12-07	ENSG00000064218	ENSG00000064218			13909	protein-coding gene	gene with protein product	"testis-specific protein"	614754	"DMRT-like family A3"	DMRTA3		11543627, 10729223	Standard	NM_021240		Approved		uc003zgw.2	Q9NQL9	OTTHUMG00000019436	ENST00000190165.2:c.1123A>G	chr9.hg19:g.990709A>G	ENSP00000190165:p.Thr375Ala	74.0	0.0		76.0	27.0	NM_021240	Q7LA03|Q7LCH8|Q96SC7|Q9NRQ9	Missense_Mutation	SNP	ENST00000190165.2	hg19	CCDS6443.1	.	.	.	.	.	.	.	.	.	.	A	17.23	3.336566	0.60963	.	.	ENSG00000064218	ENST00000190165	T	0.23552	1.9	5.15	5.15	0.70609	.	0.204155	0.40908	D	0.000995	T	0.20333	0.0489	L	0.27053	0.805	0.38314	D	0.943341	P	0.48089	0.905	B	0.40825	0.341	T	0.06698	-1.0812	10	0.45353	T	0.12	-20.5388	15.0003	0.71466	1.0:0.0:0.0:0.0	.	375	Q9NQL9	DMRT3_HUMAN	A	375	ENSP00000190165:T375A	ENSP00000190165:T375A	T	+	1	0	DMRT3	980709	1.000000	0.71417	0.976000	0.42696	0.998000	0.95712	6.447000	0.73465	1.939000	0.56221	0.533000	0.62120	ACT	.	.		0.587	DMRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051490.1	NM_021240		G	990709	A	G	990709	3	3	300	1	0	0	0	0	1	0	0	0	4589	391	14	2	1129	2	DMRT3	9	990709	Missense_Mutation	SNP	A	TCGA-G3-AAV4-01A-11D-A382-10		990709	140222722	63	43402										
C9orf24	84688	hgsc.bcm.edu	37	chr9	34380993	34380993	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	ccgcgcagacagtagtggcgGcccgagcaagcactttcgta	13	13	0	1			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr9:34380993G>T	ENST00000297623.2	-	5	807	c.609C>A	c.(607-609)ggC>ggA	p.G203G	C9orf24_ENST00000481295.1_5'Flank|C9orf24_ENST00000379127.1_Silent_p.G68G|C9orf24_ENST00000379124.1_Silent_p.G68G|C9orf24_ENST00000379126.3_Intron|C9orf24_ENST00000379133.3_Silent_p.G68G	NM_032596.3	NP_115985.2	Q8NCR6	SMRP1_HUMAN	chromosome 9 open reading frame 24	203					cell differentiation (GO:0030154)|cellular protein complex assembly (GO:0043623)|spermatogenesis (GO:0007283)	manchette (GO:0002177)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)	5			LUSC - Lung squamous cell carcinoma(29;0.0107)	GBM - Glioblastoma multiforme(74;0.123)		AGTAGTGGCGGCCCGAGCAAG	0.706																																					p.G203G		Atlas-SNP	.											.	C9orf24	15	.	0			c.C609A						.						14	18	17					9																	34380993		2116	4168	6284	SO:0001819	synonymous_variant	84688	exon5			GTGGCGGCCCGAG	BC029484	CCDS6553.1, CCDS6554.1, CCDS6555.1, CCDS59121.1	9p11.2	2013-01-11			ENSG00000164972	ENSG00000164972			19919	protein-coding gene	gene with protein product	"ciliated bronchial epithelium 1", "spermatid-specific manchette-related protein 1"					12029067	Standard	NM_147168		Approved	bA573M23.4, NYD-SP22, MGC32921, MGC33614, CBE1, SMRP1	uc003zuh.1	Q8NCR6	OTTHUMG00000000437	ENST00000297623.2:c.609C>A	chr9.hg19:g.34380993G>T		63.0	0.0		57.0	34.0	NM_032596	Q5T598|Q5T599|Q5T5A0|Q8N9G4|Q96KD1|Q96LN1	Silent	SNP	ENST00000297623.2	hg19	CCDS6554.1																																																																																			.	.		0.706	C9orf24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001098.3	NM_147169		T	34380993	G	T	34380993	2	4	300	1	0	0	0	0	0	0	0	1	2477	1190	42	3		3	C9orf24	9	34380993	Silent	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10	33390284	34380993	106832438	64	43403										
FBXO10	26267	hgsc.bcm.edu	37	chr9	37525102	37525102	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	gcagttcccatccgtacctgTgatgaggcctttgccgttct	10	13	1	2			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr9:37525102T>A	ENST00000432825.2	-	6	1822	c.1774A>T	c.(1774-1776)Aca>Tca	p.T592S	FBXO10_ENST00000543968.1_5'UTR|RP11-613M10.8_ENST00000544475.1_5'UTR|FBXO10_ENST00000541829.1_Missense_Mutation_p.T117S	NM_012166.2	NP_036298.2	Q9UK96	FBX10_HUMAN	F-box protein 10	592					apoptotic process (GO:0006915)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(5)|large_intestine(11)|lung(15)|prostate(1)|upper_aerodigestive_tract(1)	34				GBM - Glioblastoma multiforme(29;0.0107)		TCCGTACCTGTGATGAGGCCT	0.577																																					p.T592S		Atlas-SNP	.											.	FBXO10	75	.	0			c.A1774T						.						34	34	34					9																	37525102		2022	4153	6175	SO:0001583	missense	26267	exon6			TACCTGTGATGAG	AF174598	CCDS47966.1	9p13.1	2014-01-29	2004-06-15		ENSG00000147912	ENSG00000147912		"F-boxes /  "other""	13589	protein-coding gene	gene with protein product		609092	"F-box only protein 10"			10531035, 10531037, 19300908	Standard	NM_012166		Approved	FBX10	uc004aab.3	Q9UK96	OTTHUMG00000019926	ENST00000432825.2:c.1774A>T	chr9.hg19:g.37525102T>A	ENSP00000403802:p.Thr592Ser	76.0	0.0		82.0	37.0	NM_012166	Q08AL3|Q08AL4|Q5JRT8|Q9UKC3	Missense_Mutation	SNP	ENST00000432825.2	hg19	CCDS47966.1	.	.	.	.	.	.	.	.	.	.	T	18.03	3.532211	0.64972	.	.	ENSG00000147912	ENST00000432825;ENST00000541829	T;T	0.79749	-1.15;-1.3	4.96	3.75	0.43078	Pectin lyase fold/virulence factor (1);Carbohydrate-binding/sugar hydrolysis domain (1);	0.000000	0.85682	D	0.000000	T	0.78521	0.4296	N	0.20401	0.57	0.48762	D	0.999709	P;B;D	0.69078	0.816;0.267;0.997	B;B;D	0.65773	0.265;0.089;0.938	T	0.75246	-0.3385	10	0.27082	T	0.32	.	10.5322	0.44983	0.0:0.0:0.1621:0.8378	.	471;117;592	Q59F51;Q08AL4;Q9UK96	.;.;FBX10_HUMAN	S	592;117	ENSP00000403802:T592S;ENSP00000441307:T117S	ENSP00000403802:T592S	T	-	1	0	FBXO10	37515102	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.746000	0.62133	1.858000	0.53909	0.533000	0.62120	ACA	.	.		0.577	FBXO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052472.3			A	37525102	T	A	37525102	3	1	300	1	0	0	0	0	1	0	0	0	5734	1696	59	4	1120	4	FBXO10	9	37525102	Missense_Mutation	SNP	T	TCGA-G3-AAV4-01A-11D-A382-10	3144109	37525102	103688329	65	43404										
PGM5	5239	hgsc.bcm.edu	37	chr9	71006638	71006638	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	gagctgcatttgatgctgatGgggtaagtaggaaagctgtc	15	5	0	2			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr9:71006638G>T	ENST00000396396.1	+	5	1115	c.886G>T	c.(886-888)Ggg>Tgg	p.G296W	PGM5_ENST00000604870.2_3'UTR|PGM5_ENST00000396392.1_Missense_Mutation_p.G296W	NM_021965.3	NP_068800.2	Q15124	PGM5_HUMAN	phosphoglucomutase 5	296					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)	cell-cell adherens junction (GO:0005913)|costamere (GO:0043034)|cytoplasmic side of plasma membrane (GO:0009898)|dystrophin-associated glycoprotein complex (GO:0016010)|focal adhesion (GO:0005925)|intercalated disc (GO:0014704)|sarcolemma (GO:0042383)|spot adherens junction (GO:0005914)|stress fiber (GO:0001725)|Z disc (GO:0030018)	intramolecular transferase activity, phosphotransferases (GO:0016868)|magnesium ion binding (GO:0000287)|structural molecule activity (GO:0005198)			endometrium(5)|kidney(1)|large_intestine(5)|liver(2)|lung(15)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	34						TGATGCTGATGGGGTAAGTAG	0.458																																					p.G296W		Atlas-SNP	.											.	PGM5	80	.	0			c.G886T						.						84	79	81					9																	71006638		2201	4298	6499	SO:0001583	missense	5239	exon5			GCTGATGGGGTAA	L40933	CCDS6622.2	9q13	2008-02-05			ENSG00000154330	ENSG00000154330			8908	protein-coding gene	gene with protein product	"phosphoglucomutase-related protein"	600981				8586438, 8631316	Standard	NM_021965		Approved	PGMRP	uc004agr.3	Q15124	OTTHUMG00000019966	ENST00000396396.1:c.886G>T	chr9.hg19:g.71006638G>T	ENSP00000379678:p.Gly296Trp	130.0	0.0		145.0	63.0	NM_021965	B1AM46|B4DLQ6|Q5VYV3|Q8N527|Q9UDH4	Missense_Mutation	SNP	ENST00000396396.1	hg19	CCDS6622.2	.	.	.	.	.	.	.	.	.	.	.	23.7	4.449125	0.84101	.	.	ENSG00000154330	ENST00000396396;ENST00000396392	T;T	0.67523	-0.25;-0.27	5.13	5.13	0.70059	Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III (2);Alpha-D-phosphohexomutase, alpha/beta/alpha domain II (1);	0.000000	0.85682	D	0.000000	D	0.88526	0.6460	H	0.97564	4.03	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92693	0.6168	10	0.87932	D	0	.	17.3325	0.87269	0.0:0.0:1.0:0.0	.	296	Q15124	PGM5_HUMAN	W	296	ENSP00000379678:G296W;ENSP00000379674:G296W	ENSP00000379674:G296W	G	+	1	0	PGM5	70196458	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	9.736000	0.98828	2.386000	0.81285	0.555000	0.69702	GGG	.	.		0.458	PGM5-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052548.2	NM_021965		T	71006638	G	T	71006638	3	4	300	1	0	0	0	0	1	0	0	0	11810	1348	47	3	904	3	PGM5	9	71006638	Missense_Mutation	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10	33481536	71006638	70206793	66	43405										
PCSK5	5125	hgsc.bcm.edu	37	chr9	78722181	78722181	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	ttccagatcactacagatctGaggcagcgttgcacggacaa	10	11	2	3			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr9:78722181G>A	ENST00000545128.1	+	9	1660	c.1122G>A	c.(1120-1122)ctG>ctA	p.L374L	PCSK5_ENST00000376767.3_Silent_p.L374L|PCSK5_ENST00000376752.4_Silent_p.L374L	NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	374	Peptidase S8.				anterior/posterior pattern specification (GO:0009952)|cell-cell signaling (GO:0007267)|cytokine biosynthetic process (GO:0042089)|embryo implantation (GO:0007566)|embryonic digestive tract development (GO:0048566)|embryonic skeletal system development (GO:0048706)|heart development (GO:0007507)|kidney development (GO:0001822)|limb morphogenesis (GO:0035108)|nerve growth factor processing (GO:0032455)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|protein processing (GO:0016485)|renin secretion into blood stream (GO:0002001)|respiratory tube development (GO:0030323)|signal peptide processing (GO:0006465)|viral life cycle (GO:0019058)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|secretory granule (GO:0030141)	peptidase activity (GO:0008233)|peptide binding (GO:0042277)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|liver(2)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55						CTACAGATCTGAGGCAGCGTT	0.473																																					p.L374L		Atlas-SNP	.											.	PCSK5	329	.	0			c.G1122A						.						61	54	57					9																	78722181		2203	4300	6503	SO:0001819	synonymous_variant	5125	exon9			AGATCTGAGGCAG		CCDS6652.1, CCDS55320.1	9q21.13	2013-09-24			ENSG00000099139	ENSG00000099139			8747	protein-coding gene	gene with protein product		600488				7782070	Standard	NM_001190482		Approved	PC5, PC6, SPC6	uc004akc.2	Q92824	OTTHUMG00000020039	ENST00000545128.1:c.1122G>A	chr9.hg19:g.78722181G>A		52.0	0.0		65.0	25.0	NM_006200	F5H2G7|Q13527|Q96EP4	Silent	SNP	ENST00000545128.1	hg19	CCDS55320.1																																																																																			.	.		0.473	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	78722181	G	A	78722181	2	1	300	1	0	0	0	0	0	0	0	1	11612	1277	45	3		3	PCSK5	9	78722181	Silent	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10	7715543	78722181	62491250	67	43406										
PIP5KL1	138429	hgsc.bcm.edu	37	chr9	130688228	130688228	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	tcaggggcgggatccacccaGcggctcacctcgcagccttt	12	16	2	0			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr9:130688228G>A	ENST00000388747.4	-	8	725	c.681C>T	c.(679-681)cgC>cgT	p.R227R	PIP5KL1_ENST00000300432.3_Silent_p.R24R|PIP5KL1_ENST00000490773.1_Intron	NM_001135219.1	NP_001128691.1	Q5T9C9	PI5L1_HUMAN	phosphatidylinositol-4-phosphate 5-kinase-like 1	227	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.					cell projection (GO:0042995)|cytoplasm (GO:0005737)|membrane (GO:0016020)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)			endometrium(1)|kidney(2)|large_intestine(1)|lung(3)|skin(1)	8						GATCCACCCAGCGGCTCACCT	0.572																																					p.R227R		Atlas-SNP	.											.	PIP5KL1	38	.	0			c.C681T						.						43	45	44					9																	130688228		2203	4300	6503	SO:0001819	synonymous_variant	138429	exon8			CACCCAGCGGCTC	BC042184	CCDS6885.1, CCDS48030.1	9q34.13	2008-02-05			ENSG00000167103	ENSG00000167103			28711	protein-coding gene	gene with protein product		612865				12477932	Standard	NM_001135219		Approved	bA203J24.5, MGC46424	uc011mao.2	Q5T9C9	OTTHUMG00000020719	ENST00000388747.4:c.681C>T	chr9.hg19:g.130688228G>A		75.0	0.0		56.0	28.0	NM_001135219	Q8IVS3	Silent	SNP	ENST00000388747.4	hg19	CCDS48030.1																																																																																			.	.		0.572	PIP5KL1-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054289.2	NM_173492		A	130688228	G	A	130688228	2	1	300	1	0	0	0	0	0	0	0	1	11951	958	34	3		3	PIP5KL1	9	130688228	Silent	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10	51966047	130688228	10525203	68	43407										
USP20	10868	hgsc.bcm.edu	37	chr9	132614914	132614914	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	ggacttgctgctcaaatctaAggtaaagggtcagaccttac	10	9	3	1			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr9:132614914A>G	ENST00000315480.4	+	3	238	c.80A>G	c.(79-81)aAg>aGg	p.K27R	USP20_ENST00000358355.1_Splice_Site_p.K27R|USP20_ENST00000372429.3_Splice_Site_p.K27R			Q9Y2K6	UBP20_HUMAN	ubiquitin specific peptidase 20	27					endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|urinary_tract(1)	11		Ovarian(14;0.00556)				CTCAAATCTAAGGTAAAGGGT	0.567																																					p.K27R		Atlas-SNP	.											.	USP20	186	.	0			c.A80G						.						26	27	27					9																	132614914		1895	4111	6006	SO:0001630	splice_region_variant	10868	exon3			AATCTAAGGTAAA	AB023220	CCDS43892.1	9q34.2	2014-07-15	2005-08-08		ENSG00000136878	ENSG00000136878		"Ubiquitin-specific peptidases"	12619	protein-coding gene	gene with protein product		615143	"ubiquitin specific protease 20"			12838346	Standard	NM_006676		Approved	KIAA1003	uc004byr.3	Q9Y2K6	OTTHUMG00000020793	ENST00000315480.4:c.81+1A>G	chr9.hg19:g.132614914A>G		121.0	0.0		125.0	55.0	NM_001008563	Q541F1|Q8IXQ1|Q96LG5|Q9UQN8|Q9UQP0	Missense_Mutation	SNP	ENST00000315480.4	hg19	CCDS43892.1	.	.	.	.	.	.	.	.	.	.	A	18.46	3.629852	0.67015	.	.	ENSG00000136878	ENST00000372429;ENST00000315480;ENST00000358355	T;T;T	0.18810	2.19;2.19;2.19	5.69	5.69	0.88448	Zinc finger, RING/FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	T	0.38081	0.1027	L	0.50333	1.59	0.80722	D	1	D	0.71674	0.998	D	0.76071	0.987	T	0.06320	-1.0833	10	0.20519	T	0.43	.	13.9059	0.63836	1.0:0.0:0.0:0.0	.	27	Q9Y2K6	UBP20_HUMAN	R	27	ENSP00000361506:K27R;ENSP00000313811:K27R;ENSP00000351122:K27R	ENSP00000313811:K27R	K	+	2	0	USP20	131654735	1.000000	0.71417	1.000000	0.80357	0.476000	0.33039	8.165000	0.89663	2.163000	0.67991	0.533000	0.62120	AAG	.	.		0.567	USP20-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054604.2		Missense_Mutation	G	132614914	A	G	132614914	5	3	300	1	0	0	0	0	0	0	1	0	17067	86	3	2	82	2	USP20	9	132614914	Splice_Site	SNP	A	TCGA-G3-AAV4-01A-11D-A382-10	1926686	132614914	8598517	69	43408										
BAT2L1	84726	hgsc.bcm.edu	37	chr9	134323169	134323169	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	ggccttgacgatctggacgcCgatgccgatgatggctgggc	16	11	1	2	rs569503281		TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr9:134323169C>G	ENST00000357304.4	+	8	1153	c.1098C>G	c.(1096-1098)gcC>gcG	p.A366A	PRRC2B_ENST00000372249.1_5'UTR|PRRC2B_ENST00000458550.1_Silent_p.A366A|PRRC2B_ENST00000405995.1_Silent_p.A366A	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	366							poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						ATCTGGACGCCGATGCCGATG	0.602																																					p.A366A		Atlas-SNP	.											.	PRRC2B	266	.	0			c.C1098G						.						41	43	42					9																	134323169		2013	4173	6186	SO:0001819	synonymous_variant	84726	exon8			GGACGCCGATGCC	AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"KIAA0515", "HLA-B associated transcript 2-like", "HLA-B associated transcript 2-like 1"	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.1098C>G	chr9.hg19:g.134323169C>G		85.0	0.0		62.0	27.0	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Silent	SNP	ENST00000357304.4	hg19	CCDS48044.1																																																																																			.	.		0.602	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				G	134323169	C	G	134323169	2	3	300	1	0	0	0	0	0	0	0	1	1320	639	23	4		4	BAT2L1	9	134323169	Silent	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	1708255	134323169	6890262	70	43409										
EGFL7	51162	hgsc.bcm.edu	37	chr9	139564771	139564772	+	Missense_Mutation	DNP	CC	CC	AA													0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	agggccccccagggtggcccCcaacccgacaggtaaacagc							TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr9:139564771_139564772CC>AA	ENST00000371699.1	+	7	1471_1472	c.560_561CC>AA	c.(559-561)cCC>cAA	p.P187Q	EGFL7_ENST00000308874.7_Missense_Mutation_p.P187Q|EGFL7_ENST00000492002.1_3'UTR|EGFL7_ENST00000406555.3_Missense_Mutation_p.P187Q|EGFL7_ENST00000371698.3_Missense_Mutation_p.P187Q|MIR126_ENST00000362291.1_RNA			Q9UHF1	EGFL7_HUMAN	EGF-like-domain, multiple 7	187					angiogenesis (GO:0001525)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|negative regulation of cell migration (GO:0030336)|negative regulation of Notch signaling pathway (GO:0045746)|positive regulation of endothelial cell proliferation (GO:0001938)|vasculogenesis (GO:0001570)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)			kidney(2)|ovary(1)|prostate(2)|urinary_tract(1)	6	all_cancers(76;0.109)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.87e-06)|Epithelial(140;0.000123)		AGGGTGGCCCCCAACCCGACAG	0.663																																					p.P187H|p.P187P		Atlas-SNP	.											.	EGFL7	11	.	0			c.C560A|c.C561A						.																																			SO:0001583	missense	51162	exon8			TGGCCCCCAACCC|GGCCCCCAACCCG	AF186111	CCDS7002.1	9q34.3	2008-02-05			ENSG00000172889	ENSG00000172889			20594	protein-coding gene	gene with protein product		608582					Standard	NM_016215		Approved	ZNEU1	uc004cih.3	Q9UHF1	OTTHUMG00000020938	Exception_encountered	chr9.hg19:g.139564771_139564772delinsAA	ENSP00000360764:p.Pro187Gln	138.0|135.0	0.0		136.0|134.0	61.0|60.0	NM_016215	B3KRP0|M9VTX9|Q5M7Y5|Q5VUD5|Q96EG0	Missense_Mutation|Silent	SNP	ENST00000371699.1	hg19	CCDS7002.1																																																																																			.	.		0.663	EGFL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055094.1	NM_016215		AA	139564772	CC	AA	139564771	3	1	300	1	0	0	0	0	1	0	0	0	4966	623	22	3	578	3	EGFL7	9	139564771	Missense_Mutation	DNP	CC	TCGA-G3-AAV4-01A-11D-A382-10	5241602	139564771	1648660	71	43410										
PCDH15	65217	hgsc.bcm.edu	37	chr10	55955639	55955639	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	caggaagaggatgaccattgTcttgttcagcctaaaattga	10	7	2	3			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr10:55955639T>A	ENST00000320301.6	-	11	1503	c.1109A>T	c.(1108-1110)gAc>gTc	p.D370V	PCDH15_ENST00000373957.3_Missense_Mutation_p.D348V|PCDH15_ENST00000373965.2_Missense_Mutation_p.D370V|PCDH15_ENST00000395433.1_Missense_Mutation_p.D348V|PCDH15_ENST00000395445.1_Missense_Mutation_p.D370V|PCDH15_ENST00000361849.3_Missense_Mutation_p.D370V|PCDH15_ENST00000395440.1_Missense_Mutation_p.D370V|PCDH15_ENST00000395438.1_Missense_Mutation_p.D370V|PCDH15_ENST00000395446.1_Missense_Mutation_p.D370V|PCDH15_ENST00000373955.1_Missense_Mutation_p.D370V|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395430.1_Missense_Mutation_p.D370V|PCDH15_ENST00000395432.2_Missense_Mutation_p.D333V|PCDH15_ENST00000409834.1_5'UTR|PCDH15_ENST00000437009.1_Missense_Mutation_p.D370V|PCDH15_ENST00000414778.1_Missense_Mutation_p.D375V	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	370	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				ATGACCATTGTCTTGTTCAGC	0.348										HNSCC(58;0.16)																											p.D375V		Atlas-SNP	.											.	PCDH15	1715	.	0			c.A1124T						.						97	95	96					10																	55955639		2203	4300	6503	SO:0001583	missense	65217	exon12			CCATTGTCTTGTT	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.1109A>T	chr10.hg19:g.55955639T>A	ENSP00000322604:p.Asp370Val	116.0	0.0		106.0	34.0	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	hg19	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	T	19.70	3.876232	0.72180	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000395445;ENST00000395446;ENST00000395440;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000373957;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009;ENST00000373955	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.37584	1.19;1.19;1.19;1.19;1.19;1.19;2.48;1.19;1.19;1.19;1.19;1.19;1.19;1.19	5.17	5.17	0.71159	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.52092	0.1713	M	0.64567	1.98	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;0.999;0.999;1.0;1.0;1.0;1.0;1.0;0.999;0.974;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;P;D;D;D;D	0.97110	0.998;0.991;0.986;0.96;0.999;0.991;0.998;0.987;0.991;0.986;0.841;0.993;1.0;0.999;0.993	T	0.51309	-0.8722	9	0.06365	T	0.9	.	14.6657	0.68907	0.0:0.0:0.0:1.0	.	348;370;370;375;370;333;370;370;370;370;370;375;370;348;370	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;A2A3D8;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	V	370;375;370;370;370;370;370;333;370;348;348;370;370;375;370;370	ENSP00000363076:D370V;ENSP00000410304:D375V;ENSP00000378826:D370V;ENSP00000378832:D370V;ENSP00000378833:D370V;ENSP00000378827:D370V;ENSP00000378820:D333V;ENSP00000354950:D370V;ENSP00000378821:D348V;ENSP00000363068:D348V;ENSP00000322604:D370V;ENSP00000378818:D370V;ENSP00000412628:D370V;ENSP00000363066:D370V	ENSP00000322604:D370V	D	-	2	0	PCDH15	55625645	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	8.008000	0.88588	1.963000	0.57068	0.482000	0.46254	GAC	.	.		0.348	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		A	55955639	T	A	55955639	3	1	300	1	0	0	0	0	1	0	0	0	11520	1667	58	4	6494	4	PCDH15	10	55955639	Missense_Mutation	SNP	T	TCGA-G3-AAV4-01A-11D-A382-10		55955639	79579108	72	43411										
IFIT2	3433	hgsc.bcm.edu	37	chr10	91066639	91066653	+	In_Frame_Del	DEL	AAAGAAAGTTACTGG	AAAGAAAGTTACTGG	-													0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	agagaatggaatgtatgggaAaagaaagttactggaactaa							TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	AAAGAAAGTTACTGG	AAAGAAAGTTACTGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr10:91066639_91066653delAAAGAAAGTTACTGG	ENST00000371826.3	+	2	1095_1109	c.926_940delAAAGAAAGTTACTGG	c.(925-942)aaaagaaagttactggaa>aaa	p.RKLLE310del	LIPA_ENST00000487618.1_Intron|LIPA_ENST00000371837.1_Intron	NM_001547.4	NP_001538.4	P09913	IFIT2_HUMAN	interferon-induced protein with tetratricopeptide repeats 2	310					apoptotic mitochondrial changes (GO:0008637)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|negative regulation of protein binding (GO:0032091)|positive regulation of apoptotic process (GO:0043065)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	poly(A) RNA binding (GO:0044822)	p.R310I(1)		endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|skin(1)	12		Colorectal(252;0.0161)				ATGTATGGGAAAAGAAAGTTACTGGAACTAATAGG	0.437																																					p.309_313del		Atlas-Indel,Pindel	.											.	IFIT2	39	.	1	Substitution - Missense(1)	large_intestine(1)	c.925_939del						.																																			SO:0001651	inframe_deletion	3433	exon2			.	M14660	CCDS41548.1	10q23.31	2013-01-11			ENSG00000119922	ENSG00000119922		"Tetratricopeptide (TTC) repeat domain containing"	5409	protein-coding gene	gene with protein product		147040		IFI54, G10P2		3175763, 3360121	Standard	NM_001547		Approved	IFI-54, ISG-54K, cig42, GARG-39	uc009xts.3	P09913	OTTHUMG00000018707	ENST00000371826.3:c.926_940delAAAGAAAGTTACTGG	chr10.hg19:g.91066639_91066653delAAAGAAAGTTACTGG	ENSP00000360891:p.Arg310_Glu314del	117.0	0.0		86.0	14.0	NM_001547	Q5T767	In_Frame_Del	DEL	ENST00000371826.3	hg19	CCDS41548.1																																																																																			.	.		0.437	IFIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049293.1	NM_001547		-	91066653	AAAGAAAGTTACTGG	-	91066639	7	5	300	1	0	1	0	1	0	0	0	0	7532	14	1	0	932	0	IFIT2	10	91066639	In_Frame_Del	DEL	AAAGAAAGTTACTGG	TCGA-G3-AAV4-01A-11D-A382-10	35111000	91066639	44468108	73	43412										
CDKN1C	1028	hgsc.bcm.edu	37	chr11	2906108	2906108	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	gcgggggccggggccggggcCggggccggggctggggccgg	28	12	0	0			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr11:2906108C>T	ENST00000414822.3	-	1	1003	c.612G>A	c.(610-612)ccG>ccA	p.P204P	CDKN1C_ENST00000313407.6_Silent_p.P193P|CDKN1C_ENST00000380725.1_Intron|CDKN1C_ENST00000440480.2_Silent_p.P193P|CDKN1C_ENST00000430149.2_Silent_p.P204P	NM_000076.2	NP_000067.1	P49918	CDN1C_HUMAN	cyclin-dependent kinase inhibitor 1C (p57, Kip2)	204	9 X 4 AA repeats of P-A-P-A.				adrenal gland development (GO:0030325)|aging (GO:0007568)|camera-type eye development (GO:0043010)|cell cycle arrest (GO:0007050)|digestive system development (GO:0055123)|embryonic placenta morphogenesis (GO:0060669)|genetic imprinting (GO:0071514)|kidney development (GO:0001822)|multicellular organism growth (GO:0035264)|myeloid cell differentiation (GO:0030099)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of kinase activity (GO:0033673)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron maturation (GO:0042551)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|skeletal system development (GO:0001501)|uterus development (GO:0060065)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)			central_nervous_system(1)|lung(1)	2		all_epithelial(84;0.000187)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|Breast(177;0.00328)|all_neural(188;0.00681)|all_lung(207;0.157)|Lung NSC(207;0.216)		BRCA - Breast invasive adenocarcinoma(625;0.0025)|LUSC - Lung squamous cell carcinoma(625;0.19)		gggccggggccggggccgggg	0.866																																					p.P204P	GBM(111;59 1151 2497 5746 16112 18241 29216)	Atlas-SNP	.											.	CDKN1C	4	.	0			c.G612A						.						1	1	1					11																	2906108		7	20	27	SO:0001819	synonymous_variant	1028	exon1			CGGGGCCGGGGCC	D64137	CCDS7738.1, CCDS44519.1	11p15.5	2014-09-17	2004-02-13		ENSG00000129757	ENSG00000129757			1786	protein-coding gene	gene with protein product		600856	"Beckwith-Wiedemann syndrome"	BWCR, BWS		7729684	Standard	NM_000076		Approved	P57, KIP2	uc001lws.4	P49918	OTTHUMG00000010040	ENST00000414822.3:c.612G>A	chr11.hg19:g.2906108C>T		13.0	0.0		22.0	9.0	NM_000076		Silent	SNP	ENST00000414822.3	hg19	CCDS7738.1																																																																																			.	.		0.866	CDKN1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027774.2	NM_000076		T	2906108	C	T	2906108	2	4	300	1	0	0	0	0	0	0	0	1	3162	639	23	1		1	CDKN1C	11	2906108	Silent	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10		2906108	132100408	74	43413										
CPSF7	79869	hgsc.bcm.edu	37	chr11	61196760	61196760	+	5'UTR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	tggacaaagtaaggaagatgCcactgcgggattcggaaaaa	13	6	0	1			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr11:61196760C>T	ENST00000394888.4	-	0	120				CPSF7_ENST00000439958.3_5'UTR|SDHAF2_ENST00000301761.2_5'Flank|CPSF7_ENST00000340437.4_Missense_Mutation_p.G26D|SDHAF2_ENST00000534878.1_5'Flank|RP11-286N22.8_ENST00000543044.1_5'Flank|SDHAF2_ENST00000543265.1_5'Flank|CPSF7_ENST00000448745.1_5'UTR|SDHAF2_ENST00000542074.1_5'Flank|CPSF7_ENST00000541963.1_5'UTR|SDHAF2_ENST00000537782.1_5'Flank	NM_001136040.2	NP_001129512.1	Q8N684	CPSF7_HUMAN	cleavage and polyadenylation specific factor 7, 59kDa						gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|protein tetramerization (GO:0051262)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)|mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	22						AAGGAAGATGCCACTGCGGGA	0.512																																					p.G26D		Atlas-SNP	.											.	CPSF7	46	.	0			c.G77A						.						75	66	69					11																	61196760		692	1591	2283	SO:0001623	5_prime_UTR_variant	79869	exon2			AAGATGCCACTGC		CCDS8006.2, CCDS44619.1, CCDS44620.1	11q12.2	2013-06-18			ENSG00000149532	ENSG00000149532		"RNA binding motif (RRM) containing"	30098	protein-coding gene	gene with protein product	"pre mRNA cleavage factor I, 59 kDa subunit", "cleavage factor Im complex 59 kDa subunit"					12477932	Standard	NM_024811		Approved	FLJ12529	uc001nrp.3	Q8N684	OTTHUMG00000168198	ENST00000394888.4:c.-53G>A	chr11.hg19:g.61196760C>T		59.0	0.0		65.0	4.0	NM_024811	B3KU04|C9K0Q4|Q7Z3H9|Q9H025|Q9H9V1	Missense_Mutation	SNP	ENST00000394888.4	hg19	CCDS44619.1	.	.	.	.	.	.	.	.	.	.	C	14.43	2.532142	0.45073	.	.	ENSG00000149532	ENST00000340437	.	.	.	4.82	3.89	0.44902	.	.	.	.	.	T	0.60183	0.2249	.	.	.	0.80722	D	1	D	0.61080	0.989	P	0.49252	0.604	T	0.65022	-0.6269	7	0.87932	D	0	.	10.4887	0.44737	0.1941:0.8059:0.0:0.0	.	26	Q8N684-3	.	D	26	.	ENSP00000345412:G26D	G	-	2	0	CPSF7	60953336	1.000000	0.71417	1.000000	0.80357	0.452000	0.32318	1.572000	0.36461	1.367000	0.46095	0.563000	0.77884	GGC	.	.		0.512	CPSF7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347835.2	NM_024811		T	61196760	C	T	61196760	1	4	300	0	1	0	0	0	0	0	0	0	3832	739	26	3		3	CPSF7	11	61196760	5'UTR	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	58290652	61196760	73809756	75	43414										
MAML2	84441	hgsc.bcm.edu	37	chr11	95712358	95712358	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	agggatggtggctggttgatGcccgtcctcgactgattcaa	14	9	1	2			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr11:95712358G>A	ENST00000524717.1	-	5	4509	c.3225C>T	c.(3223-3225)ggC>ggT	p.G1075G		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	1075					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				GCTGGTTGATGCCCGTCCTCG	0.502			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																p.G1075G		Atlas-SNP	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2	94	.	0			c.C3225T						.						140	139	139					11																	95712358		1977	4160	6137	SO:0001819	synonymous_variant	84441	exon5			GTTGATGCCCGTC	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"mastermind (Drosophila)-like 2"			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.3225C>T	chr11.hg19:g.95712358G>A		67.0	0.0		77.0	29.0	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	hg19	CCDS44714.1																																																																																			.	.		0.502	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			A	95712358	G	A	95712358	2	1	300	1	0	0	0	0	0	0	0	1	9215	1306	46	3		3	MAML2	11	95712358	Silent	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10	34515598	95712358	39294158	76	43415										
PRDM10	56980	hgsc.bcm.edu	37	chr11	129814881	129814881	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	gtgcttcggacacactgaagCatgcgcgttattgcactcct	10	12	0	1			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr11:129814881C>A	ENST00000360871.3	-	6	778	c.547G>T	c.(547-549)Gct>Tct	p.A183S	PRDM10_ENST00000423662.2_Missense_Mutation_p.A97S|PRDM10_ENST00000358825.5_Missense_Mutation_p.A183S|PRDM10_ENST00000304538.6_Missense_Mutation_p.A97S|PRDM10_ENST00000526082.1_Missense_Mutation_p.A97S|PRDM10_ENST00000528746.1_Missense_Mutation_p.A157S	NM_199437.1	NP_955469.1	Q9NQV6	PRD10_HUMAN	PR domain containing 10	183					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			breast(2)|endometrium(6)|kidney(3)|large_intestine(14)|lung(15)|pancreas(2)|skin(1)|stomach(3)|urinary_tract(2)	48	all_hematologic(175;0.0537)	Breast(109;0.000496)|Lung NSC(97;0.000693)|all_lung(97;0.00151)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0174)|Lung(977;0.176)|LUSC - Lung squamous cell carcinoma(976;0.185)		CACACTGAAGCATGCGCGTTA	0.557																																					p.A183S		Atlas-SNP	.											.	PRDM10	120	.	0			c.G547T						.						47	46	47					11																	129814881		2201	4297	6498	SO:0001583	missense	56980	exon6			CTGAAGCATGCGC	AF275817	CCDS8484.1, CCDS8485.1, CCDS44771.1, CCDS44772.1	11q24.3	2013-01-08			ENSG00000170325	ENSG00000170325		"Zinc fingers, C2H2-type"	13995	protein-coding gene	gene with protein product	"PRDM zinc finger transcription factor", "PR-domain family member 7", "tristanin"					12175877	Standard	NM_020228		Approved	KIAA1231, PFM7, MGC131802	uc001qfm.3	Q9NQV6	OTTHUMG00000165762	ENST00000360871.3:c.547G>T	chr11.hg19:g.129814881C>A	ENSP00000354118:p.Ala183Ser	289.0	0.0		282.0	134.0	NM_020228	B7ZL71|G3XAE5|J3KP23|Q17R90|Q2KHR4|Q863Z2|Q9NXI4|Q9ULI9	Missense_Mutation	SNP	ENST00000360871.3	hg19	CCDS8484.1	.	.	.	.	.	.	.	.	.	.	A	9.276	1.046957	0.19748	.	.	ENSG00000170325	ENST00000358825;ENST00000304538;ENST00000360871;ENST00000423662;ENST00000528746;ENST00000526082	T;T;T;T;T;T	0.39056	1.1;1.1;1.1;1.1;1.1;1.1	5.5	4.37	0.52481	.	0.067621	0.64402	N	0.000014	T	0.19248	0.0462	N	0.14661	0.345	0.22412	N	0.999128	B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0;0.0;0.0	T	0.18555	-1.0333	10	0.11794	T	0.64	-14.9963	2.9904	0.05981	0.5479:0.2324:0.2197:0.0	.	97;183;183;183;97;97;97	B7ZL72;Q9NQV6-4;G3XAE5;Q9NQV6;Q9NQV6-5;Q9NQV6-2;Q9NQV6-1	.;.;.;PRD10_HUMAN;.;.;.	S	183;97;183;97;157;97	ENSP00000351686:A183S;ENSP00000302669:A97S;ENSP00000354118:A183S;ENSP00000398431:A97S;ENSP00000431262:A157S;ENSP00000432237:A97S	ENSP00000302669:A97S	A	-	1	0	PRDM10	129320091	1.000000	0.71417	0.969000	0.41365	0.987000	0.75469	4.106000	0.57804	1.026000	0.39733	-0.264000	0.10439	GCT	.	.		0.557	PRDM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386076.1	NM_199437		A	129814881	C	A	129814881	3	1	300	1	0	0	0	0	1	0	0	0	12463	710	25	3	3003	3	PRDM10	11	129814881	Missense_Mutation	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	34102523	129814881	5191635	77	43416										
JAM3	83700	hgsc.bcm.edu	37	chr11	134018672	134018672	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	ctcatagttacaagaacccaGggaaaccagatggagttaac	9	9	1	2			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr11:134018672G>A	ENST00000299106.4	+	8	1015	c.856G>A	c.(856-858)Ggg>Agg	p.G286R	NCAPD3_ENST00000526787.2_5'Flank|JAM3_ENST00000441717.3_Missense_Mutation_p.G235R|JAM3_ENST00000529443.2_Missense_Mutation_p.G331R			Q9BX67	JAM3_HUMAN	junctional adhesion molecule 3	286					adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|establishment of cell polarity (GO:0030010)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|myelination (GO:0042552)|myeloid progenitor cell differentiation (GO:0002318)|neutrophil homeostasis (GO:0001780)|regulation of actin cytoskeleton organization by cell-cell adhesion (GO:0090138)|regulation of neutrophil chemotaxis (GO:0090022)|spermatid development (GO:0007286)|transmission of nerve impulse (GO:0019226)	cell-cell contact zone (GO:0044291)|desmosome (GO:0030057)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|paranodal junction (GO:0033010)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	integrin binding (GO:0005178)			breast(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)	10	all_hematologic(175;0.127)	all_cancers(12;1.06e-21)|all_epithelial(12;3.37e-16)|all_lung(97;7.03e-06)|Lung NSC(97;1.67e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0506)|Esophageal squamous(93;0.0566)		Epithelial(10;1.55e-09)|BRCA - Breast invasive adenocarcinoma(10;1.35e-08)|all cancers(11;2.81e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00402)|Lung(977;0.245)		CAAGAACCCAGGGAAACCAGA	0.448																																					p.G286R		Atlas-SNP	.											.	JAM3	41	.	0			c.G856A						.						79	76	77					11																	134018672		2201	4297	6498	SO:0001583	missense	83700	exon8			AACCCAGGGAAAC	AF356518	CCDS8494.1, CCDS55799.1, CCDS8494.2	11q25	2013-01-29			ENSG00000166086	ENSG00000166086		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15532	protein-coding gene	gene with protein product		606871					Standard	NM_032801		Approved	JAM-C, JAMC	uc001qhb.3	Q9BX67	OTTHUMG00000167130	ENST00000299106.4:c.856G>A	chr11.hg19:g.134018672G>A	ENSP00000299106:p.Gly286Arg	256.0	0.0		262.0	150.0	NM_032801	B3KWG9|Q8WWL8|Q96FL1	Missense_Mutation	SNP	ENST00000299106.4	hg19	CCDS8494.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.9|20.9	4.068672|4.068672	0.76301|0.76301	.|.	.|.	ENSG00000166086|ENSG00000166086	ENST00000299106;ENST00000441717|ENST00000529443	T|.	0.77877|.	-1.13|.	6.04|6.04	6.04|6.04	0.98038|0.98038	.|.	0.059506|.	0.64402|.	D|.	0.000003|.	T|T	0.51736|0.51736	0.1692|0.1692	L|L	0.36672|0.36672	1.1|1.1	0.35080|0.35080	D|D	0.763311|0.763311	P;P|.	0.47302|.	0.893;0.893|.	B;B|.	0.42319|.	0.383;0.383|.	T|T	0.58358|0.58358	-0.7650|-0.7650	10|5	0.13108|.	T|.	0.6|.	.|.	13.0035|13.0035	0.58690|0.58690	0.0735:0.0:0.9265:0.0|0.0735:0.0:0.9265:0.0	.|.	235;286|.	B3KWG9;Q9BX67|.	.;JAM3_HUMAN|.	R|K	331;235|239	ENSP00000395742:G235R|.	ENSP00000299106:G331R|.	G|R	+|+	1|2	0|0	JAM3|JAM3	133523882|133523882	1.000000|1.000000	0.71417|0.71417	0.974000|0.974000	0.42286|0.42286	0.952000|0.952000	0.60782|0.60782	5.576000|5.576000	0.67437|0.67437	2.873000|2.873000	0.98535|0.98535	0.563000|0.563000	0.77884|0.77884	GGG|AGG	.	.		0.448	JAM3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000393303.4	NM_032801		A	134018672	G	A	134018672	3	1	300	1	0	0	0	0	1	0	0	0	7953	1000	35	3	1021	3	JAM3	11	134018672	Missense_Mutation	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10	4203791	134018672	987844	78	43417										
ARID2	196528	hgsc.bcm.edu	37	chr12	46230522	46230549	+	Splice_Site	DEL	TTGTAGAAGGTACATCAGGAGAATGGAT	TTGTAGAAGGTACATCAGGAGAATGGAT	-													0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	aaatatgtattttctattgtAgaaggtacatcaggagaatg					rs200449496|rs143391973|rs201031100|rs372591699		TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	TTGTAGAAGGTACATCAGGAGAATGGAT	TTGTAGAAGGTACATCAGGAGAATGGAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr12:46230522_46230549delTTGTAGAAGGTACATCAGGAGAATGGAT	ENST00000334344.6	+	8	944_970	c.772_798delTTGTAGAAGGTACATCAGGAGAATGGAT	c.(772-798)ttgtagaaggtacatcaggagaatggadel	p.L*KVHQENG258fs	ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000444670.1_5'Flank|ARID2_ENST00000422737.1_Splice_Site_p.L*KVHQENG109fs	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	258					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		TTTCTATTGTAGAAGGTACATCAGGAGAATGGATTTGGGAGTCTTTAT	0.342			"N, S, F"		hepatocellular carcinoma																																p.258_265del		Atlas-Indel,Pindel	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	311	.	0			c.773_793del						.																																			SO:0001630	splice_region_variant	196528	exon8			.		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.773-1TTGTAGAAGGTACATCAGGAGAATGGAT>-	chr12.hg19:g.46230522_46230549delTTGTAGAAGGTACATCAGGAGAATGGAT		184.0	0.0		145.0	30.0	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	In_Frame_Del	DEL	ENST00000334344.6	hg19	CCDS31783.1																																																																																			.	.		0.342	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875	Frame_Shift_Del	-	46230549	TTGTAGAAGGTACATCAGGAGAATGGAT	-	46230522	8	5	300	1	0	1	0	1	0	0	1	0	915	434	15	0	801	0	ARID2	12	46230522	Splice_Site	DEL	TTGTAGAAGGTACATCAGGAGAATGGAT	TCGA-G3-AAV4-01A-11D-A382-10		46230522	87621373	79	43418										
ARID2	196528	hgsc.bcm.edu	37	chr12	46243941	46243941	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	aaggtgttcatactgtggcaCaaactgtttcaagaattcca	8	8	2	1			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr12:46243941C>T	ENST00000334344.6	+	15	2207	c.2035C>T	c.(2035-2037)Caa>Taa	p.Q679*	ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000444670.1_Nonsense_Mutation_p.Q289*|ARID2_ENST00000422737.1_Nonsense_Mutation_p.Q530*|ARID2_ENST00000457135.1_5'Flank	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	679					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		TACTGTGGCACAAACTGTTTC	0.413			"N, S, F"		hepatocellular carcinoma																																p.Q679X		Atlas-SNP	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	311	.	0			c.C2035T						.						146	139	142					12																	46243941		2203	4300	6503	SO:0001587	stop_gained	196528	exon15			GTGGCACAAACTG		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.2035C>T	chr12.hg19:g.46243941C>T	ENSP00000335044:p.Gln679*	178.0	0.0		175.0	68.0	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Nonsense_Mutation	SNP	ENST00000334344.6	hg19	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	C	40	7.956362	0.98580	.	.	ENSG00000189079	ENST00000334344;ENST00000422737;ENST00000444670	.	.	.	5.95	5.95	0.96441	.	0.325040	0.32002	N	0.006735	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08599	T	0.76	-3.6635	18.5659	0.91116	0.0:1.0:0.0:0.0	.	.	.	.	X	679;530;289	.	ENSP00000335044:Q679X	Q	+	1	0	ARID2	44530208	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.036000	0.70948	2.825000	0.97269	0.655000	0.94253	CAA	.	.		0.413	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		T	46243941	C	T	46243941	4	4	300	1	0	0	0	0	0	1	0	0	915	479	17	3	2093	3	ARID2	12	46243941	Nonsense_Mutation	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	13419	46243941	87607954	80	43419										
CEP290	80184	hgsc.bcm.edu	37	chr12	88447463	88447463	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	tcagctccactttggtccttGttagcttctatctgatggat	8	10	3	1			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr12:88447463G>T	ENST00000552810.1	-	52	7438	c.7095C>A	c.(7093-7095)aaC>aaA	p.N2365K	CEP290_ENST00000309041.7_Missense_Mutation_p.N2367K|CEP290_ENST00000397838.3_Missense_Mutation_p.N1425K|RNA5SP364_ENST00000516938.1_RNA|CEP290_ENST00000547691.2_Missense_Mutation_p.N1425K	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	2365					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						TTTGGTCCTTGTTAGCTTCTA	0.333																																					p.N2365K		Atlas-SNP	.											.	CEP290	195	.	0			c.C7095A						.						104	93	97					12																	88447463		1815	4068	5883	SO:0001583	missense	80184	exon52			GTCCTTGTTAGCT	AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"Joubert syndrome 5", "nephrocystin-6", "cancer/testis antigen 87", "POC3 centriolar protein homolog (Chlamydomonas)", "Meckel syndrome, type 4"	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.7095C>A	chr12.hg19:g.88447463G>T	ENSP00000448012:p.Asn2365Lys	39.0	0.0		73.0	26.0	NM_025114	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Missense_Mutation	SNP	ENST00000552810.1	hg19	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	G	4.353	0.064952	0.08388	.	.	ENSG00000198707	ENST00000547691;ENST00000552810;ENST00000309041;ENST00000397838	T;T;T;T	0.62639	0.59;0.01;0.01;0.59	4.95	2.09	0.27110	.	0.977834	0.08439	N	0.945765	T	0.47173	0.1431	L	0.40543	1.245	0.09310	N	1	B	0.18166	0.026	B	0.20767	0.031	T	0.34775	-0.9815	10	0.06099	T	0.92	.	7.1342	0.25519	0.4593:0.0:0.5407:0.0	.	2365	O15078	CE290_HUMAN	K	1425;2365;2367;1425	ENSP00000446905:N1425K;ENSP00000448012:N2365K;ENSP00000308021:N2367K;ENSP00000380938:N1425K	ENSP00000308021:N2367K	N	-	3	2	CEP290	86971594	0.005000	0.15991	0.731000	0.30826	0.138000	0.21146	0.712000	0.25779	0.634000	0.30469	-0.136000	0.14681	AAC	.	.		0.333	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		T	88447463	G	T	88447463	3	4	300	1	0	0	0	0	1	0	0	0	3255	1368	48	3	356	3	CEP290	12	88447463	Missense_Mutation	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10	42203522	88447463	45404432	81	43420										
PARP4	143	hgsc.bcm.edu	37	chr13	25068806	25068806	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	cagttcttcaatgtaattttCaaagtattcacttgcatctt	4	8	5	0	rs145170390		TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr13:25068806C>T	ENST00000381989.3	-	7	751	c.646G>A	c.(646-648)Gaa>Aaa	p.E216K		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	216					cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		ATGTAATTTTCAAAGTATTCA	0.338																																					p.E216K		Atlas-SNP	.											.	PARP4	142	.	0			c.G646A						.						142	139	140					13																	25068806		2203	4300	6503	SO:0001583	missense	143	exon7			AATTTTCAAAGTA	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"Poly (ADP-ribose) polymerases"	271	protein-coding gene	gene with protein product	"von Willebrand factor A domain containing 5C"	607519	"ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.646G>A	chr13.hg19:g.25068806C>T	ENSP00000371419:p.Glu216Lys	87.0	0.0		54.0	17.0	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	hg19	CCDS9307.1	.	.	.	.	.	.	.	.	.	.	C	14.06	2.421784	0.43020	.	.	ENSG00000102699	ENST00000381989	T	0.46819	0.86	4.52	4.52	0.55395	.	0.214121	0.36972	N	0.002302	T	0.63908	0.2551	M	0.73598	2.24	0.31828	N	0.625074	D	0.67145	0.996	D	0.65443	0.935	T	0.65751	-0.6092	10	0.18276	T	0.48	-20.4413	14.772	0.69688	0.0:1.0:0.0:0.0	.	216	Q9UKK3	PARP4_HUMAN	K	216	ENSP00000371419:E216K	ENSP00000371419:E216K	E	-	1	0	PARP4	23966806	0.997000	0.39634	0.621000	0.29145	0.045000	0.14185	2.644000	0.46613	2.361000	0.80049	0.549000	0.68633	GAA	.	C|1.000;G|0.000		0.338	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437		T	25068806	C	T	25068806	3	4	300	1	0	0	0	0	1	0	0	0	11472	835	29	3	4640	3	PARP4	13	25068806	Missense_Mutation	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10		25068806	90101072	82	43421										
TM9SF2	9375	hgsc.bcm.edu	37	chr13	100193842	100193842	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	ttccctggtcattgttctctTcttatctggaatggtagcta	8	9	4	0			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr13:100193842T>A	ENST00000376387.4	+	9	1128	c.938T>A	c.(937-939)tTc>tAc	p.F313Y		NM_004800.1	NP_004791.1	Q99805	TM9S2_HUMAN	transmembrane 9 superfamily member 2	313					transport (GO:0006810)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)	17	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.218)					ATTGTTCTCTTCTTATCTGGA	0.353																																					p.F313Y		Atlas-SNP	.											.	TM9SF2	52	.	0			c.T938A						.						245	218	227					13																	100193842		2203	4300	6503	SO:0001583	missense	9375	exon9			TTCTCTTCTTATC	U81006	CCDS9493.1	13q32.2	2011-03-28			ENSG00000125304	ENSG00000125304			11865	protein-coding gene	gene with protein product		604678				9729438	Standard	NM_004800		Approved	P76	uc001voj.2	Q99805	OTTHUMG00000017272	ENST00000376387.4:c.938T>A	chr13.hg19:g.100193842T>A	ENSP00000365567:p.Phe313Tyr	145.0	0.0		95.0	49.0	NM_004800	A8K399|Q2TAY5	Missense_Mutation	SNP	ENST00000376387.4	hg19	CCDS9493.1	.	.	.	.	.	.	.	.	.	.	T	32	5.158203	0.94686	.	.	ENSG00000125304	ENST00000376387	T	0.59906	0.23	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	D	0.84352	0.5453	H	0.98218	4.175	0.80722	D	1	D;D	0.69078	0.997;0.996	D;D	0.71656	0.968;0.974	D	0.90402	0.4403	10	0.87932	D	0	-24.4181	15.1335	0.72545	0.0:0.0:0.0:1.0	.	279;313	E9PHW5;Q99805	.;TM9S2_HUMAN	Y	313	ENSP00000365567:F313Y	ENSP00000365567:F313Y	F	+	2	0	TM9SF2	98991843	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.015000	0.88690	1.965000	0.57142	0.477000	0.44152	TTC	.	.		0.353	TM9SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045602.3			A	100193842	T	A	100193842	3	1	300	1	0	0	0	0	1	0	0	0	15993	1783	62	4	972	4	TM9SF2	13	100193842	Missense_Mutation	SNP	T	TCGA-G3-AAV4-01A-11D-A382-10	75125036	100193842	14976036	83	43422										
KTN1	3895	hgsc.bcm.edu	37	chr14	56139682	56139682	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	gaacatttggaaatggaactAgaaaaggcagagatggaacg	13	4	0	2			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr14:56139682A>G	ENST00000395314.3	+	39	3707	c.3639A>G	c.(3637-3639)ctA>ctG	p.L1213L	KTN1_ENST00000413890.2_Silent_p.L1190L|KTN1_ENST00000438792.2_Silent_p.L1184L|KTN1_ENST00000395308.1_Silent_p.L1190L|KTN1_ENST00000395311.1_Silent_p.L1190L|KTN1_ENST00000416613.1_Silent_p.L1213L|KTN1_ENST00000554507.1_Silent_p.L479L|KTN1_ENST00000555573.1_Silent_p.L218L|KTN1_ENST00000395309.3_Silent_p.L1213L	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	1213					microtubule-based movement (GO:0007018)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|large_intestine(8)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	19						AAATGGAACTAGAAAAGGCAG	0.353			T	RET	papillary thryoid																																p.L1213L		Atlas-SNP	.		Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	.	KTN1	147	.	0			c.A3639G						.						104	99	101					14																	56139682		2203	4300	6503	SO:0001819	synonymous_variant	3895	exon39			GGAACTAGAAAAG		CCDS41957.1, CCDS41958.1, CCDS41959.1	14q22.1	2008-05-02			ENSG00000126777	ENSG00000126777			6467	protein-coding gene	gene with protein product		600381				9605849	Standard	NM_001079521		Approved	KIAA0004, CG1	uc001xcc.3	Q86UP2	OTTHUMG00000140312	ENST00000395314.3:c.3639A>G	chr14.hg19:g.56139682A>G		171.0	0.0		234.0	98.0	NM_001079521	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Silent	SNP	ENST00000395314.3	hg19	CCDS41957.1	.	.	.	.	.	.	.	.	.	.	A	8.283	0.815967	0.16607	.	.	ENSG00000126777	ENST00000554294	.	.	.	6.17	3.57	0.40892	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-5.4107	4.9122	0.13827	0.6628:0.0:0.2113:0.1259	.	.	.	.	W	12	.	.	X	+	2	0	KTN1	55209435	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.611000	0.46334	0.444000	0.26612	0.533000	0.62120	TAG	.	.		0.353	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2			G	56139682	A	G	56139682	2	3	300	1	0	0	0	0	0	0	0	1	8594	407	15	2		2	KTN1	14	56139682	Silent	SNP	A	TCGA-G3-AAV4-01A-11D-A382-10		56139682	51209858	84	43423										
PLEKHH1	57475	hgsc.bcm.edu	37	chr14	68028676	68028676	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	tttctttttgctcagcttgaGatggagaatcagcatctgaa	9	7	4	3			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr14:68028676G>A	ENST00000329153.5	+	6	561	c.429G>A	c.(427-429)gaG>gaA	p.E143E		NM_020715.2	NP_065766.1	Q9ULM0	PKHH1_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 1	143						cytoskeleton (GO:0005856)				endometrium(2)|kidney(4)|lung(12)|urinary_tract(1)	19				all cancers(60;0.000771)|OV - Ovarian serous cystadenocarcinoma(108;0.00502)|BRCA - Breast invasive adenocarcinoma(234;0.011)		CTCAGCTTGAGATGGAGAATC	0.438																																					p.E143E		Atlas-SNP	.											.	PLEKHH1	118	.	0			c.G429A						.						67	68	67					14																	68028676		1949	4145	6094	SO:0001819	synonymous_variant	57475	exon6			GCTTGAGATGGAG	AB033026	CCDS45128.1	14q24.1	2013-01-10				ENSG00000054690		"Pleckstrin homology (PH) domain containing"	17733	protein-coding gene	gene with protein product						10574462	Standard	NM_020715		Approved	KIAA1200	uc001xjl.1	Q9ULM0		ENST00000329153.5:c.429G>A	chr14.hg19:g.68028676G>A		182.0	0.0		169.0	92.0	NM_020715	A6H8X6|Q6PJL4|Q6ZWC7	Silent	SNP	ENST00000329153.5	hg19	CCDS45128.1																																																																																			.	.		0.438	PLEKHH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412730.3	XM_031054		A	68028676	G	A	68028676	2	1	300	1	0	0	0	0	0	0	0	1	12085	933	33	3		3	PLEKHH1	14	68028676	Silent	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10	11888994	68028676	39320864	85	43424										
TBL3	10607	hgsc.bcm.edu	37	chr16	2026919	2026919	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	cacagccccagacaacggccCtatcctcctgcaggcccaga	8	19	0	2			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr16:2026919C>T	ENST00000568546.1	+	14	1525	c.1397C>T	c.(1396-1398)cCt>cTt	p.P466L		NM_006453.2	NP_006444.2	Q12788	TBL3_HUMAN	transducin (beta)-like 3	466					G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|intracellular signal transduction (GO:0035556)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)			breast(1)|endometrium(2)|kidney(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	18						GACAACGGCCCTATCCTCCTG	0.607																																					p.P466L	Melanoma(118;616 1651 35077 38081 48633)	Atlas-SNP	.											.	TBL3	54	.	0			c.C1397T						.						110	89	96					16																	2026919		2198	4300	6498	SO:0001583	missense	10607	exon14			ACGGCCCTATCCT	U02609	CCDS10453.1	16p13.3	2013-01-10			ENSG00000183751	ENSG00000183751		"WD repeat domain containing"	11587	protein-coding gene	gene with protein product		605915				8307582	Standard	NM_006453		Approved	SAZD, UTP13	uc002cnu.1	Q12788	OTTHUMG00000128710	ENST00000568546.1:c.1397C>T	chr16.hg19:g.2026919C>T	ENSP00000454836:p.Pro466Leu	129.0	0.0		101.0	56.0	NM_006453	Q59GD6|Q8IVB7|Q96A78	Missense_Mutation	SNP	ENST00000568546.1	hg19	CCDS10453.1	.	.	.	.	.	.	.	.	.	.	C	3.105	-0.183853	0.06340	.	.	ENSG00000183751	ENST00000332704	.	.	.	5.27	3.28	0.37604	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.283721	0.29239	N	0.012723	T	0.42675	0.1213	M	0.71036	2.16	0.18873	N	0.999981	B;B	0.06786	0.0;0.001	B;B	0.06405	0.002;0.001	T	0.29212	-1.0019	9	0.27082	T	0.32	-13.1892	8.2339	0.31614	0.0:0.7559:0.0:0.2441	.	228;466	A0JLS5;Q12788	.;TBL3_HUMAN	L	466	.	ENSP00000331815:P466L	P	+	2	0	TBL3	1966920	0.137000	0.22531	0.007000	0.13788	0.015000	0.08874	1.400000	0.34577	1.182000	0.42928	0.561000	0.74099	CCT	.	.		0.607	TBL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250615.3	NM_006453		T	2026919	C	T	2026919	3	4	300	1	0	0	0	0	1	0	0	0	15658	681	24	3	1451	3	TBL3	16	2026919	Missense_Mutation	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10		2026919	88327834	86	43425										
C16orf7	9605	hgsc.bcm.edu	37	chr16	89777150	89777150	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	tggcaatccagatgcggtgtCccccaggggtgagggagacc	16	11	0	3			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr16:89777150C>A	ENST00000389386.3	-	10	1226	c.1102G>T	c.(1102-1104)Gac>Tac	p.D368Y	VPS9D1_ENST00000565452.1_5'Flank|VPS9D1-AS1_ENST00000562866.1_RNA|VPS9D1_ENST00000561976.1_Missense_Mutation_p.D298Y	NM_004913.2	NP_004904.2	Q9Y2B5	VP9D1_HUMAN	VPS9 domain containing 1	368					ATP synthesis coupled proton transport (GO:0015986)		GTPase activator activity (GO:0005096)|transporter activity (GO:0005215)										GATGCGGTGTCCCCCAGGGGT	0.731																																					p.D368Y		Atlas-SNP	.											.	.	.	.	0			c.G1102T						.						7	8	7					16																	89777150		1864	4077	5941	SO:0001583	missense	9605	exon10			CGGTGTCCCCCAG	AB018551	CCDS42220.1	16q24.3	2012-10-09	2012-10-09	2012-10-09	ENSG00000075399	ENSG00000075399			13526	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 7"	C16orf7		10231027	Standard	NM_004913		Approved	ATP-BL	uc002fom.1	Q9Y2B5	OTTHUMG00000173219	ENST00000389386.3:c.1102G>T	chr16.hg19:g.89777150C>A	ENSP00000374037:p.Asp368Tyr	148.0	0.0		122.0	13.0	NM_004913		Missense_Mutation	SNP	ENST00000389386.3	hg19	CCDS42220.1	.	.	.	.	.	.	.	.	.	.	C	5.460	0.269970	0.10349	.	.	ENSG00000075399	ENST00000389386	.	.	.	4.02	1.96	0.26148	.	0.443923	0.25086	N	0.033260	T	0.31420	0.0796	L	0.36672	1.1	0.09310	N	1	B	0.29136	0.234	B	0.22753	0.041	T	0.21930	-1.0231	9	0.72032	D	0.01	-1.6351	12.2821	0.54769	0.0:0.4574:0.5426:0.0	.	368	Q9Y2B5	CP007_HUMAN	Y	368	.	ENSP00000374037:D368Y	D	-	1	0	C16orf7	88304651	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.408000	0.21065	0.258000	0.21686	0.561000	0.74099	GAC	.	.		0.731	VPS9D1-002	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422508.1	NM_004913		A	89777150	C	A	89777150	3	1	300	1	0	0	0	0	1	0	0	0	1830	855	30	3	817	3	C16orf7	16	89777150	Missense_Mutation	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	87750231	89777150	577603	87	43426										
TP53	7157	hgsc.bcm.edu	37	chr17	7578177	7578177	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	accccagttgcaaaccagacCtcaggcggctcatagggcac	10	15	2	1	rs267605076		TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr17:7578177C>T	ENST00000269305.4	-	6	861	c.672G>A	c.(670-672)gaG>gaA	p.E224E	TP53_ENST00000359597.4_Splice_Site_p.E224E|TP53_ENST00000413465.2_Splice_Site_p.E224E|TP53_ENST00000455263.2_Splice_Site_p.E224E|TP53_ENST00000574684.1_Intron|TP53_ENST00000420246.2_Splice_Site_p.E224E|TP53_ENST00000445888.2_Splice_Site_p.E224E	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	224	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		E -> D (in sporadic cancers; somatic mutation).|E -> G (in sporadic cancers; somatic mutation).|E -> K (in sporadic cancers; somatic mutation).|E -> V (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.E224D(20)|p.?(13)|p.E224E(12)|p.0?(8)|p.E131D(3)|p.E131E(2)|p.V218_E224delVPYEPPE(1)|p.V225fs*24(1)|p.E224_V225insXX(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CAAACCAGACCTCAGGCGGCT	0.532		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.E224E	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,colon,carcinoma,0,1	TP53	33396	.	61	Substitution - Missense(23)|Substitution - coding silent(14)|Unknown(13)|Whole gene deletion(8)|Deletion - In frame(1)|Insertion - Frameshift(1)|Insertion - In frame(1)	lung(23)|large_intestine(7)|bone(6)|biliary_tract(5)|endometrium(5)|oesophagus(3)|breast(3)|stomach(2)|central_nervous_system(2)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)|ovary(1)|liver(1)	c.G672A						.						81	76	78					17																	7578177		2203	4300	6503	SO:0001630	splice_region_variant	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	CCAGACCTCAGGC	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.672+1G>A	chr17.hg19:g.7578177C>T		134.0	0.0		56.0	41.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Silent	SNP	ENST00000269305.4	hg19	CCDS11118.1																																																																																			.	.		0.532	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	Silent	T	7578177	C	T	7578177	5	4	300	1	0	0	0	0	0	0	1	0	16396	695	24	3	622	3	TP53	17	7578177	Splice_Site	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10		7578177	73617033	88	43427										
DNAH2	146754	hgsc.bcm.edu	37	chr17	7695575	7695575	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	acatgccctccttaggacacGgtatatgagtattttgtgga	10	8	0	1			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr17:7695575G>A	ENST00000572933.1	+	46	8519	c.7059G>A	c.(7057-7059)acG>acA	p.T2353T	DNAH2_ENST00000389173.2_Silent_p.T2353T			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	2353					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				CTTAGGACACGGTATATGAGT	0.532																																					p.T2353T		Atlas-SNP	.											.	DNAH2	498	.	0			c.G7059A						.						84	79	81					17																	7695575		2203	4300	6503	SO:0001819	synonymous_variant	146754	exon45			GGACACGGTATAT	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.7059G>A	chr17.hg19:g.7695575G>A		122.0	0.0		45.0	32.0	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Silent	SNP	ENST00000572933.1	hg19	CCDS32551.1																																																																																			.	.		0.532	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		A	7695575	G	A	7695575	2	1	300	1	0	0	0	0	0	0	0	1	4604	1103	39	1		1	DNAH2	17	7695575	Silent	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10	117398	7695575	73499635	89	43428										
RCVRN	5957	hgsc.bcm.edu	37	chr17	9808459	9808459	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	ttcagctgcagctcctccagGatctccttggacagggcccc	10	16	2	0			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr17:9808459G>T	ENST00000226193.5	-	1	479	c.39C>A	c.(37-39)atC>atA	p.I13I		NM_002903.2	NP_002894.1	P35243	RECO_HUMAN	recoverin	13					phototransduction, visible light (GO:0007603)|positive regulation of guanylate cyclase activity (GO:0031284)|regulation of calcium ion transport (GO:0051924)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|visual perception (GO:0007601)	dendrite (GO:0030425)	calcium ion binding (GO:0005509)|calcium sensitive guanylate cyclase activator activity (GO:0008048)			endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|upper_aerodigestive_tract(1)	12						GCTCCTCCAGGATCTCCTTGG	0.637																																					p.I13I		Atlas-SNP	.											.	RCVRN	34	.	0			c.C39A						.						26	25	26					17																	9808459		2203	4300	6503	SO:0001819	synonymous_variant	5957	exon1			CTCCAGGATCTCC	BC001720	CCDS11151.1	17p13.1	2013-01-10		2006-09-26	ENSG00000109047	ENSG00000109047		"EF-hand domain containing"	9937	protein-coding gene	gene with protein product		179618		RCV1		1387789, 12507501, 1467959, 12789533	Standard	NM_002903		Approved		uc002gme.1	P35243	OTTHUMG00000130268	ENST00000226193.5:c.39C>A	chr17.hg19:g.9808459G>T		71.0	0.0		42.0	38.0	NM_002903	Q53XL0	Silent	SNP	ENST00000226193.5	hg19	CCDS11151.1																																																																																			.	.		0.637	RCVRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252600.2	NM_002903		T	9808459	G	T	9808459	2	4	300	1	0	0	0	0	0	0	0	1	13201	1164	41	3		3	RCVRN	17	9808459	Silent	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10	2112884	9808459	71386751	90	43429										
SYNRG	11276	hgsc.bcm.edu	37	chr17	35913872	35913872	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	aatgctgtcatagtagcagcAgaacctgttgactgtggtgt	12	7	1	2			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr17:35913872A>T	ENST00000339208.6	-	14	2093	c.1953T>A	c.(1951-1953)tcT>tcA	p.S651S	SYNRG_ENST00000345615.4_Silent_p.S573S|SYNRG_ENST00000585472.1_Silent_p.S572S|SYNRG_ENST00000588194.1_5'UTR|SYNRG_ENST00000591288.1_Silent_p.S490S|SYNRG_ENST00000502449.2_Silent_p.S573S|SYNRG_ENST00000346661.4_Silent_p.S651S|SYNRG_ENST00000394378.2_Silent_p.S573S	NM_001163544.1|NM_001163545.1|NM_007247.4	NP_001157016.1|NP_001157017.1|NP_009178.3	Q9UMZ2	SYNRG_HUMAN	synergin, gamma	651	Interaction with A1P1G1 and A1P1G2.				endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)	AP-1 adaptor complex (GO:0030121)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						TAGTAGCAGCAGAACCTGTTG	0.408																																					p.S651S		Atlas-SNP	.											.	SYNRG	101	.	0			c.T1953A						.						94	86	89					17																	35913872		2203	4300	6503	SO:0001819	synonymous_variant	11276	exon14			AGCAGCAGAACCT	AF169548	CCDS11321.1, CCDS11322.1, CCDS11322.2, CCDS54113.1, CCDS54114.1, CCDS59284.1, CCDS59285.1	17q12	2014-04-16	2009-07-20	2009-07-20	ENSG00000006114	ENSG00000275066			557	protein-coding gene	gene with protein product	"gamma-synergin", "adaptor-related protein complex 1 gamma subunit-binding protein 1"	607291	"AP1 gamma subunit binding protein 1"	AP1GBP1		10477754	Standard	XM_005256980		Approved	SYNG, MGC104959	uc010wdf.2	Q9UMZ2	OTTHUMG00000188473	ENST00000339208.6:c.1953T>A	chr17.hg19:g.35913872A>T		122.0	0.0		91.0	39.0	NM_007247	A8MWU4|B7ZKZ2|B7ZKZ3|Q17RI2|Q5BKU5|Q6ZT17	Silent	SNP	ENST00000339208.6	hg19	CCDS11321.1																																																																																			.	.		0.408	SYNRG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256811.2	NM_007247		T	35913872	A	T	35913872	2	4	300	1	0	0	0	0	0	0	0	1	15475	175	7	4		4	SYNRG	17	35913872	Silent	SNP	A	TCGA-G3-AAV4-01A-11D-A382-10	26105413	35913872	45281338	91	43430										
FASN	2194	hgsc.bcm.edu	37	chr17	80038356	80038356	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	ggagcacatttcaaaggccaCgcaggccccgtaggagtagc	13	12	1	0			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr17:80038356C>T	ENST00000306749.2	-	40	7155	c.6937G>A	c.(6937-6939)Gtg>Atg	p.V2313M	FASN_ENST00000579758.1_Intron	NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	2313	Thioesterase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	TCAAAGGCCACGCAGGCCCCG	0.657																																					p.V2313M	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.G6937A						.						18	17	17					17																	80038356		2171	4278	6449	SO:0001583	missense	2194	exon40			AGGCCACGCAGGC	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.6937G>A	chr17.hg19:g.80038356C>T	ENSP00000304592:p.Val2313Met	86.0	0.0		63.0	31.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	hg19	CCDS11801.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.397298	0.83120	.	.	ENSG00000169710	ENST00000306749	T	0.32988	1.43	4.63	3.63	0.41609	Thioesterase (1);	0.073354	0.53938	D	0.000048	T	0.57475	0.2056	M	0.83384	2.64	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.65496	-0.6154	10	0.87932	D	0	-25.8076	13.9652	0.64205	0.1529:0.8471:0.0:0.0	.	2313	P49327	FAS_HUMAN	M	2313	ENSP00000304592:V2313M	ENSP00000304592:V2313M	V	-	1	0	FASN	77631645	1.000000	0.71417	0.995000	0.50966	0.945000	0.59286	7.469000	0.80959	1.128000	0.42052	0.591000	0.81541	GTG	.	.		0.657	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		T	80038356	C	T	80038356	3	4	300	1	0	0	0	0	1	0	0	0	5691	536	19	1	614	1	FASN	17	80038356	Missense_Mutation	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	44124484	80038356	1156854	92	43431										
FOXK2	3607	hgsc.bcm.edu	37	chr17	80477826	80477826	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	acccgcgggcggcggggccgGgggcggcggggccgggggcg	27	13	0	0			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr17:80477826G>C	ENST00000335255.5	+	1	236	c.62G>C	c.(61-63)gGg>gCg	p.G21A		NM_004514.3	NP_004505.2	Q01167	FOXK2_HUMAN	forkhead box K2	21	Gly-rich.			AAAAALSGAGTPPAGGGAGGGGAGGGGSPPGGWAVARLEGR EFEYLMKKRSVTIGRNSSQGSVDVSMGHSSFISRRHLEIFT PPGGGGHGGAAPELPPAQPRPDAGGDFYLRCLGKNG -> Q (in Ref. 1; CAA43200). {ECO:0000305}.	positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|urinary_tract(1)	17	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)			ggcggggccgggggcggcggg	0.846																																					p.G21A		Atlas-SNP	.											FOXK2,NS,carcinoma,0,1	FOXK2	46	.	0			c.G62C						.						1	1	1					17																	80477826		122	223	345	SO:0001583	missense	3607	exon1			GGGCCGGGGGCGG	U58196	CCDS11813.1	17q25	2006-12-15	2004-03-09	2004-03-10	ENSG00000141568	ENSG00000141568		"Forkhead boxes"	6036	protein-coding gene	gene with protein product		147685	"interleukin enhancer binding factor 1"	ILF, ILF1		3260003	Standard	NM_004514		Approved		uc002kfn.3	Q01167	OTTHUMG00000140374	ENST00000335255.5:c.62G>C	chr17.hg19:g.80477826G>C	ENSP00000335677:p.Gly21Ala	4.0	0.0		5.0	2.0	NM_004514	A6NEP5|Q13622|Q13623|Q13624	Missense_Mutation	SNP	ENST00000335255.5	hg19	CCDS11813.1	.	.	.	.	.	.	.	.	.	.	.	2.177	-0.388435	0.04932	.	.	ENSG00000141568	ENST00000335255;ENST00000335241	D	0.93076	-3.16	1.8	1.8	0.24995	.	.	.	.	.	D	0.89375	0.6697	N	0.08118	0	0.25222	N	0.98989	D;D;D	0.71674	0.998;0.996;0.998	D;D;D	0.68621	0.959;0.91;0.959	T	0.80350	-0.1419	9	0.14252	T	0.57	.	6.724	0.23346	0.0:0.0:1.0:0.0	.	21;21;21	Q01167-3;Q01167;Q01167-2	.;FOXK2_HUMAN;.	A	21	ENSP00000335677:G21A	ENSP00000334321:G21A	G	+	2	0	FOXK2	78071115	0.917000	0.31117	0.403000	0.26384	0.773000	0.43773	0.923000	0.28757	0.820000	0.34516	0.486000	0.48141	GGG	.	.		0.846	FOXK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277099.2	NM_181430		C	80477826	G	C	80477826	3	2	300	1	0	0	0	0	1	0	0	0	6023	1232	43	4	64	4	FOXK2	17	80477826	Missense_Mutation	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10	439470	80477826	717384	93	43432										
POTEC	388468	hgsc.bcm.edu	37	chr18	14542926	14542926	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	cacgttgctcgtgccgctccCcctgcagcaggggaagcagt	13	15	0	0			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr18:14542926C>A	ENST00000358970.5	-	1	219	c.220G>T	c.(220-222)Ggg>Tgg	p.G74W	POTEC_ENST00000389891.4_5'UTR	NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	74										NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						GTGCCGCTCCCCCTGCAGCAG	0.567																																					p.G74W		Atlas-SNP	.											.	POTEC	129	.	0			c.G220T						.						46	56	53					18																	14542926		692	1591	2283	SO:0001583	missense	388468	exon1			CGCTCCCCCTGCA	BX649118	CCDS45835.1	18p11.21	2013-01-10	2008-11-26	2008-11-26	ENSG00000183206	ENSG00000183206		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	33894	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 6"		"ANKRD26-like family B, member 2"	A26B2			Standard	NM_001137671		Approved	POTE18, POTE-18, DKFZp686J0529, CT104.6	uc010dln.3	B2RU33	OTTHUMG00000162963	ENST00000358970.5:c.220G>T	chr18.hg19:g.14542926C>A	ENSP00000351856:p.Gly74Trp	565.0	0.0		390.0	83.0	NM_001137671		Missense_Mutation	SNP	ENST00000358970.5	hg19	CCDS45835.1	.	.	.	.	.	.	.	.	.	.	C	9.225	1.034438	0.19590	.	.	ENSG00000183206	ENST00000358970;ENST00000389891	T	0.48522	0.81	0.429	-0.773	0.10995	.	.	.	.	.	T	0.53642	0.1809	L	0.43152	1.355	0.09310	N	1	D	0.89917	1.0	D	0.78314	0.991	T	0.43956	-0.9359	8	0.66056	D	0.02	.	.	.	.	.	74	B2RU33	POTEC_HUMAN	W	74	ENSP00000351856:G74W	ENSP00000351856:G74W	G	-	1	0	POTEC	14532926	0.001000	0.12720	0.000000	0.03702	0.039000	0.13416	-0.144000	0.10280	-0.401000	0.07644	0.175000	0.17021	GGG	.	.		0.567	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269		A	14542926	C	A	14542926	3	1	300	1	0	0	0	0	1	0	0	0	12271	623	22	3	1452	3	POTEC	18	14542926	Missense_Mutation	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10		14542926	63534322	94	43433										
ANKRD24	170961	hgsc.bcm.edu	37	chr19	4202880	4202880	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	ccccaggcttcctgcgtggtGgacgtcgtggacagcagcgg	16	13	0	0			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr19:4202880G>A	ENST00000600132.1	+	7	699	c.423G>A	c.(421-423)gtG>gtA	p.V141V	ANKRD24_ENST00000262970.5_Silent_p.V231V|ANKRD24_ENST00000318934.4_Silent_p.V141V	NM_133475.1	NP_597732.1	Q8TF21	ANR24_HUMAN	ankyrin repeat domain 24	141										endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)	21				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0233)|STAD - Stomach adenocarcinoma(1328;0.181)		CCTGCGTGGTGGACGTCGTGG	0.647																																					p.V141V		Atlas-SNP	.											.	ANKRD24	180	.	0			c.G423A						.						18	22	21					19																	4202880		2030	4184	6214	SO:0001819	synonymous_variant	170961	exon7			CGTGGTGGACGTC	AB075861	CCDS45925.1	19p13.3	2013-01-10				ENSG00000089847		"Ankyrin repeat domain containing"	29424	protein-coding gene	gene with protein product						11853319	Standard	NM_133475		Approved	KIAA1981	uc010dtt.1	Q8TF21		ENST00000600132.1:c.423G>A	chr19.hg19:g.4202880G>A		271.0	0.0		248.0	105.0	NM_133475	O75268|O95781	Silent	SNP	ENST00000600132.1	hg19	CCDS45925.1																																																																																			.	.		0.647	ANKRD24-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458188.1	XM_114000		A	4202880	G	A	4202880	2	1	300	1	0	0	0	0	0	0	0	1	653	1335	47	3		3	ANKRD24	19	4202880	Silent	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10		4202880	54926103	95	43434										
MUC16	94025	hgsc.bcm.edu	37	chr19	9066696	9066696	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	ccatggtggaggtggtatccAttggagctgtggccttggtt	16	7	0	0			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr19:9066696A>T	ENST00000397910.4	-	3	20953	c.20750T>A	c.(20749-20751)aTg>aAg	p.M6917K		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	6919	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGTGGTATCCATTGGAGCTGT	0.458																																					p.M6917K		Atlas-SNP	.											.	MUC16	4315	.	0			c.T20750A						.						306	288	294					19																	9066696		2079	4206	6285	SO:0001583	missense	94025	exon3			GTATCCATTGGAG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.20750T>A	chr19.hg19:g.9066696A>T	ENSP00000381008:p.Met6917Lys	89.0	0.0		82.0	39.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	a	4.484	0.089666	0.08632	.	.	ENSG00000181143	ENST00000397910	T	0.23754	1.89	2.77	0.355	0.16069	.	.	.	.	.	T	0.21022	0.0506	L	0.50333	1.59	.	.	.	B	0.24426	0.103	B	0.28385	0.089	T	0.31586	-0.9938	8	0.87932	D	0	.	2.757	0.05295	0.4099:0.2102:0.0:0.3799	.	6917	B5ME49	.	K	6917	ENSP00000381008:M6917K	ENSP00000381008:M6917K	M	-	2	0	MUC16	8927696	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.748000	0.01826	-0.049000	0.13379	0.334000	0.21626	ATG	.	.		0.458	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9066696	A	T	9066696	3	4	300	1	0	0	0	0	1	0	0	0	9982	217	8	4	23101	4	MUC16	19	9066696	Missense_Mutation	SNP	A	TCGA-G3-AAV4-01A-11D-A382-10	4863816	9066696	50062287	96	43435										
ZNF302	55900	hgsc.bcm.edu	37	chr19	35175888	35175888	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	aagaaaaacgctatgagtgtCgtatatgtggaaaggccttc	11	6	0	2	rs528898854	byFrequency	TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr19:35175888C>T	ENST00000446502.2	+	6	1286	c.1078C>T	c.(1078-1080)Cgt>Tgt	p.R360C	ZNF302_ENST00000505365.2_3'UTR|ZNF302_ENST00000505242.1_Missense_Mutation_p.R316C|ZNF302_ENST00000423823.2_Missense_Mutation_p.R316C|ZNF302_ENST00000457781.2_Missense_Mutation_p.R316C			Q9NR11	ZN302_HUMAN	zinc finger protein 302	395					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(2)|lung(2)|skin(1)	6	all_lung(56;6.16e-07)|Lung NSC(56;9.71e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			CTATGAGTGTCGTATATGTGG	0.408													C|||	2	0.000399361	0	0.0014	5008	,	,		22638	0.001		0	False		,,,				2504	0				p.R316C		Atlas-SNP	.											.	ZNF302	27	.	0			c.C946T						.						62	63	63					19																	35175888		2203	4300	6503	SO:0001583	missense	55900	exon5			GAGTGTCGTATAT	AF155656	CCDS46042.1, CCDS74330.1, CCDS74331.1, CCDS74332.1, CCDS74333.1	19q13.2	2013-01-08			ENSG00000089335	ENSG00000089335		"Zinc fingers, C2H2-type", "-"	13848	protein-coding gene	gene with protein product							Standard	NM_018675		Approved	ZNF327, ZNF135L, ZNF140L	uc002nvq.1	Q9NR11	OTTHUMG00000163329	ENST00000446502.2:c.1078C>T	chr19.hg19:g.35175888C>T	ENSP00000396379:p.Arg360Cys	138.0	0.0		164.0	53.0	NM_018443	Q658J3|Q9BZD8|Q9P0J4	Missense_Mutation	SNP	ENST00000446502.2	hg19		.	.	.	.	.	.	.	.	.	.	C	12.77	2.037061	0.35893	.	.	ENSG00000089335	ENST00000457781;ENST00000505242;ENST00000423823;ENST00000446502	T;T;T;T	0.15139	3.13;3.13;3.13;2.45	0.967	0.967	0.19674	.	.	.	.	.	T	0.22975	0.0555	L	0.41824	1.3	0.33248	D	0.558185	D;D	0.76494	0.999;0.999	P;P	0.61800	0.894;0.784	T	0.37361	-0.9709	9	0.87932	D	0	.	4.1867	0.10402	0.3993:0.6006:0.0:0.0	.	360;316	E7EVR1;Q9NR11-2	.;.	C	316;316;316;360	ENSP00000391067:R316C;ENSP00000421028:R316C;ENSP00000405219:R316C;ENSP00000396379:R360C	ENSP00000405219:R316C	R	+	1	0	ZNF302	39867728	0.000000	0.05858	0.999000	0.59377	0.876000	0.50452	-0.811000	0.04500	0.822000	0.34565	0.467000	0.42956	CGT	.	.		0.408	ZNF302-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000372731.1			T	35175888	C	T	35175888	3	4	300	1	0	0	0	0	1	0	0	0	17847	884	31	1	960	1	ZNF302	19	35175888	Missense_Mutation	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	26109192	35175888	23953095	97	43436										
ZNF383	163087	hgsc.bcm.edu	37	chr19	37734077	37734077	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	gagaaaccctatgaatgtaaGgaatgtggcaaagcctttac	10	7	0	2			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr19:37734077G>C	ENST00000589413.1	+	8	1522	c.939G>C	c.(937-939)aaG>aaC	p.K313N	ZNF383_ENST00000590503.1_Missense_Mutation_p.K313N|ZNF383_ENST00000352998.3_Missense_Mutation_p.K313N			Q8NA42	ZN383_HUMAN	zinc finger protein 383	313					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(8)|ovary(1)|skin(1)	15			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			ATGAATGTAAGGAATGTGGCA	0.413																																					p.K313N		Atlas-SNP	.											.	ZNF383	42	.	0			c.G939C						.						71	75	74					19																	37734077		2203	4300	6503	SO:0001583	missense	163087	exon5			ATGTAAGGAATGT	AY438646	CCDS12501.1	19q13.13	2013-01-08				ENSG00000188283		"Zinc fingers, C2H2-type", "-"	18609	protein-coding gene	gene with protein product							Standard	NM_152604		Approved	FLJ35863	uc002ofu.1	Q8NA42		ENST00000589413.1:c.939G>C	chr19.hg19:g.37734077G>C	ENSP00000464871:p.Lys313Asn	86.0	0.0		94.0	38.0	NM_152604	Q6X2C7	Missense_Mutation	SNP	ENST00000589413.1	hg19	CCDS12501.1	.	.	.	.	.	.	.	.	.	.	G	9.761	1.170025	0.21621	.	.	ENSG00000188283	ENST00000352998	T	0.07908	3.15	3.84	1.65	0.23941	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.33364	N	0.004984	T	0.05593	0.0147	N	0.03238	-0.38	0.09310	N	1	P	0.49358	0.923	P	0.59761	0.863	T	0.31447	-0.9943	10	0.08179	T	0.78	.	4.693	0.12790	0.1062:0.0:0.5101:0.3837	.	313	Q8NA42	ZN383_HUMAN	N	313	ENSP00000340132:K313N	ENSP00000340132:K313N	K	+	3	2	ZNF383	42425917	0.000000	0.05858	0.998000	0.56505	0.992000	0.81027	-1.608000	0.02068	0.394000	0.25230	0.563000	0.77884	AAG	.	.		0.413	ZNF383-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458141.1	NM_152604		C	37734077	G	C	37734077	3	2	300	1	0	0	0	0	1	0	0	0	17889	991	35	4	953	4	ZNF383	19	37734077	Missense_Mutation	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10	2558189	37734077	21394906	98	43437										
GPR4	2828	hgsc.bcm.edu	37	chr19	46094909	46094932	+	In_Frame_Del	DEL	CAGCGGCAGCGTGCAGATGTACAG	CAGCGGCAGCGTGCAGATGTACAG	-													0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	tgcaggaagtagtccacccaCagcggcagcgtgcagatgta					rs188005857		TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	CAGCGGCAGCGTGCAGATGTACAG	CAGCGGCAGCGTGCAGATGTACAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr19:46094909_46094932delCAGCGGCAGCGTGCAGATGTACAG	ENST00000323040.4	-	2	1137_1160	c.193_216delCTGTACATCTGCACGCTGCCGCTG	c.(193-216)ctgtacatctgcacgctgccgctgdel	p.LYICTLPL65del	OPA3_ENST00000544371.1_Intron|GPR4_ENST00000591614.1_5'Flank	NM_005282.2	NP_005273.1	P46093	GPR4_HUMAN	G protein-coupled receptor 4	65					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(262;0.0071)|GBM - Glioblastoma multiforme(486;0.128)|Epithelial(262;0.223)		AGTCCACCCACAGCGGCAGCGTGCAGATGTACAGCAGGTCGGCG	0.603																																					p.65_73del	Esophageal Squamous(117;181 1612 1673 14956 42937)	Atlas-Indel,Pindel	.											.	GPR4	54	.	0			c.194_217del						.																																			SO:0001651	inframe_deletion	2828	exon2			.	BC067536	CCDS12669.1	19q13.3	2012-08-21				ENSG00000177464		"GPCR / Class A : Orphans"	4497	protein-coding gene	gene with protein product		600551				8595909	Standard	NM_005282		Approved		uc002pcm.3	P46093		ENST00000323040.4:c.193_216delCTGTACATCTGCACGCTGCCGCTG	chr19.hg19:g.46094909_46094932delCAGCGGCAGCGTGCAGATGTACAG	ENSP00000319744:p.Leu65_Leu72del	147.0	0.0		92.0	23.0	NM_005282	A8K3T3|B0M0K1|Q6NWM4	In_Frame_Del	DEL	ENST00000323040.4	hg19	CCDS12669.1																																																																																			.	.		0.603	GPR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459603.1	NM_005282		-	46094932	CAGCGGCAGCGTGCAGATGTACAG	-	46094909	7	5	300	1	0	1	0	1	0	0	0	0	6702	465	17	0	876	0	GPR4	19	46094909	In_Frame_Del	DEL	CAGCGGCAGCGTGCAGATGTACAG	TCGA-G3-AAV4-01A-11D-A382-10	8360832	46094909	13034074	99	43438										
CCDC155	147872	hgsc.bcm.edu	37	chr19	49899026	49899026	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	gcctcatccctttgatacagGggattagagctggaagagga	13	8	1	3			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr19:49899026G>A	ENST00000447857.3	+	5	541	c.336G>A	c.(334-336)ggG>ggA	p.G112G		NM_144688.4	NP_653289.3	Q8N6L0	KASH5_HUMAN	coiled-coil domain containing 155	112						chromosome, telomeric region (GO:0000781)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(10)|ovary(1)|stomach(1)	22						TTTGATACAGGGGATTAGAGC	0.602																																					p.G112G		Atlas-SNP	.											.	CCDC155	46	.	0			c.G336A						.						21	23	22					19																	49899026		1948	4129	6077	SO:0001630	splice_region_variant	147872	exon5			ATACAGGGGATTA		CCDS46140.1	19q13.33	2014-01-21			ENSG00000161609	ENSG00000161609			26520	protein-coding gene	gene with protein product							Standard	NM_144688		Approved	FLJ32658, KASH5	uc002pnm.2	Q8N6L0	OTTHUMG00000183170	ENST00000447857.3:c.336-1G>A	chr19.hg19:g.49899026G>A		42.0	0.0		33.0	16.0	NM_144688	Q96MC3	Silent	SNP	ENST00000447857.3	hg19	CCDS46140.1																																																																																			.	.		0.602	CCDC155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465436.2	NM_144688	Silent	A	49899026	G	A	49899026	5	1	300	1	0	0	0	0	0	0	1	0	2790	1246	43	3	350	3	CCDC155	19	49899026	Splice_Site	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10	3804117	49899026	9229957	100	43439										
SHANK1	50944	hgsc.bcm.edu	37	chr19	51170472	51170472	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	gaggcccaggcgtgaggggcGactctggcttttcgaagctg	17	10	1	1			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr19:51170472G>T	ENST00000293441.1	-	22	4763	c.4745C>A	c.(4744-4746)tCg>tAg	p.S1582*	SHANK1_ENST00000391814.1_Nonsense_Mutation_p.S1590*|SHANK1_ENST00000359082.3_Nonsense_Mutation_p.S1573*|SHANK1_ENST00000391813.1_Nonsense_Mutation_p.S969*|SYT3_ENST00000544769.1_Intron	NM_016148.2	NP_057232.2	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	1582					adult behavior (GO:0030534)|associative learning (GO:0008306)|cytoskeletal anchoring at plasma membrane (GO:0007016)|dendritic spine morphogenesis (GO:0060997)|determination of affect (GO:0050894)|habituation (GO:0046959)|long-term memory (GO:0007616)|negative regulation of actin filament bundle assembly (GO:0032232)|neuromuscular process controlling balance (GO:0050885)|olfactory behavior (GO:0042048)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|protein complex assembly (GO:0006461)|protein localization to synapse (GO:0035418)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|righting reflex (GO:0060013)|social behavior (GO:0035176)|synapse maturation (GO:0060074)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|excitatory synapse (GO:0060076)|intracellular (GO:0005622)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ankyrin repeat binding (GO:0071532)|GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|somatostatin receptor binding (GO:0031877)			breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	64		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)		CGTGAGGGGCGACTCTGGCTT	0.682																																					p.S1582X		Atlas-SNP	.											.	SHANK1	210	.	0			c.C4745A						.						23	21	21					19																	51170472		2191	4290	6481	SO:0001587	stop_gained	50944	exon22			AGGGGCGACTCTG	AF163302	CCDS12799.1	19q13.3	2013-01-10			ENSG00000161681	ENSG00000161681		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	15474	protein-coding gene	gene with protein product	"somatostatin receptor-interacting protein"	604999				10551867	Standard	NM_016148		Approved	SSTRIP, SPANK-1, synamon	uc002psx.1	Q9Y566	OTTHUMG00000137380	ENST00000293441.1:c.4745C>A	chr19.hg19:g.51170472G>T	ENSP00000293441:p.Ser1582*	98.0	0.0		63.0	12.0	NM_016148	A8MXP5|B7WNY6|Q9NYW9	Nonsense_Mutation	SNP	ENST00000293441.1	hg19	CCDS12799.1	.	.	.	.	.	.	.	.	.	.	G	41	9.073028	0.99057	.	.	ENSG00000161681	ENST00000293441;ENST00000391813;ENST00000359082;ENST00000391814	.	.	.	2.01	2.01	0.26516	.	1.276450	0.06678	U	0.767426	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11182	T	0.66	.	11.0388	0.47818	0.0:0.0:1.0:0.0	.	.	.	.	X	1582;969;1573;1590	.	ENSP00000293441:S1582X	S	-	2	0	SHANK1	55862284	0.163000	0.22920	1.000000	0.80357	0.269000	0.26545	1.626000	0.37039	1.141000	0.42275	0.205000	0.17691	TCG	.	.		0.682	SHANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268071.1	NM_016148		T	51170472	G	T	51170472	4	4	300	1	0	0	0	0	0	1	0	0	14279	1059	37	1	1748	1	SHANK1	19	51170472	Nonsense_Mutation	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10	1271446	51170472	7958511	101	43440										
HAS1	3036	hgsc.bcm.edu	37	chr19	52222893	52222893	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	actgcgcgcggtggctgcatCcagcggcccccgcgccgccg	15	19	0	0			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr19:52222893C>A	ENST00000222115.1	-	2	302	c.268G>T	c.(268-270)Gat>Tat	p.D90Y	HAS1_ENST00000601714.1_Missense_Mutation_p.D97Y|HAS1_ENST00000540069.2_Missense_Mutation_p.D89Y|HAS1_ENST00000594621.1_5'Flank	NM_001523.2	NP_001514.2	Q92839	HYAS1_HUMAN	hyaluronan synthase 1	90					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|negative regulation of fibroblast migration (GO:0010764)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronan synthase activity (GO:0050501)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	40		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00102)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		GTGGCTGCATCCAgcggcccc	0.741																																					p.D90Y	NSCLC(132;636 2450 45807 47979)	Atlas-SNP	.											.	HAS1	61	.	0			c.G268T						.						2	3	3					19																	52222893		1753	3453	5206	SO:0001583	missense	3036	exon2			CTGCATCCAGCGG	U59269	CCDS12838.1, CCDS74436.1	19q13.3-q13.4	2013-02-22			ENSG00000105509	ENSG00000105509	2.4.1.212	"Glycosyltransferase family 2 domain containing"	4818	protein-coding gene	gene with protein product		601463		HAS		9169154	Standard	XM_005258834		Approved		uc002pxo.1	Q92839		ENST00000222115.1:c.268G>T	chr19.hg19:g.52222893C>A	ENSP00000222115:p.Asp90Tyr	104.0	0.0		89.0	45.0	NM_001523	Q14470|Q9NS49	Missense_Mutation	SNP	ENST00000222115.1	hg19	CCDS12838.1	.	.	.	.	.	.	.	.	.	.	.	11.01	1.511895	0.27036	.	.	ENSG00000105509	ENST00000540069;ENST00000222115	T;T	0.32988	1.43;1.43	3.8	2.47	0.30058	.	22.652400	0.00649	U	0.000543	T	0.20088	0.0483	N	0.24115	0.695	0.09310	N	0.999999	B;B;P	0.34699	0.092;0.056;0.464	B;B;B	0.27796	0.077;0.035;0.083	T	0.28996	-1.0026	10	0.66056	D	0.02	-4.7942	3.3268	0.07070	0.0:0.5427:0.265:0.1923	.	89;90;89	G3V1S7;Q92839;Q8IYH3	.;HAS1_HUMAN;.	Y	89;90	ENSP00000445021:D89Y;ENSP00000222115:D90Y	ENSP00000222115:D90Y	D	-	1	0	HAS1	56914705	0.000000	0.05858	0.018000	0.16275	0.012000	0.07955	0.212000	0.17497	1.815000	0.52974	0.397000	0.26171	GAT	.	.		0.741	HAS1-005	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466953.1	NM_001523		A	52222893	C	A	52222893	3	1	300	1	0	0	0	0	1	0	0	0	6970	855	30	3	1484	3	HAS1	19	52222893	Missense_Mutation	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	1052421	52222893	6906090	102	43441										
ZNF628	89887	hgsc.bcm.edu	37	chr19	55995321	55995321	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	ccagcactggtgtggtccagGatgtcctctttgagacactc	11	12	1	1			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr19:55995321G>T	ENST00000598519.1	+	3	3314	c.2761G>T	c.(2761-2763)Gat>Tat	p.D921Y	ZNF628_ENST00000391718.2_Missense_Mutation_p.D917Y|NAT14_ENST00000591590.1_5'Flank|NAT14_ENST00000205194.4_5'Flank|NAT14_ENST00000587400.1_5'Flank			Q5EBL2	ZN628_HUMAN	zinc finger protein 628	921					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|lung(2)	7	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0531)		TGTGGTCCAGGATGTCCTCTT	0.657																																					p.D921Y		Atlas-SNP	.											.	ZNF628	75	.	0			c.G2761T						.						43	32	36					19																	55995321		2201	4299	6500	SO:0001583	missense	89887	exon3			GTCCAGGATGTCC	AF367249	CCDS33116.3	19q13.43	2013-01-08			ENSG00000197483	ENSG00000197483		"Zinc fingers, C2H2-type"	28054	protein-coding gene	gene with protein product	"Zinc finger expressed in Embryonal cells and Certain adult organs"	610671					Standard	NM_033113		Approved	ZEC, Zfp628	uc002qld.3	Q5EBL2	OTTHUMG00000150396	ENST00000598519.1:c.2761G>T	chr19.hg19:g.55995321G>T	ENSP00000469591:p.Asp921Tyr	96.0	0.0		108.0	47.0	NM_033113	Q86X34	Missense_Mutation	SNP	ENST00000598519.1	hg19	CCDS33116.3	.	.	.	.	.	.	.	.	.	.	.	13.80	2.344801	0.41498	.	.	ENSG00000197483	ENST00000391718	T	0.13307	2.6	3.81	3.81	0.43845	.	0.000000	0.48286	U	0.000191	T	0.16300	0.0392	N	0.19112	0.55	0.25303	N	0.989265	D	0.61080	0.989	P	0.53912	0.737	T	0.04078	-1.0979	10	0.87932	D	0	.	13.5636	0.61804	0.0:0.0:1.0:0.0	.	917	Q5EBL2	ZN628_HUMAN	Y	917	ENSP00000375598:D917Y	ENSP00000375598:D917Y	D	+	1	0	ZNF628	60687133	0.998000	0.40836	0.990000	0.47175	0.834000	0.47266	3.860000	0.55995	1.850000	0.53721	0.289000	0.19496	GAT	.	.		0.657	ZNF628-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317934.2	XM_058964		T	55995321	G	T	55995321	3	4	300	1	0	0	0	0	1	0	0	0	18067	1174	41	3	2751	3	ZNF628	19	55995321	Missense_Mutation	SNP	G	TCGA-G3-AAV4-01A-11D-A382-10	3772428	55995321	3133662	103	43442										
ZNF304	57343	hgsc.bcm.edu	37	chr19	57867488	57867488	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	caggactgctgagtcaggtcTtttccagaaagcacacccat	9	12	2	2			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr19:57867488T>A	ENST00000282286.5	+	3	424	c.251T>A	c.(250-252)cTt>cAt	p.L84H	ZNF304_ENST00000391705.3_Missense_Mutation_p.L84H|ZNF304_ENST00000598744.1_Missense_Mutation_p.L42H|ZNF304_ENST00000443917.2_Missense_Mutation_p.L131H			Q9HCX3	ZN304_HUMAN	zinc finger protein 304	84	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)	26		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0265)		GAGTCAGGTCTTTTCCAGAAA	0.488																																					p.L84H		Atlas-SNP	.											.	ZNF304	74	.	0			c.T251A						.						119	101	107					19																	57867488		2203	4300	6503	SO:0001583	missense	57343	exon3			CAGGTCTTTTCCA	AJ276316	CCDS12950.1, CCDS74462.1	19q13.4	2013-01-08				ENSG00000131845		"Zinc fingers, C2H2-type", "-"	13505	protein-coding gene	gene with protein product		613840					Standard	XM_005259090		Approved		uc010ygw.2	Q9HCX3		ENST00000282286.5:c.251T>A	chr19.hg19:g.57867488T>A	ENSP00000282286:p.Leu84His	187.0	0.0		156.0	66.0	NM_020657		Missense_Mutation	SNP	ENST00000282286.5	hg19	CCDS12950.1	.	.	.	.	.	.	.	.	.	.	T	2.328	-0.354132	0.05173	.	.	ENSG00000131845	ENST00000282286;ENST00000391705;ENST00000443917	T;T;T	0.08807	3.05;3.05;3.05	3.37	-2.58	0.06228	Krueppel-associated box (1);	.	.	.	.	T	0.03263	0.0095	N	0.19112	0.55	0.09310	N	1	B;B	0.33379	0.41;0.41	B;B	0.28849	0.044;0.095	T	0.41858	-0.9485	9	0.15499	T	0.54	.	0.3201	0.00302	0.1943:0.2914:0.1923:0.322	.	84;131	Q9HCX3;E7EQD3	ZN304_HUMAN;.	H	84;84;131	ENSP00000282286:L84H;ENSP00000375586:L84H;ENSP00000401642:L131H	ENSP00000282286:L84H	L	+	2	0	ZNF304	62559300	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-1.184000	0.03076	-0.329000	0.08527	-1.247000	0.01520	CTT	.	.		0.488	ZNF304-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465785.1			A	57867488	T	A	57867488	3	1	300	1	0	0	0	0	1	0	0	0	17848	1609	56	4	261	4	ZNF304	19	57867488	Missense_Mutation	SNP	T	TCGA-G3-AAV4-01A-11D-A382-10	1872167	57867488	1261495	104	43443										
TPX2	22974	hgsc.bcm.edu	37	chr20	30381706	30381706	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	tgtgccacattatggggtgcCttttaagccccaaatcccag	9	12	0	0			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr20:30381706C>T	ENST00000300403.6	+	14	2093	c.1565C>T	c.(1564-1566)cCt>cTt	p.P522L	TPX2_ENST00000340513.4_Missense_Mutation_p.P558L	NM_012112.4	NP_036244.2	Q9ULW0	TPX2_HUMAN	TPX2, microtubule-associated	522					activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|mitotic nuclear division (GO:0007067)|regulation of mitotic spindle organization (GO:0060236)	axon hillock (GO:0043203)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28			Epithelial(4;0.000771)|Colorectal(19;0.00306)|all cancers(5;0.004)|COAD - Colon adenocarcinoma(19;0.0347)|OV - Ovarian serous cystadenocarcinoma(3;0.0656)			TATGGGGTGCCTTTTAAGCCC	0.433																																					p.P522L		Atlas-SNP	.											.	TPX2	61	.	0			c.C1565T						.						167	172	170					20																	30381706		2203	4300	6503	SO:0001583	missense	22974	exon14			GGGTGCCTTTTAA	AF098158	CCDS13190.1	20q11.2	2013-07-23	2013-07-23	2003-10-08	ENSG00000088325	ENSG00000088325			1249	protein-coding gene	gene with protein product		605917	"chromosome 20 open reading frame 1", "TPX2, microtubule-associated, homolog (Xenopus laevis)"	C20orf2, C20orf1		9207457, 10393424	Standard	NM_012112		Approved	p100, DIL-2	uc002wwp.1	Q9ULW0	OTTHUMG00000032190	ENST00000300403.6:c.1565C>T	chr20.hg19:g.30381706C>T	ENSP00000300403:p.Pro522Leu	230.0	0.0		226.0	91.0	NM_012112	Q9H1R4|Q9NRA3|Q9UFN9|Q9UL00|Q9Y2M1	Missense_Mutation	SNP	ENST00000300403.6	hg19	CCDS13190.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.981270	0.93044	.	.	ENSG00000088325	ENST00000300403;ENST00000340513	T	0.56103	0.48	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.78188	0.4244	M	0.86343	2.81	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.80476	-0.1366	10	0.87932	D	0	-12.8529	19.545	0.95291	0.0:1.0:0.0:0.0	.	558;522	Q96RR5;Q9ULW0	.;TPX2_HUMAN	L	522;558	ENSP00000341145:P558L	ENSP00000300403:P522L	P	+	2	0	TPX2	29845367	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.824000	0.75288	2.861000	0.98227	0.655000	0.94253	CCT	.	.		0.433	TPX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078569.2			T	30381706	C	T	30381706	3	4	300	1	0	0	0	0	1	0	0	0	16447	681	24	3	1611	3	TPX2	20	30381706	Missense_Mutation	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10		30381706	32643814	105	43444										
PRDM15	63977	hgsc.bcm.edu	37	chr21	43221607	43221607	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	ttgatgaaatgggccacagaCtgtgggttcgaggcttccgg	15	8	0	3			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr21:43221607C>T	ENST00000269844.3	-	31	4427	c.4317G>A	c.(4315-4317)caG>caA	p.Q1439Q	PRDM15_ENST00000422911.1_Silent_p.Q1130Q|PRDM15_ENST00000470586.1_5'UTR|PRDM15_ENST00000398548.1_Silent_p.Q1110Q|PRDM15_ENST00000447207.2_Silent_p.Q1073Q|PRDM15_ENST00000538201.1_Silent_p.Q1093Q	NM_022115.3	NP_071398.3	P57071	PRD15_HUMAN	PR domain containing 15	1439					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(3)|skin(2)|stomach(2)|urinary_tract(1)	43						GGGCCACAGACTGTGGGTTCG	0.612																																					p.Q1439Q		Atlas-SNP	.											.	PRDM15	110	.	0			c.G4317A						.						111	92	98					21																	43221607		2203	4300	6503	SO:0001819	synonymous_variant	63977	exon31			CACAGACTGTGGG	AF276513	CCDS13676.1, CCDS42932.1, CCDS63370.1	21q22.3	2013-01-08	2002-07-31		ENSG00000141956	ENSG00000141956		"Zinc fingers, C2H2-type"	13999	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 83"	ZNF298, C21orf83		12036297, 12036298	Standard	NM_022115		Approved		uc002yzq.1	P57071	OTTHUMG00000086781	ENST00000269844.3:c.4317G>A	chr21.hg19:g.43221607C>T		226.0	0.0		131.0	74.0	NM_022115	E9PDJ6|E9PF37|E9PGL3|Q4W8S0|Q4W8S3|Q4W8S4|Q4W8S5|Q8N0X3|Q8NEX0|Q9NQV3	Silent	SNP	ENST00000269844.3	hg19	CCDS13676.1																																																																																			.	.		0.612	PRDM15-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022115		T	43221607	C	T	43221607	2	4	300	1	0	0	0	0	0	0	0	1	12468	564	20	3		3	PRDM15	21	43221607	Silent	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10		43221607	4908288	106	43445										
CDC42EP1	11135	hgsc.bcm.edu	37	chr22	37964811	37964811	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	tgcggatgctgaggaggatgAtgaggtcaaggtgtgagggg	21	3	1	4			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr22:37964811A>G	ENST00000249014.4	+	3	1580	c.1160A>G	c.(1159-1161)gAt>gGt	p.D387G		NM_152243.2	NP_689449.1	Q00587	BORG5_HUMAN	CDC42 effector protein (Rho GTPase binding) 1	387					positive regulation of pseudopodium assembly (GO:0031274)|regulation of cell shape (GO:0008360)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(4)|prostate(5)	15	Melanoma(58;0.0574)					GAGGAGGATGATGAGGTCAAG	0.637																																					p.D387G		Atlas-SNP	.											.	CDC42EP1	53	.	0			c.A1160G						.						28	32	31					22																	37964811		2203	4300	6503	SO:0001583	missense	11135	exon3			AGGATGATGAGGT	M88338	CCDS13949.1	22q13.1	2008-06-11			ENSG00000128283	ENSG00000128283			17014	protein-coding gene	gene with protein product	"55 kDa bone marrow stromal/endothelial cell protein", "serum constituent protein"	606084				1629197, 10430899	Standard	NM_152243		Approved	MSE55, CEP1, Borg5	uc003asz.4	Q00587	OTTHUMG00000150591	ENST00000249014.4:c.1160A>G	chr22.hg19:g.37964811A>G	ENSP00000249014:p.Asp387Gly	214.0	0.0		191.0	77.0	NM_152243	A8K825|Q96GN1	Missense_Mutation	SNP	ENST00000249014.4	hg19	CCDS13949.1	.	.	.	.	.	.	.	.	.	.	A	19.57	3.851629	0.71719	.	.	ENSG00000128283	ENST00000249014	T	0.51325	0.71	4.67	4.67	0.58626	.	0.385400	0.22547	N	0.058645	T	0.46229	0.1382	L	0.32530	0.975	0.41557	D	0.988603	D	0.58268	0.982	P	0.50314	0.637	T	0.50980	-0.8763	10	0.87932	D	0	-9.1493	12.161	0.54103	1.0:0.0:0.0:0.0	.	387	Q00587	BORG5_HUMAN	G	387	ENSP00000249014:D387G	ENSP00000249014:D387G	D	+	2	0	CDC42EP1	36294757	0.999000	0.42202	0.881000	0.34555	0.610000	0.37248	6.580000	0.74040	1.856000	0.53863	0.459000	0.35465	GAT	.	.		0.637	CDC42EP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318993.1	NM_152243		G	37964811	A	G	37964811	3	3	300	1	0	0	0	0	1	0	0	0	3077	333	12	2	1166	2	CDC42EP1	22	37964811	Missense_Mutation	SNP	A	TCGA-G3-AAV4-01A-11D-A382-10		37964811	13339755	107	43446										
TCF20	6942	hgsc.bcm.edu	37	chr22	42608026	42608026	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	gctgctccagtctttatactCctctggttgctgttggtaca	9	11	2	0			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr22:42608026C>A	ENST00000359486.3	-	1	3422	c.3286G>T	c.(3286-3288)Gag>Tag	p.E1096*	TCF20_ENST00000404876.1_5'Flank|TCF20_ENST00000335626.4_Nonsense_Mutation_p.E1096*	NM_005650.1	NP_005641.1	Q9UGU0	TCF20_HUMAN	transcription factor 20 (AR1)	1096					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(13)|lung(22)|ovary(5)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(5)	66						TCTTTATACTCCTCTGGTTGC	0.507																																					p.E1096X		Atlas-SNP	.											.	TCF20	164	.	0			c.G3286T						.						66	65	65					22																	42608026		2203	4300	6503	SO:0001587	stop_gained	6942	exon1			TATACTCCTCTGG	U19345	CCDS14032.1, CCDS14033.1	22q13.3	2011-02-08			ENSG00000100207	ENSG00000100207			11631	protein-coding gene	gene with protein product	"stromelysin-1 platelet-derived growth factor-responsive element binding protein"	603107				9730594, 10995766	Standard	NM_005650		Approved	AR1, SPBP	uc003bcj.1	Q9UGU0	OTTHUMG00000150920	ENST00000359486.3:c.3286G>T	chr22.hg19:g.42608026C>A	ENSP00000352463:p.Glu1096*	107.0	0.0		103.0	44.0	NM_181492	A9JX12|O14528|Q13078|Q4V353|Q9H4M0	Nonsense_Mutation	SNP	ENST00000359486.3	hg19	CCDS14033.1	.	.	.	.	.	.	.	.	.	.	C	43	10.404770	0.99399	.	.	ENSG00000100207	ENST00000359486;ENST00000335626	.	.	.	5.81	5.81	0.92471	.	0.077866	0.52532	D	0.000066	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-23.5711	20.0628	0.97684	0.0:1.0:0.0:0.0	.	.	.	.	X	1096	.	ENSP00000335561:E1096X	E	-	1	0	TCF20	40937970	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.311000	0.65786	2.745000	0.94114	0.655000	0.94253	GAG	.	.		0.507	TCF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320531.1	NM_181492		A	42608026	C	A	42608026	4	1	300	1	0	0	0	0	0	1	0	0	15705	864	30	3	2634	3	TCF20	22	42608026	Nonsense_Mutation	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	4643215	42608026	8696540	108	43447										
A4GALT	53947	hgsc.bcm.edu	37	chr22	43089164	43089164	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	cgcggctctcggccaggctgCggatggaacaccacttcttg	13	14	2	0	rs549273376		TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr22:43089164C>T	ENST00000401850.1	-	2	1283	c.794G>A	c.(793-795)cGc>cAc	p.R265H	A4GALT_ENST00000381278.3_Missense_Mutation_p.R265H|A4GALT_ENST00000249005.2_Missense_Mutation_p.R265H|A4GALT_ENST00000465765.2_5'Flank			Q9NPC4	A4GAT_HUMAN	alpha 1,4-galactosyltransferase	265					globoside biosynthetic process (GO:0001576)|glycosphingolipid biosynthetic process (GO:0006688)|plasma membrane organization (GO:0007009)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	galactosyltransferase activity (GO:0008378)|lactosylceramide 4-alpha-galactosyltransferase activity (GO:0050512)|toxic substance binding (GO:0015643)			NS(1)|central_nervous_system(2)|large_intestine(6)|skin(1)|urinary_tract(1)	11						GGCCAGGCTGCGGATGGAACA	0.652																																					p.R265H		Atlas-SNP	.											.	A4GALT	35	.	0			c.G794A						.						21	19	20					22																	43089164		2194	4293	6487	SO:0001583	missense	53947	exon3			AGGCTGCGGATGG		CCDS14041.1	22q13.2	2014-07-18	2008-07-31		ENSG00000128274	ENSG00000128274	2.4.1.228		18149	protein-coding gene	gene with protein product	"Gb3 synthase", "CD77 synthase", "globotriaosylceramide synthase", "lactosylceramide 4-alpha-galactosyltransferase"	607922	"alpha 1,4-galactosyltransferase (globotriaosylceramide synthase, P blood group)"			10854428	Standard	XM_005261643		Approved	A14GALT, Gb3S, P(k)	uc003bdb.3	Q9NPC4	OTTHUMG00000150744	ENST00000401850.1:c.794G>A	chr22.hg19:g.43089164C>T	ENSP00000384794:p.Arg265His	65.0	0.0		56.0	27.0	NM_017436	B2R7C4|Q9P1X5	Missense_Mutation	SNP	ENST00000401850.1	hg19	CCDS14041.1	.	.	.	.	.	.	.	.	.	.	C	12.40	1.927372	0.34002	.	.	ENSG00000128274	ENST00000401850;ENST00000249005;ENST00000381278;ENST00000535654	T;T;T	0.72725	-0.68;-0.68;-0.68	5.29	0.791	0.18619	Alpha 1,4-glycosyltransferase domain (1);	0.242179	0.27143	N	0.020738	T	0.57301	0.2044	L	0.39397	1.21	0.25679	N	0.985815	B	0.16802	0.019	B	0.15484	0.013	T	0.49908	-0.8889	10	0.42905	T	0.14	-2.2733	9.5259	0.39165	0.0:0.7006:0.0:0.2994	.	265	Q9NPC4	A4GAT_HUMAN	H	265	ENSP00000384794:R265H;ENSP00000249005:R265H;ENSP00000370678:R265H	ENSP00000249005:R265H	R	-	2	0	A4GALT	41419108	0.001000	0.12720	1.000000	0.80357	0.562000	0.35680	-0.071000	0.11505	0.234000	0.21139	-0.258000	0.10820	CGC	.	.		0.652	A4GALT-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319917.1	NM_017436		T	43089164	C	T	43089164	3	4	300	1	0	0	0	0	1	0	0	0	6	768	27	1	271	1	A4GALT	22	43089164	Missense_Mutation	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	481138	43089164	8215402	109	43448										
ASB11	140456	hgsc.bcm.edu	37	chrX	15306022	15306022	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	ccttcacggagcaagagtgcCtgctccacgctgctttttgg	11	13	1	1			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chrX:15306022C>T	ENST00000480796.1	-	6	878	c.828G>A	c.(826-828)caG>caA	p.Q276Q	ASB11_ENST00000380470.3_Silent_p.Q259Q|ASB11_ENST00000537676.1_Silent_p.Q255Q|ASB11_ENST00000344384.4_Silent_p.Q255Q			Q8WXH4	ASB11_HUMAN	ankyrin repeat and SOCS box containing 11, E3 ubiquitin protein ligase	276	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(2)|central_nervous_system(4)|endometrium(1)|large_intestine(1)|lung(5)|ovary(2)|skin(1)	16	Hepatocellular(33;0.183)					GCAAGAGTGCCTGCTCCACGC	0.507																																					p.Q276Q		Atlas-SNP	.											.	ASB11	79	.	0			c.G828A						.						97	74	82					X																	15306022		2203	4300	6503	SO:0001819	synonymous_variant	140456	exon6			GAGTGCCTGCTCC	AF425642	CCDS14164.1, CCDS35209.1, CCDS56596.1	Xp22.31	2014-02-10	2014-02-10		ENSG00000165192	ENSG00000165192		"Ankyrin repeat domain containing"	17186	protein-coding gene	gene with protein product		300626	"ankyrin repeat and SOCS box-containing 11", "ankyrin repeat and SOCS box containing 11"			24337577	Standard	NM_080873		Approved	DKFZp779E2460	uc004cwp.2	Q8WXH4	OTTHUMG00000021173	ENST00000480796.1:c.828G>A	chrX.hg19:g.15306022C>T		189.0	0.0		143.0	35.0	NM_080873	E9PEN1|Q3SYC4|Q7Z667	Silent	SNP	ENST00000480796.1	hg19	CCDS14164.1																																																																																			.	.		0.507	ASB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055852.2			T	15306022	C	T	15306022	2	4	300	1	0	0	0	0	0	0	0	1	1015	680	24	3		3	ASB11	23	15306022	Silent	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10		15306022	139964538	110	43449										
MAGEB10	139422	hgsc.bcm.edu	37	chrX	27839801	27839801	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	cattacttgctgtacaagtaCcaaatgaaagagcccattac	6	10	0	2			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chrX:27839801C>T	ENST00000356790.2	+	3	623	c.378C>T	c.(376-378)taC>taT	p.Y126Y		NM_182506.3	NP_872312.2	Q96LZ2	MAGBA_HUMAN	melanoma antigen family B, 10	126	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.									NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	26						TGTACAAGTACCAAATGAAAG	0.443																																					p.Y126Y		Atlas-SNP	.											.	MAGEB10	107	.	0			c.C378T						.						59	54	56					X																	27839801		2202	4300	6502	SO:0001819	synonymous_variant	139422	exon3			CAAGTACCAAATG		CCDS35221.1	Xp21.3	2008-02-05			ENSG00000177689	ENSG00000177689			25377	protein-coding gene	gene with protein product		300761				11454705	Standard	NM_182506		Approved	FLJ32965	uc004dbw.3	Q96LZ2	OTTHUMG00000046084	ENST00000356790.2:c.378C>T	chrX.hg19:g.27839801C>T		391.0	0.0		264.0	146.0	NM_182506	Q494Y6|Q494Y7|Q9BZ78	Silent	SNP	ENST00000356790.2	hg19	CCDS35221.1																																																																																			.	.		0.443	MAGEB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106216.1	NM_182506		T	27839801	C	T	27839801	2	4	300	1	0	0	0	0	0	0	0	1	9182	518	18	3		3	MAGEB10	23	27839801	Silent	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	12533779	27839801	127430759	111	43450										
TAF1	6872	hgsc.bcm.edu	37	chrX	70595090	70595090	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	atgcctcctccacctccaccCccgggaccaatgaagaagga	8	17	0	2			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chrX:70595090C>T	ENST00000373790.4	+	4	537	c.486C>T	c.(484-486)ccC>ccT	p.P162P	TAF1_ENST00000449580.1_Silent_p.P162P|TAF1_ENST00000276072.3_Silent_p.P162P|TAF1_ENST00000423759.1_Silent_p.P162P	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	162	Pro-rich.|Protein kinase 1.				cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				CACCTCCACCCCCGGGACCAA	0.423																																					p.P162P		Atlas-SNP	.											.	TAF1	439	.	0			c.C486T						.						133	112	119					X																	70595090		2203	4300	6503	SO:0001819	synonymous_variant	6872	exon4			TCCACCCCCGGGA		CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"Chromatin-modifying enzymes / K-acetyltransferases"	11535	protein-coding gene	gene with protein product		313650	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD", "dystonia 3 (with Parkinsonism)"	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.486C>T	chrX.hg19:g.70595090C>T		158.0	0.0		117.0	36.0	NM_004606	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Silent	SNP	ENST00000373790.4	hg19	CCDS35325.1																																																																																			.	.		0.423	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606		T	70595090	C	T	70595090	2	4	300	1	0	0	0	0	0	0	0	1	15528	610	22	3		3	TAF1	23	70595090	Silent	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	42755289	70595090	84675470	112	43451										
BCAP31	10134	hgsc.bcm.edu	37	chrX	152966418	152966418	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	7	1	1.10821742832813	4.11623616236162	0.715867158671587	1	1	0	ttccttcttgtccatgggacCatctactgcagcctggaaag	9	12	2	0			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chrX:152966418C>T	ENST00000345046.6	-	8	1122	c.715G>A	c.(715-717)Ggt>Agt	p.G239S	BCAP31_ENST00000441714.1_Missense_Mutation_p.G239S|BCAP31_ENST00000458587.2_Missense_Mutation_p.G306S	NM_001256447.1	NP_001243376.1	P51572	BAP31_HUMAN	B-cell receptor-associated protein 31	239		Cleavage; by caspase-8. {ECO:0000255}.			antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|protein localization to endoplasmic reticulum exit site (GO:0070973)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lipid particle (GO:0005811)|membrane (GO:0016020)				endometrium(2)|large_intestine(2)|lung(2)|prostate(1)	7	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TCCATGGGACCATCTACTGCA	0.637																																					p.G306S		Atlas-SNP	.											.	BCAP31	33	.	0			c.G916A						.						121	82	95					X																	152966418		2203	4300	6503	SO:0001583	missense	10134	exon8			TGGGACCATCTAC	X81109	CCDS14727.1, CCDS48191.1	Xq28	2005-10-11			ENSG00000185825	ENSG00000185825			16695	protein-coding gene	gene with protein product		300398					Standard	NM_001139441		Approved	DXS1357E, BAP31, 6C6-Ag, CDM	uc011mza.1	P51572	OTTHUMG00000024218	ENST00000345046.6:c.715G>A	chrX.hg19:g.152966418C>T	ENSP00000343458:p.Gly239Ser	318.0	0.0		202.0	70.0	NM_001139457	B3KQ79|D3DWV5|Q13836|Q96CF0	Missense_Mutation	SNP	ENST00000345046.6	hg19	CCDS14727.1	.	.	.	.	.	.	.	.	.	.	c	12.19	1.864450	0.32977	.	.	ENSG00000185825	ENST00000441714;ENST00000345046;ENST00000426131;ENST00000458587	.	.	.	4.44	4.44	0.53790	.	0.141544	0.44483	D	0.000445	T	0.34164	0.0888	L	0.42686	1.345	0.39241	D	0.963856	B;P	0.43788	0.22;0.817	B;B	0.33454	0.024;0.164	T	0.42068	-0.9473	9	0.02654	T	1	-5.4705	12.0095	0.53278	0.0:1.0:0.0:0.0	.	239;306	P51572;B3KQ79	BAP31_HUMAN;.	S	239;239;306;306	.	ENSP00000343458:G239S	G	-	1	0	BCAP31	152619612	0.069000	0.21087	0.481000	0.27354	0.278000	0.26855	2.025000	0.41059	1.965000	0.57142	0.525000	0.51046	GGT	.	.		0.637	BCAP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061071.1	NM_005745		T	152966418	C	T	152966418	3	4	300	1	0	0	0	0	1	0	0	0	1347	594	21	3	29	3	BCAP31	23	152966418	Missense_Mutation	SNP	C	TCGA-G3-AAV4-01A-11D-A382-10	82371328	152966418	2304142	113	43452										
MIB2	142678	hgsc.bcm.edu	37	chr1	1558785	1558785	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	acaggtcccgagcagcccggCccaccatggacccctctgcc	10	20	1	0			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr1:1558785C>G	ENST00000357210.4	+	3	343	c.127C>G	c.(127-129)Ccc>Gcc	p.P43A	MIB2_ENST00000505820.2_Missense_Mutation_p.P100A|MIB2_ENST00000520777.1_Missense_Mutation_p.P100A|MIB2_ENST00000360522.4_Missense_Mutation_p.P43A|MIB2_ENST00000378710.3_Missense_Mutation_p.P43A|MIB2_ENST00000512004.1_3'UTR|MIB2_ENST00000378712.1_Intron|MIB2_ENST00000504599.1_5'UTR|MIB2_ENST00000355826.5_Intron|MIB2_ENST00000518681.1_Missense_Mutation_p.P100A|MIB2_ENST00000378708.1_Intron	NM_080875.2	NP_543151.2	Q96AX9	MIB2_HUMAN	mindbomb E3 ubiquitin protein ligase 2	43					Notch signaling pathway (GO:0007219)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)	early endosome (GO:0005769)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|lung(7)|prostate(4)|upper_aerodigestive_tract(1)	18	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;5.26e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.54e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|BRCA - Breast invasive adenocarcinoma(365;0.00786)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		AGCAGCCCGGCCCACCATGGA	0.716																																					p.P100A		Atlas-SNP	.											.	MIB2	62	.	0			c.C298G						.						11	14	13					1																	1558785		1885	4099	5984	SO:0001583	missense	142678	exon3			GCCCGGCCCACCA	AK097106	CCDS41224.1, CCDS41224.2, CCDS53261.1, CCDS53262.1, CCDS53263.1, CCDS53264.1	1p36.33	2013-01-10	2012-02-23	2005-04-01	ENSG00000197530	ENSG00000197530		"Zinc fingers, ZZ-type", "Ankyrin repeat domain containing"	30577	protein-coding gene	gene with protein product		611141	"zinc finger, ZZ type with ankyrin repeat domain 1", "mindbomb homolog 2 (Drosophila)"	ZZANK1		12761501	Standard	NM_080875		Approved	skeletrophin, ZZZ5, FLJ39787	uc001agg.3	Q96AX9	OTTHUMG00000074647	ENST00000357210.4:c.127C>G	chr1.hg19:g.1558785C>G	ENSP00000349741:p.Pro43Ala	142.0	0.0		153.0	59.0	NM_001170686	A2AGM5|A2AGM6|B3KV93|B3KVF4|B3KXY1|B4DZ57|E9PGU1|E9PHQ1|F8WA73|J3KNZ7|Q7Z437|Q8IY62|Q8N786|Q8N897|Q8N8R2|Q8N911|Q8NB36|Q8NCY1|Q8NG59|Q8NG60|Q8NG61|Q8NI59|Q8WYN1	Missense_Mutation	SNP	ENST00000357210.4	hg19		.	.	.	.	.	.	.	.	.	.	C	7.970	0.748943	0.15710	.	.	ENSG00000197530	ENST00000520777;ENST00000357210;ENST00000360522;ENST00000378710;ENST00000518681;ENST00000505820	T;T;T;T;T;T	0.32515	1.45;1.49;1.48;1.48;1.46;1.45	1.19	1.19	0.21007	.	10.323000	0.00695	U	0.000758	T	0.17408	0.0418	N	0.08118	0	0.09310	N	1	B;B;B	0.09022	0.001;0.001;0.002	B;B;B	0.04013	0.0;0.001;0.001	T	0.16719	-1.0393	10	0.36615	T	0.2	.	5.1539	0.15025	0.0:0.6231:0.3769:0.0	.	100;100;43	E9PHQ1;E9PGU1;Q96AX9	.;.;MIB2_HUMAN	A	100;43;43;43;100;100	ENSP00000428660:P100A;ENSP00000349741:P43A;ENSP00000353713:P43A;ENSP00000367982:P43A;ENSP00000428264:P100A;ENSP00000426103:P100A	ENSP00000349741:P43A	P	+	1	0	MIB2	1548648	0.000000	0.05858	0.003000	0.11579	0.350000	0.29205	-1.440000	0.02412	0.552000	0.29026	0.174000	0.16983	CCC	.	.		0.716	MIB2-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_080875		G	1558785	C	G	1558785	3	3	301	1	0	0	0	0	1	0	0	0	9576	739	26	4	308	4	MIB2	1	1558785	Missense_Mutation	SNP	C	TCGA-G3-AAV5-01A-11D-A36X-10		1558785	247691836	1	43453										
FOXD2	2306	hgsc.bcm.edu	37	chr1	47904970	47904970	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	tctgcccaccgcacttctgcGccagggcctcaagacggacg	11	17	3	1			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr1:47904970G>T	ENST00000334793.5	+	1	3282	c.1163G>T	c.(1162-1164)cGc>cTc	p.R388L		NM_004474.3	NP_004465.3	O60548	FOXD2_HUMAN	forkhead box D2	388	Ala-rich.|Gly-rich.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(4)	4				READ - Rectum adenocarcinoma(2;0.0908)		GCACTTCTGCGCCAGGGCCTC	0.721																																					p.R388L		Atlas-SNP	.											.	FOXD2	16	.	0			c.G1163T						.						2	4	3					1																	47904970		1699	3595	5294	SO:0001583	missense	2306	exon1			TTCTGCGCCAGGG	AF042832	CCDS30708.1	1p34-p32	2008-02-05			ENSG00000186564	ENSG00000186564		"Forkhead boxes"	3803	protein-coding gene	gene with protein product		602211		FKHL17		9403061, 12621056	Standard	NM_004474		Approved	FREAC9	uc001crm.3	O60548	OTTHUMG00000007950	ENST00000334793.5:c.1163G>T	chr1.hg19:g.47904970G>T	ENSP00000335493:p.Arg388Leu	13.0	0.0		12.0	6.0	NM_004474	Q5SVZ3	Missense_Mutation	SNP	ENST00000334793.5	hg19	CCDS30708.1	.	.	.	.	.	.	.	.	.	.	G	3.634	-0.074840	0.07184	.	.	ENSG00000186564	ENST00000334793	D	0.91894	-2.93	4.3	3.29	0.37713	.	385.614000	0.00550	N	0.000246	T	0.79417	0.4442	N	0.02225	-0.63	0.26708	N	0.971038	B	0.09022	0.002	B	0.08055	0.003	T	0.74272	-0.3719	10	0.08179	T	0.78	.	5.8598	0.18740	0.0:0.2945:0.4553:0.2502	.	388	O60548	FOXD2_HUMAN	L	388	ENSP00000335493:R388L	ENSP00000335493:R388L	R	+	2	0	FOXD2	47677557	0.978000	0.34361	1.000000	0.80357	0.940000	0.58332	0.518000	0.22847	1.914000	0.55421	0.561000	0.74099	CGC	.	.		0.721	FOXD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021831.1	NM_004474		T	47904970	G	T	47904970	3	4	301	1	0	0	0	0	1	0	0	0	6005	1087	38	1	1165	1	FOXD2	1	47904970	Missense_Mutation	SNP	G	TCGA-G3-AAV5-01A-11D-A36X-10	46346185	47904970	201345651	2	43454										
SCP2	6342	hgsc.bcm.edu	37	chr1	53443889	53443889	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	ttatttttacttcctcttagTcccacttcagatggtgctgc	6	11	2	1			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr1:53443889T>G	ENST00000528311.1	+	8	728	c.432T>G	c.(430-432)tgT>tgG	p.C144W	SCP2_ENST00000473584.1_3'UTR|SCP2_ENST00000407246.2_Splice_Site_p.C201W|SCP2_ENST00000371509.4_Splice_Site_p.C181W|SCP2_ENST00000371513.5_Splice_Site_p.C181W|SCP2_ENST00000371514.3_Splice_Site_p.C225W	NM_001193617.1	NP_001180546.1	Q9BX26	SYCP2_HUMAN	sterol carrier protein 2	865					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	15						TTCCTCTTAGTCCCACTTCAG	0.433																																					p.C225W		Atlas-SNP	.											SCP2,NS,carcinoma,0,1	SCP2	44	.	0			c.T675G						.						73	69	70					1																	53443889		2203	4300	6503	SO:0001630	splice_region_variant	6342	exon9			TCTTAGTCCCACT	M75884	CCDS572.1, CCDS30719.1, CCDS41338.1, CCDS44149.1, CCDS44150.1, CCDS53317.1, CCDS53318.1, CCDS53319.1	1p32	2010-08-20			ENSG00000116171	ENSG00000116171			10606	protein-coding gene	gene with protein product		184755				1703300, 1718316	Standard	NM_001007098		Approved		uc001cur.2	P22307	OTTHUMG00000008936	ENST00000528311.1:c.432-1T>G	chr1.hg19:g.53443889T>G		79.0	0.0		88.0	42.0	NM_002979	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Missense_Mutation	SNP	ENST00000528311.1	hg19	CCDS53319.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.87|17.87	3.495460|3.495460	0.64186|0.64186	.|.	.|.	ENSG00000116171|ENSG00000116171	ENST00000371514;ENST00000528311;ENST00000371509;ENST00000407246;ENST00000371513|ENST00000529363	D;T;D;D;D|.	0.94758|.	-3.51;-0.56;-3.51;-3.51;-3.51|.	5.29|5.29	-1.19|-1.19	0.09585|0.09585	Thiolase-like, subgroup (1);Thiolase-like (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.85982|0.85982	0.5824|0.5824	H|H	0.98178|0.98178	4.165|4.165	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0|.	D;D;D;D|.	0.87578|.	0.997;0.995;0.998;0.997|.	D|D	0.86946|0.86946	0.2082|0.2082	9|5	.|.	.|.	.|.	.|.	11.166|11.166	0.48543|0.48543	0.0:0.3803:0.0:0.6197|0.0:0.3803:0.0:0.6197	.|.	201;181;225;181|.	C9JC79;A6NM69;P22307;Q6NXF4|.	.;.;NLTP_HUMAN;.|.	W|R	225;144;181;201;181|171	ENSP00000360569:C225W;ENSP00000434132:C144W;ENSP00000360564:C181W;ENSP00000384569:C201W;ENSP00000360568:C181W|.	.|.	C|L	+|+	3|2	2|0	SCP2|SCP2	53216477|53216477	0.873000|0.873000	0.30073|0.30073	0.994000|0.994000	0.49952|0.49952	0.928000|0.928000	0.56348|0.56348	-0.079000|-0.079000	0.11357|0.11357	-0.106000|-0.106000	0.12110|0.12110	0.528000|0.528000	0.53228|0.53228	TGT|CTC	.	.		0.433	SCP2-010	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387558.1	NM_002979	Missense_Mutation	G	53443889	T	G	53443889	5	3	301	1	0	0	0	0	0	0	1	0	13949	1681	58	5	709	5	SCP2	1	53443889	Splice_Site	SNP	T	TCGA-G3-AAV5-01A-11D-A36X-10	5538919	53443889	195806732	3	43455										
TM2D1	83941	hgsc.bcm.edu	37	chr1	62175038	62175038	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	gggcttgaaaaaaccaacttCgttcccagtaaaatgtgttt	8	8	0	1	rs373304497		TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr1:62175038C>G	ENST00000606498.1	-	3	330	c.310G>C	c.(310-312)Gaa>Caa	p.E104Q	TM2D1_ENST00000472989.1_5'UTR|TM2D1_ENST00000371177.2_Missense_Mutation_p.E104Q|TM2D1_ENST00000294613.5_Missense_Mutation_p.E104Q|TM2D1_ENST00000371180.2_Missense_Mutation_p.E166Q			Q9BX74	TM2D1_HUMAN	TM2 domain containing 1	104					apoptotic signaling pathway (GO:0097190)	integral component of plasma membrane (GO:0005887)	beta-amyloid binding (GO:0001540)|G-protein coupled receptor activity (GO:0004930)	p.E166K(1)		large_intestine(2)|lung(3)|ovary(1)	6						AAACCAACTTCGTTCCCAGTA	0.358																																					p.E104Q		Atlas-SNP	.											TM2D1_ENST00000371177,NS,carcinoma,0,3	TM2D1	37	.	1	Substitution - Missense(1)	large_intestine(1)	c.G310C						.						92	88	89					1																	62175038		1839	4091	5930	SO:0001583	missense	83941	exon3			CAACTTCGTTCCC	AF353990	CCDS65554.1	1p32.1	2008-02-05			ENSG00000162604	ENSG00000162604			24142	protein-coding gene	gene with protein product		610080				11278849, 12553667	Standard	NM_032027		Approved	BBP	uc001czz.1	Q9BX74	OTTHUMG00000008466	ENST00000606498.1:c.310G>C	chr1.hg19:g.62175038C>G	ENSP00000475700:p.Glu104Gln	316.0	2.0		365.0	113.0	NM_032027	A6NDA8	Missense_Mutation	SNP	ENST00000606498.1	hg19		.	.	.	.	.	.	.	.	.	.	C	19.72	3.879717	0.72294	.	.	ENSG00000162604	ENST00000371180;ENST00000294613;ENST00000371178;ENST00000371177	.	.	.	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.75079	0.3801	L	0.59436	1.845	0.58432	D	0.999992	D	0.76494	0.999	D	0.79108	0.992	T	0.67401	-0.5680	9	0.18276	T	0.48	-3.277	18.396	0.90499	0.0:1.0:0.0:0.0	.	104	Q9BX74	TM2D1_HUMAN	Q	166;104;104;104	.	ENSP00000294613:E104Q	E	-	1	0	TM2D1	61947626	1.000000	0.71417	0.971000	0.41717	0.772000	0.43724	5.467000	0.66737	2.882000	0.98803	0.655000	0.94253	GAA	.	.		0.358	TM2D1-012	KNOWN	non_canonical_U12|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470779.2	NM_032027		G	62175038	C	G	62175038	3	3	301	1	0	0	0	0	1	0	0	0	15978	893	31	4	329	4	TM2D1	1	62175038	Missense_Mutation	SNP	C	TCGA-G3-AAV5-01A-11D-A36X-10	8731149	62175038	187075583	4	43456										
ARHGEF11	9826	hgsc.bcm.edu	37	chr1	156914158	156914158	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	cctggcacatacccaaggtcTtatccttgctgatcctccag	7	15	1	1			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr1:156914158T>A	ENST00000361409.2	-	30	3681	c.2939A>T	c.(2938-2940)aAg>aTg	p.K980M	ARHGEF11_ENST00000487682.1_5'UTR|ARHGEF11_ENST00000368194.3_Missense_Mutation_p.K1020M|ARHGEF11_ENST00000315174.8_Missense_Mutation_p.K396M	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	980	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cytokinesis (GO:0000910)|establishment of cell polarity (GO:0030010)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)|striated muscle contraction (GO:0006941)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(27)|ovary(4)|pancreas(2)|pleura(1)|prostate(4)|skin(7)|stomach(1)|urinary_tract(2)	81	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					ACCCAAGGTCTTATCCTTGCT	0.512																																					p.K1020M		Atlas-SNP	.											.	ARHGEF11	168	.	0			c.A3059T						.						123	115	117					1																	156914158		2203	4300	6503	SO:0001583	missense	9826	exon31			AAGGTCTTATCCT	AB002378	CCDS1162.1, CCDS1163.1	1q21	2011-11-16			ENSG00000132694	ENSG00000132694		"Rho guanine nucleotide exchange factors"	14580	protein-coding gene	gene with protein product		605708				10526156, 9205841	Standard	NM_014784		Approved	KIAA0380, GTRAP48, PDZ-RHOGEF	uc001fqn.3	O15085	OTTHUMG00000041292	ENST00000361409.2:c.2939A>T	chr1.hg19:g.156914158T>A	ENSP00000354644:p.Lys980Met	71.0	0.0		142.0	32.0	NM_198236	D3DVD0|Q5VY40|Q6PFW2	Missense_Mutation	SNP	ENST00000361409.2	hg19	CCDS1162.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.562143	0.86335	.	.	ENSG00000132694	ENST00000368194;ENST00000361409;ENST00000315174	T;T;T	0.69435	-0.4;-0.4;-0.4	5.13	5.13	0.70059	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.64402	D	0.000020	T	0.81418	0.4818	M	0.88181	2.935	0.80722	D	1	D;D;D	0.89917	0.996;1.0;0.999	D;D;D	0.85130	0.985;0.995;0.997	D	0.85571	0.1234	10	0.87932	D	0	-31.1983	14.7535	0.69546	0.0:0.0:0.0:1.0	.	396;980;1020	F8W8P9;O15085;O15085-2	.;ARHGB_HUMAN;.	M	1020;980;396	ENSP00000357177:K1020M;ENSP00000354644:K980M;ENSP00000313470:K396M	ENSP00000313470:K396M	K	-	2	0	ARHGEF11	155180782	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	5.990000	0.70595	2.147000	0.66899	0.459000	0.35465	AAG	.	.		0.512	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236		A	156914158	T	A	156914158	3	1	301	1	0	0	0	0	1	0	0	0	896	1609	56	4	1673	4	ARHGEF11	1	156914158	Missense_Mutation	SNP	T	TCGA-G3-AAV5-01A-11D-A36X-10	94739120	156914158	92336463	5	43457										
RASAL2	9462	hgsc.bcm.edu	37	chr1	178427542	178427542	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	gtgcttctttacgtagcaccGggagcatgtcagtggtgtcc	13	10	2	0	rs368617203		TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr1:178427542G>A	ENST00000462775.1	+	12	2817	c.2692G>A	c.(2692-2694)Ggg>Agg	p.G898R	RASAL2_ENST00000367649.3_Missense_Mutation_p.G1039R|RASAL2_ENST00000448150.3_Missense_Mutation_p.G1028R	NM_004841.3	NP_004832.1	Q9UJF2	NGAP_HUMAN	RAS protein activator like 2	898					negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Ras GTPase activator activity (GO:0005099)	p.G1039R(1)|p.G1028R(1)		biliary_tract(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(2)|lung(25)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54						ACGTAGCACCGGGAGCATGTC	0.627													G|||	1	0.000199681	0	0.0014	5008	,	,		17455	0		0	False		,,,				2504	0				p.G1039R		Atlas-SNP	.											RASAL2_ENST00000462775,NS,lymphoid_neoplasm,0,5	RASAL2	334	.	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	c.G3115A						.	G	ARG/GLY,ARG/GLY	1,4405	2.1+/-5.4	0,1,2202	55	56	55		2692,3115	5.5	1	1		55	0,8600		0,0,4300	no	missense,missense	RASAL2	NM_004841.3,NM_170692.2	125,125	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign	898/1140,1039/1281	178427542	1,13005	2203	4300	6503	SO:0001583	missense	9462	exon14			AGCACCGGGAGCA	AF047711	CCDS1321.1, CCDS1322.1, CCDS1321.2	1q25	2013-01-10			ENSG00000075391	ENSG00000075391		"Pleckstrin homology (PH) domain containing"	9874	protein-coding gene	gene with protein product	"Ras GTPase activating protein-like", "Ras protein activator like 1"	606136				9877179	Standard	NM_004841		Approved	nGAP	uc001glq.3	Q9UJF2	OTTHUMG00000035022	ENST00000462775.1:c.2692G>A	chr1.hg19:g.178427542G>A	ENSP00000420558:p.Gly898Arg	94.0	0.0		174.0	33.0	NM_170692	F8W755|O95174|Q2TB22|Q5TFU9	Missense_Mutation	SNP	ENST00000462775.1	hg19	CCDS1322.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.03|19.03	3.747873|3.747873	0.69533|0.69533	2.27E-4|2.27E-4	0.0|0.0	ENSG00000075391|ENSG00000075391	ENST00000448150;ENST00000367649;ENST00000462775|ENST00000433130	T;T;T|.	0.15487|.	2.42;2.42;2.42|.	5.46|5.46	5.46|5.46	0.80206|0.80206	.|.	0.257336|.	0.37530|.	N|.	0.002042|.	T|T	0.70710|0.70710	0.3255|0.3255	L|L	0.50333|0.50333	1.59|1.59	0.47621|0.47621	D|D	0.99947|0.99947	P;D;P|.	0.60160|.	0.952;0.987;0.862|.	B;P;B|.	0.53518|.	0.363;0.728;0.2|.	T|T	0.66897|0.66897	-0.5807|-0.5807	10|5	0.20046|.	T|.	0.44|.	.|.	19.321|19.321	0.94240|0.94240	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1028;898;1039|.	B1AKC7;Q9UJF2;F8W755|.	.;NGAP_HUMAN;.|.	R|Q	1028;1039;898|448	ENSP00000407768:G1028R;ENSP00000356621:G1039R;ENSP00000420558:G898R|.	ENSP00000356621:G1039R|.	G|R	+|+	1|2	0|0	RASAL2|RASAL2	176694165|176694165	1.000000|1.000000	0.71417|0.71417	0.958000|0.958000	0.39756|0.39756	0.965000|0.965000	0.64279|0.64279	3.270000|3.270000	0.51600|0.51600	2.548000|2.548000	0.85928|0.85928	0.591000|0.591000	0.81541|0.81541	GGG|CGG	.	.		0.627	RASAL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000084758.3	NM_170692		A	178427542	G	A	178427542	3	1	301	1	0	0	0	0	1	0	0	0	13079	1116	39	1	3207	1	RASAL2	1	178427542	Missense_Mutation	SNP	G	TCGA-G3-AAV5-01A-11D-A36X-10	21513384	178427542	70823079	6	43458										
NPHS2	7827	hgsc.bcm.edu	37	chr1	179544879	179544879	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	gcccgacggctcgggcccagCctcctggcgcccgcggcctc	14	21	0	0			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr1:179544879C>T	ENST00000367615.4	-	1	189	c.121G>A	c.(121-123)Gct>Act	p.A41T	NPHS2_ENST00000367616.4_Missense_Mutation_p.A41T|RNU5F-2P_ENST00000516066.1_RNA	NM_014625.2	NP_055440.1	Q9NP85	PODO_HUMAN	nephrosis 2, idiopathic, steroid-resistant (podocin)	41					actin cytoskeleton reorganization (GO:0031532)|excretion (GO:0007588)|metanephric glomerular visceral epithelial cell development (GO:0072249)	cell-cell junction (GO:0005911)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)				NS(1)|endometrium(1)|large_intestine(3)|lung(10)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	20						TCGGGCCCAGCCTCCTGGCGC	0.771																																					p.A41T		Atlas-SNP	.											.	NPHS2	46	.	0			c.G121A						.						2	2	2					1																	179544879		1330	3093	4423	SO:0001583	missense	7827	exon1			GCCCAGCCTCCTG	AJ279254	CCDS1331.1, CCDS72988.1	1q25-q31	2014-06-27			ENSG00000116218	ENSG00000116218			13394	protein-coding gene	gene with protein product		604766				8589695, 10742096	Standard	XM_005245483		Approved	SRN1, PDCN	uc001gmq.4	Q9NP85	OTTHUMG00000035252	ENST00000367615.4:c.121G>A	chr1.hg19:g.179544879C>T	ENSP00000356587:p.Ala41Thr	51.0	0.0		52.0	18.0	NM_014625	B1AM32|B1AM33|Q8N6Q5	Missense_Mutation	SNP	ENST00000367615.4	hg19	CCDS1331.1	.	.	.	.	.	.	.	.	.	.	C	10.65	1.409212	0.25378	.	.	ENSG00000116218	ENST00000367615;ENST00000367616	D;D	0.99797	-6.79;-6.79	3.9	0.652	0.17823	.	1.401580	0.04659	U	0.408558	D	0.98479	0.9493	L	0.36672	1.1	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.06405	0.002;0.0	D	0.99978	1.2355	10	0.21014	T	0.42	-1.8085	2.7606	0.05306	0.1858:0.52:0.1817:0.1126	.	41;41	Q9NP85-2;Q9NP85	.;PODO_HUMAN	T	41	ENSP00000356587:A41T;ENSP00000356588:A41T	ENSP00000356587:A41T	A	-	1	0	NPHS2	177811502	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.213000	0.17521	0.198000	0.20407	0.467000	0.42956	GCT	.	.		0.771	NPHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085283.1			T	179544879	C	T	179544879	3	4	301	1	0	0	0	0	1	0	0	0	10592	739	26	3	1062	3	NPHS2	1	179544879	Missense_Mutation	SNP	C	TCGA-G3-AAV5-01A-11D-A36X-10	1117337	179544879	69705742	7	43459										
MRPL55	128308	hgsc.bcm.edu	37	chr1	228295710	228295710	+	Intron	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	cccgtgccggggcaggatgaGcctcggggcttcctcaggag	17	13	1	1			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr1:228295710G>C	ENST00000411464.2	-	4	820				MRPL55_ENST00000366740.1_Intron|MRPL55_ENST00000366744.1_Intron|MRPL55_ENST00000366736.1_Intron|MRPL55_ENST00000430433.1_Silent_p.G34G|MRPL55_ENST00000295008.4_Intron|MRPL55_ENST00000366747.3_Intron|MRPL55_ENST00000366733.1_Intron|MRPL55_ENST00000391867.3_Intron|MRPL55_ENST00000366732.1_Intron|MRPL55_ENST00000336300.5_Intron|MRPL55_ENST00000348259.5_Intron|MRPL55_ENST00000366746.3_Intron|MRPL55_ENST00000366735.1_Intron|MRPL55_ENST00000336520.3_Intron|MRPL55_ENST00000366738.1_Silent_p.G34G|MRPL55_ENST00000366731.5_Silent_p.G34G|MRPL55_ENST00000366742.1_Intron|C1orf35_ENST00000472617.1_5'Flank|MRPL55_ENST00000366741.1_Intron|MRPL55_ENST00000465397.1_5'UTR|MRPL55_ENST00000366734.1_Intron|MRPL55_ENST00000366739.1_Intron			Q7Z7F7	RM55_HUMAN	mitochondrial ribosomal protein L55						translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)	structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|lung(4)	5		Prostate(94;0.0405)				GGCAGGATGAGCCTCGGGGCT	0.637																																					p.G34G		Atlas-SNP	.											.	MRPL55	27	.	0			c.C102G						.						26	35	32					1																	228295710		692	1591	2283	SO:0001627	intron_variant	128308	exon4			GGATGAGCCTCGG	AK056987	CCDS1567.1, CCDS44325.1	1q42.13	2012-09-13			ENSG00000162910	ENSG00000162910		"Mitochondrial ribosomal proteins / large subunits"	16686	protein-coding gene	gene with protein product		611859					Standard	NM_181463		Approved		uc001hrz.4	Q7Z7F7	OTTHUMG00000037965	ENST00000411464.2:c.27-140C>G	chr1.hg19:g.228295710G>C		129.0	0.0		237.0	105.0	NM_181462	Q5TBY3|Q5TBY6|Q6UWI8	Silent	SNP	ENST00000411464.2	hg19	CCDS1567.1																																																																																			.	.		0.637	MRPL55-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092808.1	XM_059233		C	228295710	G	C	228295710	1	2	301	0	1	0	0	0	0	0	0	0	9828	958	34	4		4	MRPL55	1	228295710	Intron	SNP	G	TCGA-G3-AAV5-01A-11D-A36X-10	48750831	228295710	20954911	8	43460										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228504446	228504446	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	cctggagcctctgaaaaacgCggcggtccgggccggcgcac	15	15	1	1			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr1:228504446C>T	ENST00000422127.1	+	51	13366	c.13322C>T	c.(13321-13323)gCg>gTg	p.A4441V	OBSCN_ENST00000570156.2_Missense_Mutation_p.A5398V|OBSCN_ENST00000284548.11_Missense_Mutation_p.A4441V|OBSCN_ENST00000366709.4_Missense_Mutation_p.A1560V|OBSCN_ENST00000366707.4_Missense_Mutation_p.A2075V	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4441	Ig-like 46.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CTGAAAAACGCGGCGGTCCGG	0.677																																					p.A5398V		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C16193T						.																																			SO:0001583	missense	84033	exon62			AAAACGCGGCGGT	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.13322C>T	chr1.hg19:g.228504446C>T	ENSP00000409493:p.Ala4441Val	118.0	0.0		244.0	11.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	c	15.55	2.866931	0.51588	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.74209	-0.82;-0.82;0.23;0.74	5.14	-10.3	0.00346	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	1.577390	0.03472	N	0.213753	T	0.47581	0.1453	N	0.03294	-0.36	0.09310	N	1	B;B	0.25235	0.0;0.121	B;B	0.17722	0.0;0.019	T	0.57676	-0.7770	10	0.02654	T	1	.	19.934	0.97130	0.0:0.6833:0.0:0.3167	.	4441;4441	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	V	4441;4441;2075;1560	ENSP00000284548:A4441V;ENSP00000409493:A4441V;ENSP00000355668:A2075V;ENSP00000355670:A1560V	ENSP00000284548:A4441V	A	+	2	0	OBSCN	226571069	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.970000	0.03810	-2.566000	0.00470	-1.049000	0.02347	GCG	.	.		0.677	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228504446	C	T	228504446	3	4	301	1	0	0	0	0	1	0	0	0	10821	768	27	1	13520	1	OBSCN	1	228504446	Missense_Mutation	SNP	C	TCGA-G3-AAV5-01A-11D-A36X-10	208736	228504446	20746175	9	43461										
DYSF	8291	hgsc.bcm.edu	37	chr2	71743345	71743345	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	ttgtttgactctcctggggaGctgtttgatgagcccatctt	11	9	2	3			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr2:71743345G>C	ENST00000258104.3	+	8	1105	c.828G>C	c.(826-828)gaG>gaC	p.E276D	DYSF_ENST00000409744.1_Missense_Mutation_p.E277D|DYSF_ENST00000409651.1_Missense_Mutation_p.E308D|DYSF_ENST00000409582.3_Missense_Mutation_p.E307D|DYSF_ENST00000409762.1_Missense_Mutation_p.E307D|DYSF_ENST00000410020.3_Missense_Mutation_p.E308D|DYSF_ENST00000410041.1_Missense_Mutation_p.E308D|DYSF_ENST00000429174.2_Missense_Mutation_p.E276D|DYSF_ENST00000394120.2_Missense_Mutation_p.E277D|DYSF_ENST00000413539.2_Missense_Mutation_p.E307D|DYSF_ENST00000409366.1_Missense_Mutation_p.E277D	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	276	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						CTCCTGGGGAGCTGTTTGATG	0.502																																					p.E308D		Atlas-SNP	.											.	DYSF	536	.	0			c.G924C						.						224	184	197					2																	71743345		2203	4300	6503	SO:0001583	missense	8291	exon9			TGGGGAGCTGTTT	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"fer-1-like family member 1"	603009	"limb girdle muscular dystrophy 2B (autosomal recessive)"	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.828G>C	chr2.hg19:g.71743345G>C	ENSP00000258104:p.Glu276Asp	85.0	0.0		93.0	35.0	NM_001130982	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Missense_Mutation	SNP	ENST00000258104.3	hg19	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	G	6.419	0.445454	0.12164	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	T;T;T;T;T;T;T;T;T;T;T	0.68479	-0.33;-0.33;-0.33;-0.33;-0.33;-0.33;-0.33;-0.33;-0.33;-0.33;-0.33	4.46	0.0465	0.14256	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.263965	0.37095	N	0.002249	T	0.47173	0.1431	L	0.39245	1.2	0.31905	N	0.61538	B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.06786	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.001;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.17098	0.002;0.007;0.007;0.007;0.017;0.017;0.017;0.017;0.002;0.017;0.011;0.007;0.002;0.003	T	0.25572	-1.0128	10	0.31617	T	0.26	-19.1238	1.5034	0.02481	0.2717:0.1436:0.4381:0.1466	.	308;308;277;277;308;277;307;276;307;307;276;276;277;276	O75923-8;O75923-13;O75923-10;O75923-9;O75923-11;O75923-12;O75923-5;O75923-6;O75923-2;O75923-7;O75923-4;O75923-3;O75923-14;O75923	.;.;.;.;.;.;.;.;.;.;.;.;.;DYSF_HUMAN	D	307;307;307;276;276;308;277;277;277;308;308	ENSP00000407046:E307D;ENSP00000387137:E307D;ENSP00000386547:E307D;ENSP00000398305:E276D;ENSP00000258104:E276D;ENSP00000386683:E308D;ENSP00000377678:E277D;ENSP00000386285:E277D;ENSP00000386512:E277D;ENSP00000386881:E308D;ENSP00000386617:E308D	ENSP00000258104:E276D	E	+	3	2	DYSF	71596853	0.995000	0.38212	0.920000	0.36463	0.279000	0.26890	0.286000	0.18902	0.081000	0.16988	-0.275000	0.10095	GAG	.	.		0.502	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494		C	71743345	G	C	71743345	3	2	301	1	0	0	0	0	1	0	0	0	4861	962	34	4	1050	4	DYSF	2	71743345	Missense_Mutation	SNP	G	TCGA-G3-AAV5-01A-11D-A36X-10		71743345	171456028	10	43462										
IRS1	3667	hgsc.bcm.edu	37	chr2	227660609	227660609	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	cctgccaggctgccctccggCccggccccaggtccatcttc	10	21	1	0			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr2:227660609C>T	ENST00000305123.5	-	1	3866	c.2846G>A	c.(2845-2847)gGc>gAc	p.G949D	IRS1_ENST00000498335.1_5'Flank	NM_005544.2	NP_005535.1	P35568	IRS1_HUMAN	insulin receptor substrate 1	949					cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid catabolic process (GO:0016042)|mammary gland development (GO:0030879)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein kinase B signaling (GO:0043491)|protein localization to nucleus (GO:0034504)|regulation of gene expression (GO:0010468)|response to insulin (GO:0032868)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)	caveola (GO:0005901)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|insulin receptor complex (GO:0005899)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein kinase C binding (GO:0005080)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)			autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(10)|lung(33)|ovary(6)|pancreas(1)|prostate(1)|urinary_tract(2)	69		Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23)		Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137)		TGCCCTCCGGCCCGGCCCCAG	0.652																																					p.G949D		Atlas-SNP	.											.	IRS1	141	.	0			c.G2846A						.						46	53	51					2																	227660609		2203	4300	6503	SO:0001583	missense	3667	exon1			CTCCGGCCCGGCC		CCDS2463.1	2q36	2013-01-10			ENSG00000169047	ENSG00000169047		"Pleckstrin homology (PH) domain containing"	6125	protein-coding gene	gene with protein product		147545				1648180	Standard	NM_005544		Approved	HIRS-1	uc002voh.4	P35568	OTTHUMG00000133179	ENST00000305123.5:c.2846G>A	chr2.hg19:g.227660609C>T	ENSP00000304895:p.Gly949Asp	102.0	0.0		96.0	39.0	NM_005544		Missense_Mutation	SNP	ENST00000305123.5	hg19	CCDS2463.1	.	.	.	.	.	.	.	.	.	.	C	10.64	1.406880	0.25378	.	.	ENSG00000169047	ENST00000305123	T	0.56275	0.47	5.04	4.13	0.48395	.	0.458108	0.19622	N	0.109883	T	0.28599	0.0708	N	0.08118	0	0.33660	D	0.609567	B	0.17038	0.02	B	0.10450	0.005	T	0.28364	-1.0046	10	0.12103	T	0.63	-21.179	11.0555	0.47915	0.0:0.7412:0.2588:0.0	.	949	P35568	IRS1_HUMAN	D	949	ENSP00000304895:G949D	ENSP00000304895:G949D	G	-	2	0	IRS1	227368853	0.978000	0.34361	0.998000	0.56505	0.858000	0.48976	1.423000	0.34837	2.613000	0.88420	0.655000	0.94253	GGC	.	.		0.652	IRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256886.3	NM_005544		T	227660609	C	T	227660609	3	4	301	1	0	0	0	0	1	0	0	0	7849	739	26	3	886	3	IRS1	2	227660609	Missense_Mutation	SNP	C	TCGA-G3-AAV5-01A-11D-A36X-10	155917264	227660609	15538764	11	43463										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266097	41266097	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	ggcagcaacagtcttacctgGactctggaatccattctggt	10	11	3	0	rs28931588|rs121913416|rs121913417		TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr3:41266097G>A	ENST00000349496.5	+	3	374	c.94G>A	c.(94-96)Gac>Aac	p.D32N	CTNNB1_ENST00000396185.3_Missense_Mutation_p.D32N|CTNNB1_ENST00000396183.3_Missense_Mutation_p.D32N|CTNNB1_ENST00000405570.1_Missense_Mutation_p.D32N|CTNNB1_ENST00000453024.1_Missense_Mutation_p.D25N	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	32			D -> A (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|D -> G (in PTR and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629}.|D -> Y (in PTR, hepatoblastoma and hepatocellular carcinoma; dbSNP:rs28931588). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:11703283, ECO:0000269|PubMed:9927029}.|Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.D32Y(128)|p.D32N(82)|p.A5_A80del(53)|p.D32H(40)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.WQQQSYLD25?(5)|p.W25_D32del(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.S29_H36del(1)|p.D32del(1)|p.M14_S45del(1)|p.Q28_D32>H(1)|p.Q28fs*20(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.D32fs*9(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GTCTTACCTGGACTCTGGAAT	0.478	D32N(KE39_STOMACH)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.D32N	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,0,2	CTNNB1	4904	.	397	Substitution - Missense(250)|Deletion - In frame(120)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)|Complex - frameshift(1)	liver(155)|central_nervous_system(55)|endometrium(40)|stomach(36)|pancreas(28)|large_intestine(22)|pituitary(22)|skin(11)|ovary(9)|soft_tissue(4)|prostate(4)|small_intestine(2)|haematopoietic_and_lymphoid_tissue(2)|bone(2)|adrenal_gland(1)|biliary_tract(1)|urinary_tract(1)|lung(1)|NS(1)	c.G94A						.						92	77	82					3																	41266097		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	TACCTGGACTCTG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.94G>A	chr3.hg19:g.41266097G>A	ENSP00000344456:p.Asp32Asn	160.0	0.0		172.0	76.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	G	30	5.054970	0.93793	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.49432	0.78;0.78;0.78;0.78;0.78;0.78;0.78;0.78;0.78	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.71567	0.3355	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.72982	0.979	T	0.73824	-0.3861	10	0.87932	D	0	0.3843	19.9596	0.97236	0.0:0.0:1.0:0.0	.	32	P35222	CTNB1_HUMAN	N	25;32;32;32;32;25;32;32;32	ENSP00000400508:D25N;ENSP00000385604:D32N;ENSP00000412219:D32N;ENSP00000379486:D32N;ENSP00000344456:D32N;ENSP00000411226:D25N;ENSP00000379488:D32N;ENSP00000409302:D32N;ENSP00000401599:D32N	ENSP00000344456:D32N	D	+	1	0	CTNNB1	41241101	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.726000	0.93360	0.655000	0.94253	GAC	.	.		0.478	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		A	41266097	G	A	41266097	3	1	301	1	0	0	0	0	1	0	0	0	4018	1174	41	3	100	3	CTNNB1	3	41266097	Missense_Mutation	SNP	G	TCGA-G3-AAV5-01A-11D-A36X-10		41266097	156756333	12	43464										
RBM6	10180	hgsc.bcm.edu	37	chr3	50091780	50091780	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	ccttacagtgtaaggcaaacAttggtgggcaccgatcttcc	10	11	1	0			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr3:50091780A>G	ENST00000266022.4	+	8	1904	c.1645A>G	c.(1645-1647)Att>Gtt	p.I549V	RBM6_ENST00000539992.1_5'UTR|RBM6_ENST00000422955.1_Missense_Mutation_p.I27V|RBM6_ENST00000441115.1_3'UTR|RBM6_ENST00000442092.1_Missense_Mutation_p.I27V|RBM6_ENST00000443081.1_Missense_Mutation_p.I417V	NM_005777.2	NP_005768.1	P78332	RBM6_HUMAN	RNA binding motif protein 6	549					RNA processing (GO:0006396)	nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(3)|prostate(1)|skin(4)|urinary_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)		TAAGGCAAACATTGGTGGGCA	0.378																																					p.I549V		Atlas-SNP	.											.	RBM6	85	.	0			c.A1645G						.						198	204	202					3																	50091780		2203	4300	6503	SO:0001583	missense	10180	exon8			GCAAACATTGGTG	AF069517	CCDS2809.1, CCDS54586.1	3p21.3	2013-01-28			ENSG00000004534	ENSG00000004534		"RNA binding motif (RRM) containing", "G patch domain containing"	9903	protein-coding gene	gene with protein product		606886				10352938	Standard	NM_001167582		Approved	DEF-3, 3G2, NY-LU-12, g16, DEF3	uc003cyc.3	P78332	OTTHUMG00000156736	ENST00000266022.4:c.1645A>G	chr3.hg19:g.50091780A>G	ENSP00000266022:p.Ile549Val	169.0	0.0		203.0	86.0	NM_005777	O60549|O75524|Q86SS3	Missense_Mutation	SNP	ENST00000266022.4	hg19	CCDS2809.1	.	.	.	.	.	.	.	.	.	.	A	0.523	-0.861118	0.02610	.	.	ENSG00000004534	ENST00000442092;ENST00000266022;ENST00000443081;ENST00000422955;ENST00000446471	T;T;T;T;D	0.83673	1.01;1.61;1.62;1.01;-1.75	5.42	4.25	0.50352	.	0.590922	0.17228	N	0.182053	T	0.59432	0.2193	N	0.02539	-0.55	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.49418	-0.8942	9	.	.	.	0.5443	8.9942	0.36041	0.9113:0.0:0.0887:0.0	.	417;549	E9PGM9;P78332	.;RBM6_HUMAN	V	27;549;417;27;27	ENSP00000393530:I27V;ENSP00000266022:I549V;ENSP00000396466:I417V;ENSP00000392939:I27V;ENSP00000394336:I27V	.	I	+	1	0	RBM6	50066784	0.862000	0.29867	0.893000	0.35052	0.563000	0.35712	3.749000	0.55150	0.878000	0.35920	0.528000	0.53228	ATT	.	.		0.378	RBM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345528.4	NM_005777		G	50091780	A	G	50091780	3	3	301	1	0	0	0	0	1	0	0	0	13159	217	8	2	1671	2	RBM6	3	50091780	Missense_Mutation	SNP	A	TCGA-G3-AAV5-01A-11D-A36X-10	8825683	50091780	147930650	13	43465										
MUC4	4585	hgsc.bcm.edu	37	chr3	195477874	195477874	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	cgcctccaccaccgcggccaGcagctggttgttcaggaagt	12	15	1	0	rs542498469		TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr3:195477874G>A	ENST00000346145.4	-	22	3088	c.3049C>T	c.(3049-3051)Ctg>Ttg	p.L1017L	MUC4_ENST00000475231.1_Silent_p.L5201L|MUC4_ENST00000463781.3_Silent_p.L5253L|MUC4_ENST00000349607.4_Silent_p.L966L	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	2010	Repeat.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACCGCGGCCAGCAGCTGGTTG	0.632													.|||	1	0.000199681	0	0.0014	5008	,	,		11533	0		0	False		,,,				2504	0				p.L5253L		Atlas-SNP	.											.	MUC4	1505	.	0			c.C15757T						.						54	51	52					3																	195477874		2203	4300	6503	SO:0001819	synonymous_variant	4585	exon23			CGGCCAGCAGCTG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"Mucins"	7514	protein-coding gene	gene with protein product		158372	"mucin 4, tracheobronchial"			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000346145.4:c.3049C>T	chr3.hg19:g.195477874G>A		102.0	0.0		128.0	57.0	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000346145.4	hg19	CCDS3310.1																																																																																			.	.		0.632	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406		A	195477874	G	A	195477874	2	1	301	1	0	0	0	0	0	0	0	1	9987	962	34	3		3	MUC4	3	195477874	Silent	SNP	G	TCGA-G3-AAV5-01A-11D-A36X-10	145386094	195477874	2544556	14	43466										
TAPT1	202018	hgsc.bcm.edu	37	chr4	16204107	16204107	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	taagccatagcaaggcaaagTgaggagcctgaatagtgcca	12	8	0	2			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr4:16204107T>C	ENST00000405303.2	-	3	510	c.427A>G	c.(427-429)Act>Gct	p.T143A	TAPT1_ENST00000399920.3_Missense_Mutation_p.T32A|TAPT1_ENST00000508888.1_5'UTR	NM_153365.2	NP_699196.2	Q6NXT6	TAPT1_HUMAN	transmembrane anterior posterior transformation 1	143					embryonic skeletal system development (GO:0048706)|G-protein coupled receptor signaling pathway (GO:0007186)|in utero embryonic development (GO:0001701)|post-embryonic development (GO:0009791)	integral component of membrane (GO:0016021)	growth hormone-releasing hormone receptor activity (GO:0016520)			NS(1)|breast(2)|cervix(1)|kidney(2)|large_intestine(2)|lung(1)|prostate(1)	10						CAAGGCAAAGTGAGGAGCCTG	0.378																																					p.T143A		Atlas-SNP	.											.	TAPT1	31	.	0			c.A427G						.						39	37	37					4																	16204107		1845	4047	5892	SO:0001583	missense	202018	exon3			GCAAAGTGAGGAG	AK074494	CCDS47030.1	4p15.32	2014-01-28			ENSG00000169762	ENSG00000169762			26887	protein-coding gene	gene with protein product		612758				12477932	Standard	NM_153365		Approved	FLJ90013	uc010ied.1	Q6NXT6	OTTHUMG00000160177	ENST00000405303.2:c.427A>G	chr4.hg19:g.16204107T>C	ENSP00000385347:p.Thr143Ala	358.0	1.0		440.0	168.0	NM_153365	Q8N2S3|Q9NZK9	Missense_Mutation	SNP	ENST00000405303.2	hg19	CCDS47030.1	.	.	.	.	.	.	.	.	.	.	T	12.87	2.067615	0.36470	.	.	ENSG00000169762	ENST00000405303;ENST00000542770;ENST00000399920	T;T	0.33216	1.42;1.45	5.07	3.88	0.44766	.	0.046390	0.85682	N	0.000000	T	0.25195	0.0612	L	0.53249	1.67	0.80722	D	1	B	0.15141	0.012	B	0.12156	0.007	T	0.05468	-1.0883	10	0.10636	T	0.68	-29.6464	9.7879	0.40688	0.0:0.0863:0.0:0.9137	.	143	Q6NXT6	TAPT1_HUMAN	A	143;143;32	ENSP00000385347:T143A;ENSP00000382803:T32A	ENSP00000382803:T32A	T	-	1	0	TAPT1	15813205	1.000000	0.71417	0.988000	0.46212	0.997000	0.91878	5.900000	0.69853	0.867000	0.35654	0.533000	0.62120	ACT	.	.		0.378	TAPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359568.1	NM_153365		C	16204107	T	C	16204107	3	2	301	1	0	0	0	0	1	0	0	0	15569	1696	59	2	1324	2	TAPT1	4	16204107	Missense_Mutation	SNP	T	TCGA-G3-AAV5-01A-11D-A36X-10		16204107	174950169	15	43467										
GPR125	166647	hgsc.bcm.edu	37	chr4	22390453	22390453	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	tccttaagctcatatttgcgCtcagggtgtcttttcaactg	8	10	4	0			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr4:22390453C>T	ENST00000334304.5	-	19	3110	c.2841G>A	c.(2839-2841)gaG>gaA	p.E947E	GPR125_ENST00000282943.5_5'UTR	NM_145290.3	NP_660333.2	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125	947					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(33)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	56		Breast(46;0.198)				CATATTTGCGCTCAGGGTGTC	0.443																																					p.E947E		Atlas-SNP	.											.	GPR125	118	.	0			c.G2841A						.						76	79	78					4																	22390453		2203	4300	6503	SO:0001819	synonymous_variant	166647	exon19			TTTGCGCTCAGGG	AK095866	CCDS33964.1	4p15.31	2014-08-08			ENSG00000152990	ENSG00000152990		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / I-set domain containing"	13839	protein-coding gene	gene with protein product		612303				12565841	Standard	NM_145290		Approved	FLJ38547, PGR21	uc003gqm.2	Q8IWK6	OTTHUMG00000160926	ENST00000334304.5:c.2841G>A	chr4.hg19:g.22390453C>T		107.0	0.0		98.0	37.0	NM_145290	Q6UXK9|Q86SQ5|Q8TC55	Silent	SNP	ENST00000334304.5	hg19	CCDS33964.1																																																																																			.	.		0.443	GPR125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362960.3			T	22390453	C	T	22390453	2	4	301	1	0	0	0	0	0	0	0	1	6647	796	28	3		3	GPR125	4	22390453	Silent	SNP	C	TCGA-G3-AAV5-01A-11D-A36X-10	6186346	22390453	168763823	16	43468										
ALB	213	hgsc.bcm.edu	37	chr4	74274517	74274518	+	Frame_Shift_Ins	INS	-	-	A													0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	acaatgaagagacatttttgINSaaaaagtaagtaatcagatg							TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr4:74274517_74274518insA	ENST00000295897.4	+	4	566_567	c.477_478insA	c.(478-480)aaafs	p.K160fs	ALB_ENST00000509063.1_Frame_Shift_Ins_p.K160fs|ALB_ENST00000505649.1_3'UTR|ALB_ENST00000415165.2_Intron|ALB_ENST00000503124.1_Intron|ALB_ENST00000401494.3_Intron	NM_000477.5	NP_000468.1	Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			AGACATTTTTGAAAAAGTAAGT	0.351																																					p.L159fs		Atlas-INDEL	.											.	ALB	132	.	0			c.477_478insA						.																																			SO:0001589	frameshift_variant	213	exon4			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000295897.4:c.483dupA	chr4.hg19:g.74274522_74274522dupA	ENSP00000295897:p.Lys160fs	83.0	0.0		98.0	34.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Frame_Shift_Ins	INS	ENST00000295897.4	hg19	CCDS3555.1																																																																																			.	.		0.351	ALB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252173.3	NM_000477		A	74274518	-	A	74274517	7	5	301	1	0	1	1	0	0	0	0	0	486	1281	45	0	491	0	ALB	4	74274517	Frame_Shift_Ins	INS	-	TCGA-G3-AAV5-01A-11D-A36X-10	51884064	74274517	116879759	17	43469										
ALB	213	hgsc.bcm.edu	37	chr4	74283386	74283387	+	Splice_Site	DEL	TG	TG	-													0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	atgccctgtgcagaagactaTgtgagtctttaaaaaaatat					rs78527483		TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr4:74283386_74283387delTG	ENST00000503124.1	+	9	1185	c.978delTG	c.(976-978)tat>ta	p.Y326fs	ALB_ENST00000509063.1_Splice_Site_p.Y476fs|ALB_ENST00000505649.1_Intron|ALB_ENST00000415165.2_Splice_Site_p.Y284fs|ALB_ENST00000295897.4_Splice_Site_p.Y476fs|ALB_ENST00000401494.3_Splice_Site_p.Y361fs			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CAGAAGACTATGTGAGTCttta	0.332																																					p.476_476del		Atlas-INDEL	.											.	ALB	132	.	0			c.1427_1428del						.																																			SO:0001630	splice_region_variant	213	exon11			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.978+1TG>-	chr4.hg19:g.74283388_74283389delTG		137.0	0.0		157.0	62.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Frame_Shift_Del	DEL	ENST00000503124.1	hg19																																																																																				.	.		0.332	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477	Frame_Shift_Del	-	74283387	TG	-	74283386	8	5	301	1	0	1	0	1	0	0	1	0	486	1478	51	0	1470	0	ALB	4	74283386	Splice_Site	DEL	TG	TCGA-G3-AAV5-01A-11D-A36X-10	8869	74283386	116870890	18	43470										
AFM	173	hgsc.bcm.edu	37	chr4	74361077	74361078	+	Frame_Shift_Ins	INS	-	-	GA													0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	taccagagcttttaagaattINSgttcaaatatacaaagatct							TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr4:74361077_74361078insGA	ENST00000226355.3	+	9	1212_1213	c.1119_1120insGA	c.(1120-1122)gttfs	p.V374fs		NM_001133.2	NP_001124.1	P43652	AFAM_HUMAN	afamin	374	Albumin 2. {ECO:0000255|PROSITE- ProRule:PRU00769}.				vitamin transport (GO:0051180)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	vitamin E binding (GO:0008431)			breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	Breast(15;0.00102)		Epithelial(6;5.69e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000324)|all cancers(17;0.000555)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TTTTAAGAATTGTTCAAATATA	0.361																																					p.I373fs		Atlas-INDEL	.											.	AFM	101	.	0			c.1119_1120insGA						.																																			SO:0001589	frameshift_variant	173	exon9			.	L32140	CCDS3557.1	4q13.3	2008-06-11			ENSG00000079557	ENSG00000079557			316	protein-coding gene	gene with protein product		104145				7517938	Standard	NM_001133		Approved	ALB2, ALBA	uc003hhb.3	P43652	OTTHUMG00000130004	Exception_encountered	chr4.hg19:g.74361077_74361078insGA	ENSP00000226355:p.Val374fs	103.0	0.0		107.0	37.0	NM_001133	A8K3E1|Q32MR3|Q4W5C5	Frame_Shift_Ins	INS	ENST00000226355.3	hg19	CCDS3557.1																																																																																			.	.		0.361	AFM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252275.2			GA	74361078	-	GA	74361077	7	5	301	1	0	1	1	0	0	0	0	0	361	1800	63	0	1153	0	AFM	4	74361077	Frame_Shift_Ins	INS	-	TCGA-G3-AAV5-01A-11D-A36X-10	77691	74361077	116793199	19	43471										
SCAND3	114821	hgsc.bcm.edu	37	chr6	28540012	28540013	+	Frame_Shift_Ins	INS	-	-	G													0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	cctgtagagttacagttaaaINStttaagttatcttttgatga							TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr6:28540012_28540013insG	ENST00000452236.2	-	4	4270_4271	c.3653_3654insC	c.(3652-3654)aatfs	p.N1218fs		NM_052923.1	NP_443155.1														NS(3)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(14)|liver(1)|lung(29)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(3)	71						ttacagttaaatttaagttatc	0.317																																					p.N1218fs		Atlas-INDEL	.											.	SCAND3	156	.	0			c.3654_3655insC						.																																			SO:0001589	frameshift_variant	114821	exon4			.																												ENST00000452236.2:c.3653_3654insC	chr6.hg19:g.28540012_28540013insG	ENSP00000395259:p.Asn1218fs	129.0	0.0		180.0	11.0	NM_052923		Frame_Shift_Ins	INS	ENST00000452236.2	hg19	CCDS34355.1																																																																																			.	.		0.317	SCAND3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000043551.3			G	28540013	-	G	28540012	7	5	301	1	0	1	1	0	0	0	0	0	13891	98	4	0	327	0	SCAND3	6	28540012	Frame_Shift_Ins	INS	-	TCGA-G3-AAV5-01A-11D-A36X-10		28540012	142575055	20	43472										
TAF11	6882	hgsc.bcm.edu	37	chr6	34846457	34846457	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	tccctcatatgtttgggttgTagtggtggcatttctcccca	10	10	2	0			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr6:34846457T>C	ENST00000361288.4	-	5	677	c.546A>G	c.(544-546)ctA>ctG	p.L182L	TAF11_ENST00000420584.2_Missense_Mutation_p.Y150C|UHRF1BP1_ENST00000452449.2_Intron	NM_005643.3	NP_005634.1	Q15544	TAF11_HUMAN	TAF11 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 28kDa	182					gene expression (GO:0010467)|positive regulation by host of viral transcription (GO:0043923)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|protein N-terminus binding (GO:0047485)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|vitamin D receptor binding (GO:0042809)			endometrium(2)|kidney(1)|large_intestine(2)|lung(1)	6						GTTTGGGTTGTAGTGGTGGCA	0.398																																					p.Y150C		Atlas-SNP	.											.	TAF11	15	.	0			c.A449G						.						198	175	183					6																	34846457		2203	4300	6503	SO:0001819	synonymous_variant	6882	exon4			GGGTTGTAGTGGT	X83928	CCDS4797.1, CCDS59014.1	6p21	2008-02-05	2002-08-29	2001-12-07	ENSG00000064995	ENSG00000064995			11544	protein-coding gene	gene with protein product		600772	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, I, 28kD"	TAF2I		7729427, 8820923	Standard	NM_005643		Approved	TAFII28	uc003ojw.2	Q15544	OTTHUMG00000014556	ENST00000361288.4:c.546A>G	chr6.hg19:g.34846457T>C		73.0	0.0		74.0	27.0	NM_001270488	B2R8R3|B4DY18|Q9UHS0	Missense_Mutation	SNP	ENST00000361288.4	hg19	CCDS4797.1	.	.	.	.	.	.	.	.	.	.	T	12.67	2.008001	0.35415	.	.	ENSG00000064995	ENST00000420584	T	0.49720	0.77	5.46	-9.19	0.00685	.	.	.	.	.	T	0.12817	0.0311	.	.	.	0.24960	N	0.991735	B	0.02656	0.0	B	0.01281	0.0	T	0.31586	-0.9938	8	0.44086	T	0.13	.	10.9019	0.47056	0.0:0.4852:0.2847:0.2301	.	150	B4DY18	.	C	150	ENSP00000408121:Y150C	ENSP00000408121:Y150C	Y	-	2	0	TAF11	34954435	0.007000	0.16637	0.210000	0.23637	0.854000	0.48673	-1.240000	0.02914	-1.528000	0.01756	-1.209000	0.01634	TAC	.	.		0.398	TAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040259.1	NM_005643		C	34846457	T	C	34846457	2	2	301	1	0	0	0	0	0	0	0	1	15530	1625	57	2		2	TAF11	6	34846457	Silent	SNP	T	TCGA-G3-AAV5-01A-11D-A36X-10	6306445	34846457	136268610	21	43473										
PCMT1	5110	hgsc.bcm.edu	37	chr6	150114716	150114716	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	tggaaaagtcataggaattgAtcacattaaagagctagtag	10	4	2	2			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr6:150114716A>G	ENST00000367380.5	+	5	536	c.329A>G	c.(328-330)gAt>gGt	p.D110G	PCMT1_ENST00000367378.1_Missense_Mutation_p.D168G|PCMT1_ENST00000367384.2_Missense_Mutation_p.D168G|PCMT1_ENST00000544496.1_Missense_Mutation_p.D75G|RP11-350J20.5_ENST00000455607.2_RNA|PCMT1_ENST00000464889.1_Missense_Mutation_p.D168G	NM_001252049.1|NM_001252050.1|NM_001252051.1|NM_001252052.1|NM_005389.2	NP_001238978.1|NP_001238979.1|NP_001238980.1|NP_001238981.1|NP_005380.2	P22061	PIMT_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase	110					protein methylation (GO:0006479)|protein repair (GO:0030091)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)			kidney(1)|large_intestine(2)|lung(4)|ovary(1)	8		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.221)	OV - Ovarian serous cystadenocarcinoma(155;5.63e-13)|GBM - Glioblastoma multiforme(68;0.207)		ATAGGAATTGATCACATTAAA	0.363																																					p.D168G		Atlas-SNP	.											.	PCMT1	27	.	0			c.A503G						.						71	74	73					6																	150114716		2203	4299	6502	SO:0001583	missense	5110	exon5			GAATTGATCACAT		CCDS5219.1, CCDS5219.2, CCDS59041.1, CCDS75533.1, CCDS75534.1	6q22.3-q24	2008-02-05			ENSG00000120265	ENSG00000120265	2.1.1.77		8728	protein-coding gene	gene with protein product		176851				1478665, 10343128	Standard	NM_005389		Approved		uc003qne.3	P22061	OTTHUMG00000015794	ENST00000367380.5:c.329A>G	chr6.hg19:g.150114716A>G	ENSP00000356350:p.Asp110Gly	199.0	0.0		227.0	77.0	NM_005389	A8K109|J3KP72|Q14661|Q16556|Q5VYC1|Q5VYC2|Q93061|Q96II9|Q99625|Q9BQV7|Q9BQV8|Q9NP03	Missense_Mutation	SNP	ENST00000367380.5	hg19		.	.	.	.	.	.	.	.	.	.	A	28.5	4.927466	0.92389	.	.	ENSG00000120265	ENST00000367384;ENST00000367378;ENST00000464889;ENST00000367380;ENST00000544496;ENST00000495487	T;T;T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19;0.85;1.03	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	D	0.84047	0.5386	H	0.96604	3.85	0.80722	D	1	P;D;D	0.89917	0.92;1.0;0.992	P;D;P	0.76071	0.678;0.987;0.905	D	0.89692	0.3898	10	0.87932	D	0	-16.0912	16.0958	0.81123	1.0:0.0:0.0:0.0	.	75;110;110	B7Z972;P22061-2;P22061	.;.;PIMT_HUMAN	G	168;168;168;110;75;79	ENSP00000356354:D168G;ENSP00000356348:D168G;ENSP00000420813:D168G;ENSP00000356350:D110G;ENSP00000438247:D75G;ENSP00000418881:D79G	ENSP00000356348:D168G	D	+	2	0	PCMT1	150156409	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.175000	0.94831	2.203000	0.70933	0.482000	0.46254	GAT	.	.		0.363	PCMT1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				G	150114716	A	G	150114716	3	3	301	1	0	0	0	0	1	0	0	0	11594	333	12	2	521	2	PCMT1	6	150114716	Missense_Mutation	SNP	A	TCGA-G3-AAV5-01A-11D-A36X-10	115268259	150114716	21000351	22	43474										
C7orf30	115416	hgsc.bcm.edu	37	chr7	23338987	23338987	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	ctgctatggggccgggcggcCgtgtggcgcggctgctcgcc	19	14	0	0	rs375849242	byFrequency	TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr7:23338987C>T	ENST00000466681.1	+	1	169	c.16C>T	c.(16-18)Cgt>Tgt	p.R6C	MALSU1_ENST00000479974.1_Intron	NM_138446.1	NP_612455.1	Q96EH3	MASU1_HUMAN	mitochondrial assembly of ribosomal large subunit 1	6					negative regulation of mitochondrial translation (GO:0070130)|ribosomal large subunit biogenesis (GO:0042273)	mitochondrion (GO:0005739)											GCCGGGCGGCCGTGTGGCGCG	0.716													C|||	3	0.000599042	0.0023	0	5008	,	,		14891	0		0	False		,,,				2504	0				p.R6C		Atlas-SNP	.											.	.	.	.	0			c.C16T						.	C	CYS/ARG	2,3838		0,2,1918	6	8	7		16	-0.2	0	7		7	0,8006		0,0,4003	no	missense	C7orf30	NM_138446.1	180	0,2,5921	TT,TC,CC		0.0,0.0521,0.0169	benign	6/235	23338987	2,11844	1920	4003	5923	SO:0001583	missense	115416	exon1			GGCGGCCGTGTGG	BC012331	CCDS5381.1	7p15.3	2013-05-24	2012-02-20	2012-02-20	ENSG00000156928	ENSG00000156928			21721	protein-coding gene	gene with protein product		614624	"chromosome 7 open reading frame 30"	C7orf30		22238376, 22238375	Standard	NM_138446		Approved	mtRsfA	uc003swd.1	Q96EH3	OTTHUMG00000128443	ENST00000466681.1:c.16C>T	chr7.hg19:g.23338987C>T	ENSP00000419370:p.Arg6Cys	79.0	0.0		123.0	32.0	NM_138446	A4D154	Missense_Mutation	SNP	ENST00000466681.1	hg19	CCDS5381.1	.	.	.	.	.	.	.	.	.	.	C	11.22	1.575492	0.28092	5.21E-4	0.0	ENSG00000156928	ENST00000466681	.	.	.	3.57	-0.161	0.13371	.	1.153800	0.06419	N	0.722092	T	0.13798	0.0334	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.23976	-1.0173	9	0.25751	T	0.34	-0.0559	5.8948	0.18933	0.0:0.3614:0.0:0.6386	.	6	Q96EH3	CG030_HUMAN	C	6	.	ENSP00000419370:R6C	R	+	1	0	C7orf30	23305512	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.227000	0.02950	-0.025000	0.13918	-0.238000	0.12139	CGT	.	.		0.716	MALSU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250241.2	NM_138446		T	23338987	C	T	23338987	3	4	301	1	0	0	0	0	1	0	0	0	2388	652	23	1	18	1	C7orf30	7	23338987	Missense_Mutation	SNP	C	TCGA-G3-AAV5-01A-11D-A36X-10		23338987	135799676	23	43475										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48431534	48431534	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	gcagatccatgttgacggggCtccaccctcccacttctgga	10	15	1	2			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr7:48431534C>T	ENST00000435803.1	+	38	11695	c.11671C>T	c.(11671-11673)Ctc>Ttc	p.L3891F		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	3891	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						GTTGACGGGGCTCCACCCTCC	0.532																																					p.L3891F		Atlas-SNP	.											.	ABCA13	1192	.	0			c.C11671T						.						74	74	74					7																	48431534		2014	4167	6181	SO:0001583	missense	154664	exon38			ACGGGGCTCCACC	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.11671C>T	chr7.hg19:g.48431534C>T	ENSP00000411096:p.Leu3891Phe	99.0	0.0		166.0	33.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	C	13.00	2.106013	0.37145	.	.	ENSG00000179869	ENST00000435803	D	0.94862	-3.54	4.95	4.06	0.47325	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.31922	U	0.006851	D	0.95658	0.8588	L	0.53729	1.69	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.95304	0.8406	10	0.72032	D	0.01	.	10.6604	0.45698	0.0:0.907:0.0:0.093	.	1593;3891	Q86UQ4-3;Q86UQ4	.;ABCAD_HUMAN	F	3891	ENSP00000411096:L3891F	ENSP00000411096:L3891F	L	+	1	0	ABCA13	48402080	0.988000	0.35896	0.058000	0.19502	0.140000	0.21249	2.848000	0.48278	2.296000	0.77279	0.467000	0.42956	CTC	.	.		0.532	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		T	48431534	C	T	48431534	3	4	301	1	0	0	0	0	1	0	0	0	31	797	28	3	11650	3	ABCA13	7	48431534	Missense_Mutation	SNP	C	TCGA-G3-AAV5-01A-11D-A36X-10	25092547	48431534	110707129	24	43476										
GPC2	221914	hgsc.bcm.edu	37	chr7	99768966	99768966	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	cggagctgtagccgacgccgCcgtgtcgggacatcggggcc	17	14	0	0			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr7:99768966C>T	ENST00000292377.2	-	9	1571	c.1404G>A	c.(1402-1404)cgG>cgA	p.R468R	GAL3ST4_ENST00000423751.1_5'Flank|GAL3ST4_ENST00000360039.4_5'Flank|GPC2_ENST00000471050.1_5'UTR	NM_152742.1	NP_689955.1	Q8N158	GPC2_HUMAN	glypican 2	468					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|neuron differentiation (GO:0030182)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|smoothened signaling pathway (GO:0007224)	anchored component of membrane (GO:0031225)|endoplasmic reticulum (GO:0005783)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|pancreas(1)|skin(3)	18	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GCCGACGCCGCCGTGTCGGGA	0.711																																					p.R468R		Atlas-SNP	.											.	GPC2	49	.	0			c.G1404A						.						7	9	8					7																	99768966		2082	4132	6214	SO:0001819	synonymous_variant	221914	exon9			ACGCCGCCGTGTC	BX375153	CCDS5689.1	7q22.1	2007-02-16	2007-02-15		ENSG00000213420	ENSG00000213420		"Proteoglycans / Cell Surface : Glypicans"	4450	protein-coding gene	gene with protein product	"glypican proteoglycan 2, cerebroglycan proteoglycan"		"glypican 2 (cerebroglycan)"			8294498	Standard	NM_152742		Approved	cerebroglycan, FLJ38962, DKFZp547M109	uc003utv.3	Q8N158	OTTHUMG00000154894	ENST00000292377.2:c.1404G>A	chr7.hg19:g.99768966C>T		105.0	0.0		223.0	66.0	NM_152742	A4D2A7	Silent	SNP	ENST00000292377.2	hg19	CCDS5689.1																																																																																			.	.		0.711	GPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337556.1	NM_152742		T	99768966	C	T	99768966	2	4	301	1	0	0	0	0	0	0	0	1	6606	726	26	3		3	GPC2	7	99768966	Silent	SNP	C	TCGA-G3-AAV5-01A-11D-A36X-10	51337432	99768966	59369697	25	43477										
ZNF862	643641	hgsc.bcm.edu	37	chr7	149543298	149543298	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	ggacgagggccagagccatgGcttggcagcgtccagggcca	17	12	0	1			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr7:149543298G>A	ENST00000223210.4	+	3	440	c.195G>A	c.(193-195)tgG>tgA	p.W65*		NM_001099220.1	NP_001092690.1	O60290	ZN862_HUMAN	zinc finger protein 862	65	KRAB 1. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(1)	34						CAGAGCCATGGCTTGGCAGCG	0.567																																					p.W65X		Atlas-SNP	.											.	ZNF862	97	.	0			c.G195A						.						30	33	32					7																	149543298		2015	4185	6200	SO:0001587	stop_gained	643641	exon3			GCCATGGCTTGGC	AB011115	CCDS47741.1	7q36.1	2013-01-11			ENSG00000106479	ENSG00000106479		"Zinc fingers, C2H2-type", "-"	34519	protein-coding gene	gene with protein product							Standard	NM_001099220		Approved		uc010lpn.3	O60290	OTTHUMG00000158093	ENST00000223210.4:c.195G>A	chr7.hg19:g.149543298G>A	ENSP00000223210:p.Trp65*	229.0	0.0		359.0	199.0	NM_001099220	A0AUL8	Nonsense_Mutation	SNP	ENST00000223210.4	hg19	CCDS47741.1	.	.	.	.	.	.	.	.	.	.	G	37	6.512028	0.97624	.	.	ENSG00000106479	ENST00000223210	.	.	.	4.78	4.78	0.61160	.	0.000000	0.45867	D	0.000322	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-33.042	13.3385	0.60530	0.0:0.0:1.0:0.0	.	.	.	.	X	65	.	ENSP00000223210:W65X	W	+	3	0	ZNF862	149174231	0.997000	0.39634	0.970000	0.41538	0.910000	0.53928	3.992000	0.56980	2.192000	0.70111	0.655000	0.94253	TGG	.	.		0.567	ZNF862-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350165.1	NM_001099220		A	149543298	G	A	149543298	4	1	301	1	0	0	0	0	0	1	0	0	18210	1212	42	3	205	3	ZNF862	7	149543298	Nonsense_Mutation	SNP	G	TCGA-G3-AAV5-01A-11D-A36X-10	49774332	149543298	9595365	26	43478										
EN2	2020	hgsc.bcm.edu	37	chr7	155251300	155251300	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	ttcatcgacaacatcctgcgGcccgagttcggccggcgaaa	11	14	1	0			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr7:155251300G>A	ENST00000297375.4	+	1	477	c.228G>A	c.(226-228)cgG>cgA	p.R76R	AC008060.8_ENST00000419225.1_lincRNA	NM_001427.3	NP_001418.2	P19622	HME2_HUMAN	engrailed homeobox 2	76					hindbrain development (GO:0030902)|midbrain development (GO:0030901)|multicellular organismal development (GO:0007275)|neuron development (GO:0048666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|large_intestine(1)|lung(2)	4	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		ACATCCTGCGGCCCGAGTTCG	0.746																																					p.R76R		Atlas-SNP	.											.	EN2	14	.	0			c.G228A						.						8	6	7					7																	155251300		2007	3913	5920	SO:0001819	synonymous_variant	2020	exon1			CCTGCGGCCCGAG		CCDS5940.1	7q36.2	2011-06-20	2007-02-15		ENSG00000164778	ENSG00000164778		"Homeoboxes / ANTP class : NKL subclass"	3343	protein-coding gene	gene with protein product		131310					Standard	NM_001427		Approved		uc003wmb.3	P19622	OTTHUMG00000151354	ENST00000297375.4:c.228G>A	chr7.hg19:g.155251300G>A		82.0	0.0		70.0	38.0	NM_001427	A4D252|Q549U3|Q9UD58	Silent	SNP	ENST00000297375.4	hg19	CCDS5940.1																																																																																			.	.		0.746	EN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322337.1	NM_001427		A	155251300	G	A	155251300	2	1	301	1	0	0	0	0	0	0	0	1	5112	1190	42	3		3	EN2	7	155251300	Silent	SNP	G	TCGA-G3-AAV5-01A-11D-A36X-10	5708002	155251300	3887363	27	43479										
TRIB1	10221	hgsc.bcm.edu	37	chr8	126443458	126443458	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	cctagccgagcgcgagcatgTgtcccgggcgctgtgcatcc	14	15	0	0			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr8:126443458T>C	ENST00000311922.3	+	1	896	c.314T>C	c.(313-315)gTg>gCg	p.V105A	TRIB1_ENST00000519576.1_5'Flank|TRIB1_ENST00000520847.1_5'Flank	NM_001282985.1|NM_025195.2	NP_001269914.1|NP_079471.1			tribbles pseudokinase 1											NS(1)|large_intestine(2)|lung(2)|prostate(2)|urinary_tract(1)	8	all_hematologic(1;4.97e-05)|Ovarian(258;0.00167)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)			CGCGAGCATGTGTCCCGGGCG	0.781																																					p.V105A		Atlas-SNP	.											.	TRIB1	73	.	0			c.T314C						.						2	2	2					8																	126443458		1534	3303	4837	SO:0001583	missense	10221	exon1			AGCATGTGTCCCG	AF205437	CCDS6357.1, CCDS64971.1	8q24.13	2013-10-03	2013-10-03			ENSG00000173334			16891	protein-coding gene	gene with protein product		609461	"tribbles homolog 1 (Drosophila)"			9342215, 16715410	Standard	NM_001282985		Approved	C8FW, GIG2, TRB1	uc003yrx.3	Q96RU8		ENST00000311922.3:c.314T>C	chr8.hg19:g.126443458T>C	ENSP00000312150:p.Val105Ala	22.0	0.0		52.0	10.0	NM_025195		Missense_Mutation	SNP	ENST00000311922.3	hg19	CCDS6357.1	.	.	.	.	.	.	.	.	.	.	T	13.88	2.368782	0.42003	.	.	ENSG00000173334	ENST00000311922	D	0.84146	-1.81	3.22	3.22	0.36961	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.30492	U	0.009509	D	0.86268	0.5892	M	0.81341	2.54	0.80722	D	1	B	0.29232	0.238	B	0.37731	0.257	D	0.86597	0.1864	10	0.87932	D	0	-11.7931	9.7899	0.40699	0.0:0.0:0.0:1.0	.	105	Q96RU8	TRIB1_HUMAN	A	105	ENSP00000312150:V105A	ENSP00000312150:V105A	V	+	2	0	TRIB1	126512640	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.614000	0.61183	1.455000	0.47813	0.379000	0.24179	GTG	.	.		0.781	TRIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381430.1	NM_025195		C	126443458	T	C	126443458	3	2	301	1	0	0	0	0	1	0	0	0	16497	1696	59	2	316	2	TRIB1	8	126443458	Missense_Mutation	SNP	T	TCGA-G3-AAV5-01A-11D-A36X-10		126443458	19920564	28	43480										
TG	7038	hgsc.bcm.edu	37	chr8	133899121	133899121	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	ttaacttcagtcaatttttcCagcaacttggtcttgcaagc	6	10	3	0			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr8:133899121C>T	ENST00000220616.4	+	9	1544	c.1504C>T	c.(1504-1506)Cag>Tag	p.Q502*	TG_ENST00000377869.1_Nonsense_Mutation_p.Q502*	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	502					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		TCAATTTTTCCAGCAACTTGG	0.443																																					p.Q502X		Atlas-SNP	.											.	TG	416	.	0			c.C1504T						.						61	63	62					8																	133899121		2203	4300	6503	SO:0001587	stop_gained	7038	exon9			TTTTTCCAGCAAC	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.1504C>T	chr8.hg19:g.133899121C>T	ENSP00000220616:p.Gln502*	126.0	0.0		296.0	68.0	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Nonsense_Mutation	SNP	ENST00000220616.4	hg19	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	C	38	6.916995	0.97932	.	.	ENSG00000042832	ENST00000377869;ENST00000220616;ENST00000535932	.	.	.	5.81	5.81	0.92471	.	0.794825	0.11388	N	0.569117	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	15.5096	0.75769	0.1386:0.8614:0.0:0.0	.	.	.	.	X	502	.	ENSP00000220616:Q502X	Q	+	1	0	TG	133968303	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	1.404000	0.34623	2.752000	0.94435	0.557000	0.71058	CAG	.	.		0.443	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		T	133899121	C	T	133899121	4	4	301	1	0	0	0	0	0	1	0	0	15828	595	21	3	1538	3	TG	8	133899121	Nonsense_Mutation	SNP	C	TCGA-G3-AAV5-01A-11D-A36X-10	7455663	133899121	12464901	29	43481										
EPPK1	83481	hgsc.bcm.edu	37	chr8	144940731	144940732	+	Missense_Mutation	DNP	CC	CC	AG													0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	gggctggtccttggcgggcaCcaggacgcccgcgatgcagc							TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr8:144940731_144940732CC>AG	ENST00000525985.1	-	2	6761_6762	c.6690_6691GG>CT	c.(6688-6693)ctGGtg>ctCTtg	p.V2231L				P58107	EPIPL_HUMAN	epiplakin 1	2231						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)	p.L2230L(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TTGGCGGGCACCAGGACGCCCG	0.683																																					p.V2231L|p.L2230L		Atlas-SNP	.											.|EPPK1,NS,carcinoma,0,1	EPPK1	199	.	1	Substitution - coding silent(1)	kidney(1)	c.G6691T|c.G6690C						.																																			SO:0001583	missense	83481	exon1			CGGGCACCAGGAC|GGGCACCAGGACG	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"epidermal autoantigen 450K"	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.6690_6691delinsAG	chr8.hg19:g.144940731_144940732delinsAG	ENSP00000436337:p.Val2231Leu	45.0|48.0	0.0		109.0|111.0	24.0|23.0	NM_031308	Q76E58|Q9NSU9	Missense_Mutation|Silent	SNP	ENST00000525985.1	hg19																																																																																				.	.		0.683	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		AG	144940732	CC	AG	144940731	3	1	301	1	0	0	0	0	1	0	0	0	5192	507	18	3	575	3	EPPK1	8	144940731	Missense_Mutation	DNP	CC	TCGA-G3-AAV5-01A-11D-A36X-10	11041610	144940731	1423291	30	43482										
PARP10	84875	hgsc.bcm.edu	37	chr8	145057702	145057702	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	gggggctgctccagcagggaGagggttagggcttgccgcag	20	9	0	1			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr8:145057702G>A	ENST00000313028.7	-	8	2149	c.2055C>T	c.(2053-2055)ctC>ctT	p.L685L	PARP10_ENST00000524918.1_Silent_p.L676L|PARP10_ENST00000525773.1_Silent_p.L697L|PARP10_ENST00000533665.1_5'Flank	NM_032789.3	NP_116178.2	Q53GL7	PAR10_HUMAN	poly (ADP-ribose) polymerase family, member 10	685	Glu-rich.				negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of gene expression (GO:0010629)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of protein K63-linked ubiquitination (GO:1900045)|negative regulation of viral genome replication (GO:0045071)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein poly-ADP-ribosylation (GO:0070212)|regulation of chromatin assembly (GO:0010847)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	K63-linked polyubiquitin binding (GO:0070530)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(4)|pancreas(1)|upper_aerodigestive_tract(2)	27	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.31e-40)|Epithelial(56;1.16e-39)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CCAGCAGGGAGAGGGTTAGGG	0.672																																					p.L685L		Atlas-SNP	.											.	PARP10	57	.	0			c.C2055T						.						14	16	16					8																	145057702		2201	4296	6497	SO:0001819	synonymous_variant	84875	exon8			CAGGGAGAGGGTT	AK027370	CCDS34960.1	8q24	2010-02-16				ENSG00000178685		"Poly (ADP-ribose) polymerases"	25895	protein-coding gene	gene with protein product		609564				15273990	Standard	NM_032789		Approved	FLJ14464	uc003zal.4	Q53GL7		ENST00000313028.7:c.2055C>T	chr8.hg19:g.145057702G>A		59.0	0.0		171.0	21.0	NM_032789	Q8N2I0|Q8WV05|Q96CH7|Q96K72	Silent	SNP	ENST00000313028.7	hg19	CCDS34960.1																																																																																			.	.		0.672	PARP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383866.1	NM_032789		A	145057702	G	A	145057702	2	1	301	1	0	0	0	0	0	0	0	1	11464	929	33	3		3	PARP10	8	145057702	Silent	SNP	G	TCGA-G3-AAV5-01A-11D-A36X-10	116971	145057702	1306320	31	43483										
COL27A1	85301	hgsc.bcm.edu	37	chr9	117020825	117020825	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	tttctcctcttcccagggtcCtccaggatctcgaggcccac	8	17	3	0			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr9:117020825C>T	ENST00000356083.3	+	28	3537	c.3146C>T	c.(3145-3147)cCt>cTt	p.P1049L		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	1049	Collagen-like 7.|Pro-rich.|Triple-helical region.				extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						TCCCAGGGTCCTCCAGGATCT	0.622																																					p.P1049L		Atlas-SNP	.											.	COL27A1	200	.	0			c.C3146T						.						48	47	47					9																	117020825		2203	4300	6503	SO:0001583	missense	85301	exon28			AGGGTCCTCCAGG	AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"Collagens"	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.3146C>T	chr9.hg19:g.117020825C>T	ENSP00000348385:p.Pro1049Leu	67.0	0.0		95.0	40.0	NM_032888	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	hg19	CCDS6802.1	.	.	.	.	.	.	.	.	.	.	C	7.822	0.717979	0.15372	.	.	ENSG00000196739	ENST00000356083;ENST00000357257	D	0.96041	-3.89	5.09	5.09	0.68999	.	.	.	.	.	D	0.91405	0.7288	L	0.39898	1.24	0.58432	D	0.999999	P	0.50066	0.931	B	0.42112	0.376	D	0.89816	0.3985	9	0.07990	T	0.79	.	13.9936	0.64382	0.0:1.0:0.0:0.0	.	1049	Q8IZC6	CORA1_HUMAN	L	1049	ENSP00000348385:P1049L	ENSP00000348385:P1049L	P	+	2	0	COL27A1	116060646	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	2.797000	0.47877	2.365000	0.80145	0.462000	0.41574	CCT	.	.		0.622	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888		T	117020825	C	T	117020825	3	4	301	1	0	0	0	0	1	0	0	0	3687	681	24	3	3256	3	COL27A1	9	117020825	Missense_Mutation	SNP	C	TCGA-G3-AAV5-01A-11D-A36X-10		117020825	24192606	32	43484										
BTAF1	9044	hgsc.bcm.edu	37	chr10	93716306	93716306	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	aatgatagcactgatggggaGccagaagaaaagagacggaa	14	5	0	5			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr10:93716306G>A	ENST00000265990.6	+	7	1031	c.723G>A	c.(721-723)gaG>gaA	p.E241E		NM_003972.2	NP_003963.1	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170kDa	241					negative regulation of chromatin binding (GO:0035562)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(2)|urinary_tract(6)	59		Colorectal(252;0.0846)				CTGATGGGGAGCCAGAAGAAA	0.318																																					p.E241E		Atlas-SNP	.											.	BTAF1	148	.	0			c.G723A						.						72	65	68					10																	93716306		2203	4300	6503	SO:0001819	synonymous_variant	9044	exon7			TGGGGAGCCAGAA	AJ001017	CCDS7419.1	10q22-q23	2013-05-01	2013-05-01		ENSG00000095564	ENSG00000095564			17307	protein-coding gene	gene with protein product	"Mot1 homolog (S. cerevisiae)"	605191	"BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170 kD (Mot1 homolog, S. cerevisiae)"			9342322, 9488487	Standard	NM_003972		Approved	TAFII170, TAF172, MOT1, TAF-172, TAF(II)170	uc001khr.3	O14981	OTTHUMG00000018752	ENST00000265990.6:c.723G>A	chr10.hg19:g.93716306G>A		52.0	0.0		107.0	31.0	NM_003972	B4E0W6|O43578	Silent	SNP	ENST00000265990.6	hg19	CCDS7419.1																																																																																			.	.		0.318	BTAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049380.4	NM_003972		A	93716306	G	A	93716306	2	1	301	1	0	0	0	0	0	0	0	1	1538	962	34	3		3	BTAF1	10	93716306	Silent	SNP	G	TCGA-G3-AAV5-01A-11D-A36X-10		93716306	41818441	33	43485										
SUFU	51684	hgsc.bcm.edu	37	chr10	104389858	104389858	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	gagtacagctggcctgaaaaGaagctgaaggtctccatcct	11	10	1	3			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr10:104389858G>T	ENST00000369902.3	+	12	1567	c.1401G>T	c.(1399-1401)aaG>aaT	p.K467N		NM_016169.3	NP_057253.2	Q9UMX1	SUFU_HUMAN	suppressor of fused homolog (Drosophila)	467					cytoplasmic sequestering of transcription factor (GO:0042994)|heart looping (GO:0001947)|multicellular organismal development (GO:0007275)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|negative regulation of transcription factor import into nucleus (GO:0042992)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|skin development (GO:0043588)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|primary cilium (GO:0072372)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(7)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(2)	24		Colorectal(252;0.207)		Epithelial(162;1.36e-08)|all cancers(201;3.81e-07)|BRCA - Breast invasive adenocarcinoma(275;0.242)		GGCCTGAAAAGAAGCTGAAGG	0.577			"D, F, S"		medulloblastoma	medulloblastoma			Medulloblastoma, associated with Germline SUFU Mutation																												p.K467N		Atlas-SNP	.	yes	Rec	yes	Medulloblastoma predisposition	10	10q24.32	51684	suppressor of fused homolog (Drosophila)		O	.	SUFU	44	.	0			c.G1401T						.						230	197	208					10																	104389858		2203	4300	6503	SO:0001583	missense	51684	exon12	Familial Cancer Database		TGAAAAGAAGCTG	AF175770	CCDS7537.1, CCDS53571.1	10q24.32	2014-09-17			ENSG00000107882	ENSG00000107882			16466	protein-coding gene	gene with protein product		607035				15367681	Standard	NM_016169		Approved	SUFUH, SUFUXL, PRO1280	uc001kvy.2	Q9UMX1	OTTHUMG00000018966	ENST00000369902.3:c.1401G>T	chr10.hg19:g.104389858G>T	ENSP00000358918:p.Lys467Asn	113.0	0.0		164.0	43.0	NM_016169	Q7LCP7|Q9NT90|Q9NZ07|Q9UHK2|Q9UHM8|Q9UMY0	Missense_Mutation	SNP	ENST00000369902.3	hg19	CCDS7537.1	.	.	.	.	.	.	.	.	.	.	G	17.41	3.382920	0.61845	.	.	ENSG00000107882	ENST00000369902	T	0.49432	0.78	5.59	5.59	0.84812	Suppressor of fused C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.48589	0.1508	L	0.56769	1.78	0.80722	D	1	B	0.22080	0.064	B	0.24269	0.052	T	0.39583	-0.9607	10	0.40728	T	0.16	-14.1683	17.7787	0.88517	0.0:0.0:1.0:0.0	.	467	Q9UMX1	SUFU_HUMAN	N	467	ENSP00000358918:K467N	ENSP00000358918:K467N	K	+	3	2	SUFU	104379848	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.533000	0.60615	2.644000	0.89710	0.561000	0.74099	AAG	.	.		0.577	SUFU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050089.1	NM_016169		T	104389858	G	T	104389858	3	4	301	1	0	0	0	0	1	0	0	0	15383	933	33	3	1457	3	SUFU	10	104389858	Missense_Mutation	SNP	G	TCGA-G3-AAV5-01A-11D-A36X-10	10673552	104389858	31144889	34	43486										
OR5W2	390148	hgsc.bcm.edu	37	chr11	55681633	55681633	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	taaaccccagtcaagagtagAtagcacactctgctagacat	7	11	2	3			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr11:55681633A>G	ENST00000344514.1	-	1	425	c.426T>C	c.(424-426)taT>taC	p.Y142Y		NM_001001960.1	NP_001001960.1	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W, member 2	142						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(28)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						TCAAGAGTAGATAGCACACTC	0.463																																					p.Y142Y	Melanoma(48;171 1190 15239 43886 49348)	Atlas-SNP	.											.	OR5W2	112	.	0			c.T426C						.						69	63	65					11																	55681633		2201	4296	6497	SO:0001819	synonymous_variant	390148	exon1			GAGTAGATAGCAC	BK004398	CCDS31513.1	11q11	2012-08-09		2004-03-10	ENSG00000187612	ENSG00000187612		"GPCR / Class A : Olfactory receptors"	15299	protein-coding gene	gene with protein product				OR5W2P, OR5W3P			Standard	NM_001001960		Approved		uc010rir.2	Q8NH69	OTTHUMG00000166818	ENST00000344514.1:c.426T>C	chr11.hg19:g.55681633A>G		66.0	0.0		90.0	30.0	NM_001001960		Silent	SNP	ENST00000344514.1	hg19	CCDS31513.1																																																																																			.	.		0.463	OR5W2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391523.1	NM_001001960		G	55681633	A	G	55681633	2	3	301	1	0	0	0	0	0	0	0	1	11194	340	12	2		2	OR5W2	11	55681633	Silent	SNP	A	TCGA-G3-AAV5-01A-11D-A36X-10		55681633	79324883	35	43487										
WDR74	54663	hgsc.bcm.edu	37	chr11	62601897	62601897	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	cccttcccctctaaacactcActtgcctcccggagtgaggg	8	17	2	1			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr11:62601897A>G	ENST00000525239.1	-	8	1257		c.e8+1		STX5_ENST00000394690.1_5'Flank|WDR74_ENST00000540620.1_5'Flank|STX5_ENST00000541317.1_5'Flank|WDR74_ENST00000525752.1_Splice_Site|WDR74_ENST00000278856.4_Splice_Site|RP11-727F15.9_ENST00000535817.1_RNA|STX5_ENST00000294179.3_5'Flank|RP11-727F15.9_ENST00000535867.1_RNA|WDR74_ENST00000529106.1_Splice_Site|WDR74_ENST00000311713.7_Splice_Site|STX5_ENST00000377897.4_5'Flank			Q6RFH5	WDR74_HUMAN	WD repeat domain 74						blastocyst formation (GO:0001825)|RNA metabolic process (GO:0016070)	nucleolus (GO:0005730)|nucleus (GO:0005634)				kidney(2)|large_intestine(1)|liver(1)|lung(3)|ovary(1)	8						CTAAACACTCACTTGCCTCCC	0.592																																					.		Atlas-SNP	.											.	WDR74	36	.	0			c.719+2T>C						.						29	29	29					11																	62601897		1848	4097	5945	SO:0001630	splice_region_variant	54663	exon9			ACACTCACTTGCC		CCDS44630.1	11q12.3	2013-01-09				ENSG00000133316		"WD repeat domain containing"	25529	protein-coding gene	gene with protein product							Standard	NM_018093		Approved	FLJ10439	uc001nvm.2	Q6RFH5		ENST00000525239.1:c.719+1T>C	chr11.hg19:g.62601897A>G		40.0	0.0		43.0	16.0	NM_018093	A8K8G5|Q9BRC9|Q9H6X8|Q9NVY2	Splice_Site	SNP	ENST00000525239.1	hg19	CCDS44630.1	.	.	.	.	.	.	.	.	.	.	A	16.27	3.074562	0.55646	.	.	ENSG00000133316	ENST00000311713;ENST00000529106;ENST00000525239;ENST00000278856;ENST00000525752	.	.	.	3.88	3.88	0.44766	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.0273	0.36239	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	WDR74	62358473	0.764000	0.28473	0.997000	0.53966	0.968000	0.65278	0.922000	0.28734	1.614000	0.50241	0.379000	0.24179	.	.	.		0.592	WDR74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395678.1	NM_018093	Intron	G	62601897	A	G	62601897	5	3	301	1	0	0	0	0	0	0	1	0	17339	173	6	2	456	2	WDR74	11	62601897	Splice_Site	SNP	A	TCGA-G3-AAV5-01A-11D-A36X-10	6920264	62601897	72404619	36	43488										
EIF1AD	84285	hgsc.bcm.edu	37	chr11	65767088	65767088	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	tggtccttgcagagcacaaaCgagatttcagccttcacctt	8	12	2	2			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr11:65767088C>T	ENST00000312234.2	-	4	589	c.255G>A	c.(253-255)tcG>tcA	p.S85S	EIF1AD_ENST00000533544.1_Silent_p.S85S|EIF1AD_ENST00000529964.1_Silent_p.S85S|EIF1AD_ENST00000525767.1_Silent_p.S33S|BANF1_ENST00000445560.2_5'Flank|EIF1AD_ENST00000527249.1_Silent_p.S85S|BANF1_ENST00000533166.1_5'Flank|EIF1AD_ENST00000526451.1_Silent_p.S85S|BANF1_ENST00000312175.2_5'Flank	NM_001242481.1|NM_001242482.1|NM_001242483.1|NM_032325.3	NP_001229410.1|NP_001229411.1|NP_001229412.1|NP_115701.2	Q8N9N8	EIF1A_HUMAN	eukaryotic translation initiation factor 1A domain containing	85	S1-like. {ECO:0000255|PROSITE- ProRule:PRU00181}.					intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	translation initiation factor activity (GO:0003743)			lung(5)	5						AGAGCACAAACGAGATTTCAG	0.512																																					p.S85S		Atlas-SNP	.											.	EIF1AD	10	.	0			c.G255A						.						130	115	120					11																	65767088		2201	4296	6497	SO:0001819	synonymous_variant	84285	exon4			CACAAACGAGATT	AK094129	CCDS8124.1	11q13.1	2009-05-27				ENSG00000175376			28147	protein-coding gene	gene with protein product						12477932	Standard	NM_001242482		Approved	MGC11102, haponin	uc001ogn.2	Q8N9N8		ENST00000312234.2:c.255G>A	chr11.hg19:g.65767088C>T		115.0	0.0		126.0	56.0	NM_001242483	B2R4N5|Q9BSC1	Silent	SNP	ENST00000312234.2	hg19	CCDS8124.1																																																																																			.	.		0.512	EIF1AD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391072.1	NM_032325		T	65767088	C	T	65767088	2	4	301	1	0	0	0	0	0	0	0	1	4993	523	19	1		1	EIF1AD	11	65767088	Silent	SNP	C	TCGA-G3-AAV5-01A-11D-A36X-10	3165191	65767088	69239428	37	43489										
ATP5B	506	hgsc.bcm.edu	37	chr12	57037707	57037707	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	cctgctcaacactcatttccAtgaactctggagcctcagca	6	15	4	1			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr12:57037707A>G	ENST00000262030.3	-	4	571	c.521T>C	c.(520-522)aTg>aCg	p.M174T	SNORD59A_ENST00000384304.1_RNA|ATP5B_ENST00000552919.1_Missense_Mutation_p.M174T|ATP5B_ENST00000550162.1_5'Flank	NM_001686.3	NP_001677.2	P06576	ATPB_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide	174					angiogenesis (GO:0001525)|ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|ATP hydrolysis coupled proton transport (GO:0015991)|cellular metabolic process (GO:0044237)|generation of precursor metabolites and energy (GO:0006091)|lipid metabolic process (GO:0006629)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|osteoblast differentiation (GO:0001649)|proton transport (GO:0015992)|regulation of intracellular pH (GO:0051453)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial nucleoid (GO:0042645)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase, catalytic core (GO:0005754)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|MHC class I protein binding (GO:0042288)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transmembrane transporter activity (GO:0022857)|transporter activity (GO:0005215)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						ACTCATTTCCATGAACTCTGG	0.408																																					p.M174T		Atlas-SNP	.											.	ATP5B	48	.	0			c.T521C						.						111	95	101					12																	57037707		2203	4300	6503	SO:0001583	missense	506	exon4			ATTTCCATGAACT	M27132	CCDS8924.1	12p13.3	2012-10-12			ENSG00000110955	ENSG00000110955	3.6.3.14	"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	830	protein-coding gene	gene with protein product		102910		ATPSB		2687158	Standard	NM_001686		Approved		uc001slr.3	P06576	OTTHUMG00000170291	ENST00000262030.3:c.521T>C	chr12.hg19:g.57037707A>G	ENSP00000262030:p.Met174Thr	74.0	0.0		81.0	27.0	NM_001686	A8K4X0|Q14283	Missense_Mutation	SNP	ENST00000262030.3	hg19	CCDS8924.1	.	.	.	.	.	.	.	.	.	.	A	11.34	1.608718	0.28623	.	.	ENSG00000110955	ENST00000262030;ENST00000552919;ENST00000551020	T;T;T	0.81078	-1.45;-1.45;-1.45	5.68	5.68	0.88126	.	0.516257	0.24534	N	0.037691	T	0.59959	0.2232	N	0.02266	-0.62	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48352	-0.9043	10	0.26408	T	0.33	1.8835	14.9317	0.70919	1.0:0.0:0.0:0.0	.	174	P06576	ATPB_HUMAN	T	174;174;113	ENSP00000262030:M174T;ENSP00000450297:M174T;ENSP00000446677:M113T	ENSP00000262030:M174T	M	-	2	0	ATP5B	55323974	0.669000	0.27502	0.402000	0.26371	0.853000	0.48598	4.649000	0.61433	2.174000	0.68829	0.379000	0.24179	ATG	.	.		0.408	ATP5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408380.1	NM_001686		G	57037707	A	G	57037707	3	3	301	1	0	0	0	0	1	0	0	0	1148	217	8	2	1096	2	ATP5B	12	57037707	Missense_Mutation	SNP	A	TCGA-G3-AAV5-01A-11D-A36X-10		57037707	76814188	38	43490										
ARHGAP9	64333	hgsc.bcm.edu	37	chr12	57868703	57868703	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	gagccgcaaaaagctgggcaCcgtgtctccttcccgctggc	12	15	1	0			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr12:57868703C>A	ENST00000356411.2	-	13	1801	c.1663G>T	c.(1663-1665)Gtg>Ttg	p.V555L	ARHGAP9_ENST00000430041.2_Missense_Mutation_p.V352L|ARHGAP9_ENST00000550288.1_Missense_Mutation_p.V615L|ARHGAP9_ENST00000393791.3_Missense_Mutation_p.V536L|ARHGAP9_ENST00000424809.2_Missense_Mutation_p.V536L|ARHGAP9_ENST00000393797.2_Missense_Mutation_p.V626L|ARHGAP9_ENST00000550454.1_5'Flank			Q9BRR9	RHG09_HUMAN	Rho GTPase activating protein 9	555	Lipid binding.|Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)			endometrium(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(1)	30			GBM - Glioblastoma multiforme(3;3.37e-34)			AAGCTGGGCACCGTGTCTCCT	0.547																																					p.V536L		Atlas-SNP	.											.	ARHGAP9	79	.	0			c.G1606T						.						56	53	54					12																	57868703		2203	4300	6503	SO:0001583	missense	64333	exon12			TGGGCACCGTGTC	AB051853	CCDS8941.2, CCDS44928.1, CCDS44929.1	12q13.3	2013-01-10			ENSG00000123329	ENSG00000123329		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	14130	protein-coding gene	gene with protein product		610576				11396949	Standard	NM_032496		Approved	MGC1295, 10C	uc001soc.3	Q9BRR9	OTTHUMG00000150147	ENST00000356411.2:c.1663G>T	chr12.hg19:g.57868703C>A	ENSP00000348782:p.Val555Leu	59.0	0.0		73.0	25.0	NM_001080157	B4DVI3|E9PDX9|Q8NAF3|Q8TCJ3|Q8WYR0|Q96EZ2|Q96S74	Missense_Mutation	SNP	ENST00000356411.2	hg19		.	.	.	.	.	.	.	.	.	.	C	34	5.351428	0.95830	.	.	ENSG00000123329	ENST00000393791;ENST00000356411;ENST00000423291;ENST00000424809;ENST00000393797;ENST00000340423;ENST00000430041;ENST00000550130	T;T;T;T;T;T	0.45668	0.89;0.89;2.63;0.89;0.89;2.63	5.2	5.2	0.72013	Rho GTPase-activating protein domain (3);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.60818	0.2298	L	0.53249	1.67	0.58432	D	0.999999	D;D;D;D;D	0.89917	0.999;0.994;1.0;0.999;0.998	D;D;D;D;D	0.83275	0.987;0.97;0.994;0.996;0.963	T	0.61816	-0.6985	10	0.87932	D	0	.	16.5038	0.84263	0.0:1.0:0.0:0.0	.	615;555;536;536;352	Q6ZN13;Q9BRR9;Q9BRR9-2;E9PDX9;B4DVI3	.;RHG09_HUMAN;.;.;.	L	536;555;206;536;626;585;352;43	ENSP00000377380:V536L;ENSP00000348782:V555L;ENSP00000394307:V536L;ENSP00000377386:V626L;ENSP00000397950:V352L;ENSP00000448423:V43L	ENSP00000344852:V585L	V	-	1	0	ARHGAP9	56154970	0.996000	0.38824	0.984000	0.44739	0.998000	0.95712	3.474000	0.53129	2.822000	0.97130	0.650000	0.86243	GTG	.	.		0.547	ARHGAP9-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_032496		A	57868703	C	A	57868703	3	1	301	1	0	0	0	0	1	0	0	0	889	507	18	3	613	3	ARHGAP9	12	57868703	Missense_Mutation	SNP	C	TCGA-G3-AAV5-01A-11D-A36X-10	830996	57868703	75983192	39	43491										
RASSF3	283349	hgsc.bcm.edu	37	chr12	65085254	65085254	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	ttgtttctttacccagtctaCgcctgcaagctctcagaccg	7	14	3	1			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr12:65085254C>T	ENST00000542104.1	+	4	582	c.462C>T	c.(460-462)taC>taT	p.Y154Y	RASSF3_ENST00000336061.2_Silent_p.Y154Y	NM_178169.3	NP_835463.1	Q86WH2	RASF3_HUMAN	Ras association (RalGDS/AF-6) domain family member 3	154	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10			Lung(2;0.00133)|LUAD - Lung adenocarcinoma(6;0.0665)|LUSC - Lung squamous cell carcinoma(43;0.132)	GBM - Glioblastoma multiforme(28;0.0611)		ACCCAGTCTACGCCTGCAAGC	0.488																																					p.Y154Y		Atlas-SNP	.											.	RASSF3	18	.	0			c.C462T						.						99	82	88					12																	65085254		2203	4300	6503	SO:0001819	synonymous_variant	283349	exon4			AGTCTACGCCTGC		CCDS8969.1	12q14.2	2008-02-22	2008-02-22		ENSG00000153179	ENSG00000153179			14271	protein-coding gene	gene with protein product		607019					Standard	NM_178169		Approved		uc001ssd.3	Q86WH2	OTTHUMG00000168812	ENST00000542104.1:c.462C>T	chr12.hg19:g.65085254C>T		100.0	0.0		77.0	32.0	NM_178169	Q86WH1	Silent	SNP	ENST00000542104.1	hg19	CCDS8969.1																																																																																			.	.		0.488	RASSF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401161.1			T	65085254	C	T	65085254	2	4	301	1	0	0	0	0	0	0	0	1	13102	547	19	1		1	RASSF3	12	65085254	Silent	SNP	C	TCGA-G3-AAV5-01A-11D-A36X-10	7216551	65085254	68766641	40	43492										
TRPV4	59341	hgsc.bcm.edu	37	chr12	110238504	110238504	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	gacatcagctccctgggccaCgagaagttccacgtagtgtt	11	12	1	1	rs138419280		TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr12:110238504C>A	ENST00000418703.2	-	4	866	c.772G>T	c.(772-774)Gtg>Ttg	p.V258L	TRPV4_ENST00000537083.1_Missense_Mutation_p.V258L|TRPV4_ENST00000541794.1_Intron|TRPV4_ENST00000392719.2_Intron|TRPV4_ENST00000261740.2_Missense_Mutation_p.V258L|TRPV4_ENST00000536838.1_Missense_Mutation_p.V224L|TRPV4_ENST00000346520.2_Missense_Mutation_p.V258L|TRPV4_ENST00000544971.1_Intron	NM_001177431.1	NP_001170902.1	Q9HBA0	TRPV4_HUMAN	transient receptor potential cation channel, subfamily V, member 4	258					actin cytoskeleton reorganization (GO:0031532)|actin filament organization (GO:0007015)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cell death (GO:0008219)|cell volume homeostasis (GO:0006884)|cell-cell junction assembly (GO:0007043)|cellular calcium ion homeostasis (GO:0006874)|cellular hypotonic response (GO:0071476)|cellular response to heat (GO:0034605)|cellular response to osmotic stress (GO:0071470)|cortical microtubule organization (GO:0043622)|hyperosmotic salinity response (GO:0042538)|ion transmembrane transport (GO:0034220)|microtubule polymerization (GO:0046785)|negative regulation of neuron projection development (GO:0010977)|osmosensory signaling pathway (GO:0007231)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of microtubule depolymerization (GO:0031117)|regulation of response to osmotic stress (GO:0047484)|response to mechanical stimulus (GO:0009612)|transmembrane transport (GO:0055085)|vasopressin secretion (GO:0030103)	adherens junction (GO:0005912)|cell surface (GO:0009986)|cilium (GO:0005929)|cortical actin cytoskeleton (GO:0030864)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|beta-tubulin binding (GO:0048487)|calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)|cation channel activity (GO:0005261)|microtubule binding (GO:0008017)|osmosensor activity (GO:0005034)|protein kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|SH2 domain binding (GO:0042169)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(7)|ovary(3)|prostate(2)|skin(4)|stomach(1)	35						CCCTGGGCCACGAGAAGTTCC	0.642																																					p.V258L		Atlas-SNP	.											.	TRPV4	88	.	0			c.G772T						.						84	67	73					12																	110238504		2203	4300	6503	SO:0001583	missense	59341	exon4			GGGCCACGAGAAG	AF263523	CCDS9134.1, CCDS9135.1, CCDS53827.1, CCDS53828.1, CCDS53829.1	12q24.1	2014-09-17				ENSG00000111199		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	18083	protein-coding gene	gene with protein product	"osmosensitive transient receptor potential channel 4"	605427				11025659, 11081638, 16382100, 20037587	Standard	NM_147204		Approved	OTRPC4, TRP12, VROAC, VRL-2, VR-OAC, CMT2C	uc001tpk.2	Q9HBA0		ENST00000418703.2:c.772G>T	chr12.hg19:g.110238504C>A	ENSP00000406191:p.Val258Leu	47.0	0.0		65.0	17.0	NM_147204	B7ZKQ6|Q17R79|Q2Y122|Q2Y123|Q2Y124|Q86YZ6|Q8NDY7|Q8NG64|Q96Q92|Q96RS7|Q9HBC0	Missense_Mutation	SNP	ENST00000418703.2	hg19	CCDS9134.1	.	.	.	.	.	.	.	.	.	.	C	14.98	2.698659	0.48307	.	.	ENSG00000111199	ENST00000418703;ENST00000261740;ENST00000346520;ENST00000537083;ENST00000536838	T;T;T;T;T	0.51817	0.69;0.69;0.69;0.69;0.69	4.92	4.03	0.46877	Ankyrin repeat-containing domain (3);	0.184267	0.47852	D	0.000214	T	0.32285	0.0824	N	0.00778	-1.195	0.36571	D	0.872994	D;B;B	0.76494	0.999;0.262;0.312	D;B;B	0.79784	0.993;0.047;0.147	T	0.39014	-0.9634	10	0.08599	T	0.76	-12.1954	12.0442	0.53471	0.0:0.9156:0.0:0.0844	.	258;258;224	Q9HBA0-2;Q9HBA0;Q9HBA0-5	.;TRPV4_HUMAN;.	L	258;258;258;258;224	ENSP00000406191:V258L;ENSP00000261740:V258L;ENSP00000319003:V258L;ENSP00000442738:V258L;ENSP00000444336:V224L	ENSP00000261740:V258L	V	-	1	0	TRPV4	108722887	1.000000	0.71417	0.963000	0.40424	0.371000	0.29859	3.548000	0.53670	1.210000	0.43336	0.655000	0.94253	GTG	.	C|1.000;T|0.000		0.642	TRPV4-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403270.1	NM_021625		A	110238504	C	A	110238504	3	1	301	1	0	0	0	0	1	0	0	0	16613	536	19	1	1891	1	TRPV4	12	110238504	Missense_Mutation	SNP	C	TCGA-G3-AAV5-01A-11D-A36X-10	45153250	110238504	23613391	41	43493										
C12orf51	283450	hgsc.bcm.edu	37	chr12	112617070	112617070	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	tggggtctgggagttgatctGctctttgctaagataaatgt	13	5	3	2			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr12:112617070G>A	ENST00000430131.2	-	62	10998	c.9853C>T	c.(9853-9855)Cag>Tag	p.Q3285*	HECTD4_ENST00000550722.1_Nonsense_Mutation_p.Q3561*|HECTD4_ENST00000377560.5_Nonsense_Mutation_p.Q3535*			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	3285					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										GAGTTGATCTGCTCTTTGCTA	0.532																																					p.Q3573X		Atlas-SNP	.											.	.	.	.	0			c.C10717T						.						89	98	95					12																	112617070		2029	4187	6216	SO:0001587	stop_gained	283450	exon63			TGATCTGCTCTTT	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 51"	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.9853C>T	chr12.hg19:g.112617070G>A	ENSP00000404379:p.Gln3285*	109.0	0.0		130.0	49.0	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Nonsense_Mutation	SNP	ENST00000430131.2	hg19		.	.	.	.	.	.	.	.	.	.	G	56	25.940885	0.99967	.	.	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722	.	.	.	5.62	5.62	0.85841	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.6433	0.95764	0.0:0.0:1.0:0.0	.	.	.	.	X	3535;3285;3561	.	ENSP00000366783:Q3535X	Q	-	1	0	C12orf51	111101453	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.334000	0.96470	2.638000	0.89438	0.591000	0.81541	CAG	.	.		0.532	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		A	112617070	G	A	112617070	4	1	301	1	0	0	0	0	0	1	0	0	1698	1328	46	3	2193	3	C12orf51	12	112617070	Nonsense_Mutation	SNP	G	TCGA-G3-AAV5-01A-11D-A36X-10	2378566	112617070	21234825	42	43494										
TBX3	6926	hgsc.bcm.edu	37	chr12	115118848	115118848	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	catccaccgagaattgtgaaAtttataacgacagtcatcag	7	9	2	2			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr12:115118848A>T	ENST00000257566.3	-	2	882	c.493T>A	c.(493-495)Ttt>Att	p.F165I	TBX3_ENST00000349155.2_Missense_Mutation_p.F165I	NM_016569.3	NP_057653.3	O15119	TBX3_HUMAN	T-box 3	165					anterior/posterior axis specification, embryo (GO:0008595)|atrioventricular bundle cell differentiation (GO:0003167)|blood vessel development (GO:0001568)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cardiac muscle cell fate commitment (GO:0060923)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|female genitalia development (GO:0030540)|follicle-stimulating hormone secretion (GO:0046884)|forelimb morphogenesis (GO:0035136)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|limbic system development (GO:0021761)|luteinizing hormone secretion (GO:0032275)|male genitalia development (GO:0030539)|mammary gland development (GO:0030879)|mammary placode formation (GO:0060596)|mesoderm morphogenesis (GO:0048332)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sinoatrial node cell development (GO:0060931)|skeletal system development (GO:0001501)|specification of organ position (GO:0010159)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum morphogenesis (GO:0060412)	nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			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)		GAATTGTGAAATTTATAACGA	0.448																																					p.F165I		Atlas-SNP	.											.	TBX3	106	.	0			c.T493A						.						122	125	124					12																	115118848		2203	4300	6503	SO:0001583	missense	6926	exon2			TGTGAAATTTATA	BC025258	CCDS9175.1, CCDS9176.1	12q24.21	2013-09-05	2008-07-31		ENSG00000135111	ENSG00000135111		"T-boxes"	11602	protein-coding gene	gene with protein product		601621	"ulnar mammary syndrome"	UMS		8988164	Standard	NM_005996		Approved	TBX3-ISO, XHL	uc001tvt.1	O15119	OTTHUMG00000169586	ENST00000257566.3:c.493T>A	chr12.hg19:g.115118848A>T	ENSP00000257566:p.Phe165Ile	165.0	0.0		211.0	82.0	NM_005996	Q8TB20|Q9UKF8	Missense_Mutation	SNP	ENST00000257566.3	hg19	CCDS9176.1	.	.	.	.	.	.	.	.	.	.	A	36	5.599905	0.96614	.	.	ENSG00000135111	ENST00000349155;ENST00000257566;ENST00000361100	D;D	0.92495	-3.05;-3.05	5.81	5.81	0.92471	p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.97362	0.9137	H	0.96015	3.755	0.80722	D	1	D;D;D	0.89917	0.986;1.0;0.997	D;D;D	0.81914	0.961;0.995;0.99	D	0.98543	1.0633	10	0.87932	D	0	.	15.352	0.74396	1.0:0.0:0.0:0.0	.	165;165;165	B4E3A6;O15119-2;O15119	.;.;TBX3_HUMAN	I	165	ENSP00000257567:F165I;ENSP00000257566:F165I	ENSP00000257566:F165I	F	-	1	0	TBX3	113603231	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.962000	0.93254	2.225000	0.72522	0.533000	0.62120	TTT	.	.		0.448	TBX3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404947.2	NM_016569, NM_005996		T	115118848	A	T	115118848	3	4	301	1	0	0	0	0	1	0	0	0	15674	101	4	4	1766	4	TBX3	12	115118848	Missense_Mutation	SNP	A	TCGA-G3-AAV5-01A-11D-A36X-10	2501778	115118848	18733047	43	43495										
MPHOSPH8	54737	hgsc.bcm.edu	37	chr13	20237193	20237193	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	ttcatagaactttttaacaaCagtggctattcttttggaag	7	6	2	1			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr13:20237193C>T	ENST00000361479.5	+	9	2014	c.1946C>T	c.(1945-1947)aCa>aTa	p.T649I	MPHOSPH8_ENST00000414242.2_Missense_Mutation_p.T649I	NM_017520.3	NP_059990.2	Q99549	MPP8_HUMAN	M-phase phosphoprotein 8	649					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of DNA methylation (GO:0044030)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear heterochromatin (GO:0005720)|nuclear nucleosome (GO:0000788)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	methylated histone binding (GO:0035064)			breast(2)|endometrium(1)|large_intestine(2)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		all_cancers(29;2.83e-16)|all_lung(29;1.16e-17)|all_epithelial(30;8.13e-16)|Lung NSC(5;6.91e-15)|Lung SC(185;0.0367)		all cancers(112;8.43e-05)|Epithelial(112;0.000426)|OV - Ovarian serous cystadenocarcinoma(117;0.00596)|Lung(94;0.015)|LUSC - Lung squamous cell carcinoma(192;0.0795)		TTTTTAACAACAGTGGCTATT	0.343																																					p.T649I		Atlas-SNP	.											.	MPHOSPH8	58	.	0			c.C1946T						.						101	108	106					13																	20237193		2203	4300	6503	SO:0001583	missense	54737	exon9			TAACAACAGTGGC	AK056785, AJ293409	CCDS9287.1	13q12.11	2013-01-10			ENSG00000196199	ENSG00000196199		"Ankyrin repeat domain containing"	29810	protein-coding gene	gene with protein product		611626				8885239	Standard	NM_017520		Approved	mpp8, HSMPP8	uc001umh.3	Q99549	OTTHUMG00000016498	ENST00000361479.5:c.1946C>T	chr13.hg19:g.20237193C>T	ENSP00000355388:p.Thr649Ile	79.0	0.0		73.0	26.0	NM_017520	B7Z6F9|Q5JPE5|Q5JTQ0|Q86TK3|Q96MK4|Q9BTP1	Missense_Mutation	SNP	ENST00000361479.5	hg19	CCDS9287.1	.	.	.	.	.	.	.	.	.	.	C	17.37	3.372171	0.61624	.	.	ENSG00000196199	ENST00000414242;ENST00000361479	T;T	0.61274	0.12;0.12	5.33	5.33	0.75918	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.59390	0.2190	N	0.04746	-0.17	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.68146	-0.5486	10	0.46703	T	0.11	.	19.0094	0.92867	0.0:1.0:0.0:0.0	.	649;649	Q99549;Q99549-2	MPP8_HUMAN;.	I	649	ENSP00000414663:T649I;ENSP00000355388:T649I	ENSP00000355388:T649I	T	+	2	0	MPHOSPH8	19135193	1.000000	0.71417	0.720000	0.30636	0.541000	0.35023	7.210000	0.77924	2.479000	0.83701	0.555000	0.69702	ACA	.	.		0.343	MPHOSPH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044028.2	NM_017520		T	20237193	C	T	20237193	3	4	301	1	0	0	0	0	1	0	0	0	9736	478	17	3	1980	3	MPHOSPH8	13	20237193	Missense_Mutation	SNP	C	TCGA-G3-AAV5-01A-11D-A36X-10		20237193	94932685	44	43496										
ARHGEF7	8874	hgsc.bcm.edu	37	chr13	111767970	111767970	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	acccggagggctttctgcagGcgtcgctgaaggatggggtg	18	9	1	1			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr13:111767970G>A	ENST00000375741.2	+	1	347	c.97G>A	c.(97-99)Gcg>Acg	p.A33T	ARHGEF7_ENST00000317133.5_Missense_Mutation_p.A33T|ARHGEF7-AS2_ENST00000425094.2_RNA|ARHGEF7_ENST00000370623.3_Missense_Mutation_p.A33T|ARHGEF7_ENST00000375739.2_Missense_Mutation_p.A33T	NM_001113511.1|NM_145735.2	NP_001106983.1|NP_663788.1	Q14155	ARHG7_HUMAN	Rho guanine nucleotide exchange factor (GEF) 7	33	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				apoptotic signaling pathway (GO:0097190)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|hematopoietic progenitor cell differentiation (GO:0002244)|lamellipodium assembly (GO:0030032)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of GTPase activity (GO:0043547)|positive regulation of lamellipodium morphogenesis (GO:2000394)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase binding (GO:0019901)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	41	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)			CTTTCTGCAGGCGTCGCTGAA	0.657																																					p.A33T		Atlas-SNP	.											.	ARHGEF7	157	.	0			c.G97A						.						21	21	21					13																	111767970		2202	4299	6501	SO:0001583	missense	8874	exon1			CTGCAGGCGTCGC	D63476	CCDS9521.1, CCDS32009.1, CCDS45068.1, CCDS45069.1	13q33.3	2013-01-10			ENSG00000102606	ENSG00000102606		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	15607	protein-coding gene	gene with protein product	"SH3 domain-containing proline-rich protein", "PAK-interacting exchange factor beta", "rho", "guanine nucleotide exchange factor 7"	605477				9207241, 9726964	Standard	NM_003899		Approved	KIAA0142, PIXB, DKFZp761K1021, Nbla10314, DKFZp686C12170, BETA-PIX, COOL1, P85SPR, P85, P85COOL1, P50BP, PAK3, P50	uc001vrs.2	Q14155	OTTHUMG00000017357	ENST00000375741.2:c.97G>A	chr13.hg19:g.111767970G>A	ENSP00000364893:p.Ala33Thr	28.0	0.0		22.0	7.0	NM_001113512	B1ALK6|B1ALK8|Q3LIA4|Q5W9H0|Q6P9G3|Q6PII2|Q86W63|Q8N3M1	Missense_Mutation	SNP	ENST00000375741.2	hg19	CCDS45068.1	.	.	.	.	.	.	.	.	.	.	g	4.575	0.106728	0.08780	.	.	ENSG00000102606	ENST00000317133;ENST00000375741;ENST00000375739;ENST00000370623;ENST00000545635	D;D;T;D	0.94723	-3.5;-3.5;0.69;-3.5	3.1	-0.988	0.10245	Calponin homology domain (5);	0.537042	0.15754	U	0.246273	D	0.82504	0.5051	N	0.11845	0.185	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.002;0.003;0.0	T	0.66420	-0.5928	10	0.11182	T	0.66	.	3.3069	0.07003	0.1088:0.1185:0.4698:0.303	.	33;33;33	Q14155-2;Q14155;Q14155-3	.;ARHG7_HUMAN;.	T	33;33;33;33;31	ENSP00000325994:A33T;ENSP00000364893:A33T;ENSP00000364891:A33T;ENSP00000359657:A33T	ENSP00000325994:A33T	A	+	1	0	ARHGEF7	110565971	0.961000	0.32948	0.972000	0.41901	0.803000	0.45373	0.015000	0.13355	-0.097000	0.12307	0.306000	0.20318	GCG	.	.		0.657	ARHGEF7-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001113511		A	111767970	G	A	111767970	3	1	301	1	0	0	0	0	1	0	0	0	911	1203	42	3	99	3	ARHGEF7	13	111767970	Missense_Mutation	SNP	G	TCGA-G3-AAV5-01A-11D-A36X-10	91530777	111767970	3401908	45	43497										
UPF3A	65110	hgsc.bcm.edu	37	chr13	115067260	115067260	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	gtggagagatctcaagaacaAgaatctgaagcacaaagata	10	6	2	5			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr13:115067260A>G	ENST00000375299.3	+	9	1118	c.1062A>G	c.(1060-1062)caA>caG	p.Q354Q	UPF3A_ENST00000351487.5_Silent_p.Q321Q|UPF3A_ENST00000475218.2_3'UTR	NM_023011.3	NP_075387.1	Q9H1J1	REN3A_HUMAN	UPF3 regulator of nonsense transcripts homolog A (yeast)	354					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA transport (GO:0051028)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nucleocytoplasmic transport (GO:0006913)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			autonomic_ganglia(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	16	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)	OV - Ovarian serous cystadenocarcinoma(48;0.195)|Epithelial(10;0.2)		CTCAAGAACAAGAATCTGAAG	0.498																																					p.Q354Q		Atlas-SNP	.											.	UPF3A	47	.	0			c.A1062G						.						68	57	61					13																	115067260		2203	4300	6503	SO:0001819	synonymous_variant	65110	exon9			AGAACAAGAATCT	AF318575	CCDS9543.1, CCDS9544.1	13q34	2010-04-30			ENSG00000169062	ENSG00000169062			20332	protein-coding gene	gene with protein product		605530				11113196, 11163187	Standard	NM_023011		Approved	RENT3A, UPF3, HUPF3A	uc001vup.3	Q9H1J1	OTTHUMG00000017403	ENST00000375299.3:c.1062A>G	chr13.hg19:g.115067260A>G		238.0	0.0		251.0	106.0	NM_023011	A2A366|Q5T8C3|Q5T8C9|Q7Z6N3|Q86YK1|Q9BZI8	Silent	SNP	ENST00000375299.3	hg19	CCDS9543.1																																																																																			.	.		0.498	UPF3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045968.2			G	115067260	A	G	115067260	2	3	301	1	0	0	0	0	0	0	0	1	17020	69	3	2		2	UPF3A	13	115067260	Silent	SNP	A	TCGA-G3-AAV5-01A-11D-A36X-10	3299290	115067260	102618	46	43498										
METT11D1	64745	hgsc.bcm.edu	37	chr14	21460771	21460771	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	ctttgcagcagtctccagagCattccatgaggtgaaagtcc	10	11	1	3			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr14:21460771C>T	ENST00000339374.6	+	5	751	c.518C>T	c.(517-519)gCa>gTa	p.A173V	METTL17_ENST00000556670.2_Missense_Mutation_p.A173V|METTL17_ENST00000382985.4_Missense_Mutation_p.A173V	NM_001029991.1|NM_022734.2	NP_001025162.1|NP_073571.1	Q9H7H0	MET17_HUMAN	methyltransferase like 17	173					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	copper ion binding (GO:0005507)|methyltransferase activity (GO:0008168)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|skin(2)	20						GTCTCCAGAGCATTCCATGAG	0.448																																					p.A173V		Atlas-SNP	.											.	METTL17	46	.	0			c.C518T						.						109	110	110					14																	21460771		2203	4300	6503	SO:0001583	missense	64745	exon5			CCAGAGCATTCCA	AK024512	CCDS9562.1, CCDS41913.1	14q11.2	2011-03-03	2011-03-02	2011-03-02	ENSG00000165792	ENSG00000165792			19280	protein-coding gene	gene with protein product			"methyltransferase 11 domain containing 1"	METT11D1		11278769	Standard	XM_006720235		Approved	FLJ20859	uc001vyn.3	Q9H7H0	OTTHUMG00000029610	ENST00000339374.6:c.518C>T	chr14.hg19:g.21460771C>T	ENSP00000343041:p.Ala173Val	80.0	0.0		107.0	41.0	NM_022734	Q9BSH1|Q9BZH2|Q9BZH3	Missense_Mutation	SNP	ENST00000339374.6	hg19	CCDS9562.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.343522	0.61073	.	.	ENSG00000165792	ENST00000339374;ENST00000382985;ENST00000553564;ENST00000554751;ENST00000555670	T;T;T;T	0.28255	1.62;1.62;1.62;1.62	5.86	5.86	0.93980	.	0.196755	0.43747	D	0.000525	T	0.28267	0.0698	N	0.10707	0.03	0.44168	D	0.996974	D;D;D	0.59357	0.978;0.985;0.981	P;P;P	0.62560	0.709;0.904;0.845	T	0.04307	-1.0961	10	0.02654	T	1	.	15.6803	0.77364	0.0:1.0:0.0:0.0	.	173;173;173	Q9H7H0-3;Q9H7H0;Q9H7H0-2	.;MET17_HUMAN;.	V	173;173;91;91;91	ENSP00000343041:A173V;ENSP00000372445:A173V;ENSP00000451478:A91V;ENSP00000451049:A91V	ENSP00000343041:A173V	A	+	2	0	METTL17	20530611	0.995000	0.38212	1.000000	0.80357	0.972000	0.66771	3.222000	0.51223	2.777000	0.95525	0.655000	0.94253	GCA	.	.		0.448	METTL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073804.4	NM_022734		T	21460771	C	T	21460771	3	4	301	1	0	0	0	0	1	0	0	0	9500	710	25	3	536	3	METT11D1	14	21460771	Missense_Mutation	SNP	C	TCGA-G3-AAV5-01A-11D-A36X-10		21460771	85888769	47	43499										
NOVA1	4857	hgsc.bcm.edu	37	chr14	27064670	27064670	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	ggtggctccagtttctttttGcaactgaacaattgtctgtc	9	9	2	1			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr14:27064670G>A	ENST00000344429.5	-	2	229	c.226C>T	c.(226-228)Caa>Taa	p.Q76*	NOVA1_ENST00000547619.1_Nonsense_Mutation_p.Q76*|NOVA1_ENST00000539517.2_Nonsense_Mutation_p.Q76*|NOVA1_ENST00000551754.1_5'Flank|RP11-483C6.1_ENST00000572358.1_RNA|NOVA1_ENST00000267422.7_5'UTR|NOVA1_ENST00000465357.2_Nonsense_Mutation_p.Q76*|NOVA1-AS1_ENST00000547786.1_RNA|NOVA1_ENST00000574031.1_Nonsense_Mutation_p.Q76*	NM_006491.2	NP_006482.1	P51513	NOVA1_HUMAN	neuro-oncological ventral antigen 1	76	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.				locomotory behavior (GO:0007626)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA metabolic process (GO:0051252)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(265;0.0135)		GTTTCTTTTTGCAACTGAACA	0.428																																					p.Q76X		Atlas-SNP	.											.	NOVA1	146	.	0			c.C226T						.						156	147	150					14																	27064670		2203	4300	6503	SO:0001587	stop_gained	4857	exon2			CTTTTTGCAACTG	U04840	CCDS9635.1, CCDS32060.1, CCDS32061.1	14q12	2006-06-09			ENSG00000139910	ENSG00000139910			7886	protein-coding gene	gene with protein product		602157				8558240	Standard	NM_006489		Approved		uc001wpy.3	P51513	OTTHUMG00000029385	ENST00000344429.5:c.226C>T	chr14.hg19:g.27064670G>A	ENSP00000342387:p.Gln76*	135.0	0.0		131.0	38.0	NM_006489	A8K0S4|A8K4Q7|D3DS81|D3DS82|Q6B004	Nonsense_Mutation	SNP	ENST00000344429.5	hg19	CCDS9635.1	.	.	.	.	.	.	.	.	.	.	G	36	5.707513	0.96821	.	.	ENSG00000139910	ENST00000465357;ENST00000539517;ENST00000449198;ENST00000549571;ENST00000344429;ENST00000547619	.	.	.	5.1	5.1	0.69264	.	0.103804	0.42420	D	0.000718	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	-3.4345	18.8679	0.92300	0.0:0.0:1.0:0.0	.	.	.	.	X	76;76;35;39;76;76	.	ENSP00000342387:Q76X	Q	-	1	0	NOVA1	26134510	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	9.751000	0.98889	2.523000	0.85059	0.561000	0.74099	CAA	.	.		0.428	NOVA1-001	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276557.1	NM_006491		A	27064670	G	A	27064670	4	1	301	1	0	0	0	0	0	1	0	0	10563	1328	46	3	1344	3	NOVA1	14	27064670	Nonsense_Mutation	SNP	G	TCGA-G3-AAV5-01A-11D-A36X-10	5603899	27064670	80284870	48	43500										
NRXN3	9369	hgsc.bcm.edu	37	chr14	80130128	80130128	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	ttctttattataggaacaggGgaaaattggagttgtcttca	10	4	3	0			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr14:80130128G>T	ENST00000557594.1	+	3	1390	c.437G>T	c.(436-438)gGg>gTg	p.G146V	RP11-242P2.1_ENST00000553322.1_RNA|NRXN3_ENST00000556003.1_3'UTR|NRXN3_ENST00000554719.1_Missense_Mutation_p.G778V|NRXN3_ENST00000428277.2_Missense_Mutation_p.G146V|NRXN3_ENST00000335750.5_Missense_Mutation_p.G778V|NRXN3_ENST00000281127.7_Missense_Mutation_p.G146V	NM_001272020.1	NP_001258949.1	Q9HDB5	NRX3B_HUMAN	neurexin 3	146	Laminin G-like. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|angiogenesis (GO:0001525)|learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(23)|lung(40)|ovary(3)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(9)|urinary_tract(1)	104		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		TAGGAACAGGGGAAAATTGGA	0.428																																					p.G778V		Atlas-SNP	.											.	NRXN3	342	.	0			c.G2333T						.						87	84	85					14																	80130128		2203	4300	6503	SO:0001583	missense	9369	exon14			AACAGGGGAAAAT	AB018286	CCDS9870.1, CCDS9871.1, CCDS45145.1, CCDS61515.1	14q31	2010-01-19				ENSG00000021645			8010	protein-coding gene	gene with protein product		600567	"chromosome 14 open reading frame 60"	C14orf60		11944992, 12379233	Standard	NM_004796		Approved	KIAA0743	uc001xun.4	Q9HDB5		ENST00000557594.1:c.437G>T	chr14.hg19:g.80130128G>T	ENSP00000451672:p.Gly146Val	128.0	0.0		178.0	59.0	NM_004796	A5PKW8|A8MPU5|B3KPM7|Q6NUR0|Q8IUD8	Missense_Mutation	SNP	ENST00000557594.1	hg19		.	.	.	.	.	.	.	.	.	.	G	29.7	5.028051	0.93518	.	.	ENSG00000021645	ENST00000330071;ENST00000332068;ENST00000554719;ENST00000335750;ENST00000557594;ENST00000281127;ENST00000428277	D;D;T;T;T	0.88509	-2.39;-2.39;0.04;0.04;0.04	5.74	5.74	0.90152	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.85682	D	0.000000	D	0.95667	0.8591	M	0.89214	3.015	0.80722	D	1	D;D;D;P	0.89917	1.0;1.0;1.0;0.949	D;D;D;P	0.91635	0.999;0.998;0.994;0.834	D	0.95303	0.8405	9	.	.	.	.	20.2982	0.98569	0.0:0.0:1.0:0.0	.	146;146;146;778	Q9HDB5-4;Q9HDB5-2;Q9HDB5;Q9Y4C0-3	.;.;NRX3B_HUMAN;.	V	1151;1140;778;778;146;146;146	ENSP00000451648:G778V;ENSP00000338349:G778V;ENSP00000451672:G146V;ENSP00000281127:G146V;ENSP00000394426:G146V	.	G	+	2	0	NRXN3	79199881	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.796000	0.99103	2.873000	0.98535	0.563000	0.77884	GGG	.	.		0.428	NRXN3-004	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000413790.1	NM_001105250		T	80130128	G	T	80130128	3	4	301	1	0	0	0	0	1	0	0	0	10676	1232	43	3	2630	3	NRXN3	14	80130128	Missense_Mutation	SNP	G	TCGA-G3-AAV5-01A-11D-A36X-10	53065458	80130128	27219412	49	43501										
MGA	23269	hgsc.bcm.edu	37	chr15	41988500	41988500	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	gaaacagctaaagaggcacaAtaaagttgacaacccagaag	9	8	0	3			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr15:41988500A>G	ENST00000570161.1	+	2	1292	c.1292A>G	c.(1291-1293)aAt>aGt	p.N431S	MGA_ENST00000389936.4_Missense_Mutation_p.N431S|MGA_ENST00000545763.1_Missense_Mutation_p.N431S|MGA_ENST00000568630.1_3'UTR|MGA_ENST00000566586.1_Missense_Mutation_p.N431S|MGA_ENST00000219905.7_Missense_Mutation_p.N431S			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	Maltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	AAGAGGCACAATAAAGTTGAC	0.418																																					p.N431S		Atlas-SNP	.											.	MGA	264	.	0			c.A1292G						.						79	74	76					15																	41988500		1903	4123	6026	SO:0001583	missense	23269	exon3			GGCACAATAAAGT	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.1292A>G	chr15.hg19:g.41988500A>G	ENSP00000457035:p.Asn431Ser	86.0	0.0		113.0	45.0	NM_001080541	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	hg19	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	A	11.07	1.531003	0.27387	.	.	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	D;D;D	0.83163	-1.69;-1.68;-1.68	5.53	3.21	0.36854	.	1.321340	0.04131	N	0.317906	T	0.76097	0.3940	L	0.38531	1.155	0.24664	N	0.993459	B;B	0.26363	0.147;0.005	B;B	0.29176	0.099;0.005	T	0.60717	-0.7208	10	0.32370	T	0.25	.	4.0427	0.09758	0.5008:0.1799:0.3193:0.0	.	431;431	F5H7K2;E7ENI0	.;.	S	431	ENSP00000219905:N431S;ENSP00000374586:N431S;ENSP00000442467:N431S	ENSP00000219905:N431S	N	+	2	0	MGA	39775792	0.999000	0.42202	1.000000	0.80357	0.951000	0.60555	0.807000	0.27140	0.936000	0.37367	0.459000	0.35465	AAT	.	.		0.418	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		G	41988500	A	G	41988500	3	3	301	1	0	0	0	0	1	0	0	0	9549	101	4	2	1298	2	MGA	15	41988500	Missense_Mutation	SNP	A	TCGA-G3-AAV5-01A-11D-A36X-10		41988500	60542892	50	43502										
CDAN1	146059	hgsc.bcm.edu	37	chr15	43020923	43020923	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	gatctccaacagctgggctgGgtctcccccttcctctccct	8	18	3	0			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr15:43020923G>C	ENST00000356231.3	-	20	2754	c.2731C>G	c.(2731-2733)Cca>Gca	p.P911A		NM_138477.2	NP_612486.2	Q8IWY9	CDAN1_HUMAN	codanin 1	911					chromatin assembly (GO:0031497)|chromatin organization (GO:0006325)|negative regulation of DNA replication (GO:0008156)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	24		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;2.49e-07)		AGCTGGGCTGGGTCTCCCCCT	0.627																																					p.P911A		Atlas-SNP	.											.	CDAN1	70	.	0			c.C2731G						.						74	61	65					15																	43020923		2203	4299	6502	SO:0001583	missense	146059	exon20			GGGCTGGGTCTCC	AF525398	CCDS32209.1	15q15.2	2012-04-25	2012-04-25			ENSG00000140326			1713	protein-coding gene	gene with protein product		607465	"congenital dyserythropoietic anemia, type I"			8634422, 12434312	Standard	XM_005254177		Approved	CDA-I, CDAI	uc001zql.3	Q8IWY9		ENST00000356231.3:c.2731C>G	chr15.hg19:g.43020923G>C	ENSP00000348564:p.Pro911Ala	122.0	0.0		136.0	46.0	NM_138477	Q6NYD0|Q7Z7L5|Q969N3	Missense_Mutation	SNP	ENST00000356231.3	hg19	CCDS32209.1	.	.	.	.	.	.	.	.	.	.	G	10.96	1.498782	0.26861	.	.	ENSG00000140326	ENST00000356231;ENST00000267892	D	0.86230	-2.09	5.92	2.95	0.34219	.	0.355893	0.32608	N	0.005872	T	0.74419	0.3714	L	0.27053	0.805	0.31173	N	0.70298	B;B	0.09022	0.002;0.001	B;B	0.06405	0.001;0.002	T	0.63265	-0.6676	10	0.16896	T	0.51	-4.7948	6.0952	0.20017	0.1902:0.3029:0.5069:0.0	.	911;909	Q8IWY9;C9K0H8	CDAN1_HUMAN;.	A	911;909	ENSP00000348564:P911A	ENSP00000267892:P909A	P	-	1	0	CDAN1	40808215	1.000000	0.71417	0.993000	0.49108	0.877000	0.50540	2.485000	0.45250	0.791000	0.33826	0.561000	0.74099	CCA	.	.		0.627	CDAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431103.1	XM_085300		C	43020923	G	C	43020923	3	2	301	1	0	0	0	0	1	0	0	0	3056	1232	43	4	988	4	CDAN1	15	43020923	Missense_Mutation	SNP	G	TCGA-G3-AAV5-01A-11D-A36X-10	1032423	43020923	59510469	51	43503										
ADAMTS17	170691	hgsc.bcm.edu	37	chr15	100821591	100821591	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	cccgcgaaggcctgccccacGtcggcttcttcttttctaga	9	16	3	1			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr15:100821591G>A	ENST00000268070.4	-	4	737	c.632C>T	c.(631-633)aCg>aTg	p.T211M		NM_139057.2	NP_620688.2	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 17	211						proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)	50	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)		CCTGCCCCACGTCGGCTTCTT	0.587																																					p.T211M		Atlas-SNP	.											.	ADAMTS17	127	.	0			c.C632T						.																																			SO:0001583	missense	170691	exon4			CCCCACGTCGGCT	AJ315735	CCDS10383.1	15q24	2014-01-28	2005-08-19		ENSG00000140470	ENSG00000140470		"ADAM metallopeptidases with thrombospondin type 1 motif"	17109	protein-coding gene	gene with protein product		607511	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 17"			11867212	Standard	NM_139057		Approved	FLJ32769, FLJ16363	uc002bvv.1	Q8TE56	OTTHUMG00000149867	ENST00000268070.4:c.632C>T	chr15.hg19:g.100821591G>A	ENSP00000268070:p.Thr211Met	30.0	0.0		48.0	20.0	NM_139057	Q2I7G4|Q6ZN75	Missense_Mutation	SNP	ENST00000268070.4	hg19	CCDS10383.1	.	.	.	.	.	.	.	.	.	.	G	7.849	0.723675	0.15439	.	.	ENSG00000140470	ENST00000268070	T	0.62232	0.04	4.62	-1.79	0.07932	.	0.612483	0.16044	N	0.232269	T	0.32852	0.0843	N	0.14661	0.345	0.09310	N	1	P	0.36660	0.564	B	0.27796	0.083	T	0.16453	-1.0402	10	0.45353	T	0.12	.	5.5803	0.17247	0.0:0.2988:0.1495:0.5517	.	211	Q8TE56	ATS17_HUMAN	M	211	ENSP00000268070:T211M	ENSP00000268070:T211M	T	-	2	0	ADAMTS17	98639114	0.000000	0.05858	0.004000	0.12327	0.122000	0.20287	0.043000	0.13971	-0.203000	0.10251	-0.375000	0.07067	ACG	.	.		0.587	ADAMTS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313595.1	NM_139057		A	100821591	G	A	100821591	3	1	301	1	0	0	0	0	1	0	0	0	262	1145	40	1	2731	1	ADAMTS17	15	100821591	Missense_Mutation	SNP	G	TCGA-G3-AAV5-01A-11D-A36X-10	57800668	100821591	1709801	52	43504										
PDIA2	64714	hgsc.bcm.edu	37	chr16	335324	335324	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	tactgtagacgtctgccaagAtcttcgcggccaggatcctc	10	13	2	2			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr16:335324A>T	ENST00000219406.6	+	6	826	c.808A>T	c.(808-810)Atc>Ttc	p.I270F	PDIA2_ENST00000462950.1_3'UTR|PDIA2_ENST00000404312.1_Missense_Mutation_p.I267F	NM_006849.2	NP_006840.2	Q13087	PDIA2_HUMAN	protein disulfide isomerase family A, member 2	270					cell redox homeostasis (GO:0045454)|peptidyl-proline hydroxylation (GO:0019511)|protein folding (GO:0006457)|protein retention in ER lumen (GO:0006621)|regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902175)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)	protein disulfide isomerase activity (GO:0003756)|steroid binding (GO:0005496)			breast(1)|central_nervous_system(4)|kidney(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	17		all_cancers(16;6.71e-07)|all_epithelial(16;1.59e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00769)|all_lung(18;0.0186)				GTCTGCCAAGATCTTCGCGGC	0.647																																					p.I270F		Atlas-SNP	.											.	PDIA2	51	.	0			c.A808T						.						43	49	47					16																	335324		2106	4222	6328	SO:0001583	missense	64714	exon6			GCCAAGATCTTCG	U19948	CCDS42089.1	16p13.3	2009-11-20	2005-06-29	2005-03-03	ENSG00000185615	ENSG00000185615	5.3.4.1	"Protein disulfide isomerases"	14180	protein-coding gene	gene with protein product		608012	"protein disulfide isomerase, pancreatic", "protein disulfide isomerase-associated 2"	PDIP		8561901	Standard	NM_006849		Approved	PDA2, PDI, PDIR	uc002cgo.1	Q13087	OTTHUMG00000064891	ENST00000219406.6:c.808A>T	chr16.hg19:g.335324A>T	ENSP00000219406:p.Ile270Phe	54.0	0.0		74.0	33.0	NM_006849	A6ZJ64|B4DI27|Q2WGM4|Q4TT67|Q6B010|Q96KJ6|Q9BW95	Missense_Mutation	SNP	ENST00000219406.6	hg19	CCDS42089.1	.	.	.	.	.	.	.	.	.	.	a	15.51	2.854347	0.51270	.	.	ENSG00000185615	ENST00000219406;ENST00000455994;ENST00000404312	T;T	0.30714	1.52;1.52	3.97	3.97	0.46021	Thioredoxin-like fold (1);	0.055535	0.64402	D	0.000001	T	0.56572	0.1994	M	0.83223	2.63	0.58432	D	0.999998	D	0.89917	1.0	D	0.85130	0.997	T	0.63528	-0.6617	10	0.87932	D	0	.	11.9446	0.52920	1.0:0.0:0.0:0.0	.	270	Q13087	PDIA2_HUMAN	F	270;239;267	ENSP00000219406:I270F;ENSP00000384410:I267F	ENSP00000219406:I270F	I	+	1	0	PDIA2	275325	1.000000	0.71417	0.998000	0.56505	0.334000	0.28698	3.334000	0.52097	1.675000	0.50919	0.454000	0.30748	ATC	.	.		0.647	PDIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139315.3	NM_006849		T	335324	A	T	335324	3	4	301	1	0	0	0	0	1	0	0	0	11677	333	12	4	830	4	PDIA2	16	335324	Missense_Mutation	SNP	A	TCGA-G3-AAV5-01A-11D-A36X-10		335324	90019429	53	43505										
RAB11FIP3	9727	hgsc.bcm.edu	37	chr16	570189	570197	+	In_Frame_Del	DEL	GGGGCCGCA	GGGGCCGCA	-													0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	gctggaggccgagcagcggcGgggccgcagcagcagcatgg					rs559245815|rs371078762|rs537339281	byFrequency	TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	GGGGCCGCA	GGGGCCGCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr16:570189_570197delGGGGCCGCA	ENST00000262305.4	+	12	2316_2324	c.1928_1936delGGGGCCGCA	c.(1927-1938)cggggccgcagc>cgc	p.GRS644del	RAB11FIP3_ENST00000450428.1_In_Frame_Del_p.GRS348del|RAB11FIP3_ENST00000457159.1_In_Frame_Del_p.GRS689del	NM_014700.3	NP_055515.1	O75154	RFIP3_HUMAN	RAB11 family interacting protein 3 (class II)	644					cytokinesis (GO:0000910)|endocytic recycling (GO:0032456)|vesicle-mediated transport (GO:0016192)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|endosome (GO:0005768)|intercellular bridge (GO:0045171)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)|recycling endosome (GO:0055037)	ADP-ribosylation factor binding (GO:0030306)|calcium ion binding (GO:0005509)|protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(2)|kidney(3)|lung(5)|upper_aerodigestive_tract(1)	12		Hepatocellular(16;0.0218)				GAGCAGCGGCGGGGCCGCAGCAGCAGCAT	0.713																																					p.643_645del	Melanoma(160;2366 2595 4474 8099)	Atlas-INDEL	.											.	RAB11FIP3	31	.	0			c.1927_1935del						.																																			SO:0001651	inframe_deletion	9727	exon12			.	AB014565	CCDS32351.1, CCDS45364.1	16p13.3	2013-01-10			ENSG00000090565	ENSG00000090565		"EF-hand domain containing"	17224	protein-coding gene	gene with protein product		608738				9734811, 11481332	Standard	NM_014700		Approved	KIAA0665, Rab11-FIP3, eferin	uc002chf.3	O75154	OTTHUMG00000047843	ENST00000262305.4:c.1928_1936delGGGGCCGCA	chr16.hg19:g.570189_570197delGGGGCCGCA	ENSP00000262305:p.Gly644_Ser646del	63.0	0.0		60.0	18.0	NM_014700	B0QYI8|B0QYT8|B1AHQ0|B4DEI7|B4DZR6|Q4VXV7|Q7Z5E9|Q9H155|Q9H1G0|Q9NUI0	In_Frame_Del	DEL	ENST00000262305.4	hg19	CCDS32351.1																																																																																			.	.		0.713	RAB11FIP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109066.4	NM_014700		-	570197	GGGGCCGCA	-	570189	7	5	301	1	0	1	0	1	0	0	0	0	12910	1116	39	0	1993	0	RAB11FIP3	16	570189	In_Frame_Del	DEL	GGGGCCGCA	TCGA-G3-AAV5-01A-11D-A36X-10	234865	570189	89784564	54	43506										
BAIAP3	8938	hgsc.bcm.edu	37	chr16	1391408	1391408	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	gcaagggcagcaagcgcggtGgacccctgcctgccaagtgc	15	14	0	0			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr16:1391408G>A	ENST00000324385.5	+	8	912	c.754G>A	c.(754-756)Gga>Aga	p.G252R	BAIAP3_ENST00000562208.1_Missense_Mutation_p.G194R|BAIAP3_ENST00000421665.2_Missense_Mutation_p.G217R|BAIAP3_ENST00000568887.1_Missense_Mutation_p.G189R|BAIAP3_ENST00000397488.2_Missense_Mutation_p.G234R|BAIAP3_ENST00000397489.1_Missense_Mutation_p.G234R|BAIAP3_ENST00000426824.3_Missense_Mutation_p.G217R	NM_003933.4	NP_003924.2	O94812	BAIP3_HUMAN	BAI1-associated protein 3	252	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				G-protein coupled receptor signaling pathway (GO:0007186)|neurotransmitter secretion (GO:0007269)		protein C-terminus binding (GO:0008022)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(25)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42		Hepatocellular(780;0.0893)				CAAGCGCGGTGGACCCCTGCC	0.662																																					p.G252R		Atlas-SNP	.											.	BAIAP3	88	.	0			c.G754A						.						57	52	53					16																	1391408		2197	4295	6492	SO:0001583	missense	8938	exon8			CGCGGTGGACCCC	AB017111	CCDS10434.1, CCDS55978.1, CCDS55979.1, CCDS58402.1, CCDS58403.1, CCDS66894.1	16p13.3	2008-07-04			ENSG00000007516	ENSG00000007516			948	protein-coding gene	gene with protein product		604009				9790924	Standard	NM_003933		Approved	BAP3, KIAA0734	uc002clk.2	O94812	OTTHUMG00000047833	ENST00000324385.5:c.754G>A	chr16.hg19:g.1391408G>A	ENSP00000324510:p.Gly252Arg	167.0	0.0		172.0	70.0	NM_003933	A2A2B2|B2RCD7|B4DGS5|B4DIK3|B4DRK9|B4DRP1|E7EUB9|H3BUH8|H3BVI3|H7C2Q1|O94839|Q2M226|Q658J2|Q76N05|Q96RZ3|Q9UJK1	Missense_Mutation	SNP	ENST00000324385.5	hg19	CCDS10434.1	.	.	.	.	.	.	.	.	.	.	G	10.93	1.490603	0.26686	.	.	ENSG00000007516	ENST00000426824;ENST00000397488;ENST00000324385;ENST00000397489;ENST00000421665	T;T;T;T;T	0.71341	-0.55;-0.56;-0.56;-0.56;-0.5	4.72	-4.98	0.03019	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.384288	0.25566	N	0.029796	T	0.57621	0.2066	N	0.25245	0.725	0.09310	N	1	P;P;B;P;P	0.51537	0.681;0.946;0.379;0.608;0.845	P;P;B;B;P	0.52386	0.507;0.697;0.29;0.29;0.507	T	0.59316	-0.7477	10	0.62326	D	0.03	-21.123	7.1411	0.25556	0.5911:0.0:0.2883:0.1206	.	217;269;194;252;234	E7EUB9;B4DGA2;B4DIK3;O94812;A2A2B2	.;.;.;BAIP3_HUMAN;.	R	217;234;252;234;217	ENSP00000407242:G217R;ENSP00000380625:G234R;ENSP00000324510:G252R;ENSP00000380626:G234R;ENSP00000409533:G217R	ENSP00000324510:G252R	G	+	1	0	BAIAP3	1331409	0.677000	0.27577	0.000000	0.03702	0.002000	0.02628	1.266000	0.33039	-0.834000	0.04239	-0.657000	0.03884	GGA	.	.		0.662	BAIAP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109056.3			A	1391408	G	A	1391408	3	1	301	1	0	0	0	0	1	0	0	0	1304	1349	47	3	784	3	BAIAP3	16	1391408	Missense_Mutation	SNP	G	TCGA-G3-AAV5-01A-11D-A36X-10	821219	1391408	88963345	55	43507										
SMG1	23049	hgsc.bcm.edu	37	chr16	18861619	18861619	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	caagagagtttgtacaggctGaatattctatctacaacttt	7	7	2	2			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr16:18861619G>A	ENST00000446231.2	-	34	5635	c.5223C>T	c.(5221-5223)ttC>ttT	p.F1741F	SMG1_ENST00000389467.3_Silent_p.F1741F			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	1741	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.|Interaction with SMG8 and SMG9.				DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						TGTACAGGCTGAATATTCTAT	0.388																																					p.F1741F		Atlas-SNP	.											.	SMG1	401	.	0			c.C5223T						.						98	92	94					16																	18861619		1841	4095	5936	SO:0001819	synonymous_variant	23049	exon34			CAGGCTGAATATT	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase-related kinase"	607032	"smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.5223C>T	chr16.hg19:g.18861619G>A		81.0	0.0		74.0	38.0	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Silent	SNP	ENST00000446231.2	hg19	CCDS45430.1																																																																																			.	.		0.388	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		A	18861619	G	A	18861619	2	1	301	1	0	0	0	0	0	0	0	1	14810	1281	45	3		3	SMG1	16	18861619	Silent	SNP	G	TCGA-G3-AAV5-01A-11D-A36X-10	17470211	18861619	71493134	56	43508										
C16orf86	388284	hgsc.bcm.edu	37	chr16	67701908	67701919	+	In_Frame_Del	DEL	AAAAAAGCCAAG	AAAAAAGCCAAG	-													0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	caccatctgccaaacagcacAaaaaagccaagaagcgcaag							TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	AAAAAAGCCAAG	AAAAAAGCCAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr16:67701908_67701919delAAAAAAGCCAAG	ENST00000403458.4	+	3	615_626	c.460_471delAAAAAAGCCAAG	c.(460-471)aaaaaagccaagdel	p.KKAK154del	ENKD1_ENST00000243878.4_5'Flank|C16orf86_ENST00000602974.1_3'UTR|ENKD1_ENST00000602409.1_5'Flank|ENKD1_ENST00000602644.1_5'Flank	NM_001012984.2	NP_001013002.2	Q6ZW13	CP086_HUMAN	chromosome 16 open reading frame 86	154										endometrium(2)|lung(4)	6		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.047)|all cancers(182;0.228)		CAAACAGCACAAAAAAGCCAAGAAGCGCAAGA	0.608											OREG0023886	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.153_157del		Atlas-INDEL	.											.	C16orf86	20	.	0			c.459_470del						.																																			SO:0001651	inframe_deletion	388284	exon3			.		CCDS32468.2	16q22.1	2008-10-30			ENSG00000159761	ENSG00000159761			33755	protein-coding gene	gene with protein product							Standard	NM_001012984		Approved	FLJ41802	uc002ety.3	Q6ZW13	OTTHUMG00000150527	ENST00000403458.4:c.460_471delAAAAAAGCCAAG	chr16.hg19:g.67701908_67701919delAAAAAAGCCAAG	ENSP00000384117:p.Lys154_Lys157del	134.0	0.0	1101	115.0	25.0	NM_001012984	B5MCW6	In_Frame_Del	DEL	ENST00000403458.4	hg19	CCDS32468.2																																																																																			.	.		0.608	C16orf86-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318767.2	NM_001012984		-	67701919	AAAAAAGCCAAG	-	67701908	7	5	301	1	0	1	0	1	0	0	0	0	1841	131	5	0	470	0	C16orf86	16	67701908	In_Frame_Del	DEL	AAAAAAGCCAAG	TCGA-G3-AAV5-01A-11D-A36X-10	48840289	67701908	22652845	57	43509										
USP22	23326	hgsc.bcm.edu	37	chr17	20921295	20921295	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	tctcacagaccagacaggagCtggggctctgcatctcacag	11	13	3	2			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr17:20921295C>T	ENST00000261497.4	-	5	853	c.650G>A	c.(649-651)aGc>aAc	p.S217N	USP22_ENST00000537526.2_Missense_Mutation_p.S205N|USP22_ENST00000455117.2_Intron	NM_015276.1	NP_056091.1	Q9UPT9	UBP22_HUMAN	ubiquitin specific peptidase 22	217	USP.				cell cycle (GO:0007049)|chromatin organization (GO:0006325)|embryo development (GO:0009790)|histone deubiquitination (GO:0016578)|histone H4 acetylation (GO:0043967)|histone ubiquitination (GO:0016574)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|protein deubiquitination (GO:0016579)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	SAGA complex (GO:0000124)	enzyme binding (GO:0019899)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|transcription coactivator activity (GO:0003713)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)	15						CAGACAGGAGCTGGGGCTCTG	0.527																																					p.S217N		Atlas-SNP	.											.	USP22	45	.	0			c.G650A						.						88	96	93					17																	20921295		2034	4187	6221	SO:0001583	missense	23326	exon5			CAGGAGCTGGGGC	AB028986	CCDS42285.1	17p11.2	2006-11-24	2005-08-08		ENSG00000124422	ENSG00000124422		"Ubiquitin-specific peptidases"	12621	protein-coding gene	gene with protein product		612116	"ubiquitin specific protease 22", "ubiquitin specific peptidase 3-like"	USP3L		12838346	Standard	NM_015276		Approved	KIAA1063	uc002gym.4	Q9UPT9	OTTHUMG00000133621	ENST00000261497.4:c.650G>A	chr17.hg19:g.20921295C>T	ENSP00000261497:p.Ser217Asn	51.0	0.0		46.0	19.0	NM_015276	A0JNS3|Q2NLE2|Q6MZY4|Q8TBS8|Q96IW5	Missense_Mutation	SNP	ENST00000261497.4	hg19	CCDS42285.1	.	.	.	.	.	.	.	.	.	.	c	13.61	2.289910	0.40494	.	.	ENSG00000124422	ENST00000455117;ENST00000537526;ENST00000261497	T;T	0.30981	1.51;1.51	4.22	4.22	0.49857	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.64402	D	0.000002	T	0.18759	0.0450	N	0.21617	0.685	0.39370	D	0.966078	B;B	0.06786	0.001;0.0	B;B	0.12837	0.005;0.008	T	0.08207	-1.0733	10	0.15499	T	0.54	.	10.6249	0.45502	0.0:0.9091:0.0:0.0909	.	205;217	Q9UPT9-2;Q9UPT9	.;UBP22_HUMAN	N	285;205;217	ENSP00000440950:S205N;ENSP00000261497:S217N	ENSP00000261497:S217N	S	-	2	0	USP22	20861887	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.138000	0.64795	2.054000	0.61138	0.563000	0.77884	AGC	.	.		0.527	USP22-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444169.1			T	20921295	C	T	20921295	3	4	301	1	0	0	0	0	1	0	0	0	17069	797	28	3	963	3	USP22	17	20921295	Missense_Mutation	SNP	C	TCGA-G3-AAV5-01A-11D-A36X-10		20921295	60273915	58	43510										
LASP1	3927	hgsc.bcm.edu	37	chr17	37074888	37074888	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	gcgcggtgtatgactacagcGccgccgacgaggacgaggtc	16	12	0	1			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr17:37074888G>A	ENST00000318008.6	+	7	974	c.643G>A	c.(643-645)Gcc>Acc	p.A215T	LASP1_ENST00000435347.3_Missense_Mutation_p.A215T|LASP1_ENST00000433206.2_Missense_Mutation_p.A159T|RP1-56K13.3_ENST00000580121.1_RNA	NM_006148.2	NP_006139.1	Q14847	LASP1_HUMAN	LIM and SH3 protein 1	215	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				ion transport (GO:0006811)|positive regulation of signal transduction (GO:0009967)	cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	ion transmembrane transporter activity (GO:0015075)|SH3/SH2 adaptor activity (GO:0005070)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(2)|lung(4)|urinary_tract(2)	9						TGACTACAGCGCCGCCGACGA	0.627			T	MLL	AML																																p.A215T		Atlas-SNP	.		Dom	yes		17	17q11-q21.3	3927	LIM and SH3 protein 1		L	.	LASP1	24	.	0			c.G643A						.						103	92	96					17																	37074888		2203	4300	6503	SO:0001583	missense	3927	exon7			TACAGCGCCGCCG		CCDS11331.1, CCDS62164.1	17q11-q21.3	2008-07-18			ENSG00000002834	ENSG00000002834			6513	protein-coding gene	gene with protein product		602920				7490069	Standard	NM_006148		Approved	MLN50, Lasp-1	uc010cvq.3	Q14847	OTTHUMG00000133182	ENST00000318008.6:c.643G>A	chr17.hg19:g.37074888G>A	ENSP00000325240:p.Ala215Thr	106.0	0.0		137.0	34.0	NM_006148	B4DGQ0|Q96ED2|Q96IG0	Missense_Mutation	SNP	ENST00000318008.6	hg19	CCDS11331.1	.	.	.	.	.	.	.	.	.	.	G	36	5.888562	0.97068	.	.	ENSG00000002834	ENST00000318008;ENST00000433206;ENST00000435347	T;T;T	0.52754	0.65;0.65;0.65	5.39	5.39	0.77823	Src homology-3 domain (5);	3.527180	0.02460	N	0.086506	T	0.81889	0.4918	M	0.93939	3.475	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.68108	-0.5496	10	0.87932	D	0	.	17.7153	0.88335	0.0:0.0:1.0:0.0	.	159;215	B4DGQ0;Q14847	.;LASP1_HUMAN	T	215;159;215	ENSP00000325240:A215T;ENSP00000401048:A159T;ENSP00000392853:A215T	ENSP00000325240:A215T	A	+	1	0	LASP1	34328414	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	9.779000	0.99018	2.540000	0.85666	0.462000	0.41574	GCC	.	.		0.627	LASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256890.3	NM_006148		A	37074888	G	A	37074888	3	1	301	1	0	0	0	0	1	0	0	0	8646	1087	38	1	669	1	LASP1	17	37074888	Missense_Mutation	SNP	G	TCGA-G3-AAV5-01A-11D-A36X-10	16153593	37074888	44120322	59	43511										
KRT35	3886	hgsc.bcm.edu	37	chr17	39635730	39635730	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	gatgtctgactccaccagctGccgcagggacacctccgtct	10	16	2	1			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr17:39635730G>T	ENST00000393989.1	-	3	622	c.580C>A	c.(580-582)Cag>Aag	p.Q194K	KRT35_ENST00000246639.2_Missense_Mutation_p.Q164K	NM_002280.4	NP_002271.3	Q92764	KRT35_HUMAN	keratin 35	194	Coil 1B.|Rod.				anatomical structure morphogenesis (GO:0009653)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	29		Breast(137;0.000286)				TCCACCAGCTGCCGCAGGGAC	0.587																																					p.Q194K		Atlas-SNP	.											.	KRT35	58	.	0			c.C580A						.						86	81	83					17																	39635730		2203	4300	6503	SO:0001583	missense	3886	exon3			CCAGCTGCCGCAG	X90762	CCDS11394.2	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000197079	ENSG00000197079		"-", "Intermediate filaments type I, keratins (acidic)"	6453	protein-coding gene	gene with protein product	"hard keratin type I 5"	602764	"keratin, hair, acidic, 5"	KRTHA5		8823373, 16831889	Standard	NM_002280		Approved	Ha-5	uc002hws.3	Q92764	OTTHUMG00000133425	ENST00000393989.1:c.580C>A	chr17.hg19:g.39635730G>T	ENSP00000377558:p.Gln194Lys	72.0	0.0		112.0	63.0	NM_002280	O76012|Q92651	Missense_Mutation	SNP	ENST00000393989.1	hg19	CCDS11394.2	.	.	.	.	.	.	.	.	.	.	G	18.42	3.619124	0.66787	.	.	ENSG00000197079	ENST00000246639;ENST00000393989	D;D	0.88896	-2.44;-2.44	4.47	4.47	0.54385	Filament (1);	0.000000	0.48767	D	0.000178	D	0.91965	0.7455	M	0.78916	2.43	0.31625	N	0.649795	P	0.44260	0.83	P	0.53760	0.734	D	0.92381	0.5913	10	0.59425	D	0.04	.	11.8454	0.52381	0.0:0.0:0.8253:0.1747	.	194	Q92764	KRT35_HUMAN	K	164;194	ENSP00000246639:Q164K;ENSP00000377558:Q194K	ENSP00000246639:Q164K	Q	-	1	0	KRT35	36889256	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	3.799000	0.55529	2.456000	0.83038	0.655000	0.94253	CAG	.	.		0.587	KRT35-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_002280		T	39635730	G	T	39635730	3	4	301	1	0	0	0	0	1	0	0	0	8481	1328	46	3	807	3	KRT35	17	39635730	Missense_Mutation	SNP	G	TCGA-G3-AAV5-01A-11D-A36X-10	2560842	39635730	41559480	60	43512										
THOC4	10189	hgsc.bcm.edu	37	chr17	79848595	79848595	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	gcgtctgagactccaaaatcCagattggacaccagcagttt	9	11	1	2			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr17:79848595C>T	ENST00000331204.4	-	2	365	c.339G>A	c.(337-339)ctG>ctA	p.L113L	ANAPC11_ENST00000392376.3_5'Flank|ANAPC11_ENST00000579133.1_5'Flank|ANAPC11_ENST00000571570.1_5'Flank|ANAPC11_ENST00000357385.3_5'Flank|ANAPC11_ENST00000577747.1_5'Flank|ANAPC11_ENST00000583839.1_5'Flank|ANAPC11_ENST00000572851.2_5'Flank|ALYREF_ENST00000505490.2_Silent_p.L120L|ANAPC11_ENST00000571024.2_5'Flank|ANAPC11_ENST00000572639.1_5'Flank|ANAPC11_ENST00000574924.2_5'Flank|ANAPC11_ENST00000582222.1_5'Flank|ANAPC11_ENST00000571874.2_5'Flank|ANAPC11_ENST00000577425.1_5'Flank|ANAPC11_ENST00000584314.1_5'Flank|ANAPC11_ENST00000578550.1_5'Flank|ANAPC11_ENST00000579978.1_5'Flank|ALYREF_ENST00000512673.1_5'UTR|ANAPC11_ENST00000344877.5_5'Flank|ANAPC11_ENST00000578544.1_5'Flank	NM_005782.3	NP_005773.3	Q86V81	THOC4_HUMAN	Aly/REF export factor	113	Ala/Arg/Gly-rich.|Interaction with HHV-8 ORF57 protein and with ICP27 from HHV-1. {ECO:0000250}.|RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|regulation of DNA recombination (GO:0000018)|replication fork processing (GO:0031297)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)|viral mRNA export from host cell nucleus (GO:0046784)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|transcription export complex (GO:0000346)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|single-stranded DNA binding (GO:0003697)										CTCCAAAATCCAGATTGGACA	0.567																																					p.L120L		Atlas-SNP	.											.	.	.	.	0			c.G360A						.						87	80	82					17																	79848595		2203	4300	6503	SO:0001819	synonymous_variant	10189	exon2			AAAATCCAGATTG	AF047002	CCDS32768.1, CCDS32768.2	17q25.3	2013-02-12	2011-12-12	2011-12-12	ENSG00000183684	ENSG00000183684		"THO complex subunits", "RNA binding motif (RRM) containing"	19071	protein-coding gene	gene with protein product		604171	"THO complex 4"	THOC4		11032328	Standard	NM_005782		Approved	ALY, BEF, ALY/REF, REF	uc002kbu.2	Q86V81	OTTHUMG00000160470	ENST00000331204.4:c.339G>A	chr17.hg19:g.79848595C>T		62.0	0.0		124.0	61.0	NM_005782	O43672	Silent	SNP	ENST00000331204.4	hg19																																																																																				.	.		0.567	ALYREF-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_005782		T	79848595	C	T	79848595	2	4	301	1	0	0	0	0	0	0	0	1	15882	581	21	3		3	THOC4	17	79848595	Silent	SNP	C	TCGA-G3-AAV5-01A-11D-A36X-10	40212865	79848595	1346615	61	43513										
C19orf20	91978	hgsc.bcm.edu	37	chr19	519341	519341	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	ccgcgccgtcggggggcggcGgcccagcgcgcccatgaccc	17	19	0	1	rs550238099	byFrequency	TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr19:519341G>T	ENST00000359315.5	+	2	999	c.791G>T	c.(790-792)cGg>cTg	p.R264L		NM_033513.2	NP_277048.2	Q6ZTW0	TPGS1_HUMAN	tubulin polyglutamylase complex subunit 1	264					adult behavior (GO:0030534)|multicellular organismal development (GO:0007275)|protein polyglutamylation (GO:0018095)|sperm axoneme assembly (GO:0007288)|synaptic transmission (GO:0007268)|vesicle localization (GO:0051648)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)	tubulin-glutamic acid ligase activity (GO:0070740)										GGGGGGCGGCGGCCCAGCGCG	0.791													g|||	7	0.00139776	8e-04	0	5008	,	,		4409	0		0.005	False		,,,				2504	0.001				p.R264L		Atlas-SNP	.											.	.	.	.	0			c.G791T						.																																			SO:0001583	missense	91978	exon2			GGCGGCGGCCCAG	BC009520	CCDS42454.1	19p13.3	2011-11-23	2011-11-23	2011-11-23	ENSG00000141933	ENSG00000141933			25058	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 20"	C19orf20		11441184, 12972506	Standard	NM_033513		Approved	GTRGEO22, PGs1	uc002lou.3	Q6ZTW0		ENST00000359315.5:c.791G>T	chr19.hg19:g.519341G>T	ENSP00000352265:p.Arg264Leu	0.0	0.0		7.0	6.0	NM_033513	Q96GE2	Missense_Mutation	SNP	ENST00000359315.5	hg19	CCDS42454.1	.	.	.	.	.	.	.	.	.	.	G	13.90	2.374462	0.42105	.	.	ENSG00000141933	ENST00000359315	.	.	.	3.61	2.49	0.30216	.	.	.	.	.	T	0.15522	0.0374	N	0.24115	0.695	0.09310	N	1	P	0.37176	0.586	B	0.31337	0.128	T	0.09487	-1.0672	8	0.42905	T	0.14	-16.7894	3.4176	0.07381	0.3759:0.0:0.6241:0.0	.	264	Q6ZTW0	TPGS1_HUMAN	L	264	.	ENSP00000352265:R264L	R	+	2	0	C19orf20	470341	1.000000	0.71417	0.114000	0.21550	0.854000	0.48673	3.687000	0.54692	1.910000	0.55303	0.444000	0.29173	CGG	.	.		0.791	TPGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451887.2	NM_033513		T	519341	G	T	519341	3	4	301	1	0	0	0	0	1	0	0	0	1914	1116	39	1	797	1	C19orf20	19	519341	Missense_Mutation	SNP	G	TCGA-G3-AAV5-01A-11D-A36X-10		519341	58609642	62	43514										
CD97	976	hgsc.bcm.edu	37	chr19	14517933	14517933	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	ggctgcacctgggtctttggCctgttcatcttcgacgatcg	12	12	3	0			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr19:14517933C>G	ENST00000242786.5	+	18	2348	c.2268C>G	c.(2266-2268)ggC>ggG	p.G756G	CTC-548K16.5_ENST00000590626.1_RNA|CD97_ENST00000358600.3_Silent_p.G663G|CD97_ENST00000357355.3_Silent_p.G707G|DDX39A_ENST00000592927.1_5'Flank	NM_078481.3	NP_510966.1	P48960	CD97_HUMAN	CD97 molecule	756					cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						GGGTCTTTGGCCTGTTCATCT	0.627																																					p.G756G		Atlas-SNP	.											.	CD97	86	.	0			c.C2268G						.						155	115	129					19																	14517933		2203	4300	6503	SO:0001819	synonymous_variant	976	exon18			CTTTGGCCTGTTC		CCDS32929.1, CCDS32930.1, CCDS32931.1	19p13	2014-08-08	2006-03-28			ENSG00000123146		"CD molecules", "-", "GPCR / Class B : Orphans"	1711	protein-coding gene	gene with protein product	"leukocyte antigen CD97", "seven-span transmembrane protein", "seven-transmembrane, heterodimeric receptor associated with inflammation", "seven transmembrane helix receptor"	601211	"CD97 antigen"			7636245, 8786105	Standard	NM_078481		Approved	TM7LN1	uc002myl.3	P48960		ENST00000242786.5:c.2268C>G	chr19.hg19:g.14517933C>G		65.0	0.0		70.0	22.0	NM_078481	A8K7Z4|B2RBJ9|O00718|O76101|Q8NG72|Q8TBQ7	Silent	SNP	ENST00000242786.5	hg19	CCDS32929.1																																																																																			.	.		0.627	CD97-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459821.2	NM_078481		G	14517933	C	G	14517933	2	3	301	1	0	0	0	0	0	0	0	1	3051	726	26	4		4	CD97	19	14517933	Silent	SNP	C	TCGA-G3-AAV5-01A-11D-A36X-10	13998592	14517933	44611050	63	43515										
QPCTL	54814	hgsc.bcm.edu	37	chr19	46196071	46196071	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	accgcgggttcggctcttgcCtctgttgctggcgctggccg	15	14	2	0			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr19:46196071C>T	ENST00000012049.5	+	1	331	c.110C>T	c.(109-111)cCt>cTt	p.P37L	SNRPD2_ENST00000391932.3_5'Flank|SNRPD2_ENST00000588599.1_5'Flank|SNRPD2_ENST00000588301.1_5'Flank|SNRPD2_ENST00000587367.1_5'Flank|SNRPD2_ENST00000590212.1_5'Flank|SNRPD2_ENST00000587579.1_5'Flank|QPCTL_ENST00000366382.4_Missense_Mutation_p.P37L|SNRPD2_ENST00000585392.1_5'Flank|SNRPD2_ENST00000342669.3_5'Flank	NM_017659.3	NP_060129.2	Q9NXS2	QPCTL_HUMAN	glutaminyl-peptide cyclotransferase-like	37					peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase (GO:0017186)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glutaminyl-peptide cyclotransferase activity (GO:0016603)|zinc ion binding (GO:0008270)			breast(1)|cervix(2)|endometrium(1)|lung(5)|skin(1)|stomach(1)	11		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0059)|GBM - Glioblastoma multiforme(486;0.0882)|Epithelial(262;0.208)		CGGCTCTTGCCTCTGTTGCTG	0.731																																					p.P37L		Atlas-SNP	.											.	QPCTL	24	.	0			c.C110T						.						12	13	12					19																	46196071		2172	4255	6427	SO:0001583	missense	54814	exon1			TCTTGCCTCTGTT	AK000091	CCDS12672.1, CCDS54282.1	19q13.32	2014-09-04			ENSG00000011478	ENSG00000011478			25952	protein-coding gene	gene with protein product	"glutaminyl cyclase-like"						Standard	NM_017659		Approved	FLJ20084	uc010xxr.2	Q9NXS2	OTTHUMG00000182131	ENST00000012049.5:c.110C>T	chr19.hg19:g.46196071C>T	ENSP00000012049:p.Pro37Leu	100.0	0.0		117.0	56.0	NM_017659	Q53HE4|Q96F74	Missense_Mutation	SNP	ENST00000012049.5	hg19	CCDS12672.1	.	.	.	.	.	.	.	.	.	.	C	16.98	3.271883	0.59649	.	.	ENSG00000011478	ENST00000012049;ENST00000366382	T;T	0.15017	2.46;2.46	5.01	5.01	0.66863	.	0.382752	0.26939	N	0.021731	T	0.33876	0.0878	L	0.60455	1.87	0.42686	D	0.993568	D	0.89917	1.0	D	0.83275	0.996	T	0.02437	-1.1159	10	0.11485	T	0.65	.	13.9992	0.64421	0.0:1.0:0.0:0.0	.	37	Q9NXS2	QPCTL_HUMAN	L	37	ENSP00000012049:P37L;ENSP00000387944:P37L	ENSP00000012049:P37L	P	+	2	0	QPCTL	50887911	0.182000	0.23173	0.990000	0.47175	0.475000	0.33008	1.182000	0.32029	2.768000	0.95171	0.561000	0.74099	CCT	.	.		0.731	QPCTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459656.1	NM_017659		T	46196071	C	T	46196071	3	4	301	1	0	0	0	0	1	0	0	0	12890	681	24	3	112	3	QPCTL	19	46196071	Missense_Mutation	SNP	C	TCGA-G3-AAV5-01A-11D-A36X-10	31678138	46196071	12932912	64	43516										
BAX	581	hgsc.bcm.edu	37	chr19	49459465	49459465	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	tctcctgcaggatgattgccGccgtggacacagactccccc	10	16	1	2			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr19:49459465G>T	ENST00000345358.7	+	4	296	c.244G>T	c.(244-246)Gcc>Tcc	p.A82S	BAX_ENST00000354470.3_Missense_Mutation_p.A33S|BAX_ENST00000391871.3_3'UTR|BAX_ENST00000539787.1_Missense_Mutation_p.A82S|BAX_ENST00000293288.8_Missense_Mutation_p.A82S|BAX_ENST00000415969.2_Missense_Mutation_p.A82S	NM_138761.3|NM_138764.4	NP_620116.1|NP_620119.2	Q07812	BAX_HUMAN	BCL2-associated X protein	82					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|apoptotic mitochondrial changes (GO:0008637)|apoptotic process (GO:0006915)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|apoptotic process involved in patterning of blood vessels (GO:1902262)|apoptotic signaling pathway (GO:0097190)|B cell apoptotic process (GO:0001783)|B cell homeostasis (GO:0001782)|B cell homeostatic proliferation (GO:0002358)|B cell negative selection (GO:0002352)|B cell receptor apoptotic signaling pathway (GO:1990117)|blood vessel remodeling (GO:0001974)|cellular response to organic substance (GO:0071310)|cellular response to UV (GO:0034644)|cerebral cortex development (GO:0021987)|development of secondary sexual characteristics (GO:0045136)|ectopic germ cell programmed cell death (GO:0035234)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|establishment or maintenance of transmembrane electrochemical gradient (GO:0010248)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|fertilization (GO:0009566)|germ cell development (GO:0007281)|glycosphingolipid metabolic process (GO:0006687)|homeostasis of number of cells within a tissue (GO:0048873)|hypothalamus development (GO:0021854)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|kidney development (GO:0001822)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial fusion (GO:0008053)|mitochondrion morphogenesis (GO:0070584)|myeloid cell homeostasis (GO:0002262)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein binding (GO:0032091)|neuron apoptotic process (GO:0051402)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|ovarian follicle development (GO:0001541)|positive regulation of apoptotic DNA fragmentation (GO:1902512)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of B cell apoptotic process (GO:0002904)|positive regulation of developmental pigmentation (GO:0048087)|positive regulation of endoplasmic reticulum unfolded protein response (GO:1900103)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|post-embryonic camera-type eye morphogenesis (GO:0048597)|protein homooligomerization (GO:0051260)|protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:0001844)|protein oligomerization (GO:0051259)|regulation of cell cycle (GO:0051726)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|regulation of mitochondrial membrane permeability involved in programmed necrotic cell death (GO:1902445)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of nitrogen utilization (GO:0006808)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|release of cytochrome c from mitochondria (GO:0001836)|release of matrix enzymes from mitochondria (GO:0032976)|response to axon injury (GO:0048678)|response to gamma radiation (GO:0010332)|response to salt stress (GO:0009651)|response to toxic substance (GO:0009636)|retina development in camera-type eye (GO:0060041)|retinal cell apoptotic process (GO:1990009)|retinal cell programmed cell death (GO:0046666)|Sertoli cell proliferation (GO:0060011)|spermatid differentiation (GO:0048515)|T cell homeostatic proliferation (GO:0001777)|thymocyte apoptotic process (GO:0070242)|transformed cell apoptotic process (GO:0006927)|vagina development (GO:0060068)|viral process (GO:0016032)	BAX complex (GO:0097144)|Bcl-2 family protein complex (GO:0097136)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrial permeability transition pore complex (GO:0005757)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|pore complex (GO:0046930)	BH3 domain binding (GO:0051434)|channel activity (GO:0015267)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(7)|skin(2)|urinary_tract(4)	17		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000159)|all cancers(93;0.00047)|GBM - Glioblastoma multiforme(486;0.018)|Epithelial(262;0.0279)		GATGATTGCCGCCGTGGACAC	0.567																																					p.A82S		Atlas-SNP	.											.	BAX	69	.	0			c.G244T						.						71	77	75					19																	49459465		2203	4300	6503	SO:0001583	missense	581	exon4			ATTGCCGCCGTGG		CCDS12742.1, CCDS12743.1, CCDS12744.1, CCDS12745.1, CCDS12745.2	19q13.3-q13.4	2014-03-07			ENSG00000087088	ENSG00000087088			959	protein-coding gene	gene with protein product		600040				8358790	Standard	NM_138761		Approved	BCL2L4	uc002plf.1	Q07812	OTTHUMG00000160476	ENST00000345358.7:c.244G>T	chr19.hg19:g.49459465G>T	ENSP00000263262:p.Ala82Ser	96.0	0.0		69.0	19.0	NM_004324	A8K4W1|P55269|Q07814|Q07815|Q8WZ49|Q9NR76|Q9NYG7|Q9UCZ6|Q9UCZ7|Q9UQD6	Missense_Mutation	SNP	ENST00000345358.7	hg19	CCDS12742.1	.	.	.	.	.	.	.	.	.	.	G	0.038	-1.298992	0.01364	.	.	ENSG00000087088	ENST00000539787;ENST00000345358;ENST00000415969;ENST00000354470;ENST00000293288	T;T;T;T;T	0.10860	2.83;2.83;2.83;2.83;2.83	4.05	4.05	0.47172	Apoptosis regulator, Bcl2-like (1);Apoptosis regulator, Bcl-2, BH (2);	0.354374	0.29015	N	0.013411	T	0.05593	0.0147	N	0.12182	0.205	0.28733	N	0.902377	B;B;B;B	0.15930	0.002;0.003;0.001;0.015	B;B;B;B	0.14023	0.004;0.005;0.008;0.01	T	0.27938	-1.0059	10	0.08381	T	0.77	-2.9585	12.029	0.53388	0.0:0.0:1.0:0.0	.	33;82;82;82	Q07812-4;Q07812;Q07812-8;Q07812-2	.;BAX_HUMAN;.;.	S	82;82;82;33;82	ENSP00000441413:A82S;ENSP00000263262:A82S;ENSP00000389971:A82S;ENSP00000346461:A33S;ENSP00000293288:A82S	ENSP00000293288:A82S	A	+	1	0	BAX	54151277	0.002000	0.14202	0.008000	0.14137	0.051000	0.14879	0.943000	0.29030	2.549000	0.85964	0.563000	0.77884	GCC	.	.		0.567	BAX-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360767.1	NM_138763		T	49459465	G	T	49459465	3	4	301	1	0	0	0	0	1	0	0	0	1328	1087	38	1	258	1	BAX	19	49459465	Missense_Mutation	SNP	G	TCGA-G3-AAV5-01A-11D-A36X-10	3263394	49459465	9669518	65	43517										
TSKS	60385	hgsc.bcm.edu	37	chr19	50250010	50250010	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	cagctcggcctcctgccgtcGcggcgtctcatcctgcagct	11	18	1	0			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr19:50250010G>A	ENST00000246801.3	-	6	791	c.709C>T	c.(709-711)Cga>Tga	p.R237*	TSKS_ENST00000358830.3_Nonsense_Mutation_p.R37*	NM_021733.1	NP_068379.1	Q9UJT2	TSKS_HUMAN	testis-specific serine kinase substrate	237					negative regulation of phosphatase activity (GO:0010923)	centriole (GO:0005814)	protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(9)|prostate(3)|skin(3)	38		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(134;0.0145)		tcctgccgtcgcggcgtctca	0.677																																					p.R237X		Atlas-SNP	.											.	TSKS	97	.	0			c.C709T						.						17	16	17					19																	50250010		2186	4263	6449	SO:0001587	stop_gained	60385	exon6			GCCGTCGCGGCGT	BC058862	CCDS12780.1	19q13.3	2014-06-13							30719	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 161"	608253				11444856, 18495105	Standard	NM_021733		Approved	TSSKS, PPP1R161	uc002ppm.3	Q9UJT2		ENST00000246801.3:c.709C>T	chr19.hg19:g.50250010G>A	ENSP00000246801:p.Arg237*	48.0	0.0		43.0	16.0	NM_021733	Q8WXJ0	Nonsense_Mutation	SNP	ENST00000246801.3	hg19	CCDS12780.1	.	.	.	.	.	.	.	.	.	.	-	32	5.142036	0.94560	.	.	ENSG00000126467	ENST00000246801;ENST00000358830	.	.	.	4.78	1.13	0.20643	.	0.000000	0.42964	D	0.000627	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-21.0456	10.5632	0.45156	0.0:0.0:0.4723:0.5277	.	.	.	.	X	237;37	.	ENSP00000246801:R237X	R	-	1	2	TSKS	54941822	0.699000	0.27786	0.436000	0.26797	0.580000	0.36256	1.064000	0.30579	0.556000	0.29098	0.591000	0.81541	CGA	.	.		0.677	TSKS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465795.1	NM_021733		A	50250010	G	A	50250010	4	1	301	1	0	0	0	0	0	1	0	0	16641	1095	38	1	1093	1	TSKS	19	50250010	Nonsense_Mutation	SNP	G	TCGA-G3-AAV5-01A-11D-A36X-10	790545	50250010	8878973	66	43518										
PTPRA	5786	hgsc.bcm.edu	37	chr20	3005219	3005219	+	Nonsense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	acccacctgcagaaaatttaCaacaaaatcccagggaccag	6	13	0	1			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr20:3005219C>G	ENST00000216877.6	+	16	1939	c.1539C>G	c.(1537-1539)taC>taG	p.Y513*	PTPRA_ENST00000399903.2_Nonsense_Mutation_p.Y522*|PTPRA_ENST00000318266.5_Nonsense_Mutation_p.Y513*|PTPRA_ENST00000356147.3_Nonsense_Mutation_p.Y513*|PTPRA_ENST00000380393.3_Nonsense_Mutation_p.Y522*|PTPRA_ENST00000358719.4_Nonsense_Mutation_p.Y378*|PTPRA_ENST00000425918.2_Nonsense_Mutation_p.Y533*	NM_080840.2	NP_543030.1	P18433	PTPRA_HUMAN	protein tyrosine phosphatase, receptor type, A	522					axon guidance (GO:0007411)|insulin receptor signaling pathway (GO:0008286)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein phosphorylation (GO:0006468)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						AGAAAATTTACAACAAAATCC	0.438																																					p.Y522X		Atlas-SNP	.											.	PTPRA	75	.	0			c.C1566G						.						121	124	123					20																	3005219		2203	4300	6503	SO:0001587	stop_gained	5786	exon21			AATTTACAACAAA		CCDS13038.1, CCDS13039.1	20p13	2011-06-09			ENSG00000132670	ENSG00000132670		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9664	protein-coding gene	gene with protein product		176884		PTPRL2, PTPA		2172030, 2169617	Standard	NM_080840		Approved	LRP, HLPR, HPTPA, RPTPA	uc002whn.3	P18433	OTTHUMG00000031718	ENST00000216877.6:c.1539C>G	chr20.hg19:g.3005219C>G	ENSP00000216877:p.Tyr513*	139.0	0.0		161.0	54.0	NM_002836	A8K2G8|D3DVX5|Q14513|Q7Z2I2|Q96TD9	Nonsense_Mutation	SNP	ENST00000216877.6	hg19	CCDS13039.1	.	.	.	.	.	.	.	.	.	.	C	41	8.620370	0.98888	.	.	ENSG00000132670	ENST00000380393;ENST00000216877;ENST00000399903;ENST00000358719;ENST00000542217;ENST00000425918;ENST00000318266;ENST00000356147	.	.	.	6.04	3.07	0.35406	.	0.000000	0.85682	U	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.891	0.41290	0.0:0.7259:0.0:0.2741	.	.	.	.	X	522;513;522;378;132;533;513;513	.	ENSP00000216877:Y513X	Y	+	3	2	PTPRA	2953219	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.582000	0.36568	0.439000	0.26476	0.561000	0.74099	TAC	.	.		0.438	PTPRA-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077682.3			G	3005219	C	G	3005219	4	3	301	1	0	0	0	0	0	1	0	0	12810	489	17	4	1620	4	PTPRA	20	3005219	Nonsense_Mutation	SNP	C	TCGA-G3-AAV5-01A-11D-A36X-10		3005219	60020301	67	43519										
ADNP	23394	hgsc.bcm.edu	37	chr20	49510049	49510049	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	ttaactggcccgatgagagaGaagaggcattagcagactgc	13	8	0	4			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr20:49510049G>C	ENST00000396029.3	-	5	1769	c.1202C>G	c.(1201-1203)tCt>tGt	p.S401C	ADNP_ENST00000349014.3_Missense_Mutation_p.S401C|ADNP_ENST00000396032.3_Missense_Mutation_p.S401C|ADNP_ENST00000371602.4_Missense_Mutation_p.S401C	NM_001282531.1|NM_015339.2	NP_001269460.1|NP_056154.1	Q9H2P0	ADNP_HUMAN	activity-dependent neuroprotector homeobox	401					negative regulation of neuron apoptotic process (GO:0043524)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(4)|endometrium(7)|kidney(1)|large_intestine(13)|lung(7)|ovary(2)|prostate(2)|skin(2)	39						CGATGAGAGAGAAGAGGCATT	0.542																																					p.S401C		Atlas-SNP	.											.	ADNP	106	.	0			c.C1202G						.						113	115	114					20																	49510049		2203	4300	6503	SO:0001583	missense	23394	exon5			GAGAGAGAAGAGG	AF250860	CCDS13433.1	20q13.13	2011-06-20	2007-07-17		ENSG00000101126	ENSG00000101126		"Homeoboxes / ZF class"	15766	protein-coding gene	gene with protein product	"ADNP homeobox 1"	611386	"activity-dependent neuroprotector"			9872452, 11013255	Standard	NM_015339		Approved	KIAA0784, ADNP1	uc002xvu.1	Q9H2P0	OTTHUMG00000032737	ENST00000396029.3:c.1202C>G	chr20.hg19:g.49510049G>C	ENSP00000379346:p.Ser401Cys	45.0	0.0		35.0	15.0	NM_015339	E1P5Y2|O94881|Q5BKU2|Q9UG34	Missense_Mutation	SNP	ENST00000396029.3	hg19	CCDS13433.1	.	.	.	.	.	.	.	.	.	.	G	13.29	2.193589	0.38707	.	.	ENSG00000101126	ENST00000371602;ENST00000349014;ENST00000396029;ENST00000396032	.	.	.	6.17	6.17	0.99709	.	0.451467	0.26052	N	0.026638	T	0.63931	0.2553	N	0.19112	0.55	0.38892	D	0.95713	D	0.64830	0.994	D	0.73708	0.981	T	0.67118	-0.5751	9	0.59425	D	0.04	-28.6145	16.2608	0.82541	0.0:0.1316:0.8683:0.0	.	401	Q9H2P0	ADNP_HUMAN	C	401	.	ENSP00000342905:S401C	S	-	2	0	ADNP	48943456	0.992000	0.36948	0.073000	0.20177	0.709000	0.40893	4.910000	0.63321	2.941000	0.99782	0.655000	0.94253	TCT	.	.		0.542	ADNP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079705.2	NM_181442		C	49510049	G	C	49510049	3	2	301	1	0	0	0	0	1	0	0	0	323	942	33	4	2110	4	ADNP	20	49510049	Missense_Mutation	SNP	G	TCGA-G3-AAV5-01A-11D-A36X-10	46504830	49510049	13515471	68	43520										
C20orf107	388799	hgsc.bcm.edu	37	chr20	55111382	55111382	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	cgaagtgcagaatcttaaagGtgccatggcaacaggcagtg	13	8	1	1			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr20:55111382G>A	ENST00000371325.1	+	2	500	c.404G>A	c.(403-405)gGt>gAt	p.G135D		NM_001013646.2	NP_001013668.2	Q5JX69	F209B_HUMAN	family with sequence similarity 209, member B	135						integral component of membrane (GO:0016021)|nucleus (GO:0005634)											AATCTTAAAGGTGCCATGGCA	0.413																																					p.G135D		Atlas-SNP	.											.	.	.	.	0			c.G404A						.						101	100	100					20																	55111382		2203	4300	6503	SO:0001583	missense	388799	exon2			TTAAAGGTGCCAT	AL109806	CCDS33494.1	20q13.31	2011-11-24	2011-11-24	2011-11-24	ENSG00000213714	ENSG00000213714			16101	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 107"	C20orf107			Standard	NM_001013646		Approved	dJ1153D9.4	uc002xxz.4	Q5JX69	OTTHUMG00000032800	ENST00000371325.1:c.404G>A	chr20.hg19:g.55111382G>A	ENSP00000360376:p.Gly135Asp	179.0	0.0		213.0	10.0	NM_001013646	Q3KRB5	Missense_Mutation	SNP	ENST00000371325.1	hg19	CCDS33494.1	.	.	.	.	.	.	.	.	.	.	G	2.124	-0.400622	0.04865	.	.	ENSG00000213714	ENST00000371325	T	0.07688	3.17	3.55	-3.85	0.04243	.	0.740081	0.11437	N	0.564191	T	0.04724	0.0128	L	0.29908	0.895	0.09310	N	1	P	0.35982	0.531	B	0.32289	0.143	T	0.26292	-1.0107	10	0.48119	T	0.1	-3.4122	5.3394	0.15974	0.0:0.4265:0.1759:0.3976	.	135	Q5JX69	CT107_HUMAN	D	135	ENSP00000360376:G135D	ENSP00000360376:G135D	G	+	2	0	C20orf107	54544789	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.658000	0.05329	-0.919000	0.03803	-1.694000	0.00725	GGT	.	.		0.413	FAM209B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079816.1			A	55111382	G	A	55111382	3	1	301	1	0	0	0	0	1	0	0	0	2079	1261	44	3	410	3	C20orf107	20	55111382	Missense_Mutation	SNP	G	TCGA-G3-AAV5-01A-11D-A36X-10	5601333	55111382	7914138	69	43521										
SLC5A1	6523	hgsc.bcm.edu	37	chr22	32495294	32495294	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0428571428571429	3	1	0.652290303390839	1.11432926829268	0.540280857354028	1	1	0	acttgggaccacccattgcgGctgtcttcctgcttgctatt	9	13	1	0			TCGA-G3-AAV5-01A-11D-A36X-10	TCGA-G3-AAV5-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b43b12f-f84d-4283-9cd3-10dab5e6e45a	6f867add-e781-468a-96fe-bb81275f0c31	g.chr22:32495294G>A	ENST00000266088.4	+	12	1655	c.1405G>A	c.(1405-1407)Gct>Act	p.A469T	SLC5A1_ENST00000543737.1_Missense_Mutation_p.A342T	NM_000343.3	NP_000334.1	P13866	SC5A1_HUMAN	solute carrier family 5 (sodium/glucose cotransporter), member 1	469					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|intestinal absorption (GO:0050892)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	glucose:sodium symporter activity (GO:0005412)			NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(2)|skin(4)|urinary_tract(1)	37					Canagliflozin(DB08907)	ACCCATTGCGGCTGTCTTCCT	0.493																																					p.A469T		Atlas-SNP	.											.	SLC5A1	80	.	0			c.G1405A						.						235	220	225					22																	32495294		2203	4300	6503	SO:0001583	missense	6523	exon12			ATTGCGGCTGTCT		CCDS13902.1, CCDS58805.1	22q12.3	2013-05-22			ENSG00000100170	ENSG00000100170		"Solute carriers"	11036	protein-coding gene	gene with protein product	"sodium/glucose cotransporter 1"	182380		SGLT1		8195156	Standard	NM_000343		Approved	D22S675, NAGT	uc003amc.3	P13866	OTTHUMG00000030768	ENST00000266088.4:c.1405G>A	chr22.hg19:g.32495294G>A	ENSP00000266088:p.Ala469Thr	68.0	0.0		84.0	4.0	NM_000343	B2R7E2|B7Z4Q9|B7ZA69	Missense_Mutation	SNP	ENST00000266088.4	hg19	CCDS13902.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.861702	0.91433	.	.	ENSG00000100170	ENST00000266088;ENST00000543737	D;D	0.89343	-2.5;-2.5	5.61	5.61	0.85477	.	0.048412	0.85682	D	0.000000	D	0.91536	0.7327	M	0.67700	2.07	0.80722	D	1	D	0.53462	0.96	P	0.54924	0.764	D	0.91825	0.5470	10	0.62326	D	0.03	.	13.578	0.61885	0.0:0.0:0.8447:0.1553	.	469	P13866	SC5A1_HUMAN	T	469;342	ENSP00000266088:A469T;ENSP00000444898:A342T	ENSP00000266088:A469T	A	+	1	0	SLC5A1	30825294	1.000000	0.71417	0.996000	0.52242	0.884000	0.51177	4.488000	0.60300	2.647000	0.89833	0.557000	0.71058	GCT	.	.		0.493	SLC5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075656.3	NM_000343		A	32495294	G	A	32495294	3	1	301	1	0	0	0	0	1	0	0	0	14676	1203	42	3	1451	3	SLC5A1	22	32495294	Missense_Mutation	SNP	G	TCGA-G3-AAV5-01A-11D-A36X-10		32495294	18809272	70	43522										
ELTD1	64123	hgsc.bcm.edu	37	chr1	79357333	79357333	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	gaaccccaaagatccaggtgGtgccgagaaggaacagaaga	13	9	0	4			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr1:79357333G>T	ENST00000370742.3	-	14	1949	c.1886C>A	c.(1885-1887)aCc>aAc	p.T629N		NM_022159.3	NP_071442.2	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain containing 1	629					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.T629I(1)		NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(45)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	69				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)		GATCCAGGTGGTGCCGAGAAG	0.463																																					p.T629N		Atlas-SNP	.											ELTD1,NS,carcinoma,0,1	ELTD1	143	.	1	Substitution - Missense(1)	lung(1)	c.C1886A						.						64	65	64					1																	79357333		1972	4144	6116	SO:0001583	missense	64123	exon14			CAGGTGGTGCCGA	AF192403	CCDS41352.1	1p33-p32	2014-08-08			ENSG00000162618	ENSG00000162618		"-", "GPCR / Class B : Orphans"	20822	protein-coding gene	gene with protein product						11050079	Standard	NM_022159		Approved	ETL	uc001diq.4	Q9HBW9	OTTHUMG00000009738	ENST00000370742.3:c.1886C>A	chr1.hg19:g.79357333G>T	ENSP00000359778:p.Thr629Asn	82.0	0.0		56.0	6.0	NM_022159	B1AR71|Q5KU34	Missense_Mutation	SNP	ENST00000370742.3	hg19	CCDS41352.1	.	.	.	.	.	.	.	.	.	.	G	18.64	3.666751	0.67814	.	.	ENSG00000162618	ENST00000370742;ENST00000401034	T;T	0.44881	0.91;0.91	5.59	5.59	0.84812	GPCR, family 2-like (1);	0.185125	0.48767	D	0.000172	T	0.39545	0.1082	L	0.46819	1.47	0.32403	N	0.551694	P	0.48834	0.916	P	0.56865	0.808	T	0.31280	-0.9949	9	.	.	.	.	12.8706	0.57962	0.0745:0.0:0.9255:0.0	.	629	Q9HBW9	ELTD1_HUMAN	N	629;87	ENSP00000359778:T629N;ENSP00000383813:T87N	.	T	-	2	0	ELTD1	79129921	1.000000	0.71417	0.998000	0.56505	0.892000	0.51952	5.720000	0.68470	2.612000	0.88384	0.655000	0.94253	ACC	.	.		0.463	ELTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026859.1	NM_022159		T	79357333	G	T	79357333	3	4	302	1	0	0	0	0	1	0	0	0	5086	1261	44	3	194	3	ELTD1	1	79357333	Missense_Mutation	SNP	G	TCGA-G3-AAV6-01A-21D-A36X-10		79357333	169893288	1	43523										
PTPN14	5784	hgsc.bcm.edu	37	chr1	214557166	214557166	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	gtggctgcctgacccctcctCgggcggtccctgctcccgga	13	18	0	1			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr1:214557166C>T	ENST00000366956.5	-	13	2226	c.2032G>A	c.(2032-2034)Gag>Aag	p.E678K	PTPN14_ENST00000543945.1_3'UTR	NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type 14	678					lymphangiogenesis (GO:0001946)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of protein export from nucleus (GO:0046825)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)			NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	58				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		GACCCCTCCTCGGGCGGTCCC	0.627																																					p.E678K	Colon(92;557 1424 24372 34121 40073)	Atlas-SNP	.											.	PTPN14	168	.	0			c.G2032A						.						42	42	42					1																	214557166		2203	4300	6503	SO:0001583	missense	5784	exon13			CCTCCTCGGGCGG	X82676	CCDS1514.1	1q32.2	2011-06-09			ENSG00000152104	ENSG00000152104		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9647	protein-coding gene	gene with protein product		603155				7733990	Standard	NM_005401		Approved	PEZ	uc001hkk.2	Q15678	OTTHUMG00000037039	ENST00000366956.5:c.2032G>A	chr1.hg19:g.214557166C>T	ENSP00000355923:p.Glu678Lys	69.0	0.0		67.0	20.0	NM_005401	Q5VSI0	Missense_Mutation	SNP	ENST00000366956.5	hg19	CCDS1514.1	.	.	.	.	.	.	.	.	.	.	C	1.191	-0.635274	0.03584	.	.	ENSG00000152104	ENST00000366956	T	0.67345	-0.26	3.45	1.09	0.20402	.	0.598863	0.17926	N	0.157360	T	0.50463	0.1617	L	0.52759	1.655	0.45883	D	0.998739	B	0.20052	0.041	B	0.06405	0.002	T	0.24905	-1.0147	10	0.16420	T	0.52	.	4.1616	0.10287	0.0:0.5742:0.1878:0.2379	.	678	Q15678	PTN14_HUMAN	K	678	ENSP00000355923:E678K	ENSP00000355923:E678K	E	-	1	0	PTPN14	212623789	0.966000	0.33281	0.113000	0.21522	0.017000	0.09413	2.761000	0.47589	0.327000	0.23409	0.563000	0.77884	GAG	.	.		0.627	PTPN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089918.2	NM_005401		T	214557166	C	T	214557166	3	4	302	1	0	0	0	0	1	0	0	0	12796	893	31	1	1559	1	PTPN14	1	214557166	Missense_Mutation	SNP	C	TCGA-G3-AAV6-01A-21D-A36X-10	135199833	214557166	34693455	2	43524										
APOB	338	hgsc.bcm.edu	37	chr2	21239420	21239421	+	Frame_Shift_Ins	INS	-	-	TCCGAGGTCAACATCAAAA													0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	tcattaactctgaggattgtINStccgaggtcaacatcaaaat							TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr2:21239420_21239421insTCCGAGGTCAACATCAAAA	ENST00000233242.1	-	21	3349_3350	c.3222_3223insTTTTGATGTTGACCTCGGA	c.(3220-3225)ggaacafs	p.T1075fs		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	1075					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTGAGGATTGTTCCGAGGTCAA	0.45																																					p.T1075_I1076delinsFX		Atlas-INDEL	.											.	APOB	761	.	0			c.3223_3224insTTTTGATGTTGACCTCGGA						.																																			SO:0001589	frameshift_variant	338	exon21			.	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.3204_3222dupTTTTGATGTTGACCTCGGA	chr2.hg19:g.21239420_21239421insTCCGAGGTCAACATCAAAA	ENSP00000233242:p.Thr1075fs	165.0	0.0		145.0	10.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Frame_Shift_Ins	INS	ENST00000233242.1	hg19	CCDS1703.1																																																																																			.	.		0.45	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			TCCGAGGTCAACATCAAAA	21239421	-	TCCGAGGTCAACATCAAAA	21239420	7	5	302	1	0	1	1	0	0	0	0	0	785	1725	60	0	10504	0	APOB	2	21239420	Frame_Shift_Ins	INS	-	TCGA-G3-AAV6-01A-21D-A36X-10		21239420	221959953	3	43525										
CYP1B1	1545	hgsc.bcm.edu	37	chr2	38301854	38301854	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	cgcccgaactcttcgttgtgGctgagcagctcacggaactc	11	14	2	1			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr2:38301854G>C	ENST00000260630.3	-	2	1079	c.678C>G	c.(676-678)agC>agG	p.S226R	CYP1B1-AS1_ENST00000589303.1_RNA|CYP1B1_ENST00000407341.1_Missense_Mutation_p.S226R|CYP1B1-AS1_ENST00000431999.1_RNA|CYP1B1_ENST00000494864.1_Intron	NM_000104.3	NP_000095	Q16678	CP1B1_HUMAN	cytochrome P450, family 1, subfamily B, polypeptide 1	226					angiogenesis (GO:0001525)|arachidonic acid metabolic process (GO:0019369)|blood vessel morphogenesis (GO:0048514)|cell adhesion (GO:0007155)|cellular aromatic compound metabolic process (GO:0006725)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to organic cyclic compound (GO:0071407)|collagen fibril organization (GO:0030199)|endothelial cell migration (GO:0043542)|endothelial cell-cell adhesion (GO:0071603)|epoxygenase P450 pathway (GO:0019373)|estrogen metabolic process (GO:0008210)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|membrane lipid catabolic process (GO:0046466)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nitric oxide biosynthetic process (GO:0006809)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to toxic substance (GO:0009636)|retinal blood vessel morphogenesis (GO:0061304)|retinal metabolic process (GO:0042574)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|toxin metabolic process (GO:0009404)|trabecular meshwork development (GO:0002930)|visual perception (GO:0007601)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)	13		all_hematologic(82;0.21)			Amodiaquine(DB00613)|Arsenic trioxide(DB01169)|Biotin(DB00121)|Caffeine(DB00201)|Clozapine(DB00363)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Flutamide(DB00499)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Melatonin(DB01065)|Mitoxantrone(DB01204)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Primaquine(DB01087)|Procarbazine(DB01168)|Progesterone(DB00396)|Propofol(DB00818)|Tamoxifen(DB00675)|Testosterone(DB00624)|Theophylline(DB00277)	CTTCGTTGTGGCTGAGCAGCT	0.677																																					p.S226R		Atlas-SNP	.											.	CYP1B1	39	.	0			c.C678G						.						19	21	20					2																	38301854		2200	4296	6496	SO:0001583	missense	1545	exon2			GTTGTGGCTGAGC	U56438	CCDS1793.1	2p22.2	2008-02-05	2003-01-14		ENSG00000138061	ENSG00000138061		"Cytochrome P450s"	2597	protein-coding gene	gene with protein product		601771	"cytochrome P450, subfamily I (dioxin-inducible), polypeptide 1 (glaucoma 3, primary infantile)"	GLC3A		8175734, 15128046	Standard	NM_000104		Approved	CP1B	uc002rqo.2	Q16678	OTTHUMG00000100970	ENST00000260630.3:c.678C>G	chr2.hg19:g.38301854G>C	ENSP00000260630:p.Ser226Arg	289.0	0.0		320.0	27.0	NM_000104	Q5TZW8|Q93089|Q9H316	Missense_Mutation	SNP	ENST00000260630.3	hg19	CCDS1793.1	.	.	.	.	.	.	.	.	.	.	G	14.66	2.601532	0.46423	.	.	ENSG00000138061	ENST00000260630;ENST00000407341	T;T	0.67698	-0.28;-0.28	4.5	3.63	0.41609	.	0.048810	0.85682	D	0.000000	T	0.51346	0.1669	N	0.21545	0.675	0.36414	D	0.863895	P	0.42785	0.79	B	0.40565	0.333	T	0.61739	-0.7001	10	0.56958	D	0.05	.	10.0864	0.42421	0.0976:0.0:0.9024:0.0	.	226	Q53TK1	.	R	226	ENSP00000260630:S226R;ENSP00000384972:S226R	ENSP00000260630:S226R	S	-	3	2	CYP1B1	38155358	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	0.784000	0.26816	1.127000	0.42034	0.650000	0.86243	AGC	.	.		0.677	CYP1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218580.3	NM_000104		C	38301854	G	C	38301854	3	2	302	1	0	0	0	0	1	0	0	0	4153	1194	42	4	961	4	CYP1B1	2	38301854	Missense_Mutation	SNP	G	TCGA-G3-AAV6-01A-21D-A36X-10	17062434	38301854	204897519	4	43526										
PNPT1	87178	hgsc.bcm.edu	37	chr2	55871841	55871846	+	In_Frame_Del	DEL	GAACCT	GAACCT	-													0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	ttttgctcgttttgataatgGaacctgaacagtttctggaa							TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	GAACCT	GAACCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr2:55871841_55871846delGAACCT	ENST00000447944.2	-	23	1918_1923	c.1832_1837delAGGTTC	c.(1831-1839)caggttcca>cca	p.QV611del		NM_033109.3	NP_149100.2	Q8TCS8	PNPT1_HUMAN	polyribonucleotide nucleotidyltransferase 1	611	KH. {ECO:0000255|PROSITE- ProRule:PRU00117}.				cellular response to interferon-beta (GO:0035458)|cellular response to oxidative stress (GO:0034599)|mitochondrial mRNA catabolic process (GO:0000958)|mitochondrial mRNA polyadenylation (GO:0097222)|mitochondrial RNA 3'-end processing (GO:0000965)|mitochondrial RNA 5'-end processing (GO:0000964)|mitochondrial RNA catabolic process (GO:0000957)|mitochondrion morphogenesis (GO:0070584)|mitotic cell cycle arrest (GO:0071850)|mRNA catabolic process (GO:0006402)|negative regulation of growth (GO:0045926)|nuclear polyadenylation-dependent mRNA catabolic process (GO:0071042)|positive regulation of miRNA catabolic process (GO:2000627)|positive regulation of mitochondrial RNA catabolic process (GO:0000962)|positive regulation of mRNA catabolic process (GO:0061014)|protein homooligomerization (GO:0051260)|protein homotrimerization (GO:0070207)|regulation of cellular respiration (GO:0043457)|regulation of cellular senescence (GO:2000772)|RNA catabolic process (GO:0006401)|RNA import into mitochondrion (GO:0035927)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|RNA polyadenylation (GO:0043631)|rRNA import into mitochondrion (GO:0035928)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrial degradosome (GO:0045025)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)	3'-5'-exoribonuclease activity (GO:0000175)|miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|polyribonucleotide nucleotidyltransferase activity (GO:0004654)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(9)|skin(2)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			TTTGATAATGGAACCTGAACAGTTTC	0.325																																					p.611_613del		Atlas-INDEL	.											.	PNPT1	68	.	0			c.1833_1838del						.																																			SO:0001651	inframe_deletion	87178	exon23			.	BC053660	CCDS1856.1	2p15	2013-01-08			ENSG00000138035	ENSG00000138035			23166	protein-coding gene	gene with protein product	"polynucleotide phosphorylase", "3'-5' RNA exonuclease"	610316	"deafness, autosomal recessive 70"	DFNB70		12419256	Standard	NM_033109		Approved	PNPase, OLD35, old-35	uc002rzf.3	Q8TCS8	OTTHUMG00000129335	ENST00000447944.2:c.1832_1837delAGGTTC	chr2.hg19:g.55871841_55871846delGAACCT	ENSP00000400646:p.Gln611_Val612del	43.0	0.0		51.0	10.0	NM_033109	Q53SU0|Q68CN1|Q7Z7D1|Q8IWX1|Q96T05|Q9BRU3|Q9BVX0	In_Frame_Del	DEL	ENST00000447944.2	hg19	CCDS1856.1																																																																																			.	.		0.325	PNPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251481.2	NM_033109		-	55871846	GAACCT	-	55871841	7	5	302	1	0	1	0	1	0	0	0	0	12182	1174	41	0	538	0	PNPT1	2	55871841	In_Frame_Del	DEL	GAACCT	TCGA-G3-AAV6-01A-21D-A36X-10	17569987	55871841	187327532	5	43527										
XPO1	7514	hgsc.bcm.edu	37	chr2	61719221	61719221	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	ttaatgttgttcaaaatttcAtcaataaatggcatcacttc	4	7	4	0			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr2:61719221A>C	ENST00000401558.2	-	16	2563	c.1836T>G	c.(1834-1836)gaT>gaG	p.D612E	XPO1_ENST00000406957.1_Missense_Mutation_p.D612E|XPO1_ENST00000404992.2_Missense_Mutation_p.D612E	NM_003400.3	NP_003391.1	O14980	XPO1_HUMAN	exportin 1	612	Necessary for HTLV-1 Rex-mediated mRNA export.				gene expression (GO:0010467)|intracellular transport of virus (GO:0075733)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|mRNA transport (GO:0051028)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein export from nucleus (GO:0006611)|protein localization to nucleus (GO:0034504)|regulation of centrosome duplication (GO:0010824)|regulation of protein catabolic process (GO:0042176)|regulation of protein export from nucleus (GO:0046825)|response to drug (GO:0042493)|ribosomal large subunit export from nucleus (GO:0000055)|ribosomal small subunit export from nucleus (GO:0000056)|RNA metabolic process (GO:0016070)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)	annulate lamellae (GO:0005642)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleocytoplasmic transporter activity (GO:0005487)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	39			LUSC - Lung squamous cell carcinoma(7;5.71e-05)|Epithelial(17;0.0662)|all cancers(80;0.226)			TCAAAATTTCATCAATAAATG	0.358			Mis		CLL																																p.D612E		Atlas-SNP	.	-'	Dom	yes		2	2p15	7514	"exportin 1 (CRM1 homolog, yeast)"		L	.	XPO1	108	.	0			c.T1836G						.						85	81	82					2																	61719221		2203	4300	6503	SO:0001583	missense	7514	exon16			AATTTCATCAATA	Y08614	CCDS33205.1	2p15	2014-02-19	2014-02-19		ENSG00000082898	ENSG00000082898		"Exportins"	12825	protein-coding gene	gene with protein product	"chromosome region maintenance 1 homolog (yeast)"	602559	"exportin 1 (CRM1, yeast, homolog)", "exportin 1 (CRM1 homolog, yeast)"			9205132, 9368044	Standard	XM_005264544		Approved	CRM1, emb	uc002sbj.3	O14980	OTTHUMG00000152316	ENST00000401558.2:c.1836T>G	chr2.hg19:g.61719221A>C	ENSP00000384863:p.Asp612Glu	156.0	0.0		138.0	42.0	NM_003400	A6NL14|A8K1K5|D6W5E2|Q63HP8|Q68CP3|Q99433	Missense_Mutation	SNP	ENST00000401558.2	hg19	CCDS33205.1	.	.	.	.	.	.	.	.	.	.	A	7.343	0.621214	0.14193	.	.	ENSG00000082898	ENST00000401558;ENST00000404992;ENST00000406957	T;T;T	0.66280	-0.2;-0.2;-0.2	5.73	4.57	0.56435	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.31295	0.0792	N	0.02412	-0.56	0.53688	D	0.999977	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.29761	-1.0001	10	0.02654	T	1	-25.5132	12.1353	0.53968	0.9327:0.0:0.0673:0.0	.	259;612	B3KWD0;O14980	.;XPO1_HUMAN	E	612	ENSP00000384863:D612E;ENSP00000385942:D612E;ENSP00000385559:D612E	ENSP00000384863:D612E	D	-	3	2	XPO1	61572725	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.518000	0.45537	1.090000	0.41315	0.533000	0.62120	GAT	.	.		0.358	XPO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325872.3	NM_003400		C	61719221	A	C	61719221	3	2	302	1	0	0	0	0	1	0	0	0	17460	214	8	5	1419	5	XPO1	2	61719221	Missense_Mutation	SNP	A	TCGA-G3-AAV6-01A-21D-A36X-10	5847380	61719221	181480152	6	43528										
DCTN1	1639	hgsc.bcm.edu	37	chr2	74598683	74598683	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	ccttggatggggaaggaagcGgggggactgctccaggagag	20	7	0	1	rs112725508		TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr2:74598683G>C	ENST00000361874.3	-	8	943	c.626C>G	c.(625-627)cCg>cGg	p.P209R	DCTN1_ENST00000409438.1_Missense_Mutation_p.P75R|DCTN1_ENST00000394003.3_Missense_Mutation_p.P202R|DCTN1_ENST00000409567.3_Missense_Mutation_p.P189R|DCTN1_ENST00000409868.1_Missense_Mutation_p.P192R|DCTN1_ENST00000409240.1_Missense_Mutation_p.P172R|DCTN1_ENST00000407639.2_Missense_Mutation_p.P75R	NM_004082.4	NP_004073.2	Q14203	DCTN1_HUMAN	dynactin 1	209					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|G2/M transition of mitotic cell cycle (GO:0000086)|melanosome transport (GO:0032402)|microtubule-based transport (GO:0010970)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|nervous system development (GO:0007399)	cell leading edge (GO:0031252)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|dynein complex (GO:0030286)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(1)|skin(3)	45						GGAAGGAAGCGGGGGGACTGC	0.617																																					p.P209R		Atlas-SNP	.											.,1	DCTN1	110	.	0			c.C626G						.						18	19	18					2																	74598683		2197	4292	6489	SO:0001583	missense	1639	exon8			GGAAGCGGGGGGA		CCDS1939.1, CCDS46341.1, CCDS46342.1, CCDS54368.1, CCDS54369.1	2p13	2014-09-17	2010-06-24		ENSG00000204843	ENSG00000204843			2711	protein-coding gene	gene with protein product	"p150 glued homolog (Drosophila)"	601143	"dynactin 1 (p150, Glued (Drosophila) homolog)"			1828535	Standard	NM_001190836		Approved		uc002skx.3	Q14203	OTTHUMG00000129963	ENST00000361874.3:c.626C>G	chr2.hg19:g.74598683G>C	ENSP00000354791:p.Pro209Arg	118.0	0.0		98.0	25.0	NM_004082	A8MY36|B4DM45|E9PFS5|E9PGE1|G5E9H4|O95296|Q6IQ37|Q9BRM9|Q9UIU1|Q9UIU2	Missense_Mutation	SNP	ENST00000361874.3	hg19	CCDS1939.1	.	.	.	.	.	.	.	.	.	.	G	18.20	3.571405	0.65765	.	.	ENSG00000204843	ENST00000361874;ENST00000394003;ENST00000393999;ENST00000407639;ENST00000409438;ENST00000409240;ENST00000409868;ENST00000409567	T;T;T;T;T;T;T	0.78364	-0.79;-0.94;-0.73;-0.73;-1.17;-0.97;-0.95	5.39	5.39	0.77823	.	0.000000	0.42964	D	0.000631	T	0.71693	0.3370	N	0.24115	0.695	0.58432	D	0.999994	P;B;P;P;P;D	0.53885	0.746;0.017;0.938;0.789;0.881;0.963	B;B;B;B;B;P	0.49922	0.222;0.007;0.422;0.164;0.333;0.626	T	0.73503	-0.3962	10	0.54805	T	0.06	-7.0089	11.4861	0.50354	0.0825:0.0:0.9175:0.0	.	189;172;209;202;75;75	E9PGE1;E9PFS5;Q14203;A8MY36;Q14203-2;G5E9H4	.;.;DCTN1_HUMAN;.;.;.	R	209;202;192;75;75;172;192;189	ENSP00000354791:P209R;ENSP00000377571:P202R;ENSP00000384844:P75R;ENSP00000387270:P75R;ENSP00000386406:P172R;ENSP00000387327:P192R;ENSP00000386843:P189R	ENSP00000354791:P209R	P	-	2	0	DCTN1	74452191	1.000000	0.71417	0.914000	0.36105	0.740000	0.42216	3.674000	0.54598	2.795000	0.96236	0.655000	0.94253	CCG	.	G|0.500;C|0.500		0.617	DCTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252227.3	NM_004082		C	74598683	G	C	74598683	3	2	302	1	0	0	0	0	1	0	0	0	4308	1116	39	4	3310	4	DCTN1	2	74598683	Missense_Mutation	SNP	G	TCGA-G3-AAV6-01A-21D-A36X-10	12879462	74598683	168600690	7	43529										
KDM3A	55818	hgsc.bcm.edu	37	chr2	86707311	86707311	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	cttctttagctggagaaaaaCcgactcttggtgcagtgctc	10	10	2	1			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr2:86707311C>T	ENST00000409556.1	+	17	2703	c.2338C>T	c.(2338-2340)Ccg>Tcg	p.P780S	KDM3A_ENST00000542128.1_Missense_Mutation_p.P728S|KDM3A_ENST00000312912.5_Missense_Mutation_p.P780S|KDM3A_ENST00000409064.1_Missense_Mutation_p.P780S			Q9Y4C1	KDM3A_HUMAN	lysine (K)-specific demethylase 3A	780					androgen receptor signaling pathway (GO:0030521)|formaldehyde biosynthetic process (GO:0046293)|histone H3-K9 demethylation (GO:0033169)|histone H3-K9 dimethylation (GO:0036123)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of histone H3-K9 methylation (GO:0051573)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatid nucleus elongation (GO:0007290)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|dioxygenase activity (GO:0051213)|iron ion binding (GO:0005506)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|liver(1)|lung(13)|ovary(1)|prostate(3)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	47						TGGAGAAAAACCGACTCTTGG	0.498																																					p.P780S	NSCLC(96;1150 1523 6936 46253 49736)	Atlas-SNP	.											.	KDM3A	179	.	0			c.C2338T						.						61	63	62					2																	86707311		2203	4300	6503	SO:0001583	missense	55818	exon16			GAAAAACCGACTC	AB018285	CCDS1990.1	2p11.2	2011-07-01	2009-04-06	2009-04-06	ENSG00000115548	ENSG00000115548		"Chromatin-modifying enzymes / K-demethylases"	20815	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 2A"	611512	"jumonji domain containing 1", "jumonji domain containing 1A"	JMJD1, JMJD1A		9872452	Standard	NM_018433		Approved	TSGA, KIAA0742, JHMD2A	uc010ytj.2	Q9Y4C1	OTTHUMG00000130204	ENST00000409556.1:c.2338C>T	chr2.hg19:g.86707311C>T	ENSP00000386660:p.Pro780Ser	90.0	0.0		82.0	41.0	NM_001146688	D6W5M3|Q53S72|Q68D47|Q68UT9|Q6N050|Q8IY08	Missense_Mutation	SNP	ENST00000409556.1	hg19	CCDS1990.1	.	.	.	.	.	.	.	.	.	.	C	6.811	0.518633	0.13005	.	.	ENSG00000115548	ENST00000409556;ENST00000540058;ENST00000312912;ENST00000409064;ENST00000542128	T;T;T;T	0.58210	0.35;0.35;0.35;0.36	5.86	-1.08	0.09936	.	1.069350	0.07175	N	0.853032	T	0.22513	0.0543	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.18745	-1.0327	10	0.06365	T	0.9	.	1.4047	0.02278	0.1203:0.3442:0.2362:0.2993	.	728;780	F5H070;Q9Y4C1	.;KDM3A_HUMAN	S	780;780;780;780;728	ENSP00000386660:P780S;ENSP00000323659:P780S;ENSP00000386516:P780S;ENSP00000438324:P728S	ENSP00000323659:P780S	P	+	1	0	KDM3A	86560822	0.006000	0.16342	0.006000	0.13384	0.100000	0.18952	-0.012000	0.12699	-0.155000	0.11098	0.650000	0.86243	CCG	.	.		0.498	KDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252522.2	NM_018433		T	86707311	C	T	86707311	3	4	302	1	0	0	0	0	1	0	0	0	8135	507	18	3	2396	3	KDM3A	2	86707311	Missense_Mutation	SNP	C	TCGA-G3-AAV6-01A-21D-A36X-10	12108628	86707311	156492062	8	43530										
FAM128B	80097	hgsc.bcm.edu	37	chr2	130948160	130948160	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	gctaccaggctgcccaagggGggcgggcctgggaagagccc	18	13	0	1	rs376967942		TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr2:130948160G>A	ENST00000281871.6	+	3	793	c.438G>A	c.(436-438)ggG>ggA	p.G146G	MZT2B_ENST00000409255.1_Silent_p.G206G	NM_025029.3	NP_079305.2	Q6NZ67	MZT2B_HUMAN	mitotic spindle organizing protein 2B	146						centrosome (GO:0005813)|gamma-tubulin ring complex (GO:0008274)|spindle (GO:0005819)				lung(1)	1						TGCCCAAGGGGGGCGGGCCTG	0.647																																					p.G146G		Atlas-SNP	.											.	MZT2B	5	.	0			c.G438A						.						35	41	39					2																	130948160		2192	4295	6487	SO:0001819	synonymous_variant	80097	exon3			CAAGGGGGGCGGG	BC066296	CCDS2157.1	2q21.1	2013-10-11	2010-07-22	2010-07-22	ENSG00000152082	ENSG00000152082			25886	protein-coding gene	gene with protein product	"mitotic-spindle organizing protein associated with a ring of gamma-tubulin 2B"	613450	"family with sequence similarity 128, member B"	FAM128B		20360068	Standard	NM_025029		Approved	FLJ14346, MOZART2B	uc002tqu.3	Q6NZ67	OTTHUMG00000131625	ENST00000281871.6:c.438G>A	chr2.hg19:g.130948160G>A		227.0	0.0		391.0	56.0	NM_025029	Q96CG4	Silent	SNP	ENST00000281871.6	hg19	CCDS2157.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	2.742|2.742	-0.261905|-0.261905	0.05791|0.05791	.|.	.|.	ENSG00000152082|ENSG00000152082	ENST00000425361|ENST00000455239	T|.	0.31510|.	1.49|.	3.59|3.59	0.564|0.564	0.17302|0.17302	.|.	0.572258|0.572258	0.17506|0.17506	N|N	0.171814|0.171814	T|T	0.58836|0.58836	0.2150|0.2150	.|.	.|.	.|.	0.52099|0.52099	D|D	0.999945|0.999945	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.54022|0.54022	-0.8355|-0.8355	7|6	0.56958|0.54805	D|T	0.05|0.06	-15.9954|-15.9954	6.1906|6.1906	0.20522|0.20522	0.1909:0.2824:0.5267:0.0|0.1909:0.2824:0.5267:0.0	.|.	.|.	.|.	.|.	E|R	110|87	ENSP00000398749:G110E|.	ENSP00000398749:G110E|ENSP00000404629:G87R	G|G	+|+	2|1	0|0	MZT2B|MZT2B	130664630|130664630	0.838000|0.838000	0.29461|0.29461	0.111000|0.111000	0.21465|0.21465	0.321000|0.321000	0.28281|0.28281	0.106000|0.106000	0.15354|0.15354	-0.256000|-0.256000	0.09473|0.09473	-1.644000|-1.644000	0.00765|0.00765	GGG|GGG	.	.		0.647	MZT2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254518.1	NM_025029		A	130948160	G	A	130948160	2	1	302	1	0	0	0	0	0	0	0	1	5440	1219	43	3		3	FAM128B	2	130948160	Silent	SNP	G	TCGA-G3-AAV6-01A-21D-A36X-10	44240849	130948160	112251213	9	43531										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141625315	141625315	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	ttcactcccatatagagacaCagcaaagggatgggaaaggt	11	8	1	1			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr2:141625315C>A	ENST00000389484.3	-	27	5394	c.4423G>T	c.(4423-4425)Gtg>Ttg	p.V1475L		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1475					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TATAGAGACACAGCAAAGGGA	0.433										TSP Lung(27;0.18)																											p.V1475L	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.G4423T						.						152	145	147					2																	141625315		2203	4300	6503	SO:0001583	missense	53353	exon27			GAGACACAGCAAA	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.4423G>T	chr2.hg19:g.141625315C>A	ENSP00000374135:p.Val1475Leu	139.0	0.0		198.0	55.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	14.76	2.631826	0.46944	.	.	ENSG00000168702	ENST00000389484;ENST00000544579;ENST00000434794	D;D	0.90004	-2.6;-2.6	5.42	5.42	0.78866	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	D	0.000003	D	0.85305	0.5666	N	0.20483	0.58	0.53688	D	0.999974	P;D	0.53312	0.879;0.959	P;P	0.52031	0.688;0.556	T	0.81326	-0.0983	10	0.02654	T	1	.	19.2069	0.93734	0.0:1.0:0.0:0.0	.	658;1475	Q96NT6;Q9NZR2	.;LRP1B_HUMAN	L	1475;1413;620	ENSP00000374135:V1475L;ENSP00000413239:V620L	ENSP00000374135:V1475L	V	-	1	0	LRP1B	141341785	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.723000	0.84788	2.547000	0.85894	0.655000	0.94253	GTG	.	.		0.433	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		A	141625315	C	A	141625315	3	1	302	1	0	0	0	0	1	0	0	0	8964	478	17	3	9636	3	LRP1B	2	141625315	Missense_Mutation	SNP	C	TCGA-G3-AAV6-01A-21D-A36X-10	10677155	141625315	101574058	10	43532										
TTN	7273	hgsc.bcm.edu	37	chr2	179433557	179433557	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	tacagcaacaactctaaaaaGatattcttccccttgagtta	4	10	2	2	rs541266544	byFrequency	TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr2:179433557G>T	ENST00000591111.1	-	276	72603	c.72379C>A	c.(72379-72381)Ctt>Att	p.L24127I	TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.L16895I|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.L25768I|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.L16828I|TTN_ENST00000460472.2_Missense_Mutation_p.L16703I|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.L23200I|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA			Q8WZ42	TITIN_HUMAN	titin	24127	Fibronectin type-III 75. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACTCTAAAAAGATATTCTTCC	0.418													G|||	2	0.000399361	0	0	5008	,	,		24017	0		0	False		,,,				2504	0.002				p.L25768I		Atlas-SNP	.											.	TTN	18412	.	0			c.C77302A						.						95	93	94					2																	179433557		1882	4109	5991	SO:0001583	missense	7273	exon326			TAAAAAGATATTC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.72379C>A	chr2.hg19:g.179433557G>T	ENSP00000465570:p.Leu24127Ile	83.0	0.0		111.0	15.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	12.91	2.079889	0.36662	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.56776	0.44;0.44;0.44;0.44	5.83	5.83	0.93111	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.38719	0.1051	N	0.05280	-0.08	0.44417	D	0.997331	B;B;B;B	0.25772	0.134;0.134;0.134;0.134	B;B;B;B	0.27170	0.077;0.077;0.077;0.077	T	0.36696	-0.9737	9	0.87932	D	0	.	20.111	0.97911	0.0:0.0:1.0:0.0	.	16703;16828;16895;24127	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	I	23200;16703;16895;16828;16701	ENSP00000343764:L23200I;ENSP00000434586:L16703I;ENSP00000340554:L16895I;ENSP00000352154:L16828I	ENSP00000340554:L16895I	L	-	1	0	TTN	179141803	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.263000	0.58853	2.747000	0.94245	0.650000	0.86243	CTT	.	.		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179433557	G	T	179433557	3	4	302	1	0	0	0	0	1	0	0	0	16750	942	33	3	30825	3	TTN	2	179433557	Missense_Mutation	SNP	G	TCGA-G3-AAV6-01A-21D-A36X-10	37808242	179433557	63765816	11	43533										
FZD7	8324	hgsc.bcm.edu	37	chr2	202900925	202900925	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	ccgtgccctgcccgcccggcCacttcccgcccatgagcccc	9	24	0	1			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr2:202900925C>T	ENST00000286201.1	+	1	1616	c.1555C>T	c.(1555-1557)Cac>Tac	p.H519Y	RP11-107N15.1_ENST00000608741.1_lincRNA	NM_003507.1	NP_003498.1	O75084	FZD7_HUMAN	frizzled class receptor 7	519					axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|mesenchymal to epithelial transition (GO:0060231)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of ectodermal cell fate specification (GO:0042666)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|positive regulation of JNK cascade (GO:0046330)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of catenin import into nucleus (GO:0035412)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration (GO:0014834)|somatic stem cell division (GO:0048103)|stem cell maintenance (GO:0019827)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell differentiation in thymus (GO:0033077)|vasculature development (GO:0001944)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(1)|endometrium(6)|large_intestine(6)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	31						CCCGCCCGGCCACTTCCCGCC	0.627											OREG0015146	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.H519Y		Atlas-SNP	.											.	FZD7	70	.	0			c.C1555T						.						55	58	57					2																	202900925		2203	4300	6503	SO:0001583	missense	8324	exon1			CCCGGCCACTTCC	AB010881	CCDS2351.1	2q33	2014-01-29	2014-01-29		ENSG00000155760	ENSG00000155760		"GPCR / Class F : Frizzled receptors"	4045	protein-coding gene	gene with protein product		603410	"frizzled (Drosophila) homolog 7", "frizzled homolog 7 (Drosophila)", "frizzled 7, seven transmembrane spanning receptor", "frizzled family receptor 7"			9707618, 9813155	Standard	NM_003507		Approved	FzE3	uc002uyw.1	O75084	OTTHUMG00000132841	ENST00000286201.1:c.1555C>T	chr2.hg19:g.202900925C>T	ENSP00000286201:p.His519Tyr	64.0	0.0	2133	103.0	60.0	NM_003507	O94816|Q53S59|Q96B74	Missense_Mutation	SNP	ENST00000286201.1	hg19	CCDS2351.1	.	.	.	.	.	.	.	.	.	.	C	1.901	-0.453086	0.04540	.	.	ENSG00000155760	ENST00000286201	D	0.81821	-1.54	5.72	5.72	0.89469	GPCR, family 2-like (1);	0.110494	0.64402	D	0.000015	T	0.61362	0.2341	N	0.04508	-0.205	0.45378	D	0.998366	B	0.06786	0.001	B	0.04013	0.001	T	0.58418	-0.7640	10	0.16420	T	0.52	.	14.686	0.69049	0.1451:0.8549:0.0:0.0	.	519	O75084	FZD7_HUMAN	Y	519	ENSP00000286201:H519Y	ENSP00000286201:H519Y	H	+	1	0	FZD7	202609170	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.585000	0.46111	2.711000	0.92665	0.655000	0.94253	CAC	.	.		0.627	FZD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256314.1	NM_003507		T	202900925	C	T	202900925	3	4	302	1	0	0	0	0	1	0	0	0	6143	594	21	3	1557	3	FZD7	2	202900925	Missense_Mutation	SNP	C	TCGA-G3-AAV6-01A-21D-A36X-10	23467368	202900925	40298448	12	43534										
CCDC108	255101	hgsc.bcm.edu	37	chr2	219888857	219888857	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	ccgggtgccacaaggcccgaAgtgggccgaaggatgacgtc	16	12	0	1			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr2:219888857A>C	ENST00000341552.5	-	15	2558	c.2475T>G	c.(2473-2475)acT>acG	p.T825T	CCDC108_ENST00000441968.1_Silent_p.T825T|CCDC108_ENST00000453220.1_Silent_p.T825T	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108	825						integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(1)|lung(34)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CAAGGCCCGAAGTGGGCCGAA	0.612																																					p.T825T		Atlas-SNP	.											.	CCDC108	208	.	0			c.T2475G						.						59	65	63					2																	219888857		2203	4300	6503	SO:0001819	synonymous_variant	255101	exon15			GCCCGAAGTGGGC	NM_194302, AL833882, AK127189	CCDS2430.2, CCDS2431.2, CCDS63125.1, CCDS63126.1	2q35	2008-02-05			ENSG00000181378	ENSG00000181378			25325	protein-coding gene	gene with protein product		614270				12477932	Standard	NM_194302		Approved	DKFZp434O0527, MGC35338	uc002vjl.2	Q6ZU64	OTTHUMG00000133013	ENST00000341552.5:c.2475T>G	chr2.hg19:g.219888857A>C		168.0	0.0		232.0	30.0	NM_194302	A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Silent	SNP	ENST00000341552.5	hg19	CCDS2430.2																																																																																			.	.		0.612	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4	NM_194302		C	219888857	A	C	219888857	2	2	302	1	0	0	0	0	0	0	0	1	2745	59	3	5		5	CCDC108	2	219888857	Silent	SNP	A	TCGA-G3-AAV6-01A-21D-A36X-10	16987932	219888857	23310516	13	43535										
ABCB6	10058	hgsc.bcm.edu	37	chr2	220079752	220079752	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	gaagaacatgctgaagtagaTgatgccaatgatgatgtcgg	13	5	0	6			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr2:220079752T>C	ENST00000265316.3	-	6	1523	c.1207A>G	c.(1207-1209)Atc>Gtc	p.I403V	ABCB6_ENST00000439002.2_Missense_Mutation_p.I357V	NM_005689.2	NP_005680.1	Q9NP58	ABCB6_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 6 (Langereis blood group)	403	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				brain development (GO:0007420)|cellular iron ion homeostasis (GO:0006879)|heme transport (GO:0015886)|porphyrin-containing compound biosynthetic process (GO:0006779)|skin development (GO:0043588)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial envelope (GO:0005740)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|efflux transmembrane transporter activity (GO:0015562)|heme binding (GO:0020037)|heme transporter activity (GO:0015232)|heme-transporting ATPase activity (GO:0015439)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	34		Renal(207;0.0474)		Epithelial(149;1.22e-06)|all cancers(144;0.000201)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CTGAAGTAGATGATGCCAATG	0.527																																					p.I403V		Atlas-SNP	.											.	ABCB6	76	.	0			c.A1207G						.						228	171	191					2																	220079752		2203	4300	6503	SO:0001583	missense	10058	exon6			AGTAGATGATGCC	AF070598	CCDS2436.1	2q36	2014-08-27	2014-08-27		ENSG00000115657	ENSG00000115657		"ATP binding cassette transporters / subfamily B"	47	protein-coding gene	gene with protein product	"ATP-binding cassette half-transporter"	605452	"ATP-binding cassette, sub-family B (MDR/TAP), member 6"			8894702, 9110174	Standard	NM_005689		Approved	EST45597, umat, MTABC3	uc002vkc.2	Q9NP58	OTTHUMG00000133131	ENST00000265316.3:c.1207A>G	chr2.hg19:g.220079752T>C	ENSP00000265316:p.Ile403Val	86.0	0.0		148.0	20.0	NM_005689	O75542|Q49A66|Q59GQ5|Q6ZME6|Q96ME8|Q9HAQ6|Q9HAQ7	Missense_Mutation	SNP	ENST00000265316.3	hg19	CCDS2436.1	.	.	.	.	.	.	.	.	.	.	T	9.985	1.229178	0.22542	.	.	ENSG00000115657	ENST00000265316;ENST00000439002	D;D	0.89485	-2.52;-2.52	5.97	-1.62	0.08372	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.285044	0.39475	N	0.001353	T	0.69975	0.3171	N	0.04203	-0.255	0.80722	D	1	B;B	0.06786	0.0;0.001	B;B	0.12837	0.003;0.008	T	0.59144	-0.7509	10	0.05721	T	0.95	-10.2155	12.8957	0.58098	0.0:0.6679:0.0:0.3321	.	357;403	Q9NP58-4;Q9NP58	.;ABCB6_HUMAN	V	403;357	ENSP00000265316:I403V;ENSP00000394333:I357V	ENSP00000265316:I403V	I	-	1	0	ABCB6	219787996	0.924000	0.31332	0.993000	0.49108	0.997000	0.91878	-0.003000	0.12901	-0.265000	0.09352	0.533000	0.62120	ATC	.	.		0.527	ABCB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256820.2	NM_005689		C	220079752	T	C	220079752	3	2	302	1	0	0	0	0	1	0	0	0	45	1464	51	2	1377	2	ABCB6	2	220079752	Missense_Mutation	SNP	T	TCGA-G3-AAV6-01A-21D-A36X-10	190895	220079752	23119621	14	43536										
ATG7	10533	hgsc.bcm.edu	37	chr3	11406156	11406156	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	ctatgccattgccagcagcaGtgacgatcggatgaatgagc	12	10	0	3			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr3:11406156G>T	ENST00000354449.3	+	16	1848	c.1823G>T	c.(1822-1824)aGt>aTt	p.S608I	ATG7_ENST00000354956.5_Missense_Mutation_p.S608I|ATG7_ENST00000446450.2_Missense_Mutation_p.S569I	NM_006395.2	NP_006386.1	O95352	ATG7_HUMAN	autophagy related 7	608					adult walking behavior (GO:0007628)|C-terminal protein lipidation (GO:0006501)|cardiac muscle cell development (GO:0055013)|cellular amino acid metabolic process (GO:0006520)|cellular protein modification process (GO:0006464)|cellular response to hyperoxia (GO:0071455)|cellular response to nitrogen starvation (GO:0006995)|cellular response to starvation (GO:0009267)|central nervous system neuron axonogenesis (GO:0021955)|cerebellar Purkinje cell layer development (GO:0021680)|cerebral cortex development (GO:0021987)|late nucleophagy (GO:0044805)|liver development (GO:0001889)|membrane fusion (GO:0061025)|mitochondrion degradation (GO:0000422)|mitochondrion organization (GO:0007005)|negative regulation of apoptotic process (GO:0043066)|negative stranded viral RNA replication (GO:0039689)|neurological system process (GO:0050877)|piecemeal microautophagy of nucleus (GO:0034727)|positive regulation of apoptotic process (GO:0043065)|positive regulation of autophagy (GO:0010508)|positive regulation of macroautophagy (GO:0016239)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein modification process (GO:0031401)|post-embryonic development (GO:0009791)|protein catabolic process (GO:0030163)|protein lipidation (GO:0006497)|protein modification by small protein conjugation (GO:0032446)|protein transport (GO:0015031)|pyramidal neuron development (GO:0021860)|regulation of protein ubiquitination (GO:0031396)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|pre-autophagosomal structure (GO:0000407)	Atg12 activating enzyme activity (GO:0019778)|Atg8 activating enzyme (GO:0019779)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)|ubiquitin activating enzyme activity (GO:0004839)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(14)|prostate(1)|skin(2)|urinary_tract(1)	34						GCCAGCAGCAGTGACGATCGG	0.473																																					p.S608I		Atlas-SNP	.											.	ATG7	56	.	0			c.G1823T						.						204	183	190					3																	11406156		2203	4300	6503	SO:0001583	missense	10533	exon16			GCAGCAGTGACGA	AF094516	CCDS2605.1, CCDS46752.1, CCDS46753.1	3p25.3-p25.2	2014-02-18	2012-06-06	2005-09-11	ENSG00000197548	ENSG00000197548		"Ubiquitin-like modifier activating enzymes"	16935	protein-coding gene	gene with protein product	"ubiquitin-activating enzyme E1-like protein"	608760	"APG7 autophagy 7-like (S. cerevisiae)", "ATG7 autophagy related 7 homolog (S. cerevisiae)"	APG7L		10233149	Standard	NM_006395		Approved	GSA7, DKFZp434N0735	uc003bwc.3	O95352	OTTHUMG00000129740	ENST00000354449.3:c.1823G>T	chr3.hg19:g.11406156G>T	ENSP00000346437:p.Ser608Ile	97.0	0.0		85.0	4.0	NM_001136031	B4E170|E9PB95|Q7L8L0|Q9BWP2|Q9UFH4	Missense_Mutation	SNP	ENST00000354449.3	hg19	CCDS2605.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	25.9|25.9|25.9	4.689319|4.689319|4.689319	0.88735|0.88735|0.88735	.|.|.	.|.|.	ENSG00000197548|ENSG00000197548|ENSG00000197548	ENST00000446110|ENST00000446450;ENST00000354956;ENST00000354449;ENST00000414717|ENST00000427759	.|T;T;T|.	.|0.48836|.	.|0.83;0.8;0.84|.	5.32|5.32|5.32	5.32|5.32|5.32	0.75619|0.75619|0.75619	.|Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);|.	.|0.000000|.	.|0.85682|.	.|D|.	.|0.000000|.	T|T|T	0.76054|0.76054|0.76054	0.3934|0.3934|0.3934	M|M|M	0.70595|0.70595|0.70595	2.14|2.14|2.14	0.58432|0.58432|0.58432	D|D|D	0.999996|0.999996|0.999996	.|P;D;D|.	.|0.61080|.	.|0.947;0.989;0.981|.	.|P;P;P|.	.|0.59288|.	.|0.591;0.855;0.629|.	T|T|T	0.74728|0.74728|0.74728	-0.3567|-0.3567|-0.3567	5|10|5	.|0.54805|.	.|T|.	.|0.06|.	-15.5238|-15.5238|-15.5238	19.3933|19.3933|19.3933	0.94594|0.94594|0.94594	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.|.	.|569;608;608|.	.|E9PB95;O95352-2;O95352|.	.|.;.;ATG7_HUMAN|.	H|I|L	8|569;608;608;9|9	.|ENSP00000412580:S569I;ENSP00000347042:S608I;ENSP00000346437:S608I|.	.|ENSP00000346437:S608I|.	Q|S|V	+|+|+	3|2|1	2|0|0	ATG7|ATG7|ATG7	11381156|11381156|11381156	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.997000|0.997000|0.997000	0.91878|0.91878|0.91878	9.079000|9.079000|9.079000	0.94032|0.94032|0.94032	2.648000|2.648000|2.648000	0.89879|0.89879|0.89879	0.650000|0.650000|0.650000	0.86243|0.86243|0.86243	CAG|AGT|GTG	.	.		0.473	ATG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251951.3	NM_006395		T	11406156	G	T	11406156	3	4	302	1	0	0	0	0	1	0	0	0	1101	1029	36	3	1881	3	ATG7	3	11406156	Missense_Mutation	SNP	G	TCGA-G3-AAV6-01A-21D-A36X-10		11406156	186616274	15	43537										
IQSEC1	9922	hgsc.bcm.edu	37	chr3	12944273	12944273	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	cagaggcgcttcctacttacTtccacattgctctctagcga	7	14	1	1			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr3:12944273T>G	ENST00000273221.4	-	13	3063	c.2847A>C	c.(2845-2847)gaA>gaC	p.E949D		NM_014869.5	NP_055684.3	Q6DN90	IQEC1_HUMAN	IQ motif and Sec7 domain 1	949					actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						TCCTACTTACTTCCACATTGC	0.517																																					p.E949D		Atlas-SNP	.											.	IQSEC1	88	.	0			c.A2847C						.						81	65	70					3																	12944273		2203	4300	6503	SO:0001630	splice_region_variant	9922	exon13			ACTTACTTCCACA	BC010267	CCDS33703.1, CCDS74902.1	3p25.2	2011-09-23			ENSG00000144711	ENSG00000144711			29112	protein-coding gene	gene with protein product	"brefeldin A-resistant ARF-GEF2"	610166				9872452, 8619474	Standard	NM_001134382		Approved	KIAA0763, GEP100, BRAG2, ARF-GEP100	uc011auw.2	Q6DN90	OTTHUMG00000155398	ENST00000273221.4:c.2847+1A>C	chr3.hg19:g.12944273T>G		258.0	0.0		252.0	17.0	NM_014869	O94863|Q96D85	Missense_Mutation	SNP	ENST00000273221.4	hg19	CCDS33703.1	.	.	.	.	.	.	.	.	.	.	N	33	5.202967	0.94997	.	.	ENSG00000144711	ENST00000273221;ENST00000435445;ENST00000429247	T;T	0.53423	0.62;0.62	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.67363	0.2885	.	.	.	0.80722	D	1	D;D	0.71674	0.998;0.996	D;P	0.67900	0.954;0.876	T	0.69183	-0.5212	8	.	.	.	.	15.6315	0.76912	0.0:0.0:0.0:1.0	.	935;949	E9PG60;Q6DN90	.;IQEC1_HUMAN	D	949;935;935	ENSP00000273221:E949D;ENSP00000402299:E935D	.	E	-	3	2	IQSEC1	12919273	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	5.655000	0.67981	2.084000	0.62774	0.528000	0.53228	GAA	.	.		0.517	IQSEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339865.2	NM_014869	Missense_Mutation	G	12944273	T	G	12944273	5	3	302	1	0	0	0	0	0	0	1	0	7826	1623	56	5	597	5	IQSEC1	3	12944273	Splice_Site	SNP	T	TCGA-G3-AAV6-01A-21D-A36X-10	1538117	12944273	185078157	16	43538										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266136	41266136	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	gtgccactaccacagctcctTctctgagtggtaaaggcaat	9	12	1	1	rs121913407		TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr3:41266136T>C	ENST00000349496.5	+	3	413	c.133T>C	c.(133-135)Tct>Cct	p.S45P	CTNNB1_ENST00000405570.1_Missense_Mutation_p.S45P|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S45P|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S38P|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S45P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	45			Missing (in colorectal cancer). {ECO:0000269|PubMed:9065402}.|S -> F (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> P (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S45P(168)|p.A5_A80del(53)|p.S45del(50)|p.S45A(11)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.S45_G48del(1)|p.Q28_Q61del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.S45_L46del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.P44_N51del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.T40_L46del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.S45E(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.S45T(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.T42_K49>Q(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CACAGCTCCTTCTCTGAGTGG	0.502		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S45P	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,carcinoma,0,1	CTNNB1	4904	.	355	Substitution - Missense(181)|Deletion - In frame(149)|Complex - deletion inframe(18)|Unknown(7)	liver(151)|kidney(53)|soft_tissue(47)|large_intestine(37)|adrenal_gland(28)|endometrium(9)|stomach(7)|skin(6)|pituitary(3)|prostate(3)|thyroid(2)|small_intestine(2)|bone(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)	c.T133C						.						84	74	78					3																	41266136		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	GCTCCTTCTCTGA	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.133T>C	chr3.hg19:g.41266136T>C	ENSP00000344456:p.Ser45Pro	180.0	0.0		116.0	45.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.440246	0.83993	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.65903	0.2736	M	0.65677	2.01	0.80722	D	1	D	0.60575	0.988	P	0.62649	0.905	T	0.69083	-0.5239	10	0.87932	D	0	-13.6823	16.3453	0.83126	0.0:0.0:0.0:1.0	.	45	P35222	CTNB1_HUMAN	P	38;45;45;45;45;38;45;45;45	ENSP00000400508:S38P;ENSP00000385604:S45P;ENSP00000412219:S45P;ENSP00000379486:S45P;ENSP00000344456:S45P;ENSP00000411226:S38P;ENSP00000379488:S45P;ENSP00000409302:S45P;ENSP00000401599:S45P	ENSP00000344456:S45P	S	+	1	0	CTNNB1	41241140	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.261000	0.74972	0.533000	0.62120	TCT	.	.		0.502	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266136	T	C	41266136	3	2	302	1	0	0	0	0	1	0	0	0	4018	1783	62	2	139	2	CTNNB1	3	41266136	Missense_Mutation	SNP	T	TCGA-G3-AAV6-01A-21D-A36X-10	28321863	41266136	156756294	17	43539										
TMF1	7110	hgsc.bcm.edu	37	chr3	69101099	69101099	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	gctcctctctctcttacccgGctctccatacggaatggtct	7	16	4	0			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr3:69101099G>A	ENST00000398559.2	-	1	355	c.139C>T	c.(139-141)Ccg>Tcg	p.P47S	CTD-2013N24.2_ENST00000595925.1_RNA|TMF1_ENST00000543976.1_Missense_Mutation_p.P47S|MIR3136_ENST00000583498.1_RNA			P82094	TMF1_HUMAN	TATA element modulatory factor 1	47					acrosome assembly (GO:0001675)|cellular response to organic cyclic compound (GO:0071407)|defense response to bacterium (GO:0042742)|Leydig cell differentiation (GO:0033327)|luteinizing hormone secretion (GO:0032275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|positive regulation of cytokine production (GO:0001819)|positive regulation of testosterone secretion (GO:2000845)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of transcription, DNA-templated (GO:0006355)|sperm motility (GO:0030317)|spermatid nucleus differentiation (GO:0007289)|transcription from RNA polymerase II promoter (GO:0006366)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription cofactor activity (GO:0003712)			cervix(1)|kidney(1)|large_intestine(4)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;4.48e-05)|Epithelial(33;0.000274)|LUSC - Lung squamous cell carcinoma(21;0.0123)|KIRC - Kidney renal clear cell carcinoma(39;0.211)|Kidney(39;0.247)		CTCTTACCCGGCTCTCCATAC	0.587																																					p.P47S		Atlas-SNP	.											.	TMF1	77	.	0			c.C139T						.						70	76	74					3																	69101099		1915	4133	6048	SO:0001583	missense	7110	exon1			TACCCGGCTCTCC		CCDS43105.1	3p21-p12	2009-02-11			ENSG00000144747	ENSG00000144747			11870	protein-coding gene	gene with protein product		601126				1409643	Standard	NM_007114		Approved	ARA160, TMF	uc003dnn.3	P82094	OTTHUMG00000158771	ENST00000398559.2:c.139C>T	chr3.hg19:g.69101099G>A	ENSP00000381567:p.Pro47Ser	77.0	0.0		70.0	4.0	NM_007114	B7ZLJ2|Q17R87|Q59GK0	Missense_Mutation	SNP	ENST00000398559.2	hg19	CCDS43105.1	.	.	.	.	.	.	.	.	.	.	G	12.68	2.010581	0.35511	.	.	ENSG00000144747	ENST00000398559;ENST00000543976;ENST00000356248;ENST00000438636	T;T	0.16457	2.34;2.34	5.31	5.31	0.75309	.	0.325662	0.33477	N	0.004864	T	0.16128	0.0388	L	0.54323	1.7	0.39156	D	0.962329	B;B	0.27140	0.169;0.064	B;B	0.24006	0.05;0.023	T	0.04752	-1.0929	10	0.08837	T	0.75	.	14.058	0.64781	0.0:0.1505:0.8495:0.0	.	47;47	P82094-2;P82094	.;TMF1_HUMAN	S	47	ENSP00000381567:P47S;ENSP00000438706:P47S	ENSP00000348582:P47S	P	-	1	0	TMF1	69183789	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	2.680000	0.46918	2.633000	0.89246	0.591000	0.81541	CCG	.	.		0.587	TMF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352106.1	NM_007114		A	69101099	G	A	69101099	3	1	302	1	0	0	0	0	1	0	0	0	16243	1203	42	3	3210	3	TMF1	3	69101099	Missense_Mutation	SNP	G	TCGA-G3-AAV6-01A-21D-A36X-10	27834963	69101099	128921331	18	43540										
KLHL6	89857	hgsc.bcm.edu	37	chr3	183212026	183212026	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	atctgaatccacttgttgatCgaagaattatatttccaaac	5	8	1	3	rs2256061	byFrequency	TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr3:183212026C>A	ENST00000341319.3	-	5	1226	c.1191G>T	c.(1189-1191)tcG>tcT	p.S397S		NM_130446.2	NP_569713.2	Q8WZ60	KLHL6_HUMAN	kelch-like family member 6	397					B cell receptor signaling pathway (GO:0050853)|germinal center formation (GO:0002467)					breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44	all_cancers(143;9.2e-12)|Ovarian(172;0.0172)		all cancers(12;1.29e-44)|Epithelial(37;1.24e-38)|LUSC - Lung squamous cell carcinoma(7;2.58e-24)|Lung(8;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.32e-22)			ACTTGTTGATCGAAGAATTAT	0.418																																					p.S397S		Atlas-SNP	.											.	KLHL6	100	.	0			c.G1191T						.						154	151	152					3																	183212026		2203	4300	6503	SO:0001819	synonymous_variant	89857	exon5			GTTGATCGAAGAA	AF441792	CCDS3245.2	3q27.3	2013-01-30	2013-01-30		ENSG00000172578	ENSG00000172578		"Kelch-like", "BTB/POZ domain containing"	18653	protein-coding gene	gene with protein product	"kelch-like protein KLHL6"	614214	"kelch-like 6 (Drosophila)"			11214971, 12617994	Standard	NM_130446		Approved	FLJ00029	uc003flr.3	Q8WZ60	OTTHUMG00000148673	ENST00000341319.3:c.1191G>T	chr3.hg19:g.183212026C>A		129.0	0.0		91.0	18.0	NM_130446	B2RB31|D3DNS8|Q8N5I1|Q8N892	Silent	SNP	ENST00000341319.3	hg19	CCDS3245.2																																																																																			.	C|0.818;T|0.182		0.418	KLHL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309024.1	NM_130446		A	183212026	C	A	183212026	2	1	302	1	0	0	0	0	0	0	0	1	8402	871	31	1		1	KLHL6	3	183212026	Silent	SNP	C	TCGA-G3-AAV6-01A-21D-A36X-10	114110927	183212026	14810404	19	43541										
ATP10D	57205	hgsc.bcm.edu	37	chr4	47527592	47527592	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	aggactctgaagttgatcctGagaagttttccagtaggata	11	6	1	3			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr4:47527592G>A	ENST00000273859.3	+	5	978	c.709G>A	c.(709-711)Gag>Aag	p.E237K	ATP10D_ENST00000504445.1_Missense_Mutation_p.E237K	NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	237					cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|endometrium(5)|kidney(5)|large_intestine(14)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	66						AGTTGATCCTGAGAAGTTTTC	0.348																																					p.E237K		Atlas-SNP	.											.	ATP10D	168	.	0			c.G709A						.						79	80	79					4																	47527592		2203	4300	6503	SO:0001583	missense	57205	exon5			GATCCTGAGAAGT	AB040920	CCDS3476.1	4p12	2010-04-20	2007-09-19		ENSG00000145246	ENSG00000145246		"ATPases / P-type"	13549	protein-coding gene	gene with protein product			"ATPase, Class V, type 10D"			12532265	Standard	NM_020453		Approved	ATPVD, KIAA1487	uc003gxk.1	Q9P241	OTTHUMG00000160784	ENST00000273859.3:c.709G>A	chr4.hg19:g.47527592G>A	ENSP00000273859:p.Glu237Lys	89.0	0.0		93.0	46.0	NM_020453	A2RRC8|D6REN2|Q8NC70|Q96SR3	Missense_Mutation	SNP	ENST00000273859.3	hg19	CCDS3476.1	.	.	.	.	.	.	.	.	.	.	G	16.66	3.186022	0.57909	.	.	ENSG00000145246	ENST00000273859;ENST00000504445	T;T	0.74526	-0.85;-0.85	5.76	5.76	0.90799	ATPase, P-type, ATPase-associated domain (1);	0.115441	0.64402	D	0.000020	T	0.70090	0.3184	L	0.37630	1.12	0.39974	D	0.974832	B;B	0.33549	0.417;0.236	B;B	0.40982	0.345;0.261	T	0.64024	-0.6504	10	0.09084	T	0.74	-15.5687	19.3193	0.94231	0.0:0.0:1.0:0.0	.	237;237	Q9P241;Q6PEW3	AT10D_HUMAN;.	K	237	ENSP00000273859:E237K;ENSP00000420909:E237K	ENSP00000273859:E237K	E	+	1	0	ATP10D	47222349	1.000000	0.71417	0.997000	0.53966	0.926000	0.56050	7.654000	0.83653	2.871000	0.98454	0.655000	0.94253	GAG	.	.		0.348	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453		A	47527592	G	A	47527592	3	1	302	1	0	0	0	0	1	0	0	0	1118	1291	45	3	723	3	ATP10D	4	47527592	Missense_Mutation	SNP	G	TCGA-G3-AAV6-01A-21D-A36X-10		47527592	143626684	20	43542										
SCD5	79966	hgsc.bcm.edu	37	chr4	83719510	83719510	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	gatgagcaccagggagtacaCggcccccaagtggagcaagc	14	12	0	1			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr4:83719510C>T	ENST00000319540.4	-	1	500	c.181G>A	c.(181-183)Gtg>Atg	p.V61M	SCD5_ENST00000282709.4_Missense_Mutation_p.V61M|SCD5_ENST00000273908.4_Missense_Mutation_p.V61M	NM_001037582.2	NP_001032671.2	Q86SK9	SCD5_HUMAN	stearoyl-CoA desaturase 5	61					fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	iron ion binding (GO:0005506)|stearoyl-CoA 9-desaturase activity (GO:0004768)			endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)	13		Colorectal(4;0.0323)|Hepatocellular(203;0.115)				AGGGAGTACACGGCCCCCAAG	0.711																																					p.V61M		Atlas-SNP	.											.	SCD5	58	.	0			c.G181A						.						52	45	47					4																	83719510		2203	4300	6503	SO:0001583	missense	79966	exon1			AGTACACGGCCCC	AF389338	CCDS3595.1, CCDS34024.1	4q21.3	2013-01-25	2005-06-09	2005-06-09	ENSG00000145284	ENSG00000145284		"Fatty acid desaturases"	21088	protein-coding gene	gene with protein product		608370	"stearoyl-CoA desaturase 4"	SCD4		12477932	Standard	NM_024906		Approved	ACOD4, FLJ21032, FADS4, HSCD5	uc003hna.2	Q86SK9	OTTHUMG00000130293	ENST00000319540.4:c.181G>A	chr4.hg19:g.83719510C>T	ENSP00000316329:p.Val61Met	140.0	0.0		97.0	4.0	NM_024906	B2RPG0|Q4W5Q5|Q8NDS0|Q9H7D1	Missense_Mutation	SNP	ENST00000319540.4	hg19	CCDS34024.1	.	.	.	.	.	.	.	.	.	.	C	19.21	3.782740	0.70222	.	.	ENSG00000145284	ENST00000319540;ENST00000273908;ENST00000282709	T	0.49432	0.78	4.77	0.537	0.17144	.	0.566432	0.17256	N	0.180944	T	0.56217	0.1970	L	0.51422	1.61	0.32879	D	0.510265	D;D;D	0.76494	0.999;0.998;0.963	D;D;P	0.65233	0.913;0.933;0.489	T	0.64859	-0.6308	10	0.72032	D	0.01	0.0619	10.0677	0.42315	0.1298:0.4496:0.4206:0.0	.	61;61;61	Q9BSN4;Q86SK9-2;Q86SK9	.;.;SCD5_HUMAN	M	61	ENSP00000316329:V61M	ENSP00000273908:V61M	V	-	1	0	SCD5	83938534	0.797000	0.28877	0.996000	0.52242	0.989000	0.77384	0.069000	0.14552	0.158000	0.19367	0.542000	0.68232	GTG	.	.		0.711	SCD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252635.1	NM_024906		T	83719510	C	T	83719510	3	4	302	1	0	0	0	0	1	0	0	0	13902	536	19	1	1037	1	SCD5	4	83719510	Missense_Mutation	SNP	C	TCGA-G3-AAV6-01A-21D-A36X-10	36191918	83719510	107434766	21	43543										
CWC27	10283	hgsc.bcm.edu	37	chr5	64267604	64267604	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	agtatgaagctttgaggaagCaacagtcaaagaagggaact	12	5	1	3			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr5:64267604C>A	ENST00000381070.3	+	12	1334	c.1117C>A	c.(1117-1119)Caa>Aaa	p.Q373K	CWC27_ENST00000545000.1_3'UTR	NM_005869.2	NP_005860.2	Q6UX04	CWC27_HUMAN	CWC27 spliceosome-associated protein homolog (S. cerevisiae)	373					mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(5)|prostate(1)	21						TTTGAGGAAGCAACAGTCAAA	0.368																																					p.Q373K		Atlas-SNP	.											.	CWC27	47	.	0			c.C1117A						.						58	60	59					5																	64267604		2203	4300	6503	SO:0001583	missense	10283	exon12			AGGAAGCAACAGT	AF039692	CCDS3982.2, CCDS75252.1	5q12.3	2010-01-26	2010-01-26	2010-01-26	ENSG00000153015	ENSG00000153015			10664	protein-coding gene	gene with protein product			"serologically defined colon cancer antigen 10"	SDCCAG10		9610721, 19941820	Standard	XM_005248399		Approved	NY-CO-10	uc003jtn.1	Q6UX04	OTTHUMG00000074069	ENST00000381070.3:c.1117C>A	chr5.hg19:g.64267604C>A	ENSP00000370460:p.Gln373Lys	266.0	0.0		217.0	43.0	NM_005869	O60529|O60530|Q96EM3	Missense_Mutation	SNP	ENST00000381070.3	hg19	CCDS3982.2	.	.	.	.	.	.	.	.	.	.	C	5.965	0.361948	0.11296	.	.	ENSG00000153015	ENST00000381070;ENST00000538793	T	0.21543	2.0	6.01	6.01	0.97437	.	0.117930	0.64402	D	0.000017	T	0.13030	0.0316	N	0.17723	0.515	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.10450	0.005;0.0	T	0.05370	-1.0889	10	0.02654	T	1	.	15.2612	0.73625	0.1402:0.8598:0.0:0.0	.	373;373	Q6UX04-2;Q6UX04	.;CWC27_HUMAN	K	373	ENSP00000370460:Q373K	ENSP00000370460:Q373K	Q	+	1	0	CWC27	64303360	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.829000	0.55760	2.861000	0.98227	0.650000	0.86243	CAA	.	.		0.368	CWC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157247.4	NM_005869		A	64267604	C	A	64267604	3	1	302	1	0	0	0	0	1	0	0	0	4072	711	25	3	1163	3	CWC27	5	64267604	Missense_Mutation	SNP	C	TCGA-G3-AAV6-01A-21D-A36X-10		64267604	116647656	22	43544										
DMXL1	1657	hgsc.bcm.edu	37	chr5	118485628	118485628	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	agctgaatctaatcatgaacGccgccttaggtctctcacaa	7	12	4	2			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr5:118485628G>A	ENST00000311085.8	+	18	4186	c.4106G>A	c.(4105-4107)cGc>cAc	p.R1369H	DMXL1_ENST00000539542.1_Missense_Mutation_p.R1369H	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	1369										breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		AATCATGAACGCCGCCTTAGG	0.463																																					p.R1369H		Atlas-SNP	.											DMXL1,NS,carcinoma,0,1	DMXL1	268	.	0			c.G4106A						.						78	78	78					5																	118485628		2202	4300	6502	SO:0001583	missense	1657	exon18			ATGAACGCCGCCT	AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"WD repeat domain containing"	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.4106G>A	chr5.hg19:g.118485628G>A	ENSP00000309690:p.Arg1369His	81.0	0.0		80.0	16.0	NM_005509		Missense_Mutation	SNP	ENST00000311085.8	hg19	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	G	16.21	3.057785	0.55325	.	.	ENSG00000172869	ENST00000311085;ENST00000539542	T;T	0.42513	0.97;0.97	5.56	5.56	0.83823	.	0.045776	0.85682	D	0.000000	T	0.45438	0.1342	M	0.83012	2.62	0.43756	D	0.99626	B;B	0.33379	0.41;0.329	B;B	0.26094	0.058;0.066	T	0.52540	-0.8562	10	0.72032	D	0.01	-8.6645	12.6884	0.56960	0.1185:0.0:0.8815:0.0	.	1369;1369	F5H269;Q9Y485	.;DMXL1_HUMAN	H	1369	ENSP00000309690:R1369H;ENSP00000439479:R1369H	ENSP00000309690:R1369H	R	+	2	0	DMXL1	118513527	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.343000	0.52167	2.778000	0.95560	0.655000	0.94253	CGC	.	.		0.463	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		A	118485628	G	A	118485628	3	1	302	1	0	0	0	0	1	0	0	0	4596	1087	38	1	4176	1	DMXL1	5	118485628	Missense_Mutation	SNP	G	TCGA-G3-AAV6-01A-21D-A36X-10	54218024	118485628	62429632	23	43545										
CTXN3	613212	hgsc.bcm.edu	37	chr5	126993411	126993411	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	ccaacctctacctgggctgaTggacttgaaggcctggagaa	12	11	1	3			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr5:126993411T>C	ENST00000379445.3	+	3	749	c.198T>C	c.(196-198)gaT>gaC	p.D66D	CTC-548H10.2_ENST00000512352.1_RNA|CTXN3_ENST00000395322.3_Silent_p.D66D	NM_001048252.2	NP_001041717.1	Q4LDR2	CTXN3_HUMAN	cortexin 3	66						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)|lung(1)	4		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0128)|COAD - Colon adenocarcinoma(49;0.0234)|OV - Ovarian serous cystadenocarcinoma(64;0.038)		CCTGGGCTGATGGACTTGAAG	0.498																																					p.D66D		Atlas-SNP	.											.	CTXN3	19	.	0			c.T198C						.						92	86	88					5																	126993411		2203	4300	6503	SO:0001819	synonymous_variant	613212	exon3			GGCTGATGGACTT	AB219764	CCDS34221.1	5q23.2	2006-09-21				ENSG00000205279			31110	protein-coding gene	gene with protein product							Standard	NM_001048252		Approved		uc003kum.4	Q4LDR2		ENST00000379445.3:c.198T>C	chr5.hg19:g.126993411T>C		148.0	0.0		112.0	27.0	NM_001048252	B2RV32|D3DQ82	Silent	SNP	ENST00000379445.3	hg19	CCDS34221.1																																																																																			.	.		0.498	CTXN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372467.1	XM_932841		C	126993411	T	C	126993411	2	2	302	1	0	0	0	0	0	0	0	1	4052	1461	51	2		2	CTXN3	5	126993411	Silent	SNP	T	TCGA-G3-AAV6-01A-21D-A36X-10	8507783	126993411	53921849	24	43546										
STK32A	202374	hgsc.bcm.edu	37	chr5	146750236	146750236	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	gagaccgtatcatattcgctCcagtacttccagcaaggaaa	8	11	1	1			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr5:146750236C>G	ENST00000397936.3	+	9	1013	c.680C>G	c.(679-681)tCc>tGc	p.S227C	STK32A_ENST00000398523.3_Missense_Mutation_p.S227C	NM_001112724.1	NP_001106195.1	Q8WU08	ST32A_HUMAN	serine/threonine kinase 32A	227	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.S227F(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|prostate(1)|skin(1)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CATATTCGCTCCAGTACTTCC	0.373																																					p.S227C		Atlas-SNP	.											STK32A,NS,carcinoma,0,1	STK32A	54	.	1	Substitution - Missense(1)	lung(1)	c.C680G						.						172	150	156					5																	146750236		1568	3582	5150	SO:0001583	missense	202374	exon9			TTCGCTCCAGTAC		CCDS47299.1, CCDS75351.1	5q32	2008-02-05			ENSG00000169302	ENSG00000169302			28317	protein-coding gene	gene with protein product						12477932	Standard	NM_001112724		Approved	MGC22688, YANK1	uc010jgn.1	Q8WU08	OTTHUMG00000163411	ENST00000397936.3:c.680C>G	chr5.hg19:g.146750236C>G	ENSP00000381030:p.Ser227Cys	107.0	0.0		74.0	21.0	NM_001112724	B3KSY0	Missense_Mutation	SNP	ENST00000397936.3	hg19	CCDS47299.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.486314	0.84854	.	.	ENSG00000169302	ENST00000397936;ENST00000398523	T;T	0.27720	1.65;1.65	5.52	5.52	0.82312	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.47093	D	0.000250	T	0.54111	0.1838	L	0.60455	1.87	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77004	0.989;0.985;0.987	T	0.53690	-0.8403	10	0.87932	D	0	.	18.563	0.91107	0.0:1.0:0.0:0.0	.	227;227;227	B7Z9H7;Q8WU08;Q8WU08-3	.;ST32A_HUMAN;.	C	227	ENSP00000381030:S227C;ENSP00000381535:S227C	ENSP00000381030:S227C	S	+	2	0	STK32A	146730429	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.980000	0.76160	2.761000	0.94854	0.655000	0.94253	TCC	.	.		0.373	STK32A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373306.1	NM_145001		G	146750236	C	G	146750236	3	3	302	1	0	0	0	0	1	0	0	0	15312	855	30	4	743	4	STK32A	5	146750236	Missense_Mutation	SNP	C	TCGA-G3-AAV6-01A-21D-A36X-10	19756825	146750236	34165024	25	43547										
ANKRD6	22881	hgsc.bcm.edu	37	chr6	90312775	90312775	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	agaccgccttgcaccgggccAcagtggtggggaacacggag	16	12	0	1			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr6:90312775A>C	ENST00000522441.1	+	4	888	c.247A>C	c.(247-249)Aca>Cca	p.T83P	ANKRD6_ENST00000339746.4_Missense_Mutation_p.T83P|ANKRD6_ENST00000520793.1_Missense_Mutation_p.T83P|ANKRD6_ENST00000485637.1_Missense_Mutation_p.T83P|ANKRD6_ENST00000369408.5_Missense_Mutation_p.T83P|ANKRD6_ENST00000520886.2_3'UTR|ANKRD6_ENST00000447838.2_Missense_Mutation_p.T83P	NM_001242811.1	NP_001229740.1	Q9Y2G4	ANKR6_HUMAN	ankyrin repeat domain 6	83					negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of JNK cascade (GO:0046330)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(3)|large_intestine(7)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|stomach(2)	21		all_cancers(76;1.22e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;1.83e-05)|Lung NSC(302;0.239)		BRCA - Breast invasive adenocarcinoma(108;0.0209)		GCACCGGGCCACAGTGGTGGG	0.602																																					p.T83P		Atlas-SNP	.											.	ANKRD6	51	.	0			c.A247C						.						36	42	40					6																	90312775		2110	4219	6329	SO:0001583	missense	22881	exon4			CGGGCCACAGTGG	AB023174	CCDS47460.1, CCDS56441.1, CCDS56442.1, CCDS56443.1	6q14.2-q16.1	2013-03-20			ENSG00000135299	ENSG00000135299		"Ankyrin repeat domain containing"	17280	protein-coding gene	gene with protein product		610583					Standard	NM_001242809		Approved	KIAA0957	uc003pni.4	Q9Y2G4	OTTHUMG00000015202	ENST00000522441.1:c.247A>C	chr6.hg19:g.90312775A>C	ENSP00000430985:p.Thr83Pro	78.0	0.0		55.0	7.0	NM_001242809	B3KUC3|Q5JUJ4|Q5JUJ5|Q8IUQ8|Q9NU24|Q9UFQ9	Missense_Mutation	SNP	ENST00000522441.1	hg19	CCDS56441.1	.	.	.	.	.	.	.	.	.	.	A	19.19	3.778898	0.70107	.	.	ENSG00000135299	ENST00000369408;ENST00000339746;ENST00000447838;ENST00000465722;ENST00000523798;ENST00000522441;ENST00000522779;ENST00000485637;ENST00000522705;ENST00000520793	T;T;T;T;T;T;T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14;-0.14;-0.14;0.93;-0.14;-0.14;-0.14	5.93	-2.33	0.06724	Ankyrin repeat-containing domain (4);	0.462791	0.20253	N	0.096025	T	0.41811	0.1175	L	0.54965	1.715	0.80722	D	1	B;P;P;B	0.44006	0.324;0.824;0.789;0.25	B;P;B;B	0.44772	0.268;0.46;0.33;0.197	T	0.49123	-0.8972	10	0.72032	D	0.01	-1.773	7.9158	0.29816	0.3798:0.0:0.4991:0.1211	.	83;83;83;83	B3KUC3;Q9Y2G4;Q9Y2G4-1;C9JJE8	.;ANKR6_HUMAN;.;.	P	83;83;83;83;83;83;50;83;83;83	ENSP00000358416:T83P;ENSP00000345767:T83P;ENSP00000396771:T83P;ENSP00000429431:T83P;ENSP00000428377:T83P;ENSP00000430985:T83P;ENSP00000429337:T50P;ENSP00000430954:T83P;ENSP00000428309:T83P;ENSP00000429782:T83P	ENSP00000345767:T83P	T	+	1	0	ANKRD6	90369494	0.958000	0.32768	0.827000	0.32855	0.903000	0.53119	1.096000	0.30976	-0.066000	0.12998	0.533000	0.62120	ACA	.	.		0.602	ANKRD6-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376594.1			C	90312775	A	C	90312775	3	2	302	1	0	0	0	0	1	0	0	0	685	159	6	5	257	5	ANKRD6	6	90312775	Missense_Mutation	SNP	A	TCGA-G3-AAV6-01A-21D-A36X-10		90312775	80802292	26	43548										
PHF14	9678	hgsc.bcm.edu	37	chr7	11082380	11082380	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	atacctgtaaactacattacCatcttggatgtctggatcct	6	10	2	0			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr7:11082380C>G	ENST00000403050.3	+	13	2703	c.2251C>G	c.(2251-2253)Cat>Gat	p.H751D	PHF14_ENST00000445996.2_Missense_Mutation_p.H466D	NM_014660.3	NP_055475.2	O94880	PHF14_HUMAN	PHD finger protein 14	751					lung alveolus development (GO:0048286)|negative regulation of mesenchymal cell proliferation involved in lung development (GO:2000791)|negative regulation of platelet-derived growth factor receptor-alpha signaling pathway (GO:2000584)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(2)|breast(1)|endometrium(4)|kidney(5)|large_intestine(5)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	35				UCEC - Uterine corpus endometrioid carcinoma (126;0.205)		ACTACATTACCATCTTGGATG	0.348																																					p.H751D		Atlas-SNP	.											.	PHF14	90	.	0			c.C2251G						.						115	106	109					7																	11082380		1840	4093	5933	SO:0001583	missense	9678	exon13			CATTACCATCTTG	AB018326	CCDS47542.1	7p21.3	2013-01-28			ENSG00000106443	ENSG00000106443		"Zinc fingers, PHD-type"	22203	protein-coding gene	gene with protein product						9872452	Standard	NM_014660		Approved	KIAA0783	uc003sry.2	O94880	OTTHUMG00000150463	ENST00000403050.3:c.2251C>G	chr7.hg19:g.11082380C>G	ENSP00000385795:p.His751Asp	67.0	0.0		89.0	38.0	NM_014660	A7MCZ3|B4DI82	Missense_Mutation	SNP	ENST00000403050.3	hg19	CCDS47542.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.287471	0.80803	.	.	ENSG00000106443	ENST00000403050;ENST00000445996	D;D	0.99005	-5.32;-5.32	5.5	5.5	0.81552	Zinc finger, PHD-finger (2);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.049085	0.85682	D	0.000000	D	0.99674	0.9878	H	0.99325	4.515	0.80722	D	1	P;D;D;D	0.76494	0.948;0.968;0.992;0.999	B;D;P;D	0.75484	0.279;0.954;0.817;0.986	D	0.97259	0.9903	10	0.87932	D	0	.	19.4032	0.94639	0.0:1.0:0.0:0.0	.	466;466;751;751	O94880-2;B4DG57;A8MSQ1;O94880	.;.;.;PHF14_HUMAN	D	751;466	ENSP00000385795:H751D;ENSP00000403907:H466D	ENSP00000385795:H751D	H	+	1	0	PHF14	11048905	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	7.748000	0.85085	2.590000	0.87494	0.591000	0.81541	CAT	.	.		0.348	PHF14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318212.1	NM_014660		G	11082380	C	G	11082380	3	3	302	1	0	0	0	0	1	0	0	0	11834	594	21	4	2301	4	PHF14	7	11082380	Missense_Mutation	SNP	C	TCGA-G3-AAV6-01A-21D-A36X-10		11082380	148056283	27	43549										
AMPH	273	hgsc.bcm.edu	37	chr7	38429486	38429486	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	tcatcagaatttgctgcctcAaaatcatgcagtgtttccac	6	11	4	1			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr7:38429486A>G	ENST00000356264.2	-	20	2114	c.1899T>C	c.(1897-1899)ttT>ttC	p.F633F	AMPH_ENST00000428293.2_Silent_p.F591F|AMPH_ENST00000471913.1_5'Flank|AMPH_ENST00000325590.5_Silent_p.F591F	NM_001635.3	NP_001626.1	P49418	AMPH_HUMAN	amphiphysin	633	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				endocytosis (GO:0006897)|learning (GO:0007612)|synaptic transmission (GO:0007268)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|leading edge membrane (GO:0031256)|synaptic vesicle (GO:0008021)	phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|kidney(3)|large_intestine(12)|liver(3)|lung(27)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)	62						TTGCTGCCTCAAAATCATGCA	0.418																																					p.F633F		Atlas-SNP	.											.	AMPH	157	.	0			c.T1899C						.						154	145	148					7																	38429486		2203	4300	6503	SO:0001819	synonymous_variant	273	exon20			TGCCTCAAAATCA		CCDS5456.1, CCDS47574.1	7p14-p13	2007-06-19	2007-06-19		ENSG00000078053	ENSG00000078053			471	protein-coding gene	gene with protein product		600418	"amphiphysin (Stiff-Mann syndrome with breast cancer 128kD autoantigen)", "amphiphysin (Stiff-Man syndrome with breast cancer 128kDa autoantigen)"			8245793	Standard	NM_139316		Approved		uc003tgu.3	P49418	OTTHUMG00000023725	ENST00000356264.2:c.1899T>C	chr7.hg19:g.38429486A>G		69.0	0.0		60.0	29.0	NM_001635	A4D1X8|A4D1X9|O43538|Q75MJ8|Q75MK5|Q75MM3|Q8N4G0	Silent	SNP	ENST00000356264.2	hg19	CCDS5456.1	.	.	.	.	.	.	.	.	.	.	A	10.33	1.319136	0.23994	.	.	ENSG00000078053	ENST00000441628	.	.	.	5.04	-0.846	0.10734	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-16.6732	9.4145	0.38512	0.6506:0.0:0.3494:0.0	.	.	.	.	R	516	.	.	X	-	1	0	AMPH	38396011	0.998000	0.40836	0.996000	0.52242	0.986000	0.74619	0.684000	0.25364	-0.197000	0.10350	0.383000	0.25322	TGA	.	.		0.418	AMPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226953.2	NM_001635		G	38429486	A	G	38429486	2	3	302	1	0	0	0	0	0	0	0	1	588	127	5	2		2	AMPH	7	38429486	Silent	SNP	A	TCGA-G3-AAV6-01A-21D-A36X-10	27347106	38429486	120709177	28	43550										
ROR2	4920	hgsc.bcm.edu	37	chr9	94487147	94487147	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	ctcaggggctggtccttggtCaccacgcccagcaggcagac	13	15	2	1			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr9:94487147C>T	ENST00000375708.3	-	9	1827	c.1629G>A	c.(1627-1629)gtG>gtA	p.V543V	ROR2_ENST00000375715.1_Silent_p.V403V|ROR2_ENST00000550066.1_5'UTR	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	543	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|embryonic genitalia morphogenesis (GO:0030538)|inner ear morphogenesis (GO:0042472)|JNK cascade (GO:0007254)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	clathrin-coated endocytic vesicle membrane (GO:0030669)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						GGTCCTTGGTCACCACGCCCA	0.647																																					p.V543V		Atlas-SNP	.											.	ROR2	167	.	0			c.G1629A						.						71	70	71					9																	94487147		2203	4300	6503	SO:0001819	synonymous_variant	4920	exon9			CTTGGTCACCACG	M97639	CCDS6691.1	9q22	2013-01-11			ENSG00000169071	ENSG00000169071		"Immunoglobulin superfamily / I-set domain containing"	10257	protein-coding gene	gene with protein product		602337		NTRKR2, BDB, BDB1		1334494, 10700182	Standard	NM_004560		Approved		uc004arj.2	Q01974	OTTHUMG00000020211	ENST00000375708.3:c.1629G>A	chr9.hg19:g.94487147C>T		47.0	0.0		48.0	15.0	NM_004560	Q59GF5|Q5SPI5|Q9HAY7|Q9HB61	Silent	SNP	ENST00000375708.3	hg19	CCDS6691.1																																																																																			.	.		0.647	ROR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053040.1			T	94487147	C	T	94487147	2	4	302	1	0	0	0	0	0	0	0	1	13542	813	29	3		3	ROR2	9	94487147	Silent	SNP	C	TCGA-G3-AAV6-01A-21D-A36X-10		94487147	46726284	29	43551										
ACTL7B	10880	hgsc.bcm.edu	37	chr9	111617803	111617803	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	tcggggaggatcttcatggcGgtgcggaagatgtactccca	15	9	2	1			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr9:111617803G>A	ENST00000374667.3	-	1	1436	c.408C>T	c.(406-408)acC>acT	p.T136T		NM_006686.3	NP_006677.1	Q9Y614	ACL7B_HUMAN	actin-like 7B	136						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	structural constituent of cytoskeleton (GO:0005200)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						TCTTCATGGCGGTGCGGAAGA	0.622																																					p.T136T		Atlas-SNP	.											.	ACTL7B	57	.	0			c.C408T						.						68	49	55					9																	111617803		2203	4300	6503	SO:0001819	synonymous_variant	10880	exon1			CATGGCGGTGCGG	BC033789	CCDS6771.1	9q31	2009-05-15			ENSG00000148156	ENSG00000148156			162	protein-coding gene	gene with protein product		604304				10373328, 12907721	Standard	NM_006686		Approved	Tact1	uc004bdi.3	Q9Y614	OTTHUMG00000020462	ENST00000374667.3:c.408C>T	chr9.hg19:g.111617803G>A		74.0	0.0		86.0	14.0	NM_006686	B2R9Q2|Q5JSV1	Silent	SNP	ENST00000374667.3	hg19	CCDS6771.1																																																																																			.	.		0.622	ACTL7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053571.1	NM_006686		A	111617803	G	A	111617803	2	1	302	1	0	0	0	0	0	0	0	1	201	1103	39	1		1	ACTL7B	9	111617803	Silent	SNP	G	TCGA-G3-AAV6-01A-21D-A36X-10	17130656	111617803	29595628	30	43552										
FBXW5	54461	hgsc.bcm.edu	37	chr9	139836598	139836598	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	ggtggcttggtgtggccctgGgccagcagctcggccacctt	16	13	0	0			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr9:139836598G>C	ENST00000325285.3	-	6	1075	c.996C>G	c.(994-996)gcC>gcG	p.A332A	FBXW5_ENST00000483559.1_5'UTR	NM_018998.3	NP_061871.1	Q969U6	FBXW5_HUMAN	F-box and WD repeat domain containing 5	332					centrosome duplication (GO:0051298)|mitotic nuclear division (GO:0007067)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	protein kinase binding (GO:0019901)			breast(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	12	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.19)	OV - Ovarian serous cystadenocarcinoma(145;7.8e-06)|Epithelial(140;0.000106)		TGTGGCCCTGGGCCAGCAGCT	0.662																																					p.A332A		Atlas-SNP	.											.	FBXW5	36	.	0			c.C996G						.						76	82	80					9																	139836598		2195	4297	6492	SO:0001819	synonymous_variant	54461	exon6			GCCCTGGGCCAGC	BC014130	CCDS7014.1	9q34.3	2013-01-09	2007-02-08		ENSG00000159069	ENSG00000159069		"F-boxes / WD-40 domains", "WD repeat domain containing"	13613	protein-coding gene	gene with protein product		609072	"F-box and WD-40 domain protein 5"				Standard	NM_018998		Approved	DKFZP434B205, MGC20962, Fbw5	uc004cjx.3	Q969U6	OTTHUMG00000020967	ENST00000325285.3:c.996C>G	chr9.hg19:g.139836598G>C		54.0	0.0		72.0	23.0	NM_018998	B2RDZ6|Q59ET5|Q5SPZ8|Q5SPZ9|Q5SQ00|Q5SQ02|Q5SQ03|Q5SQ04|Q8WY79|Q96GJ6|Q9BSU8|Q9H6A8|Q9HBQ6|Q9NSZ3	Silent	SNP	ENST00000325285.3	hg19	CCDS7014.1																																																																																			.	.		0.662	FBXW5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055227.1	NM_018998		C	139836598	G	C	139836598	2	2	302	1	0	0	0	0	0	0	0	1	5776	1219	43	4		4	FBXW5	9	139836598	Silent	SNP	G	TCGA-G3-AAV6-01A-21D-A36X-10	28218795	139836598	1376833	31	43553										
CACNA1B	774	hgsc.bcm.edu	37	chr9	140773613	140773613	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	gcccatgtccgagcggctggTgagtgcccggctgggcctga	17	13	0	2	rs201604190		TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr9:140773613T>C	ENST00000371372.1	+	2	535		c.e2+2		RP11-188C12.3_ENST00000371390.1_RNA|CACNA1B_ENST00000371355.4_Splice_Site|CACNA1B_ENST00000371363.1_Splice_Site|CACNA1B_ENST00000371357.1_Splice_Site|CACNA1B_ENST00000277549.5_Splice_Site|CACNA1B_ENST00000277551.2_Splice_Site	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit						calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)	p.?(2)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	GAGCGGCTGGTGAGTGCCCGG	0.632																																					.		Atlas-SNP	.											CACNA1B,colon,carcinoma,0,8	CACNA1B	266	.	2	Unknown(2)	lung(1)|breast(1)	c.390+2T>C						.						25	29	28					9																	140773613		2104	4235	6339	SO:0001630	splice_region_variant	774	exon2			GGCTGGTGAGTGC	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.390+2T>C	chr9.hg19:g.140773613T>C		54.0	0.0		49.0	0.0	NM_001243812	B1AQK5	Splice_Site	SNP	ENST00000371372.1	hg19	CCDS59522.1	.	.	.	.	.	.	.	.	.	.	T	19.61	3.860228	0.71834	.	.	ENSG00000148408	ENST00000371372;ENST00000277551;ENST00000371363;ENST00000371357;ENST00000371355	.	.	.	4.73	3.57	0.40892	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.6445	0.51253	0.0:0.0:0.1485:0.8515	.	.	.	.	.	-1	.	.	.	+	.	.	CACNA1B	139893434	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.830000	0.86741	0.644000	0.30656	0.459000	0.35465	.	.	.		0.632	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718	Intron	C	140773613	T	C	140773613	5	2	302	1	0	0	0	0	0	0	1	0	2541	1710	59	2	398	2	CACNA1B	9	140773613	Splice_Site	SNP	T	TCGA-G3-AAV6-01A-21D-A36X-10	937015	140773613	439818	32	43554										
BMS1	9790	hgsc.bcm.edu	37	chr10	43312903	43312903	+	Nonsense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	gatgaaggagaaagcacataTtttgatgatcttaaaggaga	11	3	1	5			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr10:43312903T>G	ENST00000374518.5	+	15	2604	c.2541T>G	c.(2539-2541)taT>taG	p.Y847*		NM_014753.3	NP_055568.3	Q14692	BMS1_HUMAN	BMS1 ribosome biogenesis factor	847					ribosome assembly (GO:0042255)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(23)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						AAAGCACATATTTTGATGATC	0.408																																					p.Y847X		Atlas-SNP	.											.	BMS1	132	.	0			c.T2541G						.						45	47	46					10																	43312903		2126	3979	6105	SO:0001587	stop_gained	9790	exon15			CACATATTTTGAT	BC043345	CCDS7199.1	10q11.21	2013-05-01	2013-05-01	2007-03-20	ENSG00000165733	ENSG00000165733			23505	protein-coding gene	gene with protein product		611448	"BMS1-like, ribosome assembly protein (yeast)", "BMS1 homolog, ribosome assembly protein (yeast)"	BMS1L		11779832	Standard	NM_014753		Approved	KIAA0187	uc001jaj.3	Q14692	OTTHUMG00000018020	ENST00000374518.5:c.2541T>G	chr10.hg19:g.43312903T>G	ENSP00000363642:p.Tyr847*	81.0	0.0		72.0	21.0	NM_014753	Q5QPT5|Q86XJ9	Nonsense_Mutation	SNP	ENST00000374518.5	hg19	CCDS7199.1	.	.	.	.	.	.	.	.	.	.	T	39	7.516801	0.98332	.	.	ENSG00000165733	ENST00000374518	.	.	.	5.56	-4.7	0.03288	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	17.5885	0.87989	0.0:0.7442:0.0:0.2558	.	.	.	.	X	847	.	ENSP00000363642:Y847X	Y	+	3	2	BMS1	42632909	0.953000	0.32496	0.935000	0.37517	0.998000	0.95712	0.119000	0.15626	-0.894000	0.03925	0.451000	0.29950	TAT	.	.		0.408	BMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047690.2	NM_014753		G	43312903	T	G	43312903	4	3	302	1	0	0	0	0	0	1	0	0	1472	1500	52	5	2595	5	BMS1	10	43312903	Nonsense_Mutation	SNP	T	TCGA-G3-AAV6-01A-21D-A36X-10		43312903	92221844	33	43555										
ERCC6	2074	hgsc.bcm.edu	37	chr10	50681069	50681069	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	agaagaaacacaaatatggaTgtgtcctagaggtaagacac	10	6	0	4			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr10:50681069T>C	ENST00000355832.5	-	15	2793	c.2715A>G	c.(2713-2715)acA>acG	p.T905T	ERCC6_ENST00000542458.1_Silent_p.T275T|ERCC6_ENST00000465653.1_5'Flank|RP11-123B3.2_ENST00000423283.1_RNA	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	905	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|photoreceptor cell maintenance (GO:0045494)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of protein tyrosine kinase activity (GO:0061098)|pyrimidine dimer repair (GO:0006290)|regulation of DNA-templated transcription, elongation (GO:0032784)|response to gamma radiation (GO:0010332)|response to oxidative stress (GO:0006979)|response to superoxide (GO:0000303)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein N-terminus binding (GO:0047485)|protein tyrosine kinase activator activity (GO:0030296)			breast(5)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						CAAATATGGATGTGTCCTAGA	0.493								Direct reversal of damage;Nucleotide excision repair (NER)																													p.X905W		Atlas-SNP	.											.	ERCC6	162	.	0			c.A2715G						.						69	63	65					10																	50681069		2203	4300	6503	SO:0001819	synonymous_variant	2074	exon15			TATGGATGTGTCC	L04791	CCDS7229.1	10q11	2014-09-17	2014-03-07		ENSG00000225830	ENSG00000225830			3438	protein-coding gene	gene with protein product	"Cockayne syndrome B protein"	609413	"excision repair cross-complementing rodent repair deficiency, complementation group 6"	CKN2		1339317, 19179336	Standard	NM_000124		Approved	CSB, RAD26, ARMD5	uc001jhs.5	Q03468	OTTHUMG00000018195	ENST00000355832.5:c.2715A>G	chr10.hg19:g.50681069T>C		196.0	0.0		215.0	70.0	NM_000124	D3DX94|Q5W0L9	Missense_Mutation	SNP	ENST00000355832.5	hg19	CCDS7229.1																																																																																			.	.		0.493	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124		C	50681069	T	C	50681069	2	2	302	1	0	0	0	0	0	0	0	1	5219	1451	51	2		2	ERCC6	10	50681069	Silent	SNP	T	TCGA-G3-AAV6-01A-21D-A36X-10	7368166	50681069	84853678	34	43556										
EGR2	1959	hgsc.bcm.edu	37	chr10	64573833	64573833	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	ggaggtggtggctgctgacaGgaacgcagaagggtcctggt	19	7	0	2			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr10:64573833G>A	ENST00000242480.3	-	2	890	c.565C>T	c.(565-567)Ctg>Ttg	p.L189L	EGR2_ENST00000493899.2_5'Flank|EGR2_ENST00000439032.1_Silent_p.L189L|EGR2_ENST00000411732.1_Silent_p.L139L	NM_000399.3|NM_001136177.1	NP_000390.2|NP_001129649.1	P11161	EGR2_HUMAN	early growth response 2	189					brain development (GO:0007420)|brain segmentation (GO:0035284)|cell death (GO:0008219)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|facial nerve structural organization (GO:0021612)|fat cell differentiation (GO:0045444)|learning or memory (GO:0007611)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of apoptotic process (GO:0043066)|peripheral nervous system development (GO:0007422)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein export from nucleus (GO:0006611)|protein sumoylation (GO:0016925)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of ossification (GO:0030278)|response to insulin (GO:0032868)|rhombomere 3 formation (GO:0021660)|rhombomere 5 formation (GO:0021666)|rhythmic behavior (GO:0007622)|Schwann cell differentiation (GO:0014037)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|lung(13)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)	36	Prostate(12;0.0297)|all_hematologic(501;0.228)					GCTGCTGACAGGAACGCAGAA	0.622																																					p.L189L		Atlas-SNP	.											.	EGR2	77	.	0			c.C565T						.						94	93	93					10																	64573833		2203	4300	6503	SO:0001819	synonymous_variant	1959	exon2			CTGACAGGAACGC	BC035625	CCDS7267.1, CCDS44409.1	10q21.1	2014-09-17	2009-04-23		ENSG00000122877	ENSG00000122877		"Zinc fingers, C2H2-type"	3239	protein-coding gene	gene with protein product	"Krox-20 homolog, Drosophila"	129010	"early growth response 2 (Krox-20 homolog, Drosophila)"	KROX20			Standard	NM_000399		Approved		uc001jmi.3	P11161	OTTHUMG00000018308	ENST00000242480.3:c.565C>T	chr10.hg19:g.64573833G>A		144.0	0.0		157.0	14.0	NM_000399	B2R724|B3KRD7|Q68CZ5|Q8IV26|Q9UNA6	Silent	SNP	ENST00000242480.3	hg19	CCDS7267.1																																																																																			.	.		0.622	EGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048245.2	NM_000399		A	64573833	G	A	64573833	2	1	302	1	0	0	0	0	0	0	0	1	4974	991	35	3		3	EGR2	10	64573833	Silent	SNP	G	TCGA-G3-AAV6-01A-21D-A36X-10	13892764	64573833	70960914	35	43557										
HKDC1	80201	hgsc.bcm.edu	37	chr10	71010157	71010157	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	gtacaacaagatcttcgccaTccccctggagatcatgcagg	9	13	2	2			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr10:71010157T>C	ENST00000354624.5	+	11	1815	c.1682T>C	c.(1681-1683)aTc>aCc	p.I561T	HKDC1_ENST00000395086.2_Missense_Mutation_p.I561T	NM_025130.3	NP_079406	Q2TB90	HKDC1_HUMAN	hexokinase domain containing 1	561	Hexokinase type-1 2.				carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)	cytosol (GO:0005829)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|mannokinase activity (GO:0019158)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						ATCTTCGCCATCCCCCTGGAG	0.592																																					p.I561T		Atlas-SNP	.											.	HKDC1	98	.	0			c.T1682C						.						114	99	104					10																	71010157		2203	4300	6503	SO:0001583	missense	80201	exon11			TCGCCATCCCCCT		CCDS7288.1	10q22.1	2006-10-24			ENSG00000156510	ENSG00000156510			23302	protein-coding gene	gene with protein product						12477932	Standard	NM_025130		Approved	FLJ37767, FLJ22761	uc001jpf.4	Q2TB90	OTTHUMG00000018371	ENST00000354624.5:c.1682T>C	chr10.hg19:g.71010157T>C	ENSP00000346643:p.Ile561Thr	88.0	0.0		79.0	4.0	NM_025130	B5MDN9|Q2TB91|Q5VTC7|Q7Z373|Q8WU37|Q96EH2|Q9H5Y9	Missense_Mutation	SNP	ENST00000354624.5	hg19	CCDS7288.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.417035	0.83449	.	.	ENSG00000156510	ENST00000354624;ENST00000395087;ENST00000395086	D;D	0.98717	-5.09;-5.09	4.98	4.98	0.66077	Hexokinase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.99217	0.9728	M	0.90542	3.125	0.54753	D	0.999989	P	0.48230	0.907	D	0.69479	0.964	D	0.99075	1.0835	10	0.72032	D	0.01	-20.7428	14.8099	0.69985	0.0:0.0:0.0:1.0	.	561	Q2TB90	HKDC1_HUMAN	T	561	ENSP00000346643:I561T;ENSP00000378521:I561T	ENSP00000346643:I561T	I	+	2	0	HKDC1	70680163	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.831000	0.86748	2.090000	0.63153	0.459000	0.35465	ATC	.	.		0.592	HKDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048389.1	NM_025130		C	71010157	T	C	71010157	3	2	302	1	0	0	0	0	1	0	0	0	7202	1435	50	2	1724	2	HKDC1	10	71010157	Missense_Mutation	SNP	T	TCGA-G3-AAV6-01A-21D-A36X-10	6436324	71010157	64524590	36	43558										
OPN4	94233	hgsc.bcm.edu	37	chr10	88422074	88422074	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	tgtatcacgccggcacagtcGcccctaccccagctaccgct	8	19	1	0	rs150092638		TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr10:88422074G>A	ENST00000241891.5	+	8	1306	c.1139G>A	c.(1138-1140)cGc>cAc	p.R380H	OPN4_ENST00000372071.2_Missense_Mutation_p.R391H	NM_033282.3	NP_150598.1	Q9UHM6	OPN4_HUMAN	opsin 4	380					phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|rhodopsin mediated signaling pathway (GO:0016056)|rhythmic process (GO:0048511)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	11-cis retinal binding (GO:0005502)|G-protein coupled photoreceptor activity (GO:0008020)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(5)|ovary(3)	18						CGGCACAGTCGCCCCTACCCC	0.682																																					p.R391H		Atlas-SNP	.											.	OPN4	61	.	0			c.G1172A						.	G	HIS/ARG,HIS/ARG	0,4406		0,0,2203	38	29	32		1172,1139	0.6	0.1	10	dbSNP_134	32	1,8597		0,1,4298	no	missense,missense	OPN4	NM_001030015.2,NM_033282.3	29,29	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	391/490,380/479	88422074	1,13003	2203	4299	6502	SO:0001583	missense	94233	exon9			ACAGTCGCCCCTA	AF147788	CCDS7376.1, CCDS31237.1	10q22	2012-08-08	2008-04-16		ENSG00000122375	ENSG00000122375		"GPCR / Class A : Opsin receptors"	14449	protein-coding gene	gene with protein product	"melanopsin"	606665	"opsin 4 (melanopsin)"			10632589	Standard	NM_001030015		Approved	MOP, melanopsin	uc001kdp.3	Q9UHM6	OTTHUMG00000018654	ENST00000241891.5:c.1139G>A	chr10.hg19:g.88422074G>A	ENSP00000241891:p.Arg380His	59.0	0.0		72.0	13.0	NM_001030015	B7ZLB3|Q14D01|Q2PP22|Q8NGQ9	Missense_Mutation	SNP	ENST00000241891.5	hg19	CCDS7376.1	.	.	.	.	.	.	.	.	.	.	G	5.796	0.331258	0.10956	0.0	1.16E-4	ENSG00000122375	ENST00000372071;ENST00000241891;ENST00000443292	T;T;T	0.69435	-0.35;0.03;-0.4	5.39	0.571	0.17352	.	0.846040	0.10657	N	0.649149	T	0.45074	0.1324	N	0.14661	0.345	0.09310	N	1	B;B;B	0.10296	0.002;0.002;0.003	B;B;B	0.06405	0.001;0.001;0.002	T	0.24119	-1.0169	10	0.22706	T	0.39	.	8.5819	0.33634	0.187:0.1204:0.6926:0.0	.	391;380;391	C9JWU6;Q9UHM6;Q9UHM6-2	.;OPN4_HUMAN;.	H	391;380;391	ENSP00000361141:R391H;ENSP00000241891:R380H;ENSP00000393132:R391H	ENSP00000241891:R380H	R	+	2	0	OPN4	88412054	0.001000	0.12720	0.095000	0.20976	0.944000	0.59088	0.583000	0.23849	0.097000	0.17492	-0.940000	0.02684	CGC	.	G|1.000;A|0.000		0.682	OPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049158.2	NM_033282		A	88422074	G	A	88422074	3	1	302	1	0	0	0	0	1	0	0	0	10891	1087	38	1	1206	1	OPN4	10	88422074	Missense_Mutation	SNP	G	TCGA-G3-AAV6-01A-21D-A36X-10	17411917	88422074	47112673	37	43559										
SEC31B	25956	hgsc.bcm.edu	37	chr10	102256096	102256096	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	aggttggcatactgagtgacCctgtaggttgtggcagggcc	16	8	0	2			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr10:102256096C>A	ENST00000370345.3	-	18	2326	c.2229G>T	c.(2227-2229)agG>agT	p.R743S	SEC31B_ENST00000494350.1_5'Flank	NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	743					protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|vesicle coat (GO:0030120)				NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(3)|lung(17)|ovary(1)|urinary_tract(1)	36		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)		ACTGAGTGACCCTGTAGGTTG	0.597																																					p.R743S		Atlas-SNP	.											.	SEC31B	84	.	0			c.G2229T						.						102	92	95					10																	102256096		2203	4300	6503	SO:0001583	missense	25956	exon18			AGTGACCCTGTAG	AF274863	CCDS7495.1	10q24.32	2013-01-10	2006-10-05	2006-09-07	ENSG00000075826	ENSG00000075826		"WD repeat domain containing"	23197	protein-coding gene	gene with protein product		610258	"SEC31-like 2 (S. cerevisiae)"	SEC31L2		16495487	Standard	NM_015490		Approved	SEC31B-1, DKFZP434M183	uc001krc.1	Q9NQW1	OTTHUMG00000019342	ENST00000370345.3:c.2229G>T	chr10.hg19:g.102256096C>A	ENSP00000359370:p.Arg743Ser	99.0	0.0		85.0	10.0	NM_015490	B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Missense_Mutation	SNP	ENST00000370345.3	hg19	CCDS7495.1	.	.	.	.	.	.	.	.	.	.	C	15.18	2.758444	0.49468	.	.	ENSG00000075826	ENST00000370345	T	0.51817	0.69	5.78	-4.52	0.03472	.	0.270914	0.46442	N	0.000291	T	0.37517	0.1006	M	0.73598	2.24	0.25990	N	0.98226	B;B	0.11235	0.004;0.003	B;B	0.18561	0.022;0.01	T	0.30475	-0.9977	10	0.54805	T	0.06	-3.0951	3.7149	0.08434	0.1345:0.5199:0.1152:0.2304	.	742;743	Q9NQW1-5;Q9NQW1	.;SC31B_HUMAN	S	743	ENSP00000359370:R743S	ENSP00000359370:R743S	R	-	3	2	SEC31B	102246086	0.003000	0.15002	0.001000	0.08648	0.996000	0.88848	0.005000	0.13129	-0.776000	0.04578	0.455000	0.32223	AGG	.	.		0.597	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	NM_015490		A	102256096	C	A	102256096	3	1	302	1	0	0	0	0	1	0	0	0	14014	622	22	3	1346	3	SEC31B	10	102256096	Missense_Mutation	SNP	C	TCGA-G3-AAV6-01A-21D-A36X-10	13834022	102256096	33278651	38	43560										
QSER1	79832	hgsc.bcm.edu	37	chr11	32954330	32954330	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	taaaacattgactttttctgGgtcatctcagactgtaactc	6	9	3	2			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr11:32954330G>T	ENST00000399302.2	+	4	1474	c.1139G>T	c.(1138-1140)gGg>gTg	p.G380V	QSER1_ENST00000527788.1_Intron	NM_001076786.1	NP_001070254.1	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	380	Ser-rich.									breast(5)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	48	Breast(20;0.158)					ACTTTTTCTGGGTCATCTCAG	0.383																																					p.G380V		Atlas-SNP	.											.	QSER1	153	.	0			c.G1139T						.						103	95	97					11																	32954330		1835	4077	5912	SO:0001583	missense	79832	exon4			TTTCTGGGTCATC	AL834141	CCDS41631.1	11p13	2014-02-12			ENSG00000060749	ENSG00000060749			26154	protein-coding gene	gene with protein product							Standard	XM_006718323		Approved	FLJ21924	uc001mty.3	Q2KHR3		ENST00000399302.2:c.1139G>T	chr11.hg19:g.32954330G>T	ENSP00000382241:p.Gly380Val	137.0	0.0		147.0	10.0	NM_001076786	Q6ZU30|Q6ZUR5	Missense_Mutation	SNP	ENST00000399302.2	hg19	CCDS41631.1	.	.	.	.	.	.	.	.	.	.	G	11.60	1.686751	0.29962	.	.	ENSG00000060749	ENST00000399302	T	0.47177	0.85	4.89	3.98	0.46160	.	0.175311	0.26109	U	0.026296	T	0.31888	0.0811	N	0.24115	0.695	0.80722	D	1	P	0.39282	0.666	B	0.33339	0.162	T	0.15464	-1.0436	10	0.48119	T	0.1	.	13.5502	0.61728	0.0762:0.0:0.9238:0.0	.	380	Q2KHR3	QSER1_HUMAN	V	380	ENSP00000382241:G380V	ENSP00000382241:G380V	G	+	2	0	QSER1	32910906	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.718000	0.54919	1.194000	0.43101	0.591000	0.81541	GGG	.	.		0.383	QSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388448.1	NM_024774		T	32954330	G	T	32954330	3	4	302	1	0	0	0	0	1	0	0	0	12897	1232	43	3	1145	3	QSER1	11	32954330	Missense_Mutation	SNP	G	TCGA-G3-AAV6-01A-21D-A36X-10		32954330	102052186	39	43561										
TCP11L1	55346	hgsc.bcm.edu	37	chr11	33076187	33076187	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	agaacttctagagacagcgaGaggtgtcaccaacatggctc	11	10	2	3			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr11:33076187G>T	ENST00000334274.4	+	3	612	c.212G>T	c.(211-213)aGa>aTa	p.R71I	TCP11L1_ENST00000530171.1_Intron|TCP11L1_ENST00000531632.2_Missense_Mutation_p.R71I|TCP11L1_ENST00000432887.1_Missense_Mutation_p.R71I	NM_018393.3	NP_060863.3	Q9NUJ3	T11L1_HUMAN	t-complex 11, testis-specific-like 1	71						microtubule (GO:0005874)				kidney(1)|liver(2)|lung(2)|skin(1)	6						GAGACAGCGAGAGGTGTCACC	0.418																																					p.R71I		Atlas-SNP	.											.	TCP11L1	40	.	0			c.G212T						.						119	118	119					11																	33076187		2202	4298	6500	SO:0001583	missense	55346	exon3			CAGCGAGAGGTGT	BC041696	CCDS7882.1	11p13	2014-08-12	2012-09-20		ENSG00000176148	ENSG00000176148			25655	protein-coding gene	gene with protein product			"t-complex 11 (mouse) like 1"				Standard	NM_001145541		Approved	FLJ11336	uc010rei.2	Q9NUJ3	OTTHUMG00000165303	ENST00000334274.4:c.212G>T	chr11.hg19:g.33076187G>T	ENSP00000335595:p.Arg71Ile	104.0	0.0		97.0	16.0	NM_001145541	D3DR01|Q8IVX4	Missense_Mutation	SNP	ENST00000334274.4	hg19	CCDS7882.1	.	.	.	.	.	.	.	.	.	.	G	15.11	2.734785	0.48939	.	.	ENSG00000176148	ENST00000530419;ENST00000334274;ENST00000531632;ENST00000432887	T;T;T;T	0.23754	1.89;2.9;2.9;2.9	5.96	3.52	0.40303	.	0.083576	0.85682	D	0.000000	T	0.15912	0.0383	N	0.19112	0.55	0.80722	D	1	B	0.14438	0.01	B	0.06405	0.002	T	0.04551	-1.0943	10	0.48119	T	0.1	-25.019	9.3351	0.38045	0.8405:0.0:0.1595:0.0	.	71	Q9NUJ3	T11L1_HUMAN	I	71	ENSP00000436428:R71I;ENSP00000335595:R71I;ENSP00000433067:R71I;ENSP00000395070:R71I	ENSP00000335595:R71I	R	+	2	0	TCP11L1	33032763	1.000000	0.71417	0.342000	0.25602	0.057000	0.15508	7.441000	0.80485	0.439000	0.26476	-0.345000	0.07892	AGA	.	.		0.418	TCP11L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383377.4	NM_018393		T	33076187	G	T	33076187	3	4	302	1	0	0	0	0	1	0	0	0	15729	942	33	3	218	3	TCP11L1	11	33076187	Missense_Mutation	SNP	G	TCGA-G3-AAV6-01A-21D-A36X-10	121857	33076187	101930329	40	43562										
ANO2	57101	hgsc.bcm.edu	37	chr12	5860094	5860094	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	aggaatgatgtatataatccCagccaggcaaaatacagtcc	8	9	0	1			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr12:5860094C>A	ENST00000356134.5	-	12	1160	c.1089G>T	c.(1087-1089)ctG>ctT	p.L363L	ANO2_ENST00000546188.1_Silent_p.L363L|ANO2_ENST00000327087.8_Silent_p.L362L	NM_001278596.1	NP_001265525.1	Q9NQ90	ANO2_HUMAN	anoctamin 2, calcium activated chloride channel	367					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(1)	58						TATATAATCCCAGCCAGGCAA	0.323																																					p.L362L		Atlas-SNP	.											.	ANO2	309	.	0			c.G1086T						.						75	70	72					12																	5860094		1830	4089	5919	SO:0001819	synonymous_variant	57101	exon11			TAATCCCAGCCAG	AJ272204	CCDS44807.1, CCDS44807.2	12p13.3	2014-04-09	2014-04-09	2008-08-28		ENSG00000047617		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	1183	protein-coding gene	gene with protein product	"transmembrane protein 16B (eight membrane-spanning domains)"	610109	"chromosome 12 open reading frame 3", "transmembrane protein 16B", "anoctamin 2"	C12orf3, TMEM16B		12739008, 15067359, 24692353	Standard	NM_001278596		Approved		uc001qnm.2	Q9NQ90		ENST00000356134.5:c.1089G>T	chr12.hg19:g.5860094C>A		164.0	0.0		241.0	11.0	NM_020373	C4N787|Q9H847	Silent	SNP	ENST00000356134.5	hg19																																																																																				.	.		0.323	ANO2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000399019.4	NM_020373		A	5860094	C	A	5860094	2	1	302	1	0	0	0	0	0	0	0	1	697	581	21	3		3	ANO2	12	5860094	Silent	SNP	C	TCGA-G3-AAV6-01A-21D-A36X-10		5860094	127991801	41	43563										
KRT6B	3854	hgsc.bcm.edu	37	chr12	52845384	52845384	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	tctgctcacgctcctcggccCgcacccgctggatggcgggg	14	17	2	0			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr12:52845384C>T	ENST00000252252.3	-	1	526	c.479G>A	c.(478-480)cGg>cAg	p.R160Q		NM_005555.3	NP_005546.2	P04259	K2C6B_HUMAN	keratin 6B	160	Head.			VR -> IG (in Ref. 2; AAA59466). {ECO:0000305}.	ectoderm development (GO:0007398)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(19)|ovary(4)|prostate(2)	40				BRCA - Breast invasive adenocarcinoma(357;0.083)		CTCCTCGGCCCGCACCCGCTG	0.597																																					p.R160Q		Atlas-SNP	.											.	KRT6B	90	.	0			c.G479A						.						53	72	65					12																	52845384		2203	4296	6499	SO:0001583	missense	3854	exon1			TCGGCCCGCACCC	BC034535	CCDS8828.1	12q13.13	2013-01-16	2004-08-11		ENSG00000185479	ENSG00000185479		"-", "Intermediate filaments type II, keratins (basic)"	6444	protein-coding gene	gene with protein product		148042	"keratin-like 1 (a type II keratin sequence)"	KRTL1		1713141, 16831889	Standard	NM_005555		Approved		uc001sak.3	P04259	OTTHUMG00000169593	ENST00000252252.3:c.479G>A	chr12.hg19:g.52845384C>T	ENSP00000252252:p.Arg160Gln	375.0	0.0		416.0	54.0	NM_005555	P48669	Missense_Mutation	SNP	ENST00000252252.3	hg19	CCDS8828.1	.	.	.	.	.	.	.	.	.	.	C	14.68	2.606483	0.46527	.	.	ENSG00000185479	ENST00000252252;ENST00000544607	D	0.85556	-2.0	3.28	0.429	0.16506	.	0.089287	0.44902	D	0.000418	D	0.88890	0.6560	M	0.94021	3.485	0.32244	N	0.572368	D	0.60160	0.987	P	0.48552	0.581	D	0.88941	0.3380	10	0.87932	D	0	.	8.7904	0.34848	0.0:0.7388:0.0:0.2612	.	160	P04259	K2C6B_HUMAN	Q	160	ENSP00000252252:R160Q	ENSP00000252252:R160Q	R	-	2	0	KRT6B	51131651	0.168000	0.22989	0.024000	0.17045	0.255000	0.26057	0.832000	0.27490	0.094000	0.17404	0.298000	0.19748	CGG	.	.		0.597	KRT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404969.1	NM_005555		T	52845384	C	T	52845384	3	4	302	1	0	0	0	0	1	0	0	0	8490	652	23	1	1251	1	KRT6B	12	52845384	Missense_Mutation	SNP	C	TCGA-G3-AAV6-01A-21D-A36X-10	46985290	52845384	81006511	42	43564										
ERCC5	2073	hgsc.bcm.edu	37	chr13	103520547	103520547	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	accaactgtgggttgtgtaaCcgccatggaaattctcaatg	10	9	1	0			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr13:103520547C>A	ENST00000355739.4	+	12	4041	c.2618C>A	c.(2617-2619)aCc>aAc	p.T873N	ERCC5_ENST00000375954.1_Missense_Mutation_p.T106N|BIVM-ERCC5_ENST00000602836.1_Missense_Mutation_p.N1298K	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	873	I-domain.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|response to UV (GO:0009411)|response to UV-C (GO:0010225)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|double-stranded DNA binding (GO:0003690)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	51	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					GGTTGTGTAACCGCCATGGAA	0.368			"Mis, N, F"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.T1327N		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (G)	13	13q33	2073	"excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))"		E	.	.	.	.	0			c.C3980A						.						85	93	90					13																	103520547		2203	4300	6503	SO:0001583	missense	0	exon20	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	GTGTAACCGCCAT	X71342	CCDS32004.1	13q22-q34	2014-09-17	2014-03-07		ENSG00000134899	ENSG00000134899			3437	protein-coding gene	gene with protein product	"Cockayne syndrome"	133530	"xeroderma pigmentosum, complementation group G", "excision repair cross-complementing rodent repair deficiency, complementation group 5"	ERCM2, XPGC		8088806	Standard	NM_000123		Approved			P28715	OTTHUMG00000017310	ENST00000355739.4:c.2618C>A	chr13.hg19:g.103520547C>A	ENSP00000347978:p.Thr873Asn	276.0	0.0		300.0	50.0	NM_001204425	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Missense_Mutation	SNP	ENST00000355739.4	hg19	CCDS32004.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.767516	0.90020	.	.	ENSG00000134899	ENST00000418659;ENST00000355739;ENST00000375955;ENST00000375954	T;T	0.67523	-0.27;-0.27	5.02	5.02	0.67125	-3&apos (1);Helix-hairpin-helix motif, class 2 (1); exonuclease, C-terminal domain (1);5&apos (1);	0.163740	0.53938	D	0.000053	T	0.61615	0.2361	L	0.42686	1.345	0.80722	D	1	P;B	0.40534	0.72;0.368	B;B	0.40982	0.345;0.159	T	0.58521	-0.7622	10	0.18276	T	0.48	-6.7919	18.34	0.90302	0.0:1.0:0.0:0.0	.	873;1298	P28715;Q59FZ7	ERCC5_HUMAN;.	N	1298;873;705;106	ENSP00000347978:T873N;ENSP00000365121:T106N	ENSP00000347978:T873N	T	+	2	0	ERCC5	102318548	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.691000	0.84191	2.353000	0.79882	0.491000	0.48974	ACC	.	.		0.368	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1			A	103520547	C	A	103520547	3	1	302	1	0	0	0	0	1	0	0	0	5218	507	18	3	2664	3	ERCC5	13	103520547	Missense_Mutation	SNP	C	TCGA-G3-AAV6-01A-21D-A36X-10		103520547	11649331	43	43565										
C14orf21	161424	hgsc.bcm.edu	37	chr14	24769239	24769239	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	aacgggggcgcggggccaagGggtcggggcgccccttacca	19	13	0	0			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr14:24769239G>A	ENST00000267425.3	+	1	172	c.79G>A	c.(79-81)Ggg>Agg	p.G27R	DHRS1_ENST00000288111.7_5'Flank|DHRS1_ENST00000396813.1_5'Flank|NOP9_ENST00000396802.3_Missense_Mutation_p.G27R	NM_174913.1	NP_777573.1	Q86U38	NOP9_HUMAN	NOP9 nucleolar protein	27							poly(A) RNA binding (GO:0044822)										CGGGGCCAAGGGGTCGGGGCG	0.731																																					p.G27R		Atlas-SNP	.											.	.	.	.	0			c.G79A						.						9	11	10					14																	24769239		1921	3913	5834	SO:0001583	missense	161424	exon1			GCCAAGGGGTCGG		CCDS9624.1, CCDS66616.1	14q12	2012-12-10	2012-12-10	2012-06-06	ENSG00000196943	ENSG00000196943			19826	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 21", "NOP9 nucleolar protein homolog (yeast)"	C14orf21		21653694	Standard	XM_005267385		Approved		uc001wol.1	Q86U38	OTTHUMG00000029342	ENST00000267425.3:c.79G>A	chr14.hg19:g.24769239G>A	ENSP00000267425:p.Gly27Arg	106.0	0.0		171.0	93.0	NM_174913	A8MY76|Q8IVF0|Q8TBS6	Missense_Mutation	SNP	ENST00000267425.3	hg19	CCDS9624.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.297802	0.81025	.	.	ENSG00000196943	ENST00000267425;ENST00000396802	T;T	0.35236	1.37;1.32	4.87	3.98	0.46160	.	0.427204	0.19988	N	0.101621	T	0.28034	0.0691	L	0.51422	1.61	0.09310	N	0.999998	P	0.36837	0.571	B	0.33799	0.17	T	0.10613	-1.0622	10	0.20519	T	0.43	-6.0855	9.0942	0.36629	0.0995:0.0:0.9005:0.0	.	27	Q86U38	CN021_HUMAN	R	27	ENSP00000267425:G27R;ENSP00000380020:G27R	ENSP00000267425:G27R	G	+	1	0	C14orf21	23839079	0.751000	0.28327	0.061000	0.19648	0.365000	0.29674	0.265000	0.18515	1.425000	0.47237	0.655000	0.94253	GGG	.	.		0.731	NOP9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073186.2			A	24769239	G	A	24769239	3	1	302	1	0	0	0	0	1	0	0	0	1771	1232	43	3	81	3	C14orf21	14	24769239	Missense_Mutation	SNP	G	TCGA-G3-AAV6-01A-21D-A36X-10		24769239	82580301	44	43566										
PSMA3	5684	hgsc.bcm.edu	37	chr14	58734222	58734222	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	tgacctgccgtgatatcgttAaagaagttgcaaaaatgtaa	9	6	0	3			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr14:58734222A>G	ENST00000216455.4	+	8	664	c.574A>G	c.(574-576)Aaa>Gaa	p.K192E	RP11-349A22.5_ENST00000556002.1_RNA|PSMA3_ENST00000412908.2_Missense_Mutation_p.K185E|RP11-349A22.5_ENST00000555275.1_RNA|CTD-2002H8.2_ENST00000557322.1_RNA|RP11-349A22.5_ENST00000555162.1_RNA|RP11-349A22.5_ENST00000554378.1_RNA|RP11-349A22.5_ENST00000554360.1_RNA|PSMA3_ENST00000557508.1_Missense_Mutation_p.K117E	NM_002788.3|NM_152132.2	NP_002779.1|NP_687033.1	P25788	PSA3_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 3	192					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|proteasome core complex, alpha-subunit complex (GO:0019773)	threonine-type endopeptidase activity (GO:0004298)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(2)	12						TGATATCGTTAAAGAAGTTGC	0.279																																					p.K192E		Atlas-SNP	.											.	PSMA3	30	.	0			c.A574G						.						54	58	57					14																	58734222		2203	4290	6493	SO:0001583	missense	5684	exon8			ATCGTTAAAGAAG		CCDS9731.1, CCDS45113.1	14q23	2008-08-29			ENSG00000100567	ENSG00000100567		"Proteasome (prosome, macropain) subunits"	9532	protein-coding gene	gene with protein product		176843				2025653, 8811196	Standard	NM_002788		Approved	HC8	uc001xdj.2	P25788	OTTHUMG00000140319	ENST00000216455.4:c.574A>G	chr14.hg19:g.58734222A>G	ENSP00000216455:p.Lys192Glu	57.0	0.0		85.0	11.0	NM_002788	B2RCK6|Q86U83|Q8N1D8|Q9BS70	Missense_Mutation	SNP	ENST00000216455.4	hg19	CCDS9731.1	.	.	.	.	.	.	.	.	.	.	A	16.94	3.261566	0.59431	.	.	ENSG00000100567	ENST00000216455;ENST00000412908;ENST00000557508	T;T;T	0.19806	2.12;2.12;2.12	4.69	4.69	0.59074	.	0.090096	0.85682	D	0.000000	T	0.25680	0.0625	M	0.62723	1.935	0.80722	D	1	B;B	0.24426	0.084;0.103	B;B	0.26969	0.045;0.075	T	0.05241	-1.0897	10	0.49607	T	0.09	-15.667	14.5987	0.68424	1.0:0.0:0.0:0.0	.	185;192	P25788-2;P25788	.;PSA3_HUMAN	E	192;185;117	ENSP00000216455:K192E;ENSP00000390491:K185E;ENSP00000452056:K117E	ENSP00000216455:K192E	K	+	1	0	PSMA3	57803975	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.472000	0.90407	2.097000	0.63578	0.477000	0.44152	AAA	.	.		0.279	PSMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276923.1	NM_002788		G	58734222	A	G	58734222	3	3	302	1	0	0	0	0	1	0	0	0	12680	363	13	2	604	2	PSMA3	14	58734222	Missense_Mutation	SNP	A	TCGA-G3-AAV6-01A-21D-A36X-10	33964983	58734222	48615318	45	43567										
RTN1	6252	hgsc.bcm.edu	37	chr14	60193689	60193689	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	ggggcgccaggacctagaggCccagggccctttgtggccgc	17	14	0	1			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr14:60193689C>A	ENST00000267484.5	-	3	2048	c.1713G>T	c.(1711-1713)ggG>ggT	p.G571G		NM_021136.2	NP_066959.1	Q16799	RTN1_HUMAN	reticulon 1	571					neuron differentiation (GO:0030182)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)				central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(30)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(108;0.0968)		GACCTAGAGGCCCAGGGCCCT	0.592																																					p.G571G		Atlas-SNP	.											.	RTN1	139	.	0			c.G1713T						.						22	23	23					14																	60193689		2203	4300	6503	SO:0001819	synonymous_variant	6252	exon3			TAGAGGCCCAGGG	L10333	CCDS9740.1, CCDS9741.1	14q21-q22	2008-08-29			ENSG00000139970	ENSG00000139970			10467	protein-coding gene	gene with protein product		600865	"neuroendocrine-specific protein"	NSP		8275708	Standard	NM_206852		Approved		uc001xen.1	Q16799	OTTHUMG00000028947	ENST00000267484.5:c.1713G>T	chr14.hg19:g.60193689C>A		181.0	0.0		188.0	22.0	NM_021136	Q16800|Q16801|Q5BKZ4|Q9BQ59	Silent	SNP	ENST00000267484.5	hg19	CCDS9740.1																																																																																			.	.		0.592	RTN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000072278.2			A	60193689	C	A	60193689	2	1	302	1	0	0	0	0	0	0	0	1	13740	726	26	3		3	RTN1	14	60193689	Silent	SNP	C	TCGA-G3-AAV6-01A-21D-A36X-10	1459467	60193689	47155851	46	43568										
RAB8B	51762	hgsc.bcm.edu	37	chr15	63547751	63547751	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	caaatgaaaaatcctttgacAatattaaaaattggatcaga	5	5	1	3			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr15:63547751A>G	ENST00000321437.4	+	4	448	c.292A>G	c.(292-294)Aat>Gat	p.N98D	RAB8B_ENST00000448330.2_Missense_Mutation_p.N98D	NM_016530.2	NP_057614.1	Q92930	RAB8B_HUMAN	RAB8B, member RAS oncogene family	98					adherens junction organization (GO:0034332)|antigen processing and presentation (GO:0019882)|GTP catabolic process (GO:0006184)|positive regulation of cell projection organization (GO:0031346)|positive regulation of corticotropin secretion (GO:0051461)|protein import into peroxisome membrane (GO:0045046)|small GTPase mediated signal transduction (GO:0007264)	cell tip (GO:0051286)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|peroxisomal membrane (GO:0005778)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|receptor binding (GO:0005102)			kidney(3)|large_intestine(2)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	9						ATCCTTTGACAATATTAAAAA	0.343																																					p.N98D		Atlas-SNP	.											.	RAB8B	23	.	0			c.A292G						.						57	61	60					15																	63547751		2203	4300	6503	SO:0001583	missense	51762	exon4			TTTGACAATATTA	AL833365	CCDS10183.1	15q22	2008-11-18			ENSG00000166128	ENSG00000166128		"RAB, member RAS oncogene"	30273	protein-coding gene	gene with protein product		613532				9030196, 18772196	Standard	XM_006720569		Approved		uc002alz.3	Q92930	OTTHUMG00000132862	ENST00000321437.4:c.292A>G	chr15.hg19:g.63547751A>G	ENSP00000312734:p.Asn98Asp	486.0	1.0		291.0	113.0	NM_016530	Q5JPC4|Q9P293	Missense_Mutation	SNP	ENST00000321437.4	hg19	CCDS10183.1	.	.	.	.	.	.	.	.	.	.	A	31	5.072778	0.93950	.	.	ENSG00000166128	ENST00000321437;ENST00000448330	T;T	0.78364	-1.17;-1.17	5.92	5.92	0.95590	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.82742	0.5103	L	0.41573	1.285	0.58432	D	0.999999	P;P	0.49635	0.854;0.926	P;P	0.62382	0.686;0.901	D	0.84440	0.0582	10	0.87932	D	0	.	15.5479	0.76123	1.0:0.0:0.0:0.0	.	98;98	F5GY21;Q92930	.;RAB8B_HUMAN	D	98	ENSP00000312734:N98D;ENSP00000405463:N98D	ENSP00000312734:N98D	N	+	1	0	RAB8B	61334804	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.279000	0.95777	2.268000	0.75426	0.454000	0.30748	AAT	.	.		0.343	RAB8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256336.1	NM_016530		G	63547751	A	G	63547751	3	3	302	1	0	0	0	0	1	0	0	0	12972	130	5	2	306	2	RAB8B	15	63547751	Missense_Mutation	SNP	A	TCGA-G3-AAV6-01A-21D-A36X-10		63547751	38983641	47	43569										
HMG20A	10363	hgsc.bcm.edu	37	chr15	77763375	77763375	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	accgtcagaaaggcaaatctCataggcaaggtatcaaaacc	8	10	3	1			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr15:77763375C>T	ENST00000381714.3	+	6	1002	c.574C>T	c.(574-576)Cat>Tat	p.H192Y	HMG20A_ENST00000336216.4_Missense_Mutation_p.H192Y	NM_018200.2	NP_060670.1	Q9NP66	HM20A_HUMAN	high mobility group 20A	192					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18						AGGCAAATCTCATAGGCAAGG	0.408																																					p.H192Y		Atlas-SNP	.											.	HMG20A	48	.	0			c.C574T						.						121	114	116					15																	77763375		2196	4294	6490	SO:0001583	missense	10363	exon6			AAATCTCATAGGC	AF146222	CCDS10295.1	15q24	2011-07-01	2011-04-05		ENSG00000140382	ENSG00000140382		"High mobility group / Non-canonical"	5001	protein-coding gene	gene with protein product	"HMG box domain containing 1"	605534	"high-mobility group 20A"			10773667	Standard	NM_018200		Approved	HMGX1, FLJ10739, HMGXB1	uc002bcr.3	Q9NP66	OTTHUMG00000143729	ENST00000381714.3:c.574C>T	chr15.hg19:g.77763375C>T	ENSP00000371133:p.His192Tyr	400.0	0.0		214.0	72.0	NM_018200	A6NHY3|D3DW78|Q53G31|Q9NSF6	Missense_Mutation	SNP	ENST00000381714.3	hg19	CCDS10295.1	.	.	.	.	.	.	.	.	.	.	C	17.30	3.353760	0.61293	.	.	ENSG00000140382	ENST00000336216;ENST00000381714	T;T	0.68181	-0.31;-0.31	5.97	5.97	0.96955	.	0.236335	0.49305	D	0.000151	T	0.64832	0.2634	L	0.44542	1.39	0.50171	D	0.999859	B	0.12013	0.005	B	0.23150	0.044	T	0.58544	-0.7618	10	0.54805	T	0.06	-17.6161	20.4388	0.99107	0.0:1.0:0.0:0.0	.	192	Q9NP66	HM20A_HUMAN	Y	192	ENSP00000336856:H192Y;ENSP00000371133:H192Y	ENSP00000336856:H192Y	H	+	1	0	HMG20A	75550430	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	5.742000	0.68646	2.836000	0.97738	0.655000	0.94253	CAT	.	.		0.408	HMG20A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419512.2	NM_018200		T	77763375	C	T	77763375	3	4	302	1	0	0	0	0	1	0	0	0	7230	826	29	3	588	3	HMG20A	15	77763375	Missense_Mutation	SNP	C	TCGA-G3-AAV6-01A-21D-A36X-10	14215624	77763375	24768017	48	43570										
ABCA3	21	hgsc.bcm.edu	37	chr16	2342161	2342161	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	cgaaggaagacttcctccatGgtggtgatggatgccccaaa	12	10	0	2			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr16:2342161G>A	ENST00000301732.5	-	19	3193	c.2493C>T	c.(2491-2493)acC>acT	p.T831T	ABCA3_ENST00000382381.3_Silent_p.T773T	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	831					response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	alveolar lamellar body (GO:0097208)|alveolar lamellar body membrane (GO:0097233)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(7)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(7)|prostate(5)|skin(6)|upper_aerodigestive_tract(1)	70		Ovarian(90;0.17)			Imatinib(DB00619)	CTTCCTCCATGGTGGTGATGG	0.483																																					p.T831T		Atlas-SNP	.											.	ABCA3	176	.	0			c.C2493T						.						144	112	123					16																	2342161		2198	4300	6498	SO:0001819	synonymous_variant	21	exon19			CTCCATGGTGGTG	U78735	CCDS10466.1	16p13.3	2012-03-14			ENSG00000167972	ENSG00000167972		"ATP binding cassette transporters / subfamily A"	33	protein-coding gene	gene with protein product		601615		ABC3		8706931	Standard	NM_001089		Approved	ABC-C, EST111653, LBM180	uc002cpy.1	Q99758	OTTHUMG00000128845	ENST00000301732.5:c.2493C>T	chr16.hg19:g.2342161G>A		102.0	0.0		104.0	15.0	NM_001089	B2RU09|Q54A95|Q6P5P9|Q92473	Silent	SNP	ENST00000301732.5	hg19	CCDS10466.1																																																																																			.	.		0.483	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089		A	2342161	G	A	2342161	2	1	302	1	0	0	0	0	0	0	0	1	33	1335	47	3		3	ABCA3	16	2342161	Silent	SNP	G	TCGA-G3-AAV6-01A-21D-A36X-10		2342161	88012592	49	43571										
ATP6V0C	527	hgsc.bcm.edu	37	chr16	2569246	2569246	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	cgctgcctatggcacagccaAgagcggtaccggcattgcgg	14	13	0	1			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr16:2569246A>C	ENST00000330398.4	+	2	341	c.107A>C	c.(106-108)aAg>aCg	p.K36T	AMDHD2_ENST00000413459.3_5'Flank|AMDHD2_ENST00000302956.4_5'Flank|ATP6V0C_ENST00000568562.1_Missense_Mutation_p.Q18H|RP11-20I23.1_ENST00000564543.1_Missense_Mutation_p.Q331H|ATP6V0C_ENST00000565223.1_5'UTR|ATP6V0C_ENST00000564973.1_5'UTR|ATP6C_ENST00000569317.1_Intron|AMDHD2_ENST00000293971.6_5'Flank	NM_001198569.1|NM_001694.3	NP_001185498.1|NP_001685.1	P27449	VATL_HUMAN	ATPase, H+ transporting, lysosomal 16kDa, V0 subunit c	36					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of Wnt signaling pathway (GO:0030177)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|phagocytic vesicle membrane (GO:0030670)|proton-transporting V-type ATPase, V0 domain (GO:0033179)	proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|ubiquitin protein ligase binding (GO:0031625)			endometrium(1)|lung(1)|ovary(1)	3		Ovarian(90;0.17)				GGCACAGCCAAGAGCGGTACC	0.622																																					p.K36T		Atlas-SNP	.											.	ATP6V0C	10	.	0			c.A107C						.						59	41	47					16																	2569246		2198	4300	6498	SO:0001583	missense	527	exon3			CAGCCAAGAGCGG	M62762	CCDS10470.1	16p13.3	2010-04-21	2002-08-29	2002-05-10	ENSG00000185883	ENSG00000185883	3.6.3.14	"ATPases / V-type"	855	protein-coding gene	gene with protein product		108745	"ATPase, H+ transporting, lysosomal (vacuolar proton pump) 16kD"	ATPL, ATP6C, ATP6L		1709739, 8250920	Standard	NM_001694		Approved	VATL, Vma3	uc021tav.1	P27449	OTTHUMG00000128865	ENST00000330398.4:c.107A>C	chr16.hg19:g.2569246A>C	ENSP00000329757:p.Lys36Thr	61.0	0.0		58.0	32.0	NM_001198569	Q6FH26	Missense_Mutation	SNP	ENST00000330398.4	hg19	CCDS10470.1	.	.	.	.	.	.	.	.	.	.	A	14.21	2.466990	0.43839	.	.	ENSG00000185883	ENST00000330398	T	0.45668	0.89	4.85	4.85	0.62838	ATPase, F0/V0 complex, subunit C (2);	0.000000	0.85682	D	0.000000	T	0.57562	0.2062	M	0.82323	2.585	0.80722	D	1	B	0.26002	0.139	B	0.41917	0.37	T	0.62205	-0.6903	10	0.59425	D	0.04	-6.3055	13.3519	0.60607	1.0:0.0:0.0:0.0	.	36	P27449	VATL_HUMAN	T	36	ENSP00000329757:K36T	ENSP00000329757:K36T	K	+	2	0	ATP6V0C	2509247	1.000000	0.71417	0.997000	0.53966	0.192000	0.23643	9.230000	0.95299	1.832000	0.53329	0.454000	0.30748	AAG	.	.		0.622	ATP6V0C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250810.1	NM_001694		C	2569246	A	C	2569246	3	2	302	1	0	0	0	0	1	0	0	0	1172	72	3	5	113	5	ATP6V0C	16	2569246	Missense_Mutation	SNP	A	TCGA-G3-AAV6-01A-21D-A36X-10	227085	2569246	87785507	50	43572										
CBFA2T3	863	hgsc.bcm.edu	37	chr16	88968033	88968033	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	tccgctggggagtccggcatCgctgaggccttagctttcct	13	13	0	1			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr16:88968033C>A	ENST00000268679.4	-	2	579	c.183G>T	c.(181-183)gcG>gcT	p.A61A	CBFA2T3_ENST00000360302.2_5'UTR|CBFA2T3_ENST00000327483.5_5'UTR|CBFA2T3_ENST00000448839.1_Intron|CBFA2T3_ENST00000436887.2_Silent_p.A61A	NM_005187.5	NP_005178.4	O75081	MTG16_HUMAN	core-binding factor, runt domain, alpha subunit 2; translocated to, 3	61	Mediates interaction with PDE7A (in isoform 2).|Mediates localization to the nucleus. {ECO:0000250}.|Pro-rich.|Required for nucleolar targeting (in isoform 1).				cell proliferation (GO:0008283)|granulocyte differentiation (GO:0030851)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	17				BRCA - Breast invasive adenocarcinoma(80;0.0275)		AGTCCGGCATCGCTGAGGCCT	0.687			T	RUNX1	AML																																p.A61A		Atlas-SNP	.		Dom	yes		16	16q24	863	"core-binding factor, runt domain, alpha subunit 2; translocated to, 3 (MTG-16)"		L	.	CBFA2T3	47	.	0			c.G183T						.						38	41	40					16																	88968033		2197	4300	6497	SO:0001819	synonymous_variant	863	exon2			CGGCATCGCTGAG	AF052213	CCDS10972.1, CCDS10973.1	16q24	2013-10-16			ENSG00000129993	ENSG00000129993		"Zinc fingers, MYND-type", "A-kinase anchor proteins"	1537	protein-coding gene	gene with protein product	"myeloid translocation gene 8 and 16b"	603870				9790752, 20150326	Standard	NM_005187		Approved	MTGR2, ZMYND4, MTG16	uc002fmm.2	O75081	OTTHUMG00000137864	ENST00000268679.4:c.183G>T	chr16.hg19:g.88968033C>A		23.0	0.0		21.0	10.0	NM_005187	D3DX78|O60615|O60616|O60617|O75082|O75107|O75108|Q0P5Z6|Q6P5W6	Silent	SNP	ENST00000268679.4	hg19	CCDS10972.1																																																																																			.	.		0.687	CBFA2T3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269545.2	NM_005187		A	88968033	C	A	88968033	2	1	302	1	0	0	0	0	0	0	0	1	2700	871	31	1		1	CBFA2T3	16	88968033	Silent	SNP	C	TCGA-G3-AAV6-01A-21D-A36X-10	86398787	88968033	1386720	51	43573										
DNAH2	146754	hgsc.bcm.edu	37	chr17	7682620	7682620	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	aacatcgaggtgctgtcagtGgtggcccaccagatcctgtg	13	11	1	1			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr17:7682620G>A	ENST00000572933.1	+	36	7061	c.5601G>A	c.(5599-5601)gtG>gtA	p.V1867V	DNAH2_ENST00000389173.2_Silent_p.V1867V			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	1867	AAA 1. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				TGCTGTCAGTGGTGGCCCACC	0.567																																					p.V1867V		Atlas-SNP	.											.	DNAH2	498	.	0			c.G5601A						.						105	82	90					17																	7682620		2203	4300	6503	SO:0001819	synonymous_variant	146754	exon35			GTCAGTGGTGGCC	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.5601G>A	chr17.hg19:g.7682620G>A		98.0	0.0		137.0	20.0	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Silent	SNP	ENST00000572933.1	hg19	CCDS32551.1																																																																																			.	.		0.567	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		A	7682620	G	A	7682620	2	1	302	1	0	0	0	0	0	0	0	1	4604	1335	47	3		3	DNAH2	17	7682620	Silent	SNP	G	TCGA-G3-AAV6-01A-21D-A36X-10		7682620	73512590	52	43574										
GAS7	8522	hgsc.bcm.edu	37	chr17	9850209	9850209	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	gggaaactgaggcgctgcttAcccagaagtagtcgcagtag	14	9	0	2			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr17:9850209A>G	ENST00000432992.2	-	6	776		c.e6+1		GAS7_ENST00000437099.2_Splice_Site|GAS7_ENST00000580865.1_Splice_Site|GAS7_ENST00000585266.1_Splice_Site|GAS7_ENST00000323816.4_Splice_Site|GAS7_ENST00000396115.2_Intron|GAS7_ENST00000583882.1_Splice_Site|GAS7_ENST00000540214.1_Intron|GAS7_ENST00000579158.1_Splice_Site|GAS7_ENST00000578655.1_Splice_Site|GAS7_ENST00000542249.1_Splice_Site	NM_201433.1	NP_958839.1	O60861	GAS7_HUMAN	growth arrest-specific 7						actin filament bundle assembly (GO:0051017)|actin filament polymerization (GO:0030041)|cell cycle arrest (GO:0007050)|neuron projection morphogenesis (GO:0048812)|regulation of cell shape (GO:0008360)|regulation of transcription, DNA-templated (GO:0006355)	actin filament (GO:0005884)|cytoplasm (GO:0005737)|ruffle (GO:0001726)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(7)|lung(18)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	39						GGCGCTGCTTACCCAGAAGTA	0.592			T	MLL	AML*																																.		Atlas-SNP	.		Dom	yes		17	17p	8522	growth arrest-specific 7		L	.	GAS7	113	.	0			c.423+2T>C						.						90	59	70					17																	9850209		2203	4299	6502	SO:0001630	splice_region_variant	8522	exon7			CTGCTTACCCAGA	AB007854	CCDS11152.1, CCDS42263.1, CCDS45611.1, CCDS58518.1	17p13.1	2004-02-18							4169	protein-coding gene	gene with protein product		603127				9736752	Standard	NM_001130831		Approved	KIAA0394, MGC1348	uc002gmg.1	O60861		ENST00000432992.2:c.615+1T>C	chr17.hg19:g.9850209A>G		52.0	0.0		65.0	6.0	NM_001130831	A8KAC2|B2RCK9|O43144|Q53Y77|Q7Z571	Splice_Site	SNP	ENST00000432992.2	hg19	CCDS11152.1	.	.	.	.	.	.	.	.	.	.	A	17.64	3.440408	0.63067	.	.	ENSG00000007237	ENST00000323816;ENST00000396115;ENST00000437099;ENST00000432992;ENST00000537970;ENST00000541114	.	.	.	5.23	5.23	0.72850	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5244	0.67878	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	GAS7	9790934	1.000000	0.71417	0.996000	0.52242	0.558000	0.35554	8.237000	0.89807	2.324000	0.78689	0.533000	0.62120	.	.	.		0.592	GAS7-017	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439883.1	NM_003644, NM_201432, NM_201433	Intron	G	9850209	A	G	9850209	5	3	302	1	0	0	0	0	0	0	1	0	6258	405	14	2	849	2	GAS7	17	9850209	Splice_Site	SNP	A	TCGA-G3-AAV6-01A-21D-A36X-10	2167589	9850209	71345001	53	43575										
GAS2L2	246176	hgsc.bcm.edu	37	chr17	34072962	34072962	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	ccacttgtagcaccaggaaaGctccttcctggtgttggggg	13	11	0	0			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr17:34072962G>A	ENST00000254466.6	-	6	1581	c.1554C>T	c.(1552-1554)agC>agT	p.S518S	GAS2L2_ENST00000587565.1_Silent_p.S502S	NM_139285.3	NP_644814.1	Q8NHY3	GA2L2_HUMAN	growth arrest-specific 2 like 2	518					cell cycle arrest (GO:0007050)|microtubule bundle formation (GO:0001578)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	actin filament binding (GO:0051015)|cytoskeletal adaptor activity (GO:0008093)|microtubule binding (GO:0008017)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CACCAGGAAAGCTCCTTCCTG	0.622																																					p.S518S		Atlas-SNP	.											.	GAS2L2	94	.	0			c.C1554T						.						39	44	42					17																	34072962		2203	4300	6503	SO:0001819	synonymous_variant	246176	exon6			AGGAAAGCTCCTT	AF508784	CCDS11298.1	17q21	2014-05-06			ENSG00000132139	ENSG00000270765			24846	protein-coding gene	gene with protein product		611398				12584248	Standard	NM_139285		Approved	GAR17	uc002hjv.2	Q8NHY3	OTTHUMG00000188386	ENST00000254466.6:c.1554C>T	chr17.hg19:g.34072962G>A		36.0	0.0		44.0	15.0	NM_139285	Q8NHY4	Silent	SNP	ENST00000254466.6	hg19	CCDS11298.1																																																																																			.	.		0.622	GAS2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256497.1	NM_139285		A	34072962	G	A	34072962	2	1	302	1	0	0	0	0	0	0	0	1	6255	962	34	3		3	GAS2L2	17	34072962	Silent	SNP	G	TCGA-G3-AAV6-01A-21D-A36X-10	24222753	34072962	47122248	54	43576										
TNS4	84951	hgsc.bcm.edu	37	chr17	38643429	38643429	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	ctggggtggagaagaccctgGttctgggcagccgttgatca	16	9	2	3			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr17:38643429G>A	ENST00000254051.6	-	4	1305	c.1147C>T	c.(1147-1149)Cca>Tca	p.P383S		NM_032865.5	NP_116254.4	Q8IZW8	TENS4_HUMAN	tensin 4	383					apoptotic process (GO:0006915)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	30		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(5;5.91e-05)			GAAGACCCTGGTTCTGGGCAG	0.602																																					p.P383S		Atlas-SNP	.											.	TNS4	72	.	0			c.C1147T						.						166	161	163					17																	38643429		2203	4300	6503	SO:0001583	missense	84951	exon4			ACCCTGGTTCTGG	AF417488	CCDS11368.1	17q21.2	2013-02-14			ENSG00000131746	ENSG00000131746		"SH2 domain containing"	24352	protein-coding gene	gene with protein product	"C terminal tensin like"	608385				12154022, 12711115	Standard	NM_032865		Approved	CTEN	uc010cxb.3	Q8IZW8	OTTHUMG00000133330	ENST00000254051.6:c.1147C>T	chr17.hg19:g.38643429G>A	ENSP00000254051:p.Pro383Ser	154.0	0.0		157.0	29.0	NM_032865	A6NMJ7|Q71RB7|Q8WV64|Q96JV4	Missense_Mutation	SNP	ENST00000254051.6	hg19	CCDS11368.1	.	.	.	.	.	.	.	.	.	.	G	15.22	2.769772	0.49680	.	.	ENSG00000131746	ENST00000377816;ENST00000254051	T	0.18502	2.21	5.4	4.39	0.52855	.	2.964170	0.00986	N	0.003445	T	0.16642	0.0400	L	0.32530	0.975	0.30280	N	0.791388	P	0.45126	0.851	B	0.37550	0.253	T	0.19386	-1.0307	10	0.23891	T	0.37	-9.8293	12.8456	0.57827	0.0:0.288:0.7119:0.0	.	383	Q8IZW8	TENS4_HUMAN	S	383	ENSP00000254051:P383S	ENSP00000254051:P383S	P	-	1	0	TNS4	35896955	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	0.726000	0.25984	2.539000	0.85634	0.655000	0.94253	CCA	.	.		0.602	TNS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257154.3	NM_032865		A	38643429	G	A	38643429	3	1	302	1	0	0	0	0	1	0	0	0	16360	1261	44	3	1040	3	TNS4	17	38643429	Missense_Mutation	SNP	G	TCGA-G3-AAV6-01A-21D-A36X-10	4570467	38643429	42551781	55	43577										
ABCA10	10349	hgsc.bcm.edu	37	chr17	67212097	67212120	+	In_Frame_Del	DEL	CATAGGTTTCCTTATTAAAACACT	CATAGGTTTCCTTATTAAAACACT	-													0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	aatccagccaaaccagcgagCataggtttccttattaaaac					rs143678315		TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	CATAGGTTTCCTTATTAAAACACT	CATAGGTTTCCTTATTAAAACACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr17:67212097_67212120delCATAGGTTTCCTTATTAAAACACT	ENST00000269081.4	-	9	1603_1626	c.694_717delAGTGTTTTAATAAGGAAACCTATG	c.(694-717)agtgttttaataaggaaacctatgdel	p.SVLIRKPM232del	ABCA10_ENST00000416101.2_In_Frame_Del_p.SVLIRKPM232del|ABCA10_ENST00000432313.2_In_Frame_Del_p.SVLIRKPM232del	NM_080282.3	NP_525021.3	Q8WWZ4	ABCAA_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 10	232					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.S232R(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(34)|ovary(2)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	81	Breast(10;6.95e-12)					AACCAGCGAGCATAGGTTTCCTTATTAAAACACTCATGAGGAAA	0.366																																					p.232_240del		Atlas-INDEL	.											.	ABCA10	209	.	1	Substitution - Missense(1)	breast(1)	c.695_718del						.																																			SO:0001651	inframe_deletion	10349	exon9			.	AY247065	CCDS11684.1	17q24	2012-03-14			ENSG00000154263	ENSG00000154263		"ATP binding cassette transporters / subfamily A"	30	protein-coding gene	gene with protein product		612508				12821155, 11435397	Standard	NM_080282		Approved	EST698739	uc010dfa.1	Q8WWZ4	OTTHUMG00000164716	ENST00000269081.4:c.694_717delAGTGTTTTAATAAGGAAACCTATG	chr17.hg19:g.67212097_67212120delCATAGGTTTCCTTATTAAAACACT	ENSP00000269081:p.Ser232_Met239del	295.0	0.0		417.0	29.0	NM_080282	C9JZH2|C9K035|Q6PIQ6|Q7Z2I9|Q7Z7P7|Q86TD2	In_Frame_Del	DEL	ENST00000269081.4	hg19	CCDS11684.1																																																																																			.	.		0.366	ABCA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379881.4	NM_080282		-	67212120	CATAGGTTTCCTTATTAAAACACT	-	67212097	7	5	302	1	0	1	0	1	0	0	0	0	29	710	25	0	4042	0	ABCA10	17	67212097	In_Frame_Del	DEL	CATAGGTTTCCTTATTAAAACACT	TCGA-G3-AAV6-01A-21D-A36X-10	28568668	67212097	13983113	56	43578										
DAZAP1	26528	hgsc.bcm.edu	37	chr19	1422373	1422373	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	gaggtagtcatgatctatgaCgccgagaagcagaggccccg	14	10	2	4			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr19:1422373C>G	ENST00000233078.4	+	6	602	c.441C>G	c.(439-441)gaC>gaG	p.D147E	DAZAP1_ENST00000336761.6_Missense_Mutation_p.D147E|DAZAP1_ENST00000586579.1_3'UTR	NM_018959.2	NP_061832.2	Q96EP5	DAZP1_HUMAN	DAZ associated protein 1	147	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|maternal placenta development (GO:0001893)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)			breast(2)|endometrium(2)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	9		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGATCTATGACGCCGAGAAGC	0.612																																					p.D147E		Atlas-SNP	.											.	DAZAP1	52	.	0			c.C441G						.						160	122	135					19																	1422373		2203	4300	6503	SO:0001583	missense	26528	exon6			CTATGACGCCGAG		CCDS12065.1, CCDS12066.1	19p13.3	2013-07-16			ENSG00000071626	ENSG00000071626		"RNA binding motif (RRM) containing"	2683	protein-coding gene	gene with protein product	"deleted in azoospermia associated protein 1"	607430				10857750, 23658607	Standard	XM_005259530		Approved	MGC19907	uc002lsn.3	Q96EP5		ENST00000233078.4:c.441C>G	chr19.hg19:g.1422373C>G	ENSP00000233078:p.Asp147Glu	81.0	0.0		80.0	31.0	NM_018959	Q96MJ3|Q9NRR9	Missense_Mutation	SNP	ENST00000233078.4	hg19	CCDS12065.1	.	.	.	.	.	.	.	.	.	.	T	13.59	2.282151	0.40394	.	.	ENSG00000071626	ENST00000233078;ENST00000336761	D;D	0.92199	-2.99;-2.99	4.3	-0.967	0.10316	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	D	0.94377	0.8192	M	0.75447	2.3	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.99	D	0.91616	0.5307	10	0.66056	D	0.02	.	10.1831	0.42980	0.0:0.5561:0.0:0.4439	.	147;147	Q96EP5;Q96EP5-2	DAZP1_HUMAN;.	E	147	ENSP00000233078:D147E;ENSP00000337132:D147E	ENSP00000233078:D147E	D	+	3	2	DAZAP1	1373373	0.912000	0.30974	0.626000	0.29213	0.120000	0.20174	0.006000	0.13152	-0.804000	0.04410	-1.390000	0.01156	GAC	.	.		0.612	DAZAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449522.3	NM_170711		G	1422373	C	G	1422373	3	3	302	1	0	0	0	0	1	0	0	0	4246	535	19	4	463	4	DAZAP1	19	1422373	Missense_Mutation	SNP	C	TCGA-G3-AAV6-01A-21D-A36X-10		1422373	57706610	57	43579										
UBA52	7311	hgsc.bcm.edu	37	chr19	18684552	18684552	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	ctctctcagactacaacatcCagaaaggtaccggggttggg	11	11	2	2			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr19:18684552C>T	ENST00000442744.2	+	3	242	c.184C>T	c.(184-186)Cag>Tag	p.Q62*	UBA52_ENST00000595158.1_Nonsense_Mutation_p.Q62*|UBA52_ENST00000597451.1_Nonsense_Mutation_p.Q62*|UBA52_ENST00000430157.2_Nonsense_Mutation_p.Q62*|UBA52_ENST00000596304.1_Nonsense_Mutation_p.Q62*|UBA52_ENST00000598780.1_Nonsense_Mutation_p.Q62*|UBA52_ENST00000599551.1_Nonsense_Mutation_p.Q62*|UBA52_ENST00000595683.1_Nonsense_Mutation_p.Q62*|CRLF1_ENST00000594325.1_Intron|UBA52_ENST00000599595.1_Nonsense_Mutation_p.Q62*|UBA52_ENST00000596273.1_Nonsense_Mutation_p.Q62*	NM_001033930.1	NP_001029102.1	P62987	RL40_HUMAN	ubiquitin A-52 residue ribosomal protein fusion product 1	62	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				activation of MAPK activity (GO:0000187)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|viral transcription (GO:0019083)|virion assembly (GO:0019068)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|ribosome (GO:0005840)	structural constituent of ribosome (GO:0003735)			endometrium(1)|large_intestine(2)	3						CTACAACATCCAGAAAGGTAC	0.582																																					p.Q62X		Atlas-SNP	.											.	UBA52	6	.	0			c.C184T						.						41	40	41					19																	18684552		2203	4300	6503	SO:0001587	stop_gained	7311	exon3			AACATCCAGAAAG		CCDS12382.1	19p13.1-p12	2011-04-06			ENSG00000221983	ENSG00000221983		"L ribosomal proteins"	12458	protein-coding gene	gene with protein product	"ribosomal protein L40", "ubiquitin-52 amino acid fusion protein", "ubiquitin carboxyl extension protein 52", "60S ribosomal protein L40", "ubiquitin-CEP52"	191321				8188300	Standard	XM_005260051		Approved	RPL40, CEP52, HUBCEP52, MGC57125, MGC126879, MGC126881, L40	uc002njs.3	P62987		ENST00000442744.2:c.184C>T	chr19.hg19:g.18684552C>T	ENSP00000388107:p.Gln62*	50.0	0.0		62.0	31.0	NM_001033930	P02248|P02249|P02250|P14793|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Nonsense_Mutation	SNP	ENST00000442744.2	hg19	CCDS12382.1	.	.	.	.	.	.	.	.	.	.	C	35	5.559118	0.96514	.	.	ENSG00000221983	ENST00000442744;ENST00000430157	.	.	.	4.81	4.81	0.61882	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-22.8343	15.3581	0.74443	0.0:1.0:0.0:0.0	.	.	.	.	X	62	.	ENSP00000396910:Q62X	Q	+	1	0	UBA52	18545552	1.000000	0.71417	1.000000	0.80357	0.687000	0.40016	7.663000	0.83820	2.220000	0.72140	0.462000	0.41574	CAG	.	.		0.582	UBA52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465117.2	NM_003333		T	18684552	C	T	18684552	4	4	302	1	0	0	0	0	0	1	0	0	16846	595	21	3	190	3	UBA52	19	18684552	Nonsense_Mutation	SNP	C	TCGA-G3-AAV6-01A-21D-A36X-10	17262179	18684552	40444431	58	43580										
ZNF208	7757	hgsc.bcm.edu	37	chr19	22170031	22170031	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	cacctacctggggattcttcCaccatctcatgtctcttcat	5	15	4	0			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr19:22170031C>A	ENST00000397126.4	-	3	361	c.213G>T	c.(211-213)gtG>gtT	p.V71V	ZNF208_ENST00000597040.1_Silent_p.V39V|ZNF208_ENST00000601773.1_Silent_p.V71V|ZNF208_ENST00000599916.1_Silent_p.V71V	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	71	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				GGGATTCTTCCACCATCTCAT	0.428																																					p.V71V		Atlas-SNP	.											.	ZNF208	817	.	0			c.G213T						.						67	69	68					19																	22170031		2196	4299	6495	SO:0001819	synonymous_variant	7757	exon3			TTCTTCCACCATC	BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"Zinc fingers, C2H2-type", "-"	12999	protein-coding gene	gene with protein product	"zinc finger protein 95"	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.213G>T	chr19.hg19:g.22170031C>A		124.0	0.0		109.0	32.0	NM_007153		Silent	SNP	ENST00000397126.4	hg19	CCDS54240.1																																																																																			.	.		0.428	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		A	22170031	C	A	22170031	2	1	302	1	0	0	0	0	0	0	0	1	17781	581	21	3		3	ZNF208	19	22170031	Silent	SNP	C	TCGA-G3-AAV6-01A-21D-A36X-10	3485479	22170031	36958952	59	43581										
ZNF91	7644	hgsc.bcm.edu	37	chr19	23543281	23543281	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	ggctgaggagtgcttaaaagCtttgccacattctttacatt	9	8	1	1			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr19:23543281C>T	ENST00000300619.7	-	4	2705	c.2500G>A	c.(2500-2502)Gct>Act	p.A834T	ZNF91_ENST00000596528.1_5'Flank|ZNF91_ENST00000397082.2_Missense_Mutation_p.A802T|ZNF91_ENST00000599743.1_Intron	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	834					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				TGCTTAAAAGCTTTGCCACAT	0.383																																					p.A834T		Atlas-SNP	.											.	ZNF91	349	.	0			c.G2500A						.						57	60	59					19																	23543281		2138	4264	6402	SO:0001583	missense	7644	exon4			TAAAAGCTTTGCC	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"Zinc fingers, C2H2-type", "-"	13166	protein-coding gene	gene with protein product		603971	"zinc finger protein 91 (HPF7, HTF10)"			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.2500G>A	chr19.hg19:g.23543281C>T	ENSP00000300619:p.Ala834Thr	61.0	0.0		71.0	31.0	NM_003430	A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	hg19	CCDS42541.1	.	.	.	.	.	.	.	.	.	.	C	3.304	-0.142327	0.06669	.	.	ENSG00000167232	ENST00000300619;ENST00000397082	T;T	0.13778	2.56;2.56	1.34	1.34	0.21922	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12561	0.0305	N	0.02721	-0.515	0.22710	N	0.998825	P;D	0.89917	0.851;1.0	B;D	0.79108	0.395;0.992	T	0.23940	-1.0174	9	0.45353	T	0.12	.	6.4545	0.21922	0.2877:0.7123:0.0:0.0	.	802;834	Q05481-2;Q05481	.;ZNF91_HUMAN	T	834;802	ENSP00000300619:A834T;ENSP00000380272:A802T	ENSP00000300619:A834T	A	-	1	0	ZNF91	23335121	0.000000	0.05858	0.324000	0.25361	0.029000	0.11900	-1.232000	0.02936	0.682000	0.31407	0.205000	0.17691	GCT	.	.		0.383	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430		T	23543281	C	T	23543281	3	4	302	1	0	0	0	0	1	0	0	0	18215	797	28	3	1079	3	ZNF91	19	23543281	Missense_Mutation	SNP	C	TCGA-G3-AAV6-01A-21D-A36X-10	1373250	23543281	35585702	60	43582										
CYP2B6	1555	hgsc.bcm.edu	37	chr19	41515201	41515201	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	tacaaaaacctgcaggaaatCaatgcttacattggccacag	7	10	1	0	rs35349987	byFrequency	TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr19:41515201C>T	ENST00000324071.4	+	5	730	c.723C>T	c.(721-723)atC>atT	p.I241I	CYP2B6_ENST00000330446.5_Intron|CYP2B6_ENST00000593831.1_Intron	NM_000767.4	NP_000758.1	P20813	CP2B6_HUMAN	cytochrome P450, family 2, subfamily B, polypeptide 6	241					cellular ketone metabolic process (GO:0042180)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			NS(1)|breast(1)|endometrium(5)|kidney(1)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	28			LUSC - Lung squamous cell carcinoma(20;0.00322)		Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Antipyrine(DB01435)|Artemether(DB06697)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzphetamine(DB00865)|Benzyl alcohol(DB06770)|Bifonazole(DB04794)|Brompheniramine(DB00835)|Bupropion(DB01156)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Cholecalciferol(DB00169)|Cinnarizine(DB00568)|Cisapride(DB00604)|Cisplatin(DB00515)|Citalopram(DB00215)|Clobazam(DB00349)|Clofibrate(DB00636)|Clopidogrel(DB00758)|Clotiazepam(DB01559)|Clotrimazole(DB00257)|Colchicine(DB01394)|Cyclophosphamide(DB00531)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diphenhydramine(DB01075)|Domperidone(DB01184)|Doxorubicin(DB00997)|Efavirenz(DB00625)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erythromycin(DB00199)|Estrone(DB00655)|Ethanol(DB00898)|Ethylmorphine(DB01466)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluoxetine(DB00472)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Fosphenytoin(DB01320)|Halothane(DB01159)|Ifosfamide(DB01181)|Imipramine(DB00458)|Irinotecan(DB00762)|Isoflurane(DB00753)|Itraconazole(DB01167)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Lidocaine(DB00281)|Loperamide(DB00836)|Lopinavir(DB01601)|Lorcaserin(DB04871)|Malathion(DB00772)|Memantine(DB01043)|Methadone(DB00333)|Methimazole(DB00763)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyltestosterone(DB06710)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midazolam(DB00683)|Modafinil(DB00745)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitric Oxide(DB00435)|Orphenadrine(DB01173)|Ospemifene(DB04938)|Paroxetine(DB00715)|Perhexiline(DB01074)|Permethrin(DB04930)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Prasugrel(DB06209)|Primidone(DB00794)|Promethazine(DB01069)|Propofol(DB00818)|Quinidine(DB00908)|Raloxifene(DB00481)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Ropivacaine(DB00296)|Roxithromycin(DB00778)|Selegiline(DB01037)|Sertraline(DB01104)|Sevoflurane(DB01236)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfaphenazole(DB06729)|Sulfinpyrazone(DB01138)|Tamoxifen(DB00675)|Temazepam(DB00231)|Testosterone(DB00624)|Thiotepa(DB04572)|Ticlopidine(DB00208)|Tramadol(DB00193)|Tretinoin(DB00755)|Valproic Acid(DB00313)|Venlafaxine(DB00285)|Verapamil(DB00661)	TGCAGGAAATCAATGCTTACA	0.512																																					p.I241I		Atlas-SNP	.											.	CYP2B6	79	.	0			c.C723T						.						100	100	100					19																	41515201		2202	4300	6502	SO:0001819	synonymous_variant	1555	exon5			GGAAATCAATGCT	AF182277	CCDS12570.1	19q13.2	2013-07-25	2003-01-14		ENSG00000197408	ENSG00000197408		"Cytochrome P450s"	2615	protein-coding gene	gene with protein product		123930	"cytochrome P450, subfamily IIB (phenobarbital-inducible), polypeptide 6", "cytochrome P450, family 2, subfamily B", "cytochrome P450, subfamily IIB (phenobarbital-inducible)"	CYP2B		7668294, 15128046	Standard	NM_000767		Approved	CPB6, CYPIIB6	uc002opr.1	P20813	OTTHUMG00000182714	ENST00000324071.4:c.723C>T	chr19.hg19:g.41515201C>T		520.0	0.0		566.0	116.0	NM_000767	B4DWP3|Q2V565|Q9UK46	Silent	SNP	ENST00000324071.4	hg19	CCDS12570.1																																																																																			.	C|0.999;A|0.001		0.512	CYP2B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463260.1	NM_000767		T	41515201	C	T	41515201	2	4	302	1	0	0	0	0	0	0	0	1	4166	816	29	3		3	CYP2B6	19	41515201	Silent	SNP	C	TCGA-G3-AAV6-01A-21D-A36X-10	17971920	41515201	17613782	61	43583										
FKRP	79147	hgsc.bcm.edu	37	chr19	47260089	47260089	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	tgccggcttcgtggcgcaggCgcctaacaactaccgccgct	12	16	0	0			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr19:47260089C>T	ENST00000318584.5	+	4	1679	c.1382C>T	c.(1381-1383)gCg>gTg	p.A461V	FKRP_ENST00000391909.3_Missense_Mutation_p.A461V|FKRP_ENST00000600646.1_Intron	NM_001039885.2|NM_024301.4	NP_001034974.1|NP_077277.1	Q9H9S5	FKRP_HUMAN	fukutin related protein	461					glycoprotein biosynthetic process (GO:0009101)|protein processing (GO:0016485)	dystrophin-associated glycoprotein complex (GO:0016010)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|rough endoplasmic reticulum (GO:0005791)|sarcolemma (GO:0042383)	transferase activity (GO:0016740)			NS(1)|large_intestine(1)|lung(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	7		all_epithelial(76;5.08e-05)|Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000541)|all cancers(93;0.00128)|Epithelial(262;0.0207)|GBM - Glioblastoma multiforme(486;0.0336)		GTGGCGCAGGCGCCTAACAAC	0.657																																					p.A461V		Atlas-SNP	.											.	FKRP	16	.	0			c.C1382T						.						14	14	14					19																	47260089		2201	4285	6486	SO:0001583	missense	79147	exon4			CGCAGGCGCCTAA	AJ314847	CCDS12691.1	19q13.32	2014-09-17			ENSG00000181027	ENSG00000181027			17997	protein-coding gene	gene with protein product		606596				11592034, 11741828	Standard	NM_024301		Approved	LGMD2I, MDC1C	uc002pfp.2	Q9H9S5		ENST00000318584.5:c.1382C>T	chr19.hg19:g.47260089C>T	ENSP00000326570:p.Ala461Val	51.0	0.0		52.0	24.0	NM_024301	A8K5G7	Missense_Mutation	SNP	ENST00000318584.5	hg19	CCDS12691.1	.	.	.	.	.	.	.	.	.	.	C	15.59	2.879511	0.51801	.	.	ENSG00000181027	ENST00000391909;ENST00000318584	D;D	0.99545	-6.13;-6.13	5.44	5.44	0.79542	.	0.247022	0.39210	N	0.001430	D	0.97567	0.9203	N	0.12746	0.255	0.45962	D	0.998785	B	0.31837	0.342	B	0.26864	0.074	D	0.97649	1.0153	10	0.33141	T	0.24	-20.4647	18.0247	0.89265	0.0:1.0:0.0:0.0	.	461	Q9H9S5	FKRP_HUMAN	V	461	ENSP00000375776:A461V;ENSP00000326570:A461V	ENSP00000326570:A461V	A	+	2	0	FKRP	51951929	1.000000	0.71417	1.000000	0.80357	0.823000	0.46562	3.970000	0.56824	2.573000	0.86826	0.305000	0.20034	GCG	.	.		0.657	FKRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465473.1	NM_024301		T	47260089	C	T	47260089	3	4	302	1	0	0	0	0	1	0	0	0	5925	768	27	1	1384	1	FKRP	19	47260089	Missense_Mutation	SNP	C	TCGA-G3-AAV6-01A-21D-A36X-10	5744888	47260089	11868894	62	43584										
NLRP11	204801	hgsc.bcm.edu	37	chr19	56320851	56320851	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	gcctctgatgtcaacgcatcAgcaagaaagtgggcatgtag	12	9	3	2			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr19:56320851A>T	ENST00000589093.1	-	3	1218	c.1125T>A	c.(1123-1125)gcT>gcA	p.A375A	NLRP11_ENST00000443188.1_Silent_p.A375A|NLRP11_ENST00000592953.1_Silent_p.A276A|NLRP11_ENST00000360133.3_Silent_p.A375A|NLRP11_ENST00000589824.2_Silent_p.A375A			P59045	NAL11_HUMAN	NLR family, pyrin domain containing 11	375	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.						ATP binding (GO:0005524)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	66		Colorectal(82;0.0002)		GBM - Glioblastoma multiforme(193;0.0325)		TCAACGCATCAGCAAGAAAGT	0.527																																					p.A375A		Atlas-SNP	.											.	NLRP11	139	.	0			c.T1125A						.						112	103	106					19																	56320851		2203	4300	6503	SO:0001819	synonymous_variant	204801	exon5			CGCATCAGCAAGA	AY095145	CCDS12935.1, CCDS74458.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179873		"Nucleotide-binding domain and leucine rich repeat containing"	22945	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 11"	609664	"NACHT, leucine rich repeat and PYD containing 11"	NALP11		12563287, 12019269	Standard	NM_145007		Approved	PYPAF6, NOD17, PAN10, CLR19.6	uc010ygf.2	P59045		ENST00000589093.1:c.1125T>A	chr19.hg19:g.56320851A>T		113.0	0.0		105.0	10.0	NM_145007	C9JSF5|Q2TV85|Q2TV86|Q53ZZ0|Q8NBF5	Silent	SNP	ENST00000589093.1	hg19	CCDS12935.1																																																																																			.	.		0.527	NLRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453657.1	NM_145007		T	56320851	A	T	56320851	2	4	302	1	0	0	0	0	0	0	0	1	10482	175	7	4		4	NLRP11	19	56320851	Silent	SNP	A	TCGA-G3-AAV6-01A-21D-A36X-10	9060762	56320851	2808132	63	43585										
TGM6	343641	hgsc.bcm.edu	37	chr20	2411162	2411162	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	acagaggacaagaagatcctGttggctgccatgtgccttgt	12	9	0	3			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr20:2411162G>C	ENST00000202625.2	+	11	1810	c.1749G>C	c.(1747-1749)ctG>ctC	p.L583L	TGM6_ENST00000381423.1_Silent_p.L583L	NM_198994.2	NP_945345.2	O95932	TGM3L_HUMAN	transglutaminase 6	583					cell death (GO:0008219)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(1)|endometrium(6)|kidney(2)|large_intestine(2)|lung(32)|ovary(4)|prostate(1)|skin(4)	52					L-Glutamine(DB00130)	AGAAGATCCTGTTGGCTGCCA	0.468																																					p.L583L		Atlas-SNP	.											.	TGM6	126	.	0			c.G1749C						.						107	92	97					20																	2411162		2203	4300	6503	SO:0001819	synonymous_variant	343641	exon11			GATCCTGTTGGCT	AF540970	CCDS13025.1, CCDS58761.1	20p13	2010-12-19	2004-07-05	2004-07-07	ENSG00000166948	ENSG00000166948		"Transglutaminases"	16255	protein-coding gene	gene with protein product	"spinocerebellar ataxia 35"	613900	"transglutaminase 3-like"	TGM3L		11390390, 21106500	Standard	NM_198994		Approved	dJ734P14.3, TGY, SCA35	uc002wfy.1	O95932	OTTHUMG00000031692	ENST00000202625.2:c.1749G>C	chr20.hg19:g.2411162G>C		116.0	0.0		118.0	7.0	NM_198994	Q5JXU4|Q5JXU5|Q719M2|Q719M3|Q9Y4U8	Silent	SNP	ENST00000202625.2	hg19	CCDS13025.1																																																																																			.	.		0.468	TGM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077581.2	NM_198994		C	2411162	G	C	2411162	2	2	302	1	0	0	0	0	0	0	0	1	15849	1364	48	4		4	TGM6	20	2411162	Silent	SNP	G	TCGA-G3-AAV6-01A-21D-A36X-10		2411162	60614358	64	43586										
ZHX3	23051	hgsc.bcm.edu	37	chr20	39832198	39832198	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	ttaatgggtgccacacctggCtgcttggggacggatgtcac	14	10	1	0			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr20:39832198C>T	ENST00000309060.3	-	4	1774	c.1359G>A	c.(1357-1359)caG>caA	p.Q453Q	ZHX3_ENST00000432768.2_Silent_p.Q453Q|ZHX3_ENST00000544979.2_Silent_p.Q453Q|ZHX3_ENST00000559234.1_Silent_p.Q453Q|ZHX3_ENST00000540170.1_Silent_p.Q453Q|ZHX3_ENST00000558993.1_Intron|ZHX3_ENST00000560361.1_Silent_p.Q453Q|ZHX3_ENST00000557816.1_Intron			Q9H4I2	ZHX3_HUMAN	zinc fingers and homeoboxes 3	453	Required for homodimerization and interaction with NFYA.|Required for repressor activity.				cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of osteoblast differentiation (GO:0045669)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(2)|kidney(5)|large_intestine(8)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		Myeloproliferative disorder(115;0.00425)				CCACACCTGGCTGCTTGGGGA	0.572																																					p.Q453Q		Atlas-SNP	.											.	ZHX3	78	.	0			c.G1359A						.						58	48	52					20																	39832198		2203	4300	6503	SO:0001819	synonymous_variant	23051	exon3			ACCTGGCTGCTTG	AB007855	CCDS13315.1	20q12	2012-03-09	2004-01-29	2004-01-30	ENSG00000174306	ENSG00000174306		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	15935	protein-coding gene	gene with protein product		609598	"triple homeobox 1"	TIX1		9455477	Standard	XM_005260343		Approved	KIAA0395	uc002xjs.1	Q9H4I2	OTTHUMG00000032481	ENST00000309060.3:c.1359G>A	chr20.hg19:g.39832198C>T		88.0	0.0		139.0	7.0	NM_015035	E1P5W5|F5H820|O43145|Q6NUJ7	Silent	SNP	ENST00000309060.3	hg19	CCDS13315.1	.	.	.	.	.	.	.	.	.	.	C	1.838	-0.468081	0.04476	.	.	ENSG00000174306	ENST00000421422	.	.	.	5.46	4.52	0.55395	.	.	.	.	.	T	0.54208	0.1844	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52609	-0.8553	4	.	.	.	-2.4736	4.7374	0.12995	0.0:0.5703:0.158:0.2718	.	.	.	.	T	162	.	.	A	-	1	0	ZHX3	39265612	0.851000	0.29673	0.996000	0.52242	0.815000	0.46073	0.911000	0.28584	1.309000	0.44985	-0.150000	0.13652	GCC	.	.		0.572	ZHX3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079262.3	NM_015035		T	39832198	C	T	39832198	2	4	302	1	0	0	0	0	0	0	0	1	17692	796	28	3		3	ZHX3	20	39832198	Silent	SNP	C	TCGA-G3-AAV6-01A-21D-A36X-10	37421036	39832198	23193322	65	43587										
IL17RA	23765	hgsc.bcm.edu	37	chr22	17590239	17590239	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	ccgctgctgggcagcccgggCgctgggcgaaatagcgtcct	16	14	0	0			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chr22:17590239C>T	ENST00000319363.6	+	13	2263	c.2130C>T	c.(2128-2130)ggC>ggT	p.G710G		NM_014339.5	NP_055154.3	Q96F46	I17RA_HUMAN	interleukin 17 receptor A	710					cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|fibroblast activation (GO:0072537)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)|positive regulation of interleukin-23 production (GO:0032747)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	interleukin-17 receptor activity (GO:0030368)			endometrium(2)|large_intestine(8)|lung(16)|ovary(1)|skin(2)|stomach(1)	30		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)		Colorectal(9;0.241)		GCAGCCCGGGCGCTGGGCGAA	0.736																																					p.G710G		Atlas-SNP	.											.	IL17RA	62	.	0			c.C2130T						.						11	12	11					22																	17590239		2188	4273	6461	SO:0001819	synonymous_variant	23765	exon13			CCCGGGCGCTGGG	U58917	CCDS13739.1	22q11.1	2014-09-17	2006-04-26	2006-04-26	ENSG00000177663	ENSG00000177663		"Interleukins and interleukin receptors", "CD molecules"	5985	protein-coding gene	gene with protein product		605461	"interleukin 17 receptor"	IL17R		9367539, 10591208	Standard	NM_014339		Approved	hIL-17R, IL-17RA, CDw217, CD217	uc002zly.4	Q96F46	OTTHUMG00000150026	ENST00000319363.6:c.2130C>T	chr22.hg19:g.17590239C>T		310.0	1.0		304.0	110.0	NM_014339	O43844|Q20WK1	Silent	SNP	ENST00000319363.6	hg19	CCDS13739.1																																																																																			.	.		0.736	IL17RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315820.1	NM_014339		T	17590239	C	T	17590239	2	4	302	1	0	0	0	0	0	0	0	1	7648	755	27	1		1	IL17RA	22	17590239	Silent	SNP	C	TCGA-G3-AAV6-01A-21D-A36X-10		17590239	33714327	66	43588										
PFKFB1	5207	hgsc.bcm.edu	37	chrX	54978348	54978348	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	cccaccctacctgcttgccgCgaactgagaggccagagtca	10	16	1	2			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chrX:54978348C>T	ENST00000375006.3	-	8	906	c.836G>A	c.(835-837)cGc>cAc	p.R279H	PFKFB1_ENST00000545676.1_Missense_Mutation_p.R214H|PFKFB1_ENST00000374992.2_Intron	NM_002625.2	NP_002616.2	P16118	F261_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1	279	Fructose-2,6-bisphosphatase.				carbohydrate metabolic process (GO:0005975)|dephosphorylation (GO:0016311)|energy reserve metabolic process (GO:0006112)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|intracellular signal transduction (GO:0035556)|organ regeneration (GO:0031100)|positive regulation of glucokinase activity (GO:0033133)|response to cAMP (GO:0051591)|response to glucagon (GO:0033762)|response to glucocorticoid (GO:0051384)|response to insulin (GO:0032868)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase complex (GO:0043540)|cytosol (GO:0005829)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)|fructose-6-phosphate binding (GO:0070095)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(11)|ovary(1)	24						CTGCTTGCCGCGAACTGAGAG	0.592																																					p.R279H		Atlas-SNP	.											.	PFKFB1	64	.	0			c.G836A						.						72	47	55					X																	54978348		2201	4297	6498	SO:0001583	missense	5207	exon8			TTGCCGCGAACTG		CCDS14364.1, CCDS65273.1	Xp11.21	2012-07-13			ENSG00000158571	ENSG00000158571	2.7.1.105, 3.1.3.46		8872	protein-coding gene	gene with protein product		311790		PFRX		9119406	Standard	NM_002625		Approved		uc004dty.2	P16118	OTTHUMG00000021643	ENST00000375006.3:c.836G>A	chrX.hg19:g.54978348C>T	ENSP00000364145:p.Arg279His	68.0	0.0		82.0	40.0	NM_002625	B2RA88|B4DUN5|Q5JXS5|Q99951	Missense_Mutation	SNP	ENST00000375006.3	hg19	CCDS14364.1	.	.	.	.	.	.	.	.	.	.	C	16.21	3.058944	0.55325	.	.	ENSG00000158571	ENST00000375006;ENST00000545676	T;T	0.72505	-0.66;-0.66	4.53	4.53	0.55603	Histidine phosphatase superfamily, clade-1 (2);	0.052657	0.85682	D	0.000000	T	0.73273	0.3566	M	0.84511	2.7	0.80722	D	1	P;B	0.41748	0.761;0.321	B;B	0.37015	0.239;0.094	T	0.80638	-0.1293	10	0.72032	D	0.01	-11.0959	15.6194	0.76793	0.0:1.0:0.0:0.0	.	214;279	B4DUN5;P16118	.;F261_HUMAN	H	279;214	ENSP00000364145:R279H;ENSP00000444074:R214H	ENSP00000364145:R279H	R	-	2	0	PFKFB1	54995073	0.921000	0.31238	0.985000	0.45067	0.301000	0.27625	4.775000	0.62346	2.015000	0.59207	0.519000	0.50382	CGC	.	.		0.592	PFKFB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056847.1			T	54978348	C	T	54978348	3	4	302	1	0	0	0	0	1	0	0	0	11769	768	27	1	607	1	PFKFB1	23	54978348	Missense_Mutation	SNP	C	TCGA-G3-AAV6-01A-21D-A36X-10		54978348	100292212	67	43589										
GJB1	2705	hgsc.bcm.edu	37	chrX	70443636	70443637	+	In_Frame_Ins	INS	-	-	TCATCT													0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	tggccgagtatggctctcggINStcatcttcatcttcagaatc							TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chrX:70443636_70443637insTCATCT	ENST00000374022.3	+	2	174_175	c.79_80insTCATCT	c.(79-81)gtc>gTCATCTtc	p.31_32insIF	GJB1_ENST00000361726.6_In_Frame_Ins_p.31_32insIF|GJB1_ENST00000374029.1_In_Frame_Ins_p.31_32insIF	NM_001097642.2	NP_001091111.1	P08034	CXB1_HUMAN	gap junction protein, beta 1, 32kDa	31					cell death (GO:0008219)|cell-cell signaling (GO:0007267)|gap junction assembly (GO:0016264)|membrane organization (GO:0061024)|nervous system development (GO:0007399)|protein oligomerization (GO:0051259)|purine ribonucleotide transport (GO:0015868)|transport (GO:0006810)	connexon complex (GO:0005922)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	gap junction channel activity (GO:0005243)			breast(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(1)	10	Renal(35;0.156)					ATGGCTCTCGGTCATCTTCATC	0.53																																					p.V27delinsVIF		Atlas-INDEL	.											.	GJB1	21	.	0			c.79_80insTCATCT						.																																			SO:0001652	inframe_insertion	2705	exon2			.	X04325	CCDS14408.1	Xq13.1	2014-09-17	2007-01-16		ENSG00000169562	ENSG00000169562		"Ion channels / Gap junction proteins (connexins)"	4283	protein-coding gene	gene with protein product	"Charcot-Marie-Tooth neuropathy, X-linked", "connexin 32"	304040	"gap junction protein, beta 1, 32kD (connexin 32, Charcot-Marie-Tooth neuropathy, X-linked)", "gap junction protein, beta 1, 32kDa (connexin 32, Charcot-Marie-Tooth neuropathy, X-linked)", "gap junction protein, beta 1, 32kDa (connexin 32)"	CMTX1, CMTX		1319395	Standard	NM_000166		Approved	CX32	uc004dzf.3	P08034	OTTHUMG00000021797	ENST00000374022.3:c.86_91dupTCATCT	chrX.hg19:g.70443637_70443642dupTCATCT	ENSP00000363134:p.Ile30_Phe31dup	116.0	0.0		86.0	16.0	NM_001097642	B2R8R2|D3DVV2|Q5U0S4	In_Frame_Ins	INS	ENST00000374022.3	hg19	CCDS14408.1																																																																																			.	.		0.53	GJB1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057133.1	NM_000166		TCATCT	70443637	-	TCATCT	70443636	7	5	302	1	0	1	1	0	0	0	0	0	6415	1261	44	0	81	0	GJB1	23	70443636	In_Frame_Ins	INS	-	TCGA-G3-AAV6-01A-21D-A36X-10	15465288	70443636	84826924	68	43590										
NKAP	79576	hgsc.bcm.edu	37	chrX	119059265	119059267	+	In_Frame_Del	DEL	TCT	TCT	-													0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	tgttctctctctttcgtctcTcttcttggttaaaggatgca							TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chrX:119059265_119059267delTCT	ENST00000371410.3	-	9	1330_1332	c.1164_1166delAGA	c.(1162-1167)gaagag>gag	p.388_389EE>E	RP3-327A19.5_ENST00000455986.1_RNA|NKAP_ENST00000477789.1_5'UTR|AC002477.1_ENST00000581061.1_RNA	NM_024528.3	NP_078804.2	Q8N5F7	NKAP_HUMAN	NFKB activating protein	388	Necessary for interaction with HDAC3 and transcriptional repression.				granulocyte differentiation (GO:0030851)|hematopoietic stem cell proliferation (GO:0071425)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|stem cell maintenance (GO:0019827)|T cell differentiation in thymus (GO:0033077)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)	20						CTTTCGTCTCTCTTCTTGGTTAA	0.448																																					p.389_389del		Atlas-INDEL	.											.	NKAP	53	.	0			c.1165_1167del						.																																			SO:0001651	inframe_deletion	79576	exon9			.	BC012770	CCDS14592.1	Xq24	2010-07-20			ENSG00000101882	ENSG00000101882			29873	protein-coding gene	gene with protein product	"NF kappaB activating protein"	300766				14550261	Standard	NM_024528		Approved	FLJ22626	uc004esh.3	Q8N5F7	OTTHUMG00000022284	ENST00000371410.3:c.1164_1166delAGA	chrX.hg19:g.119059268_119059270delTCT	ENSP00000360464:p.Glu389del	101.0	0.0		90.0	23.0	NM_024528	Q6IPW6|Q96BQ2|Q9H638	In_Frame_Del	DEL	ENST00000371410.3	hg19	CCDS14592.1																																																																																			.	.		0.448	NKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058072.1	NM_024528		-	119059267	TCT	-	119059265	7	5	302	1	0	1	0	1	0	0	0	0	10448	1551	54	0	85	0	NKAP	23	119059265	In_Frame_Del	DEL	TCT	TCGA-G3-AAV6-01A-21D-A36X-10	48615629	119059265	36211295	69	43591										
GPR112	139378	hgsc.bcm.edu	37	chrX	135428654	135428654	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	atacaatgaaatgacagaaaTgtttaattttaaccacacct	4	7	0	3			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chrX:135428654T>C	ENST00000394143.1	+	6	3080	c.2789T>C	c.(2788-2790)aTg>aCg	p.M930T	GPR112_ENST00000412101.1_Missense_Mutation_p.M725T|GPR112_ENST00000394141.1_Missense_Mutation_p.M725T|GPR112_ENST00000287534.4_Missense_Mutation_p.M867T|GPR112_ENST00000370652.1_Missense_Mutation_p.M930T	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	930					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					ATGACAGAAATGTTTAATTTT	0.393																																					p.M930T		Atlas-SNP	.											.	GPR112	459	.	0			c.T2789C						.						117	115	116					X																	135428654		2202	4299	6501	SO:0001583	missense	139378	exon6			CAGAAATGTTTAA	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"-", "GPCR / Class B : Orphans"	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.2789T>C	chrX.hg19:g.135428654T>C	ENSP00000377699:p.Met930Thr	239.0	0.0		203.0	107.0	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	hg19	CCDS35409.1	.	.	.	.	.	.	.	.	.	.	T	1.139	-0.650140	0.03506	.	.	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.27402	1.7;1.7;1.67;1.81;1.67	2.53	4.44E-4	0.14042	.	.	.	.	.	T	0.14830	0.0358	N	0.14661	0.345	0.09310	N	1	B;B;B	0.09022	0.002;0.001;0.0	B;B;B	0.06405	0.002;0.002;0.001	T	0.22487	-1.0215	9	0.52906	T	0.07	.	2.5999	0.04864	0.0:0.1782:0.3001:0.5217	.	867;725;930	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	T	930;930;725;867;725	ENSP00000377699:M930T;ENSP00000359686:M930T;ENSP00000416526:M725T;ENSP00000287534:M867T;ENSP00000377697:M725T	ENSP00000287534:M867T	M	+	2	0	GPR112	135256320	0.752000	0.28338	0.475000	0.27278	0.136000	0.21042	-0.025000	0.12413	-0.074000	0.12820	0.235000	0.17854	ATG	.	.		0.393	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1			C	135428654	T	C	135428654	3	2	302	1	0	0	0	0	1	0	0	0	6637	1464	51	2	2799	2	GPR112	23	135428654	Missense_Mutation	SNP	T	TCGA-G3-AAV6-01A-21D-A36X-10	16369389	135428654	19841906	70	43592										
CXorf1	9142	hgsc.bcm.edu	37	chrX	144909207	144909207	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0563380281690141	4	1	0.99862258953168	0	1.26748251748252	0.0606060606060606	0.491436100131752	0	attatttgaatgtattccagActattttatttaaaatcatc	3	5	1	2			TCGA-G3-AAV6-01A-21D-A36X-10	TCGA-G3-AAV6-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4543d206-bcd0-4bfc-a021-4b04cb3d5fb8	64362bb7-93d9-42fc-8259-b19ea7e0030f	g.chrX:144909207A>G	ENST00000408967.2	+	1	280	c.12A>G	c.(10-12)agA>agG	p.R4R		NM_004709.2	NP_004700.1	O96002	TM257_HUMAN	transmembrane protein 257	4						integral component of membrane (GO:0016021)											TGTATTCCAGACTATTTTATT	0.249																																					p.R4R		Atlas-SNP	.											.	.	.	.	0			c.A12G						.						22	22	22					X																	144909207		2186	4243	6429	SO:0001819	synonymous_variant	9142	exon1			TTCCAGACTATTT	Y08902	CCDS14681.1	Xq27.3	2012-12-03	2012-12-03	2012-12-03	ENSG00000221870	ENSG00000221870			2562	protein-coding gene	gene with protein product		300565	"chromosome X open reading frame 1"	CXorf1		9881668	Standard	NM_004709		Approved		uc004fch.3	O96002	OTTHUMG00000159605	ENST00000408967.2:c.12A>G	chrX.hg19:g.144909207A>G		265.0	0.0		332.0	61.0	NM_004709	Q14CW0	Silent	SNP	ENST00000408967.2	hg19	CCDS14681.1																																																																																			.	.		0.249	TMEM257-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356465.1	NM_004709		G	144909207	A	G	144909207	2	3	302	1	0	0	0	0	0	0	0	1	4102	272	10	2		2	CXorf1	23	144909207	Silent	SNP	A	TCGA-G3-AAV6-01A-21D-A36X-10	9480553	144909207	10361353	71	43593										
IPP	3652	hgsc.bcm.edu	37	chr1	46211836	46211836	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	tctgaaagattcctgcttcaAttcctagaatcggtacaaca	6	10	2	3			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr1:46211836A>G	ENST00000396478.3	-	2	350	c.248T>C	c.(247-249)aTt>aCt	p.I83T		NM_005897.2	NP_005888.1	Q9Y573	IPP_HUMAN	intracisternal A particle-promoted polypeptide	83	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.					actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	actin binding (GO:0003779)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|stomach(2)	20	Acute lymphoblastic leukemia(166;0.155)					TCCTGCTTCAATTCCTAGAAT	0.413																																					p.I83T		Atlas-SNP	.											.	IPP	66	.	0			c.T248C						.						87	85	85					1																	46211836		2203	4300	6503	SO:0001583	missense	3652	exon2			GCTTCAATTCCTA	BC032544	CCDS30702.1, CCDS44132.1	1p34-p32	2013-01-30			ENSG00000197429	ENSG00000197429		"Kelch-like", "BTB/POZ domain containing"	6108	protein-coding gene	gene with protein product	"kelch-like family member 27"	147485				1905535, 8432546	Standard	NM_005897		Approved	KLHL27	uc001cou.3	Q9Y573	OTTHUMG00000008004	ENST00000396478.3:c.248T>C	chr1.hg19:g.46211836A>G	ENSP00000379739:p.Ile83Thr	126.0	0.0		144.0	54.0	NM_001145349	A2A6V4|D3DQ11|Q8N5C3	Missense_Mutation	SNP	ENST00000396478.3	hg19	CCDS30702.1	.	.	.	.	.	.	.	.	.	.	A	18.03	3.533477	0.64972	.	.	ENSG00000197429	ENST00000359942;ENST00000396478	T;T	0.70749	-0.51;-0.51	5.57	5.57	0.84162	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.193310	0.47852	D	0.000218	T	0.74854	0.3771	M	0.71206	2.165	0.44402	D	0.997314	B;B	0.32653	0.085;0.379	B;B	0.39590	0.259;0.304	T	0.77172	-0.2685	10	0.87932	D	0	.	15.7343	0.77831	1.0:0.0:0.0:0.0	.	83;83	Q9Y573;A2A6V3	IPP_HUMAN;.	T	83	ENSP00000353024:I83T;ENSP00000379739:I83T	ENSP00000353024:I83T	I	-	2	0	IPP	45984423	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.692000	0.91284	2.115000	0.64714	0.533000	0.62120	ATT	.	.		0.413	IPP-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021974.3	NM_005897		G	46211836	A	G	46211836	3	3	303	1	0	0	0	0	1	0	0	0	7809	101	4	2	1640	2	IPP	1	46211836	Missense_Mutation	SNP	A	TCGA-G3-AAV7-01A-11D-A382-10		46211836	203038785	1	43594										
GLIS1	148979	hgsc.bcm.edu	37	chr1	54060500	54060500	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	ggcgaggcttcggcccgggaGgtccaggtctgggtgcaggc	20	11	1	0			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr1:54060500G>T	ENST00000312233.2	-	3	642	c.76C>A	c.(76-78)Ctc>Atc	p.L26I		NM_147193.2	NP_671726.2			GLIS family zinc finger 1											endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|skin(3)|urinary_tract(4)	24						CGGCCCGGGAGGTCCAGGTCT	0.706																																					p.L26I		Atlas-SNP	.											.	GLIS1	52	.	0			c.C76A						.						13	18	16					1																	54060500		2161	4208	6369	SO:0001583	missense	148979	exon3			CCGGGAGGTCCAG	AK093474	CCDS582.1	1p32.3	2008-02-05			ENSG00000174332	ENSG00000174332		"Zinc fingers, C2H2-type"	29525	protein-coding gene	gene with protein product		610378				12042312, 14500813	Standard	NM_147193		Approved	FLJ36155	uc001cvr.1	Q8NBF1	OTTHUMG00000008079	ENST00000312233.2:c.76C>A	chr1.hg19:g.54060500G>T	ENSP00000309653:p.Leu26Ile	98.0	0.0		119.0	32.0	NM_147193		Missense_Mutation	SNP	ENST00000312233.2	hg19	CCDS582.1	.	.	.	.	.	.	.	.	.	.	G	10.32	1.316674	0.23908	.	.	ENSG00000174332	ENST00000312233	T	0.13778	2.56	4.53	2.59	0.31030	.	0.134805	0.33534	N	0.004818	T	0.09818	0.0241	L	0.27053	0.805	0.24806	N	0.992671	B	0.24186	0.099	B	0.27608	0.081	T	0.22626	-1.0211	10	0.56958	D	0.05	.	8.0879	0.30784	0.0886:0.1598:0.7516:0.0	.	26	Q8NBF1	GLIS1_HUMAN	I	26	ENSP00000309653:L26I	ENSP00000309653:L26I	L	-	1	0	GLIS1	53833088	1.000000	0.71417	0.899000	0.35326	0.342000	0.28953	2.413000	0.44618	0.570000	0.29347	-0.302000	0.09304	CTC	.	.		0.706	GLIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022109.1	NM_147193		T	54060500	G	T	54060500	3	4	303	1	0	0	0	0	1	0	0	0	6453	1000	35	3	1818	3	GLIS1	1	54060500	Missense_Mutation	SNP	G	TCGA-G3-AAV7-01A-11D-A382-10	7848664	54060500	195190121	2	43595										
AGL	178	hgsc.bcm.edu	37	chr1	100381999	100382000	+	Frame_Shift_Del	DEL	AT	AT	-													0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	tgtggaatttatgacaatgcAttagacaatgacaactacaa							TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr1:100381999_100382000delAT	ENST00000294724.4	+	32	4771_4772	c.4293_4294delAT	c.(4291-4296)gcattafs	p.L1432fs	AGL_ENST00000370165.3_Frame_Shift_Del_p.L1432fs|AGL_ENST00000370163.3_Frame_Shift_Del_p.L1432fs|AGL_ENST00000361302.3_Frame_Shift_Del_p.L1416fs|AGL_ENST00000361522.4_Frame_Shift_Del_p.L1415fs|AGL_ENST00000361915.3_Frame_Shift_Del_p.L1432fs|AGL_ENST00000370161.2_Frame_Shift_Del_p.L1416fs	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	1432					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|inclusion body (GO:0016234)|isoamylase complex (GO:0043033)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)	4-alpha-glucanotransferase activity (GO:0004134)|amylo-alpha-1,6-glucosidase activity (GO:0004135)|glycogen debranching enzyme activity (GO:0004133)|polysaccharide binding (GO:0030247)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(9)|lung(35)|ovary(1)|prostate(4)|skin(3)|urinary_tract(1)	69		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		ATGACAATGCATTAGACAATGA	0.267																																					p.1431_1431del		Atlas-Indel,Pindel	.											.	AGL	137	.	0			c.4292_4293del						.																																			SO:0001589	frameshift_variant	178	exon32			.	BC078663	CCDS759.1, CCDS760.1, CCDS761.1	1p21	2010-04-27	2010-04-27		ENSG00000162688	ENSG00000162688	2.4.1.25, 3.2.1.33		321	protein-coding gene	gene with protein product	"glycogen debranching enzyme", "glycogen storage disease type III"	610860	"amylo-1, 6-glucosidase, 4-alpha-glucanotransferase"			1505983	Standard	NM_000028		Approved		uc001dsi.1	P35573	OTTHUMG00000010803	ENST00000294724.4:c.4293_4294delAT	chr1.hg19:g.100381999_100382000delAT	ENSP00000294724:p.Leu1432fs	352.0	0.0		434.0	141.0	NM_000644	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Frame_Shift_Del	DEL	ENST00000294724.4	hg19	CCDS759.1																																																																																			.	.		0.267	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028		-	100382000	AT	-	100381999	7	5	303	1	0	1	0	1	0	0	0	0	384	204	8	0	4484	0	AGL	1	100381999	Frame_Shift_Del	DEL	AT	TCGA-G3-AAV7-01A-11D-A382-10	46321499	100381999	148868622	3	43596										
AKNAD1	254268	hgsc.bcm.edu	37	chr1	109394989	109394989	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	cttagaagcgtctccttcatTtgctggaatatgaagagctg	10	8	2	3			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr1:109394989T>G	ENST00000370001.3	-	2	566	c.298A>C	c.(298-300)Aat>Cat	p.N100H	AKNAD1_ENST00000369995.3_Missense_Mutation_p.N100H|AKNAD1_ENST00000369994.1_Missense_Mutation_p.N100H|AKNAD1_ENST00000357393.4_Intron	NM_152763.4	NP_689976.2	Q5T1N1	AKND1_HUMAN	AKNA domain containing 1	100						cytoplasm (GO:0005737)				breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|prostate(6)|skin(3)|stomach(2)	32						TCTCCTTCATTTGCTGGAATA	0.398																																					p.N100H		Atlas-SNP	.											.	AKNAD1	83	.	0			c.A298C						.						108	107	107					1																	109394989		2203	4300	6503	SO:0001583	missense	254268	exon2			CTTCATTTGCTGG	AK095517	CCDS791.2	1p13.3	2009-10-29	2009-10-29	2009-10-29	ENSG00000162641	ENSG00000162641			28398	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 62"	C1orf62			Standard	NM_152763		Approved	MGC26989	uc001dwa.4	Q5T1N1	OTTHUMG00000011231	ENST00000370001.3:c.298A>C	chr1.hg19:g.109394989T>G	ENSP00000359018:p.Asn100His	80.0	0.0		97.0	33.0	NM_152763	B9EK62|Q5T1N0|Q8N990|Q8NCN9	Missense_Mutation	SNP	ENST00000370001.3	hg19	CCDS791.2	.	.	.	.	.	.	.	.	.	.	T	12.85	2.062286	0.36373	.	.	ENSG00000162641	ENST00000370001;ENST00000369994;ENST00000369995	T;T;T	0.09163	3.03;3.07;3.01	5.77	-2.28	0.06826	.	0.737789	0.13302	N	0.398178	T	0.05731	0.0150	L	0.56769	1.78	0.09310	N	1	P	0.43169	0.8	P	0.47206	0.541	T	0.18999	-1.0319	10	0.72032	D	0.01	-3.2114	6.2491	0.20835	0.1099:0.3173:0.0:0.5728	.	100	Q5T1N1	AKND1_HUMAN	H	100	ENSP00000359018:N100H;ENSP00000359011:N100H;ENSP00000359012:N100H	ENSP00000359011:N100H	N	-	1	0	AKNAD1	109196512	0.005000	0.15991	0.000000	0.03702	0.002000	0.02628	0.901000	0.28445	-0.415000	0.07484	-0.290000	0.09829	AAT	.	.		0.398	AKNAD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030923.2	NM_152763		G	109394989	T	G	109394989	3	3	303	1	0	0	0	0	1	0	0	0	464	1841	64	5	2272	5	AKNAD1	1	109394989	Missense_Mutation	SNP	T	TCGA-G3-AAV7-01A-11D-A382-10	9012990	109394989	139855632	4	43597										
ZNF687	57592	hgsc.bcm.edu	37	chr1	151259083	151259083	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	ctggaggctcagcaggagacGgggcccaggctgctggggta	19	10	1	1			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr1:151259083G>T	ENST00000368879.2	+	2	414	c.316G>T	c.(316-318)Ggg>Tgg	p.G106W		NM_020832.1	NP_065883.1	Q8N1G0	ZN687_HUMAN	zinc finger protein 687	106					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(2)	32	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			AGCAGGAGACGGGGCCCAGGC	0.592																																					p.G106W		Atlas-SNP	.											ZNF687,colon,carcinoma,0,1	ZNF687	94	.	0			c.G316T						.						53	59	57					1																	151259083		2203	4300	6503	SO:0001583	missense	57592	exon2			GGAGACGGGGCCC		CCDS992.1	1q21.2	2008-05-02			ENSG00000143373	ENSG00000143373			29277	protein-coding gene	gene with protein product		610568				10718198	Standard	NM_020832		Approved	KIAA1441	uc001exq.3	Q8N1G0	OTTHUMG00000012347	ENST00000368879.2:c.316G>T	chr1.hg19:g.151259083G>T	ENSP00000357874:p.Gly106Trp	68.0	0.0		151.0	19.0	NM_020832	D3DV17|Q68DQ8|Q9H937|Q9P2A7	Missense_Mutation	SNP	ENST00000368879.2	hg19		.	.	.	.	.	.	.	.	.	.	G	6.458	0.452661	0.12283	.	.	ENSG00000143373	ENST00000443959;ENST00000336715;ENST00000324048;ENST00000368879	T;T;T	0.01015	5.44;5.44;5.78	4.32	4.32	0.51571	.	0.220870	0.22859	N	0.054762	T	0.01454	0.0047	L	0.51422	1.61	0.20926	N	0.999826	D;D;D	0.71674	0.997;0.979;0.998	D;P;D	0.69824	0.95;0.571;0.966	T	0.46005	-0.9222	10	0.87932	D	0	.	10.082	0.42395	0.0987:0.0:0.9013:0.0	.	106;106;106	Q8N1G0-2;Q8N1G0;F8WCX2	.;ZN687_HUMAN;.	W	115;106;106;106	ENSP00000336620:G106W;ENSP00000319829:G106W;ENSP00000357874:G106W	ENSP00000319829:G106W	G	+	1	0	ZNF687	149525707	0.521000	0.26258	0.053000	0.19242	0.053000	0.15095	3.544000	0.53640	2.247000	0.74100	0.313000	0.20887	GGG	.	.		0.592	ZNF687-201	KNOWN	basic	protein_coding	protein_coding		NM_020832		T	151259083	G	T	151259083	3	4	303	1	0	0	0	0	1	0	0	0	18107	1116	39	1	318	1	ZNF687	1	151259083	Missense_Mutation	SNP	G	TCGA-G3-AAV7-01A-11D-A382-10	41864094	151259083	97991538	5	43598										
FLG2	388698	hgsc.bcm.edu	37	chr1	152324696	152324696	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	atgaccagattgagaatgtcCactggtatctcctgtctgtc	9	10	2	3			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr1:152324696C>A	ENST00000388718.5	-	3	5638	c.5566G>T	c.(5566-5568)Gga>Tga	p.G1856*	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000445097.1_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	1856					establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGAGAATGTCCACTGGTATCT	0.502																																					p.G1856X		Atlas-SNP	.											.	FLG2	431	.	0			c.G5566T						.						336	292	307					1																	152324696		2203	4300	6503	SO:0001587	stop_gained	388698	exon3			AATGTCCACTGGT	AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"EF-hand domain containing"	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.5566G>T	chr1.hg19:g.152324696C>A	ENSP00000373370:p.Gly1856*	108.0	0.0		239.0	40.0	NM_001014342	Q9H4U1	Nonsense_Mutation	SNP	ENST00000388718.5	hg19	CCDS30861.1	.	.	.	.	.	.	.	.	.	.	C	42	9.419145	0.99166	.	.	ENSG00000143520	ENST00000388718	.	.	.	3.93	-1.66	0.08265	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.13853	T	0.58	-0.1059	7.9128	0.29800	0.0:0.5261:0.0:0.4739	.	.	.	.	X	1856	.	ENSP00000373370:G1856X	G	-	1	0	FLG2	150591320	0.000000	0.05858	0.004000	0.12327	0.044000	0.14063	-0.751000	0.04803	-0.129000	0.11620	0.449000	0.29647	GGA	.	.		0.502	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		A	152324696	C	A	152324696	4	1	303	1	0	0	0	0	0	1	0	0	5931	603	21	3	1613	3	FLG2	1	152324696	Nonsense_Mutation	SNP	C	TCGA-G3-AAV7-01A-11D-A382-10	1065613	152324696	96925925	6	43599										
CREB3L4	148327	hgsc.bcm.edu	37	chr1	153941033	153941033	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	aatccctgacctgctggacgCgtggctggagcccccagagg	14	14	0	2			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr1:153941033C>G	ENST00000368607.3	+	2	298	c.32C>G	c.(31-33)gCg>gGg	p.A11G	CREB3L4_ENST00000368601.1_Missense_Mutation_p.A11G|CREB3L4_ENST00000368603.1_Missense_Mutation_p.A11G|SLC39A1_ENST00000310483.6_5'Flank|CREB3L4_ENST00000368600.3_Missense_Mutation_p.A11G|RP11-422P24.10_ENST00000608147.1_RNA|CREB3L4_ENST00000405694.3_5'UTR|CREB3L4_ENST00000271889.4_Missense_Mutation_p.A11G	NM_001255978.1|NM_001255980.1|NM_130898.3	NP_001242907.1|NP_001242909.1|NP_570968.1	Q8TEY5	CR3L4_HUMAN	cAMP responsive element binding protein 3-like 4	11					response to unfolded protein (GO:0006986)|spermatogenesis (GO:0007283)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(3)	13	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			CTGCTGGACGCGTGGCTGGAG	0.597																																					p.A11G		Atlas-SNP	.											.	CREB3L4	36	.	0			c.C32G						.						51	52	52					1																	153941033		2203	4300	6503	SO:0001583	missense	148327	exon2			TGGACGCGTGGCT	AF394167	CCDS1056.1, CCDS58029.1	1q21.2	2013-01-10			ENSG00000143578	ENSG00000143578		"basic leucine zipper proteins"	18854	protein-coding gene	gene with protein product		607138					Standard	NM_130898		Approved	AIbZIP, CREB4, CREB3, hJAL, ATCE1	uc001fdr.3	Q8TEY5	OTTHUMG00000037159	ENST00000368607.3:c.32C>G	chr1.hg19:g.153941033C>G	ENSP00000357596:p.Ala11Gly	96.0	0.0		187.0	78.0	NM_001255980	D3DV62|Q5T4L0|Q86YW6	Missense_Mutation	SNP	ENST00000368607.3	hg19	CCDS1056.1	.	.	.	.	.	.	.	.	.	.	C	12.46	1.943594	0.34283	.	.	ENSG00000143578	ENST00000449724;ENST00000368607;ENST00000271889;ENST00000368601;ENST00000368603;ENST00000368600;ENST00000431292	T;T;T;T;T;T;T	0.32515	1.45;1.45;1.45;1.45;1.45;1.45;1.45	4.24	0.289	0.15723	.	2.382990	0.01788	N	0.032160	T	0.04363	0.0120	N	0.08118	0	0.23003	N	0.99845	B;B;B	0.22146	0.065;0.049;0.039	B;B;B	0.23275	0.045;0.008;0.013	T	0.20438	-1.0275	10	0.22706	T	0.39	.	2.4672	0.04555	0.2098:0.2943:0.0:0.4959	.	11;11;11	B4E2G3;Q5T4L0;Q8TEY5	.;.;CR3L4_HUMAN	G	11	ENSP00000391847:A11G;ENSP00000357596:A11G;ENSP00000271889:A11G;ENSP00000357590:A11G;ENSP00000357592:A11G;ENSP00000357589:A11G;ENSP00000402308:A11G	ENSP00000271889:A11G	A	+	2	0	CREB3L4	152207657	0.002000	0.14202	0.219000	0.23793	0.585000	0.36419	-0.105000	0.10907	-0.058000	0.13177	0.561000	0.74099	GCG	.	.		0.597	CREB3L4-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090291.1	NM_130898		G	153941033	C	G	153941033	3	3	303	1	0	0	0	0	1	0	0	0	3861	768	27	4	34	4	CREB3L4	1	153941033	Missense_Mutation	SNP	C	TCGA-G3-AAV7-01A-11D-A382-10	1616337	153941033	95309588	7	43600										
NES	10763	hgsc.bcm.edu	37	chr1	156639400	156639400	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	caatgatgtctgcccctgggCctgcatcctccatcccactg	8	17	1	1			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr1:156639400C>T	ENST00000368223.3	-	4	4712	c.4580G>A	c.(4579-4581)gGc>gAc	p.G1527D		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin	1527	Tail.				brain development (GO:0007420)|cell projection morphogenesis (GO:0048858)|central nervous system development (GO:0007417)|embryonic camera-type eye development (GO:0031076)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of catalytic activity (GO:0043086)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein binding (GO:0032091)|positive regulation of intermediate filament depolymerization (GO:0030844)|positive regulation of neural precursor cell proliferation (GO:2000179)|stem cell proliferation (GO:0072089)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	intermediate filament binding (GO:0019215)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(30)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(4)	64	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TGCCCCTGGGCCTGCATCCTC	0.577																																					p.G1527D		Atlas-SNP	.											.	NES	196	.	0			c.G4580A						.						80	69	73					1																	156639400		2203	4300	6503	SO:0001583	missense	10763	exon4			CCTGGGCCTGCAT	X65964	CCDS1151.1	1q23	2013-01-16			ENSG00000132688	ENSG00000132688		"Intermediate filaments type IV"	7756	protein-coding gene	gene with protein product		600915				1478958, 9104587	Standard	NM_006617		Approved	FLJ21841	uc001fpq.3	P48681	OTTHUMG00000034299	ENST00000368223.3:c.4580G>A	chr1.hg19:g.156639400C>T	ENSP00000357206:p.Gly1527Asp	93.0	0.0		179.0	41.0	NM_006617	O00552|Q3LIF5|Q5SYZ6	Missense_Mutation	SNP	ENST00000368223.3	hg19	CCDS1151.1	.	.	.	.	.	.	.	.	.	.	C	3.129	-0.178864	0.06380	.	.	ENSG00000132688	ENST00000368223	D	0.86769	-2.17	3.63	-0.976	0.10286	.	.	.	.	.	T	0.65144	0.2663	L	0.50333	1.59	0.09310	N	1	B	0.12630	0.006	B	0.09377	0.004	T	0.55173	-0.8182	9	0.52906	T	0.07	.	1.9409	0.03346	0.4776:0.2559:0.1515:0.1151	.	1527	P48681	NEST_HUMAN	D	1527	ENSP00000357206:G1527D	ENSP00000357206:G1527D	G	-	2	0	NES	154906024	0.000000	0.05858	0.001000	0.08648	0.026000	0.11368	-0.333000	0.07894	0.172000	0.19760	0.313000	0.20887	GGC	.	.		0.577	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	NM_006617		T	156639400	C	T	156639400	3	4	303	1	0	0	0	0	1	0	0	0	10346	739	26	3	289	3	NES	1	156639400	Missense_Mutation	SNP	C	TCGA-G3-AAV7-01A-11D-A382-10	2698367	156639400	92611221	8	43601										
PEAR1	375033	hgsc.bcm.edu	37	chr1	156875181	156875181	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	ccgccagcgcctgcagtgctGccatggcttctatgagagca	12	14	1	1			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr1:156875181G>C	ENST00000338302.3	+	5	497	c.272G>C	c.(271-273)tGc>tCc	p.C91S	PEAR1_ENST00000292357.7_Missense_Mutation_p.C91S			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	91	EMI. {ECO:0000255|PROSITE- ProRule:PRU00384}.				recognition of apoptotic cell (GO:0043654)	integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(6)|lung(22)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)	43	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CTGCAGTGCTGCCATGGCTTC	0.642																																					p.C91S		Atlas-SNP	.											.	PEAR1	118	.	0			c.G272C						.						65	57	60					1																	156875181		2203	4300	6503	SO:0001583	missense	375033	exon4			AGTGCTGCCATGG	AK098809	CCDS30892.1	1q23.1	2008-02-05	2007-10-25	2007-10-25	ENSG00000187800	ENSG00000187800			33631	protein-coding gene	gene with protein product		610278	"multiple EGF-like-domains 12"	MEGF12		15851471	Standard	NM_001080471		Approved	JEDI, FLJ00193	uc001fqj.1	Q5VY43	OTTHUMG00000041293	ENST00000338302.3:c.272G>C	chr1.hg19:g.156875181G>C	ENSP00000344465:p.Cys91Ser	27.0	0.0		81.0	20.0	NM_001080471	Q8TEK2	Missense_Mutation	SNP	ENST00000338302.3	hg19	CCDS30892.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.154826	0.78114	.	.	ENSG00000187800	ENST00000338302;ENST00000455314;ENST00000292357	D;D;D	0.90955	-2.76;-2.53;-2.76	4.02	4.02	0.46733	EMI domain (1);	0.000000	0.44902	D	0.000417	D	0.92159	0.7514	M	0.62723	1.935	0.80722	D	1	D	0.89917	1.0	D	0.71870	0.975	D	0.91353	0.5106	10	0.39692	T	0.17	.	13.7114	0.62670	0.0:0.0:1.0:0.0	.	91	Q5VY43	PEAR1_HUMAN	S	91	ENSP00000344465:C91S;ENSP00000389742:C91S;ENSP00000292357:C91S	ENSP00000292357:C91S	C	+	2	0	PEAR1	155141805	1.000000	0.71417	0.934000	0.37439	0.637000	0.38172	8.778000	0.91785	2.073000	0.62155	0.655000	0.94253	TGC	.	.		0.642	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471		C	156875181	G	C	156875181	3	2	303	1	0	0	0	0	1	0	0	0	11721	1319	46	4	282	4	PEAR1	1	156875181	Missense_Mutation	SNP	G	TCGA-G3-AAV7-01A-11D-A382-10	235781	156875181	92375440	9	43602										
BRP44	25874	hgsc.bcm.edu	37	chr1	167905052	167905052	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	gagccggtggtaggtggcccGcaggcctcgggcaccggcgg	20	13	0	0			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr1:167905052G>A	ENST00000367846.4	-	1	226	c.28C>T	c.(28-30)Cgg>Tgg	p.R10W	MPC2_ENST00000271373.4_Missense_Mutation_p.R10W|DCAF6_ENST00000367840.3_5'Flank|DCAF6_ENST00000367843.3_5'Flank|DCAF6_ENST00000312263.6_5'Flank|DCAF6_ENST00000432587.2_5'Flank	NM_015415.3	NP_056230.1	O95563	MPC2_HUMAN	mitochondrial pyruvate carrier 2	10					cellular metabolic process (GO:0044237)|mitochondrial pyruvate transport (GO:0006850)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	pyruvate transmembrane transporter activity (GO:0050833)										TAGGTGGCCCGCAGGCCTCGG	0.642																																					p.R10W		Atlas-SNP	.											.	.	.	.	0			c.C28T						.						18	16	17					1																	167905052		2159	4214	6373	SO:0001583	missense	25874	exon2			TGGCCCGCAGGCC		CCDS1266.1	1q24	2012-07-30	2012-07-30	2012-07-30	ENSG00000143158	ENSG00000143158			24515	protein-coding gene	gene with protein product		614737	"brain protein 44"	BRP44		3022128, 22628558	Standard	NM_015415		Approved	DKFZP564B167	uc001get.3	O95563	OTTHUMG00000034570	ENST00000367846.4:c.28C>T	chr1.hg19:g.167905052G>A	ENSP00000356820:p.Arg10Trp	141.0	0.0		253.0	47.0	NM_001143674	A8K261|Q3SXR6|Q6FIF3	Missense_Mutation	SNP	ENST00000367846.4	hg19	CCDS1266.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.661706	0.88154	.	.	ENSG00000143158	ENST00000367846;ENST00000271373;ENST00000458574	T;T;T	0.65732	-0.17;-0.17;-0.16	5.22	3.34	0.38264	.	0.056233	0.64402	D	0.000002	T	0.67059	0.2853	M	0.79805	2.47	0.42037	D	0.991055	B;D	0.89917	0.016;1.0	B;D	0.66979	0.005;0.948	T	0.71354	-0.4618	9	0.72032	D	0.01	-4.3393	7.8078	0.29213	0.0829:0.0:0.7566:0.1604	.	10;10	B2R4Q7;O95563	.;BR44_HUMAN	W	10	ENSP00000356820:R10W;ENSP00000271373:R10W;ENSP00000392874:R10W	ENSP00000271373:R10W	R	-	1	2	BRP44	166171676	0.994000	0.37717	0.999000	0.59377	0.956000	0.61745	1.530000	0.36007	0.756000	0.33013	0.650000	0.86243	CGG	.	.		0.642	MPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083652.1	NM_015415		A	167905052	G	A	167905052	3	1	303	1	0	0	0	0	1	0	0	0	1520	1086	38	1	375	1	BRP44	1	167905052	Missense_Mutation	SNP	G	TCGA-G3-AAV7-01A-11D-A382-10	11029871	167905052	81345569	10	43603										
SLC19A2	10560	hgsc.bcm.edu	37	chr1	169454948	169454948	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	cggacccgagcggtccgcagGagcacagtggccgccgccgc	16	17	0	0			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr1:169454948G>T	ENST00000236137.5	-	1	293	c.57C>A	c.(55-57)ctC>ctA	p.L19L	SLC19A2_ENST00000367804.4_Silent_p.L19L	NM_006996.2	NP_008927.1	O60779	S19A2_HUMAN	solute carrier family 19 (thiamine transporter), member 2	19					folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|thiamine transport (GO:0015888)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	folic acid transporter activity (GO:0008517)|thiamine transmembrane transporter activity (GO:0015234)|thiamine uptake transmembrane transporter activity (GO:0015403)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|upper_aerodigestive_tract(1)	11	all_hematologic(923;0.208)				Thiamine(DB00152)	CGGTCCGCAGGAGCACAGTgg	0.751																																					p.L19L		Atlas-SNP	.											.	SLC19A2	35	.	0			c.C57A						.						4	6	5					1																	169454948		1792	3489	5281	SO:0001819	synonymous_variant	10560	exon1			CCGCAGGAGCACA	AF135488	CCDS1280.1	1q23.3	2013-05-22			ENSG00000117479	ENSG00000117479		"Solute carriers"	10938	protein-coding gene	gene with protein product		603941		TRMA		9399900, 10391221	Standard	NM_006996		Approved	THTR1	uc001gge.4	O60779	OTTHUMG00000035452	ENST00000236137.5:c.57C>A	chr1.hg19:g.169454948G>T		121.0	0.0		183.0	62.0	NM_006996	B2R9H0|B4E1X4|Q8WV87|Q9UBL7|Q9UKJ2|Q9UN31|Q9UN43	Silent	SNP	ENST00000236137.5	hg19	CCDS1280.1																																																																																			.	.		0.751	SLC19A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086106.1	NM_006996		T	169454948	G	T	169454948	2	4	303	1	0	0	0	0	0	0	0	1	14444	1161	41	3		3	SLC19A2	1	169454948	Silent	SNP	G	TCGA-G3-AAV7-01A-11D-A382-10	1549896	169454948	79795673	11	43604										
SCYL3	57147	hgsc.bcm.edu	37	chr1	169833605	169833605	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	gaagaggcaccaaccttgaaGctatcaattcctctgacaag	8	11	2	3			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr1:169833605G>A	ENST00000367770.1	-	8	907	c.860C>T	c.(859-861)gCt>gTt	p.A287V	SCYL3_ENST00000470238.1_5'UTR|SCYL3_ENST00000367771.6_Missense_Mutation_p.A287V|SCYL3_ENST00000367772.4_Missense_Mutation_p.A287V			Q8IZE3	PACE1_HUMAN	SCY1-like 3 (S. cerevisiae)	287					cell migration (GO:0016477)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)	ATP binding (GO:0005524)|transferase activity, transferring phosphorus-containing groups (GO:0016772)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(5)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					CAACCTTGAAGCTATCAATTC	0.458																																					p.A287V		Atlas-SNP	.											.	SCYL3	116	.	0			c.C860T						.						87	81	83					1																	169833605		2203	4300	6503	SO:0001583	missense	57147	exon9			CTTGAAGCTATCA	BC014662	CCDS1286.1, CCDS1287.1	1q24.2	2008-02-05			ENSG00000000457	ENSG00000000457			19285	protein-coding gene	gene with protein product	"ezrin-binding partner PACE-1"	608192				12651155	Standard	NM_020423		Approved	PACE-1, PACE1	uc001ggs.3	Q8IZE3	OTTHUMG00000035941	ENST00000367770.1:c.860C>T	chr1.hg19:g.169833605G>A	ENSP00000356744:p.Ala287Val	293.0	1.0		513.0	203.0	NM_020423	A8K8Z2|Q5THA6|Q5THA8|Q8IZN9|Q96C56|Q9UBK6	Missense_Mutation	SNP	ENST00000367770.1	hg19	CCDS1287.1	.	.	.	.	.	.	.	.	.	.	G	33	5.283003	0.95489	.	.	ENSG00000000457	ENST00000367772;ENST00000367771;ENST00000367770;ENST00000423670	T;T;T;T	0.24538	1.85;1.85;1.85;1.85	5.54	5.54	0.83059	Armadillo-like helical (1);Armadillo-type fold (1);	0.050565	0.85682	D	0.000000	T	0.50017	0.1591	M	0.82823	2.61	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.983	T	0.54866	-0.8229	10	0.62326	D	0.03	-16.4968	19.0844	0.93198	0.0:0.0:1.0:0.0	.	287;287	Q8IZE3-2;Q8IZE3	.;PACE1_HUMAN	V	287	ENSP00000356746:A287V;ENSP00000356745:A287V;ENSP00000356744:A287V;ENSP00000407993:A287V	ENSP00000356744:A287V	A	-	2	0	SCYL3	168100229	1.000000	0.71417	0.984000	0.44739	0.976000	0.68499	7.484000	0.81180	2.584000	0.87258	0.655000	0.94253	GCT	.	.		0.458	SCYL3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087550.4	NM_181093		A	169833605	G	A	169833605	3	1	303	1	0	0	0	0	1	0	0	0	13964	971	34	3	1392	3	SCYL3	1	169833605	Missense_Mutation	SNP	G	TCGA-G3-AAV7-01A-11D-A382-10	378657	169833605	79417016	12	43605										
TDRD5	163589	hgsc.bcm.edu	37	chr1	179631239	179631239	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	tgtcttctgttacattttagGatgagatccccactggaatg	9	8	2	1			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr1:179631239G>A	ENST00000367614.1	+	14	2520	c.2161G>A	c.(2161-2163)Gat>Aat	p.D721N	TDRD5_ENST00000444136.1_Splice_Site_p.D775N|TDRD5_ENST00000294848.8_Splice_Site_p.D721N	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	721					DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)				NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						TACATTTTAGGATGAGATCCC	0.383																																					p.D775N		Atlas-SNP	.											.	TDRD5	149	.	0			c.G2323A						.						133	117	123					1																	179631239		2203	4300	6503	SO:0001630	splice_region_variant	163589	exon15			TTTTAGGATGAGA	AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"Tudor domain containing"	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.2161-1G>A	chr1.hg19:g.179631239G>A		81.0	0.0		139.0	21.0	NM_001199085	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Missense_Mutation	SNP	ENST00000367614.1	hg19	CCDS1332.1	.	.	.	.	.	.	.	.	.	.	G	16.48	3.136361	0.56936	.	.	ENSG00000162782	ENST00000367614;ENST00000294848;ENST00000444136;ENST00000417329	T;T;T;T	0.37411	2.43;2.43;2.69;1.2	5.41	3.43	0.39272	.	0.258333	0.27846	N	0.017610	T	0.42653	0.1212	M	0.63843	1.955	0.25750	N	0.98506	D;D	0.57899	0.981;0.958	P;P	0.54174	0.744;0.477	T	0.26849	-1.0091	9	.	.	.	-13.5812	6.3659	0.21455	0.0972:0.1865:0.7164:0.0	.	775;721	Q8NAT2-1;Q8NAT2	.;TDRD5_HUMAN	N	721;721;775;231	ENSP00000356586:D721N;ENSP00000294848:D721N;ENSP00000406052:D775N;ENSP00000410744:D231N	.	D	+	1	0	TDRD5	177897862	1.000000	0.71417	1.000000	0.80357	0.714000	0.41099	2.006000	0.40874	2.699000	0.92147	0.650000	0.86243	GAT	.	.		0.383	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533	Missense_Mutation	A	179631239	G	A	179631239	5	1	303	1	0	0	0	0	0	0	1	0	15748	1188	41	3	2211	3	TDRD5	1	179631239	Splice_Site	SNP	G	TCGA-G3-AAV7-01A-11D-A382-10	9797634	179631239	69619382	13	43606										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186088414	186088414	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	ggctctgcacatcgacacgtGacccttcatgttcatggtat	9	12	3	1			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr1:186088414G>A	ENST00000271588.4	+	78	12169	c.11940G>A	c.(11938-11940)gtG>gtA	p.V3980V	HMCN1_ENST00000367492.2_Silent_p.V3980V	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	3980	Ig-like C2-type 38.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						ATCGACACGTGACCCTTCATG	0.433																																					p.V3980V		Atlas-SNP	.											.	HMCN1	797	.	0			c.G11940A						.						114	106	109					1																	186088414		2203	4300	6503	SO:0001819	synonymous_variant	83872	exon78			ACACGTGACCCTT	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.11940G>A	chr1.hg19:g.186088414G>A		222.0	0.0		386.0	64.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	hg19	CCDS30956.1																																																																																			.	.		0.433	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		A	186088414	G	A	186088414	2	1	303	1	0	0	0	0	0	0	0	1	7229	1277	45	3		3	HMCN1	1	186088414	Silent	SNP	G	TCGA-G3-AAV7-01A-11D-A382-10	6457175	186088414	63162207	14	43607										
TTC13	79573	hgsc.bcm.edu	37	chr1	231047225	231047225	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	atattacttacctggatcctCgagagagtggcattaaatta	8	7	0	1			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr1:231047225C>G	ENST00000366661.4	-	20	2307	c.2300G>C	c.(2299-2301)cGa>cCa	p.R767P	TTC13_ENST00000414259.1_Missense_Mutation_p.R714P|TTC13_ENST00000366662.4_Missense_Mutation_p.R713P	NM_024525.4	NP_078801.3	Q8NBP0	TTC13_HUMAN	tetratricopeptide repeat domain 13	767										central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	39	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)		COAD - Colon adenocarcinoma(196;0.243)		CCTGGATCCTCGAGAGAGTGG	0.308																																					p.R767P		Atlas-SNP	.											.	TTC13	74	.	0			c.G2300C						.						33	37	35					1																	231047225		2200	4281	6481	SO:0001583	missense	79573	exon20			GATCCTCGAGAGA		CCDS1588.1, CCDS44332.1, CCDS44332.2	1q42.2	2013-01-10			ENSG00000143643	ENSG00000143643		"Tetratricopeptide (TTC) repeat domain containing"	26204	protein-coding gene	gene with protein product							Standard	NM_024525		Approved	FLJ22584	uc001huf.4	Q8NBP0	OTTHUMG00000037788	ENST00000366661.4:c.2300G>C	chr1.hg19:g.231047225C>G	ENSP00000355621:p.Arg767Pro	525.0	0.0		1011.0	101.0	NM_024525	B1AQI1|B1AQI2|Q8IVP8|Q8NBI0|Q8ND20	Missense_Mutation	SNP	ENST00000366661.4	hg19	CCDS1588.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.725840	0.89298	.	.	ENSG00000143643	ENST00000366661;ENST00000366662;ENST00000414259	T;T;T	0.64260	-0.09;0.02;0.03	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.80297	0.4597	M	0.74647	2.275	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.91635	0.999;0.995;0.999;0.999	T	0.82032	-0.0658	10	0.87932	D	0	-14.7544	19.4157	0.94697	0.0:1.0:0.0:0.0	.	692;714;713;767	Q69YR0;E9PGV4;Q8NBP0-2;Q8NBP0	.;.;.;TTC13_HUMAN	P	767;713;714	ENSP00000355621:R767P;ENSP00000355622:R713P;ENSP00000416631:R714P	ENSP00000355621:R767P	R	-	2	0	TTC13	229113848	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.178000	0.77657	2.655000	0.90218	0.591000	0.81541	CGA	.	.		0.308	TTC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092229.2	NM_024525		G	231047225	C	G	231047225	3	3	303	1	0	0	0	0	1	0	0	0	16695	884	31	4	298	4	TTC13	1	231047225	Missense_Mutation	SNP	C	TCGA-G3-AAV7-01A-11D-A382-10	44958811	231047225	18203396	15	43608										
SNTG2	54221	hgsc.bcm.edu	37	chr2	1241734	1241734	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	gttttacacagcccaggatgGcaccgactggctgcgggcgg	15	12	0	0			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr2:1241734G>T	ENST00000308624.5	+	10	923	c.794G>T	c.(793-795)gGc>gTc	p.G265V	SNTG2_ENST00000407292.1_Missense_Mutation_p.G138V	NM_018968.3	NP_061841.2	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2	265					central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|syntrophin complex (GO:0016013)	PDZ domain binding (GO:0030165)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		GCCCAGGATGGCACCGACTGG	0.602																																					p.G265V		Atlas-SNP	.											.	SNTG2	125	.	0			c.G794T						.						35	40	39					2																	1241734		2194	4294	6488	SO:0001583	missense	54221	exon10			AGGATGGCACCGA	AJ003029	CCDS46220.1	2p25	2008-05-23			ENSG00000172554	ENSG00000172554			13741	protein-coding gene	gene with protein product		608715				10747910	Standard	NM_018968		Approved	SYN5, G2SYN	uc002qwq.3	Q9NY99	OTTHUMG00000151370	ENST00000308624.5:c.794G>T	chr2.hg19:g.1241734G>T	ENSP00000311837:p.Gly265Val	51.0	0.0		36.0	18.0	NM_018968	Q05AH5	Missense_Mutation	SNP	ENST00000308624.5	hg19	CCDS46220.1	.	.	.	.	.	.	.	.	.	.	G	6.878	0.531504	0.13127	.	.	ENSG00000172554	ENST00000308624;ENST00000407292	T;T	0.54675	0.56;0.56	4.68	3.8	0.43715	.	0.282778	0.44097	D	0.000496	T	0.31358	0.0794	N	0.14661	0.345	0.40631	D	0.981858	B;B	0.34015	0.435;0.112	B;B	0.28139	0.086;0.039	T	0.13019	-1.0525	10	0.30854	T	0.27	.	11.1991	0.48730	0.0923:0.0:0.9077:0.0	.	138;265	Q9NY99-2;Q9NY99	.;SNTG2_HUMAN	V	265;138	ENSP00000311837:G265V;ENSP00000385020:G138V	ENSP00000311837:G265V	G	+	2	0	SNTG2	1224285	0.997000	0.39634	0.005000	0.12908	0.076000	0.17211	2.665000	0.46791	1.083000	0.41159	0.655000	0.94253	GGC	.	.		0.602	SNTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322454.1	NM_018968		T	1241734	G	T	1241734	3	4	303	1	0	0	0	0	1	0	0	0	14890	1203	42	3	832	3	SNTG2	2	1241734	Missense_Mutation	SNP	G	TCGA-G3-AAV7-01A-11D-A382-10		1241734	241957639	16	43609										
BIRC6	57448	hgsc.bcm.edu	37	chr2	32703821	32703821	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	aactgacttcaatagaggagAtatatcttggggtggtgctt	12	5	2	3			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr2:32703821A>G	ENST00000421745.2	+	36	7321	c.7187A>G	c.(7186-7188)gAt>gGt	p.D2396G		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	2396					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					AATAGAGGAGATATATCTTGG	0.418																																					p.D2396G	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.A7187G						.						185	170	175					2																	32703821		2203	4300	6503	SO:0001583	missense	57448	exon36			GAGGAGATATATC	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.7187A>G	chr2.hg19:g.32703821A>G	ENSP00000393596:p.Asp2396Gly	115.0	0.0		100.0	11.0	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	hg19	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	A	22.3	4.273759	0.80580	.	.	ENSG00000115760	ENST00000421745	T	0.78126	-1.15	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.71187	0.3310	N	0.24115	0.695	0.54753	D	0.999981	P	0.51791	0.948	P	0.46237	0.508	T	0.76143	-0.3067	10	0.66056	D	0.02	.	15.3129	0.74048	1.0:0.0:0.0:0.0	.	2396	Q9NR09	BIRC6_HUMAN	G	2396	ENSP00000393596:D2396G	ENSP00000393596:D2396G	D	+	2	0	BIRC6	32557325	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.179000	0.77665	2.012000	0.59069	0.533000	0.62120	GAT	.	.		0.418	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		G	32703821	A	G	32703821	3	3	303	1	0	0	0	0	1	0	0	0	1438	333	12	2	7329	2	BIRC6	2	32703821	Missense_Mutation	SNP	A	TCGA-G3-AAV7-01A-11D-A382-10	31462087	32703821	210495552	17	43610										
FSIP2	401024	hgsc.bcm.edu	37	chr2	186670171	186670171	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	aaagtaacattgctatagggAtgattgctgctctaacccag	9	8	1	1			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr2:186670171A>G	ENST00000424728.1	+	17	16138	c.16138A>G	c.(16138-16140)Atg>Gtg	p.M5380V	FSIP2_ENST00000343098.5_Missense_Mutation_p.M5469V			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	5380										NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						TGCTATAGGGATGATTGCTGC	0.353																																					p.M5469V		Atlas-SNP	.											.	FSIP2	251	.	0			c.A16405G						.						112	103	106					2																	186670171		1870	4092	5962	SO:0001583	missense	401024	exon17			ATAGGGATGATTG	AK092099	CCDS54426.1	2q32.1	2010-06-18			ENSG00000188738	ENSG00000188738			21675	protein-coding gene	gene with protein product		615796				14702039	Standard	NM_173651		Approved	FLJ34780	uc002upl.3	Q5CZC0	OTTHUMG00000153874	ENST00000424728.1:c.16138A>G	chr2.hg19:g.186670171A>G	ENSP00000401306:p.Met5380Val	338.0	0.0		247.0	109.0	NM_173651	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Missense_Mutation	SNP	ENST00000424728.1	hg19		.	.	.	.	.	.	.	.	.	.	A	5.854	0.341798	0.11069	.	.	ENSG00000188738	ENST00000343098;ENST00000424728	T;T	0.46063	0.88;0.88	5.28	2.9	0.33743	.	.	.	.	.	T	0.30854	0.0778	L	0.29908	0.895	0.21105	N	0.999787	.	.	.	.	.	.	T	0.20273	-1.0280	7	0.27785	T	0.31	.	6.5993	0.22691	0.8126:0.0:0.1874:0.0	.	.	.	.	V	5469;5380	ENSP00000344403:M5469V;ENSP00000401306:M5380V	ENSP00000344403:M5469V	M	+	1	0	FSIP2	186378416	0.991000	0.36638	0.851000	0.33527	0.076000	0.17211	1.404000	0.34623	0.462000	0.27095	0.377000	0.23210	ATG	.	.		0.353	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651		G	186670171	A	G	186670171	3	3	303	1	0	0	0	0	1	0	0	0	6083	333	12	2	16471	2	FSIP2	2	186670171	Missense_Mutation	SNP	A	TCGA-G3-AAV7-01A-11D-A382-10	153966350	186670171	56529202	18	43611										
PLCL1	5334	hgsc.bcm.edu	37	chr2	198950089	198950089	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	tgggaaatgtgttcatttagTgaaacagaggccagccgcat	12	7	1	2			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr2:198950089T>C	ENST00000428675.1	+	2	2246	c.1848T>C	c.(1846-1848)agT>agC	p.S616S	PLCL1_ENST00000437704.2_Silent_p.S518S	NM_006226.3	NP_006217.3	Q15111	PLCL1_HUMAN	phospholipase C-like 1	616	PI-PLC Y-box. {ECO:0000255|PROSITE- ProRule:PRU00271}.				gamma-aminobutyric acid signaling pathway (GO:0007214)|intracellular signal transduction (GO:0035556)|lipid metabolic process (GO:0006629)|positive regulation of receptor binding (GO:1900122)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|inositol 1,4,5 trisphosphate binding (GO:0070679)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(14)|lung(44)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	80					Quinacrine(DB01103)	GTTCATTTAGTGAAACAGAGG	0.373																																					p.S616S		Atlas-SNP	.											.	PLCL1	358	.	0			c.T1848C						.						50	53	52					2																	198950089		2201	4300	6501	SO:0001819	synonymous_variant	5334	exon2			ATTTAGTGAAACA	D42108	CCDS2326.1, CCDS2326.2	2q33	2014-06-13	2002-02-18	2002-02-22	ENSG00000115896	ENSG00000115896			9063	protein-coding gene	gene with protein product	"phospholipase C related, but catalytically inactive protein", "protein phosphatase 1, regulatory subunit 127"	600597	"phospholipase C, epsilon"	PLCE		7633416	Standard	NM_006226		Approved	PLC-L, PLCL, PRIP, PPP1R127	uc010fsp.3	Q15111	OTTHUMG00000132750	ENST00000428675.1:c.1848T>C	chr2.hg19:g.198950089T>C		122.0	0.0		71.0	5.0	NM_006226	Q3MJ90|Q53SD3|Q7Z3S3	Silent	SNP	ENST00000428675.1	hg19	CCDS2326.2																																																																																			.	.		0.373	PLCL1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340210.1	NM_006226		C	198950089	T	C	198950089	2	2	303	1	0	0	0	0	0	0	0	1	12048	1693	59	2		2	PLCL1	2	198950089	Silent	SNP	T	TCGA-G3-AAV7-01A-11D-A382-10	12279918	198950089	44249284	19	43612										
NBEAL1	65065	hgsc.bcm.edu	37	chr2	204009854	204009854	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	atatgcataaacgagaccggGaaggaggggaaagcaagctc	14	7	0	1	rs369975893		TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr2:204009854G>A	ENST00000449802.1	+	32	5521	c.5188G>A	c.(5188-5190)Gaa>Aaa	p.E1730K		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	1730										NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						ACGAGACCGGGAAGGAGGGGA	0.323																																					p.E1730K		Atlas-SNP	.											.	NBEAL1	266	.	0			c.G5188A						.	G	LYS/GLU	1,3659		0,1,1829	103	98	100		5188	4.6	1	2		100	0,8160		0,0,4080	no	missense	NBEAL1	NM_001114132.1	56	0,1,5909	AA,AG,GG		0.0,0.0273,0.0085	possibly-damaging	1730/2695	204009854	1,11819	1830	4080	5910	SO:0001583	missense	65065	exon32			GACCGGGAAGGAG	AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"WD repeat domain containing"	20681	protein-coding gene	gene with protein product		609816	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17", "amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.5188G>A	chr2.hg19:g.204009854G>A	ENSP00000399903:p.Glu1730Lys	135.0	0.0		115.0	7.0	NM_001114132	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Missense_Mutation	SNP	ENST00000449802.1	hg19	CCDS46495.1	.	.	.	.	.	.	.	.	.	.	G	19.32	3.805363	0.70682	2.73E-4	0.0	ENSG00000144426	ENST00000449802;ENST00000340268	T	0.58506	0.33	5.49	4.6	0.57074	.	0.254943	0.45606	D	0.000359	T	0.58438	0.2122	M	0.72894	2.215	0.58432	D	0.999997	B;B	0.21606	0.058;0.058	B;B	0.23275	0.045;0.045	T	0.57608	-0.7782	10	0.39692	T	0.17	.	15.5608	0.76244	0.0:0.0:0.8606:0.1394	.	1730;1719	Q6ZS30;C9JGK5	NBEL1_HUMAN;.	K	1730	ENSP00000399903:E1730K	ENSP00000344985:E1730K	E	+	1	0	NBEAL1	203718099	1.000000	0.71417	0.999000	0.59377	0.987000	0.75469	9.452000	0.97615	1.432000	0.47375	0.650000	0.86243	GAA	.	.		0.323	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4			A	204009854	G	A	204009854	3	1	303	1	0	0	0	0	1	0	0	0	10197	1175	41	3	5310	3	NBEAL1	2	204009854	Missense_Mutation	SNP	G	TCGA-G3-AAV7-01A-11D-A382-10	5059765	204009854	39189519	20	43613										
C3orf20	84077	hgsc.bcm.edu	37	chr3	14724699	14724699	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	gaaggccatggtggagtctaTgtcgggtaaggcccagatgt	16	7	1	1			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr3:14724699T>C	ENST00000253697.3	+	3	931	c.479T>C	c.(478-480)aTg>aCg	p.M160T	C3orf20_ENST00000435614.1_Missense_Mutation_p.M38T|C3orf20_ENST00000412910.1_Missense_Mutation_p.M38T	NM_032137.4	NP_115513.4	Q8ND61	CC020_HUMAN	chromosome 3 open reading frame 20	160						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(13)|lung(11)|ovary(4)|skin(2)	40						GTGGAGTCTATGTCGGGTAAG	0.582																																					p.M160T		Atlas-SNP	.											.	C3orf20	109	.	0			c.T479C						.						103	93	96					3																	14724699		2201	4298	6499	SO:0001583	missense	84077	exon3			AGTCTATGTCGGG	AL136781	CCDS33706.1, CCDS54555.1	3p25.1	2011-01-25			ENSG00000131379	ENSG00000131379			25320	protein-coding gene	gene with protein product						11230166	Standard	NM_032137		Approved	DKFZP434N1817	uc003byy.3	Q8ND61	OTTHUMG00000155545	ENST00000253697.3:c.479T>C	chr3.hg19:g.14724699T>C	ENSP00000253697:p.Met160Thr	75.0	0.0		101.0	36.0	NM_032137	Q7L0U6|Q8NCP2|Q9H0I7	Missense_Mutation	SNP	ENST00000253697.3	hg19	CCDS33706.1	.	.	.	.	.	.	.	.	.	.	T	10.21	1.286714	0.23478	.	.	ENSG00000131379	ENST00000253697;ENST00000435614;ENST00000412910	T;T;T	0.07567	3.47;3.18;3.18	4.93	0.128	0.14733	.	1.294780	0.05712	N	0.596087	T	0.05364	0.0142	N	0.19112	0.55	0.09310	N	1	B	0.21452	0.056	B	0.18561	0.022	T	0.43750	-0.9372	10	0.27082	T	0.32	-1.873	3.9665	0.09434	0.178:0.2562:0.0:0.5658	.	160	Q8ND61	CC020_HUMAN	T	160;38;38	ENSP00000253697:M160T;ENSP00000402933:M38T;ENSP00000396081:M38T	ENSP00000253697:M160T	M	+	2	0	C3orf20	14699703	0.000000	0.05858	0.004000	0.12327	0.546000	0.35178	0.087000	0.14958	-0.003000	0.14444	0.482000	0.46254	ATG	.	.		0.582	C3orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340586.1	NM_032137		C	14724699	T	C	14724699	3	2	303	1	0	0	0	0	1	0	0	0	2215	1464	51	2	481	2	C3orf20	3	14724699	Missense_Mutation	SNP	T	TCGA-G3-AAV7-01A-11D-A382-10		14724699	183297731	21	43614										
SGOL1	151648	hgsc.bcm.edu	37	chr3	20225381	20225381	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	acataaaaatctcttactgaTtatttggcatggtgcagcta	7	7	1	1			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr3:20225381T>C	ENST00000263753.4	-	2	278	c.139A>G	c.(139-141)Atc>Gtc	p.I47V	SGOL1_ENST00000452020.1_Missense_Mutation_p.I47V|SGOL1-AS1_ENST00000448208.1_RNA|SGOL1_ENST00000419233.2_Missense_Mutation_p.I47V|SGOL1_ENST00000412868.1_Missense_Mutation_p.I47V|SGOL1_ENST00000437051.1_Missense_Mutation_p.I47V|SGOL1_ENST00000412997.1_Missense_Mutation_p.I47V|SGOL1_ENST00000421451.1_Missense_Mutation_p.I47V|SGOL1_ENST00000417364.1_Missense_Mutation_p.I47V|SGOL1-AS1_ENST00000441442.1_RNA|SGOL1_ENST00000443724.1_Missense_Mutation_p.I47V|SGOL1_ENST00000442720.1_Missense_Mutation_p.I47V|SGOL1_ENST00000429446.3_Missense_Mutation_p.I47V|SGOL1_ENST00000425061.1_Missense_Mutation_p.I47V|SGOL1_ENST00000306698.2_Missense_Mutation_p.I47V|SGOL1_ENST00000383774.1_Missense_Mutation_p.I47V	NM_001012410.3|NM_001199252.1	NP_001012410.1|NP_001186181.1	Q5FBB7	SGOL1_HUMAN	shugoshin-like 1 (S. pombe)	47	Necessary for interaction with PPP2CA and PPP2R1A.				attachment of spindle microtubules to kinetochore (GO:0008608)|centriole-centriole cohesion (GO:0010457)|chromosome segregation (GO:0007059)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|chromosome, centromeric region (GO:0000775)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)|spindle pole (GO:0000922)	kinase binding (GO:0019900)			kidney(1)|large_intestine(4)|lung(6)|skin(1)|urinary_tract(2)	14						CTCTTACTGATTATTTGGCAT	0.313																																					p.I47V		Atlas-SNP	.											.	SGOL1	55	.	0			c.A139G						.						95	95	95					3																	20225381		2203	4300	6503	SO:0001583	missense	151648	exon2			TACTGATTATTTG	BC001339	CCDS2635.1, CCDS33716.1, CCDS46771.1, CCDS46772.1, CCDS46773.1, CCDS46774.1, CCDS56243.1	3p24.3	2005-07-27			ENSG00000129810	ENSG00000129810			25088	protein-coding gene	gene with protein product		609168				12747765	Standard	NM_001199251		Approved	NY-BR-85	uc003cbu.3	Q5FBB7	OTTHUMG00000130479	ENST00000263753.4:c.139A>G	chr3.hg19:g.20225381T>C	ENSP00000263753:p.Ile47Val	105.0	0.0		99.0	34.0	NM_001199253	Q588H5|Q5FBB4|Q5FBB5|Q5FBB6|Q5FBB8|Q8N579|Q8WVL0|Q9BVA8|Q9H275	Missense_Mutation	SNP	ENST00000263753.4	hg19	CCDS33716.1	.	.	.	.	.	.	.	.	.	.	T	1.982	-0.433940	0.04669	.	.	ENSG00000129810	ENST00000306698;ENST00000419233;ENST00000263753;ENST00000383774;ENST00000425061;ENST00000443724;ENST00000421451;ENST00000452020;ENST00000442720;ENST00000412997;ENST00000437051;ENST00000412868;ENST00000429446;ENST00000417364	T;T;T;T;T;T;T;T;T;T	0.46063	0.88;2.98;0.93;0.88;0.93;2.98;1.49;0.89;1.49;0.89	5.53	-1.58	0.08479	Shugoshin, N-terminal (1);	1.230160	0.05183	N	0.501710	T	0.32645	0.0836	L	0.34521	1.04	0.09310	N	1	B;P;B;P;B;B;B	0.43412	0.114;0.454;0.114;0.806;0.114;0.27;0.114	B;B;B;P;B;B;B	0.44647	0.053;0.192;0.053;0.456;0.053;0.192;0.053	T	0.18493	-1.0335	10	0.30078	T	0.28	.	3.7402	0.08527	0.1082:0.1351:0.4447:0.312	.	47;47;47;47;47;47;47	Q5FBB7-7;B5BUA4;Q5FBB7-5;Q5FBB7-4;Q5FBB7-2;Q5FBB7;Q5FBB7-3	.;.;.;.;.;SGOL1_HUMAN;.	V	47	ENSP00000394625:I47V;ENSP00000263753:I47V;ENSP00000373284:I47V;ENSP00000414960:I47V;ENSP00000413070:I47V;ENSP00000414129:I47V;ENSP00000410458:I47V;ENSP00000389034:I47V;ENSP00000406880:I47V;ENSP00000394613:I47V	ENSP00000263753:I47V	I	-	1	0	SGOL1	20200385	0.024000	0.19004	0.000000	0.03702	0.012000	0.07955	0.342000	0.19926	-0.403000	0.07622	0.533000	0.62120	ATC	.	.		0.313	SGOL1-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000340498.1	NM_138484		C	20225381	T	C	20225381	3	2	303	1	0	0	0	0	1	0	0	0	14231	1493	52	2	1598	2	SGOL1	3	20225381	Missense_Mutation	SNP	T	TCGA-G3-AAV7-01A-11D-A382-10	5500682	20225381	177797049	22	43615										
MYRIP	25924	hgsc.bcm.edu	37	chr3	40251524	40251524	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	cccaagacagaatctgagaaCcagaaggaaagtctgtcctc	9	11	2	4			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr3:40251524C>A	ENST00000302541.6	+	11	2187	c.1845C>A	c.(1843-1845)aaC>aaA	p.N615K	RN7SL411P_ENST00000585204.1_RNA|MYRIP_ENST00000459828.1_3'UTR|MYRIP_ENST00000425621.1_Missense_Mutation_p.N615K|MYRIP_ENST00000396217.3_Missense_Mutation_p.N526K|MYRIP_ENST00000539167.1_Missense_Mutation_p.N428K|MYRIP_ENST00000444716.1_Missense_Mutation_p.N615K	NM_001284423.1|NM_001284426.1|NM_015460.2	NP_001271352.1|NP_001271355.1|NP_056275.2	Q8NFW9	MYRIP_HUMAN	myosin VIIA and Rab interacting protein	615	Actin-binding.				intracellular protein transport (GO:0006886)|positive regulation of insulin secretion (GO:0032024)	actin cytoskeleton (GO:0015629)|dense core granule (GO:0031045)|exocyst (GO:0000145)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)|photoreceptor outer segment (GO:0001750)|synapse (GO:0045202)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(2)|lung(10)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				KIRC - Kidney renal clear cell carcinoma(284;0.174)|Kidney(284;0.206)		AATCTGAGAACCAGAAGGAAA	0.493																																					p.N615K		Atlas-SNP	.											.	MYRIP	98	.	0			c.C1845A						.						58	57	57					3																	40251524		2203	4300	6503	SO:0001583	missense	25924	exon11			TGAGAACCAGAAG	AF396687	CCDS2689.1, CCDS68390.1, CCDS68391.1, CCDS68392.1	3p21.33	2010-08-20			ENSG00000170011	ENSG00000170011		"A-kinase anchor proteins"	19156	protein-coding gene	gene with protein product	"synaptotagmin-like protein homologue lacking C2 domains-c", "rab effector MYRIP", "Slp homologue lacking C2 domains"	611790				11964381, 12221080	Standard	NM_001284425		Approved	DKFZp586F1018, exophilin-8, MyRIP, SLAC2-C, SLAC2C	uc003cka.3	Q8NFW9	OTTHUMG00000131392	ENST00000302541.6:c.1845C>A	chr3.hg19:g.40251524C>A	ENSP00000301972:p.Asn615Lys	284.0	0.0		345.0	114.0	NM_015460	B3KWM3|B3KWW4|B7Z2H1|B7Z9V3|G3XAI8|Q32M41|Q32M42|Q569F7|Q8IUF5|Q9Y3V4	Missense_Mutation	SNP	ENST00000302541.6	hg19	CCDS2689.1	.	.	.	.	.	.	.	.	.	.	C	13.89	2.370859	0.42003	.	.	ENSG00000170011	ENST00000444716;ENST00000302541;ENST00000425621;ENST00000396217;ENST00000539167	T;T;T;T;T	0.25579	1.79;1.79;1.79;1.79;1.79	5.52	0.972	0.19704	Myelin-associated oligodendrocytic basic protein (MOBP) (1);	0.735153	0.12786	N	0.439242	T	0.30355	0.0762	L	0.55481	1.735	0.36855	D	0.888095	P;P;B	0.48834	0.916;0.634;0.04	P;B;B	0.51701	0.677;0.124;0.025	T	0.29397	-1.0013	9	.	.	.	.	5.6033	0.17365	0.0:0.5718:0.1492:0.279	.	526;615;615	Q32M42;G3XAI8;Q8NFW9	.;.;MYRIP_HUMAN	K	615;615;615;526;428	ENSP00000398665:N615K;ENSP00000301972:N615K;ENSP00000389323:N615K;ENSP00000379519:N526K;ENSP00000438297:N428K	.	N	+	3	2	MYRIP	40226528	0.190000	0.23276	0.997000	0.53966	0.999000	0.98932	-0.038000	0.12144	0.248000	0.21435	0.655000	0.94253	AAC	.	.		0.493	MYRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254181.2	NM_015460		A	40251524	C	A	40251524	3	1	303	1	0	0	0	0	1	0	0	0	10109	506	18	3	1883	3	MYRIP	3	40251524	Missense_Mutation	SNP	C	TCGA-G3-AAV7-01A-11D-A382-10	20026143	40251524	157770906	23	43616										
TRAK1	22906	hgsc.bcm.edu	37	chr3	42236385	42236385	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	aacctccggaacaaaaccatGcccaataccacgtctcggcg	7	16	1	0			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr3:42236385G>C	ENST00000327628.5	+	10	1465	c.1065G>C	c.(1063-1065)atG>atC	p.M355I	TRAK1_ENST00000396175.1_Missense_Mutation_p.M297I|TRAK1_ENST00000341421.3_Missense_Mutation_p.M297I|TRAK1_ENST00000449246.1_Missense_Mutation_p.M281I|TRAK1_ENST00000487159.1_3'UTR	NM_001042646.2	NP_001036111.1	Q9UPV9	TRAK1_HUMAN	trafficking protein, kinesin binding 1	355					endosome to lysosome transport (GO:0008333)|protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	22						ACAAAACCATGCCCAATACCA	0.592																																					p.M355I	GBM(44;195 884 22595 31865 41850)	Atlas-SNP	.											.	TRAK1	188	.	0			c.G1065C						.						139	101	114					3																	42236385		2203	4300	6503	SO:0001583	missense	22906	exon10			AACCATGCCCAAT		CCDS2695.1, CCDS43072.1, CCDS58826.1, CCDS74922.1	3p22.1	2012-03-05			ENSG00000182606	ENSG00000182606			29947	protein-coding gene	gene with protein product	"OGT(O Glc NAc transferase) interacting protein 106 KDa", "O-linked N-acetylglucosamine transferase interacting protein 106", "milton homolog 1 (Drosophila)"	608112				10470851, 12435728, 16380713, 20230862	Standard	NM_014965		Approved	OIP106, KIAA1042, MILT1	uc003cky.4	Q9UPV9	OTTHUMG00000131795	ENST00000327628.5:c.1065G>C	chr3.hg19:g.42236385G>C	ENSP00000328998:p.Met355Ile	91.0	0.0		113.0	31.0	NM_001265608	E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	Missense_Mutation	SNP	ENST00000327628.5	hg19	CCDS43072.1	.	.	.	.	.	.	.	.	.	.	G	13.95	2.391120	0.42410	.	.	ENSG00000182606	ENST00000327628;ENST00000543338;ENST00000449246;ENST00000396175;ENST00000341421;ENST00000427771	T;T;T;T;T	0.14516	3.09;3.05;3.08;3.07;2.5	6.06	6.06	0.98353	.	0.180581	0.64402	D	0.000017	T	0.14874	0.0359	L	0.44542	1.39	0.43555	D	0.995862	B;B;B;B;B;B	0.25850	0.051;0.002;0.003;0.032;0.136;0.002	B;B;B;B;B;B	0.20577	0.01;0.002;0.006;0.013;0.03;0.003	T	0.07790	-1.0754	10	0.20046	T	0.44	.	19.609	0.95594	0.0:0.0:1.0:0.0	.	281;297;355;297;281;355	B7Z218;C9JC32;B7Z347;Q9UPV9-2;E9PDS2;Q9UPV9	.;.;.;.;.;TRAK1_HUMAN	I	355;355;281;297;297;73	ENSP00000328998:M355I;ENSP00000410717:M281I;ENSP00000379478:M297I;ENSP00000340702:M297I;ENSP00000413729:M73I	ENSP00000328998:M355I	M	+	3	0	TRAK1	42211389	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	5.053000	0.64269	2.882000	0.98803	0.655000	0.94253	ATG	.	.		0.592	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343413.1	NM_014965		C	42236385	G	C	42236385	3	2	303	1	0	0	0	0	1	0	0	0	16464	1319	46	4	1219	4	TRAK1	3	42236385	Missense_Mutation	SNP	G	TCGA-G3-AAV7-01A-11D-A382-10	1984861	42236385	155786045	24	43617										
HYAL1	3373	hgsc.bcm.edu	37	chr3	50339584	50339584	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	gccacagccacacggaatgcCtcggccacacggtgttgcac	11	16	0	0			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr3:50339584C>G	ENST00000266031.4	-	1	1419	c.804G>C	c.(802-804)gaG>gaC	p.E268D	HYAL3_ENST00000336307.1_5'Flank|NAT6_ENST00000354862.4_5'Flank|HYAL1_ENST00000395144.2_Missense_Mutation_p.E268D|NAT6_ENST00000443842.1_5'Flank|HYAL3_ENST00000513170.1_5'Flank|HYAL1_ENST00000320295.8_Missense_Mutation_p.E268D|HYAL3_ENST00000415204.1_5'Flank|HYAL1_ENST00000447605.2_Missense_Mutation_p.E9D|HYAL3_ENST00000450982.1_5'Flank|HYAL1_ENST00000395143.2_Missense_Mutation_p.E268D|HYAL1_ENST00000457214.2_Missense_Mutation_p.E86D|NAT6_ENST00000443094.2_5'Flank			Q12794	HYAL1_HUMAN	hyaluronoglucosaminidase 1	268			E -> K (in MPS9). {ECO:0000269|PubMed:10339581}.		carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to interleukin-1 (GO:0071347)|cellular response to pH (GO:0071467)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to UV-B (GO:0071493)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal joint morphogenesis (GO:0060272)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|inflammatory response (GO:0006954)|negative regulation of cell growth (GO:0030308)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of growth (GO:0045927)|positive regulation of hyaluranon cable assembly (GO:1900106)|response to antibiotic (GO:0046677)|response to reactive oxygen species (GO:0000302)|response to virus (GO:0009615)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|hyaluranon cable (GO:0036117)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	hyaluronan synthase activity (GO:0050501)|hyalurononglucosaminidase activity (GO:0004415)|transcription factor binding (GO:0008134)			cervix(1)|endometrium(2)|large_intestine(1)|lung(6)|prostate(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		CACGGAATGCCTCGGCCACAC	0.592																																					p.E268D		Atlas-SNP	.											.	HYAL1	28	.	0			c.G804C						.						83	79	80					3																	50339584		2203	4300	6503	SO:0001583	missense	3373	exon2			GAATGCCTCGGCC	U90094	CCDS2816.1, CCDS2817.1, CCDS46832.1, CCDS46833.1	3p21.31	2014-07-17			ENSG00000114378	ENSG00000114378	3.2.1.35		5320	protein-coding gene	gene with protein product		607071				9223416, 9409739	Standard	NM_153281		Approved	LUCA1, HYAL-1, FUS2, NAT6	uc003czp.4	Q12794	OTTHUMG00000156941	ENST00000266031.4:c.804G>C	chr3.hg19:g.50339584C>G	ENSP00000266031:p.Glu268Asp	293.0	0.0		367.0	116.0	NM_033159	Q6FH23|Q6PIZ6|Q7KYU2|Q7LE34|Q8NFK5|Q8NFK6|Q8NFK7|Q8NFK8|Q8NFK9|Q93013|Q9UKD5|Q9UNI8	Missense_Mutation	SNP	ENST00000266031.4	hg19	CCDS2816.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.516568	0.85495	.	.	ENSG00000114378	ENST00000395144;ENST00000266031;ENST00000320295;ENST00000395143;ENST00000457214;ENST00000447605	T;T;T;T;T;T	0.56275	0.47;0.47;0.47;0.47;0.47;0.47	5.46	4.59	0.56863	Aldolase-type TIM barrel (1);Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	T	0.78767	0.4335	H	0.94698	3.57	0.44780	D	0.997789	D;D;D	0.89917	0.962;1.0;0.998	P;D;D	0.72625	0.64;0.978;0.938	D	0.84551	0.0644	10	0.87932	D	0	-26.9725	13.1397	0.59428	0.0:0.9219:0.0:0.0781	.	268;268;268	Q12794-7;Q12794-2;Q12794	.;.;HYAL1_HUMAN	D	268;268;268;268;86;9	ENSP00000378576:E268D;ENSP00000266031:E268D;ENSP00000346068:E268D;ENSP00000378575:E268D;ENSP00000393358:E86D;ENSP00000390149:E9D	ENSP00000266031:E268D	E	-	3	2	HYAL1	50314588	1.000000	0.71417	1.000000	0.80357	0.784000	0.44337	3.629000	0.54266	1.322000	0.45245	0.655000	0.94253	GAG	.	.		0.592	HYAL1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346703.1			G	50339584	C	G	50339584	3	3	303	1	0	0	0	0	1	0	0	0	7472	680	24	4	515	4	HYAL1	3	50339584	Missense_Mutation	SNP	C	TCGA-G3-AAV7-01A-11D-A382-10	8103199	50339584	147682846	25	43618										
TRPC1	7220	hgsc.bcm.edu	37	chr3	142467157	142467157	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	caactatggatgttgcacctGtcattttagctgctcatcgt	8	10	2	0			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr3:142467157G>A	ENST00000476941.1	+	4	973	c.487G>A	c.(487-489)Gtc>Atc	p.V163I	TRPC1_ENST00000273482.6_Missense_Mutation_p.V129I	NM_001251845.1	NP_001238774.1	P48995	TRPC1_HUMAN	transient receptor potential cation channel, subfamily C, member 1	163					axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|response to calcium ion (GO:0051592)|saliva secretion (GO:0046541)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|sarcomere (GO:0030017)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|inositol 1,4,5 trisphosphate binding (GO:0070679)|ion channel binding (GO:0044325)|store-operated calcium channel activity (GO:0015279)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(2)|stomach(3)|urinary_tract(1)	37						TGTTGCACCTGTCATTTTAGC	0.358																																					p.V163I		Atlas-SNP	.											.	TRPC1	82	.	0			c.G487A						.						124	125	125					3																	142467157		2203	4300	6503	SO:0001583	missense	7220	exon4			GCACCTGTCATTT	X89066	CCDS3126.1, CCDS58856.1	3q23	2011-12-14			ENSG00000144935	ENSG00000144935		"Voltage-gated ion channels / Transient receptor potential cation channels"	12333	protein-coding gene	gene with protein product		602343				7568191, 16382100	Standard	NM_001251845		Approved	HTRP-1	uc003evc.3	P48995	OTTHUMG00000159301	ENST00000476941.1:c.487G>A	chr3.hg19:g.142467157G>A	ENSP00000419313:p.Val163Ile	212.0	0.0		243.0	78.0	NM_001251845	Q14CE4	Missense_Mutation	SNP	ENST00000476941.1	hg19	CCDS58856.1	.	.	.	.	.	.	.	.	.	.	G	13.47	2.247341	0.39697	.	.	ENSG00000144935	ENST00000476941;ENST00000273482	T;T	0.63255	0.7;-0.03	5.59	5.59	0.84812	Ankyrin repeat-containing domain (2);	0.000000	0.85682	D	0.000000	T	0.61110	0.2321	N	0.11651	0.15	0.80722	D	1	D;P	0.63046	0.992;0.51	D;B	0.77004	0.989;0.147	T	0.54450	-0.8292	10	0.05833	T	0.94	-29.8276	19.5934	0.95525	0.0:0.0:1.0:0.0	.	163;129	P48995;P48995-2	TRPC1_HUMAN;.	I	163;129	ENSP00000419313:V163I;ENSP00000273482:V129I	ENSP00000273482:V129I	V	+	1	0	TRPC1	143949847	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	9.441000	0.97557	2.641000	0.89580	0.460000	0.39030	GTC	.	.		0.358	TRPC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354520.1	NM_003304		A	142467157	G	A	142467157	3	1	303	1	0	0	0	0	1	0	0	0	16593	1377	48	3	395	3	TRPC1	3	142467157	Missense_Mutation	SNP	G	TCGA-G3-AAV7-01A-11D-A382-10	92127573	142467157	55555273	26	43619										
MSX1	4487	hgsc.bcm.edu	37	chr4	4861842	4861842	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	ctcatggccgaccacaggaaGccgggggccaaggagagcgc	16	13	1	1			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr4:4861842G>A	ENST00000382723.4	+	1	450	c.216G>A	c.(214-216)aaG>aaA	p.K72K		NM_002448.3	NP_002439.2	P28360	MSX1_HUMAN	msh homeobox 1	72					activation of meiosis (GO:0090427)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway involved in heart development (GO:0061312)|bone morphogenesis (GO:0060349)|cartilage morphogenesis (GO:0060536)|cell morphogenesis (GO:0000902)|cellular response to nicotine (GO:0071316)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic nail plate morphogenesis (GO:0035880)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|mammary gland epithelium development (GO:0061180)|mesenchymal cell proliferation (GO:0010463)|midbrain development (GO:0030901)|middle ear morphogenesis (GO:0042474)|muscle organ development (GO:0007517)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pituitary gland development (GO:0021983)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator (GO:1902255)|positive regulation of mesenchymal cell apoptotic process (GO:2001055)|protein localization to nucleus (GO:0034504)|protein stabilization (GO:0050821)|regulation of odontogenesis (GO:0042481)|signal transduction involved in regulation of gene expression (GO:0023019)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	p53 binding (GO:0002039)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			endometrium(3)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	11				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		ACCACAGGAAGCCGGGGGCCA	0.761																																					p.K72K		Atlas-SNP	.											.	MSX1	19	.	0			c.G216A						.						7	8	7					4																	4861842		1578	2871	4449	SO:0001819	synonymous_variant	4487	exon1			CAGGAAGCCGGGG	M97676	CCDS3378.2	4p16.2	2011-06-20	2006-11-21		ENSG00000163132	ENSG00000163132		"Homeoboxes / ANTP class : NKL subclass"	7391	protein-coding gene	gene with protein product		142983	"msh (Drosophila) homeo box homolog 1 (formerly homeo box 7)", "msh homeobox homolog 1 (Drosophila)"	HOX7		1685479, 1973146	Standard	NM_002448		Approved	HYD1, OFC5	uc003gif.3	P28360	OTTHUMG00000090335	ENST00000382723.4:c.216G>A	chr4.hg19:g.4861842G>A		805.0	0.0		1014.0	281.0	NM_002448	A0SZU5|A8K3M1|Q96NY4	Silent	SNP	ENST00000382723.4	hg19	CCDS3378.2																																																																																			.	.		0.761	MSX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206700.3			A	4861842	G	A	4861842	2	1	303	1	0	0	0	0	0	0	0	1	9904	962	34	3		3	MSX1	4	4861842	Silent	SNP	G	TCGA-G3-AAV7-01A-11D-A382-10		4861842	186292434	27	43620										
BRD9	65980	hgsc.bcm.edu	37	chr5	891776	891776	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	tttcgcttccttctttcctcAtcgtccagatgcttctcctt	4	15	3	1			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr5:891776A>C	ENST00000467963.1	-	2	412	c.246T>G	c.(244-246)gaT>gaG	p.D82E	BRD9_ENST00000388890.4_5'Flank|BRD9_ENST00000323510.4_5'Flank|BRD9_ENST00000483173.1_Missense_Mutation_p.M31R|TRIP13_ENST00000166345.3_5'Flank|BRD9_ENST00000435709.2_5'UTR	NM_023924.4	NP_076413.3	Q9H8M2	BRD9_HUMAN	bromodomain containing 9	82	Lys-rich.				chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		lysine-acetylated histone binding (GO:0070577)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(3)	29			Epithelial(17;0.00202)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00815)|Lung(60;0.185)			TTCTTTCCTCATCGTCCAGAT	0.557																																					p.D82E		Atlas-SNP	.											.	BRD9	113	.	0			c.T246G						.						101	90	93					5																	891776		692	1591	2283	SO:0001583	missense	65980	exon2			TTCCTCATCGTCC	AK023503	CCDS34127.1, CCDS34128.1, CCDS34127.2, CCDS34128.2	5p15.33	2008-02-05			ENSG00000028310	ENSG00000028310			25818	protein-coding gene	gene with protein product						12477932	Standard	NM_023924		Approved	FLJ13441	uc003jbq.3	Q9H8M2	OTTHUMG00000159258	ENST00000467963.1:c.246T>G	chr5.hg19:g.891776A>C	ENSP00000419765:p.Asp82Glu	43.0	0.0		94.0	34.0	NM_023924	A6NFY8|B4DMQ2|B4DR93|Q2XUS1|Q6UWU9|Q8IUS4|Q9H5Q5|Q9H7R9	Missense_Mutation	SNP	ENST00000467963.1	hg19	CCDS34127.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	6.592|6.592	0.477509|0.477509	0.12521|0.12521	.|.	.|.	ENSG00000028310|ENSG00000028310	ENST00000467963|ENST00000483173	T|T	0.08896|0.39056	3.04|1.1	5.02|5.02	-8.26|-8.26	0.01021|0.01021	.|.	.|.	.|.	.|.	.|.	T|T	0.28234|0.28234	0.0697|0.0697	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	B|B	0.02656|0.02656	0.0|0.0	B|B	0.08055|0.01281	0.003|0.0	T|T	0.05194|0.05194	-1.0900|-1.0900	8|8	0.18710|0.87932	T|D	0.47|0	.|.	10.3454|10.3454	0.43903|0.43903	0.1561:0.4074:0.4364:0.0|0.1561:0.4074:0.4364:0.0	.|.	82|31	Q9H8M2|B4DMQ2	BRD9_HUMAN|.	E|R	82|31	ENSP00000419765:D82E|ENSP00000419845:M31R	ENSP00000419765:D82E|ENSP00000420397:M31R	D|M	-|-	3|2	2|0	BRD9|BRD9	944776|944776	0.002000|0.002000	0.14202|0.14202	0.316000|0.316000	0.25252|0.25252	0.691000|0.691000	0.40173|0.40173	-1.212000|-1.212000	0.02994|0.02994	-1.619000|-1.619000	0.01566|0.01566	0.533000|0.533000	0.62120|0.62120	GAT|ATG	.	.		0.557	BRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354113.1	NM_023924		C	891776	A	C	891776	3	2	303	1	0	0	0	0	1	0	0	0	1509	217	8	5	1607	5	BRD9	5	891776	Missense_Mutation	SNP	A	TCGA-G3-AAV7-01A-11D-A382-10		891776	180023484	28	43621										
HIST1H3C	8352	hgsc.bcm.edu	37	chr6	26045843	26045843	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	tgatccggaagctgccgttcCagcgcctggtgcgagaaatc	13	12	0	2			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr6:26045843C>T	ENST00000540144.1	+	1	205	c.205C>T	c.(205-207)Cag>Tag	p.Q69*	HIST1H2BB_ENST00000357905.2_5'Flank	NM_003531.2	NP_003522.1	P68431	H31_HUMAN	histone cluster 1, H3c	69					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(1)|skin(1)	8						GCTGCCGTTCCAGCGCCTGGT	0.622																																					p.Q69X		Atlas-SNP	.											.	HIST1H3C	34	.	0			c.C205T						.						50	52	51					6																	26045843		2203	4300	6503	SO:0001587	stop_gained	8352	exon1			CCGTTCCAGCGCC	X57128	CCDS4576.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000196532	ENSG00000278272		"Histones / Replication-dependent"	4768	protein-coding gene	gene with protein product		602812	"H3 histone family, member C", "histone 1, H3c"	H3FC		8227173, 9119399, 12408966	Standard	NM_003531		Approved	H3/c, H3.1	uc003nfv.3	P68431	OTTHUMG00000014416	ENST00000540144.1:c.205C>T	chr6.hg19:g.26045843C>T	ENSP00000439493:p.Gln69*	117.0	0.0		200.0	52.0	NM_003531	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Nonsense_Mutation	SNP	ENST00000540144.1	hg19	CCDS4576.1	.	.	.	.	.	.	.	.	.	.	C	13.82	2.350369	0.41599	.	.	ENSG00000196532	ENST00000540144	.	.	.	4.38	4.38	0.52667	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	16.8064	0.85706	0.0:1.0:0.0:0.0	.	.	.	.	X	69	.	ENSP00000439493:Q69X	Q	+	1	0	HIST1H3C	26153822	1.000000	0.71417	1.000000	0.80357	0.036000	0.12997	4.821000	0.62679	2.378000	0.81104	0.491000	0.48974	CAG	.	.		0.622	HIST1H3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040078.1	NM_003531		T	26045843	C	T	26045843	4	4	303	1	0	0	0	0	0	1	0	0	7166	595	21	3	207	3	HIST1H3C	6	26045843	Nonsense_Mutation	SNP	C	TCGA-G3-AAV7-01A-11D-A382-10		26045843	145069224	29	43622										
SYNGAP1	8831	hgsc.bcm.edu	37	chr6	33405540	33405540	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	tactactgtgagctctgcctGgatgacatgctgtatgcacg	11	10	1	2			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr6:33405540G>T	ENST00000418600.2	+	8	959	c.858G>T	c.(856-858)ctG>ctT	p.L286L	SYNGAP1_ENST00000496374.1_3'UTR|MIR5004_ENST00000579078.1_RNA|SYNGAP1_ENST00000293748.5_Silent_p.L286L|SYNGAP1_ENST00000428982.2_Silent_p.L227L	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	286	C2.				dendrite development (GO:0016358)|negative regulation of axonogenesis (GO:0050771)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|pattern specification process (GO:0007389)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|receptor clustering (GO:0043113)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of MAPK cascade (GO:0043408)|regulation of synapse structure and activity (GO:0050803)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Rab GTPase activator activity (GO:0005097)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(15)|ovary(7)|pancreas(1)|stomach(1)|urinary_tract(1)	43						AGCTCTGCCTGGATGACATGC	0.607																																					p.L286L		Atlas-SNP	.											.	SYNGAP1	202	.	0			c.G858T						.						87	92	90					6																	33405540		2203	4300	6503	SO:0001819	synonymous_variant	8831	exon8			CTGCCTGGATGAC	AB067525	CCDS34434.2	6p21.3	2010-06-25	2010-06-25		ENSG00000197283	ENSG00000197283			11497	protein-coding gene	gene with protein product		603384	"synaptic Ras GTPase activating protein 1 homolog (rat)"			9581761, 18323856	Standard	NM_006772		Approved	SYNGAP, RASA5, KIAA1938	uc011dri.2	Q96PV0	OTTHUMG00000031096	ENST00000418600.2:c.858G>T	chr6.hg19:g.33405540G>T		105.0	0.0		130.0	35.0	NM_006772	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Silent	SNP	ENST00000418600.2	hg19	CCDS34434.2																																																																																			.	.		0.607	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407		T	33405540	G	T	33405540	2	4	303	1	0	0	0	0	0	0	0	1	15462	1335	47	3		3	SYNGAP1	6	33405540	Silent	SNP	G	TCGA-G3-AAV7-01A-11D-A382-10	7359697	33405540	137709527	30	43623										
RIMS1	22999	hgsc.bcm.edu	37	chr6	73001644	73001644	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	tttttgcctgcagaatgcacCgacagagaagtccaacacaa	8	11	0	2			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr6:73001644C>A	ENST00000521978.1	+	26	3745	c.3745C>A	c.(3745-3747)Cga>Aga	p.R1249R	RIMS1_ENST00000538414.1_Silent_p.R45R|RIMS1_ENST00000425662.2_Silent_p.R489R|RIMS1_ENST00000348717.5_Silent_p.R1041R|RIMS1_ENST00000517960.1_Silent_p.R1041R|RIMS1_ENST00000401910.3_Silent_p.R569R|RIMS1_ENST00000518273.1_Silent_p.R1100R|RIMS1_ENST00000264839.7_Silent_p.R1098R|RIMS1_ENST00000523963.1_Silent_p.R546R|RIMS1_ENST00000520567.1_Silent_p.R1071R|RIMS1_ENST00000522291.1_Silent_p.R1020R|RIMS1_ENST00000517827.1_Silent_p.R555R|RIMS1_ENST00000491071.2_Silent_p.R1072R	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	1249					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				CAGAATGCACCGACAGAGAAG	0.468																																					p.R1249R		Atlas-SNP	.											.	RIMS1	278	.	0			c.C3745A						.						21	21	21					6																	73001644		1964	4130	6094	SO:0001819	synonymous_variant	22999	exon26			ATGCACCGACAGA	AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"Rab3-interacting molecule"	606629	"RAB3 interacting protein 2"	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.3745C>A	chr6.hg19:g.73001644C>A		184.0	0.0		192.0	47.0	NM_014989	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Silent	SNP	ENST00000521978.1	hg19	CCDS47449.1	.	.	.	.	.	.	.	.	.	.	C	8.210	0.800214	0.16397	.	.	ENSG00000079841	ENST00000517433	.	.	.	5.57	1.62	0.23740	.	.	.	.	.	T	0.43700	0.1259	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.32561	-0.9902	4	.	.	.	-13.4053	9.5	0.39011	0.3654:0.5705:0.0:0.0641	.	.	.	.	Q	594	.	.	P	+	2	0	RIMS1	73058365	1.000000	0.71417	0.942000	0.38095	0.807000	0.45602	3.391000	0.52530	0.061000	0.16311	0.650000	0.86243	CCG	.	.		0.468	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1			A	73001644	C	A	73001644	2	1	303	1	0	0	0	0	0	0	0	1	13382	644	23	1		1	RIMS1	6	73001644	Silent	SNP	C	TCGA-G3-AAV7-01A-11D-A382-10	39596104	73001644	98113423	31	43624										
MANEA	79694	hgsc.bcm.edu	37	chr6	96034580	96034584	+	Frame_Shift_Del	DEL	TCTGA	TCTGA	-													0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	ctatgaaaccttccaaagccTctgaacttaacttggatgaa							TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	TCTGA	TCTGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr6:96034580_96034584delTCTGA	ENST00000358812.4	+	2	399_403	c.265_269delTCTGA	c.(265-270)tctgaafs	p.SE89fs	MANEA_ENST00000369293.1_Frame_Shift_Del_p.SE89fs	NM_024641.3	NP_078917.2	Q5SRI9	MANEA_HUMAN	mannosidase, endo-alpha	89	Catalytic. {ECO:0000305}.				cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	glycoprotein endo-alpha-1,2-mannosidase activity (GO:0004569)			breast(2)|endometrium(3)|kidney(2)|liver(2)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26		all_cancers(76;1.01e-06)|Acute lymphoblastic leukemia(125;3.58e-09)|all_hematologic(75;1.22e-06)|all_epithelial(107;0.00433)|Colorectal(196;0.0341)		BRCA - Breast invasive adenocarcinoma(108;0.148)		TTCCAAAGCCTCTGAACTTAACTTG	0.322																																					p.88_90del		Atlas-INDEL	.											.	MANEA	58	.	0			c.264_268del						.																																			SO:0001589	frameshift_variant	79694	exon2			.	AK022900	CCDS5032.1	6q16.2	2008-02-05			ENSG00000172469	ENSG00000172469			21072	protein-coding gene	gene with protein product		612327					Standard	NM_024641		Approved	FLJ12838, mandaselin	uc003poo.2	Q5SRI9	OTTHUMG00000016296	ENST00000358812.4:c.265_269delTCTGA	chr6.hg19:g.96034580_96034584delTCTGA	ENSP00000351669:p.Ser89fs	119.0	0.0		112.0	18.0	NM_024641	A6H8M6|Q5SRJ0|Q6MZV0|Q70JE9|Q7Z3V7|Q8WWX5|Q9H9D2	Frame_Shift_Del	DEL	ENST00000358812.4	hg19	CCDS5032.1																																																																																			.	.		0.322	MANEA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043644.1	NM_024641		-	96034584	TCTGA	-	96034580	7	5	303	1	0	1	0	1	0	0	0	0	9230	1551	54	0	267	0	MANEA	6	96034580	Frame_Shift_Del	DEL	TCTGA	TCGA-G3-AAV7-01A-11D-A382-10	23032936	96034580	75080487	32	43625	230	3								
MANEA	79694	hgsc.bcm.edu	37	chr6	96034587	96034590	+	Frame_Shift_Del	DEL	TTAA	TTAA	-													0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	accttccaaagcctctgaacTtaacttggatgaactaccac							TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	TTAA	TTAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr6:96034587_96034590delTTAA	ENST00000358812.4	+	2	406_409	c.272_275delTTAA	c.(271-276)cttaacfs	p.LN91fs	MANEA_ENST00000369293.1_Frame_Shift_Del_p.LN91fs	NM_024641.3	NP_078917.2	Q5SRI9	MANEA_HUMAN	mannosidase, endo-alpha	91	Catalytic. {ECO:0000305}.				cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	glycoprotein endo-alpha-1,2-mannosidase activity (GO:0004569)			breast(2)|endometrium(3)|kidney(2)|liver(2)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26		all_cancers(76;1.01e-06)|Acute lymphoblastic leukemia(125;3.58e-09)|all_hematologic(75;1.22e-06)|all_epithelial(107;0.00433)|Colorectal(196;0.0341)		BRCA - Breast invasive adenocarcinoma(108;0.148)		GCCTCTGAACTTAACTTGGATGAA	0.309																																					p.91_92del		Atlas-INDEL	.											.	MANEA	58	.	0			c.271_274del						.																																			SO:0001589	frameshift_variant	79694	exon2			.	AK022900	CCDS5032.1	6q16.2	2008-02-05			ENSG00000172469	ENSG00000172469			21072	protein-coding gene	gene with protein product		612327					Standard	NM_024641		Approved	FLJ12838, mandaselin	uc003poo.2	Q5SRI9	OTTHUMG00000016296	ENST00000358812.4:c.272_275delTTAA	chr6.hg19:g.96034587_96034590delTTAA	ENSP00000351669:p.Leu91fs	121.0	0.0		108.0	18.0	NM_024641	A6H8M6|Q5SRJ0|Q6MZV0|Q70JE9|Q7Z3V7|Q8WWX5|Q9H9D2	Frame_Shift_Del	DEL	ENST00000358812.4	hg19	CCDS5032.1																																																																																			.	.		0.309	MANEA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043644.1	NM_024641		-	96034590	TTAA	-	96034587	7	5	303	1	0	1	0	1	0	0	0	0	9230	1609	56	0	274	0	MANEA	6	96034587	Frame_Shift_Del	DEL	TTAA	TCGA-G3-AAV7-01A-11D-A382-10	7	96034587	75080480	33	43626	230	3								
MANEA	79694	hgsc.bcm.edu	37	chr6	96034593	96034595	+	In_Frame_Del	DEL	TGG	TGG	-													0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	caaagcctctgaacttaactTggatgaactaccacctctga							TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	TGG	TGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr6:96034593_96034595delTGG	ENST00000358812.4	+	2	412_414	c.278_280delTGG	c.(277-282)ttggat>tat	p.93_94LD>Y	MANEA_ENST00000369293.1_In_Frame_Del_p.93_94LD>Y	NM_024641.3	NP_078917.2	Q5SRI9	MANEA_HUMAN	mannosidase, endo-alpha	93	Catalytic. {ECO:0000305}.				cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	glycoprotein endo-alpha-1,2-mannosidase activity (GO:0004569)			breast(2)|endometrium(3)|kidney(2)|liver(2)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26		all_cancers(76;1.01e-06)|Acute lymphoblastic leukemia(125;3.58e-09)|all_hematologic(75;1.22e-06)|all_epithelial(107;0.00433)|Colorectal(196;0.0341)		BRCA - Breast invasive adenocarcinoma(108;0.148)		GAACTTAACTTGGATGAACTACC	0.325																																					p.93_93del		Atlas-INDEL	.											.	MANEA	58	.	0			c.277_279del						.																																			SO:0001651	inframe_deletion	79694	exon2			.	AK022900	CCDS5032.1	6q16.2	2008-02-05			ENSG00000172469	ENSG00000172469			21072	protein-coding gene	gene with protein product		612327					Standard	NM_024641		Approved	FLJ12838, mandaselin	uc003poo.2	Q5SRI9	OTTHUMG00000016296	ENST00000358812.4:c.278_280delTGG	chr6.hg19:g.96034593_96034595delTGG	ENSP00000351669:p.Leu93_Asp94delinsTyr	122.0	0.0		97.0	18.0	NM_024641	A6H8M6|Q5SRJ0|Q6MZV0|Q70JE9|Q7Z3V7|Q8WWX5|Q9H9D2	In_Frame_Del	DEL	ENST00000358812.4	hg19	CCDS5032.1																																																																																			.	.		0.325	MANEA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043644.1	NM_024641		-	96034595	TGG	-	96034593	7	5	303	1	0	1	0	1	0	0	0	0	9230	1821	63	0	280	0	MANEA	6	96034593	In_Frame_Del	DEL	TGG	TCGA-G3-AAV7-01A-11D-A382-10	6	96034593	75080474	34	43627	230	3								
FHL5	9457	hgsc.bcm.edu	37	chr6	97053798	97053798	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	gttcccgcaaaatggaatttAagggaaactactggcatgaa	10	7	0	1			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr6:97053798A>G	ENST00000326771.2	+	5	735	c.355A>G	c.(355-357)Aag>Gag	p.K119E	FHL5_ENST00000541107.1_Missense_Mutation_p.K119E	NM_020482.4	NP_065228.4	Q5TD97	FHL5_HUMAN	four and a half LIM domains 5	119	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|urinary_tract(1)	27		all_cancers(76;1.57e-07)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00266)|Colorectal(196;0.0341)|Lung NSC(302;0.204)		BRCA - Breast invasive adenocarcinoma(108;0.0948)		AATGGAATTTAAGGGAAACTA	0.363																																					p.K119E		Atlas-SNP	.											.	FHL5	73	.	0			c.A355G						.						77	74	75					6																	97053798		2203	4300	6503	SO:0001583	missense	9457	exon5			GAATTTAAGGGAA	AF278541	CCDS5035.1	6q16.1-q16.3	2008-02-05			ENSG00000112214	ENSG00000112214			17371	protein-coding gene	gene with protein product		605126					Standard	NM_020482		Approved	FLJ33049, ACT, dJ393D12.2	uc003pot.2	Q5TD97	OTTHUMG00000015239	ENST00000326771.2:c.355A>G	chr6.hg19:g.97053798A>G	ENSP00000326022:p.Lys119Glu	149.0	0.0		147.0	29.0	NM_020482	B2RBD1|E1P526|Q5TD98|Q8WW21|Q9NQU2	Missense_Mutation	SNP	ENST00000326771.2	hg19	CCDS5035.1	.	.	.	.	.	.	.	.	.	.	A	16.63	3.177873	0.57692	.	.	ENSG00000112214	ENST00000541107;ENST00000326771;ENST00000450218	D;D;D	0.87334	-2.24;-2.24;-2.24	6.06	3.58	0.41010	Zinc finger, LIM-type (5);	0.000000	0.47455	D	0.000232	T	0.67316	0.2880	N	0.17674	0.51	0.44899	D	0.997912	B	0.27951	0.195	B	0.28011	0.085	T	0.71196	-0.4664	10	0.51188	T	0.08	.	9.5385	0.39237	0.8127:0.1222:0.0651:0.0	.	119	Q5TD97	FHL5_HUMAN	E	119	ENSP00000442357:K119E;ENSP00000326022:K119E;ENSP00000396390:K119E	ENSP00000326022:K119E	K	+	1	0	FHL5	97160519	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.015000	0.64035	2.323000	0.78572	0.528000	0.53228	AAG	.	.		0.363	FHL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041559.1	NM_020482		G	97053798	A	G	97053798	3	3	303	1	0	0	0	0	1	0	0	0	5889	363	13	2	365	2	FHL5	6	97053798	Missense_Mutation	SNP	A	TCGA-G3-AAV7-01A-11D-A382-10	1019205	97053798	74061269	35	43628										
ARMC2	84071	hgsc.bcm.edu	37	chr6	109232114	109232114	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	ctctgcagcttaaagtgagtAgaaagaatcttcttaatgtc	8	7	3	3			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr6:109232114A>G	ENST00000392644.4	+	9	1204	c.1036A>G	c.(1036-1038)Aga>Gga	p.R346G	ARMC2_ENST00000368972.3_Missense_Mutation_p.R181G	NM_032131.4	NP_115507.4	Q8NEN0	ARMC2_HUMAN	armadillo repeat containing 2	346										endometrium(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(1)|skin(1)	24		all_cancers(87;1.14e-07)|Acute lymphoblastic leukemia(125;2.3e-10)|all_hematologic(75;3.3e-08)|all_epithelial(87;0.000111)|Colorectal(196;0.03)|all_lung(197;0.11)		Epithelial(106;0.000197)|BRCA - Breast invasive adenocarcinoma(108;0.000236)|all cancers(137;0.000279)|OV - Ovarian serous cystadenocarcinoma(136;0.00434)		TAAAGTGAGTAGAAAGAATCT	0.308																																					p.R346G		Atlas-SNP	.											.	ARMC2	56	.	0			c.A1036G						.						36	36	36					6																	109232114		2200	4293	6493	SO:0001583	missense	84071	exon9			GTGAGTAGAAAGA	BC030603	CCDS5069.2, CCDS69168.1	6q21	2013-02-14			ENSG00000118690	ENSG00000118690		"Armadillo repeat containing"	23045	protein-coding gene	gene with protein product							Standard	XM_005267154		Approved	DKFZp434P0714, bA787I22.1	uc003pss.4	Q8NEN0	OTTHUMG00000015335	ENST00000392644.4:c.1036A>G	chr6.hg19:g.109232114A>G	ENSP00000376417:p.Arg346Gly	67.0	0.0		63.0	18.0	NM_032131	A8K8Y4|B4DGF5|G5E993|Q5VVY8|Q9H0K9	Missense_Mutation	SNP	ENST00000392644.4	hg19	CCDS5069.2	.	.	.	.	.	.	.	.	.	.	A	2.282	-0.364408	0.05103	.	.	ENSG00000118690	ENST00000368972;ENST00000392644	T;T	0.18810	2.22;2.19	5.19	1.57	0.23409	.	0.096535	0.64402	N	0.000001	T	0.01029	0.0034	N	0.00563	-1.375	0.27212	N	0.959877	B	0.02656	0.0	B	0.01281	0.0	T	0.47341	-0.9125	10	0.02654	T	1	.	7.7902	0.29116	0.2971:0.0:0.7029:0.0	.	346	Q8NEN0	ARMC2_HUMAN	G	181;346	ENSP00000357968:R181G;ENSP00000376417:R346G	ENSP00000357968:R181G	R	+	1	2	ARMC2	109338807	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	2.528000	0.45624	0.317000	0.23160	0.482000	0.46254	AGA	.	.		0.308	ARMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041732.2	NM_032131		G	109232114	A	G	109232114	3	3	303	1	0	0	0	0	1	0	0	0	951	412	15	2	1066	2	ARMC2	6	109232114	Missense_Mutation	SNP	A	TCGA-G3-AAV7-01A-11D-A382-10	12178316	109232114	61882953	36	43629										
SERAC1	84947	hgsc.bcm.edu	37	chr6	158535993	158535993	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	gcttccaacagcatctttttGacaagaagacctagccacag	7	12	1	3			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr6:158535993G>A	ENST00000367104.3	-	15	1643	c.1512C>T	c.(1510-1512)gtC>gtT	p.V504V	SERAC1_ENST00000367101.1_Missense_Mutation_p.S519L|SERAC1_ENST00000367102.2_Missense_Mutation_p.S519L	NM_032861.3	NP_116250.3	Q96JX3	SRAC1_HUMAN	serine active site containing 1	504					extracellular matrix organization (GO:0030198)|GPI anchor metabolic process (GO:0006505)|intracellular protein transport (GO:0006886)|phospholipid biosynthetic process (GO:0008654)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)			endometrium(1)|kidney(2)|large_intestine(6)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	15		Breast(66;0.00519)|Ovarian(120;0.123)|Prostate(117;0.178)		OV - Ovarian serous cystadenocarcinoma(65;1.37e-18)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)		GCATCTTTTTGACAAGAAGAC	0.363																																					p.V504V		Atlas-SNP	.											.	SERAC1	31	.	0			c.C1512T						.						121	127	125					6																	158535993		2203	4300	6503	SO:0001819	synonymous_variant	84947	exon15			CTTTTTGACAAGA	BC001705	CCDS5255.1	6q25.3	2003-05-12			ENSG00000122335	ENSG00000122335			21061	protein-coding gene	gene with protein product		614725					Standard	NM_032861		Approved	FLJ14917	uc003qrc.2	Q96JX3	OTTHUMG00000015905	ENST00000367104.3:c.1512C>T	chr6.hg19:g.158535993G>A		95.0	0.0		116.0	5.0	NM_032861	Q49AT1|Q5VTX3|Q6PKF3	Silent	SNP	ENST00000367104.3	hg19	CCDS5255.1	.	.	.	.	.	.	.	.	.	.	.	15.00	2.703391	0.48412	.	.	ENSG00000122335	ENST00000367102;ENST00000367101	D;D	0.85629	-2.01;-2.01	5.93	0.961	0.19638	.	.	.	.	.	T	0.79149	0.4397	.	.	.	0.36661	D	0.877974	.	.	.	.	.	.	T	0.79918	-0.1600	6	0.87932	D	0	-25.448	3.4109	0.07357	0.1806:0.3091:0.4045:0.1058	.	.	.	.	L	519	ENSP00000356069:S519L;ENSP00000356068:S519L	ENSP00000356068:S519L	S	-	2	0	SERAC1	158455981	0.692000	0.27719	1.000000	0.80357	0.977000	0.68977	-0.205000	0.09411	2.271000	0.75665	0.533000	0.62120	TCA	.	.		0.363	SERAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042862.1	NM_032861		A	158535993	G	A	158535993	2	1	303	1	0	0	0	0	0	0	0	1	14089	1277	45	3		3	SERAC1	6	158535993	Silent	SNP	G	TCGA-G3-AAV7-01A-11D-A382-10	49303879	158535993	12579074	37	43630										
SUN1	23353	hgsc.bcm.edu	37	chr7	878543	878543	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	ttgcgcctggccacgacagcAtgcaccctgggggatggtga	15	12	0	1			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr7:878543A>C	ENST00000405266.1	+	2	210	c.186A>C	c.(184-186)gcA>gcC	p.A62A	SUN1_ENST00000469755.1_3'UTR|SUN1_ENST00000456758.2_Silent_p.A120A|SUN1_ENST00000457378.2_Silent_p.A83A|SUN1_ENST00000425407.2_Silent_p.A12A|SUN1_ENST00000401592.1_Silent_p.A62A|SUN1_ENST00000452783.2_Silent_p.A62A|SUN1_ENST00000403868.1_Silent_p.A62A|SUN1_ENST00000389574.3_Silent_p.A12A			O94901	SUN1_HUMAN	Sad1 and UNC84 domain containing 1	62	LMNA-binding.				cytoskeletal anchoring at nuclear membrane (GO:0090286)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)	acrosomal membrane (GO:0002080)|integral component of nuclear inner membrane (GO:0005639)|nuclear envelope (GO:0005635)|SUN-KASH complex (GO:0034993)				NS(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(17)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						CCACGACAGCATGCACCCTGG	0.597																																					p.A83A		Atlas-SNP	.											.	SUN1	157	.	0			c.A249C						.						39	39	39					7																	878543		2035	4190	6225	SO:0001819	synonymous_variant	23353	exon4			GACAGCATGCACC	AF202724	CCDS43533.1, CCDS47525.1, CCDS55078.1, CCDS55079.1, CCDS55080.1	7p22.3	2010-01-27	2010-01-27	2010-01-27	ENSG00000164828	ENSG00000164828			18587	protein-coding gene	gene with protein product	"Sad1 unc-84 domain protein 1"	607723	"unc-84 homolog A (C. elegans)"	UNC84A		11593002	Standard	NM_001130965		Approved	KIAA0810, FLJ12407	uc021zym.1	O94901	OTTHUMG00000151426	ENST00000405266.1:c.186A>C	chr7.hg19:g.878543A>C		61.0	0.0		61.0	12.0	NM_001171945	A5PL20|B3KMV7|B4DZF7|B7WNY4|B7WP53|E9PDU4|E9PF23|F8WD13|Q96CZ7|Q9HA14|Q9UH98	Silent	SNP	ENST00000405266.1	hg19																																																																																				.	.		0.597	SUN1-001	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000322566.1	NM_025154		C	878543	A	C	878543	2	2	303	1	0	0	0	0	0	0	0	1	15406	204	8	5		5	SUN1	7	878543	Silent	SNP	A	TCGA-G3-AAV7-01A-11D-A382-10		878543	158260120	38	43631										
SRPK2	6733	hgsc.bcm.edu	37	chr7	104767483	104767483	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	ccagaatgtggttcaaacaaAtaatctcccgttgccagctc	7	12	2	1			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr7:104767483A>G	ENST00000393651.3	-	14	1866	c.1779T>C	c.(1777-1779)taT>taC	p.Y593Y	SRPK2_ENST00000489828.1_Silent_p.Y582Y|SRPK2_ENST00000357311.3_Silent_p.Y582Y	NM_182692.1	NP_872634.1			SRSF protein kinase 2											NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|kidney(11)|large_intestine(6)|lung(4)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	35						GTTCAAACAAATAATCTCCCG	0.478																																					p.Y593Y		Atlas-SNP	.											.	SRPK2	76	.	0			c.T1779C						.						137	117	124					7																	104767483		2203	4300	6503	SO:0001819	synonymous_variant	6733	exon14			AAACAAATAATCT	U88666	CCDS5735.1, CCDS34724.1	7q22-q31.1	2010-06-23	2010-06-23		ENSG00000135250	ENSG00000135250			11306	protein-coding gene	gene with protein product	"SR protein kinase 2", "serine/arginine-rich splicing factor kinase 2"	602980	"SFRS protein kinase 2"			8208298, 9472028	Standard	NM_182692		Approved	SFRSK2	uc003vcv.4	P78362	OTTHUMG00000157405	ENST00000393651.3:c.1779T>C	chr7.hg19:g.104767483A>G		125.0	0.0		136.0	48.0	NM_182692		Silent	SNP	ENST00000393651.3	hg19	CCDS34724.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.47|10.47	1.359425|1.359425	0.24598|0.24598	.|.	.|.	ENSG00000135250|ENSG00000135250	ENST00000477925|ENST00000474770	.|.	.|.	.|.	5.68|5.68	0.786|0.786	0.18590|0.18590	.|.	.|.	.|.	.|.	.|.	T|T	0.58264|0.58264	0.2110|0.2110	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.52533|0.52533	-0.8563|-0.8563	4|4	.|.	.|.	.|.	-17.0746|-17.0746	10.1801|10.1801	0.42963|0.42963	0.6661:0.0:0.3339:0.0|0.6661:0.0:0.3339:0.0	.|.	.|.	.|.	.|.	L|T	189|67	.|.	.|.	F|I	-|-	1|2	0|0	SRPK2|SRPK2	104554719|104554719	0.997000|0.997000	0.39634|0.39634	0.999000|0.999000	0.59377|0.59377	0.994000|0.994000	0.84299|0.84299	0.687000|0.687000	0.25407|0.25407	0.178000|0.178000	0.19917|0.19917	0.460000|0.460000	0.39030|0.39030	TTT|ATT	.	.		0.478	SRPK2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348723.1	NM_182691		G	104767483	A	G	104767483	2	3	303	1	0	0	0	0	0	0	0	1	15175	108	4	2		2	SRPK2	7	104767483	Silent	SNP	A	TCGA-G3-AAV7-01A-11D-A382-10	103888940	104767483	54371180	39	43632										
DGKI	9162	hgsc.bcm.edu	37	chr7	137170153	137170153	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	ctctgggagccagaagaaacTgactgtaggtcctaatgaga	12	8	1	4			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr7:137170153T>A	ENST00000288490.5	-	24	2394	c.2394A>T	c.(2392-2394)tcA>tcT	p.S798S	DGKI_ENST00000446122.1_Silent_p.S780S|DGKI_ENST00000424189.2_Silent_p.S801S|DGKI_ENST00000453654.2_Silent_p.S498S	NM_004717.2	NP_004708.1	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	798					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|positive regulation of Ras protein signal transduction (GO:0046579)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of Rap GTPase activity (GO:0032317)	cytoplasm (GO:0005737)|guanyl-nucleotide exchange factor complex (GO:0032045)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(46)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	84						CAGAAGAAACTGACTGTAGGT	0.368																																					p.S798S		Atlas-SNP	.											.	DGKI	335	.	0			c.A2394T						.						81	80	80					7																	137170153		2203	4300	6503	SO:0001819	synonymous_variant	9162	exon24			AGAAACTGACTGT	AF061936	CCDS5845.1	7q32.3-q33	2013-01-10			ENSG00000157680	ENSG00000157680		"Ankyrin repeat domain containing"	2855	protein-coding gene	gene with protein product		604072				9830018	Standard	NM_004717		Approved	DGK-IOTA	uc003vtt.3	O75912	OTTHUMG00000155697	ENST00000288490.5:c.2394A>T	chr7.hg19:g.137170153T>A		258.0	0.0		339.0	110.0	NM_004717	A4D1Q9|Q9NZ49	Silent	SNP	ENST00000288490.5	hg19	CCDS5845.1																																																																																			.	.		0.368	DGKI-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341286.3	NM_004717		A	137170153	T	A	137170153	2	1	303	1	0	0	0	0	0	0	0	1	4473	1567	55	4		4	DGKI	7	137170153	Silent	SNP	T	TCGA-G3-AAV7-01A-11D-A382-10	32402670	137170153	21968510	40	43633										
WEE2	494551	hgsc.bcm.edu	37	chr7	141416059	141416059	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	aggaaggcaagggagggctgCctgccaaggtaagcgtagtt	17	7	0	0			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr7:141416059C>T	ENST00000397541.2	+	3	983	c.577C>T	c.(577-579)Cct>Tct	p.P193S	WEE2-AS1_ENST00000459753.1_RNA|WEE2-AS1_ENST00000471512.1_RNA|WEE2-AS1_ENST00000488785.1_RNA|WEE2-AS1_ENST00000462383.1_RNA|WEE2-AS1_ENST00000465110.1_RNA|WEE2-AS1_ENST00000495800.1_RNA|WEE2-AS1_ENST00000478332.1_RNA	NM_001105558.1	NP_001099028.1	P0C1S8	WEE2_HUMAN	WEE1 homolog 2 (S. pombe)	193					female meiotic division (GO:0007143)|female pronucleus assembly (GO:0035038)|mitotic nuclear division (GO:0007067)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of oocyte maturation (GO:1900194)|regulation of meiosis I (GO:0060631)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(2)|stomach(1)	31	Melanoma(164;0.0171)					GGGAGGGCTGCCTGCCAAGGT	0.438																																					p.P193S		Atlas-SNP	.											.	WEE2	59	.	0			c.C577T						.						126	127	127					7																	141416059		1959	4137	6096	SO:0001583	missense	494551	exon3			GGGCTGCCTGCCA	AK131218	CCDS43660.1	7q32	2008-07-02			ENSG00000214102	ENSG00000214102			19684	protein-coding gene	gene with protein product		614084					Standard	NM_001105558		Approved	FLJ16107	uc003vwn.2	P0C1S8	OTTHUMG00000157536	ENST00000397541.2:c.577C>T	chr7.hg19:g.141416059C>T	ENSP00000380675:p.Pro193Ser	34.0	0.0		37.0	13.0	NM_001105558		Missense_Mutation	SNP	ENST00000397541.2	hg19	CCDS43660.1	.	.	.	.	.	.	.	.	.	.	C	13.40	2.224820	0.39300	.	.	ENSG00000214102	ENST00000397541	T	0.24908	1.83	4.34	4.34	0.51931	.	0.158837	0.42294	U	0.000723	T	0.35682	0.0940	M	0.77103	2.36	0.42515	D	0.99298	P	0.42785	0.79	B	0.44108	0.441	T	0.37174	-0.9717	10	0.66056	D	0.02	.	12.5171	0.56038	0.0:1.0:0.0:0.0	.	193	P0C1S8	WEE2_HUMAN	S	193	ENSP00000380675:P193S	ENSP00000380675:P193S	P	+	1	0	WEE2	141062528	1.000000	0.71417	0.982000	0.44146	0.121000	0.20230	1.177000	0.31969	2.414000	0.81942	0.561000	0.74099	CCT	.	.		0.438	WEE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349091.1	NM_001105558		T	141416059	C	T	141416059	3	4	303	1	0	0	0	0	1	0	0	0	17360	739	26	3	587	3	WEE2	7	141416059	Missense_Mutation	SNP	C	TCGA-G3-AAV7-01A-11D-A382-10	4245906	141416059	17722604	41	43634										
PTPRN2	5799	hgsc.bcm.edu	37	chr7	157959681	157959681	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	ggtgaaggccacttctggggGgcggctggtgccagcaaagg	19	9	1	1			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr7:157959681G>C	ENST00000389418.4	-	6	861	c.852C>G	c.(850-852)gcC>gcG	p.A284A	PTPRN2_ENST00000389413.3_Silent_p.A284A|PTPRN2_ENST00000404321.2_Silent_p.A307A|PTPRN2_ENST00000409483.1_Silent_p.A246A|PTPRN2_ENST00000389416.4_Silent_p.A267A	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	284					negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		ACTTCTGGGGGGCGGCTGGTG	0.652																																					p.A284A		Atlas-SNP	.											.	PTPRN2	243	.	0			c.C852G						.						12	12	12					7																	157959681		2117	4144	6261	SO:0001819	synonymous_variant	5799	exon6			CTGGGGGGCGGCT	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9677	protein-coding gene	gene with protein product	"IAR PTPRP"	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.852C>G	chr7.hg19:g.157959681G>C		104.0	0.0		126.0	37.0	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Silent	SNP	ENST00000389418.4	hg19	CCDS5947.1																																																																																			.	.		0.652	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1			C	157959681	G	C	157959681	2	2	303	1	0	0	0	0	0	0	0	1	12823	1219	43	4		4	PTPRN2	7	157959681	Silent	SNP	G	TCGA-G3-AAV7-01A-11D-A382-10	16543622	157959681	1178982	42	43635										
ESYT2	57488	hgsc.bcm.edu	37	chr7	158540904	158540904	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	cctcaacttcaaggtcctggCgcttgggattgtgaatgaag	12	9	2	2			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr7:158540904C>T	ENST00000251527.5	-	15	1771	c.1706G>A	c.(1705-1707)cGc>cAc	p.R569H		NM_020728.2	NP_065779.1	A0FGR8	ESYT2_HUMAN	extended synaptotagmin-like protein 2	597	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				endocytosis (GO:0006897)|lipid transport (GO:0006869)	extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|membrane (GO:0016020)|organelle membrane contact site (GO:0044232)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|identical protein binding (GO:0042802)|phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(16)|prostate(2)	32						AAGGTCCTGGCGCTTGGGATT	0.338																																					p.R569H		Atlas-SNP	.											.	ESYT2	70	.	0			c.G1706A						.						120	124	123					7																	158540904		2203	4300	6503	SO:0001583	missense	57488	exon15			TCCTGGCGCTTGG	AB033054	CCDS34791.1	7q36.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000117868	ENSG00000117868		"Synaptotagmins"	22211	protein-coding gene	gene with protein product			"family with sequence similarity 62 (C2 domain containing), member B"	FAM62B		17672888	Standard	NM_020728		Approved	KIAA1228, CHR2SYT	uc003wob.1	A0FGR8	OTTHUMG00000151436	ENST00000251527.5:c.1706G>A	chr7.hg19:g.158540904C>T	ENSP00000251527:p.Arg569His	121.0	0.0		152.0	10.0	NM_020728	A4D229|Q69YJ2|Q6UKI4|Q6ZTU0|Q6ZVU1|Q9BQS0|Q9NW47|Q9ULJ2	Missense_Mutation	SNP	ENST00000251527.5	hg19	CCDS34791.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.949205	0.73787	.	.	ENSG00000117868	ENST00000251527;ENST00000421679;ENST00000275418;ENST00000429474	T;T	0.69040	-0.37;-0.37	4.98	4.98	0.66077	.	0.117564	0.52532	D	0.000062	T	0.75975	0.3923	L	0.44542	1.39	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.70016	0.967;0.939	T	0.76647	-0.2882	10	0.48119	T	0.1	-21.6892	17.2579	0.87062	0.0:1.0:0.0:0.0	.	618;569	A0FGR8-6;A0FGR8-2	.;.	H	569;618;560;393	ENSP00000251527:R569H;ENSP00000275418:R560H	ENSP00000251527:R569H	R	-	2	0	ESYT2	158233665	0.859000	0.29813	1.000000	0.80357	0.998000	0.95712	1.507000	0.35758	2.308000	0.77769	0.563000	0.77884	CGC	.	.		0.338	ESYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322647.1	NM_020728		T	158540904	C	T	158540904	3	4	303	1	0	0	0	0	1	0	0	0	5267	768	27	1	1007	1	ESYT2	7	158540904	Missense_Mutation	SNP	C	TCGA-G3-AAV7-01A-11D-A382-10	581223	158540904	597759	43	43636										
PLEC	5339	hgsc.bcm.edu	37	chr8	144990483	144990518	+	In_Frame_Del	DEL	GCGGGAGCCGGCCCGGGAGCCGGTGCGCGAGCCGGT	GCGGGAGCCGGCCCGGGAGCCGGTGCGCGAGCCGGT	-													0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	gtggcgtcaaagctgccgcgGcgggagccggcccgggagcc					rs567240737		TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	GCGGGAGCCGGCCCGGGAGCCGGTGCGCGAGCCGGT	GCGGGAGCCGGCCCGGGAGCCGGTGCGCGAGCCGGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr8:144990483_144990518delGCGGGAGCCGGCCCGGGAGCCGGTGCGCGAGCCGGT	ENST00000322810.4	-	32	14051_14086	c.13882_13917delACCGGCTCGCGCACCGGCTCCCGGGCCGGCTCCCGC	c.(13882-13917)accggctcgcgcaccggctcccgggccggctcccgcdel	p.TGSRTGSRAGSR4628del	PLEC_ENST00000354958.2_In_Frame_Del_p.TGSRTGSRAGSR4469del|PLEC_ENST00000356346.3_In_Frame_Del_p.TGSRTGSRAGSR4477del|PLEC_ENST00000345136.3_In_Frame_Del_p.TGSRTGSRAGSR4491del|PLEC_ENST00000398774.2_In_Frame_Del_p.TGSRTGSRAGSR4459del|PLEC_ENST00000527096.1_In_Frame_Del_p.TGSRTGSRAGSR4514del|PLEC_ENST00000436759.2_In_Frame_Del_p.TGSRTGSRAGSR4518del|PLEC_ENST00000354589.3_In_Frame_Del_p.TGSRTGSRAGSR4491del|PLEC_ENST00000357649.2_In_Frame_Del_p.TGSRTGSRAGSR4495del	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	4628	4 X 4 AA tandem repeats of G-S-R-X.|Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						AGCTGCCGCGGCGGGAGCCGGCCCGGGAGCCGGTGCGCGAGCCGGTGCGGGAGCCA	0.725																																					p.4628_4640del		Atlas-Indel,Pindel	.											.	PLEC	1144	.	0			c.13883_13918del						.																																			SO:0001651	inframe_deletion	5339	exon32			.	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"plectin 1, intermediate filament binding protein, 500kD", "epidermolysis bullosa simplex 1 (Ogna)", "plectin 1, intermediate filament binding protein 500kDa"	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.13882_13917delACCGGCTCGCGCACCGGCTCCCGGGCCGGCTCCCGC	chr8.hg19:g.144990483_144990518delGCGGGAGCCGGCCCGGGAGCCGGTGCGCGAGCCGGT	ENSP00000323856:p.Thr4628_Arg4639del	104.0	0.0		173.0	32.0	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	In_Frame_Del	DEL	ENST00000322810.4	hg19	CCDS43772.1																																																																																			.	.		0.725	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		-	144990518	GCGGGAGCCGGCCCGGGAGCCGGTGCGCGAGCCGGT	-	144990483	7	5	303	1	0	1	0	1	0	0	0	0	12061	1190	42	0	141	0	PLEC	8	144990483	In_Frame_Del	DEL	GCGGGAGCCGGCCCGGGAGCCGGTGCGCGAGCCGGT	TCGA-G3-AAV7-01A-11D-A382-10		144990483	1373539	44	43637										
TLN1	7094	hgsc.bcm.edu	37	chr9	35703773	35703773	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	tgctctcattctctccaaccTtggcagagttctttagctgc	7	13	3	1			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr9:35703773T>C	ENST00000314888.9	-	47	6709	c.6356A>G	c.(6355-6357)aAg>aGg	p.K2119R	TLN1_ENST00000464379.1_5'UTR|TLN1_ENST00000540444.1_Splice_Site_p.K2013R	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	2119					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			CTCTCCAACCTTGGCAGAGTT	0.507																																					p.K2119R		Atlas-SNP	.											.	TLN1	185	.	0			c.A6356G						.						90	84	86					9																	35703773		2203	4300	6503	SO:0001630	splice_region_variant	7094	exon47			CCAACCTTGGCAG	AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.6357+1A>G	chr9.hg19:g.35703773T>C		62.0	0.0		51.0	15.0	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	hg19	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	T	17.21	3.332809	0.60853	.	.	ENSG00000137076	ENST00000314888;ENST00000540444	T;T	0.09073	3.02;3.02	4.98	4.98	0.66077	.	0.000000	0.85682	D	0.000000	T	0.12646	0.0307	M	0.74389	2.26	0.80722	D	1	P	0.36616	0.561	B	0.33454	0.164	T	0.03315	-1.1049	10	0.37606	T	0.19	-19.6436	14.6742	0.68967	0.0:0.0:0.0:1.0	.	2119	Q9Y490	TLN1_HUMAN	R	2119;2013	ENSP00000316029:K2119R;ENSP00000442981:K2013R	ENSP00000316029:K2119R	K	-	2	0	TLN1	35693773	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	5.148000	0.64857	1.879000	0.54435	0.459000	0.35465	AAG	.	.		0.507	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289	Missense_Mutation	C	35703773	T	C	35703773	5	2	303	1	0	0	0	0	0	0	1	0	15962	1623	56	2	1313	2	TLN1	9	35703773	Splice_Site	SNP	T	TCGA-G3-AAV7-01A-11D-A382-10		35703773	105509658	45	43638										
IARS	3376	hgsc.bcm.edu	37	chr9	95007263	95007270	+	Frame_Shift_Del	DEL	AATTGCGC	AATTGCGC	-													0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	gagcatctgagtgtgcttcaAattgcgcagtcccacctgtg					rs139380974		TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	AATTGCGC	AATTGCGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr9:95007263_95007270delAATTGCGC	ENST00000375643.3	-	27	3141_3148	c.2875_2882delGCGCAATT	c.(2875-2883)gcgcaatttfs	p.AQF959fs	IARS_ENST00000443024.2_Frame_Shift_Del_p.AQF959fs|IARS_ENST00000375629.3_Frame_Shift_Del_p.AQF12fs|IARS_ENST00000375627.1_Frame_Shift_Del_p.AQF12fs|IARS_ENST00000474340.1_5'Flank|IARS_ENST00000447699.2_Frame_Shift_Del_p.AQF849fs	NM_013417.2	NP_038203.2	P41252	SYIC_HUMAN	isoleucyl-tRNA synthetase	959					gene expression (GO:0010467)|isoleucyl-tRNA aminoacylation (GO:0006428)|osteoblast differentiation (GO:0001649)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|isoleucine-tRNA ligase activity (GO:0004822)			breast(3)|endometrium(2)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	35					L-Isoleucine(DB00167)	GTGTGCTTCAAATTGCGCAGTCCCACCT	0.457																																					p.959_961del		Pindel	.											.	IARS	74	.	0			c.2876_2883del						.																																			SO:0001589	frameshift_variant	3376	exon27			.	AB209234	CCDS6694.1	9q21	2011-07-01	2007-02-26		ENSG00000196305	ENSG00000196305	6.1.1.5	"Aminoacyl tRNA synthetases / Class I"	5330	protein-coding gene	gene with protein product	"isoleucine tRNA ligase 1, cytoplasmic"	600709				8812440	Standard	NM_002161		Approved	ILRS, IARS1	uc004aru.4	P41252	OTTHUMG00000020219	ENST00000375643.3:c.2875_2882delGCGCAATT	chr9.hg19:g.95007263_95007270delAATTGCGC	ENSP00000364794:p.Ala959fs	106.0	0.0		103.0	13.0	NM_002161	A8KAE9|Q5TCD0|Q7Z3T4|Q9H588	Frame_Shift_Del	DEL	ENST00000375643.3	hg19	CCDS6694.1																																																																																			.	.		0.457	IARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053059.2	NM_002161		-	95007270	AATTGCGC	-	95007263	7	5	303	1	0	1	0	1	0	0	0	0	7482	14	1	0	938	0	IARS	9	95007263	Frame_Shift_Del	DEL	AATTGCGC	TCGA-G3-AAV7-01A-11D-A382-10	59303490	95007263	46206168	46	43639										
KIAA1529	100499483	hgsc.bcm.edu	37	chr9	100117288	100117288	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	tgcaagtgaaaatcaagtgcCaggtaggatagattcattct	10	6	3	2			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr9:100117288C>G	ENST00000357054.1	+	35	4242	c.3307C>G	c.(3307-3309)Cag>Gag	p.Q1103E	CCDC180_ENST00000395220.1_3'UTR|CCDC180_ENST00000375202.2_Missense_Mutation_p.Q1132E|CCDC180_ENST00000529487.1_Missense_Mutation_p.Q1132E|RP11-23J9.4_ENST00000534123.1_RNA			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	1103						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											AATCAAGTGCCAGGTAGGATA	0.463																																					p.Q1132E		Atlas-SNP	.											.	.	.	.	0			c.C3394G						.						54	52	53					9																	100117288		2203	4300	6503	SO:0001583	missense	0	exon24			AAGTGCCAGGTAG	AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"Behcet's Disease Associated Gene 1"		"KIAA1529", "chromosome 9 open reading frame 174"	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.3307C>G	chr9.hg19:g.100117288C>G	ENSP00000349562:p.Gln1103Glu	48.0	0.0		74.0	31.0	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Missense_Mutation	SNP	ENST00000357054.1	hg19		.	.	.	.	.	.	.	.	.	.	C	12.24	1.879224	0.33162	.	.	ENSG00000197816	ENST00000357054;ENST00000375202;ENST00000529487	T;T;T	0.05199	3.48;3.8;3.8	5.16	3.3	0.37823	.	0.101074	0.43579	N	0.000552	T	0.01730	0.0055	N	0.01003	-1.06	0.80722	D	1	B;B	0.20261	0.001;0.043	B;B	0.15052	0.003;0.012	T	0.42531	-0.9446	10	0.02654	T	1	-13.779	8.8157	0.34993	0.0:0.2507:0.6308:0.1185	.	1271;1103	B7ZMG3;Q9P1Z9	.;CI174_HUMAN	E	1103;1132;1132	ENSP00000349562:Q1103E;ENSP00000364348:Q1132E;ENSP00000434727:Q1132E	ENSP00000349562:Q1103E	Q	+	1	0	C9orf174	99157109	1.000000	0.71417	0.981000	0.43875	0.937000	0.57800	4.043000	0.57354	0.671000	0.31185	-0.175000	0.13238	CAG	.	.		0.463	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893		G	100117288	C	G	100117288	3	3	303	1	0	0	0	0	1	0	0	0	8249	595	21	4	3401	4	KIAA1529	9	100117288	Missense_Mutation	SNP	C	TCGA-G3-AAV7-01A-11D-A382-10	5110025	100117288	41096143	47	43640										
FOXE1	2304	hgsc.bcm.edu	37	chr9	100616728	100616728	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	ccgccgccgccgccgccgccGccgccatcttcccaggcgcg	12	24	1	0			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr9:100616728G>A	ENST00000375123.3	+	1	1193	c.532G>A	c.(532-534)Gcc>Acc	p.A178T		NM_004473.3	NP_004464.2	O00358	FOXE1_HUMAN	forkhead box E1 (thyroid transcription factor 2)	178	Ala-rich.				anatomical structure morphogenesis (GO:0009653)|cell migration (GO:0016477)|embryonic organ morphogenesis (GO:0048562)|hair follicle morphogenesis (GO:0031069)|hard palate development (GO:0060022)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pharynx development (GO:0060465)|positive regulation of transcription, DNA-templated (GO:0045893)|soft palate development (GO:0060023)|thymus development (GO:0048538)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|lung(2)|upper_aerodigestive_tract(1)	5		Acute lymphoblastic leukemia(62;0.158)				cgccgccgccgccgccATCTT	0.791																																					p.A178T		Atlas-SNP	.											.	FOXE1	19	.	0			c.G532A						.						2	2	2					9																	100616728		529	1359	1888	SO:0001583	missense	2304	exon1			GCCGCCGCCGCCA	U89995	CCDS35078.1	9q22	2008-09-05			ENSG00000178919	ENSG00000178919		"Forkhead boxes"	3806	protein-coding gene	gene with protein product		602617	"forkhead box E2"	FKHL15, TITF2, FOXE2		9169137, 9697705	Standard	NM_004473		Approved	TTF-2, HFKH4	uc004axu.3	O00358	OTTHUMG00000020333	ENST00000375123.3:c.532G>A	chr9.hg19:g.100616728G>A	ENSP00000364265:p.Ala178Thr	194.0	0.0		194.0	10.0	NM_004473	O75765|Q5T109|Q99526	Missense_Mutation	SNP	ENST00000375123.3	hg19	CCDS35078.1	.	.	.	.	.	.	.	.	.	.	G	15.77	2.930555	0.52866	.	.	ENSG00000178919	ENST00000375123	D	0.93953	-3.32	3.94	3.02	0.34903	.	0.612880	0.14474	U	0.317365	D	0.83087	0.5178	L	0.34521	1.04	0.22571	N	0.998979	P	0.47253	0.892	B	0.30251	0.113	T	0.72969	-0.4130	10	0.13108	T	0.6	.	6.9037	0.24297	0.0993:0.1791:0.7216:0.0	.	178	O00358	FOXE1_HUMAN	T	178	ENSP00000364265:A178T	ENSP00000364265:A178T	A	+	1	0	FOXE1	99656549	0.087000	0.21565	0.898000	0.35279	0.822000	0.46500	0.422000	0.21296	0.758000	0.33059	0.557000	0.71058	GCC	.	.		0.791	FOXE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053341.1			A	100616728	G	A	100616728	3	1	303	1	0	0	0	0	1	0	0	0	6011	1087	38	1	534	1	FOXE1	9	100616728	Missense_Mutation	SNP	G	TCGA-G3-AAV7-01A-11D-A382-10	499440	100616728	40596703	48	43641										
PAEP	5047	hgsc.bcm.edu	37	chr9	138457313	138457313	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	attcatcagggctttcaggcCcctgcccaggcacctatggt	10	14	3	0	rs373981009		TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr9:138457313C>A	ENST00000479141.1	+	5	523	c.479C>A	c.(478-480)cCc>cAc	p.P160H	PAEP_ENST00000277508.5_Missense_Mutation_p.P160H|PAEP_ENST00000371766.2_Missense_Mutation_p.P160H	NM_002571.2	NP_002562.2	P09466	PAEP_HUMAN	progestagen-associated endometrial protein	160					multicellular organismal development (GO:0007275)|transport (GO:0006810)	extracellular region (GO:0005576)	small molecule binding (GO:0036094)			cervix(1)|endometrium(1)|lung(1)|prostate(1)|skin(1)|stomach(1)	6				OV - Ovarian serous cystadenocarcinoma(145;3.39e-07)|Epithelial(140;1.11e-06)|all cancers(34;2.04e-05)		GCTTTCAGGCCCCTGCCCAGG	0.597																																					p.P160H		Atlas-SNP	.											.	PAEP	16	.	0			c.C479A						.	C	HIS/PRO,HIS/PRO	0,4406		0,0,2203	76	73	74		479,479	0.1	0	9		74	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	PAEP	NM_001018049.1,NM_002571.2	77,77	0,1,6502	AA,AC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	160/181,160/181	138457313	1,13005	2203	4300	6503	SO:0001583	missense	5047	exon5			TCAGGCCCCTGCC		CCDS35173.1	9q34	2011-11-15	2008-07-31		ENSG00000122133	ENSG00000122133		"Lipocalins"	8573	protein-coding gene	gene with protein product	"glycodelin-A", "glycodelin-S", "glycodelin-F", "progesterone-associated endometrial protein", "glycodelin", "PP14 protein (placental protein 14)", "pregnancy-associated endometrial alpha-2-globulin", "alpha uterine protein"	173310				3320533, 2016092	Standard	XM_005263405		Approved	PEP, PP14, GdA, GdS, GdF, PAEG, GD, MGC138509, MGC142288	uc004cgd.1	P09466	OTTHUMG00000020914	ENST00000479141.1:c.479C>A	chr9.hg19:g.138457313C>A	ENSP00000417898:p.Pro160His	79.0	0.0		91.0	29.0	NM_002571	Q5T6T1|Q9UG92	Missense_Mutation	SNP	ENST00000479141.1	hg19	CCDS35173.1	.	.	.	.	.	.	.	.	.	.	c	9.835	1.189520	0.21954	0.0	1.16E-4	ENSG00000122133	ENST00000479141;ENST00000371767;ENST00000344007;ENST00000371766;ENST00000277508;ENST00000418284	T;T;T;T	0.07567	3.18;3.18;3.18;3.18	1.06	0.109	0.14578	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	.	.	.	.	T	0.15046	0.0363	L	0.42245	1.32	0.09310	N	1	D;D;P;D	0.76494	0.995;0.998;0.939;0.999	P;D;P;D	0.69142	0.612;0.935;0.669;0.962	T	0.16129	-1.0413	9	0.72032	D	0.01	.	3.3802	0.07252	0.0:0.7085:0.0:0.2915	.	138;142;123;160	P09466-2;B2R4F9;A6XNE0;P09466	.;.;.;PAEP_HUMAN	H	160;125;66;160;160;112	ENSP00000417898:P160H;ENSP00000360831:P160H;ENSP00000277508:P160H;ENSP00000401933:P112H	ENSP00000277508:P160H	P	+	2	0	PAEP	137597134	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.162000	0.16501	0.029000	0.15352	-0.382000	0.06688	CCC	.	.		0.597	PAEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055010.1	NM_001018049		A	138457313	C	A	138457313	3	1	303	1	0	0	0	0	1	0	0	0	11391	623	22	3	497	3	PAEP	9	138457313	Missense_Mutation	SNP	C	TCGA-G3-AAV7-01A-11D-A382-10	37840585	138457313	2756118	49	43642										
CUBN	8029	hgsc.bcm.edu	37	chr10	16955931	16955931	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	agatccggccatgaggatttGggttcgggtagttgggagaa	17	5	0	3			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr10:16955931G>C	ENST00000377833.4	-	48	7477	c.7412C>G	c.(7411-7413)cCa>cGa	p.P2471R		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2471	CUB 18. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ATGAGGATTTGGGTTCGGGTA	0.522																																					p.P2471R		Atlas-SNP	.											.	CUBN	515	.	0			c.C7412G						.						102	99	100					10																	16955931		2203	4300	6503	SO:0001583	missense	8029	exon48			GGATTTGGGTTCG	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.7412C>G	chr10.hg19:g.16955931G>C	ENSP00000367064:p.Pro2471Arg	54.0	0.0		50.0	10.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	G	3.525	-0.097014	0.07010	.	.	ENSG00000107611	ENST00000377833	T	0.30714	1.52	4.89	4.89	0.63831	CUB (5);	0.157695	0.30151	N	0.010294	T	0.20941	0.0504	L	0.41356	1.27	0.80722	D	1	B	0.06786	0.001	B	0.09377	0.004	T	0.09400	-1.0676	10	0.17369	T	0.5	.	6.5831	0.22607	0.1533:0.1566:0.6901:0.0	.	2471	O60494	CUBN_HUMAN	R	2471	ENSP00000367064:P2471R	ENSP00000367064:P2471R	P	-	2	0	CUBN	16995937	0.998000	0.40836	0.874000	0.34290	0.889000	0.51656	3.177000	0.50871	2.553000	0.86117	0.591000	0.81541	CCA	.	.		0.522	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		C	16955931	G	C	16955931	3	2	303	1	0	0	0	0	1	0	0	0	4053	1348	47	4	3539	4	CUBN	10	16955931	Missense_Mutation	SNP	G	TCGA-G3-AAV7-01A-11D-A382-10		16955931	118578816	50	43643										
CUBN	8029	hgsc.bcm.edu	37	chr10	17142085	17142085	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	gagatgaaaatagagagcatTgtcactgctgaggagttcat	12	5	2	4			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr10:17142085T>C	ENST00000377833.4	-	14	1749	c.1684A>G	c.(1684-1686)Aat>Gat	p.N562D		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	562	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TAGAGAGCATTGTCACTGCTG	0.428																																					p.N562D		Atlas-SNP	.											.	CUBN	515	.	0			c.A1684G						.						118	118	118					10																	17142085		2203	4300	6503	SO:0001583	missense	8029	exon14			GAGCATTGTCACT	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.1684A>G	chr10.hg19:g.17142085T>C	ENSP00000367064:p.Asn562Asp	235.0	0.0		243.0	80.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.273220	0.80580	.	.	ENSG00000107611	ENST00000377833	T	0.65732	-0.17	5.51	5.51	0.81932	CUB (5);	0.145914	0.31450	N	0.007623	T	0.67906	0.2943	M	0.67517	2.055	0.80722	D	1	P	0.38300	0.626	P	0.44623	0.455	T	0.68899	-0.5287	10	0.44086	T	0.13	.	15.6269	0.76867	0.0:0.0:0.0:1.0	.	562	O60494	CUBN_HUMAN	D	562	ENSP00000367064:N562D	ENSP00000367064:N562D	N	-	1	0	CUBN	17182091	1.000000	0.71417	0.975000	0.42487	0.774000	0.43823	4.491000	0.60326	2.091000	0.63221	0.528000	0.53228	AAT	.	.		0.428	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		C	17142085	T	C	17142085	3	2	303	1	0	0	0	0	1	0	0	0	4053	1812	63	2	9403	2	CUBN	10	17142085	Missense_Mutation	SNP	T	TCGA-G3-AAV7-01A-11D-A382-10	186154	17142085	118392662	51	43644										
SLC16A9	220963	hgsc.bcm.edu	37	chr10	61412663	61412663	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	gcaggacgcagaagccactaAaataaaatgcaatatcatag	8	8	1	1			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr10:61412663A>T	ENST00000395348.3	-	6	2033	c.1397T>A	c.(1396-1398)tTt>tAt	p.F466Y	SLC16A9_ENST00000395347.1_Missense_Mutation_p.F466Y	NM_194298.2	NP_919274.1	Q7RTY1	MOT9_HUMAN	solute carrier family 16, member 9	466					urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)	p.F466C(1)		kidney(3)|large_intestine(5)|lung(5)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	23						GAAGCCACTAAAATAAAATGC	0.438																																					p.F466Y		Atlas-SNP	.											SLC16A9,larynx,carcinoma,0,1	SLC16A9	58	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.T1397A						.						70	77	74					10																	61412663		2203	4300	6503	SO:0001583	missense	220963	exon6			CCACTAAAATAAA	AK125791	CCDS7256.1	10q21.3	2013-07-18	2013-07-18	2004-01-21	ENSG00000165449	ENSG00000165449		"Solute carriers"	23520	protein-coding gene	gene with protein product	"monocarboxylic acid transporter 9"	614242	"chromosome 10 open reading frame 36", "solute carrier family 16 (monocarboxylic acid transporters), member 9", "solute carrier family 16, member 9 (monocarboxylic acid transporter 9)"	C10orf36			Standard	NM_194298		Approved	FLJ43803, MCT9	uc010qig.1	Q7RTY1	OTTHUMG00000018283	ENST00000395348.3:c.1397T>A	chr10.hg19:g.61412663A>T	ENSP00000378757:p.Phe466Tyr	265.0	0.0		356.0	115.0	NM_194298	Q6ZMI2|Q9UFH8	Missense_Mutation	SNP	ENST00000395348.3	hg19	CCDS7256.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.412625	0.83340	.	.	ENSG00000165449	ENST00000395348;ENST00000395347	T;T	0.81330	-1.48;-1.48	5.57	5.57	0.84162	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.256104	0.48286	D	0.000189	D	0.84920	0.5579	L	0.61387	1.9	0.46061	D	0.998841	D	0.58268	0.982	P	0.58577	0.841	T	0.81901	-0.0720	10	0.14252	T	0.57	.	15.7166	0.77672	1.0:0.0:0.0:0.0	.	466	Q7RTY1	MOT9_HUMAN	Y	466	ENSP00000378757:F466Y;ENSP00000378756:F466Y	ENSP00000378756:F466Y	F	-	2	0	SLC16A9	61082669	1.000000	0.71417	0.997000	0.53966	0.853000	0.48598	8.523000	0.90576	2.103000	0.63969	0.528000	0.53228	TTT	.	.		0.438	SLC16A9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048174.2	NM_194298		T	61412663	A	T	61412663	3	4	303	1	0	0	0	0	1	0	0	0	14430	14	1	4	136	4	SLC16A9	10	61412663	Missense_Mutation	SNP	A	TCGA-G3-AAV7-01A-11D-A382-10	44270578	61412663	74122084	52	43645										
LRIT1	26103	hgsc.bcm.edu	37	chr10	85997354	85997354	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	ctcgccaggaaccctgcgtaTggccgtccgctccaggcgca	12	17	0	0			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr10:85997354T>C	ENST00000372105.3	-	2	232	c.211A>G	c.(211-213)Ata>Gta	p.I71V		NM_015613.2	NP_056428.1	Q9P2V4	LRIT1_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 1	71						integral component of endoplasmic reticulum membrane (GO:0030176)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|skin(1)	23						ACCCTGCGTATGGCCGTCCGC	0.682																																					p.I71V		Atlas-SNP	.											.	LRIT1	73	.	0			c.A211G						.						24	29	27					10																	85997354		2172	4251	6423	SO:0001583	missense	26103	exon2			TGCGTATGGCCGT	AB031547	CCDS7373.1	10q23	2013-02-11	2007-06-19	2007-06-19	ENSG00000148602	ENSG00000148602		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	23404	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 9"		"leucine rich repeat containing 21"	LRRC21		10777785	Standard	NM_015613		Approved	PAL, DKFZP434K091, FIGLER9	uc001kcz.1	Q9P2V4	OTTHUMG00000018632	ENST00000372105.3:c.211A>G	chr10.hg19:g.85997354T>C	ENSP00000361177:p.Ile71Val	58.0	0.0		84.0	15.0	NM_015613	Q0QD41|Q9Y4N7	Missense_Mutation	SNP	ENST00000372105.3	hg19	CCDS7373.1	.	.	.	.	.	.	.	.	.	.	T	14.03	2.413596	0.42817	.	.	ENSG00000148602	ENST00000372105	T	0.56941	0.43	5.46	-1.35	0.09114	.	0.355643	0.28694	N	0.014445	T	0.49558	0.1564	M	0.85630	2.765	0.52501	D	0.99995	B	0.13594	0.008	B	0.14578	0.011	T	0.31336	-0.9947	10	0.48119	T	0.1	.	6.382	0.21540	0.0:0.1536:0.4385:0.408	.	71	Q9P2V4	LRIT1_HUMAN	V	71	ENSP00000361177:I71V	ENSP00000361177:I71V	I	-	1	0	LRIT1	85987334	1.000000	0.71417	0.109000	0.21407	0.922000	0.55478	1.610000	0.36869	-0.513000	0.06496	0.533000	0.62120	ATA	.	.		0.682	LRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049109.1	NM_015613		C	85997354	T	C	85997354	3	2	303	1	0	0	0	0	1	0	0	0	8956	1464	51	2	1672	2	LRIT1	10	85997354	Missense_Mutation	SNP	T	TCGA-G3-AAV7-01A-11D-A382-10	24584691	85997354	49537393	53	43646										
GRID1	2894	hgsc.bcm.edu	37	chr10	87373360	87373360	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	ccatgtgcggccaccacttcTgcttcagcacatccaggtcc	8	17	2	0			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr10:87373360T>C	ENST00000327946.7	-	15	2490	c.2405A>G	c.(2404-2406)cAg>cGg	p.Q802R	GRID1_ENST00000552278.2_5'Flank|GRID1_ENST00000536331.1_Missense_Mutation_p.Q373R	NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	802					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|social behavior (GO:0035176)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|ionotropic glutamate receptor complex (GO:0008328)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(46)|ovary(5)|prostate(4)|skin(5)|stomach(4)|upper_aerodigestive_tract(5)	106						CCACCACTTCTGCTTCAGCAC	0.607										Multiple Myeloma(13;0.14)																											p.Q802R		Atlas-SNP	.											.	GRID1	204	.	0			c.A2405G						.						77	82	80					10																	87373360		2203	4300	6503	SO:0001583	missense	2894	exon15			CACTTCTGCTTCA	AB033046	CCDS31236.1	10q22	2012-08-29			ENSG00000182771	ENSG00000182771		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4575	protein-coding gene	gene with protein product		610659					Standard	NM_017551		Approved	GluD1, KIAA1220	uc001kdl.1	Q9ULK0	OTTHUMG00000018650	ENST00000327946.7:c.2405A>G	chr10.hg19:g.87373360T>C	ENSP00000330148:p.Gln802Arg	122.0	0.0		193.0	61.0	NM_017551	B3KXD5|B7Z7L0|Q8IXT3	Missense_Mutation	SNP	ENST00000327946.7	hg19	CCDS31236.1	.	.	.	.	.	.	.	.	.	.	T	17.16	3.318270	0.60524	.	.	ENSG00000182771	ENST00000327946;ENST00000536331	T;T	0.27104	1.69;1.69	5.46	5.46	0.80206	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.052929	0.85682	D	0.000000	T	0.21921	0.0528	N	0.21142	0.635	0.80722	D	1	B	0.27286	0.174	B	0.32211	0.142	T	0.05616	-1.0874	10	0.59425	D	0.04	.	14.7069	0.69198	0.0:0.0:0.0:1.0	.	802	Q9ULK0	GRID1_HUMAN	R	802;373	ENSP00000330148:Q802R;ENSP00000444455:Q373R	ENSP00000330148:Q802R	Q	-	2	0	GRID1	87363340	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.698000	0.84413	2.075000	0.62263	0.454000	0.30748	CAG	.	.		0.607	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3	XM_043613		C	87373360	T	C	87373360	3	2	303	1	0	0	0	0	1	0	0	0	6780	1580	55	2	632	2	GRID1	10	87373360	Missense_Mutation	SNP	T	TCGA-G3-AAV7-01A-11D-A382-10	1376006	87373360	48161387	54	43647										
CHUK	1147	hgsc.bcm.edu	37	chr10	101950685	101950685	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	aatagtgcttaaatggccaaGgcagttcaaattttcttcta	7	7	3	0			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr10:101950685G>T	ENST00000370397.7	-	20	2235	c.2149C>A	c.(2149-2151)Ctt>Att	p.L717I	CHUK_ENST00000590930.1_5'UTR|ERLIN1_ENST00000421367.2_5'Flank|RP11-316M21.7_ENST00000443919.1_RNA	NM_001278.3	NP_001269.3	O15111	IKKA_HUMAN	conserved helix-loop-helix ubiquitous kinase	717					anatomical structure morphogenesis (GO:0009653)|cellular response to tumor necrosis factor (GO:0071356)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|morphogenesis of an epithelial sheet (GO:0002011)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hydroperoxide (GO:0033194)|response to lipopolysaccharide (GO:0032496)|response to toxic substance (GO:0009636)|response to virus (GO:0009615)|Rho protein signal transduction (GO:0007266)|skeletal muscle contraction (GO:0003009)|striated muscle cell differentiation (GO:0051146)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|scaffold protein binding (GO:0097110)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(9)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	27		Colorectal(252;0.117)		Epithelial(162;2.05e-10)|all cancers(201;1.91e-08)	Acetylcysteine(DB06151)|Aminosalicylic Acid(DB00233)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	AAATGGCCAAGGCAGTTCAAA	0.398																																					p.L717I	Ovarian(159;52 1904 10536 35305 37148)	Atlas-SNP	.											.	CHUK	71	.	0			c.C2149A						.						234	214	221					10																	101950685		2203	4300	6503	SO:0001583	missense	1147	exon20			GGCCAAGGCAGTT	AF009225	CCDS7488.1	10q24-q25	2008-08-01			ENSG00000213341	ENSG00000213341			1974	protein-coding gene	gene with protein product		600664		TCF16		7558004, 16902410	Standard	XR_246062		Approved	IKK1, IKK-alpha, IkBKA, NFKBIKA, IKKA	uc001kqp.3	O15111	OTTHUMG00000018899	ENST00000370397.7:c.2149C>A	chr10.hg19:g.101950685G>T	ENSP00000359424:p.Leu717Ile	118.0	0.0		127.0	23.0	NM_001278	O14666|Q13132|Q5W0I4|Q92467	Missense_Mutation	SNP	ENST00000370397.7	hg19	CCDS7488.1	.	.	.	.	.	.	.	.	.	.	G	16.89	3.247910	0.59103	.	.	ENSG00000213341	ENST00000370397	T	0.33216	1.42	5.89	5.89	0.94794	I-kappa-kinase-beta NEMO binding domain (1);	0.063063	0.64402	D	0.000005	T	0.47322	0.1439	L	0.59436	1.845	0.49582	D	0.999806	D	0.61080	0.989	P	0.59643	0.861	T	0.14504	-1.0470	10	0.30854	T	0.27	-15.3343	15.7448	0.77929	0.0:0.0:1.0:0.0	.	717	O15111	IKKA_HUMAN	I	717	ENSP00000359424:L717I	ENSP00000359424:L717I	L	-	1	0	CHUK	101940675	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	5.393000	0.66279	2.790000	0.95986	0.609000	0.83330	CTT	.	.		0.398	CHUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049836.1	NM_001278		T	101950685	G	T	101950685	3	4	303	1	0	0	0	0	1	0	0	0	3418	1000	35	3	96	3	CHUK	10	101950685	Missense_Mutation	SNP	G	TCGA-G3-AAV7-01A-11D-A382-10	14577325	101950685	33584062	55	43648										
KRTAP5-4	387267	hgsc.bcm.edu	37	chr11	1642908	1642908	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	agcagggcttacagcagctgCactgggagcagccacaagag	14	11	0	1			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr11:1642908C>G	ENST00000399682.1	-	1	460	c.416G>C	c.(415-417)tGc>tCc	p.C139S		NM_001012709.1	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	0	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				NS(1)|endometrium(9)|kidney(2)|lung(2)|pancreas(1)|prostate(3)|skin(2)	20		all_epithelial(84;0.00819)|Breast(177;0.00832)|Ovarian(85;0.0256)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		ACAGCAGCTGCACTGGGAGCA	0.642																																					p.C139S		Atlas-SNP	.											.	KRTAP5-4	78	.	0			c.G416C						.						16	31	26					11																	1642908		692	1589	2281	SO:0001583	missense	387267	exon1			CAGCTGCACTGGG	AB126073		11p15.5	2012-04-19			ENSG00000241598	ENSG00000241598		"Keratin associated proteins"	23599	protein-coding gene	gene with protein product						15144888	Standard	NM_001012709		Approved	KRTAP5.4	uc009ycy.1	Q6L8H1	OTTHUMG00000057553	ENST00000399682.1:c.416G>C	chr11.hg19:g.1642908C>G	ENSP00000382590:p.Cys139Ser	164.0	0.0		144.0	6.0	NM_001012709		Missense_Mutation	SNP	ENST00000399682.1	hg19		.	.	.	.	.	.	.	.	.	.	C	0.001	-3.519974	0.00010	.	.	ENSG00000241598	ENST00000399682;ENST00000328953	T	0.00695	5.83	2.21	1.25	0.21368	.	.	.	.	.	T	0.00300	0.0009	N	0.00621	-1.32	0.20638	N	0.999873	B	0.02656	0.0	B	0.01281	0.0	T	0.42899	-0.9424	9	0.02654	T	1	.	4.6118	0.12406	0.0:0.2511:0.5007:0.2483	.	199	Q6L8H1	KRA54_HUMAN	S	139	ENSP00000382590:C139S	ENSP00000331603:C139S	C	-	2	0	KRTAP5-4	1599484	0.001000	0.12720	0.020000	0.16555	0.001000	0.01503	0.013000	0.13310	0.265000	0.21872	-0.989000	0.02550	TGC	.	.		0.642	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709		G	1642908	C	G	1642908	3	3	303	1	0	0	0	0	1	0	0	0	8572	710	25	4	274	4	KRTAP5-4	11	1642908	Missense_Mutation	SNP	C	TCGA-G3-AAV7-01A-11D-A382-10		1642908	133363608	56	43649										
PCNXL3	399909	hgsc.bcm.edu	37	chr11	65404386	65404386	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	atgggtgccctgggcgactgGcctgcccctattgaggagcg	16	12	0	1			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr11:65404386G>T	ENST00000355703.3	+	35	6581	c.6042G>T	c.(6040-6042)tgG>tgT	p.W2014C	SIPA1_ENST00000527525.1_5'Flank|SIPA1_ENST00000534313.1_5'Flank|MIR4690_ENST00000578459.1_RNA	NM_032223.2	NP_115599.2	Q9H6A9	PCX3_HUMAN	pecanex-like 3 (Drosophila)	2014						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)	13						TGGGCGACTGGCCTGCCCCTA	0.637																																					p.W2014C		Atlas-SNP	.											.	PCNXL3	140	.	0			c.G6042T						.						15	18	17					11																	65404386		1935	4129	6064	SO:0001583	missense	399909	exon35			CGACTGGCCTGCC	BX640978	CCDS44650.1	11q12.1	2008-07-21			ENSG00000197136	ENSG00000197136			18760	protein-coding gene	gene with protein product						15146197	Standard	NM_032223		Approved	FLJ22427	uc001oey.2	Q9H6A9	OTTHUMG00000166539	ENST00000355703.3:c.6042G>T	chr11.hg19:g.65404386G>T	ENSP00000347931:p.Trp2014Cys	61.0	0.0		53.0	21.0	NM_032223	Q6MZN8	Missense_Mutation	SNP	ENST00000355703.3	hg19	CCDS44650.1	.	.	.	.	.	.	.	.	.	.	G	11.72	1.721775	0.30503	.	.	ENSG00000197136	ENST00000355703	T	0.08807	3.05	5.17	4.23	0.50019	.	0.000000	0.35013	N	0.003508	T	0.06826	0.0174	N	0.24115	0.695	0.46609	D	0.999129	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.19549	-1.0302	10	0.56958	D	0.05	.	11.5486	0.50708	0.0:0.1809:0.8191:0.0	.	901;2014	Q9H6A9-3;Q9H6A9	.;PCX3_HUMAN	C	2014	ENSP00000347931:W2014C	ENSP00000347931:W2014C	W	+	3	0	PCNXL3	65160962	1.000000	0.71417	1.000000	0.80357	0.090000	0.18270	3.522000	0.53480	1.141000	0.42275	0.462000	0.41574	TGG	.	.		0.637	PCNXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390321.1	NM_032223		T	65404386	G	T	65404386	3	4	303	1	0	0	0	0	1	0	0	0	11602	1212	42	3	6180	3	PCNXL3	11	65404386	Missense_Mutation	SNP	G	TCGA-G3-AAV7-01A-11D-A382-10	63761478	65404386	69602130	57	43650										
ST14	6768	hgsc.bcm.edu	37	chr11	130079716	130079716	+	Stop_Codon_Del	DEL	T	T	-													0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	tcaaagagaacactggggtaTaggggccggggccacccaaa							TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr11:130079716delT	ENST00000278742.5	+	0	2984					NM_021978.3	NP_068813.1	Q9Y5Y6	ST14_HUMAN	suppression of tumorigenicity 14 (colon carcinoma)						keratinocyte differentiation (GO:0030216)|proteolysis (GO:0006508)	basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|ovary(3)|pancreas(2)|prostate(1)|skin(3)	32	all_hematologic(175;0.0429)	Lung NSC(97;0.000602)|Breast(109;0.000962)|all_lung(97;0.00126)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0183)|Lung(977;0.228)	Urokinase(DB00013)	CACTGGGGTATAGGGGCCGGG	0.627																																					p.V855fs		Atlas-Indel,Pindel	.											.	ST14	82	.	0			c.2565delA						.						66	74	71					11																	130079716		2201	4297	6498	SO:0001567	stop_retained_variant	6768	exon19			.	AF118224	CCDS8487.1	11q24-q25	2011-08-31	2005-11-19		ENSG00000149418	ENSG00000149418		"Serine peptidases / Transmembrane"	11344	protein-coding gene	gene with protein product	"epithin", "matriptase"	606797		PRSS14		9925927, 10373424	Standard	NM_021978		Approved	SNC19, HAI, MT-SP1, TMPRSS14	uc001qfw.3	Q9Y5Y6	OTTHUMG00000165768	Exception_encountered	chr11.hg19:g.130079716delT		55.0	0.0		89.0	21.0	NM_021978	Q9BS01|Q9H3S0|Q9HB36|Q9HCA3	Frame_Shift_Del	DEL	ENST00000278742.5	hg19	CCDS8487.1																																																																																			.	.		0.627	ST14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386119.1			-	130079716	T	-	130079716	7	5	303	1	0	1	0	1	0	0	0	0	15226	1419	49	0	2640	0	ST14	11	130079716	Stop_Codon_Del	DEL	T	TCGA-G3-AAV7-01A-11D-A382-10	64675330	130079716	4926800	58	43651										
PLEKHA5	54477	hgsc.bcm.edu	37	chr12	19501413	19501413	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	gaatctaatggagaagaaaaAtcagaacctgtttcagagat	9	5	3	4			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr12:19501413A>G	ENST00000299275.6	+	19	2487	c.2481A>G	c.(2479-2481)aaA>aaG	p.K827K	PLEKHA5_ENST00000543806.1_Silent_p.K809K|PLEKHA5_ENST00000538714.1_Silent_p.K885K|PLEKHA5_ENST00000429027.2_Silent_p.K993K|PLEKHA5_ENST00000355397.3_Silent_p.K885K|PLEKHA5_ENST00000317589.4_Silent_p.K890K|PLEKHA5_ENST00000539256.1_Silent_p.K585K|PLEKHA5_ENST00000424268.1_Silent_p.K816K|PLEKHA5_ENST00000359180.3_Intron	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5	827					reproductive system development (GO:0061458)	cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					GAGAAGAAAAATCAGAACCTG	0.353																																					p.K993K	Pancreas(196;329 2193 11246 14234 19524)	Atlas-SNP	.											.	PLEKHA5	198	.	0			c.A2979G						.						92	92	92					12																	19501413		2203	4300	6503	SO:0001819	synonymous_variant	54477	exon25			AGAAAAATCAGAA	AF302150	CCDS8682.1, CCDS44840.1, CCDS44840.2, CCDS55809.1, CCDS58213.1, CCDS58214.1	12p12	2013-01-10			ENSG00000052126	ENSG00000052126		"Pleckstrin homology (PH) domain containing"	30036	protein-coding gene	gene with protein product		607770				11214970, 11001876	Standard	NM_001143821		Approved	PEPP2, KIAA1686, FLJ10667	uc031qgo.1	Q9HAU0	OTTHUMG00000167921	ENST00000299275.6:c.2481A>G	chr12.hg19:g.19501413A>G		158.0	0.0		123.0	52.0	NM_001256470	A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	Silent	SNP	ENST00000299275.6	hg19	CCDS8682.1																																																																																			.	.		0.353	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	NM_019012		G	19501413	A	G	19501413	2	3	303	1	0	0	0	0	0	0	0	1	12068	98	4	2		2	PLEKHA5	12	19501413	Silent	SNP	A	TCGA-G3-AAV7-01A-11D-A382-10		19501413	114350482	59	43652										
CALCOCO1	57658	hgsc.bcm.edu	37	chr12	54118961	54118961	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	ttggtgttggggatgtaggtCcgggctacattgagaaagtt	16	4	0	1			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr12:54118961C>A	ENST00000550804.1	-	2	126	c.66G>T	c.(64-66)cgG>cgT	p.R22R	CALCOCO1_ENST00000430117.2_Silent_p.R22R|CALCOCO1_ENST00000548263.1_Silent_p.R22R|CALCOCO1_ENST00000262059.4_Silent_p.R22R|CALCOCO1_ENST00000547885.1_5'UTR			Q9P1Z2	CACO1_HUMAN	calcium binding and coiled-coil domain 1	22	N-terminal AD (CTNNB1 binding site). {ECO:0000250}.|p300 KIX-binding. {ECO:0000250}.				intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	28						GGATGTAGGTCCGGGCTACAT	0.532																																					p.R22R		Atlas-SNP	.											.	CALCOCO1	50	.	0			c.G66T						.						201	155	171					12																	54118961		2203	4300	6503	SO:0001819	synonymous_variant	57658	exon2			GTAGGTCCGGGCT	AL136895	CCDS8864.1, CCDS44908.1	12q13.13	2014-01-02			ENSG00000012822	ENSG00000012822			29306	protein-coding gene	gene with protein product	"coiled-coil leucine zipper coactivator 1", "inorganic pyrophosphatase activator"					10819331, 11230166	Standard	NM_020898		Approved	KIAA1536, calphoglin, Cocoa	uc001sef.3	Q9P1Z2	OTTHUMG00000170095	ENST00000550804.1:c.66G>T	chr12.hg19:g.54118961C>A		170.0	0.0		226.0	40.0	NM_020898	B3KVA8|Q6FI59|Q71RC3|Q86WF8|Q96JU3|Q9H090	Silent	SNP	ENST00000550804.1	hg19	CCDS8864.1																																																																																			.	.		0.532	CALCOCO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407233.2	NM_020898		A	54118961	C	A	54118961	2	1	303	1	0	0	0	0	0	0	0	1	2579	842	30	3		3	CALCOCO1	12	54118961	Silent	SNP	C	TCGA-G3-AAV7-01A-11D-A382-10	34617548	54118961	79732934	60	43653										
AGAP2	116986	hgsc.bcm.edu	37	chr12	58131025	58131025	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	cggtcacgagtggatgctcgGcccccctcccggccccgttt	12	18	1	0			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr12:58131025G>T	ENST00000547588.1	-	1	1004	c.1005C>A	c.(1003-1005)ggC>ggA	p.G335G	AGAP2_ENST00000257897.3_Intron	NM_001122772.2	NP_001116244.1	Q99490	AGAP2_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	335	Interaction with PLCG1. {ECO:0000250}.				axon guidance (GO:0007411)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|large_intestine(7)|lung(20)|prostate(3)|skin(1)|stomach(1)	48						TGGATGCTCGGCCCCCCTCCC	0.682																																					p.G335G		Atlas-SNP	.											.	AGAP2	167	.	0			c.C1005A						.						13	19	17					12																	58131025		1563	3580	5143	SO:0001819	synonymous_variant	116986	exon1			TGCTCGGCCCCCC	AF413077	CCDS8951.1, CCDS44932.1	12q13.2	2013-05-30	2008-09-22	2008-09-22	ENSG00000135439	ENSG00000135439		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16921	protein-coding gene	gene with protein product		605476	"centaurin, gamma 1"	CENTG1			Standard	NM_001122772		Approved		uc001spq.3	Q99490	OTTHUMG00000170285	ENST00000547588.1:c.1005C>A	chr12.hg19:g.58131025G>T		107.0	0.0		155.0	50.0	NM_001122772	A8K9F7|O00578|Q548E0|Q8IWU3	Silent	SNP	ENST00000547588.1	hg19	CCDS44932.1	.	.	.	.	.	.	.	.	.	.	G	6.884	0.532513	0.13127	.	.	ENSG00000135439	ENST00000328568	.	.	.	4.3	2.41	0.29592	.	.	.	.	.	T	0.55449	0.1921	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50608	-0.8808	4	.	.	.	.	7.2698	0.26250	0.0992:0.1769:0.7238:0.0	.	.	.	.	T	199	.	.	P	-	1	0	AGAP2	56417292	0.981000	0.34729	1.000000	0.80357	0.992000	0.81027	0.326000	0.19646	1.128000	0.42052	0.555000	0.69702	CCG	.	.		0.682	AGAP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408367.1	NM_014770		T	58131025	G	T	58131025	2	4	303	1	0	0	0	0	0	0	0	1	368	1190	42	3		3	AGAP2	12	58131025	Silent	SNP	G	TCGA-G3-AAV7-01A-11D-A382-10	4012064	58131025	75720870	61	43654										
AGAP2	116986	hgsc.bcm.edu	37	chr12	58131661	58131661	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	tcggggctcagtcccccggaGagcgggggtcccggagggac	19	13	1	1			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr12:58131661G>T	ENST00000547588.1	-	1	368	c.369C>A	c.(367-369)ctC>ctA	p.L123L	AGAP2_ENST00000257897.3_Intron	NM_001122772.2	NP_001116244.1	Q99490	AGAP2_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	123					axon guidance (GO:0007411)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|large_intestine(7)|lung(20)|prostate(3)|skin(1)|stomach(1)	48						GTCCCCCGGAGAGCGGGGGTC	0.811																																					p.L123L		Atlas-SNP	.											.	AGAP2	167	.	0			c.C369A						.						1	1	1					12																	58131661		432	1106	1538	SO:0001819	synonymous_variant	116986	exon1			CCCGGAGAGCGGG	AF413077	CCDS8951.1, CCDS44932.1	12q13.2	2013-05-30	2008-09-22	2008-09-22	ENSG00000135439	ENSG00000135439		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16921	protein-coding gene	gene with protein product		605476	"centaurin, gamma 1"	CENTG1			Standard	NM_001122772		Approved		uc001spq.3	Q99490	OTTHUMG00000170285	ENST00000547588.1:c.369C>A	chr12.hg19:g.58131661G>T		23.0	0.0		33.0	5.0	NM_001122772	A8K9F7|O00578|Q548E0|Q8IWU3	Silent	SNP	ENST00000547588.1	hg19	CCDS44932.1																																																																																			.	.		0.811	AGAP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408367.1	NM_014770		T	58131661	G	T	58131661	2	4	303	1	0	0	0	0	0	0	0	1	368	929	33	3		3	AGAP2	12	58131661	Silent	SNP	G	TCGA-G3-AAV7-01A-11D-A382-10	636	58131661	75720234	62	43655										
ANKS1B	56899	hgsc.bcm.edu	37	chr12	99145188	99145188	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	tgggtttggagggtttgtttTcaaagctttctggaagtgtg	15	3	2	0			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr12:99145188T>C	ENST00000547776.2	-	25	3616	c.3617A>G	c.(3616-3618)gAa>gGa	p.E1206G	ANKS1B_ENST00000549493.2_Missense_Mutation_p.E456G|ANKS1B_ENST00000549025.2_Missense_Mutation_p.E304G|ANKS1B_ENST00000333732.7_Missense_Mutation_p.E236G|ANKS1B_ENST00000549558.2_Missense_Mutation_p.E372G|ANKS1B_ENST00000341752.7_Missense_Mutation_p.E212G|ANKS1B_ENST00000546960.1_Missense_Mutation_p.E432G|ANKS1B_ENST00000332712.7_Missense_Mutation_p.E396G|ANKS1B_ENST00000329257.7_Missense_Mutation_p.E1206G|ANKS1B_ENST00000550693.2_Missense_Mutation_p.E396G|ANKS1B_ENST00000547446.1_Missense_Mutation_p.E341G|ANKS1B_ENST00000547010.1_Missense_Mutation_p.E722G|ANKS1B_ENST00000546568.1_Missense_Mutation_p.E372G	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	1206	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.					cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(15)|lung(38)|pancreas(1)|prostate(2)|skin(1)	70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		GGGTTTGTTTTCAAAGCTTTC	0.483																																					p.E1206G		Atlas-SNP	.											ANKS1B_ENST00000549493,lower_third,carcinoma,0,2	ANKS1B	180	.	0			c.A3617G						.						141	145	144					12																	99145188		1870	4101	5971	SO:0001583	missense	56899	exon25			TTGTTTTCAAAGC	AF145204	CCDS55864.1, CCDS55865.1, CCDS55866.1, CCDS55867.1, CCDS55868.1, CCDS55869.1, CCDS55870.1, CCDS55871.1, CCDS55872.1	12q23.1	2013-01-10						"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	24600	protein-coding gene	gene with protein product		607815				10490826, 12415113	Standard	NM_020140		Approved	EB-1, AIDA-1, cajalin-2, ANKS2	uc001tge.2	Q7Z6G8		ENST00000547776.2:c.3617A>G	chr12.hg19:g.99145188T>C	ENSP00000449629:p.Glu1206Gly	155.0	0.0		187.0	43.0	NM_152788	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Missense_Mutation	SNP	ENST00000547776.2	hg19	CCDS55872.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.48|18.48	3.633442|3.633442	0.67015|0.67015	.|.	.|.	ENSG00000185046|ENSG00000185046	ENST00000341752;ENST00000549558;ENST00000547776;ENST00000547010;ENST00000329257;ENST00000538702;ENST00000550693;ENST00000549025;ENST00000549493;ENST00000547446;ENST00000333732;ENST00000546568;ENST00000332712;ENST00000407362;ENST00000546960|ENST00000550778	T;T;T;T;T;T;T;T;T;T;T;T;T|.	0.72394|.	-0.25;-0.23;0.86;0.11;0.86;-0.27;0.36;-0.25;-0.65;-0.21;-0.27;0.05;-0.23|.	4.78|4.78	4.78|4.78	0.61160|0.61160	.|.	0.074001|.	0.51477|.	D|.	0.000081|.	T|T	0.69324|0.69324	0.3098|0.3098	L|L	0.60455|0.60455	1.87|1.87	0.40129|0.40129	D|D	0.976694|0.976694	B;B;B;P;B;P;B;P;P;B;B;D;B|.	0.76494|.	0.007;0.386;0.267;0.768;0.332;0.547;0.004;0.855;0.528;0.004;0.296;0.999;0.018|.	B;B;B;P;B;B;B;P;B;B;B;D;B|.	0.75484|.	0.022;0.108;0.05;0.543;0.167;0.11;0.025;0.69;0.167;0.012;0.192;0.986;0.024|.	T|T	0.69960|0.69960	-0.5003|-0.5003	10|5	0.87932|.	D|.	0|.	-13.3509|-13.3509	14.5949|14.5949	0.68397|0.68397	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	341;236;236;432;396;346;420;372;456;304;722;1206;372|.	F8VPM3;F8VR14;B7Z9I9;Q7Z6G8-4;Q7Z6G8-5;B1VKB5;F8VQW6;Q7Z6G8-2;Q7Z6G8-3;F8VZR9;Q7Z6G8-6;Q7Z6G8;Q7Z6G8-7|.	.;.;.;.;.;.;.;.;.;.;.;ANS1B_HUMAN;.|.	G|E	212;372;1206;722;1206;721;396;304;456;341;236;372;396;297;432|478	ENSP00000345510:E212G;ENSP00000448993:E372G;ENSP00000449629:E1206G;ENSP00000448512:E722G;ENSP00000331381:E1206G;ENSP00000447999:E396G;ENSP00000447312:E304G;ENSP00000448203:E456G;ENSP00000450015:E341G;ENSP00000331256:E236G;ENSP00000448205:E372G;ENSP00000332683:E396G;ENSP00000447839:E432G|.	ENSP00000331381:E1206G|.	E|K	-|-	2|1	0|0	ANKS1B|ANKS1B	97669319|97669319	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.651000|7.651000	0.83577|0.83577	1.918000|1.918000	0.55548|0.55548	0.459000|0.459000	0.35465|0.35465	GAA|AAA	.	.		0.483	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140		C	99145188	T	C	99145188	3	2	303	1	0	0	0	0	1	0	0	0	689	1783	62	2	252	2	ANKS1B	12	99145188	Missense_Mutation	SNP	T	TCGA-G3-AAV7-01A-11D-A382-10	41013527	99145188	34706707	63	43656										
RFX4	5992	hgsc.bcm.edu	37	chr12	107103177	107103177	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	aaagtggctctccacgacctCccagaaaacttgcgaaacat	7	13	1	1			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr12:107103177C>T	ENST00000392842.1	+	9	1317	c.903C>T	c.(901-903)ctC>ctT	p.L301L	RFX4_ENST00000229387.5_Silent_p.L207L|RP11-144F15.1_ENST00000551505.1_Intron|RFX4_ENST00000357881.4_Silent_p.L310L	NM_213594.2	NP_998759.1	Q33E94	RFX4_HUMAN	regulatory factor X, 4 (influences HLA class II expression)	301					cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|dorsal spinal cord development (GO:0021516)|midbrain development (GO:0030901)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein processing (GO:0070613)|telencephalon development (GO:0021537)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(20)|pancreas(1)|upper_aerodigestive_tract(1)	35						TCCACGACCTCCCAGAAAACT	0.398																																					p.L310L		Atlas-SNP	.											.	RFX4	218	.	0			c.C930T						.						90	79	83					12																	107103177		2203	4300	6503	SO:0001819	synonymous_variant	5992	exon9			CGACCTCCCAGAA	AB044245	CCDS9106.1, CCDS9108.1, CCDS55880.1	12q24	2008-08-05			ENSG00000111783	ENSG00000111783			9985	protein-coding gene	gene with protein product		603958				8600444, 11682486	Standard	NM_213594		Approved		uc001tlt.3	Q33E94	OTTHUMG00000169173	ENST00000392842.1:c.903C>T	chr12.hg19:g.107103177C>T		134.0	0.0		140.0	43.0	NM_001206691	A8K5Y0|B2RDW4|Q33DW6|Q33DW7|Q33E95|Q6YM53|Q8MHQ1|Q8NC78|Q8NDF9|Q8SNA1|Q96S80|Q9BXI0	Silent	SNP	ENST00000392842.1	hg19	CCDS9106.1																																																																																			.	.		0.398	RFX4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402707.1	NM_032491		T	107103177	C	T	107103177	2	4	303	1	0	0	0	0	0	0	0	1	13280	842	30	3		3	RFX4	12	107103177	Silent	SNP	C	TCGA-G3-AAV7-01A-11D-A382-10	7957989	107103177	26748718	64	43657										
OXGR1	27199	hgsc.bcm.edu	37	chr13	97639005	97639005	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	agtaaatgaaatatttcaagGgttgtttgagtaactaattt	8	2	1	2			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr13:97639005G>A	ENST00000298440.1	-	4	1252	c.1009C>T	c.(1009-1011)Cct>Tct	p.P337S	OXGR1_ENST00000543457.1_Missense_Mutation_p.P337S	NM_080818.3	NP_543008.3	Q96P68	OXGR1_HUMAN	oxoglutarate (alpha-ketoglutarate) receptor 1	337					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|large_intestine(1)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	15	all_neural(89;0.0982)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.186)			ATATTTCAAGGGTTGTTTGAG	0.413																																					p.P337S		Atlas-SNP	.											.	OXGR1	46	.	0			c.C1009T						.						87	91	90					13																	97639005		2203	4299	6502	SO:0001583	missense	27199	exon4			TTCAAGGGTTGTT	AF411109	CCDS9482.1	13q32.2	2014-04-09	2004-07-08	2004-07-09	ENSG00000165621	ENSG00000165621		"GPCR / Class A : Orphans"	4531	protein-coding gene	gene with protein product	"2-oxoglutarate receptor 1", "alpha-ketoglutarate receptor 1"	606922	"G protein-coupled receptor 80"	GPR99, GPR80		15141213, 12098360	Standard	NM_080818		Approved	P2RY15, P2Y15, aKGR	uc001vmx.1	Q96P68	OTTHUMG00000017236	ENST00000298440.1:c.1009C>T	chr13.hg19:g.97639005G>A	ENSP00000298440:p.Pro337Ser	33.0	0.0		22.0	12.0	NM_080818	Q5T5A7|Q86TL1	Missense_Mutation	SNP	ENST00000298440.1	hg19	CCDS9482.1	.	.	.	.	.	.	.	.	.	.	G	10.78	1.446444	0.25987	.	.	ENSG00000165621	ENST00000298440;ENST00000543457	T;T	0.64260	-0.09;-0.09	5.87	5.02	0.67125	.	1.111910	0.06682	N	0.768183	T	0.44008	0.1273	N	0.08118	0	0.09310	N	1	B	0.13594	0.008	B	0.11329	0.006	T	0.14531	-1.0469	10	0.66056	D	0.02	.	7.4682	0.27334	0.1231:0.0:0.7238:0.1532	.	337	Q96P68	OXGR1_HUMAN	S	337	ENSP00000298440:P337S;ENSP00000438800:P337S	ENSP00000298440:P337S	P	-	1	0	OXGR1	96437006	0.042000	0.20092	0.746000	0.31095	0.073000	0.16967	1.065000	0.30592	2.941000	0.99782	0.655000	0.94253	CCT	.	.		0.413	OXGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045521.3	NM_080818		A	97639005	G	A	97639005	3	1	303	1	0	0	0	0	1	0	0	0	11341	1232	43	3	8	3	OXGR1	13	97639005	Missense_Mutation	SNP	G	TCGA-G3-AAV7-01A-11D-A382-10		97639005	17530873	65	43658										
JUB	84962	hgsc.bcm.edu	37	chr14	23450783	23450783	+	Nonsense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	gggctgcccagggccgggggAtacgagtggcggctttcctg	19	11	0	0			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr14:23450783A>C	ENST00000262713.2	-	1	1068	c.693T>G	c.(691-693)taT>taG	p.Y231*	RP11-298I3.4_ENST00000556503.1_RNA|RP11-298I3.4_ENST00000557615.1_RNA|AJUBA_ENST00000361265.4_Nonsense_Mutation_p.Y231*|RP11-298I3.5_ENST00000555074.1_Intron|RP11-298I3.4_ENST00000555294.1_RNA	NM_032876.4	NP_116265.1	Q96IF1	AJUBA_HUMAN	ajuba LIM protein	231	PreLIM.				calcium-dependent cell-cell adhesion (GO:0016339)|cellular protein localization (GO:0034613)|focal adhesion assembly (GO:0048041)|G2/M transition of mitotic cell cycle (GO:0000086)|gene silencing by miRNA (GO:0035195)|glycerophospholipid biosynthetic process (GO:0046474)|lamellipodium assembly (GO:0030032)|mitotic cell cycle (GO:0000278)|negative regulation of hippo signaling (GO:0035331)|negative regulation of kinase activity (GO:0033673)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cellular biosynthetic process (GO:0031328)|positive regulation of gene silencing by miRNA (GO:2000637)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein complex assembly (GO:0031334)|regulation of cell migration (GO:0030334)|regulation of cellular response to hypoxia (GO:1900037)|regulation of GTPase activity (GO:0043087)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)|wound healing, spreading of epidermal cells (GO:0035313)	cell-cell junction (GO:0005911)|cytoplasmic mRNA processing body (GO:0000932)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|transcription factor complex (GO:0005667)	alpha-catenin binding (GO:0045294)|chromatin binding (GO:0003682)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)										GGGCCGGGGGATACGAGTGGC	0.736																																					p.Y231X		Atlas-SNP	.											.	.	.	.	0			c.T693G						.						3	4	4					14																	23450783		1689	3541	5230	SO:0001587	stop_gained	84962	exon1			CGGGGGATACGAG	AK025567	CCDS9581.1, CCDS9582.1	14q11.2	2011-11-10	2011-11-10	2011-11-10	ENSG00000129474	ENSG00000129474			20250	protein-coding gene	gene with protein product		609066	"jub, ajuba homolog (Xenopus laevis)"	JUB		10330178	Standard	NM_032876		Approved	MGC15563	uc001whz.3	Q96IF1	OTTHUMG00000028711	ENST00000262713.2:c.693T>G	chr14.hg19:g.23450783A>C	ENSP00000262713:p.Tyr231*	64.0	0.0		57.0	26.0	NM_032876	A8MX18|D3DS37	Nonsense_Mutation	SNP	ENST00000262713.2	hg19	CCDS9581.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	35|35	5.451101|5.451101	0.96205|0.96205	.|.	.|.	ENSG00000129474|ENSG00000129474	ENST00000553736|ENST00000262713;ENST00000361265	.|.	.|.	.|.	4.58|4.58	-3.49|-3.49	0.04724|0.04724	.|.	.|0.280130	.|0.29266	.|N	.|0.012654	T|.	0.13200|.	0.0320|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.41520|.	-0.9504|.	3|.	.|0.02654	.|T	.|1	.|.	6.5722|6.5722	0.22545|0.22545	0.3653:0.0:0.4943:0.1404|0.3653:0.0:0.4943:0.1404	.|.	.|.	.|.	.|.	A|X	5|231	.|.	.|ENSP00000262713:Y231X	S|Y	-|-	1|3	0|2	JUB|JUB	22520623|22520623	0.320000|0.320000	0.24616|0.24616	0.461000|0.461000	0.27105|0.27105	0.971000|0.971000	0.66376|0.66376	-0.043000|-0.043000	0.12043|0.12043	-0.565000|-0.565000	0.06061|0.06061	0.459000|0.459000	0.35465|0.35465	TCC|TAT	.	.		0.736	AJUBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071685.2			C	23450783	A	C	23450783	4	2	303	1	0	0	0	0	0	1	0	0	7977	340	12	5	955	5	JUB	14	23450783	Nonsense_Mutation	SNP	A	TCGA-G3-AAV7-01A-11D-A382-10		23450783	83898757	66	43659										
TMEM63C	57156	hgsc.bcm.edu	37	chr14	77685213	77685213	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	aggttacagaacatgacagtGgatgaatgcttccagtctcg	11	8	1	3			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr14:77685213G>T	ENST00000298351.4	+	3	201	c.57G>T	c.(55-57)gtG>gtT	p.V19V	RP11-463C8.4_ENST00000557752.1_3'UTR	NM_020431.2	NP_065164.2	Q9P1W3	CSC1_HUMAN	transmembrane protein 63C	19					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)	integral component of membrane (GO:0016021)	calcium activated cation channel activity (GO:0005227)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(1)	23			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0342)		ACATGACAGTGGATGAATGCT	0.597																																					p.V19V		Atlas-SNP	.											.	TMEM63C	77	.	0			c.G57T						.						58	65	62					14																	77685213		2076	4225	6301	SO:0001819	synonymous_variant	57156	exon3			GACAGTGGATGAA		CCDS45141.1	14q24.3	2014-05-30	2005-07-25	2005-07-25	ENSG00000165548	ENSG00000165548			23787	protein-coding gene	gene with protein product	"calcium permeable stress-gated cation channel 1 homolog (Arabidopsis)"		"chromosome 14 open reading frame 171"	C14orf171		24503647	Standard	NM_020431		Approved	DKFZp434P0111, CSC1, hsCSC1	uc001xtf.2	Q9P1W3	OTTHUMG00000171557	ENST00000298351.4:c.57G>T	chr14.hg19:g.77685213G>T		79.0	0.0		88.0	45.0	NM_020431	B2RN22|B3KWJ5|Q86TS3|Q86TS4|Q9NSQ4|Q9P1W1	Silent	SNP	ENST00000298351.4	hg19	CCDS45141.1																																																																																			.	.		0.597	TMEM63C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414193.1			T	77685213	G	T	77685213	2	4	303	1	0	0	0	0	0	0	0	1	16207	1335	47	3		3	TMEM63C	14	77685213	Silent	SNP	G	TCGA-G3-AAV7-01A-11D-A382-10	54234430	77685213	29664327	67	43660										
CCNDBP1	23582	hgsc.bcm.edu	37	chr15	43477752	43477752	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	caccctggcttcgcctttggAgcagctccggcacttggcgg	13	15	0	0			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr15:43477752A>C	ENST00000300213.4	+	1	298	c.56A>C	c.(55-57)gAg>gCg	p.E19A	RP11-473C18.3_ENST00000565685.1_RNA|CCNDBP1_ENST00000356633.5_5'UTR|EPB42_ENST00000563128.1_Intron	NM_012142.4	NP_036274.3	O95273	CCDB1_HUMAN	cyclin D-type binding-protein 1	19	Interaction with RPLP0.|Interaction with TCF3.|Required for interaction with CCND1.				cell cycle (GO:0007049)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)	13		all_cancers(109;3.31e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.42e-07)		TCGCCTTTGGAGCAGCTCCGG	0.692																																					p.E19A		Atlas-SNP	.											.	CCNDBP1	22	.	0			c.A56C						.						7	8	7					15																	43477752		2170	4231	6401	SO:0001583	missense	23582	exon1			CTTTGGAGCAGCT	AF082569	CCDS10092.1	15q14-q15	2008-07-18			ENSG00000166946	ENSG00000166946			1587	protein-coding gene	gene with protein product	"D-type cyclin-interacting protein 1", "MAID protein", "HHM Protein", "grap2 cyclin interacting protein"	607089				10801854	Standard	NM_012142		Approved	DIP1, GCIP	uc001zqv.3	O95273	OTTHUMG00000130703	ENST00000300213.4:c.56A>C	chr15.hg19:g.43477752A>C	ENSP00000300213:p.Glu19Ala	94.0	0.0		71.0	36.0	NM_012142	A8K3Q0|A8K3U2|Q6ZQN9|Q7Z519|Q8NBS7|Q8NBY2|Q9NS19|Q9NYH3|Q9UHX9	Missense_Mutation	SNP	ENST00000300213.4	hg19	CCDS10092.1	.	.	.	.	.	.	.	.	.	.	A	12.92	2.082185	0.36758	.	.	ENSG00000166946	ENST00000300213	T	0.50001	0.76	5.17	0.111	0.14619	.	0.436377	0.23727	N	0.045172	T	0.24890	0.0604	N	0.17082	0.46	0.21579	N	0.999632	B;B	0.14805	0.011;0.002	B;B	0.14578	0.011;0.003	T	0.09509	-1.0671	10	0.42905	T	0.14	-1.2368	4.3059	0.10947	0.5377:0.1835:0.2789:0.0	.	19;19	O95273-2;O95273	.;CCDB1_HUMAN	A	19	ENSP00000300213:E19A	ENSP00000300213:E19A	E	+	2	0	CCNDBP1	41265044	0.546000	0.26457	0.046000	0.18839	0.044000	0.14063	0.266000	0.18534	0.110000	0.17919	-1.004000	0.02495	GAG	.	.		0.692	CCNDBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253203.1	NM_012142		C	43477752	A	C	43477752	3	2	303	1	0	0	0	0	1	0	0	0	2921	304	11	5	58	5	CCNDBP1	15	43477752	Missense_Mutation	SNP	A	TCGA-G3-AAV7-01A-11D-A382-10		43477752	59053640	68	43661										
RASGRF1	5923	hgsc.bcm.edu	37	chr15	79296322	79296322	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	ttggagttgcagctgagggcGgccaggtccagggccttgcc	17	11	0	1	rs147952942		TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr15:79296322G>A	ENST00000419573.3	-	16	2593	c.2319C>T	c.(2317-2319)gcC>gcT	p.A773A	RASGRF1_ENST00000394745.3_5'UTR|RASGRF1_ENST00000558480.2_Silent_p.A757A|RASGRF1_ENST00000560334.1_5'UTR	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	773					activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						AGCTGAGGGCGGCCAGGTCCA	0.617																																					p.A773A		Atlas-SNP	.											.	RASGRF1	168	.	0			c.C2319T						.	G	,,	2,4390	4.2+/-10.8	0,2,2194	61	54	57		2271,2319,	-2.1	1	15	dbSNP_134	57	0,8586		0,0,4293	no	coding-synonymous,coding-synonymous,utr-5	RASGRF1	NM_001145648.1,NM_002891.4,NM_153815.2	,,	0,2,6487	AA,AG,GG		0.0,0.0455,0.0154	,,	757/1258,773/1274,	79296322	2,12976	2196	4293	6489	SO:0001819	synonymous_variant	5923	exon16			GAGGGCGGCCAGG	M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.2319C>T	chr15.hg19:g.79296322G>A		74.0	0.0		69.0	41.0	NM_002891	F8VPA5|H0YKF2|J3KQP9|Q16027	Silent	SNP	ENST00000419573.3	hg19	CCDS10309.1																																																																																			.	G|1.000;A|0.000		0.617	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891		A	79296322	G	A	79296322	2	1	303	1	0	0	0	0	0	0	0	1	13087	1103	39	1		1	RASGRF1	15	79296322	Silent	SNP	G	TCGA-G3-AAV7-01A-11D-A382-10	35818570	79296322	23235070	69	43662										
AXIN1	8312	hgsc.bcm.edu	37	chr16	364646	364647	+	Frame_Shift_Ins	INS	-	-	A													0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	agggcatagccggcattgacINSataataggggttgactggct					rs192381684		TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr16:364646_364647insA	ENST00000262320.3	-	3	1286_1287	c.915_916insT	c.(913-918)tatgtcfs	p.V306fs	AXIN1_ENST00000354866.3_Frame_Shift_Ins_p.V306fs|AXIN1_ENST00000481769.1_5'UTR	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	306	Interaction with TP53. {ECO:0000250}.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)	p.Y305*(1)		biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				CCGGCATTGACATAATAGGGGT	0.579																																					p.V306fs		Atlas-Indel,Pindel	.											.	AXIN1	290	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.916_917insT						.																																			SO:0001589	frameshift_variant	8312	exon3			.	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.916dupT	chr16.hg19:g.364647_364647dupA	ENSP00000262320:p.Val306fs	53.0	0.0		59.0	30.0	NM_003502	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Frame_Shift_Ins	INS	ENST00000262320.3	hg19	CCDS10405.1																																																																																			.	.		0.579	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3			A	364647	-	A	364646	7	5	303	1	0	1	1	0	0	0	0	0	1236	478	17	0	1708	0	AXIN1	16	364646	Frame_Shift_Ins	INS	-	TCGA-G3-AAV7-01A-11D-A382-10		364646	89990107	70	43663										
TSC2	7249	hgsc.bcm.edu	37	chr16	2124225	2124225	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	agatggtctactgcctggagCagggcctcatccaccgctgt	12	13	2	1	rs45517233|rs397515282		TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr16:2124225C>T	ENST00000219476.3	+	22	3010	c.2380C>T	c.(2380-2382)Cag>Tag	p.Q794*	TSC2_ENST00000401874.2_Nonsense_Mutation_p.Q794*|TSC2_ENST00000382538.6_Nonsense_Mutation_p.Q745*|TSC2_ENST00000353929.4_Nonsense_Mutation_p.Q794*|TSC2_ENST00000350773.4_Nonsense_Mutation_p.Q794*|TSC2_ENST00000568454.1_Nonsense_Mutation_p.Q805*|TSC2_ENST00000439673.2_Nonsense_Mutation_p.Q757*	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	794					acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)	p.E793fs*9(1)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				CTGCCTGGAGCAGGGCCTCAT	0.642			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.Q794X		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"E, O"	.	TSC2	364	.	1	Deletion - Frameshift(1)	pancreas(1)	c.C2380T	GRCh37	CM091029	TSC2	M	rs45517233	.						74	58	64					16																	2124225		2198	4299	6497	SO:0001587	stop_gained	7249	exon22	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	CTGGAGCAGGGCC	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 160"	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.2380C>T	chr16.hg19:g.2124225C>T	ENSP00000219476:p.Gln794*	26.0	0.0		34.0	15.0	NM_001114382	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Nonsense_Mutation	SNP	ENST00000219476.3	hg19	CCDS10458.1	.	.	.	.	.	.	.	.	.	.	C	39	7.595681	0.98381	.	.	ENSG00000103197	ENST00000219476;ENST00000401874;ENST00000353929;ENST00000439673;ENST00000382538;ENST00000350773	.	.	.	5.35	5.35	0.76521	.	0.246642	0.34178	N	0.004196	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13470	T	0.59	-13.2208	13.9587	0.64166	0.1517:0.8483:0.0:0.0	rs45517233	.	.	.	X	794;794;794;757;745;794	.	ENSP00000219476:Q794X	Q	+	1	0	TSC2	2064226	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	4.254000	0.58798	2.500000	0.84329	0.313000	0.20887	CAG	.	.		0.642	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548		T	2124225	C	T	2124225	4	4	303	1	0	0	0	0	0	1	0	0	16621	711	25	3	2462	3	TSC2	16	2124225	Nonsense_Mutation	SNP	C	TCGA-G3-AAV7-01A-11D-A382-10	1759579	2124225	88230528	71	43664										
HEATR3	55027	hgsc.bcm.edu	37	chr16	50120257	50120257	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	gtcacagctgcttttttctcAaccaggtatttagactttat	6	9	2	1			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr16:50120257A>G	ENST00000299192.7	+	11	1696	c.1505A>G	c.(1504-1506)cAa>cGa	p.Q502R	HEATR3_ENST00000285767.4_Missense_Mutation_p.Q416R|HEATR3_ENST00000564942.1_3'UTR	NM_182922.2	NP_891552.1	Q7Z4Q2	HEAT3_HUMAN	HEAT repeat containing 3	502										cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	28						CTTTTTTCTCAACCAGGTATT	0.468																																					p.Q502R		Atlas-SNP	.											.	HEATR3	59	.	0			c.A1505G						.						29	29	29					16																	50120257		2198	4300	6498	SO:0001583	missense	55027	exon11			TTTCTCAACCAGG	BC018730	CCDS10739.1	16q12.1	2008-02-05			ENSG00000155393	ENSG00000155393			26087	protein-coding gene	gene with protein product		614951				12477932	Standard	XM_005256013		Approved	FLJ20718	uc002efw.3	Q7Z4Q2	OTTHUMG00000133174	ENST00000299192.7:c.1505A>G	chr16.hg19:g.50120257A>G	ENSP00000299192:p.Gln502Arg	64.0	0.0		47.0	21.0	NM_182922	A8K1N4|Q8N525|Q8WV56|Q96CC9|Q9NWN7	Missense_Mutation	SNP	ENST00000299192.7	hg19	CCDS10739.1	.	.	.	.	.	.	.	.	.	.	A	10.31	1.314944	0.23908	.	.	ENSG00000155393	ENST00000285767;ENST00000299192	T;T	0.46819	0.86;0.87	5.82	4.73	0.59995	Armadillo-type fold (1);	0.285641	0.40640	N	0.001043	T	0.42337	0.1198	M	0.62723	1.935	0.32892	D	0.511992	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.49466	-0.8937	10	0.12103	T	0.63	.	12.0214	0.53346	0.9323:0.0:0.0677:0.0	.	416;502	B7WNW7;Q7Z4Q2	.;HEAT3_HUMAN	R	416;502	ENSP00000285767:Q416R;ENSP00000299192:Q502R	ENSP00000285767:Q416R	Q	+	2	0	HEATR3	48677758	1.000000	0.71417	1.000000	0.80357	0.603000	0.37013	4.101000	0.57769	1.013000	0.39391	0.528000	0.53228	CAA	.	.		0.468	HEATR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256880.2	NM_182922		G	50120257	A	G	50120257	3	3	303	1	0	0	0	0	1	0	0	0	7038	130	5	2	1547	2	HEATR3	16	50120257	Missense_Mutation	SNP	A	TCGA-G3-AAV7-01A-11D-A382-10	47996032	50120257	40234496	72	43665										
RFWD3	55159	hgsc.bcm.edu	37	chr16	74660446	74660446	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	cacttcgtatggtggtgtgaTttttatctatgggacagaga	12	5	1	2			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr16:74660446T>C	ENST00000361070.4	-	12	2073	c.1976A>G	c.(1975-1977)aAt>aGt	p.N659S	RFWD3_ENST00000571750.1_Missense_Mutation_p.N659S	NM_018124.3	NP_060594.3	Q6PCD5	RFWD3_HUMAN	ring finger and WD repeat domain 3	659					DNA repair (GO:0006281)|mitotic G1 DNA damage checkpoint (GO:0031571)|protein ubiquitination (GO:0016567)|regulation of DNA damage checkpoint (GO:2000001)|response to ionizing radiation (GO:0010212)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|MDM2/MDM4 family protein binding (GO:0097371)|p53 binding (GO:0002039)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	26						GGTGGTGTGATTTTTATCTAT	0.448																																					p.N659S		Atlas-SNP	.											.	RFWD3	49	.	0			c.A1976G						.						79	77	78					16																	74660446		2198	4300	6498	SO:0001583	missense	55159	exon12			GTGTGATTTTTAT	AK001382	CCDS32486.1	16q22.3	2013-01-09						"WD repeat domain containing", "RING-type (C3HC4) zinc fingers"	25539	protein-coding gene	gene with protein product		614151				21504906	Standard	XM_005256021		Approved	FLJ10520, RNF201	uc002fda.3	Q6PCD5		ENST00000361070.4:c.1976A>G	chr16.hg19:g.74660446T>C	ENSP00000354361:p.Asn659Ser	98.0	0.0		90.0	53.0	NM_018124	A8K585|B2RE35|D3DUJ8|Q5XKR3|Q9H9Q3|Q9NVT4	Missense_Mutation	SNP	ENST00000361070.4	hg19	CCDS32486.1	.	.	.	.	.	.	.	.	.	.	T	2.364	-0.345935	0.05208	.	.	ENSG00000168411	ENST00000361070;ENST00000444004	T	0.17854	2.25	5.49	2.44	0.29823	.	0.329029	0.37437	N	0.002082	T	0.06142	0.0159	N	0.13327	0.33	0.27598	N	0.949054	B	0.18461	0.028	B	0.16289	0.015	T	0.35871	-0.9771	10	0.06365	T	0.9	-9.7062	1.5086	0.02492	0.1306:0.2008:0.1354:0.5331	.	659	Q6PCD5	RFWD3_HUMAN	S	659;148	ENSP00000354361:N659S	ENSP00000354361:N659S	N	-	2	0	RFWD3	73217947	0.993000	0.37304	0.988000	0.46212	0.478000	0.33099	0.271000	0.18626	0.157000	0.19338	0.459000	0.35465	AAT	.	.		0.448	RFWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436506.2	NM_018124		C	74660446	T	C	74660446	3	2	303	1	0	0	0	0	1	0	0	0	13276	1493	52	2	356	2	RFWD3	16	74660446	Missense_Mutation	SNP	T	TCGA-G3-AAV7-01A-11D-A382-10	24540189	74660446	15694307	73	43666										
TP53	7157	hgsc.bcm.edu	37	chr17	7577153	7577153	+	Frame_Shift_Del	DEL	C	C	-													0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	tgttccgtcccagtagattaCcactactcaggataggaaaa							TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr17:7577153delC	ENST00000269305.4	-	8	974	c.785delG	c.(784-786)ggtfs	p.G262fs	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Intron|TP53_ENST00000445888.2_Frame_Shift_Del_p.G262fs|TP53_ENST00000359597.4_Frame_Shift_Del_p.G262fs|TP53_ENST00000455263.2_Frame_Shift_Del_p.G262fs|TP53_ENST00000420246.2_Frame_Shift_Del_p.G262fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	262	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		G -> C (in a sporadic cancer; somatic mutation).|G -> D (in sporadic cancers; somatic mutation).|G -> H (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|G -> S (in sporadic cancers; somatic mutation).|G -> V (in sporadic cancers; somatic mutation). {ECO:0000269|Ref.23}.|GN -> PD (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.G262V(19)|p.0?(8)|p.G262D(4)|p.?(3)|p.G262_F270delGNLLGRNSF(2)|p.G262fs*83(2)|p.G262_S269delGNLLGRNS(2)|p.G262del(2)|p.G262H(1)|p.E258fs*71(1)|p.S261_L264>R(1)|p.G262fs*2(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CAGTAGATTACCACTACTCAG	0.517		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.G262fs	Pancreas(47;798 1329 9957 10801)	Atlas-Indel,Pindel	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,NS,carcinoma,-1,2	TP53	33396	.	46	Substitution - Missense(24)|Whole gene deletion(8)|Deletion - In frame(6)|Deletion - Frameshift(4)|Unknown(3)|Complex - deletion inframe(1)	lung(8)|large_intestine(5)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(5)|ovary(5)|upper_aerodigestive_tract(4)|bone(4)|endometrium(2)|urinary_tract(2)|pancreas(2)|eye(1)|liver(1)|breast(1)|stomach(1)	c.786delT						.						40	37	38					17																	7577153		2203	4299	6502	SO:0001589	frameshift_variant	7157	exon8	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	.	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.785delG	chr17.hg19:g.7577153delC	ENSP00000269305:p.Gly262fs	78.0	0.0		72.0	28.0	NM_001126112	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Del	DEL	ENST00000269305.4	hg19	CCDS11118.1																																																																																			.	.		0.517	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		-	7577153	C	-	7577153	7	5	303	1	0	1	0	1	0	0	0	0	16396	507	18	0	501	0	TP53	17	7577153	Frame_Shift_Del	DEL	C	TCGA-G3-AAV7-01A-11D-A382-10		7577153	73618057	74	43667										
RNF112	7732	hgsc.bcm.edu	37	chr17	19316310	19316310	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	cgcatcaatgcctctgggggCctcatccttaggatgggggc	14	12	3	0			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr17:19316310C>A	ENST00000461366.1	+	4	656	c.441C>A	c.(439-441)ggC>ggA	p.G147G	CTB-187M2.2_ENST00000579897.1_RNA|RNF112_ENST00000580109.1_Intron	NM_007148.4	NP_009079.2	Q9ULX5	RN112_HUMAN	ring finger protein 112	147						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|zinc ion binding (GO:0008270)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)|urinary_tract(1)	12						CCTCTGGGGGCCTCATCCTTA	0.662																																					p.G147G		Atlas-SNP	.											.	RNF112	37	.	0			c.C441A						.						18	21	20					17																	19316310		2092	4221	6313	SO:0001819	synonymous_variant	7732	exon4			TGGGGGCCTCATC	AF054587	CCDS58529.1	17p11.2	2013-01-16	2008-06-13	2008-06-13	ENSG00000128482	ENSG00000128482		"RING-type (C3HC4) zinc fingers"	12968	protein-coding gene	gene with protein product		601237	"zinc finger protein 179"	ZNF179		8660987, 9806830	Standard	NM_007148		Approved	BFP	uc010vyw.2	Q9ULX5	OTTHUMG00000059601	ENST00000461366.1:c.441C>A	chr17.hg19:g.19316310C>A		128.0	0.0		157.0	57.0	NM_007148	O60633|Q7Z5V9	Silent	SNP	ENST00000461366.1	hg19	CCDS58529.1																																																																																			.	.		0.662	RNF112-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132549.4	NM_007148		A	19316310	C	A	19316310	2	1	303	1	0	0	0	0	0	0	0	1	13441	726	26	3		3	RNF112	17	19316310	Silent	SNP	C	TCGA-G3-AAV7-01A-11D-A382-10	11739157	19316310	61878900	75	43668										
LRRC37A2	474170	hgsc.bcm.edu	37	chr17	44630766	44630766	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	tgcgttttcttctaaaacagAtatgttgtcaccgaaggtca	8	8	4	1			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr17:44630766A>T	ENST00000576629.1	+	12	5305	c.4810A>T	c.(4810-4812)Ata>Tta	p.I1604L	ARL17A_ENST00000445552.2_Intron|ARL17A_ENST00000329240.4_Intron|ARL17A_ENST00000337845.7_Intron|LRRC37A2_ENST00000333412.3_Splice_Site_p.I1604L|ARL17A_ENST00000570550.1_Intron|ARL17A_ENST00000573185.1_Intron			A6NM11	L37A2_HUMAN	leucine rich repeat containing 37, member A2	1604						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|pancreas(4)|prostate(2)	15		Melanoma(429;0.211)		BRCA - Breast invasive adenocarcinoma(366;0.232)		TCTAAAACAGATATGTTGTCA	0.333																																					p.I1604L		Atlas-SNP	.											.	LRRC37A2	37	.	0			c.A4810T						.						69	125	106					17																	44630766		2198	4294	6492	SO:0001630	splice_region_variant	474170	exon11			AAACAGATATGTT	AY386262	CCDS42353.1	17q21.31	2013-05-14			ENSG00000238083	ENSG00000238083			32404	protein-coding gene	gene with protein product	"c114 SLIT-like testicular protein"						Standard	NM_001006607		Approved	FLJ45049	uc002ikn.1	A6NM11	OTTHUMG00000178032	ENST00000576629.1:c.4810-1A>T	chr17.hg19:g.44630766A>T		605.0	1.0		696.0	192.0	NM_001006607	B7ZMC3	Missense_Mutation	SNP	ENST00000576629.1	hg19	CCDS42353.1	.	.	.	.	.	.	.	.	.	.	a	14.71	2.616204	0.46631	.	.	ENSG00000238083	ENST00000333412	T	0.50001	0.76	2.45	1.28	0.21552	.	.	.	.	.	T	0.51295	0.1666	L	0.53249	1.67	0.58432	D	0.999995	D;P	0.62365	0.991;0.59	P;B	0.59643	0.861;0.243	T	0.46162	-0.9211	8	.	.	.	.	4.628	0.12488	0.8352:0.0:0.1648:0.0	.	565;1604	B3KRJ4;A6NM11	.;L37A2_HUMAN	L	1604	ENSP00000333071:I1604L	.	I	+	1	0	LRRC37A2	41986082	0.812000	0.29077	0.556000	0.28293	0.019000	0.09904	0.383000	0.20651	0.340000	0.23745	0.128000	0.15822	ATA	.	.		0.333	LRRC37A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440299.2	NM_001006607	Missense_Mutation	T	44630766	A	T	44630766	5	4	303	1	0	0	0	0	0	0	1	0	9001	347	12	4	4852	4	LRRC37A2	17	44630766	Splice_Site	SNP	A	TCGA-G3-AAV7-01A-11D-A382-10	25314456	44630766	36564444	76	43669										
SDK2	54549	hgsc.bcm.edu	37	chr17	71503638	71503638	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	gagccacttgaactccagtgGccagctgccctcggccatgc	11	16	0	1			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr17:71503638G>T	ENST00000392650.3	-	2	163	c.163C>A	c.(163-165)Cca>Aca	p.P55T	SDK2_ENST00000388726.3_Missense_Mutation_p.P55T	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	55	Ig-like C2-type 1.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(15)|lung(31)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	86						AACTCCAGTGGCCAGCTGCCC	0.582																																					p.P55T		Atlas-SNP	.											.	SDK2	219	.	0			c.C163A						.						96	94	95					17																	71503638		692	1591	2283	SO:0001583	missense	54549	exon2			CCAGTGGCCAGCT	AB040947	CCDS45769.1	17q21.31	2013-02-11	2011-12-09		ENSG00000069188	ENSG00000069188		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19308	protein-coding gene	gene with protein product		607217	"sidekick homolog 2 (chicken)"			12230981, 15213259	Standard	NM_001144952		Approved	FLJ10832, KIAA1514	uc010dfm.3	Q58EX2	OTTHUMG00000152726	ENST00000392650.3:c.163C>A	chr17.hg19:g.71503638G>T	ENSP00000376421:p.Pro55Thr	70.0	0.0		67.0	16.0	NM_001144952	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Missense_Mutation	SNP	ENST00000392650.3	hg19	CCDS45769.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.769011	0.90020	.	.	ENSG00000069188	ENST00000392650;ENST00000388726;ENST00000316893	T;T	0.22743	1.94;1.94	5.41	5.41	0.78517	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.000000	0.56097	U	0.000036	T	0.39226	0.1070	L	0.52206	1.635	0.58432	D	0.999999	D	0.55172	0.97	P	0.62298	0.9	T	0.01894	-1.1252	10	0.28530	T	0.3	.	18.8016	0.92021	0.0:0.0:1.0:0.0	.	55	Q58EX2	SDK2_HUMAN	T	55	ENSP00000376421:P55T;ENSP00000373378:P55T	ENSP00000324967:P55T	P	-	1	0	SDK2	69015233	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.696000	0.98695	2.539000	0.85634	0.561000	0.74099	CCA	.	.		0.582	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064		T	71503638	G	T	71503638	3	4	303	1	0	0	0	0	1	0	0	0	13984	1203	42	3	6531	3	SDK2	17	71503638	Missense_Mutation	SNP	G	TCGA-G3-AAV7-01A-11D-A382-10	26872872	71503638	9691572	77	43670										
SUMO2	6613	hgsc.bcm.edu	37	chr17	73177179	73177179	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	tcacaataggctttcattagTttactaagtggtgtatgcct	8	7	2	0			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr17:73177179T>C	ENST00000420826.2	-	2	274	c.126A>G	c.(124-126)aaA>aaG	p.K42K	SUMO2_ENST00000314523.7_Silent_p.K42K|SUMO2_ENST00000578238.1_5'UTR	NM_006937.3	NP_008868.3			small ubiquitin-like modifier 2											NS(1)	1	all_lung(278;0.14)|Lung NSC(278;0.168)					CTTTCATTAGTTTACTAAGTG	0.368																																					p.K42K		Atlas-SNP	.											.	SUMO2	4	.	0			c.A126G						.						76	83	81					17																	73177179		2203	4300	6503	SO:0001819	synonymous_variant	6613	exon2			CATTAGTTTACTA		CCDS45773.1, CCDS45774.1	17q25	2013-06-05	2013-06-05	2004-05-19	ENSG00000188612	ENSG00000188612			11125	protein-coding gene	gene with protein product		603042	"SMT3 (suppressor of mif two 3, yeast) homolog 2", "SMT3 suppressor of mif two 3 homolog 2 (yeast)", "SMT3 suppressor of mif two 3 homolog 2 (S. cerevisiae)"	SMT3H2		8630065	Standard	NM_006937		Approved	SMT3B	uc002jne.3	P61956		ENST00000420826.2:c.126A>G	chr17.hg19:g.73177179T>C		415.0	0.0		539.0	121.0	NM_006937		Silent	SNP	ENST00000420826.2	hg19	CCDS45774.1																																																																																			.	.		0.368	SUMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446614.1	NM_006937		C	73177179	T	C	73177179	2	2	303	1	0	0	0	0	0	0	0	1	15403	1722	60	2		2	SUMO2	17	73177179	Silent	SNP	T	TCGA-G3-AAV7-01A-11D-A382-10	1673541	73177179	8018031	78	43671										
TMC8	147138	hgsc.bcm.edu	37	chr17	76129505	76129505	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	aggccttcaccaacacctatCtcttctacggtgcgtaccga	7	15	3	0			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr17:76129505C>A	ENST00000318430.5	+	6	924	c.550C>A	c.(550-552)Ctc>Atc	p.L184I	TMC8_ENST00000589691.1_5'UTR|TMC6_ENST00000322914.3_5'Flank	NM_152468.4	NP_689681.2	Q8IU68	TMC8_HUMAN	transmembrane channel-like 8	184					ion transport (GO:0006811)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|regulation of cell growth (GO:0001558)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|zinc ion homeostasis (GO:0055069)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	receptor binding (GO:0005102)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	12			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)|OV - Ovarian serous cystadenocarcinoma(97;0.192)			CAACACCTATCTCTTCTACGG	0.607																																					p.L184I		Atlas-SNP	.											.	TMC8	44	.	0			c.C550A						.						145	132	137					17																	76129505		2203	4300	6503	SO:0001583	missense	147138	exon6			ACCTATCTCTTCT	AY057380	CCDS32749.1	17q25.3	2014-09-17	2005-11-10	2005-11-10	ENSG00000167895	ENSG00000167895			20474	protein-coding gene	gene with protein product		605829	"epidermodysplasia verruciformis 2"	EVER2		12426567	Standard	NM_152468		Approved	EVIN2	uc002jup.2	Q8IU68		ENST00000318430.5:c.550C>A	chr17.hg19:g.76129505C>A	ENSP00000325561:p.Leu184Ile	72.0	0.0		68.0	21.0	NM_152468	Q2YDC0|Q8IWU7|Q8N358|Q8NF04	Missense_Mutation	SNP	ENST00000318430.5	hg19	CCDS32749.1	.	.	.	.	.	.	.	.	.	.	C	17.75	3.466793	0.63625	.	.	ENSG00000167895	ENST00000318430;ENST00000301627	T	0.61980	0.06	4.08	4.08	0.47627	.	0.154254	0.64402	D	0.000016	T	0.79131	0.4394	M	0.82517	2.595	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.82653	-0.0351	10	0.72032	D	0.01	-35.7095	13.2975	0.60305	0.0:1.0:0.0:0.0	.	184	Q8IU68	TMC8_HUMAN	I	184	ENSP00000325561:L184I	ENSP00000301627:L184I	L	+	1	0	TMC8	73641100	0.990000	0.36364	0.991000	0.47740	0.403000	0.30841	3.263000	0.51546	2.097000	0.63578	0.561000	0.74099	CTC	.	.		0.607	TMC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436900.3			A	76129505	C	A	76129505	3	1	303	1	0	0	0	0	1	0	0	0	16006	913	32	3	568	3	TMC8	17	76129505	Missense_Mutation	SNP	C	TCGA-G3-AAV7-01A-11D-A382-10	2952326	76129505	5065705	79	43672										
EPB41L3	23136	hgsc.bcm.edu	37	chr18	5434095	5434095	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	ccttccggacacgatgtcatCtcgcaactgcaagcagaggt	10	13	2	1			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr18:5434095C>G	ENST00000341928.2	-	7	971	c.631G>C	c.(631-633)Gat>Cat	p.D211H	EPB41L3_ENST00000544123.1_Missense_Mutation_p.D211H|EPB41L3_ENST00000342933.3_Missense_Mutation_p.D211H|EPB41L3_ENST00000400111.3_Missense_Mutation_p.D211H|EPB41L3_ENST00000542652.2_5'UTR|EPB41L3_ENST00000540638.2_Missense_Mutation_p.D211H	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	211	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						ACGATGTCATCTCGCAACTGC	0.527																																					p.D211H		Atlas-SNP	.											.	EPB41L3	222	.	0			c.G631C						.						87	71	77					18																	5434095		2203	4300	6503	SO:0001583	missense	23136	exon7			TGTCATCTCGCAA	AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.631G>C	chr18.hg19:g.5434095C>G	ENSP00000343158:p.Asp211His	163.0	0.0		150.0	7.0	NM_012307	B7Z4I5|F5GX05|O95713|Q9BRP5	Missense_Mutation	SNP	ENST00000341928.2	hg19	CCDS11838.1	.	.	.	.	.	.	.	.	.	.	C	33	5.284359	0.95517	.	.	ENSG00000082397	ENST00000341928;ENST00000540638;ENST00000544123;ENST00000545076;ENST00000342933;ENST00000400111;ENST00000542652	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	6.02	6.02	0.97574	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.191558	0.56097	D	0.000037	D	0.84584	0.5504	L	0.38692	1.165	0.80722	D	1	D;P;D;D;P	0.89917	1.0;0.867;1.0;1.0;0.899	D;B;D;D;P	0.91635	0.999;0.272;0.984;0.985;0.619	D	0.84023	0.0355	10	0.54805	T	0.06	.	20.5373	0.99239	0.0:1.0:0.0:0.0	.	211;211;102;211;211	F5GX05;Q9Y2J2-3;A8K968;Q9Y2J2-2;Q9Y2J2	.;.;.;.;E41L3_HUMAN	H	211;102;211;102;211;211;292	ENSP00000343158:D211H;ENSP00000441174:D211H;ENSP00000341138:D211H;ENSP00000382981:D211H	ENSP00000343158:D211H	D	-	1	0	EPB41L3	5424095	1.000000	0.71417	0.988000	0.46212	0.965000	0.64279	7.818000	0.86416	2.857000	0.98124	0.650000	0.86243	GAT	.	.		0.527	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307		G	5434095	C	G	5434095	3	3	303	1	0	0	0	0	1	0	0	0	5156	913	32	4	2696	4	EPB41L3	18	5434095	Missense_Mutation	SNP	C	TCGA-G3-AAV7-01A-11D-A382-10		5434095	72643153	80	43673										
ANKRD29	147463	hgsc.bcm.edu	37	chr18	21197723	21197723	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	ataccaagagtgggtgagaaTttaagcaactcttttatgac	9	6	1	3			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr18:21197723T>A	ENST00000592179.1	-	8	850	c.696A>T	c.(694-696)aaA>aaT	p.K232N	ANKRD29_ENST00000586511.1_5'Flank|ANKRD29_ENST00000284207.7_Missense_Mutation_p.K232N|ANKRD29_ENST00000322980.9_Missense_Mutation_p.K232N	NM_173505.2	NP_775776.2	Q8N6D5	ANR29_HUMAN	ankyrin repeat domain 29	232										breast(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(3)|prostate(1)|skin(1)	13	all_cancers(21;5.07e-05)|all_epithelial(16;2.49e-07)|Lung NSC(20;0.00211)|all_lung(20;0.00676)|Colorectal(14;0.0202)|Ovarian(20;0.127)					TGGGTGAGAATTTAAGCAACT	0.353																																					p.K232N		Atlas-SNP	.											.	ANKRD29	24	.	0			c.A696T						.						141	130	133					18																	21197723		2202	4300	6502	SO:0001583	missense	147463	exon8			TGAGAATTTAAGC	AK057782	CCDS11879.1	18q11.2	2013-01-10			ENSG00000154065	ENSG00000154065		"Ankyrin repeat domain containing"	27110	protein-coding gene	gene with protein product							Standard	NM_173505		Approved	FLJ25053	uc002kun.3	Q8N6D5	OTTHUMG00000131875	ENST00000592179.1:c.696A>T	chr18.hg19:g.21197723T>A	ENSP00000468354:p.Lys232Asn	92.0	0.0		138.0	34.0	NM_173505	B2R972|Q6ZWE8|Q96LU9	Missense_Mutation	SNP	ENST00000592179.1	hg19	CCDS11879.1	.	.	.	.	.	.	.	.	.	.	T	18.08	3.543892	0.65198	.	.	ENSG00000154065	ENST00000322980;ENST00000284207	T;T	0.64618	-0.11;-0.11	5.4	0.328	0.15918	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.60792	0.2296	N	0.17922	0.545	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.91635	0.943;0.999	T	0.56715	-0.7933	10	0.41790	T	0.15	.	9.6631	0.39967	0.0:0.2947:0.0:0.7053	.	232;232	Q8N6D5-3;Q8N6D5	.;ANR29_HUMAN	N	232	ENSP00000323387:K232N;ENSP00000284207:K232N	ENSP00000284207:K232N	K	-	3	2	ANKRD29	19451721	0.992000	0.36948	0.998000	0.56505	0.936000	0.57629	0.254000	0.18314	0.118000	0.18165	-0.475000	0.04921	AAA	.	.		0.353	ANKRD29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254825.1	NM_173505		A	21197723	T	A	21197723	3	1	303	1	0	0	0	0	1	0	0	0	657	1490	52	4	221	4	ANKRD29	18	21197723	Missense_Mutation	SNP	T	TCGA-G3-AAV7-01A-11D-A382-10	15763628	21197723	56879525	81	43674										
DSEL	92126	hgsc.bcm.edu	37	chr18	65179555	65179555	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	taaatccaaaggggaaaataAtcctatcatgtcttacaggc	7	8	2	0			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr18:65179555A>G	ENST00000310045.7	-	2	3794	c.2321T>C	c.(2320-2322)aTt>aCt	p.I774T	CTD-2541J13.2_ENST00000583493.1_RNA|CTD-2541J13.2_ENST00000581951.1_RNA	NM_032160.2	NP_115536.1	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	764					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	isomerase activity (GO:0016853)|sulfotransferase activity (GO:0008146)			NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(25)|lung(23)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)				GGGGAAAATAATCCTATCATG	0.383																																					p.I774T		Atlas-SNP	.											.	DSEL	196	.	0			c.T2321C						.						47	51	50					18																	65179555		2202	4300	6502	SO:0001583	missense	92126	exon2			AAAATAATCCTAT	AF480435	CCDS11995.1	18q22.1	2007-01-29	2007-01-29	2007-01-29	ENSG00000171451	ENSG00000171451			18144	protein-coding gene	gene with protein product		611125	"chromosome 18 open reading frame 4"	C18orf4		16505484	Standard	NM_032160		Approved	NCAG1, FLJ11477	uc002lke.1	Q8IZU8	OTTHUMG00000132804	ENST00000310045.7:c.2321T>C	chr18.hg19:g.65179555A>G	ENSP00000310565:p.Ile774Thr	95.0	0.0		114.0	39.0	NM_032160	Q17RH1|Q6P5Z3	Missense_Mutation	SNP	ENST00000310045.7	hg19	CCDS11995.1	.	.	.	.	.	.	.	.	.	.	A	3.010	-0.204131	0.06180	.	.	ENSG00000171451	ENST00000310045;ENST00000397964	T	0.16597	2.33	4.98	2.63	0.31362	.	0.369879	0.24542	U	0.037623	T	0.05640	0.0148	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34477	-0.9827	10	0.20519	T	0.43	.	3.6484	0.08194	0.5976:0.0:0.2453:0.1571	.	764	Q8IZU8	DSEL_HUMAN	T	774;764	ENSP00000310565:I774T	ENSP00000310565:I774T	I	-	2	0	DSEL	63330535	0.003000	0.15002	0.263000	0.24496	0.567000	0.35839	1.478000	0.35442	0.757000	0.33036	0.374000	0.22700	ATT	.	.		0.383	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160		G	65179555	A	G	65179555	3	3	303	1	0	0	0	0	1	0	0	0	4777	101	4	2	1351	2	DSEL	18	65179555	Missense_Mutation	SNP	A	TCGA-G3-AAV7-01A-11D-A382-10	43981832	65179555	12897693	82	43675										
ZNF254	9534	hgsc.bcm.edu	37	chr19	24309680	24309681	+	Frame_Shift_Del	DEL	CT	CT	-													0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	aattcatactggagagaaacCttacaagtgtgaagaatgtg							TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr19:24309680_24309681delCT	ENST00000357002.4	+	4	993_994	c.878_879delCT	c.(877-879)cctfs	p.P293fs	ZNF254_ENST00000342944.6_Frame_Shift_Del_p.P208fs	NM_001278661.1|NM_001278662.1|NM_001278664.1|NM_001278677.1|NM_001278678.1|NM_203282.2	NP_001265590.1|NP_001265591.1|NP_001265593.1|NP_001265606.1|NP_001265607.1|NP_975011.3	O75437	ZN254_HUMAN	zinc finger protein 254	293					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)						all_cancers(12;0.086)|all_lung(12;0.00528)|Lung NSC(12;0.00731)|all_epithelial(12;0.0186)				GGAGAGAAACCTTACAAGTGTG	0.366																																					p.293_293del		Atlas-INDEL	.											.	ZNF254	88	.	0			c.877_878del						.																																			SO:0001589	frameshift_variant	9534	exon4			.	AF054180	CCDS32983.1, CCDS62622.1, CCDS62623.1, CCDS74323.1, CCDS74324.1	19p13	2013-01-08				ENSG00000213096		"Zinc fingers, C2H2-type", "-"	13047	protein-coding gene	gene with protein product		604768	"zinc finger protein 539"	ZNF91L, ZNF539		9653160	Standard	NM_001278661		Approved	HD-ZNF1, BMZF-5	uc002nru.3	O75437		ENST00000357002.4:c.878_879delCT	chr19.hg19:g.24309680_24309681delCT	ENSP00000349494:p.Pro293fs	159.0	0.0		183.0	17.0	NM_203282	A4QPC0|Q86XL7	Frame_Shift_Del	DEL	ENST00000357002.4	hg19	CCDS32983.1																																																																																			.	.		0.366	ZNF254-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466453.1	NM_004876		-	24309681	CT	-	24309680	7	5	303	1	0	1	0	1	0	0	0	0	17813	681	24	0	892	0	ZNF254	19	24309680	Frame_Shift_Del	DEL	CT	TCGA-G3-AAV7-01A-11D-A382-10		24309680	34819303	83	43676										
THAP8	199745	hgsc.bcm.edu	37	chr19	36530605	36530605	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	gactggcttctgggtgcttcGggtcctccgctgactctgga	14	12	2	1	rs201068048	byFrequency	TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr19:36530605G>A	ENST00000292894.1	-	3	836	c.292C>T	c.(292-294)Cga>Tga	p.R98*	THAP8_ENST00000538849.1_5'UTR|AC002116.7_ENST00000586962.1_RNA|THAP8_ENST00000524106.1_5'Flank	NM_152658.2	NP_689871.1	Q8NA92	THAP8_HUMAN	THAP domain containing 8	98							DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	8	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			TGGGTGCTTCGGGTCCTCCGC	0.632													g|||	2	0.000399361	0	0.0014	5008	,	,		15167	0		0	False		,,,				2504	0.001				p.R98X		Atlas-SNP	.											.	THAP8	11	.	0			c.C292T						.		stop/ARG	0,4064		0,0,2032	23	22	22		292	0	0	19		22	1,7843		0,1,3921	yes	stop-gained	THAP8	NM_152658.2		0,1,5953	AA,AG,GG		0.0127,0.0,0.0084		98/275	36530605	1,11907	2032	3922	5954	SO:0001587	stop_gained	199745	exon3			TGCTTCGGGTCCT	AK057453	CCDS33000.1	19q13.13	2013-01-25			ENSG00000161277	ENSG00000161277		"THAP (C2CH-type zinc finger) domain containing"	23191	protein-coding gene	gene with protein product		612536				12575992	Standard	NM_152658		Approved	FLJ32891	uc002oda.1	Q8NA92	OTTHUMG00000048138	ENST00000292894.1:c.292C>T	chr19.hg19:g.36530605G>A	ENSP00000292894:p.Arg98*	88.0	0.0		122.0	40.0	NM_152658	Q0P5Z7|Q96M21	Nonsense_Mutation	SNP	ENST00000292894.1	hg19	CCDS33000.1	.	.	.	.	.	.	.	.	.	.	g	21.7	4.181972	0.78677	0.0	1.27E-4	ENSG00000161277	ENST00000292894;ENST00000392182	.	.	.	3.71	0.0427	0.14218	.	2587.460000	0.00166	U	0.000000	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-22.4094	3.028	0.06097	0.2199:0.0:0.3864:0.3938	.	.	.	.	X	98	.	ENSP00000292894:R98X	R	-	1	2	THAP8	41222445	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.526000	0.06207	0.000000	0.14550	0.552000	0.68991	CGA	.	.		0.632	THAP8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379036.1	NM_152658		A	36530605	G	A	36530605	4	1	303	1	0	0	0	0	0	1	0	0	15865	1124	39	1	540	1	THAP8	19	36530605	Nonsense_Mutation	SNP	G	TCGA-G3-AAV7-01A-11D-A382-10	12220925	36530605	22598378	84	43677										
SYMPK	8189	hgsc.bcm.edu	37	chr19	46332347	46332347	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	gcgttgtactcctggtagagCcaggcgaaggccaggtccag	15	11	0	1			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr19:46332347C>A	ENST00000245934.7	-	14	2110	c.1866G>T	c.(1864-1866)tgG>tgT	p.W622C	AC092301.3_ENST00000601618.1_RNA	NM_004819.2	NP_004810.2	Q92797	SYMPK_HUMAN	symplekin	622					cell adhesion (GO:0007155)|mRNA polyadenylation (GO:0006378)|positive regulation of protein dephosphorylation (GO:0035307)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)		p.W622C(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(25)|ovary(1)|urinary_tract(1)	45		all_neural(266;0.0299)|Ovarian(192;0.0308)		OV - Ovarian serous cystadenocarcinoma(262;0.00509)|GBM - Glioblastoma multiforme(486;0.0593)		CCTGGTAGAGCCAGGCGAAGG	0.642																																					p.W622C		Atlas-SNP	.											SYMPK,NS,carcinoma,0,1	SYMPK	104	.	1	Substitution - Missense(1)	lung(1)	c.G1866T						.						66	63	64					19																	46332347		2203	4300	6503	SO:0001583	missense	8189	exon14			GTAGAGCCAGGCG	U49240	CCDS12676.2	19q13.3	2008-02-05			ENSG00000125755	ENSG00000125755			22935	protein-coding gene	gene with protein product		602388				9330635	Standard	NM_004819		Approved	SYM, SPK	uc002pdn.3	Q92797	OTTHUMG00000150151	ENST00000245934.7:c.1866G>T	chr19.hg19:g.46332347C>A	ENSP00000245934:p.Trp622Cys	148.0	1.0		213.0	66.0	NM_004819	O00521|O00689|O00733|Q59GT5|Q8N2U5	Missense_Mutation	SNP	ENST00000245934.7	hg19	CCDS12676.2	.	.	.	.	.	.	.	.	.	.	C	13.84	2.358645	0.41801	.	.	ENSG00000125755	ENST00000245934	.	.	.	4.94	4.94	0.65067	Armadillo-type fold (1);	0.074050	0.56097	D	0.000029	T	0.53722	0.1814	L	0.47016	1.485	0.80722	D	1	P;B	0.45634	0.863;0.256	B;B	0.41440	0.357;0.151	T	0.60850	-0.7181	9	0.62326	D	0.03	.	15.7509	0.77986	0.0:1.0:0.0:0.0	.	637;622	Q4LE61;Q92797	.;SYMPK_HUMAN	C	622	.	ENSP00000245934:W622C	W	-	3	0	SYMPK	51024187	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	3.779000	0.55379	2.312000	0.78011	0.456000	0.33151	TGG	.	.		0.642	SYMPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316581.1	NM_004819		A	46332347	C	A	46332347	3	1	303	1	0	0	0	0	1	0	0	0	15454	740	26	3	2014	3	SYMPK	19	46332347	Missense_Mutation	SNP	C	TCGA-G3-AAV7-01A-11D-A382-10	9801742	46332347	12796636	85	43678										
PRR12	57479	hgsc.bcm.edu	37	chr19	50119403	50119403	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	ctgaaggaggcaggcggcaaCgctacagcaggcgggggccc	18	12	0	1	rs563050549		TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr19:50119403C>T	ENST00000418929.2	+	9	5436	c.5424C>T	c.(5422-5424)aaC>aaT	p.N1808N		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	987							DNA binding (GO:0003677)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)|prostate(2)	11		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		CAGGCGGCAACGCTACAGCAG	0.672													c|||	1	0.000199681	0	0	5008	,	,		14230	0.001		0	False		,,,				2504	0				p.N1808N		Atlas-SNP	.											.	PRR12	157	.	0			c.C5424T						.						11	15	14					19																	50119403		2052	4167	6219	SO:0001819	synonymous_variant	57479	exon9			CGGCAACGCTACA	AB033031	CCDS46143.1	19q13.33	2008-07-02	2006-02-06	2006-02-06		ENSG00000126464			29217	protein-coding gene	gene with protein product			"KIAA1205"	KIAA1205		10574462	Standard	NM_020719		Approved		uc002poo.4	Q9ULL5		ENST00000418929.2:c.5424C>T	chr19.hg19:g.50119403C>T		217.0	0.0		310.0	84.0	NM_020719	E9PB06|Q8N4J6	Silent	SNP	ENST00000418929.2	hg19	CCDS46143.1																																																																																			.	.		0.672	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719		T	50119403	C	T	50119403	2	4	303	1	0	0	0	0	0	0	0	1	12596	535	19	1		1	PRR12	19	50119403	Silent	SNP	C	TCGA-G3-AAV7-01A-11D-A382-10	3787056	50119403	9009580	86	43679										
C19orf75	284369	hgsc.bcm.edu	37	chr19	51769106	51769106	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	ctatgcgggaattgtaattgCgctgctcttcctctgcctcc	9	13	2	0	rs149546733		TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr19:51769106C>T	ENST00000316401.7	+	4	761	c.380C>T	c.(379-381)gCg>gTg	p.A127V	SIGLECL1_ENST00000597824.1_Missense_Mutation_p.A33V|CTD-3187F8.2_ENST00000597569.1_RNA|SIGLECL1_ENST00000593968.1_3'UTR	NM_173635.1	NP_775906.1	Q96PQ1	SIG12_HUMAN	SIGLEC family like 1	489	Ig-like V-type 1.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.A127V(1)									ATTGTAATTGCGCTGCTCTTC	0.557																																					p.A127V		Atlas-SNP	.											C19orf75,rectum,carcinoma,0,1	.	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C380T						.	C	VAL/ALA	0,4406		0,0,2203	243	224	230		380	0.9	0	19	dbSNP_134	230	2,8598	2.2+/-6.3	0,2,4298	yes	missense	C19orf75	NM_173635.1	64	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	possibly-damaging	127/198	51769106	2,13004	2203	4300	6503	SO:0001583	missense	284369	exon4			TAATTGCGCTGCT	AK097554	CCDS12827.1	19q13.33	2013-03-20	2012-07-20	2012-07-20	ENSG00000179213	ENSG00000179213			26856	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 75", "sialic acid binding Ig-like lectin 23, pseudogene", "sialic acid binding Ig-like lectin, pseudogene 7"	C19orf75, SIGLEC23P, SIGLECP7			Standard	NM_173635		Approved	FLJ40235	uc002pwb.1	Q8N7X8	OTTHUMG00000182881	ENST00000316401.7:c.380C>T	chr19.hg19:g.51769106C>T	ENSP00000321249:p.Ala127Val	98.0	0.0		89.0	19.0	NM_173635	Q8IYH7	Missense_Mutation	SNP	ENST00000316401.7	hg19	CCDS12827.1	.	.	.	.	.	.	.	.	.	.	C	11.31	1.599762	0.28534	0.0	2.33E-4	ENSG00000179213	ENST00000316401	T	0.38560	1.13	4.38	0.863	0.19062	.	1.625570	0.03695	N	0.247752	T	0.42040	0.1185	L	0.55017	1.72	0.09310	N	1	B;D	0.56287	0.0;0.975	B;P	0.46299	0.001;0.511	T	0.28170	-1.0052	10	0.41790	T	0.15	.	4.069	0.09874	0.0:0.5631:0.2137:0.2231	.	33;127	B7ZLS6;Q8N7X8	.;CS075_HUMAN	V	127	ENSP00000321249:A127V	ENSP00000321249:A127V	A	+	2	0	C19orf75	56460918	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.247000	0.08866	0.507000	0.28148	-0.128000	0.14901	GCG	.	C|1.000;T|0.000		0.557	SIGLECL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464161.2	NM_173635		T	51769106	C	T	51769106	3	4	303	1	0	0	0	0	1	0	0	0	1951	768	27	1	390	1	C19orf75	19	51769106	Missense_Mutation	SNP	C	TCGA-G3-AAV7-01A-11D-A382-10	1649703	51769106	7359877	87	43680										
CECR6	27439	hgsc.bcm.edu	37	chr22	17600295	17600295	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	tcaccctcaattctgagaggCcacagccagggtgttgacat	10	12	3	2			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr22:17600295C>G	ENST00000331437.3	-	1	1848	c.1723G>C	c.(1723-1725)Gcc>Ccc	p.A575P	CECR6_ENST00000399875.1_Missense_Mutation_p.A220P|AC006946.15_ENST00000441544.1_5'Flank	NM_031890.3	NP_114096.1	Q9BXQ6	CECR6_HUMAN	cat eye syndrome chromosome region, candidate 6	575										haematopoietic_and_lymphoid_tissue(1)	1		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)		Colorectal(9;0.221)		TTCTGAGAGGCCACAGCCAGG	0.587																																					p.A575P		Atlas-SNP	.											.	CECR6	11	.	0			c.G1723C						.						27	26	26					22																	17600295		2201	4300	6501	SO:0001583	missense	27439	exon1			GAGAGGCCACAGC	AF307451	CCDS13740.1, CCDS54494.1	22q11.2	2008-06-12			ENSG00000183307	ENSG00000183307			1844	protein-coding gene	gene with protein product						11381032	Standard	NM_031890		Approved		uc002zmb.2	Q9BXQ6	OTTHUMG00000030471	ENST00000331437.3:c.1723G>C	chr22.hg19:g.17600295C>G	ENSP00000329318:p.Ala575Pro	93.0	0.0		131.0	49.0	NM_031890	A8MYY1	Missense_Mutation	SNP	ENST00000331437.3	hg19	CCDS13740.1	.	.	.	.	.	.	.	.	.	.	C	12.94	2.088080	0.36855	.	.	ENSG00000183307	ENST00000399875;ENST00000331437	.	.	.	4.26	0.765	0.18470	.	0.549745	0.15959	U	0.236366	T	0.33059	0.0850	N	0.19112	0.55	0.33729	D	0.618048	P	0.50617	0.937	P	0.52424	0.698	T	0.47169	-0.9138	9	0.72032	D	0.01	.	4.3691	0.11239	0.1622:0.5443:0.0:0.2935	.	575	Q9BXQ6	CECR6_HUMAN	P	220;575	.	ENSP00000329318:A575P	A	-	1	0	CECR6	15980295	0.967000	0.33354	0.965000	0.40720	0.723000	0.41478	0.466000	0.22019	0.552000	0.29026	0.561000	0.74099	GCC	.	.		0.587	CECR6-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000075359.4	NM_031890		G	17600295	C	G	17600295	3	3	303	1	0	0	0	0	1	0	0	0	3210	739	26	4	17	4	CECR6	22	17600295	Missense_Mutation	SNP	C	TCGA-G3-AAV7-01A-11D-A382-10		17600295	33704271	88	43681										
PRR5	55615	hgsc.bcm.edu	37	chr22	45132983	45132983	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	cccacccgcagctccctgccCcgctccagcccggagaacct	8	23	0	1			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr22:45132983C>T	ENST00000336985.6	+	8	1300	c.1023C>T	c.(1021-1023)ccC>ccT	p.P341P	PRR5-ARHGAP8_ENST00000352766.7_Intron|PRR5_ENST00000006251.7_Silent_p.P332P|PRR5_ENST00000403581.1_Silent_p.P364P|ARHGAP8_ENST00000517296.3_Intron|PRR5_ENST00000477331.1_3'UTR|PRR5-ARHGAP8_ENST00000361473.5_Intron|ARHGAP8_ENST00000389773.5_Intron	NM_181333.3	NP_851850.1	P85299	PRR5_HUMAN	proline rich 5 (renal)	341					cell cycle (GO:0007049)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)	TORC2 complex (GO:0031932)				central_nervous_system(1)|endometrium(2)|lung(6)|prostate(1)|skin(1)	11		all_neural(38;0.00409)|Ovarian(80;0.024)|Glioma(61;0.0647)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)		GCTCCCTGCCCCGCTCCAGCC	0.682																																					p.P364P		Atlas-SNP	.											.	PRR5	75	.	0			c.C1092T						.						22	25	24					22																	45132983		2202	4295	6497	SO:0001819	synonymous_variant	55615	exon10			CCTGCCCCGCTCC	AF177331	CCDS14058.1, CCDS14059.1, CCDS56232.1, CCDS74875.1	22q13.3	2011-02-10			ENSG00000186654	ENSG00000186654			31682	protein-coding gene	gene with protein product	"protein observed with Rictor-1"	609406				15718101, 17599906	Standard	NM_001017528		Approved	PP610, FLJ20185k, Protor-1		P85299	OTTHUMG00000150460	ENST00000336985.6:c.1023C>T	chr22.hg19:g.45132983C>T		107.0	0.0		133.0	45.0	NM_001198721	B1AHF6|B1AHG5|B3KP73|O75983|O95695|Q5BIW2|Q5EAJ8|Q5EAJ9|Q5XKJ6|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Silent	SNP	ENST00000336985.6	hg19	CCDS14058.1	.	.	.	.	.	.	.	.	.	.	C	0.712	-0.786794	0.02907	.	.	ENSG00000186654	ENST00000455389	T	0.52295	0.67	5.29	-0.903	0.10534	.	.	.	.	.	T	0.29588	0.0738	.	.	.	0.26598	N	0.97308	.	.	.	.	.	.	T	0.26573	-1.0099	5	.	.	.	.	3.0859	0.06278	0.1224:0.3422:0.361:0.1743	.	.	.	.	L	301	ENSP00000405404:P301L	.	P	+	2	0	PRR5	43511647	0.003000	0.15002	0.001000	0.08648	0.042000	0.13812	0.196000	0.17176	0.071000	0.16664	0.561000	0.74099	CCC	.	.		0.682	PRR5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318200.2	NM_001017528		T	45132983	C	T	45132983	2	4	303	1	0	0	0	0	0	0	0	1	12612	610	22	3		3	PRR5	22	45132983	Silent	SNP	C	TCGA-G3-AAV7-01A-11D-A382-10	27532688	45132983	6171583	89	43682										
TBC1D22A	25771	hgsc.bcm.edu	37	chr22	47193446	47193446	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	cagcactctcagcagctcagCgctgagcgaaagagaggcct	12	13	2	2			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chr22:47193446C>T	ENST00000337137.4	+	4	732	c.566C>T	c.(565-567)gCg>gTg	p.A189V	TBC1D22A_ENST00000406733.1_Missense_Mutation_p.A142V|TBC1D22A_ENST00000407381.3_Intron|TBC1D22A_ENST00000355704.3_Intron|TBC1D22A_ENST00000380995.1_Missense_Mutation_p.A142V	NM_001284304.1|NM_001284305.1|NM_014346.2	NP_001271233.1|NP_001271234.1|NP_055161.1	Q8WUA7	TB22A_HUMAN	TBC1 domain family, member 22A	189							protein homodimerization activity (GO:0042803)|Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(3)|large_intestine(10)|lung(5)|ovary(2)|prostate(1)	22		all_cancers(38;4.44e-05)|all_epithelial(38;0.000507)|Breast(42;0.0488)|all_lung(38;0.0682)|Ovarian(80;0.0731)|all_neural(38;0.0966)|Glioma(61;0.222)|Lung SC(80;0.236)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0347)|BRCA - Breast invasive adenocarcinoma(115;0.231)		AGCAGCTCAGCGCTGAGCGAA	0.652											OREG0026659	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A189V		Atlas-SNP	.											.	TBC1D22A	54	.	0			c.C566T						.						39	34	36					22																	47193446		2203	4300	6503	SO:0001583	missense	25771	exon4			GCTCAGCGCTGAG	AK125705	CCDS14078.1, CCDS63511.1, CCDS63512.1, CCDS74877.1	22q13	2008-01-22	2005-01-05	2005-01-05	ENSG00000054611	ENSG00000054611			1309	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 4"	C22orf4			Standard	XM_005261496		Approved		uc003bib.3	Q8WUA7	OTTHUMG00000150332	ENST00000337137.4:c.566C>T	chr22.hg19:g.47193446C>T	ENSP00000336724:p.Ala189Val	220.0	0.0	945	220.0	59.0	NM_014346	B0QYI2|B0QYI3|B9A6M3|Q5TE47|Q6ZUH2|Q92680|Q9BVD6|Q9UGG0|Q9UGT2|Q9UGU6|Q9UH25|Q9Y4W5	Missense_Mutation	SNP	ENST00000337137.4	hg19	CCDS14078.1	.	.	.	.	.	.	.	.	.	.	C	12.58	1.980250	0.34942	.	.	ENSG00000054611	ENST00000337137;ENST00000380995;ENST00000406733	T;T;T	0.49432	1.8;0.78;1.8	4.55	3.53	0.40419	.	0.107163	0.64402	N	0.000005	T	0.35856	0.0946	L	0.52364	1.645	0.40273	D	0.978305	B;B	0.17667	0.023;0.023	B;B	0.11329	0.006;0.006	T	0.13872	-1.0493	10	0.17832	T	0.49	.	6.7892	0.23689	0.1742:0.7341:0.0:0.0917	.	189;189	B9A6M3;Q8WUA7	.;TB22A_HUMAN	V	189;142;142	ENSP00000336724:A189V;ENSP00000370383:A142V;ENSP00000385634:A142V	ENSP00000336724:A189V	A	+	2	0	TBC1D22A	45572110	0.796000	0.28864	0.018000	0.16275	0.854000	0.48673	1.475000	0.35409	1.129000	0.42072	0.442000	0.29010	GCG	.	.		0.652	TBC1D22A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317600.3	NM_014346		T	47193446	C	T	47193446	3	4	303	1	0	0	0	0	1	0	0	0	15626	768	27	1	580	1	TBC1D22A	22	47193446	Missense_Mutation	SNP	C	TCGA-G3-AAV7-01A-11D-A382-10	2060463	47193446	4111120	90	43683										
VCX2	51480	hgsc.bcm.edu	37	chrX	8138182	8138182	+	Frame_Shift_Del	DEL	A	A	-													0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	ccacctcgctctcctgactcAgggggtcgtgctgggtcccc					rs41305169		TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chrX:8138182delA	ENST00000317103.4	-	3	617	c.311delT	c.(310-312)ctgfs	p.L104fs		NM_016378.2	NP_057462.2	Q9H322	VCX2_HUMAN	variable charge, X-linked 2	104	2 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.		L -> P (in dbSNP:rs41305169). {ECO:0000269|PubMed:10607842, ECO:0000269|PubMed:10903929, ECO:0000269|PubMed:15489334}.							endometrium(1)	1		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				CTCCTGACTCAGGGGGTCGTG	0.667																																					p.L104fs		Atlas-INDEL	.											.	VCX2	16	.	0			c.312delG						.						27	34	32					X																	8138182		2157	4235	6392	SO:0001589	frameshift_variant	51480	exon3			.	AF159127	CCDS35200.1	Xp22.32	2008-02-05			ENSG00000177504	ENSG00000177504			18158	protein-coding gene	gene with protein product		300532				10607842	Standard	NM_016378		Approved	VCX-2r, VCX-2R	uc004csb.3	Q9H322	OTTHUMG00000021105	ENST00000317103.4:c.311delT	chrX.hg19:g.8138182delA	ENSP00000321309:p.Leu104fs	138.0	0.0		166.0	11.0	NM_016378	A3KPB6|Q4V9T2|Q9P0H5	Frame_Shift_Del	DEL	ENST00000317103.4	hg19	CCDS35200.1																																																																																			.	.		0.667	VCX2-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055690.1	NM_016378		-	8138182	A	-	8138182	7	5	303	1	0	1	0	1	0	0	0	0	17158	188	7	0	112	0	VCX2	23	8138182	Frame_Shift_Del	DEL	A	TCGA-G3-AAV7-01A-11D-A382-10		8138182	147132378	91	43684										
OFD1	8481	hgsc.bcm.edu	37	chrX	13778504	13778504	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0333333333333333	3	1	0.770559680182753	0.727750809061489	0.793909973521624	1	1	0	caaagagcttcagcaagaggCcgaacgcttggaaaaggctt	12	9	1	2			TCGA-G3-AAV7-01A-11D-A382-10	TCGA-G3-AAV7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7a120ba7-e59d-48f3-9e72-4b0466e25e4c	07777f2e-37eb-4fc2-9804-a93484b12424	g.chrX:13778504C>G	ENST00000340096.6	+	16	2252	c.1925C>G	c.(1924-1926)gCc>gGc	p.A642G	OFD1_ENST00000380567.1_Missense_Mutation_p.A502G|OFD1_ENST00000380550.3_Missense_Mutation_p.A602G|OFD1_ENST00000490265.1_3'UTR	NM_003611.2	NP_003602.1	O75665	OFD1_HUMAN	oral-facial-digital syndrome 1	642	Mediates homooligomerization.|Mediates the interaction with SDCCAG8.				axoneme assembly (GO:0035082)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation (GO:2000314)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|gamma-tubulin binding (GO:0043015)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	25						CAGCAAGAGGCCGAACGCTTG	0.478																																					p.A642G		Atlas-SNP	.											.	OFD1	109	.	0			c.C1925G						.						91	80	84					X																	13778504		2203	4300	6503	SO:0001583	missense	8481	exon16			AAGAGGCCGAACG	Y15164	CCDS14157.1	Xp22	2014-06-18			ENSG00000046651	ENSG00000046651			2567	protein-coding gene	gene with protein product		300170	"retinitis pigmentosa 23 (X-linked recessive)"	CXorf5, RP23		9722947, 9215688, 22619378	Standard	NM_003611		Approved	71-7A, JBTS10	uc004cvp.4	O75665	OTTHUMG00000021159	ENST00000340096.6:c.1925C>G	chrX.hg19:g.13778504C>G	ENSP00000344314:p.Ala642Gly	101.0	0.0		110.0	67.0	NM_003611	B9ZVU5|O75666|Q4VAK4	Missense_Mutation	SNP	ENST00000340096.6	hg19	CCDS14157.1	.	.	.	.	.	.	.	.	.	.	.	15.81	2.942782	0.53079	.	.	ENSG00000046651	ENST00000380550;ENST00000340096;ENST00000380567	D;D;D	0.98996	-5.31;-5.18;-2.97	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	D	0.99260	0.9742	M	0.77103	2.36	0.80722	D	1	D;P;D;D;D	0.89917	0.968;0.876;1.0;1.0;0.968	P;B;D;D;P	0.91635	0.569;0.337;0.999;0.999;0.469	D	0.99727	1.1011	10	0.56958	D	0.05	-13.2959	18.8223	0.92102	0.0:1.0:0.0:0.0	.	642;602;310;502;642	A8K2T9;O75665-3;B4DLQ3;A6NF31;O75665	.;.;.;.;OFD1_HUMAN	G	602;642;502	ENSP00000369923:A602G;ENSP00000344314:A642G;ENSP00000369941:A502G	ENSP00000344314:A642G	A	+	2	0	OFD1	13688425	1.000000	0.71417	0.894000	0.35097	0.331000	0.28603	4.838000	0.62803	2.391000	0.81399	0.529000	0.55759	GCC	.	.		0.478	OFD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055808.1	NM_003611		G	13778504	C	G	13778504	3	3	303	1	0	0	0	0	1	0	0	0	10847	739	26	4	1987	4	OFD1	23	13778504	Missense_Mutation	SNP	C	TCGA-G3-AAV7-01A-11D-A382-10	5640322	13778504	141492056	92	43685										
HIVEP3	59269	hgsc.bcm.edu	37	chr1	42047687	42047687	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	ctggctcgggctgcgagacaGaggcacagaggactcgaagc	16	11	0	3			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr1:42047687G>T	ENST00000372583.1	-	4	3667	c.2782C>A	c.(2782-2784)Ctg>Atg	p.L928M	HIVEP3_ENST00000429157.2_Missense_Mutation_p.L928M|HIVEP3_ENST00000460604.1_5'Flank|HIVEP3_ENST00000372584.1_Missense_Mutation_p.L928M|HIVEP3_ENST00000247584.5_Missense_Mutation_p.L928M	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	928	No DNA binding activity or transactivation activity, but complete prevention of TRAF-dependent NF-Kappa-B activation; associates with TRAF2 and JUN. {ECO:0000250}.|Ser-rich.				positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				CTGCGAGACAGAGGCACAGAG	0.602																																					p.L928M		Atlas-SNP	.											.	HIVEP3	235	.	0			c.C2782A						.						85	92	90					1																	42047687		2203	4300	6503	SO:0001583	missense	59269	exon4			GAGACAGAGGCAC	AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"Zinc fingers, C2H2-type"	13561	protein-coding gene	gene with protein product	"kappabinding protein-1"	606649	"human immunodeficiency virus type I enhancer-binding protein 3"			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.2782C>A	chr1.hg19:g.42047687G>T	ENSP00000361664:p.Leu928Met	137.0	0.0		127.0	9.0	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Missense_Mutation	SNP	ENST00000372583.1	hg19	CCDS463.1	.	.	.	.	.	.	.	.	.	.	G	19.21	3.784173	0.70222	.	.	ENSG00000127124	ENST00000372584;ENST00000372583;ENST00000247584;ENST00000429157	T;T;T;T	0.59906	0.23;0.23;0.23;0.23	4.95	4.95	0.65309	.	0.000000	0.39210	N	0.001427	T	0.75852	0.3906	M	0.75615	2.305	0.44006	D	0.996712	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.997	T	0.77376	-0.2611	10	0.52906	T	0.07	-0.2663	16.9056	0.86127	0.0:0.0:1.0:0.0	.	928;928	Q5T1R4-2;Q5T1R4	.;ZEP3_HUMAN	M	928	ENSP00000361665:L928M;ENSP00000361664:L928M;ENSP00000247584:L928M;ENSP00000410828:L928M	ENSP00000247584:L928M	L	-	1	2	HIVEP3	41820274	1.000000	0.71417	0.996000	0.52242	0.948000	0.59901	6.278000	0.72614	2.562000	0.86427	0.462000	0.41574	CTG	.	.		0.602	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503		T	42047687	G	T	42047687	3	4	304	1	0	0	0	0	1	0	0	0	7197	933	33	3	4462	3	HIVEP3	1	42047687	Missense_Mutation	SNP	G	TCGA-GJ-A3OU-01A-31D-A382-10		42047687	207202934	1	43686										
SLC44A3	126969	hgsc.bcm.edu	37	chr1	95307574	95307574	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	agttgtctgcggtgttttatGgtggctgtattatgactata	12	4	1	1			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr1:95307574G>C	ENST00000271227.6	+	8	881	c.779G>C	c.(778-780)tGg>tCg	p.W260S	SLC44A3_ENST00000530397.1_3'UTR|SLC44A3_ENST00000446120.2_Missense_Mutation_p.W224S|SLC44A3_ENST00000527077.1_Missense_Mutation_p.W192S|RP11-465K1.2_ENST00000422162.1_RNA|SLC44A3_ENST00000532427.1_Missense_Mutation_p.W180S|SLC44A3_ENST00000467909.1_Missense_Mutation_p.W212S|SLC44A3_ENST00000529450.1_Missense_Mutation_p.W228S	NM_001114106.2|NM_001258340.1|NM_001258341.1	NP_001107578.1|NP_001245269.1|NP_001245270.1	Q8N4M1	CTL3_HUMAN	solute carrier family 44, member 3	260					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(6)|prostate(2)|stomach(1)|urinary_tract(1)	23		all_lung(203;0.000712)|Lung NSC(277;0.00316)		all cancers(265;0.039)|Epithelial(280;0.124)	Choline(DB00122)	GGTGTTTTATGGTGGCTGTAT	0.478																																					p.W260S		Atlas-SNP	.											.	SLC44A3	109	.	0			c.G779C						.						251	241	245					1																	95307574		2203	4300	6503	SO:0001583	missense	126969	exon8			TTTTATGGTGGCT	BC033858	CCDS751.1, CCDS44176.1, CCDS58011.1, CCDS58012.1, CCDS58013.1, CCDS72827.1	1p22.1	2013-05-22	2005-09-06		ENSG00000143036	ENSG00000143036		"Solute carriers"	28689	protein-coding gene	gene with protein product			"solute carrier family, member 3"			15715662, 12975309	Standard	NM_001114106		Approved	MGC45474, CTL3	uc001dqv.5	Q8N4M1	OTTHUMG00000010700	ENST00000271227.6:c.779G>C	chr1.hg19:g.95307574G>C	ENSP00000271227:p.Trp260Ser	80.0	0.0		106.0	7.0	NM_001114106	B4DVY4|B4E1M4|B7ZA08|E9PJH2|E9PJY8|Q6UWT1|Q7Z6C5|Q9BWY7	Missense_Mutation	SNP	ENST00000271227.6	hg19	CCDS44176.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.163387	0.78226	.	.	ENSG00000143036	ENST00000446120;ENST00000271227;ENST00000527077;ENST00000529450;ENST00000467909;ENST00000532427	T;T;T;T;T;T	0.20463	2.57;2.77;2.08;2.09;2.57;2.07	5.93	5.93	0.95920	.	0.000000	0.64402	D	0.000006	T	0.43986	0.1272	M	0.74881	2.28	0.80722	D	1	D;D;D;D;D	0.89917	0.999;1.0;0.999;0.999;0.999	D;D;D;D;D	0.85130	0.996;0.997;0.996;0.996;0.996	T	0.34403	-0.9830	10	0.87932	D	0	-14.3105	20.0189	0.97489	0.0:0.0:1.0:0.0	.	180;224;192;228;260	E9PIC5;Q8N4M1-3;E9PJY8;E9PJH2;Q8N4M1	.;.;.;.;CTL3_HUMAN	S	224;260;192;228;212;180	ENSP00000389143:W224S;ENSP00000271227:W260S;ENSP00000433641:W192S;ENSP00000431836:W228S;ENSP00000432789:W212S;ENSP00000436661:W180S	ENSP00000271227:W260S	W	+	2	0	SLC44A3	95080162	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	7.165000	0.77544	2.833000	0.97629	0.650000	0.86243	TGG	.	.		0.478	SLC44A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029544.3	NM_152369		C	95307574	G	C	95307574	3	2	304	1	0	0	0	0	1	0	0	0	14652	1357	47	4	809	4	SLC44A3	1	95307574	Missense_Mutation	SNP	G	TCGA-GJ-A3OU-01A-31D-A382-10	53259887	95307574	153943047	2	43687										
ASH1L	55870	hgsc.bcm.edu	37	chr1	155449069	155449069	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	tccaattccactatcactggGaatggtctcatcactatgag	7	11	3	1			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr1:155449069G>T	ENST00000368346.3	-	3	4231	c.3592C>A	c.(3592-3594)Ccc>Acc	p.P1198T	ASH1L_ENST00000392403.3_Missense_Mutation_p.P1198T			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	1198					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			CTATCACTGGGAATGGTCTCA	0.418																																					p.P1198T		Atlas-SNP	.											.	ASH1L	279	.	0			c.C3592A						.						111	115	114					1																	155449069		2203	4300	6503	SO:0001583	missense	55870	exon3			CACTGGGAATGGT	AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.3592C>A	chr1.hg19:g.155449069G>T	ENSP00000357330:p.Pro1198Thr	102.0	0.0		140.0	31.0	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	hg19		.	.	.	.	.	.	.	.	.	.	G	17.02	3.281267	0.59758	.	.	ENSG00000116539	ENST00000368346;ENST00000392403	D;D	0.90563	-2.69;-2.69	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	D	0.92116	0.7501	L	0.36672	1.1	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	D	0.92626	0.6112	10	0.62326	D	0.03	.	18.5192	0.90945	0.0:0.0:1.0:0.0	.	1198;1198	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	T	1198	ENSP00000357330:P1198T;ENSP00000376204:P1198T	ENSP00000357330:P1198T	P	-	1	0	ASH1L	153715693	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.657000	0.98554	2.705000	0.92388	0.591000	0.81541	CCC	.	.		0.418	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		T	155449069	G	T	155449069	3	4	304	1	0	0	0	0	1	0	0	0	1041	1174	41	3	5406	3	ASH1L	1	155449069	Missense_Mutation	SNP	G	TCGA-GJ-A3OU-01A-31D-A382-10	60141495	155449069	93801552	3	43688										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158646003	158646003	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	gctcccagctggagaccagaTcttctttcatctcctggatc	8	14	4	2			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr1:158646003T>C	ENST00000368147.4	-	8	1220	c.1040A>G	c.(1039-1041)gAt>gGt	p.D347G		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	347					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					GGAGACCAGATCTTCTTTCAT	0.473																																					p.D347G		Atlas-SNP	.											.	SPTA1	720	.	0			c.A1040G						.						194	184	187					1																	158646003		1922	4138	6060	SO:0001583	missense	6708	exon8			ACCAGATCTTCTT	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.1040A>G	chr1.hg19:g.158646003T>C	ENSP00000357129:p.Asp347Gly	67.0	0.0		129.0	39.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.414391	0.83449	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.36157	1.27;1.27	4.95	4.95	0.65309	.	0.248593	0.21031	N	0.081342	T	0.43986	0.1272	M	0.66939	2.045	0.53005	D	0.999966	P	0.46987	0.888	P	0.57009	0.811	T	0.46162	-0.9211	10	0.72032	D	0.01	.	13.6012	0.62020	0.0:0.0:0.0:1.0	.	347	P02549	SPTA1_HUMAN	G	347	ENSP00000357130:D347G;ENSP00000357129:D347G	ENSP00000357129:D347G	D	-	2	0	SPTA1	156912627	1.000000	0.71417	0.938000	0.37757	0.996000	0.88848	6.821000	0.75272	2.060000	0.61445	0.533000	0.62120	GAT	.	.		0.473	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		C	158646003	T	C	158646003	3	2	304	1	0	0	0	0	1	0	0	0	15131	1435	50	2	6399	2	SPTA1	1	158646003	Missense_Mutation	SNP	T	TCGA-GJ-A3OU-01A-31D-A382-10	3196934	158646003	90604618	4	43689										
C1orf112	55732	hgsc.bcm.edu	37	chr1	169775144	169775144	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	ttctgttatctttctttgcaGttattcattctttattggat	5	6	5	0			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr1:169775144G>C	ENST00000286031.6	+	7	1178		c.e7-1		C1orf112_ENST00000359326.4_Splice_Site|C1orf112_ENST00000456684.1_Splice_Site|C1orf112_ENST00000498289.1_Splice_Site|C1orf112_ENST00000413811.2_Splice_Site	NM_018186.2	NP_060656.2	Q9NSG2	CA112_HUMAN	chromosome 1 open reading frame 112											breast(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|stomach(1)	34	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					TTTCTTTGCAGTTATTCATTC	0.308																																					.		Atlas-SNP	.											.	C1orf112	74	.	0			c.479-1G>C						.						98	88	91					1																	169775144		2200	4292	6492	SO:0001630	splice_region_variant	55732	exon7			TTTGCAGTTATTC	AL354614	CCDS1285.1	1q24.2	2012-06-26			ENSG00000000460	ENSG00000000460			25565	protein-coding gene	gene with protein product						12477932	Standard	NM_018186		Approved	FLJ10706	uc001ggq.3	Q9NSG2	OTTHUMG00000035821	ENST00000286031.6:c.479-1G>C	chr1.hg19:g.169775144G>C		37.0	0.0		54.0	11.0	NM_018186	A6NFP1|B3KU42|Q3KNQ1|Q9H8L5|Q9NVJ0	Splice_Site	SNP	ENST00000286031.6	hg19	CCDS1285.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.164168	0.78339	.	.	ENSG00000000460	ENST00000413811;ENST00000359326;ENST00000456684;ENST00000286031	.	.	.	5.34	5.34	0.76211	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.9676	0.89103	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	C1orf112	168041768	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.637000	0.91014	2.657000	0.90304	0.655000	0.94253	.	.	.		0.308	C1orf112-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087126.3	NM_018186	Intron	C	169775144	G	C	169775144	5	2	304	1	0	0	0	0	0	0	1	0	1987	1043	36	4	496	4	C1orf112	1	169775144	Splice_Site	SNP	G	TCGA-GJ-A3OU-01A-31D-A382-10	11129141	169775144	79475477	5	43690										
ACBD6	84320	hgsc.bcm.edu	37	chr1	180471265	180471265	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	ggtgcgcggcagccttctcaAacagctcggccaggcaactg	13	14	1	0			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr1:180471265A>C	ENST00000367595.3	-	1	824	c.137T>G	c.(136-138)tTt>tGt	p.F46C		NM_032360.3	NP_115736.1	Q9BR61	ACBD6_HUMAN	acyl-CoA binding domain containing 6	46	ACB. {ECO:0000255|PROSITE- ProRule:PRU00573}.					cytoplasm (GO:0005737)	fatty-acyl-CoA binding (GO:0000062)|lipid binding (GO:0008289)		ACBD6/RRP15(2)	haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|ovary(1)	7						AGCCTTCTCAAACAGCTCGGC	0.612																																					p.F46C		Atlas-SNP	.											.	ACBD6	20	.	0			c.T137G						.						39	39	39					1																	180471265		2203	4300	6503	SO:0001583	missense	84320	exon1			TTCTCAAACAGCT	BC006505	CCDS1339.1	1q25.1	2013-10-11	2010-04-30		ENSG00000135847			"Ankyrin repeat domain containing"	23339	protein-coding gene	gene with protein product			"acyl-Coenzyme A binding domain containing 6"			18268358	Standard	NM_032360		Approved	MGC2404	uc001gog.3	Q9BR61	OTTHUMG00000035117	ENST00000367595.3:c.137T>G	chr1.hg19:g.180471265A>C	ENSP00000356567:p.Phe46Cys	206.0	0.0		208.0	51.0	NM_032360		Missense_Mutation	SNP	ENST00000367595.3	hg19	CCDS1339.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.028709	0.75504	.	.	ENSG00000135847	ENST00000367595	T	0.60171	0.21	4.9	4.9	0.64082	FERM/acyl-CoA-binding protein, 3-helical bundle (1);Acyl-CoA-binding protein, ACBP (4);	0.000000	0.85682	D	0.000000	D	0.83198	0.5202	H	0.97131	3.945	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88563	0.3124	10	0.72032	D	0.01	-10.0939	13.6262	0.62165	1.0:0.0:0.0:0.0	.	46	Q9BR61	ACBD6_HUMAN	C	46	ENSP00000356567:F46C	ENSP00000356567:F46C	F	-	2	0	ACBD6	178737888	1.000000	0.71417	1.000000	0.80357	0.847000	0.48162	4.552000	0.60747	2.057000	0.61298	0.260000	0.18958	TTT	.	.		0.612	ACBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084998.1	NM_032360		C	180471265	A	C	180471265	3	2	304	1	0	0	0	0	1	0	0	0	126	14	1	5	743	5	ACBD6	1	180471265	Missense_Mutation	SNP	A	TCGA-GJ-A3OU-01A-31D-A382-10	10696121	180471265	68779356	6	43691										
NEK2	4751	hgsc.bcm.edu	37	chr1	211842562	211842562	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	tggaatcctgcgatttttctGgctctcctaattgtcgccct	8	12	2	0			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr1:211842562G>C	ENST00000366999.4	-	6	1016	c.878C>G	c.(877-879)cCa>cGa	p.P293R	NEK2_ENST00000462283.1_5'UTR|NEK2_ENST00000540251.1_Missense_Mutation_p.P250R|NEK2_ENST00000366998.3_Missense_Mutation_p.P293R	NM_002497.3	NP_002488.1	P51955	NEK2_HUMAN	NIMA-related kinase 2	293	Interaction with PCNT.				blastocyst development (GO:0001824)|centrosome separation (GO:0051299)|chromosome segregation (GO:0007059)|G2/M transition of mitotic cell cycle (GO:0000086)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of centriole-centriole cohesion (GO:1903126)|negative regulation of DNA binding (GO:0043392)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of mitosis (GO:0007088)|regulation of mitotic centrosome separation (GO:0046602)|spindle assembly (GO:0051225)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|microtubule (GO:0005874)|midbody (GO:0030496)|nucleus (GO:0005634)|protein complex (GO:0043234)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|stomach(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.00203)|all cancers(67;0.0339)|Epithelial(68;0.0546)		CGATTTTTCTGGCTCTCCTAA	0.438																																					p.P293R		Atlas-SNP	.											.	NEK2	49	.	0			c.C878G						.						134	136	136					1																	211842562		2203	4300	6503	SO:0001583	missense	4751	exon6			TTTTCTGGCTCTC	U11050	CCDS1500.1, CCDS55682.1, CCDS73024.1	1q32.3	2014-06-12	2012-11-15		ENSG00000117650	ENSG00000117650			7745	protein-coding gene	gene with protein product	"HsPK 21", "protein phosphatase 1, regulatory subunit 111"	604043	"NIMA (never in mitosis gene a)-related kinase 2"			8274451, 24043777	Standard	NM_002497		Approved	NLK1, NEK2A, RP67, PPP1R111	uc001hir.2	P51955	OTTHUMG00000037121	ENST00000366999.4:c.878C>G	chr1.hg19:g.211842562G>C	ENSP00000355966:p.Pro293Arg	53.0	0.0		53.0	10.0	NM_002497	Q53FD6|Q5I1Z9|Q5VXZ1|Q6NZX8|Q7Z634|Q86XH2|Q96QN9	Missense_Mutation	SNP	ENST00000366999.4	hg19	CCDS1500.1	.	.	.	.	.	.	.	.	.	.	G	9.414	1.081309	0.20309	.	.	ENSG00000117650	ENST00000366999;ENST00000540251;ENST00000366998	D;D;T	0.87412	-2.25;-2.25;-0.59	4.91	4.91	0.64330	.	0.269488	0.42964	D	0.000629	D	0.83894	0.5353	L	0.54323	1.7	0.50467	D	0.999877	B;B;B	0.18610	0.0;0.001;0.029	B;B;B	0.26202	0.002;0.002;0.067	T	0.79009	-0.1978	10	0.28530	T	0.3	.	12.2836	0.54779	0.0:0.0:0.7038:0.2962	.	293;293;293	P51955-2;P51955;P51955-4	.;NEK2_HUMAN;.	R	293;250;293	ENSP00000355966:P293R;ENSP00000440237:P250R;ENSP00000355965:P293R	ENSP00000355965:P293R	P	-	2	0	NEK2	209909185	1.000000	0.71417	0.889000	0.34880	0.939000	0.58152	3.935000	0.56560	2.432000	0.82394	0.585000	0.79938	CCA	.	.		0.438	NEK2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090154.1	NM_002497		C	211842562	G	C	211842562	3	2	304	1	0	0	0	0	1	0	0	0	10333	1348	47	4	471	4	NEK2	1	211842562	Missense_Mutation	SNP	G	TCGA-GJ-A3OU-01A-31D-A382-10	31371297	211842562	37408059	7	43692										
GUK1	2987	hgsc.bcm.edu	37	chr1	228328057	228328057	+	5'UTR	DEL	A	A	-													0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	gccgccctgggccgggccccAccggacggtgagtacgacaa							TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr1:228328057delA	ENST00000312726.4	+	0	67				GUK1_ENST00000366730.1_Intron|GUK1_ENST00000366726.1_5'UTR|GUK1_ENST00000366728.2_Frame_Shift_Del_p.P19fs|GUK1_ENST00000366722.1_5'UTR|GUK1_ENST00000366723.1_Frame_Shift_Del_p.P19fs|GUK1_ENST00000391865.3_Frame_Shift_Del_p.P19fs|GUK1_ENST00000366721.1_5'UTR	NM_000858.5	NP_000849.1	Q16774	KGUA_HUMAN	guanylate kinase 1						ATP metabolic process (GO:0046034)|dATP metabolic process (GO:0046060)|dGDP biosynthetic process (GO:0006185)|dGMP metabolic process (GO:0046054)|drug metabolic process (GO:0017144)|GDP biosynthetic process (GO:0046711)|GDP-mannose metabolic process (GO:0019673)|glycoprotein transport (GO:0034436)|GMP metabolic process (GO:0046037)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleotide metabolic process (GO:0006163)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanylate kinase activity (GO:0004385)			endometrium(2)|lung(5)|prostate(1)|soft_tissue(1)	9		Prostate(94;0.0405)				GCCGGGCCCCACCGGACGGTG	0.751																																					p.P18fs		Atlas-INDEL	.											.	GUK1	34	.	0			c.53delC						.						4	5	5					1																	228328057		1420	3333	4753	SO:0001623	5_prime_UTR_variant	2987	exon1			.	BC006249	CCDS1568.1, CCDS53481.1, CCDS55689.1	1q32-q41	2012-10-02			ENSG00000143774	ENSG00000143774	2.7.4.8		4693	protein-coding gene	gene with protein product		139270				8647247	Standard	NM_000858		Approved		uc021pkf.1	Q16774	OTTHUMG00000039503	ENST00000312726.4:c.-175A>-	chr1.hg19:g.228328057delA		80.0	0.0		72.0	12.0	NM_001242840	B1ANH1	Frame_Shift_Del	DEL	ENST00000312726.4	hg19	CCDS1568.1																																																																																			.	.		0.751	GUK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000095312.3	NM_000858		-	228328057	A	-	228328057	6	5	304	0	1	1	0	1	0	0	0	0	6909	146	6	0		0	GUK1	1	228328057	5'UTR	DEL	A	TCGA-GJ-A3OU-01A-31D-A382-10	16485495	228328057	20922564	8	43693										
FAM36A	116228	hgsc.bcm.edu	37	chr1	244999029	244999029	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	tagtcctcatggccgccccgCcggagcccggtgagcccgag	14	17	1	1			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr1:244999029C>G	ENST00000411948.2	+	1	406	c.13C>G	c.(13-15)Ccg>Gcg	p.P5A	COX20_ENST00000366528.3_Missense_Mutation_p.P5A|COX20_ENST00000498262.1_3'UTR	NM_198076.4	NP_932342.1	Q5RI15	COX20_HUMAN	COX20 cytochrome C oxidase assembly factor	5						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)											GGCCGCCCCGCCGGAGCCCGG	0.766																																					p.P5A		Atlas-SNP	.											.	.	.	.	0			c.C13G						.						2	2	2					1																	244999029		1279	2666	3945	SO:0001583	missense	116228	exon1			GCCCCGCCGGAGC	BC062419	CCDS31080.1	1q44	2013-05-24	2013-05-23	2012-02-24	ENSG00000203667	ENSG00000203667		"Mitochondrial respiratory chain complex assembly factors"	26970	protein-coding gene	gene with protein product		614698	"family with sequence similarity 36, member A", "COX20 Cox2 chaperone homolog (S. cerevisiae)"	FAM36A		22356826, 23125284	Standard	NM_198076		Approved	FLJ43269	uc001iar.3	Q5RI15	OTTHUMG00000040401	ENST00000411948.2:c.13C>G	chr1.hg19:g.244999029C>G	ENSP00000406327:p.Pro5Ala	54.0	0.0		83.0	19.0	NM_198076	Q8WV86	Missense_Mutation	SNP	ENST00000411948.2	hg19	CCDS31080.1	.	.	.	.	.	.	.	.	.	.	C	12.60	1.987183	0.35036	.	.	ENSG00000203667	ENST00000411948;ENST00000366528	.	.	.	4.27	0.442	0.16582	.	0.876418	0.09914	N	0.739379	T	0.14313	0.0346	N	0.08118	0	0.09310	N	1	B	0.19073	0.033	B	0.15052	0.012	T	0.25222	-1.0138	9	0.23891	T	0.37	1.9105	0.8223	0.01113	0.228:0.4031:0.1517:0.2172	.	5	Q5RI15	FA36A_HUMAN	A	5	.	ENSP00000355486:P5A	P	+	1	0	FAM36A	243065652	0.012000	0.17670	0.052000	0.19188	0.036000	0.12997	-0.233000	0.09041	0.338000	0.23692	0.455000	0.32223	CCG	.	.		0.766	COX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097174.1	NM_198076		G	244999029	C	G	244999029	3	3	304	1	0	0	0	0	1	0	0	0	5562	739	26	4	15	4	FAM36A	1	244999029	Missense_Mutation	SNP	C	TCGA-GJ-A3OU-01A-31D-A382-10	16670972	244999029	4251592	9	43694										
SNTG2	54221	hgsc.bcm.edu	37	chr2	1271232	1271232	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	aggccctattgcttcagcatCgtggccggccatgggaagag	14	11	1	1	rs370848778		TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr2:1271232C>A	ENST00000308624.5	+	14	1302	c.1173C>A	c.(1171-1173)atC>atA	p.I391I	SNTG2_ENST00000407292.1_Silent_p.I264I	NM_018968.3	NP_061841.2	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2	391	PH.		I -> V (in dbSNP:rs13023962).		central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|syntrophin complex (GO:0016013)	PDZ domain binding (GO:0030165)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		GCTTCAGCATCGTGGCCGGCC	0.522																																					p.I391I		Atlas-SNP	.											.	SNTG2	125	.	0			c.C1173A						.						53	52	52					2																	1271232		1937	4132	6069	SO:0001819	synonymous_variant	54221	exon14			CAGCATCGTGGCC	AJ003029	CCDS46220.1	2p25	2008-05-23			ENSG00000172554	ENSG00000172554			13741	protein-coding gene	gene with protein product		608715				10747910	Standard	NM_018968		Approved	SYN5, G2SYN	uc002qwq.3	Q9NY99	OTTHUMG00000151370	ENST00000308624.5:c.1173C>A	chr2.hg19:g.1271232C>A		158.0	0.0		164.0	20.0	NM_018968	Q05AH5	Silent	SNP	ENST00000308624.5	hg19	CCDS46220.1																																																																																			.	.		0.522	SNTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322454.1	NM_018968		A	1271232	C	A	1271232	2	1	304	1	0	0	0	0	0	0	0	1	14890	874	31	1		1	SNTG2	2	1271232	Silent	SNP	C	TCGA-GJ-A3OU-01A-31D-A382-10		1271232	241928141	10	43695										
SLC8A1	6546	hgsc.bcm.edu	37	chr2	40656037	40656037	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	aggcttaaacaccacagttcCttcagtaaattcataatcag	5	10	3	0			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr2:40656037C>T	ENST00000403092.1	-	2	1417	c.1384G>A	c.(1384-1386)Gga>Aga	p.G462R	SLC8A1_ENST00000332839.4_Missense_Mutation_p.G462R|SLC8A1_ENST00000406391.2_Missense_Mutation_p.G462R|SLC8A1_ENST00000542756.1_Missense_Mutation_p.G462R|SLC8A1_ENST00000405901.3_Missense_Mutation_p.G462R|SLC8A1_ENST00000402441.1_Missense_Mutation_p.G462R|SLC8A1_ENST00000542024.1_Missense_Mutation_p.G462R|SLC8A1_ENST00000405269.1_Missense_Mutation_p.G462R|SLC8A1_ENST00000406785.2_Missense_Mutation_p.G462R|SLC8A1_ENST00000408028.2_Missense_Mutation_p.G462R			P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 1	462	Calx-beta 1.				blood coagulation (GO:0007596)|calcium ion export (GO:1901660)|calcium ion homeostasis (GO:0055074)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|cardiac muscle cell development (GO:0055013)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular response to caffeine (GO:0071313)|cellular response to reactive oxygen species (GO:0034614)|cellular sodium ion homeostasis (GO:0006883)|cytosolic calcium ion transport (GO:0060401)|embryonic heart tube development (GO:0035050)|embryonic placenta development (GO:0001892)|heart morphogenesis (GO:0003007)|ion transport (GO:0006811)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|muscle contraction (GO:0006936)|muscle fiber development (GO:0048747)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|post-embryonic development (GO:0009791)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|relaxation of smooth muscle (GO:0044557)|sodium ion export (GO:0071436)|sodium ion import (GO:0097369)|transmembrane transport (GO:0055085)|vascular smooth muscle contraction (GO:0014829)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|calcium:sodium antiporter activity (GO:0005432)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)	p.G462R(1)		NS(1)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|liver(1)|lung(57)|ovary(2)|pancreas(1)|skin(7)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)	100					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)	ACCACAGTTCCTTCAGTAAAT	0.418																																					p.G462R		Atlas-SNP	.											SLC8A1,face,carcinoma,0,1	SLC8A1	221	.	1	Substitution - Missense(1)	skin(1)	c.G1384A						.						81	71	75					2																	40656037		2203	4300	6503	SO:0001583	missense	6546	exon1			CAGTTCCTTCAGT		CCDS1806.1, CCDS46264.1, CCDS46265.1, CCDS59430.1	2p22.1	2013-07-15			ENSG00000183023	ENSG00000183023		"Solute carriers"	11068	protein-coding gene	gene with protein product	"Na+/Ca++ exchanger"	182305		NCX1		1559714	Standard	NM_021097		Approved		uc002rrx.3	P32418	OTTHUMG00000102183	ENST00000403092.1:c.1384G>A	chr2.hg19:g.40656037C>T	ENSP00000384763:p.Gly462Arg	72.0	0.0		54.0	4.0	NM_001252624	A8K6N1|D6W595|O95849|Q4QQG6|Q587I6|Q59GN4|Q9UBL8|Q9UD55|Q9UDN1|Q9UDN2|Q9UKX6	Missense_Mutation	SNP	ENST00000403092.1	hg19	CCDS1806.1	.	.	.	.	.	.	.	.	.	.	C	19.63	3.863057	0.71949	.	.	ENSG00000183023	ENST00000406785;ENST00000378715;ENST00000542756;ENST00000403092;ENST00000405901;ENST00000402441;ENST00000405269;ENST00000332839;ENST00000408028;ENST00000535962;ENST00000406391;ENST00000542024	T;T;T;T;T;T;T;T;T;T	0.50001	0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76	6.17	6.17	0.99709	Na-Ca exchanger/integrin-beta4 (2);	0.000000	0.85682	D	0.000000	T	0.76723	0.4027	M	0.90977	3.165	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.999;1.0;1.0;1.0	T	0.80555	-0.1330	10	0.87932	D	0	.	18.3732	0.90420	0.0:1.0:0.0:0.0	.	462;462;462;462;462	P32418-4;P32418-2;P32418-3;F6VPY9;P32418	.;.;.;.;NAC1_HUMAN	R	462	ENSP00000383886:G462R;ENSP00000440727:G462R;ENSP00000384763:G462R;ENSP00000385678:G462R;ENSP00000385188:G462R;ENSP00000385535:G462R;ENSP00000332931:G462R;ENSP00000384908:G462R;ENSP00000385811:G462R;ENSP00000443515:G462R	ENSP00000332931:G462R	G	-	1	0	SLC8A1	40509541	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.663000	0.83820	2.941000	0.99782	0.655000	0.94253	GGA	.	.		0.418	SLC8A1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326065.1	NM_021097		T	40656037	C	T	40656037	3	4	304	1	0	0	0	0	1	0	0	0	14721	690	24	3	1685	3	SLC8A1	2	40656037	Missense_Mutation	SNP	C	TCGA-GJ-A3OU-01A-31D-A382-10	39384805	40656037	202543336	11	43696										
VRK2	7444	hgsc.bcm.edu	37	chr2	58276008	58276008	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	aaatacaaacttcctattccAtttccagaaggcaaggttct	5	10	1	1			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr2:58276008A>G	ENST00000435505.2	+	5	787	c.42A>G	c.(40-42)ccA>ccG	p.P14P	VRK2_ENST00000412104.2_Silent_p.P14P|VRK2_ENST00000417641.2_Silent_p.P14P|VRK2_ENST00000340157.4_Silent_p.P14P|VRK2_ENST00000440705.2_Intron			Q86Y07	VRK2_HUMAN	vaccinia related kinase 2	14					cellular response to oxidative stress (GO:0034599)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interleukin-1-mediated signaling pathway (GO:2000659)|regulation of MAPK cascade (GO:0043408)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(4)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)	24						TTCCTATTCCATTTCCAGAAG	0.383																																					p.P14P		Atlas-SNP	.											.	VRK2	46	.	0			c.A42G						.						93	98	96					2																	58276008		2203	4300	6503	SO:0001819	synonymous_variant	7444	exon2			TATTCCATTTCCA	AK058199	CCDS1859.1, CCDS46291.1, CCDS46292.1	2p16.1	2008-05-15			ENSG00000028116	ENSG00000028116			12719	protein-coding gene	gene with protein product		602169					Standard	NM_001130480		Approved		uc002rzv.3	Q86Y07	OTTHUMG00000129348	ENST00000435505.2:c.42A>G	chr2.hg19:g.58276008A>G		189.0	0.0		183.0	22.0	NM_001130480	B4DKL0|D6W5D4|D6W5D6|Q49AK9|Q53EU9|Q53S39|Q53S77|Q53TU1|Q86Y08|Q86Y09|Q86Y10|Q86Y11|Q86Y12|Q8IXI5|Q99987	Silent	SNP	ENST00000435505.2	hg19	CCDS1859.1																																																																																			.	.		0.383	VRK2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325304.2	NM_006296		G	58276008	A	G	58276008	2	3	304	1	0	0	0	0	0	0	0	1	17235	204	8	2		2	VRK2	2	58276008	Silent	SNP	A	TCGA-GJ-A3OU-01A-31D-A382-10	17619971	58276008	184923365	12	43697										
UGGT1	56886	hgsc.bcm.edu	37	chr2	128877939	128877939	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	gtttcttttagagatctgcaCcccgacctggagggacagtt	11	10	2	1			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr2:128877939C>T	ENST00000259253.6	+	9	929	c.882C>T	c.(880-882)caC>caT	p.H294H	UGGT1_ENST00000375990.3_Silent_p.H270H|RN7SL206P_ENST00000580933.1_RNA	NM_020120.3	NP_064505.1	Q9NYU2	UGGG1_HUMAN	UDP-glucose glycoprotein glucosyltransferase 1	294					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)|unfolded protein binding (GO:0051082)			NS(1)|breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(14)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						GAGATCTGCACCCCGACCTGG	0.388																																					p.H294H		Atlas-SNP	.											.	UGGT1	126	.	0			c.C882T						.						111	115	114					2																	128877939		2203	4300	6503	SO:0001819	synonymous_variant	56886	exon9			TCTGCACCCCGAC	AF227905	CCDS2154.1	2q14.3	2009-07-23	2009-07-23	2009-07-23	ENSG00000136731	ENSG00000136731			15663	protein-coding gene	gene with protein product		605897	"UDP-glucose ceramide glucosyltransferase-like 1"	UGCGL1		10694380	Standard	NM_020120		Approved	HUGT1	uc002tps.3	Q9NYU2	OTTHUMG00000131570	ENST00000259253.6:c.882C>T	chr2.hg19:g.128877939C>T		93.0	0.0		98.0	17.0	NM_020120	Q53QP2|Q53SL3|Q8IW30|Q9H8I4	Silent	SNP	ENST00000259253.6	hg19	CCDS2154.1																																																																																			.	.		0.388	UGGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254435.2	NM_020120		T	128877939	C	T	128877939	2	4	304	1	0	0	0	0	0	0	0	1	16956	506	18	3		3	UGGT1	2	128877939	Silent	SNP	C	TCGA-GJ-A3OU-01A-31D-A382-10	70601931	128877939	114321434	13	43698										
RBM44	375316	hgsc.bcm.edu	37	chr2	238726871	238726871	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	taaaagttgctcatagcagtAccacaaagaaaacatgcttt	6	8	1	1			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr2:238726871A>G	ENST00000409864.1	+	3	1566	c.1312A>G	c.(1312-1314)Acc>Gcc	p.T438A	RBM44_ENST00000316997.4_Missense_Mutation_p.T438A|RBM44_ENST00000444524.2_Intron			Q6ZP01	RBM44_HUMAN	RNA binding motif protein 44	437						cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)	nucleotide binding (GO:0000166)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)			breast(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(7)|ovary(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	33		Breast(86;0.0042)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;3.74e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.3e-11)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000118)|Lung(119;0.0112)|LUSC - Lung squamous cell carcinoma(224;0.0266)		TCATAGCAGTACCACAAAGAA	0.383																																					p.T438A		Atlas-SNP	.											.	RBM44	167	.	0			c.A1312G						.						63	59	60					2																	238726871		1915	4127	6042	SO:0001583	missense	375316	exon3			AGCAGTACCACAA	AK097730	CCDS46554.1	2q37.3	2013-02-12			ENSG00000177483	ENSG00000177483		"RNA binding motif (RRM) containing"	24756	protein-coding gene	gene with protein product							Standard	NM_001080504		Approved	FLJ40411	uc002vxi.4	Q6ZP01	OTTHUMG00000152937	ENST00000409864.1:c.1312A>G	chr2.hg19:g.238726871A>G	ENSP00000386727:p.Thr438Ala	160.0	0.0		184.0	14.0	NM_001080504	A0AUW3	Missense_Mutation	SNP	ENST00000409864.1	hg19	CCDS46554.1	.	.	.	.	.	.	.	.	.	.	A	5.916	0.353160	0.11182	.	.	ENSG00000177483	ENST00000316997;ENST00000409864	T;T	0.19669	2.13;2.13	5.86	-11.3	0.00108	.	1.049540	0.07417	N	0.893371	T	0.10981	0.0268	N	0.21448	0.665	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.33240	-0.9876	10	0.20519	T	0.43	7.7019	14.0856	0.64954	0.1871:0.1966:0.6163:0.0	.	437	Q6ZP01	RBM44_HUMAN	A	438	ENSP00000321179:T438A;ENSP00000386727:T438A	ENSP00000321179:T438A	T	+	1	0	RBM44	238391610	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.362000	0.07602	-1.946000	0.01035	-0.462000	0.05337	ACC	.	.		0.383	RBM44-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328733.2	NM_001080504		G	238726871	A	G	238726871	3	3	304	1	0	0	0	0	1	0	0	0	13153	391	14	2	1318	2	RBM44	2	238726871	Missense_Mutation	SNP	A	TCGA-GJ-A3OU-01A-31D-A382-10	109848932	238726871	4472502	14	43699										
CACNA2D2	9254	hgsc.bcm.edu	37	chr3	50416567	50416567	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	ctcaaagacgtcctgcacgcGgtcctcaccaccatccgtga	8	17	2	2			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr3:50416567G>T	ENST00000479441.1	-	12	1215	c.1216C>A	c.(1216-1218)Cgc>Agc	p.R406S	CACNA2D2_ENST00000424201.2_Missense_Mutation_p.R406S|CACNA2D2_ENST00000435965.1_Missense_Mutation_p.R406S|CACNA2D2_ENST00000266039.3_Missense_Mutation_p.R406S|CACNA2D2_ENST00000360963.3_Missense_Mutation_p.R337S|CACNA2D2_ENST00000429770.1_Missense_Mutation_p.R406S|CACNA2D2_ENST00000423994.2_Missense_Mutation_p.R406S|CACNA2D2_ENST00000395083.1_Missense_Mutation_p.R406S			Q9NY47	CA2D2_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 2	406	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				energy reserve metabolic process (GO:0006112)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|positive regulation of organ growth (GO:0046622)|regulation of insulin secretion (GO:0050796)|regulation of multicellular organism growth (GO:0040014)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|cervix(1)|endometrium(4)|large_intestine(4)|lung(8)|ovary(2)|prostate(4)|skin(4)|urinary_tract(1)	31				BRCA - Breast invasive adenocarcinoma(193;0.000365)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)	Amiodarone(DB01118)|Bepridil(DB01244)|Felodipine(DB01023)|Gabapentin(DB00996)|Isradipine(DB00270)|Nitrendipine(DB01054)|Spironolactone(DB00421)	TCCTGCACGCGGTCCTCACCA	0.597																																					p.R406S		Atlas-SNP	.											.	CACNA2D2	82	.	0			c.C1216A						.						164	125	138					3																	50416567		2203	4300	6503	SO:0001583	missense	9254	exon12			GCACGCGGTCCTC	AF040709	CCDS33763.1, CCDS54588.1, CCDS63647.1	3p21.3	2004-02-27			ENSG00000007402	ENSG00000007402		"Calcium channel subunits"	1400	protein-coding gene	gene with protein product	"gene 26"	607082					Standard	XM_005265581		Approved	KIAA0558	uc003daq.3	Q9NY47	OTTHUMG00000156887	ENST00000479441.1:c.1216C>A	chr3.hg19:g.50416567G>T	ENSP00000418081:p.Arg406Ser	56.0	0.0		57.0	13.0	NM_001174051	A7MD15|Q9NY48|Q9UEW0|Q9Y268	Missense_Mutation	SNP	ENST00000479441.1	hg19	CCDS54588.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.163305	0.78226	.	.	ENSG00000007402	ENST00000423994;ENST00000429770;ENST00000266039;ENST00000360963;ENST00000435965;ENST00000395083;ENST00000424201;ENST00000479441	T;T;T;T;T;T;T;T	0.12984	2.63;2.63;2.63;2.63;2.63;2.63;2.63;2.63	4.82	4.82	0.62117	von Willebrand factor, type A (3);	0.000000	0.85682	D	0.000000	T	0.18130	0.0435	L	0.34521	1.04	0.80722	D	1	P;P	0.47409	0.895;0.872	P;P	0.48982	0.597;0.567	T	0.02173	-1.1201	10	0.27785	T	0.31	-14.7364	18.2971	0.90150	0.0:0.0:1.0:0.0	.	406;406	Q9NY47;Q9NY47-2	CA2D2_HUMAN;.	S	406;406;406;337;406;406;406;406	ENSP00000407393:R406S;ENSP00000404631:R406S;ENSP00000266039:R406S;ENSP00000354228:R337S;ENSP00000390526:R406S;ENSP00000378519:R406S;ENSP00000390329:R406S;ENSP00000418081:R406S	ENSP00000266039:R406S	R	-	1	0	CACNA2D2	50391571	1.000000	0.71417	1.000000	0.80357	0.652000	0.38707	5.472000	0.66768	2.407000	0.81776	0.650000	0.86243	CGC	.	.		0.597	CACNA2D2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346457.1	NM_006030		T	50416567	G	T	50416567	3	4	304	1	0	0	0	0	1	0	0	0	2551	1116	39	1	2354	1	CACNA2D2	3	50416567	Missense_Mutation	SNP	G	TCGA-GJ-A3OU-01A-31D-A382-10		50416567	147605863	15	43700										
CACNA1D	776	hgsc.bcm.edu	37	chr3	53834294	53834294	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	aggcgggattaaggacactgCatgacattgggccagaaatc	13	8	0	2			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr3:53834294C>T	ENST00000350061.5	+	41	5453	c.4942C>T	c.(4942-4944)Cat>Tat	p.H1648Y	CACNA1D_ENST00000288139.4_Missense_Mutation_p.H1668Y|RP11-884K10.6_ENST00000607740.1_RNA|CACNA1D_ENST00000544977.1_Missense_Mutation_p.H27Y|CACNA1D_ENST00000422281.2_Missense_Mutation_p.H1633Y	NM_001128840.1	NP_001122312.1	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type, alpha 1D subunit	1648					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|energy reserve metabolic process (GO:0006112)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during SA node cell action potential (GO:0086052)|positive regulation of calcium ion transport (GO:0051928)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|ankyrin binding (GO:0030506)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)|voltage-gated calcium channel activity involved in cardiac muscle cell action potential (GO:0086007)|voltage-gated calcium channel activity involved SA node cell action potential (GO:0086059)			breast(3)|central_nervous_system(9)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(13)|liver(1)|lung(29)|ovary(6)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	90				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	AAGGACACTGCATGACATTGG	0.502																																					p.H1668Y		Atlas-SNP	.											.	CACNA1D	324	.	0			c.C5002T						.						226	200	209					3																	53834294		2203	4300	6503	SO:0001583	missense	776	exon42			ACACTGCATGACA	AB209171	CCDS2872.1, CCDS46848.1, CCDS46849.1	3p14.3	2012-03-07			ENSG00000157388	ENSG00000157388		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1391	protein-coding gene	gene with protein product		114206		CCHL1A2, CACNL1A2		1664412	Standard	NM_000720		Approved	Cav1.3, CACH3, CACN4	uc003dgu.5	Q01668	OTTHUMG00000158278	ENST00000350061.5:c.4942C>T	chr3.hg19:g.53834294C>T	ENSP00000288133:p.His1648Tyr	94.0	0.0		92.0	11.0	NM_000720	B0FYA3|Q13916|Q13931|Q71UT1|Q9UDC3	Missense_Mutation	SNP	ENST00000350061.5	hg19	CCDS46848.1	.	.	.	.	.	.	.	.	.	.	c	23.8	4.455961	0.84209	.	.	ENSG00000157388	ENST00000350061;ENST00000288139;ENST00000422281;ENST00000481478;ENST00000544977	D;D;D;D	0.96716	-4.07;-4.1;-4.09;-4.09	4.62	4.62	0.57501	.	0.542544	0.17149	N	0.185141	D	0.97757	0.9264	M	0.78916	2.43	0.51767	D	0.999933	D;B;D;D	0.64830	0.959;0.406;0.994;0.989	P;B;P;P	0.61201	0.643;0.375;0.885;0.852	D	0.98662	1.0684	10	0.87932	D	0	.	17.518	0.87779	0.0:1.0:0.0:0.0	.	1633;1341;1648;1668	B0FYA3;Q59GD8;Q01668;Q01668-2	.;.;CAC1D_HUMAN;.	Y	1648;1668;1633;1341;27	ENSP00000288133:H1648Y;ENSP00000288139:H1668Y;ENSP00000409174:H1633Y;ENSP00000418014:H1341Y	ENSP00000288139:H1668Y	H	+	1	0	CACNA1D	53809334	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.478000	0.81082	2.121000	0.65114	0.450000	0.29827	CAT	.	.		0.502	CACNA1D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350557.1	NM_000720		T	53834294	C	T	53834294	3	4	304	1	0	0	0	0	1	0	0	0	2543	710	25	3	5276	3	CACNA1D	3	53834294	Missense_Mutation	SNP	C	TCGA-GJ-A3OU-01A-31D-A382-10	3417727	53834294	144188136	16	43701										
FOXP1	27086	hgsc.bcm.edu	37	chr3	71008538	71008538	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	ctcttctttgacgtgtacagGatgcctggaaaaaatatgca	9	8	2	1			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr3:71008538G>T	ENST00000318789.4	-	21	2419	c.1894C>A	c.(1894-1896)Cct>Act	p.P632T	FOXP1_ENST00000491238.1_Missense_Mutation_p.P634T|FOXP1_ENST00000493089.1_Missense_Mutation_p.P631T|FOXP1_ENST00000498215.1_Missense_Mutation_p.P632T|FOXP1_ENST00000484350.1_Missense_Mutation_p.P556T|FOXP1_ENST00000475937.1_Missense_Mutation_p.P632T|FOXP1_ENST00000468577.1_Missense_Mutation_p.P568T	NM_001244810.1|NM_001244813.1|NM_032682.5	NP_001231739.1|NP_001231742.1|NP_116071.2	Q9H334	FOXP1_HUMAN	forkhead box P1	632					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	31		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)		ACGTGTACAGGATGCCTGGAA	0.517			T	PAX5	ALL																																p.P648T		Atlas-SNP	.		Dom	yes		3	3p14.1	27086	forkhead box P1		L	.	FOXP1	104	.	0			c.C1942A						.						99	91	94					3																	71008538		2203	4300	6503	SO:0001583	missense	27086	exon21			GTACAGGATGCCT	AF146696	CCDS2914.1, CCDS33785.1, CCDS58837.1, CCDS58838.1, CCDS58839.1, CCDS74963.1, CCDS74964.1	3p14.1	2008-07-18			ENSG00000114861	ENSG00000114861		"Forkhead boxes"	3823	protein-coding gene	gene with protein product	"fork head-related protein like B", "glutamine-rich factor 1", "PAX5/FOXP1 fusion protein"	605515				8265594, 11751404	Standard	NM_032682		Approved	QRF1, 12CC4, HSPC215, hFKH1B	uc003doj.3	Q9H334	OTTHUMG00000158803	ENST00000318789.4:c.1894C>A	chr3.hg19:g.71008538G>T	ENSP00000318902:p.Pro632Thr	64.0	0.0		73.0	9.0	NM_001244810	A3QVP8|B3KV70|G5E9V8|Q8NAN6|Q9BSG9|Q9H332|Q9H333|Q9P0R1	Missense_Mutation	SNP	ENST00000318789.4	hg19	CCDS2914.1	.	.	.	.	.	.	.	.	.	.	G	15.65	2.895777	0.52121	.	.	ENSG00000114861	ENST00000318789;ENST00000358280;ENST00000475937;ENST00000497355;ENST00000491238;ENST00000493089;ENST00000498215;ENST00000484350;ENST00000468577	D;D;D;D;D;D;D;D	0.89552	-2.42;-2.42;-2.53;-2.53;-2.42;-2.42;-2.43;-2.21	6.16	6.16	0.99307	.	0.089396	0.85682	D	0.000000	D	0.85762	0.5772	N	0.24115	0.695	0.80722	D	1	P;P;P	0.47253	0.892;0.645;0.645	B;B;B	0.44163	0.443;0.23;0.297	D	0.85573	0.1235	10	0.46703	T	0.11	.	20.8598	0.99761	0.0:0.0:1.0:0.0	.	631;556;632	G5E9V8;Q8NAN6;Q9H334	.;.;FOXP1_HUMAN	T	632;444;632;528;634;631;632;556;568	ENSP00000318902:P632T;ENSP00000419393:P632T;ENSP00000418225:P528T;ENSP00000420736:P634T;ENSP00000418524:P631T;ENSP00000418102:P632T;ENSP00000417857:P556T;ENSP00000418883:P568T	ENSP00000318902:P632T	P	-	1	0	FOXP1	71091228	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	9.476000	0.97823	2.937000	0.99478	0.650000	0.86243	CCT	.	.		0.517	FOXP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352250.1	NM_032682		T	71008538	G	T	71008538	3	4	304	1	0	0	0	0	1	0	0	0	6034	1174	41	3	143	3	FOXP1	3	71008538	Missense_Mutation	SNP	G	TCGA-GJ-A3OU-01A-31D-A382-10	17174244	71008538	127013892	17	43702										
MGLL	11343	hgsc.bcm.edu	37	chr3	127441291	127441291	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	accatggagtggcccagaagGaagacaggaagcccagggta	15	9	0	2			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr3:127441291G>C	ENST00000434178.2	-	4	1247	c.351C>G	c.(349-351)ttC>ttG	p.F117L	MGLL_ENST00000265052.5_Missense_Mutation_p.F127L|MGLL_ENST00000453507.2_Missense_Mutation_p.F127L|MGLL_ENST00000398101.3_Missense_Mutation_p.F91L|MGLL_ENST00000398104.1_Missense_Mutation_p.F117L			Q99685	MGLL_HUMAN	monoglyceride lipase	117					acylglycerol acyl-chain remodeling (GO:0036155)|acylglycerol catabolic process (GO:0046464)|arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|fatty acid biosynthetic process (GO:0006633)|glycerophospholipid biosynthetic process (GO:0046474)|inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|long term synaptic depression (GO:0060292)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|regulation of endocannabinoid signaling pathway (GO:2000124)|regulation of inflammatory response (GO:0050727)|regulation of sensory perception of pain (GO:0051930)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acylglycerol lipase activity (GO:0047372)|lipid binding (GO:0008289)|lysophospholipase activity (GO:0004622)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	6						GGCCCAGAAGGAAGACAGGAA	0.557																																					p.F127L		Atlas-SNP	.											.	MGLL	19	.	0			c.C381G						.						86	90	88					3																	127441291		1955	4158	6113	SO:0001583	missense	11343	exon4			CAGAAGGAAGACA	BC000551	CCDS43148.1, CCDS46902.1, CCDS58852.1	3p13-q13.33	2014-03-14			ENSG00000074416	ENSG00000074416	3.1.1.23		17038	protein-coding gene	gene with protein product		609699				9495531	Standard	NM_007283		Approved	HU-K5, MGL	uc003ejx.4	Q99685	OTTHUMG00000159641	ENST00000434178.2:c.351C>G	chr3.hg19:g.127441291G>C	ENSP00000402798:p.Phe117Leu	91.0	0.0		82.0	10.0	NM_007283	B3KRC2|B7Z9D1|Q6IBG9|Q96AA5	Missense_Mutation	SNP	ENST00000434178.2	hg19	CCDS43148.1	.	.	.	.	.	.	.	.	.	.	G	14.67	2.605530	0.46527	.	.	ENSG00000074416	ENST00000434178;ENST00000265052;ENST00000398104;ENST00000398101;ENST00000487473;ENST00000536024;ENST00000453507;ENST00000484451;ENST00000493611	T;T;T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;-0.2;-0.2;-0.2	4.69	3.81	0.43845	.	0.108393	0.64402	N	0.000005	T	0.62073	0.2398	M	0.62088	1.915	0.48288	D	0.99962	B;B;B;B;B	0.31949	0.329;0.098;0.059;0.269;0.348	B;B;B;B;B	0.41666	0.126;0.08;0.116;0.363;0.28	T	0.62530	-0.6835	10	0.62326	D	0.03	-37.1633	6.7379	0.23419	0.2831:0.0:0.7169:0.0	.	127;117;117;127;91	B7Z9D1;B2ZGL7;Q99685;B3KRC2;E7EWX8	.;.;MGLL_HUMAN;.;.	L	117;127;117;91;41;127;127;41;54	ENSP00000402798:F117L;ENSP00000265052:F127L;ENSP00000381176:F117L;ENSP00000381173:F91L;ENSP00000420125:F41L;ENSP00000419340:F41L;ENSP00000417689:F54L	ENSP00000265052:F127L	F	-	3	2	MGLL	128923981	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	2.045000	0.41250	0.976000	0.38417	0.306000	0.20318	TTC	.	.		0.557	MGLL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356637.2	NM_007283		C	127441291	G	C	127441291	3	2	304	1	0	0	0	0	1	0	0	0	9565	1165	41	4	580	4	MGLL	3	127441291	Missense_Mutation	SNP	G	TCGA-GJ-A3OU-01A-31D-A382-10	56432753	127441291	70581139	18	43703										
XRN1	54464	hgsc.bcm.edu	37	chr3	142030413	142030413	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	tttcttgattttcttcttgaAgaagagattggtgttgactt	9	4	3	5			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr3:142030413A>T	ENST00000264951.4	-	42	5178	c.5061T>A	c.(5059-5061)tcT>tcA	p.S1687S	XRN1_ENST00000392981.2_Silent_p.S1675S	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	1687					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA catabolic process (GO:0016075)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)	5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(6)|kidney(12)|large_intestine(11)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	61						TTCTTCTTGAAGAAGAGATTG	0.363																																					p.S1687S		Atlas-SNP	.											.	XRN1	138	.	0			c.T5061A						.						113	124	120					3																	142030413		2203	4300	6503	SO:0001819	synonymous_variant	54464	exon42			TCTTGAAGAAGAG	AY137776	CCDS3123.1, CCDS63801.1, CCDS75028.1	3q23	2008-02-05			ENSG00000114127	ENSG00000114127			30654	protein-coding gene	gene with protein product		607994				12515382	Standard	XM_005247544		Approved	SEP1	uc003eus.3	Q8IZH2	OTTHUMG00000159251	ENST00000264951.4:c.5061T>A	chr3.hg19:g.142030413A>T		144.0	0.0		143.0	23.0	NM_019001	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Silent	SNP	ENST00000264951.4	hg19	CCDS3123.1																																																																																			.	.		0.363	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001		T	142030413	A	T	142030413	2	4	304	1	0	0	0	0	0	0	0	1	17474	59	3	4		4	XRN1	3	142030413	Silent	SNP	A	TCGA-GJ-A3OU-01A-31D-A382-10	14589122	142030413	55992017	19	43704										
KCTD8	386617	hgsc.bcm.edu	37	chr4	44449696	44449696	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	ggaagccggcctcggacaggCgatcaaaggcctgctccaag	14	13	1	0			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr4:44449696C>A	ENST00000360029.3	-	1	1128	c.845G>T	c.(844-846)cGc>cTc	p.R282L	AC131951.1_ENST00000584757.1_RNA	NM_198353.2	NP_938167.1	Q6ZWB6	KCTD8_HUMAN	potassium channel tetramerization domain containing 8	282					protein homooligomerization (GO:0051260)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)		p.R282H(1)		central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(5)|lung(19)|ovary(1)|prostate(3)|upper_aerodigestive_tract(4)	41						CTCGGACAGGCGATCAAAGGC	0.632										HNSCC(17;0.042)																											p.R282L		Atlas-SNP	.											KCTD8,NS,carcinoma,0,1	KCTD8	96	.	1	Substitution - Missense(1)	endometrium(1)	c.G845T						.						51	45	47					4																	44449696		2203	4300	6503	SO:0001583	missense	386617	exon1			GACAGGCGATCAA	AK123347	CCDS3467.1	4p13	2013-06-20	2013-06-20		ENSG00000183783	ENSG00000183783			22394	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 8"				Standard	NM_198353		Approved		uc003gwu.3	Q6ZWB6	OTTHUMG00000099409	ENST00000360029.3:c.845G>T	chr4.hg19:g.44449696C>A	ENSP00000353129:p.Arg282Leu	98.0	1.0		66.0	9.0	NM_198353	A2RU39	Missense_Mutation	SNP	ENST00000360029.3	hg19	CCDS3467.1	.	.	.	.	.	.	.	.	.	.	C	15.41	2.825489	0.50739	.	.	ENSG00000183783	ENST00000360029	T	0.38887	1.11	4.19	4.19	0.49359	.	0.000000	0.64402	D	0.000002	T	0.35566	0.0936	L	0.34521	1.04	0.42680	D	0.993545	P	0.47841	0.901	B	0.42214	0.38	T	0.34204	-0.9838	10	0.51188	T	0.08	.	15.7002	0.77536	0.0:1.0:0.0:0.0	.	282	Q6ZWB6	KCTD8_HUMAN	L	282	ENSP00000353129:R282L	ENSP00000353129:R282L	R	-	2	0	KCTD8	44144453	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.777000	0.55364	2.173000	0.68751	0.585000	0.79938	CGC	.	.		0.632	KCTD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216868.1			A	44449696	C	A	44449696	3	1	304	1	0	0	0	0	1	0	0	0	8124	768	27	1	584	1	KCTD8	4	44449696	Missense_Mutation	SNP	C	TCGA-GJ-A3OU-01A-31D-A382-10		44449696	146704580	20	43705										
CCDC125	202243	hgsc.bcm.edu	37	chr5	68609823	68609823	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	agtacctacctctaaagtttCattaagacattgccttaatt	4	9	2	1			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr5:68609823C>G	ENST00000396496.2	-	3	462	c.355G>C	c.(355-357)Gaa>Caa	p.E119Q	CCDC125_ENST00000396499.1_Missense_Mutation_p.E119Q|CCDC125_ENST00000383374.2_Missense_Mutation_p.E118Q|CCDC125_ENST00000511257.1_5'UTR|CCDC125_ENST00000460090.1_Intron			Q86Z20	CC125_HUMAN	coiled-coil domain containing 125	119						cytoplasm (GO:0005737)				breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(7)|urinary_tract(1)	19		Lung NSC(167;7.26e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.2e-56)|Epithelial(20;2.31e-52)|all cancers(19;5.85e-48)|Lung(70;0.0183)		TCTAAAGTTTCATTAAGACAT	0.398																																					p.E119Q		Atlas-SNP	.											.	CCDC125	41	.	0			c.G355C						.						118	130	126					5																	68609823		2203	4300	6503	SO:0001583	missense	202243	exon2			AAGTTTCATTAAG	AB024691	CCDS4000.1, CCDS75255.1	5q13.2	2008-02-05			ENSG00000183323	ENSG00000183323			28924	protein-coding gene	gene with protein product		613781					Standard	XM_005248461		Approved	KENAE	uc003jvv.1	Q86Z20	OTTHUMG00000131259	ENST00000396496.2:c.355G>C	chr5.hg19:g.68609823C>G	ENSP00000379754:p.Glu119Gln	93.0	0.0		76.0	9.0	NM_176816	Q86Z19	Missense_Mutation	SNP	ENST00000396496.2	hg19	CCDS4000.1	.	.	.	.	.	.	.	.	.	.	C	7.639	0.680469	0.14907	.	.	ENSG00000183323	ENST00000396496;ENST00000396499;ENST00000383374	T;T;T	0.49720	0.77;0.77;0.77	5.49	4.58	0.56647	.	0.058284	0.64402	D	0.000003	T	0.35128	0.0921	L	0.29908	0.895	0.33313	D	0.566287	B	0.09022	0.002	B	0.16722	0.016	T	0.43065	-0.9414	10	0.48119	T	0.1	-2.5396	9.4893	0.38948	0.0:0.8957:0.0:0.1043	.	119	Q86Z20	CC125_HUMAN	Q	119;119;118	ENSP00000379754:E119Q;ENSP00000379756:E119Q;ENSP00000372865:E118Q	ENSP00000372865:E118Q	E	-	1	0	CCDC125	68645579	0.998000	0.40836	0.942000	0.38095	0.009000	0.06853	4.633000	0.61318	1.235000	0.43724	-0.389000	0.06534	GAA	.	.		0.398	CCDC125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254027.4	NM_176816		G	68609823	C	G	68609823	3	3	304	1	0	0	0	0	1	0	0	0	2763	835	29	4	1220	4	CCDC125	5	68609823	Missense_Mutation	SNP	C	TCGA-GJ-A3OU-01A-31D-A382-10		68609823	112305437	21	43706										
PCDHA5	56143	hgsc.bcm.edu	37	chr5	140203606	140203606	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	cgcggtggggagctggtcgtActcgcagcagaggagacaga	18	9	0	3			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr5:140203606A>G	ENST00000529859.1	+	1	2246	c.2246A>G	c.(2245-2247)tAc>tGc	p.Y749C	PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000378126.3_Missense_Mutation_p.Y749C|PCDHA5_ENST00000529619.1_Missense_Mutation_p.Y749C	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	749					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(3)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCTGGTCGTACTCGCAGCAG	0.647																																					p.Y749C		Atlas-SNP	.											.	PCDHA5	361	.	0			c.A2246G						.						73	66	68					5																	140203606		2203	4300	6503	SO:0001583	missense	56143	exon1			GGTCGTACTCGCA	AF152483	CCDS54917.1	5q31	2010-11-26				ENSG00000204965		"Cadherins / Protocadherins : Clustered"	8671	other	complex locus constituent	"ortholog of mouse CNR6", "KIAA0345-like 9"	606311		CNRS6		10380929, 10662547	Standard	NM_018908		Approved	CNR6, CRNR6, CNRN6, PCDH-ALPHA5		Q9Y5H7		ENST00000529859.1:c.2246A>G	chr5.hg19:g.140203606A>G	ENSP00000436557:p.Tyr749Cys	156.0	0.0		168.0	16.0	NM_018908	O75284|Q8N4R3	Missense_Mutation	SNP	ENST00000529859.1	hg19	CCDS54917.1	.	.	.	.	.	.	.	.	.	.	A	3.368	-0.129001	0.06753	.	.	ENSG00000204965	ENST00000529619;ENST00000529859;ENST00000378126	T;T;T	0.15372	2.43;2.43;2.43	3.92	-1.96	0.07525	.	.	.	.	.	T	0.27489	0.0675	M	0.91717	3.235	0.09310	N	1	B;B;B	0.26547	0.053;0.152;0.152	B;B;B	0.31547	0.043;0.132;0.132	T	0.32295	-0.9912	9	0.62326	D	0.03	.	7.3622	0.26752	0.6049:0.1096:0.2854:0.0	.	749;749;749	Q9Y5H7;Q9Y5H7-3;Q9Y5H7-2	PCDA5_HUMAN;.;.	C	749	ENSP00000433416:Y749C;ENSP00000436557:Y749C;ENSP00000367366:Y749C	ENSP00000367366:Y749C	Y	+	2	0	PCDHA5	140183790	0.056000	0.20664	0.002000	0.10522	0.001000	0.01503	0.220000	0.17660	-1.067000	0.03160	-1.751000	0.00678	TAC	.	.		0.647	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908		G	140203606	A	G	140203606	3	3	304	1	0	0	0	0	1	0	0	0	11536	391	14	2	2248	2	PCDHA5	5	140203606	Missense_Mutation	SNP	A	TCGA-GJ-A3OU-01A-31D-A382-10	71593783	140203606	40711654	22	43707										
PCDHA7	56141	hgsc.bcm.edu	37	chr5	140215307	140215307	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	gcgtgtccgtggaggtggccGacgtgaacgacaacgccccg	16	13	0	1			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr5:140215307G>A	ENST00000525929.1	+	1	1339	c.1339G>A	c.(1339-1341)Gac>Aac	p.D447N	PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA7_ENST00000378125.3_Missense_Mutation_p.D447N|PCDHA2_ENST00000526136.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA5_ENST00000529619.1_Intron	NM_018910.2	NP_061733.1	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7	447	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|biliary_tract(1)|breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGAGGTGGCCGACGTGAACGA	0.667																																					p.D447N	NSCLC(160;258 2013 5070 22440 28951)	Atlas-SNP	.											.	PCDHA7	367	.	0			c.G1339A						.						71	75	74					5																	140215307		2203	4298	6501	SO:0001583	missense	56141	exon1			GTGGCCGACGTGA	AF152485	CCDS54918.1	5q31	2010-11-26				ENSG00000204963		"Cadherins / Protocadherins : Clustered"	8673	other	complex locus constituent	"KIAA0345-like 7", "ortholog to mouse CNR4"	606313		CNRS4		10380929, 10662547	Standard	NM_018910		Approved	CNR4, CRNR4		Q9UN72		ENST00000525929.1:c.1339G>A	chr5.hg19:g.140215307G>A	ENSP00000436426:p.Asp447Asn	182.0	0.0		161.0	11.0	NM_031852	O75282	Missense_Mutation	SNP	ENST00000525929.1	hg19	CCDS54918.1	.	.	.	.	.	.	.	.	.	.	G	19.12	3.765133	0.69878	.	.	ENSG00000204963	ENST00000525929;ENST00000378125	D;D	0.84298	-1.83;-1.83	4.04	4.04	0.47022	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	0.000000	0.33180	U	0.005193	D	0.94178	0.8132	M	0.93638	3.44	0.44309	D	0.997182	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95982	0.8978	10	0.87932	D	0	.	16.5697	0.84608	0.0:0.0:1.0:0.0	.	447;447	Q9UN72-2;Q9UN72	.;PCDA7_HUMAN	N	447	ENSP00000436426:D447N;ENSP00000367365:D447N	ENSP00000367365:D447N	D	+	1	0	PCDHA7	140195491	1.000000	0.71417	0.992000	0.48379	0.247000	0.25773	7.816000	0.86201	1.955000	0.56771	0.305000	0.20034	GAC	.	.		0.667	PCDHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372887.2	NM_018910		A	140215307	G	A	140215307	3	1	304	1	0	0	0	0	1	0	0	0	11538	1058	37	1	1341	1	PCDHA7	5	140215307	Missense_Mutation	SNP	G	TCGA-GJ-A3OU-01A-31D-A382-10	11701	140215307	40699953	23	43708										
HIST1H1A	3024	hgsc.bcm.edu	37	chr6	26017773	26017773	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	ccagcgcctttttaagagctGccaacgacacaccaccacgc	7	17	0	1			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr6:26017773G>A	ENST00000244573.3	-	1	267	c.188C>T	c.(187-189)gCa>gTa	p.A63V	HIST1H3A_ENST00000357647.3_5'Flank	NM_005325.3	NP_005316.1	Q02539	H11_HUMAN	histone cluster 1, H1a	63	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				nucleosome assembly (GO:0006334)|spermatogenesis (GO:0007283)	nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|ovary(3)|prostate(1)	13						TTTAAGAGCTGCCAACGACAC	0.577																																					p.A63V		Atlas-SNP	.											.	HIST1H1A	25	.	0			c.C188T						.						51	52	52					6																	26017773		2203	4300	6503	SO:0001583	missense	3024	exon1			AGAGCTGCCAACG	AF531299	CCDS4569.1	6p22.1	2012-11-16	2006-10-11	2003-02-21	ENSG00000124610	ENSG00000124610		"Histones / Replication-dependent"	4715	protein-coding gene	gene with protein product		142709	"H1 histone family, member 1", "histone 1, H1a"	H1F1		2759094, 12408966	Standard	NM_005325		Approved	H1.1, H1a	uc003nfo.3	Q02539	OTTHUMG00000016413	ENST00000244573.3:c.188C>T	chr6.hg19:g.26017773G>A	ENSP00000244573:p.Ala63Val	102.0	0.0		85.0	9.0	NM_005325	Q3MJ34	Missense_Mutation	SNP	ENST00000244573.3	hg19	CCDS4569.1	.	.	.	.	.	.	.	.	.	.	N	17.52	3.411253	0.62399	.	.	ENSG00000124610	ENST00000244573	T	0.15372	2.43	4.2	4.2	0.49525	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.111728	0.64402	D	0.000012	T	0.26521	0.0648	L	0.59967	1.855	0.80722	D	1	D	0.54397	0.966	D	0.64687	0.928	T	0.01156	-1.1434	10	0.39692	T	0.17	-1.553	16.4244	0.83809	0.0:0.0:1.0:0.0	.	63	Q02539	H11_HUMAN	V	63	ENSP00000244573:A63V	ENSP00000244573:A63V	A	-	2	0	HIST1H1A	26125752	1.000000	0.71417	0.197000	0.23402	0.015000	0.08874	9.771000	0.98977	2.260000	0.74910	0.609000	0.83330	GCA	.	.		0.577	HIST1H1A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043884.1	NM_005325		A	26017773	G	A	26017773	3	1	304	1	0	0	0	0	1	0	0	0	7131	1319	46	3	463	3	HIST1H1A	6	26017773	Missense_Mutation	SNP	G	TCGA-GJ-A3OU-01A-31D-A382-10		26017773	145097294	24	43709										
HIST1H2AG	8969	hgsc.bcm.edu	37	chr6	27101160	27101160	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	tgctgggcaaagtcaccatcGcacagggcggtgtcctgccc	13	14	1	0			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr6:27101160G>A	ENST00000359193.2	+	1	329	c.310G>A	c.(310-312)Gca>Aca	p.A104T	HIST1H2BJ_ENST00000541790.1_5'Flank|HIST1H2BJ_ENST00000607124.1_5'Flank|HIST1H2BJ_ENST00000339812.2_5'Flank	NM_021064.4	NP_066408.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2ag	104						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)			biliary_tract(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(1)	17						AGTCACCATCGCACAGGGCGG	0.572																																					p.A104T		Atlas-SNP	.											HIST1H2AG,NS,carcinoma,0,1	HIST1H2AG	37	.	0			c.G310A						.						111	104	106					6																	27101160		2203	4300	6503	SO:0001583	missense	8969	exon1			ACCATCGCACAGG	L19778	CCDS4619.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000196787	ENSG00000196787		"Histones / Replication-dependent"	4737	protein-coding gene	gene with protein product		615012	"H2A histone family, member P", "histone 1, H2ag"	H2AFP		8179821, 12408966	Standard	NM_021064		Approved	pH2A/f, H2A/p, H2A.1b	uc003niw.3	P0C0S8	OTTHUMG00000014469	ENST00000359193.2:c.310G>A	chr6.hg19:g.27101160G>A	ENSP00000352119:p.Ala104Thr	189.0	1.0		141.0	19.0	NM_021064	P02261|Q2M1R2|Q76PA6	Missense_Mutation	SNP	ENST00000359193.2	hg19	CCDS4619.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.553793	0.86231	.	.	ENSG00000196787	ENST00000359193	T	0.44482	0.92	4.08	4.08	0.47627	Histone-fold (2);Histone H2A (2);	0.000000	0.39909	N	0.001235	T	0.54565	0.1866	.	.	.	0.39429	D	0.967052	D	0.89917	1.0	D	0.65443	0.935	T	0.62248	-0.6894	9	0.87932	D	0	.	14.6102	0.68510	0.0:0.0:1.0:0.0	.	104	P0C0S8	H2A1_HUMAN	T	104	ENSP00000352119:A104T	ENSP00000352119:A104T	A	+	1	0	HIST1H2AG	27209139	1.000000	0.71417	0.996000	0.52242	0.950000	0.60333	6.919000	0.75793	2.217000	0.71921	0.655000	0.94253	GCA	.	.		0.572	HIST1H2AG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040137.1	NM_021064		A	27101160	G	A	27101160	3	1	304	1	0	0	0	0	1	0	0	0	7142	1087	38	1	312	1	HIST1H2AG	6	27101160	Missense_Mutation	SNP	G	TCGA-GJ-A3OU-01A-31D-A382-10	1083387	27101160	144013907	25	43710										
CDC5L	988	hgsc.bcm.edu	37	chr6	44394452	44394452	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	gaaaagttctccaaagaagaGctgaaaaaggtatgattgag	11	4	1	5			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr6:44394452G>C	ENST00000371477.3	+	13	2183	c.1884G>C	c.(1882-1884)gaG>gaC	p.E628D		NM_001253.3	NP_001244.1	Q99459	CDC5L_HUMAN	cell division cycle 5-like	628	Interaction with DAPK3. {ECO:0000250|UniProtKB:O08837}.				cell cycle (GO:0007049)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)|Prp19 complex (GO:0000974)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|WD40-repeat domain binding (GO:0071987)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|skin(4)	29	all_lung(25;0.00433)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CCAAAGAAGAGCTGAAAAAGG	0.348																																					p.E628D		Atlas-SNP	.											.	CDC5L	86	.	0			c.G1884C						.						75	75	75					6																	44394452		2202	4299	6501	SO:0001583	missense	988	exon13			AGAAGAGCTGAAA	D85423	CCDS4912.1	6p21.1	2013-01-17	2013-01-17		ENSG00000096401	ENSG00000096401			1743	protein-coding gene	gene with protein product		602868	"CDC5 (cell division cycle 5, S. pombe, homolog)-like", "CDC5 cell division cycle 5-like (S. pombe)"			9598309, 9038199	Standard	NM_001253		Approved	PCDC5RP, hCDC5, CEF1, CDC5	uc003oxl.3	Q99459	OTTHUMG00000014767	ENST00000371477.3:c.1884G>C	chr6.hg19:g.44394452G>C	ENSP00000360532:p.Glu628Asp	97.0	0.0		102.0	10.0	NM_001253	Q76N46|Q99974	Missense_Mutation	SNP	ENST00000371477.3	hg19	CCDS4912.1	.	.	.	.	.	.	.	.	.	.	G	8.203	0.798535	0.16397	.	.	ENSG00000096401	ENST00000371477	T	0.47869	0.83	5.71	-1.18	0.09617	.	0.261207	0.44688	N	0.000436	T	0.08133	0.0203	N	0.17723	0.515	0.40698	D	0.982455	B	0.06786	0.001	B	0.08055	0.003	T	0.15492	-1.0435	10	0.13470	T	0.59	-12.0426	0.8339	0.01136	0.25:0.1085:0.2463:0.3952	.	628	Q99459	CDC5L_HUMAN	D	628	ENSP00000360532:E628D	ENSP00000360532:E628D	E	+	3	2	CDC5L	44502430	0.007000	0.16637	0.973000	0.42090	0.994000	0.84299	-1.079000	0.03410	0.061000	0.16311	0.650000	0.86243	GAG	.	.		0.348	CDC5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040743.1			C	44394452	G	C	44394452	3	2	304	1	0	0	0	0	1	0	0	0	3084	962	34	4	1934	4	CDC5L	6	44394452	Missense_Mutation	SNP	G	TCGA-GJ-A3OU-01A-31D-A382-10	17293292	44394452	126720615	26	43711										
COL9A1	1297	hgsc.bcm.edu	37	chr6	70964854	70964854	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	actacagctcaggacataccGtgtctcctttgggcccaggg	11	13	2	0	rs141895443		TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr6:70964854G>A	ENST00000357250.6	-	23	1768	c.1610C>T	c.(1609-1611)aCg>aTg	p.T537M	COL9A1_ENST00000489611.1_5'UTR|COL9A1_ENST00000370499.4_Splice_Site_p.T294M|COL9A1_ENST00000320755.7_Splice_Site_p.T294M	NM_001851.4	NP_001842.3	P20849	CO9A1_HUMAN	collagen, type IX, alpha 1	537	Triple-helical region (COL2).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|organ morphogenesis (GO:0009887)|tissue homeostasis (GO:0001894)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(44)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)	80						AGGACATACCGTGTCTCCTTT	0.433																																					p.T537M		Atlas-SNP	.											.	COL9A1	228	.	0			c.C1610T						.	G	MET/THR,MET/THR	1,4405	2.1+/-5.4	0,1,2202	162	164	163		1610,881	4	1	6	dbSNP_134	163	1,8599	1.2+/-3.3	0,1,4299	yes	missense-near-splice,missense-near-splice	COL9A1	NM_001851.4,NM_078485.3	81,81	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	benign,benign	537/922,294/679	70964854	2,13004	2203	4300	6503	SO:0001630	splice_region_variant	1297	exon23			CATACCGTGTCTC		CCDS4971.1, CCDS47447.1	6q13	2013-05-07			ENSG00000112280	ENSG00000112280		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2217	protein-coding gene	gene with protein product		120210				1429648	Standard	NM_001851		Approved		uc003pfg.4	P20849	OTTHUMG00000014988	ENST00000357250.6:c.1611+1C>T	chr6.hg19:g.70964854G>A		123.0	0.0		118.0	14.0	NM_001851	Q13699|Q13700|Q5TF52|Q6P467|Q96BM8|Q99225|Q9H151|Q9H152|Q9Y6P2|Q9Y6P3	Missense_Mutation	SNP	ENST00000357250.6	hg19	CCDS4971.1	.	.	.	.	.	.	.	.	.	.	G	9.413	1.081059	0.20309	2.27E-4	1.16E-4	ENSG00000112280	ENST00000357250;ENST00000320755;ENST00000370499	D;D;D	0.93659	-3.26;-3.26;-3.26	5.92	3.99	0.46301	.	0.423225	0.27901	N	0.017395	T	0.72938	0.3523	N	0.16790	0.44	0.30352	N	0.784694	P;P;B	0.38992	0.653;0.521;0.006	B;B;B	0.21151	0.023;0.033;0.007	T	0.70967	-0.4728	10	0.48119	T	0.1	.	9.0928	0.36621	0.0804:0.0:0.7134:0.2062	.	537;294;110	P20849;P20849-2;B3KWS8	CO9A1_HUMAN;.;.	M	537;294;294	ENSP00000349790:T537M;ENSP00000315252:T294M;ENSP00000359530:T294M	ENSP00000315252:T294M	T	-	2	0	COL9A1	71021575	1.000000	0.71417	1.000000	0.80357	0.862000	0.49288	1.358000	0.34102	1.507000	0.48752	0.655000	0.94253	ACG	.	G|1.000;A|0.000		0.433	COL9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041131.2		Missense_Mutation	A	70964854	G	A	70964854	5	1	304	1	0	0	0	0	0	0	1	0	3709	1159	40	1	1219	1	COL9A1	6	70964854	Splice_Site	SNP	G	TCGA-GJ-A3OU-01A-31D-A382-10	26570402	70964854	100150213	27	43712										
CPSF4	10898	hgsc.bcm.edu	37	chr7	99047916	99047917	+	Frame_Shift_Ins	INS	-	-	A													0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	aggggagtgcagcaacaaggINSaatgtcccttcctgcacatc							TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr7:99047916_99047917insA	ENST00000292476.5	+	4	335_336	c.325_326insA	c.(325-327)gaafs	p.E109fs	CPSF4_ENST00000451876.1_Intron|ATP5J2-PTCD1_ENST00000437572.1_Intron|PTCD1_ENST00000555673.1_Intron|CPSF4_ENST00000471455.1_3'UTR|ATP5J2-PTCD1_ENST00000413834.1_Intron|CPSF4_ENST00000436336.2_Frame_Shift_Ins_p.E109fs|CPSF4_ENST00000441580.1_Frame_Shift_Ins_p.E56fs|ATP5J2_ENST00000466753.1_Intron			O95639	CPSF4_HUMAN	cleavage and polyadenylation specific factor 4, 30kDa	109					modification by virus of host mRNA processing (GO:0046778)|modulation by virus of host morphology or physiology (GO:0019048)|modulation by virus of host process (GO:0019054)|mRNA processing (GO:0006397)|viral life cycle (GO:0019058)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(5)|lung(5)	14	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					CAGCAACAAGGAATGTCCCTTC	0.599																																					p.E109fs		Atlas-INDEL	.											.	CPSF4	24	.	0			c.325_326insA						.																																			SO:0001589	frameshift_variant	10898	exon4			.		CCDS5664.1, CCDS47652.1	7q22	2007-10-18	2002-08-29		ENSG00000160917	ENSG00000160917			2327	protein-coding gene	gene with protein product		603052	"cleavage and polyadenylation specific factor 4, 30kD subunit"			9651582, 9224719	Standard	NM_006693		Approved	NAR, CPSF30	uc003uqj.3	O95639	OTTHUMG00000154599	ENST00000292476.5:c.327dupA	chr7.hg19:g.99047918_99047918dupA	ENSP00000292476:p.Glu109fs	113.0	0.0		110.0	28.0	NM_001081559	D6W5S8|Q6FGE6|Q86TF8|Q9BTW6	Frame_Shift_Ins	INS	ENST00000292476.5	hg19	CCDS5664.1																																																																																			.	.		0.599	CPSF4-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000336254.1			A	99047917	-	A	99047916	7	5	304	1	0	1	1	0	0	0	0	0	3830	1175	41	0	339	0	CPSF4	7	99047916	Frame_Shift_Ins	INS	-	TCGA-GJ-A3OU-01A-31D-A382-10		99047916	60090747	28	43713										
CPA5	93979	hgsc.bcm.edu	37	chr7	130007818	130007818	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	gagtacatttttggcagcatCagcaccaccctctgtgagtg	10	11	2	1			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr7:130007818C>T	ENST00000485477.1	+	11	2239	c.1110C>T	c.(1108-1110)atC>atT	p.I370I	CPA5_ENST00000474905.1_Silent_p.I370I|CPA5_ENST00000393213.3_Silent_p.I370I|CPA5_ENST00000461828.1_Silent_p.I370I|CPA5_ENST00000431780.2_Intron|CPA5_ENST00000466363.2_Silent_p.I370I|CPA5_ENST00000355388.3_Silent_p.I370I			Q8WXQ8	CBPA5_HUMAN	carboxypeptidase A5	370						extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(2)|large_intestine(7)|lung(4)|ovary(3)|pancreas(1)|skin(2)	23	Melanoma(18;0.0435)					TTGGCAGCATCAGCACCACCC	0.572																																					p.I370I		Atlas-SNP	.											.	CPA5	61	.	0			c.C1110T						.						129	92	104					7																	130007818		2203	4300	6503	SO:0001819	synonymous_variant	93979	exon12			CAGCATCAGCACC	AF384667	CCDS5819.1, CCDS47713.1	7q32	2008-07-18			ENSG00000158525	ENSG00000158525			15722	protein-coding gene	gene with protein product		609561				11836249	Standard	NM_080385		Approved		uc003vps.2	Q8WXQ8	OTTHUMG00000157824	ENST00000485477.1:c.1110C>T	chr7.hg19:g.130007818C>T		81.0	0.0		57.0	6.0	NM_080385	G3V0G8|Q6ZNI6|Q86SE2|Q86XM3|Q8NA08	Silent	SNP	ENST00000485477.1	hg19	CCDS5819.1																																																																																			.	.		0.572	CPA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349712.1	NM_001127441		T	130007818	C	T	130007818	2	4	304	1	0	0	0	0	0	0	0	1	3795	816	29	3		3	CPA5	7	130007818	Silent	SNP	C	TCGA-GJ-A3OU-01A-31D-A382-10	30959902	130007818	29130845	29	43714										
ASB10	136371	hgsc.bcm.edu	37	chr7	150883497	150883497	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	actcaagggtgccaggccccCggcagagatgcagggggcgt	17	12	1	1			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr7:150883497C>A	ENST00000420175.2	-	2	590	c.566G>T	c.(565-567)cGg>cTg	p.R189L	ASB10_ENST00000275838.1_Missense_Mutation_p.R189L|ASB10_ENST00000422024.1_Missense_Mutation_p.R234L|ASB10_ENST00000377867.3_Missense_Mutation_p.R174L|ASB10_ENST00000434669.1_Missense_Mutation_p.R234L			Q8WXI3	ASB10_HUMAN	ankyrin repeat and SOCS box containing 10	189			R -> W. {ECO:0000269|PubMed:22156576}.		intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(2)|lung(7)|skin(2)	12			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GCCAGGCCCCCGGCAGAGATG	0.617																																					p.R189L		Atlas-SNP	.											.	ASB10	99	.	0			c.G566T						.						13	13	13					7																	150883497		2192	4276	6468	SO:0001583	missense	136371	exon2			GGCCCCCGGCAGA	AK055536	CCDS5921.2, CCDS47749.1, CCDS47750.1, CCDS47749.2, CCDS47750.2	7q35	2014-02-04	2011-01-25		ENSG00000146926	ENSG00000146926		"Ankyrin repeat domain containing"	17185	protein-coding gene	gene with protein product		615054	"ankyrin repeat and SOCS box-containing 10", "glaucoma 1, open angle, F (adult-onset)"	GLC1F		22156576	Standard	NM_080871		Approved		uc003wjm.1	Q8WXI3	OTTHUMG00000157013	ENST00000420175.2:c.566G>T	chr7.hg19:g.150883497C>A	ENSP00000391137:p.Arg189Leu	98.0	0.0		117.0	9.0	NM_001142459	A0AVH0|Q6ZUL6	Missense_Mutation	SNP	ENST00000420175.2	hg19	CCDS47750.2	.	.	.	.	.	.	.	.	.	.	C	12.36	1.915657	0.33815	.	.	ENSG00000146926	ENST00000275838;ENST00000377867;ENST00000422024;ENST00000434669;ENST00000420175	T;T;T;T;T	0.62788	-0.0;-0.0;-0.0;-0.0;-0.0	4.96	-1.53	0.08611	Ankyrin repeat-containing domain (4);	1.056820	0.07338	N	0.880316	T	0.44787	0.1310	N	0.04148	-0.265	0.09310	N	1	B;B;B	0.31705	0.123;0.256;0.336	B;B;B	0.39339	0.085;0.297;0.165	T	0.49437	-0.8940	10	0.54805	T	0.06	-1.5839	11.208	0.48782	0.0:0.3265:0.0:0.6735	.	174;189;234	Q8WXI3-3;Q8WXI3;D5MNW9	.;ASB10_HUMAN;.	L	189;174;234;234;189	ENSP00000275838:R189L;ENSP00000367098:R174L;ENSP00000401369:R234L;ENSP00000398247:R234L;ENSP00000391137:R189L	ENSP00000275838:R189L	R	-	2	0	ASB10	150514430	0.062000	0.20869	0.216000	0.23742	0.973000	0.67179	0.056000	0.14256	-0.272000	0.09259	-0.218000	0.12543	CGG	.	.		0.617	ASB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347096.3	NM_080871		A	150883497	C	A	150883497	3	1	304	1	0	0	0	0	1	0	0	0	1014	652	23	1	853	1	ASB10	7	150883497	Missense_Mutation	SNP	C	TCGA-GJ-A3OU-01A-31D-A382-10	20875679	150883497	8255166	30	43715										
CSMD1	64478	hgsc.bcm.edu	37	chr8	2823435	2823435	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	ggtgaagtcggtcccaaactGgatgccatttgctagtgtgc	13	9	0	1			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr8:2823435G>A	ENST00000520002.1	-	60	9700	c.9145C>T	c.(9145-9147)Cag>Tag	p.Q3049*	CSMD1_ENST00000537824.1_Nonsense_Mutation_p.Q3048*|CSMD1_ENST00000602723.1_Intron|CSMD1_ENST00000400186.3_Intron|CSMD1_ENST00000542608.1_Intron|CSMD1_ENST00000602557.1_Nonsense_Mutation_p.Q3049*			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	3049	Sushi 24. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		GTCCCAAACTGGATGCCATTT	0.433																																					p.Q3048X		Atlas-SNP	.											.	CSMD1	1469	.	0			c.C9142T						.						93	93	93					8																	2823435		2048	4195	6243	SO:0001587	stop_gained	64478	exon59			CAAACTGGATGCC			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.9145C>T	chr8.hg19:g.2823435G>A	ENSP00000430733:p.Gln3049*	142.0	0.0		348.0	19.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Nonsense_Mutation	SNP	ENST00000520002.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	48|48	14.003373|14.003373	0.99774|0.99774	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000335551|ENST00000520002;ENST00000318252;ENST00000537824	.|.	.|.	.|.	5.42|5.42	5.42|5.42	0.78866|0.78866	.|.	.|0.265060	.|0.31381	.|N	.|0.007758	T|.	0.72053|.	0.3413|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.67405|.	-0.5679|.	4|.	.|0.29301	.|T	.|0.29	.|.	19.2323|19.2323	0.93845|0.93845	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	L|X	2465|3049;2910;3048	.|.	.|ENSP00000320445:Q2910X	P|Q	-|-	2|1	0|0	CSMD1|CSMD1	2810842|2810842	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.843000|0.843000	0.47879|0.47879	4.550000|4.550000	0.60733|0.60733	2.541000|2.541000	0.85698|0.85698	0.655000|0.655000	0.94253|0.94253	CCA|CAG	.	.		0.433	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		A	2823435	G	A	2823435	4	1	304	1	0	0	0	0	0	1	0	0	3946	1357	47	3	1600	3	CSMD1	8	2823435	Nonsense_Mutation	SNP	G	TCGA-GJ-A3OU-01A-31D-A382-10		2823435	143540587	31	43716										
APBA1	320	hgsc.bcm.edu	37	chr9	72071259	72071259	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	ttctcctgggagttggagcgAggcatccgccggcgggccat	16	12	1	0			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr9:72071259A>T	ENST00000265381.4	-	8	1914	c.1692T>A	c.(1690-1692)ccT>ccA	p.P564P	APBA1_ENST00000470082.1_5'UTR	NM_001163.3	NP_001154.2	Q02410	APBA1_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 1	564	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				axon cargo transport (GO:0008088)|cell adhesion (GO:0007155)|gamma-aminobutyric acid secretion (GO:0014051)|glutamate secretion (GO:0014047)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein complex assembly (GO:0006461)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synaptic vesicle (GO:0008021)	beta-amyloid binding (GO:0001540)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(4)|kidney(2)|large_intestine(12)|lung(13)|prostate(3)|skin(3)	37						AGTTGGAGCGAGGCATCCGCC	0.567																																					p.P564P		Atlas-SNP	.											.	APBA1	96	.	0			c.T1692A						.						245	232	237					9																	72071259		2203	4300	6503	SO:0001819	synonymous_variant	320	exon8			GGAGCGAGGCATC	AF029106	CCDS6630.1	9q13-q21	2008-07-18	2008-07-18		ENSG00000107282	ENSG00000107282			578	protein-coding gene	gene with protein product		602414		MINT1		7678331, 7719031	Standard	NM_001163		Approved	D9S411E, X11	uc004ahh.2	Q02410	OTTHUMG00000019984	ENST00000265381.4:c.1692T>A	chr9.hg19:g.72071259A>T		69.0	0.0		75.0	13.0	NM_001163	O14914|O60570|Q5VYR8	Silent	SNP	ENST00000265381.4	hg19	CCDS6630.1																																																																																			.	.		0.567	APBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052589.2	NM_001163		T	72071259	A	T	72071259	2	4	304	1	0	0	0	0	0	0	0	1	756	291	11	4		4	APBA1	9	72071259	Silent	SNP	A	TCGA-GJ-A3OU-01A-31D-A382-10		72071259	69142172	32	43717										
GALNT12	79695	hgsc.bcm.edu	37	chr9	101589127	101589127	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	agagggcctggtgcgagcccGgctgctgggggcgtctgcgg	21	11	1	1			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr9:101589127G>A	ENST00000375011.3	+	3	635	c.635G>A	c.(634-636)cGg>cAg	p.R212Q		NM_024642.4	NP_078918.3	Q8IXK2	GLT12_HUMAN	polypeptide N-acetylgalactosaminyltransferase 12	212	Catalytic subdomain A.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(1)|endometrium(2)|large_intestine(3)|lung(8)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	17		Acute lymphoblastic leukemia(62;0.0559)				GTGCGAGCCCGGCTGCTGGGG	0.652																																					p.R212Q		Atlas-SNP	.											.	GALNT12	37	.	0			c.G635A						.						27	27	27					9																	101589127		2203	4300	6503	SO:0001583	missense	79695	exon3			GAGCCCGGCTGCT	AB078146	CCDS6737.1	9q22.33	2014-03-13	2014-03-13		ENSG00000119514	ENSG00000119514	2.4.1.41	"Glycosyltransferase family 2 domain containing"	19877	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 12"	610290	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 12 (GalNAc-T12)"			12135769	Standard	NM_024642		Approved	GalNAc-T12	uc004ayz.3	Q8IXK2	OTTHUMG00000020348	ENST00000375011.3:c.635G>A	chr9.hg19:g.101589127G>A	ENSP00000364150:p.Arg212Gln	80.0	0.0		64.0	14.0	NM_024642	Q5TCF7|Q8NG54|Q96CT9|Q9H771	Missense_Mutation	SNP	ENST00000375011.3	hg19	CCDS6737.1	.	.	.	.	.	.	.	.	.	.	G	37	5.993299	0.97184	.	.	ENSG00000119514	ENST00000375011	T	0.64085	-0.08	5.96	5.96	0.96718	Glycosyl transferase, family 2 (1);	0.000000	0.85682	D	0.000000	D	0.86727	0.6002	H	0.96720	3.87	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.90450	0.4438	10	0.87932	D	0	.	17.902	0.88907	0.0:0.0:1.0:0.0	.	212	Q8IXK2	GLT12_HUMAN	Q	212	ENSP00000364150:R212Q	ENSP00000364150:R212Q	R	+	2	0	GALNT12	100628948	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.809000	0.99208	2.814000	0.96858	0.655000	0.94253	CGG	.	.		0.652	GALNT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053382.1	NM_024642		A	101589127	G	A	101589127	3	1	304	1	0	0	0	0	1	0	0	0	6218	1116	39	1	645	1	GALNT12	9	101589127	Missense_Mutation	SNP	G	TCGA-GJ-A3OU-01A-31D-A382-10	29517868	101589127	39624304	33	43718										
SAA2	6289	hgsc.bcm.edu	37	chr11	18266927	18266927	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	cagagtgaagaggaagctcaGtatttctcaggcaggccagc	13	9	2	3			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr11:18266927G>A	ENST00000526900.1	-	4	549	c.366C>T	c.(364-366)taC>taT	p.Y122Y	SAA2_ENST00000256733.4_Silent_p.Y122Y|SAA2_ENST00000528349.1_Intron|SAA2_ENST00000529528.1_Silent_p.Y122Y|SAA2_ENST00000530400.1_Intron|SAA2-SAA4_ENST00000524555.1_RNA|SAA2_ENST00000414546.2_Intron			P0DJI9	SAA2_HUMAN	serum amyloid A2	122					acute-phase response (GO:0006953)	extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)				central_nervous_system(1)|large_intestine(2)|lung(2)|prostate(1)	6						AGGAAGCTCAGTATTTCTCAG	0.562																																					p.Y122Y		Atlas-SNP	.											.	SAA2	22	.	0			c.C366T						.						90	82	85					11																	18266927		2199	4293	6492	SO:0001819	synonymous_variant	6289	exon4			AGCTCAGTATTTC	M26152	CCDS7833.1, CCDS44548.1	11p15.1-p14	2008-07-21			ENSG00000134339	ENSG00000134339			10514	protein-coding gene	gene with protein product		104751				7686132	Standard	NM_030754		Approved			P0DJI9	OTTHUMG00000166484	ENST00000526900.1:c.366C>T	chr11.hg19:g.18266927G>A		96.0	0.0		104.0	10.0	NM_030754	G3XAK9|P02735|P02736|P02737|Q16730|Q16834|Q16835|Q16879|Q3KRB3|Q6FG67|Q96QN0|Q9UCK9|Q9UCL0	Silent	SNP	ENST00000526900.1	hg19	CCDS7833.1																																																																																			.	.		0.562	SAA2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389983.1	NM_030754		A	18266927	G	A	18266927	2	1	304	1	0	0	0	0	0	0	0	1	13814	1024	36	3		3	SAA2	11	18266927	Silent	SNP	G	TCGA-GJ-A3OU-01A-31D-A382-10		18266927	116739589	34	43719										
MTA2	9219	hgsc.bcm.edu	37	chr11	62364838	62364839	+	Nonsense_Mutation	DNP	GC	GC	AT													0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	actcatgtgcaagcttggctGccgaatggagctgctacaat							TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr11:62364838_62364839GC>AT	ENST00000278823.2	-	8	1031_1032	c.642_643GC>AT	c.(640-645)cgGCag>cgATag	p.Q215*	MTA2_ENST00000527204.1_Nonsense_Mutation_p.Q42*|MTA2_ENST00000524902.1_Nonsense_Mutation_p.Q42*	NM_004739.3	NP_004730.2	O94776	MTA2_HUMAN	metastasis associated 1 family, member 2	215	ELM2. {ECO:0000255|PROSITE- ProRule:PRU00512}.				ATP-dependent chromatin remodeling (GO:0043044)|chromatin assembly or disassembly (GO:0006333)|DNA methylation (GO:0006306)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	histone deacetylase complex (GO:0000118)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|histone deacetylase activity (GO:0004407)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	26						AAGCTTGGCTGCCGAATGGAGC	0.51																																					p.Q215X|p.R214R		Atlas-SNP	.											.	MTA2	54	.	0			c.C643T|c.G642A						.																																			SO:0001587	stop_gained	9219	exon8			TTGGCTGCCGAAT|TGGCTGCCGAATG	AB016591	CCDS8022.1	11q12-q13.1	2013-01-25	2004-12-15	2003-12-17	ENSG00000149480	ENSG00000149480		"GATA zinc finger domain containing"	7411	protein-coding gene	gene with protein product		603947	"metastasis associated gene family, member 2"	MTA1L1		9929979	Standard	NM_004739		Approved	MTA1-L1	uc001ntq.2	O94776	OTTHUMG00000167684	ENST00000278823.2:c.642_643delinsAT	chr11.hg19:g.62364838_62364839delinsAT	ENSP00000278823:p.Gln215*	141.0	0.0		135.0|134.0	19.0|18.0	NM_004739	Q68DB1|Q9UQB5	Nonsense_Mutation|Silent	SNP	ENST00000278823.2	hg19	CCDS8022.1																																																																																			.	.		0.51	MTA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395578.1	NM_004739		AT	62364839	GC	AT	62364838	4	1	304	1	0	0	0	0	0	1	0	0	9918	1328	46	3	1407	3	MTA2	11	62364838	Nonsense_Mutation	DNP	GC	TCGA-GJ-A3OU-01A-31D-A382-10	44097911	62364838	72641678	35	43720										
NEDD1	121441	hgsc.bcm.edu	37	chr12	97331084	97331084	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	attccggaattgtcagagaaGcacctgccacgtccattgcc	9	13	1	1			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr12:97331084G>C	ENST00000266742.4	+	9	1369	c.1030G>C	c.(1030-1032)Gca>Cca	p.A344P	NEDD1_ENST00000429527.2_Missense_Mutation_p.A344P|NEDD1_ENST00000457368.2_Missense_Mutation_p.A255P|NEDD1_ENST00000411739.2_Missense_Mutation_p.A255P|NEDD1_ENST00000557644.1_Missense_Mutation_p.A351P	NM_152905.3	NP_690869.1	Q8NHV4	NEDD1_HUMAN	neural precursor cell expressed, developmentally down-regulated 1	344					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	apical part of cell (GO:0045177)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|pericentriolar material (GO:0000242)|spindle pole (GO:0000922)				breast(2)|endometrium(1)|kidney(2)|large_intestine(9)|lung(8)	22						TGTCAGAGAAGCACCTGCCAC	0.433																																					p.A351P		Atlas-SNP	.											.	NEDD1	47	.	0			c.G1051C						.						152	129	137					12																	97331084		2203	4300	6503	SO:0001583	missense	121441	exon8			AGAGAAGCACCTG		CCDS9063.1, CCDS44955.1, CCDS44956.1	12q23.1	2013-01-10			ENSG00000139350	ENSG00000139350		"WD repeat domain containing"	7723	protein-coding gene	gene with protein product		600372					Standard	NM_001135175		Approved	GCP-WD, TUBGCP7	uc001tev.4	Q8NHV4	OTTHUMG00000170604	ENST00000266742.4:c.1030G>C	chr12.hg19:g.97331084G>C	ENSP00000266742:p.Ala344Pro	114.0	0.0		129.0	17.0	NM_001135175	B0AZN0|B4E145|G3V3F1|Q8NA30	Missense_Mutation	SNP	ENST00000266742.4	hg19	CCDS9063.1	.	.	.	.	.	.	.	.	.	.	G	13.28	2.189720	0.38707	.	.	ENSG00000139350	ENST00000266742;ENST00000429527;ENST00000411739;ENST00000557644;ENST00000457368	T;T;T;T;T	0.50001	0.76;0.76;1.54;0.76;1.54	5.65	-1.02	0.10135	.	1.346880	0.04337	N	0.353378	T	0.30230	0.0758	N	0.24115	0.695	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.0	T	0.23655	-1.0182	10	0.45353	T	0.12	.	2.0603	0.03591	0.1584:0.1195:0.2492:0.4729	.	351;344	G3V3F1;Q8NHV4	.;NEDD1_HUMAN	P	344;344;255;351;255	ENSP00000266742:A344P;ENSP00000404978:A344P;ENSP00000411307:A255P;ENSP00000451211:A351P;ENSP00000407964:A255P	ENSP00000266742:A344P	A	+	1	0	NEDD1	95855215	0.000000	0.05858	0.185000	0.23176	0.213000	0.24496	-0.690000	0.05138	0.274000	0.22072	0.591000	0.81541	GCA	.	.		0.433	NEDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409792.1			C	97331084	G	C	97331084	3	2	304	1	0	0	0	0	1	0	0	0	10318	971	34	4	1081	4	NEDD1	12	97331084	Missense_Mutation	SNP	G	TCGA-GJ-A3OU-01A-31D-A382-10		97331084	36520811	36	43721										
ANKRD13A	88455	hgsc.bcm.edu	37	chr12	110457106	110457106	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	ccctgtcattaacaccagccTcgatactaaaaatattgctt	4	12	1	0			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr12:110457106T>G	ENST00000261739.4	+	6	873	c.707T>G	c.(706-708)cTc>cGc	p.L236R	ANKRD13A_ENST00000550404.1_3'UTR	NM_033121.1	NP_149112.1	Q8IZ07	AN13A_HUMAN	ankyrin repeat domain 13A	236						endosome (GO:0005768)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(8)|lung(3)|urinary_tract(1)	16						AACACCAGCCTCGATACTAAA	0.418																																					p.L236R		Atlas-SNP	.											.	ANKRD13A	39	.	0			c.T707G						.						57	58	58					12																	110457106		2203	4300	6503	SO:0001583	missense	88455	exon6			CCAGCCTCGATAC	AF064604	CCDS9140.1	12q24.12	2013-01-10	2006-06-30	2006-06-30		ENSG00000076513		"Ankyrin repeat domain containing"	21268	protein-coding gene	gene with protein product		615123	"ankyrin repeat domain 13"	ANKRD13		10508479	Standard	NM_033121		Approved	NY-REN-25	uc001tpx.3	Q8IZ07	OTTHUMG00000169314	ENST00000261739.4:c.707T>G	chr12.hg19:g.110457106T>G	ENSP00000261739:p.Leu236Arg	213.0	0.0		192.0	21.0	NM_033121	O60736	Missense_Mutation	SNP	ENST00000261739.4	hg19	CCDS9140.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	24.8|24.8	4.566066|4.566066	0.86439|0.86439	.|.	.|.	ENSG00000076513|ENSG00000076513	ENST00000261738;ENST00000261739|ENST00000547639	T|.	0.56275|.	0.47|.	5.61|5.61	5.61|5.61	0.85477|0.85477	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.77725|0.77725	0.4173|0.4173	M|M	0.82323|0.82323	2.585|2.585	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.77557|.	0.99;0.99;0.99|.	T|T	0.79645|0.79645	-0.1717|-0.1717	10|5	0.87932|.	D|.	0|.	-21.5323|-21.5323	14.9746|14.9746	0.71261|0.71261	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	236;236;236|.	B4DYP5;Q3ZTS7;Q8IZ07|.	.;.;AN13A_HUMAN|.	R|A	21;236|90	ENSP00000261739:L236R|.	ENSP00000261738:L21R|.	L|S	+|+	2|1	0|0	ANKRD13A|ANKRD13A	108941489|108941489	1.000000|1.000000	0.71417|0.71417	0.960000|0.960000	0.40013|0.40013	0.996000|0.996000	0.88848|0.88848	7.989000|7.989000	0.88205|0.88205	2.136000|2.136000	0.66102|0.66102	0.482000|0.482000	0.46254|0.46254	CTC|TCG	.	.		0.418	ANKRD13A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403430.1	NM_033121		G	110457106	T	G	110457106	3	3	304	1	0	0	0	0	1	0	0	0	641	1551	54	5	729	5	ANKRD13A	12	110457106	Missense_Mutation	SNP	T	TCGA-GJ-A3OU-01A-31D-A382-10	13126022	110457106	23394789	37	43722										
KIF26A	26153	hgsc.bcm.edu	37	chr14	104638072	104638072	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	tgccccaggtgaaggttatgCtgcggatctggcccgcacag	14	12	1	1	rs368488344		TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr14:104638072C>T	ENST00000423312.2	+	6	1126	c.1126C>T	c.(1126-1128)Ctg>Ttg	p.L376L	KIF26A_ENST00000315264.7_Silent_p.L237L	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	376	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|enteric nervous system development (GO:0048484)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of signal transduction (GO:0009968)|regulation of cell growth by extracellular stimulus (GO:0001560)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	21		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767)	Epithelial(46;0.152)	Epithelial(152;0.161)		GAAGGTTATGCTGCGGATCTG	0.672																																					p.L376L		Atlas-SNP	.											.	KIF26A	84	.	0			c.C1126T						.						9	13	12					14																	104638072		1956	4113	6069	SO:0001819	synonymous_variant	26153	exon6			GTTATGCTGCGGA	AB033062	CCDS45171.1	14q32.33	2009-03-19			ENSG00000066735	ENSG00000066735		"Kinesins"	20226	protein-coding gene	gene with protein product		613231				10574462, 11416179	Standard	NM_015656		Approved	KIAA1236, DKFZP434N178	uc001yos.4	Q9ULI4	OTTHUMG00000154986	ENST00000423312.2:c.1126C>T	chr14.hg19:g.104638072C>T		90.0	0.0		85.0	6.0	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Silent	SNP	ENST00000423312.2	hg19	CCDS45171.1																																																																																			.	.		0.672	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1			T	104638072	C	T	104638072	2	4	304	1	0	0	0	0	0	0	0	1	8303	796	28	3		3	KIF26A	14	104638072	Silent	SNP	C	TCGA-GJ-A3OU-01A-31D-A382-10		104638072	2711468	38	43723										
CHRNA3	1136	hgsc.bcm.edu	37	chr15	78894061	78894061	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	caaaaatcatggtgaacaggAggtactctccaatcaggggg	12	8	3	1			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr15:78894061A>C	ENST00000326828.5	-	5	1307	c.923T>G	c.(922-924)cTc>cGc	p.L308R	CHRNA3_ENST00000348639.3_Missense_Mutation_p.L308R	NM_000743.4	NP_000734.2	P32297	ACHA3_HUMAN	cholinergic receptor, nicotinic, alpha 3 (neuronal)	308					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of dendrite morphogenesis (GO:0048814)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of membrane potential (GO:0042391)|regulation of smooth muscle contraction (GO:0006940)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18					Bupropion(DB01156)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Levomethadyl Acetate(DB01227)|Nicotine(DB00184)|Pentolinium(DB01090)|Varenicline(DB01273)	GGTGAACAGGAGGTACTCTCC	0.532																																					p.L308R		Atlas-SNP	.											.	CHRNA3	56	.	0			c.T923G						.						135	115	122					15																	78894061		2196	4293	6489	SO:0001583	missense	1136	exon5			AACAGGAGGTACT		CCDS10305.1, CCDS53964.1	15q24	2012-02-11	2012-02-07		ENSG00000080644	ENSG00000080644		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1957	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 3 (neuronal)"	118503	"cholinergic receptor, nicotinic, alpha polypeptide 3"			2004777	Standard	NM_000743		Approved		uc002bec.3	P32297	OTTHUMG00000143863	ENST00000326828.5:c.923T>G	chr15.hg19:g.78894061A>C	ENSP00000315602:p.Leu308Arg	105.0	0.0		91.0	18.0	NM_000743	Q15823|Q4KMN8|Q86U77|Q96RH3|Q99553|Q9BQ93|Q9BRR4	Missense_Mutation	SNP	ENST00000326828.5	hg19	CCDS10305.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.512654	0.85389	.	.	ENSG00000080644	ENST00000348639;ENST00000326828;ENST00000326858	T;T	0.75589	-0.95;-0.95	6.02	6.02	0.97574	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.057150	0.64402	D	0.000001	D	0.91112	0.7202	H	0.97051	3.93	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.93883	0.7173	10	0.87932	D	0	.	16.5446	0.84426	1.0:0.0:0.0:0.0	.	308;308	P32297;P32297-3	ACHA3_HUMAN;.	R	308;308;172	ENSP00000267951:L308R;ENSP00000315602:L308R	ENSP00000315602:L308R	L	-	2	0	CHRNA3	76681116	1.000000	0.71417	0.995000	0.50966	0.995000	0.86356	9.332000	0.96446	2.311000	0.77944	0.533000	0.62120	CTC	.	.		0.532	CHRNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290111.3			C	78894061	A	C	78894061	3	2	304	1	0	0	0	0	1	0	0	0	3386	304	11	5	687	5	CHRNA3	15	78894061	Missense_Mutation	SNP	A	TCGA-GJ-A3OU-01A-31D-A382-10		78894061	23637331	39	43724										
CRAMP1L	57585	hgsc.bcm.edu	37	chr16	1691138	1691138	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	tatttattttttccatttaaAggtatggatgacaagaatgc	7	4	0	2			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr16:1691138A>C	ENST00000397412.3	+	6	877		c.e6-1		CRAMP1L_ENST00000436138.3_Splice_Site|LA16c-431H6.6_ENST00000454337.1_Splice_Site|CRAMP1L_ENST00000293925.5_Splice_Site			Q96RY5	CRML_HUMAN	Crm, cramped-like (Drosophila)							nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(6)|pancreas(1)	22						TTCCATTTAAAGGTATGGATG	0.378																																					.		Atlas-SNP	.											.	CRAMP1L	60	.	0			c.779-2A>C						.						104	102	103					16																	1691138		1862	4108	5970	SO:0001630	splice_region_variant	57585	exon5			ATTTAAAGGTATG	AB037847	CCDS10440.2	16p13.3	2008-07-30	2001-11-28		ENSG00000007545	ENSG00000007545			14122	protein-coding gene	gene with protein product			"Crm (Cramped Drosophila)-like"				Standard	NM_020825		Approved	KIAA1426	uc010uvh.2	Q96RY5	OTTHUMG00000074087	ENST00000397412.3:c.779-1A>C	chr16.hg19:g.1691138A>C		49.0	0.0		53.0	12.0	NM_020825	A8MZL1|B1AJY1|Q8NDN1|Q9P2C1	Splice_Site	SNP	ENST00000397412.3	hg19	CCDS10440.2	.	.	.	.	.	.	.	.	.	.	A	13.50	2.256505	0.39896	.	.	ENSG00000007545	ENST00000397412;ENST00000293925;ENST00000436138	.	.	.	5.46	5.46	0.80206	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.5282	0.75928	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CRAMP1L	1631139	1.000000	0.71417	0.995000	0.50966	0.942000	0.58702	8.836000	0.92105	2.076000	0.62316	0.459000	0.35465	.	.	.		0.378	CRAMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157297.4		Intron	C	1691138	A	C	1691138	5	2	304	1	0	0	0	0	0	0	1	0	3848	86	3	5	795	5	CRAMP1L	16	1691138	Splice_Site	SNP	A	TCGA-GJ-A3OU-01A-31D-A382-10		1691138	88663615	40	43725										
LPCAT2	54947	hgsc.bcm.edu	37	chr16	55562430	55562430	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	cctcattcaacattctttgaTggaattgcctgtgttgtagc	8	9	3	1			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr16:55562430T>A	ENST00000262134.5	+	3	637	c.453T>A	c.(451-453)gaT>gaA	p.D151E		NM_017839.4	NP_060309.2	Q7L5N7	PCAT2_HUMAN	lysophosphatidylcholine acyltransferase 2	151					glycerophospholipid biosynthetic process (GO:0046474)|membrane organization (GO:0061024)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)|1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)|1-alkylglycerophosphocholine O-acetyltransferase activity (GO:0047192)|calcium ion binding (GO:0005509)			endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	12						CATTCTTTGATGGAATTGCCT	0.408																																					p.D151E		Atlas-SNP	.											.	LPCAT2	35	.	0			c.T453A						.						206	188	194					16																	55562430		2198	4300	6498	SO:0001583	missense	54947	exon3			CTTTGATGGAATT	AK000488	CCDS10753.1	16q12.2	2013-01-10	2007-12-17	2007-12-17	ENSG00000087253	ENSG00000087253		"EF-hand domain containing"	26032	protein-coding gene	gene with protein product		612040	"acyltransferase like 1"	AYTL1		16704971	Standard	NM_017839		Approved	FLJ20481	uc002eie.4	Q7L5N7	OTTHUMG00000133238	ENST00000262134.5:c.453T>A	chr16.hg19:g.55562430T>A	ENSP00000262134:p.Asp151Glu	197.0	0.0		169.0	26.0	NM_017839	A3KBM1|Q6MZJ6|Q9NX23	Missense_Mutation	SNP	ENST00000262134.5	hg19	CCDS10753.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.101343	0.76983	.	.	ENSG00000087253	ENST00000262134	D	0.99933	-8.27	5.8	0.861	0.19048	Phospholipid/glycerol acyltransferase (2);	0.000000	0.85682	D	0.000000	D	0.99908	0.9956	M	0.84219	2.685	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.97501	1.0060	10	0.45353	T	0.12	-35.2268	10.0072	0.41964	0.0:0.2502:0.0:0.7498	.	151	Q7L5N7	PCAT2_HUMAN	E	151	ENSP00000262134:D151E	ENSP00000262134:D151E	D	+	3	2	LPCAT2	54119931	1.000000	0.71417	0.997000	0.53966	0.986000	0.74619	1.225000	0.32551	-0.115000	0.11915	0.477000	0.44152	GAT	.	.		0.408	LPCAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256977.2	NM_017839		A	55562430	T	A	55562430	3	1	304	1	0	0	0	0	1	0	0	0	8920	1461	51	4	463	4	LPCAT2	16	55562430	Missense_Mutation	SNP	T	TCGA-GJ-A3OU-01A-31D-A382-10	53871292	55562430	34792323	41	43726										
TP53	7157	hgsc.bcm.edu	37	chr17	7577115	7577115	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	gtctctcccaggacaggcacAaacacgcacctcaaagctgt	8	15	2	0			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr17:7577115A>G	ENST00000269305.4	-	8	1012	c.823T>C	c.(823-825)Tgt>Cgt	p.C275R	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.C275R|TP53_ENST00000455263.2_Missense_Mutation_p.C275R|TP53_ENST00000445888.2_Missense_Mutation_p.C275R|TP53_ENST00000420246.2_Missense_Mutation_p.C275R|TP53_ENST00000413465.2_Intron	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	275	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		C -> F (in sporadic cancers; somatic mutation).|C -> G (in sporadic cancers; somatic mutation).|C -> R (in sporadic cancers; somatic mutation).|C -> S (in sporadic cancers; somatic mutation).|C -> W (in sporadic cancers; somatic mutation).|C -> Y (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:7887414}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.C275G(7)|p.C275R(7)|p.C275fs*31(2)|p.?(2)|p.C275fs*20(1)|p.L265_K305del41(1)|p.R273_C275delRVC(1)|p.F270_D281del12(1)|p.V274_P278del(1)|p.S269fs*21(1)|p.C275fs*67(1)|p.C275fs*70(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGACAGGCACAAACACGCACC	0.552		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.C275R	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,NS,other,+1,2	TP53	33396	.	36	Substitution - Missense(14)|Whole gene deletion(8)|Deletion - In frame(6)|Deletion - Frameshift(4)|Insertion - Frameshift(2)|Unknown(2)	bone(5)|stomach(4)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(4)|breast(4)|upper_aerodigestive_tract(3)|ovary(3)|large_intestine(2)|oesophagus(2)|peritoneum(1)|urinary_tract(1)|skin(1)|lung(1)|prostate(1)	c.T823C						.						70	60	64					17																	7577115		2203	4300	6503	SO:0001583	missense	7157	exon8	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AGGCACAAACACG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.823T>C	chr17.hg19:g.7577115A>G	ENSP00000269305:p.Cys275Arg	77.0	0.0		76.0	13.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.225244	0.79576	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99874	-7.39;-7.39;-7.39;-7.39;-7.39;-7.39	4.92	4.92	0.64577	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99873	0.9940	M	0.92738	3.34	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.997;1.0;0.996;0.997	D	0.96415	0.9307	10	0.87932	D	0	-17.2181	12.5624	0.56288	1.0:0.0:0.0:0.0	.	275;275;275;275	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	R	275;275;275;275;275;264;143	ENSP00000352610:C275R;ENSP00000269305:C275R;ENSP00000398846:C275R;ENSP00000391127:C275R;ENSP00000391478:C275R;ENSP00000425104:C143R	ENSP00000269305:C275R	C	-	1	0	TP53	7517840	1.000000	0.71417	0.957000	0.39632	0.850000	0.48378	9.060000	0.93907	2.067000	0.61834	0.379000	0.24179	TGT	.	.		0.552	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		G	7577115	A	G	7577115	3	3	304	1	0	0	0	0	1	0	0	0	16396	130	5	2	463	2	TP53	17	7577115	Missense_Mutation	SNP	A	TCGA-GJ-A3OU-01A-31D-A382-10		7577115	73618095	42	43727										
WNT9B	7484	hgsc.bcm.edu	37	chr17	44954034	44954034	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	tgcagtggtgctgctacgtgGagtgccagcaatgtgtgcag	16	8	0	0			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr17:44954034G>C	ENST00000290015.2	+	4	1077	c.1024G>C	c.(1024-1026)Gag>Cag	p.E342Q	WNT9B_ENST00000393461.2_Intron	NM_003396.1	NP_003387.1	O14905	WNT9B_HUMAN	wingless-type MMTV integration site family, member 9B	342					branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to retinoic acid (GO:0071300)|cellular response to starvation (GO:0009267)|collecting duct development (GO:0072044)|cornea development in camera-type eye (GO:0061303)|embryonic cranial skeleton morphogenesis (GO:0048701)|establishment of planar polarity involved in nephron morphogenesis (GO:0072046)|in utero embryonic development (GO:0001701)|kidney rudiment formation (GO:0072003)|male genitalia development (GO:0030539)|mesenchymal stem cell maintenance involved in nephron morphogenesis (GO:0072038)|mesonephric duct formation (GO:0072181)|metanephric tubule formation (GO:0072174)|multicellular organismal development (GO:0007275)|neuron differentiation (GO:0030182)|palate development (GO:0060021)|positive regulation of catalytic activity (GO:0043085)|regulation of asymmetric cell division (GO:0009786)|regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003339)|regulation of protein phosphorylation (GO:0001932)|regulation of tube size (GO:0035150)|response to retinoic acid (GO:0032526)|uterus morphogenesis (GO:0061038)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			large_intestine(2)|lung(8)	10			BRCA - Breast invasive adenocarcinoma(9;0.0257)			CTGCTACGTGGAGTGCCAGCA	0.647																																					p.E342Q		Atlas-SNP	.											.	WNT9B	37	.	0			c.G1024C						.						40	38	39					17																	44954034		2203	4299	6502	SO:0001583	missense	7484	exon4			TACGTGGAGTGCC	AF028703	CCDS11506.1	17q21	2008-01-07	2003-03-11	2003-03-14		ENSG00000158955		"Wingless-type MMTV integration sites"	12779	protein-coding gene	gene with protein product		602864	"wingless-type MMTV integration site family, member 15"	WNT15		9441749, 11713592	Standard	NM_003396		Approved	WNT14B	uc002ikw.1	O14905		ENST00000290015.2:c.1024G>C	chr17.hg19:g.44954034G>C	ENSP00000290015:p.Glu342Gln	167.0	0.0		173.0	24.0	NM_003396	Q6UXT4|Q96Q09	Missense_Mutation	SNP	ENST00000290015.2	hg19	CCDS11506.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.206995	0.79127	.	.	ENSG00000158955	ENST00000376843;ENST00000290015	T	0.75938	-0.98	5.39	5.39	0.77823	.	0.103621	0.64402	D	0.000004	T	0.82089	0.4961	L	0.46947	1.48	0.80722	D	1	D	0.69078	0.997	D	0.63192	0.912	D	0.83371	0.0007	10	0.66056	D	0.02	.	19.1452	0.93463	0.0:0.0:1.0:0.0	.	342	O14905	WNT9B_HUMAN	Q	336;342	ENSP00000290015:E342Q	ENSP00000290015:E342Q	E	+	1	0	WNT9B	42309033	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.059000	0.89462	2.517000	0.84864	0.561000	0.74099	GAG	.	.		0.647	WNT9B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440433.1	NM_003396		C	44954034	G	C	44954034	3	2	304	1	0	0	0	0	1	0	0	0	17414	1175	41	4	1038	4	WNT9B	17	44954034	Missense_Mutation	SNP	G	TCGA-GJ-A3OU-01A-31D-A382-10	37376919	44954034	36241176	43	43728										
ACTL9	284382	hgsc.bcm.edu	37	chr19	8808811	8808811	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	ggcgggtttcttgggctggcAgcccaggatggtggccacgg	19	10	1	0			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr19:8808811A>T	ENST00000324436.3	-	1	361	c.241T>A	c.(241-243)Tgc>Agc	p.C81S		NM_178525.3	NP_848620.3	Q8TC94	ACTL9_HUMAN	actin-like 9	81						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(15)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	36						TTGGGCTGGCAGCCCAGGATG	0.652																																					p.C81S		Atlas-SNP	.											.	ACTL9	74	.	0			c.T241A						.						23	25	25					19																	8808811		2203	4297	6500	SO:0001583	missense	284382	exon1			GCTGGCAGCCCAG		CCDS12207.1	19p13.2	2014-08-08			ENSG00000181786	ENSG00000181786			28494	protein-coding gene	gene with protein product							Standard	NM_178525		Approved	MGC33407	uc002mkl.2	Q8TC94	OTTHUMG00000182194	ENST00000324436.3:c.241T>A	chr19.hg19:g.8808811A>T	ENSP00000316674:p.Cys81Ser	78.0	0.0		84.0	10.0	NM_178525	A8K893|Q6X960	Missense_Mutation	SNP	ENST00000324436.3	hg19	CCDS12207.1	.	.	.	.	.	.	.	.	.	.	A	10.86	1.470112	0.26423	.	.	ENSG00000181786	ENST00000324436	D	0.93763	-3.28	4.0	4.0	0.46444	.	2.153300	0.02187	U	0.061029	D	0.88119	0.6351	N	0.20610	0.595	0.32051	N	0.596937	B	0.14805	0.011	B	0.13407	0.009	T	0.79692	-0.1697	10	0.56958	D	0.05	.	4.3137	0.10982	0.6879:0.2057:0.1064:0.0	.	81	Q8TC94	ACTL9_HUMAN	S	81	ENSP00000316674:C81S	ENSP00000316674:C81S	C	-	1	0	ACTL9	8669811	0.400000	0.25295	0.730000	0.30809	0.412000	0.31113	3.215000	0.51169	1.827000	0.53221	0.379000	0.24179	TGC	.	.		0.652	ACTL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459953.1	NM_178525		T	8808811	A	T	8808811	3	4	304	1	0	0	0	0	1	0	0	0	203	188	7	4	1013	4	ACTL9	19	8808811	Missense_Mutation	SNP	A	TCGA-GJ-A3OU-01A-31D-A382-10		8808811	50320172	44	43729										
ZNF317	57693	hgsc.bcm.edu	37	chr19	9267979	9267979	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	caagatgtcgctgtggacttTaccgagaaggagtggccctt	13	9	0	2			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr19:9267979T>C	ENST00000247956.6	+	4	503	c.198T>C	c.(196-198)ttT>ttC	p.F66F	ZNF317_ENST00000360385.3_Silent_p.F66F	NM_020933.4	NP_065984.3	Q96PQ6	ZN317_HUMAN	zinc finger protein 317	66	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	27						CTGTGGACTTTACCGAGAAGG	0.498																																					p.F66F		Atlas-SNP	.											.	ZNF317	61	.	0			c.T198C						.						100	92	94					19																	9267979		2203	4300	6503	SO:0001819	synonymous_variant	57693	exon4			GGACTTTACCGAG	AF275255	CCDS12210.1, CCDS54213.1	19p13	2013-01-08				ENSG00000130803		"Zinc fingers, C2H2-type", "-"	13507	protein-coding gene	gene with protein product		613864				10997877, 11688974	Standard	NM_020933		Approved		uc002mku.3	Q96PQ6		ENST00000247956.6:c.198T>C	chr19.hg19:g.9267979T>C		107.0	0.0		103.0	20.0	NM_020933	Q6DCA9|Q96PM0|Q96PM1|Q96PT2|Q9HCI4	Silent	SNP	ENST00000247956.6	hg19	CCDS12210.1																																																																																			.	.		0.498	ZNF317-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448995.1	NM_020933		C	9267979	T	C	9267979	2	2	304	1	0	0	0	0	0	0	0	1	17850	1751	61	2		2	ZNF317	19	9267979	Silent	SNP	T	TCGA-GJ-A3OU-01A-31D-A382-10	459168	9267979	49861004	45	43730										
ZNF432	9668	hgsc.bcm.edu	37	chr19	52537481	52537481	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	cacattcactgcacctgtaaGgtttctctccagtatgagtt	7	11	2	1			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr19:52537481G>C	ENST00000594154.1	-	5	1663	c.1451C>G	c.(1450-1452)cCt>cGt	p.P484R	ZNF432_ENST00000221315.5_Missense_Mutation_p.P484R			O94892	ZN432_HUMAN	zinc finger protein 432	484					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	29		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.0054)|OV - Ovarian serous cystadenocarcinoma(262;0.0182)		GCACCTGTAAGGTTTCTCTCC	0.458																																					p.P484R		Atlas-SNP	.											.	ZNF432	172	.	0			c.C1451G						.						66	61	63					19																	52537481		2203	4300	6503	SO:0001583	missense	9668	exon5			CTGTAAGGTTTCT	AB018341	CCDS12848.1	19q13.41	2013-01-08				ENSG00000256087		"Zinc fingers, C2H2-type", "-"	20810	protein-coding gene	gene with protein product						9872452	Standard	NM_014650		Approved	KIAA0798	uc002pyk.3	O94892		ENST00000594154.1:c.1451C>G	chr19.hg19:g.52537481G>C	ENSP00000470488:p.Pro484Arg	67.0	0.0		79.0	9.0	NM_014650		Missense_Mutation	SNP	ENST00000594154.1	hg19	CCDS12848.1	.	.	.	.	.	.	.	.	.	.	G	17.19	3.327008	0.60743	.	.	ENSG00000256087	ENST00000221315	T	0.17213	2.29	2.81	2.81	0.32909	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.35008	0.0917	L	0.55017	1.72	0.38389	D	0.945357	D	0.89917	1.0	D	0.91635	0.999	T	0.35201	-0.9798	9	0.87932	D	0	.	12.7967	0.57564	0.0:0.0:1.0:0.0	.	484	O94892	ZN432_HUMAN	R	484	ENSP00000221315:P484R	ENSP00000221315:P484R	P	-	2	0	ZNF432	57229293	1.000000	0.71417	0.858000	0.33744	0.929000	0.56500	4.486000	0.60286	1.577000	0.49804	0.655000	0.94253	CCT	.	.		0.458	ZNF432-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462410.1	NM_014650		C	52537481	G	C	52537481	3	2	304	1	0	0	0	0	1	0	0	0	17921	1000	35	4	511	4	ZNF432	19	52537481	Missense_Mutation	SNP	G	TCGA-GJ-A3OU-01A-31D-A382-10	43269502	52537481	6591502	46	43731										
C20orf7	79133	hgsc.bcm.edu	37	chr20	13797788	13797788	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	gaccagctgaaagaggttccGcaactgtgtcatttggagag	13	8	1	3	rs142611230		TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr20:13797788G>A	ENST00000378106.5	+	11	1089	c.970G>A	c.(970-972)Gca>Aca	p.A324T	NDUFAF5_ENST00000463598.1_Missense_Mutation_p.A296T|NDUFAF5_ENST00000475968.1_3'UTR	NM_024120.4	NP_077025.2	Q5TEU4	NDUF5_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 5	324					mitochondrial respiratory chain complex I assembly (GO:0032981)	extrinsic component of mitochondrial inner membrane (GO:0031314)	methyltransferase activity (GO:0008168)	p.A324T(1)									AAGAGGTTCCGCAACTGTGTC	0.353																																					p.A324T		Atlas-SNP	.											C20orf7,colon,carcinoma,0,1	.	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G970A						.	G	THR/ALA,THR/ALA	0,4406		0,0,2203	99	113	108		886,970	4.4	0.8	20	dbSNP_134	108	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	C20orf7	NM_001039375.2,NM_024120.4	58,58	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	296/318,324/346	13797788	1,13005	2203	4300	6503	SO:0001583	missense	79133	exon11			GGTTCCGCAACTG		CCDS13118.1, CCDS33441.1	20p12.1	2012-10-12	2012-05-08	2012-05-08	ENSG00000101247	ENSG00000101247		"Mitochondrial respiratory chain complex assembly factors"	15899	protein-coding gene	gene with protein product		612360	"chromosome 20 open reading frame 7"	C20orf7		18940309, 21607760	Standard	NM_024120		Approved	dJ842G6.1	uc002wom.3	Q5TEU4	OTTHUMG00000031909	ENST00000378106.5:c.970G>A	chr20.hg19:g.13797788G>A	ENSP00000367346:p.Ala324Thr	148.0	0.0		166.0	20.0	NM_024120	A8K166|Q6GPH3|Q9H6F4	Missense_Mutation	SNP	ENST00000378106.5	hg19	CCDS13118.1	.	.	.	.	.	.	.	.	.	.	G	15.45	2.838556	0.51057	0.0	1.16E-4	ENSG00000101247	ENST00000378106;ENST00000463598	D;T	0.83419	-1.72;-1.48	5.33	4.37	0.52481	.	0.000000	0.85682	D	0.000000	D	0.90335	0.6976	M	0.90870	3.155	0.54753	D	0.999987	D;D	0.59767	0.986;0.976	P;P	0.54815	0.761;0.581	D	0.91889	0.5522	10	0.62326	D	0.03	-49.6394	13.6665	0.62398	0.0:0.0:0.8451:0.1549	.	296;324	Q5TEU4-2;Q5TEU4	.;CT007_HUMAN	T	324;296	ENSP00000367346:A324T;ENSP00000420497:A296T	ENSP00000367346:A324T	A	+	1	0	C20orf7	13745788	1.000000	0.71417	0.849000	0.33467	0.069000	0.16628	8.052000	0.89448	1.224000	0.43551	-0.181000	0.13052	GCA	.	G|1.000;A|0.000		0.353	NDUFAF5-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078057.2	NM_001039375		A	13797788	G	A	13797788	3	1	304	1	0	0	0	0	1	0	0	0	2117	1087	38	1	1032	1	C20orf7	20	13797788	Missense_Mutation	SNP	G	TCGA-GJ-A3OU-01A-31D-A382-10		13797788	49227732	47	43732										
HRH3	11255	hgsc.bcm.edu	37	chr20	60791400	60791400	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	caccatcttcatgcgcttctCcagcgaggccgaggacgccg	11	16	3	0			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr20:60791400C>T	ENST00000340177.5	-	3	1284	c.1000G>A	c.(1000-1002)Gag>Aag	p.E334K	HRH3_ENST00000317393.6_Missense_Mutation_p.E334K	NM_007232.2	NP_009163.2	Q9Y5N1	HRH3_HUMAN	histamine receptor H3	334					brain development (GO:0007420)|drinking behavior (GO:0042756)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|learning (GO:0007612)|memory (GO:0007613)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of blood pressure (GO:0045776)|negative regulation of gamma-aminobutyric acid secretion (GO:0014053)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of serotonin secretion (GO:0014063)|neurotransmitter secretion (GO:0007269)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of epithelial cell proliferation (GO:0050679)|regulation of norepinephrine secretion (GO:0014061)|response to organic cyclic compound (GO:0014070)	integral component of plasma membrane (GO:0005887)|myelin sheath (GO:0043209)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|histamine receptor activity (GO:0004969)			breast(1)|endometrium(1)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	9	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;7.08e-07)		Betahistine(DB06698)|Histamine Phosphate(DB00667)|Mirtazapine(DB00370)	ATGCGCTTCTCCAGCGAGGCC	0.647																																					p.E334K		Atlas-SNP	.											.	HRH3	25	.	0			c.G1000A						.						16	16	16					20																	60791400		2196	4294	6490	SO:0001583	missense	11255	exon3			GCTTCTCCAGCGA	AF140538	CCDS13493.1	20q13.33	2013-09-19			ENSG00000101180	ENSG00000101180		"GPCR / Class A : Histamine receptors"	5184	protein-coding gene	gene with protein product		604525				10347254	Standard	NM_007232		Approved	GPCR97	uc002ycf.2	Q9Y5N1	OTTHUMG00000032899	ENST00000340177.5:c.1000G>A	chr20.hg19:g.60791400C>T	ENSP00000342560:p.Glu334Lys	93.0	0.0		84.0	12.0	NM_007232	Q4QRI7|Q9GZX2|Q9H4K8	Missense_Mutation	SNP	ENST00000340177.5	hg19	CCDS13493.1	.	.	.	.	.	.	.	.	.	.	C	17.58	3.425300	0.62733	.	.	ENSG00000101180	ENST00000340177;ENST00000317393;ENST00000370797	T;T	0.66995	-0.21;-0.24	4.61	4.61	0.57282	GPCR, rhodopsin-like superfamily (1);	0.342793	0.31797	N	0.007053	T	0.62295	0.2416	L	0.50333	1.59	0.35106	D	0.765707	P;B	0.43287	0.802;0.316	B;B	0.43508	0.422;0.23	T	0.66006	-0.6030	10	0.07644	T	0.81	-29.3882	17.4157	0.87499	0.0:1.0:0.0:0.0	.	334;334	Q9Y5N1-2;Q9Y5N1	.;HRH3_HUMAN	K	334;334;304	ENSP00000342560:E334K;ENSP00000321482:E334K	ENSP00000321482:E334K	E	-	1	0	HRH3	60224795	1.000000	0.71417	0.993000	0.49108	0.973000	0.67179	5.930000	0.70104	2.077000	0.62373	0.407000	0.27541	GAG	.	.		0.647	HRH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079994.1	NM_007232		T	60791400	C	T	60791400	3	4	304	1	0	0	0	0	1	0	0	0	7366	864	30	3	341	3	HRH3	20	60791400	Missense_Mutation	SNP	C	TCGA-GJ-A3OU-01A-31D-A382-10	46993612	60791400	2234120	48	43733										
PKDREJ	10343	hgsc.bcm.edu	37	chr22	46656291	46656291	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	acctgtcgtcttcttcaaggAcccatcaacctcgctgttgg	8	14	4	0			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chr22:46656291A>G	ENST00000253255.5	-	1	2928	c.2929T>C	c.(2929-2931)Tcc>Ccc	p.S977P		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	977					acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		TTCTTCAAGGACCCATCAACC	0.483																																					p.S977P		Atlas-SNP	.											.	PKDREJ	195	.	0			c.T2929C						.						145	142	143					22																	46656291		2203	4300	6503	SO:0001583	missense	10343	exon1			TCAAGGACCCATC	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like", "polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like", "polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.2929T>C	chr22.hg19:g.46656291A>G	ENSP00000253255:p.Ser977Pro	126.0	0.0		129.0	7.0	NM_006071	B1AJY3|O95850	Missense_Mutation	SNP	ENST00000253255.5	hg19	CCDS14073.1	.	.	.	.	.	.	.	.	.	.	A	12.05	1.821371	0.32237	.	.	ENSG00000130943	ENST00000253255	T	0.36157	1.27	4.91	0.123	0.14709	.	1.498420	0.03733	N	0.253852	T	0.27967	0.0689	L	0.40543	1.245	0.09310	N	1	B	0.12630	0.006	B	0.08055	0.003	T	0.12967	-1.0527	10	0.27082	T	0.32	-4.8539	4.3796	0.11288	0.3684:0.3815:0.2501:0.0	.	977	Q9NTG1	PKDRE_HUMAN	P	977	ENSP00000253255:S977P	ENSP00000253255:S977P	S	-	1	0	PKDREJ	45034955	0.000000	0.05858	0.005000	0.12908	0.210000	0.24377	-0.734000	0.04893	-0.003000	0.14444	-0.331000	0.08364	TCC	.	.		0.483	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071		G	46656291	A	G	46656291	3	3	304	1	0	0	0	0	1	0	0	0	11979	275	10	2	3836	2	PKDREJ	22	46656291	Missense_Mutation	SNP	A	TCGA-GJ-A3OU-01A-31D-A382-10		46656291	4648275	49	43734										
POLA1	5422	hgsc.bcm.edu	37	chrX	24861714	24861714	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	gcagtaacatcgattgtaagGcttcacctctgacctttaca	7	11	2	1			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chrX:24861714G>A	ENST00000379059.3	+	34	3964	c.3949G>A	c.(3949-3951)Gct>Act	p.A1317T	POLA1_ENST00000379068.3_Missense_Mutation_p.A1323T	NM_016937.3	NP_058633.2	P09884	DPOLA_HUMAN	polymerase (DNA directed), alpha 1, catalytic subunit	1317	DNA-binding region. {ECO:0000255}.				cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via nonhomologous end joining (GO:0006303)|G1/S transition of mitotic cell cycle (GO:0000082)|lagging strand elongation (GO:0006273)|leading strand elongation (GO:0006272)|mitotic cell cycle (GO:0000278)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|translesion synthesis (GO:0019985)|viral process (GO:0016032)	alpha DNA polymerase:primase complex (GO:0005658)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleoside binding (GO:0001882)|nucleotide binding (GO:0000166)|protein kinase binding (GO:0019901)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|skin(2)	11					Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Nelarabine(DB01280)	CGATTGTAAGGCTTCACCTCT	0.358																																					p.A1317T		Atlas-SNP	.											.	POLA1	117	.	0			c.G3949A						.						153	114	127					X																	24861714		2203	4300	6503	SO:0001583	missense	5422	exon34			TGTAAGGCTTCAC		CCDS14214.1	Xp22.1-p21.3	2014-01-30	2008-08-07	2006-09-26	ENSG00000101868	ENSG00000101868	2.7.7.7	"DNA polymerases"	9173	protein-coding gene	gene with protein product		312040	"polymerase (DNA directed), alpha", "polymerase (DNA directed), alpha 1", "N syndrome (mental retardation, malformations, chromosome breakage)"	POLA, NSX		1689958	Standard	NM_016937		Approved	p180	uc004dbl.3	P09884	OTTHUMG00000021277	ENST00000379059.3:c.3949G>A	chrX.hg19:g.24861714G>A	ENSP00000368349:p.Ala1317Thr	220.0	0.0		234.0	20.0	NM_016937	Q86UQ7	Missense_Mutation	SNP	ENST00000379059.3	hg19	CCDS14214.1	.	.	.	.	.	.	.	.	.	.	G	10.57	1.385879	0.25031	.	.	ENSG00000101868	ENST00000379068;ENST00000379059	T;T	0.18016	2.24;2.24	5.82	4.06	0.47325	Zinc finger, DNA-directed DNA polymerase, family B, alpha (1);	0.370388	0.31134	N	0.008182	T	0.10637	0.0260	N	0.20807	0.61	0.28163	N	0.928914	B	0.18968	0.032	B	0.15052	0.012	T	0.24764	-1.0151	10	0.18710	T	0.47	-3.5293	11.3692	0.49690	0.1512:0.0:0.8488:0.0	.	1317	P09884	DPOLA_HUMAN	T	1323;1317	ENSP00000368358:A1323T;ENSP00000368349:A1317T	ENSP00000368349:A1317T	A	+	1	0	POLA1	24771635	0.996000	0.38824	0.998000	0.56505	0.981000	0.71138	3.081000	0.50120	0.614000	0.30107	0.594000	0.82650	GCT	.	.		0.358	POLA1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056111.1	NM_016937		A	24861714	G	A	24861714	3	1	304	1	0	0	0	0	1	0	0	0	12196	1203	42	3	4083	3	POLA1	23	24861714	Missense_Mutation	SNP	G	TCGA-GJ-A3OU-01A-31D-A382-10		24861714	130408846	50	43735										
RAB40AL	282808	hgsc.bcm.edu	37	chrX	102192893	102192893	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0392156862745098	2	1	0.656377952755905	0.820472440944882	0.546981627296588	1	1	0	ggacaagctcccgctccccaTtgccttaagaagccacctca	7	17	1	1			TCGA-GJ-A3OU-01A-31D-A382-10	TCGA-GJ-A3OU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ee0963bc-f3c2-4738-bad9-84f54c572b69	a277f049-e97c-460c-8166-8424f4301d13	g.chrX:102192893T>C	ENST00000218249.5	+	1	694	c.647T>C	c.(646-648)aTt>aCt	p.I216T	LL0XNC01-237H1.3_ENST00000413528.1_RNA	NM_001031834.1	NP_001027004.1	P0C0E4	RB40L_HUMAN	RAB40A, member RAS oncogene family-like	216	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			endometrium(4)|large_intestine(2)|lung(3)|ovary(3)	12						CCGCTCCCCATTGCCTTAAGA	0.597																																					p.I216T		Atlas-SNP	.											.	RAB40AL	33	.	0			c.T647C						.						159	130	140					X																	102192893		2203	4300	6503	SO:0001583	missense	282808	exon1			TCCCCATTGCCTT	BC101169	CCDS35353.1	Xq22.2	2008-02-05			ENSG00000102128	ENSG00000102128			25410	protein-coding gene	gene with protein product	"Ras like GTPase"	300405					Standard	NM_001031834		Approved	RAR2, RLGP	uc004ejs.3	P0C0E4	OTTHUMG00000022084	ENST00000218249.5:c.647T>C	chrX.hg19:g.102192893T>C	ENSP00000218249:p.Ile216Thr	116.0	0.0		116.0	6.0	NM_001031834	Q495H3	Missense_Mutation	SNP	ENST00000218249.5	hg19	CCDS35353.1	.	.	.	.	.	.	.	.	.	.	.	9.632	1.136683	0.21123	.	.	ENSG00000102128	ENST00000218249	T	0.39229	1.09	0.819	0.819	0.18785	SOCS protein, C-terminal (4);	0.157212	0.24363	U	0.039163	T	0.08980	0.0222	N	0.00413	-1.525	0.23010	N	0.998434	B	0.02656	0.0	B	0.09377	0.004	T	0.37753	-0.9692	10	0.07175	T	0.84	.	5.6153	0.17428	0.0:1.0E-4:0.0:0.9999	.	216	P0C0E4	RB40L_HUMAN	T	216	ENSP00000218249:I216T	ENSP00000218249:I216T	I	+	2	0	RAB40AL	102079549	1.000000	0.71417	0.079000	0.20413	0.380000	0.30137	2.842000	0.48230	0.563000	0.29222	0.376000	0.23039	ATT	.	.		0.597	RAB40AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057679.1	NM_001031834		C	102192893	T	C	102192893	3	2	304	1	0	0	0	0	1	0	0	0	12955	1493	52	2	649	2	RAB40AL	23	102192893	Missense_Mutation	SNP	T	TCGA-GJ-A3OU-01A-31D-A382-10	77331179	102192893	53077667	51	43736										
PRAMEF4	400735	hgsc.bcm.edu	37	chr1	12942173	12942173	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0909090909090909	3	1	1.44	0	1.69411764705882	0.1	0.617038875103394	0	tcctcttggcattgaggaagCacccatgggccatagcttca	10	12	2	1	rs201789683		TCGA-GJ-A6C0-01A-12D-A30V-10	TCGA-GJ-A6C0-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36b33892-0a4d-42f1-8a5c-b51efd4d40a1	6fbe0c9d-a6ae-4737-8e50-926b0b027cdb	g.chr1:12942173C>G	ENST00000235349.5	-	3	447	c.377G>C	c.(376-378)tGc>tCc	p.C126S		NM_001009611.2	NP_001009611.1	O60810	PRAM4_HUMAN	PRAME family member 4	126					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(3)|skin(1)	24	Ovarian(185;0.249)	Lung NSC(185;3.67e-05)|all_lung(284;4.03e-05)|Renal(390;0.000147)|Breast(348;0.000278)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		ATTGAGGAAGCACCCATGGGC	0.493																																					p.C126S		Atlas-SNP	.											PRAMEF4,NS,carcinoma,0,1	PRAMEF4	62	.	0			c.G377C						.						44	56	52					1																	12942173		1381	2629	4010	SO:0001583	missense	400735	exon3			AGGAAGCACCCAT		CCDS30592.1	1p36.21	2013-01-17			ENSG00000243073	ENSG00000243073		"-"	31971	protein-coding gene	gene with protein product							Standard	NM_001009611		Approved	RP5-845O24.6	uc001aun.2	O60810	OTTHUMG00000001987	ENST00000235349.5:c.377G>C	chr1.hg19:g.12942173C>G	ENSP00000235349:p.Cys126Ser	22.0	1.0		45.0	3.0	NM_001009611	Q5LJB5	Missense_Mutation	SNP	ENST00000235349.5	hg19	CCDS30592.1	.	.	.	.	.	.	.	.	.	.	c	8.575	0.881031	0.17467	.	.	ENSG00000243073	ENST00000235349	T	0.18016	2.24	1.35	0.315	0.15852	.	1.371720	0.04624	N	0.402516	T	0.19406	0.0466	L	0.53671	1.685	0.09310	N	1	P	0.50272	0.933	P	0.44811	0.461	T	0.23190	-1.0195	10	0.33940	T	0.23	.	5.2546	0.15540	0.0:0.6297:0.3703:0.0	.	126	O60810	PRAM4_HUMAN	S	126	ENSP00000235349:C126S	ENSP00000235349:C126S	C	-	2	0	PRAMEF4	12864760	0.002000	0.14202	0.003000	0.11579	0.008000	0.06430	0.188000	0.17018	0.112000	0.17975	0.194000	0.17425	TGC	.	C|0.500;G|0.500		0.493	PRAMEF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005518.1	NM_001009611		G	12942173	C	G	12942173	3	3	305	1	0	0	0	0	1	0	0	0	12449	710	25	4	1067	4	PRAMEF4	1	12942173	Missense_Mutation	SNP	C	TCGA-GJ-A6C0-01A-12D-A30V-10		12942173	236308448	1	43737										
ABCA4	24	hgsc.bcm.edu	37	chr1	94564351	94564351	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0909090909090909	3	1	1.44	0	1.69411764705882	0.1	0.617038875103394	0	agccaaacccctcccttaccAcacggaagagcttgaagaag	8	14	0	3			TCGA-GJ-A6C0-01A-12D-A30V-10	TCGA-GJ-A6C0-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36b33892-0a4d-42f1-8a5c-b51efd4d40a1	6fbe0c9d-a6ae-4737-8e50-926b0b027cdb	g.chr1:94564351A>G	ENST00000370225.3	-	6	853	c.767T>C	c.(766-768)gTg>gCg	p.V256A	ABCA4_ENST00000535735.1_Splice_Site_p.V256A	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	256					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			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)		CTCCCTTACCACACGGAAGAG	0.572																																					p.V256A		Atlas-SNP	.											.	ABCA4	275	.	0			c.T767C						.						86	83	84					1																	94564351		2203	4300	6503	SO:0001630	splice_region_variant	24	exon6			CTTACCACACGGA	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.768+1T>C	chr1.hg19:g.94564351A>G		56.0	0.0		55.0	21.0	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	hg19	CCDS747.1	.	.	.	.	.	.	.	.	.	.	A	11.42	1.634269	0.29068	.	.	ENSG00000198691	ENST00000370225;ENST00000535735	D;D	0.90955	-2.64;-2.76	5.83	5.83	0.93111	.	0.258733	0.28146	U	0.016425	T	0.81029	0.4738	L	0.50333	1.59	0.39881	D	0.973643	B;B	0.18968	0.032;0.012	B;B	0.25884	0.064;0.004	T	0.77281	-0.2646	10	0.08599	T	0.76	.	15.8674	0.79074	1.0:0.0:0.0:0.0	.	256;256	F5H6E5;P78363	.;ABCA4_HUMAN	A	256	ENSP00000359245:V256A;ENSP00000437682:V256A	ENSP00000359245:V256A	V	-	2	0	ABCA4	94336939	1.000000	0.71417	0.998000	0.56505	0.237000	0.25408	6.888000	0.75622	2.225000	0.72522	0.460000	0.39030	GTG	.	.		0.572	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350	Missense_Mutation	G	94564351	A	G	94564351	5	3	305	1	0	0	0	0	0	0	1	0	34	173	6	2	6234	2	ABCA4	1	94564351	Splice_Site	SNP	A	TCGA-GJ-A6C0-01A-12D-A30V-10	81622178	94564351	154686270	2	43738										
CYP1B1	1545	hgsc.bcm.edu	37	chr2	38301745	38301745	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0909090909090909	3	1	1.44	0	1.69411764705882	0.1	0.617038875103394	0	gctgaagttgcggttgagctGctcgaattcgcggaaaacgg	15	8	0	2			TCGA-GJ-A6C0-01A-12D-A30V-10	TCGA-GJ-A6C0-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36b33892-0a4d-42f1-8a5c-b51efd4d40a1	6fbe0c9d-a6ae-4737-8e50-926b0b027cdb	g.chr2:38301745G>A	ENST00000260630.3	-	2	1188	c.787C>T	c.(787-789)Cag>Tag	p.Q263*	CYP1B1_ENST00000407341.1_Nonsense_Mutation_p.Q263*|CYP1B1-AS1_ENST00000431999.1_RNA|CYP1B1_ENST00000494864.1_Intron|CYP1B1-AS1_ENST00000589303.1_RNA	NM_000104.3	NP_000095	Q16678	CP1B1_HUMAN	cytochrome P450, family 1, subfamily B, polypeptide 1	263					angiogenesis (GO:0001525)|arachidonic acid metabolic process (GO:0019369)|blood vessel morphogenesis (GO:0048514)|cell adhesion (GO:0007155)|cellular aromatic compound metabolic process (GO:0006725)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to organic cyclic compound (GO:0071407)|collagen fibril organization (GO:0030199)|endothelial cell migration (GO:0043542)|endothelial cell-cell adhesion (GO:0071603)|epoxygenase P450 pathway (GO:0019373)|estrogen metabolic process (GO:0008210)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|membrane lipid catabolic process (GO:0046466)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nitric oxide biosynthetic process (GO:0006809)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to toxic substance (GO:0009636)|retinal blood vessel morphogenesis (GO:0061304)|retinal metabolic process (GO:0042574)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|toxin metabolic process (GO:0009404)|trabecular meshwork development (GO:0002930)|visual perception (GO:0007601)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)	13		all_hematologic(82;0.21)			Amodiaquine(DB00613)|Arsenic trioxide(DB01169)|Biotin(DB00121)|Caffeine(DB00201)|Clozapine(DB00363)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Flutamide(DB00499)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Melatonin(DB01065)|Mitoxantrone(DB01204)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Primaquine(DB01087)|Procarbazine(DB01168)|Progesterone(DB00396)|Propofol(DB00818)|Tamoxifen(DB00675)|Testosterone(DB00624)|Theophylline(DB00277)	CGGTTGAGCTGCTCGAATTCG	0.642																																					p.Q263X		Atlas-SNP	.											.	CYP1B1	39	.	0			c.C787T						.						43	39	40					2																	38301745		2203	4300	6503	SO:0001587	stop_gained	1545	exon2			TGAGCTGCTCGAA	U56438	CCDS1793.1	2p22.2	2008-02-05	2003-01-14		ENSG00000138061	ENSG00000138061		"Cytochrome P450s"	2597	protein-coding gene	gene with protein product		601771	"cytochrome P450, subfamily I (dioxin-inducible), polypeptide 1 (glaucoma 3, primary infantile)"	GLC3A		8175734, 15128046	Standard	NM_000104		Approved	CP1B	uc002rqo.2	Q16678	OTTHUMG00000100970	ENST00000260630.3:c.787C>T	chr2.hg19:g.38301745G>A	ENSP00000260630:p.Gln263*	204.0	0.0		194.0	11.0	NM_000104	Q5TZW8|Q93089|Q9H316	Nonsense_Mutation	SNP	ENST00000260630.3	hg19	CCDS1793.1	.	.	.	.	.	.	.	.	.	.	G	38	6.657105	0.97739	.	.	ENSG00000138061	ENST00000260630;ENST00000407341	.	.	.	4.51	-0.0439	0.13857	.	0.534588	0.20863	N	0.084312	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	.	7.9908	0.30239	0.0:0.255:0.4596:0.2854	.	.	.	.	X	263	.	ENSP00000260630:Q263X	Q	-	1	0	CYP1B1	38155249	0.000000	0.05858	0.906000	0.35671	0.943000	0.58893	0.097000	0.15168	0.128000	0.18479	0.650000	0.86243	CAG	.	.		0.642	CYP1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218580.3	NM_000104		A	38301745	G	A	38301745	4	1	305	1	0	0	0	0	0	1	0	0	4153	1328	46	3	852	3	CYP1B1	2	38301745	Nonsense_Mutation	SNP	G	TCGA-GJ-A6C0-01A-12D-A30V-10		38301745	204897628	3	43739										
BAZ2B	29994	hgsc.bcm.edu	37	chr2	160206490	160206490	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0909090909090909	3	1	1.44	0	1.69411764705882	0.1	0.617038875103394	0	tccctggaccacttgaaccaGtattaaacagattattagag	7	9	0	3	rs372658436		TCGA-GJ-A6C0-01A-12D-A30V-10	TCGA-GJ-A6C0-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36b33892-0a4d-42f1-8a5c-b51efd4d40a1	6fbe0c9d-a6ae-4737-8e50-926b0b027cdb	g.chr2:160206490G>A	ENST00000392783.2	-	28	5087	c.4592C>T	c.(4591-4593)aCt>aTt	p.T1531I	BAZ2B_ENST00000343439.5_Missense_Mutation_p.T1431I|BAZ2B_ENST00000392782.1_Missense_Mutation_p.T1495I|BAZ2B_ENST00000355831.2_Missense_Mutation_p.T1497I	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	1531					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						ACTTGAACCAGTATTAAACAG	0.418																																					p.T1531I		Atlas-SNP	.											.	BAZ2B	196	.	0			c.C4592T						.						147	140	142					2																	160206490		1997	4184	6181	SO:0001583	missense	29994	exon28			GAACCAGTATTAA	AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636		"Zinc fingers, PHD-type"	963	protein-coding gene	gene with protein product		605683				10662543	Standard	XM_005246488		Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.4592C>T	chr2.hg19:g.160206490G>A	ENSP00000376534:p.Thr1531Ile	135.0	0.0		134.0	11.0	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	hg19	CCDS2209.2	.	.	.	.	.	.	.	.	.	.	G	1.684	-0.505713	0.04261	.	.	ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831;ENST00000343439	T;T;T;T	0.06849	3.25;3.25;3.25;3.25	6.17	4.35	0.52113	.	0.501674	0.14458	U	0.318345	T	0.06462	0.0166	N	0.22421	0.69	0.09310	N	1	B;B	0.33739	0.045;0.422	B;B	0.24848	0.045;0.056	T	0.28364	-1.0046	10	0.38643	T	0.18	2.0E-4	13.6731	0.62438	0.0:0.1195:0.7559:0.1246	.	1495;1531	Q9UIF8-5;Q9UIF8	.;BAZ2B_HUMAN	I	1495;1531;1497;1431	ENSP00000376533:T1495I;ENSP00000376534:T1531I;ENSP00000348087:T1497I;ENSP00000339670:T1431I	ENSP00000339670:T1431I	T	-	2	0	BAZ2B	159914736	0.928000	0.31464	0.001000	0.08648	0.042000	0.13812	5.458000	0.66679	0.906000	0.36621	-0.150000	0.13652	ACT	.	.		0.418	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2			A	160206490	G	A	160206490	3	1	305	1	0	0	0	0	1	0	0	0	1332	1029	36	3	1954	3	BAZ2B	2	160206490	Missense_Mutation	SNP	G	TCGA-GJ-A6C0-01A-12D-A30V-10	121904745	160206490	82992883	4	43740										
CHST13	166012	hgsc.bcm.edu	37	chr3	126260674	126260674	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0909090909090909	3	1	1.44	0	1.69411764705882	0.1	0.617038875103394	0	cggcagcgcctgctacagccGgaggacctgcggcacgtgct	15	15	0	0			TCGA-GJ-A6C0-01A-12D-A30V-10	TCGA-GJ-A6C0-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36b33892-0a4d-42f1-8a5c-b51efd4d40a1	6fbe0c9d-a6ae-4737-8e50-926b0b027cdb	g.chr3:126260674G>A	ENST00000319340.2	+	3	329	c.279G>A	c.(277-279)ccG>ccA	p.P93P		NM_152889.2	NP_690849.1	Q8NET6	CHSTD_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 13	93					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin 4-sulfotransferase activity (GO:0047756)|N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)			central_nervous_system(1)|large_intestine(2)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(114;0.151)		TGCTACAGCCGGAGGACCTGC	0.706																																					p.P93P		Atlas-SNP	.											.	CHST13	21	.	0			c.G279A						.						17	13	14					3																	126260674		2181	4259	6440	SO:0001819	synonymous_variant	166012	exon3			ACAGCCGGAGGAC	AY120869	CCDS3039.1	3q21.3	2008-02-05			ENSG00000180767	ENSG00000180767	2.8.2.5	"Sulfotransferases, membrane-bound"	21755	protein-coding gene	gene with protein product		610124				12080076	Standard	NM_152889		Approved	C4ST3	uc003eja.3	Q8NET6	OTTHUMG00000162721	ENST00000319340.2:c.279G>A	chr3.hg19:g.126260674G>A		50.0	0.0		49.0	15.0	NM_152889	Q3SYA3|Q3SYA5	Silent	SNP	ENST00000319340.2	hg19	CCDS3039.1																																																																																			.	.		0.706	CHST13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370201.2	NM_152889		A	126260674	G	A	126260674	2	1	305	1	0	0	0	0	0	0	0	1	3403	1103	39	1		1	CHST13	3	126260674	Silent	SNP	G	TCGA-GJ-A6C0-01A-12D-A30V-10		126260674	71761756	5	43741										
C4orf14	84273	hgsc.bcm.edu	37	chr4	57842963	57842963	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0909090909090909	3	1	1.44	0	1.69411764705882	0.1	0.617038875103394	0	tcccacagtcgctcccgcagCctctgccggtagccaggagc	11	18	1	0			TCGA-GJ-A6C0-01A-12D-A30V-10	TCGA-GJ-A6C0-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36b33892-0a4d-42f1-8a5c-b51efd4d40a1	6fbe0c9d-a6ae-4737-8e50-926b0b027cdb	g.chr4:57842963C>T	ENST00000264230.4	-	1	2026	c.789G>A	c.(787-789)agG>agA	p.R263R	POLR2B_ENST00000381227.1_5'Flank|POLR2B_ENST00000441246.2_5'Flank|POLR2B_ENST00000314595.5_5'Flank|POLR2B_ENST00000431623.2_5'Flank	NM_032313.2	NP_115689.1	Q8NC60	NOA1_HUMAN	nitric oxide associated 1	263	CP-type G. {ECO:0000255|PROSITE- ProRule:PRU01058}.				apoptotic process (GO:0006915)|GTP catabolic process (GO:0006184)|mitochondrial translation (GO:0032543)|regulation of cell death (GO:0010941)|regulation of cellular respiration (GO:0043457)|ribosome biogenesis (GO:0042254)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)										GCTCCCGCAGCCTCTGCCGGT	0.701																																					p.R263R		Atlas-SNP	.											.	.	.	.	0			c.G789A						.						28	34	32					4																	57842963		2195	4279	6474	SO:0001819	synonymous_variant	84273	exon1			CCGCAGCCTCTGC	AK098215	CCDS3510.1	4q12	2013-05-24	2011-10-19	2011-10-19	ENSG00000084092	ENSG00000084092			28473	protein-coding gene	gene with protein product	"nitric oxide synthase, mitochondrial (putative)", "mitochondrial GTPase 3 homolog (S. cerevisiae)"	614919	"chromosome 4 open reading frame 14"	C4orf14		16380119, 2118999, 21771794, 22447445	Standard	NM_032313		Approved	MGC3232, hAtNOS1, hNOA1, MTG3	uc003hck.3	Q8NC60	OTTHUMG00000128773	ENST00000264230.4:c.789G>A	chr4.hg19:g.57842963C>T		84.0	0.0		64.0	10.0	NM_032313	Q8N7L6|Q9BSQ9	Silent	SNP	ENST00000264230.4	hg19	CCDS3510.1																																																																																			.	.		0.701	NOA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250694.2	NM_032313		T	57842963	C	T	57842963	2	4	305	1	0	0	0	0	0	0	0	1	2253	738	26	3		3	C4orf14	4	57842963	Silent	SNP	C	TCGA-GJ-A6C0-01A-12D-A30V-10		57842963	133311313	6	43742										
IRX2	153572	hgsc.bcm.edu	37	chr5	2751518	2751518	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0909090909090909	3	1	1.44	0	1.69411764705882	0.1	0.617038875103394	0	ctggtacaggtagccctgcgGgtaggacatggtgggcgcgg	19	9	0	0			TCGA-GJ-A6C0-01A-12D-A30V-10	TCGA-GJ-A6C0-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36b33892-0a4d-42f1-8a5c-b51efd4d40a1	6fbe0c9d-a6ae-4737-8e50-926b0b027cdb	g.chr5:2751518G>T	ENST00000382611.6	-	1	258	c.10C>A	c.(10-12)Ccg>Acg	p.P4T	IRX2_ENST00000302057.5_Missense_Mutation_p.P4T|C5orf38_ENST00000457752.2_5'Flank|IRX2_ENST00000502957.1_Intron|C5orf38_ENST00000397835.4_5'Flank|C5orf38_ENST00000515640.1_5'Flank|C5orf38_ENST00000505778.1_5'Flank|C5orf38_ENST00000334000.3_5'Flank	NM_001134222.1	NP_001127694.1	Q9BZI1	IRX2_HUMAN	iroquois homeobox 2	4					proximal/distal pattern formation involved in metanephric nephron development (GO:0072272)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(1)|central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(2)|lung(12)|prostate(1)|skin(2)	26				GBM - Glioblastoma multiforme(108;0.204)		TAGCCCTGCGGGTAGGACATG	0.801																																					p.P4T		Atlas-SNP	.											.	IRX2	60	.	0			c.C10A						.						2	2	2					5																	2751518		1323	2902	4225	SO:0001583	missense	153572	exon1			CCTGCGGGTAGGA	AF319967	CCDS3868.1	5p15.33	2011-06-20	2007-07-13		ENSG00000170561	ENSG00000170561		"Homeoboxes / TALE class"	14359	protein-coding gene	gene with protein product		606198				11435706	Standard	NM_033267		Approved		uc003jdb.3	Q9BZI1	OTTHUMG00000090377	ENST00000382611.6:c.10C>A	chr5.hg19:g.2751518G>T	ENSP00000372056:p.Pro4Thr	32.0	0.0		23.0	10.0	NM_001134222	Q68A19|Q7Z2I7	Missense_Mutation	SNP	ENST00000382611.6	hg19	CCDS3868.1	.	.	.	.	.	.	.	.	.	.	G	15.29	2.788514	0.49997	.	.	ENSG00000170561	ENST00000382611;ENST00000302057	D;D	0.87256	-2.23;-2.23	3.23	2.34	0.29019	.	0.061211	0.64402	U	0.000002	D	0.91680	0.7370	M	0.76574	2.34	0.58432	D	0.999994	D	0.89917	1.0	D	0.69307	0.963	D	0.91658	0.5340	10	0.87932	D	0	-20.0605	11.948	0.52938	0.0:0.0:0.8245:0.1755	.	4	Q9BZI1	IRX2_HUMAN	T	4	ENSP00000372056:P4T;ENSP00000307006:P4T	ENSP00000307006:P4T	P	-	1	0	IRX2	2804518	1.000000	0.71417	0.996000	0.52242	0.965000	0.64279	7.723000	0.84788	0.716000	0.32124	0.289000	0.19496	CCG	.	.		0.801	IRX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206749.2			T	2751518	G	T	2751518	3	4	305	1	0	0	0	0	1	0	0	0	7853	1232	43	3	1421	3	IRX2	5	2751518	Missense_Mutation	SNP	G	TCGA-GJ-A6C0-01A-12D-A30V-10		2751518	178163742	7	43743										
RAPGEF5	9771	hgsc.bcm.edu	37	chr7	22347988	22347988	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0909090909090909	3	1	1.44	0	1.69411764705882	0.1	0.617038875103394	0	tgccacctctggcaggaatgAgaggcacaagttgcagtaaa	12	9	1	1			TCGA-GJ-A6C0-01A-12D-A30V-10	TCGA-GJ-A6C0-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36b33892-0a4d-42f1-8a5c-b51efd4d40a1	6fbe0c9d-a6ae-4737-8e50-926b0b027cdb	g.chr7:22347988A>T	ENST00000405243.1	-	5	733	c.650T>A	c.(649-651)cTc>cAc	p.L217H	RAPGEF5_ENST00000344041.6_Missense_Mutation_p.L64H			Q92565	RPGF5_HUMAN	Rap guanine nucleotide exchange factor (GEF) 5	0					nervous system development (GO:0007399)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|small GTPase mediated signal transduction (GO:0007264)	nucleus (GO:0005634)	GTP-dependent protein binding (GO:0030742)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(2)|ovary(1)	6						GGCAGGAATGAGAGGCACAAG	0.403																																					p.L64H		Atlas-SNP	.											.	RAPGEF5	96	.	0			c.T191A						.						70	66	67					7																	22347988		1937	4120	6057	SO:0001583	missense	9771	exon5			GGAATGAGAGGCA	D87467	CCDS55093.1	7p15.3	2004-03-01			ENSG00000136237	ENSG00000136237			16862	protein-coding gene	gene with protein product	"M-Ras-regulated GEF"	609527				9039502, 10486569	Standard	NM_012294		Approved	KIAA0277, GFR, MR-GEF	uc003svg.3	Q92565	OTTHUMG00000152525	ENST00000405243.1:c.650T>A	chr7.hg19:g.22347988A>T	ENSP00000384870:p.Leu217His	61.0	0.0		64.0	19.0	NM_012294	A4D140|Q8IXU5	Missense_Mutation	SNP	ENST00000405243.1	hg19		.	.	.	.	.	.	.	.	.	.	A	10.46	1.357644	0.24598	.	.	ENSG00000136237	ENST00000344041;ENST00000405243	T;T	0.13778	2.56;2.56	5.92	5.92	0.95590	.	0.415413	0.20130	N	0.098603	T	0.14700	0.0355	L	0.38175	1.15	0.39726	D	0.971546	B	0.18741	0.03	B	0.15052	0.012	T	0.02781	-1.1111	10	0.72032	D	0.01	.	16.371	0.83361	1.0:0.0:0.0:0.0	.	64	A8MQ07	.	H	64;217	ENSP00000343656:L64H;ENSP00000384870:L217H	ENSP00000343656:L64H	L	-	2	0	RAPGEF5	22314513	0.990000	0.36364	0.998000	0.56505	0.964000	0.63967	4.549000	0.60726	2.267000	0.75376	0.477000	0.44152	CTC	.	.		0.403	RAPGEF5-002	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000326591.1	NM_012294		T	22347988	A	T	22347988	3	4	305	1	0	0	0	0	1	0	0	0	13062	304	11	4	2089	4	RAPGEF5	7	22347988	Missense_Mutation	SNP	A	TCGA-GJ-A6C0-01A-12D-A30V-10		22347988	136790675	8	43744										
MUC17	140453	hgsc.bcm.edu	37	chr7	100683043	100683043	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0909090909090909	3	1	1.44	0	1.69411764705882	0.1	0.617038875103394	0	gttgacaccagcatacctgtCaccacttctactgaagccag	7	14	2	2	rs371681290		TCGA-GJ-A6C0-01A-12D-A30V-10	TCGA-GJ-A6C0-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36b33892-0a4d-42f1-8a5c-b51efd4d40a1	6fbe0c9d-a6ae-4737-8e50-926b0b027cdb	g.chr7:100683043C>T	ENST00000306151.4	+	3	8410	c.8346C>T	c.(8344-8346)gtC>gtT	p.V2782V		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2782	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)	p.V2782V(1)		NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					GCATACCTGTCACCACTTCTA	0.473																																					p.V2782V		Atlas-SNP	.											MUC17,NS,carcinoma,0,1	MUC17	804	.	1	Substitution - coding silent(1)	lung(1)	c.C8346T						.	C		0,4406		0,0,2203	252	244	246		8346	-2.4	0	7		246	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MUC17	NM_001040105.1		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		2782/4494	100683043	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			ACCTGTCACCACT	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.8346C>T	chr7.hg19:g.100683043C>T		84.0	2.0		74.0	11.0	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	hg19	CCDS34711.1																																																																																			.	.		0.473	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		T	100683043	C	T	100683043	2	4	305	1	0	0	0	0	0	0	0	1	9983	813	29	3		3	MUC17	7	100683043	Silent	SNP	C	TCGA-GJ-A6C0-01A-12D-A30V-10	78335055	100683043	58455620	9	43745										
ARHGEF10	9639	hgsc.bcm.edu	37	chr8	1871942	1871942	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0909090909090909	3	1	1.44	0	1.69411764705882	0.1	0.617038875103394	0	gtctgttgtttctggcagatCtgggcgaccgacgttcttta	12	9	4	1			TCGA-GJ-A6C0-01A-12D-A30V-10	TCGA-GJ-A6C0-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36b33892-0a4d-42f1-8a5c-b51efd4d40a1	6fbe0c9d-a6ae-4737-8e50-926b0b027cdb	g.chr8:1871942C>T	ENST00000398564.1	+	21	2465	c.2465C>T	c.(2464-2466)tCt>tTt	p.S822F	ARHGEF10_ENST00000520359.1_Missense_Mutation_p.S759F|ARHGEF10_ENST00000262112.6_Missense_Mutation_p.S822F|ARHGEF10_ENST00000349830.3_Missense_Mutation_p.S797F|ARHGEF10_ENST00000518288.1_Missense_Mutation_p.S821F			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	822					centrosome duplication (GO:0051298)|myelination in peripheral nervous system (GO:0022011)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|cytosol (GO:0005829)	kinesin binding (GO:0019894)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(3)|large_intestine(11)|lung(11)|prostate(3)|skin(3)|stomach(3)|urinary_tract(1)	35		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)		TCTGGCAGATCTGGGCGACCG	0.468																																					p.S797F		Atlas-SNP	.											.	ARHGEF10	255	.	0			c.C2390T						.						134	110	118					8																	1871942		2203	4300	6503	SO:0001583	missense	9639	exon21			GCAGATCTGGGCG	AF009205	CCDS34794.1	8p23	2014-09-17			ENSG00000104728	ENSG00000104728		"Rho guanine nucleotide exchange factors"	14103	protein-coding gene	gene with protein product		608136				9205841, 16896804	Standard	XM_005266039		Approved	KIAA0294, Gef10	uc003wpr.3	O15013	OTTHUMG00000163626	ENST00000398564.1:c.2465C>T	chr8.hg19:g.1871942C>T	ENSP00000381571:p.Ser822Phe	137.0	0.0		110.0	10.0	NM_014629	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Missense_Mutation	SNP	ENST00000398564.1	hg19		.	.	.	.	.	.	.	.	.	.	C	19.97	3.924475	0.73213	.	.	ENSG00000104728	ENST00000349830;ENST00000520359;ENST00000518288;ENST00000398564;ENST00000262112;ENST00000522435	T;T;T;T;T;T	0.61742	0.09;0.14;0.08;0.08;0.11;0.27	5.32	5.32	0.75619	.	0.062472	0.64402	D	0.000003	T	0.79293	0.4421	M	0.86651	2.83	0.80722	D	1	D;D;D	0.60160	0.978;0.987;0.963	P;P;D	0.64687	0.77;0.885;0.928	T	0.83299	-0.0029	10	0.87932	D	0	-28.0951	18.993	0.92801	0.0:1.0:0.0:0.0	.	822;759;797	O15013;O15013-7;O15013-5	ARHGA_HUMAN;.;.	F	797;759;821;822;822;470	ENSP00000340297:S797F;ENSP00000427909:S759F;ENSP00000431012:S821F;ENSP00000381571:S822F;ENSP00000262112:S822F;ENSP00000427768:S470F	ENSP00000262112:S822F	S	+	2	0	ARHGEF10	1859349	0.988000	0.35896	0.962000	0.40283	0.508000	0.34012	2.669000	0.46825	2.465000	0.83290	0.655000	0.94253	TCT	.	.		0.468	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding				T	1871942	C	T	1871942	3	4	305	1	0	0	0	0	1	0	0	0	894	913	32	3	2468	3	ARHGEF10	8	1871942	Missense_Mutation	SNP	C	TCGA-GJ-A6C0-01A-12D-A30V-10		1871942	144492080	10	43746										
MUC2	4583	hgsc.bcm.edu	37	chr11	1085941	1085941	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0909090909090909	3	1	1.44	0	1.69411764705882	0.1	0.617038875103394	0	ctctcctccgggcagaggacGgagctgaagttggaagacaa	14	10	1	3			TCGA-GJ-A6C0-01A-12D-A30V-10	TCGA-GJ-A6C0-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36b33892-0a4d-42f1-8a5c-b51efd4d40a1	6fbe0c9d-a6ae-4737-8e50-926b0b027cdb	g.chr11:1085941G>T	ENST00000441003.2	+	22	2808	c.2781G>T	c.(2779-2781)acG>acT	p.T927T	MUC2_ENST00000359061.5_Silent_p.T927T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	927	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.T927T(2)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	GGCAGAGGACGGAGCTGAAGT	0.652																																					p.T927T		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	.	2	Substitution - coding silent(2)	lung(2)	c.G2781T						.						49	56	54					11																	1085941		2122	4215	6337	SO:0001819	synonymous_variant	4583	exon22			GAGGACGGAGCTG	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.2781G>T	chr11.hg19:g.1085941G>T		25.0	0.0		27.0	3.0	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	hg19																																																																																				.	.		0.652	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1085941	G	T	1085941	2	4	305	1	0	0	0	0	0	0	0	1	9984	1103	39	1		1	MUC2	11	1085941	Silent	SNP	G	TCGA-GJ-A6C0-01A-12D-A30V-10		1085941	133920575	11	43747										
RRM1	6240	hgsc.bcm.edu	37	chr11	4148364	4148364	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0909090909090909	3	1	1.44	0	1.69411764705882	0.1	0.617038875103394	0	acccttttgagagtgcagaaGcccagttactgaataagcag	10	9	0	3			TCGA-GJ-A6C0-01A-12D-A30V-10	TCGA-GJ-A6C0-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36b33892-0a4d-42f1-8a5c-b51efd4d40a1	6fbe0c9d-a6ae-4737-8e50-926b0b027cdb	g.chr11:4148364G>T	ENST00000300738.5	+	14	1774	c.1570G>T	c.(1570-1572)Gcc>Tcc	p.A524S	RRM1_ENST00000534285.1_Missense_Mutation_p.A302S|RRM1_ENST00000423050.2_Missense_Mutation_p.A427S|RRM1_ENST00000537197.1_Missense_Mutation_p.A186S	NM_001033.3	NP_001024.1	P23921	RIR1_HUMAN	ribonucleotide reductase M1	524					cell proliferation in forebrain (GO:0021846)|deoxyribonucleotide biosynthetic process (GO:0009263)|DNA replication (GO:0006260)|male gonad development (GO:0008584)|mitotic cell cycle (GO:0000278)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein heterotetramerization (GO:0051290)|pyrimidine nucleobase metabolic process (GO:0006206)|response to ionizing radiation (GO:0010212)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor (GO:0004748)			breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|skin(2)	14		Medulloblastoma(188;0.0025)|Breast(177;0.00502)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0848)|LUSC - Lung squamous cell carcinoma(625;0.205)	Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Hydroxyurea(DB01005)	GAGTGCAGAAGCCCAGTTACT	0.468																																					p.A524S	NSCLC(45;1345 1376 6258 22925)|Ovarian(34;894 1053 6175 12768)	Atlas-SNP	.											.	RRM1	31	.	0			c.G1570T						.						116	119	118					11																	4148364		2201	4298	6499	SO:0001583	missense	6240	exon14			GCAGAAGCCCAGT	X59543	CCDS7750.1	11p15.5	2009-07-10	2008-03-11		ENSG00000167325	ENSG00000167325	1.17.14.1		10451	protein-coding gene	gene with protein product		180410	"ribonucleotide reductase M1 polypeptide"			7557993	Standard	NM_001033		Approved		uc001lyw.4	P23921	OTTHUMG00000133361	ENST00000300738.5:c.1570G>T	chr11.hg19:g.4148364G>T	ENSP00000300738:p.Ala524Ser	102.0	0.0		91.0	4.0	NM_001033	Q9UNN2	Missense_Mutation	SNP	ENST00000300738.5	hg19	CCDS7750.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.099144	0.76983	.	.	ENSG00000167325	ENST00000300738;ENST00000423050;ENST00000536894;ENST00000534285;ENST00000543838;ENST00000537197	T;T;T;T	0.54071	0.59;0.59;0.59;0.59	5.54	5.54	0.83059	Ribonucleoside-diphosphate reductase, alpha subunit (1);Ribonucleotide reductase large subunit, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.73776	0.3630	M	0.85777	2.775	0.80722	D	1	P	0.38250	0.624	P	0.53689	0.732	T	0.75045	-0.3456	10	0.59425	D	0.04	-10.2399	18.4056	0.90535	0.0:0.0:1.0:0.0	.	524	P23921	RIR1_HUMAN	S	524;427;437;302;302;186	ENSP00000300738:A524S;ENSP00000390539:A427S;ENSP00000431464:A302S;ENSP00000442148:A186S	ENSP00000300738:A524S	A	+	1	0	RRM1	4104940	1.000000	0.71417	1.000000	0.80357	0.456000	0.32438	9.352000	0.97076	2.775000	0.95449	0.655000	0.94253	GCC	.	.		0.468	RRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257197.1	NM_001033		T	4148364	G	T	4148364	3	4	305	1	0	0	0	0	1	0	0	0	13696	971	34	3	1624	3	RRM1	11	4148364	Missense_Mutation	SNP	G	TCGA-GJ-A6C0-01A-12D-A30V-10	3062423	4148364	130858152	12	43748										
MRGPRX3	117195	hgsc.bcm.edu	37	chr11	18159634	18159634	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0909090909090909	3	1	1.44	0	1.69411764705882	0.1	0.617038875103394	0	ctggttctccagagggctctGcaggacacgcctgaggtgga	15	11	2	2			TCGA-GJ-A6C0-01A-12D-A30V-10	TCGA-GJ-A6C0-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36b33892-0a4d-42f1-8a5c-b51efd4d40a1	6fbe0c9d-a6ae-4737-8e50-926b0b027cdb	g.chr11:18159634G>T	ENST00000396275.2	+	3	1246	c.885G>T	c.(883-885)ctG>ctT	p.L295L		NM_054031.3	NP_473372.3	Q96LB0	MRGX3_HUMAN	MAS-related GPR, member X3	295						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						AGAGGGCTCTGCAGGACACGC	0.557																																					p.L295L		Atlas-SNP	.											.	MRGPRX3	59	.	0			c.G885T						.																																			SO:0001819	synonymous_variant	117195	exon3			GGCTCTGCAGGAC		CCDS7830.1	11p15.1	2013-10-10			ENSG00000179826	ENSG00000179826		"GPCR / Class A : Orphans"	17980	protein-coding gene	gene with protein product		607229				11551509	Standard	NM_054031		Approved	MRGX3	uc001mnu.3	Q96LB0	OTTHUMG00000166435	ENST00000396275.2:c.885G>T	chr11.hg19:g.18159634G>T		51.0	0.0		53.0	19.0	NM_054031	B0M0L1|Q8TDE0|Q8TDE1	Silent	SNP	ENST00000396275.2	hg19	CCDS7830.1																																																																																			.	.		0.557	MRGPRX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389767.1	NM_054031		T	18159634	G	T	18159634	2	4	305	1	0	0	0	0	0	0	0	1	9777	1306	46	3		3	MRGPRX3	11	18159634	Silent	SNP	G	TCGA-GJ-A6C0-01A-12D-A30V-10	14011270	18159634	116846882	13	43749										
OR6M1	390261	hgsc.bcm.edu	37	chr11	123676932	123676932	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0909090909090909	3	1	1.44	0	1.69411764705882	0.1	0.617038875103394	0	atccatatcagggagatgatGgtgatgtttcctgttgctgt	12	6	1	3			TCGA-GJ-A6C0-01A-12D-A30V-10	TCGA-GJ-A6C0-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36b33892-0a4d-42f1-8a5c-b51efd4d40a1	6fbe0c9d-a6ae-4737-8e50-926b0b027cdb	g.chr11:123676932G>T	ENST00000309154.2	-	1	163	c.126C>A	c.(124-126)acC>acA	p.T42T		NM_001005325.1	NP_001005325.1	Q8NGM8	OR6M1_HUMAN	olfactory receptor, family 6, subfamily M, member 1	42						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|prostate(2)|skin(5)|urinary_tract(1)	29		Breast(109;0.0109)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.028)		GGGAGATGATGGTGATGTTTC	0.413																																					p.T42T		Atlas-SNP	.											.	OR6M1	60	.	0			c.C126A						.						155	134	141					11																	123676932		2202	4299	6501	SO:0001819	synonymous_variant	390261	exon1			GATGATGGTGATG	AB065762	CCDS31696.1	11q24.1	2012-08-09			ENSG00000196099	ENSG00000196099		"GPCR / Class A : Olfactory receptors"	14711	protein-coding gene	gene with protein product							Standard	NM_001005325		Approved		uc010rzz.2	Q8NGM8	OTTHUMG00000166012	ENST00000309154.2:c.126C>A	chr11.hg19:g.123676932G>T		129.0	0.0		100.0	15.0	NM_001005325	B2RNK0|Q6IEW9|Q96R37	Silent	SNP	ENST00000309154.2	hg19	CCDS31696.1																																																																																			.	.		0.413	OR6M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387437.1	NM_001005325		T	123676932	G	T	123676932	2	4	305	1	0	0	0	0	0	0	0	1	11214	1335	47	3		3	OR6M1	11	123676932	Silent	SNP	G	TCGA-GJ-A6C0-01A-12D-A30V-10	105517298	123676932	11329584	14	43750										
HEPACAM	220296	hgsc.bcm.edu	37	chr11	124794662	124794662	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0909090909090909	3	1	1.44	0	1.69411764705882	0.1	0.617038875103394	0	tggtcttctccccagtgaagGtgtcgtcggtgatggagatc	14	9	2	3			TCGA-GJ-A6C0-01A-12D-A30V-10	TCGA-GJ-A6C0-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36b33892-0a4d-42f1-8a5c-b51efd4d40a1	6fbe0c9d-a6ae-4737-8e50-926b0b027cdb	g.chr11:124794662G>C	ENST00000298251.4	-	2	794	c.389C>G	c.(388-390)aCc>aGc	p.T130S		NM_152722.4	NP_689935.2			hepatic and glial cell adhesion molecule											breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22	all_hematologic(175;0.215)	Breast(109;0.00222)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.54e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0308)		CCCAGTGAAGGTGTCGTCGGT	0.562																																					p.T130S		Atlas-SNP	.											.	HEPACAM	64	.	0			c.C389G						.						201	190	193					11																	124794662		2201	4299	6500	SO:0001583	missense	220296	exon2			GTGAAGGTGTCGT	AK098396	CCDS8456.1	11q24.2	2013-01-29	2011-02-11		ENSG00000165478	ENSG00000165478		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	26361	protein-coding gene	gene with protein product	"glial cell adhesion molecule"	611642	"hepatocyte cell adhesion molecule"			15885354, 15917256	Standard	NM_152722		Approved	FLJ25530, hepaCAM, GLIALCAM	uc001qbk.3	Q14CZ8	OTTHUMG00000165938	ENST00000298251.4:c.389C>G	chr11.hg19:g.124794662G>C	ENSP00000298251:p.Thr130Ser	64.0	0.0		34.0	13.0	NM_152722		Missense_Mutation	SNP	ENST00000298251.4	hg19	CCDS8456.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.288620	0.80914	.	.	ENSG00000165478	ENST00000298251;ENST00000374961	T	0.65178	-0.14	5.97	5.97	0.96955	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	0.041711	0.85682	D	0.000000	T	0.65396	0.2687	L	0.41027	1.25	0.51482	D	0.999922	P;D	0.52996	0.845;0.957	P;P	0.50490	0.55;0.642	T	0.60042	-0.7340	10	0.32370	T	0.25	-34.4757	20.428	0.99075	0.0:0.0:1.0:0.0	.	130;130	Q14CZ8-2;Q14CZ8	.;HECAM_HUMAN	S	130	ENSP00000298251:T130S	ENSP00000298251:T130S	T	-	2	0	HEPACAM	124299872	1.000000	0.71417	1.000000	0.80357	0.865000	0.49528	5.581000	0.67471	2.837000	0.97791	0.655000	0.94253	ACC	.	.		0.562	HEPACAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387125.1	NM_152722		C	124794662	G	C	124794662	3	2	305	1	0	0	0	0	1	0	0	0	7061	1261	44	4	885	4	HEPACAM	11	124794662	Missense_Mutation	SNP	G	TCGA-GJ-A6C0-01A-12D-A30V-10	1117730	124794662	10211854	15	43751										
NCKAP5L	57701	hgsc.bcm.edu	37	chr12	50186524	50186524	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0909090909090909	3	1	1.44	0	1.69411764705882	0.1	0.617038875103394	0	tagcagtgcagggaaggctgGcatgctggggtgccgcccac	17	11	0	0			TCGA-GJ-A6C0-01A-12D-A30V-10	TCGA-GJ-A6C0-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36b33892-0a4d-42f1-8a5c-b51efd4d40a1	6fbe0c9d-a6ae-4737-8e50-926b0b027cdb	g.chr12:50186524G>A	ENST00000335999.6	-	11	3787	c.3586C>T	c.(3586-3588)Cca>Tca	p.P1196S		NM_001037806.3	NP_001032895.2	Q9HCH0	NCK5L_HUMAN	NCK-associated protein 5-like	1192	Pro-rich.									central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(8)|prostate(2)	18						GGGAAGGCTGGCATGCTGGGG	0.697																																					p.P1196S		Atlas-SNP	.											.	NCKAP5L	142	.	0			c.C3586T						.						11	14	13					12																	50186524		2166	4266	6432	SO:0001583	missense	57701	exon11			AGGCTGGCATGCT	AB046822	CCDS41781.2	12q13.12	2009-08-14	2009-08-14	2009-08-14	ENSG00000167566	ENSG00000167566			29321	protein-coding gene	gene with protein product		615104	"KIAA1602"	KIAA1602			Standard	NM_001037806		Approved		uc009zlk.2	Q9HCH0	OTTHUMG00000156969	ENST00000335999.6:c.3586C>T	chr12.hg19:g.50186524G>A	ENSP00000337998:p.Pro1196Ser	57.0	0.0		96.0	29.0	NM_001037806	Q2TB26|Q71RH1|Q8N4W1|Q96HX2	Missense_Mutation	SNP	ENST00000335999.6	hg19	CCDS41781.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.94|16.94	3.259505|3.259505	0.59321|0.59321	.|.	.|.	ENSG00000167566|ENSG00000167566	ENST00000433948|ENST00000335999;ENST00000354423	.|T	.|0.46451	.|0.87	4.3|4.3	4.3|4.3	0.51218|0.51218	.|.	.|0.000000	.|0.43260	.|D	.|0.000592	T|T	0.36880|0.36880	0.0983|0.0983	L|L	0.40543|0.40543	1.245|1.245	0.37241|0.37241	D|D	0.906101|0.906101	.|P;P;P	.|0.41393	.|0.748;0.518;0.748	.|B;B;B	.|0.43225	.|0.412;0.33;0.412	T|T	0.24977|0.24977	-1.0145|-1.0145	5|10	.|0.18276	.|T	.|0.48	-11.7271|-11.7271	14.1922|14.1922	0.65646|0.65646	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1170;1192;1192	.|E2QRB5;Q9HCH0;Q9HCH0-2	.|.;NCK5L_HUMAN;.	V|S	910|1196;1170	.|ENSP00000337998:P1196S	.|ENSP00000337998:P1196S	A|P	-|-	2|1	0|0	NCKAP5L|NCKAP5L	48472791|48472791	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.988000|0.988000	0.76386|0.76386	5.348000|5.348000	0.66004|0.66004	2.420000|2.420000	0.82092|0.82092	0.561000|0.561000	0.74099|0.74099	GCC|CCA	.	.		0.697	NCKAP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346884.2	XM_035497		A	50186524	G	A	50186524	3	1	305	1	0	0	0	0	1	0	0	0	10233	1203	42	3	430	3	NCKAP5L	12	50186524	Missense_Mutation	SNP	G	TCGA-GJ-A6C0-01A-12D-A30V-10		50186524	83665371	16	43752										
OS9	10956	hgsc.bcm.edu	37	chr12	58087958	58087958	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0909090909090909	3	1	1.44	0	1.69411764705882	0.1	0.617038875103394	0	acgaaagatggcggcggaaaCgctgctgtccagtttgttag	14	8	0	1	rs150848860	byFrequency	TCGA-GJ-A6C0-01A-12D-A30V-10	TCGA-GJ-A6C0-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36b33892-0a4d-42f1-8a5c-b51efd4d40a1	6fbe0c9d-a6ae-4737-8e50-926b0b027cdb	g.chr12:58087958C>T	ENST00000315970.7	+	1	55	c.14C>T	c.(13-15)aCg>aTg	p.T5M	OS9_ENST00000552285.1_Missense_Mutation_p.T5M|OS9_ENST00000389146.6_Missense_Mutation_p.T5M|RP11-571M6.7_ENST00000549477.1_RNA|OS9_ENST00000413095.2_Missense_Mutation_p.T5M|OS9_ENST00000257966.8_Missense_Mutation_p.T5M|OS9_ENST00000435406.2_Missense_Mutation_p.T5M|OS9_ENST00000551035.1_Missense_Mutation_p.T5M|OS9_ENST00000439210.2_Missense_Mutation_p.T5M|OS9_ENST00000389142.5_Missense_Mutation_p.T5M	NM_001017958.2|NM_006812.3	NP_001017958.1|NP_006803.1	Q13438	OS9_HUMAN	osteosarcoma amplified 9, endoplasmic reticulum lectin	5					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein retention in ER lumen (GO:0006621)|protein targeting (GO:0006605)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum lumen (GO:0005788)|Hrd1p ubiquitin ligase complex (GO:0000836)	carbohydrate binding (GO:0030246)|glycoprotein binding (GO:0001948)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	21	all_neural(12;0.00548)|Glioma(12;0.0126)|Melanoma(17;0.122)		BRCA - Breast invasive adenocarcinoma(9;0.109)			GCGGCGGAAACGCTGCTGTCC	0.582																																					p.T5M		Atlas-SNP	.											.	OS9	55	.	0			c.C14T						.						139	138	138					12																	58087958		2203	4300	6503	SO:0001583	missense	10956	exon1			CGGAAACGCTGCT	AB002806	CCDS31843.1, CCDS31844.1, CCDS31845.1, CCDS31846.1, CCDS58246.1, CCDS58247.1, CCDS58248.1, CCDS58249.1	12q13	2009-08-26	2009-08-26						16994	protein-coding gene	gene with protein product	"endoplasmic reticulum lectin 2", "erlectin 2"	609677				8634085, 9498564, 19346256, 18264092	Standard	NM_006812		Approved	OS-9, ERLEC2	uc001spj.3	Q13438	OTTHUMG00000170284	ENST00000315970.7:c.14C>T	chr12.hg19:g.58087958C>T	ENSP00000318165:p.Thr5Met	80.0	0.0		124.0	32.0	NM_001261423	A6NDD1|A6NFR7|A6NLB2|A8K5Q9|B4DE28|B4DPX1|B4E1I6|E7ENT8|E7EW91|F8VUH2|G3XA88|O00579|Q6IBL2|Q8IZ58|Q9BW99	Missense_Mutation	SNP	ENST00000315970.7	hg19	CCDS31843.1	.	.	.	.	.	.	.	.	.	.	C	13.44	2.239248	0.39598	.	.	ENSG00000135506	ENST00000552285;ENST00000315970;ENST00000547079;ENST00000439210;ENST00000389146;ENST00000413095;ENST00000551035;ENST00000257966;ENST00000435406;ENST00000550372;ENST00000389142	T;T;T;T;T;T;T;T;T;T	0.46451	1.87;1.87;0.87;1.86;1.87;1.46;1.88;1.87;1.87;1.87	5.0	0.892	0.19230	.	0.694322	0.14596	N	0.309924	T	0.19406	0.0466	N	0.08118	0	0.19300	N	0.999973	B;B;B;D;D;P;P;P	0.59767	0.007;0.029;0.002;0.957;0.986;0.834;0.798;0.834	B;B;B;P;B;B;B;B	0.44811	0.004;0.01;0.002;0.461;0.425;0.272;0.212;0.182	T	0.08046	-1.0741	10	0.38643	T	0.18	-1.205	1.4232	0.02317	0.1516:0.4555:0.1473:0.2455	.	5;5;5;5;5;5;5;5	E7EW91;F8VUH2;B4E321;G3XA88;E9PEY5;Q9BW99;A6NLB2;Q13438	.;.;.;.;.;.;.;OS9_HUMAN	M	5	ENSP00000450010:T5M;ENSP00000318165:T5M;ENSP00000447031:T5M;ENSP00000407360:T5M;ENSP00000373798:T5M;ENSP00000413112:T5M;ENSP00000447866:T5M;ENSP00000257966:T5M;ENSP00000389632:T5M;ENSP00000373794:T5M	ENSP00000257966:T5M	T	+	2	0	OS9	56374225	0.002000	0.14202	0.919000	0.36401	0.865000	0.49528	0.151000	0.16283	0.061000	0.16311	0.563000	0.77884	ACG	.	C|0.997;G|0.003		0.582	OS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408344.1	NM_006812		T	58087958	C	T	58087958	3	4	305	1	0	0	0	0	1	0	0	0	11281	536	19	1	16	1	OS9	12	58087958	Missense_Mutation	SNP	C	TCGA-GJ-A6C0-01A-12D-A30V-10	7901434	58087958	75763937	17	43753										
FANCM	57697	hgsc.bcm.edu	37	chr14	45658377	45658377	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0909090909090909	3	1	1.44	0	1.69411764705882	0.1	0.617038875103394	0	gatcttctgcgcagtccaagGtgcgttctactccaagagtt	10	11	3	1	rs371629950		TCGA-GJ-A6C0-01A-12D-A30V-10	TCGA-GJ-A6C0-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36b33892-0a4d-42f1-8a5c-b51efd4d40a1	6fbe0c9d-a6ae-4737-8e50-926b0b027cdb	g.chr14:45658377G>A	ENST00000267430.5	+	20	5237	c.5152G>A	c.(5152-5154)Gtg>Atg	p.V1718M	FANCM_ENST00000542564.2_Missense_Mutation_p.V1692M	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1718					DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						GCAGTCCAAGGTGCGTTCTAC	0.408								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.V1718M		Atlas-SNP	.											.	FANCM	225	.	0			c.G5152A						.	G	MET/VAL	0,4406		0,0,2203	140	139	139		5152	2.5	0	14		139	1,8599	1.2+/-3.3	0,1,4299	no	missense	FANCM	NM_020937.2	21	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	1718/2049	45658377	1,13005	2203	4300	6503	SO:0001583	missense	57697	exon20	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TCCAAGGTGCGTT	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"Fanconi anemia, complementation groups"	23168	protein-coding gene	gene with protein product		609644	"KIAA1596"	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.5152G>A	chr14.hg19:g.45658377G>A	ENSP00000267430:p.Val1718Met	174.0	0.0		176.0	77.0	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	hg19	CCDS32070.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.608|7.608	0.674106|0.674106	0.14841|0.14841	0.0|0.0	1.16E-4|1.16E-4	ENSG00000187790|ENSG00000187790	ENST00000554809|ENST00000267430;ENST00000542564;ENST00000556250	.|T;T;T	.|0.77358	.|-1.09;-1.09;-1.09	5.28|5.28	2.45|2.45	0.29901|0.29901	.|.	.|1.660690	.|0.03081	.|N	.|0.158562	T|T	0.63022|0.63022	0.2476|0.2476	N|N	0.04959|0.04959	-0.14|-0.14	0.09310|0.09310	N|N	1|1	.|B;B	.|0.14012	.|0.009;0.001	.|B;B	.|0.11329	.|0.006;0.003	T|T	0.52366|0.52366	-0.8585|-0.8585	5|10	.|0.45353	.|T	.|0.12	.|.	10.0425|10.0425	0.42166|0.42166	0.3005:0.0:0.6995:0.0|0.3005:0.0:0.6995:0.0	.|.	.|1692;1718	.|B2RTQ9;Q8IYD8	.|.;FANCM_HUMAN	D|M	650|1718;1692;1234	.|ENSP00000267430:V1718M;ENSP00000442493:V1692M;ENSP00000452033:V1234M	.|ENSP00000267430:V1718M	G|V	+|+	2|1	0|0	FANCM|FANCM	44728127|44728127	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	0.713000|0.713000	0.25794|0.25794	0.068000|0.068000	0.16574|0.16574	-1.761000|-1.761000	0.00669|0.00669	GGT|GTG	.	.		0.408	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		A	45658377	G	A	45658377	3	1	305	1	0	0	0	0	1	0	0	0	5679	1261	44	3	5230	3	FANCM	14	45658377	Missense_Mutation	SNP	G	TCGA-GJ-A6C0-01A-12D-A30V-10		45658377	61691163	18	43754										
TMEM30B	161291	hgsc.bcm.edu	37	chr14	61747549	61747549	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0909090909090909	3	1	1.44	0	1.69411764705882	0.1	0.617038875103394	0	cgtagtagaggtacactgggCcctggaagagctcgggcagc	16	10	0	2			TCGA-GJ-A6C0-01A-12D-A30V-10	TCGA-GJ-A6C0-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36b33892-0a4d-42f1-8a5c-b51efd4d40a1	6fbe0c9d-a6ae-4737-8e50-926b0b027cdb	g.chr14:61747549C>T	ENST00000555868.1	-	1	1009	c.317G>A	c.(316-318)gGc>gAc	p.G106D	TMEM30B_ENST00000557163.1_5'UTR|TMEM30B_ENST00000355702.2_Missense_Mutation_p.G106D	NM_001017970.2	NP_001017970.1	Q3MIR4	CC50B_HUMAN	transmembrane protein 30B	106					lipid transport (GO:0006869)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|large_intestine(1)|lung(1)|prostate(1)|stomach(1)	6				OV - Ovarian serous cystadenocarcinoma(108;0.107)|BRCA - Breast invasive adenocarcinoma(234;0.181)		GTACACTGGGCCCTGGAAGAG	0.697																																					p.G106D		Atlas-SNP	.											.	TMEM30B	13	.	0			c.G317A						.						10	10	10					14																	61747549		2118	4155	6273	SO:0001583	missense	161291	exon1			ACTGGGCCCTGGA	AK091169	CCDS32093.1	14q23.1	2006-09-20				ENSG00000182107			27254	protein-coding gene	gene with protein product		611029				15375526	Standard	NM_001017970		Approved	CDC50B	uc001xfl.3	Q3MIR4		ENST00000555868.1:c.317G>A	chr14.hg19:g.61747549C>T	ENSP00000450842:p.Gly106Asp	14.0	0.0		25.0	9.0	NM_001017970	B3KR84|Q14D00	Missense_Mutation	SNP	ENST00000555868.1	hg19	CCDS32093.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.498253	0.85069	.	.	ENSG00000182107	ENST00000555868;ENST00000355702	.	.	.	4.14	4.14	0.48551	.	0.000000	0.85682	D	0.000000	T	0.75339	0.3836	M	0.85041	2.73	0.49798	D	0.999824	P	0.52170	0.951	P	0.54270	0.747	T	0.80190	-0.1485	9	0.56958	D	0.05	-16.3792	14.0112	0.64498	0.0:1.0:0.0:0.0	.	106	Q3MIR4	CC50B_HUMAN	D	106	.	ENSP00000347930:G106D	G	-	2	0	TMEM30B	60817302	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.314000	0.51943	2.163000	0.67991	0.650000	0.86243	GGC	.	.		0.697	TMEM30B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413358.1	XM_090844		T	61747549	C	T	61747549	3	4	305	1	0	0	0	0	1	0	0	0	16169	739	26	3	742	3	TMEM30B	14	61747549	Missense_Mutation	SNP	C	TCGA-GJ-A6C0-01A-12D-A30V-10	16089172	61747549	45601991	19	43755										
DLST	1743	hgsc.bcm.edu	37	chr14	75359658	75359658	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0909090909090909	3	1	1.44	0	1.69411764705882	0.1	0.617038875103394	0	actcagatgccaccggtgccCtcgccctcacagcctccttc	7	20	2	1			TCGA-GJ-A6C0-01A-12D-A30V-10	TCGA-GJ-A6C0-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36b33892-0a4d-42f1-8a5c-b51efd4d40a1	6fbe0c9d-a6ae-4737-8e50-926b0b027cdb	g.chr14:75359658C>T	ENST00000334220.4	+	8	625	c.564C>T	c.(562-564)ccC>ccT	p.P188P	DLST_ENST00000334212.6_Silent_p.P102P|DLST_ENST00000555190.1_3'UTR	NM_001933.4	NP_001924.2	P36957	ODO2_HUMAN	dihydrolipoamide S-succinyltransferase (E2 component of 2-oxo-glutarate complex)	188					cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|generation of precursor metabolites and energy (GO:0006091)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|oxoglutarate dehydrogenase complex (GO:0045252)	dihydrolipoyllysine-residue succinyltransferase activity (GO:0004149)			breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(234;0.00698)		CACCGGTGCCCTCGCCCTCAC	0.572																																					p.P188P		Atlas-SNP	.											.	DLST	42	.	0			c.C564T						.						67	56	60					14																	75359658		2203	4300	6503	SO:0001819	synonymous_variant	1743	exon8			GGTGCCCTCGCCC		CCDS9833.1	14q23.1	2008-08-11			ENSG00000119689	ENSG00000119689	2.3.1.61		2911	protein-coding gene	gene with protein product		126063		DLTS		8009371	Standard	NM_001933		Approved		uc001xqv.2	P36957		ENST00000334220.4:c.564C>T	chr14.hg19:g.75359658C>T		62.0	0.0		78.0	8.0	NM_001933	B7Z5W8|E7ESY5|Q7LDY7|Q9BQ32	Silent	SNP	ENST00000334220.4	hg19	CCDS9833.1																																																																																			.	.		0.572	DLST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413637.1			T	75359658	C	T	75359658	2	4	305	1	0	0	0	0	0	0	0	1	4571	668	24	3		3	DLST	14	75359658	Silent	SNP	C	TCGA-GJ-A6C0-01A-12D-A30V-10	13612109	75359658	31989882	20	43756										
IL16	3603	hgsc.bcm.edu	37	chr15	81593848	81593848	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0909090909090909	3	1	1.44	0	1.69411764705882	0.1	0.617038875103394	0	aggttctggatgaagcaacaTtaaaggtaggtttcctttgt	11	5	1	1			TCGA-GJ-A6C0-01A-12D-A30V-10	TCGA-GJ-A6C0-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36b33892-0a4d-42f1-8a5c-b51efd4d40a1	6fbe0c9d-a6ae-4737-8e50-926b0b027cdb	g.chr15:81593848T>G	ENST00000302987.4	+	14	3313	c.3313T>G	c.(3313-3315)Tta>Gta	p.L1105V	IL16_ENST00000394652.2_Missense_Mutation_p.L404V|RP11-761I4.4_ENST00000607019.1_RNA|IL16_ENST00000394660.2_Missense_Mutation_p.L1105V			Q14005	IL16_HUMAN	interleukin 16	1105	Interaction with HTLV-1 tax.				immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						TGAAGCAACATTAAAGGTAGG	0.473																																					p.L1105V		Atlas-SNP	.											.	IL16	254	.	0			c.T3313G						.						95	93	94					15																	81593848		2203	4300	6503	SO:0001583	missense	3603	exon15			GCAACATTAAAGG	U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"Interleukins and interleukin receptors"	5980	protein-coding gene	gene with protein product	"prointerleukin 16", "lymphocyte chemoattractant factor"	603035	"interleukin 16 (lymphocyte chemoattractant factor)"			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.3313T>G	chr15.hg19:g.81593848T>G	ENSP00000302935:p.Leu1105Val	56.0	0.0		63.0	19.0	NM_001172128	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Missense_Mutation	SNP	ENST00000302987.4	hg19	CCDS42069.1	.	.	.	.	.	.	.	.	.	.	T	10.34	1.323405	0.24080	.	.	ENSG00000172349	ENST00000394660;ENST00000355368;ENST00000302987;ENST00000329842;ENST00000394653;ENST00000394652;ENST00000394656	T;T;T	0.13307	2.6;2.61;3.24	4.87	-3.11	0.05299	PDZ/DHR/GLGF (1);	0.000000	0.30565	N	0.009356	T	0.21962	0.0529	L	0.36672	1.1	0.32316	N	0.563122	D;D;D;P;D;B	0.63880	0.983;0.993;0.981;0.843;0.977;0.152	D;D;P;D;D;P	0.83275	0.986;0.996;0.727;0.956;0.985;0.558	T	0.03662	-1.1015	10	0.59425	D	0.04	.	12.1584	0.54091	0.0:0.5327:0.0:0.4673	.	937;598;642;495;1105;1105	F8W7Z5;Q6ZTT5;B7Z8M3;B3KY62;Q14005;Q14005-2	.;.;.;.;IL16_HUMAN;.	V	1105;937;1105;642;495;404;404	ENSP00000378155:L1105V;ENSP00000302935:L1105V;ENSP00000378147:L404V	ENSP00000302935:L1105V	L	+	1	2	IL16	79380903	0.007000	0.16637	0.001000	0.08648	0.141000	0.21300	-0.021000	0.12504	-0.667000	0.05303	0.459000	0.35465	TTA	.	.		0.473	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217		G	81593848	T	G	81593848	3	3	305	1	0	0	0	0	1	0	0	0	7642	1490	52	5	3367	5	IL16	15	81593848	Missense_Mutation	SNP	T	TCGA-GJ-A6C0-01A-12D-A30V-10		81593848	20937544	21	43757										
ITGAD	3681	hgsc.bcm.edu	37	chr16	31414896	31414896	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0909090909090909	3	1	1.44	0	1.69411764705882	0.1	0.617038875103394	0	tccggaccagcccgagccagCagagcctggtggatcccatc	12	16	0	1			TCGA-GJ-A6C0-01A-12D-A30V-10	TCGA-GJ-A6C0-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36b33892-0a4d-42f1-8a5c-b51efd4d40a1	6fbe0c9d-a6ae-4737-8e50-926b0b027cdb	g.chr16:31414896C>T	ENST00000389202.2	+	7	683	c.634C>T	c.(634-636)Cag>Tag	p.Q212*	RP11-120K18.2_ENST00000567545.1_RNA	NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	212	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				activated T cell proliferation (GO:0050798)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)	cell surface (GO:0009986)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(43)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						CCCGAGCCAGCAGAGCCTGGT	0.602																																					p.Q212X		Atlas-SNP	.											.	ITGAD	154	.	0			c.C634T						.						107	86	93					16																	31414896		2197	4300	6497	SO:0001587	stop_gained	3681	exon7			AGCCAGCAGAGCC	U40274	CCDS32438.1	16p13.1-p11	2010-03-23				ENSG00000156886		"CD molecules", "Integrins"	6146	protein-coding gene	gene with protein product		602453				8666289, 9598326	Standard	NM_005353		Approved	CD11d, ADB2	uc002ebv.1	Q13349		ENST00000389202.2:c.634C>T	chr16.hg19:g.31414896C>T	ENSP00000373854:p.Gln212*	62.0	0.0		76.0	27.0	NM_005353	Q15575|Q15576	Nonsense_Mutation	SNP	ENST00000389202.2	hg19	CCDS32438.1	.	.	.	.	.	.	.	.	.	.	C	16.80	3.223352	0.58668	.	.	ENSG00000156886	ENST00000316569;ENST00000444228;ENST00000389202	.	.	.	4.69	3.7	0.42460	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05525	T	0.97	.	7.1887	0.25814	0.1785:0.625:0.1964:0.0	.	.	.	.	X	76;228;212	.	ENSP00000323325:Q76X	Q	+	1	0	ITGAD	31322397	0.000000	0.05858	0.227000	0.23927	0.034000	0.12701	0.172000	0.16704	2.430000	0.82344	0.503000	0.49774	CAG	.	.		0.602	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353		T	31414896	C	T	31414896	4	4	305	1	0	0	0	0	0	1	0	0	7893	711	25	3	660	3	ITGAD	16	31414896	Nonsense_Mutation	SNP	C	TCGA-GJ-A6C0-01A-12D-A30V-10		31414896	58939857	22	43758										
ANKRD13B	124930	hgsc.bcm.edu	37	chr17	27940598	27940598	+	Nonstop_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0909090909090909	3	1	1.44	0	1.69411764705882	0.1	0.617038875103394	0	ggctctcactgaccgagcagTagcgccccctgccgggaccc	12	18	1	1			TCGA-GJ-A6C0-01A-12D-A30V-10	TCGA-GJ-A6C0-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36b33892-0a4d-42f1-8a5c-b51efd4d40a1	6fbe0c9d-a6ae-4737-8e50-926b0b027cdb	g.chr17:27940598T>C	ENST00000394859.3	+	15	2033	c.1879T>C	c.(1879-1881)Tag>Cag	p.*627Q	RP11-68I3.2_ENST00000581474.1_RNA|CORO6_ENST00000577909.1_5'Flank	NM_152345.4	NP_689558.4	Q86YJ7	AN13B_HUMAN	ankyrin repeat domain 13B	0						endosome (GO:0005768)|plasma membrane (GO:0005886)				cervix(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(2)	16						GACCGAGCAGTAGCGCCCCCT	0.741																																					p.X627Q		Atlas-SNP	.											.	ANKRD13B	39	.	0			c.T1879C						.						6	11	9					17																	27940598		1747	3446	5193	SO:0001578	stop_lost	124930	exon15			GAGCAGTAGCGCC	AK092673	CCDS11251.1	17q11.2	2013-01-10			ENSG00000198720	ENSG00000198720		"Ankyrin repeat domain containing"	26363	protein-coding gene	gene with protein product		615124					Standard	NM_152345		Approved	FLJ25555	uc002hei.3	Q86YJ7	OTTHUMG00000132731	ENST00000394859.3:c.1879T>C	chr17.hg19:g.27940598T>C	ENSP00000378328:p.*627Glnext*108	24.0	0.0		20.0	8.0	NM_152345	Q8N7S9	Missense_Mutation	SNP	ENST00000394859.3	hg19	CCDS11251.1	.	.	.	.	.	.	.	.	.	.	T	18.36	3.606729	0.66558	.	.	ENSG00000198720	ENST00000394859	.	.	.	5.0	2.6	0.31112	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.2728	0.31855	0.1314:0.0:0.1375:0.7311	.	.	.	.	Q	627	.	.	X	+	1	0	ANKRD13B	24964724	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.733000	0.68571	0.898000	0.36418	0.460000	0.39030	TAG	.	.		0.741	ANKRD13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256077.1	NM_152345		C	27940598	T	C	27940598	4	2	305	1	0	0	0	0	0	0	0	0	642	1651	57	2	1937	2	ANKRD13B	17	27940598	Nonstop_Mutation	SNP	T	TCGA-GJ-A6C0-01A-12D-A30V-10		27940598	53254612	23	43759										
SLC16A6	9120	hgsc.bcm.edu	37	chr17	66268836	66268836	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0909090909090909	3	1	1.44	0	1.69411764705882	0.1	0.617038875103394	0	tggaagcaactgcagtgactAtggaacgtcttttgccaaaa	10	8	1	1			TCGA-GJ-A6C0-01A-12D-A30V-10	TCGA-GJ-A6C0-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36b33892-0a4d-42f1-8a5c-b51efd4d40a1	6fbe0c9d-a6ae-4737-8e50-926b0b027cdb	g.chr17:66268836A>G	ENST00000327268.4	-	5	613	c.449T>C	c.(448-450)aTa>aCa	p.I150T	SLC16A6_ENST00000580666.1_Missense_Mutation_p.I150T|ARSG_ENST00000448504.2_Intron	NM_001174166.1	NP_001167637.1	O15403	MOT7_HUMAN	solute carrier family 16, member 6	150					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)			large_intestine(3)|lung(8)|prostate(1)|skin(1)|urinary_tract(2)	15	all_cancers(12;1.24e-09)		BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)		Pyruvic acid(DB00119)	TGCAGTGACTATGGAACGTCT	0.428																																					p.I150T		Atlas-SNP	.											.	SLC16A6	56	.	0			c.T449C						.						190	165	174					17																	66268836		2203	4300	6503	SO:0001583	missense	9120	exon5			GTGACTATGGAAC	U79745	CCDS11675.1	17q24.2	2013-07-18	2013-07-18		ENSG00000108932	ENSG00000108932		"Solute carriers"	10927	protein-coding gene	gene with protein product		603880	"solute carrier family 16 (monocarboxylic acid transporters), member 6", "solute carrier family 16, member 6 (monocarboxylic acid transporter 7)"			9425115	Standard	NM_004694		Approved	MCT6, MCT7	uc002jgz.2	O15403	OTTHUMG00000179812	ENST00000327268.4:c.449T>C	chr17.hg19:g.66268836A>G	ENSP00000319991:p.Ile150Thr	107.0	0.0		135.0	32.0	NM_001174166	Q6P1X3	Missense_Mutation	SNP	ENST00000327268.4	hg19	CCDS11675.1	.	.	.	.	.	.	.	.	.	.	A	10.24	1.296930	0.23650	.	.	ENSG00000108932	ENST00000327268	T	0.38722	1.12	5.41	5.41	0.78517	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.443462	0.22581	N	0.058217	T	0.31167	0.0788	N	0.14661	0.345	0.32400	N	0.55204	B	0.29955	0.263	B	0.32928	0.155	T	0.48080	-0.9066	10	0.87932	D	0	.	14.9216	0.70843	1.0:0.0:0.0:0.0	.	150	O15403	MOT7_HUMAN	T	150	ENSP00000319991:I150T	ENSP00000319991:I150T	I	-	2	0	SLC16A6	63780431	0.995000	0.38212	0.010000	0.14722	0.383000	0.30230	8.673000	0.91186	2.171000	0.68590	0.533000	0.62120	ATA	.	.		0.428	SLC16A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448323.1	NM_004694		G	66268836	A	G	66268836	3	3	305	1	0	0	0	0	1	0	0	0	14427	449	16	2	1134	2	SLC16A6	17	66268836	Missense_Mutation	SNP	A	TCGA-GJ-A6C0-01A-12D-A30V-10	38328238	66268836	14926374	24	43760										
STRN4	29888	hgsc.bcm.edu	37	chr19	47231256	47231256	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0909090909090909	3	1	1.44	0	1.69411764705882	0.1	0.617038875103394	0	aatgccttggagtttgacccGacggctttctgcagggtcga	13	10	1	1			TCGA-GJ-A6C0-01A-12D-A30V-10	TCGA-GJ-A6C0-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36b33892-0a4d-42f1-8a5c-b51efd4d40a1	6fbe0c9d-a6ae-4737-8e50-926b0b027cdb	g.chr19:47231256G>C	ENST00000263280.6	-	8	1097	c.1048C>G	c.(1048-1050)Cgg>Ggg	p.R350G	STRN4_ENST00000594357.2_5'UTR|CTB-174O21.2_ENST00000600716.1_RNA|STRN4_ENST00000391910.3_Missense_Mutation_p.R350G|STRN4_ENST00000539396.1_Missense_Mutation_p.R231G	NM_001039877.1|NM_013403.2	NP_001034966.1|NP_037535.2	Q9NRL3	STRN4_HUMAN	striatin, calmodulin binding protein 4	350						cell projection (GO:0042995)|cytoplasm (GO:0005737)|membrane (GO:0016020)	armadillo repeat domain binding (GO:0070016)|calmodulin binding (GO:0005516)|protein complex binding (GO:0032403)|protein phosphatase 2A binding (GO:0051721)			NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000563)|all cancers(93;0.00138)|Epithelial(262;0.0217)|GBM - Glioblastoma multiforme(486;0.035)		AGTTTGACCCGACGGCTTTCT	0.657																																					p.R350G		Atlas-SNP	.											.	STRN4	33	.	0			c.C1048G						.						46	41	43					19																	47231256		2203	4300	6503	SO:0001583	missense	29888	exon8			TGACCCGACGGCT	AF212940	CCDS12690.1, CCDS42581.1	19q13.32	2013-01-10			ENSG00000090372	ENSG00000090372		"WD repeat domain containing"	15721	protein-coding gene	gene with protein product		614767				10748158	Standard	XM_006723171		Approved	zinedin, ZIN	uc002pfm.3	Q9NRL3		ENST00000263280.6:c.1048C>G	chr19.hg19:g.47231256G>C	ENSP00000263280:p.Arg350Gly	50.0	0.0		51.0	13.0	NM_001039877	A0A024R0V2|B4DQH7|F8VYA6|Q8NE53	Missense_Mutation	SNP	ENST00000263280.6	hg19	CCDS12690.1	.	.	.	.	.	.	.	.	.	.	G	18.27	3.588039	0.66105	.	.	ENSG00000090372	ENST00000391910;ENST00000263280;ENST00000539396	T;T;T	0.70631	-0.5;-0.32;-0.18	4.6	4.6	0.57074	.	0.000000	0.85682	D	0.000000	T	0.80592	0.4652	M	0.72353	2.195	0.80722	D	1	D;D	0.76494	0.999;0.993	D;D	0.74674	0.984;0.972	T	0.80511	-0.1350	10	0.45353	T	0.12	-20.9293	10.2599	0.43421	0.0:0.0:0.8026:0.1974	.	350;350	F8VYA6;Q9NRL3	.;STRN4_HUMAN	G	350;350;231	ENSP00000375777:R350G;ENSP00000263280:R350G;ENSP00000440901:R231G	ENSP00000263280:R350G	R	-	1	2	STRN4	51923096	0.999000	0.42202	0.996000	0.52242	0.984000	0.73092	2.112000	0.41892	2.107000	0.64212	0.561000	0.74099	CGG	.	.		0.657	STRN4-001	KNOWN	NMD_exception|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466607.2			C	47231256	G	C	47231256	3	2	305	1	0	0	0	0	1	0	0	0	15346	1057	37	4	1274	4	STRN4	19	47231256	Missense_Mutation	SNP	G	TCGA-GJ-A6C0-01A-12D-A30V-10		47231256	11897727	25	43761										
LILRB1	10859	hgsc.bcm.edu	37	chr19	55148029	55148029	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0909090909090909	3	1	1.44	0	1.69411764705882	0.1	0.617038875103394	0	ggagagaaatggcctctcctCcttccccactgtctggggaa	11	13	2	1	rs370268778		TCGA-GJ-A6C0-01A-12D-A30V-10	TCGA-GJ-A6C0-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36b33892-0a4d-42f1-8a5c-b51efd4d40a1	6fbe0c9d-a6ae-4737-8e50-926b0b027cdb	g.chr19:55148029C>T	ENST00000396331.1	+	15	2089	c.1732C>T	c.(1732-1734)Cct>Tct	p.P578S	LILRB1_ENST00000427581.2_Missense_Mutation_p.P629S|LILRB1_ENST00000448689.1_3'UTR|LILRB1_ENST00000396327.3_Missense_Mutation_p.P579S|LILRB1_ENST00000396332.4_Missense_Mutation_p.P579S|LILRB1_ENST00000434867.2_Missense_Mutation_p.P578S|LILRB1_ENST00000462628.1_3'UTR|LILRB1_ENST00000396321.2_Missense_Mutation_p.P578S|LILRB1_ENST00000396317.1_Missense_Mutation_p.P562S|LILRB1_ENST00000324602.7_Missense_Mutation_p.P580S|AC009892.10_ENST00000456337.1_Intron|LILRB1_ENST00000396315.1_Missense_Mutation_p.P580S|LILRB1_ENST00000418536.2_Missense_Mutation_p.P562S	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	578					cellular response to lipopolysaccharide (GO:0071222)|defense response to virus (GO:0051607)|dendritic cell differentiation (GO:0097028)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma production (GO:0032609)|interferon-gamma secretion (GO:0072643)|negative regulation of alpha-beta T cell activation (GO:0046636)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of CD8-positive, alpha-beta T cell activation (GO:2001186)|negative regulation of cell cycle (GO:0045786)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of endocytosis (GO:0045806)|negative regulation of interferon-beta secretion (GO:0035548)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-12 secretion (GO:2001183)|negative regulation of mononuclear cell proliferation (GO:0032945)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of osteoclast development (GO:2001205)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transforming growth factor-beta secretion (GO:2001202)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of gamma-delta T cell activation involved in immune response (GO:2001193)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor internalization (GO:0031623)|regulation of immune response (GO:0050776)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation involved in immune response (GO:0002309)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	HLA-A specific inhibitory MHC class I receptor activity (GO:0030107)|HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)|MHC class I protein binding (GO:0042288)|MHC class I receptor activity (GO:0032393)|protein homodimerization activity (GO:0042803)|protein phosphatase 1 binding (GO:0008157)|SH2 domain binding (GO:0042169)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	74				GBM - Glioblastoma multiforme(193;0.0188)		GGCCTCTCCTCCTTCCCCACT	0.582										HNSCC(37;0.09)																											p.P580S		Atlas-SNP	.											LILRB1,NS,carcinoma,0,1	LILRB1	140	.	0			c.C1738T						.						112	96	101					19																	55148029		2201	4298	6499	SO:0001583	missense	10859	exon14			TCTCCTCCTTCCC	AF009220	CCDS42614.1, CCDS42615.1, CCDS42616.1, CCDS42617.1, CCDS62803.1	19q13.4	2013-01-11						"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6605	protein-coding gene	gene with protein product		604811				9285411, 9382880	Standard	XM_006726246		Approved	LIR-1, ILT2, MIR-7, CD85, LIR1, CD85j	uc002qgm.3	Q8NHL6		ENST00000396331.1:c.1732C>T	chr19.hg19:g.55148029C>T	ENSP00000379622:p.Pro578Ser	134.0	0.0		122.0	10.0	NM_001081637	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Missense_Mutation	SNP	ENST00000396331.1	hg19	CCDS42617.1	.	.	.	.	.	.	.	.	.	.	C	7.396	0.631747	0.14322	.	.	ENSG00000104972	ENST00000396321;ENST00000418536;ENST00000396331;ENST00000396327;ENST00000324602;ENST00000434867;ENST00000396332;ENST00000427581;ENST00000396317;ENST00000396315	T;T;T;T;T;T;T;T;T;T	0.00518	7.0;6.92;7.0;7.03;6.99;7.0;7.02;6.86;6.92;6.99	1.59	0.511	0.16989	.	.	.	.	.	T	0.01124	0.0037	M	0.82323	2.585	0.09310	N	1	B;D;B;P;D	0.63046	0.411;0.992;0.339;0.882;0.964	B;P;B;P;P	0.58928	0.055;0.848;0.035;0.528;0.601	T	0.47328	-0.9126	9	0.52906	T	0.07	.	3.7747	0.08656	0.0:0.7538:0.0:0.2462	.	562;580;579;579;578	A8MVE2;Q8NHL6-3;A2IXV4;Q8NHL6-2;Q8NHL6	.;.;.;.;LIRB1_HUMAN	S	578;562;578;579;580;578;579;629;562;580	ENSP00000379614:P578S;ENSP00000391514:P562S;ENSP00000379622:P578S;ENSP00000379618:P579S;ENSP00000315997:P580S;ENSP00000405243:P578S;ENSP00000379623:P579S;ENSP00000395004:P629S;ENSP00000379610:P562S;ENSP00000379608:P580S	ENSP00000315997:P580S	P	+	1	0	LILRB1	59839841	0.003000	0.15002	0.001000	0.08648	0.091000	0.18340	0.942000	0.29017	0.254000	0.21573	0.194000	0.17425	CCT	.	.		0.582	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4			T	55148029	C	T	55148029	3	4	305	1	0	0	0	0	1	0	0	0	8799	855	30	3	1788	3	LILRB1	19	55148029	Missense_Mutation	SNP	C	TCGA-GJ-A6C0-01A-12D-A30V-10	7916773	55148029	3980954	26	43762										
ADRA1D	146	hgsc.bcm.edu	37	chr20	4228867	4228867	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0909090909090909	3	1	1.44	0	1.69411764705882	0.1	0.617038875103394	0	cccgcctcctcggtgataccGcagaagcgctcgtcaggggg	14	15	1	2	rs140080149	byFrequency	TCGA-GJ-A6C0-01A-12D-A30V-10	TCGA-GJ-A6C0-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36b33892-0a4d-42f1-8a5c-b51efd4d40a1	6fbe0c9d-a6ae-4737-8e50-926b0b027cdb	g.chr20:4228867G>T	ENST00000379453.4	-	1	854	c.738C>A	c.(736-738)tgC>tgA	p.C246*		NM_000678.3	NP_000669.1	P25100	ADA1D_HUMAN	adrenoceptor alpha 1D	246					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|DNA metabolic process (GO:0006259)|G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)|negative regulation of the force of heart contraction involved in baroreceptor response to increased systemic arterial blood pressure (GO:0001986)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|positive regulation of cell proliferation (GO:0008284)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha1-adrenergic receptor activity (GO:0004937)			endometrium(1)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	14					Alfuzosin(DB00346)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Dapiprazole(DB00298)|Desipramine(DB01151)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|Labetalol(DB00598)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Mianserin(DB06148)|Midodrine(DB00211)|Mirtazapine(DB00370)|Nicardipine(DB00622)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Oxymetazoline(DB00935)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Prazosin(DB00457)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Silodosin(DB06207)|Tamsulosin(DB00706)|Terazosin(DB01162)|Xylometazoline(DB06694)	CGGTGATACCGCAGAAGCGCT	0.672																																					p.C246X		Atlas-SNP	.											.	ADRA1D	36	.	0			c.C738A						.						29	27	28					20																	4228867		2198	4300	6498	SO:0001587	stop_gained	146	exon1			GATACCGCAGAAG	U03864	CCDS13079.1	20p13	2012-08-08	2012-05-09		ENSG00000171873	ENSG00000171873		"GPCR / Class A : Adrenoceptors : alpha"	280	protein-coding gene	gene with protein product		104219	"adrenergic, alpha-1D-, receptor"			8039425	Standard	NM_000678		Approved	ADRA1R, ADRA1A, ADRA1	uc002wkr.2	P25100	OTTHUMG00000031779	ENST00000379453.4:c.738C>A	chr20.hg19:g.4228867G>T	ENSP00000368766:p.Cys246*	97.0	0.0		86.0	35.0	NM_000678	Q9NPY0	Nonsense_Mutation	SNP	ENST00000379453.4	hg19	CCDS13079.1	.	.	.	.	.	.	.	.	.	.	g	38	6.699864	0.97772	.	.	ENSG00000171873	ENST00000379453	.	.	.	4.25	1.16	0.20824	.	0.000000	0.85682	U	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.5193	0.22266	0.4102:0.0:0.5898:0.0	.	.	.	.	X	246	.	ENSP00000368766:C246X	C	-	3	2	ADRA1D	4176867	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	1.685000	0.37659	0.448000	0.26722	0.552000	0.68991	TGC	.	G|0.996;A|0.004		0.672	ADRA1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077812.2	NM_000678		T	4228867	G	T	4228867	4	4	305	1	0	0	0	0	0	1	0	0	336	1079	38	1	988	1	ADRA1D	20	4228867	Nonsense_Mutation	SNP	G	TCGA-GJ-A6C0-01A-12D-A30V-10		4228867	58796653	27	43763										
SLC9A8	23315	hgsc.bcm.edu	37	chr20	48497559	48497559	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0909090909090909	3	1	1.44	0	1.69411764705882	0.1	0.617038875103394	0	acaccgaagatgatgttcatCatgtggtttagtggtaagtc	11	6	2	2			TCGA-GJ-A6C0-01A-12D-A30V-10	TCGA-GJ-A6C0-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36b33892-0a4d-42f1-8a5c-b51efd4d40a1	6fbe0c9d-a6ae-4737-8e50-926b0b027cdb	g.chr20:48497559C>T	ENST00000361573.2	+	13	1299	c.1257C>T	c.(1255-1257)atC>atT	p.I419I	SLC9A8_ENST00000541138.1_Silent_p.I119I|SLC9A8_ENST00000417961.1_Silent_p.I435I|SLC9A8_ENST00000539601.1_Silent_p.I200I			Q9Y2E8	SL9A8_HUMAN	solute carrier family 9, subfamily A (NHE8, cation proton antiporter 8), member 8	419					ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	potassium:proton antiporter activity (GO:0015386)|sodium:proton antiporter activity (GO:0015385)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	30			BRCA - Breast invasive adenocarcinoma(9;3.91e-07)			TGATGTTCATCATGTGGTTTA	0.458																																					p.I435I		Atlas-SNP	.											.	SLC9A8	63	.	0			c.C1305T						.						144	128	133					20																	48497559		2203	4300	6503	SO:0001819	synonymous_variant	23315	exon13			GTTCATCATGTGG	AB023156	CCDS13421.1, CCDS58774.1	20q13.13	2013-05-22	2012-03-22		ENSG00000197818	ENSG00000197818		"Solute carriers"	20728	protein-coding gene	gene with protein product		612730	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 8", "solute carrier family 9 (sodium/hydrogen exchanger), member 8"			12409279	Standard	NM_001260491		Approved	KIAA0939, NHE8	uc002xuv.2	Q9Y2E8	OTTHUMG00000032710	ENST00000361573.2:c.1257C>T	chr20.hg19:g.48497559C>T		115.0	0.0		113.0	34.0	NM_001260491	B4DTQ8|Q2M1U9|Q68CZ8|Q9BX15|Q9Y507	Silent	SNP	ENST00000361573.2	hg19	CCDS13421.1																																																																																			.	.		0.458	SLC9A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106483.3	XM_030524		T	48497559	C	T	48497559	2	4	305	1	0	0	0	0	0	0	0	1	14735	816	29	3		3	SLC9A8	20	48497559	Silent	SNP	C	TCGA-GJ-A6C0-01A-12D-A30V-10	44268692	48497559	14527961	28	43764										
ZNF512B	57473	hgsc.bcm.edu	37	chr20	62594086	62594086	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0909090909090909	3	1	1.44	0	1.69411764705882	0.1	0.617038875103394	0	gcttggggtccgctccacacCcagcgggtcctcagcctcag	12	17	2	0			TCGA-GJ-A6C0-01A-12D-A30V-10	TCGA-GJ-A6C0-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36b33892-0a4d-42f1-8a5c-b51efd4d40a1	6fbe0c9d-a6ae-4737-8e50-926b0b027cdb	g.chr20:62594086C>T	ENST00000450537.1	-	13	2077	c.2017G>A	c.(2017-2019)Ggt>Agt	p.G673S	ZNF512B_ENST00000369888.1_Missense_Mutation_p.G673S|ZNF512B_ENST00000217130.3_Missense_Mutation_p.G673S			Q96KM6	Z512B_HUMAN	zinc finger protein 512B	673					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(4)|skin(1)	33	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					CGCTCCACACCCAGCGGGTCC	0.692																																					p.G673S		Atlas-SNP	.											.	ZNF512B	72	.	0			c.G2017A						.						10	11	11					20																	62594086		2180	4261	6441	SO:0001583	missense	57473	exon13			CCACACCCAGCGG	AB033022	CCDS13548.1	20q13.33	2011-02-09			ENSG00000196700	ENSG00000196700			29212	protein-coding gene	gene with protein product						10574462	Standard	NM_020713		Approved	GM632, MGC149845, MGC149846	uc002yhl.2	Q96KM6	OTTHUMG00000033008	ENST00000450537.1:c.2017G>A	chr20.hg19:g.62594086C>T	ENSP00000393795:p.Gly673Ser	77.0	0.0		69.0	21.0	NM_020713	Q08AK9|Q9ULM4	Missense_Mutation	SNP	ENST00000450537.1	hg19	CCDS13548.1	.	.	.	.	.	.	.	.	.	.	C	17.61	3.431940	0.62844	.	.	ENSG00000196700	ENST00000369888;ENST00000450537;ENST00000217130	T;T;T	0.22134	1.97;1.97;1.97	5.22	4.27	0.50696	.	0.135951	0.46442	D	0.000283	T	0.10423	0.0255	N	0.03608	-0.345	0.35703	D	0.815806	B	0.06786	0.001	B	0.13407	0.009	T	0.14559	-1.0468	10	0.35671	T	0.21	-12.2131	14.0508	0.64734	0.0:0.926:0.0:0.074	.	673	Q96KM6	Z512B_HUMAN	S	673	ENSP00000358904:G673S;ENSP00000393795:G673S;ENSP00000217130:G673S	ENSP00000217130:G673S	G	-	1	0	ZNF512B	62064530	0.988000	0.35896	1.000000	0.80357	0.936000	0.57629	4.424000	0.59868	2.434000	0.82447	0.563000	0.77884	GGT	.	.		0.692	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713		T	62594086	C	T	62594086	3	4	305	1	0	0	0	0	1	0	0	0	17972	623	22	3	681	3	ZNF512B	20	62594086	Missense_Mutation	SNP	C	TCGA-GJ-A6C0-01A-12D-A30V-10	14096527	62594086	431434	29	43765										
EIF4ENIF1	56478	hgsc.bcm.edu	37	chr22	31845450	31845450	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0909090909090909	3	1	1.44	0	1.69411764705882	0.1	0.617038875103394	0	gtaaagatgttgtaggctccAagctccccataaggccactc	9	12	0	1			TCGA-GJ-A6C0-01A-12D-A30V-10	TCGA-GJ-A6C0-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36b33892-0a4d-42f1-8a5c-b51efd4d40a1	6fbe0c9d-a6ae-4737-8e50-926b0b027cdb	g.chr22:31845450A>C	ENST00000397525.1	-	12	1875	c.1652T>G	c.(1651-1653)tTg>tGg	p.L551W	EIF4ENIF1_ENST00000344710.5_Missense_Mutation_p.L376W|EIF4ENIF1_ENST00000330125.5_Missense_Mutation_p.L551W|EIF4ENIF1_ENST00000382180.2_Missense_Mutation_p.L206W|EIF4ENIF1_ENST00000397523.1_Missense_Mutation_p.L527W	NM_001164501.1	NP_001157973.1	Q9NRA8	4ET_HUMAN	eukaryotic translation initiation factor 4E nuclear import factor 1	551						cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						TGTAGGCTCCAAGCTCCCCAT	0.507																																					p.L551W		Atlas-SNP	.											.	EIF4ENIF1	80	.	0			c.T1652G						.						118	118	118					22																	31845450		2203	4300	6503	SO:0001583	missense	56478	exon12			GGCTCCAAGCTCC	AF240775	CCDS13898.1, CCDS54520.1	22q11.2	2007-01-16			ENSG00000184708	ENSG00000184708			16687	protein-coding gene	gene with protein product		607445				10856257	Standard	NM_019843		Approved	4E-T, FLJ21601, Clast4, 2610509L04Rik	uc003akz.2	Q9NRA8	OTTHUMG00000030793	ENST00000397525.1:c.1652T>G	chr22.hg19:g.31845450A>C	ENSP00000380659:p.Leu551Trp	77.0	0.0		72.0	24.0	NM_019843	B1AKL2|B1AKL3|B2RBF1|Q8NCF2|Q9H708	Missense_Mutation	SNP	ENST00000397525.1	hg19	CCDS13898.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.017915	0.75275	.	.	ENSG00000184708	ENST00000344710;ENST00000397525;ENST00000330125;ENST00000397523;ENST00000382180	.	.	.	5.93	4.89	0.63831	.	0.197661	0.43110	D	0.000604	T	0.74696	0.3750	L	0.59436	1.845	0.44694	D	0.997684	D;D;D;B	0.89917	1.0;1.0;1.0;0.013	D;D;D;B	0.91635	0.999;0.999;0.988;0.013	T	0.75204	-0.3400	9	0.54805	T	0.06	-7.5621	12.6931	0.56988	0.8624:0.1376:0.0:0.0	.	376;551;376;527	B1AKL3;Q9NRA8;Q9NRA8-2;B1AKL4	.;4ET_HUMAN;.;.	W	376;551;551;527;206	.	ENSP00000328103:L551W	L	-	2	0	EIF4ENIF1	30175450	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.629000	0.61290	1.050000	0.40346	0.455000	0.32223	TTG	.	.		0.507	EIF4ENIF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127926.1	NM_019843		C	31845450	A	C	31845450	3	2	305	1	0	0	0	0	1	0	0	0	5037	131	5	5	1340	5	EIF4ENIF1	22	31845450	Missense_Mutation	SNP	A	TCGA-GJ-A6C0-01A-12D-A30V-10		31845450	19459116	30	43766										
EP300	2033	hgsc.bcm.edu	37	chr22	41574846	41574846	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0909090909090909	3	1	1.44	0	1.69411764705882	0.1	0.617038875103394	0	tcaatgctttctcagcttgcTagcaatccaggcatggcaaa	8	11	2	0			TCGA-GJ-A6C0-01A-12D-A30V-10	TCGA-GJ-A6C0-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36b33892-0a4d-42f1-8a5c-b51efd4d40a1	6fbe0c9d-a6ae-4737-8e50-926b0b027cdb	g.chr22:41574846T>C	ENST00000263253.7	+	31	8350	c.7131T>C	c.(7129-7131)gcT>gcC	p.A2377A	RP1-85F18.5_ENST00000420537.1_RNA|RP1-85F18.6_ENST00000415054.1_RNA	NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	2377					apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						CTCAGCTTGCTAGCAATCCAG	0.542			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																												p.A2377A		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	.	EP300	367	.	0			c.T7131C						.						50	51	50					22																	41574846		2203	4300	6503	SO:0001819	synonymous_variant	2033	exon31	Familial Cancer Database	Broad Thumb-Hallux syndrome	GCTTGCTAGCAAT	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.7131T>C	chr22.hg19:g.41574846T>C		87.0	0.0		63.0	22.0	NM_001429	B1AKC2	Silent	SNP	ENST00000263253.7	hg19	CCDS14010.1																																																																																			.	.		0.542	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		C	41574846	T	C	41574846	2	2	305	1	0	0	0	0	0	0	0	1	5150	1509	53	2		2	EP300	22	41574846	Silent	SNP	T	TCGA-GJ-A6C0-01A-12D-A30V-10	9729396	41574846	9729720	31	43767										
SHROOM4	57477	hgsc.bcm.edu	37	chrX	50378093	50378093	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0909090909090909	3	1	1.44	0	1.69411764705882	0.1	0.617038875103394	0	cttggtcatgcccactgaggCaacagaacctattagggttc	10	11	1	2			TCGA-GJ-A6C0-01A-12D-A30V-10	TCGA-GJ-A6C0-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36b33892-0a4d-42f1-8a5c-b51efd4d40a1	6fbe0c9d-a6ae-4737-8e50-926b0b027cdb	g.chrX:50378093C>T	ENST00000289292.7	-	4	1263	c.980G>A	c.(979-981)tGc>tAc	p.C327Y	SHROOM4_ENST00000460112.3_Missense_Mutation_p.C211Y|SHROOM4_ENST00000376020.2_Missense_Mutation_p.C327Y			Q9ULL8	SHRM4_HUMAN	shroom family member 4	327					actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					CCCACTGAGGCAACAGAACCT	0.552																																					p.C327Y		Atlas-SNP	.											.	SHROOM4	171	.	0			c.G980A						.						59	43	48					X																	50378093		2203	4300	6503	SO:0001583	missense	57477	exon4			CTGAGGCAACAGA	AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.980G>A	chrX.hg19:g.50378093C>T	ENSP00000289292:p.Cys327Tyr	76.0	0.0		101.0	32.0	NM_020717	A7E2X9|D6RFW0|Q96LA0	Missense_Mutation	SNP	ENST00000289292.7	hg19	CCDS35277.1	.	.	.	.	.	.	.	.	.	.	C	4.540	0.100320	0.08731	.	.	ENSG00000158352	ENST00000289292;ENST00000376020;ENST00000460112	T;T;T	0.15603	2.86;2.86;2.41	5.81	4.93	0.64822	.	0.331162	0.27668	N	0.018342	T	0.22166	0.0534	M	0.65975	2.015	0.39464	D	0.967615	P	0.49961	0.93	P	0.44732	0.459	T	0.03773	-1.1005	10	0.59425	D	0.04	.	8.6758	0.34179	0.171:0.667:0.1619:0.0	.	327	Q9ULL8	SHRM4_HUMAN	Y	327;327;211	ENSP00000289292:C327Y;ENSP00000365188:C327Y;ENSP00000421450:C211Y	ENSP00000289292:C327Y	C	-	2	0	SHROOM4	50394833	0.963000	0.33076	0.924000	0.36721	0.191000	0.23601	2.125000	0.42016	1.171000	0.42768	0.600000	0.82982	TGC	.	.		0.552	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717		T	50378093	C	T	50378093	3	4	305	1	0	0	0	0	1	0	0	0	14311	710	25	3	3525	3	SHROOM4	23	50378093	Missense_Mutation	SNP	C	TCGA-GJ-A6C0-01A-12D-A30V-10		50378093	104892467	32	43768										
MAGEE1	57692	hgsc.bcm.edu	37	chrX	75648383	75648383	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0909090909090909	3	1	1.44	0	1.69411764705882	0.1	0.617038875103394	0	cgcgttgcaaaggctactgcGcacaacagcagctggggcga	14	12	0	0			TCGA-GJ-A6C0-01A-12D-A30V-10	TCGA-GJ-A6C0-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	36b33892-0a4d-42f1-8a5c-b51efd4d40a1	6fbe0c9d-a6ae-4737-8e50-926b0b027cdb	g.chrX:75648383G>A	ENST00000361470.2	+	1	338	c.60G>A	c.(58-60)gcG>gcA	p.A20A		NM_020932.2	NP_065983.1	Q9HCI5	MAGE1_HUMAN	melanoma antigen family E, 1	20						dendrite (GO:0030425)|dystrophin-associated glycoprotein complex (GO:0016010)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	51						AGGCTACTGCGCACAACAGCA	0.662																																					p.A20A		Atlas-SNP	.											.	MAGEE1	236	.	0			c.G60A						.						16	17	17					X																	75648383		2199	4289	6488	SO:0001819	synonymous_variant	57692	exon1			TACTGCGCACAAC	AF490507	CCDS14433.1	Xq13	2008-02-05			ENSG00000198934	ENSG00000198934			24934	protein-coding gene	gene with protein product		300759				14623885	Standard	NM_020932		Approved	KIAA1587, DAMAGE	uc004ecm.2	Q9HCI5	OTTHUMG00000021879	ENST00000361470.2:c.60G>A	chrX.hg19:g.75648383G>A		152.0	0.0		138.0	15.0	NM_020932	Q5JXC7|Q86TG0|Q8TD92|Q9H216	Silent	SNP	ENST00000361470.2	hg19	CCDS14433.1																																																																																			.	.		0.662	MAGEE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057298.1	NM_020932		A	75648383	G	A	75648383	2	1	305	1	0	0	0	0	0	0	0	1	9194	1074	38	1		1	MAGEE1	23	75648383	Silent	SNP	G	TCGA-GJ-A6C0-01A-12D-A30V-10	25270290	75648383	79622177	33	43769										
TP73	7161	hgsc.bcm.edu	37	chr1	3599744	3599744	+	Splice_Site	DEL	G	G	-													0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	ggcatgactacatctgtcatGgtgagtgggggggctgccct							TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr1:3599744delG	ENST00000378295.4	+	3	341	c.186delG	c.(184-186)atg>at	p.M62fs	TP73_ENST00000604074.1_Splice_Site_p.M62fs|TP73_ENST00000346387.4_Splice_Site_p.M62fs|TP73_ENST00000604479.1_Splice_Site_p.M62fs|TP73_ENST00000357733.3_Splice_Site_p.M62fs|TP73_ENST00000354437.4_Splice_Site_p.M62fs|TP73_ENST00000603362.1_Splice_Site_p.M62fs	NM_001204185.1|NM_005427.3	NP_001191114.1|NP_005418.1	O15350	P73_HUMAN	tumor protein p73	62					activation of MAPK activity (GO:0000187)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|cerebrospinal fluid secretion (GO:0033326)|digestive tract morphogenesis (GO:0048546)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|hippocampus development (GO:0021766)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|kidney development (GO:0001822)|mismatch repair (GO:0006298)|mitotic G1 DNA damage checkpoint (GO:0031571)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron development (GO:0048666)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell size (GO:0045793)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902167)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|protein tetramerization (GO:0051262)|release of cytochrome c from mitochondria (GO:0001836)|response to gamma radiation (GO:0010332)|response to organonitrogen compound (GO:0010243)|response to X-ray (GO:0010165)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|cytosol (GO:0005829)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|lung(8)|ovary(1)|prostate(1)	20	all_cancers(77;0.0395)|Ovarian(185;0.0634)|Lung NSC(156;0.188)|all_lung(157;0.198)	all_epithelial(116;7.42e-17)|all_lung(118;1.86e-06)|Lung NSC(185;0.000163)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.109)|Ovarian(437;0.127)		Epithelial(90;5.57e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.87e-22)|GBM - Glioblastoma multiforme(42;5.72e-16)|Colorectal(212;2.22e-05)|COAD - Colon adenocarcinoma(227;8.48e-05)|Kidney(185;0.000539)|BRCA - Breast invasive adenocarcinoma(365;0.000868)|STAD - Stomach adenocarcinoma(132;0.0072)|KIRC - Kidney renal clear cell carcinoma(229;0.00751)|Lung(427;0.226)		CATCTGTCATGGTGAGTGGGG	0.587																																					p.M62fs		Atlas-INDEL	.											.	TP73	54	.	0			c.185delT						.						75	75	75					1																	3599744		2203	4300	6503	SO:0001630	splice_region_variant	7161	exon3			.	AB055065	CCDS49.1, CCDS44049.1, CCDS44050.1, CCDS44051.1, CCDS55566.1, CCDS55567.1, CCDS55568.1, CCDS55569.1, CCDS59965.1	1p36.3	2010-06-15			ENSG00000078900	ENSG00000078900			12003	protein-coding gene	gene with protein product		601990				9296498, 9288759	Standard	NM_001204186		Approved	P73	uc001akp.3	O15350	OTTHUMG00000000610	ENST00000378295.4:c.186+1G>-	chr1.hg19:g.3599744delG		110.0	0.0		84.0	25.0	NM_005427	B7Z7J4|B7Z8Z1|B7Z9C1|C9J521|O15351|Q17RN8|Q5TBV5|Q5TBV6|Q8NHW9|Q8TDY5|Q8TDY6|Q9NTK8	Frame_Shift_Del	DEL	ENST00000378295.4	hg19	CCDS49.1																																																																																			.	.		0.587	TP73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001468.4	NM_005427	Frame_Shift_Del	-	3599744	G	-	3599744	8	5	306	1	0	1	0	1	0	0	1	0	16408	1362	47	0	192	0	TP73	1	3599744	Splice_Site	DEL	G	TCGA-GJ-A9DB-01A-11D-A36X-10		3599744	245650877	1	43770										
CHD5	26038	hgsc.bcm.edu	37	chr1	6214807	6214807	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	tagcggaggggagatggtgaCcgtctctacagccgcagcca	15	11	1	2			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr1:6214807C>T	ENST00000262450.3	-	5	757	c.658G>A	c.(658-660)Gtc>Atc	p.V220I	CHD5_ENST00000378021.1_5'UTR	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5	0					tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		GAGATGGTGACCGTCTCTACA	0.687																																					p.V220I		Atlas-SNP	.											.	CHD5	267	.	0			c.G658A						.						22	21	22					1																	6214807		2203	4299	6502	SO:0001583	missense	26038	exon5			TGGTGACCGTCTC	AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"Zinc fingers, PHD-type"	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.658G>A	chr1.hg19:g.6214807C>T	ENSP00000262450:p.Val220Ile	134.0	0.0		118.0	34.0	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Missense_Mutation	SNP	ENST00000262450.3	hg19	CCDS57.1	.	.	.	.	.	.	.	.	.	.	C	15.14	2.744928	0.49151	.	.	ENSG00000116254	ENST00000262450	D	0.90844	-2.74	3.84	3.84	0.44239	.	0.000000	0.64402	D	0.000008	D	0.92935	0.7752	L	0.55481	1.735	0.80722	D	1	D	0.56521	0.976	P	0.62184	0.899	D	0.92951	0.6380	10	0.45353	T	0.12	-40.9189	16.1333	0.81461	0.0:1.0:0.0:0.0	.	220	Q8TDI0	CHD5_HUMAN	I	220	ENSP00000262450:V220I	ENSP00000262450:V220I	V	-	1	0	CHD5	6137394	1.000000	0.71417	0.920000	0.36463	0.062000	0.15995	4.437000	0.59955	1.876000	0.54355	0.313000	0.20887	GTC	.	.		0.687	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557		T	6214807	C	T	6214807	3	4	306	1	0	0	0	0	1	0	0	0	3330	507	18	3	5354	3	CHD5	1	6214807	Missense_Mutation	SNP	C	TCGA-GJ-A9DB-01A-11D-A36X-10	2615063	6214807	243035814	2	43771										
KDM1A	23028	hgsc.bcm.edu	37	chr1	23370953	23370953	+	Intron	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	acttcaagacgacagttctgGagggtatggagacggccaag	14	8	2	2			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr1:23370953G>C	ENST00000356634.3	+	3	666				MIR3115_ENST00000577915.1_RNA|KDM1A_ENST00000542151.1_Missense_Mutation_p.G184A|KDM1A_ENST00000400181.4_Missense_Mutation_p.G184A|RP1-184J9.2_ENST00000427154.1_RNA	NM_015013.3	NP_055828.2	O60341	KDM1A_HUMAN	lysine (K)-specific demethylase 1A						blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|granulocyte differentiation (GO:0030851)|histone H3-K4 demethylation (GO:0034720)|histone H3-K9 demethylation (GO:0033169)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of DNA binding (GO:0043392)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of protein binding (GO:0032091)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pituitary gland development (GO:0021983)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein demethylation (GO:0006482)|regulation of primitive erythrocyte differentiation (GO:0010725)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|demethylase activity (GO:0032451)|enzyme binding (GO:0019899)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-K4 specific) (GO:0032453)|histone demethylase activity (H3-K9 specific) (GO:0032454)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|MRF binding (GO:0043426)|oxidoreductase activity (GO:0016491)|p53 binding (GO:0002039)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(2)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						GACAGTTCTGGAGGGTATGGA	0.478																																					p.G184A		Atlas-SNP	.											.	KDM1A	49	.	0			c.G551C						.						56	50	52					1																	23370953		1568	3582	5150	SO:0001627	intron_variant	23028	exon3			GTTCTGGAGGGTA	AL031428	CCDS30627.1, CCDS53278.1	1p36.12	2011-07-01	2009-09-29	2009-09-29	ENSG00000004487	ENSG00000004487		"Chromatin-modifying enzymes / K-demethylases"	29079	protein-coding gene	gene with protein product		609132	"amine oxidase (flavin containing) domain 2", "lysine (K)-specific demethylase 1"	AOF2, KDM1		9628581, 12493763	Standard	NM_015013		Approved	KIAA0601, BHC110, LSD1	uc001bgj.2	O60341	OTTHUMG00000003220	ENST00000356634.3:c.518-5927G>C	chr1.hg19:g.23370953G>C		109.0	0.0		114.0	19.0	NM_001009999	A8MWP9|Q5TH94|Q5TH95|Q86VT7|Q8IXK4|Q8NDP6|Q8TAZ3|Q96AW4	Missense_Mutation	SNP	ENST00000356634.3	hg19	CCDS30627.1	.	.	.	.	.	.	.	.	.	.	G	10.25	1.298385	0.23650	.	.	ENSG00000004487	ENST00000400181;ENST00000542151	T;T	0.28454	1.61;1.61	5.55	5.55	0.83447	.	0.496724	0.19159	N	0.121250	T	0.32133	0.0819	N	0.08118	0	0.44908	D	0.997929	D	0.61697	0.99	D	0.72625	0.978	T	0.03993	-1.0986	10	0.06625	T	0.88	-18.6337	17.0077	0.86397	0.0:0.0:1.0:0.0	.	184	O60341-2	.	A	184	ENSP00000383042:G184A;ENSP00000439072:G184A	ENSP00000383042:G184A	G	+	2	0	KDM1A	23243540	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.008000	0.70739	2.755000	0.94549	0.655000	0.94253	GGA	.	.		0.478	KDM1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008880.3	NM_015013		C	23370953	G	C	23370953	1	2	306	0	1	0	0	0	0	0	0	0	8131	1174	41	4		4	KDM1A	1	23370953	Intron	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10	17156146	23370953	225879668	3	43772										
COL8A2	1296	hgsc.bcm.edu	37	chr1	36565003	36565003	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	ggttttcctgggaagccaggGgggccagggggaccccgagg	20	10	0	0			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr1:36565003G>C	ENST00000397799.1	-	4	503	c.279C>G	c.(277-279)ccC>ccG	p.P93P	COL8A2_ENST00000481785.1_Silent_p.P28P|COL8A2_ENST00000303143.4_Silent_p.P93P			P25067	CO8A2_HUMAN	collagen, type VIII, alpha 2	93	Triple-helical region.				angiogenesis (GO:0001525)|camera-type eye morphogenesis (GO:0048593)|collagen catabolic process (GO:0030574)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			NS(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GGAAGCCAGGGGGGCCAGGGG	0.677																																					p.P93P		Atlas-SNP	.											.	COL8A2	41	.	0			c.C279G						.						3	4	4					1																	36565003		1619	3636	5255	SO:0001819	synonymous_variant	1296	exon2			GCCAGGGGGGCCA	M60832	CCDS403.1, CCDS72756.1	1p34.2-p32.3	2014-02-14			ENSG00000171812	ENSG00000171812		"Collagens"	2216	protein-coding gene	gene with protein product		120252		FECD		11689488	Standard	XM_005270477		Approved	PPCD, FECD1, PPCD2	uc001bzv.2	P25067	OTTHUMG00000007665	ENST00000397799.1:c.279C>G	chr1.hg19:g.36565003G>C		46.0	0.0		46.0	15.0	NM_005202	Q5JV31|Q8TEJ5	Silent	SNP	ENST00000397799.1	hg19	CCDS403.1																																																																																			.	.		0.677	COL8A2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313674.1	NM_005202		C	36565003	G	C	36565003	2	2	306	1	0	0	0	0	0	0	0	1	3708	1219	43	4		4	COL8A2	1	36565003	Silent	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10	13194050	36565003	212685618	4	43773										
HIVEP3	59269	hgsc.bcm.edu	37	chr1	42041241	42041241	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	tcgaagattttgatcctcgcCggctcccctctctgggaggc	11	14	1	2			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr1:42041241C>T	ENST00000372583.1	-	5	6066	c.5181G>A	c.(5179-5181)ccG>ccA	p.P1727P	HIVEP3_ENST00000372584.1_Silent_p.P1727P|HIVEP3_ENST00000247584.5_Silent_p.P1727P|HIVEP3_ENST00000429157.2_Silent_p.P1727P|HIVEP3_ENST00000460604.1_5'UTR	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	1727					positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				TGATCCTCGCCGGCTCCCCTC	0.557																																					p.P1727P		Atlas-SNP	.											.	HIVEP3	235	.	0			c.G5181A						.						151	161	158					1																	42041241		2203	4300	6503	SO:0001819	synonymous_variant	59269	exon5			CCTCGCCGGCTCC	AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"Zinc fingers, C2H2-type"	13561	protein-coding gene	gene with protein product	"kappabinding protein-1"	606649	"human immunodeficiency virus type I enhancer-binding protein 3"			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.5181G>A	chr1.hg19:g.42041241C>T		61.0	0.0		87.0	31.0	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Silent	SNP	ENST00000372583.1	hg19	CCDS463.1																																																																																			.	.		0.557	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503		T	42041241	C	T	42041241	2	4	306	1	0	0	0	0	0	0	0	1	7197	639	23	1		1	HIVEP3	1	42041241	Silent	SNP	C	TCGA-GJ-A9DB-01A-11D-A36X-10	5476238	42041241	207209380	5	43774										
CYP4A22	284541	hgsc.bcm.edu	37	chr1	47610597	47610597	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	tgccaggcattggaagagagCtcagcactcccgtcaccttc	10	14	2	1			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr1:47610597C>T	ENST00000371891.3	+	9	1208	c.1177C>T	c.(1177-1179)Ctc>Ttc	p.L393F	CYP4A22_ENST00000294337.3_Missense_Mutation_p.L393F|CYP4A22_ENST00000371890.3_Missense_Mutation_p.L295F|CYP4A22_ENST00000485117.1_3'UTR|CYP4A22-AS1_ENST00000444042.2_lincRNA	NM_001010969.2	NP_001010969.2	Q5TCH4	CP4AM_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 22	393						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TGGAAGAGAGCTCAGCACTCC	0.577																																					p.L393F	Pancreas(88;1240 1470 2099 14214 37557)	Atlas-SNP	.											.	CYP4A22	60	.	0			c.C1177T						.						126	104	111					1																	47610597		2203	4300	6503	SO:0001583	missense	284541	exon9			AGAGAGCTCAGCA		CCDS30707.1	1p33	2007-12-14			ENSG00000162365	ENSG00000162365		"Cytochrome P450s"	20575	protein-coding gene	gene with protein product		615341					Standard	XM_005270768		Approved		uc001cqv.1	Q5TCH4	OTTHUMG00000007845	ENST00000371891.3:c.1177C>T	chr1.hg19:g.47610597C>T	ENSP00000360958:p.Leu393Phe	169.0	0.0		174.0	55.0	NM_001010969	Q5TCH3|Q6JXK7|Q6JXK8|Q9NRM4	Missense_Mutation	SNP	ENST00000371891.3	hg19	CCDS30707.1	.	.	.	.	.	.	.	.	.	.	c	15.82	2.946698	0.53186	.	.	ENSG00000162365	ENST00000371890;ENST00000371891;ENST00000294337	T;T;T	0.70164	-0.46;-0.4;-0.4	1.51	0.497	0.16902	.	0.323945	0.34435	N	0.003974	T	0.74596	0.3737	M	0.81112	2.525	0.34446	D	0.70009	P;P	0.46952	0.887;0.779	P;P	0.56648	0.803;0.589	T	0.78481	-0.2187	10	0.87932	D	0	.	7.6464	0.28323	0.0:0.859:0.0:0.141	.	295;393	Q5TCH5;Q5TCH4	.;CP4AM_HUMAN	F	295;393;393	ENSP00000360957:L295F;ENSP00000360958:L393F;ENSP00000294337:L393F	ENSP00000294337:L393F	L	+	1	0	CYP4A22	47383184	0.011000	0.17503	0.253000	0.24343	0.455000	0.32408	0.635000	0.24629	0.000000	0.14550	0.194000	0.17425	CTC	.	.		0.577	CYP4A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021635.1	XM_208213		T	47610597	C	T	47610597	3	4	306	1	0	0	0	0	1	0	0	0	4186	797	28	3	1211	3	CYP4A22	1	47610597	Missense_Mutation	SNP	C	TCGA-GJ-A9DB-01A-11D-A36X-10	5569356	47610597	201640024	6	43775										
L1TD1	54596	hgsc.bcm.edu	37	chr1	62672399	62672399	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	agagagcagttaacagaaacTgataaggacatagctccggt	11	7	0	3			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr1:62672399T>A	ENST00000498273.1	+	3	394	c.99T>A	c.(97-99)acT>acA	p.T33T		NM_001164835.1|NM_019079.4	NP_001158307.1|NP_061952.3	Q5T7N2	LITD1_HUMAN	LINE-1 type transposase domain containing 1	33										breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	35						taacagaaactgataaggaca	0.328																																					p.T33T		Atlas-SNP	.											.	L1TD1	114	.	0			c.T99A						.						26	23	24					1																	62672399		2025	3947	5972	SO:0001819	synonymous_variant	54596	exon4			AGAAACTGATAAG	BC060808	CCDS619.1	1p31.3	2009-01-12			ENSG00000240563	ENSG00000240563			25595	protein-coding gene	gene with protein product						12477932	Standard	NM_001164835		Approved	FLJ10884, ECAT11	uc001dae.4	Q5T7N2	OTTHUMG00000008914	ENST00000498273.1:c.99T>A	chr1.hg19:g.62672399T>A		324.0	0.0		371.0	27.0	NM_001164835	Q8NDA1|Q9NUV8|Q9NV78	Silent	SNP	ENST00000498273.1	hg19	CCDS619.1																																																																																			.	.		0.328	L1TD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024688.1	NM_019079		A	62672399	T	A	62672399	2	1	306	1	0	0	0	0	0	0	0	1	8598	1567	55	4		4	L1TD1	1	62672399	Silent	SNP	T	TCGA-GJ-A9DB-01A-11D-A36X-10	15061802	62672399	186578222	7	43776										
FOXD3	27022	hgsc.bcm.edu	37	chr1	63788897	63788897	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	ccgccggagctgcgcctggaCgaggcggacgaggtgccccc	17	16	0	0			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr1:63788897C>T	ENST00000371116.2	+	1	168	c.168C>T	c.(166-168)gaC>gaT	p.D56D	RP4-792G4.2_ENST00000427268.1_RNA|RP4-792G4.2_ENST00000418244.1_RNA|RP4-792G4.2_ENST00000426393.1_RNA|RP4-792G4.2_ENST00000431294.1_RNA|RP4-792G4.2_ENST00000449386.1_RNA	NM_012183.2	NP_036315.1	Q9UJU5	FOXD3_HUMAN	forkhead box D3	56					embryonic placenta development (GO:0001892)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|trophectodermal cell differentiation (GO:0001829)	nuclear chromatin (GO:0000790)	double-stranded DNA binding (GO:0003690)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|lung(2)|upper_aerodigestive_tract(1)	5						TGCGCCTGGACGAGGCGGACG	0.731																																					p.D56D	Pancreas(68;276 1750 11966 31252)	Atlas-SNP	.											.	FOXD3	15	.	0			c.C168T						.						12	13	13					1																	63788897		2054	4035	6089	SO:0001819	synonymous_variant	27022	exon1			CCTGGACGAGGCG	AF197560	CCDS624.1	1p31.3	2008-04-10			ENSG00000187140	ENSG00000187140		"Forkhead boxes"	3804	protein-coding gene	gene with protein product		611539				8499623	Standard	NM_012183		Approved	Genesis, HFH2	uc001dax.2	Q9UJU5	OTTHUMG00000009141	ENST00000371116.2:c.168C>T	chr1.hg19:g.63788897C>T		147.0	0.0		111.0	38.0	NM_012183	Q9BYM2|Q9UDD1	Silent	SNP	ENST00000371116.2	hg19	CCDS624.1																																																																																			.	.		0.731	FOXD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025331.1			T	63788897	C	T	63788897	2	4	306	1	0	0	0	0	0	0	0	1	6006	535	19	1		1	FOXD3	1	63788897	Silent	SNP	C	TCGA-GJ-A9DB-01A-11D-A36X-10	1116498	63788897	185461724	8	43777										
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	145075831	145075831	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	agccaaagtcgcatcggcggCggcagcaggacccgctgtct	14	14	1	0			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr1:145075831C>A	ENST00000530740.1	-	1	70	c.32G>T	c.(31-33)cGc>cTc	p.R11L	PDE4DIP_ENST00000369345.4_Missense_Mutation_p.R11L|PDE4DIP_ENST00000369348.3_Missense_Mutation_p.R11L|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.R11L			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	0					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		GCATCGGCGGCGGCAGCAGGA	0.667			T	PDGFRB	MPD																																p.R11L		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.G32T						.						39	47	44					1																	145075831		2173	4272	6445	SO:0001583	missense	9659	exon1			CGGCGGCGGCAGC	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"myomegalin"	608117	"cardiomyopathy associated 2"	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000530740.1:c.32G>T	chr1.hg19:g.145075831C>A	ENSP00000435654:p.Arg11Leu	182.0	0.0		220.0	25.0	NM_022359	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000530740.1	hg19		.	.	.	.	.	.	.	.	.	.	C	17.02	3.281053	0.59758	.	.	ENSG00000178104	ENST00000530740;ENST00000369359;ENST00000369348;ENST00000369345	T;T;T	0.13657	4.08;4.06;2.57	2.04	1.11	0.20524	.	.	.	.	.	T	0.04770	0.0129	N	0.19112	0.55	0.22571	N	0.99898	P;B	0.50443	0.935;0.159	P;B	0.50825	0.651;0.063	T	0.25606	-1.0127	9	0.87932	D	0	.	4.3682	0.11235	0.0:0.8:0.0:0.2	.	11;11	Q5TB27;E9PJ64	.;.	L	11	ENSP00000435654:R11L;ENSP00000358366:R11L;ENSP00000358354:R11L	ENSP00000358351:R11L	R	-	2	0	PDE4DIP	143787188	0.004000	0.15560	0.986000	0.45419	0.758000	0.43043	0.890000	0.28295	0.411000	0.25702	0.511000	0.50034	CGC	.	.		0.667	PDE4DIP-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000384663.2	NM_022359		A	145075831	C	A	145075831	3	1	306	1	0	0	0	0	1	0	0	0	11652	768	27	1	8780	1	PDE4DIP	1	145075831	Missense_Mutation	SNP	C	TCGA-GJ-A9DB-01A-11D-A36X-10	81286934	145075831	104174790	9	43778										
CD5L	922	hgsc.bcm.edu	37	chr1	157803090	157803090	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	ccctgagcaacgaacattatCcagccagatgcggccaaccc	8	16	0	2			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr1:157803090C>A	ENST00000368174.4	-	5	1027	c.931G>T	c.(931-933)Gat>Tat	p.D311Y	CD5L_ENST00000484609.1_5'Flank	NM_005894.2	NP_005885.1	O43866	CD5L_HUMAN	CD5 molecule-like	311	SRCR 3. {ECO:0000255|PROSITE- ProRule:PRU00196}.				apoptotic process (GO:0006915)|cellular defense response (GO:0006968)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	scavenger receptor activity (GO:0005044)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	52	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			CGAACATTATCCAGCCAGATG	0.582																																					p.D311Y		Atlas-SNP	.											CD5L,right_upper_lobe,carcinoma,0,1	CD5L	112	.	0			c.G931T						.						100	100	100					1																	157803090		2203	4300	6503	SO:0001583	missense	922	exon5			CATTATCCAGCCA	U82812	CCDS1171.1	1q21-q23	2008-02-05	2006-03-28		ENSG00000073754	ENSG00000073754			1690	protein-coding gene	gene with protein product		602592	"apoptosis inhibitor 6", "CD5 antigen-like (scavenger receptor cysteine rich family)"	API6		9045627	Standard	NM_005894		Approved	Spalpha	uc001frk.4	O43866	OTTHUMG00000022440	ENST00000368174.4:c.931G>T	chr1.hg19:g.157803090C>A	ENSP00000357156:p.Asp311Tyr	125.0	0.0		125.0	28.0	NM_005894	A8K7M5|Q6UX63	Missense_Mutation	SNP	ENST00000368174.4	hg19	CCDS1171.1	.	.	.	.	.	.	.	.	.	.	C	18.51	3.640674	0.67244	.	.	ENSG00000073754	ENST00000368174	T	0.37235	1.21	5.06	5.06	0.68205	Speract/scavenger receptor (3);Speract/scavenger receptor-related (2);	0.222845	0.34555	N	0.003876	T	0.58352	0.2116	M	0.92367	3.3	0.36566	D	0.872727	D	0.89917	1.0	D	0.81914	0.995	T	0.68588	-0.5369	10	0.72032	D	0.01	.	9.3594	0.38186	0.0:0.905:0.0:0.095	.	311	O43866	CD5L_HUMAN	Y	311	ENSP00000357156:D311Y	ENSP00000357156:D311Y	D	-	1	0	CD5L	156069714	1.000000	0.71417	0.998000	0.56505	0.897000	0.52465	3.695000	0.54749	2.615000	0.88500	0.655000	0.94253	GAT	.	.		0.582	CD5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058346.1	NM_005894		A	157803090	C	A	157803090	3	1	306	1	0	0	0	0	1	0	0	0	3029	855	30	3	120	3	CD5L	1	157803090	Missense_Mutation	SNP	C	TCGA-GJ-A9DB-01A-11D-A36X-10	12727259	157803090	91447531	10	43779										
PRG4	10216	hgsc.bcm.edu	37	chr1	186277296	186277296	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	gggcccacatccaccacctcTgacaagcctgctccaactac	6	19	1	1			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr1:186277296T>C	ENST00000445192.2	+	7	2490	c.2445T>C	c.(2443-2445)tcT>tcC	p.S815S	PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367483.4_Silent_p.S774S|PRG4_ENST00000367485.4_Silent_p.S722S|PRG4_ENST00000367486.3_Silent_p.S772S	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	815	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						CCACCACCTCTGACAAGCCTG	0.592																																					p.S815S		Atlas-SNP	.											PRG4,NS,carcinoma,0,1	PRG4	259	.	0			c.T2445C						.						216	243	234					1																	186277296		2203	4300	6503	SO:0001819	synonymous_variant	10216	exon7			CACCTCTGACAAG	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"lubricin", "megakaryocyte stimulating factor", "articular superficial zone protein", "Jacobs camptodactyly-arthropathy-pericarditis syndrome", "camptodactyly, arthropathy, coxa vara, pericarditis syndrome", "bG174L6.2 (MSF: megakaryocyte stimulating factor )"	604283	"proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.2445T>C	chr1.hg19:g.186277296T>C		130.0	1.0		163.0	67.0	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Silent	SNP	ENST00000445192.2	hg19	CCDS1369.1																																																																																			.	.		0.592	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807		C	186277296	T	C	186277296	2	2	306	1	0	0	0	0	0	0	0	1	12493	1567	55	2		2	PRG4	1	186277296	Silent	SNP	T	TCGA-GJ-A9DB-01A-11D-A36X-10	28474206	186277296	62973325	11	43780										
CNTN2	6900	hgsc.bcm.edu	37	chr1	205027106	205027106	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	gcctgtctttgaagaccagcCcctcagtgtgctattcccag	9	14	2	2			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr1:205027106C>T	ENST00000331830.4	+	3	412	c.128C>T	c.(127-129)cCc>cTc	p.P43L		NM_005076.3	NP_005067.1	Q02246	CNTN2_HUMAN	contactin 2 (axonal)	43	Ig-like C2-type 1.				adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|central nervous system myelination (GO:0022010)|cerebral cortex GABAergic interneuron migration (GO:0021853)|clustering of voltage-gated potassium channels (GO:0045163)|establishment of protein localization to juxtaparanode region of axon (GO:0071206)|learning (GO:0007612)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|positive regulation of protein processing (GO:0010954)|presynaptic membrane organization (GO:0097090)|receptor internalization (GO:0031623)|regulation of astrocyte differentiation (GO:0048710)|regulation of axon diameter (GO:0031133)|regulation of neuronal synaptic plasticity (GO:0048168)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|juxtaparanode region of axon (GO:0044224)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated potassium channel complex (GO:0008076)	carbohydrate binding (GO:0030246)|identical protein binding (GO:0042802)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(11)|lung(23)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	54	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			GAAGACCAGCCCCTCAGTGTG	0.627																																					p.P43L	Melanoma(183;2548 2817 37099 41192)	Atlas-SNP	.											.	CNTN2	116	.	0			c.C128T						.						48	46	47					1																	205027106		2203	4300	6503	SO:0001583	missense	6900	exon3			ACCAGCCCCTCAG	X67734	CCDS1449.1	1q32.1	2013-02-11			ENSG00000184144	ENSG00000184144		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2172	protein-coding gene	gene with protein product		190197		TAX, AXT		8307567, 8586965	Standard	NM_005076		Approved	TAG-1, TAX1	uc001hbr.3	Q02246	OTTHUMG00000037105	ENST00000331830.4:c.128C>T	chr1.hg19:g.205027106C>T	ENSP00000330633:p.Pro43Leu	213.0	0.0		181.0	54.0	NM_005076	P78432|Q5T054	Missense_Mutation	SNP	ENST00000331830.4	hg19	CCDS1449.1	.	.	.	.	.	.	.	.	.	.	C	19.92	3.916184	0.73098	.	.	ENSG00000184144	ENST00000331830	T	0.44083	0.93	5.4	5.4	0.78164	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.52532	D	0.000061	T	0.65923	0.2738	M	0.74389	2.26	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.69495	-0.5130	10	0.87932	D	0	.	16.9422	0.86221	0.0:1.0:0.0:0.0	.	43	Q02246	CNTN2_HUMAN	L	43	ENSP00000330633:P43L	ENSP00000330633:P43L	P	+	2	0	CNTN2	203293729	1.000000	0.71417	0.850000	0.33497	0.195000	0.23768	7.072000	0.76777	2.508000	0.84585	0.655000	0.94253	CCC	.	.		0.627	CNTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090080.3	NM_005076		T	205027106	C	T	205027106	3	4	306	1	0	0	0	0	1	0	0	0	3643	623	22	3	134	3	CNTN2	1	205027106	Missense_Mutation	SNP	C	TCGA-GJ-A9DB-01A-11D-A36X-10	18749810	205027106	44223515	12	43781										
NUP133	55746	hgsc.bcm.edu	37	chr1	229631653	229631653	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	tcttacccaaatagcatcggTaatgttttccttcagggctc	7	11	2	0			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr1:229631653T>C	ENST00000261396.3	-	7	1052	c.961A>G	c.(961-963)Acc>Gcc	p.T321A	NUP133_ENST00000537506.1_Missense_Mutation_p.T305A	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	321					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore organization (GO:0006999)|paraxial mesoderm development (GO:0048339)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)			NS(1)|breast(7)|endometrium(1)|kidney(6)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(4)	56	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				ATAGCATCGGTAATGTTTTCC	0.328																																					p.T321A		Atlas-SNP	.											.	NUP133	111	.	0			c.A961G						.						120	121	120					1																	229631653		2203	4300	6503	SO:0001583	missense	55746	exon7			CATCGGTAATGTT		CCDS1579.1	1q42.13	2008-02-05	2002-08-29		ENSG00000069248	ENSG00000069248			18016	protein-coding gene	gene with protein product		607613	"nucleoporin 133kD"			11684705	Standard	NM_018230		Approved	FLJ10814	uc001htn.3	Q8WUM0	OTTHUMG00000039462	ENST00000261396.3:c.961A>G	chr1.hg19:g.229631653T>C	ENSP00000261396:p.Thr321Ala	33.0	0.0		28.0	9.0	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Missense_Mutation	SNP	ENST00000261396.3	hg19	CCDS1579.1	.	.	.	.	.	.	.	.	.	.	T	8.283	0.815938	0.16607	.	.	ENSG00000069248	ENST00000366681;ENST00000261396;ENST00000366679;ENST00000537506	T;T;T	0.40225	1.04;1.04;1.04	5.57	0.468	0.16732	WD40/YVTN repeat-like-containing domain (1);Nucleoporin, Nup133/Nup155-like, N-terminal (1);	0.434585	0.28322	N	0.015769	T	0.18257	0.0438	N	0.13043	0.29	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.24012	-1.0172	10	0.08837	T	0.75	-27.3619	6.0272	0.19662	0.1233:0.3829:0.0:0.4937	.	321	Q8WUM0	NU133_HUMAN	A	321;321;321;305	ENSP00000261396:T321A;ENSP00000355640:T321A;ENSP00000443496:T305A	ENSP00000261396:T321A	T	-	1	0	NUP133	227698276	0.001000	0.12720	0.063000	0.19743	0.974000	0.67602	0.011000	0.13264	0.045000	0.15804	0.528000	0.53228	ACC	.	.		0.328	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230		C	229631653	T	C	229631653	3	2	306	1	0	0	0	0	1	0	0	0	10763	1638	57	2	2589	2	NUP133	1	229631653	Missense_Mutation	SNP	T	TCGA-GJ-A9DB-01A-11D-A36X-10	24604547	229631653	19618968	13	43782										
LGALS8	3964	hgsc.bcm.edu	37	chr1	236703931	236703931	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	cccagagaaaatagacactcTgggcatttatggcaaagtga	10	8	1	3			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr1:236703931T>C	ENST00000366584.4	+	5	979	c.413T>C	c.(412-414)cTg>cCg	p.L138P	LGALS8_ENST00000341872.6_Missense_Mutation_p.L138P|LGALS8_ENST00000352231.2_Missense_Mutation_p.L138P|RP11-385F5.4_ENST00000433131.1_RNA|LGALS8_ENST00000526634.1_Missense_Mutation_p.L138P|LGALS8_ENST00000323938.6_Missense_Mutation_p.L111P|LGALS8_ENST00000526589.1_Missense_Mutation_p.L138P|LGALS8_ENST00000450372.2_Missense_Mutation_p.L138P|LGALS8_ENST00000527974.1_Missense_Mutation_p.L138P|LGALS8_ENST00000525042.1_Intron|LGALS8_ENST00000416919.2_Intron	NM_201544.2	NP_963838.1	O00214	LEG8_HUMAN	lectin, galactoside-binding, soluble, 8	138	Galectin 1. {ECO:0000255|PROSITE- ProRule:PRU00639}.				plasma cell differentiation (GO:0002317)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(5)	20	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.0253)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			ATAGACACTCTGGGCATTTAT	0.478																																					p.L138P		Atlas-SNP	.											.	LGALS8	42	.	0			c.T413C						.						172	175	174					1																	236703931		2203	4300	6503	SO:0001583	missense	3964	exon6			ACACTCTGGGCAT	X91790	CCDS1611.1, CCDS1612.1	1q43	2011-08-04	2008-07-25		ENSG00000116977	ENSG00000116977		"Lectins, galactoside-binding"	6569	protein-coding gene	gene with protein product	"galectin 8"	606099				7852431, 8692978	Standard	NM_201545		Approved	PCTA-1	uc001hxy.2	O00214	OTTHUMG00000039953	ENST00000366584.4:c.413T>C	chr1.hg19:g.236703931T>C	ENSP00000355543:p.Leu138Pro	51.0	0.0		57.0	17.0	NM_006499	O15215|Q5T3P5|Q5T3Q4|Q8TEV1|Q96B92|Q9BXC8|Q9H584|Q9H585|Q9UEZ6|Q9UP32|Q9UP33|Q9UP34	Missense_Mutation	SNP	ENST00000366584.4	hg19	CCDS1612.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.462896	0.84425	.	.	ENSG00000116977	ENST00000454943;ENST00000527974;ENST00000352231;ENST00000406509;ENST00000526589;ENST00000341872;ENST00000450372;ENST00000366584;ENST00000356238;ENST00000323938;ENST00000526634	T;T;T;T;T;T;T;T;T;T	0.10573	2.86;2.86;2.86;2.86;2.86;2.86;2.86;2.86;2.86;2.86	5.46	5.46	0.80206	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	0.300108	0.32218	N	0.006418	T	0.48572	0.1507	H	0.96996	3.92	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.66728	-0.5850	10	0.87932	D	0	-3.484	15.7119	0.77635	0.0:0.0:0.0:1.0	.	138;138	O00214;O00214-2	LEG8_HUMAN;.	P	138;138;138;138;138;138;138;138;138;111;138	ENSP00000405504:L138P;ENSP00000431398:L138P;ENSP00000309576:L138P;ENSP00000385999:L138P;ENSP00000435460:L138P;ENSP00000342139:L138P;ENSP00000408657:L138P;ENSP00000355543:L138P;ENSP00000434860:L111P;ENSP00000437040:L138P	ENSP00000434860:L111P	L	+	2	0	LGALS8	234770554	1.000000	0.71417	0.994000	0.49952	0.959000	0.62525	7.340000	0.79292	2.291000	0.77112	0.533000	0.62120	CTG	.	.		0.478	LGALS8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000096365.2	NM_006499		C	236703931	T	C	236703931	3	2	306	1	0	0	0	0	1	0	0	0	8756	1580	55	2	427	2	LGALS8	1	236703931	Missense_Mutation	SNP	T	TCGA-GJ-A9DB-01A-11D-A36X-10	7072278	236703931	12546690	14	43783										
FOXN2	3344	hgsc.bcm.edu	37	chr2	48602270	48602270	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	tccctgtcttctgtggatgaGgtatatgaatttatcccaaa	8	8	2	2			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr2:48602270G>C	ENST00000340553.3	+	7	1245	c.984G>C	c.(982-984)gaG>gaC	p.E328D		NM_002158.3	NP_002149.2	P32314	FOXN2_HUMAN	forkhead box N2	328					transcription, DNA-templated (GO:0006351)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	13		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.0272)|LUSC - Lung squamous cell carcinoma(58;0.036)			CTGTGGATGAGGTATATGAAT	0.438																																					p.E328D		Atlas-SNP	.											.	FOXN2	39	.	0			c.G984C						.						123	106	112					2																	48602270		2203	4300	6503	SO:0001583	missense	3344	exon7			GGATGAGGTATAT		CCDS1838.1	2p22-p16	2008-02-05	2006-10-02	2006-10-02	ENSG00000170802	ENSG00000170802		"Forkhead boxes"	5281	protein-coding gene	gene with protein product		143089	"human T-cell leukemia virus enhancer factor"	HTLF		1639393	Standard	NM_002158		Approved		uc002rwh.1	P32314	OTTHUMG00000129168	ENST00000340553.3:c.984G>C	chr2.hg19:g.48602270G>C	ENSP00000343633:p.Glu328Asp	100.0	0.0		107.0	16.0	NM_002158	Q15769|Q6P4Q2	Missense_Mutation	SNP	ENST00000340553.3	hg19	CCDS1838.1	.	.	.	.	.	.	.	.	.	.	G	10.62	1.400247	0.25291	.	.	ENSG00000170802	ENST00000304367;ENST00000340553	D	0.92647	-3.08	4.69	1.92	0.25849	.	0.165824	0.51477	D	0.000098	D	0.90092	0.6905	L	0.28344	0.845	0.40539	D	0.981003	D	0.63880	0.993	D	0.70016	0.967	D	0.84567	0.0653	10	0.13470	T	0.59	.	7.9389	0.29946	0.3965:0.0:0.6035:0.0	.	328	P32314	FOXN2_HUMAN	D	237;328	ENSP00000343633:E328D	ENSP00000305685:E237D	E	+	3	2	FOXN2	48455774	1.000000	0.71417	0.949000	0.38748	0.976000	0.68499	0.692000	0.25482	0.311000	0.23014	-0.145000	0.13849	GAG	.	.		0.438	FOXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251240.3	NM_002158		C	48602270	G	C	48602270	3	2	306	1	0	0	0	0	1	0	0	0	6028	991	35	4	1002	4	FOXN2	2	48602270	Missense_Mutation	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10		48602270	194597103	15	43784										
VPS54	51542	hgsc.bcm.edu	37	chr2	64208898	64208898	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	atgtttttgtgaagaagtcaGattctctttttgctaatcta	7	5	3	3			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr2:64208898G>T	ENST00000272322.4	-	3	414	c.260C>A	c.(259-261)tCt>tAt	p.S87Y	VPS54_ENST00000409558.4_Missense_Mutation_p.S75Y			Q9P1Q0	VPS54_HUMAN	vacuolar protein sorting 54 homolog (S. cerevisiae)	87					growth (GO:0040007)|homeostasis of number of cells within a tissue (GO:0048873)|musculoskeletal movement (GO:0050881)|neurofilament cytoskeleton organization (GO:0060052)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	GARP complex (GO:0000938)				endometrium(3)|kidney(4)|large_intestine(8)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	27						GAAGAAGTCAGATTCTCTTTT	0.393																																					p.S87Y		Atlas-SNP	.											.	VPS54	57	.	0			c.C260A						.						245	224	231					2																	64208898		2203	4300	6503	SO:0001583	missense	51542	exon3			AAGTCAGATTCTC	AF102177	CCDS33208.1, CCDS46302.1	2p15-p14	2014-06-13	2006-12-19		ENSG00000143952	ENSG00000143952			18652	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 164"	614633	"vacuolar protein sorting 54 (yeast)"			12039048	Standard	NM_016516		Approved	HCC8, PPP1R164	uc002scq.3	Q9P1Q0	OTTHUMG00000152627	ENST00000272322.4:c.260C>A	chr2.hg19:g.64208898G>T	ENSP00000272322:p.Ser87Tyr	142.0	0.0		101.0	41.0	NM_016516	Q5VIR5|Q86YF7|Q8N6G3|Q9NPV0|Q9NT07|Q9NUJ0	Missense_Mutation	SNP	ENST00000272322.4	hg19	CCDS33208.1	.	.	.	.	.	.	.	.	.	.	G	29.6	5.018588	0.93404	.	.	ENSG00000143952	ENST00000272322;ENST00000409558;ENST00000483277;ENST00000394400	T;T	0.35236	1.32;1.32	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.62122	0.2402	M	0.71036	2.16	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.67548	0.915;0.952	T	0.60697	-0.7212	10	0.72032	D	0.01	.	20.8598	0.99761	0.0:0.0:1.0:0.0	.	87;75	Q9P1Q0;Q9P1Q0-4	VPS54_HUMAN;.	Y	87;75;75;87	ENSP00000272322:S87Y;ENSP00000386980:S75Y	ENSP00000272322:S87Y	S	-	2	0	VPS54	64062402	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.564000	0.98151	2.937000	0.99478	0.650000	0.86243	TCT	.	.		0.393	VPS54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327062.2	NM_016516		T	64208898	G	T	64208898	3	4	306	1	0	0	0	0	1	0	0	0	17231	942	33	3	2757	3	VPS54	2	64208898	Missense_Mutation	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10	15606628	64208898	178990475	16	43785										
MOGS	7841	hgsc.bcm.edu	37	chr2	74689306	74689306	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	aggcatgcaggcggggcaagGcctttcggaggaaagccaag	17	9	0	0			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr2:74689306G>A	ENST00000233616.4	-	4	1772	c.1610C>T	c.(1609-1611)gCc>gTc	p.A537V	MOGS_ENST00000452063.2_Missense_Mutation_p.A431V|MOGS_ENST00000409065.1_3'UTR|MOGS_ENST00000462443.1_5'Flank	NM_006302.2	NP_006293.2	Q13724	MOGS_HUMAN	mannosyl-oligosaccharide glucosidase	537					cellular protein metabolic process (GO:0044267)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucosidase activity (GO:0015926)|mannosyl-oligosaccharide glucosidase activity (GO:0004573)			cervix(1)|endometrium(6)|large_intestine(3)|lung(10)|prostate(1)|urinary_tract(2)	23						GCGGGGCAAGGCCTTTCGGAG	0.607																																					p.A537V		Atlas-SNP	.											.	MOGS	58	.	0			c.C1610T						.						75	82	80					2																	74689306		1986	4160	6146	SO:0001583	missense	7841	exon4			GGCAAGGCCTTTC	X87237	CCDS42700.1, CCDS54370.1	2p13.1	2012-01-31			ENSG00000115275	ENSG00000115275	3.2.1.106		24862	protein-coding gene	gene with protein product	"glucosidase I", "processing A-glucosidase I"	601336				7635146, 8786151	Standard	NM_006302		Approved	GCS1, CWH41, DER7	uc010ffj.3	Q13724	OTTHUMG00000152886	ENST00000233616.4:c.1610C>T	chr2.hg19:g.74689306G>A	ENSP00000233616:p.Ala537Val	137.0	0.0		119.0	32.0	NM_006302	A8K938|F5H6D0|Q17RN9|Q8TCT5	Missense_Mutation	SNP	ENST00000233616.4	hg19	CCDS42700.1	.	.	.	.	.	.	.	.	.	.	G	4.979	0.181823	0.09495	.	.	ENSG00000115275	ENST00000233616;ENST00000452063;ENST00000448666	T;T;T	0.38077	1.16;1.16;1.16	5.19	5.19	0.71726	Six-hairpin glycosidase-like (1);	0.320352	0.30630	N	0.009205	T	0.25044	0.0608	N	0.20807	0.61	0.80722	D	1	B	0.29612	0.251	B	0.29862	0.108	T	0.05484	-1.0882	10	0.15066	T	0.55	-15.8438	16.2431	0.82426	0.0:0.0:1.0:0.0	.	537	Q13724	MOGS_HUMAN	V	537;431;431	ENSP00000233616:A537V;ENSP00000388201:A431V;ENSP00000410992:A431V	ENSP00000233616:A537V	A	-	2	0	MOGS	74542814	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	5.399000	0.66314	2.710000	0.92621	0.655000	0.94253	GCC	.	.		0.607	MOGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328382.1	NM_006302		A	74689306	G	A	74689306	3	1	306	1	0	0	0	0	1	0	0	0	9706	1203	42	3	907	3	MOGS	2	74689306	Missense_Mutation	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10	10480408	74689306	168510067	17	43786										
BIN1	274	hgsc.bcm.edu	37	chr2	127808484	127808484	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	ccaccacgacagcaggaagaGagctctggtggcagaggtac	14	11	1	2			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr2:127808484G>T	ENST00000316724.5	-	17	1877	c.1466C>A	c.(1465-1467)tCt>tAt	p.S489Y	BIN1_ENST00000466111.1_5'UTR|BIN1_ENST00000393041.3_Missense_Mutation_p.S371Y|BIN1_ENST00000393040.3_Missense_Mutation_p.S378Y|BIN1_ENST00000346226.3_Missense_Mutation_p.S414Y|BIN1_ENST00000259238.4_Missense_Mutation_p.S393Y|BIN1_ENST00000376113.2_Missense_Mutation_p.S320Y|BIN1_ENST00000357970.3_Missense_Mutation_p.S446Y|BIN1_ENST00000348750.4_Missense_Mutation_p.S305Y|BIN1_ENST00000351659.3_Missense_Mutation_p.S402Y|BIN1_ENST00000409400.1_Missense_Mutation_p.S335Y|BIN1_ENST00000352848.3_Missense_Mutation_p.S350Y	NM_139343.2	NP_647593.1	O00499	BIN1_HUMAN	bridging integrator 1	489					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|lipid tube assembly (GO:0060988)|muscle cell differentiation (GO:0042692)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of endocytosis (GO:0045807)|positive regulation of GTPase activity (GO:0043547)|regulation of cell cycle arrest (GO:0071156)|regulation of neuron differentiation (GO:0045664)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|axon initial segment (GO:0043194)|axon terminus (GO:0043679)|cerebellar mossy fiber (GO:0044300)|cytoplasm (GO:0005737)|I band (GO:0031674)|lipid tube (GO:0060987)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)|T-tubule (GO:0030315)|varicosity (GO:0043196)|Z disc (GO:0030018)	identical protein binding (GO:0042802)|tau protein binding (GO:0048156)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(3)|skin(3)	24	Colorectal(110;0.0831)			BRCA - Breast invasive adenocarcinoma(221;0.073)		AGCAGGAAGAGAGCTCTGGTG	0.662																																					p.S489Y		Atlas-SNP	.											.	BIN1	85	.	0			c.C1466A						.						49	51	51					2																	127808484		2203	4300	6503	SO:0001583	missense	274	exon17			GGAAGAGAGCTCT	U68485	CCDS2137.1, CCDS2138.1, CCDS2139.1, CCDS2140.1, CCDS2141.1, CCDS2142.1, CCDS2143.1, CCDS42743.1, CCDS42744.1, CCDS46403.1	2q14	2014-09-17			ENSG00000136717	ENSG00000136717			1052	protein-coding gene	gene with protein product	"amphiphysin II"	601248		AMPHL		8725406, 8782822, 17676042	Standard	NM_004305		Approved	SH3P9, AMPH2	uc002tns.2	O00499	OTTHUMG00000131465	ENST00000316724.5:c.1466C>A	chr2.hg19:g.127808484G>T	ENSP00000316779:p.Ser489Tyr	323.0	0.0		215.0	31.0	NM_139343	O00297|O00545|O43867|O60552|O60553|O60554|O60555|O75514|O75515|O75516|O75517|O75518|Q659B7|Q92944|Q99688	Missense_Mutation	SNP	ENST00000316724.5	hg19	CCDS2138.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.419808	0.83559	.	.	ENSG00000136717	ENST00000376113;ENST00000357970;ENST00000393040;ENST00000348750;ENST00000259238;ENST00000346226;ENST00000393041;ENST00000351659;ENST00000352848;ENST00000316724;ENST00000409400	T;T;T;T;T;T;T;T;T;T;T	0.65916	0.39;-0.18;0.35;0.38;0.37;0.39;0.32;0.32;0.36;-0.18;0.4	4.82	4.82	0.62117	.	0.216060	0.41001	D	0.000975	T	0.69450	0.3112	L	0.27053	0.805	0.38360	D	0.944577	D;P;D;D;D;D;D;D;D;D;D;D;D	0.76494	0.997;0.94;0.999;0.999;0.997;0.997;0.988;0.994;0.999;0.997;0.998;0.997;0.995	P;P;D;D;D;D;D;P;D;D;D;D;D	0.91635	0.854;0.61;0.998;0.968;0.999;0.964;0.972;0.854;0.999;0.976;0.968;0.935;0.943	T	0.75513	-0.3291	10	0.72032	D	0.01	-22.7633	16.8717	0.86041	0.0:0.0:1.0:0.0	.	366;281;371;335;378;414;402;350;393;446;320;305;489	B7Z2Z2;B7Z6Y2;O00499-4;O00499-7;O00499-6;O00499-2;O00499-3;O00499-8;O00499-11;O00499-5;O00499-10;O00499-9;O00499	.;.;.;.;.;.;.;.;.;.;.;.;BIN1_HUMAN	Y	320;446;378;305;393;414;371;402;350;489;335	ENSP00000365281:S320Y;ENSP00000350654:S446Y;ENSP00000376760:S378Y;ENSP00000259237:S305Y;ENSP00000259238:S393Y;ENSP00000315411:S414Y;ENSP00000376761:S371Y;ENSP00000315388:S402Y;ENSP00000315284:S350Y;ENSP00000316779:S489Y;ENSP00000386797:S335Y	ENSP00000259238:S393Y	S	-	2	0	BIN1	127524954	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.561000	0.73955	2.506000	0.84524	0.555000	0.69702	TCT	.	.		0.662	BIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254298.2	NM_139343		T	127808484	G	T	127808484	3	4	306	1	0	0	0	0	1	0	0	0	1432	942	33	3	327	3	BIN1	2	127808484	Missense_Mutation	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10	53119178	127808484	115390889	18	43787										
TMEFF2	23671	hgsc.bcm.edu	37	chr2	192820997	192820997	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	ttacctgcaagatggctcctGcatattgatagaatgctcac	8	10	1	3			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr2:192820997G>A	ENST00000272771.5	-	8	2037	c.853C>T	c.(853-855)Cag>Tag	p.Q285*	TMEFF2_ENST00000392314.1_Nonsense_Mutation_p.Q285*|AC098617.1_ENST00000424116.2_RNA|AC098617.1_ENST00000428980.2_RNA	NM_016192.2	NP_057276.2	Q9UIK5	TEFF2_HUMAN	transmembrane protein with EGF-like and two follistatin-like domains 2	285	EGF-like. {ECO:0000255|PROSITE- ProRule:PRU00076}.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				breast(2)|cervix(1)|kidney(2)|large_intestine(4)|liver(1)|lung(12)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27			OV - Ovarian serous cystadenocarcinoma(117;0.0835)			GATGGCTCCTGCATATTGATA	0.353																																					p.Q285X	Pancreas(50;1277 1381 28487 47072)	Atlas-SNP	.											.	TMEFF2	54	.	0			c.C853T						.						127	111	116					2																	192820997		2202	4300	6502	SO:0001587	stop_gained	23671	exon8			GCTCCTGCATATT	AB017269	CCDS2314.1	2q32.3	2010-05-04			ENSG00000144339	ENSG00000144339			11867	protein-coding gene	gene with protein product	"transmembrane protein TENB2", "tomoregulin", "cancer/testis antigen family 120, member 2"	605734				10903839	Standard	NM_016192		Approved	TENB2, HPP1, TR, TPEF, CT120.2	uc002utc.3	Q9UIK5	OTTHUMG00000132723	ENST00000272771.5:c.853C>T	chr2.hg19:g.192820997G>A	ENSP00000272771:p.Gln285*	72.0	0.0		84.0	11.0	NM_016192	Q2FA44|Q4ZFW4|Q53H90|Q53RE1|Q8N2R5|Q9NR15|Q9NSS5|Q9P2Y9|Q9UK65	Nonsense_Mutation	SNP	ENST00000272771.5	hg19	CCDS2314.1	.	.	.	.	.	.	.	.	.	.	G	47	13.140383	0.99722	.	.	ENSG00000144339	ENST00000392314;ENST00000272771	.	.	.	4.55	4.55	0.56014	.	0.469460	0.22838	N	0.055005	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.22109	T	0.4	-7.7253	17.8495	0.88740	0.0:0.0:1.0:0.0	.	.	.	.	X	285	.	ENSP00000272771:Q285X	Q	-	1	0	TMEFF2	192529242	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.180000	0.50895	2.499000	0.84300	0.491000	0.48974	CAG	.	.		0.353	TMEFF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256065.2	NM_016192		A	192820997	G	A	192820997	4	1	306	1	0	0	0	0	0	1	0	0	16029	1328	46	3	283	3	TMEFF2	2	192820997	Nonsense_Mutation	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10	65012513	192820997	50378376	19	43788										
MTMR14	64419	hgsc.bcm.edu	37	chr3	9739394	9739394	+	Splice_Site	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	tctctctcctctctgccccaGatcagtggaccatcccctgc	6	19	4	1			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr3:9739394G>T	ENST00000296003.4	+	18	1735		c.e18-1		MTMR14_ENST00000420925.1_Intron|MTMR14_ENST00000351233.5_Intron|MTMR14_ENST00000353332.5_Intron	NM_001077525.2	NP_001070993.1	Q8NCE2	MTMRE_HUMAN	myotubularin related protein 14						phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)	p.?(1)		breast(1)|endometrium(3)|kidney(2)|lung(10)|skin(3)|upper_aerodigestive_tract(2)	21	Medulloblastoma(99;0.227)					CTCTGCCCCAGATCAGTGGAC	0.617																																					.		Atlas-SNP	.											MTMR14,NS,carcinoma,0,1	MTMR14	43	.	1	Unknown(1)	lung(1)	c.1614-1G>T						.						126	128	127					3																	9739394		1982	4176	6158	SO:0001630	splice_region_variant	64419	exon18			GCCCCAGATCAGT	BC001674	CCDS43043.1, CCDS43044.1, CCDS43045.1	3p26	2011-06-09	2006-12-18	2006-12-18	ENSG00000163719	ENSG00000163719		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	26190	protein-coding gene	gene with protein product	"egg-derived tyrosine phosphatase homolog (Drosophila)"	611089	"chromosome 3 open reading frame 29"	C3orf29		15186772	Standard	NM_022485		Approved	FLJ22405, FLJ90311, hJumpy, hEDTP	uc003brz.3	Q8NCE2	OTTHUMG00000155111	ENST00000296003.4:c.1614-1G>T	chr3.hg19:g.9739394G>T		50.0	0.0		57.0	29.0	NM_001077525	Q0JTH5|Q0JU83|Q6PIZ4|Q6QE21|Q86VK9|Q8IYK1|Q8TCM7|Q9H6C0	Splice_Site	SNP	ENST00000296003.4	hg19	CCDS43043.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.417945	0.83449	.	.	ENSG00000163719	ENST00000296003	.	.	.	5.64	5.64	0.86602	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.7013	0.96054	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MTMR14	9714394	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.856000	0.75450	2.657000	0.90304	0.655000	0.94253	.	.	.		0.617	MTMR14-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338435.1	NM_022485	Intron	T	9739394	G	T	9739394	5	4	306	1	0	0	0	0	0	0	1	0	9951	956	33	3	1683	3	MTMR14	3	9739394	Splice_Site	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10		9739394	188283036	20	43789										
CLCN2	1181	hgsc.bcm.edu	37	chr3	184071474	184071474	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	ggactccactagggccagcaTtcggcccttggtcctgtgca	12	14	0	0			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr3:184071474T>A	ENST00000265593.4	-	16	2002	c.1831A>T	c.(1831-1833)Atg>Ttg	p.M611L	CLCN2_ENST00000475279.1_5'Flank|CLCN2_ENST00000434054.2_Missense_Mutation_p.M567L|CLCN2_ENST00000423355.2_3'UTR|CLCN2_ENST00000457512.1_Missense_Mutation_p.M611L|EIF2B5_ENST00000444495.1_Intron|CLCN2_ENST00000344937.7_Missense_Mutation_p.M594L	NM_004366.5	NP_004357.3	P51788	CLCN2_HUMAN	chloride channel, voltage-sensitive 2	611	CBS 1. {ECO:0000255|PROSITE- ProRule:PRU00703}.				cell differentiation involved in salivary gland development (GO:0060689)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|retina development in camera-type eye (GO:0060041)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|voltage-gated chloride channel activity (GO:0005247)			breast(2)|central_nervous_system(4)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	27	all_cancers(143;6.66e-11)|Ovarian(172;0.0339)		Epithelial(37;2.22e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		Lubiprostone(DB01046)	AGGGCCAGCATTCGGCCCTTG	0.657																																					p.M611L		Atlas-SNP	.											.	CLCN2	74	.	0			c.A1831T						.						38	37	37					3																	184071474		2202	4300	6502	SO:0001583	missense	1181	exon16			CCAGCATTCGGCC	S77770	CCDS3263.1, CCDS54690.1, CCDS54691.1, CCDS54692.1	3q27.1	2013-09-19	2012-02-23		ENSG00000114859	ENSG00000114859		"Ion channels / Chloride channels : Voltage-sensitive"	2020	protein-coding gene	gene with protein product		600570	"chloride channel 2"			7795595	Standard	NM_004366		Approved	CLC2, EJM6, ClC-2	uc003foi.4	P51788	OTTHUMG00000156747	ENST00000265593.4:c.1831A>T	chr3.hg19:g.184071474T>A	ENSP00000265593:p.Met611Leu	68.0	0.0		82.0	22.0	NM_004366	B4DQT9|B4DZ58|E9PBD9|E9PCD2|O14864|Q6IPA9|Q8WU13	Missense_Mutation	SNP	ENST00000265593.4	hg19	CCDS3263.1	.	.	.	.	.	.	.	.	.	.	t	16.38	3.107384	0.56291	.	.	ENSG00000114859	ENST00000265593;ENST00000344937;ENST00000434054;ENST00000457512	D;D;D;D	0.87334	-2.24;-2.24;-2.24;-2.24	5.0	3.81	0.43845	Cystathionine beta-synthase, core (1);	0.387182	0.31709	N	0.007192	T	0.76364	0.3977	N	0.22421	0.69	0.80722	D	1	B;B;B;B;B	0.16166	0.016;0.009;0.015;0.004;0.009	B;B;B;B;B	0.15052	0.005;0.005;0.012;0.005;0.005	T	0.69172	-0.5215	10	0.62326	D	0.03	-12.1521	5.9788	0.19395	0.1445:0.0793:0.0:0.7762	.	567;611;594;611;567	E9PBD9;E9PCD2;P51788-3;P51788;B4DZ58	.;.;.;CLCN2_HUMAN;.	L	611;594;567;611	ENSP00000265593:M611L;ENSP00000345056:M594L;ENSP00000400425:M567L;ENSP00000391928:M611L	ENSP00000265593:M611L	M	-	1	0	CLCN2	185554168	1.000000	0.71417	0.997000	0.53966	0.988000	0.76386	3.305000	0.51873	0.734000	0.32515	0.460000	0.39030	ATG	.	.		0.657	CLCN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345571.1			A	184071474	T	A	184071474	3	1	306	1	0	0	0	0	1	0	0	0	3465	1493	52	4	901	4	CLCN2	3	184071474	Missense_Mutation	SNP	T	TCGA-GJ-A9DB-01A-11D-A36X-10	174332080	184071474	13950956	21	43790										
C3orf43	255798	hgsc.bcm.edu	37	chr3	196242031	196242031	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	tccctatagccctcagcaacCttttcattgcctccttcaag	4	16	3	0			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr3:196242031C>T	ENST00000397537.2	-	1	206	c.50G>A	c.(49-51)aGa>aAa	p.R17K		NM_001077657.1	NP_001071125.1	Q147U7	SMCO1_HUMAN	single-pass membrane protein with coiled-coil domains 1	17						integral component of membrane (GO:0016021)											CCTCAGCAACCTTTTCATTGC	0.408																																					p.R17K		Atlas-SNP	.											.	C3orf43	25	.	0			c.G50A						.						218	213	215					3																	196242031		1866	4107	5973	SO:0001630	splice_region_variant	255798	exon1			AGCAACCTTTTCA	AK123917	CCDS43192.1	3q29	2013-03-08	2013-03-08	2013-03-08	ENSG00000214097	ENSG00000214097			27407	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 43"	C3orf43			Standard	NM_001077657		Approved	FLJ41923, DKFZp313B0440		Q147U7	OTTHUMG00000155581	ENST00000397537.2:c.50+1G>A	chr3.hg19:g.196242031C>T		62.0	0.0		65.0	24.0	NM_001077657	B3KW20	Missense_Mutation	SNP	ENST00000397537.2	hg19	CCDS43192.1	.	.	.	.	.	.	.	.	.	.	C	19.56	3.851109	0.71719	.	.	ENSG00000214097	ENST00000397537	T	0.36340	1.26	5.09	5.09	0.68999	.	.	.	.	.	T	0.47116	0.1428	N	0.24115	0.695	0.37112	D	0.900407	D	0.76494	0.999	D	0.80764	0.994	T	0.57665	-0.7772	9	0.87932	D	0	-10.7046	16.279	0.82658	0.0:1.0:0.0:0.0	.	17	Q147U7	CC043_HUMAN	K	17	ENSP00000380671:R17K	ENSP00000380671:R17K	R	-	2	0	C3orf43	197726428	1.000000	0.71417	0.998000	0.56505	0.366000	0.29705	4.032000	0.57274	2.372000	0.80975	0.313000	0.20887	AGA	.	.		0.408	SMCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340776.1	NM_001006109	Missense_Mutation	T	196242031	C	T	196242031	5	4	306	1	0	0	0	0	0	0	1	0	2232	695	24	3	606	3	C3orf43	3	196242031	Splice_Site	SNP	C	TCGA-GJ-A9DB-01A-11D-A36X-10	12170557	196242031	1780399	22	43791										
PIGZ	80235	hgsc.bcm.edu	37	chr3	196674641	196674641	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	cagatagcagggccagaggcAtgaagtagaggagaaggaga	17	5	0	6			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr3:196674641A>C	ENST00000412723.1	-	3	1273	c.1127T>G	c.(1126-1128)aTg>aGg	p.M376R		NM_025163.2	NP_079439.2	Q86VD9	PIGZ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Z	376					GPI anchor biosynthetic process (GO:0006506)|mannosylation (GO:0097502)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	alpha-1,2-mannosyltransferase activity (GO:0000026)|mannosyltransferase activity (GO:0000030)			breast(1)|endometrium(1)|lung(7)|ovary(3)|prostate(1)|urinary_tract(1)	14	all_cancers(143;1.05e-08)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.29e-24)|all cancers(36;2.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00603)		GGCCAGAGGCATGAAGTAGAG	0.627																																					p.M376R		Atlas-SNP	.											.	PIGZ	34	.	0			c.T1127G						.						54	65	61					3																	196674641		2203	4300	6503	SO:0001583	missense	80235	exon3			AGAGGCATGAAGT	BC018804	CCDS3324.1	3q29	2013-02-26	2006-06-28		ENSG00000119227	ENSG00000119227		"Dolichyl D-mannosyl phosphate dependent mannosyltransferases", "Phosphatidylinositol glycan anchor biosynthesis"	30596	protein-coding gene	gene with protein product	"GPI mannosyltransferase 4", "dol-P-Man dependent GPI mannosyltransferase"	611671	"phosphatidylinositol glycan, class Z"			15208306	Standard	NM_025163		Approved	FLJ12768, MGC52163, SMP3	uc003fxh.3	Q86VD9	OTTHUMG00000155522	ENST00000412723.1:c.1127T>G	chr3.hg19:g.196674641A>C	ENSP00000413405:p.Met376Arg	269.0	0.0		246.0	77.0	NM_025163	Q9H9G6	Missense_Mutation	SNP	ENST00000412723.1	hg19	CCDS3324.1	.	.	.	.	.	.	.	.	.	.	a	3.946	-0.013307	0.07727	.	.	ENSG00000119227	ENST00000412723	T	0.63096	-0.02	5.17	-10.3	0.00346	.	1.714580	0.03005	N	0.148641	T	0.53997	0.1831	L	0.43152	1.355	0.09310	N	0.999999	B	0.24768	0.111	B	0.26693	0.072	T	0.45542	-0.9254	10	0.39692	T	0.17	0.6406	16.9534	0.86251	0.7203:0.0:0.2797:0.0	.	376	Q86VD9	PIGZ_HUMAN	R	376	ENSP00000413405:M376R	ENSP00000413405:M376R	M	-	2	0	PIGZ	198159038	0.006000	0.16342	0.000000	0.03702	0.027000	0.11550	-0.189000	0.09629	-2.234000	0.00715	-1.325000	0.01285	ATG	.	.		0.627	PIGZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340486.2	NM_025163		C	196674641	A	C	196674641	3	2	306	1	0	0	0	0	1	0	0	0	11914	217	8	5	616	5	PIGZ	3	196674641	Missense_Mutation	SNP	A	TCGA-GJ-A9DB-01A-11D-A36X-10	432610	196674641	1347789	23	43792										
NFXL1	152518	hgsc.bcm.edu	37	chr4	47887522	47887522	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	attattcccttaccctgccaGtctgctttattaatgcttga	5	11	1	1			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr4:47887522G>T	ENST00000507489.1	-	14	1993	c.1817C>A	c.(1816-1818)aCt>aAt	p.T606N	NFXL1_ENST00000329043.3_Missense_Mutation_p.T606N|NFXL1_ENST00000381538.3_Missense_Mutation_p.T606N	NM_001278624.1	NP_001265553.1	Q6ZNB6	NFXL1_HUMAN	nuclear transcription factor, X-box binding-like 1	606						integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(4)	27						TACCCTGCCAGTCTGCTTTAT	0.398																																					p.T606N		Atlas-SNP	.											.	NFXL1	79	.	0			c.C1817A						.						146	141	143					4																	47887522		2203	4300	6503	SO:0001583	missense	152518	exon14			CTGCCAGTCTGCT	AY134856	CCDS3478.2	4p12	2008-02-05			ENSG00000170448	ENSG00000170448			18726	protein-coding gene	gene with protein product	"ovarian zinc finger protein"						Standard	NM_152995		Approved	HOZFP	uc003gxp.3	Q6ZNB6	OTTHUMG00000128621	ENST00000507489.1:c.1817C>A	chr4.hg19:g.47887522G>T	ENSP00000422037:p.Thr606Asn	131.0	0.0		115.0	46.0	NM_152995	B1Q2K1|Q86VG1|Q8WVH1	Missense_Mutation	SNP	ENST00000507489.1	hg19	CCDS3478.2	.	.	.	.	.	.	.	.	.	.	G	12.25	1.880432	0.33255	.	.	ENSG00000170448	ENST00000381538;ENST00000507489;ENST00000329043	T;T;T	0.28666	1.6;1.6;1.6	5.66	5.66	0.87406	Zinc finger, NF-X1-type (1);	0.610086	0.16413	N	0.215518	T	0.30166	0.0756	L	0.53249	1.67	0.36092	D	0.843556	B	0.29253	0.239	B	0.28709	0.093	T	0.22034	-1.0228	10	0.17369	T	0.5	-2.7067	14.5822	0.68300	0.0:0.0:0.854:0.146	.	606	Q6ZNB6	NFXL1_HUMAN	N	606	ENSP00000370949:T606N;ENSP00000422037:T606N;ENSP00000333113:T606N	ENSP00000333113:T606N	T	-	2	0	NFXL1	47582279	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	4.461000	0.60115	2.663000	0.90544	0.555000	0.69702	ACT	.	.		0.398	NFXL1-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361636.1	NM_152995		T	47887522	G	T	47887522	3	4	306	1	0	0	0	0	1	0	0	0	10397	1029	36	3	958	3	NFXL1	4	47887522	Missense_Mutation	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10		47887522	143266754	24	43793										
PAICS	10606	hgsc.bcm.edu	37	chr4	57312864	57312864	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	tggttatcaatatgtaggtaTtaaaactgccttcaccagaa	7	7	2	1			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr4:57312864T>G	ENST00000512576.1	+	3	379	c.218T>G	c.(217-219)aTt>aGt	p.I73S	PAICS_ENST00000514888.1_De_novo_Start_InFrame|PAICS_ENST00000399688.3_Missense_Mutation_p.I80S|PAICS_ENST00000264221.2_Missense_Mutation_p.I73S	NM_001079524.1	NP_001072992.1	P22234	PUR6_HUMAN	phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase	73	SAICAR synthetase.				'de novo' IMP biosynthetic process (GO:0006189)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|phosphoribosylaminoimidazole carboxylase activity (GO:0004638)|phosphoribosylaminoimidazolesuccinocarboxamide synthase activity (GO:0004639)			endometrium(1)|kidney(2)|large_intestine(1)|urinary_tract(1)	5	Glioma(25;0.08)|all_neural(26;0.101)				L-Aspartic Acid(DB00128)	TATGTAGGTATTAAAACTGCC	0.363																																					p.I80S	GBM(53;429 1144 8755 40726)	Atlas-SNP	.											.	PAICS	21	.	0			c.T239G						.						30	28	29					4																	57312864		1830	4092	5922	SO:0001583	missense	10606	exon4			TAGGTATTAAAAC	X53793	CCDS47060.1, CCDS47061.1	4q12	2012-07-13			ENSG00000128050	ENSG00000128050	4.1.1.21, 6.3.2.6		8587	protein-coding gene	gene with protein product		172439		PAIS		2253271, 8106516	Standard	NM_006452		Approved	ADE2H1, AIRC	uc003hbt.1	P22234	OTTHUMG00000160957	ENST00000512576.1:c.218T>G	chr4.hg19:g.57312864T>G	ENSP00000421096:p.Ile73Ser	208.0	0.0		234.0	61.0	NM_001079525	E9PDH9|Q68CQ5	Missense_Mutation	SNP	ENST00000512576.1	hg19	CCDS47061.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.048076	0.75846	.	.	ENSG00000128050	ENST00000264221;ENST00000505164;ENST00000399688;ENST00000512576	T;T;T;T	0.55052	0.54;0.54;0.69;0.54	5.43	5.43	0.79202	.	0.046141	0.85682	D	0.000000	T	0.81079	0.4748	H	0.96239	3.79	0.80722	D	1	D;D;D	0.71674	0.998;0.997;0.998	D;D;D	0.72075	0.976;0.972;0.976	D	0.87427	0.2386	10	0.87932	D	0	-17.5636	15.7797	0.78249	0.0:0.0:0.0:1.0	.	73;80;73	E9PBS1;P22234-2;P22234	.;.;PUR6_HUMAN	S	73;73;80;73	ENSP00000264221:I73S;ENSP00000424053:I73S;ENSP00000382595:I80S;ENSP00000421096:I73S	ENSP00000264221:I73S	I	+	2	0	PAICS	57007621	1.000000	0.71417	1.000000	0.80357	0.717000	0.41224	7.901000	0.87382	2.195000	0.70347	0.477000	0.44152	ATT	.	.		0.363	PAICS-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363136.2	NM_006452		G	57312864	T	G	57312864	3	3	306	1	0	0	0	0	1	0	0	0	11404	1493	52	5	253	5	PAICS	4	57312864	Missense_Mutation	SNP	T	TCGA-GJ-A9DB-01A-11D-A36X-10	9425342	57312864	133841412	25	43794										
SLC39A8	64116	hgsc.bcm.edu	37	chr4	103265762	103265762	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	ccctggcccctccgccactcCtccgaggccggcggccgcca	11	23	0	0			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr4:103265762C>A	ENST00000394833.2	-	1	534	c.58G>T	c.(58-60)Gga>Tga	p.G20*	SLC39A8_ENST00000510255.1_Intron|SLC39A8_ENST00000356736.4_Nonsense_Mutation_p.G20*|SLC39A8_ENST00000424970.2_Nonsense_Mutation_p.G20*	NM_001135148.1|NM_022154.5	NP_001128620.1|NP_071437.3	Q9C0K1	S39A8_HUMAN	solute carrier family 39 (zinc transporter), member 8	20					transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)|organelle membrane (GO:0031090)|plasma membrane (GO:0005886)	metal ion transmembrane transporter activity (GO:0046873)			large_intestine(1)|lung(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	9		Hepatocellular(203;0.217)		all cancers(1;9.78e-10)|OV - Ovarian serous cystadenocarcinoma(123;1.52e-09)|GBM - Glioblastoma multiforme(1;0.000142)		TCCGCCACTCCTCCGAGGCCG	0.736																																					p.G20X		Atlas-SNP	.											.	SLC39A8	24	.	0			c.G58T						.						3	6	5					4																	103265762		1732	3670	5402	SO:0001587	stop_gained	64116	exon1			CCACTCCTCCGAG		CCDS3656.1, CCDS47117.1	4q22-q24	2013-05-22			ENSG00000138821	ENSG00000138821		"Solute carriers"	20862	protein-coding gene	gene with protein product		608732	"solute carrier family 39 (metal ion transporter), member 8"			12504855, 12659941	Standard	NM_001135146		Approved	BIGM103	uc003hwc.2	Q9C0K1	OTTHUMG00000131120	ENST00000394833.2:c.58G>T	chr4.hg19:g.103265762C>A	ENSP00000378310:p.Gly20*	115.0	0.0		128.0	40.0	NM_022154	B4E2H3|Q96SM9|Q9BVC0|Q9NSA4	Nonsense_Mutation	SNP	ENST00000394833.2	hg19	CCDS3656.1	.	.	.	.	.	.	.	.	.	.	C	39	7.442824	0.98286	.	.	ENSG00000138821	ENST00000424970;ENST00000356736;ENST00000394833	.	.	.	3.87	0.948	0.19561	.	0.907354	0.09048	U	0.856272	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08599	T	0.76	-13.5435	5.995	0.19489	0.0:0.4967:0.3895:0.1138	.	.	.	.	X	20	.	ENSP00000349174:G20X	G	-	1	0	SLC39A8	103484785	0.003000	0.15002	0.179000	0.23059	0.808000	0.45660	0.071000	0.14594	0.274000	0.22072	0.491000	0.48974	GGA	.	.		0.736	SLC39A8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253798.1	NM_022154		A	103265762	C	A	103265762	4	1	306	1	0	0	0	0	0	1	0	0	14639	690	24	3	1455	3	SLC39A8	4	103265762	Nonsense_Mutation	SNP	C	TCGA-GJ-A9DB-01A-11D-A36X-10	45952898	103265762	87888514	26	43795										
ANKRD50	57182	hgsc.bcm.edu	37	chr4	125592001	125592001	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	gactgtcctaccttcactatCaatactatccacagctgcac	4	15	2	0			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr4:125592001C>T	ENST00000504087.1	-	4	3468	c.2431G>A	c.(2431-2433)Gat>Aat	p.D811N	ANKRD50_ENST00000515641.1_Missense_Mutation_p.D632N	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	811										NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(14)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	55						CCTTCACTATCAATACTATCC	0.443																																					p.D811N		Atlas-SNP	.											.	ANKRD50	136	.	0			c.G2431A						.						141	129	133					4																	125592001		2203	4300	6503	SO:0001583	missense	57182	exon4			CACTATCAATACT	AB033049	CCDS34060.1, CCDS54802.1	4q28.1	2013-01-10			ENSG00000151458	ENSG00000151458		"Ankyrin repeat domain containing"	29223	protein-coding gene	gene with protein product							Standard	NM_020337		Approved	KIAA1223	uc010inw.3	Q9ULJ7	OTTHUMG00000161398	ENST00000504087.1:c.2431G>A	chr4.hg19:g.125592001C>T	ENSP00000425658:p.Asp811Asn	89.0	0.0		95.0	35.0	NM_020337	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Missense_Mutation	SNP	ENST00000504087.1	hg19	CCDS34060.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.279626	0.80692	.	.	ENSG00000151458	ENST00000504087;ENST00000515641	T;T	0.17854	2.25;2.25	4.99	4.99	0.66335	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.42426	0.1202	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.22034	-1.0228	10	0.54805	T	0.06	.	18.4729	0.90781	0.0:1.0:0.0:0.0	.	811	Q9ULJ7	ANR50_HUMAN	N	811;632	ENSP00000425658:D811N;ENSP00000425355:D632N	ENSP00000425658:D811N	D	-	1	0	ANKRD50	125811451	1.000000	0.71417	0.977000	0.42913	0.995000	0.86356	7.164000	0.77533	2.606000	0.88127	0.561000	0.74099	GAT	.	.		0.443	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337		T	125592001	C	T	125592001	3	4	306	1	0	0	0	0	1	0	0	0	677	826	29	3	1862	3	ANKRD50	4	125592001	Missense_Mutation	SNP	C	TCGA-GJ-A9DB-01A-11D-A36X-10	22326239	125592001	65562275	27	43796										
INTU	27152	hgsc.bcm.edu	37	chr4	128625405	128625405	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	cgaggattactatgacatgaGgcggctgtatacaattttgg	12	6	0	2			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr4:128625405G>C	ENST00000335251.6	+	10	1629	c.1526G>C	c.(1525-1527)aGg>aCg	p.R509T	INTU_ENST00000512995.1_3'UTR	NM_015693.3	NP_056508.2	Q9ULD6	INTU_HUMAN	inturned planar cell polarity protein	509					cilium assembly (GO:0042384)|hair follicle morphogenesis (GO:0031069)|keratinocyte differentiation (GO:0030216)|limb development (GO:0060173)|negative regulation of cell division (GO:0051782)|negative regulation of keratinocyte proliferation (GO:0010839)|nervous system development (GO:0007399)|positive regulation of smoothened signaling pathway (GO:0045880)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord dorsal/ventral patterning (GO:0021513)	cytoplasm (GO:0005737)				breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	43						TATGACATGAGGCGGCTGTAT	0.313																																					p.R509T		Atlas-SNP	.											.	INTU	92	.	0			c.G1526C						.						123	127	125					4																	128625405		2203	4300	6503	SO:0001583	missense	27152	exon10			ACATGAGGCGGCT	BC051698	CCDS34061.1	4q28.2	2013-03-05	2013-03-05	2006-10-24	ENSG00000164066	ENSG00000164066			29239	protein-coding gene	gene with protein product		610621	"PDZ domain containing 6", "inturned planar cell polarity effector homolog (Drosophila)"	PDZK6, PDZD6		10574462, 21761479	Standard	NM_015693		Approved	KIAA1284	uc003ifk.2	Q9ULD6	OTTHUMG00000161202	ENST00000335251.6:c.1526G>C	chr4.hg19:g.128625405G>C	ENSP00000334003:p.Arg509Thr	74.0	0.0		80.0	18.0	NM_015693	A1L4N5|D6RAE6|D6RBT4|Q4W5I8|Q86V55	Missense_Mutation	SNP	ENST00000335251.6	hg19	CCDS34061.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.782416	0.90282	.	.	ENSG00000164066	ENST00000335251	T	0.30448	1.53	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	T	0.58061	0.2096	M	0.74881	2.28	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.61252	-0.7100	10	0.72032	D	0.01	-16.4587	18.4011	0.90516	0.0:0.0:1.0:0.0	.	509	Q9ULD6	PDZD6_HUMAN	T	509	ENSP00000334003:R509T	ENSP00000334003:R509T	R	+	2	0	INTU	128844855	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.131000	0.94446	2.672000	0.90937	0.555000	0.69702	AGG	.	.		0.313	INTU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364147.2	XM_371707		C	128625405	G	C	128625405	3	2	306	1	0	0	0	0	1	0	0	0	7795	1000	35	4	1564	4	INTU	4	128625405	Missense_Mutation	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10	3033404	128625405	62528871	28	43797										
ARHGAP10	79658	hgsc.bcm.edu	37	chr4	148787952	148787952	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	cactacaaaatggaactacaGatcaacattcagaatgtaag	6	8	2	2			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr4:148787952G>A	ENST00000336498.3	+	7	926	c.687G>A	c.(685-687)caG>caA	p.Q229Q		NM_024605.3	NP_078881.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 10	0					establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			autonomic_ganglia(2)|endometrium(5)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		TGGAACTACAGATCAACATTC	0.333											OREG0016355	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q229Q		Atlas-SNP	.											.	ARHGAP10	92	.	0			c.G687A						.						109	102	105					4																	148787952		2203	4300	6503	SO:0001819	synonymous_variant	79658	exon7			ACTACAGATCAAC	BC047914	CCDS34075.1	4q31.23	2013-09-20			ENSG00000071205	ENSG00000071205		"Rho GTPase activating proteins"	26099	protein-coding gene	gene with protein product		609746				8288572	Standard	NM_024605		Approved	FLJ20896, FLJ41791, GRAF2	uc003ilf.3	A1A4S6	OTTHUMG00000161460	ENST00000336498.3:c.687G>A	chr4.hg19:g.148787952G>A		218.0	0.0	1720	231.0	41.0	NM_024605	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Silent	SNP	ENST00000336498.3	hg19	CCDS34075.1																																																																																			.	.		0.333	ARHGAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365005.1	NM_024605		A	148787952	G	A	148787952	2	1	306	1	0	0	0	0	0	0	0	1	862	933	33	3		3	ARHGAP10	4	148787952	Silent	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10	20162547	148787952	42366324	29	43798										
TRIML1	339976	hgsc.bcm.edu	37	chr4	189061021	189061021	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	aggatgcccaccactgccaaGgcgctctccgatgacgagca	11	15	1	1			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr4:189061021G>A	ENST00000332517.3	+	1	449	c.309G>A	c.(307-309)aaG>aaA	p.K103K	RP11-366H4.3_ENST00000501322.2_RNA	NM_178556.3	NP_848651.2	Q8N9V2	TRIML_HUMAN	tripartite motif family-like 1	103					multicellular organismal development (GO:0007275)|protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	60		all_cancers(14;1.33e-43)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)|all_hematologic(60;0.062)		OV - Ovarian serous cystadenocarcinoma(60;1.52e-11)|BRCA - Breast invasive adenocarcinoma(30;4.19e-06)|GBM - Glioblastoma multiforme(59;0.000232)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.156)		CCACTGCCAAGGCGCTCTCCG	0.647																																					p.K103K	Melanoma(31;213 1036 16579 23968 32372)	Atlas-SNP	.											.	TRIML1	126	.	0			c.G309A						.						42	41	41					4																	189061021		2203	4300	6503	SO:0001819	synonymous_variant	339976	exon1			TGCCAAGGCGCTC	AK093499	CCDS3851.1	4q35.2	2013-01-09			ENSG00000184108	ENSG00000184108		"RING-type (C3HC4) zinc fingers"	26698	protein-coding gene	gene with protein product						12477932	Standard	NM_178556		Approved	FLJ36180, RNF209	uc003izm.1	Q8N9V2	OTTHUMG00000160237	ENST00000332517.3:c.309G>A	chr4.hg19:g.189061021G>A		135.0	0.0		138.0	46.0	NM_178556	Q96BE5	Silent	SNP	ENST00000332517.3	hg19	CCDS3851.1																																																																																			.	.		0.647	TRIML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359813.1	NM_178556		A	189061021	G	A	189061021	2	1	306	1	0	0	0	0	0	0	0	1	16565	991	35	3		3	TRIML1	4	189061021	Silent	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10	40273069	189061021	2093255	30	43799										
RASGRF2	5924	hgsc.bcm.edu	37	chr5	80388721	80388721	+	Frame_Shift_Del	DEL	T	T	-													0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	gagagagacaatgcttcttaTttacaaaacactttttaata							TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr5:80388721delT	ENST00000265080.4	+	10	1559	c.1492delT	c.(1492-1494)tttfs	p.F498fs		NM_006909.2	NP_008840.1	O14827	RGRF2_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 2	498	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			biliary_tract(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(28)|ovary(5)|prostate(3)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)		ATGCTTCTTATTTACAAAACA	0.393																																					p.L497fs		Atlas-INDEL	.											.	RASGRF2	165	.	0			c.1491delA						.						113	114	113					5																	80388721		2203	4300	6503	SO:0001589	frameshift_variant	5924	exon10			.	AF023130	CCDS4052.1	5q13	2013-01-10			ENSG00000113319	ENSG00000113319		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9876	protein-coding gene	gene with protein product		606614					Standard	NM_006909		Approved	GRF2, Ras-GRF2	uc003kha.2	O14827	OTTHUMG00000119015	ENST00000265080.4:c.1492delT	chr5.hg19:g.80388721delT	ENSP00000265080:p.Phe498fs	129.0	0.0		135.0	36.0	NM_006909	B9EG89|Q9UK56	Frame_Shift_Del	DEL	ENST00000265080.4	hg19	CCDS4052.1																																																																																			.	.		0.393	RASGRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239215.2	NM_006909		-	80388721	T	-	80388721	7	5	306	1	0	1	0	1	0	0	0	0	13088	1493	52	0	1530	0	RASGRF2	5	80388721	Frame_Shift_Del	DEL	T	TCGA-GJ-A9DB-01A-11D-A36X-10		80388721	100526539	31	43800										
PCDHA11	56138	hgsc.bcm.edu	37	chr5	140250310	140250310	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	gagcgcgcgcgatgcgggcgTgccgcctctgagcagcaacg	17	14	1	1			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr5:140250310T>G	ENST00000398640.2	+	1	1622	c.1622T>G	c.(1621-1623)gTg>gGg	p.V541G	PCDHA6_ENST00000529310.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA7_ENST00000525929.1_Intron	NM_018902.3	NP_061725.1	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11	541	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(1)|lung(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GATGCGGGCGTGCCGCCTCTG	0.687																																					p.V541G		Atlas-SNP	.											.	PCDHA11	209	.	0			c.T1622G						.						72	80	77					5																	140250310		2202	4298	6500	SO:0001583	missense	56138	exon1			CGGGCGTGCCGCC	AF152476	CCDS47284.1, CCDS75326.1	5q31	2010-11-26			ENSG00000249158	ENSG00000249158		"Cadherins / Protocadherins : Clustered"	8665	other	complex locus constituent	"KIAA0345-like 3", "ortholog of mouse CNR7"	606317		CNRS7		10380929, 10662547	Standard	NM_018902		Approved	CNR7, CRNR7, CNRN7, PCDH-ALPHA11		Q9Y5I1	OTTHUMG00000163369	ENST00000398640.2:c.1622T>G	chr5.hg19:g.140250310T>G	ENSP00000381636:p.Val541Gly	75.0	0.0		88.0	28.0	NM_018902	B2RN58|O75279	Missense_Mutation	SNP	ENST00000398640.2	hg19	CCDS47284.1	.	.	.	.	.	.	.	.	.	.	T	15.17	2.754905	0.49362	.	.	ENSG00000249158	ENST00000398640	T	0.48836	0.8	5.15	5.15	0.70609	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.35566	0.0936	N	0.12611	0.24	0.38941	D	0.958148	P;P	0.42123	0.771;0.678	B;P	0.45794	0.211;0.493	T	0.32052	-0.9921	9	0.37606	T	0.19	.	11.5782	0.50877	0.0:0.0:0.1489:0.8511	.	541;541	Q9Y5I1-2;Q9Y5I1	.;PCDAB_HUMAN	G	541	ENSP00000381636:V541G	ENSP00000381636:V541G	V	+	2	0	PCDHA11	140230494	0.000000	0.05858	0.999000	0.59377	0.943000	0.58893	-0.427000	0.06999	1.942000	0.56320	0.454000	0.30748	GTG	.	.		0.687	PCDHA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372885.2	NM_018902		G	140250310	T	G	140250310	3	3	306	1	0	0	0	0	1	0	0	0	11530	1696	59	5	1624	5	PCDHA11	5	140250310	Missense_Mutation	SNP	T	TCGA-GJ-A9DB-01A-11D-A36X-10	59861589	140250310	40664950	32	43801										
RBM27	54439	hgsc.bcm.edu	37	chr5	145664265	145664265	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	aaggtaccatctatatccacTgagactgaagaagaagaagt	9	7	1	5			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr5:145664265T>A	ENST00000265271.5	+	20	3235	c.3069T>A	c.(3067-3069)acT>acA	p.T1023T	RBM27_ENST00000506502.1_Intron	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	1023					mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTATATCCACTGAGACTGAAG	0.353																																					p.T1023T		Atlas-SNP	.											.	RBM27	119	.	0			c.T3069A						.						91	87	88					5																	145664265		1568	3582	5150	SO:0001819	synonymous_variant	54439	exon20			ATCCACTGAGACT	AL833706	CCDS43378.1	5q32	2013-01-09				ENSG00000091009		"Zinc fingers, CCCH-type domain containing", "RNA binding motif (RRM) containing"	29243	protein-coding gene	gene with protein product	"acidic rich RS domain containing 1"					10718198, 15741184	Standard	NM_018989		Approved	KIAA1311, ARRS1, Psc1, ZC3H18	uc003lnz.4	Q9P2N5		ENST00000265271.5:c.3069T>A	chr5.hg19:g.145664265T>A		277.0	0.0		393.0	169.0	NM_018989	Q8IYW9	Silent	SNP	ENST00000265271.5	hg19	CCDS43378.1																																																																																			.	.		0.353	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373420.1	XM_291128		A	145664265	T	A	145664265	2	1	306	1	0	0	0	0	0	0	0	1	13142	1567	55	4		4	RBM27	5	145664265	Silent	SNP	T	TCGA-GJ-A9DB-01A-11D-A36X-10	5413955	145664265	35250995	33	43802										
KIF13A	63971	hgsc.bcm.edu	37	chr6	17837188	17837188	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	cttttgcgttggggtcctcaTtcacaacagcatggttcaca	9	11	3	0			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr6:17837188T>A	ENST00000259711.6	-	11	1181	c.1076A>T	c.(1075-1077)aAt>aTt	p.N359I	KIF13A_ENST00000378843.2_Missense_Mutation_p.N359I|KIF13A_ENST00000378816.5_Missense_Mutation_p.N359I|KIF13A_ENST00000378814.5_Missense_Mutation_p.N359I|KIF13A_ENST00000378826.2_Missense_Mutation_p.N359I	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	359					ATP catabolic process (GO:0006200)|cargo loading into vesicle (GO:0035459)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|Golgi to plasma membrane protein transport (GO:0043001)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)	centrosome (GO:0005813)|endosome membrane (GO:0010008)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|trans-Golgi network membrane (GO:0032588)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	64	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			GGGGTCCTCATTCACAACAGC	0.512																																					p.N359I		Atlas-SNP	.											.	KIF13A	276	.	0			c.A1076T						.						294	287	289					6																	17837188		1991	4170	6161	SO:0001583	missense	63971	exon11			TCCTCATTCACAA	AJ291578	CCDS47380.1, CCDS47381.1, CCDS54967.1, CCDS54968.1, CCDS58998.1	6p23	2008-10-21			ENSG00000137177	ENSG00000137177		"Kinesins"	14566	protein-coding gene	gene with protein product		605433				11106728	Standard	NM_022113		Approved	bA500C11.2	uc003ncg.4	Q9H1H9	OTTHUMG00000014313	ENST00000259711.6:c.1076A>T	chr6.hg19:g.17837188T>A	ENSP00000259711:p.Asn359Ile	108.0	0.0		117.0	50.0	NM_001105567	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Missense_Mutation	SNP	ENST00000259711.6	hg19	CCDS47381.1	.	.	.	.	.	.	.	.	.	.	T	27.9	4.873838	0.91664	.	.	ENSG00000137177	ENST00000378814;ENST00000259711;ENST00000378826;ENST00000378843;ENST00000378816	D;D;D;D;D	0.89415	-2.51;-2.51;-2.51;-2.51;-2.51	6.03	6.03	0.97812	Kinesin, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.95633	0.8580	M	0.93638	3.44	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.999;0.999;1.0;0.999	D	0.96637	0.9471	10	0.87932	D	0	.	16.5724	0.84622	0.0:0.0:0.0:1.0	.	330;359;359;359;359	E7ER65;Q9H1H9-4;Q9H1H9-2;Q9H1H9;Q9H1H9-3	.;.;.;KI13A_HUMAN;.	I	359	ENSP00000368091:N359I;ENSP00000259711:N359I;ENSP00000368103:N359I;ENSP00000368120:N359I;ENSP00000368093:N359I	ENSP00000259711:N359I	N	-	2	0	KIF13A	17945167	1.000000	0.71417	0.995000	0.50966	0.908000	0.53690	7.997000	0.88414	2.313000	0.78055	0.455000	0.32223	AAT	.	.		0.512	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4			A	17837188	T	A	17837188	3	1	306	1	0	0	0	0	1	0	0	0	8283	1493	52	4	4482	4	KIF13A	6	17837188	Missense_Mutation	SNP	T	TCGA-GJ-A9DB-01A-11D-A36X-10		17837188	153277879	34	43803										
HLA-DQA1	3117	hgsc.bcm.edu	37	chr6	32610000	32610000	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	actgcaaggtggagcactggGgcctggaccagcctcttctg	14	12	2	0			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr6:32610000G>A	ENST00000343139.5	+	3	685	c.583G>A	c.(583-585)Ggc>Agc	p.G195S	HLA-DQA1_ENST00000374949.2_Missense_Mutation_p.G195S|HLA-DQA1_ENST00000395363.1_Missense_Mutation_p.G195S	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	194	Alpha-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						GGAGCACTGGGGCCTGGACCA	0.458																																					p.G195S		Atlas-SNP	.											.	HLA-DQA1	52	.	0			c.G583A						.						94	99	97					6																	32610000		1507	2706	4213	SO:0001583	missense	3117	exon3			CACTGGGGCCTGG		CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.583G>A	chr6.hg19:g.32610000G>A	ENSP00000339398:p.Gly195Ser	261.0	0.0		245.0	111.0	NM_002122	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Missense_Mutation	SNP	ENST00000343139.5	hg19	CCDS4752.1	.	.	.	.	.	.	.	.	.	.	.	20.2	3.951973	0.73787	.	.	ENSG00000196735	ENST00000343139;ENST00000395364;ENST00000395363;ENST00000496318;ENST00000374949	T;T;T;T	0.02709	4.19;4.19;4.19;4.19	4.1	4.1	0.47936	.	0.234509	0.35615	N	0.003094	T	0.05502	0.0145	L	0.39692	1.235	0.40836	D	0.983632	D;P	0.89917	1.0;0.918	D;P	0.97110	1.0;0.797	T	0.38478	-0.9659	10	0.66056	D	0.02	.	14.2269	0.65866	0.0:0.0:1.0:0.0	.	201;195	Q59F33;G4XQK2	.;.	S	195	ENSP00000339398:G195S;ENSP00000378767:G195S;ENSP00000437302:G195S;ENSP00000364087:G195S	ENSP00000339398:G195S	G	+	1	0	HLA-DQA1	32717978	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	4.303000	0.59098	2.291000	0.77112	0.655000	0.94253	GGC	.	.		0.458	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122		A	32610000	G	A	32610000	3	1	306	1	0	0	0	0	1	0	0	0	7213	1232	43	3	593	3	HLA-DQA1	6	32610000	Missense_Mutation	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10	14772812	32610000	138505067	35	43804										
FRS3	10817	hgsc.bcm.edu	37	chr6	41740590	41740590	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	ctcagcggggtggctattgcGggtgatgatgacaggctctt	16	8	2	3	rs545980178		TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr6:41740590G>T	ENST00000373018.3	-	5	612	c.361C>A	c.(361-363)Cgc>Agc	p.R121S	FRS3_ENST00000259748.2_Missense_Mutation_p.R121S	NM_006653.3	NP_006644.1	O43559	FRS3_HUMAN	fibroblast growth factor receptor substrate 3	121					fibroblast growth factor receptor signaling pathway (GO:0008543)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	fibroblast growth factor receptor binding (GO:0005104)	p.R121C(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;8.38e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			TGGCTATTGCGGGTGATGATG	0.547																																					p.R121S		Atlas-SNP	.											FRS3,colon,carcinoma,0,4	FRS3	53	.	1	Substitution - Missense(1)	ovary(1)	c.C361A						.						124	125	125					6																	41740590		2203	4300	6503	SO:0001583	missense	10817	exon5			TATTGCGGGTGAT	AF036718	CCDS4860.1	6p21.1	2010-08-05			ENSG00000137218	ENSG00000137218			16970	protein-coding gene	gene with protein product		607744				8761293, 9660748	Standard	NM_006653		Approved	SNT-2, FRS2beta, FRS2B	uc003orc.1	O43559	OTTHUMG00000014686	ENST00000373018.3:c.361C>A	chr6.hg19:g.41740590G>T	ENSP00000362109:p.Arg121Ser	76.0	0.0		76.0	4.0	NM_006653	Q5T3D5	Missense_Mutation	SNP	ENST00000373018.3	hg19	CCDS4860.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.589072	0.86851	.	.	ENSG00000137218	ENST00000373018;ENST00000259748;ENST00000426290	D;D	0.82433	-1.61;-1.61	5.46	3.49	0.39957	.	0.207707	0.33875	N	0.004468	D	0.83312	0.5227	M	0.68593	2.085	0.58432	D	0.999998	D	0.76494	0.999	D	0.85130	0.997	T	0.80200	-0.1481	10	0.08179	T	0.78	-37.7643	12.373	0.55265	0.0:0.0:0.6461:0.3539	.	121	O43559	FRS3_HUMAN	S	121;121;145	ENSP00000362109:R121S;ENSP00000259748:R121S	ENSP00000259748:R121S	R	-	1	0	FRS3	41848568	1.000000	0.71417	0.996000	0.52242	0.966000	0.64601	4.032000	0.57274	2.573000	0.86826	0.655000	0.94253	CGC	.	.		0.547	FRS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040532.2	NM_006653		T	41740590	G	T	41740590	3	4	306	1	0	0	0	0	1	0	0	0	6070	1116	39	1	1129	1	FRS3	6	41740590	Missense_Mutation	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10	9130590	41740590	129374477	36	43805										
USP49	25862	hgsc.bcm.edu	37	chr6	41774615	41774615	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	gggagcacttgaggcaggccCacacggactcggtggtggca	17	11	0	1			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr6:41774615C>T	ENST00000394253.3	-	3	436	c.107G>A	c.(106-108)tGg>tAg	p.W36*	USP49_ENST00000373009.3_Nonsense_Mutation_p.W36*|USP49_ENST00000373006.1_Nonsense_Mutation_p.W36*|USP49_ENST00000373010.1_Nonsense_Mutation_p.W36*|USP49_ENST00000297229.2_Nonsense_Mutation_p.W36*			Q70CQ1	UBP49_HUMAN	ubiquitin specific peptidase 49	36					histone H2B conserved C-terminal lysine deubiquitination (GO:0035616)|mRNA splicing, via spliceosome (GO:0000398)|protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|histone binding (GO:0042393)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(2)|skin(2)	23	Ovarian(28;0.0919)|Colorectal(47;0.121)		STAD - Stomach adenocarcinoma(11;0.000204)|Epithelial(12;0.000309)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			GAGGCAGGCCCACACGGACTC	0.602																																					p.W36X		Atlas-SNP	.											.	USP49	58	.	0			c.G107A						.						79	82	81					6																	41774615		2203	4300	6503	SO:0001587	stop_gained	25862	exon4			CAGGCCCACACGG	AJ586139	CCDS4861.1, CCDS69111.1	6p12.1	2008-02-05	2005-08-08		ENSG00000164663	ENSG00000164663		"Ubiquitin-specific peptidases"	20078	protein-coding gene	gene with protein product			"ubiquitin specific protease 49"			14715245	Standard	NM_018561		Approved	MGC20741	uc003ori.3	Q70CQ1	OTTHUMG00000014688	ENST00000394253.3:c.107G>A	chr6.hg19:g.41774615C>T	ENSP00000377797:p.Trp36*	113.0	0.0		97.0	34.0	NM_018561	Q5T3D9|Q5T3E0|Q96CK4	Nonsense_Mutation	SNP	ENST00000394253.3	hg19		.	.	.	.	.	.	.	.	.	.	C	19.30	3.800986	0.70567	.	.	ENSG00000164663	ENST00000394253;ENST00000373010;ENST00000373009;ENST00000373006;ENST00000297229;ENST00000437061	.	.	.	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.8314	18.203	0.89844	0.0:1.0:0.0:0.0	.	.	.	.	X	36	.	ENSP00000297229:W36X	W	-	2	0	USP49	41882593	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.272000	0.78516	2.624000	0.88883	0.655000	0.94253	TGG	.	.		0.602	USP49-007	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000316513.3	NM_018561		T	41774615	C	T	41774615	4	4	306	1	0	0	0	0	0	1	0	0	17095	595	21	3	1831	3	USP49	6	41774615	Nonsense_Mutation	SNP	C	TCGA-GJ-A9DB-01A-11D-A36X-10	34025	41774615	129340452	37	43806										
TTBK1	84630	hgsc.bcm.edu	37	chr6	43222834	43222834	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	acggttcgctatgcctcagtCaatgcccacaagaaccgggt	10	13	2	1			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr6:43222834C>T	ENST00000259750.4	+	7	707	c.624C>T	c.(622-624)gtC>gtT	p.V208V	TTBK1_ENST00000304139.5_Silent_p.V157V	NM_032538.1	NP_115927.1	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	208	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(10)|liver(1)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)			ATGCCTCAGTCAATGCCCACA	0.632																																					p.V208V		Atlas-SNP	.											.	TTBK1	124	.	0			c.C624T						.						116	90	98					6																	43222834		2203	4300	6503	SO:0001819	synonymous_variant	84630	exon7			CTCAGTCAATGCC	AB058758	CCDS34455.1	6p21.1	2008-02-05			ENSG00000146216	ENSG00000146216			19140	protein-coding gene	gene with protein product						11347906	Standard	XM_006715229		Approved	KIAA1855	uc003ouq.1	Q5TCY1	OTTHUMG00000014725	ENST00000259750.4:c.624C>T	chr6.hg19:g.43222834C>T		86.0	0.0		107.0	14.0	NM_032538	A2A2U5|Q2L6C6|Q6ZNH0|Q8N444|Q96JH2	Silent	SNP	ENST00000259750.4	hg19	CCDS34455.1																																																																																			.	.		0.632	TTBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040584.3			T	43222834	C	T	43222834	2	4	306	1	0	0	0	0	0	0	0	1	16691	813	29	3		3	TTBK1	6	43222834	Silent	SNP	C	TCGA-GJ-A9DB-01A-11D-A36X-10	1448219	43222834	127892233	38	43807										
AARS2	57505	hgsc.bcm.edu	37	chr6	44272421	44272421	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	aggtagccacggtctgaagcCtggcccccctgttctgcgta	12	14	2	1			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr6:44272421C>T	ENST00000244571.4	-	12	1715	c.1713G>A	c.(1711-1713)caG>caA	p.Q571Q	TMEM151B_ENST00000438774.2_Intron|RP11-444E17.6_ENST00000505802.1_Intron	NM_020745.3	NP_065796			alanyl-tRNA synthetase 2, mitochondrial											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(2)|stomach(1)	34	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			GGTCTGAAGCCTGGCCCCCCT	0.622											OREG0017473	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q571Q		Atlas-SNP	.											.	AARS2	77	.	0			c.G1713A						.						62	59	60					6																	44272421		2203	4300	6503	SO:0001819	synonymous_variant	57505	exon12			TGAAGCCTGGCCC	AB033096	CCDS34464.1	6p21.1	2012-10-26	2012-10-26	2007-02-23	ENSG00000124608	ENSG00000124608	6.1.1.7	"Aminoacyl tRNA synthetases / Class II"	21022	protein-coding gene	gene with protein product	"alanine tRNA ligase 2, mitochondrial"	612035	"alanyl-tRNA synthetase like", "alanyl-tRNA synthetase 2, mitochondrial (putative)"	AARSL		15779907, 21549344	Standard	NM_020745		Approved	KIAA1270, bA444E17.1	uc010jza.1	Q5JTZ9	OTTHUMG00000014766	ENST00000244571.4:c.1713G>A	chr6.hg19:g.44272421C>T		149.0	0.0	922	185.0	67.0	NM_020745		Silent	SNP	ENST00000244571.4	hg19	CCDS34464.1																																																																																			.	.		0.622	AARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040741.2	NM_020745		T	44272421	C	T	44272421	2	4	306	1	0	0	0	0	0	0	0	1	20	680	24	3		3	AARS2	6	44272421	Silent	SNP	C	TCGA-GJ-A9DB-01A-11D-A36X-10	1049587	44272421	126842646	39	43808										
FAM46A	55603	hgsc.bcm.edu	37	chr6	82461742	82461742	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	ccgccaccgccgaagtcgccGccgccgaagtcgccgccgcc	12	22	0	0			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr6:82461742G>A	ENST00000320172.6	-	2	431	c.117C>T	c.(115-117)ggC>ggT	p.G39G	FAM46A_ENST00000369756.3_Silent_p.G120G|FAM46A_ENST00000369754.3_Silent_p.G58G	NM_017633.2	NP_060103.2	Q96IP4	FA46A_HUMAN	family with sequence similarity 46, member A	39			Missing. {ECO:0000269|PubMed:12054608, ECO:0000269|PubMed:16545789}.		regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)		poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(5)|skin(1)|urinary_tract(1)	12		all_cancers(76;6.74e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000282)|all_epithelial(107;0.0104)		BRCA - Breast invasive adenocarcinoma(397;0.0428)		cgaagtcgccgccgccgaagt	0.667																																					p.G39G		Atlas-SNP	.											.	FAM46A	37	.	0			c.C117T						.						7	8	8					6																	82461742		1601	3424	5025	SO:0001819	synonymous_variant	55603	exon2			GTCGCCGCCGCCG	AF350451	CCDS34489.1	6q14	2008-07-03	2004-08-19	2004-08-26	ENSG00000112773	ENSG00000112773			18345	protein-coding gene	gene with protein product		611357	"chromosome 6 open reading frame 37"	C6orf37		12054608, 17803723	Standard	NM_017633		Approved	FLJ20037	uc003pjg.3	Q96IP4	OTTHUMG00000015097	ENST00000320172.6:c.117C>T	chr6.hg19:g.82461742G>A		53.0	0.0		70.0	9.0	NM_017633	A8K7U4|Q5TF86|Q8NFZ9|Q9BW32|Q9NXV5	Silent	SNP	ENST00000320172.6	hg19	CCDS34489.1																																																																																			.	.		0.667	FAM46A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041331.1			A	82461742	G	A	82461742	2	1	306	1	0	0	0	0	0	0	0	1	5573	1074	38	1		1	FAM46A	6	82461742	Silent	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10	38189321	82461742	88653325	40	43809										
ZBTB2	57621	hgsc.bcm.edu	37	chr6	151687782	151687782	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	tggtggcttgtctcaactgaTgatctgcaatctgaatgcca	10	9	3	3			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr6:151687782T>C	ENST00000325144.4	-	3	559	c.419A>G	c.(418-420)cAt>cGt	p.H140R		NM_020861.1	NP_065912.1	Q8N680	ZBTB2_HUMAN	zinc finger and BTB domain containing 2	140					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|large_intestine(2)|lung(6)|skin(1)	12			BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.63e-11)		TCTCAACTGATGATCTGCAAT	0.537																																					p.H140R		Atlas-SNP	.											.	ZBTB2	30	.	0			c.A419G						.						102	96	98					6																	151687782		2203	4300	6503	SO:0001583	missense	57621	exon3			AACTGATGATCTG	BC020172	CCDS5231.1	6q25.1	2013-01-09			ENSG00000181472	ENSG00000181472		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	20868	protein-coding gene	gene with protein product						10819331	Standard	NM_020861		Approved	KIAA1483, ZNF437, bA351K16.2	uc003qoh.3	Q8N680	OTTHUMG00000015834	ENST00000325144.4:c.419A>G	chr6.hg19:g.151687782T>C	ENSP00000323183:p.His140Arg	131.0	0.0		132.0	41.0	NM_020861	A8K7C7|Q5SZ81|Q9P245	Missense_Mutation	SNP	ENST00000325144.4	hg19	CCDS5231.1	.	.	.	.	.	.	.	.	.	.	T	8.118	0.780319	0.16120	.	.	ENSG00000181472	ENST00000325144	T	0.04758	3.56	5.76	4.58	0.56647	.	0.046141	0.85682	D	0.000000	T	0.01661	0.0053	N	0.24115	0.695	0.50632	D	0.999885	B	0.34015	0.435	B	0.30572	0.117	T	0.53982	-0.8361	10	0.52906	T	0.07	-36.1224	13.0429	0.58910	0.0:0.0:0.1346:0.8654	.	140	Q8N680	ZBTB2_HUMAN	R	140	ENSP00000323183:H140R	ENSP00000323183:H140R	H	-	2	0	ZBTB2	151729475	1.000000	0.71417	0.176000	0.23000	0.830000	0.47004	7.691000	0.84191	0.986000	0.38683	-0.313000	0.08912	CAT	.	.		0.537	ZBTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042715.1	NM_020861		C	151687782	T	C	151687782	3	2	306	1	0	0	0	0	1	0	0	0	17543	1464	51	2	1129	2	ZBTB2	6	151687782	Missense_Mutation	SNP	T	TCGA-GJ-A9DB-01A-11D-A36X-10	69226040	151687782	19427285	41	43810										
THSD7A	221981	hgsc.bcm.edu	37	chr7	11416199	11416199	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	aattatttaaacactcaccaAgctagataaatcatggagac	5	8	2	2			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr7:11416199A>T	ENST00000423059.4	-	27	5138	c.4887T>A	c.(4885-4887)gcT>gcA	p.A1629A	AC004538.3_ENST00000445839.1_RNA|AC004538.3_ENST00000599875.1_RNA|AC004538.3_ENST00000595972.1_RNA|AC004538.3_ENST00000428967.1_RNA|AC004538.3_ENST00000421121.1_RNA	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	1629					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		ACACTCACCAAGCTAGATAAA	0.358										HNSCC(18;0.044)																											p.A1629A		Atlas-SNP	.											.	THSD7A	219	.	0			c.T4887A						.						48	49	49					7																	11416199		1842	4082	5924	SO:0001819	synonymous_variant	221981	exon26			TCACCAAGCTAGA		CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.4887T>A	chr7.hg19:g.11416199A>T		35.0	0.0		71.0	24.0	NM_015204		Silent	SNP	ENST00000423059.4	hg19	CCDS47543.1																																																																																			.	.		0.358	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2		T	11416199	A	T	11416199	2	4	306	1	0	0	0	0	0	0	0	1	15894	59	3	4		4	THSD7A	7	11416199	Silent	SNP	A	TCGA-GJ-A9DB-01A-11D-A36X-10		11416199	147722464	42	43811										
CCT6A	908	hgsc.bcm.edu	37	chr7	56127966	56127966	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	ttttttctacacatagggagAagagaagtttacctttattg	8	5	1	2			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr7:56127966A>G	ENST00000275603.4	+	10	1289	c.1070A>G	c.(1069-1071)gAa>gGa	p.E357G	SNORA15_ENST00000384439.1_RNA|CCT6A_ENST00000540286.1_Missense_Mutation_p.E326G|CCT6A_ENST00000335503.3_Missense_Mutation_p.E312G	NM_001762.3	NP_001753.1	P40227	TCPZ_HUMAN	chaperonin containing TCP1, subunit 6A (zeta 1)	357					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(1)|cervix(2)|endometrium(1)|large_intestine(4)|lung(5)|stomach(1)|upper_aerodigestive_tract(1)	15	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			ACATAGGGAGAAGAGAAGTTT	0.353																																					p.E357G		Atlas-SNP	.											.	CCT6A	44	.	0			c.A1070G						.						67	64	65					7																	56127966		2203	4300	6503	SO:0001583	missense	908	exon10			AGGGAGAAGAGAA	M94083	CCDS5523.1, CCDS34640.1	7p11.2	2011-09-02			ENSG00000146731	ENSG00000146731		"Heat Shock Proteins / Chaperonins"	1620	protein-coding gene	gene with protein product		104613		CCT6		1352881, 8034610	Standard	NM_001762		Approved	TTCP20, TCPZ, Cctz, HTR3, TCP20	uc003trl.1	P40227	OTTHUMG00000022842	ENST00000275603.4:c.1070A>G	chr7.hg19:g.56127966A>G	ENSP00000275603:p.Glu357Gly	149.0	0.0		139.0	58.0	NM_001762	A6NCD2|Q3KP28|Q75LP4|Q96S46	Missense_Mutation	SNP	ENST00000275603.4	hg19	CCDS5523.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.409710	0.83340	.	.	ENSG00000146731	ENST00000275603;ENST00000335503;ENST00000540286;ENST00000539340	T;T;T	0.67523	-0.27;-0.27;-0.27	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	T	0.70815	0.3267	L	0.60957	1.885	0.80722	D	1	B;P;B	0.40731	0.286;0.728;0.127	P;B;B	0.48677	0.586;0.33;0.39	T	0.67337	-0.5696	10	0.23891	T	0.37	-26.5914	15.1098	0.72346	1.0:0.0:0.0:0.0	.	326;312;357	B4DPJ8;A6NCD2;P40227	.;.;TCPZ_HUMAN	G	357;312;326;215	ENSP00000275603:E357G;ENSP00000352019:E312G;ENSP00000438488:E326G	ENSP00000275603:E357G	E	+	2	0	CCT6A	56095460	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.561000	0.90715	2.162000	0.67917	0.482000	0.46254	GAA	.	.		0.353	CCT6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251526.2	NM_001762		G	56127966	A	G	56127966	3	3	306	1	0	0	0	0	1	0	0	0	2959	246	9	2	1108	2	CCT6A	7	56127966	Missense_Mutation	SNP	A	TCGA-GJ-A9DB-01A-11D-A36X-10	44711767	56127966	103010697	43	43812										
WBSCR22	114049	hgsc.bcm.edu	37	chr7	73097969	73097969	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	cgtgagaatggcgtcccgcgGccggcgtccggagcatggcg	18	13	0	1			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr7:73097969G>C	ENST00000265758.2	+	1	72	c.14G>C	c.(13-15)gGc>gCc	p.G5A	WBSCR22_ENST00000423166.2_5'UTR|WBSCR22_ENST00000464615.1_Intron|WBSCR22_ENST00000423497.1_Missense_Mutation_p.G5A|DNAJC30_ENST00000395176.2_5'Flank	NM_017528.4	NP_059998.2	O43709	WBS22_HUMAN	Williams Beuren syndrome chromosome region 22	5					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|rRNA processing (GO:0006364)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|large_intestine(2)|lung(9)|prostate(1)	13		Lung NSC(55;0.0908)|all_lung(88;0.198)				GCGTCCCGCGGCCGGCGTCCG	0.667																																					p.G5A		Atlas-SNP	.											.	WBSCR22	27	.	0			c.G14C						.						11	14	13					7																	73097969		2193	4294	6487	SO:0001583	missense	114049	exon1			CCCGCGGCCGGCG	AF420248	CCDS5557.1, CCDS56490.1	7q11.23	2012-06-12			ENSG00000071462	ENSG00000071462			16405	protein-coding gene	gene with protein product	"metastasis-related methyltransferase 1"	615733				12073013, 11978965, 21148752	Standard	NM_001202560		Approved	MGC19709, MGC2022, MGC5140, PP3381, WBMT, MERM1	uc003tyt.3	O43709	OTTHUMG00000023306	ENST00000265758.2:c.14G>C	chr7.hg19:g.73097969G>C	ENSP00000265758:p.Gly5Ala	134.0	0.0		116.0	6.0	NM_001202560	A8K501|C9K060|Q96P12|Q9BQ58|Q9HBP9	Missense_Mutation	SNP	ENST00000265758.2	hg19	CCDS5557.1	.	.	.	.	.	.	.	.	.	.	G	0.100	-1.153666	0.01700	.	.	ENSG00000071462	ENST00000265758;ENST00000423497	T;T	0.39406	1.08;1.08	4.97	4.08	0.47627	.	0.549084	0.19896	N	0.103624	T	0.21267	0.0512	N	0.14661	0.345	0.28468	N	0.915572	B;B	0.16166	0.016;0.012	B;B	0.14023	0.007;0.01	T	0.19128	-1.0315	10	0.07813	T	0.8	-15.7673	8.4949	0.33121	0.0:0.1692:0.6555:0.1753	.	5;5	C9K060;O43709	.;WBS22_HUMAN	A	5	ENSP00000265758:G5A;ENSP00000401191:G5A	ENSP00000265758:G5A	G	+	2	0	WBSCR22	72735905	0.936000	0.31750	0.013000	0.15412	0.003000	0.03518	4.495000	0.60353	1.427000	0.47276	-0.302000	0.09304	GGC	.	.		0.667	WBSCR22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252303.1			C	73097969	G	C	73097969	3	2	306	1	0	0	0	0	1	0	0	0	17280	1203	42	4	16	4	WBSCR22	7	73097969	Missense_Mutation	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10	16970003	73097969	86040694	44	43813										
TMEM130	222865	hgsc.bcm.edu	37	chr7	98445808	98445808	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	cacatctggcagcagcacctGaccccagagggtggctccgg	13	15	1	2			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr7:98445808G>A	ENST00000416379.2	-	8	1183	c.1179C>T	c.(1177-1179)gtC>gtT	p.V393V	TMEM130_ENST00000345589.4_Silent_p.V279V|TMEM130_ENST00000546258.1_Silent_p.V362V|TMEM130_ENST00000474857.1_5'Flank|TMEM130_ENST00000339375.4_Silent_p.V381V|TMEM130_ENST00000450876.1_Silent_p.V297V			Q8N3G9	TM130_HUMAN	transmembrane protein 130	393						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	25	all_cancers(62;4.05e-09)|all_epithelial(64;2.62e-09)|Lung NSC(181;0.01)|all_lung(186;0.0115)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			AGCAGCACCTGACCCCAGAGG	0.562																																					p.V393V		Atlas-SNP	.											.	TMEM130	54	.	0			c.C1179T						.						51	49	50					7																	98445808		2203	4300	6503	SO:0001819	synonymous_variant	222865	exon8			GCACCTGACCCCA		CCDS5658.1, CCDS47649.1, CCDS47650.1	7q22.1	2006-03-09			ENSG00000166448	ENSG00000166448			25429	protein-coding gene	gene with protein product						12975309	Standard	NM_152913		Approved	DKFZp761L1417, FLJ42643	uc003upo.3	Q8N3G9	OTTHUMG00000154419	ENST00000416379.2:c.1179C>T	chr7.hg19:g.98445808G>A		302.0	0.0		269.0	100.0	NM_001134450	A4D266|B7Z364|Q8IY46|Q8N0W9|Q8N3R2	Silent	SNP	ENST00000416379.2	hg19	CCDS47650.1																																																																																			.	.		0.562	TMEM130-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000380713.1	NM_152913		A	98445808	G	A	98445808	2	1	306	1	0	0	0	0	0	0	0	1	16058	1277	45	3		3	TMEM130	7	98445808	Silent	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10	25347839	98445808	60692855	45	43814										
MUC17	140453	hgsc.bcm.edu	37	chr7	100679095	100679095	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	atacctgtcagcaacacgccGgtggccaattctgaggctag	11	12	2	1	rs527976330	byFrequency	TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr7:100679095G>A	ENST00000306151.4	+	3	4462	c.4398G>A	c.(4396-4398)ccG>ccA	p.P1466P		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1466	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					GCAACACGCCGGTGGCCAATT	0.478													A|||	23	0.00459265	0.0106	0.0014	5008	,	,		24214	0.005		0.001	False		,,,				2504	0.002				p.P1466P		Atlas-SNP	.											.	MUC17	804	.	0			c.G4398A						.						181	195	190					7																	100679095		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			CACGCCGGTGGCC	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.4398G>A	chr7.hg19:g.100679095G>A		78.0	0.0		82.0	27.0	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	hg19	CCDS34711.1																																																																																			.	.		0.478	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		A	100679095	G	A	100679095	2	1	306	1	0	0	0	0	0	0	0	1	9983	1103	39	1		1	MUC17	7	100679095	Silent	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10	2233287	100679095	58459568	46	43815										
ST18	9705	hgsc.bcm.edu	37	chr8	53074116	53074116	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	aaattgaattcaatttgcttCaccaaacttgtcctggagag	7	8	2	2			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr8:53074116C>T	ENST00000276480.7	-	14	2096	c.1413G>A	c.(1411-1413)gtG>gtA	p.V471V		NM_014682.2	NP_055497.1	O60284	ST18_HUMAN	suppression of tumorigenicity 18, zinc finger	471					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(14)|lung(38)|ovary(4)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	85		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)				CAATTTGCTTCACCAAACTTG	0.408																																					p.V471V		Atlas-SNP	.											.	ST18	212	.	0			c.G1413A						.						109	102	104					8																	53074116		2203	4300	6503	SO:0001819	synonymous_variant	9705	exon14			TTGCTTCACCAAA	AB011107	CCDS6149.1	8q11.23	2014-03-24	2014-03-24	2002-12-13	ENSG00000147488	ENSG00000147488		"Zinc fingers, C2HC-type containing"	18695	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 3"		"zinc finger protein 387", "suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein)"	ZNF387		15489893	Standard	NM_014682		Approved	KIAA0535, ZC2HC10, NZF3	uc003xra.2	O60284	OTTHUMG00000164233	ENST00000276480.7:c.1413G>A	chr8.hg19:g.53074116C>T		190.0	0.0		196.0	69.0	NM_014682	Q17RY1	Silent	SNP	ENST00000276480.7	hg19	CCDS6149.1																																																																																			.	.		0.408	ST18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377867.1			T	53074116	C	T	53074116	2	4	306	1	0	0	0	0	0	0	0	1	15227	813	29	3		3	ST18	8	53074116	Silent	SNP	C	TCGA-GJ-A9DB-01A-11D-A36X-10		53074116	93289906	47	43816										
KCNB2	9312	hgsc.bcm.edu	37	chr8	73848416	73848416	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	ttgatttgctggccatcttgCcgtactatgtcaccattttt	7	10	2	1			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr8:73848416C>A	ENST00000523207.1	+	3	1414	c.826C>A	c.(826-828)Ccg>Acg	p.P276T		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	276					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	GGCCATCTTGCCGTACTATGT	0.468																																					p.P276T		Atlas-SNP	.											.	KCNB2	228	.	0			c.C826A						.						133	126	128					8																	73848416		2203	4300	6503	SO:0001583	missense	9312	exon3			ATCTTGCCGTACT	U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.826C>A	chr8.hg19:g.73848416C>A	ENSP00000430846:p.Pro276Thr	140.0	0.0		171.0	69.0	NM_004770	Q7Z7D0|Q9BXD3	Missense_Mutation	SNP	ENST00000523207.1	hg19	CCDS6209.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.956102	0.92726	.	.	ENSG00000182674	ENST00000523207	D	0.98345	-4.88	5.74	5.74	0.90152	Ion transport (1);	0.000000	0.45126	D	0.000385	D	0.99477	0.9814	H	0.98466	4.24	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98119	1.0424	10	0.87932	D	0	.	19.91	0.97023	0.0:1.0:0.0:0.0	.	276	Q92953	KCNB2_HUMAN	T	276	ENSP00000430846:P276T	ENSP00000430846:P276T	P	+	1	0	KCNB2	74010970	1.000000	0.71417	0.967000	0.41034	0.979000	0.70002	7.818000	0.86416	2.702000	0.92279	0.655000	0.94253	CCG	.	.		0.468	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770		A	73848416	C	A	73848416	3	1	306	1	0	0	0	0	1	0	0	0	8022	739	26	3	832	3	KCNB2	8	73848416	Missense_Mutation	SNP	C	TCGA-GJ-A9DB-01A-11D-A36X-10	20774300	73848416	72515606	48	43817										
TRPS1	7227	hgsc.bcm.edu	37	chr8	116616728	116616728	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	ctgattaatgacagagccccTggaaagcttatcatttaact	7	9	1	3			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr8:116616728T>C	ENST00000220888.5	-	3	1588	c.1429A>G	c.(1429-1431)Agg>Ggg	p.R477G	TRPS1_ENST00000519674.1_Missense_Mutation_p.R477G|TRPS1_ENST00000395715.3_Missense_Mutation_p.R490G|TRPS1_ENST00000519076.1_Intron|TRPS1_ENST00000520276.1_Missense_Mutation_p.R481G			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	477					chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			ACAGAGCCCCTGGAAAGCTTA	0.453									Langer-Giedion syndrome																												p.R490G		Atlas-SNP	.											.	TRPS1	516	.	0			c.A1468G						.						65	63	63					8																	116616728		1896	4121	6017	SO:0001583	missense	7227	exon4	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	AGCCCCTGGAAAG	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"GATA zinc finger domain containing", "Zinc fingers, C2H2-type"	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.1429A>G	chr8.hg19:g.116616728T>C	ENSP00000220888:p.Arg477Gly	92.0	0.0		85.0	25.0	NM_014112	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Missense_Mutation	SNP	ENST00000220888.5	hg19		.	.	.	.	.	.	.	.	.	.	T	15.55	2.867237	0.51588	.	.	ENSG00000104447	ENST00000395715;ENST00000220888;ENST00000520276;ENST00000519674	D;D;D;T	0.98822	-5.16;-5.13;-5.13;0.66	5.6	1.7	0.24286	.	0.053759	0.64402	D	0.000001	D	0.97745	0.9260	N	0.19112	0.55	0.41707	D	0.989439	D;D;D	0.61080	0.989;0.981;0.989	D;D;D	0.75020	0.985;0.966;0.985	D	0.96955	0.9697	10	0.87932	D	0	.	13.4229	0.61009	0.0:0.0:0.3737:0.6263	.	481;477;490	Q9UHF7-3;Q9UHF7;Q9UHF7-2	.;TRPS1_HUMAN;.	G	490;477;481;477	ENSP00000379065:R490G;ENSP00000220888:R477G;ENSP00000428680:R481G;ENSP00000429174:R477G	ENSP00000220888:R477G	R	-	1	2	TRPS1	116685903	1.000000	0.71417	0.994000	0.49952	0.921000	0.55340	1.895000	0.39778	0.107000	0.17824	-0.435000	0.05868	AGG	.	.		0.453	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112		C	116616728	T	C	116616728	3	2	306	1	0	0	0	0	1	0	0	0	16608	1579	55	2	2432	2	TRPS1	8	116616728	Missense_Mutation	SNP	T	TCGA-GJ-A9DB-01A-11D-A36X-10	42768312	116616728	29747294	49	43818										
PTPRD	5789	hgsc.bcm.edu	37	chr9	8500869	8500869	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	tccagctgttccaaaaggtaTttggtagtgtccgaaggaat	11	7	0	0			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr9:8500869T>G	ENST00000381196.4	-	21	2556	c.2013A>C	c.(2011-2013)aaA>aaC	p.K671N	PTPRD_ENST00000358503.5_Missense_Mutation_p.K658N|PTPRD_ENST00000486161.1_Intron|PTPRD_ENST00000537002.1_Intron|PTPRD_ENST00000356435.5_Missense_Mutation_p.K671N|PTPRD_ENST00000360074.4_Missense_Mutation_p.K658N|PTPRD_ENST00000471274.1_5'UTR|PTPRD_ENST00000397606.3_Intron|PTPRD_ENST00000540109.1_Missense_Mutation_p.K671N|PTPRD_ENST00000355233.5_Intron|PTPRD_ENST00000397611.3_Intron|PTPRD_ENST00000397617.3_Intron	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	671	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		CCAAAAGGTATTTGGTAGTGT	0.478										TSP Lung(15;0.13)																											p.K671N		Atlas-SNP	.											.	PTPRD	1348	.	0			c.A2013C						.						236	223	228					9																	8500869		2203	4300	6503	SO:0001583	missense	5789	exon24			AAGGTATTTGGTA	X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.2013A>C	chr9.hg19:g.8500869T>G	ENSP00000370593:p.Lys671Asn	195.0	0.0		127.0	63.0	NM_002839	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Missense_Mutation	SNP	ENST00000381196.4	hg19	CCDS43786.1	.	.	.	.	.	.	.	.	.	.	T	12.95	2.092206	0.36952	.	.	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000540109	T;T;T;T;T	0.56776	0.44;0.44;0.44;0.44;0.44	5.64	-1.98	0.07480	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.220732	0.48286	D	0.000194	T	0.23886	0.0578	N	0.02011	-0.69	0.36524	D	0.8703	B;B;B	0.26081	0.141;0.033;0.045	B;B;B	0.33121	0.133;0.025;0.158	T	0.13202	-1.0518	9	.	.	.	.	13.0381	0.58882	0.0:0.7342:0.0:0.2658	.	658;671;671	G3XAE2;Q2HXI4;P23468	.;.;PTPRD_HUMAN	N	671;671;658;658;671	ENSP00000370593:K671N;ENSP00000348812:K671N;ENSP00000353187:K658N;ENSP00000351293:K658N;ENSP00000438164:K671N	.	K	-	3	2	PTPRD	8490869	0.255000	0.24002	0.977000	0.42913	0.996000	0.88848	-0.230000	0.09083	-0.418000	0.07450	0.459000	0.35465	AAA	.	.		0.478	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3			G	8500869	T	G	8500869	3	3	306	1	0	0	0	0	1	0	0	0	12814	1490	52	5	3885	5	PTPRD	9	8500869	Missense_Mutation	SNP	T	TCGA-GJ-A9DB-01A-11D-A36X-10		8500869	132712562	50	43819										
BNC2	54796	hgsc.bcm.edu	37	chr9	16436852	16436852	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	ctttgtcatagaatgtcttcCcacatgcattacagaacact	5	11	2	2			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr9:16436852C>T	ENST00000380672.4	-	6	1397	c.1340G>A	c.(1339-1341)gGg>gAg	p.G447E	BNC2_ENST00000545497.1_Missense_Mutation_p.G352E|BNC2_ENST00000380667.2_Missense_Mutation_p.G380E|BNC2_ENST00000380666.2_Missense_Mutation_p.G447E	NM_017637.5	NP_060107.3			basonuclin 2											NS(2)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(16)|liver(1)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(50;9.01e-08)		GAATGTCTTCCCACATGCATT	0.423																																					p.G447E		Atlas-SNP	.											.	BNC2	166	.	0			c.G1340A						.						107	99	102					9																	16436852		2203	4300	6503	SO:0001583	missense	54796	exon6			GTCTTCCCACATG	AK092247	CCDS6482.2	9p22.2	2013-05-20			ENSG00000173068	ENSG00000173068		"Zinc fingers, C2H2-type"	30988	protein-coding gene	gene with protein product		608669				14702039	Standard	XM_006716784		Approved	BSN2, FLJ20043	uc003zml.3	Q6ZN30	OTTHUMG00000019593	ENST00000380672.4:c.1340G>A	chr9.hg19:g.16436852C>T	ENSP00000370047:p.Gly447Glu	80.0	0.0		69.0	38.0	NM_017637		Missense_Mutation	SNP	ENST00000380672.4	hg19	CCDS6482.2	.	.	.	.	.	.	.	.	.	.	C	12.07	1.827916	0.32329	.	.	ENSG00000173068	ENST00000380672;ENST00000418777;ENST00000380667;ENST00000545497;ENST00000544198;ENST00000380666;ENST00000540340	T;T;T;T;T	0.20598	2.06;2.06;2.06;2.06;2.06	6.17	6.17	0.99709	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.000000	0.85682	D	0.000000	T	0.34250	0.0891	L	0.33093	0.98	0.80722	D	1	P;D;D;B;D;D;D;D;D	0.89917	0.51;1.0;1.0;0.08;1.0;1.0;1.0;1.0;1.0	B;D;D;B;D;D;D;D;D	0.97110	0.147;0.997;1.0;0.086;0.999;0.999;0.993;0.997;1.0	T	0.01591	-1.1317	10	0.02654	T	1	-19.5438	20.8794	0.99867	0.0:1.0:0.0:0.0	.	352;380;447;273;447;404;447;352;212	F5H586;B1APH0;Q6ZN30-2;B4E3J2;F5H8G9;Q5H9S4;Q6ZN30;B4DR27;D3DRJ1	.;.;.;.;.;.;BNC2_HUMAN;.;.	E	447;404;380;352;273;447;447	ENSP00000370047:G447E;ENSP00000408370:G404E;ENSP00000370042:G380E;ENSP00000444640:G352E;ENSP00000370041:G447E	ENSP00000370041:G447E	G	-	2	0	BNC2	16426852	1.000000	0.71417	1.000000	0.80357	0.851000	0.48451	4.968000	0.63728	2.941000	0.99782	0.655000	0.94253	GGG	.	.		0.423	BNC2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216901.5	NM_017637		T	16436852	C	T	16436852	3	4	306	1	0	0	0	0	1	0	0	0	1475	623	22	3	1967	3	BNC2	9	16436852	Missense_Mutation	SNP	C	TCGA-GJ-A9DB-01A-11D-A36X-10	7935983	16436852	124776579	51	43820										
MTAP	4507	hgsc.bcm.edu	37	chr9	21837985	21837985	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	tgccatattccaatggctgaGccgttttgccccaaaacgag	9	12	0	1			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr9:21837985G>C	ENST00000460874.2	+	5	702	c.477G>C	c.(475-477)gaG>gaC	p.E159D	RP11-145E5.5_ENST00000404796.2_Intron|MTAP_ENST00000380172.4_Missense_Mutation_p.E142D|MTAP_ENST00000580900.1_Missense_Mutation_p.E142D					methylthioadenosine phosphorylase									p.0(1)|p.E142E(1)|p.0?(1)		central_nervous_system(1)|endometrium(2)|kidney(3)|lung(3)|pancreas(1)	10		all_cancers(5;0)|Hepatocellular(5;0.00162)|Colorectal(97;0.173)		GBM - Glioblastoma multiforme(3;0)|Lung(24;2.24e-57)|LUSC - Lung squamous cell carcinoma(38;1.97e-36)|STAD - Stomach adenocarcinoma(4;3.26e-05)|OV - Ovarian serous cystadenocarcinoma(39;0.00931)|COAD - Colon adenocarcinoma(8;0.15)		CAATGGCTGAGCCGTTTTGCC	0.458																																					p.E142D		Atlas-SNP	.											MTAP,NS,carcinoma,0,1	MTAP	23	.	3	Whole gene deletion(2)|Substitution - coding silent(1)	lung(2)|endometrium(1)	c.G426C						.						249	249	249					9																	21837985		2203	4300	6503	SO:0001583	missense	4507	exon5			GGCTGAGCCGTTT	AB062485	CCDS6509.1	9p21	2013-05-29			ENSG00000099810	ENSG00000099810	2.4.2.28		7413	protein-coding gene	gene with protein product	"S-methyl-5'-thioadenosine phosphorylase"	156540				11126361	Standard	NM_002451		Approved	MSAP, c86fus	uc003zph.3	Q13126	OTTHUMG00000019690	ENST00000460874.2:c.477G>C	chr9.hg19:g.21837985G>C	ENSP00000461932:p.Glu159Asp	110.0	0.0		67.0	33.0	NM_002451		Missense_Mutation	SNP	ENST00000460874.2	hg19		.	.	.	.	.	.	.	.	.	.	G	12.89	2.074830	0.36566	.	.	ENSG00000099810	ENST00000380172	D	0.86865	-2.18	5.54	-1.69	0.08186	Nucleoside phosphorylase domain (1);	0.050401	0.85682	N	0.000000	T	0.70281	0.3206	L	0.27944	0.81	0.54753	D	0.999985	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.58154	-0.7686	10	0.02654	T	1	-15.3699	7.2062	0.25909	0.6104:0.1375:0.2521:0.0	.	159;142	B4DUC8;Q13126	.;MTAP_HUMAN	D	142	ENSP00000369519:E142D	ENSP00000369519:E142D	E	+	3	2	MTAP	21827985	0.999000	0.42202	0.607000	0.28956	0.990000	0.78478	0.391000	0.20784	-0.382000	0.07870	0.655000	0.94253	GAG	.	.		0.458	MTAP-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000051929.2	NM_002451		C	21837985	G	C	21837985	3	2	306	1	0	0	0	0	1	0	0	0	9920	962	34	4	444	4	MTAP	9	21837985	Missense_Mutation	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10	5401133	21837985	119375446	52	43821										
SLC28A3	64078	hgsc.bcm.edu	37	chr9	86894924	86894924	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	gtcatgaagcaggccacggtCcccgcaatcagagctctcac	10	15	3	2			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr9:86894924C>T	ENST00000376238.4	-	16	1843	c.1794G>A	c.(1792-1794)ggG>ggA	p.G598G	SLC28A3_ENST00000537648.1_Silent_p.G529G|RP11-380F14.2_ENST00000419815.1_RNA	NM_001199633.1|NM_022127.2	NP_001186562.1|NP_071410.1	Q9HAS3	S28A3_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 3	598					pyrimidine nucleoside transport (GO:0015864)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|purine-specific nucleoside:sodium symporter activity (GO:0015390)|pyrimidine- and adenine-specific:sodium symporter activity (GO:0015389)			endometrium(2)|large_intestine(6)|lung(17)|ovary(1)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31					Adenosine(DB00640)|Cladribine(DB00242)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Mercaptopurine(DB01033)|Ribavirin(DB00811)	AGGCCACGGTCCCCGCAATCA	0.572																																					p.G598G	Ovarian(106;425 1539 34835 42413 43572)	Atlas-SNP	.											.	SLC28A3	72	.	0			c.G1794A						.						87	72	77					9																	86894924		2203	4300	6503	SO:0001819	synonymous_variant	64078	exon16			CACGGTCCCCGCA	AF305210	CCDS6670.1	9q21.33	2013-07-17	2013-07-17		ENSG00000197506	ENSG00000197506		"Solute carriers"	16484	protein-coding gene	gene with protein product		608269	"solute carrier family 28 (sodium-coupled nucleoside transporter), member 3"			11032837	Standard	NM_001199633		Approved	CNT3	uc010mpz.3	Q9HAS3	OTTHUMG00000020117	ENST00000376238.4:c.1794G>A	chr9.hg19:g.86894924C>T		39.0	0.0		40.0	18.0	NM_001199633	A8K9Y4|B1AML0|B2RA51|B4E2S8|F5GYE3	Silent	SNP	ENST00000376238.4	hg19	CCDS6670.1																																																																																			.	.		0.572	SLC28A3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052874.1	NM_022127		T	86894924	C	T	86894924	2	4	306	1	0	0	0	0	0	0	0	1	14548	842	30	3		3	SLC28A3	9	86894924	Silent	SNP	C	TCGA-GJ-A9DB-01A-11D-A36X-10	65056939	86894924	54318507	53	43822										
CUBN	8029	hgsc.bcm.edu	37	chr10	16979768	16979768	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	aattaggcgggcgtgaatgcTaggcccatcatagatctgta	12	8	2	2			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr10:16979768T>C	ENST00000377833.4	-	39	5814	c.5749A>G	c.(5749-5751)Agc>Ggc	p.S1917G		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	1917	CUB 13. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GCGTGAATGCTAGGCCCATCA	0.343																																					p.S1917G		Atlas-SNP	.											.	CUBN	515	.	0			c.A5749G						.						56	59	58					10																	16979768		2203	4300	6503	SO:0001583	missense	8029	exon39			GAATGCTAGGCCC	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.5749A>G	chr10.hg19:g.16979768T>C	ENSP00000367064:p.Ser1917Gly	68.0	0.0		63.0	11.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	T	0.079	-1.187462	0.01620	.	.	ENSG00000107611	ENST00000377833	T	0.36699	1.24	5.14	1.71	0.24356	CUB (5);	0.865227	0.09619	N	0.777837	T	0.23766	0.0575	L	0.35341	1.055	0.09310	N	1	B	0.11235	0.004	B	0.10450	0.005	T	0.30995	-0.9959	10	0.13108	T	0.6	.	6.6094	0.22743	0.0:0.526:0.0:0.474	.	1917	O60494	CUBN_HUMAN	G	1917	ENSP00000367064:S1917G	ENSP00000367064:S1917G	S	-	1	0	CUBN	17019774	0.002000	0.14202	0.012000	0.15200	0.078000	0.17371	1.214000	0.32419	0.636000	0.30508	-0.462000	0.05337	AGC	.	.		0.343	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		C	16979768	T	C	16979768	3	2	306	1	0	0	0	0	1	0	0	0	4053	1522	53	2	5238	2	CUBN	10	16979768	Missense_Mutation	SNP	T	TCGA-GJ-A9DB-01A-11D-A36X-10		16979768	118554979	54	43823										
MYO3A	53904	hgsc.bcm.edu	37	chr10	26432443	26432443	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	aggataactggcccctcttaGatatgtttctgcaaaagcca	8	10	2	1			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr10:26432443G>C	ENST00000265944.5	+	21	2495	c.2329G>C	c.(2329-2331)Gat>Cat	p.D777H	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	777	Myosin motor.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.D777Y(1)		NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						GCCCCTCTTAGATATGTTTCT	0.373																																					p.D777H		Atlas-SNP	.											MYO3A,NS,carcinoma,0,1	MYO3A	371	.	1	Substitution - Missense(1)	kidney(1)	c.G2329C						.						146	143	144					10																	26432443		2203	4300	6503	SO:0001583	missense	53904	exon21			CTCTTAGATATGT	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.2329G>C	chr10.hg19:g.26432443G>C	ENSP00000265944:p.Asp777His	133.0	0.0		137.0	13.0	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	hg19	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.277643	0.80692	.	.	ENSG00000095777	ENST00000265944	D	0.90444	-2.67	6.02	5.12	0.69794	Myosin head, motor domain (3);	0.134780	0.64402	D	0.000004	D	0.96377	0.8818	M	0.92459	3.31	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.97317	0.9941	10	0.87932	D	0	.	15.5933	0.76558	0.0656:0.0:0.9344:0.0	.	777	Q8NEV4	MYO3A_HUMAN	H	777	ENSP00000265944:D777H	ENSP00000265944:D777H	D	+	1	0	MYO3A	26472449	1.000000	0.71417	0.999000	0.59377	0.928000	0.56348	9.869000	0.99810	1.570000	0.49709	-0.127000	0.14921	GAT	.	.		0.373	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		C	26432443	G	C	26432443	3	2	306	1	0	0	0	0	1	0	0	0	10085	942	33	4	2403	4	MYO3A	10	26432443	Missense_Mutation	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10	9452675	26432443	109102304	55	43824										
TSPAN15	23555	hgsc.bcm.edu	37	chr10	71244958	71244958	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	tggtggcgtggtggccttgaCcttccggaaccaggtgggcc	17	11	0	1			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr10:71244958C>A	ENST00000373290.2	+	3	466	c.344C>A	c.(343-345)aCc>aAc	p.T115N		NM_012339.3	NP_036471.1	O95858	TSN15_HUMAN	tetraspanin 15	115					establishment of protein localization to plasma membrane (GO:0090002)|protein maturation (GO:0051604)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	enzyme binding (GO:0019899)			breast(1)|endometrium(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)	9						GTGGCCTTGACCTTCCGGAAC	0.552																																					p.T115N		Atlas-SNP	.											.	TSPAN15	22	.	0			c.C344A						.						277	209	232					10																	71244958		2203	4300	6503	SO:0001583	missense	23555	exon3			CCTTGACCTTCCG	AY358934	CCDS7294.1	10q22.1	2013-02-14	2005-03-21	2005-03-21	ENSG00000099282	ENSG00000099282		"Tetraspanins"	23298	protein-coding gene	gene with protein product		613140	"transmembrane 4 superfamily member 15"	TM4SF15		11739647, 10719184	Standard	NM_012339		Approved	NET-7	uc001jpo.1	O95858	OTTHUMG00000018381	ENST00000373290.2:c.344C>A	chr10.hg19:g.71244958C>A	ENSP00000362387:p.Thr115Asn	142.0	0.0		189.0	8.0	NM_012339	Q6UW79	Missense_Mutation	SNP	ENST00000373290.2	hg19	CCDS7294.1	.	.	.	.	.	.	.	.	.	.	C	11.93	1.786716	0.31593	.	.	ENSG00000099282	ENST00000373290;ENST00000452130	T;T	0.79352	-1.26;-1.26	5.04	1.2	0.21068	Tetraspanin, EC2 domain (1);	0.354234	0.29266	N	0.012645	T	0.67496	0.2899	L	0.38175	1.15	0.22240	N	0.999265	B	0.26876	0.162	B	0.31495	0.131	T	0.61855	-0.6977	10	0.87932	D	0	-22.0167	9.3633	0.38208	0.0:0.1995:0.0:0.8005	.	115	O95858	TSN15_HUMAN	N	115;24	ENSP00000362387:T115N;ENSP00000404528:T24N	ENSP00000362387:T115N	T	+	2	0	TSPAN15	70914964	0.996000	0.38824	1.000000	0.80357	0.792000	0.44763	0.292000	0.19011	0.266000	0.21894	-1.012000	0.02466	ACC	.	.		0.552	TSPAN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048444.1	NM_012339		A	71244958	C	A	71244958	3	1	306	1	0	0	0	0	1	0	0	0	16654	507	18	3	354	3	TSPAN15	10	71244958	Missense_Mutation	SNP	C	TCGA-GJ-A9DB-01A-11D-A36X-10	44812515	71244958	64289789	56	43825										
EBF3	253738	hgsc.bcm.edu	37	chr10	131761727	131761727	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	agcacgaagtggaagaaattGgatttccggaggttggaagg	16	4	0	1			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr10:131761727G>T	ENST00000355311.5	-	2	267	c.195C>A	c.(193-195)tcC>tcA	p.S65S	EBF3_ENST00000368648.3_Silent_p.S65S			Q9H4W6	COE3_HUMAN	early B-cell factor 3	65	Interaction with DNA. {ECO:0000250}.				multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	44		all_cancers(35;1.8e-08)|all_epithelial(44;8.26e-08)|Lung NSC(174;0.0091)|all_lung(145;0.0123)|Breast(234;0.039)|all_neural(114;0.0722)|Colorectal(57;0.0764)		OV - Ovarian serous cystadenocarcinoma(35;0.00513)		GGAAGAAATTGGATTTCCGGA	0.607																																					p.S65S		Atlas-SNP	.											.	EBF3	193	.	0			c.C195A						.						54	59	58					10																	131761727		2203	4300	6503	SO:0001819	synonymous_variant	253738	exon2			GAAATTGGATTTC		CCDS31314.1	10q26.3	2007-03-30			ENSG00000108001	ENSG00000108001			19087	protein-coding gene	gene with protein product		607407				12355068	Standard	NM_001005463		Approved	COE3, DKFZp667B0210	uc001lki.2	Q9H4W6	OTTHUMG00000019265	ENST00000355311.5:c.195C>A	chr10.hg19:g.131761727G>T		74.0	0.0		78.0	28.0	NM_001005463	A0AUY1|Q5T6H9|Q9H4W5	Silent	SNP	ENST00000355311.5	hg19																																																																																				.	.		0.607	EBF3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051015.2	NM_001005463		T	131761727	G	T	131761727	2	4	306	1	0	0	0	0	0	0	0	1	4884	1335	47	3		3	EBF3	10	131761727	Silent	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10	60516769	131761727	3773020	57	43826										
TOLLIP	54472	hgsc.bcm.edu	37	chr11	1309926	1309926	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	ccgctcaggctgtaccacttGtcctccaccttgccctgcct	7	19	1	0			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr11:1309926G>A	ENST00000317204.6	-	4	570	c.447C>T	c.(445-447)gaC>gaT	p.D149D	TOLLIP_ENST00000528719.1_5'UTR|TOLLIP_ENST00000525159.1_Silent_p.D88D|TOLLIP_ENST00000527886.1_Silent_p.D80D|TOLLIP_ENST00000263646.7_Silent_p.D121D|TOLLIP_ENST00000542915.1_Silent_p.D99D|TOLLIP_ENST00000527938.1_Intron	NM_019009.3	NP_061882.2	Q9H0E2	TOLIP_HUMAN	toll interacting protein	149					autophagy (GO:0006914)|cell-cell signaling (GO:0007267)|epithelial cell differentiation (GO:0030855)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|leukocyte activation (GO:0045321)|phosphorylation (GO:0016310)|positive regulation of protein sumoylation (GO:0033235)|protein localization to endosome (GO:0036010)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|interleukin-1 receptor complex (GO:0045323)|interleukin-18 receptor complex (GO:0045092)|nuclear body (GO:0016604)|perinuclear region of cytoplasm (GO:0048471)	kinase binding (GO:0019900)|signal transducer activity (GO:0004871)|Toll-like receptor binding (GO:0035325)			large_intestine(1)|lung(4)|upper_aerodigestive_tract(1)	6		all_cancers(49;7.62e-05)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0256)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.00152)|Lung(200;0.09)|LUSC - Lung squamous cell carcinoma(625;0.107)		TGTACCACTTGTCCTCCACCT	0.647																																					p.D149D		Atlas-SNP	.											.	TOLLIP	25	.	0			c.C447T						.						177	101	127					11																	1309926		2202	4298	6500	SO:0001819	synonymous_variant	54472	exon4			CCACTTGTCCTCC	AJ242972	CCDS7723.1	11p	2008-02-05			ENSG00000078902	ENSG00000078902			16476	protein-coding gene	gene with protein product		606277				9426216, 10854325	Standard	NM_019009		Approved	IL-1RAcPIP	uc001lte.3	Q9H0E2	OTTHUMG00000133333	ENST00000317204.6:c.447C>T	chr11.hg19:g.1309926G>A		89.0	0.0		72.0	26.0	NM_019009	B3KXC6|Q9H9E6|Q9UJ69	Silent	SNP	ENST00000317204.6	hg19	CCDS7723.1																																																																																			.	.		0.647	TOLLIP-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000257162.2	NM_019009		A	1309926	G	A	1309926	2	1	306	1	0	0	0	0	0	0	0	1	16365	1368	48	3		3	TOLLIP	11	1309926	Silent	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10		1309926	133696590	58	43827										
OR52E4	390081	hgsc.bcm.edu	37	chr11	5905748	5905748	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	ctatgattgatctgggtctgTccacatccactatccccaaa	6	13	2	2			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr11:5905748T>C	ENST00000316987.2	+	1	248	c.226T>C	c.(226-228)Tcc>Ccc	p.S76P		NM_001005165.1	NP_001005165.1	Q8NGH9	O52E4_HUMAN	olfactory receptor, family 52, subfamily E, member 4	76						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(2)|prostate(1)|skin(2)	30		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.24e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCTGGGTCTGTCCACATCCAC	0.438																																					p.S76P		Atlas-SNP	.											.	OR52E4	65	.	0			c.T226C						.						164	139	148					11																	5905748		2201	4296	6497	SO:0001583	missense	390081	exon1			GGTCTGTCCACAT	AB065817	CCDS31401.1	11p15.4	2012-08-09			ENSG00000180974	ENSG00000180974		"GPCR / Class A : Olfactory receptors"	15213	protein-coding gene	gene with protein product							Standard	NM_001005165		Approved		uc010qzs.2	Q8NGH9	OTTHUMG00000168804	ENST00000316987.2:c.226T>C	chr11.hg19:g.5905748T>C	ENSP00000321426:p.Ser76Pro	73.0	0.0		63.0	13.0	NM_001005165	Q6IFG0	Missense_Mutation	SNP	ENST00000316987.2	hg19	CCDS31401.1	.	.	.	.	.	.	.	.	.	.	T	15.89	2.966462	0.53507	.	.	ENSG00000180974	ENST00000316987	T	0.00832	5.64	5.04	5.04	0.67666	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49305	D	0.000153	T	0.06371	0.0164	M	0.90082	3.085	0.09310	N	1	D	0.69078	0.997	D	0.70227	0.968	T	0.07271	-1.0781	10	0.87932	D	0	.	10.488	0.44733	0.0:0.0:0.1627:0.8373	.	76	Q8NGH9	O52E4_HUMAN	P	76	ENSP00000321426:S76P	ENSP00000321426:S76P	S	+	1	0	OR52E4	5862324	0.000000	0.05858	0.887000	0.34795	0.997000	0.91878	-0.252000	0.08806	2.106000	0.64143	0.523000	0.50628	TCC	.	.		0.438	OR52E4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401146.1	NM_001005165		C	5905748	T	C	5905748	3	2	306	1	0	0	0	0	1	0	0	0	11125	1667	58	2	228	2	OR52E4	11	5905748	Missense_Mutation	SNP	T	TCGA-GJ-A9DB-01A-11D-A36X-10	4595822	5905748	129100768	59	43828										
DKK3	27122	hgsc.bcm.edu	37	chr11	11990020	11990020	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	atgctgggcccacagtcctcGtcgatgatgcactcctgggg	13	13	0	1			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr11:11990020G>A	ENST00000396505.2	-	5	688	c.450C>T	c.(448-450)gaC>gaT	p.D150D	DKK3_ENST00000525493.1_Silent_p.D150D|DKK3_ENST00000450094.2_Silent_p.D122D|DKK3_ENST00000326932.4_Silent_p.D150D|DKK3_ENST00000527132.1_Intron	NM_015881.5	NP_056965.3	Q9UBP4	DKK3_HUMAN	dickkopf WNT signaling pathway inhibitor 3	150	DKK-type Cys-1.				adrenal gland development (GO:0030325)|anatomical structure morphogenesis (GO:0009653)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of transcription, DNA-templated (GO:0045892)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)				breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(1)|pancreas(1)	8				Epithelial(150;0.000502)		CACAGTCCTCGTCGATGATGC	0.632																																					p.D150D		Atlas-SNP	.											.	DKK3	35	.	0			c.C450T						.						89	75	79					11																	11990020		2201	4294	6495	SO:0001819	synonymous_variant	27122	exon4			GTCCTCGTCGATG	AF177396	CCDS7808.1	11p15.3	2013-05-15	2013-05-15		ENSG00000050165	ENSG00000050165			2893	protein-coding gene	gene with protein product	"regulated in glioma"	605416	"dickkopf (Xenopus laevis) homolog 3", "dickkopf 3 homolog (Xenopus laevis)"			10570958	Standard	XM_006718177		Approved	REIC, RIG	uc001mjv.3	Q9UBP4	OTTHUMG00000165709	ENST00000396505.2:c.450C>T	chr11.hg19:g.11990020G>A		71.0	0.0		66.0	19.0	NM_001018057	A8K1I2|D3DQW1|Q9ULB7	Silent	SNP	ENST00000396505.2	hg19	CCDS7808.1																																																																																			.	.		0.632	DKK3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385863.1	NM_013253		A	11990020	G	A	11990020	2	1	306	1	0	0	0	0	0	0	0	1	4548	1136	40	1		1	DKK3	11	11990020	Silent	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10	6084272	11990020	123016496	60	43829										
IGSF22	283284	hgsc.bcm.edu	37	chr11	18733863	18733863	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	attgtcctttggggccttccActtcatgtgcacacaactac	7	13	1	0			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr11:18733863A>G	ENST00000513874.1	-	15	2303	c.2164T>C	c.(2164-2166)Tgg>Cgg	p.W722R	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	721	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.									NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						GGGGCCTTCCACTTCATGTGC	0.557																																					p.W722R		Atlas-SNP	.											.	IGSF22	211	.	0			c.T2164C						.						96	82	86					11																	18733863		692	1591	2283	SO:0001583	missense	283284	exon15			CCTTCCACTTCAT	AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	26750	protein-coding gene	gene with protein product							Standard	NM_173588		Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.2164T>C	chr11.hg19:g.18733863A>G	ENSP00000421191:p.Trp722Arg	188.0	0.0		180.0	54.0	NM_173588	A6NNA0|D6RGV7	Missense_Mutation	SNP	ENST00000513874.1	hg19	CCDS41625.2	.	.	.	.	.	.	.	.	.	.	a	14.49	2.550306	0.45383	.	.	ENSG00000179057	ENST00000513874	D	0.91011	-2.77	4.24	3.12	0.35913	.	.	.	.	.	D	0.93177	0.7827	H	0.98155	4.16	0.31692	N	0.64175	B	0.34161	0.439	B	0.33196	0.159	D	0.92150	0.5727	9	0.59425	D	0.04	.	7.9731	0.30138	0.9039:0.0:0.0961:0.0	.	722	D6RGV7	.	R	722	ENSP00000421191:W722R	ENSP00000421191:W722R	W	-	1	0	IGSF22	18690439	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.410000	0.66381	0.696000	0.31696	0.524000	0.50904	TGG	.	.		0.557	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588		G	18733863	A	G	18733863	3	3	306	1	0	0	0	0	1	0	0	0	7609	159	6	2	1852	2	IGSF22	11	18733863	Missense_Mutation	SNP	A	TCGA-GJ-A9DB-01A-11D-A36X-10	6743843	18733863	116272653	61	43830										
FAT3	120114	hgsc.bcm.edu	37	chr11	92087690	92087690	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	ctccttaatatcaccatctaTgacttaggtaatccacagaa	4	11	2	2			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr11:92087690T>C	ENST00000298047.6	+	1	2429	c.2412T>C	c.(2410-2412)taT>taC	p.Y804Y	FAT3_ENST00000541502.1_Silent_p.Y804Y|FAT3_ENST00000525166.1_Silent_p.Y654Y|FAT3_ENST00000409404.2_Silent_p.Y804Y			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	804	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				TCACCATCTATGACTTAGGTA	0.408										TCGA Ovarian(4;0.039)																											p.Y804Y		Atlas-SNP	.											.	FAT3	1822	.	0			c.T2412C						.						102	97	99					11																	92087690		1964	4168	6132	SO:0001819	synonymous_variant	120114	exon1			CATCTATGACTTA	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.2412T>C	chr11.hg19:g.92087690T>C		84.0	0.0		92.0	34.0	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	hg19																																																																																				.	.		0.408	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		C	92087690	T	C	92087690	2	2	306	1	0	0	0	0	0	0	0	1	5699	1471	51	2		2	FAT3	11	92087690	Silent	SNP	T	TCGA-GJ-A9DB-01A-11D-A36X-10	73353827	92087690	42918826	62	43831										
BCO2	83875	hgsc.bcm.edu	37	chr11	112064319	112064319	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	ggccaacagtgctaaaaaccGaattgtgatctcagaatttg	9	8	1	2			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr11:112064319G>A	ENST00000357685.5	+	3	551	c.416G>A	c.(415-417)cGa>cAa	p.R139Q	BCO2_ENST00000526088.1_Missense_Mutation_p.R105Q|BCO2_ENST00000532593.1_Missense_Mutation_p.R34Q|SDHD_ENST00000525468.1_3'UTR|AP002884.3_ENST00000532612.1_Missense_Mutation_p.R110Q|BCO2_ENST00000393032.2_Missense_Mutation_p.R105Q|BCO2_ENST00000531169.1_Missense_Mutation_p.R105Q|BCO2_ENST00000438022.1_Missense_Mutation_p.R105Q|BCO2_ENST00000361053.4_Missense_Mutation_p.R139Q			Q9BYV7	BCDO2_HUMAN	beta-carotene oxygenase 2	139					carotene catabolic process (GO:0016121)|carotene metabolic process (GO:0016119)|carotenoid metabolic process (GO:0016116)|oxidation-reduction process (GO:0055114)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of reactive oxygen species metabolic process (GO:2000377)|retinal metabolic process (GO:0042574)|retinoic acid metabolic process (GO:0042573)	intracellular (GO:0005622)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			NS(1)|breast(1)|kidney(3)|large_intestine(1)|lung(9)|skin(1)	16						GCTAAAAACCGAATTGTGATC	0.463																																					p.R139Q	GBM(177;1916 2099 21049 29541 39946)	Atlas-SNP	.											BCO2,NS,carcinoma,+1,2	BCO2	44	.	0			c.G416A						.						132	111	119					11																	112064319		2201	4297	6498	SO:0001583	missense	83875	exon3			AAAACCGAATTGT	AJ290393	CCDS8358.2, CCDS41716.1, CCDS58181.1, CCDS58182.1, CCDS58183.1	11q23.1	2014-05-12	2008-04-15	2008-04-15	ENSG00000197580	ENSG00000197580	1.13.11.71		18503	protein-coding gene	gene with protein product	"beta-carotene 9',10' oxygenase", "carotenoid-9',10'-cleaving dioxygenase"	611740	"beta-carotene dioxygenase 2"	BCDO2		11278918, 15983114, 15949678	Standard	NM_031938		Approved	FLJ34464, B-DIOX-II	uc001pnf.3	Q9BYV7	OTTHUMG00000167155	ENST00000357685.5:c.416G>A	chr11.hg19:g.112064319G>A	ENSP00000350314:p.Arg139Gln	158.0	0.0		152.0	49.0	NM_001256398	B0YIX5|B4DNC3|E9PBI8|E9PJJ1|Q8IUS0|Q96JC8|Q96JY5	Missense_Mutation	SNP	ENST00000357685.5	hg19	CCDS8358.2	.	.	.	.	.	.	.	.	.	.	G	31	5.068707	0.93950	.	.	ENSG00000197580	ENST00000357685;ENST00000393032;ENST00000361053;ENST00000438022;ENST00000526088;ENST00000532593;ENST00000531169	D;D;D;D;D;D;D	0.95137	-3.62;-3.62;-3.62;-3.62;-3.62;-3.62;-3.62	5.58	4.66	0.58398	.	0.057288	0.64402	N	0.000001	D	0.97583	0.9208	M	0.90369	3.11	0.80722	D	1	D;P;D	0.89917	1.0;0.944;1.0	D;P;D	0.91635	0.999;0.488;0.999	D	0.98202	1.0468	9	.	.	.	-1.3105	14.8123	0.70006	0.0697:0.0:0.9303:0.0	.	116;139;139	C9JEZ9;E9PBI8;Q9BYV7	.;.;BCDO2_HUMAN	Q	139;105;139;105;105;34;105	ENSP00000350314:R139Q;ENSP00000376752:R105Q;ENSP00000354338:R139Q;ENSP00000414843:R105Q;ENSP00000436615:R105Q;ENSP00000431802:R34Q;ENSP00000437053:R105Q	.	R	+	2	0	BCO2	111569529	1.000000	0.71417	0.876000	0.34364	0.938000	0.57974	7.266000	0.78452	1.346000	0.45694	0.655000	0.94253	CGA	.	.		0.463	BCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256570.3	NM_001037290		A	112064319	G	A	112064319	3	1	306	1	0	0	0	0	1	0	0	0	1385	1058	37	1	426	1	BCO2	11	112064319	Missense_Mutation	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10	19976629	112064319	22942197	63	43832										
FAM55D	54827	hgsc.bcm.edu	37	chr11	114453434	114453434	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	catcctggccctcaggaaatCcccgccatattgcttcctgc	7	17	1	0			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr11:114453434C>G	ENST00000375478.3	-	3	586	c.406G>C	c.(406-408)Gat>Cat	p.D136H	NXPE4_ENST00000424261.2_Intron	NM_001077639.1	NP_001071107.1	Q6UWF7	NXPE4_HUMAN	neurexophilin and PC-esterase domain family, member 4	136						extracellular vesicular exosome (GO:0070062)											CTCAGGAAATCCCCGCCATAT	0.577																																					p.D136H		Atlas-SNP	.											.	.	.	.	0			c.G406C						.						80	85	83					11																	114453434		2198	4296	6494	SO:0001583	missense	54827	exon3			GGAAATCCCCGCC	AK000134	CCDS41718.1, CCDS44737.1	11q23.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000137634	ENSG00000137634			23117	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 33", "family with sequence similarity 55, member D"	C11orf33, FAM55D		20056006	Standard	NM_017678		Approved	FLJ20127	uc001ppc.3	Q6UWF7	OTTHUMG00000168291	ENST00000375478.3:c.406G>C	chr11.hg19:g.114453434C>G	ENSP00000364627:p.Asp136His	135.0	0.0		131.0	31.0	NM_001077639	Q6QDB4|Q9NXP5	Missense_Mutation	SNP	ENST00000375478.3	hg19	CCDS41718.1	.	.	.	.	.	.	.	.	.	.	C	15.65	2.895503	0.52121	.	.	ENSG00000137634	ENST00000375478	T	0.49432	0.78	5.01	5.01	0.66863	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.079753	0.50627	D	0.000114	T	0.76765	0.4033	H	0.95365	3.66	0.42043	D	0.991088	D	0.89917	1.0	D	0.91635	0.999	D	0.83736	0.0201	10	0.87932	D	0	.	13.1986	0.59754	0.1599:0.8401:0.0:0.0	.	136	Q6UWF7	FA55D_HUMAN	H	136	ENSP00000364627:D136H	ENSP00000364627:D136H	D	-	1	0	FAM55D	113958644	1.000000	0.71417	0.960000	0.40013	0.369000	0.29798	4.592000	0.61027	2.479000	0.83701	0.591000	0.81541	GAT	.	.		0.577	NXPE4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399179.1	NM_017678		G	114453434	C	G	114453434	3	3	306	1	0	0	0	0	1	0	0	0	5595	855	30	4	1244	4	FAM55D	11	114453434	Missense_Mutation	SNP	C	TCGA-GJ-A9DB-01A-11D-A36X-10	2389115	114453434	20553082	64	43833										
OR8A1	390275	hgsc.bcm.edu	37	chr11	124440405	124440405	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	gttgccatctgccaccctttGctttacaacatcattatgtc	5	13	2	0			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr11:124440405G>A	ENST00000284287.3	+	1	513	c.441G>A	c.(439-441)ttG>ttA	p.L147L		NM_001005194.1	NP_001005194.1	Q8NGG7	OR8A1_HUMAN	olfactory receptor, family 8, subfamily A, member 1	147					axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			haematopoietic_and_lymphoid_tissue(1)|lung(16)|ovary(2)|prostate(1)|skin(2)	22		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0214)		GCCACCCTTTGCTTTACAACA	0.493																																					p.L147L		Atlas-SNP	.											.	OR8A1	61	.	0			c.G441A						.						164	138	147					11																	124440405		2201	4299	6500	SO:0001819	synonymous_variant	390275	exon1			CCCTTTGCTTTAC	BK004495	CCDS31712.1	11q24.2	2012-08-09			ENSG00000196119	ENSG00000196119		"GPCR / Class A : Olfactory receptors"	8469	protein-coding gene	gene with protein product							Standard	NM_001005194		Approved	OST025	uc010san.2	Q8NGG7	OTTHUMG00000165923	ENST00000284287.3:c.441G>A	chr11.hg19:g.124440405G>A		57.0	0.0		65.0	20.0	NM_001005194	Q6IEW7|Q96RC6	Silent	SNP	ENST00000284287.3	hg19	CCDS31712.1																																																																																			.	.		0.493	OR8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387062.1	NM_001005194		A	124440405	G	A	124440405	2	1	306	1	0	0	0	0	0	0	0	1	11234	1310	46	3		3	OR8A1	11	124440405	Silent	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10	9986971	124440405	10566111	65	43834										
ZCRB1	85437	hgsc.bcm.edu	37	chr12	42717863	42717863	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	agggaaaaaggcaagttggaTacatacactgtgctcttact	10	7	1	0			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr12:42717863T>A	ENST00000266529.3	-	2	225	c.42A>T	c.(40-42)gtA>gtT	p.V14V	PPHLN1_ENST00000358314.7_5'Flank|PPHLN1_ENST00000337898.6_5'Flank|PPHLN1_ENST00000395580.3_5'Flank|PPHLN1_ENST00000317560.9_5'Flank|PPHLN1_ENST00000549190.1_Intron|ZCRB1_ENST00000551102.1_5'Flank|PPHLN1_ENST00000395568.2_5'Flank|PPHLN1_ENST00000432191.2_5'Flank|PPHLN1_ENST00000449194.2_5'Flank|ZCRB1_ENST00000552673.1_Intron|PPHLN1_ENST00000552761.1_5'Flank|PPHLN1_ENST00000256678.8_5'Flank	NM_033114.3	NP_149105.3	Q8TBF4	ZCRB1_HUMAN	zinc finger CCHC-type and RNA binding motif 1	14	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	U12-type spliceosomal complex (GO:0005689)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(2)|lung(1)|skin(2)	8	all_cancers(12;0.000348)|Breast(8;0.221)	Lung NSC(34;0.123)		GBM - Glioblastoma multiforme(48;0.0689)		GCAAGTTGGATACATACACTG	0.368																																					p.V14V		Atlas-SNP	.											.	ZCRB1	20	.	0			c.A42T						.						138	130	133					12																	42717863		2203	4300	6503	SO:0001819	synonymous_variant	85437	exon2			GTTGGATACATAC	BC022543	CCDS8740.1	12q12	2013-02-12				ENSG00000139168		"Zinc fingers, CCHC domain containing", "RNA binding motif (RRM) containing"	29620	protein-coding gene	gene with protein product	"U11/U12 snRNP 31K"	610750				15146077, 16959469	Standard	NM_033114		Approved	MADP-1, MADP1, RBM36, ZCCHC19, SNRNP31	uc001rmz.3	Q8TBF4	OTTHUMG00000169382	ENST00000266529.3:c.42A>T	chr12.hg19:g.42717863T>A		127.0	0.0		114.0	32.0	NM_033114	Q6PJX0|Q96TA6	Silent	SNP	ENST00000266529.3	hg19	CCDS8740.1																																																																																			.	.		0.368	ZCRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403813.1	NM_033114		A	42717863	T	A	42717863	2	1	306	1	0	0	0	0	0	0	0	1	17611	1393	49	4		4	ZCRB1	12	42717863	Silent	SNP	T	TCGA-GJ-A9DB-01A-11D-A36X-10		42717863	91134032	66	43835										
LMBR1L	55716	hgsc.bcm.edu	37	chr12	49491852	49491852	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	aattgcccagccagttgaagCgtccaaagtcacccagcagg	10	13	1	1	rs367631047		TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr12:49491852C>A	ENST00000267102.8	-	16	1619	c.1277G>T	c.(1276-1278)cGc>cTc	p.R426L	LMBR1L_ENST00000547382.1_Missense_Mutation_p.R406L|LMBR1L_ENST00000395141.4_Missense_Mutation_p.R421L	NM_018113.2	NP_060583.2	Q6UX01	LMBRL_HUMAN	limb development membrane protein 1-like	426					endocytosis (GO:0006897)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						CCAGTTGAAGCGTCCAAAGTC	0.557											OREG0021783	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R426L		Atlas-SNP	.											.	LMBR1L	61	.	0			c.G1277T						.						145	139	141					12																	49491852		2203	4300	6503	SO:0001583	missense	55716	exon16			TTGAAGCGTCCAA	AB033000	CCDS8780.2, CCDS73466.1	12q13.12	2013-08-05	2013-08-05		ENSG00000139636	ENSG00000139636			18268	protein-coding gene	gene with protein product		610007	"limb region 1 homolog (mouse)-like"			10574461, 11287427	Standard	XM_005269022		Approved	FLJ10494, KIAA1174	uc001rth.4	Q6UX01	OTTHUMG00000150511	ENST00000267102.8:c.1277G>T	chr12.hg19:g.49491852C>A	ENSP00000267102:p.Arg426Leu	66.0	0.0	962	60.0	15.0	NM_018113	Q969J4|Q96BY8|Q96HN8|Q9NT09|Q9NVE1|Q9NVU9|Q9ULP6	Missense_Mutation	SNP	ENST00000267102.8	hg19	CCDS8780.2	.	.	.	.	.	.	.	.	.	.	C	34	5.296074	0.95574	.	.	ENSG00000139636	ENST00000267102;ENST00000547382;ENST00000395141	T;T;T	0.32515	1.45;1.45;1.45	5.54	5.54	0.83059	LMBR1-like membrane protein (1);	0.000000	0.85682	D	0.000000	T	0.58481	0.2125	M	0.74881	2.28	0.80722	D	1	D;D;D	0.89917	0.996;0.997;1.0	D;D;D	0.87578	0.977;0.992;0.998	T	0.60094	-0.7330	10	0.72032	D	0.01	.	18.6171	0.91306	0.0:1.0:0.0:0.0	.	406;426;421	Q6UX01-3;Q6UX01;Q6UX01-4	.;LMBRL_HUMAN;.	L	426;406;421	ENSP00000267102:R426L;ENSP00000447329:R406L;ENSP00000378573:R421L	ENSP00000267102:R426L	R	-	2	0	LMBR1L	47778119	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.756000	0.85195	2.769000	0.95229	0.563000	0.77884	CGC	.	.		0.557	LMBR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318696.1	NM_018113		A	49491852	C	A	49491852	3	1	306	1	0	0	0	0	1	0	0	0	8850	768	27	1	200	1	LMBR1L	12	49491852	Missense_Mutation	SNP	C	TCGA-GJ-A9DB-01A-11D-A36X-10	6773989	49491852	84360043	67	43836										
DHX37	57647	hgsc.bcm.edu	37	chr12	125470692	125470692	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	tttctgcagcactttcttctCcttcttggtcagaggcttct	7	12	6	1			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr12:125470692C>A	ENST00000308736.2	-	2	324	c.226G>T	c.(226-228)Gag>Tag	p.E76*		NM_032656.3	NP_116045.2	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	76							ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(5)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|liver(1)|lung(27)|ovary(1)|prostate(2)|skin(3)	65	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)		ACTTTCTTCTCCTTCTTGGTC	0.512																																					p.E76X		Atlas-SNP	.											.	DHX37	114	.	0			c.G226T						.						190	186	187					12																	125470692		2203	4300	6503	SO:0001587	stop_gained	57647	exon2			TCTTCTCCTTCTT	AB040950	CCDS9261.1	12q24.31	2004-03-25	2003-06-13	2003-06-20		ENSG00000150990		"DEAH-boxes"	17210	protein-coding gene	gene with protein product			"DEAD/DEAH box helicase DDX37"	DDX37		10819331	Standard	NM_032656		Approved	KIAA1517, MGC4322, MGC2695	uc001ugy.3	Q8IY37		ENST00000308736.2:c.226G>T	chr12.hg19:g.125470692C>A	ENSP00000311135:p.Glu76*	57.0	0.0		74.0	21.0	NM_032656	Q9BUI7|Q9P211	Nonsense_Mutation	SNP	ENST00000308736.2	hg19	CCDS9261.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.891854	0.91889	.	.	ENSG00000150990	ENST00000308736	.	.	.	4.04	4.04	0.47022	.	0.131071	0.51477	D	0.000086	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.35671	T	0.21	-1.2702	10.9356	0.47243	0.0:0.67:0.33:0.0	.	.	.	.	X	76	.	ENSP00000311135:E76X	E	-	1	0	DHX37	124036645	1.000000	0.71417	0.992000	0.48379	0.499000	0.33736	2.925000	0.48884	1.948000	0.56530	0.491000	0.48974	GAG	.	.		0.512	DHX37-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032656		A	125470692	C	A	125470692	4	1	306	1	0	0	0	0	0	1	0	0	4512	864	30	3	3351	3	DHX37	12	125470692	Nonsense_Mutation	SNP	C	TCGA-GJ-A9DB-01A-11D-A36X-10	75978840	125470692	8381203	68	43837										
LTB4R	1241	hgsc.bcm.edu	37	chr14	24785802	24785802	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	ggctccgaggcgtccagcacGcgccgcgggggcagcctggg	19	15	0	0			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr14:24785802G>A	ENST00000396789.4	+	2	2670	c.945G>A	c.(943-945)acG>acA	p.T315T	LTB4R_ENST00000396782.2_Silent_p.T315T|LTB4R_ENST00000345363.3_Silent_p.T315T	NM_181657.3	NP_858043.1	Q15722	LT4R1_HUMAN	leukotriene B4 receptor	315					cellular component movement (GO:0006928)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|muscle contraction (GO:0006936)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	leukotriene B4 receptor activity (GO:0001632)|leukotriene receptor activity (GO:0004974)|nucleotide binding (GO:0000166)			endometrium(1)|kidney(2)|large_intestine(1)|lung(3)|stomach(1)	8				GBM - Glioblastoma multiforme(265;0.018)		CGTCCAGCACGCGCCGCGGGG	0.751																																					p.T315T		Atlas-SNP	.											.	LTB4R	18	.	0			c.G945A						.						2	2	2					14																	24785802		1271	2627	3898	SO:0001819	synonymous_variant	1241	exon2			CAGCACGCGCCGC	X98356	CCDS9626.1	14q11.2-q12	2012-08-10			ENSG00000213903	ENSG00000213903		"GPCR / Class A : Leukotriene receptors"	6713	protein-coding gene	gene with protein product		601531		P2RY7, GPR16, CMKRL1		8921391, 8702478	Standard	NM_181657		Approved	BLTR, P2Y7, LTB4R1	uc001wos.3	Q15722	OTTHUMG00000029346	ENST00000396789.4:c.945G>A	chr14.hg19:g.24785802G>A		25.0	0.0		31.0	10.0	NM_181657	Q13305|Q53XV5|Q92641|Q9BSU5	Silent	SNP	ENST00000396789.4	hg19	CCDS9626.1																																																																																			.	.		0.751	LTB4R-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073198.4			A	24785802	G	A	24785802	2	1	306	1	0	0	0	0	0	0	0	1	9080	1074	38	1		1	LTB4R	14	24785802	Silent	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10		24785802	82563738	69	43838										
NKX2-1	7080	hgsc.bcm.edu	37	chr14	36986874	36986874	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	gttgctgctgcgggcacccgGtgcccccgccgcccccgccg	14	21	0	0			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr14:36986874G>C	ENST00000518149.1	-	3	1330	c.725C>G	c.(724-726)aCc>aGc	p.T242S	NKX2-1_ENST00000522719.2_Missense_Mutation_p.T242S|NKX2-1_ENST00000354822.5_Missense_Mutation_p.T272S|RP11-896J10.3_ENST00000521945.1_RNA|NKX2-1-AS1_ENST00000521292.2_RNA|NKX2-1_ENST00000498187.2_Missense_Mutation_p.T242S			P43699	NKX21_HUMAN	NK2 homeobox 1	242	Poly-Gly.				anatomical structure formation involved in morphogenesis (GO:0048646)|axon guidance (GO:0007411)|brain development (GO:0007420)|cerebral cortex cell migration (GO:0021795)|cerebral cortex GABAergic interneuron differentiation (GO:0021892)|Clara cell differentiation (GO:0060486)|developmental induction (GO:0031128)|endoderm development (GO:0007492)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|forebrain development (GO:0030900)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain neuron fate commitment (GO:0021877)|globus pallidus development (GO:0021759)|hippocampus development (GO:0021766)|Leydig cell differentiation (GO:0033327)|locomotory behavior (GO:0007626)|lung development (GO:0030324)|lung saccule development (GO:0060430)|menarche (GO:0042696)|negative regulation of cell migration (GO:0030336)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron migration (GO:0001764)|oligodendrocyte differentiation (GO:0048709)|phospholipid metabolic process (GO:0006644)|pituitary gland development (GO:0021983)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|rhythmic process (GO:0048511)|thyroid gland development (GO:0030878)|Type II pneumocyte differentiation (GO:0060510)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(2)	7	all_cancers(3;4.47e-51)|Hepatocellular(127;0.158)|Esophageal squamous(585;0.164)|Breast(36;0.165)		Lung(8;1.8e-08)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.014)|all cancers(34;0.0366)|LUSC - Lung squamous cell carcinoma(13;0.132)	GBM - Glioblastoma multiforme(112;0.0171)		cgggcacccggtgcccccgcc	0.711			A		NSCLC																																p.T272S		Atlas-SNP	.		Dom	yes		14	14q13	7080	NK2 homeobox 1		E	.	NKX2-1	21	.	0			c.C815G						.						4	4	4					14																	36986874		1946	3771	5717	SO:0001583	missense	7080	exon3			CACCCGGTGCCCC		CCDS9659.1, CCDS41945.1	14q13.3	2012-03-09	2007-07-26	2007-07-26	ENSG00000136352	ENSG00000136352		"Homeoboxes / ANTP class : NKL subclass"	11825	protein-coding gene	gene with protein product		600635	"benign chorea", "thyroid transcription factor 1"	NKX2A, BCH, TITF1		1976511	Standard	NM_001079668		Approved	TTF-1, TTF1	uc001wtu.3	P43699	OTTHUMG00000140225	ENST00000518149.1:c.725C>G	chr14.hg19:g.36986874G>C	ENSP00000428341:p.Thr242Ser	228.0	0.0		217.0	28.0	NM_001079668	D3DSA3|O14954|O14955|Q7KZF6|Q9BRJ8	Missense_Mutation	SNP	ENST00000518149.1	hg19	CCDS9659.1	.	.	.	.	.	.	.	.	.	.	G	2.562	-0.301694	0.05495	.	.	ENSG00000136352	ENST00000354822;ENST00000498187;ENST00000518149;ENST00000522719	D;D;D;D	0.90385	-2.66;-2.65;-2.65;-2.65	2.73	2.73	0.32206	.	1.530320	0.04717	N	0.418568	T	0.79476	0.4452	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.66073	-0.6014	10	0.07030	T	0.85	.	9.1075	0.36707	0.0:0.0:1.0:0.0	.	272;242	P43699-3;P43699	.;NKX21_HUMAN	S	272;242;242;242	ENSP00000346879:T272S;ENSP00000429607:T242S;ENSP00000428341:T242S;ENSP00000429519:T242S	ENSP00000346879:T272S	T	-	2	0	NKX2-1	36056625	0.974000	0.33945	0.996000	0.52242	0.944000	0.59088	0.000000	0.12993	1.844000	0.53588	0.455000	0.32223	ACC	.	.		0.711	NKX2-1-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376225.2	NM_003317		C	36986874	G	C	36986874	3	2	306	1	0	0	0	0	1	0	0	0	10458	1261	44	4	394	4	NKX2-1	14	36986874	Missense_Mutation	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10	12201072	36986874	70362666	70	43839										
CDKL1	8814	hgsc.bcm.edu	37	chr14	50862544	50862544	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	acatttgaaaacaactccatAggatccttctccaattttcc	3	12	1	1			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr14:50862544A>G	ENST00000216378.2	-	2	690	c.46T>C	c.(46-48)Tat>Cat	p.Y16H	RP11-247L20.3_ENST00000556713.1_lincRNA|CDKL1_ENST00000356146.1_5'UTR|CDKL1_ENST00000395834.1_Missense_Mutation_p.Y16H	NM_001282236.1	NP_001269165.1	Q00532	CDKL1_HUMAN	cyclin-dependent kinase-like 1 (CDC2-related kinase)	15	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				heart development (GO:0007507)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|stomach(1)	12	all_epithelial(31;0.000746)|Breast(41;0.0102)					ACAACTCCATAGGATCCTTCT	0.403																																					p.Y16H		Atlas-SNP	.											.	CDKL1	50	.	0			c.T46C						.						81	84	83					14																	50862544		2203	4300	6503	SO:0001583	missense	8814	exon1			CTCCATAGGATCC	AF390028	CCDS9699.1, CCDS73637.1	14q21.3	2011-11-04			ENSG00000100490	ENSG00000100490		"Cyclin-dependent kinases"	1781	protein-coding gene	gene with protein product		603441				1639063, 7595554	Standard	XM_005268157		Approved	KKIALRE	uc010anu.2	Q00532	OTTHUMG00000140290	ENST00000216378.2:c.46T>C	chr14.hg19:g.50862544A>G	ENSP00000216378:p.Tyr16His	138.0	0.0		129.0	38.0	NM_004196	Q2M3A4|Q6QUA0|Q8WXQ5	Missense_Mutation	SNP	ENST00000216378.2	hg19		.	.	.	.	.	.	.	.	.	.	A	17.85	3.491299	0.64074	.	.	ENSG00000100490	ENST00000395834;ENST00000216378	T;T	0.51071	0.72;0.72	4.34	4.34	0.51931	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.65544	0.2701	M	0.69248	2.105	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	T	0.69826	-0.5040	9	0.87932	D	0	.	13.2349	0.59965	1.0:0.0:0.0:0.0	.	205;15	Q00532-2;Q00532	.;CDKL1_HUMAN	H	16	ENSP00000379176:Y16H;ENSP00000216378:Y16H	ENSP00000216378:Y16H	Y	-	1	0	CDKL1	49932294	1.000000	0.71417	1.000000	0.80357	0.401000	0.30781	8.712000	0.91403	1.918000	0.55548	0.459000	0.35465	TAT	.	.		0.403	CDKL1-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000382103.1			G	50862544	A	G	50862544	3	3	306	1	0	0	0	0	1	0	0	0	3155	420	15	2	1066	2	CDKL1	14	50862544	Missense_Mutation	SNP	A	TCGA-GJ-A9DB-01A-11D-A36X-10	13875670	50862544	56486996	71	43840										
KIAA0317	9870	hgsc.bcm.edu	37	chr14	75130767	75130767	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	tggaaaccacagtccaaaacCacctcatgacctggcaggga	9	13	1	1			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr14:75130767C>T	ENST00000356357.4	-	19	2719	c.2204G>A	c.(2203-2205)tGg>tAg	p.W735*	AREL1_ENST00000557401.1_5'UTR	NM_001039479.1	NP_001034568.1	O15033	AREL1_HUMAN	apoptosis resistant E3 ubiquitin protein ligase 1	735	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										AGTCCAAAACCACCTCATGAC	0.542																																					p.W735X		Atlas-SNP	.											.	KIAA0317	68	.	0			c.G2204A						.						49	49	49					14																	75130767		2011	4189	6200	SO:0001587	stop_gained	9870	exon19			CAAAACCACCTCA	AB002315	CCDS41971.1	14q24.2	2013-04-15	2013-04-15	2013-04-15	ENSG00000119682	ENSG00000119682			20363	protein-coding gene	gene with protein product		615380	"KIAA0317"	KIAA0317		9205841, 23479728	Standard	XM_006720344		Approved		uc001xqb.3	O15033	OTTHUMG00000154499	ENST00000356357.4:c.2204G>A	chr14.hg19:g.75130767C>T	ENSP00000348714:p.Trp735*	91.0	0.0		91.0	26.0	NM_001039479	B4E2C7|Q7LDY1|Q8IYY9	Nonsense_Mutation	SNP	ENST00000356357.4	hg19	CCDS41971.1	.	.	.	.	.	.	.	.	.	.	C	46	12.871266	0.99702	.	.	ENSG00000119682	ENST00000356357;ENST00000543377;ENST00000556202	.	.	.	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.9084	0.97016	0.0:1.0:0.0:0.0	.	.	.	.	X	735;574;574	.	ENSP00000348714:W735X	W	-	2	0	KIAA0317	74200520	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.711000	0.92665	0.650000	0.86243	TGG	.	.		0.542	AREL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335517.2	NM_014821		T	75130767	C	T	75130767	4	4	306	1	0	0	0	0	0	1	0	0	8176	595	21	3	275	3	KIAA0317	14	75130767	Nonsense_Mutation	SNP	C	TCGA-GJ-A9DB-01A-11D-A36X-10	24268223	75130767	32218773	72	43841										
C14orf80	283643	hgsc.bcm.edu	37	chr14	105958483	105958483	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	gaagtcagcactatgctcccAgggctacccgaggctggcac	12	14	1	0			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr14:105958483A>T	ENST00000392523.4	+	3	387	c.266A>T	c.(265-267)cAg>cTg	p.Q89L	C14orf80_ENST00000329886.7_Missense_Mutation_p.Q50L|C14orf80_ENST00000334656.7_Missense_Mutation_p.Q48L|C14orf80_ENST00000392522.3_Missense_Mutation_p.Q89L|C14orf80_ENST00000551054.1_3'UTR|C14orf80_ENST00000450383.1_De_novo_Start_OutOfFrame|C14orf80_ENST00000354560.6_Missense_Mutation_p.Q89L|C14orf80_ENST00000392527.1_Missense_Mutation_p.Q48L			Q86SX3	CN080_HUMAN	chromosome 14 open reading frame 80	89										central_nervous_system(1)	1		Melanoma(154;0.226)	OV - Ovarian serous cystadenocarcinoma(23;0.00596)|Epithelial(46;0.0188)	Epithelial(152;0.239)		CTATGCTCCCAGGGCTACCCG	0.632																																					p.Q89L		Atlas-SNP	.											.	C14orf80	19	.	0			c.A266T						.						63	59	60					14																	105958483		692	1591	2283	SO:0001583	missense	283643	exon3			GCTCCCAGGGCTA		CCDS45180.1, CCDS45181.1, CCDS45182.1, CCDS55955.1	14q32.33	2012-09-25			ENSG00000185347	ENSG00000185347			20127	protein-coding gene	gene with protein product							Standard	NM_001134875		Approved		uc001yrn.3	Q86SX3	OTTHUMG00000170426	ENST00000392523.4:c.266A>T	chr14.hg19:g.105958483A>T	ENSP00000376308:p.Gln89Leu	44.0	0.0		58.0	20.0	NM_001134876	B5MDG3|E9PAQ4|Q86TT3|Q86TT4|Q86TT5|Q96B41|Q9H7H4	Missense_Mutation	SNP	ENST00000392523.4	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	1.991|1.991	-0.431879|-0.431879	0.04669|0.04669	.|.	.|.	ENSG00000185347|ENSG00000185347	ENST00000548920|ENST00000329886;ENST00000427614;ENST00000455454;ENST00000432805;ENST00000392527;ENST00000443229;ENST00000334656;ENST00000392522;ENST00000392523;ENST00000354560	.|.	.|.	.|.	5.22|5.22	-1.26|-1.26	0.09376|0.09376	.|.	.|0.820114	.|0.10824	.|N	.|0.630078	.|T	.|0.31670	.|0.0804	L|L	0.47716|0.47716	1.5|1.5	0.09310|0.09310	N|N	1|1	.|B;B;B;B;B	.|0.26547	.|0.144;0.066;0.144;0.152;0.11	.|B;B;B;B;B	.|0.28011	.|0.037;0.053;0.037;0.085;0.059	.|T	.|0.34675	.|-0.9819	.|9	.|0.10636	.|T	.|0.68	.|-8.2165	10.392|10.392	0.44179|0.44179	0.5163:0.0:0.4837:0.0|0.5163:0.0:0.4837:0.0	.|.	.|89;89;89;48;50	.|Q86SX3-2;E9PAQ4;Q86SX3;B5MDG3;Q86SX3-3	.|.;.;CN080_HUMAN;.;.	.|L	-1|50;48;48;48;48;48;48;89;89;89	.|.	.|ENSP00000333010:Q50L	.|Q	+|+	.|2	.|0	C14orf80|C14orf80	105029528|105029528	0.000000|0.000000	0.05858|0.05858	0.070000|0.070000	0.20053|0.20053	0.191000|0.191000	0.23601|0.23601	-0.434000|-0.434000	0.06939|0.06939	-0.240000|-0.240000	0.09696|0.09696	-0.421000|-0.421000	0.06004|0.06004	.|CAG	.	.		0.632	C14orf80-017	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409090.1	NM_001134875		T	105958483	A	T	105958483	3	4	306	1	0	0	0	0	1	0	0	0	1783	188	7	4	304	4	C14orf80	14	105958483	Missense_Mutation	SNP	A	TCGA-GJ-A9DB-01A-11D-A36X-10	30827716	105958483	1391057	73	43842										
AP4E1	23431	hgsc.bcm.edu	37	chr15	51289823	51289823	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	cattgtttgctaataacaacAtggaaatttttcaccctcct	4	10	1	0			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr15:51289823A>G	ENST00000261842.5	+	18	2753	c.2647A>G	c.(2647-2649)Atg>Gtg	p.M883V	AP4E1_ENST00000560508.1_Missense_Mutation_p.M808V	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	883					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	coated pit (GO:0005905)|Golgi apparatus (GO:0005794)|membrane coat (GO:0030117)				breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(5)|skin(2)	27				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		TAATAACAACATGGAAATTTT	0.388																																					p.M883V		Atlas-SNP	.											.	AP4E1	78	.	0			c.A2647G						.						105	101	103					15																	51289823		2196	4294	6490	SO:0001583	missense	23431	exon18			AACAACATGGAAA	AB030653	CCDS32240.1, CCDS58362.1	15q21.2	2014-09-17			ENSG00000081014	ENSG00000081014			573	protein-coding gene	gene with protein product		607244				10436028, 21620353	Standard	NM_007347		Approved	AP-4-EPSILON, SPG51	uc001zyx.2	Q9UPM8	OTTHUMG00000172458	ENST00000261842.5:c.2647A>G	chr15.hg19:g.51289823A>G	ENSP00000261842:p.Met883Val	69.0	0.0		89.0	18.0	NM_007347	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	Missense_Mutation	SNP	ENST00000261842.5	hg19	CCDS32240.1	.	.	.	.	.	.	.	.	.	.	A	5.845	0.340125	0.11069	.	.	ENSG00000081014	ENST00000261842	T	0.15952	2.38	5.47	2.99	0.34606	Coatomer, beta subunit, C-terminal (1);	0.288944	0.38164	N	0.001791	T	0.12305	0.0299	L	0.50333	1.59	0.37071	D	0.89855	B	0.02656	0.0	B	0.04013	0.001	T	0.12502	-1.0545	10	0.07482	T	0.82	-12.0471	7.1219	0.25450	0.7026:0.1375:0.0:0.1599	.	883	Q9UPM8	AP4E1_HUMAN	V	883	ENSP00000261842:M883V	ENSP00000261842:M883V	M	+	1	0	AP4E1	49077115	0.985000	0.35326	0.947000	0.38551	0.676000	0.39594	1.983000	0.40648	0.883000	0.36040	0.383000	0.25322	ATG	.	.		0.388	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418656.1			G	51289823	A	G	51289823	3	3	306	1	0	0	0	0	1	0	0	0	752	217	8	2	2717	2	AP4E1	15	51289823	Missense_Mutation	SNP	A	TCGA-GJ-A9DB-01A-11D-A36X-10		51289823	51241569	74	43843										
EFTUD1	79631	hgsc.bcm.edu	37	chr15	82444220	82444220	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	caaatctcggtatctactggCttcttttgaagctttgtcag	8	9	4	1			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr15:82444220C>T	ENST00000268206.7	-	18	2743	c.2575G>A	c.(2575-2577)Gcc>Acc	p.A859T	EFTUD1_ENST00000359445.3_Missense_Mutation_p.A808T	NM_024580.5	NP_078856.4	Q7Z2Z2	ETUD1_HUMAN	elongation factor Tu GTP binding domain containing 1	859					GTP catabolic process (GO:0006184)|mature ribosome assembly (GO:0042256)		GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ribosome binding (GO:0043022)|translation elongation factor activity (GO:0003746)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(14)|ovary(1)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32						TATCTACTGGCTTCTTTTGAA	0.463																																					p.A859T		Atlas-SNP	.											.	EFTUD1	74	.	0			c.G2575A						.						51	51	51					15																	82444220		1880	4109	5989	SO:0001583	missense	79631	exon18			TACTGGCTTCTTT	AK056656	CCDS42070.1, CCDS42071.1	15q25.2	2012-07-04			ENSG00000140598	ENSG00000140598			25789	protein-coding gene	gene with protein product	"ribosome assembly 1 homolog (yeast)"					14702039	Standard	NM_024580		Approved	FLJ13119, FAM42A, HsT19294, RIA1	uc002bgt.1	Q7Z2Z2	OTTHUMG00000172573	ENST00000268206.7:c.2575G>A	chr15.hg19:g.82444220C>T	ENSP00000268206:p.Ala859Thr	113.0	0.0		109.0	35.0	NM_024580	A6NKY5|B7Z6I0|Q9H8Z6	Missense_Mutation	SNP	ENST00000268206.7	hg19	CCDS42071.1	.	.	.	.	.	.	.	.	.	.	C	4.706	0.131297	0.08981	.	.	ENSG00000140598	ENST00000268206;ENST00000359445	T;T	0.24538	1.85;1.85	6.06	3.17	0.36434	Ribosomal protein S5 domain 2-type fold (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);	0.303968	0.22942	N	0.053780	T	0.10766	0.0263	N	0.08118	0	0.31224	N	0.697124	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.001	T	0.21759	-1.0236	10	0.14252	T	0.57	2.6917	7.4321	0.27134	0.1176:0.691:0.0:0.1914	.	808;859	Q7Z2Z2-2;Q7Z2Z2	.;ETUD1_HUMAN	T	859;808	ENSP00000268206:A859T;ENSP00000352418:A808T	ENSP00000268206:A859T	A	-	1	0	EFTUD1	80231275	0.151000	0.22747	0.073000	0.20177	0.098000	0.18820	0.977000	0.29475	0.906000	0.36621	-0.142000	0.14014	GCC	.	.		0.463	EFTUD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419252.1	NM_024580		T	82444220	C	T	82444220	3	4	306	1	0	0	0	0	1	0	0	0	4962	797	28	3	799	3	EFTUD1	15	82444220	Missense_Mutation	SNP	C	TCGA-GJ-A9DB-01A-11D-A36X-10	31154397	82444220	20087172	75	43844										
NLRC3	197358	hgsc.bcm.edu	37	chr16	3613191	3613191	+	RNA	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	gctctccatggcctcctccaCgctgcgggccagctcggtgt	12	17	1	0			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr16:3613191C>T	ENST00000301749.7	-	0	2152				NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000603507.1_RNA|NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000324659.8_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GCCTCCTCCACGCTGCGGGCC	0.711																																					p.V583M		Atlas-SNP	.											.	NLRC3	103	.	0			c.G1747A						.						9	12	11					16																	3613191		2107	4212	6319			197358	exon5			CCTCCACGCTGCG	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"Nucleotide-binding domain and leucine rich repeat containing"	29889	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3", "NOD-like receptor C3"	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		chr16.hg19:g.3613191C>T		103.0	0.0		118.0	43.0	NM_178844	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Missense_Mutation	SNP	ENST00000301749.7	hg19		.	.	.	.	.	.	.	.	.	.	C	4.380	0.070128	0.08436	.	.	ENSG00000167984	ENST00000419350;ENST00000301749;ENST00000359128;ENST00000448023;ENST00000324659	D;D;D;D	0.85484	-1.99;-1.99;-1.99;-1.99	4.89	1.73	0.24493	.	0.220217	0.38058	N	0.001827	T	0.76572	0.4006	.	.	.	0.20489	N	0.999892	B	0.14438	0.01	B	0.08055	0.003	T	0.65615	-0.6125	9	0.56958	D	0.05	.	8.4145	0.32664	0.0:0.7195:0.0:0.2805	.	630	C9JLH9	.	M	583;583;583;630;565	ENSP00000301749:V583M;ENSP00000352039:V583M;ENSP00000414415:V630M;ENSP00000323897:V565M	ENSP00000301749:V583M	V	-	1	0	NLRC3	3553192	0.520000	0.26250	0.257000	0.24404	0.021000	0.10359	1.184000	0.32053	0.089000	0.17243	-1.105000	0.02106	GTG	.	.		0.711	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844		T	3613191	C	T	3613191	1	4	306	0	1	0	0	0	0	0	0	0	10477	536	19	1		1	NLRC3	16	3613191	RNA	SNP	C	TCGA-GJ-A9DB-01A-11D-A36X-10		3613191	86741562	76	43845										
SPN	6693	hgsc.bcm.edu	37	chr16	29675716	29675716	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	gcggggccagtggaccccagGtctctagcgtaaaactatct	12	12	2	0			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr16:29675716G>A	ENST00000360121.3	+	2	759	c.667G>A	c.(667-669)Gtc>Atc	p.V223I	SPN_ENST00000395389.2_Missense_Mutation_p.V223I	NM_001030288.2|NM_003123.4	NP_001025459.1|NP_003114.1	O75398	DEAF1_HUMAN	sialophorin	0	SAND. {ECO:0000255|PROSITE- ProRule:PRU00185}.				anatomical structure morphogenesis (GO:0009653)|embryonic skeletal system development (GO:0048706)|germ cell development (GO:0007281)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|skin(2)|stomach(1)	15						TGGACCCCAGGTCTCTAGCGT	0.577																																					p.V223I		Atlas-SNP	.											.	SPN	44	.	0			c.G667A						.						74	75	75					16																	29675716		2197	4300	6497	SO:0001583	missense	6693	exon2			CCCCAGGTCTCTA	J04536	CCDS10650.1	16p11.2	2008-07-31	2008-07-31		ENSG00000197471	ENSG00000197471		"CD molecules"	11249	protein-coding gene	gene with protein product	"leukosialin"	182160	"sialophorin (gpL115, leukosialin, CD43)"			2784859, 2521952	Standard	NM_001030288		Approved	LSN, CD43, GPL115	uc002dtm.4	P16150	OTTHUMG00000097765	ENST00000360121.3:c.667G>A	chr16.hg19:g.29675716G>A	ENSP00000353238:p.Val223Ile	99.0	0.0		85.0	18.0	NM_001030288	A8K1F8|A8K5R8|C7T5V5|O15152|O75399|O75510|O75511|O75512|O75513|Q9UET1	Missense_Mutation	SNP	ENST00000360121.3	hg19	CCDS10650.1	.	.	.	.	.	.	.	.	.	.	.	9.300	1.052914	0.19907	.	.	ENSG00000197471	ENST00000395389;ENST00000436527;ENST00000360121	T;T;T	0.79845	-1.31;-1.31;-1.31	4.57	-3.69	0.04450	.	2.677570	0.01419	N	0.014316	T	0.73164	0.3552	L	0.47016	1.485	0.09310	N	1	B	0.27229	0.172	B	0.29598	0.104	T	0.55805	-0.8083	10	0.11182	T	0.66	-0.7568	10.1697	0.42902	0.5878:0.0:0.4122:0.0	.	223	P16150	LEUK_HUMAN	I	223	ENSP00000378787:V223I;ENSP00000412907:V223I;ENSP00000353238:V223I	ENSP00000353238:V223I	V	+	1	0	SPN	29583217	0.000000	0.05858	0.000000	0.03702	0.090000	0.18270	-0.847000	0.04331	-0.586000	0.05898	0.591000	0.81541	GTC	.	.		0.577	SPN-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215001.2			A	29675716	G	A	29675716	3	1	306	1	0	0	0	0	1	0	0	0	15088	1261	44	3	669	3	SPN	16	29675716	Missense_Mutation	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10	26062525	29675716	60679037	77	43846										
SRCAP	10847	hgsc.bcm.edu	37	chr16	30748580	30748584	+	Frame_Shift_Del	DEL	CAAGG	CAAGG	-													0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	gtggagcccgggctgagactCaaggggcaaaccacactcct							TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	CAAGG	CAAGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr16:30748580_30748584delCAAGG	ENST00000262518.4	+	34	7604_7608	c.7219_7223delCAAGG	c.(7219-7224)caagggfs	p.QG2407fs	SRCAP_ENST00000395059.2_Frame_Shift_Del_p.QG2345fs|SRCAP_ENST00000344771.4_Frame_Shift_Del_p.QG2249fs	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	2407					histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			GGCTGAGACTCAAGGGGCAAACCAC	0.639																																					p.2406_2408del		Atlas-INDEL	.											.	SRCAP	298	.	0			c.7218_7222del						.																																			SO:0001589	frameshift_variant	10847	exon34			.	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.7219_7223delCAAGG	chr16.hg19:g.30748580_30748584delCAAGG	ENSP00000262518:p.Gln2407fs	92.0	0.0		102.0	33.0	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Frame_Shift_Del	DEL	ENST00000262518.4	hg19	CCDS10689.2																																																																																			.	.		0.639	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		-	30748584	CAAGG	-	30748580	7	5	306	1	0	1	0	1	0	0	0	0	15150	827	29	0	7345	0	SRCAP	16	30748580	Frame_Shift_Del	DEL	CAAGG	TCGA-GJ-A9DB-01A-11D-A36X-10	1072864	30748580	59606173	78	43847										
SETD1A	9739	hgsc.bcm.edu	37	chr16	30982811	30982811	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	agctcttccagctcctcatcCtcctcctcctcctcgtcctc	3	22	2	0	rs531337171|rs569719496	byFrequency	TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr16:30982811C>A	ENST00000262519.8	+	13	3815	c.3129C>A	c.(3127-3129)tcC>tcA	p.S1043S		NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A	1043	Ser-rich. {ECO:0000255}.				histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(21)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	59						Gctcctcatcctcctcctcct	0.542																																					p.S1043S		Atlas-SNP	.											.	SETD1A	143	.	0			c.C3129A						.						79	79	79					16																	30982811		2197	4300	6497	SO:0001819	synonymous_variant	9739	exon13			CTCATCCTCCTCC	AB002337	CCDS32435.1	16p11.2	2013-02-12			ENSG00000099381	ENSG00000099381		"Chromatin-modifying enzymes / K-methyltransferases", "RNA binding motif (RRM) containing"	29010	protein-coding gene	gene with protein product		611052				9205841, 12670868	Standard	XM_005255723		Approved	KIAA0339, Set1, KMT2F	uc002ead.1	O15047	OTTHUMG00000150474	ENST00000262519.8:c.3129C>A	chr16.hg19:g.30982811C>A		89.0	0.0		96.0	4.0	NM_014712	A6NP62|Q6PIF3|Q8TAJ6	Silent	SNP	ENST00000262519.8	hg19	CCDS32435.1																																																																																			.	.		0.542	SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318244.2	NM_014712		A	30982811	C	A	30982811	2	1	306	1	0	0	0	0	0	0	0	1	14145	668	24	3		3	SETD1A	16	30982811	Silent	SNP	C	TCGA-GJ-A9DB-01A-11D-A36X-10	234231	30982811	59371942	79	43848										
KATNB1	10300	hgsc.bcm.edu	37	chr16	57788908	57788908	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	tgtgcagttcccggtgccaaAtgtatgtccatggagggagc	14	9	0	0			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr16:57788908A>C	ENST00000379661.3	+	14	1687	c.1295A>C	c.(1294-1296)aAt>aCt	p.N432T		NM_005886.2	NP_005877.2			katanin p80 (WD repeat containing) subunit B 1											cervix(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16		all_neural(199;0.223)				CCGGTGCCAAATGTATGTCCA	0.627																																					p.N432T		Atlas-SNP	.											.	KATNB1	35	.	0			c.A1295C						.						107	110	109					16																	57788908		2198	4300	6498	SO:0001630	splice_region_variant	10300	exon14			TGCCAAATGTATG	AF052432	CCDS10788.1	16q12.2	2013-01-09	2003-03-13		ENSG00000140854	ENSG00000140854		"WD repeat domain containing"	6217	protein-coding gene	gene with protein product		602703	"katanin p80 (WD40-containing) subunit B 1"			9568719	Standard	XM_006721121		Approved		uc002eml.1	Q9BVA0	OTTHUMG00000133467	ENST00000379661.3:c.1296+1A>C	chr16.hg19:g.57788908A>C		86.0	0.0		75.0	23.0	NM_005886		Missense_Mutation	SNP	ENST00000379661.3	hg19	CCDS10788.1	.	.	.	.	.	.	.	.	.	.	A	8.820	0.937297	0.18206	.	.	ENSG00000140854	ENST00000379661	T	0.54479	0.57	5.24	4.12	0.48240	.	0.246207	0.47093	D	0.000242	T	0.39963	0.1098	L	0.36672	1.1	0.80722	D	1	B	0.19331	0.035	B	0.17433	0.018	T	0.15954	-1.0419	10	0.33141	T	0.24	-29.7787	8.918	0.35594	0.9126:0.0:0.0874:0.0	.	432	Q9BVA0	KTNB1_HUMAN	T	432	ENSP00000368982:N432T	ENSP00000368982:N432T	N	+	2	0	KATNB1	56346409	0.934000	0.31675	0.722000	0.30670	0.020000	0.10135	1.962000	0.40442	0.806000	0.34183	0.477000	0.44152	AAT	.	.		0.627	KATNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257343.3		Missense_Mutation	C	57788908	A	C	57788908	5	2	306	1	0	0	0	0	0	0	1	0	7996	115	4	5	1345	5	KATNB1	16	57788908	Splice_Site	SNP	A	TCGA-GJ-A9DB-01A-11D-A36X-10	26806097	57788908	32565845	80	43849										
FHOD1	29109	hgsc.bcm.edu	37	chr16	67263800	67263800	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	ggtccatgatctcatctgatGtatcactgggtaaactggag	11	8	3	2			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr16:67263800G>A	ENST00000258201.4	-	21	3555	c.3308C>T	c.(3307-3309)aCa>aTa	p.T1103I	LRRC29_ENST00000462169.1_5'Flank|AC040160.1_ENST00000454102.2_5'Flank|LRRC29_ENST00000409509.1_5'Flank|LRRC29_ENST00000341546.3_5'Flank	NM_013241.2	NP_037373.2	Q9Y613	FHOD1_HUMAN	formin homology 2 domain containing 1	1103	DAD.				positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			breast(4)|endometrium(3)|kidney(3)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	34		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000691)|Epithelial(162;0.00462)|all cancers(182;0.0434)		CTCATCTGATGTATCACTGGG	0.587																																					p.T1103I		Atlas-SNP	.											.	FHOD1	86	.	0			c.C3308T						.						72	74	73					16																	67263800		2198	4300	6498	SO:0001583	missense	29109	exon21			TCTGATGTATCAC	AF113615	CCDS10834.1	16q22	2008-02-22			ENSG00000135723	ENSG00000135723			17905	protein-coding gene	gene with protein product		606881				10352228, 16112087	Standard	NM_013241		Approved	FHOS	uc002esl.3	Q9Y613	OTTHUMG00000137521	ENST00000258201.4:c.3308C>T	chr16.hg19:g.67263800G>A	ENSP00000258201:p.Thr1103Ile	86.0	0.0		94.0	27.0	NM_013241	Q59F76|Q6Y1F2|Q76MS8|Q8N521	Missense_Mutation	SNP	ENST00000258201.4	hg19	CCDS10834.1	.	.	.	.	.	.	.	.	.	.	G	14.54	2.567245	0.45694	.	.	ENSG00000135723	ENST00000258201	T	0.36699	1.24	5.46	4.49	0.54785	.	0.156564	0.56097	D	0.000030	T	0.33644	0.0870	L	0.53249	1.67	0.38355	D	0.944434	B	0.26708	0.157	B	0.25291	0.059	T	0.17961	-1.0352	10	0.34782	T	0.22	.	13.4633	0.61239	0.077:0.0:0.923:0.0	.	1103	Q9Y613	FHOD1_HUMAN	I	1103	ENSP00000258201:T1103I	ENSP00000258201:T1103I	T	-	2	0	FHOD1	65821301	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.469000	0.80959	2.840000	0.97914	0.655000	0.94253	ACA	.	.		0.587	FHOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268844.2			A	67263800	G	A	67263800	3	1	306	1	0	0	0	0	1	0	0	0	5890	1377	48	3	194	3	FHOD1	16	67263800	Missense_Mutation	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10	9474892	67263800	23090953	81	43850										
CYBA	1535	hgsc.bcm.edu	37	chr16	88713210	88713210	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	taattcctggtaaagggcccGaacagcttcaccacggcggt	11	12	1	0	rs373948664		TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr16:88713210G>T	ENST00000261623.3	-	4	378	c.240C>A	c.(238-240)ttC>ttA	p.F80L	CYBA_ENST00000567174.1_Missense_Mutation_p.F80L|CYBA_ENST00000569359.1_Missense_Mutation_p.F80L|CYBA_ENST00000561972.1_5'Flank	NM_000101.3	NP_000092.2	P13498	CY24A_HUMAN	cytochrome b-245, alpha polypeptide	80					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular response to amino acid stimulus (GO:0071230)|cellular response to gamma radiation (GO:0071480)|cellular response to glucose stimulus (GO:0071333)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic cyclic compound (GO:0071407)|cellular response to tumor necrosis factor (GO:0071356)|cytochrome complex assembly (GO:0017004)|hydrogen peroxide biosynthetic process (GO:0050665)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|negative regulation of glomerular filtration by angiotensin (GO:0003106)|oxidation-reduction process (GO:0055114)|phagosome maturation (GO:0090382)|positive regulation of cell growth (GO:0030307)|positive regulation of endothelial cell proliferation (GO:0001938)|respiratory burst (GO:0045730)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|response to nutrient levels (GO:0031667)|smooth muscle hypertrophy (GO:0014895)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	apical plasma membrane (GO:0016324)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|neuronal cell body (GO:0043025)|phagocytic vesicle membrane (GO:0030670)|secretory granule (GO:0030141)	electron carrier activity (GO:0009055)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|SH3 domain binding (GO:0017124)|superoxide-generating NADPH oxidase activity (GO:0016175)			endometrium(1)|liver(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0478)	Dextromethorphan(DB00514)	TAAAGGGCCCGAACAGCTTCA	0.652																																					p.F80L		Atlas-SNP	.											.	CYBA	12	.	0			c.C240A						.						82	91	88					16																	88713210		2198	4300	6498	SO:0001583	missense	1535	exon4			GGGCCCGAACAGC		CCDS32504.1	16q24	2014-09-17				ENSG00000051523		"Cytochrome b genes"	2577	protein-coding gene	gene with protein product	"flavocytochrome b-558 alpha polypeptide"	608508				2243141	Standard	NM_000101		Approved	p22-PHOX	uc002flb.4	P13498		ENST00000261623.3:c.240C>A	chr16.hg19:g.88713210G>T	ENSP00000261623:p.Phe80Leu	66.0	0.0		71.0	23.0	NM_000101	Q14090|Q9BR72	Missense_Mutation	SNP	ENST00000261623.3	hg19	CCDS32504.1	.	.	.	.	.	.	.	.	.	.	G	11.19	1.564713	0.27915	.	.	ENSG00000051523	ENST00000261623	D	0.82893	-1.66	4.46	-8.91	0.00778	.	0.213482	0.49305	N	0.000147	T	0.61578	0.2358	L	0.34521	1.04	0.33695	D	0.613844	B;B	0.15930	0.015;0.015	B;B	0.20184	0.028;0.028	T	0.58769	-0.7578	10	0.06099	T	0.92	-3.6037	8.2117	0.31488	0.5075:0.2727:0.2197:0.0	.	16;80	B4DT46;P13498	.;CY24A_HUMAN	L	80	ENSP00000261623:F80L	ENSP00000261623:F80L	F	-	3	2	CYBA	87240711	0.008000	0.16893	0.254000	0.24359	0.809000	0.45718	-1.150000	0.03178	-1.895000	0.01104	-0.362000	0.07510	TTC	.	.		0.652	CYBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422765.1	NM_000101		T	88713210	G	T	88713210	3	4	306	1	0	0	0	0	1	0	0	0	4133	1049	37	1	359	1	CYBA	16	88713210	Missense_Mutation	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10	21449410	88713210	1641543	82	43851										
MYBBP1A	10514	hgsc.bcm.edu	37	chr17	4451500	4451500	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	gtggtcacgttgtggctgtgAttcaacaggaggtctgcgaa	15	7	3	1			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr17:4451500A>G	ENST00000254718.4	-	12	1968	c.1662T>C	c.(1660-1662)aaT>aaC	p.N554N	MYBBP1A_ENST00000381556.2_Silent_p.N554N			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	554	Interaction with MYB. {ECO:0000250}.				cellular response to glucose starvation (GO:0042149)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|osteoblast differentiation (GO:0001649)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|NLS-dependent protein nuclear import complex (GO:0042564)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)	24						TGTGGCTGTGATTCAACAGGA	0.652																																					p.N554N		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.T1662C						.						67	61	63					17																	4451500		2203	4300	6503	SO:0001819	synonymous_variant	10514	exon12			GCTGTGATTCAAC	AF147709	CCDS11046.1, CCDS42238.1	17p13.3	2008-07-18			ENSG00000132382	ENSG00000132382			7546	protein-coding gene	gene with protein product	"p53-activated protein-2"	604885				10644447	Standard	NM_014520		Approved	P160, PAP2, FLJ37886	uc002fxz.4	Q9BQG0	OTTHUMG00000090747	ENST00000254718.4:c.1662T>C	chr17.hg19:g.4451500A>G		67.0	0.0		59.0	14.0	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Silent	SNP	ENST00000254718.4	hg19	CCDS11046.1																																																																																			.	.		0.652	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520		G	4451500	A	G	4451500	2	3	306	1	0	0	0	0	0	0	0	1	10017	330	12	2		2	MYBBP1A	17	4451500	Silent	SNP	A	TCGA-GJ-A9DB-01A-11D-A36X-10		4451500	76743710	83	43852										
SBNO2	22904	hgsc.bcm.edu	37	chr19	1119995	1119995	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	cttggtggagccggcattctTggctttgtgacactcgtcga	13	10	1	1			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr19:1119995T>C	ENST00000361757.3	-	12	1414	c.1177A>G	c.(1177-1179)Aag>Gag	p.K393E	SBNO2_ENST00000438103.2_Missense_Mutation_p.K336E|SBNO2_ENST00000587024.1_Missense_Mutation_p.K393E	NM_014963.2	NP_055778.2	Q9Y2G9	SBNO2_HUMAN	strawberry notch homolog 2 (Drosophila)	393					bone mineralization (GO:0030282)|bone trabecula morphogenesis (GO:0061430)|macrophage activation involved in immune response (GO:0002281)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoclast fusion (GO:0072675)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of inflammatory response (GO:0050727)|transcription, DNA-templated (GO:0006351)					NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCGGCATTCTTGGCTTTGTGA	0.627																																					p.K393E		Atlas-SNP	.											.	SBNO2	112	.	0			c.A1177G						.						49	52	51					19																	1119995		1990	4019	6009	SO:0001583	missense	22904	exon12			CATTCTTGGCTTT	AK074102	CCDS45894.1, CCDS45895.1	19p13.3	2008-02-05	2006-10-06	2006-10-06		ENSG00000064932			29158	protein-coding gene	gene with protein product		615729	"KIAA0963"	KIAA0963		10231032	Standard	NM_014963		Approved	FLJ00173, Stno, Sno	uc002lrk.4	Q9Y2G9		ENST00000361757.3:c.1177A>G	chr19.hg19:g.1119995T>C	ENSP00000354733:p.Lys393Glu	74.0	0.0		68.0	11.0	NM_014963	A8K8P2|B3KWJ1|O75257|Q3KQX0|Q8TEM0	Missense_Mutation	SNP	ENST00000361757.3	hg19	CCDS45894.1	.	.	.	.	.	.	.	.	.	.	T	18.13	3.556292	0.65425	.	.	ENSG00000064932	ENST00000361757;ENST00000438103;ENST00000250872	D;D	0.95171	-3.63;-3.63	3.91	3.91	0.45181	.	0.000000	0.85682	D	0.000000	D	0.96846	0.8970	M	0.88775	2.98	0.58432	D	0.999995	D;P;D;D	0.57571	0.98;0.925;0.963;0.975	P;P;P;P	0.61003	0.846;0.882;0.789;0.761	D	0.97202	0.9865	10	0.72032	D	0.01	-42.3101	11.9804	0.53117	0.0:0.0:0.0:1.0	.	336;393;393;336	B4DL53;B4DV91;Q9Y2G9;Q9Y2G9-3	.;.;SBNO2_HUMAN;.	E	393;336;417	ENSP00000354733:K393E;ENSP00000400762:K336E	ENSP00000250872:K417E	K	-	1	0	SBNO2	1070995	1.000000	0.71417	1.000000	0.80357	0.169000	0.22640	7.738000	0.84966	1.747000	0.51819	0.450000	0.29827	AAG	.	.		0.627	SBNO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458065.2	NM_014963		C	1119995	T	C	1119995	3	2	306	1	0	0	0	0	1	0	0	0	13878	1821	63	2	3007	2	SBNO2	19	1119995	Missense_Mutation	SNP	T	TCGA-GJ-A9DB-01A-11D-A36X-10		1119995	58008988	84	43853										
DPP9	91039	hgsc.bcm.edu	37	chr19	4683489	4683489	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	cggccaggggtgggacccacCttgaacacctggggcttgtg	16	12	0	1			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr19:4683489C>A	ENST00000598800.1	-	20	2749	c.2244G>T	c.(2242-2244)aaG>aaT	p.K748N	DPP9_ENST00000262960.9_Splice_Site_p.K777N|DPP9_ENST00000601173.1_5'UTR|DPP9_ENST00000594671.1_Splice_Site_p.K748N|AC005594.3_ENST00000381796.1_RNA			Q86TI2	DPP9_HUMAN	dipeptidyl-peptidase 9	748						cytoplasm (GO:0005737)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|identical protein binding (GO:0042802)|serine-type peptidase activity (GO:0008236)			cervix(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00884)		TGGGACCCACCTTGAACACCT	0.672																																					p.K777N		Atlas-SNP	.											.	DPP9	59	.	0			c.G2331T						.						34	43	40					19																	4683489		1950	4130	6080	SO:0001630	splice_region_variant	91039	exon19			ACCCACCTTGAAC	AF452102	CCDS45928.1	19p13.3	2014-06-11	2006-01-12		ENSG00000142002	ENSG00000142002			18648	protein-coding gene	gene with protein product		608258	"dipeptidylpeptidase 9"				Standard	NM_139159		Approved		uc002mba.3	Q86TI2	OTTHUMG00000182040	ENST00000598800.1:c.2244+1G>T	chr19.hg19:g.4683489C>A		121.0	0.0		110.0	31.0	NM_139159	O75273|O75868|Q1ZZB8|Q6AI37|Q6UAL0|Q6ZMT2|Q6ZNJ5|Q8N2J7|Q8N3F5|Q8WXD8|Q96NT8|Q9BVR3	Missense_Mutation	SNP	ENST00000598800.1	hg19		.	.	.	.	.	.	.	.	.	.	C	22.8	4.341751	0.81911	.	.	ENSG00000142002	ENST00000357909;ENST00000381797;ENST00000262960	T	0.51817	0.69	4.0	4.0	0.46444	.	0.000000	0.85682	D	0.000000	T	0.72985	0.3529	M	0.90759	3.145	0.80722	D	1	D	0.71674	0.998	D	0.72625	0.978	T	0.80214	-0.1475	9	.	.	.	-33.276	15.3398	0.74287	0.0:1.0:0.0:0.0	.	777	Q1ZZB8	.	N	856;718;777	ENSP00000262960:K777N	.	K	-	3	2	DPP9	4634489	1.000000	0.71417	1.000000	0.80357	0.861000	0.49209	7.590000	0.82653	2.092000	0.63282	0.456000	0.33151	AAG	.	.		0.672	DPP9-026	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000459343.2		Missense_Mutation	A	4683489	C	A	4683489	5	1	306	1	0	0	0	0	0	0	1	0	4735	695	24	3	363	3	DPP9	19	4683489	Splice_Site	SNP	C	TCGA-GJ-A9DB-01A-11D-A36X-10	3563494	4683489	54445494	85	43854										
MCOLN1	57192	hgsc.bcm.edu	37	chr19	7593583	7593583	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	ctccttcgaggcttcctgctGcagaacgtgaggcttctgcg	12	13	1	2			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr19:7593583G>A	ENST00000264079.6	+	8	1103	c.978G>A	c.(976-978)ctG>ctA	p.L326L		NM_020533.2	NP_065394.1	Q9GZU1	MCLN1_HUMAN	mucolipin 1	326					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular iron ion homeostasis (GO:0006879)|ion transmembrane transport (GO:0034220)|release of sequestered calcium ion into cytosol (GO:0051209)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cation channel activity (GO:0005261)|NAADP-sensitive calcium-release channel activity (GO:0072345)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						GCTTCCTGCTGCAGAACGTGA	0.627																																					p.L326L		Atlas-SNP	.											.	MCOLN1	54	.	0			c.G978A						.						128	82	97					19																	7593583		2203	4300	6503	SO:0001819	synonymous_variant	57192	exon8			CCTGCTGCAGAAC	AF249319	CCDS12180.1	19p13.2	2011-12-16				ENSG00000090674		"Voltage-gated ion channels / Transient receptor potential cation channels"	13356	protein-coding gene	gene with protein product		605248				16382100	Standard	NM_020533		Approved	TRPML1, ML4, MLIV, MST080, MSTP080, TRPM-L1	uc002mgo.3	Q9GZU1		ENST00000264079.6:c.978G>A	chr19.hg19:g.7593583G>A		82.0	0.0		102.0	37.0	NM_020533	D6W647|Q7Z4F7|Q9H292|Q9H4B3|Q9H4B5	Silent	SNP	ENST00000264079.6	hg19	CCDS12180.1																																																																																			.	.		0.627	MCOLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458974.2	NM_020533		A	7593583	G	A	7593583	2	1	306	1	0	0	0	0	0	0	0	1	9404	1306	46	3		3	MCOLN1	19	7593583	Silent	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10	2910094	7593583	51535400	86	43855										
ZNF442	79973	hgsc.bcm.edu	37	chr19	12461659	12461659	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	ttagataggaactgtaaataGggaaggctttacaacactgc	10	6	0	1			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr19:12461659G>C	ENST00000242804.4	-	6	1322	c.740C>G	c.(739-741)cCt>cGt	p.P247R	ZNF442_ENST00000438182.1_Missense_Mutation_p.P178R|CTD-3105H18.13_ENST00000563695.2_lincRNA	NM_030824.2	NP_110451.1	Q9H7R0	ZN442_HUMAN	zinc finger protein 442	247					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P247R(1)		breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	31						ACTGTAAATAGGGAAGGCTTT	0.408																																					p.P247R		Atlas-SNP	.											ZNF442,NS,carcinoma,0,2	ZNF442	102	.	1	Substitution - Missense(1)	lung(1)	c.C740G						.						164	165	165					19																	12461659		2203	4300	6503	SO:0001583	missense	79973	exon6			TAAATAGGGAAGG	AK024418	CCDS12271.1	19p13.13	2013-01-08			ENSG00000198342	ENSG00000198342		"Zinc fingers, C2H2-type", "-"	20877	protein-coding gene	gene with protein product							Standard	NM_030824		Approved	FLJ14356	uc002mtr.1	Q9H7R0	OTTHUMG00000156411	ENST00000242804.4:c.740C>G	chr19.hg19:g.12461659G>C	ENSP00000242804:p.Pro247Arg	106.0	0.0		103.0	20.0	NM_030824	B4DJ48	Missense_Mutation	SNP	ENST00000242804.4	hg19	CCDS12271.1	.	.	.	.	.	.	.	.	.	.	G	0.023	-1.402021	0.01165	.	.	ENSG00000198342	ENST00000242804;ENST00000438182	T;T	0.14144	2.53;2.53	0.832	-1.66	0.08265	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04272	0.0118	N	0.02315	-0.6	0.09310	N	1	B	0.06786	0.001	B	0.13407	0.009	T	0.40831	-0.9542	9	0.20519	T	0.43	.	5.0246	0.14378	0.0:0.4253:0.3888:0.1859	.	247	Q9H7R0	ZN442_HUMAN	R	247;178	ENSP00000242804:P247R;ENSP00000388634:P178R	ENSP00000242804:P247R	P	-	2	0	ZNF442	12322659	.	.	0.000000	0.03702	0.335000	0.28730	.	.	-1.607000	0.01589	-0.656000	0.03901	CCT	.	.		0.408	ZNF442-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344109.1	NM_030824		C	12461659	G	C	12461659	3	2	306	1	0	0	0	0	1	0	0	0	17930	1000	35	4	1147	4	ZNF442	19	12461659	Missense_Mutation	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10	4868076	12461659	46667324	87	43856										
SLC25A42	284439	hgsc.bcm.edu	37	chr19	19217109	19217109	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	cttggcctcgcctcttcgccGgcgcactggctggaacgaca	12	16	1	0			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr19:19217109G>A	ENST00000318596.7	+	6	563	c.412G>A	c.(412-414)Ggc>Agc	p.G138S	SLC25A42_ENST00000600275.1_3'UTR	NM_178526.4	NP_848621.2	Q86VD7	S2542_HUMAN	solute carrier family 25, member 42	138					ADP transport (GO:0015866)|AMP transport (GO:0080121)|ATP transport (GO:0015867)|coenzyme A transmembrane transport (GO:0035349)|metabolic process (GO:0008152)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	adenosine-diphosphatase activity (GO:0043262)|ADP transmembrane transporter activity (GO:0015217)|AMP transmembrane transporter activity (GO:0080122)|ATP transmembrane transporter activity (GO:0005347)|coenzyme A transmembrane transporter activity (GO:0015228)			cervix(1)|large_intestine(2)|lung(3)	6			OV - Ovarian serous cystadenocarcinoma(5;5.4e-06)|Epithelial(12;0.000497)			CCTCTTCGCCGGCGCACTGGC	0.647																																					p.G138S		Atlas-SNP	.											.	SLC25A42	18	.	0			c.G412A						.						62	66	64					19																	19217109		2203	4300	6503	SO:0001583	missense	284439	exon6			TTCGCCGGCGCAC		CCDS32966.1	19p13.11	2013-05-22			ENSG00000181035	ENSG00000181035		"Solute carriers"	28380	protein-coding gene	gene with protein product		610823				16949250, 19429682	Standard	NM_178526		Approved	MGC26694	uc002nlf.3	Q86VD7		ENST00000318596.7:c.412G>A	chr19.hg19:g.19217109G>A	ENSP00000326693:p.Gly138Ser	44.0	0.0		58.0	6.0	NM_178526	D2T2J5|O14553|O43378	Missense_Mutation	SNP	ENST00000318596.7	hg19	CCDS32966.1	.	.	.	.	.	.	.	.	.	.	G	32	5.186075	0.94885	.	.	ENSG00000181035	ENST00000318596	D	0.91686	-2.89	4.5	4.5	0.54988	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.96364	0.8814	M	0.87971	2.92	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97237	0.9888	10	0.87932	D	0	-0.0015	15.7734	0.78190	0.0:0.0:1.0:0.0	.	190;138	B7Z8R5;Q86VD7	.;S2542_HUMAN	S	138	ENSP00000326693:G138S	ENSP00000326693:G138S	G	+	1	0	SLC25A42	19078109	1.000000	0.71417	0.038000	0.18304	0.701000	0.40568	8.756000	0.91651	2.056000	0.61249	0.491000	0.48974	GGC	.	.		0.647	SLC25A42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465931.1	NM_178526		A	19217109	G	A	19217109	3	1	306	1	0	0	0	0	1	0	0	0	14522	1116	39	1	430	1	SLC25A42	19	19217109	Missense_Mutation	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10	6755450	19217109	39911874	88	43857										
ZNF565	147929	hgsc.bcm.edu	37	chr19	36686037	36686037	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	cagagagaactctatggccaCgtccctgaatgtcaccagtc	9	13	2	3			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr19:36686037C>T	ENST00000355114.5	-	3	877	c.151G>A	c.(151-153)Gtg>Atg	p.V51M	ZNF565_ENST00000392173.2_Missense_Mutation_p.V11M|ZNF565_ENST00000304116.5_Missense_Mutation_p.V11M			Q8N9K5	ZN565_HUMAN	zinc finger protein 565	51	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(4)|lung(4)|ovary(1)|skin(2)	11	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.206)			TCTATGGCCACGTCCCTGAAT	0.433																																					p.V11M		Atlas-SNP	.											.	ZNF565	46	.	0			c.G31A						.						132	117	122					19																	36686037		2203	4300	6503	SO:0001583	missense	147929	exon3			TGGCCACGTCCCT	AK094310	CCDS12491.1	19q13.12	2013-09-20			ENSG00000196357	ENSG00000196357		"Zinc fingers, C2H2-type", "-"	26726	protein-coding gene	gene with protein product		614275					Standard	NM_001042474		Approved	FLJ36991	uc002odn.3	Q8N9K5	OTTHUMG00000180508	ENST00000355114.5:c.151G>A	chr19.hg19:g.36686037C>T	ENSP00000347234:p.Val51Met	187.0	0.0		178.0	64.0	NM_001042474	B3KQ35|Q6NUS2	Missense_Mutation	SNP	ENST00000355114.5	hg19		.	.	.	.	.	.	.	.	.	.	C	18.89	3.720472	0.68959	.	.	ENSG00000196357	ENST00000392173;ENST00000304116;ENST00000355114	T;T;T	0.10382	2.88;2.88;2.88	4.44	4.44	0.53790	Krueppel-associated box (4);	0.000000	0.29676	U	0.011496	T	0.35422	0.0931	M	0.85041	2.73	0.25777	N	0.984779	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.14783	-1.0460	10	0.66056	D	0.02	.	12.4231	0.55532	0.0:1.0:0.0:0.0	.	51;11	B3KQ35;Q8N9K5	.;ZN565_HUMAN	M	11;11;51	ENSP00000376013:V11M;ENSP00000306869:V11M;ENSP00000347234:V51M	ENSP00000306869:V11M	V	-	1	0	ZNF565	41377877	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.814000	0.55643	2.276000	0.75962	0.555000	0.69702	GTG	.	.		0.433	ZNF565-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000451697.1	NM_152477		T	36686037	C	T	36686037	3	4	306	1	0	0	0	0	1	0	0	0	18011	536	19	1	1480	1	ZNF565	19	36686037	Missense_Mutation	SNP	C	TCGA-GJ-A9DB-01A-11D-A36X-10	17468928	36686037	22442946	89	43858										
CEACAM8	1088	hgsc.bcm.edu	37	chr19	43093887	43093887	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	tggagggcttgggagtctccGctgtgcagaaaacagagaga	16	7	1	3	rs142428970		TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr19:43093887G>T	ENST00000244336.5	-	3	526	c.425C>A	c.(424-426)cCg>cAg	p.P142Q	LIPE-AS1_ENST00000594688.1_RNA|CEACAM8_ENST00000599005.1_Intron|LIPE-AS1_ENST00000594624.2_RNA	NM_001816.3	NP_001807.2	P31997	CEAM8_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 8	142	Ig-like V-type.				immune response (GO:0006955)	anchored component of membrane (GO:0031225)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.P142L(1)		endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	16		Prostate(69;0.00899)				GGGAGTCTCCGCTGTGCAGAA	0.527																																					p.P142Q		Atlas-SNP	.											CEACAM8,NS,carcinoma,0,1	CEACAM8	44	.	1	Substitution - Missense(1)	prostate(1)	c.C425A						.						132	130	131					19																	43093887		2203	4300	6503	SO:0001630	splice_region_variant	1088	exon3			GTCTCCGCTGTGC	D90064	CCDS12610.1	19q13.2	2013-01-29			ENSG00000124469	ENSG00000124469		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1820	protein-coding gene	gene with protein product		615747		CGM6		2208113, 2306228	Standard	NM_001816		Approved	CD66b	uc002oud.2	P31997	OTTHUMG00000151124	ENST00000244336.5:c.425-1C>A	chr19.hg19:g.43093887G>T		54.0	0.0		51.0	13.0	NM_001816	O60399|Q16574	Missense_Mutation	SNP	ENST00000244336.5	hg19	CCDS12610.1	.	.	.	.	.	.	.	.	.	.	g	3.053	-0.195049	0.06259	.	.	ENSG00000124469	ENST00000244336	T	0.19938	2.11	2.7	-1.51	0.08664	.	.	.	.	.	T	0.15392	0.0371	L	0.42686	1.345	0.09310	N	1	B	0.21452	0.056	B	0.29440	0.102	T	0.39272	-0.9622	9	0.22706	T	0.39	.	4.7298	0.12959	0.143:0.4359:0.4211:0.0	.	142	P31997	CEAM8_HUMAN	Q	142	ENSP00000244336:P142Q	ENSP00000244336:P142Q	P	-	2	0	CEACAM8	47785727	0.000000	0.05858	0.001000	0.08648	0.017000	0.09413	-2.633000	0.00869	-0.343000	0.08351	-0.657000	0.03884	CCG	.	G|1.000;A|0.000		0.527	CEACAM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321430.1		Missense_Mutation	T	43093887	G	T	43093887	5	4	306	1	0	0	0	0	0	0	1	0	3200	1101	38	1	636	1	CEACAM8	19	43093887	Splice_Site	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10	6407850	43093887	16035096	90	43859										
MYPOP	339344	hgsc.bcm.edu	37	chr19	46394252	46394252	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	tccctgtcgaagggtgccggCcagctcccggatggcgttgg	16	13	0	0			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr19:46394252C>T	ENST00000322217.5	-	3	915	c.829G>A	c.(829-831)Gcc>Acc	p.A277T		NM_001012643.2	NP_001012661.1	Q86VE0	MYPOP_HUMAN	Myb-related transcription factor, partner of profilin	277	Pro-rich.					nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			large_intestine(2)|lung(1)|skin(1)	4						AGGGTGCCGGCCAGCTCCCGG	0.692																																					p.A277T		Atlas-SNP	.											.	MYPOP	23	.	0			c.G829A						.						8	7	7					19																	46394252		2159	4222	6381	SO:0001583	missense	339344	exon3			TGCCGGCCAGCTC	BC044311	CCDS33055.1	19q13.32	2014-06-13			ENSG00000176182	ENSG00000176182			20178	protein-coding gene	gene with protein product	"p42 Myb-related transcription factor, partner of profilin"					15615774	Standard	NM_001012643		Approved	P42pop	uc002pdt.3	Q86VE0	OTTHUMG00000182486	ENST00000322217.5:c.829G>A	chr19.hg19:g.46394252C>T	ENSP00000325402:p.Ala277Thr	88.0	0.0		101.0	44.0	NM_001012643		Missense_Mutation	SNP	ENST00000322217.5	hg19	CCDS33055.1	.	.	.	.	.	.	.	.	.	.	C	12.01	1.808608	0.31961	.	.	ENSG00000176182	ENST00000322217	T	0.45668	0.89	4.5	3.45	0.39498	.	0.416780	0.19022	N	0.124790	T	0.18718	0.0449	N	0.08118	0	0.23645	N	0.997215	B	0.26363	0.147	B	0.20384	0.029	T	0.20706	-1.0267	10	0.11182	T	0.66	-3.7428	8.404	0.32603	0.0:0.8886:0.0:0.1114	.	277	Q86VE0	MYPOP_HUMAN	T	277	ENSP00000325402:A277T	ENSP00000325402:A277T	A	-	1	0	MYPOP	51086092	0.997000	0.39634	0.988000	0.46212	0.989000	0.77384	1.362000	0.34148	0.866000	0.35629	0.561000	0.74099	GCC	.	.		0.692	MYPOP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461684.1	NM_001012643		T	46394252	C	T	46394252	3	4	306	1	0	0	0	0	1	0	0	0	10108	739	26	3	374	3	MYPOP	19	46394252	Missense_Mutation	SNP	C	TCGA-GJ-A9DB-01A-11D-A36X-10	3300365	46394252	12734731	91	43860										
KLK9	284366	hgsc.bcm.edu	37	chr19	51507011	51507011	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	cccgcacagagcatgctgtcCgagatgtgtccagggtatgc	13	12	0	2	rs147491832		TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr19:51507011C>T	ENST00000594211.1	-	4	552	c.552G>A	c.(550-552)tcG>tcA	p.S184S	KLK8_ENST00000593490.1_5'Flank|KLK8_ENST00000320838.5_5'Flank|KLK8_ENST00000600767.1_5'Flank|KLK8_ENST00000391806.2_5'Flank|KLK8_ENST00000347619.4_5'Flank|CTB-147C22.9_ENST00000594512.1_RNA|KLK9_ENST00000376832.4_Silent_p.S184S|KLK9_ENST00000250366.6_Silent_p.S184S|KLK8_ENST00000291726.7_5'Flank			Q9UKQ9	KLK9_HUMAN	kallikrein-related peptidase 9	184	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|skin(1)	7		all_neural(266;0.0652)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00885)		GCATGCTGTCCGAGATGTGTC	0.567																																					p.S184S		Atlas-SNP	.											.	KLK9	27	.	0			c.G552A						.	C		1,4405	2.1+/-5.4	0,1,2202	106	79	88		552	-9.4	0	19	dbSNP_134	88	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	KLK9	NM_012315.1		0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231		184/251	51507011	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	284366	exon4			GCTGTCCGAGATG	AF135026	CCDS12816.1	19q13.33	2008-02-05	2006-10-27					"Kallikreins"	6370	protein-coding gene	gene with protein product		605504	"kallikrein 9"			16800724, 16800723	Standard	NM_012315		Approved	KLK-L3	uc002pux.1	Q9UKQ9		ENST00000594211.1:c.552G>A	chr19.hg19:g.51507011C>T		99.0	0.0		111.0	37.0	NM_012315	Q6QA55	Silent	SNP	ENST00000594211.1	hg19	CCDS12816.1																																																																																			.	C|1.000;T|0.000		0.567	KLK9-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465226.1	NM_012315		T	51507011	C	T	51507011	2	4	306	1	0	0	0	0	0	0	0	1	8420	639	23	1		1	KLK9	19	51507011	Silent	SNP	C	TCGA-GJ-A9DB-01A-11D-A36X-10	5112759	51507011	7621972	92	43861										
VN1R2	317701	hgsc.bcm.edu	37	chr19	53761895	53761895	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	aaacccaccaaacctgtgggGctggaccctacactattcca	7	15	0	0			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr19:53761895G>T	ENST00000341702.3	+	1	351	c.267G>T	c.(265-267)ggG>ggT	p.G89G		NM_173856.2	NP_776255.2	Q8NFZ6	VN1R2_HUMAN	vomeronasal 1 receptor 2	89					response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(134;0.00301)		aacctgtggggctggacccta	0.423																																					p.G89G		Atlas-SNP	.											.	VN1R2	71	.	0			c.G267T						.						46	48	48					19																	53761895		2184	4282	6466	SO:0001819	synonymous_variant	317701	exon1			TGTGGGGCTGGAC	AF370359	CCDS12862.1	19q13.42	2012-08-22			ENSG00000196131	ENSG00000196131		"Vomeronasal receptors / Type 1", "GPCR / Unclassified : Vomeronasal receptors, type 1"	19872	protein-coding gene	gene with protein product						12123587	Standard	NM_173856		Approved	V1RL2	uc002qbi.2	Q8NFZ6		ENST00000341702.3:c.267G>T	chr19.hg19:g.53761895G>T		133.0	0.0		150.0	49.0	NM_173856	A1L411|Q8TDU4	Silent	SNP	ENST00000341702.3	hg19	CCDS12862.1																																																																																			.	.		0.423	VN1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464285.1	NM_173856		T	53761895	G	T	53761895	2	4	306	1	0	0	0	0	0	0	0	1	17194	1190	42	3		3	VN1R2	19	53761895	Silent	SNP	G	TCGA-GJ-A9DB-01A-11D-A36X-10	2254884	53761895	5367088	93	43862										
OLIG2	10215	hgsc.bcm.edu	37	chr21	34399755	34399755	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0638297872340425	6	1	1.18905279503106	0.911607142857143	1.26612103174603	0.131221719457014	0.709357990687916	0	tgcggcggcctggcgcactcCgcgcccctgcccgccgccac	13	22	0	0			TCGA-GJ-A9DB-01A-11D-A36X-10	TCGA-GJ-A9DB-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84dd6525-b3f4-4225-854b-d8ea04ae087d	1feb671e-5b85-48f9-b96b-19e5a877a13e	g.chr21:34399755C>A	ENST00000333337.3	+	1	1513	c.585C>A	c.(583-585)tcC>tcA	p.S195S	OLIG2_ENST00000382357.3_Silent_p.S195S|AP000282.2_ENST00000454622.1_RNA|AP000282.2_ENST00000420356.1_RNA			Q13516	OLIG2_HUMAN	oligodendrocyte lineage transcription factor 2	195					myelination (GO:0042552)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron fate commitment (GO:0048663)|positive regulation of oligodendrocyte differentiation (GO:0048714)|spinal cord motor neuron differentiation (GO:0021522)|spinal cord oligodendrocyte cell fate specification (GO:0021530)|thalamus development (GO:0021794)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			breast(1)|central_nervous_system(2)	3						TGGCGCACTCCGCGCCCCTGC	0.751			T	TRA@	T-ALL																																p.S195S		Atlas-SNP	.		Dom	yes		21	21q22.11	10215	oligodendrocyte lineage transcription factor 2 (BHLHB1)		L	.	OLIG2	22	.	0			c.C585A						.						4	4	4					21																	34399755		1684	3217	4901	SO:0001819	synonymous_variant	10215	exon2			GCACTCCGCGCCC	U48250	CCDS13620.1	21q22.11	2013-05-21	2001-12-04	2001-12-07	ENSG00000205927	ENSG00000205927		"Basic helix-loop-helix proteins"	9398	protein-coding gene	gene with protein product	"oligodendrocyte-specific bHLH transcription factor 2", "protein kinase C binding protein 2", "human protein kinase C-binding protein RACK17", "basic domain, helix-loop-helix protein, class B, 1"	606386	"protein kinase C binding protein 2"	PRKCBP2, BHLHB1		11526205	Standard	NM_005806		Approved	RACK17, OLIGO2, bHLHe19	uc002yqx.2	Q13516	OTTHUMG00000065032	ENST00000333337.3:c.585C>A	chr21.hg19:g.34399755C>A		34.0	0.0		46.0	15.0	NM_005806	B3KRF3|Q05BP9|Q49AL3|Q86X04|Q9NZ14	Silent	SNP	ENST00000333337.3	hg19	CCDS13620.1																																																																																			.	.		0.751	OLIG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139663.1	NM_005806		A	34399755	C	A	34399755	2	1	306	1	0	0	0	0	0	0	0	1	10870	639	23	1		1	OLIG2	21	34399755	Silent	SNP	C	TCGA-GJ-A9DB-01A-11D-A36X-10		34399755	13730140	94	43863										
IFI16	3428	hgsc.bcm.edu	37	chr1	159002321	159002321	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	tgaatactttcagataaagaAaaaaacaaacccgagaaaca	5	7	1	4			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr1:159002321A>G	ENST00000295809.7	+	7	1424	c.1169A>G	c.(1168-1170)aAa>aGa	p.K390R	IFI16_ENST00000448393.2_Missense_Mutation_p.K390R|IFI16_ENST00000368132.3_Missense_Mutation_p.K390R|IFI16_ENST00000340979.6_Missense_Mutation_p.K390R|IFI16_ENST00000359709.3_Missense_Mutation_p.K334R|IFI16_ENST00000430894.2_Missense_Mutation_p.K338R|IFI16_ENST00000368131.4_Missense_Mutation_p.K390R			Q16666	IF16_HUMAN	interferon, gamma-inducible protein 16	390	Interaction with TP53 C-terminus.				activation of cysteine-type endopeptidase activity (GO:0097202)|activation of innate immune response (GO:0002218)|autophagy (GO:0006914)|cell proliferation (GO:0008283)|cellular response to glucose starvation (GO:0042149)|cellular response to ionizing radiation (GO:0071479)|defense response to virus (GO:0051607)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|monocyte differentiation (GO:0030224)|myeloid cell differentiation (GO:0030099)|negative regulation of cysteine-type endopeptidase activity (GO:2000117)|negative regulation of DNA binding (GO:0043392)|negative regulation of innate immune response (GO:0045824)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|positive regulation of cytokine production (GO:0001819)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of autophagy (GO:0010506)|regulation of gene expression, epigenetic (GO:0040029)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_hematologic(112;0.0429)					CAGATAAAGAAAAAAACAAAC	0.383																																					p.K390R		Atlas-SNP	.											.	IFI16	111	.	0			c.A1169G						.						56	57	57					1																	159002321		2203	4300	6503	SO:0001583	missense	3428	exon7			TAAAGAAAAAAAC	M63838	CCDS1180.3, CCDS58039.1	1q22	2008-02-05			ENSG00000163565	ENSG00000163565			5395	protein-coding gene	gene with protein product		147586				1526658, 7959953	Standard	NM_005531		Approved	IFNGIP1, PYHIN2	uc010pis.2	Q16666	OTTHUMG00000037108	ENST00000295809.7:c.1169A>G	chr1.hg19:g.159002321A>G	ENSP00000295809:p.Lys390Arg	36.0	0.0		41.0	4.0	NM_005531	B4DJT8|H3BLV7|Q59GX0|Q5T3W7|Q5T3W8|Q5T3X0|Q5T3X1|Q5T3X2|Q8N9E5|Q8NEQ7|Q96AJ5|Q9UH78	Missense_Mutation	SNP	ENST00000295809.7	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	7.414|7.414	0.635294|0.635294	0.14322|0.14322	.|.	.|.	ENSG00000163565|ENSG00000163565	ENST00000448393|ENST00000295809;ENST00000340979;ENST00000368131;ENST00000368132;ENST00000430894	.|T;T;T;T;T	.|0.06068	.|3.58;3.53;3.53;3.53;3.35	1.9|1.9	-0.624|-0.624	0.11552|0.11552	.|.	.|.	.|.	.|.	.|.	T|T	0.02888|0.02888	0.0086|0.0086	L|L	0.48642|0.48642	1.525|1.525	0.09310|0.09310	N|N	1|1	.|B;P	.|0.47762	.|0.009;0.9	.|B;P	.|0.48795	.|0.001;0.59	T|T	0.36432|0.36432	-0.9748|-0.9748	6|9	0.35671|0.45353	T|T	0.21|0.12	.|.	4.2894|4.2894	0.10870|0.10870	0.601:0.0:0.399:0.0|0.601:0.0:0.399:0.0	.|.	.|338;390	.|E7EPR3;Q16666-2	.|.;.	E|R	211|390;390;390;390;338	.|ENSP00000295809:K390R;ENSP00000342741:K390R;ENSP00000357113:K390R;ENSP00000357114:K390R;ENSP00000394935:K338R	ENSP00000404325:K211E|ENSP00000295809:K390R	K|K	+|+	1|2	0|0	IFI16|IFI16	157268945|157268945	0.000000|0.000000	0.05858|0.05858	0.003000|0.003000	0.11579|0.11579	0.690000|0.690000	0.40134|0.40134	0.185000|0.185000	0.16958|0.16958	-0.173000|-0.173000	0.10761|0.10761	0.379000|0.379000	0.24179|0.24179	AAA|AAA	.	.		0.383	IFI16-013	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000421720.1	NM_005531		G	159002321	A	G	159002321	3	3	307	1	0	0	0	0	1	0	0	0	7520	14	1	2	1191	2	IFI16	1	159002321	Missense_Mutation	SNP	A	TCGA-HP-A5MZ-01A-21D-A27I-10		159002321	90248300	1	43864										
PLXNA2	5362	hgsc.bcm.edu	37	chr1	208269429	208269429	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	ggtgctgacaaatatcttccCtgtctccttggacctcagct	8	13	3	1			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr1:208269429C>A	ENST00000367033.3	-	8	2684	c.1927G>T	c.(1927-1929)Ggg>Tgg	p.G643W		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	643					axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		AATATCTTCCCTGTCTCCTTG	0.498																																					p.G643W		Atlas-SNP	.											.	PLXNA2	178	.	0			c.G1927T						.						256	269	265					1																	208269429		2203	4300	6503	SO:0001583	missense	5362	exon8			TCTTCCCTGTCTC	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"Plexins"	9100	protein-coding gene	gene with protein product	"plexin 2", "plexin-A2", "semaphorin receptor OCT", "transmembrane protein OCT"	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.1927G>T	chr1.hg19:g.208269429C>A	ENSP00000356000:p.Gly643Trp	109.0	0.0		179.0	17.0	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	hg19	CCDS31013.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.774232	0.90108	.	.	ENSG00000076356	ENST00000367033	T	0.01092	5.35	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	T	0.08582	0.0213	M	0.83118	2.625	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.00766	-1.1575	10	0.87932	D	0	.	18.6344	0.91371	0.0:1.0:0.0:0.0	.	643	O75051	PLXA2_HUMAN	W	643	ENSP00000356000:G643W	ENSP00000356000:G643W	G	-	1	0	PLXNA2	206336052	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.650000	0.67944	2.635000	0.89317	0.650000	0.86243	GGG	.	.		0.498	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179		A	208269429	C	A	208269429	3	1	307	1	0	0	0	0	1	0	0	0	12129	681	24	3	3857	3	PLXNA2	1	208269429	Missense_Mutation	SNP	C	TCGA-HP-A5MZ-01A-21D-A27I-10	49267108	208269429	40981192	2	43865										
LPGAT1	9926	hgsc.bcm.edu	37	chr1	211952355	211952355	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	ggataagctatcgttgtatcTattatccactggaggccttt	9	8	1	0			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr1:211952355T>C	ENST00000366997.4	-	6	985	c.759A>G	c.(757-759)atA>atG	p.I253M	LPGAT1_ENST00000366996.1_Missense_Mutation_p.I253M	NM_014873.2	NP_055688.1	Q92604	LGAT1_HUMAN	lysophosphatidylglycerol acyltransferase 1	253					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity, transferring acyl groups (GO:0016746)			breast(1)|endometrium(2)|large_intestine(1)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				OV - Ovarian serous cystadenocarcinoma(81;0.00773)|all cancers(67;0.0765)|Epithelial(68;0.114)		TCGTTGTATCTATTATCCACT	0.343																																					p.I253M		Atlas-SNP	.											.	LPGAT1	32	.	0			c.A759G						.						152	156	155					1																	211952355		2203	4300	6503	SO:0001583	missense	9926	exon6			TGTATCTATTATC	D86960	CCDS31018.1	1q32.3	2008-05-14	2004-11-25	2004-11-26	ENSG00000123684	ENSG00000123684			28985	protein-coding gene	gene with protein product		610473	"family with sequence similarity 34, member A"	FAM34A		9039502, 15485873	Standard	NM_014873		Approved	KIAA0205, FAM34A1, NET8	uc001hiv.3	Q92604	OTTHUMG00000037120	ENST00000366997.4:c.759A>G	chr1.hg19:g.211952355T>C	ENSP00000355964:p.Ile253Met	60.0	0.0		80.0	4.0	NM_014873	Q53YL2	Missense_Mutation	SNP	ENST00000366997.4	hg19	CCDS31018.1	.	.	.	.	.	.	.	.	.	.	T	29.1	4.975289	0.92919	.	.	ENSG00000123684	ENST00000366997;ENST00000366996	T;T	0.32272	1.46;1.46	5.89	5.89	0.94794	.	0.036291	0.85682	D	0.000000	T	0.50735	0.1633	M	0.73962	2.25	0.80722	D	1	D	0.57899	0.981	P	0.55161	0.77	T	0.55042	-0.8202	10	0.72032	D	0.01	-29.7876	16.3625	0.83273	0.0:0.0:0.0:1.0	.	253	Q92604	LGAT1_HUMAN	M	253	ENSP00000355964:I253M;ENSP00000355963:I253M	ENSP00000355963:I253M	I	-	3	3	LPGAT1	210018978	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.244000	0.43124	2.265000	0.75225	0.449000	0.29647	ATA	.	.		0.343	LPGAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090150.1	NM_014873		C	211952355	T	C	211952355	3	2	307	1	0	0	0	0	1	0	0	0	8923	1512	53	2	365	2	LPGAT1	1	211952355	Missense_Mutation	SNP	T	TCGA-HP-A5MZ-01A-21D-A27I-10	3682926	211952355	37298266	3	43866										
RAB4A	5867	hgsc.bcm.edu	37	chr1	229434759	229434759	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	aaacaagtgcgctcacagggGagaatgtagaagaggctttt	13	6	1	3			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr1:229434759G>T	ENST00000366690.4	+	6	689	c.481G>T	c.(481-483)Gag>Tag	p.E161*	RAB4A_ENST00000473894.1_3'UTR	NM_004578.2	NP_004569.2	P20338	RAB4A_HUMAN	RAB4A, member RAS oncogene family	161					antigen processing and presentation (GO:0019882)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|regulation of endocytosis (GO:0030100)|small GTPase mediated signal transduction (GO:0007264)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|protein transporter activity (GO:0008565)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|skin(1)	11	Breast(184;0.0858)|Ovarian(103;0.103)	Prostate(94;0.178)				GCTCACAGGGGAGAATGTAGA	0.333																																					p.E161X	Esophageal Squamous(11;250 603 9619 16563)	Atlas-SNP	.											.	RAB4A	29	.	0			c.G481T						.						119	117	118					1																	229434759		2203	4300	6503	SO:0001587	stop_gained	5867	exon6			ACAGGGGAGAATG	BC004309	CCDS31050.1, CCDS73046.1	1q42-q43	2014-04-03		2002-02-28	ENSG00000168118	ENSG00000168118		"RAB, member RAS oncogene"	9781	protein-coding gene	gene with protein product		179511		RAB4			Standard	NM_004578		Approved	HRES-1/RAB4	uc001hth.4	P20338	OTTHUMG00000037627	ENST00000366690.4:c.481G>T	chr1.hg19:g.229434759G>T	ENSP00000355651:p.Glu161*	85.0	0.0		155.0	23.0	NM_004578	Q5T7P7|Q9BQ44	Nonsense_Mutation	SNP	ENST00000366690.4	hg19	CCDS31050.1	.	.	.	.	.	.	.	.	.	.	G	38	7.082605	0.98051	.	.	ENSG00000168118	ENST00000366690	.	.	.	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	.	19.5035	0.95105	0.0:0.0:1.0:0.0	.	.	.	.	X	161	.	ENSP00000355651:E161X	E	+	1	0	RAB4A	227501382	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.781000	0.99029	2.674000	0.91012	0.655000	0.94253	GAG	.	.		0.333	RAB4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091727.3	NM_004578		T	229434759	G	T	229434759	4	4	307	1	0	0	0	0	0	1	0	0	12961	1175	41	3	503	3	RAB4A	1	229434759	Nonsense_Mutation	SNP	G	TCGA-HP-A5MZ-01A-21D-A27I-10	17482404	229434759	19815862	4	43867										
APOB	338	hgsc.bcm.edu	37	chr2	21259995	21259995	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	gcctttgatgagagcaagtgGgctgatgcctgtgcggatgg	17	7	0	3			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr2:21259995G>A	ENST00000233242.1	-	6	797	c.670C>T	c.(670-672)Cca>Tca	p.P224S	APOB_ENST00000399256.4_Missense_Mutation_p.P224S	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	224	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.				artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGAGCAAGTGGGCTGATGCCT	0.498																																					p.P224S		Atlas-SNP	.											.	APOB	761	.	0			c.C670T						.						154	124	134					2																	21259995		2203	4300	6503	SO:0001583	missense	338	exon6			CAAGTGGGCTGAT	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.670C>T	chr2.hg19:g.21259995G>A	ENSP00000233242:p.Pro224Ser	204.0	0.0		219.0	24.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.631711	0.87660	.	.	ENSG00000084674	ENST00000233242;ENST00000535079;ENST00000399256	T;T	0.38401	1.14;1.14	5.64	5.64	0.86602	Lipid transport protein, beta-sheet shell (1);Lipid transport protein, N-terminal (3);Vitellinogen, beta-sheet N-terminal (1);	0.000000	0.56097	D	0.000027	T	0.65333	0.2681	M	0.80847	2.515	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	T	0.66444	-0.5922	10	0.59425	D	0.04	.	20.0869	0.97801	0.0:0.0:1.0:0.0	.	224	P04114	APOB_HUMAN	S	224	ENSP00000233242:P224S;ENSP00000382200:P224S	ENSP00000233242:P224S	P	-	1	0	APOB	21113500	1.000000	0.71417	0.998000	0.56505	0.732000	0.41865	8.485000	0.90448	2.831000	0.97527	0.650000	0.86243	CCA	.	.		0.498	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			A	21259995	G	A	21259995	3	1	307	1	0	0	0	0	1	0	0	0	785	1232	43	3	13117	3	APOB	2	21259995	Missense_Mutation	SNP	G	TCGA-HP-A5MZ-01A-21D-A27I-10		21259995	221939378	5	43868										
CIB4	130106	hgsc.bcm.edu	37	chr2	26852279	26852279	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	cccaccatcctggactcaccCgcagagctggcagggagctg	12	16	1	1	rs374300070		TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr2:26852279C>T	ENST00000288861.4	-	3	238	c.185G>A	c.(184-186)cGg>cAg	p.R62Q		NM_001029881.1	NP_001025052.1	A0PJX0	CIB4_HUMAN	calcium and integrin binding family member 4	62	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGGACTCACCCGCAGAGCTGG	0.627																																					p.R62Q		Atlas-SNP	.											.	CIB4	15	.	0			c.G185A						.						67	47	54					2																	26852279		2201	4290	6491	SO:0001630	splice_region_variant	130106	exon3			CTCACCCGCAGAG		CCDS33160.1	2p23.3	2013-01-10			ENSG00000157884	ENSG00000157884		"EF-hand domain containing"	33703	protein-coding gene	gene with protein product		610646				15574431	Standard	NM_001029881		Approved		uc002rhm.3	A0PJX0	OTTHUMG00000151993	ENST00000288861.4:c.186+1G>A	chr2.hg19:g.26852279C>T		77.0	0.0		96.0	19.0	NM_001029881	B2RU18	Missense_Mutation	SNP	ENST00000288861.4	hg19	CCDS33160.1	.	.	.	.	.	.	.	.	.	.	C	17.65	3.442532	0.63067	.	.	ENSG00000157884	ENST00000288861	T	0.66638	-0.22	5.26	5.26	0.73747	EF-hand-like domain (1);	0.000000	0.53938	D	0.000044	T	0.51007	0.1649	L	0.28344	0.845	0.80722	D	1	B	0.33073	0.396	B	0.22880	0.042	T	0.54139	-0.8338	10	0.44086	T	0.13	.	14.3709	0.66838	0.0:1.0:0.0:0.0	.	62	A0PJX0	CIB4_HUMAN	Q	62	ENSP00000288861:R62Q	ENSP00000288861:R62Q	R	-	2	0	CIB4	26705783	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	3.458000	0.53014	2.459000	0.83118	0.563000	0.77884	CGG	.	.		0.627	CIB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324709.1		Missense_Mutation	T	26852279	C	T	26852279	5	4	307	1	0	0	0	0	0	0	1	0	3425	666	23	1	392	1	CIB4	2	26852279	Splice_Site	SNP	C	TCGA-HP-A5MZ-01A-21D-A27I-10	5592284	26852279	216347094	6	43869										
ETAA1	54465	hgsc.bcm.edu	37	chr2	67631603	67631603	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	ttaaagcatgtcatcaattaGataatacctgggaagcagat	8	6	2	2			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr2:67631603G>C	ENST00000272342.5	+	5	1919	c.1789G>C	c.(1789-1791)Gat>Cat	p.D597H	ETAA1_ENST00000462772.1_Intron	NM_019002.3	NP_061875.2	Q9NY74	ETAA1_HUMAN	Ewing tumor-associated antigen 1	597						cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	33						TCATCAATTAGATAATACCTG	0.353																																					p.D597H		Atlas-SNP	.											.	ETAA1	88	.	0			c.G1789C						.						101	105	104					2																	67631603		2202	4300	6502	SO:0001583	missense	54465	exon5			CAATTAGATAATA	AJ242682	CCDS1882.1	2p14	2014-02-12	2007-10-04		ENSG00000143971	ENSG00000143971			24648	protein-coding gene	gene with protein product		613196	"Ewing's tumor-associated antigen 1"			16003559	Standard	XM_005264374		Approved	ETAA16	uc002sdz.1	Q9NY74	OTTHUMG00000129545	ENST00000272342.5:c.1789G>C	chr2.hg19:g.67631603G>C	ENSP00000272342:p.Asp597His	73.0	0.0		81.0	11.0	NM_019002	Q05BT7|Q53SC4	Missense_Mutation	SNP	ENST00000272342.5	hg19	CCDS1882.1	.	.	.	.	.	.	.	.	.	.	G	11.77	1.738893	0.30774	.	.	ENSG00000143971	ENST00000272342	T	0.18016	2.24	5.83	4.95	0.65309	.	0.238496	0.38605	N	0.001624	T	0.22820	0.0551	L	0.39898	1.24	0.45150	D	0.998163	D	0.53151	0.958	P	0.51135	0.66	T	0.01010	-1.1482	10	0.66056	D	0.02	-17.7595	12.0508	0.53505	0.0664:0.1221:0.8115:0.0	.	597	Q9NY74	ETAA1_HUMAN	H	597	ENSP00000272342:D597H	ENSP00000272342:D597H	D	+	1	0	ETAA1	67485107	0.999000	0.42202	0.413000	0.26509	0.254000	0.26022	2.979000	0.49313	1.456000	0.47831	0.655000	0.94253	GAT	.	.		0.353	ETAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251735.1	NM_019002		C	67631603	G	C	67631603	3	2	307	1	0	0	0	0	1	0	0	0	5269	942	33	4	1807	4	ETAA1	2	67631603	Missense_Mutation	SNP	G	TCGA-HP-A5MZ-01A-21D-A27I-10	40779324	67631603	175567770	7	43870										
PMS1	5378	hgsc.bcm.edu	37	chr2	190742031	190742031	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	gtctatccagacaattacccAtgtacttatcaaaagaggac	6	10	2	2	rs537745271		TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr2:190742031A>G	ENST00000441310.2	+	13	2901	c.2668A>G	c.(2668-2670)Atg>Gtg	p.M890V	PMS1_ENST00000409823.3_Missense_Mutation_p.M851V|PMS1_ENST00000447232.2_Missense_Mutation_p.M728V|PMS1_ENST00000432292.3_Missense_Mutation_p.M714V|PMS1_ENST00000418224.3_Missense_Mutation_p.M714V	NM_000534.4	NP_000525.1	P54277	PMS1_HUMAN	PMS1 postmeiotic segregation increased 1 (S. cerevisiae)	890					ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)	MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|mismatched DNA binding (GO:0030983)|single-stranded DNA binding (GO:0003697)	p.M890L(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(16)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			OV - Ovarian serous cystadenocarcinoma(117;0.0013)|Epithelial(96;0.0263)|all cancers(119;0.0751)			ACAATTACCCATGTACTTATC	0.403			"Mis, N"			"colorectal, endometrial, ovarian"		Direct reversal of damage;Mismatch excision repair (MMR)																													p.M890V		Atlas-SNP	.	yes	Rec		Hereditary non-polyposis colorectal cancer	2	2q31-q33	5378	PMS1 postmeiotic segregation increased 1 (S. cerevisiae)		E	PMS1,NS,carcinoma,0,1	PMS1	78	.	1	Substitution - Missense(1)	lung(1)	c.A2668G						.						129	119	122					2																	190742031		2203	4300	6503	SO:0001583	missense	5378	exon13			TTACCCATGTACT		CCDS2302.1, CCDS46473.1, CCDS46474.1, CCDS74615.1	2q31-q33	2014-09-17	2001-11-28		ENSG00000064933	ENSG00000064933			9121	protein-coding gene	gene with protein product		600258	"postmeiotic segregation increased (S. cerevisiae) 1"	PMSL1		8072530	Standard	NM_000534		Approved		uc002urh.4	P54277	OTTHUMG00000132664	ENST00000441310.2:c.2668A>G	chr2.hg19:g.190742031A>G	ENSP00000406490:p.Met890Val	111.0	1.0		152.0	16.0	NM_000534	D3DPI1|Q4VAL4|Q5FBZ3|Q5FBZ6|Q5FBZ8	Missense_Mutation	SNP	ENST00000441310.2	hg19	CCDS2302.1	.	.	.	.	.	.	.	.	.	.	A	13.46	2.245289	0.39697	.	.	ENSG00000064933	ENST00000441310;ENST00000418224;ENST00000409823;ENST00000447232;ENST00000432292;ENST00000409593	D;D;D;D;D;D	0.96168	-2.24;-1.93;-2.4;-2.77;-1.93;-3.93	5.87	3.45	0.39498	.	0.252228	0.46145	D	0.000312	D	0.90024	0.6885	L	0.40543	1.245	0.31561	N	0.657558	B;B;B;B;B	0.26195	0.01;0.029;0.05;0.144;0.029	B;B;B;B;B	0.21546	0.002;0.021;0.013;0.035;0.013	D	0.84270	0.0488	10	0.20046	T	0.44	-20.2265	7.2379	0.26079	0.6946:0.1118:0.0:0.1936	.	206;513;851;728;890	Q5FBZ4;Q5FBZ6;Q5FBZ3;Q5FBZ8;P54277	.;.;.;.;PMS1_HUMAN	V	890;714;851;728;714;513	ENSP00000406490:M890V;ENSP00000404492:M714V;ENSP00000387125:M851V;ENSP00000401064:M728V;ENSP00000398378:M714V;ENSP00000387169:M513V	ENSP00000387169:M513V	M	+	1	0	PMS1	190450276	0.671000	0.27521	1.000000	0.80357	0.981000	0.71138	0.811000	0.27198	2.371000	0.80710	0.533000	0.62120	ATG	.	.		0.403	PMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255918.2			G	190742031	A	G	190742031	3	3	307	1	0	0	0	0	1	0	0	0	12151	217	8	2	2714	2	PMS1	2	190742031	Missense_Mutation	SNP	A	TCGA-HP-A5MZ-01A-21D-A27I-10	123110428	190742031	52457342	8	43871										
USP4	7375	hgsc.bcm.edu	37	chr3	49321560	49321560	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	tgttgatgcttcttacagttGggacagtacctaaaaagaga	10	6	1	2			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr3:49321560G>A	ENST00000265560.4	-	19	2446	c.2400C>T	c.(2398-2400)ccC>ccT	p.P800P	USP4_ENST00000351842.4_Silent_p.P753P	NM_003363.3	NP_003354.2	Q13107	UBP4_HUMAN	ubiquitin specific peptidase 4 (proto-oncogene)	800	USP.				negative regulation of protein ubiquitination (GO:0031397)|protein deubiquitination (GO:0016579)|protein localization to cell surface (GO:0034394)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	adenosine receptor binding (GO:0031685)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33		Ovarian(412;0.00308)|Myeloproliferative disorder(1037;0.0255)|Hepatocellular(537;0.121)		OV - Ovarian serous cystadenocarcinoma(275;4.74e-26)|Kidney(197;2.22e-07)|KIRC - Kidney renal clear cell carcinoma(197;5.14e-06)|BRCA - Breast invasive adenocarcinoma(193;9.46e-05)		TCTTACAGTTGGGACAGTACC	0.517																																					p.P800P		Atlas-SNP	.											.	USP4	72	.	0			c.C2400T						.						122	108	113					3																	49321560		2203	4300	6503	SO:0001819	synonymous_variant	7375	exon19			ACAGTTGGGACAG	U20657	CCDS2793.1, CCDS2794.1, CCDS58832.1	3p21.3	2005-10-11	2005-08-08		ENSG00000114316	ENSG00000114316		"Ubiquitin-specific peptidases"	12627	protein-coding gene	gene with protein product		603486	"ubiquitin specific protease 4 (proto-oncogene)"	UNP		12838346, 9464533	Standard	NM_199443		Approved	Unph	uc003cwq.2	Q13107	OTTHUMG00000156825	ENST00000265560.4:c.2400C>T	chr3.hg19:g.49321560G>A		202.0	0.0		253.0	37.0	NM_003363	A8K6Y0|C9IY91|O43452|O43453|Q08AK8	Silent	SNP	ENST00000265560.4	hg19	CCDS2793.1	.	.	.	.	.	.	.	.	.	.	G	8.788	0.929803	0.18131	.	.	ENSG00000114316	ENST00000431357	.	.	.	5.36	2.1	0.27182	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-19.5461	5.4554	0.16588	0.2197:0.3045:0.4758:0.0	.	.	.	.	X	539	.	.	Q	-	1	0	USP4	49296564	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.780000	0.38634	0.633000	0.30452	0.655000	0.94253	CAA	.	.		0.517	USP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346069.1	NM_199443		A	49321560	G	A	49321560	2	1	307	1	0	0	0	0	0	0	0	1	17086	1335	47	3		3	USP4	3	49321560	Silent	SNP	G	TCGA-HP-A5MZ-01A-21D-A27I-10		49321560	148700870	9	43872										
UBA7	7318	hgsc.bcm.edu	37	chr3	49849633	49849633	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	tgtctccaatctccagggacCcatcctctgagggagttcca	9	14	3	1			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr3:49849633C>A	ENST00000333486.3	-	7	859	c.701G>T	c.(700-702)gGg>gTg	p.G234V	UBA7_ENST00000494212.1_5'Flank	NM_003335.2	NP_003326.2	P41226	UBA7_HUMAN	ubiquitin-like modifier activating enzyme 7	234	2 approximate repeats.				cellular protein modification process (GO:0006464)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|modification-dependent protein catabolic process (GO:0019941)|negative regulation of type I interferon production (GO:0032480)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ISG15 activating enzyme activity (GO:0019782)|ubiquitin activating enzyme activity (GO:0004839)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(15)|large_intestine(4)|lung(7)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;3.58e-06)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		CTCCAGGGACCCATCCTCTGA	0.517																																					p.G234V		Atlas-SNP	.											.	UBA7	64	.	0			c.G701T						.						151	140	143					3																	49849633		2203	4300	6503	SO:0001583	missense	7318	exon7			AGGGACCCATCCT	BC006378	CCDS2805.1	3p21	2007-11-30	2007-11-30	2007-11-30	ENSG00000182179	ENSG00000182179		"Ubiquitin-like modifier activating enzymes"	12471	protein-coding gene	gene with protein product	"UBA1, ubiquitin-activating enzyme E1 homolog B (yeast)", "UBA7, ubiquitin-activating enzyme E1"	191325	"ubiquitin-activating enzyme E1-like"	UBE1L		8327486	Standard	NM_003335		Approved	D8, UBE2, UBA1B	uc003cxr.3	P41226	OTTHUMG00000158267	ENST00000333486.3:c.701G>T	chr3.hg19:g.49849633C>A	ENSP00000333266:p.Gly234Val	165.0	0.0		196.0	32.0	NM_003335	Q9BRB2	Missense_Mutation	SNP	ENST00000333486.3	hg19	CCDS2805.1	.	.	.	.	.	.	.	.	.	.	C	14.47	2.545034	0.45280	.	.	ENSG00000182179	ENST00000333486	T	0.28454	1.61	5.78	5.78	0.91487	Molybdenum cofactor biosynthesis, MoeB (1);	0.583161	0.21006	N	0.081779	T	0.35158	0.0922	M	0.68317	2.08	0.52099	D	0.999944	B	0.22683	0.073	B	0.25759	0.063	T	0.14615	-1.0466	10	0.66056	D	0.02	-8.2445	12.4467	0.55654	0.1674:0.8326:0.0:0.0	.	234	P41226	UBA7_HUMAN	V	234	ENSP00000333266:G234V	ENSP00000333266:G234V	G	-	2	0	UBA7	49824637	0.000000	0.05858	0.787000	0.31911	0.906000	0.53458	0.635000	0.24629	2.739000	0.93911	0.561000	0.74099	GGG	.	.		0.517	UBA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350503.1	NM_003335		A	49849633	C	A	49849633	3	1	307	1	0	0	0	0	1	0	0	0	16848	623	22	3	2409	3	UBA7	3	49849633	Missense_Mutation	SNP	C	TCGA-HP-A5MZ-01A-21D-A27I-10	528073	49849633	148172797	10	43873										
DNAH12	201625	hgsc.bcm.edu	37	chr3	57391435	57391435	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	tgtgaaatgattctttaaaaTggtcctttataacagtttta	6	4	1	2			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr3:57391435T>C	ENST00000351747.2	-	41	6644	c.6464A>G	c.(6463-6465)cAt>cGt	p.H2155R		NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	2155					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						TTCTTTAAAATGGTCCTTTAT	0.358																																					p.H2155R		Atlas-SNP	.											.	DNAH12	182	.	0			c.A6464G						.						76	60	65					3																	57391435		692	1591	2283	SO:0001583	missense	201625	exon41			TTAAAATGGTCCT	U53532, AK126276	CCDS33771.1	3p21.1	2009-02-04	2006-09-04		ENSG00000174844	ENSG00000174844		"Axonemal dyneins"	2943	protein-coding gene	gene with protein product		603340	"dynein, axonemal, heavy polypeptide 12", "dynein heavy chain domain 2", "dynein heavy domain 2", "dynein, axonemal, heavy chain 12-like", "dynein, axonemal, heavy chain 7-like"	DNHD2, DNAH12L, DNAH7L		8812413, 8666668	Standard	NM_198564		Approved	DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290	uc003dit.2	Q6ZR08	OTTHUMG00000158598	ENST00000351747.2:c.6464A>G	chr3.hg19:g.57391435T>C	ENSP00000295937:p.His2155Arg	90.0	0.0		121.0	26.0	NM_178504	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Missense_Mutation	SNP	ENST00000351747.2	hg19		.	.	.	.	.	.	.	.	.	.	T	14.26	2.483586	0.44147	.	.	ENSG00000174844	ENST00000351747;ENST00000495027	T;T	0.23754	2.04;1.89	5.92	5.92	0.95590	.	.	.	.	.	T	0.31888	0.0811	M	0.71206	2.165	0.80722	D	1	B	0.24258	0.1	B	0.24006	0.05	T	0.05273	-1.0895	9	0.29301	T	0.29	.	16.3678	0.83341	0.0:0.0:0.0:1.0	.	2155	Q6ZR08	DYH12_HUMAN	R	2155;2174	ENSP00000295937:H2155R;ENSP00000418137:H2174R	ENSP00000295937:H2155R	H	-	2	0	DNAH12	57366475	1.000000	0.71417	0.999000	0.59377	0.489000	0.33432	7.896000	0.87350	2.254000	0.74563	0.528000	0.53228	CAT	.	.		0.358	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504		C	57391435	T	C	57391435	3	2	307	1	0	0	0	0	1	0	0	0	4602	1464	51	2	2890	2	DNAH12	3	57391435	Missense_Mutation	SNP	T	TCGA-HP-A5MZ-01A-21D-A27I-10	7541802	57391435	140630995	11	43874										
LRRC58	116064	hgsc.bcm.edu	37	chr3	120067725	120067725	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	ccgctgaggttgagcacctgGaggctgcggcagagcggcga	18	11	0	3			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr3:120067725G>T	ENST00000295628.3	-	1	461	c.366C>A	c.(364-366)ctC>ctA	p.L122L	RP11-174O3.3_ENST00000494869.1_RNA	NM_001099678.1	NP_001093148.1	Q96CX6	LRC58_HUMAN	leucine rich repeat containing 58	122										large_intestine(2)|lung(5)	7				GBM - Glioblastoma multiforme(114;0.147)		TGAGCACCTGGAGGCTGCGGC	0.701																																					p.L122L		Atlas-SNP	.											.	LRRC58	18	.	0			c.C366A						.						8	11	10					3																	120067725		1915	4114	6029	SO:0001819	synonymous_variant	116064	exon1			CACCTGGAGGCTG	BC013757	CCDS46892.1	3q13.33	2006-01-06			ENSG00000163428	ENSG00000163428			26968	protein-coding gene	gene with protein product							Standard	NM_001099678		Approved		uc003edr.2	Q96CX6	OTTHUMG00000159407	ENST00000295628.3:c.366C>A	chr3.hg19:g.120067725G>T		31.0	0.0		73.0	14.0	NM_001099678		Silent	SNP	ENST00000295628.3	hg19	CCDS46892.1																																																																																			.	.		0.701	LRRC58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355142.1	XM_057296		T	120067725	G	T	120067725	2	4	307	1	0	0	0	0	0	0	0	1	9023	1161	41	3		3	LRRC58	3	120067725	Silent	SNP	G	TCGA-HP-A5MZ-01A-21D-A27I-10	62676290	120067725	77954705	12	43875										
TIPARP	25976	hgsc.bcm.edu	37	chr3	156422743	156422766	+	In_Frame_Del	DEL	CAGTCATGGCATGAGAAGGCCCCC	CAGTCATGGCATGAGAAGGCCCCC	-													0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	acgggcagatacacaatgggCagtcatggcatgagaaggcc					rs267599664		TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	CAGTCATGGCATGAGAAGGCCCCC	CAGTCATGGCATGAGAAGGCCCCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr3:156422743_156422766delCAGTCATGGCATGAGAAGGCCCCC	ENST00000461166.1	+	6	2385_2408	c.1797_1820delCAGTCATGGCATGAGAAGGCCCCC	c.(1795-1821)ggcagtcatggcatgagaaggcccccg>ggg	p.SHGMRRPP600del	TIPARP_ENST00000295924.7_In_Frame_Del_p.SHGMRRPP600del|TIPARP_ENST00000486483.1_In_Frame_Del_p.SHGMRRPP600del|TIPARP_ENST00000542783.1_In_Frame_Del_p.SHGMRRPP600del	NM_001184717.1	NP_001171646.1	Q7Z3E1	PARPT_HUMAN	TCDD-inducible poly(ADP-ribose) polymerase	600	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				androgen metabolic process (GO:0008209)|cellular response to organic cyclic compound (GO:0071407)|estrogen metabolic process (GO:0008210)|face morphogenesis (GO:0060325)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|kidney development (GO:0001822)|multicellular organismal metabolic process (GO:0044236)|negative regulation of gene expression (GO:0010629)|nitrogen compound metabolic process (GO:0006807)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of protein catabolic process (GO:0045732)|post-embryonic development (GO:0009791)|protein ADP-ribosylation (GO:0006471)|skeletal system morphogenesis (GO:0048705)|smooth muscle tissue development (GO:0048745)|vasculogenesis (GO:0001570)	nucleus (GO:0005634)	enhancer binding (GO:0035326)|metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	23			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			ACACAATGGGCAGTCATGGCATGAGAAGGCCCCCGCCAGTCaat	0.455																																					p.599_607del	Ovarian(171;276 1987 3319 6837 11197)	Pindel	.											.	TIPARP	50	.	0			c.1796_1819del						.																																			SO:0001651	inframe_deletion	25976	exon6			.	BX537965	CCDS3177.1	3q25.31	2011-06-22			ENSG00000163659	ENSG00000163659		"Poly (ADP-ribose) polymerases"	23696	protein-coding gene	gene with protein product		612480				12851707	Standard	NM_001184717		Approved	DKFZP434J214, DKFZp686N0351, DDF1, PARP7, PARP-7, PARP-1, pART14, RM1	uc021xgg.1	Q7Z3E1	OTTHUMG00000158646	ENST00000461166.1:c.1797_1820delCAGTCATGGCATGAGAAGGCCCCC	chr3.hg19:g.156422743_156422766delCAGTCATGGCATGAGAAGGCCCCC	ENSP00000420612:p.Ser600_Pro607del	117.0	0.0		151.0	14.0	NM_001184717	D3DNK6|Q68CY9|Q86VP4|Q9Y4P7	In_Frame_Del	DEL	ENST00000461166.1	hg19	CCDS3177.1																																																																																			.	.		0.455	TIPARP-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351618.1	NM_015508		-	156422766	CAGTCATGGCATGAGAAGGCCCCC	-	156422743	7	5	307	1	0	1	0	1	0	0	0	0	15939	697	25	0	1815	0	TIPARP	3	156422743	In_Frame_Del	DEL	CAGTCATGGCATGAGAAGGCCCCC	TCGA-HP-A5MZ-01A-21D-A27I-10	36355018	156422743	41599687	13	43876										
DSPP	1834	hgsc.bcm.edu	37	chr4	88537069	88537070	+	In_Frame_Ins	INS	-	-	GATAGCAGC													0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	gtgatagcagtgaaagcagtINSgatagcagtgacagcagcaa							TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr4:88537069_88537070insGATAGCAGC	ENST00000282478.7	+	4	3288_3289	c.3255_3256insGATAGCAGC	c.(3256-3258)gat>GATAGCAGCgat	p.1086_1086D>DSSD	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_In_Frame_Ins_p.1086_1086D>DSSD			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1086	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			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)		gtgaaagcagtgatagcagtga	0.545																																					p.S1085delinsSDSS		Atlas-INDEL	.											.	DSPP	174	.	0			c.3255_3256insGATAGCAGC						.																																			SO:0001652	inframe_insertion	1834	exon5			.	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	Exception_encountered	chr4.hg19:g.88537069_88537070insGATAGCAGC	ENSP00000282478:p.SerSerAsp1089dup	128.0	0.0		144.0	78.0	NM_014208	A8MUI0|O95815	In_Frame_Ins	INS	ENST00000282478.7	hg19	CCDS43248.1																																																																																			.	.		0.545	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		GATAGCAGC	88537070	-	GATAGCAGC	88537069	7	5	307	1	0	1	1	0	0	0	0	0	4784	1693	59	0	3269	0	DSPP	4	88537069	In_Frame_Ins	INS	-	TCGA-HP-A5MZ-01A-21D-A27I-10		88537069	102617207	14	43877										
SLC10A7	84068	hgsc.bcm.edu	37	chr4	147179851	147179851	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	tctggggactcaccttctgcCttgataccatccaagacttg	8	13	3	2			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr4:147179851C>T	ENST00000507030.1	-	11	985	c.986G>A	c.(985-987)aGg>aAg	p.R329K	SLC10A7_ENST00000264986.3_3'UTR|SLC10A7_ENST00000335472.7_Missense_Mutation_p.R329K|SLC10A7_ENST00000432059.2_Missense_Mutation_p.R316K|SLC10A7_ENST00000394062.3_Missense_Mutation_p.R329K			Q0GE19	NTCP7_HUMAN	solute carrier family 10, member 7	329					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			endometrium(1)|kidney(3)|large_intestine(3)|lung(8)|skin(1)	16	all_hematologic(180;0.151)					CACCTTCTGCCTTGATACCAT	0.423																																					p.R329K		Atlas-SNP	.											.	SLC10A7	32	.	0			c.G986A						.						140	132	135					4																	147179851		2203	4300	6503	SO:0001583	missense	84068	exon11			TTCTGCCTTGATA	AY346324	CCDS3768.1, CCDS34073.1, CCDS75198.1	4q31.2	2013-07-18	2013-07-18	2006-12-19	ENSG00000120519	ENSG00000120519		"Solute carriers"	23088	protein-coding gene	gene with protein product		611459	"chromosome 4 open reading frame 13"	C4orf13		15932064	Standard	NM_032128		Approved	MGC25043, DKFZp566M114, DKFZp313H0531, DKFZp779O2438	uc003ikr.2	Q0GE19	OTTHUMG00000161437	ENST00000507030.1:c.986G>A	chr4.hg19:g.147179851C>T	ENSP00000421275:p.Arg329Lys	64.0	0.0		97.0	12.0	NM_001029998	A7E2E6|A7MAX9|Q0VAP9|Q45NG1|Q45NG2|Q5H9S6|Q6P4E6|Q8IZ62|Q8NBP8|Q9H0M9	Missense_Mutation	SNP	ENST00000507030.1	hg19	CCDS34073.1	.	.	.	.	.	.	.	.	.	.	C	17.25	3.340848	0.60963	.	.	ENSG00000120519	ENST00000432059;ENST00000335472;ENST00000507030;ENST00000394062	.	.	.	5.6	5.6	0.85130	.	0.044235	0.85682	D	0.000000	T	0.38108	0.1028	N	0.08118	0	0.80722	D	1	B;B;B	0.21071	0.022;0.013;0.051	B;B;B	0.18871	0.023;0.007;0.023	T	0.32561	-0.9902	9	0.07813	T	0.8	-15.5529	19.9855	0.97347	0.0:1.0:0.0:0.0	.	316;329;329	Q0GE19-3;Q0GE19;Q0GE19-2	.;NTCP7_HUMAN;.	K	316;329;329;329	.	ENSP00000334594:R329K	R	-	2	0	SLC10A7	147399301	1.000000	0.71417	0.984000	0.44739	0.927000	0.56198	2.309000	0.43699	2.806000	0.96561	0.655000	0.94253	AGG	.	.		0.423	SLC10A7-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000366932.1	NM_032128		T	147179851	C	T	147179851	3	4	307	1	0	0	0	0	1	0	0	0	14394	681	24	3	44	3	SLC10A7	4	147179851	Missense_Mutation	SNP	C	TCGA-HP-A5MZ-01A-21D-A27I-10	58642782	147179851	43974425	15	43878										
SLC22A5	6584	hgsc.bcm.edu	37	chr5	131721132	131721132	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	tttgcttacttcatccgagaCtggcggatgctgctggtggc	13	10	1	1			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr5:131721132C>G	ENST00000245407.3	+	4	986	c.765C>G	c.(763-765)gaC>gaG	p.D255E	SLC22A5_ENST00000435065.2_Missense_Mutation_p.D279E	NM_003060.3	NP_003051.1	O76082	S22A5_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 5	255					carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|positive regulation of intestinal epithelial structure maintenance (GO:0060731)|quaternary ammonium group transport (GO:0015697)|quorum sensing involved in interaction with host (GO:0052106)|sodium ion transport (GO:0006814)|sodium-dependent organic cation transport (GO:0070715)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antibiotic transporter activity (GO:0042895)|ATP binding (GO:0005524)|carnitine transmembrane transporter activity (GO:0015226)|drug transmembrane transporter activity (GO:0015238)|PDZ domain binding (GO:0030165)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|symporter activity (GO:0015293)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|stomach(1)	8		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Acetylcarnitine(DB08842)|Aminohippurate(DB00345)|Amphetamine(DB00182)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benzylpenicillin(DB01053)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefradine(DB01333)|Ceftazidime(DB00438)|Cephalexin(DB00567)|Cephaloglycin(DB00689)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Creatine(DB00148)|Cyclacillin(DB01000)|Dactinomycin(DB00970)|Desipramine(DB01151)|Diphenhydramine(DB01075)|Dopamine(DB00988)|Epinephrine(DB00668)|Furosemide(DB00695)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Ipratropium bromide(DB00332)|L-Arginine(DB00125)|L-Carnitine(DB00583)|Lidocaine(DB00281)|Lomefloxacin(DB00978)|Mepyramine(DB06691)|Methamphetamine(DB01577)|Niacin(DB00627)|Nicotine(DB00184)|Norepinephrine(DB00368)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Probenecid(DB01032)|Procainamide(DB01035)|Quinidine(DB00908)|Quinine(DB00468)|Sparfloxacin(DB01208)|Thiamine(DB00152)|Tiotropium(DB01409)|Valproic Acid(DB00313)|Verapamil(DB00661)	TCATCCGAGACTGGCGGATGC	0.532											OREG0016766	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D255E		Atlas-SNP	.											.	SLC22A5	34	.	0			c.C765G						.						129	118	121					5																	131721132		2203	4300	6503	SO:0001583	missense	6584	exon4			CCGAGACTGGCGG	AF057164	CCDS4154.1	5q23.3	2013-05-22	2008-01-11		ENSG00000197375	ENSG00000197375		"Solute carriers"	10969	protein-coding gene	gene with protein product		603377		CDSP		9618255, 9916797, 9685390	Standard	NM_003060		Approved	OCTN2, SCD	uc003kww.4	O76082	OTTHUMG00000059634	ENST00000245407.3:c.765C>G	chr5.hg19:g.131721132C>G	ENSP00000245407:p.Asp255Glu	151.0	0.0	1589	274.0	78.0	NM_003060	A2Q0V1|B2R844|D3DQ87|Q6ZQZ8|Q96EH6	Missense_Mutation	SNP	ENST00000245407.3	hg19	CCDS4154.1	.	.	.	.	.	.	.	.	.	.	C	16.19	3.053816	0.55218	.	.	ENSG00000197375	ENST00000245407;ENST00000435065;ENST00000415928	T;T;T	0.59364	0.27;0.27;0.27	5.9	3.95	0.45737	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.131317	0.64402	D	0.000002	T	0.52354	0.1729	L	0.54908	1.71	0.48830	D	0.999711	B;B	0.18610	0.023;0.029	B;B	0.27887	0.068;0.084	T	0.54221	-0.8326	10	0.54805	T	0.06	.	9.6	0.39598	0.1266:0.7369:0.0:0.1365	.	279;255	A2Q0V1;O76082	.;S22A5_HUMAN	E	255;279;178	ENSP00000245407:D255E;ENSP00000402760:D279E;ENSP00000388838:D178E	ENSP00000245407:D255E	D	+	3	2	SLC22A5	131749031	0.996000	0.38824	1.000000	0.80357	0.902000	0.53008	0.519000	0.22862	1.496000	0.48567	0.650000	0.86243	GAC	.	.		0.532	SLC22A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132631.1	NM_003060		G	131721132	C	G	131721132	3	3	307	1	0	0	0	0	1	0	0	0	14472	564	20	4	779	4	SLC22A5	5	131721132	Missense_Mutation	SNP	C	TCGA-HP-A5MZ-01A-21D-A27I-10		131721132	49194128	16	43879										
PCDHB4	56131	hgsc.bcm.edu	37	chr5	140503231	140503231	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	cgctggtgcgcgtgctggtgCtggacaccaacgacaactcg	14	13	0	0			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr5:140503231C>T	ENST00000194152.1	+	1	1651	c.1651C>T	c.(1651-1653)Ctg>Ttg	p.L551L	AC005754.8_ENST00000606030.1_lincRNA	NM_018938.2	NP_061761.1	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4	551	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|lung(35)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	67			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGTGCTGGTGCTGGACACCAA	0.701																																					p.L551L		Atlas-SNP	.											.	PCDHB4	177	.	0			c.C1651T						.						40	44	43					5																	140503231		2200	4294	6494	SO:0001819	synonymous_variant	56131	exon1			CTGGTGCTGGACA	AF152497	CCDS4246.1	5q31	2010-01-26			ENSG00000081818	ENSG00000081818		"Cadherins / Protocadherins : Clustered"	8689	other	protocadherin		606330				10380929	Standard	NM_018938		Approved	PCDH-BETA4	uc003lip.1	Q9Y5E5	OTTHUMG00000129617	ENST00000194152.1:c.1651C>T	chr5.hg19:g.140503231C>T		8.0	0.0		19.0	4.0	NM_018938	Q4V761	Silent	SNP	ENST00000194152.1	hg19	CCDS4246.1																																																																																			.	.		0.701	PCDHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251812.2	NM_018938		T	140503231	C	T	140503231	2	4	307	1	0	0	0	0	0	0	0	1	11553	796	28	3		3	PCDHB4	5	140503231	Silent	SNP	C	TCGA-HP-A5MZ-01A-21D-A27I-10	8782099	140503231	40412029	17	43880										
FLOT1	10211	hgsc.bcm.edu	37	chr6	30698721	30698721	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	tgcctcggctaggcgctccaGcttgtagcgctccgcttccg	12	16	0	0	rs576921685		TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr6:30698721G>C	ENST00000376389.3	-	9	1100	c.880C>G	c.(880-882)Ctg>Gtg	p.L294V	FLOT1_ENST00000456573.2_Missense_Mutation_p.L246V	NM_005803.2	NP_005794.1	P41440	S19A1_HUMAN	flotillin 1	0					folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|methotrexate transporter activity (GO:0015350)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|prostate(1)	13					Methotrexate(DB00563)|Pralatrexate(DB06813)	AGGCGCTCCAGCTTGTAGCGC	0.657																																					p.L294V		Atlas-SNP	.											.	FLOT1	28	.	0			c.C880G						.						49	52	51					6																	30698721		2196	4296	6492	SO:0001583	missense	10211	exon9			GCTCCAGCTTGTA	AF089750	CCDS4688.1	6p21.3	2010-02-17			ENSG00000137312	ENSG00000137312			3757	protein-coding gene	gene with protein product		606998					Standard	XM_005248780		Approved		uc003nrm.3	O75955	OTTHUMG00000031151	ENST00000376389.3:c.880C>G	chr6.hg19:g.30698721G>C	ENSP00000365569:p.Leu294Val	31.0	0.0		53.0	6.0	NM_005803	B2R7U8|B7Z8C3|E9PFY4|O00553|O60227|Q13026|Q9BTX8	Missense_Mutation	SNP	ENST00000376389.3	hg19	CCDS4688.1	.	.	.	.	.	.	.	.	.	.	G	6.247	0.413784	0.11812	.	.	ENSG00000137312	ENST00000376389;ENST00000456573;ENST00000413165	T;T	0.36340	1.26;1.36	4.67	3.79	0.43588	.	0.367801	0.25555	N	0.029879	T	0.11281	0.0275	N	0.20610	0.595	0.34549	D	0.711124	P;B	0.35600	0.511;0.36	B;B	0.39119	0.291;0.291	T	0.09729	-1.0661	10	0.17369	T	0.5	-0.595	10.9181	0.47148	0.0922:0.0:0.9078:0.0	.	246;294	B4DVY7;O75955	.;FLOT1_HUMAN	V	294;246;231	ENSP00000365569:L294V;ENSP00000394375:L246V	ENSP00000365569:L294V	L	-	1	2	FLOT1	30806700	0.995000	0.38212	0.952000	0.39060	0.823000	0.46562	1.053000	0.30442	1.339000	0.45563	0.650000	0.86243	CTG	.	.		0.657	FLOT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076276.2			C	30698721	G	C	30698721	3	2	307	1	0	0	0	0	1	0	0	0	5944	962	34	4	423	4	FLOT1	6	30698721	Missense_Mutation	SNP	G	TCGA-HP-A5MZ-01A-21D-A27I-10		30698721	140416346	18	43881										
CUL9	23113	hgsc.bcm.edu	37	chr6	43166474	43166474	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	ctgtgccgtgagggcagcccCggaggtgccgtgaggcccct	17	14	0	2			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr6:43166474C>A	ENST00000252050.4	+	12	3015	c.2931C>A	c.(2929-2931)ccC>ccA	p.P977P	CUL9_ENST00000372647.2_Silent_p.P977P|CUL9_ENST00000354495.3_Silent_p.P867P	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	977					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						AGGGCAGCCCCGGAGGTGCCG	0.642																																					p.P977P		Atlas-SNP	.											.	CUL9	248	.	0			c.C2931A						.						77	82	81					6																	43166474		2203	4300	6503	SO:0001819	synonymous_variant	23113	exon12			CAGCCCCGGAGGT	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"parkin-like cytoplasmic p53 binding protein", "p53-associated parkin-like cytoplasmic protein"	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.2931C>A	chr6.hg19:g.43166474C>A		42.0	0.0		72.0	12.0	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Silent	SNP	ENST00000252050.4	hg19	CCDS4890.1																																																																																			.	.		0.642	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		A	43166474	C	A	43166474	2	1	307	1	0	0	0	0	0	0	0	1	4063	639	23	1		1	CUL9	6	43166474	Silent	SNP	C	TCGA-HP-A5MZ-01A-21D-A27I-10	12467753	43166474	127948593	19	43882										
IMPG1	3617	hgsc.bcm.edu	37	chr6	76731919	76731919	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	agtgagagggaaaggcccaaGtgagacgttggcaacatctg	15	7	1	2			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr6:76731919G>T	ENST00000369950.3	-	6	769	c.580C>A	c.(580-582)Ctt>Att	p.L194I	IMPG1_ENST00000369963.3_3'UTR	NM_001282368.1|NM_001563.2	NP_001269297.1|NP_001554.2			interphotoreceptor matrix proteoglycan 1											breast(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(8)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	63		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				AAAGGCCCAAGTGAGACGTTG	0.378																																					p.L194I	Pancreas(37;839 1141 2599 26037)	Atlas-SNP	.											.	IMPG1	143	.	0			c.C580A						.						143	128	133					6																	76731919		2203	4300	6503	SO:0001583	missense	3617	exon6			GCCCAAGTGAGAC	AF017776	CCDS4985.1, CCDS75483.1	6q14.2-q15	2008-02-05	2004-05-25		ENSG00000112706	ENSG00000112706			6055	protein-coding gene	gene with protein product		602870	"sialoprotein associated with cones and rods"	SPACR			Standard	NM_001282368		Approved	IPM150, GP147	uc003pik.1	Q17R60	OTTHUMG00000015063	ENST00000369950.3:c.580C>A	chr6.hg19:g.76731919G>T	ENSP00000358966:p.Leu194Ile	63.0	0.0		65.0	12.0	NM_001563		Missense_Mutation	SNP	ENST00000369950.3	hg19	CCDS4985.1	.	.	.	.	.	.	.	.	.	.	G	3.488	-0.104447	0.06967	.	.	ENSG00000112706	ENST00000369950	T	0.20881	2.04	5.2	3.31	0.37934	.	0.616116	0.14303	N	0.328140	T	0.07638	0.0192	M	0.66939	2.045	0.09310	N	1	B	0.18461	0.028	B	0.19946	0.027	T	0.31806	-0.9930	10	0.17832	T	0.49	.	6.0581	0.19822	0.1707:0.1572:0.6721:0.0	.	194	Q17R60	IMPG1_HUMAN	I	194	ENSP00000358966:L194I	ENSP00000358966:L194I	L	-	1	0	IMPG1	76788639	0.002000	0.14202	0.020000	0.16555	0.007000	0.05969	0.323000	0.19593	1.178000	0.42870	-0.145000	0.13849	CTT	.	.		0.378	IMPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041288.1	NM_001563		T	76731919	G	T	76731919	3	4	307	1	0	0	0	0	1	0	0	0	7737	1029	36	3	1861	3	IMPG1	6	76731919	Missense_Mutation	SNP	G	TCGA-HP-A5MZ-01A-21D-A27I-10	33565445	76731919	94383148	20	43883										
C6orf170	221322	hgsc.bcm.edu	37	chr6	121563360	121563360	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	ttcatacctgtaatttttttGcatatcgattgaatataaat	4	5	1	1			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr6:121563360G>A	ENST00000398212.2	-	18	2193	c.2144C>T	c.(2143-2145)gCa>gTa	p.A715V	TBC1D32_ENST00000275159.6_Missense_Mutation_p.A715V	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	715					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)										TAATTTTTTTGCATATCGATT	0.343																																					p.A715V		Atlas-SNP	.											.	C6orf170	146	.	0			c.C2144T						.						93	86	88					6																	121563360		1827	4089	5916	SO:0001583	missense	221322	exon18			TTTTTTGCATATC	AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"broad-minded homolog"	615867	"chromosome 6 open reading frame 171", "chromosome 6 open reading frame 170"	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.2144C>T	chr6.hg19:g.121563360G>A	ENSP00000381270:p.Ala715Val	43.0	0.0		50.0	7.0	NM_152730	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Missense_Mutation	SNP	ENST00000398212.2	hg19	CCDS43501.1	.	.	.	.	.	.	.	.	.	.	G	14.99	2.699992	0.48307	.	.	ENSG00000146350	ENST00000275159;ENST00000398212	T;T	0.20069	2.1;2.1	5.0	5.0	0.66597	.	0.352762	0.28595	N	0.014787	T	0.33614	0.0869	M	0.62723	1.935	0.33657	D	0.609255	D;B	0.71674	0.998;0.08	D;B	0.80764	0.994;0.067	T	0.04607	-1.0939	10	0.30078	T	0.28	.	18.2399	0.89963	0.0:0.0:1.0:0.0	.	715;715	Q96NH3-4;Q96NH3	.;BROMI_HUMAN	V	715	ENSP00000275159:A715V;ENSP00000381270:A715V	ENSP00000275159:A715V	A	-	2	0	C6orf170	121605059	1.000000	0.71417	0.997000	0.53966	0.870000	0.49936	5.603000	0.67619	2.492000	0.84095	0.585000	0.79938	GCA	.	.		0.343	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730		A	121563360	G	A	121563360	3	1	307	1	0	0	0	0	1	0	0	0	2346	1319	46	3	1689	3	C6orf170	6	121563360	Missense_Mutation	SNP	G	TCGA-HP-A5MZ-01A-21D-A27I-10	44831441	121563360	49551707	21	43884										
LPA	4018	hgsc.bcm.edu	37	chr6	160966524	160966524	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	tttcttggattcattgtgtaGcaccagggaccattgatgtc	10	8	2	1			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr6:160966524G>A	ENST00000316300.5	-	33	5390	c.5346C>T	c.(5344-5346)tgC>tgT	p.C1782C	LPA_ENST00000447678.1_Silent_p.C1782C			P08519	APOA_HUMAN	lipoprotein, Lp(a)	4290	Kringle 16. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	TCATTGTGTAGCACCAGGGAC	0.448																																					p.C1782C		Atlas-SNP	.											.	LPA	237	.	0			c.C5346T						.						136	139	138					6																	160966524		2203	4300	6503	SO:0001819	synonymous_variant	4018	exon34			TGTGTAGCACCAG	X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.5346C>T	chr6.hg19:g.160966524G>A		107.0	0.0		133.0	6.0	NM_005577	Q5VTD7|Q9UD88	Silent	SNP	ENST00000316300.5	hg19	CCDS43523.1																																																																																			.	.		0.448	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577		A	160966524	G	A	160966524	2	1	307	1	0	0	0	0	0	0	0	1	8912	963	34	3		3	LPA	6	160966524	Silent	SNP	G	TCGA-HP-A5MZ-01A-21D-A27I-10	39403164	160966524	10148543	22	43885										
SDK1	221935	hgsc.bcm.edu	37	chr7	4277393	4277393	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	cgtcctgcacgggcagaataAgaagtataagaactgcagca	11	9	0	3			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr7:4277393A>G	ENST00000404826.2	+	42	6246	c.6107A>G	c.(6106-6108)aAg>aGg	p.K2036R	SDK1_ENST00000466611.1_3'UTR|SDK1_ENST00000389531.3_Missense_Mutation_p.K2016R	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	2036					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		GGGCAGAATAAGAAGTATAAG	0.567																																					p.K2036R		Atlas-SNP	.											.	SDK1	361	.	0			c.A6107G						.						139	128	132					7																	4277393		2203	4300	6503	SO:0001583	missense	221935	exon42			AGAATAAGAAGTA	AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19307	protein-coding gene	gene with protein product		607216	"sidekick homolog 1 (chicken)", "sidekick homolog 1, cell adhesion molecule (chicken)"			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.6107A>G	chr7.hg19:g.4277393A>G	ENSP00000385899:p.Lys2036Arg	205.0	0.0		287.0	51.0	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	hg19	CCDS34590.1	.	.	.	.	.	.	.	.	.	.	A	3.009	-0.204260	0.06180	.	.	ENSG00000146555	ENST00000404826;ENST00000446104;ENST00000389531	T;T	0.62105	0.05;0.06	5.27	1.39	0.22231	.	0.072732	0.52532	N	0.000065	T	0.45637	0.1352	L	0.38649	1.16	0.23542	N	0.997453	B;B;B;B	0.20052	0.041;0.003;0.011;0.002	B;B;B;B	0.23419	0.046;0.012;0.033;0.002	T	0.28038	-1.0056	10	0.12103	T	0.63	.	8.9492	0.35779	0.7743:0.0:0.2257:0.0	.	2016;96;523;2036	F8W6X9;Q7Z5N4-2;F2Z3E9;Q7Z5N4	.;.;.;SDK1_HUMAN	R	2036;284;2016	ENSP00000385899:K2036R;ENSP00000374182:K2016R	ENSP00000374182:K2016R	K	+	2	0	SDK1	4243919	0.998000	0.40836	0.008000	0.14137	0.743000	0.42351	2.149000	0.42244	-0.004000	0.14419	0.496000	0.49642	AAG	.	.		0.567	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744		G	4277393	A	G	4277393	3	3	307	1	0	0	0	0	1	0	0	0	13983	72	3	2	6273	2	SDK1	7	4277393	Missense_Mutation	SNP	A	TCGA-HP-A5MZ-01A-21D-A27I-10		4277393	154861270	23	43886										
VWC2	375567	hgsc.bcm.edu	37	chr7	49951654	49951654	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	aaactgctttgcagaaaccgCggtgatccctgctggcagag	12	11	0	3			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr7:49951654C>T	ENST00000340652.4	+	4	1407	c.851C>T	c.(850-852)gCg>gTg	p.A284V	ZPBP_ENST00000491129.1_Intron	NM_198570.3	NP_940972.2	Q2TAL6	VWC2_HUMAN	von Willebrand factor C domain containing 2	284					negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of neuron differentiation (GO:0045666)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|basement membrane (GO:0005604)|cell junction (GO:0030054)|extracellular space (GO:0005615)|interstitial matrix (GO:0005614)|synapse (GO:0045202)				cervix(1)|endometrium(2)|large_intestine(1)|lung(3)|prostate(1)	8						GCAGAAACCGCGGTGATCCCT	0.418																																					p.A284V		Atlas-SNP	.											.	VWC2	30	.	0			c.C851T						.						92	82	86					7																	49951654		2203	4300	6503	SO:0001583	missense	375567	exon4			AAACCGCGGTGAT	AY358393	CCDS5508.1	7p12.3-p12.2	2007-07-19			ENSG00000188730	ENSG00000188730			30200	protein-coding gene	gene with protein product	"brorin", "brain-specific chordin-like"	611108				17400546	Standard	NM_198570		Approved	PSST739, UNQ739	uc003tot.1	Q2TAL6	OTTHUMG00000129265	ENST00000340652.4:c.851C>T	chr7.hg19:g.49951654C>T	ENSP00000341819:p.Ala284Val	141.0	0.0		143.0	22.0	NM_198570	Q6UXE2	Missense_Mutation	SNP	ENST00000340652.4	hg19	CCDS5508.1	.	.	.	.	.	.	.	.	.	.	C	14.34	2.506945	0.44558	.	.	ENSG00000188730	ENST00000340652	T	0.13538	2.58	5.82	5.82	0.92795	.	0.298945	0.26711	N	0.022886	T	0.06917	0.0176	N	0.08118	0	0.45554	D	0.998505	B	0.27351	0.176	B	0.15484	0.013	T	0.40308	-0.9570	10	0.29301	T	0.29	.	11.3891	0.49804	0.0:0.8609:0.0:0.1391	.	284	Q2TAL6	VWC2_HUMAN	V	284	ENSP00000341819:A284V	ENSP00000341819:A284V	A	+	2	0	VWC2	49922200	0.210000	0.23517	0.898000	0.35279	0.907000	0.53573	2.647000	0.46639	2.751000	0.94390	0.650000	0.86243	GCG	.	.		0.418	VWC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251375.2	NM_198570		T	49951654	C	T	49951654	3	4	307	1	0	0	0	0	1	0	0	0	17258	768	27	1	861	1	VWC2	7	49951654	Missense_Mutation	SNP	C	TCGA-HP-A5MZ-01A-21D-A27I-10	45674261	49951654	109187009	24	43887										
MPDZ	8777	hgsc.bcm.edu	37	chr9	13126733	13126733	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	atgatgactccactgagtgtAtcttcttcgctgatagcaat	8	9	2	4			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr9:13126733A>G	ENST00000319217.7	-	33	4750	c.4503T>C	c.(4501-4503)gaT>gaC	p.D1501D	MPDZ_ENST00000381015.4_Silent_p.D1501D|MPDZ_ENST00000447879.1_Silent_p.D1468D|MPDZ_ENST00000541718.1_Silent_p.D1501D|MPDZ_ENST00000538841.1_Silent_p.D360D|MPDZ_ENST00000546205.1_Silent_p.D1515D|MPDZ_ENST00000541093.1_5'UTR|MPDZ_ENST00000381022.2_Silent_p.D1501D|MPDZ_ENST00000536827.1_Silent_p.D1468D	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	1501	PDZ 9. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		CACTGAGTGTATCTTCTTCGC	0.413																																					p.D1501D		Atlas-SNP	.											.	MPDZ	324	.	0			c.T4503C						.						115	110	111					9																	13126733		1896	4124	6020	SO:0001819	synonymous_variant	8777	exon33			GAGTGTATCTTCT	AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.4503T>C	chr9.hg19:g.13126733A>G		91.0	0.0		152.0	26.0	NM_003829	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Silent	SNP	ENST00000319217.7	hg19																																																																																				.	.		0.413	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829		G	13126733	A	G	13126733	2	3	307	1	0	0	0	0	0	0	0	1	9731	446	16	2		2	MPDZ	9	13126733	Silent	SNP	A	TCGA-HP-A5MZ-01A-21D-A27I-10		13126733	128086698	25	43888										
ATRNL1	26033	hgsc.bcm.edu	37	chr10	117486766	117486766	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	aaccccctccagcaactgctTcgagaacgacagcagatggc	9	15	0	2			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr10:117486766T>C	ENST00000355044.3	+	27	3930	c.3804T>C	c.(3802-3804)ctT>ctC	p.L1268L	ATRNL1_ENST00000303745.7_Silent_p.L61L|ATRNL1_ENST00000423111.2_Silent_p.L319L	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	1268					G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(11)|liver(2)|lung(44)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		AGCAACTGCTTCGAGAACGAC	0.433																																					p.L1268L		Atlas-SNP	.											.	ATRNL1	219	.	0			c.T3804C						.						47	45	46					10																	117486766		2203	4300	6503	SO:0001819	synonymous_variant	26033	exon27			ACTGCTTCGAGAA	AB011106	CCDS7592.1, CCDS73204.1	10q26	2004-03-04			ENSG00000107518	ENSG00000107518			29063	protein-coding gene	gene with protein product		612869				9628581	Standard	NM_001276282		Approved	KIAA0534, FLJ45344, ALP	uc001lcg.3	Q5VV63	OTTHUMG00000019096	ENST00000355044.3:c.3804T>C	chr10.hg19:g.117486766T>C		20.0	0.0		37.0	10.0	NM_207303	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Silent	SNP	ENST00000355044.3	hg19	CCDS7592.1																																																																																			.	.		0.433	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349		C	117486766	T	C	117486766	2	2	307	1	0	0	0	0	0	0	0	1	1207	1770	62	2		2	ATRNL1	10	117486766	Silent	SNP	T	TCGA-HP-A5MZ-01A-21D-A27I-10		117486766	18047981	26	43889										
DMBT1	1755	hgsc.bcm.edu	37	chr10	124335946	124335946	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	ggtttggccctgaggctggtGaatggagatggcaggtgtca	18	6	1	3			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr10:124335946G>A	ENST00000338354.3	+	7	421	c.315G>A	c.(313-315)gtG>gtA	p.V105V	DMBT1_ENST00000330163.4_Silent_p.V105V|DMBT1_ENST00000368956.2_Silent_p.V105V|DMBT1_ENST00000368909.3_Silent_p.V105V|DMBT1_ENST00000359586.6_Silent_p.V105V|DMBT1_ENST00000368955.3_Silent_p.V105V|DMBT1_ENST00000344338.3_Silent_p.V105V			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	105	SRCR 1. {ECO:0000255|PROSITE- ProRule:PRU00196}.				defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				TGAGGCTGGTGAATGGAGATG	0.567																																					p.V105V	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											.	DMBT1	677	.	0			c.G315A						.						134	137	136					10																	124335946		2030	4224	6254	SO:0001819	synonymous_variant	1755	exon7			GCTGGTGAATGGA		CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.315G>A	chr10.hg19:g.124335946G>A		70.0	0.0		120.0	22.0	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Silent	SNP	ENST00000338354.3	hg19																																																																																				.	.		0.567	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406		A	124335946	G	A	124335946	2	1	307	1	0	0	0	0	0	0	0	1	4579	1277	45	3		3	DMBT1	10	124335946	Silent	SNP	G	TCGA-HP-A5MZ-01A-21D-A27I-10	6849180	124335946	11198801	27	43890										
DPYSL4	10570	hgsc.bcm.edu	37	chr10	134015481	134015481	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	gatggacgagaatgagttcgTcgcggtgaccagtacaaatg	14	7	0	3			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr10:134015481T>G	ENST00000338492.4	+	11	1306	c.1142T>G	c.(1141-1143)gTc>gGc	p.V381G	DPYSL4_ENST00000368627.1_Missense_Mutation_p.V281G|DPYSL4_ENST00000368629.1_Missense_Mutation_p.V281G	NM_006426.2	NP_006417.2	O14531	DPYL4_HUMAN	dihydropyrimidinase-like 4	381					axon guidance (GO:0007411)|nervous system development (GO:0007399)|pyrimidine nucleobase catabolic process (GO:0006208)	cytosol (GO:0005829)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		all_cancers(35;4.33e-08)|all_epithelial(44;6.75e-06)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)|Colorectal(31;0.19)		OV - Ovarian serous cystadenocarcinoma(35;7.21e-05)|Epithelial(32;8.01e-05)|all cancers(32;9.29e-05)|BRCA - Breast invasive adenocarcinoma(275;0.206)		AATGAGTTCGTCGCGGTGACC	0.577																																					p.V381G		Atlas-SNP	.											.	DPYSL4	91	.	0			c.T1142G						.						97	94	95					10																	134015481		2203	4300	6503	SO:0001583	missense	10570	exon11			AGTTCGTCGCGGT	AB006713	CCDS7665.1	10q25.2-q26	2008-05-14			ENSG00000151640	ENSG00000151640			3016	protein-coding gene	gene with protein product		608407				8973361, 9652388	Standard	NM_006426		Approved	ULIP4, DRP-4	uc009ybb.3	O14531	OTTHUMG00000019283	ENST00000338492.4:c.1142T>G	chr10.hg19:g.134015481T>G	ENSP00000339850:p.Val381Gly	87.0	0.0		120.0	11.0	NM_006426	B2RMQ1|D3DRG5|O00240|Q5T0Q7	Missense_Mutation	SNP	ENST00000338492.4	hg19	CCDS7665.1	.	.	.	.	.	.	.	.	.	.	T	13.83	2.354506	0.41700	.	.	ENSG00000151640	ENST00000338492;ENST00000368629;ENST00000368627	D;D;D	0.91351	-2.83;-2.83;-2.83	4.48	4.48	0.54585	Amidohydrolase 1 (1);Metal-dependent hydrolase, composite domain (1);	0.066345	0.64402	D	0.000014	D	0.93083	0.7798	H	0.94385	3.53	0.80722	D	1	B	0.25105	0.118	B	0.26693	0.072	D	0.93042	0.6458	10	0.87932	D	0	-11.8436	13.9972	0.64409	0.0:0.0:0.0:1.0	.	381	O14531	DPYL4_HUMAN	G	381;281;281	ENSP00000339850:V381G;ENSP00000357618:V281G;ENSP00000357616:V281G	ENSP00000339850:V381G	V	+	2	0	DPYSL4	133865471	1.000000	0.71417	0.724000	0.30704	0.364000	0.29643	7.454000	0.80714	1.879000	0.54435	0.529000	0.55759	GTC	.	.		0.577	DPYSL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051050.2			G	134015481	T	G	134015481	3	3	307	1	0	0	0	0	1	0	0	0	4751	1667	58	5	1184	5	DPYSL4	10	134015481	Missense_Mutation	SNP	T	TCGA-HP-A5MZ-01A-21D-A27I-10	9679535	134015481	1519266	28	43891										
AHNAK	79026	hgsc.bcm.edu	37	chr11	62286109	62286109	+	Frame_Shift_Del	DEL	G	G	-													0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	ctcaagtctccttcaagagaGggtagctgggcatggacctc							TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr11:62286109delG	ENST00000378024.4	-	5	16054	c.15780delC	c.(15778-15780)cccfs	p.P5260fs	AHNAK_ENST00000525875.1_5'Flank|AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	5260					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				CTTCAAGAGAGGGTAGCTGGG	0.522																																					p.S5261fs		Atlas-Indel,Pindel	.											.	AHNAK	532	.	0			c.15781delT						.						94	91	92					11																	62286109		2202	4299	6501	SO:0001589	frameshift_variant	79026	exon5			.	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.15780delC	chr11.hg19:g.62286109delG	ENSP00000367263:p.Pro5260fs	101.0	0.0		87.0	12.0	NM_001620	A1A586	Frame_Shift_Del	DEL	ENST00000378024.4	hg19	CCDS31584.1																																																																																			.	.		0.522	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		-	62286109	G	-	62286109	7	5	307	1	0	1	0	1	0	0	0	0	414	987	35	0	2012	0	AHNAK	11	62286109	Frame_Shift_Del	DEL	G	TCGA-HP-A5MZ-01A-21D-A27I-10		62286109	72720407	29	43892										
GDPD5	81544	hgsc.bcm.edu	37	chr11	75150967	75150967	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	gatgagggtgaaggagaccaGgtcggcagtgacccacatga	16	8	0	5			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr11:75150967G>A	ENST00000336898.3	-	15	2350	c.1513C>T	c.(1513-1515)Ctg>Ttg	p.L505L	GDPD5_ENST00000529721.1_Silent_p.L505L|GDPD5_ENST00000526177.1_Silent_p.L367L|GDPD5_ENST00000376282.3_Silent_p.L386L|GDPD5_ENST00000533784.1_Silent_p.L386L|GDPD5_ENST00000443276.2_3'UTR|GDPD5_ENST00000533805.1_Silent_p.L260L	NM_030792.6	NP_110419.5	Q8WTR4	GDPD5_HUMAN	glycerophosphodiester phosphodiesterase domain containing 5	505					cerebral cortex neuron differentiation (GO:0021895)|glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)|negative regulation of Notch signaling pathway (GO:0045746)|neuron projection development (GO:0031175)|positive regulation of neuron differentiation (GO:0045666)|regulation of timing of cell differentiation (GO:0048505)|spinal cord motor neuron differentiation (GO:0021522)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(3)|skin(2)	20						AAGGAGACCAGGTCGGCAGTG	0.622																																					p.L505L		Atlas-SNP	.											.	GDPD5	49	.	0			c.C1513T						.						127	103	111					11																	75150967		2200	4293	6493	SO:0001819	synonymous_variant	81544	exon15			AGACCAGGTCGGC	AF318377	CCDS8238.1	11q13.4-q13.5	2011-01-25				ENSG00000158555			28804	protein-coding gene	gene with protein product		609632				18667693, 17275818	Standard	NM_030792		Approved	PP1665, GDE2	uc001owp.4	Q8WTR4		ENST00000336898.3:c.1513C>T	chr11.hg19:g.75150967G>A		107.0	0.0		163.0	27.0	NM_030792	Q49AQ5|Q6UX76|Q7Z4S0|Q8N781|Q8NCB7|Q8TB77	Silent	SNP	ENST00000336898.3	hg19	CCDS8238.1																																																																																			.	.		0.622	GDPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384409.1	NM_030792		A	75150967	G	A	75150967	2	1	307	1	0	0	0	0	0	0	0	1	6335	991	35	3		3	GDPD5	11	75150967	Silent	SNP	G	TCGA-HP-A5MZ-01A-21D-A27I-10	12864858	75150967	59855549	30	43893										
THRSP	7069	hgsc.bcm.edu	37	chr11	77774945	77774946	+	Missense_Mutation	DNP	GC	GC	AG													0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	accatgcaggtgctaaccaaGcgttaccccaagaactgcct							TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr11:77774945_77774946GC>AG	ENST00000281030.2	+	1	39_40	c.18_19GC>AG	c.(16-21)aaGCgt>aaAGgt	p.R7G	NDUFC2-KCTD14_ENST00000530054.1_Intron|NDUFC2-KCTD14_ENST00000528251.1_Intron	NM_003251.3	NP_003242.1	Q92748	THRSP_HUMAN	thyroid hormone responsive	7					lipid metabolic process (GO:0006629)|regulation of lipid biosynthetic process (GO:0046890)|regulation of transcription, DNA-templated (GO:0006355)|regulation of triglyceride biosynthetic process (GO:0010866)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)		p.R7C(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	7	all_cancers(14;2.23e-19)|all_epithelial(13;7.49e-22)|Breast(9;6.38e-17)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;2.15e-25)			TGCTAACCAAGCGTTACCCCAA	0.569																																					p.K6K|p.R7G		Atlas-SNP	.											.|THRSP,colon,carcinoma,-1,1	THRSP	18	.	1	Substitution - Missense(1)	breast(1)	c.G18A|c.C19G						.																																			SO:0001583	missense	7069	exon1			AACCAAGCGTTAC|ACCAAGCGTTACC	Y08409	CCDS8256.1	11q14.1	2012-06-19	2010-06-25		ENSG00000151365	ENSG00000151365			11800	protein-coding gene	gene with protein product	"SPOT14 homolog (rat)"	601926	"thyroid hormone responsive SPOT14 (rat) homolog", "lipogenic protein 1"	LPGP1		9003802	Standard	NM_003251		Approved	SPOT14, Lpgp, S14, THRP	uc001oyx.3	Q92748	OTTHUMG00000166632	Exception_encountered	chr11.hg19:g.77774945_77774946delinsAG	ENSP00000281030:p.Arg7Gly	89.0	0.0		111.0|112.0	15.0	NM_003251	B2R4W7	Silent|Missense_Mutation	SNP	ENST00000281030.2	hg19	CCDS8256.1																																																																																			.	.		0.569	THRSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390939.1	NM_003251		AG	77774946	GC	AG	77774945	3	1	307	1	0	0	0	0	1	0	0	0	15891	962	34	3	20	3	THRSP	11	77774945	Missense_Mutation	DNP	GC	TCGA-HP-A5MZ-01A-21D-A27I-10	2623978	77774945	57231571	31	43894										
CDON	50937	hgsc.bcm.edu	37	chr11	125885319	125885319	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	ccaggtacagttgggggctgGgttcccatgaacgtcgcagg	16	10	0	1			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr11:125885319G>A	ENST00000392693.3	-	7	1142	c.1015C>T	c.(1015-1017)Cca>Tca	p.P339S	CDON_ENST00000263577.7_Missense_Mutation_p.P339S	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	339	Ig-like C2-type 4.				anterior/posterior pattern specification (GO:0009952)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cerebral cortex development (GO:0021987)|embryonic body morphogenesis (GO:0010172)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|lens development in camera-type eye (GO:0002088)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein heterodimerization activity (GO:0043497)|skeletal muscle satellite cell differentiation (GO:0014816)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(9)|ovary(3)|prostate(2)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	61	all_hematologic(175;0.177)	Breast(109;0.00157)|Lung NSC(97;0.0127)|all_lung(97;0.0133)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.51e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0604)		TTGGGGGCTGGGTTCCCATGA	0.463																																					p.P339S		Atlas-SNP	.											.	CDON	137	.	0			c.C1015T						.						100	84	89					11																	125885319		2201	4299	6500	SO:0001583	missense	50937	exon7			GGGCTGGGTTCCC	AF004841	CCDS8468.1, CCDS58192.1	11q24.2	2013-02-11	2012-12-07		ENSG00000064309	ENSG00000064309		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	17104	protein-coding gene	gene with protein product	"cell adhesion molecule-related/down-regulated by oncogenes"	608707	"Cdon homolog (mouse)"			9214393	Standard	NM_016952		Approved	ORCAM, CDO, CDON1	uc009zbw.3	Q4KMG0	OTTHUMG00000165862	ENST00000392693.3:c.1015C>T	chr11.hg19:g.125885319G>A	ENSP00000376458:p.Pro339Ser	164.0	0.0		272.0	48.0	NM_016952	O14631	Missense_Mutation	SNP	ENST00000392693.3	hg19	CCDS58192.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.08|16.08	3.021587|3.021587	0.54576|0.54576	.|.	.|.	ENSG00000064309|ENSG00000064309	ENST00000534661|ENST00000392693;ENST00000263577	.|T;T	.|0.73897	.|-0.79;-0.79	5.58|5.58	4.67|4.67	0.58626|0.58626	.|Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000|0.000000	0.49305|0.49305	D|D	0.000147|0.000147	D|D	0.89602|0.89602	0.6762|0.6762	H|H	0.94183|0.94183	3.505|3.505	0.45899|0.45899	D|D	0.998747|0.998747	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|1.0;1.0	D|D	0.92328|0.92328	0.5871|0.5871	6|10	.|0.87932	.|D	.|0	-11.4224|-11.4224	14.4906|14.4906	0.67647|0.67647	0.0707:0.0:0.9293:0.0|0.0707:0.0:0.9293:0.0	.|.	.|339;339	.|Q4KMG0;Q4KMG0-2	.|CDON_HUMAN;.	L|S	314|339	.|ENSP00000376458:P339S;ENSP00000263577:P339S	.|ENSP00000263577:P339S	P|P	-|-	2|1	0|0	CDON|CDON	125390529|125390529	1.000000|1.000000	0.71417|0.71417	0.985000|0.985000	0.45067|0.45067	0.144000|0.144000	0.21451|0.21451	7.203000|7.203000	0.77864|0.77864	1.363000|1.363000	0.46019|0.46019	-0.258000|-0.258000	0.10820|0.10820	CCC|CCA	.	.		0.463	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952		A	125885319	G	A	125885319	3	1	307	1	0	0	0	0	1	0	0	0	3172	1232	43	3	2835	3	CDON	11	125885319	Missense_Mutation	SNP	G	TCGA-HP-A5MZ-01A-21D-A27I-10	48110374	125885319	9121197	32	43895										
ITPR2	3709	hgsc.bcm.edu	37	chr12	26816709	26816709	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	gtgcatatctttgatcccccAgatcttcaagtctcagcatc	6	13	4	2			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr12:26816709A>C	ENST00000381340.3	-	15	2038	c.1622T>G	c.(1621-1623)cTg>cGg	p.L541R		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	541					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	TTGATCCCCCAGATCTTCAAG	0.468																																					p.L541R		Atlas-SNP	.											.	ITPR2	270	.	0			c.T1622G						.						264	261	262					12																	26816709		1882	4119	6001	SO:0001583	missense	3709	exon15			TCCCCCAGATCTT	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"Ion channels / Inositol triphosphate receptors"	6181	protein-coding gene	gene with protein product	"cilia and flagella associated protein 48"	600144	"inositol 1,4,5-triphosphate receptor, type 2"			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.1622T>G	chr12.hg19:g.26816709A>C	ENSP00000370744:p.Leu541Arg	58.0	0.0		94.0	13.0	NM_002223	O94773	Missense_Mutation	SNP	ENST00000381340.3	hg19	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.455523	0.84209	.	.	ENSG00000123104	ENST00000381340	D	0.91124	-2.79	4.7	4.7	0.59300	Intracellular calcium-release channel (1);	0.075309	0.56097	D	0.000034	D	0.96015	0.8702	M	0.91196	3.185	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	D	0.96784	0.9577	10	0.66056	D	0.02	.	14.6573	0.68844	1.0:0.0:0.0:0.0	.	541	Q14571	ITPR2_HUMAN	R	541	ENSP00000370744:L541R	ENSP00000370744:L541R	L	-	2	0	ITPR2	26707976	1.000000	0.71417	0.935000	0.37517	0.961000	0.63080	9.123000	0.94387	2.099000	0.63709	0.533000	0.62120	CTG	.	.		0.468	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		C	26816709	A	C	26816709	3	2	307	1	0	0	0	0	1	0	0	0	7930	188	7	5	6655	5	ITPR2	12	26816709	Missense_Mutation	SNP	A	TCGA-HP-A5MZ-01A-21D-A27I-10		26816709	107035186	33	43896										
ATP5B	506	hgsc.bcm.edu	37	chr12	57037684	57037684	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	cttgataccagtcaccagaaTttcctgctcaacactcattt	4	13	3	2			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr12:57037684T>C	ENST00000262030.3	-	4	594	c.544A>G	c.(544-546)Att>Gtt	p.I182V	ATP5B_ENST00000552919.1_Missense_Mutation_p.I182V|SNORD59A_ENST00000384304.1_RNA|ATP5B_ENST00000550162.1_5'Flank	NM_001686.3	NP_001677.2	P06576	ATPB_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide	182					angiogenesis (GO:0001525)|ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|ATP hydrolysis coupled proton transport (GO:0015991)|cellular metabolic process (GO:0044237)|generation of precursor metabolites and energy (GO:0006091)|lipid metabolic process (GO:0006629)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|osteoblast differentiation (GO:0001649)|proton transport (GO:0015992)|regulation of intracellular pH (GO:0051453)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial nucleoid (GO:0042645)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase, catalytic core (GO:0005754)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|MHC class I protein binding (GO:0042288)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transmembrane transporter activity (GO:0022857)|transporter activity (GO:0005215)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GTCACCAGAATTTCCTGCTCA	0.423																																					p.I182V		Atlas-SNP	.											.	ATP5B	48	.	0			c.A544G						.						127	107	114					12																	57037684		2203	4300	6503	SO:0001583	missense	506	exon4			CCAGAATTTCCTG	M27132	CCDS8924.1	12p13.3	2012-10-12			ENSG00000110955	ENSG00000110955	3.6.3.14	"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	830	protein-coding gene	gene with protein product		102910		ATPSB		2687158	Standard	NM_001686		Approved		uc001slr.3	P06576	OTTHUMG00000170291	ENST00000262030.3:c.544A>G	chr12.hg19:g.57037684T>C	ENSP00000262030:p.Ile182Val	131.0	0.0		179.0	33.0	NM_001686	A8K4X0|Q14283	Missense_Mutation	SNP	ENST00000262030.3	hg19	CCDS8924.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.73|16.73	3.202852|3.202852	0.58234|0.58234	.|.	.|.	ENSG00000110955|ENSG00000110955	ENST00000262030;ENST00000552919;ENST00000551020|ENST00000552959	T;T;T|.	0.81330|.	-1.48;-1.48;-1.48|.	5.56|5.56	5.56|5.56	0.83823|0.83823	.|.	0.047019|.	0.85682|.	D|.	0.000000|.	T|T	0.72145|0.72145	0.3424|0.3424	M|M	0.66939|0.66939	2.045|2.045	0.80722|0.80722	D|D	1|1	B|.	0.06786|.	0.001|.	B|.	0.06405|.	0.002|.	T|T	0.71988|0.71988	-0.4426|-0.4426	10|5	0.35671|.	T|.	0.21|.	-9.2759|-9.2759	14.7018|14.7018	0.69162|0.69162	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	182|.	P06576|.	ATPB_HUMAN|.	V|S	182;182;121|118	ENSP00000262030:I182V;ENSP00000450297:I182V;ENSP00000446677:I121V|.	ENSP00000262030:I182V|.	I|N	-|-	1|2	0|0	ATP5B|ATP5B	55323951|55323951	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.975000|0.975000	0.68041|0.68041	7.314000|7.314000	0.78988|0.78988	2.123000|2.123000	0.65237|0.65237	0.260000|0.260000	0.18958|0.18958	ATT|AAT	.	.		0.423	ATP5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408380.1	NM_001686		C	57037684	T	C	57037684	3	2	307	1	0	0	0	0	1	0	0	0	1148	1493	52	2	1073	2	ATP5B	12	57037684	Missense_Mutation	SNP	T	TCGA-HP-A5MZ-01A-21D-A27I-10	30220975	57037684	76814211	34	43897										
TPH2	121278	hgsc.bcm.edu	37	chr12	72416191	72416191	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	ttcttcagtgctatttcttcAcaatcgagtttggcctttgc	7	10	4	0			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr12:72416191A>T	ENST00000333850.3	+	9	1222	c.1081A>T	c.(1081-1083)Aca>Tca	p.T361S		NM_173353.3	NP_775489.2	Q8IWU9	TPH2_HUMAN	tryptophan hydroxylase 2	361					aromatic amino acid family metabolic process (GO:0009072)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to lithium ion (GO:0071285)|circadian rhythm (GO:0007623)|indolalkylamine biosynthetic process (GO:0046219)|response to activity (GO:0014823)|response to calcium ion (GO:0051592)|response to estrogen (GO:0043627)|response to glucocorticoid (GO:0051384)|response to nutrient levels (GO:0031667)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|neuron projection (GO:0043005)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|tryptophan 5-monooxygenase activity (GO:0004510)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	41					L-Tryptophan(DB00150)	CTATTTCTTCACAATCGAGTT	0.423																																					p.T361S		Atlas-SNP	.											.	TPH2	81	.	0			c.A1081T						.						117	106	110					12																	72416191		2203	4300	6503	SO:0001583	missense	121278	exon9			TTCTTCACAATCG	AY098914	CCDS31859.1	12q15	2008-02-07				ENSG00000139287	1.14.16.4		20692	protein-coding gene	gene with protein product		607478				12511643	Standard	NM_173353		Approved	NTPH, FLJ37295	uc009zrw.1	Q8IWU9		ENST00000333850.3:c.1081A>T	chr12.hg19:g.72416191A>T	ENSP00000329093:p.Thr361Ser	67.0	0.0		58.0	8.0	NM_173353	A6NGA4|Q14CB0	Missense_Mutation	SNP	ENST00000333850.3	hg19	CCDS31859.1	.	.	.	.	.	.	.	.	.	.	A	26.9	4.783657	0.90282	.	.	ENSG00000139287	ENST00000333850	D	0.99820	-6.93	5.98	5.98	0.97165	Aromatic amino acid hydroxylase, C-terminal (3);	0.150965	0.64402	N	0.000014	D	0.99429	0.9798	M	0.67569	2.06	0.80722	D	1	P	0.39094	0.659	B	0.39971	0.315	D	0.99113	1.0847	10	0.59425	D	0.04	-18.4464	16.4696	0.84102	1.0:0.0:0.0:0.0	.	361	Q8IWU9	TPH2_HUMAN	S	361	ENSP00000329093:T361S	ENSP00000329093:T361S	T	+	1	0	TPH2	70702458	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.339000	0.96797	2.289000	0.77006	0.482000	0.46254	ACA	.	.		0.423	TPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405234.1	NM_173353		T	72416191	A	T	72416191	3	4	307	1	0	0	0	0	1	0	0	0	16417	159	6	4	1115	4	TPH2	12	72416191	Missense_Mutation	SNP	A	TCGA-HP-A5MZ-01A-21D-A27I-10	15378507	72416191	61435704	35	43898										
SPATA13	221178	hgsc.bcm.edu	37	chr13	24861041	24861041	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	ccaacgtcatccgggagatcAtggacaccgagcgggtgtac	13	12	2	1			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr13:24861041A>G	ENST00000382095.4	+	6	1152	c.745A>G	c.(745-747)Atg>Gtg	p.M249V	SPATA13_ENST00000382108.3_Missense_Mutation_p.M874V|SPATA13_ENST00000343003.6_Missense_Mutation_p.M193V|SPATA13_ENST00000409126.1_Intron|SPATA13_ENST00000424834.2_Missense_Mutation_p.M874V|RP11-307N16.6_ENST00000382141.4_Missense_Mutation_p.M752V|SPATA13_ENST00000399949.2_Missense_Mutation_p.M171V	NM_153023.2	NP_694568.1	Q96N96	SPT13_HUMAN	spermatogenesis associated 13	249	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				cell migration (GO:0016477)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell migration (GO:0030334)	cytoplasm (GO:0005737)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			breast(4)|endometrium(2)|large_intestine(9)|lung(4)|ovary(1)|prostate(1)|skin(2)	23		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)		CCGGGAGATCATGGACACCGA	0.607																																					p.M874V		Atlas-SNP	.											.	SPATA13	92	.	0			c.A2620G						.						117	100	106					13																	24861041		2203	4300	6503	SO:0001583	missense	221178	exon7			GAGATCATGGACA	AK055770	CCDS9305.1, CCDS53857.1, CCDS66517.1, CCDS66518.1, CCDS73553.1	13q12.13	2013-01-10			ENSG00000182957	ENSG00000182957		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	23222	protein-coding gene	gene with protein product		613324					Standard	NM_001286795		Approved	FLJ31208, ARHGEF29	uc021rhg.1	Q96N96	OTTHUMG00000016578	ENST00000382095.4:c.745A>G	chr13.hg19:g.24861041A>G	ENSP00000371527:p.Met249Val	112.0	0.0		140.0	27.0	NM_001166271	A2VEA9|A6NF85|B4DQB1|B4DSZ0|B4DVM8|J3KPJ7|J3KQH2|Q5VX68|Q6ZML1|Q8N873|Q8TEK6	Missense_Mutation	SNP	ENST00000382095.4	hg19	CCDS9305.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.39|13.39	2.222784|2.222784	0.39300|0.39300	.|.	.|.	ENSG00000182957|ENSG00000182957	ENST00000424834|ENST00000382108;ENST00000382095;ENST00000438694;ENST00000399949;ENST00000343003	.|T;T;T;T	.|0.60424	.|0.19;0.19;0.19;0.19	4.96|4.96	3.78|3.78	0.43462|0.43462	.|Src homology-3 domain (1);Dbl homology (DH) domain (5);	.|0.038199	.|0.85682	.|D	.|0.000000	T|T	0.27524|0.27524	0.0676|0.0676	N|N	0.01438|0.01438	-0.865|-0.865	0.51482|0.51482	D|D	0.999923|0.999923	.|B;B;B;B	.|0.15141	.|0.0;0.012;0.0;0.0	.|B;B;B;B	.|0.15484	.|0.004;0.012;0.004;0.013	T|T	0.10474|0.10474	-1.0628|-1.0628	5|10	.|0.35671	.|T	.|0.21	.|.	9.5763|9.5763	0.39459|0.39459	0.9165:0.0:0.0835:0.0|0.9165:0.0:0.0835:0.0	.|.	.|193;195;171;249	.|Q96N96-3;Q96N96-4;Q96N96-2;Q96N96	.|.;.;.;SPT13_HUMAN	R|V	911|874;249;195;171;193	.|ENSP00000371542:M874V;ENSP00000371527:M249V;ENSP00000382830:M171V;ENSP00000343631:M193V	.|ENSP00000343631:M193V	H|M	+|+	2|1	0|0	SPATA13|SPATA13	23759041|23759041	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.818000|0.818000	0.46254|0.46254	4.179000|4.179000	0.58290|0.58290	1.985000|1.985000	0.57927|0.57927	0.459000|0.459000	0.35465|0.35465	CAT|ATG	.	.		0.607	SPATA13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044180.2	NM_153023		G	24861041	A	G	24861041	3	3	307	1	0	0	0	0	1	0	0	0	15015	217	8	2	2642	2	SPATA13	13	24861041	Missense_Mutation	SNP	A	TCGA-HP-A5MZ-01A-21D-A27I-10		24861041	90308837	36	43899										
NUBPL	80224	hgsc.bcm.edu	37	chr14	32257020	32257020	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	actggactacttagttgtagAcatgccaccaggaactggag	11	9	0	1			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr14:32257020A>G	ENST00000281081.7	+	7	593	c.548A>G	c.(547-549)gAc>gGc	p.D183G	NUBPL_ENST00000418681.2_3'UTR|NUBPL_ENST00000536705.1_Missense_Mutation_p.D87G	NM_001201573.1|NM_001201574.1|NM_025152.2	NP_001188502.1|NP_001188503.1|NP_079428.2	Q8TB37	NUBPL_HUMAN	nucleotide binding protein-like	183					mitochondrial respiratory chain complex I assembly (GO:0032981)|mitochondrion morphogenesis (GO:0070584)	mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			endometrium(1)|lung(2)|prostate(1)|skin(1)	5	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.214)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0677)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0102)		TTAGTTGTAGACATGCCACCA	0.313																																					p.D183G		Atlas-SNP	.											.	NUBPL	21	.	0			c.A548G						.						97	89	92					14																	32257020		1867	4097	5964	SO:0001583	missense	80224	exon7			TTGTAGACATGCC	AK022722	CCDS41940.1	14q12	2012-10-12	2005-01-07	2005-01-07	ENSG00000151413	ENSG00000151413		"Mitochondrial respiratory chain complex assembly factors"	20278	protein-coding gene	gene with protein product	"iron-sulfur protein required for NADH dehydrogenase"	613621	"chromosome 14 open reading frame 127"	C14orf127			Standard	NM_025152		Approved	FLJ12660, IND1, huInd1	uc001wrk.4	Q8TB37	OTTHUMG00000170521	ENST00000281081.7:c.548A>G	chr14.hg19:g.32257020A>G	ENSP00000281081:p.Asp183Gly	50.0	0.0		75.0	13.0	NM_025152	B4DHZ1|Q86TZ4|Q9H9M2	Missense_Mutation	SNP	ENST00000281081.7	hg19	CCDS41940.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.422610	0.83559	.	.	ENSG00000151413	ENST00000281081;ENST00000551314;ENST00000536705	T;D;T	0.81821	-1.41;-1.54;-1.41	5.86	5.86	0.93980	Mrp, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.94574	0.8252	H	0.99746	4.745	0.58432	D	0.999999	D;D	0.89917	0.999;1.0	D;D	0.83275	0.996;0.992	D	0.96700	0.9517	10	0.87932	D	0	-31.2323	14.2085	0.65750	1.0:0.0:0.0:0.0	.	87;183	B4DWB0;Q8TB37	.;NUBPL_HUMAN	G	183;131;87	ENSP00000281081:D183G;ENSP00000447234:D131G;ENSP00000439286:D87G	ENSP00000281081:D183G	D	+	2	0	NUBPL	31326771	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.472000	0.80996	2.235000	0.73313	0.533000	0.62120	GAC	.	.		0.313	NUBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409519.1	NM_025152		G	32257020	A	G	32257020	3	3	307	1	0	0	0	0	1	0	0	0	10726	275	10	2	574	2	NUBPL	14	32257020	Missense_Mutation	SNP	A	TCGA-HP-A5MZ-01A-21D-A27I-10		32257020	75092520	37	43900										
EXOC5	10640	hgsc.bcm.edu	37	chr14	57698355	57698355	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	aaataggaaatgaaaatggaTttgataagcttagacaagaa	9	2	0	4			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr14:57698355T>C	ENST00000413566.2	-	11	1376	c.1017A>G	c.(1015-1017)aaA>aaG	p.K339K	EXOC5_ENST00000340918.7_Silent_p.K274K	NM_006544.3	NP_006535.1	O00471	EXOC5_HUMAN	exocyst complex component 5	339					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|vesicle docking (GO:0048278)	cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(3)|endometrium(1)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	22						TGAAAATGGATTTGATAAGCT	0.363																																					p.K339K		Atlas-SNP	.											.	EXOC5	45	.	0			c.A1017G						.						71	67	69					14																	57698355		1829	4077	5906	SO:0001819	synonymous_variant	10640	exon11			AATGGATTTGATA	U85946	CCDS45111.1	14q22.3	2013-01-22	2005-11-01	2005-11-01	ENSG00000070367	ENSG00000070367			10696	protein-coding gene	gene with protein product		604469	"SEC10 (S. cerevisiae)-like 1", "SEC10-like 1 (S. cerevisiae)"	SEC10L1		9119050	Standard	XM_005267272		Approved	SEC10, SEC10P	uc001xct.3	O00471	OTTHUMG00000171309	ENST00000413566.2:c.1017A>G	chr14.hg19:g.57698355T>C		72.0	0.0		93.0	8.0	NM_006544	B2R6C5	Silent	SNP	ENST00000413566.2	hg19	CCDS45111.1																																																																																			.	.		0.363	EXOC5-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412905.1	NM_006544		C	57698355	T	C	57698355	2	2	307	1	0	0	0	0	0	0	0	1	5309	1490	52	2		2	EXOC5	14	57698355	Silent	SNP	T	TCGA-HP-A5MZ-01A-21D-A27I-10	25441335	57698355	49651185	38	43901										
KIF26A	26153	hgsc.bcm.edu	37	chr14	104644901	104644901	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	ttccaggtctgcagcggcggCgcctgattcccgccccactg	12	17	1	1	rs375944046		TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr14:104644901C>T	ENST00000423312.2	+	13	5125	c.5125C>T	c.(5125-5127)Cgc>Tgc	p.R1709C	KIF26A_ENST00000315264.7_Missense_Mutation_p.R1570C	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	1709					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|enteric nervous system development (GO:0048484)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of signal transduction (GO:0009968)|regulation of cell growth by extracellular stimulus (GO:0001560)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	21		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767)	Epithelial(46;0.152)	Epithelial(152;0.161)		GCAGCGGCGGCGCCTGATTCC	0.756													C|||	1	0.000199681	0	0	5008	,	,		11748	0		0	False		,,,				2504	0.001				p.R1709C		Atlas-SNP	.											.	KIF26A	84	.	0			c.C5125T						.	C	CYS/ARG	0,3446		0,0,1723	4	5	4		5125	1.9	1	14		4	1,7591		0,1,3795	no	missense	KIF26A	NM_015656.1	180	0,1,5518	TT,TC,CC		0.0132,0.0,0.0091	probably-damaging	1709/1883	104644901	1,11037	1723	3796	5519	SO:0001583	missense	26153	exon13			CGGCGGCGCCTGA	AB033062	CCDS45171.1	14q32.33	2009-03-19			ENSG00000066735	ENSG00000066735		"Kinesins"	20226	protein-coding gene	gene with protein product		613231				10574462, 11416179	Standard	NM_015656		Approved	KIAA1236, DKFZP434N178	uc001yos.4	Q9ULI4	OTTHUMG00000154986	ENST00000423312.2:c.5125C>T	chr14.hg19:g.104644901C>T	ENSP00000388241:p.Arg1709Cys	3.0	0.0		8.0	6.0	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Missense_Mutation	SNP	ENST00000423312.2	hg19	CCDS45171.1	.	.	.	.	.	.	.	.	.	.	C	12.15	1.850260	0.32699	0.0	1.32E-4	ENSG00000066735	ENST00000423312;ENST00000315264	D;D	0.89270	-2.49;-2.49	4.02	1.91	0.25777	.	.	.	.	.	D	0.93390	0.7892	M	0.82323	2.585	0.50039	D	0.99984	D	0.89917	1.0	D	0.67231	0.95	D	0.93059	0.6472	9	0.87932	D	0	.	11.4699	0.50261	0.5384:0.4616:0.0:0.0	.	1709	Q9ULI4	KI26A_HUMAN	C	1709;1570	ENSP00000388241:R1709C;ENSP00000325452:R1570C	ENSP00000325452:R1570C	R	+	1	0	KIF26A	103714654	0.382000	0.25148	0.976000	0.42696	0.076000	0.17211	0.974000	0.29436	0.616000	0.30141	0.462000	0.41574	CGC	.	.		0.756	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1			T	104644901	C	T	104644901	3	4	307	1	0	0	0	0	1	0	0	0	8303	768	27	1	5175	1	KIF26A	14	104644901	Missense_Mutation	SNP	C	TCGA-HP-A5MZ-01A-21D-A27I-10	46946546	104644901	2704639	39	43902										
GJD2	57369	hgsc.bcm.edu	37	chr15	35044889	35044889	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	gcaaacatgaacactagaaaGacagtcttctcagttggccg	9	10	2	3			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr15:35044889G>A	ENST00000290374.4	-	2	1232	c.756C>T	c.(754-756)gtC>gtT	p.V252V	RP11-814P5.1_ENST00000503496.1_RNA|RP11-814P5.1_ENST00000558707.1_RNA	NM_020660.2	NP_065711.1	Q9UKL4	CXD2_HUMAN	gap junction protein, delta 2, 36kDa	252					action potential (GO:0001508)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|urinary_tract(1)	19		all_lung(180;9.67e-07)		all cancers(64;2.75e-18)|GBM - Glioblastoma multiforme(113;1.9e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0156)		ACACTAGAAAGACAGTCTTCT	0.507																																					p.V252V		Atlas-SNP	.											.	GJD2	49	.	0			c.C756T						.						151	118	129					15																	35044889		2201	4298	6499	SO:0001819	synonymous_variant	57369	exon2			TAGAAAGACAGTC	AB037509	CCDS10040.1	15q13.1	2008-02-04	2007-11-06	2007-11-06	ENSG00000159248	ENSG00000159248		"Ion channels / Gap junction proteins (connexins)"	19154	protein-coding gene	gene with protein product	"connexin 36"	607058	"gap junction protein, alpha 9, 36kDa"	GJA9		10462698	Standard	NM_020660		Approved	CX36	uc001zis.2	Q9UKL4	OTTHUMG00000129674	ENST00000290374.4:c.756C>T	chr15.hg19:g.35044889G>A		213.0	0.0		276.0	37.0	NM_020660	Q2M241|Q9P2R0	Silent	SNP	ENST00000290374.4	hg19	CCDS10040.1																																																																																			.	.		0.507	GJD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251875.2			A	35044889	G	A	35044889	2	1	307	1	0	0	0	0	0	0	0	1	6425	929	33	3		3	GJD2	15	35044889	Silent	SNP	G	TCGA-HP-A5MZ-01A-21D-A27I-10		35044889	67486503	40	43903										
CEP152	22995	hgsc.bcm.edu	37	chr15	49054803	49054803	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	taaggtcttctttttcattgCctttatagtttgatccagct	6	8	3	1			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr15:49054803C>T	ENST00000380950.2	-	18	2534	c.2347G>A	c.(2347-2349)Gca>Aca	p.A783T	CEP152_ENST00000325747.5_Missense_Mutation_p.A690T|CEP152_ENST00000399334.3_Missense_Mutation_p.A783T	NM_001194998.1|NM_014985.3	NP_001181927.1|NP_055800.2	O94986	CE152_HUMAN	centrosomal protein 152kDa	783					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)			breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		TTTTTCATTGCCTTTATAGTT	0.373																																					p.A783T		Atlas-SNP	.											.	CEP152	145	.	0			c.G2347A						.						108	102	104					15																	49054803		1851	4093	5944	SO:0001583	missense	22995	exon18			TCATTGCCTTTAT	AB020719	CCDS42033.1, CCDS58361.1	15q21.1	2014-02-20							29298	protein-coding gene	gene with protein product	"asterless"	613529	"microcephaly, primary autosomal recessive 4"	MCPH4		14654843, 21131973	Standard	NM_014985		Approved	KIAA0912, SCKL5	uc001zwz.3	O94986		ENST00000380950.2:c.2347G>A	chr15.hg19:g.49054803C>T	ENSP00000370337:p.Ala783Thr	58.0	0.0		78.0	9.0	NM_014985	E7ER66|Q17RV1|Q6NTA0	Missense_Mutation	SNP	ENST00000380950.2	hg19	CCDS58361.1	.	.	.	.	.	.	.	.	.	.	C	10.36	1.327365	0.24080	.	.	ENSG00000103995	ENST00000380950;ENST00000325747;ENST00000399334	T;T;T	0.53640	0.61;0.63;0.62	4.93	4.01	0.46588	.	0.656922	0.15090	N	0.281144	T	0.35682	0.0940	L	0.38838	1.175	0.33487	D	0.588207	B;B;B	0.22909	0.01;0.077;0.005	B;B;B	0.23275	0.007;0.045;0.006	T	0.40251	-0.9573	10	0.13470	T	0.59	-2.8577	11.5024	0.50446	0.0:0.9161:0.0:0.0839	.	690;783;783	O94986-1;E7ER66;O94986	.;.;CE152_HUMAN	T	783;690;783	ENSP00000370337:A783T;ENSP00000321000:A690T;ENSP00000382271:A783T	ENSP00000321000:A690T	A	-	1	0	CEP152	46842095	0.889000	0.30405	0.160000	0.22671	0.907000	0.53573	2.409000	0.44583	1.435000	0.47434	0.655000	0.94253	GCA	.	.		0.373	CEP152-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417365.1	NM_014985		T	49054803	C	T	49054803	3	4	307	1	0	0	0	0	1	0	0	0	3250	739	26	3	2653	3	CEP152	15	49054803	Missense_Mutation	SNP	C	TCGA-HP-A5MZ-01A-21D-A27I-10	14009914	49054803	53476589	41	43904										
KRT33A	3883	hgsc.bcm.edu	37	chr17	39502874	39502874	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	gcacctgggacagctgggagCtgtagcgggcctcgctctct	15	13	1	0	rs371555388		TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr17:39502874C>T	ENST00000007735.3	-	6	967	c.923G>A	c.(922-924)aGc>aAc	p.S308N		NM_004138.3	NP_004129.2	O76009	KT33A_HUMAN	keratin 33A	308	Coil 2.|Rod.					extracellular space (GO:0005615)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	21		Breast(137;0.000496)				CAGCTGGGAGCTGTAGCGGGC	0.587																																					p.S308N		Atlas-SNP	.											.	KRT33A	53	.	0			c.G923A						.	C	ASN/SER	0,4406		0,0,2203	60	59	60		923	4.6	1	17		60	1,8599	1.2+/-3.3	0,1,4299	no	missense	KRT33A	NM_004138.2	46	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	308/405	39502874	1,13005	2203	4300	6503	SO:0001583	missense	3883	exon6			TGGGAGCTGTAGC	Y16788	CCDS11388.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000006059	ENSG00000006059		"-", "Intermediate filaments type I, keratins (acidic)"	6450	protein-coding gene	gene with protein product	"hard keratin type I 3I"	602761	"keratin, hair, acidic, 3A"	KRTHA3A		7565656, 16831889	Standard	NM_004138		Approved	Ha-3I, Krt1-3	uc002hwk.2	O76009	OTTHUMG00000133432	ENST00000007735.3:c.923G>A	chr17.hg19:g.39502874C>T	ENSP00000007735:p.Ser308Asn	61.0	0.0		87.0	23.0	NM_004138	B2RA87|Q6NTB9|Q6ZZB9	Missense_Mutation	SNP	ENST00000007735.3	hg19	CCDS11388.1	.	.	.	.	.	.	.	.	.	.	C	18.14	3.557484	0.65425	0.0	1.16E-4	ENSG00000006059	ENST00000007735	D	0.89050	-2.46	4.55	4.55	0.56014	Filament (1);	0.000000	0.85682	D	0.000000	D	0.91095	0.7197	L	0.48986	1.54	0.35220	D	0.775908	P	0.45212	0.853	P	0.54590	0.756	D	0.94197	0.7446	10	0.59425	D	0.04	.	16.8343	0.85953	0.0:1.0:0.0:0.0	.	308	O76009	KT33A_HUMAN	N	308	ENSP00000007735:S308N	ENSP00000007735:S308N	S	-	2	0	KRT33A	36756400	0.000000	0.05858	1.000000	0.80357	0.982000	0.71751	0.305000	0.19254	2.501000	0.84356	0.655000	0.94253	AGC	.	.		0.587	KRT33A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257295.1	NM_004138		T	39502874	C	T	39502874	3	4	307	1	0	0	0	0	1	0	0	0	8478	797	28	3	299	3	KRT33A	17	39502874	Missense_Mutation	SNP	C	TCGA-HP-A5MZ-01A-21D-A27I-10		39502874	41692336	42	43905										
KRT36	8689	hgsc.bcm.edu	37	chr17	39643887	39643887	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	ctccaccagggcctcgtactGgcatctcatatcctccagga	8	16	1	0			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr17:39643887G>A	ENST00000328119.6	-	4	801	c.802C>T	c.(802-804)Cag>Tag	p.Q268*	KRT36_ENST00000393986.2_Nonsense_Mutation_p.Q218*	NM_003771.4	NP_003762.1	O76013	KRT36_HUMAN	keratin 36	268	Coil 2.|Rod.				regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural constituent of epidermis (GO:0030280)			breast(2)|cervix(1)|kidney(2)|large_intestine(3)|lung(8)|skin(1)	17		Breast(137;0.000286)				GCCTCGTACTGGCATCTCATA	0.602																																					p.Q268X		Atlas-SNP	.											.	KRT36	52	.	0			c.C802T						.						131	116	121					17																	39643887		2203	4300	6503	SO:0001587	stop_gained	8689	exon4			CGTACTGGCATCT	Y16792	CCDS11395.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000126337	ENSG00000126337		"-", "Intermediate filaments type I, keratins (acidic)"	6454	protein-coding gene	gene with protein product		604540	"keratin, hair, acidic, 6"	KRTHA6		9756910, 16831889	Standard	XM_005257762		Approved		uc002hwt.3	O76013	OTTHUMG00000133431	ENST00000328119.6:c.802C>T	chr17.hg19:g.39643887G>A	ENSP00000329165:p.Gln268*	137.0	0.0		209.0	27.0	NM_003771	Q86XG4	Nonsense_Mutation	SNP	ENST00000328119.6	hg19	CCDS11395.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.922657	0.92319	.	.	ENSG00000126337	ENST00000393986;ENST00000328119	.	.	.	5.83	5.83	0.93111	.	0.000000	0.47852	D	0.000206	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	16.5841	0.84723	0.0:0.1386:0.8614:0.0	.	.	.	.	X	218;268	.	ENSP00000329165:Q268X	Q	-	1	0	KRT36	36897413	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	3.761000	0.55242	2.769000	0.95229	0.655000	0.94253	CAG	.	.		0.602	KRT36-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259508.1	NM_003771		A	39643887	G	A	39643887	4	1	307	1	0	0	0	0	0	1	0	0	8482	1357	47	3	617	3	KRT36	17	39643887	Nonsense_Mutation	SNP	G	TCGA-HP-A5MZ-01A-21D-A27I-10	141013	39643887	41551323	43	43906										
FECH	2235	hgsc.bcm.edu	37	chr18	55226447	55226447	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	tctcaagtggaaaatggtccAgttcctttagaatatgatct	8	7	2	2			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr18:55226447A>T	ENST00000262093.5	-	7	885	c.734T>A	c.(733-735)cTg>cAg	p.L245Q	FECH_ENST00000382873.3_Missense_Mutation_p.L251Q	NM_000140.3|NM_001012515.2	NP_000131.2|NP_001012533.1	P22830	HEMH_HUMAN	ferrochelatase	245					cellular response to dexamethasone stimulus (GO:0071549)|cholesterol metabolic process (GO:0008203)|detection of UV (GO:0009589)|erythrocyte differentiation (GO:0030218)|generation of precursor metabolites and energy (GO:0006091)|heme biosynthetic process (GO:0006783)|iron ion homeostasis (GO:0055072)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX metabolic process (GO:0046501)|regulation of eIF2 alpha phosphorylation by heme (GO:0010999)|regulation of gene expression (GO:0010468)|regulation of hemoglobin biosynthetic process (GO:0046984)|response to arsenic-containing substance (GO:0046685)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to insecticide (GO:0017085)|response to lead ion (GO:0010288)|response to light stimulus (GO:0009416)|response to methylmercury (GO:0051597)|response to platinum ion (GO:0070541)|small molecule metabolic process (GO:0044281)|very-low-density lipoprotein particle assembly (GO:0034379)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)	2 iron, 2 sulfur cluster binding (GO:0051537)|ferrochelatase activity (GO:0004325)|ferrous iron binding (GO:0008198)|heme binding (GO:0020037)|iron-responsive element binding (GO:0030350)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	15		Colorectal(73;0.227)				AAAATGGTCCAGTTCCTTTAG	0.393																																					p.L251Q		Atlas-SNP	.											.	FECH	42	.	0			c.T752A	GRCh37	CM042047	FECH	M		.						108	99	102					18																	55226447		2203	4300	6503	SO:0001583	missense	2235	exon7			TGGTCCAGTTCCT	D00726	CCDS11964.1, CCDS32836.1	18q21.2-q21.3	2010-05-11	2010-05-11		ENSG00000066926	ENSG00000066926	4.99.1.1		3647	protein-coding gene	gene with protein product	"protoporphyria"	612386	"ferrochelatase (protoporphyria)"			1838349	Standard	NM_001012515		Approved		uc002lgp.4	P22830	OTTHUMG00000132740	ENST00000262093.5:c.734T>A	chr18.hg19:g.55226447A>T	ENSP00000262093:p.Leu245Gln	49.0	0.0		62.0	11.0	NM_001012515	A8KA72|Q8IXN1|Q8NAN0	Missense_Mutation	SNP	ENST00000262093.5	hg19	CCDS11964.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.382203	0.82792	.	.	ENSG00000066926	ENST00000262093;ENST00000382873	D;D	0.97772	-4.53;-4.53	4.97	4.97	0.65823	.	0.000000	0.85682	D	0.000000	D	0.99152	0.9707	H	0.97077	3.935	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	D	0.99078	1.0836	10	0.87932	D	0	-13.2122	14.6203	0.68579	1.0:0.0:0.0:0.0	.	245;251	P22830;P22830-2	HEMH_HUMAN;.	Q	245;251	ENSP00000262093:L245Q;ENSP00000372326:L251Q	ENSP00000262093:L245Q	L	-	2	0	FECH	53377445	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	8.463000	0.90377	1.993000	0.58246	0.459000	0.35465	CTG	.	.		0.393	FECH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256098.1			T	55226447	A	T	55226447	3	4	307	1	0	0	0	0	1	0	0	0	5816	188	7	4	557	4	FECH	18	55226447	Missense_Mutation	SNP	A	TCGA-HP-A5MZ-01A-21D-A27I-10		55226447	22850801	44	43907										
CIRBP	1153	hgsc.bcm.edu	37	chr19	1271998	1271998	+	Frame_Shift_Del	DEL	C	C	-													0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	agccggagtcagagtggtggCtacagtgaccggagctcggg							TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr19:1271998delC	ENST00000588030.1	+	6	710	c.450delC	c.(448-450)ggcfs	p.G150fs	CIRBP_ENST00000588090.1_Frame_Shift_Del_p.G150fs|CIRBP_ENST00000589660.1_Frame_Shift_Del_p.G150fs|CIRBP_ENST00000589235.1_Frame_Shift_Del_p.G150fs|CIRBP_ENST00000587896.1_Frame_Shift_Del_p.G150fs|CIRBP_ENST00000591935.1_Frame_Shift_Del_p.G150fs|CIRBP-AS1_ENST00000600215.1_RNA|CIRBP_ENST00000586472.1_Frame_Shift_Del_p.G150fs|CIRBP-AS1_ENST00000585832.1_RNA|CIRBP_ENST00000586773.1_Frame_Shift_Del_p.G150fs|CIRBP_ENST00000589710.1_Frame_Shift_Del_p.G150fs|CIRBP_ENST00000444172.2_Frame_Shift_Del_p.G97fs|CIRBP_ENST00000413636.2_Frame_Shift_Del_p.G116fs|CIRBP_ENST00000320936.5_Frame_Shift_Del_p.G150fs|CIRBP_ENST00000589686.1_Frame_Shift_Del_p.G150fs|CIRBP_ENST00000588230.1_Frame_Shift_Del_p.G150fs|CIRBP_ENST00000585630.1_Frame_Shift_Del_p.G150fs|CIRBP_ENST00000587323.1_Frame_Shift_Del_p.G150fs			Q14011	CIRBP_HUMAN	cold inducible RNA binding protein	150	Gly-rich.				mRNA stabilization (GO:0048255)|positive regulation of translation (GO:0045727)|response to cold (GO:0009409)|response to UV (GO:0009411)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|small ribosomal subunit rRNA binding (GO:0070181)|translation repressor activity (GO:0030371)			endometrium(1)|large_intestine(1)|lung(3)	5		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000332)|all_lung(49;0.000498)|Breast(49;0.0014)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AGAGTGGTGGCTACAGTGACC	0.612																																					p.G150fs		Atlas-Indel,Pindel	.											.	CIRBP	19	.	0			c.449delG						.						123	105	111					19																	1271998		2203	4300	6503	SO:0001589	frameshift_variant	1153	exon6			.	D78134	CCDS12059.1, CCDS74244.1, CCDS74245.1	19p13.3	2013-02-12	2001-11-28		ENSG00000099622	ENSG00000099622		"RNA binding motif (RRM) containing"	1982	protein-coding gene	gene with protein product	"Cold-inducible RNA-binding protein", "glycine-rich RNA binding protein"	602649	"cold inducible RNA-binding protein"			9434172, 9151692	Standard	NM_001280		Approved	CIRP	uc002lrr.4	Q14011		ENST00000588030.1:c.450delC	chr19.hg19:g.1271998delC	ENSP00000468788:p.Gly150fs	388.0	0.0		449.0	86.0	NM_001280	B3KT17|B4E2X2	Frame_Shift_Del	DEL	ENST00000588030.1	hg19	CCDS12059.1																																																																																			.	.		0.612	CIRBP-011	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449969.1	NM_001280		-	1271998	C	-	1271998	7	5	307	1	0	1	0	1	0	0	0	0	3435	784	28	0	468	0	CIRBP	19	1271998	Frame_Shift_Del	DEL	C	TCGA-HP-A5MZ-01A-21D-A27I-10		1271998	57856985	45	43908										
TUBB4	10382	hgsc.bcm.edu	37	chr19	6495513	6495513	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	gctgctgttcttgctctgcaCgctcagcatctgctcgtcca	9	15	4	0			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr19:6495513C>T	ENST00000264071.2	-	4	1368	c.997G>A	c.(997-999)Gtg>Atg	p.V333M	CTD-2396E7.9_ENST00000599292.1_RNA|TUBB4A_ENST00000540257.1_Missense_Mutation_p.V333M|CTD-2396E7.10_ENST00000596027.1_RNA			P04350	TBB4A_HUMAN	tubulin, beta 4A class IVa	333					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|internode region of axon (GO:0033269)|microtubule (GO:0005874)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)										TTGCTCTGCACGCTCAGCATC	0.672																																					p.V333M		Atlas-SNP	.											.	.	.	.	0			c.G997A						.						174	139	151					19																	6495513		2203	4300	6503	SO:0001583	missense	10382	exon4			TCTGCACGCTCAG	AK075307	CCDS12168.1	19p13.3	2014-02-05	2011-10-11	2011-10-10	ENSG00000104833	ENSG00000104833		"Tubulins"	20774	protein-coding gene	gene with protein product	"class IVa beta-tubulin"	602662	"tubulin, beta 4", "tubulin, beta 4 class IVa", "dystonia 4, torsion (autosomal dominant)"	TUBB4, DYT4		6865944, 6462917, 23595291	Standard	NM_001289123		Approved	beta-5	uc002mfg.1	P04350		ENST00000264071.2:c.997G>A	chr19.hg19:g.6495513C>T	ENSP00000264071:p.Val333Met	61.0	0.0		76.0	8.0	NM_006087	B3KQP4|Q969E5	Missense_Mutation	SNP	ENST00000264071.2	hg19	CCDS12168.1	.	.	.	.	.	.	.	.	.	.	C	14.58	2.577392	0.45902	.	.	ENSG00000104833	ENST00000264071;ENST00000540257;ENST00000412858	D;D	0.83075	-1.68;-1.68	3.43	3.43	0.39272	.	0.000000	0.64402	U	0.000014	D	0.85452	0.5700	L	0.39085	1.19	0.51482	D	0.999924	D	0.53885	0.963	D	0.64595	0.927	D	0.87123	0.2192	10	0.87932	D	0	.	13.6752	0.62449	0.0:1.0:0.0:0.0	.	333	P04350	TBB4A_HUMAN	M	333;333;251	ENSP00000264071:V333M;ENSP00000443590:V333M	ENSP00000264071:V333M	V	-	1	0	TUBB4	6446513	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.793000	0.62474	1.473000	0.48159	0.306000	0.20318	GTG	.	.		0.672	TUBB4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457841.1	NM_006087		T	6495513	C	T	6495513	3	4	307	1	0	0	0	0	1	0	0	0	16773	536	19	1	341	1	TUBB4	19	6495513	Missense_Mutation	SNP	C	TCGA-HP-A5MZ-01A-21D-A27I-10	5223515	6495513	52633470	46	43909										
LRRC8E	80131	hgsc.bcm.edu	37	chr19	7964686	7964686	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	agctggccctctgcatgctgCcgggtctgcccgacaccgtc	12	17	2	0			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr19:7964686C>T	ENST00000306708.6	+	3	1380	c.1279C>T	c.(1279-1281)Ccg>Tcg	p.P427S	RN7SL115P_ENST00000392196.5_RNA|AC010336.1_ENST00000539278.1_Missense_Mutation_p.G194D	NM_001268284.1|NM_001268285.1|NM_025061.4	NP_001255213.1|NP_001255214.1|NP_079337.2	Q6NSJ5	LRC8E_HUMAN	leucine rich repeat containing 8 family, member E	427					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(10)	35						CTGCATGCTGCCGGGTCTGCC	0.632																																					p.P427S		Atlas-SNP	.											LRRC8E,NS,carcinoma,0,1	LRRC8E	67	.	0			c.C1279T						.						29	28	29					19																	7964686		2203	4299	6502	SO:0001583	missense	80131	exon4			ATGCTGCCGGGTC		CCDS12189.1	19p13.2	2008-02-05				ENSG00000171017			26272	protein-coding gene	gene with protein product		612891				12477932	Standard	NM_025061		Approved	FLJ23420	uc002mir.3	Q6NSJ5		ENST00000306708.6:c.1279C>T	chr19.hg19:g.7964686C>T	ENSP00000306524:p.Pro427Ser	27.0	0.0		55.0	9.0	NM_001268284	B3KR78|Q2YDY3|Q7L236|Q8N3B0|Q9H5H8	Missense_Mutation	SNP	ENST00000306708.6	hg19	CCDS12189.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.53|11.53	1.666529|1.666529	0.29604|0.29604	.|.	.|.	ENSG00000214248|ENSG00000171017	ENST00000539278|ENST00000306708	.|T	.|0.12361	.|2.69	4.49|4.49	4.49|4.49	0.54785|0.54785	.|.	.|0.123338	.|0.56097	.|D	.|0.000039	T|T	0.06188|0.06188	0.0160|0.0160	N|N	0.03948|0.03948	-0.315|-0.315	0.58432|0.58432	D|D	0.999993|0.999993	.|B	.|0.30870	.|0.298	.|B	.|0.34242	.|0.178	T|T	0.18178|0.18178	-1.0345|-1.0345	6|10	0.87932|0.02654	D|T	0|1	.|.	14.7209|14.7209	0.69305|0.69305	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|427	.|Q6NSJ5	.|LRC8E_HUMAN	D|S	194|427	.|ENSP00000306524:P427S	ENSP00000441047:G194D|ENSP00000306524:P427S	G|P	-|+	2|1	0|0	AC010336.2|LRRC8E	7870686|7870686	0.984000|0.984000	0.35163|0.35163	0.971000|0.971000	0.41717|0.41717	0.236000|0.236000	0.25371|0.25371	1.690000|1.690000	0.37711|0.37711	2.340000|2.340000	0.79590|0.79590	0.555000|0.555000	0.69702|0.69702	GGC|CCG	.	.		0.632	LRRC8E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461354.1	NM_025061		T	7964686	C	T	7964686	3	4	307	1	0	0	0	0	1	0	0	0	9034	739	26	3	1285	3	LRRC8E	19	7964686	Missense_Mutation	SNP	C	TCGA-HP-A5MZ-01A-21D-A27I-10	1469173	7964686	51164297	47	43910										
SLC5A5	6528	hgsc.bcm.edu	37	chr19	18001723	18001723	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	aagcgcagcaccctggccccGggattgttgtggtgggacct	15	12	0	0	rs149937279		TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr19:18001723G>A	ENST00000222248.3	+	14	2027	c.1680G>A	c.(1678-1680)ccG>ccA	p.P560P		NM_000453.2	NP_000444.1	Q92911	SC5A5_HUMAN	solute carrier family 5 (sodium/iodide cotransporter), member 5	560					cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|iodide transport (GO:0015705)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	iodide transmembrane transporter activity (GO:0015111)|sodium:iodide symporter activity (GO:0008507)			NS(2)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|skin(3)	31						CCCTGGCCCCGGGATTGTTGT	0.602																																					p.P560P	Melanoma(65;1008 1708 7910 46650)	Atlas-SNP	.											.	SLC5A5	67	.	0			c.G1680A						.	G		1,4405	2.1+/-5.4	0,1,2202	101	104	103		1680	-6.5	0.4	19	dbSNP_134	103	0,8600		0,0,4300	no	coding-synonymous	SLC5A5	NM_000453.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		560/644	18001723	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	6528	exon14			GGCCCCGGGATTG		CCDS12368.1	19p13.11	2013-07-19	2013-07-19		ENSG00000105641	ENSG00000105641		"Solute carriers"	11040	protein-coding gene	gene with protein product		601843	"solute carrier family 5 (sodium iodide symporter), member 5"			9231811	Standard	NM_000453		Approved	NIS	uc002nhr.4	Q92911		ENST00000222248.3:c.1680G>A	chr19.hg19:g.18001723G>A		64.0	0.0		78.0	20.0	NM_000453	O43702|Q2M335|Q9NYB6	Silent	SNP	ENST00000222248.3	hg19	CCDS12368.1																																																																																			.	G|1.000;C|0.000		0.602	SLC5A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466690.1			A	18001723	G	A	18001723	2	1	307	1	0	0	0	0	0	0	0	1	14683	1103	39	1		1	SLC5A5	19	18001723	Silent	SNP	G	TCGA-HP-A5MZ-01A-21D-A27I-10	10037037	18001723	41127260	48	43911										
MLL4	9757	hgsc.bcm.edu	37	chr19	36219035	36219035	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	tcggctggttcgacgcccacGaccccaagtactggcgacgg	13	15	0	0			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr19:36219035G>A	ENST00000222270.7	+	19	4534	c.4534G>A	c.(4534-4536)Gac>Aac	p.D1512N	KMT2B_ENST00000420124.1_Missense_Mutation_p.D1512N|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	1512					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										CGACGCCCACGACCCCAAGTA	0.637																																					p.D1512N		Atlas-SNP	.											.	MLL4	229	.	0			c.G4534A						.						16	16	16					19																	36219035		2003	4172	6175	SO:0001583	missense	8085	exon19			GCCCACGACCCCA	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"Chromatin-modifying enzymes / K-methyltransferases"	15840	protein-coding gene	gene with protein product	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.4534G>A	chr19.hg19:g.36219035G>A	ENSP00000222270:p.Asp1512Asn	102.0	0.0		112.0	16.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Missense_Mutation	SNP	ENST00000222270.7	hg19	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	G	19.03	3.748430	0.69533	.	.	ENSG00000105663	ENST00000222270;ENST00000420124	D;D	0.84146	-1.81;-1.81	5.31	5.31	0.75309	.	0.000000	0.44285	D	0.000470	D	0.89305	0.6677	L	0.43152	1.355	0.53005	D	0.999965	D	0.89917	1.0	D	0.77557	0.99	D	0.89192	0.3551	10	0.54805	T	0.06	.	16.0062	0.80363	0.0:0.0:1.0:0.0	.	1512	Q9UMN6	MLL4_HUMAN	N	1512	ENSP00000222270:D1512N;ENSP00000398837:D1512N	ENSP00000222270:D1512N	D	+	1	0	AD000671.1	40910875	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.554000	0.67294	2.765000	0.95021	0.655000	0.94253	GAC	.	.		0.637	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727		A	36219035	G	A	36219035	3	1	307	1	0	0	0	0	1	0	0	0	9632	1058	37	1	4608	1	MLL4	19	36219035	Missense_Mutation	SNP	G	TCGA-HP-A5MZ-01A-21D-A27I-10	18217312	36219035	22909948	49	43912										
PPP5C	5536	hgsc.bcm.edu	37	chr19	46857241	46857241	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	gggccgcgctgcgagactacGagacggtgagctggggagtg	20	9	0	3			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr19:46857241G>C	ENST00000012443.4	+	2	461	c.358G>C	c.(358-360)Gag>Cag	p.E120Q	PPP5C_ENST00000391919.1_Missense_Mutation_p.E14Q	NM_006247.3	NP_006238.1	P53041	PPP5_HUMAN	protein phosphatase 5, catalytic subunit	120					cell death (GO:0008219)|DNA repair (GO:0006281)|mitotic nuclear division (GO:0007067)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein dephosphorylation (GO:0006470)|protein heterooligomerization (GO:0051291)|response to morphine (GO:0043278)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|RNA binding (GO:0003723)|signal transducer activity (GO:0004871)			endometrium(4)|kidney(1)|large_intestine(5)|liver(2)|lung(4)|ovary(1)|pancreas(1)	18		Ovarian(192;0.0731)|all_neural(266;0.196)		OV - Ovarian serous cystadenocarcinoma(262;0.000196)|all cancers(93;0.00192)|GBM - Glioblastoma multiforme(486;0.0499)|Epithelial(262;0.0504)		GCGAGACTACGAGACGGTGAG	0.642																																					p.E120Q		Atlas-SNP	.											.	PPP5C	44	.	0			c.G358C						.						21	18	19					19																	46857241		2201	4299	6500	SO:0001583	missense	5536	exon2			GACTACGAGACGG		CCDS12684.1	19q13.3	2013-01-10			ENSG00000011485	ENSG00000011485	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits", "Tetratricopeptide (TTC) repeat domain containing"	9322	protein-coding gene	gene with protein product		600658		PPP5		8666404	Standard	NM_006247		Approved	PP5	uc002pem.3	P53041	OTTHUMG00000134287	ENST00000012443.4:c.358G>C	chr19.hg19:g.46857241G>C	ENSP00000012443:p.Glu120Gln	62.0	0.0		128.0	24.0	NM_006247	Q16722|Q53XV2	Missense_Mutation	SNP	ENST00000012443.4	hg19	CCDS12684.1	.	.	.	.	.	.	.	.	.	.	G	16.75	3.208645	0.58343	.	.	ENSG00000011485	ENST00000012443;ENST00000451918;ENST00000391919	T;T	0.64260	-0.09;1.5	5.07	5.07	0.68467	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	U	0.000000	T	0.55609	0.1931	L	0.45698	1.435	0.80722	D	1	P;B	0.41624	0.757;0.392	B;B	0.39094	0.29;0.075	T	0.54036	-0.8353	10	0.23891	T	0.37	-21.617	16.3322	0.83039	0.0:0.0:1.0:0.0	.	120;120	B2R6R6;P53041	.;PPP5_HUMAN	Q	120;107;14	ENSP00000012443:E120Q;ENSP00000375786:E14Q	ENSP00000012443:E120Q	E	+	1	0	PPP5C	51549081	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.102000	0.77005	2.528000	0.85240	0.462000	0.41574	GAG	.	.		0.642	PPP5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258969.2	NM_006247		C	46857241	G	C	46857241	3	2	307	1	0	0	0	0	1	0	0	0	12418	1059	37	4	364	4	PPP5C	19	46857241	Missense_Mutation	SNP	G	TCGA-HP-A5MZ-01A-21D-A27I-10	10638206	46857241	12271742	50	43913										
ZBTB45	84878	hgsc.bcm.edu	37	chr19	59029036	59029036	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	gatgcacagcctctgcagccGccatctgcacagaacaagag	10	14	2	2			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr19:59029036G>A	ENST00000594051.1	-	2	485	c.5C>T	c.(4-6)gCg>gTg	p.A2V	ZBTB45_ENST00000600990.1_Missense_Mutation_p.A2V|ZBTB45_ENST00000354590.3_Missense_Mutation_p.A2V			Q96K62	ZBT45_HUMAN	zinc finger and BTB domain containing 45	2					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|lung(5)|urinary_tract(1)	11		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0165)|Lung(386;0.18)		CTCTGCAGCCGCCATCTGCAC	0.592																																					p.A2V	NSCLC(164;1383 2017 5233 27540 46677)	Atlas-SNP	.											.	ZBTB45	37	.	0			c.C5T						.						34	40	38					19																	59029036		2197	4296	6493	SO:0001583	missense	84878	exon2			GCAGCCGCCATCT	AK027392	CCDS12984.1	19q13.43	2013-10-10	2006-09-19	2006-09-19	ENSG00000119574	ENSG00000119574		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	23715	protein-coding gene	gene with protein product			"zinc finger protein 499"	ZNF499			Standard	NM_032792		Approved	FLJ14486	uc002qtd.3	Q96K62	OTTHUMG00000183545	ENST00000594051.1:c.5C>T	chr19.hg19:g.59029036G>A	ENSP00000469089:p.Ala2Val	94.0	0.0		127.0	6.0	NM_032792		Missense_Mutation	SNP	ENST00000594051.1	hg19	CCDS12984.1	.	.	.	.	.	.	.	.	.	.	g	16.63	3.176981	0.57692	.	.	ENSG00000119574	ENST00000354590	T	0.10668	2.85	3.88	3.88	0.44766	.	0.284575	0.23618	U	0.046276	T	0.08537	0.0212	N	0.19112	0.55	0.31566	N	0.656973	D	0.63880	0.993	P	0.44897	0.463	T	0.04481	-1.0948	10	0.87932	D	0	.	9.8862	0.41264	0.0:0.2097:0.7903:0.0	.	2	Q96K62	ZBT45_HUMAN	V	2	ENSP00000346603:A2V	ENSP00000346603:A2V	A	-	2	0	ZBTB45	63720848	0.047000	0.20315	0.951000	0.38953	0.393000	0.30537	1.354000	0.34056	1.883000	0.54544	0.289000	0.19496	GCG	.	.		0.592	ZBTB45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467067.1	NM_032792		A	59029036	G	A	59029036	3	1	307	1	0	0	0	0	1	0	0	0	17561	1087	38	1	1538	1	ZBTB45	19	59029036	Missense_Mutation	SNP	G	TCGA-HP-A5MZ-01A-21D-A27I-10	12171795	59029036	99947	51	43914										
ACSS2	55902	hgsc.bcm.edu	37	chr20	33464506	33464506	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	ggagccggggccaggaggaaGctggagccggaggccgggcg	23	10	0	0			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr20:33464506G>A	ENST00000360596.2	+	1	269	c.58G>A	c.(58-60)Gct>Act	p.A20T	ACSS2_ENST00000336325.4_Intron|ACSS2_ENST00000253382.5_Missense_Mutation_p.A20T|ACSS2_ENST00000476922.1_3'UTR	NM_018677.3	NP_061147.1	Q9NR19	ACSA_HUMAN	acyl-CoA synthetase short-chain family member 2	20					acetate biosynthetic process (GO:0019413)|acetyl-CoA biosynthetic process from acetate (GO:0019427)|ethanol oxidation (GO:0006069)|lipid biosynthetic process (GO:0008610)|propionate biosynthetic process (GO:0019542)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	acetate-CoA ligase activity (GO:0003987)|AMP binding (GO:0016208)|ATP binding (GO:0005524)			cervix(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(9)	21					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	CCAGGAGGAAGCTGGAGCCGG	0.746																																					p.A20T		Atlas-SNP	.											.	ACSS2	75	.	0			c.G58A						.						3	4	4					20																	33464506		1732	3698	5430	SO:0001583	missense	55902	exon1			GAGGAAGCTGGAG	AF263614	CCDS13243.1, CCDS42868.1, CCDS42868.2	20q11.22	2012-07-13	2005-09-08	2005-09-08	ENSG00000131069	ENSG00000131069	6.2.1.1	"Acyl-CoA synthetase family"	15814	protein-coding gene	gene with protein product		605832	"acetyl-Coenzyme A synthetase 2 (ADP forming)"	ACAS2		10843999	Standard	NM_018677		Approved	ACS, ACSA, AceCS, dJ1161H23.1	uc010gey.2	Q9NR19	OTTHUMG00000032317	ENST00000360596.2:c.58G>A	chr20.hg19:g.33464506G>A	ENSP00000353804:p.Ala20Thr	1.0	0.0		9.0	6.0	NM_001076552	A6NE90|Q5QPH2|Q5QPH3|Q8N238|Q96EL0|Q9NQP7|Q9UJ15	Missense_Mutation	SNP	ENST00000360596.2	hg19	CCDS13243.1	.	.	.	.	.	.	.	.	.	.	G	12.83	2.056168	0.36277	.	.	ENSG00000131069	ENST00000360596;ENST00000374693;ENST00000484354;ENST00000493805;ENST00000473172;ENST00000253382	T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92	4.54	-3.35	0.04928	.	0.658399	0.14855	N	0.294412	T	0.14141	0.0342	N	0.08118	0	0.25084	N	0.990901	B;B;B	0.18610	0.0;0.029;0.0	B;B;B	0.08055	0.001;0.003;0.0	T	0.13045	-1.0524	10	0.22109	T	0.4	-13.8251	0.7722	0.01026	0.1832:0.2778:0.2564:0.2826	.	20;20;20	Q5QPH3;B4DEH9;Q9NR19	.;.;ACSA_HUMAN	T	20	ENSP00000353804:A20T;ENSP00000419167:A20T;ENSP00000418812:A20T;ENSP00000419925:A20T;ENSP00000253382:A20T	ENSP00000253382:A20T	A	+	1	0	ACSS2	32928167	0.001000	0.12720	0.004000	0.12327	0.886000	0.51366	0.052000	0.14163	-0.666000	0.05310	0.462000	0.41574	GCT	.	.		0.746	ACSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078823.3	NM_018677		A	33464506	G	A	33464506	3	1	307	1	0	0	0	0	1	0	0	0	189	971	34	3	60	3	ACSS2	20	33464506	Missense_Mutation	SNP	G	TCGA-HP-A5MZ-01A-21D-A27I-10		33464506	29561014	52	43915										
EPB41L1	2036	hgsc.bcm.edu	37	chr20	34797717	34797717	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	tgagggcctgctgttctcccGggatctcaacaagggggccc	14	13	2	1	rs140677677		TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr20:34797717G>T	ENST00000338074.2	+	15	2137	c.1976G>T	c.(1975-1977)cGg>cTg	p.R659L	EPB41L1_ENST00000202028.5_Missense_Mutation_p.R585L|EPB41L1_ENST00000373941.1_Missense_Mutation_p.R659L|EPB41L1_ENST00000441639.1_Missense_Mutation_p.R585L|EPB41L1_ENST00000479336.1_3'UTR|EPB41L1_ENST00000373946.3_Intron|EPB41L1_ENST00000373950.2_Missense_Mutation_p.R550L	NM_001258329.1|NM_012156.2	NP_001245258.1|NP_036288.2	Q9H4G0	E41L1_HUMAN	erythrocyte membrane protein band 4.1-like 1	659					cortical actin cytoskeleton organization (GO:0030866)|synaptic transmission (GO:0007268)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)	p.R948L(1)|p.R659L(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(10)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	37	Breast(12;0.0239)					CTGTTCTCCCGGGATCTCAAC	0.637																																					p.R659L		Atlas-SNP	.											EPB41L1_ENST00000344237,NS,carcinoma,0,2	EPB41L1	111	.	2	Substitution - Missense(2)	lung(2)	c.G1976T						.						32	35	34					20																	34797717		2203	4300	6503	SO:0001583	missense	2036	exon16			TCTCCCGGGATCT	AB002336	CCDS13271.1, CCDS13272.1, CCDS58771.1	20q11.2-q12	2003-03-17			ENSG00000088367	ENSG00000088367			3378	protein-coding gene	gene with protein product		602879				9570967, 9828140	Standard	NM_012156		Approved	KIAA0338	uc002xfb.3	Q9H4G0	OTTHUMG00000032378	ENST00000338074.2:c.1976G>T	chr20.hg19:g.34797717G>T	ENSP00000337168:p.Arg659Leu	82.0	1.0		105.0	26.0	NM_001258329	O15046|Q4VXM6|Q4VXM7|Q4VXM8|Q4VXN4|Q6ZT61|Q8IUU7|Q96CV5|Q96L65	Missense_Mutation	SNP	ENST00000338074.2	hg19	CCDS13271.1	.	.	.	.	.	.	.	.	.	.	G	14.66	2.602254	0.46423	.	.	ENSG00000088367	ENST00000202028;ENST00000373950;ENST00000397315;ENST00000373951;ENST00000441639;ENST00000344237;ENST00000338074;ENST00000373941	D;D;D;D;D	0.83837	-1.77;-1.68;-1.77;-1.75;-1.75	5.87	3.91	0.45181	.	0.193405	0.49916	D	0.000132	T	0.75228	0.3821	N	0.24115	0.695	0.33013	D	0.527767	B;D;B;B;B;B	0.59767	0.026;0.986;0.016;0.039;0.18;0.15	B;P;B;B;B;B	0.51355	0.011;0.667;0.007;0.029;0.028;0.049	T	0.77411	-0.2598	10	0.32370	T	0.25	-8.0653	6.2374	0.20770	0.3153:0.0:0.6847:0.0	.	659;948;659;550;550;585	B7Z653;E9PCJ3;Q9H4G0;Q9H4G0-3;B3KUB6;Q9H4G0-2	.;.;E41L1_HUMAN;.;.;.	L	585;550;659;550;585;948;659;659	ENSP00000202028:R585L;ENSP00000363061:R550L;ENSP00000399214:R585L;ENSP00000337168:R659L;ENSP00000363052:R659L	ENSP00000202028:R585L	R	+	2	0	EPB41L1	34261131	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	2.031000	0.41117	1.616000	0.50265	0.655000	0.94253	CGG	.	G|1.000;A|0.000		0.637	EPB41L1-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078978.3	NM_012156		T	34797717	G	T	34797717	3	4	307	1	0	0	0	0	1	0	0	0	5154	1116	39	1	2030	1	EPB41L1	20	34797717	Missense_Mutation	SNP	G	TCGA-HP-A5MZ-01A-21D-A27I-10	1333211	34797717	28227803	53	43916										
ITSN1	6453	hgsc.bcm.edu	37	chr21	35183471	35183471	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0555555555555556	3	1	0.858974358974359	1.86111111111111	0.676767676767677	1	1	0	agacccccgcccctttggcaGtaacctcttcagagccctcc	7	19	2	2			TCGA-HP-A5MZ-01A-21D-A27I-10	TCGA-HP-A5MZ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36213e4-c057-46f5-ada5-f1f921855bb4	09ea881b-e60d-4cbe-9c35-d556da8bf86c	g.chr21:35183471G>T	ENST00000381318.3	+	21	2800	c.2512G>T	c.(2512-2514)Gta>Tta	p.V838L	AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000437442.2_Missense_Mutation_p.V833L|ITSN1_ENST00000399355.2_Missense_Mutation_p.V838L|ITSN1_ENST00000381285.4_Missense_Mutation_p.V838L|ITSN1_ENST00000399326.3_Missense_Mutation_p.V833L|ITSN1_ENST00000399353.1_Missense_Mutation_p.V796L|ITSN1_ENST00000399352.1_Missense_Mutation_p.V833L|ITSN1_ENST00000399338.4_Missense_Mutation_p.V833L|ITSN1_ENST00000381291.4_Missense_Mutation_p.V838L|ITSN1_ENST00000399367.3_Missense_Mutation_p.V833L|ITSN1_ENST00000399349.1_Missense_Mutation_p.V833L|ITSN1_ENST00000379960.5_Missense_Mutation_p.V833L	NM_003024.2	NP_003015.2	Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)	838					apoptotic signaling pathway (GO:0097190)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|kinase activator activity (GO:0019209)|proline-rich region binding (GO:0070064)|protein complex scaffold (GO:0032947)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(26)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	67						CCCTTTGGCAGTAACCTCTTC	0.542																																					p.V838L		Atlas-SNP	.											.	ITSN1	166	.	0			c.G2512T						.						84	82	82					21																	35183471		2203	4300	6503	SO:0001583	missense	6453	exon21			TTGGCAGTAACCT	AF064244	CCDS33545.1, CCDS33546.1	21q22.1-q22.2	2013-01-10			ENSG00000205726	ENSG00000205726		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "EF-hand domain containing"	6183	protein-coding gene	gene with protein product	"SH3 domain protein-1A", "human intersectin-SH3 domain-containing protein SH3P17", "Src homology 3 domain-containing protein", "intersectin 1 short form variant, 11", "intersectin 1 short form variant 3", "intersectin short variant 12"	602442		SH3D1A, ITSN		9799604, 9813051	Standard	NM_003024		Approved	SH3P17, MGC134948, MGC134949	uc002yta.1	Q15811	OTTHUMG00000065284	ENST00000381318.3:c.2512G>T	chr21.hg19:g.35183471G>T	ENSP00000370719:p.Val838Leu	146.0	0.0		179.0	36.0	NM_001001132	A7Y322|A8CTX8|A8CTY3|A8CTY7|A8D7D0|A8DCP3|B4DTM2|E7ERJ1|E9PE44|E9PG01|E9PHV2|O95216|Q0PW94|Q0PW95|Q0PW97|Q14BD3|Q1ED40|Q20BK3|Q9UET5|Q9UK60|Q9UNK1|Q9UNK2|Q9UQ92	Missense_Mutation	SNP	ENST00000381318.3	hg19	CCDS33545.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.240|8.240	0.806515|0.806515	0.16467|0.16467	.|.	.|.	ENSG00000205726|ENSG00000205726	ENST00000440794|ENST00000399353;ENST00000381318;ENST00000381291;ENST00000381285;ENST00000381288;ENST00000381289;ENST00000399367;ENST00000399352;ENST00000399355;ENST00000399349;ENST00000399338;ENST00000437442;ENST00000399326;ENST00000379960	.|T;T;T;T;T;T;T;T;T;T;T;T	.|0.44881	.|1.48;0.91;0.99;0.94;1.04;1.47;0.98;1.39;2.03;1.02;2.01;2.06	5.66|5.66	0.391|0.391	0.16282|0.16282	.|.	.|0.794609	.|0.11149	.|N	.|0.594338	T|T	0.19087|0.19087	0.0458|0.0458	N|N	0.03608|0.03608	-0.345|-0.345	0.09310|0.09310	N|N	1|1	.|B;P;B;B;P;B;B;B;B;P	.|0.37688	.|0.442;0.456;0.02;0.128;0.527;0.006;0.227;0.07;0.202;0.605	.|B;B;B;B;B;B;B;B;B;B	.|0.36766	.|0.17;0.084;0.01;0.101;0.232;0.01;0.079;0.028;0.153;0.175	T|T	0.14062|0.14062	-1.0486|-1.0486	5|10	.|0.41790	.|T	.|0.15	.|.	8.241|8.241	0.31660|0.31660	0.2745:0.1627:0.5628:0.0|0.2745:0.1627:0.5628:0.0	.|.	.|801;801;796;833;838;833;833;838;833;796	.|A8D7D0;A7XZY7;A8CTY7;A8CTY3;F8W7U0;E7ERJ1;A8CTX8;Q15811;Q15811-3;E7ERJ0	.|.;.;.;.;.;.;.;ITSN1_HUMAN;.;.	I|L	72|796;838;838;838;838;833;833;833;838;833;833;833;833;833	.|ENSP00000382290:V796L;ENSP00000370719:V838L;ENSP00000370691:V838L;ENSP00000370685:V838L;ENSP00000382301:V833L;ENSP00000382289:V833L;ENSP00000382292:V838L;ENSP00000382286:V833L;ENSP00000382275:V833L;ENSP00000387377:V833L;ENSP00000382265:V833L;ENSP00000369294:V833L	.|ENSP00000369294:V833L	S|V	+|+	2|1	0|0	ITSN1|ITSN1	34105341|34105341	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.924000|0.924000	0.55760|0.55760	0.526000|0.526000	0.22971|0.22971	0.343000|0.343000	0.23821|0.23821	0.563000|0.563000	0.77884|0.77884	AGT|GTA	.	.		0.542	ITSN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000140070.4	NM_003024		T	35183471	G	T	35183471	3	4	307	1	0	0	0	0	1	0	0	0	7935	1029	36	3	2590	3	ITSN1	21	35183471	Missense_Mutation	SNP	G	TCGA-HP-A5MZ-01A-21D-A27I-10		35183471	12946424	54	43917										
CASZ1	54897	hgsc.bcm.edu	37	chr1	10713785	10713785	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	tgagccaggcaggccctgggGcagcagccccgagatcttgc	15	14	1	2			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr1:10713785G>A	ENST00000377022.3	-	11	2646	c.2329C>T	c.(2329-2331)Ccc>Tcc	p.P777S	RP4-734G22.3_ENST00000606802.1_RNA|CASZ1_ENST00000344008.5_Missense_Mutation_p.P777S	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	777					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		AGGCCCTGGGGCAGCAGCCCC	0.706																																					p.P777S		Atlas-SNP	.											.	CASZ1	150	.	0			c.C2329T						.						29	38	35					1																	10713785		2190	4296	6486	SO:0001583	missense	54897	exon11			CCTGGGGCAGCAG	AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"Zinc fingers, C2H2-type"	26002	protein-coding gene	gene with protein product	"zinc finger protein 693", "survival related gene"	609895	"castor homolog 1, zinc finger (Drosophila)"			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.2329C>T	chr1.hg19:g.10713785G>A	ENSP00000366221:p.Pro777Ser	86.0	0.0		56.0	14.0	NM_001079843	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Missense_Mutation	SNP	ENST00000377022.3	hg19	CCDS41246.1	.	.	.	.	.	.	.	.	.	.	G	2.369	-0.344827	0.05208	.	.	ENSG00000130940	ENST00000377022;ENST00000344008	.	.	.	4.83	1.48	0.22813	.	0.388541	0.32273	N	0.006338	T	0.12050	0.0293	N	0.00347	-1.61	0.42382	D	0.992497	B;B;B	0.11235	0.004;0.0;0.0	B;B;B	0.09377	0.004;0.001;0.001	T	0.07790	-1.0754	9	0.12766	T	0.61	-13.782	7.5763	0.27937	0.1715:0.5908:0.2377:0.0	.	801;777;777	B7Z1S3;Q86V15-2;Q86V15	.;.;CASZ1_HUMAN	S	777	.	ENSP00000339445:P777S	P	-	1	0	CASZ1	10636372	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.719000	0.38011	0.065000	0.16485	0.655000	0.94253	CCC	.	.		0.706	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766		A	10713785	G	A	10713785	3	1	308	1	0	0	0	0	1	0	0	0	2687	1203	42	3	2998	3	CASZ1	1	10713785	Missense_Mutation	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10		10713785	238536836	1	43918										
EXTL1	2134	hgsc.bcm.edu	37	chr1	26355761	26355761	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	tcccgaggctgcctcgcgctTcctccaagccctgcaggtac	10	18	0	0			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr1:26355761T>C	ENST00000374280.3	+	2	1724	c.857T>C	c.(856-858)tTc>tCc	p.F286S	EXTL1_ENST00000484339.1_3'UTR	NM_004455.2	NP_004446.2	Q92935	EXTL1_HUMAN	exostosin-like glycosyltransferase 1	286					protein glycosylation (GO:0006486)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)	p.F286Y(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|stomach(1)|urinary_tract(1)	23		Colorectal(325;3.46e-05)|Lung NSC(340;6.18e-05)|all_lung(284;9.43e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00594)|READ - Rectum adenocarcinoma(331;0.0649)		GCCTCGCGCTTCCTCCAAGCC	0.622																																					p.F286S		Atlas-SNP	.											EXTL1,NS,carcinoma,0,1	EXTL1	61	.	1	Substitution - Missense(1)	kidney(1)	c.T857C						.						92	86	88					1																	26355761		2203	4300	6503	SO:0001583	missense	2134	exon2			CGCGCTTCCTCCA	U67191	CCDS271.1	1p36.1	2013-03-01	2013-03-01		ENSG00000158008	ENSG00000158008	2.4.1.224	"Exostosin glycosyltransferase family"	3515	protein-coding gene	gene with protein product	"glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase", "alpha-N-acetylglucosaminyltransferase II", "glucuronyl-N-acetylglucosaminylproteoglycan alpha-1,4-N- acetylglucosaminyltransferase", "exostosin-L"	601738	"exostoses (multiple)-like 1"			9037597	Standard	NM_004455		Approved	EXTL, MGC70794	uc001blf.3	Q92935	OTTHUMG00000007509	ENST00000374280.3:c.857T>C	chr1.hg19:g.26355761T>C	ENSP00000363398:p.Phe286Ser	148.0	0.0		142.0	50.0	NM_004455	Q6GSC1	Missense_Mutation	SNP	ENST00000374280.3	hg19	CCDS271.1	.	.	.	.	.	.	.	.	.	.	T	19.64	3.864795	0.71949	.	.	ENSG00000158008	ENST00000374280	D	0.97688	-4.49	3.91	3.91	0.45181	.	0.067410	0.64402	D	0.000013	D	0.98030	0.9351	M	0.86268	2.805	0.58432	D	0.999998	D	0.55385	0.971	P	0.56278	0.795	D	0.98202	1.0468	10	0.87932	D	0	-20.1562	9.3164	0.37937	0.0:0.0:0.0:1.0	.	286	Q92935	EXTL1_HUMAN	S	286	ENSP00000363398:F286S	ENSP00000363398:F286S	F	+	2	0	EXTL1	26228348	1.000000	0.71417	0.996000	0.52242	0.773000	0.43773	5.471000	0.66762	1.783000	0.52377	0.459000	0.35465	TTC	.	.		0.622	EXTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019749.1	NM_004455		C	26355761	T	C	26355761	3	2	308	1	0	0	0	0	1	0	0	0	5327	1783	62	2	863	2	EXTL1	1	26355761	Missense_Mutation	SNP	T	TCGA-HP-A5N0-01A-11D-A28X-10	15641976	26355761	222894860	2	43919										
EBNA1BP2	10969	hgsc.bcm.edu	37	chr1	43630464	43630464	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	ttctggtttttataccgtcgTttagcactgggcctggaaaa	10	8	1	0			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr1:43630464T>C	ENST00000236051.2	-	8	861	c.720A>G	c.(718-720)aaA>aaG	p.K240K	EBNA1BP2_ENST00000431635.2_Silent_p.K295K	NM_006824.2	NP_006815.2	Q99848	EBP2_HUMAN	EBNA1 binding protein 2	240					ribosome biogenesis (GO:0042254)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(4)|lung(9)	16	Ovarian(52;0.00579)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				TATACCGTCGTTTAGCACTGG	0.463																																					p.K295K		Atlas-SNP	.											.	EBNA1BP2	37	.	0			c.A885G						.						71	68	69					1																	43630464		2203	4300	6503	SO:0001819	synonymous_variant	10969	exon9			CCGTCGTTTAGCA	U86602	CCDS478.1, CCDS53308.1	1p35-p33	2011-02-10	2001-11-28		ENSG00000117395	ENSG00000117395			15531	protein-coding gene	gene with protein product		614443	"EBNA1-binding protein 2"			10074103, 11438656	Standard	NM_001159936		Approved	NOBP, EBP2, P40	uc010ojx.2	Q99848	OTTHUMG00000007284	ENST00000236051.2:c.720A>G	chr1.hg19:g.43630464T>C		98.0	0.0		83.0	4.0	NM_001159936	Q96A66	Silent	SNP	ENST00000236051.2	hg19	CCDS478.1																																																																																			.	.		0.463	EBNA1BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019015.1			C	43630464	T	C	43630464	2	2	308	1	0	0	0	0	0	0	0	1	4887	1722	60	2		2	EBNA1BP2	1	43630464	Silent	SNP	T	TCGA-HP-A5N0-01A-11D-A28X-10	17274703	43630464	205620157	3	43920										
KCNA2	3737	hgsc.bcm.edu	37	chr1	111147065	111147065	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	ttctcccagctcataaaaccGaatttcttcagagaatatat	4	10	4	1			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr1:111147065G>A	ENST00000485317.1	-	3	1013	c.340C>T	c.(340-342)Cgg>Tgg	p.R114W	KCNA2_ENST00000369770.3_Missense_Mutation_p.R114W|KCNA2_ENST00000440270.1_Missense_Mutation_p.R114W|KCNA2_ENST00000316361.4_Missense_Mutation_p.R114W|KCNA2_ENST00000525120.1_Intron			P16389	KCNA2_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 2	114					optic nerve structural organization (GO:0021633)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	juxtaparanode region of axon (GO:0044224)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		all_cancers(81;5.55e-06)|all_epithelial(167;1.87e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Colorectal(144;0.00878)|Lung(183;0.0234)|all cancers(265;0.0492)|Epithelial(280;0.0529)|COAD - Colon adenocarcinoma(174;0.131)|LUSC - Lung squamous cell carcinoma(189;0.133)|READ - Rectum adenocarcinoma(129;0.191)	Dalfampridine(DB06637)	TCATAAAACCGAATTTCTTCA	0.478																																					p.R114W	Pancreas(18;568 735 10587 23710 36357)	Atlas-SNP	.											.	KCNA2	61	.	0			c.C340T						.						41	43	42					1																	111147065		2203	4300	6503	SO:0001583	missense	3737	exon3			AAAACCGAATTTC	L02752	CCDS827.1, CCDS55625.1	1p13	2012-07-05			ENSG00000177301	ENSG00000177301		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6220	protein-coding gene	gene with protein product		176262				16382104	Standard	NM_004974		Approved	Kv1.2, HK4	uc009wfw.3	P16389	OTTHUMG00000011567	ENST00000485317.1:c.340C>T	chr1.hg19:g.111147065G>A	ENSP00000433109:p.Arg114Trp	76.0	0.0		46.0	15.0	NM_001204269	Q86XG6	Missense_Mutation	SNP	ENST00000485317.1	hg19	CCDS827.1	.	.	.	.	.	.	.	.	.	.	G	16.88	3.243998	0.58995	.	.	ENSG00000177301	ENST00000369770;ENST00000485317;ENST00000440270;ENST00000316361	T;T;T;T	0.78003	-1.14;-1.14;-1.14;-1.14	6.02	6.02	0.97574	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.057269	0.64402	D	0.000001	D	0.86847	0.6031	M	0.81802	2.56	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77557	0.99;0.975	D	0.87668	0.2539	10	0.87932	D	0	.	16.0721	0.80941	0.0:0.0:0.8655:0.1345	.	114;114	Q86XG6;P16389	.;KCNA2_HUMAN	W	114	ENSP00000358785:R114W;ENSP00000433109:R114W;ENSP00000415257:R114W;ENSP00000314520:R114W	ENSP00000314520:R114W	R	-	1	2	KCNA2	110948588	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.442000	0.66575	2.865000	0.98341	0.655000	0.94253	CGG	.	.		0.478	KCNA2-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128001.2	NM_004974		A	111147065	G	A	111147065	3	1	308	1	0	0	0	0	1	0	0	0	8012	1057	37	1	1163	1	KCNA2	1	111147065	Missense_Mutation	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10	67516601	111147065	138103556	4	43921										
NES	10763	hgsc.bcm.edu	37	chr1	156641173	156641173	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	gcagctcctgtccctcctccTccagagacctcagtgactct	7	18	2	2			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr1:156641173T>A	ENST00000368223.3	-	4	2939	c.2807A>T	c.(2806-2808)gAg>gTg	p.E936V		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin	936	Tail.				brain development (GO:0007420)|cell projection morphogenesis (GO:0048858)|central nervous system development (GO:0007417)|embryonic camera-type eye development (GO:0031076)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of catalytic activity (GO:0043086)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein binding (GO:0032091)|positive regulation of intermediate filament depolymerization (GO:0030844)|positive regulation of neural precursor cell proliferation (GO:2000179)|stem cell proliferation (GO:0072089)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	intermediate filament binding (GO:0019215)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(30)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(4)	64	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TCCCTCCTCCTCCAGAGACCT	0.542																																					p.E936V		Atlas-SNP	.											.	NES	196	.	0			c.A2807T						.						145	160	155					1																	156641173		2203	4300	6503	SO:0001583	missense	10763	exon4			TCCTCCTCCAGAG	X65964	CCDS1151.1	1q23	2013-01-16			ENSG00000132688	ENSG00000132688		"Intermediate filaments type IV"	7756	protein-coding gene	gene with protein product		600915				1478958, 9104587	Standard	NM_006617		Approved	FLJ21841	uc001fpq.3	P48681	OTTHUMG00000034299	ENST00000368223.3:c.2807A>T	chr1.hg19:g.156641173T>A	ENSP00000357206:p.Glu936Val	73.0	0.0		113.0	6.0	NM_006617	O00552|Q3LIF5|Q5SYZ6	Missense_Mutation	SNP	ENST00000368223.3	hg19	CCDS1151.1	.	.	.	.	.	.	.	.	.	.	T	16.39	3.109586	0.56398	.	.	ENSG00000132688	ENST00000368223	D	0.90261	-2.64	5.14	-1.44	0.08856	.	0.836085	0.09754	N	0.760216	T	0.74427	0.3715	L	0.54323	1.7	0.09310	N	0.999993	P	0.44877	0.845	B	0.36719	0.231	T	0.66862	-0.5816	10	0.72032	D	0.01	.	5.0384	0.14447	0.0:0.333:0.1556:0.5114	.	936	P48681	NEST_HUMAN	V	936	ENSP00000357206:E936V	ENSP00000357206:E936V	E	-	2	0	NES	154907797	0.000000	0.05858	0.001000	0.08648	0.125000	0.20455	0.165000	0.16564	-0.545000	0.06224	0.379000	0.24179	GAG	.	.		0.542	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	NM_006617		A	156641173	T	A	156641173	3	1	308	1	0	0	0	0	1	0	0	0	10346	1551	54	4	2062	4	NES	1	156641173	Missense_Mutation	SNP	T	TCGA-HP-A5N0-01A-11D-A28X-10	45494108	156641173	92609448	5	43922										
OR10Z1	128368	hgsc.bcm.edu	37	chr1	158576234	158576234	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	gatatacctctcagaatgggGcagaccaacgtaacctcctg	9	12	1	2			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr1:158576234G>T	ENST00000361284.1	+	1	6	c.6G>T	c.(4-6)ggG>ggT	p.G2G		NM_001004478.1	NP_001004478.1	Q8NGY1	O10Z1_HUMAN	olfactory receptor, family 10, subfamily Z, member 1	2						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(6)|lung(21)|pancreas(1)|prostate(3)|skin(4)	37	all_hematologic(112;0.0378)					TCAGAATGGGGCAGACCAACG	0.453																																					p.G2G		Atlas-SNP	.											.	OR10Z1	99	.	0			c.G6T						.						105	106	106					1																	158576234		2203	4300	6503	SO:0001819	synonymous_variant	128368	exon1			AATGGGGCAGACC	AB065635	CCDS30901.1	1q23.1	2012-08-23			ENSG00000198967	ENSG00000198967		"GPCR / Class A : Olfactory receptors"	14996	protein-coding gene	gene with protein product							Standard	NM_001004478		Approved		uc010pio.2	Q8NGY1	OTTHUMG00000019637	ENST00000361284.1:c.6G>T	chr1.hg19:g.158576234G>T		93.0	0.0		72.0	39.0	NM_001004478	Q5VYL0|Q6IFR7	Silent	SNP	ENST00000361284.1	hg19	CCDS30901.1																																																																																			.	.		0.453	OR10Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051853.1	NM_001004478		T	158576234	G	T	158576234	2	4	308	1	0	0	0	0	0	0	0	1	10932	1190	42	3		3	OR10Z1	1	158576234	Silent	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10	1935061	158576234	90674387	6	43923										
CD244	51744	hgsc.bcm.edu	37	chr1	160806007	160806007	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	gggactggatcatagagtagAtggtgctcccccctccagga	13	11	1	2			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr1:160806007A>G	ENST00000368033.3	-	6	969	c.887T>C	c.(886-888)aTc>aCc	p.I296T	CD244_ENST00000368034.4_Missense_Mutation_p.I291T|CD244_ENST00000322302.7_Missense_Mutation_p.I199T|CD244_ENST00000368032.2_Missense_Mutation_p.I291T|CD244_ENST00000481677.1_Intron			Q9BZW8	CD244_HUMAN	CD244 molecule, natural killer cell receptor 2B4	296					blood coagulation (GO:0007596)|leukocyte migration (GO:0050900)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			central_nervous_system(1)|large_intestine(3)|lung(12)|ovary(1)|urinary_tract(1)	18	all_cancers(52;2.72e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)			CATAGAGTAGATGGTGCTCCC	0.502																																					p.I296T		Atlas-SNP	.											.	CD244	77	.	0			c.T887C						.						117	103	108					1																	160806007		2203	4300	6503	SO:0001583	missense	51744	exon6			GAGTAGATGGTGC	AF105261	CCDS1210.1, CCDS53398.1, CCDS53399.1	1q23.1	2013-01-11	2006-03-29		ENSG00000122223	ENSG00000122223		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18171	protein-coding gene	gene with protein product		605554	"natural killer cell receptor 2B4", "CD244 natural killer cell receptor 2B4"			3772297, 10458320	Standard	NM_016382		Approved	2B4, NAIL, NKR2B4, Nmrk, SLAMF4	uc009wtq.3	Q9BZW8	OTTHUMG00000028606	ENST00000368033.3:c.887T>C	chr1.hg19:g.160806007A>G	ENSP00000357012:p.Ile296Thr	105.0	0.0		97.0	46.0	NM_001166663	Q5VYI2|Q5VYI6|Q5VYI7|Q96T47|Q9NQD2|Q9NQD3|Q9Y288	Missense_Mutation	SNP	ENST00000368033.3	hg19	CCDS53399.1	.	.	.	.	.	.	.	.	.	.	A	18.44	3.625010	0.66901	.	.	ENSG00000122223	ENST00000368034;ENST00000368033;ENST00000322302;ENST00000368032	T;T;T;T	0.56103	0.48;0.48;1.16;0.48	3.72	3.72	0.42706	.	4.060120	0.00879	N	0.002112	T	0.46889	0.1416	L	0.29908	0.895	0.28017	N	0.934669	D;P;P	0.65815	0.995;0.675;0.782	P;B;B	0.61592	0.891;0.158;0.3	T	0.45848	-0.9233	10	0.72032	D	0.01	-15.7478	9.1278	0.36826	1.0:0.0:0.0:0.0	.	199;296;291	Q9BZW8-4;Q9BZW8;Q9BZW8-2	.;CD244_HUMAN;.	T	291;296;199;291	ENSP00000357013:I291T;ENSP00000357012:I296T;ENSP00000313619:I199T;ENSP00000357011:I291T	ENSP00000313619:I199T	I	-	2	0	CD244	159072631	1.000000	0.71417	0.991000	0.47740	0.510000	0.34073	3.095000	0.50235	1.935000	0.56089	0.459000	0.35465	ATC	.	.		0.502	CD244-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071469.1	NM_016382		G	160806007	A	G	160806007	3	3	308	1	0	0	0	0	1	0	0	0	2989	333	12	2	241	2	CD244	1	160806007	Missense_Mutation	SNP	A	TCGA-HP-A5N0-01A-11D-A28X-10	2229773	160806007	88444614	7	43924										
DCAF6	55827	hgsc.bcm.edu	37	chr1	167962525	167962525	+	Frame_Shift_Del	DEL	T	T	-													0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	tttattccttcccatcttaaTaataagtcctgcagagtgac							TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr1:167962525delT	ENST00000312263.6	+	7	954	c.750delT	c.(748-750)aatfs	p.N251fs	DCAF6_ENST00000432587.2_Frame_Shift_Del_p.N220fs|DCAF6_ENST00000367843.3_Frame_Shift_Del_p.N251fs|DCAF6_ENST00000367840.3_Frame_Shift_Del_p.N251fs	NM_001017977.2	NP_001017977.1	Q58WW2	DCAF6_HUMAN	DDB1 and CUL4 associated factor 6	251					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	36						CCCATCTTAATAATAAGTCCT	0.358																																					p.N250fs		Atlas-Indel,Pindel	.											.	DCAF6	99	.	0			c.749delA						.						98	95	96					1																	167962525		2203	4300	6503	SO:0001589	frameshift_variant	55827	exon7			.	AL136738	CCDS1267.2, CCDS30933.1, CCDS55657.1, CCDS55658.1	1q23.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000143164	ENSG00000143164		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	30002	protein-coding gene	gene with protein product		610494	"IQ motif and WD repeats 1"	IQWD1		12032826	Standard	NM_018442		Approved	PC326	uc001gex.3	Q58WW2	OTTHUMG00000034572	ENST00000312263.6:c.750delT	chr1.hg19:g.167962525delT	ENSP00000311949:p.Asn251fs	153.0	0.0		153.0	37.0	NM_001198956	A2A295|B4DNB8|Q7L8I0|Q8IXH3|Q8TB19	Frame_Shift_Del	DEL	ENST00000312263.6	hg19	CCDS30933.1																																																																																			.	.		0.358	DCAF6-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083661.2	NM_018442		-	167962525	T	-	167962525	7	5	308	1	0	1	0	1	0	0	0	0	4276	1403	49	0	776	0	DCAF6	1	167962525	Frame_Shift_Del	DEL	T	TCGA-HP-A5N0-01A-11D-A28X-10	7156518	167962525	81288096	8	43925										
TNR	7143	hgsc.bcm.edu	37	chr1	175299224	175299224	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	aggtacccgcagtgccgttgTagcttcctatgcggagtttg	13	10	0	0			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr1:175299224T>C	ENST00000367674.2	-	21	4487	c.3779A>G	c.(3778-3780)tAc>tGc	p.Y1260C	RP3-518E13.2_ENST00000569593.1_RNA|TNR_ENST00000263525.2_Missense_Mutation_p.Y1260C			Q92752	TENR_HUMAN	tenascin R	1260	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)		p.Y1260C(1)		NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					AGTGCCGTTGTAGCTTCCTAT	0.597																																					p.Y1260C		Atlas-SNP	.											TNR,NS,carcinoma,0,1	TNR	399	.	1	Substitution - Missense(1)	endometrium(1)	c.A3779G						.						96	78	84					1																	175299224		2203	4300	6503	SO:0001583	missense	7143	exon21			CCGTTGTAGCTTC	X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11953	protein-coding gene	gene with protein product	"restrictin", "janusin"	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.3779A>G	chr1.hg19:g.175299224T>C	ENSP00000356646:p.Tyr1260Cys	91.0	0.0		106.0	27.0	NM_003285	C9J563|Q15568|Q5R3G0	Missense_Mutation	SNP	ENST00000367674.2	hg19	CCDS1318.1	.	.	.	.	.	.	.	.	.	.	T	14.33	2.503794	0.44558	.	.	ENSG00000116147	ENST00000367674;ENST00000263525;ENST00000367673	D;D	0.84589	-1.87;-1.87	5.64	5.64	0.86602	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.000000	0.85682	D	0.000000	D	0.94228	0.8147	H	0.96333	3.805	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	D	0.95210	0.8324	10	0.87932	D	0	.	10.7341	0.46115	0.1421:0.0:0.0:0.8579	.	1260	Q92752	TENR_HUMAN	C	1260;1260;1170	ENSP00000356646:Y1260C;ENSP00000263525:Y1260C	ENSP00000263525:Y1260C	Y	-	2	0	TNR	173565847	1.000000	0.71417	0.995000	0.50966	0.046000	0.14306	3.689000	0.54706	2.144000	0.66660	0.533000	0.62120	TAC	.	.		0.597	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285		C	175299224	T	C	175299224	3	2	308	1	0	0	0	0	1	0	0	0	16353	1638	57	2	309	2	TNR	1	175299224	Missense_Mutation	SNP	T	TCGA-HP-A5N0-01A-11D-A28X-10	7336699	175299224	73951397	9	43926										
EDEM3	80267	hgsc.bcm.edu	37	chr1	184702094	184702094	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	tcacctttttctttcagcatGattgccagggagtgcccacc	8	13	3	1			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr1:184702094G>T	ENST00000318130.8	-	6	755	c.489C>A	c.(487-489)atC>atA	p.I163I	EDEM3_ENST00000367512.3_Silent_p.I120I	NM_025191.3	NP_079467.3	Q9BZQ6	EDEM3_HUMAN	ER degradation enhancer, mannosidase alpha-like 3	163					cellular protein metabolic process (GO:0044267)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|glycoprotein endo-alpha-1,2-mannosidase activity (GO:0004569)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						CTTTCAGCATGATTGCCAGGG	0.388																																					p.I163I		Atlas-SNP	.											.	EDEM3	63	.	0			c.C489A						.						118	115	116					1																	184702094		2203	4300	6503	SO:0001819	synonymous_variant	80267	exon6			CAGCATGATTGCC	AF288393	CCDS1363.2	1q25	2008-02-05	2006-03-31	2006-03-31	ENSG00000116406	ENSG00000116406			16787	protein-coding gene	gene with protein product		610214	"chromosome 1 open reading frame 22"	C1orf22		15537790, 15579471	Standard	NM_025191		Approved		uc010pok.2	Q9BZQ6	OTTHUMG00000035387	ENST00000318130.8:c.489C>A	chr1.hg19:g.184702094G>T		86.0	0.0		75.0	12.0	NM_025191	B2RCH6|B7ZLZ2|Q0VGM5|Q5TEZ0|Q9HCW1|Q9UFV7	Silent	SNP	ENST00000318130.8	hg19	CCDS1363.2																																																																																			.	.		0.388	EDEM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085785.3	NM_025191		T	184702094	G	T	184702094	2	4	308	1	0	0	0	0	0	0	0	1	4915	1280	45	3		3	EDEM3	1	184702094	Silent	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10	9402870	184702094	64548527	10	43927										
FAM5C	339479	hgsc.bcm.edu	37	chr1	190195248	190195248	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	actgttgtaagctttccaggTttcagttattcgaagaagat	9	6	1	2			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr1:190195248T>G	ENST00000367462.3	-	6	1156	c.925A>C	c.(925-927)Acc>Ccc	p.T309P	BRINP3_ENST00000463404.1_5'UTR|BRINP3_ENST00000534846.1_Missense_Mutation_p.T207P	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	309					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)											GCTTTCCAGGTTTCAGTTATT	0.363																																					p.T309P		Atlas-SNP	.											.	FAM5C	343	.	0			c.A925C						.						70	68	69					1																	190195248		2203	4299	6502	SO:0001583	missense	339479	exon6			TCCAGGTTTCAGT	AB111893	CCDS1373.1	1q31.1	2013-09-18	2013-09-18	2013-09-18	ENSG00000162670	ENSG00000162670			22393	protein-coding gene	gene with protein product			"family with sequence similarity 5, member C"	FAM5C		16018821, 15193423	Standard	NM_199051		Approved	DBCCR1L, DBCCR1L1	uc001gse.1	Q76B58	OTTHUMG00000035533	ENST00000367462.3:c.925A>C	chr1.hg19:g.190195248T>G	ENSP00000356432:p.Thr309Pro	72.0	0.0		57.0	29.0	NM_199051	B3KVP1|B7Z260|O95726|Q2M330	Missense_Mutation	SNP	ENST00000367462.3	hg19	CCDS1373.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.965554	0.74131	.	.	ENSG00000162670	ENST00000367462;ENST00000534846	T;T	0.18657	2.47;2.2	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.31796	0.0808	L	0.46157	1.445	0.53005	D	0.99996	D;P	0.55385	0.971;0.917	P;B	0.52343	0.696;0.348	T	0.02037	-1.1225	10	0.72032	D	0.01	.	14.5927	0.68378	0.0:0.0:0.0:1.0	.	207;309	B7Z260;Q76B58	.;FAM5C_HUMAN	P	309;207	ENSP00000356432:T309P;ENSP00000438022:T207P	ENSP00000356432:T309P	T	-	1	0	FAM5C	188461871	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.944000	0.49034	2.326000	0.78906	0.533000	0.62120	ACC	.	.		0.363	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086278.1	NM_199051		G	190195248	T	G	190195248	3	3	308	1	0	0	0	0	1	0	0	0	5602	1725	60	5	1387	5	FAM5C	1	190195248	Missense_Mutation	SNP	T	TCGA-HP-A5N0-01A-11D-A28X-10	5493154	190195248	59055373	11	43928										
ASPM	259266	hgsc.bcm.edu	37	chr1	197111554	197111554	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	tttcttaacagctgatgtttTaggctctgagggagaaaaat	10	5	2	3			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr1:197111554T>C	ENST00000367409.4	-	3	2084	c.1828A>G	c.(1828-1830)Aaa>Gaa	p.K610E	ASPM_ENST00000294732.7_Missense_Mutation_p.K610E	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	610					developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						GCTGATGTTTTAGGCTCTGAG	0.383																																					p.K610E		Atlas-SNP	.											.	ASPM	444	.	0			c.A1828G						.						199	211	207					1																	197111554		2203	4300	6503	SO:0001583	missense	259266	exon3			ATGTTTTAGGCTC	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"microcephaly, primary autosomal recessive 5", "asp (abnormal spindle)-like, microcephaly associated (Drosophila)"	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.1828A>G	chr1.hg19:g.197111554T>C	ENSP00000356379:p.Lys610Glu	92.0	0.0		93.0	27.0	NM_001206846	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	hg19	CCDS1389.1	.	.	.	.	.	.	.	.	.	.	T	7.881	0.730257	0.15507	.	.	ENSG00000066279	ENST00000367409;ENST00000294732	T;T	0.57907	0.37;1.64	5.65	3.3	0.37823	.	0.601453	0.17303	N	0.179187	T	0.37865	0.1019	L	0.38175	1.15	0.09310	N	1	B;B	0.10296	0.003;0.0	B;B	0.08055	0.003;0.0	T	0.22556	-1.0213	10	0.33940	T	0.23	.	5.7189	0.17976	0.0:0.1416:0.2682:0.5903	.	610;610	Q4G1H1;Q8IZT6	.;ASPM_HUMAN	E	610	ENSP00000356379:K610E;ENSP00000294732:K610E	ENSP00000294732:K610E	K	-	1	0	ASPM	195378177	0.004000	0.15560	0.160000	0.22671	0.131000	0.20780	0.374000	0.20501	0.483000	0.27608	0.523000	0.50628	AAA	.	.		0.383	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136		C	197111554	T	C	197111554	3	2	308	1	0	0	0	0	1	0	0	0	1056	1763	61	2	8709	2	ASPM	1	197111554	Missense_Mutation	SNP	T	TCGA-HP-A5N0-01A-11D-A28X-10	6916306	197111554	52139067	12	43929										
DEGS1	8560	hgsc.bcm.edu	37	chr1	224371102	224371102	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	ccgaccagccgcacgccgacCggcgccgggagatcctgggt	15	17	0	1			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr1:224371102C>T	ENST00000323699.4	+	1	230	c.64C>T	c.(64-66)Cgg>Tgg	p.R22W	DEGS1_ENST00000391877.3_Missense_Mutation_p.R22W	NM_003676.3	NP_003667.1	O15121	DEGS1_HUMAN	delta(4)-desaturase, sphingolipid 1	22					small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|unsaturated fatty acid biosynthetic process (GO:0006636)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)			breast(1)|kidney(3)|large_intestine(2)|lung(4)	10	Breast(184;0.193)			GBM - Glioblastoma multiforme(131;0.00643)		GCACGCCGACCGGCGCCGGGA	0.741																																					p.R22W		Atlas-SNP	.											.	DEGS1	24	.	0			c.C64T						.						10	11	11					1																	224371102		1603	2945	4548	SO:0001583	missense	8560	exon1			GCCGACCGGCGCC	AF002668	CCDS1540.1	1q42.11	2013-09-02	2011-12-09	2004-12-14	ENSG00000143753	ENSG00000143753		"Fatty acid desaturases"	13709	protein-coding gene	gene with protein product	"sphingolipid delta(4)-desaturase 1", "dihydroceramide desaturase 1"	615843	"degenerative spermatocyte homolog 1, lipid desaturase (Drosophila)"			9188692, 20105137	Standard	NM_003676		Approved	MLD, Des-1, DES1, FADS7, DEGS-1	uc001hoj.3	O15121	OTTHUMG00000037496	ENST00000323699.4:c.64C>T	chr1.hg19:g.224371102C>T	ENSP00000316476:p.Arg22Trp	73.0	0.0		90.0	22.0	NM_003676		Missense_Mutation	SNP	ENST00000323699.4	hg19	CCDS1540.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.613556	0.87359	.	.	ENSG00000143753	ENST00000323699;ENST00000391877	D;D	0.88741	-2.42;-2.42	4.01	4.01	0.46588	Sphingolipid delta4-desaturase, N-terminal (1);	0.000000	0.64402	D	0.000002	D	0.96109	0.8732	H	0.95504	3.68	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.97747	1.0212	10	0.87932	D	0	-13.795	16.502	0.84260	0.0:1.0:0.0:0.0	.	22	O15121	DEGS1_HUMAN	W	22	ENSP00000316476:R22W;ENSP00000375749:R22W	ENSP00000316476:R22W	R	+	1	2	DEGS1	222437725	0.876000	0.30132	0.832000	0.32986	0.962000	0.63368	1.687000	0.37680	1.935000	0.56089	0.491000	0.48974	CGG	.	.		0.741	DEGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091285.2			T	224371102	C	T	224371102	3	4	308	1	0	0	0	0	1	0	0	0	4424	643	23	1	66	1	DEGS1	1	224371102	Missense_Mutation	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	27259548	224371102	24879519	13	43930										
TTC13	79573	hgsc.bcm.edu	37	chr1	231060591	231060591	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	ctgagatgttagttaccttcTccatttaactgcaatgtcaa	6	9	2	1			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr1:231060591T>C	ENST00000366661.4	-	14	1724	c.1717A>G	c.(1717-1719)Aga>Gga	p.R573G	TTC13_ENST00000366662.4_Missense_Mutation_p.R520G|TTC13_ENST00000414259.1_Missense_Mutation_p.R520G	NM_024525.4	NP_078801.3	Q8NBP0	TTC13_HUMAN	tetratricopeptide repeat domain 13	573										central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	39	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)		COAD - Colon adenocarcinoma(196;0.243)		AGTTACCTTCTCCATTTAACT	0.408																																					p.R573G		Atlas-SNP	.											.	TTC13	74	.	0			c.A1717G						.						213	176	189					1																	231060591		2203	4300	6503	SO:0001583	missense	79573	exon14			ACCTTCTCCATTT		CCDS1588.1, CCDS44332.1, CCDS44332.2	1q42.2	2013-01-10			ENSG00000143643	ENSG00000143643		"Tetratricopeptide (TTC) repeat domain containing"	26204	protein-coding gene	gene with protein product							Standard	NM_024525		Approved	FLJ22584	uc001huf.4	Q8NBP0	OTTHUMG00000037788	ENST00000366661.4:c.1717A>G	chr1.hg19:g.231060591T>C	ENSP00000355621:p.Arg573Gly	120.0	0.0		136.0	27.0	NM_024525	B1AQI1|B1AQI2|Q8IVP8|Q8NBI0|Q8ND20	Missense_Mutation	SNP	ENST00000366661.4	hg19	CCDS1588.1	.	.	.	.	.	.	.	.	.	.	T	19.38	3.817492	0.70912	.	.	ENSG00000143643	ENST00000366661;ENST00000366662;ENST00000414259;ENST00000486879	T;T;T	0.33438	1.41;1.41;1.41	5.47	4.26	0.50523	.	0.000000	0.85682	D	0.000000	T	0.53850	0.1822	M	0.75615	2.305	0.80722	D	1	D;D;D;D	0.89917	1.0;0.993;1.0;0.999	D;D;D;D	0.85130	0.975;0.977;0.997;0.961	T	0.58244	-0.7670	10	0.66056	D	0.02	.	12.6453	0.56731	0.0:0.0:0.2148:0.7852	.	498;520;520;573	Q69YR0;E9PGV4;Q8NBP0-2;Q8NBP0	.;.;.;TTC13_HUMAN	G	573;520;520;7	ENSP00000355621:R573G;ENSP00000355622:R520G;ENSP00000416631:R520G	ENSP00000355621:R573G	R	-	1	2	TTC13	229127214	1.000000	0.71417	1.000000	0.80357	0.817000	0.46193	2.851000	0.48302	2.200000	0.70718	0.533000	0.62120	AGA	.	.		0.408	TTC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092229.2	NM_024525		C	231060591	T	C	231060591	3	2	308	1	0	0	0	0	1	0	0	0	16695	1559	54	2	905	2	TTC13	1	231060591	Missense_Mutation	SNP	T	TCGA-HP-A5N0-01A-11D-A28X-10	6689489	231060591	18190030	14	43931										
ACVR2A	92	hgsc.bcm.edu	37	chr2	148680560	148680560	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	aggttggtacccggaggtacAtggctccagaggtattagag	15	7	0	2			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr2:148680560A>G	ENST00000241416.7	+	9	1732	c.1096A>G	c.(1096-1098)Atg>Gtg	p.M366V	ACVR2A_ENST00000535787.1_Missense_Mutation_p.M258V|ACVR2A_ENST00000404590.1_Missense_Mutation_p.M366V	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	366	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		CCGGAGGTACATGGCTCCAGA	0.383																																					p.M366V		Atlas-SNP	.											.	ACVR2A	125	.	0			c.A1096G						.						172	176	174					2																	148680560		2203	4300	6503	SO:0001583	missense	92	exon9			AGGTACATGGCTC		CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"activin A receptor, type II"	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.1096A>G	chr2.hg19:g.148680560A>G	ENSP00000241416:p.Met366Val	168.0	0.0		97.0	38.0	NM_001616	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	Missense_Mutation	SNP	ENST00000241416.7	hg19	CCDS33301.1	.	.	.	.	.	.	.	.	.	.	A	23.6	4.432475	0.83776	.	.	ENSG00000121989	ENST00000241416;ENST00000535787;ENST00000404590	D;D;D	0.94232	-3.38;-3.38;-3.38	5.65	5.65	0.86999	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.96513	0.8862	M	0.79258	2.445	0.80722	D	1	D	0.76494	0.999	D	0.77004	0.989	D	0.96984	0.9717	10	0.87932	D	0	.	16.0399	0.80667	1.0:0.0:0.0:0.0	.	366	P27037	AVR2A_HUMAN	V	366;258;366	ENSP00000241416:M366V;ENSP00000439988:M258V;ENSP00000384338:M366V	ENSP00000241416:M366V	M	+	1	0	ACVR2A	148397030	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.113000	0.94321	2.371000	0.80710	0.533000	0.62120	ATG	.	.		0.383	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616		G	148680560	A	G	148680560	3	3	308	1	0	0	0	0	1	0	0	0	223	217	8	2	1130	2	ACVR2A	2	148680560	Missense_Mutation	SNP	A	TCGA-HP-A5N0-01A-11D-A28X-10		148680560	94518813	15	43932										
NEB	4703	hgsc.bcm.edu	37	chr2	152528994	152528994	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	acattggtagcgacatcctgGgccatctttgcagctgtgat	11	10	1	1			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr2:152528994G>T	ENST00000172853.10	-	37	4335	c.4188C>A	c.(4186-4188)gcC>gcA	p.A1396A	NEB_ENST00000603639.1_Silent_p.A1396A|NEB_ENST00000397345.3_Silent_p.A1396A|NEB_ENST00000604864.1_Silent_p.A1396A|NEB_ENST00000427231.2_Silent_p.A1396A|NEB_ENST00000409198.1_Silent_p.A1396A			P20929	NEBU_HUMAN	nebulin	1396					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		CGACATCCTGGGCCATCTTTG	0.463																																					p.A1396A		Atlas-SNP	.											.	NEB	1697	.	0			c.C4188A						.						181	171	175					2																	152528994		2054	4216	6270	SO:0001819	synonymous_variant	4703	exon37			ATCCTGGGCCATC	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.4188C>A	chr2.hg19:g.152528994G>T		344.0	0.0		210.0	91.0	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	hg19																																																																																				.	.		0.463	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		T	152528994	G	T	152528994	2	4	308	1	0	0	0	0	0	0	0	1	10311	1219	43	3		3	NEB	2	152528994	Silent	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10	3848434	152528994	90670379	16	43933										
SDPR	8436	hgsc.bcm.edu	37	chr2	192700908	192700908	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	ccagagcgctggcgagggacGcttcggaatgaccctctgca	14	13	1	2			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr2:192700908G>T	ENST00000304141.4	-	2	1348	c.1019C>A	c.(1018-1020)gCg>gAg	p.A340E		NM_004657.5	NP_004648.1			serum deprivation response											NS(1)|central_nervous_system(1)|cervix(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|urinary_tract(3)	23			OV - Ovarian serous cystadenocarcinoma(117;0.0647)			GGCGAGGGACGCTTCGGAATG	0.567																																					p.A340E		Atlas-SNP	.											.	SDPR	67	.	0			c.C1019A						.						105	105	105					2																	192700908		2203	4300	6503	SO:0001583	missense	8436	exon2			AGGGACGCTTCGG	AF085481	CCDS2313.1	2q32-q33	2011-04-20	2009-09-18		ENSG00000168497	ENSG00000168497			10690	protein-coding gene	gene with protein product	"phosphatidylserine binding protein"	606728	"serum deprivation response (phosphatidylserine-binding protein)", "serum deprivation response (phosphatidylserine binding protein)"			10191091, 8241023	Standard	NM_004657		Approved	SDR, PS-p68, cavin-2, CAVIN2	uc002utb.3	O95810	OTTHUMG00000154309	ENST00000304141.4:c.1019C>A	chr2.hg19:g.192700908G>T	ENSP00000305675:p.Ala340Glu	120.0	0.0		84.0	4.0	NM_004657		Missense_Mutation	SNP	ENST00000304141.4	hg19	CCDS2313.1	.	.	.	.	.	.	.	.	.	.	G	14.14	2.446819	0.43429	.	.	ENSG00000168497	ENST00000304141	T	0.64438	-0.1	5.01	4.11	0.48088	.	0.633297	0.16592	N	0.207720	T	0.46502	0.1396	L	0.44542	1.39	0.09310	N	1	B	0.26483	0.15	B	0.22601	0.04	T	0.25813	-1.0121	10	0.20519	T	0.43	-15.7112	3.9134	0.09213	0.1993:0.2237:0.577:0.0	.	340	O95810	SDPR_HUMAN	E	340	ENSP00000305675:A340E	ENSP00000305675:A340E	A	-	2	0	SDPR	192409153	0.275000	0.24201	0.043000	0.18650	0.007000	0.05969	2.139000	0.42149	1.299000	0.44798	0.563000	0.77884	GCG	.	.		0.567	SDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334791.2	NM_004657		T	192700908	G	T	192700908	3	4	308	1	0	0	0	0	1	0	0	0	13985	1087	38	1	262	1	SDPR	2	192700908	Missense_Mutation	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10	40171914	192700908	50498465	17	43934										
SPAG16	79582	hgsc.bcm.edu	37	chr2	215274960	215274960	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	gatgggccacgaaaacgaggCacacacggttgtgttttctc	12	10	1	0			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr2:215274960C>A	ENST00000331683.5	+	16	1912	c.1817C>A	c.(1816-1818)gCa>gAa	p.A606E	AC107218.3_ENST00000412896.1_RNA|VWC2L_ENST00000312504.5_5'Flank|VWC2L_ENST00000427124.1_5'Flank|AC107218.3_ENST00000437883.1_RNA|SPAG16_ENST00000374309.3_Missense_Mutation_p.A512E	NM_024532.4	NP_078808.3	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16	606					cilium assembly (GO:0042384)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|microtubule cytoskeleton (GO:0015630)|motile cilium (GO:0031514)|nucleus (GO:0005634)				endometrium(4)|kidney(1)|large_intestine(15)|lung(27)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	56		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)		GAAAACGAGGCACACACGGTT	0.502																																					p.A606E		Atlas-SNP	.											.	SPAG16	134	.	0			c.C1817A						.						136	130	132					2																	215274960		2203	4300	6503	SO:0001583	missense	79582	exon16			ACGAGGCACACAC	AF310672	CCDS2396.1, CCDS46508.1	2q34	2013-05-21			ENSG00000144451	ENSG00000144451		"WD repeat domain containing"	23225	protein-coding gene	gene with protein product		612173				12391165, 11867345	Standard	NM_024532		Approved	PF20, FLJ22724, DKFZp666P1710, WDR29	uc002veq.4	Q8N0X2	OTTHUMG00000133015	ENST00000331683.5:c.1817C>A	chr2.hg19:g.215274960C>A	ENSP00000332592:p.Ala606Glu	216.0	0.0		186.0	47.0	NM_024532	Q498B7|Q658W1|Q68DB3|Q6I9Z6|Q8N9C7|Q9H601	Missense_Mutation	SNP	ENST00000331683.5	hg19	CCDS2396.1	.	.	.	.	.	.	.	.	.	.	C	14.11	2.436431	0.43224	.	.	ENSG00000144451	ENST00000331683;ENST00000374309;ENST00000451561	T;T;T	0.60171	0.21;0.21;0.21	5.48	0.291	0.15732	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.802457	0.10745	N	0.638995	T	0.59824	0.2222	L	0.46670	1.46	0.21256	N	0.999742	D;P;D	0.58970	0.97;0.757;0.984	P;B;P	0.54815	0.761;0.433;0.761	T	0.52003	-0.8633	10	0.87932	D	0	.	8.4277	0.32739	0.0:0.3662:0.0:0.6338	.	512;546;606	B4DYB5;Q4G1A2;Q8N0X2	.;.;SPG16_HUMAN	E	606;512;230	ENSP00000332592:A606E;ENSP00000363428:A512E;ENSP00000416600:A230E	ENSP00000332592:A606E	A	+	2	0	SPAG16	214983205	0.527000	0.26306	0.746000	0.31095	0.165000	0.22458	0.128000	0.15810	0.051000	0.15978	-0.217000	0.12591	GCA	.	.		0.502	SPAG16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256601.2	NM_024532		A	215274960	C	A	215274960	3	1	308	1	0	0	0	0	1	0	0	0	14993	710	25	3	1895	3	SPAG16	2	215274960	Missense_Mutation	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	22574052	215274960	27924413	18	43935										
SLC16A14	151473	hgsc.bcm.edu	37	chr2	230914503	230914503	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	cgactccaaaagtaatgaagAgataatgcacgtttgcagca	9	8	0	2			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr2:230914503A>C	ENST00000295190.4	-	3	835	c.377T>G	c.(376-378)cTc>cGc	p.L126R		NM_152527.4	NP_689740.2	Q7RTX9	MOT14_HUMAN	solute carrier family 16, member 14	126						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			NS(1)|cervix(1)|endometrium(7)|large_intestine(7)|lung(3)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.149)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;7.31e-13)|all cancers(144;5.1e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00948)		AGTAATGAAGAGATAATGCAC	0.448																																					p.L126R		Atlas-SNP	.											.	SLC16A14	75	.	0			c.T377G						.						93	91	92					2																	230914503		2203	4300	6503	SO:0001583	missense	151473	exon3			ATGAAGAGATAAT	BN000146	CCDS2473.1	2q37.1	2013-07-18	2013-07-18		ENSG00000163053	ENSG00000163053		"Solute carriers"	26417	protein-coding gene	gene with protein product	"monocarboxylic acid transporter 14"		"solute carrier family 16 (monocarboxylic acid transporters), member 14"				Standard	NM_152527		Approved	FLJ30794, MCT14	uc002vqd.2	Q7RTX9	OTTHUMG00000133205	ENST00000295190.4:c.377T>G	chr2.hg19:g.230914503A>C	ENSP00000295190:p.Leu126Arg	252.0	0.0		248.0	43.0	NM_152527	A8KA08|Q53R92|Q96NI7	Missense_Mutation	SNP	ENST00000295190.4	hg19	CCDS2473.1	.	.	.	.	.	.	.	.	.	.	A	19.47	3.833629	0.71258	.	.	ENSG00000163053	ENST00000295190;ENST00000457406;ENST00000412034	D;D;D	0.86097	-2.07;-2.07;-2.07	4.8	4.8	0.61643	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.50627	D	0.000107	D	0.92430	0.7597	M	0.91140	3.18	0.49915	D	0.999839	P;D	0.64830	0.953;0.994	P;P	0.60012	0.84;0.867	D	0.93688	0.7004	10	0.62326	D	0.03	.	13.1076	0.59255	1.0:0.0:0.0:0.0	.	126;126	E7EMG7;Q7RTX9	.;MOT14_HUMAN	R	126	ENSP00000295190:L126R;ENSP00000400352:L126R;ENSP00000395775:L126R	ENSP00000295190:L126R	L	-	2	0	SLC16A14	230622747	1.000000	0.71417	0.983000	0.44433	0.930000	0.56654	6.002000	0.70693	2.017000	0.59298	0.533000	0.62120	CTC	.	.		0.448	SLC16A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256918.2	NM_152527		C	230914503	A	C	230914503	3	2	308	1	0	0	0	0	1	0	0	0	14422	304	11	5	1167	5	SLC16A14	2	230914503	Missense_Mutation	SNP	A	TCGA-HP-A5N0-01A-11D-A28X-10	15639543	230914503	12284870	19	43936										
COL6A3	1293	hgsc.bcm.edu	37	chr2	238280705	238280705	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	cttgaagatgttcctggacaCgtactccagggcattgccca	10	12	0	2			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr2:238280705C>A	ENST00000295550.4	-	9	4407	c.3955G>T	c.(3955-3957)Gtg>Ttg	p.V1319L	COL6A3_ENST00000472056.1_Missense_Mutation_p.V712L|COL6A3_ENST00000392004.3_Missense_Mutation_p.V1113L|COL6A3_ENST00000409809.1_Missense_Mutation_p.V1113L|COL6A3_ENST00000353578.4_Missense_Mutation_p.V1113L|COL6A3_ENST00000392003.2_Missense_Mutation_p.V912L|COL6A3_ENST00000347401.3_Missense_Mutation_p.V1118L|COL6A3_ENST00000346358.4_Missense_Mutation_p.V1119L	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1319	Nonhelical region.|VWFA 7. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		TTCCTGGACACGTACTCCAGG	0.607																																					p.V1319L		Atlas-SNP	.											.	COL6A3	608	.	0			c.G3955T						.						48	45	46					2																	238280705		2203	4300	6503	SO:0001583	missense	1293	exon9			TGGACACGTACTC	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.3955G>T	chr2.hg19:g.238280705C>A	ENSP00000295550:p.Val1319Leu	88.0	0.0		77.0	20.0	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	hg19	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.188379	0.78789	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358;ENST00000392004;ENST00000392003	D;D;D;D;D;D;D;D	0.84730	-1.89;-1.89;-1.89;-1.89;-1.89;-1.89;-1.89;-1.89	5.84	5.84	0.93424	von Willebrand factor, type A (3);	0.000000	0.49305	D	0.000154	D	0.89880	0.6843	L	0.41824	1.3	0.58432	D	0.999999	D;D;D;D;P	0.89917	1.0;0.999;1.0;1.0;0.893	D;D;D;D;P	0.91635	0.999;0.986;0.999;0.999;0.644	D	0.88577	0.3134	10	0.42905	T	0.14	.	20.1346	0.98019	0.0:1.0:0.0:0.0	.	712;912;1113;1113;1319	E9PFQ6;A8MT30;E9PGQ9;P12111-2;P12111	.;.;.;.;CO6A3_HUMAN	L	1319;1118;1113;712;1113;1119;1113;912	ENSP00000295550:V1319L;ENSP00000315609:V1118L;ENSP00000315873:V1113L;ENSP00000418285:V712L;ENSP00000386844:V1113L;ENSP00000295546:V1119L;ENSP00000375861:V1113L;ENSP00000375860:V912L	ENSP00000295550:V1319L	V	-	1	0	COL6A3	237945444	0.998000	0.40836	0.881000	0.34555	0.800000	0.45204	3.846000	0.55888	2.765000	0.95021	0.655000	0.94253	GTG	.	.		0.607	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		A	238280705	C	A	238280705	3	1	308	1	0	0	0	0	1	0	0	0	3703	536	19	1	5769	1	COL6A3	2	238280705	Missense_Mutation	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	7366202	238280705	4918668	20	43937										
GRM7	2917	hgsc.bcm.edu	37	chr3	7494474	7494474	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	caagaagttgctgaagtataTacgcaatgttaatttcaatg	8	5	1	2			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr3:7494474T>C	ENST00000357716.4	+	6	1629	c.1355T>C	c.(1354-1356)aTa>aCa	p.I452T	GRM7_ENST00000403881.1_Missense_Mutation_p.I452T|GRM7_ENST00000486284.1_Missense_Mutation_p.I452T|GRM7_ENST00000458641.2_3'UTR|GRM7_ENST00000389336.4_Missense_Mutation_p.I452T|GRM7_ENST00000402647.2_Missense_Mutation_p.I452T	NM_000844.3	NP_000835.1	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7	452					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|adult behavior (GO:0030534)|conditioned taste aversion (GO:0001661)|multicellular organismal response to stress (GO:0033555)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of glutamate secretion (GO:0014050)|regulation of cyclase activity (GO:0031279)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|short-term memory (GO:0007614)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	adenylate cyclase inhibitor activity (GO:0010855)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|glutamate binding (GO:0016595)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|PDZ domain binding (GO:0030165)|serine binding (GO:0070905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(35)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	76						CTGAAGTATATACGCAATGTT	0.423																																					p.I452T		Atlas-SNP	.											.	GRM7	223	.	0			c.T1355C						.						67	59	62					3																	7494474		2203	4300	6503	SO:0001583	missense	2917	exon6			AGTATATACGCAA	U92458	CCDS43042.1	3p26-p25	2014-06-12			ENSG00000196277	ENSG00000196277		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4599	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 87"	604101				8288585, 8840028	Standard	NM_000844		Approved	GLUR7, GPRC1G, mGlu7, MGLUR7, PPP1R87	uc003bql.2	Q14831	OTTHUMG00000125549	ENST00000357716.4:c.1355T>C	chr3.hg19:g.7494474T>C	ENSP00000350348:p.Ile452Thr	159.0	0.0		124.0	43.0	NM_000844	Q8NFS2|Q8NFS3|Q8NFS4	Missense_Mutation	SNP	ENST00000357716.4	hg19	CCDS43042.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.368242	0.82463	.	.	ENSG00000196277	ENST00000357716;ENST00000486284;ENST00000389336;ENST00000403881;ENST00000525747;ENST00000402647;ENST00000413492;ENST00000445087	D;D;D;D;D;D	0.87571	-2.27;-2.27;-2.27;-2.27;-2.27;-2.27	5.88	5.88	0.94601	Extracellular ligand-binding receptor (1);	0.051654	0.85682	D	0.000000	D	0.92714	0.7684	M	0.87547	2.89	0.58432	D	0.999999	P;P;P;D	0.56035	0.728;0.896;0.77;0.974	B;B;B;P	0.55785	0.272;0.393;0.393;0.784	D	0.93829	0.7126	10	0.87932	D	0	.	15.1249	0.72475	0.0:0.0:0.0:1.0	.	452;207;452;452	Q14831-5;Q59G95;Q14831;Q14831-2	.;.;GRM7_HUMAN;.	T	452;452;452;452;452;452;452;109	ENSP00000350348:I452T;ENSP00000417536:I452T;ENSP00000373987:I452T;ENSP00000385664:I452T;ENSP00000384585:I452T;ENSP00000395035:I109T	ENSP00000350348:I452T	I	+	2	0	GRM7	7469474	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	8.040000	0.89188	2.246000	0.74042	0.533000	0.62120	ATA	.	.		0.423	GRM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246895.3	NM_000844		C	7494474	T	C	7494474	3	2	308	1	0	0	0	0	1	0	0	0	6811	1406	49	2	1377	2	GRM7	3	7494474	Missense_Mutation	SNP	T	TCGA-HP-A5N0-01A-11D-A28X-10		7494474	190527956	21	43938										
CSPG5	10675	hgsc.bcm.edu	37	chr3	47618646	47618646	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	tcatcttctaggtctccaccTcctactgcatctttgtcatc	4	15	6	0			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr3:47618646T>C	ENST00000383738.2	-	2	2968	c.870A>G	c.(868-870)ggA>ggG	p.G290G	CSPG5_ENST00000465441.1_5'Flank|CSPG5_ENST00000456150.1_Silent_p.G152G|CSPG5_ENST00000264723.4_Silent_p.G290G	NM_001206943.1|NM_001206945.1	NP_001193872.1|NP_001193874.1	O95196	CSPG5_HUMAN	chondroitin sulfate proteoglycan 5 (neuroglycan C)	290	Interaction with TNC and TNR. {ECO:0000250}.				axon regeneration (GO:0031103)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|intracellular transport (GO:0046907)|nervous system development (GO:0007399)|regulation of growth (GO:0040008)|regulation of synaptic transmission (GO:0050804)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|Golgi-associated vesicle membrane (GO:0030660)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	growth factor activity (GO:0008083)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|prostate(2)	22				BRCA - Breast invasive adenocarcinoma(193;0.000266)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		GGTctccacctcctactgcat	0.542																																					p.G290G		Atlas-SNP	.											.	CSPG5	46	.	0			c.A870G						.						23	23	23					3																	47618646		2203	4300	6503	SO:0001819	synonymous_variant	10675	exon2			TCCACCTCCTACT	AF059274	CCDS2757.1, CCDS56252.1, CCDS56253.1, CCDS74930.1	3p21.3	2008-07-18			ENSG00000114646	ENSG00000114646			2467	protein-coding gene	gene with protein product		606775				9950058	Standard	NM_006574		Approved	NGC	uc003crp.4	O95196	OTTHUMG00000133518	ENST00000383738.2:c.870A>G	chr3.hg19:g.47618646T>C		65.0	0.0		63.0	15.0	NM_006574	Q71M39|Q71M40	Silent	SNP	ENST00000383738.2	hg19	CCDS56253.1																																																																																			.	.		0.542	CSPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257489.1	NM_006574		C	47618646	T	C	47618646	2	2	308	1	0	0	0	0	0	0	0	1	3963	1538	54	2		2	CSPG5	3	47618646	Silent	SNP	T	TCGA-HP-A5N0-01A-11D-A28X-10	40124172	47618646	150403784	22	43939										
DNAH1	25981	hgsc.bcm.edu	37	chr3	52393979	52393979	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	gggaagctgtcccgcatgcaGcgggcagtgctgtcagcgct	16	12	1	0			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr3:52393979G>A	ENST00000420323.2	+	27	4716	c.4455G>A	c.(4453-4455)caG>caA	p.Q1485Q		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	1485	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		CCCGCATGCAGCGGGCAGTGC	0.577																																					p.Q1485Q		Atlas-SNP	.											.	DNAH1	534	.	0			c.G4455A						.						162	170	168					3																	52393979		2154	4253	6407	SO:0001819	synonymous_variant	25981	exon27			CATGCAGCGGGCA	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.4455G>A	chr3.hg19:g.52393979G>A		203.0	0.0		176.0	69.0	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Silent	SNP	ENST00000420323.2	hg19	CCDS46842.1																																																																																			.	.		0.577	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		A	52393979	G	A	52393979	2	1	308	1	0	0	0	0	0	0	0	1	4599	962	34	3		3	DNAH1	3	52393979	Silent	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10	4775333	52393979	145628451	23	43940										
MYH15	22989	hgsc.bcm.edu	37	chr3	108133086	108133086	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	ttgccctactcacttggcatCctccaagtcttctgttctct	5	15	4	0			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr3:108133086C>G	ENST00000273353.3	-	31	4254	c.4198G>C	c.(4198-4200)Gat>Cat	p.D1400H		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	1400						cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						CACTTGGCATCCTCCAAGTCT	0.463																																					p.D1400H		Atlas-SNP	.											.	MYH15	223	.	0			c.G4198C						.						156	151	152					3																	108133086		1977	4158	6135	SO:0001583	missense	22989	exon31			TGGCATCCTCCAA	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"Myosins / Myosin superfamily : Class II"	31073	protein-coding gene	gene with protein product		609929	"myosin, heavy polypeptide 15"			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.4198G>C	chr3.hg19:g.108133086C>G	ENSP00000273353:p.Asp1400His	130.0	0.0		142.0	27.0	NM_014981		Missense_Mutation	SNP	ENST00000273353.3	hg19	CCDS43127.1	.	.	.	.	.	.	.	.	.	.	C	19.84	3.901987	0.72754	.	.	ENSG00000144821	ENST00000273353	T	0.80480	-1.38	5.17	3.38	0.38709	Myosin tail (1);	.	.	.	.	D	0.85314	0.5668	M	0.69523	2.12	0.36664	D	0.878096	P	0.48834	0.916	P	0.55455	0.776	D	0.87952	0.2724	9	0.87932	D	0	.	11.7857	0.52041	0.0:0.861:0.0:0.139	.	1400	Q9Y2K3	MYH15_HUMAN	H	1400	ENSP00000273353:D1400H	ENSP00000273353:D1400H	D	-	1	0	MYH15	109615776	1.000000	0.71417	0.155000	0.22561	0.897000	0.52465	3.917000	0.56424	0.679000	0.31345	0.655000	0.94253	GAT	.	.		0.463	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988		G	108133086	C	G	108133086	3	3	308	1	0	0	0	0	1	0	0	0	10043	855	30	4	1690	4	MYH15	3	108133086	Missense_Mutation	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	55739107	108133086	89889344	24	43941										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178928226	178928226	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	ttccatctcttaggaaactcCatgcttagagttggagtttg	9	8	1	1			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr3:178928226C>T	ENST00000263967.3	+	9	1569	c.1412C>T	c.(1411-1413)cCa>cTa	p.P471L		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	471	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00880}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.P471L(6)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TAGGAAACTCCATGCTTAGAG	0.368		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											p.P471L	Colon(199;1504 1750 3362 26421 31210 32040)	Atlas-SNP	.		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	PIK3CA_ENST00000263967,scalp,carcinoma,0,8	PIK3CA	8460	.	6	Substitution - Missense(6)	large_intestine(2)|endometrium(2)|skin(2)	c.C1412T						.						99	93	95					3																	178928226		1846	4090	5936	SO:0001583	missense	5290	exon9			AAACTCCATGCTT		CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1412C>T	chr3.hg19:g.178928226C>T	ENSP00000263967:p.Pro471Leu	114.0	0.0		99.0	4.0	NM_006218	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	hg19	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.756128	0.89843	.	.	ENSG00000121879	ENST00000263967	T	0.75821	-0.97	5.64	5.64	0.86602	C2 calcium/lipid-binding domain, CaLB (1);Phosphoinositide 3-kinase, C2 (1);	0.107853	0.64402	D	0.000005	D	0.83769	0.5326	M	0.74258	2.255	0.80722	D	1	D	0.56968	0.978	P	0.57620	0.824	T	0.81326	-0.0983	10	0.30854	T	0.27	-14.0418	19.6973	0.96031	0.0:1.0:0.0:0.0	.	471	P42336	PK3CA_HUMAN	L	471	ENSP00000263967:P471L	ENSP00000263967:P471L	P	+	2	0	PIK3CA	180410920	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.466000	0.80914	2.674000	0.91012	0.655000	0.94253	CCA	.	.		0.368	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			T	178928226	C	T	178928226	3	4	308	1	0	0	0	0	1	0	0	0	11922	594	21	3	1442	3	PIK3CA	3	178928226	Missense_Mutation	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	70795140	178928226	19094204	25	43942										
HTT	3064	hgsc.bcm.edu	37	chr4	3237426	3237426	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	gcagaatcgctggtcaagctGagtgtggacagagtgaacgt	15	7	1	4			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr4:3237426G>T	ENST00000355072.5	+	63	8851	c.8706G>T	c.(8704-8706)ctG>ctT	p.L2902L		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	2902					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		TGGTCAAGCTGAGTGTGGACA	0.627																																					p.L2902L		Atlas-SNP	.											.	HTT	221	.	0			c.G8706T						.						41	46	44					4																	3237426		2137	4251	6388	SO:0001819	synonymous_variant	3064	exon63			CAAGCTGAGTGTG	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.8706G>T	chr4.hg19:g.3237426G>T		97.0	0.0		56.0	27.0	NM_002111	Q9UQB7	Silent	SNP	ENST00000355072.5	hg19	CCDS43206.1																																																																																			.	.		0.627	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		T	3237426	G	T	3237426	2	4	308	1	0	0	0	0	0	0	0	1	7466	1277	45	3		3	HTT	4	3237426	Silent	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10		3237426	187916850	26	43943										
SLC34A2	10568	hgsc.bcm.edu	37	chr4	25671316	25671316	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	cttcttcaactggctgtccgTgttggtgctcttgcccgtgg	12	12	3	0			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr4:25671316T>A	ENST00000382051.3	+	7	733	c.683T>A	c.(682-684)gTg>gAg	p.V228E	SLC34A2_ENST00000504570.1_Missense_Mutation_p.V227E|SLC34A2_ENST00000503434.1_Missense_Mutation_p.V227E	NM_001177998.1|NM_006424.2	NP_001171469.1|NP_006415	O95436	NPT2B_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 2	228				V -> L (in Ref. 2; AAF31328 and 5; AAL55657). {ECO:0000305}.	aging (GO:0007568)|cellular phosphate ion homeostasis (GO:0030643)|in utero embryonic development (GO:0001701)|ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|response to fructose (GO:0009750)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	phosphate ion binding (GO:0042301)|sodium ion binding (GO:0031402)|sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|sodium:phosphate symporter activity (GO:0005436)		SLC34A2/ROS1(14)	breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|skin(4)	41		Breast(46;0.0503)				TGGCTGTCCGTGTTGGTGCTC	0.532			T	ROS1	NSCLC																																p.V228E		Atlas-SNP	.		Dom	yes		4	4p15.2	10568	"solute carrier family 34 (sodium phosphate), member 2"		E	.	SLC34A2	93	.	0			c.T683A						.						206	198	201					4																	25671316		2203	4300	6503	SO:0001583	missense	10568	exon7			TGTCCGTGTTGGT	AF111856	CCDS3435.1, CCDS54750.1	4p15.2	2013-07-17	2013-07-17		ENSG00000157765	ENSG00000157765		"Solute carriers"	11020	protein-coding gene	gene with protein product		604217	"solute carrier family 34 (sodium phosphate), member 2"			10329428, 10610722	Standard	NM_006424		Approved	NAPI-3B	uc003grr.3	O95436	OTTHUMG00000097757	ENST00000382051.3:c.683T>A	chr4.hg19:g.25671316T>A	ENSP00000371483:p.Val228Glu	186.0	0.0		171.0	57.0	NM_006424	A5PL17|Q8N2K2|Q8WYA9|Q9P0V7	Missense_Mutation	SNP	ENST00000382051.3	hg19	CCDS3435.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.705879	0.89018	.	.	ENSG00000157765	ENST00000504570;ENST00000382051;ENST00000503434	D;D;D	0.88277	-2.36;-2.36;-2.36	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	D	0.96778	0.8948	H	0.98426	4.23	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.76071	0.983;0.987	D	0.98429	1.0581	10	0.87932	D	0	-29.2286	15.5276	0.75923	0.0:0.0:0.0:1.0	.	227;228	O95436-2;O95436	.;NPT2B_HUMAN	E	227;228;227	ENSP00000425501:V227E;ENSP00000371483:V228E;ENSP00000423021:V227E	ENSP00000371483:V228E	V	+	2	0	SLC34A2	25280414	1.000000	0.71417	0.268000	0.24571	0.846000	0.48090	7.948000	0.87774	2.136000	0.66102	0.459000	0.35465	GTG	.	.		0.532	SLC34A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214990.1	NM_006424		A	25671316	T	A	25671316	3	1	308	1	0	0	0	0	1	0	0	0	14583	1696	59	4	705	4	SLC34A2	4	25671316	Missense_Mutation	SNP	T	TCGA-HP-A5N0-01A-11D-A28X-10	22433890	25671316	165482960	27	43944										
PLK4	10733	hgsc.bcm.edu	37	chr4	128816239	128816239	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	tttgtgaaaaatgttggttgGgctacacaggtgagaagttt	13	3	0	2			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr4:128816239G>T	ENST00000270861.5	+	14	2968	c.2694G>T	c.(2692-2694)tgG>tgT	p.W898C	PLK4_ENST00000507249.1_Missense_Mutation_p.W837C|PLK4_ENST00000513090.1_Missense_Mutation_p.W866C|PLK4_ENST00000515069.1_Missense_Mutation_p.W820C|PLK4_ENST00000514379.1_Missense_Mutation_p.W857C	NM_014264.4	NP_055079.3	O00444	PLK4_HUMAN	polo-like kinase 4	898	POLO box. {ECO:0000255|PROSITE- ProRule:PRU00154}.				centriole replication (GO:0007099)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of centriole replication (GO:0046601)|protein phosphorylation (GO:0006468)|trophoblast giant cell differentiation (GO:0060707)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	31						ATGTTGGTTGGGCTACACAGG	0.323																																					p.W898C	Colon(135;508 1718 19061 31832 42879)	Atlas-SNP	.											.	PLK4	65	.	0			c.G2694T						.						111	114	113					4																	128816239		2203	4300	6503	SO:0001583	missense	10733	exon14			TGGTTGGGCTACA	Y13115	CCDS3735.1, CCDS54803.1, CCDS54804.1	4q27-q28	2013-01-18	2010-06-24	2004-01-28	ENSG00000142731	ENSG00000142731			11397	protein-coding gene	gene with protein product		605031	"serine/threonine kinase 18", "polo-like kinase 4 (Drosophila)"	STK18			Standard	NM_014264		Approved	Sak	uc003ifo.3	O00444	OTTHUMG00000133301	ENST00000270861.5:c.2694G>T	chr4.hg19:g.128816239G>T	ENSP00000270861:p.Trp898Cys	79.0	0.0		37.0	13.0	NM_014264	B2RAL0|B7Z837|B7Z8G7|Q8IYF0|Q96Q95|Q9UD84|Q9UDE2	Missense_Mutation	SNP	ENST00000270861.5	hg19	CCDS3735.1	.	.	.	.	.	.	.	.	.	.	G	14.69	2.609263	0.46527	.	.	ENSG00000142731	ENST00000270861;ENST00000515069;ENST00000513090;ENST00000507249;ENST00000514379;ENST00000508113	T;T;T;T;T;T	0.11712	2.75;2.75;2.75;2.75;2.75;2.75	5.25	4.37	0.52481	POLO box duplicated domain (2);	0.056561	0.85682	D	0.000000	T	0.12475	0.0303	L	0.35723	1.085	0.80722	D	1	B;B	0.33494	0.01;0.414	B;B	0.38378	0.034;0.272	T	0.06232	-1.0838	10	0.52906	T	0.07	-1.8738	15.0412	0.71793	0.0:0.0:0.8575:0.1425	.	866;898	O00444-2;O00444	.;PLK4_HUMAN	C	898;820;866;837;857;144	ENSP00000270861:W898C;ENSP00000421774:W820C;ENSP00000427554:W866C;ENSP00000423412:W837C;ENSP00000423582:W857C;ENSP00000427568:W144C	ENSP00000270861:W898C	W	+	3	0	PLK4	129035689	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.950000	0.70265	2.730000	0.93505	0.479000	0.44913	TGG	.	.		0.323	PLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257095.3			T	128816239	G	T	128816239	3	4	308	1	0	0	0	0	1	0	0	0	12107	1241	43	3	2748	3	PLK4	4	128816239	Missense_Mutation	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10	103144923	128816239	62338037	28	43945										
UCP1	7350	hgsc.bcm.edu	37	chr4	141484571	141484571	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	tccgtggagatggctctgtgCttgaagtctgactttcacga	12	9	3	3			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr4:141484571C>T	ENST00000262999.3	-	3	502	c.427G>A	c.(427-429)Gca>Aca	p.A143T		NM_021833.4	NP_068605.1	P25874	UCP1_HUMAN	uncoupling protein 1 (mitochondrial, proton carrier)	143					brown fat cell differentiation (GO:0050873)|cellular metabolic process (GO:0044237)|mitochondrial transport (GO:0006839)|proton transport (GO:0015992)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	oxidative phosphorylation uncoupler activity (GO:0017077)			NS(1)|breast(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(1)|stomach(1)	16	all_hematologic(180;0.162)					TGGCTCTGTGCTTGAAGTCTG	0.483																																					p.A143T		Atlas-SNP	.											.	UCP1	33	.	0			c.G427A						.						155	135	142					4																	141484571		2203	4300	6503	SO:0001583	missense	7350	exon3			TCTGTGCTTGAAG	X51955	CCDS3753.1	4q28-q31	2013-05-22			ENSG00000109424	ENSG00000109424		"Solute carriers"	12517	protein-coding gene	gene with protein product		113730		UCP		2380264	Standard	NM_021833		Approved	SLC25A7	uc011chj.2	P25874	OTTHUMG00000133415	ENST00000262999.3:c.427G>A	chr4.hg19:g.141484571C>T	ENSP00000262999:p.Ala143Thr	134.0	0.0		118.0	24.0	NM_021833	Q13218|Q4KMZ3|Q68G66	Missense_Mutation	SNP	ENST00000262999.3	hg19	CCDS3753.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.058183	0.76074	.	.	ENSG00000109424	ENST00000262999	T	0.78595	-1.19	5.44	5.44	0.79542	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.86573	0.5965	M	0.64567	1.98	0.58432	D	0.999997	D;D	0.60160	0.987;0.987	D;D	0.79784	0.993;0.993	D	0.87617	0.2507	10	0.87932	D	0	.	16.744	0.85467	0.0:1.0:0.0:0.0	.	142;143	Q4KMT7;P25874	.;UCP1_HUMAN	T	143	ENSP00000262999:A143T	ENSP00000262999:A143T	A	-	1	0	UCP1	141704021	1.000000	0.71417	0.588000	0.28705	0.119000	0.20118	6.963000	0.76055	2.560000	0.86352	0.650000	0.86243	GCA	.	.		0.483	UCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257273.1			T	141484571	C	T	141484571	3	4	308	1	0	0	0	0	1	0	0	0	16945	797	28	3	510	3	UCP1	4	141484571	Missense_Mutation	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	12668332	141484571	49669705	29	43946										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155163818	155163818	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	tgtaatttccactgcttcagAggggagaaaagctggggcat	13	7	1	2			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr4:155163818A>T	ENST00000357232.4	-	22	5682	c.5683T>A	c.(5683-5685)Tct>Act	p.S1895T		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1895	Cadherin 17. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		ACTGCTTCAGAGGGGAGAAAA	0.398																																					p.S1895T		Atlas-SNP	.											.	DCHS2	594	.	0			c.T5683A						.						145	136	139					4																	155163818		2203	4300	6503	SO:0001583	missense	54798	exon22			CTTCAGAGGGGAG	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.5683T>A	chr4.hg19:g.155163818A>T	ENSP00000349768:p.Ser1895Thr	100.0	0.0		89.0	34.0	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	hg19	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	A	2.937	-0.219733	0.06061	.	.	ENSG00000197410	ENST00000357232	T	0.61510	0.1	5.15	2.59	0.31030	Cadherin (1);Cadherin-like (1);	0.523212	0.17626	N	0.167550	T	0.42698	0.1214	L	0.53780	1.695	0.09310	N	0.999999	B	0.26547	0.152	B	0.20384	0.029	T	0.24977	-1.0145	10	0.11794	T	0.64	.	4.2122	0.10517	0.5988:0.0:0.2605:0.1407	.	1895	Q6V1P9	PCD23_HUMAN	T	1895	ENSP00000349768:S1895T	ENSP00000349768:S1895T	S	-	1	0	DCHS2	155383268	0.043000	0.20138	0.032000	0.17829	0.321000	0.28281	0.406000	0.21032	0.326000	0.23384	0.482000	0.46254	TCT	.	.		0.398	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		T	155163818	A	T	155163818	3	4	308	1	0	0	0	0	1	0	0	0	4290	304	11	4	3083	4	DCHS2	4	155163818	Missense_Mutation	SNP	A	TCGA-HP-A5N0-01A-11D-A28X-10	13679247	155163818	35990458	30	43947										
RAPGEF2	9693	hgsc.bcm.edu	37	chr4	160253698	160253698	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	ttaaaaaggccagtcgctacTccattccagatcttgctgta	7	11	1	1			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr4:160253698T>C	ENST00000264431.4	+	11	1920	c.1501T>C	c.(1501-1503)Tcc>Ccc	p.S501P		NM_014247.2	NP_055062.1	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor (GEF) 2	501					adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|blood vessel development (GO:0001568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|forebrain neuron development (GO:0021884)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of cell proliferation (GO:0008285)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of melanin biosynthetic process (GO:0048022)|nerve growth factor signaling pathway (GO:0038180)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of vasculogenesis (GO:2001214)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|regulation of synaptic plasticity (GO:0048167)|small GTPase mediated signal transduction (GO:0007264)|ventricular system development (GO:0021591)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	beta-1 adrenergic receptor binding (GO:0031697)|calcium ion binding (GO:0005509)|cAMP binding (GO:0030552)|diacylglycerol binding (GO:0019992)|PDZ domain binding (GO:0030165)|Rap GTPase activator activity (GO:0046582)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	70	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		CAGTCGCTACTCCATTCCAGA	0.393																																					p.S501P		Atlas-SNP	.											.	RAPGEF2	171	.	0			c.T1501C						.						88	84	85					4																	160253698		1882	4106	5988	SO:0001583	missense	9693	exon11			CGCTACTCCATTC	AB002311	CCDS43277.1	4q32.1	2004-03-01	2004-03-01	2004-03-01					16854	protein-coding gene	gene with protein product	"Rap GEP"	609530	"PDZ domain containing guanine nucleotide exchange factor (GEF) 1"	PDZGEF1		9205841, 10934204	Standard	NM_014247		Approved	PDZ-GEF1, RA-GEF, DKFZP586O1422, KIAA0313	uc003iqg.4	Q9Y4G8		ENST00000264431.4:c.1501T>C	chr4.hg19:g.160253698T>C	ENSP00000264431:p.Ser501Pro	231.0	0.0		169.0	43.0	NM_014247	D3DP27	Missense_Mutation	SNP	ENST00000264431.4	hg19	CCDS43277.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	27.2|27.2	4.814180|4.814180	0.90790|0.90790	.|.	.|.	ENSG00000109756|ENSG00000109756	ENST00000512056|ENST00000264431	.|T	.|0.42513	.|0.97	5.63|5.63	5.63|5.63	0.86233|0.86233	.|Ras guanine nucleotide exchange factor, domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.62344|0.62344	0.2420|0.2420	M|M	0.66939|0.66939	2.045|2.045	0.80722|0.80722	D|D	1|1	.|D	.|0.64830	.|0.994	.|D	.|0.66847	.|0.947	T|T	0.65117|0.65117	-0.6246|-0.6246	5|10	.|0.62326	.|D	.|0.03	.|.	15.8417|15.8417	0.78852|0.78852	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|501	.|Q9Y4G8	.|RPGF2_HUMAN	P|P	138|501	.|ENSP00000264431:S501P	.|ENSP00000264431:S501P	L|S	+|+	2|1	0|0	RAPGEF2|RAPGEF2	160473148|160473148	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.950000|7.950000	0.87804|0.87804	2.141000|2.141000	0.66446|0.66446	0.533000|0.533000	0.62120|0.62120	CTC|TCC	.	.		0.393	RAPGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364980.2	NM_014247		C	160253698	T	C	160253698	3	2	308	1	0	0	0	0	1	0	0	0	13059	1551	54	2	1543	2	RAPGEF2	4	160253698	Missense_Mutation	SNP	T	TCGA-HP-A5N0-01A-11D-A28X-10	5089880	160253698	30900578	31	43948										
GALNTL6	442117	hgsc.bcm.edu	37	chr4	173942670	173942670	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	agatattcgacccggtgagcCactgcatacccggaaattct	9	12	1	2			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr4:173942670C>G	ENST00000506823.1	+	12	2189	c.1532C>G	c.(1531-1533)cCa>cGa	p.P511R	GALNTL6_ENST00000508122.1_Missense_Mutation_p.P494R	NM_001034845.2	NP_001030017.2	Q49A17	GLTL6_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 6	511	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.?(1)		breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(2)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	45						CCCGGTGAGCCACTGCATACC	0.483																																					p.P511R		Atlas-SNP	.											.	GALNTL6	102	.	1	Unknown(1)	breast(1)	c.C1532G						.						149	139	143					4																	173942670		2203	4300	6503	SO:0001583	missense	442117	exon12			GTGAGCCACTGCA		CCDS34104.1	4q34.1	2014-03-13	2014-03-13		ENSG00000174473	ENSG00000174473		"Glycosyltransferase family 2 domain containing"	33844	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase-like 6"	615138	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 6"				Standard	NM_001034845		Approved	GALNT17, GalNAc-T6L	uc003isv.3	Q49A17	OTTHUMG00000160807	ENST00000506823.1:c.1532C>G	chr4.hg19:g.173942670C>G	ENSP00000423313:p.Pro511Arg	168.0	0.0		113.0	44.0	NM_001034845	Q2L4S6	Missense_Mutation	SNP	ENST00000506823.1	hg19	CCDS34104.1	.	.	.	.	.	.	.	.	.	.	C	17.01	3.278701	0.59758	.	.	ENSG00000174473	ENST00000506823;ENST00000508122	T;T	0.25749	1.78;1.78	5.81	5.81	0.92471	Ricin B-related lectin (1);Ricin B lectin (3);	0.075225	0.56097	D	0.000025	T	0.50803	0.1637	M	0.65320	2	0.80722	D	1	D	0.76494	0.999	D	0.71656	0.974	T	0.40869	-0.9540	10	0.52906	T	0.07	.	20.0817	0.97778	0.0:1.0:0.0:0.0	.	511	Q49A17	GLTL6_HUMAN	R	511;494	ENSP00000423313:P511R;ENSP00000423827:P494R	ENSP00000423313:P511R	P	+	2	0	GALNTL6	174179245	1.000000	0.71417	0.969000	0.41365	0.084000	0.17831	7.458000	0.80787	2.743000	0.94032	0.650000	0.86243	CCA	.	.		0.483	GALNTL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362395.1	NM_001034845		G	173942670	C	G	173942670	3	3	308	1	0	0	0	0	1	0	0	0	6233	594	21	4	1574	4	GALNTL6	4	173942670	Missense_Mutation	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	13688972	173942670	17211606	32	43949										
SORBS2	8470	hgsc.bcm.edu	37	chr4	186544299	186544299	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	cagctcactgatgaggcggtGcaggatgctgttgtccggca	15	10	1	2			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr4:186544299G>T	ENST00000284776.7	-	13	2781	c.2272C>A	c.(2272-2274)Cac>Aac	p.H758N	SORBS2_ENST00000431808.1_Missense_Mutation_p.H758N|SORBS2_ENST00000498125.1_Intron|SORBS2_ENST00000448662.2_Intron|SORBS2_ENST00000418609.1_Missense_Mutation_p.H662N|SORBS2_ENST00000319471.9_Intron|SORBS2_ENST00000437304.2_Intron|SORBS2_ENST00000393528.3_Intron|SORBS2_ENST00000355634.5_Missense_Mutation_p.H858N|SORBS2_ENST00000449407.2_Intron	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	758					actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		ATGAGGCGGTGCAGGATGCTG	0.562																																					p.H858N	Esophageal Squamous(153;41 2433 9491 36028)	Atlas-SNP	.											.	SORBS2	300	.	0			c.C2572A						.						135	154	148					4																	186544299		2203	4300	6503	SO:0001583	missense	8470	exon16			GGCGGTGCAGGAT		CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556			24098	protein-coding gene	gene with protein product	"Arg/Abl interacting protein"					9211900, 9872452	Standard	NM_021069		Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000284776.7:c.2272C>A	chr4.hg19:g.186544299G>T	ENSP00000284776:p.His758Asn	68.0	0.0		55.0	4.0	NM_001270771	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Missense_Mutation	SNP	ENST00000284776.7	hg19	CCDS3845.1	.	.	.	.	.	.	.	.	.	.	G	14.87	2.664954	0.47572	.	.	ENSG00000154556	ENST00000284776;ENST00000431808;ENST00000418609;ENST00000355634	T;T;T;T	0.36878	1.31;1.31;1.23;1.3	5.77	5.77	0.91146	.	0.054833	0.64402	D	0.000001	T	0.59183	0.2175	L	0.56769	1.78	0.50632	D	0.999889	D;D;D	0.64830	0.994;0.993;0.994	D;D;D	0.72338	0.977;0.968;0.977	T	0.56347	-0.7994	10	0.54805	T	0.06	-28.33	19.982	0.97329	0.0:0.0:1.0:0.0	.	662;858;758	B7Z3X6;B3KPQ7;O94875	.;.;SRBS2_HUMAN	N	758;758;662;858	ENSP00000284776:H758N;ENSP00000411764:H758N;ENSP00000397482:H662N;ENSP00000347852:H858N	ENSP00000284776:H758N	H	-	1	0	SORBS2	186781293	1.000000	0.71417	1.000000	0.80357	0.266000	0.26442	7.654000	0.83653	2.737000	0.93849	0.561000	0.74099	CAC	.	.		0.562	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603		T	186544299	G	T	186544299	3	4	308	1	0	0	0	0	1	0	0	0	14943	1319	46	3	1066	3	SORBS2	4	186544299	Missense_Mutation	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10	12601629	186544299	4609977	33	43950										
LMBRD2	92255	hgsc.bcm.edu	37	chr5	36124328	36124328	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	atcaacacattttctcaatgGgtgattatacttgatgcttt	6	7	2	2			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr5:36124328G>T	ENST00000296603.4	-	7	1249	c.787C>A	c.(787-789)Cca>Aca	p.P263T		NM_001007527.1	NP_001007528.1	Q68DH5	LMBD2_HUMAN	LMBR1 domain containing 2	263						integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_lung(31;0.000146)		Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TTTCTCAATGGGTGATTATAC	0.259																																					p.P263T		Atlas-SNP	.											.	LMBRD2	89	.	0			c.C787A						.						59	57	57					5																	36124328		2195	4281	6476	SO:0001583	missense	92255	exon7			TCAATGGGTGATT		CCDS34145.1	5p13.2	2008-02-05			ENSG00000164187	ENSG00000164187			25287	protein-coding gene	gene with protein product							Standard	NM_001007527		Approved	DKFZp434H2226	uc003jkb.1	Q68DH5	OTTHUMG00000162150	ENST00000296603.4:c.787C>A	chr5.hg19:g.36124328G>T	ENSP00000296603:p.Pro263Thr	246.0	0.0		174.0	41.0	NM_001007527	B3KRB6|Q9NTC7	Missense_Mutation	SNP	ENST00000296603.4	hg19	CCDS34145.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.873167	0.91664	.	.	ENSG00000164187	ENST00000296603;ENST00000546130	T	0.28255	1.62	5.61	5.61	0.85477	LMBR1-like membrane protein (1);	0.000000	0.85682	D	0.000000	T	0.46386	0.1390	M	0.69823	2.125	0.80722	D	1	P	0.49185	0.92	P	0.50860	0.652	T	0.23084	-1.0198	10	0.23302	T	0.38	-13.0866	19.6306	0.95700	0.0:0.0:1.0:0.0	.	263	Q68DH5	LMBD2_HUMAN	T	263;157	ENSP00000296603:P263T	ENSP00000296603:P263T	P	-	1	0	LMBRD2	36160085	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.175000	0.77632	2.646000	0.89796	0.585000	0.79938	CCA	.	.		0.259	LMBRD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367552.1	NM_001007527		T	36124328	G	T	36124328	3	4	308	1	0	0	0	0	1	0	0	0	8852	1232	43	3	1348	3	LMBRD2	5	36124328	Missense_Mutation	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10		36124328	144790932	34	43951										
JMY	133746	hgsc.bcm.edu	37	chr5	78533507	78533522	+	Splice_Site	DEL	TGAGTGAGTGAGCTCC	TGAGTGAGTGAGCTCC	-													0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	caggaagcgcatccaggaggTgagtgagtgagctcctagtc					rs373550284		TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	TGAGTGAGTGAGCTCC	TGAGTGAGTGAGCTCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr5:78533507_78533522delTGAGTGAGTGAGCTCC	ENST00000396137.4	+	1	1494		c.e1+2		DMGDH_ENST00000520388.1_5'Flank	NM_152405.4	NP_689618.4	Q8N9B5	JMY_HUMAN	junction mediating and regulatory protein, p53 cofactor						'de novo' actin filament nucleation (GO:0070060)|actin polymerization-dependent cell motility (GO:0070358)|Arp2/3 complex-mediated actin nucleation (GO:0034314)|cell cycle arrest (GO:0007050)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of apoptotic process (GO:0043065)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			endometrium(4)|kidney(2)|large_intestine(2)|lung(6)|skin(1)|urinary_tract(1)	16		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;4.45e-45)|Epithelial(54;5.85e-40)|all cancers(79;2.89e-35)		ATCCAGGAGGTGAGTGAGTGAGCTCCTAGTCTGGGC	0.569																																					.		Pindel	.											.	JMY	82	.	0			.						.																																			SO:0001630	splice_region_variant	133746	.			.	AK095189	CCDS4047.3	5q14.1	2010-03-23			ENSG00000152409	ENSG00000152409			28916	protein-coding gene	gene with protein product		604279				10518217	Standard	NM_152405		Approved	FLJ37870	uc003kfx.4	Q8N9B5	OTTHUMG00000131301	ENST00000396137.4:c.1032+2TGAGTGAGTGAGCTCC>-	chr5.hg19:g.78533507_78533522delTGAGTGAGTGAGCTCC		143.0	0.0		98.0	11.0	.	A1L4P5|B5MDS2|B5MDT0	Splice_Site	DEL	ENST00000396137.4	hg19	CCDS4047.3																																																																																			.	.		0.569	JMY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254070.4	NM_152405	Intron	-	78533522	TGAGTGAGTGAGCTCC	-	78533507	8	5	308	1	0	1	0	1	0	0	1	0	7966	1710	59	0	1036	0	JMY	5	78533507	Splice_Site	DEL	TGAGTGAGTGAGCTCC	TCGA-HP-A5N0-01A-11D-A28X-10	42409179	78533507	102381753	35	43952										
PCDHGC3	5098	hgsc.bcm.edu	37	chr5	140857854	140857854	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	ttacaagtggaagcagtctaGagacctataccgagccccgg	11	11	1	1			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr5:140857854G>C	ENST00000308177.3	+	1	2275	c.2171G>C	c.(2170-2172)aGa>aCa	p.R724T	PCDHGB3_ENST00000576222.1_Intron|RN7SL68P_ENST00000488078.2_RNA|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA8_ENST00000398604.2_Intron	NM_002588.2|NM_032402.1	NP_002579.2|NP_115778.1	Q9UN70	PCDGK_HUMAN	protocadherin gamma subfamily C, 3	724					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(2)|urinary_tract(1)	29			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAGCAGTCTAGAGACCTATAC	0.527											OREG0016865	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R724T		Atlas-SNP	.											.	PCDHGC3	173	.	0			c.G2171C						.						169	199	189					5																	140857854		2203	4300	6503	SO:0001583	missense	5098	exon1			AGTCTAGAGACCT	AF152337	CCDS4261.1, CCDS75347.1, CCDS75348.1	5q31	2010-01-26			ENSG00000240184	ENSG00000240184		"Cadherins / Protocadherins : Clustered"	8716	other	protocadherin	"cadherin-like 2", "protocadherin 2", "protocadherin 43"	603627		PCDH2		9360932, 8508762	Standard	NM_032402		Approved	PC-43, PC43, PCDH-GAMMA-C3		Q9UN70	OTTHUMG00000129613	ENST00000308177.3:c.2171G>C	chr5.hg19:g.140857854G>C	ENSP00000312070:p.Arg724Thr	68.0	0.0	1659	68.0	7.0	NM_032402	O60622|Q08192|Q9Y5C4	Missense_Mutation	SNP	ENST00000308177.3	hg19	CCDS4261.1	.	.	.	.	.	.	.	.	.	.	G	13.50	2.255106	0.39896	.	.	ENSG00000240184	ENST00000308177	T	0.49139	0.79	5.46	3.66	0.41972	.	.	.	.	.	T	0.36026	0.0952	N	0.16656	0.425	0.22156	N	0.999325	B;B	0.34290	0.155;0.447	B;B	0.40602	0.071;0.334	T	0.28202	-1.0051	9	0.51188	T	0.08	.	9.1498	0.36955	0.227:0.0:0.773:0.0	.	724;724	Q9UN70;Q9UN70-2	PCDGK_HUMAN;.	T	724	ENSP00000312070:R724T	ENSP00000312070:R724T	R	+	2	0	PCDHGC3	140838038	0.012000	0.17670	1.000000	0.80357	0.949000	0.60115	0.679000	0.25291	1.540000	0.49301	0.655000	0.94253	AGA	.	.		0.527	PCDHGC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251808.2	NM_002588		C	140857854	G	C	140857854	3	2	308	1	0	0	0	0	1	0	0	0	11578	942	33	4	2173	4	PCDHGC3	5	140857854	Missense_Mutation	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10	62324347	140857854	40057406	36	43953										
ATP10B	23120	hgsc.bcm.edu	37	chr5	160113232	160113232	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	ctgtggaagacttccatggaGggcatccagttcaaaatcac	10	10	2	1			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr5:160113232G>A	ENST00000327245.5	-	6	1170	c.324C>T	c.(322-324)ccC>ccT	p.P108P	ATP10B_ENST00000518411.1_5'UTR|CTC-529G1.1_ENST00000524198.1_RNA	NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	108					phospholipid translocation (GO:0045332)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1)	75	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CTTCCATGGAGGGCATCCAGT	0.458																																					p.P108P		Atlas-SNP	.											.	ATP10B	201	.	0			c.C324T						.						77	74	75					5																	160113232		1904	4120	6024	SO:0001819	synonymous_variant	23120	exon6			CATGGAGGGCATC	AB018258	CCDS43394.1	5q34	2010-04-20	2007-09-19		ENSG00000118322	ENSG00000118322		"ATPases / P-type"	13543	protein-coding gene	gene with protein product			"ATPase, Class V, type 10B"			9872452, 11015572	Standard	NM_025153		Approved	ATPVB, KIAA0715, FLJ21477	uc003lym.1	O94823	OTTHUMG00000163551	ENST00000327245.5:c.324C>T	chr5.hg19:g.160113232G>A		154.0	0.0		145.0	40.0	NM_025153	Q9H725	Silent	SNP	ENST00000327245.5	hg19	CCDS43394.1																																																																																			.	.		0.458	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374127.1	NM_025153		A	160113232	G	A	160113232	2	1	308	1	0	0	0	0	0	0	0	1	1117	987	35	3		3	ATP10B	5	160113232	Silent	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10	19255378	160113232	20802028	37	43954										
GABRA1	2554	hgsc.bcm.edu	37	chr5	161324184	161324184	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	tccaacagcaaccagctacaCccctaatttggccaggggcg	9	15	0	0			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr5:161324184C>A	ENST00000428797.2	+	11	1482	c.1127C>A	c.(1126-1128)aCc>aAc	p.T376N	GABRA1_ENST00000023897.6_Missense_Mutation_p.T376N|GABRA1_ENST00000393943.4_Missense_Mutation_p.T376N|GABRA1_ENST00000420560.1_Missense_Mutation_p.T376N|GABRA1_ENST00000444819.1_Missense_Mutation_p.T376N|GABRA1_ENST00000437025.2_Missense_Mutation_p.T376N	NM_001127643.1	NP_001121115.1	P14867	GBRA1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 1	376					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|drug binding (GO:0008144)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.T376N(1)		NS(1)|endometrium(2)|kidney(3)|large_intestine(4)|liver(1)|lung(22)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(1)	42	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.228)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethanol(DB00898)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methohexital(DB00474)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Prazepam(DB01588)|Primidone(DB00794)|Progabide(DB00837)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiamylal(DB01154)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zaleplon(DB00962)|Zolpidem(DB00425)|Zopiclone(DB01198)	ACCAGCTACACCCCTAATTTG	0.453																																					p.T376N		Atlas-SNP	.											GABRA1,NS,carcinoma,0,2	GABRA1	132	.	1	Substitution - Missense(1)	pancreas(1)	c.C1127A						.						104	116	112					5																	161324184		2203	4300	6503	SO:0001583	missense	2554	exon11			GCTACACCCCTAA		CCDS4357.1	5q34	2012-06-22			ENSG00000022355	ENSG00000022355		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4075	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 1"	137160				1330891	Standard	NM_000806		Approved	EJM5	uc003lyx.4	P14867	OTTHUMG00000163586	ENST00000428797.2:c.1127C>A	chr5.hg19:g.161324184C>A	ENSP00000393097:p.Thr376Asn	125.0	0.0		120.0	7.0	NM_001127643	D3DQK6|Q8N629	Missense_Mutation	SNP	ENST00000428797.2	hg19	CCDS4357.1	.	.	.	.	.	.	.	.	.	.	C	15.22	2.769225	0.49680	.	.	ENSG00000022355	ENST00000023897;ENST00000428797;ENST00000393943;ENST00000437025;ENST00000420560;ENST00000444819	D;D;D;D;D;D	0.81499	-1.5;-1.5;-1.5;-1.5;-1.5;-1.5	5.32	5.32	0.75619	Neurotransmitter-gated ion-channel transmembrane domain (1);	0.174985	0.38663	U	0.001613	T	0.77928	0.4204	L	0.36672	1.1	0.49582	D	0.9998	P	0.37594	0.601	B	0.42959	0.403	T	0.73541	-0.3950	10	0.21540	T	0.41	.	19.3564	0.94416	0.0:1.0:0.0:0.0	.	376	P14867	GBRA1_HUMAN	N	376	ENSP00000023897:T376N;ENSP00000393097:T376N;ENSP00000377517:T376N;ENSP00000415441:T376N;ENSP00000408041:T376N;ENSP00000414232:T376N	ENSP00000023897:T376N	T	+	2	0	GABRA1	161256762	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.395000	0.79876	2.642000	0.89623	0.563000	0.77884	ACC	.	.		0.453	GABRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252702.2	NM_000806.5		A	161324184	C	A	161324184	3	1	308	1	0	0	0	0	1	0	0	0	6168	507	18	3	1161	3	GABRA1	5	161324184	Missense_Mutation	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	1210952	161324184	19591076	38	43955										
SLIT3	6586	hgsc.bcm.edu	37	chr5	168233531	168233531	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	tccacgatgttattgctgcaCgtgcagggcgaagggcagga	15	9	0	0	rs367972639		TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr5:168233531C>A	ENST00000519560.1	-	9	1274	c.855G>T	c.(853-855)acG>acT	p.T285T	SLIT3_ENST00000404867.3_Silent_p.T285T|SLIT3_ENST00000332966.8_Silent_p.T285T	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	285	LRRNT 2.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TATTGCTGCACGTGCAGGGCG	0.562																																					p.T285T	Ovarian(29;311 847 10864 17279 24903)	Atlas-SNP	.											SLIT3,colon,carcinoma,0,1	SLIT3	224	.	0			c.G855T						.						90	82	85					5																	168233531		2203	4300	6503	SO:0001819	synonymous_variant	6586	exon9			GCTGCACGTGCAG	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"slit (Drosophila) homolog 3"	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.855G>T	chr5.hg19:g.168233531C>A		248.0	0.0		214.0	50.0	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Silent	SNP	ENST00000519560.1	hg19	CCDS4369.1																																																																																			.	.		0.562	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062		A	168233531	C	A	168233531	2	1	308	1	0	0	0	0	0	0	0	1	14756	523	19	1		1	SLIT3	5	168233531	Silent	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	6909347	168233531	12681729	39	43956										
KCNIP1	30820	hgsc.bcm.edu	37	chr5	170145856	170145856	+	Frame_Shift_Del	DEL	G	G	-													0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	accaacttcaccaagagggaGctgcaggtcctttatcgagg							TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr5:170145856delG	ENST00000411494.1	+	3	189	c.189delG	c.(187-189)gagfs	p.E63fs	KCNIP1_ENST00000434108.1_Frame_Shift_Del_p.E52fs|KCNIP1_ENST00000520740.1_Frame_Shift_Del_p.E24fs|KCNIP1_ENST00000390656.4_Frame_Shift_Del_p.E52fs|KCNIP1_ENST00000328939.4_Frame_Shift_Del_p.E52fs|KCNIP1_ENST00000377360.4_Frame_Shift_Del_p.E61fs			Q9NZI2	KCIP1_HUMAN	Kv channel interacting protein 1	63	EF-hand 1; degenerate. {ECO:0000255|PROSITE-ProRule:PRU00448}.				detection of calcium ion (GO:0005513)|positive regulation of action potential (GO:0045760)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|potassium channel complex (GO:0034705)	calcium ion binding (GO:0005509)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|voltage-gated ion channel activity (GO:0005244)			autonomic_ganglia(1)|large_intestine(7)|lung(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	18	Renal(175;0.000159)|Lung NSC(126;0.0191)|all_lung(126;0.0297)	Medulloblastoma(196;0.0109)|all_neural(177;0.0177)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CCAAGAGGGAGCTGCAGGTCC	0.562																																					p.E63fs		Pindel	.											.	KCNIP1	66	.	0			c.188delA						.						66	62	63					5																	170145856		2203	4300	6503	SO:0001589	frameshift_variant	30820	exon3			.	AF199597	CCDS34285.1, CCDS34286.1, CCDS4374.1, CCDS64312.1, CCDS64313.1	5q35	2013-01-10			ENSG00000182132	ENSG00000182132		"EF-hand domain containing"	15521	protein-coding gene	gene with protein product		604660				10676964	Standard	NM_001278339		Approved	KCHIP1	uc003map.3	Q9NZI2	OTTHUMG00000130442	ENST00000411494.1:c.189delG	chr5.hg19:g.170145856delG	ENSP00000395323:p.Glu63fs	91.0	0.0		79.0	20.0	NM_001034837	B7Z7B4|Q3YAD0|Q3YAD1|Q3YAD2|Q3YAD3|Q5U822	Frame_Shift_Del	DEL	ENST00000411494.1	hg19	CCDS34286.1																																																																																			.	.		0.562	KCNIP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000371760.1			-	170145856	G	-	170145856	7	5	308	1	0	1	0	1	0	0	0	0	8048	962	34	0	291	0	KCNIP1	5	170145856	Frame_Shift_Del	DEL	G	TCGA-HP-A5N0-01A-11D-A28X-10	1912325	170145856	10769404	40	43957										
DOK3	79930	hgsc.bcm.edu	37	chr5	176936802	176936802	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	gaaggcagccttctcacgcaCctggttcagctgggcacgcg	13	14	2	0			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr5:176936802C>T	ENST00000357198.4	-	1	56		c.e1+1		DOK3_ENST00000312943.6_Intron|DOK3_ENST00000501403.2_Intron|DOK3_ENST00000377112.4_Intron	NM_024872.2	NP_079148.2	Q7L591	DOK3_HUMAN	docking protein 3						Ras protein signal transduction (GO:0007265)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|lung(7)	13	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.191)			TTCTCACGCACCTGGTTCAGC	0.697																																					.		Atlas-SNP	.											.	DOK3	41	.	0			c.51+1G>A						.						50	51	51					5																	176936802		2203	4300	6503	SO:0001630	splice_region_variant	79930	exon2			CACGCACCTGGTT	AK026223	CCDS4426.1, CCDS47349.1, CCDS47350.1	5q35	2008-02-05			ENSG00000146094	ENSG00000146094			24583	protein-coding gene	gene with protein product		611435				10733577, 12595900	Standard	NM_024872		Approved	FLJ22570	uc003mhk.3	Q7L591	OTTHUMG00000130850	ENST00000357198.4:c.51+1G>A	chr5.hg19:g.176936802C>T		158.0	0.0		125.0	30.0	NM_024872	E9PAT0|H7BXS0|Q8N864|Q9BQB3|Q9H666	Splice_Site	SNP	ENST00000357198.4	hg19	CCDS4426.1	.	.	.	.	.	.	.	.	.	.	C	0.625	-0.819677	0.02776	.	.	ENSG00000146094	ENST00000357198	.	.	.	3.26	0.473	0.16763	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999995	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.4785	0.16710	0.0:0.6173:0.0:0.3827	.	.	.	.	.	-1	.	.	.	-	.	.	DOK3	176869408	0.000000	0.05858	0.004000	0.12327	0.022000	0.10575	-0.074000	0.11450	0.078000	0.16900	0.491000	0.48974	.	.	.		0.697	DOK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253420.4	NM_024872	Intron	T	176936802	C	T	176936802	5	4	308	1	0	0	0	0	0	0	1	0	4700	521	18	3	1814	3	DOK3	5	176936802	Splice_Site	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	6790946	176936802	3978458	41	43958										
ATXN1	6310	hgsc.bcm.edu	37	chr6	16327885	16327885	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	tgctgctgctgctgctgctgCtgctgctgctgctgctgctg	14	13	0	0			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr6:16327885C>A	ENST00000244769.4	-	8	1593	c.657G>T	c.(655-657)caG>caT	p.Q219H	ATXN1_ENST00000436367.1_Missense_Mutation_p.Q219H	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	219	Poly-Gln.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				gctgctgctgctgctgctgct	0.652																																					p.Q219H		Atlas-SNP	.											.	ATXN1	117	.	0			c.G657T						.						5	9	8					6																	16327885		2047	4039	6086	SO:0001583	missense	6310	exon7			CTGCTGCTGCTGC	X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"Ataxins"	10548	protein-coding gene	gene with protein product		601556	"spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.657G>T	chr6.hg19:g.16327885C>A	ENSP00000244769:p.Gln219His	80.0	0.0		109.0	12.0	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	hg19	CCDS34342.1	.	.	.	.	.	.	.	.	.	.	C	4.428	0.079217	0.08533	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.57752	0.38;0.38	0.62	-0.561	0.11785	.	.	.	.	.	T	0.13157	0.0319	N	0.19112	0.55	0.09310	N	1	B	0.28713	0.22	B	0.17979	0.02	T	0.15925	-1.0420	9	0.87932	D	0	.	4.3931	0.11350	0.0:0.6364:0.0:0.3636	.	219	P54253	ATX1_HUMAN	H	219	ENSP00000244769:Q219H;ENSP00000416360:Q219H	ENSP00000244769:Q219H	Q	-	3	2	ATXN1	16435864	0.005000	0.15991	0.005000	0.12908	0.144000	0.21451	0.000000	0.12993	-0.298000	0.08921	0.205000	0.17691	CAG	.	.		0.652	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332		A	16327885	C	A	16327885	3	1	308	1	0	0	0	0	1	0	0	0	1209	796	28	3	1798	3	ATXN1	6	16327885	Missense_Mutation	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10		16327885	154787182	42	43959										
MTO1	25821	hgsc.bcm.edu	37	chr6	74183325	74183325	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	tattctaaacaagcatatacCggacaatccatccataccat	3	12	1	0			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr6:74183325C>T	ENST00000370300.4	+	4	863	c.773C>T	c.(772-774)cCg>cTg	p.P258L	MTO1_ENST00000498286.1_Missense_Mutation_p.P258L|MTO1_ENST00000415954.2_Missense_Mutation_p.P258L|MTO1_ENST00000370305.1_Missense_Mutation_p.P184L	NM_012123.3|NM_133645.2	NP_036255.2|NP_598400.1	Q9Y2Z2	MTO1_HUMAN	mitochondrial tRNA translation optimization 1	258					mitochondrial tRNA wobble uridine modification (GO:0070899)|oxidation-reduction process (GO:0055114)	mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)	27						AAGCATATACCGGACAATCCA	0.423																																					p.P258L		Atlas-SNP	.											.	MTO1	59	.	0			c.C773T						.						87	83	84					6																	74183325		2203	4300	6503	SO:0001583	missense	25821	exon4			ATATACCGGACAA	AF132937	CCDS4979.1, CCDS34485.1, CCDS47452.1	6q14.1	2013-05-07	2013-05-07		ENSG00000135297	ENSG00000135297			19261	protein-coding gene	gene with protein product		614667	"mitochondrial translation optimization 1 homolog (S. cerevisiae)"			12011058, 22608499	Standard	NM_012123		Approved		uc003pgy.4	Q9Y2Z2	OTTHUMG00000015032	ENST00000370300.4:c.773C>T	chr6.hg19:g.74183325C>T	ENSP00000359323:p.Pro258Leu	157.0	0.0		96.0	8.0	NM_133645	B3KQB5|Q5SWL2|Q5SWL3|Q5SWL4|Q8NDN7|Q8WZ57|Q96FE6|Q9BS06	Missense_Mutation	SNP	ENST00000370300.4	hg19	CCDS4979.1	.	.	.	.	.	.	.	.	.	.	C	17.46	3.395329	0.62066	.	.	ENSG00000135297	ENST00000415954;ENST00000498286;ENST00000370305;ENST00000370300	T;T;T;T	0.76186	-1.0;-1.0;-1.0;-1.0	5.7	5.7	0.88788	.	0.054502	0.85682	D	0.000000	T	0.77844	0.4191	L	0.42686	1.345	0.80722	D	1	D;D;D	0.61697	0.99;0.969;0.986	P;P;D	0.63033	0.855;0.855;0.91	T	0.79881	-0.1616	10	0.87932	D	0	-11.4426	17.9905	0.89168	0.0:1.0:0.0:0.0	.	258;258;258	Q9Y2Z2-6;Q9Y2Z2-4;Q9Y2Z2	.;.;MTO1_HUMAN	L	258;258;184;258	ENSP00000402038:P258L;ENSP00000419561:P258L;ENSP00000359328:P184L;ENSP00000359323:P258L	ENSP00000359323:P258L	P	+	2	0	MTO1	74240046	1.000000	0.71417	0.997000	0.53966	0.032000	0.12392	7.094000	0.76944	2.682000	0.91365	0.609000	0.83330	CCG	.	.		0.423	MTO1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041215.2	NM_012123		T	74183325	C	T	74183325	3	4	308	1	0	0	0	0	1	0	0	0	9962	652	23	1	787	1	MTO1	6	74183325	Missense_Mutation	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	57855440	74183325	96931742	43	43960										
CD109	135228	hgsc.bcm.edu	37	chr6	74446154	74446154	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	ggttgtcacaacaaagtgatCttggagtcatttccaaaact	8	8	3	1			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr6:74446154C>G	ENST00000287097.5	+	5	668	c.556C>G	c.(556-558)Ctt>Gtt	p.L186V	CD109_ENST00000422508.2_Missense_Mutation_p.L109V|CD109_ENST00000437994.2_Missense_Mutation_p.L186V			Q6YHK3	CD109_HUMAN	CD109 molecule	186					negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						ACAAAGTGATCTTGGAGTCAT	0.378																																					p.L186V		Atlas-SNP	.											.	CD109	170	.	0			c.C556G						.						185	185	185					6																	74446154		2203	4300	6503	SO:0001583	missense	135228	exon5			AGTGATCTTGGAG	AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"CD molecules"	21685	protein-coding gene	gene with protein product		608859	"CD109 antigen (Gov platelet alloantigens)"			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.556C>G	chr6.hg19:g.74446154C>G	ENSP00000287097:p.Leu186Val	117.0	0.0		69.0	36.0	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Missense_Mutation	SNP	ENST00000287097.5	hg19	CCDS4982.1	.	.	.	.	.	.	.	.	.	.	C	15.89	2.967589	0.53507	.	.	ENSG00000156535	ENST00000437994;ENST00000422508;ENST00000287097	T;T;T	0.73575	-0.76;-0.76;-0.76	4.74	4.74	0.60224	Alpha-2-macroglobulin, N-terminal (1);	0.405345	0.21740	N	0.069821	T	0.67599	0.2910	L	0.53249	1.67	0.35023	D	0.758072	P;D;B;B	0.56746	0.905;0.977;0.049;0.372	P;P;B;B	0.53266	0.544;0.722;0.061;0.309	T	0.66598	-0.5883	10	0.29301	T	0.29	.	10.5919	0.45314	0.0:0.9098:0.0:0.0902	.	109;186;186;186	Q6YHK3-2;Q6YHK3-3;Q6YHK3-4;Q6YHK3	.;.;.;CD109_HUMAN	V	186;109;186	ENSP00000388062:L186V;ENSP00000404475:L109V;ENSP00000287097:L186V	ENSP00000287097:L186V	L	+	1	0	CD109	74502875	0.960000	0.32886	0.951000	0.38953	0.847000	0.48162	1.200000	0.32247	2.601000	0.87937	0.655000	0.94253	CTT	.	.		0.378	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493		G	74446154	C	G	74446154	3	3	308	1	0	0	0	0	1	0	0	0	2965	913	32	4	574	4	CD109	6	74446154	Missense_Mutation	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	262829	74446154	96668913	44	43961										
ROS1	6098	hgsc.bcm.edu	37	chr6	117638330	117638330	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	gccatccgggctttacgcaaAtaagtaagaaggtctcctcc	9	12	1	1			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr6:117638330A>G	ENST00000368508.3	-	38	6309	c.6111T>C	c.(6109-6111)taT>taC	p.Y2037Y	GOPC_ENST00000467125.1_5'Flank|ROS1_ENST00000368507.3_Silent_p.Y2031Y	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	2037	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		CTTTACGCAAATAAGTAAGAA	0.398			T	"GOPC, SDC4, SLC34A2, EZR, LRIG3"	"glioblastoma, NSCLC"																																p.Y2037Y		Atlas-SNP	.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"O, E"	.	ROS1	728	.	0			c.T6111C						.						134	124	127					6																	117638330		2203	4300	6503	SO:0001819	synonymous_variant	6098	exon38			ACGCAAATAAGTA	M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"Fibronectin type III domain containing"	10261	protein-coding gene	gene with protein product		165020	"v-ros avian UR2 sarcoma virus oncogene homolog 1", "v-ros UR2 sarcoma virus oncogene homolog 1 (avian)", "c-ros oncogene 1 , receptor tyrosine kinase"			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.6111T>C	chr6.hg19:g.117638330A>G		214.0	0.0		126.0	6.0	NM_002944	Q15368|Q5TDB5	Silent	SNP	ENST00000368508.3	hg19	CCDS5116.1																																																																																			.	.		0.398	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1			G	117638330	A	G	117638330	2	3	308	1	0	0	0	0	0	0	0	1	13546	108	4	2		2	ROS1	6	117638330	Silent	SNP	A	TCGA-HP-A5N0-01A-11D-A28X-10	43192176	117638330	53476737	45	43962										
IGF2R	3482	hgsc.bcm.edu	37	chr6	160494391	160494391	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	ataagagtgtgatcagtttcGtgtgcaggcctgaggccagg	15	7	1	3	rs375863720		TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr6:160494391G>A	ENST00000356956.1	+	34	4985	c.4837G>A	c.(4837-4839)Gtg>Atg	p.V1613M		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	1613					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	GATCAGTTTCGTGTGCAGGCC	0.582													G|||	1	0.000199681	0	0	5008	,	,		20337	0.001		0	False		,,,				2504	0				p.V1613M		Atlas-SNP	.											.	IGF2R	251	.	0			c.G4837A						.	G	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	168	127	141		4837	5.3	1	6		141	0,8600		0,0,4300	no	missense	IGF2R	NM_000876.2	21	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	1613/2492	160494391	1,13005	2203	4300	6503	SO:0001583	missense	3482	exon34			AGTTTCGTGTGCA	J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"CD molecules"	5467	protein-coding gene	gene with protein product	"cation-independent mannose-6 phosphate receptor"	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.4837G>A	chr6.hg19:g.160494391G>A	ENSP00000349437:p.Val1613Met	233.0	0.0		164.0	7.0	NM_000876	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	hg19	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.058852	0.76074	2.27E-4	0.0	ENSG00000197081	ENST00000356956	T	0.12984	2.63	5.3	5.3	0.74995	Mannose-6-phosphate receptor, binding (1);	0.138533	0.50627	D	0.000118	T	0.35335	0.0928	M	0.80847	2.515	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.19844	-1.0293	10	0.72032	D	0.01	-11.0221	19.3023	0.94148	0.0:0.0:1.0:0.0	.	1613	P11717	MPRI_HUMAN	M	1613	ENSP00000349437:V1613M	ENSP00000349437:V1613M	V	+	1	0	IGF2R	160414381	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	5.163000	0.64948	2.639000	0.89480	0.561000	0.74099	GTG	.	.		0.582	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876		A	160494391	G	A	160494391	3	1	308	1	0	0	0	0	1	0	0	0	7585	1145	40	1	4971	1	IGF2R	6	160494391	Missense_Mutation	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10	42856061	160494391	10620676	46	43963										
GPR31	2853	hgsc.bcm.edu	37	chr6	167571101	167571101	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	caagcctggaggctcaggtaGaaggcggccaggaaaggcag	17	9	1	1			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr6:167571101G>A	ENST00000366834.1	-	1	716	c.219C>T	c.(217-219)ttC>ttT	p.F73F		NM_005299.2	NP_005290.2	O00270	GPR31_HUMAN	G protein-coupled receptor 31	73				F -> L (in Ref. 5; AAH95537). {ECO:0000305}.	G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(4)|large_intestine(4)|lung(7)|prostate(1)	17		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;4.81e-20)|BRCA - Breast invasive adenocarcinoma(81;4.45e-06)|GBM - Glioblastoma multiforme(31;0.00492)		GGCTCAGGTAGAAGGCGGCCA	0.667																																					p.F73F		Atlas-SNP	.											.	GPR31	44	.	0			c.C219T						.						37	32	34					6																	167571101		2201	4298	6499	SO:0001819	synonymous_variant	2853	exon1			CAGGTAGAAGGCG	U65402	CCDS5299.1	6q27	2012-08-21				ENSG00000120436		"GPCR / Class A : Orphans"	4486	protein-coding gene	gene with protein product	"hydroxyeicosatetraenoic (HETE) acid receptor 1", "12-(S)-HETE acid receptor"	602043				9205127, 21712392	Standard	NM_005299		Approved	HETER1, 12-HETER	uc011egq.2	O00270		ENST00000366834.1:c.219C>T	chr6.hg19:g.167571101G>A		265.0	0.0		170.0	47.0	NM_005299	B0M0K2|Q4VBL3|Q9NQ20	Silent	SNP	ENST00000366834.1	hg19	CCDS5299.1																																																																																			.	.		0.667	GPR31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043111.1	NM_005299		A	167571101	G	A	167571101	2	1	308	1	0	0	0	0	0	0	0	1	6695	933	33	3		3	GPR31	6	167571101	Silent	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10	7076710	167571101	3543966	47	43964										
KIF25	3834	hgsc.bcm.edu	37	chr6	168443256	168443256	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	tccaggtgtgtctggagtgaCcgggttggccctgagggaga	18	8	1	3			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr6:168443256C>G	ENST00000443060.2	+	9	1236	c.845C>G	c.(844-846)aCc>aGc	p.T282S	KIF25_ENST00000354419.2_Missense_Mutation_p.T282S|KIF25_ENST00000351261.3_Intron			Q9UIL4	KIF25_HUMAN	kinesin family member 25	282	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of autophagy (GO:0010507)|organelle organization (GO:0006996)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	29		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)		TCTGGAGTGACCGGGTTGGCC	0.647																																					p.T282S		Atlas-SNP	.											.	KIF25	75	.	0			c.C845G						.						127	118	121					6																	168443256		2203	4300	6503	SO:0001583	missense	3834	exon8			GAGTGACCGGGTT	AB012722	CCDS5305.1, CCDS43530.1	6q27	2008-02-05	2003-01-09	2003-01-10	ENSG00000125337	ENSG00000125337		"Kinesins"	6390	protein-coding gene	gene with protein product		603815	"kinesin-like 3"	KNSL3		9925910	Standard	NM_030615		Approved		uc003qwk.1	Q9UIL4	OTTHUMG00000016035	ENST00000443060.2:c.845C>G	chr6.hg19:g.168443256C>G	ENSP00000388878:p.Thr282Ser	105.0	0.0		56.0	31.0	NM_030615	O94775|Q5SZU9	Missense_Mutation	SNP	ENST00000443060.2	hg19	CCDS5305.1	.	.	.	.	.	.	.	.	.	.	C	14.90	2.674115	0.47781	.	.	ENSG00000125337	ENST00000443060;ENST00000354419	T;T	0.74315	-0.83;-0.83	4.27	2.41	0.29592	Kinesin, motor domain (4);	0.142741	0.46145	D	0.000309	T	0.45935	0.1367	L	0.39020	1.185	0.80722	D	1	P	0.38565	0.637	B	0.37091	0.241	T	0.43893	-0.9363	10	0.51188	T	0.08	-13.93	7.4262	0.27100	0.0:0.7363:0.1674:0.0963	.	282	Q9UIL4	KIF25_HUMAN	S	282	ENSP00000388878:T282S;ENSP00000346401:T282S	ENSP00000346401:T282S	T	+	2	0	KIF25	168186105	0.966000	0.33281	0.015000	0.15790	0.012000	0.07955	2.235000	0.43044	0.341000	0.23771	0.543000	0.68304	ACC	.	.		0.647	KIF25-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362509.1			G	168443256	C	G	168443256	3	3	308	1	0	0	0	0	1	0	0	0	8302	507	18	4	871	4	KIF25	6	168443256	Missense_Mutation	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	872155	168443256	2671811	48	43965										
MAGI2	9863	hgsc.bcm.edu	37	chr7	77975281	77975281	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	gggctttgttccaagttctgTgtggggcatgttatgttgct	14	6	1	0			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr7:77975281T>A	ENST00000354212.4	-	8	1436	c.1183A>T	c.(1183-1185)Aca>Tca	p.T395S	RPL13AP17_ENST00000450028.1_RNA|MAGI2_ENST00000419488.1_Missense_Mutation_p.T395S|MAGI2_ENST00000536571.1_Missense_Mutation_p.T227S|MAGI2_ENST00000522391.1_Missense_Mutation_p.T395S|MAGI2_ENST00000535697.1_Missense_Mutation_p.T232S	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	395					cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|glomerular visceral epithelial cell development (GO:0072015)|mitotic cell cycle arrest (GO:0071850)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase B signaling (GO:0051898)|nerve growth factor signaling pathway (GO:0038180)|planar cell polarity pathway involved in axis elongation (GO:0003402)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of receptor internalization (GO:0002092)|protein heterooligomerization (GO:0051291)|receptor clustering (GO:0043113)|SMAD protein signal transduction (GO:0060395)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|late endosome (GO:0005770)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)|synapse (GO:0045202)|tight junction (GO:0005923)	beta-1 adrenergic receptor binding (GO:0031697)|phosphatase binding (GO:0019902)|receptor signaling complex scaffold activity (GO:0030159)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|type II activin receptor binding (GO:0070699)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(37)|ovary(5)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(3)	84		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				CCAAGTTCTGTGTGGGGCATG	0.428																																					p.T395S		Atlas-SNP	.											.	MAGI2	246	.	0			c.A1183T						.						215	203	207					7																	77975281		2203	4300	6503	SO:0001583	missense	9863	exon8			GTTCTGTGTGGGG	AB014605	CCDS5594.1, CCDS75623.1	7q21	2005-08-09			ENSG00000187391	ENSG00000187391			18957	protein-coding gene	gene with protein product		606382				10681527, 9734811	Standard	XM_005250725		Approved	AIP1, ARIP1, KIAA0705, ACVRIP1, MAGI-2	uc003ugx.3	Q86UL8	OTTHUMG00000130697	ENST00000354212.4:c.1183A>T	chr7.hg19:g.77975281T>A	ENSP00000346151:p.Thr395Ser	106.0	0.0		83.0	4.0	NM_012301	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Missense_Mutation	SNP	ENST00000354212.4	hg19	CCDS5594.1	.	.	.	.	.	.	.	.	.	.	T	6.844	0.524956	0.13066	.	.	ENSG00000187391	ENST00000419488;ENST00000354212;ENST00000536298;ENST00000522391;ENST00000536571;ENST00000535697	T;T;T;T;T	0.10005	3.03;3.03;2.92;3.86;3.87	5.63	1.72	0.24424	.	0.412788	0.17253	U	0.181094	T	0.04634	0.0126	N	0.11201	0.11	0.32064	N	0.595244	B;B;B;B;B;B	0.24368	0.102;0.035;0.009;0.009;0.001;0.022	B;B;B;B;B;B	0.24541	0.054;0.048;0.004;0.006;0.012;0.016	T	0.36383	-0.9750	10	0.16896	T	0.51	.	5.4092	0.16339	0.0:0.1572:0.278:0.5648	.	232;227;395;395;395;395	F5GWH1;F5GWK7;B7Z4H4;E7EWI0;Q86UL8-2;Q86UL8	.;.;.;.;.;MAGI2_HUMAN	S	395;395;395;395;227;232	ENSP00000405766:T395S;ENSP00000346151:T395S;ENSP00000428389:T395S;ENSP00000441584:T227S;ENSP00000441603:T232S	ENSP00000346151:T395S	T	-	1	0	MAGI2	77813217	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.513000	0.35823	0.393000	0.25203	0.533000	0.62120	ACA	.	.		0.428	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301		A	77975281	T	A	77975281	3	1	308	1	0	0	0	0	1	0	0	0	9200	1696	59	4	3244	4	MAGI2	7	77975281	Missense_Mutation	SNP	T	TCGA-HP-A5N0-01A-11D-A28X-10		77975281	81163382	49	43966										
CALCR	799	hgsc.bcm.edu	37	chr7	93055779	93055779	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	tgatggcagatgtaaattggGatgtcgccagcctccgcagc	13	10	0	2	rs145853724		TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr7:93055779G>A	ENST00000394441.1	-	13	1629	c.1314C>T	c.(1312-1314)atC>atT	p.I438I	CALCR_ENST00000359558.2_Silent_p.I472I|CALCR_ENST00000360249.4_Silent_p.I454I|CALCR_ENST00000421592.1_Silent_p.I454I|CALCR_ENST00000426151.1_Silent_p.I438I	NM_001164738.1	NP_001158210.1	P30988	CALCR_HUMAN	calcitonin receptor	472					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|response to glucocorticoid (GO:0051384)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcitonin binding (GO:0032841)|calcitonin receptor activity (GO:0004948)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(3)	45	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Pramlintide(DB01278)|Salmon Calcitonin(DB00017)	TGTAAATTGGGATGTCGCCAG	0.557																																					p.I472I		Atlas-SNP	.											.	CALCR	200	.	0			c.C1416T						.	G	,,	0,4406		0,0,2203	125	123	124		1416,1314,1314	2.1	0	7	dbSNP_134	124	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	CALCR	NM_001164737.1,NM_001164738.1,NM_001742.3	,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,	472/509,438/475,438/475	93055779	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	799	exon16			AATTGGGATGTCG	L00587	CCDS5631.1, CCDS55125.1	7q21.3	2012-08-10			ENSG00000004948	ENSG00000004948		"GPCR / Class B : Calcitonin receptors"	1440	protein-coding gene	gene with protein product		114131				1331173	Standard	NM_001742		Approved	CTR	uc003umw.2	P30988	OTTHUMG00000023599	ENST00000394441.1:c.1314C>T	chr7.hg19:g.93055779G>A		128.0	0.0		93.0	6.0	NM_001164737	A4D1G6|F5H605|O14585|Q13941|Q5ZGL8|Q659U6|Q6DJU8|Q6T712	Silent	SNP	ENST00000394441.1	hg19	CCDS5631.1																																																																																			.	G|1.000;A|0.000		0.557	CALCR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254661.2	NM_001742		A	93055779	G	A	93055779	2	1	308	1	0	0	0	0	0	0	0	1	2581	1164	41	3		3	CALCR	7	93055779	Silent	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10	15080498	93055779	66082884	50	43967										
LMTK2	22853	hgsc.bcm.edu	37	chr7	97821009	97821009	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	caggctgctgacttacctgcGgctgcagagccagcgggact	14	13	0	2	rs531778656		TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr7:97821009G>A	ENST00000297293.5	+	11	1525	c.1232G>A	c.(1231-1233)cGg>cAg	p.R411Q		NM_014916.3	NP_055731.2	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2	411					early endosome to late endosome transport (GO:0045022)|endocytic recycling (GO:0032456)|negative regulation of catalytic activity (GO:0043086)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor recycling (GO:0001881)|transferrin transport (GO:0033572)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|myosin VI binding (GO:0070853)|protein phosphatase inhibitor activity (GO:0004864)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|pancreas(2)|skin(2)|stomach(3)	59	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)					ACTTACCTGCGGCTGCAGAGC	0.542													G|||	1	0.000199681	0	0	5008	,	,		15350	0		0	False		,,,				2504	0.001				p.R411Q		Atlas-SNP	.											.	LMTK2	228	.	0			c.G1232A						.						65	60	62					7																	97821009		2203	4300	6503	SO:0001583	missense	22853	exon11			ACCTGCGGCTGCA	AB029002	CCDS5654.1	7q22.1	2014-06-12			ENSG00000164715	ENSG00000164715			17880	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 100"	610989				15005709	Standard	NM_014916		Approved	KIAA1079, KPI2, KPI-2, cprk, LMR2, BREK, AATYK2, PPP1R100	uc003upd.2	Q8IWU2	OTTHUMG00000154256	ENST00000297293.5:c.1232G>A	chr7.hg19:g.97821009G>A	ENSP00000297293:p.Arg411Gln	127.0	0.0		86.0	23.0	NM_014916	A4D272|Q75MG7|Q9UPS3	Missense_Mutation	SNP	ENST00000297293.5	hg19	CCDS5654.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.299652	0.81136	.	.	ENSG00000164715	ENST00000297293	T	0.62105	0.05	5.41	5.41	0.78517	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.78729	0.4329	M	0.73598	2.24	0.80722	D	1	D	0.89917	1.0	D	0.71656	0.974	T	0.76782	-0.2832	10	0.37606	T	0.19	.	18.551	0.91065	0.0:0.0:1.0:0.0	.	411	Q8IWU2	LMTK2_HUMAN	Q	411	ENSP00000297293:R411Q	ENSP00000297293:R411Q	R	+	2	0	LMTK2	97658945	1.000000	0.71417	0.829000	0.32907	0.786000	0.44442	9.420000	0.97426	2.710000	0.92621	0.655000	0.94253	CGG	.	.		0.542	LMTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334560.1	NM_014916		A	97821009	G	A	97821009	3	1	308	1	0	0	0	0	1	0	0	0	8868	1116	39	1	1274	1	LMTK2	7	97821009	Missense_Mutation	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10	4765230	97821009	61317654	51	43968										
LRWD1	222229	hgsc.bcm.edu	37	chr7	102108549	102108549	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	acggccagacgacgtcccacTcagcctctctcccagcaagc	8	19	2	1			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr7:102108549T>G	ENST00000292616.5	+	6	871	c.719T>G	c.(718-720)cTc>cGc	p.L240R	MIR5090_ENST00000582533.1_RNA	NM_152892.1	NP_690852.1	Q9UFC0	LRWD1_HUMAN	leucine-rich repeats and WD repeat domain containing 1	240					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|DNA replication initiation (GO:0006270)|establishment of protein localization to chromatin (GO:0071169)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nuclear origin of replication recognition complex (GO:0005664)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|telomeric heterochromatin (GO:0031933)	chromatin binding (GO:0003682)|methyl-CpG binding (GO:0008327)|methylated histone binding (GO:0035064)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|skin(1)|stomach(2)	20						GACGTCCCACTCAGCCTCTCT	0.687																																					p.L240R		Atlas-SNP	.											.	LRWD1	41	.	0			c.T719G						.						46	49	48					7																	102108549		2201	4299	6500	SO:0001583	missense	222229	exon6			TCCCACTCAGCCT	AL133057	CCDS34715.1	7q22.1	2013-01-10			ENSG00000161036	ENSG00000161036		"WD repeat domain containing"	21769	protein-coding gene	gene with protein product	"origin recognition complex associated", "centromere protein 33"	615167				20932478, 20850016, 20180869	Standard	NM_152892		Approved	DKFZp434K1815, ORCA, CENP-33	uc003uzn.3	Q9UFC0	OTTHUMG00000157718	ENST00000292616.5:c.719T>G	chr7.hg19:g.102108549T>G	ENSP00000292616:p.Leu240Arg	111.0	0.0		86.0	21.0	NM_152892	A8K4K2|B2R9G2|Q8N0T9|Q8WV43|Q96GJ2	Missense_Mutation	SNP	ENST00000292616.5	hg19	CCDS34715.1	.	.	.	.	.	.	.	.	.	.	T	10.79	1.451106	0.26074	.	.	ENSG00000161036	ENST00000292616	T	0.61859	0.07	4.89	1.14	0.20703	.	0.695571	0.14825	N	0.296183	T	0.40171	0.1106	L	0.50333	1.59	0.09310	N	1	P	0.43169	0.8	B	0.37833	0.259	T	0.17806	-1.0357	10	0.12766	T	0.61	-3.6758	3.6134	0.08069	0.0:0.203:0.1959:0.6011	.	240	Q9UFC0	LRWD1_HUMAN	R	240	ENSP00000292616:L240R	ENSP00000292616:L240R	L	+	2	0	LRWD1	101895554	0.000000	0.05858	0.006000	0.13384	0.470000	0.32858	0.017000	0.13399	0.890000	0.36211	0.379000	0.24179	CTC	.	.		0.687	LRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349493.1	NM_152892		G	102108549	T	G	102108549	3	3	308	1	0	0	0	0	1	0	0	0	9056	1551	54	5	741	5	LRWD1	7	102108549	Missense_Mutation	SNP	T	TCGA-HP-A5N0-01A-11D-A28X-10	4287540	102108549	57030114	52	43969										
RELN	5649	hgsc.bcm.edu	37	chr7	103179712	103179712	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	tgaagcagccatttcctactAtcaagggttgtgaaatcatc	8	9	2	2			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr7:103179712A>G	ENST00000428762.1	-	45	7152	c.6993T>C	c.(6991-6993)gaT>gaC	p.D2331D	RELN_ENST00000424685.2_Silent_p.D2331D|RELN_ENST00000343529.5_Silent_p.D2331D	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	2331					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		ATTTCCTACTATCAAGGGTTG	0.428																																					p.D2331D	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.T6993C						.						64	66	66					7																	103179712		2203	4300	6503	SO:0001819	synonymous_variant	5649	exon45			CCTACTATCAAGG		CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.6993T>C	chr7.hg19:g.103179712A>G		119.0	0.0		120.0	41.0	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Silent	SNP	ENST00000428762.1	hg19	CCDS47680.1																																																																																			.	.		0.428	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		G	103179712	A	G	103179712	2	3	308	1	0	0	0	0	0	0	0	1	13235	446	16	2		2	RELN	7	103179712	Silent	SNP	A	TCGA-HP-A5N0-01A-11D-A28X-10	1071163	103179712	55958951	53	43970										
PIK3CG	5294	hgsc.bcm.edu	37	chr7	106508977	106508977	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	ggtgaggaaggaagagtggcCactggtggatgactgcacgg	19	6	0	3			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr7:106508977C>T	ENST00000359195.3	+	2	1281	c.971C>T	c.(970-972)cCa>cTa	p.P324L	PIK3CG_ENST00000440650.2_Missense_Mutation_p.P324L|PIK3CG_ENST00000496166.1_Missense_Mutation_p.P324L	NM_001282427.1|NM_002649.2	NP_001269356.1|NP_002640.2	P48736	PK3CG_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	324					adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cytokine production (GO:0001816)|dendritic cell chemotaxis (GO:0002407)|endocytosis (GO:0006897)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte apoptotic process (GO:0097284)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|natural killer cell chemotaxis (GO:0035747)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of triglyceride catabolic process (GO:0010897)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion mediated by integrin (GO:0033628)|respiratory burst involved in defense response (GO:0002679)|secretory granule localization (GO:0032252)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell proliferation (GO:0042098)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(9)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(16)|liver(4)|lung(59)|ovary(4)|pancreas(4)|prostate(3)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	132						GAAGAGTGGCCACTGGTGGAT	0.602																																					p.P324L		Atlas-SNP	.											.	PIK3CG	279	.	0			c.C971T						.						70	63	65					7																	106508977		2203	4300	6503	SO:0001583	missense	5294	exon2			AGTGGCCACTGGT		CCDS5739.1	7q22	2012-07-13	2012-07-13		ENSG00000105851	ENSG00000105851	2.7.1.153		8978	protein-coding gene	gene with protein product		601232	"phosphoinositide-3-kinase, catalytic, gamma polypeptide"				Standard	XM_005250443		Approved		uc003vdw.3	P48736	OTTHUMG00000157641	ENST00000359195.3:c.971C>T	chr7.hg19:g.106508977C>T	ENSP00000352121:p.Pro324Leu	167.0	0.0		156.0	44.0	NM_002649	A4D0Q6|Q8IV23|Q9BZC8	Missense_Mutation	SNP	ENST00000359195.3	hg19	CCDS5739.1	.	.	.	.	.	.	.	.	.	.	C	14.21	2.465987	0.43839	.	.	ENSG00000105851	ENST00000440650;ENST00000496166;ENST00000359195	T;T;T	0.70631	-0.5;-0.5;-0.5	5.6	5.6	0.85130	.	0.098021	0.64402	D	0.000001	T	0.68824	0.3043	L	0.53249	1.67	0.80722	D	1	B	0.23316	0.083	B	0.17979	0.02	T	0.64132	-0.6479	10	0.41790	T	0.15	-25.5935	19.6034	0.95572	0.0:1.0:0.0:0.0	.	324	P48736	PK3CG_HUMAN	L	324	ENSP00000392258:P324L;ENSP00000419260:P324L;ENSP00000352121:P324L	ENSP00000352121:P324L	P	+	2	0	PIK3CG	106296213	1.000000	0.71417	0.961000	0.40146	0.533000	0.34776	7.770000	0.85390	2.637000	0.89404	0.561000	0.74099	CCA	.	.		0.602	PIK3CG-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349294.1			T	106508977	C	T	106508977	3	4	308	1	0	0	0	0	1	0	0	0	11925	594	21	3	973	3	PIK3CG	7	106508977	Missense_Mutation	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	3329265	106508977	52629686	54	43971										
C7orf55	154791	hgsc.bcm.edu	37	chr7	139026139	139026139	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	aaggacaggacaatggcggcCttagggtccccgtcgcacac	13	13	0	0	rs530614678		TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr7:139026139C>T	ENST00000297534.6	+	1	262	c.9C>T	c.(7-9)gcC>gcT	p.A3A	C7orf55_ENST00000481123.1_Intron|C7orf55-LUC7L2_ENST00000541170.3_Intron|LUC7L2_ENST00000541515.3_Silent_p.A3A	NM_197964.4	NP_932068.2	Q96HJ9	CG055_HUMAN	chromosome 7 open reading frame 55	3						mitochondrion (GO:0005739)				breast(1)|lung(2)	3						CAATGGCGGCCTTAGGGTCCC	0.662											OREG0018357	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1	0.000199681	0	0	5008	,	,		15350	0		0.001	False		,,,				2504	0				p.A3A		Atlas-SNP	.											.	.	.	.	0			c.C9T						.						53	62	59					7																	139026139		2203	4300	6503	SO:0001819	synonymous_variant	100996928	exon1			GGCGGCCTTAGGG	AF161386	CCDS5853.1	7q34	2009-01-22	2009-01-22	2009-01-22	ENSG00000164898	ENSG00000164898			26946	protein-coding gene	gene with protein product	"formation of mitochondrial complexes 1 homolog (S. cerevisiae)"					12477932	Standard	NM_197964		Approved	HSPC268, FMC1		Q96HJ9	OTTHUMG00000151719	ENST00000297534.6:c.9C>T	chr7.hg19:g.139026139C>T		61.0	0.0	1645	54.0	20.0	NM_001244584	B7Z4Q3|Q75M90|Q9P0B3	Silent	SNP	ENST00000297534.6	hg19	CCDS5853.1																																																																																			.	.		0.662	C7orf55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323626.1	NM_197964		T	139026139	C	T	139026139	2	4	308	1	0	0	0	0	0	0	0	1	2405	668	24	3		3	C7orf55	7	139026139	Silent	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	32517162	139026139	20112524	55	43972										
TAS2R41	259287	hgsc.bcm.edu	37	chr7	143175239	143175239	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	tccatctacactggcacttcCtgaactcagccaccttctgg	6	16	3	1			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr7:143175239C>G	ENST00000408916.1	+	1	274	c.274C>G	c.(274-276)Ctg>Gtg	p.L92V	EPHA1-AS1_ENST00000429289.1_RNA	NM_176883.2	NP_795364.2	P59536	T2R41_HUMAN	taste receptor, type 2, member 41	92					sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|large_intestine(2)|lung(10)|pancreas(1)|prostate(2)|skin(1)	18	Melanoma(164;0.15)					CTGGCACTTCCTGAACTCAGC	0.537																																					p.L92V		Atlas-SNP	.											.	TAS2R41	43	.	0			c.C274G						.						101	100	101					7																	143175239		1998	4180	6178	SO:0001583	missense	259287	exon1			CACTTCCTGAACT	AF494232	CCDS43663.1	7q34	2012-08-22			ENSG00000221855	ENSG00000221855		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	18883	protein-coding gene	gene with protein product		613965				12379855	Standard	NM_176883		Approved	T2R59	uc003wdc.1	P59536	OTTHUMG00000155892	ENST00000408916.1:c.274C>G	chr7.hg19:g.143175239C>G	ENSP00000386201:p.Leu92Val	138.0	0.0		126.0	19.0	NM_176883	P59550|Q495I2|Q50KJ5|Q50KJ6|Q50KJ7|Q645W7	Missense_Mutation	SNP	ENST00000408916.1	hg19	CCDS43663.1	.	.	.	.	.	.	.	.	.	.	C	13.05	2.120206	0.37436	.	.	ENSG00000221855	ENST00000408916	T	0.39406	1.08	6.0	2.61	0.31194	.	0.242058	0.26883	U	0.022002	T	0.43456	0.1248	L	0.48986	1.54	0.28844	N	0.896432	P	0.42123	0.771	P	0.51550	0.673	T	0.29058	-1.0024	10	0.27082	T	0.32	.	6.5006	0.22166	0.2905:0.6053:0.0:0.1042	.	92	P59536	T2R41_HUMAN	V	92	ENSP00000386201:L92V	ENSP00000386201:L92V	L	+	1	2	TAS2R41	142885361	0.010000	0.17322	0.986000	0.45419	0.104000	0.19210	-0.450000	0.06803	0.202000	0.20498	0.655000	0.94253	CTG	.	.		0.537	TAS2R41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342149.1			G	143175239	C	G	143175239	3	3	308	1	0	0	0	0	1	0	0	0	15594	680	24	4	276	4	TAS2R41	7	143175239	Missense_Mutation	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	4149100	143175239	15963424	56	43973										
OR2A14	135941	hgsc.bcm.edu	37	chr7	143826880	143826880	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	cgcatcctggccgccatcttGaggatccagtctggggaggg	15	12	2	1			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr7:143826880G>T	ENST00000408899.2	+	1	730	c.675G>T	c.(673-675)ttG>ttT	p.L225F		NM_001001659.1	NP_001001659.1	Q96R47	O2A14_HUMAN	olfactory receptor, family 2, subfamily A, member 14	225						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(4)|lung(17)|skin(1)	22	Melanoma(164;0.0783)					CCGCCATCTTGAGGATCCAGT	0.607																																					p.L225F		Atlas-SNP	.											.	OR2A14	66	.	0			c.G675T						.						113	116	115					7																	143826880		2050	4202	6252	SO:0001583	missense	135941	exon1			CATCTTGAGGATC		CCDS43672.1	7q35	2013-09-20		2004-03-08	ENSG00000221938	ENSG00000221938		"GPCR / Class A : Olfactory receptors"	15084	protein-coding gene	gene with protein product				OR2A14P, OR2A6			Standard	NM_001001659		Approved	OST182	uc011kua.2	Q96R47	OTTHUMG00000158003	ENST00000408899.2:c.675G>T	chr7.hg19:g.143826880G>T	ENSP00000386137:p.Leu225Phe	166.0	0.0		175.0	19.0	NM_001001659	Q6IF41|Q8NGT8	Missense_Mutation	SNP	ENST00000408899.2	hg19	CCDS43672.1	.	.	.	.	.	.	.	.	.	.	G	11.52	1.661764	0.29515	.	.	ENSG00000221938	ENST00000408899	T	0.00296	8.24	4.18	0.0235	0.14137	GPCR, rhodopsin-like superfamily (1);	0.000000	0.26804	U	0.022415	T	0.00496	0.0016	M	0.71581	2.175	0.30546	N	0.765944	D	0.89917	1.0	D	0.85130	0.997	T	0.40515	-0.9559	10	0.72032	D	0.01	-10.1967	8.5074	0.33195	0.0886:0.4458:0.4655:0.0	.	225	Q96R47	O2A14_HUMAN	F	225	ENSP00000386137:L225F	ENSP00000386137:L225F	L	+	3	2	OR2A14	143457813	0.008000	0.16893	0.981000	0.43875	0.009000	0.06853	-0.048000	0.11944	-0.109000	0.12044	-0.304000	0.09214	TTG	.	.		0.607	OR2A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349980.1			T	143826880	G	T	143826880	3	4	308	1	0	0	0	0	1	0	0	0	10985	1281	45	3	677	3	OR2A14	7	143826880	Missense_Mutation	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10	651641	143826880	15311783	57	43974										
VIPR2	7434	hgsc.bcm.edu	37	chr7	158851225	158851225	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	agagacatcagagagacactGtagcccagtgtataaatggc	11	8	1	3	rs547418694		TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr7:158851225G>A	ENST00000262178.2	-	5	587	c.402C>T	c.(400-402)taC>taT	p.Y134Y	VIPR2_ENST00000402066.1_Silent_p.Y275Y|VIPR2_ENST00000377633.3_Silent_p.Y118Y	NM_003382.4	NP_003373.2	P41587	VIPR2_HUMAN	vasoactive intestinal peptide receptor 2	134					activation of adenylate cyclase activity (GO:0007190)|cell-cell signaling (GO:0007267)|negative regulation of smooth muscle cell proliferation (GO:0048662)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|vasoactive intestinal polypeptide receptor activity (GO:0004999)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	22	Ovarian(565;0.152)	all_cancers(7;1.13e-11)|all_epithelial(9;0.000545)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)|STAD - Stomach adenocarcinoma(7;0.18)		GAGAGACACTGTAGCCCAGTG	0.413													G|||	1	0.000199681	8e-04	0	5008	,	,		19344	0		0	False		,,,				2504	0				p.Y134Y	Pancreas(154;1876 1931 2329 17914 20079)	Atlas-SNP	.											.	VIPR2	53	.	0			c.C402T						.						165	157	159					7																	158851225		2203	4300	6503	SO:0001819	synonymous_variant	7434	exon5			GACACTGTAGCCC	CA449700, X95097	CCDS5950.1	7q36.3	2012-08-10			ENSG00000106018	ENSG00000106018		"GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"	12695	protein-coding gene	gene with protein product	"VIP and PACAP receptor 2"	601970				7811244	Standard	NM_003382		Approved	VPAC2, VPAC2R	uc003woh.3	P41587	OTTHUMG00000151446	ENST00000262178.2:c.402C>T	chr7.hg19:g.158851225G>A		80.0	0.0		54.0	15.0	NM_003382	Q13053|Q15870|Q53Y09|Q6ZN22|Q9UCW0	Silent	SNP	ENST00000262178.2	hg19	CCDS5950.1																																																																																			.	.		0.413	VIPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322675.1	NM_003382		A	158851225	G	A	158851225	2	1	308	1	0	0	0	0	0	0	0	1	17185	1372	48	3		3	VIPR2	7	158851225	Silent	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10	15024345	158851225	287438	58	43975										
ESCO2	157570	hgsc.bcm.edu	37	chr8	27645507	27645507	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	acaagtaaaaaaacaaaagaCcagctcatcatcgtgagtaa	6	8	2	2			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr8:27645507C>G	ENST00000305188.8	+	6	1357	c.1119C>G	c.(1117-1119)gaC>gaG	p.D373E	ESCO2_ENST00000397418.2_Missense_Mutation_p.D21E	NM_001017420.2	NP_001017420.1	Q56NI9	ESCO2_HUMAN	establishment of sister chromatid cohesion N-acetyltransferase 2	373					chromosome segregation (GO:0007059)|double-strand break repair (GO:0006302)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|post-translational protein acetylation (GO:0034421)|protein localization to chromatin (GO:0071168)|regulation of DNA replication (GO:0006275)	chromatin (GO:0000785)|chromocenter (GO:0010369)|Golgi apparatus (GO:0005794)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|XY body (GO:0001741)	lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|KIRC - Kidney renal clear cell carcinoma(542;0.0955)|Kidney(114;0.115)|Colorectal(74;0.132)		AAACAAAAGACCAGCTCATCA	0.383									SC Phocomelia syndrome																												p.D373E		Atlas-SNP	.											.	ESCO2	50	.	0			c.C1119G						.						100	98	98					8																	27645507		2203	4300	6503	SO:0001583	missense	157570	exon6	Familial Cancer Database	SC-Pseudothalidomide s., incl.: Roberts s.	AAAAGACCAGCTC	AF306679	CCDS34872.1	8p21.1	2013-05-02	2013-05-02		ENSG00000171320	ENSG00000171320			27230	protein-coding gene	gene with protein product		609353	"Roberts syndrome", "establishment of cohesion 1 homolog 2 (S. cerevisiae)"	RBS		15958495, 16775838, 15821733, 16380922	Standard	XR_247122		Approved	EFO2	uc003xgg.3	Q56NI9	OTTHUMG00000163901	ENST00000305188.8:c.1119C>G	chr8.hg19:g.27645507C>G	ENSP00000306999:p.Asp373Glu	68.0	0.0		60.0	11.0	NM_001017420	B3KW59|Q49AP4	Missense_Mutation	SNP	ENST00000305188.8	hg19	CCDS34872.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.51|13.51	2.260090|2.260090	0.39995|0.39995	.|.	.|.	ENSG00000171320|ENSG00000171320	ENST00000305188;ENST00000397418|ENST00000518262	T;T|.	0.71103|.	-0.07;-0.54|.	5.79|5.79	3.98|3.98	0.46160|0.46160	.|.	0.424311|.	0.28376|.	N|.	0.015580|.	T|T	0.52273|0.52273	0.1724|0.1724	L|L	0.34521|0.34521	1.04|1.04	0.46927|0.46927	D|D	0.999253|0.999253	D|.	0.76494|.	0.999|.	D|.	0.85130|.	0.997|.	T|T	0.46965|0.46965	-0.9153|-0.9153	10|5	0.49607|.	T|.	0.09|.	-5.5893|-5.5893	11.2049|11.2049	0.48762|0.48762	0.0:0.8458:0.0:0.1542|0.0:0.8458:0.0:0.1542	.|.	373|.	Q56NI9|.	ESCO2_HUMAN|.	E|S	373;21|78	ENSP00000306999:D373E;ENSP00000380563:D21E|.	ENSP00000306999:D373E|.	D|T	+|+	3|2	2|0	ESCO2|ESCO2	27701426|27701426	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.739000|0.739000	0.42172|0.42172	1.332000|1.332000	0.33805|0.33805	1.451000|1.451000	0.47736|0.47736	0.561000|0.561000	0.74099|0.74099	GAC|ACC	.	.		0.383	ESCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376276.1	NM_001017420		G	27645507	C	G	27645507	3	3	308	1	0	0	0	0	1	0	0	0	5251	506	18	4	1137	4	ESCO2	8	27645507	Missense_Mutation	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10		27645507	118718515	59	43976										
ZMAT4	79698	hgsc.bcm.edu	37	chr8	40554844	40554844	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	tgccttgataatgggaatcgGccaccaccgctgaagtgaat	11	10	0	3			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr8:40554844G>A	ENST00000297737.6	-	4	415	c.269C>T	c.(268-270)gCc>gTc	p.A90V	ZMAT4_ENST00000315769.7_Missense_Mutation_p.A90V	NM_024645.2	NP_078921.1	Q9H898	ZMAT4_HUMAN	zinc finger, matrin-type 4	90						nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.A90V(1)		NS(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	18	Ovarian(28;0.00724)|Colorectal(14;0.0468)	all_cancers(7;0.00936)|all_epithelial(6;3.53e-06)|all_lung(54;0.0318)|Lung NSC(58;0.0919)|Esophageal squamous(32;0.15)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;0.00722)			ATGGGAATCGGCCACCACCGC	0.498																																					p.A90V		Atlas-SNP	.											ZMAT4,rectum,carcinoma,0,1	ZMAT4	47	.	1	Substitution - Missense(1)	large_intestine(1)	c.C269T						.						151	136	141					8																	40554844		2203	4300	6503	SO:0001583	missense	79698	exon4			GAATCGGCCACCA	AK023904	CCDS34885.1, CCDS47848.1	8p11.21	2012-10-05	2010-09-15		ENSG00000165061	ENSG00000165061		"Zinc fingers, matrin-type"	25844	protein-coding gene	gene with protein product						12477932	Standard	NM_024645		Approved	FLJ13842	uc003xnr.3	Q9H898	OTTHUMG00000164049	ENST00000297737.6:c.269C>T	chr8.hg19:g.40554844G>A	ENSP00000297737:p.Ala90Val	122.0	0.0		122.0	34.0	NM_024645	Q8WUT8	Missense_Mutation	SNP	ENST00000297737.6	hg19	CCDS34885.1	.	.	.	.	.	.	.	.	.	.	G	36	5.608570	0.96626	.	.	ENSG00000165061	ENST00000315769;ENST00000297737;ENST00000519406	T;T;T	0.23348	1.91;1.91;1.91	6.17	6.17	0.99709	Zinc finger, C2H2-like (1);Zinc finger, U1-type (1);Zinc finger, C2H2 (1);	0.000000	0.85682	D	0.000000	T	0.58264	0.2110	M	0.82630	2.6	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.59573	-0.7429	10	0.87932	D	0	-18.2353	19.8676	0.96824	0.0:0.0:1.0:0.0	.	90;90	Q9H898-2;Q9H898	.;ZMAT4_HUMAN	V	90	ENSP00000319785:A90V;ENSP00000297737:A90V;ENSP00000428423:A90V	ENSP00000297737:A90V	A	-	2	0	ZMAT4	40674001	1.000000	0.71417	0.999000	0.59377	0.944000	0.59088	9.258000	0.95555	2.941000	0.99782	0.655000	0.94253	GCC	.	.		0.498	ZMAT4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376950.1	NM_024645		A	40554844	G	A	40554844	3	1	308	1	0	0	0	0	1	0	0	0	17709	1203	42	3	436	3	ZMAT4	8	40554844	Missense_Mutation	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10	12909337	40554844	105809178	60	43977										
CHRNA6	8973	hgsc.bcm.edu	37	chr8	42611206	42611206	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	ggcttgcaagcttgcctttgGcaggcctcctggcaaggcct	13	13	0	0			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr8:42611206G>T	ENST00000276410.2	-	5	1491	c.1136C>A	c.(1135-1137)gCc>gAc	p.A379D	CHRNA6_ENST00000530869.1_5'Flank|CHRNA6_ENST00000534622.1_Missense_Mutation_p.A364D	NM_004198.3	NP_004189.1	Q15825	ACHA6_HUMAN	cholinergic receptor, nicotinic, alpha 6 (neuronal)	379					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|membrane depolarization (GO:0051899)|regulation of dopamine secretion (GO:0014059)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)			endometrium(2)|large_intestine(3)|liver(1)|lung(15)|ovary(1)	22	all_lung(13;3.33e-12)|Lung NSC(13;9.17e-11)|Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00439)|Lung NSC(58;0.0124)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	Lung(22;0.0252)|LUSC - Lung squamous cell carcinoma(45;0.0869)		Galantamine(DB00674)|Nicotine(DB00184)|Varenicline(DB01273)	CTTGCCTTTGGCAGGCCTCCT	0.537																																					p.A379D		Atlas-SNP	.											.	CHRNA6	60	.	0			c.C1136A						.						76	69	72					8																	42611206		2203	4300	6503	SO:0001583	missense	8973	exon5			CCTTTGGCAGGCC	U62435	CCDS6135.1, CCDS56536.1	8p22	2012-02-11	2012-02-07					"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	15963	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 6 (neuronal)"	606888	"cholinergic receptor, nicotinic, alpha polypeptide 6"			8906617	Standard	NM_004198		Approved		uc003xpj.3	Q15825		ENST00000276410.2:c.1136C>A	chr8.hg19:g.42611206G>T	ENSP00000276410:p.Ala379Asp	116.0	0.0		124.0	42.0	NM_004198	B2R8V4|B4DQH1	Missense_Mutation	SNP	ENST00000276410.2	hg19	CCDS6135.1	.	.	.	.	.	.	.	.	.	.	G	0.840	-0.742257	0.03088	.	.	ENSG00000147434	ENST00000276410;ENST00000534622	D;D	0.85411	-1.98;-1.98	6.07	3.35	0.38373	Neurotransmitter-gated ion-channel transmembrane domain (2);	1.918270	0.02392	N	0.079793	T	0.80737	0.4680	L	0.38733	1.17	0.20074	N	0.999937	B;B	0.20550	0.046;0.002	B;B	0.32583	0.148;0.005	T	0.61128	-0.7125	10	0.10377	T	0.69	.	6.3808	0.21533	0.2193:0.1668:0.6139:0.0	.	364;379	B4DQH1;Q15825	.;ACHA6_HUMAN	D	379;364	ENSP00000276410:A379D;ENSP00000433871:A364D	ENSP00000276410:A379D	A	-	2	0	CHRNA6	42730363	0.102000	0.21896	0.415000	0.26534	0.009000	0.06853	1.419000	0.34793	0.464000	0.27142	-0.140000	0.14226	GCC	.	.		0.537	CHRNA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383156.1			T	42611206	G	T	42611206	3	4	308	1	0	0	0	0	1	0	0	0	3389	1203	42	3	356	3	CHRNA6	8	42611206	Missense_Mutation	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10	2056362	42611206	103752816	61	43978										
TRPA1	8989	hgsc.bcm.edu	37	chr8	72975703	72975703	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	aaagcctcaactcaccaaacCttagtattatttccatgcat	3	12	2	0			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr8:72975703C>T	ENST00000262209.4	-	5	863	c.656G>A	c.(655-657)aGg>aAg	p.R219K		NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	219					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	CTCACCAAACCTTAGTATTAT	0.318																																					p.R219K		Atlas-SNP	.											.	TRPA1	256	.	0			c.G656A						.						77	74	75					8																	72975703		2203	4300	6503	SO:0001583	missense	8989	exon5			CCAAACCTTAGTA	Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	497	protein-coding gene	gene with protein product		604775	"ankyrin-like with transmembrane domains 1"	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.656G>A	chr8.hg19:g.72975703C>T	ENSP00000262209:p.Arg219Lys	75.0	0.0		46.0	15.0	NM_007332	A6NIN6	Missense_Mutation	SNP	ENST00000262209.4	hg19	CCDS34908.1	.	.	.	.	.	.	.	.	.	.	C	1.753	-0.488836	0.04352	.	.	ENSG00000104321	ENST00000523582;ENST00000262209	T;T	0.49432	0.78;2.45	5.62	3.23	0.37069	Ankyrin repeat-containing domain (3);	0.434041	0.29133	N	0.013060	T	0.11024	0.0269	N	0.00289	-1.7	0.25494	N	0.987619	B	0.02656	0.0	B	0.01281	0.0	T	0.36696	-0.9737	10	0.02654	T	1	-9.6898	7.7386	0.28829	0.0:0.0754:0.1449:0.7797	.	219	O75762	TRPA1_HUMAN	K	71;219	ENSP00000428151:R71K;ENSP00000262209:R219K	ENSP00000262209:R219K	R	-	2	0	TRPA1	73138257	1.000000	0.71417	0.389000	0.26208	0.548000	0.35241	2.535000	0.45685	0.485000	0.27652	-0.312000	0.09012	AGG	.	.		0.318	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332		T	72975703	C	T	72975703	3	4	308	1	0	0	0	0	1	0	0	0	16592	681	24	3	2795	3	TRPA1	8	72975703	Missense_Mutation	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	30364497	72975703	73388319	62	43979										
KIAA1429	25962	hgsc.bcm.edu	37	chr8	95523460	95523460	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	aggcagcagctctgaaaggaGtatgagtccagaaaaaaatc	11	7	1	3			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr8:95523460G>T	ENST00000297591.5	-	13	3418	c.3343C>A	c.(3343-3345)Ctc>Atc	p.L1115I	KIAA1429_ENST00000421249.2_Missense_Mutation_p.L1115I|KIAA1429_ENST00000523405.1_5'UTR|KIAA1429_ENST00000437199.1_Missense_Mutation_p.L1115I	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	1115					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			TCTGAAAGGAGTATGAGTCCA	0.378																																					p.L1115I		Atlas-SNP	.											.	KIAA1429	176	.	0			c.C3343A						.						57	61	60					8																	95523460		2203	4300	6503	SO:0001583	missense	25962	exon13			AAAGGAGTATGAG	AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 121"					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.3343C>A	chr8.hg19:g.95523460G>T	ENSP00000297591:p.Leu1115Ile	129.0	0.0		80.0	4.0	NM_015496	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Missense_Mutation	SNP	ENST00000297591.5	hg19	CCDS34923.1	.	.	.	.	.	.	.	.	.	.	G	13.07	2.127470	0.37533	.	.	ENSG00000164944	ENST00000297591;ENST00000437199;ENST00000421249	T;T;T	0.59083	0.29;0.33;0.32	5.92	5.05	0.67936	.	0.143311	0.49305	D	0.000149	T	0.42921	0.1224	L	0.27053	0.805	0.53688	D	0.999979	B;B	0.13594	0.008;0.008	B;B	0.14578	0.011;0.011	T	0.29792	-1.0000	10	0.37606	T	0.19	-7.4637	9.9805	0.41811	0.069:0.0:0.7936:0.1374	.	1115;1115	Q69YN4-4;Q69YN4	.;VIR_HUMAN	I	1115	ENSP00000297591:L1115I;ENSP00000395600:L1115I;ENSP00000398390:L1115I	ENSP00000297591:L1115I	L	-	1	0	KIAA1429	95592636	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	5.291000	0.65667	1.505000	0.48720	-0.145000	0.13849	CTC	.	.		0.378	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496		T	95523460	G	T	95523460	3	4	308	1	0	0	0	0	1	0	0	0	8240	1029	36	3	2197	3	KIAA1429	8	95523460	Missense_Mutation	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10	22547757	95523460	50840562	63	43980										
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110539193	110539193	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	aattagctgtctggttggaaGaatgtggctcttggaaatat	12	4	2	1			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr8:110539193G>T	ENST00000378402.5	+	77	12769	c.12665G>T	c.(12664-12666)aGa>aTa	p.R4222I		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	4222					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			CTGGTTGGAAGAATGTGGCTC	0.398										HNSCC(38;0.096)																											p.R4222I		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.G12665T						.						87	93	91					8																	110539193		1986	4185	6171	SO:0001583	missense	93035	exon77			TTGGAAGAATGTG	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.12665G>T	chr8.hg19:g.110539193G>T	ENSP00000367655:p.Arg4222Ile	132.0	0.0		109.0	14.0	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	hg19	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	G	10.93	1.489194	0.26686	.	.	ENSG00000205038	ENST00000378402;ENST00000526472	D;D	0.86432	-2.12;-1.95	5.64	1.74	0.24563	.	0.586744	0.16067	N	0.231211	T	0.74891	0.3776	L	0.27053	0.805	0.22888	N	0.998608	B	0.34015	0.435	B	0.29440	0.102	T	0.65796	-0.6081	10	0.66056	D	0.02	.	5.2328	0.15432	0.2484:0.1474:0.6042:0.0	.	4222	Q86WI1	PKHL1_HUMAN	I	4222;1150	ENSP00000367655:R4222I;ENSP00000437376:R1150I	ENSP00000367655:R4222I	R	+	2	0	PKHD1L1	110608369	0.995000	0.38212	0.286000	0.24833	0.326000	0.28443	1.734000	0.38166	0.334000	0.23590	-0.157000	0.13467	AGA	.	.		0.398	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		T	110539193	G	T	110539193	3	4	308	1	0	0	0	0	1	0	0	0	11981	942	33	3	12971	3	PKHD1L1	8	110539193	Missense_Mutation	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10	15015733	110539193	35824829	64	43981										
ZNF250	58500	hgsc.bcm.edu	37	chr8	146107239	146107239	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	tcaccacacacatagggcttCtccccagtgtggactctctg	8	15	3	0			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr8:146107239C>T	ENST00000292579.7	-	6	1460	c.1344G>A	c.(1342-1344)gaG>gaA	p.E448E	ZNF250_ENST00000417550.2_Silent_p.E443E|ZNF250_ENST00000543949.1_Intron|ZNF250_ENST00000342660.6_Intron	NM_001109689.3|NM_021061.4	NP_001103159.1|NP_066405.1	P15622	ZN250_HUMAN	zinc finger protein 250	448					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(2)|lung(8)|skin(1)	15	all_cancers(97;8.72e-12)|all_epithelial(106;1.07e-10)|Lung NSC(106;7.18e-05)|all_lung(105;0.00021)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;2.53e-38)|OV - Ovarian serous cystadenocarcinoma(54;4.07e-38)|all cancers(56;2.27e-33)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.0654)		CATAGGGCTTCTCCCCAGTGT	0.557																																					p.E448E	NSCLC(16;520 556 24096 40084 43446)	Atlas-SNP	.											.	ZNF250	37	.	0			c.G1344A						.						127	119	122					8																	146107239		2203	4300	6503	SO:0001819	synonymous_variant	58500	exon6			GGGCTTCTCCCCA	AK095705	CCDS34972.1, CCDS55282.1	8q24.3	2013-01-08	2004-11-08			ENSG00000196150		"Zinc fingers, C2H2-type", "-"	13044	protein-coding gene	gene with protein product			"zinc finger protein 647"	ZNF647		12477932	Standard	NM_021061		Approved	MGC9718, ZFP647	uc003zer.4	P15622		ENST00000292579.7:c.1344G>A	chr8.hg19:g.146107239C>T		196.0	0.0		168.0	54.0	NM_021061	D3DWP1|Q59HE9|Q8N942|Q96AH9	Silent	SNP	ENST00000292579.7	hg19	CCDS34972.1																																																																																			.	.		0.557	ZNF250-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382968.1	NM_021061		T	146107239	C	T	146107239	2	4	308	1	0	0	0	0	0	0	0	1	17810	912	32	3		3	ZNF250	8	146107239	Silent	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	35568046	146107239	256783	65	43982										
FRMPD1	22844	hgsc.bcm.edu	37	chr9	37746731	37746731	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	tcacggccgccgtgttctgtTtgacccagaagttccgggca	12	13	2	2			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr9:37746731T>G	ENST00000539465.1	+	16	5295	c.4702T>G	c.(4702-4704)Ttg>Gtg	p.L1568V	FRMPD1_ENST00000377765.3_Missense_Mutation_p.L1568V|RP11-613M10.9_ENST00000540557.1_Intron			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	1568						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		CGTGTTCTGTTTGACCCAGAA	0.607																																					p.L1568V		Atlas-SNP	.											.	FRMPD1	237	.	0			c.T4702G						.						73	80	78					9																	37746731		2203	4299	6502	SO:0001583	missense	22844	exon16			TTCTGTTTGACCC	AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.4702T>G	chr9.hg19:g.37746731T>G	ENSP00000444411:p.Leu1568Val	131.0	0.0		116.0	18.0	NM_014907	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	hg19	CCDS6612.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.947019	0.73672	.	.	ENSG00000070601	ENST00000377765;ENST00000539465	T;T	0.25414	1.8;1.8	5.71	4.38	0.52667	.	0.000000	0.64402	D	0.000002	T	0.44850	0.1313	M	0.63843	1.955	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.41233	-0.9520	10	0.87932	D	0	-4.6909	9.9902	0.41865	0.0:0.0922:0.0:0.9078	.	1568	Q5SYB0	FRPD1_HUMAN	V	1568	ENSP00000366995:L1568V;ENSP00000444411:L1568V	ENSP00000366995:L1568V	L	+	1	2	FRMPD1	37736731	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	3.449000	0.52950	2.183000	0.69458	0.533000	0.62120	TTG	.	.		0.607	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907		G	37746731	T	G	37746731	3	3	308	1	0	0	0	0	1	0	0	0	6065	1838	64	5	4760	5	FRMPD1	9	37746731	Missense_Mutation	SNP	T	TCGA-HP-A5N0-01A-11D-A28X-10		37746731	103466700	66	43983										
SLC28A3	64078	hgsc.bcm.edu	37	chr9	86905113	86905113	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	cacgcttccagcaatggtagAgaacccggcggtcatgatgg	13	11	1	2			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr9:86905113A>G	ENST00000376238.4	-	11	1154	c.1105T>C	c.(1105-1107)Tct>Cct	p.S369P	RP11-380F14.2_ENST00000419815.1_RNA|SLC28A3_ENST00000537648.1_Missense_Mutation_p.S300P	NM_001199633.1|NM_022127.2	NP_001186562.1|NP_071410.1	Q9HAS3	S28A3_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 3	369					pyrimidine nucleoside transport (GO:0015864)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|purine-specific nucleoside:sodium symporter activity (GO:0015390)|pyrimidine- and adenine-specific:sodium symporter activity (GO:0015389)			endometrium(2)|large_intestine(6)|lung(17)|ovary(1)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31					Adenosine(DB00640)|Cladribine(DB00242)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Mercaptopurine(DB01033)|Ribavirin(DB00811)	GCAATGGTAGAGAACCCGGCG	0.448																																					p.S369P	Ovarian(106;425 1539 34835 42413 43572)	Atlas-SNP	.											.	SLC28A3	72	.	0			c.T1105C						.						114	108	110					9																	86905113		2203	4300	6503	SO:0001583	missense	64078	exon11			TGGTAGAGAACCC	AF305210	CCDS6670.1	9q21.33	2013-07-17	2013-07-17		ENSG00000197506	ENSG00000197506		"Solute carriers"	16484	protein-coding gene	gene with protein product		608269	"solute carrier family 28 (sodium-coupled nucleoside transporter), member 3"			11032837	Standard	NM_001199633		Approved	CNT3	uc010mpz.3	Q9HAS3	OTTHUMG00000020117	ENST00000376238.4:c.1105T>C	chr9.hg19:g.86905113A>G	ENSP00000365413:p.Ser369Pro	152.0	0.0		125.0	25.0	NM_001199633	A8K9Y4|B1AML0|B2RA51|B4E2S8|F5GYE3	Missense_Mutation	SNP	ENST00000376238.4	hg19	CCDS6670.1	.	.	.	.	.	.	.	.	.	.	A	23.6	4.432896	0.83776	.	.	ENSG00000197506	ENST00000376238;ENST00000537648	T;T	0.30714	1.52;1.52	5.82	-0.775	0.10988	Nucleoside recognition (1);	0.410917	0.26355	N	0.024852	T	0.55033	0.1895	M	0.80183	2.485	0.38193	D	0.939974	P	0.49307	0.922	P	0.60609	0.877	T	0.71397	-0.4605	10	0.87932	D	0	-5.7197	20.1898	0.98228	0.2856:0.7143:0.0:0.0	.	369	Q9HAS3	S28A3_HUMAN	P	369;300	ENSP00000365413:S369P;ENSP00000446438:S300P	ENSP00000365413:S369P	S	-	1	0	SLC28A3	86094933	0.991000	0.36638	0.966000	0.40874	0.809000	0.45718	0.500000	0.22562	-0.089000	0.12484	0.460000	0.39030	TCT	.	.		0.448	SLC28A3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052874.1	NM_022127		G	86905113	A	G	86905113	3	3	308	1	0	0	0	0	1	0	0	0	14548	304	11	2	1002	2	SLC28A3	9	86905113	Missense_Mutation	SNP	A	TCGA-HP-A5N0-01A-11D-A28X-10	49158382	86905113	54308318	67	43984										
PAPPA	5069	hgsc.bcm.edu	37	chr9	118950193	118950193	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	ttcaagcaatacaacatctcCtgggagctggacgtgctgga	11	10	2	0			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr9:118950193C>G	ENST00000328252.3	+	2	1545	c.1176C>G	c.(1174-1176)tcC>tcG	p.S392S	PAPPA_ENST00000534838.1_5'Flank	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	392	Metalloprotease.				cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|female pregnancy (GO:0007565)|response to follicle-stimulating hormone (GO:0032354)|response to glucocorticoid (GO:0051384)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(9)|kidney(2)|large_intestine(23)|lung(33)|ovary(4)|pancreas(2)|prostate(5)|skin(7)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	98						ACAACATCTCCTGGGAGCTGG	0.567																																					p.S392S		Atlas-SNP	.											.	PAPPA	243	.	0			c.C1176G						.						66	58	61					9																	118950193		2203	4300	6503	SO:0001819	synonymous_variant	5069	exon2			CATCTCCTGGGAG		CCDS6813.1	9q33.1	2014-03-05			ENSG00000182752	ENSG00000182752			8602	protein-coding gene	gene with protein product	"insulin-like growth factor-dependent IGF binding protein-4 protease", "aspecific BCL2 ARE-binding protein 2", "differentially placenta 1 expressed protein"	176385				7679961	Standard	NM_002581		Approved	PAPP-A, PAPPA1, IGFBP-4ase, PAPA, ASBABP2, DIPLA1	uc004bjn.3	Q13219	OTTHUMG00000021045	ENST00000328252.3:c.1176C>G	chr9.hg19:g.118950193C>G		130.0	0.0		150.0	43.0	NM_002581	B1AMF9|Q08371|Q68G52|Q9UDK7	Silent	SNP	ENST00000328252.3	hg19	CCDS6813.1																																																																																			.	.		0.567	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581		G	118950193	C	G	118950193	2	3	308	1	0	0	0	0	0	0	0	1	11441	668	24	4		4	PAPPA	9	118950193	Silent	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	32045080	118950193	22263238	68	43985										
HSPA14	51182	hgsc.bcm.edu	37	chr10	14890638	14890638	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	ccacaagctcagaaatacatCgcggaaagtaaatgtttagt	8	8	1	1	rs375004850		TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr10:14890638C>T	ENST00000378372.3	+	4	491	c.252C>T	c.(250-252)atC>atT	p.I84I		NM_016299.2	NP_057383.2	Q0VDF9	HSP7E_HUMAN	heat shock 70kDa protein 14	84					'de novo' cotranslational protein folding (GO:0051083)	cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)			breast(4)|endometrium(2)|kidney(2)|large_intestine(3)|lung(4)|ovary(2)	17						AGAAATACATCGCGGAAAGTA	0.328																																					p.I84I		Atlas-SNP	.											HSPA14,NS,carcinoma,0,1	HSPA14	42	.	0			c.C252T						.						108	95	99					10																	14890638		2203	4299	6502	SO:0001819	synonymous_variant	51182	exon4			ATACATCGCGGAA	AF112210	CCDS7103.1, CCDS60487.1	10p13	2011-09-02			ENSG00000187522	ENSG00000187522		"Heat shock proteins / HSP70"	29526	protein-coding gene	gene with protein product		610369				12477932	Standard	NM_016299		Approved	HSP70-4, HSP70L1	uc001ind.4	Q0VDF9	OTTHUMG00000017712	ENST00000378372.3:c.252C>T	chr10.hg19:g.14890638C>T		76.0	0.0		45.0	12.0	NM_016299	A8K8F8|B0YIY9|Q9P0X2|Q9UI07	Silent	SNP	ENST00000378372.3	hg19	CCDS7103.1	.	.	.	.	.	.	.	.	.	.	C	8.509	0.866065	0.17250	.	.	ENSG00000187522	ENST00000441647	.	.	.	5.89	4.97	0.65823	.	.	.	.	.	T	0.55909	0.1950	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54912	-0.8222	4	.	.	.	-6.1368	6.1276	0.20187	0.1413:0.6466:0.1364:0.0758	.	.	.	.	L	73	.	.	S	+	2	0	HSPA14	14930644	0.334000	0.24739	0.891000	0.34965	0.990000	0.78478	0.680000	0.25306	1.441000	0.47550	0.655000	0.94253	TCG	.	.		0.328	HSPA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046910.1	NM_016299		T	14890638	C	T	14890638	2	4	308	1	0	0	0	0	0	0	0	1	7416	874	31	1		1	HSPA14	10	14890638	Silent	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10		14890638	120644109	69	43986										
FAM171A1	221061	hgsc.bcm.edu	37	chr10	15326009	15326009	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	atcagtccccgaggtgccagAggctatggaggcctggttgg	16	10	1	1			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr10:15326009A>G	ENST00000378116.4	-	2	199	c.193T>C	c.(193-195)Tct>Cct	p.S65P		NM_001010924.1	NP_001010924.1	Q5VUB5	F1711_HUMAN	family with sequence similarity 171, member A1	65						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(6)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	52						GAGGTGCCAGAGGCTATGGAG	0.567																																					p.S65P		Atlas-SNP	.											.	FAM171A1	252	.	0			c.T193C						.						79	71	74					10																	15326009		2203	4300	6503	SO:0001583	missense	221061	exon2			TGCCAGAGGCTAT	AK022946	CCDS31154.1	10p13	2008-06-16	2008-06-16	2008-06-16	ENSG00000148468	ENSG00000148468			23522	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 38"	C10orf38			Standard	NM_001010924		Approved	FLJ12884	uc001iob.3	Q5VUB5	OTTHUMG00000017732	ENST00000378116.4:c.193T>C	chr10.hg19:g.15326009A>G	ENSP00000367356:p.Ser65Pro	143.0	0.0		97.0	35.0	NM_001010924	D3DRT9|Q32M49|Q8N4I0	Missense_Mutation	SNP	ENST00000378116.4	hg19	CCDS31154.1	.	.	.	.	.	.	.	.	.	.	A	18.63	3.665484	0.67700	.	.	ENSG00000148468	ENST00000378116;ENST00000378114;ENST00000396781;ENST00000455654	T;T	0.40476	1.03;1.03	5.25	5.25	0.73442	.	0.165668	0.56097	D	0.000036	T	0.55986	0.1955	M	0.74881	2.28	0.51482	D	0.999923	P	0.46512	0.879	P	0.50314	0.637	T	0.62666	-0.6806	10	0.87932	D	0	-13.882	15.4481	0.75248	1.0:0.0:0.0:0.0	.	65	Q5VUB5	F1711_HUMAN	P	65;65;66;65	ENSP00000367356:S65P;ENSP00000407796:S65P	ENSP00000367354:S65P	S	-	1	0	FAM171A1	15366015	1.000000	0.71417	0.991000	0.47740	0.688000	0.40055	2.921000	0.48852	2.111000	0.64477	0.482000	0.46254	TCT	.	.		0.567	FAM171A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046984.1	XM_167709		G	15326009	A	G	15326009	3	3	308	1	0	0	0	0	1	0	0	0	5495	304	11	2	2507	2	FAM171A1	10	15326009	Missense_Mutation	SNP	A	TCGA-HP-A5N0-01A-11D-A28X-10	435371	15326009	120208738	70	43987										
CDH23	64072	hgsc.bcm.edu	37	chr10	73437280	73437280	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	tggactatgagctcatccagCgcttcaccctgacgatcatt	8	13	3	2			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr10:73437280C>T	ENST00000224721.6	+	15	1602	c.1597C>T	c.(1597-1599)Cgc>Tgc	p.R533C	CDH23_ENST00000299366.7_Missense_Mutation_p.R573C	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	528	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						GCTCATCCAGCGCTTCACCCT	0.597																																					p.R528C		Atlas-SNP	.											.	CDH23	365	.	0			c.C1582T						.						40	42	41					10																	73437280		2098	4229	6327	SO:0001583	missense	64072	exon15			ATCCAGCGCTTCA	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"Cadherins / Cadherin-related"	13733	protein-coding gene	gene with protein product	"cadherin-related family member 23"	605516	"cadherin related 23", "cadherin-like 23"	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.1597C>T	chr10.hg19:g.73437280C>T	ENSP00000224721:p.Arg533Cys	148.0	0.0		120.0	9.0	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	hg19		.	.	.	.	.	.	.	.	.	.	C	35	5.530094	0.96446	.	.	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000398828;ENST00000299366;ENST00000224721;ENST00000442677	.	.	.	5.51	5.51	0.81932	Cadherin (5);Cadherin-like (1);	0.069679	0.56097	D	0.000023	D	0.82651	0.5083	M	0.79614	2.46	0.80722	D	1	D;D;D	0.89917	0.995;1.0;0.989	P;D;P	0.87578	0.893;0.998;0.67	T	0.81540	-0.0886	9	0.39692	T	0.17	.	19.473	0.94971	0.0:1.0:0.0:0.0	.	528;531;528	Q6P152;G3XCN8;Q9H251	.;.;CAD23_HUMAN	C	533;528;528;531;531;45	.	ENSP00000224721:R533C	R	+	1	0	CDH23	73107286	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.893000	0.69798	2.594000	0.87642	0.650000	0.86243	CGC	.	.		0.597	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836		T	73437280	C	T	73437280	3	4	308	1	0	0	0	0	1	0	0	0	3110	768	27	1	1867	1	CDH23	10	73437280	Missense_Mutation	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	58111271	73437280	62097467	71	43988										
TNKS2	80351	hgsc.bcm.edu	37	chr10	93558624	93558624	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	gacacggcgggcaggaaatcCaccccgctgcacttcgccgc	12	17	0	0			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr10:93558624C>T	ENST00000371627.4	+	1	556	c.177C>T	c.(175-177)tcC>tcT	p.S59S	TNKS2-AS1_ENST00000432246.1_RNA|TNKS2-AS1_ENST00000432938.1_RNA	NM_025235.3	NP_079511.1	Q9H2K2	TNKS2_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2	59					multicellular organism growth (GO:0035264)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein polyubiquitination (GO:0000209)|regulation of multicellular organism growth (GO:0040014)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			biliary_tract(1)|breast(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	48		Colorectal(252;0.162)				GCAGGAAATCCACCCCGCTGC	0.682																																					p.S59S		Atlas-SNP	.											.	TNKS2	103	.	0			c.C177T						.						11	13	12					10																	93558624		2126	4214	6340	SO:0001819	synonymous_variant	80351	exon1			GAAATCCACCCCG	AF342982	CCDS7417.1	10q23.3	2013-01-10			ENSG00000107854	ENSG00000107854		"Poly (ADP-ribose) polymerases", "Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	15677	protein-coding gene	gene with protein product		607128					Standard	NM_025235		Approved	TNKL, TANK2, PARP-5b, PARP-5c, PARP5B, PARP5C, pART6	uc001khp.3	Q9H2K2	OTTHUMG00000018747	ENST00000371627.4:c.177C>T	chr10.hg19:g.93558624C>T		69.0	0.0		62.0	28.0	NM_025235	B2RBD3|Q9H8F2|Q9HAS4	Silent	SNP	ENST00000371627.4	hg19	CCDS7417.1																																																																																			.	.		0.682	TNKS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049374.1	NM_025235		T	93558624	C	T	93558624	2	4	308	1	0	0	0	0	0	0	0	1	16336	581	21	3		3	TNKS2	10	93558624	Silent	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	20121344	93558624	41976123	72	43989										
PPRC1	23082	hgsc.bcm.edu	37	chr10	103909723	103909723	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	gacccagcacctgtaaagagCaaatttgattctcttgactt	7	10	1	3			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr10:103909723C>T	ENST00000278070.2	+	14	4971	c.4932C>T	c.(4930-4932)agC>agT	p.S1644S	NOLC1_ENST00000603742.1_5'Flank|PPRC1_ENST00000413464.2_Silent_p.S1380S|PPRC1_ENST00000370012.1_Silent_p.S611S|NOLC1_ENST00000405356.1_5'Flank|NOLC1_ENST00000488254.2_5'Flank|NOLC1_ENST00000605788.1_5'Flank	NM_015062.3	NP_055877.3	Q5VV67	PPRC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator-related 1	1644					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(10)|lung(19)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Colorectal(252;0.122)		Epithelial(162;4.97e-08)|all cancers(201;8.99e-07)		CTGTAAAGAGCAAATTTGATT	0.473																																					p.S1644S		Atlas-SNP	.											.	PPRC1	151	.	0			c.C4932T						.						149	160	156					10																	103909723		2203	4300	6503	SO:0001819	synonymous_variant	23082	exon14			AAAGAGCAAATTT	AF325193	CCDS7529.1, CCDS73186.1	10q24.32	2013-02-12	2006-10-17		ENSG00000148840	ENSG00000148840		"RNA binding motif (RRM) containing"	30025	protein-coding gene	gene with protein product			"peroxisome proliferative activated receptor, gamma, coactivator-related 1"			9628581, 11340167	Standard	XM_005269656		Approved	PRC, KIAA0595, MGC74642	uc001kum.3	Q5VV67	OTTHUMG00000018948	ENST00000278070.2:c.4932C>T	chr10.hg19:g.103909723C>T		146.0	0.0		68.0	26.0	NM_015062	Q5VV66|Q6P3U5|Q6P3W1|Q76N31|Q9BUJ3|Q9BZE5|Q9Y4E0	Silent	SNP	ENST00000278070.2	hg19	CCDS7529.1																																																																																			.	.		0.473	PPRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050021.1	NM_015062		T	103909723	C	T	103909723	2	4	308	1	0	0	0	0	0	0	0	1	12422	709	25	3		3	PPRC1	10	103909723	Silent	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	10351099	103909723	31625024	73	43990										
OR52D1	390066	hgsc.bcm.edu	37	chr11	5510297	5510297	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	agtcctcaattctacttgccAtggcctttgataggtatgtg	9	9	2	1			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr11:5510297A>T	ENST00000322641.5	+	1	383	c.361A>T	c.(361-363)Atg>Ttg	p.M121L	HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron	NM_001005163.2	NP_001005163.1	Q9H346	O52D1_HUMAN	olfactory receptor, family 52, subfamily D, member 1	121					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			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)		TCTACTTGCCATGGCCTTTGA	0.463																																					p.M121L		Atlas-SNP	.											.	OR52D1	66	.	0			c.A361T						.						173	159	164					11																	5510297		2201	4297	6498	SO:0001583	missense	390066	exon1			CTTGCCATGGCCT	BK004276	CCDS31384.1	11p15.4	2012-08-09			ENSG00000181609	ENSG00000181609		"GPCR / Class A : Olfactory receptors"	15212	protein-coding gene	gene with protein product							Standard	NM_001005163		Approved		uc010qzg.2	Q9H346	OTTHUMG00000066895	ENST00000322641.5:c.361A>T	chr11.hg19:g.5510297A>T	ENSP00000326232:p.Met121Leu	181.0	0.0		174.0	49.0	NM_001005163	B9EGY9|Q6IFI6	Missense_Mutation	SNP	ENST00000322641.5	hg19	CCDS31384.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.154485	0.78114	.	.	ENSG00000181609	ENST00000322641	T	0.00420	7.47	5.57	5.57	0.84162	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.01976	0.0062	H	0.95151	3.63	0.46631	D	0.999135	D	0.56035	0.974	D	0.69307	0.963	T	0.15435	-1.0437	10	0.72032	D	0.01	.	14.7065	0.69194	1.0:0.0:0.0:0.0	.	121	Q9H346	O52D1_HUMAN	L	121	ENSP00000326232:M121L	ENSP00000326232:M121L	M	+	1	0	OR52D1	5466873	1.000000	0.71417	1.000000	0.80357	0.679000	0.39708	7.269000	0.78482	2.340000	0.79590	0.528000	0.53228	ATG	.	.		0.463	OR52D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143372.1	NM_001005163		T	5510297	A	T	5510297	3	4	308	1	0	0	0	0	1	0	0	0	11123	217	8	4	363	4	OR52D1	11	5510297	Missense_Mutation	SNP	A	TCGA-HP-A5N0-01A-11D-A28X-10		5510297	129496219	74	43991										
ANO5	203859	hgsc.bcm.edu	37	chr11	22272304	22272304	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	cagcactgaaatctgtgaccCtgagattggtggtcagatga	12	8	2	5	rs541372136	byFrequency	TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr11:22272304C>A	ENST00000324559.8	+	11	1348	c.1031C>A	c.(1030-1032)cCt>cAt	p.P344H		NM_001142649.1|NM_213599.2	NP_001136121.1|NP_998764.1	Q75V66	ANO5_HUMAN	anoctamin 5	344					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	intracellular calcium activated chloride channel activity (GO:0005229)			breast(2)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(12)|lung(36)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						ATCTGTGACCCTGAGATTGGT	0.398																																					p.P344H		Atlas-SNP	.											.	ANO5	162	.	0			c.C1031A						.						229	184	199					11																	22272304		2203	4300	6503	SO:0001583	missense	203859	exon11			GTGACCCTGAGAT	AL833271	CCDS31444.1	11p15.1	2014-09-17	2008-08-28	2008-08-28	ENSG00000171714	ENSG00000171714		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	27337	protein-coding gene	gene with protein product		608662	"transmembrane protein 16E", "limb girdle muscular dystrophy 2L (autosomal recessive)"	TMEM16E, LGMD2L		15067359, 20096397, 24692353	Standard	NM_213599		Approved	GDD1	uc001mqi.2	Q75V66	OTTHUMG00000166051	ENST00000324559.8:c.1031C>A	chr11.hg19:g.22272304C>A	ENSP00000315371:p.Pro344His	155.0	0.0		123.0	41.0	NM_213599		Missense_Mutation	SNP	ENST00000324559.8	hg19	CCDS31444.1	.	.	.	.	.	.	.	.	.	.	C	16.56	3.157899	0.57368	.	.	ENSG00000171714	ENST00000324559	T	0.71698	-0.59	5.49	3.48	0.39840	.	0.436137	0.25780	N	0.028351	T	0.79411	0.4441	M	0.64997	1.995	0.31533	N	0.660977	D	0.65815	0.995	D	0.67900	0.954	T	0.79072	-0.1953	10	0.45353	T	0.12	.	13.1544	0.59509	0.1302:0.7549:0.1149:0.0	.	344	Q75V66	ANO5_HUMAN	H	344	ENSP00000315371:P344H	ENSP00000315371:P344H	P	+	2	0	ANO5	22228880	0.742000	0.28228	0.996000	0.52242	0.932000	0.56968	1.685000	0.37659	2.565000	0.86533	0.557000	0.71058	CCT	.	.		0.398	ANO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387615.1	NM_213599		A	22272304	C	A	22272304	3	1	308	1	0	0	0	0	1	0	0	0	700	681	24	3	1073	3	ANO5	11	22272304	Missense_Mutation	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	16762007	22272304	112734212	75	43992										
FNBP4	23360	hgsc.bcm.edu	37	chr11	47772487	47772487	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	cctttttaacttctcgcttgGctatgactggtccactttta	6	11	1	1			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr11:47772487G>T	ENST00000263773.5	-	6	899	c.887C>A	c.(886-888)gCc>gAc	p.A296D	FNBP4_ENST00000534003.1_5'UTR	NM_015308.2	NP_056123.2	Q8N3X1	FNBP4_HUMAN	formin binding protein 4	296						nucleus (GO:0005634)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	44						TTCTCGCTTGGCTATGACTGG	0.393																																					p.A296D		Atlas-SNP	.											.	FNBP4	99	.	0			c.C887A						.						171	151	157					11																	47772487		1866	4098	5964	SO:0001583	missense	23360	exon6			CGCTTGGCTATGA	BC037404	CCDS41644.1	11q12.1	2008-02-05			ENSG00000109920	ENSG00000109920			19752	protein-coding gene	gene with protein product		615265				10231032	Standard	NM_015308		Approved	KIAA1014	uc009ylv.3	Q8N3X1	OTTHUMG00000166533	ENST00000263773.5:c.887C>A	chr11.hg19:g.47772487G>T	ENSP00000263773:p.Ala296Asp	89.0	0.0		80.0	4.0	NM_015308	Q9H985|Q9NT81|Q9Y2L7	Missense_Mutation	SNP	ENST00000263773.5	hg19	CCDS41644.1	.	.	.	.	.	.	.	.	.	.	G	8.190	0.795709	0.16327	.	.	ENSG00000109920	ENST00000263773	T	0.33216	1.42	5.69	1.24	0.21308	.	0.658388	0.15866	N	0.240795	T	0.19846	0.0477	N	0.24115	0.695	0.09310	N	1	B	0.28128	0.201	B	0.32289	0.143	T	0.25117	-1.0141	10	0.23891	T	0.37	0.2091	10.0434	0.42173	0.4033:0.0:0.5967:0.0	.	296	Q8N3X1	FNBP4_HUMAN	D	296	ENSP00000263773:A296D	ENSP00000263773:A296D	A	-	2	0	FNBP4	47729063	0.400000	0.25295	0.182000	0.23118	0.139000	0.21198	1.083000	0.30815	0.353000	0.24079	0.650000	0.86243	GCC	.	.		0.393	FNBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390237.3			T	47772487	G	T	47772487	3	4	308	1	0	0	0	0	1	0	0	0	5975	1203	42	3	2214	3	FNBP4	11	47772487	Missense_Mutation	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10	25500183	47772487	87234029	76	43993										
ARRB1	408	hgsc.bcm.edu	37	chr11	74980004	74980004	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	gcagttccacggccacgtcgCtgaaacagagacccagaccc	10	16	0	3			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr11:74980004C>T	ENST00000420843.2	-	14	1120		c.e14-1		ARRB1_ENST00000393505.4_Missense_Mutation_p.S341N|ARRB1_ENST00000360025.3_Splice_Site	NM_004041.4	NP_004032.2	P49407	ARRB1_HUMAN	arrestin, beta 1						activation of MAPK activity (GO:0000187)|apoptotic DNA fragmentation (GO:0006309)|blood coagulation (GO:0007596)|follicle-stimulating hormone signaling pathway (GO:0042699)|G-protein coupled receptor internalization (GO:0002031)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of GTPase activity (GO:0034260)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein ubiquitination (GO:0031397)|Notch signaling pathway (GO:0007219)|phototransduction (GO:0007602)|platelet activation (GO:0030168)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of GTPase activity (GO:0043547)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H4 acetylation (GO:0090240)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of receptor internalization (GO:0002092)|positive regulation of Rho protein signal transduction (GO:0035025)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-Golgi vesicle-mediated transport (GO:0006892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|stress fiber assembly (GO:0043149)|transcription from RNA polymerase II promoter (GO:0006366)	basolateral plasma membrane (GO:0016323)|chromatin (GO:0000785)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|pseudopodium (GO:0031143)	angiotensin receptor binding (GO:0031701)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|enzyme inhibitor activity (GO:0004857)|GTPase activator activity (GO:0005096)|insulin-like growth factor receptor binding (GO:0005159)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			breast(4)|large_intestine(2)|lung(4)|prostate(1)	11						GGCCACGTCGCTGAAACAGAG	0.587																																					.		Atlas-SNP	.											.	ARRB1	37	.	0			c.1023-1G>A						.						101	94	96					11																	74980004		2200	4293	6493	SO:0001630	splice_region_variant	408	exon15			ACGTCGCTGAAAC	BC003636	CCDS31640.1, CCDS44684.1	11q13	2008-12-11			ENSG00000137486	ENSG00000137486			711	protein-coding gene	gene with protein product	"arrestin 2"	107940		ARR1		8486659	Standard	NM_004041		Approved		uc001owe.2	P49407	OTTHUMG00000165444	ENST00000420843.2:c.1023-1G>A	chr11.hg19:g.74980004C>T		131.0	0.0		82.0	25.0	NM_004041	B6V9G8|O75625|O75630|Q2PP20|Q9BTK8	Splice_Site	SNP	ENST00000420843.2	hg19	CCDS44684.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.92|17.92	3.506193|3.506193	0.64410|0.64410	.|.	.|.	ENSG00000137486|ENSG00000137486	ENST00000420843;ENST00000360025;ENST00000532447|ENST00000393505	.|T	.|0.18016	.|2.24	4.36|4.36	4.36|4.36	0.52297|0.52297	.|.	.|59.833200	.|0.00397	.|U	.|0.000058	.|T	.|0.30166	.|0.0756	.|.	.|.	.|.	0.47276|0.47276	D|D	0.999374|0.999374	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.02546	.|-1.1143	.|6	.|.	.|.	.|.	.|.	14.4868|14.4868	0.67622|0.67622	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	.|N	-1|341	.|ENSP00000377141:S341N	.|.	.|S	-|-	.|2	.|0	ARRB1|ARRB1	74657652|74657652	1.000000|1.000000	0.71417|0.71417	0.925000|0.925000	0.36789|0.36789	0.648000|0.648000	0.38561|0.38561	6.975000|6.975000	0.76128|0.76128	2.281000|2.281000	0.76405|0.76405	0.555000|0.555000	0.69702|0.69702	.|AGC	.	.		0.587	ARRB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384092.3	NM_004041	Intron	T	74980004	C	T	74980004	5	4	308	1	0	0	0	0	0	0	1	0	980	811	28	3	246	3	ARRB1	11	74980004	Splice_Site	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	27207517	74980004	60026512	77	43994										
SLC36A4	120103	hgsc.bcm.edu	37	chr11	92918881	92918881	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	tgccctcttgatcatcaagtTggtaatgcttctgaacaggc	9	10	4	2			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr11:92918881T>C	ENST00000326402.4	-	2	285	c.155A>G	c.(154-156)cAa>cGa	p.Q52R	SLC36A4_ENST00000529184.1_5'UTR	NM_152313.2	NP_689526.2	Q6YBV0	S36A4_HUMAN	solute carrier family 36 (proton/amino acid symporter), member 4	52					L-alanine transport (GO:0015808)|proline transport (GO:0015824)|tryptophan transport (GO:0015827)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	25		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				ATCATCAAGTTGGTAATGCTT	0.373																																					p.Q52R		Atlas-SNP	.											.	SLC36A4	61	.	0			c.A155G						.						125	115	119					11																	92918881		2201	4298	6499	SO:0001583	missense	120103	exon2			TCAAGTTGGTAAT	AY162216	CCDS8291.1, CCDS66202.1	11q21	2013-05-22			ENSG00000180773	ENSG00000180773		"Solute carriers"	19660	protein-coding gene	gene with protein product		613760					Standard	XM_005273758		Approved	PAT4, FLJ38932	uc001pdn.3	Q6YBV0	OTTHUMG00000167368	ENST00000326402.4:c.155A>G	chr11.hg19:g.92918881T>C	ENSP00000317382:p.Gln52Arg	90.0	0.0		66.0	15.0	NM_152313	Q86X30|Q8IVM5|Q8N8S6	Missense_Mutation	SNP	ENST00000326402.4	hg19	CCDS8291.1	.	.	.	.	.	.	.	.	.	.	T	3.785	-0.044776	0.07452	.	.	ENSG00000180773	ENST00000326402	T	0.03889	3.77	5.62	5.62	0.85841	.	0.092368	0.48767	D	0.000167	T	0.04092	0.0114	L	0.27053	0.805	0.80722	D	1	B	0.11235	0.004	B	0.09377	0.004	T	0.34477	-0.9827	10	0.07813	T	0.8	-7.6902	14.0451	0.64700	0.0:0.0:0.0:1.0	.	52	Q6YBV0	S36A4_HUMAN	R	52	ENSP00000317382:Q52R	ENSP00000317382:Q52R	Q	-	2	0	SLC36A4	92558529	1.000000	0.71417	0.979000	0.43373	0.507000	0.33981	3.589000	0.53972	2.134000	0.65973	0.528000	0.53228	CAA	.	.		0.373	SLC36A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394329.2			C	92918881	T	C	92918881	3	2	308	1	0	0	0	0	1	0	0	0	14611	1812	63	2	1399	2	SLC36A4	11	92918881	Missense_Mutation	SNP	T	TCGA-HP-A5N0-01A-11D-A28X-10	17938877	92918881	42087635	78	43995										
CEP164	22897	hgsc.bcm.edu	37	chr11	117282631	117282631	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	cgtgtcaagaatgaccccagGttgtatccttttacctggtt	9	10	1	2			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr11:117282631G>T	ENST00000278935.3	+	32	4431	c.4284G>T	c.(4282-4284)agG>agT	p.R1428S	CEP164_ENST00000533706.1_3'UTR	NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	1428					cilium assembly (GO:0042384)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(7)|large_intestine(12)|lung(18)|ovary(3)|prostate(3)	47	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		ATGACCCCAGGTTGTATCCTT	0.577																																					p.R1428S		Atlas-SNP	.											.	CEP164	121	.	0			c.G4284T						.						47	48	48					11																	117282631		2201	4296	6497	SO:0001583	missense	22897	exon32			CCCCAGGTTGTAT	AB028975	CCDS31683.1	11q23.3	2014-02-20			ENSG00000110274	ENSG00000110274			29182	protein-coding gene	gene with protein product		614848				10470851, 14654843	Standard	NM_014956		Approved	KIAA1052, NPHP15	uc001prc.3	Q9UPV0	OTTHUMG00000167070	ENST00000278935.3:c.4284G>T	chr11.hg19:g.117282631G>T	ENSP00000278935:p.Arg1428Ser	147.0	0.0		117.0	36.0	NM_014956	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	Missense_Mutation	SNP	ENST00000278935.3	hg19	CCDS31683.1	.	.	.	.	.	.	.	.	.	.	G	11.82	1.753185	0.31046	.	.	ENSG00000110274	ENST00000278935	T	0.56611	0.45	5.27	1.37	0.22104	.	0.235815	0.29995	N	0.010672	T	0.29491	0.0735	N	0.08118	0	0.09310	N	1	B;B	0.15473	0.013;0.013	B;B	0.19391	0.025;0.025	T	0.25710	-1.0124	10	0.72032	D	0.01	-19.1551	7.9719	0.30132	0.4035:0.0:0.5965:0.0	.	1428;1423	Q9UPV0;Q9UPV0-2	CE164_HUMAN;.	S	1428	ENSP00000278935:R1428S	ENSP00000278935:R1428S	R	+	3	2	CEP164	116787841	0.743000	0.28239	0.292000	0.24919	0.845000	0.48019	0.248000	0.18198	0.249000	0.21456	0.655000	0.94253	AGG	.	.		0.577	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1	NM_014956		T	117282631	G	T	117282631	3	4	308	1	0	0	0	0	1	0	0	0	3251	1252	44	3	4402	3	CEP164	11	117282631	Missense_Mutation	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10	24363750	117282631	17723885	79	43996										
MLL	4297	hgsc.bcm.edu	37	chr11	118362558	118362558	+	Frame_Shift_Del	DEL	A	A	-													0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	agagtggcgactggcccttgAaaaagagctgcagatttctc							TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr11:118362558delA	ENST00000389506.5	+	15	4910	c.4910delA	c.(4909-4911)gaafs	p.E1637fs	KMT2A_ENST00000354520.4_Frame_Shift_Del_p.E1599fs|KMT2A_ENST00000534358.1_Frame_Shift_Del_p.E1640fs			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	1637					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										CTGGCCCTTGAAAAAGAGCTG	0.493																																					p.E1640fs		Atlas-INDEL	.											.	MLL	548	.	0			c.4918delG						.						73	72	72					11																	118362558		2200	4296	6496	SO:0001589	frameshift_variant	4297	exon15			.	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.4910delA	chr11.hg19:g.118362558delA	ENSP00000374157:p.Glu1637fs	98.0	0.0		76.0	12.0	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Frame_Shift_Del	DEL	ENST00000389506.5	hg19	CCDS31686.1																																																																																			.	.		0.493	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		-	118362558	A	-	118362558	7	5	308	1	0	1	0	1	0	0	0	0	9629	246	9	0	4968	0	MLL	11	118362558	Frame_Shift_Del	DEL	A	TCGA-HP-A5N0-01A-11D-A28X-10	1079927	118362558	16643958	80	43997										
CLEC1B	51266	hgsc.bcm.edu	37	chr12	10147806	10147806	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	cgacttctggcgagataatcCgacccaacgaattaaatgag	9	10	1	2			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr12:10147806C>A	ENST00000298527.6	-	5	657	c.478G>T	c.(478-480)Gga>Tga	p.G160*	CLEC1B_ENST00000428126.2_Nonsense_Mutation_p.G127*|CLEC1B_ENST00000348658.4_Nonsense_Mutation_p.G127*	NM_016509.3	NP_057593.3	Q9P126	CLC1B_HUMAN	C-type lectin domain family 1, member B	160	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|platelet formation (GO:0030220)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(12)|stomach(1)|urinary_tract(1)	19						CGAGATAATCCGACCCAACGA	0.428																																					p.G160X		Atlas-SNP	.											.	CLEC1B	39	.	0			c.G478T						.						275	266	269					12																	10147806		1868	4092	5960	SO:0001587	stop_gained	51266	exon5			ATAATCCGACCCA	AF124841	CCDS41751.1, CCDS41752.1	12p13.31	2006-04-12				ENSG00000165682		"C-type lectin domain containing"	24356	protein-coding gene	gene with protein product		606783				10671229, 11745369	Standard	NM_016509		Approved	CLEC2	uc001qwu.3	Q9P126		ENST00000298527.6:c.478G>T	chr12.hg19:g.10147806C>A	ENSP00000298527:p.Gly160*	65.0	0.0		60.0	20.0	NM_016509	Q6UWX7|Q8NHR6	Nonsense_Mutation	SNP	ENST00000298527.6	hg19	CCDS41752.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.037910	0.93630	.	.	ENSG00000165682	ENST00000398937;ENST00000428126;ENST00000298527;ENST00000348658;ENST00000398939	.	.	.	3.83	3.83	0.44106	.	0.000000	0.47455	D	0.000228	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	11.1397	0.48396	0.0:1.0:0.0:0.0	.	.	.	.	X	67;127;160;127;67	.	ENSP00000298527:G160X	G	-	1	0	CLEC1B	10039073	1.000000	0.71417	1.000000	0.80357	0.735000	0.41995	3.454000	0.52986	1.954000	0.56735	0.298000	0.19748	GGA	.	.		0.428	CLEC1B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399922.1	NM_016509		A	10147806	C	A	10147806	4	1	308	1	0	0	0	0	0	1	0	0	3508	661	23	1	219	1	CLEC1B	12	10147806	Nonsense_Mutation	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10		10147806	123704089	81	43998										
KRT85	3891	hgsc.bcm.edu	37	chr12	52760929	52760929	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	catggggggctgggtccgcaCacgcccccggagcggtagcc	17	15	0	0			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr12:52760929C>T	ENST00000257901.3	-	1	336	c.261G>A	c.(259-261)gtG>gtA	p.V87V	KRT85_ENST00000544265.1_5'Flank	NM_002283.3	NP_002274.1	P78386	KRT85_HUMAN	keratin 85	87	Head.				epidermis development (GO:0008544)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(6)|kidney(1)|large_intestine(7)|liver(1)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	36	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		TGGGTCCGCACACGCCCCCGG	0.682																																					p.V87V		Atlas-SNP	.											.	KRT85	78	.	0			c.G261A						.						60	65	63					12																	52760929		2203	4300	6503	SO:0001819	synonymous_variant	3891	exon1			TCCGCACACGCCC	X99140	CCDS8824.1, CCDS73472.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000135443	ENSG00000135443		"-", "Intermediate filaments type II, keratins (basic)"	6462	protein-coding gene	gene with protein product	"hard keratin type II"	602767	"keratin, hair, basic, 5"	KRTHB5		9084137, 16831889	Standard	NM_002283		Approved	Hb-5	uc001sag.3	P78386	OTTHUMG00000169633	ENST00000257901.3:c.261G>A	chr12.hg19:g.52760929C>T		378.0	0.0		351.0	69.0	NM_002283	Q9NSB1	Silent	SNP	ENST00000257901.3	hg19	CCDS8824.1																																																																																			.	.		0.682	KRT85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405184.1	NM_002283		T	52760929	C	T	52760929	2	4	308	1	0	0	0	0	0	0	0	1	8508	465	17	3		3	KRT85	12	52760929	Silent	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	42613123	52760929	81090966	82	43999										
TMEM5	10329	hgsc.bcm.edu	37	chr12	64174920	64174920	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	tccacgaaaggaaaaacagaTctcagtgtacaaatctgggg	10	8	2	1			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr12:64174920T>A	ENST00000261234.6	+	2	449	c.291T>A	c.(289-291)gaT>gaA	p.D97E	RP11-415I12.3_ENST00000509615.2_RNA|TMEM5_ENST00000537982.1_3'UTR|TMEM5_ENST00000537373.1_5'UTR	NM_014254.1	NP_055069.1	Q9Y2B1	TMEM5_HUMAN	transmembrane protein 5	97						integral component of plasma membrane (GO:0005887)				breast(1)|large_intestine(3)|liver(2)|lung(7)|prostate(1)|skin(1)	15		Myeloproliferative disorder(1001;0.0255)	BRCA - Breast invasive adenocarcinoma(9;0.0985)	GBM - Glioblastoma multiforme(28;9e-08)|BRCA - Breast invasive adenocarcinoma(357;0.000175)		GAAAAACAGATCTCAGTGTAC	0.323																																					p.D97E		Atlas-SNP	.											.	TMEM5	35	.	0			c.T291A						.						76	84	81					12																	64174920		2203	4300	6503	SO:0001583	missense	10329	exon2			AACAGATCTCAGT	AB015633	CCDS8966.1, CCDS61179.1	12q14.1	2013-05-07			ENSG00000118600	ENSG00000118600			13530	protein-coding gene	gene with protein product		605862				10072769, 23217329	Standard	NM_014254		Approved	HP10481	uc001srq.2	Q9Y2B1	OTTHUMG00000168730	ENST00000261234.6:c.291T>A	chr12.hg19:g.64174920T>A	ENSP00000261234:p.Asp97Glu	107.0	0.0		55.0	13.0	NM_014254	A8K017|Q6PKD6	Missense_Mutation	SNP	ENST00000261234.6	hg19	CCDS8966.1	.	.	.	.	.	.	.	.	.	.	T	0.023	-1.399927	0.01165	.	.	ENSG00000118600	ENST00000261234	T	0.28454	1.61	4.34	1.4	0.22301	.	0.679416	0.15610	N	0.253407	T	0.12944	0.0314	N	0.05124	-0.11	0.21527	N	0.999653	B	0.02656	0.0	B	0.09377	0.004	T	0.31696	-0.9934	9	.	.	.	-26.0342	8.4151	0.32666	0.0:0.7387:0.1614:0.0999	.	97	Q9Y2B1	TMEM5_HUMAN	E	97	ENSP00000261234:D97E	.	D	+	3	2	TMEM5	62461187	0.955000	0.32602	0.035000	0.18076	0.133000	0.20885	0.370000	0.20433	0.160000	0.19432	-1.277000	0.01392	GAT	.	.		0.323	TMEM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400821.1	NM_014254		A	64174920	T	A	64174920	3	1	308	1	0	0	0	0	1	0	0	0	16189	1432	50	4	297	4	TMEM5	12	64174920	Missense_Mutation	SNP	T	TCGA-HP-A5N0-01A-11D-A28X-10	11413991	64174920	69676975	83	44000										
LRRIQ1	84125	hgsc.bcm.edu	37	chr12	85450892	85450892	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	aaagagacctgtgaaatgccCagccaacatgacacccgctt	8	13	0	3			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr12:85450892C>A	ENST00000393217.2	+	8	2382	c.2321C>A	c.(2320-2322)cCa>cAa	p.P774Q		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	774										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		GTGAAATGCCCAGCCAACATG	0.358																																					p.P774Q		Atlas-SNP	.											.	LRRIQ1	512	.	0			c.C2321A						.						110	126	120					12																	85450892		2203	4300	6503	SO:0001583	missense	84125	exon8			AATGCCCAGCCAA	AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.2321C>A	chr12.hg19:g.85450892C>A	ENSP00000376910:p.Pro774Gln	88.0	0.0		40.0	11.0	NM_001079910	Q567P4|Q9BS17|Q9HA36	Missense_Mutation	SNP	ENST00000393217.2	hg19	CCDS41816.1	.	.	.	.	.	.	.	.	.	.	C	14.52	2.560180	0.45590	.	.	ENSG00000133640	ENST00000256007;ENST00000378580;ENST00000393217	T	0.55234	0.53	5.56	4.68	0.58851	.	0.654660	0.13852	N	0.358317	T	0.55816	0.1944	L	0.34521	1.04	0.33335	D	0.569101	D;P	0.57899	0.981;0.481	P;B	0.55161	0.77;0.185	T	0.65257	-0.6212	10	0.54805	T	0.06	.	12.6917	0.56978	0.0:0.9238:0.0:0.0762	.	774;749	Q96JM4;C9JI57	LRIQ1_HUMAN;.	Q	774;749;774	ENSP00000376910:P774Q	ENSP00000256007:P774Q	P	+	2	0	LRRIQ1	83975023	0.973000	0.33851	0.871000	0.34182	0.167000	0.22549	3.077000	0.50089	1.354000	0.45846	0.591000	0.81541	CCA	.	.		0.358	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165		A	85450892	C	A	85450892	3	1	308	1	0	0	0	0	1	0	0	0	9038	594	21	3	2347	3	LRRIQ1	12	85450892	Missense_Mutation	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	21275972	85450892	48401003	84	44001										
SALL2	6297	hgsc.bcm.edu	37	chr14	21992350	21992350	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	aacttattgaaagcagggagTcctggagccgtggctgtgcc	14	9	0	1			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr14:21992350T>A	ENST00000327430.3	-	2	1806	c.1512A>T	c.(1510-1512)ggA>ggT	p.G504G	SALL2_ENST00000450879.2_Silent_p.G367G|SALL2_ENST00000538754.1_Intron|SALL2_ENST00000317492.5_Intron|AE000658.22_ENST00000535893.1_RNA	NM_005407.1	NP_005398.1	Q9Y467	SALL2_HUMAN	spalt-like transcription factor 2	504					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(12)|lung(12)|ovary(2)|skin(6)|urinary_tract(2)	43	all_cancers(95;0.000662)			GBM - Glioblastoma multiforme(265;0.0151)		AAGCAGGGAGTCCTGGAGCCG	0.567																																					p.G504G		Atlas-SNP	.											.	SALL2	95	.	0			c.A1512T						.						40	39	39					14																	21992350		2203	4300	6503	SO:0001819	synonymous_variant	6297	exon2			AGGGAGTCCTGGA	AB002358	CCDS32045.1	14q11.1-q12.1	2013-10-17	2013-10-17		ENSG00000165821	ENSG00000165821		"Zinc fingers, C2H2-type"	10526	protein-coding gene	gene with protein product		602219	"sal (Drosophila)-like 2", "sal-like 2 (Drosophila)"			8975705	Standard	XM_005267983		Approved	KIAA0360, Hsal2, ZNF795	uc001wbe.3	Q9Y467	OTTHUMG00000168826	ENST00000327430.3:c.1512A>T	chr14.hg19:g.21992350T>A		66.0	0.0		63.0	21.0	NM_005407	B2RMX6|B9EGK8|Q8N656|Q9Y4G1	Silent	SNP	ENST00000327430.3	hg19	CCDS32045.1	.	.	.	.	.	.	.	.	.	.	T	0.028	-1.355502	0.01256	.	.	ENSG00000165821	ENST00000546363	.	.	.	4.46	-1.66	0.08265	.	.	.	.	.	T	0.39226	0.1070	.	.	.	0.48901	D	0.999725	.	.	.	.	.	.	T	0.29150	-1.0021	4	.	.	.	-8.9817	1.1556	0.01795	0.1499:0.3012:0.1472:0.4016	.	.	.	.	V	363	.	.	D	-	2	0	SALL2	21062190	0.012000	0.17670	0.939000	0.37840	0.168000	0.22595	-0.521000	0.06245	-0.168000	0.10853	0.379000	0.24179	GAC	.	.		0.567	SALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401242.1	NM_005407		A	21992350	T	A	21992350	2	1	308	1	0	0	0	0	0	0	0	1	13826	1654	58	4		4	SALL2	14	21992350	Silent	SNP	T	TCGA-HP-A5N0-01A-11D-A28X-10		21992350	85357190	85	44002										
SOS2	6655	hgsc.bcm.edu	37	chr14	50655388	50655388	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	acagagagaaaccaaacctaTgtcatcctgatcaaacatgt	6	10	2	3			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr14:50655388T>A	ENST00000216373.5	-	5	815	c.541A>T	c.(541-543)Ata>Tta	p.I181L	SOS2_ENST00000543680.1_Missense_Mutation_p.I181L	NM_006939.2	NP_008870.2	Q07890	SOS2_HUMAN	son of sevenless homolog 2 (Drosophila)	181					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	DNA binding (GO:0003677)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(16)|ovary(2)|skin(1)	39	all_epithelial(31;0.000822)|Breast(41;0.0065)					ACCAAACCTATGTCATCCTGA	0.323																																					p.I181L		Atlas-SNP	.											.	SOS2	195	.	0			c.A541T						.						80	74	76					14																	50655388		2203	4300	6503	SO:0001583	missense	6655	exon5			AACCTATGTCATC	L13858	CCDS9697.1	14q21	2013-01-10	2001-12-04		ENSG00000100485	ENSG00000100485		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11188	protein-coding gene	gene with protein product		601247	"son of sevenless (Drosophilia) homolog 2"			8276400	Standard	NM_006939		Approved		uc001wxs.4	Q07890	OTTHUMG00000140292	ENST00000216373.5:c.541A>T	chr14.hg19:g.50655388T>A	ENSP00000216373:p.Ile181Leu	71.0	0.0		57.0	13.0	NM_006939	B7ZKT6|D3DSB4|Q15503|Q17RN1	Missense_Mutation	SNP	ENST00000216373.5	hg19	CCDS9697.1	.	.	.	.	.	.	.	.	.	.	T	12.74	2.028637	0.35797	.	.	ENSG00000100485	ENST00000216373;ENST00000543680	T;T	0.78595	-1.19;-1.03	5.43	5.43	0.79202	Histone-fold (1);	0.443755	0.27064	N	0.021116	T	0.65004	0.2650	L	0.27053	0.805	0.44908	D	0.997926	B;B	0.09022	0.002;0.001	B;B	0.06405	0.002;0.001	T	0.60419	-0.7267	10	0.09590	T	0.72	.	15.4668	0.75406	0.0:0.0:0.0:1.0	.	181;181	B7ZKT6;Q07890	.;SOS2_HUMAN	L	181	ENSP00000216373:I181L;ENSP00000445328:I181L	ENSP00000216373:I181L	I	-	1	0	SOS2	49725138	1.000000	0.71417	0.998000	0.56505	0.783000	0.44284	4.960000	0.63673	2.046000	0.60703	0.533000	0.62120	ATA	.	.		0.323	SOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276878.2			A	50655388	T	A	50655388	3	1	308	1	0	0	0	0	1	0	0	0	14952	1464	51	4	3533	4	SOS2	14	50655388	Missense_Mutation	SNP	T	TCGA-HP-A5N0-01A-11D-A28X-10	28663038	50655388	56694152	86	44003										
SPTB	6710	hgsc.bcm.edu	37	chr14	65260468	65260468	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	cccagaagaacttccagagtCgtttggactgctccagttgg	11	11	0	3	rs371216825		TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr14:65260468C>G	ENST00000389721.5	-	13	1945	c.1913G>C	c.(1912-1914)cGa>cCa	p.R638P	SPTB_ENST00000389720.3_Missense_Mutation_p.R638P|SPTB_ENST00000556626.1_Missense_Mutation_p.R638P|SPTB_ENST00000389722.3_Missense_Mutation_p.R638P|SPTB_ENST00000542895.1_Missense_Mutation_p.R638P	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	638					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		CTTCCAGAGTCGTTTGGACTG	0.557																																					p.R638P		Atlas-SNP	.											SPTB_ENST00000542895,mucosal,malignant_melanoma,0,2	SPTB	378	.	0			c.G1913C						.						75	64	68					14																	65260468		2203	4300	6503	SO:0001583	missense	6710	exon13			CAGAGTCGTTTGG		CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"Pleckstrin homology (PH) domain containing"	11274	protein-coding gene	gene with protein product	"spherocytosis, clinical type I"	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.1913G>C	chr14.hg19:g.65260468C>G	ENSP00000374371:p.Arg638Pro	101.0	1.0		81.0	28.0	NM_001024858	Q15510|Q15519	Missense_Mutation	SNP	ENST00000389721.5	hg19	CCDS32100.1	.	.	.	.	.	.	.	.	.	.	C	14.14	2.447774	0.43429	.	.	ENSG00000070182	ENST00000389723;ENST00000389722;ENST00000556626;ENST00000389721;ENST00000542895;ENST00000389720	T;T;T;T;T	0.36520	1.25;1.25;1.25;1.25;1.25	5.32	4.43	0.53597	.	0.126301	0.53938	D	0.000045	T	0.46308	0.1386	M	0.77486	2.375	0.51767	D	0.999935	B;B	0.18968	0.032;0.031	B;B	0.33690	0.168;0.054	T	0.50171	-0.8859	10	0.87932	D	0	.	12.9528	0.58411	0.0:0.9198:0.0:0.0802	.	638;642	P11277;Q59FP5	SPTB1_HUMAN;.	P	642;638;638;638;638;638	ENSP00000374372:R638P;ENSP00000451752:R638P;ENSP00000374371:R638P;ENSP00000443882:R638P;ENSP00000374370:R638P	ENSP00000374370:R638P	R	-	2	0	SPTB	64330221	0.043000	0.20138	1.000000	0.80357	0.871000	0.50021	1.437000	0.34991	1.249000	0.43950	0.561000	0.74099	CGA	.	.		0.557	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1			G	65260468	C	G	65260468	3	3	308	1	0	0	0	0	1	0	0	0	15133	884	31	4	5234	4	SPTB	14	65260468	Missense_Mutation	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	14605080	65260468	42089072	87	44004										
ATP10A	57194	hgsc.bcm.edu	37	chr15	25924784	25924785	+	Missense_Mutation	DNP	CA	CA	AC													0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	ccctcctggactcctcaggaCagcctcccctggcgcagagg							TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C|A	C|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr15:25924784_25924785CA>AC	ENST00000356865.6	-	21	4314_4315	c.4203_4204TG>GT	c.(4201-4206)gcTGtc>gcGTtc	p.V1402F		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	1402					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			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)		CTCCTCAGGACAGCCTCCCCTG	0.663																																					p.V1402F|p.A1401A		Atlas-SNP	.											.	ATP10A	270	.	0			c.G4204T|c.T4203G						.																																			SO:0001583	missense	57194	exon21			TCAGGACAGCCTC|CAGGACAGCCTCC	AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.4203_4204delinsAC	chr15.hg19:g.25924784_25924785delinsAC	ENSP00000349325:p.Val1402Phe	65.0|67.0	0.0		46.0|44.0	19.0|18.0	NM_024490	Q4G0S9|Q969I4	Missense_Mutation|Silent	SNP	ENST00000356865.6	hg19	CCDS32178.1																																																																																			.	.		0.663	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		AC	25924785	CA	AC	25924784	3	1	308	1	0	0	0	0	1	0	0	0	1116	478	17	3	299	3	ATP10A	15	25924784	Missense_Mutation	DNP	CA	TCGA-HP-A5N0-01A-11D-A28X-10		25924784	76606608	88	44005										
C15orf26	161502	hgsc.bcm.edu	37	chr15	81426689	81426689	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	cgatggcgcagaacgtgtatGgtccgggagtccggataggc	17	9	0	1			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr15:81426689G>T	ENST00000286732.4	+	1	102	c.19G>T	c.(19-21)Ggt>Tgt	p.G7C		NM_173528.2	NP_775799.2	Q6P656	CO026_HUMAN	chromosome 15 open reading frame 26	7										endometrium(1)|kidney(4)|large_intestine(5)|lung(6)|skin(1)	17						GAACGTGTATGGTCCGGGAGT	0.647																																					p.G7C		Atlas-SNP	.											.	C15orf26	33	.	0			c.G19T						.						62	79	73					15																	81426689		2106	4230	6336	SO:0001583	missense	161502	exon1			GTGTATGGTCCGG	AK095934	CCDS42068.1	15q25.1	2012-09-10			ENSG00000156206	ENSG00000156206			26782	protein-coding gene	gene with protein product						14702039	Standard	NM_173528		Approved	FLJ38615	uc002bgb.3	Q6P656	OTTHUMG00000172263	ENST00000286732.4:c.19G>T	chr15.hg19:g.81426689G>T	ENSP00000286732:p.Gly7Cys	203.0	0.0		215.0	40.0	NM_173528	Q8N906	Missense_Mutation	SNP	ENST00000286732.4	hg19	CCDS42068.1	.	.	.	.	.	.	.	.	.	.	G	14.63	2.591664	0.46214	.	.	ENSG00000156206	ENST00000286732	T	0.43294	0.95	4.85	-2.1	0.07210	.	0.996921	0.08133	N	0.992829	T	0.30386	0.0763	L	0.50333	1.59	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.37865	-0.9687	10	0.49607	T	0.09	-1.2937	0.8554	0.01181	0.4126:0.1283:0.2204:0.2387	.	7	Q6P656	CO026_HUMAN	C	7	ENSP00000286732:G7C	ENSP00000286732:G7C	G	+	1	0	C15orf26	79213744	0.013000	0.17824	0.001000	0.08648	0.004000	0.04260	0.152000	0.16302	-0.217000	0.10033	-0.150000	0.13652	GGT	.	.		0.647	C15orf26-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417587.1	NM_173528		T	81426689	G	T	81426689	3	4	308	1	0	0	0	0	1	0	0	0	1789	1348	47	3	21	3	C15orf26	15	81426689	Missense_Mutation	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10	55501905	81426689	21104703	89	44006										
NOD2	64127	hgsc.bcm.edu	37	chr16	50750836	50750836	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	aattgactgacggctgtgcaCactccatggctaagctcctt	9	12	0	2			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr16:50750836C>T	ENST00000300589.2	+	6	2686	c.2581C>T	c.(2581-2583)Cac>Tac	p.H861Y		NM_022162.1	NP_071445.1	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain containing 2	861					activation of MAPK activity (GO:0000187)|activation of MAPK activity involved in innate immune response (GO:0035419)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to peptidoglycan (GO:0071224)|cytokine production involved in immune response (GO:0002367)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|detection of biotic stimulus (GO:0009595)|detection of muramyl dipeptide (GO:0032498)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|innate immune response (GO:0045087)|innate immune response in mucosa (GO:0002227)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|macrophage inflammatory protein-1 alpha production (GO:0071608)|maintenance of gastrointestinal epithelium (GO:0030277)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-18 production (GO:0032701)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of macrophage apoptotic process (GO:2000110)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell mediated immunity (GO:0002710)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of tumor necrosis factor production (GO:0032720)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of B cell activation (GO:0050871)|positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria (GO:0006965)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell cytokine production (GO:0002732)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gamma-delta T cell activation (GO:0046645)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of prostaglandin-E synthase activity (GO:2000363)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type 2 immune response (GO:0002830)|protein oligomerization (GO:0051259)|regulation of inflammatory response (GO:0050727)|regulation of neutrophil chemotaxis (GO:0090022)|response to exogenous dsRNA (GO:0043330)|response to lipopolysaccharide (GO:0032496)|response to muramyl dipeptide (GO:0032495)|response to nutrient (GO:0007584)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|enzyme binding (GO:0019899)|muramyl dipeptide binding (GO:0032500)|peptidoglycan binding (GO:0042834)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(30)|ovary(3)|skin(3)	52		all_cancers(37;0.0156)				CGGCTGTGCACACTCCATGGC	0.473																																					p.H861Y		Atlas-SNP	.											.	NOD2	118	.	0			c.C2581T						.						194	183	187					16																	50750836		2198	4300	6498	SO:0001583	missense	64127	exon6			TGTGCACACTCCA	AF178930	CCDS10746.1	16q12	2014-09-17	2006-12-08	2006-12-08	ENSG00000167207	ENSG00000167207		"Nucleotide-binding domain and leucine rich repeat containing"	5331	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 2", "NOD-like receptor C2", "NLR family, CARD domain containing 2"	605956	"caspase recruitment domain family, member 15"	IBD1, CARD15		7809109, 8587604	Standard	XM_005256084		Approved	BLAU, CD, PSORAS1, CLR16.3, NLRC2	uc002egm.1	Q9HC29	OTTHUMG00000133171	ENST00000300589.2:c.2581C>T	chr16.hg19:g.50750836C>T	ENSP00000300589:p.His861Tyr	182.0	0.0		146.0	43.0	NM_022162	E2JEQ6|Q96RH5|Q96RH6|Q96RH8	Missense_Mutation	SNP	ENST00000300589.2	hg19	CCDS10746.1	.	.	.	.	.	.	.	.	.	.	C	8.577	0.881362	0.17467	.	.	ENSG00000167207	ENST00000526417;ENST00000300589	T	0.52295	0.67	5.76	3.77	0.43336	.	0.434813	0.24172	N	0.040897	T	0.43478	0.1249	M	0.65975	2.015	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.44590	-0.9318	10	0.66056	D	0.02	.	7.1981	0.25864	0.0:0.7348:0.1728:0.0924	.	861	Q9HC29	NOD2_HUMAN	Y	834;861	ENSP00000300589:H861Y	ENSP00000300589:H861Y	H	+	1	0	NOD2	49308337	0.017000	0.18338	0.005000	0.12908	0.138000	0.21146	1.695000	0.37763	0.735000	0.32537	0.555000	0.69702	CAC	.	.		0.473	NOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256876.2	NM_022162		T	50750836	C	T	50750836	3	4	308	1	0	0	0	0	1	0	0	0	10526	478	17	3	2603	3	NOD2	16	50750836	Missense_Mutation	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10		50750836	39603917	90	44007										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11597228	11597228	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	cgacattgactttaaagagcTagcttatgatgcccagaaaa	8	8	0	4			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr17:11597228T>G	ENST00000262442.4	+	21	4726	c.4658T>G	c.(4657-4659)cTa>cGa	p.L1553R	DNAH9_ENST00000454412.2_Missense_Mutation_p.L1553R	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	1553	Stem. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		TTTAAAGAGCTAGCTTATGAT	0.448																																					p.L1553R		Atlas-SNP	.											.	DNAH9	695	.	0			c.T4658G						.						121	116	118					17																	11597228		2203	4300	6503	SO:0001583	missense	1770	exon21			AAGAGCTAGCTTA	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.4658T>G	chr17.hg19:g.11597228T>G	ENSP00000262442:p.Leu1553Arg	108.0	0.0		55.0	32.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	hg19	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	T	19.72	3.880588	0.72294	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.66460	-0.21;-0.21	4.72	4.72	0.59763	Dynein heavy chain, domain-2 (1);	0.091849	0.44285	D	0.000466	D	0.86247	0.5887	H	0.95224	3.64	0.80722	D	1	D	0.56521	0.976	D	0.71414	0.973	D	0.90345	0.4362	10	0.87932	D	0	.	14.3297	0.66548	0.0:0.0:0.0:1.0	.	1553	Q9NYC9	DYH9_HUMAN	R	1553;1553;135	ENSP00000262442:L1553R;ENSP00000414874:L1553R	ENSP00000262442:L1553R	L	+	2	0	DNAH9	11537953	1.000000	0.71417	0.997000	0.53966	0.831000	0.47069	7.307000	0.78920	2.122000	0.65172	0.533000	0.62120	CTA	.	.		0.448	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		G	11597228	T	G	11597228	3	3	308	1	0	0	0	0	1	0	0	0	4610	1522	53	5	4740	5	DNAH9	17	11597228	Missense_Mutation	SNP	T	TCGA-HP-A5N0-01A-11D-A28X-10		11597228	69597982	91	44008										
ZNF286A	57335	hgsc.bcm.edu	37	chr17	15619991	15619991	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	atcccttgcaacacatcagaGaattcacgttggagagagac	9	10	2	3			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr17:15619991G>T	ENST00000464847.2	+	5	1506	c.953G>T	c.(952-954)aGa>aTa	p.R318I	ZNF286A_ENST00000421016.1_Missense_Mutation_p.R318I|ZNF286A_ENST00000585171.1_Intron|ZNF286A_ENST00000583566.1_Missense_Mutation_p.R318I|ZNF286A_ENST00000413242.2_Missense_Mutation_p.R318I|ZNF286A_ENST00000593105.1_Missense_Mutation_p.R308I|ZNF286A_ENST00000395894.2_3'UTR			Q9HBT8	Z286A_HUMAN	zinc finger protein 286A	318					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.0781)		ACACATCAGAGAATTCACGTT	0.388																																					p.R318I		Atlas-SNP	.											.	ZNF286A	58	.	0			c.G953T						.						46	46	46					17																	15619991		2202	4297	6499	SO:0001583	missense	57335	exon6			ATCAGAGAATTCA	AF217226	CCDS11172.1, CCDS73997.1	17p11.2	2013-02-14	2007-01-05	2007-01-05		ENSG00000187607		"Zinc fingers, C2H2-type", "-"	13501	protein-coding gene	gene with protein product			"zinc finger protein 286"	ZNF286		11347906	Standard	NM_020652		Approved	KIAA1874	uc010cot.3	Q9HBT8	OTTHUMG00000166448	ENST00000464847.2:c.953G>T	chr17.hg19:g.15619991G>T	ENSP00000464218:p.Arg318Ile	283.0	0.0		146.0	59.0	NM_020652	B4DKF9|Q96JF3	Missense_Mutation	SNP	ENST00000464847.2	hg19	CCDS11172.1	.	.	.	.	.	.	.	.	.	.	g	14.42	2.531113	0.45073	.	.	ENSG00000187607	ENST00000421016;ENST00000412988;ENST00000395894	T;T	0.24908	1.83;1.83	4.2	3.23	0.37069	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.42821	D	0.000643	T	0.29423	0.0733	M	0.77103	2.36	0.48511	D	0.999664	B	0.25235	0.121	B	0.21708	0.036	T	0.16305	-1.0407	10	0.59425	D	0.04	-19.3153	10.0158	0.42014	0.1007:0.0:0.8993:0.0	.	318	Q9HBT8	Z286A_HUMAN	I	318;308;318	ENSP00000397163:R318I;ENSP00000408168:R308I	ENSP00000435872:R318I	R	+	2	0	ZNF286A	15560716	0.973000	0.33851	1.000000	0.80357	0.934000	0.57294	2.996000	0.49449	1.122000	0.41944	-0.142000	0.14014	AGA	.	.		0.388	ZNF286A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130696.4	NM_020652		T	15619991	G	T	15619991	3	4	308	1	0	0	0	0	1	0	0	0	17838	942	33	3	971	3	ZNF286A	17	15619991	Missense_Mutation	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10	4022763	15619991	65575219	92	44009										
KRTAP1-1	81851	hgsc.bcm.edu	37	chr17	39197352	39197352	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	ctcctggccatagccaatgcCaccaccaatgccacagccag	7	18	0	0	rs370724456		TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr17:39197352C>T	ENST00000306271.4	-	1	361	c.298G>A	c.(298-300)Ggc>Agc	p.G100S		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	100			Missing (in allele KAP1.7). {ECO:0000269|PubMed:11841537}.			keratin filament (GO:0045095)				NS(2)|endometrium(2)|kidney(5)|lung(4)|prostate(1)	14		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			TAGCCAATGCCACCACCAATG	0.632																																					p.G100S		Atlas-SNP	.											.	KRTAP1-1	23	.	0			c.G298A						.						30	34	32					17																	39197352		1987	4161	6148	SO:0001583	missense	81851	exon1			CAATGCCACCACC	AJ406926	CCDS42324.1	17q21.2	2014-06-05			ENSG00000188581	ENSG00000188581		"Keratin associated proteins"	16772	protein-coding gene	gene with protein product		608819				11279113	Standard	NM_030967		Approved	KAP1.1B, HB2A, KAP1.1, KAP1.1A	uc002hvw.1	Q07627	OTTHUMG00000133592	ENST00000306271.4:c.298G>A	chr17.hg19:g.39197352C>T	ENSP00000305975:p.Gly100Ser	172.0	0.0		154.0	39.0	NM_030967	A6NC32|Q96S60|Q96S67	Missense_Mutation	SNP	ENST00000306271.4	hg19	CCDS42324.1	.	.	.	.	.	.	.	.	.	.	C	8.751	0.921274	0.17982	.	.	ENSG00000188581	ENST00000306271;ENST00000543328	T	0.29397	1.57	3.79	2.83	0.33086	.	.	.	.	.	T	0.21841	0.0526	L	0.38649	1.16	0.30133	N	0.804616	P	0.36162	0.54	B	0.36666	0.23	T	0.10870	-1.0611	9	0.20519	T	0.43	.	7.6537	0.28363	0.0:0.8839:0.0:0.1161	.	100	Q07627	KRA11_HUMAN	S	100;90	ENSP00000305975:G100S	ENSP00000305975:G100S	G	-	1	0	KRTAP1-1	36450878	0.025000	0.19082	0.724000	0.30704	0.028000	0.11728	1.202000	0.32271	1.203000	0.43233	-0.464000	0.05259	GGC	.	.		0.632	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257696.1	NM_030967		T	39197352	C	T	39197352	3	4	308	1	0	0	0	0	1	0	0	0	8511	594	21	3	239	3	KRTAP1-1	17	39197352	Missense_Mutation	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	23577361	39197352	41997858	93	44010										
B4GALNT2	124872	hgsc.bcm.edu	37	chr17	47246920	47246920	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	ggctagggaccctactcgtgGggtcatgcccagaagtgatt	14	10	1	2			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr17:47246920G>T	ENST00000300404.2	+	11	1590	c.1531G>T	c.(1531-1533)Ggg>Tgg	p.G511W	RP11-708H21.4_ENST00000575159.1_lincRNA|B4GALNT2_ENST00000504681.1_Missense_Mutation_p.G425W|B4GALNT2_ENST00000393354.2_Missense_Mutation_p.G451W	NM_153446.2	NP_703147.2	Q8NHY0	B4GN2_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 2	511					lipid glycosylation (GO:0030259)|negative regulation of cell-cell adhesion (GO:0022408)|protein glycosylation (GO:0006486)|UDP-N-acetylgalactosamine metabolic process (GO:0019276)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)			endometrium(3)|large_intestine(6)|liver(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	24			all cancers(6;0.000316)			CCTACTCGTGGGGTCATGCCC	0.522																																					p.G511W	GBM(124;244 1635 8663 18097 33175)	Atlas-SNP	.											.	B4GALNT2	67	.	0			c.G1531T						.						87	88	88					17																	47246920		2203	4300	6503	SO:0001583	missense	124872	exon11			CTCGTGGGGTCAT	AJ517770	CCDS11544.1, CCDS54139.1, CCDS54140.1	17q21.33	2013-02-22	2006-01-08	2006-01-08	ENSG00000167080	ENSG00000167080	2.4.1.-	"Beta 4-glycosyltransferases", "Glycosyltransferase family 2 domain containing"	24136	protein-coding gene	gene with protein product		111730	"UDP-GalNAc:Neu5Acalpha2-3Galbeta-R beta1,4-N-acetylgalactosaminyltransferase"	GALGT2		8782649, 12678917	Standard	NM_153446		Approved	Sda, Cad	uc002ion.2	Q8NHY0	OTTHUMG00000161307	ENST00000300404.2:c.1531G>T	chr17.hg19:g.47246920G>T	ENSP00000300404:p.Gly511Trp	53.0	0.0		69.0	26.0	NM_153446	B4DZE4|Q14CP1|Q86Y40	Missense_Mutation	SNP	ENST00000300404.2	hg19	CCDS11544.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.133884	0.77662	.	.	ENSG00000167080	ENST00000504681;ENST00000393354;ENST00000300404	T;T;T	0.25085	1.82;1.82;1.82	5.79	5.79	0.91817	.	0.069689	0.56097	D	0.000030	T	0.53302	0.1788	M	0.72894	2.215	0.58432	D	0.99999	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	T	0.53114	-0.8484	10	0.87932	D	0	-24.8208	18.7973	0.91999	0.0:0.0:1.0:0.0	.	451;511	Q8NHY0-2;Q8NHY0	.;B4GN2_HUMAN	W	425;451;511	ENSP00000425510:G425W;ENSP00000377022:G451W;ENSP00000300404:G511W	ENSP00000300404:G511W	G	+	1	0	B4GALNT2	44601919	1.000000	0.71417	1.000000	0.80357	0.510000	0.34073	8.151000	0.89636	2.745000	0.94114	0.561000	0.74099	GGG	.	.		0.522	B4GALNT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364477.1	NM_153446		T	47246920	G	T	47246920	3	4	308	1	0	0	0	0	1	0	0	0	1267	1232	43	3	1591	3	B4GALNT2	17	47246920	Missense_Mutation	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10	8049568	47246920	33948290	94	44011										
GZMM	3004	hgsc.bcm.edu	37	chr19	549779	549779	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	tggatcaggaaggtcaccggCcgatcggcctgatgccctgg	15	12	2	1			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr19:549779C>G	ENST00000264553.3	+	5	800	c.762C>G	c.(760-762)ggC>ggG	p.G254G		NM_001258351.1|NM_005317.3	NP_001245280.1|NP_005308	P51124	GRAM_HUMAN	granzyme M (lymphocyte met-ase 1)	254	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				apoptotic process (GO:0006915)|cytolysis (GO:0019835)|innate immune response (GO:0045087)	extracellular region (GO:0005576)|membrane (GO:0016020)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(1)|large_intestine(1)|prostate(1)	3		all_cancers(10;1.94e-35)|all_epithelial(18;5.94e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AGGTCACCGGCCGATCGGCCT	0.662																																					p.G254G		Atlas-SNP	.											.	GZMM	11	.	0			c.C762G						.						72	58	63					19																	549779		2203	4300	6503	SO:0001819	synonymous_variant	3004	exon5			CACCGGCCGATCG		CCDS12031.1, CCDS74240.1	19p13.3	2008-07-16				ENSG00000197540			4712	protein-coding gene	gene with protein product	"lymphocyte met-ase 1"	600311				8119738	Standard	NM_005317		Approved	MET1, LMET1	uc002low.2	P51124		ENST00000264553.3:c.762C>G	chr19.hg19:g.549779C>G		72.0	0.0		45.0	18.0	NM_005317		Silent	SNP	ENST00000264553.3	hg19	CCDS12031.1																																																																																			.	.		0.662	GZMM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451895.2	NM_005317		G	549779	C	G	549779	2	3	308	1	0	0	0	0	0	0	0	1	6928	726	26	4		4	GZMM	19	549779	Silent	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10		549779	58579204	95	44012										
ANKRD24	170961	hgsc.bcm.edu	37	chr19	4219685	4219685	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	acgggggctacggaccgaggCggaaagggctcgccaggccc	18	13	0	0			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr19:4219685C>T	ENST00000600132.1	+	19	3377	c.3101C>T	c.(3100-3102)gCg>gTg	p.A1034V	ANKRD24_ENST00000318934.4_Missense_Mutation_p.A1034V|ANKRD24_ENST00000262970.5_Missense_Mutation_p.A1124V	NM_133475.1	NP_597732.1	Q8TF21	ANR24_HUMAN	ankyrin repeat domain 24	1034										endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)	21				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0233)|STAD - Stomach adenocarcinoma(1328;0.181)		CGGACCGAGGCGGAAAGGGCT	0.662																																					p.A1034V		Atlas-SNP	.											.	ANKRD24	180	.	0			c.C3101T						.						40	49	46					19																	4219685		2101	4229	6330	SO:0001583	missense	170961	exon19			CCGAGGCGGAAAG	AB075861	CCDS45925.1	19p13.3	2013-01-10				ENSG00000089847		"Ankyrin repeat domain containing"	29424	protein-coding gene	gene with protein product						11853319	Standard	NM_133475		Approved	KIAA1981	uc010dtt.1	Q8TF21		ENST00000600132.1:c.3101C>T	chr19.hg19:g.4219685C>T	ENSP00000471252:p.Ala1034Val	148.0	0.0		122.0	38.0	NM_133475	O75268|O95781	Missense_Mutation	SNP	ENST00000600132.1	hg19	CCDS45925.1	.	.	.	.	.	.	.	.	.	.	c	13.45	2.240513	0.39598	.	.	ENSG00000089847	ENST00000318934;ENST00000262970	T;T	0.32753	1.45;1.44	3.79	3.79	0.43588	.	.	.	.	.	T	0.33614	0.0869	N	0.24115	0.695	0.29081	N	0.882692	D	0.76494	0.999	P	0.61003	0.882	T	0.05852	-1.0860	9	0.17369	T	0.5	.	11.8657	0.52493	0.0:1.0:0.0:0.0	.	1034	Q8TF21	ANR24_HUMAN	V	1034;1124	ENSP00000321731:A1034V;ENSP00000262970:A1124V	ENSP00000262970:A1124V	A	+	2	0	ANKRD24	4170685	0.996000	0.38824	0.889000	0.34880	0.412000	0.31113	3.435000	0.52849	2.080000	0.62538	0.313000	0.20887	GCG	.	.		0.662	ANKRD24-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458188.1	XM_114000		T	4219685	C	T	4219685	3	4	308	1	0	0	0	0	1	0	0	0	653	768	27	1	3171	1	ANKRD24	19	4219685	Missense_Mutation	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	3669906	4219685	54909298	96	44013										
SAFB2	9667	hgsc.bcm.edu	37	chr19	5621381	5621381	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	aactcgatgccaatttcatcAggatcttgcccctcttcttt	5	13	5	0			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr19:5621381A>G	ENST00000252542.4	-	2	477	c.213T>C	c.(211-213)ccT>ccC	p.P71P	SAFB_ENST00000454510.1_5'Flank|SAFB_ENST00000592224.1_5'Flank|SAFB_ENST00000433404.1_5'Flank|SAFB_ENST00000292123.5_5'Flank|SAFB_ENST00000538656.1_5'Flank|SAFB_ENST00000588852.1_5'Flank	NM_014649.2	NP_055464.1	Q14151	SAFB2_HUMAN	scaffold attachment factor B2	71					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				UCEC - Uterine corpus endometrioid carcinoma (162;0.000228)		CAATTTCATCAGGATCTTGCC	0.448																																					p.P71P	Ovarian(127;888 1728 23957 44128 52668)	Atlas-SNP	.											.	SAFB2	90	.	0			c.T213C						.						305	280	288					19																	5621381		2203	4300	6503	SO:0001819	synonymous_variant	9667	exon2			TTCATCAGGATCT	D50928	CCDS32879.1	19p13.3	2013-02-12				ENSG00000130254		"RNA binding motif (RRM) containing"	21605	protein-coding gene	gene with protein product		608066				12660241	Standard	NM_014649		Approved	KIAA0138	uc002mcd.3	Q14151		ENST00000252542.4:c.213T>C	chr19.hg19:g.5621381A>G		113.0	0.0		95.0	5.0	NM_014649	B4DKG3|Q8TB13	Silent	SNP	ENST00000252542.4	hg19	CCDS32879.1																																																																																			.	.		0.448	SAFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451016.1	NM_014649		G	5621381	A	G	5621381	2	3	308	1	0	0	0	0	0	0	0	1	13822	175	7	2		2	SAFB2	19	5621381	Silent	SNP	A	TCGA-HP-A5N0-01A-11D-A28X-10	1401696	5621381	53507602	97	44014										
PODNL1	79883	hgsc.bcm.edu	37	chr19	14043535	14043538	+	Frame_Shift_Del	DEL	TGTT	TGTT	-													0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	gctttaccagctaactagaaTgtttgggacgtggcagggca							TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	TGTT	TGTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr19:14043535_14043538delTGTT	ENST00000339560.5	-	8	1792_1795	c.1519_1522delAACA	c.(1519-1524)aacattfs	p.NI507fs	PODNL1_ENST00000254320.3_Frame_Shift_Del_p.NI425fs|PODNL1_ENST00000538371.2_Frame_Shift_Del_p.NI505fs|PODNL1_ENST00000538517.2_Frame_Shift_Del_p.NI416fs	NM_024825.3	NP_079101.3	Q6PEZ8	PONL1_HUMAN	podocan-like 1	507						proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(19;5.26e-23)			CTAACTAGAATGTTTGGGACGTGG	0.564																																					p.507_508del		Atlas-Indel,Pindel	.											PODNL1,NS,carcinoma,0,1	PODNL1	27	.	0			c.1520_1523del						.																																			SO:0001589	frameshift_variant	79883	exon8			.	AK027100	CCDS12300.1, CCDS54225.1, CCDS54226.1	19p13.12	2008-02-05							26275	protein-coding gene	gene with protein product						12477932	Standard	NM_024825		Approved	FLJ23447, SLRR5B	uc010xnj.2	Q6PEZ8		ENST00000339560.5:c.1519_1522delAACA	chr19.hg19:g.14043535_14043538delTGTT	ENSP00000345175:p.Asn507fs	132.0	0.0		127.0	25.0	NM_024825	B7Z564|Q9H5G9	Frame_Shift_Del	DEL	ENST00000339560.5	hg19	CCDS12300.1																																																																																			.	.		0.564	PODNL1-003	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457967.1	NM_024825		-	14043538	TGTT	-	14043535	7	5	308	1	0	1	0	1	0	0	0	0	12188	1464	51	0	20	0	PODNL1	19	14043535	Frame_Shift_Del	DEL	TGTT	TCGA-HP-A5N0-01A-11D-A28X-10	8422154	14043535	45085448	98	44015										
NWD1	284434	hgsc.bcm.edu	37	chr19	16918939	16918939	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	gcaagtggaaattcgagatgAgctacacggtgggtggcccg	16	8	0	2			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr19:16918939A>G	ENST00000552788.1	+	16	4279	c.4279A>G	c.(4279-4281)Agc>Ggc	p.S1427G	NWD1_ENST00000523826.1_Missense_Mutation_p.S1221G|NWD1_ENST00000379808.3_Missense_Mutation_p.S1427G|NWD1_ENST00000549814.1_Missense_Mutation_p.S1385G|NWD1_ENST00000524140.2_Missense_Mutation_p.S1427G|NWD1_ENST00000339803.6_Missense_Mutation_p.S1292G			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	1427							ATP binding (GO:0005524)			NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						ATTCGAGATGAGCTACACGGT	0.562																																					p.S1427G		Atlas-SNP	.											.	NWD1	303	.	0			c.A4279G						.						66	65	65					19																	16918939		2203	4300	6503	SO:0001583	missense	284434	exon18			GAGATGAGCTACA	BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"WD repeat domain containing"	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.4279A>G	chr19.hg19:g.16918939A>G	ENSP00000447224:p.Ser1427Gly	103.0	0.0		94.0	29.0	NM_001007525	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	hg19		.	.	.	.	.	.	.	.	.	.	A	7.761	0.705488	0.15172	.	.	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803	T;T;T;T;T;T	0.57436	0.4;0.93;0.4;2.19;1.42;2.19	4.46	3.44	0.39384	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.462517	0.23817	N	0.044276	T	0.41050	0.1142	L	0.58354	1.805	0.28693	N	0.904492	B;B;B	0.27229	0.172;0.122;0.075	B;B;B	0.25291	0.039;0.059;0.027	T	0.28299	-1.0048	10	0.20046	T	0.44	-11.0881	3.9765	0.09476	0.7144:0.0:0.1023:0.1833	.	1427;1427;1292	Q149M9;Q149M9-3;C9J2Y8	NWD1_HUMAN;.;.	G	1292;1427;1385;1427;1221;1427;1292	ENSP00000428579:S1427G;ENSP00000447548:S1385G;ENSP00000369136:S1427G;ENSP00000428955:S1221G;ENSP00000447224:S1427G;ENSP00000340159:S1292G	ENSP00000340159:S1292G	S	+	1	0	NWD1	16779939	1.000000	0.71417	0.977000	0.42913	0.257000	0.26127	0.763000	0.26517	0.673000	0.31224	0.533000	0.62120	AGC	.	.		0.562	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525		G	16918939	A	G	16918939	3	3	308	1	0	0	0	0	1	0	0	0	10790	304	11	2	3928	2	NWD1	19	16918939	Missense_Mutation	SNP	A	TCGA-HP-A5N0-01A-11D-A28X-10	2875404	16918939	42210044	99	44016										
RYR1	6261	hgsc.bcm.edu	37	chr19	38986916	38986965	+	Frame_Shift_Del	DEL	CACGAGACGGTCATGGAGGTCATGGTCAACGTCCTCGGGGGCGGCGAGTC	CACGAGACGGTCATGGAGGTCATGGTCAACGTCCTCGGGGGCGGCGAGTC	-													0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	tgatgagggcgctgggcatgCacgagacggtcatggaggtc					rs181195904|rs185754956|rs374630822|rs149185729|rs558202046|rs146617004|rs193922795|rs193922792|rs193922793|rs370261565|rs141646642|rs118192177|rs371006370	byFrequency	TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	CACGAGACGGTCATGGAGGTCATGGTCAACGTCCTCGGGGGCGGCGAGTC	CACGAGACGGTCATGGAGGTCATGGTCAACGTCCTCGGGGGCGGCGAGTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr19:38986916_38986965delCACGAGACGGTCATGGAGGTCATGGTCAACGTCCTCGGGGGCGGCGAGTC	ENST00000359596.3	+	40	6610_6659	c.6610_6659delCACGAGACGGTCATGGAGGTCATGGTCAACGTCCTCGGGGGCGGCGAGTC	c.(6610-6660)cacgagacggtcatggaggtcatggtcaacgtcctcgggggcggcgagtccfs	p.HETVMEVMVNVLGGGES2204fs	RYR1_ENST00000360985.3_Frame_Shift_Del_p.HETVMEVMVNVLGGGES2204fs|RYR1_ENST00000355481.4_Frame_Shift_Del_p.HETVMEVMVNVLGGGES2204fs			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	2204	6 X approximate repeats.		H -> Q (in CCD; dbSNP:rs141646642). {ECO:0000269|PubMed:21674524}.		calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GCTGGGCATGCACGAGACGGTCATGGAGGTCATGGTCAACGTCCTCGGGGGCGGCGAGTCCAAGGTGAGG	0.644																																					p.2203_2220del		Pindel	.											.	RYR1	708	.	0			c.6609_6658del	GRCh37	CM014979|CM055514|CM063120|CM981782|CM992214	RYR1	M	rs118192177	.																																			SO:0001589	frameshift_variant	6261	exon40			.	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.6610_6659delCACGAGACGGTCATGGAGGTCATGGTCAACGTCCTCGGGGGCGGCGAGTC	chr19.hg19:g.38986916_38986965delCACGAGACGGTCATGGAGGTCATGGTCAACGTCCTCGGGGGCGGCGAGTC	ENSP00000352608:p.His2204fs	89.0	0.0		98.0	20.0	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Frame_Shift_Del	DEL	ENST00000359596.3	hg19	CCDS33011.1																																																																																			.	.		0.644	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			-	38986965	CACGAGACGGTCATGGAGGTCATGGTCAACGTCCTCGGGGGCGGCGAGTC	-	38986916	7	5	308	1	0	1	0	1	0	0	0	0	13783	710	25	0	6768	0	RYR1	19	38986916	Frame_Shift_Del	DEL	CACGAGACGGTCATGGAGGTCATGGTCAACGTCCTCGGGGGCGGCGAGTC	TCGA-HP-A5N0-01A-11D-A28X-10	22067977	38986916	20142067	100	44017										
CEACAM3	1084	hgsc.bcm.edu	37	chr19	42300619	42300619	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	cagcagagaccatggggcccCcctcagcctctccccacaga	9	19	2	2			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr19:42300619C>A	ENST00000357396.3	+	1	251	c.10C>A	c.(10-12)Ccc>Acc	p.P4T	CEACAM3_ENST00000344550.4_Missense_Mutation_p.P4T|CEACAM3_ENST00000221999.4_Missense_Mutation_p.P4T|CEACAM3_ENST00000595255.1_3'UTR	NM_001815.2	NP_001806.2	P40198	CEAM3_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 3	4						integral component of membrane (GO:0016021)				endometrium(2)|kidney(4)|large_intestine(1)|lung(4)|prostate(3)|skin(4)|stomach(1)	19						CATGGGGCCCCCCTCAGCCTC	0.597																																					p.P4T		Atlas-SNP	.											.	CEACAM3	37	.	0			c.C10A						.						42	43	43					19																	42300619		2203	4300	6503	SO:0001583	missense	1084	exon1			GGGCCCCCCTCAG	E03349	CCDS12586.2, CCDS62685.1	19q13.2	2013-01-11			ENSG00000170956	ENSG00000170956		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	1815	protein-coding gene	gene with protein product		609142		CGM1			Standard	NM_001815		Approved	CD66d	uc002orn.2	P40198	OTTHUMG00000150142	ENST00000357396.3:c.10C>A	chr19.hg19:g.42300619C>A	ENSP00000349971:p.Pro4Thr	97.0	0.0		73.0	18.0	NM_001815	G5E978|Q3KPH9	Missense_Mutation	SNP	ENST00000357396.3	hg19	CCDS12586.2	.	.	.	.	.	.	.	.	.	.	C	11.58	1.680285	0.29872	.	.	ENSG00000170956	ENST00000357396;ENST00000389667;ENST00000221999;ENST00000344550	T;T;T	0.01197	5.19;5.23;5.23	3.09	0.709	0.18150	.	.	.	.	.	T	0.03178	0.0093	M	0.77313	2.365	0.09310	N	1	P;P	0.47677	0.887;0.899	P;P	0.52343	0.604;0.696	T	0.36625	-0.9740	9	0.62326	D	0.03	.	3.8124	0.08802	0.0:0.5644:0.277:0.1586	.	4;4	G5E978;P40198	.;CEAM3_HUMAN	T	4	ENSP00000349971:P4T;ENSP00000221999:P4T;ENSP00000341725:P4T	ENSP00000221999:P4T	P	+	1	0	CEACAM3	46992459	0.000000	0.05858	0.060000	0.19600	0.035000	0.12851	-0.257000	0.08745	0.374000	0.24650	0.508000	0.49915	CCC	.	.		0.597	CEACAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316509.2	NM_001815		A	42300619	C	A	42300619	3	1	308	1	0	0	0	0	1	0	0	0	3195	623	22	3	12	3	CEACAM3	19	42300619	Missense_Mutation	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	3313703	42300619	16828364	101	44018										
TMEM145	284339	hgsc.bcm.edu	37	chr19	42827878	42827878	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	cacgtctatgggaacgtgacGtttatcagcgactcggtgcc	12	11	2	1			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr19:42827878G>C	ENST00000301204.3	+	14	1379	c.1338G>C	c.(1336-1338)acG>acC	p.T446T	MEGF8_ENST00000334370.4_5'Flank|MEGF8_ENST00000251268.6_5'Flank	NM_173633.2	NP_775904.2	Q8NBT3	TM145_HUMAN	transmembrane protein 145	446					G-protein coupled receptor signaling pathway (GO:0007186)|response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(11)|prostate(4)|skin(1)|urinary_tract(1)	27		Prostate(69;0.00682)				GGAACGTGACGTTTATCAGCG	0.672																																					p.T446T		Atlas-SNP	.											.	TMEM145	55	.	0			c.G1338C						.						109	90	96					19																	42827878		2203	4300	6503	SO:0001819	synonymous_variant	284339	exon14			CGTGACGTTTATC	AK075286	CCDS12603.1	19q13.2	2008-02-05				ENSG00000167619			26912	protein-coding gene	gene with protein product							Standard	NM_173633		Approved	FLJ90805	uc002otk.1	Q8NBT3		ENST00000301204.3:c.1338G>C	chr19.hg19:g.42827878G>C		206.0	0.0		194.0	30.0	NM_173633		Silent	SNP	ENST00000301204.3	hg19	CCDS12603.1																																																																																			.	.		0.672	TMEM145-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463737.1	NM_173633		C	42827878	G	C	42827878	2	2	308	1	0	0	0	0	0	0	0	1	16074	1132	40	4		4	TMEM145	19	42827878	Silent	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10	527259	42827878	16301105	102	44019										
MEGF8	1954	hgsc.bcm.edu	37	chr19	42858165	42858165	+	Frame_Shift_Del	DEL	A	A	-													0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	ccttctcccccgacagcagcAccccctgcacggtgagcact							TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr19:42858165delA	ENST00000251268.6	+	22	4000	c.4000delA	c.(4000-4002)accfs	p.T1334fs	MEGF8_ENST00000334370.4_Frame_Shift_Del_p.T1267fs	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	1334	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)			breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				CGACAGCAGCACCCCCTGCAC	0.632																																					p.S1333fs		Atlas-INDEL	.											.	MEGF8	358	.	0			c.3999delC						.						33	28	30					19																	42858165		2200	4289	6489	SO:0001589	frameshift_variant	1954	exon22			.	AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"HBV pre s2 binding protein 1"	604267	"EGF-like-domain, multiple 4", "chromosome 19 open reading frame 49"	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.4000delA	chr19.hg19:g.42858165delA	ENSP00000251268:p.Thr1334fs	44.0	0.0		59.0	10.0	NM_001271938	A8KAY0|O75097	Frame_Shift_Del	DEL	ENST00000251268.6	hg19																																																																																				.	.		0.632	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410		-	42858165	A	-	42858165	7	5	308	1	0	1	0	1	0	0	0	0	9472	159	6	0	3881	0	MEGF8	19	42858165	Frame_Shift_Del	DEL	A	TCGA-HP-A5N0-01A-11D-A28X-10	30287	42858165	16270818	103	44020										
PSG11	5680	hgsc.bcm.edu	37	chr19	43523032	43523032	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	caccaaatagaaagagggtcCtgttggtttcagacagctgc	11	9	1	3			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr19:43523032C>A	ENST00000401740.1	-	3	702	c.599G>T	c.(598-600)aGg>aTg	p.R200M	PSG11_ENST00000403486.1_Missense_Mutation_p.R78M|PSG11_ENST00000306322.7_Missense_Mutation_p.R78M|PSG11_ENST00000320078.7_Missense_Mutation_p.R200M|PSG11_ENST00000595312.1_5'UTR			Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 11	200	Ig-like C2-type 1.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	26		Prostate(69;0.00682)				AAAGAGGGTCCTGTTGGTTTC	0.502																																					p.R200M		Atlas-SNP	.											.	PSG11	57	.	0			c.G599T						.						261	270	267					19																	43523032		2200	4298	6498	SO:0001583	missense	5680	exon3			AGGGTCCTGTTGG	U25988	CCDS12614.2, CCDS12615.2	19q13.2	2013-01-29			ENSG00000243130	ENSG00000243130		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9516	protein-coding gene	gene with protein product	"pregnancy specific beta-1-glycoprotein 13"	176401		PSG13, PSG14		7794280	Standard	NM_001113410		Approved	MGC22484	uc002ovm.1	Q9UQ72	OTTHUMG00000151546	ENST00000401740.1:c.599G>T	chr19.hg19:g.43523032C>A	ENSP00000384995:p.Arg200Met	172.0	0.0		161.0	49.0	NM_002785	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Missense_Mutation	SNP	ENST00000401740.1	hg19	CCDS12614.2	.	.	.	.	.	.	.	.	.	.	c	10.27	1.304756	0.23736	.	.	ENSG00000243130	ENST00000320078;ENST00000403486;ENST00000306322;ENST00000401740	T;T;T;T	0.00730	5.77;5.77;5.77;5.77	1.13	-0.0155	0.13976	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.04543	0.0124	M	0.93241	3.395	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.26744	-1.0094	9	0.66056	D	0.02	.	2.9657	0.05907	0.0:0.6454:0.0:0.3546	.	78;200	Q9UQ72-2;Q9UQ72	.;PSG11_HUMAN	M	200;78;78;200	ENSP00000319140:R200M;ENSP00000385427:R78M;ENSP00000304913:R78M;ENSP00000384995:R200M	ENSP00000304913:R78M	R	-	2	0	PSG11	48214872	0.995000	0.38212	0.104000	0.21259	0.023000	0.10783	0.615000	0.24329	0.567000	0.29293	0.184000	0.17185	AGG	.	.		0.502	PSG11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323079.1	NM_002785		A	43523032	C	A	43523032	3	1	308	1	0	0	0	0	1	0	0	0	12666	681	24	3	420	3	PSG11	19	43523032	Missense_Mutation	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	664867	43523032	15605951	104	44021										
GYS1	2997	hgsc.bcm.edu	37	chr19	49472819	49472819	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	ggctggagtgtcgtgacagcGagggcgacggtggcaccgag	20	9	0	1			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr19:49472819G>A	ENST00000323798.3	-	16	2136	c.1940C>T	c.(1939-1941)tCg>tTg	p.S647L	GYS1_ENST00000544287.1_Missense_Mutation_p.S280L|GYS1_ENST00000541188.1_Missense_Mutation_p.S567L|GYS1_ENST00000263276.6_Missense_Mutation_p.S583L	NM_002103.4	NP_002094.2	P13807	GYS1_HUMAN	glycogen synthase 1 (muscle)	647					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|heart development (GO:0007507)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|inclusion body (GO:0016234)|membrane (GO:0016020)	glucose binding (GO:0005536)|glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein kinase binding (GO:0019901)			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)		TCGTGACAGCGAGGGCGACGG	0.672																																					p.S647L		Atlas-SNP	.											.	GYS1	59	.	0			c.C1940T						.						31	16	21					19																	49472819		2013	3907	5920	SO:0001583	missense	2997	exon16			GACAGCGAGGGCG		CCDS12747.1, CCDS54292.1	19q13.3	2013-02-22			ENSG00000104812	ENSG00000104812	2.4.1.11	"Glycosyltransferase group 1 domain containing"	4706	protein-coding gene	gene with protein product		138570		GYS			Standard	NM_002103		Approved	GSY	uc002plp.3	P13807	OTTHUMG00000150723	ENST00000323798.3:c.1940C>T	chr19.hg19:g.49472819G>A	ENSP00000317904:p.Ser647Leu	41.0	0.0		31.0	12.0	NM_002103	Q9BTT9	Missense_Mutation	SNP	ENST00000323798.3	hg19	CCDS12747.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.596090	0.86953	.	.	ENSG00000104812	ENST00000323798;ENST00000263276;ENST00000541188;ENST00000544287	T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22	5.71	5.71	0.89125	.	0.122704	0.56097	D	0.000036	T	0.67795	0.2931	M	0.75777	2.31	0.80722	D	1	P;P;P	0.43750	0.816;0.816;0.816	B;B;B	0.38106	0.265;0.265;0.265	T	0.71852	-0.4467	10	0.48119	T	0.1	-13.9468	17.7236	0.88359	0.0:0.0:1.0:0.0	.	567;583;647	B7Z806;Q9BTT9;P13807	.;.;GYS1_HUMAN	L	647;583;567;280	ENSP00000317904:S647L;ENSP00000263276:S583L;ENSP00000437922:S567L;ENSP00000444004:S280L	ENSP00000263276:S583L	S	-	2	0	GYS1	54164631	1.000000	0.71417	0.976000	0.42696	0.985000	0.73830	9.139000	0.94554	2.854000	0.98071	0.655000	0.94253	TCG	.	.		0.672	GYS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319791.1	NM_002103		A	49472819	G	A	49472819	3	1	308	1	0	0	0	0	1	0	0	0	6921	1059	37	1	277	1	GYS1	19	49472819	Missense_Mutation	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10	5949787	49472819	9656164	105	44022										
OSCAR	126014	hgsc.bcm.edu	37	chr19	54598520	54598530	+	3'UTR	DEL	CTGCGCCAGTC	CTGCGCCAGTC	-													0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	cagcaggagcgcggttctgaCtgcgccagtcaaaagtgacc					rs148850642		TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	CTGCGCCAGTC	CTGCGCCAGTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr19:54598520_54598530delCTGCGCCAGTC	ENST00000284648.6	-	0	1459_1469				OSCAR_ENST00000359649.4_3'UTR|OSCAR_ENST00000358375.4_Frame_Shift_Del_p.DWRS250fs|OSCAR_ENST00000391761.1_3'UTR|OSCAR_ENST00000351806.4_Frame_Shift_Del_p.DWRS239fs|OSCAR_ENST00000356532.3_Frame_Shift_Del_p.DWRS254fs			Q8IYS5	OSCAR_HUMAN	osteoclast associated, immunoglobulin-like receptor							extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				large_intestine(1)|skin(1)	2	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)					GCGGTTCTGACTGCGCCAGTCAAAAGTGACC	0.682																																					p.254_257del		Atlas-Indel,Pindel	.											.	OSCAR	22	.	0			c.761_771del						.																																			SO:0001624	3_prime_UTR_variant	126014	exon6			.	AK130199	CCDS12873.1, CCDS12874.1, CCDS12875.1, CCDS12876.1, CCDS62789.1, CCDS74444.1	19q13.42	2013-01-29			ENSG00000170909	ENSG00000170909		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29960	protein-coding gene	gene with protein product		606862				11805147	Standard	NM_206818		Approved		uc002qda.3	Q8IYS5	OTTHUMG00000064966	ENST00000284648.6:c.*423GACTGGCGCAG>-	chr19.hg19:g.54598520_54598530delCTGCGCCAGTC		341.0	0.0		239.0	34.0	NM_130771	B7WNS2|Q5GRG5|Q8N763|Q8NHL4|Q8WXQ0|Q8WXQ1|Q8WXQ2	Frame_Shift_Del	DEL	ENST00000284648.6	hg19																																																																																				.	.		0.682	OSCAR-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000139493.4	NM_133169		-	54598530	CTGCGCCAGTC	-	54598520	6	5	308	0	1	1	0	1	0	0	0	0	11294	565	20	0		0	OSCAR	19	54598520	3'UTR	DEL	CTGCGCCAGTC	TCGA-HP-A5N0-01A-11D-A28X-10	5125701	54598520	4530463	106	44023										
LILRA4	23547	hgsc.bcm.edu	37	chr19	54850148	54850148	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	cagactcacctgcctgcaccCgggtcctggggcccaggctc	12	18	1	1	rs181991337		TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr19:54850148C>A	ENST00000291759.4	-	2	115	c.59G>T	c.(58-60)cGg>cTg	p.R20L	AC008984.2_ENST00000507363.1_RNA	NM_012276.3	NP_036408.3	P59901	LIRA4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 4	20					immune system process (GO:0002376)	integral component of membrane (GO:0016021)				NS(2)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(13)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	32	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0565)		TGCCTGCACCCGGGTCCTGGG	0.627											OREG0003656	type=REGULATORY REGION|Gene=LILRA4|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.R20L		Atlas-SNP	.											.	LILRA4	91	.	0			c.G59T						.						58	63	62					19																	54850148		2203	4300	6503	SO:0001583	missense	23547	exon2			TGCACCCGGGTCC	AF041261	CCDS12890.1	19q13.4	2013-01-11			ENSG00000239961	ENSG00000239961		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15503	protein-coding gene	gene with protein product		607517				10941842	Standard	NM_012276		Approved	ILT7, CD85g	uc002qfj.3	P59901	OTTHUMG00000065355	ENST00000291759.4:c.59G>T	chr19.hg19:g.54850148C>A	ENSP00000291759:p.Arg20Leu	135.0	0.0	1003	108.0	31.0	NM_012276	Q32MC4	Missense_Mutation	SNP	ENST00000291759.4	hg19	CCDS12890.1	.	.	.	.	.	.	.	.	.	.	.	0.025	-1.375492	0.01214	.	.	ENSG00000239961	ENST00000291759	T	0.00507	6.92	2.5	-5.01	0.02991	.	4.720850	0.00633	N	0.000483	T	0.00552	0.0018	L	0.53561	1.675	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.42599	-0.9442	10	0.51188	T	0.08	.	7.3356	0.26607	0.0:0.3981:0.4095:0.1924	.	20	P59901	LIRA4_HUMAN	L	20	ENSP00000291759:R20L	ENSP00000291759:R20L	R	-	2	0	LILRA4	59541960	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.432000	0.00235	-3.358000	0.00179	-1.283000	0.01379	CGG	.	C|1.000;T|0.000		0.627	LILRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140229.2	NM_012276		A	54850148	C	A	54850148	3	1	308	1	0	0	0	0	1	0	0	0	8796	652	23	1	1468	1	LILRA4	19	54850148	Missense_Mutation	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	251628	54850148	4278835	107	44024										
NLRP9	338321	hgsc.bcm.edu	37	chr19	56241199	56241199	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	ggttaacataaaacttacatGagttttcggagtttacaaac	7	6	0	1			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr19:56241199G>A	ENST00000332836.2	-	3	2019	c.1992C>T	c.(1990-1992)ctC>ctT	p.L664L		NM_176820.2	NP_789790.2	Q7RTR0	NALP9_HUMAN	NLR family, pyrin domain containing 9	664						cytoplasm (GO:0005737)	ATP binding (GO:0005524)			NS(2)|breast(5)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(15)|lung(21)|ovary(2)|prostate(3)|skin(7)|urinary_tract(3)	74		Colorectal(82;0.000133)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.123)		AAACTTACATGAGTTTTCGGA	0.438																																					p.L664L		Atlas-SNP	.											.	NLRP9	163	.	0			c.C1992T						.						68	67	67					19																	56241199		2203	4300	6503	SO:0001819	synonymous_variant	338321	exon3			TTACATGAGTTTT	AY154464	CCDS12934.1	19q13.43	2006-12-08	2006-12-08	2006-12-08				"Nucleotide-binding domain and leucine rich repeat containing"	22941	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 9"	609663	"NACHT, leucine rich repeat and PYD containing 9"	NALP9		12563287	Standard	NM_176820		Approved	NOD6, PAN12, CLR19.1	uc002qly.3	Q7RTR0		ENST00000332836.2:c.1992C>T	chr19.hg19:g.56241199G>A		88.0	0.0		69.0	19.0	NM_176820	B2RN12|Q86W27	Silent	SNP	ENST00000332836.2	hg19	CCDS12934.1																																																																																			.	.		0.438	NLRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453653.1	NM_176820		A	56241199	G	A	56241199	2	1	308	1	0	0	0	0	0	0	0	1	10493	1277	45	3		3	NLRP9	19	56241199	Silent	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10	1391051	56241199	2887784	108	44025										
NLRP13	126204	hgsc.bcm.edu	37	chr19	56416366	56416366	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	cgcacacaatagctttatgcCatcatcttggagccgattaa	7	11	2	0	rs201367180		TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr19:56416366C>A	ENST00000342929.3	-	8	2559	c.2560G>T	c.(2560-2562)Ggc>Tgc	p.G854C	NLRP13_ENST00000588751.1_Missense_Mutation_p.G854C	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	854							ATP binding (GO:0005524)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(58)|ovary(4)|pancreas(2)|prostate(2)|skin(13)|stomach(2)|urinary_tract(1)	109		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)		AGCTTTATGCCATCATCTTGG	0.493																																					p.G854C		Atlas-SNP	.											.	NLRP13	220	.	0			c.G2560T						.						147	115	126					19																	56416366		2203	4300	6503	SO:0001583	missense	126204	exon8			TTATGCCATCATC	AY154468	CCDS33119.1	19q13.43	2008-02-05	2006-12-08	2006-12-08	ENSG00000173572	ENSG00000173572		"Nucleotide-binding domain and leucine rich repeat containing"	22937	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 13"	609660	"NACHT, leucine rich repeat and PYD containing 13"	NALP13		12563287	Standard	NM_176810		Approved	NOD14, PAN13, CLR19.7	uc010ygg.2	Q86W25	OTTHUMG00000167839	ENST00000342929.3:c.2560G>T	chr19.hg19:g.56416366C>A	ENSP00000343891:p.Gly854Cys	187.0	0.0		154.0	38.0	NM_176810	Q7RTR5	Missense_Mutation	SNP	ENST00000342929.3	hg19	CCDS33119.1	.	.	.	.	.	.	.	.	.	.	C	11.29	1.594277	0.28445	.	.	ENSG00000173572	ENST00000342929	T	0.62498	0.02	2.28	1.23	0.21249	.	.	.	.	.	T	0.76054	0.3934	M	0.91196	3.185	0.09310	N	1	P	0.49862	0.929	P	0.57960	0.83	T	0.63550	-0.6612	9	0.56958	D	0.05	.	4.9121	0.13827	0.0:0.8222:0.0:0.1778	.	854	Q86W25	NAL13_HUMAN	C	854	ENSP00000343891:G854C	ENSP00000343891:G854C	G	-	1	0	NLRP13	61108178	0.002000	0.14202	0.001000	0.08648	0.001000	0.01503	1.449000	0.35123	0.541000	0.28827	0.655000	0.94253	GGC	.	C|0.999;T|0.001		0.493	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810		A	56416366	C	A	56416366	3	1	308	1	0	0	0	0	1	0	0	0	10484	594	21	3	585	3	NLRP13	19	56416366	Missense_Mutation	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	175167	56416366	2712617	109	44026										
NCOA6	23054	hgsc.bcm.edu	37	chr20	33345295	33345295	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	tgttggtgaggtggggctgcTgcaagggagttgggacccta	19	6	0	1			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr20:33345295T>A	ENST00000374796.2	-	8	3826	c.1256A>T	c.(1255-1257)cAg>cTg	p.Q419L	NCOA6_ENST00000359003.2_Missense_Mutation_p.Q419L			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	419	CREBBP-binding region.|Gln-rich.|NCOA1-binding region.|TBP/GTF2A-binding region.				brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			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						GTGGGGCTGCTGCAAGGGAGT	0.587																																					p.Q419L		Atlas-SNP	.											.	NCOA6	219	.	0			c.A1256T						.						51	54	53					20																	33345295		2203	4300	6503	SO:0001583	missense	23054	exon7			GGCTGCTGCAAGG	AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"nuclear receptor coactivator RAP250", "activating signal cointegrator-2", "peroxisome proliferator-activated receptor interacting protein"	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.1256A>T	chr20.hg19:g.33345295T>A	ENSP00000363929:p.Gln419Leu	128.0	0.0		105.0	22.0	NM_014071	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Missense_Mutation	SNP	ENST00000374796.2	hg19	CCDS13241.1	.	.	.	.	.	.	.	.	.	.	T	17.20	3.329521	0.60743	.	.	ENSG00000198646	ENST00000374796;ENST00000359003	T;T	0.33438	1.41;1.41	5.72	5.72	0.89469	.	0.000000	0.64402	D	0.000005	T	0.38506	0.1043	L	0.29908	0.895	0.51767	D	0.999931	D;D	0.63880	0.969;0.993	P;P	0.55824	0.785;0.777	T	0.14392	-1.0474	10	0.51188	T	0.08	-3.0414	15.9979	0.80265	0.0:0.0:0.0:1.0	.	419;419	F6M2K2;Q14686	.;NCOA6_HUMAN	L	419	ENSP00000363929:Q419L;ENSP00000351894:Q419L	ENSP00000351894:Q419L	Q	-	2	0	NCOA6	32808956	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.748000	0.55142	2.183000	0.69458	0.383000	0.25322	CAG	.	.		0.587	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071		A	33345295	T	A	33345295	3	1	308	1	0	0	0	0	1	0	0	0	10242	1580	55	4	4971	4	NCOA6	20	33345295	Missense_Mutation	SNP	T	TCGA-HP-A5N0-01A-11D-A28X-10		33345295	29680225	110	44027										
SNAI1	6615	hgsc.bcm.edu	37	chr20	48600475	48600475	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	catctgggactctgtcctggCgccccaagcccagccaattg	10	16	2	0	rs34261470	byFrequency	TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr20:48600475C>G	ENST00000244050.2	+	2	258	c.197C>G	c.(196-198)gCg>gGg	p.A66G		NM_005985.3	NP_005976.2	O95863	SNAI1_HUMAN	snail family zinc finger 1	66			A -> V (in dbSNP:rs34261470).		cartilage morphogenesis (GO:0060536)|cell migration (GO:0016477)|epithelial to mesenchymal transition (GO:0001837)|hair follicle morphogenesis (GO:0031069)|left/right pattern formation (GO:0060972)|mesoderm formation (GO:0001707)|negative regulation of cell differentiation involved in embryonic placenta development (GO:0060806)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|Notch signaling involved in heart development (GO:0061314)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of tight junction assembly (GO:2000810)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	kinase binding (GO:0019900)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)	17			BRCA - Breast invasive adenocarcinoma(9;4.03e-06)			TCTGTCCTGGCGCCCCAAGCC	0.657																																					p.A66G		Atlas-SNP	.											.	SNAI1	28	.	0			c.C197G						.						45	50	48					20																	48600475		2203	4300	6503	SO:0001583	missense	6615	exon2			TCCTGGCGCCCCA	AF125377	CCDS13423.1	20q13.2	2013-05-23	2013-05-23		ENSG00000124216	ENSG00000124216		"Snail homologs", "Zinc fingers, C2H2-type"	11128	protein-coding gene	gene with protein product		604238	"snail 1 (drosophila homolog), zinc finger protein", "snail homolog 1 (Drosophila)"			10585766	Standard	NM_005985		Approved	SNA, SLUGH2, SNAH, SNAIL1, SNAIL	uc002xuz.3	O95863	OTTHUMG00000033048	ENST00000244050.2:c.197C>G	chr20.hg19:g.48600475C>G	ENSP00000244050:p.Ala66Gly	21.0	0.0		31.0	8.0	NM_005985	B2R842|Q9P113|Q9UBP7|Q9UHH7	Missense_Mutation	SNP	ENST00000244050.2	hg19	CCDS13423.1	.	.	.	.	.	.	.	.	.	.	C	13.09	2.133396	0.37630	.	.	ENSG00000124216	ENST00000244050	T	0.23950	1.88	4.94	1.81	0.25067	.	1.159810	0.06133	N	0.670998	T	0.19685	0.0473	L	0.43152	1.355	0.23406	N	0.997747	B	0.32203	0.36	B	0.25506	0.061	T	0.25882	-1.0119	10	0.20519	T	0.43	-4.3384	7.28	0.26306	0.0:0.6314:0.0:0.3686	.	66	O95863	SNAI1_HUMAN	G	66	ENSP00000244050:A66G	ENSP00000244050:A66G	A	+	2	0	SNAI1	48033882	0.003000	0.15002	0.936000	0.37596	0.943000	0.58893	1.315000	0.33608	0.429000	0.26202	0.557000	0.71058	GCG	.	C|0.979;T|0.021		0.657	SNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080350.1			G	48600475	C	G	48600475	3	3	308	1	0	0	0	0	1	0	0	0	14841	768	27	4	203	4	SNAI1	20	48600475	Missense_Mutation	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	15255180	48600475	14425045	111	44028										
BHLHE23	128408	hgsc.bcm.edu	37	chr20	61637464	61637464	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	ccggagaaggcggcgcacttGtcagggcagggccccagggc	18	13	1	1			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr20:61637464G>A	ENST00000370346.2	-	1	923	c.615C>T	c.(613-615)gaC>gaT	p.D205D		NM_080606.3	NP_542173	Q8NDY6	BHE23_HUMAN	basic helix-loop-helix family, member e23	205					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)	1						CGGCGCACTTGTCAGGGCAGG	0.746																																					p.D205D		Atlas-SNP	.											.	BHLHE23	3	.	0			c.C615T						.						4	5	5					20																	61637464		2054	4053	6107	SO:0001819	synonymous_variant	128408	exon1			GCACTTGTCAGGG	AL121673	CCDS33507.1, CCDS33507.2	20q13.33	2009-01-12	2009-01-12	2009-01-12	ENSG00000125533	ENSG00000125533		"Basic helix-loop-helix proteins"	16093	protein-coding gene	gene with protein product		609331	"basic helix-loop-helix domain containing, class B, 4"	BHLHB4		11863370, 18557763	Standard	NM_080606		Approved	bA305P22.3, Beta4, bHLHe23	uc002yeb.2	Q8NDY6	OTTHUMG00000032948	ENST00000370346.2:c.615C>T	chr20.hg19:g.61637464G>A		20.0	0.0		23.0	9.0	NM_080606	B2RP69	Silent	SNP	ENST00000370346.2	hg19	CCDS33507.1																																																																																			.	.		0.746	BHLHE23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080095.2	NM_080606		A	61637464	G	A	61637464	2	1	308	1	0	0	0	0	0	0	0	1	1422	1368	48	3		3	BHLHE23	20	61637464	Silent	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10	13036989	61637464	1388056	112	44029										
BPIL2	254240	hgsc.bcm.edu	37	chr22	32829728	32829728	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	gggagagcacgttgccaaggCcttgagagttttgaacaaaa	13	7	0	3			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr22:32829728C>T	ENST00000397452.1	-	10	1066	c.956G>A	c.(955-957)gGc>gAc	p.G319D	BPIFC_ENST00000432451.2_Missense_Mutation_p.G133D|BPIFC_ENST00000300399.3_Missense_Mutation_p.G319D|BPIFC_ENST00000534972.1_Missense_Mutation_p.G43D			Q8NFQ6	BPIFC_HUMAN	BPI fold containing family C	319						extracellular region (GO:0005576)	lipopolysaccharide binding (GO:0001530)|phospholipid binding (GO:0005543)										GTTGCCAAGGCCTTGAGAGTT	0.423																																					p.G319D		Atlas-SNP	.											.	.	.	.	0			c.G956A						.						102	94	96					22																	32829728		2203	4300	6503	SO:0001583	missense	254240	exon9			CCAAGGCCTTGAG	AF465766	CCDS13906.1	22q12.3	2011-08-04	2011-08-01	2011-08-01	ENSG00000184459	ENSG00000184459		"BPI fold containing"	16503	protein-coding gene	gene with protein product		614109	"bactericidal/permeability-increasing protein-like 2"	BPIL2			Standard	NM_174932		Approved	dJ149A16.7	uc003amn.2	Q8NFQ6	OTTHUMG00000058273	ENST00000397452.1:c.956G>A	chr22.hg19:g.32829728C>T	ENSP00000380594:p.Gly319Asp	159.0	0.0		115.0	33.0	NM_174932	A2RRF1	Missense_Mutation	SNP	ENST00000397452.1	hg19	CCDS13906.1	.	.	.	.	.	.	.	.	.	.	C	18.44	3.624992	0.66901	.	.	ENSG00000184459	ENST00000397452;ENST00000300399;ENST00000534972;ENST00000432451	T;T;T;T	0.08546	3.08;3.08;3.08;3.08	5.75	3.66	0.41972	.	0.349682	0.31519	N	0.007517	T	0.16428	0.0395	M	0.80028	2.48	0.34587	D	0.715106	P;P	0.48589	0.912;0.89	P;P	0.49829	0.623;0.543	T	0.18681	-1.0329	10	0.33940	T	0.23	-9.9352	7.2304	0.26038	0.0:0.7386:0.1728:0.0886	.	133;319	A2RRF1;Q8NFQ6	.;BPIFC_HUMAN	D	319;319;43;133	ENSP00000380594:G319D;ENSP00000300399:G319D;ENSP00000439123:G43D;ENSP00000408920:G133D	ENSP00000300399:G319D	G	-	2	0	BPIFC	31159728	0.627000	0.27129	0.884000	0.34674	0.987000	0.75469	0.807000	0.27140	1.422000	0.47177	0.655000	0.94253	GGC	.	.		0.423	BPIFC-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129029.2	NM_174932		T	32829728	C	T	32829728	3	4	308	1	0	0	0	0	1	0	0	0	1494	739	26	3	595	3	BPIL2	22	32829728	Missense_Mutation	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10		32829728	18474838	113	44030										
CACNG2	10369	hgsc.bcm.edu	37	chr22	36960750	36960750	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	cgcgggccgtggcccgcagcTgtttgtgccggtcgataaac	15	13	0	0			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr22:36960750T>A	ENST00000300105.6	-	4	1601	c.620A>T	c.(619-621)cAg>cTg	p.Q207L	RP5-1119A7.17_ENST00000562756.1_RNA	NM_006078.3	NP_006069.1	Q9Y698	CCG2_HUMAN	calcium channel, voltage-dependent, gamma subunit 2	207					membrane depolarization (GO:0051899)|membrane hyperpolarization (GO:0060081)|neuromuscular junction development (GO:0007528)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	18						GGCCCGCAGCTGTTTGTGCCG	0.657																																					p.Q207L		Atlas-SNP	.											.	CACNG2	43	.	0			c.A620T						.						93	109	103					22																	36960750		2203	4300	6503	SO:0001583	missense	10369	exon4			CGCAGCTGTTTGT	AF096322	CCDS13931.1	22q13.1	2006-08-01			ENSG00000166862	ENSG00000166862		"Calcium channel subunits"	1406	protein-coding gene	gene with protein product		602911					Standard	NM_006078		Approved	stargazin, MGC138502, MGC138504	uc003aps.2	Q9Y698	OTTHUMG00000030612	ENST00000300105.6:c.620A>T	chr22.hg19:g.36960750T>A	ENSP00000300105:p.Gln207Leu	105.0	0.0		65.0	5.0	NM_006078	Q2M1M1|Q5TGT3|Q9UGZ7	Missense_Mutation	SNP	ENST00000300105.6	hg19	CCDS13931.1	.	.	.	.	.	.	.	.	.	.	T	17.76	3.468640	0.63625	.	.	ENSG00000166862	ENST00000300105	T	0.37752	1.18	5.62	5.62	0.85841	.	0.119730	0.64402	D	0.000017	T	0.35913	0.0948	L	0.46157	1.445	0.80722	D	1	B	0.23058	0.079	B	0.21546	0.035	T	0.16305	-1.0407	10	0.87932	D	0	-11.2082	15.799	0.78436	0.0:0.0:0.0:1.0	.	207	Q9Y698	CCG2_HUMAN	L	207	ENSP00000300105:Q207L	ENSP00000300105:Q207L	Q	-	2	0	CACNG2	35290696	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.662000	0.83803	2.145000	0.66743	0.533000	0.62120	CAG	.	.		0.657	CACNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075500.2			A	36960750	T	A	36960750	3	1	308	1	0	0	0	0	1	0	0	0	2559	1580	55	4	355	4	CACNG2	22	36960750	Missense_Mutation	SNP	T	TCGA-HP-A5N0-01A-11D-A28X-10	4131022	36960750	14343816	114	44031										
CACNG2	10369	hgsc.bcm.edu	37	chr22	36960792	36960792	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	tgtgcaccgccagcaccccgAccatctcggcgatgatgaag	11	15	1	2			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr22:36960792A>G	ENST00000300105.6	-	4	1559	c.578T>C	c.(577-579)gTc>gCc	p.V193A	RP5-1119A7.17_ENST00000562756.1_RNA	NM_006078.3	NP_006069.1	Q9Y698	CCG2_HUMAN	calcium channel, voltage-dependent, gamma subunit 2	193					membrane depolarization (GO:0051899)|membrane hyperpolarization (GO:0060081)|neuromuscular junction development (GO:0007528)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	18						CAGCACCCCGACCATCTCGGC	0.607																																					p.V193A		Atlas-SNP	.											.	CACNG2	43	.	0			c.T578C						.						118	135	129					22																	36960792		2203	4300	6503	SO:0001583	missense	10369	exon4			ACCCCGACCATCT	AF096322	CCDS13931.1	22q13.1	2006-08-01			ENSG00000166862	ENSG00000166862		"Calcium channel subunits"	1406	protein-coding gene	gene with protein product		602911					Standard	NM_006078		Approved	stargazin, MGC138502, MGC138504	uc003aps.2	Q9Y698	OTTHUMG00000030612	ENST00000300105.6:c.578T>C	chr22.hg19:g.36960792A>G	ENSP00000300105:p.Val193Ala	123.0	0.0		80.0	7.0	NM_006078	Q2M1M1|Q5TGT3|Q9UGZ7	Missense_Mutation	SNP	ENST00000300105.6	hg19	CCDS13931.1	.	.	.	.	.	.	.	.	.	.	A	13.37	2.215750	0.39102	.	.	ENSG00000166862	ENST00000300105	D	0.88896	-2.44	5.62	3.48	0.39840	.	0.000000	0.85682	D	0.000000	D	0.84483	0.5482	L	0.48260	1.515	0.58432	D	0.999998	P	0.42757	0.789	B	0.44224	0.444	T	0.77138	-0.2698	10	0.19147	T	0.46	-31.4349	8.4167	0.32676	0.7992:0.1323:0.0685:0.0	.	193	Q9Y698	CCG2_HUMAN	A	193	ENSP00000300105:V193A	ENSP00000300105:V193A	V	-	2	0	CACNG2	35290738	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.919000	0.92770	0.409000	0.25649	-0.316000	0.08728	GTC	.	.		0.607	CACNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075500.2			G	36960792	A	G	36960792	3	3	308	1	0	0	0	0	1	0	0	0	2559	275	10	2	397	2	CACNG2	22	36960792	Missense_Mutation	SNP	A	TCGA-HP-A5N0-01A-11D-A28X-10	42	36960792	14343774	115	44032										
CACNG2	10369	hgsc.bcm.edu	37	chr22	36983573	36983574	+	Missense_Mutation	DNP	CT	CT	AA													0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	tctgggaagtgatcaatttgCttgcacagacctttgaaatt							TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C|T	C|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chr22:36983573_36983574CT>AA	ENST00000300105.6	-	2	1214_1215	c.233_234AG>TT	c.(232-234)aAG>aTT	p.K78I	CACNG2_ENST00000480002.1_5'Flank	NM_006078.3	NP_006069.1	Q9Y698	CCG2_HUMAN	calcium channel, voltage-dependent, gamma subunit 2	78					membrane depolarization (GO:0051899)|membrane hyperpolarization (GO:0060081)|neuromuscular junction development (GO:0007528)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	18						GATCAATTTGCTTGCACAGACC	0.485																																					p.K78N|p.K78M		Atlas-SNP	.											.	CACNG2	43	.	0			c.G234T|c.A233T						.																																			SO:0001583	missense	10369	exon2			AATTTGCTTGCAC|ATTTGCTTGCACA	AF096322	CCDS13931.1	22q13.1	2006-08-01			ENSG00000166862	ENSG00000166862		"Calcium channel subunits"	1406	protein-coding gene	gene with protein product		602911					Standard	NM_006078		Approved	stargazin, MGC138502, MGC138504	uc003aps.2	Q9Y698	OTTHUMG00000030612	ENST00000300105.6:c.233_234delinsAA	chr22.hg19:g.36983573_36983574delinsAA	ENSP00000300105:p.Lys78Ile	154.0|156.0	0.0		184.0|183.0	39.0	NM_006078	Q2M1M1|Q5TGT3|Q9UGZ7	Missense_Mutation	SNP	ENST00000300105.6	hg19	CCDS13931.1																																																																																			.	.		0.485	CACNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075500.2			AA	36983574	CT	AA	36983573	3	1	308	1	0	0	0	0	1	0	0	0	2559	796	28	3	749	3	CACNG2	22	36983573	Missense_Mutation	DNP	CT	TCGA-HP-A5N0-01A-11D-A28X-10	22781	36983573	14320993	116	44033										
MXRA5	25878	hgsc.bcm.edu	37	chrX	3238423	3238423	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	gggaatgtatcctgttgtagGaacctggaataacttttctc	10	7	1	0			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chrX:3238423G>C	ENST00000217939.6	-	5	5457	c.5303C>G	c.(5302-5304)tCc>tGc	p.S1768C		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	1768						extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				CCTGTTGTAGGAACCTGGAAT	0.522																																					p.S1768C		Atlas-SNP	.											.	MXRA5	815	.	0			c.C5303G						.						88	80	83					X																	3238423		2203	4300	6503	SO:0001583	missense	25878	exon5			TTGTAGGAACCTG	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7539	protein-coding gene	gene with protein product	"adlican"					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.5303C>G	chrX.hg19:g.3238423G>C	ENSP00000217939:p.Ser1768Cys	154.0	0.0		112.0	33.0	NM_015419	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	hg19	CCDS14124.1	.	.	.	.	.	.	.	.	.	.	G	7.708	0.694503	0.15039	.	.	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.64260	-0.09	3.35	2.48	0.30137	.	0.407810	0.17792	U	0.161860	T	0.37265	0.0997	N	0.08118	0	0.09310	N	1	B	0.31519	0.327	B	0.28232	0.087	T	0.20538	-1.0272	10	0.48119	T	0.1	.	8.0364	0.30495	0.234:0.0:0.766:0.0	.	1768	Q9NR99	MXRA5_HUMAN	C	1768	ENSP00000217939:S1768C	ENSP00000217939:S1768C	S	-	2	0	MXRA5	3248423	0.001000	0.12720	0.001000	0.08648	0.039000	0.13416	0.681000	0.25320	0.317000	0.23160	-0.475000	0.04921	TCC	.	.		0.522	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		C	3238423	G	C	3238423	3	2	308	1	0	0	0	0	1	0	0	0	10012	1174	41	4	3195	4	MXRA5	23	3238423	Missense_Mutation	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10		3238423	152032137	117	44034										
PTCHD1	139411	hgsc.bcm.edu	37	chrX	23411941	23411941	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	ttacacaattgacaattgtgCtccaatgttatccacatttg	5	9	0	1			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chrX:23411941C>T	ENST00000379361.4	+	3	3166	c.2306C>T	c.(2305-2307)gCt>gTt	p.A769V		NM_173495.2	NP_775766.2	Q96NR3	PTHD1_HUMAN	patched domain containing 1	769					cognition (GO:0050890)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(4)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(4)|skin(2)|urinary_tract(2)	42						GACAATTGTGCTCCAATGTTA	0.368																																					p.A769V		Atlas-SNP	.											.	PTCHD1	213	.	0			c.C2306T						.						136	118	124					X																	23411941		2203	4300	6503	SO:0001583	missense	139411	exon3			ATTGTGCTCCAAT	AK054858	CCDS35215.2	Xp22.13	2008-02-05			ENSG00000165186	ENSG00000165186			26392	protein-coding gene	gene with protein product		300828					Standard	NM_173495		Approved	FLJ30296	uc004dal.4	Q96NR3	OTTHUMG00000021251	ENST00000379361.4:c.2306C>T	chrX.hg19:g.23411941C>T	ENSP00000368666:p.Ala769Val	126.0	0.0		107.0	11.0	NM_173495	B4DQH0|Q0IJ60|Q6P6B8	Missense_Mutation	SNP	ENST00000379361.4	hg19	CCDS35215.2	.	.	.	.	.	.	.	.	.	.	C	17.95	3.514919	0.64634	.	.	ENSG00000165186	ENST00000379361	D	0.93426	-3.22	5.18	5.18	0.71444	.	0.056326	0.64402	D	0.000001	D	0.94978	0.8375	L	0.55213	1.73	0.51767	D	0.999934	D	0.55605	0.972	P	0.59761	0.863	D	0.94409	0.7630	10	0.39692	T	0.17	.	17.8203	0.88648	0.0:1.0:0.0:0.0	.	769	Q96NR3	PTHD1_HUMAN	V	769	ENSP00000368666:A769V	ENSP00000368666:A769V	A	+	2	0	PTCHD1	23321862	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	5.933000	0.70130	2.140000	0.66376	0.523000	0.50628	GCT	.	.		0.368	PTCHD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056047.2	NM_173495		T	23411941	C	T	23411941	3	4	308	1	0	0	0	0	1	0	0	0	12744	797	28	3	2316	3	PTCHD1	23	23411941	Missense_Mutation	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	20173518	23411941	131858619	118	44035										
FAM47A	158724	hgsc.bcm.edu	37	chrX	34149907	34149907	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	tcctgggtctcacaacaagcCcaagcgtcctccagctccct	7	18	1	0			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chrX:34149907C>A	ENST00000346193.3	-	1	540	c.489G>T	c.(487-489)tgG>tgT	p.W163C		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	163										NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	97						CACAACAAGCCCAAGCGTCCT	0.557																																					p.W163C		Atlas-SNP	.											.	FAM47A	249	.	0			c.G489T						.						68	65	66					X																	34149907		2202	4300	6502	SO:0001583	missense	158724	exon1			ACAAGCCCAAGCG	BC026171	CCDS43926.1	Xp21.1	2004-08-09			ENSG00000185448	ENSG00000185448			29962	protein-coding gene	gene with protein product	"similar to hypothetical protein FLJ35782"					12477932	Standard	NM_203408		Approved	MGC27003	uc004ddg.3	Q5JRC9	OTTHUMG00000021339	ENST00000346193.3:c.489G>T	chrX.hg19:g.34149907C>A	ENSP00000345029:p.Trp163Cys	224.0	0.0		152.0	12.0	NM_203408	A8K8I9|Q8TAA0	Missense_Mutation	SNP	ENST00000346193.3	hg19	CCDS43926.1	.	.	.	.	.	.	.	.	.	.	C	2.401	-0.337539	0.05278	.	.	ENSG00000185448	ENST00000346193	T	0.15256	2.44	1.1	0.107	0.14544	.	.	.	.	.	T	0.24084	0.0583	L	0.38953	1.18	0.09310	N	0.999999	D	0.89917	1.0	D	0.78314	0.991	T	0.12630	-1.0540	9	0.41790	T	0.15	.	4.001	0.09580	0.4092:0.5908:0.0:0.0	.	163	Q5JRC9	FA47A_HUMAN	C	163	ENSP00000345029:W163C	ENSP00000345029:W163C	W	-	3	0	FAM47A	34059828	0.004000	0.15560	0.010000	0.14722	0.024000	0.10985	0.441000	0.21611	-0.027000	0.13873	0.499000	0.49734	TGG	.	.		0.557	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408		A	34149907	C	A	34149907	3	1	308	1	0	0	0	0	1	0	0	0	5577	624	22	3	1890	3	FAM47A	23	34149907	Missense_Mutation	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	10737966	34149907	121120653	119	44036										
GPR34	2857	hgsc.bcm.edu	37	chrX	41555817	41555817	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	ttgttcacaaaaccaatgagAtcatgctggttctctcatct	6	10	5	1			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chrX:41555817A>T	ENST00000378142.4	+	3	1215	c.931A>T	c.(931-933)Atc>Ttc	p.I311F	CASK_ENST00000378154.1_Intron|CASK_ENST00000442742.2_Intron|CASK_ENST00000378163.1_Intron|CASK_ENST00000318588.9_Intron|CASK_ENST00000361962.4_Intron|CASK_ENST00000378166.4_Intron|CASK_ENST00000421587.2_Intron|CASK_ENST00000378158.1_Intron|GPR34_ENST00000378138.5_Missense_Mutation_p.I311F	NM_001097579.1|NM_005300.3	NP_001091048.1|NP_005291.1	Q9UPC5	GPR34_HUMAN	G protein-coupled receptor 34	311					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(1)|large_intestine(6)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	14						AACCAATGAGATCATGCTGGT	0.358																																					p.I311F		Atlas-SNP	.											.	GPR34	42	.	0			c.A931T						.						136	111	120					X																	41555817		2203	4300	6503	SO:0001583	missense	2857	exon3			AATGAGATCATGC	AF039686	CCDS14258.1	Xp11.4	2012-08-21			ENSG00000171659	ENSG00000171659		"GPCR / Class A : Orphans"	4490	protein-coding gene	gene with protein product		300241				10395919, 10036181	Standard	NM_005300		Approved		uc004dfq.4	Q9UPC5	OTTHUMG00000021375	ENST00000378142.4:c.931A>T	chrX.hg19:g.41555817A>T	ENSP00000367384:p.Ile311Phe	143.0	0.0		103.0	36.0	NM_001097579	O95853	Missense_Mutation	SNP	ENST00000378142.4	hg19	CCDS14258.1	.	.	.	.	.	.	.	.	.	.	A	15.60	2.880484	0.51801	.	.	ENSG00000171659	ENST00000378142;ENST00000378138;ENST00000535368	T;T	0.27104	1.69;1.69	5.73	5.73	0.89815	GPCR, rhodopsin-like superfamily (1);	0.242157	0.42294	D	0.000735	T	0.37812	0.1017	L	0.40543	1.245	0.51012	D	0.999907	D	0.63880	0.993	D	0.70487	0.969	T	0.28138	-1.0053	10	0.87932	D	0	-12.6891	7.5581	0.27835	0.8626:0.0:0.1374:0.0	.	311	Q9UPC5	GPR34_HUMAN	F	311;311;264	ENSP00000367384:I311F;ENSP00000367378:I311F	ENSP00000367378:I311F	I	+	1	0	GPR34	41440761	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.255000	0.43222	1.922000	0.55676	0.481000	0.45027	ATC	.	.		0.358	GPR34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056264.1	NM_005300		T	41555817	A	T	41555817	3	4	308	1	0	0	0	0	1	0	0	0	6697	333	12	4	933	4	GPR34	23	41555817	Missense_Mutation	SNP	A	TCGA-HP-A5N0-01A-11D-A28X-10	7405910	41555817	113714743	120	44037										
GPRASP2	114928	hgsc.bcm.edu	37	chrX	101970175	101970185	+	Frame_Shift_Del	DEL	CCAGGCATGGG	CCAGGCATGGG	-													0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	gcaaggcccaaggatgaggcCcaggcatgggcccagagtga					rs61097741|rs538885190		TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	CCAGGCATGGG	CCAGGCATGGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chrX:101970175_101970185delCCAGGCATGGG	ENST00000535209.1	+	4	1209_1219	c.378_388delCCAGGCATGGG	c.(376-390)gcccaggcatgggccfs	p.AQAWA126fs	GPRASP2_ENST00000543253.1_Frame_Shift_Del_p.AQAWA126fs|GPRASP2_ENST00000332262.5_Frame_Shift_Del_p.AQAWA126fs			Q96D09	GASP2_HUMAN	G protein-coupled receptor associated sorting protein 2	126						cytoplasm (GO:0005737)	beta-amyloid binding (GO:0001540)			breast(3)|endometrium(5)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	30						AGGATGAGGCCCAGGCATGGGCCCAGAGTGA	0.583																																					p.126_129del		Atlas-Indel,Pindel	.											.	GPRASP2	89	.	0			c.377_387del						.																																			SO:0001589	frameshift_variant	114928	exon5			.	AK094646	CCDS14501.1	Xq22.1	2014-03-21			ENSG00000158301	ENSG00000158301		"Armadillo repeat containing"	25169	protein-coding gene	gene with protein product						15086532, 16221301	Standard	NM_138437		Approved	GASP2, FLJ37327		Q96D09	OTTHUMG00000022059	ENST00000535209.1:c.378_388delCCAGGCATGGG	chrX.hg19:g.101970175_101970185delCCAGGCATGGG	ENSP00000437394:p.Ala126fs	143.0	0.0		122.0	29.0	NM_001184874	D3DXA0|Q8NAB4	Frame_Shift_Del	DEL	ENST00000535209.1	hg19	CCDS14501.1																																																																																			.	.		0.583	GPRASP2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057626.2	NM_138437		-	101970185	CCAGGCATGGG	-	101970175	7	5	308	1	0	1	0	1	0	0	0	0	6732	610	22	0	380	0	GPRASP2	23	101970175	Frame_Shift_Del	DEL	CCAGGCATGGG	TCGA-HP-A5N0-01A-11D-A28X-10	60414358	101970175	53300385	121	44038										
AIFM1	9131	hgsc.bcm.edu	37	chrX	129264035	129264035	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	tagaagatgacacctttgccGtagtcctccccctggacggg	11	13	0	3			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chrX:129264035G>A	ENST00000287295.3	-	15	1910	c.1680C>T	c.(1678-1680)taC>taT	p.Y560Y	AIFM1_ENST00000319908.3_Silent_p.Y556Y|AIFM1_ENST00000535724.1_3'UTR|AIFM1_ENST00000440263.1_Silent_p.Y208Y|AIFM1_ENST00000460436.2_Silent_p.Y221Y|AIFM1_ENST00000346424.2_Silent_p.Y273Y	NM_001130847.3|NM_004208.3	NP_001124319.1|NP_004199.1	O95831	AIFM1_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 1	560					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cell redox homeostasis (GO:0045454)|chromosome condensation (GO:0030261)|DNA catabolic process (GO:0006308)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mitochondrial respiratory chain complex I assembly (GO:0032981)|neuron apoptotic process (GO:0051402)|neuron differentiation (GO:0030182)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic DNA fragmentation (GO:1902510)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|electron carrier activity (GO:0009055)|FAD binding (GO:0071949)|NAD(P)H oxidase activity (GO:0016174)|oxidoreductase activity, acting on NAD(P)H (GO:0016651)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|liver(2)|lung(8)|ovary(4)|prostate(2)|urinary_tract(1)	30					Flavin adenine dinucleotide(DB03147)	CACCTTTGCCGTAGTCCTCCC	0.537																																					p.Y560Y		Atlas-SNP	.											.	AIFM1	75	.	0			c.C1680T						.						177	165	169					X																	129264035		2203	4300	6503	SO:0001819	synonymous_variant	9131	exon15			TTTGCCGTAGTCC	AF100928	CCDS14618.1, CCDS14619.1, CCDS48167.1	Xq26.1	2014-01-30	2006-11-16	2006-11-16	ENSG00000156709	ENSG00000156709			8768	protein-coding gene	gene with protein product		300169	"programmed cell death 8 (apoptosis-inducing factor)", "neuropathy, axonal, motor-sensory with deafness and mental retardation (Cowchock syndrome)"	PDCD8, NAMSD		9989411, 23217327	Standard	NM_004208		Approved	AIF, CMTX4	uc004evg.3	O95831	OTTHUMG00000022392	ENST00000287295.3:c.1680C>T	chrX.hg19:g.129264035G>A		229.0	0.0		251.0	33.0	NM_004208	A4QPB4|B1ALN1|B2RB08|D3DTE9|Q1L6K4|Q1L6K6|Q2QKE4|Q5JUZ7|Q6I9X6|Q9Y3I3|Q9Y3I4	Silent	SNP	ENST00000287295.3	hg19	CCDS14618.1																																																																																			.	.		0.537	AIFM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058247.2			A	129264035	G	A	129264035	2	1	308	1	0	0	0	0	0	0	0	1	426	1140	40	1		1	AIFM1	23	129264035	Silent	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10	27293860	129264035	26006525	122	44039										
FAM122B	159090	hgsc.bcm.edu	37	chrX	133927919	133927919	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	aggttggaaaacctgtgaaaGgtcactgaaaaaaacaaaaa	9	5	1	2			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chrX:133927919G>A	ENST00000370790.1	-	2	1031	c.103C>T	c.(103-105)Ctt>Ttt	p.L35F	FAM122B_ENST00000298090.6_Missense_Mutation_p.L35F|FAM122B_ENST00000343004.5_Missense_Mutation_p.L35F|FAM122C_ENST00000414371.2_5'Flank|FAM122B_ENST00000493333.1_5'UTR|FAM122B_ENST00000486347.1_Missense_Mutation_p.L35F	NM_001166599.2|NM_145284.5	NP_001160071.1|NP_660327.2	Q7Z309	F122B_HUMAN	family with sequence similarity 122B	35										breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|skin(1)	6	Acute lymphoblastic leukemia(192;0.000127)					ACCTGTGAAAGGTCACTGAAA	0.328																																					p.L35F		Atlas-SNP	.											.	FAM122B	20	.	0			c.C103T						.						91	85	87					X																	133927919		2203	4300	6503	SO:0001583	missense	159090	exon2			GTGAAAGGTCACT	BX538218	CCDS14643.1, CCDS55497.1, CCDS55498.1	Xq26.3	2008-02-05			ENSG00000156504	ENSG00000156504			30490	protein-coding gene	gene with protein product						12477932	Standard	NM_145284		Approved	DKFZp686L20116, RP11-308B5.5	uc004exq.3	Q7Z309	OTTHUMG00000022461	ENST00000370790.1:c.103C>T	chrX.hg19:g.133927919G>A	ENSP00000359826:p.Leu35Phe	43.0	0.0		47.0	7.0	NM_001170756	A8K902|Q6PIM2|Q6ZU47|Q6ZV64|Q6ZVE4|Q8TB75	Missense_Mutation	SNP	ENST00000370790.1	hg19	CCDS55497.1	.	.	.	.	.	.	.	.	.	.	G	7.356	0.623892	0.14193	.	.	ENSG00000156504	ENST00000370790;ENST00000298090;ENST00000343004;ENST00000394270;ENST00000486347;ENST00000370787	T;T;T;T	0.56275	0.47;0.47;0.47;0.47	5.47	1.26	0.21427	.	0.680988	0.13649	N	0.372414	T	0.41581	0.1165	L	0.51422	1.61	0.25269	N	0.98953	B;B;B;B	0.12630	0.006;0.001;0.001;0.003	B;B;B;B	0.13407	0.009;0.004;0.004;0.006	T	0.39333	-0.9619	10	0.62326	D	0.03	.	3.8695	0.09030	0.3101:0.0:0.3565:0.3334	.	35;35;35;35	G1UD80;Q7Z309-2;Q7Z309;Q7Z309-3	.;.;F122B_HUMAN;.	F	35	ENSP00000359826:L35F;ENSP00000298090:L35F;ENSP00000339207:L35F;ENSP00000419592:L35F	ENSP00000298090:L35F	L	-	1	0	FAM122B	133755585	0.967000	0.33354	0.961000	0.40146	0.401000	0.30781	0.670000	0.25157	0.154000	0.19237	0.506000	0.49869	CTT	.	.		0.328	FAM122B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058382.1	NM_145284		A	133927919	G	A	133927919	3	1	308	1	0	0	0	0	1	0	0	0	5425	1000	35	3	810	3	FAM122B	23	133927919	Missense_Mutation	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10	4663884	133927919	21342641	123	44040										
MCF2	4168	hgsc.bcm.edu	37	chrX	138728988	138728988	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	agtaagtacttttgctattaCttcctctggtatacatctaa	5	8	2	0			TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chrX:138728988C>A	ENST00000519895.1	-	3	265	c.100G>T	c.(100-102)Gta>Tta	p.V34L	MCF2_ENST00000414978.1_Missense_Mutation_p.V34L|MCF2_ENST00000370578.4_Missense_Mutation_p.V119L|MCF2_ENST00000520602.1_Missense_Mutation_p.V34L	NM_001171876.1	NP_001165347.1	P10911	MCF2_HUMAN	MCF.2 cell line derived transforming sequence	0	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				apoptotic signaling pathway (GO:0097190)|dendrite development (GO:0016358)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(15)|lung(34)|pancreas(1)|pleura(1)|prostate(1)	62	Acute lymphoblastic leukemia(192;0.000127)					TTTGCTATTACTTCCTCTGGT	0.333																																					p.V34L		Atlas-SNP	.											.	MCF2	432	.	0			c.G100T						.						58	52	54					X																	138728988		1852	4084	5936	SO:0001583	missense	4168	exon3			CTATTACTTCCTC		CCDS14667.1, CCDS48175.1, CCDS55514.1, CCDS55515.1, CCDS55516.1, CCDS55517.1	Xq26.3-q27.1	2012-07-24			ENSG00000101977	ENSG00000101977		"Rho guanine nucleotide exchange factors"	6940	protein-coding gene	gene with protein product	"Oncogene MCF2 (oncogene DBL)"	311030				2577874, 1611909	Standard	NM_001099855		Approved	DBL, ARHGEF21	uc011mwo.1	P10911	OTTHUMG00000022537	ENST00000519895.1:c.100G>T	chrX.hg19:g.138728988C>A	ENSP00000430276:p.Val34Leu	552.0	0.0		596.0	107.0	NM_001171876	B7Z3Y5|B7Z869|B7ZAV1|E9PH77|F5H091|P14919|Q5JYJ2|Q5JYJ3|Q5JYJ4|Q8IUF3|Q8IUF4|Q9UJB3	Missense_Mutation	SNP	ENST00000519895.1	hg19	CCDS55517.1	.	.	.	.	.	.	.	.	.	.	C	13.31	2.198536	0.38806	.	.	ENSG00000101977	ENST00000520602;ENST00000370578;ENST00000414978;ENST00000519895	T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04	5.7	3.93	0.45458	.	0.064020	0.64402	D	0.000008	T	0.51058	0.1652	L	0.44542	1.39	0.09310	N	1	B;P;B	0.38617	0.05;0.64;0.221	B;B;B	0.36567	0.1;0.228;0.14	T	0.38845	-0.9642	10	0.39692	T	0.17	.	9.7869	0.40681	0.0:0.8276:0.0:0.1724	.	34;119;119	E9PH77;B7Z3Z2;Q5JYJ7	.;.;.	L	34;119;34;34	ENSP00000427745:V34L;ENSP00000359610:V119L;ENSP00000397055:V34L;ENSP00000430276:V34L	ENSP00000359610:V119L	V	-	1	0	MCF2	138556654	0.051000	0.20477	0.160000	0.22671	0.992000	0.81027	0.972000	0.29409	0.562000	0.29204	0.600000	0.82982	GTA	.	.		0.333	MCF2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377602.1	NM_005369		A	138728988	C	A	138728988	3	1	308	1	0	0	0	0	1	0	0	0	9387	565	20	3	3096	3	MCF2	23	138728988	Missense_Mutation	SNP	C	TCGA-HP-A5N0-01A-11D-A28X-10	4801069	138728988	16541572	124	44041										
MECP2	4204	hgsc.bcm.edu	37	chrX	153296110	153296110	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.04	5	1	0.84465224216777	1.27347568819141	0.689799331103679	1	1	0	cggagctctcgggctcaggtGgaggtgggggcaggggtggg	24	7	2	0	rs267608599|rs63749029|rs267608593|rs267608592|rs267608591|rs267608596|rs63749024|rs267608594|rs267608349|rs267608329|rs63009262|rs267608343|rs267608327|rs63749023|rs267608580|rs61754419|rs267608581|rs267608401|rs267608582|rs63749030|rs267608406|rs267608588|rs267608589|rs267608600|rs63749749|rs63749748|rs267608603|rs267608602|rs267608601|rs267608583|rs267608607|rs63749034|rs267608605|rs267608587|rs267608586|rs63749028|rs267608604|rs386134271|rs61753008|rs267608573|rs267608575|rs267608574|rs267608577|rs267608579|rs267608578|rs267608585|rs267608334|rs267608373|rs267608372|rs267608350|rs61752992|rs267608392		TCGA-HP-A5N0-01A-11D-A28X-10	TCGA-HP-A5N0-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed152c64-923a-45a2-a5e1-d8a649063561	06f66113-568b-43cd-a4f5-a6b4356cd508	g.chrX:153296110G>A	ENST00000303391.6	-	4	1418	c.1169C>T	c.(1168-1170)cCa>cTa	p.P390L	MECP2_ENST00000453960.2_Missense_Mutation_p.P402L|MECP2_ENST00000460227.1_5'Flank	NM_004992.3	NP_004983.1	P51608	MECP2_HUMAN	methyl CpG binding protein 2	390	Pro-rich.				adult locomotory behavior (GO:0008344)|behavioral fear response (GO:0001662)|cardiolipin metabolic process (GO:0032048)|catecholamine secretion (GO:0050432)|cerebellum development (GO:0021549)|chromatin silencing (GO:0006342)|dendrite development (GO:0016358)|glucocorticoid metabolic process (GO:0008211)|glutamine metabolic process (GO:0006541)|histone acetylation (GO:0016573)|histone methylation (GO:0016571)|inositol metabolic process (GO:0006020)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|negative regulation of histone acetylation (GO:0035067)|negative regulation of histone methylation (GO:0031061)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurological system process involved in regulation of systemic arterial blood pressure (GO:0001976)|neuron maturation (GO:0042551)|pathogenesis (GO:0009405)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of cell proliferation (GO:0008284)|positive regulation of synapse assembly (GO:0051965)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|proprioception (GO:0019230)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|sensory perception of pain (GO:0019233)|social behavior (GO:0035176)|startle response (GO:0001964)|synapse assembly (GO:0007416)|transcription, DNA-templated (GO:0006351)|ventricular system development (GO:0021591)|visual learning (GO:0008542)	cytosol (GO:0005829)|extracellular space (GO:0005615)|heterochromatin (GO:0000792)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|double-stranded methylated DNA binding (GO:0010385)|methyl-CpG binding (GO:0008327)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|protein N-terminus binding (GO:0047485)|sequence-specific DNA binding transcription factor activity (GO:0003700)|siRNA binding (GO:0035197)|transcription corepressor activity (GO:0003714)			breast(2)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(8)|prostate(2)|urinary_tract(1)	23	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GGGCTCAGGTGGAGGTGGGGG	0.667																																					p.P402L		Atlas-SNP	.											.	MECP2	41	.	0			c.C1205T						.						21	25	24					X																	153296110		2167	4173	6340	SO:0001583	missense	4204	exon3			TCAGGTGGAGGTG	AF158180	CCDS14741.1, CCDS48193.1	Xq28	2014-09-17	2014-06-18		ENSG00000169057	ENSG00000169057			6990	protein-coding gene	gene with protein product		300005	"mental retardation, X-linked 16", "mental retardation, X-linked 79", "Rett syndrome", "methyl CpG binding protein 2 (Rett syndrome)"	RTT, MRX16, MRX79		1606614, 10508514	Standard	NM_004992		Approved		uc004fjw.2	P51608	OTTHUMG00000024229	ENST00000303391.6:c.1169C>T	chrX.hg19:g.153296110G>A	ENSP00000301948:p.Pro390Leu	7.0	0.0		10.0	4.0	NM_001110792	O15233|Q6QHH9|Q7Z384	Missense_Mutation	SNP	ENST00000303391.6	hg19	CCDS14741.1	.	.	.	.	.	.	.	.	.	.	G	3.105	-0.183890	0.06340	.	.	ENSG00000169057	ENST00000303391;ENST00000453960	D;D	0.89552	-2.53;-2.52	5.27	2.5	0.30297	.	0.667809	0.15582	N	0.254853	T	0.75852	0.3906	N	0.14661	0.345	0.80722	D	1	B;B	0.23650	0.0;0.089	B;B	0.18871	0.0;0.023	T	0.65109	-0.6248	10	0.33141	T	0.24	-3.4518	5.227	0.15399	0.1767:0.0:0.6367:0.1866	.	402;390	P51608-2;P51608	.;MECP2_HUMAN	L	390;402	ENSP00000301948:P390L;ENSP00000395535:P402L	ENSP00000301948:P390L	P	-	2	0	MECP2	152949304	0.984000	0.35163	0.614000	0.29051	0.023000	0.10783	0.751000	0.26348	0.552000	0.29026	0.513000	0.50165	CCA	.	.		0.667	MECP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061144.1	NM_004992		A	153296110	G	A	153296110	3	1	308	1	0	0	0	0	1	0	0	0	9432	1348	47	3	295	3	MECP2	23	153296110	Missense_Mutation	SNP	G	TCGA-HP-A5N0-01A-11D-A28X-10	14567122	153296110	1974450	125	44042										
PGD	5226	hgsc.bcm.edu	37	chr1	10468143	10468143	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	cacaggccccacatcaagacCatcttccaaggcattgctgc	7	16	2	1			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr1:10468143C>T	ENST00000270776.8	+	6	503	c.465C>T	c.(463-465)acC>acT	p.T155T	PGD_ENST00000541529.1_Silent_p.T133T|PGD_ENST00000538557.1_Silent_p.T142T	NM_002631.2	NP_002622.2	P52209	6PGD_HUMAN	phosphogluconate dehydrogenase	155					carbohydrate metabolic process (GO:0005975)|D-gluconate metabolic process (GO:0019521)|oxidation-reduction process (GO:0055114)|pentose biosynthetic process (GO:0019322)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, oxidative branch (GO:0009051)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	NADP binding (GO:0050661)|phosphogluconate dehydrogenase (decarboxylating) activity (GO:0004616)			NS(1)|breast(1)|cervix(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	14	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.14e-07)|COAD - Colon adenocarcinoma(227;7.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000294)|Kidney(185;0.000728)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(132;0.00832)|READ - Rectum adenocarcinoma(331;0.0487)	Dacarbazine(DB00851)|Furosemide(DB00695)|Gadopentetate dimeglumine(DB00789)|Ketotifen(DB00920)|Meloxicam(DB00814)|Methotrexate(DB00563)|Ritodrine(DB00867)	ACATCAAGACCATCTTCCAAG	0.498																																					p.T155T		Atlas-SNP	.											.	PGD	39	.	0			c.C465T						.						200	197	198					1																	10468143		2203	4300	6503	SO:0001819	synonymous_variant	5226	exon6			CAAGACCATCTTC	BC000368	CCDS113.1	1p36.22	2012-10-02			ENSG00000142657	ENSG00000142657	1.1.1.43		8891	protein-coding gene	gene with protein product		172200					Standard	NM_002631		Approved		uc001arc.3	P52209	OTTHUMG00000001905	ENST00000270776.8:c.465C>T	chr1.hg19:g.10468143C>T		105.0	0.0		144.0	10.0	NM_002631	A8K2Y9|B4DQJ8|Q9BWD8	Silent	SNP	ENST00000270776.8	hg19	CCDS113.1																																																																																			.	.		0.498	PGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005398.1	NM_002631		T	10468143	C	T	10468143	2	4	309	1	0	0	0	0	0	0	0	1	11796	581	21	3		3	PGD	1	10468143	Silent	SNP	C	TCGA-K7-A5RF-01A-11D-A28X-10		10468143	238782478	1	44043										
UBR4	23352	hgsc.bcm.edu	37	chr1	19499468	19499468	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	gcagccatcttagaaaaatgCtcatccaaagagacctggac	8	11	2	2			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr1:19499468C>T	ENST00000375254.3	-	25	3438	c.3411G>A	c.(3409-3411)gaG>gaA	p.E1137E	UBR4_ENST00000375267.2_Silent_p.E1137E|UBR4_ENST00000375217.2_Silent_p.E1137E|UBR4_ENST00000375226.2_Silent_p.E1137E	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	1137					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		TAGAAAAATGCTCATCCAAAG	0.483																																					p.E1137E		Atlas-SNP	.											.	UBR4	415	.	0			c.G3411A						.						87	81	83					1																	19499468		2203	4300	6503	SO:0001819	synonymous_variant	23352	exon25			AAAATGCTCATCC	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.3411G>A	chr1.hg19:g.19499468C>T		138.0	0.0		157.0	12.0	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Silent	SNP	ENST00000375254.3	hg19	CCDS189.1																																																																																			.	.		0.483	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		T	19499468	C	T	19499468	2	4	309	1	0	0	0	0	0	0	0	1	16919	796	28	3		3	UBR4	1	19499468	Silent	SNP	C	TCGA-K7-A5RF-01A-11D-A28X-10	9031325	19499468	229751153	2	44044										
ZYG11B	79699	hgsc.bcm.edu	37	chr1	53279323	53279323	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	agtcagttactttgcagctgGaattattgcccatttaatat	7	7	1	0			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr1:53279323G>A	ENST00000294353.6	+	11	1956	c.1811G>A	c.(1810-1812)gGa>gAa	p.G604E	ZYG11B_ENST00000443756.2_Missense_Mutation_p.G534E|ZYG11B_ENST00000545132.1_3'UTR	NM_024646.2	NP_078922.1	Q9C0D3	ZY11B_HUMAN	zyg-11 family member B, cell cycle regulator	604										breast(1)|endometrium(1)|kidney(6)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	30						TTTGCAGCTGGAATTATTGCC	0.408																																					p.G604E		Atlas-SNP	.											.	ZYG11B	61	.	0			c.G1811A						.						116	105	109					1																	53279323		2203	4300	6503	SO:0001583	missense	79699	exon11			CAGCTGGAATTAT	AB051517	CCDS30717.1	1p32.3	2013-01-17	2012-12-10	2005-07-11	ENSG00000162378	ENSG00000162378		"ZYG11 cell cycle regulator family"	25820	protein-coding gene	gene with protein product			"zyg-11 homolog (C. elegans)", "zyg-11 homolog B (C. elegans)"	ZYG11		11214970	Standard	NM_024646		Approved	FLJ13456	uc001cuj.3	Q9C0D3	OTTHUMG00000008938	ENST00000294353.6:c.1811G>A	chr1.hg19:g.53279323G>A	ENSP00000294353:p.Gly604Glu	84.0	0.0		97.0	14.0	NM_024646	Q8N2X3|Q9H8L8	Missense_Mutation	SNP	ENST00000294353.6	hg19	CCDS30717.1	.	.	.	.	.	.	.	.	.	.	G	32	5.143609	0.94603	.	.	ENSG00000162378	ENST00000443756;ENST00000294353	T;T	0.49720	0.77;0.77	5.37	5.37	0.77165	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.73768	0.3629	M	0.84948	2.725	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.995;1.0	T	0.78409	-0.2215	10	0.87932	D	0	.	19.1012	0.93275	0.0:0.0:1.0:0.0	.	534;604	B4DK95;Q9C0D3	.;ZY11B_HUMAN	E	534;604	ENSP00000400522:G534E;ENSP00000294353:G604E	ENSP00000294353:G604E	G	+	2	0	ZYG11B	53051911	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.116000	0.94341	2.504000	0.84457	0.655000	0.94253	GGA	.	.		0.408	ZYG11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024749.1	NM_024646		A	53279323	G	A	53279323	3	1	309	1	0	0	0	0	1	0	0	0	18268	1174	41	3	1853	3	ZYG11B	1	53279323	Missense_Mutation	SNP	G	TCGA-K7-A5RF-01A-11D-A28X-10	33779855	53279323	195971298	3	44045										
SLAMF1	6504	hgsc.bcm.edu	37	chr1	160589594	160589594	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	tctggacttgggcatagatcGtaaggctttttttttccact	9	8	1	1			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr1:160589594G>A	ENST00000302035.6	-	5	1185	c.836C>T	c.(835-837)aCg>aTg	p.T279M	SLAMF1_ENST00000355199.3_Missense_Mutation_p.T279M|SLAMF1_ENST00000235739.5_Missense_Mutation_p.T249M|SLAMF1_ENST00000538290.1_Intron	NM_003037.2	NP_003028.1	Q13291	SLAF1_HUMAN	signaling lymphocytic activation molecule family member 1	279					lymphocyte activation (GO:0046649)|positive regulation of cell proliferation (GO:0008284)|regulation of catalytic activity (GO:0050790)|regulation of vesicle fusion (GO:0031338)|signal transduction (GO:0007165)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|phagocytic vesicle (GO:0045335)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)	p.T279K(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(52;4.94e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			GGCATAGATCGTAAGGCTTTT	0.438																																					p.T279M		Atlas-SNP	.											SLAMF1,NS,carcinoma,0,1	SLAMF1	74	.	1	Substitution - Missense(1)	endometrium(1)	c.C836T						.						265	264	264					1																	160589594		2203	4300	6503	SO:0001583	missense	6504	exon5			TAGATCGTAAGGC	U33017	CCDS1207.1	1q23.3	2013-01-11	2003-10-29	2003-10-31	ENSG00000117090	ENSG00000117090		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10903	protein-coding gene	gene with protein product		603492	"signaling lymphocytic activation molecule"	SLAM		7617038	Standard	XM_005245456		Approved	CD150	uc001fwl.4	Q13291	OTTHUMG00000024006	ENST00000302035.6:c.836C>T	chr1.hg19:g.160589594G>A	ENSP00000306190:p.Thr279Met	98.0	1.0		103.0	8.0	NM_003037	Q5W172|Q9HBE8	Missense_Mutation	SNP	ENST00000302035.6	hg19	CCDS1207.1	.	.	.	.	.	.	.	.	.	.	G	13.88	2.368198	0.42003	.	.	ENSG00000117090	ENST00000302035;ENST00000235739;ENST00000355199	T;T;T	0.56444	0.46;0.46;0.46	4.19	4.19	0.49359	.	0.194999	0.34200	N	0.004165	T	0.67458	0.2895	M	0.83852	2.665	0.45216	D	0.998226	D	0.89917	1.0	D	0.91635	0.999	T	0.70974	-0.4726	10	0.66056	D	0.02	-17.8434	12.3258	0.55009	0.0:0.0:1.0:0.0	.	279	Q13291	SLAF1_HUMAN	M	279;249;279	ENSP00000306190:T279M;ENSP00000235739:T249M;ENSP00000347333:T279M	ENSP00000235739:T249M	T	-	2	0	SLAMF1	158856218	1.000000	0.71417	0.935000	0.37517	0.225000	0.24961	3.802000	0.55553	2.632000	0.89209	0.563000	0.77884	ACG	.	.		0.438	SLAMF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060454.1			A	160589594	G	A	160589594	3	1	309	1	0	0	0	0	1	0	0	0	14382	1145	40	1	183	1	SLAMF1	1	160589594	Missense_Mutation	SNP	G	TCGA-K7-A5RF-01A-11D-A28X-10	107310271	160589594	88661027	4	44046										
ZC3H11A	9877	hgsc.bcm.edu	37	chr1	203797536	203797536	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	atatgttgatggccttttccTacctccgagcaaaagtgaga	9	9	0	2			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr1:203797536T>C	ENST00000545588.1	+	4	4111	c.284T>C	c.(283-285)cTa>cCa	p.L95P	ZC3H11A_ENST00000367212.3_Missense_Mutation_p.L95P|ZC3H11A_ENST00000367210.1_Missense_Mutation_p.L95P|ZC3H11A_ENST00000367214.1_Missense_Mutation_p.L95P|ZC3H11A_ENST00000332127.4_Missense_Mutation_p.L95P	NM_001271675.1	NP_001258604.1	O75152	ZC11A_HUMAN	zinc finger CCCH-type containing 11A	95					poly(A)+ mRNA export from nucleus (GO:0016973)		metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32	all_cancers(21;0.0904)|all_epithelial(62;0.234)		BRCA - Breast invasive adenocarcinoma(75;0.109)			GGCCTTTTCCTACCTCCGAGC	0.363																																					p.L95P		Atlas-SNP	.											.	ZC3H11A	71	.	0			c.T284C						.						52	48	49					1																	203797536		2203	4300	6503	SO:0001583	missense	9877	exon7			TTTTCCTACCTCC		CCDS30978.1	1q32.1	2012-07-05	2005-06-02	2005-06-02	ENSG00000058673	ENSG00000058673		"Zinc fingers, CCCH-type domain containing"	29093	protein-coding gene	gene with protein product		613513	"zinc finger CCCH-type domain containing 11A"	ZC3HDC11A		9734811	Standard	NM_014827		Approved	KIAA0663	uc001hac.3	O75152	OTTHUMG00000035909	ENST00000545588.1:c.284T>C	chr1.hg19:g.203797536T>C	ENSP00000438527:p.Leu95Pro	177.0	0.0		214.0	11.0	NM_014827	Q6AHY4|Q6AHY9|Q6AW79|Q6AWA1|Q6PJK4|Q86XZ7	Missense_Mutation	SNP	ENST00000545588.1	hg19	CCDS30978.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.232622	0.79688	.	.	ENSG00000058673	ENST00000453771;ENST00000367214;ENST00000537080;ENST00000367212;ENST00000332127;ENST00000545588;ENST00000367210	T;T;T;T;T	0.53857	0.6;0.6;0.6;0.6;0.6	5.02	5.02	0.67125	.	0.251367	0.34411	N	0.003994	T	0.68384	0.2995	L	0.61218	1.895	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.69150	-0.5221	10	0.45353	T	0.12	-14.2846	14.0227	0.64565	0.0:0.0:0.0:1.0	.	95	O75152	ZC11A_HUMAN	P	95;95;41;95;95;95;95	ENSP00000356183:L95P;ENSP00000356181:L95P;ENSP00000333253:L95P;ENSP00000438527:L95P;ENSP00000356179:L95P	ENSP00000333253:L95P	L	+	2	0	ZC3H11A	202064159	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.629000	0.83207	2.001000	0.58596	0.533000	0.62120	CTA	.	.		0.363	ZC3H11A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087471.3	NM_014827		C	203797536	T	C	203797536	3	2	309	1	0	0	0	0	1	0	0	0	17575	1522	53	2	294	2	ZC3H11A	1	203797536	Missense_Mutation	SNP	T	TCGA-K7-A5RF-01A-11D-A28X-10	43207942	203797536	45453085	5	44047										
CNST	163882	hgsc.bcm.edu	37	chr1	246811218	246811218	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	tgaagataaccaagacgacgActccgatctccttcaagatc	7	12	2	4			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr1:246811218A>G	ENST00000366513.4	+	9	1984	c.1715A>G	c.(1714-1716)gAc>gGc	p.D572G	CNST_ENST00000483271.1_3'UTR|CNST_ENST00000366512.3_Missense_Mutation_p.D572G	NM_152609.2	NP_689822.2	Q6PJW8	CNST_HUMAN	consortin, connexin sorting protein	572					negative regulation of phosphatase activity (GO:0010923)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)	connexin binding (GO:0071253)|phosphatase binding (GO:0019902)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|prostate(1)|urinary_tract(2)	28						CAAGACGACGACTCCGATCTC	0.413																																					p.D572G		Atlas-SNP	.											.	CNST	73	.	0			c.A1715G						.						133	139	137					1																	246811218		2203	4300	6503	SO:0001583	missense	163882	exon9			ACGACGACTCCGA	AK056563	CCDS1628.1, CCDS44343.1	1q44	2012-04-17	2009-11-03	2009-11-03	ENSG00000162852	ENSG00000162852		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	26486	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 64"	613439	"chromosome 1 open reading frame 71"	C1orf71		19864490	Standard	NM_152609		Approved	FLJ32001, PPP1R64	uc001ibp.3	Q6PJW8	OTTHUMG00000040090	ENST00000366513.4:c.1715A>G	chr1.hg19:g.246811218A>G	ENSP00000355470:p.Asp572Gly	117.0	0.0		156.0	9.0	NM_152609	Q5VSY9|Q5VTM7|Q8IYA9|Q8N3L5|Q8NB09|Q8TEI2|Q96MR5	Missense_Mutation	SNP	ENST00000366513.4	hg19	CCDS1628.1	.	.	.	.	.	.	.	.	.	.	A	12.84	2.059340	0.36373	.	.	ENSG00000162852	ENST00000366513;ENST00000366512	T;T	0.27104	1.86;1.69	5.39	3.03	0.35002	.	0.076047	0.47852	N	0.000217	T	0.24431	0.0592	M	0.64404	1.975	0.80722	D	1	B;B	0.27997	0.197;0.197	B;B	0.28465	0.09;0.09	T	0.05582	-1.0876	10	0.87932	D	0	-21.7352	6.2464	0.20820	0.783:0.0:0.0756:0.1414	.	572;572	Q6PJW8;Q6PJW8-2	CNST_HUMAN;.	G	572	ENSP00000355470:D572G;ENSP00000355469:D572G	ENSP00000355469:D572G	D	+	2	0	CNST	244877841	1.000000	0.71417	0.378000	0.26068	0.195000	0.23768	3.907000	0.56348	0.423000	0.26033	0.383000	0.25322	GAC	.	.		0.413	CNST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096780.1	NM_152609		G	246811218	A	G	246811218	3	3	309	1	0	0	0	0	1	0	0	0	3636	275	10	2	1745	2	CNST	1	246811218	Missense_Mutation	SNP	A	TCGA-K7-A5RF-01A-11D-A28X-10	43013682	246811218	2439403	6	44048										
STARD7	56910	hgsc.bcm.edu	37	chr2	96861116	96861116	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	tgggtgcctgtaattgggcgCcgccacagcttaaagtgttt	13	9	0	0			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr2:96861116C>T	ENST00000337288.5	-	2	845	c.462G>A	c.(460-462)cgG>cgA	p.R154R	STARD7_ENST00000462501.1_5'UTR	NM_020151.3	NP_064536.2	Q9NQZ5	STAR7_HUMAN	StAR-related lipid transfer (START) domain containing 7	154	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.					mitochondrion (GO:0005739)	lipid binding (GO:0008289)			endometrium(2)|kidney(1)|large_intestine(1)|lung(8)|stomach(2)	14						TAATTGGGCGCCGCCACAGCT	0.493																																					p.R154R		Atlas-SNP	.											.	STARD7	49	.	0			c.G462A						.						107	83	91					2																	96861116		2203	4299	6502	SO:0001819	synonymous_variant	56910	exon2			TGGGCGCCGCCAC	AF270647	CCDS2017.2	2p11.1	2011-09-12	2007-08-16		ENSG00000084090	ENSG00000084090		"StAR-related lipid transfer (START) domain containing"	18063	protein-coding gene	gene with protein product			"START domain containing 7"				Standard	NM_020151		Approved	GTT1	uc002svm.4	Q9NQZ5	OTTHUMG00000130457	ENST00000337288.5:c.462G>A	chr2.hg19:g.96861116C>T		85.0	0.0		154.0	13.0	NM_020151	D3DXG9|Q53T44|Q6GU43|Q969M6	Silent	SNP	ENST00000337288.5	hg19	CCDS2017.2																																																																																			.	.		0.493	STARD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252848.2			T	96861116	C	T	96861116	2	4	309	1	0	0	0	0	0	0	0	1	15277	726	26	3		3	STARD7	2	96861116	Silent	SNP	C	TCGA-K7-A5RF-01A-11D-A28X-10		96861116	146338257	7	44049										
IWS1	55677	hgsc.bcm.edu	37	chr2	128247456	128247457	+	Frame_Shift_Ins	INS	-	-	T													0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	ttctagatctctctgctcccINStttcttctcttgtcattcct							TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr2:128247456_128247457insT	ENST00000295321.4	-	11	2369_2370	c.2110_2111insA	c.(2110-2112)aggfs	p.R704fs	AC010976.2_ENST00000598065.1_RNA|AC010976.2_ENST00000454503.2_RNA|AC010976.2_ENST00000595561.1_RNA|AC010976.2_ENST00000596439.1_RNA|AC010976.2_ENST00000599001.1_RNA	NM_017969.2	NP_060439.2	Q96ST2	IWS1_HUMAN	IWS1 homolog (S. cerevisiae)	704	Interaction with SUPT6H and ALYREF.				mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|regulation of histone H3-K36 trimethylation (GO:2001253)|regulation of histone H4 acetylation (GO:0090239)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(2)|kidney(6)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0735)		TCTCTGCTCCCTTTCTTCTCTT	0.381																																					p.R704fs		Atlas-Indel,Pindel	.											.	IWS1	61	.	0			c.2111_2112insA						.																																			SO:0001589	frameshift_variant	55677	exon11			.	AK000868	CCDS2146.1	2q14.3	2006-03-17			ENSG00000163166	ENSG00000163166			25467	protein-coding gene	gene with protein product							Standard	NM_017969		Approved	DKFZp761G0123, FLJ10006, FLJ14655, FLJ32319	uc002ton.2	Q96ST2	OTTHUMG00000131527	ENST00000295321.4:c.2111dupA	chr2.hg19:g.128247459_128247459dupT	ENSP00000295321:p.Arg704fs	126.0	0.0		159.0	11.0	NM_017969	Q2TB65|Q6P157|Q8N3E8|Q96MI7|Q9NV97|Q9NWH8	Frame_Shift_Ins	INS	ENST00000295321.4	hg19	CCDS2146.1																																																																																			.	.		0.381	IWS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254384.2	NM_017969		T	128247457	-	T	128247456	7	5	309	1	0	1	1	0	0	0	0	0	7940	681	24	0	364	0	IWS1	2	128247456	Frame_Shift_Ins	INS	-	TCGA-K7-A5RF-01A-11D-A28X-10	31386340	128247456	114951917	8	44050										
CTDSPL	10217	hgsc.bcm.edu	37	chr3	37988645	37988645	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	tacaatgtggaggcccctccAcccagcagccccagtgtgct	10	16	0	0			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr3:37988645A>C	ENST00000273179.5	+	2	203	c.177A>C	c.(175-177)ccA>ccC	p.P59P	CTDSPL_ENST00000443503.2_Silent_p.P59P	NM_001008392.1	NP_001008393.1	O15194	CTDSL_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase-like	59						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			breast(1)|endometrium(2)|large_intestine(4)|skin(1)	8		Melanoma(1037;0.0122)		KIRC - Kidney renal clear cell carcinoma(284;0.0729)|Kidney(284;0.0902)		AGGCCCCTCCACCCAGCAGCC	0.567																																					p.P59P		Atlas-SNP	.											.	CTDSPL	17	.	0			c.A177C						.						76	75	75					3																	37988645		2203	4300	6503	SO:0001819	synonymous_variant	10217	exon2			CCCTCCACCCAGC	D88153	CCDS33734.1, CCDS33735.1	3p21.3	2010-06-21	2003-10-27	2003-10-29	ENSG00000144677	ENSG00000144677	3.1.3.16	"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	16890	protein-coding gene	gene with protein product	"small CTD phosphatase 3", "HYA22 protein", "RB protein serine phosphatase from chromosome 3"	608592	"chromosome 3 open reading frame 8"	C3orf8		9179494, 12543795	Standard	NM_005808		Approved	HYA22, SCP3, PSR1, RBSP3	uc003chg.3	O15194	OTTHUMG00000155942	ENST00000273179.5:c.177A>C	chr3.hg19:g.37988645A>C		50.0	0.0		71.0	5.0	NM_001008392	Q3ZTU0|Q70KI4|Q7Z5Q2	Silent	SNP	ENST00000273179.5	hg19	CCDS33734.1																																																																																			.	.		0.567	CTDSPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342392.1	NM_005808		C	37988645	A	C	37988645	2	2	309	1	0	0	0	0	0	0	0	1	4007	146	6	5		5	CTDSPL	3	37988645	Silent	SNP	A	TCGA-K7-A5RF-01A-11D-A28X-10		37988645	160033785	9	44051										
CSRNP1	64651	hgsc.bcm.edu	37	chr3	39184867	39184867	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	ccagcgtccatgctgggtggCactgaggtgccaggaaggct	16	11	0	1			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr3:39184867C>G	ENST00000273153.5	-	5	1626	c.1449G>C	c.(1447-1449)gtG>gtC	p.V483V	CSRNP1_ENST00000514182.1_Silent_p.V483V	NM_033027.3	NP_149016.2	Q96S65	CSRN1_HUMAN	cysteine-serine-rich nuclear protein 1	483					apoptotic process (GO:0006915)|face morphogenesis (GO:0060325)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|skeletal system morphogenesis (GO:0048705)	nucleus (GO:0005634)	RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(5)|lung(3)|ovary(5)|skin(3)	24						TGCTGGGTGGCACTGAGGTGC	0.557																																					p.V483V		Atlas-SNP	.											.	CSRNP1	59	.	0			c.G1449C						.						50	48	49					3																	39184867		2203	4300	6503	SO:0001819	synonymous_variant	64651	exon5			GGGTGGCACTGAG	AB053121	CCDS2682.1	3p22	2009-04-17	2009-04-17	2009-04-17	ENSG00000144655	ENSG00000144655			14300	protein-coding gene	gene with protein product		606458	"AXIN1 up-regulated 1"	AXUD1		11526492, 17726538	Standard	NM_033027		Approved	URAX1, DKFZp566F164, FAM130B, TAIP-3	uc003cjg.3	Q96S65	OTTHUMG00000131293	ENST00000273153.5:c.1449G>C	chr3.hg19:g.39184867C>G		111.0	0.0		130.0	9.0	NM_033027	Q69YY5	Silent	SNP	ENST00000273153.5	hg19	CCDS2682.1																																																																																			.	.		0.557	CSRNP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254061.1	NM_033027		G	39184867	C	G	39184867	2	3	309	1	0	0	0	0	0	0	0	1	3965	697	25	4		4	CSRNP1	3	39184867	Silent	SNP	C	TCGA-K7-A5RF-01A-11D-A28X-10	1196222	39184867	158837563	10	44052										
SEC22C	9117	hgsc.bcm.edu	37	chr3	42610528	42610528	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	gtaccacgcaggcaaaaaagAtcacggacatggtccacaag	10	11	1	1			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr3:42610528A>C	ENST00000264454.3	-	2	154	c.11T>G	c.(10-12)aTc>aGc	p.I4S	SEC22C_ENST00000493107.1_5'UTR|SEC22C_ENST00000423701.2_Missense_Mutation_p.I4S|SEC22C_ENST00000536332.1_5'UTR|SEC22C_ENST00000417572.1_Missense_Mutation_p.I4S|SEC22C_ENST00000273156.7_Missense_Mutation_p.I4S			Q9BRL7	SC22C_HUMAN	SEC22 vesicle trafficking protein homolog C (S. cerevisiae)	4					ER to Golgi vesicle-mediated transport (GO:0006888)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)	3				KIRC - Kidney renal clear cell carcinoma(284;0.222)		GGCAAAAAAGATCACGGACAT	0.507																																					p.I4S		Atlas-SNP	.											.	SEC22C	27	.	0			c.T11G						.						69	61	63					3																	42610528		2203	4300	6503	SO:0001583	missense	9117	exon2			AAAAAGATCACGG	AF039568	CCDS2699.1, CCDS2700.1, CCDS56246.1	3p24.3-p22.1	2006-04-25	2006-04-25	2006-04-25	ENSG00000093183	ENSG00000093183			16828	protein-coding gene	gene with protein product		604028	"SEC22 vesicle trafficking protein-like 3 (S. cerevisiae)"	SEC22L3		9501016, 11001058	Standard	NM_004206		Approved	MGC13261, MGC5373	uc003clj.3	Q9BRL7	OTTHUMG00000131797	ENST00000264454.3:c.11T>G	chr3.hg19:g.42610528A>C	ENSP00000264454:p.Ile4Ser	250.0	0.0		304.0	21.0	NM_001201584	O95152|Q68CX3|Q6UW18	Missense_Mutation	SNP	ENST00000264454.3	hg19	CCDS2700.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.578789	0.86645	.	.	ENSG00000093183	ENST00000423701;ENST00000273156;ENST00000417572;ENST00000264454;ENST00000456515;ENST00000450981;ENST00000416880;ENST00000420163	T;T;T;T;T;T;T;T	0.29655	1.56;1.56;1.56;1.56;1.56;1.56;1.56;1.56	5.41	5.41	0.78517	Longin (1);Longin-like (1);	0.000000	0.85682	D	0.000000	T	0.49712	0.1573	L	0.48362	1.52	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.91635	0.998;0.997;0.999	T	0.51325	-0.8720	10	0.87932	D	0	-5.9336	15.4347	0.75137	1.0:0.0:0.0:0.0	.	4;4;4	Q9BRL7-3;Q9BRL7;Q9BRL7-2	.;SC22C_HUMAN;.	S	4	ENSP00000414576:I4S;ENSP00000273156:I4S;ENSP00000407564:I4S;ENSP00000264454:I4S;ENSP00000391170:I4S;ENSP00000397170:I4S;ENSP00000391957:I4S;ENSP00000408242:I4S	ENSP00000264454:I4S	I	-	2	0	SEC22C	42585532	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.671000	0.91174	2.040000	0.60383	0.533000	0.62120	ATC	.	.		0.507	SEC22C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254734.1	NM_004206		C	42610528	A	C	42610528	3	2	309	1	0	0	0	0	1	0	0	0	14005	333	12	5	970	5	SEC22C	3	42610528	Missense_Mutation	SNP	A	TCGA-K7-A5RF-01A-11D-A28X-10	3425661	42610528	155411902	11	44053										
AP2M1	1173	hgsc.bcm.edu	37	chr3	183898651	183898651	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	atgtagacaaaagaagagcaGtcacagatcaccagccaggt	10	9	2	4	rs375328073		TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr3:183898651G>T	ENST00000292807.5	+	6	592	c.444G>T	c.(442-444)caG>caT	p.Q148H	EIF2B5_ENST00000444495.1_Intron|AP2M1_ENST00000382456.3_Missense_Mutation_p.Q146H|AP2M1_ENST00000411763.2_Missense_Mutation_p.Q173H|AP2M1_ENST00000439647.1_Missense_Mutation_p.Q146H|AP2M1_ENST00000461733.1_3'UTR	NM_004068.3	NP_004059.2	Q96CW1	AP2M1_HUMAN	adaptor-related protein complex 2, mu 1 subunit	148					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of protein localization to plasma membrane (GO:1903077)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(1)	18	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.92e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			AAGAAGAGCAGTCACAGATCA	0.517																																					p.Q146H		Atlas-SNP	.											.	AP2M1	35	.	0			c.G438T						.						147	156	153					3																	183898651		2045	4204	6249	SO:0001583	missense	1173	exon5			AGAGCAGTCACAG	U36188	CCDS43177.1, CCDS43178.1	3q28	2008-07-18			ENSG00000161203	ENSG00000161203			564	protein-coding gene	gene with protein product	"clathrin-associated/assembly/adaptor protein, medium 1", "plasma membrane adaptor AP-2 50kDA protein", "clathrin coat adaptor protein AP50", "clathrin adaptor complex AP2, mu subunit", "HA2 50 kDA subunit", "clathrin assembly protein complex 2 medium chain", "AP-2 mu 2 chain"	601024		CLAPM1		8595912	Standard	NM_004068		Approved	AP50, mu2	uc003fmw.3	Q96CW1	OTTHUMG00000156822	ENST00000292807.5:c.444G>T	chr3.hg19:g.183898651G>T	ENSP00000292807:p.Gln148His	197.0	0.0		231.0	19.0	NM_001025205	A6NE12|D3DNT1|P20172|P53679	Missense_Mutation	SNP	ENST00000292807.5	hg19	CCDS43177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.54|15.54	2.864449|2.864449	0.51482|0.51482	.|.	.|.	ENSG00000161203|ENSG00000161203	ENST00000382456;ENST00000411763;ENST00000292807;ENST00000540821;ENST00000539646;ENST00000448139;ENST00000439647;ENST00000432591|ENST00000431779	T;T;T;T|.	0.65549|.	-0.16;-0.16;-0.15;-0.16|.	5.54|5.54	0.825|0.825	0.18824|0.18824	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.63271|0.63271	0.2497|0.2497	M|M	0.68317|0.68317	2.08|2.08	0.80722|0.80722	D|D	1|1	P;P;P;P|.	0.51240|.	0.753;0.905;0.773;0.943|.	B;B;P;P|.	0.48089|.	0.297;0.358;0.566;0.561|.	T|T	0.60692|0.60692	-0.7213|-0.7213	10|6	0.51188|0.49607	T|T	0.08|0.09	.|.	10.0459|10.0459	0.42186|0.42186	0.3244:0.0:0.6756:0.0|0.3244:0.0:0.6756:0.0	.|.	18;148;173;146|.	B4DTI4;Q96CW1;E9PFW3;Q96CW1-2|.	.;AP2M1_HUMAN;.;.|.	H|F	146;173;148;88;133;150;146;148|179	ENSP00000371894:Q146H;ENSP00000403362:Q173H;ENSP00000292807:Q148H;ENSP00000409081:Q146H|.	ENSP00000292807:Q148H|ENSP00000404326:V179F	Q|V	+|+	3|1	2|0	AP2M1|AP2M1	185381345|185381345	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.943000|0.943000	0.58893|0.58893	2.026000|2.026000	0.41069|0.41069	-0.031000|-0.031000	0.13781|0.13781	-0.768000|-0.768000	0.03414|0.03414	CAG|GTC	.	.		0.517	AP2M1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346013.1	NM_004068		T	183898651	G	T	183898651	3	4	309	1	0	0	0	0	1	0	0	0	742	1029	36	3	459	3	AP2M1	3	183898651	Missense_Mutation	SNP	G	TCGA-K7-A5RF-01A-11D-A28X-10	141288123	183898651	14123779	12	44054										
KLB	152831	hgsc.bcm.edu	37	chr4	39448160	39448160	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	gtttgctctggattgggcctCggtccttcccactggcaacc	11	14	1	0			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr4:39448160C>T	ENST00000257408.4	+	4	1911	c.1814C>T	c.(1813-1815)tCg>tTg	p.S605L		NM_175737.3	NP_783864.1	Q86Z14	KLOTB_HUMAN	klotho beta	605	Glycosyl hydrolase-1 2.				carbohydrate metabolic process (GO:0005975)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fibroblast growth factor binding (GO:0017134)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|skin(6)	29						GATTGGGCCTCGGTCCTTCCC	0.542																																					p.S605L		Atlas-SNP	.											.	KLB	95	.	0			c.C1814T						.						108	113	112					4																	39448160		2203	4300	6503	SO:0001583	missense	152831	exon4			GGGCCTCGGTCCT	AB079373	CCDS3451.1	4p14	2008-02-05			ENSG00000134962	ENSG00000134962			15527	protein-coding gene	gene with protein product		611135					Standard	NM_175737		Approved		uc003gua.3	Q86Z14	OTTHUMG00000128577	ENST00000257408.4:c.1814C>T	chr4.hg19:g.39448160C>T	ENSP00000257408:p.Ser605Leu	93.0	0.0		136.0	9.0	NM_175737	Q2M3K8	Missense_Mutation	SNP	ENST00000257408.4	hg19	CCDS3451.1	.	.	.	.	.	.	.	.	.	.	C	12.36	1.914619	0.33815	.	.	ENSG00000134962	ENST00000257408	T	0.31769	1.48	5.68	3.69	0.42338	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.138816	0.49305	D	0.000151	T	0.09642	0.0237	N	0.02315	-0.6	0.26490	N	0.974953	B;B	0.11235	0.004;0.004	B;B	0.08055	0.003;0.003	T	0.13818	-1.0495	10	0.25106	T	0.35	-18.3494	2.9688	0.05916	0.0:0.4901:0.2795:0.2304	.	596;605	B7ZL50;Q86Z14	.;KLOTB_HUMAN	L	605	ENSP00000257408:S605L	ENSP00000257408:S605L	S	+	2	0	KLB	39124555	0.941000	0.31946	0.956000	0.39512	0.957000	0.61999	3.160000	0.50739	2.683000	0.91414	0.484000	0.47621	TCG	.	.		0.542	KLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250429.1	NM_175737		T	39448160	C	T	39448160	3	4	309	1	0	0	0	0	1	0	0	0	8341	893	31	1	1828	1	KLB	4	39448160	Missense_Mutation	SNP	C	TCGA-K7-A5RF-01A-11D-A28X-10		39448160	151706116	13	44055										
CORIN	10699	hgsc.bcm.edu	37	chr4	47663761	47663761	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	atcaggcatcaggcaggtttGattgtctgaattttcctctg	10	8	4	2			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr4:47663761G>T	ENST00000273857.4	-	12	1701	c.1702C>A	c.(1702-1704)Caa>Aaa	p.Q568K	CORIN_ENST00000508498.1_Missense_Mutation_p.Q429K|CORIN_ENST00000504584.1_Missense_Mutation_p.Q531K|CORIN_ENST00000505909.1_Missense_Mutation_p.Q531K|CORIN_ENST00000502252.1_Missense_Mutation_p.Q501K	NM_006587.2	NP_006578.2	Q9Y5Q5	CORIN_HUMAN	corin, serine peptidase	568	FZ 2. {ECO:0000255|PROSITE- ProRule:PRU00090}.				female pregnancy (GO:0007565)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of blood pressure (GO:0008217)|regulation of renal sodium excretion (GO:0035813)|regulation of systemic arterial blood pressure by atrial natriuretic peptide (GO:0003050)	cell surface (GO:0009986)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)			NS(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(18)|lung(39)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)	79						AGGCAGGTTTGATTGTCTGAA	0.398																																					p.Q568K		Atlas-SNP	.											.	CORIN	154	.	0			c.C1702A						.						117	112	114					4																	47663761		2203	4300	6503	SO:0001583	missense	10699	exon12			AGGTTTGATTGTC	AF133845	CCDS3477.1, CCDS63958.1, CCDS75122.1	4p13-p12	2011-08-31	2005-08-17		ENSG00000145244	ENSG00000145244		"Serine peptidases / Transmembrane"	19012	protein-coding gene	gene with protein product		605236	"corin, serine protease"			10329693	Standard	NM_006587		Approved	PRSC, CRN, ATC2, Lrp4, TMPRSS10	uc003gxm.3	Q9Y5Q5	OTTHUMG00000099441	ENST00000273857.4:c.1702C>A	chr4.hg19:g.47663761G>T	ENSP00000273857:p.Gln568Lys	64.0	0.0		108.0	6.0	NM_006587	B0ZBE3|Q2TBD2|Q4W5E5|Q4W5G6|Q9UHY2	Missense_Mutation	SNP	ENST00000273857.4	hg19	CCDS3477.1	.	.	.	.	.	.	.	.	.	.	G	14.42	2.530200	0.45073	.	.	ENSG00000145244	ENST00000273857;ENST00000508498;ENST00000502252;ENST00000505909;ENST00000504584	T;T;T;T;T	0.74737	-0.87;-0.87;-0.87;-0.87;-0.87	5.9	4.03	0.46877	Frizzled domain (5);	0.376630	0.28677	N	0.014501	T	0.69433	0.3110	L	0.39245	1.2	0.37790	D	0.927328	B;P;B;B	0.38617	0.134;0.64;0.015;0.009	B;B;B;B	0.40602	0.077;0.334;0.015;0.038	T	0.74515	-0.3640	10	0.46703	T	0.11	.	16.0384	0.80648	0.0:0.2534:0.7466:0.0	.	531;531;501;568	B7Z4R1;B4E2W9;B4E1Y7;Q9Y5Q5	.;.;.;CORIN_HUMAN	K	568;429;501;531;531	ENSP00000273857:Q568K;ENSP00000425597:Q429K;ENSP00000424212:Q501K;ENSP00000425401:Q531K;ENSP00000423216:Q531K	ENSP00000273857:Q568K	Q	-	1	0	CORIN	47358518	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	0.817000	0.27281	1.458000	0.47871	0.650000	0.86243	CAA	.	.		0.398	CORIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216906.2			T	47663761	G	T	47663761	3	4	309	1	0	0	0	0	1	0	0	0	3754	1299	45	3	1470	3	CORIN	4	47663761	Missense_Mutation	SNP	G	TCGA-K7-A5RF-01A-11D-A28X-10	8215601	47663761	143490515	14	44056										
CASP6	839	hgsc.bcm.edu	37	chr4	110615726	110615726	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	ccaaccaggctgtgacacttGtctcctttgaacaagccagt	8	13	1	2			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr4:110615726G>C	ENST00000265164.2	-	5	515	c.438C>G	c.(436-438)gaC>gaG	p.D146E	CASP6_ENST00000510324.1_5'UTR|AC004067.5_ENST00000608733.1_RNA|CASP6_ENST00000352981.3_Missense_Mutation_p.D57E	NM_001226.3	NP_001217.2	P55212	CASP6_HUMAN	caspase 6, apoptosis-related cysteine peptidase	146					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|epithelial cell differentiation (GO:0030855)|proteolysis (GO:0006508)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|identical protein binding (GO:0042802)			breast(1)|endometrium(1)|large_intestine(3)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	8		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000171)		TGTGACACTTGTCTCCTTTGA	0.383																																					p.D146E		Atlas-SNP	.											.	CASP6	25	.	0			c.C438G						.						101	90	94					4																	110615726		2203	4300	6503	SO:0001583	missense	839	exon5			ACACTTGTCTCCT	U20536	CCDS3684.1, CCDS3685.1	4q25	2008-02-05	2005-08-17		ENSG00000138794	ENSG00000138794		"Caspases"	1507	protein-coding gene	gene with protein product		601532	"caspase 6, apoptosis-related cysteine protease"			8780721, 7796396	Standard	XM_005263271		Approved	MCH2	uc003hzn.1	P55212	OTTHUMG00000131914	ENST00000265164.2:c.438C>G	chr4.hg19:g.110615726G>C	ENSP00000265164:p.Asp146Glu	216.0	0.0		271.0	16.0	NM_001226	Q9BQE7	Missense_Mutation	SNP	ENST00000265164.2	hg19	CCDS3684.1	.	.	.	.	.	.	.	.	.	.	G	19.65	3.866945	0.72065	.	.	ENSG00000138794	ENST00000352981;ENST00000265164;ENST00000503684	T;T;T	0.52983	0.64;0.64;0.64	5.31	4.47	0.54385	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase precursor p45, core (1);Peptidase C14, ICE, catalytic subunit p20 (1);	0.087933	0.85682	D	0.000000	T	0.56108	0.1963	M	0.74881	2.28	0.80722	D	1	B;B	0.31837	0.073;0.342	B;B	0.42282	0.098;0.382	T	0.60974	-0.7156	10	0.87932	D	0	.	11.6539	0.51306	0.1452:0.0:0.8548:0.0	.	57;146	P55212-2;P55212	.;CASP6_HUMAN	E	57;146;128	ENSP00000285333:D57E;ENSP00000265164:D146E;ENSP00000427669:D128E	ENSP00000265164:D146E	D	-	3	2	CASP6	110835175	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.760000	0.55235	1.361000	0.45981	0.650000	0.86243	GAC	.	.		0.383	CASP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254866.1	NM_001226		C	110615726	G	C	110615726	3	2	309	1	0	0	0	0	1	0	0	0	2677	1368	48	4	455	4	CASP6	4	110615726	Missense_Mutation	SNP	G	TCGA-K7-A5RF-01A-11D-A28X-10	62951965	110615726	80538550	15	44057										
IQGAP2	10788	hgsc.bcm.edu	37	chr5	75893275	75893275	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	catcctcagggcaggctgcaGtggaccatatcaatgctgtc	11	12	2	0			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr5:75893275G>T	ENST00000274364.6	+	10	1216	c.919G>T	c.(919-921)Gtg>Ttg	p.V307L	IQGAP2_ENST00000379730.3_5'UTR	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	307					negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		GCAGGCTGCAGTGGACCATAT	0.532																																					p.V307L		Atlas-SNP	.											.	IQGAP2	186	.	0			c.G919T						.						104	99	101					5																	75893275		2203	4300	6503	SO:0001583	missense	10788	exon10			GCTGCAGTGGACC	U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.919G>T	chr5.hg19:g.75893275G>T	ENSP00000274364:p.Val307Leu	168.0	0.0		184.0	13.0	NM_006633	A8K4V1|B7Z8A4|J3KR91	Missense_Mutation	SNP	ENST00000274364.6	hg19	CCDS34188.1	.	.	.	.	.	.	.	.	.	.	G	13.82	2.350147	0.41599	.	.	ENSG00000145703	ENST00000274364;ENST00000514350;ENST00000505766	T;T;T	0.30981	4.22;1.51;4.17	5.88	4.84	0.62591	.	0.000000	0.85682	D	0.000000	T	0.33352	0.0860	L	0.41906	1.305	0.80722	D	1	P	0.40794	0.729	P	0.50352	0.638	T	0.01879	-1.1255	10	0.02654	T	1	-25.8355	15.9192	0.79547	0.0749:0.0:0.9251:0.0	.	307	Q13576	IQGA2_HUMAN	L	307;280;257	ENSP00000274364:V307L;ENSP00000423672:V280L;ENSP00000421097:V257L	ENSP00000274364:V307L	V	+	1	0	IQGAP2	75929031	1.000000	0.71417	0.966000	0.40874	0.668000	0.39293	5.952000	0.70282	2.788000	0.95919	0.650000	0.86243	GTG	.	.		0.532	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633		T	75893275	G	T	75893275	3	4	309	1	0	0	0	0	1	0	0	0	7824	1029	36	3	957	3	IQGAP2	5	75893275	Missense_Mutation	SNP	G	TCGA-K7-A5RF-01A-11D-A28X-10		75893275	105021985	16	44058										
MSH3	4437	hgsc.bcm.edu	37	chr5	80063794	80063794	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	tgattgtcaaaactttatatCacctaaagtcagaatttcaa	4	7	4	2			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr5:80063794C>G	ENST00000265081.6	+	14	2019	c.1939C>G	c.(1939-1941)Cac>Gac	p.H647D		NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	647					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		AACTTTATATCACCTAAAGTC	0.323								Mismatch excision repair (MMR)																													p.H647D	Melanoma(88;1010 1399 13793 26548 36275)	Atlas-SNP	.											.	MSH3	129	.	0			c.C1939G						.						67	69	68					5																	80063794		2203	4299	6502	SO:0001583	missense	4437	exon14			TTATATCACCTAA	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"Divergent upstream protein", "Mismatch repair protein 1"	600887	"mutS (E. coli) homolog 3", "mutS homolog 3 (E. coli)"				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.1939C>G	chr5.hg19:g.80063794C>G	ENSP00000265081:p.His647Asp	99.0	0.0		125.0	9.0	NM_002439	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Missense_Mutation	SNP	ENST00000265081.6	hg19	CCDS34195.1	.	.	.	.	.	.	.	.	.	.	C	8.922	0.961380	0.18583	.	.	ENSG00000113318	ENST00000265081;ENST00000535995	D	0.90261	-2.64	5.66	3.89	0.44902	DNA mismatch repair protein MutS, core (3);	0.342267	0.40144	N	0.001177	T	0.82167	0.4978	N	0.14661	0.345	0.09310	N	1	P	0.39920	0.695	B	0.43331	0.416	T	0.71941	-0.4440	9	.	.	.	-1.8806	7.0908	0.25283	0.1389:0.7176:0.0:0.1436	.	647	P20585	MSH3_HUMAN	D	647;638	ENSP00000265081:H647D	.	H	+	1	0	MSH3	80099550	1.000000	0.71417	0.211000	0.23655	0.692000	0.40212	2.413000	0.44618	0.864000	0.35578	0.609000	0.83330	CAC	.	.		0.323	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439		G	80063794	C	G	80063794	3	3	309	1	0	0	0	0	1	0	0	0	9880	826	29	4	1993	4	MSH3	5	80063794	Missense_Mutation	SNP	C	TCGA-K7-A5RF-01A-11D-A28X-10	4170519	80063794	100851466	17	44059										
SH3TC2	79628	hgsc.bcm.edu	37	chr5	148407630	148407630	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	aatgctccattgagaatgtgGatggcctcctcgaagtacac	10	10	0	1			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr5:148407630G>T	ENST00000515425.1	-	11	1766	c.1665C>A	c.(1663-1665)atC>atA	p.I555I	SH3TC2_ENST00000512049.1_Silent_p.I548I|SH3TC2_ENST00000394358.2_Silent_p.I440I|SH3TC2_ENST00000513340.1_5'Flank|SH3TC2_ENST00000538184.1_Silent_p.I102I	NM_024577.3	NP_078853.2	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	555					cell death (GO:0008219)|peripheral nervous system myelin maintenance (GO:0032287)|regulation of ERBB signaling pathway (GO:1901184)|regulation of intracellular protein transport (GO:0033157)	cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGAGAATGTGGATGGCCTCCT	0.542																																					p.I555I		Atlas-SNP	.											.	SH3TC2	178	.	0			c.C1665A						.						110	105	106					5																	148407630		2203	4300	6503	SO:0001819	synonymous_variant	79628	exon11			AATGTGGATGGCC	AK127248	CCDS4293.1	5q32	2014-09-17			ENSG00000169247	ENSG00000169247		"Tetratricopeptide (TTC) repeat domain containing"	29427	protein-coding gene	gene with protein product		608206				14574644	Standard	NM_024577		Approved	KIAA1985, CMT4C	uc003lpu.3	Q8TF17	OTTHUMG00000129930	ENST00000515425.1:c.1665C>A	chr5.hg19:g.148407630G>T		186.0	0.0		262.0	17.0	NM_024577	B3KWE5|Q14CC0|Q14CF5|Q9H8I5	Silent	SNP	ENST00000515425.1	hg19	CCDS4293.1																																																																																			.	.		0.542	SH3TC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252186.2	NM_024577		T	148407630	G	T	148407630	2	4	309	1	0	0	0	0	0	0	0	1	14277	1164	41	3		3	SH3TC2	5	148407630	Silent	SNP	G	TCGA-K7-A5RF-01A-11D-A28X-10	68343836	148407630	32507630	18	44060										
CNOT6	57472	hgsc.bcm.edu	37	chr5	179956354	179956354	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	tctgaggaagcagcaaatggAaagaaatcccactgggcaga	12	8	1	3			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr5:179956354A>G	ENST00000393356.1	+	4	502	c.78A>G	c.(76-78)ggA>ggG	p.G26G	CNOT6_ENST00000502447.1_3'UTR|CNOT6_ENST00000261951.4_Silent_p.G26G			Q9ULM6	CNOT6_HUMAN	CCR4-NOT transcription complex, subunit 6	26					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|gene silencing by miRNA (GO:0035195)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, no-go decay (GO:0070966)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of ligand-dependent nuclear receptor transcription coactivator activity (GO:2000327)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	exoribonuclease activity (GO:0004532)|metal ion binding (GO:0046872)|poly(A)-specific ribonuclease activity (GO:0004535)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|skin(1)	23	all_cancers(89;3.3e-05)|all_epithelial(37;7.38e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00543)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.023)		CAGCAAATGGAAAGAAATCCC	0.393																																					p.G26G		Atlas-SNP	.											.	CNOT6	47	.	0			c.A78G						.						75	85	82					5																	179956354		2203	4300	6503	SO:0001819	synonymous_variant	57472	exon2			AAATGGAAAGAAA	AB033020	CCDS4455.1	5q35.3	2014-06-17			ENSG00000113300	ENSG00000113300			14099	protein-coding gene	gene with protein product		608951				11889047	Standard	XM_005265953		Approved	CCR4, KIAA1194, Ccr4a	uc003mlx.3	Q9ULM6	OTTHUMG00000130935	ENST00000393356.1:c.78A>G	chr5.hg19:g.179956354A>G		252.0	0.0		316.0	25.0	NM_015455	A7MD46|D3DWR0	Silent	SNP	ENST00000393356.1	hg19	CCDS4455.1																																																																																			.	.		0.393	CNOT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253532.1	NM_015455		G	179956354	A	G	179956354	2	3	309	1	0	0	0	0	0	0	0	1	3624	233	9	2		2	CNOT6	5	179956354	Silent	SNP	A	TCGA-K7-A5RF-01A-11D-A28X-10	31548724	179956354	958906	19	44061										
FLT4	2324	hgsc.bcm.edu	37	chr5	180048894	180048894	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	ttggattcgatggtgaagccGtcggggatggctgtggaggg	20	5	0	1	rs143634822		TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr5:180048894G>A	ENST00000261937.6	-	13	1746	c.1668C>T	c.(1666-1668)gaC>gaT	p.D556D	FLT4_ENST00000502649.1_Silent_p.D556D|FLT4_ENST00000393347.3_Silent_p.D556D|FLT4_ENST00000424276.2_5'UTR	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	556	Ig-like C2-type 6.				blood vessel morphogenesis (GO:0048514)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|lymph vessel development (GO:0001945)|lymphangiogenesis (GO:0001946)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein autophosphorylation (GO:0046777)|regulation of blood vessel remodeling (GO:0060312)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(6)|large_intestine(5)|liver(2)|lung(37)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TGGTGAAGCCGTCGGGGATGG	0.647																																					p.D556D	Colon(97;1075 1466 27033 27547 35871)	Atlas-SNP	.											FLT4_ENST00000376868,NS,carcinoma,0,3	FLT4	356	.	0			c.C1668T						.	G	,	1,4405	2.1+/-5.4	0,1,2202	76	90	85		1668,1668	-5.9	0.8	5	dbSNP_134	85	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous	FLT4	NM_002020.4,NM_182925.4	,	0,1,6501	AA,AG,GG		0.0,0.0227,0.0077	,	556/1299,556/1364	180048894	1,13003	2203	4299	6502	SO:0001819	synonymous_variant	2324	exon13			GAAGCCGTCGGGG	X68203	CCDS4457.1, CCDS43412.1	5q34-q35	2013-01-29			ENSG00000037280	ENSG00000037280	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3767	protein-coding gene	gene with protein product		136352				1319394	Standard	NM_002020		Approved	VEGFR3, PCL	uc003mlz.4	P35916	OTTHUMG00000130931	ENST00000261937.6:c.1668C>T	chr5.hg19:g.180048894G>A		132.0	0.0		194.0	14.0	NM_182925	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Silent	SNP	ENST00000261937.6	hg19	CCDS4457.1																																																																																			.	G|1.000;A|0.000		0.647	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4			A	180048894	G	A	180048894	2	1	309	1	0	0	0	0	0	0	0	1	5952	1136	40	1		1	FLT4	5	180048894	Silent	SNP	G	TCGA-K7-A5RF-01A-11D-A28X-10	92540	180048894	866366	20	44062										
OR2V2	285659	hgsc.bcm.edu	37	chr5	180582509	180582509	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	ctatccttgttgaagctggcCtgtgtagacacatccctgtt	9	11	0	2			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr5:180582509C>T	ENST00000328275.1	+	1	567	c.567C>T	c.(565-567)gcC>gcT	p.A189A		NM_206880.1	NP_996763.1	Q96R30	OR2V2_HUMAN	olfactory receptor, family 2, subfamily V, member 2	189						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20	all_cancers(89;8.26e-06)|all_epithelial(37;1.02e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0684)	all_cancers(40;0.0103)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.0652)|all_lung(500;0.149)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TGAAGCTGGCCTGTGTAGACA	0.463																																					p.A189A		Atlas-SNP	.											.	OR2V2	56	.	0			c.C567T						.						343	331	335					5																	180582509		2203	4300	6503	SO:0001819	synonymous_variant	285659	exon1			GCTGGCCTGTGTA	AL161615	CCDS4461.1	5q35.3	2012-08-09			ENSG00000182613	ENSG00000182613		"GPCR / Class A : Olfactory receptors"	15341	protein-coding gene	gene with protein product				OR2V3			Standard	NM_206880		Approved	OST713	uc011dhj.2	Q96R30	OTTHUMG00000130933	ENST00000328275.1:c.567C>T	chr5.hg19:g.180582509C>T		192.0	0.0		249.0	20.0	NM_206880	Q6IFL6|Q8NGV1	Silent	SNP	ENST00000328275.1	hg19	CCDS4461.1																																																																																			.	.		0.463	OR2V2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253529.1			T	180582509	C	T	180582509	2	4	309	1	0	0	0	0	0	0	0	1	11040	668	24	3		3	OR2V2	5	180582509	Silent	SNP	C	TCGA-K7-A5RF-01A-11D-A28X-10	533615	180582509	332751	21	44063										
EPM2A	7957	hgsc.bcm.edu	37	chr6	145948714	145948714	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	atcacatactggagccagccGcagacagccgcggtggagcg	14	13	1	1			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr6:145948714G>A	ENST00000367519.3	-	4	1359	c.834C>T	c.(832-834)tgC>tgT	p.C278C		NM_005670.3	NP_005661.1	O95278	EPM2A_HUMAN	epilepsy, progressive myoclonus type 2A, Lafora disease (laforin)	278	Tyrosine-protein phosphatase.				autophagy (GO:0006914)|carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen metabolic process (GO:0005977)|habituation (GO:0046959)|inositol phosphate dephosphorylation (GO:0046855)|nervous system development (GO:0007399)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polysome (GO:0005844)	carbohydrate phosphatase activity (GO:0019203)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|starch binding (GO:2001070)			kidney(1)|large_intestine(2)|lung(2)|pancreas(1)|skin(1)	7		Ovarian(120;0.162)		OV - Ovarian serous cystadenocarcinoma(155;3.38e-07)|GBM - Glioblastoma multiforme(68;0.0203)		GGAGCCAGCCGCAGACAGCCG	0.627																																					p.C278C		Atlas-SNP	.											.	EPM2A	21	.	0			c.C834T	GRCh37	HM0660	EPM2A	M		.						49	51	50					6																	145948714		2203	4300	6503	SO:0001819	synonymous_variant	7957	exon4			CCAGCCGCAGACA	AF284580	CCDS5206.1	6q24	2011-06-09			ENSG00000112425	ENSG00000112425		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	3413	protein-coding gene	gene with protein product		607566	"epilepsy, progressive myoclonus type 2, Lafora disease (laforin)"			9222970, 7485240	Standard	XM_006715564		Approved	LDE, LD	uc003qkw.3	B3EWF7	OTTHUMG00000015747	ENST00000367519.3:c.834C>T	chr6.hg19:g.145948714G>A		82.0	0.0		74.0	4.0	NM_005670	B3KMU5|B4DRZ2|O95483|Q5T3F5|Q6IS15|Q8IU96|Q8IX24|Q8IX25|Q9BS66|Q9UEN2	Silent	SNP	ENST00000367519.3	hg19	CCDS5206.1	.	.	.	.	.	.	.	.	.	.	G	9.640	1.138831	0.21123	.	.	ENSG00000112425	ENST00000435470	.	.	.	5.72	-3.8	0.04307	.	.	.	.	.	T	0.52533	0.1740	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.62464	-0.6849	4	.	.	.	-23.8817	15.1704	0.72869	0.5853:0.0:0.4147:0.0	.	.	.	.	V	198	.	.	A	-	2	0	EPM2A	145990407	0.672000	0.27530	0.387000	0.26183	0.922000	0.55478	-0.036000	0.12185	-0.644000	0.05465	-0.259000	0.10710	GCG	.	.		0.627	EPM2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042564.1			A	145948714	G	A	145948714	2	1	309	1	0	0	0	0	0	0	0	1	5185	1079	38	1		1	EPM2A	6	145948714	Silent	SNP	G	TCGA-K7-A5RF-01A-11D-A28X-10		145948714	25166353	22	44064										
EIF3B	8662	hgsc.bcm.edu	37	chr7	2406209	2406209	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	gaatgaccctggatacgcttAgcatctatgaaactcctgta	8	10	1	2			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr7:2406209A>C	ENST00000360876.4	+	8	1395	c.1339A>C	c.(1339-1341)Agc>Cgc	p.S447R	EIF3B_ENST00000397011.2_Missense_Mutation_p.S447R	NM_001037283.1	NP_001032360.1			eukaryotic translation initiation factor 3, subunit B											breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|skin(1)	24		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0833)|OV - Ovarian serous cystadenocarcinoma(56;7.76e-14)		GGATACGCTTAGCATCTATGA	0.483																																					p.S447R		Atlas-SNP	.											.	EIF3B	54	.	0			c.A1339C						.						84	83	83					7																	2406209		2203	4300	6503	SO:0001583	missense	8662	exon8			ACGCTTAGCATCT	U62583	CCDS5332.1	7p22	2013-02-12	2007-07-27	2007-07-27	ENSG00000106263	ENSG00000106263		"RNA binding motif (RRM) containing"	3280	protein-coding gene	gene with protein product		603917	"eukaryotic translation initiation factor 3, subunit 9 eta, 116kDa"	EIF3S9		8995410	Standard	NM_001037283		Approved	PRT1, eIF3b	uc003sly.3	P55884	OTTHUMG00000022839	ENST00000360876.4:c.1339A>C	chr7.hg19:g.2406209A>C	ENSP00000354125:p.Ser447Arg	131.0	0.0		172.0	17.0	NM_001037283		Missense_Mutation	SNP	ENST00000360876.4	hg19	CCDS5332.1	.	.	.	.	.	.	.	.	.	.	A	28.2	4.899914	0.91962	.	.	ENSG00000106263	ENST00000314800;ENST00000360876;ENST00000397011;ENST00000489558	T;T	0.04917	3.53;3.53	5.54	5.54	0.83059	WD40/YVTN repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.23965	0.0580	M	0.73753	2.245	0.80722	D	1	D	0.59767	0.986	D	0.63877	0.919	T	0.00529	-1.1687	10	0.87932	D	0	-34.6695	15.7372	0.77853	1.0:0.0:0.0:0.0	.	447	P55884	EIF3B_HUMAN	R	447;447;447;371	ENSP00000354125:S447R;ENSP00000380206:S447R	ENSP00000316638:S447R	S	+	1	0	EIF3B	2372735	1.000000	0.71417	0.990000	0.47175	0.994000	0.84299	9.107000	0.94261	2.120000	0.65058	0.529000	0.55759	AGC	.	.		0.483	EIF3B-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207006.1			C	2406209	A	C	2406209	3	2	309	1	0	0	0	0	1	0	0	0	5015	420	15	5	1369	5	EIF3B	7	2406209	Missense_Mutation	SNP	A	TCGA-K7-A5RF-01A-11D-A28X-10		2406209	156732454	23	44065										
MACC1	346389	hgsc.bcm.edu	37	chr7	20201371	20201371	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	acagttataaattcccatacCtgtaatattgcaactttttg	4	8	0	0			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr7:20201371C>T	ENST00000400331.5	-	4	423	c.115G>A	c.(115-117)Gaa>Aaa	p.E39K	MACC1_ENST00000471019.1_5'Flank|MACC1_ENST00000589011.1_Splice_Site_p.E39K|MACC1_ENST00000332878.4_Splice_Site_p.E39K	NM_182762.3	NP_877439.3	Q6ZN28	MACC1_HUMAN	metastasis associated in colon cancer 1	39					positive regulation of cell division (GO:0051781)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(15)|lung(12)|ovary(2)|prostate(1)|skin(3)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(1)	39						ATTCCCATACCTGTAATATTG	0.338																																					p.E39K		Atlas-SNP	.											.	MACC1	99	.	0			c.G115A						.						111	111	111					7																	20201371		2201	4298	6499	SO:0001630	splice_region_variant	346389	exon4			CCATACCTGTAAT		CCDS5369.1	7p15.3	2008-10-14			ENSG00000183742	ENSG00000183742			30215	protein-coding gene	gene with protein product		612646					Standard	NM_182762		Approved	7A5, SH3BP4L	uc003sus.4	Q6ZN28	OTTHUMG00000128415	ENST00000400331.5:c.115+1G>A	chr7.hg19:g.20201371C>T		36.0	0.0		60.0	7.0	NM_182762	A8MUS5|B2RNR9|Q6ZQN8|Q7Z5A5	Missense_Mutation	SNP	ENST00000400331.5	hg19	CCDS5369.1	.	.	.	.	.	.	.	.	.	.	C	11.76	1.733500	0.30684	.	.	ENSG00000183742	ENST00000400331;ENST00000332878	T;T	0.09630	2.96;2.96	5.51	5.51	0.81932	.	0.427052	0.22900	N	0.054274	T	0.11665	0.0284	L	0.36672	1.1	0.36053	D	0.840926	B	0.23058	0.079	B	0.24269	0.052	T	0.18461	-1.0336	9	.	.	.	.	18.5358	0.91010	0.0:1.0:0.0:0.0	.	39	Q6ZN28	MACC1_HUMAN	K	39	ENSP00000383185:E39K;ENSP00000328410:E39K	.	E	-	1	0	MACC1	20167896	1.000000	0.71417	1.000000	0.80357	0.060000	0.15804	4.563000	0.60823	2.750000	0.94351	0.655000	0.94253	GAA	.	.		0.338	MACC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250202.5	NM_182762	Missense_Mutation	T	20201371	C	T	20201371	5	4	309	1	0	0	0	0	0	0	1	0	9152	695	24	3	2459	3	MACC1	7	20201371	Splice_Site	SNP	C	TCGA-K7-A5RF-01A-11D-A28X-10	17795162	20201371	138937292	24	44066										
IL6	3569	hgsc.bcm.edu	37	chr7	22767126	22767126	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	gttgcctgctgccttccctgCcccagtacccccaggagaag	10	17	0	1			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr7:22767126C>T	ENST00000404625.1	+	3	542	c.83C>T	c.(82-84)gCc>gTc	p.A28V	IL6_ENST00000420258.2_Missense_Mutation_p.A82V|AC073072.5_ENST00000325042.2_RNA|IL6_ENST00000406575.1_Missense_Mutation_p.A28V|IL6_ENST00000401630.3_Intron|IL6_ENST00000407492.1_Intron|IL6_ENST00000401651.1_Intron|IL6_ENST00000258743.5_Missense_Mutation_p.A28V			P05231	IL6_HUMAN	interleukin 6	28					acute-phase response (GO:0006953)|aging (GO:0007568)|bone remodeling (GO:0046849)|branching involved in salivary gland morphogenesis (GO:0060445)|cell growth (GO:0016049)|cell redox homeostasis (GO:0045454)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endocrine pancreas development (GO:0031018)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|glucagon secretion (GO:0070091)|hepatic immune response (GO:0002384)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|interleukin-6-mediated signaling pathway (GO:0070102)|monocyte chemotaxis (GO:0002548)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine biosynthetic process (GO:0045079)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of hormone secretion (GO:0046888)|negative regulation of lipid storage (GO:0010888)|negative regulation of muscle organ development (GO:0048635)|negative regulation of neuron death (GO:1901215)|negative regulation of protein kinase activity (GO:0006469)|neuron projection development (GO:0031175)|neutrophil apoptotic process (GO:0001781)|neutrophil mediated immunity (GO:0002446)|platelet activation (GO:0030168)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell activation (GO:0050871)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine production (GO:0032722)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|positive regulation of type B pancreatic cell apoptotic process (GO:2000676)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of angiogenesis (GO:0045765)|regulation of cell shape (GO:0008360)|regulation of circadian sleep/wake cycle, non-REM sleep (GO:0045188)|regulation of vascular endothelial growth factor production (GO:0010574)|response to amino acid (GO:0043200)|response to antibiotic (GO:0046677)|response to caffeine (GO:0031000)|response to calcium ion (GO:0051592)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to glucocorticoid (GO:0051384)|response to heat (GO:0009408)|response to insulin (GO:0032868)|response to mechanical stimulus (GO:0009612)|response to nutrient levels (GO:0031667)|response to peptidoglycan (GO:0032494)|T-helper 17 cell lineage commitment (GO:0072540)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|interleukin-6 receptor complex (GO:0005896)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|interleukin-6 receptor binding (GO:0005138)			breast(1)|endometrium(2)|large_intestine(4)|lung(1)	8					Ginseng(DB01404)	GCCTTCCCTGCCCCAGTACCC	0.602																																					p.A28V	Esophageal Squamous(47;342 1214 13936 33513)	Atlas-SNP	.											.	IL6	30	.	0			c.C83T						.						60	62	62					7																	22767126		2203	4300	6503	SO:0001583	missense	3569	exon2			TCCCTGCCCCAGT	M18403	CCDS5375.1	7p21-p15	2014-04-04	2014-04-04		ENSG00000136244	ENSG00000136244		"Interleukins and interleukin receptors", "Interferons"	6018	protein-coding gene	gene with protein product	"interferon, beta 2"	147620	"interleukin 6 (interferon, beta 2)"	IFNB2		3294161	Standard	NM_000600		Approved	IL-6, BSF2, HGF, HSF	uc003svj.4	P05231	OTTHUMG00000023178	ENST00000404625.1:c.83C>T	chr7.hg19:g.22767126C>T	ENSP00000385675:p.Ala28Val	71.0	0.0		104.0	7.0	NM_000600	Q9UCU2|Q9UCU3|Q9UCU4	Missense_Mutation	SNP	ENST00000404625.1	hg19	CCDS5375.1	.	.	.	.	.	.	.	.	.	.	C	14.31	2.497180	0.44352	.	.	ENSG00000136244	ENST00000404625;ENST00000426291;ENST00000258743;ENST00000420258;ENST00000406575	T;T;T;T;T	0.75477	-0.94;-0.94;-0.94;0.91;-0.94	5.62	2.83	0.33086	.	0.410931	0.30830	N	0.008781	T	0.55481	0.1923	L	0.29908	0.895	0.09310	N	1	B;P;P	0.39216	0.077;0.664;0.495	B;B;B	0.32928	0.028;0.155;0.065	T	0.52586	-0.8556	10	0.87932	D	0	-9.9549	5.6418	0.17569	0.1567:0.6783:0.0:0.165	.	82;28;28	B4DNQ5;B5MC14;P05231	.;.;IL6_HUMAN	V	28;28;28;82;28	ENSP00000385675:A28V;ENSP00000405150:A28V;ENSP00000258743:A28V;ENSP00000405994:A82V;ENSP00000385227:A28V	ENSP00000258743:A28V	A	+	2	0	IL6	22733651	0.001000	0.12720	0.005000	0.12908	0.003000	0.03518	0.134000	0.15932	0.403000	0.25479	0.555000	0.69702	GCC	.	.		0.602	IL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250225.2	NM_000600		T	22767126	C	T	22767126	3	4	309	1	0	0	0	0	1	0	0	0	7710	739	26	3	89	3	IL6	7	22767126	Missense_Mutation	SNP	C	TCGA-K7-A5RF-01A-11D-A28X-10	2565755	22767126	136371537	25	44067										
CHN2	1124	hgsc.bcm.edu	37	chr7	29407578	29407578	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	acagcaagaggcacctcgtcCcaagagaatcatttgtcctc	8	13	1	2			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr7:29407578C>T	ENST00000222792.6	+	3	649	c.119C>T	c.(118-120)cCc>cTc	p.P40L	CHN2_ENST00000539389.1_Missense_Mutation_p.P40L|CHN2_ENST00000495789.2_Missense_Mutation_p.P53L|CHN2_ENST00000539406.1_Missense_Mutation_p.P115L|CHN2_ENST00000546235.1_Missense_Mutation_p.P25L|CHN2_ENST00000435288.2_Missense_Mutation_p.P40L	NM_004067.2	NP_004058.1	P52757	CHIO_HUMAN	chimerin 2	40					positive regulation of GTPase activity (GO:0043547)|positive regulation of signal transduction (GO:0009967)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(3)|large_intestine(2)|lung(12)|ovary(2)|urinary_tract(2)	23						GCACCTCGTCCCAAGAGAATC	0.413																																					p.P40L	Ovarian(1;44 48 13232 18918 31480)	Atlas-SNP	.											.	CHN2	98	.	0			c.C119T						.						114	111	112					7																	29407578		2203	4300	6503	SO:0001583	missense	1124	exon3			CTCGTCCCAAGAG	L29126	CCDS5420.1	7p15.3	2013-02-14	2012-10-17		ENSG00000106069	ENSG00000106069		"Rho GTPase activating proteins", "SH2 domain containing"	1944	protein-coding gene	gene with protein product	"beta chimerin", "chimaerin 2"	602857	"chimerin (chimaerin) 2"			8175705	Standard	XM_005249602		Approved	ARHGAP3, RhoGAP3	uc003szz.3	P52757	OTTHUMG00000023063	ENST00000222792.6:c.119C>T	chr7.hg19:g.29407578C>T	ENSP00000222792:p.Pro40Leu	35.0	0.0		59.0	6.0	NM_004067	A4D1A2|B3VCF1|B3VCF2|B3VCF3|B3VCF7|B3VCG1|C9J7B0|E9PGE0|F8QPL9|Q2M203|Q75MM2	Missense_Mutation	SNP	ENST00000222792.6	hg19	CCDS5420.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.475941	0.84640	.	.	ENSG00000106069	ENST00000439384;ENST00000539406;ENST00000222792;ENST00000435288;ENST00000409350;ENST00000495789;ENST00000539389;ENST00000546235	T;T;T;T;T;T;T;T	0.71817	-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;-0.6;-0.02	5.12	5.12	0.69794	.	0.250879	0.40144	N	0.001168	D	0.83769	0.5326	M	0.76574	2.34	0.80722	D	1	D;D;D;B;D	0.89917	1.0;0.998;1.0;0.081;0.998	D;D;D;B;D	0.97110	1.0;0.981;0.998;0.033;0.981	D	0.85912	0.1441	10	0.87932	D	0	.	16.3346	0.83053	0.0:1.0:0.0:0.0	.	25;53;115;40;40	B7Z1W9;B7Z1V0;F5H003;B3VCG1;P52757	.;.;.;.;CHIO_HUMAN	L	115;115;40;40;53;53;40;25	ENSP00000409843:P115L;ENSP00000444063:P115L;ENSP00000222792:P40L;ENSP00000400282:P40L;ENSP00000386968:P53L;ENSP00000438587:P53L;ENSP00000440526:P40L;ENSP00000442812:P25L	ENSP00000222792:P40L	P	+	2	0	CHN2	29374103	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.472000	0.66768	2.388000	0.81334	0.585000	0.79938	CCC	.	.		0.413	CHN2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214228.2	NM_004067		T	29407578	C	T	29407578	3	4	309	1	0	0	0	0	1	0	0	0	3365	623	22	3	129	3	CHN2	7	29407578	Missense_Mutation	SNP	C	TCGA-K7-A5RF-01A-11D-A28X-10	6640452	29407578	129731085	26	44068										
IKZF1	10320	hgsc.bcm.edu	37	chr7	50444279	50444279	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	tgatgaagagaatgggcgtgCctgtgaaatgaatggggaag	17	3	0	5			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr7:50444279C>A	ENST00000331340.3	+	4	364	c.209C>A	c.(208-210)gCc>gAc	p.A70D	IKZF1_ENST00000440768.2_Missense_Mutation_p.A70D|IKZF1_ENST00000359197.5_Missense_Mutation_p.A70D|IKZF1_ENST00000357364.4_Missense_Mutation_p.A70D|IKZF1_ENST00000349824.4_Missense_Mutation_p.A70D|IKZF1_ENST00000346667.4_Intron|IKZF1_ENST00000343574.5_Intron|IKZF1_ENST00000438033.1_Intron|IKZF1_ENST00000439701.1_Missense_Mutation_p.A70D	NM_001220769.1|NM_001220772.1|NM_001220773.1|NM_001220775.1|NM_006060.4	NP_001207698.1|NP_001207701.1|NP_001207702.1|NP_001207704.1|NP_006051.1	Q13422	IKZF1_HUMAN	IKAROS family zinc finger 1 (Ikaros)	70					B cell differentiation (GO:0030183)|cell cycle (GO:0007049)|chromatin modification (GO:0016568)|forebrain development (GO:0030900)|lymph node development (GO:0048535)|mesoderm development (GO:0007498)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Peyer's patch development (GO:0048541)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neutrophil differentiation (GO:0045660)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|T cell differentiation (GO:0030217)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.?(131)		haematopoietic_and_lymphoid_tissue(275)|lung(1)	276	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;7.29e-10)|all_hematologic(4;4.8e-07)				AATGGGCGTGCCTGTGAAATG	0.468			"D,T"	BCL6	"ALL, DLBCL"																																p.A70D		Atlas-SNP	.		"Rec,Dom"	yes		7	7p12.2	10320	IKAROS family zinc finger 1		L	.	IKZF1	613	.	131	Unknown(131)	haematopoietic_and_lymphoid_tissue(131)	c.C209A						.						148	155	152					7																	50444279		1980	4160	6140	SO:0001583	missense	10320	exon4			GGCGTGCCTGTGA	U40462	CCDS59055.1, CCDS69299.1, CCDS75596.1, CCDS75597.1	7p12.2	2014-06-12	2006-08-25	2006-08-25	ENSG00000185811	ENSG00000185811		"Zinc fingers, C2H2-type", "IKAROS zinc fingers"	13176	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 92"	603023	"zinc finger protein, subfamily 1A, 1 (Ikaros)"	ZNFN1A1		1439790, 7935426	Standard	NM_006060		Approved	hIk-1, LyF-1, Hs.54452, IKAROS, PPP1R92	uc003tow.4	Q13422	OTTHUMG00000155907	ENST00000331340.3:c.209C>A	chr7.hg19:g.50444279C>A	ENSP00000331614:p.Ala70Asp	89.0	0.0		122.0	12.0	NM_006060	A4D260|B4E0Z1|D3DVM5|O00598|Q53XL2|Q69BM4|Q8WVA3	Missense_Mutation	SNP	ENST00000331340.3	hg19		.	.	.	.	.	.	.	.	.	.	C	14.24	2.475096	0.43942	.	.	ENSG00000185811	ENST00000359197;ENST00000440768;ENST00000349824;ENST00000357364;ENST00000331340;ENST00000439701	T;T;T;T;T;T	0.06608	3.38;3.28;4.4;3.46;3.38;3.38	4.45	2.54	0.30619	.	0.061157	0.64402	D	0.000005	T	0.16171	0.0389	.	.	.	0.58432	D	0.999997	P;P	0.52577	0.953;0.954	P;P	0.56434	0.798;0.588	T	0.00773	-1.1572	9	0.34782	T	0.22	-6.8227	14.4497	0.67376	0.0:0.7214:0.2786:0.0	.	70;70	Q13422-7;Q13422	.;IKZF1_HUMAN	D	70	ENSP00000352123:A70D;ENSP00000401507:A70D;ENSP00000342485:A70D;ENSP00000349928:A70D;ENSP00000331614:A70D;ENSP00000413025:A70D	ENSP00000331614:A70D	A	+	2	0	IKZF1	50411773	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.910000	0.63321	0.390000	0.25115	0.313000	0.20887	GCC	.	.		0.468	IKZF1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000342242.1	NM_006060		A	50444279	C	A	50444279	3	1	309	1	0	0	0	0	1	0	0	0	7623	739	26	3	219	3	IKZF1	7	50444279	Missense_Mutation	SNP	C	TCGA-K7-A5RF-01A-11D-A28X-10	21036701	50444279	108694384	27	44069										
CYP3A5	1577	hgsc.bcm.edu	37	chr7	99273802	99273802	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	gccctggaattcccagtctcTtaaaaagtccatgtgtacgg	9	11	1	0			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr7:99273802T>C	ENST00000222982.4	-	2	200	c.101A>G	c.(100-102)aAg>aGg	p.K34R	CYP3A5_ENST00000439761.1_Missense_Mutation_p.K34R|CYP3A5_ENST00000339843.2_3'UTR|CYP3A5_ENST00000343703.5_Missense_Mutation_p.K24R|CYP3A5_ENST00000480723.1_5'UTR	NM_000777.3	NP_000768.1	P20815	CP3A5_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 5	34					alkaloid catabolic process (GO:0009822)|drug catabolic process (GO:0042737)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxygen binding (GO:0019825)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_epithelial(64;2.77e-08)|Lung NSC(181;0.00396)|all_lung(186;0.00659)|Esophageal squamous(72;0.0166)				ado-trastuzumab emtansine(DB05773)|Alfentanil(DB00802)|Alprazolam(DB00404)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Apixaban(DB06605)|Aprepitant(DB00673)|Argatroban(DB00278)|Aripiprazole(DB01238)|Artemether(DB06697)|Astemizole(DB00637)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Beclomethasone(DB00394)|Boceprevir(DB08873)|Brentuximab vedotin(DB08870)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Carbamazepine(DB00564)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Cilostazol(DB01166)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clonidine(DB00575)|Clopidogrel(DB00758)|Cocaine(DB00907)|Codeine(DB00318)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diltiazem(DB00343)|Disulfiram(DB00822)|Docetaxel(DB01248)|Dolutegravir(DB08930)|Domperidone(DB01184)|Dutasteride(DB01126)|Enzalutamide(DB08899)|Eplerenone(DB00700)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estrone(DB00655)|Ethosuximide(DB00593)|Etoposide(DB00773)|Felodipine(DB01023)|Fentanyl(DB00813)|Finasteride(DB01216)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flutamide(DB00499)|Fluticasone Propionate(DB00588)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gestodene(DB06730)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Indinavir(DB00224)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Levomethadyl Acetate(DB01227)|Lidocaine(DB00281)|Losartan(DB00678)|Lovastatin(DB00227)|Methadone(DB00333)|Midazolam(DB00683)|Mifepristone(DB00834)|Modafinil(DB00745)|Mycophenolate mofetil(DB00688)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ondansetron(DB00904)|Oxazepam(DB00842)|Oxcarbazepine(DB00776)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Pentamidine(DB00738)|Perampanel(DB08883)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Progesterone(DB00396)|Propranolol(DB00571)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinine(DB00468)|Ranitidine(DB00863)|Reserpine(DB00206)|Rifampicin(DB01045)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Rosuvastatin(DB01098)|Salmeterol(DB00938)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Teniposide(DB00444)|Testosterone(DB00624)|Thalidomide(DB01041)|Trazodone(DB00656)|Tretinoin(DB00755)|Triazolam(DB00897)|Troleandomycin(DB01361)|Udenafil(DB06267)|Valproic Acid(DB00313)|Vardenafil(DB00862)|Verapamil(DB00661)|Vincristine(DB00541)|Voriconazole(DB00582)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Ziprasidone(DB00246)|Zolpidem(DB00425)	TCCCAGTCTCTTAAAAAGTCC	0.453																																					p.K34R		Atlas-SNP	.											.	CYP3A5	46	.	0			c.A101G						.						115	105	108					7																	99273802		2203	4300	6503	SO:0001583	missense	1577	exon2			AGTCTCTTAAAAA	L26985	CCDS5672.1, CCDS55134.1	7q21.1	2007-12-14	2003-01-14		ENSG00000106258	ENSG00000106258		"Cytochrome P450s"	2638	protein-coding gene	gene with protein product		605325	"cytochrome P450, subfamily IIIA (niphedipine oxidase), polypeptide 5"				Standard	NR_033808		Approved	PCN3, P450PCN3, CP35		P20815	OTTHUMG00000156724	ENST00000222982.4:c.101A>G	chr7.hg19:g.99273802T>C	ENSP00000222982:p.Lys34Arg	169.0	0.0		273.0	28.0	NM_001190484	A4D289|B7Z5I7|Q53WY8|Q75MV0|Q9HB56	Missense_Mutation	SNP	ENST00000222982.4	hg19	CCDS5672.1	.	.	.	.	.	.	.	.	.	.	T	8.763	0.923980	0.18056	.	.	ENSG00000106258	ENST00000222982;ENST00000343703;ENST00000439761	T;T;T	0.09445	2.98;2.98;2.98	3.78	2.49	0.30216	.	0.000000	0.85682	D	0.000000	T	0.13586	0.0329	L	0.49350	1.555	0.80722	D	1	B;B;B	0.28082	0.029;0.2;0.017	B;B;B	0.40228	0.194;0.323;0.095	T	0.06320	-1.0833	10	0.66056	D	0.02	.	6.6367	0.22887	0.0:0.0:0.2448:0.7552	.	24;34;34	F5H4S0;B7Z5I7;P20815	.;.;CP3A5_HUMAN	R	34;24;34	ENSP00000222982:K34R;ENSP00000342969:K24R;ENSP00000401269:K34R	ENSP00000222982:K34R	K	-	2	0	CYP3A5	99111738	1.000000	0.71417	0.809000	0.32408	0.042000	0.13812	1.054000	0.30455	1.476000	0.48215	0.374000	0.22700	AAG	.	.		0.453	CYP3A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345469.1			C	99273802	T	C	99273802	3	2	309	1	0	0	0	0	1	0	0	0	4182	1609	56	2	1455	2	CYP3A5	7	99273802	Missense_Mutation	SNP	T	TCGA-K7-A5RF-01A-11D-A28X-10	48829523	99273802	59864861	28	44070										
GPR22	2845	hgsc.bcm.edu	37	chr7	107115727	107115727	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	tacacaactcttggatagatCctaaaagaaacaaaaaaatt	4	7	1	2			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr7:107115727C>A	ENST00000304402.4	+	3	2565	c.1222C>A	c.(1222-1224)Cct>Act	p.P408T	COG5_ENST00000475638.2_Intron|COG5_ENST00000297135.3_Intron|COG5_ENST00000347053.3_Intron|COG5_ENST00000393603.2_Intron	NM_005295.2	NP_005286.2	Q99680	GPR22_HUMAN	G protein-coupled receptor 22	408					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			large_intestine(3)|lung(6)|ovary(2)|stomach(1)	12						TTGGATAGATCCTAAAAGAAA	0.343																																					p.P408T		Atlas-SNP	.											.	GPR22	43	.	0			c.C1222A						.						37	42	41					7																	107115727		2197	4285	6482	SO:0001583	missense	2845	exon3			ATAGATCCTAAAA	U66581	CCDS5744.1	7q22-q31.1	2012-08-21			ENSG00000172209	ENSG00000172209		"GPCR / Class A : Orphans"	4477	protein-coding gene	gene with protein product		601910				9073069	Standard	NM_005295		Approved		uc003vef.3	Q99680	OTTHUMG00000154902	ENST00000304402.4:c.1222C>A	chr7.hg19:g.107115727C>A	ENSP00000302676:p.Pro408Thr	81.0	0.0		121.0	7.0	NM_005295	O14554	Missense_Mutation	SNP	ENST00000304402.4	hg19	CCDS5744.1	.	.	.	.	.	.	.	.	.	.	C	16.68	3.191150	0.58017	.	.	ENSG00000172209	ENST00000304402	T	0.29917	1.55	5.83	5.83	0.93111	.	0.163823	0.56097	D	0.000039	T	0.45196	0.1330	L	0.32530	0.975	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	T	0.08330	-1.0727	10	0.15066	T	0.55	-10.6011	20.114	0.97919	0.0:1.0:0.0:0.0	.	408	Q99680	GPR22_HUMAN	T	408	ENSP00000302676:P408T	ENSP00000302676:P408T	P	+	1	0	GPR22	106902963	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.763000	0.94921	0.585000	0.79938	CCT	.	.		0.343	GPR22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337598.1			A	107115727	C	A	107115727	3	1	309	1	0	0	0	0	1	0	0	0	6690	855	30	3	1224	3	GPR22	7	107115727	Missense_Mutation	SNP	C	TCGA-K7-A5RF-01A-11D-A28X-10	7841925	107115727	52022936	29	44071										
CSMD1	64478	hgsc.bcm.edu	37	chr8	3072177	3072177	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	caactcttgtcccattcattAtatttcctgggtcaaaacaa	4	11	3	0			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr8:3072177A>G	ENST00000520002.1	-	31	5267	c.4712T>C	c.(4711-4713)aTa>aCa	p.I1571T	CSMD1_ENST00000602723.1_Missense_Mutation_p.I1571T|CSMD1_ENST00000400186.3_Missense_Mutation_p.I1571T|CSMD1_ENST00000542608.1_Missense_Mutation_p.I1570T|CSMD1_ENST00000539096.1_Missense_Mutation_p.I1570T|CSMD1_ENST00000602557.1_Missense_Mutation_p.I1571T|CSMD1_ENST00000523387.1_5'UTR|CSMD1_ENST00000537824.1_Missense_Mutation_p.I1570T			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1571	Sushi 9. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CCCATTCATTATATTTCCTGG	0.433																																					p.I1570T		Atlas-SNP	.											.	CSMD1	1469	.	0			c.T4709C						.						73	69	70					8																	3072177		1915	4076	5991	SO:0001583	missense	64478	exon30			TTCATTATATTTC			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.4712T>C	chr8.hg19:g.3072177A>G	ENSP00000430733:p.Ile1571Thr	118.0	0.0		144.0	9.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	hg19		.	.	.	.	.	.	.	.	.	.	A	23.2	4.386921	0.82902	.	.	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096	T;T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3;-0.3	5.53	5.53	0.82687	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.64402	D	0.000001	T	0.81795	0.4898	M	0.79343	2.45	0.58432	D	0.999999	D;P;P	0.63046	0.992;0.863;0.84	D;P;P	0.72338	0.977;0.756;0.557	D	0.84104	0.0397	10	0.66056	D	0.02	.	15.6592	0.77169	1.0:0.0:0.0:0.0	.	1571;1571;1571	E5RIG2;Q96PZ7;Q96PZ7-4	.;CSMD1_HUMAN;.	T	1571;1571;1433;1570;1570;1570	ENSP00000383047:I1571T;ENSP00000430733:I1571T;ENSP00000441462:I1570T;ENSP00000446243:I1570T;ENSP00000441675:I1570T	ENSP00000320445:I1433T	I	-	2	0	CSMD1	3059584	1.000000	0.71417	0.993000	0.49108	0.984000	0.73092	9.065000	0.93941	2.095000	0.63458	0.482000	0.46254	ATA	.	.		0.433	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		G	3072177	A	G	3072177	3	3	309	1	0	0	0	0	1	0	0	0	3946	449	16	2	6149	2	CSMD1	8	3072177	Missense_Mutation	SNP	A	TCGA-K7-A5RF-01A-11D-A28X-10		3072177	143291845	30	44072										
UNC5D	137970	hgsc.bcm.edu	37	chr8	35608295	35608295	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	tggattacaacttgagagttTactgtgtggacaatacccct	9	8	0	1			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr8:35608295T>C	ENST00000404895.2	+	13	2459	c.2131T>C	c.(2131-2133)Tac>Cac	p.Y711H	UNC5D_ENST00000416672.1_Missense_Mutation_p.Y716H|UNC5D_ENST00000449677.1_Missense_Mutation_p.Y287H|UNC5D_ENST00000453357.2_Missense_Mutation_p.Y706H|UNC5D_ENST00000287272.2_Missense_Mutation_p.Y642H|UNC5D_ENST00000420357.1_Missense_Mutation_p.Y644H	NM_080872.2	NP_543148.2	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D (C. elegans)	711	Interaction with DCC. {ECO:0000250}.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|pyramidal neuron differentiation (GO:0021859)|regulation of neuron migration (GO:2001222)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(2)|breast(7)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(56)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(6)|urinary_tract(2)	112				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)		CTTGAGAGTTTACTGTGTGGA	0.433																																					p.Y711H		Atlas-SNP	.											.	UNC5D	393	.	0			c.T2131C						.						201	174	183					8																	35608295		2203	4300	6503	SO:0001583	missense	137970	exon13			AGAGTTTACTGTG	AB055056	CCDS6093.2	8p12	2013-01-11			ENSG00000156687	ENSG00000156687		"Immunoglobulin superfamily / I-set domain containing"	18634	protein-coding gene	gene with protein product						18402767	Standard	NM_080872		Approved	KIAA1777, Unc5h4	uc003xjr.2	Q6UXZ4	OTTHUMG00000157145	ENST00000404895.2:c.2131T>C	chr8.hg19:g.35608295T>C	ENSP00000385143:p.Tyr711His	204.0	0.0		284.0	23.0	NM_080872	Q8WYP7	Missense_Mutation	SNP	ENST00000404895.2	hg19	CCDS6093.2	.	.	.	.	.	.	.	.	.	.	T	16.38	3.106869	0.56291	.	.	ENSG00000156687	ENST00000404895;ENST00000420357;ENST00000287272;ENST00000416672;ENST00000453357;ENST00000449677	T;T;T;T;T;T	0.66815	-0.2;0.2;0.16;-0.2;-0.23;1.69	5.9	5.9	0.94986	.	0.052466	0.85682	D	0.000000	T	0.61578	0.2358	L	0.52364	1.645	0.58432	D	0.999998	P;B;B	0.35050	0.482;0.202;0.128	B;B;B	0.30029	0.11;0.097;0.045	T	0.64833	-0.6314	10	0.62326	D	0.03	-22.5614	16.3317	0.83023	0.0:0.0:0.0:1.0	.	287;706;711	E9PDS8;Q6UXZ4-2;Q6UXZ4	.;.;UNC5D_HUMAN	H	711;644;642;716;706;287	ENSP00000385143:Y711H;ENSP00000392739:Y644H;ENSP00000287272:Y642H;ENSP00000412652:Y716H;ENSP00000394303:Y706H;ENSP00000397211:Y287H	ENSP00000287272:Y642H	Y	+	1	0	UNC5D	35727837	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.937000	0.70162	2.264000	0.75181	0.533000	0.62120	TAC	.	.		0.433	UNC5D-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347586.2			C	35608295	T	C	35608295	3	2	309	1	0	0	0	0	1	0	0	0	17010	1754	61	2	2181	2	UNC5D	8	35608295	Missense_Mutation	SNP	T	TCGA-K7-A5RF-01A-11D-A28X-10	32536118	35608295	110755727	31	44073										
RUNX1T1	862	hgsc.bcm.edu	37	chr8	93026974	93026974	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	ggaggaggaagaagaggaagGcccattgctgaagccattgg	17	6	0	3			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr8:93026974G>A	ENST00000523629.1	-	4	755	c.301C>T	c.(301-303)Cct>Tct	p.P101S	RUNX1T1_ENST00000521553.1_Missense_Mutation_p.P64S|RUNX1T1_ENST00000422361.2_Missense_Mutation_p.P64S|RUNX1T1_ENST00000520724.1_Missense_Mutation_p.P64S|RUNX1T1_ENST00000265814.3_Missense_Mutation_p.P101S|RUNX1T1_ENST00000436581.2_Missense_Mutation_p.P112S|RUNX1T1_ENST00000360348.2_Missense_Mutation_p.P64S|RUNX1T1_ENST00000522163.1_5'Flank|RUNX1T1_ENST00000396218.1_Missense_Mutation_p.P74S|RUNX1T1_ENST00000518844.1_Missense_Mutation_p.P74S	NM_001198626.1|NM_001198630.1|NM_001198633.1|NM_175634.2	NP_001185555.1|NP_001185559.1|NP_001185562.1|NP_783552.1	Q06455	MTG8_HUMAN	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	101					fat cell differentiation (GO:0045444)|generation of precursor metabolites and energy (GO:0006091)|regulation of DNA binding (GO:0051101)|transcription, DNA-templated (GO:0006351)	nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(54)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	86			BRCA - Breast invasive adenocarcinoma(11;0.0141)			GAAGAGGAAGGCCCATTGCTG	0.537																																					p.P160S		Atlas-SNP	.											RUNX1T1_ENST00000436581,NS,carcinoma,0,3	RUNX1T1	516	.	0			c.C478T						.						59	61	60					8																	93026974		2203	4300	6503	SO:0001583	missense	862	exon4			AGGAAGGCCCATT	D43638	CCDS6256.1, CCDS6257.1, CCDS47891.1, CCDS56544.1, CCDS75766.1, CCDS75767.1	8q22	2007-01-29	2005-01-20	2005-01-22	ENSG00000079102	ENSG00000079102		"Zinc fingers, MYND-type"	1535	protein-coding gene	gene with protein product		133435	"core-binding factor, runt domain, alpha subunit 2; translocated to, 1; cyclin D-related"	AML1T1, CBFA2T1		1391946, 9790752	Standard	NM_004349		Approved	CDR, ETO, MTG8, ZMYND2	uc011lgi.2	Q06455	OTTHUMG00000164066	ENST00000523629.1:c.301C>T	chr8.hg19:g.93026974G>A	ENSP00000428543:p.Pro101Ser	66.0	0.0		110.0	7.0	NM_001198679	B7Z4P4|E7EPN4|O14784|Q06456|Q14873|Q16239|Q16346|Q16347|Q6IBL1|Q6NXH1|Q7Z4J5|Q92479|Q9BRZ0	Missense_Mutation	SNP	ENST00000523629.1	hg19	CCDS6256.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.735715	0.89482	.	.	ENSG00000079102	ENST00000523629;ENST00000396218;ENST00000265814;ENST00000360348;ENST00000422361;ENST00000520724;ENST00000436581;ENST00000518844;ENST00000521553;ENST00000518992;ENST00000521054;ENST00000519847;ENST00000517792;ENST00000522467;ENST00000517919;ENST00000521733;ENST00000520556;ENST00000521319;ENST00000520583;ENST00000523168;ENST00000518823	T;T;T;T;T;T;T;T;T;T;T	0.55234	1.14;1.08;1.14;1.02;1.02;1.02;0.81;1.08;0.54;0.53;1.18	6.05	5.18	0.71444	.	0.000000	0.85682	D	0.000000	T	0.68622	0.3021	L	0.57536	1.79	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.999;0.999;0.999;0.999	T	0.68213	-0.5468	10	0.39692	T	0.17	-11.3328	15.6276	0.76874	0.0658:0.0:0.9342:0.0	.	112;112;74;101;74	E7EPN4;B7Z4P4;B2R6I9;Q06455;Q06455-2	.;.;.;MTG8_HUMAN;.	S	101;74;101;64;64;64;112;74;64;101;64;101;64;101;101;74;64;64;101;101;74	ENSP00000428543:P101S;ENSP00000379520:P74S;ENSP00000265814:P101S;ENSP00000353504:P64S;ENSP00000390137:P64S;ENSP00000428742:P64S;ENSP00000402257:P112S;ENSP00000430728:P74S;ENSP00000429728:P64S;ENSP00000431094:P101S;ENSP00000427763:P64S	ENSP00000265814:P101S	P	-	1	0	RUNX1T1	93096150	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.823000	0.99369	1.576000	0.49790	0.650000	0.86243	CCT	.	.		0.537	RUNX1T1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377045.3	NM_004349, NM_175635		A	93026974	G	A	93026974	3	1	309	1	0	0	0	0	1	0	0	0	13762	1203	42	3	1549	3	RUNX1T1	8	93026974	Missense_Mutation	SNP	G	TCGA-K7-A5RF-01A-11D-A28X-10	57418679	93026974	53337048	32	44074										
SCRIB	23513	hgsc.bcm.edu	37	chr8	144891130	144891130	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	agggtccagggggcctcaggCtgcccctcctcgatctccct	12	17	2	0			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr8:144891130C>A	ENST00000320476.3	-	15	1770	c.1764G>T	c.(1762-1764)caG>caT	p.Q588H	SCRIB_ENST00000356994.2_Missense_Mutation_p.Q588H|SCRIB_ENST00000377533.3_Missense_Mutation_p.Q507H	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	588	Sufficient for targeting to adherens junction and to inhibit cell proliferation.				activation of Rac GTPase activity (GO:0032863)|apoptotic process involved in morphogenesis (GO:0060561)|astrocyte cell migration (GO:0043615)|asymmetric protein localization (GO:0008105)|auditory receptor cell stereocilium organization (GO:0060088)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cochlear nucleus development (GO:0021747)|establishment of apical/basal cell polarity (GO:0035089)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of mitotic cell cycle (GO:0045930)|neural tube closure (GO:0001843)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of receptor recycling (GO:0001921)|protein localization to adherens junction (GO:0071896)|single organismal cell-cell adhesion (GO:0016337)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle targeting (GO:0016080)|viral process (GO:0016032)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)|Scrib-APC-beta-catenin complex (GO:0034750)				NS(1)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(20)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	42	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			GGGCCTCAGGCTGCCCCTCCT	0.647																																					p.Q588H	Pancreas(51;966 1133 10533 14576 29674)	Atlas-SNP	.											.	SCRIB	192	.	0			c.G1764T						.						58	59	59					8																	144891130		2203	4300	6503	SO:0001583	missense	23513	exon15			CTCAGGCTGCCCC	AY062238	CCDS6411.1, CCDS6412.1	8q24.3	2013-03-05	2013-03-05		ENSG00000180900	ENSG00000180900			30377	protein-coding gene	gene with protein product		607733	"scribbled homolog (Drosophila)"			11027293, 14681682	Standard	NM_182706		Approved	KIAA0147, SCRB1, Vartul	uc003yzo.1	Q14160	OTTHUMG00000165154	ENST00000320476.3:c.1764G>T	chr8.hg19:g.144891130C>A	ENSP00000322938:p.Gln588His	101.0	0.0		97.0	5.0	NM_015356	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Missense_Mutation	SNP	ENST00000320476.3	hg19	CCDS6411.1	.	.	.	.	.	.	.	.	.	.	c	9.457	1.092161	0.20471	.	.	ENSG00000180900	ENST00000356994;ENST00000320476;ENST00000377533	T;T;T	0.36157	1.48;1.46;1.27	4.79	0.634	0.17718	.	.	.	.	.	T	0.37652	0.1011	L	0.56769	1.78	0.19300	N	0.99998	P;P	0.51240	0.943;0.928	P;P	0.50440	0.547;0.641	T	0.19549	-1.0302	9	0.45353	T	0.12	.	3.4687	0.07559	0.1626:0.4286:0.3163:0.0925	.	588;588	Q14160;Q14160-3	SCRIB_HUMAN;.	H	588;588;507	ENSP00000349486:Q588H;ENSP00000322938:Q588H;ENSP00000366756:Q507H	ENSP00000322938:Q588H	Q	-	3	2	SCRIB	144963118	0.136000	0.22515	0.087000	0.20705	0.065000	0.16274	-0.133000	0.10451	-0.189000	0.10482	-0.494000	0.04653	CAG	.	.		0.647	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356		A	144891130	C	A	144891130	3	1	309	1	0	0	0	0	1	0	0	0	13952	796	28	3	3295	3	SCRIB	8	144891130	Missense_Mutation	SNP	C	TCGA-K7-A5RF-01A-11D-A28X-10	51864156	144891130	1472892	33	44075										
RNF20	56254	hgsc.bcm.edu	37	chr9	104303192	104303192	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	ccgccgagccgtgtcccagaTtgtgactgtttatgataaat	10	10	0	3			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr9:104303192T>C	ENST00000389120.3	+	5	653	c.563T>C	c.(562-564)aTt>aCt	p.I188T		NM_019592.5	NP_062538.5	Q5VTR2	BRE1A_HUMAN	ring finger protein 20, E3 ubiquitin protein ligase	188					histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|negative regulation of cell migration (GO:0030336)|positive regulation of histone methylation (GO:0031062)|positive regulation of transcription, DNA-templated (GO:0045893)|protein polyubiquitination (GO:0000209)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)	HULC complex (GO:0033503)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|ligase activity (GO:0016874)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(6)|large_intestine(7)|lung(23)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_hematologic(171;8.99e-06)|Acute lymphoblastic leukemia(62;0.000365)|Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.88e-19)|STAD - Stomach adenocarcinoma(157;0.00311)		GTGTCCCAGATTGTGACTGTT	0.522																																					p.I188T		Atlas-SNP	.											.	RNF20	110	.	0			c.T563C						.						77	82	80					9																	104303192		2203	4300	6503	SO:0001583	missense	56254	exon5			CCCAGATTGTGAC	AF265230	CCDS35084.1	9q22	2012-02-23	2012-02-23	2008-12-12	ENSG00000155827	ENSG00000155827		"RING-type (C3HC4) zinc fingers"	10062	protein-coding gene	gene with protein product	"BRE1 E3 ubiquitin ligase homolog (S. cerevisiae)"	607699	"ring finger protein 20"			16337599, 12876294, 18832071, 19037095	Standard	NM_019592		Approved	FLJ20382, FLJ11189, KAIA2779, BRE1A, hBRE1, BRE1	uc004bbn.3	Q5VTR2	OTTHUMG00000020385	ENST00000389120.3:c.563T>C	chr9.hg19:g.104303192T>C	ENSP00000373772:p.Ile188Thr	136.0	0.0		143.0	7.0	NM_019592	A7MCT5|Q2TB34|Q69YL5|Q6P527|Q8N3J4|Q96JD3|Q9H9Y7|Q9HA51|Q9NUR4|Q9NWQ3|Q9NX83	Missense_Mutation	SNP	ENST00000389120.3	hg19	CCDS35084.1	.	.	.	.	.	.	.	.	.	.	T	10.79	1.450996	0.26074	.	.	ENSG00000155827	ENST00000389120	T	0.77750	-1.12	4.69	4.69	0.59074	.	0.114258	0.64402	D	0.000016	T	0.66963	0.2843	L	0.38175	1.15	0.48087	D	0.999589	P	0.34662	0.462	B	0.27887	0.084	T	0.68918	-0.5282	10	0.45353	T	0.12	-9.6461	14.0986	0.65039	0.0:0.0:0.0:1.0	.	188	Q5VTR2	BRE1A_HUMAN	T	188	ENSP00000373772:I188T	ENSP00000373772:I188T	I	+	2	0	RNF20	103343013	1.000000	0.71417	1.000000	0.80357	0.104000	0.19210	5.286000	0.65639	1.887000	0.54652	0.374000	0.22700	ATT	.	.		0.522	RNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356402.1	NM_019592		C	104303192	T	C	104303192	3	2	309	1	0	0	0	0	1	0	0	0	13488	1493	52	2	577	2	RNF20	9	104303192	Missense_Mutation	SNP	T	TCGA-K7-A5RF-01A-11D-A28X-10		104303192	36910239	34	44076										
PARD3	56288	hgsc.bcm.edu	37	chr10	34671814	34671814	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	accacatggaaccaaatgatGggtgtacgcatggcttggcg	13	9	0	1			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr10:34671814G>A	ENST00000374789.3	-	9	1378	c.1053C>T	c.(1051-1053)ccC>ccT	p.P351P	PARD3_ENST00000374776.1_Silent_p.P351P|PARD3_ENST00000374794.3_Silent_p.P307P|PARD3_ENST00000545693.1_Silent_p.P351P|PARD3_ENST00000340077.5_Silent_p.P351P|PARD3_ENST00000545260.1_Silent_p.P307P|PARD3_ENST00000350537.4_Silent_p.P351P|PARD3_ENST00000374788.3_Silent_p.P351P|PARD3_ENST00000544292.1_Silent_p.P81P|PARD3_ENST00000374790.3_Silent_p.P307P|PARD3_ENST00000374773.1_Silent_p.P351P|PARD3_ENST00000346874.4_Silent_p.P351P	NM_019619.3	NP_062565.2	Q8TEW0	PARD3_HUMAN	par-3 family cell polarity regulator	351	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				apical constriction (GO:0003383)|asymmetric cell division (GO:0008356)|axonogenesis (GO:0007409)|cell cycle (GO:0007049)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|centrosome localization (GO:0051642)|establishment of epithelial cell polarity (GO:0090162)|establishment or maintenance of cell polarity (GO:0007163)|microtubule cytoskeleton organization (GO:0000226)|myelination in peripheral nervous system (GO:0022011)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|positive regulation of myelination (GO:0031643)|protein complex assembly (GO:0006461)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein targeting to membrane (GO:0006612)|regulation of actin filament-based process (GO:0032970)|regulation of cellular localization (GO:0060341)|tight junction assembly (GO:0070830)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing, spreading of cells (GO:0044319)	apical part of cell (GO:0045177)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|internode region of axon (GO:0033269)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|tight junction (GO:0005923)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	63		Breast(68;0.0707)				ACCAAATGATGGGTGTACGCA	0.403																																					p.P351P		Atlas-SNP	.											.	PARD3	131	.	0			c.C1053T						.						150	139	142					10																	34671814		2203	4300	6503	SO:0001819	synonymous_variant	56288	exon9			AATGATGGGTGTA	AF252293	CCDS7178.1, CCDS53509.1, CCDS53510.1, CCDS53511.1, CCDS53512.1, CCDS53513.1, CCDS53514.1, CCDS53515.1, CCDS53516.1	10p11.22	2014-06-13	2013-08-28		ENSG00000148498	ENSG00000148498			16051	protein-coding gene	gene with protein product	"atypical PKC isotype-specific interacting protein", "par-3 family cell polarity regulator alpha", "protein phosphatase 1, regulatory subunit 118"	606745	"par-3 (partitioning defective 3, C.elegans) homolog", "par-3 partitioning defective 3 homolog (C. elegans)"			10934474	Standard	NM_001184790		Approved	PAR3, PARD3A, Bazooka, Baz, ASIP, PPP1R118	uc010qej.2	Q8TEW0	OTTHUMG00000017948	ENST00000374789.3:c.1053C>T	chr10.hg19:g.34671814G>A		229.0	0.0		249.0	16.0	NM_001184788	F5H5T0|Q5T2U1|Q5VUA2|Q5VUA3|Q5VWV0|Q5VWV1|Q5VWV3|Q5VWV4|Q5VWV5|Q6IQ47|Q8TCZ9|Q8TEW1|Q8TEW2|Q8TEW3|Q96K28|Q96RM6|Q96RM7|Q9BY57|Q9BY58|Q9HC48|Q9NWL4|Q9NYE6	Silent	SNP	ENST00000374789.3	hg19	CCDS7178.1																																																																																			.	.		0.403	PARD3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047527.1	NM_019619		A	34671814	G	A	34671814	2	1	309	1	0	0	0	0	0	0	0	1	11452	1335	47	3		3	PARD3	10	34671814	Silent	SNP	G	TCGA-K7-A5RF-01A-11D-A28X-10		34671814	100862933	35	44077										
PCDH15	65217	hgsc.bcm.edu	37	chr10	55719518	55719518	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	tcctcctgtgtgaagcgtggGatctcaccaggatgtaagac	12	10	1	2	rs370200250		TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr10:55719518G>A	ENST00000320301.6	-	23	3490	c.3096C>T	c.(3094-3096)atC>atT	p.I1032I	PCDH15_ENST00000395438.1_Silent_p.I1032I|PCDH15_ENST00000395445.1_Silent_p.I1039I|PCDH15_ENST00000373965.2_Silent_p.I1039I|PCDH15_ENST00000395432.2_Silent_p.I995I|PCDH15_ENST00000395433.1_Silent_p.I1010I|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000409834.1_Silent_p.I643I|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000395430.1_Silent_p.I1032I|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000414778.1_Silent_p.I1037I|PCDH15_ENST00000437009.1_Silent_p.I961I|PCDH15_ENST00000361849.3_Silent_p.I1032I	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1032	Cadherin 9. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				TGAAGCGTGGGATCTCACCAG	0.413										HNSCC(58;0.16)																											p.I1037I		Atlas-SNP	.											.	PCDH15	1715	.	0			c.C3111T						.						82	73	76					10																	55719518		2203	4300	6503	SO:0001819	synonymous_variant	65217	exon24			GCGTGGGATCTCA	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.3096C>T	chr10.hg19:g.55719518G>A		58.0	0.0		75.0	8.0	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Silent	SNP	ENST00000320301.6	hg19	CCDS7248.1																																																																																			.	.		0.413	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		A	55719518	G	A	55719518	2	1	309	1	0	0	0	0	0	0	0	1	11520	1164	41	3		3	PCDH15	10	55719518	Silent	SNP	G	TCGA-K7-A5RF-01A-11D-A28X-10	21047704	55719518	79815229	36	44078										
BTAF1	9044	hgsc.bcm.edu	37	chr10	93749020	93749020	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	aatgacagttacagagaccaAccaggagtggcaagtgttgc	12	8	0	2			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr10:93749020A>G	ENST00000265990.6	+	20	2845	c.2537A>G	c.(2536-2538)aAc>aGc	p.N846S	BTAF1_ENST00000471217.1_3'UTR	NM_003972.2	NP_003963.1	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170kDa	846					negative regulation of chromatin binding (GO:0035562)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(2)|urinary_tract(6)	59		Colorectal(252;0.0846)				ACAGAGACCAACCAGGAGTGG	0.413																																					p.N846S		Atlas-SNP	.											.	BTAF1	148	.	0			c.A2537G						.						89	86	87					10																	93749020		2203	4300	6503	SO:0001583	missense	9044	exon20			AGACCAACCAGGA	AJ001017	CCDS7419.1	10q22-q23	2013-05-01	2013-05-01		ENSG00000095564	ENSG00000095564			17307	protein-coding gene	gene with protein product	"Mot1 homolog (S. cerevisiae)"	605191	"BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170 kD (Mot1 homolog, S. cerevisiae)"			9342322, 9488487	Standard	NM_003972		Approved	TAFII170, TAF172, MOT1, TAF-172, TAF(II)170	uc001khr.3	O14981	OTTHUMG00000018752	ENST00000265990.6:c.2537A>G	chr10.hg19:g.93749020A>G	ENSP00000265990:p.Asn846Ser	73.0	0.0		112.0	9.0	NM_003972	B4E0W6|O43578	Missense_Mutation	SNP	ENST00000265990.6	hg19	CCDS7419.1	.	.	.	.	.	.	.	.	.	.	A	4.050	0.006909	0.07866	.	.	ENSG00000095564	ENST00000265990	D	0.89552	-2.53	4.91	4.91	0.64330	Domain of unknown function DUF3535 (1);Armadillo-type fold (1);	0.092168	0.85682	D	0.000000	T	0.73697	0.3620	N	0.04636	-0.2	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.10450	0.005;0.005	T	0.67968	-0.5533	10	0.17369	T	0.5	-0.9041	9.458	0.38767	0.9195:0.0:0.0805:0.0	.	846;846	Q2M1V9;O14981	.;BTAF1_HUMAN	S	846	ENSP00000265990:N846S	ENSP00000265990:N846S	N	+	2	0	BTAF1	93739000	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.183000	0.50918	1.988000	0.58038	0.477000	0.44152	AAC	.	.		0.413	BTAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049380.4	NM_003972		G	93749020	A	G	93749020	3	3	309	1	0	0	0	0	1	0	0	0	1538	43	2	2	2615	2	BTAF1	10	93749020	Missense_Mutation	SNP	A	TCGA-K7-A5RF-01A-11D-A28X-10	38029502	93749020	41785727	37	44079										
SH3PXD2A	9644	hgsc.bcm.edu	37	chr10	105362908	105362908	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	atggtgatggatgaggaaaaGgaggctgaggagtggttctt	18	2	1	3			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr10:105362908G>T	ENST00000369774.4	-	15	2343	c.2067C>A	c.(2065-2067)tcC>tcA	p.S689S	SH3PXD2A_ENST00000427662.2_Intron|SH3PXD2A_ENST00000538130.1_Silent_p.S524S|SH3PXD2A_ENST00000315994.6_5'UTR|SH3PXD2A_ENST00000540321.1_Silent_p.S556S|SH3PXD2A_ENST00000355946.2_Silent_p.S661S			Q5TCZ1	SPD2A_HUMAN	SH3 and PX domains 2A	689	Ser-rich.				superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|podosome (GO:0002102)	phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(18)|ovary(1)|skin(1)|urinary_tract(1)	38		Colorectal(252;0.0815)|Breast(234;0.131)		Epithelial(162;4.09e-10)|all cancers(201;2.73e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0119)		ATGAGGAAAAGGAGGCTGAGG	0.547																																					p.S661S		Atlas-SNP	.											.	SH3PXD2A	90	.	0			c.C1983A						.						118	135	129					10																	105362908		2203	4300	6503	SO:0001819	synonymous_variant	9644	exon14			GGAAAAGGAGGCT	AB007878	CCDS31278.1	10q25.1	2006-02-13	2006-02-13	2006-02-13	ENSG00000107957	ENSG00000107957			23664	protein-coding gene	gene with protein product	"five SH3 domains"		"SH3 multiple domains 1"	SH3MD1		9687503	Standard	XM_005270297		Approved	FISH, KIAA0418	uc001kxj.1	Q5TCZ1	OTTHUMG00000018997	ENST00000369774.4:c.2067C>A	chr10.hg19:g.105362908G>T		31.0	0.0		55.0	6.0	NM_014631	D3DR98|O43302|Q5TCZ2|Q5TDQ8	Silent	SNP	ENST00000369774.4	hg19		.	.	.	.	.	.	.	.	.	.	G	4.225	0.040538	0.08196	.	.	ENSG00000107957	ENST00000420222	.	.	.	5.42	3.22	0.36961	.	.	.	.	.	T	0.60248	0.2254	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57860	-0.7738	4	.	.	.	-31.4903	10.6452	0.45615	0.1865:0.0:0.8135:0.0	.	.	.	.	I	616	.	.	L	-	1	0	SH3PXD2A	105352898	1.000000	0.71417	0.998000	0.56505	0.983000	0.72400	2.843000	0.48238	1.291000	0.44653	0.561000	0.74099	CTT	.	.		0.547	SH3PXD2A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050178.1	NM_014631		T	105362908	G	T	105362908	2	4	309	1	0	0	0	0	0	0	0	1	14271	987	35	3		3	SH3PXD2A	10	105362908	Silent	SNP	G	TCGA-K7-A5RF-01A-11D-A28X-10	11613888	105362908	30171839	38	44080										
KRTAP5-2	440021	hgsc.bcm.edu	37	chr11	1619335	1619335	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	atctggagccacatcccccaCagctggagctgcagccccca	9	18	1	0			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr11:1619335C>T	ENST00000412090.1	-	1	189	c.146G>A	c.(145-147)tGt>tAt	p.C49Y	KRTAP5-AS1_ENST00000424148.1_RNA|KRTAP5-AS1_ENST00000532922.1_RNA|KRTAP5-AS1_ENST00000534077.1_RNA|KRTAP5-AS1_ENST00000524947.1_RNA	NM_001004325.1	NP_001004325.1	Q701N4	KRA52_HUMAN	keratin associated protein 5-2	49						keratin filament (GO:0045095)				large_intestine(1)|lung(2)|skin(1)	4		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		ACATCCCCCACAGCTGGAGCT	0.677																																					p.C49Y		Atlas-SNP	.											.	KRTAP5-2	38	.	0			c.G146A						.						45	55	52					11																	1619335		2201	4283	6484	SO:0001583	missense	440021	exon1			CCCCCACAGCTGG	AB126071	CCDS31331.1	11p15.5	2008-02-05				ENSG00000205867		"Keratin associated proteins"	23597	protein-coding gene	gene with protein product						15144888	Standard	NM_001004325		Approved	KRTAP5.2, KRTAP5-8	uc001ltv.3	Q701N4		ENST00000412090.1:c.146G>A	chr11.hg19:g.1619335C>T	ENSP00000400041:p.Cys49Tyr	136.0	0.0		189.0	17.0	NM_001004325	A9JTZ1	Missense_Mutation	SNP	ENST00000412090.1	hg19	CCDS31331.1	.	.	.	.	.	.	.	.	.	.	c	11.31	1.600950	0.28534	.	.	ENSG00000205867	ENST00000412090	T	0.00958	5.5	2.77	0.0567	0.14320	.	.	.	.	.	T	0.02012	0.0063	M	0.88775	2.98	0.09310	N	1	B	0.15141	0.012	B	0.14578	0.011	T	0.30794	-0.9966	9	0.35671	T	0.21	.	7.3669	0.26779	0.0:0.7692:0.0:0.2308	.	49	Q701N4	KRA52_HUMAN	Y	49	ENSP00000400041:C49Y	ENSP00000400041:C49Y	C	-	2	0	KRTAP5-2	1575911	0.975000	0.34042	0.015000	0.15790	0.501000	0.33797	1.170000	0.31883	-0.053000	0.13289	0.388000	0.25769	TGT	.	.		0.677	KRTAP5-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384775.1	NM_001004325		T	1619335	C	T	1619335	3	4	309	1	0	0	0	0	1	0	0	0	8570	478	17	3	391	3	KRTAP5-2	11	1619335	Missense_Mutation	SNP	C	TCGA-K7-A5RF-01A-11D-A28X-10		1619335	133387181	39	44081										
GANAB	23193	hgsc.bcm.edu	37	chr11	62400540	62400540	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	catagacatgctccatgcctGgcagagagaagtccaaaccc	9	13	0	3			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr11:62400540G>T	ENST00000356638.3	-	8	768	c.752C>A	c.(751-753)cCa>cAa	p.P251Q	GANAB_ENST00000540933.1_Missense_Mutation_p.P154Q|GANAB_ENST00000346178.4_Missense_Mutation_p.P273Q|GANAB_ENST00000534779.1_Missense_Mutation_p.P159Q|GANAB_ENST00000534422.1_5'UTR	NM_198334.1	NP_938148.1	Q14697	GANAB_HUMAN	glucosidase, alpha; neutral AB	251					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|glucosidase II complex (GO:0017177)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|glucan 1,3-alpha-glucosidase activity (GO:0033919)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|ovary(3)|skin(2)|urinary_tract(3)	35					Miglitol(DB00491)	CTCCATGCCTGGCAGAGAGAA	0.542																																					p.P273Q	Melanoma(23;1005 1074 15747 18937)	Atlas-SNP	.											.	GANAB	110	.	0			c.C818A						.						104	95	98					11																	62400540		2202	4299	6501	SO:0001583	missense	23193	exon9			ATGCCTGGCAGAG	AF144074	CCDS8026.1, CCDS41656.1, CCDS60817.1, CCDS60818.1	11q12.3	2012-10-02			ENSG00000089597	ENSG00000089597	3.2.1.20		4138	protein-coding gene	gene with protein product		104160				10764838, 6342981	Standard	NM_198335		Approved	GluII, G2AN, KIAA0088	uc001nua.4	Q14697	OTTHUMG00000167696	ENST00000356638.3:c.752C>A	chr11.hg19:g.62400540G>T	ENSP00000349053:p.Pro251Gln	71.0	0.0		84.0	4.0	NM_198335	A6NC20|Q8WTS9|Q9P0X0	Missense_Mutation	SNP	ENST00000356638.3	hg19	CCDS8026.1	.	.	.	.	.	.	.	.	.	.	G	17.39	3.376809	0.61735	.	.	ENSG00000089597	ENST00000346178;ENST00000356638;ENST00000534779;ENST00000540933	D;D;D;D	0.86497	-2.13;-2.13;-2.13;-2.13	5.14	5.14	0.70334	Glycoside hydrolase-type carbohydrate-binding (1);	0.000000	0.85682	D	0.000000	D	0.88695	0.6506	M	0.65677	2.01	0.80722	D	1	P;P;P;P	0.46395	0.805;0.805;0.805;0.877	B;B;B;P	0.47044	0.433;0.334;0.334;0.535	D	0.89390	0.3688	10	0.54805	T	0.06	-12.0254	16.153	0.81636	0.0:0.0:1.0:0.0	.	137;159;251;273	B4DIW2;E9PKU7;Q14697;Q14697-2	.;.;GANAB_HUMAN;.	Q	273;251;159;154	ENSP00000340466:P273Q;ENSP00000349053:P251Q;ENSP00000435306:P159Q;ENSP00000442962:P154Q	ENSP00000340466:P273Q	P	-	2	0	GANAB	62157116	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	3.145000	0.50623	2.673000	0.90976	0.557000	0.71058	CCA	.	.		0.542	GANAB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395689.1	NM_198334		T	62400540	G	T	62400540	3	4	309	1	0	0	0	0	1	0	0	0	6241	1348	47	3	2150	3	GANAB	11	62400540	Missense_Mutation	SNP	G	TCGA-K7-A5RF-01A-11D-A28X-10	60781205	62400540	72605976	40	44082										
DENND5B	160518	hgsc.bcm.edu	37	chr12	31552686	31552686	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	tgaccaatctgaacagtggtCagcttccccaagttctggca	9	12	3	2			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr12:31552686C>A	ENST00000389082.5	-	16	3234	c.2970G>T	c.(2968-2970)ctG>ctT	p.L990L	DENND5B_ENST00000306833.6_Silent_p.L1025L|DENND5B_ENST00000536562.1_Silent_p.L1025L	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	990	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				positive regulation of Rab GTPase activity (GO:0032851)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						GAACAGTGGTCAGCTTCCCCA	0.453																																					p.L990L		Atlas-SNP	.											.	DENND5B	114	.	0			c.G2970T						.						109	102	104					12																	31552686		2074	4252	6326	SO:0001819	synonymous_variant	160518	exon16			AGTGGTCAGCTTC	AF086301	CCDS44857.1	12p11.21	2012-10-03			ENSG00000170456	ENSG00000170456		"DENN/MADD domain containing"	28338	protein-coding gene	gene with protein product						12477932	Standard	NM_144973		Approved	MGC24039	uc001rki.1	Q6ZUT9	OTTHUMG00000169034	ENST00000389082.5:c.2970G>T	chr12.hg19:g.31552686C>A		144.0	0.0		205.0	11.0	NM_144973	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	Silent	SNP	ENST00000389082.5	hg19	CCDS44857.1																																																																																			.	.		0.453	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1	NM_144973		A	31552686	C	A	31552686	2	1	309	1	0	0	0	0	0	0	0	1	4439	813	29	3		3	DENND5B	12	31552686	Silent	SNP	C	TCGA-K7-A5RF-01A-11D-A28X-10		31552686	102299209	41	44083										
SPATA7	55812	hgsc.bcm.edu	37	chr14	88904449	88904449	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	caactgaatttttcatgcctAtttataaatcaaagcattca	3	8	3	1			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr14:88904449A>G	ENST00000393545.4	+	12	1772	c.1483A>G	c.(1483-1485)Att>Gtt	p.I495V	SPATA7_ENST00000556553.1_Missense_Mutation_p.I463V|SPATA7_ENST00000045347.7_Intron|SPATA7_ENST00000356583.5_Missense_Mutation_p.I463V	NM_018418.4	NP_060888.2	Q9P0W8	SPAT7_HUMAN	spermatogenesis associated 7	495					response to stimulus (GO:0050896)|visual perception (GO:0007601)					cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)	18						TTTCATGCCTATTTATAAATC	0.358																																					p.I495V		Atlas-SNP	.											.	SPATA7	58	.	0			c.A1483G						.						56	56	56					14																	88904449		2203	4300	6503	SO:0001583	missense	55812	exon12			ATGCCTATTTATA	AF144487	CCDS9883.1, CCDS32132.1	14q31.3	2011-02-17				ENSG00000042317			20423	protein-coding gene	gene with protein product		609868	"Leber congenital amaurosis 3"	LCA3		9799089, 19268277	Standard	NM_018418		Approved	HSD3	uc001xwq.3	Q9P0W8		ENST00000393545.4:c.1483A>G	chr14.hg19:g.88904449A>G	ENSP00000377176:p.Ile495Val	81.0	0.0		122.0	11.0	NM_018418	Q5BKY5|Q8WX30|Q96HF3|Q9H0X0|Q9P0W7	Missense_Mutation	SNP	ENST00000393545.4	hg19	CCDS9883.1	.	.	.	.	.	.	.	.	.	.	A	0.004	-2.283952	0.00251	.	.	ENSG00000042317	ENST00000556553;ENST00000393545;ENST00000356583	T;T;T	0.26223	1.76;1.75;1.76	5.87	-11.7	0.00046	.	1.626990	0.03178	N	0.171715	T	0.10852	0.0265	N	0.16307	0.4	0.09310	N	1	B;B;B	0.11235	0.002;0.004;0.0	B;B;B	0.11329	0.002;0.006;0.001	T	0.19484	-1.0304	10	0.02654	T	1	1.7256	9.5377	0.39233	0.3402:0.299:0.3608:0.0	.	463;463;495	A8K3L6;Q9P0W8-2;Q9P0W8	.;.;SPAT7_HUMAN	V	463;495;463	ENSP00000451128:I463V;ENSP00000377176:I495V;ENSP00000348991:I463V	ENSP00000348991:I463V	I	+	1	0	SPATA7	87974202	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-1.078000	0.03413	-3.883000	0.00095	-2.357000	0.00240	ATT	.	.		0.358	SPATA7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410172.1			G	88904449	A	G	88904449	3	3	309	1	0	0	0	0	1	0	0	0	15029	449	16	2	1529	2	SPATA7	14	88904449	Missense_Mutation	SNP	A	TCGA-K7-A5RF-01A-11D-A28X-10		88904449	18445091	42	44084										
C14orf49	161176	hgsc.bcm.edu	37	chr14	95916270	95916270	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	tggcaggaccacggttacctCgatctggggcaggaaggtgt	16	9	1	0	rs201231576	byFrequency	TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr14:95916270C>T	ENST00000334258.5	-	7	1461	c.1447G>A	c.(1447-1449)Gag>Aag	p.E483K	SYNE3_ENST00000554873.1_Missense_Mutation_p.E240K|SYNE3_ENST00000553340.1_Missense_Mutation_p.E483K|SYNE3_ENST00000557275.1_Missense_Mutation_p.E483K	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	483					cytoskeletal anchoring at nuclear membrane (GO:0090286)|cytoskeleton organization (GO:0007010)|establishment of protein localization to membrane (GO:0090150)|regulation of cell shape (GO:0008360)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear outer membrane (GO:0005640)|SUN-KASH complex (GO:0034993)	actin filament binding (GO:0051015)			breast(1)|endometrium(2)|lung(25)	28						ACGGTTACCTCGATCTGGGGC	0.662																																					p.E483K		Atlas-SNP	.											.	SYNE3	130	.	0			c.G1447A						.						26	26	26					14																	95916270		2166	4235	6401	SO:0001583	missense	161176	exon7			TTACCTCGATCTG	AK098471	CCDS9935.1	14q32.13	2012-05-31	2012-05-31	2012-05-31	ENSG00000176438	ENSG00000176438			19861	protein-coding gene	gene with protein product		610861	"chromosome 14 open reading frame 49"	C14orf49			Standard	NM_152592		Approved	FLJ25605, NET53, Nesprin-3, Nesp3	uc001yei.4	Q6ZMZ3	OTTHUMG00000171632	ENST00000334258.5:c.1447G>A	chr14.hg19:g.95916270C>T	ENSP00000334308:p.Glu483Lys	294.0	0.0		336.0	22.0	NM_152592	A6H8H3|Q86SX5|Q8N7G8	Missense_Mutation	SNP	ENST00000334258.5	hg19	CCDS9935.1	.	.	.	.	.	.	.	.	.	.	C	17.88	3.496696	0.64186	.	.	ENSG00000176438	ENST00000334258;ENST00000554873;ENST00000557275;ENST00000553340	T;T;T;T	0.17054	3.35;2.3;3.34;2.78	5.17	4.25	0.50352	.	0.000000	0.42682	D	0.000675	T	0.24005	0.0581	M	0.76574	2.34	0.54753	D	0.999987	P;D;P	0.56968	0.898;0.978;0.836	P;P;B	0.44946	0.465;0.465;0.275	T	0.05784	-1.0864	10	0.29301	T	0.29	-28.0853	12.6477	0.56744	0.0:0.8329:0.1671:0.0	.	483;483;483	Q6ZMZ3-2;Q6ZMZ3-3;Q6ZMZ3	.;.;SYNE3_HUMAN	K	483;240;483;483	ENSP00000334308:E483K;ENSP00000452154:E240K;ENSP00000450562:E483K;ENSP00000450774:E483K	ENSP00000334308:E483K	E	-	1	0	C14orf49	94986023	0.995000	0.38212	0.998000	0.56505	0.868000	0.49771	1.651000	0.37302	1.103000	0.41568	0.591000	0.81541	GAG	.	.		0.662	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592		T	95916270	C	T	95916270	3	4	309	1	0	0	0	0	1	0	0	0	1778	893	31	1	1524	1	C14orf49	14	95916270	Missense_Mutation	SNP	C	TCGA-K7-A5RF-01A-11D-A28X-10	7011821	95916270	11433270	43	44085										
PAQR4	124222	hgsc.bcm.edu	37	chr16	3021213	3021213	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	atgaccatgccctggggtcaGctgggcaaggatggctggct	16	10	1	1			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr16:3021213G>T	ENST00000318782.8	+	2	652	c.222G>T	c.(220-222)caG>caT	p.Q74H	PAQR4_ENST00000293978.8_Intron|PAQR4_ENST00000572687.1_Intron|PKMYT1_ENST00000431515.2_Intron|PAQR4_ENST00000576565.1_Missense_Mutation_p.Q7H|PKMYT1_ENST00000571102.1_5'Flank|PAQR4_ENST00000574988.1_Missense_Mutation_p.Q7H	NM_001284513.1|NM_152341.3	NP_001271442.1|NP_689554.2	Q8N4S7	PAQR4_HUMAN	progestin and adipoQ receptor family member IV	74						integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	8						CCTGGGGTCAGCTGGGCAAGG	0.612																																					p.Q74H		Atlas-SNP	.											.	PAQR4	23	.	0			c.G222T						.						50	50	50					16																	3021213		2198	4300	6498	SO:0001583	missense	124222	exon2			GGGTCAGCTGGGC		CCDS10485.1, CCDS66911.1, CCDS66912.1, CCDS73814.1	16p13	2008-05-02			ENSG00000162073	ENSG00000162073			26386	protein-coding gene	gene with protein product		614578				12477932	Standard	XM_005255112		Approved	FLJ30002	uc002csj.4	Q8N4S7	OTTHUMG00000128977	ENST00000318782.8:c.222G>T	chr16.hg19:g.3021213G>T	ENSP00000321804:p.Gln74His	111.0	0.0		145.0	8.0	NM_152341	A8K5Q8|D3DUA2|D3DUA3|Q8NAS6|Q96NW1	Missense_Mutation	SNP	ENST00000318782.8	hg19	CCDS10485.1	.	.	.	.	.	.	.	.	.	.	G	13.49	2.251369	0.39797	.	.	ENSG00000162073	ENST00000318782	T	0.29917	1.55	4.73	3.77	0.43336	.	0.062767	0.64402	D	0.000004	T	0.38825	0.1055	L	0.58101	1.795	0.52501	D	0.999955	D	0.55385	0.971	P	0.52267	0.694	T	0.12016	-1.0564	10	0.38643	T	0.18	-16.781	10.7839	0.46395	0.095:0.0:0.905:0.0	.	74	Q8N4S7	PAQR4_HUMAN	H	74	ENSP00000321804:Q74H	ENSP00000321804:Q74H	Q	+	3	2	PAQR4	2961214	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	3.467000	0.53078	0.978000	0.38470	0.462000	0.41574	CAG	.	.		0.612	PAQR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250966.1	NM_152341		T	3021213	G	T	3021213	3	4	309	1	0	0	0	0	1	0	0	0	11446	962	34	3	228	3	PAQR4	16	3021213	Missense_Mutation	SNP	G	TCGA-K7-A5RF-01A-11D-A28X-10		3021213	87333540	44	44086										
ZNF629	23361	hgsc.bcm.edu	37	chr16	30794703	30794703	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	ctcggtgcagcggtatggctTctcgcccgcgtggatcttct	13	13	3	0			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr16:30794703T>A	ENST00000262525.4	-	3	1153	c.946A>T	c.(946-948)Aag>Tag	p.K316*		NM_001080417.1	NP_001073886.1	Q9UEG4	ZN629_HUMAN	zinc finger protein 629	316					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(3)|urinary_tract(1)	22			Colorectal(24;0.198)			CGGTATGGCTTCTCGCCCGCG	0.632																																					p.K316X		Atlas-SNP	.											.	ZNF629	44	.	0			c.A946T						.						65	74	71					16																	30794703		2193	4299	6492	SO:0001587	stop_gained	23361	exon3			ATGGCTTCTCGCC	AB002324	CCDS45463.1	16p11.2	2013-01-08				ENSG00000102870		"Zinc fingers, C2H2-type"	29008	protein-coding gene	gene with protein product			"zinc finger protein 65"	ZNF65		9205841	Standard	NM_001080417		Approved	KIAA0326	uc002dzs.1	Q9UEG4		ENST00000262525.4:c.946A>T	chr16.hg19:g.30794703T>A	ENSP00000262525:p.Lys316*	157.0	0.0		223.0	14.0	NM_001080417	Q15938	Nonsense_Mutation	SNP	ENST00000262525.4	hg19	CCDS45463.1	.	.	.	.	.	.	.	.	.	.	T	36	5.843208	0.97016	.	.	ENSG00000102870	ENST00000262525	.	.	.	5.59	5.59	0.84812	.	0.000000	0.47455	D	0.000223	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-38.8667	14.74	0.69445	0.0:0.0:0.0:1.0	.	.	.	.	X	316	.	ENSP00000262525:K316X	K	-	1	0	ZNF629	30702204	0.047000	0.20315	1.000000	0.80357	0.997000	0.91878	0.651000	0.24873	2.125000	0.65367	0.459000	0.35465	AAG	.	.		0.632	ZNF629-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434291.1	NM_015309		A	30794703	T	A	30794703	4	1	309	1	0	0	0	0	0	1	0	0	18068	1792	62	4	1667	4	ZNF629	16	30794703	Nonsense_Mutation	SNP	T	TCGA-K7-A5RF-01A-11D-A28X-10	27773490	30794703	59560050	45	44087										
PRPF8	10594	hgsc.bcm.edu	37	chr17	1554786	1554786	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	tggcatgggtggtgacatccTggggtgataactgcggggac	18	7	0	2			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr17:1554786T>C	ENST00000572621.1	-	40	6837	c.6572A>G	c.(6571-6573)cAg>cGg	p.Q2191R	RILP_ENST00000301336.6_5'Flank|PRPF8_ENST00000304992.6_Missense_Mutation_p.Q2191R|PRPF8_ENST00000575116.1_5'Flank			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	2191	MPN.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		GGTGACATCCTGGGGTGATAA	0.537																																					p.Q2191R		Atlas-SNP	.											.	PRPF8	169	.	0			c.A6572G						.						121	109	113					17																	1554786		2203	4300	6503	SO:0001583	missense	10594	exon41			ACATCCTGGGGTG	AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231			17340	protein-coding gene	gene with protein product		607300	"PRP8 pre-mRNA processing factor 8 homolog (yeast)", "PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)"	RP13		11468273, 10411133	Standard	NM_006445		Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.6572A>G	chr17.hg19:g.1554786T>C	ENSP00000460348:p.Gln2191Arg	134.0	0.0		166.0	7.0	NM_006445	O14547|O75965	Missense_Mutation	SNP	ENST00000572621.1	hg19	CCDS11010.1	.	.	.	.	.	.	.	.	.	.	T	12.54	1.969587	0.34754	.	.	ENSG00000174231	ENST00000304992	T	0.54675	0.56	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.64057	0.2564	M	0.82630	2.6	0.80722	D	1	B	0.32893	0.389	B	0.43274	0.414	T	0.61931	-0.6961	10	0.19147	T	0.46	.	15.7744	0.78198	0.0:0.0:0.0:1.0	.	2191	Q6P2Q9	PRP8_HUMAN	R	2191	ENSP00000304350:Q2191R	ENSP00000304350:Q2191R	Q	-	2	0	PRPF8	1501536	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.779000	0.85648	2.122000	0.65172	0.533000	0.62120	CAG	.	.		0.537	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2			C	1554786	T	C	1554786	3	2	309	1	0	0	0	0	1	0	0	0	12587	1580	55	2	447	2	PRPF8	17	1554786	Missense_Mutation	SNP	T	TCGA-K7-A5RF-01A-11D-A28X-10		1554786	79640424	46	44088										
KCNH6	81033	hgsc.bcm.edu	37	chr17	61613103	61613103	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	cgtagcacggaagctggaccGctactctgagtatggggcgg	16	10	1	1	rs370829183		TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr17:61613103G>A	ENST00000583023.1	+	6	1186	c.1175G>A	c.(1174-1176)cGc>cAc	p.R392H	KCNH6_ENST00000314672.5_Missense_Mutation_p.R392H|KCNH6_ENST00000456941.2_Missense_Mutation_p.R392H|KCNH6_ENST00000580652.1_Missense_Mutation_p.R392H|KCNH6_ENST00000581784.1_Missense_Mutation_p.R392H	NM_030779.2	NP_110406.1	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 6	392					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(4)|large_intestine(6)|lung(20)|ovary(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	54					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	AAGCTGGACCGCTACTCTGAG	0.607																																					p.R392H		Atlas-SNP	.											KCNH6,NS,carcinoma,0,1	KCNH6	122	.	0			c.G1175A						.	G	HIS/ARG,HIS/ARG	0,4406		0,0,2203	78	69	72		1175,1175	4.4	1	17		72	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	KCNH6	NM_030779.2,NM_173092.1	29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	392/995,392/906	61613103	1,13005	2203	4300	6503	SO:0001583	missense	81033	exon6			TGGACCGCTACTC	AF311913	CCDS11638.1, CCDS11639.1, CCDS62290.1	17q23.3	2012-07-05				ENSG00000173826		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18862	protein-coding gene	gene with protein product		608168				16382104	Standard	NM_030779		Approved	Kv11.2, erg2, HERG2	uc002jay.3	Q9H252		ENST00000583023.1:c.1175G>A	chr17.hg19:g.61613103G>A	ENSP00000463533:p.Arg392His	131.0	0.0		165.0	10.0	NM_030779	Q9BRD7	Missense_Mutation	SNP	ENST00000583023.1	hg19	CCDS11638.1	.	.	.	.	.	.	.	.	.	.	G	11.47	1.648974	0.29336	0.0	1.16E-4	ENSG00000173826	ENST00000314672;ENST00000456941	D;D	0.98474	-4.95;-4.95	4.36	4.36	0.52297	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98448	0.9483	L	0.58101	1.795	0.80722	D	1	D;D;D;D;D	0.76494	0.979;0.991;0.999;0.991;0.981	P;P;D;P;P	0.74023	0.864;0.817;0.982;0.869;0.761	D	0.98732	1.0713	10	0.42905	T	0.14	.	17.0722	0.86577	0.0:0.0:1.0:0.0	.	269;392;392;392;392	B4DPJ3;B4DKC0;Q9H252-2;Q9H252;Q9H252-3	.;.;.;KCNH6_HUMAN;.	H	392	ENSP00000318212:R392H;ENSP00000396900:R392H	ENSP00000318212:R392H	R	+	2	0	KCNH6	58966835	1.000000	0.71417	1.000000	0.80357	0.111000	0.19643	9.657000	0.98554	2.244000	0.73946	0.313000	0.20887	CGC	.	.		0.607	KCNH6-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443853.1	NM_030779		A	61613103	G	A	61613103	3	1	309	1	0	0	0	0	1	0	0	0	8045	1087	38	1	1197	1	KCNH6	17	61613103	Missense_Mutation	SNP	G	TCGA-K7-A5RF-01A-11D-A28X-10	60058317	61613103	19582107	47	44089										
YIF1B	90522	hgsc.bcm.edu	37	chr19	38796124	38796124	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	tcagctgctgcgtctgccaaGatcttcagccgcagcgtccg	11	15	4	1			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr19:38796124G>C	ENST00000339413.6	-	8	858	c.813C>G	c.(811-813)atC>atG	p.I271M	YIF1B_ENST00000329420.8_Missense_Mutation_p.I256M|YIF1B_ENST00000592246.1_Missense_Mutation_p.I205M|YIF1B_ENST00000392124.3_Missense_Mutation_p.I240M|YIF1B_ENST00000592694.1_Missense_Mutation_p.I240M|YIF1B_ENST00000337679.8_3'UTR|YIF1B_ENST00000591784.1_Missense_Mutation_p.I240M	NM_001039672.2|NM_001039673.2	NP_001034761.1|NP_001034762.1	Q5BJH7	YIF1B_HUMAN	Yip1 interacting factor homolog B (S. cerevisiae)	271						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|prostate(1)	10	all_cancers(60;1.07e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CGTCTGCCAAGATCTTCAGCC	0.642																																					p.I271M		Atlas-SNP	.											.	YIF1B	47	.	0			c.C813G						.						13	16	15					19																	38796124		2184	4273	6457	SO:0001583	missense	90522	exon8			TGCCAAGATCTTC	AL833382	CCDS12512.1, CCDS33010.1, CCDS46066.1, CCDS46067.1	19q13.2	2008-02-05							30511	protein-coding gene	gene with protein product						12975309	Standard	NM_001039672		Approved	FinGER8	uc002ohz.2	Q5BJH7		ENST00000339413.6:c.813C>G	chr19.hg19:g.38796124G>C	ENSP00000343435:p.Ile271Met	242.0	0.0		281.0	23.0	NM_001039672	H7BXS8|Q5JPC2|Q8WY70|Q96C02|Q96IC4	Missense_Mutation	SNP	ENST00000339413.6	hg19	CCDS33010.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.238318	0.79800	.	.	ENSG00000167645	ENST00000339413;ENST00000329420;ENST00000392124	T;T;T	0.48836	0.8;0.81;0.81	4.96	4.96	0.65561	.	0.067243	0.64402	D	0.000010	T	0.62780	0.2456	M	0.62723	1.935	0.80722	D	1	P;P;P	0.52463	0.773;0.81;0.953	P;P;P	0.59357	0.515;0.647;0.856	T	0.65561	-0.6138	10	0.59425	D	0.04	-9.6626	15.7029	0.77555	0.0:0.0:1.0:0.0	.	240;271;268	Q5BJH7-2;Q5BJH7;Q5BJH7-3	.;YIF1B_HUMAN;.	M	271;256;240	ENSP00000343435:I271M;ENSP00000329559:I256M;ENSP00000375971:I240M	ENSP00000329559:I256M	I	-	3	3	YIF1B	43487964	1.000000	0.71417	1.000000	0.80357	0.812000	0.45895	3.311000	0.51919	2.304000	0.77564	0.462000	0.41574	ATC	.	.		0.642	YIF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460511.1	NM_033557		C	38796124	G	C	38796124	3	2	309	1	0	0	0	0	1	0	0	0	17491	932	33	4	135	4	YIF1B	19	38796124	Missense_Mutation	SNP	G	TCGA-K7-A5RF-01A-11D-A28X-10		38796124	20332859	48	44090										
ATP1A3	478	hgsc.bcm.edu	37	chr19	42486221	42486221	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	ggttcttcaccaggcagttcTtccgggccatgcgcttggcg	13	13	3	0			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr19:42486221T>A	ENST00000302102.5	-	9	1181	c.1031A>T	c.(1030-1032)aAg>aTg	p.K344M	ATP1A3_ENST00000543770.1_Missense_Mutation_p.K355M|ATP1A3_ENST00000602133.1_Missense_Mutation_p.K314M|ATP1A3_ENST00000545399.1_Missense_Mutation_p.K357M	NM_152296.4	NP_689509.1	P13637	AT1A3_HUMAN	ATPase, Na+/K+ transporting, alpha 3 polypeptide	344					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|memory (GO:0007613)|potassium ion import (GO:0010107)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	axon (GO:0030424)|dendritic spine head (GO:0044327)|dendritic spine neck (GO:0044326)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(19)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	52						caggcagttcttccGGGCCAT	0.602																																					p.K357M		Atlas-SNP	.											.	ATP1A3	117	.	0			c.A1070T						.						132	121	125					19																	42486221		2203	4300	6503	SO:0001583	missense	478	exon9			CAGTTCTTCCGGG		CCDS12594.1, CCDS58663.1, CCDS58664.1	19q13.2	2012-10-22			ENSG00000105409	ENSG00000105409	3.6.3.9	"ATPases / P-type"	801	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-3", "sodium pump subunit alpha-3", "sodium-potassium ATPase catalytic subunit alpha-3"	182350	"dystonia 12"	DYT12		17282997	Standard	NM_152296		Approved		uc002osh.4	P13637	OTTHUMG00000137384	ENST00000302102.5:c.1031A>T	chr19.hg19:g.42486221T>A	ENSP00000302397:p.Lys344Met	213.0	0.0		294.0	19.0	NM_001256214	B7Z2T0|B7Z401|F5H6J6|Q16732|Q16735|Q969K5	Missense_Mutation	SNP	ENST00000302102.5	hg19	CCDS12594.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.316293	0.81469	.	.	ENSG00000105409	ENST00000302102;ENST00000441343;ENST00000545399;ENST00000368080;ENST00000535899;ENST00000543770	D;D;D;D	0.92048	-2.96;-2.96;-2.96;-2.96	4.21	4.21	0.49690	ATPase, P-type, ATPase-associated domain (1);	0.000000	0.85682	D	0.000000	D	0.97445	0.9164	H	0.98388	4.22	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.994;0.999;0.999;0.999	D	0.97914	1.0310	10	0.87932	D	0	.	11.5777	0.50873	0.0:0.0:0.0:1.0	.	357;355;344;344	B7Z2T0;F5H6J6;E9PC51;P13637	.;.;.;AT1A3_HUMAN	M	344;344;357;314;88;355	ENSP00000302397:K344M;ENSP00000411503:K344M;ENSP00000444688:K357M;ENSP00000437577:K355M	ENSP00000302397:K344M	K	-	2	0	ATP1A3	47178061	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.841000	0.86834	1.910000	0.55303	0.459000	0.35465	AAG	.	.		0.602	ATP1A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268107.1	NM_152296		A	42486221	T	A	42486221	3	1	309	1	0	0	0	0	1	0	0	0	1130	1609	56	4	2070	4	ATP1A3	19	42486221	Missense_Mutation	SNP	T	TCGA-K7-A5RF-01A-11D-A28X-10	3690097	42486221	16642762	49	44091										
LYPD3	27076	hgsc.bcm.edu	37	chr19	43968547	43968547	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	cacttcactgtcttcatcttGttcggggagcatccgtcatc	8	13	5	0	rs368122649		TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr19:43968547G>A	ENST00000244333.3	-	2	229	c.141C>T	c.(139-141)aaC>aaT	p.N47N		NM_014400.2	NP_055215.2	O95274	LYPD3_HUMAN	LY6/PLAUR domain containing 3	47	UPAR/Ly6 1.				cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|pancreas(1)|upper_aerodigestive_tract(2)	11		Prostate(69;0.0153)				TCTTCATCTTGTTCGGGGAGC	0.672																																					p.N47N		Atlas-SNP	.											.	LYPD3	24	.	0			c.C141T						.	G		0,4406		0,0,2203	64	51	55		141	-8.2	0.8	19		55	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	LYPD3	NM_014400.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		47/347	43968547	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	27076	exon2			CATCTTGTTCGGG	AF082889	CCDS12620.1	19q13.31	2008-02-05				ENSG00000124466			24880	protein-coding gene	gene with protein product		609484				11179665, 11245483	Standard	NM_014400		Approved	C4.4A	uc002owl.1	O95274		ENST00000244333.3:c.141C>T	chr19.hg19:g.43968547G>A		95.0	0.0		111.0	12.0	NM_014400	Q9UJ74	Silent	SNP	ENST00000244333.3	hg19	CCDS12620.1																																																																																			.	.		0.672	LYPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463177.1	NM_014400		A	43968547	G	A	43968547	2	1	309	1	0	0	0	0	0	0	0	1	9120	1368	48	3		3	LYPD3	19	43968547	Silent	SNP	G	TCGA-K7-A5RF-01A-11D-A28X-10	1482326	43968547	15160436	50	44092										
SYT3	84258	hgsc.bcm.edu	37	chr19	51129160	51129160	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	cccaggaccctcacctgagaAgccagtgaggtccatcgctt	10	15	1	2			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr19:51129160A>G	ENST00000338916.4	-	5	2029	c.1396T>C	c.(1396-1398)Ttc>Ctc	p.F466L	SYT3_ENST00000593901.1_Missense_Mutation_p.F466L|SYT3_ENST00000600079.1_Missense_Mutation_p.F466L|SYT3_ENST00000544769.1_Missense_Mutation_p.F466L	NM_032298.2	NP_115674.1	Q9BQG1	SYT3_HUMAN	synaptotagmin III	466	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium ion-dependent exocytosis (GO:0017156)|positive regulation of vesicle fusion (GO:0031340)|response to calcium ion (GO:0051592)	cell junction (GO:0030054)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|metal ion binding (GO:0046872)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|prostate(2)|skin(3)|urinary_tract(2)	35		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00462)|GBM - Glioblastoma multiforme(134;0.0188)		TCACCTGAGAAGCCAGTGAGG	0.647																																					p.F466L		Atlas-SNP	.											.	SYT3	85	.	0			c.T1396C						.						53	47	49					19																	51129160		2203	4300	6503	SO:0001583	missense	84258	exon5			CTGAGAAGCCAGT	AL136594	CCDS12798.1	19q13.33	2014-07-02			ENSG00000213023	ENSG00000213023		"Synaptotagmins"	11511	protein-coding gene	gene with protein product		600327				7749232	Standard	NM_032298		Approved		uc002psv.3	Q9BQG1	OTTHUMG00000183064	ENST00000338916.4:c.1396T>C	chr19.hg19:g.51129160A>G	ENSP00000340914:p.Phe466Leu	117.0	0.0		140.0	10.0	NM_032298	Q8N5Z1|Q8N640	Missense_Mutation	SNP	ENST00000338916.4	hg19	CCDS12798.1	.	.	.	.	.	.	.	.	.	.	A	13.22	2.170708	0.38315	.	.	ENSG00000213023	ENST00000338916;ENST00000544769	T;T	0.68624	-0.34;-0.34	4.13	4.13	0.48395	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.171365	0.37053	U	0.002266	T	0.31295	0.0792	N	0.00661	-1.28	0.46298	D	0.998974	B	0.33512	0.415	B	0.35607	0.206	T	0.27640	-1.0068	10	0.13470	T	0.59	.	8.9115	0.35557	0.8117:0.1883:0.0:0.0	.	466	Q9BQG1	SYT3_HUMAN	L	466	ENSP00000340914:F466L;ENSP00000438883:F466L	ENSP00000340914:F466L	F	-	1	0	SYT3	55820972	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	2.832000	0.48152	1.662000	0.50781	0.454000	0.30748	TTC	.	.		0.647	SYT3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464910.1	NM_032298		G	51129160	A	G	51129160	3	3	309	1	0	0	0	0	1	0	0	0	15490	72	3	2	392	2	SYT3	19	51129160	Missense_Mutation	SNP	A	TCGA-K7-A5RF-01A-11D-A28X-10	7160613	51129160	7999823	51	44093										
NLRP8	126205	hgsc.bcm.edu	37	chr19	56499259	56499259	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	tcacgggaaaaagtgactgcCtatcccagattaatccttag	8	10	1	2			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr19:56499259C>G	ENST00000291971.3	+	10	3198	c.3127C>G	c.(3127-3129)Cta>Gta	p.L1043V	NLRP8_ENST00000590542.1_Missense_Mutation_p.L1024V	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	1043					neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		AAGTGACTGCCTATCCCAGAT	0.507																																					p.L1043V		Atlas-SNP	.											.	NLRP8	225	.	0			c.C3127G						.						117	98	104					19																	56499259		2203	4300	6503	SO:0001583	missense	126205	exon10			GACTGCCTATCCC	AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"Nucleotide-binding domain and leucine rich repeat containing"	22940	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"	609659	"NACHT, leucine rich repeat and PYD containing 8"	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.3127C>G	chr19.hg19:g.56499259C>G	ENSP00000291971:p.Leu1043Val	93.0	0.0		128.0	6.0	NM_176811	Q7RTR4	Missense_Mutation	SNP	ENST00000291971.3	hg19	CCDS12937.1	.	.	.	.	.	.	.	.	.	.	C	6.093	0.385410	0.11524	.	.	ENSG00000179709	ENST00000291971	T	0.75154	-0.91	1.44	0.356	0.16074	.	.	.	.	.	T	0.65923	0.2738	N	0.08118	0	0.09310	N	1	D;P	0.71674	0.998;0.461	D;B	0.73708	0.981;0.116	T	0.54403	-0.8299	9	0.33940	T	0.23	.	3.8138	0.08808	0.0:0.7566:0.0:0.2434	.	1024;1043	Q86W28-2;Q86W28	.;NALP8_HUMAN	V	1043	ENSP00000291971:L1043V	ENSP00000291971:L1043V	L	+	1	2	NLRP8	61191071	0.007000	0.16637	0.026000	0.17262	0.102000	0.19082	0.299000	0.19138	0.183000	0.20059	0.386000	0.25728	CTA	.	.		0.507	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811		G	56499259	C	G	56499259	3	3	309	1	0	0	0	0	1	0	0	0	10492	680	24	4	3165	4	NLRP8	19	56499259	Missense_Mutation	SNP	C	TCGA-K7-A5RF-01A-11D-A28X-10	5370099	56499259	2629724	52	44094										
A1BG	1	hgsc.bcm.edu	37	chr19	58863684	58863684	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	tcacagtagcgctgggctcaGagagggcgccttccccatcg	13	14	2	1			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr19:58863684G>A	ENST00000263100.3	-	4	639	c.578C>T	c.(577-579)tCt>tTt	p.S193F	A1BG-AS1_ENST00000595302.1_RNA|A1BG-AS1_ENST00000594950.1_RNA|A1BG-AS1_ENST00000593960.1_RNA|CTD-2619J13.8_ENST00000599109.1_RNA|A1BG-AS1_ENST00000600686.1_RNA|A1BG-AS1_ENST00000600379.1_RNA|A1BG-AS1_ENST00000593374.1_RNA|A1BG-AS1_ENST00000599728.1_RNA	NM_130786.3	NP_570602.2	P04217	A1BG_HUMAN	alpha-1-B glycoprotein	193	Ig-like V-type 2.					blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|prostate(2)	15		all_cancers(17;3.04e-16)|all_epithelial(17;7.77e-12)|Lung NSC(17;3.25e-05)|Colorectal(82;5.46e-05)|all_lung(17;0.000129)|all_neural(62;0.0182)|Ovarian(87;0.0443)|Breast(46;0.0889)|Renal(17;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0269)		GCTGGGCTCAGAGAGGGCGCC	0.627																																					p.S193F		Atlas-SNP	.											.	A1BG	40	.	0			c.C578T						.						100	89	93					19																	58863684		2203	4300	6503	SO:0001583	missense	1	exon4			GGCTCAGAGAGGG		CCDS12976.1	19q13.43	2013-10-15			ENSG00000121410	ENSG00000121410		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5	protein-coding gene	gene with protein product		138670				2591067	Standard	NM_130786		Approved		uc002qsd.4	P04217	OTTHUMG00000183507	ENST00000263100.3:c.578C>T	chr19.hg19:g.58863684G>A	ENSP00000263100:p.Ser193Phe	68.0	0.0		100.0	12.0	NM_130786	A8K052|Q68CK0|Q8IYJ6|Q96P39	Missense_Mutation	SNP	ENST00000263100.3	hg19	CCDS12976.1	.	.	.	.	.	.	.	.	.	.	G	15.06	2.721617	0.48728	.	.	ENSG00000121410	ENST00000263100;ENST00000453054	T	0.13307	2.6	3.39	3.39	0.38822	Immunoglobulin-like fold (1);	0.000000	0.43110	D	0.000603	T	0.40196	0.1107	M	0.88704	2.975	0.18873	N	0.999982	D	0.89917	1.0	D	0.85130	0.997	T	0.16689	-1.0394	10	0.87932	D	0	.	10.5741	0.45217	0.0:0.0:1.0:0.0	.	193	P04217	A1BG_HUMAN	F	193;71	ENSP00000263100:S193F	ENSP00000263100:S193F	S	-	2	0	A1BG	63555496	0.032000	0.19561	0.101000	0.21167	0.005000	0.04900	0.939000	0.28978	2.203000	0.70933	0.563000	0.77884	TCT	.	.		0.627	A1BG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466930.1	NM_130786		A	58863684	G	A	58863684	3	1	309	1	0	0	0	0	1	0	0	0	1	942	33	3	929	3	A1BG	19	58863684	Missense_Mutation	SNP	G	TCGA-K7-A5RF-01A-11D-A28X-10	2364425	58863684	265299	53	44095										
GNAS	2778	hgsc.bcm.edu	37	chr20	57415270	57415270	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	ccgcgctcctctggctctccTgctccatcgcgctcctccgc	8	22	2	0			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr20:57415270T>C	ENST00000313949.7	+	1	498	c.109T>C	c.(109-111)Tgc>Cgc	p.C37R	GNAS_ENST00000371075.3_Missense_Mutation_p.C37R|GNAS_ENST00000371098.2_Missense_Mutation_p.C37R|GNAS-AS1_ENST00000424094.2_RNA|GNAS-AS1_ENST00000443966.1_RNA|GNAS-AS1_ENST00000598163.1_RNA			P63092	GNAS2_HUMAN	GNAS complex locus	0					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|bone development (GO:0060348)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|cognition (GO:0050890)|developmental growth (GO:0048589)|energy reserve metabolic process (GO:0006112)|hair follicle placode formation (GO:0060789)|intracellular transport (GO:0046907)|platelet aggregation (GO:0070527)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of insulin secretion (GO:0050796)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intrinsic component of membrane (GO:0031224)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	adenylate cyclase activity (GO:0004016)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			adrenal_gland(12)|autonomic_ganglia(1)|biliary_tract(5)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(37)|liver(9)|lung(9)|ovary(16)|pancreas(56)|parathyroid(5)|pituitary(228)|prostate(2)|small_intestine(1)|stomach(1)|testis(2)|thyroid(35)|upper_aerodigestive_tract(3)|urinary_tract(1)	441	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			CTGGCTCTCCTGCTCCATCGC	0.711			Mis		pituitary adenoma		"McCune-Albright syndrome; pseudohypoparathyroidism, type IA"			TSP Lung(22;0.16)																											p.C37R	Colon(117;935 1597 6045 8307 46442)	Atlas-SNP	.		Dom	yes		20	20q13.2	2778	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	yes	E	.	GNAS	867	.	0			c.T109C						.						23	29	27					20																	57415270		2201	4293	6494	SO:0001583	missense	2778	exon1			CTCTCCTGCTCCA	M21142	CCDS13471.1, CCDS13472.1, CCDS42892.1, CCDS46622.1, CCDS46623.1, CCDS46624.1	20q13.2-q13.3	2010-03-01	2001-12-19	2001-12-20	ENSG00000087460	ENSG00000087460			4392	protein-coding gene	gene with protein product	"secretogranin VI"	139320	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	GNAS1			Standard	NM_000516		Approved	NESP55, NESP, GNASXL, GPSA, SCG6	uc002xzw.3	O95467	OTTHUMG00000033069	ENST00000313949.7:c.109T>C	chr20.hg19:g.57415270T>C	ENSP00000323571:p.Cys37Arg	53.0	0.0		70.0	4.0	NM_016592	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Missense_Mutation	SNP	ENST00000313949.7	hg19	CCDS13471.1	.	.	.	.	.	.	.	.	.	.	T	14.93	2.682219	0.47991	.	.	ENSG00000087460	ENST00000313949;ENST00000371098;ENST00000371075	.	.	.	3.72	3.72	0.42706	.	.	.	.	.	T	0.55657	0.1934	N	0.24115	0.695	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	T	0.58808	-0.7571	8	0.87932	D	0	.	9.0937	0.36625	0.0:0.0:0.0:1.0	.	37	O95467	GNAS3_HUMAN	R	37	.	ENSP00000323571:C37R	C	+	1	0	GNAS	56848665	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.026000	0.49689	1.935000	0.56089	0.377000	0.23210	TGC	.	.		0.711	GNAS-002	KNOWN	NMD_exception|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080418.7	NM_000516		C	57415270	T	C	57415270	3	2	309	1	0	0	0	0	1	0	0	0	6518	1580	55	2	111	2	GNAS	20	57415270	Missense_Mutation	SNP	T	TCGA-K7-A5RF-01A-11D-A28X-10		57415270	5610250	54	44096										
NDUFV3	4731	hgsc.bcm.edu	37	chr21	44324091	44324091	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	agagcagaggggcagctgcaAgccagtcctcctggggcggc	17	12	0	2			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr21:44324091A>G	ENST00000340344.4	+	3	235				NDUFV3_ENST00000460259.1_3'UTR|NDUFV3_ENST00000354250.2_Silent_p.Q323Q	NM_001001503.1	NP_001001503.1	P56181	NDUV3_HUMAN	NADH dehydrogenase (ubiquinone) flavoprotein 3, 10kDa						cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(2)|skin(1)	10				STAD - Stomach adenocarcinoma(101;0.0606)		GGCAGCTGCAAGCCAGTCCTC	0.647																																					p.Q323Q		Atlas-SNP	.											.	NDUFV3	23	.	0			c.A969G						.						32	39	37					21																	44324091		2199	4300	6499	SO:0001627	intron_variant	4731	exon3			GCTGCAAGCCAGT		CCDS33572.1, CCDS33573.1	21q22.3	2011-07-04	2002-08-29		ENSG00000160194	ENSG00000160194	1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7719	protein-coding gene	gene with protein product	"complex I 10kDa subunit"	602184	"NADH dehydrogenase (ubiquinone) flavoprotein 3 (10kD)"			9344673	Standard	NM_021075		Approved	CI-10k	uc002zcm.3	P56181	OTTHUMG00000086823	ENST00000340344.4:c.170-4883A>G	chr21.hg19:g.44324091A>G		73.0	0.0		110.0	6.0	NM_021075	A8K0M1|J3KNX7|Q6FGD3|Q8WU60|Q9HCR5	Silent	SNP	ENST00000340344.4	hg19	CCDS33573.1																																																																																			.	.		0.647	NDUFV3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195448.2			G	44324091	A	G	44324091	1	3	309	0	1	0	0	0	0	0	0	0	10310	69	3	2		2	NDUFV3	21	44324091	Intron	SNP	A	TCGA-K7-A5RF-01A-11D-A28X-10		44324091	3805804	55	44097										
ENTHD1	150350	hgsc.bcm.edu	37	chr22	40216999	40216999	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	tattccttaaccaatttaccTgcacccgaaagattacaaac	3	12	0	1			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chr22:40216999T>C	ENST00000325157.6	-	5	1081	c.831A>G	c.(829-831)gcA>gcG	p.A277A		NM_152512.3	NP_689725.2	Q8IYW4	ENTD1_HUMAN	ENTH domain containing 1	277										breast(2)|endometrium(1)|kidney(6)|large_intestine(6)|lung(11)|ovary(3)|skin(3)	32	Melanoma(58;0.0749)					CCAATTTACCTGCACCCGAAA	0.388																																					p.A277A		Atlas-SNP	.											.	ENTHD1	83	.	0			c.A831G						.						110	102	104					22																	40216999		2203	4300	6503	SO:0001630	splice_region_variant	150350	exon5			TTTACCTGCACCC	AK093154	CCDS13998.1	22q13.1	2006-06-26			ENSG00000176177	ENSG00000176177			26352	protein-coding gene	gene with protein product						12477932	Standard	NM_152512		Approved	FLJ25421	uc003ayg.3	Q8IYW4	OTTHUMG00000151098	ENST00000325157.6:c.832+1A>G	chr22.hg19:g.40216999T>C		49.0	0.0		76.0	7.0	NM_152512	B0QYD5|Q5H9F7|Q96LK3	Silent	SNP	ENST00000325157.6	hg19	CCDS13998.1																																																																																			.	.		0.388	ENTHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321302.1	NM_152512	Silent	C	40216999	T	C	40216999	5	2	309	1	0	0	0	0	0	0	1	0	5139	1594	55	2	1004	2	ENTHD1	22	40216999	Splice_Site	SNP	T	TCGA-K7-A5RF-01A-11D-A28X-10		40216999	11087567	56	44098										
P2RY4	5030	hgsc.bcm.edu	37	chrX	69479048	69479048	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	agggcggccccagcgtagtgCccgaagtgggtggcagatgc	18	11	0	1			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chrX:69479048C>A	ENST00000374519.2	-	1	606	c.427G>T	c.(427-429)Gca>Tca	p.A143S		NM_002565.3	NP_002556.1	P51582	P2RY4_HUMAN	pyrimidinergic receptor P2Y, G-protein coupled, 4	143					phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|transepithelial chloride transport (GO:0030321)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|uridine nucleotide receptor activity (GO:0015065)|UTP-activated nucleotide receptor activity (GO:0045030)			cervix(2)|endometrium(2)|large_intestine(8)|lung(6)	18						CAGCGTAGTGCCCGAAGTGGG	0.597																																					p.A143S		Atlas-SNP	.											.	P2RY4	39	.	0			c.G427T						.						52	48	49					X																	69479048		2203	4300	6503	SO:0001583	missense	5030	exon1			GTAGTGCCCGAAG	X91852	CCDS14398.1	Xq13	2012-08-08			ENSG00000186912	ENSG00000186912		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	8542	protein-coding gene	gene with protein product		300038				8537336	Standard	NM_002565		Approved	NRU, P2Y4, UNR, P2P	uc004dxz.1	P51582	OTTHUMG00000021769	ENST00000374519.2:c.427G>T	chrX.hg19:g.69479048C>A	ENSP00000363643:p.Ala143Ser	101.0	0.0		111.0	13.0	NM_002565	Q4VBB7|Q4VBB8|Q502W2|Q5JT22	Missense_Mutation	SNP	ENST00000374519.2	hg19	CCDS14398.1	.	.	.	.	.	.	.	.	.	.	C	0.553	-0.848501	0.02651	.	.	ENSG00000186912	ENST00000374519	T	0.36699	1.24	4.2	3.31	0.37934	GPCR, rhodopsin-like superfamily (1);	0.300514	0.31747	U	0.007130	T	0.09949	0.0244	N	0.00991	-1.07	0.39697	D	0.971137	B	0.02656	0.0	B	0.09377	0.004	T	0.26189	-1.0110	10	0.02654	T	1	.	8.8321	0.35091	0.4384:0.5616:0.0:0.0	.	143	P51582	P2RY4_HUMAN	S	143	ENSP00000363643:A143S	ENSP00000363643:A143S	A	-	1	0	P2RY4	69395773	0.948000	0.32251	0.342000	0.25602	0.862000	0.49288	2.415000	0.44635	0.877000	0.35895	0.517000	0.50305	GCA	.	.		0.597	P2RY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057058.2	NM_002565		A	69479048	C	A	69479048	3	1	309	1	0	0	0	0	1	0	0	0	11362	739	26	3	674	3	P2RY4	23	69479048	Missense_Mutation	SNP	C	TCGA-K7-A5RF-01A-11D-A28X-10		69479048	85791512	57	44099										
ATP11C	286410	hgsc.bcm.edu	37	chrX	138878508	138878508	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	cttcatcataaaagtccttaTcccatgagatgaagaaggag	8	8	2	3			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chrX:138878508T>A	ENST00000327569.3	-	12	1237	c.1139A>T	c.(1138-1140)gAt>gTt	p.D380V	ATP11C_ENST00000359686.2_Missense_Mutation_p.D380V|ATP11C_ENST00000370557.1_Missense_Mutation_p.D377V|ATP11C_ENST00000370543.1_Missense_Mutation_p.D380V|ATP11C_ENST00000460773.1_5'UTR|ATP11C_ENST00000361648.2_Missense_Mutation_p.D380V	NM_173694.4	NP_775965	Q8NB49	AT11C_HUMAN	ATPase, class VI, type 11C	380					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|positive regulation of B cell differentiation (GO:0045579)|pre-B cell differentiation (GO:0002329)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(31)|ovary(5)|prostate(1)|skin(3)	75	Acute lymphoblastic leukemia(192;0.000127)					AAAGTCCTTATCCCATGAGAT	0.363																																					p.D380V		Atlas-SNP	.											.	ATP11C	319	.	0			c.A1139T						.						62	55	57					X																	138878508		2203	4300	6503	SO:0001583	missense	286410	exon12			TCCTTATCCCATG	AJ580094	CCDS14668.1, CCDS35410.1	Xq27.1	2011-06-09	2007-09-19		ENSG00000101974	ENSG00000101974		"ATPases / P-type"	13554	protein-coding gene	gene with protein product		300516	"ATPase, Class VI, type 11C"			11015572	Standard	NM_173694		Approved	ATPIG, ATPIQ	uc004faz.3	Q8NB49	OTTHUMG00000022538	ENST00000327569.3:c.1139A>T	chrX.hg19:g.138878508T>A	ENSP00000332756:p.Asp380Val	151.0	0.0		143.0	26.0	NM_001010986	Q5JT69|Q5JT70|Q5JT71|Q5JT72|Q5JT73|Q6ZND5|Q6ZU50|Q6ZUP7|Q70IJ9|Q70IK0|Q8WX24	Missense_Mutation	SNP	ENST00000327569.3	hg19	CCDS14668.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.358385	0.82243	.	.	ENSG00000101974	ENST00000370557;ENST00000361648;ENST00000327569;ENST00000370543;ENST00000359686	T;T;T;T;T	0.72615	-0.67;-0.67;-0.67;-0.67;-0.67	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	D	0.90563	0.7042	H	0.99011	4.4	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.94021	0.7292	10	0.87932	D	0	.	14.2923	0.66286	0.0:0.0:0.0:1.0	.	380;380	Q8NB49-3;Q8NB49	.;AT11C_HUMAN	V	377;380;380;380;380	ENSP00000359588:D377V;ENSP00000355165:D380V;ENSP00000332756:D380V;ENSP00000359574:D380V;ENSP00000352715:D380V	ENSP00000332756:D380V	D	-	2	0	ATP11C	138706174	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.040000	0.89188	1.973000	0.57446	0.486000	0.48141	GAT	.	.		0.363	ATP11C-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354945.1	NM_173694		A	138878508	T	A	138878508	3	1	309	1	0	0	0	0	1	0	0	0	1121	1435	50	4	2398	4	ATP11C	23	138878508	Missense_Mutation	SNP	T	TCGA-K7-A5RF-01A-11D-A28X-10	69399460	138878508	16392052	58	44100										
KDM5D	8284	hgsc.bcm.edu	37	chrY	21901515	21901515	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0508474576271186	3	1	0.978947368421053	3.26315789473684	0.407894736842105	1	1	0	gggcttgtattccttatcttTtacctcattgtcaaacgggt	8	9	3	0			TCGA-K7-A5RF-01A-11D-A28X-10	TCGA-K7-A5RF-10B-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9ee0fd7-4827-4171-adec-2f21b3075a50	77617e95-e25c-432e-b8f7-1bb14530e30f	g.chrY:21901515T>C	ENST00000317961.4	-	6	827	c.556A>G	c.(556-558)Aaa>Gaa	p.K186E	KDM5D_ENST00000382806.2_Missense_Mutation_p.K129E|KDM5D_ENST00000541639.1_Missense_Mutation_p.K186E	NM_004653.4	NP_004644.2	Q9BY66	KDM5D_HUMAN	lysine (K)-specific demethylase 5D	186					histone H3-K4 demethylation (GO:0034720)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-K4 specific) (GO:0032453)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(9)|lung(6)|skin(1)	17					Vitamin C(DB00126)	TCCTTATCTTTTACCTCATTG	0.403																																					p.K186E		Atlas-SNP	.											.	KDM5D	40	.	0			c.A556G						.						94	109	105					Y																	21901515		597	1931	2528	SO:0001583	missense	8284	exon6			TATCTTTTACCTC	U52191	CCDS14794.1, CCDS55554.1, CCDS55555.1	Yq11	2013-01-28	2009-04-06	2009-04-06	ENSG00000012817	ENSG00000012817		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	11115	protein-coding gene	gene with protein product		426000	"Jumonji, AT rich interactive domain 1D (RBP2-like)", "Smcy homolog, Y-linked (mouse)", "jumonji, AT rich interactive domain 1D"	HYA, HY, SMCY, JARID1D		795123, 8841177	Standard	NM_001146705		Approved	KIAA0234	uc011naz.2	Q9BY66	OTTHUMG00000036508	ENST00000317961.4:c.556A>G	chrY.hg19:g.21901515T>C	ENSP00000322408:p.Lys186Glu	91.0	0.0		109.0	5.0	NM_001146705	A2RU19|A6H8V7|B7ZLX1|Q92509|Q92809|Q9HCU1	Missense_Mutation	SNP	ENST00000317961.4	hg19	CCDS14794.1																																																																																			.	.		0.403	KDM5D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088790.1	NM_004653		C	21901515	T	C	21901515	3	2	309	1	0	0	0	0	1	0	0	0	8145	1850	64	2	4248	2	KDM5D	24	21901515	Missense_Mutation	SNP	T	TCGA-K7-A5RF-01A-11D-A28X-10		21901515	37472051	59	44101										
NPHP4	261734	hgsc.bcm.edu	37	chr1	5964775	5964775	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ccagctggaccagctgcagtCgtggcgtcgttgcgggtggg	18	11	0	0	rs543023683		TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr1:5964775C>T	ENST00000378156.4	-	16	2310	c.2045G>A	c.(2044-2046)cGa>cAa	p.R682Q	NPHP4_ENST00000478423.2_5'UTR	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	682					actin cytoskeleton organization (GO:0030036)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(4)	47	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		CAGCTGCAGTCGTGGCGTCGT	0.602													C|||	1	0.000199681	0	0	5008	,	,		19337	0.001		0	False		,,,				2504	0				p.R682Q		Atlas-SNP	.											NPHP4,colon,carcinoma,0,1	NPHP4	119	.	0			c.G2045A						.						84	88	87					1																	5964775		2079	4216	6295	SO:0001583	missense	261734	exon16			TGCAGTCGTGGCG	AB014573	CCDS44052.1	1p36	2010-03-26			ENSG00000131697	ENSG00000131697			19104	protein-coding gene	gene with protein product	"nephroretinin", "nephrocystin-4", "POC10 centriolar protein homolog (Chlamydomonas)"	607215				11920287, 12205563	Standard	XR_244787		Approved	SLSN4, KIAA0673, POC10	uc001alq.2	O75161	OTTHUMG00000000701	ENST00000378156.4:c.2045G>A	chr1.hg19:g.5964775C>T	ENSP00000367398:p.Arg682Gln	210.0	2.0		297.0	33.0	NM_015102	Q8IWC0	Missense_Mutation	SNP	ENST00000378156.4	hg19	CCDS44052.1	.	.	.	.	.	.	.	.	.	.	C	19.69	3.875568	0.72180	.	.	ENSG00000131697	ENST00000378156;ENST00000378160	D	0.88509	-2.39	5.1	5.1	0.69264	.	0.091255	0.46442	D	0.000281	D	0.93485	0.7921	M	0.64404	1.975	0.47009	D	0.999283	D	0.89917	1.0	D	0.83275	0.996	D	0.93666	0.6986	10	0.54805	T	0.06	.	17.5221	0.87790	0.0:1.0:0.0:0.0	.	682	O75161	NPHP4_HUMAN	Q	682;85	ENSP00000367398:R682Q	ENSP00000367398:R682Q	R	-	2	0	NPHP4	5887362	1.000000	0.71417	0.724000	0.30704	0.558000	0.35554	4.701000	0.61810	2.364000	0.80123	0.655000	0.94253	CGA	.	.		0.602	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2			T	5964775	C	T	5964775	3	4	310	1	0	0	0	0	1	0	0	0	10590	884	31	1	2295	1	NPHP4	1	5964775	Missense_Mutation	SNP	C	TCGA-K7-A5RG-01A-11D-A28X-10		5964775	243285846	1	44102										
CELA3A	10136	hgsc.bcm.edu	37	chr1	22336295	22336295	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	tgcctttggctgcaacttcaTctggaagcccacggtgttca	10	12	3	0	rs572609699		TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr1:22336295T>C	ENST00000290122.3	+	7	759	c.740T>C	c.(739-741)aTc>aCc	p.I247T	RNU6-776P_ENST00000364403.1_RNA|RN7SL186P_ENST00000466485.2_RNA	NM_005747.4	NP_005738.4	P09093	CEL3A_HUMAN	chymotrypsin-like elastase family, member 3A	247	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cholesterol metabolic process (GO:0008203)|digestion (GO:0007586)|proteolysis (GO:0006508)		serine-type endopeptidase activity (GO:0004252)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TGCAACTTCATCTGGAAGCCC	0.612																																					p.I247T		Atlas-SNP	.											.	CELA3A	35	.	0			c.T740C						.						79	70	73					1																	22336295		2197	4300	6497	SO:0001583	missense	10136	exon7			ACTTCATCTGGAA	D00306	CCDS220.1	1p36.12	2009-05-05	2009-05-05	2009-05-05	ENSG00000142789	ENSG00000142789			15944	protein-coding gene	gene with protein product	"protease E"		"elastase 3A, pancreatic (protease E)", "elastase 3A, pancreatic"	ELA3A		2826474, 2460440	Standard	NM_005747		Approved	ELA3		P09093	OTTHUMG00000002755	ENST00000290122.3:c.740T>C	chr1.hg19:g.22336295T>C	ENSP00000290122:p.Ile247Thr	326.0	0.0		375.0	61.0	NM_005747	B1AQ53|Q9BRW4	Missense_Mutation	SNP	ENST00000290122.3	hg19	CCDS220.1	.	.	.	.	.	.	.	.	.	.	T	0.005	-2.215979	0.00289	.	.	ENSG00000142789	ENST00000290122;ENST00000400271	D;D	0.87966	-2.32;-2.32	3.65	-7.3	0.01446	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.62319	0.2418	N	0.03194	-0.395	0.09310	N	0.999999	B	0.02656	0.0	B	0.12156	0.007	T	0.53194	-0.8473	9	0.23891	T	0.37	4.6722	1.582	0.02636	0.3376:0.0804:0.2881:0.2938	.	247	P09093	CEL3A_HUMAN	T	247;55	ENSP00000290122:I247T;ENSP00000383130:I55T	ENSP00000290122:I247T	I	+	2	0	CELA3A	22208882	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.530000	0.00220	-2.937000	0.00298	-3.637000	0.00026	ATC	.	.		0.612	CELA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007791.1	NM_005747		C	22336295	T	C	22336295	3	2	310	1	0	0	0	0	1	0	0	0	3215	1435	50	2	766	2	CELA3A	1	22336295	Missense_Mutation	SNP	T	TCGA-K7-A5RG-01A-11D-A28X-10	16371520	22336295	226914326	2	44103										
C1QA	712	hgsc.bcm.edu	37	chr1	22965803	22965803	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	tcagctgcagcagggtgaccAggtctgggttgaaaaagacc	14	9	2	3			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr1:22965803A>T	ENST00000374642.3	+	3	845	c.641A>T	c.(640-642)cAg>cTg	p.Q214L	C1QA_ENST00000402322.1_Missense_Mutation_p.Q214L	NM_015991.2	NP_057075.1	P02745	C1QA_HUMAN	complement component 1, q subcomponent, A chain	214	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				cell-cell signaling (GO:0007267)|complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)	collagen trimer (GO:0005581)|complement component C1 complex (GO:0005602)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)				autonomic_ganglia(1)|liver(1)|lung(3)|skin(1)	6		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;6.41e-27)|Colorectal(126;1.52e-07)|COAD - Colon adenocarcinoma(152;1.12e-05)|GBM - Glioblastoma multiforme(114;1.63e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000541)|KIRC - Kidney renal clear cell carcinoma(1967;0.00269)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.197)	Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	CAGGGTGACCAGGTCTGGGTT	0.602																																					p.Q214L		Atlas-SNP	.											.	C1QA	31	.	0			c.A641T						.						57	62	60					1																	22965803		2203	4300	6503	SO:0001583	missense	712	exon3			GTGACCAGGTCTG	AF135157	CCDS226.1	1p36.3-p34.1	2014-09-17	2006-02-09		ENSG00000173372	ENSG00000173372		"Complement system"	1241	protein-coding gene	gene with protein product		120550	"complement component 1, q subcomponent, alpha polypeptide"			1537612	Standard	NM_015991		Approved		uc001bfy.3	P02745	OTTHUMG00000002893	ENST00000374642.3:c.641A>T	chr1.hg19:g.22965803A>T	ENSP00000363773:p.Gln214Leu	95.0	0.0		123.0	23.0	NM_015991	B2R4X2|Q5T963	Missense_Mutation	SNP	ENST00000374642.3	hg19	CCDS226.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.26|13.26	2.183717|2.183717	0.38609|0.38609	.|.	.|.	ENSG00000173372|ENSG00000173372	ENST00000374642;ENST00000438241;ENST00000402322|ENST00000339353	T;T;T|.	0.76448|.	-1.02;-1.02;-1.02|.	5.55|5.55	3.23|3.23	0.37069|0.37069	Tumour necrosis factor-like (2);Complement C1q protein (4);|.	.|0.356712	.|0.20636	.|N	.|0.088498	T|T	0.59059|0.59059	0.2166|0.2166	M|M	0.82517|0.82517	2.595|2.595	0.27136|0.27136	N|N	0.961765|0.961765	B|.	0.33238|.	0.403|.	B|.	0.35039|.	0.194|.	T|T	0.56275|0.56275	-0.8006|-0.8006	9|7	0.51188|0.87932	T|D	0.08|0	-0.9218|-0.9218	8.3424|8.3424	0.32252|0.32252	0.7679:0.0:0.2321:0.0|0.7679:0.0:0.2321:0.0	.|.	214|.	P02745|.	C1QA_HUMAN|.	L|W	214|209	ENSP00000363773:Q214L;ENSP00000416841:Q214L;ENSP00000385564:Q214L|.	ENSP00000363773:Q214L|ENSP00000341271:R209W	Q|R	+|+	2|1	0|2	C1QA|C1QA	22838390|22838390	0.384000|0.384000	0.25164|0.25164	0.998000|0.998000	0.56505|0.56505	0.265000|0.265000	0.26407|0.26407	0.792000|0.792000	0.26929|0.26929	0.395000|0.395000	0.25257|0.25257	0.459000|0.459000	0.35465|0.35465	CAG|AGG	.	.		0.602	C1QA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008087.2	NM_015991		T	22965803	A	T	22965803	3	4	310	1	0	0	0	0	1	0	0	0	1956	188	7	4	647	4	C1QA	1	22965803	Missense_Mutation	SNP	A	TCGA-K7-A5RG-01A-11D-A28X-10	629508	22965803	226284818	3	44104										
JUN	3725	hgsc.bcm.edu	37	chr1	59248012	59248012	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	cctgggactccatgtcgatgGgggacaggggcggtgtctcg	18	10	1	0			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr1:59248012G>A	ENST00000371222.2	-	1	1773	c.731C>T	c.(730-732)cCc>cTc	p.P244L	RP4-794H19.2_ENST00000419531.2_lincRNA	NM_002228.3	NP_002219.1	P05412	JUN_HUMAN	jun proto-oncogene	244					aging (GO:0007568)|angiogenesis (GO:0001525)|axon regeneration (GO:0031103)|cellular response to calcium ion (GO:0071277)|cellular response to potassium ion starvation (GO:0051365)|circadian rhythm (GO:0007623)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|leading edge cell differentiation (GO:0035026)|learning (GO:0007612)|liver development (GO:0001889)|membrane depolarization (GO:0051899)|microglial cell activation (GO:0001774)|monocyte differentiation (GO:0030224)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA binding (GO:0043392)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress (GO:1990441)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA replication (GO:0045740)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of monocyte differentiation (GO:0045657)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle (GO:0051726)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|release of cytochrome c from mitochondria (GO:0001836)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|SMAD protein import into nucleus (GO:0007184)|SMAD protein signal transduction (GO:0060395)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nuclear chromosome (GO:0000228)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	cAMP response element binding (GO:0035497)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|R-SMAD binding (GO:0070412)|Rho GTPase activator activity (GO:0005100)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|kidney(2)|lung(5)|skin(1)	10	all_cancers(7;8.55e-07)				Arsenic trioxide(DB01169)|Irbesartan(DB01029)|Pseudoephedrine(DB00852)|Vinblastine(DB00570)	CATGTCGATGGGGGACAGGGG	0.652			A		sarcoma																																p.P244L		Atlas-SNP	.		Dom	yes		1	1p32-p31	3725	jun oncogene		M	.	JUN	26	.	0			c.C731T						.						40	44	43					1																	59248012		2203	4300	6503	SO:0001583	missense	3725	exon1			TCGATGGGGGACA	AY217548	CCDS610.1	1p32-p31	2013-01-10	2010-08-27		ENSG00000177606	ENSG00000177606		"basic leucine zipper proteins"	6204	protein-coding gene	gene with protein product		165160	"v-jun avian sarcoma virus 17 oncogene homolog", "v-jun sarcoma virus 17 oncogene homolog (avian)", "jun oncogene"			3194415	Standard	NM_002228		Approved	c-Jun, AP-1	uc001cze.3	P05412	OTTHUMG00000008376	ENST00000371222.2:c.731C>T	chr1.hg19:g.59248012G>A	ENSP00000360266:p.Pro244Leu	69.0	0.0		81.0	19.0	NM_002228	Q6FHM7|Q96G93	Missense_Mutation	SNP	ENST00000371222.2	hg19	CCDS610.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.594171	0.86953	.	.	ENSG00000177606	ENST00000371222	T	0.28454	1.61	4.15	4.15	0.48705	Eukaryotic transcription factor, Skn-1-like, DNA-binding (2);	0.000000	0.85682	D	0.000000	T	0.63295	0.2499	M	0.90425	3.115	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74210	-0.3739	10	0.87932	D	0	-0.2551	16.6369	0.85061	0.0:0.0:1.0:0.0	.	244	P05412	JUN_HUMAN	L	244	ENSP00000360266:P244L	ENSP00000360266:P244L	P	-	2	0	JUN	59020600	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.544000	0.98092	2.127000	0.65507	0.561000	0.74099	CCC	.	.		0.652	JUN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023042.1	NM_002228		A	59248012	G	A	59248012	3	1	310	1	0	0	0	0	1	0	0	0	7978	1232	43	3	268	3	JUN	1	59248012	Missense_Mutation	SNP	G	TCGA-K7-A5RG-01A-11D-A28X-10	36282209	59248012	190002609	4	44105										
ABCA4	24	hgsc.bcm.edu	37	chr1	94578571	94578571	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	gttggcattccttaaccagaTcaagaccagaaataaagata	7	8	1	4			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr1:94578571T>C	ENST00000370225.3	-	2	204	c.118A>G	c.(118-120)Atc>Gtc	p.I40V	ABCA4_ENST00000535735.1_Missense_Mutation_p.I40V	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	40					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			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)		CTTAACCAGATCAAGACCAGA	0.443																																					p.I40V		Atlas-SNP	.											.	ABCA4	275	.	0			c.A118G						.						118	110	113					1																	94578571		2203	4300	6503	SO:0001583	missense	24	exon2			ACCAGATCAAGAC	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.118A>G	chr1.hg19:g.94578571T>C	ENSP00000359245:p.Ile40Val	202.0	0.0		216.0	29.0	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	hg19	CCDS747.1	.	.	.	.	.	.	.	.	.	.	T	8.344	0.829365	0.16749	.	.	ENSG00000198691	ENST00000370225;ENST00000535735	D;D	0.87256	-2.23;-2.23	5.92	4.8	0.61643	.	0.426017	0.26023	N	0.026808	T	0.54046	0.1834	N	0.05199	-0.095	0.37225	D	0.905411	B;B	0.18310	0.027;0.001	B;B	0.18871	0.023;0.001	T	0.54536	-0.8279	10	0.19590	T	0.45	.	5.8343	0.18599	0.0:0.2233:0.0:0.7767	.	40;40	F5H6E5;P78363	.;ABCA4_HUMAN	V	40	ENSP00000359245:I40V;ENSP00000437682:I40V	ENSP00000359245:I40V	I	-	1	0	ABCA4	94351159	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.749000	0.55150	2.265000	0.75225	0.448000	0.29417	ATC	.	.		0.443	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		C	94578571	T	C	94578571	3	2	310	1	0	0	0	0	1	0	0	0	34	1435	50	2	6899	2	ABCA4	1	94578571	Missense_Mutation	SNP	T	TCGA-K7-A5RG-01A-11D-A28X-10	35330559	94578571	154672050	5	44106										
EFNA3	1944	hgsc.bcm.edu	37	chr1	155057577	155057577	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ttccccacagcctgcggcgaGagggctacaccgtgcaggtg	14	14	0	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr1:155057577G>A	ENST00000368408.3	+	2	209	c.139G>A	c.(139-141)Gag>Aag	p.E47K	EFNA3_ENST00000505139.1_Missense_Mutation_p.E42K|EFNA3_ENST00000556931.1_Missense_Mutation_p.E42K|EFNA3_ENST00000418360.2_Missense_Mutation_p.E47K	NM_004952.4	NP_004943.1	P52797	EFNA3_HUMAN	ephrin-A3	47	Ephrin RBD. {ECO:0000255|PROSITE- ProRule:PRU00884}.				axon guidance (GO:0007411)|cell-cell signaling (GO:0007267)|ephrin receptor signaling pathway (GO:0048013)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ephrin receptor binding (GO:0046875)|transmembrane-ephrin receptor activity (GO:0005005)			breast(1)|central_nervous_system(1)|large_intestine(1)|lung(2)	5	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		all cancers(21;5.67e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000284)|LUSC - Lung squamous cell carcinoma(543;0.193)			CCTGCGGCGAGAGGGCTACAC	0.657											OREG0013849	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E47K		Atlas-SNP	.											.	EFNA3	15	.	0			c.G139A						.						44	50	48					1																	155057577		2203	4295	6498	SO:0001583	missense	1944	exon2			CGGCGAGAGGGCT	BC017722	CCDS1090.1	1q21-q22	2011-03-09			ENSG00000143590	ENSG00000143590		"Ephrins"	3223	protein-coding gene	gene with protein product		601381		EPLG3		8660976	Standard	NM_004952		Approved	LERK3, Ehk1-L	uc001fhf.3	P52797	OTTHUMG00000035313	ENST00000368408.3:c.139G>A	chr1.hg19:g.155057577G>A	ENSP00000357393:p.Glu47Lys	127.0	0.0	1767	137.0	27.0	NM_004952	B7ZAD3|D3DV85|Q0VGC9|Q5SR70	Missense_Mutation	SNP	ENST00000368408.3	hg19	CCDS1090.1	.	.	.	.	.	.	.	.	.	.	G	30	5.050978	0.93740	.	.	ENSG00000143590;ENSG00000143590;ENSG00000143590;ENSG00000251246	ENST00000556931;ENST00000368408;ENST00000418360;ENST00000505139	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	5.02	5.02	0.67125	Cupredoxin (2);	0.106082	0.64402	D	0.000006	T	0.30479	0.0766	L	0.33485	1.01	0.53688	D	0.999978	P;B;P	0.47350	0.894;0.04;0.894	P;B;P	0.48063	0.565;0.1;0.565	T	0.07501	-1.0769	10	0.49607	T	0.09	-11.9798	15.8307	0.78749	0.0:0.0:1.0:0.0	.	47;42;47	B7ZAD3;B4DXG7;P52797	.;.;EFNA3_HUMAN	K	42;47;47;42	ENSP00000450814:E42K;ENSP00000357393:E47K;ENSP00000391370:E47K;ENSP00000426741:E42K	ENSP00000357393:E47K	E	+	1	0	RP11-540D14.8;EFNA3	153324201	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.658000	0.83755	2.353000	0.79882	0.561000	0.74099	GAG	.	.		0.657	EFNA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085429.1	NM_004952		A	155057577	G	A	155057577	3	1	310	1	0	0	0	0	1	0	0	0	4954	943	33	3	145	3	EFNA3	1	155057577	Missense_Mutation	SNP	G	TCGA-K7-A5RG-01A-11D-A28X-10	60479006	155057577	94193044	6	44107										
CCT3	7203	hgsc.bcm.edu	37	chr1	156303388	156303388	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	caacctcttcatcctgggtcCggctaatttcgatcatggac	8	13	3	0			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr1:156303388C>G	ENST00000295688.3	-	5	534	c.254G>C	c.(253-255)cGg>cCg	p.R85P	CCT3_ENST00000472765.2_Missense_Mutation_p.R40P|CCT3_ENST00000368256.3_5'UTR|CCT3_ENST00000368259.2_Missense_Mutation_p.R47P|CCT3_ENST00000368261.3_Missense_Mutation_p.R40P	NM_005998.4	NP_005989.3	P49368	TCPG_HUMAN	chaperonin containing TCP1, subunit 3 (gamma)	85					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			endometrium(4)|large_intestine(1)|liver(1)|lung(11)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	22	Hepatocellular(266;0.158)					ATCCTGGGTCCGGCTAATTTC	0.413																																					p.R85P		Atlas-SNP	.											.	CCT3	61	.	0			c.G254C						.						136	136	136					1																	156303388		2203	4300	6503	SO:0001583	missense	7203	exon5			TGGGTCCGGCTAA	BC008019	CCDS1140.2, CCDS30888.1	1q23	2011-09-02			ENSG00000163468	ENSG00000163468		"Heat Shock Proteins / Chaperonins"	1616	protein-coding gene	gene with protein product		600114		TRIC5		8110840	Standard	NM_005998		Approved	Cctg	uc001fol.2	P49368	OTTHUMG00000024061	ENST00000295688.3:c.254G>C	chr1.hg19:g.156303388C>G	ENSP00000295688:p.Arg85Pro	52.0	0.0		55.0	5.0	NM_005998	A6NE14|Q5SZY1|Q9BR64	Missense_Mutation	SNP	ENST00000295688.3	hg19	CCDS1140.2	.	.	.	.	.	.	.	.	.	.	C	26.9	4.784350	0.90282	.	.	ENSG00000163468	ENST00000295688;ENST00000368259;ENST00000368261;ENST00000472765;ENST00000413555;ENST00000496684;ENST00000533194;ENST00000446905;ENST00000478640;ENST00000415548	T;T;T;T;T;T;T;T;T;T	0.79454	-1.27;-1.27;-1.27;-1.27;-1.27;-1.27;-1.27;-1.27;-1.27;-1.27	5.84	4.93	0.64822	.	0.000000	0.85682	D	0.000000	D	0.90314	0.6970	H	0.98005	4.125	0.58432	D	0.999997	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.995;1.0;1.0	D	0.92745	0.6211	10	0.87932	D	0	-15.7251	10.8293	0.46650	0.0:0.9134:0.0:0.0866	.	47;85;85	P49368-2;E9PAQ6;P49368	.;.;TCPG_HUMAN	P	85;47;40;40;109;85;6;71;64;85	ENSP00000295688:R85P;ENSP00000357242:R47P;ENSP00000357244:R40P;ENSP00000431543:R40P;ENSP00000413308:R109P;ENSP00000434232:R85P;ENSP00000434481:R6P;ENSP00000388799:R71P;ENSP00000435026:R64P;ENSP00000413431:R85P	ENSP00000295688:R85P	R	-	2	0	CCT3	154570012	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.192000	0.77771	1.472000	0.48140	0.650000	0.86243	CGG	.	.		0.413	CCT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060602.3	NM_005998		G	156303388	C	G	156303388	3	3	310	1	0	0	0	0	1	0	0	0	2956	652	23	4	1423	4	CCT3	1	156303388	Missense_Mutation	SNP	C	TCGA-K7-A5RG-01A-11D-A28X-10	1245811	156303388	92947233	7	44108										
ASTN1	460	hgsc.bcm.edu	37	chr1	176853524	176853524	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	tcagtgactttctcttgacgGaggaggtaatctacaatctg	10	8	4	2			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr1:176853524G>T	ENST00000367654.3	-	19	3412	c.3201C>A	c.(3199-3201)ctC>ctA	p.L1067L	ASTN1_ENST00000424564.2_Silent_p.L1059L|ASTN1_ENST00000361833.2_Silent_p.L1059L|ASTN1_ENST00000367657.3_Silent_p.L1059L	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	1067	Fibronectin type-III 1.				locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						TCTCTTGACGGAGGAGGTAAT	0.517																																					p.L1059L		Atlas-SNP	.											.	ASTN1	314	.	0			c.C3177A						.						160	133	142					1																	176853524		2203	4300	6503	SO:0001819	synonymous_variant	460	exon19			TTGACGGAGGAGG	AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"astrotactin"	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.3201C>A	chr1.hg19:g.176853524G>T		175.0	0.0		196.0	28.0	NM_004319	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Silent	SNP	ENST00000367654.3	hg19																																																																																				.	.		0.517	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319		T	176853524	G	T	176853524	2	4	310	1	0	0	0	0	0	0	0	1	1064	1161	41	3		3	ASTN1	1	176853524	Silent	SNP	G	TCGA-K7-A5RG-01A-11D-A28X-10	20550136	176853524	72397097	8	44109										
PLA2G4A	5321	hgsc.bcm.edu	37	chr1	186909157	186909157	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	tgaaggaaaaagttaatactGcacaatgccctttacctctt	6	9	1	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr1:186909157G>T	ENST00000367466.3	+	10	1116	c.964G>T	c.(964-966)Gca>Tca	p.A322S	PLA2G4A_ENST00000442353.2_Missense_Mutation_p.A262S	NM_024420.2	NP_077734	P47712	PA24A_HUMAN	phospholipase A2, group IVA (cytosolic, calcium-dependent)	322	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid metabolic process (GO:0019369)|arachidonic acid secretion (GO:0050482)|blood coagulation (GO:0007596)|cardiolipin acyl-chain remodeling (GO:0035965)|cellular response to antibiotic (GO:0071236)|glycerophospholipid biosynthetic process (GO:0046474)|icosanoid biosynthetic process (GO:0046456)|icosanoid metabolic process (GO:0006690)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|platelet activation (GO:0030168)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|calcium-dependent phospholipid binding (GO:0005544)|lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|prostate(3)|skin(4)|stomach(1)	53					Aldesleukin(DB00041)|Carbachol(DB00411)|Carbenicillin(DB00578)|Epirubicin(DB00445)|Fluocinolone Acetonide(DB00591)|Fluticasone Propionate(DB00588)|Niflumic Acid(DB04552)|Orlistat(DB01083)|Quinacrine(DB01103)|Streptokinase(DB00086)|Suramin(DB04786)	AGTTAATACTGCACAATGCCC	0.378																																					p.A322S		Atlas-SNP	.											.	PLA2G4A	125	.	0			c.G964T						.						160	150	153					1																	186909157		2203	4300	6503	SO:0001583	missense	5321	exon10			AATACTGCACAAT	M72393	CCDS1372.1	1q25	2014-09-17			ENSG00000116711	ENSG00000116711	3.1.1.4, 3.1.1.5		9035	protein-coding gene	gene with protein product		600522		PLA2G4		8175726	Standard	NM_024420		Approved	cPLA2-alpha	uc001gsc.3	P47712	OTTHUMG00000035512	ENST00000367466.3:c.964G>T	chr1.hg19:g.186909157G>T	ENSP00000356436:p.Ala322Ser	73.0	0.0		70.0	14.0	NM_024420	B1AKG4|Q29R80	Missense_Mutation	SNP	ENST00000367466.3	hg19	CCDS1372.1	.	.	.	.	.	.	.	.	.	.	G	16.02	3.004029	0.54254	.	.	ENSG00000116711	ENST00000367466;ENST00000442353	T;T	0.13538	2.58;2.58	5.67	5.67	0.87782	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	0.257363	0.44285	D	0.000464	T	0.17831	0.0428	L	0.40543	1.245	0.39919	D	0.974134	B;B	0.27559	0.181;0.152	B;B	0.33121	0.12;0.158	T	0.03524	-1.1028	10	0.72032	D	0.01	-8.2661	18.7591	0.91843	0.0:0.0:1.0:0.0	.	262;322	E7EU42;P47712	.;PA24A_HUMAN	S	322;262	ENSP00000356436:A322S;ENSP00000406892:A262S	ENSP00000356436:A322S	A	+	1	0	PLA2G4A	185175780	0.999000	0.42202	0.007000	0.13788	0.193000	0.23685	7.795000	0.85887	2.661000	0.90470	0.650000	0.86243	GCA	.	.		0.378	PLA2G4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086236.1	NM_024420		T	186909157	G	T	186909157	3	4	310	1	0	0	0	0	1	0	0	0	12010	1319	46	3	998	3	PLA2G4A	1	186909157	Missense_Mutation	SNP	G	TCGA-K7-A5RG-01A-11D-A28X-10	10055633	186909157	62341464	9	44110										
IGFN1	91156	hgsc.bcm.edu	37	chr1	201184848	201184848	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	gaggcccaggtggacctgggGgatggctacacgcggctgtg	19	10	0	0			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr1:201184848G>T	ENST00000335211.4	+	15	9307	c.9177G>T	c.(9175-9177)ggG>ggT	p.G3059G	IGFN1_ENST00000451870.2_Intron|IGFN1_ENST00000295591.8_Silent_p.G219G	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	602						nucleus (GO:0005634)|Z disc (GO:0030018)				autonomic_ganglia(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						TGGACCTGGGGGATGGCTACA	0.667																																					p.G3059G		Atlas-SNP	.											.	IGFN1	220	.	0			c.G9177T						.						45	39	41					1																	201184848		2203	4300	6503	SO:0001819	synonymous_variant	91156	exon15			CCTGGGGGATGGC	AY245430	CCDS53455.1	1q32.1	2013-02-11			ENSG00000163395	ENSG00000163395		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	24607	protein-coding gene	gene with protein product							Standard	NM_001164586		Approved	DKFZp434B1231, EEF1A2BP1	uc001gwc.3	Q86VF2	OTTHUMG00000035728	ENST00000335211.4:c.9177G>T	chr1.hg19:g.201184848G>T		193.0	0.0		213.0	37.0	NM_001164586	F8WAI1|Q9NT72	Silent	SNP	ENST00000335211.4	hg19	CCDS53455.1	.	.	.	.	.	.	.	.	.	.	G	5.843	0.339727	0.11069	.	.	ENSG00000163395	ENST00000412892	.	.	.	4.83	-4.97	0.03029	.	0.399254	0.23409	N	0.048491	.	.	.	.	.	.	0.20403	N	0.99991	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.5982	0.08014	0.5788:0.1154:0.1903:0.1155	.	.	.	.	X	477	.	.	G	+	1	0	IGFN1	199451471	0.228000	0.23718	0.191000	0.23289	0.012000	0.07955	-0.560000	0.05964	-0.773000	0.04596	-0.258000	0.10820	GGA	.	.		0.667	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275		T	201184848	G	T	201184848	2	4	310	1	0	0	0	0	0	0	0	1	7599	1219	43	3		3	IGFN1	1	201184848	Silent	SNP	G	TCGA-K7-A5RG-01A-11D-A28X-10	14275691	201184848	48065773	10	44111										
RBBP5	5929	hgsc.bcm.edu	37	chr1	205065957	205065957	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	gactgcatccggtggggggcCgtaaggattttcttctgggt	16	8	2	0			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr1:205065957C>T	ENST00000264515.6	-	12	1390	c.1249G>A	c.(1249-1251)Ggc>Agc	p.G417S	RBBP5_ENST00000367164.1_Missense_Mutation_p.G417S	NM_001193273.1|NM_005057.3	NP_001180202.1|NP_005048.2	Q15291	RBBP5_HUMAN	retinoblastoma binding protein 5	417					cellular response to DNA damage stimulus (GO:0006974)|histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	methylated histone binding (GO:0035064)|transcription regulatory region DNA binding (GO:0044212)			cervix(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	27	Breast(84;0.0505)		BRCA - Breast invasive adenocarcinoma(75;0.0923)			GGTGGGGGGCCGTAAGGATTT	0.502																																					p.G417S		Atlas-SNP	.											.	RBBP5	45	.	0			c.G1249A						.						115	123	120					1																	205065957		2203	4300	6503	SO:0001583	missense	5929	exon12			GGGGGCCGTAAGG	BC053856	CCDS30983.1, CCDS53463.1	1q32	2013-01-10	2001-11-28		ENSG00000117222	ENSG00000117222		"WD repeat domain containing"	9888	protein-coding gene	gene with protein product	"SWD1, Set1c WD40 repeat protein, homolog (S. cerevisiae)"	600697	"retinoblastoma-binding protein 5"			7558034	Standard	NM_005057		Approved	RBQ3, SWD1	uc001hbu.2	Q15291	OTTHUMG00000037104	ENST00000264515.6:c.1249G>A	chr1.hg19:g.205065957C>T	ENSP00000264515:p.Gly417Ser	111.0	0.0		124.0	22.0	NM_005057	A8K272|Q7Z6D8|Q8NDZ7	Missense_Mutation	SNP	ENST00000264515.6	hg19	CCDS30983.1	.	.	.	.	.	.	.	.	.	.	C	18.56	3.649927	0.67472	.	.	ENSG00000117222	ENST00000264515;ENST00000367164	T;T	0.59364	0.27;0.29	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.50257	0.1605	L	0.54323	1.7	0.80722	D	1	P;P;B;P	0.41313	0.714;0.745;0.281;0.591	B;B;B;B	0.30646	0.118;0.098;0.071;0.055	T	0.50206	-0.8855	10	0.20046	T	0.44	.	19.5705	0.95413	0.0:1.0:0.0:0.0	.	290;452;417;417	B4DLF8;B4DMM7;Q15291-2;Q15291	.;.;.;RBBP5_HUMAN	S	417	ENSP00000264515:G417S;ENSP00000356132:G417S	ENSP00000264515:G417S	G	-	1	0	RBBP5	203332580	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	7.487000	0.81328	2.722000	0.93159	0.650000	0.86243	GGC	.	.		0.502	RBBP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090077.1	NM_005057		T	205065957	C	T	205065957	3	4	310	1	0	0	0	0	1	0	0	0	13117	652	23	1	379	1	RBBP5	1	205065957	Missense_Mutation	SNP	C	TCGA-K7-A5RG-01A-11D-A28X-10	3881109	205065957	44184664	11	44112										
HHAT	55733	hgsc.bcm.edu	37	chr1	210847644	210847644	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ctgcaggctggccttgggtgAccctctctgtcctgggattc	13	13	1	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr1:210847644A>T	ENST00000367010.1	+	12	1632	c.1405A>T	c.(1405-1407)Acc>Tcc	p.T469S	HHAT_ENST00000261458.3_Missense_Mutation_p.T469S|HHAT_ENST00000545781.1_Missense_Mutation_p.T406S|HHAT_ENST00000413764.2_Missense_Mutation_p.T469S|HHAT_ENST00000537898.1_Missense_Mutation_p.T404S|HHAT_ENST00000367009.1_Missense_Mutation_p.T159S|HHAT_ENST00000541565.1_Missense_Mutation_p.T332S|HHAT_ENST00000545154.1_Missense_Mutation_p.T470S|HHAT_ENST00000308852.6_Missense_Mutation_p.T424S	NM_001170580.1	NP_001164051.1	Q5VTY9	HHAT_HUMAN	hedgehog acyltransferase	469					multicellular organismal development (GO:0007275)|protein palmitoylation (GO:0018345)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|palmitoyltransferase activity (GO:0016409)			breast(3)|central_nervous_system(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	27				OV - Ovarian serous cystadenocarcinoma(81;0.0136)|all cancers(67;0.161)|KIRC - Kidney renal clear cell carcinoma(1967;0.215)		GCCTTGGGTGACCCTCTCTGT	0.592																																					p.T470S		Atlas-SNP	.											.	HHAT	66	.	0			c.A1408T						.						144	117	126					1																	210847644		2203	4300	6503	SO:0001583	missense	55733	exon11			TGGGTGACCCTCT	AK001586	CCDS1495.1, CCDS53471.1, CCDS53472.1, CCDS53473.1	1q32	2008-02-05			ENSG00000054392	ENSG00000054392			18270	protein-coding gene	gene with protein product		605743				11160356	Standard	NM_001170587		Approved	FLJ10724, MART-2, MART2, Skn, ski, rasp, sit, GUP2	uc009xcx.3	Q5VTY9	OTTHUMG00000036447	ENST00000367010.1:c.1405A>T	chr1.hg19:g.210847644A>T	ENSP00000355977:p.Thr469Ser	92.0	0.0		107.0	20.0	NM_001170587	B7Z4D5|B7Z5I1|B7Z868|B7ZA75|D3DT91|F5H444|Q17RZ7|Q4G0K3|Q5CZ95|Q5TGI2|Q9NVH9|Q9Y3N8	Missense_Mutation	SNP	ENST00000367010.1	hg19	CCDS1495.1	.	.	.	.	.	.	.	.	.	.	A	14.07	2.427176	0.43122	.	.	ENSG00000054392	ENST00000413764;ENST00000541565;ENST00000545154;ENST00000537898;ENST00000545781;ENST00000261458;ENST00000308852;ENST00000367010;ENST00000367009	T;T;T;T;T;T;T;T;T	0.44881	2.19;0.91;2.16;2.22;2.18;2.19;2.19;2.19;0.92	5.51	5.51	0.81932	.	.	.	.	.	T	0.32793	0.0841	L	0.39898	1.24	0.30129	N	0.804963	P;P;P;B;P	0.42296	0.666;0.775;0.688;0.172;0.518	B;B;B;B;B	0.36464	0.112;0.225;0.095;0.039;0.079	T	0.21793	-1.0235	9	0.21540	T	0.41	.	13.2915	0.60274	1.0:0.0:0.0:0.0	.	424;470;332;404;469	B7Z2U8;F5H444;B7Z4D5;B7Z5I1;Q5VTY9	.;.;.;.;HHAT_HUMAN	S	469;332;470;404;406;469;424;469;159	ENSP00000416845:T469S;ENSP00000444995:T332S;ENSP00000438468:T470S;ENSP00000442625:T404S;ENSP00000439229:T406S;ENSP00000261458:T469S;ENSP00000308628:T424S;ENSP00000355977:T469S;ENSP00000355976:T159S	ENSP00000261458:T469S	T	+	1	0	HHAT	208914267	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.634000	0.61325	2.210000	0.71456	0.533000	0.62120	ACC	.	.		0.592	HHAT-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088662.1	NM_018194		T	210847644	A	T	210847644	3	4	310	1	0	0	0	0	1	0	0	0	7098	275	10	4	1545	4	HHAT	1	210847644	Missense_Mutation	SNP	A	TCGA-K7-A5RG-01A-11D-A28X-10	5781687	210847644	38402977	12	44113										
CHRM3	1131	hgsc.bcm.edu	37	chr1	240071769	240071769	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	gcagtgacagttggaacaacAatgatgctgctgcctccctg	11	11	0	2			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr1:240071769A>G	ENST00000255380.4	+	5	1797	c.1018A>G	c.(1018-1020)Aat>Gat	p.N340D		NM_000740.2	NP_000731.1	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	340					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|energy reserve metabolic process (GO:0006112)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of insulin secretion (GO:0050796)|regulation of vascular smooth muscle contraction (GO:0003056)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|smooth muscle contraction (GO:0006939)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)|receptor activity (GO:0004872)			breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(19)|ovary(4)|prostate(1)|skin(12)|upper_aerodigestive_tract(1)	51	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Fesoterodine(DB06702)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Isopropamide(DB01625)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methacholine(DB06709)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tramadol(DB00193)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	TTGGAACAACAATGATGCTGC	0.577																																					p.N340D		Atlas-SNP	.											.	CHRM3	118	.	0			c.A1018G						.						48	41	44					1																	240071769		2203	4299	6502	SO:0001583	missense	1131	exon5			AACAACAATGATG	U29589	CCDS1616.1	1q43	2012-09-20			ENSG00000133019	ENSG00000133019		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1952	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 3"	118494					Standard	XM_005273032		Approved		uc001hyp.3	P20309	OTTHUMG00000039649	ENST00000255380.4:c.1018A>G	chr1.hg19:g.240071769A>G	ENSP00000255380:p.Asn340Asp	167.0	0.0		185.0	26.0	NM_000740	Q0VAJ8|Q4QRI3|Q5VXY2|Q9HB60	Missense_Mutation	SNP	ENST00000255380.4	hg19	CCDS1616.1	.	.	.	.	.	.	.	.	.	.	A	11.51	1.660706	0.29515	.	.	ENSG00000133019	ENST00000255380	T	0.60424	0.19	5.97	5.97	0.96955	GPCR, rhodopsin-like superfamily (1);	0.106979	0.64402	D	0.000013	T	0.52837	0.1759	L	0.49126	1.545	0.58432	D	0.999999	B	0.26602	0.154	B	0.29176	0.099	T	0.49051	-0.8979	10	0.13108	T	0.6	-26.3872	16.4473	0.83942	1.0:0.0:0.0:0.0	.	340	P20309	ACM3_HUMAN	D	340	ENSP00000255380:N340D	ENSP00000255380:N340D	N	+	1	0	CHRM3	238138392	1.000000	0.71417	0.999000	0.59377	0.951000	0.60555	7.576000	0.82467	2.281000	0.76405	0.533000	0.62120	AAT	.	.		0.577	CHRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095644.2	NM_000740		G	240071769	A	G	240071769	3	3	310	1	0	0	0	0	1	0	0	0	3380	130	5	2	1020	2	CHRM3	1	240071769	Missense_Mutation	SNP	A	TCGA-K7-A5RG-01A-11D-A28X-10	29224125	240071769	9178852	13	44114										
ZNF238	10472	hgsc.bcm.edu	37	chr1	244217640	244217640	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	aaaagggacttggcggccgaGcctgggaacatgtggatgcg	17	8	0	0			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr1:244217640G>T	ENST00000358704.4	+	2	713	c.564G>T	c.(562-564)gaG>gaT	p.E188D		NM_001278196.1|NM_006352.4|NM_205768.2	NP_001265125.1|NP_006343.2|NP_991331.1	Q99592	ZBT18_HUMAN	zinc finger and BTB domain containing 18	179				KLNILPSKRDLAAEPGNMWMRLPSDSAGIPQAGGEAEPHAT AAGKTVASPCSSTESLSQRSVTSVRDSADVDCVLDLSVKSS LSGVENLNSSYFSSQ -> IEHPAQQKGLGGRAWEHVDAIA LRLSRHPPGWRRGRATRHSSWKNSSQPLQLNRVFVPE (in Ref. 1; AAA81368). {ECO:0000305}.	cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron development (GO:0048666)|regulation of cell division (GO:0051302)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TGGCGGCCGAGCCTGGGAACA	0.562																																					p.E188D		Atlas-SNP	.											.	.	.	.	0			c.G564T						.						50	56	54					1																	244217640		2203	4300	6503	SO:0001583	missense	10472	exon2			GGCCGAGCCTGGG	U38896	CCDS1622.1	1q44	2013-09-19	2013-01-09	2013-01-09	ENSG00000179456	ENSG00000179456		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	13030	protein-coding gene	gene with protein product		608433	"zinc finger protein 238"	ZNF238		9568537, 9013868	Standard	NM_205768		Approved	C2H2-171, TAZ-1, RP58	uc031psv.1	Q99592	OTTHUMG00000040013	ENST00000358704.4:c.564G>T	chr1.hg19:g.244217640G>T	ENSP00000351539:p.Glu188Asp	182.0	0.0		224.0	42.0	NM_205768	A8K5U3|Q13397|Q5VU40|Q8N463|Q9UD99	Missense_Mutation	SNP	ENST00000358704.4	hg19	CCDS1622.1	.	.	.	.	.	.	.	.	.	.	G	11.17	1.560715	0.27827	.	.	ENSG00000179456	ENST00000366538;ENST00000358704	T	0.12039	2.72	5.28	5.28	0.74379	.	0.050245	0.85682	D	0.000000	T	0.20981	0.0505	L	0.27053	0.805	0.58432	D	0.999994	P;P;D	0.55605	0.953;0.953;0.972	D;D;D	0.70935	0.935;0.935;0.971	T	0.04294	-1.0962	10	0.16420	T	0.52	.	12.2886	0.54805	0.0778:0.0:0.9222:0.0	.	188;179;188	B4DF20;Q99592;Q99592-2	.;ZN238_HUMAN;.	D	188	ENSP00000351539:E188D	ENSP00000351539:E188D	E	+	3	2	ZNF238	242284263	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	3.786000	0.55431	2.475000	0.83589	0.650000	0.86243	GAG	.	.		0.562	ZBTB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096513.2	NM_205768		T	244217640	G	T	244217640	3	4	310	1	0	0	0	0	1	0	0	0	17805	962	34	3	570	3	ZNF238	1	244217640	Missense_Mutation	SNP	G	TCGA-K7-A5RG-01A-11D-A28X-10	4145871	244217640	5032981	14	44115										
C2orf56	55471	hgsc.bcm.edu	37	chr2	37474750	37474750	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	acacacatttttaaaaaataTgggtattgatgtccggctga	8	6	0	2			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr2:37474750T>C	ENST00000002125.4	+	9	1128	c.1088T>C	c.(1087-1089)aTg>aCg	p.M363T	NDUFAF7_ENST00000336237.6_Missense_Mutation_p.M265T	NM_144736.4	NP_653337.1	Q7L592	NDUF7_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 7	363					methylation (GO:0032259)|mitochondrial respiratory chain complex I assembly (GO:0032981)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	enzyme binding (GO:0019899)|methyltransferase activity (GO:0008168)										TTAAAAAATATGGGTATTGAT	0.343																																					p.M363T		Atlas-SNP	.											.	.	.	.	0			c.T1088C						.						64	66	65					2																	37474750		2203	4298	6501	SO:0001583	missense	55471	exon9			AAAATATGGGTAT		CCDS1788.1, CCDS42673.1	2p22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000003509	ENSG00000003509		"Mitochondrial respiratory chain complex assembly factors"	28816	protein-coding gene	gene with protein product	"mitochondrial dysfunction protein A homolog"	615898	"chromosome 2 open reading frame 56"	C2orf56			Standard	NM_144736		Approved	PRO1853, MidA	uc002rqa.4	Q7L592	OTTHUMG00000128468	ENST00000002125.4:c.1088T>C	chr2.hg19:g.37474750T>C	ENSP00000002125:p.Met363Thr	98.0	0.0		110.0	17.0	NM_144736	Q7Z399|Q9P1G3	Missense_Mutation	SNP	ENST00000002125.4	hg19	CCDS1788.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.274872	0.80580	.	.	ENSG00000003509	ENST00000002125;ENST00000336237	T;T	0.77489	-1.1;-1.1	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	D	0.89382	0.6699	M	0.91818	3.245	0.80722	D	1	D;P;D;D	0.61080	0.97;0.884;0.959;0.989	P;P;P;P	0.61003	0.665;0.636;0.882;0.762	D	0.91558	0.5262	9	.	.	.	-32.4236	16.0663	0.80878	0.0:0.0:0.0:1.0	.	336;292;265;363	E7EUC2;B4DQY3;Q7L592-2;Q7L592	.;.;.;MIDA_HUMAN	T	363;265	ENSP00000002125:M363T;ENSP00000337431:M265T	.	M	+	2	0	C2orf56	37328254	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.374000	0.79633	2.196000	0.70406	0.533000	0.62120	ATG	.	.		0.343	NDUFAF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250267.1	NM_144736		C	37474750	T	C	37474750	3	2	310	1	0	0	0	0	1	0	0	0	2179	1464	51	2	1122	2	C2orf56	2	37474750	Missense_Mutation	SNP	T	TCGA-K7-A5RG-01A-11D-A28X-10		37474750	205724623	15	44116										
SOCS5	9655	hgsc.bcm.edu	37	chr2	46986955	46986955	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	caacagatccctgcatgcccGaattgagcagtggaatcaca	9	12	1	2			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr2:46986955G>A	ENST00000306503.5	+	2	1458	c.1286G>A	c.(1285-1287)cGa>cAa	p.R429Q	SOCS5_ENST00000394861.2_Missense_Mutation_p.R429Q	NM_014011.4	NP_054730.1	O75159	SOCS5_HUMAN	suppressor of cytokine signaling 5	429	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cell growth (GO:0016049)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|JAK-STAT cascade (GO:0007259)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of signal transduction (GO:0009968)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)		receptor tyrosine kinase binding (GO:0030971)	p.R429L(1)|p.R429Q(1)		breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(9)|ovary(2)	22		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.114)			CTGCATGCCCGAATTGAGCAG	0.498																																					p.R429Q		Atlas-SNP	.											SOCS5,NS,carcinoma,0,3	SOCS5	62	.	2	Substitution - Missense(2)	ovary(1)|lung(1)	c.G1286A						.						103	101	102					2																	46986955		2203	4300	6503	SO:0001583	missense	9655	exon2			ATGCCCGAATTGA	AB014571	CCDS1830.1	2p21	2013-02-14			ENSG00000171150	ENSG00000171150		"Suppressors of cytokine signaling", "SH2 domain containing"	16852	protein-coding gene	gene with protein product		607094				9734811, 11230166	Standard	NM_014011		Approved	KIAA0671, SOCS-5, CIS6, CISH6, Cish5	uc002rvf.3	O75159	OTTHUMG00000128852	ENST00000306503.5:c.1286G>A	chr2.hg19:g.46986955G>A	ENSP00000305133:p.Arg429Gln	245.0	0.0		216.0	25.0	NM_144949	Q53SD4|Q8IYZ4	Missense_Mutation	SNP	ENST00000306503.5	hg19	CCDS1830.1	.	.	.	.	.	.	.	.	.	.	G	16.21	3.060002	0.55325	.	.	ENSG00000171150	ENST00000306503;ENST00000394861	D;D	0.89270	-2.49;-2.49	5.43	3.64	0.41730	SH2 motif (4);	0.056973	0.64402	D	0.000001	D	0.93916	0.8053	M	0.82716	2.605	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	D	0.93888	0.7177	10	0.87932	D	0	-11.2549	11.8239	0.52256	0.1425:0.0:0.8575:0.0	.	429	O75159	SOCS5_HUMAN	Q	429	ENSP00000305133:R429Q;ENSP00000378330:R429Q	ENSP00000305133:R429Q	R	+	2	0	SOCS5	46840459	1.000000	0.71417	0.715000	0.30552	0.898000	0.52572	9.657000	0.98554	0.867000	0.35654	-0.136000	0.14681	CGA	.	.		0.498	SOCS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250791.2			A	46986955	G	A	46986955	3	1	310	1	0	0	0	0	1	0	0	0	14932	1058	37	1	1288	1	SOCS5	2	46986955	Missense_Mutation	SNP	G	TCGA-K7-A5RG-01A-11D-A28X-10	9512205	46986955	196212418	16	44117										
WDR92	116143	hgsc.bcm.edu	37	chr2	68365900	68365900	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	tttgatgtttgtctcccaccGtaatgccatatttctgagat	7	9	2	2	rs35021866		TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr2:68365900G>A	ENST00000295121.6	-	5	723	c.607C>T	c.(607-609)Cgg>Tgg	p.R203W	WDR92_ENST00000406245.2_Missense_Mutation_p.R102W|WDR92_ENST00000409164.1_Missense_Mutation_p.R203W|WDR92_ENST00000492039.2_5'UTR|RP11-474G23.1_ENST00000406334.3_3'UTR	NM_138458.3	NP_612467.1	Q96MX6	WDR92_HUMAN	WD repeat domain 92	203					apoptotic process (GO:0006915)|histone lysine methylation (GO:0034968)		methylated histone binding (GO:0035064)			endometrium(1)|kidney(3)|large_intestine(4)|lung(3)|stomach(1)	12						GTCTCCCACCGTAATGCCATA	0.378																																					p.R203W		Atlas-SNP	.											.	WDR92	21	.	0			c.C607T						.						232	233	233					2																	68365900		2203	4300	6503	SO:0001583	missense	116143	exon5			CCCACCGTAATGC	AK056303	CCDS1884.1, CCDS58712.1	2p14	2013-01-09			ENSG00000243667	ENSG00000243667		"WD repeat domain containing"	25176	protein-coding gene	gene with protein product		610729				16487927	Standard	NM_138458		Approved	FLJ31741, Monad	uc002see.2	Q96MX6	OTTHUMG00000152561	ENST00000295121.6:c.607C>T	chr2.hg19:g.68365900G>A	ENSP00000295121:p.Arg203Trp	119.0	0.0		117.0	9.0	NM_001256476	Q96CR6	Missense_Mutation	SNP	ENST00000295121.6	hg19	CCDS1884.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.438457	0.83885	.	.	ENSG00000243667	ENST00000295121;ENST00000406245;ENST00000409164	T;T;T	0.66280	1.57;1.57;-0.2	6.03	4.02	0.46733	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.53938	D	0.000054	T	0.78767	0.4335	M	0.89904	3.07	0.80722	D	1	D	0.89917	1.0	P	0.55965	0.788	D	0.84540	0.0638	10	0.59425	D	0.04	.	15.69	0.77442	0.0:0.0:0.6563:0.3437	rs35021866	203	Q96MX6	WDR92_HUMAN	W	203;102;203	ENSP00000295121:R203W;ENSP00000384518:R102W;ENSP00000386746:R203W	ENSP00000295121:R203W	R	-	1	2	WDR92	68219404	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.722000	0.54948	1.514000	0.48869	0.655000	0.94253	CGG	.	G|0.983;A|0.017		0.378	WDR92-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251754.2	NM_138458		A	68365900	G	A	68365900	3	1	310	1	0	0	0	0	1	0	0	0	17354	1144	40	1	482	1	WDR92	2	68365900	Missense_Mutation	SNP	G	TCGA-K7-A5RG-01A-11D-A28X-10	21378945	68365900	174833473	17	44118										
ITPRIPL1	150771	hgsc.bcm.edu	37	chr2	96992598	96992598	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	agaaggcagagaacttctggAcaggagacacatccagtgac	12	9	1	4			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr2:96992598A>G	ENST00000439118.2	+	3	480	c.229A>G	c.(229-231)Aca>Gca	p.T77A	ITPRIPL1_ENST00000542887.1_Missense_Mutation_p.T69A|ITPRIPL1_ENST00000536814.1_Missense_Mutation_p.T69A|ITPRIPL1_ENST00000361124.4_Missense_Mutation_p.T85A	NM_001008949.2	NP_001008949.1	Q6GPH6	IPIL1_HUMAN	inositol 1,4,5-trisphosphate receptor interacting protein-like 1	77						integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.T85P(1)		breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						GAACTTCTGGACAGGAGACAC	0.582																																					p.T85A		Atlas-SNP	.											ITPRIPL1,NS,lymphoid_neoplasm,0,2	ITPRIPL1	58	.	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.A253G						.						96	101	99					2																	96992598		2203	4300	6503	SO:0001583	missense	150771	exon1			TTCTGGACAGGAG		CCDS33250.1, CCDS46360.1, CCDS54378.1	2q11.2	2011-04-28	2011-04-28	2008-08-11	ENSG00000198885	ENSG00000198885			29371	protein-coding gene	gene with protein product			"KIAA1754-like", "inositol 1,4,5-triphosphate receptor interacting protein-like 1"	KIAA1754L		12477932	Standard	NM_178495		Approved		uc010yul.2	Q6GPH6	OTTHUMG00000155230	ENST00000439118.2:c.229A>G	chr2.hg19:g.96992598A>G	ENSP00000389308:p.Thr77Ala	130.0	0.0		138.0	18.0	NM_178495	F5H1L8|Q8NE61	Missense_Mutation	SNP	ENST00000439118.2	hg19	CCDS46360.1	.	.	.	.	.	.	.	.	.	.	A	0.421	-0.908184	0.02434	.	.	ENSG00000198885	ENST00000420176;ENST00000536814;ENST00000439118;ENST00000361124;ENST00000542887	T;T;T;T	0.17054	2.32;2.31;2.3;2.32	4.42	3.23	0.37069	.	0.466412	0.16056	N	0.231718	T	0.07098	0.0180	N	0.08118	0	0.20403	N	0.999901	B;B	0.09022	0.002;0.001	B;B	0.08055	0.003;0.001	T	0.40098	-0.9581	10	0.07813	T	0.8	-8.7959	7.9578	0.30053	0.7913:0.2087:0.0:0.0	.	85;77	Q6GPH6-2;Q6GPH6	.;IPIL1_HUMAN	A	69;69;77;85;69	ENSP00000439566:T69A;ENSP00000389308:T77A;ENSP00000355121:T85A;ENSP00000438212:T69A	ENSP00000355121:T85A	T	+	1	0	ITPRIPL1	96356325	0.987000	0.35691	1.000000	0.80357	0.713000	0.41058	0.548000	0.23314	0.817000	0.34445	0.533000	0.62120	ACA	.	.		0.582	ITPRIPL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000338896.1	NM_178495		G	96992598	A	G	96992598	3	3	310	1	0	0	0	0	1	0	0	0	7933	275	10	2	269	2	ITPRIPL1	2	96992598	Missense_Mutation	SNP	A	TCGA-K7-A5RG-01A-11D-A28X-10	28626698	96992598	146206775	18	44119										
DDX18	8886	hgsc.bcm.edu	37	chr2	118575029	118575029	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	tatttaaacaggggcctcaaAtctgaccctatcggaaactc	7	11	2	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr2:118575029A>G	ENST00000263239.2	+	2	223	c.95A>G	c.(94-96)aAt>aGt	p.N32S	DDX18_ENST00000474694.1_3'UTR	NM_006773.3	NP_006764.3	Q9NVP1	DDX18_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 18	32					ATP catabolic process (GO:0006200)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(4)|large_intestine(3)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						GGGGCCTCAAATCTGACCCTA	0.373																																					p.N32S		Atlas-SNP	.											.	DDX18	79	.	0			c.A95G						.						34	38	36					2																	118575029		2199	4296	6495	SO:0001583	missense	8886	exon2			CCTCAAATCTGAC	X98743	CCDS2120.1	2q21.2	2008-02-05	2003-06-13		ENSG00000088205	ENSG00000088205		"DEAD-boxes"	2741	protein-coding gene	gene with protein product		606355	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 18 (Myc-regulated)"			8861962	Standard	NM_006773		Approved	MrDb	uc002tlh.1	Q9NVP1	OTTHUMG00000058521	ENST00000263239.2:c.95A>G	chr2.hg19:g.118575029A>G	ENSP00000263239:p.Asn32Ser	26.0	0.0		23.0	4.0	NM_006773	Q6GTZ9|Q6IAU4|Q92732|Q9BQB7	Missense_Mutation	SNP	ENST00000263239.2	hg19	CCDS2120.1	.	.	.	.	.	.	.	.	.	.	A	0.084	-1.178179	0.01633	.	.	ENSG00000088205	ENST00000263239	T	0.01887	4.58	3.34	0.953	0.19590	.	2.062890	0.01808	N	0.033274	T	0.02230	0.0069	L	0.36672	1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.47898	-0.9081	10	0.09338	T	0.73	-0.8748	3.5617	0.07885	0.6196:0.2523:0.1281:0.0	.	32	Q9NVP1	DDX18_HUMAN	S	32	ENSP00000263239:N32S	ENSP00000263239:N32S	N	+	2	0	DDX18	118291499	0.000000	0.05858	0.285000	0.24819	0.075000	0.17131	-0.083000	0.11286	0.203000	0.20529	0.533000	0.62120	AAT	.	.		0.373	DDX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129632.3	NM_006773		G	118575029	A	G	118575029	3	3	310	1	0	0	0	0	1	0	0	0	4347	101	4	2	101	2	DDX18	2	118575029	Missense_Mutation	SNP	A	TCGA-K7-A5RG-01A-11D-A28X-10	21582431	118575029	124624344	19	44120										
TTN	7273	hgsc.bcm.edu	37	chr2	179438598	179438598	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	cttgttgaatctttgtttacCagattagtagagaaatctgc	8	6	2	3			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr2:179438598C>T	ENST00000591111.1	-	276	67562	c.67338G>A	c.(67336-67338)ctG>ctA	p.L22446L	TTN_ENST00000342175.6_Silent_p.L15214L|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Silent_p.L24087L|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000460472.2_Silent_p.L15022L|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342992.6_Silent_p.L21519L|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Silent_p.L15147L			Q8WZ42	TITIN_HUMAN	titin	22446	Ig-like 116.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTTTGTTTACCAGATTAGTAG	0.418																																					p.L24087L		Atlas-SNP	.											.	TTN	18412	.	0			c.G72261A						.						89	83	85					2																	179438598		1855	4093	5948	SO:0001819	synonymous_variant	7273	exon326			GTTTACCAGATTA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.67338G>A	chr2.hg19:g.179438598C>T		123.0	0.0		127.0	14.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179438598	C	T	179438598	2	4	310	1	0	0	0	0	0	0	0	1	16750	581	21	3		3	TTN	2	179438598	Silent	SNP	C	TCGA-K7-A5RG-01A-11D-A28X-10	60863569	179438598	63760775	20	44121										
PSMD1	5707	hgsc.bcm.edu	37	chr2	231927267	231927267	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ccggagtcggcagtttgcagCcttagtggcatctaaagtat	12	9	1	0			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr2:231927267C>T	ENST00000308696.6	+	4	344	c.182C>T	c.(181-183)gCc>gTc	p.A61V	PSMD1_ENST00000373635.4_Missense_Mutation_p.A61V|PSMD1_ENST00000409643.1_Missense_Mutation_p.A61V	NM_002807.3	NP_002798.2	Q99460	PSMD1_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	61					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)	31		Ovarian(221;0.000626)|Medulloblastoma(418;0.0109)|Renal(207;0.0112)|Lung NSC(271;0.0538)|all_lung(227;0.0713)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;4e-26)|LUSC - Lung squamous cell carcinoma(224;0.0138)|Lung(119;0.0168)	Bortezomib(DB00188)	CAGTTTGCAGCCTTAGTGGCA	0.423																																					p.A61V		Atlas-SNP	.											.	PSMD1	77	.	0			c.C182T						.						93	98	96					2																	231927267		2203	4300	6503	SO:0001583	missense	5707	exon4			TTGCAGCCTTAGT	D44466	CCDS2482.1, CCDS54436.1	2q37.1	2008-05-22			ENSG00000173692	ENSG00000173692		"Proteasome (prosome, macropain) subunits"	9554	protein-coding gene	gene with protein product						8816993	Standard	NM_002807		Approved	S1, P112, Rpn2	uc002vrn.2	Q99460	OTTHUMG00000133223	ENST00000308696.6:c.182C>T	chr2.hg19:g.231927267C>T	ENSP00000309474:p.Ala61Val	48.0	0.0		53.0	6.0	NM_002807	B8ZZH9|Q24JU0|Q53TI2|Q6GMU5|Q6P2P4|Q6PJM7|Q6PKG9|Q86VU1|Q8IV79	Missense_Mutation	SNP	ENST00000308696.6	hg19	CCDS2482.1	.	.	.	.	.	.	.	.	.	.	C	36	5.710218	0.96821	.	.	ENSG00000173692	ENST00000308696;ENST00000373635;ENST00000440838;ENST00000409643	T;T;T	0.32023	1.47;1.47;1.47	6.08	6.08	0.98989	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.69296	0.3095	H	0.94345	3.525	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.74674	0.984;0.983	T	0.76501	-0.2936	10	0.72032	D	0.01	-3.0784	20.6634	0.99662	0.0:1.0:0.0:0.0	.	61;61	Q99460;Q99460-2	PSMD1_HUMAN;.	V	61	ENSP00000309474:A61V;ENSP00000362738:A61V;ENSP00000386932:A61V	ENSP00000309474:A61V	A	+	2	0	PSMD1	231635511	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.894000	0.99253	0.655000	0.94253	GCC	.	.		0.423	PSMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256958.2			T	231927267	C	T	231927267	3	4	310	1	0	0	0	0	1	0	0	0	12704	739	26	3	196	3	PSMD1	2	231927267	Missense_Mutation	SNP	C	TCGA-K7-A5RG-01A-11D-A28X-10	52488669	231927267	11272106	21	44122										
HACL1	26061	hgsc.bcm.edu	37	chr3	15613198	15613198	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ggatgcagcttcattgctctTcattttttctctcagagttt	7	9	5	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr3:15613198T>A	ENST00000321169.5	-	12	1439	c.1072A>T	c.(1072-1074)Aag>Tag	p.K358*	HACL1_ENST00000457447.2_Intron|HACL1_ENST00000435217.2_Nonsense_Mutation_p.K117*|HACL1_ENST00000451445.2_Nonsense_Mutation_p.K276*|HACL1_ENST00000456194.2_Nonsense_Mutation_p.K331*	NM_012260.2	NP_036392.2	Q9UJ83	HACL1_HUMAN	2-hydroxyacyl-CoA lyase 1	358					cellular lipid metabolic process (GO:0044255)|fatty acid alpha-oxidation (GO:0001561)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carbon-carbon lyase activity (GO:0016830)|cofactor binding (GO:0048037)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|receptor binding (GO:0005102)|thiamine pyrophosphate binding (GO:0030976)			NS(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|skin(1)	16						TCATTGCTCTTCATTTTTTCT	0.408																																					p.K358X		Atlas-SNP	.											.	HACL1	33	.	0			c.A1072T						.						238	206	217					3																	15613198		2203	4300	6503	SO:0001587	stop_gained	26061	exon12			TGCTCTTCATTTT	AJ131753	CCDS2627.1, CCDS68360.1, CCDS68361.1, CCDS68362.1	3p24.3	2009-01-14	2006-05-16	2006-05-16	ENSG00000131373	ENSG00000131373	4.1.-.-		17856	protein-coding gene	gene with protein product		604300	"2-hydroxyphytanoyl-CoA lyase"	HPCL		10468558, 15644336	Standard	NM_001284416		Approved	2-HPCL, PHYH2	uc003caf.3	Q9UJ83	OTTHUMG00000129862	ENST00000321169.5:c.1072A>T	chr3.hg19:g.15613198T>A	ENSP00000323811:p.Lys358*	62.0	0.0		47.0	7.0	NM_012260	B4DWI1|B4DXI5|E9PEN4|Q9BV42|Q9P0A2	Nonsense_Mutation	SNP	ENST00000321169.5	hg19	CCDS2627.1	.	.	.	.	.	.	.	.	.	.	T	13.84	2.355688	0.41700	.	.	ENSG00000131373	ENST00000321169;ENST00000435217;ENST00000451445;ENST00000456194	.	.	.	5.08	-3.68	0.04463	.	1.952780	0.02237	N	0.065427	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.06891	T	0.86	.	8.2332	0.31610	0.0:0.3787:0.155:0.4663	.	.	.	.	X	358;117;276;331	.	ENSP00000323811:K358X	K	-	1	0	HACL1	15588202	0.368000	0.25031	0.251000	0.24312	0.096000	0.18686	0.694000	0.25512	-0.858000	0.04110	-0.924000	0.02725	AAG	.	.		0.408	HACL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252104.3	NM_012260		A	15613198	T	A	15613198	4	1	310	1	0	0	0	0	0	1	0	0	6950	1792	62	4	688	4	HACL1	3	15613198	Nonsense_Mutation	SNP	T	TCGA-K7-A5RG-01A-11D-A28X-10		15613198	182409232	22	44123										
TBC1D5	9779	hgsc.bcm.edu	37	chr3	17349528	17349528	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	tggctacgaagatataatctActaaacccaggctgaggccg	10	10	1	2			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr3:17349528A>G	ENST00000253692.7	-	14	2758	c.1094T>C	c.(1093-1095)gTa>gCa	p.V365A	TBC1D5_ENST00000429924.2_Missense_Mutation_p.V317A|TBC1D5_ENST00000446818.2_Missense_Mutation_p.V365A|TBC1D5_ENST00000429383.4_Missense_Mutation_p.V365A|TBC1D5_ENST00000414318.2_5'UTR	NM_014744.2	NP_055559.1	Q92609	TBCD5_HUMAN	TBC1 domain family, member 5	365						retromer complex (GO:0030904)	Rab GTPase activator activity (GO:0005097)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	36						GATATAATCTACTAAACCCAG	0.463																																					p.V365A		Atlas-SNP	.											.	TBC1D5	69	.	0			c.T1094C						.						81	78	79					3																	17349528		2203	4300	6503	SO:0001583	missense	9779	exon14			TAATCTACTAAAC	D86965	CCDS33714.1, CCDS46770.1	3p24.3	2013-07-09			ENSG00000131374	ENSG00000131374			19166	protein-coding gene	gene with protein product		615740				19531583	Standard	NM_014744		Approved	KIAA0210	uc003cbe.3	Q92609	OTTHUMG00000155488	ENST00000253692.7:c.1094T>C	chr3.hg19:g.17349528A>G	ENSP00000253692:p.Val365Ala	224.0	0.0		190.0	38.0	NM_014744	A6NP25|C9JP52	Missense_Mutation	SNP	ENST00000253692.7	hg19	CCDS33714.1	.	.	.	.	.	.	.	.	.	.	A	17.55	3.417639	0.62622	.	.	ENSG00000131374	ENST00000253692;ENST00000429383;ENST00000446818;ENST00000429924	T;T;T;T	0.11385	2.78;2.78;2.78;2.78	5.55	5.55	0.83447	Rab-GAP/TBC domain (3);	0.000000	0.85682	D	0.000000	T	0.23766	0.0575	L	0.41710	1.295	0.80722	D	1	B;P;P	0.51240	0.372;0.943;0.94	P;P;P	0.62014	0.74;0.854;0.897	T	0.00415	-1.1753	10	0.66056	D	0.02	-17.9645	15.6976	0.77512	1.0:0.0:0.0:0.0	.	317;365;365	C9J3F6;C9JP52;Q92609	.;.;TBCD5_HUMAN	A	365;365;365;317	ENSP00000253692:V365A;ENSP00000398127:V365A;ENSP00000402935:V365A;ENSP00000411925:V317A	ENSP00000253692:V365A	V	-	2	0	TBC1D5	17324532	1.000000	0.71417	0.113000	0.21522	0.443000	0.32047	9.173000	0.94815	2.115000	0.64714	0.477000	0.44152	GTA	.	.		0.463	TBC1D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340301.3	NM_014744		G	17349528	A	G	17349528	3	3	310	1	0	0	0	0	1	0	0	0	15638	391	14	2	1399	2	TBC1D5	3	17349528	Missense_Mutation	SNP	A	TCGA-K7-A5RG-01A-11D-A28X-10	1736330	17349528	180672902	23	44124										
ZNF445	353274	hgsc.bcm.edu	37	chr3	44492403	44492403	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	tggttggtgttacctggtctCccgggcacccctctctcggg	13	14	2	0			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr3:44492403C>T	ENST00000396077.2	-	5	997	c.650G>A	c.(649-651)gGa>gAa	p.G217E	ZNF445_ENST00000425708.2_Missense_Mutation_p.G217E	NM_181489.5	NP_852466.1	P59923	ZN445_HUMAN	zinc finger protein 445	217					transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|skin(3)	31				KIRC - Kidney renal clear cell carcinoma(197;0.0514)|Kidney(197;0.0646)		TACCTGGTCTCCCGGGCACCC	0.592																																					p.G217E		Atlas-SNP	.											.	ZNF445	91	.	0			c.G650A						.						87	77	81					3																	44492403		2203	4300	6503	SO:0001583	missense	353274	exon5			TGGTCTCCCGGGC	AY262260	CCDS2713.1	3p21.32	2013-01-09	2003-10-07		ENSG00000185219	ENSG00000185219		"Zinc fingers, C2H2-type", "-", "-", "-"	21018	protein-coding gene	gene with protein product			"zinc finger protein 168"	ZNF168		7814019	Standard	NM_181489		Approved	ZKSCAN15, ZSCAN47	uc003cnf.2	P59923	OTTHUMG00000133042	ENST00000396077.2:c.650G>A	chr3.hg19:g.44492403C>T	ENSP00000379387:p.Gly217Glu	110.0	0.0		125.0	9.0	NM_181489	Q3MJD1	Missense_Mutation	SNP	ENST00000396077.2	hg19	CCDS2713.1	.	.	.	.	.	.	.	.	.	.	C	12.14	1.847418	0.32606	.	.	ENSG00000185219	ENST00000425708;ENST00000396077;ENST00000340674;ENST00000430301	T;T	0.05319	3.46;3.46	4.34	0.507	0.16967	.	0.333064	0.21908	N	0.067355	T	0.03220	0.0094	N	0.24115	0.695	0.09310	N	1	B;B	0.21225	0.053;0.053	B;B	0.18263	0.021;0.021	T	0.47169	-0.9138	10	0.02654	T	1	.	7.7594	0.28944	0.0:0.6148:0.0:0.3852	.	217;217	B7ZKX2;P59923	.;ZN445_HUMAN	E	217;217;210;215	ENSP00000413073:G217E;ENSP00000379387:G217E	ENSP00000342436:G210E	G	-	2	0	ZNF445	44467407	0.000000	0.05858	0.002000	0.10522	0.270000	0.26580	-0.357000	0.07651	0.075000	0.16796	0.491000	0.48974	GGA	.	.		0.592	ZNF445-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256647.2	NM_181489		T	44492403	C	T	44492403	3	4	310	1	0	0	0	0	1	0	0	0	17933	855	30	3	2461	3	ZNF445	3	44492403	Missense_Mutation	SNP	C	TCGA-K7-A5RG-01A-11D-A28X-10	27142875	44492403	153530027	24	44125										
DPPA2	151871	hgsc.bcm.edu	37	chr3	109028174	109028174	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	gctcatttgtttgaagtagaTgacctaagacaagaatggaa	10	5	1	5			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr3:109028174T>C	ENST00000478945.1	-	4	431	c.185A>G	c.(184-186)cAt>cGt	p.H62R		NM_138815.3	NP_620170.3	Q7Z7J5	DPPA2_HUMAN	developmental pluripotency associated 2	62					lung-associated mesenchyme development (GO:0060484)|positive regulation of stem cell proliferation (GO:2000648)|regulation of histone methylation (GO:0031060)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(19)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TTGAAGTAGATGACCTAAGAC	0.398																																					p.H62R		Atlas-SNP	.											.	DPPA2	52	.	0			c.A185G						.						94	92	93					3																	109028174		2203	4300	6503	SO:0001583	missense	151871	exon4			AGTAGATGACCTA	AY283672	CCDS2956.1	3q13.13	2010-05-04			ENSG00000163530	ENSG00000163530			19197	protein-coding gene	gene with protein product	"cancer/testis antigen 100"	614445				15583978	Standard	NM_138815		Approved	PESCRG1, CT100	uc003dxo.3	Q7Z7J5	OTTHUMG00000159227	ENST00000478945.1:c.185A>G	chr3.hg19:g.109028174T>C	ENSP00000417710:p.His62Arg	73.0	0.0		111.0	18.0	NM_138815	Q8WVF0	Missense_Mutation	SNP	ENST00000478945.1	hg19	CCDS2956.1	.	.	.	.	.	.	.	.	.	.	T	5.899	0.349915	0.11182	.	.	ENSG00000163530	ENST00000478945	T	0.47528	0.84	4.76	-6.46	0.01908	.	2.299430	0.01348	N	0.011813	T	0.24661	0.0598	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.09271	-1.0682	10	0.15499	T	0.54	1.0161	0.4091	0.00438	0.2548:0.2646:0.2591:0.2215	.	62	Q7Z7J5	DPPA2_HUMAN	R	62	ENSP00000417710:H62R	ENSP00000417710:H62R	H	-	2	0	DPPA2	110510864	0.000000	0.05858	0.000000	0.03702	0.349000	0.29174	-0.479000	0.06567	-0.844000	0.04184	0.459000	0.35465	CAT	.	.		0.398	DPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353938.1	NM_138815		C	109028174	T	C	109028174	3	2	310	1	0	0	0	0	1	0	0	0	4736	1464	51	2	731	2	DPPA2	3	109028174	Missense_Mutation	SNP	T	TCGA-K7-A5RG-01A-11D-A28X-10	64535771	109028174	88994256	25	44126										
ILDR1	286676	hgsc.bcm.edu	37	chr3	121712594	121712594	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	gatgacaggtctctgatcagTgggggcaggtggatgattct	16	6	3	3			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr3:121712594T>A	ENST00000344209.5	-	7	1128	c.1002A>T	c.(1000-1002)ccA>ccT	p.P334P	ILDR1_ENST00000393631.1_Silent_p.P245P|ILDR1_ENST00000273691.3_Silent_p.P290P|ILDR1_ENST00000462014.1_Silent_p.P302P|ILDR1_ENST00000460554.1_5'UTR	NM_001199799.1	NP_001186728.1	Q86SU0	ILDR1_HUMAN	immunoglobulin-like domain containing receptor 1	334					positive regulation of peptide hormone secretion (GO:0090277)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-density lipoprotein particle receptor activity (GO:0070506)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				GBM - Glioblastoma multiforme(114;0.156)		CTCTGATCAGTGGGGGCAGGT	0.612																																					p.P334P		Atlas-SNP	.											.	ILDR1	120	.	0			c.A1002T						.						72	72	72					3																	121712594		2203	4300	6503	SO:0001819	synonymous_variant	286676	exon7			GATCAGTGGGGGC	BC044240	CCDS3008.1, CCDS56270.1, CCDS56271.1	3q21.1	2013-10-11			ENSG00000145103	ENSG00000145103			28741	protein-coding gene	gene with protein product		609739	"deafness, autosomal recessive 42"	DFNB42		15641023, 21255762	Standard	NM_175924		Approved	MGC50831	uc003ees.3	Q86SU0	OTTHUMG00000159481	ENST00000344209.5:c.1002A>T	chr3.hg19:g.121712594T>A		185.0	0.0		201.0	21.0	NM_001199799	Q6ZP61|Q7Z578	Silent	SNP	ENST00000344209.5	hg19	CCDS56271.1																																																																																			.	.		0.612	ILDR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355666.1	NM_175924		A	121712594	T	A	121712594	2	1	310	1	0	0	0	0	0	0	0	1	7718	1683	59	4		4	ILDR1	3	121712594	Silent	SNP	T	TCGA-K7-A5RG-01A-11D-A28X-10	12684420	121712594	76309836	26	44127										
ACAD11	84129	hgsc.bcm.edu	37	chr3	132297694	132297694	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ttttactccaggtgtgttcaTgggaacaagaatcatgctgt	10	7	2	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr3:132297694T>C	ENST00000264990.6	-	15	2691	c.1720A>G	c.(1720-1722)Atg>Gtg	p.M574V	ACAD11_ENST00000545291.1_Missense_Mutation_p.M99V|ACAD11_ENST00000355458.3_Intron	NM_032169.4	NP_115545	Q709F0	ACD11_HUMAN	acyl-CoA dehydrogenase family, member 11	574					fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)	mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|peroxisome (GO:0005777)	flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)|medium-chain-acyl-CoA dehydrogenase activity (GO:0070991)|transferase activity, transferring phosphorus-containing groups (GO:0016772)|very-long-chain-acyl-CoA dehydrogenase activity (GO:0017099)			breast(2)|endometrium(6)|kidney(2)|large_intestine(8)|lung(10)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	36						GGTGTGTTCATGGGAACAAGA	0.348																																					p.M574V		Atlas-SNP	.											.	ACAD11	78	.	0			c.A1720G						.						156	157	157					3																	132297694		2203	4300	6503	SO:0001583	missense	84129	exon15			TGTTCATGGGAAC	BC019607	CCDS3074.1	3q22.1	2010-04-30	2010-04-30		ENSG00000240303	ENSG00000240303			30211	protein-coding gene	gene with protein product		614288	"acyl-Coenzyme A dehydrogenase family, member 11"				Standard	NM_032169		Approved	FLJ12592		Q709F0	OTTHUMG00000159780	ENST00000264990.6:c.1720A>G	chr3.hg19:g.132297694T>C	ENSP00000264990:p.Met574Val	80.0	0.0		67.0	10.0	NM_032169	Q08AF0|Q658N9|Q658Y2|Q6ZND2|Q8WUT6|Q9H9R3	Missense_Mutation	SNP	ENST00000264990.6	hg19	CCDS3074.1	.	.	.	.	.	.	.	.	.	.	T	13.12	2.141987	0.37825	.	.	ENSG00000240303	ENST00000264990;ENST00000545291	D;D	0.98901	-5.22;-5.22	5.56	-0.072	0.13741	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA oxidase/dehydrogenase, central domain (1);	.	.	.	.	D	0.95875	0.8657	L	0.58428	1.81	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	D	0.89750	0.3939	9	0.35671	T	0.21	.	2.2763	0.04103	0.1256:0.1452:0.1303:0.5989	.	574	Q709F0	ACD11_HUMAN	V	574;99	ENSP00000264990:M574V;ENSP00000446263:M99V	ENSP00000264990:M574V	M	-	1	0	ACAD11	133780384	0.012000	0.17670	0.045000	0.18777	0.969000	0.65631	0.027000	0.13621	0.113000	0.18004	0.482000	0.46254	ATG	.	.		0.348	ACAD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357279.2	NM_032169		C	132297694	T	C	132297694	3	2	310	1	0	0	0	0	1	0	0	0	109	1464	51	2	646	2	ACAD11	3	132297694	Missense_Mutation	SNP	T	TCGA-K7-A5RG-01A-11D-A28X-10	10585100	132297694	65724736	27	44128										
A4GNT	51146	hgsc.bcm.edu	37	chr3	137843669	137843669	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	tttccagatgatggccaggcGggatgcatccgagctgatgt	14	9	0	3	rs376190351		TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr3:137843669G>A	ENST00000236709.3	-	3	661	c.460C>T	c.(460-462)Cgc>Tgc	p.R154C		NM_016161.2	NP_057245.1	Q9UNA3	A4GCT_HUMAN	alpha-1,4-N-acetylglucosaminyltransferase	154					carbohydrate metabolic process (GO:0005975)|glycoprotein biosynthetic process (GO:0009101)|negative regulation of epithelial cell proliferation (GO:0050680)|protein O-linked glycosylation (GO:0006493)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylglucosaminyltransferase activity (GO:0008375)	p.R154S(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)	16						ATGGCCAGGCGGGATGCATCC	0.572																																					p.R154C		Atlas-SNP	.											A4GNT,colon,carcinoma,0,1	A4GNT	42	.	1	Substitution - Missense(1)	large_intestine(1)	c.C460T						.						78	74	75					3																	137843669		2203	4300	6503	SO:0001583	missense	51146	exon3			CCAGGCGGGATGC	AF141315	CCDS3097.1	3p14.3	2010-12-14			ENSG00000118017	ENSG00000118017			17968	protein-coding gene	gene with protein product						10430883	Standard	NM_016161		Approved	alpha4GnT	uc003ers.2	Q9UNA3	OTTHUMG00000159820	ENST00000236709.3:c.460C>T	chr3.hg19:g.137843669G>A	ENSP00000236709:p.Arg154Cys	138.0	0.0		137.0	21.0	NM_016161	Q0VDK1|Q0VDK2	Missense_Mutation	SNP	ENST00000236709.3	hg19	CCDS3097.1	.	.	.	.	.	.	.	.	.	.	G	17.77	3.470071	0.63625	.	.	ENSG00000118017	ENST00000236709	D	0.97888	-4.59	5.27	4.31	0.51392	Glycosyltransferase, DXD sugar-binding motif (1);	0.000000	0.64402	D	0.000002	D	0.98937	0.9639	H	0.95437	3.67	0.58432	D	0.999997	D	0.89917	1.0	D	0.97110	1.0	D	0.98869	1.0765	10	0.87932	D	0	-6.1903	10.6822	0.45821	0.0:0.0:0.5672:0.4328	.	154	Q9UNA3	A4GCT_HUMAN	C	154	ENSP00000236709:R154C	ENSP00000236709:R154C	R	-	1	0	A4GNT	139326359	1.000000	0.71417	0.975000	0.42487	0.556000	0.35491	2.715000	0.47210	2.458000	0.83093	0.563000	0.77884	CGC	.	.		0.572	A4GNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357557.1	NM_016161		A	137843669	G	A	137843669	3	1	310	1	0	0	0	0	1	0	0	0	7	1116	39	1	566	1	A4GNT	3	137843669	Missense_Mutation	SNP	G	TCGA-K7-A5RG-01A-11D-A28X-10	5545975	137843669	60178761	28	44129										
ATP1B3	483	hgsc.bcm.edu	37	chr3	141632520	141632520	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ctttagaagaacagaagaacCtcacagtctgtcctgatgga	9	9	2	5			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr3:141632520C>A	ENST00000286371.3	+	4	561	c.373C>A	c.(373-375)Ctc>Atc	p.L125I	ATP1B3_ENST00000462082.1_Intron|ATP1B3_ENST00000539728.1_Missense_Mutation_p.L111I	NM_001679.2	NP_001670.1	P54709	AT1B3_HUMAN	ATPase, Na+/K+ transporting, beta 3 polypeptide	125					blood coagulation (GO:0007596)|cellular potassium ion homeostasis (GO:0030007)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|leukocyte migration (GO:0050900)|membrane repolarization (GO:0086009)|positive regulation of ATP catabolic process (GO:1903291)|positive regulation of ATPase activity (GO:0032781)|positive regulation of potassium ion import (GO:1903288)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of sodium ion export from cell (GO:1903278)|potassium ion import (GO:0010107)|protein localization to plasma membrane (GO:0072659)|protein stabilization (GO:0050821)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)|transport (GO:0006810)	caveola (GO:0005901)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|sodium:potassium-exchanging ATPase activity (GO:0005391)			cervix(1)|endometrium(1)|lung(2)	4						ACAGAAGAACCTCACAGTCTG	0.363																																					p.L125I		Atlas-SNP	.											.	ATP1B3	17	.	0			c.C373A						.						146	140	142					3																	141632520		2203	4300	6503	SO:0001583	missense	483	exon4			AAGAACCTCACAG	BC011835	CCDS3121.1	3q23	2012-10-22			ENSG00000069849	ENSG00000069849		"CD molecules", "ATPases / P-type"	806	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit beta-3", "sodium pump subunit beta-3", "sodium-potassium ATPase subunit beta 3 (non-catalytic)"	601867				8798450, 9457675	Standard	NM_001679		Approved	FLJ29027, CD298	uc003eug.1	P54709	OTTHUMG00000159081	ENST00000286371.3:c.373C>A	chr3.hg19:g.141632520C>A	ENSP00000286371:p.Leu125Ile	102.0	0.0		116.0	18.0	NM_001679	B7Z1N7	Missense_Mutation	SNP	ENST00000286371.3	hg19	CCDS3121.1	.	.	.	.	.	.	.	.	.	.	C	12.41	1.928682	0.34002	.	.	ENSG00000069849	ENST00000475483;ENST00000286371;ENST00000539728;ENST00000495216	T;T;T;T	0.30448	1.53;1.53;1.53;1.53	5.45	2.33	0.28932	.	0.162128	0.52532	D	0.000076	T	0.31638	0.0803	L	0.37561	1.115	0.80722	D	1	D;P	0.55605	0.972;0.86	P;B	0.56563	0.801;0.406	T	0.03761	-1.1006	10	0.18276	T	0.48	-7.5263	8.4834	0.33057	0.2775:0.598:0.1245:0.0	.	111;125	D3DNF9;P54709	.;AT1B3_HUMAN	I	68;125;111;111	ENSP00000417522:L68I;ENSP00000286371:L125I;ENSP00000440307:L111I;ENSP00000419962:L111I	ENSP00000286371:L125I	L	+	1	0	ATP1B3	143115210	0.105000	0.21958	0.998000	0.56505	0.546000	0.35178	0.828000	0.27435	1.279000	0.44446	0.491000	0.48974	CTC	.	.		0.363	ATP1B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353218.1	NM_001679		A	141632520	C	A	141632520	3	1	310	1	0	0	0	0	1	0	0	0	1134	681	24	3	387	3	ATP1B3	3	141632520	Missense_Mutation	SNP	C	TCGA-K7-A5RG-01A-11D-A28X-10	3788851	141632520	56389910	29	44130										
PLSCR5	389158	hgsc.bcm.edu	37	chr3	146318107	146318107	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ttctagaccaggagggagacTgactgttggcaggaaactgc	14	8	1	3			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr3:146318107T>A	ENST00000443512.1	-	2	1160	c.157A>T	c.(157-159)Agt>Tgt	p.S53C	PLSCR5_ENST00000492200.1_Missense_Mutation_p.S53C|PLSCR5_ENST00000482567.1_Intron	NM_001085420.1	NP_001078889.1	A0PG75	PLS5_HUMAN	phospholipid scramblase family, member 5	53										endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|urinary_tract(1)	12						GGAGGGAGACTGACTGTTGGC	0.453																																					p.S53C		Atlas-SNP	.											.	PLSCR5	35	.	0			c.A157T						.						43	44	44					3																	146318107		1847	4087	5934	SO:0001583	missense	389158	exon2			GGAGACTGACTGT	AY436642	CCDS46931.1	3q24	2004-06-28			ENSG00000231213	ENSG00000231213			19952	protein-coding gene	gene with protein product							Standard	NM_001085420		Approved		uc010hvc.3	A0PG75	OTTHUMG00000159437	ENST00000443512.1:c.157A>T	chr3.hg19:g.146318107T>A	ENSP00000390111:p.Ser53Cys	44.0	0.0		46.0	9.0	NM_001085420	B2RXK5	Missense_Mutation	SNP	ENST00000443512.1	hg19	CCDS46931.1	.	.	.	.	.	.	.	.	.	.	T	17.56	3.420521	0.62622	.	.	ENSG00000231213	ENST00000492200;ENST00000443512	T;T	0.24350	1.86;1.86	3.15	0.54	0.17163	.	.	.	.	.	T	0.25827	0.0629	L	0.39898	1.24	0.09310	N	1	B	0.32425	0.371	P	0.44597	0.454	T	0.41016	-0.9532	9	0.72032	D	0.01	-10.8872	3.7158	0.08437	0.2215:0.0:0.2294:0.549	.	53	A0PG75	PLS5_HUMAN	C	53	ENSP00000417184:S53C;ENSP00000390111:S53C	ENSP00000390111:S53C	S	-	1	0	PLSCR5	147800797	0.038000	0.19896	0.012000	0.15200	0.985000	0.73830	0.651000	0.24873	0.098000	0.17522	0.524000	0.50904	AGT	.	.		0.453	PLSCR5-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355365.1	XM_371670		A	146318107	T	A	146318107	3	1	310	1	0	0	0	0	1	0	0	0	12122	1580	55	4	682	4	PLSCR5	3	146318107	Missense_Mutation	SNP	T	TCGA-K7-A5RG-01A-11D-A28X-10	4685587	146318107	51704323	30	44131										
SGEF	26084	hgsc.bcm.edu	37	chr3	153840488	153840488	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	gaatccttccgtggttttgaGtacaaacagccccgccgccc	9	15	0	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr3:153840488G>T	ENST00000356448.4	+	2	991	c.707G>T	c.(706-708)aGt>aTt	p.S236I	ARHGEF26-AS1_ENST00000467912.1_RNA|ARHGEF26-AS1_ENST00000480639.1_RNA|ARHGEF26-AS1_ENST00000491862.1_RNA|ARHGEF26_ENST00000465093.1_Missense_Mutation_p.S236I|ARHGEF26-AS1_ENST00000479270.1_RNA|ARHGEF26_ENST00000465817.1_Missense_Mutation_p.S236I	NM_001251962.1	NP_001238891.1	Q96DR7	ARHGQ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 26	236					endothelial cell morphogenesis (GO:0001886)|ruffle assembly (GO:0097178)	cell projection (GO:0042995)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	23						GTGGTTTTGAGTACAAACAGC	0.502																																					p.S236I	GBM(163;191 2003 24758 29593 48540)|Ovarian(152;631 1885 20165 22910 51013)	Atlas-SNP	.											.	ARHGEF26	158	.	0			c.G707T						.						15	18	17					3																	153840488		1852	4096	5948	SO:0001583	missense	26084	exon2			TTTTGAGTACAAA	BC016628	CCDS46938.1, CCDS58858.1	3q25.2	2013-01-10			ENSG00000114790	ENSG00000114790		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	24490	protein-coding gene	gene with protein product	"Src homology 3 domain-containing guanine nucleotide exchange factor"					15133129, 12697679	Standard	NM_015595		Approved	DKFZP434D146, SGEF	uc021xgc.1	Q96DR7	OTTHUMG00000159098	ENST00000356448.4:c.707G>T	chr3.hg19:g.153840488G>T	ENSP00000348828:p.Ser236Ile	79.0	0.0		79.0	4.0	NM_001251962	B3KVP8|E9PBD0|Q68CL1|Q6AZ96|Q6Q8Q8|Q96AW8|Q96DR6|Q9H9D7|Q9H9R2|Q9UFW5	Missense_Mutation	SNP	ENST00000356448.4	hg19	CCDS46938.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.751204	0.89753	.	.	ENSG00000114790	ENST00000356448;ENST00000465093;ENST00000465817	T;T;T	0.78481	-1.18;-1.18;0.1	5.04	5.04	0.67666	.	0.085942	0.85682	D	0.000000	D	0.82761	0.5107	L	0.29908	0.895	0.58432	D	0.999999	D;D	0.76494	0.999;0.999	D;D	0.83275	0.996;0.996	D	0.85369	0.1112	10	0.87932	D	0	-13.0269	17.981	0.89141	0.0:0.0:1.0:0.0	.	236;236	E9PBD0;Q96DR7	.;ARHGQ_HUMAN	I	236	ENSP00000348828:S236I;ENSP00000423418:S236I;ENSP00000423295:S236I	ENSP00000348828:S236I	S	+	2	0	ARHGEF26	155323178	1.000000	0.71417	0.999000	0.59377	0.897000	0.52465	8.417000	0.90247	2.316000	0.78162	0.655000	0.94253	AGT	.	.		0.502	ARHGEF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353287.3	NM_015595		T	153840488	G	T	153840488	3	4	310	1	0	0	0	0	1	0	0	0	14220	1029	36	3	709	3	SGEF	3	153840488	Missense_Mutation	SNP	G	TCGA-K7-A5RG-01A-11D-A28X-10	7522381	153840488	44181942	31	44132										
VEPH1	79674	hgsc.bcm.edu	37	chr3	157188168	157188169	+	Missense_Mutation	DNP	AG	AG	TT													0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	agtgtcttcgtctttcccaaAgggtctcaggttatgttcca					rs565482063		TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	A|G	A|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr3:157188168_157188169AG>TT	ENST00000362010.2	-	3	595_596	c.288_289CT>AA	c.(286-291)ccCTtt>ccAAtt	p.F97I	VEPH1_ENST00000537559.1_Missense_Mutation_p.F97I|VEPH1_ENST00000494677.1_Missense_Mutation_p.F97I|VEPH1_ENST00000468233.1_Missense_Mutation_p.F97I|VEPH1_ENST00000392832.2_Missense_Mutation_p.F97I|VEPH1_ENST00000392833.2_Missense_Mutation_p.F97I|VEPH1_ENST00000543418.1_Missense_Mutation_p.F97I	NM_001167912.1	NP_001161384.1	Q14D04	MELT_HUMAN	ventricular zone expressed PH domain-containing 1	97						plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(5)|cervix(1)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|pancreas(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)			TCTTTCCCAAAGGGTCTCAGGT	0.455																																					p.F97I|p.P96P		Atlas-SNP	.											.	VEPH1	129	.	0			c.T289A|c.C288A						.																																			SO:0001583	missense	79674	exon3			TCCCAAAGGGTCT|CCCAAAGGGTCTC	AL713656	CCDS3179.1, CCDS54661.1, CCDS54662.1, CCDS54663.1	3q24-q25	2013-01-10	2012-12-10		ENSG00000197415	ENSG00000197415		"Pleckstrin homology (PH) domain containing"	25735	protein-coding gene	gene with protein product		609594	"ventricular zone expressed PH domain homolog 1 (zebrafish)"			11214970, 15388229	Standard	NM_024621		Approved	FLJ12604, KIAA1692	uc003fbk.2	Q14D04	OTTHUMG00000158711	ENST00000362010.2:c.288_289delinsTT	chr3.hg19:g.157188168_157188169delinsTT	ENSP00000354919:p.Phe97Ile	141.0|143.0	0.0		151.0	24.0|23.0	NM_001167911	D3DNL0|F5GZ91|Q2TAA9|Q3MIX2|Q6PEL3|Q86TL5|Q8TCR3|Q96SP7|Q9C0H1|Q9H9Q7	Missense_Mutation|Silent	SNP	ENST00000362010.2	hg19	CCDS3179.1																																																																																			.	.		0.455	VEPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351845.3	NM_024621		TT	157188169	AG	TT	157188168	3	4	310	1	0	0	0	0	1	0	0	0	17169	72	3	4	2382	4	VEPH1	3	157188168	Missense_Mutation	DNP	AG	TCGA-K7-A5RG-01A-11D-A28X-10	3347680	157188168	40834262	32	44133										
MUC20	200958	hgsc.bcm.edu	37	chr3	195452975	195452978	+	Frame_Shift_Del	DEL	CCCA	CCCA	-													0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ccacggttgggaccccactcCccactaacagcgccacagaa					rs562232731		TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	CCCA	CCCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr3:195452975_195452978delCCCA	ENST00000447234.2	+	2	1627_1630	c.1501_1504delCCCA	c.(1501-1506)cccactfs	p.PT501fs	MUC20_ENST00000445522.2_Frame_Shift_Del_p.PT466fs|MUC20_ENST00000436408.1_Frame_Shift_Del_p.PT501fs|MUC20_ENST00000320736.6_Frame_Shift_Del_p.PT330fs	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	501	Involved in oligomerization.		Missing. {ECO:0000269|PubMed:14702039}.		activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)				NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		GACCCCACTCCCCACTAACAGCGC	0.593																																					p.329_330del		Atlas-Indel,Pindel	.											.	MUC20	84	.	0			c.987_990del						.																																			SO:0001589	frameshift_variant	200958	exon3			.	AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"Mucins"	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.1501_1504delCCCA	chr3.hg19:g.195452975_195452978delCCCA	ENSP00000414350:p.Pro501fs	411.0	0.0		453.0	44.0	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Frame_Shift_Del	DEL	ENST00000447234.2	hg19																																																																																				.	.		0.593	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673		-	195452978	CCCA	-	195452975	7	5	310	1	0	1	0	1	0	0	0	0	9985	623	22	0	998	0	MUC20	3	195452975	Frame_Shift_Del	DEL	CCCA	TCGA-K7-A5RG-01A-11D-A28X-10	38264807	195452975	2569455	33	44134										
HTT	3064	hgsc.bcm.edu	37	chr4	3179109	3179109	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	gaatacattgaagtgggccaGttcaggtaatagcattttat	10	5	1	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr4:3179109G>T	ENST00000355072.5	+	34	4603	c.4458G>T	c.(4456-4458)caG>caT	p.Q1486H		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	1486					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		AAGTGGGCCAGTTCAGGTAAT	0.279																																					p.Q1486H		Atlas-SNP	.											.	HTT	221	.	0			c.G4458T						.						135	119	124					4																	3179109		1794	4065	5859	SO:0001583	missense	3064	exon34			GGGCCAGTTCAGG	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.4458G>T	chr4.hg19:g.3179109G>T	ENSP00000347184:p.Gln1486His	58.0	0.0		55.0	10.0	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	hg19	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	G	17.28	3.348668	0.61183	.	.	ENSG00000197386	ENST00000355072	T	0.05513	3.43	6.07	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.14657	0.0354	L	0.38531	1.155	0.58432	D	0.999994	D	0.69078	0.997	D	0.78314	0.991	T	0.11324	-1.0592	10	0.25751	T	0.34	.	12.1988	0.54313	0.1358:0.0:0.8642:0.0	.	1486	P42858	HD_HUMAN	H	1486	ENSP00000347184:Q1486H	ENSP00000347184:Q1486H	Q	+	3	2	HTT	3148907	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.843000	0.62838	1.578000	0.49821	0.655000	0.94253	CAG	.	.		0.279	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		T	3179109	G	T	3179109	3	4	310	1	0	0	0	0	1	0	0	0	7466	1020	36	3	4592	3	HTT	4	3179109	Missense_Mutation	SNP	G	TCGA-K7-A5RG-01A-11D-A28X-10		3179109	187975167	34	44135										
RBPJ	3516	hgsc.bcm.edu	37	chr4	26426076	26426076	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	tttcatgccagttcacagcaGtggggagccttttttattca	9	9	3	0			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr4:26426076G>T	ENST00000361572.6	+	6	842	c.648G>T	c.(646-648)caG>caT	p.Q216H	RBPJ_ENST00000504907.1_Missense_Mutation_p.Q202H|RBPJ_ENST00000507561.1_Missense_Mutation_p.Q181H|RBPJ_ENST00000355476.3_Missense_Mutation_p.Q202H|RBPJ_ENST00000342295.1_Missense_Mutation_p.Q216H|RBPJ_ENST00000348160.4_Missense_Mutation_p.Q203H|RBPJ_ENST00000342320.4_Missense_Mutation_p.Q202H|RBPJ_ENST00000345843.3_Missense_Mutation_p.Q201H			Q06330	SUH_HUMAN	recombination signal binding protein for immunoglobulin kappa J region	216					angiogenesis (GO:0001525)|arterial endothelial cell fate commitment (GO:0060844)|atrioventricular canal development (GO:0036302)|auditory receptor cell fate commitment (GO:0009912)|B cell differentiation (GO:0030183)|blood vessel endothelial cell fate specification (GO:0097101)|blood vessel lumenization (GO:0072554)|blood vessel remodeling (GO:0001974)|cardiac left ventricle morphogenesis (GO:0003214)|Clara cell differentiation (GO:0060486)|defense response to bacterium (GO:0042742)|DNA recombination (GO:0006310)|dorsal aorta morphogenesis (GO:0035912)|endocardium morphogenesis (GO:0003160)|epidermal cell fate specification (GO:0009957)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|gene expression (GO:0010467)|hair follicle maturation (GO:0048820)|humoral immune response (GO:0006959)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ossification (GO:0030279)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|pituitary gland development (GO:0021983)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:1901297)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of ephrin receptor signaling pathway (GO:1901189)|positive regulation of ERBB signaling pathway (GO:1901186)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription of Notch receptor target (GO:0007221)|regulation of timing of cell differentiation (GO:0048505)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|sebaceous gland development (GO:0048733)|secondary heart field specification (GO:0003139)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|recombinase activity (GO:0000150)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)	15		Breast(46;0.0503)				GTTCACAGCAGTGGGGAGCCT	0.368																																					p.Q216H		Atlas-SNP	.											.	RBPJ	78	.	0			c.G648T						.						124	128	127					4																	26426076		2203	4300	6503	SO:0001583	missense	3516	exon7			ACAGCAGTGGGGA	L07872	CCDS3436.1, CCDS3437.1, CCDS33969.1, CCDS43219.1	4p15.2	2013-10-18	2007-02-26	2007-02-26	ENSG00000168214	ENSG00000168214			5724	protein-coding gene	gene with protein product	"suppressor of hairless homolog (Drosophila)"	147183	"recombining binding protein suppressor of hairless (Drosophila)"	IGKJRB1, RBPSUH		8406481, 9290259	Standard	NM_005349		Approved	SUH, IGKJRB, RBPJK, KBF2, RBP-J, CBF1	uc003gsb.2	Q06330	OTTHUMG00000097793	ENST00000361572.6:c.648G>T	chr4.hg19:g.26426076G>T	ENSP00000354528:p.Gln216His	65.0	0.0		83.0	7.0	NM_005349	B4DY22|Q5XKH9|Q6P1N3	Missense_Mutation	SNP	ENST00000361572.6	hg19	CCDS3437.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.283992	0.80803	.	.	ENSG00000168214	ENST00000345843;ENST00000342295;ENST00000361572;ENST00000348160;ENST00000355476;ENST00000507561;ENST00000515573;ENST00000504907;ENST00000342320	T;T;T;T;T;T;T;T;T	0.33438	1.41;1.41;1.41;1.41;1.41;1.41;1.41;1.41;1.41	5.58	3.87	0.44632	Beta-trefoil (2);	0.000000	0.85682	D	0.000000	T	0.48409	0.1498	M	0.68593	2.085	0.80722	D	1	D;D;D;D;D;D	0.64830	0.993;0.993;0.994;0.992;0.992;0.994	P;P;P;P;P;P	0.62435	0.869;0.902;0.84;0.753;0.753;0.902	T	0.41610	-0.9499	9	.	.	.	-8.8232	12.2522	0.54605	0.1383:0.0:0.8617:0.0	.	216;202;203;202;201;216	B7Z8D8;D6R927;B4DY22;Q06330-6;Q06330-4;Q06330	.;.;.;.;.;SUH_HUMAN	H	201;216;216;203;202;181;181;202;202	ENSP00000305815:Q201H;ENSP00000345206:Q216H;ENSP00000354528:Q216H;ENSP00000339699:Q203H;ENSP00000347659:Q202H;ENSP00000423907:Q181H;ENSP00000423406:Q181H;ENSP00000423703:Q202H;ENSP00000340124:Q202H	.	Q	+	3	2	RBPJ	26035174	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.769000	0.55303	0.725000	0.32318	0.650000	0.86243	CAG	.	.		0.368	RBPJ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215046.2	NM_015874		T	26426076	G	T	26426076	3	4	310	1	0	0	0	0	1	0	0	0	13176	1020	36	3	733	3	RBPJ	4	26426076	Missense_Mutation	SNP	G	TCGA-K7-A5RG-01A-11D-A28X-10	23246967	26426076	164728200	35	44136										
AASDH	132949	hgsc.bcm.edu	37	chr4	57216008	57216008	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ggcacaactcttcctgaatgTcacatcttcatctggaacca	6	13	5	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr4:57216008T>C	ENST00000205214.6	-	11	2089	c.1909A>G	c.(1909-1911)Aca>Gca	p.T637A	AASDH_ENST00000502617.1_Missense_Mutation_p.T637A|AASDH_ENST00000434343.2_Missense_Mutation_p.T152A|AASDH_ENST00000513376.1_Missense_Mutation_p.T537A|AASDH_ENST00000602986.1_Missense_Mutation_p.T484A|AASDH_ENST00000451613.1_Missense_Mutation_p.T637A	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	637					fatty acid metabolic process (GO:0006631)		acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)			endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	40	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)				TTCCTGAATGTCACATCTTCA	0.403																																					p.T637A		Atlas-SNP	.											.	AASDH	101	.	0			c.A1909G						.						170	147	155					4																	57216008		2203	4300	6503	SO:0001583	missense	132949	exon11			TGAATGTCACATC	AF516672	CCDS3504.1, CCDS68705.1, CCDS68706.1, CCDS75126.1, CCDS75127.1	4q12	2010-12-14			ENSG00000157426	ENSG00000157426	1.2.1.31	"Acyl-CoA synthetase family"	23993	protein-coding gene	gene with protein product	"acyl-CoA synthetase family member 4"	614365				15865210, 12712191, 17762044	Standard	XM_005265721		Approved	NRPS998, LYS2, ACSF4	uc003hbn.3	Q4L235	OTTHUMG00000128841	ENST00000205214.6:c.1909A>G	chr4.hg19:g.57216008T>C	ENSP00000205214:p.Thr637Ala	153.0	0.0		137.0	19.0	NM_181806	A5D8V3|A5PL22|Q63HK2|Q63HR7|Q6IPP8|Q6TFZ6|Q7Z5Y3|Q96BW4|Q9P064	Missense_Mutation	SNP	ENST00000205214.6	hg19	CCDS3504.1	.	.	.	.	.	.	.	.	.	.	T	0.111	-1.138286	0.01742	.	.	ENSG00000157426	ENST00000205214;ENST00000513376;ENST00000434343;ENST00000451613;ENST00000503808;ENST00000502617	T;T;T;T;T	0.08720	3.06;3.06;3.06;3.06;3.06	6.06	-2.92	0.05615	.	1.387120	0.03965	N	0.290755	T	0.06554	0.0168	L	0.44542	1.39	0.09310	N	1	B;B;B;B	0.09022	0.002;0.0;0.0;0.0	B;B;B;B	0.08055	0.003;0.001;0.001;0.0	T	0.39396	-0.9616	10	0.09084	T	0.74	-0.281	4.6553	0.12615	0.0723:0.3437:0.2609:0.3232	.	484;637;637;637	E9PH98;Q4L235-4;Q4L235-3;Q4L235	.;.;.;ACSF4_HUMAN	A	637;537;152;637;484;637	ENSP00000205214:T637A;ENSP00000423760:T537A;ENSP00000392158:T152A;ENSP00000409656:T637A;ENSP00000421171:T637A	ENSP00000205214:T637A	T	-	1	0	AASDH	56910765	0.000000	0.05858	0.000000	0.03702	0.292000	0.27327	-0.549000	0.06041	-0.512000	0.06505	0.533000	0.62120	ACA	.	.		0.403	AASDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250780.1	NM_181806		C	57216008	T	C	57216008	3	2	310	1	0	0	0	0	1	0	0	0	22	1667	58	2	1407	2	AASDH	4	57216008	Missense_Mutation	SNP	T	TCGA-K7-A5RG-01A-11D-A28X-10	30789932	57216008	133938268	36	44137										
MUC7	4589	hgsc.bcm.edu	37	chr4	71346647	71346647	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	aagccgttcattagaaagtcCtataaatgtctgcacaaacg	7	9	2	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr4:71346647C>T	ENST00000304887.5	+	3	376	c.186C>T	c.(184-186)tcC>tcT	p.S62S	MUC7_ENST00000514512.1_3'UTR|MUC7_ENST00000413702.1_Silent_p.S62S|MUC7_ENST00000456088.1_Silent_p.S62S	NM_152291.2	NP_689504.2	Q8TAX7	MUC7_HUMAN	mucin 7, secreted	62					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(2)|lung(23)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	42			Lung(101;0.211)			TTAGAAAGTCCTATAAATGTC	0.453																																					p.S62S		Atlas-SNP	.											MUC7,colon,carcinoma,0,1	MUC7	91	.	0			c.C186T						.						172	168	169					4																	71346647		2203	4300	6503	SO:0001819	synonymous_variant	4589	exon4			AAAGTCCTATAAA	BC025688	CCDS3541.1	4q13.3	2008-02-05	2006-03-14		ENSG00000171195	ENSG00000171195		"Mucins"	7518	protein-coding gene	gene with protein product		158375	"mucin 7, salivary"			8838308	Standard	NM_152291		Approved	FLJ27047, MG2	uc003hfj.3	Q8TAX7	OTTHUMG00000129916	ENST00000304887.5:c.186C>T	chr4.hg19:g.71346647C>T		161.0	0.0		161.0	30.0	NM_001145007	Q9UCD7|Q9UCD8	Silent	SNP	ENST00000304887.5	hg19	CCDS3541.1																																																																																			.	.		0.453	MUC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252168.2	NM_152291		T	71346647	C	T	71346647	2	4	310	1	0	0	0	0	0	0	0	1	9990	668	24	3		3	MUC7	4	71346647	Silent	SNP	C	TCGA-K7-A5RG-01A-11D-A28X-10	14130639	71346647	119807629	37	44138										
ADH5	128	hgsc.bcm.edu	37	chr4	100003145	100003146	+	Frame_Shift_Ins	INS	-	-	C													0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ccgccttcagcttagtaactINSccctcaccaacactttccac							TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr4:100003145_100003146insC	ENST00000296412.8	-	3	286_287	c.236_237insG	c.(235-237)ggafs	p.G79fs	ADH5_ENST00000512991.1_5'UTR	NM_000671.3	NP_000662.3			alcohol dehydrogenase 5 (class III), chi polypeptide											endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)	13				OV - Ovarian serous cystadenocarcinoma(123;2.5e-07)		GCTTAGTAACTCCCTCACCAAC	0.436																																					p.G79fs		Atlas-Indel,Pindel	.											.	ADH5	23	.	0			c.237_238insG						.																																			SO:0001589	frameshift_variant	128	exon3			.	M29872	CCDS47111.1	4q23	2012-07-13	2003-06-19		ENSG00000197894	ENSG00000197894	1.1.1.284	"Alcohol dehydrogenases"	253	protein-coding gene	gene with protein product		103710	"formaldehyde dehydrogenase"	FDH		1446828, 6424546	Standard	NM_000671		Approved	ADH-3, ADHX	uc003hui.3	P11766	OTTHUMG00000161230	ENST00000296412.8:c.237dupG	chr4.hg19:g.100003148_100003148dupC	ENSP00000296412:p.Gly79fs	192.0	0.0		191.0	29.0	NM_000671		Frame_Shift_Ins	INS	ENST00000296412.8	hg19	CCDS47111.1																																																																																			.	.		0.436	ADH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364224.1	NM_000671		C	100003146	-	C	100003145	7	5	310	1	0	1	1	0	0	0	0	0	311	1538	54	0	915	0	ADH5	4	100003145	Frame_Shift_Ins	INS	-	TCGA-K7-A5RG-01A-11D-A28X-10	28656498	100003145	91151131	38	44139										
GUCY1B3	2983	hgsc.bcm.edu	37	chr4	156696144	156696144	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	gaggcacagttagatgaagaAggacagtttcttgtcagaat	12	5	2	4			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr4:156696144A>T	ENST00000264424.8	+	3	184	c.102A>T	c.(100-102)gaA>gaT	p.E34D	GUCY1B3_ENST00000513437.1_De_novo_Start_OutOfFrame|GUCY1B3_ENST00000507146.1_De_novo_Start_OutOfFrame|GUCY1B3_ENST00000502959.1_Missense_Mutation_p.E34D|GUCY1B3_ENST00000505154.1_De_novo_Start_OutOfFrame|GUCY1B3_ENST00000505764.1_Missense_Mutation_p.E14D|GUCY1B3_ENST00000503520.1_Missense_Mutation_p.E34D	NM_000857.2	NP_000848.1	Q02153	GCYB1_HUMAN	guanylate cyclase 1, soluble, beta 3	34					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|nitric oxide mediated signal transduction (GO:0007263)	cytoplasm (GO:0005737)|guanylate cyclase complex, soluble (GO:0008074)|intracellular membrane-bounded organelle (GO:0043231)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)			NS(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.148)		TAGATGAAGAAGGACAGTTTC	0.328																																					p.E34D		Atlas-SNP	.											.	GUCY1B3	65	.	0			c.A102T						.						124	122	123					4																	156696144		1834	4079	5913	SO:0001583	missense	2983	exon3			TGAAGAAGGACAG	AF020340	CCDS47154.1, CCDS75203.1	4q31.3-q33	2008-03-18			ENSG00000061918	ENSG00000061918	4.6.1.2		4687	protein-coding gene	gene with protein product		139397		GUC1B3		1352257	Standard	XM_005262959		Approved	GC-SB3, GC-S-beta-1	uc003ipc.3	Q02153	OTTHUMG00000161698	ENST00000264424.8:c.102A>T	chr4.hg19:g.156696144A>T	ENSP00000264424:p.Glu34Asp	41.0	0.0		30.0	4.0	NM_000857	B7Z426|Q86WY5	Missense_Mutation	SNP	ENST00000264424.8	hg19	CCDS47154.1	.	.	.	.	.	.	.	.	.	.	A	13.89	2.373174	0.42105	.	.	ENSG00000061918	ENST00000502959;ENST00000505764;ENST00000264424;ENST00000503520	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	5.3	4.12	0.48240	Heme-NO binding (1);NO signalling/Golgi transport  ligand-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.33235	0.0856	L	0.46885	1.475	0.80722	D	1	B;B;B;B	0.23316	0.083;0.03;0.043;0.019	B;B;B;B	0.27796	0.083;0.058;0.02;0.022	T	0.07271	-1.0781	10	0.15952	T	0.53	.	8.6366	0.33953	0.7852:0.0:0.2148:0.0	.	14;34;34;34	B7Z426;E9PCN2;Q02153-2;Q02153	.;.;.;GCYB1_HUMAN	D	34;14;34;34	ENSP00000426786:E34D;ENSP00000426319:E14D;ENSP00000264424:E34D;ENSP00000420842:E34D	ENSP00000264424:E34D	E	+	3	2	GUCY1B3	156915594	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.838000	0.48199	0.960000	0.38005	-0.281000	0.10026	GAA	.	.		0.328	GUCY1B3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365770.2			T	156696144	A	T	156696144	3	4	310	1	0	0	0	0	1	0	0	0	6904	69	3	4	112	4	GUCY1B3	4	156696144	Missense_Mutation	SNP	A	TCGA-K7-A5RG-01A-11D-A28X-10	56692999	156696144	34458132	39	44140										
GUCY1B3	2983	hgsc.bcm.edu	37	chr4	156726268	156726268	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	cttttagatgtcttatgtctCcagaaaattcagatccacaa	5	9	3	3			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr4:156726268C>A	ENST00000264424.8	+	13	1805	c.1723C>A	c.(1723-1725)Cca>Aca	p.P575T	GUCY1B3_ENST00000513437.1_Missense_Mutation_p.P507T|GUCY1B3_ENST00000507146.1_Missense_Mutation_p.P550T|GUCY1B3_ENST00000502959.1_Missense_Mutation_p.P597T|GUCY1B3_ENST00000505154.1_Missense_Mutation_p.P507T|GUCY1B3_ENST00000505764.1_Missense_Mutation_p.P555T|GUCY1B3_ENST00000503520.1_Missense_Mutation_p.P542T	NM_000857.2	NP_000848.1	Q02153	GCYB1_HUMAN	guanylate cyclase 1, soluble, beta 3	575					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|nitric oxide mediated signal transduction (GO:0007263)	cytoplasm (GO:0005737)|guanylate cyclase complex, soluble (GO:0008074)|intracellular membrane-bounded organelle (GO:0043231)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)			NS(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.148)		TCTTATGTCTCCAGAAAATTC	0.393																																					p.P575T		Atlas-SNP	.											.	GUCY1B3	65	.	0			c.C1723A						.						93	82	86					4																	156726268		1859	4095	5954	SO:0001583	missense	2983	exon13			ATGTCTCCAGAAA	AF020340	CCDS47154.1, CCDS75203.1	4q31.3-q33	2008-03-18			ENSG00000061918	ENSG00000061918	4.6.1.2		4687	protein-coding gene	gene with protein product		139397		GUC1B3		1352257	Standard	XM_005262959		Approved	GC-SB3, GC-S-beta-1	uc003ipc.3	Q02153	OTTHUMG00000161698	ENST00000264424.8:c.1723C>A	chr4.hg19:g.156726268C>A	ENSP00000264424:p.Pro575Thr	169.0	0.0		186.0	32.0	NM_000857	B7Z426|Q86WY5	Missense_Mutation	SNP	ENST00000264424.8	hg19	CCDS47154.1	.	.	.	.	.	.	.	.	.	.	C	14.04	2.417114	0.42918	.	.	ENSG00000061918	ENST00000505154;ENST00000502959;ENST00000505764;ENST00000507146;ENST00000264424;ENST00000503520;ENST00000513437	T;T;T;T;T;T;T	0.28895	1.59;1.59;1.59;1.59;1.59;1.59;1.59	5.56	3.83	0.44106	Adenylyl cyclase class-3/4/guanylyl cyclase (4);	0.173250	0.51477	D	0.000100	T	0.37433	0.1003	M	0.86178	2.8	0.45946	D	0.998779	B;B;B;B;B	0.34147	0.438;0.001;0.001;0.196;0.234	B;B;B;B;B	0.38020	0.263;0.011;0.007;0.089;0.19	T	0.22521	-1.0214	10	0.11794	T	0.64	.	11.5191	0.50541	0.0:0.8562:0.0:0.1438	.	555;597;550;542;575	B7Z426;E9PCN2;D6RC99;Q02153-2;Q02153	.;.;.;.;GCYB1_HUMAN	T	507;597;555;550;575;542;507	ENSP00000427226:P507T;ENSP00000426786:P597T;ENSP00000426319:P555T;ENSP00000422313:P550T;ENSP00000264424:P575T;ENSP00000420842:P542T;ENSP00000425065:P507T	ENSP00000264424:P575T	P	+	1	0	GUCY1B3	156945718	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	3.238000	0.51352	1.355000	0.45865	-0.142000	0.14014	CCA	.	.		0.393	GUCY1B3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365770.2			A	156726268	C	A	156726268	3	1	310	1	0	0	0	0	1	0	0	0	6904	855	30	3	1773	3	GUCY1B3	4	156726268	Missense_Mutation	SNP	C	TCGA-K7-A5RG-01A-11D-A28X-10	30124	156726268	34428008	40	44141										
SPOCK3	50859	hgsc.bcm.edu	37	chr4	168155168	168155168	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	gttccactgtccgacttcctTgtcatactgagagattgtgg	10	10	1	2			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr4:168155168T>A	ENST00000357154.3	-	2	294	c.157A>T	c.(157-159)Aag>Tag	p.K53*	SPOCK3_ENST00000421836.2_5'UTR|SPOCK3_ENST00000512681.1_Nonsense_Mutation_p.K53*|SPOCK3_ENST00000541637.1_Nonsense_Mutation_p.K53*|SPOCK3_ENST00000535728.1_5'UTR|SPOCK3_ENST00000502330.1_Nonsense_Mutation_p.K53*|SPOCK3_ENST00000511269.1_Nonsense_Mutation_p.K53*|SPOCK3_ENST00000512648.1_Nonsense_Mutation_p.K53*|SPOCK3_ENST00000357545.4_Nonsense_Mutation_p.K53*|SPOCK3_ENST00000534949.1_Silent_p.T13T|SPOCK3_ENST00000541354.1_5'UTR|SPOCK3_ENST00000506886.1_Nonsense_Mutation_p.K53*|SPOCK3_ENST00000510741.1_Nonsense_Mutation_p.K53*|SPOCK3_ENST00000511531.1_Nonsense_Mutation_p.K53*|SPOCK3_ENST00000504953.1_Nonsense_Mutation_p.K53*	NM_016950.2	NP_058646.2	Q9BQ16	TICN3_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 3	53					negative regulation of endopeptidase activity (GO:0010951)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|glycosaminoglycan binding (GO:0005539)|metalloendopeptidase inhibitor activity (GO:0008191)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	38	all_hematologic(180;0.221)	Prostate(90;0.0181)|Renal(120;0.0184)|Melanoma(52;0.0198)		GBM - Glioblastoma multiforme(119;0.02)		CCGACTTCCTTGTCATACTGA	0.647																																					p.K53X		Atlas-SNP	.											.	SPOCK3	90	.	0			c.A157T						.						67	70	69					4																	168155168		2203	4300	6503	SO:0001587	stop_gained	50859	exon2			CTTCCTTGTCATA	AJ001454	CCDS34095.1, CCDS54817.1, CCDS56343.1, CCDS56344.1, CCDS56346.1, CCDS56347.1, CCDS58931.1, CCDS75207.1	4q32.3	2011-10-10			ENSG00000196104	ENSG00000196104			13565	protein-coding gene	gene with protein product		607989				11751414	Standard	NM_001204352		Approved	testican-3	uc003iri.1	Q9BQ16	OTTHUMG00000161190	ENST00000357154.3:c.157A>T	chr4.hg19:g.168155168T>A	ENSP00000349677:p.Lys53*	141.0	0.0		141.0	27.0	NM_016950	B2R7M7|B3KR67|B4DGK5|B4DHB4|B4DHV3|B4DI46|B4DJY3|E7EP61|F5H099|O75705|Q6UW53|Q96Q26	Nonsense_Mutation	SNP	ENST00000357154.3	hg19	CCDS54817.1	.	.	.	.	.	.	.	.	.	.	T	26.4	4.738454	0.89573	.	.	ENSG00000196104	ENST00000357154;ENST00000357545;ENST00000504953;ENST00000506886;ENST00000511531;ENST00000502330;ENST00000510741;ENST00000512681;ENST00000511269;ENST00000541637;ENST00000512648;ENST00000510403;ENST00000509854;ENST00000506697;ENST00000512042	.	.	.	3.97	1.39	0.22231	.	0.487152	0.17603	U	0.168354	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.4908	6.3694	0.21473	0.0:0.0873:0.1587:0.754	.	.	.	.	X	53	.	ENSP00000349677:K53X	K	-	1	0	SPOCK3	168391743	1.000000	0.71417	0.997000	0.53966	0.001000	0.01503	2.194000	0.42668	0.075000	0.16796	-0.467000	0.05162	AAG	.	.		0.647	SPOCK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364091.1			A	168155168	T	A	168155168	4	1	310	1	0	0	0	0	0	1	0	0	15096	1821	63	4	1197	4	SPOCK3	4	168155168	Nonsense_Mutation	SNP	T	TCGA-K7-A5RG-01A-11D-A28X-10	11428900	168155168	22999108	41	44142										
SLC9A3	6550	hgsc.bcm.edu	37	chr5	481703	481703	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	tctctgagataattgtgcccGatctgtccggatatgtcctc	9	11	2	1	rs200474984		TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr5:481703G>A	ENST00000264938.3	-	9	1503	c.1494C>T	c.(1492-1494)atC>atT	p.I498I	CTD-2228K2.7_ENST00000607005.1_RNA|CTD-2228K2.7_ENST00000607286.1_RNA|CTD-2228K2.7_ENST00000606288.1_RNA|SLC9A3_ENST00000514375.1_Silent_p.I489I	NM_004174.2	NP_004165.2	P48764	SL9A3_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3	498					ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|sodium:proton antiporter activity (GO:0015385)			NS(2)|biliary_tract(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(2)|lung(16)|prostate(3)|skin(2)|urinary_tract(1)	37			Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			AATTGTGCCCGATCTGTCCGG	0.582																																					p.I498I		Atlas-SNP	.											.	SLC9A3	89	.	0			c.C1494T						.	G		1,4405	2.1+/-5.4	0,1,2202	180	185	183		1494	-7.7	0.7	5		183	0,8600		0,0,4300	no	coding-synonymous	SLC9A3	NM_004174.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		498/835	481703	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	6550	exon9			GTGCCCGATCTGT		CCDS3855.1, CCDS64116.1	5p15.3	2013-05-22	2012-03-22		ENSG00000066230	ENSG00000066230		"Solute carriers"	11073	protein-coding gene	gene with protein product		182307	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 3", "solute carrier family 9 (sodium/hydrogen exchanger), member 3"	NHE3		8096830	Standard	NM_004174		Approved		uc003jbe.2	P48764	OTTHUMG00000090315	ENST00000264938.3:c.1494C>T	chr5.hg19:g.481703G>A		129.0	0.0		141.0	13.0	NM_004174	B7ZKR2|E9PF67|Q3MIW3	Silent	SNP	ENST00000264938.3	hg19	CCDS3855.1																																																																																			.	G|0.999;A|0.001		0.582	SLC9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206677.2	NM_004174		A	481703	G	A	481703	2	1	310	1	0	0	0	0	0	0	0	1	14728	1048	37	1		1	SLC9A3	5	481703	Silent	SNP	G	TCGA-K7-A5RG-01A-11D-A28X-10		481703	180433557	42	44143										
RAI14	26064	hgsc.bcm.edu	37	chr5	34823722	34823722	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	tgttattgagaatatgaataAggagaaagcatttttgtttg	10	1	0	3			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr5:34823722A>C	ENST00000265109.3	+	15	2062	c.1775A>C	c.(1774-1776)aAg>aCg	p.K592T	RAI14_ENST00000512629.1_Missense_Mutation_p.K563T|RAI14_ENST00000515799.1_Missense_Mutation_p.K595T|RAI14_ENST00000503673.1_Missense_Mutation_p.K592T|RAI14_ENST00000428746.2_Missense_Mutation_p.K592T|RAI14_ENST00000506376.1_Missense_Mutation_p.K584T|RAI14_ENST00000397449.1_Missense_Mutation_p.K585T	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	592						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(19)|lung(22)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(31;0.000191)					AATATGAATAAGGAGAAAGCA	0.368																																					p.K595T		Atlas-SNP	.											.	RAI14	100	.	0			c.A1784C						.						57	60	59					5																	34823722		2203	4300	6503	SO:0001583	missense	26064	exon17			TGAATAAGGAGAA	AB037755	CCDS34142.1, CCDS54837.1, CCDS54838.1, CCDS54839.1	5p13.3-p13.2	2013-01-10			ENSG00000039560	ENSG00000039560		"Ankyrin repeat domain containing"	14873	protein-coding gene	gene with protein product	"novel retinal pigment epithelial"	606586				11042181	Standard	NM_015577		Approved	NORPEG, KIAA1334, RAI13, DKFZp564G013	uc011coj.2	Q9P0K7	OTTHUMG00000162019	ENST00000265109.3:c.1775A>C	chr5.hg19:g.34823722A>C	ENSP00000265109:p.Lys592Thr	121.0	0.0		151.0	30.0	NM_001145525	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Missense_Mutation	SNP	ENST00000265109.3	hg19	CCDS34142.1	.	.	.	.	.	.	.	.	.	.	A	17.71	3.456469	0.63401	.	.	ENSG00000039560	ENST00000265109;ENST00000512629;ENST00000428746;ENST00000503673;ENST00000515799;ENST00000506376;ENST00000397449	T;T;T;T;T;T;T	0.39229	1.11;1.09;1.11;1.11;1.1;1.15;1.14	5.42	5.42	0.78866	.	.	.	.	.	T	0.35913	0.0948	N	0.19112	0.55	0.40263	D	0.978206	P;P;P;P	0.44044	0.634;0.682;0.825;0.682	B;B;P;B	0.44477	0.234;0.205;0.451;0.205	T	0.37056	-0.9722	9	0.72032	D	0.01	-25.5718	15.4697	0.75432	1.0:0.0:0.0:0.0	.	584;563;595;592	Q9P0K7-3;E9PED3;Q9P0K7-2;Q9P0K7	.;.;.;RAI14_HUMAN	T	592;563;592;592;595;584;585	ENSP00000265109:K592T;ENSP00000422377:K563T;ENSP00000388725:K592T;ENSP00000422942:K592T;ENSP00000427123:K595T;ENSP00000423854:K584T;ENSP00000380591:K585T	ENSP00000265109:K592T	K	+	2	0	RAI14	34859479	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	5.159000	0.64923	2.067000	0.61834	0.454000	0.30748	AAG	.	.		0.368	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577		C	34823722	A	C	34823722	3	2	310	1	0	0	0	0	1	0	0	0	13023	72	3	5	1894	5	RAI14	5	34823722	Missense_Mutation	SNP	A	TCGA-K7-A5RG-01A-11D-A28X-10	34342019	34823722	146091538	43	44144										
HTR1A	3350	hgsc.bcm.edu	37	chr5	63256701	63256701	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	gcggcgccatcgtcaccttgCctcaccgcgccattggcgca	11	18	2	0			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr5:63256701C>T	ENST00000323865.3	-	1	1079	c.846G>A	c.(844-846)agG>agA	p.R282R	RP11-158J3.2_ENST00000502882.1_RNA	NM_000524.3	NP_000515.2	P08908	5HT1A_HUMAN	5-hydroxytryptamine (serotonin) receptor 1A, G protein-coupled	282					adenylate cyclase-inhibiting serotonin receptor signaling pathway (GO:0007198)|behavioral fear response (GO:0001662)|cell proliferation (GO:0008283)|exploration behavior (GO:0035640)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cell proliferation (GO:0008284)|regulation of behavior (GO:0050795)|regulation of dopamine metabolic process (GO:0042053)|regulation of hormone secretion (GO:0046883)|regulation of serotonin secretion (GO:0014062)|serotonin metabolic process (GO:0042428)|serotonin receptor signaling pathway (GO:0007210)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin receptor activity (GO:0004993)			cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(29)|ovary(2)|pancreas(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	56		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0575)|Colorectal(97;0.234)		Lung(70;0.105)	Acepromazine(DB01614)|Alprenolol(DB00866)|Alverine(DB01616)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bopindolol(DB08807)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinitapride(DB08810)|Clozapine(DB00363)|Desipramine(DB01151)|Dopamine(DB00988)|Doxepin(DB01142)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Methysergide(DB00247)|Mianserin(DB06148)|Molindone(DB01618)|Naratriptan(DB00952)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Ondansetron(DB00904)|Paliperidone(DB01267)|Penbutolol(DB01359)|Pergolide(DB01186)|Pindolol(DB00960)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Propranolol(DB00571)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sumatriptan(DB00669)|Thioproperazine(DB01622)|Trazodone(DB00656)|Trimipramine(DB00726)|Vilazodone(DB06684)|Yohimbine(DB01392)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)	CGTCACCTTGCCTCACCGCGC	0.642																																					p.R282R		Atlas-SNP	.											.	HTR1A	128	.	0			c.G846A						.						47	43	44					5																	63256701		2203	4300	6503	SO:0001819	synonymous_variant	3350	exon1			ACCTTGCCTCACC	AF498978	CCDS34168.1	5q11.2-q13	2012-08-08	2012-02-03			ENSG00000178394		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5286	protein-coding gene	gene with protein product		109760	"5-hydroxytryptamine (serotonin) receptor 1A"	ADRB2RL1, ADRBRL1		2591972, 12969265	Standard	NM_000524		Approved	5-HT1A	uc011cqt.3	P08908		ENST00000323865.3:c.846G>A	chr5.hg19:g.63256701C>T		105.0	0.0		132.0	19.0	NM_000524	Q6LAE7	Silent	SNP	ENST00000323865.3	hg19	CCDS34168.1																																																																																			.	.		0.642	HTR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368397.1	NM_000524		T	63256701	C	T	63256701	2	4	310	1	0	0	0	0	0	0	0	1	7445	738	26	3		3	HTR1A	5	63256701	Silent	SNP	C	TCGA-K7-A5RG-01A-11D-A28X-10	28432979	63256701	117658559	44	44145										
PAPD4	167153	hgsc.bcm.edu	37	chr5	78940987	78940987	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	agctgattcgagcaaaagtgCcaattgtgaagttcagggat	12	6	1	2			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr5:78940987C>T	ENST00000296783.3	+	9	1092	c.793C>T	c.(793-795)Cca>Tca	p.P265S	PAPD4_ENST00000453514.1_Missense_Mutation_p.P265S|PAPD4_ENST00000428308.2_Missense_Mutation_p.P265S|PAPD4_ENST00000423041.2_Missense_Mutation_p.P261S|PAPD4_ENST00000504233.1_Missense_Mutation_p.P265S			Q6PIY7	GLD2_HUMAN	PAP associated domain containing 4	265					hematopoietic progenitor cell differentiation (GO:0002244)|histone mRNA catabolic process (GO:0071044)|mRNA processing (GO:0006397)|RNA polyadenylation (GO:0043631)	cytoplasm (GO:0005737)|nuclear RNA-directed RNA polymerase complex (GO:0031380)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)			biliary_tract(1)|breast(2)|endometrium(4)|kidney(3)|large_intestine(9)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Lung NSC(167;0.00293)|all_lung(232;0.00323)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;8.61e-47)|Epithelial(54;1.32e-41)|all cancers(79;2.45e-36)		AGCAAAAGTGCCAATTGTGAA	0.343																																					p.P265S		Atlas-SNP	.											.	PAPD4	51	.	0			c.C793T						.						98	100	99					5																	78940987		2203	4300	6503	SO:0001583	missense	167153	exon9			AAAGTGCCAATTG	AL833136	CCDS4048.1, CCDS75265.1, CCDS75266.1	5q14.1	2014-03-21			ENSG00000164329	ENSG00000164329			26776	protein-coding gene	gene with protein product	"TUTase2"	614121				12477932	Standard	NM_173797		Approved	FLJ38499, GLD2, TUT2	uc003kgb.2	Q6PIY7	OTTHUMG00000108163	ENST00000296783.3:c.793C>T	chr5.hg19:g.78940987C>T	ENSP00000296783:p.Pro265Ser	183.0	0.0		184.0	24.0	NM_173797	Q86WZ2|Q8N927	Missense_Mutation	SNP	ENST00000296783.3	hg19	CCDS4048.1	.	.	.	.	.	.	.	.	.	.	C	31	5.074093	0.94000	.	.	ENSG00000164329	ENST00000453514;ENST00000423041;ENST00000504233;ENST00000428308;ENST00000296783	D;D;D;D;D	0.89875	-2.58;-2.58;-2.58;-2.58;-2.58	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	D	0.96540	0.8871	H	0.95079	3.62	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	D	0.97219	0.9876	10	0.87932	D	0	-8.8984	19.8629	0.96790	0.0:1.0:0.0:0.0	.	265;261;265	Q6PIY7;Q6PIY7-2;D6RAF2	GLD2_HUMAN;.;.	S	265;261;265;265;265	ENSP00000397563:P265S;ENSP00000393412:P261S;ENSP00000421966:P265S;ENSP00000396861:P265S;ENSP00000296783:P265S	ENSP00000296783:P265S	P	+	1	0	PAPD4	78976743	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.436000	0.80404	2.690000	0.91761	0.573000	0.79308	CCA	.	.		0.343	PAPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226967.1	NM_173797		T	78940987	C	T	78940987	3	4	310	1	0	0	0	0	1	0	0	0	11433	739	26	3	819	3	PAPD4	5	78940987	Missense_Mutation	SNP	C	TCGA-K7-A5RG-01A-11D-A28X-10	15684286	78940987	101974273	45	44146										
PCDHA2	56146	hgsc.bcm.edu	37	chr5	140175547	140175547	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	aaccccttcaatgtcaggacAttgtaaaatttcattaaaac	4	9	3	0			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr5:140175547A>T	ENST00000526136.1	+	1	998	c.998A>T	c.(997-999)cAt>cTt	p.H333L	PCDHA2_ENST00000520672.2_Missense_Mutation_p.H333L|PCDHA2_ENST00000378132.1_Missense_Mutation_p.H333L|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018905.2	NP_061728.1	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2	333	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(16)|lung(26)|ovary(4)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATGTCAGGACATTGTAAAATT	0.418																																					p.H333L		Atlas-SNP	.											.	PCDHA2	404	.	0			c.A998T						.						73	71	72					5																	140175547		2203	4300	6503	SO:0001583	missense	56146	exon1			CAGGACATTGTAA	AF152480	CCDS54914.1, CCDS64269.1	5q31	2010-11-26				ENSG00000204969		"Cadherins / Protocadherins : Clustered"	8668	other	complex locus constituent	"KIAA0345-like 12"	606308				10380929	Standard	NM_018905		Approved			Q9Y5H9		ENST00000526136.1:c.998A>T	chr5.hg19:g.140175547A>T	ENSP00000431748:p.His333Leu	182.0	0.0		207.0	31.0	NM_031495	O75287|Q9BTV3	Missense_Mutation	SNP	ENST00000526136.1	hg19	CCDS54914.1	.	.	.	.	.	.	.	.	.	.	a	18.00	3.524978	0.64747	.	.	ENSG00000204969	ENST00000520672;ENST00000378132;ENST00000526136	T;T;T	0.50277	0.75;0.75;0.75	3.92	3.92	0.45320	Cadherin (4);Cadherin-like (1);	0.000000	0.41294	U	0.000917	T	0.67192	0.2867	M	0.82056	2.57	0.32231	N	0.573901	D;D;D	0.65815	0.994;0.995;0.994	P;D;P	0.65987	0.9;0.94;0.9	T	0.77267	-0.2651	10	0.87932	D	0	.	13.2048	0.59788	1.0:0.0:0.0:0.0	.	333;333;333	Q9Y5H9-3;Q9Y5H9;Q9Y5H9-2	.;PCDA2_HUMAN;.	L	333	ENSP00000430584:H333L;ENSP00000367372:H333L;ENSP00000431748:H333L	ENSP00000367372:H333L	H	+	2	0	PCDHA2	140155731	0.999000	0.42202	0.960000	0.40013	0.892000	0.51952	6.937000	0.75898	1.769000	0.52152	0.528000	0.53228	CAT	.	.		0.418	PCDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372877.3	NM_018905		T	140175547	A	T	140175547	3	4	310	1	0	0	0	0	1	0	0	0	11533	217	8	4	1000	4	PCDHA2	5	140175547	Missense_Mutation	SNP	A	TCGA-K7-A5RG-01A-11D-A28X-10	61234560	140175547	40739713	46	44147										
TLX3	30012	hgsc.bcm.edu	37	chr5	170738472	170738472	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	agctgcaacacgacgccttcCaaaagagcctcaacgactcc	7	16	1	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr5:170738472C>T	ENST00000296921.5	+	3	827	c.745C>T	c.(745-747)Caa>Taa	p.Q249*		NM_021025.2	NP_066305.2	O43711	TLX3_HUMAN	T-cell leukemia homeobox 3	249					central nervous system development (GO:0007417)|negative regulation of neuron differentiation (GO:0045665)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of transcription, DNA-templated (GO:0006355)|respiratory gaseous exchange (GO:0007585)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)	1	Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CGACGCCTTCCAAAAGAGCCT	0.647			T	BCL11B	T-ALL																																p.Q249X	Esophageal Squamous(33;43 807 3116 3348 30094)	Atlas-SNP	.		Dom	yes		5	5q35.1	30012	"T-cell leukemia, homeobox 3 (HOX11L2)"		L	.	TLX3	23	.	0			c.C745T						.						60	53	56					5																	170738472		2203	4299	6502	SO:0001587	stop_gained	30012	exon3			GCCTTCCAAAAGA	AJ223798	CCDS34288.1	5q35.1	2011-06-20	2005-12-22	2002-05-31	ENSG00000164438	ENSG00000164438		"Homeoboxes / ANTP class : NKL subclass"	13532	protein-coding gene	gene with protein product		604640	"homeo box 11-like 2", "T-cell leukemia, homeobox 3"	HOX11L2		11435718, 11435716	Standard	NM_021025		Approved	RNX	uc003mbf.3	O43711	OTTHUMG00000163207	ENST00000296921.5:c.745C>T	chr5.hg19:g.170738472C>T	ENSP00000296921:p.Gln249*	242.0	0.0		322.0	38.0	NM_021025	Q96AD3	Nonsense_Mutation	SNP	ENST00000296921.5	hg19	CCDS34288.1	.	.	.	.	.	.	.	.	.	.	C	36	5.651979	0.96714	.	.	ENSG00000164438	ENST00000296921	.	.	.	4.25	4.25	0.50352	.	0.057953	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07325	T	0.83	.	16.2636	0.82563	0.0:1.0:0.0:0.0	.	.	.	.	X	249	.	ENSP00000296921:Q249X	Q	+	1	0	TLX3	170671077	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.392000	0.79840	1.901000	0.55032	0.491000	0.48974	CAA	.	.		0.647	TLX3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372076.3			T	170738472	C	T	170738472	4	4	310	1	0	0	0	0	0	1	0	0	15977	595	21	3	755	3	TLX3	5	170738472	Nonsense_Mutation	SNP	C	TCGA-K7-A5RG-01A-11D-A28X-10	30562925	170738472	10176788	47	44148										
CDYL	9425	hgsc.bcm.edu	37	chr6	4892439	4892439	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	tggaccccgtcgagcagggtCaggaggacacagtggcaccc	15	13	1	0			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr6:4892439C>A	ENST00000328908.5	+	4	810	c.679C>A	c.(679-681)Cag>Aag	p.Q227K	CDYL_ENST00000343762.5_Missense_Mutation_p.Q41K|CDYL_ENST00000449732.2_Missense_Mutation_p.Q41K|CDYL_ENST00000397588.3_Missense_Mutation_p.Q173K|CDYL_ENST00000472453.1_Intron			Q9Y232	CDYL1_HUMAN	chromodomain protein, Y-like	227	Interaction with EZH2.				regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|methylated histone binding (GO:0035064)|transcription corepressor activity (GO:0003714)			breast(2)|kidney(2)|large_intestine(9)|lung(13)|skin(1)|stomach(2)|urinary_tract(1)	30	Ovarian(93;0.11)	all_hematologic(90;0.0901)|Lung NSC(90;0.244)		OV - Ovarian serous cystadenocarcinoma(45;0.182)		CGAGCAGGGTCAGGAGGACAC	0.622																																					p.Q173K		Atlas-SNP	.											.	CDYL	74	.	0			c.C517A						.						46	53	51					6																	4892439		2203	4300	6503	SO:0001583	missense	9425	exon2			CAGGGTCAGGAGG	AF081258	CCDS4491.2, CCDS47364.1	6p25.1	2010-05-04	2003-09-12		ENSG00000153046	ENSG00000153046			1811	protein-coding gene	gene with protein product	"CDY-like, autosomal", "testis-specific chromodomain Y-like protein"	603778	"chromodomain protein, Y chromosome-like"			10192397	Standard	NM_001143970		Approved	DKFZP586C1622, CDYL1	uc003mwj.3	Q9Y232	OTTHUMG00000014170	ENST00000328908.5:c.679C>A	chr6.hg19:g.4892439C>A	ENSP00000330512:p.Gln227Lys	113.0	0.0		126.0	24.0	NM_004824	A8K6D6|B4DLG4|Q0VDG7|Q32NC5|Q5VX99|Q6P7T5|Q9BWZ2|Q9Y424	Missense_Mutation	SNP	ENST00000328908.5	hg19		.	.	.	.	.	.	.	.	.	.	C	15.29	2.788951	0.49997	.	.	ENSG00000153046	ENST00000328908;ENST00000397588;ENST00000449732;ENST00000343762	T;T;T;T	0.55234	0.95;0.57;0.53;0.53	5.55	3.72	0.42706	.	0.670270	0.13571	U	0.378091	T	0.23926	0.0579	L	0.38175	1.15	0.27544	N	0.950718	B;B	0.13594	0.002;0.008	B;B	0.14578	0.005;0.011	T	0.19063	-1.0317	9	.	.	.	.	15.061	0.71955	0.0:0.7303:0.2697:0.0	.	173;227	Q9Y232-2;Q9Y232	.;CDYL1_HUMAN	K	227;173;41;41	ENSP00000330512:Q227K;ENSP00000380718:Q173K;ENSP00000394076:Q41K;ENSP00000340908:Q41K	.	Q	+	1	0	CDYL	4837438	1.000000	0.71417	0.273000	0.24645	0.953000	0.61014	3.017000	0.49615	0.661000	0.30985	0.650000	0.86243	CAG	.	.		0.622	CDYL-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000039736.1	NM_004824		A	4892439	C	A	4892439	3	1	310	1	0	0	0	0	1	0	0	0	3187	827	29	3	523	3	CDYL	6	4892439	Missense_Mutation	SNP	C	TCGA-K7-A5RG-01A-11D-A28X-10		4892439	166222628	48	44149										
TMEM14C	51522	hgsc.bcm.edu	37	chr6	10728899	10728899	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ctggtaccttggctggcattAtgggaatgaggttctaccac	12	9	1	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr6:10728899A>G	ENST00000541412.1	+	5	611	c.226A>G	c.(226-228)Atg>Gtg	p.M76V	TMEM14C_ENST00000467415.1_3'UTR|TMEM14C_ENST00000229563.5_Missense_Mutation_p.M76V	NM_001165258.1	NP_001158730.1	Q9P0S9	TM14C_HUMAN	transmembrane protein 14C	76					heme biosynthetic process (GO:0006783)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				large_intestine(2)|lung(3)	5	Ovarian(93;0.107)|Breast(50;0.137)	all_hematologic(90;0.135)	Epithelial(50;0.246)			GGCTGGCATTATGGGAATGAG	0.413																																					p.M76V		Atlas-SNP	.											.	TMEM14C	8	.	0			c.A226G						.						161	144	150					6																	10728899		2203	4300	6503	SO:0001583	missense	51522	exon5			GGCATTATGGGAA	AF151028	CCDS4514.1	6p24.1	2008-02-26	2004-04-16	2004-04-21	ENSG00000111843	ENSG00000111843			20952	protein-coding gene	gene with protein product		615318	"chromosome 6 open reading frame 53"	C6orf53		11042152, 12958361	Standard	NM_016462		Approved	HSPC194, bA421M1.6, NET26	uc021ylj.1	Q9P0S9	OTTHUMG00000014242	ENST00000541412.1:c.226A>G	chr6.hg19:g.10728899A>G	ENSP00000444561:p.Met76Val	73.0	0.0		79.0	12.0	NM_001165258	Q5T4I6	Missense_Mutation	SNP	ENST00000541412.1	hg19	CCDS4514.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.30|17.30	3.354364|3.354364	0.61293|0.61293	.|.	.|.	ENSG00000111843|ENSG00000111843	ENST00000541412;ENST00000229563|ENST00000342277	T;T|.	0.46819|.	0.86;0.86|.	3.88|3.88	3.88|3.88	0.44766|0.44766	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.79834|0.79834	0.4514|0.4514	H|H	0.95187|0.95187	3.635|3.635	0.80722|0.80722	D|D	1|1	B;B|.	0.33528|.	0.416;0.416|.	P;P|.	0.44673|.	0.457;0.457|.	T|T	0.82486|0.82486	-0.0433|-0.0433	10|6	0.59425|0.37606	D|T	0.04|0.19	.|.	11.6776|11.6776	0.51438|0.51438	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	76;76|.	Q53F27;Q9P0S9|.	.;TM14C_HUMAN|.	V|C	76|75	ENSP00000444561:M76V;ENSP00000229563:M76V|.	ENSP00000229563:M76V|ENSP00000343293:Y75C	M|Y	+|+	1|2	0|0	TMEM14C|TMEM14C	10836885|10836885	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.818000|0.818000	0.46254|0.46254	7.898000|7.898000	0.87363|0.87363	1.374000|1.374000	0.46228|0.46228	0.374000|0.374000	0.22700|0.22700	ATG|TAT	.	.		0.413	TMEM14C-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039829.1	NM_016462		G	10728899	A	G	10728899	3	3	310	1	0	0	0	0	1	0	0	0	16080	449	16	2	240	2	TMEM14C	6	10728899	Missense_Mutation	SNP	A	TCGA-K7-A5RG-01A-11D-A28X-10	5836460	10728899	160386168	49	44150										
MSH5	4439	hgsc.bcm.edu	37	chr6	31726633	31726633	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ctcccgtattccttcatgcaGtgtcatctacatccctctgg	6	15	4	0			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr6:31726633G>A	ENST00000375755.3	+	15	1593	c.1307G>A	c.(1306-1308)aGt>aAt	p.S436N	MSH5_ENST00000395853.1_Missense_Mutation_p.S110N|MSH5_ENST00000375703.3_Missense_Mutation_p.S436N|MSH5_ENST00000375750.3_Missense_Mutation_p.S436N|MSH5_ENST00000431848.2_Missense_Mutation_p.S135N|MSH5_ENST00000534153.4_Missense_Mutation_p.S453N|MSH5_ENST00000375740.3_Missense_Mutation_p.S453N|MSH5-SAPCD1_ENST00000493662.2_Missense_Mutation_p.S453N|MSH5_ENST00000375742.3_Missense_Mutation_p.S453N|RNU6-850P_ENST00000516934.1_RNA	NM_002441.4	NP_002432.1	O43196	MSH5_HUMAN	mutS homolog 5	436					ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|reciprocal meiotic recombination (GO:0007131)	synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|ovary(2)|skin(2)	5						CCTTCATGCAGTGTCATCTAC	0.493								Direct reversal of damage;Mismatch excision repair (MMR)																													p.S453N		Atlas-SNP	.											.	MSH5	108	.	0			c.G1358A						.						101	96	98					6																	31726633		2203	4300	6503	SO:0001583	missense	4439	exon15			CATGCAGTGTCAT	AF070071	CCDS4720.1, CCDS34409.1, CCDS34410.1, CCDS34409.2	6p21.3	2013-09-12	2013-09-12		ENSG00000204410	ENSG00000204410			7328	protein-coding gene	gene with protein product		603382	"mutS (E. coli) homolog 5", "mutS homolog 5 (E. coli)"			9740671, 9787078, 17977839	Standard	NM_002441		Approved		uc011hbg.2	O43196	OTTHUMG00000167551	ENST00000375755.3:c.1307G>A	chr6.hg19:g.31726633G>A	ENSP00000364908:p.Ser436Asn	161.0	0.0		217.0	29.0	NM_025259	B0V033|B0V034|O60586|Q5BLU9|Q5SSR1|Q8IW44|Q9BQC7	Missense_Mutation	SNP	ENST00000375755.3	hg19	CCDS4720.1	.	.	.	.	.	.	.	.	.	.	G	13.48	2.250221	0.39797	.	.	ENSG00000204410	ENST00000375755;ENST00000375742;ENST00000375750;ENST00000534153;ENST00000375703;ENST00000375740;ENST00000450148;ENST00000431848;ENST00000395853	D;D;D;D;D;D;D;D;D	0.89196	-2.48;-2.48;-2.48;-2.48;-2.48;-2.48;-2.48;-2.48;-2.48	5.42	5.42	0.78866	DNA mismatch repair protein MutS, clamp (1);DNA mismatch repair protein MutS, core (3);	0.050593	0.85682	D	0.000000	T	0.59998	0.2235	N	0.05259	-0.085	0.32564	N	0.5307040000000001	B;B;B;B;B	0.27117	0.035;0.168;0.164;0.002;0.029	B;B;B;B;B	0.30029	0.032;0.067;0.11;0.016;0.027	T	0.55483	-0.8134	9	0.07644	T	0.81	0.3324	10.1909	0.43026	0.0904:0.0:0.9096:0.0	.	121;453;436;436;453	Q59EC5;O43196-4;O43196;O43196-2;O43196-3	.;.;MSH5_HUMAN;.;.	N	436;453;436;453;436;453;278;135;110	ENSP00000364908:S436N;ENSP00000364894:S453N;ENSP00000364903:S436N;ENSP00000431693:S453N;ENSP00000364855:S436N;ENSP00000364892:S453N;ENSP00000394971:S278N;ENSP00000416784:S135N;ENSP00000379194:S110N	ENSP00000364855:S436N	S	+	2	0	MSH5	31834612	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.685000	0.68204	2.557000	0.86248	0.591000	0.81541	AGT	.	.		0.493	MSH5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076243.4			A	31726633	G	A	31726633	3	1	310	1	0	0	0	0	1	0	0	0	9882	1029	36	3	1412	3	MSH5	6	31726633	Missense_Mutation	SNP	G	TCGA-K7-A5RG-01A-11D-A28X-10	20997734	31726633	139388434	50	44151										
HLA-DQA2	3118	hgsc.bcm.edu	37	chr6	32714164	32714164	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	tgcttccagacaccaagggcTcttatgaatcccatcctgaa	7	13	1	3	rs115121776		TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr6:32714164T>C	ENST00000374940.3	+	4	863	c.761T>C	c.(760-762)cTc>cCc	p.L254P		NM_020056.4	NP_064440.1	P01906	DQA2_HUMAN	major histocompatibility complex, class II, DQ alpha 2	254					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)			endometrium(2)|large_intestine(3)|lung(7)|skin(1)	13					"""Insulin(DB00071)"	CACCAAGGGCTCTTATGAATC	0.527																																					p.L254P		Atlas-SNP	.											.	HLA-DQA2	27	.	0			c.T761C						.						124	126	125					6																	32714164		1511	2709	4220	SO:0001583	missense	3118	exon4			AAGGGCTCTTATG		CCDS4753.1	6p21.3	2013-01-11			ENSG00000237541	ENSG00000237541		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4943	protein-coding gene	gene with protein product		613503		HLA-DXA			Standard	NM_020056		Approved		uc003obx.3	P01906	OTTHUMG00000031108	ENST00000374940.3:c.761T>C	chr6.hg19:g.32714164T>C	ENSP00000364076:p.Leu254Pro	147.0	0.0		177.0	9.0	NM_020056	A2BF37|B0V0E7|O19789|Q5SQ94|Q5SR04	Missense_Mutation	SNP	ENST00000374940.3	hg19	CCDS4753.1	.	.	.	.	.	.	.	.	.	.	.	0.001	-3.487525	0.00011	.	.	ENSG00000237541	ENST00000374940	T	0.01685	4.69	3.06	1.21	0.21127	.	1.322850	0.05780	N	0.608367	T	0.00144	0.0004	N	0.00175	-1.925	0.23107	N	0.998286	B	0.02656	0.0	B	0.01281	0.0	T	0.43147	-0.9409	10	0.02654	T	1	.	5.2607	0.15571	0.0:0.7098:0.0:0.2902	.	254	P01906	DQA2_HUMAN	P	254	ENSP00000364076:L254P	ENSP00000364076:L254P	L	+	2	0	HLA-DQA2	32822142	0.000000	0.05858	0.162000	0.22713	0.013000	0.08279	0.678000	0.25277	0.152000	0.19188	-1.188000	0.01700	CTC	.	.		0.527	HLA-DQA2-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076179.2	NM_020056		C	32714164	T	C	32714164	3	2	310	1	0	0	0	0	1	0	0	0	7214	1551	54	2	775	2	HLA-DQA2	6	32714164	Missense_Mutation	SNP	T	TCGA-K7-A5RG-01A-11D-A28X-10	987531	32714164	138400903	51	44152										
KIF6	221458	hgsc.bcm.edu	37	chr6	39607439	39607439	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ccttgggataatgcctctgtCactgtaacgctctgcacccc	8	15	3	0			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr6:39607439C>T	ENST00000287152.7	-	4	440	c.346G>A	c.(346-348)Gac>Aac	p.D116N	KIF6_ENST00000373215.3_Missense_Mutation_p.D116N|KIF6_ENST00000373216.3_Missense_Mutation_p.D116N|KIF6_ENST00000538893.1_Missense_Mutation_p.D116N	NM_145027.4	NP_659464.3	Q6ZMV9	KIF6_HUMAN	kinesin family member 6	116	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|male germ cell nucleus (GO:0001673)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(16)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						ATGCCTCTGTCACTGTAACGC	0.418																																					p.D116N		Atlas-SNP	.											.	KIF6	233	.	0			c.G346A						.						177	133	148					6																	39607439		2203	4300	6503	SO:0001583	missense	221458	exon4			CTCTGTCACTGTA	AL832634	CCDS4844.1, CCDS75449.1	6p21.2	2010-03-30			ENSG00000164627	ENSG00000164627		"Kinesins"	21202	protein-coding gene	gene with protein product		613919	"chromosome 6 open reading frame 102"	C6orf102			Standard	NM_145027		Approved	dJ1043E3.1, MGC33317, dJ137F1.4, dJ188D3.1, DKFZp451I2418	uc003oot.2	Q6ZMV9	OTTHUMG00000014648	ENST00000287152.7:c.346G>A	chr6.hg19:g.39607439C>T	ENSP00000287152:p.Asp116Asn	131.0	0.0		147.0	18.0	NM_145027	Q2MDE3|Q2MDE4|Q5T8J6|Q6ZWE3|Q86T87|Q8WTV4	Missense_Mutation	SNP	ENST00000287152.7	hg19	CCDS4844.1	.	.	.	.	.	.	.	.	.	.	C	36	5.833923	0.97003	.	.	ENSG00000164627	ENST00000287152;ENST00000373216;ENST00000373215;ENST00000538893	T;T;T;T	0.72725	-0.68;-0.68;-0.68;-0.68	5.67	5.67	0.87782	Kinesin, motor domain (4);	.	.	.	.	T	0.72969	0.3527	L	0.42686	1.345	0.80722	D	1	D;P;D	0.89917	1.0;0.729;1.0	D;B;D	0.91635	0.995;0.444;0.999	T	0.65697	-0.6105	9	0.14656	T	0.56	.	19.3678	0.94471	0.0:1.0:0.0:0.0	.	116;116;116	E7EUN7;F6VGH2;Q6ZMV9	.;.;KIF6_HUMAN	N	116	ENSP00000287152:D116N;ENSP00000362312:D116N;ENSP00000362311:D116N;ENSP00000441435:D116N	ENSP00000287152:D116N	D	-	1	0	KIF6	39715417	1.000000	0.71417	0.991000	0.47740	0.973000	0.67179	7.696000	0.84270	2.687000	0.91594	0.655000	0.94253	GAC	.	.		0.418	KIF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040455.2	NM_145027		T	39607439	C	T	39607439	3	4	310	1	0	0	0	0	1	0	0	0	8317	826	29	3	2178	3	KIF6	6	39607439	Missense_Mutation	SNP	C	TCGA-K7-A5RG-01A-11D-A28X-10	6893275	39607439	131507628	52	44153										
LRFN2	57497	hgsc.bcm.edu	37	chr6	40360391	40360391	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	tgcagaccttgtagcgcaccAtgaggatgacgatgaagacc	12	10	0	5			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr6:40360391A>G	ENST00000338305.6	-	3	2203	c.1661T>C	c.(1660-1662)aTg>aCg	p.M554T		NM_020737.1	NP_065788.1	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III domain containing 2	554						cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	58	Ovarian(28;0.0418)|Colorectal(47;0.196)					GTAGCGCACCATGAGGATGAC	0.627																																					p.M554T		Atlas-SNP	.											.	LRFN2	133	.	0			c.T1661C						.						72	57	62					6																	40360391		2203	4300	6503	SO:0001583	missense	57497	exon3			CGCACCATGAGGA	AB033072	CCDS34443.1	6p21.2-p21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000156564	ENSG00000156564		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	21226	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 2"	612808	"KIAA1246"	KIAA1246, SALM1		16495444, 16828986	Standard	NM_020737		Approved	FIGLER2	uc003oph.1	Q9ULH4	OTTHUMG00000014662	ENST00000338305.6:c.1661T>C	chr6.hg19:g.40360391A>G	ENSP00000345985:p.Met554Thr	85.0	0.0		95.0	11.0	NM_020737	A5PKU3|Q5SYP9	Missense_Mutation	SNP	ENST00000338305.6	hg19	CCDS34443.1	.	.	.	.	.	.	.	.	.	.	a	19.82	3.898442	0.72639	.	.	ENSG00000156564	ENST00000338305	T	0.61742	0.08	5.41	5.41	0.78517	.	0.113552	0.85682	D	0.000000	T	0.64405	0.2595	M	0.81802	2.56	0.80722	D	1	P	0.47253	0.892	P	0.53266	0.722	T	0.71741	-0.4501	10	0.87932	D	0	.	14.2596	0.66076	1.0:0.0:0.0:0.0	.	554	Q9ULH4	LRFN2_HUMAN	T	554	ENSP00000345985:M554T	ENSP00000345985:M554T	M	-	2	0	LRFN2	40468369	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.285000	0.95894	2.043000	0.60533	0.529000	0.55759	ATG	.	.		0.627	LRFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040488.1	XM_166372		G	40360391	A	G	40360391	3	3	310	1	0	0	0	0	1	0	0	0	8947	217	8	2	712	2	LRFN2	6	40360391	Missense_Mutation	SNP	A	TCGA-K7-A5RG-01A-11D-A28X-10	752952	40360391	130754676	53	44154										
TNFRSF21	27242	hgsc.bcm.edu	37	chr6	47251729	47251729	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ttctgggttggagtcatggaTttcttcagccctgccttttc	10	10	4	0			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr6:47251729T>A	ENST00000296861.2	-	3	1581	c.1188A>T	c.(1186-1188)aaA>aaT	p.K396N		NM_014452.3	NP_055267.1	O75509	TNR21_HUMAN	tumor necrosis factor receptor superfamily, member 21	396					adaptive immune response (GO:0002250)|apoptotic process (GO:0006915)|B cell apoptotic process (GO:0001783)|cellular lipid metabolic process (GO:0044255)|cellular response to tumor necrosis factor (GO:0071356)|humoral immune response (GO:0006959)|myelination (GO:0042552)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-13 secretion (GO:2000666)|negative regulation of interleukin-5 secretion (GO:2000663)|negative regulation of myelination (GO:0031642)|negative regulation of T cell proliferation (GO:0042130)|neuron apoptotic process (GO:0051402)|oligodendrocyte apoptotic process (GO:0097252)|regulation of oligodendrocyte differentiation (GO:0048713)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|lung(7)|pancreas(1)|skin(2)	21			Lung(136;0.189)			GAGTCATGGATTTCTTCAGCC	0.527																																					p.K396N		Atlas-SNP	.											.	TNFRSF21	61	.	0			c.A1188T						.						106	109	108					6																	47251729		2203	4300	6503	SO:0001583	missense	27242	exon3			CATGGATTTCTTC	AF068868	CCDS4921.1	6p21.1	2011-08-11			ENSG00000146072	ENSG00000146072		"Tumor necrosis factor receptor superfamily", "CD molecules"	13469	protein-coding gene	gene with protein product	"death receptor 6"	605732				9714541	Standard	NM_014452		Approved	DR6, CD358	uc003oyv.3	O75509	OTTHUMG00000014796	ENST00000296861.2:c.1188A>T	chr6.hg19:g.47251729T>A	ENSP00000296861:p.Lys396Asn	114.0	0.0		124.0	14.0	NM_014452	B2RDI9|Q0D2P5|Q96D86	Missense_Mutation	SNP	ENST00000296861.2	hg19	CCDS4921.1	.	.	.	.	.	.	.	.	.	.	T	18.46	3.628927	0.67015	.	.	ENSG00000146072	ENST00000296861;ENST00000419206	T	0.74632	-0.86	6.17	1.25	0.21368	Death (1);	0.000000	0.85682	D	0.000000	T	0.76104	0.3941	M	0.63843	1.955	0.49582	D	0.999803	D	0.89917	1.0	D	0.87578	0.998	T	0.77270	-0.2650	10	0.87932	D	0	.	10.6599	0.45696	0.0:0.3964:0.0:0.6036	.	396	O75509	TNR21_HUMAN	N	396;85	ENSP00000296861:K396N	ENSP00000296861:K396N	K	-	3	2	TNFRSF21	47359688	0.953000	0.32496	0.988000	0.46212	0.925000	0.55904	0.322000	0.19576	-0.006000	0.14370	-0.256000	0.11100	AAA	.	.		0.527	TNFRSF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040814.1	NM_014452		A	47251729	T	A	47251729	3	1	310	1	0	0	0	0	1	0	0	0	16310	1490	52	4	795	4	TNFRSF21	6	47251729	Missense_Mutation	SNP	T	TCGA-K7-A5RG-01A-11D-A28X-10	6891338	47251729	123863338	54	44155										
SAMD9	54809	hgsc.bcm.edu	37	chr7	92731170	92731170	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	gttgcaagacttctcgaagcTgatcttttagtttttcaact	7	8	3	2			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr7:92731170T>C	ENST00000379958.2	-	3	4510	c.4241A>G	c.(4240-4242)cAg>cGg	p.Q1414R		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	1414						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			TTCTCGAAGCTGATCTTTTAG	0.378																																					p.Q1414R		Atlas-SNP	.											SAMD9,right_upper_lobe,carcinoma,0,1	SAMD9	239	.	0			c.A4241G						.						138	143	141					7																	92731170		2203	4300	6503	SO:0001583	missense	54809	exon2			CGAAGCTGATCTT	AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"Sterile alpha motif (SAM) domain containing"	1348	protein-coding gene	gene with protein product		610456	"chromosome 7 open reading frame 5"	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.4241A>G	chr7.hg19:g.92731170T>C	ENSP00000369292:p.Gln1414Arg	146.0	0.0		120.0	17.0	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Missense_Mutation	SNP	ENST00000379958.2	hg19	CCDS34680.1	.	.	.	.	.	.	.	.	.	.	T	3.114	-0.182080	0.06340	.	.	ENSG00000205413	ENST00000379958	T	0.22336	1.96	4.56	3.31	0.37934	.	0.420119	0.21138	N	0.079526	T	0.14399	0.0348	L	0.46157	1.445	0.21822	N	0.999522	B	0.33694	0.421	B	0.29942	0.109	T	0.15838	-1.0423	10	0.07482	T	0.82	-5.3122	9.9689	0.41741	0.1521:0.0:0.0:0.8479	.	1414	Q5K651	SAMD9_HUMAN	R	1414	ENSP00000369292:Q1414R	ENSP00000369292:Q1414R	Q	-	2	0	SAMD9	92569106	0.541000	0.26417	1.000000	0.80357	0.947000	0.59692	1.414000	0.34736	2.034000	0.60081	0.491000	0.48974	CAG	.	.		0.378	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654		C	92731170	T	C	92731170	3	2	310	1	0	0	0	0	1	0	0	0	13841	1580	55	2	532	2	SAMD9	7	92731170	Missense_Mutation	SNP	T	TCGA-K7-A5RG-01A-11D-A28X-10		92731170	66407493	55	44156										
FBXO24	26261	hgsc.bcm.edu	37	chr7	100192090	100192090	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ggttcagctggccctgaggaAggtgtcccactacctgcctc	12	14	1	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr7:100192090A>G	ENST00000241071.6	+	6	1200	c.878A>G	c.(877-879)aAg>aGg	p.K293R	PCOLCE-AS1_ENST00000442166.2_RNA|FBXO24_ENST00000465843.1_Missense_Mutation_p.K279R|FBXO24_ENST00000360609.2_Missense_Mutation_p.K279R|FBXO24_ENST00000468962.1_Missense_Mutation_p.K281R|FBXO24_ENST00000427939.2_Missense_Mutation_p.K331R|PCOLCE-AS1_ENST00000544873.1_RNA	NM_033506.2	NP_277041.1	O75426	FBX24_HUMAN	F-box protein 24	293					protein ubiquitination (GO:0016567)	ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|ovary(3)|skin(4)|urinary_tract(2)	28	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					GCCCTGAGGAAGGTGTCCCAC	0.592																																					p.K331R		Atlas-SNP	.											.	FBXO24	125	.	0			c.A992G						.						108	84	92					7																	100192090		2203	4300	6503	SO:0001583	missense	26261	exon6			TGAGGAAGGTGTC	AF174604	CCDS5698.1, CCDS5699.1, CCDS5699.2, CCDS55138.1	7q22	2005-10-07	2004-06-15		ENSG00000106336	ENSG00000106336		"F-boxes /  "other""	13595	protein-coding gene	gene with protein product		609097	"F-box only protein 24"			10531035, 10531037	Standard	NM_012172		Approved	FBX24	uc011kjz.1	O75426	OTTHUMG00000159543	ENST00000241071.6:c.878A>G	chr7.hg19:g.100192090A>G	ENSP00000241071:p.Lys293Arg	110.0	0.0		127.0	15.0	NM_012172	A4D2D4|B4DX91|B4DY42|Q9H0G1	Missense_Mutation	SNP	ENST00000241071.6	hg19	CCDS5698.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.052596	0.75960	.	.	ENSG00000106336	ENST00000241071;ENST00000360609;ENST00000465843;ENST00000468962;ENST00000427939	T;T;T;T;T	0.80653	-1.4;0.43;0.43;-1.4;-1.4	5.03	5.03	0.67393	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.64402	D	0.000003	T	0.66761	0.2822	N	0.08118	0	0.40451	D	0.980148	D;D;D;P	0.53151	0.958;0.958;0.958;0.933	P;P;P;B	0.45276	0.475;0.475;0.475;0.359	T	0.72087	-0.4396	10	0.42905	T	0.14	-14.2967	12.7928	0.57543	1.0:0.0:0.0:0.0	.	281;331;293;279	B4DY42;B4DX91;O75426;O75426-2	.;.;FBX24_HUMAN;.	R	293;279;279;281;331	ENSP00000241071:K293R;ENSP00000353821:K279R;ENSP00000419602:K279R;ENSP00000420239:K281R;ENSP00000416558:K331R	ENSP00000241071:K293R	K	+	2	0	FBXO24	100030026	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	3.978000	0.56881	2.137000	0.66172	0.392000	0.25879	AAG	.	.		0.592	FBXO24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356104.1			G	100192090	A	G	100192090	3	3	310	1	0	0	0	0	1	0	0	0	5743	72	3	2	1057	2	FBXO24	7	100192090	Missense_Mutation	SNP	A	TCGA-K7-A5RG-01A-11D-A28X-10	7460920	100192090	58946573	56	44157										
PODXL	5420	hgsc.bcm.edu	37	chr7	131195912	131195912	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	actgtagtggtgtctgcactTtttgtgctcttggggctctc	12	9	3	0			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr7:131195912T>G	ENST00000378555.3	-	2	628	c.381A>C	c.(379-381)aaA>aaC	p.K127N	PODXL_ENST00000465001.1_5'Flank|PODXL_ENST00000537928.1_Missense_Mutation_p.K127N|PODXL_ENST00000541194.1_Missense_Mutation_p.K129N|PODXL_ENST00000322985.9_Missense_Mutation_p.K127N			O00592	PODXL_HUMAN	podocalyxin-like	127	Thr-rich.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					TGTCTGCACTTTTTGTGCTCT	0.552																																					p.K127N		Atlas-SNP	.											.	PODXL	53	.	0			c.A381C						.						238	229	232					7																	131195912		2203	4300	6503	SO:0001583	missense	5420	exon2			TGCACTTTTTGTG		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.381A>C	chr7.hg19:g.131195912T>G	ENSP00000367817:p.Lys127Asn	213.0	0.0		288.0	45.0	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Missense_Mutation	SNP	ENST00000378555.3	hg19	CCDS34755.1	.	.	.	.	.	.	.	.	.	.	T	2.626	-0.287547	0.05605	.	.	ENSG00000128567	ENST00000541194;ENST00000537928;ENST00000544955;ENST00000378555;ENST00000322985	T;T;T;T	0.12984	2.74;2.63;2.75;2.83	0.724	-1.45	0.08828	.	.	.	.	.	T	0.04907	0.0132	N	0.14661	0.345	0.09310	N	1	P;B	0.34934	0.476;0.198	B;B	0.27608	0.052;0.081	T	0.31916	-0.9926	8	0.23891	T	0.37	2.5449	.	.	.	.	127;127	O00592-2;O00592	.;PODXL_HUMAN	N	129;127;117;127;127	ENSP00000440518:K129N;ENSP00000442655:K127N;ENSP00000367817:K127N;ENSP00000319782:K127N	ENSP00000319782:K127N	K	-	3	2	PODXL	130846452	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.832000	0.01696	-1.396000	0.02071	-0.654000	0.03906	AAA	.	.		0.552	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111		G	131195912	T	G	131195912	3	3	310	1	0	0	0	0	1	0	0	0	12189	1838	64	5	1327	5	PODXL	7	131195912	Missense_Mutation	SNP	T	TCGA-K7-A5RG-01A-11D-A28X-10	31003822	131195912	27942751	57	44158										
KIAA1549	57670	hgsc.bcm.edu	37	chr7	138564336	138564336	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ttgacggctcccggcgtcttAtctcctgcgtccctctcgct	9	17	3	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr7:138564336A>G	ENST00000422774.1	-	12	4341	c.4293T>C	c.(4291-4293)gaT>gaC	p.D1431D	KIAA1549_ENST00000242365.4_Silent_p.D1381D|KIAA1549_ENST00000440172.1_Silent_p.D1431D			Q9HCM3	K1549_HUMAN	KIAA1549	1431						integral component of membrane (GO:0016021)			KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						CCGGCGTCTTATCTCCTGCGT	0.512			O	BRAF	pilocytic astrocytoma																																p.D1431D	NSCLC(119;1534 1718 44213 46230 50068)	Atlas-SNP	.		Dom	yes		7	7q34	57670	KIAA1549		O	.	KIAA1549	314	.	0			c.T4293C						.						27	29	29					7																	138564336		1869	4103	5972	SO:0001819	synonymous_variant	57670	exon12			CGTCTTATCTCCT		CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.4293T>C	chr7.hg19:g.138564336A>G		26.0	0.0		27.0	5.0	NM_020910	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Silent	SNP	ENST00000422774.1	hg19	CCDS56513.1																																																																																			.	.		0.512	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1			G	138564336	A	G	138564336	2	3	310	1	0	0	0	0	0	0	0	1	8253	446	16	2		2	KIAA1549	7	138564336	Silent	SNP	A	TCGA-K7-A5RG-01A-11D-A28X-10	7368424	138564336	20574327	58	44159										
PXDNL	137902	hgsc.bcm.edu	37	chr8	52339318	52339318	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	gttgagtaaacactgcaagaGctgtggaaacaaaccaaaat	9	7	0	2			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr8:52339318G>C	ENST00000356297.4	-	13	1626	c.1526C>G	c.(1525-1527)gCt>gGt	p.A509G	PXDNL_ENST00000543296.1_Splice_Site_p.A509G	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	509	Ig-like C2-type 4.				hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				CACTGCAAGAGCTGTGGAAAC	0.373																																					p.A509G		Atlas-SNP	.											.	PXDNL	414	.	0			c.C1526G						.						74	66	69					8																	52339318		1873	4109	5982	SO:0001630	splice_region_variant	137902	exon13			GCAAGAGCTGTGG		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"Immunoglobulin superfamily / I-set domain containing"	26359	protein-coding gene	gene with protein product	"polysomal ribonuclease 1 homolog (Xenopus)"	615904	"peroxidasin homolog-like (Drosophila)"			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.1526-1C>G	chr8.hg19:g.52339318G>C		33.0	0.0		53.0	9.0	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	hg19	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	G	3.740	-0.053773	0.07362	.	.	ENSG00000147485	ENST00000356297;ENST00000543296	T;T	0.66815	-0.2;-0.23	4.18	-5.33	0.02713	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.39306	0.1073	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.09377	0.004	T	0.19778	-1.0295	9	0.18710	T	0.47	.	2.3172	0.04201	0.5321:0.1386:0.1895:0.1398	.	509	A1KZ92	PXDNL_HUMAN	G	509	ENSP00000348645:A509G;ENSP00000444865:A509G	ENSP00000348645:A509G	A	-	2	0	PXDNL	52501871	0.009000	0.17119	0.000000	0.03702	0.005000	0.04900	-0.238000	0.08977	-1.044000	0.03254	-0.157000	0.13467	GCT	.	.		0.373	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	Missense_Mutation	C	52339318	G	C	52339318	5	2	310	1	0	0	0	0	0	0	1	0	12863	985	34	4	2909	4	PXDNL	8	52339318	Splice_Site	SNP	G	TCGA-K7-A5RG-01A-11D-A28X-10		52339318	94024704	59	44160										
EYA1	2138	hgsc.bcm.edu	37	chr8	72234031	72234031	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	tggcataggctgtagcttgtTgcattcctgtggtaaactgt	12	7	0	0			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr8:72234031T>C	ENST00000340726.3	-	6	995	c.356A>G	c.(355-357)cAa>cGa	p.Q119R	EYA1_ENST00000388742.4_Missense_Mutation_p.Q119R|EYA1_ENST00000303824.7_Missense_Mutation_p.Q118R|EYA1_ENST00000388743.2_Missense_Mutation_p.Q118R|EYA1_ENST00000419131.1_Missense_Mutation_p.Q119R|EYA1_ENST00000388741.2_Missense_Mutation_p.Q85R|EYA1_ENST00000388740.3_Missense_Mutation_p.Q86R	NM_000503.4	NP_000494.2	Q99502	EYA1_HUMAN	EYA transcriptional coactivator and phosphatase 1	119					anatomical structure morphogenesis (GO:0009653)|aorta morphogenesis (GO:0035909)|branching involved in ureteric bud morphogenesis (GO:0001658)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|double-strand break repair (GO:0006302)|embryonic skeletal system morphogenesis (GO:0048704)|establishment of mitotic spindle orientation (GO:0000132)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|histone dephosphorylation (GO:0016576)|lung epithelial cell differentiation (GO:0060487)|metanephros development (GO:0001656)|middle ear morphogenesis (GO:0042474)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|neuron fate specification (GO:0048665)|otic vesicle morphogenesis (GO:0071600)|outer ear morphogenesis (GO:0042473)|outflow tract morphogenesis (GO:0003151)|pattern specification process (GO:0007389)|pharyngeal system development (GO:0060037)|positive regulation of DNA repair (GO:0045739)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of neuron differentiation (GO:0045664)|response to ionizing radiation (GO:0010212)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|striated muscle tissue development (GO:0014706)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)|RNA binding (GO:0003723)	p.Q119L(1)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(15)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	44	Breast(64;0.046)		Epithelial(68;0.0837)|all cancers(69;0.247)			TGTAGCTTGTTGCATTCCTGT	0.488																																					p.Q119R		Atlas-SNP	.											EYA1,NS,lymphoid_neoplasm,0,2	EYA1	108	.	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.A356G						.						200	154	169					8																	72234031		2203	4300	6503	SO:0001583	missense	2138	exon5			GCTTGTTGCATTC	AJ000098	CCDS34906.1, CCDS34907.1, CCDS47873.1, CCDS75750.1	8q13.3	2014-06-19	2014-06-19		ENSG00000104313	ENSG00000104313		"Protein tyrosine phosphatases / Asp-based PTPs"	3519	protein-coding gene	gene with protein product		601653	"eyes absent (Drosophila) homolog 1", "eyes absent homolog 1 (Drosophila)"	BOR		9020840	Standard	XM_005251184		Approved		uc003xys.4	Q99502	OTTHUMG00000149894	ENST00000340726.3:c.356A>G	chr8.hg19:g.72234031T>C	ENSP00000342626:p.Gln119Arg	288.0	0.0		335.0	38.0	NM_172059	A6NHQ0|G5E9R4|Q0P516|Q8WX80	Missense_Mutation	SNP	ENST00000340726.3	hg19	CCDS34906.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.283613	0.80803	.	.	ENSG00000104313	ENST00000388742;ENST00000340726;ENST00000388744;ENST00000388740;ENST00000303824;ENST00000388741;ENST00000388743;ENST00000419131	D;D;D;D;D;D;D	0.89875	-2.58;-2.58;-2.58;-2.58;-2.58;-2.58;-2.58	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	D	0.93848	0.8032	M	0.75615	2.305	0.58432	D	0.999992	D;D;D;D;D	0.76494	0.994;0.999;0.999;0.994;0.997	D;D;D;D;D	0.87578	0.986;0.998;0.998;0.986;0.958	D	0.93917	0.7202	10	0.49607	T	0.09	-9.9561	15.3428	0.74311	0.0:0.0:0.0:1.0	.	118;46;86;119;119	A6NCB9;Q0P517;Q99502-2;Q99502;G5E9R4	.;.;.;EYA1_HUMAN;.	R	119;119;87;86;118;85;118;119	ENSP00000373394:Q119R;ENSP00000342626:Q119R;ENSP00000373392:Q86R;ENSP00000303221:Q118R;ENSP00000373393:Q85R;ENSP00000373395:Q118R;ENSP00000410176:Q119R	ENSP00000303221:Q118R	Q	-	2	0	EYA1	72396585	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.145000	0.71769	2.083000	0.62718	0.528000	0.53228	CAA	.	.		0.488	EYA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313788.2	NM_000503, NM_172060		C	72234031	T	C	72234031	3	2	310	1	0	0	0	0	1	0	0	0	5330	1812	63	2	1474	2	EYA1	8	72234031	Missense_Mutation	SNP	T	TCGA-K7-A5RG-01A-11D-A28X-10	19894713	72234031	74129991	60	44161										
ESRP1	54845	hgsc.bcm.edu	37	chr8	95676928	95676928	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ttttgcttcatccacagcagCaagatggaacttattgatga	8	8	1	3			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr8:95676928C>T	ENST00000433389.2	+	7	838	c.648C>T	c.(646-648)agC>agT	p.S216S	ESRP1_ENST00000358397.5_Silent_p.S216S|ESRP1_ENST00000423620.2_Silent_p.S216S|ESRP1_ENST00000454170.2_Silent_p.S216S	NM_001034915.2|NM_017697.3	NP_001030087.2|NP_060167.2	Q6NXG1	ESRP1_HUMAN	epithelial splicing regulatory protein 1	216					mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)		ESRP1/RAF1(4)	NS(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)|urinary_tract(2)	20						TCCACAGCAGCAAGATGGAAC	0.428																																					p.S216S		Atlas-SNP	.											.	ESRP1	148	.	0			c.C648T						.						107	99	102					8																	95676928		1954	4154	6108	SO:0001819	synonymous_variant	54845	exon7			CAGCAGCAAGATG	AK000178	CCDS47895.1, CCDS47896.1, CCDS47897.1, CCDS47898.1	8q22.1	2013-02-12	2009-03-10	2009-03-10	ENSG00000104413	ENSG00000104413		"RNA binding motif (RRM) containing"	25966	protein-coding gene	gene with protein product		612959	"RNA binding motif protein 35A"	RBM35A		12477932	Standard	NM_017697		Approved	FLJ20171	uc003ygq.4	Q6NXG1	OTTHUMG00000164587	ENST00000433389.2:c.648C>T	chr8.hg19:g.95676928C>T		137.0	0.0		190.0	18.0	NM_001122827	A6NHA8|A8MPX1|E9PB47|Q2M2B0|Q499G3|Q6PJ86|Q9NXL8	Silent	SNP	ENST00000433389.2	hg19	CCDS47897.1	.	.	.	.	.	.	.	.	.	.	C	9.963	1.223329	0.22457	.	.	ENSG00000104413	ENST00000519505	.	.	.	5.68	5.68	0.88126	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-15.7934	19.798	0.96494	0.0:1.0:0.0:0.0	.	.	.	.	X	82	.	.	Q	+	1	0	ESRP1	95746104	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.478000	0.35442	2.677000	0.91161	0.563000	0.77884	CAA	.	.		0.428	ESRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379326.1	NM_017697		T	95676928	C	T	95676928	2	4	310	1	0	0	0	0	0	0	0	1	5260	709	25	3		3	ESRP1	8	95676928	Silent	SNP	C	TCGA-K7-A5RG-01A-11D-A28X-10	23442897	95676928	50687094	61	44162										
SCRIB	23513	hgsc.bcm.edu	37	chr8	144892681	144892681	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	caagggcgacccagagtctgGctggcaagggcaggcctcgc	16	13	1	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr8:144892681G>C	ENST00000320476.3	-	13	1504	c.1498C>G	c.(1498-1500)Cca>Gca	p.P500A	MIR937_ENST00000401271.1_RNA|SCRIB_ENST00000356994.2_Missense_Mutation_p.P500A|SCRIB_ENST00000377533.3_Missense_Mutation_p.P419A	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	500	Sufficient for targeting to adherens junction and to inhibit cell proliferation.				activation of Rac GTPase activity (GO:0032863)|apoptotic process involved in morphogenesis (GO:0060561)|astrocyte cell migration (GO:0043615)|asymmetric protein localization (GO:0008105)|auditory receptor cell stereocilium organization (GO:0060088)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cochlear nucleus development (GO:0021747)|establishment of apical/basal cell polarity (GO:0035089)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of mitotic cell cycle (GO:0045930)|neural tube closure (GO:0001843)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of receptor recycling (GO:0001921)|protein localization to adherens junction (GO:0071896)|single organismal cell-cell adhesion (GO:0016337)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle targeting (GO:0016080)|viral process (GO:0016032)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)|Scrib-APC-beta-catenin complex (GO:0034750)				NS(1)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(20)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	42	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			CCAGAGTCTGGCTGGCAAGGG	0.692																																					p.P500A	Pancreas(51;966 1133 10533 14576 29674)	Atlas-SNP	.											.	SCRIB	192	.	0			c.C1498G						.						55	60	58					8																	144892681		2203	4299	6502	SO:0001583	missense	23513	exon13			AGTCTGGCTGGCA	AY062238	CCDS6411.1, CCDS6412.1	8q24.3	2013-03-05	2013-03-05		ENSG00000180900	ENSG00000180900			30377	protein-coding gene	gene with protein product		607733	"scribbled homolog (Drosophila)"			11027293, 14681682	Standard	NM_182706		Approved	KIAA0147, SCRB1, Vartul	uc003yzo.1	Q14160	OTTHUMG00000165154	ENST00000320476.3:c.1498C>G	chr8.hg19:g.144892681G>C	ENSP00000322938:p.Pro500Ala	109.0	0.0		151.0	20.0	NM_015356	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Missense_Mutation	SNP	ENST00000320476.3	hg19	CCDS6411.1	.	.	.	.	.	.	.	.	.	.	G	11.82	1.751837	0.31046	.	.	ENSG00000180900	ENST00000356994;ENST00000320476;ENST00000377533	T;T;T	0.75260	-0.92;-0.92;-0.92	4.35	4.35	0.52113	.	.	.	.	.	T	0.70369	0.3216	M	0.63843	1.955	0.09310	N	1	B;B	0.25105	0.037;0.118	B;B	0.24155	0.012;0.051	T	0.58358	-0.7650	9	0.24483	T	0.36	.	12.6158	0.56576	0.0:0.1683:0.8317:0.0	.	500;500	Q14160;Q14160-3	SCRIB_HUMAN;.	A	500;500;419	ENSP00000349486:P500A;ENSP00000322938:P500A;ENSP00000366756:P419A	ENSP00000322938:P500A	P	-	1	0	SCRIB	144964669	0.996000	0.38824	0.129000	0.21949	0.091000	0.18340	3.665000	0.54532	2.148000	0.66965	0.563000	0.77884	CCA	.	.		0.692	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356		C	144892681	G	C	144892681	3	2	310	1	0	0	0	0	1	0	0	0	13952	1203	42	4	3569	4	SCRIB	8	144892681	Missense_Mutation	SNP	G	TCGA-K7-A5RG-01A-11D-A28X-10	49215753	144892681	1471341	62	44163										
SH3GL2	6456	hgsc.bcm.edu	37	chr9	17789515	17789515	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	gatgagtctaaggaaattgcTgagtcaagcatgttcaatct	10	6	4	2			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr9:17789515T>A	ENST00000380607.4	+	6	711	c.591T>A	c.(589-591)gcT>gcA	p.A197A	SH3GL2_ENST00000537391.1_Silent_p.A150A	NM_003026.2	NP_003017.1	Q99962	SH3G2_HUMAN	SH3-domain GRB2-like 2	197	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|central nervous system development (GO:0007417)|epidermal growth factor receptor signaling pathway (GO:0007173)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of receptor internalization (GO:0002090)|signal transduction (GO:0007165)|synaptic vesicle endocytosis (GO:0048488)	clathrin-coated endocytic vesicle membrane (GO:0030669)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)			NS(1)|breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(11)|skin(3)|upper_aerodigestive_tract(1)	26				GBM - Glioblastoma multiforme(50;2.71e-10)|Lung(42;0.203)		AGGAAATTGCTGAGTCAAGCA	0.393																																					p.A197A		Atlas-SNP	.											.	SH3GL2	60	.	0			c.T591A						.						103	103	103					9																	17789515		2203	4300	6503	SO:0001819	synonymous_variant	6456	exon6			AATTGCTGAGTCA	X99657	CCDS6483.1	9p22	2008-02-05			ENSG00000107295	ENSG00000107295			10831	protein-coding gene	gene with protein product		604465				9169142	Standard	XM_005251549		Approved	SH3P4, SH3D2A, CNSA2, EEN-B1	uc003zna.3	Q99962	OTTHUMG00000019601	ENST00000380607.4:c.591T>A	chr9.hg19:g.17789515T>A		66.0	0.0		91.0	19.0	NM_003026	B2R618|Q9NQK5	Silent	SNP	ENST00000380607.4	hg19	CCDS6483.1																																																																																			.	.		0.393	SH3GL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051796.1	NM_003026		A	17789515	T	A	17789515	2	1	310	1	0	0	0	0	0	0	0	1	14266	1567	55	4		4	SH3GL2	9	17789515	Silent	SNP	T	TCGA-K7-A5RG-01A-11D-A28X-10		17789515	123423916	63	44164										
TJP2	9414	hgsc.bcm.edu	37	chr9	71836182	71836182	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ccgggaccgtgaccgcagccGcggccggagcattgaccagg	16	15	0	2			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr9:71836182G>A	ENST00000377245.4	+	5	930	c.722G>A	c.(721-723)cGc>cAc	p.R241H	TJP2_ENST00000535702.1_Missense_Mutation_p.R245H|TJP2_ENST00000453658.2_Missense_Mutation_p.R218H|TJP2_ENST00000265384.7_Missense_Mutation_p.R241H|TJP2_ENST00000348208.4_Missense_Mutation_p.R241H|TJP2_ENST00000539225.1_Missense_Mutation_p.R272H	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	241					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|hippo signaling (GO:0035329)|nucleotide phosphorylation (GO:0046939)|response to organic substance (GO:0010033)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	guanylate kinase activity (GO:0004385)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(5)|lung(9)|prostate(3)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	35						GACCGCAGCCGCGGCCGGAGC	0.726																																					p.R272H		Atlas-SNP	.											.	TJP2	120	.	0			c.G815A						.						15	20	18					9																	71836182		2189	4286	6475	SO:0001583	missense	9414	exon5			GCAGCCGCGGCCG	L27476	CCDS6627.1, CCDS6628.1, CCDS55314.1, CCDS55315.1, CCDS55316.1, CCDS55317.1	9q13-q21	2012-07-12	2012-07-12		ENSG00000119139	ENSG00000119139			11828	protein-coding gene	gene with protein product	"Friedreich ataxia region gene X104 (tight junction protein ZO-2)", "zona occludens 2"	607709	"deafness, autosomal dominant 51"	DFNA51		7951235, 20602916	Standard	NM_001170630		Approved	ZO-2, X104, ZO2	uc011lrv.2	Q9UDY2	OTTHUMG00000019978	ENST00000377245.4:c.722G>A	chr9.hg19:g.71836182G>A	ENSP00000366453:p.Arg241His	58.0	0.0		72.0	6.0	NM_001170416	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Missense_Mutation	SNP	ENST00000377245.4	hg19	CCDS6627.1	.	.	.	.	.	.	.	.	.	.	G	9.270	1.045346	0.19748	.	.	ENSG00000119139	ENST00000453658;ENST00000377245;ENST00000348208;ENST00000265384;ENST00000535702;ENST00000539225	T;T;T;T;T;T	0.61274	0.12;0.12;0.12;0.12;0.12;0.12	4.4	1.39	0.22231	.	0.379077	0.26812	N	0.022363	T	0.39682	0.1087	L	0.46157	1.445	0.24222	N	0.995431	B;B;B;B;P	0.50443	0.017;0.003;0.003;0.002;0.935	B;B;B;B;B	0.37650	0.007;0.005;0.003;0.001;0.255	T	0.34329	-0.9833	9	.	.	.	.	3.6203	0.08093	0.2475:0.0:0.4452:0.3073	.	272;245;241;241;241	F5H301;F5H886;Q9UDY2-2;Q9UDY2;Q9UDY2-5	.;.;.;ZO2_HUMAN;.	H	218;241;241;241;245;272	ENSP00000392178:R218H;ENSP00000366453:R241H;ENSP00000345893:R241H;ENSP00000265384:R241H;ENSP00000442090:R245H;ENSP00000438262:R272H	.	R	+	2	0	TJP2	71026002	0.224000	0.23674	0.013000	0.15412	0.103000	0.19146	0.665000	0.25083	0.064000	0.16427	0.655000	0.94253	CGC	.	.		0.726	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629		A	71836182	G	A	71836182	3	1	310	1	0	0	0	0	1	0	0	0	15945	1087	38	1	897	1	TJP2	9	71836182	Missense_Mutation	SNP	G	TCGA-K7-A5RG-01A-11D-A28X-10	54046667	71836182	69377249	64	44165										
GAPVD1	26130	hgsc.bcm.edu	37	chr9	128118132	128118132	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	aagatggggacatacttcgcGaccagtaagtacttctatgt	10	8	1	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr9:128118132G>A	ENST00000495955.1	+	25	4311	c.4021G>A	c.(4021-4023)Gac>Aac	p.D1341N	GAPVD1_ENST00000265956.4_Missense_Mutation_p.D1315N|GAPVD1_ENST00000394105.2_Missense_Mutation_p.D1350N|GAPVD1_ENST00000394104.2_Missense_Mutation_p.D1341N|GAPVD1_ENST00000470056.1_Missense_Mutation_p.D1296N|GAPVD1_ENST00000312123.9_Missense_Mutation_p.D1302N|GAPVD1_ENST00000297933.6_Missense_Mutation_p.D1323N|GAPVD1_ENST00000394083.2_Missense_Mutation_p.D1275N			Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1	1341	VPS9. {ECO:0000255|PROSITE- ProRule:PRU00550}.				endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|regulation of protein transport (GO:0051223)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	GTPase activating protein binding (GO:0032794)|GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						CATACTTCGCGACCAGTAAGT	0.463																																					p.D1350N		Atlas-SNP	.											.	GAPVD1	124	.	0			c.G4048A						.						93	79	84					9																	128118132		2203	4300	6503	SO:0001583	missense	26130	exon24			CTTCGCGACCAGT		CCDS65130.1, CCDS65131.1, CCDS65132.1	9q34.11	2008-02-05			ENSG00000165219	ENSG00000165219			23375	protein-coding gene	gene with protein product		611714					Standard	XM_005251901		Approved	DKFZP434C212, KIAA1521	uc004bpr.3	Q14C86	OTTHUMG00000020678	ENST00000495955.1:c.4021G>A	chr9.hg19:g.128118132G>A	ENSP00000419063:p.Asp1341Asn	214.0	0.0		221.0	35.0	NM_015635	A8MYK3|B0QZ62|B0QZ63|B0QZ64|Q14C76|Q2Q1W1|Q8ND92|Q8WU86|Q96CZ4|Q9NXQ1|Q9P207|Q9Y4N0	Missense_Mutation	SNP	ENST00000495955.1	hg19		.	.	.	.	.	.	.	.	.	.	G	36	5.778991	0.96929	.	.	ENSG00000165219	ENST00000470056;ENST00000394105;ENST00000394104;ENST00000265956;ENST00000394083;ENST00000495955;ENST00000297933;ENST00000312123;ENST00000438537	T;T;T;T;T;T;T;T	0.48522	0.81;0.81;0.81;0.81;0.81;0.81;0.81;0.81	6.03	6.03	0.97812	Vacuolar sorting protein 9 (1);	0.000000	0.85682	D	0.000000	T	0.74253	0.3692	M	0.86097	2.795	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;0.999;0.999	D;D;D;D;D;D	0.85130	0.978;0.949;0.951;0.997;0.979;0.984	T	0.76683	-0.2869	10	0.87932	D	0	.	19.5544	0.95335	0.0:0.0:1.0:0.0	.	1341;356;1296;1302;1323;1350	Q14C86;B3KTX2;Q14C86-3;Q14C86-4;Q14C86-2;Q14C86-6	GAPD1_HUMAN;.;.;.;.;.	N	1296;1350;1341;1315;1275;1341;1323;1302;34	ENSP00000419767:D1296N;ENSP00000377665:D1350N;ENSP00000377664:D1341N;ENSP00000265956:D1315N;ENSP00000377645:D1275N;ENSP00000419063:D1341N;ENSP00000297933:D1323N;ENSP00000309582:D1302N	ENSP00000265956:D1315N	D	+	1	0	GAPVD1	127157953	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	9.378000	0.97191	2.868000	0.98415	0.603000	0.83216	GAC	.	.		0.463	GAPVD1-014	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000355644.1			A	128118132	G	A	128118132	3	1	310	1	0	0	0	0	1	0	0	0	6247	1058	37	1	4138	1	GAPVD1	9	128118132	Missense_Mutation	SNP	G	TCGA-K7-A5RG-01A-11D-A28X-10	56281950	128118132	13095299	65	44166										
PCDH15	65217	hgsc.bcm.edu	37	chr10	55581783	55581783	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	agatagtttttttctatttgActgtacatgttagctactga	7	5	1	3			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr10:55581783A>G	ENST00000320301.6	-	33	6097	c.5703T>C	c.(5701-5703)agT>agC	p.S1901S	PCDH15_ENST00000373957.3_Silent_p.S755S|PCDH15_ENST00000437009.1_Silent_p.S1832S|PCDH15_ENST00000395445.1_Intron|PCDH15_ENST00000395432.2_Silent_p.S1861S|PCDH15_ENST00000395438.1_Intron|PCDH15_ENST00000361849.3_Silent_p.S1903S|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000395430.1_Silent_p.S1898S|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000414778.1_Intron|PCDH15_ENST00000409834.1_Intron|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395433.1_Silent_p.S1878S|PCDH15_ENST00000373965.2_Intron	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1901					equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				TTTCTATTTGACTGTACATGT	0.368										HNSCC(58;0.16)																											p.S1908S		Atlas-SNP	.											PCDH15_ENST00000417177,NS,carcinoma,-2,2	PCDH15	1715	.	0			c.T5724C						.						210	194	199					10																	55581783		2203	4300	6503	SO:0001819	synonymous_variant	65217	exon35			TATTTGACTGTAC	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.5703T>C	chr10.hg19:g.55581783A>G		98.0	0.0		71.0	8.0	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Silent	SNP	ENST00000320301.6	hg19	CCDS7248.1																																																																																			.	.		0.368	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		G	55581783	A	G	55581783	2	3	310	1	0	0	0	0	0	0	0	1	11520	272	10	2		2	PCDH15	10	55581783	Silent	SNP	A	TCGA-K7-A5RG-01A-11D-A28X-10		55581783	79952964	66	44167										
LDB3	11155	hgsc.bcm.edu	37	chr10	88452294	88452294	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	gctcctttctaccaacagtgCaagaccctgatgaagaagct	8	12	1	4			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr10:88452294C>A	ENST00000361373.4	+	6	883	c.862C>A	c.(862-864)Caa>Aaa	p.Q288K	LDB3_ENST00000352360.5_Intron|LDB3_ENST00000542786.1_3'UTR|LDB3_ENST00000429277.2_Missense_Mutation_p.Q356K|LDB3_ENST00000458213.2_Missense_Mutation_p.Q241K|LDB3_ENST00000310944.6_Missense_Mutation_p.Q288K|LDB3_ENST00000263066.6_Missense_Mutation_p.Q241K|LDB3_ENST00000372066.3_Missense_Mutation_p.Q241K|LDB3_ENST00000372056.4_Missense_Mutation_p.Q356K	NM_007078.2	NP_009009.1			LIM domain binding 3											breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|soft_tissue(1)	25						ACCAACAGTGCAAGACCCTGA	0.617																																					p.Q356K		Atlas-SNP	.											.	LDB3	164	.	0			c.C1066A						.						134	119	124					10																	88452294		2203	4300	6503	SO:0001583	missense	11155	exon8			ACAGTGCAAGACC	AB014513	CCDS7377.1, CCDS41544.1, CCDS41545.1, CCDS53549.1, CCDS53550.1	10q22.3-q23.2	2014-09-17			ENSG00000122367	ENSG00000122367			15710	protein-coding gene	gene with protein product	"cypher", "oracle", "Z-band alternatively spliced PDZ motif protein"	605906	"cardiomyopathy, dilated 1C (autosomal dominant)"	CMD1C		10427098, 23271734, 23996002, 14662268	Standard	NM_001080114		Approved	PDLIM6, KIAA0613, ZASP	uc001kdv.3	O75112	OTTHUMG00000018655	ENST00000361373.4:c.862C>A	chr10.hg19:g.88452294C>A	ENSP00000355296:p.Gln288Lys	122.0	0.0		133.0	6.0	NM_001171610		Missense_Mutation	SNP	ENST00000361373.4	hg19	CCDS7377.1	.	.	.	.	.	.	.	.	.	.	C	31	5.094118	0.94149	.	.	ENSG00000122367	ENST00000539402;ENST00000429277;ENST00000458213;ENST00000372066;ENST00000263066;ENST00000372056;ENST00000310944;ENST00000361373	T;T;T;T;T;T;T	0.55413	0.69;0.52;0.85;0.52;0.79;0.98;0.57	5.92	5.92	0.95590	.	.	.	.	.	T	0.53126	0.1777	L	0.37630	1.12	0.80722	D	1	B;B;B;B;B;D;P	0.54047	0.199;0.011;0.433;0.307;0.167;0.964;0.894	B;B;B;B;B;P;P	0.52554	0.06;0.025;0.127;0.06;0.066;0.702;0.676	T	0.42155	-0.9468	9	0.05436	T	0.98	.	20.3214	0.98679	0.0:1.0:0.0:0.0	.	356;288;356;288;241;288;241	B4E3K3;F5H0C2;O75112-4;O75112;O75112-2;O75112-5;O75112-6	.;.;.;LDB3_HUMAN;.;.;.	K	288;356;241;241;241;356;288;288	ENSP00000401437:Q356K;ENSP00000409148:Q241K;ENSP00000361136:Q241K;ENSP00000263066:Q241K;ENSP00000361126:Q356K;ENSP00000311913:Q288K;ENSP00000355296:Q288K	ENSP00000263066:Q241K	Q	+	1	0	LDB3	88442274	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.280000	0.78610	2.804000	0.96469	0.655000	0.94253	CAA	.	.		0.617	LDB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000049160.2			A	88452294	C	A	88452294	3	1	310	1	0	0	0	0	1	0	0	0	8706	711	25	3	1119	3	LDB3	10	88452294	Missense_Mutation	SNP	C	TCGA-K7-A5RG-01A-11D-A28X-10	32870511	88452294	47082453	67	44168										
DCHS1	8642	hgsc.bcm.edu	37	chr11	6643111	6643111	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	cccaaatggtgagacaacggGtgagcgagcagccagaggag	16	9	0	3			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr11:6643111G>A	ENST00000299441.3	-	21	10207	c.9796C>T	c.(9796-9798)Ccc>Tcc	p.P3266S	TPP1_ENST00000533371.1_5'Flank|TPP1_ENST00000534644.1_5'Flank|TPP1_ENST00000299427.6_5'Flank|RP11-732A19.5_ENST00000526456.1_RNA|RP11-732A19.9_ENST00000545572.1_RNA|TPP1_ENST00000528657.1_5'Flank	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	3266					branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GAGACAACGGGTGAGCGAGCA	0.622																																					p.P3266S		Atlas-SNP	.											.	DCHS1	277	.	0			c.C9796T						.						53	47	49					11																	6643111		2201	4296	6497	SO:0001583	missense	8642	exon21			CAACGGGTGAGCG	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"Cadherins / Cadherin-related"	13681	protein-coding gene	gene with protein product	"cadherin-related family member 6"	603057	"protocadherin 16", "dachsous 1 (Drosophila)"	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.9796C>T	chr11.hg19:g.6643111G>A	ENSP00000299441:p.Pro3266Ser	102.0	0.0		126.0	14.0	NM_003737	O15098	Missense_Mutation	SNP	ENST00000299441.3	hg19	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	G	19.08	3.758475	0.69763	.	.	ENSG00000166341	ENST00000299441	T	0.74106	-0.81	5.01	5.01	0.66863	.	0.000000	0.42053	D	0.000778	D	0.86814	0.6023	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.88512	0.3090	10	0.87932	D	0	.	17.0523	0.86523	0.0:0.0:1.0:0.0	.	3266	Q96JQ0	PCD16_HUMAN	S	3266	ENSP00000299441:P3266S	ENSP00000299441:P3266S	P	-	1	0	DCHS1	6599687	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.774000	0.85478	2.595000	0.87683	0.462000	0.41574	CCC	.	.		0.622	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		A	6643111	G	A	6643111	3	1	310	1	0	0	0	0	1	0	0	0	4289	1261	44	3	104	3	DCHS1	11	6643111	Missense_Mutation	SNP	G	TCGA-K7-A5RG-01A-11D-A28X-10		6643111	128363405	68	44169										
ASCL3	56676	hgsc.bcm.edu	37	chr11	8959174	8959174	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	aacagcaactcaaacaattcTgaacatagggtcagcatggt	8	9	3	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr11:8959174T>A	ENST00000531618.1	-	1	584	c.535A>T	c.(535-537)Aga>Tga	p.R179*	ASCL3_ENST00000325884.1_Nonsense_Mutation_p.R179*			Q9NQ33	ASCL3_HUMAN	achaete-scute family bHLH transcription factor 3	178					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)			breast(1)|large_intestine(2)|lung(5)|stomach(1)	9				Epithelial(150;1.48e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0228)		CAAACAATTCTGAACATAGGG	0.393																																					p.R179X		Atlas-SNP	.											.	ASCL3	19	.	0			c.A535T						.						141	144	143					11																	8959174		2201	4295	6496	SO:0001587	stop_gained	56676	exon2			CAATTCTGAACAT	AJ400877	CCDS7795.1	11p15.3	2013-10-17	2013-10-17			ENSG00000176009		"Basic helix-loop-helix proteins"	740	protein-coding gene	gene with protein product		609154	"achaete-scute complex (Drosophila) homolog-like 3", "achaete-scute complex homolog 3 (Drosophila)"			11528127	Standard	NM_020646		Approved	bHLHa42, HASH3, Sgn1	uc001mhd.1	Q9NQ33	OTTHUMG00000165679	ENST00000531618.1:c.535A>T	chr11.hg19:g.8959174T>A	ENSP00000435770:p.Arg179*	78.0	0.0		85.0	4.0	NM_020646	Q8WYQ6	Nonsense_Mutation	SNP	ENST00000531618.1	hg19	CCDS7795.1	.	.	.	.	.	.	.	.	.	.	T	12.74	2.028248	0.35797	.	.	ENSG00000176009	ENST00000325884;ENST00000531618	.	.	.	5.67	4.47	0.54385	.	0.325654	0.26514	N	0.023960	.	.	.	.	.	.	0.26563	N	0.973703	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.0869	9.3574	0.38175	0.0:0.0:0.18:0.82	.	.	.	.	X	179	.	ENSP00000318846:R179X	R	-	1	2	ASCL3	8915750	1.000000	0.71417	1.000000	0.80357	0.043000	0.13939	2.800000	0.47900	2.285000	0.76669	0.528000	0.53228	AGA	.	.		0.393	ASCL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385773.1			A	8959174	T	A	8959174	4	1	310	1	0	0	0	0	0	1	0	0	1035	1588	55	4	14	4	ASCL3	11	8959174	Nonsense_Mutation	SNP	T	TCGA-K7-A5RG-01A-11D-A28X-10	2316063	8959174	126047342	69	44170										
EXT2	2132	hgsc.bcm.edu	37	chr11	44255728	44255728	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	agaactgggtagatgctcatAtgaactgtgaagatattgcc	11	6	1	5			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr11:44255728A>G	ENST00000343631.3	+	12	1999	c.1870A>G	c.(1870-1872)Atg>Gtg	p.M624V	EXT2_ENST00000358681.4_Missense_Mutation_p.M634V|EXT2_ENST00000395673.3_Missense_Mutation_p.M657V|EXT2_ENST00000533608.1_Missense_Mutation_p.M624V			Q93063	EXT2_HUMAN	exostosin glycosyltransferase 2	624	Substrate binding. {ECO:0000250|UniProtKB:Q9ES89}.				carbohydrate metabolic process (GO:0005975)|cell differentiation (GO:0030154)|cellular polysaccharide biosynthetic process (GO:0033692)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0015014)|mesoderm formation (GO:0001707)|ossification (GO:0001503)|protein glycosylation (GO:0006486)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|membrane (GO:0016020)	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)|glucuronosyltransferase activity (GO:0015020)|heparan sulfate N-acetylglucosaminyltransferase activity (GO:0042328)|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity (GO:0050509)|protein heterodimerization activity (GO:0046982)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|lung(17)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	32						AGATGCTCATATGAACTGTGA	0.408			"Mis, N, F, S"			"exostoses, osteosarcoma"			Hereditary Multiple Exostoses																												p.M657V		Atlas-SNP	.	yes	Rec		Multiple Exostoses Type 2	11	11p12-p11	2132	multiple exostoses type 2 gene		M	.	EXT2	129	.	0			c.A1969G						.						115	108	111					11																	44255728		2203	4299	6502	SO:0001583	missense	2132	exon12	Familial Cancer Database	HME, Hereditary Exostoses, Multiple Osteochondromatosis, Multiple Cartilaginous Exostoses	GCTCATATGAACT		CCDS7908.1, CCDS53618.1, CCDS53619.1	11p12-p11	2014-09-17	2013-03-01		ENSG00000151348	ENSG00000151348	2.4.1.224, 2.4.1.225	"Exostosin glycosyltransferase family"	3513	protein-coding gene	gene with protein product	"Glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase", "N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase"	608210	"exostoses (multiple) 2", "exostosin 2"			8162019, 9576285	Standard	NM_000401		Approved	SOTV	uc001mya.3	Q93063	OTTHUMG00000166498	ENST00000343631.3:c.1870A>G	chr11.hg19:g.44255728A>G	ENSP00000342656:p.Met624Val	160.0	0.0		195.0	31.0	NM_000401	B2R5Z6|C9JU51|J3KPT2|O15288	Missense_Mutation	SNP	ENST00000343631.3	hg19	CCDS7908.1	.	.	.	.	.	.	.	.	.	.	A	17.15	3.315620	0.60524	.	.	ENSG00000151348	ENST00000533608;ENST00000358681;ENST00000395673;ENST00000343631	T;T;T;T	0.76448	-1.02;-1.02;-1.02;-1.02	5.64	5.64	0.86602	EXTL2, alpha-1,4-N-acetylhexosaminyltransferase (1);	0.000000	0.85682	D	0.000000	D	0.88411	0.6429	M	0.85945	2.785	0.80722	D	1	D;D;D;D;D	0.76494	0.985;0.994;0.992;0.996;0.999	D;D;D;D;D	0.72625	0.977;0.946;0.911;0.946;0.978	D	0.87648	0.2526	10	0.30078	T	0.28	-6.5982	15.8713	0.79122	1.0:0.0:0.0:0.0	.	624;634;634;624;637	Q6NUL1;C9JU51;Q93063-2;Q93063;D3DR24	.;.;.;EXT2_HUMAN;.	V	624;634;657;624	ENSP00000431173:M624V;ENSP00000351509:M634V;ENSP00000379032:M657V;ENSP00000342656:M624V	ENSP00000342656:M624V	M	+	1	0	EXT2	44212304	1.000000	0.71417	0.966000	0.40874	0.391000	0.30476	9.339000	0.96797	2.144000	0.66660	0.533000	0.62120	ATG	.	.		0.408	EXT2-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390074.1	NM_000401		G	44255728	A	G	44255728	3	3	310	1	0	0	0	0	1	0	0	0	5326	449	16	2	2112	2	EXT2	11	44255728	Missense_Mutation	SNP	A	TCGA-K7-A5RG-01A-11D-A28X-10	35296554	44255728	90750788	70	44171										
ALX4	60529	hgsc.bcm.edu	37	chr11	44289129	44289129	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	cctgctgcatctgcccaaaaCgctcccgcttcctccacttg	6	19	1	0	rs368050443		TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr11:44289129C>T	ENST00000329255.3	-	3	924	c.821G>A	c.(820-822)cGt>cAt	p.R274H		NM_021926.3	NP_068745.2	Q9H161	ALX4_HUMAN	ALX homeobox 4	274					anterior/posterior pattern specification (GO:0009952)|digestive tract development (GO:0048565)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal system morphogenesis (GO:0048704)|hair follicle development (GO:0001942)|muscle organ development (GO:0007517)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of apoptotic process (GO:0042981)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R274H(1)		central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	16						CTGCCCAAAACGCTCCCGCTT	0.597																																					p.R274H		Atlas-SNP	.											ALX4,right_upper_lobe,carcinoma,-1,1	ALX4	58	.	1	Substitution - Missense(1)	lung(1)	c.G821A						.	C	HIS/ARG	0,4406		0,0,2203	179	146	157		821	4.9	1	11		157	1,8597	1.2+/-3.3	0,1,4298	no	missense	ALX4	NM_021926.3	29	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	274/412	44289129	1,13003	2203	4299	6502	SO:0001583	missense	60529	exon3			CCAAAACGCTCCC	AF294629	CCDS31468.1	11p11.2	2011-06-20	2008-11-04		ENSG00000052850	ENSG00000052850		"Homeoboxes / PRD class"	450	protein-coding gene	gene with protein product		605420	"parietal foramina 2", "aristaless-like homeobox 4"	PFM2		11017806, 8644736	Standard	NM_021926		Approved	FPP, PFM, KIAA1788	uc001myb.3	Q9H161	OTTHUMG00000166557	ENST00000329255.3:c.821G>A	chr11.hg19:g.44289129C>T	ENSP00000332744:p.Arg274His	107.0	0.0		206.0	33.0	NM_021926	Q96JN7|Q9H198|Q9HAY9	Missense_Mutation	SNP	ENST00000329255.3	hg19	CCDS31468.1	.	.	.	.	.	.	.	.	.	.	C	36	5.646267	0.96704	0.0	1.16E-4	ENSG00000052850	ENST00000329255	D	0.92965	-3.14	4.88	4.88	0.63580	Homeobox (1);Homeodomain-like (1);	0.116529	0.64402	D	0.000018	D	0.95853	0.8650	M	0.75777	2.31	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	D	0.96120	0.9084	10	0.87932	D	0	.	18.578	0.91162	0.0:1.0:0.0:0.0	.	274	Q9H161	ALX4_HUMAN	H	274	ENSP00000332744:R274H	ENSP00000332744:R274H	R	-	2	0	ALX4	44245705	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	5.817000	0.69229	2.700000	0.92200	0.462000	0.41574	CGT	.	.		0.597	ALX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390399.1			T	44289129	C	T	44289129	3	4	310	1	0	0	0	0	1	0	0	0	558	536	19	1	422	1	ALX4	11	44289129	Missense_Mutation	SNP	C	TCGA-K7-A5RG-01A-11D-A28X-10	33401	44289129	90717387	71	44172										
NR1H3	10062	hgsc.bcm.edu	37	chr11	47282864	47282864	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ggaacaggctcatgccacatCcttgccccccagggcttcct	9	17	1	0			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr11:47282864C>T	ENST00000467728.1	+	4	1810	c.572C>T	c.(571-573)tCc>tTc	p.S191F	NR1H3_ENST00000405576.1_Missense_Mutation_p.S146F|NR1H3_ENST00000405853.3_Missense_Mutation_p.S191F|NR1H3_ENST00000527949.1_Missense_Mutation_p.S100F|NR1H3_ENST00000481889.2_Missense_Mutation_p.S146F|NR1H3_ENST00000407404.1_Missense_Mutation_p.S191F|NR1H3_ENST00000529540.1_3'UTR|NR1H3_ENST00000395397.3_Missense_Mutation_p.S146F|NR1H3_ENST00000441012.2_Missense_Mutation_p.S191F			Q13133	NR1H3_HUMAN	nuclear receptor subfamily 1, group H, member 3	191					apoptotic cell clearance (GO:0043277)|cellular lipid metabolic process (GO:0044255)|cellular response to lipopolysaccharide (GO:0071222)|cholesterol homeostasis (GO:0042632)|gene expression (GO:0010467)|lipid homeostasis (GO:0055088)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of lipid transport (GO:0032369)|negative regulation of macrophage activation (GO:0043031)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of pinocytosis (GO:0048550)|negative regulation of proteolysis (GO:0045861)|negative regulation of secretion of lysosomal enzymes (GO:0090341)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of cholesterol transport (GO:0032376)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cholesterol homeostasis (GO:2000188)|regulation of circadian rhythm (GO:0042752)|response to progesterone (GO:0032570)|sterol homeostasis (GO:0055092)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cholesterol binding (GO:0015485)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|steroid hormone receptor activity (GO:0003707)|sterol response element binding (GO:0032810)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|ovary(5)	20						CATGCCACATCCTTGCCCCCC	0.582																																					p.S197F		Atlas-SNP	.											.	NR1H3	52	.	0			c.C590T						.						63	61	62					11																	47282864		2201	4298	6499	SO:0001583	missense	10062	exon5			CCACATCCTTGCC	U22662	CCDS7929.1, CCDS44584.1, CCDS44585.1, CCDS73285.1	11p11.2	2013-01-16			ENSG00000025434	ENSG00000025434		"Nuclear hormone receptors"	7966	protein-coding gene	gene with protein product	"liver X receptor-alpha"	602423				8621574, 7744246	Standard	NM_005693		Approved	LXR-a, RLD-1	uc009ylm.3	Q13133	OTTHUMG00000150628	ENST00000467728.1:c.572C>T	chr11.hg19:g.47282864C>T	ENSP00000420656:p.Ser191Phe	165.0	0.0		210.0	32.0	NM_001251934	A8K3J9|D3DQR1|Q8IW13|Q96H87	Missense_Mutation	SNP	ENST00000467728.1	hg19	CCDS7929.1	.	.	.	.	.	.	.	.	.	.	C	13.41	2.227501	0.39399	.	.	ENSG00000025434	ENST00000395397;ENST00000405576;ENST00000481889;ENST00000436778;ENST00000531660;ENST00000407404;ENST00000444396;ENST00000449369;ENST00000441012;ENST00000436029;ENST00000467728;ENST00000405853;ENST00000527949	D;D;D;D;T;D;D;D;D;D;D;D;D	0.94613	-3.01;-3.28;-3.15;-2.49;0.85;-3.29;-2.67;-2.5;-3.02;-2.52;-3.02;-3.29;-3.47	5.33	5.33	0.75918	.	1.295660	0.05288	N	0.520526	D	0.93236	0.7845	L	0.32530	0.975	0.09310	N	1	P;B;B;P;B	0.47350	0.545;0.13;0.075;0.894;0.338	B;B;B;P;B	0.47044	0.261;0.094;0.057;0.535;0.168	D	0.84986	0.0891	10	0.62326	D	0.03	.	11.0246	0.47739	0.0:0.8852:0.0:0.1148	.	197;146;191;146;191	B4DXU5;B5MBY7;Q13133;E9PLL4;Q13133-2	.;.;NR1H3_HUMAN;.;.	F	146;146;146;191;57;191;191;191;191;191;191;191;100	ENSP00000378793:S146F;ENSP00000385073:S146F;ENSP00000433271:S146F;ENSP00000403798:S191F;ENSP00000434650:S57F;ENSP00000385801:S191F;ENSP00000391005:S191F;ENSP00000415591:S191F;ENSP00000387946:S191F;ENSP00000403696:S191F;ENSP00000420656:S191F;ENSP00000384745:S191F;ENSP00000432073:S100F	ENSP00000378793:S146F	S	+	2	0	NR1H3	47239440	0.090000	0.21635	0.010000	0.14722	0.723000	0.41478	3.648000	0.54410	2.871000	0.98454	0.655000	0.94253	TCC	.	.		0.582	NR1H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319214.3			T	47282864	C	T	47282864	3	4	310	1	0	0	0	0	1	0	0	0	10627	855	30	3	586	3	NR1H3	11	47282864	Missense_Mutation	SNP	C	TCGA-K7-A5RG-01A-11D-A28X-10	2993735	47282864	87723652	72	44173										
GLYATL2	219970	hgsc.bcm.edu	37	chr11	58602018	58602018	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	attatctgccacatggaaatAaaatgggatttctttctgag	8	6	3	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr11:58602018A>C	ENST00000287275.1	-	6	1159	c.769T>G	c.(769-771)Tat>Gat	p.Y257D	GLYATL2_ENST00000532258.1_Missense_Mutation_p.Y257D|GLYATL2_ENST00000533636.1_5'Flank	NM_145016.3	NP_659453.3	Q8WU03	GLYL2_HUMAN	glycine-N-acyltransferase-like 2	257						endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)			breast(1)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	23		Breast(21;0.0044)|all_epithelial(135;0.0216)			Glycine(DB00145)	ACATGGAAATAAAATGGGATT	0.403																																					p.Y257D		Atlas-SNP	.											.	GLYATL2	40	.	0			c.T769G						.						96	91	93					11																	58602018		1862	4102	5964	SO:0001583	missense	219970	exon6			GGAAATAAAATGG	AF426250	CCDS41649.1	11q12.1	2008-02-05				ENSG00000156689			24178	protein-coding gene	gene with protein product		614762				12477932	Standard	NM_145016		Approved	BXMAS2-10, MGC24009	uc001nnd.4	Q8WU03		ENST00000287275.1:c.769T>G	chr11.hg19:g.58602018A>C	ENSP00000287275:p.Tyr257Asp	74.0	0.0		75.0	15.0	NM_145016	A5LGC7|Q86WC3|Q96AT2	Missense_Mutation	SNP	ENST00000287275.1	hg19	CCDS41649.1	.	.	.	.	.	.	.	.	.	.	A	15.29	2.788922	0.49997	.	.	ENSG00000156689	ENST00000287275;ENST00000532258	T;T	0.18016	2.24;2.24	3.65	3.65	0.41850	Acyl-CoA N-acyltransferase (2);Glycine N-acyltransferase, C-terminal (1);	0.215315	0.30714	U	0.009036	T	0.38321	0.1036	M	0.78916	2.43	0.09310	N	1	D	0.89917	1.0	D	0.72982	0.979	T	0.11518	-1.0584	10	0.72032	D	0.01	.	8.7865	0.34823	1.0:0.0:0.0:0.0	.	257	Q8WU03	GLYL2_HUMAN	D	257	ENSP00000287275:Y257D;ENSP00000434277:Y257D	ENSP00000287275:Y257D	Y	-	1	0	GLYATL2	58358594	0.149000	0.22717	0.050000	0.19076	0.332000	0.28634	2.008000	0.40893	1.321000	0.45227	0.467000	0.42956	TAT	.	.		0.403	GLYATL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394599.1	NM_145016		C	58602018	A	C	58602018	3	2	310	1	0	0	0	0	1	0	0	0	6489	362	13	5	119	5	GLYATL2	11	58602018	Missense_Mutation	SNP	A	TCGA-K7-A5RG-01A-11D-A28X-10	11319154	58602018	76404498	73	44174										
PLA2G16	11145	hgsc.bcm.edu	37	chr11	63365558	63365558	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ggggccagatgaaccacataTccatcgccaacatagatggc	10	12	0	3			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr11:63365558T>C	ENST00000323646.5	-	2	447	c.93A>G	c.(91-93)ggA>ggG	p.G31G	PLA2G16_ENST00000415826.1_Silent_p.G31G|PLA2G16_ENST00000394613.3_5'UTR	NM_007069.3	NP_009000.2	P53816	HRSL3_HUMAN	phospholipase A2, group XVI	31					glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|negative regulation of cell cycle (GO:0045786)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	1-acyl-2-lysophosphatidylserine acylhydrolase activity (GO:0052740)|phosphatidylcholine 1-acylhydrolase activity (GO:0008970)|phosphatidylserine 1-acylhydrolase activity (GO:0052739)|phospholipase A2 activity (GO:0004623)			kidney(2)|lung(1)|ovary(1)|skin(1)	5						GAACCACATATCCATCGCCAA	0.547																																					p.G31G		Atlas-SNP	.											.	PLA2G16	12	.	0			c.A93G						.						122	99	107					11																	63365558		2201	4298	6499	SO:0001819	synonymous_variant	11145	exon3			CACATATCCATCG	X92814	CCDS8047.1	11q12.3	2014-03-14	2008-09-19	2008-09-19	ENSG00000176485	ENSG00000176485	3.1.1.4		17825	protein-coding gene	gene with protein product	"adipose-specific PLA2"	613867	"HRAS-like suppressor 3"	HRASLS3		9771974, 18614531	Standard	NM_007069		Approved	HREV107, H-REV107-1, HREV107-3, MGC118754., AdPLA	uc009you.1	P53816	OTTHUMG00000167852	ENST00000323646.5:c.93A>G	chr11.hg19:g.63365558T>C		268.0	0.0		271.0	42.0	NM_001128203	B2R7Q4|B7XAK5|Q3SYI3|Q9HDD1	Silent	SNP	ENST00000323646.5	hg19	CCDS8047.1																																																																																			.	.		0.547	PLA2G16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396632.1	NM_001128203		C	63365558	T	C	63365558	2	2	310	1	0	0	0	0	0	0	0	1	12002	1422	50	2		2	PLA2G16	11	63365558	Silent	SNP	T	TCGA-K7-A5RG-01A-11D-A28X-10	4763540	63365558	71640958	74	44175										
PRB3	5544	hgsc.bcm.edu	37	chr12	11420457	11420583	+	Frame_Shift_Del	DEL	GAGGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGAAGGTGGTCCTTCTGGCTTTCCTGGACGAGGTGGGGGACCTTGGGACTGGTTTCCTCCTTGTGGGGGTGGTCCTTCTGGCTTTCCTGGAC	GAGGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGAAGGTGGTCCTTCTGGCTTTCCTGGACGAGGTGGGGGACCTTGGGACTGGTTTCCTCCTTGTGGGGGTGGTCCTTCTGGCTTTCCTGGAC	-													0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ggtccttctggctttcctggAcgaggtgggggaccttgagg					rs367917023|rs552923329|rs12811806|rs200902635|rs570697251|rs113884749|rs11054203|rs370173277|rs28435564|rs112526960|rs375731986|rs12368171|rs200117404|rs12811811|rs539718896|rs550913655	byFrequency	TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	GAGGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGAAGGTGGTCCTTCTGGCTTTCCTGGACGAGGTGGGGGACCTTGGGACTGGTTTCCTCCTTGTGGGGGTGGTCCTTCTGGCTTTCCTGGAC	GAGGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGAAGGTGGTCCTTCTGGCTTTCCTGGACGAGGTGGGGGACCTTGGGACTGGTTTCCTCCTTGTGGGGGTGGTCCTTCTGGCTTTCCTGGAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr12:11420457_11420583delGAGGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGAAGGTGGTCCTTCTGGCTTTCCTGGACGAGGTGGGGGACCTTGGGACTGGTTTCCTCCTTGTGGGGGTGGTCCTTCTGGCTTTCCTGGAC	ENST00000279573.7	-	3	735_861	c.600_726delGTCCAGGAAAGCCAGAAGGACCACCCCCACAAGGAGGAAACCAGTCCCAAGGTCCCCCACCTCGTCCAGGAAAGCCAGAAGGACCACCTTCACAAGGAGGCAACAAACCTCAAGGTCCCCCACCCTC	c.(598-726)cggtccaggaaagccagaaggaccacccccacaaggaggaaaccagtcccaaggtcccccacctcgtccaggaaagccagaaggaccaccttcacaaggaggcaacaaacctcaaggtcccccaccctcfs	p.RSRKARRTTPTRRKPVPRSPTSSRKARRTTFTRRQQTSRSPTL200fs	PRB3_ENST00000538488.1_Splice_Site_p.RSRKARRTTPTRRKPVPRSPTSSR179fs|PRB3_ENST00000381842.3_Splice_Site_p.RSR200fs|PRB3_ENST00000440870.3_Intron			Q04118	PRB3_HUMAN	proline-rich protein BstNI subfamily 3	200	10 X 21 AA tandem repeats of [RH]-P-G-K- P-[EQ]-G-[PQS]-P-[PS]-Q-[GE]-G-N-[QK]- [SP]-[QR]-[GR]-P-P-P.|Pro-rich.		Missing (in allele S).		defense response to Gram-negative bacterium (GO:0050829)	extracellular region (GO:0005576)		p.Q193K(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|skin(5)	25			OV - Ovarian serous cystadenocarcinoma(49;0.201)			GCTTTCCTGGACGAGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGGGGGTGGTCCTTCTGGCTTTCCCGGACGAGGTGGGGGACCTTGGGACTGGTTTCCTCCTTGTGGGGGTGGTCCTTCTGGCTTTCCCGGACGAGGTGGGG	0.618																																					p.242_242del		Pindel	.											PRB3_ENST00000538488,caecum,carcinoma,0,2	PRB3	84	.	1	Substitution - Missense(1)	endometrium(1)	c.725_725del						.																																			SO:0001589	frameshift_variant	5544	exon4			.			12p13.2	2012-10-02				ENSG00000197870			9339	protein-coding gene	gene with protein product		168840				1894623	Standard	NM_006249		Approved	PRG	uc001qzs.3	Q04118		ENST00000279573.7:c.600_726delGTCCAGGAAAGCCAGAAGGACCACCCCCACAAGGAGGAAACCAGTCCCAAGGTCCCCCACCTCGTCCAGGAAAGCCAGAAGGACCACCTTCACAAGGAGGCAACAAACCTCAAGGTCCCCCACCCTC	chr12.hg19:g.11420457_11420583delGAGGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGAAGGTGGTCCTTCTGGCTTTCCTGGACGAGGTGGGGGACCTTGGGACTGGTTTCCTCCTTGTGGGGGTGGTCCTTCTGGCTTTCCTGGAC	ENSP00000279573:p.Arg200fs	85.0	0.0		100.0	13.0	NM_006249	Q15188|Q4VAY3|Q4VAY4|Q7M4M9|Q9UCT9	Frame_Shift_Del	DEL	ENST00000279573.7	hg19																																																																																				.	.		0.618	PRB3-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000402119.5	NM_006249		-	11420583	GAGGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGAAGGTGGTCCTTCTGGCTTTCCTGGACGAGGTGGGGGACCTTGGGACTGGTTTCCTCCTTGTGGGGGTGGTCCTTCTGGCTTTCCTGGAC	-	11420457	7	5	310	1	0	1	0	1	0	0	0	0	12456	289	10	0	211	0	PRB3	12	11420457	Frame_Shift_Del	DEL	GAGGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGAAGGTGGTCCTTCTGGCTTTCCTGGACGAGGTGGGGGACCTTGGGACTGGTTTCCTCCTTGTGGGGGTGGTCCTTCTGGCTTTCCTGGAC	TCGA-K7-A5RG-01A-11D-A28X-10		11420457	122431438	75	44176										
WNT1	7471	hgsc.bcm.edu	37	chr12	49374980	49374980	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	agtgcaagtgccacgggatgTccggctcatgcacggtgcgc	15	12	1	0			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr12:49374980T>C	ENST00000293549.3	+	4	706	c.670T>C	c.(670-672)Tcc>Ccc	p.S224P		NM_005430.3	NP_005421.1	P04628	WNT1_HUMAN	wingless-type MMTV integration site family, member 1	224					bone development (GO:0060348)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to peptide hormone stimulus (GO:0071375)|central nervous system morphogenesis (GO:0021551)|cerebellum formation (GO:0021588)|diencephalon development (GO:0021536)|embryonic axis specification (GO:0000578)|forebrain anterior/posterior pattern specification (GO:0021797)|hematopoietic stem cell proliferation (GO:0071425)|hepatocyte differentiation (GO:0070365)|inner ear morphogenesis (GO:0042472)|midbrain development (GO:0030901)|midbrain-hindbrain boundary maturation during brain development (GO:0022004)|myoblast fusion (GO:0007520)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell aging (GO:0090344)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron differentiation (GO:0030182)|neuron fate determination (GO:0048664)|organ regeneration (GO:0031100)|positive regulation of cell proliferation (GO:0008284)|positive regulation of dermatome development (GO:0061184)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to wounding (GO:0009611)|signal transduction in response to DNA damage (GO:0042770)|Spemann organizer formation (GO:0060061)|spinal cord association neuron differentiation (GO:0021527)|T cell differentiation in thymus (GO:0033077)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)	11				BRCA - Breast invasive adenocarcinoma(357;0.244)		CCACGGGATGTCCGGCTCATG	0.687																																					p.S224P		Atlas-SNP	.											.	WNT1	13	.	0			c.T670C						.						28	26	26					12																	49374980		2177	4263	6440	SO:0001583	missense	7471	exon4			GGGATGTCCGGCT	X03072	CCDS8776.1	12q13	2013-02-28				ENSG00000125084		"Wingless-type MMTV integration sites", "Endogenous ligands"	12774	protein-coding gene	gene with protein product		164820		INT1		2998762, 3281802	Standard	NM_005430		Approved		uc001rsu.3	P04628	OTTHUMG00000170403	ENST00000293549.3:c.670T>C	chr12.hg19:g.49374980T>C	ENSP00000293549:p.Ser224Pro	189.0	0.0		242.0	28.0	NM_005430	Q5U0N2	Missense_Mutation	SNP	ENST00000293549.3	hg19	CCDS8776.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.496640	0.85069	.	.	ENSG00000125084	ENST00000293549;ENST00000380414	D	0.83992	-1.79	4.44	4.44	0.53790	Secreted growth factor Wnt protein, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.93449	0.7910	H	0.96208	3.785	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95074	0.8207	10	0.87932	D	0	.	13.1023	0.59226	0.0:0.0:0.0:1.0	.	224	P04628	WNT1_HUMAN	P	224;60	ENSP00000293549:S224P	ENSP00000293549:S224P	S	+	1	0	WNT1	47661247	1.000000	0.71417	0.996000	0.52242	0.872000	0.50106	7.814000	0.86154	1.997000	0.58415	0.533000	0.62120	TCC	.	.		0.687	WNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408937.1			C	49374980	T	C	49374980	3	2	310	1	0	0	0	0	1	0	0	0	17396	1667	58	2	684	2	WNT1	12	49374980	Missense_Mutation	SNP	T	TCGA-K7-A5RG-01A-11D-A28X-10	37954523	49374980	84476915	76	44177										
OR6C68	403284	hgsc.bcm.edu	37	chr12	55886941	55886941	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	atcttcatctatatcaagccAtctgcaaaagaagaggtaaa	6	8	5	2			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr12:55886941A>G	ENST00000548615.1	+	1	780	c.780A>G	c.(778-780)ccA>ccG	p.P260P	RP11-110A12.2_ENST00000554049.1_RNA|RP11-110A12.2_ENST00000555138.1_RNA|RP11-110A12.2_ENST00000556750.1_RNA|OR6C68_ENST00000379662.1_Silent_p.P265P	NM_001005519.2	NP_001005519.2	A6NDL8	O6C68_HUMAN	olfactory receptor, family 6, subfamily C, member 68	260						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	15						ATATCAAGCCATCTGCAAAAG	0.353																																					p.P260P		Atlas-SNP	.											.	OR6C68	36	.	0			c.A780G						.						72	74	73					12																	55886941		2203	4300	6503	SO:0001819	synonymous_variant	403284	exon1			CAAGCCATCTGCA		CCDS31826.1, CCDS31826.2	12q13.2	2013-09-23			ENSG00000205327	ENSG00000205327		"GPCR / Class A : Olfactory receptors"	31297	protein-coding gene	gene with protein product							Standard	NM_001005519		Approved		uc031qhq.1	A6NDL8	OTTHUMG00000169958	ENST00000548615.1:c.780A>G	chr12.hg19:g.55886941A>G		109.0	0.0		76.0	15.0	NM_001005519		Silent	SNP	ENST00000548615.1	hg19	CCDS31826.2																																																																																			.	.		0.353	OR6C68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406677.1			G	55886941	A	G	55886941	2	3	310	1	0	0	0	0	0	0	0	1	11205	204	8	2		2	OR6C68	12	55886941	Silent	SNP	A	TCGA-K7-A5RG-01A-11D-A28X-10	6511961	55886941	77964954	77	44178										
OR6C4	341418	hgsc.bcm.edu	37	chr12	55945800	55945800	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	acattaatccttctgcaaaaGaaggaggtgctttcaacaaa	7	8	2	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr12:55945800G>T	ENST00000394256.2	+	1	818	c.790G>T	c.(790-792)Gaa>Taa	p.E264*	RP11-110A12.2_ENST00000555138.1_RNA|AC009779.1_ENST00000584743.1_RNA|RP11-110A12.2_ENST00000556750.1_RNA	NM_001005494.1	NP_001005494.1	Q8NGE1	OR6C4_HUMAN	olfactory receptor, family 6, subfamily C, member 4	264						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|skin(1)	11						TTCTGCAAAAGAAGGAGGTGC	0.403																																					p.E264X		Atlas-SNP	.											.	OR6C4	34	.	0			c.G790T						.						101	90	94					12																	55945800		2203	4300	6503	SO:0001587	stop_gained	341418	exon1			GCAAAAGAAGGAG	BK004261	CCDS31827.1	12q14.2	2012-08-09				ENSG00000179626		"GPCR / Class A : Olfactory receptors"	19632	protein-coding gene	gene with protein product							Standard	NM_001005494		Approved		uc010spp.2	Q8NGE1	OTTHUMG00000169959	ENST00000394256.2:c.790G>T	chr12.hg19:g.55945800G>T	ENSP00000377799:p.Glu264*	104.0	0.0		85.0	6.0	NM_001005494	A8MZG7|B2RNN2|Q6IFK1	Nonsense_Mutation	SNP	ENST00000394256.2	hg19	CCDS31827.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.370866	0.82573	.	.	ENSG00000179626	ENST00000394256	.	.	.	4.8	2.96	0.34315	.	0.310695	0.23076	N	0.052206	.	.	.	.	.	.	0.58432	D	0.999997	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	7.5657	0.27876	0.197:0.0:0.803:0.0	.	.	.	.	X	264	.	ENSP00000377799:E264X	E	+	1	0	OR6C4	54232067	0.000000	0.05858	0.836000	0.33094	0.994000	0.84299	-0.457000	0.06745	0.740000	0.32651	0.556000	0.70494	GAA	.	.		0.403	OR6C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406678.1			T	55945800	G	T	55945800	4	4	310	1	0	0	0	0	0	1	0	0	11202	943	33	3	792	3	OR6C4	12	55945800	Nonsense_Mutation	SNP	G	TCGA-K7-A5RG-01A-11D-A28X-10	58859	55945800	77906095	78	44179										
DCTN2	10540	hgsc.bcm.edu	37	chr12	57929270	57929270	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	acacacacacaacaaaccatCtcatattctccagattcata	1	14	3	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr12:57929270C>A	ENST00000548249.1	-	4	528	c.261G>T	c.(259-261)gaG>gaT	p.E87D	DCTN2_ENST00000543672.1_Missense_Mutation_p.E92D|DCTN2_ENST00000537439.1_Missense_Mutation_p.E64D|DCTN2_ENST00000434715.3_Missense_Mutation_p.E92D|DCTN2_ENST00000551400.1_5'UTR	NM_001261412.1|NM_001261413.1	NP_001248341.1|NP_001248342.1	Q13561	DCTN2_HUMAN	dynactin 2 (p50)	87					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|melanosome transport (GO:0032402)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|vesicle (GO:0031982)	motor activity (GO:0003774)|spectrin binding (GO:0030507)			endometrium(1)|large_intestine(4)|lung(2)|ovary(2)|upper_aerodigestive_tract(2)	11						AACAAACCATCTCATATTCTC	0.453																																					p.E89D		Atlas-SNP	.											.	DCTN2	51	.	0			c.G267T						.						135	129	131					12																	57929270		1931	4135	6066	SO:0001583	missense	10540	exon4			AACCATCTCATAT	U50733	CCDS44930.1, CCDS58245.1, CCDS73489.1	12q13.3	2008-05-14				ENSG00000175203			2712	protein-coding gene	gene with protein product		607376				8647893	Standard	NM_001261412		Approved	RBP50, DCTN-50	uc001som.2	Q13561	OTTHUMG00000170124	ENST00000548249.1:c.261G>T	chr12.hg19:g.57929270C>A	ENSP00000447824:p.Glu87Asp	82.0	0.0		87.0	11.0	NM_001261412	B2RBK5|Q86YN2|Q9BW17	Missense_Mutation	SNP	ENST00000548249.1	hg19	CCDS58245.1	.	.	.	.	.	.	.	.	.	.	C	19.43	3.826141	0.71143	.	.	ENSG00000175203	ENST00000548249;ENST00000434715;ENST00000543672;ENST00000537439;ENST00000354743;ENST00000550086;ENST00000550954;ENST00000546670;ENST00000550750	.	.	.	5.22	3.38	0.38709	.	0.000000	0.85682	D	0.000000	T	0.64886	0.2639	L	0.59912	1.85	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.996;0.996;0.998	T	0.62177	-0.6909	9	0.24483	T	0.36	-16.0905	5.3373	0.15965	0.0:0.6489:0.0:0.3511	.	87;92;87	F8WAG8;F5H2S7;Q13561	.;.;DCTN2_HUMAN	D	87;92;92;64;87;52;101;87;64	.	ENSP00000346785:E87D	E	-	3	2	DCTN2	56215537	0.995000	0.38212	1.000000	0.80357	0.994000	0.84299	0.264000	0.18497	1.557000	0.49525	0.655000	0.94253	GAG	.	.		0.453	DCTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407393.2	NM_006400		A	57929270	C	A	57929270	3	1	310	1	0	0	0	0	1	0	0	0	4309	912	32	3	988	3	DCTN2	12	57929270	Missense_Mutation	SNP	C	TCGA-K7-A5RG-01A-11D-A28X-10	1983470	57929270	75922625	79	44180										
TSPAN31	6302	hgsc.bcm.edu	37	chr12	58141073	58141073	+	Nonstop_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	aaccccagtgcctttctatgAgactttggatccttctgact	7	12	2	2			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr12:58141073A>G	ENST00000257910.3	+	6	907	c.633A>G	c.(631-633)tgA>tgG	p.*211W	TSPAN31_ENST00000547472.1_Nonstop_Mutation_p.*128W|CDK4_ENST00000551888.1_5'Flank|TSPAN31_ENST00000547992.1_Nonstop_Mutation_p.*127W	NM_005981.3	NP_005972.1	Q12999	TSN31_HUMAN	tetraspanin 31	0					positive regulation of cell proliferation (GO:0008284)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				endometrium(1)|kidney(1)|lung(5)	7	all_cancers(7;4.96e-69)|Lung NSC(6;5.5e-25)|all_lung(6;3.87e-23)|all_epithelial(6;1.66e-15)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)		GBM - Glioblastoma multiforme(5;4.21e-120)|all cancers(5;3.75e-83)|BRCA - Breast invasive adenocarcinoma(9;0.0294)			CCTTTCTATGAGACTTTGGAT	0.438																																					p.X211W		Atlas-SNP	.											.	TSPAN31	20	.	0			c.A633G						.						110	105	107					12																	58141073		2203	4300	6503	SO:0001578	stop_lost	6302	exon6			TCTATGAGACTTT		CCDS8952.1	12q13-q14	2013-02-14	2005-08-16	2005-08-16		ENSG00000135452		"Tetraspanins"	10539	protein-coding gene	gene with protein product		181035	"sarcoma amplified sequence"	SAS			Standard	NM_005981		Approved		uc001spt.3	Q12999		ENST00000257910.3:c.633A>G	chr12.hg19:g.58141073A>G	ENSP00000257910:p.*211Trpext*6	59.0	0.0		68.0	7.0	NM_005981	O00577|Q53X76	Missense_Mutation	SNP	ENST00000257910.3	hg19	CCDS8952.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.080989	0.76528	.	.	ENSG00000135452	ENST00000257910;ENST00000547992;ENST00000547472	.	.	.	5.18	5.18	0.71444	.	.	.	.	.	.	.	.	.	.	.	0.18873	N	0.999985	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.6273	0.51153	1.0:0.0:0.0:0.0	.	.	.	.	W	211;127;128	.	.	X	+	3	0	TSPAN31	56427340	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	5.291000	0.65667	2.317000	0.78254	0.459000	0.35465	TGA	.	.		0.438	TSPAN31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408778.1			G	58141073	A	G	58141073	4	3	310	1	0	0	0	0	0	0	0	0	16661	317	11	2	655	2	TSPAN31	12	58141073	Nonstop_Mutation	SNP	A	TCGA-K7-A5RG-01A-11D-A28X-10	211803	58141073	75710822	80	44181										
C12orf74	338809	hgsc.bcm.edu	37	chr12	93100546	93100546	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	aagccccaggccgcatctccAcctcgcccactttgaggaga	9	17	1	2			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr12:93100546A>T	ENST00000397833.3	+	2	590	c.139A>T	c.(139-141)Acc>Tcc	p.T47S	C12orf74_ENST00000544406.2_Missense_Mutation_p.T47S	NM_001037671.3|NM_001178097.2	NP_001032760.1|NP_001171568.1	Q32Q52	CL074_HUMAN	chromosome 12 open reading frame 74	47										kidney(1)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(2)	10						CCGCATCTCCACCTCGCCCAC	0.637																																					p.T47S		Atlas-SNP	.											.	C12orf74	17	.	0			c.A139T						.						42	45	44					12																	93100546		1908	4119	6027	SO:0001583	missense	338809	exon2			ATCTCCACCTCGC	BC043363	CCDS41819.1, CCDS53818.1	12q22	2012-08-16			ENSG00000214215	ENSG00000214215			27887	protein-coding gene	gene with protein product						12477932	Standard	NM_001037671		Approved		uc001tch.2	Q32Q52	OTTHUMG00000170105	ENST00000397833.3:c.139A>T	chr12.hg19:g.93100546A>T	ENSP00000380933:p.Thr47Ser	109.0	0.0		113.0	15.0	NM_001037671	F5H4P0	Missense_Mutation	SNP	ENST00000397833.3	hg19	CCDS41819.1	.	.	.	.	.	.	.	.	.	.	A	16.54	3.151659	0.57151	.	.	ENSG00000214215	ENST00000397833;ENST00000544406	.	.	.	4.98	4.98	0.66077	.	.	.	.	.	T	0.48642	0.1511	L	0.27053	0.805	0.22266	N	0.999249	D;D	0.61080	0.989;0.989	D;D	0.64776	0.929;0.929	T	0.38286	-0.9668	8	0.87932	D	0	.	10.9752	0.47461	1.0:0.0:0.0:0.0	.	47;47	F5H4P0;Q32Q52	.;CL074_HUMAN	S	47	.	ENSP00000380933:T47S	T	+	1	0	C12orf74	91624677	0.039000	0.19947	0.777000	0.31699	0.124000	0.20399	2.927000	0.48900	2.090000	0.63153	0.379000	0.24179	ACC	.	.		0.637	C12orf74-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407285.1	NM_001037671		T	93100546	A	T	93100546	3	4	310	1	0	0	0	0	1	0	0	0	1716	159	6	4	141	4	C12orf74	12	93100546	Missense_Mutation	SNP	A	TCGA-K7-A5RG-01A-11D-A28X-10	34959473	93100546	40751349	81	44182										
DAO	1610	hgsc.bcm.edu	37	chr12	109283310	109283310	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	cccagagagctggatatgttCccagattacgggtgagttta	12	8	0	3			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr12:109283310C>A	ENST00000228476.3	+	4	579	c.375C>A	c.(373-375)ttC>ttA	p.F125L	DAO_ENST00000551281.1_Intron	NM_001917.4	NP_001908.3	P14920	OXDA_HUMAN	D-amino-acid oxidase	125					cellular nitrogen compound metabolic process (GO:0034641)|D-alanine catabolic process (GO:0055130)|D-serine catabolic process (GO:0036088)|D-serine metabolic process (GO:0070178)|dopamine biosynthetic process (GO:0042416)|glyoxylate metabolic process (GO:0046487)|leucine metabolic process (GO:0006551)|proline catabolic process (GO:0006562)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	cofactor binding (GO:0048037)|D-amino-acid oxidase activity (GO:0003884)|FAD binding (GO:0071949)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|prostate(2)|skin(1)	26					Flavin adenine dinucleotide(DB03147)	TGGATATGTTCCCAGATTACG	0.557																																					p.F125L		Atlas-SNP	.											DAO,right_lower_lobe,carcinoma,0,1	DAO	58	.	0			c.C375A						.						85	78	80					12																	109283310		2203	4300	6503	SO:0001583	missense	1610	exon4			TATGTTCCCAGAT	D11370	CCDS9122.1	12q24.11	2013-09-20			ENSG00000110887	ENSG00000110887	1.4.3.3		2671	protein-coding gene	gene with protein product		124050				1356107, 8182053	Standard	NM_001917		Approved	DAMOX	uc001tnr.4	P14920	OTTHUMG00000169360	ENST00000228476.3:c.375C>A	chr12.hg19:g.109283310C>A	ENSP00000228476:p.Phe125Leu	97.0	0.0		125.0	11.0	NM_001917	B2R7I5|Q16758|Q8N6R2	Missense_Mutation	SNP	ENST00000228476.3	hg19	CCDS9122.1	.	.	.	.	.	.	.	.	.	.	C	13.12	2.141493	0.37825	.	.	ENSG00000110887	ENST00000228476;ENST00000547768;ENST00000547166	T;T;T	0.79141	-1.24;1.04;-1.24	6.17	1.59	0.23543	FAD dependent oxidoreductase (1);	0.000000	0.85682	D	0.000000	T	0.75613	0.3873	L	0.58583	1.82	0.58432	D	0.999991	D	0.53619	0.961	P	0.52598	0.703	T	0.70930	-0.4738	10	0.10636	T	0.68	-7.7819	9.5736	0.39442	0.0:0.5466:0.0:0.4534	.	125	P14920	OXDA_HUMAN	L	125;2;125	ENSP00000228476:F125L;ENSP00000449967:F2L;ENSP00000447104:F125L	ENSP00000228476:F125L	F	+	3	2	DAO	107807439	0.928000	0.31464	0.999000	0.59377	0.122000	0.20287	-0.097000	0.11042	0.406000	0.25560	-0.137000	0.14449	TTC	.	.		0.557	DAO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403682.1			A	109283310	C	A	109283310	3	1	310	1	0	0	0	0	1	0	0	0	4233	854	30	3	385	3	DAO	12	109283310	Missense_Mutation	SNP	C	TCGA-K7-A5RG-01A-11D-A28X-10	16182764	109283310	24568585	82	44183										
WDR66	144406	hgsc.bcm.edu	37	chr12	122396358	122396358	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	aaagtgtggaattatgaaaaCaaacaatatcttttcagcag	7	5	2	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr12:122396358C>A	ENST00000288912.4	+	12	2765	c.1911C>A	c.(1909-1911)aaC>aaA	p.N637K	WDR66_ENST00000397454.2_Missense_Mutation_p.N637K	NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	637							calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(13)|ovary(2)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)		ATTATGAAAACAAACAATATC	0.473																																					p.N637K	Esophageal Squamous(85;849 1794 49757 52143)	Atlas-SNP	.											.	WDR66	143	.	0			c.C1911A						.						222	217	219					12																	122396358		1886	4109	5995	SO:0001583	missense	144406	exon12			TGAAAACAAACAA	AL833930	CCDS41853.1, CCDS53840.1	12q24.31	2014-07-31			ENSG00000158023	ENSG00000158023		"WD repeat domain containing"	28506	protein-coding gene	gene with protein product						17967944	Standard	NM_001178003		Approved	MGC33630, CaM-IP4	uc009zxk.3	Q8TBY9	OTTHUMG00000168948	ENST00000288912.4:c.1911C>A	chr12.hg19:g.122396358C>A	ENSP00000288912:p.Asn637Lys	111.0	0.0		139.0	17.0	NM_001178003	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Missense_Mutation	SNP	ENST00000288912.4	hg19	CCDS41853.1	.	.	.	.	.	.	.	.	.	.	C	0.005	-2.159081	0.00321	.	.	ENSG00000158023	ENST00000288912;ENST00000397454	T;T	0.63580	1.01;-0.05	5.26	1.12	0.20585	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (2);WD40-repeat-containing domain (1);	0.899953	0.09985	N	0.730460	T	0.25531	0.0621	N	0.01048	-1.04	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.25882	-1.0119	10	0.02654	T	1	.	7.7989	0.29164	0.0712:0.5268:0.2895:0.1125	.	637	Q8TBY9	WDR66_HUMAN	K	637	ENSP00000288912:N637K;ENSP00000380595:N637K	ENSP00000288912:N637K	N	+	3	2	WDR66	120880741	0.001000	0.12720	0.030000	0.17652	0.470000	0.32858	-0.169000	0.09911	0.147000	0.19030	-0.280000	0.10049	AAC	.	.		0.473	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668		A	122396358	C	A	122396358	3	1	310	1	0	0	0	0	1	0	0	0	17332	477	17	3	1953	3	WDR66	12	122396358	Missense_Mutation	SNP	C	TCGA-K7-A5RG-01A-11D-A28X-10	13113048	122396358	11455537	83	44184										
DNAH10	196385	hgsc.bcm.edu	37	chr12	124402197	124402197	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ttacgagaggcgggagctggAggagcagcgggagcacctca	18	9	1	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr12:124402197A>G	ENST00000409039.3	+	63	10740	c.10715A>G	c.(10714-10716)gAg>gGg	p.E3572G		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	3572	AAA 5. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		CGGGAGCTGGAGGAGCAGCGG	0.647																																					p.E3572G		Atlas-SNP	.											.	DNAH10	888	.	0			c.A10715G						.						26	36	33					12																	124402197		1997	4003	6000	SO:0001583	missense	196385	exon63			AGCTGGAGGAGCA	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.10715A>G	chr12.hg19:g.124402197A>G	ENSP00000386770:p.Glu3572Gly	110.0	0.0		166.0	28.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	hg19	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	A	24.0	4.483714	0.84854	.	.	ENSG00000197653	ENST00000409039	T	0.32272	1.46	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	T	0.68997	0.3062	H	0.96777	3.88	0.58432	D	0.999996	D	0.89917	1.0	D	0.87578	0.998	T	0.80946	-0.1155	10	0.87932	D	0	.	14.8445	0.70251	1.0:0.0:0.0:0.0	.	3572	Q8IVF4	DYH10_HUMAN	G	3572	ENSP00000386770:E3572G	ENSP00000386770:E3572G	E	+	2	0	DNAH10	122968150	1.000000	0.71417	1.000000	0.80357	0.760000	0.43138	9.233000	0.95337	1.934000	0.56057	0.260000	0.18958	GAG	.	.		0.647	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			G	124402197	A	G	124402197	3	3	310	1	0	0	0	0	1	0	0	0	4600	304	11	2	10965	2	DNAH10	12	124402197	Missense_Mutation	SNP	A	TCGA-K7-A5RG-01A-11D-A28X-10	2005839	124402197	9449698	84	44185										
SLITRK5	26050	hgsc.bcm.edu	37	chr13	88328465	88328465	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ttccgcttacacggaagggaCttggacgaggtatccaagca	12	10	0	0			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr13:88328465C>A	ENST00000325089.6	+	2	1041	c.822C>A	c.(820-822)gaC>gaA	p.D274E	SLITRK5_ENST00000400028.3_Missense_Mutation_p.D33E	NM_015567.1	NP_056382.1	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5	274	LRRCT 1.				adult behavior (GO:0030534)|axonogenesis (GO:0007409)|cardiovascular system development (GO:0072358)|dendrite morphogenesis (GO:0048813)|grooming behavior (GO:0007625)|response to xenobiotic stimulus (GO:0009410)|skin development (GO:0043588)|striatum development (GO:0021756)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(14)|lung(40)|ovary(2)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(4)	81	all_neural(89;0.101)|Medulloblastoma(90;0.163)					ACGGAAGGGACTTGGACGAGG	0.522																																					p.D274E		Atlas-SNP	.											.	SLITRK5	192	.	0			c.C822A						.						83	84	84					13																	88328465		2203	4300	6503	SO:0001583	missense	26050	exon2			AAGGGACTTGGAC	AB020725	CCDS9465.1	13q31.1	2004-04-16	2004-01-08		ENSG00000165300	ENSG00000165300			20295	protein-coding gene	gene with protein product		609680	"leucine rich repeat containing 11"	LRRC11		10048485, 14557068	Standard	NM_015567		Approved	bA364G4.2, KIAA0918	uc001vln.3	O94991	OTTHUMG00000017167	ENST00000325089.6:c.822C>A	chr13.hg19:g.88328465C>A	ENSP00000366283:p.Asp274Glu	93.0	0.0		121.0	17.0	NM_015567	B3KNB8|B4DSH5|Q5VT81	Missense_Mutation	SNP	ENST00000325089.6	hg19	CCDS9465.1	.	.	.	.	.	.	.	.	.	.	C	13.79	2.341555	0.41498	.	.	ENSG00000165300	ENST00000325089;ENST00000400028	T;T	0.57436	0.4;0.4	5.76	3.0	0.34707	Cysteine-rich flanking region, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.64994	0.2649	M	0.67700	2.07	0.37937	D	0.932184	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.991	T	0.64521	-0.6388	9	.	.	.	-22.7635	7.2612	0.26203	0.0:0.6333:0.0:0.3667	.	33;274	B4DSH5;O94991	.;SLIK5_HUMAN	E	274;33	ENSP00000366283:D274E;ENSP00000442244:D33E	.	D	+	3	2	SLITRK5	87126466	0.306000	0.24490	0.998000	0.56505	0.967000	0.64934	0.274000	0.18680	0.312000	0.23038	0.491000	0.48974	GAC	.	.		0.522	SLITRK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045416.3			A	88328465	C	A	88328465	3	1	310	1	0	0	0	0	1	0	0	0	14761	564	20	3	824	3	SLITRK5	13	88328465	Missense_Mutation	SNP	C	TCGA-K7-A5RG-01A-11D-A28X-10		88328465	26841413	85	44186										
LRFN5	145581	hgsc.bcm.edu	37	chr14	42356745	42356745	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ggagggacaaagggcaacacTgaggtgcaaagccaggggag	18	7	0	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr14:42356745T>C	ENST00000298119.4	+	3	2106	c.917T>C	c.(916-918)cTg>cCg	p.L306P	LRFN5_ENST00000554171.1_Missense_Mutation_p.L306P|LRFN5_ENST00000554120.1_Missense_Mutation_p.L306P	NM_152447.3	NP_689660.2	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III domain containing 5	306	Ig-like.					integral component of membrane (GO:0016021)		p.L306P(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(67)|ovary(5)|pancreas(3)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(2)	120			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		AGGGCAACACTGAGGTGCAAA	0.458										HNSCC(30;0.082)																											p.L306P		Atlas-SNP	.											LRFN5,NS,carcinoma,0,1	LRFN5	269	.	1	Substitution - Missense(1)	endometrium(1)	c.T917C						.						115	109	111					14																	42356745		2203	4300	6503	SO:0001583	missense	145581	exon3			CAACACTGAGGTG	AK055365	CCDS9678.1	14q21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000165379	ENSG00000165379		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	20360	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 8"	612811	"chromosome 14 open reading frame 146"	C14orf146		16828986	Standard	NM_152447		Approved	FIGLER8, SALM5	uc001wvm.3	Q96NI6	OTTHUMG00000140261	ENST00000298119.4:c.917T>C	chr14.hg19:g.42356745T>C	ENSP00000298119:p.Leu306Pro	130.0	0.0		122.0	15.0	NM_152447	B3KU78|Q86XL2	Missense_Mutation	SNP	ENST00000298119.4	hg19	CCDS9678.1	.	.	.	.	.	.	.	.	.	.	T	16.71	3.198632	0.58126	.	.	ENSG00000165379	ENST00000298119;ENST00000554120;ENST00000554171	T;T;T	0.75477	-0.94;-0.94;-0.94	5.4	5.4	0.78164	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.43919	D	0.000502	D	0.91888	0.7432	H	0.99182	4.46	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.94763	0.7938	10	0.87932	D	0	.	13.6708	0.62424	0.0:0.0:0.0:1.0	.	306;306	G3V364;Q96NI6	.;LRFN5_HUMAN	P	306	ENSP00000298119:L306P;ENSP00000451897:L306P;ENSP00000451067:L306P	ENSP00000298119:L306P	L	+	2	0	LRFN5	41426495	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	7.997000	0.88414	2.165000	0.68154	0.460000	0.39030	CTG	.	.		0.458	LRFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276786.1	NM_152447		C	42356745	T	C	42356745	3	2	310	1	0	0	0	0	1	0	0	0	8950	1580	55	2	919	2	LRFN5	14	42356745	Missense_Mutation	SNP	T	TCGA-K7-A5RG-01A-11D-A28X-10		42356745	64992795	86	44187										
C14orf104	55172	hgsc.bcm.edu	37	chr14	50100800	50100800	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	gcggcgacggcgacagcgggCtcccggcgcgcggccggcag	20	16	0	0			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr14:50100800C>A	ENST00000298292.8	-	1	1148	c.1068G>T	c.(1066-1068)gaG>gaT	p.E356D	DNAAF2_ENST00000406043.3_Missense_Mutation_p.E356D	NM_018139.2	NP_060609.2	Q9NVR5	KTU_HUMAN	dynein, axonemal, assembly factor 2	356					axonemal dynein complex assembly (GO:0070286)|bacterial-type flagellum-dependent cell motility (GO:0071973)|cilium-dependent cell motility (GO:0060285)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)				kidney(1)|lung(4)	5						cgacagcgggctcccggcgcg	0.746																																					p.E356D		Atlas-SNP	.											.	DNAAF2	47	.	0			c.G1068T						.						1	1	1					14																	50100800		947	2322	3269	SO:0001583	missense	55172	exon1			AGCGGGCTCCCGG	AK001425	CCDS9691.2, CCDS45100.1	14q21.3	2012-05-03	2011-06-09	2011-06-09	ENSG00000165506	ENSG00000165506			20188	protein-coding gene	gene with protein product	"kintoun"	612517	"chromosome 14 open reading frame 104"	C14orf104			Standard	NM_001083908		Approved	FLJ10563, KTU, PF13, CILD10	uc001wws.4	Q9NVR5	OTTHUMG00000152331	ENST00000298292.8:c.1068G>T	chr14.hg19:g.50100800C>A	ENSP00000298292:p.Glu356Asp	5.0	0.0		10.0	6.0	NM_018139	B9WS54|C0JAP7|Q86TR1|Q86TY8|Q969Z5	Missense_Mutation	SNP	ENST00000298292.8	hg19	CCDS9691.2	.	.	.	.	.	.	.	.	.	.	C	12.03	1.815110	0.32053	.	.	ENSG00000165506	ENST00000298292;ENST00000406043	T;T	0.19250	2.16;2.43	4.1	-6.19	0.02078	.	.	.	.	.	T	0.08358	0.0208	N	0.19112	0.55	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36089	-0.9762	9	0.18276	T	0.48	.	1.5215	0.02517	0.1963:0.1356:0.3649:0.3033	.	356;356	Q9NVR5-2;Q9NVR5	.;KTU_HUMAN	D	356	ENSP00000298292:E356D;ENSP00000384862:E356D	ENSP00000298292:E356D	E	-	3	2	DNAAF2	49170550	0.000000	0.05858	0.000000	0.03702	0.141000	0.21300	-0.250000	0.08830	-1.195000	0.02680	-0.459000	0.05422	GAG	.	.		0.746	DNAAF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276813.1			A	50100800	C	A	50100800	3	1	310	1	0	0	0	0	1	0	0	0	1738	796	28	3	1457	3	C14orf104	14	50100800	Missense_Mutation	SNP	C	TCGA-K7-A5RG-01A-11D-A28X-10	7744055	50100800	57248740	87	44188										
YLPM1	56252	hgsc.bcm.edu	37	chr14	75245225	75245225	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	aagttcatttgccaggacacAaaaagggtcctgtggtagca	11	8	1	0	rs376895690		TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr14:75245225A>G	ENST00000552421.1	+	2	1073	c.949A>G	c.(949-951)Aaa>Gaa	p.K317E	YLPM1_ENST00000325680.7_Missense_Mutation_p.K317E|YLPM1_ENST00000238571.3_Missense_Mutation_p.K317E			P49750	YLPM1_HUMAN	YLP motif containing 1	317					regulation of telomere maintenance (GO:0032204)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	62			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		GCCAGGACACAAAAAGGGTCC	0.438																																					p.K317E		Atlas-SNP	.											.	YLPM1	298	.	0			c.A949G						.	A	GLU/LYS	1,3767		0,1,1883	65	66	66		949	5.4	1	14		66	0,8212		0,0,4106	no	missense	YLPM1	NM_019589.2	56	0,1,5989	GG,GA,AA		0.0,0.0265,0.0083	possibly-damaging	317/2147	75245225	1,11979	1884	4106	5990	SO:0001583	missense	56252	exon2			GGACACAAAAAGG	AK090435	CCDS45135.1	14q24.3	2014-06-13	2004-07-15	2004-07-15	ENSG00000119596	ENSG00000119596			17798	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 169"		"chromosome 14 open reading frame 170"	C14orf170		7596406	Standard	NM_019589		Approved	ZAP, PPP1R169	uc001xqj.4	P49750	OTTHUMG00000172503	ENST00000552421.1:c.949A>G	chr14.hg19:g.75245225A>G	ENSP00000447921:p.Lys317Glu	242.0	0.0		235.0	43.0	NM_019589	P49752|Q96I64|Q9P1V7	Missense_Mutation	SNP	ENST00000552421.1	hg19		.	.	.	.	.	.	.	.	.	.	A	15.04	2.714104	0.48622	2.65E-4	0.0	ENSG00000119596	ENST00000552421;ENST00000325680;ENST00000238571;ENST00000423680	T;T;T	0.22539	1.95;1.95;1.95	5.42	5.42	0.78866	.	0.175257	0.40469	N	0.001087	T	0.10637	0.0260	N	0.14661	0.345	0.23802	N	0.996808	P	0.39480	0.675	B	0.33454	0.164	T	0.20940	-1.0260	10	0.08837	T	0.75	-10.6533	14.0466	0.64708	1.0:0.0:0.0:0.0	.	317	P49750-4	.	E	317;317;317;30	ENSP00000447921:K317E;ENSP00000324463:K317E;ENSP00000238571:K317E	ENSP00000238571:K317E	K	+	1	0	YLPM1	74314978	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.364000	0.44187	2.050000	0.60909	0.482000	0.46254	AAA	.	.		0.438	YLPM1-008	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404450.1	NM_019589		G	75245225	A	G	75245225	3	3	310	1	0	0	0	0	1	0	0	0	17501	131	5	2	955	2	YLPM1	14	75245225	Missense_Mutation	SNP	A	TCGA-K7-A5RG-01A-11D-A28X-10	25144425	75245225	32104315	88	44189										
NEK9	91754	hgsc.bcm.edu	37	chr14	75567697	75567697	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	tgatatgtacagactcaccaTcagtggcagcaatggtaaac	9	9	2	2			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr14:75567697T>G	ENST00000238616.5	-	16	2158	c.2000A>C	c.(1999-2001)gAt>gCt	p.D667A		NM_033116.4	NP_149107.4	Q8TD19	NEK9_HUMAN	NIMA-related kinase 9	667					mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			endometrium(4)|kidney(2)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	31				BRCA - Breast invasive adenocarcinoma(234;0.00718)		AGACTCACCATCAGTGGCAGC	0.468																																					p.D667A		Atlas-SNP	.											.	NEK9	64	.	0			c.A2000C						.						95	90	92					14																	75567697		2203	4300	6503	SO:0001583	missense	91754	exon16			TCACCATCAGTGG	AY048580	CCDS9839.1	14q24.2	2012-11-15	2012-11-15		ENSG00000119638	ENSG00000119638			18591	protein-coding gene	gene with protein product		609798	"NIMA (never in mitosis gene a)- related kinase 9"			11864968	Standard	NM_033116		Approved	Nek8, NERCC, DKFZp434D0935, MGC16714	uc001xrl.3	Q8TD19	OTTHUMG00000171768	ENST00000238616.5:c.2000A>C	chr14.hg19:g.75567697T>G	ENSP00000238616:p.Asp667Ala	80.0	0.0		60.0	5.0	NM_033116	Q52LK6|Q8NCN0|Q8TCY4|Q9UPI4|Q9Y6S4|Q9Y6S5|Q9Y6S6	Missense_Mutation	SNP	ENST00000238616.5	hg19	CCDS9839.1	.	.	.	.	.	.	.	.	.	.	T	9.963	1.223341	0.22457	.	.	ENSG00000119638	ENST00000238616	T	0.80738	-1.41	5.42	5.42	0.78866	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.206143	0.49305	D	0.000142	T	0.62356	0.2421	N	0.12182	0.205	0.41644	D	0.989092	B;B	0.28082	0.0;0.2	B;B	0.28465	0.0;0.09	T	0.60073	-0.7334	10	0.08837	T	0.75	.	11.4589	0.50197	0.0:0.0:0.1504:0.8496	.	667;10	Q8TD19;Q6PKF2	NEK9_HUMAN;.	A	667	ENSP00000238616:D667A	ENSP00000238616:D667A	D	-	2	0	NEK9	74637450	1.000000	0.71417	0.990000	0.47175	0.975000	0.68041	5.024000	0.64090	2.056000	0.61249	0.460000	0.39030	GAT	.	.		0.468	NEK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415021.1	NM_033116		G	75567697	T	G	75567697	3	3	310	1	0	0	0	0	1	0	0	0	10340	1435	50	5	967	5	NEK9	14	75567697	Missense_Mutation	SNP	T	TCGA-K7-A5RG-01A-11D-A28X-10	322472	75567697	31781843	89	44190										
PSMC1	5700	hgsc.bcm.edu	37	chr14	90730490	90730490	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	atgcagatattggggggttgGacaaccaaattcaggaaatt	12	5	1	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr14:90730490G>A	ENST00000261303.8	+	6	674	c.571G>A	c.(571-573)Gac>Aac	p.D191N	PSMC1_ENST00000543772.2_Missense_Mutation_p.D118N	NM_002802.2	NP_002793.2	P62191	PRS4_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 1	191					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(2)|upper_aerodigestive_tract(2)	6		all_cancers(154;0.142)		COAD - Colon adenocarcinoma(157;0.21)		TGGGGGGTTGGACAACCAAAT	0.468																																					p.D191N		Atlas-SNP	.											.	PSMC1	27	.	0			c.G571A						.						50	51	51					14																	90730490		2203	4300	6503	SO:0001583	missense	5700	exon6			GGGTTGGACAACC	L02426	CCDS32139.1	14q32.11	2010-04-21			ENSG00000100764	ENSG00000100764		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9547	protein-coding gene	gene with protein product		602706				9473509	Standard	NM_002802		Approved	S4, p56	uc001xyf.3	P62191		ENST00000261303.8:c.571G>A	chr14.hg19:g.90730490G>A	ENSP00000261303:p.Asp191Asn	91.0	0.0		86.0	12.0	NM_002802	B4DR63|P49014|Q03527|Q6IAW0|Q6NW36|Q96AZ3	Missense_Mutation	SNP	ENST00000261303.8	hg19	CCDS32139.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.633849	0.87660	.	.	ENSG00000100764	ENST00000261303;ENST00000553835;ENST00000543772	D;D;D	0.95518	-3.71;-3.73;-3.71	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	D	0.96642	0.8904	M	0.87617	2.895	0.80722	D	1	P	0.48911	0.917	P	0.46275	0.51	D	0.97403	0.9997	10	0.87932	D	0	-18.9112	19.3931	0.94592	0.0:0.0:1.0:0.0	.	191	P62191	PRS4_HUMAN	N	191;28;118	ENSP00000261303:D191N;ENSP00000452049:D28N;ENSP00000445147:D118N	ENSP00000261303:D191N	D	+	1	0	PSMC1	89800243	1.000000	0.71417	0.988000	0.46212	0.486000	0.33341	9.712000	0.98738	2.669000	0.90835	0.655000	0.94253	GAC	.	.		0.468	PSMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411253.1	NM_002802		A	90730490	G	A	90730490	3	1	310	1	0	0	0	0	1	0	0	0	12697	1174	41	3	593	3	PSMC1	14	90730490	Missense_Mutation	SNP	G	TCGA-K7-A5RG-01A-11D-A28X-10	15162793	90730490	16619050	90	44191										
FSIP1	161835	hgsc.bcm.edu	37	chr15	40031879	40031879	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	tacatacctcaatgtttctcTtaataaaatcctggttgtgt	5	8	2	0			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr15:40031879T>C	ENST00000350221.3	-	7	976	c.767A>G	c.(766-768)aAg>aGg	p.K256R	FSIP1_ENST00000559692.1_5'UTR	NM_152597.4	NP_689810.3	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	256										NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	23		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		AATGTTTCTCTTAATAAAATC	0.338																																					p.K256R		Atlas-SNP	.											.	FSIP1	53	.	0			c.A767G						.						98	95	96					15																	40031879		2202	4295	6497	SO:0001583	missense	161835	exon7			TTTCTCTTAATAA	BC045191	CCDS10050.1	15q14	2012-11-19			ENSG00000150667	ENSG00000150667			21674	protein-coding gene	gene with protein product		615795				14702039	Standard	NM_152597		Approved	FLJ35989	uc001zki.3	Q8NA03	OTTHUMG00000172456	ENST00000350221.3:c.767A>G	chr15.hg19:g.40031879T>C	ENSP00000280236:p.Lys256Arg	30.0	0.0		25.0	6.0	NM_152597	Q6X2C8|Q86Y89	Missense_Mutation	SNP	ENST00000350221.3	hg19	CCDS10050.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.321961	0.81580	.	.	ENSG00000150667	ENST00000350221	T	0.32988	1.43	5.77	5.77	0.91146	.	0.226724	0.35495	N	0.003170	T	0.47820	0.1466	M	0.62723	1.935	0.32348	N	0.558787	D	0.69078	0.997	P	0.60949	0.881	T	0.60276	-0.7295	9	.	.	.	-13.615	12.4875	0.55881	0.0:0.0:0.0:1.0	.	256	Q8NA03	FSIP1_HUMAN	R	256	ENSP00000280236:K256R	.	K	-	2	0	FSIP1	37819171	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.948000	0.56660	2.199000	0.70637	0.533000	0.62120	AAG	.	.		0.338	FSIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252118.2	NM_152597		C	40031879	T	C	40031879	3	2	310	1	0	0	0	0	1	0	0	0	6082	1609	56	2	1002	2	FSIP1	15	40031879	Missense_Mutation	SNP	T	TCGA-K7-A5RG-01A-11D-A28X-10		40031879	62499513	91	44192										
TCF12	6938	hgsc.bcm.edu	37	chr15	57212181	57212181	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	tgagcgacctactggacttcAgtgcggtatgagagctttcc	12	10	1	2			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr15:57212181A>G	ENST00000267811.5	+	2	374	c.70A>G	c.(70-72)Agt>Ggt	p.S24G	TCF12_ENST00000438423.2_Missense_Mutation_p.S24G|TCF12_ENST00000333725.5_Missense_Mutation_p.S24G|TCF12_ENST00000452095.2_Missense_Mutation_p.S24G|ZNF280D_ENST00000559000.1_5'Flank|ZNF280D_ENST00000561122.1_5'Flank|TCF12_ENST00000557843.1_Missense_Mutation_p.S24G	NM_003205.3|NM_207038.1	NP_003196.1|NP_996921.1	Q99081	HTF4_HUMAN	transcription factor 12	24					immune response (GO:0006955)|muscle organ development (GO:0007517)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription factor binding (GO:0008134)		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)		ACTGGACTTCAGTGCGGTATG	0.502			T	TEC	extraskeletal myxoid chondrosarcoma																																p.S24G		Atlas-SNP	.		Dom	yes		15	15q21	6938	"transcription factor 12 (HTF4, helix-loop-helix transcription factors 4)"		M	.	TCF12	242	.	0			c.A70G						.						182	169	174					15																	57212181		2192	4292	6484	SO:0001583	missense	6938	exon2			GACTTCAGTGCGG	BC050556	CCDS10159.1, CCDS10160.1, CCDS42042.1	15q21	2013-05-21	2008-07-31		ENSG00000140262	ENSG00000140262		"Basic helix-loop-helix proteins"	11623	protein-coding gene	gene with protein product	"helix-loop-helix transcription factor 4"	600480				1886779	Standard	NM_003205		Approved	HEB, HTF4, HsT17266, bHLHb20	uc002aeb.3	Q99081	OTTHUMG00000132047	ENST00000267811.5:c.70A>G	chr15.hg19:g.57212181A>G	ENSP00000267811:p.Ser24Gly	149.0	0.0		143.0	20.0	NM_207036	Q7Z3D9|Q86TC1|Q86VM2	Missense_Mutation	SNP	ENST00000267811.5	hg19	CCDS10159.1	.	.	.	.	.	.	.	.	.	.	A	16.86	3.238639	0.58995	.	.	ENSG00000140262	ENST00000543236;ENST00000267811;ENST00000438423;ENST00000452095;ENST00000333725	T;T;T;T	0.24350	1.88;1.86;1.91;1.86	4.1	2.95	0.34219	.	0.046714	0.85682	D	0.000000	T	0.34250	0.0891	M	0.67397	2.05	0.50467	D	0.99987	B;P;B;B	0.41450	0.323;0.75;0.171;0.263	P;B;B;B	0.48571	0.582;0.304;0.067;0.142	T	0.07829	-1.0752	10	0.72032	D	0.01	-4.9583	8.0529	0.30587	0.8187:0.0:0.0:0.1813	.	24;76;24;24	E9PGY0;F5H6Z6;Q99081;Q99081-3	.;.;HTF4_HUMAN;.	G	76;24;24;24;24	ENSP00000267811:S24G;ENSP00000388940:S24G;ENSP00000396881:S24G;ENSP00000331057:S24G	ENSP00000267811:S24G	S	+	1	0	TCF12	54999473	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.658000	0.83755	0.601000	0.29879	0.459000	0.35465	AGT	.	.		0.502	TCF12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255069.3	NM_003205		G	57212181	A	G	57212181	3	3	310	1	0	0	0	0	1	0	0	0	15702	188	7	2	72	2	TCF12	15	57212181	Missense_Mutation	SNP	A	TCGA-K7-A5RG-01A-11D-A28X-10	17180302	57212181	45319211	92	44193										
ZNF592	9640	hgsc.bcm.edu	37	chr15	85327447	85327447	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	cctgaacctcgtcccccacaGtgttgctgcatcagtgacag	9	15	1	2			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr15:85327447G>C	ENST00000560079.2	+	4	1829	c.1541G>C	c.(1540-1542)aGt>aCt	p.S514T	ZNF592_ENST00000299927.3_Missense_Mutation_p.S514T	NM_014630.2	NP_055445.2	Q92610	ZN592_HUMAN	zinc finger protein 592	514					cell death (GO:0008219)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|kidney(1)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(143;0.0587)			GTCCCCCACAGTGTTGCTGCA	0.582																																					p.S514T		Atlas-SNP	.											.	ZNF592	95	.	0			c.G1541C						.						63	50	54					15																	85327447		2203	4299	6502	SO:0001583	missense	9640	exon4			CCCACAGTGTTGC	D86966	CCDS32317.1	15q25.2	2011-03-15				ENSG00000166716		"Zinc fingers, C2H2-type"	28986	protein-coding gene	gene with protein product		613624	"spinocerebellar ataxia, autosomal recessive 5"	SCAR5		9039502, 12030328, 20531441	Standard	NM_014630		Approved	KIAA0211, CAMOS	uc002bld.3	Q92610		ENST00000560079.2:c.1541G>C	chr15.hg19:g.85327447G>C	ENSP00000452877:p.Ser514Thr	154.0	0.0		196.0	34.0	NM_014630	Q2M1T2|Q504Y9	Missense_Mutation	SNP	ENST00000560079.2	hg19	CCDS32317.1	.	.	.	.	.	.	.	.	.	.	G	14.85	2.657638	0.47467	.	.	ENSG00000166716	ENST00000299927	T	0.00625	6.14	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.01800	0.0057	L	0.29908	0.895	0.53688	D	0.99997	D	0.76494	0.999	D	0.73380	0.98	T	0.80446	-0.1379	10	0.31617	T	0.26	-15.2806	16.5914	0.84766	0.0:0.0:1.0:0.0	.	514	Q92610	ZN592_HUMAN	T	514	ENSP00000299927:S514T	ENSP00000299927:S514T	S	+	2	0	ZNF592	83128451	1.000000	0.71417	0.972000	0.41901	0.859000	0.49053	9.438000	0.97539	2.495000	0.84180	0.655000	0.94253	AGT	.	.		0.582	ZNF592-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418779.2	NM_014630		C	85327447	G	C	85327447	3	2	310	1	0	0	0	0	1	0	0	0	18037	1029	36	4	1543	4	ZNF592	15	85327447	Missense_Mutation	SNP	G	TCGA-K7-A5RG-01A-11D-A28X-10	28115266	85327447	17203945	93	44194										
CACNA1H	8912	hgsc.bcm.edu	37	chr16	1254427	1254427	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	gatggccatccttgtcaacaCgctgagcatgggcgtggagt	14	10	1	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr16:1254427C>T	ENST00000348261.5	+	10	2668	c.2420C>T	c.(2419-2421)aCg>aTg	p.T807M	CACNA1H_ENST00000565831.1_Missense_Mutation_p.T807M|RP11-616M22.3_ENST00000564700.1_RNA|CACNA1H_ENST00000358590.4_Missense_Mutation_p.T807M	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	807					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	CTTGTCAACACGCTGAGCATG	0.647																																					p.T807M		Atlas-SNP	.											.	CACNA1H	317	.	0			c.C2420T						.						41	44	43					16																	1254427		2165	4260	6425	SO:0001583	missense	8912	exon10			TCAACACGCTGAG	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.2420C>T	chr16.hg19:g.1254427C>T	ENSP00000334198:p.Thr807Met	192.0	0.0		307.0	59.0	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	hg19	CCDS45375.1	.	.	.	.	.	.	.	.	.	.	C	18.29	3.591890	0.66219	.	.	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.97430	-4.38;-4.38	3.85	3.85	0.44370	.	0.000000	0.85682	D	0.000000	D	0.97829	0.9287	L	0.61036	1.89	0.49299	D	0.999776	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	D	0.98648	1.0678	10	0.87932	D	0	.	14.9329	0.70929	0.0:1.0:0.0:0.0	.	807;807	O95180-2;O95180	.;CAC1H_HUMAN	M	807	ENSP00000334198:T807M;ENSP00000351401:T807M	ENSP00000334198:T807M	T	+	2	0	CACNA1H	1194428	1.000000	0.71417	0.945000	0.38365	0.340000	0.28889	5.691000	0.68249	1.992000	0.58205	0.491000	0.48974	ACG	.	.		0.647	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407		T	1254427	C	T	1254427	3	4	310	1	0	0	0	0	1	0	0	0	2547	536	19	1	2454	1	CACNA1H	16	1254427	Missense_Mutation	SNP	C	TCGA-K7-A5RG-01A-11D-A28X-10		1254427	89100326	94	44195										
MEFV	4210	hgsc.bcm.edu	37	chr16	3298983	3298983	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	tctcagcttcttcagatgctCcagctgcttctgaattttct	6	12	5	2			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr16:3298983C>T	ENST00000219596.1	-	4	1321	c.1282G>A	c.(1282-1284)Gag>Aag	p.E428K	MEFV_ENST00000536379.1_Missense_Mutation_p.E217K|MEFV_ENST00000541159.1_Missense_Mutation_p.E217K|MEFV_ENST00000339854.4_Missense_Mutation_p.E248K	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	428	Required for homotrimerization and induction of pyroptosomes.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						TTCAGATGCTCCAGCTGCTTC	0.502																																					p.E428K		Atlas-SNP	.											.	MEFV	170	.	0			c.G1282A						.						146	134	138					16																	3298983		2197	4300	6497	SO:0001583	missense	4210	exon4			GATGCTCCAGCTG	AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"Tripartite motif containing / Tripartite motif containing"	6998	protein-coding gene	gene with protein product	"pyrin"	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.1282G>A	chr16.hg19:g.3298983C>T	ENSP00000219596:p.Glu428Lys	55.0	0.0		72.0	17.0	NM_000243	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Missense_Mutation	SNP	ENST00000219596.1	hg19	CCDS10498.1	.	.	.	.	.	.	.	.	.	.	C	11.58	1.681645	0.29872	.	.	ENSG00000103313	ENST00000545159;ENST00000219596;ENST00000339854;ENST00000541159;ENST00000536379;ENST00000534868	T;T;T;T	0.57595	0.39;0.39;0.39;0.39	5.5	3.56	0.40772	.	0.234539	0.30142	N	0.010311	T	0.39172	0.1068	L	0.38838	1.175	0.29396	N	0.862296	B	0.22541	0.071	B	0.20184	0.028	T	0.28744	-1.0034	10	0.30854	T	0.27	-18.0346	8.8	0.34903	0.0:0.8256:0.0:0.1744	.	428	O15553	MEFV_HUMAN	K	428;428;248;217;217;217	ENSP00000219596:E428K;ENSP00000339639:E248K;ENSP00000438711:E217K;ENSP00000445079:E217K	ENSP00000219596:E428K	E	-	1	0	MEFV	3238984	0.999000	0.42202	0.917000	0.36280	0.439000	0.31926	0.735000	0.26115	0.810000	0.34279	-0.244000	0.11960	GAG	.	.		0.502	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243		T	3298983	C	T	3298983	3	4	310	1	0	0	0	0	1	0	0	0	9468	864	30	3	1091	3	MEFV	16	3298983	Missense_Mutation	SNP	C	TCGA-K7-A5RG-01A-11D-A28X-10	2044556	3298983	87055770	95	44196										
DNAH3	55567	hgsc.bcm.edu	37	chr16	20981196	20981196	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	atgaccagtttgacagggccTggtgggttctgcatcgactt	13	9	1	2			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr16:20981196T>C	ENST00000261383.3	-	52	8375	c.8376A>G	c.(8374-8376)ccA>ccG	p.P2792P	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	2792	Stalk. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			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)		TGACAGGGCCTGGTGGGTTCT	0.597																																					p.P2792P		Atlas-SNP	.											.	DNAH3	1142	.	0			c.A8376G						.						147	127	134					16																	20981196		2201	4300	6501	SO:0001819	synonymous_variant	55567	exon52			AGGGCCTGGTGGG	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"Axonemal dyneins"	2949	protein-coding gene	gene with protein product		603334	"dynein, axonemal, heavy polypeptide 3"			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.8376A>G	chr16.hg19:g.20981196T>C		109.0	0.0		143.0	26.0	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Silent	SNP	ENST00000261383.3	hg19	CCDS10594.1																																																																																			.	.		0.597	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		C	20981196	T	C	20981196	2	2	310	1	0	0	0	0	0	0	0	1	4605	1567	55	2		2	DNAH3	16	20981196	Silent	SNP	T	TCGA-K7-A5RG-01A-11D-A28X-10	17682213	20981196	69373557	96	44197										
PHKG2	5261	hgsc.bcm.edu	37	chr16	30760208	30760208	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ccgccaaagagttttaccagAagtacgaccctaaggacgtc	9	12	0	2			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr16:30760208A>T	ENST00000563588.1	+	2	306	c.67A>T	c.(67-69)Aag>Tag	p.K23*	PHKG2_ENST00000328273.7_Nonsense_Mutation_p.K23*|PHKG2_ENST00000424889.3_Nonsense_Mutation_p.K23*|RP11-2C24.4_ENST00000483578.1_lincRNA	NM_000294.2	NP_000285.1	P15735	PHKG2_HUMAN	phosphorylase kinase, gamma 2 (testis)	23					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|positive regulation of glycogen catabolic process (GO:0045819)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)	ATP binding (GO:0005524)|phosphorylase kinase activity (GO:0004689)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			ovary(1)|skin(1)	2			Colorectal(24;0.198)			GTTTTACCAGAAGTACGACCC	0.647																																					p.K23X		Atlas-SNP	.											.	PHKG2	29	.	0			c.A67T						.						21	16	18					16																	30760208		2146	4206	6352	SO:0001587	stop_gained	5261	exon2			TACCAGAAGTACG	S73483, M31606	CCDS10690.1, CCDS54002.1	16p11.2	2008-02-05			ENSG00000156873	ENSG00000156873			8931	protein-coding gene	gene with protein product		172471				2915644, 8020963	Standard	NM_000294		Approved		uc021tgo.1	P15735	OTTHUMG00000132400	ENST00000563588.1:c.67A>T	chr16.hg19:g.30760208A>T	ENSP00000455607:p.Lys23*	186.0	0.0		214.0	33.0	NM_001172432	A8K0C7|B4DEB7|E9PEU3|P11800	Nonsense_Mutation	SNP	ENST00000563588.1	hg19	CCDS10690.1	.	.	.	.	.	.	.	.	.	.	A	39	7.741128	0.98465	.	.	ENSG00000156873	ENST00000328273;ENST00000424889	.	.	.	5.38	5.38	0.77491	.	0.000000	0.40064	U	0.001181	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-23.7362	14.4183	0.67165	1.0:0.0:0.0:0.0	.	.	.	.	X	23	.	ENSP00000329968:K23X	K	+	1	0	PHKG2	30667709	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	8.754000	0.91642	2.040000	0.60383	0.529000	0.55759	AAG	.	.		0.647	PHKG2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255531.2	NM_000294		T	30760208	A	T	30760208	4	4	310	1	0	0	0	0	0	1	0	0	11856	247	9	4	69	4	PHKG2	16	30760208	Nonsense_Mutation	SNP	A	TCGA-K7-A5RG-01A-11D-A28X-10	9779012	30760208	59594545	97	44198										
CTCF	10664	hgsc.bcm.edu	37	chr16	67655390	67655390	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ttgtcatgctcggtttacccAaagtggtaccatgaagatgc	10	9	1	2			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr16:67655390A>G	ENST00000264010.4	+	7	1697	c.1253A>G	c.(1252-1254)cAa>cGa	p.Q418R	CTCF_ENST00000401394.1_Missense_Mutation_p.Q90R	NM_006565.3	NP_006556.1	P49711	CTCF_HUMAN	CCCTC-binding factor (zinc finger protein)	418					chromatin modification (GO:0016568)|chromosome segregation (GO:0007059)|DNA methylation (GO:0006306)|maintenance of DNA methylation (GO:0010216)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome positioning (GO:0016584)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone acetylation (GO:0035065)|regulation of histone methylation (GO:0031060)|regulation of molecular function, epigenetic (GO:0040030)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin insulator sequence binding (GO:0043035)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.Q418R(1)		breast(6)|central_nervous_system(2)|cervix(1)|endometrium(34)|haematopoietic_and_lymphoid_tissue(7)|kidney(3)|large_intestine(9)|liver(1)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	79		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0166)|Epithelial(162;0.0577)		CGGTTTACCCAAAGTGGTACC	0.358																																					p.Q418R	Colon(175;1200 1966 6945 23069 27405)	Atlas-SNP	.											CTCF,brainstem,primitive_neuroectodermal_tumour-medulloblastoma,0,1	CTCF	193	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.A1253G						.						112	103	106					16																	67655390		2198	4300	6498	SO:0001583	missense	10664	exon7			TTACCCAAAGTGG	U25435	CCDS10841.1, CCDS54029.1	16q21-q22.3	2013-01-08			ENSG00000102974	ENSG00000102974		"Zinc fingers, C2H2-type"	13723	protein-coding gene	gene with protein product	"11 zinc finger transcriptional repressor"	604167				8649389, 18550811	Standard	NM_006565		Approved		uc002etl.3	P49711	OTTHUMG00000137539	ENST00000264010.4:c.1253A>G	chr16.hg19:g.67655390A>G	ENSP00000264010:p.Gln418Arg	118.0	0.0		122.0	18.0	NM_006565	B5MC38|Q53XI7|Q59EL8	Missense_Mutation	SNP	ENST00000264010.4	hg19	CCDS10841.1	.	.	.	.	.	.	.	.	.	.	A	27.9	4.875391	0.91664	.	.	ENSG00000102974	ENST00000264010;ENST00000401394	T;T	0.07216	3.21;3.21	5.83	5.83	0.93111	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	D	0.000006	T	0.13841	0.0335	N	0.10685	0.025	0.80722	D	1	D	0.59357	0.985	D	0.74023	0.982	T	0.36672	-0.9738	10	0.51188	T	0.08	-3.3406	16.1946	0.82018	1.0:0.0:0.0:0.0	.	418	P49711	CTCF_HUMAN	R	418;90	ENSP00000264010:Q418R;ENSP00000384707:Q90R	ENSP00000264010:Q418R	Q	+	2	0	CTCF	66212891	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	9.339000	0.96797	2.228000	0.72767	0.528000	0.53228	CAA	.	.		0.358	CTCF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268870.2	NM_006565		G	67655390	A	G	67655390	3	3	310	1	0	0	0	0	1	0	0	0	4002	130	5	2	1271	2	CTCF	16	67655390	Missense_Mutation	SNP	A	TCGA-K7-A5RG-01A-11D-A28X-10	36895182	67655390	22699363	98	44199										
TP53	7157	hgsc.bcm.edu	37	chr17	7576928	7576928	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ctggtgttgttgggcagtgcTaggaaagaggcaaggaaagg	18	4	0	1	rs397516439		TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr17:7576928T>C	ENST00000269305.4	-	9	1109		c.e9-2		TP53_ENST00000445888.2_Splice_Site|TP53_ENST00000413465.2_Intron|TP53_ENST00000359597.4_Splice_Site|TP53_ENST00000420246.2_Splice_Site|TP53_ENST00000455263.2_Splice_Site|TP53_ENST00000574684.1_5'Flank	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53						apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.?(28)|p.0?(8)|p.A307fs*34(1)|p.L308fs*31(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TGGGCAGTGCTAGGAAAGAGG	0.493		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											.	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,NS,carcinoma,0,37	TP53	33396	.	38	Unknown(28)|Whole gene deletion(8)|Deletion - Frameshift(2)	lung(11)|upper_aerodigestive_tract(6)|breast(5)|bone(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|urinary_tract(2)|liver(2)|large_intestine(1)|stomach(1)|gastrointestinal_tract_(site_indeterminate)(1)|ovary(1)	c.920-2A>G						.						137	124	129					17																	7576928		2203	4300	6503	SO:0001630	splice_region_variant	7157	exon10	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	CAGTGCTAGGAAA	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.920-2A>G	chr17.hg19:g.7576928T>C		173.0	1.0		193.0	38.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Splice_Site	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	8.085	0.773141	0.16051	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	.	.	.	4.71	3.58	0.41010	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.665	0.28426	0.187:0.0:0.0:0.813	.	.	.	.	.	-1	.	.	.	-	.	.	TP53	7517653	0.089000	0.21612	0.933000	0.37362	0.236000	0.25371	0.838000	0.27572	1.993000	0.58246	0.459000	0.35465	.	.	.		0.493	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	Intron	C	7576928	T	C	7576928	5	2	310	1	0	0	0	0	0	0	1	0	16396	1536	53	2	364	2	TP53	17	7576928	Splice_Site	SNP	T	TCGA-K7-A5RG-01A-11D-A28X-10		7576928	73618282	99	44200										
MYH3	4621	hgsc.bcm.edu	37	chr17	10543955	10543955	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ttttcacaggctttcttgctGtcaatgaattgtccctcagg	8	10	4	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr17:10543955G>T	ENST00000583535.1	-	20	2301	c.2214C>A	c.(2212-2214)gaC>gaA	p.D738E	MYH3_ENST00000226209.7_Missense_Mutation_p.D738E	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	738	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						CTTTCTTGCTGTCAATGAATT	0.438																																					p.D738E		Atlas-SNP	.											.	MYH3	227	.	0			c.C2214A						.						129	113	119					17																	10543955		2203	4300	6503	SO:0001583	missense	4621	exon20			CTTGCTGTCAATG		CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"Myosins / Myosin superfamily : Class II"	7573	protein-coding gene	gene with protein product	"myosin, skeletal, heavy chain, embryonic 1", "muscle embryonic myosin heavy chain 3"	160720	"myosin, heavy polypeptide 3, skeletal muscle, embryonic"			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.2214C>A	chr17.hg19:g.10543955G>T	ENSP00000464317:p.Asp738Glu	119.0	0.0		124.0	5.0	NM_002470	Q15492	Missense_Mutation	SNP	ENST00000583535.1	hg19	CCDS11157.1	.	.	.	.	.	.	.	.	.	.	G	19.59	3.855849	0.71834	.	.	ENSG00000109063	ENST00000226209	T	0.73047	-0.71	5.74	4.77	0.60923	Myosin head, motor domain (2);	.	.	.	.	T	0.78861	0.4350	L	0.53671	1.685	0.41740	D	0.989603	P	0.43392	0.805	P	0.57371	0.819	T	0.79983	-0.1573	9	0.51188	T	0.08	.	15.3689	0.74548	0.0673:0.0:0.9327:0.0	.	738	P11055	MYH3_HUMAN	E	738	ENSP00000226209:D738E	ENSP00000226209:D738E	D	-	3	2	MYH3	10484680	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	3.705000	0.54823	1.568000	0.49683	0.561000	0.74099	GAC	.	.		0.438	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470		T	10543955	G	T	10543955	3	4	310	1	0	0	0	0	1	0	0	0	10045	1368	48	3	3696	3	MYH3	17	10543955	Missense_Mutation	SNP	G	TCGA-K7-A5RG-01A-11D-A28X-10	2967027	10543955	70651255	100	44201										
PIP4K2B	8396	hgsc.bcm.edu	37	chr17	36955561	36955561	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	aggacgctgaggatcggctcGctggcccggaatagcttcac	14	12	1	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr17:36955561G>A	ENST00000269554.3	-	1	597	c.117C>T	c.(115-117)agC>agT	p.S39S	PIP4K2B_ENST00000311500.6_5'UTR	NM_003559.4	NP_003550.1	P78356	PI42B_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, beta	39	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				cell surface receptor signaling pathway (GO:0007166)|intracellular signal transduction (GO:0035556)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|1-phosphatidylinositol-5-phosphate 4-kinase activity (GO:0016309)|ATP binding (GO:0005524)|receptor signaling protein activity (GO:0005057)			endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(8)|ovary(1)	19						GGATCGGCTCGCTGGCCCGGA	0.677																																					p.S39S		Atlas-SNP	.											.	PIP4K2B	35	.	0			c.C117T						.																																			SO:0001819	synonymous_variant	8396	exon1			CGGCTCGCTGGCC	U85245	CCDS11329.1	17q21.2	2007-08-14	2007-08-14	2007-08-14		ENSG00000276293	2.7.1.149		8998	protein-coding gene	gene with protein product		603261	"phosphatidylinositol-4-phosphate 5-kinase, type II, beta"	PIP5K2B		9038203, 14691457, 9367159	Standard	NM_003559		Approved	PIP5KIIB, PIP5KIIbeta	uc002hqs.3	P78356		ENST00000269554.3:c.117C>T	chr17.hg19:g.36955561G>A		58.0	0.0		74.0	17.0	NM_003559	Q5U0E8|Q8TBP2	Silent	SNP	ENST00000269554.3	hg19	CCDS11329.1																																																																																			.	.		0.677	PIP4K2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256791.1	NM_003559		A	36955561	G	A	36955561	2	1	310	1	0	0	0	0	0	0	0	1	11946	1078	38	1		1	PIP4K2B	17	36955561	Silent	SNP	G	TCGA-K7-A5RG-01A-11D-A28X-10	26411606	36955561	44239649	101	44202										
HOXB7	3217	hgsc.bcm.edu	37	chr17	46685442	46685442	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	gggtgtaggtctggcggcctCgtttgcggtcagttcctgca	16	10	2	0			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr17:46685442C>T	ENST00000239165.7	-	2	514	c.416G>A	c.(415-417)cGa>cAa	p.R139Q	HOXB-AS3_ENST00000487849.3_RNA|HOXB-AS3_ENST00000494420.1_RNA|HOXB-AS3_ENST00000491264.1_RNA|HOXB-AS3_ENST00000466037.2_RNA|HOXB7_ENST00000567101.2_5'UTR|HOXB-AS3_ENST00000467155.2_RNA	NM_004502.3	NP_004493.3	P09629	HXB7_HUMAN	homeobox B7	139					anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|multicellular organismal development (GO:0007275)|myeloid cell differentiation (GO:0030099)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	8						CTGGCGGCCTCGTTTGCGGTC	0.577																																					p.R139Q		Atlas-SNP	.											.	HOXB7	15	.	0			c.G416A						.						57	57	57					17																	46685442		2203	4300	6503	SO:0001583	missense	3217	exon2			CGGCCTCGTTTGC		CCDS11532.1	17q21.32	2013-05-22	2005-12-22					"Homeoboxes / ANTP class : HOXL subclass"	5118	protein-coding gene	gene with protein product		142962	"homeo box B7"	HOX2, HOX2C		1973146, 1358459	Standard	NM_004502		Approved		uc002inv.3	P09629	OTTHUMG00000170231	ENST00000239165.7:c.416G>A	chr17.hg19:g.46685442C>T	ENSP00000239165:p.Arg139Gln	74.0	0.0		85.0	10.0	NM_004502	A8K3N8|Q15957|Q53FN3|Q96BQ6	Missense_Mutation	SNP	ENST00000239165.7	hg19	CCDS11532.1	.	.	.	.	.	.	.	.	.	.	C	17.34	3.364794	0.61513	.	.	ENSG00000120087	ENST00000239165	D	0.97066	-4.23	4.58	4.58	0.56647	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.64402	D	0.000003	D	0.97945	0.9324	M	0.91717	3.235	0.51012	D	0.999903	P	0.46912	0.886	P	0.48425	0.577	D	0.99655	1.0992	10	0.87932	D	0	.	17.1969	0.86895	0.0:1.0:0.0:0.0	.	139	P09629	HXB7_HUMAN	Q	139	ENSP00000239165:R139Q	ENSP00000239165:R139Q	R	-	2	0	HOXB7	44040441	0.903000	0.30736	1.000000	0.80357	0.953000	0.61014	5.743000	0.68655	2.357000	0.79964	0.563000	0.77884	CGA	.	.		0.577	HOXB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358097.3			T	46685442	C	T	46685442	3	4	310	1	0	0	0	0	1	0	0	0	7315	884	31	1	241	1	HOXB7	17	46685442	Missense_Mutation	SNP	C	TCGA-K7-A5RG-01A-11D-A28X-10	9729881	46685442	34509768	102	44203										
STARD6	147323	hgsc.bcm.edu	37	chr18	51851176	51851176	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	gaaggcatggttttttcaatTattgatggggacaattttcc	10	5	1	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr18:51851176T>G	ENST00000581310.1	-	9	922	c.549A>C	c.(547-549)atA>atC	p.I183I	STARD6_ENST00000580990.2_Silent_p.I59I|STARD6_ENST00000307844.3_Silent_p.I183I			P59095	STAR6_HUMAN	StAR-related lipid transfer (START) domain containing 6	183	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				lipid transport (GO:0006869)		lipid binding (GO:0008289)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)	8				Colorectal(16;0.021)|READ - Rectum adenocarcinoma(59;0.188)		TTTTTTCAATTATTGATGGGG	0.358																																					p.I183I		Atlas-SNP	.											.	STARD6	19	.	0			c.A549C						.						151	147	148					18																	51851176		2203	4300	6503	SO:0001819	synonymous_variant	147323	exon6			TTCAATTATTGAT	AF480305	CCDS11955.1	18q21.2	2011-09-12	2007-08-16		ENSG00000174448	ENSG00000174448		"StAR-related lipid transfer (START) domain containing"	18066	protein-coding gene	gene with protein product		607051	"START domain containing 6"			12011452	Standard	NM_139171		Approved		uc010xdt.2	P59095	OTTHUMG00000132702	ENST00000581310.1:c.549A>C	chr18.hg19:g.51851176T>G		111.0	0.0		118.0	10.0	NM_139171		Silent	SNP	ENST00000581310.1	hg19	CCDS11955.1																																																																																			.	.		0.358	STARD6-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256000.3	NM_139171		G	51851176	T	G	51851176	2	3	310	1	0	0	0	0	0	0	0	1	15276	1744	61	5		5	STARD6	18	51851176	Silent	SNP	T	TCGA-K7-A5RG-01A-11D-A28X-10		51851176	26226072	103	44204										
CD209	30835	hgsc.bcm.edu	37	chr19	7807945	7807945	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ctacgcaggaggggggtttgGggtggcaggggctggagaaa	22	5	0	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr19:7807945G>T	ENST00000315599.7	-	7	1217	c.1195C>A	c.(1195-1197)Cca>Aca	p.P399T	CD209_ENST00000204801.8_Missense_Mutation_p.P355T|CD209_ENST00000301357.8_Missense_Mutation_p.P263T|CD209_ENST00000593821.1_Missense_Mutation_p.P263T|CD209_ENST00000394173.4_Missense_Mutation_p.P238T|CD209_ENST00000602261.1_Missense_Mutation_p.P307T|CD209_ENST00000394161.5_Missense_Mutation_p.P163T|CD209_ENST00000354397.6_Missense_Mutation_p.P393T|CD209_ENST00000593660.1_Missense_Mutation_p.P329T|CD209_ENST00000601951.1_Missense_Mutation_p.P375T|CD209_ENST00000315591.8_Missense_Mutation_p.P375T	NM_001144895.1|NM_001144897.1|NM_021155.3	NP_001138367.1|NP_001138369.1|NP_066978.1	Q9NNX6	CD209_HUMAN	CD209 molecule	399					antigen processing and presentation (GO:0019882)|cell-cell recognition (GO:0009988)|endocytosis (GO:0006897)|heterophilic cell-cell adhesion (GO:0007157)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|intracellular transport of virus (GO:0075733)|leukocyte cell-cell adhesion (GO:0007159)|modulation by virus of host morphology or physiology (GO:0019048)|peptide antigen transport (GO:0046968)|regulation of T cell proliferation (GO:0042129)|viral genome replication (GO:0019079)|virion attachment to host cell (GO:0019062)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|mannose binding (GO:0005537)|metal ion binding (GO:0046872)|peptide antigen binding (GO:0042605)|virion binding (GO:0046790)			endometrium(7)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						GGGGGGTTTGGGGTGGCAGGG	0.502																																					p.P399T		Atlas-SNP	.											.	CD209	166	.	0			c.C1195A						.						83	88	87					19																	7807945		2203	4300	6503	SO:0001583	missense	30835	exon7			GGTTTGGGGTGGC	M98457	CCDS12186.1, CCDS45949.1, CCDS45950.1, CCDS45951.1, CCDS45952.1, CCDS59344.1, CCDS59345.1	19p13	2011-08-30	2006-03-28			ENSG00000090659		"C-type lectin domain containing", "CD molecules"	1641	protein-coding gene	gene with protein product		604672	"CD209 antigen"			1518869	Standard	NM_021155		Approved	DC-SIGN, CDSIGN, DC-SIGN1, CLEC4L	uc002mht.2	Q9NNX6		ENST00000315599.7:c.1195C>A	chr19.hg19:g.7807945G>T	ENSP00000315477:p.Pro399Thr	66.0	0.0		61.0	11.0	NM_021155	A8KAM4|A8MVQ9|G5E9C4|Q2TB19|Q96QP7|Q96QP8|Q96QP9|Q96QQ0|Q96QQ1|Q96QQ2|Q96QQ3|Q96QQ4|Q96QQ5|Q96QQ6|Q96QQ7|Q96QQ8	Missense_Mutation	SNP	ENST00000315599.7	hg19	CCDS12186.1	.	.	.	.	.	.	.	.	.	.	G	6.878	0.531508	0.13127	.	.	ENSG00000090659	ENST00000315599;ENST00000354397;ENST00000315591;ENST00000204801;ENST00000394173;ENST00000301357;ENST00000394161	T;T;T;T;T;T	0.08984	4.07;4.46;4.05;4.01;4.12;3.03	3.27	1.11	0.20524	.	.	.	.	.	T	0.06781	0.0173	L	0.40543	1.245	0.09310	N	1	P;P;P;P;P;P;P;B;P;P;P	0.49635	0.829;0.926;0.573;0.573;0.893;0.573;0.893;0.295;0.573;0.573;0.573	B;P;B;B;P;B;P;B;B;B;B	0.45506	0.272;0.483;0.19;0.19;0.461;0.19;0.461;0.093;0.258;0.258;0.19	T	0.11842	-1.0571	9	0.06891	T	0.86	.	5.5963	0.17329	0.2604:0.0:0.7396:0.0	.	399;163;393;355;263;375;307;399;329;375;399	B2R907;Q9NNX6-4;Q9NNX6-2;Q9NNX6-7;Q9NNX6-8;Q9NNX6-6;G5E9C4;Q9NNX6;Q9NNX6-11;Q9NNX6-10;Q9NNX6-5	.;.;.;.;.;.;.;CD209_HUMAN;.;.;.	T	399;393;375;355;307;263;163	ENSP00000315477:P399T;ENSP00000346373:P393T;ENSP00000315407:P375T;ENSP00000204801:P355T;ENSP00000301357:P263T;ENSP00000377716:P163T	ENSP00000204801:P355T	P	-	1	0	CD209	7713945	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.342000	0.07801	0.385000	0.24970	-0.448000	0.05591	CCA	.	.		0.502	CD209-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462241.1	NM_021155		T	7807945	G	T	7807945	3	4	310	1	0	0	0	0	1	0	0	0	2986	1232	43	3	23	3	CD209	19	7807945	Missense_Mutation	SNP	G	TCGA-K7-A5RG-01A-11D-A28X-10		7807945	51321038	104	44205										
MUC16	94025	hgsc.bcm.edu	37	chr19	9073366	9073366	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ggttgatgtgtctaaggcaaGtggaatctttgatgtagctc	13	5	2	2			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr19:9073366G>A	ENST00000397910.4	-	3	14283	c.14080C>T	c.(14080-14082)Ctt>Ttt	p.L4694F		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4696	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TCTAAGGCAAGTGGAATCTTT	0.478																																					p.L4694F		Atlas-SNP	.											.	MUC16	4315	.	0			c.C14080T						.						187	174	178					19																	9073366		1943	4157	6100	SO:0001583	missense	94025	exon3			AGGCAAGTGGAAT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.14080C>T	chr19.hg19:g.9073366G>A	ENSP00000381008:p.Leu4694Phe	187.0	0.0		188.0	37.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	9.006	0.981229	0.18812	.	.	ENSG00000181143	ENST00000397910	T	0.36340	1.26	1.8	-3.39	0.04868	.	.	.	.	.	T	0.22085	0.0532	L	0.29908	0.895	.	.	.	D	0.58268	0.982	B	0.41332	0.354	T	0.29610	-1.0006	8	0.87932	D	0	.	7.0444	0.25038	0.0:0.0:0.3082:0.6918	.	4694	B5ME49	.	F	4694	ENSP00000381008:L4694F	ENSP00000381008:L4694F	L	-	1	0	MUC16	8934366	0.000000	0.05858	0.000000	0.03702	0.679000	0.39708	-2.894000	0.00707	-0.653000	0.05401	0.313000	0.20887	CTT	.	.		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9073366	G	A	9073366	3	1	310	1	0	0	0	0	1	0	0	0	9982	1029	36	3	29771	3	MUC16	19	9073366	Missense_Mutation	SNP	G	TCGA-K7-A5RG-01A-11D-A28X-10	1265421	9073366	50055617	105	44206										
KEAP1	9817	hgsc.bcm.edu	37	chr19	10602442	10602442	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	cgtcgggcgagttgttcctgCcgcccacggcgtacaacagc	13	15	0	0			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr19:10602442C>A	ENST00000171111.5	-	3	1683	c.1136G>T	c.(1135-1137)gGc>gTc	p.G379V	KEAP1_ENST00000393623.2_Missense_Mutation_p.G379V|KEAP1_ENST00000588024.1_5'Flank|CTC-429L19.3_ENST00000592671.1_RNA	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	379					cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)				breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	GTTGTTCCTGCCGCCCACGGC	0.701																																					p.G379V		Atlas-SNP	.											.	KEAP1	182	.	0			c.G1136T						.						30	26	27					19																	10602442		2166	4243	6409	SO:0001583	missense	9817	exon3			TTCCTGCCGCCCA	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"Kelch-like", "BTB/POZ domain containing"	23177	protein-coding gene	gene with protein product	"kelch-like family member 19"	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.1136G>T	chr19.hg19:g.10602442C>A	ENSP00000171111:p.Gly379Val	75.0	0.0		112.0	14.0	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Missense_Mutation	SNP	ENST00000171111.5	hg19	CCDS12239.1	.	.	.	.	.	.	.	.	.	.	C	18.65	3.669347	0.67814	.	.	ENSG00000079999	ENST00000171111;ENST00000393623	D;D	0.99494	-6.01;-6.01	5.77	5.77	0.91146	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	D	0.99809	0.9917	H	0.99454	4.575	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96806	0.9593	10	0.87932	D	0	.	17.4866	0.87691	0.0:1.0:0.0:0.0	.	379	Q14145	KEAP1_HUMAN	V	379	ENSP00000171111:G379V;ENSP00000377245:G379V	ENSP00000171111:G379V	G	-	2	0	KEAP1	10463442	1.000000	0.71417	1.000000	0.80357	0.170000	0.22686	7.601000	0.82783	2.745000	0.94114	0.655000	0.94253	GGC	.	.		0.701	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289		A	10602442	C	A	10602442	3	1	310	1	0	0	0	0	1	0	0	0	8150	739	26	3	754	3	KEAP1	19	10602442	Missense_Mutation	SNP	C	TCGA-K7-A5RG-01A-11D-A28X-10	1529076	10602442	48526541	106	44207										
PIK3R2	5296	hgsc.bcm.edu	37	chr19	18279669	18279669	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	atggcaccttcctcatccgcGagagcagccagcggggctgc	13	15	1	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr19:18279669G>T	ENST00000593731.1	+	15	2502	c.1942G>T	c.(1942-1944)Gag>Tag	p.E648*	PIK3R2_ENST00000222254.8_Nonsense_Mutation_p.E648*			O00459	P85B_HUMAN	phosphoinositide-3-kinase, regulatory subunit 2 (beta)	648	SH2 2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)	phosphatidylinositol 3-kinase regulator activity (GO:0035014)|receptor tyrosine kinase binding (GO:0030971)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(3)|pancreas(1)|stomach(1)	24					Isoprenaline(DB01064)	CCTCATCCGCGAGAGCAGCCA	0.652																																					p.E648X		Atlas-SNP	.											.	PIK3R2	48	.	0			c.G1942T						.						51	34	40					19																	18279669		2203	4299	6502	SO:0001587	stop_gained	5296	exon15			ATCCGCGAGAGCA		CCDS12371.1	19p13.11	2013-03-28	2008-02-04		ENSG00000105647	ENSG00000105647		"SH2 domain containing"	8980	protein-coding gene	gene with protein product		603157				1314371	Standard	NM_005027		Approved	P85B, p85	uc002nia.2	O00459	OTTHUMG00000183383	ENST00000593731.1:c.1942G>T	chr19.hg19:g.18279669G>T	ENSP00000471914:p.Glu648*	165.0	0.0		217.0	30.0	NM_005027	Q5EAT5|Q9UPH9	Nonsense_Mutation	SNP	ENST00000593731.1	hg19	CCDS12371.1	.	.	.	.	.	.	.	.	.	.	G	44	10.678555	0.99448	.	.	ENSG00000105647	ENST00000222254	.	.	.	3.83	3.83	0.44106	.	0.061318	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	-29.5935	15.572	0.76345	0.0:0.0:1.0:0.0	.	.	.	.	X	648	.	ENSP00000222254:E648X	E	+	1	0	PIK3R2	18140669	1.000000	0.71417	0.995000	0.50966	0.817000	0.46193	7.875000	0.87205	2.091000	0.63221	0.313000	0.20887	GAG	.	.		0.652	PIK3R2-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000466386.2	NM_005027		T	18279669	G	T	18279669	4	4	310	1	0	0	0	0	0	1	0	0	11928	1059	37	1	1996	1	PIK3R2	19	18279669	Nonsense_Mutation	SNP	G	TCGA-K7-A5RG-01A-11D-A28X-10	7677227	18279669	40849314	107	44208										
ZNF536	9745	hgsc.bcm.edu	37	chr19	31040266	31040266	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	agcccaggaccccttggcggGcctgccaaagccggagcggg	16	15	0	0			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr19:31040266G>T	ENST00000355537.3	+	4	3887	c.3740G>T	c.(3739-3741)gGc>gTc	p.G1247V		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	1247					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					CCCTTGGCGGGCCTGCCAAAG	0.627																																					p.G1247V		Atlas-SNP	.											.	ZNF536	424	.	0			c.G3740T						.						18	19	19					19																	31040266		2200	4290	6490	SO:0001583	missense	9745	exon4			TGGCGGGCCTGCC		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"Zinc fingers, C2H2-type"	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.3740G>T	chr19.hg19:g.31040266G>T	ENSP00000347730:p.Gly1247Val	81.0	0.0		85.0	17.0	NM_014717	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	hg19	CCDS32984.1	.	.	.	.	.	.	.	.	.	.	G	12.95	2.092769	0.36952	.	.	ENSG00000198597	ENST00000355537	T	0.11821	2.74	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	T	0.14917	0.0360	L	0.32530	0.975	0.80722	D	1	P;P	0.50066	0.883;0.931	P;P	0.47402	0.546;0.546	T	0.00641	-1.1631	10	0.87932	D	0	-28.0219	10.3603	0.43989	0.1523:0.0:0.8477:0.0	.	1247;1247	A7E228;O15090	.;ZN536_HUMAN	V	1247	ENSP00000347730:G1247V	ENSP00000347730:G1247V	G	+	2	0	ZNF536	35732106	1.000000	0.71417	0.895000	0.35142	0.258000	0.26162	4.504000	0.60414	2.401000	0.81631	0.650000	0.86243	GGC	.	.		0.627	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		T	31040266	G	T	31040266	3	4	310	1	0	0	0	0	1	0	0	0	17989	1203	42	3	3750	3	ZNF536	19	31040266	Missense_Mutation	SNP	G	TCGA-K7-A5RG-01A-11D-A28X-10	12760597	31040266	28088717	108	44209										
ATP4A	495	hgsc.bcm.edu	37	chr19	36048727	36048727	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	agtgtcgcgggtcccgcgggTcctccagcgtatggatggac	16	12	0	0			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr19:36048727T>A	ENST00000262623.3	-	11	1551	c.1523A>T	c.(1522-1524)gAc>gTc	p.D508V		NM_000704.2	NP_000695.2	P20648	ATP4A_HUMAN	ATPase, H+/K+ exchanging, alpha polypeptide	508					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|ion transmembrane transport (GO:0034220)|pH reduction (GO:0045851)|regulation of proton transport (GO:0010155)|response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|magnesium ion binding (GO:0000287)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(26)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	53	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)	GTCCCGCGGGTCCTCCAGCGT	0.716																																					p.D508V		Atlas-SNP	.											.	ATP4A	123	.	0			c.A1523T						.						8	10	9					19																	36048727		2065	4074	6139	SO:0001583	missense	495	exon11			CGCGGGTCCTCCA		CCDS12467.1	19q13.1	2010-04-20			ENSG00000105675	ENSG00000105675	3.6.3.10	"ATPases / P-type"	819	protein-coding gene	gene with protein product	"gastric H,K-ATPase alpha subunit", "H(+)-K(+)-ATPase alpha subunit", "proton pump"	137216				1330887	Standard	NM_000704		Approved	ATP6A	uc002oal.1	P20648	OTTHUMG00000048106	ENST00000262623.3:c.1523A>T	chr19.hg19:g.36048727T>A	ENSP00000262623:p.Asp508Val	87.0	0.0		120.0	15.0	NM_000704	O00738	Missense_Mutation	SNP	ENST00000262623.3	hg19	CCDS12467.1	.	.	.	.	.	.	.	.	.	.	T	19.43	3.826776	0.71143	.	.	ENSG00000105675	ENST00000262623	T	0.81078	-1.45	3.39	3.39	0.38822	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.318910	0.22173	N	0.063615	D	0.83691	0.5309	M	0.64630	1.985	0.58432	D	0.999999	B	0.32800	0.385	P	0.48654	0.585	D	0.84275	0.0491	10	0.72032	D	0.01	.	9.8205	0.40880	0.0:0.0:0.0:1.0	.	508	P20648	ATP4A_HUMAN	V	508	ENSP00000262623:D508V	ENSP00000262623:D508V	D	-	2	0	ATP4A	40740567	1.000000	0.71417	1.000000	0.80357	0.867000	0.49689	3.912000	0.56386	1.421000	0.47157	0.397000	0.26171	GAC	.	.		0.716	ATP4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109470.2	NM_000704		A	36048727	T	A	36048727	3	1	310	1	0	0	0	0	1	0	0	0	1145	1667	58	4	1632	4	ATP4A	19	36048727	Missense_Mutation	SNP	T	TCGA-K7-A5RG-01A-11D-A28X-10	5008461	36048727	23080256	109	44210										
NFKBID	84807	hgsc.bcm.edu	37	chr19	36387302	36387302	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	agctggccataccaagagaaCtcctgggagcccgtaggtag	13	11	0	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr19:36387302C>T	ENST00000396901.1	-	7	970	c.397G>A	c.(397-399)Gtt>Att	p.V133I	NFKBID_ENST00000606253.1_Missense_Mutation_p.V133I|NFKBID_ENST00000352614.2_Missense_Mutation_p.V285I|NFKBID_ENST00000585544.1_5'Flank	NM_139239.1	NP_640332.1	Q8NI38	IKBD_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, delta	133					inflammatory response (GO:0006954)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell differentiation in thymus (GO:0033085)|positive regulation of thymocyte apoptotic process (GO:0070245)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	14						ACCAAGAGAACTCCTGGGAGC	0.607																																					p.V133I		Atlas-SNP	.											.	NFKBID	30	.	0			c.G397A						.						71	81	78					19																	36387302		1922	4131	6053	SO:0001583	missense	84807	exon7			AGAGAACTCCTGG	AF385434	CCDS42552.1	19q13.12	2013-01-10				ENSG00000167604		"Ankyrin repeat domain containing"	15671	protein-coding gene	gene with protein product						12477932	Standard	NM_139239		Approved	TA-NFKBH, IkappaBNS	uc002oci.1	Q8NI38		ENST00000396901.1:c.397G>A	chr19.hg19:g.36387302C>T	ENSP00000380109:p.Val133Ile	82.0	0.0		106.0	9.0	NM_139239	Q8NI39|Q9BRG9	Missense_Mutation	SNP	ENST00000396901.1	hg19	CCDS42552.1	.	.	.	.	.	.	.	.	.	.	C	16.69	3.193820	0.58017	.	.	ENSG00000167604	ENST00000352614;ENST00000396901	T;T	0.63913	-0.07;-0.07	4.81	4.81	0.61882	Ankyrin repeat-containing domain (4);	0.072360	0.56097	D	0.000030	T	0.60586	0.2280	N	0.05199	-0.095	0.80722	D	1	D;P	0.61697	0.99;0.729	D;P	0.75484	0.986;0.535	T	0.66337	-0.5949	10	0.37606	T	0.19	.	15.3604	0.74469	0.0:1.0:0.0:0.0	.	285;133	Q8NI38-2;Q8NI38	.;IKBD_HUMAN	I	285;133	ENSP00000252985:V285I;ENSP00000380109:V133I	ENSP00000252985:V285I	V	-	1	0	NFKBID	41079142	0.998000	0.40836	0.939000	0.37840	0.279000	0.26890	3.897000	0.56273	2.199000	0.70637	0.561000	0.74099	GTT	.	.		0.607	NFKBID-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000452927.3	NM_032721		T	36387302	C	T	36387302	3	4	310	1	0	0	0	0	1	0	0	0	10388	565	20	3	568	3	NFKBID	19	36387302	Missense_Mutation	SNP	C	TCGA-K7-A5RG-01A-11D-A28X-10	338575	36387302	22741681	110	44211										
ZNF790	388536	hgsc.bcm.edu	37	chr19	37310227	37310227	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	aagctttcccacactccttaCattcataaggtttttcacca	3	13	2	0	rs375770964		TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr19:37310227C>G	ENST00000356725.4	-	5	1139	c.1019G>C	c.(1018-1020)tGt>tCt	p.C340S	CTD-2162K18.5_ENST00000588906.1_RNA|CTD-2162K18.5_ENST00000587278.1_RNA	NM_001242802.1|NM_206894.3	NP_001229731.1|NP_996777.2	Q6PG37	ZN790_HUMAN	zinc finger protein 790	340					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			biliary_tract(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	32	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			ACACTCCTTACATTCATAAGG	0.378																																					p.C340S		Atlas-SNP	.											.	ZNF790	89	.	0			c.G1019C						.	C	SER/CYS,SER/CYS,SER/CYS,SER/CYS	1,4405	2.1+/-5.4	0,1,2202	60	61	61		1019,1019,1019,1019	3.1	0.9	19		61	0,8600		0,0,4300	no	missense,missense,missense,missense	ZNF790	NM_001242800.1,NM_001242801.1,NM_001242802.1,NM_206894.3	112,112,112,112	0,1,6502	GG,GC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	340/637,340/637,340/637,340/637	37310227	1,13005	2203	4300	6503	SO:0001583	missense	388536	exon5			TCCTTACATTCAT	BC057245	CCDS12496.1	19q13.12	2013-01-08			ENSG00000197863	ENSG00000197863		"Zinc fingers, C2H2-type", "-"	33114	protein-coding gene	gene with protein product							Standard	NM_206894		Approved	MGC62100, FLJ20350	uc021utm.1	Q6PG37	OTTHUMG00000165616	ENST00000356725.4:c.1019G>C	chr19.hg19:g.37310227C>G	ENSP00000349161:p.Cys340Ser	79.0	0.0		77.0	14.0	NM_206894		Missense_Mutation	SNP	ENST00000356725.4	hg19	CCDS12496.1	.	.	.	.	.	.	.	.	.	.	C	17.79	3.475659	0.63737	2.27E-4	0.0	ENSG00000197863	ENST00000356725	D	0.85171	-1.95	3.14	3.14	0.36123	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.93648	0.7971	M	0.93638	3.44	0.44337	D	0.997221	D	0.89917	1.0	D	0.97110	1.0	D	0.95038	0.8175	9	0.87932	D	0	.	13.5234	0.61580	0.0:1.0:0.0:0.0	.	340	Q6PG37	ZN790_HUMAN	S	340	ENSP00000349161:C340S	ENSP00000349161:C340S	C	-	2	0	ZNF790	42002067	0.999000	0.42202	0.895000	0.35142	0.815000	0.46073	4.770000	0.62309	1.753000	0.51906	0.491000	0.48974	TGT	.	.		0.378	ZNF790-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385341.2	NM_206894		G	37310227	C	G	37310227	3	3	310	1	0	0	0	0	1	0	0	0	18177	478	17	4	895	4	ZNF790	19	37310227	Missense_Mutation	SNP	C	TCGA-K7-A5RG-01A-11D-A28X-10	922925	37310227	21818756	111	44212										
ZNF546	339327	hgsc.bcm.edu	37	chr19	40520371	40520371	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	aaggcctttagtcatggctcAtaccttgttcaacatcagaa	7	10	4	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr19:40520371A>T	ENST00000347077.4	+	7	1410	c.1194A>T	c.(1192-1194)tcA>tcT	p.S398S	ZNF546_ENST00000600094.1_Silent_p.S372S|ZNF546_ENST00000596894.1_Intron	NM_178544.3	NP_848639.2	Q86UE3	ZN546_HUMAN	zinc finger protein 546	398					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(15)|lung(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(3)	34	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					GTCATGGCTCATACCTTGTTC	0.378																																					p.S398S		Atlas-SNP	.											.	ZNF546	93	.	0			c.A1194T						.						47	45	46					19																	40520371		2203	4300	6503	SO:0001819	synonymous_variant	339327	exon7			TGGCTCATACCTT	BC045649	CCDS12548.1	19q13.2	2013-01-08				ENSG00000187187		"Zinc fingers, C2H2-type", "-"	28671	protein-coding gene	gene with protein product				ZNF49		12477932	Standard	XM_005258853		Approved	MGC43537	uc002oms.2	Q86UE3		ENST00000347077.4:c.1194A>T	chr19.hg19:g.40520371A>T		101.0	0.0		80.0	13.0	NM_178544	A8K913	Silent	SNP	ENST00000347077.4	hg19	CCDS12548.1																																																																																			.	.		0.378	ZNF546-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462495.2	NM_178544		T	40520371	A	T	40520371	2	4	310	1	0	0	0	0	0	0	0	1	17993	204	8	4		4	ZNF546	19	40520371	Silent	SNP	A	TCGA-K7-A5RG-01A-11D-A28X-10	3210144	40520371	18608612	112	44213										
KPTN	11133	hgsc.bcm.edu	37	chr19	47983128	47983128	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	cccagagctcacccttggcgGccgagaggctgaacacaatc	11	15	1	3	rs547863250		TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr19:47983128G>T	ENST00000338134.3	-	8	886	c.779C>A	c.(778-780)gCc>gAc	p.A260D	KPTN_ENST00000536339.1_Missense_Mutation_p.A20D|KPTN_ENST00000595484.1_5'Flank	NM_007059.2	NP_008990.2	Q9Y664	KPTN_HUMAN	kaptin (actin binding protein)	260					actin filament organization (GO:0007015)|cellular component movement (GO:0006928)|sensory perception of sound (GO:0007605)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	actin binding (GO:0003779)			breast(1)|lung(3)|ovary(2)|pancreas(2)	8		all_cancers(25;1.55e-10)|all_epithelial(76;3.4e-08)|all_lung(116;1.73e-07)|Lung NSC(112;3.95e-07)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		OV - Ovarian serous cystadenocarcinoma(262;0.000428)|all cancers(93;0.000631)|Epithelial(262;0.0153)|GBM - Glioblastoma multiforme(486;0.0694)		ACCCTTGGCGGCCGAGAGGCT	0.602													g|||	1	0.000199681	0	0	5008	,	,		10019	0.001		0	False		,,,				2504	0				p.A260D		Atlas-SNP	.											.	KPTN	34	.	0			c.C779A						.						38	43	41					19																	47983128		1992	4150	6142	SO:0001583	missense	11133	exon8			TTGGCGGCCGAGA	AF105369	CCDS42583.1	19q13.32	2014-08-13	2001-11-28		ENSG00000118162	ENSG00000118162			6404	protein-coding gene	gene with protein product		615620	"kaptin (actin-binding protein)"			10099934	Standard	XM_005258467		Approved	2E4	uc002pgy.3	Q9Y664	OTTHUMG00000183443	ENST00000338134.3:c.779C>A	chr19.hg19:g.47983128G>T	ENSP00000337850:p.Ala260Asp	50.0	0.0		88.0	4.0	NM_007059	B3KN86|B4DQ76|Q96GT1	Missense_Mutation	SNP	ENST00000338134.3	hg19	CCDS42583.1	.	.	.	.	.	.	.	.	.	.	G	13.34	2.207593	0.39003	.	.	ENSG00000118162	ENST00000338134;ENST00000536339	.	.	.	4.16	3.09	0.35607	.	0.608900	0.16534	N	0.210260	T	0.42426	0.1202	L	0.54323	1.7	0.09310	N	1	B	0.30281	0.275	B	0.32624	0.149	T	0.28713	-1.0035	9	0.36615	T	0.2	-12.7416	9.6832	0.40082	0.0:0.2134:0.7866:0.0	.	260	Q9Y664	KPTN_HUMAN	D	260;20	.	ENSP00000337850:A260D	A	-	2	0	KPTN	52674940	1.000000	0.71417	0.002000	0.10522	0.724000	0.41520	0.768000	0.26590	0.698000	0.31739	0.306000	0.20318	GCC	.	.		0.602	KPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466672.2			T	47983128	G	T	47983128	3	4	310	1	0	0	0	0	1	0	0	0	8446	1203	42	3	551	3	KPTN	19	47983128	Missense_Mutation	SNP	G	TCGA-K7-A5RG-01A-11D-A28X-10	7462757	47983128	11145855	113	44214										
OSCAR	126014	hgsc.bcm.edu	37	chr19	54600387	54600387	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ctcaaggtcacgttgaccccAggggtcacaactgtagccgg	12	13	3	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr19:54600387A>T	ENST00000284648.6	-	4	332	c.135T>A	c.(133-135)ccT>ccA	p.P45P	OSCAR_ENST00000391760.1_Intron|OSCAR_ENST00000359649.4_Silent_p.P49P|OSCAR_ENST00000356532.3_Silent_p.P49P|OSCAR_ENST00000391761.1_Silent_p.P34P|OSCAR_ENST00000358375.4_Silent_p.P45P|OSCAR_ENST00000351806.4_Silent_p.P34P			Q8IYS5	OSCAR_HUMAN	osteoclast associated, immunoglobulin-like receptor	45	Ig-like 1.					extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				large_intestine(1)|skin(1)	2	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)					CGTTGACCCCAGGGGTCACAA	0.607																																					p.P49P		Atlas-SNP	.											.	OSCAR	22	.	0			c.T147A						.						63	68	66					19																	54600387		2203	4300	6503	SO:0001819	synonymous_variant	126014	exon4			GACCCCAGGGGTC	AK130199	CCDS12873.1, CCDS12874.1, CCDS12875.1, CCDS12876.1, CCDS62789.1, CCDS74444.1	19q13.42	2013-01-29			ENSG00000170909	ENSG00000170909		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29960	protein-coding gene	gene with protein product		606862				11805147	Standard	NM_206818		Approved		uc002qda.3	Q8IYS5	OTTHUMG00000064966	ENST00000284648.6:c.135T>A	chr19.hg19:g.54600387A>T		95.0	0.0		93.0	16.0	NM_130771	B7WNS2|Q5GRG5|Q8N763|Q8NHL4|Q8WXQ0|Q8WXQ1|Q8WXQ2	Silent	SNP	ENST00000284648.6	hg19																																																																																				.	.		0.607	OSCAR-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000139493.4	NM_133169		T	54600387	A	T	54600387	2	4	310	1	0	0	0	0	0	0	0	1	11294	175	7	4		4	OSCAR	19	54600387	Silent	SNP	A	TCGA-K7-A5RG-01A-11D-A28X-10	6617259	54600387	4528596	114	44215										
JAG1	182	hgsc.bcm.edu	37	chr20	10644621	10644621	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	cgatacttacgaacggtgtcAttactggaatcccacgcctc	8	13	1	0			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr20:10644621A>G	ENST00000254958.5	-	3	944	c.429T>C	c.(427-429)aaT>aaC	p.N143N	JAG1_ENST00000423891.2_5'Flank	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	143					angiogenesis (GO:0001525)|aorta morphogenesis (GO:0035909)|auditory receptor cell differentiation (GO:0042491)|blood vessel remodeling (GO:0001974)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cell fate determination (GO:0001709)|ciliary body morphogenesis (GO:0061073)|distal tubule development (GO:0072017)|endocardial cushion cell development (GO:0061444)|endothelial cell differentiation (GO:0045446)|hemopoiesis (GO:0030097)|keratinocyte differentiation (GO:0030216)|loop of Henle development (GO:0072070)|morphogenesis of an epithelial sheet (GO:0002011)|myoblast differentiation (GO:0045445)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of stem cell differentiation (GO:2000737)|nervous system development (GO:0007399)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|response to muramyl dipeptide (GO:0032495)|T cell mediated immunity (GO:0002456)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|urinary_tract(1)	44						GAACGGTGTCATTACTGGAAT	0.468									Alagille Syndrome																												p.N143N		Atlas-SNP	.											.	JAG1	213	.	0			c.T429C						.						180	140	154					20																	10644621		2203	4300	6503	SO:0001819	synonymous_variant	182	exon3	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	GGTGTCATTACTG	U61276	CCDS13112.1	20p12.1-p11.23	2011-05-12	2010-06-24		ENSG00000101384	ENSG00000101384		"CD molecules"	6188	protein-coding gene	gene with protein product		601920	"Alagille syndrome"	AGS, JAGL1		7697721, 9207788	Standard	NM_000214		Approved	AHD, AWS, HJ1, CD339	uc002wnw.2	P78504	OTTHUMG00000031872	ENST00000254958.5:c.429T>C	chr20.hg19:g.10644621A>G		164.0	0.0		193.0	17.0	NM_000214	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Silent	SNP	ENST00000254958.5	hg19	CCDS13112.1																																																																																			.	.		0.468	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214		G	10644621	A	G	10644621	2	3	310	1	0	0	0	0	0	0	0	1	7943	214	8	2		2	JAG1	20	10644621	Silent	SNP	A	TCGA-K7-A5RG-01A-11D-A28X-10		10644621	52380899	115	44216										
PTPRT	11122	hgsc.bcm.edu	37	chr20	40980734	40980734	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	gcagagatacctgaaattttGgtggcaatccgagtggtgac	13	7	0	3			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr20:40980734G>T	ENST00000373187.1	-	10	1751	c.1752C>A	c.(1750-1752)acC>acA	p.T584T	PTPRT_ENST00000373201.1_Silent_p.T584T|PTPRT_ENST00000373190.1_Silent_p.T584T|PTPRT_ENST00000373198.4_Silent_p.T584T|PTPRT_ENST00000373184.1_Silent_p.T584T|PTPRT_ENST00000356100.2_Silent_p.T584T|PTPRT_ENST00000373193.3_Silent_p.T584T			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	584	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)	p.T584T(1)		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)				CTGAAATTTTGGTGGCAATCC	0.468																																					p.T584T		Atlas-SNP	.											PTPRT,NS,carcinoma,0,1	PTPRT	372	.	1	Substitution - coding silent(1)	lung(1)	c.C1752A						.						77	79	79					20																	40980734		1891	4122	6013	SO:0001819	synonymous_variant	11122	exon10			AATTTTGGTGGCA	AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.1752C>A	chr20.hg19:g.40980734G>T		102.0	0.0		139.0	10.0	NM_007050	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Silent	SNP	ENST00000373187.1	hg19	CCDS42874.1																																																																																			.	.		0.468	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			T	40980734	G	T	40980734	2	4	310	1	0	0	0	0	0	0	0	1	12827	1335	47	3		3	PTPRT	20	40980734	Silent	SNP	G	TCGA-K7-A5RG-01A-11D-A28X-10	30336113	40980734	22044786	116	44217										
PCK1	5105	hgsc.bcm.edu	37	chr20	56139664	56139664	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	tatctttggaggccgtagacCtgctggtgaggctctccttc	12	11	2	2			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr20:56139664C>T	ENST00000319441.4	+	8	1477	c.1313C>T	c.(1312-1314)cCt>cTt	p.P438L	PCK1_ENST00000535860.1_3'UTR|PCK1_ENST00000543666.1_Missense_Mutation_p.P121L	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	438					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			GGCCGTAGACCTGCTGGTGAG	0.552																																					p.P438L		Atlas-SNP	.											.	PCK1	95	.	0			c.C1313T						.						105	101	103					20																	56139664		2203	4300	6503	SO:0001583	missense	5105	exon8			GTAGACCTGCTGG		CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.1313C>T	chr20.hg19:g.56139664C>T	ENSP00000319814:p.Pro438Leu	30.0	0.0		40.0	7.0	NM_002591	A8K437|B4DT64|Q8TCA3|Q9UJD2	Missense_Mutation	SNP	ENST00000319441.4	hg19	CCDS13460.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.448695	0.84101	.	.	ENSG00000124253	ENST00000540165;ENST00000319441;ENST00000543666	T;T	0.04360	3.64;3.64	5.8	5.8	0.92144	Phosphoenolpyruvate carboxykinase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.38904	0.1058	H	0.97214	3.96	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.993	T	0.59215	-0.7496	10	0.87932	D	0	-9.5935	20.063	0.97692	0.0:1.0:0.0:0.0	.	121;438	B4DT64;P35558	.;PCKGC_HUMAN	L	120;438;121	ENSP00000319814:P438L;ENSP00000445767:P121L	ENSP00000319814:P438L	P	+	2	0	PCK1	55573070	1.000000	0.71417	0.982000	0.44146	0.529000	0.34654	7.285000	0.78660	2.735000	0.93741	0.655000	0.94253	CCT	.	.		0.552	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2			T	56139664	C	T	56139664	3	4	310	1	0	0	0	0	1	0	0	0	11590	681	24	3	1339	3	PCK1	20	56139664	Missense_Mutation	SNP	C	TCGA-K7-A5RG-01A-11D-A28X-10	15158930	56139664	6885856	117	44218										
RANGAP1	5905	hgsc.bcm.edu	37	chr22	41652812	41652812	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	aattaatcacctccacctgcCgcaaggtcttcaaggtctgt	7	13	4	0	rs567605253		TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chr22:41652812C>T	ENST00000455915.2	-	7	2260	c.791G>A	c.(790-792)cGg>cAg	p.R264Q	RANGAP1_ENST00000407260.4_Missense_Mutation_p.R209Q|RANGAP1_ENST00000405486.1_Missense_Mutation_p.R264Q|RANGAP1_ENST00000356244.3_Missense_Mutation_p.R264Q			P46060	RAGP1_HUMAN	Ran GTPase activating protein 1	264					mitotic cell cycle (GO:0000278)|negative regulation of protein export from nucleus (GO:0046826)|positive regulation of Ran GTPase activity (GO:0032853)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear pore (GO:0005643)|perinuclear region of cytoplasm (GO:0048471)	Ran GTPase activator activity (GO:0005098)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						CTCCACCTGCCGCAAGGTCTT	0.632													C|||	1	0.000199681	8e-04	0	5008	,	,		13657	0		0	False		,,,				2504	0				p.R264Q		Atlas-SNP	.											.	RANGAP1	47	.	0			c.G791A						.						47	45	45					22																	41652812		2203	4300	6503	SO:0001583	missense	5905	exon8			ACCTGCCGCAAGG	X82260	CCDS14012.1	22q13	2013-01-17			ENSG00000100401	ENSG00000100401			9854	protein-coding gene	gene with protein product		602362	"segregation distorter homolog (Drosophila)"	SD		7878053	Standard	NM_002883		Approved	Fug1, KIAA1835	uc003azu.3	P46060	OTTHUMG00000150940	ENST00000455915.2:c.791G>A	chr22.hg19:g.41652812C>T	ENSP00000401470:p.Arg264Gln	64.0	0.0		74.0	10.0	NM_002883	Q96JJ2	Missense_Mutation	SNP	ENST00000455915.2	hg19	CCDS14012.1	.	.	.	.	.	.	.	.	.	.	C	14.00	2.405842	0.42715	.	.	ENSG00000100401	ENST00000405486;ENST00000356244;ENST00000405383;ENST00000455915;ENST00000407260	T;T;T;T	0.52295	0.67;0.67;0.67;0.68	5.55	5.55	0.83447	.	0.105475	0.64402	D	0.000007	T	0.32466	0.0830	N	0.14661	0.345	0.51482	D	0.999925	B;B	0.26363	0.147;0.091	B;B	0.18263	0.021;0.004	T	0.10706	-1.0618	10	0.16896	T	0.51	-21.1076	19.4978	0.95081	0.0:1.0:0.0:0.0	.	209;264	F8W7I9;P46060	.;RAGP1_HUMAN	Q	264;264;264;264;209	ENSP00000385866:R264Q;ENSP00000348577:R264Q;ENSP00000401470:R264Q;ENSP00000385354:R209Q	ENSP00000348577:R264Q	R	-	2	0	RANGAP1	39982758	0.972000	0.33761	1.000000	0.80357	0.623000	0.37688	3.959000	0.56744	2.608000	0.88229	0.462000	0.41574	CGG	.	.		0.632	RANGAP1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320606.1	NM_002883		T	41652812	C	T	41652812	3	4	310	1	0	0	0	0	1	0	0	0	13048	652	23	1	1008	1	RANGAP1	22	41652812	Missense_Mutation	SNP	C	TCGA-K7-A5RG-01A-11D-A28X-10		41652812	9651754	118	44219										
IL1RAPL1	11141	hgsc.bcm.edu	37	chrX	29973747	29973747	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ctatgagtacgacgtacctcCtaccggcaccctgcctctta	7	16	1	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chrX:29973747C>T	ENST00000378993.1	+	11	2574	c.1901C>T	c.(1900-1902)cCt>cTt	p.P634L	IL1RAPL1_ENST00000302196.4_Missense_Mutation_p.P634L	NM_014271.3	NP_055086.1	Q9NZN1	IRPL1_HUMAN	interleukin 1 receptor accessory protein-like 1	634	Interaction with NCS1.				calcium ion transmembrane transport (GO:0070588)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of exocytosis (GO:0045920)|neuron differentiation (GO:0030182)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor binding (GO:0005102)|voltage-gated calcium channel activity (GO:0005245)			biliary_tract(1)|breast(1)|endometrium(5)|large_intestine(9)|lung(38)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62						GACGTACCTCCTACCGGCACC	0.512																																					p.P634L		Atlas-SNP	.											.	IL1RAPL1	311	.	0			c.C1901T						.						84	43	57					X																	29973747		2202	4300	6502	SO:0001583	missense	11141	exon11			TACCTCCTACCGG	AJ243874	CCDS14218.1	Xp22.1-p21.3	2013-01-29	2004-02-13		ENSG00000169306	ENSG00000169306		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5996	protein-coding gene	gene with protein product		300206	"mental retardation, X-linked 34", "mental retardation, X-linked 21", "mental retardation, X-linked 10"	IL1RAPL, MRX34, MRX21, MRX10		10471494, 10757639	Standard	NM_014271		Approved	OPHN4, TIGIRR-2, IL1R8	uc004dby.2	Q9NZN1	OTTHUMG00000021317	ENST00000378993.1:c.1901C>T	chrX.hg19:g.29973747C>T	ENSP00000368278:p.Pro634Leu	77.0	0.0		118.0	32.0	NM_014271	A0AVG4|Q9UJ53	Missense_Mutation	SNP	ENST00000378993.1	hg19	CCDS14218.1	.	.	.	.	.	.	.	.	.	.	C	13.51	2.259525	0.39995	.	.	ENSG00000169306	ENST00000378993;ENST00000302196	T;T	0.04119	3.7;3.7	5.25	5.25	0.73442	.	0.100017	0.64402	D	0.000001	T	0.05181	0.0138	L	0.36672	1.1	0.80722	D	1	P	0.38020	0.615	B	0.33454	0.164	T	0.52245	-0.8601	9	.	.	.	.	16.1248	0.81383	0.0:1.0:0.0:0.0	.	634	Q9NZN1	IRPL1_HUMAN	L	634	ENSP00000368278:P634L;ENSP00000305200:P634L	.	P	+	2	0	IL1RAPL1	29883668	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	4.655000	0.61476	2.174000	0.68829	0.600000	0.82982	CCT	.	.		0.512	IL1RAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056155.1	NM_014271		T	29973747	C	T	29973747	3	4	310	1	0	0	0	0	1	0	0	0	7670	681	24	3	1939	3	IL1RAPL1	23	29973747	Missense_Mutation	SNP	C	TCGA-K7-A5RG-01A-11D-A28X-10		29973747	125296813	119	44220										
FAM123B	139285	hgsc.bcm.edu	37	chrX	63412208	63412208	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ctgtcaatgaatcaaagcttTtcagggatgtcacatcccca	7	11	4	1			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chrX:63412208T>A	ENST00000330258.3	-	2	1231	c.959A>T	c.(958-960)aAa>aTa	p.K320I	AMER1_ENST00000374869.3_Missense_Mutation_p.K320I|AMER1_ENST00000403336.1_Missense_Mutation_p.K320I	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	320					adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)									ATCAAAGCTTTTCAGGGATGT	0.527																																					p.K320I		Atlas-SNP	.											.	.	.	.	67	Whole gene deletion(67)	kidney(65)|ovary(1)|large_intestine(1)	c.A959T						.						135	117	123					X																	63412208		2203	4300	6503	SO:0001583	missense	139285	exon2			AAGCTTTTCAGGG	AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"-"	26837	protein-coding gene	gene with protein product	"Wilms Tumor on the X", "adenomatous polyposis coli membrane recruitment 1"	300647	"family with sequence similarity 123B"	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.959A>T	chrX.hg19:g.63412208T>A	ENSP00000329117:p.Lys320Ile	45.0	0.0		58.0	6.0	NM_152424	A2IB86|Q8N885	Missense_Mutation	SNP	ENST00000330258.3	hg19	CCDS14377.2	.	.	.	.	.	.	.	.	.	.	T	18.01	3.527713	0.64860	.	.	ENSG00000184675	ENST00000374869;ENST00000330258;ENST00000403336	T;T;T	0.32023	1.47;1.47;1.47	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	T	0.54886	0.1886	M	0.74647	2.275	0.46823	D	0.999212	D	0.89917	1.0	D	0.91635	0.999	T	0.59867	-0.7373	10	0.87932	D	0	-18.0894	12.9334	0.58301	0.0:0.0:0.0:1.0	.	320	Q5JTC6	F123B_HUMAN	I	320	ENSP00000364003:K320I;ENSP00000329117:K320I;ENSP00000384722:K320I	ENSP00000329117:K320I	K	-	2	0	FAM123B	63328933	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.525000	0.81892	2.003000	0.58678	0.430000	0.28490	AAA	.	.		0.527	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		A	63412208	T	A	63412208	3	1	310	1	0	0	0	0	1	0	0	0	5428	1841	64	4	2452	4	FAM123B	23	63412208	Missense_Mutation	SNP	T	TCGA-K7-A5RG-01A-11D-A28X-10	33438461	63412208	91858352	120	44221										
IL1RAPL2	26280	hgsc.bcm.edu	37	chrX	104999216	104999216	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0165289256198347	2	1	0.369630973986691	0	0.425635667014977	0.444444444444444	1	0	ctcttacacaaaagtggaccAagatactttagactgtgaca	7	9	1	3			TCGA-K7-A5RG-01A-11D-A28X-10	TCGA-K7-A5RG-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95bf87d5-3675-43fb-9dad-5e8968afcf13	c34592de-1c9f-4df8-8565-e1ed94a51992	g.chrX:104999216A>G	ENST00000372582.1	+	10	1994	c.1238A>G	c.(1237-1239)cAa>cGa	p.Q413R	IL1RAPL2_ENST00000485671.1_3'UTR|IL1RAPL2_ENST00000344799.4_Missense_Mutation_p.Q413R	NM_017416.1	NP_059112.1	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2	413	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				central nervous system development (GO:0007417)|cytokine-mediated signaling pathway (GO:0019221)	integral component of membrane (GO:0016021)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)			breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(23)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						AAAGTGGACCAAGATACTTTA	0.373																																					p.Q413R		Atlas-SNP	.											.	IL1RAPL2	105	.	0			c.A1238G						.						127	115	119					X																	104999216		2203	4300	6503	SO:0001583	missense	26280	exon10			TGGACCAAGATAC	AF181285	CCDS14517.1	Xq22	2013-01-11			ENSG00000189108	ENSG00000189108		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5997	protein-coding gene	gene with protein product		300277				10757639	Standard	NM_017416		Approved	IL-1R9, TIGIRR-1, IL1RAPL-2, IL1R9	uc004elz.1	Q9NP60	OTTHUMG00000022141	ENST00000372582.1:c.1238A>G	chrX.hg19:g.104999216A>G	ENSP00000361663:p.Gln413Arg	144.0	0.0		169.0	40.0	NM_017416	Q2M3U3|Q9NZN0	Missense_Mutation	SNP	ENST00000372582.1	hg19	CCDS14517.1	.	.	.	.	.	.	.	.	.	.	A	14.26	2.481888	0.44147	.	.	ENSG00000189108	ENST00000372582;ENST00000344799;ENST00000538500	T;T;T	0.04194	3.99;3.99;3.68	5.62	4.51	0.55191	Toll/interleukin-1 receptor homology (TIR) domain (4);	0.101165	0.43747	D	0.000539	T	0.02767	0.0083	N	0.08118	0	0.35755	D	0.819711	B	0.28400	0.21	B	0.32677	0.15	T	0.48790	-0.9004	10	0.11182	T	0.66	.	9.5508	0.39308	0.5691:0.4309:0.0:0.0	.	413	Q9NP60	IRPL2_HUMAN	R	413;413;18	ENSP00000361663:Q413R;ENSP00000344976:Q413R;ENSP00000445576:Q18R	ENSP00000344976:Q413R	Q	+	2	0	IL1RAPL2	104885872	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	5.108000	0.64609	1.881000	0.54492	0.486000	0.48141	CAA	.	.		0.373	IL1RAPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057785.1	NM_017416		G	104999216	A	G	104999216	3	3	310	1	0	0	0	0	1	0	0	0	7671	130	5	2	1272	2	IL1RAPL2	23	104999216	Missense_Mutation	SNP	A	TCGA-K7-A5RG-01A-11D-A28X-10	41587008	104999216	50271344	121	44222										
PADI1	29943	hgsc.bcm.edu	37	chr1	17565194	17565194	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	gagggttatggggaggcagcCcagtttgatggtgagtgcca	18	6	0	2			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr1:17565194C>T	ENST00000375471.4	+	13	1634	c.1542C>T	c.(1540-1542)gcC>gcT	p.A514A	PADI1_ENST00000413717.2_Silent_p.A71A|PADI1_ENST00000536552.1_5'UTR|PADI1_ENST00000537499.1_Silent_p.A71A	NM_013358.2	NP_037490.2	Q9ULC6	PADI1_HUMAN	peptidyl arginine deiminase, type I	514					protein citrullination (GO:0018101)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|skin(1)|stomach(1)|urinary_tract(1)	28		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00054)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00522)|BRCA - Breast invasive adenocarcinoma(304;1.3e-05)|COAD - Colon adenocarcinoma(227;1.31e-05)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(196;0.0069)|READ - Rectum adenocarcinoma(331;0.0681)|Lung(427;0.197)	L-Citrulline(DB00155)	GGGAGGCAGCCCAGTTTGATG	0.612																																					p.A514A	Esophageal Squamous(80;414 1257 4580 27746 50832)	Atlas-SNP	.											.	PADI1	77	.	0			c.C1542T						.						42	39	40					1																	17565194		2203	4300	6503	SO:0001819	synonymous_variant	29943	exon13			GGCAGCCCAGTTT	AB033768	CCDS178.1	1p36.13	2008-07-18			ENSG00000142623	ENSG00000142623	3.5.3.15	"Peptidyl arginine deiminases"	18367	protein-coding gene	gene with protein product	"peptidylarginine deiminase type I", "protein-arginine deiminase type-1", "hPAD-colony 10"	607934				12416996	Standard	NM_013358		Approved	HPAD10, PDI1, PDI, PAD1	uc001bah.1	Q9ULC6	OTTHUMG00000002294	ENST00000375471.4:c.1542C>T	chr1.hg19:g.17565194C>T		120.0	0.0		55.0	18.0	NM_013358	A1L4K6|Q70SX6	Silent	SNP	ENST00000375471.4	hg19	CCDS178.1																																																																																			.	.		0.612	PADI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006621.1	NM_013358		T	17565194	C	T	17565194	2	4	311	1	0	0	0	0	0	0	0	1	11386	610	22	3		3	PADI1	1	17565194	Silent	SNP	C	TCGA-K7-A6G5-01A-11D-A30V-10		17565194	231685427	1	44223										
TFAP2E	339488	hgsc.bcm.edu	37	chr1	36060160	36060160	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	atctgtgctgccctcactgcCttccagaactatttgctgga	8	13	2	1			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr1:36060160C>T	ENST00000373235.3	+	7	1420	c.1212C>T	c.(1210-1212)gcC>gcT	p.A404A		NM_178548.3	NP_848643.2			transcription factor AP-2 epsilon (activating enhancer binding protein 2 epsilon)											endometrium(1)|large_intestine(1)	2		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.196)				CCCTCACTGCCTTCCAGAACT	0.557																																					p.A404A		Atlas-SNP	.											.	TFAP2E	13	.	0			c.C1212T						.						112	97	102					1																	36060160		2203	4300	6503	SO:0001819	synonymous_variant	339488	exon7			CACTGCCTTCCAG	BC041175	CCDS393.2	1p34.3	2008-02-05			ENSG00000116819	ENSG00000116819			30774	protein-coding gene	gene with protein product		614428				14636996	Standard	NM_178548		Approved	AP2E	uc010ohy.2	Q6VUC0	OTTHUMG00000004388	ENST00000373235.3:c.1212C>T	chr1.hg19:g.36060160C>T		73.0	0.0		44.0	10.0	NM_178548		Silent	SNP	ENST00000373235.3	hg19	CCDS393.2																																																																																			.	.		0.557	TFAP2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012732.1	NM_178548		T	36060160	C	T	36060160	2	4	311	1	0	0	0	0	0	0	0	1	15806	668	24	3		3	TFAP2E	1	36060160	Silent	SNP	C	TCGA-K7-A6G5-01A-11D-A30V-10	18494966	36060160	213190461	2	44224										
VPS72	6944	hgsc.bcm.edu	37	chr1	151158055	151158055	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	gccttctgagagctaccagcCggggtgttgacctttcgagg	14	11	1	2			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr1:151158055C>A	ENST00000354473.4	-	3	348	c.312G>T	c.(310-312)ccG>ccT	p.P104P	VPS72_ENST00000496809.1_5'UTR			Q15906	VPS72_HUMAN	vacuolar protein sorting 72 homolog (S. cerevisiae)	104					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(6)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	14	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			AGCTACCAGCCGGGGTGTTGA	0.498																																					p.P104P	Pancreas(109;1131 2287 3209 24201)	Atlas-SNP	.											.	VPS72	31	.	0			c.G312T						.						194	192	192					1																	151158055		2203	4300	6503	SO:0001819	synonymous_variant	6944	exon3			ACCAGCCGGGGTG	D43642	CCDS989.1, CCDS59201.1	1q21	2008-02-05	2006-12-19	2005-09-08	ENSG00000163159	ENSG00000163159			11644	protein-coding gene	gene with protein product		600607	"transcription factor-like 1", "vacuolar protein sorting 72 (yeast)"	TCFL1		7702631	Standard	NM_001271087		Approved	YL-1, YL1, Swc2	uc001exe.2	Q15906	OTTHUMG00000012345	ENST00000354473.4:c.312G>T	chr1.hg19:g.151158055C>A		97.0	0.0		139.0	36.0	NM_001271087	A6NLK9|A6PW55|Q53GJ2|Q5U0R4	Silent	SNP	ENST00000354473.4	hg19	CCDS59201.1																																																																																			.	.		0.498	VPS72-002	NOVEL	mRNA_start_NF|basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000034394.3	NM_005997		A	151158055	C	A	151158055	2	1	311	1	0	0	0	0	0	0	0	1	17232	639	23	1		1	VPS72	1	151158055	Silent	SNP	C	TCGA-K7-A6G5-01A-11D-A30V-10	115097895	151158055	98092566	3	44225										
SPRR1B	6699	hgsc.bcm.edu	37	chr1	153004986	153004986	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	tgccaccccaaagtgcccgaGccctgccagcccaaggttcc	9	19	0	0			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr1:153004986G>A	ENST00000307098.4	+	2	230	c.165G>A	c.(163-165)gaG>gaA	p.E55E	SPRR1B_ENST00000392661.3_Intron	NM_003125.2	NP_003116.2	P22528	SPR1B_HUMAN	small proline-rich protein 1B	55	6 X 8 AA approximate tandem repeats.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)	p.C41_P64delCHPKVPEPCHPKVPEPCQPKVPEP(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|ovary(2)|skin(2)	9	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			AAGTGCCCGAGCCCTGCCAGC	0.627																																					p.E55E		Atlas-SNP	.											.	SPRR1B	18	.	1	Deletion - In frame(1)	ovary(1)	c.G165A						.						111	111	111					1																	153004986		2203	4298	6501	SO:0001819	synonymous_variant	6699	exon2			GCCCGAGCCCTGC	M84757	CCDS30863.1	1q21-q22	2010-06-25	2010-06-25		ENSG00000169469	ENSG00000169469			11260	protein-coding gene	gene with protein product	"cornifin"	182266		SPRR1		8325635, 1438308	Standard	NM_003125		Approved	GADD33	uc001fba.3	P22528	OTTHUMG00000013869	ENST00000307098.4:c.165G>A	chr1.hg19:g.153004986G>A		86.0	0.0		66.0	9.0	NM_003125	B2R5H7|P22529|P22530|Q5T524	Silent	SNP	ENST00000307098.4	hg19	CCDS30863.1																																																																																			.	.		0.627	SPRR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038906.1	NM_003125		A	153004986	G	A	153004986	2	1	311	1	0	0	0	0	0	0	0	1	15111	962	34	3		3	SPRR1B	1	153004986	Silent	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10	1846931	153004986	96245635	4	44226										
TPO	7173	hgsc.bcm.edu	37	chr2	1499804	1499804	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	tcttcacggatgcacagaggCgtgagctggagaagcactcc	13	11	2	3			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr2:1499804C>T	ENST00000345913.4	+	12	2141	c.2050C>T	c.(2050-2052)Cgt>Tgt	p.R684C	TPO_ENST00000349624.3_Missense_Mutation_p.R511C|TPO_ENST00000346956.3_Missense_Mutation_p.R684C|TPO_ENST00000497517.2_Intron|TPO_ENST00000337415.3_Missense_Mutation_p.R684C|TPO_ENST00000382198.1_Missense_Mutation_p.R511C|TPO_ENST00000329066.4_Missense_Mutation_p.R684C|TPO_ENST00000382201.3_Missense_Mutation_p.R627C	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	684					cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)	p.R684C(1)		breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	TGCACAGAGGCGTGAGCTGGA	0.577																																					p.R684C		Atlas-SNP	.											TPO,NS,carcinoma,0,1	TPO	224	.	1	Substitution - Missense(1)	ovary(1)	c.C2050T						.						78	63	68					2																	1499804		2203	4300	6503	SO:0001583	missense	7173	exon12			CAGAGGCGTGAGC		CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.2050C>T	chr2.hg19:g.1499804C>T	ENSP00000318820:p.Arg684Cys	32.0	0.0		36.0	12.0	NM_001206744	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	hg19	CCDS1643.1	.	.	.	.	.	.	.	.	.	.	C	7.302	0.613147	0.14066	.	.	ENSG00000115705	ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000329066;ENST00000382201;ENST00000382198;ENST00000422464;ENST00000469607	T;T;T;T;T;T;T;T;T	0.73575	-0.76;-0.76;-0.76;-0.76;-0.76;-0.76;-0.76;-0.76;-0.76	4.52	4.52	0.55395	.	1.024840	0.07679	N	0.936752	T	0.71837	0.3387	M	0.80332	2.49	0.80722	D	1	B;P;B;B	0.36789	0.028;0.57;0.051;0.035	B;B;B;B	0.24269	0.01;0.052;0.014;0.017	T	0.72093	-0.4394	10	0.49607	T	0.09	-9.0606	8.7369	0.34534	0.0:0.8284:0.0:0.1716	.	684;511;627;684	P07202-4;P07202-5;P07202-2;P07202	.;.;.;PERT_HUMAN	C	684;684;684;511;684;627;511;613;158	ENSP00000337263:R684C;ENSP00000318820:R684C;ENSP00000263886:R684C;ENSP00000332044:R511C;ENSP00000329869:R684C;ENSP00000371636:R627C;ENSP00000371633:R511C;ENSP00000405788:R613C;ENSP00000419461:R158C	ENSP00000329869:R684C	R	+	1	0	TPO	1478811	0.036000	0.19791	0.197000	0.23402	0.084000	0.17831	0.320000	0.19540	2.239000	0.73571	0.561000	0.74099	CGT	.	.		0.577	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547		T	1499804	C	T	1499804	3	4	311	1	0	0	0	0	1	0	0	0	16425	768	27	1	2092	1	TPO	2	1499804	Missense_Mutation	SNP	C	TCGA-K7-A6G5-01A-11D-A30V-10		1499804	241699569	5	44227										
ASXL2	55252	hgsc.bcm.edu	37	chr2	25965885	25965885	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	cttctgccagcaaaacccagCatgaacctctggcttgtgga	9	13	2	1			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr2:25965885C>A	ENST00000435504.4	-	13	3614	c.3321G>T	c.(3319-3321)atG>atT	p.M1107I	ASXL2_ENST00000272341.4_Missense_Mutation_p.M590I|ASXL2_ENST00000404843.1_Missense_Mutation_p.M590I|ASXL2_ENST00000336112.4_Missense_Mutation_p.M1079I			Q76L83	ASXL2_HUMAN	additional sex combs like transcriptional regulator 2	1107					adult heart development (GO:0007512)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of histone H3-K27 trimethylation (GO:1902466)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(7)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(3)	33	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CAAAACCCAGCATGAACCTCT	0.522																																					p.M1107I		Atlas-SNP	.											.	ASXL2	217	.	0			c.G3321T						.						145	144	144					2																	25965885		1985	4165	6150	SO:0001583	missense	55252	exon12			ACCCAGCATGAAC			2p24.1	2014-06-17	2014-06-17		ENSG00000143970	ENSG00000143970			23805	protein-coding gene	gene with protein product		612991	"additional sex combs like 2 (Drosophila)"			12888926	Standard	NM_018263		Approved	ASXH2, FLJ10898, KIAA1685	uc002rgs.2	Q76L83	OTTHUMG00000152176	ENST00000435504.4:c.3321G>T	chr2.hg19:g.25965885C>A	ENSP00000391447:p.Met1107Ile	35.0	0.0		57.0	13.0	NM_018263	Q53TC9|Q5H9U4|Q76L81|Q86XM1|Q9C0H8|Q9NV67	Missense_Mutation	SNP	ENST00000435504.4	hg19		.	.	.	.	.	.	.	.	.	.	C	17.10	3.303628	0.60305	.	.	ENSG00000143970	ENST00000435504;ENST00000336112;ENST00000404843;ENST00000272341	T;T;T;T	0.18174	2.24;2.24;2.23;2.23	6.07	6.07	0.98685	.	0.124467	0.64402	D	0.000001	T	0.40670	0.1126	M	0.69823	2.125	0.23724	N	0.997014	P;P	0.50528	0.77;0.936	B;P	0.61201	0.366;0.885	T	0.16748	-1.0392	10	0.31617	T	0.26	-17.8188	19.2077	0.93739	0.0:1.0:0.0:0.0	.	590;1107	Q76L83-2;Q76L83	.;ASXL2_HUMAN	I	1107;1079;590;590	ENSP00000391447:M1107I;ENSP00000337250:M1079I;ENSP00000383920:M590I;ENSP00000272341:M590I	ENSP00000272341:M590I	M	-	3	0	ASXL2	25819389	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.451000	0.44952	2.884000	0.98904	0.655000	0.94253	ATG	.	.		0.522	ASXL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000325593.3	NM_018263		A	25965885	C	A	25965885	3	1	311	1	0	0	0	0	1	0	0	0	1067	710	25	3	990	3	ASXL2	2	25965885	Missense_Mutation	SNP	C	TCGA-K7-A6G5-01A-11D-A30V-10	24466081	25965885	217233488	6	44228										
NFU1	27247	hgsc.bcm.edu	37	chr2	69650764	69650764	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	ggggtgggaaaatccatggtCcttgtctcaagaactggttt	13	7	1	1			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr2:69650764C>A	ENST00000410022.2	-	3	457	c.252G>T	c.(250-252)agG>agT	p.R84S	NFU1_ENST00000303698.3_Missense_Mutation_p.R60S|NFU1_ENST00000471185.1_Intron|NFU1_ENST00000394305.1_Intron	NM_001002755.2	NP_001002755.1	Q9UMS0	NFU1_HUMAN	NFU1 iron-sulfur cluster scaffold	84					iron-sulfur cluster assembly (GO:0016226)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|iron ion binding (GO:0005506)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|prostate(1)|skin(1)	7						AATCCATGGTCCTTGTCTCAA	0.373																																					p.R84S		Atlas-SNP	.											.	NFU1	19	.	0			c.G252T						.						100	100	100					2																	69650764		2203	4300	6503	SO:0001583	missense	27247	exon3			CATGGTCCTTGTC	AJ132584	CCDS33217.1, CCDS42694.1, CCDS46315.1	2p15-p13	2014-07-03	2014-07-03	2006-10-24	ENSG00000169599	ENSG00000169599			16287	protein-coding gene	gene with protein product		608100	"HIRA interacting protein 5", "NFU1 iron-sulfur cluster scaffold homolog (S. cerevisiae)"	HIRIP5		11342215, 12886008	Standard	NR_045631		Approved	CGI-33, NifU, NIFUC	uc002sfk.3	Q9UMS0	OTTHUMG00000152668	ENST00000410022.2:c.252G>T	chr2.hg19:g.69650764C>A	ENSP00000387219:p.Arg84Ser	98.0	0.0		90.0	25.0	NM_001002755	B4DUL9|Q53QE5|Q6VNZ8|Q7Z5B1|Q7Z5B2|Q9Y322	Missense_Mutation	SNP	ENST00000410022.2	hg19	CCDS33217.1	.	.	.	.	.	.	.	.	.	.	C	14.41	2.528097	0.44969	.	.	ENSG00000169599	ENST00000410022;ENST00000303698	T;T	0.62498	0.02;0.03	5.45	5.45	0.79879	NIF system FeS cluster assembly, NifU-like scaffold, N-terminal (4);	0.096119	0.64402	D	0.000001	T	0.42630	0.1211	N	0.05467	-0.045	0.80722	D	1	B;B	0.18310	0.007;0.027	B;B	0.22152	0.007;0.038	T	0.37174	-0.9717	10	0.48119	T	0.1	-0.0521	11.7654	0.51928	0.0:0.92:0.0:0.08	.	60;84	Q9UMS0-3;Q9UMS0	.;NFU1_HUMAN	S	84;60	ENSP00000387219:R84S;ENSP00000306965:R60S	ENSP00000306965:R60S	R	-	3	2	NFU1	69504268	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.088000	0.30877	2.566000	0.86566	0.638000	0.83543	AGG	.	.		0.373	NFU1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327279.3	NM_015700		A	69650764	C	A	69650764	3	1	311	1	0	0	0	0	1	0	0	0	10395	854	30	3	536	3	NFU1	2	69650764	Missense_Mutation	SNP	C	TCGA-K7-A6G5-01A-11D-A30V-10	43684879	69650764	173548609	7	44229										
CYP26B1	56603	hgsc.bcm.edu	37	chr2	72374800	72374800	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	tctctccgatgagcgggaagCccatggatcccttggggatg	14	11	1	1			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr2:72374800C>A	ENST00000001146.2	-	1	367	c.164G>T	c.(163-165)gGc>gTc	p.G55V	CYP26B1_ENST00000546307.1_Missense_Mutation_p.G55V	NM_001277742.1|NM_019885.2	NP_001264671.1|NP_063938.1	Q9NR63	CP26B_HUMAN	cytochrome P450, family 26, subfamily B, polypeptide 1	55					bone morphogenesis (GO:0060349)|cell fate determination (GO:0001709)|cellular response to retinoic acid (GO:0071300)|cornification (GO:0070268)|embryonic limb morphogenesis (GO:0030326)|establishment of skin barrier (GO:0061436)|male meiosis (GO:0007140)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|oxidation-reduction process (GO:0055114)|positive regulation of gene expression (GO:0010628)|positive regulation of tongue muscle cell differentiation (GO:2001037)|proximal/distal pattern formation (GO:0009954)|retinoic acid catabolic process (GO:0034653)|retinoic acid receptor signaling pathway (GO:0048384)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|tongue morphogenesis (GO:0043587)|vitamin metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|retinoic acid 4-hydroxylase activity (GO:0008401)|retinoic acid binding (GO:0001972)			breast(1)|kidney(3)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)	28						GAGCGGGAAGCCCATGGATCC	0.701																																					p.G55V		Atlas-SNP	.											.	CYP26B1	73	.	0			c.G164T						.						21	21	21					2																	72374800		2200	4297	6497	SO:0001583	missense	56603	exon1			GGGAAGCCCATGG		CCDS1919.1, CCDS62934.1	2p12	2006-11-24			ENSG00000003137	ENSG00000003137		"Cytochrome P450s"	20581	protein-coding gene	gene with protein product		605207				10545224	Standard	NM_019885		Approved	P450RAI-2	uc002sih.2	Q9NR63	OTTHUMG00000129756	ENST00000001146.2:c.164G>T	chr2.hg19:g.72374800C>A	ENSP00000001146:p.Gly55Val	63.0	0.0		49.0	11.0	NM_019885	B2R8M7|B7Z2K6|B7Z2P4|B7Z3B8|E4W5W7|Q32MC0|Q53TW1|Q9NP41	Missense_Mutation	SNP	ENST00000001146.2	hg19	CCDS1919.1	.	.	.	.	.	.	.	.	.	.	C	16.13	3.036330	0.54896	.	.	ENSG00000003137	ENST00000001146;ENST00000546307;ENST00000474509	T;T;T	0.79749	-0.46;-1.3;-0.27	3.97	3.97	0.46021	.	0.000000	0.64402	D	0.000011	D	0.89501	0.6733	M	0.83852	2.665	0.58432	D	0.999998	D;D	0.76494	0.999;0.997	D;D	0.87578	0.998;0.992	D	0.91111	0.4922	10	0.87932	D	0	-3.3777	13.9139	0.63885	0.0:1.0:0.0:0.0	.	55;55	B7Z2K6;Q9NR63	.;CP26B_HUMAN	V	55	ENSP00000001146:G55V;ENSP00000443304:G55V;ENSP00000430888:G55V	ENSP00000001146:G55V	G	-	2	0	CYP26B1	72228308	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.324000	0.79115	2.225000	0.72522	0.462000	0.41574	GGC	.	.		0.701	CYP26B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251969.1	NM_019885		A	72374800	C	A	72374800	3	1	311	1	0	0	0	0	1	0	0	0	4158	739	26	3	1398	3	CYP26B1	2	72374800	Missense_Mutation	SNP	C	TCGA-K7-A6G5-01A-11D-A30V-10	2724036	72374800	170824573	8	44230										
SCN2A	6326	hgsc.bcm.edu	37	chr2	166229735	166229735	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	gtgttgctttttctgtatagGtctcactggttagcttaact	9	7	2	0			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr2:166229735G>C	ENST00000375437.2	+	21	4140	c.3850G>C	c.(3850-3852)Gtc>Ctc	p.V1284L	SCN2A_ENST00000357398.3_Splice_Site_p.V1284L|SCN2A_ENST00000375427.2_Splice_Site_p.V1284L|SCN2A_ENST00000283256.6_Splice_Site_p.V1284L	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	1284					intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TTCTGTATAGGTCTCACTGGT	0.393																																					p.V1284L		Atlas-SNP	.											.	SCN2A	589	.	0			c.G3850C						.						142	142	142					2																	166229735		2203	4300	6503	SO:0001630	splice_region_variant	6326	exon20			GTATAGGTCTCAC	AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10588	protein-coding gene	gene with protein product		182390	"sodium channel, voltage-gated, type II, alpha 2 polypeptide", "sodium channel, voltage-gated, type II, alpha 1 polypeptide"	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.3850-1G>C	chr2.hg19:g.166229735G>C		102.0	0.0		96.0	21.0	NM_001040143	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Missense_Mutation	SNP	ENST00000375437.2	hg19	CCDS33314.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.643486	0.87859	.	.	ENSG00000136531	ENST00000375437;ENST00000357398;ENST00000283256;ENST00000375427	D;D;D;D	0.97279	-4.32;-4.32;-4.32;-4.32	5.78	5.78	0.91487	Ion transport (1);	0.190914	0.36815	N	0.002394	D	0.97974	0.9333	M	0.72894	2.215	0.58432	D	0.999996	D;D	0.71674	0.998;0.996	D;D	0.85130	0.971;0.997	D	0.97450	1.0027	9	.	.	.	.	13.5635	0.61804	0.0711:0.0:0.9289:0.0	.	1284;1284	Q99250-2;Q99250	.;SCN2A_HUMAN	L	1284	ENSP00000364586:V1284L;ENSP00000349973:V1284L;ENSP00000283256:V1284L;ENSP00000364576:V1284L	.	V	+	1	0	SCN2A	165937981	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.872000	0.75536	2.894000	0.99253	0.655000	0.94253	GTC	.	.		0.393	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007	Missense_Mutation	C	166229735	G	C	166229735	5	2	311	1	0	0	0	0	0	0	1	0	13931	1275	44	4	4024	4	SCN2A	2	166229735	Splice_Site	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10	93854935	166229735	76969638	9	44231										
PPIG	9360	hgsc.bcm.edu	37	chr2	170460700	170460700	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	actaccttctttttcagctgGaagagttgtctttgaattat	7	7	3	2			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr2:170460700G>T	ENST00000260970.3	+	4	285	c.65G>T	c.(64-66)gGa>gTa	p.G22V	PPIG_ENST00000448752.2_Missense_Mutation_p.G22V|PPIG_ENST00000462903.1_Missense_Mutation_p.G22V|PPIG_ENST00000409714.3_Missense_Mutation_p.G22V	NM_004792.2	NP_004783.2	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G (cyclophilin G)	22	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				protein folding (GO:0006457)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(17)|ovary(2)|stomach(1)|urinary_tract(1)	43					L-Proline(DB00172)	TTTTCAGCTGGAAGAGTTGTC	0.323																																					p.G22V		Atlas-SNP	.											.	PPIG	100	.	0			c.G65T						.						126	127	126					2																	170460700		2202	4300	6502	SO:0001583	missense	9360	exon4			CAGCTGGAAGAGT	X99717	CCDS2235.1	2q31.1	2010-07-23	2006-01-12		ENSG00000138398	ENSG00000138398	6.1.1.16		14650	protein-coding gene	gene with protein product	"SR-related CTD-associated factor 10"	606093	"peptidyl-prolyl isomerase G (cyclophilin G)"			8973360, 9153302	Standard	NM_004792		Approved	CARS-Cyp, SRCyp, SCAF10	uc002uez.3	Q13427	OTTHUMG00000132206	ENST00000260970.3:c.65G>T	chr2.hg19:g.170460700G>T	ENSP00000260970:p.Gly22Val	89.0	0.0		70.0	26.0	NM_004792	D3DPC5|D3DPC6|O00706|Q53R40|Q53SN4|Q96DG9	Missense_Mutation	SNP	ENST00000260970.3	hg19	CCDS2235.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.709286	0.89018	.	.	ENSG00000138398	ENST00000260970;ENST00000530133;ENST00000409714;ENST00000462903;ENST00000448752;ENST00000418888;ENST00000414307	D;D;D;D;D;D	0.83506	-1.73;-1.73;-1.73;-1.73;-1.73;-1.73	5.13	5.13	0.70059	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (3);Cyclophilin-like (1);	0.000000	0.85682	D	0.000000	D	0.94716	0.8295	H	0.97491	4.015	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;0.999;1.0	D	0.96502	0.9372	10	0.87932	D	0	-19.8119	18.9436	0.92613	0.0:0.0:1.0:0.0	.	22;22;22;22	E9PG73;Q2NKQ6;Q13427-2;Q13427	.;.;.;PPIG_HUMAN	V	22	ENSP00000260970:G22V;ENSP00000386245:G22V;ENSP00000435987:G22V;ENSP00000407083:G22V;ENSP00000394202:G22V;ENSP00000402222:G22V	ENSP00000260970:G22V	G	+	2	0	PPIG	170168946	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.694000	0.98686	2.541000	0.85698	0.591000	0.81541	GGA	.	.		0.323	PPIG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255264.2			T	170460700	G	T	170460700	3	4	311	1	0	0	0	0	1	0	0	0	12336	1174	41	3	71	3	PPIG	2	170460700	Missense_Mutation	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10	4230965	170460700	72738673	10	44232										
TTN	7273	hgsc.bcm.edu	37	chr2	179439946	179439946	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	caatgaccagtttctgatagAtgccacggagatccagctct	9	11	2	4			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr2:179439946A>C	ENST00000591111.1	-	276	66214	c.65990T>G	c.(65989-65991)aTc>aGc	p.I21997S	RP11-171I2.5_ENST00000604215.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.I14765S|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.I23638S|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.I14698S|TTN_ENST00000460472.2_Missense_Mutation_p.I14573S|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.I21070S			Q8WZ42	TITIN_HUMAN	titin	21997	Ig-like 115.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTTCTGATAGATGCCACGGAG	0.517																																					p.I23638S		Atlas-SNP	.											.	TTN	18412	.	0			c.T70913G						.						36	36	36					2																	179439946		1996	4184	6180	SO:0001583	missense	7273	exon326			TGATAGATGCCAC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.65990T>G	chr2.hg19:g.179439946A>C	ENSP00000465570:p.Ile21997Ser	77.0	0.0		53.0	15.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	13.11	2.140505	0.37825	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.63744	-0.06;0.18;0.16;0.15	5.6	5.6	0.85130	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.69637	0.3133	L	0.29908	0.895	0.58432	D	0.999996	D;D;D;D	0.71674	0.994;0.997;0.997;0.998	P;D;D;D	0.69824	0.892;0.939;0.939;0.966	T	0.73616	-0.3926	9	0.87932	D	0	.	15.7826	0.78272	1.0:0.0:0.0:0.0	.	14573;14698;14765;21997	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	S	21070;14573;14765;14698;14571	ENSP00000343764:I21070S;ENSP00000434586:I14573S;ENSP00000340554:I14765S;ENSP00000352154:I14698S	ENSP00000340554:I14765S	I	-	2	0	TTN	179148192	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.281000	0.95811	2.142000	0.66516	0.477000	0.44152	ATC	.	.		0.517	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179439946	A	C	179439946	3	2	311	1	0	0	0	0	1	0	0	0	16750	333	12	5	37214	5	TTN	2	179439946	Missense_Mutation	SNP	A	TCGA-K7-A6G5-01A-11D-A30V-10	8979246	179439946	63759427	11	44233										
ZNF804A	91752	hgsc.bcm.edu	37	chr2	185800549	185800549	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	atgttcaaatcaacaactgtTactgtgagagaaaactgtaa	7	6	2	2			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr2:185800549T>C	ENST00000302277.6	+	4	1020	c.426T>C	c.(424-426)gtT>gtC	p.V142V		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	142							metal ion binding (GO:0046872)			NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						CAACAACTGTTACTGTGAGAG	0.353																																					p.V142V		Atlas-SNP	.											.	ZNF804A	322	.	0			c.T426C						.						57	56	56					2																	185800549		2203	4298	6501	SO:0001819	synonymous_variant	91752	exon4			AACTGTTACTGTG	AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.426T>C	chr2.hg19:g.185800549T>C		70.0	0.0		66.0	19.0	NM_194250	A7E253|Q6ZN26	Silent	SNP	ENST00000302277.6	hg19	CCDS2291.1																																																																																			.	.		0.353	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250		C	185800549	T	C	185800549	2	2	311	1	0	0	0	0	0	0	0	1	18185	1741	61	2		2	ZNF804A	2	185800549	Silent	SNP	T	TCGA-K7-A6G5-01A-11D-A30V-10	6360603	185800549	57398824	12	44234										
COL5A2	1290	hgsc.bcm.edu	37	chr2	189907465	189907465	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	ctcttgggccaaatggtccaGggattccagcacttccttgt	10	12	1	0			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr2:189907465G>C	ENST00000374866.3	-	49	3780	c.3506C>G	c.(3505-3507)cCt>cGt	p.P1169R		NM_000393.3	NP_000384.2	P05997	CO5A2_HUMAN	collagen, type V, alpha 2	1169					axon guidance (GO:0007411)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|negative regulation of endodermal cell differentiation (GO:1903225)|skeletal system development (GO:0001501)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(53)|ovary(3)|prostate(2)|skin(6)|urinary_tract(3)	95			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			AAATGGTCCAGGGATTCCAGC	0.373																																					p.P1169R		Atlas-SNP	.											.	COL5A2	230	.	0			c.C3506G						.						92	80	84					2																	189907465		2203	4300	6503	SO:0001583	missense	1290	exon49			GGTCCAGGGATTC	Y14690	CCDS33350.1	2q14-q32	2014-09-17			ENSG00000204262	ENSG00000204262		"Collagens"	2210	protein-coding gene	gene with protein product	"AB collagen"	120190				1572660	Standard	NM_000393		Approved		uc002uqk.3	P05997	OTTHUMG00000149842	ENST00000374866.3:c.3506C>G	chr2.hg19:g.189907465G>C	ENSP00000364000:p.Pro1169Arg	46.0	0.0		42.0	17.0	NM_000393	P78440|Q13908|Q53WR4|Q59GR4|Q6LDJ5|Q7KZ55|Q86XF6|Q96QB0|Q96QB3	Missense_Mutation	SNP	ENST00000374866.3	hg19	CCDS33350.1	.	.	.	.	.	.	.	.	.	.	G	11.78	1.740792	0.30865	.	.	ENSG00000204262	ENST00000374866;ENST00000452536	D	0.98684	-5.07	5.76	5.76	0.90799	.	0.000000	0.51477	D	0.000088	D	0.97791	0.9275	M	0.67397	2.05	0.41356	D	0.987395	P;P	0.42584	0.586;0.784	B;P	0.45167	0.377;0.472	D	0.96744	0.9549	10	0.31617	T	0.26	.	13.5317	0.61625	0.0713:0.0:0.9287:0.0	.	809;1169	Q5PR22;P05997	.;CO5A2_HUMAN	R	1169;809	ENSP00000364000:P1169R	ENSP00000364000:P1169R	P	-	2	0	COL5A2	189615710	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.742000	0.47434	2.871000	0.98454	0.655000	0.94253	CCT	.	.		0.373	COL5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313523.1	NM_000393		C	189907465	G	C	189907465	3	2	311	1	0	0	0	0	1	0	0	0	3699	1000	35	4	1017	4	COL5A2	2	189907465	Missense_Mutation	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10	4106916	189907465	53291908	13	44235										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41268766	41268766	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	gaggacctatacttacgaaaAactactgtggaccacaagca	8	10	0	0			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr3:41268766A>C	ENST00000349496.5	+	7	1284	c.1004A>C	c.(1003-1005)aAa>aCa	p.K335T	CTNNB1_ENST00000396183.3_Missense_Mutation_p.K335T|CTNNB1_ENST00000405570.1_Missense_Mutation_p.K335T|CTNNB1_ENST00000453024.1_Missense_Mutation_p.K328T|CTNNB1_ENST00000396185.3_Missense_Mutation_p.K335T	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	335					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.K335I(8)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		ACTTACGAAAAACTACTGTGG	0.383		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.K335T	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,colon,carcinoma,-1,11	CTNNB1	4904	.	8	Substitution - Missense(8)	liver(7)|kidney(1)	c.A1004C						.						110	108	109					3																	41268766		2203	4300	6503	SO:0001583	missense	1499	exon7	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	ACGAAAAACTACT	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.1004A>C	chr3.hg19:g.41268766A>C	ENSP00000344456:p.Lys335Thr	94.0	0.0		111.0	24.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	26.4	4.732055	0.89390	.	.	ENSG00000168036	ENST00000405570;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185	T;T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14;-0.14	5.5	5.5	0.81552	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.82121	0.4968	M	0.89287	3.02	0.80722	D	1	D;D	0.71674	0.981;0.998	D;D	0.76575	0.913;0.988	D	0.85665	0.1291	10	0.66056	D	0.02	-3.7939	15.5934	0.76558	1.0:0.0:0.0:0.0	.	263;335	B4DSW9;P35222	.;CTNB1_HUMAN	T	335;335;335;328;335	ENSP00000385604:K335T;ENSP00000379486:K335T;ENSP00000344456:K335T;ENSP00000411226:K328T;ENSP00000379488:K335T	ENSP00000344456:K335T	K	+	2	0	CTNNB1	41243770	1.000000	0.71417	0.998000	0.56505	0.968000	0.65278	9.339000	0.96797	2.094000	0.63399	0.482000	0.46254	AAA	.	.		0.383	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41268766	A	C	41268766	3	2	311	1	0	0	0	0	1	0	0	0	4018	14	1	5	1026	5	CTNNB1	3	41268766	Missense_Mutation	SNP	A	TCGA-K7-A6G5-01A-11D-A30V-10		41268766	156753664	14	44236										
HIGD1A	25994	hgsc.bcm.edu	37	chr3	42826810	42826810	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	ccgatacatggaatagcccaTacctaaagaaaaagaatgct	7	9	0	2	rs368330989		TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr3:42826810T>C	ENST00000321331.7	-	4	352	c.235A>G	c.(235-237)Atg>Gtg	p.M79V	HIGD1A_ENST00000470543.1_5'UTR|HIGD1A_ENST00000452906.2_Missense_Mutation_p.M93V|HIGD1A_ENST00000430190.1_Missense_Mutation_p.Y84C|HIGD1A_ENST00000418900.2_Missense_Mutation_p.M79V	NM_001099669.1|NM_014056.3	NP_001093139.1|NP_054775.2	Q9Y241	HIG1A_HUMAN	HIG1 hypoxia inducible domain family, member 1A	79	HIG1. {ECO:0000255|PROSITE- ProRule:PRU00836}.				cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|protein complex (GO:0043234)|respiratory chain (GO:0070469)				lung(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.217)		GAATAGCCCATACCTAAAGAA	0.363																																					p.M93V		Atlas-SNP	.											.	HIGD1A	12	.	0			c.A277G						.	T	VAL/MET,VAL/MET,VAL/MET	0,3628		0,0,1814	95	88	90		235,235,277	4.4	1	3		90	1,8155		0,1,4077	no	missense,missense,missense	HIGD1A	NM_014056.3,NM_001099669.1,NM_001099668.1	21,21,21	0,1,5891	CC,CT,TT		0.0123,0.0,0.0085	benign,benign,benign	79/94,79/94,93/108	42826810	1,11783	1814	4078	5892	SO:0001583	missense	25994	exon4			AGCCCATACCTAA	BC009583	CCDS43073.1, CCDS46806.1	3p22.1	2014-02-12	2009-03-17		ENSG00000181061	ENSG00000181061			29527	protein-coding gene	gene with protein product	"hypoxia inducible gene 1"		"HIG1 domain family, member 1A"			11042152, 11230166	Standard	NM_001099668		Approved	HIG1, DKFZP564K247	uc010hid.3	Q9Y241	OTTHUMG00000156277	ENST00000321331.7:c.235A>G	chr3.hg19:g.42826810T>C	ENSP00000319393:p.Met79Val	648.0	0.0		538.0	108.0	NM_001099668	Q9UFZ2	Missense_Mutation	SNP	ENST00000321331.7	hg19	CCDS43073.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.358|0.358	-0.941198|-0.941198	0.02322|0.02322	0.0|0.0	1.23E-4|1.23E-4	ENSG00000181061|ENSG00000181061	ENST00000321331;ENST00000418900;ENST00000452906|ENST00000430190	T;T;T|.	0.27256|.	1.7;1.7;1.68|.	4.42|4.42	4.42|4.42	0.53409|0.53409	Hypoxia induced protein, domain (1);|.	0.086182|.	0.85682|.	D|.	0.000000|.	T|T	0.52125|0.52125	0.1715|0.1715	.|.	.|.	.|.	0.30552|0.30552	N|N	0.765356|0.765356	B;B|.	0.11235|.	0.004;0.0|.	B;B|.	0.13407|.	0.009;0.001|.	T|T	0.57505|0.57505	-0.7800|-0.7800	9|5	0.02654|0.62326	T|D	1|0.03	-6.03|-6.03	10.2143|10.2143	0.43160|0.43160	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	93;79|.	Q9Y241-2;Q9Y241|.	.;HIG1A_HUMAN|.	V|C	79;79;93|84	ENSP00000319393:M79V;ENSP00000402160:M79V;ENSP00000398064:M93V|.	ENSP00000319393:M79V|ENSP00000408289:Y84C	M|Y	-|-	1|2	0|0	HIGD1A|HIGD1A	42801814|42801814	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.971000|0.971000	0.66376|0.66376	2.221000|2.221000	0.42917|0.42917	1.987000|1.987000	0.57996|0.57996	0.402000|0.402000	0.26972|0.26972	ATG|TAT	.	.		0.363	HIGD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343686.1	NM_014056		C	42826810	T	C	42826810	3	2	311	1	0	0	0	0	1	0	0	0	7115	1406	49	2	50	2	HIGD1A	3	42826810	Missense_Mutation	SNP	T	TCGA-K7-A6G5-01A-11D-A30V-10	1558044	42826810	155195620	15	44237										
SETD2	29072	hgsc.bcm.edu	37	chr3	47162395	47162395	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	agtgcaagccatccacatgtGgtatctcacaagaggaagaa	10	9	1	2			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr3:47162395G>A	ENST00000409792.3	-	3	3773	c.3731C>T	c.(3730-3732)cCa>cTa	p.P1244L		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1244					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		ATCCACATGTGGTATCTCACA	0.443			"N, F, S, Mis"		clear cell renal carcinoma																																p.P1244L		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.C3731T						.						110	110	110					3																	47162395		2203	4300	6503	SO:0001583	missense	29072	exon3			ACATGTGGTATCT	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.3731C>T	chr3.hg19:g.47162395G>A	ENSP00000386759:p.Pro1244Leu	79.0	0.0		71.0	7.0	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	hg19	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	G	9.177	1.022546	0.19433	.	.	ENSG00000181555	ENST00000451092;ENST00000543224;ENST00000409792;ENST00000412450	D;T	0.87809	-2.3;1.57	5.28	5.28	0.74379	.	0.104145	0.43260	D	0.000581	T	0.78285	0.4259	N	0.08118	0	0.35744	D	0.818904	B;B	0.19817	0.039;0.039	B;B	0.16722	0.016;0.01	T	0.78069	-0.2348	10	0.87932	D	0	.	19.111	0.93317	0.0:0.0:1.0:0.0	.	1244;1244	F2Z317;Q9BYW2	.;SETD2_HUMAN	L	1244;1244;1244;1200	ENSP00000386759:P1244L;ENSP00000416401:P1200L	ENSP00000386759:P1244L	P	-	2	0	SETD2	47137399	0.922000	0.31269	0.309000	0.25155	0.008000	0.06430	3.949000	0.56668	2.756000	0.94617	0.655000	0.94253	CCA	.	.		0.443	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		A	47162395	G	A	47162395	3	1	311	1	0	0	0	0	1	0	0	0	14146	1348	47	3	4039	3	SETD2	3	47162395	Missense_Mutation	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10	4335585	47162395	150860035	16	44238										
CBLB	868	hgsc.bcm.edu	37	chr3	105586253	105586253	+	Splice_Site	DEL	C	C	-													0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	gcaacgtcagacagaacttaCcactttgtccatgagcttcc							TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr3:105586253delC	ENST00000264122.4	-	2	490		c.e2+1		CBLB_ENST00000403724.1_Splice_Site|CBLB_ENST00000545639.1_Splice_Site|CBLB_ENST00000394027.3_Splice_Site|CBLB_ENST00000405772.1_Splice_Site	NM_170662.3	NP_733762.2	Q13191	CBLB_HUMAN	Cbl proto-oncogene B, E3 ubiquitin protein ligase						cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of alpha-beta T cell proliferation (GO:0046642)|negative regulation of T cell receptor signaling pathway (GO:0050860)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of T cell anergy (GO:0002669)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(2)|urinary_tract(2)	49						ACAGAACTTACCACTTTGTCC	0.443			Mis S		AML																																.	GBM(93;588 1337 9788 29341 43499)	Atlas-Indel,Pindel	.		Rec	yes		3	3q13.11	868	Cas-Br-M (murine) ecotropic retroviral transforming sequence b		L	.	CBLB	118	.	0			c.168+2G>-						.						162	151	155					3																	105586253		2203	4300	6503	SO:0001630	splice_region_variant	868	exon3			.	U26710	CCDS2948.1	3q	2013-07-09	2013-07-09		ENSG00000114423	ENSG00000114423		"RING-type (C3HC4) zinc fingers"	1542	protein-coding gene	gene with protein product		604491	"Cas-Br-M (murine) ectropic retroviral transforming sequence b", "Cas-Br-M (murine) ecotropic retroviral transforming sequence b"			7784085	Standard	XM_005247853		Approved	RNF56, Cbl-b	uc003dwc.3	Q13191	OTTHUMG00000150654	ENST00000264122.4:c.168+1G>-	chr3.hg19:g.105586253delC		67.0	0.0		56.0	19.0	NM_170662	A8K9S7|B7WNM4|Q13192|Q13193|Q3LIC0|Q63Z43|Q8IVC5	Splice_Site	DEL	ENST00000264122.4	hg19	CCDS2948.1																																																																																			.	.		0.443	CBLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319417.2	NM_170662	Intron	-	105586253	C	-	105586253	8	5	311	1	0	1	0	1	0	0	1	0	2703	521	18	0	2851	0	CBLB	3	105586253	Splice_Site	DEL	C	TCGA-K7-A6G5-01A-11D-A30V-10	58423858	105586253	92436177	17	44239										
KIAA0232	9778	hgsc.bcm.edu	37	chr4	6863165	6863165	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	attcatactggaagtagtagCagtagcagcagtggttctgt	12	6	2	0			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr4:6863165C>T	ENST00000307659.5	+	7	1511	c.1056C>T	c.(1054-1056)agC>agT	p.S352S	KIAA0232_ENST00000425103.1_Silent_p.S352S	NM_014743.2	NP_055558.2	Q92628	K0232_HUMAN	KIAA0232	352	Poly-Ser.						ATP binding (GO:0005524)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(12)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	41						GAAGTAGTAGCAGTAGCAGCA	0.463																																					p.S352S		Atlas-SNP	.											.	KIAA0232	102	.	0			c.C1056T						.						73	75	74					4																	6863165		1915	4125	6040	SO:0001819	synonymous_variant	9778	exon7			TAGTAGCAGTAGC	D86985	CCDS43209.1	4p16.1	2012-11-29			ENSG00000170871	ENSG00000170871			28992	protein-coding gene	gene with protein product						9039502	Standard	NM_014743		Approved		uc003gjq.4	Q92628	OTTHUMG00000160072	ENST00000307659.5:c.1056C>T	chr4.hg19:g.6863165C>T		107.0	0.0		86.0	21.0	NM_014743	A7E2D2	Silent	SNP	ENST00000307659.5	hg19	CCDS43209.1																																																																																			.	.		0.463	KIAA0232-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359102.2	NM_014743		T	6863165	C	T	6863165	2	4	311	1	0	0	0	0	0	0	0	1	8172	709	25	3		3	KIAA0232	4	6863165	Silent	SNP	C	TCGA-K7-A6G5-01A-11D-A30V-10		6863165	184291111	18	44240										
ALB	213	hgsc.bcm.edu	37	chr4	74283386	74283387	+	Splice_Site	DEL	TG	TG	-													0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	atgccctgtgcagaagactaTgtgagtctttaaaaaaatat					rs78527483		TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr4:74283386_74283387delTG	ENST00000503124.1	+	9	1185	c.978delTG	c.(976-978)tat>ta	p.Y326fs	ALB_ENST00000415165.2_Splice_Site_p.Y284fs|ALB_ENST00000401494.3_Splice_Site_p.Y361fs|ALB_ENST00000509063.1_Splice_Site_p.Y476fs|ALB_ENST00000295897.4_Splice_Site_p.Y476fs|ALB_ENST00000505649.1_Intron			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CAGAAGACTATGTGAGTCttta	0.332																																					p.476_476del		Atlas-Indel,Pindel	.											.	ALB	132	.	0			c.1427_1428del						.																																			SO:0001630	splice_region_variant	213	exon11			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.978+1TG>-	chr4.hg19:g.74283388_74283389delTG		111.0	0.0		68.0	23.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Frame_Shift_Del	DEL	ENST00000503124.1	hg19																																																																																				.	.		0.332	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477	Frame_Shift_Del	-	74283387	TG	-	74283386	8	5	311	1	0	1	0	1	0	0	1	0	486	1478	51	0	1470	0	ALB	4	74283386	Splice_Site	DEL	TG	TCGA-K7-A6G5-01A-11D-A30V-10	67420221	74283386	116870890	19	44241										
ALB	213	hgsc.bcm.edu	37	chr4	74285295	74285296	+	Frame_Shift_Ins	INS	-	-	C													0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	aaagctgttatggatgatttINScgcagcttttgtagagaagt							TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr4:74285295_74285296insC	ENST00000503124.1	+	11	1481_1482	c.1274_1275insC	c.(1273-1278)ttcgcafs	p.A426fs	ALB_ENST00000415165.2_Frame_Shift_Ins_p.A384fs|ALB_ENST00000401494.3_Frame_Shift_Ins_p.A461fs|ALB_ENST00000509063.1_Frame_Shift_Ins_p.A576fs|ALB_ENST00000295897.4_Frame_Shift_Ins_p.A576fs|ALB_ENST00000505649.1_3'UTR			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			ATGGATGATTTCGCAGCTTTTG	0.411																																					p.F575fs		Atlas-Indel,Pindel	.											.	ALB	132	.	0			c.1724_1725insC						.																																			SO:0001589	frameshift_variant	213	exon13			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.1275dupC	chr4.hg19:g.74285296_74285296dupC	ENSP00000421027:p.Ala426fs	51.0	0.0		62.0	18.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Frame_Shift_Ins	INS	ENST00000503124.1	hg19																																																																																				.	.		0.411	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		C	74285296	-	C	74285295	7	5	311	1	0	1	1	0	0	0	0	0	486	1783	62	0	1774	0	ALB	4	74285295	Frame_Shift_Ins	INS	-	TCGA-K7-A6G5-01A-11D-A30V-10	1909	74285295	116868981	20	44242										
BMPR1B	658	hgsc.bcm.edu	37	chr4	96052422	96052422	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	ggacccagttgtacctaatcAcagactatcatgaaaatggt	8	9	2	2			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr4:96052422A>G	ENST00000515059.1	+	10	1118	c.835A>G	c.(835-837)Aca>Gca	p.T279A	BMPR1B_ENST00000440890.2_Missense_Mutation_p.T309A|BMPR1B_ENST00000264568.4_Missense_Mutation_p.T279A|BMPR1B_ENST00000394931.1_Missense_Mutation_p.T279A	NM_001203.2	NP_001194.1	O00238	BMR1B_HUMAN	bone morphogenetic protein receptor, type IB	279	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				BMP signaling pathway (GO:0030509)|cartilage condensation (GO:0001502)|chondrocyte differentiation (GO:0002062)|dorsal/ventral pattern formation (GO:0009953)|eye development (GO:0001654)|inflammatory response (GO:0006954)|limb morphogenesis (GO:0035108)|ovarian cumulus expansion (GO:0001550)|ovulation cycle (GO:0042698)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cell differentiation (GO:0045597)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of osteoblast differentiation (GO:0045669)|protein phosphorylation (GO:0006468)|retina development in camera-type eye (GO:0060041)|retinal ganglion cell axon guidance (GO:0031290)|skeletal system development (GO:0001501)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta receptor activity, type I (GO:0005025)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(8)|ovary(1)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.51e-07)		GTACCTAATCACAGACTATCA	0.403																																					p.T309A		Atlas-SNP	.											.	BMPR1B	121	.	0			c.A925G						.						92	77	82					4																	96052422		2203	4300	6503	SO:0001583	missense	658	exon8			CTAATCACAGACT	D89675	CCDS3642.1, CCDS58919.1	4q23-q24	2008-02-05			ENSG00000138696	ENSG00000138696		"CD molecules"	1077	protein-coding gene	gene with protein product		603248				8140412, 9730621	Standard	NM_001203		Approved	ALK6, CDw293	uc031sgn.1	O00238	OTTHUMG00000130991	ENST00000515059.1:c.835A>G	chr4.hg19:g.96052422A>G	ENSP00000426617:p.Thr279Ala	162.0	0.0		132.0	33.0	NM_001256793	B2R953|B4DSV1|P78366	Missense_Mutation	SNP	ENST00000515059.1	hg19	CCDS3642.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.258231	0.80246	.	.	ENSG00000138696	ENST00000515059;ENST00000512312;ENST00000509540;ENST00000440890;ENST00000264568;ENST00000394931	D;D;D;D;D;D	0.93859	-3.3;-3.3;-3.3;-3.3;-3.3;-3.3	6.06	6.06	0.98353	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.97629	0.9223	M	0.93328	3.405	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98565	1.0643	10	0.87932	D	0	.	16.6093	0.84858	1.0:0.0:0.0:0.0	.	279	O00238	BMR1B_HUMAN	A	279;279;279;309;279;279	ENSP00000426617:T279A;ENSP00000425444:T279A;ENSP00000421671:T279A;ENSP00000401907:T309A;ENSP00000264568:T279A;ENSP00000378389:T279A	ENSP00000264568:T279A	T	+	1	0	BMPR1B	96271445	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.274000	0.78538	2.324000	0.78689	0.533000	0.62120	ACA	.	.		0.403	BMPR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253609.3	NM_001203		G	96052422	A	G	96052422	3	3	311	1	0	0	0	0	1	0	0	0	1470	159	6	2	861	2	BMPR1B	4	96052422	Missense_Mutation	SNP	A	TCGA-K7-A6G5-01A-11D-A30V-10	21767127	96052422	95101854	21	44243										
EIF4E	1977	hgsc.bcm.edu	37	chr4	99850252	99850252	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	aaggcaatactcaccggttcGacagtcgccatcttagatcg	9	12	2	1			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr4:99850252G>A	ENST00000450253.2	-	1	1536	c.12C>T	c.(10-12)gtC>gtT	p.V4V	EIF4E_ENST00000505992.1_Silent_p.V4V|AC019131.1_ENST00000459306.1_RNA|EIF4E_ENST00000504472.1_5'UTR|EIF4E_ENST00000280892.6_5'Flank|EIF4E_ENST00000504432.1_5'UTR|RP11-571L19.7_ENST00000583654.1_RNA	NM_001968.3	NP_001959.1	P06730	IF4E_HUMAN	eukaryotic translation initiation factor 4E	4					cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of mitotic cell cycle (GO:0045931)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|extracellular vesicular exosome (GO:0070062)|mRNA cap binding complex (GO:0005845)|RISC complex (GO:0016442)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation initiation factor activity (GO:0003743)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)	13				OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)|LUSC - Lung squamous cell carcinoma(721;0.00227)		TCACCGGTTCGACAGTCGCCA	0.612																																					p.V4V		Atlas-SNP	.											.	EIF4E	18	.	0			c.C12T						.						12	12	12					4																	99850252		2191	4282	6473	SO:0001819	synonymous_variant	1977	exon1			CGGTTCGACAGTC	M15353	CCDS34031.1, CCDS47109.1, CCDS54779.1	4q21-q25	2008-02-05			ENSG00000151247	ENSG00000151247			3287	protein-coding gene	gene with protein product		133440		EIF4EL1, EIF4F		9330633, 1916814	Standard	NM_001968		Approved	EIF4E1	uc011cea.1	P06730	OTTHUMG00000161090	ENST00000450253.2:c.12C>T	chr4.hg19:g.99850252G>A		54.0	0.0		46.0	12.0	NM_001130679	B7Z6V1|D6RCQ6|Q96E95	Silent	SNP	ENST00000450253.2	hg19	CCDS34031.1	.	.	.	.	.	.	.	.	.	.	G	10.92	1.487573	0.26686	.	.	ENSG00000151247	ENST00000511644	.	.	.	4.53	3.69	0.42338	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.7273	0.51716	0.0:0.8112:0.1888:0.0	.	.	.	.	X	1	.	.	R	-	1	2	EIF4E	100069275	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.084000	0.41625	1.126000	0.42016	-0.171000	0.13296	CGA	.	.		0.612	EIF4E-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000363739.1	NM_001968		A	99850252	G	A	99850252	2	1	311	1	0	0	0	0	0	0	0	1	5030	1045	37	1		1	EIF4E	4	99850252	Silent	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10	3797830	99850252	91304024	22	44244										
C4orf17	84103	hgsc.bcm.edu	37	chr4	100463066	100463066	+	Splice_Site	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	agatttttttctctatttcaGaggctgagcacaagcctcca	7	10	2	3			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr4:100463066G>C	ENST00000326581.4	+	9	1242		c.e9-1			NM_032149.2	NP_115525.2	Q53FE4	CD017_HUMAN	chromosome 4 open reading frame 17											central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|prostate(1)|urinary_tract(3)	18				OV - Ovarian serous cystadenocarcinoma(123;2.08e-08)		CTCTATTTCAGAGGCTGAGCA	0.328																																					.		Atlas-SNP	.											.	C4orf17	42	.	0			c.881-1G>C						.						26	28	28					4																	100463066		2200	4295	6495	SO:0001630	splice_region_variant	84103	exon9			ATTTCAGAGGCTG	AL136838	CCDS3649.1	4q23	2008-02-05			ENSG00000138813	ENSG00000138813			25274	protein-coding gene	gene with protein product						11230166	Standard	NM_032149		Approved	DKFZP434G072	uc003huw.3	Q53FE4	OTTHUMG00000131027	ENST00000326581.4:c.881-1G>C	chr4.hg19:g.100463066G>C		232.0	0.0		176.0	10.0	NM_032149	Q6FI84|Q6IS77|Q8NA78|Q9H0D9	Splice_Site	SNP	ENST00000326581.4	hg19	CCDS3649.1	.	.	.	.	.	.	.	.	.	.	G	13.04	2.118326	0.37339	.	.	ENSG00000138813	ENST00000326581	.	.	.	5.32	4.44	0.53790	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.4052	0.49894	0.0:0.0:0.821:0.179	.	.	.	.	.	-1	.	.	.	+	.	.	C4orf17	100682089	1.000000	0.71417	1.000000	0.80357	0.566000	0.35808	2.399000	0.44495	2.764000	0.94973	0.650000	0.86243	.	.	.		0.328	C4orf17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253670.2	NM_032149	Intron	C	100463066	G	C	100463066	5	2	311	1	0	0	0	0	0	0	1	0	2254	956	33	4	910	4	C4orf17	4	100463066	Splice_Site	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10	612814	100463066	90691210	23	44245										
PCDH10	57575	hgsc.bcm.edu	37	chr4	134071449	134071449	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	ttacaaaactttcggctcgcGggtttcagacggtgcccaac	10	12	1	1			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr4:134071449G>A	ENST00000264360.5	+	1	980	c.154G>A	c.(154-156)Ggg>Agg	p.G52R	RP11-9G1.3_ENST00000505289.1_lincRNA	NM_032961.1	NP_116586.1	Q9P2E7	PCD10_HUMAN	protocadherin 10	52	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.G52W(1)		NS(2)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(30)|liver(1)|lung(72)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(2)	136				LUSC - Lung squamous cell carcinoma(193;0.227)		TTCGGCTCGCGGGTTTCAGAC	0.522																																					p.G52R		Atlas-SNP	.											PCDH10,NS,carcinoma,0,1	PCDH10	290	.	1	Substitution - Missense(1)	lung(1)	c.G154A						.						100	101	100					4																	134071449		2203	4300	6503	SO:0001583	missense	57575	exon1			GCTCGCGGGTTTC	AB037821	CCDS34063.1, CCDS75192.1	4q28.3	2010-01-26				ENSG00000138650		"Cadherins / Protocadherins : Non-clustered"	13404	protein-coding gene	gene with protein product		608286				10835267	Standard	NM_020815		Approved	OL-PCDH, KIAA1400	uc003iha.3	Q9P2E7		ENST00000264360.5:c.154G>A	chr4.hg19:g.134071449G>A	ENSP00000264360:p.Gly52Arg	94.0	0.0		79.0	19.0	NM_032961	Q4W5F6|Q96SF0	Missense_Mutation	SNP	ENST00000264360.5	hg19	CCDS34063.1	.	.	.	.	.	.	.	.	.	.	G	0.290	-0.980606	0.02197	.	.	ENSG00000138650	ENST00000264360;ENST00000394248	T	0.28069	1.63	4.77	-2.74	0.05932	Cadherin, N-terminal (1);Cadherin (2);Cadherin-like (1);	0.568307	0.14595	N	0.310037	T	0.08044	0.0201	N	0.01284	-0.91	0.29296	N	0.869002	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.34950	-0.9808	10	0.19590	T	0.45	.	6.4676	0.21990	0.3755:0.3283:0.2962:0.0	.	52;52	Q9P2E7;Q96SF0	PCD10_HUMAN;.	R	52	ENSP00000264360:G52R	ENSP00000264360:G52R	G	+	1	0	PCDH10	134290899	1.000000	0.71417	0.994000	0.49952	0.913000	0.54294	1.734000	0.38166	-0.267000	0.09325	-0.378000	0.06908	GGG	.	.		0.522	PCDH10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000364457.2	NM_032961		A	134071449	G	A	134071449	3	1	311	1	0	0	0	0	1	0	0	0	11516	1116	39	1	156	1	PCDH10	4	134071449	Missense_Mutation	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10	33608383	134071449	57082827	24	44246										
PRMT10	90826	hgsc.bcm.edu	37	chr4	148579096	148579097	+	Frame_Shift_Ins	INS	-	-	AGGCTTTTTAGTTGCA													0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	acaggaataccaatcttatcINSaggctttttagttgcaagac							TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr4:148579096_148579097insAGGCTTTTTAGTTGCA	ENST00000322396.6	-	8	1418_1419	c.1176_1177insTGCAACTAAAAAGCCT	c.(1174-1179)cctgatfs	p.D393fs	TMEM184C_ENST00000508208.1_Intron|PRMT10_ENST00000541232.1_Frame_Shift_Ins_p.D280fs	NM_138364.2	NP_612373.2	Q6P2P2	ANM9_HUMAN		393	SAM-dependent MTase PRMT-type 1. {ECO:0000255|PROSITE-ProRule:PRU01015}.					cytoplasm (GO:0005737)	protein methyltransferase activity (GO:0008276)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28						CCAATCTTATCAGGCTTTTTAG	0.332																																					p.D393_K394delinsCNX		Atlas-Indel,Pindel	.											.	PRMT10	68	.	0			c.1177_1178insTGCAACTAAAAAGCCT						.																																			SO:0001589	frameshift_variant	90826	exon8			.																												ENST00000322396.6:c.1161_1176dupTGCAACTAAAAAGCCT	chr4.hg19:g.148579096_148579097insAGGCTTTTTAGTTGCA	ENSP00000314396:p.Asp393fs	102.0	0.0		119.0	20.0	NM_138364	A8KA39|B3KU92|Q6ZR58|Q8N383|Q9BT55|Q9NT98	Frame_Shift_Ins	INS	ENST00000322396.6	hg19	CCDS3771.1																																																																																			.	.		0.332	PRMT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364650.1			AGGCTTTTTAGTTGCA	148579097	-	AGGCTTTTTAGTTGCA	148579096	7	5	311	1	0	1	1	0	0	0	0	0	12548	826	29	0	1380	0	PRMT10	4	148579096	Frame_Shift_Ins	INS	-	TCGA-K7-A6G5-01A-11D-A30V-10	14507647	148579096	42575180	25	44247										
ZNF608	57507	hgsc.bcm.edu	37	chr5	123979216	123979216	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	aggcttacagcaggagacttGctgcggtattggttagcatg	14	7	0	1			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr5:123979216G>A	ENST00000306315.5	-	6	4719	c.4284C>T	c.(4282-4284)agC>agT	p.S1428S	ZNF608_ENST00000513985.1_5'UTR|ZNF608_ENST00000504926.1_Silent_p.S1001S	NM_020747.2	NP_065798.2	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	1428							metal ion binding (GO:0046872)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(12)|ovary(3)|skin(6)|urinary_tract(1)	46		all_cancers(142;0.186)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783)		CAGGAGACTTGCTGCGGTATT	0.428																																					p.S1428S		Atlas-SNP	.											.	ZNF608	117	.	0			c.C4284T						.						194	161	173					5																	123979216		2203	4300	6503	SO:0001819	synonymous_variant	57507	exon6			AGACTTGCTGCGG	AB033107	CCDS34219.1	5q23.2	2008-05-02			ENSG00000168916	ENSG00000168916		"Zinc fingers, C2H2-type"	29238	protein-coding gene	gene with protein product						10574462, 10508479	Standard	NM_020747		Approved	KIAA1281, DKFZp434M098, NY-REN-36	uc003ktq.1	Q9ULD9	OTTHUMG00000162999	ENST00000306315.5:c.4284C>T	chr5.hg19:g.123979216G>A		119.0	0.0		110.0	27.0	NM_020747	A7E2W9|Q3SYM6|Q68D12|Q8IY05|Q9Y5A1	Silent	SNP	ENST00000306315.5	hg19	CCDS34219.1																																																																																			.	.		0.428	ZNF608-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371300.1	XM_114432		A	123979216	G	A	123979216	2	1	311	1	0	0	0	0	0	0	0	1	18049	1310	46	3		3	ZNF608	5	123979216	Silent	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10		123979216	56936044	26	44248										
PCDHA7	56141	hgsc.bcm.edu	37	chr5	140214367	140214367	+	Frame_Shift_Del	DEL	C	C	-													0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	aacgacaaccctccggtgttCccagcgacacaaaggaatct							TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr5:140214367delC	ENST00000525929.1	+	1	399	c.399delC	c.(397-399)ttcfs	p.F133fs	PCDHA5_ENST00000529859.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA7_ENST00000378125.3_Frame_Shift_Del_p.F133fs|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA6_ENST00000529310.1_Intron	NM_018910.2	NP_061733.1	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7	133	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|biliary_tract(1)|breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCCGGTGTTCCCAGCGACAC	0.582																																					p.F133fs	NSCLC(160;258 2013 5070 22440 28951)	Atlas-INDEL	.											PCDHA7_ENST00000525929,lower_third,carcinoma,0,2	PCDHA7	367	.	0			c.398delT						.						106	101	103					5																	140214367		2203	4300	6503	SO:0001589	frameshift_variant	56141	exon1			.	AF152485	CCDS54918.1	5q31	2010-11-26				ENSG00000204963		"Cadherins / Protocadherins : Clustered"	8673	other	complex locus constituent	"KIAA0345-like 7", "ortholog to mouse CNR4"	606313		CNRS4		10380929, 10662547	Standard	NM_018910		Approved	CNR4, CRNR4		Q9UN72		ENST00000525929.1:c.399delC	chr5.hg19:g.140214367delC	ENSP00000436426:p.Phe133fs	399.0	0.0		322.0	94.0	NM_018910	O75282	Frame_Shift_Del	DEL	ENST00000525929.1	hg19	CCDS54918.1																																																																																			.	.		0.582	PCDHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372887.2	NM_018910		-	140214367	C	-	140214367	7	5	311	1	0	1	0	1	0	0	0	0	11538	854	30	0	401	0	PCDHA7	5	140214367	Frame_Shift_Del	DEL	C	TCGA-K7-A6G5-01A-11D-A30V-10	16235151	140214367	40700893	27	44249										
GRPEL2	134266	hgsc.bcm.edu	37	chr5	148725167	148725167	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	cctactggcctggagtgccgCgtgggagagcaagtaagcat	15	10	0	1			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr5:148725167C>G	ENST00000329271.3	+	1	175	c.65C>G	c.(64-66)gCg>gGg	p.A22G	GRPEL2_ENST00000416916.2_Missense_Mutation_p.A22G|GRPEL2_ENST00000513661.1_Missense_Mutation_p.A22G|GRPEL2-AS1_ENST00000521295.1_RNA	NM_152407.3	NP_689620.2	Q8TAA5	GRPE2_HUMAN	GrpE-like 2, mitochondrial (E. coli)	22					cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|protein targeting to mitochondrion (GO:0006626)	mitochondrial inner membrane (GO:0005743)	adenyl-nucleotide exchange factor activity (GO:0000774)			breast(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGAGTGCCGCGTGGGAGAGC	0.682																																					p.A22G		Atlas-SNP	.											.	GRPEL2	18	.	0			c.C65G						.						15	18	17					5																	148725167		2200	4299	6499	SO:0001583	missense	134266	exon1			GTGCCGCGTGGGA	AL832325	CCDS4295.1	5q33.1	2008-02-05			ENSG00000164284	ENSG00000164284			21060	protein-coding gene	gene with protein product							Standard	NM_152407		Approved	DKFZp451C205, Mt-GrpE#2, FLJ23713	uc003lqj.3	Q8TAA5	OTTHUMG00000130048	ENST00000329271.3:c.65C>G	chr5.hg19:g.148725167C>G	ENSP00000329558:p.Ala22Gly	133.0	0.0		91.0	18.0	NM_152407	B4DFA6|Q49AJ6	Missense_Mutation	SNP	ENST00000329271.3	hg19	CCDS4295.1	.	.	.	.	.	.	.	.	.	.	C	14.99	2.699566	0.48307	.	.	ENSG00000164284	ENST00000513661;ENST00000329271;ENST00000416916	.	.	.	4.96	0.83	0.18854	.	0.904049	0.09399	N	0.807544	T	0.21103	0.0508	N	0.19112	0.55	0.09310	N	1	B;B	0.32396	0.369;0.093	B;B	0.34385	0.181;0.028	T	0.23940	-1.0174	9	0.36615	T	0.2	-3.3056	3.322	0.07053	0.1659:0.4169:0.3229:0.0943	.	22;22	B4DFA6;Q8TAA5	.;GRPE2_HUMAN	G	22	.	ENSP00000329558:A22G	A	+	2	0	GRPEL2	148705360	0.000000	0.05858	0.002000	0.10522	0.051000	0.14879	0.278000	0.18753	0.030000	0.15379	0.561000	0.74099	GCG	.	.		0.682	GRPEL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252327.1	NM_152407		G	148725167	C	G	148725167	3	3	311	1	0	0	0	0	1	0	0	0	6816	768	27	4	67	4	GRPEL2	5	148725167	Missense_Mutation	SNP	C	TCGA-K7-A6G5-01A-11D-A30V-10	8510800	148725167	32190093	28	44250										
CPLX2	10814	hgsc.bcm.edu	37	chr5	175306952	175306952	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	cccaagaaggccatccctgcGggctgcggggacgaggagga	17	12	0	1	rs150632571	byFrequency	TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr5:175306952G>T	ENST00000359546.4	+	5	952	c.309G>T	c.(307-309)gcG>gcT	p.A103A	CPLX2_ENST00000515094.1_Silent_p.A103A|CPLX2_ENST00000393745.3_Silent_p.A103A	NM_001008220.1|NM_006650.3	NP_001008221.1|NP_006641.1	Q6PUV4	CPLX2_HUMAN	complexin 2	103					cell differentiation (GO:0030154)|mast cell degranulation (GO:0043303)|nervous system development (GO:0007399)|positive regulation of synaptic plasticity (GO:0031915)|regulation of exocytosis (GO:0017157)|synaptic vesicle exocytosis (GO:0016079)|vesicle docking involved in exocytosis (GO:0006904)	dendrite (GO:0030425)|mast cell granule (GO:0042629)|neuronal cell body (GO:0043025)|synapse (GO:0045202)|synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex (GO:0070033)|synaptobrevin 2-SNAP-25-syntaxin-3-complexin complex (GO:0070554)		p.A103A(2)		endometrium(3)|kidney(2)|lung(3)|ovary(2)	10	all_cancers(89;0.004)|Renal(175;0.000269)|Lung NSC(126;0.00441)|all_lung(126;0.00747)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			CCATCCCTGCGGGCTGCGGGG	0.622																																					p.A103A		Atlas-SNP	.											.	CPLX2	42	.	2	Substitution - coding silent(2)	kidney(2)	c.G309T						.						34	38	37					5																	175306952		2203	4300	6503	SO:0001819	synonymous_variant	10814	exon5			CCCTGCGGGCTGC	U35100	CCDS4396.1	5q35.2	2008-05-23			ENSG00000145920	ENSG00000145920			2310	protein-coding gene	gene with protein product		605033				7553862, 16162394	Standard	XM_005265798		Approved	CPX-2, DKFZp547D155	uc003mdf.1	Q6PUV4	OTTHUMG00000130665	ENST00000359546.4:c.309G>T	chr5.hg19:g.175306952G>T		155.0	0.0		119.0	5.0	NM_006650	B2RAG2|O09056|Q13329|Q28184|Q52M15|Q64386	Silent	SNP	ENST00000359546.4	hg19	CCDS4396.1																																																																																			.	G|1.000;A|0.000		0.622	CPLX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253157.2			T	175306952	G	T	175306952	2	4	311	1	0	0	0	0	0	0	0	1	3807	1103	39	1		1	CPLX2	5	175306952	Silent	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10	26581785	175306952	5608308	29	44251										
TNXB	7148	hgsc.bcm.edu	37	chr6	32037937	32037937	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	ggcagtgagagggccatggcGcttcttgcccaggaggccat	16	11	1	1			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr6:32037937G>T	ENST00000375244.3	-	14	5446	c.5245C>A	c.(5245-5247)Cgc>Agc	p.R1749S	TNXB_ENST00000375247.2_Missense_Mutation_p.R1749S			P22105	TENX_HUMAN	tenascin XB	1831	Fibronectin type-III 9. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						GGGCCATGGCGCTTCTTGCCC	0.652																																					p.R1749S		Atlas-SNP	.											TNXB_ENST00000375247,NS,carcinoma,0,2	TNXB	553	.	0			c.C5245A						.						25	29	28					6																	32037937		2017	4186	6203	SO:0001583	missense	7148	exon14			CATGGCGCTTCTT	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.5245C>A	chr6.hg19:g.32037937G>T	ENSP00000364393:p.Arg1749Ser	46.0	0.0		30.0	3.0	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	hg19		.	.	.	.	.	.	.	.	.	.	G	18.80	3.701296	0.68501	.	.	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.04706	3.57;3.57	5.15	4.27	0.50696	.	0.000000	0.53938	D	0.000046	T	0.12987	0.0315	M	0.87097	2.86	0.09310	N	1	D	0.76494	0.999	D	0.85130	0.997	T	0.05338	-1.0891	10	0.38643	T	0.18	.	11.3566	0.49620	0.0886:0.0:0.9114:0.0	.	1749	P22105-3	.	S	1749	ENSP00000364393:R1749S;ENSP00000364396:R1749S	ENSP00000364393:R1749S	R	-	1	0	TNXB	32145915	0.991000	0.36638	0.756000	0.31282	0.821000	0.46438	3.761000	0.55242	2.403000	0.81681	0.561000	0.74099	CGC	.	.		0.652	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		T	32037937	G	T	32037937	3	4	311	1	0	0	0	0	1	0	0	0	16361	1087	38	1	9592	1	TNXB	6	32037937	Missense_Mutation	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10		32037937	139077130	30	44252										
CAPN11	11131	hgsc.bcm.edu	37	chr6	44147887	44147887	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	ttcgggtcttcaccgagaagCacagcgagtcatggtaaggg	14	9	3	1			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr6:44147887C>A	ENST00000398776.1	+	14	1665	c.1627C>A	c.(1627-1629)Cac>Aac	p.H543N	CAPN11_ENST00000542245.1_Missense_Mutation_p.H543N	NM_007058.3	NP_008989.2	Q9UMQ6	CAN11_HUMAN	calpain 11	543	Domain III.				proteolysis (GO:0006508)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|peptidase activity (GO:0008233)			breast(3)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)	36	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CACCGAGAAGCACAGCGAGTC	0.587																																					p.H543N		Atlas-SNP	.											.	CAPN11	66	.	0			c.C1627A						.						25	25	25					6																	44147887		2055	4218	6273	SO:0001583	missense	11131	exon14			GAGAAGCACAGCG	AJ242832	CCDS47436.1	6p12	2013-01-10			ENSG00000137225	ENSG00000137225		"EF-hand domain containing"	1478	protein-coding gene	gene with protein product		604822				10409436	Standard	NM_007058		Approved		uc003owt.1	Q9UMQ6	OTTHUMG00000014758	ENST00000398776.1:c.1627C>A	chr6.hg19:g.44147887C>A	ENSP00000381758:p.His543Asn	37.0	0.0		31.0	8.0	NM_007058	B2RA64|Q5T3G1|Q8N4R5	Missense_Mutation	SNP	ENST00000398776.1	hg19	CCDS47436.1	.	.	.	.	.	.	.	.	.	.	C	16.81	3.224609	0.58668	.	.	ENSG00000137225	ENST00000398776;ENST00000542245	D;D	0.87809	-2.3;-2.3	4.67	3.8	0.43715	Peptidase C2, calpain, large subunit, domain III (2);Peptidase C2, calpain, domain III (1);	0.135690	0.34555	N	0.003869	T	0.78604	0.4309	L	0.43923	1.385	0.31109	N	0.7102	P;P	0.52692	0.891;0.955	P;P	0.52343	0.494;0.696	T	0.75303	-0.3365	10	0.45353	T	0.12	.	5.8402	0.18629	0.1908:0.7111:0.0:0.098	.	197;543	B4DT90;Q9UMQ6	.;CAN11_HUMAN	N	543	ENSP00000381758:H543N;ENSP00000441078:H543N	ENSP00000381758:H543N	H	+	1	0	CAPN11	44255865	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	3.729000	0.54999	1.333000	0.45449	0.609000	0.83330	CAC	.	.		0.587	CAPN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040714.3			A	44147887	C	A	44147887	3	1	311	1	0	0	0	0	1	0	0	0	2626	710	25	3	1681	3	CAPN11	6	44147887	Missense_Mutation	SNP	C	TCGA-K7-A6G5-01A-11D-A30V-10	12109950	44147887	126967180	31	44253										
EYS	346007	hgsc.bcm.edu	37	chr6	65149117	65149117	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	atctactaaatttgagtcttGcttgacatacagcagaagtc	7	8	2	3			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr6:65149117G>T	ENST00000370621.3	-	27	6299	c.5773C>A	c.(5773-5775)Caa>Aaa	p.Q1925K	EYS_ENST00000370616.2_Missense_Mutation_p.Q1925K|EYS_ENST00000503581.1_Missense_Mutation_p.Q1925K			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	1925	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						TTTGAGTCTTGCTTGACATAC	0.289																																					p.Q1925K		Atlas-SNP	.											.	EYS	527	.	0			c.C5773A						.						60	53	55					6																	65149117		692	1590	2282	SO:0001583	missense	346007	exon27			AGTCTTGCTTGAC		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.5773C>A	chr6.hg19:g.65149117G>T	ENSP00000359655:p.Gln1925Lys	146.0	0.0		90.0	16.0	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	hg19		.	.	.	.	.	.	.	.	.	.	G	4.459	0.085035	0.08583	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	T;T;T	0.68624	-0.34;-0.34;-0.34	4.33	1.35	0.21983	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.	.	.	.	T	0.35219	0.0924	N	0.19112	0.55	0.41592	D	0.9888	B;B	0.34181	0.386;0.44	B;B	0.38378	0.178;0.272	T	0.20075	-1.0286	9	0.49607	T	0.09	.	9.4444	0.38688	0.0819:0.4505:0.4676:0.0	.	1925;1925	Q5T1H1-1;Q5T1H1	.;EYS_HUMAN	K	1925	ENSP00000424243:Q1925K;ENSP00000359655:Q1925K;ENSP00000359650:Q1925K	ENSP00000359650:Q1925K	Q	-	1	0	EYS	65205838	0.991000	0.36638	0.113000	0.21522	0.009000	0.06853	0.955000	0.29188	0.243000	0.21327	-0.274000	0.10170	CAA	.	.		0.289	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		T	65149117	G	T	65149117	3	4	311	1	0	0	0	0	1	0	0	0	5334	1328	46	3	3574	3	EYS	6	65149117	Missense_Mutation	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10	21001230	65149117	105965950	32	44254										
KCNQ5	56479	hgsc.bcm.edu	37	chr6	73843259	73843259	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	caagcaccgacatcacagccGagggcagtcccaccaaagtg	10	15	1	0			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr6:73843259G>A	ENST00000370398.1	+	10	1472	c.1363G>A	c.(1363-1365)Gag>Aag	p.E455K	KCNQ5_ENST00000355635.3_Missense_Mutation_p.E456K|KCNQ5_ENST00000355194.4_Missense_Mutation_p.E455K|KCNQ5-AS1_ENST00000429832.1_RNA|KCNQ5_ENST00000414165.2_Intron|KCNQ5_ENST00000342056.2_Missense_Mutation_p.E474K|KCNQ5_ENST00000403813.2_Missense_Mutation_p.E446K|KCNQ5_ENST00000402622.2_Missense_Mutation_p.E465K	NM_019842.3	NP_062816.2	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 5	455					protein complex assembly (GO:0006461)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|inward rectifier potassium channel activity (GO:0005242)			breast(1)|cervix(1)|endometrium(6)|kidney(7)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	57		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)	Ezogabine(DB04953)	CATCACAGCCGAGGGCAGTCC	0.592																																					p.E474K	GBM(142;1375 1859 14391 23261 44706)	Atlas-SNP	.											KCNQ5,bladder,carcinoma,0,1	KCNQ5	153	.	0			c.G1420A						.						102	102	102					6																	73843259		2203	4300	6503	SO:0001583	missense	56479	exon11			ACAGCCGAGGGCA	AF202977	CCDS4976.1, CCDS55034.1	6q14	2012-07-05			ENSG00000185760	ENSG00000185760		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6299	protein-coding gene	gene with protein product		607357				10787416, 10816588, 16382104	Standard	NM_019842		Approved	Kv7.5	uc011dyh.2	Q9NR82	OTTHUMG00000015020	ENST00000370398.1:c.1363G>A	chr6.hg19:g.73843259G>A	ENSP00000359425:p.Glu455Lys	92.0	0.0		48.0	12.0	NM_001160133	A6NKT6|A6PVT6|A8MSQ5|B4DS33|B5MC83|B7ZL37|F5GZV0|Q17RE1|Q5VVP3|Q86W40|Q9NRN0|Q9NYA6	Missense_Mutation	SNP	ENST00000370398.1	hg19	CCDS4976.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	34|34	5.356508|5.356508	0.95854|0.95854	.|.	.|.	ENSG00000185760|ENSG00000185760	ENST00000342056;ENST00000451840;ENST00000355194;ENST00000370398;ENST00000402622;ENST00000355635;ENST00000403813|ENST00000427928	D;D;D;D;D;D|.	0.99660|.	-6.32;-6.32;-6.32;-6.32;-6.32;-6.32|.	5.59|5.59	5.59|5.59	0.84812|0.84812	Potassium channel, voltage dependent, KCNQ, C-terminal (1);|.	0.268023|.	0.35838|.	N|.	0.002948|.	T|T	0.57607|0.57607	0.2065|0.2065	L|L	0.41492|0.41492	1.28|1.28	0.80722|0.80722	D|D	1|1	P;P;P;P|.	0.49783|.	0.928;0.588;0.753;0.793|.	B;B;B;B|.	0.36534|.	0.216;0.225;0.194;0.227|.	T|T	0.52518|0.52518	-0.8565|-0.8565	10|5	0.52906|.	T|.	0.07|.	.|.	18.1396|18.1396	0.89634|0.89634	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	465;474;446;455|.	Q9NR82-3;A6PVT6;Q9NR82-2;Q9NR82|.	.;.;.;KCNQ5_HUMAN|.	K|Q	474;474;455;455;465;456;446|46	ENSP00000345055:E474K;ENSP00000347326:E455K;ENSP00000359425:E455K;ENSP00000385501:E465K;ENSP00000347853:E456K;ENSP00000384453:E446K|.	ENSP00000345055:E474K|.	E|R	+|+	1|2	0|0	KCNQ5|KCNQ5	73899980|73899980	1.000000|1.000000	0.71417|0.71417	0.990000|0.990000	0.47175|0.47175	0.979000|0.979000	0.70002|0.70002	7.582000|7.582000	0.82546|0.82546	2.797000|2.797000	0.96272|0.96272	0.563000|0.563000	0.77884|0.77884	GAG|CGA	.	.		0.592	KCNQ5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041198.3	NM_019842		A	73843259	G	A	73843259	3	1	311	1	0	0	0	0	1	0	0	0	8095	1059	37	1	1462	1	KCNQ5	6	73843259	Missense_Mutation	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10	8694142	73843259	97271808	33	44255										
C6orf204	387119	hgsc.bcm.edu	37	chr6	118887408	118887408	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	gctggaattagacggcatcaCatgggcagtaggaagagtaa	14	6	1	2			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr6:118887408C>A	ENST00000368491.3	-	3	925	c.304G>T	c.(304-306)Gtg>Ttg	p.V102L	CEP85L_ENST00000360290.3_5'UTR|CEP85L_ENST00000472713.1_5'UTR|CEP85L_ENST00000392500.3_Missense_Mutation_p.V105L|CEP85L_ENST00000419517.2_Missense_Mutation_p.V102L|CEP85L_ENST00000368488.5_Missense_Mutation_p.V105L	NM_001042475.2	NP_001035940.1	Q5SZL2	CE85L_HUMAN	centrosomal protein 85kDa-like	102						centrosome (GO:0005813)|cytoplasm (GO:0005737)											GACGGCATCACATGGGCAGTA	0.393																																					p.V105L		Atlas-SNP	.											.	CEP85L	26	.	0			c.G313T						.						51	51	51					6																	118887408		2203	4300	6503	SO:0001583	missense	387119	exon4			GCATCACATGGGC	AF308284	CCDS5119.2, CCDS43498.1, CCDS55052.1	6q22.31	2011-11-25	2011-11-25	2011-11-25	ENSG00000111860	ENSG00000111860			21638	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 204"	C6orf204			Standard	NM_206921		Approved	NY-BR-15, bA57K17.2	uc003pya.2	Q5SZL2	OTTHUMG00000015465	ENST00000368491.3:c.304G>T	chr6.hg19:g.118887408C>A	ENSP00000357477:p.Val102Leu	61.0	0.0		46.0	13.0	NM_001178035	A1A4E1|A2A3P2|A2IDE5|F8W6J2|G3V0H3|Q2TAM2|Q5T323|Q7Z5K7|Q9H289	Missense_Mutation	SNP	ENST00000368491.3	hg19	CCDS43498.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.862730	0.91511	.	.	ENSG00000111860	ENST00000368491;ENST00000368488;ENST00000434604;ENST00000392500;ENST00000419517	T;T;T;T;T	0.21932	1.98;1.98;1.98;1.98;1.98	5.96	5.96	0.96718	.	0.150870	0.43747	D	0.000534	T	0.34687	0.0906	L	0.46819	1.47	0.45837	D	0.998704	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.68621	0.959;0.945;0.945;0.945	T	0.03423	-1.1038	10	0.87932	D	0	-12.4625	20.422	0.99049	0.0:1.0:0.0:0.0	.	105;102;105;102	Q5SZL2-2;G3V0H3;F8W6J2;Q5SZL2	.;.;.;CF204_HUMAN	L	102;105;105;105;102	ENSP00000357477:V102L;ENSP00000357474:V105L;ENSP00000392131:V105L;ENSP00000376288:V105L;ENSP00000393317:V102L	ENSP00000357474:V105L	V	-	1	0	C6orf204	118994101	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.473000	0.73572	2.832000	0.97577	0.655000	0.94253	GTG	.	.		0.393	CEP85L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041996.2	NM_001042475		A	118887408	C	A	118887408	3	1	311	1	0	0	0	0	1	0	0	0	2355	478	17	3	2211	3	C6orf204	6	118887408	Missense_Mutation	SNP	C	TCGA-K7-A6G5-01A-11D-A30V-10	45044149	118887408	52227659	34	44256										
PNLDC1	154197	hgsc.bcm.edu	37	chr6	160237044	160237044	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	ctggaccagagattgttcacGcgagcaggtgtgagaaatat	13	7	1	2	rs137878641	byFrequency	TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr6:160237044G>T	ENST00000610273.1	+	13	1177	c.1006G>T	c.(1006-1008)Gcg>Tcg	p.A336S	PNLDC1_ENST00000392167.3_Missense_Mutation_p.A347S	NM_001271862.1|NM_173516.1	NP_001258791.1|NP_775787.1	Q8NA58	PNDC1_HUMAN	poly(A)-specific ribonuclease (PARN)-like domain containing 1	336						integral component of membrane (GO:0016021)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(9)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	31		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;1.55e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		GATTGTTCACGCGAGCAGGTG	0.448																																					p.A336S		Atlas-SNP	.											.	PNLDC1	66	.	0			c.G1006T						.						124	108	114					6																	160237044		2203	4300	6503	SO:0001583	missense	154197	exon13			GTTCACGCGAGCA	AK097559	CCDS5271.1, CCDS5271.2, CCDS64561.1	6q25.3	2008-02-05			ENSG00000146453	ENSG00000146453			21185	protein-coding gene	gene with protein product							Standard	NM_001271862		Approved	FLJ40240, dJ195P10.2	uc003qsy.2	Q8NA58	OTTHUMG00000015941	ENST00000610273.1:c.1006G>T	chr6.hg19:g.160237044G>T	ENSP00000476448:p.Ala336Ser	47.0	0.0		41.0	11.0	NM_173516	Q5TAP7|Q8N7X5	Missense_Mutation	SNP	ENST00000610273.1	hg19	CCDS5271.1	.	.	.	.	.	.	.	.	.	.	G	7.262	0.605325	0.14002	.	.	ENSG00000146453	ENST00000275275;ENST00000392167	T;T	0.20463	2.07;2.07	4.78	0.623	0.17654	Ribonuclease H-like (1);	0.721130	0.12837	N	0.435169	T	0.06096	0.0158	L	0.35644	1.08	0.09310	N	1	B;P	0.48230	0.405;0.907	B;B	0.43052	0.115;0.406	T	0.32455	-0.9906	10	0.12103	T	0.63	.	12.0983	0.53767	0.0:0.0:0.3997:0.6002	.	347;336	Q8NA58-2;Q8NA58	.;PNDC1_HUMAN	S	336;347	ENSP00000275275:A336S;ENSP00000376007:A347S	ENSP00000275275:A336S	A	+	1	0	PNLDC1	160157034	0.557000	0.26546	0.002000	0.10522	0.039000	0.13416	2.252000	0.43196	-0.070000	0.12908	-0.558000	0.04189	GCG	.	G|0.999;A|0.001		0.448	PNLDC1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_173516		T	160237044	G	T	160237044	3	4	311	1	0	0	0	0	1	0	0	0	12157	1087	38	1	1052	1	PNLDC1	6	160237044	Missense_Mutation	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10	41349636	160237044	10878023	35	44257										
NPTX2	4885	hgsc.bcm.edu	37	chr7	98257930	98257930	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	agacgtgtgaggagcgtctcCttgacttgtagccgccttct	12	11	2	3			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr7:98257930C>T	ENST00000265634.3	+	5	1450	c.1285C>T	c.(1285-1287)Ctt>Ttt	p.L429F		NM_002523.2	NP_002514.1	P47972	NPTX2_HUMAN	neuronal pentraxin II	429	Pentaxin.				synaptic transmission (GO:0007268)	extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			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)			GGAGCGTCTCCTTGACTTGTA	0.577																																					p.L429F		Atlas-SNP	.											.	NPTX2	45	.	0			c.C1285T						.						39	37	37					7																	98257930		2202	4300	6502	SO:0001583	missense	4885	exon5			CGTCTCCTTGACT		CCDS5657.1	7q21.3-q22.1	2008-04-30			ENSG00000106236	ENSG00000106236			7953	protein-coding gene	gene with protein product	"apexin"	600750				8530029	Standard	NM_002523		Approved		uc003upl.2	P47972	OTTHUMG00000154369	ENST00000265634.3:c.1285C>T	chr7.hg19:g.98257930C>T	ENSP00000265634:p.Leu429Phe	64.0	0.0		50.0	12.0	NM_002523	A4D267|Q86XV7|Q96G70	Missense_Mutation	SNP	ENST00000265634.3	hg19	CCDS5657.1	.	.	.	.	.	.	.	.	.	.	C	11.46	1.643911	0.29246	.	.	ENSG00000106236	ENST00000265634	T	0.12147	2.71	5.94	5.06	0.68205	.	0.061993	0.64402	D	0.000006	T	0.04452	0.0122	N	0.00926	-1.1	0.35814	D	0.824057	B	0.06786	0.001	B	0.06405	0.002	T	0.27739	-1.0065	10	0.31617	T	0.26	-5.8534	8.9727	0.35917	0.1474:0.779:0.0:0.0736	.	429	P47972	NPTX2_HUMAN	F	429	ENSP00000265634:L429F	ENSP00000265634:L429F	L	+	1	0	NPTX2	98095866	0.675000	0.27558	0.980000	0.43619	0.796000	0.44982	1.270000	0.33086	1.531000	0.49152	0.561000	0.74099	CTT	.	.		0.577	NPTX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334982.1	NM_002523		T	98257930	C	T	98257930	3	4	311	1	0	0	0	0	1	0	0	0	10612	681	24	3	1303	3	NPTX2	7	98257930	Missense_Mutation	SNP	C	TCGA-K7-A6G5-01A-11D-A30V-10		98257930	60880733	36	44258										
WNT2	7472	hgsc.bcm.edu	37	chr7	116960721	116960721	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	tggcattctgctgtccactcGgccacgccctggctaatggc	11	15	1	0	rs139486726	byFrequency	TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr7:116960721G>A	ENST00000265441.3	-	2	509	c.210C>T	c.(208-210)gcC>gcT	p.A70A	AC002465.2_ENST00000436097.1_RNA	NM_003391.2	NP_003382.1	P09544	WNT2_HUMAN	wingless-type MMTV integration site family member 2	70					atrial cardiac muscle tissue morphogenesis (GO:0055009)|canonical Wnt signaling pathway (GO:0060070)|cardiac epithelial to mesenchymal transition (GO:0060317)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|iris morphogenesis (GO:0061072)|labyrinthine layer blood vessel development (GO:0060716)|lens development in camera-type eye (GO:0002088)|lung development (GO:0030324)|lung induction (GO:0060492)|mammary gland epithelium development (GO:0061180)|neuron differentiation (GO:0030182)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)			breast(2)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|ovary(3)|prostate(1)|skin(2)	31	all_epithelial(6;2.24e-06)|Lung NSC(10;0.000936)|all_lung(10;0.00109)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		CTGTCCACTCGGCCACGCCCT	0.602													G|||	2	0.000399361	0	0	5008	,	,		19823	0.002		0	False		,,,				2504	0				p.A70A		Atlas-SNP	.											.	WNT2	56	.	0			c.C210T						.	G		2,4404	4.2+/-10.8	0,2,2201	75	58	64		210	-10.6	0.1	7	dbSNP_134	64	0,8600		0,0,4300	no	coding-synonymous	WNT2	NM_003391.2		0,2,6501	AA,AG,GG		0.0,0.0454,0.0154		70/361	116960721	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	7472	exon2			CCACTCGGCCACG	X07876	CCDS5771.1	7q31	2013-02-28			ENSG00000105989	ENSG00000105989		"Wingless-type MMTV integration sites", "Endogenous ligands"	12780	protein-coding gene	gene with protein product	"secreted growth factor"	147870		INT1L1		2971536	Standard	NM_003391		Approved	IRP	uc003viz.3	P09544	OTTHUMG00000023428	ENST00000265441.3:c.210C>T	chr7.hg19:g.116960721G>A		36.0	0.0		50.0	13.0	NM_003391	A4D0V1|Q75N05|Q9UDP9	Silent	SNP	ENST00000265441.3	hg19	CCDS5771.1																																																																																			.	G|1.000;A|0.000		0.602	WNT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059749.3	NM_003391		A	116960721	G	A	116960721	2	1	311	1	0	0	0	0	0	0	0	1	17401	1103	39	1		1	WNT2	7	116960721	Silent	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10	18702791	116960721	42177942	37	44259										
TSTA3	7264	hgsc.bcm.edu	37	chr8	144695934	144695934	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	tacccaccggagaggatgatGggctccacttcattgtactc	10	12	1	2			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr8:144695934G>A	ENST00000425753.2	-	8	820	c.717C>T	c.(715-717)ccC>ccT	p.P239P	TSTA3_ENST00000529064.1_Silent_p.P239P	NM_003313.3	NP_003304.1	Q13630	FCL_HUMAN	tissue specific transplantation antigen P35B	239					'de novo' GDP-L-fucose biosynthetic process (GO:0042351)|cytolysis (GO:0019835)|GDP-mannose metabolic process (GO:0019673)|leukocyte cell-cell adhesion (GO:0007159)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	coenzyme binding (GO:0050662)|electron carrier activity (GO:0009055)|GDP-4-dehydro-D-rhamnose reductase activity (GO:0042356)|GDP-L-fucose synthase activity (GO:0050577)|isomerase activity (GO:0016853)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|skin(1)	9	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.17e-38)|Epithelial(56;7.17e-37)|all cancers(56;2.46e-32)|Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)			AGAGGATGATGGGCTCCACTT	0.607																																					p.P239P		Atlas-SNP	.											.	TSTA3	23	.	0			c.C717T						.						33	30	31					8																	144695934		2083	4025	6108	SO:0001819	synonymous_variant	7264	exon8			GATGATGGGCTCC	U58766	CCDS6408.1	8q24.3	2012-02-22			ENSG00000104522	ENSG00000104522	1.1.1.271	"Short chain dehydrogenase/reductase superfamily / Extended SDR fold"	12390	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 4E, member 1", "GDP-L-fucose synthase"	137020				7803801, 1348494, 19027726	Standard	NM_003313		Approved	FX, P35B, SDR4E1	uc003yzb.2	Q13630	OTTHUMG00000165159	ENST00000425753.2:c.717C>T	chr8.hg19:g.144695934G>A		70.0	0.0		122.0	43.0	NM_003313	B2R8Y7|D3DWK5|Q567Q9|Q9UDG7	Silent	SNP	ENST00000425753.2	hg19	CCDS6408.1																																																																																			.	.		0.607	TSTA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382263.1	NM_003313		A	144695934	G	A	144695934	2	1	311	1	0	0	0	0	0	0	0	1	16689	1335	47	3		3	TSTA3	8	144695934	Silent	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10		144695934	1668088	38	44260										
NOL6	65083	hgsc.bcm.edu	37	chr9	33465828	33465828	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	gcgagatcatcccctctgggCtctgcacctccttcaggatc	9	16	4	1			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr9:33465828C>T	ENST00000379471.2	-	19	2519	c.2432G>A	c.(2431-2433)aGc>aAc	p.S811N	NOL6_ENST00000455041.2_Missense_Mutation_p.S759N|NOL6_ENST00000464829.1_Intron			Q9H6R4	NOL6_HUMAN	nucleolar protein 6 (RNA-associated)	811					rRNA processing (GO:0006364)	condensed nuclear chromosome (GO:0000794)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|skin(2)	27			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.152)		CCCCTCTGGGCTCTGCACCTC	0.572																																					p.S811N		Atlas-SNP	.											.	NOL6	85	.	0			c.G2432A						.						78	66	70					9																	33465828		2203	4300	6503	SO:0001583	missense	65083	exon19			TCTGGGCTCTGCA	AF361079	CCDS6543.1, CCDS6544.1	9p12	2013-02-22	2013-02-22		ENSG00000165271	ENSG00000165271			19910	protein-coding gene	gene with protein product		611532	"nucleolar protein family 6 (RNA-associated)"			11895476, 15590835	Standard	NM_022917		Approved	bA311H10.1, Nrap, FLJ21959, MGC14896, MGC14921, MGC20838, UTP22	uc003zsz.3	Q9H6R4	OTTHUMG00000000394	ENST00000379471.2:c.2432G>A	chr9.hg19:g.33465828C>T	ENSP00000368784:p.Ser811Asn	45.0	0.0		41.0	12.0	NM_022917	Q5T5M3|Q5T5M4|Q7L4G6|Q8N6I0|Q8TEY9|Q8TEZ0|Q8TEZ1|Q9H675	Missense_Mutation	SNP	ENST00000379471.2	hg19		.	.	.	.	.	.	.	.	.	.	C	11.09	1.535200	0.27475	.	.	ENSG00000165271	ENST00000297990;ENST00000379471;ENST00000541373;ENST00000325914;ENST00000455041	T;T;T	0.43688	0.94;0.94;0.94	5.94	4.06	0.47325	.	0.123193	0.85682	N	0.000000	T	0.27169	0.0666	L	0.29908	0.895	0.40134	D	0.976759	B;B;B;B	0.18741	0.03;0.01;0.024;0.03	B;B;B;B	0.17098	0.017;0.006;0.01;0.017	T	0.08229	-1.0732	10	0.16420	T	0.52	.	8.618	0.33845	0.0:0.565:0.3433:0.0916	.	759;808;811;811	B4DF80;Q9H6R4-4;Q9H6R4-2;Q9H6R4	.;.;.;NOL6_HUMAN	N	811;811;367;811;759	ENSP00000297990:S811N;ENSP00000368784:S811N;ENSP00000395915:S759N	ENSP00000297990:S811N	S	-	2	0	NOL6	33455828	1.000000	0.71417	0.999000	0.59377	0.355000	0.29361	1.888000	0.39708	1.513000	0.48852	0.563000	0.77884	AGC	.	.		0.572	NOL6-005	NOVEL	non_canonical_TEC|basic	protein_coding	protein_coding	OTTHUMT00000001019.2	NM_022917		T	33465828	C	T	33465828	3	4	311	1	0	0	0	0	1	0	0	0	10534	797	28	3	1040	3	NOL6	9	33465828	Missense_Mutation	SNP	C	TCGA-K7-A6G5-01A-11D-A30V-10		33465828	107747603	39	44261										
PRUNE2	158471	hgsc.bcm.edu	37	chr9	79320343	79320343	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	gtctgaggctagcaaagcatCaggaaccaaggcaggattct	12	9	3	1			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr9:79320343C>T	ENST00000376718.3	-	8	6970	c.6847G>A	c.(6847-6849)Gat>Aat	p.D2283N	PRUNE2_ENST00000428286.1_Missense_Mutation_p.D1924N	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	2283					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						AGCAAAGCATCAGGAACCAAG	0.473																																					p.D2283N		Atlas-SNP	.											.	PRUNE2	331	.	0			c.G6847A						.						56	51	53					9																	79320343		1568	3582	5150	SO:0001583	missense	158471	exon8			AAGCATCAGGAAC	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.6847G>A	chr9.hg19:g.79320343C>T	ENSP00000365908:p.Asp2283Asn	93.0	0.0		90.0	16.0	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	hg19	CCDS47982.1	.	.	.	.	.	.	.	.	.	.	C	17.04	3.288435	0.59976	.	.	ENSG00000106772	ENST00000376718;ENST00000428286;ENST00000422033	T;T	0.53857	0.6;0.62	5.66	3.77	0.43336	.	0.797388	0.11280	N	0.580461	T	0.49304	0.1549	M	0.62723	1.935	0.23346	N	0.997861	B	0.18461	0.028	B	0.15052	0.012	T	0.38628	-0.9652	10	0.32370	T	0.25	-1.1507	10.0639	0.42292	0.0:0.7902:0.1368:0.073	.	2283	Q8WUY3	PRUN2_HUMAN	N	2283;1924;2282	ENSP00000365908:D2283N;ENSP00000397425:D1924N	ENSP00000365908:D2283N	D	-	1	0	PRUNE2	78510163	0.002000	0.14202	0.001000	0.08648	0.758000	0.43043	1.527000	0.35975	0.691000	0.31592	0.655000	0.94253	GAT	.	.		0.473	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		T	79320343	C	T	79320343	3	4	311	1	0	0	0	0	1	0	0	0	12653	826	29	3	2467	3	PRUNE2	9	79320343	Missense_Mutation	SNP	C	TCGA-K7-A6G5-01A-11D-A30V-10	45854515	79320343	61893088	40	44262										
LAMC3	10319	hgsc.bcm.edu	37	chr9	133942439	133942439	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	gccaccagtgccagtgtagcGggaacgtggaccccaatgcc	13	14	0	0	rs529385350		TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr9:133942439G>A	ENST00000361069.4	+	14	2573	c.2440G>A	c.(2440-2442)Ggg>Agg	p.G814R	LAMC3_ENST00000480883.1_Intron	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	814	Laminin EGF-like 8. {ECO:0000255|PROSITE- ProRule:PRU00460}.				astrocyte development (GO:0014002)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|extracellular matrix organization (GO:0030198)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	structural molecule activity (GO:0005198)	p.G814R(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(31)|ovary(3)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	69	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		CCAGTGTAGCGGGAACGTGGA	0.642																																					p.G814R		Atlas-SNP	.											LAMC3,NS,carcinoma,0,1	LAMC3	167	.	1	Substitution - Missense(1)	ovary(1)	c.G2440A						.						65	56	59					9																	133942439		2203	4300	6503	SO:0001583	missense	10319	exon14			TGTAGCGGGAACG	AF041835	CCDS6938.1	9q31-q34	2013-03-01			ENSG00000050555	ENSG00000050555		"Laminins"	6494	protein-coding gene	gene with protein product		604349				10225960	Standard	NM_006059		Approved	DKFZp434E202	uc004caa.1	Q9Y6N6	OTTHUMG00000020819	ENST00000361069.4:c.2440G>A	chr9.hg19:g.133942439G>A	ENSP00000354360:p.Gly814Arg	42.0	0.0		26.0	10.0	NM_006059	B1APX9|B1APY0|Q59H72	Missense_Mutation	SNP	ENST00000361069.4	hg19	CCDS6938.1	.	.	.	.	.	.	.	.	.	.	G	14.94	2.684891	0.47991	.	.	ENSG00000050555	ENST00000361069;ENST00000355048	T	0.66995	-0.24	4.8	3.89	0.44902	EGF-like, laminin (3);	0.299825	0.35903	N	0.002908	T	0.76478	0.3993	H	0.95816	3.725	0.52501	D	0.999959	P	0.37525	0.598	B	0.41135	0.348	T	0.78881	-0.2029	10	0.54805	T	0.06	.	9.275	0.37694	0.168:0.0:0.832:0.0	.	814	Q9Y6N6	LAMC3_HUMAN	R	814	ENSP00000354360:G814R	ENSP00000347156:G814R	G	+	1	0	LAMC3	132932260	1.000000	0.71417	0.694000	0.30210	0.378000	0.30076	4.898000	0.63238	1.128000	0.42052	0.650000	0.86243	GGG	.	.		0.642	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3	NM_006059		A	133942439	G	A	133942439	3	1	311	1	0	0	0	0	1	0	0	0	8625	1116	39	1	2494	1	LAMC3	9	133942439	Missense_Mutation	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10	54622096	133942439	7270992	41	44263										
NOTCH1	4851	hgsc.bcm.edu	37	chr9	139405212	139405212	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	ggcaggatgcgccgtgccggCacgggctcagaacgcactcg	16	14	1	1			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr9:139405212C>T	ENST00000277541.6	-	17	2708	c.2633G>A	c.(2632-2634)tGc>tAc	p.C878Y		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	878	EGF-like 23; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		GCCGTGCCGGCACGGGCTCAG	0.701			"T, Mis, O"	TRB@	T-ALL					HNSCC(8;0.001)																											p.C878Y		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"Notch homolog 1, translocation-associated (Drosophila) (TAN1)"		L	.	NOTCH1	1980	.	0			c.G2633A						.						32	40	37					9																	139405212		2041	4168	6209	SO:0001583	missense	4851	exon17			TGCCGGCACGGGC	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"Ankyrin repeat domain containing"	7881	protein-coding gene	gene with protein product		190198	"Notch (Drosophila) homolog 1 (translocation-associated)", "Notch homolog 1, translocation-associated (Drosophila)"	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.2633G>A	chr9.hg19:g.139405212C>T	ENSP00000277541:p.Cys878Tyr	73.0	0.0		38.0	17.0	NM_017617	Q59ED8|Q5SXM3	Missense_Mutation	SNP	ENST00000277541.6	hg19	CCDS43905.1	.	.	.	.	.	.	.	.	.	.	C	19.44	3.828185	0.71143	.	.	ENSG00000148400	ENST00000277541	D	0.99445	-5.91	4.88	4.88	0.63580	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.99832	0.9924	H	0.99916	4.945	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96194	0.9140	10	0.87932	D	0	.	17.0189	0.86428	0.0:1.0:0.0:0.0	.	878	P46531	NOTC1_HUMAN	Y	878	ENSP00000277541:C878Y	ENSP00000277541:C878Y	C	-	2	0	NOTCH1	138525033	1.000000	0.71417	0.990000	0.47175	0.328000	0.28507	7.633000	0.83260	2.253000	0.74438	0.561000	0.74099	TGC	.	.		0.701	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		T	139405212	C	T	139405212	3	4	311	1	0	0	0	0	1	0	0	0	10556	710	25	3	5106	3	NOTCH1	9	139405212	Missense_Mutation	SNP	C	TCGA-K7-A6G5-01A-11D-A30V-10	5462773	139405212	1808219	42	44264										
PRKCQ	5588	hgsc.bcm.edu	37	chr10	6498670	6498670	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	agtcaggtgtcccacagaagGtattcgtcttggcatctcct	10	11	3	1			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr10:6498670G>T	ENST00000263125.5	-	15	1712	c.1613C>A	c.(1612-1614)aCc>aAc	p.T538N	PRKCQ_ENST00000397176.2_Missense_Mutation_p.T538N|PRKCQ_ENST00000539722.1_Missense_Mutation_p.T413N	NM_001282644.1|NM_006257.3	NP_001269573.1|NP_006248.1	Q04759	KPCT_HUMAN	protein kinase C, theta	538	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of T cell apoptotic process (GO:0070233)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of T-helper 2 cell activation (GO:2000570)|protein ubiquitination (GO:0016567)|regulation of cell growth (GO:0001558)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of transcription, DNA-templated (GO:0006355)|rhodopsin mediated signaling pathway (GO:0016056)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(2)	45					Tamoxifen(DB00675)	CCCACAGAAGGTATTCGTCTT	0.493																																					p.T538N	Ovarian(50;572 1126 10530 25349 30594)	Atlas-SNP	.											.	PRKCQ	113	.	0			c.C1613A						.						274	209	231					10																	6498670		2203	4300	6503	SO:0001583	missense	5588	exon15			CAGAAGGTATTCG	L07032	CCDS7079.1, CCDS55701.1, CCDS60482.1	10p15	2009-07-10			ENSG00000065675	ENSG00000065675	2.7.11.1		9410	protein-coding gene	gene with protein product		600448				8444877	Standard	NM_001282645		Approved		uc001ijj.2	Q04759	OTTHUMG00000017623	ENST00000263125.5:c.1613C>A	chr10.hg19:g.6498670G>T	ENSP00000263125:p.Thr538Asn	50.0	0.0		72.0	16.0	NM_006257	B4DF52|Q14DH6|Q3MJF1|Q64FY5|Q9H508|Q9H549	Missense_Mutation	SNP	ENST00000263125.5	hg19	CCDS7079.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.81|17.81	3.481039|3.481039	0.63849|0.63849	.|.	.|.	ENSG00000065675|ENSG00000065675	ENST00000397178|ENST00000263125;ENST00000397176;ENST00000539722	.|T;T;T	.|0.67171	.|-0.25;-0.25;-0.25	5.4|5.4	5.4|5.4	0.78164|0.78164	.|Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.84005|0.84005	0.5377|0.5377	M|M	0.82630|0.82630	2.6|2.6	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;0.999	.|D;D;D;D	.|0.91635	.|0.998;0.994;0.999;0.997	D|D	0.86216|0.86216	0.1628|0.1628	5|10	.|0.87932	.|D	.|0	.|.	19.1852|19.1852	0.93641|0.93641	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|413;310;538;538	.|B4DF52;Q5JUN8;Q04759-2;Q04759	.|.;.;.;KPCT_HUMAN	T|N	311|538;538;413	.|ENSP00000263125:T538N;ENSP00000380361:T538N;ENSP00000441752:T413N	.|ENSP00000263125:T538N	P|T	-|-	1|2	0|0	PRKCQ|PRKCQ	6538676|6538676	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.085000|0.085000	0.17905|0.17905	9.551000|9.551000	0.98112|0.98112	2.510000|2.510000	0.84645|0.84645	0.557000|0.557000	0.71058|0.71058	CCT|ACC	.	.		0.493	PRKCQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046665.1	NM_006257		T	6498670	G	T	6498670	3	4	311	1	0	0	0	0	1	0	0	0	12527	1261	44	3	523	3	PRKCQ	10	6498670	Missense_Mutation	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10		6498670	129036077	43	44265										
KIAA1217	56243	hgsc.bcm.edu	37	chr10	24508649	24508649	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	aatggaaacagtcgtggttcAgtttccaagtcttcccgcaa	9	10	2	0			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr10:24508649A>G	ENST00000376454.3	+	2	195	c.165A>G	c.(163-165)tcA>tcG	p.S55S	KIAA1217_ENST00000458595.1_Silent_p.S55S|KIAA1217_ENST00000376462.1_5'UTR|KIAA1217_ENST00000376452.3_Silent_p.S55S	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	55					embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						GTCGTGGTTCAGTTTCCAAGT	0.488																																					p.S55S		Atlas-SNP	.											.	KIAA1217	235	.	0			c.A165G						.						77	72	74					10																	24508649		2203	4300	6503	SO:0001819	synonymous_variant	56243	exon2			TGGTTCAGTTTCC	BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"sickle tail"					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.165A>G	chr10.hg19:g.24508649A>G		80.0	0.0		66.0	22.0	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Silent	SNP	ENST00000376454.3	hg19	CCDS31165.1																																																																																			.	.		0.488	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590		G	24508649	A	G	24508649	2	3	311	1	0	0	0	0	0	0	0	1	8225	175	7	2		2	KIAA1217	10	24508649	Silent	SNP	A	TCGA-K7-A6G5-01A-11D-A30V-10	18009979	24508649	111026098	44	44266										
MAT1A	4143	hgsc.bcm.edu	37	chr10	82036284	82036284	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	gtcttcgttgtgctgcacagAgatgacgatggtgtggatgc	15	7	1	2			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr10:82036284A>C	ENST00000372213.3	-	6	876	c.616T>G	c.(616-618)Tct>Gct	p.S206A	MAT1A_ENST00000485270.1_5'Flank	NM_000429.2	NP_000420.1	Q00266	METK1_HUMAN	methionine adenosyltransferase I, alpha	206					cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|S-adenosylmethionine biosynthetic process (GO:0006556)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methionine adenosyltransferase activity (GO:0004478)			endometrium(4)|large_intestine(7)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26			Colorectal(32;0.229)		L-Methionine(DB00134)|S-Adenosylmethionine(DB00118)	TGCTGCACAGAGATGACGATG	0.577																																					p.S206A		Atlas-SNP	.											.	MAT1A	52	.	0			c.T616G						.						202	161	175					10																	82036284		2203	4300	6503	SO:0001583	missense	4143	exon6			GCACAGAGATGAC		CCDS7365.1	10q22	2008-08-01			ENSG00000151224	ENSG00000151224			6903	protein-coding gene	gene with protein product	"S-adenosylmethionine synthetase"	610550				8393662	Standard	XM_005269842		Approved	MAT, SAMS, MATA1, SAMS1	uc001kbw.3	Q00266	OTTHUMG00000018613	ENST00000372213.3:c.616T>G	chr10.hg19:g.82036284A>C	ENSP00000361287:p.Ser206Ala	19.0	0.0		16.0	8.0	NM_000429	D3DWD5|Q5QP09	Missense_Mutation	SNP	ENST00000372213.3	hg19	CCDS7365.1	.	.	.	.	.	.	.	.	.	.	A	17.39	3.377786	0.61735	.	.	ENSG00000151224	ENST00000372213;ENST00000372206;ENST00000455001	D;D	0.86562	-2.14;-2.14	4.84	4.84	0.62591	S-adenosylmethionine synthetase, central domain (1);S-adenosylmethionine synthetase superfamily (1);	0.000000	0.85682	D	0.000000	D	0.93897	0.8047	H	0.96576	3.845	0.80722	D	1	B	0.20887	0.049	B	0.42214	0.38	D	0.93781	0.7084	10	0.72032	D	0.01	-28.2539	12.7009	0.57032	1.0:0.0:0.0:0.0	.	206	Q00266	METK1_HUMAN	A	206;206;143	ENSP00000361287:S206A;ENSP00000414961:S143A	ENSP00000361280:S206A	S	-	1	0	MAT1A	82026264	1.000000	0.71417	0.998000	0.56505	0.946000	0.59487	8.761000	0.91691	2.164000	0.68074	0.533000	0.62120	TCT	.	.		0.577	MAT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049070.1	NM_000429		C	82036284	A	C	82036284	3	2	311	1	0	0	0	0	1	0	0	0	9338	304	11	5	587	5	MAT1A	10	82036284	Missense_Mutation	SNP	A	TCGA-K7-A6G5-01A-11D-A30V-10	57527635	82036284	53498463	45	44267										
ENTPD1	953	hgsc.bcm.edu	37	chr10	97624496	97624496	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	tctagataaaaacatcttacGctggagtaaaggagaagtac	9	6	2	2			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr10:97624496G>T	ENST00000371205.4	+	9	1487	c.1204G>T	c.(1204-1206)Gct>Tct	p.A402S	ENTPD1-AS1_ENST00000416301.1_RNA|ENTPD1_ENST00000371203.5_Missense_Mutation_p.A264S|RP11-429G19.3_ENST00000433113.1_RNA|ENTPD1_ENST00000371207.3_Missense_Mutation_p.A414S|ENTPD1_ENST00000543964.1_Missense_Mutation_p.A294S|RP11-248J23.7_ENST00000491114.1_Silent_p.T17T|ENTPD1_ENST00000453258.2_Missense_Mutation_p.A409S|ENTPD1-AS1_ENST00000451364.1_RNA|ENTPD1_ENST00000539125.1_Missense_Mutation_p.A264S			P49961	ENTP1_HUMAN	ectonucleoside triphosphate diphosphohydrolase 1	402					ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|purine ribonucleoside diphosphate catabolic process (GO:0009181)	basal lamina (GO:0005605)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|nucleoside-diphosphatase activity (GO:0017110)|nucleoside-triphosphatase activity (GO:0017111)			cervix(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(3)|prostate(1)|skin(1)	16		Colorectal(252;0.0821)		Epithelial(162;1.31e-07)|all cancers(201;5.33e-06)		AACATCTTACGCTGGAGTAAA	0.453																																					p.A414S		Atlas-SNP	.											.	ENTPD1	44	.	0			c.G1240T						.						132	105	114					10																	97624496		2203	4300	6503	SO:0001583	missense	953	exon9			TCTTACGCTGGAG	S73813	CCDS7444.1, CCDS53556.1, CCDS53557.1, CCDS53558.1, CCDS41554.1	10q24.1	2014-03-03			ENSG00000138185	ENSG00000138185		"CD molecules"	3363	protein-coding gene	gene with protein product		601752		CD39		9226376, 24482476	Standard	NM_001098175		Approved	NTPDase-1, ATPDase, SPG64	uc010qoj.2	P49961	OTTHUMG00000018818	ENST00000371205.4:c.1204G>T	chr10.hg19:g.97624496G>T	ENSP00000360248:p.Ala402Ser	66.0	0.0		63.0	4.0	NM_001164178	A9Z1X8|B4DWB9|B4E1X1|B7Z599|G3XAF6|Q5T561|Q5T562|Q86VV3|Q9UQQ9|Q9Y3Q9	Missense_Mutation	SNP	ENST00000371205.4	hg19	CCDS7444.1	.	.	.	.	.	.	.	.	.	.	G	13.79	2.341222	0.41498	.	.	ENSG00000138185	ENST00000453258;ENST00000371207;ENST00000543964;ENST00000539125;ENST00000371203;ENST00000371205	T;T;T;T;T;T	0.11063	2.81;2.81;2.81;2.81;2.81;2.81	5.28	-4.14	0.03892	.	1.377460	0.04341	N	0.354005	T	0.04363	0.0120	N	0.10972	0.075	0.09310	N	1	P;P;B;P	0.44627	0.839;0.807;0.053;0.839	B;B;B;B	0.38712	0.28;0.184;0.068;0.28	T	0.30504	-0.9976	10	0.16896	T	0.51	0.6554	3.9178	0.09230	0.3007:0.4481:0.1567:0.0944	.	414;414;409;402	B4DWB9;G3XAF6;P49961-2;P49961	.;.;.;ENTP1_HUMAN	S	409;414;294;264;264;402	ENSP00000390955:A409S;ENSP00000360250:A414S;ENSP00000442968:A294S;ENSP00000440027:A264S;ENSP00000360246:A264S;ENSP00000360248:A402S	ENSP00000360246:A264S	A	+	1	0	ENTPD1	97614486	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	0.205000	0.17356	-0.376000	0.07943	-0.137000	0.14449	GCT	.	.		0.453	ENTPD1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049566.1	NM_001776		T	97624496	G	T	97624496	3	4	311	1	0	0	0	0	1	0	0	0	5140	1087	38	1	1335	1	ENTPD1	10	97624496	Missense_Mutation	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10	15588212	97624496	37910251	46	44268										
OR51I1	390063	hgsc.bcm.edu	37	chr11	5462429	5462429	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	catgaaggagaaagtgtggaTgaagaacatctggaccaggc	14	6	1	4			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr11:5462429T>C	ENST00000380211.1	-	1	315	c.316A>G	c.(316-318)Atc>Gtc	p.I106V	HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001005288.2	NP_001005288.1	Q9H343	O51I1_HUMAN	olfactory receptor, family 51, subfamily I, member 1	106					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	30		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AAAGTGTGGATGAAGAACATC	0.458																																					p.I106V		Atlas-SNP	.											.	OR51I1	66	.	0			c.A316G						.						141	121	128					11																	5462429		2201	4297	6498	SO:0001583	missense	390063	exon1			TGTGGATGAAGAA	BK004429	CCDS31382.1	11p15.4	2012-08-09			ENSG00000167359	ENSG00000167359		"GPCR / Class A : Olfactory receptors"	15200	protein-coding gene	gene with protein product							Standard	NM_001005288		Approved		uc010qze.2	Q9H343	OTTHUMG00000066908	ENST00000380211.1:c.316A>G	chr11.hg19:g.5462429T>C	ENSP00000369559:p.Ile106Val	75.0	0.0		70.0	20.0	NM_001005288	B9EKW2|Q6IF33	Missense_Mutation	SNP	ENST00000380211.1	hg19	CCDS31382.1	.	.	.	.	.	.	.	.	.	.	T	12.05	1.820884	0.32237	.	.	ENSG00000167359	ENST00000317283;ENST00000321307;ENST00000380211	T	0.03004	4.08	5.64	5.64	0.86602	GPCR, rhodopsin-like superfamily (1);	0.110949	0.39687	N	0.001296	T	0.05181	0.0138	L	0.50847	1.595	0.26143	N	0.980245	B	0.21753	0.06	B	0.18263	0.021	T	0.19647	-1.0299	10	0.66056	D	0.02	.	10.0601	0.42270	0.0:0.0793:0.0:0.9207	.	106	Q9H343	O51I1_HUMAN	V	91;103;106	ENSP00000369559:I106V	ENSP00000348350:I91V	I	-	1	0	OR51I1	5419005	0.206000	0.23470	1.000000	0.80357	0.898000	0.52572	0.817000	0.27281	2.169000	0.68431	0.450000	0.29827	ATC	.	.		0.458	OR51I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143399.1	NM_001005288		C	5462429	T	C	5462429	3	2	311	1	0	0	0	0	1	0	0	0	11109	1464	51	2	632	2	OR51I1	11	5462429	Missense_Mutation	SNP	T	TCGA-K7-A6G5-01A-11D-A30V-10		5462429	129544087	47	44269										
EIF4G2	1982	hgsc.bcm.edu	37	chr11	10824602	10824602	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	ctgcatcttgacgaatttgaTtgatcgtctttggtccattg	9	8	2	3			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr11:10824602T>C	ENST00000526148.1	-	11	1481	c.971A>G	c.(970-972)aAt>aGt	p.N324S	EIF4G2_ENST00000396525.2_Missense_Mutation_p.N324S|EIF4G2_ENST00000525995.1_5'Flank|EIF4G2_ENST00000339995.5_Missense_Mutation_p.N324S|EIF4G2_ENST00000525681.1_Missense_Mutation_p.N324S|SNORD97_ENST00000459187.1_RNA|RP11-685M7.5_ENST00000532365.1_RNA	NM_001172705.1	NP_001166176			eukaryotic translation initiation factor 4 gamma, 2											NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	43				all cancers(16;2.8e-07)|Epithelial(150;4.18e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		ACGAATTTGATTGATCGTCTT	0.378																																					p.N324S		Atlas-SNP	.											.	EIF4G2	89	.	0			c.A971G						.						81	76	78					11																	10824602		2201	4294	6495	SO:0001583	missense	1982	exon11			ATTTGATTGATCG	U73824	CCDS31428.1, CCDS41618.1	11p15	2005-09-29			ENSG00000110321	ENSG00000110321			3297	protein-coding gene	gene with protein product		602325				9030685, 9032289	Standard	NM_001042559		Approved	DAP5, NAT1, p97	uc001mjc.3	P78344	OTTHUMG00000165823	ENST00000526148.1:c.971A>G	chr11.hg19:g.10824602T>C	ENSP00000433664:p.Asn324Ser	58.0	0.0		54.0	15.0	NM_001172705		Missense_Mutation	SNP	ENST00000526148.1	hg19	CCDS31428.1	.	.	.	.	.	.	.	.	.	.	T	13.16	2.153337	0.38021	.	.	ENSG00000110321	ENST00000526148;ENST00000525681;ENST00000339995;ENST00000396525;ENST00000429377;ENST00000531416	T;T;T;T;T	0.21191	2.32;2.32;2.32;2.32;2.02	6.07	6.07	0.98685	.	0.127499	0.64402	D	0.000001	T	0.21103	0.0508	L	0.50333	1.59	0.34552	D	0.711409	B;B;B	0.26318	0.022;0.049;0.146	B;B;B	0.18871	0.023;0.016;0.016	T	0.20371	-1.0277	9	0.56958	D	0.05	-11.3161	12.4822	0.55850	0.0:0.0:0.1393:0.8607	.	324;324;397	P78344-2;P78344;B4DZF2	.;IF4G2_HUMAN;.	S	324;324;324;324;397;324	ENSP00000433664:N324S;ENSP00000433371:N324S;ENSP00000340281:N324S;ENSP00000379778:N324S;ENSP00000431583:N324S	ENSP00000340281:N324S	N	-	2	0	EIF4G2	10781178	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.230000	0.51286	2.326000	0.78906	0.533000	0.62120	AAT	.	.		0.378	EIF4G2-006	KNOWN	alternative_5_UTR|non_ATG_start|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386603.1	NM_001418		C	10824602	T	C	10824602	3	2	311	1	0	0	0	0	1	0	0	0	5039	1493	52	2	1800	2	EIF4G2	11	10824602	Missense_Mutation	SNP	T	TCGA-K7-A6G5-01A-11D-A30V-10	5362173	10824602	124181914	48	44270										
PSMA1	5682	hgsc.bcm.edu	37	chr11	14535383	14535383	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	atcataaccagcaataaggaGaccaacaccatatggtctcc	6	12	2	1			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr11:14535383G>C	ENST00000396394.2	-	6	790	c.394C>G	c.(394-396)Ctc>Gtc	p.L132V	PSMA1_ENST00000530457.1_Missense_Mutation_p.L107V|PSMA1_ENST00000419365.2_Intron|PSMA1_ENST00000418988.2_Missense_Mutation_p.L138V|PSMA1_ENST00000555531.1_Intron|PSMA1_ENST00000524606.1_5'Flank|PSMA1_ENST00000396393.1_Missense_Mutation_p.L132V	NM_002786.3	NP_002777.1	P25786	PSA1_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 1	132					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|polysome (GO:0005844)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|proteasome core complex, alpha-subunit complex (GO:0019773)	RNA binding (GO:0003723)|threonine-type endopeptidase activity (GO:0004298)			large_intestine(1)|skin(1)|upper_aerodigestive_tract(1)	3						GCAATAAGGAGACCAACACCA	0.318																																					p.L138V		Atlas-SNP	.											.	PSMA1	22	.	0			c.C412G						.						74	72	72					11																	14535383		2200	4294	6494	SO:0001583	missense	5682	exon7			TAAGGAGACCAAC	X61969	CCDS7816.1, CCDS31431.1	11p15.1	2005-10-10			ENSG00000129084	ENSG00000129084		"Proteasome (prosome, macropain) subunits"	9530	protein-coding gene	gene with protein product		602854				1398136, 2025653	Standard	NM_148976		Approved	HC2, NU, PROS30, MGC14542, MGC14575, MGC14751, MGC1667, MGC21459, MGC22853, MGC23915	uc001mlk.3	P25786	OTTHUMG00000165825	ENST00000396394.2:c.394C>G	chr11.hg19:g.14535383G>C	ENSP00000379676:p.Leu132Val	82.0	0.0		61.0	17.0	NM_148976	A8K400|Q53YE8|Q9BRV9	Missense_Mutation	SNP	ENST00000396394.2	hg19	CCDS7816.1	.	.	.	.	.	.	.	.	.	.	G	19.84	3.902099	0.72754	.	.	ENSG00000129084	ENST00000396394;ENST00000396393;ENST00000530457;ENST00000418988	T;T;T;T	0.26660	1.72;1.72;1.72;1.72	5.4	4.49	0.54785	.	0.000000	0.85682	D	0.000000	T	0.53722	0.1814	H	0.94698	3.57	0.80722	D	1	D;D	0.54601	0.959;0.967	P;P	0.53360	0.602;0.724	T	0.69224	-0.5201	10	0.72032	D	0.01	-9.63	14.0814	0.64925	0.0727:0.0:0.9273:0.0	.	138;132	P25786-2;P25786	.;PSA1_HUMAN	V	132;132;107;138	ENSP00000379676:L132V;ENSP00000379675:L132V;ENSP00000441166:L107V;ENSP00000414359:L138V	ENSP00000379675:L132V	L	-	1	0	PSMA1	14491959	1.000000	0.71417	0.999000	0.59377	0.923000	0.55619	3.492000	0.53259	1.287000	0.44583	0.591000	0.81541	CTC	.	.		0.318	PSMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386421.3	NM_002786		C	14535383	G	C	14535383	3	2	311	1	0	0	0	0	1	0	0	0	12678	942	33	4	417	4	PSMA1	11	14535383	Missense_Mutation	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10	3710781	14535383	120471133	49	44271										
LDHAL6A	160287	hgsc.bcm.edu	37	chr11	18499168	18499168	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	tggtttcttctatctacagtGgctatgagatggtcaaaatg	10	6	4	1			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr11:18499168G>T	ENST00000280706.2	+	6	1509	c.712G>T	c.(712-714)Ggc>Tgc	p.G238C	TSG101_ENST00000536719.1_Intron|LDHAL6A_ENST00000396213.3_Splice_Site_p.G238C	NM_144972.4	NP_659409.2	Q6ZMR3	LDH6A_HUMAN	lactate dehydrogenase A-like 6A	238					cellular carbohydrate metabolic process (GO:0044262)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	L-lactate dehydrogenase activity (GO:0004459)			large_intestine(3)|lung(9)|urinary_tract(1)	13						TATCTACAGTGGCTATGAGAT	0.363																																					p.G238C		Atlas-SNP	.											.	LDHAL6A	35	.	0			c.G712T						.						190	187	188					11																	18499168		2199	4293	6492	SO:0001630	splice_region_variant	160287	exon6			TACAGTGGCTATG	AK131523	CCDS7841.1	11p15.1	2011-01-27			ENSG00000166800	ENSG00000166800			28335	protein-coding gene	gene with protein product						12477932	Standard	NM_001144071		Approved	MGC23940, LDH6A	uc001mop.1	Q6ZMR3	OTTHUMG00000167724	ENST00000280706.2:c.711-1G>T	chr11.hg19:g.18499168G>T		105.0	0.0		75.0	16.0	NM_144972	D3DQY5	Missense_Mutation	SNP	ENST00000280706.2	hg19	CCDS7841.1	.	.	.	.	.	.	.	.	.	.	G	19.12	3.766755	0.69878	.	.	ENSG00000166800	ENST00000396213;ENST00000280706	T;T	0.79749	-1.3;-1.3	3.89	3.89	0.44902	Lactate/malate dehydrogenase, C-terminal (1);Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal (2);	0.164274	0.39759	U	0.001278	D	0.91219	0.7233	M	0.93854	3.465	0.38191	D	0.939909	D	0.62365	0.991	D	0.65233	0.933	D	0.94666	0.7852	10	0.87932	D	0	.	14.8202	0.70068	0.0:0.0:1.0:0.0	.	238	Q6ZMR3	LDH6A_HUMAN	C	238	ENSP00000379516:G238C;ENSP00000280706:G238C	ENSP00000280706:G238C	G	+	1	0	LDHAL6A	18455744	1.000000	0.71417	0.114000	0.21550	0.753000	0.42808	6.550000	0.73905	1.859000	0.53934	0.563000	0.77884	GGC	.	.		0.363	LDHAL6A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395904.1	NM_144972	Missense_Mutation	T	18499168	G	T	18499168	5	4	311	1	0	0	0	0	0	0	1	0	8708	1362	47	3	734	3	LDHAL6A	11	18499168	Splice_Site	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10	3963785	18499168	116507348	50	44272										
NELL1	4745	hgsc.bcm.edu	37	chr11	21592455	21592455	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	gtatcgaagtggagacaattGgacccatagctgtcagcagt	12	8	1	1			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr11:21592455G>T	ENST00000357134.5	+	18	2278	c.2126G>T	c.(2125-2127)tGg>tTg	p.W709L	NELL1_ENST00000532434.1_Missense_Mutation_p.W662L|NELL1_ENST00000298925.5_Missense_Mutation_p.W737L|NELL1_ENST00000529218.1_3'UTR|NELL1_ENST00000325319.5_Missense_Mutation_p.W652L	NM_006157.3|NM_201551.1	NP_006148.2|NP_963845.1	Q92832	NELL1_HUMAN	NEL-like 1 (chicken)	709	VWFC 2. {ECO:0000255|PROSITE- ProRule:PRU00220}.				cell differentiation (GO:0030154)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of osteoblast proliferation (GO:0033689)|nervous system development (GO:0007399)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of gene expression (GO:0010468)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(5)|kidney(3)|large_intestine(15)|lung(36)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	70						GGAGACAATTGGACCCATAGC	0.448																																					p.W709L		Atlas-SNP	.											.	NELL1	179	.	0			c.G2126T						.						197	186	190					11																	21592455		2203	4300	6503	SO:0001583	missense	4745	exon18			ACAATTGGACCCA	AK127805	CCDS7855.1, CCDS44555.1, CCDS73267.1, CCDS73268.1	11p15.1	2008-02-01	2001-11-28		ENSG00000165973	ENSG00000165973			7750	protein-coding gene	gene with protein product		602319	"nel (chicken)-like 1"			8975702	Standard	NM_006157		Approved	IDH3GL, FLJ45906	uc001mqe.3	Q92832	OTTHUMG00000166042	ENST00000357134.5:c.2126G>T	chr11.hg19:g.21592455G>T	ENSP00000349654:p.Trp709Leu	82.0	0.0		69.0	12.0	NM_006157	B2CKC1|Q4VB90|Q4VB91|Q6NSY8|Q9Y472	Missense_Mutation	SNP	ENST00000357134.5	hg19	CCDS7855.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.995299	0.93167	.	.	ENSG00000165973	ENST00000298925;ENST00000357134;ENST00000325319;ENST00000532434	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	6.16	6.16	0.99307	von Willebrand factor, type C (3);	0.000000	0.85682	D	0.000000	D	0.92133	0.7506	H	0.94423	3.535	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.997;0.998;0.999;1.0;0.998	D	0.92447	0.5967	10	0.56958	D	0.05	-24.1435	20.8598	0.99761	0.0:0.0:1.0:0.0	.	652;737;254;662;709	F5H6I3;B3KXR2;Q8N9Z6;Q92832-2;Q92832	.;.;.;.;NELL1_HUMAN	L	737;709;652;662	ENSP00000298925:W737L;ENSP00000349654:W709L;ENSP00000317837:W652L;ENSP00000437170:W662L	ENSP00000298925:W737L	W	+	2	0	NELL1	21549031	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.447000	0.97595	2.937000	0.99478	0.650000	0.86243	TGG	.	.		0.448	NELL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387588.1	NM_006157		T	21592455	G	T	21592455	3	4	311	1	0	0	0	0	1	0	0	0	10342	1357	47	3	2196	3	NELL1	11	21592455	Missense_Mutation	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10	3093287	21592455	113414061	51	44273										
IL18BP	10068	hgsc.bcm.edu	37	chr11	71711533	71711533	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	gacccctgcccctcccagccCccagtgttcccagcagctaa	7	21	0	0	rs369922984		TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr11:71711533C>T	ENST00000393703.4	+	3	702	c.165C>T	c.(163-165)ccC>ccT	p.P55P	IL18BP_ENST00000393707.4_Silent_p.P55P|IL18BP_ENST00000260049.5_Silent_p.P55P|IL18BP_ENST00000404792.1_Silent_p.P55P|IL18BP_ENST00000531053.1_Silent_p.P55P|IL18BP_ENST00000497194.2_Silent_p.P55P|IL18BP_ENST00000393705.4_Silent_p.P55P|IL18BP_ENST00000337131.5_Silent_p.P55P	NM_001039660.1	NP_001034749.1	O95998	I18BP_HUMAN	interleukin 18 binding protein	55					cellular response to hydrogen peroxide (GO:0070301)|cellular response to tumor necrosis factor (GO:0071356)|extracellular negative regulation of signal transduction (GO:1900116)|response to lipopolysaccharide (GO:0032496)|T-helper 1 type immune response (GO:0042088)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	interleukin-18 binding (GO:0042007)|receptor antagonist activity (GO:0048019)			endometrium(2)|kidney(1)|large_intestine(3)|lung(1)	7						CCTCCCAGCCCCCAGTGTTCC	0.597																																					p.P55P		Atlas-SNP	.											.	IL18BP	15	.	0			c.C165T						.	C	,,,,,,	0,4134		0,0,2067	76	85	82		165,165,165,165,165,165,165	-1.7	0	11		82	1,8445		0,1,4222	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IL18BP	NM_001039659.1,NM_001039660.1,NM_001145055.1,NM_001145057.1,NM_005699.3,NM_173042.2,NM_173044.2	,,,,,,	0,1,6289	TT,TC,CC		0.0118,0.0,0.0079	,,,,,,	55/195,55/195,55/116,55/195,55/200,55/195,55/164	71711533	1,12579	2067	4223	6290	SO:0001819	synonymous_variant	10068	exon3			CCAGCCCCCAGTG	AF110798	CCDS8206.2, CCDS44666.1	11q13	2013-01-11			ENSG00000137496	ENSG00000137496		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5987	protein-coding gene	gene with protein product	"MC51L-53L-54L homolog gene product"	604113				10023777	Standard	NM_001145055		Approved	IL18BPa	uc001orf.1	O95998	OTTHUMG00000133713	ENST00000393703.4:c.165C>T	chr11.hg19:g.71711533C>T		26.0	0.0		20.0	6.0	NM_001145057	B3KUZ0|B7WPK4|O95993|O96027|Q9NZA9|Q9UBR7	Silent	SNP	ENST00000393703.4	hg19	CCDS8206.2																																																																																			.	.		0.597	IL18BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000258012.2	NM_173042		T	71711533	C	T	71711533	2	4	311	1	0	0	0	0	0	0	0	1	7655	610	22	3		3	IL18BP	11	71711533	Silent	SNP	C	TCGA-K7-A6G5-01A-11D-A30V-10	50119078	71711533	63294983	52	44274										
C2CD3	26005	hgsc.bcm.edu	37	chr11	73824849	73824849	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	atctgtaattttactggaggCgagtcgaacaacctcagtga	10	8	2	1			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr11:73824849C>A	ENST00000334126.7	-	11	2045	c.1819G>T	c.(1819-1821)Gcc>Tcc	p.A607S	C2CD3_ENST00000313663.7_Missense_Mutation_p.A607S			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	607					brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					TTACTGGAGGCGAGTCGAACA	0.383																																					p.A607S		Atlas-SNP	.											.	C2CD3	288	.	0			c.G1819T						.						129	126	127					11																	73824849		2200	4293	6493	SO:0001583	missense	26005	exon11			TGGAGGCGAGTCG	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.1819G>T	chr11.hg19:g.73824849C>A	ENSP00000334379:p.Ala607Ser	47.0	0.0		51.0	5.0	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	hg19		.	.	.	.	.	.	.	.	.	.	C	27.0	4.788968	0.90367	.	.	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681	T;T	0.12569	2.67;2.68	5.27	5.27	0.74061	C2 calcium-dependent membrane targeting (1);	0.058320	0.64402	D	0.000002	T	0.37156	0.0993	M	0.68952	2.095	0.37577	D	0.919663	D;D	0.89917	1.0;1.0	D;D	0.91635	0.996;0.999	T	0.30534	-0.9975	10	0.66056	D	0.02	-11.788	16.6638	0.85247	0.0:1.0:0.0:0.0	.	607;607	Q4AC94;Q4AC94-1	C2CD3_HUMAN;.	S	607	ENSP00000334379:A607S;ENSP00000323339:A607S	ENSP00000323339:A607S	A	-	1	0	C2CD3	73502497	1.000000	0.71417	0.998000	0.56505	0.922000	0.55478	5.933000	0.70130	2.466000	0.83321	0.455000	0.32223	GCC	.	.		0.383	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531		A	73824849	C	A	73824849	3	1	311	1	0	0	0	0	1	0	0	0	2156	768	27	1	4156	1	C2CD3	11	73824849	Missense_Mutation	SNP	C	TCGA-K7-A6G5-01A-11D-A30V-10	2113316	73824849	61181667	53	44275										
PDE3A	5139	hgsc.bcm.edu	37	chr12	20766493	20766493	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	gtgtgcacatccttgagagcCgtgagcaacttgctcagcac	11	12	1	2			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr12:20766493C>A	ENST00000359062.3	+	3	1168	c.1128C>A	c.(1126-1128)gcC>gcA	p.A376A	PDE3A_ENST00000544307.1_3'UTR	NM_000921.4|NM_001244683.1	NP_000912.3|NP_001231612.1	Q14432	PDE3A_HUMAN	phosphodiesterase 3A, cGMP-inhibited	376					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP-mediated signaling (GO:0019934)|diterpenoid metabolic process (GO:0016101)|lipid metabolic process (GO:0006629)|negative regulation of apoptotic process (GO:0043066)|negative regulation of vascular permeability (GO:0043116)|oocyte maturation (GO:0001556)|positive regulation of oocyte development (GO:0060282)|positive regulation of vascular permeability (GO:0043117)|regulation of meiosis (GO:0040020)|response to cAMP (GO:0051591)|response to drug (GO:0042493)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(7)|lung(29)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	58	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Caffeine(DB00201)|Cilostazol(DB01166)|Enoximone(DB04880)|Ibudilast(DB05266)|Levosimendan(DB00922)|Milrinone(DB00235)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Tofisopam(DB08811)	CCTTGAGAGCCGTGAGCAACT	0.552																																					p.A376A		Atlas-SNP	.											PDE3A,NS,carcinoma,0,1	PDE3A	184	.	0			c.C1128A						.						109	100	103					12																	20766493		2203	4300	6503	SO:0001819	synonymous_variant	5139	exon3			GAGAGCCGTGAGC		CCDS31754.1	12p12.2	2011-04-15			ENSG00000172572	ENSG00000172572	3.1.4.17	"Phosphodiesterases"	8778	protein-coding gene	gene with protein product		123805				1315035, 10679291	Standard	NM_000921		Approved	CGI-PDE	uc001reh.2	Q14432	OTTHUMG00000168962	ENST00000359062.3:c.1128C>A	chr12.hg19:g.20766493C>A		73.0	0.0		71.0	22.0	NM_000921	O60865|Q13348|Q17RD1	Silent	SNP	ENST00000359062.3	hg19	CCDS31754.1																																																																																			.	.		0.552	PDE3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401756.2			A	20766493	C	A	20766493	2	1	311	1	0	0	0	0	0	0	0	1	11646	639	23	1		1	PDE3A	12	20766493	Silent	SNP	C	TCGA-K7-A6G5-01A-11D-A30V-10		20766493	113085402	54	44276										
KRT81	3887	hgsc.bcm.edu	37	chr12	52681386	52681386	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	cagatgccccatacctggcaCttggcattctccacctcggc	8	17	1	1			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr12:52681386C>A	ENST00000327741.5	-	6	1088	c.1020G>T	c.(1018-1020)aaG>aaT	p.K340N	KRT86_ENST00000544024.1_Intron|KRT86_ENST00000423955.2_Intron	NM_002281.3	NP_002272.2	Q14533	KRT81_HUMAN	keratin 81	340	Coil 2.|Rod.					extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(2)|endometrium(3)|large_intestine(3)|lung(6)|prostate(1)|stomach(1)	16				BRCA - Breast invasive adenocarcinoma(357;0.189)		ATACCTGGCACTTGGCATTCT	0.582																																					p.K340N		Atlas-SNP	.											.	KRT81	46	.	0			c.G1020T						.						94	81	85					12																	52681386		2203	4300	6503	SO:0001583	missense	3887	exon6			CTGGCACTTGGCA	X81420	CCDS31805.1	12q13	2013-01-16	2006-07-17	2006-07-17	ENSG00000205426	ENSG00000205426		"-", "Intermediate filaments type II, keratins (basic)"	6458	protein-coding gene	gene with protein product	"hard keratin type II 1"	602153	"keratin, hair, basic, 1"	KRTHB1		7556444, 16831889	Standard	NM_002281		Approved	Hb-1	uc001sab.3	Q14533	OTTHUMG00000167574	ENST00000327741.5:c.1020G>T	chr12.hg19:g.52681386C>A	ENSP00000369349:p.Lys340Asn	57.0	0.0		50.0	18.0	NM_002281	Q14846|Q16274|Q17R48|Q8WU52|Q9BR74	Missense_Mutation	SNP	ENST00000327741.5	hg19	CCDS31805.1	.	.	.	.	.	.	.	.	.	.	C	19.72	3.880810	0.72294	.	.	ENSG00000205426	ENST00000327741;ENST00000389388	D	0.90324	-2.65	4.7	4.7	0.59300	Filament (1);	0.000000	0.45867	U	0.000321	D	0.95503	0.8539	M	0.93420	3.415	0.37266	D	0.907216	D	0.89917	1.0	D	0.80764	0.994	D	0.96140	0.9099	10	0.72032	D	0.01	.	6.1684	0.20404	0.164:0.6956:0.0:0.1404	.	340	Q14533	KRT81_HUMAN	N	340	ENSP00000369349:K340N	ENSP00000369349:K340N	K	-	3	2	KRT81	50967653	0.000000	0.05858	1.000000	0.80357	0.994000	0.84299	-0.107000	0.10873	2.139000	0.66308	0.561000	0.74099	AAG	.	.		0.582	KRT81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395128.2	NM_002281		A	52681386	C	A	52681386	3	1	311	1	0	0	0	0	1	0	0	0	8504	564	20	3	513	3	KRT81	12	52681386	Missense_Mutation	SNP	C	TCGA-K7-A6G5-01A-11D-A30V-10	31914893	52681386	81170509	55	44277										
NCKAP1L	3071	hgsc.bcm.edu	37	chr12	54910687	54910687	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	ttttcttccttagtggccagTttcattgtcaacggcggcaa	9	10	3	0			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr12:54910687T>C	ENST00000293373.6	+	11	1085	c.1006T>C	c.(1006-1008)Ttt>Ctt	p.F336L	NCKAP1L_ENST00000552211.1_3'UTR|NCKAP1L_ENST00000545638.2_Missense_Mutation_p.F286L	NM_005337.4	NP_005328.2	P55160	NCKPL_HUMAN	NCK-associated protein 1-like	336					actin polymerization-dependent cell motility (GO:0070358)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|chemotaxis (GO:0006935)|cortical actin cytoskeleton organization (GO:0030866)|erythrocyte development (GO:0048821)|maintenance of cell polarity (GO:0030011)|myeloid cell homeostasis (GO:0002262)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of myosin-light-chain-phosphatase activity (GO:0035509)|neutrophil chemotaxis (GO:0030593)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of CD8-positive, alpha-beta T cell differentiation (GO:0043378)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of lymphocyte differentiation (GO:0045621)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of T cell proliferation (GO:0042102)|protein complex assembly (GO:0006461)|response to drug (GO:0042493)|T cell homeostasis (GO:0043029)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|SCAR complex (GO:0031209)	protein complex binding (GO:0032403)|protein kinase activator activity (GO:0030295)|Rac GTPase activator activity (GO:0030675)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(37)|ovary(3)|prostate(3)|skin(3)|stomach(2)	80						TAGTGGCCAGTTTCATTGTCA	0.502																																					p.F336L		Atlas-SNP	.											.	NCKAP1L	180	.	0			c.T1006C						.						125	117	120					12																	54910687		2203	4300	6503	SO:0001583	missense	3071	exon11			GGCCAGTTTCATT	AI924363	CCDS31813.1, CCDS53799.1	12q13.1	2005-10-11	2005-10-11	2005-10-11		ENSG00000123338			4862	protein-coding gene	gene with protein product		141180	"hematopoietic protein 1"	HEM1		1932118	Standard	NM_005337		Approved		uc001sgc.4	P55160	OTTHUMG00000169843	ENST00000293373.6:c.1006T>C	chr12.hg19:g.54910687T>C	ENSP00000293373:p.Phe336Leu	97.0	0.0		78.0	19.0	NM_005337	B4DUT5|Q52LW0	Missense_Mutation	SNP	ENST00000293373.6	hg19	CCDS31813.1	.	.	.	.	.	.	.	.	.	.	T	13.50	2.257099	0.39896	.	.	ENSG00000123338	ENST00000293373;ENST00000545638	T;T	0.22134	1.97;1.97	5.19	5.19	0.71726	.	0.185508	0.51477	N	0.000097	T	0.08447	0.0210	N	0.03948	-0.315	0.37102	D	0.899939	B	0.06786	0.001	B	0.09377	0.004	T	0.13522	-1.0506	10	0.02654	T	1	-10.4278	13.278	0.60198	0.0:0.0:0.0:1.0	.	336	P55160	NCKPL_HUMAN	L	336;286	ENSP00000293373:F336L;ENSP00000445596:F286L	ENSP00000293373:F336L	F	+	1	0	NCKAP1L	53196954	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.527000	0.35975	2.084000	0.62774	0.482000	0.46254	TTT	.	.		0.502	NCKAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406195.1	NM_005337		C	54910687	T	C	54910687	3	2	311	1	0	0	0	0	1	0	0	0	10231	1725	60	2	1048	2	NCKAP1L	12	54910687	Missense_Mutation	SNP	T	TCGA-K7-A6G5-01A-11D-A30V-10	2229301	54910687	78941208	56	44278										
POSTN	10631	hgsc.bcm.edu	37	chr13	38162065	38162065	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	ttctcttattaatcatgtgaCtatgtaaagcattcagtaat	5	6	3	1			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr13:38162065C>T	ENST00000379747.4	-	5	617	c.500G>A	c.(499-501)aGt>aAt	p.S167N	POSTN_ENST00000541179.1_Missense_Mutation_p.S167N|POSTN_ENST00000379743.4_Missense_Mutation_p.S167N|POSTN_ENST00000541481.1_Missense_Mutation_p.S167N|POSTN_ENST00000379742.4_Missense_Mutation_p.S167N|POSTN_ENST00000379749.4_Missense_Mutation_p.S167N	NM_006475.2	NP_006466.2	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor	167	FAS1 1. {ECO:0000255|PROSITE- ProRule:PRU00082, ECO:0000305}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of Notch signaling pathway (GO:0008593)|skeletal system development (GO:0001501)|tissue development (GO:0009888)	proteinaceous extracellular matrix (GO:0005578)|trans-Golgi network (GO:0005802)	heparin binding (GO:0008201)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(16)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	59		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)		AATCATGTGACTATGTAAAGC	0.323																																					p.S167N		Atlas-SNP	.											.	POSTN	161	.	0			c.G500A						.						109	106	107					13																	38162065		2203	4295	6498	SO:0001583	missense	10631	exon5			ATGTGACTATGTA	D13665	CCDS9364.1, CCDS45034.1, CCDS53864.1, CCDS66530.1, CCDS66531.1	13q13.3	2008-02-05			ENSG00000133110	ENSG00000133110			16953	protein-coding gene	gene with protein product		608777				8363580, 12235007	Standard	NM_006475		Approved	OSF-2, PN, periostin	uc001uwo.4	Q15063	OTTHUMG00000016751	ENST00000379747.4:c.500G>A	chr13.hg19:g.38162065C>T	ENSP00000369071:p.Ser167Asn	356.0	0.0		317.0	102.0	NM_006475	B1ALD8|C0IMJ1|C0IMJ2|C0IMJ4|D2KRH7|F5H628|Q15064|Q29XZ0|Q3KPJ5|Q5VSY5|Q8IZF9	Missense_Mutation	SNP	ENST00000379747.4	hg19	CCDS9364.1	.	.	.	.	.	.	.	.	.	.	C	6.583	0.475857	0.12521	.	.	ENSG00000133110	ENST00000541179;ENST00000379749;ENST00000379747;ENST00000379743;ENST00000379742;ENST00000541481;ENST00000538347	D;D;D;D;D;D	0.89875	-2.58;-2.58;-2.58;-2.58;-2.58;-2.58	5.82	4.03	0.46877	FAS1 domain (5);	0.230310	0.53938	D	0.000058	T	0.72087	0.3417	N	0.02916	-0.46	0.24834	N	0.992509	B;B;B;B;B;B;B	0.13145	0.007;0.003;0.004;0.003;0.005;0.002;0.004	B;B;B;B;B;B;B	0.18561	0.022;0.013;0.012;0.013;0.013;0.007;0.012	T	0.62163	-0.6912	10	0.48119	T	0.1	-19.1093	5.578	0.17235	0.0:0.4952:0.3483:0.1564	.	167;167;167;167;167;167;167	C0IMJ4;F5H628;B1ALD8;Q15063-3;Q15063-4;Q15063-2;Q15063	.;.;.;.;.;.;POSTN_HUMAN	N	167;167;167;167;167;167;84	ENSP00000437959:S167N;ENSP00000369073:S167N;ENSP00000369071:S167N;ENSP00000369067:S167N;ENSP00000369066:S167N;ENSP00000437953:S167N	ENSP00000369066:S167N	S	-	2	0	POSTN	37060065	1.000000	0.71417	0.967000	0.41034	0.005000	0.04900	4.633000	0.61318	0.745000	0.32763	-0.499000	0.04595	AGT	.	.		0.323	POSTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044566.2	NM_006475		T	38162065	C	T	38162065	3	4	311	1	0	0	0	0	1	0	0	0	12268	565	20	3	2086	3	POSTN	13	38162065	Missense_Mutation	SNP	C	TCGA-K7-A6G5-01A-11D-A30V-10		38162065	77007813	57	44279										
COQ6	51004	hgsc.bcm.edu	37	chr14	74428466	74428466	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	tgagccacctcacaggttatGaaacagaaagacagcgtcac	9	11	2	4			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr14:74428466G>T	ENST00000334571.2	+	11	1277	c.1237G>T	c.(1237-1239)Gaa>Taa	p.E413*	COQ6_ENST00000394026.4_Nonsense_Mutation_p.E388*|COQ6_ENST00000554920.1_Intron|COQ6_ENST00000238709.4_Nonsense_Mutation_p.E338*|ENTPD5_ENST00000557325.1_Intron	NM_182476.2	NP_872282.1	Q9Y2Z9	COQ6_HUMAN	coenzyme Q6 monooxygenase	413					small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	cell projection (GO:0042995)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)			breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	16				BRCA - Breast invasive adenocarcinoma(234;0.00337)		CACAGGTTATGAAACAGAAAG	0.463																																					p.E413X		Atlas-SNP	.											.	COQ6	27	.	0			c.G1237T						.						159	152	154					14																	74428466		2203	4300	6503	SO:0001587	stop_gained	51004	exon11			GGTTATGAAACAG	AF132944	CCDS9823.1, CCDS9824.1, CCDS9824.2	14q24.1	2013-05-01	2013-05-01		ENSG00000119723	ENSG00000119723			20233	protein-coding gene	gene with protein product		614647	"coenzyme Q6 homolog (yeast)", "coenzyme Q6 homolog, monooxygenase (yeast)", "coenzyme Q6 homolog, monooxygenase (S. cerevisiae)"			21540551	Standard	NM_182476		Approved	CGI-10	uc001xph.3	Q9Y2Z9	OTTHUMG00000171260	ENST00000334571.2:c.1237G>T	chr14.hg19:g.74428466G>T	ENSP00000333946:p.Glu413*	52.0	0.0		40.0	13.0	NM_182476	B7Z3K8|Q53GG6|Q86U30|Q96CA1|Q96CK2	Nonsense_Mutation	SNP	ENST00000334571.2	hg19	CCDS9823.1	.	.	.	.	.	.	.	.	.	.	G	38	7.084039	0.98051	.	.	ENSG00000119723	ENST00000394026;ENST00000555376;ENST00000238709;ENST00000334571;ENST00000556299	.	.	.	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-7.3024	19.2367	0.93864	0.0:0.0:1.0:0.0	.	.	.	.	X	388;338;338;413;101	.	ENSP00000238709:E338X	E	+	1	0	COQ6	73498219	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	9.411000	0.97342	2.776000	0.95493	0.655000	0.94253	GAA	.	.		0.463	COQ6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412616.1			T	74428466	G	T	74428466	4	4	311	1	0	0	0	0	0	1	0	0	3751	1291	45	3	1279	3	COQ6	14	74428466	Nonsense_Mutation	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10		74428466	32921074	58	44280										
HERC2	8924	hgsc.bcm.edu	37	chr15	28419597	28419597	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	ggaagaggacgggctcgtggAcagagggcgtggccacatcc	18	10	0	2			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr15:28419597A>C	ENST00000261609.7	-	65	10109	c.10001T>G	c.(10000-10002)gTc>gGc	p.V3334G		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		GGGCTCGTGGACAGAGGGCGT	0.517																																					p.V3334G		Atlas-SNP	.											.	HERC2	501	.	0			c.T10001G						.						38	30	32					15																	28419597		2203	4297	6500	SO:0001583	missense	8924	exon65			TCGTGGACAGAGG	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.10001T>G	chr15.hg19:g.28419597A>C	ENSP00000261609:p.Val3334Gly	211.0	0.0		211.0	67.0	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	hg19	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	A	9.760	1.169822	0.21621	.	.	ENSG00000128731	ENST00000261609	T	0.39056	1.1	5.5	4.38	0.52667	.	0.063358	0.64402	D	0.000008	T	0.33933	0.0880	L	0.51422	1.61	0.80722	D	1	P	0.42456	0.78	B	0.38106	0.265	T	0.08659	-1.0711	10	0.23302	T	0.38	.	10.8049	0.46512	0.9259:0.0:0.074:0.0	.	3334	O95714	HERC2_HUMAN	G	3334	ENSP00000261609:V3334G	ENSP00000261609:V3334G	V	-	2	0	HERC2	26093192	1.000000	0.71417	0.964000	0.40570	0.108000	0.19459	7.473000	0.81007	2.091000	0.63221	0.482000	0.46254	GTC	.	.		0.517	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		C	28419597	A	C	28419597	3	2	311	1	0	0	0	0	1	0	0	0	7067	275	10	5	4619	5	HERC2	15	28419597	Missense_Mutation	SNP	A	TCGA-K7-A6G5-01A-11D-A30V-10		28419597	74111795	59	44281										
ARHGAP11B	89839	hgsc.bcm.edu	37	chr15	30926529	30926529	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	aacagttaggcacagaggaaAagaataaagctatactgttg	10	5	0	2			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr15:30926529A>G	ENST00000428041.2	+	4	599	c.454A>G	c.(454-456)Aag>Gag	p.K152E		NM_001039841.1	NP_001034930.1	Q3KRB8	RHGBB_HUMAN	Rho GTPase activating protein 11B	152	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			endometrium(2)|kidney(1)|large_intestine(3)|lung(1)|prostate(1)	8		all_lung(180;2.71e-09)|Breast(32;0.00116)		all cancers(64;1.9e-15)|Epithelial(43;3.59e-12)|GBM - Glioblastoma multiforme(186;9e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)|Lung(196;0.153)		CACAGAGGAAAAGAATAAAGC	0.413																																					p.K152E		Atlas-SNP	.											.	ARHGAP11B	14	.	0			c.A454G						.						133	129	130					15																	30926529		2201	4300	6501	SO:0001583	missense	89839	exon4			GAGGAAAAGAATA	BC105788	CCDS32185.1	15q13.2	2011-07-13				ENSG00000187951		"Rho GTPase activating proteins"	15782	protein-coding gene	gene with protein product	"GAP (1-8)"		"family with sequence similarity 7, member B1"	FAM7B1		11829490	Standard	NM_001039841		Approved	B'-T	uc001zet.1	Q3KRB8		ENST00000428041.2:c.454A>G	chr15.hg19:g.30926529A>G	ENSP00000392760:p.Lys152Glu	461.0	0.0		431.0	113.0	NM_001039841		Missense_Mutation	SNP	ENST00000428041.2	hg19	CCDS32185.1	.	.	.	.	.	.	.	.	.	.	.	8.092	0.774720	0.16051	.	.	ENSG00000187951	ENST00000428041	T	0.19250	2.16	1.53	1.53	0.23141	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.350015	0.10494	U	0.668138	T	0.24236	0.0587	L	0.53671	1.685	0.22034	N	0.999408	B	0.29212	0.237	B	0.39152	0.292	T	0.34153	-0.9840	10	0.39692	T	0.17	.	7.1208	0.25444	1.0:0.0:0.0:0.0	.	152	Q3KRB8	RHGBB_HUMAN	E	152	ENSP00000392760:K152E	ENSP00000392760:K152E	K	+	1	0	ARHGAP11B	28713821	1.000000	0.71417	0.951000	0.38953	0.463000	0.32649	4.023000	0.57211	0.949000	0.37715	0.136000	0.15936	AAG	.	.		0.413	ARHGAP11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430729.1	NM_001039841		G	30926529	A	G	30926529	3	3	311	1	0	0	0	0	1	0	0	0	864	15	1	2	468	2	ARHGAP11B	15	30926529	Missense_Mutation	SNP	A	TCGA-K7-A6G5-01A-11D-A30V-10	2506932	30926529	71604863	60	44282										
CTDSPL2	51496	hgsc.bcm.edu	37	chr15	44816346	44816346	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	acatcagagacagatttcgcTtgcatgatttgctgccccca	8	12	1	3			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr15:44816346T>C	ENST00000260327.4	+	13	1938	c.1375T>C	c.(1375-1377)Ttg>Ctg	p.L459L	CTDSPL2_ENST00000558966.1_Silent_p.L459L|CTDSPL2_ENST00000558373.1_Silent_p.L387L|CTDSPL2_ENST00000396780.1_Silent_p.L387L	NM_016396.2	NP_057480.2	Q05D32	CTSL2_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2	459							phosphoprotein phosphatase activity (GO:0004721)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(2)	13		all_cancers(109;4.36e-14)|all_epithelial(112;9.8e-12)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.0122)		all cancers(107;1.02e-20)|GBM - Glioblastoma multiforme(94;1.49e-06)|COAD - Colon adenocarcinoma(120;0.0857)|Colorectal(105;0.0905)		CAGATTTCGCTTGCATGATTT	0.388																																					p.L459L		Atlas-SNP	.											.	CTDSPL2	31	.	0			c.T1375C						.						107	102	103					15																	44816346		2198	4298	6496	SO:0001819	synonymous_variant	51496	exon13			TTTCGCTTGCATG	AF161478	CCDS10110.1	15q15.3-q21.1	2010-06-21			ENSG00000137770	ENSG00000137770		"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	26936	protein-coding gene	gene with protein product							Standard	NM_016396		Approved	HSPC129, FLJ10523	uc001ztr.3	Q05D32	OTTHUMG00000131159	ENST00000260327.4:c.1375T>C	chr15.hg19:g.44816346T>C		46.0	0.0		49.0	24.0	NM_016396	Q3ZTU1|Q6AI06|Q8IYI9|Q9NVT2|Q9NZX8|Q9P030	Silent	SNP	ENST00000260327.4	hg19	CCDS10110.1																																																																																			.	.		0.388	CTDSPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253851.1	NM_016396		C	44816346	T	C	44816346	2	2	311	1	0	0	0	0	0	0	0	1	4008	1606	56	2		2	CTDSPL2	15	44816346	Silent	SNP	T	TCGA-K7-A6G5-01A-11D-A30V-10	13889817	44816346	57715046	61	44283										
VPS13C	54832	hgsc.bcm.edu	37	chr15	62226473	62226473	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	gagattcaaagtgaaagtcaAattggagactgacaatctgg	11	5	3	4			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr15:62226473A>C	ENST00000261517.5	-	49	5886	c.5813T>G	c.(5812-5814)tTt>tGt	p.F1938C	VPS13C_ENST00000395896.4_Missense_Mutation_p.F1938C|VPS13C_ENST00000249837.3_Missense_Mutation_p.F1895C|VPS13C_ENST00000395898.3_Missense_Mutation_p.F1895C	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						GTGAAAGTCAAATTGGAGACT	0.313																																					p.F1938C		Atlas-SNP	.											.	VPS13C	506	.	0			c.T5813G						.						129	140	136					15																	62226473		2203	4298	6501	SO:0001583	missense	54832	exon49			AAGTCAAATTGGA	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"vacuolar protein sorting 13C (yeast)"				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.5813T>G	chr15.hg19:g.62226473A>C	ENSP00000261517:p.Phe1938Cys	280.0	0.0		236.0	10.0	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	hg19	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	A	15.05	2.719375	0.48728	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.17370	2.28;2.28;2.28	5.19	4.04	0.47022	.	0.112294	0.64402	D	0.000009	T	0.36908	0.0984	M	0.69823	2.125	0.58432	D	0.999999	D;D;D;D	0.76494	0.999;0.999;0.998;0.999	D;D;D;P	0.70016	0.967;0.951;0.967;0.894	T	0.08785	-1.0705	10	0.87932	D	0	.	9.2205	0.37373	0.7103:0.0:0.0:0.2897	.	1895;1938;1895;1938	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	C	1895;1938;1938;1938	ENSP00000249837:F1895C;ENSP00000261517:F1938C;ENSP00000379233:F1938C	ENSP00000249837:F1895C	F	-	2	0	VPS13C	60013765	1.000000	0.71417	0.969000	0.41365	0.633000	0.38033	3.665000	0.54532	0.773000	0.33404	0.528000	0.53228	TTT	.	.		0.313	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		C	62226473	A	C	62226473	3	2	311	1	0	0	0	0	1	0	0	0	17206	14	1	5	5624	5	VPS13C	15	62226473	Missense_Mutation	SNP	A	TCGA-K7-A6G5-01A-11D-A30V-10	17410127	62226473	40304919	62	44284										
TLN2	83660	hgsc.bcm.edu	37	chr15	63031555	63031555	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	tgttccccacagctacctccAagcacgaagcctttccagga	7	16	0	0			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr15:63031555A>G	ENST00000561311.1	+	30	3926	c.3696A>G	c.(3694-3696)ccA>ccG	p.P1232P	TLN2_ENST00000306829.6_Silent_p.P1232P|TLN2_ENST00000559908.1_3'UTR			Q9Y4G6	TLN2_HUMAN	talin 2	1232					cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						AGCTACCTCCAAGCACGAAGC	0.562																																					p.P1232P		Atlas-SNP	.											.	TLN2	253	.	0			c.A3696G						.						78	68	71					15																	63031555		2203	4300	6503	SO:0001819	synonymous_variant	83660	exon28			ACCTCCAAGCACG	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.3696A>G	chr15.hg19:g.63031555A>G		37.0	0.0		37.0	7.0	NM_015059	A6NLB8	Silent	SNP	ENST00000561311.1	hg19	CCDS32261.1																																																																																			.	.		0.562	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			G	63031555	A	G	63031555	2	3	311	1	0	0	0	0	0	0	0	1	15963	117	5	2		2	TLN2	15	63031555	Silent	SNP	A	TCGA-K7-A6G5-01A-11D-A30V-10	805082	63031555	39499837	63	44285										
AEN	64782	hgsc.bcm.edu	37	chr15	89169543	89169543	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	agaggcacaagagaaggagcCgacagcaccagcggttcatg	14	10	1	2	rs199532354		TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr15:89169543C>T	ENST00000332810.3	+	2	254	c.103C>T	c.(103-105)Cga>Tga	p.R35*	AEN_ENST00000379231.3_Nonsense_Mutation_p.R35*	NM_022767.3	NP_073604.3	Q8WTP8	AEN_HUMAN	apoptosis enhancing nuclease	35					intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|response to ionizing radiation (GO:0010212)	nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)			NS(1)|kidney(1)|large_intestine(1)|lung(4)	7						GAGAAGGAGCCGACAGCACCA	0.637																																					p.R35X		Atlas-SNP	.											.	AEN	29	.	0			c.C103T						.						32	28	29					15																	89169543		2200	4299	6499	SO:0001587	stop_gained	64782	exon2			AGGAGCCGACAGC	BC020988	CCDS10344.1	15q26.1	2008-07-15	2008-07-15	2008-07-15	ENSG00000181026	ENSG00000181026			25722	protein-coding gene	gene with protein product		610177	"interferon stimulated exonuclease gene 20kDa-like 1"	ISG20L1		18264133, 16171785	Standard	NM_022767		Approved	FLJ12484, FLJ12562	uc002bmt.2	Q8WTP8	OTTHUMG00000148681	ENST00000332810.3:c.103C>T	chr15.hg19:g.89169543C>T	ENSP00000331944:p.Arg35*	15.0	0.0		23.0	5.0	NM_022767	C9J571|Q9BSA5|Q9H9X7	Nonsense_Mutation	SNP	ENST00000332810.3	hg19	CCDS10344.1	.	.	.	.	.	.	.	.	.	.	C	39	7.883288	0.98542	.	.	ENSG00000181026	ENST00000332810;ENST00000379231	.	.	.	5.02	5.02	0.67125	.	1.364360	0.05327	N	0.527595	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	4.6706	17.3342	0.87275	0.0:1.0:0.0:0.0	.	.	.	.	X	35	.	ENSP00000331944:R35X	R	+	1	2	AEN	86970547	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.714000	0.54889	2.315000	0.78130	0.563000	0.77884	CGA	.	C|0.998;T|0.002		0.637	AEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309071.1	NM_022767		T	89169543	C	T	89169543	4	4	311	1	0	0	0	0	0	1	0	0	351	644	23	1	105	1	AEN	15	89169543	Nonsense_Mutation	SNP	C	TCGA-K7-A6G5-01A-11D-A30V-10	26137988	89169543	13361849	64	44286										
SEZ6L2	26470	hgsc.bcm.edu	37	chr16	29891311	29891311	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	gaaggttgccagtgcccctgGgcgatactcagggtccgtgg	16	11	1	0			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr16:29891311G>A	ENST00000308713.5	-	9	1974	c.1447C>T	c.(1447-1449)Cca>Tca	p.P483S	SEZ6L2_ENST00000350527.3_Missense_Mutation_p.P413S|SEZ6L2_ENST00000537485.1_Missense_Mutation_p.P439S|SEZ6L2_ENST00000346932.5_Missense_Mutation_p.P369S	NM_001114099.2|NM_201575.3	NP_001107571.1|NP_963869.2	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2	483	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						AGTGCCCCTGGGCGATACTCA	0.592																																					p.P483S		Atlas-SNP	.											.	SEZ6L2	137	.	0			c.C1447T						.						89	77	81					16																	29891311		2197	4300	6497	SO:0001583	missense	26470	exon9			CCCCTGGGCGATA	AY358404	CCDS10658.1, CCDS10659.1, CCDS45458.1, CCDS58447.1, CCDS73865.1	16p12.1	2008-02-05			ENSG00000174938	ENSG00000174938			30844	protein-coding gene	gene with protein product	"type I transmembrane receptor (seizure related protein)"					12975309	Standard	NM_012410		Approved	PSK-1, FLJ90517	uc010vec.2	Q6UXD5	OTTHUMG00000132112	ENST00000308713.5:c.1447C>T	chr16.hg19:g.29891311G>A	ENSP00000312550:p.Pro483Ser	61.0	0.0		50.0	14.0	NM_001243332	B7Z1N0|F5H293|H7BXQ6|Q9BW82|Q9UJ45|Q9UJ46|Q9UJ47	Missense_Mutation	SNP	ENST00000308713.5	hg19	CCDS10659.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.026869	0.75390	.	.	ENSG00000174938	ENST00000350527;ENST00000308713;ENST00000346932;ENST00000537485	T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1	5.26	5.26	0.73747	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.56097	D	0.000028	T	0.61751	0.2372	L	0.40543	1.245	0.42829	D	0.994015	B;B;D;P;P;B	0.53312	0.008;0.01;0.959;0.879;0.901;0.008	B;B;P;B;P;B	0.50049	0.012;0.012;0.629;0.399;0.534;0.013	T	0.64672	-0.6352	10	0.59425	D	0.04	.	13.3502	0.60597	0.0:0.0:0.8416:0.1584	.	439;483;369;413;483;413	F5H293;B7Z5L4;Q9BW82;Q6UXD5-2;Q6UXD5;Q6UXD5-3	.;.;.;.;SE6L2_HUMAN;.	S	413;483;369;439	ENSP00000310206:P413S;ENSP00000312550:P483S;ENSP00000319215:P369S;ENSP00000439412:P439S	ENSP00000312550:P483S	P	-	1	0	SEZ6L2	29798812	0.964000	0.33143	1.000000	0.80357	0.869000	0.49853	1.419000	0.34793	2.735000	0.93741	0.655000	0.94253	CCA	.	.		0.592	SEZ6L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255154.2	NM_012410		A	29891311	G	A	29891311	3	1	311	1	0	0	0	0	1	0	0	0	14159	1232	43	3	1364	3	SEZ6L2	16	29891311	Missense_Mutation	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10		29891311	60463442	65	44287										
GAN	8139	hgsc.bcm.edu	37	chr16	81390417	81390417	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	tgaaggatgttatgtcagctCtgtgggtttcagggttggac	15	5	3	1			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr16:81390417C>T	ENST00000568107.2	+	4	823	c.661C>T	c.(661-663)Ctg>Ttg	p.L221L		NM_022041.3	NP_071324.1	Q9H2C0	GAN_HUMAN	gigaxonin	221	BACK.				cell death (GO:0008219)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)	25		Colorectal(91;0.153)				TATGTCAGCTCTGTGGGTTTC	0.413																																					p.L221L	GBM(106;1239 1507 7582 9741 33976)	Atlas-SNP	.											.	GAN	59	.	0			c.C661T						.						121	110	114					16																	81390417		2202	4300	6502	SO:0001819	synonymous_variant	8139	exon4			TCAGCTCTGTGGG	AF291673	CCDS10935.1	16q24.1	2014-09-17	2008-08-01		ENSG00000261609	ENSG00000261609		"Kelch-like", "BTB/POZ domain containing"	4137	protein-coding gene	gene with protein product	"kelch-like family member 16"	605379	"giant axonal neuropathy (gigaxonin)"			9450783, 11062483	Standard	NM_022041		Approved	GAN1, KLHL16	uc002fgo.3	Q9H2C0	OTTHUMG00000137627	ENST00000568107.2:c.661C>T	chr16.hg19:g.81390417C>T		132.0	0.0		149.0	46.0	NM_022041		Silent	SNP	ENST00000568107.2	hg19	CCDS10935.1																																																																																			.	.		0.413	GAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269050.3			T	81390417	C	T	81390417	2	4	311	1	0	0	0	0	0	0	0	1	6240	912	32	3		3	GAN	16	81390417	Silent	SNP	C	TCGA-K7-A6G5-01A-11D-A30V-10	51499106	81390417	8964336	66	44288										
SLC47A1	55244	hgsc.bcm.edu	37	chr17	19459199	19459199	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	gtgcatggagtggtgggcctAtgaggtcgggagcttcctca	17	8	1	1			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr17:19459199A>G	ENST00000270570.4	+	9	916	c.830A>G	c.(829-831)tAt>tGt	p.Y277C	SLC47A1_ENST00000542886.1_Silent_p.L244L|SLC47A1_ENST00000436810.2_Missense_Mutation_p.Y254C|SLC47A1_ENST00000575023.1_Intron|SLC47A1_ENST00000571335.1_Missense_Mutation_p.Y82C|SNORA59B_ENST00000458926.1_RNA|SLC47A1_ENST00000457293.1_Missense_Mutation_p.Y277C|SLC47A1_ENST00000395585.1_Missense_Mutation_p.Y277C	NM_018242.2	NP_060712.2	Q96FL8	S47A1_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 1	277					organic cation transport (GO:0015695)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane-bounded vesicle (GO:0031988)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|monovalent cation:proton antiporter activity (GO:0005451)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(4)|lung(5)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	23	all_cancers(12;2.49e-05)|all_epithelial(12;0.00263)|Hepatocellular(7;0.00345)				Aciclovir(DB00787)|Bromodiphenhydramine(DB01237)|Cephalexin(DB00567)|Cimetidine(DB00501)|Metformin(DB00331)|Sirolimus(DB00877)	TGGTGGGCCTATGAGGTCGGG	0.642																																					p.Y277C		Atlas-SNP	.											.	SLC47A1	55	.	0			c.A830G						.						41	37	39					17																	19459199		2203	4300	6503	SO:0001583	missense	55244	exon9			GGGCCTATGAGGT		CCDS11209.1	17p11.2	2013-07-17	2013-07-17		ENSG00000142494	ENSG00000142494		"Solute carriers"	25588	protein-coding gene	gene with protein product	"multidrug and toxin extrusion 1"	609832				16330770, 16996621, 16928787	Standard	NM_018242		Approved	FLJ10847, MATE1	uc002gvy.1	Q96FL8	OTTHUMG00000059466	ENST00000270570.4:c.830A>G	chr17.hg19:g.19459199A>G	ENSP00000270570:p.Tyr277Cys	25.0	0.0		22.0	7.0	NM_018242	Q53HF5|Q6PD77|Q86VL4|Q9NVA3	Missense_Mutation	SNP	ENST00000270570.4	hg19	CCDS11209.1	.	.	.	.	.	.	.	.	.	.	A	17.86	3.492914	0.64074	.	.	ENSG00000142494	ENST00000436810;ENST00000270570;ENST00000457293;ENST00000395585;ENST00000455670	T;T;T;T	0.30448	1.53;1.53;1.53;1.53	5.54	5.54	0.83059	.	0.110737	0.64402	D	0.000005	T	0.62405	0.2425	M	0.92880	3.355	0.80722	D	1	D;D;D;D;D	0.89917	0.999;1.0;0.999;1.0;1.0	D;D;D;D;D	0.85130	0.984;0.997;0.99;0.994;0.987	T	0.70769	-0.4782	10	0.87932	D	0	-9.0532	10.161	0.42851	0.8514:0.0:0.0:0.1486	.	11;254;11;277;277	E7ENC3;E7EX57;B4DDH5;Q96FL8;Q96FL8-3	.;.;.;S47A1_HUMAN;.	C	254;277;277;277;11	ENSP00000407155:Y254C;ENSP00000270570:Y277C;ENSP00000415586:Y277C;ENSP00000378951:Y277C	ENSP00000270570:Y277C	Y	+	2	0	SLC47A1	19399791	0.036000	0.19791	0.999000	0.59377	0.994000	0.84299	0.423000	0.21313	2.104000	0.64026	0.533000	0.62120	TAT	.	.		0.642	SLC47A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132250.1	NM_018242		G	19459199	A	G	19459199	3	3	311	1	0	0	0	0	1	0	0	0	14662	449	16	2	864	2	SLC47A1	17	19459199	Missense_Mutation	SNP	A	TCGA-K7-A6G5-01A-11D-A30V-10		19459199	61736011	67	44289										
CCDC55	84081	hgsc.bcm.edu	37	chr17	28506153	28506156	+	Frame_Shift_Del	DEL	AAGG	AAGG	-													0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	aagcagttgagatcagaaaaAaggaacaggaaaaaagaatg							TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	AAGG	AAGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr17:28506153_28506156delAAGG	ENST00000247026.5	+	5	409_412	c.346_349delAAGG	c.(346-351)aaggaafs	p.KE116fs	NSRP1_ENST00000540900.3_3'UTR	NM_001261467.1|NM_032141.3	NP_001248396.1|NP_115517.1	Q9H0G5	NSRP1_HUMAN	nuclear speckle splicing regulatory protein 1	116	Necessary for alternative splicing activity.				developmental process (GO:0032502)|mRNA processing (GO:0006397)|nucleocytoplasmic transport (GO:0006913)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	14						GATCAGAAAAAAGGAACAGGAAAA	0.304																																					p.115_116del		Atlas-Indel,Pindel	.											.	NSRP1	49	.	0			c.345_348del						.																																			SO:0001589	frameshift_variant	84081	exon5			.	AL136806	CCDS11255.1, CCDS74025.1	17q11.2	2011-05-24	2011-05-24	2011-05-24	ENSG00000126653	ENSG00000126653			25305	protein-coding gene	gene with protein product			"coiled-coil domain containing 55"	CCDC55		11230166	Standard	NM_032141		Approved	DKFZP434K1421, NSrp70	uc002heu.4	Q9H0G5	OTTHUMG00000132754	ENST00000247026.5:c.346_349delAAGG	chr17.hg19:g.28506153_28506156delAAGG	ENSP00000247026:p.Lys116fs	290.0	0.0		253.0	58.0	NM_032141	Q6FI71	Frame_Shift_Del	DEL	ENST00000247026.5	hg19	CCDS11255.1																																																																																			.	.		0.304	NSRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256121.2	NM_032141		-	28506156	AAGG	-	28506153	7	5	311	1	0	1	0	1	0	0	0	0	2827	15	1	0	364	0	CCDC55	17	28506153	Frame_Shift_Del	DEL	AAGG	TCGA-K7-A6G5-01A-11D-A30V-10	9046954	28506153	52689057	68	44290										
EFTUD2	9343	hgsc.bcm.edu	37	chr17	42964016	42964016	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	ctcaggaccatacacctcctCggctgttgggtagtacttct	9	13	2	0			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr17:42964016C>T	ENST00000426333.2	-	3	505	c.208G>A	c.(208-210)Gag>Aag	p.E70K	EFTUD2_ENST00000591382.1_Missense_Mutation_p.E70K|RN7SL405P_ENST00000582502.1_RNA|EFTUD2_ENST00000589211.1_5'Flank|EFTUD2_ENST00000592576.1_Missense_Mutation_p.E70K|EFTUD2_ENST00000402521.3_Missense_Mutation_p.E35K	NM_001142605.1|NM_001258354.1|NM_004247.3	NP_001136077.1|NP_001245283.1|NP_004238.3	Q15029	U5S1_HUMAN	elongation factor Tu GTP binding domain containing 2	70					gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	32		Prostate(33;0.109)				TACACCTCCTCGGCTGTTGGG	0.532																																					p.E70K	Ovarian(10;65 485 10258 29980 30707)	Atlas-SNP	.											.	EFTUD2	85	.	0			c.G208A						.						219	144	170					17																	42964016		2203	4300	6503	SO:0001583	missense	9343	exon3			CCTCCTCGGCTGT	D21163	CCDS11489.1, CCDS45707.1, CCDS59295.1	17q21.31	2014-08-12			ENSG00000108883	ENSG00000108883			30858	protein-coding gene	gene with protein product	"U5 snRNP specific protein, 116 kD"	603892				9233818	Standard	NM_004247		Approved	U5-116KD, Snrp116, Snu114, SNRNP116	uc002ihn.2	Q15029	OTTHUMG00000179865	ENST00000426333.2:c.208G>A	chr17.hg19:g.42964016C>T	ENSP00000392094:p.Glu70Lys	58.0	0.0		50.0	12.0	NM_004247	B4DK30|B4DMC0|D3DX58|K7EJ81|Q9BUR0	Missense_Mutation	SNP	ENST00000426333.2	hg19	CCDS11489.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.964151	0.74131	.	.	ENSG00000108883	ENST00000426333;ENST00000402521	T;T	0.70869	-0.52;-0.52	6.11	6.11	0.99139	.	0.000000	0.85682	D	0.000000	T	0.71384	0.3333	M	0.76574	2.34	0.80722	D	1	B;B	0.27765	0.188;0.188	B;B	0.21360	0.034;0.034	T	0.66559	-0.5893	10	0.19147	T	0.46	-18.5037	20.7342	0.99715	0.0:1.0:0.0:0.0	.	70;70	B4DMC0;Q15029	.;U5S1_HUMAN	K	70;35	ENSP00000392094:E70K;ENSP00000385873:E35K	ENSP00000385873:E35K	E	-	1	0	EFTUD2	40319542	1.000000	0.71417	0.981000	0.43875	0.805000	0.45488	7.433000	0.80362	2.906000	0.99361	0.655000	0.94253	GAG	.	.		0.532	EFTUD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448672.1	NM_004247		T	42964016	C	T	42964016	3	4	311	1	0	0	0	0	1	0	0	0	4963	893	31	1	2814	1	EFTUD2	17	42964016	Missense_Mutation	SNP	C	TCGA-K7-A6G5-01A-11D-A30V-10	14457863	42964016	38231194	69	44291										
INTS2	57508	hgsc.bcm.edu	37	chr17	59947136	59947136	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	agcaatgttgggatctgcaaTgtacatttggtgcaagagac	12	6	1	1			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr17:59947136T>C	ENST00000444766.3	-	21	3091	c.3016A>G	c.(3016-3018)Att>Gtt	p.I1006V	INTS2_ENST00000251334.6_Missense_Mutation_p.I998V	NM_020748.2	NP_065799	Q9H0H0	INT2_HUMAN	integrator complex subunit 2	1006					snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|intracellular (GO:0005622)|membrane (GO:0016020)				NS(1)|breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	38						GGATCTGCAATGTACATTTGG	0.413																																					p.I1006V		Atlas-SNP	.											.	INTS2	89	.	0			c.A3016G						.						226	219	221					17																	59947136		1925	4140	6065	SO:0001583	missense	57508	exon21			CTGCAATGTACAT	AB033113	CCDS45750.1	17q23.2	2006-04-26	2006-03-15	2006-03-15		ENSG00000108506			29241	protein-coding gene	gene with protein product		611346	"KIAA1287"	KIAA1287		16239144	Standard	NR_026641		Approved	INT2	uc002izn.3	Q9H0H0		ENST00000444766.3:c.3016A>G	chr17.hg19:g.59947136T>C	ENSP00000414237:p.Ile1006Val	71.0	0.0		70.0	22.0	NM_020748	Q9ULD3	Missense_Mutation	SNP	ENST00000444766.3	hg19	CCDS45750.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.338158	0.81911	.	.	ENSG00000108506	ENST00000444766;ENST00000251334	T	0.59906	0.23	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.72407	0.3456	M	0.76838	2.35	0.80722	D	1	P	0.38863	0.65	P	0.54140	0.743	T	0.72636	-0.4233	9	.	.	.	-16.9128	14.2898	0.66270	0.0:0.0:0.0:1.0	.	1006	Q9H0H0	INT2_HUMAN	V	1006;1005	ENSP00000414237:I1006V	.	I	-	1	0	INTS2	57301918	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.673000	0.83973	1.975000	0.57531	0.528000	0.53228	ATT	.	.		0.413	INTS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000445368.1	NM_020748		C	59947136	T	C	59947136	3	2	311	1	0	0	0	0	1	0	0	0	7787	1464	51	2	618	2	INTS2	17	59947136	Missense_Mutation	SNP	T	TCGA-K7-A6G5-01A-11D-A30V-10	16983120	59947136	21248074	70	44292										
AFG3L2	10939	hgsc.bcm.edu	37	chr18	12356735	12356735	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	aacatctccaaaaactcagaTccactaacggtgatgaaggg	8	10	2	3			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr18:12356735T>G	ENST00000269143.3	-	9	1353	c.1122A>C	c.(1120-1122)ggA>ggC	p.G374G		NM_006796.2	NP_006787.2	Q9Y4W6	AFG32_HUMAN	AFG3-like AAA ATPase 2	374					axonogenesis (GO:0007409)|cell death (GO:0008219)|cristae formation (GO:0042407)|mitochondrial fusion (GO:0008053)|mitochondrial protein processing (GO:0034982)|muscle fiber development (GO:0048747)|myelination (GO:0042552)|nerve development (GO:0021675)|neuromuscular junction development (GO:0007528)|regulation of multicellular organism growth (GO:0040014)|righting reflex (GO:0060013)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metalloendopeptidase activity (GO:0004222)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(12)|prostate(3)|skin(1)|stomach(3)|urinary_tract(1)	27					Adenosine triphosphate(DB00171)	AAAACTCAGATCCACTAACGG	0.542																																					p.G374G		Atlas-SNP	.											.	AFG3L2	60	.	0			c.A1122C						.						193	145	162					18																	12356735		2203	4300	6503	SO:0001819	synonymous_variant	10939	exon9			CTCAGATCCACTA	Y18314	CCDS11859.1	18p11.21	2014-09-17	2013-10-17		ENSG00000141385	ENSG00000141385		"ATPases / AAA-type"	315	protein-coding gene	gene with protein product		604581	"AFG3 (ATPase family gene 3, yeast)-like 2", "spinocerebellar ataxia 28", "AFG3 ATPase family gene 3-like 2 (yeast)", "AFG3 ATPase family gene 3-like 2 (S. cerevisiae)", "AFG3 ATPase family member 3-like 2 (S. cerevisiae)"	SCA28		10395799, 18769991	Standard	NM_006796		Approved	SPAX5	uc002kqz.2	Q9Y4W6	OTTHUMG00000131695	ENST00000269143.3:c.1122A>C	chr18.hg19:g.12356735T>G		58.0	0.0		51.0	11.0	NM_006796	Q6P1L0	Silent	SNP	ENST00000269143.3	hg19	CCDS11859.1																																																																																			.	.		0.542	AFG3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254603.2	NM_006796		G	12356735	T	G	12356735	2	3	311	1	0	0	0	0	0	0	0	1	360	1422	50	5		5	AFG3L2	18	12356735	Silent	SNP	T	TCGA-K7-A6G5-01A-11D-A30V-10		12356735	65720513	71	44293										
ZCCHC2	54877	hgsc.bcm.edu	37	chr18	60241963	60241963	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	ggactcaatcaaatggtgccTcaaattgagggaaacacagg	11	8	3	1			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr18:60241963T>G	ENST00000269499.5	+	13	3067	c.2649T>G	c.(2647-2649)ccT>ccG	p.P883P	ZCCHC2_ENST00000586834.1_Silent_p.P562P	NM_017742.4	NP_060212.4	Q9C0B9	ZCHC2_HUMAN	zinc finger, CCHC domain containing 2	883						cytoplasm (GO:0005737)	nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(10)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	25						AAATGGTGCCTCAAATTGAGG	0.527																																					p.P883P		Atlas-SNP	.											.	ZCCHC2	64	.	0			c.T2649G						.						109	106	107					18																	60241963		2022	4196	6218	SO:0001819	synonymous_variant	54877	exon13			GGTGCCTCAAATT	AB051531	CCDS45880.1	18q21.33	2012-04-19			ENSG00000141664	ENSG00000141664		"Zinc fingers, CCHC domain containing"	22916	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 49"	C18orf49		11214970	Standard	NM_017742		Approved	FLJ20281, KIAA1744, FLJ20222	uc002lip.4	Q9C0B9		ENST00000269499.5:c.2649T>G	chr18.hg19:g.60241963T>G		114.0	0.0		102.0	25.0	NM_017742	B2RPG6|Q8N3S1|Q9NXF6	Silent	SNP	ENST00000269499.5	hg19	CCDS45880.1																																																																																			.	.		0.527	ZCCHC2-005	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450083.1	NM_017742		G	60241963	T	G	60241963	2	3	311	1	0	0	0	0	0	0	0	1	17602	1538	54	5		5	ZCCHC2	18	60241963	Silent	SNP	T	TCGA-K7-A6G5-01A-11D-A30V-10	47885228	60241963	17835285	72	44294										
LRRC8E	80131	hgsc.bcm.edu	37	chr19	7960521	7960521	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	gccgagttcaagcagttcacGgaacagcagcctgcgttcaa	11	12	3	0			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr19:7960521G>A	ENST00000306708.6	+	2	134	c.33G>A	c.(31-33)acG>acA	p.T11T		NM_001268284.1|NM_001268285.1|NM_025061.4	NP_001255213.1|NP_001255214.1|NP_079337.2	Q6NSJ5	LRC8E_HUMAN	leucine rich repeat containing 8 family, member E	11					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(10)	35						AGCAGTTCACGGAACAGCAGC	0.622																																					p.T11T		Atlas-SNP	.											.	LRRC8E	67	.	0			c.G33A						.						145	103	118					19																	7960521		2203	4300	6503	SO:0001819	synonymous_variant	80131	exon3			GTTCACGGAACAG		CCDS12189.1	19p13.2	2008-02-05				ENSG00000171017			26272	protein-coding gene	gene with protein product		612891				12477932	Standard	NM_025061		Approved	FLJ23420	uc002mir.3	Q6NSJ5		ENST00000306708.6:c.33G>A	chr19.hg19:g.7960521G>A		109.0	0.0		56.0	21.0	NM_001268284	B3KR78|Q2YDY3|Q7L236|Q8N3B0|Q9H5H8	Silent	SNP	ENST00000306708.6	hg19	CCDS12189.1																																																																																			.	.		0.622	LRRC8E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461354.1	NM_025061		A	7960521	G	A	7960521	2	1	311	1	0	0	0	0	0	0	0	1	9034	1103	39	1		1	LRRC8E	19	7960521	Silent	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10		7960521	51168462	73	44295										
MAN2B1	4125	hgsc.bcm.edu	37	chr19	12757461	12757461	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	tccacctccttccattgaacTgaggccaggaaagtgcggat	10	12	0	2			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr19:12757461T>C	ENST00000456935.2	-	24	3049	c.3009A>G	c.(3007-3009)tcA>tcG	p.S1003S	CTD-2192J16.22_ENST00000597692.1_Missense_Mutation_p.S190G|MAN2B1_ENST00000221363.4_Silent_p.S1002S	NM_000528.3|NM_001173498.1	NP_000519.2|NP_001166969.1	O00754	MA2B1_HUMAN	mannosidase, alpha, class 2B, member 1	1003					cellular protein modification process (GO:0006464)|mannose metabolic process (GO:0006013)|protein deglycosylation (GO:0006517)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						TCCATTGAACTGAGGCCAGGA	0.617																																					p.S1003S		Atlas-SNP	.											.	MAN2B1	91	.	0			c.A3009G						.						167	130	143					19																	12757461		2203	4300	6503	SO:0001819	synonymous_variant	4125	exon24			TTGAACTGAGGCC		CCDS32919.1, CCDS54224.1	19p13.2	2013-09-20			ENSG00000104774	ENSG00000104774	3.2.1.24		6826	protein-coding gene	gene with protein product		609458		MANB			Standard	NM_000528		Approved	LAMAN	uc002mub.2	O00754	OTTHUMG00000156397	ENST00000456935.2:c.3009A>G	chr19.hg19:g.12757461T>C		72.0	0.0		62.0	13.0	NM_000528	G5E928|O15330|Q16680|Q93094|Q9BW13	Silent	SNP	ENST00000456935.2	hg19	CCDS32919.1																																																																																			.	.		0.617	MAN2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344062.1			C	12757461	T	C	12757461	2	2	311	1	0	0	0	0	0	0	0	1	9225	1567	55	2		2	MAN2B1	19	12757461	Silent	SNP	T	TCGA-K7-A6G5-01A-11D-A30V-10	4796940	12757461	46371522	74	44296										
ZNF230	7773	hgsc.bcm.edu	37	chr19	44515439	44515440	+	Frame_Shift_Ins	INS	-	-	A													0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	ataagaaactccactgccggINSaaaaaacccttcaaatgtga							TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr19:44515439_44515440insA	ENST00000429154.2	+	5	1476_1477	c.1248_1249insA	c.(1249-1251)aaafs	p.K417fs		NM_006300.3	NP_006291.2	Q9UIE0	ZN230_HUMAN	zinc finger protein 230	417					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(10)|skin(1)|stomach(3)|urinary_tract(2)	22		Prostate(69;0.0352)				TCCACTGCCGGAAAAAACCCTT	0.431																																					p.R416fs	GBM(175;914 2069 22996 47111 52600)	Atlas-Indel,Pindel	.											ZNF230,colon,carcinoma,0,1	ZNF230	44	.	0			c.1248_1249insA						.																																			SO:0001589	frameshift_variant	7773	exon5			.	U95044	CCDS33044.1	19q13.31	2013-01-08				ENSG00000159882		"Zinc fingers, C2H2-type", "-"	13024	protein-coding gene	gene with protein product							Standard	NM_006300		Approved	FDZF2	uc002oyb.1	Q9UIE0		ENST00000429154.2:c.1254dupA	chr19.hg19:g.44515445_44515445dupA	ENSP00000409318:p.Lys417fs	120.0	0.0		113.0	24.0	NM_006300	O15322|Q504X7|Q86W84|Q9P1U6	Frame_Shift_Ins	INS	ENST00000429154.2	hg19	CCDS33044.1																																																																																			.	.		0.431	ZNF230-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460456.1			A	44515440	-	A	44515439	7	5	311	1	0	1	1	0	0	0	0	0	17799	1161	41	0	1262	0	ZNF230	19	44515439	Frame_Shift_Ins	INS	-	TCGA-K7-A6G5-01A-11D-A30V-10	31757978	44515439	14613544	75	44297										
GLTSCR1	29998	hgsc.bcm.edu	37	chr19	48205339	48205339	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	ctgaagggccccccgccagaGcccgcagccagcgccgccca	12	21	0	2			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr19:48205339G>T	ENST00000396720.3	+	15	4544	c.4350G>T	c.(4348-4350)gaG>gaT	p.E1450D	CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_015711.3	NP_056526.3	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1	1450										breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|pancreas(3)|prostate(4)|skin(2)	20		all_cancers(25;1.8e-07)|all_lung(116;5.73e-06)|Lung NSC(112;9.69e-06)|all_epithelial(76;2.42e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000358)|OV - Ovarian serous cystadenocarcinoma(262;0.000576)|Epithelial(262;0.0212)|GBM - Glioblastoma multiforme(486;0.0355)		CCCCGCCAGAGCCCGCAGCCA	0.746																																					p.E1450D		Atlas-SNP	.											.	GLTSCR1	79	.	0			c.G4350T						.						2	2	2					19																	48205339		1194	2863	4057	SO:0001583	missense	29998	exon15			GCCAGAGCCCGCA	AF182077	CCDS46134.1	19q13.3	2012-11-29			ENSG00000063169	ENSG00000063169			4332	protein-coding gene	gene with protein product		605690				10708517	Standard	NM_015711		Approved		uc002phh.4	Q9NZM4		ENST00000396720.3:c.4350G>T	chr19.hg19:g.48205339G>T	ENSP00000379946:p.Glu1450Asp	4.0	0.0		12.0	9.0	NM_015711	A8MW01	Missense_Mutation	SNP	ENST00000396720.3	hg19	CCDS46134.1	.	.	.	.	.	.	.	.	.	.	G	1.685	-0.505580	0.04261	.	.	ENSG00000063169	ENST00000396720	T	0.30714	1.52	3.27	-0.671	0.11381	.	.	.	.	.	T	0.08670	0.0215	N	0.01576	-0.805	0.09310	N	1	B	0.11235	0.004	B	0.11329	0.006	T	0.37934	-0.9684	9	0.12103	T	0.63	.	4.19	0.10416	0.233:0.376:0.391:0.0	.	1450	Q9NZM4	GSCR1_HUMAN	D	1450	ENSP00000379946:E1450D	ENSP00000379946:E1450D	E	+	3	2	GLTSCR1	52897151	0.051000	0.20477	0.003000	0.11579	0.171000	0.22731	0.042000	0.13949	0.111000	0.17947	0.313000	0.20887	GAG	.	.		0.746	GLTSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465846.1	NM_015711		T	48205339	G	T	48205339	3	4	311	1	0	0	0	0	1	0	0	0	6482	962	34	3	4400	3	GLTSCR1	19	48205339	Missense_Mutation	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10	3689900	48205339	10923644	76	44298										
SIGLEC9	27180	hgsc.bcm.edu	37	chr19	51630358	51630358	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	ctctgcgcctggtctgtgcaGttgatgcagttgacagcaat	12	10	2	2			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr19:51630358G>A	ENST00000250360.3	+	4	887	c.820G>A	c.(820-822)Gtt>Att	p.V274I	SIGLEC9_ENST00000440804.3_Missense_Mutation_p.V274I	NM_014441.2	NP_055256.1	Q9Y336	SIGL9_HUMAN	sialic acid binding Ig-like lectin 9	274	Ig-like C2-type 2.				cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(3)|lung(25)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	45		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.000826)|OV - Ovarian serous cystadenocarcinoma(262;0.00295)		GGTCTGTGCAGTTGATGCAGT	0.587																																					p.V274I		Atlas-SNP	.											.	SIGLEC9	85	.	0			c.G820A						.						107	103	104					19																	51630358		2203	4300	6503	SO:0001583	missense	27180	exon4			TGTGCAGTTGATG	AF135027	CCDS12825.1, CCDS56100.1	19q13.3-q13.4	2013-01-29			ENSG00000129450	ENSG00000129450		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10878	protein-coding gene	gene with protein product		605640				10903842	Standard	NM_014441		Approved	CD329	uc002pvu.3	Q9Y336		ENST00000250360.3:c.820G>A	chr19.hg19:g.51630358G>A	ENSP00000250360:p.Val274Ile	52.0	0.0		40.0	8.0	NM_001198558	Q6GTU4|Q9BYI9	Missense_Mutation	SNP	ENST00000250360.3	hg19	CCDS12825.1	.	.	.	.	.	.	.	.	.	.	.	8.166	0.790530	0.16258	.	.	ENSG00000129450	ENST00000440804;ENST00000250360	T;T	0.12672	2.66;2.66	.	.	.	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.114660	0.07119	N	0.843648	T	0.10680	0.0261	L	0.36672	1.1	0.09310	N	1	B	0.26002	0.139	B	0.21360	0.034	T	0.37244	-0.9714	8	0.62326	D	0.03	.	.	.	.	.	274	Q9Y336	SIGL9_HUMAN	I	274	ENSP00000413861:V274I;ENSP00000250360:V274I	ENSP00000250360:V274I	V	+	1	0	SIGLEC9	56322170	0.523000	0.26274	0.105000	0.21289	0.118000	0.20060	0.064000	0.14437	0.088000	0.17205	0.089000	0.15464	GTT	.	.		0.587	SIGLEC9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464224.1	NM_014441		A	51630358	G	A	51630358	3	1	311	1	0	0	0	0	1	0	0	0	14330	1029	36	3	834	3	SIGLEC9	19	51630358	Missense_Mutation	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10	3425019	51630358	7498625	77	44299										
PLCB4	5332	hgsc.bcm.edu	37	chr20	9449315	9449315	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	tcaagaataaagcagaacggGaaaggtaagtctgagagtgt	13	4	2	3			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr20:9449315G>T	ENST00000378493.1	+	32	3325	c.3310G>T	c.(3310-3312)Gaa>Taa	p.E1104*	PLCB4_ENST00000378501.2_Nonsense_Mutation_p.E1104*|PLCB4_ENST00000378473.3_Nonsense_Mutation_p.E1116*|PLCB4_ENST00000278655.4_Nonsense_Mutation_p.E1104*|PLCB4_ENST00000334005.3_Nonsense_Mutation_p.E1104*|PLCB4_ENST00000414679.2_Nonsense_Mutation_p.E1116*|PLCB4_ENST00000492632.1_3'UTR			Q15147	PLCB4_HUMAN	phospholipase C, beta 4	1104					inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|smooth endoplasmic reticulum (GO:0005790)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(2)|breast(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(11)|liver(4)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(19)|upper_aerodigestive_tract(1)	87						AGCAGAACGGGAAAGGTAAGT	0.418																																					p.E1116X		Atlas-SNP	.											PLCB4,mucosal,malignant_melanoma,0,2	PLCB4	204	.	0			c.G3346T						.						109	98	102					20																	9449315		2203	4300	6503	SO:0001587	stop_gained	5332	exon35			GAACGGGAAAGGT		CCDS13104.1, CCDS13105.1, CCDS54447.1	20p12	2008-03-18			ENSG00000101333	ENSG00000101333	3.1.4.11		9059	protein-coding gene	gene with protein product		600810				8530101	Standard	NM_000933		Approved		uc021wam.1	Q15147	OTTHUMG00000031853	ENST00000378493.1:c.3310G>T	chr20.hg19:g.9449315G>T	ENSP00000367754:p.Glu1104*	57.0	0.0		49.0	18.0	NM_001172646	B7ZLK6|E2QRH8|Q17R56|Q5JYS8|Q5JYS9|Q5JYT0|Q5JYT3|Q5JYT4|Q9BQW5|Q9BQW6|Q9BQW8|Q9UJQ2	Nonsense_Mutation	SNP	ENST00000378493.1	hg19	CCDS13105.1	.	.	.	.	.	.	.	.	.	.	G	44	11.195880	0.99529	.	.	ENSG00000101333	ENST00000334005;ENST00000378473;ENST00000278655;ENST00000378493;ENST00000378501;ENST00000414679	.	.	.	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	19.9433	0.97172	0.0:0.0:1.0:0.0	.	.	.	.	X	1104;1116;1104;1104;1104;952	.	ENSP00000278655:E1104X	E	+	1	0	PLCB4	9397315	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	9.054000	0.93866	2.716000	0.92895	0.655000	0.94253	GAA	.	.		0.418	PLCB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077948.2			T	9449315	G	T	9449315	4	4	311	1	0	0	0	0	0	1	0	0	12039	1175	41	3	3476	3	PLCB4	20	9449315	Nonsense_Mutation	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10		9449315	53576205	78	44300										
CD93	22918	hgsc.bcm.edu	37	chr20	23066708	23066708	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	cggcagcgctcagcttgcccGagtgggccgtgtagcaggcg	17	13	1	0			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr20:23066708G>T	ENST00000246006.4	-	1	269	c.122C>A	c.(121-123)tCg>tAg	p.S41*		NM_012072.3	NP_036204.2	Q9NPY3	C1QR1_HUMAN	CD93 molecule	41	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				macrophage activation (GO:0042116)|phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|complement component C1q binding (GO:0001849)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(10)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	39	Colorectal(13;0.0352)|Lung NSC(19;0.0542)|all_lung(19;0.118)					CAGCTTGCCCGAGTGGGCCGT	0.697																																					p.S41X		Atlas-SNP	.											.	CD93	84	.	0			c.C122A						.						26	23	24					20																	23066708		2200	4296	6496	SO:0001587	stop_gained	22918	exon1			TTGCCCGAGTGGG	U94333	CCDS13149.1	20p11.21	2009-01-29	2006-03-28	2006-02-22	ENSG00000125810	ENSG00000125810		"CD molecules"	15855	protein-coding gene	gene with protein product		120577	"matrix-remodelling associated 4", "complement component 1, q subcomponent, receptor 1", "CD93 antigen"	MXRA4, C1QR1		9047234, 10648005	Standard	NM_012072		Approved	C1qRP, C1qR(P), dJ737E23.1, CDw93, ECSM3	uc002wsv.3	Q9NPY3	OTTHUMG00000032058	ENST00000246006.4:c.122C>A	chr20.hg19:g.23066708G>T	ENSP00000246006:p.Ser41*	33.0	0.0		13.0	4.0	NM_012072	O00274	Nonsense_Mutation	SNP	ENST00000246006.4	hg19	CCDS13149.1	.	.	.	.	.	.	.	.	.	.	G	38	6.967644	0.97971	.	.	ENSG00000125810	ENST00000246006;ENST00000413585	.	.	.	5.88	3.96	0.45880	.	0.558192	0.16514	N	0.211139	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.14252	T	0.57	-11.1266	11.0412	0.47831	0.1357:0.5987:0.2657:0.0	.	.	.	.	X	41	.	ENSP00000246006:S41X	S	-	2	0	CD93	23014708	0.975000	0.34042	0.998000	0.56505	0.961000	0.63080	1.617000	0.36943	0.817000	0.34445	-0.133000	0.14855	TCG	.	.		0.697	CD93-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078312.2	NM_012072		T	23066708	G	T	23066708	4	4	311	1	0	0	0	0	0	1	0	0	3049	1059	37	1	1844	1	CD93	20	23066708	Nonsense_Mutation	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10	13617393	23066708	39958812	79	44301										
C20orf186	149954	hgsc.bcm.edu	37	chr20	31672781	31672781	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	ctacctgagcttgtacacccGtgtggccatcaacgggaaga	11	12	1	2			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr20:31672781G>A	ENST00000375483.3	+	4	761	c.761G>A	c.(760-762)cGt>cAt	p.R254H		NM_182519.2	NP_872325.2	P59827	BPIB4_HUMAN	BPI fold containing family B, member 4	254						cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										TTGTACACCCGTGTGGCCATC	0.637																																					p.R254H		Atlas-SNP	.											.	.	.	.	0			c.G761A						.						53	43	46					20																	31672781		2203	4300	6503	SO:0001583	missense	149954	exon4			ACACCCGTGTGGC	AF549190	CCDS13213.2	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186191	ENSG00000186191		"BPI fold containing"	16179	protein-coding gene	gene with protein product		615718	"chromosome 20 open reading frame 186"	C20orf186		11971875, 21787333	Standard	NM_182519		Approved	dJ726C3.5, LPLUNC4	uc010zue.2	P59827	OTTHUMG00000032235	ENST00000375483.3:c.761G>A	chr20.hg19:g.31672781G>A	ENSP00000364632:p.Arg254His	32.0	0.0		33.0	12.0	NM_182519	Q5TDX6	Missense_Mutation	SNP	ENST00000375483.3	hg19	CCDS13213.2	.	.	.	.	.	.	.	.	.	.	G	12.42	1.932778	0.34096	.	.	ENSG00000186191	ENST00000375483	T	0.05580	3.42	3.39	3.39	0.38822	.	0.369375	0.23125	N	0.051659	T	0.06600	0.0169	N	0.22421	0.69	0.30416	N	0.778544	D	0.58620	0.983	P	0.50270	0.636	T	0.14671	-1.0464	10	0.16896	T	0.51	-0.4489	10.14	0.42730	0.0:0.0:1.0:0.0	.	254	P59827	BPIB4_HUMAN	H	254	ENSP00000364632:R254H	ENSP00000364632:R254H	R	+	2	0	BPIFB4	31136442	0.141000	0.22595	0.981000	0.43875	0.370000	0.29829	1.778000	0.38614	1.749000	0.51849	0.484000	0.47621	CGT	.	.		0.637	BPIFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078655.5	NM_182519		A	31672781	G	A	31672781	3	1	311	1	0	0	0	0	1	0	0	0	2100	1145	40	1	775	1	C20orf186	20	31672781	Missense_Mutation	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10	8606073	31672781	31352739	80	44302										
ADAMTS5	11096	hgsc.bcm.edu	37	chr21	28296456	28296456	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	gctaacttccggtttccatcCtggcactgcaccgttctggt	9	14	1	0			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr21:28296456C>T	ENST00000284987.5	-	8	2830	c.2709G>A	c.(2707-2709)caG>caA	p.Q903Q	AP001601.2_ENST00000426771.1_RNA	NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 5	903	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	72						GGTTTCCATCCTGGCACTGCA	0.537																																					p.Q903Q	Esophageal Squamous(53;683 1080 10100 14424 45938)	Atlas-SNP	.											.	ADAMTS5	184	.	0			c.G2709A						.						94	79	84					21																	28296456		2203	4300	6503	SO:0001819	synonymous_variant	11096	exon8			TCCATCCTGGCAC	AF142099	CCDS13579.1	21q21.3	2008-07-31	2008-07-31		ENSG00000154736	ENSG00000154736		"ADAM metallopeptidases with thrombospondin type 1 motif"	221	protein-coding gene	gene with protein product	"aggrecanase-2"	605007	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"			10438522	Standard	NM_007038		Approved	ADMP-2, ADAMTS11	uc002ymg.3	Q9UNA0	OTTHUMG00000078686	ENST00000284987.5:c.2709G>A	chr21.hg19:g.28296456C>T		56.0	0.0		43.0	15.0	NM_007038	Q52LV4|Q9UKP2	Silent	SNP	ENST00000284987.5	hg19	CCDS13579.1																																																																																			.	.		0.537	ADAMTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171648.1			T	28296456	C	T	28296456	2	4	311	1	0	0	0	0	0	0	0	1	269	680	24	3		3	ADAMTS5	21	28296456	Silent	SNP	C	TCGA-K7-A6G5-01A-11D-A30V-10		28296456	19833439	81	44303										
BRWD1	54014	hgsc.bcm.edu	37	chr21	40619671	40619671	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	atttccagaagataactcacGccagctacgatttcttctac	5	12	3	2	rs201010892		TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr21:40619671G>T	ENST00000333229.2	-	21	2764	c.2437C>A	c.(2437-2439)Cgt>Agt	p.R813S	BRWD1_ENST00000342449.3_Missense_Mutation_p.R813S|BRWD1_ENST00000380800.3_Missense_Mutation_p.R813S	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	813					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				GATAACTCACGCCAGCTACGA	0.353																																					p.R813S	Melanoma(170;988 1986 4794 16843 39731)	Atlas-SNP	.											.	BRWD1	325	.	0			c.C2437A						.						97	91	93					21																	40619671		2203	4300	6503	SO:0001583	missense	54014	exon21			ACTCACGCCAGCT	AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"WD repeat domain containing"	12760	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 107", "WD repeat domain 9"	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.2437C>A	chr21.hg19:g.40619671G>T	ENSP00000330753:p.Arg813Ser	88.0	0.0		89.0	4.0	NM_018963	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Missense_Mutation	SNP	ENST00000333229.2	hg19	CCDS13662.1	.	.	.	.	.	.	.	.	.	.	G	2.675	-0.276698	0.05679	.	.	ENSG00000185658	ENST00000333229;ENST00000342449;ENST00000380800	T;T;T	0.54866	0.55;0.57;0.65	5.44	0.108	0.14548	.	1.538240	0.03654	N	0.241530	T	0.31389	0.0795	N	0.14661	0.345	0.09310	N	1	B;B	0.13594	0.008;0.005	B;B	0.16722	0.016;0.008	T	0.07927	-1.0747	10	0.19590	T	0.45	0.1546	1.6167	0.02705	0.2407:0.1314:0.472:0.1559	.	813;813	Q9NSI6-2;Q9NSI6	.;BRWD1_HUMAN	S	813	ENSP00000330753:R813S;ENSP00000344333:R813S;ENSP00000370178:R813S	ENSP00000330753:R813S	R	-	1	0	BRWD1	39541541	0.000000	0.05858	0.000000	0.03702	0.063000	0.16089	0.655000	0.24933	-0.200000	0.10300	0.591000	0.81541	CGT	.	G|0.999;A|0.001		0.353	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656		T	40619671	G	T	40619671	3	4	311	1	0	0	0	0	1	0	0	0	1527	1087	38	1	4852	1	BRWD1	21	40619671	Missense_Mutation	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10	12323215	40619671	7510224	82	44304										
EWSR1	2130	hgsc.bcm.edu	37	chr22	29664336	29664336	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	aggagagaaaatggcgtccaCgggtgagtatggtggaactg	17	5	0	2			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr22:29664336C>G	ENST00000397938.2	+	1	330	c.11C>G	c.(10-12)aCg>aGg	p.T4R	RHBDD3_ENST00000216085.7_5'Flank|EWSR1_ENST00000414183.2_Missense_Mutation_p.T4R|EWSR1_ENST00000332035.6_Missense_Mutation_p.T4R|EWSR1_ENST00000332050.6_Missense_Mutation_p.T4R|EWSR1_ENST00000406548.1_Missense_Mutation_p.T4R|EWSR1_ENST00000333395.6_Missense_Mutation_p.T4R|EWSR1_ENST00000331029.7_Missense_Mutation_p.T4R	NM_001163285.1|NM_001163286.1|NM_005243.3|NM_013986.3	NP_001156757.1|NP_001156758.1|NP_005234.1|NP_053733.2	Q01844	EWS_HUMAN	EWS RNA-binding protein 1	4	EAD (Gln/Pro/Thr-rich).				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		EWSR1/ATF1(347)|EWSR1/POU5F1(10)|EWSR1/PBX1(3)|EWSR1/DDIT3(45)|EWSR1/FEV(11)|EWSR1/CREB1(44)|EWSR1/SMARCA5(2)|EWSR1/ETV4(6)|EWSR1/ERG(178)|EWSR1/ZNF384(4)|EWSR1/ETV1(7)|EWSR1/FLI1(2569)|EWSR1/NR4A3(146)|EWSR1/SP3(3)|EWSR1/PATZ1(2)|EWSR1/WT1(234)|EWSR1/NFATC2(9)	breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|liver(1)|lung(6)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						ATGGCGTCCACGGGTGAGTAT	0.622			T	"FLI1, ERG, ZNF278, NR4A3, FEV, ATF1, ETV1, ETV4, WT1, ZNF384, CREB1, POU5F1,  PBX1"	"Ewing sarcoma,  desmoplastic small round cell tumor , ALL, clear cell sarcoma, sarcoma, myoepithelioma"																																p.T4R		Atlas-SNP	.		Dom	yes		22	22q12	2130	Ewing sarcoma breakpoint region 1 (EWS)		"L, M"	.	EWSR1	104	.	0			c.C11G						.						174	169	171					22																	29664336		2203	4300	6503	SO:0001583	missense	2130	exon1			CGTCCACGGGTGA		CCDS13851.1, CCDS13852.1, CCDS13852.2, CCDS54512.1, CCDS54513.1, CCDS54514.1	22q12.2	2013-05-24	2013-05-24		ENSG00000182944	ENSG00000182944		"RNA binding motif (RRM) containing"	3508	protein-coding gene	gene with protein product		133450	"Ewing sarcoma breakpoint region 1"			1522903	Standard	NM_005243		Approved	EWS	uc003aev.3	Q01844	OTTHUMG00000151107	ENST00000397938.2:c.11C>G	chr22.hg19:g.29664336C>G	ENSP00000381031:p.Thr4Arg	56.0	0.0		43.0	11.0	NM_013986	B0QYK1|Q5THL0|Q92635|Q96FE8|Q96MN4|Q96MX4|Q9BWA2	Missense_Mutation	SNP	ENST00000397938.2	hg19	CCDS13851.1	.	.	.	.	.	.	.	.	.	.	C	16.62	3.173199	0.57584	.	.	ENSG00000182944	ENST00000444626;ENST00000332050;ENST00000397938;ENST00000436425;ENST00000447973;ENST00000406548;ENST00000437155;ENST00000415761;ENST00000331029;ENST00000414183;ENST00000333395;ENST00000455726;ENST00000332035	T;T;T;T;T;T;T;T;T;T;T;T	0.29655	1.56;1.56;1.56;1.56;1.56;1.56;1.56;1.56;1.56;1.56;1.56;1.56	4.06	3.02	0.34903	.	0.336013	0.26345	U	0.024901	T	0.36026	0.0952	L	0.27053	0.805	0.37572	D	0.919475	P;D;D;P;P	0.76494	0.923;0.994;0.999;0.923;0.954	P;D;D;P;P	0.72625	0.657;0.92;0.978;0.657;0.814	T	0.35076	-0.9803	10	0.87932	D	0	.	7.0125	0.24871	0.0:0.8739:0.0:0.126	.	4;4;4;4;4	Q96FE8;B0QYK1;Q96MX4;Q01844;Q9BWA2	.;.;.;EWS_HUMAN;.	R	4	ENSP00000416171:T4R;ENSP00000330896:T4R;ENSP00000381031:T4R;ENSP00000406824:T4R;ENSP00000405947:T4R;ENSP00000385726:T4R;ENSP00000412670:T4R;ENSP00000330516:T4R;ENSP00000400142:T4R;ENSP00000327456:T4R;ENSP00000393637:T4R;ENSP00000331699:T4R	ENSP00000330516:T4R	T	+	2	0	EWSR1	27994336	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.882000	0.39648	1.964000	0.57103	0.467000	0.42956	ACG	.	.		0.622	EWSR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321345.1	NM_005243		G	29664336	C	G	29664336	3	3	311	1	0	0	0	0	1	0	0	0	5298	536	19	4	13	4	EWSR1	22	29664336	Missense_Mutation	SNP	C	TCGA-K7-A6G5-01A-11D-A30V-10		29664336	21640230	83	44305										
FBLN1	2192	hgsc.bcm.edu	37	chr22	45960824	45960824	+	Intron	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	tcaagtaaagaggactgcagGgttcttccatggaagcaggg	14	7	2	1	rs373139240		TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chr22:45960824G>T	ENST00000327858.6	+	15	1792				FBLN1_ENST00000442170.2_Missense_Mutation_p.R586S|FBLN1_ENST00000348697.2_Missense_Mutation_p.R586S	NM_006486.2	NP_006477	P23142	FBLN1_HUMAN	fibulin 1						embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|viral process (GO:0016032)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)|peptidase activator activity (GO:0016504)			biliary_tract(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)	30		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		AGGACTGCAGGGTTCTTCCAT	0.542																																					p.R586S		Atlas-SNP	.											.	FBLN1	143	.	0			c.G1758T						.	G	SER/ARG,	0,4406		0,0,2203	138	114	122		1758,	0.5	0	22		122	2,8598	2.2+/-6.3	0,2,4298	no	missense,intron	FBLN1	NM_006485.3,NM_006486.2	110,	0,2,6501	TT,TG,GG		0.0233,0.0,0.0154	,	586/602,	45960824	2,13004	2203	4300	6503	SO:0001627	intron_variant	2192	exon15			CTGCAGGGTTCTT		CCDS14067.1, CCDS14068.1, CCDS14069.1, CCDS43028.1	22q13.31	2010-06-15			ENSG00000077942	ENSG00000077942		"Fibulins"	3600	protein-coding gene	gene with protein product		135820				2269669, 1400330	Standard	NM_006485		Approved	FBLN	uc003bgj.1	P23142	OTTHUMG00000151340	ENST00000327858.6:c.1698-9567G>T	chr22.hg19:g.45960824G>T		55.0	0.0		41.0	15.0	NM_006485	B0QY42|B1AHL4|P23143|P23144|P37888|Q5TIC4|Q8TBH8|Q9HBQ5|Q9UC21|Q9UGR4|Q9UH41	Missense_Mutation	SNP	ENST00000327858.6	hg19	CCDS14067.1	.	.	.	.	.	.	.	.	.	.	G	6.256	0.415325	0.11870	0.0	2.33E-4	ENSG00000077942	ENST00000348697;ENST00000442170	D;D	0.82526	-1.58;-1.62	1.58	0.543	0.17179	.	.	.	.	.	T	0.65749	0.2721	L	0.27053	0.805	0.09310	N	1	B	0.15473	0.013	B	0.15052	0.012	T	0.46965	-0.9153	9	0.09590	T	0.72	.	3.9389	0.09318	0.2276:0.0:0.7724:0.0	.	586	B1AHL4	.	S	586	ENSP00000262723:R586S;ENSP00000393812:R586S	ENSP00000262723:R586S	R	+	3	2	FBLN1	44339488	0.005000	0.15991	0.000000	0.03702	0.001000	0.01503	1.122000	0.31295	0.233000	0.21120	-0.373000	0.07131	AGG	.	.		0.542	FBLN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322287.1	NM_006486		T	45960824	G	T	45960824	1	4	311	0	1	0	0	0	0	0	0	0	5706	1223	43	3		3	FBLN1	22	45960824	Intron	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10	16296488	45960824	5343742	84	44306										
MXRA5	25878	hgsc.bcm.edu	37	chrX	3248697	3248697	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	gggtttacctgaagagagctGaggtctcttaaagctccatc	11	9	1	3			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chrX:3248697G>A	ENST00000217939.6	-	3	460	c.306C>T	c.(304-306)ctC>ctT	p.L102L		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	102						extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				GAAGAGAGCTGAGGTCTCTTA	0.428																																					p.L102L		Atlas-SNP	.											.	MXRA5	815	.	0			c.C306T						.						136	122	126					X																	3248697		2203	4300	6503	SO:0001819	synonymous_variant	25878	exon3			AGAGCTGAGGTCT	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7539	protein-coding gene	gene with protein product	"adlican"					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.306C>T	chrX.hg19:g.3248697G>A		55.0	0.0		35.0	17.0	NM_015419	Q6P1M7|Q9Y3Y8	Silent	SNP	ENST00000217939.6	hg19	CCDS14124.1																																																																																			.	.		0.428	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		A	3248697	G	A	3248697	2	1	311	1	0	0	0	0	0	0	0	1	10012	1277	45	3		3	MXRA5	23	3248697	Silent	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10		3248697	152021863	85	44307										
VSIG4	11326	hgsc.bcm.edu	37	chrX	65253415	65253415	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	gtagtggctccggtcatccaTctccagggtgctcaattgga	12	11	3	0			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chrX:65253415T>C	ENST00000374737.4	-	2	421	c.313A>G	c.(313-315)Atg>Gtg	p.M105V	VSIG4_ENST00000455586.2_Missense_Mutation_p.M105V|VSIG4_ENST00000412866.2_Missense_Mutation_p.M105V	NM_001257403.1|NM_007268.2	NP_001244332.1|NP_009199.1	Q9Y279	VSIG4_HUMAN	V-set and immunoglobulin domain containing 4	105	Ig-like 1.				complement activation, alternative pathway (GO:0006957)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of T cell proliferation (GO:0042130)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CGGTCATCCATCTCCAGGGTG	0.542																																					p.M105V		Atlas-SNP	.											.	VSIG4	54	.	0			c.A313G						.						138	118	125					X																	65253415		2203	4300	6503	SO:0001583	missense	11326	exon2			CATCCATCTCCAG	AJ132502	CCDS14383.1, CCDS48132.1, CCDS55435.1	Xq12-q13.3	2013-01-29			ENSG00000155659	ENSG00000155659		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17032	protein-coding gene	gene with protein product		300353				10899594, 11004523, 17016555, 17016562	Standard	NM_007268		Approved	Z39IG	uc004dwh.2	Q9Y279	OTTHUMG00000021727	ENST00000374737.4:c.313A>G	chrX.hg19:g.65253415T>C	ENSP00000363869:p.Met105Val	52.0	0.0		62.0	27.0	NM_001100431	Q6UXI4	Missense_Mutation	SNP	ENST00000374737.4	hg19	CCDS14383.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.16|13.16	2.155569|2.155569	0.38021|0.38021	.|.	.|.	ENSG00000155659|ENSG00000155659	ENST00000427538|ENST00000374737;ENST00000455586;ENST00000412866	.|T;T;T	.|0.63913	.|-0.07;-0.07;-0.07	4.88|4.88	4.88|4.88	0.63580|0.63580	.|Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.|0.153579	.|0.46442	.|D	.|0.000293	T|T	0.63319|0.63319	0.2501|0.2501	M|M	0.68317|0.68317	2.08|2.08	0.34905|0.34905	D|D	0.746931|0.746931	.|B;B;B;B;B	.|0.31009	.|0.211;0.137;0.303;0.284;0.202	.|B;B;B;B;B	.|0.41860	.|0.202;0.096;0.368;0.177;0.204	T|T	0.65833|0.65833	-0.6072|-0.6072	5|10	.|0.15066	.|T	.|0.55	-15.2845|-15.2845	9.9597|9.9597	0.41688|0.41688	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|105;105;95;105;105	.|C9J1L3;Q9Y279-2;C9JH67;Q9Y279-3;Q9Y279	.|.;.;.;.;VSIG4_HUMAN	G|V	31|105	.|ENSP00000363869:M105V;ENSP00000411581:M105V;ENSP00000394143:M105V	.|ENSP00000363869:M105V	D|M	-|-	2|1	0|0	VSIG4|VSIG4	65170140|65170140	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.752000|0.752000	0.42762|0.42762	3.569000|3.569000	0.53827|0.53827	1.614000|1.614000	0.50241|0.50241	0.481000|0.481000	0.45027|0.45027	GAT|ATG	.	.		0.542	VSIG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056986.1	NM_007268		C	65253415	T	C	65253415	3	2	311	1	0	0	0	0	1	0	0	0	17240	1435	50	2	918	2	VSIG4	23	65253415	Missense_Mutation	SNP	T	TCGA-K7-A6G5-01A-11D-A30V-10	62004718	65253415	90017145	86	44308										
GABRQ	55879	hgsc.bcm.edu	37	chrX	151821124	151821124	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0574712643678161	5	1	1.05936920222635	2.11873840445269	0.794526901669759	1	1	0	cctccgagcaggcccagctgGccacctcggaaagcctcagc	11	18	1	0			TCGA-K7-A6G5-01A-11D-A30V-10	TCGA-K7-A6G5-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ba1022c-bdf7-464b-a527-f69dd5bac5be	9878f24b-c9b2-4b3b-9cf2-d4ad1132ee86	g.chrX:151821124G>C	ENST00000370306.2	+	9	1299	c.1279G>C	c.(1279-1281)Gcc>Ccc	p.A427P		NM_018558.2	NP_061028.3	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) A receptor, theta	427					neurotransmitter transport (GO:0006836)|signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|neurotransmitter transporter activity (GO:0005326)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(9)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	52	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GGCCCAGCTGGCCACCTCGGA	0.662																																					p.A427P		Atlas-SNP	.											.	GABRQ	131	.	0			c.G1279C						.						58	58	58					X																	151821124		2203	4300	6503	SO:0001583	missense	55879	exon9			CAGCTGGCCACCT	U47334	CCDS14707.1	Xq28	2012-06-22	2012-02-03		ENSG00000147402	ENSG00000268089		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	14454	protein-coding gene	gene with protein product	"GABA(A) receptor, theta"	300349	"gamma-aminobutyric acid (GABA) receptor, theta"			10804200, 10449790	Standard	NM_018558		Approved	THETA	uc004ffp.1	Q9UN88	OTTHUMG00000022649	ENST00000370306.2:c.1279G>C	chrX.hg19:g.151821124G>C	ENSP00000359329:p.Ala427Pro	64.0	0.0		84.0	44.0	NM_018558	A6NFN1|Q32MB4|Q9NZK8	Missense_Mutation	SNP	ENST00000370306.2	hg19	CCDS14707.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.295250	0.81025	.	.	ENSG00000147402	ENST00000370306	T	0.80824	-1.42	4.49	4.49	0.54785	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.36815	N	0.002398	D	0.85008	0.5599	L	0.48642	1.525	0.36231	D	0.85261	D	0.89917	1.0	D	0.91635	0.999	D	0.87900	0.2690	10	0.62326	D	0.03	.	11.4043	0.49889	0.0:0.0:1.0:0.0	.	427	Q9UN88	GBRT_HUMAN	P	427	ENSP00000359329:A427P	ENSP00000359329:A427P	A	+	1	0	GABRQ	151571780	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.817000	0.55668	2.464000	0.83262	0.600000	0.82982	GCC	.	.		0.662	GABRQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058763.2	NM_018558		C	151821124	G	C	151821124	3	2	311	1	0	0	0	0	1	0	0	0	6183	1203	42	4	1313	4	GABRQ	23	151821124	Missense_Mutation	SNP	G	TCGA-K7-A6G5-01A-11D-A30V-10	86567709	151821124	3449436	87	44309										
UBXN10	127733	hgsc.bcm.edu	37	chr1	20517668	20517668	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	gttgctgcttgctgttagatCaccaacaggccaaaggtttg	11	9	1	1			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr1:20517668C>T	ENST00000375099.3	+	2	698	c.614C>T	c.(613-615)tCa>tTa	p.S205L		NM_152376.3	NP_689589.1	Q96LJ8	UBX10_HUMAN	UBX domain protein 10	205	UBX. {ECO:0000255|PROSITE- ProRule:PRU00215}.									endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|ovary(2)|skin(2)	14						GCTGTTAGATCACCAACAGGC	0.493																																					p.S205L		Atlas-SNP	.											.	UBXN10	29	.	0			c.C614T						.						124	119	120					1																	20517668		2203	4300	6503	SO:0001583	missense	127733	exon2			TTAGATCACCAAC	AK058158	CCDS205.1	1p36.13	2008-07-25	2008-07-25	2008-07-25	ENSG00000162543	ENSG00000162543		"UBX domain containing"	26354	protein-coding gene	gene with protein product			"UBX domain containing 3"	UBXD3		12477932	Standard	NM_152376		Approved	FLJ25429	uc001bdb.3	Q96LJ8	OTTHUMG00000002708	ENST00000375099.3:c.614C>T	chr1.hg19:g.20517668C>T	ENSP00000364240:p.Ser205Leu	66.0	0.0		61.0	20.0	NM_152376	Q5R386	Missense_Mutation	SNP	ENST00000375099.3	hg19	CCDS205.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.250616	0.80135	.	.	ENSG00000162543	ENST00000375099	.	.	.	4.92	4.92	0.64577	UBX (3);	0.114875	0.37136	N	0.002227	T	0.73892	0.3645	L	0.50333	1.59	0.49798	D	0.999826	D	0.76494	0.999	D	0.72982	0.979	T	0.73151	-0.4073	9	0.42905	T	0.14	-15.0667	16.8349	0.85954	0.0:1.0:0.0:0.0	.	205	Q96LJ8	UBX10_HUMAN	L	205	.	ENSP00000364240:S205L	S	+	2	0	UBXN10	20390255	1.000000	0.71417	0.253000	0.24343	0.748000	0.42578	6.810000	0.75216	2.543000	0.85770	0.591000	0.81541	TCA	.	.		0.493	UBXN10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007693.1	NM_152376		T	20517668	C	T	20517668	3	4	312	1	0	0	0	0	1	0	0	0	16927	838	29	3	616	3	UBXN10	1	20517668	Missense_Mutation	SNP	C	TCGA-K7-AAU7-01A-11D-A382-10		20517668	228732953	1	44310										
CCDC21	64793	hgsc.bcm.edu	37	chr1	26603246	26603246	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	tctctccctgctcctgggcaTtcactgtgagtcctcagacc	8	16	3	2			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr1:26603246T>A	ENST00000252992.4	+	13	2254	c.2123T>A	c.(2122-2124)aTt>aAt	p.I708N	CEP85_ENST00000451429.2_Missense_Mutation_p.I657N|CEP85_ENST00000469609.1_3'UTR|SH3BGRL3_ENST00000270792.5_5'Flank	NM_001281517.1|NM_022778.2	NP_001268446.1|NP_073615.2	Q6P2H3	CEP85_HUMAN	centrosomal protein 85kDa	708						centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|spindle pole (GO:0000922)				breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(11)|skin(2)	25						CTCCTGGGCATTCACTGTGAG	0.552																																					p.I708N		Atlas-SNP	.											.	CEP85	61	.	0			c.T2123A						.						40	32	35					1																	26603246		2203	4300	6503	SO:0001583	missense	64793	exon13			TGGGCATTCACTG	AK024038	CCDS277.1, CCDS60038.1	1p36.11	2014-02-20	2011-05-06	2011-05-06	ENSG00000130695	ENSG00000130695			25309	protein-coding gene	gene with protein product			"coiled-coil domain containing 21"	CCDC21		12477932	Standard	NM_022778		Approved	DKFZP434L0117	uc001bls.1	Q6P2H3	OTTHUMG00000003380	ENST00000252992.4:c.2123T>A	chr1.hg19:g.26603246T>A	ENSP00000252992:p.Ile708Asn	133.0	0.0		105.0	29.0	NM_022778	B4DRL1|D3DPK4|F8W7K4|Q5VY68|Q5VY70|Q9H6Q1|Q9H828|Q9UF52	Missense_Mutation	SNP	ENST00000252992.4	hg19	CCDS277.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.2|25.2	4.609720|4.609720	0.87258|0.87258	.|.	.|.	ENSG00000130695|ENSG00000130695	ENST00000453146|ENST00000451429;ENST00000252992	.|T;T	.|0.11169	.|2.8;2.8	5.51|5.51	5.51|5.51	0.81932|0.81932	.|.	.|0.048397	.|0.85682	.|D	.|0.000000	T|T	0.34048|0.34048	0.0884|0.0884	M|M	0.75264|0.75264	2.295|2.295	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|0.999;1.0;1.0	.|D;D;D	.|0.78314	.|0.965;0.977;0.991	T|T	0.07578|0.07578	-1.0765|-1.0765	5|10	.|0.72032	.|D	.|0.01	-7.3726|-7.3726	15.6105|15.6105	0.76713|0.76713	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|657;708;708	.|F8W7K4;Q6P2H3;Q6P2H3-2	.|.;CEP85_HUMAN;.	I|N	382|657;708	.|ENSP00000417002:I657N;ENSP00000252992:I708N	.|ENSP00000252992:I708N	F|I	+|+	1|2	0|0	CEP85|CEP85	26475833|26475833	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.910000|0.910000	0.53928|0.53928	7.665000|7.665000	0.83852|0.83852	2.105000|2.105000	0.64084|0.64084	0.454000|0.454000	0.30748|0.30748	TTC|ATT	.	.		0.552	CEP85-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009492.2	NM_022778		A	26603246	T	A	26603246	3	1	312	1	0	0	0	0	1	0	0	0	2798	1493	52	4	2169	4	CCDC21	1	26603246	Missense_Mutation	SNP	T	TCGA-K7-AAU7-01A-11D-A382-10	6085578	26603246	222647375	2	44311										
KIAA1324	57535	hgsc.bcm.edu	37	chr1	109734359	109734359	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	tgggttcagggtgtgaattcTaggaccaacactcctgtgga	13	8	2	1			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr1:109734359T>C	ENST00000369939.3	+	13	1740	c.1557T>C	c.(1555-1557)tcT>tcC	p.S519S	KIAA1324_ENST00000369938.1_3'UTR|KIAA1324_ENST00000529753.1_Silent_p.S432S	NM_020775.4	NP_065826	Q6UXG2	K1324_HUMAN	KIAA1324	519					cellular response to starvation (GO:0009267)|macroautophagy (GO:0016236)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|positive regulation of autophagic vacuole assembly (GO:2000786)|positive regulation of vacuole organization (GO:0044090)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34		all_epithelial(167;0.000102)|all_lung(203;0.000323)|Lung NSC(277;0.00063)		Colorectal(144;0.0188)|Lung(183;0.0527)|COAD - Colon adenocarcinoma(174;0.14)|Epithelial(280;0.21)|all cancers(265;0.249)		GTGTGAATTCTAGGACCAACA	0.557																																					p.S519S		Atlas-SNP	.											.	KIAA1324	77	.	0			c.T1557C						.						139	131	133					1																	109734359		2203	4300	6503	SO:0001819	synonymous_variant	57535	exon13			GAATTCTAGGACC	AK057647	CCDS794.1, CCDS58015.1	1p13.3	2008-09-18			ENSG00000116299	ENSG00000116299			29618	protein-coding gene	gene with protein product	"estrogen induced gene 121"	611298				10718198, 16322283	Standard	NM_020775		Approved	maba1, EIG121	uc021orb.1	Q6UXG2	OTTHUMG00000011725	ENST00000369939.3:c.1557T>C	chr1.hg19:g.109734359T>C		88.0	0.0		83.0	15.0	NM_020775	Q08AE6|Q5T5C9|Q5T5D0|Q5T5D1|Q9P2M2	Silent	SNP	ENST00000369939.3	hg19	CCDS794.1																																																																																			.	.		0.557	KIAA1324-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032389.2	NM_020775		C	109734359	T	C	109734359	2	2	312	1	0	0	0	0	0	0	0	1	8232	1509	53	2		2	KIAA1324	1	109734359	Silent	SNP	T	TCGA-K7-AAU7-01A-11D-A382-10	83131113	109734359	139516262	3	44312										
RFWD2	64326	hgsc.bcm.edu	37	chr1	175957534	175957534	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	ctacattccacagttttagcTgactgtctgttgagctgagg	10	9	1	3			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr1:175957534T>A	ENST00000367669.3	-	17	2376	c.1862A>T	c.(1861-1863)cAg>cTg	p.Q621L	RFWD2_ENST00000308769.8_Missense_Mutation_p.Q597L	NM_022457.5	NP_071902.2	Q8NHY2	RFWD2_HUMAN	ring finger and WD repeat domain 2, E3 ubiquitin protein ligase	621					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin protein ligase activity (GO:0061630)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						CAGTTTTAGCTGACTGTCTGT	0.393																																					p.Q621L	Ovarian(134;1413 1765 5706 35534 51541)	Atlas-SNP	.											.	RFWD2	67	.	0			c.A1862T						.						126	109	115					1																	175957534		2203	4300	6503	SO:0001583	missense	64326	exon17			TTTAGCTGACTGT	AK001278	CCDS30944.1, CCDS44279.1	1q25.1-q25.2	2013-01-09	2012-02-23		ENSG00000143207	ENSG00000143207		"WD repeat domain containing", "RING-type (C3HC4) zinc fingers"	17440	protein-coding gene	gene with protein product		608067	"ring finger and WD repeat domain 2"			10395541	Standard	XM_005245447		Approved	FLJ10416, COP1, RNF200	uc001gku.1	Q8NHY2	OTTHUMG00000034986	ENST00000367669.3:c.1862A>T	chr1.hg19:g.175957534T>A	ENSP00000356641:p.Gln621Leu	116.0	0.0		100.0	28.0	NM_022457	E9PKI0|Q504W6|Q6H103|Q9H6L7|X5D9B4	Missense_Mutation	SNP	ENST00000367669.3	hg19	CCDS30944.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.465121	0.84425	.	.	ENSG00000143207	ENST00000367665;ENST00000367669;ENST00000367666;ENST00000308769	T;T;T	0.41400	1.0;1.0;1.0	4.98	4.98	0.66077	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.41743	0.1172	N	0.04686	-0.185	0.80722	D	1	D;P;D;P;P	0.67145	0.97;0.705;0.996;0.925;0.705	P;P;P;D;P	0.65140	0.79;0.6;0.899;0.932;0.6	T	0.55140	-0.8187	10	0.72032	D	0.01	-8.4906	14.6158	0.68547	0.0:0.0:0.0:1.0	.	396;381;597;621;621	Q8NHY2-3;B1AMD2;Q8NHY2-2;Q8NHY2;Q504W6	.;.;.;RFWD2_HUMAN;.	L	396;621;456;597	ENSP00000356641:Q621L;ENSP00000356638:Q456L;ENSP00000310943:Q597L	ENSP00000310943:Q597L	Q	-	2	0	RFWD2	174224157	1.000000	0.71417	1.000000	0.80357	0.827000	0.46813	7.806000	0.86020	1.978000	0.57642	0.482000	0.46254	CAG	.	.		0.393	RFWD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084672.2	NM_022457		A	175957534	T	A	175957534	3	1	312	1	0	0	0	0	1	0	0	0	13275	1580	55	4	349	4	RFWD2	1	175957534	Missense_Mutation	SNP	T	TCGA-K7-AAU7-01A-11D-A382-10	66223175	175957534	73293087	4	44313										
PTPN14	5784	hgsc.bcm.edu	37	chr1	214557934	214557934	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	gctcgggatgtagtcggcccGcatgatgtcactcccaggga	14	12	1	1			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr1:214557934G>A	ENST00000366956.5	-	13	1458	c.1264C>T	c.(1264-1266)Cgg>Tgg	p.R422W	PTPN14_ENST00000543945.1_3'UTR	NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type 14	422					lymphangiogenesis (GO:0001946)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of protein export from nucleus (GO:0046825)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)			NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	58				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		TAGTCGGCCCGCATGATGTCA	0.587																																					p.R422W	Colon(92;557 1424 24372 34121 40073)	Atlas-SNP	.											.	PTPN14	168	.	0			c.C1264T						.						136	126	129					1																	214557934		2203	4300	6503	SO:0001583	missense	5784	exon13			CGGCCCGCATGAT	X82676	CCDS1514.1	1q32.2	2011-06-09			ENSG00000152104	ENSG00000152104		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9647	protein-coding gene	gene with protein product		603155				7733990	Standard	NM_005401		Approved	PEZ	uc001hkk.2	Q15678	OTTHUMG00000037039	ENST00000366956.5:c.1264C>T	chr1.hg19:g.214557934G>A	ENSP00000355923:p.Arg422Trp	103.0	0.0		100.0	30.0	NM_005401	Q5VSI0	Missense_Mutation	SNP	ENST00000366956.5	hg19	CCDS1514.1	.	.	.	.	.	.	.	.	.	.	G	17.85	3.489143	0.64074	.	.	ENSG00000152104	ENST00000366956	T	0.73363	-0.74	5.5	2.23	0.28157	.	0.000000	0.85682	D	0.000000	T	0.82250	0.4996	M	0.71036	2.16	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.81428	-0.0937	10	0.87932	D	0	.	8.6931	0.34278	0.0:0.113:0.3439:0.5431	.	422	Q15678	PTN14_HUMAN	W	422	ENSP00000355923:R422W	ENSP00000355923:R422W	R	-	1	2	PTPN14	212624557	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.522000	0.45572	0.590000	0.29694	0.655000	0.94253	CGG	.	.		0.587	PTPN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089918.2	NM_005401		A	214557934	G	A	214557934	3	1	312	1	0	0	0	0	1	0	0	0	12796	1086	38	1	2327	1	PTPN14	1	214557934	Missense_Mutation	SNP	G	TCGA-K7-AAU7-01A-11D-A382-10	38600400	214557934	34692687	5	44314										
MYT1L	23040	hgsc.bcm.edu	37	chr2	1895870	1895870	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	gcggcatctcgcggcagcgcGtggacaggttgaggatggcg	19	10	1	1			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr2:1895870G>A	ENST00000399161.2	-	15	2969	c.2222C>T	c.(2221-2223)aCg>aTg	p.T741M	MYT1L_ENST00000428368.2_Missense_Mutation_p.T739M	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	741					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		GCGGCAGCGCGTGGACAGGTT	0.701																																					p.T739M		Atlas-SNP	.											.	MYT1L	241	.	0			c.C2216T						.						11	23	19					2																	1895870		1685	3108	4793	SO:0001583	missense	23040	exon15			CAGCGCGTGGACA	AF036943	CCDS46222.1	2p25.3	2013-01-10			ENSG00000186487	ENSG00000186487		"Zinc fingers, C2HC-type containing"	7623	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 1"	613084				9373037	Standard	XM_006711862		Approved	KIAA1106, NZF1, ZC2HC4B	uc002qxd.3	Q9UL68	OTTHUMG00000151407	ENST00000399161.2:c.2222C>T	chr2.hg19:g.1895870G>A	ENSP00000382114:p.Thr741Met	65.0	0.0		66.0	21.0	NM_015025	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Missense_Mutation	SNP	ENST00000399161.2	hg19		.	.	.	.	.	.	.	.	.	.	G	32	5.153386	0.94645	.	.	ENSG00000186487	ENST00000399161;ENST00000295067;ENST00000428368	T;T	0.58652	0.32;0.32	4.93	4.93	0.64822	Myelin transcription factor 1 (1);	0.000000	0.85682	D	0.000000	T	0.78811	0.4342	M	0.83953	2.67	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.983	T	0.82790	-0.0283	10	0.87932	D	0	-28.9357	18.1375	0.89624	0.0:0.0:1.0:0.0	.	741;739	Q9UL68;Q9UL68-4	MYT1L_HUMAN;.	M	741;687;739	ENSP00000382114:T741M;ENSP00000396103:T739M	ENSP00000295067:T687M	T	-	2	0	MYT1L	1874877	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.749000	0.98871	2.298000	0.77334	0.467000	0.42956	ACG	.	.		0.701	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025		A	1895870	G	A	1895870	3	1	312	1	0	0	0	0	1	0	0	0	10116	1145	40	1	1382	1	MYT1L	2	1895870	Missense_Mutation	SNP	G	TCGA-K7-AAU7-01A-11D-A382-10		1895870	241303503	6	44315										
LTBP1	4052	hgsc.bcm.edu	37	chr2	33518280	33518280	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	caaatggtgattgttccaacCttgaaggctcctacatgtgt	9	9	0	2			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr2:33518280C>T	ENST00000404816.2	+	20	3519	c.3166C>T	c.(3166-3168)Ctt>Ttt	p.L1056F	LTBP1_ENST00000418533.2_Missense_Mutation_p.L730F|LTBP1_ENST00000354476.3_Missense_Mutation_p.L1057F|LTBP1_ENST00000407925.1_Missense_Mutation_p.L730F|LTBP1_ENST00000272273.5_5'UTR|LTBP1_ENST00000404525.1_Missense_Mutation_p.L677F|LTBP1_ENST00000390003.4_Missense_Mutation_p.L731F|LTBP1_ENST00000402934.1_Missense_Mutation_p.L677F|LTBP1_ENST00000498013.1_3'UTR			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	1056	EGF-like 8; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				TTGTTCCAACCTTGAAGGCTC	0.433																																					p.L1056F		Atlas-SNP	.											.	LTBP1	317	.	0			c.C3166T						.						109	97	101					2																	33518280		2203	4300	6503	SO:0001583	missense	4052	exon20			TCCAACCTTGAAG		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"Latent transforming growth factor, beta binding proteins"	6714	protein-coding gene	gene with protein product	"TGF-beta1-BP-1"	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.3166C>T	chr2.hg19:g.33518280C>T	ENSP00000386043:p.Leu1056Phe	414.0	1.0		356.0	98.0	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	hg19	CCDS33177.2	.	.	.	.	.	.	.	.	.	.	C	22.7	4.330116	0.81690	.	.	ENSG00000049323	ENST00000404816;ENST00000354476;ENST00000390003;ENST00000418533;ENST00000402934;ENST00000404525;ENST00000407925	D;D;D;D;D;D;D	0.91996	-2.95;-2.95;-2.95;-2.95;-2.95;-2.95;-2.95	5.66	5.66	0.87406	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	.	.	.	.	D	0.94922	0.8358	M	0.64997	1.995	0.80722	D	1	D;D;B;D;B;D	0.57257	0.979;0.975;0.154;0.974;0.035;0.974	D;P;B;P;B;P	0.63033	0.91;0.791;0.16;0.756;0.045;0.854	D	0.95073	0.8206	9	0.72032	D	0.01	.	17.2525	0.87046	0.0:1.0:0.0:0.0	.	1056;730;677;730;731;1057	Q14766;E7EV71;Q14766-3;Q14766-2;Q14766-5;Q14766-4	LTBP1_HUMAN;.;.;.;.;.	F	1056;1057;731;730;677;677;730	ENSP00000386043:L1056F;ENSP00000346467:L1057F;ENSP00000374653:L731F;ENSP00000393057:L730F;ENSP00000384373:L677F;ENSP00000385359:L677F;ENSP00000384091:L730F	ENSP00000346467:L1057F	L	+	1	0	LTBP1	33371784	0.998000	0.40836	0.998000	0.56505	0.995000	0.86356	2.025000	0.41059	2.663000	0.90544	0.555000	0.69702	CTT	.	.		0.433	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943		T	33518280	C	T	33518280	3	4	312	1	0	0	0	0	1	0	0	0	9082	681	24	3	3299	3	LTBP1	2	33518280	Missense_Mutation	SNP	C	TCGA-K7-AAU7-01A-11D-A382-10	31622410	33518280	209681093	7	44316										
TTN	7273	hgsc.bcm.edu	37	chr2	179571276	179571276	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	ctttcaatttcaccatgttcGttaaatgccacgcatcggta	6	11	2	0	rs377442695	byFrequency	TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr2:179571276G>A	ENST00000591111.1	-	100	28598	c.28374C>T	c.(28372-28374)aaC>aaT	p.N9458N	TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000589042.1_Silent_p.N9775N|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Silent_p.N8531N|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13552	Ig-like 77.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CACCATGTTCGTTAAATGCCA	0.403													G|||	2	0.000399361	0	0	5008	,	,		18712	0.002		0	False		,,,				2504	0				p.N9775N		Atlas-SNP	.											.	TTN	18412	.	0			c.C29325T						.	G	,,,	0,3818		0,0,1909	177	162	167		,25593,,	3.6	1	2		167	1,8259		0,1,4129	no	intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	0,1,6038	AA,AG,GG		0.0121,0.0,0.0083	,,,	,8531/33424,,	179571276	1,12077	1909	4130	6039	SO:0001819	synonymous_variant	7273	exon102			ATGTTCGTTAAAT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.28374C>T	chr2.hg19:g.179571276G>A		119.0	0.0		113.0	20.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179571276	G	A	179571276	2	1	312	1	0	0	0	0	0	0	0	1	16750	1136	40	1		1	TTN	2	179571276	Silent	SNP	G	TCGA-K7-AAU7-01A-11D-A382-10	146052996	179571276	63628097	8	44317										
CELSR3	1951	hgsc.bcm.edu	37	chr3	48699034	48699034	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	ggtcctgagcaaccacgcgtAgcaccgcggtgcctgctgcc	13	16	0	1			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr3:48699034A>G	ENST00000164024.4	-	1	1314	c.1034T>C	c.(1033-1035)cTa>cCa	p.L345P	RP11-148G20.1_ENST00000421275.1_RNA|CELSR3_ENST00000544264.1_Missense_Mutation_p.L345P	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	345	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		AACCACGCGTAGCACCGCGGT	0.672																																					p.L345P		Atlas-SNP	.											.	CELSR3	237	.	0			c.T1034C						.						39	44	42					3																	48699034		2192	4285	6477	SO:0001583	missense	1951	exon1			ACGCGTAGCACCG	AF231023	CCDS2775.1	3p21.31	2014-08-08	2013-02-18		ENSG00000008300	ENSG00000008300		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3230	protein-coding gene	gene with protein product	"flamingo homolog 1 (Drosophila)"	604264	"cadherin EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog"	EGFL1		9693030	Standard	NM_001407		Approved	MEGF2, HFMI1, FMI1, CDHF11	uc003cuf.1	Q9NYQ7	OTTHUMG00000133544	ENST00000164024.4:c.1034T>C	chr3.hg19:g.48699034A>G	ENSP00000164024:p.Leu345Pro	80.0	0.0		54.0	20.0	NM_001407	O75092	Missense_Mutation	SNP	ENST00000164024.4	hg19	CCDS2775.1	.	.	.	.	.	.	.	.	.	.	A	19.17	3.776616	0.70107	.	.	ENSG00000008300	ENST00000164024;ENST00000544264	T;T	0.56444	0.46;0.46	5.83	5.83	0.93111	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.73659	0.3615	M	0.82630	2.6	0.80722	D	1	D;D	0.71674	0.988;0.998	P;D	0.66979	0.904;0.948	T	0.76386	-0.2978	9	0.49607	T	0.09	.	15.8624	0.79035	1.0:0.0:0.0:0.0	.	345;415	Q9NYQ7;Q5Y190	CELR3_HUMAN;.	P	345	ENSP00000164024:L345P;ENSP00000445694:L345P	ENSP00000164024:L345P	L	-	2	0	CELSR3	48674038	0.499000	0.26083	0.998000	0.56505	0.335000	0.28730	4.433000	0.59929	2.235000	0.73313	0.533000	0.62120	CTA	.	.		0.672	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407		G	48699034	A	G	48699034	3	3	312	1	0	0	0	0	1	0	0	0	3225	420	15	2	9044	2	CELSR3	3	48699034	Missense_Mutation	SNP	A	TCGA-K7-AAU7-01A-11D-A382-10		48699034	149323396	9	44318										
DCUN1D4	23142	hgsc.bcm.edu	37	chr4	52757946	52757946	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	gtagttatgcttgtcctagcTtggaaattggatgcacaaaa	10	6	0	0			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr4:52757946T>G	ENST00000334635.5	+	7	615	c.435T>G	c.(433-435)gcT>gcG	p.A145A	DCUN1D4_ENST00000451288.2_Silent_p.A189A|DCUN1D4_ENST00000381441.3_Silent_p.A145A|DCUN1D4_ENST00000381437.4_Silent_p.A85A	NM_001040402.1	NP_001035492.1	Q92564	DCNL4_HUMAN	DCN1, defective in cullin neddylation 1, domain containing 4	145	DCUN1. {ECO:0000255|PROSITE- ProRule:PRU00574}.					nucleus (GO:0005634)				endometrium(2)|large_intestine(2)|lung(2)|ovary(2)|skin(1)	9			GBM - Glioblastoma multiforme(4;1.93e-11)|LUSC - Lung squamous cell carcinoma(32;0.00654)			TTGTCCTAGCTTGGAAATTGG	0.323																																					p.A145A		Atlas-SNP	.											.	DCUN1D4	26	.	0			c.T435G						.						112	115	114					4																	52757946		2203	4300	6503	SO:0001819	synonymous_variant	23142	exon7			CCTAGCTTGGAAA	D87466	CCDS3487.2, CCDS33982.1, CCDS75123.1	4q11	2013-06-10	2013-06-10		ENSG00000109184	ENSG00000109184			28998	protein-coding gene	gene with protein product		612977	"DCN1, defective in cullin neddylation 1, domain containing 4 (S. cerevisiae)"			15988528	Standard	XM_005265731		Approved	KIAA0276	uc003gze.3	Q92564	OTTHUMG00000128700	ENST00000334635.5:c.435T>G	chr4.hg19:g.52757946T>G		60.0	0.0		75.0	15.0	NM_015115	B4DH25|Q7Z3F3|Q7Z6B8	Silent	SNP	ENST00000334635.5	hg19	CCDS33982.1																																																																																			.	.		0.323	DCUN1D4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250599.2	NM_015115		G	52757946	T	G	52757946	2	3	312	1	0	0	0	0	0	0	0	1	4318	1596	56	5		5	DCUN1D4	4	52757946	Silent	SNP	T	TCGA-K7-AAU7-01A-11D-A382-10		52757946	138396330	10	44319										
ALB	213	hgsc.bcm.edu	37	chr4	74274379	74274380	+	Frame_Shift_Ins	INS	-	-	AGCA													0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	cctatggtgaaatggctgacINStgctgtgcaaaacaagaacc							TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr4:74274379_74274380insAGCA	ENST00000295897.4	+	4	428_429	c.339_340insAGCA	c.(340-342)tgcfs	p.C114fs	ALB_ENST00000401494.3_Intron|ALB_ENST00000415165.2_Intron|ALB_ENST00000503124.1_Intron|ALB_ENST00000509063.1_Frame_Shift_Ins_p.C114fs|ALB_ENST00000505649.1_3'UTR	NM_000477.5	NP_000468.1	Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			AAATGGCTGACTGCTGTGCAAA	0.441																																					p.D113fs		Atlas-INDEL	.											.	ALB	132	.	0			c.339_340insAGCA						.																																			SO:0001589	frameshift_variant	213	exon4			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	Exception_encountered	chr4.hg19:g.74274379_74274380insAGCA	ENSP00000295897:p.Cys114fs	118.0	0.0		95.0	19.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Frame_Shift_Ins	INS	ENST00000295897.4	hg19	CCDS3555.1																																																																																			.	.		0.441	ALB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252173.3	NM_000477		AGCA	74274380	-	AGCA	74274379	7	5	312	1	0	1	1	0	0	0	0	0	486	564	20	0	353	0	ALB	4	74274379	Frame_Shift_Ins	INS	-	TCGA-K7-AAU7-01A-11D-A382-10	21516433	74274379	116879897	11	44320										
C4orf26	152816	hgsc.bcm.edu	37	chr4	76481309	76481309	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	agccatggctcgcagacactGcttctcctactggttactgg	10	13	1	1			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr4:76481309G>C	ENST00000311623.4	+	1	52	c.17G>C	c.(16-18)tGc>tCc	p.C6S	C4orf26_ENST00000514064.1_3'UTR|C4orf26_ENST00000435974.2_Missense_Mutation_p.C6S	NM_001257072.1|NM_178497.3	NP_001244001.1|NP_848592.2	Q17RF5	CD026_HUMAN	chromosome 4 open reading frame 26	6						extracellular region (GO:0005576)				kidney(1)|large_intestine(4)|stomach(1)	6			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			CGCAGACACTGCTTCTCCTAC	0.473																																					p.C6S		Atlas-SNP	.											.	C4orf26	24	.	0			c.G17C						.						159	144	149					4																	76481309		2203	4300	6503	SO:0001583	missense	152816	exon1			GACACTGCTTCTC	AK074237	CCDS3569.1, CCDS56334.1, CCDS75142.1	4q21.1	2012-10-31			ENSG00000174792	ENSG00000174792			26300	protein-coding gene	gene with protein product		614829				22901946	Standard	NM_001206981		Approved	FLJ23657	uc011cbo.2	Q17RF5	OTTHUMG00000130104	ENST00000311623.4:c.17G>C	chr4.hg19:g.76481309G>C	ENSP00000311307:p.Cys6Ser	116.0	0.0		107.0	24.0	NM_001257072	B4DTI3|E7ETQ0|Q8TEC3	Missense_Mutation	SNP	ENST00000311623.4	hg19	CCDS3569.1	.	.	.	.	.	.	.	.	.	.	G	4.674	0.125313	0.08931	.	.	ENSG00000174792	ENST00000311623;ENST00000435974	T;T	0.60040	1.4;0.22	4.96	2.78	0.32641	.	0.285410	0.25241	N	0.032094	T	0.33990	0.0882	L	0.27053	0.805	0.09310	N	1	B;B	0.22003	0.063;0.002	B;B	0.15484	0.013;0.005	T	0.15636	-1.0430	10	0.09338	T	0.73	.	4.2792	0.10824	0.152:0.0:0.6466:0.2014	.	6;6	E7ETQ0;Q17RF5	.;CD026_HUMAN	S	6	ENSP00000311307:C6S;ENSP00000406925:C6S	ENSP00000311307:C6S	C	+	2	0	C4orf26	76700333	0.004000	0.15560	0.014000	0.15608	0.044000	0.14063	0.394000	0.20834	0.527000	0.28560	-0.181000	0.13052	TGC	.	.		0.473	C4orf26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252410.1	NM_178497		C	76481309	G	C	76481309	3	2	312	1	0	0	0	0	1	0	0	0	2259	1319	46	4	19	4	C4orf26	4	76481309	Missense_Mutation	SNP	G	TCGA-K7-AAU7-01A-11D-A382-10	2206930	76481309	114672967	12	44321										
HPSE	10855	hgsc.bcm.edu	37	chr4	84216608	84216608	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	ttttccattaaaggtggcaaGgtttgatcatccaccatctt	7	9	2	1			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr4:84216608G>A	ENST00000405413.2	-	13	1657	c.1521C>T	c.(1519-1521)acC>acT	p.T507T	HPSE_ENST00000513463.1_Silent_p.T449T|HPSE_ENST00000311412.5_Silent_p.T507T|HPSE_ENST00000512196.1_Silent_p.T433T	NM_006665.5	NP_006656.2	Q9Y251	HPSE_HUMAN	heparanase	507					carbohydrate metabolic process (GO:0005975)|cell-matrix adhesion (GO:0007160)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan catabolic process (GO:0030200)|positive regulation of blood coagulation (GO:0030194)|positive regulation of hair follicle development (GO:0051798)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation vascular endothelial growth factor production (GO:0010575)|proteoglycan metabolic process (GO:0006029)|regulation of hair follicle development (GO:0051797)|small molecule metabolic process (GO:0044281)|vascular wound healing (GO:0061042)	extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|membrane raft (GO:0045121)|nucleus (GO:0005634)	beta-glucuronidase activity (GO:0004566)|heparanase activity (GO:0030305)|protein dimerization activity (GO:0046983)|syndecan binding (GO:0045545)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	20		Hepatocellular(203;0.114)		COAD - Colon adenocarcinoma(81;0.141)	Dalteparin(DB06779)|Heparin(DB01109)	AAGGTGGCAAGGTTTGATCAT	0.448																																					p.T507T		Atlas-SNP	.											.	HPSE	55	.	0			c.C1521T						.						95	96	96					4																	84216608		2203	4300	6503	SO:0001819	synonymous_variant	10855	exon12			TGGCAAGGTTTGA	AF144325	CCDS3602.1, CCDS54774.1, CCDS56337.1	4q21.3	2008-02-05			ENSG00000173083	ENSG00000173083			5164	protein-coding gene	gene with protein product		604724				10395325, 10395326	Standard	NM_006665		Approved	HPA, HSE1, HPSE1	uc003hoj.4	Q9Y251	OTTHUMG00000130425	ENST00000405413.2:c.1521C>T	chr4.hg19:g.84216608G>A		149.0	0.0		135.0	35.0	NM_001098540	A9JIG7|C7F7I3|C7F7I4|E9PCA9|E9PGR1|Q53GE5|Q9UL39	Silent	SNP	ENST00000405413.2	hg19	CCDS3602.1																																																																																			.	.		0.448	HPSE-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252812.2	NM_006665		A	84216608	G	A	84216608	2	1	312	1	0	0	0	0	0	0	0	1	7353	987	35	3		3	HPSE	4	84216608	Silent	SNP	G	TCGA-K7-AAU7-01A-11D-A382-10	7735299	84216608	106937668	13	44322										
MTNR1A	4543	hgsc.bcm.edu	37	chr4	187455203	187455203	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	acaaaattcctgaagtcctgTggtttcagtttgggtttgcg	11	7	1	1			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr4:187455203T>C	ENST00000307161.5	-	2	894	c.693A>G	c.(691-693)ccA>ccG	p.P231P	RP11-215A19.2_ENST00000509111.1_Intron	NM_005958.3	NP_005949.1	P48039	MTR1A_HUMAN	melatonin receptor 1A	231					circadian rhythm (GO:0007623)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|mating behavior (GO:0007617)|positive regulation of cGMP biosynthetic process (GO:0030828)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	hormone binding (GO:0042562)|melatonin receptor activity (GO:0008502)|organic cyclic compound binding (GO:0097159)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	14		all_cancers(14;6.39e-56)|all_epithelial(14;1.48e-41)|all_lung(41;2.45e-15)|Lung NSC(41;7.26e-15)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00335)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Colorectal(36;0.0161)|Renal(120;0.0183)|all_neural(102;0.202)		OV - Ovarian serous cystadenocarcinoma(60;7.63e-12)|BRCA - Breast invasive adenocarcinoma(30;6.68e-07)|GBM - Glioblastoma multiforme(59;3.44e-05)|LUSC - Lung squamous cell carcinoma(40;0.000106)|STAD - Stomach adenocarcinoma(60;0.000279)|READ - Rectum adenocarcinoma(43;0.159)	Agomelatine(DB06594)|Melatonin(DB01065)|Ramelteon(DB00980)	TGAAGTCCTGTGGTTTCAGTT	0.488																																					p.P231P		Atlas-SNP	.											.	MTNR1A	46	.	0			c.A693G						.						140	149	146					4																	187455203		2203	4300	6503	SO:0001819	synonymous_variant	4543	exon2			GTCCTGTGGTTTC		CCDS3848.1	4q35	2012-08-08				ENSG00000168412		"GPCR / Class A : Melatonin receptors"	7463	protein-coding gene	gene with protein product		600665				7558006	Standard	NM_005958		Approved	MEL-1A-R	uc003izd.1	P48039		ENST00000307161.5:c.693A>G	chr4.hg19:g.187455203T>C		164.0	0.0		137.0	32.0	NM_005958	A0AVC5|B0M0L2	Silent	SNP	ENST00000307161.5	hg19	CCDS3848.1																																																																																			.	.		0.488	MTNR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360189.1			C	187455203	T	C	187455203	2	2	312	1	0	0	0	0	0	0	0	1	9960	1683	59	2		2	MTNR1A	4	187455203	Silent	SNP	T	TCGA-K7-AAU7-01A-11D-A382-10	103238595	187455203	3699073	14	44323										
IL7R	3575	hgsc.bcm.edu	37	chr5	35867558	35867558	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	tgcaaaaaaatagacctaacCactataggtaagaagttgta	7	6	0	2			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr5:35867558C>T	ENST00000303115.3	+	3	501	c.372C>T	c.(370-372)acC>acT	p.T124T	IL7R_ENST00000506850.1_Silent_p.T124T|IL7R_ENST00000511982.1_Silent_p.T124T|IL7R_ENST00000511031.1_3'UTR|IL7R_ENST00000343305.4_Silent_p.T124T	NM_002185.3	NP_002176.2	P16871	IL7RA_HUMAN	interleukin 7 receptor	124					B cell proliferation (GO:0042100)|cell growth (GO:0016049)|cell morphogenesis (GO:0000902)|cell surface receptor signaling pathway (GO:0007166)|homeostasis of number of cells (GO:0048872)|immune response (GO:0006955)|immunoglobulin production (GO:0002377)|interleukin-7-mediated signaling pathway (GO:0038111)|lymph node development (GO:0048535)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|positive regulation of gene expression (GO:0010628)|positive regulation of T cell differentiation in thymus (GO:0033089)|regulation of cell size (GO:0008361)|regulation of DNA recombination (GO:0000018)|signal transduction (GO:0007165)|T cell differentiation (GO:0030217)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|interleukin-7 receptor activity (GO:0004917)	p.T124T(1)		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)			TAGACCTAACCACTATAGGTA	0.343			"Mis, O"		"ALL, ETP ALL"		Severe combined immune deficiency																														p.T124T		Atlas-SNP	.		Dom	yes		5	5p13	146661	interleukin 7 receptor	yes	L	IL7R,NS,carcinoma,0,1	IL7R	200	.	1	Substitution - coding silent(1)	lung(1)	c.C372T						.						71	72	72					5																	35867558		2203	4300	6503	SO:0001819	synonymous_variant	3575	exon3			CCTAACCACTATA	M29696	CCDS3911.1	5p13	2014-09-17			ENSG00000168685	ENSG00000168685		"Interleukins and interleukin receptors", "CD molecules", "Fibronectin type III domain containing"	6024	protein-coding gene	gene with protein product		146661				2317865	Standard	NM_002185		Approved	CD127	uc003jjs.4	P16871	OTTHUMG00000090791	ENST00000303115.3:c.372C>T	chr5.hg19:g.35867558C>T		57.0	0.0		54.0	9.0	NM_002185	B2RCS6|B4DVT1|Q05CU8|Q6NSP4|Q6NWM0|Q6NWM1|Q6NWM2|Q6NWM3|Q6SV45|Q9UPC1	Silent	SNP	ENST00000303115.3	hg19	CCDS3911.1																																																																																			.	.		0.343	IL7R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207577.2			T	35867558	C	T	35867558	2	4	312	1	0	0	0	0	0	0	0	1	7714	581	21	3		3	IL7R	5	35867558	Silent	SNP	C	TCGA-K7-AAU7-01A-11D-A382-10		35867558	145047702	15	44324										
FST	10468	hgsc.bcm.edu	37	chr5	52776663	52776663	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	ccgggtgggctttgcctcctGctgctgctgctctgccagtt	13	14	1	0			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr5:52776663G>C	ENST00000256759.3	+	1	425	c.42G>C	c.(40-42)ctG>ctC	p.L14L	FST_ENST00000396947.3_Silent_p.L14L	NM_013409.2	NP_037541.1	P19883	FST_HUMAN	follistatin	14					BMP signaling pathway (GO:0030509)|female gonad development (GO:0008585)|gamete generation (GO:0007276)|hair follicle morphogenesis (GO:0031069)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinocyte proliferation (GO:0043616)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|pattern specification process (GO:0007389)|positive regulation of hair follicle development (GO:0051798)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleus (GO:0005634)	activin binding (GO:0048185)|signal transducer activity (GO:0004871)	p.L14L(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(7)|prostate(1)|urinary_tract(1)	15		Ovarian(174;1.78e-06)|Lung NSC(810;3.55e-06)|Breast(144;4.08e-05)				TTTGCCTCCTGCTGCTGCTGC	0.731																																					p.L14L		Atlas-SNP	.											FST,colon,carcinoma,0,1	FST	42	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G42C						.						20	15	17					5																	52776663		2000	3838	5838	SO:0001819	synonymous_variant	10468	exon1			CCTCCTGCTGCTG	M19481	CCDS3959.1, CCDS43315.1	5q11.2	2008-02-05			ENSG00000134363	ENSG00000134363			3971	protein-coding gene	gene with protein product		136470				10411917, 3380788	Standard	NM_006350		Approved	FS	uc003jpd.3	P19883	OTTHUMG00000131183	ENST00000256759.3:c.42G>C	chr5.hg19:g.52776663G>C		85.0	0.0		63.0	3.0	NM_013409	B5BU94|Q9BTH0	Silent	SNP	ENST00000256759.3	hg19	CCDS3959.1																																																																																			.	.		0.731	FST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253906.1	NM_013409		C	52776663	G	C	52776663	2	2	312	1	0	0	0	0	0	0	0	1	6084	1306	46	4		4	FST	5	52776663	Silent	SNP	G	TCGA-K7-AAU7-01A-11D-A382-10	16909105	52776663	128138597	16	44325										
PDE4D	5144	hgsc.bcm.edu	37	chr5	59189173	59189173	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	cccgctcgaggcgtagcggcCgcgggcagccccgggcggcg	19	17	0	0			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr5:59189173C>T	ENST00000340635.6	-	1	452	c.277G>A	c.(277-279)Ggc>Agc	p.G93S	PDE4D_ENST00000502484.2_Intron|PDE4D_ENST00000546160.1_Intron	NM_001104631.1	NP_001098101.1	Q08499	PDE4D_HUMAN	phosphodiesterase 4D, cAMP-specific	93					adrenergic receptor signaling pathway (GO:0071875)|adrenergic receptor signaling pathway involved in positive regulation of heart rate (GO:0086024)|aging (GO:0007568)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to lipopolysaccharide (GO:0071222)|establishment of endothelial barrier (GO:0061028)|multicellular organism growth (GO:0035264)|negative regulation of heart contraction (GO:0045822)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of relaxation of cardiac muscle (GO:1901898)|neutrophil chemotaxis (GO:0030593)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-5 production (GO:0032754)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of receptor activity (GO:0010469)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|smooth muscle contraction (GO:0006939)|T cell receptor signaling pathway (GO:0050852)	calcium channel complex (GO:0034704)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|ATPase binding (GO:0051117)|beta-2 adrenergic receptor binding (GO:0031698)|cAMP binding (GO:0030552)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|pancreas(1)	15		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Caffeine(DB00201)|Dyphylline(DB00651)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Roflumilast(DB01656)	GCGTAGCGGCCGCGGGCAGCC	0.801																																					p.G93S		Atlas-SNP	.											.	PDE4D	345	.	0			c.G277A						.						2	2	2					5																	59189173		926	2138	3064	SO:0001583	missense	5144	exon1			AGCGGCCGCGGGC		CCDS47213.1, CCDS54858.1, CCDS54859.1, CCDS56369.1, CCDS56370.1, CCDS56371.1, CCDS56372.1, CCDS56373.1	5q12	2010-06-24	2010-06-24				3.1.4.17	"Phosphodiesterases"	8783	protein-coding gene	gene with protein product	"phosphodiesterase E3 dunce homolog (Drosophila)"	600129	"phosphodiesterase 4D, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E3)"	DPDE3			Standard	NM_006203		Approved		uc003jsa.2	Q08499		ENST00000340635.6:c.277G>A	chr5.hg19:g.59189173C>T	ENSP00000345502:p.Gly93Ser	362.0	0.0		272.0	67.0	NM_001104631	O43433|Q13549|Q13550|Q13551|Q7Z2L8|Q8IV84|Q8IVA9|Q8IVD2|Q8IVD3|Q96HL4|Q9HCX7	Missense_Mutation	SNP	ENST00000340635.6	hg19	CCDS47213.1	.	.	.	.	.	.	.	.	.	.	C	15.80	2.941440	0.53079	.	.	ENSG00000113448	ENST00000340635	T	0.65364	-0.15	4.09	3.22	0.36961	.	.	.	.	.	T	0.41558	0.1164	N	0.24115	0.695	0.58432	D	0.999991	B	0.28208	0.203	B	0.17433	0.018	T	0.17806	-1.0357	9	0.21540	T	0.41	.	8.6276	0.33899	0.0:0.8226:0.0:0.1774	.	93	Q08499	PDE4D_HUMAN	S	93	ENSP00000345502:G93S	ENSP00000345502:G93S	G	-	1	0	PDE4D	59224930	0.995000	0.38212	0.064000	0.19789	0.787000	0.44495	1.519000	0.35888	1.057000	0.40506	0.484000	0.47621	GGC	.	.		0.801	PDE4D-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367940.3			T	59189173	C	T	59189173	3	4	312	1	0	0	0	0	1	0	0	0	11651	652	23	1	2263	1	PDE4D	5	59189173	Missense_Mutation	SNP	C	TCGA-K7-AAU7-01A-11D-A382-10	6412510	59189173	121726087	17	44326										
PCDHA7	56141	hgsc.bcm.edu	37	chr5	140215179	140215179	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	ggtgtccaccttcaagaattActattcattggtgctggaca	9	9	2	1			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr5:140215179A>G	ENST00000525929.1	+	1	1211	c.1211A>G	c.(1210-1212)tAc>tGc	p.Y404C	PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA7_ENST00000378125.3_Missense_Mutation_p.Y404C	NM_018910.2	NP_061733.1	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7	404	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|biliary_tract(1)|breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCAAGAATTACTATTCATTG	0.577																																					p.Y404C	NSCLC(160;258 2013 5070 22440 28951)	Atlas-SNP	.											.	PCDHA7	367	.	0			c.A1211G						.						128	128	128					5																	140215179		2203	4299	6502	SO:0001583	missense	56141	exon1			AGAATTACTATTC	AF152485	CCDS54918.1	5q31	2010-11-26				ENSG00000204963		"Cadherins / Protocadherins : Clustered"	8673	other	complex locus constituent	"KIAA0345-like 7", "ortholog to mouse CNR4"	606313		CNRS4		10380929, 10662547	Standard	NM_018910		Approved	CNR4, CRNR4		Q9UN72		ENST00000525929.1:c.1211A>G	chr5.hg19:g.140215179A>G	ENSP00000436426:p.Tyr404Cys	152.0	0.0		115.0	23.0	NM_031852	O75282	Missense_Mutation	SNP	ENST00000525929.1	hg19	CCDS54918.1	.	.	.	.	.	.	.	.	.	.	A	12.05	1.821903	0.32237	.	.	ENSG00000204963	ENST00000525929;ENST00000378125	T;T	0.01745	4.66;4.66	4.04	4.04	0.47022	Cadherin (4);Cadherin-like (1);	0.000000	0.29537	U	0.011878	T	0.14184	0.0343	H	0.94264	3.515	0.31404	N	0.676281	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	T	0.13335	-1.0513	10	0.87932	D	0	.	10.7335	0.46111	0.8409:0.1591:0.0:0.0	.	404;404	Q9UN72-2;Q9UN72	.;PCDA7_HUMAN	C	404	ENSP00000436426:Y404C;ENSP00000367365:Y404C	ENSP00000367365:Y404C	Y	+	2	0	PCDHA7	140195363	0.011000	0.17503	0.984000	0.44739	0.207000	0.24258	2.361000	0.44160	1.592000	0.50018	0.254000	0.18369	TAC	.	.		0.577	PCDHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372887.2	NM_018910		G	140215179	A	G	140215179	3	3	312	1	0	0	0	0	1	0	0	0	11538	391	14	2	1213	2	PCDHA7	5	140215179	Missense_Mutation	SNP	A	TCGA-K7-AAU7-01A-11D-A382-10	81026006	140215179	40700081	18	44327										
PCDHA9	9752	hgsc.bcm.edu	37	chr5	140229434	140229434	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	tggccgacgtgaacgacaacGcaccagcgttcgcgcagtcc	12	15	0	1	rs145248721		TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr5:140229434G>A	ENST00000532602.1	+	1	2387	c.1354G>A	c.(1354-1356)Gca>Aca	p.A452T	PCDHA9_ENST00000378122.3_Missense_Mutation_p.A452T|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	452	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAACGACAACGCACCAGCGTT	0.672																																					p.A452T	Melanoma(55;1800 1972 14909)	Atlas-SNP	.											.	PCDHA9	373	.	0			c.G1354A						.	G	THR/ALA,,,,,,,,,,,THR/ALA	1,4391	2.1+/-5.4	0,1,2195	89	82	85		1354,,,,,,,,,,,1354	3.6	1	5	dbSNP_134	85	0,8538		0,0,4269	no	missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense	PCDHA9,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_014005.3,NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1	58,,,,,,,,,,,58	0,1,6464	AA,AG,GG		0.0,0.0228,0.0077	,,,,,,,,,,,	452/843,,,,,,,,,,,452/951	140229434	1,12929	2196	4269	6465	SO:0001583	missense	9752	exon1			GACAACGCACCAG	AF152487	CCDS54920.1	5q31	2010-11-26				ENSG00000204961		"Cadherins / Protocadherins : Clustered"	8675	other	complex locus constituent	"KIAA0345-like 5"	606315				10380929	Standard	NM_031857		Approved	KIAA0345, PCDH-ALPHA9		Q9Y5H5		ENST00000532602.1:c.1354G>A	chr5.hg19:g.140229434G>A	ENSP00000436042:p.Ala452Thr	207.0	0.0		212.0	60.0	NM_031857	O15053|Q2M3S5	Missense_Mutation	SNP	ENST00000532602.1	hg19	CCDS54920.1	.	.	.	.	.	.	.	.	.	.	G	17.30	3.354424	0.61293	2.28E-4	0.0	ENSG00000204961	ENST00000532602;ENST00000378122	T;T	0.61742	0.08;0.08	3.56	3.56	0.40772	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	0.000000	0.31519	U	0.007517	T	0.77811	0.4186	M	0.86028	2.79	0.23524	N	0.997498	P;D	0.89917	0.925;1.0	B;D	0.87578	0.135;0.998	T	0.71590	-0.4547	10	0.87932	D	0	.	15.7535	0.78005	0.0:0.0:1.0:0.0	.	452;452	Q9Y5H5;Q9Y5H5-2	PCDA9_HUMAN;.	T	452	ENSP00000436042:A452T;ENSP00000367362:A452T	ENSP00000367362:A452T	A	+	1	0	PCDHA9	140209618	0.000000	0.05858	1.000000	0.80357	0.449000	0.32228	0.847000	0.27696	1.973000	0.57446	0.306000	0.20318	GCA	.	G|1.000;A|0.000		0.672	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857		A	140229434	G	A	140229434	3	1	312	1	0	0	0	0	1	0	0	0	11540	1087	38	1	1356	1	PCDHA9	5	140229434	Missense_Mutation	SNP	G	TCGA-K7-AAU7-01A-11D-A382-10	14255	140229434	40685826	19	44328										
NT5E	4907	hgsc.bcm.edu	37	chr6	86176881	86176881	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	tgcaaacattaaagcaaaggGgccactagcatctcaaatat	7	9	1	0			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr6:86176881G>A	ENST00000257770.3	+	2	492	c.443G>A	c.(442-444)gGg>gAg	p.G148E	NT5E_ENST00000369646.3_Missense_Mutation_p.G148E|NT5E_ENST00000369651.3_Missense_Mutation_p.G148E	NM_002526.3	NP_002517.1	P21589	5NTD_HUMAN	5'-nucleotidase, ecto (CD73)	148					adenosine biosynthetic process (GO:0046086)|AMP catabolic process (GO:0006196)|dephosphorylation (GO:0016311)|DNA metabolic process (GO:0006259)|negative regulation of inflammatory response (GO:0050728)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	5'-nucleotidase activity (GO:0008253)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(76;0.000215)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0427)		BRCA - Breast invasive adenocarcinoma(108;0.0417)	Cytarabine(DB00987)|Pentoxifylline(DB00806)	AAAGCAAAGGGGCCACTAGCA	0.413																																					p.G148E	Melanoma(140;797 1765 2035 2752 18208)	Atlas-SNP	.											.	NT5E	56	.	0			c.G443A						.						134	124	127					6																	86176881		2203	4300	6503	SO:0001583	missense	4907	exon2			CAAAGGGGCCACT	X55740	CCDS5002.1, CCDS56439.1	6q14-q21	2013-08-28	2002-04-18	2002-04-19	ENSG00000135318	ENSG00000135318	3.1.3.5	"CD molecules"	8021	protein-coding gene	gene with protein product		129190	"5' nucleotidase (CD73)"	NT5			Standard	NM_002526		Approved	CD73, eN, eNT, CALJA	uc003pko.4	P21589	OTTHUMG00000015139	ENST00000257770.3:c.443G>A	chr6.hg19:g.86176881G>A	ENSP00000257770:p.Gly148Glu	159.0	0.0		113.0	31.0	NM_001204813	B3KQI8|O75520|Q5W116	Missense_Mutation	SNP	ENST00000257770.3	hg19	CCDS5002.1	.	.	.	.	.	.	.	.	.	.	G	8.409	0.843766	0.16963	.	.	ENSG00000135318	ENST00000257770;ENST00000369646;ENST00000369651	D;D;D	0.83837	-1.77;-1.77;-1.77	5.57	1.26	0.21427	Metallophosphoesterase domain (1);	0.851095	0.11050	N	0.605173	T	0.41003	0.1140	N	0.11313	0.125	0.09310	N	1	B;B;B	0.09022	0.001;0.0;0.002	B;B;B	0.11329	0.006;0.006;0.006	T	0.32955	-0.9887	10	0.15952	T	0.53	-4.0844	5.8042	0.18430	0.4144:0.1461:0.4395:0.0	.	148;148;148	B3KQI8;P21589;Q96B60	.;5NTD_HUMAN;.	E	148	ENSP00000257770:G148E;ENSP00000358660:G148E;ENSP00000358665:G148E	ENSP00000257770:G148E	G	+	2	0	NT5E	86233600	0.000000	0.05858	0.383000	0.26132	0.978000	0.69477	-0.059000	0.11731	0.313000	0.23062	0.462000	0.41574	GGG	.	.		0.413	NT5E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041388.1			A	86176881	G	A	86176881	3	1	312	1	0	0	0	0	1	0	0	0	10702	1232	43	3	449	3	NT5E	6	86176881	Missense_Mutation	SNP	G	TCGA-K7-AAU7-01A-11D-A382-10		86176881	84938186	20	44329										
AKAP12	9590	hgsc.bcm.edu	37	chr6	151671011	151671011	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	ctgtccaaaccccccgaaggCgttgtgagtgaggtggaaat	13	10	0	2	rs370245999		TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr6:151671011C>T	ENST00000253332.1	+	3	1674	c.1485C>T	c.(1483-1485)ggC>ggT	p.G495G	snoU13_ENST00000458767.1_RNA|AKAP12_ENST00000354675.6_Silent_p.G397G|AKAP12_ENST00000402676.2_Silent_p.G495G|AKAP12_ENST00000359755.5_Silent_p.G390G			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	495	Involved in PKC-binding. {ECO:0000305}.				G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of protein kinase C signaling (GO:0090036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	68		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)		CCCCCGAAGGCGTTGTGAGTG	0.502																																					p.G495G	Melanoma(141;1616 1805 10049 24534 51979)	Atlas-SNP	.											.	AKAP12	170	.	0			c.C1485T						.	C	,	1,4405	2.1+/-5.4	0,1,2202	107	113	111		1485,1191	4.2	0.1	6		111	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	AKAP12	NM_005100.3,NM_144497.2	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	495/1783,397/1685	151671011	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9590	exon4			CGAAGGCGTTGTG	U81607	CCDS5229.1, CCDS5230.1	6q24-q25	2011-07-01	2008-08-29		ENSG00000131016	ENSG00000131016		"A-kinase anchor proteins"	370	protein-coding gene	gene with protein product	"gravin", "Src-Suppressed C Kinase Substrate"	604698	"A kinase (PRKA) anchor protein (gravin) 12"			9000000	Standard	NM_144497		Approved	AKAP250, SSeCKS	uc011eep.2	Q02952	OTTHUMG00000015833	ENST00000253332.1:c.1485C>T	chr6.hg19:g.151671011C>T		85.0	0.0		93.0	23.0	NM_005100	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Silent	SNP	ENST00000253332.1	hg19	CCDS5229.1																																																																																			.	.		0.502	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1			T	151671011	C	T	151671011	2	4	312	1	0	0	0	0	0	0	0	1	448	755	27	1		1	AKAP12	6	151671011	Silent	SNP	C	TCGA-K7-AAU7-01A-11D-A382-10	65494130	151671011	19444056	21	44330										
AEBP1	165	hgsc.bcm.edu	37	chr7	44149650	44149650	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	gatggagtcacaccgtattgAggacaaccagatccgagcct	11	11	1	2			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr7:44149650A>T	ENST00000223357.3	+	10	1492	c.1187A>T	c.(1186-1188)gAg>gTg	p.E396V	AEBP1_ENST00000454218.1_3'UTR|MIR4649_ENST00000582839.1_RNA|AEBP1_ENST00000450684.2_5'Flank	NM_001129.3	NP_001120.3	Q8IUX7	AEBP1_HUMAN	AE binding protein 1	396	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.|Required for DNA-binding and interaction with NFKBIA. {ECO:0000250}.				cell adhesion (GO:0007155)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(13)|upper_aerodigestive_tract(2)	33						CACCGTATTGAGGACAACCAG	0.627																																					p.E396V		Atlas-SNP	.											.	AEBP1	102	.	0			c.A1187T						.						60	52	55					7																	44149650		2203	4300	6503	SO:0001583	missense	165	exon10			GTATTGAGGACAA	D86479	CCDS5476.1	7p	2008-07-18	2001-11-28		ENSG00000106624	ENSG00000106624			303	protein-coding gene	gene with protein product	"aortic carboxypeptidase-like protein", "adipocyte enhancer binding protein 1"	602981	"AE-binding protein 1"			8920928	Standard	NM_001129		Approved	ACLP	uc003tkb.4	Q8IUX7	OTTHUMG00000023362	ENST00000223357.3:c.1187A>T	chr7.hg19:g.44149650A>T	ENSP00000223357:p.Glu396Val	90.0	0.0		81.0	22.0	NM_001129	Q14113|Q59ER7|Q6ZSC7|Q7KZ79	Missense_Mutation	SNP	ENST00000223357.3	hg19	CCDS5476.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.520613	0.85495	.	.	ENSG00000106624	ENST00000223357	D	0.97186	-4.28	5.05	5.05	0.67936	Coagulation factor 5/8 C-terminal type domain (2);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	D	0.96380	0.8819	L	0.39514	1.22	0.80722	D	1	P	0.51933	0.949	P	0.56343	0.796	D	0.96381	0.9281	10	0.87932	D	0	-38.7085	10.6252	0.45504	0.839:0.161:0.0:0.0	.	396	Q8IUX7	AEBP1_HUMAN	V	396	ENSP00000223357:E396V	ENSP00000223357:E396V	E	+	2	0	AEBP1	44116175	1.000000	0.71417	0.994000	0.49952	0.977000	0.68977	5.984000	0.70548	1.908000	0.55244	0.459000	0.35465	GAG	.	.		0.627	AEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250993.2	NM_001129		T	44149650	A	T	44149650	3	4	312	1	0	0	0	0	1	0	0	0	349	304	11	4	1225	4	AEBP1	7	44149650	Missense_Mutation	SNP	A	TCGA-K7-AAU7-01A-11D-A382-10		44149650	114989013	22	44331										
DUS4L	11062	hgsc.bcm.edu	37	chr7	107217956	107217956	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	aagggtatttaatgctctgtCaagcacatcagcaatcatag	8	8	4	0			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr7:107217956C>G	ENST00000265720.3	+	8	1267	c.905C>G	c.(904-906)tCa>tGa	p.S302*	BCAP29_ENST00000379117.2_5'Flank|BCAP29_ENST00000005259.4_5'Flank|BCAP29_ENST00000465919.1_5'Flank|RP4-593H12.1_ENST00000610269.1_RNA|BCAP29_ENST00000445771.2_5'Flank|DUS4L_ENST00000402620.1_Nonsense_Mutation_p.S181*	NM_001270419.1|NM_181581.2	NP_001257348.1|NP_853559.1	O95620	DUS4L_HUMAN	dihydrouridine synthase 4-like (S. cerevisiae)	302							flavin adenine dinucleotide binding (GO:0050660)|tRNA dihydrouridine synthase activity (GO:0017150)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(1)|stomach(1)	8						AATGCTCTGTCAAGCACATCA	0.358																																					p.S302X		Atlas-SNP	.											.	DUS4L	27	.	0			c.C905G						.						124	130	128					7																	107217956		2203	4300	6503	SO:0001587	stop_gained	11062	exon8			CTCTGTCAAGCAC	U62767	CCDS5745.1	7q22-q31	2007-12-04			ENSG00000105865	ENSG00000105865			21517	protein-coding gene	gene with protein product	"protein similar to E.coli yhdg and R. capsulatus nifR3"						Standard	NM_181581		Approved	PP35, DUS4	uc031syv.1	O95620	OTTHUMG00000154763	ENST00000265720.3:c.905C>G	chr7.hg19:g.107217956C>G	ENSP00000265720:p.Ser302*	118.0	0.0		103.0	25.0	NM_001270419	B4DLX0|Q2NKK1	Nonsense_Mutation	SNP	ENST00000265720.3	hg19	CCDS5745.1	.	.	.	.	.	.	.	.	.	.	C	38	7.261954	0.98171	.	.	ENSG00000105865	ENST00000265720;ENST00000402620	.	.	.	5.67	4.79	0.61399	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	.	15.1503	0.72692	0.0:0.9319:0.0:0.0681	.	.	.	.	X	302;181	.	ENSP00000265720:S302X	S	+	2	0	DUS4L	107005192	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.447000	0.60020	1.536000	0.49237	0.655000	0.94253	TCA	.	.		0.358	DUS4L-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336967.2	NM_181581		G	107217956	C	G	107217956	4	3	312	1	0	0	0	0	0	1	0	0	4810	838	29	4	927	4	DUS4L	7	107217956	Nonsense_Mutation	SNP	C	TCGA-K7-AAU7-01A-11D-A382-10	63068306	107217956	51920707	23	44332										
CTTNBP2	83992	hgsc.bcm.edu	37	chr7	117431557	117431557	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	cctgctgctgtctataataaCcttgagttgggggtgtggtg	14	7	1	1			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr7:117431557C>A	ENST00000160373.3	-	4	1784	c.1693G>T	c.(1693-1695)Gtt>Ttt	p.V565F	CTTNBP2_ENST00000487820.1_5'Flank	NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	565					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)				breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		TCTATAATAACCTTGAGTTGG	0.512																																					p.V565F		Atlas-SNP	.											.	CTTNBP2	200	.	0			c.G1693T						.						112	119	117					7																	117431557		2203	4300	6503	SO:0001583	missense	83992	exon4			TAATAACCTTGAG		CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"Ankyrin repeat domain containing"	15679	protein-coding gene	gene with protein product		609772	"cortactin binding protein 2"	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.1693G>T	chr7.hg19:g.117431557C>A	ENSP00000160373:p.Val565Phe	188.0	0.0		177.0	43.0	NM_033427	O43389|Q7LG11|Q9C0A5	Missense_Mutation	SNP	ENST00000160373.3	hg19	CCDS5774.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.49|16.49	3.138871|3.138871	0.56936|0.56936	.|.	.|.	ENSG00000077063|ENSG00000077063	ENST00000446636|ENST00000160373	.|T	.|0.68025	.|-0.3	5.37|5.37	3.5|3.5	0.40072|0.40072	.|.	.|0.289894	.|0.37809	.|N	.|0.001924	T|T	0.68210|0.68210	0.2976|0.2976	M|M	0.83852|0.83852	2.665|2.665	0.31045|0.31045	N|N	0.71585|0.71585	.|P	.|0.39576	.|0.679	.|B	.|0.38562	.|0.276	T|T	0.72887|0.72887	-0.4156|-0.4156	5|10	.|0.66056	.|D	.|0.02	-1.9558|-1.9558	11.3863|11.3863	0.49787|0.49787	0.0:0.862:0.0:0.138|0.0:0.862:0.0:0.138	.|.	.|565	.|Q8WZ74	.|CTTB2_HUMAN	V|F	93|565	.|ENSP00000160373:V565F	.|ENSP00000160373:V565F	G|V	-|-	2|1	0|0	CTTNBP2|CTTNBP2	117218793|117218793	1.000000|1.000000	0.71417|0.71417	0.778000|0.778000	0.31720|0.31720	0.996000|0.996000	0.88848|0.88848	4.037000|4.037000	0.57311|0.57311	0.691000|0.691000	0.31592|0.31592	0.563000|0.563000	0.77884|0.77884	GGT|GTT	.	.		0.512	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		A	117431557	C	A	117431557	3	1	312	1	0	0	0	0	1	0	0	0	4047	507	18	3	3378	3	CTTNBP2	7	117431557	Missense_Mutation	SNP	C	TCGA-K7-AAU7-01A-11D-A382-10	10213601	117431557	41707106	24	44333										
IMPDH1	3614	hgsc.bcm.edu	37	chr7	128034577	128034577	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	gatgcctgctatgaggtaggGcacgaacttctgaatggatc	13	8	1	2			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr7:128034577G>A	ENST00000480861.1	-	12	1434	c.1357C>T	c.(1357-1359)Ccc>Tcc	p.P453S	IMPDH1_ENST00000338791.6_Missense_Mutation_p.P543S|IMPDH1_ENST00000419067.2_Missense_Mutation_p.P510S|IMPDH1_ENST00000348127.6_Missense_Mutation_p.P507S|IMPDH1_ENST00000470772.1_Missense_Mutation_p.P457S|IMPDH1_ENST00000354269.5_Missense_Mutation_p.P533S|IMPDH1_ENST00000496200.1_Missense_Mutation_p.P433S|IMPDH1_ENST00000343214.4_Missense_Mutation_p.P433S|IMPDH1_ENST00000378717.4_Missense_Mutation_p.P474S	NM_001142574.1	NP_001136046.1			IMP (inosine 5'-monophosphate) dehydrogenase 1											breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(3)	22						ATGAGGTAGGGCACGAACTTC	0.602																																					p.P543S		Atlas-SNP	.											.	IMPDH1	38	.	0			c.C1627T						.						92	87	89					7																	128034577		2203	4300	6503	SO:0001583	missense	3614	exon15			GGTAGGGCACGAA		CCDS34748.1, CCDS34749.1, CCDS43643.1, CCDS47699.1, CCDS47700.1, CCDS55161.1	7q31.3-q32	2013-01-08	2010-04-29		ENSG00000106348	ENSG00000106348	1.1.1.205		6052	protein-coding gene	gene with protein product		146690	"retinitis pigmentosa 10 (autosomal dominant)", "IMP (inosine monophosphate) dehydrogenase 1"	RP10		1969416, 11875049, 11875050	Standard	NM_000883		Approved	sWSS2608, LCA11	uc003vmu.2	P20839	OTTHUMG00000157713	ENST00000480861.1:c.1357C>T	chr7.hg19:g.128034577G>A	ENSP00000420185:p.Pro453Ser	40.0	0.0		45.0	15.0	NM_000883		Missense_Mutation	SNP	ENST00000480861.1	hg19	CCDS55161.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.714827	0.89112	.	.	ENSG00000106348	ENST00000419067;ENST00000338791;ENST00000496200;ENST00000354269;ENST00000378717;ENST00000348127;ENST00000343214;ENST00000470772;ENST00000480861	T;T;T;T;T;T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16;-1.16;-1.16;-1.16;-1.16;-1.16	5.18	5.18	0.71444	Aldolase-type TIM barrel (1);IMP dehydrogenase/GMP reductase (1);	0.000000	0.85682	D	0.000000	D	0.87325	0.6149	M	0.83223	2.63	0.80722	D	1	P;P;D;P;D;D;D;P	0.65815	0.939;0.928;0.964;0.928;0.973;0.981;0.995;0.911	P;P;P;P;P;P;P;P	0.61722	0.762;0.629;0.629;0.629;0.846;0.599;0.893;0.496	D	0.87986	0.2746	10	0.46703	T	0.11	-28.3939	16.1961	0.82025	0.0:0.0:1.0:0.0	.	510;453;458;474;533;507;543;433	C9JV30;B4DE09;P20839;E7EQS0;Q5H9Q6;P20839-3;A4D0Z6;P20839-2	.;.;IMDH1_HUMAN;.;.;.;.;.	S	510;543;433;533;474;507;433;457;453	ENSP00000399400:P510S;ENSP00000345096:P543S;ENSP00000420803:P433S;ENSP00000346219:P533S;ENSP00000367989:P474S;ENSP00000265385:P507S;ENSP00000342438:P433S;ENSP00000417296:P457S;ENSP00000420185:P453S	ENSP00000345096:P543S	P	-	1	0	IMPDH1	127821813	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.912000	0.92726	2.409000	0.81822	0.561000	0.74099	CCC	.	.		0.602	IMPDH1-009	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000349462.1	NM_000883		A	128034577	G	A	128034577	3	1	312	1	0	0	0	0	1	0	0	0	7735	1203	42	3	184	3	IMPDH1	7	128034577	Missense_Mutation	SNP	G	TCGA-K7-AAU7-01A-11D-A382-10	10603020	128034577	31104086	25	44334										
OR9A2	135924	hgsc.bcm.edu	37	chr7	142723576	142723576	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	ggatggtggagataatgtagGtgtaggagacaatcgtaggg	18	2	0	2			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr7:142723576G>A	ENST00000350513.2	-	1	706	c.644C>T	c.(643-645)aCc>aTc	p.T215I		NM_001001658.1	NP_001001658.1	Q8NGT5	OR9A2_HUMAN	olfactory receptor, family 9, subfamily A, member 2	215						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(3)|endometrium(4)|large_intestine(1)|lung(14)|skin(3)	25	Melanoma(164;0.059)					GATAATGTAGGTGTAGGAGAC	0.453																																					p.T215I		Atlas-SNP	.											.	OR9A2	52	.	0			c.C644T						.						84	90	88					7																	142723576		2203	4300	6503	SO:0001583	missense	135924	exon1			ATGTAGGTGTAGG		CCDS34767.1	7q34	2014-07-10			ENSG00000179468	ENSG00000179468		"GPCR / Class A : Olfactory receptors"	15093	protein-coding gene	gene with protein product							Standard	NM_001001658		Approved		uc003wcc.1	Q8NGT5	OTTHUMG00000158386	ENST00000350513.2:c.644C>T	chr7.hg19:g.142723576G>A	ENSP00000316518:p.Thr215Ile	72.0	0.0		68.0	11.0	NM_001001658	B9EH51|Q6IF71|Q8NGD9	Missense_Mutation	SNP	ENST00000350513.2	hg19	CCDS34767.1	.	.	.	.	.	.	.	.	.	.	G	2.387	-0.340807	0.05243	.	.	ENSG00000179468	ENST00000350513	T	0.00054	8.8	4.62	2.77	0.32553	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41294	U	0.000918	T	0.00073	0.0002	N	0.12746	0.255	0.27876	N	0.939866	B	0.14805	0.011	B	0.20955	0.032	T	0.01786	-1.1274	10	0.17369	T	0.5	-12.5647	4.7669	0.13137	0.1932:0.1803:0.6266:0.0	.	215	Q8NGT5	OR9A2_HUMAN	I	215	ENSP00000316518:T215I	ENSP00000316518:T215I	T	-	2	0	OR9A2	142433698	0.001000	0.12720	1.000000	0.80357	0.047000	0.14425	0.700000	0.25601	0.639000	0.30564	0.561000	0.74099	ACC	.	.		0.453	OR9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350862.1			A	142723576	G	A	142723576	3	1	312	1	0	0	0	0	1	0	0	0	11257	1261	44	3	292	3	OR9A2	7	142723576	Missense_Mutation	SNP	G	TCGA-K7-AAU7-01A-11D-A382-10	14688999	142723576	16415087	26	44335										
C8orf74	203076	hgsc.bcm.edu	37	chr8	10557811	10557811	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	tcctgcaggagctgctgcagCgccagatccagaacacattc	10	14	0	2			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr8:10557811C>T	ENST00000304519.5	+	4	744	c.715C>T	c.(715-717)Cgc>Tgc	p.R239C	RP1L1_ENST00000329335.3_Intron	NM_001040032.1	NP_001035121	Q6P047	CH074_HUMAN	chromosome 8 open reading frame 74	239										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|urinary_tract(1)	13				COAD - Colon adenocarcinoma(149;0.0811)		GCTGCTGCAGCGCCAGATCCA	0.602																																					p.R239C		Atlas-SNP	.											.	C8orf74	28	.	0			c.C715T						.						79	88	85					8																	10557811		2020	4192	6212	SO:0001583	missense	203076	exon4			CTGCAGCGCCAGA	BC038534	CCDS47800.1	8p23.1	2012-04-17			ENSG00000171060	ENSG00000171060			32296	protein-coding gene	gene with protein product							Standard	NM_001040032		Approved		uc003wtd.1	Q6P047	OTTHUMG00000163807	ENST00000304519.5:c.715C>T	chr8.hg19:g.10557811C>T	ENSP00000307129:p.Arg239Cys	84.0	0.0		57.0	27.0	NM_001040032	A2RUD6	Missense_Mutation	SNP	ENST00000304519.5	hg19	CCDS47800.1	.	.	.	.	.	.	.	.	.	.	C	3.345	-0.133780	0.06711	.	.	ENSG00000171060	ENST00000304519	T	0.30448	1.53	5.01	-4.92	0.03075	.	1.842940	0.02311	N	0.072098	T	0.09423	0.0232	N	0.01352	-0.895	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.15752	-1.0426	10	0.38643	T	0.18	.	2.082	0.03637	0.1564:0.3974:0.1444:0.3018	.	239	Q6P047	CH074_HUMAN	C	239	ENSP00000307129:R239C	ENSP00000307129:R239C	R	+	1	0	C8orf74	10595221	0.000000	0.05858	0.011000	0.14972	0.001000	0.01503	-1.050000	0.03510	-0.483000	0.06772	-1.149000	0.01842	CGC	.	.		0.602	C8orf74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375675.1	NM_001040032		T	10557811	C	T	10557811	3	4	312	1	0	0	0	0	1	0	0	0	2438	768	27	1	729	1	C8orf74	8	10557811	Missense_Mutation	SNP	C	TCGA-K7-AAU7-01A-11D-A382-10		10557811	135806211	27	44336										
PLEKHA2	59339	hgsc.bcm.edu	37	chr8	38793565	38793565	+	Silent	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	ttgcagctgacctacatctcGaaggtaatgttgacctggaa	10	9	1	2			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr8:38793565G>C	ENST00000521746.1	+	3	429	c.195G>C	c.(193-195)tcG>tcC	p.S65S	PLEKHA2_ENST00000388745.4_3'UTR|PLEKHA2_ENST00000420274.1_Silent_p.S65S			Q9HB19	PKHA2_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 2	65	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				positive regulation of cell-matrix adhesion (GO:0001954)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	fibronectin binding (GO:0001968)|laminin binding (GO:0043236)|lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	13		all_lung(54;0.0413)|Lung NSC(58;0.115)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;4.68e-08)|COAD - Colon adenocarcinoma(9;0.235)			CCTACATCTCGAAGGTAATGT	0.458																																					p.S65S		Atlas-SNP	.											.	PLEKHA2	22	.	0			c.G195C						.						144	142	142					8																	38793565		1934	4152	6086	SO:0001819	synonymous_variant	59339	exon3			CATCTCGAAGGTA	AF286164	CCDS75732.1	8p11.21	2013-01-10	2002-01-14			ENSG00000169499		"Pleckstrin homology (PH) domain containing"	14336	protein-coding gene	gene with protein product	"tandem PH Domain containing protein-2"	607773	"pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2"			11001876	Standard	NM_021623		Approved	TAPP2	uc003xmi.4	Q9HB19		ENST00000521746.1:c.195G>C	chr8.hg19:g.38793565G>C		56.0	0.0		33.0	8.0	NM_021623		Silent	SNP	ENST00000521746.1	hg19																																																																																				.	.		0.458	PLEKHA2-002	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000377068.1	NM_021623		C	38793565	G	C	38793565	2	2	312	1	0	0	0	0	0	0	0	1	12065	1045	37	4		4	PLEKHA2	8	38793565	Silent	SNP	G	TCGA-K7-AAU7-01A-11D-A382-10	28235754	38793565	107570457	28	44337										
C8orf76	84933	hgsc.bcm.edu	37	chr8	124238821	124238821	+	Frame_Shift_Del	DEL	C	C	-													0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	tcctgctgagtccttaagttCctctccaaagcaaacgatgt							TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr8:124238821delC	ENST00000276704.4	-	5	918	c.867delG	c.(865-867)aggfs	p.R289fs	ZHX1-C8ORF76_ENST00000357082.4_Frame_Shift_Del_p.R257fs|C8orf76_ENST00000521310.1_5'UTR	NM_032847.2	NP_116236.1	Q96K31	CH076_HUMAN	chromosome 8 open reading frame 76	289										NS(1)|lung(9)|ovary(2)|prostate(1)|urinary_tract(4)	17	Lung NSC(37;1.25e-09)|Ovarian(258;0.0154)		STAD - Stomach adenocarcinoma(47;0.00527)			TCCTTAAGTTCCTCTCCAAAG	0.453																																					p.N290fs		Atlas-INDEL	.											.	C8orf76	26	.	0			c.868delA						.						86	81	83					8																	124238821		2203	4300	6503	SO:0001589	frameshift_variant	84933	exon5			.	AK027731	CCDS6341.1	8q24.13	2012-06-27			ENSG00000189376	ENSG00000189376			25924	protein-coding gene	gene with protein product							Standard	NM_032847		Approved	FLJ14825	uc003yqc.2	Q96K31	OTTHUMG00000172562	ENST00000276704.4:c.867delG	chr8.hg19:g.124238821delC	ENSP00000276704:p.Arg289fs	67.0	0.0		151.0	88.0	NM_032847	Q53HC1	Frame_Shift_Del	DEL	ENST00000276704.4	hg19	CCDS6341.1																																																																																			.	.		0.453	C8orf76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381748.1	NM_032847		-	124238821	C	-	124238821	7	5	312	1	0	1	0	1	0	0	0	0	2439	854	30	0	283	0	C8orf76	8	124238821	Frame_Shift_Del	DEL	C	TCGA-K7-AAU7-01A-11D-A382-10	85445256	124238821	22125201	29	44338										
MTSS1	9788	hgsc.bcm.edu	37	chr8	125568510	125568510	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	cagtcatgctccgtggtctcTgagcctcctcagctgctgca	10	15	3	1			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr8:125568510T>C	ENST00000518547.1	-	12	1840	c.1367A>G	c.(1366-1368)cAg>cGg	p.Q456R	MTSS1_ENST00000524090.1_Missense_Mutation_p.Q346R|MTSS1_ENST00000378017.3_Missense_Mutation_p.Q431R|MTSS1_ENST00000431961.2_Missense_Mutation_p.Q174R|MTSS1_ENST00000523587.1_5'UTR|MTSS1_ENST00000395508.2_Missense_Mutation_p.Q230R|MTSS1_ENST00000354184.4_Missense_Mutation_p.Q174R|MTSS1_ENST00000325064.5_Missense_Mutation_p.Q460R|NDUFB9_ENST00000522532.1_Intron	NM_001282971.1|NM_014751.4	NP_001269900.1|NP_055566.3	O43312	MTSS1_HUMAN	metastasis suppressor 1	456					actin cytoskeleton organization (GO:0030036)|actin filament polymerization (GO:0030041)|adherens junction maintenance (GO:0034334)|bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|cellular response to fluid shear stress (GO:0071498)|epithelial cell proliferation involved in renal tubule morphogenesis (GO:2001013)|filopodium assembly (GO:0046847)|glomerulus morphogenesis (GO:0072102)|in utero embryonic development (GO:0001701)|magnesium ion homeostasis (GO:0010960)|microspike assembly (GO:0030035)|negative regulation of epithelial cell proliferation (GO:0050680)|nephron tubule epithelial cell differentiation (GO:0072160)|positive regulation of actin filament bundle assembly (GO:0032233)|renal tubule morphogenesis (GO:0061333)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			CCGTGGTCTCTGAGCCTCCTC	0.632																																					p.Q456R	Esophageal Squamous(160;622 1893 3862 8546 12509)	Atlas-SNP	.											.	MTSS1	79	.	0			c.A1367G						.						87	73	78					8																	125568510		2203	4300	6503	SO:0001583	missense	9788	exon12			GGTCTCTGAGCCT	AF086645	CCDS6353.1, CCDS64968.1, CCDS64969.1	8p22	2008-02-05			ENSG00000170873	ENSG00000170873			20443	protein-coding gene	gene with protein product		608486				12482861, 12082544	Standard	XM_005251111		Approved	KIAA0429, MIMA, MIMB, MIM	uc003yrk.2	O43312	OTTHUMG00000048189	ENST00000518547.1:c.1367A>G	chr8.hg19:g.125568510T>C	ENSP00000429064:p.Gln456Arg	73.0	0.0		126.0	21.0	NM_014751	J3KNK6|Q8TCA2|Q96RX2	Missense_Mutation	SNP	ENST00000518547.1	hg19	CCDS6353.1	.	.	.	.	.	.	.	.	.	.	T	13.93	2.385426	0.42308	.	.	ENSG00000170873	ENST00000378017;ENST00000518547;ENST00000354184;ENST00000395508;ENST00000325064;ENST00000431961;ENST00000524090	T;T;T;T;T;T;T	0.32272	1.48;1.47;1.49;1.48;1.47;1.49;1.46	4.65	4.65	0.58169	.	0.333994	0.29172	N	0.012922	T	0.28300	0.0699	L	0.36672	1.1	0.40924	D	0.984332	B;P;B;P;D	0.56968	0.0;0.824;0.0;0.89;0.978	B;B;B;B;P	0.49085	0.001;0.258;0.0;0.245;0.6	T	0.03840	-1.0999	10	0.16896	T	0.51	-16.8762	10.2923	0.43603	0.0:0.0:0.1656:0.8344	.	346;230;456;431;174	E7EWW5;B7Z3B6;O43312;O43312-4;O43312-2	.;.;MTSS1_HUMAN;.;.	R	431;456;174;230;460;174;346	ENSP00000367256:Q431R;ENSP00000429064:Q456R;ENSP00000346119:Q174R;ENSP00000378884:Q230R;ENSP00000322804:Q460R;ENSP00000393606:Q174R;ENSP00000428319:Q346R	ENSP00000322804:Q460R	Q	-	2	0	MTSS1	125637691	1.000000	0.71417	0.996000	0.52242	0.924000	0.55760	5.383000	0.66219	1.733000	0.51620	0.374000	0.22700	CAG	.	.		0.632	MTSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109625.3	NM_014751		C	125568510	T	C	125568510	3	2	312	1	0	0	0	0	1	0	0	0	9971	1580	55	2	912	2	MTSS1	8	125568510	Missense_Mutation	SNP	T	TCGA-K7-AAU7-01A-11D-A382-10	1329689	125568510	20795512	30	44339										
ADCY8	114	hgsc.bcm.edu	37	chr8	132052016	132052016	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	gtgagtttggtcagcacgtcCagcacgttcatcaccacttc	9	13	3	1	rs80098122		TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr8:132052016C>T	ENST00000286355.5	-	1	2656	c.564G>A	c.(562-564)ctG>ctA	p.L188L	ADCY8_ENST00000377928.3_Silent_p.L188L	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	188					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			TCAGCACGTCCAGCACGTTCA	0.582										HNSCC(32;0.087)																											p.L188L		Atlas-SNP	.											.	ADCY8	291	.	0			c.G564A						.						99	100	100					8																	132052016		2203	4300	6503	SO:0001819	synonymous_variant	114	exon1			CACGTCCAGCACG	Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"Adenylate cyclases"	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.564G>A	chr8.hg19:g.132052016C>T		116.0	0.0		182.0	22.0	NM_001115		Silent	SNP	ENST00000286355.5	hg19	CCDS6363.1																																																																																			.	.		0.582	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			T	132052016	C	T	132052016	2	4	312	1	0	0	0	0	0	0	0	1	300	581	21	3		3	ADCY8	8	132052016	Silent	SNP	C	TCGA-K7-AAU7-01A-11D-A382-10	6483506	132052016	14312006	31	44340										
NPR2	4882	hgsc.bcm.edu	37	chr9	35806115	35806115	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	catatttccggccaagcattGaccggacccaactgaatgaa	8	12	0	3			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr9:35806115G>T	ENST00000342694.2	+	15	2512	c.2257G>T	c.(2257-2259)Gac>Tac	p.D753Y		NM_003995.3	NP_003986.2	P20594	ANPRB_HUMAN	natriuretic peptide receptor 2	753	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				bone development (GO:0060348)|cell surface receptor signaling pathway (GO:0007166)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cGMP biosynthetic process (GO:0006182)|intracellular signal transduction (GO:0035556)|negative regulation of meiotic cell cycle (GO:0051447)|negative regulation of oocyte maturation (GO:1900194)|ossification (GO:0001503)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|signal transduction (GO:0007165)|single organism reproductive process (GO:0044702)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(2)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)		Erythrityl Tetranitrate(DB01613)|Nesiritide(DB04899)	GCCAAGCATTGACCGGACCCA	0.512																																					p.D753Y		Atlas-SNP	.											.	NPR2	162	.	0			c.G2257T						.						71	72	71					9																	35806115		2203	4300	6503	SO:0001583	missense	4882	exon15			AGCATTGACCGGA	AJ005282	CCDS6590.1	9p21-p12	2014-03-03	2014-03-03		ENSG00000159899	ENSG00000159899			7944	protein-coding gene	gene with protein product	"guanylate cyclase B"	108961	"acromesomelic dysplasia, Maroteaux type", "atrionatriuretic peptide receptor B", "natriuretic peptide receptor B"	ANPRB, NPRB, AMDM		9634515, 15146390	Standard	XM_005251478		Approved	GUCY2B, ANPb	uc003zyd.3	P20594	OTTHUMG00000019871	ENST00000342694.2:c.2257G>T	chr9.hg19:g.35806115G>T	ENSP00000341083:p.Asp753Tyr	63.0	0.0		49.0	15.0	NM_003995	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	Missense_Mutation	SNP	ENST00000342694.2	hg19	CCDS6590.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.81|19.81	3.897022|3.897022	0.72639|0.72639	.|.	.|.	ENSG00000159899|ENSG00000159899	ENST00000342694;ENST00000447210|ENST00000421267	T;D|.	0.85556|.	0.0;-2.0|.	5.82|5.82	5.82|5.82	0.92795|0.92795	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.46442|.	D|.	0.000291|.	T|T	0.77164|0.77164	0.4090|0.4090	M|M	0.76727|0.76727	2.345|2.345	0.80722|0.80722	D|D	1|1	D;P|.	0.89917|.	1.0;0.804|.	D;P|.	0.72075|.	0.976;0.643|.	T|T	0.76005|0.76005	-0.3117|-0.3117	10|5	0.66056|.	D|.	0.02|.	.|.	18.6867|18.6867	0.91567|0.91567	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	753;753|.	P20594-2;P20594|.	.;ANPRB_HUMAN|.	Y|F	753;12|99	ENSP00000341083:D753Y;ENSP00000393029:D12Y|.	ENSP00000341083:D753Y|.	D|L	+|+	1|3	0|2	NPR2|NPR2	35796115|35796115	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	2.865000|2.865000	0.48412|0.48412	2.756000|2.756000	0.94617|0.94617	0.563000|0.563000	0.77884|0.77884	GAC|TTG	.	.		0.512	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1			T	35806115	G	T	35806115	3	4	312	1	0	0	0	0	1	0	0	0	10604	1290	45	3	2315	3	NPR2	9	35806115	Missense_Mutation	SNP	G	TCGA-K7-AAU7-01A-11D-A382-10		35806115	105407316	32	44341										
FAM108B1	51104	hgsc.bcm.edu	37	chr9	74485146	74485146	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	ctgtccctatactttggccaTatataatcacattttcaggg	6	10	2	0			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr9:74485146T>C	ENST00000333421.6	-	3	611	c.500A>G	c.(499-501)tAt>tGt	p.Y167C	ABHD17B_ENST00000377041.2_Missense_Mutation_p.Y167C	NM_001025780.1	NP_001020951.1	Q5VST6	AB17B_HUMAN	abhydrolase domain containing 17B	167						extracellular region (GO:0005576)|membrane (GO:0016020)	hydrolase activity (GO:0016787)										ACTTTGGCCATATATAATCAC	0.408																																					p.Y167C		Atlas-SNP	.											.	FAM108B1	24	.	0			c.A500G						.						146	139	141					9																	74485146		2203	4300	6503	SO:0001583	missense	51104	exon3			TGGCCATATATAA	AF151825	CCDS35042.1, CCDS35043.1	9q21.2	2013-03-15	2013-03-15	2013-03-15	ENSG00000107362	ENSG00000107362		"Abhydrolase domain containing"	24278	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 77", "family with sequence similarity 108, member B1"	C9orf77, FAM108B1		10810093	Standard	XM_006717134		Approved	CGI-67	uc004ail.3	Q5VST6	OTTHUMG00000020001	ENST00000333421.6:c.500A>G	chr9.hg19:g.74485146T>C	ENSP00000330222:p.Tyr167Cys	97.0	0.0		71.0	19.0	NM_016014	A8KAJ5|Q5VST7|Q86YB6|Q8IY03|Q9Y377	Missense_Mutation	SNP	ENST00000333421.6	hg19	CCDS35043.1	.	.	.	.	.	.	.	.	.	.	T	15.18	2.757528	0.49468	.	.	ENSG00000107362	ENST00000377041;ENST00000333421	T;T	0.44083	0.93;0.93	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.73369	0.3578	M	0.93808	3.46	0.80722	D	1	D;P	0.89917	1.0;0.926	D;P	0.97110	1.0;0.814	T	0.81575	-0.0870	10	0.87932	D	0	-3.7809	15.6113	0.76721	0.0:0.0:0.0:1.0	.	167;167	Q5VST6;Q5VST6-2	F108B_HUMAN;.	C	167	ENSP00000366240:Y167C;ENSP00000330222:Y167C	ENSP00000330222:Y167C	Y	-	2	0	FAM108B1	73674966	1.000000	0.71417	1.000000	0.80357	0.045000	0.14185	7.884000	0.87274	2.151000	0.67156	0.533000	0.62120	TAT	.	.		0.408	ABHD17B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052625.1	NM_016014		C	74485146	T	C	74485146	3	2	312	1	0	0	0	0	1	0	0	0	5397	1406	49	2	405	2	FAM108B1	9	74485146	Missense_Mutation	SNP	T	TCGA-K7-AAU7-01A-11D-A382-10	38679031	74485146	66728285	33	44342										
GAPVD1	26130	hgsc.bcm.edu	37	chr9	128074846	128074846	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	gaggtgttggtcatttccttAggtacaggtccccagcttac	11	10	1	0			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr9:128074846A>G	ENST00000495955.1	+	9	1847	c.1557A>G	c.(1555-1557)ttA>ttG	p.L519L	GAPVD1_ENST00000394105.2_Silent_p.L519L|GAPVD1_ENST00000470056.1_Silent_p.L519L|GAPVD1_ENST00000394083.2_Silent_p.L519L|GAPVD1_ENST00000297933.6_Silent_p.L519L|GAPVD1_ENST00000265956.4_Silent_p.L519L|GAPVD1_ENST00000312123.9_Silent_p.L519L|GAPVD1_ENST00000394104.2_Silent_p.L519L			Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1	519					endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|regulation of protein transport (GO:0051223)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	GTPase activating protein binding (GO:0032794)|GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						TCATTTCCTTAGGTACAGGTC	0.438																																					p.L519L		Atlas-SNP	.											.	GAPVD1	124	.	0			c.A1557G						.						171	143	152					9																	128074846		2203	4300	6503	SO:0001819	synonymous_variant	26130	exon7			TTCCTTAGGTACA		CCDS65130.1, CCDS65131.1, CCDS65132.1	9q34.11	2008-02-05			ENSG00000165219	ENSG00000165219			23375	protein-coding gene	gene with protein product		611714					Standard	XM_005251901		Approved	DKFZP434C212, KIAA1521	uc004bpr.3	Q14C86	OTTHUMG00000020678	ENST00000495955.1:c.1557A>G	chr9.hg19:g.128074846A>G		102.0	0.0		80.0	19.0	NM_015635	A8MYK3|B0QZ62|B0QZ63|B0QZ64|Q14C76|Q2Q1W1|Q8ND92|Q8WU86|Q96CZ4|Q9NXQ1|Q9P207|Q9Y4N0	Silent	SNP	ENST00000495955.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.885|9.885	1.202557|1.202557	0.22121|0.22121	.|.	.|.	ENSG00000165219|ENSG00000165219	ENST00000436712|ENST00000431329	.|.	.|.	.|.	5.8|5.8	4.67|4.67	0.58626|0.58626	.|.	.|.	.|.	.|.	.|.	T|.	0.55737|.	0.1939|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.54649|.	-0.8262|.	4|.	.|.	.|.	.|.	.|.	6.0598|6.0598	0.19832|0.19832	0.839:0.0:0.161:0.0|0.839:0.0:0.161:0.0	.|.	.|.	.|.	.|.	G|W	377|382	.|.	.|.	R|X	+|+	1|2	2|0	GAPVD1|GAPVD1	127114667|127114667	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	2.793000|2.793000	0.47845|0.47845	2.216000|2.216000	0.71823|0.71823	0.402000|0.402000	0.26972|0.26972	AGG|TAG	.	.		0.438	GAPVD1-014	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000355644.1			G	128074846	A	G	128074846	2	3	312	1	0	0	0	0	0	0	0	1	6247	417	15	2		2	GAPVD1	9	128074846	Silent	SNP	A	TCGA-K7-AAU7-01A-11D-A382-10	53589700	128074846	13138585	34	44343										
FBXO18	84893	hgsc.bcm.edu	37	chr10	5952981	5952981	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	atccagcgactgctcttctgCctccggagacccagctccac	8	18	2	1			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr10:5952981C>T	ENST00000362091.4	+	6	1216	c.1101C>T	c.(1099-1101)tgC>tgT	p.C367C	FBXO18_ENST00000379999.5_Silent_p.C418C|FBXO18_ENST00000397269.3_5'UTR	NM_001258453.1|NM_178150.2	NP_001245382.1|NP_835363.1	Q8NFZ0	FBX18_HUMAN	F-box protein, helicase, 18	367					DNA catabolic process, endonucleolytic (GO:0000737)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|positive regulation of protein phosphorylation (GO:0001934)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)			NS(2)|breast(2)|kidney(2)|large_intestine(16)|lung(9)|ovary(2)|prostate(3)|skin(3)|stomach(1)	40						TGCTCTTCTGCCTCCGGAGAC	0.597																																					p.C418C		Atlas-SNP	.											.	FBXO18	108	.	0			c.C1254T						.						104	94	97					10																	5952981		2203	4300	6503	SO:0001819	synonymous_variant	84893	exon7			CTTCTGCCTCCGG	AK095343	CCDS7072.1, CCDS7073.1, CCDS73064.1	10p15.1	2004-08-24	2004-06-15		ENSG00000134452	ENSG00000134452		"F-boxes /  "other""	13620	protein-coding gene	gene with protein product		607222	"F-box only protein 18"			10531037, 11956208	Standard	NM_032807		Approved	FBH1, FLJ14590, Fbx18	uc001iit.4	Q8NFZ0	OTTHUMG00000017609	ENST00000362091.4:c.1101C>T	chr10.hg19:g.5952981C>T		46.0	0.0		39.0	11.0	NM_032807	Q5JVB0|Q5JVB1|Q7Z4Q6|Q7Z4R0|Q8N1P5|Q8N586|Q96E82|Q96K67|Q96SW7|Q9UFB2	Silent	SNP	ENST00000362091.4	hg19	CCDS7072.1																																																																																			.	.		0.597	FBXO18-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046596.1	NM_032807		T	5952981	C	T	5952981	2	4	312	1	0	0	0	0	0	0	0	1	5739	747	26	3		3	FBXO18	10	5952981	Silent	SNP	C	TCGA-K7-AAU7-01A-11D-A382-10		5952981	129581766	35	44344										
SGPL1	8879	hgsc.bcm.edu	37	chr10	72636985	72636985	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	gcatggcccagacaactgttGacaggaatatggttgcagaa	12	8	0	3			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr10:72636985G>A	ENST00000373202.3	+	15	1800	c.1600G>A	c.(1600-1602)Gac>Aac	p.D534N		NM_003901.3	NP_003892.2	O95470	SGPL1_HUMAN	sphingosine-1-phosphate lyase 1	534					androgen metabolic process (GO:0008209)|apoptotic signaling pathway (GO:0097190)|ceramide metabolic process (GO:0006672)|estrogen metabolic process (GO:0008210)|face morphogenesis (GO:0060325)|fatty acid metabolic process (GO:0006631)|fibroblast migration (GO:0010761)|hemopoiesis (GO:0030097)|kidney development (GO:0001822)|Leydig cell differentiation (GO:0033327)|luteinization (GO:0001553)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic development (GO:0009791)|regulation of multicellular organism growth (GO:0040014)|skeletal system morphogenesis (GO:0048705)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid catabolic process (GO:0030149)|sphingolipid metabolic process (GO:0006665)|vasculogenesis (GO:0001570)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)|sphinganine-1-phosphate aldolase activity (GO:0008117)			large_intestine(4)	4						GACAACTGTTGACAGGAATAT	0.473																																					p.D534N	Colon(151;1054 2458 6676 40971)	Atlas-SNP	.											.	SGPL1	37	.	0			c.G1600A						.						116	102	107					10																	72636985		2203	4300	6503	SO:0001583	missense	8879	exon15			ACTGTTGACAGGA	AI128825	CCDS31216.1	10q21	2008-08-01			ENSG00000166224	ENSG00000166224			10817	protein-coding gene	gene with protein product		603729				9464245, 17090686	Standard	NM_003901		Approved	SPL	uc001jrm.3	O95470	OTTHUMG00000018421	ENST00000373202.3:c.1600G>A	chr10.hg19:g.72636985G>A	ENSP00000362298:p.Asp534Asn	82.0	0.0		59.0	21.0	NM_003901	B2RBD4|Q7Z732|Q9ULG8|Q9UN89	Missense_Mutation	SNP	ENST00000373202.3	hg19	CCDS31216.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.248405	0.80024	.	.	ENSG00000166224	ENST00000373202	T	0.49139	0.79	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.65091	0.2658	L	0.52011	1.625	0.80722	D	1	D	0.69078	0.997	D	0.70016	0.967	T	0.62671	-0.6805	10	0.49607	T	0.09	-28.5977	19.9035	0.96999	0.0:0.0:1.0:0.0	.	534	O95470	SGPL1_HUMAN	N	534	ENSP00000362298:D534N	ENSP00000362298:D534N	D	+	1	0	SGPL1	72306991	1.000000	0.71417	0.962000	0.40283	0.121000	0.20230	9.434000	0.97515	2.712000	0.92718	0.650000	0.86243	GAC	.	.		0.473	SGPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048533.1	NM_003901		A	72636985	G	A	72636985	3	1	312	1	0	0	0	0	1	0	0	0	14233	1290	45	3	1654	3	SGPL1	10	72636985	Missense_Mutation	SNP	G	TCGA-K7-AAU7-01A-11D-A382-10	66684004	72636985	62897762	36	44345										
TNKS2	80351	hgsc.bcm.edu	37	chr10	93579739	93579739	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	aggatataacagagtaaagaTtgtacagctgttactgcaac	9	6	0	2			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr10:93579739T>C	ENST00000371627.4	+	6	1056	c.677T>C	c.(676-678)aTt>aCt	p.I226T		NM_025235.3	NP_079511.1	Q9H2K2	TNKS2_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2	226					multicellular organism growth (GO:0035264)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein polyubiquitination (GO:0000209)|regulation of multicellular organism growth (GO:0040014)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			biliary_tract(1)|breast(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	48		Colorectal(252;0.162)				AGAGTAAAGATTGTACAGCTG	0.313																																					p.I226T		Atlas-SNP	.											.	TNKS2	103	.	0			c.T677C						.						116	121	119					10																	93579739		2203	4300	6503	SO:0001583	missense	80351	exon6			TAAAGATTGTACA	AF342982	CCDS7417.1	10q23.3	2013-01-10			ENSG00000107854	ENSG00000107854		"Poly (ADP-ribose) polymerases", "Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	15677	protein-coding gene	gene with protein product		607128					Standard	NM_025235		Approved	TNKL, TANK2, PARP-5b, PARP-5c, PARP5B, PARP5C, pART6	uc001khp.3	Q9H2K2	OTTHUMG00000018747	ENST00000371627.4:c.677T>C	chr10.hg19:g.93579739T>C	ENSP00000360689:p.Ile226Thr	381.0	0.0		365.0	93.0	NM_025235	B2RBD3|Q9H8F2|Q9HAS4	Missense_Mutation	SNP	ENST00000371627.4	hg19	CCDS7417.1	.	.	.	.	.	.	.	.	.	.	T	15.80	2.940586	0.52972	.	.	ENSG00000107854	ENST00000371627	T	0.67171	-0.25	5.46	5.46	0.80206	Ankyrin repeat-containing domain (4);	0.178092	0.35179	N	0.003392	T	0.62889	0.2465	L	0.45051	1.395	0.58432	D	0.999999	B	0.13594	0.008	B	0.28305	0.088	T	0.59547	-0.7434	10	0.42905	T	0.14	.	15.5302	0.75952	0.0:0.0:0.0:1.0	.	226	Q9H2K2	TNKS2_HUMAN	T	226	ENSP00000360689:I226T	ENSP00000360689:I226T	I	+	2	0	TNKS2	93569719	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.199000	0.72112	2.070000	0.61991	0.455000	0.32223	ATT	.	.		0.313	TNKS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049374.1	NM_025235		C	93579739	T	C	93579739	3	2	312	1	0	0	0	0	1	0	0	0	16336	1493	52	2	699	2	TNKS2	10	93579739	Missense_Mutation	SNP	T	TCGA-K7-AAU7-01A-11D-A382-10	20942754	93579739	41955008	37	44346										
PDZD8	118987	hgsc.bcm.edu	37	chr10	119044292	119044292	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	ccacttcttgctttgctaaaAattgcttaggtgcagctgca	8	10	1	0			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr10:119044292A>C	ENST00000334464.5	-	5	2191	c.1952T>G	c.(1951-1953)tTt>tGt	p.F651C	PDZD8_ENST00000482496.1_5'UTR	NM_173791.3	NP_776152.1	Q8NEN9	PDZD8_HUMAN	PDZ domain containing 8	651					cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|regulation of cell morphogenesis (GO:0022604)|viral process (GO:0016032)	membrane (GO:0016020)	metal ion binding (GO:0046872)			kidney(3)|large_intestine(8)|lung(24)|upper_aerodigestive_tract(3)	38		Colorectal(252;0.19)		all cancers(201;0.0121)		CTTTGCTAAAAATTGCTTAGG	0.448																																					p.F651C		Atlas-SNP	.											.	PDZD8	85	.	0			c.T1952G						.						80	80	80					10																	119044292		2203	4300	6503	SO:0001583	missense	118987	exon5			GCTAAAAATTGCT	AL122051	CCDS7600.1	10q26.12	2006-01-24		2006-01-24	ENSG00000165650	ENSG00000165650			26974	protein-coding gene	gene with protein product		614235		PDZK8		12477932	Standard	NM_173791		Approved	bA129M16.2, FLJ34427	uc001lde.1	Q8NEN9	OTTHUMG00000019122	ENST00000334464.5:c.1952T>G	chr10.hg19:g.119044292A>C	ENSP00000334642:p.Phe651Cys	109.0	0.0		86.0	26.0	NM_173791	Q86WE0|Q86WE5|Q9UFF1	Missense_Mutation	SNP	ENST00000334464.5	hg19	CCDS7600.1	.	.	.	.	.	.	.	.	.	.	A	11.13	1.547795	0.27652	.	.	ENSG00000165650	ENST00000334464	D	0.85339	-1.97	5.61	-1.25	0.09405	.	1.196990	0.05874	N	0.625197	T	0.72391	0.3454	N	0.14661	0.345	0.09310	N	1	B	0.30709	0.291	B	0.31191	0.125	T	0.60692	-0.7213	10	0.40728	T	0.16	0.149	7.6998	0.28617	0.3852:0.1342:0.4806:0.0	.	651	Q8NEN9	PDZD8_HUMAN	C	651	ENSP00000334642:F651C	ENSP00000334642:F651C	F	-	2	0	PDZD8	119034282	0.000000	0.05858	0.000000	0.03702	0.154000	0.21943	0.025000	0.13577	-0.063000	0.13065	0.482000	0.46254	TTT	.	.		0.448	PDZD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050565.1	NM_173791		C	119044292	A	C	119044292	3	2	312	1	0	0	0	0	1	0	0	0	11714	14	1	5	1516	5	PDZD8	10	119044292	Missense_Mutation	SNP	A	TCGA-K7-AAU7-01A-11D-A382-10	25464553	119044292	16490455	38	44347										
NAT10	55226	hgsc.bcm.edu	37	chr11	34135326	34135326	+	Frame_Shift_Del	DEL	C	C	-													0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	aaacagtggaaggtggtgggCtagtggtcatcctcctacgg							TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr11:34135326delC	ENST00000257829.3	+	5	642	c.436delC	c.(436-438)ctafs	p.L146fs	NAT10_ENST00000531159.2_Frame_Shift_Del_p.L74fs|NAT10_ENST00000527971.1_Frame_Shift_Del_p.L146fs	NM_024662.2	NP_078938	Q9H0A0	NAT10_HUMAN	N-acetyltransferase 10 (GCN5-related)	146						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|N-acetyltransferase activity (GO:0008080)|poly(A) RNA binding (GO:0044822)			endometrium(4)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	23		Acute lymphoblastic leukemia(5;0.0119)|all_hematologic(20;0.0231)				AGGTGGTGGGCTAGTGGTCAT	0.463																																					p.G145fs		Atlas-INDEL	.											.	NAT10	78	.	0			c.435delG						.						139	123	128					11																	34135326		2202	4298	6500	SO:0001589	frameshift_variant	55226	exon5			.	AF489535	CCDS7889.1, CCDS44568.1	11p13	2011-11-16	2008-09-24		ENSG00000135372	ENSG00000135372	2.3.1.-		29830	protein-coding gene	gene with protein product		609221	"N-acetyltransferase 10"			14592445, 21177859	Standard	NM_024662		Approved	hALP, FLJ10774, FLJ12179, NET43, KIAA1709	uc001mvk.3	Q9H0A0	OTTHUMG00000166249	ENST00000257829.3:c.436delC	chr11.hg19:g.34135326delC	ENSP00000257829:p.Leu146fs	143.0	0.0		128.0	39.0	NM_024662	B4DFD5|E7ESU4|E9PMN9|Q86WK5|Q9C0F4|Q9HA61|Q9NVF2	Frame_Shift_Del	DEL	ENST00000257829.3	hg19	CCDS7889.1																																																																																			.	.		0.463	NAT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388693.1	NM_024662		-	34135326	C	-	34135326	7	5	312	1	0	1	0	1	0	0	0	0	10183	796	28	0	450	0	NAT10	11	34135326	Frame_Shift_Del	DEL	C	TCGA-K7-AAU7-01A-11D-A382-10		34135326	100871190	39	44348										
OR5L1	219437	hgsc.bcm.edu	37	chr11	55579074	55579074	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	acgttgttagccaacctgggCatgattgcactgattcaggt	11	9	1	2			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr11:55579074C>A	ENST00000333973.2	+	1	221	c.132C>A	c.(130-132)ggC>ggA	p.G44G		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, member 1	44						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(4)|liver(4)|lung(36)|ovary(2)|pancreas(1)|prostate(5)|skin(9)|stomach(4)|upper_aerodigestive_tract(3)	78		all_epithelial(135;0.208)				CCAACCTGGGCATGATTGCAC	0.483																																					p.G44G		Atlas-SNP	.											.	OR5L1	145	.	0			c.C132A						.						328	286	300					11																	55579074		2200	4296	6496	SO:0001819	synonymous_variant	219437	exon1			CCTGGGCATGATT	AB065780	CCDS31509.1	11q11	2012-08-09			ENSG00000186117	ENSG00000186117		"GPCR / Class A : Olfactory receptors"	8350	protein-coding gene	gene with protein product							Standard	NM_001004738		Approved	OST262	uc001nhw.1	Q8NGL2	OTTHUMG00000166810	ENST00000333973.2:c.132C>A	chr11.hg19:g.55579074C>A		61.0	0.0		78.0	17.0	NM_001004738	B2RNK6|Q6IFD0	Silent	SNP	ENST00000333973.2	hg19	CCDS31509.1																																																																																			.	.		0.483	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738		A	55579074	C	A	55579074	2	1	312	1	0	0	0	0	0	0	0	1	11179	697	25	3		3	OR5L1	11	55579074	Silent	SNP	C	TCGA-K7-AAU7-01A-11D-A382-10	21443748	55579074	79427442	40	44349										
LTBP3	4054	hgsc.bcm.edu	37	chr11	65314273	65314273	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	cgggccccgccctcaccgcgAcaggccccgcccccctggct	11	24	1	0			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr11:65314273A>C	ENST00000301873.5	-	15	2494	c.2226T>G	c.(2224-2226)tgT>tgG	p.C742W	LTBP3_ENST00000529189.1_5'Flank|LTBP3_ENST00000536982.1_Missense_Mutation_p.C368W|LTBP3_ENST00000322147.4_Missense_Mutation_p.C742W|LTBP3_ENST00000530785.1_5'Flank|LTBP3_ENST00000532932.1_Missense_Mutation_p.C172W	NM_001130144.2	NP_001123616.1	Q9NS15	LTBP3_HUMAN	latent transforming growth factor beta binding protein 3	742	Cys-rich.				bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|extracellular matrix organization (GO:0030198)|lung saccule development (GO:0060430)|negative regulation of bone mineralization (GO:0030502)|negative regulation of chondrocyte differentiation (GO:0032331)|positive regulation of bone resorption (GO:0045780)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of mesenchymal stem cell proliferation (GO:1902462)|transforming growth factor beta activation (GO:0036363)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|prostate(2)|upper_aerodigestive_tract(3)	23						CCTCACCGCGACAGGCCCCGC	0.716																																					p.C742W		Atlas-SNP	.											LTBP3,NS,carcinoma,0,1	LTBP3	55	.	0			c.T2226G						.						18	22	21					11																	65314273		2188	4279	6467	SO:0001583	missense	4054	exon15			ACCGCGACAGGCC	AF135960	CCDS8103.1, CCDS44647.1	11q12	2011-10-20			ENSG00000168056	ENSG00000168056		"Latent transforming growth factor, beta binding proteins"	6716	protein-coding gene	gene with protein product		602090		LTBP2		7719025	Standard	NM_001164266		Approved		uc001oej.3	Q9NS15	OTTHUMG00000166575	ENST00000301873.5:c.2226T>G	chr11.hg19:g.65314273A>C	ENSP00000301873:p.Cys742Trp	15.0	0.0		18.0	6.0	NM_001130144	O15107|Q96HB9|Q9H7K2|Q9UFN4	Missense_Mutation	SNP	ENST00000301873.5	hg19	CCDS44647.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.50|19.50	3.838964|3.838964	0.71373|0.71373	.|.	.|.	ENSG00000168056|ENSG00000168056	ENST00000322147;ENST00000301873;ENST00000532932;ENST00000536982;ENST00000530866;ENST00000527339|ENST00000526927	D;D;D;D;D;D|.	0.99445|.	-5.91;-5.91;-5.91;-5.91;-5.91;-5.91|.	4.85|4.85	-2.96|-2.96	0.05547|0.05547	EGF-like calcium-binding (2);|.	0.701264|.	0.15043|.	N|.	0.283773|.	T|T	0.69360|0.69360	0.3102|0.3102	M|M	0.86864|0.86864	2.845|2.845	0.80722|0.80722	D|D	1|1	P;D;D;D;D;D|.	0.65815|.	0.93;0.995;0.968;0.957;0.989;0.973|.	P;P;P;P;P;P|.	0.62491|.	0.547;0.844;0.794;0.601;0.878;0.903|.	T|T	0.68112|0.68112	-0.5495|-0.5495	10|5	0.72032|.	D|.	0.01|.	.|.	4.9009|4.9009	0.13773|0.13773	0.4993:0.0:0.3576:0.1431|0.4993:0.0:0.3576:0.1431	.|.	653;368;625;742;742;172|.	E9PKW1;F5GWC4;B9EG76;Q9NS15;Q9NS15-2;E9PJR2|.	.;.;.;LTBP3_HUMAN;.;.|.	W|A	742;742;172;368;653;82|393	ENSP00000326647:C742W;ENSP00000301873:C742W;ENSP00000435530:C172W;ENSP00000441912:C368W;ENSP00000435276:C653W;ENSP00000432121:C82W|.	ENSP00000301873:C742W|.	C|S	-|-	3|1	2|0	LTBP3|LTBP3	65070849|65070849	0.989000|0.989000	0.36119|0.36119	0.985000|0.985000	0.45067|0.45067	0.918000|0.918000	0.54935|0.54935	0.252000|0.252000	0.18278|0.18278	-0.476000|-0.476000	0.06842|0.06842	-0.486000|-0.486000	0.04755|0.04755	TGT|TCG	.	.		0.716	LTBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390538.1	NM_021070		C	65314273	A	C	65314273	3	2	312	1	0	0	0	0	1	0	0	0	9084	273	10	5	1741	5	LTBP3	11	65314273	Missense_Mutation	SNP	A	TCGA-K7-AAU7-01A-11D-A382-10	9735199	65314273	69692243	41	44350										
HTR3B	9177	hgsc.bcm.edu	37	chr11	113775680	113775680	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	tgtcaagtgtaatggctcccCtgtgggcctgcatcctggtg	13	11	1	0			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr11:113775680C>T	ENST00000260191.2	+	1	282	c.25C>T	c.(25-27)Ctg>Ttg	p.L9L		NM_006028.4	NP_006019.1	O95264	5HT3B_HUMAN	5-hydroxytryptamine (serotonin) receptor 3B, ionotropic	9					cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ion channel activity (GO:0005216)|serotonin receptor activity (GO:0004993)|serotonin-activated cation-selective channel activity (GO:0005232)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(11)	20		all_cancers(61;6.81e-18)|all_epithelial(67;6.67e-11)|all_hematologic(158;4.67e-05)|Melanoma(852;0.000316)|Acute lymphoblastic leukemia(157;0.000976)|Breast(348;0.0101)|Prostate(24;0.0154)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.04e-06)|Epithelial(105;1.98e-05)|all cancers(92;0.000201)|OV - Ovarian serous cystadenocarcinoma(223;0.151)	Ergoloid mesylate(DB01049)	AATGGCTCCCCTGTGGGCCTG	0.438																																					p.L9L		Atlas-SNP	.											.	HTR3B	50	.	0			c.C25T						.						118	105	110					11																	113775680		2201	4296	6497	SO:0001819	synonymous_variant	9177	exon1			GCTCCCCTGTGGG	AF080582	CCDS8364.1	11q23.1	2012-05-22	2012-02-03		ENSG00000149305	ENSG00000149305		"5-HT (serotonin) receptors", "Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"	5298	protein-coding gene	gene with protein product		604654	"5-hydroxytryptamine (serotonin) receptor 3B"			9950429, 10521471	Standard	NM_006028		Approved	5-HT3B	uc001pok.3	O95264	OTTHUMG00000168210	ENST00000260191.2:c.25C>T	chr11.hg19:g.113775680C>T		73.0	0.0		60.0	16.0	NM_006028	B0YJ23|Q0VJC3	Silent	SNP	ENST00000260191.2	hg19	CCDS8364.1																																																																																			.	.		0.438	HTR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398842.1	NM_006028		T	113775680	C	T	113775680	2	4	312	1	0	0	0	0	0	0	0	1	7454	680	24	3		3	HTR3B	11	113775680	Silent	SNP	C	TCGA-K7-AAU7-01A-11D-A382-10	48461407	113775680	21230836	42	44351										
ARNTL2	56938	hgsc.bcm.edu	37	chr12	27521282	27521282	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	aagaccaacagctatggggtCtttcagctcacacatgacag	9	11	3	2			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr12:27521282C>G	ENST00000266503.5	+	2	137	c.119C>G	c.(118-120)tCt>tGt	p.S40C	ARNTL2_ENST00000261178.5_Missense_Mutation_p.S40C|ARNTL2_ENST00000395901.2_Missense_Mutation_p.S51C|ARNTL2_ENST00000544915.1_Missense_Mutation_p.S40C|ARNTL2_ENST00000311001.5_Missense_Mutation_p.S40C|ARNTL2_ENST00000539558.1_3'UTR|ARNTL2_ENST00000542388.1_Missense_Mutation_p.S3C|ARNTL2_ENST00000546179.1_Missense_Mutation_p.S51C			Q8WYA1	BMAL2_HUMAN	aryl hydrocarbon receptor nuclear translocator-like 2	40					circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	E-box binding (GO:0070888)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(1)|skin(2)|urinary_tract(1)	21	Colorectal(261;0.0847)|Lung SC(9;0.184)					GCTATGGGGTCTTTCAGCTCA	0.498																																					p.S51C		Atlas-SNP	.											.	ARNTL2	54	.	0			c.C152G						.						139	115	123					12																	27521282		2203	4300	6503	SO:0001583	missense	56938	exon2			TGGGGTCTTTCAG	AF246961	CCDS8712.1, CCDS58219.1, CCDS58220.1, CCDS58221.1, CCDS58222.1	12p12.2-p11.2	2013-05-21			ENSG00000029153	ENSG00000029153		"Basic helix-loop-helix proteins"	18984	protein-coding gene	gene with protein product		614517				10864977, 10964693	Standard	NM_020183		Approved	BMAL2, MOP9, CLIF, PASD9, bHLHe6	uc001rht.2	Q8WYA1	OTTHUMG00000169257	ENST00000266503.5:c.119C>G	chr12.hg19:g.27521282C>G	ENSP00000266503:p.Ser40Cys	125.0	0.0		663.0	549.0	NM_001248003	B7Z429|F5H402|Q8WYA2|Q8WYA3|Q8WYA4|Q96J63|Q9H2M4|Q9NS70|Q9NYQ4|Q9NYQ5	Missense_Mutation	SNP	ENST00000266503.5	hg19	CCDS8712.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.66|13.66	2.303931|2.303931	0.40795|0.40795	.|.	.|.	ENSG00000029153|ENSG00000029153	ENST00000457040|ENST00000544915;ENST00000395901;ENST00000546179;ENST00000311001;ENST00000261178;ENST00000266503;ENST00000542388	.|T;T;T;T;T;T;T	.|0.10960	.|3.13;3.21;3.06;3.21;3.19;2.82;3.21	3.39|3.39	2.47|2.47	0.30058|0.30058	.|.	.|1.073310	.|0.07291	.|N	.|0.872413	T|T	0.20455|0.20455	0.0492|0.0492	N|N	0.24115|0.24115	0.695|0.695	0.09310|0.09310	N|N	1|1	.|D;D;D;D;D;D	.|0.89917	.|1.0;0.999;0.998;0.998;0.995;1.0	.|D;D;D;D;P;D	.|0.76071	.|0.987;0.959;0.967;0.967;0.847;0.968	T|T	0.39502|0.39502	-0.9611|-0.9611	5|10	.|0.72032	.|D	.|0.01	.|.	10.4321|10.4321	0.44413|0.44413	0.0:0.7997:0.2003:0.0|0.0:0.7997:0.2003:0.0	.|.	.|51;40;51;40;40;40	.|F5H402;Q8WYA1-5;Q8WYA1-3;Q8WYA1-4;Q8WYA1-2;Q8WYA1	.|.;.;.;.;.;BMAL2_HUMAN	V|C	19|40;51;51;40;40;40;3	.|ENSP00000442438:S40C;ENSP00000379238:S51C;ENSP00000438545:S51C;ENSP00000312247:S40C;ENSP00000261178:S40C;ENSP00000266503:S40C;ENSP00000445836:S3C	.|ENSP00000261178:S40C	L|S	+|+	1|2	0|0	ARNTL2|ARNTL2	27412549|27412549	0.002000|0.002000	0.14202|0.14202	0.184000|0.184000	0.23157|0.23157	0.105000|0.105000	0.19272|0.19272	0.813000|0.813000	0.27225|0.27225	0.981000|0.981000	0.38548|0.38548	-0.479000|-0.479000	0.04858|0.04858	CTT|TCT	.	.		0.498	ARNTL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403162.1	NM_020183		G	27521282	C	G	27521282	3	3	312	1	0	0	0	0	1	0	0	0	968	913	32	4	125	4	ARNTL2	12	27521282	Missense_Mutation	SNP	C	TCGA-K7-AAU7-01A-11D-A382-10		27521282	106330613	43	44352										
C12orf35	55196	hgsc.bcm.edu	37	chr12	32138704	32138704	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	aaattagaaagttcacccagGaagcttcataaagataagag	8	6	2	3			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr12:32138704G>A	ENST00000312561.4	+	4	5229	c.4815G>A	c.(4813-4815)agG>agA	p.R1605R	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	1605																	GTTCACCCAGGAAGCTTCATA	0.343																																					p.R1605R		Atlas-SNP	.											.	.	.	.	0			c.G4815A						.						63	69	67					12																	32138704		2203	4300	6503	SO:0001819	synonymous_variant	55196	exon4			ACCCAGGAAGCTT	AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 35"	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.4815G>A	chr12.hg19:g.32138704G>A		327.0	1.0		1406.0	1059.0	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Silent	SNP	ENST00000312561.4	hg19	CCDS8725.2																																																																																			.	.		0.343	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169		A	32138704	G	A	32138704	2	1	312	1	0	0	0	0	0	0	0	1	1684	1165	41	3		3	C12orf35	12	32138704	Silent	SNP	G	TCGA-K7-AAU7-01A-11D-A382-10	4617422	32138704	101713191	44	44353										
ACSS3	79611	hgsc.bcm.edu	37	chr12	81503455	81503455	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	tgttacaaacactaaagcaaCctttacctataaagaagttc	4	9	0	1			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr12:81503455C>T	ENST00000548058.1	+	2	1338	c.428C>T	c.(427-429)aCc>aTc	p.T143I	ACSS3_ENST00000261206.3_Missense_Mutation_p.T142I|RP11-543H12.1_ENST00000547123.1_RNA			Q9H6R3	ACSS3_HUMAN	acyl-CoA synthetase short-chain family member 3	143						mitochondrion (GO:0005739)	acetate-CoA ligase activity (GO:0003987)|ATP binding (GO:0005524)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(7)|liver(3)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)	51						ACTAAAGCAACCTTTACCTAT	0.299																																					p.T143I		Atlas-SNP	.											ACSS3,NS,malignant_melanoma,0,1	ACSS3	118	.	0			c.C428T						.						95	94	94					12																	81503455		2203	4300	6503	SO:0001583	missense	79611	exon2			AAGCAACCTTTAC		CCDS9022.1	12q21.31	2014-08-08			ENSG00000111058	ENSG00000111058		"Acyl-CoA synthetase family"	24723	protein-coding gene	gene with protein product		614356				17762044	Standard	NM_024560		Approved	FLJ21963	uc001szl.1	Q9H6R3	OTTHUMG00000170179	ENST00000548058.1:c.428C>T	chr12.hg19:g.81503455C>T	ENSP00000449535:p.Thr143Ile	214.0	1.0		303.0	111.0	NM_024560	Q8NC66	Missense_Mutation	SNP	ENST00000548058.1	hg19	CCDS9022.1	.	.	.	.	.	.	.	.	.	.	C	12.47	1.948545	0.34377	.	.	ENSG00000111058	ENST00000549175;ENST00000548058;ENST00000261206	T;T;T	0.45276	0.9;0.9;0.9	6.07	3.1	0.35709	.	0.571636	0.19562	N	0.111320	T	0.32823	0.0842	L	0.45470	1.425	0.45452	D	0.998423	B	0.02656	0.0	B	0.01281	0.0	T	0.12268	-1.0554	10	0.44086	T	0.13	-5.1204	6.9619	0.24601	0.131:0.6726:0.1265:0.0699	.	143	Q9H6R3	ACSS3_HUMAN	I	35;143;142	ENSP00000447748:T35I;ENSP00000449535:T143I;ENSP00000261206:T142I	ENSP00000261206:T142I	T	+	2	0	ACSS3	80027586	0.993000	0.37304	0.993000	0.49108	0.969000	0.65631	1.781000	0.38644	0.874000	0.35823	0.655000	0.94253	ACC	.	.		0.299	ACSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407794.1	NM_024560		T	81503455	C	T	81503455	3	4	312	1	0	0	0	0	1	0	0	0	190	507	18	3	434	3	ACSS3	12	81503455	Missense_Mutation	SNP	C	TCGA-K7-AAU7-01A-11D-A382-10	49364751	81503455	52348440	45	44354										
SLC6A15	55117	hgsc.bcm.edu	37	chr12	85285776	85285776	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	atctttctcttcctggccatCaacaattagttcacttgtct	4	12	5	0			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr12:85285776C>T	ENST00000266682.5	-	2	665	c.124G>A	c.(124-126)Gat>Aat	p.D42N	SLC6A15_ENST00000450363.3_Missense_Mutation_p.D42N|SLC6A15_ENST00000551388.1_Intron|SLC6A15_ENST00000552192.1_Intron	NM_182767.5	NP_877499.1	Q9H2J7	S6A15_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 15	42					amino acid transport (GO:0006865)|ion transport (GO:0006811)|leucine transport (GO:0015820)|neurotransmitter transport (GO:0006836)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)|proline:sodium symporter activity (GO:0005298)			kidney(1)|large_intestine(18)|lung(15)|ovary(1)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	44						TCCTGGCCATCAACAATTAGT	0.393																																					p.D42N		Atlas-SNP	.											.	SLC6A15	159	.	0			c.G124A						.						235	214	221					12																	85285776		2203	4300	6503	SO:0001583	missense	55117	exon2			GGCCATCAACAAT	AF265577	CCDS9026.1, CCDS9027.1, CCDS53816.1	12q21.31	2013-07-15	2008-09-02		ENSG00000072041	ENSG00000072041		"Solute carriers"	13621	protein-coding gene	gene with protein product	"homolog of rat orphan transporter v7-3", "sodium/chloride dependent neurotransmitter transporter Homo sapiens orphan neurotransmitter transporter NTT7"	607971	"solute carrier family 6 (neurotransmitter transporter), member 15"			10471414, 11112352, 16185194	Standard	NM_182767		Approved	hv7-3, NTT73, FLJ10316, V7-3, SBAT1	uc001szv.4	Q9H2J7	OTTHUMG00000169742	ENST00000266682.5:c.124G>A	chr12.hg19:g.85285776C>T	ENSP00000266682:p.Asp42Asn	100.0	0.0		115.0	42.0	NM_018057	A8K592|B7Z2P7|E7ESJ5|Q9H9F5	Missense_Mutation	SNP	ENST00000266682.5	hg19	CCDS9026.1	.	.	.	.	.	.	.	.	.	.	C	8.929	0.962924	0.18583	.	.	ENSG00000072041	ENST00000266682;ENST00000450363;ENST00000549540	T;T;T	0.73363	-0.74;-0.42;0.86	5.44	5.44	0.79542	.	0.312106	0.38548	N	0.001651	T	0.66867	0.2833	L	0.57536	1.79	0.30931	N	0.726914	B;B	0.06786	0.001;0.0	B;B	0.06405	0.001;0.002	T	0.60167	-0.7316	10	0.17369	T	0.5	.	10.1725	0.42920	0.0:0.8513:0.0:0.1487	.	42;42	Q9H9F5;Q9H2J7	.;S6A15_HUMAN	N	42	ENSP00000266682:D42N;ENSP00000390706:D42N;ENSP00000448308:D42N	ENSP00000266682:D42N	D	-	1	0	SLC6A15	83809907	0.985000	0.35326	0.996000	0.52242	0.285000	0.27093	1.482000	0.35486	2.702000	0.92279	0.591000	0.81541	GAT	.	.		0.393	SLC6A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405678.1	NM_018057, NM_182767		T	85285776	C	T	85285776	3	4	312	1	0	0	0	0	1	0	0	0	14693	826	29	3	2226	3	SLC6A15	12	85285776	Missense_Mutation	SNP	C	TCGA-K7-AAU7-01A-11D-A382-10	3782321	85285776	48566119	46	44355										
TMEM132B	114795	hgsc.bcm.edu	37	chr12	125834194	125834194	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	cgagccaggacaccccctatTatcaatgccagctatggccc	8	16	1	0			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr12:125834194T>C	ENST00000299308.3	+	2	257	c.249T>C	c.(247-249)atT>atC	p.I83I	TMEM132B_ENST00000418253.2_3'UTR	NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	83						integral component of membrane (GO:0016021)		p.I83I(1)		NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		CACCCCCTATTATCAATGCCA	0.498																																					p.I83I		Atlas-SNP	.											TMEM132B,NS,carcinoma,0,1	TMEM132B	207	.	1	Substitution - coding silent(1)	kidney(1)	c.T249C						.						106	105	105					12																	125834194		1868	4104	5972	SO:0001819	synonymous_variant	114795	exon2			CCCTATTATCAAT	AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.249T>C	chr12.hg19:g.125834194T>C		123.0	0.0		121.0	30.0	NM_052907	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Silent	SNP	ENST00000299308.3	hg19	CCDS41859.1																																																																																			.	.		0.498	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907		C	125834194	T	C	125834194	2	2	312	1	0	0	0	0	0	0	0	1	16061	1742	61	2		2	TMEM132B	12	125834194	Silent	SNP	T	TCGA-K7-AAU7-01A-11D-A382-10	40548418	125834194	8017701	47	44356										
FREM2	341640	hgsc.bcm.edu	37	chr13	39263249	39263257	+	In_Frame_Del	DEL	GATTCAGAT	GATTCAGAT	-													0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	ccctgagtgcaactgacatgGattcagatgattctctgctg					rs368864300		TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	GATTCAGAT	GATTCAGAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr13:39263249_39263257delGATTCAGAT	ENST00000280481.7	+	1	1984_1992	c.1768_1776delGATTCAGAT	c.(1768-1776)gattcagatdel	p.DSD590del		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	590					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		AACTGACATGGATTCAGATGATTCTCTGC	0.541																																					p.589_592del		Atlas-INDEL	.											.	FREM2	385	.	0			c.1767_1775del						.																																			SO:0001651	inframe_deletion	341640	exon1			.	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.1768_1776delGATTCAGAT	chr13.hg19:g.39263249_39263257delGATTCAGAT	ENSP00000280481:p.Asp590_Asp592del	41.0	0.0		48.0	13.0	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	In_Frame_Del	DEL	ENST00000280481.7	hg19	CCDS31960.1																																																																																			.	.		0.541	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		-	39263257	GATTCAGAT	-	39263249	7	5	312	1	0	1	0	1	0	0	0	0	6053	1174	41	0	1770	0	FREM2	13	39263249	In_Frame_Del	DEL	GATTCAGAT	TCGA-K7-AAU7-01A-11D-A382-10		39263249	75906629	48	44357										
BCL11B	64919	hgsc.bcm.edu	37	chr14	99641663	99641663	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	gaggccctcgcccgccagctCgctggtgccgggctcggggg	18	16	0	0			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr14:99641663C>A	ENST00000357195.3	-	4	1519	c.1510G>T	c.(1510-1512)Gag>Tag	p.E504*	BCL11B_ENST00000443726.2_Nonsense_Mutation_p.E310*|BCL11B_ENST00000345514.2_Nonsense_Mutation_p.E433*	NM_001282237.1|NM_138576.2	NP_001269166.1|NP_612808.1	Q9C0K0	BC11B_HUMAN	B-cell CLL/lymphoma 11B (zinc finger protein)	504					alpha-beta T cell differentiation (GO:0046632)|epithelial cell morphogenesis (GO:0003382)|keratinocyte development (GO:0003334)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|odontogenesis of dentin-containing tooth (GO:0042475)|olfactory bulb axon guidance (GO:0071678)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive T cell selection (GO:0043368)|post-embryonic camera-type eye development (GO:0031077)|regulation of keratinocyte proliferation (GO:0010837)|regulation of lipid metabolic process (GO:0019216)|regulation of neuron differentiation (GO:0045664)|striatal medium spiny neuron differentiation (GO:0021773)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|thymus development (GO:0048538)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(3)|breast(1)|central_nervous_system(9)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(9)|prostate(2)|skin(2)	34		Melanoma(154;0.0866)|all_epithelial(191;0.241)		COAD - Colon adenocarcinoma(157;0.103)		CCCGCCAGCTCGCTGGTGCCG	0.736			T	TLX3	T-ALL																																p.E504X		Atlas-SNP	.		Dom	yes		14	14q32.1	64919	B-cell CLL/lymphoma 11B  (CTIP2)		L	.	BCL11B	108	.	0			c.G1510T						.						3	3	3					14																	99641663		1526	3256	4782	SO:0001587	stop_gained	64919	exon4			CCAGCTCGCTGGT	AJ404614	CCDS9949.1, CCDS9950.1	14q32	2013-01-08			ENSG00000127152	ENSG00000127152		"Zinc fingers, C2H2-type"	13222	protein-coding gene	gene with protein product		606558		ZNF856B		11719382, 16950772	Standard	NM_138576		Approved	CTIP-2, CTIP2, hRIT1-alpha	uc001yga.3	Q9C0K0	OTTHUMG00000028967	ENST00000357195.3:c.1510G>T	chr14.hg19:g.99641663C>A	ENSP00000349723:p.Glu504*	30.0	0.0		19.0	4.0	NM_138576	Q9H162	Nonsense_Mutation	SNP	ENST00000357195.3	hg19	CCDS9950.1	.	.	.	.	.	.	.	.	.	.	C	38	6.851263	0.97885	.	.	ENSG00000127152	ENST00000357195;ENST00000345514;ENST00000443726	.	.	.	3.62	3.62	0.41486	.	0.188974	0.32952	N	0.005445	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.14656	T	0.56	-13.0736	15.6477	0.77068	0.0:1.0:0.0:0.0	.	.	.	.	X	504;433;310	.	ENSP00000280435:E433X	E	-	1	0	BCL11B	98711416	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	6.823000	0.75282	1.745000	0.51790	0.462000	0.41574	GAG	.	.		0.736	BCL11B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000072332.2	NM_138576		A	99641663	C	A	99641663	4	1	312	1	0	0	0	0	0	1	0	0	1364	893	31	1	1178	1	BCL11B	14	99641663	Nonsense_Mutation	SNP	C	TCGA-K7-AAU7-01A-11D-A382-10		99641663	7707877	49	44358										
FES	2242	hgsc.bcm.edu	37	chr15	91430578	91430578	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	tgcggtcactgcaggacctgCacgaggagatggcttgcatc	14	11	1	1			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr15:91430578C>T	ENST00000328850.3	+	5	788	c.646C>T	c.(646-648)Cac>Tac	p.H216Y	FES_ENST00000394302.1_Missense_Mutation_p.H158Y|FES_ENST00000414248.2_Missense_Mutation_p.H158Y|FES_ENST00000450438.2_Missense_Mutation_p.H158Y|FES_ENST00000444422.2_Missense_Mutation_p.H216Y|FES_ENST00000394300.3_Missense_Mutation_p.H158Y	NM_002005.3	NP_001996.1	P07332	FES_HUMAN	FES proto-oncogene, tyrosine kinase	216	Important for interaction with membranes containing phosphoinositides.				axon guidance (GO:0007411)|cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of neuron projection development (GO:0010976)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell adhesion (GO:0030155)|regulation of cell differentiation (GO:0045595)|regulation of cell motility (GO:2000145)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of mast cell degranulation (GO:0043304)|regulation of vesicle-mediated transport (GO:0060627)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|microtubule cytoskeleton (GO:0015630)	ATP binding (GO:0005524)|immunoglobulin receptor binding (GO:0034987)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphatidylinositol binding (GO:0035091)|protein tyrosine kinase activity (GO:0004713)			lung(2)|ovary(1)	3	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)			GCAGGACCTGCACGAGGAGAT	0.687																																					p.H216Y		Atlas-SNP	.											.	FES	102	.	0			c.C646T						.						27	28	28					15																	91430578		2198	4296	6494	SO:0001583	missense	2242	exon4			GACCTGCACGAGG	X52192	CCDS10365.1, CCDS45349.1, CCDS45350.1, CCDS45351.1	15q26.1	2014-06-26	2014-06-26		ENSG00000182511	ENSG00000182511	2.7.10.1	"SH2 domain containing"	3657	protein-coding gene	gene with protein product	"Oncogene FES, feline sarcoma virus", "c-fes/fps protein"	190030	"feline sarcoma (Snyder-Theilen) viral (v-fes)/Fujinami avian sarcoma (PRCII) viral (v-fps) oncogene homolog", "feline sarcoma oncogene"			1870997	Standard	NM_002005		Approved	FPS	uc002bpv.3	P07332	OTTHUMG00000044456	ENST00000328850.3:c.646C>T	chr15.hg19:g.91430578C>T	ENSP00000331504:p.His216Tyr	92.0	0.0		57.0	19.0	NM_001143784	B2R6E6|B4DUD0|E9PC94|E9PC95|Q2VXS7|Q2VXS8|Q2VXT0|Q6GTU5	Missense_Mutation	SNP	ENST00000328850.3	hg19	CCDS10365.1	.	.	.	.	.	.	.	.	.	.	C	16.70	3.195079	0.58017	.	.	ENSG00000182511	ENST00000328850;ENST00000414248;ENST00000394302;ENST00000444422;ENST00000394300;ENST00000450438	T;T;T;T;T;T	0.13538	2.58;2.58;2.58;2.58;2.58;2.58	3.87	3.87	0.44632	.	0.112232	0.64402	D	0.000007	T	0.20659	0.0497	L	0.54323	1.7	0.46954	D	0.999263	B;B;D;B;B;B	0.59357	0.0;0.045;0.985;0.004;0.115;0.0	B;B;P;B;B;B	0.47206	0.002;0.061;0.541;0.004;0.07;0.002	T	0.06285	-1.0835	10	0.87932	D	0	-37.5682	16.4539	0.84007	0.0:1.0:0.0:0.0	.	198;158;158;158;216;216	B4DUD9;P07332-2;E7ENM8;P07332-3;P07332-4;P07332	.;.;.;.;.;FES_HUMAN	Y	216;158;158;216;158;158	ENSP00000331504:H216Y;ENSP00000414629:H158Y;ENSP00000377839:H158Y;ENSP00000400868:H216Y;ENSP00000377837:H158Y;ENSP00000409915:H158Y	ENSP00000331504:H216Y	H	+	1	0	FES	89231582	1.000000	0.71417	1.000000	0.80357	0.834000	0.47266	5.363000	0.66104	2.194000	0.70268	0.555000	0.69702	CAC	.	.		0.687	FES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313497.1	NM_002005		T	91430578	C	T	91430578	3	4	312	1	0	0	0	0	1	0	0	0	5828	710	25	3	660	3	FES	15	91430578	Missense_Mutation	SNP	C	TCGA-K7-AAU7-01A-11D-A382-10		91430578	11100814	50	44359										
TRAF7	84231	hgsc.bcm.edu	37	chr16	2215890	2215890	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	ctccctctagaccagaatggAaacgaccttcggacccgcct	8	16	1	2			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr16:2215890A>C	ENST00000326181.6	+	3	224	c.92A>C	c.(91-93)gAa>gCa	p.E31A		NM_032271.2	NP_115647.2	Q6Q0C0	TRAF7_HUMAN	TNF receptor-associated factor 7, E3 ubiquitin protein ligase	31					activation of MAPKKK activity (GO:0000185)|apoptotic process (GO:0006915)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of MAPK cascade (GO:0043410)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic vesicle (GO:0031410)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	23						ACCAGAATGGAAACGACCTTC	0.602																																					p.E31A		Atlas-SNP	.											.	TRAF7	158	.	0			c.A92C						.						156	115	128					16																	2215890		2198	4300	6498	SO:0001583	missense	84231	exon3			GAATGGAAACGAC	AL136921	CCDS10461.1	16p13.3	2013-01-10	2012-02-23	2004-06-04	ENSG00000131653	ENSG00000131653		"RING-type (C3HC4) zinc fingers", "WD repeat domain containing"	20456	protein-coding gene	gene with protein product		606692	"ring finger and WD repeat domain 1", "TNF receptor-associated factor 7"	RFWD1		11230166, 15001576	Standard	NM_032271		Approved	RNF119, DKFZp586I021, MGC7807	uc002cow.3	Q6Q0C0	OTTHUMG00000128826	ENST00000326181.6:c.92A>C	chr16.hg19:g.2215890A>C	ENSP00000318944:p.Glu31Ala	72.0	0.0		43.0	10.0	NM_032271	Q9H073	Missense_Mutation	SNP	ENST00000326181.6	hg19	CCDS10461.1	.	.	.	.	.	.	.	.	.	.	A	17.39	3.377927	0.61735	.	.	ENSG00000131653	ENST00000326181	D	0.86230	-2.09	5.17	5.17	0.71159	.	0.053109	0.85682	D	0.000000	T	0.80486	0.4632	L	0.34521	1.04	0.58432	D	0.999999	P	0.45348	0.856	B	0.37601	0.254	D	0.83375	0.0009	10	0.66056	D	0.02	-19.8128	14.1854	0.65603	1.0:0.0:0.0:0.0	.	31	Q6Q0C0	TRAF7_HUMAN	A	31	ENSP00000318944:E31A	ENSP00000318944:E31A	E	+	2	0	TRAF7	2155891	1.000000	0.71417	1.000000	0.80357	0.670000	0.39368	7.769000	0.85360	1.967000	0.57214	0.374000	0.22700	GAA	.	.		0.602	TRAF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250762.1	NM_032271		C	2215890	A	C	2215890	3	2	312	1	0	0	0	0	1	0	0	0	16461	246	9	5	98	5	TRAF7	16	2215890	Missense_Mutation	SNP	A	TCGA-K7-AAU7-01A-11D-A382-10		2215890	88138863	51	44360										
NLRC3	197358	hgsc.bcm.edu	37	chr16	3613511	3613511	+	RNA	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	cgctctcagtgaagaggtcgAagatggccctcctggatgcg	14	11	1	3			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr16:3613511A>T	ENST00000301749.7	-	0	1832				NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000603507.1_RNA|NLRC3_ENST00000324659.8_RNA|NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000419350.2_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GAAGAGGTCGAAGATGGCCCT	0.627																																					p.F476Y		Atlas-SNP	.											.	NLRC3	103	.	0			c.T1427A						.						26	28	28					16																	3613511		2042	4178	6220			197358	exon5			AGGTCGAAGATGG	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"Nucleotide-binding domain and leucine rich repeat containing"	29889	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3", "NOD-like receptor C3"	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		chr16.hg19:g.3613511A>T		93.0	0.0		79.0	19.0	NM_178844	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Missense_Mutation	SNP	ENST00000301749.7	hg19		.	.	.	.	.	.	.	.	.	.	A	18.11	3.551124	0.65311	.	.	ENSG00000167984	ENST00000419350;ENST00000301749;ENST00000359128;ENST00000448023;ENST00000324659	D;D;D;D	0.84070	-1.8;-1.8;-1.8;-1.8	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	D	0.83613	0.5292	.	.	.	0.28132	N	0.93014	D	0.71674	0.998	D	0.76575	0.988	T	0.73043	-0.4107	9	0.05620	T	0.96	.	12.8296	0.57738	1.0:0.0:0.0:0.0	.	523	C9JLH9	.	Y	476;476;476;523;458	ENSP00000301749:F476Y;ENSP00000352039:F476Y;ENSP00000414415:F523Y;ENSP00000323897:F458Y	ENSP00000301749:F476Y	F	-	2	0	NLRC3	3553512	1.000000	0.71417	0.998000	0.56505	0.459000	0.32528	9.190000	0.94934	1.910000	0.55303	0.533000	0.62120	TTC	.	.		0.627	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844		T	3613511	A	T	3613511	1	4	312	0	1	0	0	0	0	0	0	0	10477	246	9	4		4	NLRC3	16	3613511	RNA	SNP	A	TCGA-K7-AAU7-01A-11D-A382-10	1397621	3613511	86741242	52	44361										
BTBD12	84464	hgsc.bcm.edu	37	chr16	3641076	3641076	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	ctgagtagctgcaaattcatAaatttcttccatttctgctt	5	9	3	1			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr16:3641076A>C	ENST00000294008.3	-	12	3203	c.2563T>G	c.(2563-2565)Tat>Gat	p.Y855D		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	855	Glu-rich.|Interaction with PLK1 and TERF2-TERF2IP.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						GCAAATTCATAAATTTCTTCC	0.507								Direct reversal of damage																													p.Y855D		Atlas-SNP	.											.	SLX4	173	.	0			c.T2563G						.						127	127	127					16																	3641076		2197	4300	6497	SO:0001583	missense	84464	exon12			ATTCATAAATTTC	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"Fanconi anemia, complementation groups", "BTB/POZ domain containing"	23845	protein-coding gene	gene with protein product	"Fanconi anemia, complementation group P"	613278	"BTB (POZ) domain containing 12", "SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.2563T>G	chr16.hg19:g.3641076A>C	ENSP00000294008:p.Tyr855Asp	71.0	0.0		55.0	10.0	NM_032444	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	hg19	CCDS10506.2	.	.	.	.	.	.	.	.	.	.	A	24.0	4.479563	0.84747	.	.	ENSG00000188827	ENST00000294008	T	0.02280	4.36	5.57	5.57	0.84162	.	0.000000	0.64402	D	0.000009	T	0.11452	0.0279	M	0.65975	2.015	0.40284	D	0.978426	D	0.89917	1.0	D	0.87578	0.998	T	0.00465	-1.1723	10	0.72032	D	0.01	.	14.9117	0.70761	1.0:0.0:0.0:0.0	.	855	Q8IY92	SLX4_HUMAN	D	855	ENSP00000294008:Y855D	ENSP00000294008:Y855D	Y	-	1	0	SLX4	3581077	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	7.286000	0.78671	2.117000	0.64856	0.459000	0.35465	TAT	.	.		0.507	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444		C	3641076	A	C	3641076	3	2	312	1	0	0	0	0	1	0	0	0	1542	362	13	5	2957	5	BTBD12	16	3641076	Missense_Mutation	SNP	A	TCGA-K7-AAU7-01A-11D-A382-10	27565	3641076	86713677	53	44362										
CBLN1	869	hgsc.bcm.edu	37	chr16	49315146	49315146	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	atgatcatggtgcgattactCatctcggacggctcgtggtt	12	9	3	1			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr16:49315146C>G	ENST00000219197.6	-	1	596	c.231G>C	c.(229-231)atG>atC	p.M77I	CBLN1_ENST00000536749.1_Missense_Mutation_p.M77I	NM_004352.3	NP_004343.1	P23435	CBLN1_HUMAN	cerebellin 1 precursor	77	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.|Necessary for interaction with CBLN3, and homotrimerization. {ECO:0000250}.				cerebellar granule cell differentiation (GO:0021707)|heterophilic cell-cell adhesion (GO:0007157)|nervous system development (GO:0007399)|positive regulation of synapse assembly (GO:0051965)|protein secretion (GO:0009306)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|extracellular region (GO:0005576)|postsynaptic membrane (GO:0045211)				breast(1)|kidney(3)|large_intestine(2)|lung(3)	9		all_cancers(37;0.0766)|all_lung(18;0.24)				TGCGATTACTCATCTCGGACG	0.607																																					p.M77I		Atlas-SNP	.											.	CBLN1	26	.	0			c.G231C						.						72	74	73					16																	49315146		2200	4300	6500	SO:0001583	missense	869	exon1			ATTACTCATCTCG	M58583	CCDS10736.1	16q12.1	2008-02-05			ENSG00000102924	ENSG00000102924			1543	protein-coding gene	gene with protein product		600432				7877445, 1704129	Standard	NM_004352		Approved		uc002efq.3	P23435	OTTHUMG00000133148	ENST00000219197.6:c.231G>C	chr16.hg19:g.49315146C>G	ENSP00000219197:p.Met77Ile	84.0	0.0		77.0	16.0	NM_004352	B2RAN9|P02682|Q52M09	Missense_Mutation	SNP	ENST00000219197.6	hg19	CCDS10736.1	.	.	.	.	.	.	.	.	.	.	C	17.71	3.456052	0.63401	.	.	ENSG00000102924	ENST00000219197;ENST00000536749	T;T	0.36520	1.25;1.25	4.47	4.47	0.54385	Tumour necrosis factor-like (2);Complement C1q protein (4);	0.083709	0.85682	D	0.000000	T	0.28764	0.0713	N	0.25201	0.72	0.80722	D	1	B	0.24186	0.099	B	0.25140	0.058	T	0.10894	-1.0610	10	0.51188	T	0.08	-20.4485	16.9081	0.86133	0.0:1.0:0.0:0.0	.	77	P23435	CBLN1_HUMAN	I	77	ENSP00000219197:M77I;ENSP00000444651:M77I	ENSP00000219197:M77I	M	-	3	0	CBLN1	47872647	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.270000	0.78493	2.314000	0.78098	0.462000	0.41574	ATG	.	.		0.607	CBLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256845.4	NM_004352		G	49315146	C	G	49315146	3	3	312	1	0	0	0	0	1	0	0	0	2706	826	29	4	362	4	CBLN1	16	49315146	Missense_Mutation	SNP	C	TCGA-K7-AAU7-01A-11D-A382-10	45674070	49315146	41039607	54	44363										
SMPD3	55512	hgsc.bcm.edu	37	chr16	68405459	68405459	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	cgtcacccttgtactccacaGaggctgtcctcttaatgctc	7	15	2	1			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr16:68405459G>A	ENST00000219334.5	-	3	1229	c.626C>T	c.(625-627)tCt>tTt	p.S209F	SMPD3_ENST00000566009.1_5'Flank|SMPD3_ENST00000568373.1_Missense_Mutation_p.S209F|SMPD3_ENST00000563226.1_Missense_Mutation_p.S209F	NM_018667.3	NP_061137.1	Q9NY59	NSMA2_HUMAN	sphingomyelin phosphodiesterase 3, neutral membrane (neutral sphingomyelinase II)	209					cell cycle (GO:0007049)|glycosphingolipid metabolic process (GO:0006687)|hematopoietic progenitor cell differentiation (GO:0002244)|peptide hormone secretion (GO:0030072)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)	Golgi cis cisterna (GO:0000137)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)			breast(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0184)|Epithelial(162;0.0785)	Phosphatidylserine(DB00144)	GTACTCCACAGAGGCTGTCCT	0.682																																					p.S209F		Atlas-SNP	.											.	SMPD3	52	.	0			c.C626T						.						17	21	20					16																	68405459		2194	4298	6492	SO:0001583	missense	55512	exon3			TCCACAGAGGCTG	AJ250460	CCDS10867.1	16q22.1	2008-02-05			ENSG00000103056	ENSG00000103056			14240	protein-coding gene	gene with protein product		605777				10823942	Standard	NM_018667		Approved	NSMASE2	uc002ewa.3	Q9NY59	OTTHUMG00000137559	ENST00000219334.5:c.626C>T	chr16.hg19:g.68405459G>A	ENSP00000219334:p.Ser209Phe	13.0	0.0		23.0	7.0	NM_018667	B7ZL82|Q2M1S8	Missense_Mutation	SNP	ENST00000219334.5	hg19	CCDS10867.1	.	.	.	.	.	.	.	.	.	.	G	16.66	3.185210	0.57909	.	.	ENSG00000103056	ENST00000219334	.	.	.	4.74	4.74	0.60224	.	0.101538	0.64402	D	0.000001	T	0.63803	0.2542	L	0.29908	0.895	0.50171	D	0.999856	D;D;D	0.69078	0.997;0.997;0.997	D;D;D	0.63597	0.916;0.916;0.916	T	0.68108	-0.5496	9	0.72032	D	0.01	-15.5338	15.5658	0.76290	0.0:0.0:1.0:0.0	.	209;209;209	B7ZL82;B7ZL84;Q9NY59	.;.;NSMA2_HUMAN	F	209	.	ENSP00000219334:S209F	S	-	2	0	SMPD3	66962960	1.000000	0.71417	0.999000	0.59377	0.686000	0.39977	4.896000	0.63222	2.335000	0.79485	0.561000	0.74099	TCT	.	.		0.682	SMPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268895.3	NM_018667		A	68405459	G	A	68405459	3	1	312	1	0	0	0	0	1	0	0	0	14821	942	33	3	1369	3	SMPD3	16	68405459	Missense_Mutation	SNP	G	TCGA-K7-AAU7-01A-11D-A382-10	19090313	68405459	21949294	55	44364										
AARS	16	hgsc.bcm.edu	37	chr16	70293021	70293021	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	ttctggtcagcttccccaagCactgagcgcagggcgaagtt	12	12	2	1			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr16:70293021C>T	ENST00000261772.8	-	14	1997	c.1854G>A	c.(1852-1854)gtG>gtA	p.V618V	AARS_ENST00000564359.1_5'UTR	NM_001605.2	NP_001596.2			alanyl-tRNA synthetase											breast(3)|cervix(2)|endometrium(5)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)	27		Ovarian(137;0.0365)		BRCA - Breast invasive adenocarcinoma(221;0.161)		CTTCCCCAAGCACTGAGCGCA	0.562																																					p.V618V		Atlas-SNP	.											.	AARS	62	.	0			c.G1854A						.						178	160	166					16																	70293021		2198	4300	6498	SO:0001819	synonymous_variant	16	exon14			CCCAAGCACTGAG	D32050	CCDS32474.1	16q22.1	2014-09-17			ENSG00000090861	ENSG00000090861	6.1.1.7	"Aminoacyl tRNA synthetases / Class II"	20	protein-coding gene	gene with protein product	"alanine tRNA ligase 1, cytoplasmic"	601065				8595897	Standard	NM_001605		Approved		uc002eyn.1	P49588	OTTHUMG00000177042	ENST00000261772.8:c.1854G>A	chr16.hg19:g.70293021C>T		95.0	0.0		63.0	14.0	NM_001605		Silent	SNP	ENST00000261772.8	hg19	CCDS32474.1																																																																																			.	.		0.562	AARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435021.2	NM_001605		T	70293021	C	T	70293021	2	4	312	1	0	0	0	0	0	0	0	1	19	697	25	3		3	AARS	16	70293021	Silent	SNP	C	TCGA-K7-AAU7-01A-11D-A382-10	1887562	70293021	20061732	56	44365										
GAN	8139	hgsc.bcm.edu	37	chr16	81385202	81385202	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	tcttaggacaaagttaaactAtaatcctccaaaagatgatg	6	7	1	2			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr16:81385202A>G	ENST00000568107.2	+	2	344	c.182A>G	c.(181-183)tAt>tGt	p.Y61C		NM_022041.3	NP_071324.1	Q9H2C0	GAN_HUMAN	gigaxonin	61	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				cell death (GO:0008219)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)	25		Colorectal(91;0.153)				AAGTTAAACTATAATCCTCCA	0.313																																					p.Y61C	GBM(106;1239 1507 7582 9741 33976)	Atlas-SNP	.											.	GAN	59	.	0			c.A182G						.						90	85	87					16																	81385202		2202	4300	6502	SO:0001583	missense	8139	exon2			TAAACTATAATCC	AF291673	CCDS10935.1	16q24.1	2014-09-17	2008-08-01		ENSG00000261609	ENSG00000261609		"Kelch-like", "BTB/POZ domain containing"	4137	protein-coding gene	gene with protein product	"kelch-like family member 16"	605379	"giant axonal neuropathy (gigaxonin)"			9450783, 11062483	Standard	NM_022041		Approved	GAN1, KLHL16	uc002fgo.3	Q9H2C0	OTTHUMG00000137627	ENST00000568107.2:c.182A>G	chr16.hg19:g.81385202A>G	ENSP00000476795:p.Tyr61Cys	60.0	0.0		58.0	12.0	NM_022041		Missense_Mutation	SNP	ENST00000568107.2	hg19	CCDS10935.1	.	.	.	.	.	.	.	.	.	.	A	18.94	3.729425	0.69074	.	.	ENSG00000127688	ENST00000248272	T	0.67171	-0.25	5.75	5.75	0.90469	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.139673	0.49916	D	0.000129	T	0.75049	0.3797	L	0.36672	1.1	0.80722	D	1	D	0.71674	0.998	D	0.72075	0.976	T	0.77624	-0.2518	10	0.72032	D	0.01	.	16.0549	0.80794	1.0:0.0:0.0:0.0	.	61	Q9H2C0	GAN_HUMAN	C	61	ENSP00000248272:Y61C	ENSP00000248272:Y61C	Y	+	2	0	GAN	79942703	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.339000	0.96797	2.192000	0.70111	0.459000	0.35465	TAT	.	.		0.313	GAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269050.3			G	81385202	A	G	81385202	3	3	312	1	0	0	0	0	1	0	0	0	6240	449	16	2	188	2	GAN	16	81385202	Missense_Mutation	SNP	A	TCGA-K7-AAU7-01A-11D-A382-10	11092181	81385202	8969551	57	44366										
RPL13	6137	hgsc.bcm.edu	37	chr16	89628070	89628070	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	acaagtccacggagtccctgCaggccaacgtgcagcggctg	13	14	0	0			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr16:89628070C>T	ENST00000393099.3	+	3	580	c.331C>T	c.(331-333)Cag>Tag	p.Q111*	RPL13_ENST00000452368.3_Intron|RPL13_ENST00000567815.1_Nonsense_Mutation_p.Q111*|SNORD68_ENST00000363214.1_RNA|RPL13_ENST00000311528.5_Nonsense_Mutation_p.Q111*	NM_033251.2	NP_150254.1	P26373	RL13_HUMAN	ribosomal protein L13	111					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|cytosolic ribosome (GO:0022626)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			lung(3)|skin(1)|upper_aerodigestive_tract(2)	6		all_hematologic(23;0.0748)		all cancers(4;1.15e-07)|OV - Ovarian serous cystadenocarcinoma(4;7.8e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0139)		GGAGTCCCTGCAGGCCAACGT	0.612																																					p.Q111X		Atlas-SNP	.											.	RPL13	11	.	0			c.C331T						.						44	43	43					16																	89628070		2198	4299	6497	SO:0001587	stop_gained	6137	exon4			TCCCTGCAGGCCA	AB007172	CCDS10979.1, CCDS58492.1	16q24.3	2011-04-06			ENSG00000167526	ENSG00000167526		"L ribosomal proteins"	10303	protein-coding gene	gene with protein product		113703				9582194	Standard	NM_000977		Approved	D16S444E, BBC1, L13	uc002fnm.2	P26373	OTTHUMG00000133770	ENST00000393099.3:c.331C>T	chr16.hg19:g.89628070C>T	ENSP00000376811:p.Gln111*	209.0	0.0		160.0	42.0	NM_000977	B4DLX3|F5H1S2|Q3KQT8|Q567Q8|Q9BPX0	Nonsense_Mutation	SNP	ENST00000393099.3	hg19	CCDS10979.1	.	.	.	.	.	.	.	.	.	.	C	36	5.630997	0.96682	.	.	ENSG00000167526	ENST00000311528;ENST00000393099	.	.	.	4.29	4.29	0.51040	.	0.066901	0.64402	U	0.000009	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-8.4789	17.1115	0.86676	0.0:1.0:0.0:0.0	.	.	.	.	X	111	.	ENSP00000307889:Q111X	Q	+	1	0	RPL13	88155571	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.622000	0.83099	2.106000	0.64143	0.462000	0.41574	CAG	.	.		0.612	RPL13-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258294.2	NM_000977		T	89628070	C	T	89628070	4	4	312	1	0	0	0	0	0	1	0	0	13574	711	25	3	341	3	RPL13	16	89628070	Nonsense_Mutation	SNP	C	TCGA-K7-AAU7-01A-11D-A382-10	8242868	89628070	726683	58	44367										
TP53	7157	hgsc.bcm.edu	37	chr17	7578463	7578463	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	agatggccatggcgcggacgCgggtgccgggcgggggtgtg	23	9	0	1	rs371524413		TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr17:7578463C>G	ENST00000269305.4	-	5	656	c.467G>C	c.(466-468)cGc>cCc	p.R156P	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Missense_Mutation_p.R156P|TP53_ENST00000445888.2_Missense_Mutation_p.R156P|TP53_ENST00000420246.2_Missense_Mutation_p.R156P|TP53_ENST00000359597.4_Missense_Mutation_p.R156P|TP53_ENST00000455263.2_Missense_Mutation_p.R156P	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	156	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		R -> C (in sporadic cancers; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:7682763}.|R -> S (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R156P(24)|p.R156H(10)|p.0?(8)|p.?(5)|p.R156L(3)|p.R156_I162delRVRAMAI(2)|p.T155fs*23(2)|p.P153fs*22(2)|p.T155_R156delTR(1)|p.R156_A161delRVRAMA(1)|p.P151_V173del23(1)|p.R156del(1)|p.R156_R158delRVR(1)|p.R156fs*12(1)|p.R156fs*14(1)|p.R156fs*18(1)|p.R156_A161del(1)|p.R156_V157del(1)|p.D148fs*23(1)|p.S149fs*72(1)|p.T155_A161delTRVRAMA(1)|p.G154fs*22(1)|p.R156fs*25(1)|p.G154_R156delGTR(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGCGCGGACGCGGGTGCCGGG	0.612		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.R156P	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,right_upper_lobe,carcinoma,0,5	TP53	33396	.	72	Substitution - Missense(37)|Deletion - In frame(11)|Deletion - Frameshift(10)|Whole gene deletion(8)|Unknown(5)|Insertion - Frameshift(1)	breast(9)|lung(8)|ovary(8)|stomach(7)|upper_aerodigestive_tract(6)|large_intestine(5)|skin(5)|bone(5)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(3)|urinary_tract(3)|kidney(2)|liver(2)|oesophagus(2)|biliary_tract(1)|prostate(1)|pancreas(1)	c.G467C	GRCh37	CM984589	TP53	M		.						50	52	51					17																	7578463		2203	4300	6503	SO:0001583	missense	7157	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	CGGACGCGGGTGC	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.467G>C	chr17.hg19:g.7578463C>G	ENSP00000269305:p.Arg156Pro	139.0	0.0		80.0	29.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	12.90	2.076061	0.36662	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793	D;D;D;D;D;D;D;D;D	0.99766	-6.69;-6.69;-6.69;-6.69;-6.69;-6.69;-6.69;-6.69;-6.69	5.47	3.45	0.39498	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.599272	0.17934	N	0.157074	D	0.99576	0.9847	M	0.73598	2.24	0.09310	N	1	D;D;D;D;D;D;D	0.89917	1.0;0.988;0.96;0.985;0.982;0.996;1.0	D;P;P;D;P;D;D	0.74674	0.984;0.887;0.614;0.924;0.902;0.953;0.958	D	0.99552	1.0966	10	0.54805	T	0.06	-1.0137	6.8349	0.23931	0.3112:0.607:0.0:0.0817	.	117;156;156;63;156;156;156	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	P	156;156;156;156;156;156;145;63;24;63;24;156	ENSP00000410739:R156P;ENSP00000352610:R156P;ENSP00000269305:R156P;ENSP00000398846:R156P;ENSP00000391127:R156P;ENSP00000391478:R156P;ENSP00000425104:R24P;ENSP00000423862:R63P;ENSP00000424104:R156P	ENSP00000269305:R156P	R	-	2	0	TP53	7519188	0.333000	0.24731	0.002000	0.10522	0.138000	0.21146	4.631000	0.61304	0.779000	0.33543	0.563000	0.77884	CGC	.	.		0.612	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		G	7578463	C	G	7578463	3	3	312	1	0	0	0	0	1	0	0	0	16396	768	27	4	831	4	TP53	17	7578463	Missense_Mutation	SNP	C	TCGA-K7-AAU7-01A-11D-A382-10		7578463	73616747	59	44368										
SLFN12L	100506736	hgsc.bcm.edu	37	chr17	33802437	33802437	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	tcacatattaattgcttaagTccttcatgttgtgagaacag	7	7	2	1			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr17:33802437T>C	ENST00000260908.7	-	4	1389	c.1272A>G	c.(1270-1272)ggA>ggG	p.G424G	RP11-686D22.9_ENST00000587076.1_RNA|SLFN12L_ENST00000361112.4_Silent_p.G453G|SLFN12L_ENST00000449046.1_Silent_p.G455G	NM_001195790.1	NP_001182719.1	Q6IEE8	SN12L_HUMAN	schlafen family member 12-like	424						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)			breast(1)|endometrium(4)|kidney(5)|large_intestine(2)|lung(3)|ovary(1)	16						ATTGCTTAAGTCCTTCATGTT	0.393																																					p.G424G		Atlas-SNP	.											.	SLFN12L	140	.	0			c.A1272G						.						62	51	54					17																	33802437		692	1591	2283	SO:0001819	synonymous_variant	100506736	exon4			CTTAAGTCCTTCA	AK172761	CCDS56026.1	17q12	2011-05-24				ENSG00000205045			33920	protein-coding gene	gene with protein product		614956				9846487	Standard	NM_001195790		Approved		uc021tuy.1	Q6IEE8		ENST00000260908.7:c.1272A>G	chr17.hg19:g.33802437T>C		88.0	0.0		55.0	14.0	NM_001195790	F5H6G3	Silent	SNP	ENST00000260908.7	hg19	CCDS56026.1																																																																																			.	.		0.393	SLFN12L-004	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395748.2	XM_496206		C	33802437	T	C	33802437	2	2	312	1	0	0	0	0	0	0	0	1	14750	1654	58	2		2	SLFN12L	17	33802437	Silent	SNP	T	TCGA-K7-AAU7-01A-11D-A382-10	26223974	33802437	47392773	60	44369										
GPR179	440435	hgsc.bcm.edu	37	chr17	36482914	36482914	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	ttccccagggcagactgcctCctgctctctgggctttgctg	11	15	1	1			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr17:36482914C>T	ENST00000342292.4	-	11	6558	c.6538G>A	c.(6538-6540)Gag>Aag	p.E2180K	GPR179_ENST00000584976.1_Intron	NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	2180					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				CAGACTGCCTCCTGCTCTCTG	0.582																																					p.E2180K		Atlas-SNP	.											.	GPR179	170	.	0			c.G6538A						.						96	99	98					17																	36482914		2119	4231	6350	SO:0001583	missense	440435	exon11			CTGCCTCCTGCTC		CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"GPCR / Class C : Orphans"	31371	protein-coding gene	gene with protein product		614515	"GPR158-like 1", "GPR179"	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.6538G>A	chr17.hg19:g.36482914C>T	ENSP00000345060:p.Glu2180Lys	63.0	0.0		38.0	6.0	NM_001004334		Missense_Mutation	SNP	ENST00000342292.4	hg19	CCDS42308.1	.	.	.	.	.	.	.	.	.	.	C	13.62	2.291736	0.40594	.	.	ENSG00000188888	ENST00000342292	T	0.53640	0.61	3.24	3.24	0.37175	.	0.000000	0.40144	N	0.001173	T	0.41581	0.1165	L	0.55743	1.74	0.09310	N	1	B	0.28713	0.22	B	0.21708	0.036	T	0.39121	-0.9629	10	0.38643	T	0.18	-12.2637	14.4268	0.67220	0.0:1.0:0.0:0.0	.	2180	Q6PRD1	GP179_HUMAN	K	2180	ENSP00000345060:E2180K	ENSP00000345060:E2180K	E	-	1	0	GPR179	33736440	0.891000	0.30450	0.132000	0.22025	0.055000	0.15305	1.003000	0.29809	2.115000	0.64714	0.460000	0.39030	GAG	.	.		0.582	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2			T	36482914	C	T	36482914	3	4	312	1	0	0	0	0	1	0	0	0	6682	864	30	3	569	3	GPR179	17	36482914	Missense_Mutation	SNP	C	TCGA-K7-AAU7-01A-11D-A382-10	2680477	36482914	44712296	61	44370										
WDR18	57418	hgsc.bcm.edu	37	chr19	992023	992023	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	gctcagacttcaggcccagcCtgccgctgccccacttcaac	8	19	3	1			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr19:992023C>G	ENST00000251289.5	+	8	1023	c.1000C>G	c.(1000-1002)Ctg>Gtg	p.L334V	WDR18_ENST00000587001.2_Missense_Mutation_p.L334V	NM_024100.3	NP_077005.2	Q9BV38	WDR18_HUMAN	WD repeat domain 18	334					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|lung(2)|skin(2)	7		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGGCCCAGCCTGCCGCTGCC	0.721																																					p.L334V		Atlas-SNP	.											.	WDR18	20	.	0			c.C1000G						.						10	11	11					19																	992023		2143	4187	6330	SO:0001583	missense	57418	exon8			CCCAGCCTGCCGC		CCDS12051.1	19p13.3	2013-01-09				ENSG00000065268		"WD repeat domain containing"	17956	protein-coding gene	gene with protein product	"Involved in Processing ITS2 3 homolog (S. cerevisiae)"					22190735	Standard	NM_024100		Approved	Ipi3	uc002lqm.1	Q9BV38		ENST00000251289.5:c.1000C>G	chr19.hg19:g.992023C>G	ENSP00000251289:p.Leu334Val	63.0	0.0		58.0	17.0	NM_024100	O60390|Q9BWR2	Missense_Mutation	SNP	ENST00000251289.5	hg19	CCDS12051.1	.	.	.	.	.	.	.	.	.	.	C	8.908	0.958045	0.18507	.	.	ENSG00000065268	ENST00000251289	T	0.68331	-0.32	4.28	4.28	0.50868	.	0.162347	0.41097	D	0.000942	T	0.44307	0.1287	L	0.31207	0.915	0.32238	N	0.573086	B	0.14438	0.01	B	0.06405	0.002	T	0.43212	-0.9405	10	0.02654	T	1	.	6.0096	0.19567	0.0:0.7023:0.1947:0.103	.	334	Q9BV38	WDR18_HUMAN	V	334	ENSP00000251289:L334V	ENSP00000251289:L334V	L	+	1	2	WDR18	943023	0.999000	0.42202	1.000000	0.80357	0.981000	0.71138	1.101000	0.31037	2.227000	0.72691	0.491000	0.48974	CTG	.	.		0.721	WDR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458225.2			G	992023	C	G	992023	3	3	312	1	0	0	0	0	1	0	0	0	17293	680	24	4	1030	4	WDR18	19	992023	Missense_Mutation	SNP	C	TCGA-K7-AAU7-01A-11D-A382-10		992023	58136960	62	44371										
ATP4A	495	hgsc.bcm.edu	37	chr19	36047937	36047937	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	aaagttcatggcctctacgtCgaaggcatagccaggcgggt	13	10	2	0	rs200791532		TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr19:36047937C>T	ENST00000262623.3	-	12	1775	c.1747G>A	c.(1747-1749)Gac>Aac	p.D583N		NM_000704.2	NP_000695.2	P20648	ATP4A_HUMAN	ATPase, H+/K+ exchanging, alpha polypeptide	583					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|ion transmembrane transport (GO:0034220)|pH reduction (GO:0045851)|regulation of proton transport (GO:0010155)|response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|magnesium ion binding (GO:0000287)	p.D583N(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(26)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	53	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)	GCCTCTACGTCGAAGGCATAG	0.582																																					p.D583N		Atlas-SNP	.											ATP4A,NS,carcinoma,0,1	ATP4A	123	.	1	Substitution - Missense(1)	prostate(1)	c.G1747A						.						78	73	75					19																	36047937		2203	4300	6503	SO:0001583	missense	495	exon12			CTACGTCGAAGGC		CCDS12467.1	19q13.1	2010-04-20			ENSG00000105675	ENSG00000105675	3.6.3.10	"ATPases / P-type"	819	protein-coding gene	gene with protein product	"gastric H,K-ATPase alpha subunit", "H(+)-K(+)-ATPase alpha subunit", "proton pump"	137216				1330887	Standard	NM_000704		Approved	ATP6A	uc002oal.1	P20648	OTTHUMG00000048106	ENST00000262623.3:c.1747G>A	chr19.hg19:g.36047937C>T	ENSP00000262623:p.Asp583Asn	93.0	0.0		86.0	23.0	NM_000704	O00738	Missense_Mutation	SNP	ENST00000262623.3	hg19	CCDS12467.1	.	.	.	.	.	.	.	.	.	.	C	11.33	1.605498	0.28623	.	.	ENSG00000105675	ENST00000262623	T	0.80393	-1.37	5.14	2.91	0.33838	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.074877	0.48767	D	0.000176	T	0.66626	0.2808	N	0.20574	0.59	0.48511	D	0.999666	B	0.18310	0.027	B	0.29267	0.1	T	0.59778	-0.7390	10	0.28530	T	0.3	.	9.0288	0.36247	0.0:0.8056:0.0:0.1944	.	583	P20648	ATP4A_HUMAN	N	583	ENSP00000262623:D583N	ENSP00000262623:D583N	D	-	1	0	ATP4A	40739777	0.998000	0.40836	0.896000	0.35187	0.180000	0.23129	3.898000	0.56281	1.400000	0.46741	0.591000	0.81541	GAC	.	C|0.999;T|0.001		0.582	ATP4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109470.2	NM_000704		T	36047937	C	T	36047937	3	4	312	1	0	0	0	0	1	0	0	0	1145	884	31	1	1404	1	ATP4A	19	36047937	Missense_Mutation	SNP	C	TCGA-K7-AAU7-01A-11D-A382-10	35055914	36047937	23081046	63	44372										
IZUMO1	284359	hgsc.bcm.edu	37	chr19	49244274	49244274	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	tgaaatcgatcaccttccttCgacgaaatatcctaggggtg	9	10	1	1			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr19:49244274C>T	ENST00000332955.2	-	10	1491	c.944G>A	c.(943-945)cGa>cAa	p.R315Q	RASIP1_ENST00000594232.1_5'Flank|RASIP1_ENST00000222145.4_5'Flank	NM_182575.2	NP_872381.2	Q8IYV9	IZUM1_HUMAN	izumo sperm-egg fusion 1	315					cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	acrosomal membrane (GO:0002080)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			endometrium(4)|kidney(3)|large_intestine(4)|lung(2)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	17		all_lung(116;0.000156)|Lung NSC(112;0.000251)|all_epithelial(76;0.000761)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000348)|Epithelial(262;0.019)|GBM - Glioblastoma multiforme(486;0.022)		CACCTTCCTTCGACGAAATAT	0.547																																					p.R315Q		Atlas-SNP	.											.	IZUMO1	30	.	0			c.G944A						.						102	92	95					19																	49244274		2203	4300	6503	SO:0001583	missense	284359	exon10			TTCCTTCGACGAA	BC034769	CCDS12732.1	19q13.33	2014-07-23			ENSG00000182264	ENSG00000182264		"-"	28539	protein-coding gene	gene with protein product	"oocyte binding/fusion factor"	609278				15759005, 18952059, 19658160, 22957301	Standard	NM_182575		Approved	IZUMO, MGC34799, OBF	uc002pkj.3	Q8IYV9	OTTHUMG00000183324	ENST00000332955.2:c.944G>A	chr19.hg19:g.49244274C>T	ENSP00000327786:p.Arg315Gln	55.0	0.0		51.0	9.0	NM_182575	Q6Q8P6|Q6Q8P7	Missense_Mutation	SNP	ENST00000332955.2	hg19	CCDS12732.1	.	.	.	.	.	.	.	.	.	.	C	12.87	2.066391	0.36470	.	.	ENSG00000182264	ENST00000332955	T	0.23552	1.9	4.39	-2.09	0.07232	.	2.702910	0.01922	N	0.040588	T	0.18045	0.0433	L	0.39898	1.24	0.09310	N	1	B	0.22276	0.067	B	0.11329	0.006	T	0.09618	-1.0666	10	0.22706	T	0.39	3.134	2.5771	0.04809	0.1022:0.2153:0.4382:0.2442	.	315	Q8IYV9	IZUM1_HUMAN	Q	315	ENSP00000327786:R315Q	ENSP00000327786:R315Q	R	-	2	0	IZUMO1	53936086	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-0.518000	0.06267	-0.183000	0.10585	-0.150000	0.13652	CGA	.	.		0.547	IZUMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466189.1	NM_182575		T	49244274	C	T	49244274	3	4	312	1	0	0	0	0	1	0	0	0	7942	884	31	1	112	1	IZUMO1	19	49244274	Missense_Mutation	SNP	C	TCGA-K7-AAU7-01A-11D-A382-10	13196337	49244274	9884709	64	44373										
PLCB1	23236	hgsc.bcm.edu	37	chr20	8769114	8769114	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	agcttattcaaaagttgacgGatgtcgcagaagagtgtcag	12	6	2	3			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr20:8769114G>A	ENST00000338037.6	+	28	3157	c.3130G>A	c.(3130-3132)Gat>Aat	p.D1044N	PLCB1_ENST00000378637.2_Missense_Mutation_p.D1044N|PLCB1_ENST00000378641.3_Missense_Mutation_p.D1044N|PLCB1_ENST00000494924.1_3'UTR	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	1044					activation of meiosis involved in egg activation (GO:0060466)|cerebral cortex development (GO:0021987)|fat cell differentiation (GO:0045444)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G2/M transition of mitotic cell cycle (GO:0000086)|glutamate receptor signaling pathway (GO:0007215)|inositol phosphate metabolic process (GO:0043647)|insulin-like growth factor receptor signaling pathway (GO:0048009)|interleukin-1-mediated signaling pathway (GO:0070498)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-15-mediated signaling pathway (GO:0035723)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|memory (GO:0007613)|negative regulation of monocyte extravasation (GO:2000438)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of CD24 biosynthetic process (GO:2000560)|positive regulation of developmental growth (GO:0048639)|positive regulation of embryonic development (GO:0040019)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of GTPase activity (GO:0043547)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fertilization (GO:0080154)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						AAAGTTGACGGATGTCGCAGA	0.388																																					p.K1044K		Atlas-SNP	.											.	PLCB1	394	.	0			c.A3130A						.						73	70	71					20																	8769114		2203	4300	6503	SO:0001583	missense	23236	exon28			TTGACGGATGTCG	AB011153	CCDS13102.1, CCDS13103.1	20p12	2008-03-18			ENSG00000182621	ENSG00000182621	3.1.4.11		15917	protein-coding gene	gene with protein product		607120				10760467, 11118617	Standard	NM_015192		Approved	KIAA0581, PLC-I, PLC154	uc002wnb.4	Q9NQ66	OTTHUMG00000031849	ENST00000338037.6:c.3130G>A	chr20.hg19:g.8769114G>A	ENSP00000338185:p.Asp1044Asn	169.0	0.0		177.0	49.0	NM_015192	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Silent	SNP	ENST00000338037.6	hg19	CCDS13102.1	.	.	.	.	.	.	.	.	.	.	G	17.79	3.475396	0.63737	.	.	ENSG00000182621	ENST00000378641;ENST00000338037;ENST00000378637;ENST00000441163;ENST00000535719	T;T;T	0.48522	0.81;0.81;0.81	5.28	5.28	0.74379	PLC-beta, C-terminal (1);	0.343372	0.33217	N	0.005146	T	0.44477	0.1295	L	0.40543	1.245	0.34571	D	0.713448	P;B	0.35124	0.485;0.336	B;B	0.35550	0.179;0.205	T	0.57539	-0.7794	10	0.49607	T	0.09	.	19.2861	0.94072	0.0:0.0:1.0:0.0	.	1044;1044	Q9NQ66;Q9NQ66-2	PLCB1_HUMAN;.	N	1044;1044;1044;964;964	ENSP00000367908:D1044N;ENSP00000338185:D1044N;ENSP00000367904:D1044N	ENSP00000338185:D1044N	D	+	1	0	PLCB1	8717114	1.000000	0.71417	0.994000	0.49952	0.972000	0.66771	4.005000	0.57075	2.640000	0.89533	0.563000	0.77884	GAT	.	.		0.388	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3			A	8769114	G	A	8769114	3	1	312	1	0	0	0	0	1	0	0	0	12036	1174	41	3	3240	3	PLCB1	20	8769114	Missense_Mutation	SNP	G	TCGA-K7-AAU7-01A-11D-A382-10		8769114	54256406	65	44374										
SEC23B	10483	hgsc.bcm.edu	37	chr20	18491492	18491492	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	tttagactatggcgacatacCtggagttcatccagcagaat	9	9	1	2			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr20:18491492C>G	ENST00000336714.3	+	2	445	c.13C>G	c.(13-15)Ctg>Gtg	p.L5V	SEC23B_ENST00000377465.1_Missense_Mutation_p.L5V|SEC23B_ENST00000377475.3_Missense_Mutation_p.L5V|SEC23B_ENST00000262544.2_Missense_Mutation_p.L5V	NM_006363.4|NM_032985.4|NM_032986.3	NP_006354.2|NP_116780.1|NP_116781.1	Q15437	SC23B_HUMAN	Sec23 homolog B (S. cerevisiae)	5					ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	32						GGCGACATACCTGGAGTTCAT	0.428																																					p.L5V		Atlas-SNP	.											.	SEC23B	70	.	0			c.C13G						.						122	112	115					20																	18491492		2203	4300	6503	SO:0001583	missense	10483	exon2			ACATACCTGGAGT	X97065	CCDS13137.1	20p11.23	2010-02-09	2001-11-28		ENSG00000101310	ENSG00000101310			10702	protein-coding gene	gene with protein product		610512	"Sec23 (S. cerevisiae) homolog B", "congenital dyserythropoietic anemia, type II"	CDAN2		8898360, 10329445, 19621418	Standard	NM_032985		Approved	CDA-II, CDAII, HEMPAS	uc002wrb.2	Q15437	OTTHUMG00000031976	ENST00000336714.3:c.13C>G	chr20.hg19:g.18491492C>G	ENSP00000338844:p.Leu5Val	209.0	0.0		160.0	38.0	NM_032985	D3DW33|Q503A9|Q5W183|Q9BS15|Q9BSI2|Q9H1D7	Missense_Mutation	SNP	ENST00000336714.3	hg19	CCDS13137.1	.	.	.	.	.	.	.	.	.	.	C	13.50	2.254860	0.39896	.	.	ENSG00000101310	ENST00000450074;ENST00000336714;ENST00000262544;ENST00000377475;ENST00000377465	D;D;D;D;D	0.86956	-1.6;-2.19;-2.19;-2.19;-2.19	5.08	3.15	0.36227	.	0.068699	0.64402	D	0.000014	T	0.77253	0.4103	L	0.27053	0.805	0.41804	D	0.989939	B;B	0.11235	0.004;0.004	B;B	0.09377	0.004;0.004	T	0.69881	-0.5025	10	0.46703	T	0.11	-7.8413	8.0822	0.30752	0.0:0.756:0.0:0.244	.	5;5	B4DJW8;Q15437	.;SC23B_HUMAN	V	5	ENSP00000403971:L5V;ENSP00000338844:L5V;ENSP00000262544:L5V;ENSP00000366695:L5V;ENSP00000366685:L5V	ENSP00000262544:L5V	L	+	1	2	SEC23B	18439492	0.982000	0.34865	0.999000	0.59377	0.989000	0.77384	1.255000	0.32909	0.738000	0.32606	0.655000	0.94253	CTG	.	.		0.428	SEC23B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078184.5			G	18491492	C	G	18491492	3	3	312	1	0	0	0	0	1	0	0	0	14007	680	24	4	15	4	SEC23B	20	18491492	Missense_Mutation	SNP	C	TCGA-K7-AAU7-01A-11D-A382-10	9722378	18491492	44534028	66	44375										
TTC38	55020	hgsc.bcm.edu	37	chr22	46681166	46681166	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.104477611940299	7	1	1.61273344651952	2.91827956989247	1.20756395995551	1	1	0	tgaggccgcgctgaccatctAcgatacccacgtaagttgca	10	13	1	2			TCGA-K7-AAU7-01A-11D-A382-10	TCGA-K7-AAU7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad39f207-eb8e-4719-8887-cd482741dd5f	16cd1e7f-a4ad-474d-8aa1-d578f2f2db0c	g.chr22:46681166A>G	ENST00000381031.3	+	9	900	c.824A>G	c.(823-825)tAc>tGc	p.Y275C	TTC38_ENST00000445282.2_Missense_Mutation_p.Y217C	NM_017931.2	NP_060401	Q5R3I4	TTC38_HUMAN	tetratricopeptide repeat domain 38	275						extracellular vesicular exosome (GO:0070062)				endometrium(4)|large_intestine(3)|lung(4)|ovary(1)	12						CTGACCATCTACGATACCCAC	0.453																																					p.Y275C		Atlas-SNP	.											.	TTC38	40	.	0			c.A824G						.						137	128	131					22																	46681166		1953	4146	6099	SO:0001583	missense	55020	exon9			CCATCTACGATAC		CCDS43030.1	22q13	2013-01-11			ENSG00000075234	ENSG00000075234		"Tetratricopeptide (TTC) repeat domain containing"	26082	protein-coding gene	gene with protein product							Standard	NM_017931		Approved	FLJ20699	uc003bhi.3	Q5R3I4	OTTHUMG00000150494	ENST00000381031.3:c.824A>G	chr22.hg19:g.46681166A>G	ENSP00000370419:p.Tyr275Cys	106.0	0.0		67.0	23.0	NM_017931	Q8WV27|Q9NWP8	Missense_Mutation	SNP	ENST00000381031.3	hg19	CCDS43030.1	.	.	.	.	.	.	.	.	.	.	A	8.490	0.861838	0.17178	.	.	ENSG00000075234	ENST00000381031;ENST00000445282	T;T	0.81415	1.29;-1.49	5.03	2.87	0.33458	Tetratricopeptide-like helical (1);	0.167804	0.53938	D	0.000044	D	0.89787	0.6816	M	0.88241	2.94	0.18873	N	0.999989	D;D	0.89917	0.995;1.0	D;D	0.74023	0.931;0.982	T	0.83056	-0.0150	10	0.72032	D	0.01	-1.4444	11.7344	0.51757	0.7644:0.0:0.0:0.2356	.	217;275	E7ES35;Q5R3I4	.;TTC38_HUMAN	C	275;217	ENSP00000370419:Y275C;ENSP00000393960:Y217C	ENSP00000370419:Y275C	Y	+	2	0	TTC38	45059830	0.969000	0.33509	0.000000	0.03702	0.001000	0.01503	1.755000	0.38379	0.015000	0.14971	-2.489000	0.00195	TAC	.	.		0.453	TTC38-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000318469.1	NM_017931		G	46681166	A	G	46681166	3	3	312	1	0	0	0	0	1	0	0	0	16721	391	14	2	858	2	TTC38	22	46681166	Missense_Mutation	SNP	A	TCGA-K7-AAU7-01A-11D-A382-10		46681166	4623400	67	44376										
PPT1	5538	hgsc.bcm.edu	37	chr1	40539787	40539787	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	cattcttcagacaactgaagAtggtccccttctgtagccag	8	12	3	3			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr1:40539787A>G	ENST00000433473.3	-	9	1331	c.867T>C	c.(865-867)caT>caC	p.H289H	PPT1_ENST00000372775.2_5'UTR|PPT1_ENST00000530076.1_Silent_p.H70H|PPT1_ENST00000449045.2_Silent_p.H186H	NM_000310.3	NP_000301.1	P50897	PPT1_HUMAN	palmitoyl-protein thioesterase 1	289					adult locomotory behavior (GO:0008344)|associative learning (GO:0008306)|brain development (GO:0007420)|cell death (GO:0008219)|cellular protein catabolic process (GO:0044257)|cofactor metabolic process (GO:0051186)|cofactor transport (GO:0051181)|grooming behavior (GO:0007625)|lipid catabolic process (GO:0016042)|lysosomal lumen acidification (GO:0007042)|membrane raft organization (GO:0031579)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)|neuron development (GO:0048666)|neurotransmitter secretion (GO:0007269)|pinocytosis (GO:0006907)|positive regulation of pinocytosis (GO:0048549)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein catabolic process (GO:0030163)|protein depalmitoylation (GO:0002084)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|regulation of phospholipase A2 activity (GO:0032429)|regulation of synapse structure and activity (GO:0050803)|sphingolipid catabolic process (GO:0030149)|visual perception (GO:0007601)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)	palmitoyl-(protein) hydrolase activity (GO:0008474)|palmitoyl-CoA hydrolase activity (GO:0016290)			endometrium(5)|large_intestine(1)|lung(3)|ovary(1)|stomach(1)	11	Lung NSC(20;3.43e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1e-18)|Epithelial(16;3.6e-17)|all cancers(16;1.1e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			ACAACTGAAGATGGTCCCCTT	0.458																																					p.H289H		Atlas-SNP	.											.	PPT1	18	.	0			c.T867C						.						154	144	148					1																	40539787		2203	4300	6503	SO:0001819	synonymous_variant	5538	exon9			CTGAAGATGGTCC	U44772	CCDS447.1, CCDS44119.1	1p32	2014-09-17	2008-07-31		ENSG00000131238	ENSG00000131238	3.1.2.22		9325	protein-coding gene	gene with protein product	"ceroid-lipofuscinosis, neuronal 1, infantile"	600722		PPT		7637805, 8325646	Standard	NM_000310		Approved	CLN1, INCL	uc001cfb.2	P50897	OTTHUMG00000004495	ENST00000433473.3:c.867T>C	chr1.hg19:g.40539787A>G		83.0	0.0		78.0	16.0	NM_000310	B4DY24|Q6FGQ4	Silent	SNP	ENST00000433473.3	hg19	CCDS447.1																																																																																			.	.		0.458	PPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000013126.2	NM_000310		G	40539787	A	G	40539787	2	3	313	1	0	0	0	0	0	0	0	1	12423	330	12	2		2	PPT1	1	40539787	Silent	SNP	A	TCGA-KR-A7K0-01A-12D-A33Q-10		40539787	208710834	1	44377										
CTPS	1503	hgsc.bcm.edu	37	chr1	41457492	41457492	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	agtgaaggagaaaatatcaaTgttctgccatgttgagcctg	11	6	2	3			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr1:41457492T>C	ENST00000372621.4	+	7	1203	c.695T>C	c.(694-696)aTg>aCg	p.M232T	CTPS1_ENST00000372616.1_Missense_Mutation_p.M232T|CTPS1_ENST00000541520.1_Start_Codon_SNP_p.M1T|CTPS1_ENST00000543104.1_Missense_Mutation_p.M239T	NM_001905.2	NP_001896.2			CTP synthase 1											endometrium(3)|lung(10)	13						AAAATATCAATGTTCTGCCAT	0.393																																					p.M232T		Atlas-SNP	.											.	CTPS1	34	.	0			c.T695C						.						123	113	117					1																	41457492		2203	4300	6503	SO:0001583	missense	1503	exon7			TATCAATGTTCTG	BC009408	CCDS459.1	1p34.1	2012-05-02	2012-05-02	2012-05-02	ENSG00000171793	ENSG00000171793	6.3.4.2		2519	protein-coding gene	gene with protein product		123860	"CTP synthase"	CTPS		1783378	Standard	XM_005270536		Approved		uc001cgk.4	P17812	OTTHUMG00000005712	ENST00000372621.4:c.695T>C	chr1.hg19:g.41457492T>C	ENSP00000361704:p.Met232Thr	137.0	0.0		158.0	51.0	NM_001905		Missense_Mutation	SNP	ENST00000372621.4	hg19	CCDS459.1	.	.	.	.	.	.	.	.	.	.	T	18.70	3.679250	0.68042	.	.	ENSG00000171793	ENST00000372621;ENST00000541520;ENST00000543104;ENST00000372616	T;T;T	0.50277	0.99;0.75;0.99	6.17	6.17	0.99709	CTP synthase, N-terminal (1);	0.032670	0.85682	D	0.000000	T	0.49949	0.1587	M	0.64080	1.96	0.80722	D	1	B;B	0.19583	0.009;0.037	B;B	0.29077	0.021;0.098	T	0.41716	-0.9493	10	0.32370	T	0.25	.	15.6463	0.77055	0.0:0.0:0.0:1.0	.	239;232	B7Z9C4;P17812	.;PYRG1_HUMAN	T	232;1;239;232	ENSP00000361704:M232T;ENSP00000442646:M1T;ENSP00000361699:M232T	ENSP00000361699:M232T	M	+	2	0	CTPS	41230079	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	7.617000	0.83032	2.371000	0.80710	0.533000	0.62120	ATG	.	.		0.393	CTPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015629.1	NM_001905		C	41457492	T	C	41457492	3	2	313	1	0	0	0	0	1	0	0	0	4024	1464	51	2	717	2	CTPS	1	41457492	Missense_Mutation	SNP	T	TCGA-KR-A7K0-01A-12D-A33Q-10	917705	41457492	207793129	2	44378										
FRRS1	391059	hgsc.bcm.edu	37	chr1	100214255	100214256	+	Frame_Shift_Ins	INS	-	-	A													0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	tgtgttacttttccattgggINSataattagccacataactaa							TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr1:100214255_100214256insA	ENST00000414213.1	-	3	670_671	c.69_70insT	c.(67-72)tatcccfs	p.P24fs	FRRS1_ENST00000287474.5_Frame_Shift_Ins_p.P24fs			Q6ZNA5	FRRS1_HUMAN	ferric-chelate reductase 1	24	Reelin. {ECO:0000255|PROSITE- ProRule:PRU00363}.					integral component of membrane (GO:0016021)	ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(12)|pancreas(1)|skin(1)|urinary_tract(1)	26		all_epithelial(167;2.09e-06)|all_lung(203;0.000435)|Lung NSC(277;0.00201)		Epithelial(280;0.0718)|all cancers(265;0.126)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.206)		TTTCCATTGGGATAATTAGCCA	0.406																																					p.P24fs		Atlas-Indel,Pindel	.											.	FRRS1	50	.	0			c.70_71insT						.																																			SO:0001589	frameshift_variant	391059	exon3			.	AK131302	CCDS30780.1	1p21.3	2009-11-30	2006-02-22	2006-02-22	ENSG00000156869	ENSG00000156869			27622	protein-coding gene	gene with protein product		611578	"stromal cell derived factor receptor 2 homolog (mouse)"	SDFR2			Standard	NM_001013660		Approved	SDR2	uc001dsh.1	Q6ZNA5	OTTHUMG00000010768	ENST00000414213.1:c.70dupT	chr1.hg19:g.100214256_100214256dupA	ENSP00000393884:p.Pro24fs	215.0	0.0		265.0	72.0	NM_001013660	A6NLN7	Frame_Shift_Ins	INS	ENST00000414213.1	hg19																																																																																				.	.		0.406	FRRS1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001013660		A	100214256	-	A	100214255	7	5	313	1	0	1	1	0	0	0	0	0	6068	1174	41	0	1870	0	FRRS1	1	100214255	Frame_Shift_Ins	INS	-	TCGA-KR-A7K0-01A-12D-A33Q-10	58756763	100214255	149036366	3	44379										
ATP1A1	476	hgsc.bcm.edu	37	chr1	116932324	116932324	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	cggaaggtttgctggccactGtcacggtaagaggcaggtga	16	8	1	2			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr1:116932324G>A	ENST00000295598.5	+	8	1270	c.1018G>A	c.(1018-1020)Gtc>Atc	p.V340I	ATP1A1_ENST00000491156.1_3'UTR|ATP1A1_ENST00000369496.4_Missense_Mutation_p.V309I|ATP1A1_ENST00000537345.1_Missense_Mutation_p.V340I	NM_000701.7	NP_000692.2	P05023	AT1A1_HUMAN	ATPase, Na+/K+ transporting, alpha 1 polypeptide	340					ATP biosynthetic process (GO:0006754)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|membrane hyperpolarization (GO:0060081)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of glucocorticoid biosynthetic process (GO:0031947)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart contraction (GO:0045823)|positive regulation of striated muscle contraction (GO:0045989)|potassium ion import (GO:0010107)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of sodium ion transport (GO:0002028)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|chaperone binding (GO:0051087)|phosphatase activity (GO:0016791)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(2)|breast(2)|cervix(3)|endometrium(2)|kidney(5)|large_intestine(9)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47	Lung SC(450;0.225)	all_cancers(81;1.28e-06)|all_epithelial(167;3.48e-07)|all_lung(203;2.64e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0164)|LUSC - Lung squamous cell carcinoma(189;0.0548)|Colorectal(144;0.0825)|COAD - Colon adenocarcinoma(174;0.127)|all cancers(265;0.24)	Acetyldigitoxin(DB00511)|Almitrine(DB01430)|Aluminium(DB01370)|Bepridil(DB01244)|Bretylium(DB01158)|Ciclopirox(DB01188)|Deslanoside(DB01078)|Diazoxide(DB01119)|Digitoxin(DB01396)|Digoxin(DB00390)|Ethacrynic acid(DB00903)|Hydroflumethiazide(DB00774)|Ouabain(DB01092)|Trichlormethiazide(DB01021)	GCTGGCCACTGTCACGGTAAG	0.488																																					p.V340I		Atlas-SNP	.											.	ATP1A1	87	.	0			c.G1018A						.						109	85	93					1																	116932324		2203	4300	6503	SO:0001583	missense	476	exon8			GCCACTGTCACGG	D00099	CCDS887.1, CCDS53351.1, CCDS53352.1	1p13	2012-10-22			ENSG00000163399	ENSG00000163399	3.6.3.9	"ATPases / P-type"	799	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-1", "sodium pump subunit alpha-1", "sodium-potassium ATPase catalytic subunit alpha-1"	182310					Standard	NM_000701		Approved		uc001ege.3	P05023	OTTHUMG00000012109	ENST00000295598.5:c.1018G>A	chr1.hg19:g.116932324G>A	ENSP00000295598:p.Val340Ile	62.0	0.0		95.0	34.0	NM_001160233	B2RBR6|B7Z2T5|B7Z3U6|F5H3A1|Q16689|Q6LDM4|Q9UCN1|Q9UJ20|Q9UJ21	Missense_Mutation	SNP	ENST00000295598.5	hg19	CCDS887.1	.	.	.	.	.	.	.	.	.	.	G	35	5.498466	0.96355	.	.	ENSG00000163399	ENST00000295598;ENST00000537345;ENST00000339159;ENST00000369496	D;D;D	0.91792	-2.91;-2.91;-2.91	4.87	4.87	0.63330	ATPase, P-type, ATPase-associated domain (1);	0.000000	0.85682	D	0.000000	D	0.95322	0.8482	M	0.72894	2.215	0.80722	D	1	D;D	0.65815	0.994;0.995	D;D	0.91635	0.998;0.999	D	0.95618	0.8678	10	0.87932	D	0	.	18.2082	0.89861	0.0:0.0:1.0:0.0	.	340;340	F5H3A1;P05023	.;AT1A1_HUMAN	I	340;340;339;309	ENSP00000295598:V340I;ENSP00000445306:V340I;ENSP00000358508:V309I	ENSP00000295598:V340I	V	+	1	0	ATP1A1	116733847	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	9.657000	0.98554	2.558000	0.86282	0.650000	0.86243	GTC	.	.		0.488	ATP1A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033481.5	NM_001160233		A	116932324	G	A	116932324	3	1	313	1	0	0	0	0	1	0	0	0	1128	1377	48	3	1064	3	ATP1A1	1	116932324	Missense_Mutation	SNP	G	TCGA-KR-A7K0-01A-12D-A33Q-10	16718069	116932324	132318297	4	44380										
RUSC1	23623	hgsc.bcm.edu	37	chr1	155292686	155292686	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	gtcaccaccttcaaggaactCcggtcccgaagccgggcccc	10	18	2	0			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr1:155292686C>A	ENST00000368352.5	+	2	1273	c.1122C>A	c.(1120-1122)ctC>ctA	p.L374L	RUSC1-AS1_ENST00000543656.1_RNA|RUSC1_ENST00000368354.3_Silent_p.L374L|RUSC1-AS1_ENST00000443642.1_RNA|RUSC1-AS1_ENST00000446880.1_RNA|RUSC1-AS1_ENST00000450199.1_RNA|RUSC1_ENST00000368347.4_5'Flank|RUSC1_ENST00000368349.4_5'Flank|RUSC1_ENST00000292254.4_5'Flank	NM_001105203.1	NP_001098673.1	Q9BVN2	RUSC1_HUMAN	RUN and SH3 domain containing 1	374					positive regulation of signal transduction (GO:0009967)|protein polyubiquitination (GO:0000209)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(2)|skin(1)|urinary_tract(1)	21	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;1.55e-10)|all cancers(21;4.15e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)			TCAAGGAACTCCGGTCCCGAA	0.731																																					p.L374L		Atlas-SNP	.											.	RUSC1	85	.	0			c.C1122A						.						9	11	10					1																	155292686		1765	3994	5759	SO:0001819	synonymous_variant	23623	exon2			GGAACTCCGGTCC	AB026894	CCDS1112.1, CCDS41410.1, CCDS41411.1, CCDS41412.1	1q21-q22	2011-04-28			ENSG00000160753	ENSG00000160753			17153	protein-coding gene	gene with protein product						10760598	Standard	NM_001105203		Approved	NESCA	uc001fkj.2	Q9BVN2	OTTHUMG00000013910	ENST00000368352.5:c.1122C>A	chr1.hg19:g.155292686C>A		99.0	0.0		131.0	38.0	NM_001105203	B3KWM9|Q5T9U9|Q5T9V0|Q5T9V1|Q5T9V2|Q9UPY4|Q9Y4T5	Silent	SNP	ENST00000368352.5	hg19	CCDS41410.1																																																																																			.	.		0.731	RUSC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039071.1			A	155292686	C	A	155292686	2	1	313	1	0	0	0	0	0	0	0	1	13765	842	30	3		3	RUSC1	1	155292686	Silent	SNP	C	TCGA-KR-A7K0-01A-12D-A33Q-10	38360362	155292686	93957935	5	44381										
GON4L	54856	hgsc.bcm.edu	37	chr1	155736387	155736387	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	tcactccccaactccaaattGtctttttctaggcttcgatc	4	14	3	0			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr1:155736387G>A	ENST00000368331.1	-	21	2925	c.2877C>T	c.(2875-2877)gaC>gaT	p.D959D	GON4L_ENST00000471341.1_5'UTR|GON4L_ENST00000437809.1_Silent_p.D959D|GON4L_ENST00000271883.5_Silent_p.D959D|GON4L_ENST00000361040.5_Silent_p.D959D	NM_001282858.1|NM_001282860.1	NP_001269787.1|NP_001269789.1	Q3T8J9	GON4L_HUMAN	gon-4-like (C. elegans)	959					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	45	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					ACTCCAAATTGTCTTTTTCTA	0.502																																					p.D959D		Atlas-SNP	.											.	GON4L	392	.	0			c.C2877T						.						137	130	132					1																	155736387		2203	4300	6503	SO:0001819	synonymous_variant	54856	exon21			CAAATTGTCTTTT	AB046826	CCDS1121.1, CCDS44242.1, CCDS60296.1	1q22	2013-10-31	2006-11-08	2006-02-16	ENSG00000116580	ENSG00000116580			25973	protein-coding gene	gene with protein product		610393	"gon-4 homolog (C.elegans)"	GON4		16545939, 21454521	Standard	XM_005245283		Approved	FLJ20203, GON-4	uc001fly.1	Q3T8J9	OTTHUMG00000014106	ENST00000368331.1:c.2877C>T	chr1.hg19:g.155736387G>A		117.0	0.0		186.0	39.0	NM_001037533	B7ZBL4|Q14C93|Q3T8J8|Q5VYZ5|Q5W0D5|Q6AWA6|Q6P1Q6|Q7Z3L3|Q8IY79|Q9BQI1|Q9HCG6	Silent	SNP	ENST00000368331.1	hg19																																																																																				.	.		0.502	GON4L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_032292		A	155736387	G	A	155736387	2	1	313	1	0	0	0	0	0	0	0	1	6580	1368	48	3		3	GON4L	1	155736387	Silent	SNP	G	TCGA-KR-A7K0-01A-12D-A33Q-10	443701	155736387	93514234	6	44382										
HMCN1	83872	hgsc.bcm.edu	37	chr1	185985310	185985310	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	gaaattgatcgaggacagtaCatatgcgtggctaccagtgt	12	7	0	1			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr1:185985310C>A	ENST00000271588.4	+	32	5359	c.5130C>A	c.(5128-5130)taC>taA	p.Y1710*	HMCN1_ENST00000367492.2_Nonsense_Mutation_p.Y1710*	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	1710	Ig-like C2-type 14.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						GAGGACAGTACATATGCGTGG	0.433																																					p.Y1710X		Atlas-SNP	.											.	HMCN1	797	.	0			c.C5130A						.						118	109	112					1																	185985310		2203	4300	6503	SO:0001587	stop_gained	83872	exon32			ACAGTACATATGC	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.5130C>A	chr1.hg19:g.185985310C>A	ENSP00000271588:p.Tyr1710*	138.0	0.0		205.0	111.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Nonsense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	C	45	11.801259	0.99604	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	.	.	.	5.87	-1.26	0.09376	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.6458	0.62281	0.0:0.5833:0.0:0.4167	.	.	.	.	X	1710	.	ENSP00000271588:Y1710X	Y	+	3	2	HMCN1	184251933	0.031000	0.19500	0.528000	0.27938	0.755000	0.42902	-0.013000	0.12678	-0.368000	0.08040	-0.345000	0.07892	TAC	.	.		0.433	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		A	185985310	C	A	185985310	4	1	313	1	0	0	0	0	0	1	0	0	7229	489	17	3	5256	3	HMCN1	1	185985310	Nonsense_Mutation	SNP	C	TCGA-KR-A7K0-01A-12D-A33Q-10	30248923	185985310	63265311	7	44383										
CFH	3075	hgsc.bcm.edu	37	chr1	196684870	196684870	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	ttccatagtgtgtggttacaAtggttggtctgatttaccca	10	7	1	1			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr1:196684870A>T	ENST00000367429.4	+	11	1907	c.1667A>T	c.(1666-1668)aAt>aTt	p.N556I		NM_000186.3	NP_000177.2	P08603	CFAH_HUMAN	complement factor H	556	Sushi 9. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)			NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						TGTGGTTACAATGGTTGGTCT	0.333																																					p.N556I		Atlas-SNP	.											.	CFH	251	.	0			c.A1667T						.						238	225	229					1																	196684870		2203	4300	6503	SO:0001583	missense	3075	exon11			GTTACAATGGTTG	Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971		"Complement system"	4883	protein-coding gene	gene with protein product	"beta-1H", "H factor 2 (complement)", "age-related maculopathy susceptibility 1"	134370	"H factor 1 (complement)"	HF, HF1, HF2		2889480, 2963625	Standard	NM_000186		Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000367429.4:c.1667A>T	chr1.hg19:g.196684870A>T	ENSP00000356399:p.Asn556Ile	149.0	0.0		176.0	83.0	NM_000186	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Missense_Mutation	SNP	ENST00000367429.4	hg19	CCDS1385.1	.	.	.	.	.	.	.	.	.	.	A	12.62	1.993812	0.35131	.	.	ENSG00000000971	ENST00000367429	T	0.69040	-0.37	5.42	1.73	0.24493	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.64294	0.2585	M	0.64997	1.995	0.09310	N	1	B	0.31640	0.333	B	0.40741	0.339	T	0.53041	-0.8494	9	0.20519	T	0.43	.	7.3773	0.26835	0.74:0.0:0.26:0.0	.	556	P08603	CFAH_HUMAN	I	556	ENSP00000356399:N556I	ENSP00000356399:N556I	N	+	2	0	CFH	194951493	0.022000	0.18835	0.012000	0.15200	0.002000	0.02628	0.610000	0.24253	0.038000	0.15604	0.533000	0.62120	AAT	.	.		0.333	CFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086412.2	NM_000186		T	196684870	A	T	196684870	3	4	313	1	0	0	0	0	1	0	0	0	3285	101	4	4	1727	4	CFH	1	196684870	Missense_Mutation	SNP	A	TCGA-KR-A7K0-01A-12D-A33Q-10	10699560	196684870	52565751	8	44384										
USH2A	7399	hgsc.bcm.edu	37	chr1	215932021	215932021	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	gatttcttctggtgttgacaTaggtgtttgaacaatgtaat	10	4	2	2			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr1:215932021T>A	ENST00000307340.3	-	58	11691	c.11305A>T	c.(11305-11307)Atg>Ttg	p.M3769L	USH2A_ENST00000366943.2_Missense_Mutation_p.M3769L	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3769	Fibronectin type-III 22. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			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)		GGTGTTGACATAGGTGTTTGA	0.333										HNSCC(13;0.011)																											p.M3769L		Atlas-SNP	.											.	USH2A	1168	.	0			c.A11305T						.						174	173	173					1																	215932021		2203	4300	6503	SO:0001583	missense	7399	exon58			TTGACATAGGTGT	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.11305A>T	chr1.hg19:g.215932021T>A	ENSP00000305941:p.Met3769Leu	81.0	0.0		125.0	18.0	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	T	5.979	0.364568	0.11296	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.52057	0.68;0.68	5.9	-8.63	0.00878	Fibronectin, type III (1);Immunoglobulin-like fold (1);	2.808690	0.01404	N	0.013724	T	0.17109	0.0411	N	0.04508	-0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21930	-1.0231	10	0.09843	T	0.71	.	1.637	0.02744	0.1762:0.1496:0.257:0.4172	.	3769	O75445	USH2A_HUMAN	L	3769	ENSP00000305941:M3769L;ENSP00000355910:M3769L	ENSP00000305941:M3769L	M	-	1	0	USH2A	213998644	0.000000	0.05858	0.000000	0.03702	0.181000	0.23173	-2.366000	0.01078	-2.241000	0.00709	-0.480000	0.04831	ATG	.	.		0.333	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		A	215932021	T	A	215932021	3	1	313	1	0	0	0	0	1	0	0	0	17051	1406	49	4	4363	4	USH2A	1	215932021	Missense_Mutation	SNP	T	TCGA-KR-A7K0-01A-12D-A33Q-10	19247151	215932021	33318600	9	44385										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228560355	228560355	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	tcaggtgatgcggaggcggcCgacacaatatccctggacat	13	11	1	1	rs372263588		TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr1:228560355C>T	ENST00000422127.1	+	94	21920	c.21876C>T	c.(21874-21876)gcC>gcT	p.A7292A	OBSCN_ENST00000366707.4_Silent_p.A4926A|OBSCN_ENST00000570156.2_Silent_p.A8249A	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	7292					apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CGGAGGCGGCCGACACAATAT	0.592																																					p.A8249A		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C24747T						.	C		0,4028		0,0,2014	25	29	27		21876	-10.6	0	1		27	1,8331		0,1,4165	no	coding-synonymous	OBSCN	NM_001098623.1		0,1,6179	TT,TC,CC		0.012,0.0,0.0081		7292/7969	228560355	1,12359	2014	4166	6180	SO:0001819	synonymous_variant	84033	exon105			GGCGGCCGACACA	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.21876C>T	chr1.hg19:g.228560355C>T		296.0	0.0		382.0	178.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	C	8.089	0.774173	0.16051	0.0	1.2E-4	ENSG00000154358	ENST00000441106	.	.	.	5.31	-10.6	0.00265	.	.	.	.	.	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.2076	0.15299	0.3201:0.4181:0.1221:0.1397	.	.	.	.	X	1909	.	.	R	+	1	2	OBSCN	226626978	0.000000	0.05858	0.002000	0.10522	0.129000	0.20672	-5.329000	0.00131	-5.289000	0.00017	-1.579000	0.00862	CGA	.	.		0.592	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228560355	C	T	228560355	2	4	313	1	0	0	0	0	0	0	0	1	10821	639	23	1		1	OBSCN	1	228560355	Silent	SNP	C	TCGA-KR-A7K0-01A-12D-A33Q-10	12628334	228560355	20690266	10	44386										
CMPK2	129607	hgsc.bcm.edu	37	chr2	7003632	7003632	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	tcgatggcaacaacctggaaCtttcctttctggatctgttt	8	10	2	0			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr2:7003632C>A	ENST00000256722.5	-	2	752	c.753G>T	c.(751-753)aaG>aaT	p.K251N	CMPK2_ENST00000404168.1_Missense_Mutation_p.K251N|CMPK2_ENST00000478738.1_5'UTR|CMPK2_ENST00000458098.1_Missense_Mutation_p.K251N	NM_207315.3	NP_997198.2	Q5EBM0	CMPK2_HUMAN	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	251					cellular response to lipopolysaccharide (GO:0071222)|dTDP biosynthetic process (GO:0006233)|dUDP biosynthetic process (GO:0006227)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)|thymidylate kinase activity (GO:0004798)|UMP kinase activity (GO:0033862)			large_intestine(1)|lung(13)|prostate(1)|upper_aerodigestive_tract(1)	16	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					CAACCTGGAACTTTCCTTTCT	0.448																																					p.K251N		Atlas-SNP	.											.	CMPK2	30	.	0			c.G753T						.						134	132	133					2																	7003632		1900	4114	6014	SO:0001583	missense	129607	exon2			CTGGAACTTTCCT		CCDS42648.1, CCDS58695.1, CCDS58696.1	2p25.2	2008-01-25			ENSG00000134326	ENSG00000134326	2.7.4.14		27015	protein-coding gene	gene with protein product	"cytidylate kinase 2"	611787				17999954	Standard	NM_207315		Approved	TYKi, UMP-CMPK2	uc002qyo.4	Q5EBM0	OTTHUMG00000151629	ENST00000256722.5:c.753G>T	chr2.hg19:g.7003632C>A	ENSP00000256722:p.Lys251Asn	103.0	0.0		138.0	40.0	NM_001256478	A2RUB0|A5D8T2|B7ZM18|Q6ZRU2|Q96AL8	Missense_Mutation	SNP	ENST00000256722.5	hg19	CCDS42648.1	.	.	.	.	.	.	.	.	.	.	C	9.644	1.139675	0.21205	.	.	ENSG00000134326	ENST00000458098;ENST00000256722;ENST00000404168	T	0.50277	0.75	5.21	2.19	0.27852	.	0.722742	0.13832	N	0.359641	T	0.37210	0.0995	L	0.47716	1.5	0.30938	N	0.72609	B;B	0.18863	0.021;0.031	B;B	0.15484	0.013;0.009	T	0.39014	-0.9634	10	0.48119	T	0.1	-21.4232	6.5483	0.22418	0.2564:0.5791:0.0:0.1645	.	251;251	Q5EBM0-3;Q5EBM0	.;CMPK2_HUMAN	N	251	ENSP00000256722:K251N	ENSP00000256722:K251N	K	-	3	2	CMPK2	6921083	0.053000	0.20554	0.998000	0.56505	0.477000	0.33069	0.277000	0.18734	1.193000	0.43086	0.557000	0.71058	AAG	.	.		0.448	CMPK2-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323339.2	NM_207315		A	7003632	C	A	7003632	3	1	313	1	0	0	0	0	1	0	0	0	3583	564	20	3	612	3	CMPK2	2	7003632	Missense_Mutation	SNP	C	TCGA-KR-A7K0-01A-12D-A33Q-10		7003632	236195741	11	44387										
APOB	338	hgsc.bcm.edu	37	chr2	21232581	21232585	+	Frame_Shift_Del	DEL	TTATC	TTATC	-													0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	caatttctcaaagtaatcttTtatcttaacttgttgtagga							TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	TTATC	TTATC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr2:21232581_21232585delTTATC	ENST00000233242.1	-	26	7282_7286	c.7155_7159delGATAA	c.(7153-7161)aagataaaafs	p.KIK2385fs		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	2385					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AAGTAATCTTTTATCTTAACTTGTT	0.312																																					p.2386_2387del		Atlas-Indel,Pindel	.											.	APOB	761	.	0			c.7156_7160del	GRCh37	CD930898	APOB	D		.																																			SO:0001589	frameshift_variant	338	exon26			.	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.7155_7159delGATAA	chr2.hg19:g.21232581_21232585delTTATC	ENSP00000233242:p.Lys2385fs	171.0	0.0		217.0	67.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Frame_Shift_Del	DEL	ENST00000233242.1	hg19	CCDS1703.1																																																																																			.	.		0.312	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			-	21232585	TTATC	-	21232581	7	5	313	1	0	1	0	1	0	0	0	0	785	1850	64	0	6548	0	APOB	2	21232581	Frame_Shift_Del	DEL	TTATC	TCGA-KR-A7K0-01A-12D-A33Q-10	14228949	21232581	221966792	12	44388										
ANTXR1	84168	hgsc.bcm.edu	37	chr2	69379340	69379340	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	ccatcgccctgctgatcctgTtcctgctcctagccctggct	8	18	0	1			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr2:69379340T>C	ENST00000303714.4	+	13	1313	c.991T>C	c.(991-993)Ttc>Ctc	p.F331L	ANTXR1_ENST00000409349.3_Missense_Mutation_p.F331L	NM_032208.2	NP_115584.1	Q9H6X2	ANTR1_HUMAN	anthrax toxin receptor 1	331					actin cytoskeleton reorganization (GO:0031532)|reproductive process (GO:0022414)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|integral component of membrane (GO:0016021)|lamellipodium membrane (GO:0031258)	actin filament binding (GO:0051015)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|transmembrane signaling receptor activity (GO:0004888)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(16)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	29						GCTGATCCTGTTCCTGCTCCT	0.612									Familial Infantile Hemangioma																												p.F331L		Atlas-SNP	.											.	ANTXR1	128	.	0			c.T991C						.						227	162	184					2																	69379340		2203	4300	6503	SO:0001583	missense	84168	exon13	Familial Cancer Database	Infantile Capillary Hemangioma, HCI, Hereditary Capillary Hemangioma	ATCCTGTTCCTGC	AF421380	CCDS1892.1, CCDS46313.1, CCDS46314.1	2p13.1	2006-04-12			ENSG00000169604	ENSG00000169604			21014	protein-coding gene	gene with protein product	"anthrax toxin receptor", "tumor endothelial marker 8 precursor"	606410				10947988, 11559528	Standard	NM_032208		Approved	TEM8, FLJ21776, FLJ10601, ATR	uc002sfg.3	Q9H6X2	OTTHUMG00000129575	ENST00000303714.4:c.991T>C	chr2.hg19:g.69379340T>C	ENSP00000301945:p.Phe331Leu	70.0	0.0		71.0	14.0	NM_032208	A8K7U8|J7K7G4|J7KF88|Q4ZFV6|Q53QD8|Q96P02|Q9NVP3	Missense_Mutation	SNP	ENST00000303714.4	hg19	CCDS1892.1	.	.	.	.	.	.	.	.	.	.	T	7.991	0.753210	0.15778	.	.	ENSG00000169604	ENST00000303714;ENST00000409349	T;T	0.26957	1.7;2.14	5.85	5.85	0.93711	.	0.092384	0.85682	D	0.000000	T	0.14056	0.0340	N	0.12961	0.28	0.47737	D	0.999506	B;B	0.13145	0.007;0.002	B;B	0.13407	0.009;0.008	T	0.06481	-1.0824	10	0.02654	T	1	-23.9755	14.1824	0.65583	0.0:0.0:0.0:1.0	.	331;331	Q9H6X2;Q9H6X2-2	ANTR1_HUMAN;.	L	331	ENSP00000301945:F331L;ENSP00000386494:F331L	ENSP00000301945:F331L	F	+	1	0	ANTXR1	69232844	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	2.920000	0.48844	2.233000	0.73108	0.533000	0.62120	TTC	.	.		0.612	ANTXR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251770.2	NM_032208		C	69379340	T	C	69379340	3	2	313	1	0	0	0	0	1	0	0	0	711	1725	60	2	1096	2	ANTXR1	2	69379340	Missense_Mutation	SNP	T	TCGA-KR-A7K0-01A-12D-A33Q-10	48146759	69379340	173820033	13	44389										
SCN7A	6332	hgsc.bcm.edu	37	chr2	167298065	167298065	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	tcatgcatgtgccagcgtggGagttgacagtctttgtctat	12	8	3	1			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr2:167298065G>T	ENST00000409855.1	-	14	2124	c.1998C>A	c.(1996-1998)ctC>ctA	p.L666L		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	666					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	GCCAGCGTGGGAGTTGACAGT	0.448																																					p.L666L		Atlas-SNP	.											.	SCN7A	410	.	0			c.C1998A						.						119	124	122					2																	167298065		2203	4300	6503	SO:0001819	synonymous_variant	6332	exon14			GCGTGGGAGTTGA	M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10594	protein-coding gene	gene with protein product		182392	"sodium channel, voltage-gated, type VI, alpha", "sodium channel, voltage-gated, type VII, alpha"	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.1998C>A	chr2.hg19:g.167298065G>T		204.0	0.0		247.0	82.0	NM_002976		Silent	SNP	ENST00000409855.1	hg19	CCDS46442.1																																																																																			.	.		0.448	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1			T	167298065	G	T	167298065	2	4	313	1	0	0	0	0	0	0	0	1	13938	1161	41	3		3	SCN7A	2	167298065	Silent	SNP	G	TCGA-KR-A7K0-01A-12D-A33Q-10	97918725	167298065	75901308	14	44390										
TLK1	9874	hgsc.bcm.edu	37	chr2	171853223	171853223	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	acttctgtggcttttaatatTgtattttcttgaagaatgtc	7	5	2	2			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr2:171853223T>C	ENST00000431350.2	-	20	2468	c.2064A>G	c.(2062-2064)acA>acG	p.T688T	TLK1_ENST00000521943.1_Silent_p.T640T|TLK1_ENST00000360843.3_Silent_p.T709T|TLK1_ENST00000442919.2_Silent_p.T640T|TLK1_ENST00000434911.2_Silent_p.T592T			Q9UKI8	TLK1_HUMAN	tousled-like kinase 1	688	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of chromatin assembly or disassembly (GO:0001672)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|liver(3)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	33						CTTTTAATATTGTATTTTCTT	0.299																																					p.T688T		Atlas-SNP	.											.	TLK1	134	.	0			c.A2064G						.						95	99	98					2																	171853223		2203	4300	6503	SO:0001819	synonymous_variant	9874	exon20			TAATATTGTATTT	AB004885	CCDS2241.1, CCDS46447.1, CCDS46448.1	2q31.1	2010-04-19			ENSG00000198586	ENSG00000198586			11841	protein-coding gene	gene with protein product		608438				9427565, 12660173	Standard	NM_012290		Approved	KIAA0137, PKU-BETA	uc002ugp.2	Q9UKI8	OTTHUMG00000132243	ENST00000431350.2:c.2064A>G	chr2.hg19:g.171853223T>C		59.0	0.0		65.0	12.0	NM_012290	B3KR15|B4DX87|Q14150|Q8N591|Q9NYH2|Q9Y4F6	Silent	SNP	ENST00000431350.2	hg19	CCDS2241.1																																																																																			.	.		0.299	TLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255314.1	NM_012290		C	171853223	T	C	171853223	2	2	313	1	0	0	0	0	0	0	0	1	15958	1799	63	2		2	TLK1	2	171853223	Silent	SNP	T	TCGA-KR-A7K0-01A-12D-A33Q-10	4555158	171853223	71346150	15	44391										
TTN	7273	hgsc.bcm.edu	37	chr2	179438088	179438088	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	ttatcacgccgttccacaatAtaattgatgatttcacttcc	4	11	2	2			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr2:179438088A>G	ENST00000591111.1	-	276	68072	c.67848T>C	c.(67846-67848)taT>taC	p.Y22616Y	TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Silent_p.Y15317Y|TTN_ENST00000460472.2_Silent_p.Y15192Y|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000589042.1_Silent_p.Y24257Y|TTN_ENST00000342992.6_Silent_p.Y21689Y|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Silent_p.Y15384Y|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA			Q8WZ42	TITIN_HUMAN	titin	22616	Fibronectin type-III 64. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTTCCACAATATAATTGATGA	0.408																																					p.Y24257Y		Atlas-SNP	.											.	TTN	18412	.	0			c.T72771C						.						73	72	72					2																	179438088		1918	4136	6054	SO:0001819	synonymous_variant	7273	exon326			CACAATATAATTG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.67848T>C	chr2.hg19:g.179438088A>G		65.0	0.0		63.0	17.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179438088	A	G	179438088	2	3	313	1	0	0	0	0	0	0	0	1	16750	456	16	2		2	TTN	2	179438088	Silent	SNP	A	TCGA-KR-A7K0-01A-12D-A33Q-10	7584865	179438088	63761285	16	44392										
MAP2	4133	hgsc.bcm.edu	37	chr2	210594614	210594614	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	gagagtgtaaaactagatttCaaagaaaaggcccaagctaa	9	6	1	3			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr2:210594614C>T	ENST00000360351.4	+	14	5702	c.5196C>T	c.(5194-5196)ttC>ttT	p.F1732F	MAP2_ENST00000392194.1_Silent_p.F376F|MAP2_ENST00000361559.4_Silent_p.F376F|MAP2_ENST00000447185.1_Silent_p.F1728F|MAP2_ENST00000199940.6_Silent_p.F464F	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	1732					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	AACTAGATTTCAAAGAAAAGG	0.388																																					p.F1732F	Pancreas(27;423 979 28787 29963)	Atlas-SNP	.											.	MAP2	372	.	0			c.C5196T						.						115	109	111					2																	210594614		2203	4300	6503	SO:0001819	synonymous_variant	4133	exon14			AGATTTCAAAGAA		CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"A-kinase anchor proteins"	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.5196C>T	chr2.hg19:g.210594614C>T		123.0	0.0		133.0	25.0	NM_002374	Q17S04|Q8IUX2|Q99975|Q99976	Silent	SNP	ENST00000360351.4	hg19	CCDS2384.1																																																																																			.	.		0.388	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538		T	210594614	C	T	210594614	2	4	313	1	0	0	0	0	0	0	0	1	9244	825	29	3		3	MAP2	2	210594614	Silent	SNP	C	TCGA-KR-A7K0-01A-12D-A33Q-10	31156526	210594614	32604759	17	44393										
CNOT10	25904	hgsc.bcm.edu	37	chr3	32774933	32774933	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	agacttctgaacaagaaactAaaggccttcccagcaaaaaa	6	10	1	3			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr3:32774933A>G	ENST00000328834.5	+	11	1550	c.1234A>G	c.(1234-1236)Aaa>Gaa	p.K412E	CNOT10-AS1_ENST00000475395.2_RNA|CNOT10_ENST00000331889.6_Missense_Mutation_p.K412E|CNOT10_ENST00000454516.2_Missense_Mutation_p.K472E|CNOT10_ENST00000538368.1_Missense_Mutation_p.K184E	NM_015442.2	NP_056257.1	Q9H9A5	CNO10_HUMAN	CCR4-NOT transcription complex, subunit 10	412					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(3)	23						ACAAGAAACTAAAGGCCTTCC	0.318																																					p.K472E		Atlas-SNP	.											.	CNOT10	57	.	0			c.A1414G						.						73	76	75					3																	32774933		2203	4298	6501	SO:0001583	missense	25904	exon11			GAAACTAAAGGCC	BC002928	CCDS2655.1, CCDS58821.1, CCDS58822.1	3p23	2013-01-10			ENSG00000182973	ENSG00000182973		"Tetratricopeptide (TTC) repeat domain containing"	23817	protein-coding gene	gene with protein product							Standard	NR_046352		Approved	FLJ12890, FLJ13165	uc011axj.2	Q9H9A5	OTTHUMG00000130748	ENST00000328834.5:c.1234A>G	chr3.hg19:g.32774933A>G	ENSP00000330060:p.Lys412Glu	275.0	0.0		272.0	80.0	NM_001256742	B7Z7L1|F8WAF2|Q9BU30|Q9H5J7|Q9H8X1|Q9H9W0|Q9HAH3|Q9UFJ2	Missense_Mutation	SNP	ENST00000328834.5	hg19	CCDS2655.1	.	.	.	.	.	.	.	.	.	.	A	16.58	3.163325	0.57476	.	.	ENSG00000182973	ENST00000331889;ENST00000328834;ENST00000540405;ENST00000538368;ENST00000454516	T;T;T;T	0.44482	1.57;1.57;0.92;1.57	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	T	0.49184	0.1542	L	0.40543	1.245	0.80722	D	1	P;P;D;P	0.59767	0.774;0.885;0.986;0.817	B;P;P;B	0.58520	0.296;0.465;0.84;0.217	T	0.31998	-0.9923	10	0.11794	T	0.64	-28.9566	16.5885	0.84745	1.0:0.0:0.0:0.0	.	472;412;411;412	F8WAF2;Q9H9A5-3;Q9H9A5-2;Q9H9A5	.;.;.;CNOTA_HUMAN	E	412;412;312;184;472	ENSP00000329376:K412E;ENSP00000330060:K412E;ENSP00000442552:K184E;ENSP00000399862:K472E	ENSP00000330060:K412E	K	+	1	0	CNOT10	32749937	1.000000	0.71417	0.998000	0.56505	0.982000	0.71751	9.208000	0.95075	2.317000	0.78254	0.460000	0.39030	AAA	.	.		0.318	CNOT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253248.2	NM_015442		G	32774933	A	G	32774933	3	3	313	1	0	0	0	0	1	0	0	0	3620	363	13	2	1276	2	CNOT10	3	32774933	Missense_Mutation	SNP	A	TCGA-KR-A7K0-01A-12D-A33Q-10		32774933	165247497	18	44394										
CTDSPL	10217	hgsc.bcm.edu	37	chr3	38017293	38017293	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	tttttcatcgtgggaactacGtgaaggacctgagtcgcctt	11	9	1	2			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr3:38017293G>T	ENST00000273179.5	+	7	639	c.613G>T	c.(613-615)Gtg>Ttg	p.V205L	CTDSPL_ENST00000310189.3_3'UTR|CTDSPL_ENST00000443503.2_Missense_Mutation_p.V194L	NM_001008392.1	NP_001008393.1	O15194	CTDSL_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase-like	205	FCP1 homology. {ECO:0000255|PROSITE- ProRule:PRU00336}.					extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			breast(1)|endometrium(2)|large_intestine(4)|skin(1)	8		Melanoma(1037;0.0122)		KIRC - Kidney renal clear cell carcinoma(284;0.0729)|Kidney(284;0.0902)		TGGGAACTACGTGAAGGACCT	0.532																																					p.V205L		Atlas-SNP	.											.	CTDSPL	17	.	0			c.G613T						.						117	119	118					3																	38017293		2203	4300	6503	SO:0001583	missense	10217	exon7			AACTACGTGAAGG	D88153	CCDS33734.1, CCDS33735.1	3p21.3	2010-06-21	2003-10-27	2003-10-29	ENSG00000144677	ENSG00000144677	3.1.3.16	"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	16890	protein-coding gene	gene with protein product	"small CTD phosphatase 3", "HYA22 protein", "RB protein serine phosphatase from chromosome 3"	608592	"chromosome 3 open reading frame 8"	C3orf8		9179494, 12543795	Standard	NM_005808		Approved	HYA22, SCP3, PSR1, RBSP3	uc003chg.3	O15194	OTTHUMG00000155942	ENST00000273179.5:c.613G>T	chr3.hg19:g.38017293G>T	ENSP00000273179:p.Val205Leu	71.0	0.0		64.0	25.0	NM_001008392	Q3ZTU0|Q70KI4|Q7Z5Q2	Missense_Mutation	SNP	ENST00000273179.5	hg19	CCDS33734.1	.	.	.	.	.	.	.	.	.	.	G	28.6	4.936838	0.92458	.	.	ENSG00000144677	ENST00000443503;ENST00000273179;ENST00000447745	T;T;T	0.16743	2.32;2.32;2.32	4.79	4.79	0.61399	NLI interacting factor (3);Dullard phosphatase domain, eukaryotic (1);HAD-like domain (2);	0.000000	0.85682	D	0.000000	T	0.45054	0.1323	M	0.82132	2.575	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.67725	0.922;0.953	T	0.51655	-0.8678	10	0.87932	D	0	-2.4139	18.2041	0.89848	0.0:0.0:1.0:0.0	.	194;205	O15194-2;O15194	.;CTDSL_HUMAN	L	194;205;94	ENSP00000398288:V194L;ENSP00000273179:V205L;ENSP00000407443:V94L	ENSP00000273179:V205L	V	+	1	0	CTDSPL	37992297	1.000000	0.71417	0.983000	0.44433	0.941000	0.58515	9.667000	0.98616	2.386000	0.81285	0.561000	0.74099	GTG	.	.		0.532	CTDSPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342392.1	NM_005808		T	38017293	G	T	38017293	3	4	313	1	0	0	0	0	1	0	0	0	4007	1145	40	1	639	1	CTDSPL	3	38017293	Missense_Mutation	SNP	G	TCGA-KR-A7K0-01A-12D-A33Q-10	5242360	38017293	160005137	19	44395										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266112	41266112	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	acctggactctggaatccatTctggtgccactaccacagct	8	14	2	0	rs121913416|rs121913228		TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr3:41266112T>G	ENST00000349496.5	+	3	389	c.109T>G	c.(109-111)Tct>Gct	p.S37A	CTNNB1_ENST00000405570.1_Missense_Mutation_p.S37A|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S37A|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S37A|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S30A	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	37			S -> A (in MDB and hepatocellular carcinoma; enhances transactivation of target genes). {ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10666372}.|S -> C (in PTR, hepatoblastoma and ovarian cancer). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10391090, ECO:0000269|PubMed:9927029}.|S -> F (in PTR). {ECO:0000269|PubMed:10192393}.|S -> Y (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|SG -> W (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S37A(62)|p.A5_A80del(53)|p.S37P(21)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.I35_S37>T(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.S37T(1)|p.I35_K170del(1)|p.H24_G38del(1)|p.I35_T41del(1)|p.I35_G38del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.D32fs*9(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.GIHS34?(1)|p.S37_G38>W(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TGGAATCCATTCTGGTGCCAC	0.498	S37P(HEC108_ENDOMETRIUM)|S37P(SNGM_ENDOMETRIUM)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S37A	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,-1,1	CTNNB1	4904	.	214	Deletion - In frame(102)|Substitution - Missense(84)|Complex - deletion inframe(18)|Unknown(7)|Deletion - Frameshift(3)	liver(108)|large_intestine(33)|stomach(21)|endometrium(13)|small_intestine(10)|parathyroid(9)|central_nervous_system(8)|skin(3)|ovary(3)|pancreas(2)|adrenal_gland(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|pituitary(1)	c.T109G						.						94	79	84					3																	41266112		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	ATCCATTCTGGTG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.109T>G	chr3.hg19:g.41266112T>G	ENSP00000344456:p.Ser37Ala	163.0	0.0		162.0	25.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.591559	0.86953	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92;0.92;0.92;0.92;0.92	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.67468	0.2896	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.72357	-0.4318	10	0.87932	D	0	-15.9763	16.0677	0.80897	0.0:0.0:0.0:1.0	.	37	P35222	CTNB1_HUMAN	A	30;37;37;37;37;30;37;37;37	ENSP00000400508:S30A;ENSP00000385604:S37A;ENSP00000412219:S37A;ENSP00000379486:S37A;ENSP00000344456:S37A;ENSP00000411226:S30A;ENSP00000379488:S37A;ENSP00000409302:S37A;ENSP00000401599:S37A	ENSP00000344456:S37A	S	+	1	0	CTNNB1	41241116	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.201000	0.70794	0.533000	0.62120	TCT	.	.		0.498	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266112	T	G	41266112	3	3	313	1	0	0	0	0	1	0	0	0	4018	1783	62	5	115	5	CTNNB1	3	41266112	Missense_Mutation	SNP	T	TCGA-KR-A7K0-01A-12D-A33Q-10	3248819	41266112	156756318	20	44396										
PXK	54899	hgsc.bcm.edu	37	chr3	58383369	58383369	+	Nonsense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	tgtccactgctttggccactTactgtatgaaatgacttatg	8	9	0	2			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr3:58383369T>G	ENST00000356151.2	+	11	1131	c.1022T>G	c.(1021-1023)tTa>tGa	p.L341*	PXK_ENST00000536660.1_Nonsense_Mutation_p.L204*|PXK_ENST00000463280.1_Nonsense_Mutation_p.L308*|PXK_ENST00000383716.3_Nonsense_Mutation_p.L308*|PXK_ENST00000302779.5_Nonsense_Mutation_p.L324*|PXK_ENST00000479241.1_Nonsense_Mutation_p.L324*|PXK_ENST00000484288.1_Nonsense_Mutation_p.L341*|PXK_ENST00000383715.4_Nonsense_Mutation_p.L324*	NM_017771.3	NP_060241.2			PX domain containing serine/threonine kinase											cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000249)|KIRC - Kidney renal clear cell carcinoma(10;0.00346)|Kidney(10;0.00368)|OV - Ovarian serous cystadenocarcinoma(275;0.22)		TTTGGCCACTTACTGTATGAA	0.552																																					p.L341X		Atlas-SNP	.											.	PXK	89	.	0			c.T1022G						.						228	207	214					3																	58383369		2203	4300	6503	SO:0001587	stop_gained	54899	exon11			GCCACTTACTGTA	AY274811	CCDS2889.1, CCDS74952.1, CCDS74954.1, CCDS74955.1	3p21.2	2008-02-05			ENSG00000168297	ENSG00000168297			23326	protein-coding gene	gene with protein product		611450					Standard	XM_005265255		Approved	FLJ20335	uc003djz.1	Q7Z7A4	OTTHUMG00000159149	ENST00000356151.2:c.1022T>G	chr3.hg19:g.58383369T>G	ENSP00000348472:p.Leu341*	124.0	0.0		98.0	28.0	NM_017771		Nonsense_Mutation	SNP	ENST00000356151.2	hg19	CCDS2889.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	38|38	6.889215|6.889215	0.97912|0.97912	.|.	.|.	ENSG00000168297|ENSG00000168297	ENST00000356151;ENST00000302779;ENST00000383716;ENST00000463280;ENST00000383715;ENST00000484288;ENST00000479241;ENST00000536660;ENST00000536750|ENST00000479134	.|.	.|.	.|.	5.52|5.52	5.52|5.52	0.82312|0.82312	.|.	0.068230|.	0.64402|.	D|.	0.000009|.	.|T	.|0.71567	.|0.3355	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.73786	.|-0.3873	.|3	0.02654|.	T|.	1|.	-10.2912|-10.2912	15.8062|15.8062	0.78513|0.78513	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|.	.|.	.|.	X|D	341;324;308;308;324;341;324;204;204|96	.|.	ENSP00000305045:L324X|.	L|Y	+|+	2|1	0|0	PXK|PXK	58358409|58358409	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.960000|0.960000	0.62799|0.62799	5.472000|5.472000	0.66768|0.66768	2.317000|2.317000	0.78254|0.78254	0.460000|0.460000	0.39030|0.39030	TTA|TAC	.	.		0.552	PXK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353499.1	NM_017771		G	58383369	T	G	58383369	4	3	313	1	0	0	0	0	0	1	0	0	12864	1764	61	5	1064	5	PXK	3	58383369	Nonsense_Mutation	SNP	T	TCGA-KR-A7K0-01A-12D-A33Q-10	17117257	58383369	139639061	21	44397										
CCDC80	151887	hgsc.bcm.edu	37	chr3	112358134	112358134	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	gggctgctccaggatctggcCctcgctggtgatccttctca	12	14	2	1			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr3:112358134C>T	ENST00000206423.3	-	2	1572	c.619G>A	c.(619-621)Ggc>Agc	p.G207S	CCDC80_ENST00000475181.1_5'Flank|CCDC80_ENST00000439685.2_Missense_Mutation_p.G207S	NM_199511.1|NM_199512.1	NP_955805.1|NP_955806.1	Q76M96	CCD80_HUMAN	coiled-coil domain containing 80	207					extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(21)|ovary(3)|pancreas(2)|prostate(4)	51						AGGATCTGGCCCTCGCTGGTG	0.572																																					p.G207S		Atlas-SNP	.											.	CCDC80	100	.	0			c.G619A						.						102	89	93					3																	112358134		2203	4300	6503	SO:0001583	missense	151887	exon2			TCTGGCCCTCGCT	AY333429	CCDS2968.1	3q13.2	2010-12-24			ENSG00000091986	ENSG00000091986			30649	protein-coding gene	gene with protein product	"steroid sensitive gene 1"	608298				15325258, 18178152	Standard	XM_005247135		Approved	URB, SSG1, DRO1	uc003dzf.3	Q76M96	OTTHUMG00000159265	ENST00000206423.3:c.619G>A	chr3.hg19:g.112358134C>T	ENSP00000206423:p.Gly207Ser	98.0	0.0		93.0	27.0	NM_199511	D3DN67|Q5PR20|Q6GPG9|Q8IVT6|Q8NBV1|Q8NHY8	Missense_Mutation	SNP	ENST00000206423.3	hg19	CCDS2968.1	.	.	.	.	.	.	.	.	.	.	C	34	5.310534	0.95629	.	.	ENSG00000091986	ENST00000206423;ENST00000439685	T;T	0.78003	-1.14;-1.14	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.88500	0.6453	M	0.76574	2.34	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.89092	0.3483	10	0.72032	D	0.01	-23.7373	19.5067	0.95121	0.0:1.0:0.0:0.0	.	218;207;207	Q76M96-2;A3KC71;Q76M96	.;.;CCD80_HUMAN	S	207	ENSP00000206423:G207S;ENSP00000411814:G207S	ENSP00000206423:G207S	G	-	1	0	CCDC80	113840824	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.786000	0.85741	2.609000	0.88269	0.650000	0.86243	GGC	.	.		0.572	CCDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354219.1	NM_199511		T	112358134	C	T	112358134	3	4	313	1	0	0	0	0	1	0	0	0	2856	623	22	3	2261	3	CCDC80	3	112358134	Missense_Mutation	SNP	C	TCGA-KR-A7K0-01A-12D-A33Q-10	53974765	112358134	85664296	22	44398										
EVC	2121	hgsc.bcm.edu	37	chr4	5798959	5798959	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	tggcagctgctcagggccctGgtaagaccagcatggtggcc	15	12	1	1	rs201083145		TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr4:5798959G>T	ENST00000264956.6	+	14	2281	c.2097G>T	c.(2095-2097)ctG>ctT	p.L699L	EVC_ENST00000382674.2_Splice_Site_p.L699L|EVC_ENST00000515113.1_3'UTR	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	699					cartilage development (GO:0051216)|endochondral bone growth (GO:0003416)|muscle organ development (GO:0007517)|positive regulation of smoothened signaling pathway (GO:0045880)|skeletal system development (GO:0001501)|smoothened signaling pathway (GO:0007224)	ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|stomach(1)	28		Myeloproliferative disorder(84;0.117)				TCAGGGCCCTGGTAAGACCAG	0.647																																					p.L699L		Atlas-SNP	.											.	EVC	90	.	0			c.G2097T						.						17	17	17					4																	5798959		2203	4298	6501	SO:0001630	splice_region_variant	2121	exon14			GGCCCTGGTAAGA	AF216184	CCDS3383.1	4p16	2008-07-03			ENSG00000072840	ENSG00000072840			3497	protein-coding gene	gene with protein product		604831				10700184	Standard	NM_153717		Approved	DWF-1	uc003gil.1	P57679	OTTHUMG00000090427	ENST00000264956.6:c.2097+1G>T	chr4.hg19:g.5798959G>T		109.0	0.0		109.0	38.0	NM_153717		Silent	SNP	ENST00000264956.6	hg19	CCDS3383.1																																																																																			.	G|1.000;A|0.000		0.647	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1		Silent	T	5798959	G	T	5798959	5	4	313	1	0	0	0	0	0	0	1	0	5287	1362	47	3	2151	3	EVC	4	5798959	Splice_Site	SNP	G	TCGA-KR-A7K0-01A-12D-A33Q-10		5798959	185355317	23	44399										
EPHA5	2044	hgsc.bcm.edu	37	chr4	66467891	66467891	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	gtaaatttgagttctatgaaGattctggaagcaccttcatt	8	6	3	3	rs55882537		TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr4:66467891G>T	ENST00000273854.3	-	3	978	c.378C>A	c.(376-378)atC>atA	p.I126I	EPHA5_ENST00000511294.1_Silent_p.I126I|EPHA5_ENST00000432638.2_Silent_p.I126I|EPHA5_ENST00000354839.4_Silent_p.I126I	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	126	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						GTTCTATGAAGATTCTGGAAG	0.438										TSP Lung(17;0.13)																											p.I126I		Atlas-SNP	.											.	EPHA5	315	.	0			c.C378A						.						95	100	98					4																	66467891		2203	4300	6503	SO:0001819	synonymous_variant	2044	exon3			TATGAAGATTCTG	L36644	CCDS3513.1, CCDS3514.1, CCDS75131.1, CCDS75132.1, CCDS75133.1	4q13.1	2013-02-11	2004-10-28		ENSG00000145242	ENSG00000145242		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3389	protein-coding gene	gene with protein product		600004	"EphA5"			9267020, 7528718	Standard	NM_004439		Approved	Hek7, TYRO4, CEK7, EHK1	uc003hcy.3	P54756	OTTHUMG00000129273	ENST00000273854.3:c.378C>A	chr4.hg19:g.66467891G>T		56.0	0.0		55.0	17.0	NM_004439	Q7Z3F2	Silent	SNP	ENST00000273854.3	hg19	CCDS3513.1																																																																																			.	.		0.438	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439		T	66467891	G	T	66467891	2	4	313	1	0	0	0	0	0	0	0	1	5172	932	33	3		3	EPHA5	4	66467891	Silent	SNP	G	TCGA-KR-A7K0-01A-12D-A33Q-10	60668932	66467891	124686385	24	44400										
BTC	685	hgsc.bcm.edu	37	chr4	75675929	75675929	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	ccaatgtagccttcatcacaGctataaaacaagacgagggc	8	11	2	1	rs146656652		TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr4:75675929G>T	ENST00000395743.3	-	4	642	c.282C>A	c.(280-282)gtC>gtA	p.V94V		NM_001729.2	NP_001720.1	P35070	BTC_HUMAN	betacellulin	94	EGF-like. {ECO:0000255|PROSITE- ProRule:PRU00076}.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mitosis (GO:0045840)|positive regulation of urine volume (GO:0035810)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)			central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	10			Lung(101;0.219)			CTTCATCACAGCTATAAAACA	0.368																																					p.V94V		Atlas-SNP	.											.	BTC	23	.	0			c.C282A						.						156	166	163					4																	75675929		2203	4300	6503	SO:0001630	splice_region_variant	685	exon4			ATCACAGCTATAA	S55606	CCDS3566.1	4q13.3	2012-09-20			ENSG00000174808	ENSG00000174808			1121	protein-coding gene	gene with protein product		600345				8439318, 11522793	Standard	NM_001729		Approved		uc003hig.2	P35070	OTTHUMG00000130107	ENST00000395743.3:c.282-1C>A	chr4.hg19:g.75675929G>T		381.0	0.0		410.0	107.0	NM_001729	Q96F48	Silent	SNP	ENST00000395743.3	hg19	CCDS3566.1																																																																																			.	G|1.000;C|0.000		0.368	BTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252413.1		Silent	T	75675929	G	T	75675929	5	4	313	1	0	0	0	0	0	0	1	0	1551	985	34	3	262	3	BTC	4	75675929	Splice_Site	SNP	G	TCGA-KR-A7K0-01A-12D-A33Q-10	9208038	75675929	115478347	25	44401										
IBSP	3381	hgsc.bcm.edu	37	chr4	88732574	88732609	+	In_Frame_Del	DEL	GAAGAGGAAGGAAATGAAAACGAAGAAAGCGAAGCA	GAAGAGGAAGGAAATGAAAACGAAGAAAGCGAAGCA	-													0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	gtgatgaagaagaagaggagGaagaggaaggaaatgaaaac					rs200405481		TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	GAAGAGGAAGGAAATGAAAACGAAGAAAGCGAAGCA	GAAGAGGAAGGAAATGAAAACGAAGAAAGCGAAGCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr4:88732574_88732609delGAAGAGGAAGGAAATGAAAACGAAGAAAGCGAAGCA	ENST00000226284.5	+	7	533_568	c.466_501delGAAGAGGAAGGAAATGAAAACGAAGAAAGCGAAGCA	c.(466-501)gaagaggaaggaaatgaaaacgaagaaagcgaagcadel	p.EEEGNENEESEA156del		NM_004967.3	NP_004958.2	P21815	SIAL_HUMAN	integrin-binding sialoprotein	156	Asp/Glu-rich (acidic).|Poly-Glu.				biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|cellular response to growth factor stimulus (GO:0071363)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|membrane-bounded vesicle (GO:0031988)		p.E163K(1)|p.S165S(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(10)	21		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000333)|COAD - Colon adenocarcinoma(81;0.154)		agaagaggaggaagaggaaggaaatgaaaacgaagaaagcgaagcagaagTGGATG	0.449																																					p.155_167del		Atlas-Indel,Pindel	.											.	IBSP	53	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	c.465_500del						.																																			SO:0001651	inframe_deletion	3381	exon7			.		CCDS3624.1	4q21.1	2008-07-28	2008-07-28		ENSG00000029559	ENSG00000029559			5341	protein-coding gene	gene with protein product	"bone sialoprotein", "bone sialoprotein II"	147563				8406493	Standard	NM_004967		Approved	BSP, SP-II, BSP-II	uc003hqx.4	P21815	OTTHUMG00000130600	ENST00000226284.5:c.466_501delGAAGAGGAAGGAAATGAAAACGAAGAAAGCGAAGCA	chr4.hg19:g.88732574_88732609delGAAGAGGAAGGAAATGAAAACGAAGAAAGCGAAGCA	ENSP00000226284:p.Glu156_Ala167del	133.0	0.0		108.0	18.0	NM_004967		In_Frame_Del	DEL	ENST00000226284.5	hg19	CCDS3624.1																																																																																			.	.		0.449	IBSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253050.2			-	88732609	GAAGAGGAAGGAAATGAAAACGAAGAAAGCGAAGCA	-	88732574	7	5	313	1	0	1	0	1	0	0	0	0	7484	1175	41	0	488	0	IBSP	4	88732574	In_Frame_Del	DEL	GAAGAGGAAGGAAATGAAAACGAAGAAAGCGAAGCA	TCGA-KR-A7K0-01A-12D-A33Q-10	13056645	88732574	102421702	26	44402										
PDHA2	5161	hgsc.bcm.edu	37	chr4	96761797	96761797	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	atgggggcaatggcatcgtcGgtgcacagggccccctgggc	17	12	0	0			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr4:96761797G>A	ENST00000295266.4	+	1	559	c.496G>A	c.(496-498)Ggt>Agt	p.G166S		NM_005390.4	NP_005381.1	P29803	ODPAT_HUMAN	pyruvate dehydrogenase (lipoamide) alpha 2	166					glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|pyruvate metabolic process (GO:0006090)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	pyruvate dehydrogenase (acetyl-transferring) activity (GO:0004739)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(23)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	46		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.23e-06)		TGGCATCGTCGGTGCACAGGG	0.507																																					p.G166S		Atlas-SNP	.											PDHA2,NS,carcinoma,0,1	PDHA2	118	.	0			c.G496A						.						67	70	69					4																	96761797		2203	4300	6503	SO:0001583	missense	5161	exon1			ATCGTCGGTGCAC		CCDS3644.1	4q22-q23	2009-11-09			ENSG00000163114	ENSG00000163114	1.2.4.1		8807	protein-coding gene	gene with protein product		179061		PDHAL			Standard	NM_005390		Approved		uc003htr.4	P29803	OTTHUMG00000130990	ENST00000295266.4:c.496G>A	chr4.hg19:g.96761797G>A	ENSP00000295266:p.Gly166Ser	71.0	0.0		75.0	22.0	NM_005390	B2R9Q3|Q0VDI5|Q4VC02|Q6NXQ1	Missense_Mutation	SNP	ENST00000295266.4	hg19	CCDS3644.1	.	.	.	.	.	.	.	.	.	.	G	16.81	3.226337	0.58668	.	.	ENSG00000163114	ENST00000295266	D	0.98381	-4.9	4.67	4.67	0.58626	Dehydrogenase, E1 component (1);	0.000000	0.85682	D	0.000000	D	0.99111	0.9694	M	0.92970	3.365	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	D	0.99091	1.0840	10	0.87932	D	0	-13.8878	15.4624	0.75369	0.0:0.0:1.0:0.0	.	166	P29803	ODPAT_HUMAN	S	166	ENSP00000295266:G166S	ENSP00000295266:G166S	G	+	1	0	PDHA2	96980820	1.000000	0.71417	0.170000	0.22879	0.038000	0.13279	6.965000	0.76067	2.587000	0.87381	0.467000	0.42956	GGT	.	.		0.507	PDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253608.1			A	96761797	G	A	96761797	3	1	313	1	0	0	0	0	1	0	0	0	11674	1116	39	1	498	1	PDHA2	4	96761797	Missense_Mutation	SNP	G	TCGA-KR-A7K0-01A-12D-A33Q-10	8029223	96761797	94392479	27	44403										
TMEM192	201931	hgsc.bcm.edu	37	chr4	166000907	166000907	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	gcttcaggtattcaatggtgTctccttgcttttcaacaatt	7	9	4	0			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr4:166000907T>A	ENST00000306480.6	-	6	864	c.719A>T	c.(718-720)gAc>gTc	p.D240V	TMEM192_ENST00000506087.1_Missense_Mutation_p.D236V	NM_001100389.1	NP_001093859.1	Q8IY95	TM192_HUMAN	transmembrane protein 192	240						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)	protein homodimerization activity (GO:0042803)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)	7	all_hematologic(180;0.221)	Prostate(90;0.0959)|Melanoma(52;0.18)		GBM - Glioblastoma multiforme(119;0.0926)		TTCAATGGTGTCTCCTTGCTT	0.423																																					p.D240V		Atlas-SNP	.											.	TMEM192	21	.	0			c.A719T						.						122	113	116					4																	166000907		1902	4127	6029	SO:0001583	missense	201931	exon6			ATGGTGTCTCCTT	BC036301	CCDS43279.1	4q32.3	2008-04-22			ENSG00000170088	ENSG00000170088			26775	protein-coding gene	gene with protein product						12477932	Standard	NM_001100389		Approved	FLJ38482	uc003iqz.4	Q8IY95	OTTHUMG00000161254	ENST00000306480.6:c.719A>T	chr4.hg19:g.166000907T>A	ENSP00000305069:p.Asp240Val	73.0	0.0		97.0	37.0	NM_001100389	Q7Z3A1|Q8N928	Missense_Mutation	SNP	ENST00000306480.6	hg19	CCDS43279.1	.	.	.	.	.	.	.	.	.	.	T	18.90	3.722608	0.68959	.	.	ENSG00000170088	ENST00000306480;ENST00000506087	.	.	.	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.80232	0.4585	M	0.83012	2.62	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.81595	-0.0861	9	0.48119	T	0.1	-31.8821	14.3903	0.66973	0.0:0.0:0.0:1.0	.	240	Q8IY95	TM192_HUMAN	V	240;236	.	ENSP00000305069:D240V	D	-	2	0	TMEM192	166220357	1.000000	0.71417	0.999000	0.59377	0.620000	0.37586	5.164000	0.64954	2.287000	0.76781	0.482000	0.46254	GAC	.	.		0.423	TMEM192-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364310.3	NM_152681		A	166000907	T	A	166000907	3	1	313	1	0	0	0	0	1	0	0	0	16130	1667	58	4	100	4	TMEM192	4	166000907	Missense_Mutation	SNP	T	TCGA-KR-A7K0-01A-12D-A33Q-10	69239110	166000907	25153369	28	44404										
CLCN3	1182	hgsc.bcm.edu	37	chr4	170618416	170618417	+	In_Frame_Ins	INS	-	-	CAT													0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	gctgcatttgttttgaggtcINScatcaatccatttggtaaca							TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr4:170618416_170618417insCAT	ENST00000513761.1	+	9	1653_1654	c.1094_1095insCAT	c.(1093-1098)tccatc>tcCATcatc	p.366_367insI	CLCN3_ENST00000504131.2_In_Frame_Ins_p.349_350insI|CLCN3_ENST00000360642.3_In_Frame_Ins_p.339_340insI|CLCN3_ENST00000347613.4_In_Frame_Ins_p.366_367insI	NM_001829.3	NP_001820.2	P51790	CLCN3_HUMAN	chloride channel, voltage-sensitive 3	366					chloride transmembrane transport (GO:1902476)|endosomal lumen acidification (GO:0048388)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|voltage-gated chloride channel activity (GO:0005247)			breast(5)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	29		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0233)|LUSC - Lung squamous cell carcinoma(193;0.131)		GTTTTGAGGTCCATCAATCCAT	0.351																																					p.S365delinsSI		Atlas-INDEL	.											CLCN3,right_upper_lobe,carcinoma,0,1	CLCN3	85	.	0			c.1094_1095insCAT						.																																			SO:0001652	inframe_insertion	1182	exon9			.	X78520	CCDS34100.1, CCDS34101.1, CCDS58932.1, CCDS75208.1	4q	2012-09-26	2012-02-23		ENSG00000109572	ENSG00000109572		"Ion channels / Chloride channels : Voltage-sensitive"	2021	protein-coding gene	gene with protein product		600580	"chloride channel 3"				Standard	NM_001243374		Approved	CLC3, ClC-3	uc003ish.3	P51790	OTTHUMG00000160973	ENST00000513761.1:c.1095_1097dupCAT	chr4.hg19:g.170618417_170618419dupCAT	ENSP00000424603:p.Ile366_Ile366dup	183.0	0.0		218.0	54.0	NM_001829	B7Z932|B9EGJ9|D3DP34|E9PB97|O14918|Q86Z21	In_Frame_Ins	INS	ENST00000513761.1	hg19	CCDS34101.1																																																																																			.	.		0.351	CLCN3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363210.2			CAT	170618417	-	CAT	170618416	7	5	313	1	0	1	1	0	0	0	0	0	3466	855	30	0	1124	0	CLCN3	4	170618416	In_Frame_Ins	INS	-	TCGA-KR-A7K0-01A-12D-A33Q-10	4617509	170618416	20535860	29	44405	231	3								
CLCN3	1182	hgsc.bcm.edu	37	chr4	170618422	170618424	+	In_Frame_Del	DEL	ATC	ATC	-													0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	atttgttttgaggtccatcaAtccatttggtaacagccgtc							TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	ATC	ATC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr4:170618422_170618424delATC	ENST00000513761.1	+	9	1659_1661	c.1100_1102delATC	c.(1099-1104)aatcca>aca	p.367_368NP>T	CLCN3_ENST00000504131.2_In_Frame_Del_p.350_351NP>T|CLCN3_ENST00000360642.3_In_Frame_Del_p.340_341NP>T|CLCN3_ENST00000347613.4_In_Frame_Del_p.367_368NP>T	NM_001829.3	NP_001820.2	P51790	CLCN3_HUMAN	chloride channel, voltage-sensitive 3	367					chloride transmembrane transport (GO:1902476)|endosomal lumen acidification (GO:0048388)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|voltage-gated chloride channel activity (GO:0005247)	p.P368A(1)		breast(5)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	29		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0233)|LUSC - Lung squamous cell carcinoma(193;0.131)		AGGTCCATCAATCCATTTGGTAA	0.365																																					p.367_367del		Pindel	.											.	CLCN3	85	.	1	Substitution - Missense(1)	lung(1)	c.1099_1101del						.																																			SO:0001651	inframe_deletion	1182	exon9			.	X78520	CCDS34100.1, CCDS34101.1, CCDS58932.1, CCDS75208.1	4q	2012-09-26	2012-02-23		ENSG00000109572	ENSG00000109572		"Ion channels / Chloride channels : Voltage-sensitive"	2021	protein-coding gene	gene with protein product		600580	"chloride channel 3"				Standard	NM_001243374		Approved	CLC3, ClC-3	uc003ish.3	P51790	OTTHUMG00000160973	ENST00000513761.1:c.1100_1102delATC	chr4.hg19:g.170618422_170618424delATC	ENSP00000424603:p.Asn367_Pro368delinsThr	183.0	0.0		226.0	39.0	NM_001829	B7Z932|B9EGJ9|D3DP34|E9PB97|O14918|Q86Z21	In_Frame_Del	DEL	ENST00000513761.1	hg19	CCDS34101.1																																																																																			.	.		0.365	CLCN3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363210.2			-	170618424	ATC	-	170618422	7	5	313	1	0	1	0	1	0	0	0	0	3466	101	4	0	1130	0	CLCN3	4	170618422	In_Frame_Del	DEL	ATC	TCGA-KR-A7K0-01A-12D-A33Q-10	6	170618422	20535854	30	44406	231	3								
CLCN3	1182	hgsc.bcm.edu	37	chr4	170618424	170618424	+	Frame_Shift_Del	DEL	C	C	-													0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	ttgttttgaggtccatcaatCcatttggtaacagccgtctg							TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr4:170618424delC	ENST00000513761.1	+	9	1661	c.1102delC	c.(1102-1104)ccafs	p.P368fs	CLCN3_ENST00000504131.2_Frame_Shift_Del_p.P351fs|CLCN3_ENST00000360642.3_Frame_Shift_Del_p.P341fs|CLCN3_ENST00000347613.4_Frame_Shift_Del_p.P368fs	NM_001829.3	NP_001820.2	P51790	CLCN3_HUMAN	chloride channel, voltage-sensitive 3	368					chloride transmembrane transport (GO:1902476)|endosomal lumen acidification (GO:0048388)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|voltage-gated chloride channel activity (GO:0005247)	p.P368A(1)		breast(5)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	29		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0233)|LUSC - Lung squamous cell carcinoma(193;0.131)		GTCCATCAATCCATTTGGTAA	0.363																																					p.N367fs		Atlas-INDEL	.											.	CLCN3	85	.	1	Substitution - Missense(1)	lung(1)	c.1101delT						.						108	107	107					4																	170618424		2203	4300	6503	SO:0001589	frameshift_variant	1182	exon9			.	X78520	CCDS34100.1, CCDS34101.1, CCDS58932.1, CCDS75208.1	4q	2012-09-26	2012-02-23		ENSG00000109572	ENSG00000109572		"Ion channels / Chloride channels : Voltage-sensitive"	2021	protein-coding gene	gene with protein product		600580	"chloride channel 3"				Standard	NM_001243374		Approved	CLC3, ClC-3	uc003ish.3	P51790	OTTHUMG00000160973	ENST00000513761.1:c.1102delC	chr4.hg19:g.170618424delC	ENSP00000424603:p.Pro368fs	180.0	0.0		224.0	62.0	NM_001829	B7Z932|B9EGJ9|D3DP34|E9PB97|O14918|Q86Z21	Frame_Shift_Del	DEL	ENST00000513761.1	hg19	CCDS34101.1																																																																																			.	.		0.363	CLCN3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363210.2			-	170618424	C	-	170618424	7	5	313	1	0	1	0	1	0	0	0	0	3466	855	30	0	1132	0	CLCN3	4	170618424	Frame_Shift_Del	DEL	C	TCGA-KR-A7K0-01A-12D-A33Q-10	2	170618424	20535852	31	44407	231	3								
PDZD2	23037	hgsc.bcm.edu	37	chr5	32089543	32089543	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	agcctgttcctgagcaaggcAtgtggagcaggttccacatg	13	10	0	1			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr5:32089543A>T	ENST00000438447.1	+	20	6377	c.5989A>T	c.(5989-5991)Atg>Ttg	p.M1997L	PDZD2_ENST00000282493.3_Missense_Mutation_p.M1997L			O15018	PDZD2_HUMAN	PDZ domain containing 2	1997					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				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						TGAGCAAGGCATGTGGAGCAG	0.587																																					p.M1997L		Atlas-SNP	.											.	PDZD2	306	.	0			c.A5989T						.						113	111	112					5																	32089543		2203	4300	6503	SO:0001583	missense	23037	exon19			CAAGGCATGTGGA	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"PDZ domain containing 3"	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.5989A>T	chr5.hg19:g.32089543A>T	ENSP00000402033:p.Met1997Leu	43.0	0.0		48.0	13.0	NM_178140	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	hg19	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	A	7.550	0.662443	0.14645	.	.	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.05382	3.45;3.45	3.86	-2.28	0.06826	.	1.089650	0.07116	N	0.843028	T	0.02929	0.0087	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.46275	-0.9203	10	0.07482	T	0.82	.	4.2959	0.10901	0.5079:0.0:0.3255:0.1666	.	1997	O15018	PDZD2_HUMAN	L	1997;1798;1997	ENSP00000402033:M1997L;ENSP00000282493:M1997L	ENSP00000282493:M1997L	M	+	1	0	PDZD2	32125300	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.405000	0.07196	-0.560000	0.06102	-0.802000	0.03209	ATG	.	.		0.587	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			T	32089543	A	T	32089543	3	4	313	1	0	0	0	0	1	0	0	0	11710	217	8	4	6063	4	PDZD2	5	32089543	Missense_Mutation	SNP	A	TCGA-KR-A7K0-01A-12D-A33Q-10		32089543	148825717	32	44408										
ZFR	51663	hgsc.bcm.edu	37	chr5	32404160	32404160	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	tgaggctttcaatgcagcttCtttttttttatgtttctgtc	7	7	3	1			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr5:32404160C>T	ENST00000265069.8	-	7	1177	c.1075G>A	c.(1075-1077)Gaa>Aaa	p.E359K		NM_016107.3	NP_057191.2	Q96KR1	ZFR_HUMAN	zinc finger RNA binding protein	359					multicellular organismal development (GO:0007275)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|upper_aerodigestive_tract(2)	32				STAD - Stomach adenocarcinoma(35;0.19)		AATGCAGCTTCTTTTTTTTTA	0.353																																					p.E359K		Atlas-SNP	.											.,1	ZFR	98	.	0			c.G1075A						.						148	146	147					5																	32404160		2203	4300	6503	SO:0001583	missense	51663	exon7			CAGCTTCTTTTTT	AF100742	CCDS34139.1	5p15.2	2014-03-03			ENSG00000056097	ENSG00000056097			17277	protein-coding gene	gene with protein product		615635				11574164, 24482476	Standard	NM_016107		Approved	ZFR1, SPG71	uc003jhr.1	Q96KR1	OTTHUMG00000161979	ENST00000265069.8:c.1075G>A	chr5.hg19:g.32404160C>T	ENSP00000265069:p.Glu359Lys	100.0	2.0		88.0	14.0	NM_016107	B2RNR5|Q05C08|Q3B7X5|Q6P5A3|Q86UA0|Q9H6V4|Q9NTI1|Q9Y687	Missense_Mutation	SNP	ENST00000265069.8	hg19	CCDS34139.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.284022	0.80803	.	.	ENSG00000056097	ENST00000265069;ENST00000382126	T	0.44083	0.93	5.73	5.73	0.89815	Zinc finger, U1-type (1);	0.176085	0.64402	D	0.000010	T	0.57431	0.2053	M	0.91459	3.21	0.80722	D	1	B	0.27498	0.18	B	0.29353	0.101	T	0.63220	-0.6686	10	0.87932	D	0	.	18.0665	0.89392	0.0:1.0:0.0:0.0	.	359	Q96KR1	ZFR_HUMAN	K	359;337	ENSP00000265069:E359K	ENSP00000265069:E359K	E	-	1	0	ZFR	32439917	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.707000	0.92482	0.555000	0.69702	GAA	.	.		0.353	ZFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366586.1			T	32404160	C	T	32404160	3	4	313	1	0	0	0	0	1	0	0	0	17674	922	32	3	2205	3	ZFR	5	32404160	Missense_Mutation	SNP	C	TCGA-KR-A7K0-01A-12D-A33Q-10	314617	32404160	148511100	33	44409										
PRKAA1	5562	hgsc.bcm.edu	37	chr5	40762932	40762932	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	acatctcaaaaaattctattGtgtgacttccaggtcttgga	7	8	3	1			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr5:40762932G>T	ENST00000397128.2	-	9	1636	c.1628C>A	c.(1627-1629)aCa>aAa	p.T543K	PRKAA1_ENST00000354209.3_Missense_Mutation_p.T558K	NM_006251.5|NM_206907.3	NP_006242.5|NP_996790.3	Q13131	AAPK1_HUMAN	protein kinase, AMP-activated, alpha 1 catalytic subunit	543					activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|cell cycle arrest (GO:0007050)|cellular response to ethanol (GO:0071361)|cellular response to glucose starvation (GO:0042149)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|cholesterol biosynthetic process (GO:0006695)|cold acclimation (GO:0009631)|fatty acid biosynthetic process (GO:0006633)|fatty acid homeostasis (GO:0055089)|fatty acid oxidation (GO:0019395)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glucose import in response to insulin stimulus (GO:2001274)|negative regulation of glucosylceramide biosynthetic process (GO:0046318)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of gene expression (GO:0010628)|positive regulation of glycolytic process (GO:0045821)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|regulation of energy homeostasis (GO:2000505)|regulation of transcription, DNA-templated (GO:0006355)|regulation of vesicle-mediated transport (GO:0060627)|response to activity (GO:0014823)|response to caffeine (GO:0031000)|response to camptothecin (GO:1901563)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	AMP-activated protein kinase complex (GO:0031588)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)	[acetyl-CoA carboxylase] kinase activity (GO:0050405)|[hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity (GO:0047322)|AMP-activated protein kinase activity (GO:0004679)|ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)|chromatin binding (GO:0003682)|histone serine kinase activity (GO:0035174)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|tau-protein kinase activity (GO:0050321)			breast(1)	1					Acetylsalicylic acid(DB00945)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Phenformin(DB00914)	AAATTCTATTGTGTGACTTCC	0.368																																					p.T558K		Atlas-SNP	.											.	PRKAA1	27	.	0			c.C1673A						.						69	67	67					5																	40762932		1836	4095	5931	SO:0001583	missense	5562	exon10			TCTATTGTGTGAC		CCDS3932.2, CCDS3933.2	5p13.1	2012-10-03			ENSG00000132356	ENSG00000132356			9376	protein-coding gene	gene with protein product	"AMPK, alpha, 1"	602739				8557660	Standard	XM_006714481		Approved	AMPKa1	uc003jmb.3	Q13131	OTTHUMG00000162269	ENST00000397128.2:c.1628C>A	chr5.hg19:g.40762932G>T	ENSP00000380317:p.Thr543Lys	153.0	0.0		116.0	25.0	NM_206907	A8MTQ6|B2R7E1|O00286|Q5D0E1|Q86VS1|Q9UNQ4	Missense_Mutation	SNP	ENST00000397128.2	hg19	CCDS3932.2	.	.	.	.	.	.	.	.	.	.	G	28.9	4.961707	0.92791	.	.	ENSG00000132356	ENST00000397128;ENST00000354209	T;T	0.76060	-0.89;-0.99	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	D	0.85826	0.5787	L	0.61218	1.895	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	D	0.85873	0.1417	10	0.87932	D	0	-20.0768	20.3465	0.98790	0.0:0.0:1.0:0.0	.	543;558	Q13131;Q13131-2	AAPK1_HUMAN;.	K	543;558	ENSP00000380317:T543K;ENSP00000346148:T558K	ENSP00000346148:T558K	T	-	2	0	AC008810.1	40798689	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.660000	0.83776	2.798000	0.96311	0.655000	0.94253	ACA	.	.		0.368	PRKAA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253833.2	NM_006251		T	40762932	G	T	40762932	3	4	313	1	0	0	0	0	1	0	0	0	12505	1377	48	3	55	3	PRKAA1	5	40762932	Missense_Mutation	SNP	G	TCGA-KR-A7K0-01A-12D-A33Q-10	8358772	40762932	140152328	34	44410										
DEPDC1B	55789	hgsc.bcm.edu	37	chr5	59940645	59940645	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	tggatgatgaacttcgaattGacaagtttgacgtctaaaac	9	6	1	4			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr5:59940645G>T	ENST00000265036.5	-	5	703	c.636C>A	c.(634-636)gtC>gtA	p.V212V	DEPDC1B_ENST00000545085.1_Silent_p.V185V|DEPDC1B_ENST00000453022.2_Silent_p.V212V	NM_018369.2	NP_060839.2	Q8WUY9	DEP1B_HUMAN	DEP domain containing 1B	212	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(2)|skin(2)	17		Lung NSC(810;0.000214)|Prostate(74;0.0147)|Breast(144;0.0991)|Ovarian(174;0.17)				ACTTCGAATTGACAAGTTTGA	0.299																																					p.V212V		Atlas-SNP	.											.	DEPDC1B	56	.	0			c.C636A						.						91	89	90					5																	59940645		2203	4300	6503	SO:0001819	synonymous_variant	55789	exon5			CGAATTGACAAGT	AF303178	CCDS3977.1, CCDS47214.1	5q12	2008-02-05			ENSG00000035499	ENSG00000035499			24902	protein-coding gene	gene with protein product	"breast cancer cell 3"					12477932	Standard	NM_001145208		Approved	XTP1, BRCC3	uc003jsh.3	Q8WUY9	OTTHUMG00000097083	ENST00000265036.5:c.636C>A	chr5.hg19:g.59940645G>T		137.0	0.0		158.0	53.0	NM_001145208	A8K3R9|B4DUT4|Q86WJ3|Q8IZY6|Q9NUN3|Q9NW57	Silent	SNP	ENST00000265036.5	hg19	CCDS3977.1																																																																																			.	.		0.299	DEPDC1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214207.1	NM_018369		T	59940645	G	T	59940645	2	4	313	1	0	0	0	0	0	0	0	1	4442	1277	45	3		3	DEPDC1B	5	59940645	Silent	SNP	G	TCGA-KR-A7K0-01A-12D-A33Q-10	19177713	59940645	120974615	35	44411										
ST8SIA4	7903	hgsc.bcm.edu	37	chr5	100147642	100147642	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	attctaatggcattctgtgaGggcttgcattggaaaagtac	11	6	2	1			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr5:100147642G>T	ENST00000231461.5	-	5	1299	c.989C>A	c.(988-990)cCt>cAt	p.P330H		NM_005668.4	NP_005659.1	Q92187	SIA8D_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	330					axon guidance (GO:0007411)|cellular protein modification process (GO:0006464)|ganglioside biosynthetic process (GO:0001574)|N-glycan processing (GO:0006491)|nervous system development (GO:0007399)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(11)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)	25		all_cancers(142;1.5e-07)|all_epithelial(76;1.43e-10)|Prostate(80;0.000644)|Lung NSC(167;0.0059)|all_lung(232;0.00914)|Ovarian(225;0.024)|Colorectal(57;0.09)|Breast(839;0.203)		COAD - Colon adenocarcinoma(37;0.00402)		CATTCTGTGAGGGCTTGCATT	0.348																																					p.P330H		Atlas-SNP	.											.	ST8SIA4	77	.	0			c.C989A						.						126	115	119					5																	100147642		2203	4300	6503	SO:0001583	missense	7903	exon5			CTGTGAGGGCTTG	L41680	CCDS4091.1, CCDS47252.1	5q21	2013-03-01	2003-01-14	2005-02-07	ENSG00000113532	ENSG00000113532		"Sialyltransferases"	10871	protein-coding gene	gene with protein product	"ST8Sia IV"	602547	"sialyltransferase 8 (alpha-2, 8-polysialytransferase) D"	SIAT8D		7624364	Standard	NM_005668		Approved	PST, PST1	uc003knk.3	Q92187	OTTHUMG00000128727	ENST00000231461.5:c.989C>A	chr5.hg19:g.100147642G>T	ENSP00000231461:p.Pro330His	108.0	0.0		88.0	21.0	NM_005668	A8KA07|G3V104|Q8N1F4|Q92693	Missense_Mutation	SNP	ENST00000231461.5	hg19	CCDS4091.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.316374	0.81469	.	.	ENSG00000113532	ENST00000231461	T	0.29397	1.57	5.62	5.62	0.85841	.	0.126814	0.53938	D	0.000057	T	0.34890	0.0913	L	0.61036	1.89	0.80722	D	1	B	0.33103	0.397	B	0.35240	0.198	T	0.09143	-1.0688	10	0.15499	T	0.54	-4.8664	18.6327	0.91366	0.0:0.0:1.0:0.0	.	330	Q92187	SIA8D_HUMAN	H	330	ENSP00000231461:P330H	ENSP00000231461:P330H	P	-	2	0	ST8SIA4	100175541	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	9.827000	0.99397	2.646000	0.89796	0.655000	0.94253	CCT	.	.		0.348	ST8SIA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250632.3	NM_005668		T	100147642	G	T	100147642	3	4	313	1	0	0	0	0	1	0	0	0	15249	1000	35	3	94	3	ST8SIA4	5	100147642	Missense_Mutation	SNP	G	TCGA-KR-A7K0-01A-12D-A33Q-10	40206997	100147642	80767618	36	44412										
STK32A	202374	hgsc.bcm.edu	37	chr5	146752851	146752851	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	aggctcattccaggtttcatTcctaatgtgagtcaatccta	7	10	3	1			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr5:146752851T>C	ENST00000397936.3	+	10	1230	c.897T>C	c.(895-897)atT>atC	p.I299I	STK32A_ENST00000398523.3_Silent_p.I299I	NM_001112724.1	NP_001106195.1	Q8WU08	ST32A_HUMAN	serine/threonine kinase 32A	299							ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|prostate(1)|skin(1)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGGTTTCATTCCTAATGTGA	0.408																																					p.I299I		Atlas-SNP	.											.	STK32A	54	.	0			c.T897C						.						78	70	73					5																	146752851		1568	3582	5150	SO:0001819	synonymous_variant	202374	exon10			TTTCATTCCTAAT		CCDS47299.1, CCDS75351.1	5q32	2008-02-05			ENSG00000169302	ENSG00000169302			28317	protein-coding gene	gene with protein product						12477932	Standard	NM_001112724		Approved	MGC22688, YANK1	uc010jgn.1	Q8WU08	OTTHUMG00000163411	ENST00000397936.3:c.897T>C	chr5.hg19:g.146752851T>C		72.0	0.0		95.0	38.0	NM_001112724	B3KSY0	Silent	SNP	ENST00000397936.3	hg19	CCDS47299.1																																																																																			.	.		0.408	STK32A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373306.1	NM_145001		C	146752851	T	C	146752851	2	2	313	1	0	0	0	0	0	0	0	1	15312	1771	62	2		2	STK32A	5	146752851	Silent	SNP	T	TCGA-KR-A7K0-01A-12D-A33Q-10	46605209	146752851	34162409	37	44413										
DOCK2	1794	hgsc.bcm.edu	37	chr5	169186741	169186741	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	aaatacatcccatctgtcctGcatgatgtagaaatggtctt	7	9	2	2			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr5:169186741G>T	ENST00000256935.8	+	24	2489	c.2409G>T	c.(2407-2409)ctG>ctT	p.L803L	DOCK2_ENST00000520908.1_Silent_p.L295L|DOCK2_ENST00000540750.1_5'UTR	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	803					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CATCTGTCCTGCATGATGTAG	0.463																																					p.L803L		Atlas-SNP	.											.	DOCK2	389	.	0			c.G2409T						.						259	235	243					5																	169186741		2203	4300	6503	SO:0001819	synonymous_variant	1794	exon24			TGTCCTGCATGAT	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.2409G>T	chr5.hg19:g.169186741G>T		83.0	0.0		81.0	23.0	NM_004946	Q2M3I0|Q96AK7	Silent	SNP	ENST00000256935.8	hg19	CCDS4371.1																																																																																			.	.		0.463	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		T	169186741	G	T	169186741	2	4	313	1	0	0	0	0	0	0	0	1	4689	1306	46	3		3	DOCK2	5	169186741	Silent	SNP	G	TCGA-KR-A7K0-01A-12D-A33Q-10	22433890	169186741	11728519	38	44414										
PRELID1	27166	hgsc.bcm.edu	37	chr5	176732936	176732936	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	tggctggactgaaatccgccGggaagcctgggtctcctcta	13	12	2	1			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr5:176732936G>A	ENST00000303204.4	+	3	595	c.383G>A	c.(382-384)cGg>cAg	p.R128Q	RAB24_ENST00000393611.2_5'Flank|MXD3_ENST00000427908.2_3'UTR|RAB24_ENST00000303251.6_5'Flank|RAB24_ENST00000303270.6_5'Flank|PRELID1_ENST00000503216.1_Missense_Mutation_p.R128Q			Q9Y255	PRLD1_HUMAN	PRELI domain containing 1	128	PRELI/MSF1. {ECO:0000255|PROSITE- ProRule:PRU00158}.				apoptotic process (GO:0006915)|immune response (GO:0006955)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mitochondrial membrane potential (GO:0010917)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|phospholipid transport (GO:0015914)|positive regulation of cellular respiration (GO:1901857)|positive regulation of endopeptidase activity (GO:0010950)|positive regulation of phospholipid transport (GO:2001140)|positive regulation of T cell apoptotic process (GO:0070234)|regulation of membrane lipid distribution (GO:0097035)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of T cell differentiation (GO:0045580)	mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)				endometrium(1)|kidney(2)|lung(2)|prostate(1)|stomach(1)	7	all_cancers(89;2.49e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GAAATCCGCCGGGAAGCCTGG	0.552																																					p.R128Q		Atlas-SNP	.											.	PRELID1	10	.	0			c.G383A						.						85	80	81					5																	176732936		2203	4300	6503	SO:0001583	missense	27166	exon3			TCCGCCGGGAAGC	BC013748	CCDS4415.1, CCDS64328.1	5q35.3	2010-01-18			ENSG00000169230	ENSG00000169230			30255	protein-coding gene	gene with protein product	"protein of relevant evolutionary and lymphoid interest", "px19-like protein"	605733				10784606, 14640972	Standard	NM_013237		Approved	CGI-106, PX19, PRELI	uc003mfx.4	Q9Y255	OTTHUMG00000130847	ENST00000303204.4:c.383G>A	chr5.hg19:g.176732936G>A	ENSP00000302114:p.Arg128Gln	70.0	0.0		53.0	12.0	NM_013237	B2R5F7|D6RD25|Q549N2|Q9UI13|Q9UJS9	Missense_Mutation	SNP	ENST00000303204.4	hg19	CCDS4415.1	.	.	.	.	.	.	.	.	.	.	G	35	5.496477	0.96355	.	.	ENSG00000169230	ENST00000303204;ENST00000503216	T;T	0.12147	2.71;2.71	4.48	4.48	0.54585	PRELI/MSF1 (2);	0.056777	0.64402	D	0.000001	T	0.24431	0.0592	L	0.39245	1.2	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77004	0.985;0.989	T	0.01781	-1.1275	10	0.02654	T	1	-11.7669	17.3571	0.87340	0.0:0.0:1.0:0.0	.	128;128	D6RD25;Q9Y255	.;PRLD1_HUMAN	Q	128	ENSP00000302114:R128Q;ENSP00000427097:R128Q	ENSP00000302114:R128Q	R	+	2	0	PRELID1	176665542	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.257000	0.78362	2.332000	0.79248	0.561000	0.74099	CGG	.	.		0.552	PRELID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253414.1	NM_013237		A	176732936	G	A	176732936	3	1	313	1	0	0	0	0	1	0	0	0	12483	1116	39	1	393	1	PRELID1	5	176732936	Missense_Mutation	SNP	G	TCGA-KR-A7K0-01A-12D-A33Q-10	7546195	176732936	4182324	39	44415										
PRPF4B	8899	hgsc.bcm.edu	37	chr6	4032471	4032471	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	gatcaagcaaggaaatcaaaAtcccctacccttagaaggcg	8	11	2	1			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr6:4032471A>G	ENST00000337659.6	+	2	820	c.720A>G	c.(718-720)aaA>aaG	p.K240K	PRPF4B_ENST00000538861.1_Silent_p.K226K	NM_003913.4	NP_003904.3	Q13523	PRP4B_HUMAN	pre-mRNA processing factor 4B	240	Arg/Lys-rich (basic).				mRNA splicing, via spliceosome (GO:0000398)|protein phosphorylation (GO:0006468)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|chromosome (GO:0005694)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(6)|endometrium(3)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	22	Ovarian(93;0.0925)	all_hematologic(90;0.0895)				GGAAATCAAAATCCCCTACCC	0.358																																					p.K240K		Atlas-SNP	.											.	PRPF4B	140	.	0			c.A720G						.						132	144	140					6																	4032471		2203	4300	6503	SO:0001819	synonymous_variant	8899	exon2			ATCAAAATCCCCT	U48736	CCDS4488.1	6p24.2	2013-10-03	2013-10-03		ENSG00000112739	ENSG00000112739			17346	protein-coding gene	gene with protein product		602338	"PRP4 pre-mRNA processing factor 4 homolog B (yeast)"			9628581, 11418604	Standard	XR_241936		Approved	Prp4, PR4H, KIAA0536	uc003mvv.3	Q13523	OTTHUMG00000014157	ENST00000337659.6:c.720A>G	chr6.hg19:g.4032471A>G		152.0	0.0		178.0	47.0	NM_003913	A8K5C9|Q5D0F6|Q5TAY8|Q8IVC3|Q8TDP2|Q96QT7|Q9UEE6	Silent	SNP	ENST00000337659.6	hg19	CCDS4488.1																																																																																			.	.		0.358	PRPF4B-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314018.2			G	4032471	A	G	4032471	2	3	313	1	0	0	0	0	0	0	0	1	12585	98	4	2		2	PRPF4B	6	4032471	Silent	SNP	A	TCGA-KR-A7K0-01A-12D-A33Q-10		4032471	167082596	40	44416										
VARS2	57176	hgsc.bcm.edu	37	chr6	30893707	30893707	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	ctgttagccgcccgaaggtaCaagttgcagaagcagcttga	12	10	0	2			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr6:30893707C>T	ENST00000321897.5	+	28	3644	c.3012C>T	c.(3010-3012)taC>taT	p.Y1004Y	VARS2_ENST00000542001.1_Silent_p.Y864Y|VARS2_ENST00000541562.1_Silent_p.Y1034Y|VARS2_ENST00000476162.1_3'UTR|VARS2_ENST00000416670.2_Silent_p.Y1004Y			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	1004					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						CCCGAAGGTACAAGTTGCAGA	0.612																																					p.Y1034Y		Atlas-SNP	.											.	VARS2	60	.	0			c.C3102T						.						76	75	75					6																	30893707		1509	2709	4218	SO:0001819	synonymous_variant	57176	exon29			AAGGTACAAGTTG	AB067472	CCDS34387.1, CCDS54980.1	6p21.33	2012-10-26	2012-10-26	2007-02-23	ENSG00000137411	ENSG00000137411	6.1.1.9	"Aminoacyl tRNA synthetases / Class I"	21642	protein-coding gene	gene with protein product	"valine tRNA ligase 2, mitochondrial"	612802	"valyl-tRNA synthetase 2-like", "valyl-tRNA synthetase like", "valyl-tRNA synthetase 2, mitochondrial (putative)"	VARS2L, VARSL		1898367, 11572484, 18400783	Standard	NM_001167734		Approved	DKFZP434L1435, KIAA1885, G7a	uc011dmz.2	Q5ST30	OTTHUMG00000031263	ENST00000321897.5:c.3012C>T	chr6.hg19:g.30893707C>T		151.0	0.0		147.0	59.0	NM_001167734	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Silent	SNP	ENST00000321897.5	hg19	CCDS34387.1																																																																																			.	.		0.612	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442		T	30893707	C	T	30893707	2	4	313	1	0	0	0	0	0	0	0	1	17139	489	17	3		3	VARS2	6	30893707	Silent	SNP	C	TCGA-KR-A7K0-01A-12D-A33Q-10	26861236	30893707	140221360	41	44417										
PBX2	5089	hgsc.bcm.edu	37	chr6	32156140	32156140	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	caggggacacaccaccaccaGaggctgcagcggctgcagct	13	15	0	1			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr6:32156140G>C	ENST00000375050.4	-	3	707	c.437C>G	c.(436-438)tCt>tGt	p.S146C	XXbac-BPG300A18.13_ENST00000559458.1_RNA	NM_002586.4	NP_002577.2	P40425	PBX2_HUMAN	pre-B-cell leukemia homeobox 2	146					embryonic limb morphogenesis (GO:0030326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(1)|kidney(1)|lung(9)|ovary(1)|prostate(2)	14						ACCACCACCAGAGGCTGCAGC	0.597																																					p.S146C		Atlas-SNP	.											.	PBX2	29	.	0			c.C437G						.						47	53	51					6																	32156140		2203	4300	6503	SO:0001583	missense	5089	exon3			CCACCAGAGGCTG		CCDS4748.1	6p21.32	2011-06-20	2007-01-30		ENSG00000204304	ENSG00000204304		"Homeoboxes / TALE class"	8633	protein-coding gene	gene with protein product		176311	"pre-B-cell leukemia transcription factor 2"			7835890	Standard	NM_002586		Approved	G17, HOX12, PBX2MHC	uc003oav.1	P40425	OTTHUMG00000031116	ENST00000375050.4:c.437C>G	chr6.hg19:g.32156140G>C	ENSP00000364190:p.Ser146Cys	59.0	0.0		57.0	16.0	NM_002586	A2BFJ2	Missense_Mutation	SNP	ENST00000375050.4	hg19	CCDS4748.1	.	.	.	.	.	.	.	.	.	.	G	19.18	3.776810	0.70107	.	.	ENSG00000204304	ENST00000375050	D	0.89552	-2.53	5.02	5.02	0.67125	PBX (1);	0.000000	0.64402	D	0.000013	D	0.90696	0.7081	L	0.50333	1.59	0.80722	D	1	D;D	0.62365	0.984;0.991	P;D	0.64506	0.886;0.926	D	0.91871	0.5507	10	0.72032	D	0.01	-1.7648	15.8313	0.78752	0.0:0.0:1.0:0.0	.	146;146	Q7KZE5;P40425	.;PBX2_HUMAN	C	146	ENSP00000364190:S146C	ENSP00000364190:S146C	S	-	2	0	PBX2	32264118	1.000000	0.71417	0.978000	0.43139	0.504000	0.33889	5.878000	0.69682	2.327000	0.79052	0.561000	0.74099	TCT	.	.		0.597	PBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076194.4			C	32156140	G	C	32156140	3	2	313	1	0	0	0	0	1	0	0	0	11502	942	33	4	883	4	PBX2	6	32156140	Missense_Mutation	SNP	G	TCGA-KR-A7K0-01A-12D-A33Q-10	1262433	32156140	138958927	42	44418										
TULP1	7287	hgsc.bcm.edu	37	chr6	35471363	35471363	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	ggccggatggggaccctctcGttctccgcactcatgccagg	13	15	3	0			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr6:35471363G>A	ENST00000229771.6	-	13	1375	c.1296C>T	c.(1294-1296)aaC>aaT	p.N432N	TULP1_ENST00000322263.4_Silent_p.N379N	NM_003322.3	NP_003313.3	O00294	TULP1_HUMAN	tubby like protein 1	432					dendrite development (GO:0016358)|detection of light stimulus involved in visual perception (GO:0050908)|eye photoreceptor cell development (GO:0042462)|phagocytosis (GO:0006909)|photoreceptor cell maintenance (GO:0045494)|phototransduction (GO:0007602)|positive regulation of phagocytosis (GO:0050766)|retina development in camera-type eye (GO:0060041)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|synapse (GO:0045202)	actin filament binding (GO:0051015)|G-protein coupled photoreceptor activity (GO:0008020)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	19						GGACCCTCTCGTTCTCCGCAC	0.622																																					p.N432N	GBM(55;1027 1091 11115 23439)	Atlas-SNP	.											.	TULP1	51	.	0			c.C1296T						.						20	20	20					6																	35471363		2200	4296	6496	SO:0001819	synonymous_variant	7287	exon13			CCTCTCGTTCTCC	U82468	CCDS4807.1, CCDS75436.1	6p21.3	2014-01-28			ENSG00000112041	ENSG00000112041			12423	protein-coding gene	gene with protein product		602280		RP14		9096357, 9521870	Standard	NM_003322		Approved	TUBL1, LCA15	uc003okv.4	O00294	OTTHUMG00000014575	ENST00000229771.6:c.1296C>T	chr6.hg19:g.35471363G>A		81.0	0.0		73.0	10.0	NM_003322	O43536|Q5TGM5|Q8N571	Silent	SNP	ENST00000229771.6	hg19	CCDS4807.1																																																																																			.	.		0.622	TULP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040307.2			A	35471363	G	A	35471363	2	1	313	1	0	0	0	0	0	0	0	1	16788	1136	40	1		1	TULP1	6	35471363	Silent	SNP	G	TCGA-KR-A7K0-01A-12D-A33Q-10	3315223	35471363	135643704	43	44419										
PKHD1	5314	hgsc.bcm.edu	37	chr6	51523772	51523772	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	atagccaatgactccctttgActgagtaactagtaaggccc	8	11	0	3			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr6:51523772A>G	ENST00000371117.3	-	61	11427	c.11152T>C	c.(11152-11154)Tca>Cca	p.S3718P		NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3718					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					ACTCCCTTTGACTGAGTAACT	0.393																																					p.S3718P		Atlas-SNP	.											.	PKHD1	927	.	0			c.T11152C						.						113	112	113					6																	51523772		2203	4300	6503	SO:0001583	missense	5314	exon61			CCTTTGACTGAGT	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.11152T>C	chr6.hg19:g.51523772A>G	ENSP00000360158:p.Ser3718Pro	81.0	0.0		74.0	13.0	NM_138694	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	hg19	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	A	8.722	0.914653	0.17907	.	.	ENSG00000170927	ENST00000371117	D	0.85702	-2.02	5.56	-1.23	0.09465	.	0.530450	0.18404	N	0.142280	T	0.53012	0.1770	L	0.33485	1.01	0.58432	D	0.999999	B	0.10296	0.003	B	0.06405	0.002	T	0.52711	-0.8539	10	0.02654	T	1	.	11.2078	0.48780	0.3946:0.0:0.6054:0.0	.	3718	P08F94	PKHD1_HUMAN	P	3718	ENSP00000360158:S3718P	ENSP00000360158:S3718P	S	-	1	0	PKHD1	51631731	0.116000	0.22171	0.161000	0.22692	0.930000	0.56654	-0.085000	0.11250	-0.190000	0.10465	-0.408000	0.06270	TCA	.	.		0.393	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		G	51523772	A	G	51523772	3	3	313	1	0	0	0	0	1	0	0	0	11980	275	10	2	1100	2	PKHD1	6	51523772	Missense_Mutation	SNP	A	TCGA-KR-A7K0-01A-12D-A33Q-10	16052409	51523772	119591295	44	44420										
EEF1A1	1915	hgsc.bcm.edu	37	chr6	74227627	74227628	+	Missense_Mutation	DNP	GT	GT	AA													0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	tgatgacacccaccgcaactGtctgtctcatatcacgaaca							TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	G|T	G|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr6:74227627_74227628GT>AA	ENST00000316292.9	-	7	2285_2286	c.1294_1295AC>TT	c.(1294-1296)ACa>TTa	p.T432L	EEF1A1_ENST00000309268.6_Missense_Mutation_p.T432L|EEF1A1_ENST00000331523.2_Missense_Mutation_p.T432L|EEF1A1_ENST00000491404.1_Intron	NM_001402.5	NP_001393.1	P68104	EF1A1_HUMAN	eukaryotic translation elongation factor 1 alpha 1	432					cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation elongation factor activity (GO:0003746)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(6)|prostate(2)|skin(3)	18						CACCGCAACTGTCTGTCTCATA	0.401											OREG0003893	type=REGULATORY REGION|Gene=BC038897|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.T432I|p.T432S		Atlas-SNP	.											.	EEF1A1	56	.	0			c.C1295T|c.A1294T						.																																			SO:0001583	missense	1915	exon8			GCAACTGTCTGTC|CAACTGTCTGTCT	BC019669	CCDS4980.1	6q14.1	2010-06-30	2004-11-19		ENSG00000156508	ENSG00000156508			3189	protein-coding gene	gene with protein product		130590	"leukocyte receptor cluster (LRC) member 7"	EF1A, EEF1A, LENG7		8812466, 10941842	Standard	NM_001402		Approved	EE1A1	uc003phj.3	P68104	OTTHUMG00000015031	ENST00000316292.9:c.1294_1295delinsAA	chr6.hg19:g.74227627_74227628delinsAA	ENSP00000339063:p.Thr432Leu	380.0	0.0	1151	358.0|359.0	115.0	NM_001402	P04719|P04720|Q6IQ15	Missense_Mutation	SNP	ENST00000316292.9	hg19	CCDS4980.1																																																																																			.	.		0.401	EEF1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041210.2	NM_001402		AA	74227628	GT	AA	74227627	3	1	313	1	0	0	0	0	1	0	0	0	4925	1377	48	3	97	3	EEF1A1	6	74227627	Missense_Mutation	DNP	GT	TCGA-KR-A7K0-01A-12D-A33Q-10	22703855	74227627	96887440	45	44421										
POU3F2	5454	hgsc.bcm.edu	37	chr6	99283906	99283906	+	Frame_Shift_Del	DEL	C	C	-													0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	ctcggcccaggagatcacctCcctcgcggacagcttacagc							TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr6:99283906delC	ENST00000328345.5	+	1	1327	c.1157delC	c.(1156-1158)tccfs	p.S386fs		NM_005604.3	NP_005595.2	P20265	PO3F2_HUMAN	POU class 3 homeobox 2	386					astrocyte development (GO:0014002)|cellular response to organic substance (GO:0071310)|cerebral cortex radially oriented cell migration (GO:0021799)|epidermis development (GO:0008544)|forebrain ventricular zone progenitor cell division (GO:0021869)|hypothalamus cell differentiation (GO:0021979)|myelination in peripheral nervous system (GO:0022011)|neurohypophysis development (GO:0021985)|neuron differentiation (GO:0030182)|positive regulation of cell proliferation (GO:0008284)|positive regulation of multicellular organism growth (GO:0040018)|regulation of axonogenesis (GO:0050770)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	identical protein binding (GO:0042802)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|large_intestine(3)|lung(5)	10		all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197)		BRCA - Breast invasive adenocarcinoma(108;0.0355)		GAGATCACCTCCCTCGCGGAC	0.577																																					p.S386fs		Atlas-Indel,Pindel	.											.	POU3F2	33	.	0			c.1156delT						.						53	61	58					6																	99283906		2203	4300	6503	SO:0001589	frameshift_variant	5454	exon1			.	Z11933	CCDS5040.1	6q16.2	2011-06-20	2007-07-13		ENSG00000184486	ENSG00000184486		"Homeoboxes / POU class"	9215	protein-coding gene	gene with protein product		600494	"POU domain class 3, transcription factor 2"	OTF7		8441633	Standard	NM_005604		Approved	POUF3, BRN2, OCT7	uc003ppe.3	P20265	OTTHUMG00000015258	ENST00000328345.5:c.1157delC	chr6.hg19:g.99283906delC	ENSP00000329170:p.Ser386fs	80.0	0.0		110.0	29.0	NM_005604	Q14960|Q86V54|Q9UJL0	Frame_Shift_Del	DEL	ENST00000328345.5	hg19	CCDS5040.1																																																																																			.	.		0.577	POU3F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041586.2			-	99283906	C	-	99283906	7	5	313	1	0	1	0	1	0	0	0	0	12284	855	30	0	1159	0	POU3F2	6	99283906	Frame_Shift_Del	DEL	C	TCGA-KR-A7K0-01A-12D-A33Q-10	25056279	99283906	71831161	46	44422										
FRMD1	79981	hgsc.bcm.edu	37	chr6	168464373	168464373	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	ctccttggggctcaggccctGgcgctcacggtgcagggtag	16	13	2	0			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr6:168464373G>A	ENST00000283309.6	-	6	776	c.712C>T	c.(712-714)Cag>Tag	p.Q238*	FRMD1_ENST00000440994.2_Nonsense_Mutation_p.Q170*|FRMD1_ENST00000432403.1_5'UTR|FRMD1_ENST00000537786.1_Nonsense_Mutation_p.Q9*	NM_024919.3	NP_079195.3	Q8N878	FRMD1_HUMAN	FERM domain containing 1	238	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoskeleton (GO:0005856)				endometrium(3)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|urinary_tract(1)	19		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)		CTCAGGCCCTGGCGCTCACGG	0.642																																					p.Q238X	GBM(50;8 1094 9538 34399)|Ovarian(80;676 1857 8675 49015)	Atlas-SNP	.											.	FRMD1	52	.	0			c.C712T						.						91	77	81					6																	168464373		2203	4300	6503	SO:0001587	stop_gained	79981	exon6			GGCCCTGGCGCTC		CCDS5306.1, CCDS47518.1	6q27	2008-10-23			ENSG00000153303	ENSG00000153303			21240	protein-coding gene	gene with protein product							Standard	NM_001122841		Approved	FLJ00181, DKFZp434O0117, FLJ40260, FLJ22615, bA164L23.1	uc003qwo.4	Q8N878	OTTHUMG00000016037	ENST00000283309.6:c.712C>T	chr6.hg19:g.168464373G>A	ENSP00000283309:p.Gln238*	120.0	0.0		109.0	21.0	NM_024919	B2RNV8|B3KUM6|Q5SZU7|Q9UFB0	Nonsense_Mutation	SNP	ENST00000283309.6	hg19	CCDS5306.1	.	.	.	.	.	.	.	.	.	.	G	19.50	3.839819	0.71488	.	.	ENSG00000153303	ENST00000283309;ENST00000440994;ENST00000537786	.	.	.	2.83	2.83	0.33086	.	0.493026	0.18335	U	0.144344	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	.	7.9508	0.30014	0.1171:0.0:0.8829:0.0	.	.	.	.	X	238;170;9	.	ENSP00000283309:Q238X	Q	-	1	0	FRMD1	168207222	0.309000	0.24518	0.367000	0.25926	0.234000	0.25298	1.415000	0.34748	1.425000	0.47237	0.305000	0.20034	CAG	.	.		0.642	FRMD1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362513.2	NM_024919		A	168464373	G	A	168464373	4	1	313	1	0	0	0	0	0	1	0	0	6057	1357	47	3	961	3	FRMD1	6	168464373	Nonsense_Mutation	SNP	G	TCGA-KR-A7K0-01A-12D-A33Q-10	69180467	168464373	2650694	47	44423										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48467381	48467381	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	aggtgtttttgatgcttttgCaagattccaacaagaaatct	8	6	1	3			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr7:48467381C>G	ENST00000435803.1	+	42	12502	c.12478C>G	c.(12478-12480)Caa>Gaa	p.Q4160E		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	4160					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						GATGCTTTTGCAAGATTCCAA	0.408																																					p.Q4160E		Atlas-SNP	.											.	ABCA13	1192	.	0			c.C12478G						.						56	52	53					7																	48467381		1850	4114	5964	SO:0001583	missense	154664	exon42			CTTTTGCAAGATT	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.12478C>G	chr7.hg19:g.48467381C>G	ENSP00000411096:p.Gln4160Glu	64.0	0.0		67.0	24.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	C	7.101	0.574091	0.13623	.	.	ENSG00000179869	ENST00000435803	T	0.74421	-0.84	4.74	2.83	0.33086	.	0.144123	0.32041	N	0.006677	T	0.64034	0.2562	L	0.44542	1.39	0.80722	D	1	B;B	0.15473	0.002;0.013	B;B	0.12837	0.006;0.008	T	0.56098	-0.8035	10	0.27082	T	0.32	.	11.1741	0.48588	0.0:0.6397:0.3603:0.0	.	1862;4160	Q86UQ4-3;Q86UQ4	.;ABCAD_HUMAN	E	4160	ENSP00000411096:Q4160E	ENSP00000411096:Q4160E	Q	+	1	0	ABCA13	48437927	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	1.772000	0.38552	0.643000	0.30638	0.655000	0.94253	CAA	.	.		0.408	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		G	48467381	C	G	48467381	3	3	313	1	0	0	0	0	1	0	0	0	31	711	25	4	12473	4	ABCA13	7	48467381	Missense_Mutation	SNP	C	TCGA-KR-A7K0-01A-12D-A33Q-10		48467381	110671282	48	44424										
LAT2	7462	hgsc.bcm.edu	37	chr7	73631176	73631176	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	tgcaaagaggtcagagaaaaTctaccagcagagaagtctgt	11	7	3	3			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr7:73631176T>G	ENST00000460943.1	+	4	1005	c.116T>G	c.(115-117)aTc>aGc	p.I39S	LAT2_ENST00000344995.5_Missense_Mutation_p.I39S|LAT2_ENST00000398475.1_Missense_Mutation_p.I39S|LAT2_ENST00000275635.7_Missense_Mutation_p.I39S	NM_032464.2	NP_115853.2	Q9UHI5	LAT2_HUMAN	linker for activation of T cells family, member 2	0					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|metal ion homeostasis (GO:0055065)|neutral amino acid transport (GO:0015804)|organic cation transport (GO:0015695)|response to toxic substance (GO:0009636)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-amino acid transmembrane transporter activity (GO:0015179)|neutral amino acid transmembrane transporter activity (GO:0015175)|organic cation transmembrane transporter activity (GO:0015101)|peptide antigen binding (GO:0042605)|toxin transporter activity (GO:0019534)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|prostate(1)	6					L-Alanine(DB00160)|L-DOPA(DB01235)|L-Glutamine(DB00130)|L-Phenylalanine(DB00120)	TCAGAGAAAATCTACCAGCAG	0.547																																					p.I39S		Atlas-SNP	.											.	LAT2	24	.	0			c.T116G						.						94	102	99					7																	73631176		1965	4156	6121	SO:0001583	missense	7462	exon4			AGAAAATCTACCA	AF257135	CCDS5566.2	7q11.23	2011-11-01	2005-04-26	2005-04-26	ENSG00000086730	ENSG00000086730			12749	protein-coding gene	gene with protein product	"linker for activation of B cells", "non-T cell activation linker", "linker for activation of T cells, transmembrane adaptor 2"	605719	"Williams-Beuren syndrome chromosome region 5"	WBSCR15, WBSCR5		8812460, 12514734	Standard	NM_032464		Approved	WSCR5, HSPC046, LAB, NTAL	uc003uai.3	Q9GZY6	OTTHUMG00000130151	ENST00000460943.1:c.116T>G	chr7.hg19:g.73631176T>G	ENSP00000420494:p.Ile39Ser	86.0	0.0		98.0	27.0	NM_032464	B2R8Q4|B4DKT4|B4DTV6|D3DS46|F2Z2J4|Q86U05|Q9UKQ6|Q9UKQ7|Q9UKQ8|Q9Y445	Missense_Mutation	SNP	ENST00000460943.1	hg19	CCDS5566.2	.	.	.	.	.	.	.	.	.	.	T	16.62	3.173245	0.57584	.	.	ENSG00000086730	ENST00000465116;ENST00000344995;ENST00000460943;ENST00000475494;ENST00000398475;ENST00000361082;ENST00000275635	T;T;T;T;T;T;T	0.07021	3.23;3.23;3.23;3.23;3.23;3.23;3.23	3.84	3.84	0.44239	.	0.000000	0.38272	N	0.001746	T	0.16428	0.0395	L	0.34521	1.04	0.37639	D	0.921989	D	0.76494	0.999	D	0.83275	0.996	T	0.02950	-1.1090	10	0.72032	D	0.01	-26.2421	9.3054	0.37872	0.0:0.0:0.0:1.0	.	39	Q9GZY6	NTAL_HUMAN	S	39	ENSP00000420549:I39S;ENSP00000344881:I39S;ENSP00000420494:I39S;ENSP00000417533:I39S;ENSP00000381492:I39S;ENSP00000354374:I39S;ENSP00000275635:I39S	ENSP00000275635:I39S	I	+	2	0	LAT2	73269112	1.000000	0.71417	1.000000	0.80357	0.865000	0.49528	2.857000	0.48349	1.970000	0.57323	0.459000	0.35465	ATC	.	.		0.547	LAT2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277062.1			G	73631176	T	G	73631176	3	3	313	1	0	0	0	0	1	0	0	0	8654	1435	50	5	122	5	LAT2	7	73631176	Missense_Mutation	SNP	T	TCGA-KR-A7K0-01A-12D-A33Q-10	25163795	73631176	85507487	49	44425										
ZNF804B	219578	hgsc.bcm.edu	37	chr7	88965181	88965181	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	agaggctccttcgcaagtccCatgcacaattcaacttgcac	7	14	1	1			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr7:88965181C>T	ENST00000333190.4	+	4	3494	c.2885C>T	c.(2884-2886)cCa>cTa	p.P962L		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	962							metal ion binding (GO:0046872)	p.P962L(1)|p.P962Q(1)		NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			TCGCAAGTCCCATGCACAATT	0.388										HNSCC(36;0.09)																											p.P962L		Atlas-SNP	.											ZNF804B,NS,carcinoma,0,1	ZNF804B	322	.	2	Substitution - Missense(2)	lung(2)	c.C2885T						.						114	115	115					7																	88965181		2203	4300	6503	SO:0001583	missense	219578	exon4			AAGTCCCATGCAC	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"zinc finger 804B"				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.2885C>T	chr7.hg19:g.88965181C>T	ENSP00000329638:p.Pro962Leu	283.0	0.0		299.0	100.0	NM_181646	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	hg19	CCDS5613.1	.	.	.	.	.	.	.	.	.	.	C	0.012	-1.658293	0.00779	.	.	ENSG00000182348	ENST00000333190	T	0.04809	3.55	5.34	0.244	0.15507	.	0.393600	0.24476	N	0.038181	T	0.01870	0.0059	N	0.08118	0	0.09310	N	1	B	0.23185	0.081	B	0.16289	0.015	T	0.47787	-0.9090	10	0.11182	T	0.66	-0.299	4.835	0.13460	0.3735:0.4483:0.0681:0.1101	.	962	A4D1E1	Z804B_HUMAN	L	962	ENSP00000329638:P962L	ENSP00000329638:P962L	P	+	2	0	ZNF804B	88803117	0.131000	0.22433	0.000000	0.03702	0.070000	0.16714	1.579000	0.36536	-0.098000	0.12285	-0.274000	0.10170	CCA	.	.		0.388	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646		T	88965181	C	T	88965181	3	4	313	1	0	0	0	0	1	0	0	0	18186	594	21	3	2899	3	ZNF804B	7	88965181	Missense_Mutation	SNP	C	TCGA-KR-A7K0-01A-12D-A33Q-10	15334005	88965181	70173482	50	44426										
GTPBP10	85865	hgsc.bcm.edu	37	chr7	89982211	89982211	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	atcctcgtttaggtggagaaGgtggaaaaggtggtgatgtc	16	4	0	2			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr7:89982211G>A	ENST00000222511.6	+	2	181	c.115G>A	c.(115-117)Ggt>Agt	p.G39S	GTPBP10_ENST00000257659.8_Missense_Mutation_p.G39S	NM_033107.3	NP_149098.2	A4D1E9	GTPBA_HUMAN	GTP-binding protein 10 (putative)	39					ribosome biogenesis (GO:0042254)	chromosome (GO:0005694)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(3)|lung(4)	10						AGGTGGAGAAGGTGGAAAAGG	0.433																																					p.G39S		Atlas-SNP	.											GTPBP10,right_lower_lobe,carcinoma,0,1	GTPBP10	31	.	0			c.G115A						.						186	181	182					7																	89982211		2203	4300	6503	SO:0001583	missense	85865	exon2			GGAGAAGGTGGAA		CCDS5617.1, CCDS43614.1	7q21.13	2006-08-15			ENSG00000105793	ENSG00000105793			25106	protein-coding gene	gene with protein product		610920				12477932	Standard	NM_001042717		Approved	DKFZP686A10121, FLJ38242	uc003ukm.2	A4D1E9	OTTHUMG00000023655	ENST00000222511.6:c.115G>A	chr7.hg19:g.89982211G>A	ENSP00000222511:p.Gly39Ser	144.0	0.0		164.0	48.0	NM_001042717	B4DFY6|Q3B7A6|Q5H9V2|Q8IXG8|Q8N982|Q8WU16|Q9BSP1|Q9Y6T6	Missense_Mutation	SNP	ENST00000222511.6	hg19	CCDS5617.1	.	.	.	.	.	.	.	.	.	.	G	36	5.798025	0.96952	.	.	ENSG00000105793	ENST00000426366;ENST00000450619;ENST00000257659;ENST00000222511;ENST00000417207	T;T;T;T;T	0.61274	0.12;0.12;0.12;0.12;0.12	6.07	6.07	0.98685	GTP1/OBG subdomain (3);	0.049416	0.85682	N	0.000000	D	0.87261	0.6133	H	0.98936	4.375	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.997;1.0;1.0;1.0	D	0.91409	0.5149	9	.	.	.	-8.5243	20.6525	0.99598	0.0:0.0:1.0:0.0	.	39;39;30;56	A4D1E9-2;A4D1E9;C9J8R7;C9JNI1	.;GTPBA_HUMAN;.;.	S	30;56;39;39;39	ENSP00000405697:G30S;ENSP00000389510:G56S;ENSP00000257659:G39S;ENSP00000222511:G39S;ENSP00000416596:G39S	.	G	+	1	0	GTPBP10	89820147	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	9.145000	0.94634	2.890000	0.99128	0.585000	0.79938	GGT	.	.		0.433	GTPBP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059976.3	NM_033107		A	89982211	G	A	89982211	3	1	313	1	0	0	0	0	1	0	0	0	6888	1000	35	3	121	3	GTPBP10	7	89982211	Missense_Mutation	SNP	G	TCGA-KR-A7K0-01A-12D-A33Q-10	1017030	89982211	69156452	51	44427										
TEX15	56154	hgsc.bcm.edu	37	chr8	30694575	30694575	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	cttgcaactgtggtcaacagCccagaaggagatggctgtac	12	10	1	2	rs547808449		TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr8:30694575C>A	ENST00000256246.2	-	3	8150	c.8076G>T	c.(8074-8076)ggG>ggT	p.G2692G		NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	2692					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)					NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		TGGTCAACAGCCCAGAAGGAG	0.453													C|||	1	0.000199681	8e-04	0	5008	,	,		21606	0		0	False		,,,				2504	0				p.G2692G		Atlas-SNP	.											.	TEX15	350	.	0			c.G8076T						.						133	128	129					8																	30694575		2203	4300	6503	SO:0001819	synonymous_variant	56154	exon3			CAACAGCCCAGAA	AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"cancer/testis antigen 42"	605795	"testis expressed sequence 15"			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.8076G>T	chr8.hg19:g.30694575C>A		109.0	0.0		121.0	40.0	NM_031271		Silent	SNP	ENST00000256246.2	hg19	CCDS6080.1																																																																																			.	.		0.453	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			A	30694575	C	A	30694575	2	1	313	1	0	0	0	0	0	0	0	1	15794	726	26	3		3	TEX15	8	30694575	Silent	SNP	C	TCGA-KR-A7K0-01A-12D-A33Q-10		30694575	115669447	52	44428										
UNC5D	137970	hgsc.bcm.edu	37	chr8	35631938	35631938	+	Frame_Shift_Del	DEL	C	C	-													0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	gatttgtgctacatttgataCccccaatgccaaaggcaagg							TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr8:35631938delC	ENST00000404895.2	+	16	2928	c.2600delC	c.(2599-2601)accfs	p.T867fs	UNC5D_ENST00000420357.1_Frame_Shift_Del_p.T800fs|UNC5D_ENST00000287272.2_Frame_Shift_Del_p.T798fs|UNC5D_ENST00000416672.1_Frame_Shift_Del_p.T872fs|UNC5D_ENST00000449677.1_Frame_Shift_Del_p.T443fs|UNC5D_ENST00000453357.2_Frame_Shift_Del_p.T862fs	NM_080872.2	NP_543148.2	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D (C. elegans)	867	Death.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|pyramidal neuron differentiation (GO:0021859)|regulation of neuron migration (GO:2001222)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(2)|breast(7)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(56)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(6)|urinary_tract(2)	112				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)		ACATTTGATACCCCCAATGCC	0.478																																					p.T867fs		Pindel	.											.	UNC5D	393	.	0			c.2599delA						.						125	114	118					8																	35631938		2203	4300	6503	SO:0001589	frameshift_variant	137970	exon16			.	AB055056	CCDS6093.2	8p12	2013-01-11			ENSG00000156687	ENSG00000156687		"Immunoglobulin superfamily / I-set domain containing"	18634	protein-coding gene	gene with protein product						18402767	Standard	NM_080872		Approved	KIAA1777, Unc5h4	uc003xjr.2	Q6UXZ4	OTTHUMG00000157145	ENST00000404895.2:c.2600delC	chr8.hg19:g.35631938delC	ENSP00000385143:p.Thr867fs	119.0	0.0		144.0	29.0	NM_080872	Q8WYP7	Frame_Shift_Del	DEL	ENST00000404895.2	hg19	CCDS6093.2																																																																																			.	.		0.478	UNC5D-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347586.2			-	35631938	C	-	35631938	7	5	313	1	0	1	0	1	0	0	0	0	17010	507	18	0	2662	0	UNC5D	8	35631938	Frame_Shift_Del	DEL	C	TCGA-KR-A7K0-01A-12D-A33Q-10	4937363	35631938	110732084	53	44429										
TGS1	96764	hgsc.bcm.edu	37	chr8	56698309	56698309	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	acagaagaagaggaaggtggTtattcctgtggtactgcaga	14	5	0	4			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr8:56698309T>C	ENST00000260129.5	+	3	675	c.198T>C	c.(196-198)ggT>ggC	p.G66G		NM_024831.6	NP_079107.6	Q96RS0	TGS1_HUMAN	trimethylguanosine synthase 1	66					7-methylguanosine cap hypermethylation (GO:0036261)|7-methylguanosine RNA capping (GO:0009452)|cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|regulation of transcription, DNA-templated (GO:0006355)|ribonucleoprotein complex biogenesis (GO:0022613)|ribonucleoprotein complex import into nucleus (GO:0071167)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)	RNA trimethylguanosine synthase activity (GO:0071164)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		all_lung(136;0.119)|all_epithelial(80;0.125)|Lung NSC(129;0.147)	Epithelial(17;0.00027)|all cancers(17;0.00251)			AGGAAGGTGGTTATTCCTGTG	0.413																																					p.G66G	Esophageal Squamous(34;275 823 4842 34837 48447)	Atlas-SNP	.											.	TGS1	66	.	0			c.T198C						.						132	120	124					8																	56698309		2203	4300	6503	SO:0001819	synonymous_variant	96764	exon3			AGGTGGTTATTCC	AY028423	CCDS34894.1	8q11	2010-06-25	2010-06-25	2006-11-27	ENSG00000137574	ENSG00000137574	2.1.1.-		17843	protein-coding gene	gene with protein product		606461	"nuclear receptor coactivator 6 interacting protein", "trimethylguanosine synthase homolog (S. cerevisiae)"	NCOA6IP		11517327, 11983179, 19307714	Standard	NM_024831		Approved	PIMT	uc003xsj.4	Q96RS0	OTTHUMG00000164294	ENST00000260129.5:c.198T>C	chr8.hg19:g.56698309T>C		161.0	0.0		209.0	57.0	NM_024831	A6NJQ5|Q5GH23|Q8TDG9|Q96QU3|Q9H5V3	Silent	SNP	ENST00000260129.5	hg19	CCDS34894.1																																																																																			.	.		0.413	TGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378152.1	NM_024831		C	56698309	T	C	56698309	2	2	313	1	0	0	0	0	0	0	0	1	15852	1712	60	2		2	TGS1	8	56698309	Silent	SNP	T	TCGA-KR-A7K0-01A-12D-A33Q-10	21066371	56698309	89665713	54	44430										
TRAPPC9	83696	hgsc.bcm.edu	37	chr8	141370238	141370238	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	tccccatccttcgggaggcgTagaccaattcatggagcaaa	10	12	1	1			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr8:141370238T>C	ENST00000438773.2	-	9	1539	c.1406A>G	c.(1405-1407)tAc>tGc	p.Y469C	TRAPPC9_ENST00000389328.4_Missense_Mutation_p.Y567C|TRAPPC9_ENST00000389327.3_Missense_Mutation_p.Y460C	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	469					cell differentiation (GO:0030154)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	47						TCGGGAGGCGTAGACCAATTC	0.547																																					p.Y567C		Atlas-SNP	.											.	TRAPPC9	114	.	0			c.A1700G						.						90	80	83					8																	141370238		2203	4300	6503	SO:0001583	missense	83696	exon9			GAGGCGTAGACCA	BC006206	CCDS34946.1, CCDS55278.1	8q24.3	2010-10-22			ENSG00000167632	ENSG00000167632		"Trafficking protein particle complex"	30832	protein-coding gene	gene with protein product	"TRAPP 120 kDa subunit", "tularik gene 1"	611966				11572484	Standard	NM_031466		Approved	IKBKBBP, NIBP, KIAA1882, T1, TRS120, MRT13	uc003yvh.2	Q96Q05	OTTHUMG00000164187	ENST00000438773.2:c.1406A>G	chr8.hg19:g.141370238T>C	ENSP00000405060:p.Tyr469Cys	92.0	0.0		116.0	13.0	NM_031466	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Missense_Mutation	SNP	ENST00000438773.2	hg19	CCDS55278.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.158619	0.78226	.	.	ENSG00000167632	ENST00000389328;ENST00000389327;ENST00000438773	.	.	.	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.69940	0.3167	L	0.47716	1.5	0.58432	D	0.999991	D;D;D	0.89917	1.0;0.996;0.999	D;D;D	0.75484	0.986;0.918;0.951	T	0.71364	-0.4615	9	0.52906	T	0.07	.	15.4136	0.74945	0.0:0.0:0.0:1.0	.	469;460;567	Q96Q05;Q96Q05-3;Q96Q05-2	TPPC9_HUMAN;.;.	C	567;460;469	.	ENSP00000373978:Y460C	Y	-	2	0	TRAPPC9	141439420	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.803000	0.85983	2.054000	0.61138	0.533000	0.62120	TAC	.	.		0.547	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466		C	141370238	T	C	141370238	3	2	313	1	0	0	0	0	1	0	0	0	16480	1638	57	2	2100	2	TRAPPC9	8	141370238	Missense_Mutation	SNP	T	TCGA-KR-A7K0-01A-12D-A33Q-10	84671929	141370238	4993784	55	44431										
KIAA1797	54914	hgsc.bcm.edu	37	chr9	20926369	20926369	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	atacactcttggtcattgtgGatagccattaccaacccaga	7	11	2	1			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr9:20926369G>T	ENST00000380249.1	+	28	3395	c.3031G>T	c.(3031-3033)Gat>Tat	p.D1011Y	FOCAD_ENST00000605086.1_Missense_Mutation_p.D447Y|FOCAD_ENST00000338382.6_Missense_Mutation_p.D1011Y	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	1011						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)											GGTCATTGTGGATAGCCATTA	0.348																																					p.D1011Y		Atlas-SNP	.											.	.	.	.	0			c.G3031T						.						121	112	115					9																	20926369		2203	4300	6503	SO:0001583	missense	54914	exon28			ATTGTGGATAGCC	AB058700	CCDS34993.1	9p21	2012-03-23	2012-03-23	2012-03-23	ENSG00000188352	ENSG00000188352			23377	protein-coding gene	gene with protein product		614606	"KIAA1797"	KIAA1797		22427331	Standard	XM_006716794		Approved	FLJ20375	uc003zog.1	Q5VW36	OTTHUMG00000066930	ENST00000380249.1:c.3031G>T	chr9.hg19:g.20926369G>T	ENSP00000369599:p.Asp1011Tyr	105.0	0.0		106.0	27.0	NM_017794	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Missense_Mutation	SNP	ENST00000380249.1	hg19	CCDS34993.1	.	.	.	.	.	.	.	.	.	.	G	18.52	3.641896	0.67244	.	.	ENSG00000188352	ENST00000380249;ENST00000338382	T;T	0.11385	2.78;2.78	5.84	5.84	0.93424	Armadillo-type fold (1);	0.139822	0.64402	D	0.000004	T	0.29620	0.0739	M	0.62723	1.935	0.40454	D	0.980178	D	0.89917	1.0	D	0.68192	0.956	T	0.00544	-1.1679	10	0.87932	D	0	-6.1902	14.3704	0.66836	0.0725:0.0:0.9275:0.0	.	1011	Q5VW36	K1797_HUMAN	Y	1011	ENSP00000369599:D1011Y;ENSP00000344307:D1011Y	ENSP00000344307:D1011Y	D	+	1	0	KIAA1797	20916369	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.268000	0.58883	2.776000	0.95493	0.586000	0.80456	GAT	.	.		0.348	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794		T	20926369	G	T	20926369	3	4	313	1	0	0	0	0	1	0	0	0	8267	1174	41	3	3129	3	KIAA1797	9	20926369	Missense_Mutation	SNP	G	TCGA-KR-A7K0-01A-12D-A33Q-10		20926369	120287062	56	44432										
TTC16	158248	hgsc.bcm.edu	37	chr9	130489325	130489325	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	cacccagatagcccacctggCcaggctgcagctggagcaga	12	15	0	2			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr9:130489325C>T	ENST00000373289.3	+	11	1582	c.1502C>T	c.(1501-1503)gCc>gTc	p.A501V	TTC16_ENST00000489226.1_3'UTR|PTRH1_ENST00000419060.1_5'Flank|PTRH1_ENST00000429848.1_5'Flank	NM_144965.1	NP_659402.1	Q8NEE8	TTC16_HUMAN	tetratricopeptide repeat domain 16	501										central_nervous_system(2)|endometrium(3)|lung(7)|ovary(3)|pancreas(2)|prostate(4)|skin(1)	22						GCCCACCTGGCCAGGCTGCAG	0.652																																					p.A501V		Atlas-SNP	.											.	TTC16	55	.	0			c.C1502T						.						39	40	40					9																	130489325		2203	4300	6503	SO:0001583	missense	158248	exon11			ACCTGGCCAGGCT	AK057342	CCDS6875.1	9q34.13	2013-01-10			ENSG00000167094	ENSG00000167094		"Tetratricopeptide (TTC) repeat domain containing"	26536	protein-coding gene	gene with protein product						12477932	Standard	NM_144965		Approved	FLJ32780	uc004brq.1	Q8NEE8	OTTHUMG00000020711	ENST00000373289.3:c.1502C>T	chr9.hg19:g.130489325C>T	ENSP00000362386:p.Ala501Val	43.0	0.0		49.0	18.0	NM_144965	B4DYG4|B5ME24|Q5JU66|Q96M72	Missense_Mutation	SNP	ENST00000373289.3	hg19	CCDS6875.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.049540	0.75846	.	.	ENSG00000167094	ENST00000373289;ENST00000373288	T	0.19394	2.15	5.9	5.9	0.94986	.	0.208186	0.33854	N	0.004482	T	0.37019	0.0988	L	0.54323	1.7	0.80722	D	1	D;D	0.69078	0.997;0.997	P;P	0.56751	0.805;0.805	T	0.00681	-1.1612	10	0.32370	T	0.25	-24.4927	17.8179	0.88640	0.0:1.0:0.0:0.0	.	488;501	B4DZ42;Q8NEE8	.;TTC16_HUMAN	V	501;279	ENSP00000362386:A501V	ENSP00000362385:A279V	A	+	2	0	TTC16	129529146	0.999000	0.42202	0.960000	0.40013	0.212000	0.24457	4.444000	0.60001	2.811000	0.96726	0.555000	0.69702	GCC	.	.		0.652	TTC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054224.1	NM_144965		T	130489325	C	T	130489325	3	4	313	1	0	0	0	0	1	0	0	0	16698	739	26	3	1544	3	TTC16	9	130489325	Missense_Mutation	SNP	C	TCGA-KR-A7K0-01A-12D-A33Q-10	109562956	130489325	10724106	57	44433										
USP20	10868	hgsc.bcm.edu	37	chr9	132632793	132632793	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	tcgtcaccctggaagactgcCttgctgccttctttgccgct	9	15	2	1			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr9:132632793C>T	ENST00000315480.4	+	15	1785	c.1627C>T	c.(1627-1629)Ctt>Ttt	p.L543F	USP20_ENST00000372429.3_Missense_Mutation_p.L543F|USP20_ENST00000358355.1_Missense_Mutation_p.L543F			Q9Y2K6	UBP20_HUMAN	ubiquitin specific peptidase 20	543	USP.				endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|urinary_tract(1)	11		Ovarian(14;0.00556)				GGAAGACTGCCTTGCTGCCTT	0.617																																					p.L543F		Atlas-SNP	.											.	USP20	186	.	0			c.C1627T						.						93	95	94					9																	132632793		2004	4165	6169	SO:0001583	missense	10868	exon15			GACTGCCTTGCTG	AB023220	CCDS43892.1	9q34.2	2014-07-15	2005-08-08		ENSG00000136878	ENSG00000136878		"Ubiquitin-specific peptidases"	12619	protein-coding gene	gene with protein product		615143	"ubiquitin specific protease 20"			12838346	Standard	NM_006676		Approved	KIAA1003	uc004byr.3	Q9Y2K6	OTTHUMG00000020793	ENST00000315480.4:c.1627C>T	chr9.hg19:g.132632793C>T	ENSP00000313811:p.Leu543Phe	88.0	0.0		90.0	21.0	NM_001008563	Q541F1|Q8IXQ1|Q96LG5|Q9UQN8|Q9UQP0	Missense_Mutation	SNP	ENST00000315480.4	hg19	CCDS43892.1	.	.	.	.	.	.	.	.	.	.	C	17.05	3.288985	0.59976	.	.	ENSG00000136878	ENST00000372429;ENST00000315480;ENST00000358355	T;T;T	0.09350	2.99;2.99;2.99	5.36	5.36	0.76844	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.21307	0.0513	M	0.63428	1.95	0.80722	D	1	P	0.36199	0.543	B	0.43658	0.426	T	0.00518	-1.1693	10	0.46703	T	0.11	.	18.4511	0.90704	0.0:1.0:0.0:0.0	.	543	Q9Y2K6	UBP20_HUMAN	F	543	ENSP00000361506:L543F;ENSP00000313811:L543F;ENSP00000351122:L543F	ENSP00000313811:L543F	L	+	1	0	USP20	131672614	1.000000	0.71417	0.993000	0.49108	0.288000	0.27193	5.736000	0.68597	2.666000	0.90696	0.655000	0.94253	CTT	.	.		0.617	USP20-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054604.2			T	132632793	C	T	132632793	3	4	313	1	0	0	0	0	1	0	0	0	17067	681	24	3	1677	3	USP20	9	132632793	Missense_Mutation	SNP	C	TCGA-KR-A7K0-01A-12D-A33Q-10	2143468	132632793	8580638	58	44434										
PSD	5662	hgsc.bcm.edu	37	chr10	104173644	104173644	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	ctcctcctcccctctctgtgTccaaggaccatcagcagcag	7	18	2	0			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr10:104173644T>C	ENST00000020673.5	-	5	1961	c.1435A>G	c.(1435-1437)Aca>Gca	p.T479A	PSD_ENST00000492902.2_5'Flank|PSD_ENST00000406432.1_Missense_Mutation_p.T479A	NM_001270966.1|NM_002779.4	NP_001257895.1|NP_002770.3	A5PKW4	PSD1_HUMAN	pleckstrin and Sec7 domain containing	479					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)|signal transducer activity (GO:0004871)			breast(4)|endometrium(2)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				Epithelial(162;1.27e-08)|all cancers(201;2.85e-07)		CCTCTCTGTGTCCAAGGACCA	0.677																																					p.T479A		Atlas-SNP	.											.	PSD	164	.	0			c.A1435G						.						32	37	36					10																	104173644		2203	4300	6503	SO:0001583	missense	5662	exon6			TCTGTGTCCAAGG	X99688	CCDS31272.1, CCDS73187.1	10q24	2013-01-10	2004-04-28		ENSG00000059915	ENSG00000059915		"Pleckstrin homology (PH) domain containing"	9507	protein-coding gene	gene with protein product		602327	"pleckstrin and Sec7 domain protein"			9417912	Standard	NM_002779		Approved	KIAA2011, TYL, PSD1	uc009xxd.2	A5PKW4	OTTHUMG00000018954	ENST00000020673.5:c.1435A>G	chr10.hg19:g.104173644T>C	ENSP00000020673:p.Thr479Ala	172.0	0.0		160.0	19.0	NM_001270965	B1AKX7|D3DR87|Q15673|Q8IVG0	Missense_Mutation	SNP	ENST00000020673.5	hg19	CCDS31272.1	.	.	.	.	.	.	.	.	.	.	T	14.68	2.607718	0.46527	.	.	ENSG00000059915	ENST00000020673;ENST00000541902;ENST00000406432	T;T	0.19394	2.15;2.15	4.65	4.65	0.58169	.	.	.	.	.	T	0.14184	0.0343	N	0.24115	0.695	0.24261	N	0.995286	B	0.19817	0.039	B	0.16722	0.016	T	0.17961	-1.0352	9	0.08179	T	0.78	.	14.1315	0.65257	0.0:0.0:0.0:1.0	.	479	A5PKW4	PSD1_HUMAN	A	479;382;479	ENSP00000020673:T479A;ENSP00000384830:T479A	ENSP00000020673:T479A	T	-	1	0	PSD	104163634	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	3.511000	0.53400	1.749000	0.51849	0.374000	0.22700	ACA	.	.		0.677	PSD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050041.2			C	104173644	T	C	104173644	3	2	313	1	0	0	0	0	1	0	0	0	12658	1667	58	2	1691	2	PSD	10	104173644	Missense_Mutation	SNP	T	TCGA-KR-A7K0-01A-12D-A33Q-10		104173644	31361103	59	44435										
OR51E2	81285	hgsc.bcm.edu	37	chr11	4703454	4703454	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	agtggcagaaggccagccgcTtgatcagcagaggcagtggg	17	9	1	3			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr11:4703454T>G	ENST00000396950.3	-	2	727	c.488A>C	c.(487-489)aAg>aCg	p.K163T		NM_030774.3	NP_110401.1	Q9H255	O51E2_HUMAN	olfactory receptor, family 51, subfamily E, member 2	163					cellular response to fatty acid (GO:0071398)|detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|positive regulation of blood pressure (GO:0045777)|positive regulation of renin secretion into blood stream (GO:1900135)|steroid hormone mediated signaling pathway (GO:0043401)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)|signaling receptor activity (GO:0038023)|steroid hormone receptor activity (GO:0003707)			NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(3)	23		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;3e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00476)|LUSC - Lung squamous cell carcinoma(625;0.2)		GGCCAGCCGCTTGATCAGCAG	0.532																																					p.K163T		Atlas-SNP	.											.	OR51E2	77	.	0			c.A488C						.						74	72	73					11																	4703454		2201	4298	6499	SO:0001583	missense	81285	exon2			AGCCGCTTGATCA	AY033942	CCDS7751.1	11p15	2012-08-09			ENSG00000167332	ENSG00000167332		"GPCR / Class A : Olfactory receptors"	15195	protein-coding gene	gene with protein product		611268				11118034	Standard	NM_030774		Approved	PSGR	uc001lzk.2	Q9H255	OTTHUMG00000133362	ENST00000396950.3:c.488A>C	chr11.hg19:g.4703454T>G	ENSP00000380153:p.Lys163Thr	70.0	0.0		97.0	24.0	NM_030774	B2RA63|Q6IF94	Missense_Mutation	SNP	ENST00000396950.3	hg19	CCDS7751.1	.	.	.	.	.	.	.	.	.	.	T	14.28	2.488814	0.44249	.	.	ENSG00000167332	ENST00000396950	T	0.00058	8.79	5.0	5.0	0.66597	GPCR, rhodopsin-like superfamily (1);	0.134424	0.33610	N	0.004723	T	0.00300	0.0009	M	0.81112	2.525	0.28552	N	0.911585	P	0.41546	0.754	P	0.48141	0.568	T	0.18524	-1.0334	10	0.52906	T	0.07	.	11.0275	0.47753	0.0:0.0:0.0:1.0	.	163	Q9H255	O51E2_HUMAN	T	163	ENSP00000380153:K163T	ENSP00000380153:K163T	K	-	2	0	OR51E2	4660030	0.000000	0.05858	0.932000	0.37286	0.475000	0.33008	-0.327000	0.07955	2.112000	0.64535	0.533000	0.62120	AAG	.	.		0.532	OR51E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257198.1	NM_030774		G	4703454	T	G	4703454	3	3	313	1	0	0	0	0	1	0	0	0	11104	1609	56	5	478	5	OR51E2	11	4703454	Missense_Mutation	SNP	T	TCGA-KR-A7K0-01A-12D-A33Q-10		4703454	130303062	60	44436										
CNGA4	1262	hgsc.bcm.edu	37	chr11	6265537	6265537	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	actcgagagtggccaatgccCgaggacctggctgaggctga	15	11	0	3	rs560979109		TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr11:6265537C>T	ENST00000379936.2	+	6	1741	c.1626C>T	c.(1624-1626)ccC>ccT	p.P542P		NM_001037329.3	NP_001032406.1	Q8IV77	CNGA4_HUMAN	cyclic nucleotide gated channel alpha 4	542					phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sensory perception of smell (GO:0007608)	integral component of plasma membrane (GO:0005887)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)	p.P542P(1)		endometrium(2)|kidney(1)|large_intestine(9)|lung(24)|prostate(3)|skin(1)	40		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.04e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGCCAATGCCCGAGGACCTGG	0.607													C|||	1	0.000199681	0	0.0014	5008	,	,		17683	0		0	False		,,,				2504	0				p.P542P		Atlas-SNP	.											CNGA4,NS,carcinoma,0,1	CNGA4	96	.	1	Substitution - coding silent(1)	lung(1)	c.C1626T						.						51	53	53					11																	6265537		2201	4296	6497	SO:0001819	synonymous_variant	1262	exon6			AATGCCCGAGGAC	AK122736	CCDS31408.1	11p15.4	2011-07-05		2002-01-18		ENSG00000132259		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2152	protein-coding gene	gene with protein product		609472	"cyclic nucleotide gated channel beta 2"	CNCA2, CNGB2		11764791, 16382102	Standard	NM_001037329		Approved	OCNC2, OCNCb, CNG5	uc001mco.3	Q8IV77		ENST00000379936.2:c.1626C>T	chr11.hg19:g.6265537C>T		64.0	0.0		57.0	20.0	NM_001037329		Silent	SNP	ENST00000379936.2	hg19	CCDS31408.1																																																																																			.	.		0.607	CNGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383765.2	NM_001037329		T	6265537	C	T	6265537	2	4	313	1	0	0	0	0	0	0	0	1	3601	639	23	1		1	CNGA4	11	6265537	Silent	SNP	C	TCGA-KR-A7K0-01A-12D-A33Q-10	1562083	6265537	128740979	61	44437										
RAG1	5896	hgsc.bcm.edu	37	chr11	36597509	36597509	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	cacgaggctctgagggagctGatggatctttacctgaagat	13	8	2	4			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr11:36597509G>A	ENST00000299440.5	+	2	2767	c.2655G>A	c.(2653-2655)ctG>ctA	p.L885L		NM_000448.2	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	885			L -> R (in OS; dbSNP:rs199474691). {ECO:0000269|PubMed:10606976}.		adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|DNA recombination (GO:0006310)|histone monoubiquitination (GO:0010390)|immune response (GO:0006955)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|pre-B cell allelic exclusion (GO:0002331)|protein autoubiquitination (GO:0051865)|regulation of T cell differentiation (GO:0045580)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	65	all_lung(20;0.226)	all_hematologic(20;0.107)				TGAGGGAGCTGATGGATCTTT	0.488									Familial Hemophagocytic Lymphohistiocytosis																												p.L885L	Pancreas(43;321 1249 3212 48200)|Esophageal Squamous(38;49 1003 17530 24363)	Atlas-SNP	.											.	RAG1	151	.	0			c.G2655A						.						151	143	146					11																	36597509		2202	4298	6500	SO:0001819	synonymous_variant	5896	exon2	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	GGAGCTGATGGAT	M29474	CCDS7902.1	11p13	2014-09-17				ENSG00000166349		"RING-type (C3HC4) zinc fingers"	9831	protein-coding gene	gene with protein product	"recombination activating protein 1", "RING finger protein 74", "V(D)J recombination-activating protein 1"	179615				1612612, 1283330	Standard	NM_000448		Approved	RNF74, MGC43321	uc001mwu.4	P15918		ENST00000299440.5:c.2655G>A	chr11.hg19:g.36597509G>A		60.0	0.0		74.0	29.0	NM_000448	E9PPC4|Q8IY72|Q8NER2	Silent	SNP	ENST00000299440.5	hg19	CCDS7902.1																																																																																			.	.		0.488	RAG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389535.1	NM_000448		A	36597509	G	A	36597509	2	1	313	1	0	0	0	0	0	0	0	1	13018	1277	45	3		3	RAG1	11	36597509	Silent	SNP	G	TCGA-KR-A7K0-01A-12D-A33Q-10	30331972	36597509	98409007	62	44438										
LRRC4C	57689	hgsc.bcm.edu	37	chr11	40136207	40136207	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	cttcctcatcttgtagaaaaTgaccagcatcactgcagcca	6	13	3	2			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr11:40136207T>C	ENST00000278198.2	-	2	3599	c.1636A>G	c.(1636-1638)Att>Gtt	p.I546V	LRRC4C_ENST00000528697.1_Missense_Mutation_p.I546V|LRRC4C_ENST00000527150.1_Missense_Mutation_p.I546V|LRRC4C_ENST00000530763.1_Missense_Mutation_p.I546V			Q9HCJ2	LRC4C_HUMAN	leucine rich repeat containing 4C	546					regulation of axonogenesis (GO:0050770)	cell junction (GO:0030054)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)				NS(2)|central_nervous_system(3)|endometrium(1)|large_intestine(14)|lung(43)|ovary(5)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	86		all_lung(304;0.0575)|Lung NSC(402;0.138)				TTGTAGAAAATGACCAGCATC	0.453																																					p.I546V		Atlas-SNP	.											.	LRRC4C	190	.	0			c.A1636G						.						149	134	139					11																	40136207		2203	4300	6503	SO:0001583	missense	57689	exon7			AGAAAATGACCAG	AB046800	CCDS31464.1	11p12	2013-01-14				ENSG00000148948		"Immunoglobulin superfamily / I-set domain containing"	29317	protein-coding gene	gene with protein product		608817				14595443	Standard	NM_020929		Approved	KIAA1580, NGL-1	uc031pzu.1	Q9HCJ2		ENST00000278198.2:c.1636A>G	chr11.hg19:g.40136207T>C	ENSP00000278198:p.Ile546Val	99.0	0.0		93.0	24.0	NM_001258419	A8K0T1|Q7L0N3	Missense_Mutation	SNP	ENST00000278198.2	hg19	CCDS31464.1	.	.	.	.	.	.	.	.	.	.	T	0.644	-0.812120	0.02798	.	.	ENSG00000148948	ENST00000278198;ENST00000527150;ENST00000528697;ENST00000530763	T;T;T;T	0.25579	1.79;1.79;1.79;1.79	5.99	5.99	0.97316	.	0.000000	0.85682	D	0.000000	T	0.15349	0.0370	N	0.16307	0.4	0.58432	D	0.999999	B	0.11235	0.004	B	0.12156	0.007	T	0.06391	-1.0829	10	0.02654	T	1	.	15.6754	0.77316	0.0:0.0:0.0:1.0	.	546	Q9HCJ2	LRC4C_HUMAN	V	546	ENSP00000278198:I546V;ENSP00000436976:I546V;ENSP00000437132:I546V;ENSP00000434761:I546V	ENSP00000278198:I546V	I	-	1	0	LRRC4C	40092783	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.040000	0.89188	2.291000	0.77112	0.533000	0.62120	ATT	.	.		0.453	LRRC4C-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389499.1	NM_020929		C	40136207	T	C	40136207	3	2	313	1	0	0	0	0	1	0	0	0	9017	1464	51	2	290	2	LRRC4C	11	40136207	Missense_Mutation	SNP	T	TCGA-KR-A7K0-01A-12D-A33Q-10	3538698	40136207	94870309	63	44439										
SYT7	9066	hgsc.bcm.edu	37	chr11	61323666	61323666	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	gcagagaccagcaggacgtcGcgcgagggcgcccctgggga	18	13	0	1	rs547867914		TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr11:61323666G>A	ENST00000263846.4	-	2	372	c.45C>T	c.(43-45)cgC>cgT	p.R15R	SYT7_ENST00000540677.1_Silent_p.R15R|SYT7_ENST00000542670.1_Silent_p.R15R|SYT7_ENST00000542836.1_Silent_p.R15R|SYT7_ENST00000535826.1_Silent_p.R15R|SYT7_ENST00000539008.1_Silent_p.R15R	NM_004200.3	NP_004191.2	O43581	SYT7_HUMAN	synaptotagmin VII	15					exocytosis (GO:0006887)|plasma membrane repair (GO:0001778)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of insulin secretion (GO:0050796)	cell junction (GO:0030054)|dense core granule (GO:0031045)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			kidney(2)|large_intestine(3)|lung(4)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						GCAGGACGTCGCGCGAGGGCG	0.657													G|||	1	0.000199681	8e-04	0	5008	,	,		18141	0		0	False		,,,				2504	0				p.R15R		Atlas-SNP	.											.	SYT7	39	.	0			c.C45T						.						67	58	61					11																	61323666		2202	4299	6501	SO:0001819	synonymous_variant	9066	exon2			GACGTCGCGCGAG	AF038535	CCDS31577.1, CCDS58139.1, CCDS73298.1	11q12-q13.1	2013-01-21			ENSG00000011347	ENSG00000011347		"Synaptotagmins"	11514	protein-coding gene	gene with protein product		604146	"prostate cancer associated protein 7"	PCANAP7		9615227	Standard	NM_001252065		Approved	IPCA-7, SYT-VII, MGC150517	uc009ynr.3	O43581	OTTHUMG00000168199	ENST00000263846.4:c.45C>T	chr11.hg19:g.61323666G>A		78.0	0.0		85.0	20.0	NM_001252065	F5GZU9|Q08AH6	Silent	SNP	ENST00000263846.4	hg19	CCDS31577.1																																																																																			.	.		0.657	SYT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398733.1	NM_004200		A	61323666	G	A	61323666	2	1	313	1	0	0	0	0	0	0	0	1	15494	1074	38	1		1	SYT7	11	61323666	Silent	SNP	G	TCGA-KR-A7K0-01A-12D-A33Q-10	21187459	61323666	73682850	64	44440										
ENDOD1	23052	hgsc.bcm.edu	37	chr11	94823277	94823277	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	tgtcagcgcgcggagggtgcTgagcgcttcgccaccctcta	14	14	2	1			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr11:94823277T>G	ENST00000278505.4	+	1	304	c.186T>G	c.(184-186)gcT>gcG	p.A62A		NM_015036.2	NP_055851.1	O94919	ENDD1_HUMAN	endonuclease domain containing 1	62						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.00824)				CGGAGGGTGCTGAGCGCTTCG	0.716																																					p.A62A		Atlas-SNP	.											.	ENDOD1	26	.	0			c.T186G						.						12	16	15					11																	94823277		1882	4104	5986	SO:0001819	synonymous_variant	23052	exon1			GGGTGCTGAGCGC	BC026191	CCDS41699.1	11q21	2010-03-19			ENSG00000149218	ENSG00000149218			29129	protein-coding gene	gene with protein product						10048485	Standard	NM_015036		Approved	KIAA0830	uc001pfh.3	O94919	OTTHUMG00000167835	ENST00000278505.4:c.186T>G	chr11.hg19:g.94823277T>G		76.0	0.0		100.0	29.0	NM_015036	A8K6K8|Q6GQY5|Q8TAQ8	Silent	SNP	ENST00000278505.4	hg19	CCDS41699.1																																																																																			.	.		0.716	ENDOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396545.1	NM_015036		G	94823277	T	G	94823277	2	3	313	1	0	0	0	0	0	0	0	1	5116	1567	55	5		5	ENDOD1	11	94823277	Silent	SNP	T	TCGA-KR-A7K0-01A-12D-A33Q-10	33499611	94823277	40183239	65	44441										
PPP2R1B	5519	hgsc.bcm.edu	37	chr11	111636082	111636082	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	agtgctagggcaattgttgaTaacttcttaatactgttgag	10	5	1	2			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr11:111636082T>C	ENST00000527614.1	-	2	206	c.141A>G	c.(139-141)ttA>ttG	p.L47L	PPP2R1B_ENST00000393055.2_Silent_p.L47L|PPP2R1B_ENST00000341980.6_Silent_p.L47L|PPP2R1B_ENST00000426998.2_Intron|PPP2R1B_ENST00000311129.5_Silent_p.L47L|PPP2R1B_ENST00000427203.2_5'UTR	NM_001177562.1|NM_002716.4	NP_001171033.1|NP_002707.3	P30154	2AAB_HUMAN	protein phosphatase 2, regulatory subunit A, beta	47					apoptotic process involved in morphogenesis (GO:0060561)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)	extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|liver(1)|lung(10)|prostate(1)|urinary_tract(2)	22		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|Epithelial(105;2.36e-06)|all cancers(92;3.78e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0761)		CAATTGTTGATAACTTCTTAA	0.368																																					p.L47L		Atlas-SNP	.											.	PPP2R1B	44	.	0			c.A141G						.						110	110	110					11																	111636082		2201	4297	6498	SO:0001819	synonymous_variant	5519	exon2			TGTTGATAACTTC	AF087438	CCDS8348.1, CCDS8349.1, CCDS53706.1, CCDS53707.1, CCDS53708.1	11q23.1	2010-06-18	2010-04-14		ENSG00000137713	ENSG00000137713	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9303	protein-coding gene	gene with protein product	"PP2A-A-beta", "protein phosphatase 2A, regulatory subunit A, beta isoform"	603113	"protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), beta isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit A, beta isoform"			2159327, 9795170	Standard	NM_181699		Approved	PR65B, PP2A-Abeta	uc001plw.1	P30154	OTTHUMG00000166741	ENST00000527614.1:c.141A>G	chr11.hg19:g.111636082T>C		111.0	0.0		101.0	17.0	NM_001177562	A8MY67|B0YJ69|B4DGQ6|B4DK91|B4DWW5|F8W8G1|O75620|Q8NHV8	Silent	SNP	ENST00000527614.1	hg19	CCDS8349.1																																																																																			.	.		0.368	PPP2R1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391298.1	NM_002716		C	111636082	T	C	111636082	2	2	313	1	0	0	0	0	0	0	0	1	12395	1403	49	2		2	PPP2R1B	11	111636082	Silent	SNP	T	TCGA-KR-A7K0-01A-12D-A33Q-10	16812805	111636082	23370434	66	44442										
C1QTNF5	114902	hgsc.bcm.edu	37	chr11	119210937	119210945	+	In_Frame_Del	DEL	GCCGTCGCG	GCCGTCGCG	-													0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	tctcccggagccccgggcgcGccgtcgcggccgtcgcggcc							TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	GCCGTCGCG	GCCGTCGCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr11:119210937_119210945delGCCGTCGCG	ENST00000528368.1	-	2	394_402	c.163_171delCGCGACGGC	c.(163-171)cgcgacggcdel	p.RDG55del	RP11-334E6.10_ENST00000501918.2_RNA|C1QTNF5_ENST00000445041.2_In_Frame_Del_p.RDG55del|MFRP_ENST00000530681.1_3'UTR|C1QTNF5_ENST00000525657.1_Intron|MFRP_ENST00000555262.1_3'UTR	NM_001278431.1	NP_001265360.1	Q9BXJ0	C1QT5_HUMAN	C1q and tumor necrosis factor related protein 5	55	Collagen-like.					collagen trimer (GO:0005581)|extracellular vesicular exosome (GO:0070062)				endometrium(1)|lung(2)	3		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;3.78e-05)		CCCCGGGCGCgccgtcgcggccgtcgcgg	0.766																																					p.55_58del		Atlas-Indel,Pindel	.											.	C1QTNF5	12	.	0			c.164_172del						.																																			SO:0001651	inframe_deletion	114902	exon14			.	AF329841	CCDS8420.1	11q23.3	2013-05-10				ENSG00000223953			14344	protein-coding gene	gene with protein product	"complement-c1q tumor necrosis factor-related protein 5", "complement C1q tumor necrosis factor-related protein 5 precursor variant 3"	608752				12944416	Standard	NM_015645		Approved	CTRP5, DKFZp586B0621, LORD		Q9BXJ0	OTTHUMG00000166198	ENST00000528368.1:c.163_171delCGCGACGGC	chr11.hg19:g.119210946_119210954delGCCGTCGCG	ENSP00000431140:p.Arg55_Gly57del	4.0	0.0		26.0	11.0	NM_015645	A6NDD3|B0YJ35|Q335M2|Q8N6P2|Q9UFX4	In_Frame_Del	DEL	ENST00000528368.1	hg19	CCDS8420.1																																																																																			.	.		0.766	C1QTNF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388354.1	NM_015645		-	119210945	GCCGTCGCG	-	119210937	7	5	313	1	0	1	0	1	0	0	0	0	1968	1074	38	0	568	0	C1QTNF5	11	119210937	In_Frame_Del	DEL	GCCGTCGCG	TCGA-KR-A7K0-01A-12D-A33Q-10	7574855	119210937	15795579	67	44443										
MANSC1	54682	hgsc.bcm.edu	37	chr12	12483617	12483617	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	aggcagcagatgagctatttCttgatcagaggaaaattgtg	12	5	2	4			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr12:12483617C>A	ENST00000535902.1	-	4	1203	c.640G>T	c.(640-642)Gaa>Taa	p.E214*	MANSC1_ENST00000545735.1_Nonsense_Mutation_p.E133*|MANSC1_ENST00000396349.3_Nonsense_Mutation_p.E180*			Q9H8J5	MANS1_HUMAN	MANSC domain containing 1	214						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|skin(1)|stomach(4)	23		Prostate(47;0.0865)		BRCA - Breast invasive adenocarcinoma(232;0.185)		TGAGCTATTTCTTGATCAGAG	0.483																																					p.E214X		Atlas-SNP	.											.	MANSC1	38	.	0			c.G640T						.						94	98	96					12																	12483617		2203	4300	6503	SO:0001587	stop_gained	54682	exon4			CTATTTCTTGATC	AK001160	CCDS8648.1	12p13.2	2006-04-12				ENSG00000111261			25505	protein-coding gene	gene with protein product						12975309	Standard	NM_018050		Approved	FLJ10298, LOH12CR3	uc001rai.1	Q9H8J5		ENST00000535902.1:c.640G>T	chr12.hg19:g.12483617C>A	ENSP00000438205:p.Glu214*	90.0	0.0		94.0	32.0	NM_018050	Q8NEC1|Q9NW60	Nonsense_Mutation	SNP	ENST00000535902.1	hg19	CCDS8648.1	.	.	.	.	.	.	.	.	.	.	C	37	6.407185	0.97542	.	.	ENSG00000111261	ENST00000535902;ENST00000396349;ENST00000355566;ENST00000545735	.	.	.	5.03	-2.99	0.05497	.	1.727610	0.03237	N	0.179831	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05959	T	0.93	-0.8017	5.7843	0.18324	0.0:0.3877:0.1432:0.469	.	.	.	.	X	214;180;133;133	.	ENSP00000347765:E133X	E	-	1	0	MANSC1	12374884	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.052000	0.11865	-0.566000	0.06054	0.491000	0.48974	GAA	.	.		0.483	MANSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400144.1	NM_018050		A	12483617	C	A	12483617	4	1	313	1	0	0	0	0	0	1	0	0	9233	922	32	3	659	3	MANSC1	12	12483617	Nonsense_Mutation	SNP	C	TCGA-KR-A7K0-01A-12D-A33Q-10		12483617	121368278	68	44444										
PLEKHA5	54477	hgsc.bcm.edu	37	chr12	19285332	19285332	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	tatgtattgttttagatttgCctactggctgggaagaagca	11	5	0	2			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr12:19285332C>T	ENST00000299275.6	+	3	181	c.175C>T	c.(175-177)Cct>Tct	p.P59S	PLEKHA5_ENST00000317589.4_Missense_Mutation_p.P59S|PLEKHA5_ENST00000538714.1_Missense_Mutation_p.P59S|PLEKHA5_ENST00000355397.3_Missense_Mutation_p.P59S|PLEKHA5_ENST00000539256.1_5'UTR|PLEKHA5_ENST00000429027.2_Missense_Mutation_p.P59S|PLEKHA5_ENST00000540972.1_Missense_Mutation_p.P59S|PLEKHA5_ENST00000359180.3_Missense_Mutation_p.P59S|PLEKHA5_ENST00000309364.4_Missense_Mutation_p.P59S	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5	59	WW 2. {ECO:0000255|PROSITE- ProRule:PRU00224}.				reproductive system development (GO:0061458)	cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					TTTAGATTTGCCTACTGGCTG	0.284																																					p.P59S	Pancreas(196;329 2193 11246 14234 19524)	Atlas-SNP	.											.	PLEKHA5	198	.	0			c.C175T						.						105	107	106					12																	19285332		2203	4298	6501	SO:0001583	missense	54477	exon3			GATTTGCCTACTG	AF302150	CCDS8682.1, CCDS44840.1, CCDS44840.2, CCDS55809.1, CCDS58213.1, CCDS58214.1	12p12	2013-01-10			ENSG00000052126	ENSG00000052126		"Pleckstrin homology (PH) domain containing"	30036	protein-coding gene	gene with protein product		607770				11214970, 11001876	Standard	NM_001143821		Approved	PEPP2, KIAA1686, FLJ10667	uc031qgo.1	Q9HAU0	OTTHUMG00000167921	ENST00000299275.6:c.175C>T	chr12.hg19:g.19285332C>T	ENSP00000299275:p.Pro59Ser	98.0	0.0		99.0	24.0	NM_001143821	A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	Missense_Mutation	SNP	ENST00000299275.6	hg19	CCDS8682.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.321850	0.81580	.	.	ENSG00000052126	ENST00000317589;ENST00000355397;ENST00000359180;ENST00000542828;ENST00000309364;ENST00000412219;ENST00000540972;ENST00000429027;ENST00000299275;ENST00000538714	D;D;D;D;D;D;D	0.88277	-2.36;-2.36;-2.36;-2.36;-2.36;-2.36;-2.36	4.8	4.8	0.61643	WW/Rsp5/WWP (3);	0.354218	0.20979	N	0.082251	D	0.94905	0.8353	M	0.87038	2.855	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.998	D	0.95324	0.8423	10	0.87932	D	0	-8.9638	15.0659	0.71996	0.0:1.0:0.0:0.0	.	59;59;59	B4DHK5;Q9HAU0;Q9HAU0-2	.;PKHA5_HUMAN;.	S	59	ENSP00000325155:P59S;ENSP00000347560:P59S;ENSP00000352104:P59S;ENSP00000311239:P59S;ENSP00000404296:P59S;ENSP00000299275:P59S;ENSP00000439673:P59S	ENSP00000299275:P59S	P	+	1	0	PLEKHA5	19176599	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.407000	0.73280	2.656000	0.90262	0.557000	0.71058	CCT	.	.		0.284	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	NM_019012		T	19285332	C	T	19285332	3	4	313	1	0	0	0	0	1	0	0	0	12068	739	26	3	185	3	PLEKHA5	12	19285332	Missense_Mutation	SNP	C	TCGA-KR-A7K0-01A-12D-A33Q-10	6801715	19285332	114566563	69	44445										
KRT7	3855	hgsc.bcm.edu	37	chr12	52635403	52635403	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	gcagccgggctgaggctgaaGcctggtaccagaccaaggtg	16	11	0	3			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr12:52635403G>A	ENST00000331817.5	+	5	1024	c.841G>A	c.(841-843)Gcc>Acc	p.A281T		NM_005556.3	NP_005547.3	P08729	K2C7_HUMAN	keratin 7	281	Coil 2.|Rod.				viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(2)|stomach(1)|urinary_tract(1)	14				BRCA - Breast invasive adenocarcinoma(357;0.105)	Primaquine(DB01087)	TGAGGCTGAAGCCTGGTACCA	0.592																																					p.A281T		Atlas-SNP	.											.	KRT7	48	.	0			c.G841A						.						73	67	69					12																	52635403		2203	4300	6503	SO:0001583	missense	3855	exon5			GCTGAAGCCTGGT		CCDS8822.1	12q13.13	2013-01-16			ENSG00000135480	ENSG00000135480		"-", "Intermediate filaments type II, keratins (basic)"	6445	protein-coding gene	gene with protein product	"keratin, type II cytoskeletal 7", "cytokeratin 7", "sarcolectin", "keratin, 55K type II cytoskeletal"	148059				1713141, 16831889	Standard	XR_245927		Approved	K7, CK7, K2C7, SCL	uc001saa.1	P08729	OTTHUMG00000169580	ENST00000331817.5:c.841G>A	chr12.hg19:g.52635403G>A	ENSP00000329243:p.Ala281Thr	61.0	0.0		57.0	12.0	NM_005556	Q92676|Q9BUD8|Q9Y3R7	Missense_Mutation	SNP	ENST00000331817.5	hg19	CCDS8822.1	.	.	.	.	.	.	.	.	.	.	G	9.058	0.993758	0.19043	.	.	ENSG00000135480	ENST00000331817;ENST00000422319;ENST00000551537	T	0.77877	-1.13	4.88	-7.1	0.01547	Prefoldin (1);Filament (1);	0.424132	0.17542	N	0.170505	T	0.60170	0.2248	L	0.37850	1.14	0.09310	N	0.999996	B;B	0.22080	0.0;0.064	B;B	0.24006	0.008;0.05	T	0.46373	-0.9196	10	0.54805	T	0.06	.	7.293	0.26376	0.4708:0.0:0.3269:0.2023	.	281;281	F8VZY5;P08729	.;K2C7_HUMAN	T	281;257;281	ENSP00000329243:A281T	ENSP00000329243:A281T	A	+	1	0	KRT7	50921670	0.000000	0.05858	0.000000	0.03702	0.556000	0.35491	-0.730000	0.04915	-1.328000	0.02261	-0.181000	0.13052	GCC	.	.		0.592	KRT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404897.1	NM_005556		A	52635403	G	A	52635403	3	1	313	1	0	0	0	0	1	0	0	0	8492	971	34	3	859	3	KRT7	12	52635403	Missense_Mutation	SNP	G	TCGA-KR-A7K0-01A-12D-A33Q-10	33350071	52635403	81216492	70	44446										
NAA25	80018	hgsc.bcm.edu	37	chr12	112481516	112481516	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	cgaagaatatcaatccgggaGgataccccattctcggcagt	10	11	2	1			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr12:112481516G>C	ENST00000261745.4	-	18	2411	c.2163C>G	c.(2161-2163)tcC>tcG	p.S721S		NM_024953.3	NP_079229.2	Q14CX7	NAA25_HUMAN	N(alpha)-acetyltransferase 25, NatB auxiliary subunit	721						cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(1)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	46						CAATCCGGGAGGATACCCCAT	0.478																																					p.S721S		Atlas-SNP	.											.	NAA25	105	.	0			c.C2163G						.						86	88	87					12																	112481516		2203	4300	6503	SO:0001819	synonymous_variant	80018	exon18			CCGGGAGGATACC	AB054990	CCDS9159.1	12q24.13	2013-10-11	2010-01-14	2010-01-14		ENSG00000111300		"N(alpha)-acetyltransferase subunits"	25783	protein-coding gene	gene with protein product		612755	"chromosome 12 open reading frame 30"	C12orf30		19660095	Standard	NM_024953		Approved	FLJ13089	uc001ttm.3	Q14CX7	OTTHUMG00000169638	ENST00000261745.4:c.2163C>G	chr12.hg19:g.112481516G>C		91.0	0.0		72.0	26.0	NM_024953	A0JLU7|Q6MZH1|Q7Z4N6|Q9H911	Silent	SNP	ENST00000261745.4	hg19	CCDS9159.1																																																																																			.	.		0.478	NAA25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405205.1	NM_024953		C	112481516	G	C	112481516	2	2	313	1	0	0	0	0	0	0	0	1	10130	987	35	4		4	NAA25	12	112481516	Silent	SNP	G	TCGA-KR-A7K0-01A-12D-A33Q-10	59846113	112481516	21370379	71	44447										
ANKLE2	23141	hgsc.bcm.edu	37	chr12	133319812	133319812	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	tgtgacgaaagcacgttgacTacatctgcatttccaaactt	7	10	1	2			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr12:133319812T>G	ENST00000357997.5	-	6	1370	c.1281A>C	c.(1279-1281)gtA>gtC	p.V427V	ANKLE2_ENST00000337516.5_Silent_p.V427V|ANKLE2_ENST00000539605.1_Silent_p.V365V	NM_015114.1	NP_055929.1	Q86XL3	ANKL2_HUMAN	ankyrin repeat and LEM domain containing 2	427					mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope reassembly (GO:0007084)|negative regulation of phosphorylation (GO:0042326)|positive regulation of protein dephosphorylation (GO:0035307)|regulation of catalytic activity (GO:0050790)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	protein phosphatase 2A binding (GO:0051721)|protein phosphatase type 2A regulator activity (GO:0008601)			NS(2)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|lung(20)|ovary(1)|urinary_tract(2)	45	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.3e-08)|Epithelial(86;1.56e-07)|all cancers(50;4.94e-06)		GCACGTTGACTACATCTGCAT	0.368																																					p.V427V		Atlas-SNP	.											.	ANKLE2	76	.	0			c.A1281C						.						135	119	124					12																	133319812		1899	4113	6012	SO:0001819	synonymous_variant	23141	exon6			GTTGACTACATCT	AB014592	CCDS41869.1	12q24.33	2013-01-11	2008-03-25	2008-03-25	ENSG00000176915	ENSG00000176915		"Ankyrin repeat domain containing"	29101	protein-coding gene	gene with protein product	"LEM domain containing 7"		"KIAA0692"	KIAA0692		9734811	Standard	XM_005266159		Approved	LEMD7, Lem4	uc001ukx.2	Q86XL3	OTTHUMG00000168046	ENST00000357997.5:c.1281A>C	chr12.hg19:g.133319812T>G		89.0	0.0		84.0	18.0	NM_015114	A8KAG3|B3KN97|B3KSF8|O75176|Q6P6A5|Q8TAZ9|Q96DH4	Silent	SNP	ENST00000357997.5	hg19	CCDS41869.1																																																																																			.	.		0.368	ANKLE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397712.1			G	133319812	T	G	133319812	2	3	313	1	0	0	0	0	0	0	0	1	633	1509	53	5		5	ANKLE2	12	133319812	Silent	SNP	T	TCGA-KR-A7K0-01A-12D-A33Q-10	20838296	133319812	532083	72	44448										
MTMR6	9107	hgsc.bcm.edu	37	chr13	25842077	25842077	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	gaggcaatatggtggtgtaaTatctacagcatgaaaaaaca	10	5	1	1			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr13:25842077T>C	ENST00000381801.5	-	3	905	c.144A>G	c.(142-144)atA>atG	p.I48M	MTMR6_ENST00000540661.1_Missense_Mutation_p.I48M	NM_004685.3	NP_004676.3	Q9Y217	MTMR6_HUMAN	myotubularin related protein 6	48					peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|potassium ion transmembrane transport (GO:0071805)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	calcium-activated potassium channel activity (GO:0015269)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(5)|stomach(3)	36		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.00927)|Epithelial(112;0.0474)|OV - Ovarian serous cystadenocarcinoma(117;0.164)		GGTGGTGTAATATCTACAGCA	0.373																																					p.I48M		Atlas-SNP	.											.	MTMR6	75	.	0			c.A144G						.						115	106	109					13																	25842077		2203	4300	6503	SO:0001583	missense	9107	exon3			GTGTAATATCTAC	AF072928	CCDS9313.1	13q12	2011-06-09			ENSG00000139505	ENSG00000139505		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7453	protein-coding gene	gene with protein product		603561				9736772	Standard	NM_004685		Approved		uc001uqf.4	Q9Y217	OTTHUMG00000016606	ENST00000381801.5:c.144A>G	chr13.hg19:g.25842077T>C	ENSP00000371221:p.Ile48Met	63.0	0.0		86.0	18.0	NM_004685	B2RBB5|B3KSB4|Q5JRG6|Q86TB7|Q86YH4|Q96P80	Missense_Mutation	SNP	ENST00000381801.5	hg19	CCDS9313.1	.	.	.	.	.	.	.	.	.	.	T	16.10	3.028241	0.54790	.	.	ENSG00000139505	ENST00000540661;ENST00000541021;ENST00000381801	D;D	0.84660	-1.88;-1.88	5.56	-0.333	0.12671	Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	D	0.92041	0.7478	M	0.93283	3.4	0.54753	D	0.999984	D;D	0.76494	0.992;0.999	D;D	0.76071	0.983;0.987	D	0.89324	0.3642	10	0.87932	D	0	.	6.6463	0.22936	0.3425:0.0:0.2327:0.4248	.	48;48	Q9Y217;Q9Y217-2	MTMR6_HUMAN;.	M	48	ENSP00000443161:I48M;ENSP00000371221:I48M	ENSP00000371221:I48M	I	-	3	3	MTMR6	24740077	0.785000	0.28726	0.782000	0.31804	0.966000	0.64601	0.032000	0.13732	0.029000	0.15352	-0.480000	0.04831	ATA	.	.		0.373	MTMR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044225.1	NM_004685		C	25842077	T	C	25842077	3	2	313	1	0	0	0	0	1	0	0	0	9956	1396	49	2	1769	2	MTMR6	13	25842077	Missense_Mutation	SNP	T	TCGA-KR-A7K0-01A-12D-A33Q-10		25842077	89327801	73	44449										
C14orf28	122525	hgsc.bcm.edu	37	chr14	45373642	45373642	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	ccaacgaattttctgccatgGggcacccccttttgttgtct	8	13	2	0			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr14:45373642G>C	ENST00000325192.3	+	4	934	c.659G>C	c.(658-660)gGg>gCg	p.G220A	C14orf28_ENST00000553841.1_3'UTR|RP11-857B24.5_ENST00000555157.1_RNA|C14orf28_ENST00000557112.1_Missense_Mutation_p.G190A	NM_001017923.1	NP_001017923.1	Q4W4Y0	CN028_HUMAN	chromosome 14 open reading frame 28	220										endometrium(1)|large_intestine(3)|liver(1)|lung(4)|ovary(2)	11						TTCTGCCATGGGGCACCCCCT	0.398																																					p.G220A		Atlas-SNP	.											.	C14orf28	32	.	0			c.G659C						.						187	182	184					14																	45373642		2203	4300	6503	SO:0001583	missense	122525	exon4			GCCATGGGGCACC	AA496212	CCDS32069.1	14q21.2	2012-08-16			ENSG00000179476	ENSG00000179476			19834	protein-coding gene	gene with protein product	"dopamine receptor interacting protein 1"						Standard	XM_005267316		Approved	DRIP-1	uc001wvo.3	Q4W4Y0	OTTHUMG00000170722	ENST00000325192.3:c.659G>C	chr14.hg19:g.45373642G>C	ENSP00000326846:p.Gly220Ala	104.0	0.0		93.0	28.0	NM_001017923		Missense_Mutation	SNP	ENST00000325192.3	hg19	CCDS32069.1	.	.	.	.	.	.	.	.	.	.	G	19.59	3.857032	0.71834	.	.	ENSG00000179476	ENST00000325192;ENST00000557112	T;T	0.30714	1.52;1.52	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.43211	0.1237	N	0.19112	0.55	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	T	0.39761	-0.9598	10	0.87932	D	0	.	17.9074	0.88923	0.0:0.0:1.0:0.0	.	220	Q4W4Y0	CN028_HUMAN	A	220;190	ENSP00000326846:G220A;ENSP00000451791:G190A	ENSP00000326846:G220A	G	+	2	0	C14orf28	44443392	1.000000	0.71417	0.998000	0.56505	0.945000	0.59286	7.714000	0.84703	2.835000	0.97688	0.591000	0.81541	GGG	.	.		0.398	C14orf28-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410086.1	NM_001017923		C	45373642	G	C	45373642	3	2	313	1	0	0	0	0	1	0	0	0	1772	1232	43	4	669	4	C14orf28	14	45373642	Missense_Mutation	SNP	G	TCGA-KR-A7K0-01A-12D-A33Q-10		45373642	61975898	74	44450										
C14orf183	196913	hgsc.bcm.edu	37	chr14	50550627	50550627	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	ccaccaacaccgcacccaccTgtggggcctccagcctcttg	8	20	1	0			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr14:50550627T>C	ENST00000305273.1	-	5	716	c.717A>G	c.(715-717)acA>acG	p.T239T	RP11-58E21.7_ENST00000556019.2_lincRNA|RP11-58E21.5_ENST00000603228.1_lincRNA	NM_001014830.1	NP_001014830.1	Q8WXQ3	CN183_HUMAN	chromosome 14 open reading frame 183	239										endometrium(2)|large_intestine(2)|lung(3)	7						CGCACCCACCTGTGGGGCCTC	0.667																																					p.T239T		Atlas-SNP	.											.	C14orf183	9	.	0			c.A717G						.						11	13	13					14																	50550627		1861	4054	5915	SO:0001819	synonymous_variant	196913	exon5			CCCACCTGTGGGG	AF390030	CCDS45101.1	14q21.3	2012-09-26			ENSG00000168260	ENSG00000168260			27285	protein-coding gene	gene with protein product							Standard	NM_001014830		Approved		uc010tqk.2	Q8WXQ3	OTTHUMG00000170858	ENST00000305273.1:c.717A>G	chr14.hg19:g.50550627T>C		133.0	0.0		160.0	45.0	NM_001014830		Silent	SNP	ENST00000305273.1	hg19	CCDS45101.1																																																																																			.	.		0.667	C14orf183-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000410705.1	NM_001014830		C	50550627	T	C	50550627	2	2	313	1	0	0	0	0	0	0	0	1	1768	1567	55	2		2	C14orf183	14	50550627	Silent	SNP	T	TCGA-KR-A7K0-01A-12D-A33Q-10	5176985	50550627	56798913	75	44451										
FUT8	2530	hgsc.bcm.edu	37	chr14	66082780	66082780	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	cttgttaaggccaaagaacaGattgaaaattacaagaaaca	7	6	0	4			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr14:66082780G>A	ENST00000360689.5	+	4	2015	c.288G>A	c.(286-288)caG>caA	p.Q96Q	FUT8_ENST00000394585.1_Silent_p.Q96Q|FUT8_ENST00000358307.2_5'UTR|FUT8_ENST00000394586.2_Silent_p.Q96Q|FUT8_ENST00000557164.1_5'UTR	NM_004480.4|NM_178155.2	NP_004471.4|NP_835368.1	Q9BYC5	FUT8_HUMAN	fucosyltransferase 8 (alpha (1,6) fucosyltransferase)	96					cell migration (GO:0016477)|cellular protein metabolic process (GO:0044267)|GDP-L-fucose metabolic process (GO:0046368)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|L-fucose catabolic process (GO:0042355)|N-glycan fucosylation (GO:0036071)|N-glycan processing (GO:0006491)|oligosaccharide biosynthetic process (GO:0009312)|post-translational protein modification (GO:0043687)|protein glycosylation in Golgi (GO:0033578)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|receptor metabolic process (GO:0043112)|respiratory gaseous exchange (GO:0007585)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycoprotein 6-alpha-L-fucosyltransferase activity (GO:0008424)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	22				all cancers(60;0.00109)|OV - Ovarian serous cystadenocarcinoma(108;0.00242)|BRCA - Breast invasive adenocarcinoma(234;0.0114)		CCAAAGAACAGATTGAAAATT	0.418																																					p.Q96Q		Atlas-SNP	.											.	FUT8	101	.	0			c.G288A						.						91	91	91					14																	66082780		2203	4300	6503	SO:0001819	synonymous_variant	2530	exon4			AGAACAGATTGAA	AB049740	CCDS9775.1, CCDS9776.1, CCDS9776.2	14q24.3	2013-02-26			ENSG00000033170	ENSG00000033170		"Fucosyltransferases"	4019	protein-coding gene	gene with protein product		602589				9368041	Standard	NM_178155		Approved		uc001xio.3	Q9BYC5	OTTHUMG00000142818	ENST00000360689.5:c.288G>A	chr14.hg19:g.66082780G>A		141.0	0.0		139.0	43.0	NM_178155	B4DFS7|G3V5N0|O00235|Q8IUA5|Q9BYC6|Q9P2U5|Q9P2U6	Silent	SNP	ENST00000360689.5	hg19	CCDS9775.1																																																																																			.	.		0.418	FUT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286406.1	NM_004480		A	66082780	G	A	66082780	2	1	313	1	0	0	0	0	0	0	0	1	6118	933	33	3		3	FUT8	14	66082780	Silent	SNP	G	TCGA-KR-A7K0-01A-12D-A33Q-10	15532153	66082780	41266760	76	44452										
GPR132	29933	hgsc.bcm.edu	37	chr14	105518034	105518034	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	ggcggccccgactctccagcGcgtacaccacggccacgaag	12	18	1	0	rs376299075		TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr14:105518034G>A	ENST00000329797.3	-	4	1351	c.440C>T	c.(439-441)gCg>gTg	p.A147V	GPR132_ENST00000392585.2_Missense_Mutation_p.A138V|GPR132_ENST00000546679.1_5'UTR|GPR132_ENST00000539291.2_Missense_Mutation_p.A147V	NM_001278694.1|NM_001278696.1|NM_013345.2	NP_001265623.1|NP_001265625.1|NP_037477.1	Q9UNW8	GP132_HUMAN	G protein-coupled receptor 132	147					G1/S transition of mitotic cell cycle (GO:0000082)|response to stress (GO:0006950)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)	18		all_cancers(154;0.0953)|Melanoma(154;0.155)|all_epithelial(191;0.219)	OV - Ovarian serous cystadenocarcinoma(23;0.00778)|all cancers(16;0.00936)|Epithelial(46;0.0227)	Epithelial(152;0.02)|all cancers(159;0.0419)|OV - Ovarian serous cystadenocarcinoma(161;0.0521)		ACTCTCCAGCGCGTACACCAC	0.627																																					p.A147V		Atlas-SNP	.											.	GPR132	40	.	0			c.C440T						.	G	VAL/ALA	0,4406		0,0,2203	82	76	78		440	5	0.1	14		78	1,8599	1.2+/-3.3	0,1,4299	no	missense	GPR132	NM_013345.2	64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	147/381	105518034	1,13005	2203	4300	6503	SO:0001583	missense	29933	exon4			TCCAGCGCGTACA	AF083955	CCDS9997.1, CCDS61567.1	14q32.3	2012-08-21			ENSG00000183484	ENSG00000183484		"GPCR / Class A : Orphans"	17482	protein-coding gene	gene with protein product	"G2 accumulation"	606167				12086852	Standard	NM_013345		Approved	G2A	uc001yqd.3	Q9UNW8	OTTHUMG00000140173	ENST00000329797.3:c.440C>T	chr14.hg19:g.105518034G>A	ENSP00000328818:p.Ala147Val	108.0	0.0		123.0	33.0	NM_013345	A8K7X7|B4E144|Q9BSU2	Missense_Mutation	SNP	ENST00000329797.3	hg19	CCDS9997.1	.	.	.	.	.	.	.	.	.	.	G	16.76	3.212011	0.58452	0.0	1.16E-4	ENSG00000183484	ENST00000329797;ENST00000392585;ENST00000539291	T;T;T	0.37915	1.17;1.17;1.17	4.97	4.97	0.65823	GPCR, rhodopsin-like superfamily (1);	0.224717	0.36972	N	0.002304	T	0.65460	0.2693	M	0.86953	2.85	0.27577	N	0.949692	D;D	0.89917	0.999;1.0	D;D	0.71414	0.953;0.973	T	0.65249	-0.6214	10	0.87932	D	0	.	17.2051	0.86915	0.0:0.0:1.0:0.0	.	138;147	B4E144;Q9UNW8	.;GP132_HUMAN	V	147;138;147	ENSP00000328818:A147V;ENSP00000376364:A138V;ENSP00000438094:A147V	ENSP00000328818:A147V	A	-	2	0	GPR132	104589079	0.981000	0.34729	0.105000	0.21289	0.019000	0.09904	6.191000	0.72063	2.283000	0.76528	0.563000	0.77884	GCG	.	.		0.627	GPR132-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409278.1	NM_013345		A	105518034	G	A	105518034	3	1	313	1	0	0	0	0	1	0	0	0	6650	1087	38	1	706	1	GPR132	14	105518034	Missense_Mutation	SNP	G	TCGA-KR-A7K0-01A-12D-A33Q-10	39435254	105518034	1831506	77	44453										
BNC1	646	hgsc.bcm.edu	37	chr15	83932609	83932609	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	tgtttgggaaggctggttggCctttggaatcctctcctgaa	13	8	1	1	rs144958076		TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr15:83932609C>G	ENST00000345382.2	-	4	1479	c.1394G>C	c.(1393-1395)gGc>gCc	p.G465A	RP11-382A20.4_ENST00000565495.1_RNA|BNC1_ENST00000569704.1_Missense_Mutation_p.G458A	NM_001717.3	NP_001708.3	Q01954	BNC1_HUMAN	basonuclin 1	465					chromosome organization (GO:0051276)|epidermis development (GO:0008544)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	56						GGCTGGTTGGCCTTTGGAATC	0.552																																					p.G465A		Atlas-SNP	.											.	BNC1	149	.	0			c.G1394C						.						88	80	83					15																	83932609		2203	4300	6503	SO:0001583	missense	646	exon4			GGTTGGCCTTTGG	L03427	CCDS10324.1, CCDS73771.1	15q25.1	2013-05-20	2004-04-30	2004-05-04	ENSG00000169594	ENSG00000169594		"Zinc fingers, C2H2-type"	1081	protein-coding gene	gene with protein product		601930	"basonuclin"	BNC		1332044	Standard	NM_001717		Approved	HsT19447	uc002bjt.1	Q01954	OTTHUMG00000147362	ENST00000345382.2:c.1394G>C	chr15.hg19:g.83932609C>G	ENSP00000307041:p.Gly465Ala	151.0	0.0		142.0	43.0	NM_001717	Q15840	Missense_Mutation	SNP	ENST00000345382.2	hg19	CCDS10324.1	.	.	.	.	.	.	.	.	.	.	C	0	-2.612797	0.00120	.	.	ENSG00000169594	ENST00000345382;ENST00000541809	T	0.40476	1.03	5.51	4.51	0.55191	.	0.607917	0.18385	N	0.142845	T	0.35189	0.0923	L	0.57536	1.79	0.32099	N	0.590858	B;B	0.27068	0.167;0.104	B;B	0.20955	0.032;0.022	T	0.39542	-0.9609	10	0.02654	T	1	-16.8072	15.3486	0.74363	0.226:0.774:0.0:0.0	.	458;465	F5GY04;Q01954	.;BNC1_HUMAN	A	465;458	ENSP00000307041:G465A	ENSP00000307041:G465A	G	-	2	0	BNC1	81723613	1.000000	0.71417	0.907000	0.35723	0.024000	0.10985	3.412000	0.52679	2.589000	0.87451	0.655000	0.94253	GGC	.	C|1.000;A|0.000		0.552	BNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304006.1	NM_001717		G	83932609	C	G	83932609	3	3	313	1	0	0	0	0	1	0	0	0	1474	739	26	4	1598	4	BNC1	15	83932609	Missense_Mutation	SNP	C	TCGA-KR-A7K0-01A-12D-A33Q-10		83932609	18598783	78	44454										
ABAT	18	hgsc.bcm.edu	37	chr16	8866725	8866725	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	ccagtccgagggtggagacaAccacgcatccgatgacttct	11	13	1	2			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr16:8866725A>G	ENST00000396600.2	+	12	1843	c.905A>G	c.(904-906)aAc>aGc	p.N302S	ABAT_ENST00000569156.1_Missense_Mutation_p.N302S|ABAT_ENST00000567812.1_Missense_Mutation_p.N317S|ABAT_ENST00000268251.8_Missense_Mutation_p.N302S|ABAT_ENST00000425191.2_Missense_Mutation_p.N302S	NM_000663.4	NP_000654.2	P80404	GABT_HUMAN	4-aminobutyrate aminotransferase	302					behavioral response to cocaine (GO:0048148)|copulation (GO:0007620)|gamma-aminobutyric acid catabolic process (GO:0009450)|locomotory behavior (GO:0007626)|negative regulation of blood pressure (GO:0045776)|neurotransmitter catabolic process (GO:0042135)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to iron ion (GO:0010039)|response to nicotine (GO:0035094)|synaptic transmission (GO:0007268)	4-aminobutyrate transaminase complex (GO:0032144)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	(S)-3-amino-2-methylpropionate transaminase activity (GO:0047298)|4-aminobutyrate transaminase activity (GO:0003867)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|succinate-semialdehyde dehydrogenase binding (GO:0032145)			breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|skin(3)|upper_aerodigestive_tract(2)	26					L-Alanine(DB00160)|Phenelzine(DB00780)|Pyruvic acid(DB00119)|Valproic Acid(DB00313)|Vigabatrin(DB01080)	GGTGGAGACAACCACGCATCC	0.542																																					p.N302S		Atlas-SNP	.											.	ABAT	46	.	0			c.A905G						.						95	78	84					16																	8866725		2197	4300	6497	SO:0001583	missense	18	exon12			GAGACAACCACGC	L32961	CCDS10534.1	16p13.2	2011-01-10			ENSG00000183044	ENSG00000183044	2.6.1.19		23	protein-coding gene	gene with protein product	"4-aminobutyrate transaminase"	137150				7721088	Standard	NM_020686		Approved	GABAT	uc002czc.4	P80404	OTTHUMG00000048201	ENST00000396600.2:c.905A>G	chr16.hg19:g.8866725A>G	ENSP00000379845:p.Asn302Ser	94.0	0.0		96.0	21.0	NM_001127448	A8K386|Q16260|Q8N5W2|Q96BG2|Q99800	Missense_Mutation	SNP	ENST00000396600.2	hg19	CCDS10534.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.468739	0.84533	.	.	ENSG00000183044	ENST00000268251;ENST00000396600;ENST00000425191	T;T;T	0.76316	-1.01;-1.01;-1.01	5.05	5.05	0.67936	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.91243	0.7240	H	0.96720	3.87	0.80722	D	1	D	0.76494	0.999	D	0.66351	0.943	D	0.93943	0.7225	10	0.87932	D	0	-7.7274	13.9748	0.64265	1.0:0.0:0.0:0.0	.	302	P80404	GABT_HUMAN	S	302	ENSP00000268251:N302S;ENSP00000379845:N302S;ENSP00000411916:N302S	ENSP00000268251:N302S	N	+	2	0	ABAT	8774226	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	9.083000	0.94067	1.893000	0.54813	0.459000	0.35465	AAC	.	.		0.542	ABAT-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433620.2	NM_020686		G	8866725	A	G	8866725	3	3	313	1	0	0	0	0	1	0	0	0	27	43	2	2	947	2	ABAT	16	8866725	Missense_Mutation	SNP	A	TCGA-KR-A7K0-01A-12D-A33Q-10		8866725	81488028	79	44455										
SPNS1	83985	hgsc.bcm.edu	37	chr16	28995279	28995279	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	ggcacagctgcacgtgcaggGtcagttaggagctgtgcccg	16	11	1	0			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr16:28995279G>A	ENST00000311008.11	+	11	1869		c.e11+1		LAT_ENST00000566177.1_5'Flank|RP11-264B17.3_ENST00000569969.1_RNA|SPNS1_ENST00000323081.8_Splice_Site|LAT_ENST00000360872.5_5'Flank|LAT_ENST00000395456.2_5'Flank|LAT_ENST00000564277.1_5'Flank|LAT_ENST00000395461.3_5'Flank|SPNS1_ENST00000334536.8_Splice_Site|LAT_ENST00000454369.2_5'Flank|SPNS1_ENST00000352260.7_Splice_Site|SPNS1_ENST00000565975.1_Splice_Site|LAT_ENST00000354453.4_5'Flank	NM_032038.2	NP_114427.1	Q9H2V7	SPNS1_HUMAN	spinster homolog 1 (Drosophila)						lipid transport (GO:0006869)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrial inner membrane (GO:0005743)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)|urinary_tract(1)	21						CACGTGCAGGGTCAGTTAGGA	0.647																																					.		Atlas-SNP	.											.	SPNS1	47	.	0			c.1492+1G>A						.						23	25	24					16																	28995279		2192	4292	6484	SO:0001630	splice_region_variant	83985	exon11			TGCAGGGTCAGTT	BC006156	CCDS10646.1, CCDS45452.1, CCDS45453.1, CCDS45454.1	16p11.2	2007-04-12			ENSG00000169682	ENSG00000169682			30621	protein-coding gene	gene with protein product		612583				11340170, 12815463	Standard	NM_032038		Approved	HSpin1, nrs, SPINL, PP2030, SPIN1, LAT	uc010vdi.1	Q9H2V7	OTTHUMG00000131762	ENST00000311008.11:c.1492+1G>A	chr16.hg19:g.28995279G>A		11.0	0.0		18.0	6.0	NM_032038	B5MDM9|Q6P182|Q71RB5|Q7L541|Q86VU7|Q8N953|Q8TCS5|Q9BRN5	Splice_Site	SNP	ENST00000311008.11	hg19	CCDS10646.1	.	.	.	.	.	.	.	.	.	.	G	14.98	2.698045	0.48307	.	.	ENSG00000169682	ENST00000311008;ENST00000334536;ENST00000352260;ENST00000323081	.	.	.	4.75	4.75	0.60458	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3031	0.73969	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SPNS1	28902780	1.000000	0.71417	1.000000	0.80357	0.519000	0.34347	5.893000	0.69798	2.470000	0.83445	0.655000	0.94253	.	.	.		0.647	SPNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254690.2	NM_032038	Intron	A	28995279	G	A	28995279	5	1	313	1	0	0	0	0	0	0	1	0	15089	1275	44	3	1535	3	SPNS1	16	28995279	Splice_Site	SNP	G	TCGA-KR-A7K0-01A-12D-A33Q-10	20128554	28995279	61359474	80	44456										
CES2	8824	hgsc.bcm.edu	37	chr16	66976600	66976600	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	ttccagcatcagcccagctgGctcaagaacatcaggccacc	8	16	3	1			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr16:66976600G>A	ENST00000317091.4	+	10	2508	c.1524G>A	c.(1522-1524)tgG>tgA	p.W508*	CES2_ENST00000417689.1_Nonsense_Mutation_p.W508*|RP11-361L15.4_ENST00000566869.1_RNA	NM_003869.5	NP_003860.2	O00748	EST2_HUMAN	carboxylesterase 2	444					catabolic process (GO:0009056)	endoplasmic reticulum (GO:0005783)	carboxylic ester hydrolase activity (GO:0052689)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)			breast(1)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|prostate(1)|urinary_tract(1)	12		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0663)|Epithelial(162;0.166)	Dabigatran etexilate(DB06695)|Irinotecan(DB00762)|Mycophenolate mofetil(DB00688)|Prasugrel(DB06209)	AGCCCAGCTGGCTCAAGAACA	0.552																																					p.W508X	Ovarian(70;1230 1691 37888 38351)	Atlas-SNP	.											.	CES2	43	.	0			c.G1524A						.						81	74	76					16																	66976600		2200	4300	6500	SO:0001587	stop_gained	8824	exon10			CAGCTGGCTCAAG	BC032095	CCDS10825.1, CCDS45507.1	16q22.1	2010-10-12	2010-10-12		ENSG00000172831	ENSG00000172831		"Carboxylesterases"	1864	protein-coding gene	gene with protein product		605278	"carboxylesterase 2 (intestine, liver)"			9169443, 9144407, 20931200	Standard	NM_198061		Approved	CE-2, iCE, CES2A1	uc002eqr.3	O00748	OTTHUMG00000137517	ENST00000317091.4:c.1524G>A	chr16.hg19:g.66976600G>A	ENSP00000317842:p.Trp508*	90.0	0.0		87.0	21.0	NM_003869	A8K367|Q16859|Q5MAB8|Q7Z366|Q8IUP4|Q8TCP8	Nonsense_Mutation	SNP	ENST00000317091.4	hg19	CCDS10825.1	.	.	.	.	.	.	.	.	.	.	G	10.76	1.442395	0.25987	.	.	ENSG00000172831	ENST00000417689;ENST00000317091	.	.	.	5.12	-0.345	0.12624	.	0.849215	0.10425	N	0.676178	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.36615	T	0.2	.	0.8934	0.01259	0.277:0.2983:0.2498:0.1748	.	.	.	.	X	508	.	ENSP00000317842:W508X	W	+	3	0	CES2	65534101	0.000000	0.05858	0.002000	0.10522	0.005000	0.04900	-0.954000	0.03873	0.329000	0.23460	-0.171000	0.13296	TGG	.	.		0.552	CES2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268838.2	NM_003869		A	66976600	G	A	66976600	4	1	313	1	0	0	0	0	0	1	0	0	3272	1212	42	3	1562	3	CES2	16	66976600	Nonsense_Mutation	SNP	G	TCGA-KR-A7K0-01A-12D-A33Q-10	37981321	66976600	23378153	81	44457										
HYDIN	54768	hgsc.bcm.edu	37	chr16	70902688	70902688	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	acacccagggtggaggtggcCcatctaggaaagagcctggt	15	10	1	1			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr16:70902688C>A	ENST00000393567.2	-	66	11245	c.11095G>T	c.(11095-11097)Ggc>Tgc	p.G3699C	SNORD112_ENST00000515891.1_RNA	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	3699					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				TGGAGGTGGCCCATCTAGGAA	0.483																																					p.G3699C		Atlas-SNP	.											.	HYDIN	788	.	0			c.G11095T						.						48	40	42					16																	70902688		1935	4109	6044	SO:0001583	missense	54768	exon66			GGTGGCCCATCTA	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.11095G>T	chr16.hg19:g.70902688C>A	ENSP00000377197:p.Gly3699Cys	47.0	0.0		40.0	14.0	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	hg19	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.287363	0.80803	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.04454	3.62	5.03	5.03	0.67393	.	0.000000	0.33382	U	0.004963	T	0.25269	0.0614	M	0.82323	2.585	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.01869	-1.1257	10	0.56958	D	0.05	.	17.9383	0.89019	0.0:1.0:0.0:0.0	.	3698	F8WD23	.	C	3699;3698	ENSP00000377197:G3699C	ENSP00000313052:G3698C	G	-	1	0	HYDIN	69460189	1.000000	0.71417	0.988000	0.46212	0.896000	0.52359	6.392000	0.73213	2.327000	0.79052	0.511000	0.50034	GGC	.	.		0.483	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			A	70902688	C	A	70902688	3	1	313	1	0	0	0	0	1	0	0	0	7476	623	22	3	4354	3	HYDIN	16	70902688	Missense_Mutation	SNP	C	TCGA-KR-A7K0-01A-12D-A33Q-10	3926088	70902688	19452065	82	44458										
WFDC1	58189	hgsc.bcm.edu	37	chr16	84358060	84358060	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	gacacaaactttacaaagaaTatccaggtaaaagaagaaac	6	7	0	3			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr16:84358060T>C	ENST00000219454.5	+	5	924	c.598T>C	c.(598-600)Tat>Cat	p.Y200H	WFDC1_ENST00000568638.1_Missense_Mutation_p.Y200H	NM_001282466.1|NM_001282467.1	NP_001269395.1|NP_001269396.1	Q9HC57	WFDC1_HUMAN	WAP four-disulfide core domain 1	200					negative regulation of cell growth (GO:0030308)|negative regulation of epithelial cell proliferation (GO:0050680)|response to drug (GO:0042493)|response to estradiol (GO:0032355)	extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)	9						TTACAAAGAATATCCAGGTAA	0.368																																					p.Y200H		Atlas-SNP	.											.	WFDC1	17	.	0			c.T598C						.						100	99	99					16																	84358060		2200	4300	6500	SO:0001583	missense	58189	exon5			AAAGAATATCCAG	AF302109	CCDS10946.1	16q24.1	2013-01-21			ENSG00000103175	ENSG00000103175		"WAP four-disulfide core domain containing"	15466	protein-coding gene	gene with protein product		605322				10967136	Standard	NM_021197		Approved	PS20	uc002fhw.3	Q9HC57	OTTHUMG00000137641	ENST00000219454.5:c.598T>C	chr16.hg19:g.84358060T>C	ENSP00000219454:p.Tyr200His	83.0	0.0		79.0	23.0	NM_021197	D3DUL7|Q8NC27|Q9HAU1	Missense_Mutation	SNP	ENST00000219454.5	hg19	CCDS10946.1	.	.	.	.	.	.	.	.	.	.	T	10.34	1.324302	0.24080	.	.	ENSG00000103175	ENST00000219454	T	0.33654	1.4	4.55	2.12	0.27331	.	0.151761	0.45606	N	0.000347	T	0.20941	0.0504	L	0.29908	0.895	0.44492	D	0.99743	B	0.12013	0.005	B	0.12156	0.007	T	0.09930	-1.0652	10	0.49607	T	0.09	-8.9944	2.49	0.04607	0.1478:0.0893:0.1521:0.6108	.	200	Q9HC57	WFDC1_HUMAN	H	200	ENSP00000219454:Y200H	ENSP00000219454:Y200H	Y	+	1	0	WFDC1	82915561	0.980000	0.34600	0.955000	0.39395	0.448000	0.32197	1.051000	0.30417	0.883000	0.36040	0.528000	0.53228	TAT	.	.		0.368	WFDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269083.2			C	84358060	T	C	84358060	3	2	313	1	0	0	0	0	1	0	0	0	17361	1406	49	2	616	2	WFDC1	16	84358060	Missense_Mutation	SNP	T	TCGA-KR-A7K0-01A-12D-A33Q-10	13455372	84358060	5996693	83	44459										
DNAH2	146754	hgsc.bcm.edu	37	chr17	7636408	7636408	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	tgctgtcttccatgcagaccCagaaccagcttgtctacttc	7	14	2	2			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr17:7636408C>A	ENST00000572933.1	+	5	1863	c.403C>A	c.(403-405)Cag>Aag	p.Q135K	DNAH2_ENST00000570791.1_Missense_Mutation_p.Q135K|DNAH2_ENST00000082259.3_Missense_Mutation_p.Q135K|DNAH2_ENST00000389173.2_Missense_Mutation_p.Q135K			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	135	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				CATGCAGACCCAGAACCAGCT	0.562																																					p.Q135K		Atlas-SNP	.											.	DNAH2	498	.	0			c.C403A						.						75	68	71					17																	7636408		2203	4300	6503	SO:0001583	missense	146754	exon4			CAGACCCAGAACC	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.403C>A	chr17.hg19:g.7636408C>A	ENSP00000458355:p.Gln135Lys	71.0	0.0		67.0	26.0	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	hg19	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	C	11.32	1.604300	0.28534	.	.	ENSG00000183914	ENST00000360606;ENST00000389173;ENST00000082259	T;T	0.41065	1.01;1.01	4.67	4.67	0.58626	.	0.778438	0.11639	N	0.544033	T	0.30665	0.0772	L	0.27053	0.805	0.46874	D	0.999231	B;P	0.36660	0.329;0.564	B;B	0.40101	0.038;0.319	T	0.03130	-1.1069	10	0.02654	T	1	.	12.6852	0.56944	0.0:0.8333:0.1667:0.0	.	135;135	Q9P225;Q9P225-3	DYH2_HUMAN;.	K	135	ENSP00000373825:Q135K;ENSP00000082259:Q135K	ENSP00000082259:Q135K	Q	+	1	0	DNAH2	7577133	0.962000	0.33011	1.000000	0.80357	0.823000	0.46562	1.993000	0.40747	2.596000	0.87737	0.655000	0.94253	CAG	.	.		0.562	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		A	7636408	C	A	7636408	3	1	313	1	0	0	0	0	1	0	0	0	4604	595	21	3	417	3	DNAH2	17	7636408	Missense_Mutation	SNP	C	TCGA-KR-A7K0-01A-12D-A33Q-10		7636408	73558802	84	44460										
TLK2	11011	hgsc.bcm.edu	37	chr17	60637386	60637386	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	tctcattgaaggccaactgtGatttgagacggcagattgat	11	7	1	5			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr17:60637386G>A	ENST00000326270.9	+	10	998	c.730G>A	c.(730-732)Gat>Aat	p.D244N	TLK2_ENST00000346027.5_Missense_Mutation_p.D244N|TLK2_ENST00000343388.7_Missense_Mutation_p.D212N|TLK2_ENST00000582809.1_Missense_Mutation_p.D95N|TLK2_ENST00000542523.1_Missense_Mutation_p.D212N	NM_001284333.1	NP_001271262.1	Q86UE8	TLK2_HUMAN	tousled-like kinase 2	244					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|chromatin modification (GO:0016568)|chromosome segregation (GO:0007059)|intracellular signal transduction (GO:0035556)|negative regulation of autophagy (GO:0010507)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of chromatin assembly or disassembly (GO:0001672)	intermediate filament (GO:0005882)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(4)|large_intestine(6)|liver(2)|lung(10)|prostate(1)|stomach(1)|urinary_tract(1)	39						GGCCAACTGTGATTTGAGACG	0.328																																					p.D244N		Atlas-SNP	.											.	TLK2	223	.	0			c.G730A						.						42	43	43					17																	60637386		2203	4297	6500	SO:0001583	missense	11011	exon10			AACTGTGATTTGA	AB004884	CCDS11633.1, CCDS45753.1, CCDS62283.1	17q23	2008-07-18							11842	protein-coding gene	gene with protein product		608439				9427565, 10523312	Standard	NM_006852		Approved	PKU-ALPHA, MGC44450	uc002izz.4	Q86UE8		ENST00000326270.9:c.730G>A	chr17.hg19:g.60637386G>A	ENSP00000316512:p.Asp244Asn	442.0	0.0		450.0	117.0	NM_006852	D3DU07|Q9UKI7|Q9Y4F7	Missense_Mutation	SNP	ENST00000326270.9	hg19		.	.	.	.	.	.	.	.	.	.	G	16.56	3.158107	0.57368	.	.	ENSG00000146872	ENST00000346027;ENST00000343388;ENST00000326270;ENST00000542523	T;T;T;T	0.50813	0.73;0.73;0.73;0.73	4.69	4.69	0.59074	.	0.000000	0.85682	D	0.000000	T	0.67599	0.2910	M	0.65975	2.015	0.80722	D	1	D;D;D;D	0.89917	1.0;0.984;0.967;0.998	D;P;P;D	0.91635	0.999;0.879;0.879;0.954	T	0.71265	-0.4644	10	0.87932	D	0	.	17.1608	0.86803	0.0:0.0:1.0:0.0	.	244;212;244;244	Q86UE8;Q86UE8-3;Q86UE8-2;D3DU05	TLK2_HUMAN;.;.;.	N	244;212;244;212	ENSP00000275780:D244N;ENSP00000340800:D212N;ENSP00000316512:D244N;ENSP00000442311:D212N	ENSP00000316512:D244N	D	+	1	0	TLK2	57991118	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.504000	0.97986	2.593000	0.87608	0.655000	0.94253	GAT	.	.		0.328	TLK2-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000445140.1	NM_006852		A	60637386	G	A	60637386	3	1	313	1	0	0	0	0	1	0	0	0	15959	1290	45	3	764	3	TLK2	17	60637386	Missense_Mutation	SNP	G	TCGA-KR-A7K0-01A-12D-A33Q-10	53000978	60637386	20557824	85	44461										
CSHL1	1444	hgsc.bcm.edu	37	chr17	61987600	61987600	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	tccgaggtgtcatacaccagGttgttggtgaaggtactcct	12	9	1	1			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr17:61987600G>T	ENST00000309894.5	-	4	392	c.393C>A	c.(391-393)aaC>aaA	p.N131K	CSHL1_ENST00000558099.1_5'UTR|CSHL1_ENST00000259003.10_Missense_Mutation_p.N69K|CSHL1_ENST00000561003.1_Missense_Mutation_p.N48K|CSHL1_ENST00000346606.6_Missense_Mutation_p.N37K|CSHL1_ENST00000392824.4_3'UTR|CSHL1_ENST00000438387.2_Missense_Mutation_p.N48K|CSHL1_ENST00000450719.3_Missense_Mutation_p.N37K	NM_022579.1	NP_072101.1	Q14406	CSHL_HUMAN	chorionic somatomammotropin hormone-like 1	131						extracellular region (GO:0005576)	hormone activity (GO:0005179)|metal ion binding (GO:0046872)			endometrium(3)|lung(6)	9						CATACACCAGGTTGTTGGTGA	0.582																																					p.N131K		Atlas-SNP	.											.	CSHL1	42	.	0			c.C393A						.						81	70	73					17																	61987600		2203	4300	6503	SO:0001583	missense	1444	exon4			CACCAGGTTGTTG	BC029365	CCDS11652.1, CCDS42370.1, CCDS45759.1	17q22-q24	2012-10-02							2442	protein-coding gene	gene with protein product	"chorionic somatomammotropin CS-5"	603515		CSHP1		8083227	Standard	NM_001318		Approved	hCS-L, CSL, CS-5, MGC149868	uc002jda.1	Q14406		ENST00000309894.5:c.393C>A	chr17.hg19:g.61987600G>T	ENSP00000309524:p.Asn131Lys	137.0	0.0		141.0	19.0	NM_022579	D3DU26|D3DU27|Q0VDB2	Missense_Mutation	SNP	ENST00000309894.5	hg19	CCDS11652.1	.	.	.	.	.	.	.	.	.	.	g	6.762	0.509428	0.12883	.	.	ENSG00000204414	ENST00000309894;ENST00000438387;ENST00000259003;ENST00000346606;ENST00000450719	D;D;D	0.89270	-2.49;-2.49;-2.49	3.07	3.07	0.35406	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.521808	0.22290	N	0.062013	T	0.81460	0.4827	L	0.38175	1.15	0.80722	D	1	B;B;B;B	0.06786	0.0;0.0;0.001;0.0	B;B;B;B	0.15870	0.001;0.003;0.014;0.008	T	0.78507	-0.2177	10	0.72032	D	0.01	.	6.1657	0.20388	0.1431:0.0:0.8569:0.0	.	37;48;131;108	Q14406-4;Q14406-3;Q14406;Q14406-2	.;.;CSHL_HUMAN;.	K	131;48;126;37;126	ENSP00000309524:N131K;ENSP00000402632:N48K;ENSP00000316360:N37K	ENSP00000259003:N126K	N	-	3	2	GH1	59341332	1.000000	0.71417	0.930000	0.37139	0.003000	0.03518	2.131000	0.42074	1.730000	0.51580	0.305000	0.20034	AAC	.	.		0.582	CSHL1-009	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444557.1	NM_022579		T	61987600	G	T	61987600	3	4	313	1	0	0	0	0	1	0	0	0	3944	1252	44	3	283	3	CSHL1	17	61987600	Missense_Mutation	SNP	G	TCGA-KR-A7K0-01A-12D-A33Q-10	1350214	61987600	19207610	86	44462										
HELZ	9931	hgsc.bcm.edu	37	chr17	65116628	65116628	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	aaggaataggagatcctcgtCcatgtgtctgtaataggttc	11	7	1	1			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr17:65116628C>A	ENST00000358691.5	-	27	3897	c.3731G>T	c.(3730-3732)gGa>gTa	p.G1244V	HELZ_ENST00000580168.1_Missense_Mutation_p.G1245V	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	1244						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					AGATCCTCGTCCATGTGTCTG	0.463																																					p.G1244V		Atlas-SNP	.											.	HELZ	160	.	0			c.G3731T						.						247	221	229					17																	65116628		1976	4174	6150	SO:0001583	missense	9931	exon27			CCTCGTCCATGTG	D29677	CCDS42374.1	17q24.2	2013-01-18			ENSG00000198265	ENSG00000198265		"Zinc fingers, CCCH-type domain containing"	16878	protein-coding gene	gene with protein product	"down-regulated in human cancers"	606699				10471385, 12691822	Standard	NM_014877		Approved	KIAA0054, HUMORF5, DHRC	uc002jfx.4	P42694	OTTHUMG00000179555	ENST00000358691.5:c.3731G>T	chr17.hg19:g.65116628C>A	ENSP00000351524:p.Gly1244Val	147.0	0.0		197.0	45.0	NM_014877	I6L9H4	Missense_Mutation	SNP	ENST00000358691.5	hg19	CCDS42374.1	.	.	.	.	.	.	.	.	.	.	C	13.05	2.120896	0.37436	.	.	ENSG00000198265	ENST00000358691	D	0.83914	-1.78	5.78	5.78	0.91487	.	0.140104	0.64402	D	0.000004	D	0.86543	0.5958	L	0.29908	0.895	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.63597	0.916;0.916	D	0.87651	0.2528	10	0.87932	D	0	-17.6146	20.0203	0.97492	0.0:1.0:0.0:0.0	.	1245;1244	B7ZLW2;P42694	.;HELZ_HUMAN	V	1244	ENSP00000351524:G1244V	ENSP00000351524:G1244V	G	-	2	0	HELZ	62547090	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	4.267000	0.58877	2.730000	0.93505	0.655000	0.94253	GGA	.	.		0.463	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		A	65116628	C	A	65116628	3	1	313	1	0	0	0	0	1	0	0	0	7058	855	30	3	2125	3	HELZ	17	65116628	Missense_Mutation	SNP	C	TCGA-KR-A7K0-01A-12D-A33Q-10	3129028	65116628	16078582	87	44463										
ST6GALNAC1	55808	hgsc.bcm.edu	37	chr17	74625607	74625607	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	tcctgctcctccggcggtgcCtggttggcctcctttcctct	10	17	1	0			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr17:74625607C>A	ENST00000156626.7	-	2	517	c.318G>T	c.(316-318)caG>caT	p.Q106H	ST6GALNAC1_ENST00000590878.1_5'UTR	NM_018414.3	NP_060884.1	Q9NSC7	SIA7A_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 1	106					oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity (GO:0001665)|sialyltransferase activity (GO:0008373)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(11)|prostate(1)|upper_aerodigestive_tract(1)	22						CCGGCGGTGCCTGGTTGGCCT	0.577																																					p.Q106H		Atlas-SNP	.											.	ST6GALNAC1	42	.	0			c.G318T						.						133	121	125					17																	74625607		2203	4300	6503	SO:0001583	missense	55808	exon2			CGGTGCCTGGTTG	Y11339	CCDS11748.1	17q25.3	2013-03-01	2005-02-07	2005-02-07	ENSG00000070526	ENSG00000070526		"Sialyltransferases"	23614	protein-coding gene	gene with protein product		610138	"sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) A"	SIAT7A			Standard	NM_001289107		Approved	ST6GalNAcI	uc002jsh.3	Q9NSC7	OTTHUMG00000180369	ENST00000156626.7:c.318G>T	chr17.hg19:g.74625607C>A	ENSP00000156626:p.Gln106His	167.0	0.0		170.0	47.0	NM_018414	Q6UW90|Q9NSC6	Missense_Mutation	SNP	ENST00000156626.7	hg19	CCDS11748.1	.	.	.	.	.	.	.	.	.	.	C	9.919	1.211733	0.22289	.	.	ENSG00000070526	ENST00000156626;ENST00000359088	T;T	0.25085	1.86;1.82	4.04	1.98	0.26296	.	3.353760	0.00792	N	0.001352	T	0.18964	0.0455	N	0.22421	0.69	0.09310	N	1	P	0.36944	0.574	B	0.31751	0.135	T	0.24693	-1.0153	10	0.59425	D	0.04	-0.0411	7.1483	0.25595	0.0:0.7762:0.0:0.2238	.	106	Q9NSC7	SIA7A_HUMAN	H	106	ENSP00000156626:Q106H;ENSP00000351991:Q106H	ENSP00000156626:Q106H	Q	-	3	2	ST6GALNAC1	72137202	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	0.736000	0.26130	0.421000	0.25980	0.491000	0.48974	CAG	.	.		0.577	ST6GALNAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450974.1	NM_018414		A	74625607	C	A	74625607	3	1	313	1	0	0	0	0	1	0	0	0	15238	680	24	3	1516	3	ST6GALNAC1	17	74625607	Missense_Mutation	SNP	C	TCGA-KR-A7K0-01A-12D-A33Q-10	9508979	74625607	6569603	88	44464										
MYOM1	8736	hgsc.bcm.edu	37	chr18	3067314	3067314	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	aaggcggccatcctcgcctcCtcctctgggatgaacacgct	10	16	1	1			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr18:3067314C>T	ENST00000356443.4	-	38	5337	c.5004G>A	c.(5002-5004)gaG>gaA	p.E1668E	MYOM1_ENST00000261606.7_Silent_p.E1572E|MYOM1_ENST00000400569.3_Silent_p.E1668E	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	1668					muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						TCCTCGCCTCCTCCTCTGGGA	0.612																																					p.E1668E		Atlas-SNP	.											.	MYOM1	192	.	0			c.G5004A						.						32	38	36					18																	3067314		2200	4300	6500	SO:0001819	synonymous_variant	8736	exon38			CGCCTCCTCCTCT	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7613	protein-coding gene	gene with protein product	"skelemin"	603508	"myomesin 1 (skelemin) (185kD)", "myomesin 1 (skelemin) 185kDa", "myomesin 1, 185kDa"			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.5004G>A	chr18.hg19:g.3067314C>T		106.0	0.0		110.0	25.0	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Silent	SNP	ENST00000356443.4	hg19	CCDS45824.1																																																																																			.	.		0.612	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803		T	3067314	C	T	3067314	2	4	313	1	0	0	0	0	0	0	0	1	10100	680	24	3		3	MYOM1	18	3067314	Silent	SNP	C	TCGA-KR-A7K0-01A-12D-A33Q-10		3067314	75009934	89	44465										
ATCAY	85300	hgsc.bcm.edu	37	chr19	3908298	3908298	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	aaggcctcaacgccatcatcGtcttcgcagcctgcttcctt	7	16	3	0			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr19:3908298G>A	ENST00000450849.2	+	6	1044	c.577G>A	c.(577-579)Gtc>Atc	p.V193I	ATCAY_ENST00000398448.3_Missense_Mutation_p.V199I|ATCAY_ENST00000600960.1_Missense_Mutation_p.V193I|ATCAY_ENST00000301260.6_Missense_Mutation_p.V193I	NM_033064.4	NP_149053.1	Q86WG3	ATCAY_HUMAN	ataxia, cerebellar, Cayman type	193	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.|Mediates interaction with GLS.				apoptotic process (GO:0006915)|mitochondrion distribution (GO:0048311)|negative regulation of glutamate metabolic process (GO:2000212)|neuron projection development (GO:0031175)|regulation of protein localization (GO:0032880)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrial membrane (GO:0031966)|neuron projection (GO:0043005)|synapse (GO:0045202)	kinesin binding (GO:0019894)			breast(1)|endometrium(2)|kidney(2)|lung(2)	7		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00485)|STAD - Stomach adenocarcinoma(1328;0.183)		CGCCATCATCGTCTTCGCAGC	0.642																																					p.V193I		Atlas-SNP	.											.	ATCAY	84	.	0			c.G577A						.						36	44	41					19																	3908298		2143	4248	6391	SO:0001583	missense	85300	exon6			ATCATCGTCTTCG		CCDS45923.1	19p13.3	2014-06-24	2008-07-18		ENSG00000167654	ENSG00000167654			779	protein-coding gene	gene with protein product	"Cayman ataxia", "caytaxin"	608179				8845847, 14556008	Standard	NM_033064		Approved		uc002lyy.4	Q86WG3	OTTHUMG00000181836	ENST00000450849.2:c.577G>A	chr19.hg19:g.3908298G>A	ENSP00000390941:p.Val193Ile	209.0	0.0		201.0	59.0	NM_033064	Q8NAQ2|Q8TAQ3|Q96HC6|Q96JF5	Missense_Mutation	SNP	ENST00000450849.2	hg19	CCDS45923.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.869593	0.91587	.	.	ENSG00000167654	ENST00000450849;ENST00000301260;ENST00000357694;ENST00000398448;ENST00000539301	T;T;T	0.63913	-0.07;-0.07;-0.07	5.14	5.14	0.70334	Cellular retinaldehyde-binding/triple function, C-terminal (2);	0.192296	0.44483	D	0.000448	T	0.79885	0.4523	M	0.83953	2.67	0.48762	D	0.9997	D;D	0.71674	0.998;0.99	D;D	0.65140	0.932;0.926	T	0.81947	-0.0700	10	0.51188	T	0.08	-52.2715	17.7669	0.88481	0.0:0.0:1.0:0.0	.	199;193	B4DS11;Q86WG3	.;ATCAY_HUMAN	I	193;193;193;199;171	ENSP00000390941:V193I;ENSP00000301260:V193I;ENSP00000381466:V199I	ENSP00000301260:V193I	V	+	1	0	ATCAY	3859298	1.000000	0.71417	0.998000	0.56505	0.821000	0.46438	9.164000	0.94755	2.438000	0.82558	0.644000	0.83932	GTC	.	.		0.642	ATCAY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457872.2			A	3908298	G	A	3908298	3	1	313	1	0	0	0	0	1	0	0	0	1077	1145	40	1	595	1	ATCAY	19	3908298	Missense_Mutation	SNP	G	TCGA-KR-A7K0-01A-12D-A33Q-10		3908298	55220685	90	44466										
MUC16	94025	hgsc.bcm.edu	37	chr19	9074794	9074794	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	tgtactgctcaaattgggagGtaaacttgtgccaggttcca	11	8	1	0			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr19:9074794G>A	ENST00000397910.4	-	3	12855	c.12652C>T	c.(12652-12654)Cct>Tct	p.P4218S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4220	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AAATTGGGAGGTAAACTTGTG	0.493																																					p.P4218S		Atlas-SNP	.											.	MUC16	4315	.	0			c.C12652T						.						78	74	75					19																	9074794		1942	4163	6105	SO:0001583	missense	94025	exon3			TGGGAGGTAAACT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.12652C>T	chr19.hg19:g.9074794G>A	ENSP00000381008:p.Pro4218Ser	141.0	0.0		128.0	31.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	2.003	-0.428953	0.04701	.	.	ENSG00000181143	ENST00000397910	T	0.18338	2.22	1.31	0.243	0.15503	.	.	.	.	.	T	0.11623	0.0283	L	0.36672	1.1	.	.	.	B	0.12013	0.005	B	0.09377	0.004	T	0.22173	-1.0224	8	0.87932	D	0	.	3.4538	0.07507	0.272:0.0:0.728:0.0	.	4218	B5ME49	.	S	4218	ENSP00000381008:P4218S	ENSP00000381008:P4218S	P	-	1	0	MUC16	8935794	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.814000	0.04486	0.118000	0.18165	0.313000	0.20887	CCT	.	.		0.493	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9074794	G	A	9074794	3	1	313	1	0	0	0	0	1	0	0	0	9982	1261	44	3	31199	3	MUC16	19	9074794	Missense_Mutation	SNP	G	TCGA-KR-A7K0-01A-12D-A33Q-10	5166496	9074794	50054189	91	44467										
LPHN1	22859	hgsc.bcm.edu	37	chr19	14271099	14271099	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	cgatgttggccgcgttctccCcactcttgatctgcatgagg	11	13	3	2			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr19:14271099C>T	ENST00000340736.6	-	9	1937	c.1640G>A	c.(1639-1641)gGg>gAg	p.G547E	LPHN1_ENST00000591528.1_5'Flank|LPHN1_ENST00000361434.3_Missense_Mutation_p.G542E|CTB-55O6.12_ENST00000588387.1_RNA|CTB-55O6.12_ENST00000592086.1_RNA	NM_001008701.2	NP_001008701.1	O94910	LPHN1_HUMAN	latrophilin 1	547					calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|heterophilic cell-cell adhesion (GO:0007157)|neuropeptide signaling pathway (GO:0007218)|positive regulation of synapse maturation (GO:0090129)	axon (GO:0030424)|cell junction (GO:0030054)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)			central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						CGCGTTCTCCCCACTCTTGAT	0.667																																					p.G547E		Atlas-SNP	.											.	LPHN1	107	.	0			c.G1640A						.						37	48	44					19																	14271099		2202	4300	6502	SO:0001583	missense	22859	exon9			TTCTCCCCACTCT	AB020628	CCDS12307.1, CCDS32928.1	19p13.2	2014-08-08				ENSG00000072071		"-", "GPCR / Class B : Orphans"	20973	protein-coding gene	gene with protein product						10994649	Standard	NM_014921		Approved	KIAA0821, CIRL1, LEC2	uc010xnn.2	O94910		ENST00000340736.6:c.1640G>A	chr19.hg19:g.14271099C>T	ENSP00000340688:p.Gly547Glu	80.0	0.0		64.0	22.0	NM_001008701	Q96IE7|Q9BU07|Q9HAR3	Missense_Mutation	SNP	ENST00000340736.6	hg19	CCDS32928.1	.	.	.	.	.	.	.	.	.	.	C	18.66	3.672480	0.67928	.	.	ENSG00000072071	ENST00000340736;ENST00000361434	T;T	0.12147	2.71;2.71	5.17	5.17	0.71159	Domain of unknown function DUF3497 (1);	0.000000	0.85682	D	0.000000	T	0.39911	0.1096	M	0.79475	2.455	0.80722	D	1	D;D	0.67145	0.989;0.996	D;D	0.76071	0.962;0.987	T	0.26916	-1.0089	10	0.87932	D	0	.	16.52	0.84311	0.0:1.0:0.0:0.0	.	542;547	O94910-2;O94910	.;LPHN1_HUMAN	E	547;542	ENSP00000340688:G547E;ENSP00000355328:G542E	ENSP00000340688:G547E	G	-	2	0	LPHN1	14132099	1.000000	0.71417	0.948000	0.38648	0.092000	0.18411	7.776000	0.85560	2.571000	0.86741	0.491000	0.48974	GGG	.	.		0.667	LPHN1-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459696.1	NM_014921		T	14271099	C	T	14271099	3	4	313	1	0	0	0	0	1	0	0	0	8924	623	22	3	2848	3	LPHN1	19	14271099	Missense_Mutation	SNP	C	TCGA-KR-A7K0-01A-12D-A33Q-10	5196305	14271099	44857884	92	44468										
NWD1	284434	hgsc.bcm.edu	37	chr19	16918475	16918475	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	gcagcgcaagctcctatttaCgggcctcgtgtcgggggtcg	15	12	0	0			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr19:16918475C>T	ENST00000552788.1	+	16	3815	c.3815C>T	c.(3814-3816)aCg>aTg	p.T1272M	NWD1_ENST00000339803.6_Missense_Mutation_p.T1137M|NWD1_ENST00000524140.2_Missense_Mutation_p.T1272M|NWD1_ENST00000523826.1_Missense_Mutation_p.T1066M|NWD1_ENST00000379808.3_Missense_Mutation_p.T1272M|NWD1_ENST00000549814.1_Missense_Mutation_p.T1230M			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	1272							ATP binding (GO:0005524)	p.T1272M(1)|p.T1137M(1)		NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						CTCCTATTTACGGGCCTCGTG	0.567																																					p.T1272M		Atlas-SNP	.											NWD1_ENST00000524140,colon,carcinoma,0,8	NWD1	303	.	2	Substitution - Missense(2)	endometrium(2)	c.C3815T						.						81	84	83					19																	16918475		2203	4300	6503	SO:0001583	missense	284434	exon18			TATTTACGGGCCT	BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"WD repeat domain containing"	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.3815C>T	chr19.hg19:g.16918475C>T	ENSP00000447224:p.Thr1272Met	100.0	0.0		142.0	34.0	NM_001007525	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	hg19		.	.	.	.	.	.	.	.	.	.	C	10.56	1.385067	0.25031	.	.	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803	T;T;T;T;T;T	0.74002	-0.45;-0.8;-0.45;1.9;1.3;1.9	5.27	5.27	0.74061	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.411545	0.25964	N	0.027180	T	0.78444	0.4284	L	0.43152	1.355	0.09310	N	1	D;D;D	0.76494	0.998;0.999;0.998	P;D;P	0.63703	0.732;0.917;0.828	T	0.70741	-0.4789	10	0.72032	D	0.01	-10.5953	9.9171	0.41442	0.0:0.906:0.0:0.094	.	1272;1272;1137	Q149M9;Q149M9-3;C9J2Y8	NWD1_HUMAN;.;.	M	1137;1272;1230;1272;1066;1272;1137	ENSP00000428579:T1272M;ENSP00000447548:T1230M;ENSP00000369136:T1272M;ENSP00000428955:T1066M;ENSP00000447224:T1272M;ENSP00000340159:T1137M	ENSP00000340159:T1137M	T	+	2	0	NWD1	16779475	0.047000	0.20315	0.014000	0.15608	0.005000	0.04900	2.135000	0.42112	2.457000	0.83068	0.655000	0.94253	ACG	.	.		0.567	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525		T	16918475	C	T	16918475	3	4	313	1	0	0	0	0	1	0	0	0	10790	536	19	1	3464	1	NWD1	19	16918475	Missense_Mutation	SNP	C	TCGA-KR-A7K0-01A-12D-A33Q-10	2647376	16918475	42210508	93	44469										
LRFN3	79414	hgsc.bcm.edu	37	chr19	36431219	36431219	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	ttgtctgcgagccgcccgtgGtgactcaccgctcaccacct	10	17	3	1			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr19:36431219G>A	ENST00000588831.1	+	3	1946	c.892G>A	c.(892-894)Gtg>Atg	p.V298M	LRFN3_ENST00000246529.3_Missense_Mutation_p.V298M			Q9BTN0	LRFN3_HUMAN	leucine rich repeat and fibronectin type III domain containing 3	298	Ig-like.				cell adhesion (GO:0007155)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				cervix(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(2)|upper_aerodigestive_tract(1)	12	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			GCCGCCCGTGGTGACTCACCG	0.731																																					p.V298M		Atlas-SNP	.											.	LRFN3	43	.	0			c.G892A						.						8	9	9					19																	36431219		2044	4014	6058	SO:0001583	missense	79414	exon2			CCCGTGGTGACTC	BC003578	CCDS12483.1	19q13.13	2013-02-11				ENSG00000126243		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	28370	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 1"	612809				12975309, 16495444, 16828986	Standard	NM_024509		Approved	MGC2656, SALM4, FIGLER1	uc002oco.3	Q9BTN0		ENST00000588831.1:c.892G>A	chr19.hg19:g.36431219G>A	ENSP00000466989:p.Val298Met	28.0	0.0		25.0	7.0	NM_024509	Q6UY10	Missense_Mutation	SNP	ENST00000588831.1	hg19	CCDS12483.1	.	.	.	.	.	.	.	.	.	.	G	16.46	3.129974	0.56721	.	.	ENSG00000126243	ENST00000246529	T	0.68765	-0.35	4.97	3.93	0.45458	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.33290	N	0.005076	T	0.64875	0.2638	N	0.21097	0.63	0.39690	D	0.971038	D	0.54207	0.965	D	0.64321	0.924	T	0.67669	-0.5611	10	0.66056	D	0.02	.	6.6904	0.23167	0.1979:0.0:0.8021:0.0	.	298	Q9BTN0	LRFN3_HUMAN	M	298	ENSP00000246529:V298M	ENSP00000246529:V298M	V	+	1	0	LRFN3	41123059	1.000000	0.71417	1.000000	0.80357	0.623000	0.37688	6.949000	0.75971	2.299000	0.77371	0.460000	0.39030	GTG	.	.		0.731	LRFN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457403.2	NM_024509		A	36431219	G	A	36431219	3	1	313	1	0	0	0	0	1	0	0	0	8948	1261	44	3	894	3	LRFN3	19	36431219	Missense_Mutation	SNP	G	TCGA-KR-A7K0-01A-12D-A33Q-10	19512744	36431219	22697764	94	44470										
ERCC2	2068	hgsc.bcm.edu	37	chr19	45856053	45856053	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	aggggacgccaaacatgatgAcggcccgcccgtagtggtgc	15	12	0	2			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr19:45856053A>C	ENST00000391945.4	-	20	1930	c.1853T>G	c.(1852-1854)gTc>gGc	p.V618G	ERCC2_ENST00000391944.3_Missense_Mutation_p.V540G	NM_000400.3	NP_000391.1	P18074	ERCC2_HUMAN	excision repair cross-complementation group 2	618	Mediates interaction with MMS19.				7-methylguanosine mRNA capping (GO:0006370)|aging (GO:0007568)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|central nervous system myelin formation (GO:0032289)|chromosome segregation (GO:0007059)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|embryonic cleavage (GO:0040016)|erythrocyte maturation (GO:0043249)|extracellular matrix organization (GO:0030198)|gene expression (GO:0010467)|hair cell differentiation (GO:0035315)|hair follicle maturation (GO:0048820)|hematopoietic stem cell differentiation (GO:0060218)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|spinal cord development (GO:0021510)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)|viral process (GO:0016032)	cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|MMXD complex (GO:0071817)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			large_intestine(4)|lung(2)|ovary(1)|pancreas(1)|stomach(1)	9		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		AAACATGATGACGGCCCGCCC	0.617			"Mis, N, F, S"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.V618G		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (D)	19	19q13.2-q13.3	2068	"excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D)"		E	.	ERCC2	78	.	0			c.T1853G						.						67	61	63					19																	45856053		2203	4300	6503	SO:0001583	missense	2068	exon20	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	ATGATGACGGCCC		CCDS33049.1, CCDS46112.1	19q13.3	2014-09-17	2014-03-07		ENSG00000104884	ENSG00000104884	3.6.4.12	"General transcription factor IIH complex subunits"	3434	protein-coding gene	gene with protein product	"excision repair cross-complementing rodent repair deficiency, complementation group 2 protein", "TFIIH basal transcription factor complex helicase XPB subunit"	126340	"xeroderma pigmentosum complementary group D", "excision repair cross-complementing rodent repair deficiency, complementation group 2"	XPD		8413672, 2184031	Standard	NM_000400		Approved	MAG, EM9, MGC102762, MGC126218, MGC126219, TFIIH	uc002pbj.2	P18074	OTTHUMG00000048190	ENST00000391945.4:c.1853T>G	chr19.hg19:g.45856053A>C	ENSP00000375809:p.Val618Gly	80.0	0.0		67.0	18.0	NM_000400	Q2TB78|Q2YDY2|Q7KZU6|Q8N721	Missense_Mutation	SNP	ENST00000391945.4	hg19	CCDS33049.1	.	.	.	.	.	.	.	.	.	.	A	27.1	4.801712	0.90538	.	.	ENSG00000104884	ENST00000391941;ENST00000391942;ENST00000391945;ENST00000391944	D;D	0.83591	-1.74;-1.74	5.13	5.13	0.70059	Helicase, ATP-dependent, c2 type (1);	0.000000	0.85682	D	0.000000	D	0.95114	0.8417	H	0.99626	4.665	0.80722	D	1	D;D;D	0.76494	0.999;0.998;0.999	D;D;D	0.77557	0.99;0.986;0.988	D	0.96671	0.9496	10	0.87932	D	0	-64.0864	12.9281	0.58272	1.0:0.0:0.0:0.0	.	540;618;311	E7EVE9;P18074;Q6ZNQ5	.;ERCC2_HUMAN;.	G	568;594;618;540	ENSP00000375809:V618G;ENSP00000375808:V540G	ENSP00000375805:V568G	V	-	2	0	ERCC2	50547893	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.988000	0.63863	2.154000	0.67381	0.459000	0.35465	GTC	.	.		0.617	ERCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109626.2	NM_000400		C	45856053	A	C	45856053	3	2	313	1	0	0	0	0	1	0	0	0	5215	275	10	5	445	5	ERCC2	19	45856053	Missense_Mutation	SNP	A	TCGA-KR-A7K0-01A-12D-A33Q-10	9424834	45856053	13272930	95	44471										
PAX1	5075	hgsc.bcm.edu	37	chr20	21687274	21687274	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	cgagaccggctccattctgcCcggggccatcggggggagca	16	14	1	1			TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr20:21687274C>T	ENST00000398485.2	+	2	539	c.485C>T	c.(484-486)cCc>cTc	p.P162L	PAX1_ENST00000444366.2_Missense_Mutation_p.P138L|PAX1_ENST00000460221.1_Intron	NM_001257096.1|NM_006192.4	NP_001244025.1|NP_006183.2	P15863	PAX1_HUMAN	paired box 1	162	Paired. {ECO:0000255|PROSITE- ProRule:PRU00381}.				bone morphogenesis (GO:0060349)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cell proliferation (GO:0008283)|parathyroid gland development (GO:0060017)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sclerotome development (GO:0061056)|skeletal system development (GO:0001501)|somitogenesis (GO:0001756)|thymus development (GO:0048538)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(21)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	38						TCCATTCTGCCCGGGGCCATC	0.647																																					p.P162L		Atlas-SNP	.											.	PAX1	152	.	0			c.C485T						.						49	53	51					20																	21687274		2203	4299	6502	SO:0001583	missense	5075	exon2			TTCTGCCCGGGGC		CCDS13146.2, CCDS74709.1	20p11.22	2007-07-12	2007-07-12		ENSG00000125813	ENSG00000125813		"Paired boxes"	8615	protein-coding gene	gene with protein product		167411	"paired box gene 1"			1358810	Standard	NM_006192		Approved		uc002wsj.3	P15863	OTTHUMG00000032034	ENST00000398485.2:c.485C>T	chr20.hg19:g.21687274C>T	ENSP00000381499:p.Pro162Leu	42.0	0.0		52.0	20.0	NM_006192	B4E0D6|Q642X9|Q6NTC0|Q9Y558	Missense_Mutation	SNP	ENST00000398485.2	hg19	CCDS13146.2	.	.	.	.	.	.	.	.	.	.	C	16.08	3.021041	0.54576	.	.	ENSG00000125813	ENST00000398485;ENST00000444366	D;D	0.99709	-6.48;-6.48	5.39	3.43	0.39272	Paired box protein, N-terminal (4);Winged helix-turn-helix transcription repressor DNA-binding (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99732	0.9895	H	0.94925	3.6	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.956	D	0.98276	1.0506	10	0.87932	D	0	.	10.031	0.42101	0.1378:0.7901:0.0:0.0721	.	138;68;162	P15863-2;C9J775;P15863	.;.;PAX1_HUMAN	L	162;138	ENSP00000381499:P162L;ENSP00000410355:P138L	ENSP00000381499:P162L	P	+	2	0	PAX1	21635274	1.000000	0.71417	0.987000	0.45799	0.016000	0.09150	7.653000	0.83643	0.642000	0.30620	0.655000	0.94253	CCC	.	.		0.647	PAX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078282.3			T	21687274	C	T	21687274	3	4	313	1	0	0	0	0	1	0	0	0	11487	623	22	3	491	3	PAX1	20	21687274	Missense_Mutation	SNP	C	TCGA-KR-A7K0-01A-12D-A33Q-10		21687274	41338246	96	44472										
XPNPEP3	63929	hgsc.bcm.edu	37	chr22	41320402	41320416	+	In_Frame_Del	DEL	TACCTCGGGATGGAT	TACCTCGGGATGGAT	-													0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	gtcctcatcatgttggccacTacctcgggatggatgtccat							TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	TACCTCGGGATGGAT	TACCTCGGGATGGAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr22:41320402_41320416delTACCTCGGGATGGAT	ENST00000357137.4	+	9	1357_1371	c.1273_1287delTACCTCGGGATGGAT	c.(1273-1287)tacctcgggatggatdel	p.YLGMD425del	XPNPEP3_ENST00000544094.1_In_Frame_Del_p.YLGMD402del	NM_022098.3	NP_071381.1	Q9NQH7	XPP3_HUMAN	X-prolyl aminopeptidase (aminopeptidase P) 3, putative	425					glomerular filtration (GO:0003094)|protein processing (GO:0016485)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metallopeptidase activity (GO:0008237)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	17						TGTTGGCCACTACCTCGGGATGGATGTCCATGACA	0.488																																					p.424_429del	Ovarian(145;306 1841 7037 21878 30110)	Atlas-Indel,Pindel	.											.	XPNPEP3	46	.	0			c.1272_1286del						.																																			SO:0001651	inframe_deletion	63929	exon9			.		CCDS14007.1, CCDS74869.1	22q13.2	2010-07-20			ENSG00000196236	ENSG00000196236			28052	protein-coding gene	gene with protein product		613553				15708373, 20179356	Standard	NM_022098		Approved	APP3, NPHPL1	uc003azh.3	Q9NQH7	OTTHUMG00000151312	ENST00000357137.4:c.1273_1287delTACCTCGGGATGGAT	chr22.hg19:g.41320402_41320416delTACCTCGGGATGGAT	ENSP00000349658:p.Tyr425_Asp429del	131.0	0.0		96.0	20.0	NM_022098	B2R9G1|B7Z790|B7Z7B2|Q6I9V9|Q8NDA6|Q9BV27|Q9BVH0	In_Frame_Del	DEL	ENST00000357137.4	hg19	CCDS14007.1																																																																																			.	.		0.488	XPNPEP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322201.2	NM_022098		-	41320416	TACCTCGGGATGGAT	-	41320402	7	5	313	1	0	1	0	1	0	0	0	0	17459	1522	53	0	1307	0	XPNPEP3	22	41320402	In_Frame_Del	DEL	TACCTCGGGATGGAT	TCGA-KR-A7K0-01A-12D-A33Q-10		41320402	9984164	97	44473										
PLXNB2	23654	hgsc.bcm.edu	37	chr22	50728375	50728379	+	Frame_Shift_Del	DEL	GGTGG	GGTGG	-													0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	gccacgaactgctgtgtgttGgtggacaggtagccggcctt							TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	GGTGG	GGTGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr22:50728375_50728379delGGTGG	ENST00000449103.1	-	3	775_779	c.635_639delCCACC	c.(634-639)tccaccfs	p.ST212fs	PLXNB2_ENST00000359337.4_Frame_Shift_Del_p.ST212fs			O15031	PLXB2_HUMAN	plexin B2	212	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				brain development (GO:0007420)|neural tube closure (GO:0001843)|neuroblast proliferation (GO:0007405)|positive regulation of axonogenesis (GO:0050772)|regulation of cell shape (GO:0008360)|regulation of neuron migration (GO:2001222)|regulation of protein phosphorylation (GO:0001932)|regulation of Rho GTPase activity (GO:0032319)|semaphorin-plexin signaling pathway (GO:0071526)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	GTPase activator activity (GO:0005096)|semaphorin receptor activity (GO:0017154)			breast(2)|central_nervous_system(4)|cervix(2)|endometrium(11)|kidney(4)|large_intestine(3)|liver(1)|lung(20)|ovary(5)|prostate(6)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	66		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|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)		GCTGTGTGTTGGTGGACAGGTAGCC	0.624																																					p.212_214del		Atlas-INDEL	.											.	PLXNB2	172	.	0			c.636_640del						.																																			SO:0001589	frameshift_variant	23654	exon3			.		CCDS43035.1	22q13.33	2008-06-12			ENSG00000196576	ENSG00000196576		"Plexins"	9104	protein-coding gene	gene with protein product		604293				10520995, 12183458	Standard	NM_012401		Approved	MM1, KIAA0315, PLEXB2	uc003bkv.4	O15031	OTTHUMG00000150219	ENST00000449103.1:c.635_639delCCACC	chr22.hg19:g.50728375_50728379delGGTGG	ENSP00000409171:p.Ser212fs	106.0	0.0		69.0	16.0	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Frame_Shift_Del	DEL	ENST00000449103.1	hg19	CCDS43035.1																																																																																			.	.		0.624	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401		-	50728379	GGTGG	-	50728375	7	5	313	1	0	1	0	1	0	0	0	0	12133	1335	47	0	5017	0	PLXNB2	22	50728375	Frame_Shift_Del	DEL	GGTGG	TCGA-KR-A7K0-01A-12D-A33Q-10	9407973	50728375	576191	98	44474	232	2								
PLXNB2	23654	hgsc.bcm.edu	37	chr22	50728381	50728387	+	Frame_Shift_Del	DEL	CAGGTAG	CAGGTAG	-													0.0625	6	1	1.17310167310167	1.4468253968254	1.13033234126984	0.131221719457014	0.709357990687916	0	aactgctgtgtgttggtggaCaggtagccggccttgtaggt							TCGA-KR-A7K0-01A-12D-A33Q-10	TCGA-KR-A7K0-10A-01D-A33Q-10	CAGGTAG	CAGGTAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	683468d5-b681-43be-9025-724ad958d4f7	7266f903-8881-4952-9391-525e33241f67	g.chr22:50728381_50728387delCAGGTAG	ENST00000449103.1	-	3	767_773	c.627_633delCTACCTG	c.(625-633)ggctacctgfs	p.GYL209fs	PLXNB2_ENST00000359337.4_Frame_Shift_Del_p.GYL209fs			O15031	PLXB2_HUMAN	plexin B2	209	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				brain development (GO:0007420)|neural tube closure (GO:0001843)|neuroblast proliferation (GO:0007405)|positive regulation of axonogenesis (GO:0050772)|regulation of cell shape (GO:0008360)|regulation of neuron migration (GO:2001222)|regulation of protein phosphorylation (GO:0001932)|regulation of Rho GTPase activity (GO:0032319)|semaphorin-plexin signaling pathway (GO:0071526)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	GTPase activator activity (GO:0005096)|semaphorin receptor activity (GO:0017154)			breast(2)|central_nervous_system(4)|cervix(2)|endometrium(11)|kidney(4)|large_intestine(3)|liver(1)|lung(20)|ovary(5)|prostate(6)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	66		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|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)		TGTTGGTGGACAGGTAGCCGGCCTTGT	0.623																																					p.210_212del		Atlas-INDEL	.											.	PLXNB2	172	.	0			c.628_634del						.																																			SO:0001589	frameshift_variant	23654	exon3			.		CCDS43035.1	22q13.33	2008-06-12			ENSG00000196576	ENSG00000196576		"Plexins"	9104	protein-coding gene	gene with protein product		604293				10520995, 12183458	Standard	NM_012401		Approved	MM1, KIAA0315, PLEXB2	uc003bkv.4	O15031	OTTHUMG00000150219	ENST00000449103.1:c.627_633delCTACCTG	chr22.hg19:g.50728381_50728387delCAGGTAG	ENSP00000409171:p.Gly209fs	108.0	0.0		64.0	15.0	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Frame_Shift_Del	DEL	ENST00000449103.1	hg19	CCDS43035.1																																																																																			.	.		0.623	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401		-	50728387	CAGGTAG	-	50728381	7	5	313	1	0	1	0	1	0	0	0	0	12133	465	17	0	5023	0	PLXNB2	22	50728381	Frame_Shift_Del	DEL	CAGGTAG	TCGA-KR-A7K0-01A-12D-A33Q-10	6	50728381	576185	99	44475	232	2								
PLOD1	5351	hgsc.bcm.edu	37	chr1	12023642	12023642	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	ctacttcagcgtggatgctgAcgtggccctgaccgagccca	12	14	1	2			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr1:12023642A>C	ENST00000196061.4	+	11	1178	c.1151A>C	c.(1150-1152)gAc>gCc	p.D384A	PLOD1_ENST00000376369.3_Missense_Mutation_p.D431A	NM_000302.3	NP_000293.2	Q02809	PLOD1_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1	384					cellular protein modification process (GO:0006464)|epidermis development (GO:0008544)|extracellular matrix organization (GO:0030198)|hydroxylysine biosynthetic process (GO:0046947)|oxidation-reduction process (GO:0055114)|response to hypoxia (GO:0001666)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-lysine 5-dioxygenase activity (GO:0008475)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	29	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.06e-06)|COAD - Colon adenocarcinoma(227;0.000273)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000809)|KIRC - Kidney renal clear cell carcinoma(229;0.00267)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)	Succinic acid(DB00139)|Vitamin C(DB00126)	GTGGATGCTGACGTGGCCCTG	0.627																																					p.D384A		Atlas-SNP	.											.	PLOD1	75	.	0			c.A1151C						.						57	44	48					1																	12023642		2202	4299	6501	SO:0001583	missense	5351	exon11			ATGCTGACGTGGC	BC016657	CCDS142.1	1p36.22	2011-08-25	2011-08-24	2004-12-14	ENSG00000083444	ENSG00000083444	1.14.11.4		9081	protein-coding gene	gene with protein product	"lysyl hydroxlase 1"	153454	"procollagen-lysine 1, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase, Ehlers-Danlos syndrome type VI)"	LLH, PLOD		1577494	Standard	NM_000302		Approved	LH1	uc001atm.3	Q02809	OTTHUMG00000002393	ENST00000196061.4:c.1151A>C	chr1.hg19:g.12023642A>C	ENSP00000196061:p.Asp384Ala	61.0	0.0		49.0	12.0	NM_000302	B4DR87|Q96AV9|Q9H132	Missense_Mutation	SNP	ENST00000196061.4	hg19	CCDS142.1	.	.	.	.	.	.	.	.	.	.	A	18.46	3.629557	0.67015	.	.	ENSG00000083444	ENST00000376369;ENST00000196061	D;D	0.98120	-4.73;-4.73	5.01	5.01	0.66863	.	0.319876	0.33534	N	0.004811	D	0.98009	0.9344	M	0.77103	2.36	0.80722	D	1	D;B	0.62365	0.991;0.22	P;B	0.56127	0.792;0.115	D	0.98290	1.0513	10	0.59425	D	0.04	.	13.616	0.62108	1.0:0.0:0.0:0.0	.	431;384	B4DR87;Q02809	.;PLOD1_HUMAN	A	431;384	ENSP00000365548:D431A;ENSP00000196061:D384A	ENSP00000196061:D384A	D	+	2	0	PLOD1	11946229	1.000000	0.71417	0.945000	0.38365	0.862000	0.49288	9.205000	0.95048	1.879000	0.54435	0.529000	0.55759	GAC	.	.		0.627	PLOD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000006865.1	NM_000302		C	12023642	A	C	12023642	3	2	314	1	0	0	0	0	1	0	0	0	12110	275	10	5	1193	5	PLOD1	1	12023642	Missense_Mutation	SNP	A	TCGA-KR-A7K2-01A-12D-A33Q-10		12023642	237226979	1	44476										
NCDN	23154	hgsc.bcm.edu	37	chr1	36024726	36024726	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	agttgggcaaggcgagcatcAtggcctcggattgcgagcca	15	10	1	0			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr1:36024726A>T	ENST00000373243.2	+	2	435	c.52A>T	c.(52-54)Atg>Ttg	p.M18L	NCDN_ENST00000373253.3_Start_Codon_SNP_p.M1L|KIAA0319L_ENST00000325722.3_5'Flank|NCDN_ENST00000459931.1_3'UTR|NCDN_ENST00000356090.4_Missense_Mutation_p.M18L	NM_014284.2	NP_055099.1	Q9UBB6	NCDN_HUMAN	neurochondrin	18					bone resorption (GO:0045453)|neuron projection development (GO:0031175)|regulation of neuronal synaptic plasticity (GO:0048168)	cytosol (GO:0005829)|dendrite (GO:0030425)|membrane (GO:0016020)|neuronal cell body (GO:0043025)				breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|pancreas(1)|skin(2)	16		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				GGCGAGCATCATGGCCTCGGA	0.637																																					p.M18L		Atlas-SNP	.											.	NCDN	79	.	0			c.A52T						.						52	50	51					1																	36024726		2203	4300	6503	SO:0001583	missense	23154	exon2			AGCATCATGGCCT	AB011179	CCDS392.1, CCDS30672.1	1p34.3	2008-02-05			ENSG00000020129	ENSG00000020129			17597	protein-coding gene	gene with protein product		608458				15007648	Standard	NM_014284		Approved	NCDN-1, NCDN-2	uc001bza.3	Q9UBB6	OTTHUMG00000059204	ENST00000373243.2:c.52A>T	chr1.hg19:g.36024726A>T	ENSP00000362340:p.Met18Leu	166.0	0.0		138.0	68.0	NM_014284	D3DPR9|Q9UBY2|Q9Y4A6|Q9Y4D9	Missense_Mutation	SNP	ENST00000373243.2	hg19	CCDS392.1	.	.	.	.	.	.	.	.	.	.	A	14.82	2.648594	0.47258	.	.	ENSG00000020129	ENST00000373253;ENST00000356090;ENST00000373243;ENST00000437806	.	.	.	4.89	4.89	0.63831	.	0.400531	0.25275	N	0.031846	T	0.35624	0.0938	N	0.19112	0.55	0.34181	D	0.670955	B	0.29136	0.234	B	0.14578	0.011	T	0.49093	-0.8975	9	0.36615	T	0.2	.	13.3409	0.60545	1.0:0.0:0.0:0.0	.	18	Q9UBB6	NCDN_HUMAN	L	1;18;18;1	.	ENSP00000348394:M18L	M	+	1	0	NCDN	35797313	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.210000	0.58500	1.809000	0.52856	0.379000	0.24179	ATG	.	.		0.637	NCDN-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131298.1	NM_014284		T	36024726	A	T	36024726	3	4	314	1	0	0	0	0	1	0	0	0	10223	217	8	4	58	4	NCDN	1	36024726	Missense_Mutation	SNP	A	TCGA-KR-A7K2-01A-12D-A33Q-10	24001084	36024726	213225895	2	44477										
GBP5	115362	hgsc.bcm.edu	37	chr1	89726418	89726419	+	Frame_Shift_Del	DEL	AC	AC	-													0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	cacatggatcatcgttattaAcagtcctctgggcgtgctgg							TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr1:89726418_89726419delAC	ENST00000370459.3	-	11	1856_1857	c.1729_1730delGT	c.(1729-1731)gttfs	p.V577fs	GBP5_ENST00000471171.1_5'UTR|GBP5_ENST00000343435.5_Frame_Shift_Del_p.V577fs|RP4-620F22.2_ENST00000437128.1_RNA			Q96PP8	GBP5_HUMAN	guanylate binding protein 5	577	Required for tetramerization. {ECO:0000250}.					cytoplasm (GO:0005737)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			breast(1)|endometrium(1)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)	24				all cancers(265;0.00784)|Epithelial(280;0.0286)		ATCGTTATTAACAGTCCTCTGG	0.406																																					p.577_577del		Atlas-Indel,Pindel	.											.	GBP5	65	.	0			c.1730_1731del						.																																			SO:0001589	frameshift_variant	115362	exon12			.	AF430642	CCDS722.1	1p22.2	2008-02-05			ENSG00000154451	ENSG00000154451			19895	protein-coding gene	gene with protein product		611467					Standard	NM_052942		Approved		uc001dnd.3	Q96PP8	OTTHUMG00000010006	ENST00000370459.3:c.1729_1730delGT	chr1.hg19:g.89726418_89726419delAC	ENSP00000359488:p.Val577fs	51.0	0.0		50.0	15.0	NM_052942	B2RCE1|Q86TM5	Frame_Shift_Del	DEL	ENST00000370459.3	hg19	CCDS722.1																																																																																			.	.		0.406	GBP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027700.1	NM_052942		-	89726419	AC	-	89726418	7	5	314	1	0	1	0	1	0	0	0	0	6285	43	2	0	34	0	GBP5	1	89726418	Frame_Shift_Del	DEL	AC	TCGA-KR-A7K2-01A-12D-A33Q-10	53701692	89726418	159524203	3	44478										
CAPZA1	829	hgsc.bcm.edu	37	chr1	113212621	113212621	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	ttatctattgcagacagcaaTtagtgaaaactatcaaacaa	5	7	2	2			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr1:113212621T>G	ENST00000263168.3	+	10	1400	c.728T>G	c.(727-729)aTt>aGt	p.I243S	CAPZA1_ENST00000476936.1_3'UTR	NM_006135.2	NP_006126.1	P52907	CAZA1_HUMAN	capping protein (actin filament) muscle Z-line, alpha 1	243					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)	actin cytoskeleton (GO:0015629)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|F-actin capping protein complex (GO:0008290)|WASH complex (GO:0071203)	actin binding (GO:0003779)			breast(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(1)	9	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CAGACAGCAATTAGTGAAAAC	0.423																																					p.I243S		Atlas-SNP	.											.	CAPZA1	16	.	0			c.T728G						.						69	68	68					1																	113212621		2202	4300	6502	SO:0001583	missense	829	exon10			CAGCAATTAGTGA	U56637	CCDS30805.1	1p13.2	2014-05-09			ENSG00000116489	ENSG00000116489			1488	protein-coding gene	gene with protein product		601580				7665558, 9119363	Standard	NM_006135		Approved		uc001ecj.1	P52907	OTTHUMG00000011769	ENST00000263168.3:c.728T>G	chr1.hg19:g.113212621T>G	ENSP00000263168:p.Ile243Ser	142.0	0.0		125.0	62.0	NM_006135	Q53FQ6|Q6FHD5	Missense_Mutation	SNP	ENST00000263168.3	hg19	CCDS30805.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.761273	0.89932	.	.	ENSG00000116489	ENST00000263168	.	.	.	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.80929	0.4718	M	0.86178	2.8	0.80722	D	1	D	0.76494	0.999	D	0.97110	1.0	D	0.84490	0.0610	9	0.87932	D	0	-15.1678	15.8615	0.79026	0.0:0.0:0.0:1.0	.	243	P52907	CAZA1_HUMAN	S	243	.	ENSP00000263168:I243S	I	+	2	0	CAPZA1	113014144	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.979000	0.88103	2.285000	0.76669	0.528000	0.53228	ATT	.	.		0.423	CAPZA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032567.2	NM_006135		G	113212621	T	G	113212621	3	3	314	1	0	0	0	0	1	0	0	0	2642	1493	52	5	766	5	CAPZA1	1	113212621	Missense_Mutation	SNP	T	TCGA-KR-A7K2-01A-12D-A33Q-10	23486203	113212621	136038000	4	44479										
XPR1	9213	hgsc.bcm.edu	37	chr1	180794056	180794056	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	aacttaatccgagaagcaatTtgtctcatcaacatctcttt	4	10	3	1			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr1:180794056T>C	ENST00000367590.4	+	8	1129	c.931T>C	c.(931-933)Ttg>Ctg	p.L311L	AL590085.1_ENST00000579998.1_RNA|XPR1_ENST00000367589.3_Silent_p.L311L	NM_004736.3	NP_004727.2	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor 1	311					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|virus receptor activity (GO:0001618)			breast(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	35						GAGAAGCAATTTGTCTCATCA	0.378																																					p.L311L		Atlas-SNP	.											.	XPR1	76	.	0			c.T931C						.						129	119	122					1																	180794056		2203	4300	6503	SO:0001819	synonymous_variant	9213	exon8			AGCAATTTGTCTC	AF099082	CCDS1340.1, CCDS44284.1	1q25.1	2013-07-18	2010-04-23		ENSG00000143324	ENSG00000143324			12827	protein-coding gene	gene with protein product		605237	"xenotropic and polytropic retrovirus receptor"			9990033	Standard	NM_004736		Approved	SYG1, X3	uc001goi.3	Q9UBH6	OTTHUMG00000035116	ENST00000367590.4:c.931T>C	chr1.hg19:g.180794056T>C		53.0	0.0		111.0	16.0	NM_004736	O95719|Q7L8K9|Q8IW20|Q9NT19|Q9UFB9	Silent	SNP	ENST00000367590.4	hg19	CCDS1340.1																																																																																			.	.		0.378	XPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084996.2	NM_004736		C	180794056	T	C	180794056	2	2	314	1	0	0	0	0	0	0	0	1	17466	1838	64	2		2	XPR1	1	180794056	Silent	SNP	T	TCGA-KR-A7K2-01A-12D-A33Q-10	67581435	180794056	68456565	5	44480										
RYR2	6262	hgsc.bcm.edu	37	chr1	237670087	237670087	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	gaactctgggttatgaataaAattgagcttggctggcagta	12	5	1	2			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr1:237670087A>G	ENST00000366574.2	+	23	3008	c.2691A>G	c.(2689-2691)aaA>aaG	p.K897K	RYR2_ENST00000542537.1_Silent_p.K881K|RYR2_ENST00000360064.6_Silent_p.K895K	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	897	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TTATGAATAAAATTGAGCTTG	0.323																																					p.K897K		Atlas-SNP	.											.	RYR2	1273	.	0			c.A2691G						.						116	117	117					1																	237670087		1822	4080	5902	SO:0001819	synonymous_variant	6262	exon23			GAATAAAATTGAG	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.2691A>G	chr1.hg19:g.237670087A>G		40.0	0.0		86.0	25.0	NM_001035	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	hg19	CCDS55691.1																																																																																			.	.		0.323	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		G	237670087	A	G	237670087	2	3	314	1	0	0	0	0	0	0	0	1	13784	11	1	2		2	RYR2	1	237670087	Silent	SNP	A	TCGA-KR-A7K2-01A-12D-A33Q-10	56876031	237670087	11580534	6	44481										
TAF1B	9014	hgsc.bcm.edu	37	chr2	9994549	9994563	+	Splice_Site	DEL	CGGTAAGTCACAAGT	CGGTAAGTCACAAGT	-													0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	taccactggaaggaaacctaCggtaagtcacaagtctgaaa					rs35681700		TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	CGGTAAGTCACAAGT	CGGTAAGTCACAAGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr2:9994549_9994563delCGGTAAGTCACAAGT	ENST00000263663.5	+	5	586_587	c.398_399delCGGTAAGTCACAAGT	c.(397-399)acg>a	p.T133del	TAF1B_ENST00000396242.3_5'UTR|TAF1B_ENST00000402170.1_3'UTR	NM_005680.2	NP_005671	Q53T94	TAF1B_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa	133	N-terminal cyclin fold.				gene expression (GO:0010467)|RNA polymerase I transcriptional preinitiation complex assembly at the promoter for the nuclear large rRNA transcript (GO:0001189)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RNA polymerase I core factor complex (GO:0070860)	metal ion binding (GO:0046872)|RNA polymerase I CORE element sequence-specific DNA binding (GO:0001164)|RNA polymerase I CORE element sequence-specific DNA binding transcription factor recruiting transcription factor activity (GO:0001187)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TBP-class protein binding (GO:0017025)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	14	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					AGGAAACCTACGGTAAGTCACAAGTCTGAAAAGTT	0.391																																					p.133_133del		Atlas-Indel,Pindel	.											.	TAF1B	62	.	0			c.397_399del						.																																			SO:0001630	splice_region_variant	9014	exon5			.	L39061	CCDS33143.1	2p25	2008-06-02	2002-08-29		ENSG00000115750	ENSG00000115750			11533	protein-coding gene	gene with protein product		604904	"TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kD"			7801123	Standard	NM_005680		Approved	TAFI63, SL1, RAF1B, RAFI63	uc002qzz.3	Q53T94	OTTHUMG00000151673	ENST00000263663.5:c.399+1CGGTAAGTCACAAGT>-	chr2.hg19:g.9994549_9994563delCGGTAAGTCACAAGT		94.0	0.0		79.0	11.0	NM_005680	B4DI42|F8WD72|Q15574|Q8WVC3	In_Frame_Del	DEL	ENST00000263663.5	hg19	CCDS33143.1																																																																																			.	.		0.391	TAF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323426.2	NM_005680	In_Frame_Del	-	9994563	CGGTAAGTCACAAGT	-	9994549	8	5	314	1	0	1	0	1	0	0	1	0	15535	550	19	0	416	0	TAF1B	2	9994549	Splice_Site	DEL	CGGTAAGTCACAAGT	TCGA-KR-A7K2-01A-12D-A33Q-10		9994549	233204824	7	44482										
GREB1	9687	hgsc.bcm.edu	37	chr2	11738866	11738866	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	gaagcagagggtggaacagtAtgttctgaagctagacacgg	15	6	1	3			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr2:11738866A>G	ENST00000381486.2	+	15	2513	c.2213A>G	c.(2212-2214)tAt>tGt	p.Y738C	GREB1_ENST00000234142.5_Missense_Mutation_p.Y738C	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	738						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		GTGGAACAGTATGTTCTGAAG	0.448																																					p.Y738C	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											GREB1_ENST00000381486,NS,carcinoma,0,1	GREB1	308	.	0			c.A2213G						.						197	200	199					2																	11738866		1985	4175	6160	SO:0001583	missense	9687	exon15			AACAGTATGTTCT		CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"gene regulated by estrogen in breast cancer"	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.2213A>G	chr2.hg19:g.11738866A>G	ENSP00000370896:p.Tyr738Cys	70.0	0.0		67.0	17.0	NM_014668	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	hg19	CCDS42655.1	.	.	.	.	.	.	.	.	.	.	A	14.44	2.536364	0.45176	.	.	ENSG00000196208	ENST00000381486;ENST00000234142;ENST00000432985	T;T;T	0.55930	2.81;2.81;0.49	5.04	5.04	0.67666	.	0.247626	0.35235	N	0.003342	T	0.67107	0.2858	M	0.65975	2.015	0.58432	D	0.999998	D;D	0.63046	0.992;0.992	P;P	0.59761	0.863;0.863	T	0.71842	-0.4470	10	0.87932	D	0	-44.4277	14.781	0.69766	1.0:0.0:0.0:0.0	.	372;738	C9JIG0;Q4ZG55	.;GREB1_HUMAN	C	738;738;372	ENSP00000370896:Y738C;ENSP00000234142:Y738C;ENSP00000403886:Y372C	ENSP00000234142:Y738C	Y	+	2	0	GREB1	11656317	1.000000	0.71417	0.007000	0.13788	0.004000	0.04260	7.021000	0.76425	1.900000	0.55004	0.460000	0.39030	TAT	.	.		0.448	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668		G	11738866	A	G	11738866	3	3	314	1	0	0	0	0	1	0	0	0	6769	449	16	2	2375	2	GREB1	2	11738866	Missense_Mutation	SNP	A	TCGA-KR-A7K2-01A-12D-A33Q-10	1744317	11738866	231460507	8	44483										
APOB	338	hgsc.bcm.edu	37	chr2	21229489	21229489	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	gacacttccatatttttcgtGgttaagctcacagtactgtt	7	9	1	0	rs374560333		TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr2:21229489G>T	ENST00000233242.1	-	26	10378	c.10251C>A	c.(10249-10251)acC>acA	p.T3417T		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	3417	Heparin-binding.				artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TATTTTTCGTGGTTAAGCTCA	0.393																																					p.T3417T		Atlas-SNP	.											.	APOB	761	.	0			c.C10251A						.						175	173	174					2																	21229489		2203	4300	6503	SO:0001819	synonymous_variant	338	exon26			TTTCGTGGTTAAG	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.10251C>A	chr2.hg19:g.21229489G>T		61.0	0.0		58.0	14.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Silent	SNP	ENST00000233242.1	hg19	CCDS1703.1																																																																																			.	.		0.393	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			T	21229489	G	T	21229489	2	4	314	1	0	0	0	0	0	0	0	1	785	1335	47	3		3	APOB	2	21229489	Silent	SNP	G	TCGA-KR-A7K2-01A-12D-A33Q-10	9490623	21229489	221969884	9	44484										
CNGA3	1261	hgsc.bcm.edu	37	chr2	99012595	99012595	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	ccactggaatgcctgcatctActttgccatttccaagttca	6	13	2	0			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr2:99012595A>G	ENST00000272602.2	+	7	1001	c.962A>G	c.(961-963)tAc>tGc	p.Y321C	CNGA3_ENST00000409937.1_Missense_Mutation_p.Y325C|CNGA3_ENST00000393504.1_Missense_Mutation_p.Y321C|CNGA3_ENST00000436404.2_Missense_Mutation_p.Y303C			Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3	321					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to magnesium ion (GO:0032026)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|photoreceptor outer segment membrane (GO:0042622)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(17)|ovary(5)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	49						GCCTGCATCTACTTTGCCATT	0.473																																					p.Y321C		Atlas-SNP	.											.	CNGA3	118	.	0			c.A962G						.						111	113	112					2																	99012595		2203	4300	6503	SO:0001583	missense	1261	exon8			GCATCTACTTTGC	S76069	CCDS2034.1, CCDS42719.1	2q11.2	2013-01-08			ENSG00000144191	ENSG00000144191		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2150	protein-coding gene	gene with protein product		600053		CNCG3, ACHM2		7532814, 9517456, 16382102	Standard	NM_001298		Approved	CCNC1, CCNCa, CNG3	uc002syt.3	Q16281	OTTHUMG00000130561	ENST00000272602.2:c.962A>G	chr2.hg19:g.99012595A>G	ENSP00000272602:p.Tyr321Cys	105.0	0.0		82.0	50.0	NM_001298	E9PF93|Q4VAP7|Q53RD2|Q6ZNA7|Q9UP64	Missense_Mutation	SNP	ENST00000272602.2	hg19	CCDS2034.1	.	.	.	.	.	.	.	.	.	.	A	13.45	2.240853	0.39598	.	.	ENSG00000144191	ENST00000393504;ENST00000436404;ENST00000272602;ENST00000409937	D;D;D;D	0.98777	-5.13;-5.13;-5.13;-5.13	4.99	4.99	0.66335	Ion transport (1);	0.116998	0.64402	D	0.000013	D	0.99312	0.9759	H	0.95850	3.73	0.53005	D	0.999966	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.994;0.992;0.998	D	0.99215	1.0877	10	0.87932	D	0	.	9.6218	0.39725	0.8435:0.0:0.0:0.1565	.	325;303;321	E9PF93;Q4VAP7;Q16281	.;.;CNGA3_HUMAN	C	321;303;321;325	ENSP00000377140:Y321C;ENSP00000410070:Y303C;ENSP00000272602:Y321C;ENSP00000386761:Y325C	ENSP00000272602:Y321C	Y	+	2	0	CNGA3	98379027	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.464000	0.53057	2.098000	0.63641	0.460000	0.39030	TAC	.	.		0.473	CNGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252986.1	NM_001298		G	99012595	A	G	99012595	3	3	314	1	0	0	0	0	1	0	0	0	3600	391	14	2	988	2	CNGA3	2	99012595	Missense_Mutation	SNP	A	TCGA-KR-A7K2-01A-12D-A33Q-10	77783106	99012595	144186778	10	44485										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168108386	168108386	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	aagagtttttaaaggcctggGatatgcaaccgcagatgctt	11	7	0	2			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr2:168108386G>T	ENST00000409195.1	+	9	10573	c.10484G>T	c.(10483-10485)gGa>gTa	p.G3495V	XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.G3495V|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.G3273V	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	3320					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AAAGGCCTGGGATATGCAACC	0.383																																					p.G3495V		Atlas-SNP	.											.	XIRP2	914	.	0			c.G10484T						.						65	64	64					2																	168108386		1856	4083	5939	SO:0001583	missense	129446	exon9			GCCTGGGATATGC	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.10484G>T	chr2.hg19:g.168108386G>T	ENSP00000386840:p.Gly3495Val	76.0	0.0		52.0	15.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	hg19	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	G	12.52	1.961144	0.34565	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273;ENST00000413534	T;T;T	0.22743	2.01;2.01;1.94	5.94	5.07	0.68467	.	0.054870	0.64402	D	0.000001	T	0.46964	0.1420	M	0.74258	2.255	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.97110	0.999;1.0;0.985	T	0.50808	-0.8784	10	0.87932	D	0	-16.2881	14.0553	0.64764	0.073:0.0:0.927:0.0	.	3320;3320;3273	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	V	3495;3495;3273;909	ENSP00000386840:G3495V;ENSP00000295237:G3495V;ENSP00000387255:G3273V	ENSP00000295237:G3495V	G	+	2	0	XIRP2	167816632	1.000000	0.71417	0.528000	0.27938	0.067000	0.16453	7.888000	0.87302	1.535000	0.49220	-0.142000	0.14014	GGA	.	.		0.383	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		T	168108386	G	T	168108386	3	4	314	1	0	0	0	0	1	0	0	0	17445	1174	41	3	10514	3	XIRP2	2	168108386	Missense_Mutation	SNP	G	TCGA-KR-A7K2-01A-12D-A33Q-10	69095791	168108386	75090987	11	44486										
ABCB11	8647	hgsc.bcm.edu	37	chr2	169847362	169847362	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	cagccactgttctcattgatGaaatgacttcatcagccacc	6	13	3	3			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr2:169847362G>A	ENST00000263817.6	-	9	981	c.857C>T	c.(856-858)tCa>tTa	p.S286L		NM_003742.2	NP_003733.2	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 11	286	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|canalicular bile acid transport (GO:0015722)|small molecule metabolic process (GO:0044281)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|bile acid-exporting ATPase activity (GO:0015432)|canalicular bile acid transmembrane transporter activity (GO:0015126)|sodium-exporting ATPase activity, phosphorylative mechanism (GO:0008554)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(16)|lung(26)|ovary(3)|stomach(1)	57					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Chlorpromazine(DB00477)|Cimetidine(DB00501)|Clofazimine(DB00845)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Digoxin(DB00390)|Doxorubicin(DB00997)|Ethinyl Estradiol(DB00977)|Fluorescein(DB00693)|Fusidic Acid(DB02703)|Glyburide(DB01016)|Ketoconazole(DB01026)|Novobiocin(DB01051)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Ponatinib(DB08901)|Pravastatin(DB00175)|Progesterone(DB00396)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Rosuvastatin(DB01098)|Tamoxifen(DB00675)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	TCTCATTGATGAAATGACTTC	0.393																																					p.S286L		Atlas-SNP	.											.	ABCB11	136	.	0			c.C857T						.						194	196	195					2																	169847362		1910	4121	6031	SO:0001583	missense	8647	exon9			ATTGATGAAATGA	AF091582	CCDS46444.1	2q24	2012-03-14			ENSG00000073734	ENSG00000073734		"ATP binding cassette transporters / subfamily B"	42	protein-coding gene	gene with protein product	"ABC member 16, MDR/TAP subfamily"	603201	"progressive familial intrahepatic cholestasis 2", "bile salt export pump"	BSEP, PFIC2		9806540	Standard	NM_003742		Approved	ABC16, SPGP, PFIC-2, PGY4	uc002ueo.1	O95342	OTTHUMG00000154039	ENST00000263817.6:c.857C>T	chr2.hg19:g.169847362G>A	ENSP00000263817:p.Ser286Leu	64.0	0.0		47.0	22.0	NM_003742	Q53TL2|Q9UNB2	Missense_Mutation	SNP	ENST00000263817.6	hg19	CCDS46444.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.117789	0.77323	.	.	ENSG00000073734	ENST00000263817	D	0.82344	-1.6	5.53	5.53	0.82687	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.88855	0.6550	M	0.87097	2.86	0.80722	D	1	B	0.28350	0.208	B	0.38264	0.269	D	0.87958	0.2728	10	0.72032	D	0.01	1.3303	19.8195	0.96586	0.0:0.0:1.0:0.0	.	286	O95342	ABCBB_HUMAN	L	286	ENSP00000263817:S286L	ENSP00000263817:S286L	S	-	2	0	ABCB11	169555608	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.923000	0.87546	2.756000	0.94617	0.655000	0.94253	TCA	.	.		0.393	ABCB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333616.2	NM_003742		A	169847362	G	A	169847362	3	1	314	1	0	0	0	0	1	0	0	0	42	1294	45	3	3188	3	ABCB11	2	169847362	Missense_Mutation	SNP	G	TCGA-KR-A7K2-01A-12D-A33Q-10	1738976	169847362	73352011	12	44487										
VIL1	7429	hgsc.bcm.edu	37	chr2	219305556	219305556	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	acaagcctgtagaggagctcCccgagggtgtggaccccagc	14	13	0	1			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr2:219305556C>T	ENST00000248444.5	+	19	2429	c.2341C>T	c.(2341-2343)Ccc>Tcc	p.P781S	VIL1_ENST00000392114.2_Missense_Mutation_p.P470S	NM_007127.2	NP_009058.2	P09327	VILI_HUMAN	villin 1	781	HP. {ECO:0000255|PROSITE- ProRule:PRU00595}.|Headpiece.				actin filament capping (GO:0051693)|actin filament depolymerization (GO:0030042)|actin filament polymerization (GO:0030041)|actin filament severing (GO:0051014)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cytoplasmic actin-based contraction involved in cell motility (GO:0060327)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell differentiation (GO:0030855)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell migration (GO:0010634)|protein complex assembly (GO:0006461)|regulation of actin nucleation (GO:0051125)|regulation of cell shape (GO:0008360)|regulation of lamellipodium morphogenesis (GO:2000392)|regulation of wound healing (GO:0061041)|response to bacterium (GO:0009617)	actin filament bundle (GO:0032432)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|microvillus (GO:0005902)|ruffle (GO:0001726)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|identical protein binding (GO:0042802)|lysophosphatidic acid binding (GO:0035727)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(20)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Renal(207;0.0474)		Epithelial(149;6.88e-07)|all cancers(144;0.00013)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGAGGAGCTCCCCGAGGGTGT	0.537																																					p.P781S		Atlas-SNP	.											.	VIL1	65	.	0			c.C2341T						.						47	47	47					2																	219305556		2203	4300	6503	SO:0001583	missense	7429	exon19			GAGCTCCCCGAGG	X12901	CCDS2417.1	2q35	2012-10-02			ENSG00000127831	ENSG00000127831			12690	protein-coding gene	gene with protein product		193040		VIL		2846586	Standard	NM_007127		Approved	D2S1471	uc002via.3	P09327	OTTHUMG00000133112	ENST00000248444.5:c.2341C>T	chr2.hg19:g.219305556C>T	ENSP00000248444:p.Pro781Ser	86.0	0.0		86.0	39.0	NM_007127	B2R9A7|Q53S11|Q96AC8	Missense_Mutation	SNP	ENST00000248444.5	hg19	CCDS2417.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.105774	0.77096	.	.	ENSG00000127831	ENST00000248444;ENST00000392114	T;T	0.25749	1.78;1.9	5.85	5.85	0.93711	Villin headpiece (3);	0.000000	0.85682	D	0.000000	T	0.44973	0.1319	M	0.91140	3.18	0.80722	D	1	B	0.29162	0.235	B	0.29524	0.103	T	0.52419	-0.8578	10	0.87932	D	0	-12.1305	20.1729	0.98161	0.0:1.0:0.0:0.0	.	781	P09327	VILI_HUMAN	S	781;470	ENSP00000248444:P781S;ENSP00000375962:P470S	ENSP00000248444:P781S	P	+	1	0	VIL1	219013800	1.000000	0.71417	0.998000	0.56505	0.797000	0.45037	7.536000	0.82023	2.775000	0.95449	0.603000	0.83216	CCC	.	.		0.537	VIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256778.3	NM_007127		T	219305556	C	T	219305556	3	4	314	1	0	0	0	0	1	0	0	0	17179	623	22	3	2411	3	VIL1	2	219305556	Missense_Mutation	SNP	C	TCGA-KR-A7K2-01A-12D-A33Q-10	49458194	219305556	23893817	13	44488										
SPHKAP	80309	hgsc.bcm.edu	37	chr2	228882606	228882606	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	tgtttcctcacagcggtcccGctcccctggctctctttctt	7	17	3	0			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr2:228882606G>A	ENST00000392056.3	-	7	3010	c.2964C>T	c.(2962-2964)agC>agT	p.S988S	SPHKAP_ENST00000344657.5_Silent_p.S988S	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	988						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)	p.S988R(2)		NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		CAGCGGTCCCGCTCCCCTGGC	0.532																																					p.S988S		Atlas-SNP	.											SPHKAP_ENST00000392056,NS,carcinoma,0,2	SPHKAP	750	.	2	Substitution - Missense(2)	lung(2)	c.C2964T						.						74	69	70					2																	228882606		2203	4300	6503	SO:0001819	synonymous_variant	80309	exon7			GGTCCCGCTCCCC		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"A-kinase anchor proteins"	30619	protein-coding gene	gene with protein product	"sphingosine kinase type 1-interacting protein"	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.2964C>T	chr2.hg19:g.228882606G>A		77.0	0.0		48.0	14.0	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Silent	SNP	ENST00000392056.3	hg19	CCDS46537.1																																																																																			.	.		0.532	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623		A	228882606	G	A	228882606	2	1	314	1	0	0	0	0	0	0	0	1	15063	1078	38	1		1	SPHKAP	2	228882606	Silent	SNP	G	TCGA-KR-A7K2-01A-12D-A33Q-10	9577050	228882606	14316767	14	44489										
MYH15	22989	hgsc.bcm.edu	37	chr3	108117574	108117574	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	tctgtctgctcttgcagggaCcttagatcctctagttcaga	9	11	5	2			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr3:108117574C>T	ENST00000273353.3	-	36	5159	c.5103G>A	c.(5101-5103)agG>agA	p.R1701R		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	1701						cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						CTTGCAGGGACCTTAGATCCT	0.532																																					p.R1701R		Atlas-SNP	.											.	MYH15	223	.	0			c.G5103A						.						192	193	193					3																	108117574		1998	4187	6185	SO:0001819	synonymous_variant	22989	exon36			CAGGGACCTTAGA	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"Myosins / Myosin superfamily : Class II"	31073	protein-coding gene	gene with protein product		609929	"myosin, heavy polypeptide 15"			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.5103G>A	chr3.hg19:g.108117574C>T		61.0	0.0		43.0	14.0	NM_014981		Silent	SNP	ENST00000273353.3	hg19	CCDS43127.1																																																																																			.	.		0.532	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988		T	108117574	C	T	108117574	2	4	314	1	0	0	0	0	0	0	0	1	10043	506	18	3		3	MYH15	3	108117574	Silent	SNP	C	TCGA-KR-A7K2-01A-12D-A33Q-10		108117574	89904856	15	44490										
RUVBL1	8607	hgsc.bcm.edu	37	chr3	127831762	127831762	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	cggaagttctccatcagcacCtctgtcttcttgatctcagt	7	13	6	1			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr3:127831762C>T	ENST00000322623.5	-	3	429	c.330G>A	c.(328-330)gaG>gaA	p.E110E	RUVBL1_ENST00000464873.1_Silent_p.E50E|RUVBL1_ENST00000417360.1_Silent_p.E110E	NM_003707.2	NP_003698.1	Q9Y265	RUVB1_HUMAN	RuvB-like AAA ATPase 1	110					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Ino80 complex (GO:0031011)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)			endometrium(1)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26				GBM - Glioblastoma multiforme(114;0.181)		CCATCAGCACCTCTGTCTTCT	0.527																																					p.E110E		Atlas-SNP	.											.	RUVBL1	38	.	0			c.G330A						.						161	146	151					3																	127831762		2203	4300	6503	SO:0001819	synonymous_variant	8607	exon3			CAGCACCTCTGTC	AF070735	CCDS3047.1	3q21	2013-09-12	2013-09-12		ENSG00000175792	ENSG00000175792		"INO80 complex subunits", "ATPases / AAA-type"	10474	protein-coding gene	gene with protein product	"pontin", "INO80 complex subunit H"	603449	"RuvB (E coli homolog)-like 1", "RuvB-like 1 (E. coli)", "RuvB-like AAA ATPase"			9774387, 9588198	Standard	NM_003707		Approved	TIP49, NMP238, RVB1, TIP49a, Pontin52, ECP54, TIH1, Rvb1, INO80H	uc003ekh.3	Q9Y265	OTTHUMG00000159658	ENST00000322623.5:c.330G>A	chr3.hg19:g.127831762C>T		120.0	0.0		59.0	11.0	NM_003707	B2R5S0|P82276|Q1KMR0|Q53HK5|Q53HL7|Q53Y27|Q9BSX9	Silent	SNP	ENST00000322623.5	hg19	CCDS3047.1																																																																																			.	.		0.527	RUVBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356728.2			T	127831762	C	T	127831762	2	4	314	1	0	0	0	0	0	0	0	1	13767	680	24	3		3	RUVBL1	3	127831762	Silent	SNP	C	TCGA-KR-A7K2-01A-12D-A33Q-10	19714188	127831762	70190668	16	44491										
GRK7	131890	hgsc.bcm.edu	37	chr3	141497429	141497429	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	ctggccgaggagggacccacCaaagacagcgcgctgcaggg	16	13	0	1			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr3:141497429C>A	ENST00000264952.2	+	1	440	c.303C>A	c.(301-303)acC>acA	p.T101T		NM_139209.2	NP_631948.1	Q8WTQ7	GRK7_HUMAN	G protein-coupled receptor kinase 7	101	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				protein autophosphorylation (GO:0046777)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual perception (GO:0007601)	membrane (GO:0016020)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|rhodopsin kinase activity (GO:0050254)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	26						AGGGACCCACCAAAGACAGCG	0.672																																					p.T101T		Atlas-SNP	.											.	GRK7	65	.	0			c.C303A						.						25	27	26					3																	141497429		2201	4298	6499	SO:0001819	synonymous_variant	131890	exon1			ACCCACCAAAGAC		CCDS3120.1	3q24	2004-02-04	2004-02-04	2004-02-04	ENSG00000114124	ENSG00000114124			17031	protein-coding gene	gene with protein product		606987		GPRK7		11717351, 11754336	Standard	NM_139209		Approved		uc011bnd.2	Q8WTQ7	OTTHUMG00000159068	ENST00000264952.2:c.303C>A	chr3.hg19:g.141497429C>A		94.0	0.0		68.0	20.0	NM_139209		Silent	SNP	ENST00000264952.2	hg19	CCDS3120.1																																																																																			.	.		0.672	GRK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353168.1	NM_139209		A	141497429	C	A	141497429	2	1	314	1	0	0	0	0	0	0	0	1	6803	581	21	3		3	GRK7	3	141497429	Silent	SNP	C	TCGA-KR-A7K2-01A-12D-A33Q-10	13665667	141497429	56525001	17	44492										
GPR149	344758	hgsc.bcm.edu	37	chr3	154055628	154055628	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	tgtgtctggaatggagatatTaatatcaccatcaggattac	9	6	3	1			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr3:154055628T>C	ENST00000389740.2	-	4	2155	c.2056A>G	c.(2056-2058)Aat>Gat	p.N686D		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	686					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			ATGGAGATATTAATATCACCA	0.433																																					p.N686D		Atlas-SNP	.											.	GPR149	134	.	0			c.A2056G						.						260	239	246					3																	154055628		1914	4140	6054	SO:0001583	missense	344758	exon4			AGATATTAATATC	AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"GPCR / Class A : Orphans"	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.2056A>G	chr3.hg19:g.154055628T>C	ENSP00000374390:p.Asn686Asp	91.0	0.0		113.0	60.0	NM_001038705		Missense_Mutation	SNP	ENST00000389740.2	hg19	CCDS43162.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.391436	0.83011	.	.	ENSG00000174948	ENST00000389740	.	.	.	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.61999	0.2392	N	0.24115	0.695	0.53688	D	0.999975	D	0.67145	0.996	P	0.60541	0.876	T	0.67090	-0.5758	9	0.87932	D	0	-21.6473	16.1538	0.81644	0.0:0.0:0.0:1.0	.	686	Q86SP6	GP149_HUMAN	D	686	.	ENSP00000374390:N686D	N	-	1	0	GPR149	155538322	1.000000	0.71417	0.985000	0.45067	0.656000	0.38851	7.706000	0.84615	2.213000	0.71641	0.528000	0.53228	AAT	.	.		0.433	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580		C	154055628	T	C	154055628	3	2	314	1	0	0	0	0	1	0	0	0	6662	1754	61	2	143	2	GPR149	3	154055628	Missense_Mutation	SNP	T	TCGA-KR-A7K2-01A-12D-A33Q-10	12558199	154055628	43966802	18	44493										
PDS5A	23244	hgsc.bcm.edu	37	chr4	39905761	39905761	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	gcttcaccatgaagacagtaTttcttataaagctgagccag	8	9	2	3			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr4:39905761T>C	ENST00000303538.8	-	12	1823	c.1284A>G	c.(1282-1284)aaA>aaG	p.K428K	PDS5A_ENST00000503396.1_Silent_p.K428K	NM_001100399.1	NP_001093869.1			PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae)											breast(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(14)|prostate(3)|skin(1)|urinary_tract(1)	39						GAAGACAGTATTTCTTATAAA	0.373																																					p.K428K		Atlas-SNP	.											.	PDS5A	114	.	0			c.A1284G						.						71	62	65					4																	39905761		1858	4113	5971	SO:0001819	synonymous_variant	23244	exon12			ACAGTATTTCTTA	AF294791	CCDS47045.1, CCDS54759.1	4p14	2007-06-20			ENSG00000121892	ENSG00000121892			29088	protein-coding gene	gene with protein product		613200				11076961, 15855230	Standard	NM_001100399		Approved	KIAA0648, PIG54, SCC-112	uc003guv.4	Q29RF7	OTTHUMG00000160582	ENST00000303538.8:c.1284A>G	chr4.hg19:g.39905761T>C		48.0	0.0		56.0	32.0	NM_001100399		Silent	SNP	ENST00000303538.8	hg19	CCDS47045.1	.	.	.	.	.	.	.	.	.	.	T	9.138	1.013147	0.19277	.	.	ENSG00000121892	ENST00000513798	.	.	.	5.04	2.55	0.30701	.	.	.	.	.	T	0.57740	0.2074	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50171	-0.8859	4	.	.	.	-16.4527	8.6341	0.33936	0.0:0.2974:0.0:0.7026	.	.	.	.	S	66	.	.	N	-	2	0	PDS5A	39582156	0.246000	0.23909	1.000000	0.80357	0.977000	0.68977	-0.288000	0.08377	0.338000	0.23692	-0.290000	0.09829	AAT	.	.		0.373	PDS5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361287.1	NM_015200		C	39905761	T	C	39905761	2	2	314	1	0	0	0	0	0	0	0	1	11700	1490	52	2		2	PDS5A	4	39905761	Silent	SNP	T	TCGA-KR-A7K2-01A-12D-A33Q-10		39905761	151248515	19	44494										
GABRG1	2565	hgsc.bcm.edu	37	chr4	46066470	46066470	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	ttacttacagcttgaaaattCcagtggacaggaatgttcat	8	7	1	1			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr4:46066470C>G	ENST00000295452.4	-	5	780	c.613G>C	c.(613-615)Gaa>Caa	p.E205Q		NM_173536.3	NP_775807.2	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 1	205					gamma-aminobutyric acid signaling pathway (GO:0007214)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(2)|central_nervous_system(5)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(2)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	76				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CTTGAAAATTCCAGTGGACAG	0.274																																					p.E205Q		Atlas-SNP	.											.	GABRG1	172	.	0			c.G613C						.						65	73	70					4																	46066470		2202	4287	6489	SO:0001583	missense	2565	exon5			AAAATTCCAGTGG	BC031087	CCDS3470.1	4p12	2012-06-22			ENSG00000163285	ENSG00000163285		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4086	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma"	137166				1321425	Standard	NM_173536		Approved		uc003gxb.3	Q8N1C3	OTTHUMG00000128609	ENST00000295452.4:c.613G>C	chr4.hg19:g.46066470C>G	ENSP00000295452:p.Glu205Gln	344.0	0.0		319.0	90.0	NM_173536	Q5H9T8	Missense_Mutation	SNP	ENST00000295452.4	hg19	CCDS3470.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.716852	0.89205	.	.	ENSG00000163285	ENST00000295452;ENST00000540030	T	0.79940	-1.32	5.8	5.8	0.92144	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	D	0.83459	0.5259	L	0.37561	1.115	0.80722	D	1	D	0.57257	0.979	P	0.62740	0.906	T	0.77640	-0.2512	10	0.13108	T	0.6	.	19.0345	0.92971	0.0:1.0:0.0:0.0	.	205	Q8N1C3	GBRG1_HUMAN	Q	205	ENSP00000295452:E205Q	ENSP00000295452:E205Q	E	-	1	0	GABRG1	45761227	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	6.012000	0.70767	2.729000	0.93468	0.561000	0.74099	GAA	.	.		0.274	GABRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250470.1	NM_173536		G	46066470	C	G	46066470	3	3	314	1	0	0	0	0	1	0	0	0	6179	864	30	4	804	4	GABRG1	4	46066470	Missense_Mutation	SNP	C	TCGA-KR-A7K2-01A-12D-A33Q-10	6160709	46066470	145087806	20	44495										
KDR	3791	hgsc.bcm.edu	37	chr4	55946235	55946235	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	cactggagtacacggtggtgTctgtgtcatcggagtgatat	14	7	2	1			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr4:55946235T>C	ENST00000263923.4	-	30	4239	c.3944A>G	c.(3943-3945)gAc>gGc	p.D1315G	RP11-530I17.1_ENST00000511222.1_RNA	NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	1315					angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CACGGTGGTGTCTGTGTCATC	0.537			Mis		"NSCLC, angiosarcoma"					TSP Lung(20;0.16)																											p.D1315G		Atlas-SNP	.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	.	KDR	307	.	0			c.A3944G						.						203	190	194					4																	55946235		2203	4300	6503	SO:0001583	missense	3791	exon30			GTGGTGTCTGTGT	AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.3944A>G	chr4.hg19:g.55946235T>C	ENSP00000263923:p.Asp1315Gly	129.0	0.0		91.0	44.0	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Missense_Mutation	SNP	ENST00000263923.4	hg19	CCDS3497.1	.	.	.	.	.	.	.	.	.	.	T	16.49	3.137104	0.56936	.	.	ENSG00000128052	ENST00000263923	T	0.76186	-1.0	5.62	5.62	0.85841	.	0.100113	0.64402	D	0.000002	T	0.73321	0.3572	L	0.31065	0.9	0.80722	D	1	D	0.65815	0.995	P	0.58928	0.848	T	0.68413	-0.5415	10	0.06757	T	0.87	.	15.8235	0.78678	0.0:0.0:0.0:1.0	.	1315	P35968	VGFR2_HUMAN	G	1315	ENSP00000263923:D1315G	ENSP00000263923:D1315G	D	-	2	0	KDR	55640992	1.000000	0.71417	0.982000	0.44146	0.923000	0.55619	7.698000	0.84413	2.149000	0.67028	0.528000	0.53228	GAC	.	.		0.537	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1			C	55946235	T	C	55946235	3	2	314	1	0	0	0	0	1	0	0	0	8148	1667	58	2	130	2	KDR	4	55946235	Missense_Mutation	SNP	T	TCGA-KR-A7K2-01A-12D-A33Q-10	9879765	55946235	135208041	21	44496										
NFKB1	4790	hgsc.bcm.edu	37	chr4	103518690	103518690	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	cttacagataacctctttctAgagaaggctatgcagcttgc	8	10	2	2			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr4:103518690A>G	ENST00000505458.1	+	15	1783	c.1506A>G	c.(1504-1506)ctA>ctG	p.L502L	NFKB1_ENST00000600343.1_Silent_p.L322L|NFKB1_ENST00000394820.4_Silent_p.L502L|NFKB1_ENST00000226574.4_Silent_p.L503L			P19838	NFKB1_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 1	502	Interaction with CFLAR.				apoptotic process (GO:0006915)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of calcidiol 1-monooxygenase activity (GO:0010956)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of cytokine production (GO:0001818)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-12 biosynthetic process (GO:0045083)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|response to copper ion (GO:0046688)|response to oxidative stress (GO:0006979)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I-kappaB/NF-kappaB complex (GO:0033256)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleic acid binding transcription factor activity (GO:0001071)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			biliary_tract(1)|breast(4)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	27		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.59e-08)	Acetylsalicylic acid(DB00945)|Pranlukast(DB01411)|Thalidomide(DB01041)|Triflusal(DB08814)	ACCTCTTTCTAGAGAAGGCTA	0.483																																					p.L503L		Atlas-SNP	.											.	NFKB1	78	.	0			c.A1509G						.						101	93	96					4																	103518690		2203	4300	6503	SO:0001819	synonymous_variant	4790	exon15			CTTTCTAGAGAAG	M58603	CCDS3657.1, CCDS54783.1	4q24	2013-01-10	2008-07-28		ENSG00000109320	ENSG00000109320		"Ankyrin repeat domain containing"	7794	protein-coding gene	gene with protein product		164011				1992489	Standard	NM_003998		Approved	KBF1, p105, NFKB-p50, p50, NF-kappaB, NFkappaB, NF-kB1	uc011cep.2	P19838	OTTHUMG00000161080	ENST00000505458.1:c.1506A>G	chr4.hg19:g.103518690A>G		33.0	0.0		23.0	8.0	NM_003998	A8K5Y5|B3KVE8|Q68D84|Q86V43|Q8N4X7|Q9NZC0	Silent	SNP	ENST00000505458.1	hg19	CCDS54783.1																																																																																			.	.		0.483	NFKB1-003	KNOWN	alternative_5_UTR|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363411.1			G	103518690	A	G	103518690	2	3	314	1	0	0	0	0	0	0	0	1	10384	407	15	2		2	NFKB1	4	103518690	Silent	SNP	A	TCGA-KR-A7K2-01A-12D-A33Q-10	47572455	103518690	87635586	22	44497										
SC4MOL	6307	hgsc.bcm.edu	37	chr4	166259057	166259058	+	Frame_Shift_Ins	INS	-	-	A													0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	attttacagagtatttcaatINSattccttatgattgggaaag					rs148185089		TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr4:166259057_166259058insA	ENST00000261507.6	+	3	545_546	c.372_373insA	c.(373-375)attfs	p.I125fs	MSMO1_ENST00000393766.2_5'UTR|MSMO1_ENST00000504317.1_Frame_Shift_Ins_p.I125fs	NM_006745.4	NP_006736.1	Q15800	MSMO1_HUMAN	methylsterol monooxygenase 1	125					cholesterol biosynthetic process (GO:0006695)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C-4 methylsterol oxidase activity (GO:0000254)|iron ion binding (GO:0005506)										AGTATTTCAATATTCCTTATGA	0.332																																					p.N124fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.372_373insA						.																																			SO:0001589	frameshift_variant	6307	exon3			.	U93162	CCDS3809.1, CCDS43280.1	4q32-q34	2013-03-04	2011-09-01	2011-09-01	ENSG00000052802	ENSG00000052802	1.14.13.72	"Fatty acid hydroxylase domain containing"	10545	protein-coding gene	gene with protein product		607545	"sterol-C4-methyl oxidase-like"	SC4MOL		8663358	Standard	NM_006745		Approved	DESP4, ERG25	uc003ire.3	Q15800	OTTHUMG00000161126	ENST00000261507.6:c.373dupA	chr4.hg19:g.166259058_166259058dupA	ENSP00000261507:p.Ile125fs	63.0	0.0		68.0	31.0	NM_006745	A8K8Q3|A8MYF6|D3DP32|Q32Q24	Frame_Shift_Ins	INS	ENST00000261507.6	hg19	CCDS3809.1																																																																																			.	.		0.332	MSMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363880.1	NM_006745		A	166259058	-	A	166259057	7	5	314	1	0	1	1	0	0	0	0	0	13880	1403	49	0	378	0	SC4MOL	4	166259057	Frame_Shift_Ins	INS	-	TCGA-KR-A7K2-01A-12D-A33Q-10	62740367	166259057	24895219	23	44498										
CDH18	1016	hgsc.bcm.edu	37	chr5	19747162	19747162	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	ctcggattcaggctcaagagGtttgtttgtacgtctatcaa	10	8	4	1			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr5:19747162G>T	ENST00000507958.1	-	6	1402	c.412C>A	c.(412-414)Cct>Act	p.P138T	CDH18_ENST00000274170.4_Missense_Mutation_p.P138T|CDH18_ENST00000511273.1_Missense_Mutation_p.P138T|CDH18_ENST00000502796.1_Missense_Mutation_p.P138T|CDH18_ENST00000382275.1_Missense_Mutation_p.P138T|CDH18_ENST00000506372.1_Missense_Mutation_p.P138T			Q13634	CAD18_HUMAN	cadherin 18, type 2	138	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					GGCTCAAGAGGTTTGTTTGTA	0.433																																					p.P138T		Atlas-SNP	.											.	CDH18	561	.	0			c.C412A						.						228	206	213					5																	19747162		2203	4300	6503	SO:0001583	missense	1016	exon4			CAAGAGGTTTGTT	U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"Cadherins / Major cadherins"	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.412C>A	chr5.hg19:g.19747162G>T	ENSP00000425093:p.Pro138Thr	105.0	0.0		106.0	54.0	NM_001167667	A8K0I2|B4DHG6|Q8N5Z2	Missense_Mutation	SNP	ENST00000507958.1	hg19	CCDS3889.1	.	.	.	.	.	.	.	.	.	.	G	16.69	3.194529	0.58017	.	.	ENSG00000145526	ENST00000382275;ENST00000507958;ENST00000542864;ENST00000274170;ENST00000506372;ENST00000502796;ENST00000515257;ENST00000511273	T;T;T;T;T;T;T	0.56275	0.47;0.47;0.47;0.47;0.47;0.47;0.47	5.04	5.04	0.67666	Cadherin (4);Cadherin-like (1);	0.058569	0.64402	D	0.000001	T	0.70002	0.3174	M	0.79343	2.45	0.53005	D	0.999961	P;D	0.52996	0.812;0.957	P;P	0.58820	0.773;0.846	T	0.72384	-0.4310	9	.	.	.	.	16.957	0.86262	0.0:0.0:1.0:0.0	.	138;138	B4DHG6;Q13634	.;CAD18_HUMAN	T	138;138;138;138;138;138;84;138	ENSP00000371710:P138T;ENSP00000425093:P138T;ENSP00000274170:P138T;ENSP00000424931:P138T;ENSP00000422138:P138T;ENSP00000427383:P84T;ENSP00000425854:P138T	.	P	-	1	0	CDH18	19782919	1.000000	0.71417	0.997000	0.53966	0.624000	0.37722	3.924000	0.56476	2.338000	0.79540	0.591000	0.81541	CCT	.	.		0.433	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934		T	19747162	G	T	19747162	3	4	314	1	0	0	0	0	1	0	0	0	3105	1261	44	3	2000	3	CDH18	5	19747162	Missense_Mutation	SNP	G	TCGA-KR-A7K2-01A-12D-A33Q-10		19747162	161168098	24	44499										
FBN2	2201	hgsc.bcm.edu	37	chr5	127744387	127744387	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	cgatgcatcgagagccatctGttgaggttacatatccacgt	10	10	1	2			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr5:127744387G>A	ENST00000508053.1	-	14	2032	c.1058C>T	c.(1057-1059)aCa>aTa	p.T353I	FBN2_ENST00000262464.4_Missense_Mutation_p.T353I|FBN2_ENST00000508989.1_Missense_Mutation_p.T320I			P35556	FBN2_HUMAN	fibrillin 2	353	EGF-like 5; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		AGAGCCATCTGTTGAGGTTAC	0.448																																					p.T353I		Atlas-SNP	.											.	FBN2	858	.	0			c.C1058T						.						137	118	124					5																	127744387		2203	4300	6503	SO:0001583	missense	2201	exon8			CCATCTGTTGAGG	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.1058C>T	chr5.hg19:g.127744387G>A	ENSP00000424571:p.Thr353Ile	221.0	0.0		271.0	107.0	NM_001999	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	hg19	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	G	13.27	2.188296	0.38609	.	.	ENSG00000138829	ENST00000262464;ENST00000508053;ENST00000508989	D;D;D	0.92446	-2.24;-2.24;-3.04	4.89	4.89	0.63831	EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.142496	0.46758	D	0.000262	D	0.84942	0.5584	N	0.16478	0.41	0.36875	D	0.889126	B;B	0.26744	0.158;0.158	B;B	0.25405	0.06;0.041	D	0.84128	0.0410	10	0.35671	T	0.21	.	14.1899	0.65633	0.0:0.1504:0.8496:0.0	.	320;353	D6RJI3;P35556	.;FBN2_HUMAN	I	353;353;320	ENSP00000262464:T353I;ENSP00000424571:T353I;ENSP00000425596:T320I	ENSP00000262464:T353I	T	-	2	0	FBN2	127772286	0.983000	0.35010	1.000000	0.80357	0.610000	0.37248	3.218000	0.51192	2.647000	0.89833	0.555000	0.69702	ACA	.	.		0.448	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		A	127744387	G	A	127744387	3	1	314	1	0	0	0	0	1	0	0	0	5711	1377	48	3	7912	3	FBN2	5	127744387	Missense_Mutation	SNP	G	TCGA-KR-A7K2-01A-12D-A33Q-10	107997225	127744387	53170873	25	44500										
RREB1	6239	hgsc.bcm.edu	37	chr6	7231437	7231437	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	ctcgtgggcagctcagccctCctgagtggcacagccttgct	12	15	1	1			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr6:7231437C>A	ENST00000349384.6	+	10	3419	c.3105C>A	c.(3103-3105)ctC>ctA	p.L1035L	RREB1_ENST00000379938.2_Silent_p.L1035L|RREB1_ENST00000334984.6_Silent_p.L1035L|RREB1_ENST00000379933.3_Silent_p.L1035L	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	1035	Pro-rich.				multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				GCTCAGCCCTCCTGAGTGGCA	0.672																																					p.L1035L		Atlas-SNP	.											.	RREB1	242	.	0			c.C3105A						.						30	35	33					6																	7231437		2203	4296	6499	SO:0001819	synonymous_variant	6239	exon10			AGCCCTCCTGAGT	U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"Zinc fingers, C2H2-type"	10449	protein-coding gene	gene with protein product	"hindsight homolog (drosophila)"	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.3105C>A	chr6.hg19:g.7231437C>A		41.0	0.0		47.0	12.0	NM_001003700	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Silent	SNP	ENST00000349384.6	hg19	CCDS34336.1																																																																																			.	.		0.672	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1			A	7231437	C	A	7231437	2	1	314	1	0	0	0	0	0	0	0	1	13694	842	30	3		3	RREB1	6	7231437	Silent	SNP	C	TCGA-KR-A7K2-01A-12D-A33Q-10		7231437	163883630	26	44501										
NOTCH4	4855	hgsc.bcm.edu	37	chr6	32163286	32163286	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	ggaccacagtcaagttgaggTgatccccgctccggggacgg	15	12	1	2			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr6:32163286T>C	ENST00000375023.3	-	30	6078	c.5940A>G	c.(5938-5940)tcA>tcG	p.S1980S	GPSM3_ENST00000487761.1_5'Flank|GPSM3_ENST00000375043.3_5'UTR|GPSM3_ENST00000375040.3_5'Flank	NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	1980					cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						CAAGTTGAGGTGATCCCCGCT	0.552																																					p.S1980S		Atlas-SNP	.											.	NOTCH4	201	.	0			c.A5940G						.						95	112	106					6																	32163286		1509	2708	4217	SO:0001819	synonymous_variant	4855	exon30			TTGAGGTGATCCC		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"Ankyrin repeat domain containing"	7884	protein-coding gene	gene with protein product		164951	"Notch (Drosophila) homolog 4", "Notch homolog 4 (Drosophila)"	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.5940A>G	chr6.hg19:g.32163286T>C		84.0	0.0		61.0	7.0	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Silent	SNP	ENST00000375023.3	hg19	CCDS34420.1																																																																																			.	.		0.552	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2			C	32163286	T	C	32163286	2	2	314	1	0	0	0	0	0	0	0	1	10560	1683	59	2		2	NOTCH4	6	32163286	Silent	SNP	T	TCGA-KR-A7K2-01A-12D-A33Q-10	24931849	32163286	138951781	27	44502										
FIG4	9896	hgsc.bcm.edu	37	chr6	110098138	110098138	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	tttttagatgccgatagacaAgattccattaatctcttcct	5	9	1	3			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr6:110098138A>G	ENST00000230124.3	+	16	1888	c.1764A>G	c.(1762-1764)caA>caG	p.Q588Q	FIG4_ENST00000441478.2_Silent_p.Q311Q	NM_014845.5	NP_055660.1	Q92562	FIG4_HUMAN	FIG4 phosphoinositide 5-phosphatase	588					cell death (GO:0008219)|locomotory behavior (GO:0007626)|myelin assembly (GO:0032288)|negative regulation of myelination (GO:0031642)|neuron development (GO:0048666)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of neuron projection development (GO:0010976)|small molecule metabolic process (GO:0044281)|vacuole organization (GO:0007033)	early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)	phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphatidylinositol-4-phosphate phosphatase activity (GO:0043812)			central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)	32		all_cancers(87;8.63e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000124)|all_lung(197;0.0187)|Colorectal(196;0.0492)|Lung SC(18;0.0548)		OV - Ovarian serous cystadenocarcinoma(136;0.0355)|Epithelial(106;0.038)|all cancers(137;0.0425)|BRCA - Breast invasive adenocarcinoma(108;0.079)		CCGATAGACAAGATTCCATTA	0.358																																					p.Q588Q		Atlas-SNP	.											.	FIG4	77	.	0			c.A1764G						.						57	62	60					6																	110098138		2203	4300	6503	SO:0001819	synonymous_variant	9896	exon16			TAGACAAGATTCC	D87464	CCDS5078.1	6q21	2014-09-17	2014-08-04	2007-07-30	ENSG00000112367	ENSG00000112367			16873	protein-coding gene	gene with protein product		609390	"KIAA0274", "FIG4 homolog (S. cerevisiae)", "FIG4 homolog, SAC1 lipid phosphatase domain containing (S. cerevisiae)"	KIAA0274		9039502, 11274189, 17572665	Standard	NM_014845		Approved	SAC3, hSac3, dJ249I4.1, ALS11, CMT4J	uc003ptt.2	Q92562	OTTHUMG00000015352	ENST00000230124.3:c.1764A>G	chr6.hg19:g.110098138A>G		98.0	0.0		98.0	4.0	NM_014845	Q53H49|Q5TCS6	Silent	SNP	ENST00000230124.3	hg19	CCDS5078.1	.	.	.	.	.	.	.	.	.	.	A	7.368	0.626218	0.14257	.	.	ENSG00000112367	ENST00000415980	.	.	.	5.35	2.95	0.34219	.	.	.	.	.	T	0.45418	0.1341	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37220	-0.9715	4	.	.	.	-18.0992	9.7067	0.40220	0.8586:0.0:0.1414:0.0	.	.	.	.	G	61	.	.	R	+	1	2	FIG4	110204831	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	1.263000	0.33004	0.433000	0.26313	0.459000	0.35465	AGA	.	.		0.358	FIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041768.1	NM_014845		G	110098138	A	G	110098138	2	3	314	1	0	0	0	0	0	0	0	1	5896	69	3	2		2	FIG4	6	110098138	Silent	SNP	A	TCGA-KR-A7K2-01A-12D-A33Q-10	77934852	110098138	61016929	28	44503										
ECT2L	345930	hgsc.bcm.edu	37	chr6	139134461	139134461	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	ctggacaccttttagcaacaAgtcattaaatagacaggtaa	7	8	1	1	rs369742195		TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr6:139134461A>T	ENST00000423192.1	+	2	211	c.50A>T	c.(49-51)aAg>aTg	p.K17M	ECT2L_ENST00000367682.2_Missense_Mutation_p.K17M|ECT2L_ENST00000541398.1_5'Flank			Q008S8	ECT2L_HUMAN	epithelial cell transforming 2 like	17							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			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						TTTAGCAACAAGTCATTAAAT	0.388			"N, Splice, Mis"		ETP ALL																																p.K17M		Atlas-SNP	.		Rec	yes		6	6q24.1	345930	epithelial cell transforming sequence 2 oncogene-like		L	.	ECT2L	75	.	0			c.A50T						.						78	72	73					6																	139134461		1828	4087	5915	SO:0001583	missense	345930	exon2			GCAACAAGTCATT		CCDS43508.1	6q24.1	2014-03-11	2014-03-11		ENSG00000203734	ENSG00000203734		"Rho guanine nucleotide exchange factors", "F-boxes /  "other""	21118	protein-coding gene	gene with protein product	"lung specific F-box and DH domain containing protein", "F-box protein 49"		"chromosome 6 open reading frame 91", "epithelial cell transforming sequence 2 oncogene-like"	C6orf91			Standard	NM_001077706		Approved	ARHGEF32, FBXO49, LFDH	uc021zfx.1	Q008S8	OTTHUMG00000015679	ENST00000423192.1:c.50A>T	chr6.hg19:g.139134461A>T	ENSP00000387388:p.Lys17Met	65.0	0.0		91.0	16.0	NM_001195037	B2RUV6|Q5JWK2|Q5JWK3|Q5JWK4	Missense_Mutation	SNP	ENST00000423192.1	hg19	CCDS43508.1	.	.	.	.	.	.	.	.	.	.	A	12.25	1.880305	0.33162	.	.	ENSG00000203734	ENST00000423192;ENST00000401414;ENST00000367682	T;T;T	0.63096	-0.02;0.76;-0.02	6.08	2.2	0.27929	.	.	.	.	.	T	0.24661	0.0598	N	0.14661	0.345	0.80722	D	1	B	0.23058	0.079	B	0.23716	0.048	T	0.09207	-1.0685	9	0.72032	D	0.01	-1.2885	7.498	0.27500	0.5852:0.2806:0.0:0.1341	.	17	Q008S8	ECT2L_HUMAN	M	17	ENSP00000387388:K17M;ENSP00000385187:K17M;ENSP00000356655:K17M	ENSP00000356655:K17M	K	+	2	0	ECT2L	139176154	0.942000	0.31987	0.971000	0.41717	0.099000	0.18886	0.780000	0.26760	0.137000	0.18759	-1.263000	0.01449	AAG	.	.		0.388	ECT2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042441.3	NM_001077706		T	139134461	A	T	139134461	3	4	314	1	0	0	0	0	1	0	0	0	4904	72	3	4	52	4	ECT2L	6	139134461	Missense_Mutation	SNP	A	TCGA-KR-A7K2-01A-12D-A33Q-10	29036323	139134461	31980606	29	44504										
C6orf120	387263	hgsc.bcm.edu	37	chr6	170102922	170102922	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	tcggcgtctatggacaccccTcccacctggagagcgagttc	11	15	1	1			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr6:170102922T>A	ENST00000332290.2	+	1	666	c.367T>A	c.(367-369)Tcc>Acc	p.S123T	C6orf120_ENST00000439249.1_Missense_Mutation_p.S142T|WDR27_ENST00000333572.6_5'Flank|WDR27_ENST00000448612.1_5'Flank|WDR27_ENST00000423258.1_5'Flank|WDR27_ENST00000420344.2_5'Flank	NM_001029863.1	NP_001025034.1	Q7Z4R8	CF120_HUMAN	chromosome 6 open reading frame 120	123					apoptotic process (GO:0006915)	extracellular vesicular exosome (GO:0070062)				endometrium(1)|lung(2)	3		Breast(66;0.000338)		OV - Ovarian serous cystadenocarcinoma(33;9.65e-22)|BRCA - Breast invasive adenocarcinoma(81;1.29e-07)|GBM - Glioblastoma multiforme(31;0.0015)		TGGACACCCCTCCCACCTGGA	0.692																																					p.S123T		Atlas-SNP	.											.	C6orf120	5	.	0			c.T367A						.						28	29	29					6																	170102922		2203	4298	6501	SO:0001583	missense	387263	exon1			CACCCCTCCCACC	AF055030	CCDS34575.1	6q27	2012-06-21			ENSG00000185127	ENSG00000185127			21247	protein-coding gene	gene with protein product						8619474, 9110174, 22340178	Standard	NM_001029863		Approved	bA160E12.4	uc003qxb.3	Q7Z4R8	OTTHUMG00000016057	ENST00000332290.2:c.367T>A	chr6.hg19:g.170102922T>A	ENSP00000346931:p.Ser123Thr	44.0	0.0		35.0	14.0	NM_001029863	B4DHE9|E1P5C9	Missense_Mutation	SNP	ENST00000332290.2	hg19	CCDS34575.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.184594	0.78677	.	.	ENSG00000185127	ENST00000439249;ENST00000332290	.	.	.	5.48	5.48	0.80851	.	0.000000	0.85682	U	0.000000	T	0.76572	0.4006	M	0.85373	2.75	0.58432	D	0.999999	D;D	0.76494	0.999;0.999	D;D	0.70935	0.971;0.971	T	0.81088	-0.1091	9	0.66056	D	0.02	-20.1084	15.0314	0.71710	0.0:0.0:0.0:1.0	.	142;123	B4DJ79;Q7Z4R8	.;CF120_HUMAN	T	142;123	.	ENSP00000346931:S123T	S	+	1	0	C6orf120	169844847	1.000000	0.71417	0.095000	0.20976	0.031000	0.12232	5.941000	0.70195	2.195000	0.70347	0.533000	0.62120	TCC	.	.		0.692	C6orf120-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043214.1	NM_001029863		A	170102922	T	A	170102922	3	1	314	1	0	0	0	0	1	0	0	0	2326	1551	54	4	369	4	C6orf120	6	170102922	Missense_Mutation	SNP	T	TCGA-KR-A7K2-01A-12D-A33Q-10	30968461	170102922	1012145	30	44505										
NPC1L1	29881	hgsc.bcm.edu	37	chr7	44555486	44555486	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	gaggttgaggcggaagaagaAgatctgaatgagctgggcct	17	5	1	6			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr7:44555486A>T	ENST00000289547.4	-	19	3848	c.3793T>A	c.(3793-3795)Ttc>Atc	p.F1265I	NPC1L1_ENST00000546276.1_Missense_Mutation_p.F1192I|NPC1L1_ENST00000381160.3_Missense_Mutation_p.F1238I	NM_013389.2	NP_037521.2	Q9UHC9	NPCL1_HUMAN	NPC1-like 1	1265					cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intestinal cholesterol absorption (GO:0030299)|lipoprotein metabolic process (GO:0042157)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)	brush border membrane (GO:0031526)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|hedgehog receptor activity (GO:0008158)|myosin V binding (GO:0031489)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(7)|lung(27)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	57					Ezetimibe(DB00973)	CGGAAGAAGAAGATCTGAATG	0.612																																					p.F1265I		Atlas-SNP	.											.	NPC1L1	141	.	0			c.T3793A						.						70	71	71					7																	44555486		2203	4300	6503	SO:0001583	missense	29881	exon19			AGAAGAAGATCTG		CCDS5491.1, CCDS43575.1, CCDS75587.1	7p13	2012-11-15	2012-11-15		ENSG00000015520	ENSG00000015520			7898	protein-coding gene	gene with protein product		608010	"NPC1 (Niemann-Pick disease, type C1, gene)-like 1"			10783261	Standard	NM_013389		Approved		uc003tlb.3	Q9UHC9	OTTHUMG00000023691	ENST00000289547.4:c.3793T>A	chr7.hg19:g.44555486A>T	ENSP00000289547:p.Phe1265Ile	90.0	0.0		75.0	55.0	NM_013389	A4D2J7|B7ZLE6|D3DVK9|Q17RV5|Q6R3Q4|Q9UHC8	Missense_Mutation	SNP	ENST00000289547.4	hg19	CCDS5491.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.708856	0.89018	.	.	ENSG00000015520	ENST00000289547;ENST00000381160;ENST00000546276	D;D;D	0.94966	-3.57;-3.57;-3.57	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	D	0.97639	0.9226	M	0.91972	3.26	0.51233	D	0.999915	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.998;0.999	D	0.98419	1.0576	10	0.72032	D	0.01	-43.9093	13.5148	0.61535	1.0:0.0:0.0:0.0	.	1192;1238;1265	B7ZLE6;Q17RV5;D3DVK9	.;.;.	I	1265;1238;1192	ENSP00000289547:F1265I;ENSP00000370552:F1238I;ENSP00000438033:F1192I	ENSP00000289547:F1265I	F	-	1	0	NPC1L1	44522011	1.000000	0.71417	1.000000	0.80357	0.809000	0.45718	8.575000	0.90766	2.092000	0.63282	0.459000	0.35465	TTC	.	.		0.612	NPC1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251256.1	NM_013389		T	44555486	A	T	44555486	3	4	314	1	0	0	0	0	1	0	0	0	10580	72	3	4	294	4	NPC1L1	7	44555486	Missense_Mutation	SNP	A	TCGA-KR-A7K2-01A-12D-A33Q-10		44555486	114583177	31	44506										
PCLO	27445	hgsc.bcm.edu	37	chr7	82451998	82451998	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	gatttctcaatggtgggaacCtgcatgtctggtcacaaaag	11	8	3	0			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr7:82451998C>A	ENST00000333891.9	-	20	14941	c.14604G>T	c.(14602-14604)caG>caT	p.Q4868H	PCLO_ENST00000426442.2_5'UTR|PCLO_ENST00000423517.2_Missense_Mutation_p.Q4868H	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TGGTGGGAACCTGCATGTCTG	0.413																																					p.Q4868H		Atlas-SNP	.											.	PCLO	1506	.	0			c.G14604T						.						208	203	205					7																	82451998		1956	4170	6126	SO:0001583	missense	27445	exon20			GGGAACCTGCATG	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.14604G>T	chr7.hg19:g.82451998C>A	ENSP00000334319:p.Gln4868His	24.0	0.0		32.0	20.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	C	13.06	2.123340	0.37436	.	.	ENSG00000186472	ENST00000333891;ENST00000423517;ENST00000380195	T;T	0.18174	2.23;2.24	5.05	5.05	0.67936	.	.	.	.	.	T	0.32823	0.0842	L	0.29908	0.895	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.986;0.996	D;D;P;D	0.91635	0.999;0.999;0.814;0.986	T	0.10337	-1.0634	9	0.87932	D	0	.	18.7616	0.91853	0.0:1.0:0.0:0.0	.	4868;4868;289;356	Q9Y6V0-5;Q9Y6V0-6;Q9Y6V0-3;Q32P40	.;.;.;.	H	4868;4868;355	ENSP00000334319:Q4868H;ENSP00000388393:Q4868H	ENSP00000334319:Q4868H	Q	-	3	2	PCLO	82289934	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.304000	0.59104	2.500000	0.84329	0.655000	0.94253	CAG	.	.		0.413	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82451998	C	A	82451998	3	1	314	1	0	0	0	0	1	0	0	0	11592	680	24	3	865	3	PCLO	7	82451998	Missense_Mutation	SNP	C	TCGA-KR-A7K2-01A-12D-A33Q-10	37896512	82451998	76686665	32	44507										
MDFIC	29969	hgsc.bcm.edu	37	chr7	114619638	114619638	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	aaataggcaagataaagaacGgccacacaggtctgagcaat	10	8	1	3	rs548881845	byFrequency	TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr7:114619638G>C	ENST00000393486.1	+	4	885	c.295G>C	c.(295-297)Ggc>Cgc	p.G99R	MDFIC_ENST00000257724.3_Missense_Mutation_p.G208R	NM_001166345.1|NM_199072.4	NP_001159817.1|NP_951038.1			MyoD family inhibitor domain containing											breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	8						GATAAAGAACGGCCACACAGG	0.473																																					p.G208R		Atlas-SNP	.											.	MDFIC	30	.	0			c.G622C						.						85	81	83					7																	114619638		2203	4300	6503	SO:0001583	missense	29969	exon4			AAGAACGGCCACA	AF054589	CCDS34737.1, CCDS55155.1	7q31.1-q31.2	2006-01-11			ENSG00000135272	ENSG00000135272			28870	protein-coding gene	gene with protein product		614511				10671520	Standard	NM_199072		Approved	HIC	uc003vhf.3	Q9P1T7	OTTHUMG00000023647	ENST00000393486.1:c.295G>C	chr7.hg19:g.114619638G>C	ENSP00000377126:p.Gly99Arg	150.0	0.0		156.0	19.0	NM_199072		Missense_Mutation	SNP	ENST00000393486.1	hg19	CCDS55155.1	.	.	.	.	.	.	.	.	.	.	G	18.09	3.546299	0.65198	.	.	ENSG00000135272	ENST00000257724;ENST00000393486;ENST00000427207;ENST00000498196	.	.	.	5.98	3.14	0.36123	.	0.319263	0.28470	N	0.015223	T	0.67429	0.2892	M	0.77103	2.36	0.80722	D	1	D	0.54397	0.966	P	0.56474	0.799	T	0.67684	-0.5607	9	0.56958	D	0.05	0.0177	8.0155	0.30379	0.1349:0.0:0.7227:0.1424	.	99	Q9P1T7	MDFIC_HUMAN	R	208;99;85;44	.	ENSP00000257724:G208R	G	+	1	0	MDFIC	114406874	0.962000	0.33011	0.742000	0.31022	0.627000	0.37826	1.491000	0.35583	0.793000	0.33875	0.591000	0.81541	GGC	.	.		0.473	MDFIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059968.4	NM_199072		C	114619638	G	C	114619638	3	2	314	1	0	0	0	0	1	0	0	0	9414	1116	39	4	678	4	MDFIC	7	114619638	Missense_Mutation	SNP	G	TCGA-KR-A7K2-01A-12D-A33Q-10	32167640	114619638	44519025	33	44508										
PODXL	5420	hgsc.bcm.edu	37	chr7	131193749	131193751	+	In_Frame_Del	DEL	CTC	CTC	-													0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	aggttcaggacgagctgcttCtcactctgtgtctgtgtctc							TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr7:131193749_131193751delCTC	ENST00000378555.3	-	5	1307_1309	c.1060_1062delGAG	c.(1060-1062)gagdel	p.E354del	PODXL_ENST00000537928.1_Intron|PODXL_ENST00000541194.1_In_Frame_Del_p.E356del|PODXL_ENST00000322985.9_In_Frame_Del_p.E322del|PODXL_ENST00000465001.1_5'Flank			O00592	PODXL_HUMAN	podocalyxin-like	354					cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					CGAGCTGCTTCTCACTCTGTGTC	0.532																																					p.354_355del		Atlas-INDEL	.											.	PODXL	53	.	0			c.1061_1063del						.																																			SO:0001651	inframe_deletion	5420	exon5			.		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.1060_1062delGAG	chr7.hg19:g.131193749_131193751delCTC	ENSP00000367817:p.Glu354del	165.0	0.0		147.0	19.0	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	In_Frame_Del	DEL	ENST00000378555.3	hg19	CCDS34755.1																																																																																			.	.		0.532	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111		-	131193751	CTC	-	131193749	7	5	314	1	0	1	0	1	0	0	0	0	12189	912	32	0	634	0	PODXL	7	131193749	In_Frame_Del	DEL	CTC	TCGA-KR-A7K2-01A-12D-A33Q-10	16574111	131193749	27944914	34	44509	233	2								
PODXL	5420	hgsc.bcm.edu	37	chr7	131193753	131193756	+	Frame_Shift_Del	DEL	CTCT	CTCT	-													0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	tcaggacgagctgcttctcaCtctgtgtctgtgtctcaaga							TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	CTCT	CTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr7:131193753_131193756delCTCT	ENST00000378555.3	-	5	1302_1305	c.1055_1058delAGAG	c.(1054-1059)cagagtfs	p.QS352fs	PODXL_ENST00000537928.1_Intron|PODXL_ENST00000541194.1_Frame_Shift_Del_p.QS354fs|PODXL_ENST00000322985.9_Frame_Shift_Del_p.QS320fs|PODXL_ENST00000465001.1_5'Flank			O00592	PODXL_HUMAN	podocalyxin-like	352					cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					CTGCTTCTCACTCTGTGTCTGTGT	0.52																																					p.352_353del		Atlas-INDEL	.											.	PODXL	53	.	0			c.1056_1059del						.																																			SO:0001589	frameshift_variant	5420	exon5			.		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.1055_1058delAGAG	chr7.hg19:g.131193753_131193756delCTCT	ENSP00000367817:p.Gln352fs	164.0	0.0		145.0	18.0	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Frame_Shift_Del	DEL	ENST00000378555.3	hg19	CCDS34755.1																																																																																			.	.		0.52	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111		-	131193756	CTCT	-	131193753	7	5	314	1	0	1	0	1	0	0	0	0	12189	565	20	0	638	0	PODXL	7	131193753	Frame_Shift_Del	DEL	CTCT	TCGA-KR-A7K2-01A-12D-A33Q-10	4	131193753	27944910	35	44510	233	2								
ADAM28	10863	hgsc.bcm.edu	37	chr8	24157559	24157559	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	tataagacttcatccactgcAtaaaagagaggccaaagagc	8	9	1	3			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr8:24157559A>G	ENST00000265769.4	+	2	229	c.119A>G	c.(118-120)cAt>cGt	p.H40R	ADAM28_ENST00000437154.2_Missense_Mutation_p.H40R|RP11-624C23.1_ENST00000523578.1_RNA|RP11-624C23.1_ENST00000518988.1_RNA|ADAM28_ENST00000540823.1_5'UTR|RP11-624C23.1_ENST00000519689.1_RNA|ADAM28_ENST00000397649.3_5'UTR|RP11-624C23.1_ENST00000523700.1_RNA	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	40					spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(7)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		CATCCACTGCATAAAAGAGAG	0.343																																					p.H40R	NSCLC(193;488 2149 22258 34798 40734)	Atlas-SNP	.											.	ADAM28	100	.	0			c.A119G						.						98	103	101					8																	24157559		2203	4300	6503	SO:0001583	missense	10863	exon2			CACTGCATAAAAG	AJ242015	CCDS34865.1, CCDS47830.1	8p21.2	2005-11-29	2005-08-18		ENSG00000042980	ENSG00000042980		"ADAM metallopeptidase domain containing"	206	protein-coding gene	gene with protein product		606188	"a disintegrin and metalloproteinase domain 28"				Standard	XM_005273378		Approved	eMDCII, MDC-Lm, MDC-Ls, ADAM23	uc003xdy.3	Q9UKQ2	OTTHUMG00000163780	ENST00000265769.4:c.119A>G	chr8.hg19:g.24157559A>G	ENSP00000265769:p.His40Arg	28.0	0.0		23.0	17.0	NM_014265	B2RMV5|Q9Y339|Q9Y3S0	Missense_Mutation	SNP	ENST00000265769.4	hg19	CCDS34865.1	.	.	.	.	.	.	.	.	.	.	A	1.003	-0.690273	0.03303	.	.	ENSG00000042980	ENST00000265769;ENST00000437154	T;T	0.06142	3.34;3.34	4.31	1.8	0.24995	Peptidase M12B, propeptide (1);	.	.	.	.	T	0.03608	0.0103	N	0.13299	0.325	0.21897	N	0.999487	B;B	0.12013	0.001;0.005	B;B	0.15052	0.004;0.012	T	0.47935	-0.9078	9	0.19590	T	0.45	.	6.3711	0.21481	0.7939:0.0:0.2061:0.0	.	40;40	Q9UKQ2;Q9UKQ2-2	ADA28_HUMAN;.	R	40	ENSP00000265769:H40R;ENSP00000393699:H40R	ENSP00000265769:H40R	H	+	2	0	ADAM28	24213504	0.123000	0.22298	0.096000	0.21009	0.066000	0.16364	0.957000	0.29215	0.257000	0.21650	-0.736000	0.03550	CAT	.	.		0.343	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778		G	24157559	A	G	24157559	3	3	314	1	0	0	0	0	1	0	0	0	246	217	8	2	125	2	ADAM28	8	24157559	Missense_Mutation	SNP	A	TCGA-KR-A7K2-01A-12D-A33Q-10		24157559	122206463	36	44511										
CHD7	55636	hgsc.bcm.edu	37	chr8	61654307	61654307	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	cgtctccgcactcgcagtatCacacccctcccgttcctcag	6	20	3	0			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr8:61654307C>T	ENST00000423902.2	+	2	795	c.316C>T	c.(316-318)Cac>Tac	p.H106Y	CHD7_ENST00000524602.1_Missense_Mutation_p.H106Y|CHD7_ENST00000525508.1_Missense_Mutation_p.H106Y	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	106					adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			CTCGCAGTATCACACCCCTCC	0.547																																					p.H106Y		Atlas-SNP	.											.	CHD7	534	.	0			c.C316T						.						52	58	56					8																	61654307		2161	4250	6411	SO:0001583	missense	55636	exon2			CAGTATCACACCC	AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"CHARGE association"	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.316C>T	chr8.hg19:g.61654307C>T	ENSP00000392028:p.His106Tyr	82.0	0.0		119.0	29.0	NM_017780	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Missense_Mutation	SNP	ENST00000423902.2	hg19	CCDS47865.1	.	.	.	.	.	.	.	.	.	.	C	13.59	2.281219	0.40394	.	.	ENSG00000171316	ENST00000307121;ENST00000423902;ENST00000524602;ENST00000525508	T;T;T	0.52526	0.66;0.66;0.66	5.36	5.36	0.76844	.	0.000000	0.42294	D	0.000728	T	0.42404	0.1201	L	0.40543	1.245	0.47698	D	0.999493	D	0.53885	0.963	B	0.41036	0.346	T	0.29150	-1.0021	10	0.30854	T	0.27	-15.0176	19.0882	0.93215	0.0:1.0:0.0:0.0	.	106	Q9P2D1	CHD7_HUMAN	Y	106	ENSP00000392028:H106Y;ENSP00000437061:H106Y;ENSP00000436027:H106Y	ENSP00000307304:H106Y	H	+	1	0	CHD7	61816861	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.698000	0.61789	2.531000	0.85337	0.585000	0.79938	CAC	.	.		0.547	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762		T	61654307	C	T	61654307	3	4	314	1	0	0	0	0	1	0	0	0	3332	826	29	3	318	3	CHD7	8	61654307	Missense_Mutation	SNP	C	TCGA-KR-A7K2-01A-12D-A33Q-10	37496748	61654307	84709715	37	44512										
VPS13B	157680	hgsc.bcm.edu	37	chr8	100883103	100883103	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	ccaggctccaaacagccatgTcaaatatgtctggtaaaatt	7	10	2	0			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr8:100883103T>G	ENST00000358544.2	+	60	11669	c.11558T>G	c.(11557-11559)gTc>gGc	p.V3853G	VPS13B_ENST00000357162.2_Missense_Mutation_p.V3828G|VPS13B_ENST00000395996.1_3'UTR	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	3853					protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			AACAGCCATGTCAAATATGTC	0.438																																					p.V3853G	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											.	VPS13B	811	.	0			c.T11558G						.						77	74	75					8																	100883103		2203	4300	6503	SO:0001583	missense	157680	exon60			GCCATGTCAAATA	AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.11558T>G	chr8.hg19:g.100883103T>G	ENSP00000351346:p.Val3853Gly	176.0	0.0		345.0	73.0	NM_017890	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	hg19	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.961594	0.74016	.	.	ENSG00000132549	ENST00000357162;ENST00000358544	T;T	0.70749	-0.51;-0.51	5.73	5.73	0.89815	.	0.067596	0.64402	D	0.000012	T	0.66548	0.2800	L	0.32530	0.975	0.80722	D	1	P;D	0.61080	0.763;0.989	B;P	0.47299	0.387;0.543	T	0.67444	-0.5669	10	0.39692	T	0.17	.	16.0175	0.80455	0.0:0.0:0.0:1.0	.	3828;3853	Q7Z7G8-2;Q7Z7G8	.;VP13B_HUMAN	G	3828;3853	ENSP00000349685:V3828G;ENSP00000351346:V3853G	ENSP00000349685:V3828G	V	+	2	0	VPS13B	100952279	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.772000	0.68889	2.184000	0.69523	0.533000	0.62120	GTC	.	.		0.438	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		G	100883103	T	G	100883103	3	3	314	1	0	0	0	0	1	0	0	0	17205	1667	58	5	11986	5	VPS13B	8	100883103	Missense_Mutation	SNP	T	TCGA-KR-A7K2-01A-12D-A33Q-10	39228796	100883103	45480919	38	44513										
TMEM71	137835	hgsc.bcm.edu	37	chr8	133734323	133734323	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	gattaagcacacagcaagcaGgattgcctgaaagaagacct	10	9	0	3			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr8:133734323G>C	ENST00000356838.3	-	7	800	c.658C>G	c.(658-660)Ctg>Gtg	p.L220V	TMEM71_ENST00000377901.4_Missense_Mutation_p.L176V|TMEM71_ENST00000523829.1_Missense_Mutation_p.L239V	NM_144649.2	NP_653250.2	Q6P5X7	TMM71_HUMAN	transmembrane protein 71	239						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|skin(2)	16	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			ACAGCAAGCAGGATTGCCTGA	0.348																																					p.L220V		Atlas-SNP	.											.	TMEM71	55	.	0			c.C658G						.						119	116	117					8																	133734323		2203	4300	6503	SO:0001583	missense	137835	exon7			CAAGCAGGATTGC	AK057631	CCDS6366.1, CCDS47921.1	8q24.22	2005-09-02				ENSG00000165071			26572	protein-coding gene	gene with protein product						12477932	Standard	NM_144649		Approved	FLJ33069	uc003ytn.3	Q6P5X7		ENST00000356838.3:c.658C>G	chr8.hg19:g.133734323G>C	ENSP00000349296:p.Leu220Val	415.0	1.0		710.0	308.0	NM_144649	Q3KRC2|Q8WVZ4|Q96LX9	Missense_Mutation	SNP	ENST00000356838.3	hg19	CCDS6366.1	.	.	.	.	.	.	.	.	.	.	G	13.17	2.156402	0.38119	.	.	ENSG00000165071	ENST00000523829;ENST00000356838;ENST00000377901	.	.	.	5.72	1.63	0.23807	.	0.581878	0.15507	N	0.258724	T	0.51770	0.1694	L	0.55481	1.735	0.09310	N	1	D;D;P	0.89917	1.0;1.0;0.946	D;D;B	0.83275	0.996;0.996;0.41	T	0.30679	-0.9970	9	0.87932	D	0	-0.0331	3.7446	0.08542	0.0873:0.3059:0.4493:0.1575	.	239;176;220	Q6P5X7;Q6P5X7-3;Q6P5X7-2	TMM71_HUMAN;.;.	V	239;220;176	.	ENSP00000349296:L220V	L	-	1	2	TMEM71	133803505	0.171000	0.23029	0.053000	0.19242	0.729000	0.41735	0.530000	0.23036	0.840000	0.34995	0.650000	0.86243	CTG	.	.		0.348	TMEM71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379591.1	NM_144649		C	133734323	G	C	133734323	3	2	314	1	0	0	0	0	1	0	0	0	16215	991	35	4	188	4	TMEM71	8	133734323	Missense_Mutation	SNP	G	TCGA-KR-A7K2-01A-12D-A33Q-10	32851220	133734323	12629699	39	44514										
PSCA	8000	hgsc.bcm.edu	37	chr8	143763524	143763524	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	tgctccctgcactcggcctgCtgctctggggacccggccag	13	17	1	0			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr8:143763524C>T	ENST00000301258.4	+	3	402	c.319C>T	c.(319-321)Ctg>Ttg	p.L107L		NM_005672.4	NP_005663.2	O43653	PSCA_HUMAN	prostate stem cell antigen	116						anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(1)	2	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					ACTCGGCCTGCTGCTCTGGGG	0.697																																					p.L107L		Atlas-SNP	.											.	PSCA	9	.	0			c.C319T						.						21	24	23					8																	143763524		2121	4232	6353	SO:0001819	synonymous_variant	8000	exon3			GGCCTGCTGCTCT	AF043498	CCDS47925.1, CCDS47925.2	8q24.2	2004-02-03				ENSG00000167653			9500	protein-coding gene	gene with protein product		602470				9465086	Standard	NM_005672		Approved		uc022bcd.1	O43653		ENST00000301258.4:c.319C>T	chr8.hg19:g.143763524C>T		12.0	0.0		40.0	8.0	NM_005672	Q6UW92	Silent	SNP	ENST00000301258.4	hg19	CCDS47925.2																																																																																			.	.		0.697	PSCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367112.2	NM_005672		T	143763524	C	T	143763524	2	4	314	1	0	0	0	0	0	0	0	1	12657	796	28	3		3	PSCA	8	143763524	Silent	SNP	C	TCGA-KR-A7K2-01A-12D-A33Q-10	10029201	143763524	2600498	40	44515										
GSN	2934	hgsc.bcm.edu	37	chr9	124065340	124065340	+	Nonsense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	ttcaagtctggcctgaagtaCaaggtgggttgggccccacc	13	11	2	1			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr9:124065340C>G	ENST00000373818.4	+	3	570	c.501C>G	c.(499-501)taC>taG	p.Y167*	GSN_ENST00000449733.1_Nonsense_Mutation_p.Y116*|GSN_ENST00000412819.1_Nonsense_Mutation_p.Y116*|GSN_ENST00000373808.2_Nonsense_Mutation_p.Y116*|GSN_ENST00000373823.3_Nonsense_Mutation_p.Y116*|GSN_ENST00000436847.1_Nonsense_Mutation_p.Y127*|GSN_ENST00000341272.2_Nonsense_Mutation_p.Y116*|GSN_ENST00000545652.1_Nonsense_Mutation_p.Y124*|GSN_ENST00000394353.2_Nonsense_Mutation_p.Y127*	NM_000177.4|NM_001258029.1	NP_000168.1|NP_001244958.1	P06396	GELS_HUMAN	gelsolin	167	Actin-severing. {ECO:0000255}.|Polyphosphoinositide binding. {ECO:0000250}.				actin filament polymerization (GO:0030041)|actin filament severing (GO:0051014)|aging (GO:0007568)|apoptotic process (GO:0006915)|barbed-end actin filament capping (GO:0051016)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to cadmium ion (GO:0071276)|cilium morphogenesis (GO:0060271)|oligodendrocyte development (GO:0014003)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of cell adhesion (GO:0030155)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|tissue regeneration (GO:0042246)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)	21						GCCTGAAGTACAAGGTGGGTT	0.592																																					p.Y167X		Atlas-SNP	.											.	GSN	81	.	0			c.C501G						.						45	46	46					9																	124065340		2203	4300	6503	SO:0001587	stop_gained	2934	exon3			GAAGTACAAGGTG	X04412	CCDS6828.1, CCDS6829.1, CCDS48011.1, CCDS65118.1, CCDS75890.1, CCDS75891.1	9q33	2010-04-27	2010-04-27		ENSG00000148180	ENSG00000148180			4620	protein-coding gene	gene with protein product	"amyloidosis, Finnish type"	137350	"gelsolin (amyloidosis, Finnish type)"			1652889	Standard	NM_001127662		Approved	DKFZp313L0718	uc004blf.1	P06396	OTTHUMG00000020584	ENST00000373818.4:c.501C>G	chr9.hg19:g.124065340C>G	ENSP00000362924:p.Tyr167*	27.0	0.0		38.0	10.0	NM_000177	A2A418|A8MUD1|A8MYN7|B7Z373|B7Z5V1|F5H1A8|Q5T0I2|Q8WVV7	Nonsense_Mutation	SNP	ENST00000373818.4	hg19	CCDS6828.1	.	.	.	.	.	.	.	.	.	.	C	37	6.203764	0.97371	.	.	ENSG00000148180	ENST00000373823;ENST00000432226;ENST00000449773;ENST00000436847;ENST00000394353;ENST00000449733;ENST00000412819;ENST00000341272;ENST00000373808;ENST00000394352;ENST00000456109;ENST00000545652;ENST00000373818	.	.	.	5.91	4.02	0.46733	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-22.4785	10.3205	0.43762	0.0:0.8344:0.0:0.1656	.	.	.	.	X	116;116;127;127;127;116;116;116;116;100;90;124;167	.	ENSP00000340888:Y116X	Y	+	3	2	GSN	123105161	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.104000	0.57790	0.765000	0.33221	-0.150000	0.13652	TAC	.	.		0.592	GSN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053861.1	NM_000177		G	124065340	C	G	124065340	4	3	314	1	0	0	0	0	0	1	0	0	6834	489	17	4	539	4	GSN	9	124065340	Nonsense_Mutation	SNP	C	TCGA-KR-A7K2-01A-12D-A33Q-10		124065340	17148091	41	44516										
SLC39A12	221074	hgsc.bcm.edu	37	chr10	18289660	18289660	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	agcctgcataattttgcagaTggcctagccataggagcagc	11	10	0	1			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr10:18289660T>C	ENST00000377369.2	+	11	1938	c.1665T>C	c.(1663-1665)gaT>gaC	p.D555D	SLC39A12_ENST00000377371.3_Silent_p.D554D|SLC39A12-AS1_ENST00000439319.1_RNA|SLC39A12-AS1_ENST00000445287.1_RNA|SLC39A12_ENST00000539911.1_Silent_p.D421D|SLC39A12_ENST00000377374.4_Silent_p.D518D	NM_001145195.1|NM_001282733.1|NM_001282734.1	NP_001138667.1|NP_001269662.1|NP_001269663.1	Q504Y0	S39AC_HUMAN	solute carrier family 39 (zinc transporter), member 12	555					regulation of microtubule polymerization (GO:0031113)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)|zinc ion transmembrane import (GO:0071578)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	zinc ion transmembrane transporter activity (GO:0005385)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(5)|lung(38)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	60						ATTTTGCAGATGGCCTAGCCA	0.433																																					p.D555D		Atlas-SNP	.											.	SLC39A12	181	.	0			c.T1665C						.						159	139	146					10																	18289660		2203	4300	6503	SO:0001819	synonymous_variant	221074	exon11			TGCAGATGGCCTA		CCDS7124.1, CCDS44362.1, CCDS60493.1, CCDS60494.1	10p12.33	2013-05-22			ENSG00000148482	ENSG00000148482		"Solute carriers"	20860	protein-coding gene	gene with protein product		608734	"solute carrier family 39 (metal ion transporter), member 12"			12659941	Standard	NM_152725		Approved	FLJ30499	uc001ipo.2	Q504Y0	OTTHUMG00000017759	ENST00000377369.2:c.1665T>C	chr10.hg19:g.18289660T>C		78.0	0.0		62.0	32.0	NM_001145195	B7ZL35|C9JJL4|Q49AN8|Q4G0L3|Q5VWV8|Q5VWV9|Q6NZY5|Q96NN4	Silent	SNP	ENST00000377369.2	hg19	CCDS44362.1																																																																																			.	.		0.433	SLC39A12-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_152725		C	18289660	T	C	18289660	2	2	314	1	0	0	0	0	0	0	0	1	14630	1461	51	2		2	SLC39A12	10	18289660	Silent	SNP	T	TCGA-KR-A7K2-01A-12D-A33Q-10		18289660	117245087	42	44517										
FRMPD2	143162	hgsc.bcm.edu	37	chr10	49447719	49447719	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	tctggtgagctctgggtctcCgtgcttctttctgaaactaa	10	10	5	2			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr10:49447719C>A	ENST00000374201.3	-	7	1019	c.717G>T	c.(715-717)acG>acT	p.T239T	FRMPD2_ENST00000305531.3_Silent_p.T215T|FRMPD2_ENST00000407470.4_Silent_p.T208T	NM_001018071.3|NM_001042512.2	NP_001018081|NP_001035977.2	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2	239			T -> M (in dbSNP:rs55802136).		tight junction assembly (GO:0070830)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)	1-phosphatidylinositol binding (GO:0005545)			NS(2)|autonomic_ganglia(2)|breast(5)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(15)|lung(24)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	66				Kidney(211;0.201)		TCTGGGTCTCCGTGCTTCTTT	0.517																																					p.T239T		Atlas-SNP	.											.	FRMPD2	157	.	0			c.G717T						.						111	90	97					10																	49447719		2203	4300	6503	SO:0001819	synonymous_variant	143162	exon7			GGTCTCCGTGCTT	AK123038	CCDS31195.1	10q11	2010-10-13			ENSG00000170324	ENSG00000170324			28572	protein-coding gene	gene with protein product		613323	"PDZ domain containing 5C"	PDZD5C, PDZK5C			Standard	NM_001018071		Approved	MGC35285	uc001jdv.3	Q68DX3	OTTHUMG00000018171	ENST00000374201.3:c.717G>T	chr10.hg19:g.49447719C>A		49.0	0.0		45.0	21.0	NM_001018071	B7WNW0|B7ZML5|Q2VY07|Q6GMQ9|Q6ZN38|Q6ZWI2|Q8N5T9	Silent	SNP	ENST00000374201.3	hg19	CCDS31195.1																																																																																			.	.		0.517	FRMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047923.3	NM_152428		A	49447719	C	A	49447719	2	1	314	1	0	0	0	0	0	0	0	1	6066	639	23	1		1	FRMPD2	10	49447719	Silent	SNP	C	TCGA-KR-A7K2-01A-12D-A33Q-10	31158059	49447719	86087028	43	44518										
NOX4	50507	hgsc.bcm.edu	37	chr11	89069106	89069106	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	gtgcatgatatttttctccaAttatcttctgccaaaaagaa	5	8	3	2			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr11:89069106A>C	ENST00000263317.4	-	17	1761	c.1523T>G	c.(1522-1524)aTt>aGt	p.I508S	NOX4_ENST00000532825.1_Missense_Mutation_p.I444S|NOX4_ENST00000527956.1_Missense_Mutation_p.I484S|NOX4_ENST00000528341.1_Missense_Mutation_p.I483S|NOX4_ENST00000535633.1_Missense_Mutation_p.I484S|NOX4_ENST00000413594.2_Missense_Mutation_p.I529S|NOX4_ENST00000527626.1_Missense_Mutation_p.I321S|NOX4_ENST00000542487.1_Missense_Mutation_p.I484S|NOX4_ENST00000525196.1_Missense_Mutation_p.I272S|NOX4_ENST00000375979.3_Missense_Mutation_p.I201S|NOX4_ENST00000343727.5_Missense_Mutation_p.I484S|NOX4_ENST00000534731.1_Missense_Mutation_p.I468S|NOX4_ENST00000424319.1_Missense_Mutation_p.I484S|NOX4_ENST00000531342.1_Missense_Mutation_p.I161S			Q9NPH5	NOX4_HUMAN	NADPH oxidase 4	508	Mediates interaction with TLR4.				bone resorption (GO:0045453)|cardiac muscle cell differentiation (GO:0055007)|cell aging (GO:0007569)|cell morphogenesis (GO:0000902)|cellular response to cAMP (GO:0071320)|cellular response to gamma radiation (GO:0071480)|cellular response to glucose stimulus (GO:0071333)|cellular response to transforming growth factor beta stimulus (GO:0071560)|homocysteine metabolic process (GO:0050667)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|oxidation-reduction process (GO:0055114)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of stress fiber assembly (GO:0051496)|reactive oxygen species metabolic process (GO:0072593)|response to hypoxia (GO:0001666)|superoxide anion generation (GO:0042554)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|modified amino acid binding (GO:0072341)|NAD(P)H oxidase activity (GO:0016174)|nucleotide binding (GO:0000166)|oxygen sensor activity (GO:0019826)|superoxide-generating NADPH oxidase activity (GO:0016175)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(20)|ovary(2)|prostate(3)|skin(2)	44		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)				TTTTTCTCCAATTATCTTCTG	0.363																																					p.I508S		Atlas-SNP	.											.	NOX4	101	.	0			c.T1523G						.						61	62	62					11																	89069106		2201	4297	6498	SO:0001583	missense	50507	exon17			TCTCCAATTATCT	AF254621	CCDS8285.1, CCDS44695.1, CCDS44696.1, CCDS73361.1, CCDS73362.1	11q14.2-q21	2008-02-05			ENSG00000086991	ENSG00000086991			7891	protein-coding gene	gene with protein product		605261					Standard	NM_001143837		Approved	KOX-1, KOX	uc001pct.3	Q9NPH5	OTTHUMG00000167298	ENST00000263317.4:c.1523T>G	chr11.hg19:g.89069106A>C	ENSP00000263317:p.Ile508Ser	196.0	0.0		219.0	116.0	NM_016931	A8K715|B7Z520|E7EMD7|Q5K3R4|Q5K3R5|Q5K3R6|Q5K3R8|Q7Z7G3|Q86V92	Missense_Mutation	SNP	ENST00000263317.4	hg19	CCDS8285.1	.	.	.	.	.	.	.	.	.	.	A	9.882	1.201756	0.22121	.	.	ENSG00000086991	ENST00000424319;ENST00000535633;ENST00000343727;ENST00000534731;ENST00000525196;ENST00000263317;ENST00000532825;ENST00000527956;ENST00000542487;ENST00000527626;ENST00000528341;ENST00000413594;ENST00000531342;ENST00000375979	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.93859	-3.27;-3.27;-3.27;-3.27;-3.27;-3.27;-3.27;-3.27;-3.27;-3.3;-3.27;-3.27;-3.27;-3.27	4.33	4.33	0.51752	Ferric reductase, NAD binding (1);	0.420567	0.26421	N	0.024474	D	0.87038	0.6078	N	0.12853	0.265	0.46542	D	0.999093	B;B;B;B;B;B;B;B	0.33448	0.036;0.277;0.412;0.321;0.05;0.023;0.2;0.014	B;B;B;B;B;B;B;B	0.38921	0.03;0.164;0.164;0.285;0.047;0.006;0.069;0.065	D	0.84513	0.0623	9	.	.	.	-12.5691	13.8139	0.63278	1.0:0.0:0.0:0.0	.	444;321;483;272;161;201;468;508	E9PMY6;E9PR43;E9PPP2;E9PI95;Q9NPH5-3;Q9NPH5-4;Q9NPH5-6;Q9NPH5	.;.;.;.;.;.;.;NOX4_HUMAN	S	484;484;484;468;272;508;444;484;484;321;483;529;161;201	ENSP00000412446:I484S;ENSP00000440172:I484S;ENSP00000344747:I484S;ENSP00000436892:I468S;ENSP00000436716:I272S;ENSP00000263317:I508S;ENSP00000434924:I444S;ENSP00000433797:I484S;ENSP00000439373:I484S;ENSP00000436093:I321S;ENSP00000436970:I483S;ENSP00000405705:I529S;ENSP00000435039:I161S;ENSP00000365146:I201S	.	I	-	2	0	NOX4	88708754	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.663000	0.61532	1.729000	0.51567	0.460000	0.39030	ATT	.	.		0.363	NOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394054.1	NM_016931		C	89069106	A	C	89069106	3	2	314	1	0	0	0	0	1	0	0	0	10567	101	4	5	221	5	NOX4	11	89069106	Missense_Mutation	SNP	A	TCGA-KR-A7K2-01A-12D-A33Q-10		89069106	45937410	44	44519										
GNPNAT1	64841	hgsc.bcm.edu	37	chr14	53245074	53245074	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	tagttttcttcagatacagtAtatccaaactttttatagaa	4	6	2	2			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr14:53245074A>G	ENST00000216410.3	-	6	697	c.510T>C	c.(508-510)taT>taC	p.Y170Y	GNPNAT1_ENST00000554230.1_Silent_p.Y99Y|RP11-589M4.1_ENST00000555969.1_RNA|RP11-589M4.1_ENST00000555689.1_RNA|GNPNAT1_ENST00000554421.1_5'Flank	NM_198066.3	NP_932332.1	Q96EK6	GNA1_HUMAN	glucosamine-phosphate N-acetyltransferase 1	170	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|glucosamine metabolic process (GO:0006041)|liver development (GO:0001889)|N-acetylglucosamine metabolic process (GO:0006044)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine biosynthetic process (GO:0006048)	cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|membrane (GO:0016020)	glucosamine 6-phosphate N-acetyltransferase activity (GO:0004343)|monosaccharide binding (GO:0048029)			liver(1)|lung(1)|prostate(1)|skin(1)	4	Breast(41;0.176)					CAGATACAGTATATCCAAACT	0.343																																					p.Y170Y		Atlas-SNP	.											.	GNPNAT1	14	.	0			c.T510C						.						53	55	54					14																	53245074		2203	4295	6498	SO:0001819	synonymous_variant	64841	exon6			TACAGTATATCCA	AK001469	CCDS9712.1	14q22.1	2011-11-16			ENSG00000100522	ENSG00000100522	2.3.1.4		19980	protein-coding gene	gene with protein product							Standard	NM_198066		Approved	Gpnat1, FLJ10607	uc001xab.3	Q96EK6	OTTHUMG00000152334	ENST00000216410.3:c.510T>C	chr14.hg19:g.53245074A>G		167.0	0.0		179.0	10.0	NM_198066		Silent	SNP	ENST00000216410.3	hg19	CCDS9712.1																																																																																			.	.		0.343	GNPNAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276898.1			G	53245074	A	G	53245074	2	3	314	1	0	0	0	0	0	0	0	1	6552	456	16	2		2	GNPNAT1	14	53245074	Silent	SNP	A	TCGA-KR-A7K2-01A-12D-A33Q-10		53245074	54104466	45	44520										
CATSPER2	117155	hgsc.bcm.edu	37	chr15	43924421	43924421	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	aaactcttgtaacttcttacGttcctctaggttatactgaa	5	9	3	1	rs148790135		TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr15:43924421G>T	ENST00000321596.5	-	12	1736	c.1537C>A	c.(1537-1539)Cgt>Agt	p.R513S	CATSPER2_ENST00000354127.4_Missense_Mutation_p.R511S|STRC_ENST00000541030.1_Intron|CATSPER2_ENST00000381761.1_Missense_Mutation_p.R517S|CATSPER2_ENST00000396879.1_Missense_Mutation_p.R511S|CATSPER2_ENST00000355438.2_3'UTR			Q96P56	CTSR2_HUMAN	cation channel, sperm associated 2	513					calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	22		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		AACTTCTTACGTTCCTCTAGG	0.453																																					p.R513S		Atlas-SNP	.											.	CATSPER2	49	.	0			c.C1537A						.						93	86	88					15																	43924421		2199	4297	6496	SO:0001583	missense	117155	exon12			TCTTACGTTCCTC	AF411817	CCDS10099.1, CCDS32216.1, CCDS73714.1	15q15.3	2011-07-05			ENSG00000166762	ENSG00000166762		"Voltage-gated ion channels / Cation channels, sperm associated"	18810	protein-coding gene	gene with protein product		607249				11675491, 16382101	Standard	NM_172095		Approved		uc001zsh.3	Q96P56	OTTHUMG00000059902	ENST00000321596.5:c.1537C>A	chr15.hg19:g.43924421G>T	ENSP00000321463:p.Arg513Ser	80.0	0.0		59.0	35.0	NM_172095	Q8NHT9|Q96P54|Q96P55	Missense_Mutation	SNP	ENST00000321596.5	hg19	CCDS10099.1	.	.	.	.	.	.	.	.	.	.	G	18.53	3.643235	0.67244	.	.	ENSG00000166762	ENST00000396879;ENST00000299989;ENST00000381761;ENST00000321596;ENST00000354127	D;D;D;D	0.99060	-5.35;-5.38;-5.32;-5.35	4.43	3.51	0.40186	.	0.000000	0.47093	D	0.000246	D	0.98972	0.9650	M	0.77616	2.38	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.99572	1.0971	10	0.87932	D	0	.	8.2994	0.32006	0.1087:0.0:0.8913:0.0	.	517;513	F8W9H2;Q96P56	.;CTSR2_HUMAN	S	511;513;517;513;511	ENSP00000380088:R511S;ENSP00000371180:R517S;ENSP00000321463:R513S;ENSP00000339137:R511S	ENSP00000299989:R513S	R	-	1	0	CATSPER2	41711713	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.973000	0.56845	1.210000	0.43336	0.644000	0.83932	CGT	.	G|1.000;A|0.000		0.453	CATSPER2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133151.2	NM_054020		T	43924421	G	T	43924421	3	4	314	1	0	0	0	0	1	0	0	0	2690	1145	40	1	63	1	CATSPER2	15	43924421	Missense_Mutation	SNP	G	TCGA-KR-A7K2-01A-12D-A33Q-10		43924421	58606971	46	44521										
ABCC1	4363	hgsc.bcm.edu	37	chr16	16139804	16139804	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	accctcgtgctgcaccagtaCttccacatctgcttcgtcag	7	16	2	0			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr16:16139804C>T	ENST00000399410.3	+	9	1327	c.1152C>T	c.(1150-1152)taC>taT	p.Y384Y	ABCC1_ENST00000399408.2_Silent_p.Y384Y|ABCC1_ENST00000345148.5_Silent_p.Y384Y|ABCC1_ENST00000346370.5_Silent_p.Y384Y|ABCC1_ENST00000351154.5_Silent_p.Y384Y|ABCC1_ENST00000349029.5_Silent_p.Y384Y	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	384	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				arachidonic acid metabolic process (GO:0019369)|ATP catabolic process (GO:0006200)|cobalamin metabolic process (GO:0009235)|leukotriene metabolic process (GO:0006691)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(5)|prostate(1)|skin(3)	56					Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	TGCACCAGTACTTCCACATCT	0.577											OREG0023639	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y384Y		Atlas-SNP	.											.	ABCC1	156	.	0			c.C1152T						.						77	79	79					16																	16139804		2124	4240	6364	SO:0001819	synonymous_variant	4363	exon9			CCAGTACTTCCAC	L05628	CCDS42122.1	16p13.1	2012-03-14			ENSG00000103222	ENSG00000103222		"ATP binding cassette transporters / subfamily C"	51	protein-coding gene	gene with protein product		158343	"multidrug resistance associated protein 1"	MRP, MRP1		8098549, 1360704	Standard	NM_004996		Approved	GS-X	uc010bvi.3	P33527	OTTHUMG00000048267	ENST00000399410.3:c.1152C>T	chr16.hg19:g.16139804C>T		86.0	0.0	708	101.0	12.0	NM_004996	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Silent	SNP	ENST00000399410.3	hg19	CCDS42122.1																																																																																			.	.		0.577	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996		T	16139804	C	T	16139804	2	4	314	1	0	0	0	0	0	0	0	1	49	576	20	3		3	ABCC1	16	16139804	Silent	SNP	C	TCGA-KR-A7K2-01A-12D-A33Q-10		16139804	74214949	47	44522										
MLKL	197259	hgsc.bcm.edu	37	chr16	74708937	74708937	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	agctctgaagggcagtcttcAcccagtggctcctgctgccg	12	14	3	1			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr16:74708937A>C	ENST00000308807.7	-	10	1765	c.1302T>G	c.(1300-1302)ggT>ggG	p.G434G	MLKL_ENST00000306247.7_Silent_p.G226G	NM_152649.2	NP_689862.1			mixed lineage kinase domain-like											breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(6)|skin(1)|stomach(2)	19						GGCAGTCTTCACCCAGTGGCT	0.547																																					p.G434G		Atlas-SNP	.											.	MLKL	51	.	0			c.T1302G						.						50	52	51					16																	74708937		2198	4300	6498	SO:0001819	synonymous_variant	197259	exon10			GTCTTCACCCAGT	AK091708	CCDS32487.1, CCDS45528.1	16q22.3	2008-02-05				ENSG00000168404			26617	protein-coding gene	gene with protein product		615153				12477932	Standard	NM_152649		Approved	FLJ34389	uc002fdb.2	Q8NB16		ENST00000308807.7:c.1302T>G	chr16.hg19:g.74708937A>C		92.0	0.0		128.0	53.0	NM_152649		Silent	SNP	ENST00000308807.7	hg19	CCDS32487.1																																																																																			.	.		0.547	MLKL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436403.3	NM_152649		C	74708937	A	C	74708937	2	2	314	1	0	0	0	0	0	0	0	1	9628	146	6	5		5	MLKL	16	74708937	Silent	SNP	A	TCGA-KR-A7K2-01A-12D-A33Q-10	58569133	74708937	15645816	48	44523										
MNT	4335	hgsc.bcm.edu	37	chr17	2290484	2290484	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	gcacagtgatgtgcccaatgGggggtgtggcaggcgccagt	18	9	0	1			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr17:2290484G>T	ENST00000174618.4	-	6	1865	c.1460C>A	c.(1459-1461)cCc>cAc	p.P487H	MNT_ENST00000575374.1_5'Flank|RP1-59D14.1_ENST00000571775.1_RNA	NM_020310.2	NP_064706.1	Q99583	MNT_HUMAN	MAX network transcriptional repressor	487					cell aging (GO:0007569)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of cell cycle (GO:0051726)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			endometrium(4)|large_intestine(5)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	12				Colorectal(2;1.37e-05)|READ - Rectum adenocarcinoma(2;8.68e-05)		GTGCCCAATGGGGGGTGTGGC	0.682																																					p.P487H		Atlas-SNP	.											.	MNT	35	.	0			c.C1460A						.						23	25	24					17																	2290484		2201	4297	6498	SO:0001583	missense	4335	exon6			CCAATGGGGGGTG	Y13444	CCDS11018.1	17p13.3	2013-11-15	2013-11-15		ENSG00000070444	ENSG00000070444		"MAX dimerization proteins", "Basic helix-loop-helix proteins"	7188	protein-coding gene	gene with protein product	"myc antagonist", "Max-interacting protein"	603039	"MAX binding protein", "MNT, MAX dimerization protein"			9598315	Standard	NM_020310		Approved	ROX, MXD6, MAD6, bHLHd3	uc002fur.3	Q99583	OTTHUMG00000090603	ENST00000174618.4:c.1460C>A	chr17.hg19:g.2290484G>T	ENSP00000174618:p.Pro487His	37.0	0.0		32.0	11.0	NM_020310	A8K6D1|D3DTI7|Q1ED38	Missense_Mutation	SNP	ENST00000174618.4	hg19	CCDS11018.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.329680	0.81690	.	.	ENSG00000070444	ENST00000174618;ENST00000404961	D	0.87334	-2.24	4.91	4.91	0.64330	.	0.182095	0.38005	N	0.001842	D	0.87313	0.6146	N	0.24115	0.695	0.53688	D	0.99997	D	0.69078	0.997	P	0.58013	0.831	D	0.89619	0.3847	10	0.87932	D	0	-12.3015	17.0679	0.86564	0.0:0.0:1.0:0.0	.	487	Q99583	MNT_HUMAN	H	487	ENSP00000174618:P487H	ENSP00000174618:P487H	P	-	2	0	MNT	2237234	1.000000	0.71417	0.998000	0.56505	0.910000	0.53928	7.435000	0.80391	2.274000	0.75844	0.591000	0.81541	CCC	.	.		0.682	MNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207158.1	NM_020310		T	2290484	G	T	2290484	3	4	314	1	0	0	0	0	1	0	0	0	9687	1232	43	3	292	3	MNT	17	2290484	Missense_Mutation	SNP	G	TCGA-KR-A7K2-01A-12D-A33Q-10		2290484	78904726	49	44524										
KRTAP9-2	83899	hgsc.bcm.edu	37	chr17	39383271	39383271	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	ctgcagaagaacctgctactAccccacgactgtctgcctgc	8	16	1	2			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr17:39383271A>G	ENST00000377721.3	+	1	372	c.365A>G	c.(364-366)tAc>tGc	p.Y122C	KRTAP9-2_ENST00000455970.2_Missense_Mutation_p.Y106C	NM_031961.2	NP_114167.2	Q9BYQ4	KRA92_HUMAN	keratin associated protein 9-2	122	17 X 5 AA repeats of C-C-[RQVSGE]-[SPTQ]- [TASP].					keratin filament (GO:0045095)				large_intestine(1)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			ACCTGCTACTACCCCACGACT	0.627																																					p.Y122C		Atlas-SNP	.											.	KRTAP9-2	24	.	0			c.A365G						.						162	155	157					17																	39383271		2203	4300	6503	SO:0001583	missense	83899	exon1			GCTACTACCCCAC	AJ406946	CCDS32651.1	17q21.2	2013-06-25			ENSG00000239886	ENSG00000239886		"Keratin associated proteins"	16926	protein-coding gene	gene with protein product						11279113	Standard	NM_031961		Approved	KAP9.2	uc002hwf.3	Q9BYQ4	OTTHUMG00000133609	ENST00000377721.3:c.365A>G	chr17.hg19:g.39383271A>G	ENSP00000366950:p.Tyr122Cys	140.0	0.0		131.0	70.0	NM_031961	Q17RK8|Q2TB15|Q6ISF6	Missense_Mutation	SNP	ENST00000377721.3	hg19	CCDS32651.1	.	.	.	.	.	.	.	.	.	.	.	11.10	1.539129	0.27475	.	.	ENSG00000239886	ENST00000377721;ENST00000455970	T;T	0.01335	5.0;5.0	2.68	0.349	0.16032	.	.	.	.	.	T	0.00845	0.0028	N	0.08118	0	0.09310	N	1	B	0.16166	0.016	B	0.12156	0.007	T	0.48281	-0.9049	9	0.42905	T	0.14	.	2.2922	0.04141	0.5096:0.0:0.27:0.2204	.	122	Q9BYQ4	KRA92_HUMAN	C	122;106	ENSP00000366950:Y122C;ENSP00000398325:Y106C	ENSP00000366950:Y122C	Y	+	2	0	KRTAP9-2	36636797	0.000000	0.05858	0.547000	0.28179	0.130000	0.20726	0.009000	0.13219	0.033000	0.15463	0.451000	0.29950	TAC	.	.		0.627	KRTAP9-2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257717.1			G	39383271	A	G	39383271	3	3	314	1	0	0	0	0	1	0	0	0	8582	391	14	2	367	2	KRTAP9-2	17	39383271	Missense_Mutation	SNP	A	TCGA-KR-A7K2-01A-12D-A33Q-10	37092787	39383271	41811939	50	44525										
PTPRM	5797	hgsc.bcm.edu	37	chr18	8143692	8143692	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	aacccgagaaacagacagacCatacagttaaaattgctgga	8	9	0	3			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr18:8143692C>T	ENST00000332175.8	+	14	3252	c.2215C>T	c.(2215-2217)Cat>Tat	p.H739Y	PTPRM_ENST00000444013.1_Missense_Mutation_p.H526Y|PTPRM_ENST00000580170.1_Missense_Mutation_p.H739Y|PTPRM_ENST00000400060.4_Missense_Mutation_p.H739Y|PTPRM_ENST00000400053.4_Missense_Mutation_p.H677Y	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	739					homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				ACAGACAGACCATACAGTTAA	0.443																																					p.H739Y		Atlas-SNP	.											.	PTPRM	185	.	0			c.C2215T						.						151	148	149					18																	8143692		2203	4300	6503	SO:0001583	missense	5797	exon14			ACAGACCATACAG	X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.2215C>T	chr18.hg19:g.8143692C>T	ENSP00000331418:p.His739Tyr	68.0	0.0		81.0	22.0	NM_001105244	A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	ENST00000332175.8	hg19	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.982410	0.93044	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053;ENST00000444013	T;T;T;T	0.46819	1.18;1.19;1.0;0.86	5.92	5.92	0.95590	.	0.049790	0.85682	D	0.000000	T	0.65291	0.2677	L	0.51422	1.61	0.58432	D	0.999997	P;D;D	0.57899	0.754;0.981;0.981	B;D;D	0.67900	0.424;0.954;0.954	T	0.63019	-0.6730	10	0.56958	D	0.05	.	20.3206	0.98668	0.0:1.0:0.0:0.0	.	526;739;739	E7EVX9;A7MBN1;P28827	.;.;PTPRM_HUMAN	Y	739;739;677;526	ENSP00000331418:H739Y;ENSP00000382933:H739Y;ENSP00000382927:H677Y;ENSP00000387608:H526Y	ENSP00000331418:H739Y	H	+	1	0	PTPRM	8133692	1.000000	0.71417	0.997000	0.53966	0.964000	0.63967	7.478000	0.81082	2.809000	0.96659	0.655000	0.94253	CAT	.	.		0.443	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			T	8143692	C	T	8143692	3	4	314	1	0	0	0	0	1	0	0	0	12821	594	21	3	2269	3	PTPRM	18	8143692	Missense_Mutation	SNP	C	TCGA-KR-A7K2-01A-12D-A33Q-10		8143692	69933556	51	44526										
DENND1C	79958	hgsc.bcm.edu	37	chr19	6472968	6472968	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	aggtgccccaggcttctgggCcaagaagacttcctcactga	11	13	2	3			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr19:6472968C>G	ENST00000381480.2	-	15	1202	c.1090G>C	c.(1090-1092)Gcc>Ccc	p.A364P	DENND1C_ENST00000543576.1_Missense_Mutation_p.A320P	NM_024898.2	NP_079174.2	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	364	dDENN. {ECO:0000255|PROSITE- ProRule:PRU00306}.				positive regulation of Rab GTPase activity (GO:0032851)	cytoplasmic vesicle (GO:0031410)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(3)|kidney(3)|large_intestine(1)|lung(3)	10						GGCTTCTGGGCCAAGAAGACT	0.612																																					p.A364P		Atlas-SNP	.											.	DENND1C	93	.	0			c.G1090C						.						26	30	29					19																	6472968		1934	4130	6064	SO:0001583	missense	79958	exon15			TCTGGGCCAAGAA	AL713770	CCDS45938.1	19p13.3	2014-02-06	2005-08-17	2005-08-17	ENSG00000205744	ENSG00000205744		"DENN/MADD domain containing"	26225	protein-coding gene	gene with protein product		613634	"family with sequence similarity 31, member C"	FAM31C		12477932	Standard	XM_005259646		Approved	FLJ22757	uc002mfe.3	Q8IV53	OTTHUMG00000180853	ENST00000381480.2:c.1090G>C	chr19.hg19:g.6472968C>G	ENSP00000370889:p.Ala364Pro	29.0	0.0		35.0	6.0	NM_024898	B4E051|D3PFD4|Q8NDB1|Q9H5Z2	Missense_Mutation	SNP	ENST00000381480.2	hg19	CCDS45938.1	.	.	.	.	.	.	.	.	.	.	c	16.87	3.241085	0.58995	.	.	ENSG00000205744	ENST00000381480;ENST00000543576	T;T	0.44881	0.91;0.91	4.57	3.51	0.40186	dDENN (3);	0.575922	0.18100	N	0.151725	T	0.42988	0.1227	L	0.40543	1.245	0.22873	N	0.998626	P	0.41041	0.736	P	0.49451	0.611	T	0.23655	-1.0182	10	0.54805	T	0.06	-10.532	8.8932	0.35446	0.0:0.8922:0.0:0.1078	.	364	Q8IV53	DEN1C_HUMAN	P	364;320	ENSP00000370889:A364P;ENSP00000437805:A320P	ENSP00000370889:A364P	A	-	1	0	DENND1C	6423968	0.946000	0.32159	0.997000	0.53966	0.981000	0.71138	0.867000	0.27968	0.902000	0.36520	0.457000	0.33378	GCC	.	.		0.612	DENND1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453332.2	NM_024898		G	6472968	C	G	6472968	3	3	314	1	0	0	0	0	1	0	0	0	4430	739	26	4	1351	4	DENND1C	19	6472968	Missense_Mutation	SNP	C	TCGA-KR-A7K2-01A-12D-A33Q-10		6472968	52656015	52	44527										
ZNF792	126375	hgsc.bcm.edu	37	chr19	35449077	35449077	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	cacattcgctgcattcgtaaGgcctgtctggtttgtgaact	10	10	1	1			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr19:35449077G>A	ENST00000404801.1	-	4	2068	c.1682C>T	c.(1681-1683)cCt>cTt	p.P561L	ZNF792_ENST00000605484.1_Missense_Mutation_p.P494L	NM_175872.4	NP_787068.3	Q3KQV3	ZN792_HUMAN	zinc finger protein 792	561					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(5)	12	all_lung(56;4.18e-08)|Lung NSC(56;6.62e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			GCATTCGTAAGGCCTGTCTGG	0.522																																					p.P561L	GBM(1;7 183 21053 22581 22847)	Atlas-SNP	.											.	ZNF792	46	.	0			c.C1682T						.						123	94	104					19																	35449077		2203	4300	6503	SO:0001583	missense	126375	exon4			TCGTAAGGCCTGT	AK095770	CCDS12440.2	19q13.11	2013-01-08			ENSG00000180884	ENSG00000180884		"Zinc fingers, C2H2-type", "-"	24751	protein-coding gene	gene with protein product						8889548	Standard	NM_175872		Approved	FLJ38451	uc002nxh.1	Q3KQV3	OTTHUMG00000150339	ENST00000404801.1:c.1682C>T	chr19.hg19:g.35449077G>A	ENSP00000385099:p.Pro561Leu	148.0	0.0		173.0	75.0	NM_175872	B4E333|Q495L1|Q495L3|Q8N932	Missense_Mutation	SNP	ENST00000404801.1	hg19	CCDS12440.2	.	.	.	.	.	.	.	.	.	.	g	9.146	1.015163	0.19355	.	.	ENSG00000180884	ENST00000404801;ENST00000379189	T	0.17054	2.3	2.81	1.78	0.24846	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.16085	0.0387	L	0.56769	1.78	0.09310	N	1	B	0.24721	0.11	B	0.23716	0.048	T	0.27606	-1.0069	9	0.72032	D	0.01	.	4.1938	0.10433	0.1364:0.2417:0.6219:0.0	.	561	Q3KQV3	ZN792_HUMAN	L	561;321	ENSP00000385099:P561L	ENSP00000368487:P321L	P	-	2	0	ZNF792	40140917	1.000000	0.71417	0.001000	0.08648	0.219000	0.24729	3.738000	0.55067	0.768000	0.33290	-0.253000	0.11424	CCT	.	.		0.522	ZNF792-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317673.1	NM_175872		A	35449077	G	A	35449077	3	1	314	1	0	0	0	0	1	0	0	0	18179	1000	35	3	220	3	ZNF792	19	35449077	Missense_Mutation	SNP	G	TCGA-KR-A7K2-01A-12D-A33Q-10	28976109	35449077	23679906	53	44528										
PRPF6	57473	hgsc.bcm.edu	37	chr20	62659867	62659867	+	Intron	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	ctggagtaccgtgcggggctGaagaacatcgcaaatacact	12	10	0	2			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr20:62659867G>A	ENST00000450537.1	-	1	56				ZNF512B_ENST00000217130.3_Intron|PRPF6_ENST00000535781.1_Silent_p.L752L			Q96KM6	Z512B_HUMAN	zinc finger protein 512B						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(4)|skin(1)	33	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					GTGCGGGGCTGAAGAACATCG	0.632																																					p.L792L		Atlas-SNP	.											.	PRPF6	88	.	0			c.G2376A						.						75	71	73					20																	62659867		2203	4300	6503	SO:0001627	intron_variant	24148	exon18			GGGGCTGAAGAAC	AB033022	CCDS13548.1	20q13.33	2011-02-09			ENSG00000196700	ENSG00000196700			29212	protein-coding gene	gene with protein product						10574462	Standard	NM_020713		Approved	GM632, MGC149845, MGC149846	uc002yhl.2	Q96KM6	OTTHUMG00000033008	ENST00000450537.1:c.4+20190C>T	chr20.hg19:g.62659867G>A		44.0	0.0		40.0	14.0	NM_012469	Q08AK9|Q9ULM4	Silent	SNP	ENST00000450537.1	hg19	CCDS13548.1																																																																																			.	.		0.632	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713		A	62659867	G	A	62659867	1	1	314	0	1	0	0	0	0	0	0	0	12586	1277	45	3		3	PRPF6	20	62659867	Intron	SNP	G	TCGA-KR-A7K2-01A-12D-A33Q-10		62659867	365653	54	44529										
MORC3	23515	hgsc.bcm.edu	37	chr21	37736428	37736428	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	gtttcggccaactgctctttCaactccaagcttttcttctc	5	14	4	0			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr21:37736428C>A	ENST00000400485.1	+	14	1566	c.1490C>A	c.(1489-1491)tCa>tAa	p.S497*	MORC3_ENST00000487909.1_3'UTR|AP000692.9_ENST00000397184.2_RNA	NM_015358.2	NP_056173.1	Q14149	MORC3_HUMAN	MORC family CW-type zinc finger 3	497					cell aging (GO:0007569)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of fibroblast proliferation (GO:0048147)|peptidyl-serine phosphorylation (GO:0018105)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)	PML body (GO:0016605)	zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	35						ACTGCTCTTTCAACTCCAAGC	0.378																																					p.S497X		Atlas-SNP	.											.	MORC3	78	.	0			c.C1490A						.						126	114	118					21																	37736428		1857	4089	5946	SO:0001587	stop_gained	23515	exon14			CTCTTTCAACTCC	AK025327	CCDS42924.1	21q22.13	2005-06-15	2005-06-15	2005-06-15	ENSG00000159256	ENSG00000159256			23572	protein-coding gene	gene with protein product		610078	"zinc finger, CW-type with coiled-coil domain 3", "zinc finger, CW type with coiled-coil domain 3"	ZCWCC3		14607086	Standard	NM_015358		Approved	ZCW5, NXP2, KIAA0136	uc002yvi.3	Q14149	OTTHUMG00000086620	ENST00000400485.1:c.1490C>A	chr21.hg19:g.37736428C>A	ENSP00000383333:p.Ser497*	82.0	0.0		84.0	32.0	NM_015358	A8KA92|Q9UEZ2	Nonsense_Mutation	SNP	ENST00000400485.1	hg19	CCDS42924.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.951012	0.73787	.	.	ENSG00000159256	ENST00000400485	.	.	.	5.24	3.42	0.39159	.	1.062980	0.07374	N	0.886261	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06494	T	0.89	-0.8832	9.18	0.37136	0.0:0.8287:0.0:0.1713	.	.	.	.	X	497	.	ENSP00000383333:S497X	S	+	2	0	MORC3	36658298	0.059000	0.20769	0.005000	0.12908	0.007000	0.05969	1.175000	0.31944	0.696000	0.31696	-0.258000	0.10820	TCA	.	.		0.378	MORC3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000194640.1	NM_015358		A	37736428	C	A	37736428	4	1	314	1	0	0	0	0	0	1	0	0	9712	838	29	3	1544	3	MORC3	21	37736428	Nonsense_Mutation	SNP	C	TCGA-KR-A7K2-01A-12D-A33Q-10		37736428	10393467	55	44530										
TYMP	1890	hgsc.bcm.edu	37	chr22	50968105	50968105	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	gaagtcaccaggcgcgggtgGggccccggttcccggggtca	18	13	2	0			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr22:50968105G>A	ENST00000252029.3	-	2	196	c.34C>T	c.(34-36)Cca>Tca	p.P12S	TYMP_ENST00000395681.1_Missense_Mutation_p.P12S|TYMP_ENST00000395678.3_Missense_Mutation_p.P12S|TYMP_ENST00000395680.1_Missense_Mutation_p.P12S	NM_001113755.2|NM_001113756.2|NM_001257988.1|NM_001257989.1|NM_001953.4	NP_001107227.1|NP_001107228.1|NP_001244917.1|NP_001244918.1|NP_001944.1	P19971	TYPH_HUMAN	thymidine phosphorylase	12					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|chemotaxis (GO:0006935)|DNA replication (GO:0006260)|mitochondrial genome maintenance (GO:0000002)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside salvage (GO:0043097)|pyrimidine nucleotide metabolic process (GO:0006220)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	phosphorylase activity (GO:0004645)|platelet-derived growth factor receptor binding (GO:0005161)|pyrimidine-nucleoside phosphorylase activity (GO:0016154)|thymidine phosphorylase activity (GO:0009032)|transferase activity, transferring pentosyl groups (GO:0016763)			large_intestine(1)|lung(2)|ovary(1)|prostate(1)	5		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;0.206)|LUAD - Lung adenocarcinoma(64;0.247)	Capecitabine(DB01101)|Cidofovir(DB00369)|Floxuridine(DB00322)|Fluorouracil(DB00544)|Trifluridine(DB00432)	GGCGCGGGTGGGGCCCCGGTT	0.706																																					p.P12S		Atlas-SNP	.											.	TYMP	25	.	0			c.C34T						.						12	16	14					22																	50968105		2192	4291	6483	SO:0001583	missense	1890	exon2			CGGGTGGGGCCCC	M63193	CCDS14096.1, CCDS58811.1	22q13	2014-09-17	2008-01-21	2008-01-21	ENSG00000025708	ENSG00000025708	2.4.2.4		3148	protein-coding gene	gene with protein product	"gliostatin"	131222	"endothelial cell growth factor 1 (platelet-derived)"	MNGIE, ECGF1		1590793, 11733540	Standard	NM_001113755		Approved		uc003bme.5	P19971	OTTHUMG00000150249	ENST00000252029.3:c.34C>T	chr22.hg19:g.50968105G>A	ENSP00000252029:p.Pro12Ser	110.0	0.0		57.0	27.0	NM_001257989	A8MW15|H9KVA0|Q13390|Q8WVB7	Missense_Mutation	SNP	ENST00000252029.3	hg19	CCDS14096.1	.	.	.	.	.	.	.	.	.	.	G	18.37	3.609082	0.66558	.	.	ENSG00000025708	ENST00000395680;ENST00000395681;ENST00000252029;ENST00000395678;ENST00000425169	D;D;D;D;D	0.98666	-4.76;-4.75;-4.76;-4.76;-5.06	4.4	-3.91	0.04168	.	0.562517	0.13620	N	0.374461	D	0.92802	0.7711	N	0.08118	0	0.09310	N	1	B;B;B;B	0.14438	0.01;0.002;0.002;0.002	B;B;B;B	0.12156	0.007;0.001;0.002;0.002	D	0.86787	0.1983	10	0.87932	D	0	0.0036	4.9868	0.14194	0.5954:0.0:0.2412:0.1634	.	12;12;12;12	B4DVR2;B2RBL3;E5KRG5;P19971	.;.;.;TYPH_HUMAN	S	12	ENSP00000379037:P12S;ENSP00000379038:P12S;ENSP00000252029:P12S;ENSP00000379036:P12S;ENSP00000395875:P12S	ENSP00000252029:P12S	P	-	1	0	TYMP	49314971	0.000000	0.05858	0.000000	0.03702	0.053000	0.15095	-0.547000	0.06055	-0.481000	0.06792	0.462000	0.41574	CCA	.	.		0.706	TYMP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317081.1	NM_001953		A	50968105	G	A	50968105	3	1	314	1	0	0	0	0	1	0	0	0	16826	1232	43	3	1450	3	TYMP	22	50968105	Missense_Mutation	SNP	G	TCGA-KR-A7K2-01A-12D-A33Q-10		50968105	336461	56	44531										
DMD	1756	hgsc.bcm.edu	37	chrX	32486815	32486815	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	actttgttgctcttgcagagAactttgtaaagcctaaaaaa	7	7	1	1			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chrX:32486815A>G	ENST00000357033.4	-	23	3168	c.2962T>C	c.(2962-2964)Tct>Cct	p.S988P	DMD_ENST00000378677.2_Missense_Mutation_p.S984P	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	988					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				TCTTGCAGAGAACTTTGTAAA	0.333																																					p.S988P		Atlas-SNP	.											.	DMD	2127	.	0			c.T2962C						.						51	46	47					X																	32486815		2201	4297	6498	SO:0001583	missense	1756	exon23			GCAGAGAACTTTG	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.2962T>C	chrX.hg19:g.32486815A>G	ENSP00000354923:p.Ser988Pro	124.0	0.0		140.0	115.0	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	hg19	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	A	15.65	2.895466	0.52121	.	.	ENSG00000198947	ENST00000534884;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280	T;T	0.35789	1.29;1.29	5.12	3.86	0.44501	.	0.000000	0.33772	U	0.004578	T	0.43722	0.1260	L	0.34521	1.04	0.80722	D	1	D;D;D	0.71674	0.982;0.998;0.986	P;D;P	0.66847	0.802;0.947;0.875	T	0.23619	-1.0183	10	0.37606	T	0.19	.	10.9111	0.47110	0.8452:0.1548:0.0:0.0	.	980;988;984	P11532-4;P11532;E9PDN5	.;DMD_HUMAN;.	P	980;984;988;988;865	ENSP00000367948:S984P;ENSP00000354923:S988P	ENSP00000354923:S988P	S	-	1	0	DMD	32396736	1.000000	0.71417	0.999000	0.59377	0.729000	0.41735	3.240000	0.51368	1.789000	0.52484	0.437000	0.28790	TCT	.	.		0.333	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		G	32486815	A	G	32486815	3	3	314	1	0	0	0	0	1	0	0	0	4582	246	9	2	8566	2	DMD	23	32486815	Missense_Mutation	SNP	A	TCGA-KR-A7K2-01A-12D-A33Q-10		32486815	122783745	57	44532										
CSTF2	1478	hgsc.bcm.edu	37	chrX	100086583	100086583	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	acccctcgaggcttgttaggAgatgctccgaatgatccacg	11	12	0	2			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chrX:100086583A>G	ENST00000372972.2	+	9	985	c.969A>G	c.(967-969)ggA>ggG	p.G323G	CSTF2_ENST00000415585.2_Silent_p.G343G	NM_001325.2	NP_001316.1	P33240	CSTF2_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa	323	Gly/Pro-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cleavage body (GO:0071920)|mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|skin(2)|stomach(1)	13						GCTTGTTAGGAGATGCTCCGA	0.522																																					p.G323G		Atlas-SNP	.											.	CSTF2	47	.	0			c.A969G						.						119	100	106					X																	100086583		2203	4300	6503	SO:0001819	synonymous_variant	1478	exon9			GTTAGGAGATGCT	BC017712	CCDS14473.1	Xq22.1	2013-02-12	2002-08-29		ENSG00000101811	ENSG00000101811		"RNA binding motif (RRM) containing"	2484	protein-coding gene	gene with protein product		300907	"cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kD"			1741396	Standard	XM_006724622		Approved		uc004egh.3	P33240	OTTHUMG00000022709	ENST00000372972.2:c.969A>G	chrX.hg19:g.100086583A>G		68.0	0.0		72.0	35.0	NM_001325	Q5H951|Q6LA74|Q8N502	Silent	SNP	ENST00000372972.2	hg19	CCDS14473.1																																																																																			.	.		0.522	CSTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058926.1	NM_001325		G	100086583	A	G	100086583	2	3	314	1	0	0	0	0	0	0	0	1	3986	291	11	2		2	CSTF2	23	100086583	Silent	SNP	A	TCGA-KR-A7K2-01A-12D-A33Q-10	67599768	100086583	55183977	58	44533										
FAM127A	8933	hgsc.bcm.edu	37	chrX	134166686	134166686	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0517241379310345	3	1	1.04356060606061	0	1.44493006993007	0.166666666666667	0.751940625889747	0	aagaaggagagccccctcctCaatgattaccggggctttct	10	12	2	3			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chrX:134166686C>A	ENST00000257013.7	+	1	354	c.273C>A	c.(271-273)ctC>ctA	p.L91L	FAM127A_ENST00000464369.1_Intron	NM_001078171.1	NP_001071639.1	O15255	CXX1_HUMAN	family with sequence similarity 127, member A	0						plasma membrane (GO:0005886)				endometrium(3)|urinary_tract(1)	4	Acute lymphoblastic leukemia(192;0.000127)					GCCCCCTCCTCAATGATTACC	0.637																																					p.L91L		Atlas-SNP	.											.	FAM127A	21	.	0			c.C273A						.						42	45	44					X																	134166686		2187	4291	6478	SO:0001819	synonymous_variant	8933	exon1			CCTCCTCAATGAT	Y13374	CCDS43997.1	Xq26	2014-05-16	2006-11-16	2006-11-16	ENSG00000134590	ENSG00000134590			2569	protein-coding gene	gene with protein product		300213	"CAAX box 1"	CXX1		9403077, 15716091, 16093683	Standard	NM_001078171		Approved	Mart8, Mar8, MAR8C	uc004eyd.3	A6ZKI3	OTTHUMG00000022465	ENST00000257013.7:c.273C>A	chrX.hg19:g.134166686C>A		136.0	0.0		129.0	50.0	NM_001078171	Q6IBF1	Silent	SNP	ENST00000257013.7	hg19	CCDS43997.1																																																																																			.	.		0.637	FAM127A-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058391.2	NM_001078171		A	134166686	C	A	134166686	2	1	314	1	0	0	0	0	0	0	0	1	5436	813	29	3		3	FAM127A	23	134166686	Silent	SNP	C	TCGA-KR-A7K2-01A-12D-A33Q-10	34080103	134166686	21103874	59	44534										
PRDM2	7799	hgsc.bcm.edu	37	chr1	14105088	14105088	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	gcttgtgaggtgaatgatttGggggaagaggaggaggagga	21	1	0	4			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr1:14105088G>T	ENST00000235372.7	+	8	1654	c.798G>T	c.(796-798)ttG>ttT	p.L266F	PRDM2_ENST00000311066.5_Missense_Mutation_p.L266F|PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000413440.1_Missense_Mutation_p.L65F|PRDM2_ENST00000503842.1_Intron|PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000343137.4_Missense_Mutation_p.L65F	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	266					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		TGAATGATTTgggggaagagg	0.547																																					p.L266F		Atlas-SNP	.											.	PRDM2	147	.	0			c.G798T						.						43	45	45					1																	14105088		2203	4300	6503	SO:0001583	missense	7799	exon8			TGATTTGGGGGAA	U17838	CCDS150.1, CCDS151.1, CCDS30603.1, CCDS44061.1	1p36	2011-07-01			ENSG00000116731	ENSG00000116731		"Chromatin-modifying enzymes / K-methyltransferases"	9347	protein-coding gene	gene with protein product	"retinoblastoma protein-binding zinc finger protein", "retinoblastoma protein-interacting zinc finger protein", "MTE-binding protein", "zinc-finger DNA-binding protein", "GATA-3 binding protein G3B"	601196				7538672	Standard	NM_012231		Approved	RIZ, RIZ1, RIZ2, KMT8, MTB-ZF, HUMHOXY1	uc001avi.3	Q13029	OTTHUMG00000007917	ENST00000235372.7:c.798G>T	chr1.hg19:g.14105088G>T	ENSP00000235372:p.Leu266Phe	174.0	0.0		131.0	8.0	NM_015866	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Missense_Mutation	SNP	ENST00000235372.7	hg19	CCDS150.1	.	.	.	.	.	.	.	.	.	.	G	11.18	1.562032	0.27915	.	.	ENSG00000116731	ENST00000235372;ENST00000311066;ENST00000400800;ENST00000413440;ENST00000343137;ENST00000407521	T;T;T;T	0.01787	4.78;4.64;4.68;4.68	5.66	5.66	0.87406	.	0.816321	0.11400	N	0.567889	T	0.02047	0.0064	L	0.46157	1.445	0.36063	D	0.841608	P;P;P	0.37636	0.468;0.468;0.603	B;B;B	0.30495	0.086;0.054;0.116	T	0.55237	-0.8172	10	0.10902	T	0.67	.	11.7344	0.51757	0.0807:0.0:0.9193:0.0	.	124;266;266	Q5THJ0;Q13029;Q13029-2	.;PRDM2_HUMAN;.	F	266;266;266;65;65;65	ENSP00000235372:L266F;ENSP00000312352:L266F;ENSP00000411103:L65F;ENSP00000341621:L65F	ENSP00000235372:L266F	L	+	3	2	PRDM2	13977675	0.981000	0.34729	0.996000	0.52242	0.853000	0.48598	0.977000	0.29475	2.662000	0.90505	0.555000	0.69702	TTG	.	.		0.547	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231		T	14105088	G	T	14105088	3	4	315	1	0	0	0	0	1	0	0	0	12470	1339	47	3	824	3	PRDM2	1	14105088	Missense_Mutation	SNP	G	TCGA-KR-A7K7-01A-11D-A33K-10		14105088	235145533	1	44535										
MAP7D1	55700	hgsc.bcm.edu	37	chr1	36638161	36638161	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	gcgccggctggaggagcaacGtcttaaagccgagcaacgcc	14	13	1	0			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr1:36638161G>A	ENST00000373151.2	+	4	773	c.557G>A	c.(556-558)cGt>cAt	p.R186H	MAP7D1_ENST00000316156.4_Missense_Mutation_p.R186H|MAP7D1_ENST00000474796.1_3'UTR|MAP7D1_ENST00000373150.4_Missense_Mutation_p.R186H	NM_018067.3	NP_060537.3	Q3KQU3	MA7D1_HUMAN	MAP7 domain containing 1	186					microtubule cytoskeleton organization (GO:0000226)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)				breast(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	19		Myeloproliferative disorder(586;0.0393)				GAGGAGCAACGTCTTAAAGCC	0.632																																					p.R186H		Atlas-SNP	.											.	MAP7D1	62	.	0			c.G557A						.						21	21	21					1																	36638161		2202	4299	6501	SO:0001583	missense	55700	exon4			AGCAACGTCTTAA	AK096341	CCDS30673.1, CCDS65492.1, CCDS65493.1	1p34.3	2008-02-05	2007-02-08	2007-02-08	ENSG00000116871	ENSG00000116871			25514	protein-coding gene	gene with protein product			"proline arginine rich coiled coil 1", "arginine/proline rich coiled-coil 1"	PARCC1, RPRC1		10574461	Standard	XM_005271024		Approved	FLJ10350, FLJ39022	uc001bzz.3	Q3KQU3	OTTHUMG00000007714	ENST00000373151.2:c.557G>A	chr1.hg19:g.36638161G>A	ENSP00000362244:p.Arg186His	327.0	0.0		213.0	17.0	NM_018067	D3DPS4|Q7L8J5|Q8N905|Q8TAK0|Q9HBQ2|Q9NW29|Q9ULN3	Missense_Mutation	SNP	ENST00000373151.2	hg19	CCDS30673.1	.	.	.	.	.	.	.	.	.	.	G	36	5.662200	0.96734	.	.	ENSG00000116871	ENST00000429533;ENST00000316156;ENST00000373150;ENST00000373151	T;T;T;T	0.12569	2.67;2.67;2.67;2.67	5.41	5.41	0.78517	.	0.000000	0.37348	N	0.002128	T	0.39118	0.1066	M	0.70595	2.14	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.996;0.998	T	0.15492	-1.0435	10	0.87932	D	0	-19.004	17.7518	0.88436	0.0:0.0:1.0:0.0	.	186;186;186	Q3KQU3-2;Q3KQU3-4;Q3KQU3	.;.;MA7D1_HUMAN	H	147;186;186;186	ENSP00000390091:R147H;ENSP00000320228:R186H;ENSP00000362243:R186H;ENSP00000362244:R186H	ENSP00000320228:R186H	R	+	2	0	MAP7D1	36410748	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	8.620000	0.90943	2.532000	0.85374	0.655000	0.94253	CGT	.	.		0.632	MAP7D1-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382095.1	NM_018067		A	36638161	G	A	36638161	3	1	315	1	0	0	0	0	1	0	0	0	9276	1145	40	1	571	1	MAP7D1	1	36638161	Missense_Mutation	SNP	G	TCGA-KR-A7K7-01A-11D-A33K-10	22533073	36638161	212612460	2	44536										
NASP	4678	hgsc.bcm.edu	37	chr1	46073372	46073372	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	aaaggaggtcaggagaagcaGggagaggtaattgtgagcat	17	3	1	3	rs202027114		TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr1:46073372G>C	ENST00000350030.3	+	6	876	c.789G>C	c.(787-789)caG>caC	p.Q263H	NASP_ENST00000372052.4_Intron|NASP_ENST00000537798.1_Missense_Mutation_p.Q199H|NASP_ENST00000402363.3_Missense_Mutation_p.Q265H|NASP_ENST00000351223.3_Intron	NM_002482.3	NP_002473.2	P49321	NASP_HUMAN	nuclear autoantigenic sperm protein (histone-binding)	263	Glu-rich (acidic).				blastocyst development (GO:0001824)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone exchange (GO:0043486)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	Hsp90 protein binding (GO:0051879)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	17	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.211)					AGGAGAAGCAGGGAGAGGTAA	0.478																																					p.Q263H		Atlas-SNP	.											.	NASP	77	.	0			c.G789C						.						44	47	46					1																	46073372		2203	4300	6503	SO:0001583	missense	4678	exon6			GAAGCAGGGAGAG	M97856	CCDS524.1, CCDS525.1, CCDS55597.1	1p34.1	2013-01-10			ENSG00000132780	ENSG00000132780		"Tetratricopeptide (TTC) repeat domain containing"	7644	protein-coding gene	gene with protein product		603185				1426632	Standard	NM_002482		Approved	FLB7527, FLJ31599, FLJ35510, MGC19722, MGC20372, MGC2297, DKFZp547F162, PRO1999	uc001coi.2	P49321	OTTHUMG00000007826	ENST00000350030.3:c.789G>C	chr1.hg19:g.46073372G>C	ENSP00000255120:p.Gln263His	143.0	0.0		137.0	7.0	NM_002482	A8K6H2|B4DQP3|D3DQ07|F5H3J2|Q53GW5|Q5T622|Q5T625|Q96A69|Q9BTW2	Missense_Mutation	SNP	ENST00000350030.3	hg19	CCDS524.1	.	.	.	.	.	.	.	.	.	.	G	11.36	1.615555	0.28801	.	.	ENSG00000132780	ENST00000537798;ENST00000402363;ENST00000341288;ENST00000350030;ENST00000470768	D;D;D;D	0.94650	-3.48;-3.48;-3.48;-3.48	5.37	5.37	0.77165	.	0.433338	0.26122	N	0.026214	D	0.92113	0.7500	N	0.17082	0.46	0.32940	D	0.518256	D;D;D;D;D	0.69078	0.994;0.996;0.997;0.99;0.994	P;D;D;P;P	0.64321	0.861;0.924;0.924;0.73;0.861	D	0.90293	0.4324	9	.	.	.	-5.1147	6.1073	0.20081	0.113:0.0:0.6989:0.188	.	199;263;163;263;265	F5H3J2;Q53H03;B4DS57;P49321;P49321-3	.;.;.;NASP_HUMAN;.	H	199;265;163;263;226	ENSP00000438871:Q199H;ENSP00000384529:Q265H;ENSP00000255120:Q263H;ENSP00000436924:Q226H	.	Q	+	3	2	NASP	45845959	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.932000	0.48940	2.902000	0.99343	0.650000	0.86243	CAG	.	G|0.995;C|0.005		0.478	NASP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021533.2	NM_002482		C	46073372	G	C	46073372	3	2	315	1	0	0	0	0	1	0	0	0	10181	991	35	4	888	4	NASP	1	46073372	Missense_Mutation	SNP	G	TCGA-KR-A7K7-01A-11D-A33K-10	9435211	46073372	203177249	3	44537										
HIPK1	204851	hgsc.bcm.edu	37	chr1	114483116	114483116	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	tgggatgtttcaggacagagTagcaacgacaaatattatac	10	6	1	1			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr1:114483116T>A	ENST00000369558.1	+	2	343	c.111T>A	c.(109-111)agT>agA	p.S37R	HIPK1_ENST00000369561.4_Missense_Mutation_p.S37R|HIPK1_ENST00000369555.2_Missense_Mutation_p.S37R|HIPK1_ENST00000369559.4_Missense_Mutation_p.S37R|HIPK1_ENST00000426820.2_Missense_Mutation_p.S37R|HIPK1_ENST00000369554.2_Missense_Mutation_p.S37R			Q86Z02	HIPK1_HUMAN	homeodomain interacting protein kinase 1	37					anterior/posterior pattern specification (GO:0009952)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|neuron differentiation (GO:0030182)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|retina layer formation (GO:0010842)|smoothened signaling pathway (GO:0007224)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(15)|ovary(4)|prostate(2)	39	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CAGGACAGAGTAGCAACGACA	0.507																																					p.S37R		Atlas-SNP	.											.	HIPK1	195	.	0			c.T111A						.						221	237	231					1																	114483116		2203	4300	6503	SO:0001583	missense	204851	exon2			ACAGAGTAGCAAC	AB089957	CCDS867.1, CCDS868.1, CCDS869.1, CCDS41370.1	1p13.1	2008-02-05			ENSG00000163349	ENSG00000163349			19006	protein-coding gene	gene with protein product		608003					Standard	NM_198268		Approved	KIAA0630, Myak, MGC26642, Nbak2, MGC33446, MGC33548	uc001eem.3	Q86Z02	OTTHUMG00000011983	ENST00000369558.1:c.111T>A	chr1.hg19:g.114483116T>A	ENSP00000358571:p.Ser37Arg	121.0	0.0		69.0	17.0	NM_198268	A6NJ34|O75125|Q5SQL2|Q5SQL4|Q5SQL5|Q8IYD7|Q8NDN5|Q8NEB6|Q8TBZ1	Missense_Mutation	SNP	ENST00000369558.1	hg19	CCDS867.1	.	.	.	.	.	.	.	.	.	.	T	13.83	2.353273	0.41700	.	.	ENSG00000163349	ENST00000426820;ENST00000369559;ENST00000443627;ENST00000369554;ENST00000369555;ENST00000369558;ENST00000369561;ENST00000514621;ENST00000503968	T;T;T;T;T;T;T;T;T	0.49139	0.84;0.86;0.89;0.9;0.9;0.89;0.91;0.8;0.79	4.92	4.0	0.46444	.	0.204155	0.43919	D	0.000502	T	0.14830	0.0358	N	0.19112	0.55	0.80722	D	1	P;P	0.44195	0.61;0.828	B;P	0.45232	0.207;0.474	T	0.06006	-1.0851	10	0.07175	T	0.84	.	7.6757	0.28484	0.0:0.74:0.0:0.26	.	37;37	Q86Z02;Q86Z02-2	HIPK1_HUMAN;.	R	108;37;37;37;37;37;37;37;37	ENSP00000407442:S108R;ENSP00000358572:S37R;ENSP00000409673:S37R;ENSP00000358567:S37R;ENSP00000358568:S37R;ENSP00000358571:S37R;ENSP00000358574:S37R;ENSP00000422322:S37R;ENSP00000426695:S37R	ENSP00000358567:S37R	S	+	3	2	HIPK1	114284639	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.324000	0.43831	1.037000	0.40024	-0.248000	0.11899	AGT	.	.		0.507	HIPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000033127.1	NM_198268		A	114483116	T	A	114483116	3	1	315	1	0	0	0	0	1	0	0	0	7125	1635	57	4	113	4	HIPK1	1	114483116	Missense_Mutation	SNP	T	TCGA-KR-A7K7-01A-11D-A33K-10	68409744	114483116	134767505	4	44538										
OR10J1	26476	hgsc.bcm.edu	37	chr1	159410510	159410510	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	tgttggtgggaagttttcctGaccatgtaggaagagttctc	13	6	1	2			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr1:159410510G>A	ENST00000423932.3	+	1	999	c.962G>A	c.(961-963)tGa>tAa	p.*321*	RP11-550P17.5_ENST00000431862.1_RNA	NM_012351.2	NP_036483.2	P30954	O10J1_HUMAN	olfactory receptor, family 10, subfamily J, member 1	0					G-protein coupled receptor signaling pathway (GO:0007186)|sensory perception of chemical stimulus (GO:0007606)|single fertilization (GO:0007338)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|skin(2)|stomach(1)	25	all_hematologic(112;0.0429)					AAGTTTTCCTGACCATGTAGG	0.488																																					p.X321X		Atlas-SNP	.											.	OR10J1	118	.	0			c.G962A						.						63	64	63					1																	159410510		2203	4300	6503	SO:0001819	synonymous_variant	26476	exon1			TTTCCTGACCATG	X64995	CCDS1185.1	1q23.2	2012-08-09			ENSG00000196184	ENSG00000196184		"GPCR / Class A : Olfactory receptors"	8175	protein-coding gene	gene with protein product						1370859	Standard	NM_012351		Approved	HGMP07J, HSHGMP07J	uc010piv.2	P30954	OTTHUMG00000022737	ENST00000423932.3:c.962G>A	chr1.hg19:g.159410510G>A		40.0	0.0		42.0	25.0	NM_012351	Q2M1M8|Q5VSV1|Q6IET5|Q96R56	Silent	SNP	ENST00000423932.3	hg19	CCDS1185.1																																																																																			.	.		0.488	OR10J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059020.1	NM_012351		A	159410510	G	A	159410510	2	1	315	1	0	0	0	0	0	0	0	1	10919	1285	45	3		3	OR10J1	1	159410510	Silent	SNP	G	TCGA-KR-A7K7-01A-11D-A33K-10	44927394	159410510	89840111	5	44539										
SMYD1	150572	hgsc.bcm.edu	37	chr2	88383836	88383836	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	cttctttctccatttccagcCttgttaattttgtgtgccac	5	12	2	0			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr2:88383836C>T	ENST00000419482.2	+	2	224	c.139C>T	c.(139-141)Ctt>Ttt	p.L47F	SMYD1_ENST00000468008.1_3'UTR|MIR4780_ENST00000584268.1_RNA|SMYD1_ENST00000444564.2_Splice_Site_p.L47F|SMYD1_ENST00000438570.1_Splice_Site_p.L47F	NM_198274.3	NP_938015.1	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	47	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of myotube differentiation (GO:0010831)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			NS(1)|breast(4)|central_nervous_system(1)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	41						CATTTCCAGCCTTGTTAATTT	0.542																																					p.L47F		Atlas-SNP	.											.	SMYD1	95	.	0			c.C139T						.						86	77	80					2																	88383836		2203	4300	6503	SO:0001630	splice_region_variant	150572	exon2			TCCAGCCTTGTTA	AF086123	CCDS33240.1	2p11.1	2011-07-01			ENSG00000115593	ENSG00000115593		"Zinc fingers, MYND-type", "Chromatin-modifying enzymes / K-methyltransferases"	20986	protein-coding gene	gene with protein product		606846				11923873	Standard	NM_198274		Approved	BOP, ZMYND22, KMT3D	uc002ssr.3	Q8NB12	OTTHUMG00000155045	ENST00000419482.2:c.138-1C>T	chr2.hg19:g.88383836C>T		109.0	0.0		119.0	54.0	NM_198274	A0AV30|A6NE13	Missense_Mutation	SNP	ENST00000419482.2	hg19	CCDS33240.1	.	.	.	.	.	.	.	.	.	.	C	13.09	2.133213	0.37630	.	.	ENSG00000115593	ENST00000419482;ENST00000444564;ENST00000438570	T;T;T	0.81078	-1.45;-1.45;2.44	5.78	4.72	0.59763	SET domain (2);	0.132566	0.52532	D	0.000074	T	0.73156	0.3551	L	0.46157	1.445	0.54753	D	0.999983	B;B	0.21225	0.053;0.005	B;B	0.22601	0.04;0.004	T	0.66031	-0.6024	10	0.10636	T	0.68	-16.8945	14.8066	0.69962	0.0:0.919:0.0:0.081	.	47;47	Q8NB12;C9JUP3	SMYD1_HUMAN;.	F	47	ENSP00000393453:L47F;ENSP00000407888:L47F;ENSP00000387482:L47F	ENSP00000393453:L47F	L	+	1	0	SMYD1	88164951	1.000000	0.71417	0.997000	0.53966	0.832000	0.47134	3.488000	0.53229	2.736000	0.93811	0.555000	0.69702	CTT	.	.		0.542	SMYD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338229.2	XM_097915	Missense_Mutation	T	88383836	C	T	88383836	5	4	315	1	0	0	0	0	0	0	1	0	14836	695	24	3	145	3	SMYD1	2	88383836	Splice_Site	SNP	C	TCGA-KR-A7K7-01A-11D-A33K-10		88383836	154815537	6	44540										
TRIP12	9320	hgsc.bcm.edu	37	chr2	230668295	230668295	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	atatgacattaccttctcttCtgaagtaaacactaaaaata	3	8	2	2			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr2:230668295C>T	ENST00000283943.5	-	19	2943	c.2765G>A	c.(2764-2766)aGa>aAa	p.R922K	TRIP12_ENST00000389045.3_Missense_Mutation_p.R652K|TRIP12_ENST00000543084.1_Intron|TRIP12_ENST00000389044.4_Missense_Mutation_p.R970K	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	922					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		ACCTTCTCTTCTGAAGTAAAC	0.338																																					p.R922K		Atlas-SNP	.											.	TRIP12	207	.	0			c.G2765A						.						44	45	45					2																	230668295		2203	4300	6503	SO:0001583	missense	9320	exon19			TCTCTTCTGAAGT	L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.2765G>A	chr2.hg19:g.230668295C>T	ENSP00000283943:p.Arg922Lys	150.0	0.0		158.0	67.0	NM_004238	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Missense_Mutation	SNP	ENST00000283943.5	hg19	CCDS33391.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.876613	0.91664	.	.	ENSG00000153827	ENST00000283943;ENST00000389045;ENST00000389044	T;T;T	0.34072	1.38;1.38;1.38	5.88	5.88	0.94601	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.47451	0.1446	L	0.35723	1.085	0.80722	D	1	P;P;P	0.44690	0.841;0.841;0.841	P;P;P	0.57204	0.815;0.815;0.815	T	0.06110	-1.0845	10	0.17832	T	0.49	.	20.2314	0.98350	0.0:1.0:0.0:0.0	.	652;970;922	Q14CF1;Q14CA3;Q14669	.;.;TRIPC_HUMAN	K	922;652;970	ENSP00000283943:R922K;ENSP00000373697:R652K;ENSP00000373696:R970K	ENSP00000283943:R922K	R	-	2	0	TRIP12	230376539	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.461000	0.80834	2.789000	0.95967	0.591000	0.81541	AGA	.	.		0.338	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238		T	230668295	C	T	230668295	3	4	315	1	0	0	0	0	1	0	0	0	16571	913	32	3	3305	3	TRIP12	2	230668295	Missense_Mutation	SNP	C	TCGA-KR-A7K7-01A-11D-A33K-10	142284459	230668295	12531078	7	44541										
MAP4	4134	hgsc.bcm.edu	37	chr3	47958322	47958322	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	ctgtgggcagtaccacattcTtggctgaagatacatctgtt	10	9	2	2			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr3:47958322T>G	ENST00000360240.6	-	7	1513	c.995A>C	c.(994-996)aAg>aCg	p.K332T	MAP4_ENST00000395734.3_Missense_Mutation_p.K332T|MAP4_ENST00000426837.2_Missense_Mutation_p.K349T|MAP4_ENST00000383737.4_Intron	NM_002375.4	NP_002366.2	P27816	MAP4_HUMAN	microtubule-associated protein 4	332	17 X 14 AA tandem repeats.				cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|microtubule sliding (GO:0051012)|mitotic spindle organization (GO:0007052)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|microtubule cytoskeleton (GO:0015630)|mitotic spindle (GO:0072686)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(2)	32				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)	Docetaxel(DB01248)|Paclitaxel(DB01229)	TACCACATTCTTGGCTGAAGA	0.478																																					p.K332T		Atlas-SNP	.											.	MAP4	176	.	0			c.A995C						.						260	243	249					3																	47958322		2203	4300	6503	SO:0001583	missense	4134	exon7			ACATTCTTGGCTG		CCDS33750.1, CCDS46818.1, CCDS46821.1	3p21	2008-07-18			ENSG00000047849	ENSG00000047849			6862	protein-coding gene	gene with protein product		157132				1905296	Standard	NM_002375		Approved		uc003csb.2	P27816	OTTHUMG00000156828	ENST00000360240.6:c.995A>C	chr3.hg19:g.47958322T>G	ENSP00000353375:p.Lys332Thr	98.0	0.0		70.0	17.0	NM_001134364	Q13082|Q59FT2|Q68D74|Q6ZUW9|Q86V26|Q96A76|Q96NS9	Missense_Mutation	SNP	ENST00000360240.6	hg19	CCDS33750.1	.	.	.	.	.	.	.	.	.	.	T	13.44	2.237820	0.39598	.	.	ENSG00000047849	ENST00000395734;ENST00000426837;ENST00000360240	T;T;T	0.08984	3.05;3.05;3.03	4.92	3.69	0.42338	.	.	.	.	.	T	0.17746	0.0426	M	0.67397	2.05	0.09310	N	0.999999	B;D;B	0.56968	0.41;0.978;0.102	B;P;B	0.55303	0.164;0.773;0.045	T	0.06499	-1.0823	9	0.54805	T	0.06	-1.9123	7.0975	0.25317	0.2151:0.0:0.0:0.7849	.	309;332;332	C9JFC3;P27816-6;P27816	.;.;MAP4_HUMAN	T	332;349;332	ENSP00000379083:K332T;ENSP00000407602:K349T;ENSP00000353375:K332T	ENSP00000353375:K332T	K	-	2	0	MAP4	47933326	0.001000	0.12720	0.042000	0.18584	0.021000	0.10359	1.014000	0.29950	2.044000	0.60594	0.533000	0.62120	AAG	.	.		0.478	MAP4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346085.1	NM_002375		G	47958322	T	G	47958322	3	3	315	1	0	0	0	0	1	0	0	0	9267	1609	56	5	3874	5	MAP4	3	47958322	Missense_Mutation	SNP	T	TCGA-KR-A7K7-01A-11D-A33K-10		47958322	150064108	8	44542										
BSN	8927	hgsc.bcm.edu	37	chr3	49693730	49693730	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	ctgacacgtgtgcccatgatTgccccccgggtacctcttgg	11	15	1	2			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr3:49693730T>G	ENST00000296452.4	+	5	6855	c.6741T>G	c.(6739-6741)atT>atG	p.I2247M		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	2247					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		TGCCCATGATTGCCCCCCGGG	0.592																																					p.I2247M		Atlas-SNP	.											.	BSN	272	.	0			c.T6741G						.						83	79	80					3																	49693730		2203	4300	6503	SO:0001583	missense	8927	exon5			CATGATTGCCCCC	AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"zinc finger protein 231", "neuronal double zinc finger protein"	604020	"bassoon (presynaptic cytomatrix protein)"	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.6741T>G	chr3.hg19:g.49693730T>G	ENSP00000296452:p.Ile2247Met	104.0	0.0		61.0	22.0	NM_003458	O43161|Q7LGH3	Missense_Mutation	SNP	ENST00000296452.4	hg19	CCDS2800.1	.	.	.	.	.	.	.	.	.	.	T	11.40	1.626460	0.28978	.	.	ENSG00000164061	ENST00000296452	T	0.19938	2.11	5.53	3.02	0.34903	.	0.132337	0.51477	D	0.000086	T	0.12732	0.0309	N	0.11427	0.14	0.29390	N	0.862707	P	0.49961	0.93	P	0.48030	0.564	T	0.03695	-1.1012	10	0.41790	T	0.15	-7.132	5.7893	0.18351	0.0:0.1611:0.144:0.6949	.	2247	Q9UPA5	BSN_HUMAN	M	2247	ENSP00000296452:I2247M	ENSP00000296452:I2247M	I	+	3	3	BSN	49668734	0.974000	0.33945	1.000000	0.80357	0.994000	0.84299	0.098000	0.15189	0.946000	0.37632	0.533000	0.62120	ATT	.	.		0.592	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458		G	49693730	T	G	49693730	3	3	315	1	0	0	0	0	1	0	0	0	1532	1800	63	5	6759	5	BSN	3	49693730	Missense_Mutation	SNP	T	TCGA-KR-A7K7-01A-11D-A33K-10	1735408	49693730	148328700	9	44543										
ZBTB20	26137	hgsc.bcm.edu	37	chr3	114070355	114070355	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	acgttctgtgacacgatgcgCgtgcactcgtcgatgactgt	12	11	1	2			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr3:114070355C>T	ENST00000474710.1	-	4	748	c.570G>A	c.(568-570)acG>acA	p.T190T	ZBTB20_ENST00000464560.1_Silent_p.T117T|ZBTB20_ENST00000462705.1_Silent_p.T117T|ZBTB20_ENST00000471418.1_Silent_p.T117T|ZBTB20_ENST00000393785.2_Silent_p.T117T|ZBTB20-AS1_ENST00000467304.1_RNA|ZBTB20_ENST00000357258.3_Silent_p.T117T|ZBTB20-AS1_ENST00000496219.1_RNA|ZBTB20_ENST00000481632.1_Silent_p.T117T|ZBTB20-AS1_ENST00000475939.1_RNA	NM_001164342.1	NP_001157814.1	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20	190						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)	p.T117T(1)		breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(8)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	48				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)		ACACGATGCGCGTGCACTCGT	0.637																																					p.T190T	NSCLC(69;748 1344 9802 11203 30933)	Atlas-SNP	.											ZBTB20,NS,carcinoma,0,1	ZBTB20	157	.	1	Substitution - coding silent(1)	lung(1)	c.G570A						.						74	60	65					3																	114070355		2203	4300	6503	SO:0001819	synonymous_variant	26137	exon4			GATGCGCGTGCAC	AF139460	CCDS2981.1, CCDS54626.1	3q13.2	2013-01-08	2004-07-16	2004-07-16	ENSG00000181722	ENSG00000181722		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	13503	protein-coding gene	gene with protein product		606025	"zinc finger protein 288"	ZNF288		10965110, 11352661	Standard	XM_005247339		Approved	ODA-8S, DKFZp566F123, DPZF	uc003ebi.3	Q9HC78	OTTHUMG00000159366	ENST00000474710.1:c.570G>A	chr3.hg19:g.114070355C>T		36.0	0.0		41.0	7.0	NM_001164342	Q63HP6|Q8N6R5|Q9Y410	Silent	SNP	ENST00000474710.1	hg19	CCDS54626.1																																																																																			.	.		0.637	ZBTB20-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354951.1	NM_015642		T	114070355	C	T	114070355	2	4	315	1	0	0	0	0	0	0	0	1	17544	755	27	1		1	ZBTB20	3	114070355	Silent	SNP	C	TCGA-KR-A7K7-01A-11D-A33K-10	64376625	114070355	83952075	10	44544										
HEG1	57493	hgsc.bcm.edu	37	chr3	124731574	124731574	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	tggaaacaactgtggtttggGgagaaggagatgttccgagg	17	4	0	2			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr3:124731574G>A	ENST00000311127.4	-	6	2916	c.2849C>T	c.(2848-2850)cCc>cTc	p.P950L	HEG1_ENST00000477536.1_5'Flank	NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	950					cardiac atrium morphogenesis (GO:0003209)|cell-cell junction assembly (GO:0007043)|endothelial cell morphogenesis (GO:0001886)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|lymph circulation (GO:0003017)|lymph vessel development (GO:0001945)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|post-embryonic development (GO:0009791)|regulation of body fluid levels (GO:0050878)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|ventricular septum development (GO:0003281)	cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(24)|ovary(2)|urinary_tract(4)	47						TGTGGTTTGGGGAGAAGGAGA	0.507																																					p.P950L		Atlas-SNP	.											.	HEG1	109	.	0			c.C2849T						.						144	162	156					3																	124731574		2061	4199	6260	SO:0001583	missense	57493	exon6			GTTTGGGGAGAAG	AK074987	CCDS46898.1	3q21.2	2013-03-08	2013-03-08		ENSG00000173706	ENSG00000173706			29227	protein-coding gene	gene with protein product	"heart of glass"	614182	"HEG homolog 1 (zebrafish)"			10574462, 19151727, 23007647	Standard	NM_020733		Approved	KIAA1237, HEG	uc003ehs.4	Q9ULI3	OTTHUMG00000159486	ENST00000311127.4:c.2849C>T	chr3.hg19:g.124731574G>A	ENSP00000311502:p.Pro950Leu	74.0	0.0		45.0	15.0	NM_020733	Q6NX66|Q8NC40|Q9BSV0	Missense_Mutation	SNP	ENST00000311127.4	hg19	CCDS46898.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.990566	0.74589	.	.	ENSG00000173706	ENST00000311127	D	0.89123	-2.47	4.09	3.21	0.36854	.	0.457587	0.16144	U	0.227570	D	0.85431	0.5695	M	0.66939	2.045	0.09310	N	0.999999	P;P	0.42908	0.793;0.689	B;B	0.40940	0.344;0.186	T	0.78099	-0.2336	10	0.51188	T	0.08	.	4.4008	0.11385	0.2045:0.1885:0.6069:0.0	.	950;950	Q9ULI3-2;Q9ULI3	.;HEG1_HUMAN	L	950	ENSP00000311502:P950L	ENSP00000311502:P950L	P	-	2	0	HEG1	126214264	0.000000	0.05858	0.010000	0.14722	0.929000	0.56500	-0.113000	0.10774	1.062000	0.40625	0.655000	0.94253	CCC	.	.		0.507	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386		A	124731574	G	A	124731574	3	1	315	1	0	0	0	0	1	0	0	0	7053	1232	43	3	1344	3	HEG1	3	124731574	Missense_Mutation	SNP	G	TCGA-KR-A7K7-01A-11D-A33K-10	10661219	124731574	73290856	11	44545										
SLC6A19	340024	hgsc.bcm.edu	37	chr5	1221849	1221849	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	aatcccagaagatctcctacCcgaactgggtgtatgtggtg	11	10	1	2			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr5:1221849C>A	ENST00000304460.10	+	12	1791	c.1735C>A	c.(1735-1737)Ccg>Acg	p.P579T		NM_001003841.2	NP_001003841.1	Q695T7	S6A19_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 19	579					amino acid transport (GO:0006865)|ion transport (GO:0006811)|response to nutrient (GO:0007584)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)|neutral amino acid transmembrane transporter activity (GO:0015175)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(25)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10)		Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			GATCTCCTACCCGAACTGGGT	0.567																																					p.P579T		Atlas-SNP	.											.	SLC6A19	99	.	0			c.C1735A						.						114	103	107					5																	1221849		2203	4300	6503	SO:0001583	missense	340024	exon12			TCCTACCCGAACT	AK096054	CCDS34130.1	5p15	2013-07-19			ENSG00000174358	ENSG00000174358		"Solute carriers"	27960	protein-coding gene	gene with protein product	"Hartnup disease"	608893					Standard	NM_001003841		Approved		uc003jbw.4	Q695T7	OTTHUMG00000161636	ENST00000304460.10:c.1735C>A	chr5.hg19:g.1221849C>A	ENSP00000305302:p.Pro579Thr	142.0	0.0		127.0	61.0	NM_001003841	A8K446	Missense_Mutation	SNP	ENST00000304460.10	hg19	CCDS34130.1	.	.	.	.	.	.	.	.	.	.	C	15.10	2.733358	0.48939	.	.	ENSG00000174358	ENST00000304460	D	0.86769	-2.17	4.73	4.73	0.59995	.	0.158475	0.56097	D	0.000024	D	0.95554	0.8555	H	0.95079	3.62	0.58432	D	0.999999	D	0.89917	1.0	D	0.77004	0.989	D	0.97151	0.9831	10	0.87932	D	0	.	17.6827	0.88248	0.0:1.0:0.0:0.0	.	579	Q695T7	S6A19_HUMAN	T	579	ENSP00000305302:P579T	ENSP00000305302:P579T	P	+	1	0	SLC6A19	1274849	1.000000	0.71417	0.780000	0.31762	0.010000	0.07245	6.480000	0.73604	2.197000	0.70478	0.561000	0.74099	CCG	.	.		0.567	SLC6A19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365557.1	XM_291120		A	1221849	C	A	1221849	3	1	315	1	0	0	0	0	1	0	0	0	14697	623	22	3	1781	3	SLC6A19	5	1221849	Missense_Mutation	SNP	C	TCGA-KR-A7K7-01A-11D-A33K-10		1221849	179693411	12	44546										
APC	324	hgsc.bcm.edu	37	chr5	112174286	112174286	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	gtaagttttgcagttatggtCaatacccagccgacctagcc	9	11	1	0	rs75239284		TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr5:112174286C>T	ENST00000457016.1	+	16	3375	c.2995C>T	c.(2995-2997)Caa>Taa	p.Q999*	APC_ENST00000257430.4_Nonsense_Mutation_p.Q999*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.Q999*			P25054	APC_HUMAN	adenomatous polyposis coli	999	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CAGTTATGGTCAATACCCAGC	0.348		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											p.Q999X	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-SNP	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	.	APC	4158	.	1	Unknown(1)	skin(1)	c.C2995T	GRCh37	CM994279	APC	M	rs75239284	.						87	83	84					5																	112174286		2202	4300	6502	SO:0001587	stop_gained	324	exon17	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	TATGGTCAATACC	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.2995C>T	chr5.hg19:g.112174286C>T	ENSP00000413133:p.Gln999*	96.0	0.0		104.0	48.0	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	hg19	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	38	6.647106	0.97730	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.76	5.76	0.90799	.	0.106709	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.13470	T	0.59	-13.0393	16.9398	0.86215	0.0:0.8726:0.1274:0.0	.	.	.	.	X	999;981;999;999;999	.	ENSP00000257430:Q999X	Q	+	1	0	APC	112202185	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	3.594000	0.54008	2.726000	0.93360	0.655000	0.94253	CAA	.	.		0.348	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112174286	C	T	112174286	4	4	315	1	0	0	0	0	0	1	0	0	763	827	29	3	3053	3	APC	5	112174286	Nonsense_Mutation	SNP	C	TCGA-KR-A7K7-01A-11D-A33K-10	110952437	112174286	68740974	13	44547										
PCDHGA5	56110	hgsc.bcm.edu	37	chr5	140745479	140745479	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	actatgagcagttgagagacCtacagttgtgggtgacagcc	13	8	0	4			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr5:140745479C>A	ENST00000518069.1	+	1	1582	c.1582C>A	c.(1582-1584)Cta>Ata	p.L528I	PCDHGA4_ENST00000571252.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018918.2|NM_032054.1	NP_061741.1|NP_114443.1	Q9Y5G8	PCDG5_HUMAN	protocadherin gamma subfamily A, 5	528	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(5)|upper_aerodigestive_tract(3)	18			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTTGAGAGACCTACAGTTGTG	0.537																																					p.L528I		Atlas-SNP	.											.	PCDHGA5	215	.	0			c.C1582A						.						189	207	201					5																	140745479		2200	4298	6498	SO:0001583	missense	56110	exon1			AGAGACCTACAGT	AF152512	CCDS54925.1, CCDS75333.1	5q31	2010-01-26				ENSG00000253485		"Cadherins / Protocadherins : Clustered"	8703	other	protocadherin	"cadherin ME3"	606292				10380929	Standard	NM_018918		Approved	CDH-GAMMA-A5, ME3, PCDH-GAMMA-A5		Q9Y5G8		ENST00000518069.1:c.1582C>A	chr5.hg19:g.140745479C>A	ENSP00000429834:p.Leu528Ile	81.0	0.0		82.0	16.0	NM_032054	Q2M3F5|Q9Y5D2	Missense_Mutation	SNP	ENST00000518069.1	hg19	CCDS54925.1	.	.	.	.	.	.	.	.	.	.	.	5.391	0.257373	0.10239	.	.	ENSG00000253485	ENST00000518069	T	0.51325	0.71	4.84	-0.0812	0.13703	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.29716	0.0742	N	0.10645	0.015	0.09310	N	1	B;P	0.38440	0.242;0.631	B;P	0.44811	0.331;0.461	T	0.21314	-1.0249	9	0.42905	T	0.14	.	5.47	0.16664	0.1268:0.4324:0.0:0.4408	.	528;528	Q9Y5G8-2;Q9Y5G8	.;PCDG5_HUMAN	I	528	ENSP00000429834:L528I	ENSP00000429834:L528I	L	+	1	2	PCDHGA5	140725663	0.000000	0.05858	0.353000	0.25747	0.524000	0.34500	-1.327000	0.02682	-0.261000	0.09405	-0.471000	0.05019	CTA	.	.		0.537	PCDHGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374742.1	NM_018918		A	140745479	C	A	140745479	3	1	315	1	0	0	0	0	1	0	0	0	11566	680	24	3	1584	3	PCDHGA5	5	140745479	Missense_Mutation	SNP	C	TCGA-KR-A7K7-01A-11D-A33K-10	28571193	140745479	40169781	14	44548										
MBOAT1	154141	hgsc.bcm.edu	37	chr6	20124766	20124766	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	aggcaggtgacaggaaaggtCttcgttagcgtcaaaaacaa	12	7	2	1			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr6:20124766C>A	ENST00000324607.7	-	8	944	c.780G>T	c.(778-780)aaG>aaT	p.K260N	MBOAT1_ENST00000541730.1_Missense_Mutation_p.K111N	NM_001080480.1	NP_001073949.1	Q6ZNC8	MBOA1_HUMAN	membrane bound O-acyltransferase domain containing 1	260					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transferase activity, transferring acyl groups other than amino-acyl groups (GO:0016747)			breast(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(5)	20	all_cancers(95;0.244)|Breast(50;0.0379)|Ovarian(93;0.0473)|all_epithelial(95;0.109)		OV - Ovarian serous cystadenocarcinoma(7;0.00392)|all cancers(50;0.0117)|Epithelial(50;0.0454)			CAGGAAAGGTCTTCGTTAGCG	0.473																																					p.K260N		Atlas-SNP	.											.	MBOAT1	48	.	0			c.G780T						.						179	154	163					6																	20124766		2203	4300	6503	SO:0001583	missense	154141	exon8			AAAGGTCTTCGTT	AK093994	CCDS34346.1	6p22.3	2013-10-11	2006-06-29	2006-06-29	ENSG00000172197	ENSG00000172197			21579	protein-coding gene	gene with protein product	"lysophosphatidylethanolamine acyltransferase 1"	611732	"O-acyltransferase (membrane bound) domain containing 1"	OACT1		18287005	Standard	NM_001080480		Approved	MGC44669, dJ434O11.1, LPEAT1	uc003ncx.2	Q6ZNC8	OTTHUMG00000014334	ENST00000324607.7:c.780G>T	chr6.hg19:g.20124766C>A	ENSP00000324944:p.Lys260Asn	147.0	0.0		172.0	75.0	NM_001080480	A9EDQ5|B4DL59|B4E3J4|Q86XC2|Q8N9R5	Missense_Mutation	SNP	ENST00000324607.7	hg19	CCDS34346.1	.	.	.	.	.	.	.	.	.	.	C	15.82	2.945034	0.53079	.	.	ENSG00000172197	ENST00000541730;ENST00000324607	T;T	0.72725	-0.68;-0.68	5.48	4.6	0.57074	.	0.150507	0.64402	D	0.000015	T	0.58075	0.2097	L	0.48218	1.51	0.80722	D	1	B;P	0.43885	0.1;0.82	B;P	0.47786	0.049;0.557	T	0.53982	-0.8361	10	0.15499	T	0.54	-14.2729	14.0304	0.64613	0.0:0.9272:0.0:0.0728	.	111;260	Q6ZNC8-2;Q6ZNC8	.;MBOA1_HUMAN	N	111;260	ENSP00000441568:K111N;ENSP00000324944:K260N	ENSP00000324944:K260N	K	-	3	2	MBOAT1	20232745	1.000000	0.71417	0.999000	0.59377	0.699000	0.40488	2.991000	0.49409	2.739000	0.93911	0.561000	0.74099	AAG	.	.		0.473	MBOAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039980.1			A	20124766	C	A	20124766	3	1	315	1	0	0	0	0	1	0	0	0	9365	912	32	3	731	3	MBOAT1	6	20124766	Missense_Mutation	SNP	C	TCGA-KR-A7K7-01A-11D-A33K-10		20124766	150990301	15	44549										
CDSN	170679	hgsc.bcm.edu	37	chr6	31084730	31084730	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	tgcagggagagtcggggatgTccgaactacagggacgctgg	18	8	0	1			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr6:31084730T>C	ENST00000259881.9	+	1	61				PSORS1C1_ENST00000467107.1_3'UTR|CDSN_ENST00000376288.2_Missense_Mutation_p.D221G	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1											kidney(1)|ovary(2)|prostate(1)|skin(1)	5						GTCGGGGATGTCCGAACTACA	0.622																																					p.D221G		Atlas-SNP	.											.	CDSN	48	.	0			c.A662G						.						69	75	73					6																	31084730		2203	4300	6503	SO:0001627	intron_variant	1041	exon2			GGGATGTCCGAAC	AB031479	CCDS34390.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204540	ENSG00000204540			17202	protein-coding gene	gene with protein product		613525	"chromosome 6 open reading frame 16"	C6orf16			Standard	NM_014068		Approved	SEEK1	uc003nsl.2	Q9UIG5	OTTHUMG00000031077	ENST00000259881.9:c.-229+2062T>C	chr6.hg19:g.31084730T>C		96.0	0.0		125.0	66.0	NM_001264	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Missense_Mutation	SNP	ENST00000259881.9	hg19	CCDS34390.1	.	.	.	.	.	.	.	.	.	.	T	12.88	2.071726	0.36566	.	.	ENSG00000204539	ENST00000376288	T	0.07114	3.22	4.63	3.47	0.39725	.	0.406771	0.20659	N	0.088043	T	0.01976	0.0062	L	0.32530	0.975	0.09310	N	1	B	0.15930	0.015	B	0.14023	0.01	T	0.41627	-0.9498	10	0.30854	T	0.27	-8.5713	6.1252	0.20176	0.0:0.115:0.0:0.885	.	221	Q15517	CDSN_HUMAN	G	221	ENSP00000365465:D221G	ENSP00000365465:D221G	D	-	2	0	CDSN	31192709	0.014000	0.17966	0.040000	0.18447	0.044000	0.14063	1.456000	0.35201	1.723000	0.51488	0.368000	0.22195	GAC	.	.		0.622	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068		C	31084730	T	C	31084730	1	2	315	0	1	0	0	0	0	0	0	0	3181	1667	58	2		2	CDSN	6	31084730	Intron	SNP	T	TCGA-KR-A7K7-01A-11D-A33K-10	10959964	31084730	140030337	16	44550										
UBR2	23304	hgsc.bcm.edu	37	chr6	42610159	42610159	+	Nonsense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	tacttttttttttagatttaTtactaccataatgtgaaatg	4	4	0	2			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr6:42610159T>G	ENST00000372899.1	+	18	2295	c.2037T>G	c.(2035-2037)taT>taG	p.Y679*	UBR2_ENST00000372883.3_Nonsense_Mutation_p.Y183*|UBR2_ENST00000372901.1_Nonsense_Mutation_p.Y679*	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	679					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			TTTAGATTTATTACTACCATA	0.328																																					p.Y679X		Atlas-SNP	.											.	UBR2	134	.	0			c.T2037G						.						53	56	55					6																	42610159		2202	4300	6502	SO:0001587	stop_gained	23304	exon18			GATTTATTACTAC	BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"Ubiquitin protein ligase E3 component n-recognins"	21289	protein-coding gene	gene with protein product		609134	"chromosome 6 open reading frame 133"	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.2037T>G	chr6.hg19:g.42610159T>G	ENSP00000361990:p.Tyr679*	56.0	0.0		56.0	27.0	NM_015255	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Nonsense_Mutation	SNP	ENST00000372899.1	hg19	CCDS4870.1	.	.	.	.	.	.	.	.	.	.	T	41	9.092070	0.99062	.	.	ENSG00000024048	ENST00000372899;ENST00000372901;ENST00000372883	.	.	.	5.77	3.38	0.38709	.	0.057993	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.0098	9.0257	0.36227	0.0:0.2089:0.0:0.7911	.	.	.	.	X	679;679;183	.	ENSP00000361974:Y183X	Y	+	3	2	UBR2	42718137	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.866000	0.39489	0.450000	0.26774	0.533000	0.62120	TAT	.	.		0.328	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255		G	42610159	T	G	42610159	4	3	315	1	0	0	0	0	0	1	0	0	16917	1500	52	5	2253	5	UBR2	6	42610159	Nonsense_Mutation	SNP	T	TCGA-KR-A7K7-01A-11D-A33K-10	11525429	42610159	128504908	17	44551										
CRIP3	401262	hgsc.bcm.edu	37	chr6	43274193	43274193	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	ctgttacttaccaaaatagaCgggctccccacagccagggc	9	14	0	1			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr6:43274193C>T	ENST00000274990.4	-	5	395	c.391G>A	c.(391-393)Gtc>Atc	p.V131I	CRIP3_ENST00000372569.3_Missense_Mutation_p.V131I|ZNF318_ENST00000607252.1_5'Flank			Q6Q6R5	CRIP3_HUMAN	cysteine-rich protein 3	131	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				T cell proliferation (GO:0042098)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)			CCAAAATAGACGGGCTCCCCA	0.577																																					p.V131I		Atlas-SNP	.											.	CRIP3	30	.	0			c.G391A						.						66	65	65					6																	43274193		2203	4300	6503	SO:0001583	missense	401262	exon5			AATAGACGGGCTC	AY555741	CCDS4894.2	6p21	2008-02-05			ENSG00000146215	ENSG00000146215			17751	protein-coding gene	gene with protein product						15380775	Standard	NM_206922		Approved	TLP-A, bA480N24.2, TLP	uc003ouu.1	Q6Q6R5	OTTHUMG00000014727	ENST00000274990.4:c.391G>A	chr6.hg19:g.43274193C>T	ENSP00000274990:p.Val131Ile	89.0	0.0		90.0	5.0	NM_206922	A2A436|Q5T043|Q6Q6R4|Q6Q6R6|Q6Q6R7	Missense_Mutation	SNP	ENST00000274990.4	hg19		.	.	.	.	.	.	.	.	.	.	C	24.9	4.584821	0.86748	.	.	ENSG00000146215	ENST00000372569;ENST00000451294;ENST00000274990	D;D;D	0.84298	-1.83;-1.83;-1.83	4.75	4.75	0.60458	Zinc finger, LIM-type (5);	0.171388	0.36444	N	0.002583	D	0.87795	0.6267	L	0.46885	1.475	0.51233	D	0.999912	D;D	0.76494	0.999;0.999	D;D	0.79108	0.992;0.991	D	0.89414	0.3705	10	0.87932	D	0	-35.3784	15.6048	0.76658	0.0:1.0:0.0:0.0	.	131;131	Q6Q6R5;Q6Q6R5-3	CRIP3_HUMAN;.	I	131;3;131	ENSP00000361650:V131I;ENSP00000397775:V3I;ENSP00000274990:V131I	ENSP00000274990:V131I	V	-	1	0	CRIP3	43382171	0.999000	0.42202	0.976000	0.42696	0.916000	0.54674	4.501000	0.60393	2.343000	0.79666	0.561000	0.74099	GTC	.	.		0.577	CRIP3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000313968.1			T	43274193	C	T	43274193	3	4	315	1	0	0	0	0	1	0	0	0	3878	536	19	1	239	1	CRIP3	6	43274193	Missense_Mutation	SNP	C	TCGA-KR-A7K7-01A-11D-A33K-10	664034	43274193	127840874	18	44552										
COL19A1	1310	hgsc.bcm.edu	37	chr6	70894595	70894595	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	aatcctttttttctttatagGgaataaatggaaaagatgga	8	3	1	1			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr6:70894595G>A	ENST00000322773.4	+	45	2878	c.2776G>A	c.(2776-2778)Gga>Aga	p.G926R	COL19A1_ENST00000393344.1_Splice_Site_p.G548R	NM_001858.4	NP_001849.2	Q14993	COJA1_HUMAN	collagen, type XIX, alpha 1	926	Collagen-like 10.|Triple-helical region 5 (COL5).				cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)|skeletal muscle tissue development (GO:0007519)|skeletal system development (GO:0001501)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(8)|lung(54)|ovary(3)|prostate(2)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	109						TTCTTTATAGGGAATAAATGG	0.308																																					p.G926R		Atlas-SNP	.											.	COL19A1	232	.	0			c.G2776A						.						83	91	88					6																	70894595		2203	4300	6503	SO:0001630	splice_region_variant	1310	exon45			TTATAGGGAATAA		CCDS4970.1	6q12-q13	2013-01-16			ENSG00000082293	ENSG00000082293		"Collagens"	2196	protein-coding gene	gene with protein product		120165				7916703, 9143499	Standard	NM_001858		Approved		uc003pfc.1	Q14993	OTTHUMG00000014987	ENST00000322773.4:c.2776-1G>A	chr6.hg19:g.70894595G>A		88.0	0.0		97.0	31.0	NM_001858	Q00559|Q05850|Q12885|Q13676|Q14DH1|Q5JUF0|Q5T424|Q9H572|Q9NPZ2|Q9NQP2	Missense_Mutation	SNP	ENST00000322773.4	hg19	CCDS4970.1	.	.	.	.	.	.	.	.	.	.	G	16.51	3.142801	0.57044	.	.	ENSG00000082293	ENST00000322773;ENST00000393344;ENST00000393333	D;D	0.97161	-4.27;-4.27	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	D	0.99211	0.9726	H	0.98089	4.145	0.53688	D	0.999973	D	0.89917	1.0	D	0.91635	0.999	D	0.99063	1.0831	9	.	.	.	.	18.5553	0.91081	0.0:0.0:1.0:0.0	.	926	Q14993	COJA1_HUMAN	R	926;548;1	ENSP00000316030:G926R;ENSP00000377013:G548R	.	G	+	1	0	COL19A1	70951316	1.000000	0.71417	1.000000	0.80357	0.692000	0.40212	5.303000	0.65738	2.817000	0.96982	0.563000	0.77884	GGA	.	.		0.308	COL19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041127.1		Missense_Mutation	A	70894595	G	A	70894595	5	1	315	1	0	0	0	0	0	0	1	0	3678	1246	43	3	2950	3	COL19A1	6	70894595	Splice_Site	SNP	G	TCGA-KR-A7K7-01A-11D-A33K-10	27620402	70894595	100220472	19	44553										
RARS2	57038	hgsc.bcm.edu	37	chr6	88227931	88227931	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	acagactgtggctcttgtaaAcaagcagtgttgaagtcatt	10	7	2	2			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr6:88227931A>G	ENST00000369536.5	-	17	1512	c.1467T>C	c.(1465-1467)tgT>tgC	p.C489C	RARS2_ENST00000497828.1_5'Flank	NM_020320.3	NP_064716.2	Q5T160	SYRM_HUMAN	arginyl-tRNA synthetase 2, mitochondrial	489					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	22		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0456)		GCTCTTGTAAACAAGCAGTGT	0.353																																					p.C489C		Atlas-SNP	.											.	RARS2	61	.	0			c.T1467C						.						168	167	167					6																	88227931		2203	4300	6503	SO:0001819	synonymous_variant	57038	exon17			TTGTAAACAAGCA	AK093934	CCDS5011.1	6q16.1	2011-07-01	2007-09-27	2007-02-23	ENSG00000146282	ENSG00000146282	6.1.1.19	"Aminoacyl tRNA synthetases / Class I"	21406	protein-coding gene	gene with protein product	"arginine tRNA ligase 2, mitochondrial (putative)"	611524	"arginyl-tRNA synthetase-like"	RARSL		17847012	Standard	NM_020320		Approved	MGC14993, MGC23778, PRO1992, dJ382I10.6, DALRD2	uc003pme.3	Q5T160	OTTHUMG00000015178	ENST00000369536.5:c.1467T>C	chr6.hg19:g.88227931A>G		106.0	0.0		123.0	20.0	NM_020320	B2RDT7|Q96FU5|Q9H8K8	Silent	SNP	ENST00000369536.5	hg19	CCDS5011.1																																																																																			.	.		0.353	RARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041448.1	NM_020320		G	88227931	A	G	88227931	2	3	315	1	0	0	0	0	0	0	0	1	13074	41	2	2		2	RARS2	6	88227931	Silent	SNP	A	TCGA-KR-A7K7-01A-11D-A33K-10	17333336	88227931	82887136	20	44554										
CAV1	857	hgsc.bcm.edu	37	chr7	116165144	116165144	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	ggggcaaatacgtagactcgGaggtaggcatccgtgggggg	19	7	0	1	rs370105972		TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr7:116165144G>A	ENST00000341049.2	+	1	306	c.28G>A	c.(28-30)Gag>Aag	p.E10K	CAV1_ENST00000393468.1_5'Flank|CAV1_ENST00000393470.1_Missense_Mutation_p.E10K|CAV1_ENST00000405348.1_5'Flank|CAV1_ENST00000393467.1_5'Flank	NM_001753.4	NP_001744.2	Q03135	CAV1_HUMAN	caveolin 1, caveolae protein, 22kDa	10					angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|calcium ion homeostasis (GO:0055074)|calcium ion transport (GO:0006816)|caveola assembly (GO:0070836)|caveolin-mediated endocytosis (GO:0072584)|cellular calcium ion homeostasis (GO:0006874)|cellular response to hyperoxia (GO:0071455)|cellular response to starvation (GO:0009267)|cholesterol homeostasis (GO:0042632)|cholesterol transport (GO:0030301)|cytosolic calcium ion homeostasis (GO:0051480)|inactivation of MAPK activity (GO:0000188)|lactation (GO:0007595)|leukocyte migration (GO:0050900)|lipid storage (GO:0019915)|maintenance of protein location in cell (GO:0032507)|mammary gland development (GO:0030879)|mammary gland involution (GO:0060056)|MAPK cascade (GO:0000165)|membrane depolarization (GO:0051899)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of pinocytosis (GO:0048550)|negative regulation of protein binding (GO:0032091)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|nitric oxide homeostasis (GO:0033484)|nitric oxide metabolic process (GO:0046209)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of vasoconstriction (GO:0045907)|protein homooligomerization (GO:0051260)|protein localization (GO:0008104)|receptor internalization involved in canonical Wnt signaling pathway (GO:2000286)|regulation of blood coagulation (GO:0030193)|regulation of fatty acid metabolic process (GO:0019217)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidase activity (GO:0052547)|regulation of smooth muscle contraction (GO:0006940)|regulation of the force of heart contraction by chemical signal (GO:0003057)|response to calcium ion (GO:0051592)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to ischemia (GO:0002931)|response to progesterone (GO:0032570)|skeletal muscle tissue development (GO:0007519)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|vasculogenesis (GO:0001570)|vasoconstriction (GO:0042310)|vesicle organization (GO:0016050)|viral process (GO:0016032)	acrosomal membrane (GO:0002080)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|cell cortex (GO:0005938)|cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lipid particle (GO:0005811)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	cholesterol binding (GO:0015485)|enzyme binding (GO:0019899)|nitric-oxide synthase binding (GO:0050998)|patched binding (GO:0005113)|peptidase activator activity (GO:0016504)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)|structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4	all_epithelial(6;1.42e-06)|Lung NSC(10;0.0056)|all_lung(10;0.00609)		STAD - Stomach adenocarcinoma(10;0.00878)			CGTAGACTCGGAGGTAGGCAT	0.622																																					p.E10K		Atlas-SNP	.											.	CAV1	13	.	0			c.G28A						.						84	97	92					7																	116165144		2203	4300	6503	SO:0001583	missense	857	exon1			GACTCGGAGGTAG	AF125348	CCDS5767.1, CCDS55156.1	7q31	2006-02-09	2002-08-29		ENSG00000105974	ENSG00000105974			1527	protein-coding gene	gene with protein product		601047	"caveolin 1, caveolae protein, 22kD"	CAV		10087206	Standard	NM_001753		Approved		uc003vif.2	Q03135	OTTHUMG00000023413	ENST00000341049.2:c.28G>A	chr7.hg19:g.116165144G>A	ENSP00000339191:p.Glu10Lys	105.0	0.0		104.0	22.0	NM_001753	Q9UGP1|Q9UNG1|Q9UQH6	Missense_Mutation	SNP	ENST00000341049.2	hg19	CCDS5767.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.258727	0.80246	.	.	ENSG00000105974	ENST00000341049;ENST00000393470	D;D	0.93189	-3.18;-3.1	4.71	4.71	0.59529	.	0.499327	0.21587	N	0.072152	D	0.90988	0.7166	L	0.47716	1.5	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	D	0.87983	0.2744	10	0.59425	D	0.04	-11.0741	16.9495	0.86240	0.0:0.0:1.0:0.0	.	10	Q03135	CAV1_HUMAN	K	10	ENSP00000339191:E10K;ENSP00000377113:E10K	ENSP00000339191:E10K	E	+	1	0	CAV1	115952380	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.802000	0.69122	2.583000	0.87209	0.650000	0.86243	GAG	.	.		0.622	CAV1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000059734.4	NM_001753		A	116165144	G	A	116165144	3	1	315	1	0	0	0	0	1	0	0	0	2695	1175	41	3	30	3	CAV1	7	116165144	Missense_Mutation	SNP	G	TCGA-KR-A7K7-01A-11D-A33K-10		116165144	42973519	21	44555										
FBXO43	286151	hgsc.bcm.edu	37	chr8	101153180	101153180	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	ggggtctttgataaattcttTaagctaaaggtcaaatcccc	8	8	3	1			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr8:101153180T>C	ENST00000428847.2	-	2	1618	c.1302A>G	c.(1300-1302)ttA>ttG	p.L434L		NM_001029860.3	NP_001025031.2	Q4G163	FBX43_HUMAN	F-box protein 43	434					meiotic nuclear division (GO:0007126)|negative regulation of meiosis (GO:0045835)|negative regulation of protein catabolic process (GO:0042177)|protein ubiquitination (GO:0016567)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(5)|lung(14)|prostate(1)|skin(5)|urinary_tract(1)	31	all_cancers(14;0.000139)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000274)|all_lung(17;0.000798)		Epithelial(11;1.17e-09)|all cancers(13;1.34e-07)|OV - Ovarian serous cystadenocarcinoma(57;3.82e-05)|STAD - Stomach adenocarcinoma(118;0.0957)			ATAAATTCTTTAAGCTAAAGG	0.428																																					p.L434L		Atlas-SNP	.											.	FBXO43	155	.	0			c.A1302G						.						118	113	114					8																	101153180		1890	4127	6017	SO:0001819	synonymous_variant	286151	exon2			ATTCTTTAAGCTA	BC028709	CCDS47904.1	8q22.3	2004-08-24			ENSG00000156509	ENSG00000156509		"F-boxes /  "other""	28521	protein-coding gene	gene with protein product		609110					Standard	NR_036491		Approved	Fbx43	uc003yjd.3	Q4G163	OTTHUMG00000164803	ENST00000428847.2:c.1302A>G	chr8.hg19:g.101153180T>C		151.0	0.0		354.0	38.0	NM_001029860		Silent	SNP	ENST00000428847.2	hg19	CCDS47904.1																																																																																			.	.		0.428	FBXO43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380380.1	XM_209918		C	101153180	T	C	101153180	2	2	315	1	0	0	0	0	0	0	0	1	5760	1751	61	2		2	FBXO43	8	101153180	Silent	SNP	T	TCGA-KR-A7K7-01A-11D-A33K-10		101153180	45210842	22	44556										
KCNV1	27012	hgsc.bcm.edu	37	chr8	110980791	110980791	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	agcagtaggccgacttcttcGtaacactgggtgattgtcat	11	9	2	1			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr8:110980791G>A	ENST00000524391.1	-	4	2061	c.1029C>T	c.(1027-1029)taC>taT	p.Y343Y	KCNV1_ENST00000297404.1_Silent_p.Y343Y			Q6PIU1	KCNV1_HUMAN	potassium channel, subfamily V, member 1	343					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|ion channel inhibitor activity (GO:0008200)|potassium channel regulator activity (GO:0015459)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(20)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_neural(195;0.219)		OV - Ovarian serous cystadenocarcinoma(57;5.35e-13)			CGACTTCTTCGTAACACTGGG	0.463																																					p.Y343Y		Atlas-SNP	.											.	KCNV1	101	.	0			c.C1029T						.						73	62	66					8																	110980791		2203	4300	6503	SO:0001819	synonymous_variant	27012	exon3			TTCTTCGTAACAC	AF167082	CCDS6314.1	8q23.2	2011-07-05				ENSG00000164794		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18861	protein-coding gene	gene with protein product		608164				8670833, 16382104	Standard	NM_014379		Approved	Kv8.1	uc003ynr.4	Q6PIU1		ENST00000524391.1:c.1029C>T	chr8.hg19:g.110980791G>A		55.0	0.0		109.0	21.0	NM_014379	Q9UHJ4	Silent	SNP	ENST00000524391.1	hg19	CCDS6314.1																																																																																			.	.		0.463	KCNV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385525.1	NM_014379		A	110980791	G	A	110980791	2	1	315	1	0	0	0	0	0	0	0	1	8103	1140	40	1		1	KCNV1	8	110980791	Silent	SNP	G	TCGA-KR-A7K7-01A-11D-A33K-10	9827611	110980791	35383231	23	44557										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113347573	113347574	+	Frame_Shift_Ins	INS	-	-	A													0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	caaccgtgataactgagcacINSaaaaaagccacttgttgtga							TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr8:113347573_113347574insA	ENST00000297405.5	-	45	7393_7394	c.7149_7150insT	c.(7147-7152)tttgtgfs	p.V2384fs	CSMD3_ENST00000352409.3_Frame_Shift_Ins_p.V2314fs|CSMD3_ENST00000343508.3_Frame_Shift_Ins_p.V2344fs|CSMD3_ENST00000455883.2_Frame_Shift_Ins_p.V2280fs	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2384	CUB 13. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TAACTGAGCACAAAAAAGCCAC	0.351										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.V2384fs		Atlas-Indel,Pindel	.											.	CSMD3	2325	.	0			c.7150_7151insT						.																																			SO:0001589	frameshift_variant	114788	exon45			.	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.7150dupT	chr8.hg19:g.113347579_113347579dupA	ENSP00000297405:p.Val2384fs	96.0	0.0		197.0	21.0	NM_198123	Q96PZ3	Frame_Shift_Ins	INS	ENST00000297405.5	hg19	CCDS6315.1																																																																																			.	.		0.351	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	113347574	-	A	113347573	7	5	315	1	0	1	1	0	0	0	0	0	3948	478	17	0	4081	0	CSMD3	8	113347573	Frame_Shift_Ins	INS	-	TCGA-KR-A7K7-01A-11D-A33K-10	2366782	113347573	33016449	24	44558										
ARHGAP39	80728	hgsc.bcm.edu	37	chr8	145755886	145755886	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	catctccttgcgggtgttctCgaagatgacgcgcgggtcgt	14	11	2	2			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr8:145755886C>G	ENST00000276826.5	-	10	3373	c.3172G>C	c.(3172-3174)Gag>Cag	p.E1058Q	ARHGAP39_ENST00000377307.2_Missense_Mutation_p.E1089Q|C8orf82_ENST00000313465.5_5'Flank|C8orf82_ENST00000524821.1_5'Flank|ARHGAP39_ENST00000540274.1_Missense_Mutation_p.E1058Q			Q9C0H5	RHG39_HUMAN	Rho GTPase activating protein 39	1058	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				axon guidance (GO:0007411)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	22						CGGGTGTTCTCGAAGATGACG	0.647																																					p.E1089Q		Atlas-SNP	.											.	ARHGAP39	80	.	0			c.G3265C						.						38	33	35					8																	145755886		2194	4295	6489	SO:0001583	missense	80728	exon13			TGTTCTCGAAGAT		CCDS34971.1	8q24.3	2011-06-29			ENSG00000147799	ENSG00000147799		"Rho GTPase activating proteins"	29351	protein-coding gene	gene with protein product	"RhoGAP93B homolog (Drosophila)", "crossGAP homolog (Drosophila)"	615880				15755809	Standard	XM_005272344		Approved	KIAA1688, Vilse, CrGAP	uc003zds.1	Q9C0H5	OTTHUMG00000165182	ENST00000276826.5:c.3172G>C	chr8.hg19:g.145755886C>G	ENSP00000276826:p.Glu1058Gln	99.0	0.0		203.0	28.0	NM_025251	B4E1I1	Missense_Mutation	SNP	ENST00000276826.5	hg19		.	.	.	.	.	.	.	.	.	.	C	29.7	5.029724	0.93518	.	.	ENSG00000147799	ENST00000276826;ENST00000377307;ENST00000540274	T;T;T	0.60424	0.19;0.19;0.19	4.79	4.79	0.61399	Rho GTPase-activating protein domain (3);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.70605	0.3243	L	0.49350	1.555	0.58432	D	0.999997	D;D	0.89917	1.0;0.999	D;D	0.85130	0.967;0.997	T	0.72730	-0.4205	10	0.56958	D	0.05	-35.7706	15.3199	0.74112	0.0:1.0:0.0:0.0	.	1058;1089	Q9C0H5;Q9C0H5-2	RHG39_HUMAN;.	Q	1058;1089;1058	ENSP00000276826:E1058Q;ENSP00000366522:E1089Q;ENSP00000445075:E1058Q	ENSP00000276826:E1058Q	E	-	1	0	ARHGAP39	145726694	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.265000	0.78442	2.197000	0.70478	0.561000	0.74099	GAG	.	.		0.647	ARHGAP39-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382509.1			G	145755886	C	G	145755886	3	3	315	1	0	0	0	0	1	0	0	0	884	893	31	4	83	4	ARHGAP39	8	145755886	Missense_Mutation	SNP	C	TCGA-KR-A7K7-01A-11D-A33K-10	32408313	145755886	608136	25	44559										
UBQLN1	29979	hgsc.bcm.edu	37	chr9	86297921	86297921	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	gtagagttactattaggagtTgatgatgtagtaacattgct	11	3	0	3			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr9:86297921T>C	ENST00000376395.4	-	3	916	c.393A>G	c.(391-393)tcA>tcG	p.S131S	UBQLN1_ENST00000257468.7_Silent_p.S131S	NM_013438.4|NM_053067.2	NP_038466.2|NP_444295.1	Q9UMX0	UBQL1_HUMAN	ubiquilin 1	131					cellular response to hypoxia (GO:0071456)|regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902175)|regulation of protein ubiquitination (GO:0031396)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|proteasome complex (GO:0000502)|protein complex (GO:0043234)	kinase binding (GO:0019900)			breast(4)|endometrium(2)|kidney(4)|large_intestine(6)|lung(10)|prostate(1)	27						TATTAGGAGTTGATGATGTAG	0.403																																					p.S131S	Melanoma(186;1284 2073 12755 14558 18426)	Atlas-SNP	.											.	UBQLN1	49	.	0			c.A393G						.						183	166	172					9																	86297921		2203	4300	6503	SO:0001819	synonymous_variant	29979	exon3			AGGAGTTGATGAT	AF176069	CCDS6663.1, CCDS6664.1	9q22	2013-02-12			ENSG00000135018	ENSG00000135018		"Ubiquilin family"	12508	protein-coding gene	gene with protein product		605046				9303440, 10807547	Standard	NM_013438		Approved	DSK2, PLIC-1, XDRP1, DA41	uc004amv.3	Q9UMX0	OTTHUMG00000020104	ENST00000376395.4:c.393A>G	chr9.hg19:g.86297921T>C		92.0	0.0		64.0	6.0	NM_053067	Q5T6J5|Q5T6J9|Q8IXS9|Q8N2Q3|Q9H0T8|Q9H3R4|Q9HAZ5	Silent	SNP	ENST00000376395.4	hg19	CCDS6663.1																																																																																			.	.		0.403	UBQLN1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000052834.1	NM_013438		C	86297921	T	C	86297921	2	2	315	1	0	0	0	0	0	0	0	1	16911	1799	63	2		2	UBQLN1	9	86297921	Silent	SNP	T	TCGA-KR-A7K7-01A-11D-A33K-10		86297921	54915510	26	44560										
KCNMA1	3778	hgsc.bcm.edu	37	chr10	79397093	79397093	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	tccgccagagcaagatgatgAagaggcccccgaagaaagtc	12	11	0	6			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr10:79397093A>T	ENST00000286628.8	-	1	307	c.308T>A	c.(307-309)tTc>tAc	p.F103Y	KCNMA1_ENST00000372440.1_Missense_Mutation_p.F103Y|KCNMA1_ENST00000372443.1_Missense_Mutation_p.F103Y|KCNMA1_ENST00000481070.1_Missense_Mutation_p.F103Y|KCNMA1_ENST00000406533.3_Missense_Mutation_p.F103Y|KCNMA1_ENST00000480683.1_Missense_Mutation_p.F103Y|KCNMA1_ENST00000286627.5_Missense_Mutation_p.F103Y|KCNMA1_ENST00000404771.3_Missense_Mutation_p.F103Y|KCNMA1_ENST00000354353.5_Missense_Mutation_p.F103Y|KCNMA1_ENST00000404857.1_Missense_Mutation_p.F103Y	NM_001161352.1	NP_001154824.1	Q12791	KCMA1_HUMAN	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	103					blood coagulation (GO:0007596)|cellular potassium ion homeostasis (GO:0030007)|micturition (GO:0060073)|negative regulation of cell volume (GO:0045794)|positive regulation of apoptotic process (GO:0043065)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|response to calcium ion (GO:0051592)|response to carbon monoxide (GO:0034465)|response to hypoxia (GO:0001666)|response to osmotic stress (GO:0006970)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	actin binding (GO:0003779)|calcium-activated potassium channel activity (GO:0015269)|large conductance calcium-activated potassium channel activity (GO:0060072)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(17)|lung(23)|ovary(2)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	68	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Chlorzoxazone(DB00356)|Cromoglicic acid(DB01003)|Diazoxide(DB01119)|Halothane(DB01159)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Miconazole(DB01110)|Procaine(DB00721)	CAAGATGATGAAGAGGCCCCC	0.657																																					p.F103Y		Atlas-SNP	.											.	KCNMA1	370	.	0			c.T308A						.						64	62	63					10																	79397093		2203	4300	6503	SO:0001583	missense	3778	exon1			ATGATGAAGAGGC	U11717	CCDS7352.1, CCDS60569.1, CCDS60571.1, CCDS60572.1, CCDS73156.1	10q22	2012-07-05			ENSG00000156113	ENSG00000156113		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6284	protein-coding gene	gene with protein product	"BK channel alpha subunit"	600150		SLO		7987297, 16382103	Standard	NM_002247		Approved	KCa1.1, mSLO1	uc001jxn.3	Q12791	OTTHUMG00000018543	ENST00000286628.8:c.308T>A	chr10.hg19:g.79397093A>T	ENSP00000286628:p.Phe103Tyr	113.0	0.0		60.0	22.0	NM_001161352	F8WA96|Q12886|Q12917|Q12921|Q12960|Q13150|Q5JQ23|Q5SQR9|Q96LG8|Q9UBB0|Q9UCX0|Q9UQK6	Missense_Mutation	SNP	ENST00000286628.8	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	27.1|27.1	4.803963|4.803963	0.90623|0.90623	.|.	.|.	ENSG00000156113|ENSG00000156113	ENST00000372440;ENST00000372408;ENST00000372437;ENST00000457953;ENST00000404771;ENST00000372443;ENST00000286627;ENST00000286628;ENST00000406533;ENST00000354353;ENST00000404857|ENST00000372403	T;T;T;T;T;T;T;T;T|.	0.47869|.	0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83|.	4.08|4.08	2.93|2.93	0.34026|0.34026	.|.	0.137185|.	0.48767|.	D|.	0.000168|.	T|T	0.52980|0.52980	0.1768|0.1768	L|L	0.39898|0.39898	1.24|1.24	0.44677|0.44677	D|D	0.997665|0.997665	B;P;D;P;P;D;P|.	0.56521|.	0.329;0.831;0.959;0.951;0.918;0.976;0.918|.	B;P;B;P;P;P;P|.	0.57679|.	0.191;0.825;0.424;0.628;0.544;0.732;0.544|.	T|T	0.47548|0.47548	-0.9109|-0.9109	10|5	0.87932|.	D|.	0|.	-3.6688|-3.6688	9.0031|9.0031	0.36094|0.36094	0.91:0.0:0.09:0.0|0.91:0.0:0.09:0.0	.|.	103;103;103;103;103;103;103|.	D5MRH1;Q12791-6;B7ZMF5;Q12791-2;Q12791;Q12791-5;Q5SVJ7|.	.;.;.;.;KCMA1_HUMAN;.;.|.	Y|T	103;40;38;77;40;103;103;77;103;103;103|54	ENSP00000361517:F103Y;ENSP00000361485:F40Y;ENSP00000361514:F38Y;ENSP00000396608:F77Y;ENSP00000361520:F103Y;ENSP00000286627:F103Y;ENSP00000385552:F103Y;ENSP00000346321:F103Y;ENSP00000385806:F103Y|.	ENSP00000286627:F103Y|.	F|S	-|-	2|1	0|0	KCNMA1|KCNMA1	79067099|79067099	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.980000|0.980000	0.70556|0.70556	5.551000|5.551000	0.67274|0.67274	1.617000|1.617000	0.50277|0.50277	0.374000|0.374000	0.22700|0.22700	TTC|TCA	.	.		0.657	KCNMA1-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000048885.3	NM_002247		T	79397093	A	T	79397093	3	4	315	1	0	0	0	0	1	0	0	0	8082	246	9	4	3686	4	KCNMA1	10	79397093	Missense_Mutation	SNP	A	TCGA-KR-A7K7-01A-11D-A33K-10		79397093	56137654	27	44561										
SORCS3	22986	hgsc.bcm.edu	37	chr10	106849559	106849559	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	ggccggattggataaggaggCggacctggtgcacatggagg	19	7	0	0	rs550554404	byFrequency	TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr10:106849559C>T	ENST00000369701.3	+	6	1282	c.1055C>T	c.(1054-1056)gCg>gTg	p.A352V		NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	352					learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		GATAAGGAGGCGGACCTGGTG	0.597													C|||	2	0.000399361	8e-04	0.0014	5008	,	,		18789	0		0	False		,,,				2504	0				p.A352V	NSCLC(116;1497 1690 7108 13108 14106)	Atlas-SNP	.											.	SORCS3	282	.	0			c.C1055T						.						106	91	96					10																	106849559		2203	4300	6503	SO:0001583	missense	22986	exon6			AGGAGGCGGACCT	AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.1055C>T	chr10.hg19:g.106849559C>T	ENSP00000358715:p.Ala352Val	117.0	0.0		117.0	40.0	NM_014978	Q5VXF9|Q9NQJ2	Missense_Mutation	SNP	ENST00000369701.3	hg19	CCDS7558.1	.	.	.	.	.	.	.	.	.	.	C	17.92	3.506937	0.64410	.	.	ENSG00000156395	ENST00000369701	T	0.32023	1.47	6.17	5.26	0.73747	VPS10 (1);	0.312497	0.35936	N	0.002894	T	0.20536	0.0494	N	0.22421	0.69	0.30867	N	0.732918	P	0.38250	0.624	B	0.31812	0.136	T	0.17623	-1.0363	10	0.72032	D	0.01	.	12.9709	0.58511	0.1616:0.8384:0.0:0.0	.	352	Q9UPU3	SORC3_HUMAN	V	352	ENSP00000358715:A352V	ENSP00000358715:A352V	A	+	2	0	SORCS3	106839549	0.967000	0.33354	0.984000	0.44739	0.971000	0.66376	2.275000	0.43399	1.606000	0.50161	-0.182000	0.12963	GCG	.	.		0.597	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978		T	106849559	C	T	106849559	3	4	315	1	0	0	0	0	1	0	0	0	14947	768	27	1	1077	1	SORCS3	10	106849559	Missense_Mutation	SNP	C	TCGA-KR-A7K7-01A-11D-A33K-10	27452466	106849559	28685188	28	44562										
PHRF1	57661	hgsc.bcm.edu	37	chr11	610529	610529	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	ccccggcctgccgcctgcccCggcccagccctcaagcatcc	9	24	1	0	rs201225978		TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr11:610529C>T	ENST00000264555.5	+	16	4573	c.4445C>T	c.(4444-4446)cCg>cTg	p.P1482L	PHRF1_ENST00000416188.2_Missense_Mutation_p.P1481L|PHRF1_ENST00000533464.1_Missense_Mutation_p.P1478L|PHRF1_ENST00000413872.2_Missense_Mutation_p.P1480L	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	1482					mRNA processing (GO:0006397)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)	RNA polymerase binding (GO:0070063)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|urinary_tract(2)	28						CCGCCTGCCCCGGCCCAGCCC	0.687													C|||	1	0.000199681	0	0	5008	,	,		15432	0		0	False		,,,				2504	0.001				p.P1481L		Atlas-SNP	.											.	PHRF1	188	.	0			c.C4442T						.		LEU/PRO	2,3954		0,2,1976	14	18	17		4442	-5.4	0	11		17	3,8263		0,3,4130	no	missense	PHRF1	NM_020901.2	98	0,5,6106	TT,TC,CC		0.0363,0.0506,0.0409	benign	1481/1649	610529	5,12217	1978	4133	6111	SO:0001583	missense	57661	exon16			CTGCCCCGGCCCA	BC004950	CCDS44507.1, CCDS65987.1, CCDS65988.1, CCDS65989.1	11p15.5	2014-06-13			ENSG00000070047	ENSG00000070047		"RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	24351	protein-coding gene	gene with protein product	"CTD binding SR like protein rA9", "protein phosphatase 1, regulatory subunit 125"	611780		RNF221			Standard	XM_005253027		Approved	KIAA1542, PPP1R125	uc010qwc.2	Q9P1Y6	OTTHUMG00000165141	ENST00000264555.5:c.4445C>T	chr11.hg19:g.610529C>T	ENSP00000264555:p.Pro1482Leu	23.0	0.0		15.0	7.0	NM_020901	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Missense_Mutation	SNP	ENST00000264555.5	hg19		.	.	.	.	.	.	.	.	.	.	c	5.063	0.197280	0.09599	5.06E-4	3.63E-4	ENSG00000070047	ENST00000264555;ENST00000413872;ENST00000416188;ENST00000533464	T;T;T;T	0.80480	-1.38;-1.38;-1.38;-1.38	3.77	-5.37	0.02681	.	1.440870	0.05223	N	0.508816	T	0.63534	0.2519	N	0.12746	0.255	0.09310	N	1	B;B;B;B	0.09022	0.002;0.0;0.0;0.0	B;B;B;B	0.06405	0.002;0.001;0.0;0.0	T	0.50030	-0.8875	10	0.33141	T	0.24	-0.3714	11.4847	0.50346	0.0:0.3298:0.0:0.6702	.	1478;1480;1481;1482	E9PJ24;F8WEF5;Q9P1Y6-3;Q9P1Y6	.;.;.;PHRF1_HUMAN	L	1482;1480;1481;1478	ENSP00000264555:P1482L;ENSP00000388589:P1480L;ENSP00000410626:P1481L;ENSP00000431870:P1478L	ENSP00000264555:P1482L	P	+	2	0	PHRF1	600529	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.001000	0.12947	-1.143000	0.02866	-0.452000	0.05504	CCG	.	.		0.687	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901		T	610529	C	T	610529	3	4	315	1	0	0	0	0	1	0	0	0	11870	652	23	1	4500	1	PHRF1	11	610529	Missense_Mutation	SNP	C	TCGA-KR-A7K7-01A-11D-A33K-10		610529	134395987	29	44563										
OR51G2	81282	hgsc.bcm.edu	37	chr11	4936112	4936112	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	gatggatgacagagaggccaAtcatgggagtgtagaagagc	16	5	1	4			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr11:4936112A>G	ENST00000322013.3	-	1	810	c.782T>C	c.(781-783)aTt>aCt	p.I261T	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001005238.1	NP_001005238.1	Q8NGK0	O51G2_HUMAN	olfactory receptor, family 51, subfamily G, member 2	261						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|endometrium(1)|large_intestine(9)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		AGAGAGGCCAATCATGGGAGT	0.542																																					p.I261T		Atlas-SNP	.											.	OR51G2	70	.	0			c.T782C						.						147	127	134					11																	4936112		2201	4298	6499	SO:0001583	missense	81282	exon1			AGGCCAATCATGG	AB065794	CCDS31365.1	11p15.4	2012-08-09			ENSG00000176893	ENSG00000176893		"GPCR / Class A : Olfactory receptors"	15198	protein-coding gene	gene with protein product							Standard	NM_001005238		Approved		uc001lzr.1	Q8NGK0	OTTHUMG00000066501	ENST00000322013.3:c.782T>C	chr11.hg19:g.4936112A>G	ENSP00000322593:p.Ile261Thr	118.0	0.0		110.0	23.0	NM_001005238	Q6IFH7	Missense_Mutation	SNP	ENST00000322013.3	hg19	CCDS31365.1	.	.	.	.	.	.	.	.	.	.	A	16.97	3.269426	0.59540	.	.	ENSG00000176893	ENST00000322013	T	0.00152	8.66	5.48	5.48	0.80851	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	D	0.000099	T	0.00695	0.0023	M	0.93375	3.41	0.37194	D	0.90405	D	0.89917	1.0	D	0.91635	0.999	T	0.59451	-0.7452	10	0.72032	D	0.01	.	14.5252	0.67884	1.0:0.0:0.0:0.0	.	261	Q8NGK0	O51G2_HUMAN	T	261	ENSP00000322593:I261T	ENSP00000322593:I261T	I	-	2	0	OR51G2	4892688	0.182000	0.23173	1.000000	0.80357	0.896000	0.52359	4.338000	0.59316	2.297000	0.77311	0.533000	0.62120	ATT	.	.		0.542	OR51G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142174.1	NM_001005238		G	4936112	A	G	4936112	3	3	315	1	0	0	0	0	1	0	0	0	11108	101	4	2	166	2	OR51G2	11	4936112	Missense_Mutation	SNP	A	TCGA-KR-A7K7-01A-11D-A33K-10	4325583	4936112	130070404	30	44564										
CELF1	10658	hgsc.bcm.edu	37	chr11	47510522	47510522	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	tggcccacaaacatcttgatAgcatcaagatctggttggtc	9	10	3	2			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr11:47510522A>T	ENST00000358597.3	-	1	44	c.45T>A	c.(43-45)gcT>gcA	p.A15A	CELF1_ENST00000532048.1_Silent_p.A42A|CELF1_ENST00000310513.5_Silent_p.A15A|CELF1_ENST00000361904.3_Silent_p.A15A|CELF1_ENST00000531165.1_Silent_p.A42A|CELF1_ENST00000395292.2_Silent_p.A15A|CELF1_ENST00000395290.2_Silent_p.A15A			Q92879	CELF1_HUMAN	CUGBP, Elav-like family member 1	15					embryo development (GO:0009790)|germ cell development (GO:0007281)|mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|negative regulation of translation (GO:0017148)|positive regulation of multicellular organism growth (GO:0040018)|regulation of RNA splicing (GO:0043484)|RNA interference (GO:0016246)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	BRE binding (GO:0042835)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation repressor activity, nucleic acid binding (GO:0000900)			central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|ovary(2)	18						ACATCTTGATAGCATCAAGAT	0.433																																					p.A42A	Pancreas(163;1949 1966 9906 43218 43785)	Atlas-SNP	.											.	CELF1	43	.	0			c.T126A						.						104	104	104					11																	47510522		2201	4298	6499	SO:0001819	synonymous_variant	10658	exon4			CTTGATAGCATCA	U63289	CCDS7938.1, CCDS7939.1, CCDS31482.1, CCDS53622.1, CCDS53623.1	11p11	2013-02-12	2010-02-19	2010-02-19				"RNA binding motif (RRM) containing"	2549	protein-coding gene	gene with protein product	"CUG RNA-binding protein", "nuclear polyadenylated RNA-binding protein, 50-kD", "bruno-like 2", "embryo deadenylation element binding protein"	601074	"CUG triplet repeat, RNA-binding protein 1", "CUG triplet repeat, RNA binding protein 1"	CUGBP1		8948631, 9371827	Standard	NM_006560		Approved	CUG-BP, hNab50, BRUNOL2, NAB50, CUGBP, NAPOR, EDEN-BP	uc001nfl.3	Q92879		ENST00000358597.3:c.45T>A	chr11.hg19:g.47510522A>T		143.0	0.0		143.0	31.0	NM_001172639	B4E2U5|D3DQS0|F8W940|Q4LE52|Q9NP83|Q9NR06	Silent	SNP	ENST00000358597.3	hg19	CCDS31482.1																																																																																			.	.		0.433	CELF1-024	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398352.1	NM_006560		T	47510522	A	T	47510522	2	4	315	1	0	0	0	0	0	0	0	1	3217	407	15	4		4	CELF1	11	47510522	Silent	SNP	A	TCGA-KR-A7K7-01A-11D-A33K-10	42574410	47510522	87495994	31	44565										
NEU3	10825	hgsc.bcm.edu	37	chr11	74716816	74716816	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	catcccttcctggttcttttGcttccagctaccatgtaaaa	5	13	1	0			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr11:74716816G>A	ENST00000544263.1	+	4	736	c.566G>A	c.(565-567)tGc>tAc	p.C189Y	NEU3_ENST00000529024.1_Intron|NEU3_ENST00000294064.4_Missense_Mutation_p.C222Y|NEU3_ENST00000531509.1_Missense_Mutation_p.C222Y|NEU3_ENST00000532963.1_3'UTR|NEU3_ENST00000545272.1_Missense_Mutation_p.C113Y			Q9UQ49	NEUR3_HUMAN	sialidase 3 (membrane sialidase)	189					carbohydrate metabolic process (GO:0005975)|ganglioside catabolic process (GO:0006689)|glycosphingolipid metabolic process (GO:0006687)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha-sialidase activity (GO:0016997)|exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)|exo-alpha-sialidase activity (GO:0004308)			kidney(2)|large_intestine(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	11						TGGTTCTTTTGCTTCCAGCTA	0.522																																					p.C222Y		Atlas-SNP	.											.	NEU3	50	.	0			c.G665A						.						117	113	115					11																	74716816		2004	4181	6185	SO:0001583	missense	10825	exon3			TCTTTTGCTTCCA	AB008185	CCDS44682.1	11q13.5	2008-02-05				ENSG00000162139			7760	protein-coding gene	gene with protein product		604617				10405317	Standard	NM_006656		Approved		uc001ovw.3	Q9UQ49		ENST00000544263.1:c.566G>A	chr11.hg19:g.74716816G>A	ENSP00000445591:p.Cys189Tyr	46.0	0.0		44.0	15.0	NM_006656	A8K327|Q9NQE1	Missense_Mutation	SNP	ENST00000544263.1	hg19		.	.	.	.	.	.	.	.	.	.	G	11.75	1.732755	0.30684	.	.	ENSG00000162139	ENST00000294064;ENST00000531509;ENST00000544263;ENST00000545272	D;D;D;D	0.83419	-1.72;-1.72;-1.72;-1.72	5.44	4.51	0.55191	Neuraminidase (2);	0.250108	0.48286	D	0.000184	D	0.90170	0.6928	M	0.82323	2.585	0.32312	N	0.563545	D;D	0.61697	0.98;0.99	P;D	0.63877	0.816;0.919	D	0.92456	0.5974	10	0.59425	D	0.04	-8.5172	13.2135	0.59839	0.0:0.0:0.84:0.16	.	189;222	Q9UQ49;A8K327	NEUR3_HUMAN;.	Y	222;222;189;113	ENSP00000294064:C222Y;ENSP00000432097:C222Y;ENSP00000445591:C189Y;ENSP00000439908:C113Y	ENSP00000294064:C222Y	C	+	2	0	NEU3	74394464	0.000000	0.05858	0.804000	0.32291	0.079000	0.17450	0.299000	0.19138	1.481000	0.48307	0.655000	0.94253	TGC	.	.		0.522	NEU3-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_006656		A	74716816	G	A	74716816	3	1	315	1	0	0	0	0	1	0	0	0	10352	1319	46	3	675	3	NEU3	11	74716816	Missense_Mutation	SNP	G	TCGA-KR-A7K7-01A-11D-A33K-10	27206294	74716816	60289700	32	44566										
NEU3	10825	hgsc.bcm.edu	37	chr11	74717089	74717089	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	tgagcccccacatggttgccAagggagtgtggtaagtttcc	13	10	0	1			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr11:74717089A>G	ENST00000544263.1	+	4	1009	c.839A>G	c.(838-840)cAa>cGa	p.Q280R	NEU3_ENST00000529024.1_Intron|NEU3_ENST00000294064.4_Missense_Mutation_p.Q313R|NEU3_ENST00000531509.1_Missense_Mutation_p.Q313R|NEU3_ENST00000532963.1_3'UTR|NEU3_ENST00000545272.1_Missense_Mutation_p.Q204R			Q9UQ49	NEUR3_HUMAN	sialidase 3 (membrane sialidase)	280					carbohydrate metabolic process (GO:0005975)|ganglioside catabolic process (GO:0006689)|glycosphingolipid metabolic process (GO:0006687)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha-sialidase activity (GO:0016997)|exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)|exo-alpha-sialidase activity (GO:0004308)			kidney(2)|large_intestine(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	11						CATGGTTGCCAAGGGAGTGTG	0.592																																					p.Q313R		Atlas-SNP	.											.	NEU3	50	.	0			c.A938G						.						42	45	44					11																	74717089		1982	4153	6135	SO:0001583	missense	10825	exon3			GTTGCCAAGGGAG	AB008185	CCDS44682.1	11q13.5	2008-02-05				ENSG00000162139			7760	protein-coding gene	gene with protein product		604617				10405317	Standard	NM_006656		Approved		uc001ovw.3	Q9UQ49		ENST00000544263.1:c.839A>G	chr11.hg19:g.74717089A>G	ENSP00000445591:p.Gln280Arg	37.0	0.0		31.0	6.0	NM_006656	A8K327|Q9NQE1	Missense_Mutation	SNP	ENST00000544263.1	hg19		.	.	.	.	.	.	.	.	.	.	A	20.3	3.968491	0.74131	.	.	ENSG00000162139	ENST00000294064;ENST00000531509;ENST00000544263;ENST00000545272	D;D;D;D	0.85861	-2.04;-2.04;-2.04;-2.04	5.35	5.35	0.76521	Neuraminidase (2);	0.105769	0.64402	D	0.000003	D	0.92919	0.7747	M	0.88979	2.995	0.49299	D	0.99977	D;D	0.76494	0.999;0.999	D;D	0.79108	0.992;0.992	D	0.93778	0.7081	10	0.62326	D	0.03	-16.2685	13.3289	0.60475	1.0:0.0:0.0:0.0	.	280;313	Q9UQ49;A8K327	NEUR3_HUMAN;.	R	313;313;280;204	ENSP00000294064:Q313R;ENSP00000432097:Q313R;ENSP00000445591:Q280R;ENSP00000439908:Q204R	ENSP00000294064:Q313R	Q	+	2	0	NEU3	74394737	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.761000	0.91691	2.247000	0.74100	0.482000	0.46254	CAA	.	.		0.592	NEU3-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_006656		G	74717089	A	G	74717089	3	3	315	1	0	0	0	0	1	0	0	0	10352	130	5	2	948	2	NEU3	11	74717089	Missense_Mutation	SNP	A	TCGA-KR-A7K7-01A-11D-A33K-10	273	74717089	60289427	33	44567										
TIMELESS	8914	hgsc.bcm.edu	37	chr12	56822710	56822710	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	cttgcggtcagtcagcatcaTctcatagtagttggtgaggt	12	8	4	1			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr12:56822710T>A	ENST00000553532.1	-	11	1411	c.1261A>T	c.(1261-1263)Atg>Ttg	p.M421L	TIMELESS_ENST00000229201.4_Missense_Mutation_p.M420L|TIMELESS_ENST00000554616.1_Intron					timeless circadian clock											NS(1)|breast(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(8)|lung(14)|ovary(7)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	49						GTCAGCATCATCTCATAGTAG	0.542																																					p.M421L		Atlas-SNP	.											.	TIMELESS	107	.	0			c.A1261T						.						127	110	116					12																	56822710		2203	4300	6503	SO:0001583	missense	8914	exon11			GCATCATCTCATA	AF098162	CCDS8918.1	12q13.3	2012-12-14	2012-12-14		ENSG00000111602	ENSG00000111602			11813	protein-coding gene	gene with protein product	"Tof1 homolog (S. cerevisiae)", "timeless circadian clock 1"	603887	"timeless (Drosophila) homolog", "timeless homolog (Drosophila)"			9856465	Standard	NM_003920		Approved	hTIM, TIM, TIM1	uc001slf.2	Q9UNS1	OTTHUMG00000170600	ENST00000553532.1:c.1261A>T	chr12.hg19:g.56822710T>A	ENSP00000450607:p.Met421Leu	83.0	0.0		91.0	37.0	NM_003920		Missense_Mutation	SNP	ENST00000553532.1	hg19	CCDS8918.1	.	.	.	.	.	.	.	.	.	.	T	33	5.244422	0.95272	.	.	ENSG00000111602	ENST00000229201;ENST00000553532	T;T	0.06608	3.28;3.28	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.18173	0.0436	M	0.77820	2.39	0.80722	D	1	P;P	0.51933	0.949;0.915	P;P	0.51895	0.683;0.485	T	0.00516	-1.1694	10	0.46703	T	0.11	-22.9615	14.8632	0.70397	0.0:0.0:0.0:1.0	.	420;421	Q9UNS1-2;Q9UNS1	.;TIM_HUMAN	L	420;421	ENSP00000229201:M420L;ENSP00000450607:M421L	ENSP00000229201:M421L	M	-	1	0	TIMELESS	55108977	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	5.982000	0.70532	2.214000	0.71695	0.459000	0.35465	ATG	.	.		0.542	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920		A	56822710	T	A	56822710	3	1	315	1	0	0	0	0	1	0	0	0	15919	1435	50	4	2441	4	TIMELESS	12	56822710	Missense_Mutation	SNP	T	TCGA-KR-A7K7-01A-11D-A33K-10		56822710	77029185	34	44568										
MYO1A	4640	hgsc.bcm.edu	37	chr12	57432386	57432386	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	gtctcggaagagtaggtcatTattcttgtcaataaagctgg	11	6	4	1			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr12:57432386T>A	ENST00000442789.2	-	18	1857	c.1570A>T	c.(1570-1572)Aat>Tat	p.N524Y	MYO1A_ENST00000300119.3_Missense_Mutation_p.N524Y|MYO1A_ENST00000476795.1_5'UTR|MYO1A_ENST00000544473.1_Missense_Mutation_p.N362Y	NM_001256041.1	NP_001242970.1	Q9UBC5	MYO1A_HUMAN	myosin IA	524	Myosin motor.				microvillus assembly (GO:0030033)|sensory perception of sound (GO:0007605)|vesicle localization (GO:0051648)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|brush border (GO:0005903)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|lateral plasma membrane (GO:0016328)|microvillus (GO:0005902)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(7)|urinary_tract(3)	50						AGTAGGTCATTATTCTTGTCA	0.532																																					p.N524Y		Atlas-SNP	.											.	MYO1A	122	.	0			c.A1570T						.						93	84	87					12																	57432386		2203	4300	6503	SO:0001583	missense	4640	exon17			GGTCATTATTCTT	L29137	CCDS8929.1	12q13-q15	2011-09-27			ENSG00000166866	ENSG00000166866		"Myosins / Myosin superfamily : Class I"	7595	protein-coding gene	gene with protein product		601478		MYHL, DFNA48		8884266, 12736868	Standard	NM_001256041		Approved		uc009zpd.3	Q9UBC5	OTTHUMG00000149899	ENST00000442789.2:c.1570A>T	chr12.hg19:g.57432386T>A	ENSP00000393392:p.Asn524Tyr	89.0	0.0		83.0	13.0	NM_005379	Q9UQD7	Missense_Mutation	SNP	ENST00000442789.2	hg19	CCDS8929.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.395588	0.83011	.	.	ENSG00000166866	ENST00000300119;ENST00000442789;ENST00000544473	D;D;D	0.87809	-2.3;-2.3;-2.3	4.94	4.94	0.65067	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.93926	0.8056	M	0.88450	2.955	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.94816	0.7983	10	0.87932	D	0	.	12.8538	0.57873	0.0:0.0:0.0:1.0	.	524	Q9UBC5	MYO1A_HUMAN	Y	524;524;362	ENSP00000300119:N524Y;ENSP00000393392:N524Y;ENSP00000440514:N362Y	ENSP00000300119:N524Y	N	-	1	0	MYO1A	55718653	1.000000	0.71417	0.989000	0.46669	0.995000	0.86356	8.040000	0.89188	2.004000	0.58718	0.459000	0.35465	AAT	.	.		0.532	MYO1A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313833.2	NM_005379		A	57432386	T	A	57432386	3	1	315	1	0	0	0	0	1	0	0	0	10077	1754	61	4	1609	4	MYO1A	12	57432386	Missense_Mutation	SNP	T	TCGA-KR-A7K7-01A-11D-A33K-10	609676	57432386	76419509	35	44569										
MTERFD3	80298	hgsc.bcm.edu	37	chr12	107372216	107372216	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	ttccaaaatactggctacagCagtctcatcggcacctagtt	7	12	1	0			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr12:107372216C>G	ENST00000552029.1	-	2	2345	c.277G>C	c.(277-279)Gct>Cct	p.A93P	MTERFD3_ENST00000240050.4_Missense_Mutation_p.A93P|MTERFD3_ENST00000392830.2_Missense_Mutation_p.A93P|C12orf23_ENST00000551237.1_3'UTR			Q49AM1	MTEF2_HUMAN		93					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)	transcription regulatory region DNA binding (GO:0044212)			breast(1)|kidney(1)|large_intestine(2)|lung(3)	7						CTGGCTACAGCAGTCTCATCG	0.418																																					p.A93P		Atlas-SNP	.											.	MTERFD3	32	.	0			c.G277C						.						125	133	131					12																	107372216		2203	4300	6503	SO:0001583	missense	80298	exon3			CTACAGCAGTCTC																												ENST00000552029.1:c.277G>C	chr12.hg19:g.107372216C>G	ENSP00000447651:p.Ala93Pro	75.0	0.0		80.0	43.0	NM_001033050	Q53HM2|Q9H4L6|Q9H7Y9	Missense_Mutation	SNP	ENST00000552029.1	hg19	CCDS9111.1	.	.	.	.	.	.	.	.	.	.	C	15.83	2.949348	0.53186	.	.	ENSG00000120832	ENST00000392830;ENST00000240050;ENST00000552029;ENST00000548101	T;T;T;T	0.11712	2.75;2.75;2.75;2.75	5.82	1.89	0.25635	.	0.587930	0.18669	N	0.134515	T	0.09992	0.0245	L	0.54323	1.7	0.09310	N	1	P	0.47484	0.896	B	0.42827	0.399	T	0.18618	-1.0331	10	0.31617	T	0.26	0.387	4.1989	0.10457	0.3743:0.3815:0.0:0.2442	.	93	Q49AM1	MTER3_HUMAN	P	93	ENSP00000376575:A93P;ENSP00000240050:A93P;ENSP00000447651:A93P;ENSP00000448343:A93P	ENSP00000240050:A93P	A	-	1	0	MTERFD3	105896346	0.000000	0.05858	0.001000	0.08648	0.989000	0.77384	-0.185000	0.09684	0.349000	0.23975	0.557000	0.71058	GCT	.	.		0.418	MTERFD3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406835.1			G	107372216	C	G	107372216	3	3	315	1	0	0	0	0	1	0	0	0	9930	710	25	4	884	4	MTERFD3	12	107372216	Missense_Mutation	SNP	C	TCGA-KR-A7K7-01A-11D-A33K-10	49939830	107372216	26479679	36	44570										
KSR2	283455	hgsc.bcm.edu	37	chr12	118199277	118199277	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	acgggattgttctccttcccCgtctctgtcgtgggccactg	11	14	2	0			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr12:118199277C>T	ENST00000339824.5	-	4	1252	c.525G>A	c.(523-525)acG>acA	p.T175T	KSR2_ENST00000425217.1_Silent_p.T146T			Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2	175					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.T207T(2)		NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(25)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TCTCCTTCCCCGTCTCTGTCG	0.602																																					p.T146T		Atlas-SNP	.											KSR2,NS,carcinoma,0,1	KSR2	208	.	2	Substitution - coding silent(2)	lung(1)|endometrium(1)	c.G438A						.						70	72	71					12																	118199277		1955	4138	6093	SO:0001819	synonymous_variant	283455	exon4			CTTCCCCGTCTCT	AY345972	CCDS61250.1	12q24.22-q24.23	2014-08-12			ENSG00000171435	ENSG00000171435			18610	protein-coding gene	gene with protein product		610737				12471243	Standard	NM_173598		Approved	FLJ25965	uc001two.2	Q6VAB6	OTTHUMG00000169020	ENST00000339824.5:c.525G>A	chr12.hg19:g.118199277C>T		82.0	0.0		70.0	29.0	NM_173598	A0PJT2|Q3B828|Q8N775	Silent	SNP	ENST00000339824.5	hg19																																																																																				.	.		0.602	KSR2-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401987.2	NM_173598		T	118199277	C	T	118199277	2	4	315	1	0	0	0	0	0	0	0	1	8591	639	23	1		1	KSR2	12	118199277	Silent	SNP	C	TCGA-KR-A7K7-01A-11D-A33K-10	10827061	118199277	15652618	37	44571										
FREM2	341640	hgsc.bcm.edu	37	chr13	39264296	39264296	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	atgtccggccagtggatgatGaagtgcccatactgagccat	12	10	0	3			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr13:39264296G>T	ENST00000280481.7	+	1	3031	c.2815G>T	c.(2815-2817)Gaa>Taa	p.E939*		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	939					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		AGTGGATGATGAAGTGCCCAT	0.493																																					p.E939X		Atlas-SNP	.											.	FREM2	385	.	0			c.G2815T						.						69	60	63					13																	39264296		2203	4300	6503	SO:0001587	stop_gained	341640	exon1			GATGATGAAGTGC	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.2815G>T	chr13.hg19:g.39264296G>T	ENSP00000280481:p.Glu939*	68.0	0.0		72.0	15.0	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Nonsense_Mutation	SNP	ENST00000280481.7	hg19	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	G	41	8.871636	0.98984	.	.	ENSG00000150893	ENST00000280481	.	.	.	5.59	5.59	0.84812	.	0.049447	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.19147	T	0.46	.	19.6034	0.95572	0.0:0.0:1.0:0.0	.	.	.	.	X	939	.	ENSP00000280481:E939X	E	+	1	0	FREM2	38162296	1.000000	0.71417	0.012000	0.15200	0.012000	0.07955	7.988000	0.88194	2.645000	0.89757	0.655000	0.94253	GAA	.	.		0.493	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		T	39264296	G	T	39264296	4	4	315	1	0	0	0	0	0	1	0	0	6053	1291	45	3	2817	3	FREM2	13	39264296	Nonsense_Mutation	SNP	G	TCGA-KR-A7K7-01A-11D-A33K-10		39264296	75905582	38	44572										
MGAT2	4247	hgsc.bcm.edu	37	chr14	50089030	50089030	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	gatgattataactgggactgGactcttcaatacttgactgt	9	7	2	2			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr14:50089030G>A	ENST00000305386.2	+	1	1542	c.1044G>A	c.(1042-1044)tgG>tgA	p.W348*	RPL36AL_ENST00000298289.6_5'Flank|RP11-649E7.5_ENST00000555043.1_RNA	NM_002408.3	NP_002399.1	Q10469	MGAT2_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,2-N-acetylglucosaminyltransferase	348					cellular protein metabolic process (GO:0044267)|oligosaccharide biosynthetic process (GO:0009312)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	alpha-1,6-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity (GO:0008455)|carbohydrate binding (GO:0030246)			cervix(1)|endometrium(3)|large_intestine(1)|lung(6)	11	all_epithelial(31;0.0021)|Breast(41;0.0124)					ACTGGGACTGGACTCTTCAAT	0.438																																					p.W348X		Atlas-SNP	.											.	MGAT2	26	.	0			c.G1044A						.						143	136	138					14																	50089030		2203	4300	6503	SO:0001587	stop_gained	4247	exon1			GGACTGGACTCTT	U15128	CCDS9690.1	14q21	2013-02-25			ENSG00000168282	ENSG00000168282	2.4.1.143	"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	7045	protein-coding gene	gene with protein product		602616				7635144	Standard	NM_002408		Approved	GNT-II	uc001wwr.3	Q10469	OTTHUMG00000140271	ENST00000305386.2:c.1044G>A	chr14.hg19:g.50089030G>A	ENSP00000307423:p.Trp348*	92.0	0.0		90.0	22.0	NM_002408	B3KPC5|B3KQM0	Nonsense_Mutation	SNP	ENST00000305386.2	hg19	CCDS9690.1	.	.	.	.	.	.	.	.	.	.	G	40	8.467835	0.98825	.	.	ENSG00000168282	ENST00000305386;ENST00000504161	.	.	.	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.3904	19.7004	0.96050	0.0:0.0:1.0:0.0	.	.	.	.	X	348;354	.	ENSP00000307423:W348X	W	+	3	0	MGAT2	49158780	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.029000	0.88807	2.657000	0.90304	0.555000	0.69702	TGG	.	.		0.438	MGAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276807.1	NM_002408		A	50089030	G	A	50089030	4	1	315	1	0	0	0	0	0	1	0	0	9552	1183	41	3	1046	3	MGAT2	14	50089030	Nonsense_Mutation	SNP	G	TCGA-KR-A7K7-01A-11D-A33K-10		50089030	57260510	39	44573										
TOMM20L	387990	hgsc.bcm.edu	37	chr14	58874094	58874094	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	gcaatgcccttttagtgtgcGagcaaccacgggaacttctg	11	11	1	0	rs141434824		TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr14:58874094G>A	ENST00000360945.2	+	4	355	c.313G>A	c.(313-315)Gag>Aag	p.E105K	TIMM9_ENST00000216463.4_5'Flank|RP11-517O13.1_ENST00000556734.1_RNA	NM_207377.2	NP_997260.1	Q6UXN7	TO20L_HUMAN	translocase of outer mitochondrial membrane 20 homolog (yeast)-like	105					protein targeting (GO:0006605)	integral component of membrane (GO:0016021)|mitochondrial outer membrane translocase complex (GO:0005742)				large_intestine(2)|lung(2)	4						TTTAGTGTGCGAGCAACCACG	0.433													G|||	1	0.000199681	0	0	5008	,	,		18053	0		0.001	False		,,,				2504	0				p.E105K		Atlas-SNP	.											TOMM20L,NS,carcinoma,0,1	TOMM20L	8	.	0			c.G313A						.	G	LYS/GLU	0,4406		0,0,2203	103	98	100		313	1.9	0.8	14	dbSNP_134	100	2,8598	2.2+/-6.3	0,2,4298	yes	missense	TOMM20L	NM_207377.2	56	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign	105/153	58874094	2,13004	2203	4300	6503	SO:0001583	missense	387990	exon4			GTGTGCGAGCAAC		CCDS9734.1	14q23.1	2009-01-14			ENSG00000196860	ENSG00000196860			33752	protein-coding gene	gene with protein product	"translocase of outer mitochondrial membrane 20 homolog type I"					15733919	Standard	NM_207377		Approved	UNQ9438	uc001xdr.1	Q6UXN7	OTTHUMG00000140323	ENST00000360945.2:c.313G>A	chr14.hg19:g.58874094G>A	ENSP00000354204:p.Glu105Lys	127.0	1.0		93.0	4.0	NM_207377	B2RPR0	Missense_Mutation	SNP	ENST00000360945.2	hg19	CCDS9734.1	.	.	.	.	.	.	.	.	.	.	G	10.72	1.430831	0.25726	0.0	2.33E-4	ENSG00000196860	ENST00000360945	T	0.30448	1.53	4.77	1.92	0.25849	Mitochondrial outer membrane translocase complex, subunit Tom20 domain (2);	0.636489	0.13862	N	0.357595	T	0.13841	0.0335	N	0.14661	0.345	0.24401	N	0.994702	B	0.15141	0.012	B	0.08055	0.003	T	0.21895	-1.0232	10	0.28530	T	0.3	0.1489	1.754	0.02978	0.1785:0.1641:0.4877:0.1697	.	105	Q6UXN7	TO20L_HUMAN	K	105	ENSP00000354204:E105K	ENSP00000354204:E105K	E	+	1	0	TOMM20L	57943847	0.736000	0.28164	0.792000	0.32020	0.173000	0.22820	0.781000	0.26774	0.225000	0.20959	-0.152000	0.13540	GAG	.	G|1.000;A|0.000		0.433	TOMM20L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276937.1	NM_207377		A	58874094	G	A	58874094	3	1	315	1	0	0	0	0	1	0	0	0	16370	1059	37	1	327	1	TOMM20L	14	58874094	Missense_Mutation	SNP	G	TCGA-KR-A7K7-01A-11D-A33K-10	8785064	58874094	48475446	40	44574										
HDDC3	374659	hgsc.bcm.edu	37	chr15	91475134	91475134	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	gtagctccacctcatccaggGtggtgtctgtgtcctccacc	10	15	2	0			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr15:91475134G>A	ENST00000394272.3	-	3	237	c.209C>T	c.(208-210)aCc>aTc	p.T70I	HDDC3_ENST00000330334.3_Missense_Mutation_p.T70I|AC068831.3_ENST00000448987.1_RNA|HDDC3_ENST00000559898.1_Missense_Mutation_p.T70I|UNC45A_ENST00000394275.2_Intron|AC068831.3_ENST00000438890.1_RNA			Q8N4P3	MESH1_HUMAN	HD domain containing 3	70	HD.						guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity (GO:0008893)|metal ion binding (GO:0046872)			NS(1)|ovary(1)	2	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			CTCATCCAGGGTGGTGTCTGT	0.592											OREG0023475	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T70I		Atlas-SNP	.											.	HDDC3	8	.	0			c.C209T						.						81	74	77					15																	91475134		2198	4298	6496	SO:0001583	missense	374659	exon3			TCCAGGGTGGTGT	AK057584	CCDS10366.1, CCDS66866.1	15q26.1	2005-08-22			ENSG00000184508	ENSG00000184508			30522	protein-coding gene	gene with protein product						12477932	Standard	NM_001286451		Approved	MGC45386	uc002bqe.4	Q8N4P3	OTTHUMG00000141260	ENST00000394272.3:c.209C>T	chr15.hg19:g.91475134G>A	ENSP00000377814:p.Thr70Ile	36.0	0.0	1282	23.0	8.0	NM_198527		Missense_Mutation	SNP	ENST00000394272.3	hg19		.	.	.	.	.	.	.	.	.	.	G	29.6	5.022380	0.93462	.	.	ENSG00000184508	ENST00000394272;ENST00000330334	.	.	.	4.97	4.97	0.65823	Metal-dependent phosphohydrolase, HD domain (1);Metal-dependent phosphohydrolase, HD subdomain (1);	0.102055	0.64402	D	0.000004	D	0.89784	0.6815	H	0.97659	4.05	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.79108	0.992;0.975	D	0.93277	0.6657	9	0.87932	D	0	-6.9392	17.0399	0.86486	0.0:0.0:1.0:0.0	.	70;70	Q8N4P3;Q8N4P3-2	MESH1_HUMAN;.	I	70	.	ENSP00000330721:T70I	T	-	2	0	HDDC3	89276138	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.725000	0.61979	2.585000	0.87301	0.555000	0.69702	ACC	.	.		0.592	HDDC3-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000280403.2	NM_198527		A	91475134	G	A	91475134	3	1	315	1	0	0	0	0	1	0	0	0	7026	1261	44	3	221	3	HDDC3	15	91475134	Missense_Mutation	SNP	G	TCGA-KR-A7K7-01A-11D-A33K-10		91475134	11056258	41	44575										
IRX6	79190	hgsc.bcm.edu	37	chr16	55362664	55362664	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	cggctgagtgacctggaagaCctggaggaagaggaggagga	19	6	0	4	rs143272826		TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr16:55362664C>G	ENST00000290552.7	+	5	2106	c.774C>G	c.(772-774)gaC>gaG	p.D258E	RP11-26L20.3_ENST00000558730.2_RNA	NM_024335.2	NP_077311.2	P78412	IRX6_HUMAN	iroquois homeobox 6	258					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(5)|endometrium(3)|kidney(2)|large_intestine(6)|liver(2)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	33						ACCTGGAAGACCTggaggaag	0.617																																					p.D258E		Atlas-SNP	.											.	IRX6	66	.	0			c.C774G						.						33	40	38					16																	55362664		2191	4286	6477	SO:0001583	missense	79190	exon5			GGAAGACCTGGAG	AF319966	CCDS32449.1	16q12.2	2011-06-20	2007-07-13	2003-01-10		ENSG00000159387		"Homeoboxes / TALE class"	14675	protein-coding gene	gene with protein product		606196	"iroquois homeobox protein 7", "iroquois homeobox protein 6"	IRX7			Standard	NM_024335		Approved	IRX-3	uc002ehy.3	P78412		ENST00000290552.7:c.774C>G	chr16.hg19:g.55362664C>G	ENSP00000290552:p.Asp258Glu	46.0	0.0		30.0	11.0	NM_024335	B2RN06|Q7Z2K0	Missense_Mutation	SNP	ENST00000290552.7	hg19	CCDS32449.1	.	.	.	.	.	.	.	.	.	.	C	16.69	3.192126	0.58017	.	.	ENSG00000159387	ENST00000290552	D	0.91295	-2.82	5.27	3.29	0.37713	.	0.833479	0.10461	N	0.671932	D	0.90703	0.7083	L	0.27053	0.805	0.43814	D	0.996374	D	0.76494	0.999	D	0.83275	0.996	D	0.84033	0.0360	10	0.36615	T	0.2	-36.4803	7.5295	0.27674	0.0:0.7312:0.0:0.2688	.	258	P78412	IRX6_HUMAN	E	258	ENSP00000290552:D258E	ENSP00000290552:D258E	D	+	3	2	IRX6	53920165	0.904000	0.30761	1.000000	0.80357	0.844000	0.47949	1.470000	0.35354	0.588000	0.29660	0.462000	0.41574	GAC	.	C|1.000;A|0.000		0.617	IRX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417445.4	NM_024335		G	55362664	C	G	55362664	3	3	315	1	0	0	0	0	1	0	0	0	7857	506	18	4	792	4	IRX6	16	55362664	Missense_Mutation	SNP	C	TCGA-KR-A7K7-01A-11D-A33K-10		55362664	34992089	42	44576										
CTU2	348180	hgsc.bcm.edu	37	chr16	88776364	88776364	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	agggactgtttcaaggccttCtacgtccacaagttcagagc	10	11	3	1			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr16:88776364C>G	ENST00000453996.2	+	3	230	c.162C>G	c.(160-162)ttC>ttG	p.F54L	CTU2_ENST00000567949.1_Missense_Mutation_p.F54L|CTU2_ENST00000378384.3_Intron|CTU2_ENST00000312060.5_Missense_Mutation_p.F54L	NM_001012759.1	NP_001012777.1			cytosolic thiouridylase subunit 2 homolog (S. pombe)											NS(1)|breast(1)|endometrium(1)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	11						TCAAGGCCTTCTACGTCCACA	0.607																																					p.F54L		Atlas-SNP	.											.	CTU2	66	.	0			c.C162G						.						169	164	166					16																	88776364		2198	4300	6498	SO:0001583	missense	348180	exon3			GGCCTTCTACGTC	BC021056	CCDS32506.1, CCDS45545.1	16q24.3	2013-10-11	2009-08-19	2009-08-19		ENSG00000174177			28005	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 84"	C16orf84		19017811	Standard	NM_001012759		Approved	NCS2	uc002flm.3	Q2VPK5		ENST00000453996.2:c.162C>G	chr16.hg19:g.88776364C>G	ENSP00000388320:p.Phe54Leu	66.0	0.0		39.0	11.0	NM_001012759		Missense_Mutation	SNP	ENST00000453996.2	hg19	CCDS45545.1	.	.	.	.	.	.	.	.	.	.	C	13.28	2.190379	0.38707	.	.	ENSG00000174177	ENST00000312060;ENST00000453996	T;T	0.38722	1.12;1.12	3.88	-1.97	0.07503	.	0.268590	0.37623	N	0.002017	T	0.24661	0.0598	L	0.38175	1.15	0.80722	D	1	B;B	0.13145	0.006;0.007	B;B	0.13407	0.009;0.004	T	0.02829	-1.1105	10	0.30854	T	0.27	.	5.2425	0.15479	0.0:0.4496:0.1587:0.3918	.	54;54	Q2VPK5-5;Q2VPK5	.;CTU2_HUMAN	L	54	ENSP00000308617:F54L;ENSP00000388320:F54L	ENSP00000308617:F54L	F	+	3	2	CTU2	87303865	0.993000	0.37304	0.022000	0.16811	0.902000	0.53008	0.245000	0.18142	-0.160000	0.11002	0.297000	0.19635	TTC	.	.		0.607	CTU2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423025.1	NM_001012762		G	88776364	C	G	88776364	3	3	315	1	0	0	0	0	1	0	0	0	4050	912	32	4	172	4	CTU2	16	88776364	Missense_Mutation	SNP	C	TCGA-KR-A7K7-01A-11D-A33K-10	33413700	88776364	1578389	43	44577										
SREBF1	6720	hgsc.bcm.edu	37	chr17	17723609	17723613	+	Frame_Shift_Del	DEL	TGGAG	TGGAG	-													0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	atggacgggtacatcttcaaTggagtgggtgcaggctgggg					rs368174566		TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	TGGAG	TGGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr17:17723609_17723613delTGGAG	ENST00000261646.5	-	2	498_502	c.314_318delCTCCA	c.(313-318)actccafs	p.TP105fs	SREBF1_ENST00000338854.5_Frame_Shift_Del_p.TP105fs|SREBF1_ENST00000583732.1_Intron|SREBF1_ENST00000435530.2_Frame_Shift_Del_p.TP105fs|SREBF1_ENST00000395757.1_5'Flank|SREBF1_ENST00000355815.4_Frame_Shift_Del_p.TP135fs	NM_004176.4	NP_004167.3	P36956	SRBP1_HUMAN	sterol regulatory element binding transcription factor 1	105	Pro/Ser-rich.				aging (GO:0007568)|cellular lipid metabolic process (GO:0044255)|cellular response to fatty acid (GO:0071398)|cellular response to starvation (GO:0009267)|cholesterol metabolic process (GO:0008203)|circadian rhythm (GO:0007623)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|lipid metabolic process (GO:0006629)|lung development (GO:0030324)|negative regulation of insulin secretion (GO:0046676)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of fatty acid metabolic process (GO:0019217)|regulation of heart rate by chemical signal (GO:0003062)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to drug (GO:0042493)|response to food (GO:0032094)|response to glucagon (GO:0033762)|response to glucose (GO:0009749)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|sterol response element binding (GO:0032810)			cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	14						ACATCTTCAATGGAGTGGGTGCAGG	0.634																																					p.135_137del		Atlas-Indel,Pindel	.											.	SREBF1	47	.	0			c.405_409del						.																																			SO:0001589	frameshift_variant	6720	exon3			.	BC057388	CCDS11189.1, CCDS32583.1	17p11.2	2013-05-21			ENSG00000072310	ENSG00000072310		"Basic helix-loop-helix proteins"	11289	protein-coding gene	gene with protein product		184756				8402897, 7759101	Standard	NM_001005291		Approved	SREBP1, bHLHd1, SREBP-1c	uc002grt.2	P36956	OTTHUMG00000059313	ENST00000261646.5:c.314_318delCTCCA	chr17.hg19:g.17723609_17723613delTGGAG	ENSP00000261646:p.Thr105fs	48.0	0.0		53.0	24.0	NM_001005291	B0I4X3|B0I4X4|D3DXC4|Q16062|Q59F52|Q6P4R7|Q6PFW7|Q6PJ36|Q8TAK9	Frame_Shift_Del	DEL	ENST00000261646.5	hg19	CCDS11189.1																																																																																			.	.		0.634	SREBF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131771.1	NM_004176		-	17723613	TGGAG	-	17723609	7	5	315	1	0	1	0	1	0	0	0	0	15156	1451	51	0	3197	0	SREBF1	17	17723609	Frame_Shift_Del	DEL	TGGAG	TCGA-KR-A7K7-01A-11D-A33K-10		17723609	63471601	44	44578										
EFCAB3	146779	hgsc.bcm.edu	37	chr17	60464748	60464748	+	Frame_Shift_Del	DEL	A	A	-													0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	atgccaattacaacacaaagAaaagaagctaagtgcttcac							TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr17:60464748delA	ENST00000305286.3	+	3	200	c.122delA	c.(121-123)gaafs	p.E41fs	EFCAB3_ENST00000450662.2_Frame_Shift_Del_p.E93fs	NM_173503.3	NP_775774.1	Q8N7B9	EFCB3_HUMAN	EF-hand calcium binding domain 3	41							calcium ion binding (GO:0005509)			cervix(1)|endometrium(2)|large_intestine(5)|lung(6)|skin(3)	17			BRCA - Breast invasive adenocarcinoma(2;2.27e-11)			CAACACAAAGAAAAGAAGCTA	0.363																																					p.E93fs		Atlas-Indel,Pindel	.											.	EFCAB3	71	.	0			c.277delG						.						94	86	89					17																	60464748		2203	4300	6503	SO:0001589	frameshift_variant	146779	exon5			.	AK098684	CCDS11632.1, CCDS45751.1	17q23.3	2013-01-10			ENSG00000172421	ENSG00000172421		"EF-hand domain containing"	26379	protein-coding gene	gene with protein product						12477932	Standard	NM_173503		Approved	FLJ25818	uc010wpc.2	Q8N7B9	OTTHUMG00000179175	ENST00000305286.3:c.122delA	chr17.hg19:g.60464748delA	ENSP00000302649:p.Glu41fs	63.0	0.0		91.0	39.0	NM_001144933	J3KQM8	Frame_Shift_Del	DEL	ENST00000305286.3	hg19	CCDS11632.1																																																																																			.	.		0.363	EFCAB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379114.1	NM_173503		-	60464748	A	-	60464748	7	5	315	1	0	1	0	1	0	0	0	0	4937	246	9	0	296	0	EFCAB3	17	60464748	Frame_Shift_Del	DEL	A	TCGA-KR-A7K7-01A-11D-A33K-10	42741139	60464748	20730462	45	44579										
ANKRD12	23253	hgsc.bcm.edu	37	chr18	9208758	9208758	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	ccactctctgagcgaaaacaGatggcacttcttatgcagat	8	11	2	3			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr18:9208758G>C	ENST00000262126.4	+	5	648	c.408G>C	c.(406-408)caG>caC	p.Q136H	ANKRD12_ENST00000540578.2_3'UTR|ANKRD12_ENST00000383440.2_Missense_Mutation_p.Q113H|ANKRD12_ENST00000400020.3_Missense_Mutation_p.Q113H	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	136						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						AGCGAAAACAGATGGCACTTC	0.408																																					p.Q136H		Atlas-SNP	.											.	ANKRD12	167	.	0			c.G408C						.						213	187	196					18																	9208758		2203	4300	6503	SO:0001583	missense	23253	exon5			AAAACAGATGGCA	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.408G>C	chr18.hg19:g.9208758G>C	ENSP00000262126:p.Gln136His	174.0	0.0		169.0	49.0	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Missense_Mutation	SNP	ENST00000262126.4	hg19	CCDS11843.1	.	.	.	.	.	.	.	.	.	.	G	13.74	2.326098	0.41197	.	.	ENSG00000101745	ENST00000383440;ENST00000546007;ENST00000262126;ENST00000540578	T;T;T	0.52295	3.38;0.67;3.43	5.82	4.04	0.47022	.	0.000000	0.85682	D	0.000000	T	0.57417	0.2052	L	0.36672	1.1	0.80722	D	1	D;D;D	0.76494	0.997;0.999;0.998	D;D;D	0.85130	0.99;0.997;0.993	T	0.59010	-0.7534	10	0.87932	D	0	-21.6665	12.0274	0.53380	0.1385:0.0:0.8615:0.0	.	136;113;136	Q6PG48;Q6UB98-2;Q6UB98	.;.;ANR12_HUMAN	H	113;113;136;136	ENSP00000372932:Q113H;ENSP00000441510:Q113H;ENSP00000262126:Q136H	ENSP00000262126:Q136H	Q	+	3	2	ANKRD12	9198758	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.946000	0.63576	0.807000	0.34208	0.467000	0.42956	CAG	.	.		0.408	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		C	9208758	G	C	9208758	3	2	315	1	0	0	0	0	1	0	0	0	640	933	33	4	422	4	ANKRD12	18	9208758	Missense_Mutation	SNP	G	TCGA-KR-A7K7-01A-11D-A33K-10		9208758	68868490	46	44580										
SETBP1	26040	hgsc.bcm.edu	37	chr18	42643643	42643643	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	agaggaagtcccgagggagtGagagcgaggtccttccctag	16	9	0	2			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr18:42643643G>C	ENST00000282030.5	+	6	5067	c.4771G>C	c.(4771-4773)Gag>Cag	p.E1591Q		NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	1591						nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(20)|lung(47)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	104				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		CCGAGGGAGTGAGAGCGAGGT	0.692									Schinzel-Giedion syndrome																												p.E1591Q		Atlas-SNP	.											.	SETBP1	577	.	0			c.G4771C						.						13	18	17					18																	42643643		2134	4112	6246	SO:0001583	missense	26040	exon6	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	GGGAGTGAGAGCG	AB022660	CCDS11923.2, CCDS45859.1	18q21.1	2008-08-01			ENSG00000152217	ENSG00000152217			15573	protein-coding gene	gene with protein product		611060				11231286	Standard	NM_015559		Approved	SEB, KIAA0437	uc010dni.3	Q9Y6X0	OTTHUMG00000132613	ENST00000282030.5:c.4771G>C	chr18.hg19:g.42643643G>C	ENSP00000282030:p.Glu1591Gln	280.0	0.0		206.0	55.0	NM_015559	A6H8W5|Q6P6C3|Q9UEF3	Missense_Mutation	SNP	ENST00000282030.5	hg19	CCDS11923.2	.	.	.	.	.	.	.	.	.	.	G	24.7	4.564599	0.86439	.	.	ENSG00000152217	ENST00000282030	T	0.71817	-0.6	4.97	4.97	0.65823	.	0.000000	0.56097	D	0.000037	T	0.75474	0.3854	N	0.24115	0.695	0.36753	D	0.882857	D	0.67145	0.996	D	0.78314	0.991	T	0.82068	-0.0640	10	0.87932	D	0	.	16.778	0.85556	0.0:0.0:1.0:0.0	.	1591	Q9Y6X0	SETBP_HUMAN	Q	1591	ENSP00000282030:E1591Q	ENSP00000282030:E1591Q	E	+	1	0	SETBP1	40897641	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.139000	0.71728	2.443000	0.82685	0.655000	0.94253	GAG	.	.		0.692	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110		C	42643643	G	C	42643643	3	2	315	1	0	0	0	0	1	0	0	0	14144	1291	45	4	4982	4	SETBP1	18	42643643	Missense_Mutation	SNP	G	TCGA-KR-A7K7-01A-11D-A33K-10	33434885	42643643	35433605	47	44581										
TNFRSF11A	8792	hgsc.bcm.edu	37	chr18	60036567	60036567	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	gtggacccttgccccagtgcGcctatggcatgggccttccc	12	16	0	0			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr18:60036567G>A	ENST00000586569.1	+	9	1455	c.1417G>A	c.(1417-1419)Gcc>Acc	p.A473T	TNFRSF11A_ENST00000269485.7_Intron	NM_001270949.1|NM_003839.3	NP_001257878.1|NP_003830.1	Q9Y6Q6	TNR11_HUMAN	tumor necrosis factor receptor superfamily, member 11a, NFKB activator	473					adaptive immune response (GO:0002250)|cell-cell signaling (GO:0007267)|circadian temperature homeostasis (GO:0060086)|lymph node development (GO:0048535)|mammary gland alveolus development (GO:0060749)|monocyte chemotaxis (GO:0002548)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade via TNFSF11-mediated signaling (GO:0071848)|positive regulation of fever generation by positive regulation of prostaglandin secretion (GO:0071812)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|response to cytokine (GO:0034097)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to radiation (GO:0009314)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|TNFSF11-mediated signaling pathway (GO:0071847)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|tumor necrosis factor-activated receptor activity (GO:0005031)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(13)|skin(3)|upper_aerodigestive_tract(1)	29		Colorectal(73;0.188)				GCCCCAGTGCGCCTATGGCAT	0.652																																					p.A473T		Atlas-SNP	.											TNFRSF11A,NS,NS,0,1	TNFRSF11A	51	.	0			c.G1417A						.																																			SO:0001583	missense	8792	exon9			CAGTGCGCCTATG	AF018253	CCDS11980.1, CCDS59324.1, CCDS74227.1, CCDS74228.1	18q22.1	2014-09-17			ENSG00000141655	ENSG00000141655		"Tumor necrosis factor receptor superfamily", "CD molecules"	11908	protein-coding gene	gene with protein product		603499	"tumor necrosis factor receptor superfamily, member 11a, activator of NFKB", "Paget disease of bone 2", "loss of heterozygosity, 18, chromosomal region 1"	PDB2, LOH18CR1		9367155, 10615125	Standard	NM_001270951		Approved	RANK, CD265, FEO	uc002lin.4	Q9Y6Q6	OTTHUMG00000132779	ENST00000586569.1:c.1417G>A	chr18.hg19:g.60036567G>A	ENSP00000465500:p.Ala473Thr	35.0	0.0		26.0	7.0	NM_003839	I4EC36|I4EC38|I4EC39|I7JE63|N0GVH0|Q59EP9	Missense_Mutation	SNP	ENST00000586569.1	hg19	CCDS11980.1	.	.	.	.	.	.	.	.	.	.	G	6.414	0.444590	0.12164	.	.	ENSG00000141655	ENST00000269485	.	.	.	5.03	1.67	0.24075	.	4.700340	0.00481	N	0.000137	T	0.28433	0.0703	N	0.21448	0.665	0.22796	N	0.998722	B	0.24823	0.112	B	0.15484	0.013	T	0.11446	-1.0587	8	.	.	.	-8.869	4.468	0.11698	0.2877:0.1863:0.5261:0.0	.	473	Q9Y6Q6	TNR11_HUMAN	T	473	.	.	A	+	1	0	TNFRSF11A	58187547	0.605000	0.26941	0.159000	0.22649	0.622000	0.37654	0.996000	0.29719	0.492000	0.27815	-0.244000	0.11960	GCC	.	.		0.652	TNFRSF11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256186.2			A	60036567	G	A	60036567	3	1	315	1	0	0	0	0	1	0	0	0	16299	1087	38	1	1451	1	TNFRSF11A	18	60036567	Missense_Mutation	SNP	G	TCGA-KR-A7K7-01A-11D-A33K-10	17392924	60036567	18040681	48	44582										
ADNP2	22850	hgsc.bcm.edu	37	chr18	77896211	77896211	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	tggtgaagtgatgcatgattCcagtttttctgttaagagaa	11	4	1	4			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr18:77896211C>A	ENST00000262198.4	+	4	3370	c.2915C>A	c.(2914-2916)tCc>tAc	p.S972Y		NM_014913.3	NP_055728.1	Q6IQ32	ADNP2_HUMAN	ADNP homeobox 2	972					cellular response to oxidative stress (GO:0034599)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell death (GO:0060548)|neuron differentiation (GO:0030182)|positive regulation of cell growth (GO:0030307)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(9)|liver(1)|lung(15)|ovary(5)|prostate(2)	42		all_cancers(4;1.06e-15)|all_epithelial(4;2.36e-10)|all_lung(4;0.000302)|Lung NSC(4;0.000518)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0256)|all_hematologic(56;0.15)|Melanoma(33;0.2)		Epithelial(2;1.1e-11)|OV - Ovarian serous cystadenocarcinoma(15;7.54e-09)|BRCA - Breast invasive adenocarcinoma(31;0.00247)|STAD - Stomach adenocarcinoma(84;0.164)		ATGCATGATTCCAGTTTTTCT	0.542																																					p.S972Y		Atlas-SNP	.											.	ADNP2	102	.	0			c.C2915A						.						71	77	75					18																	77896211		2203	4300	6503	SO:0001583	missense	22850	exon4			ATGATTCCAGTTT	AB020670	CCDS32853.1	18q23	2013-01-07	2007-07-17	2007-07-17	ENSG00000101544	ENSG00000101544		"Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	23803	protein-coding gene	gene with protein product			"zinc finger protein 508"	ZNF508			Standard	NM_014913		Approved	KIAA0863	uc002lnw.3	Q6IQ32	OTTHUMG00000172535	ENST00000262198.4:c.2915C>A	chr18.hg19:g.77896211C>A	ENSP00000262198:p.Ser972Tyr	49.0	0.0		52.0	18.0	NM_014913	A8K951|O94943|Q9H9P3	Missense_Mutation	SNP	ENST00000262198.4	hg19	CCDS32853.1	.	.	.	.	.	.	.	.	.	.	C	0.010	-1.746738	0.00669	.	.	ENSG00000101544	ENST00000262198	.	.	.	5.03	5.03	0.67393	.	0.996198	0.08135	N	0.992473	T	0.45074	0.1324	L	0.44542	1.39	0.09310	N	1	P	0.48016	0.904	P	0.44946	0.465	T	0.40496	-0.9560	8	.	.	.	-6.3646	15.3834	0.74679	0.0:1.0:0.0:0.0	.	972	Q6IQ32	ADNP2_HUMAN	Y	972	.	.	S	+	2	0	ADNP2	75997202	0.002000	0.14202	0.005000	0.12908	0.001000	0.01503	1.657000	0.37366	2.612000	0.88384	0.655000	0.94253	TCC	.	.		0.542	ADNP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418979.1	NM_014913		A	77896211	C	A	77896211	3	1	315	1	0	0	0	0	1	0	0	0	324	855	30	3	2925	3	ADNP2	18	77896211	Missense_Mutation	SNP	C	TCGA-KR-A7K7-01A-11D-A33K-10	17859644	77896211	181037	49	44583										
COL5A3	50509	hgsc.bcm.edu	37	chr19	10080566	10080566	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	ttggcacctttctccccttcTctgccttctcgacccatgtg	6	17	3	0			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr19:10080566T>A	ENST00000264828.3	-	55	4054	c.3969A>T	c.(3967-3969)agA>agT	p.R1323S		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	1323	Triple-helical region.				axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			TCTCCCCTTCTCTGCCTTCTC	0.612																																					p.R1323S		Atlas-SNP	.											.	COL5A3	243	.	0			c.A3969T						.						126	100	109					19																	10080566		2203	4300	6503	SO:0001583	missense	50509	exon55			CCCTTCTCTGCCT	AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573		"Collagens"	14864	protein-coding gene	gene with protein product		120216				10722718	Standard	NM_015719		Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.3969A>T	chr19.hg19:g.10080566T>A	ENSP00000264828:p.Arg1323Ser	110.0	0.0		95.0	41.0	NM_015719	Q9NZQ6	Missense_Mutation	SNP	ENST00000264828.3	hg19	CCDS12222.1	.	.	.	.	.	.	.	.	.	.	T	15.05	2.718942	0.48622	.	.	ENSG00000080573	ENST00000264828	D	0.94000	-3.33	4.16	4.16	0.48862	.	0.209970	0.39834	N	0.001243	D	0.84129	0.5404	N	0.17922	0.545	0.27075	N	0.963235	B	0.30482	0.281	B	0.25405	0.06	T	0.71111	-0.4687	10	0.07482	T	0.82	.	11.2176	0.48835	0.0:0.0:0.0:1.0	.	1323	P25940	CO5A3_HUMAN	S	1323	ENSP00000264828:R1323S	ENSP00000264828:R1323S	R	-	3	2	COL5A3	9941566	0.915000	0.31059	1.000000	0.80357	0.839000	0.47603	0.795000	0.26972	1.743000	0.51761	0.402000	0.26972	AGA	.	.		0.612	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719		A	10080566	T	A	10080566	3	1	315	1	0	0	0	0	1	0	0	0	3700	1548	54	4	1320	4	COL5A3	19	10080566	Missense_Mutation	SNP	T	TCGA-KR-A7K7-01A-11D-A33K-10		10080566	49048417	50	44584										
ZNF844	284391	hgsc.bcm.edu	37	chr19	12187711	12187711	+	Frame_Shift_Del	DEL	A	A	-													0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	atgaatgtaaagagtgtgacAaagcattcatatctgccaag							TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr19:12187711delA	ENST00000439326.3	+	4	1951	c.1776delA	c.(1774-1776)acafs	p.T592fs	ZNF844_ENST00000441304.2_3'UTR	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN	zinc finger protein 844	592					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(1)|prostate(1)	10						AGAGTGTGACAAAGCATTCAT	0.383																																					p.T592fs		Atlas-Indel,Pindel	.											.	ZNF844	69	.	0			c.1775delC						.						122	109	113					19																	12187711		692	1591	2283	SO:0001589	frameshift_variant	284391	exon4			.	AL832297	CCDS45985.1	19p13.2	2013-01-08			ENSG00000223547	ENSG00000223547		"Zinc fingers, C2H2-type", "-"	25932	protein-coding gene	gene with protein product							Standard	NM_001136501		Approved	FLJ14959	uc002mtb.2	Q08AG5	OTTHUMG00000156405	ENST00000439326.3:c.1776delA	chr19.hg19:g.12187711delA	ENSP00000392024:p.Thr592fs	104.0	0.0		110.0	28.0	NM_001136501	Q5JPI8	Frame_Shift_Del	DEL	ENST00000439326.3	hg19	CCDS45985.1																																																																																			.	.		0.383	ZNF844-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344086.2			-	12187711	A	-	12187711	7	5	315	1	0	1	0	1	0	0	0	0	18205	117	5	0	1790	0	ZNF844	19	12187711	Frame_Shift_Del	DEL	A	TCGA-KR-A7K7-01A-11D-A33K-10	2107145	12187711	46941272	51	44585										
ZNF567	163081	hgsc.bcm.edu	37	chr19	37203683	37203683	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	gtctttttttcacttttcagGgtgtcacatgaccaaacctg	7	10	4	1			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr19:37203683G>A	ENST00000536254.2	+	5	359	c.137G>A	c.(136-138)gGg>gAg	p.G46E	ZNF567_ENST00000360729.4_Splice_Site_p.G15E|ZNF567_ENST00000585696.1_Splice_Site_p.G15E|ZNF567_ENST00000392163.2_Splice_Site_p.G15E|ZNF567_ENST00000588311.1_Splice_Site_p.G15E			Q8N184	ZN567_HUMAN	zinc finger protein 567	46	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			CACTTTTCAGGGTGTCACATG	0.428																																					p.G15E		Atlas-SNP	.											.	ZNF567	61	.	0			c.G44A						.						134	116	122					19																	37203683		2203	4300	6503	SO:0001630	splice_region_variant	163081	exon3			TTTCAGGGTGTCA	AK093034	CCDS12495.1, CCDS74349.1	19q13.12	2013-10-08				ENSG00000189042		"Zinc fingers, C2H2-type", "-"	28696	protein-coding gene	gene with protein product						12477932	Standard	XM_006723064		Approved	MGC45586	uc002oep.4	Q8N184		ENST00000536254.2:c.137-1G>A	chr19.hg19:g.37203683G>A		103.0	0.0		89.0	50.0	NM_152603	B3KX49|Q6N044	Missense_Mutation	SNP	ENST00000536254.2	hg19		.	.	.	.	.	.	.	.	.	.	G	17.21	3.330426	0.60743	.	.	ENSG00000189042	ENST00000536254;ENST00000378686;ENST00000360729;ENST00000423498;ENST00000392163	T;T;T	0.02552	4.25;5.31;5.31	4.42	3.38	0.38709	Krueppel-associated box (4);	0.164522	0.29139	N	0.013032	T	0.13543	0.0328	M	0.84585	2.705	0.28026	N	0.934321	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.00934	-1.1509	9	.	.	.	.	7.3491	0.26680	0.1174:0.0:0.8826:0.0	.	46;15	Q8N184;F8WEL6	ZN567_HUMAN;.	E	46;46;15;45;15	ENSP00000441838:G46E;ENSP00000353957:G15E;ENSP00000376003:G15E	.	G	+	2	0	ZNF567	41895523	0.816000	0.29132	0.996000	0.52242	0.834000	0.47266	2.002000	0.40835	2.382000	0.81193	0.462000	0.41574	GGG	.	.		0.428	ZNF567-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000453549.1	NM_152603	Missense_Mutation	A	37203683	G	A	37203683	5	1	315	1	0	0	0	0	0	0	1	0	18013	1246	43	3	50	3	ZNF567	19	37203683	Splice_Site	SNP	G	TCGA-KR-A7K7-01A-11D-A33K-10	25015972	37203683	21925300	52	44586										
ERF	2077	hgsc.bcm.edu	37	chr19	42754547	42754547	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	cttgcgaacgccccacagccGggccacctcatcagggtctt	10	17	3	0			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr19:42754547G>A	ENST00000222329.4	-	2	350	c.193C>T	c.(193-195)Cgg>Tgg	p.R65W	AC006486.9_ENST00000594664.1_Intron|ERF_ENST00000595941.1_5'Flank|ERF_ENST00000440177.2_5'UTR	NM_006494.2	NP_006485.2	P50548	ERF_HUMAN	Ets2 repressor factor	65			R -> Q (in CRS4). {ECO:0000269|PubMed:23354439}.		cell cycle (GO:0007049)|cell differentiation (GO:0030154)|chorio-allantoic fusion (GO:0060710)|ectodermal cell differentiation (GO:0010668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)|trophoblast giant cell differentiation (GO:0060707)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(1)	17		Prostate(69;0.00682)				CCCCACAGCCGGGCCACCTCA	0.622																																					p.R65W		Atlas-SNP	.											.	ERF	47	.	0			c.C193T						.						47	47	47					19																	42754547		2203	4300	6503	SO:0001583	missense	2077	exon2			ACAGCCGGGCCAC	U58535	CCDS12600.1	19q13	2008-07-16				ENSG00000105722			3444	protein-coding gene	gene with protein product	"Ets2 repressor factor"	611888				7588608, 9192842	Standard	XM_005258644		Approved	PE-2, PE2	uc002ote.4	P50548		ENST00000222329.4:c.193C>T	chr19.hg19:g.42754547G>A	ENSP00000222329:p.Arg65Trp	86.0	0.0		82.0	41.0	NM_006494	B2RAP1|B7Z4R0|Q59G38|Q9UPI7	Missense_Mutation	SNP	ENST00000222329.4	hg19	CCDS12600.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.753389	0.89753	.	.	ENSG00000105722	ENST00000222329	T	0.29397	1.57	5.55	4.52	0.55395	Winged helix-turn-helix transcription repressor DNA-binding (1);Ets (4);	0.000000	0.85682	D	0.000000	T	0.63307	0.2500	M	0.92738	3.34	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.72808	-0.4181	10	0.87932	D	0	.	12.5983	0.56483	0.0808:0.0:0.9192:0.0	.	65	P50548	ERF_HUMAN	W	65	ENSP00000222329:R65W	ENSP00000222329:R65W	R	-	1	2	ERF	47446387	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.790000	0.99075	1.505000	0.48720	0.655000	0.94253	CGG	.	.		0.622	ERF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463684.1	NM_006494		A	42754547	G	A	42754547	3	1	315	1	0	0	0	0	1	0	0	0	5223	1115	39	1	1465	1	ERF	19	42754547	Missense_Mutation	SNP	G	TCGA-KR-A7K7-01A-11D-A33K-10	5550864	42754547	16374436	53	44587										
ZFP28	140612	hgsc.bcm.edu	37	chr19	57058902	57058902	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	ggtgacatttggggatgtggCtgtagatttctcccaagagg	15	6	1	3			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr19:57058902C>T	ENST00000301318.3	+	3	397	c.326C>T	c.(325-327)gCt>gTt	p.A109V	AC007228.11_ENST00000596587.1_RNA|ZFP28_ENST00000591844.1_Missense_Mutation_p.A109V	NM_020828.1	NP_065879.1	Q8NHY6	ZFP28_HUMAN	ZFP28 zinc finger protein	109	KRAB 1. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(6)|ovary(1)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	35		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0302)		GGGGATGTGGCTGTAGATTTC	0.493																																					p.A109V	Ovarian(124;554 1662 19430 21141 52494)	Atlas-SNP	.											.	ZFP28	99	.	0			c.C326T						.						155	132	139					19																	57058902		2203	4300	6503	SO:0001583	missense	140612	exon3			ATGTGGCTGTAGA		CCDS12946.1	19q13.43	2013-01-08	2012-11-27			ENSG00000196867		"Zinc fingers, C2H2-type", "-"	17801	protein-coding gene	gene with protein product			"zinc finger protein 28 homolog (mouse)"				Standard	NM_020828		Approved	KIAA1431, mkr5	uc002qnj.3	Q8NHY6		ENST00000301318.3:c.326C>T	chr19.hg19:g.57058902C>T	ENSP00000301318:p.Ala109Val	160.0	0.0		175.0	35.0	NM_020828	A0JNV6|K7ES88|Q8NHU8|Q9BY30|Q9P2B6	Missense_Mutation	SNP	ENST00000301318.3	hg19	CCDS12946.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.344857	0.61073	.	.	ENSG00000196867	ENST00000301318	T	0.03301	3.98	3.58	1.36	0.22044	Krueppel-associated box (4);	0.219701	0.23254	N	0.050205	T	0.16642	0.0400	M	0.88181	2.935	0.28655	N	0.906432	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	T	0.02115	-1.1211	10	0.48119	T	0.1	.	6.6417	0.22913	0.1782:0.722:0.0:0.0999	.	109;109	Q8NHY6;A8K0L8	ZFP28_HUMAN;.	V	109	ENSP00000301318:A109V	ENSP00000301318:A109V	A	+	2	0	ZFP28	61750714	0.259000	0.24043	0.408000	0.26446	0.932000	0.56968	0.560000	0.23500	0.293000	0.22520	0.563000	0.77884	GCT	.	.		0.493	ZFP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458409.1	NM_020828		T	57058902	C	T	57058902	3	4	315	1	0	0	0	0	1	0	0	0	17657	797	28	3	336	3	ZFP28	19	57058902	Missense_Mutation	SNP	C	TCGA-KR-A7K7-01A-11D-A33K-10	14304355	57058902	2070081	54	44588										
ZNF470	388566	hgsc.bcm.edu	37	chr19	57086027	57086027	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	gtctttgcatttctaaaccaGatgtgatctccttactggag	8	9	3	2			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr19:57086027G>T	ENST00000330619.8	+	5	894	c.208G>T	c.(208-210)Gat>Tat	p.D70Y	ZNF470_ENST00000391709.3_Missense_Mutation_p.D70Y|ZNF470_ENST00000601902.1_Missense_Mutation_p.D70Y	NM_001001668.3	NP_001001668.3	Q6ECI4	ZN470_HUMAN	zinc finger protein 470	70	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(7)|large_intestine(12)|lung(11)|ovary(1)|pancreas(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	41		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0294)		TTCTAAACCAGATGTGATCTC	0.408																																					p.D70Y		Atlas-SNP	.											.	ZNF470	103	.	0			c.G208T						.						82	80	81					19																	57086027		2203	4300	6503	SO:0001583	missense	388566	exon5			AAACCAGATGTGA	AK129686	CCDS33122.1	19q13.43	2013-01-08				ENSG00000197016		"Zinc fingers, C2H2-type", "-"	22220	protein-coding gene	gene with protein product						15302581	Standard	NM_001001668		Approved	CZF-1, FLJ26175	uc002qnl.4	Q6ECI4		ENST00000330619.8:c.208G>T	chr19.hg19:g.57086027G>T	ENSP00000333223:p.Asp70Tyr	92.0	0.0		83.0	45.0	NM_001001668	A8MTW0|B9EGU1|Q6ZPA1|Q9Y2N9	Missense_Mutation	SNP	ENST00000330619.8	hg19	CCDS33122.1	.	.	.	.	.	.	.	.	.	.	G	4.264	0.048051	0.08243	.	.	ENSG00000197016	ENST00000391709;ENST00000330619	T;T	0.00976	5.48;5.48	3.73	2.67	0.31697	Krueppel-associated box (3);	.	.	.	.	T	0.01353	0.0044	L	0.58969	1.84	0.22489	N	0.99906	P	0.36733	0.567	B	0.33521	0.165	T	0.46428	-0.9192	9	0.48119	T	0.1	.	9.1886	0.37184	0.0:0.2231:0.7769:0.0	.	70	Q6ECI4	ZN470_HUMAN	Y	70	ENSP00000375590:D70Y;ENSP00000333223:D70Y	ENSP00000333223:D70Y	D	+	1	0	ZNF470	61777839	0.255000	0.24002	0.976000	0.42696	0.036000	0.12997	1.291000	0.33330	0.893000	0.36288	-0.175000	0.13238	GAT	.	.		0.408	ZNF470-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459707.2	NM_001001668		T	57086027	G	T	57086027	3	4	315	1	0	0	0	0	1	0	0	0	17944	942	33	3	218	3	ZNF470	19	57086027	Missense_Mutation	SNP	G	TCGA-KR-A7K7-01A-11D-A33K-10	27125	57086027	2042956	55	44589										
MAVS	57506	hgsc.bcm.edu	37	chr20	3845079	3845079	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	tggcctctgcaggggctgcaGagggtaaacagggtgcagag	18	8	1	2			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr20:3845079G>T	ENST00000428216.2	+	6	930	c.802G>T	c.(802-804)Gag>Tag	p.E268*	MAVS_ENST00000358134.6_3'UTR|MAVS_ENST00000416600.2_Nonsense_Mutation_p.E127*	NM_020746.4	NP_065797.2	Q7Z434	MAVS_HUMAN	mitochondrial antiviral signaling protein	268					activation of innate immune response (GO:0002218)|cellular response to exogenous dsRNA (GO:0071360)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|negative regulation of viral genome replication (GO:0045071)|positive regulation of chemokine (C-C motif) ligand 5 production (GO:0071651)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of IP-10 production (GO:0071660)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of peroxisome organization (GO:1900063)|RIG-I signaling pathway (GO:0039529)|signal transduction (GO:0007165)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)	CARD domain binding (GO:0050700)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			autonomic_ganglia(1)|breast(3)|endometrium(1)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	14						AGGGGCTGCAGAGGGTAAACA	0.622																																					p.E268X		Atlas-SNP	.											.	MAVS	34	.	0			c.G802T						.						55	50	51					20																	3845079		2203	4300	6503	SO:0001587	stop_gained	57506	exon6			GCTGCAGAGGGTA	DQ174270	CCDS33437.1, CCDS56176.1	20p13	2009-04-02			ENSG00000088888	ENSG00000088888			29233	protein-coding gene	gene with protein product	"virus-induced signaling adaptor", "IFN-B promoter stimulator 1", "CARD adaptor inducing IFN-beta"	609676				16125763, 16153868	Standard	NM_020746		Approved	VISA, KIAA1271, IPS-1, Cardif	uc002wjw.4	Q7Z434	OTTHUMG00000031765	ENST00000428216.2:c.802G>T	chr20.hg19:g.3845079G>T	ENSP00000401980:p.Glu268*	55.0	0.0		53.0	21.0	NM_020746	A8K6X0|B2BD33|B2BD34|F5H6C8|Q2HWT5|Q3I0Y2|Q5T7I6|Q86VY7|Q9H1H3|Q9H4Y1|Q9H8D3|Q9ULE9	Nonsense_Mutation	SNP	ENST00000428216.2	hg19	CCDS33437.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.965305	0.92855	.	.	ENSG00000088888	ENST00000416600;ENST00000428216	.	.	.	4.3	2.34	0.29019	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22706	T	0.39	.	6.6829	0.23129	0.2193:0.0:0.7807:0.0	.	.	.	.	X	127;268	.	ENSP00000413749:E127X	E	+	1	0	MAVS	3793079	0.207000	0.23482	0.010000	0.14722	0.014000	0.08584	1.591000	0.36665	0.567000	0.29293	0.467000	0.42956	GAG	.	.		0.622	MAVS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077784.3	NM_020746		T	3845079	G	T	3845079	4	4	315	1	0	0	0	0	0	1	0	0	9347	943	33	3	820	3	MAVS	20	3845079	Nonsense_Mutation	SNP	G	TCGA-KR-A7K7-01A-11D-A33K-10		3845079	59180441	56	44590										
NCOA5	57727	hgsc.bcm.edu	37	chr20	44695721	44695721	+	Frame_Shift_Del	DEL	G	G	-													0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	gtttgttgaccacaatcacaGaacaatcaacgggcctttcg							TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr20:44695721delG	ENST00000290231.6	-	5	766	c.602delC	c.(601-603)tctfs	p.S201fs		NM_020967.2	NP_066018.1	Q9HCD5	NCOA5_HUMAN	nuclear receptor coactivator 5	201					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|extracellular space (GO:0005615)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|skin(2)|urinary_tract(1)	21		Myeloproliferative disorder(115;0.0122)				CACAATCACAGAACAATCAAC	0.443																																					p.S201fs		Atlas-Indel,Pindel	.											.	NCOA5	58	.	0			c.603delT						.						105	101	102					20																	44695721		2203	4300	6503	SO:0001589	frameshift_variant	57727	exon5			.		CCDS13392.1	20q12-q13.12	2008-07-02			ENSG00000124160	ENSG00000124160			15909	protein-coding gene	gene with protein product	"coactivator independent of AF-2"					11780052, 11113208	Standard	XM_005260474		Approved	bA465L10.6, CIA	uc002xre.3	Q9HCD5	OTTHUMG00000032639	ENST00000290231.6:c.602delC	chr20.hg19:g.44695721delG	ENSP00000290231:p.Ser201fs	138.0	0.0		164.0	71.0	NM_020967	B2RTV9|E1P5R0|Q6HA99|Q9H1F2|Q9H2T2|Q9H4Y9	Frame_Shift_Del	DEL	ENST00000290231.6	hg19	CCDS13392.1																																																																																			.	.		0.443	NCOA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079559.1	NM_020967		-	44695721	G	-	44695721	7	5	315	1	0	1	0	1	0	0	0	0	10241	942	33	0	1153	0	NCOA5	20	44695721	Frame_Shift_Del	DEL	G	TCGA-KR-A7K7-01A-11D-A33K-10	40850642	44695721	18329799	57	44591										
SLC2A10	81031	hgsc.bcm.edu	37	chr20	45354604	45354604	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	ctgtgccctcatggccctgtCcgtcagtggcataggcctcg	12	15	2	0			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chr20:45354604C>G	ENST00000359271.2	+	2	1179	c.929C>G	c.(928-930)tCc>tGc	p.S310C		NM_030777.3	NP_110404.1	O95528	GTR10_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 10	310					glucose transport (GO:0015758)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sugar:proton symporter activity (GO:0005351)			central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|liver(2)|lung(13)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	34		Myeloproliferative disorder(115;0.0122)				ATGGCCCTGTCCGTCAGTGGC	0.667																																					p.S310C		Atlas-SNP	.											SLC2A10,NS,carcinoma,0,1	SLC2A10	75	.	0			c.C929G						.						72	64	66					20																	45354604		2203	4300	6503	SO:0001583	missense	81031	exon2			CCCTGTCCGTCAG	AL137188	CCDS13402.1	20q13.12	2013-05-22			ENSG00000197496	ENSG00000197496		"Solute carriers"	13444	protein-coding gene	gene with protein product		606145				11247674	Standard	NM_030777		Approved	GLUT10	uc002xsl.3	O95528	OTTHUMG00000032657	ENST00000359271.2:c.929C>G	chr20.hg19:g.45354604C>G	ENSP00000352216:p.Ser310Cys	43.0	0.0		59.0	24.0	NM_030777	A8K4J6|Q3MIX5|Q9H4I6	Missense_Mutation	SNP	ENST00000359271.2	hg19	CCDS13402.1	.	.	.	.	.	.	.	.	.	.	C	12.15	1.850299	0.32699	.	.	ENSG00000197496	ENST00000359271	T	0.70869	-0.52	5.76	4.82	0.62117	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.334814	0.31624	N	0.007338	T	0.63486	0.2515	L	0.41632	1.29	0.38279	D	0.942386	B	0.20052	0.041	B	0.26770	0.073	T	0.62348	-0.6873	10	0.37606	T	0.19	-1.0384	14.2173	0.65802	0.0:0.9287:0.0:0.0713	.	310	O95528	GTR10_HUMAN	C	310	ENSP00000352216:S310C	ENSP00000352216:S310C	S	+	2	0	SLC2A10	44788011	0.525000	0.26290	0.919000	0.36401	0.333000	0.28666	1.948000	0.40303	2.728000	0.93425	0.655000	0.94253	TCC	.	.		0.667	SLC2A10-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079578.2			G	45354604	C	G	45354604	3	3	315	1	0	0	0	0	1	0	0	0	14554	855	30	4	935	4	SLC2A10	20	45354604	Missense_Mutation	SNP	C	TCGA-KR-A7K7-01A-11D-A33K-10	658883	45354604	17670916	58	44592										
COL4A6	1288	hgsc.bcm.edu	37	chrX	107422545	107422545	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.101694915254237	6	1	1.42911392405063	2.67958860759494	0.97439585730725	1	1	0	caccattttcagcaccaaagAtgtcaccagtggctcccttg	7	14	2	1			TCGA-KR-A7K7-01A-11D-A33K-10	TCGA-KR-A7K7-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c81cbc1f-0de9-4578-a35e-014fb80c54a4	9edcdb8d-6a27-4c45-a22e-30466a7e13cd	g.chrX:107422545A>C	ENST00000372216.4	-	26	2358	c.2258T>G	c.(2257-2259)aTc>aGc	p.I753S	COL4A6_ENST00000394872.2_Missense_Mutation_p.I753S|COL4A6_ENST00000538570.1_Missense_Mutation_p.I752S|COL4A6_ENST00000545689.1_Missense_Mutation_p.I752S|COL4A6_ENST00000334504.7_Missense_Mutation_p.I752S	NM_001847.2	NP_001838.2	Q14031	CO4A6_HUMAN	collagen, type IV, alpha 6	753	Triple-helical region.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(41)|ovary(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	92						AGCACCAAAGATGTCACCAGT	0.547									Alport syndrome with Diffuse Leiomyomatosis																												p.I753S	Melanoma(87;1895 1945 2589 7165)	Atlas-SNP	.											.	COL4A6	270	.	0			c.T2258G						.						96	76	83					X																	107422545		2203	4300	6503	SO:0001583	missense	1288	exon26	Familial Cancer Database		CCAAAGATGTCAC	U04845	CCDS14541.1, CCDS14542.1, CCDS76008.1, CCDS76009.1, CCDS76010.1	Xq22	2014-09-17			ENSG00000197565	ENSG00000197565		"Collagens"	2208	protein-coding gene	gene with protein product		303631				8356449	Standard	NM_033641		Approved		uc004env.4	Q14031	OTTHUMG00000022179	ENST00000372216.4:c.2258T>G	chrX.hg19:g.107422545A>C	ENSP00000361290:p.Ile753Ser	349.0	0.0		363.0	165.0	NM_001847	Q12823|Q14053|Q5JYH6|Q5JYH8|Q9NQM5|Q9NTX3|Q9UJ76|Q9UMG6|Q9Y4L4	Missense_Mutation	SNP	ENST00000372216.4	hg19	CCDS14541.1	.	.	.	.	.	.	.	.	.	.	A	15.34	2.803421	0.50315	.	.	ENSG00000197565	ENST00000372216;ENST00000334504;ENST00000394872;ENST00000541389;ENST00000545689;ENST00000538570	D;D;D;D;D	0.96396	-4.0;-4.0;-4.0;-3.2;-3.2	4.59	4.59	0.56863	.	0.172537	0.27871	N	0.017518	D	0.95529	0.8547	N	0.25825	0.765	0.40204	D	0.977556	D;D;D;D	0.76494	0.995;0.999;0.999;0.999	P;D;D;D	0.83275	0.835;0.996;0.988;0.979	D	0.93048	0.6463	10	0.09338	T	0.73	.	13.7531	0.62919	1.0:0.0:0.0:0.0	.	752;752;753;752	F5H851;F5H3Q5;Q14031;Q14031-2	.;.;CO4A6_HUMAN;.	S	753;752;753;752;752;752	ENSP00000361290:I753S;ENSP00000334733:I752S;ENSP00000378340:I753S;ENSP00000443707:I752S;ENSP00000445236:I752S	ENSP00000334733:I752S	I	-	2	0	COL4A6	107309201	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	6.281000	0.72632	1.780000	0.52325	0.425000	0.28330	ATC	.	.		0.547	COL4A6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057875.2			C	107422545	A	C	107422545	3	2	315	1	0	0	0	0	1	0	0	0	3697	333	12	5	2897	5	COL4A6	23	107422545	Missense_Mutation	SNP	A	TCGA-KR-A7K7-01A-11D-A33K-10		107422545	47848015	59	44593										
RUNX3	864	hgsc.bcm.edu	37	chr1	25229111	25229111	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	gttggcagcgtggggaaggaGcggtcaaactggcgggggtc	21	7	1	0			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr1:25229111G>A	ENST00000308873.6	-	5	758	c.750C>T	c.(748-750)cgC>cgT	p.R250R	RUNX3_ENST00000399916.1_Silent_p.R264R|RUNX3_ENST00000540420.1_Silent_p.R157R|RUNX3_ENST00000338888.3_Silent_p.R264R|RUNX3_ENST00000496967.1_5'UTR	NM_004350.2	NP_004341.1	Q13761	RUNX3_HUMAN	runt-related transcription factor 3	250	Pro/Ser/Thr-rich.				axon guidance (GO:0007411)|cell maturation (GO:0048469)|chondrocyte differentiation (GO:0002062)|hair follicle morphogenesis (GO:0031069)|interferon-gamma production (GO:0032609)|negative regulation of cell cycle (GO:0045786)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peripheral nervous system neuron development (GO:0048935)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(3)	18		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00131)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0419)|OV - Ovarian serous cystadenocarcinoma(117;2.85e-26)|Colorectal(126;4.35e-08)|COAD - Colon adenocarcinoma(152;1.92e-06)|GBM - Glioblastoma multiforme(114;0.000102)|STAD - Stomach adenocarcinoma(196;0.000766)|KIRC - Kidney renal clear cell carcinoma(1967;0.00148)|BRCA - Breast invasive adenocarcinoma(304;0.00173)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.136)		TGGGGAAGGAGCGGTCAAACT	0.647																																					p.R264R		Atlas-SNP	.											.	RUNX3	72	.	0			c.C792T						.						78	75	76					1																	25229111		2192	4290	6482	SO:0001819	synonymous_variant	864	exon6			GAAGGAGCGGTCA	BC013362	CCDS257.1, CCDS30633.1	1p36	2008-02-05			ENSG00000020633	ENSG00000020633			10473	protein-coding gene	gene with protein product		600210		CBFA3		7835892	Standard	NM_001031680		Approved	AML2, PEBP2A3	uc001bjq.3	Q13761	OTTHUMG00000003316	ENST00000308873.6:c.750C>T	chr1.hg19:g.25229111G>A		141.0	0.0		105.0	17.0	NM_001031680	B1AJV5|Q12969|Q13760	Silent	SNP	ENST00000308873.6	hg19	CCDS257.1																																																																																			.	.		0.647	RUNX3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000009284.1	NM_004350		A	25229111	G	A	25229111	2	1	316	1	0	0	0	0	0	0	0	1	13764	958	34	3		3	RUNX3	1	25229111	Silent	SNP	G	TCGA-KR-A7K8-01A-11D-A33K-10		25229111	224021510	1	44594										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27106176	27106176	+	Frame_Shift_Del	DEL	T	T	-													0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	accgaggatggagctaagagTtcagaggccatcaaggagag							TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr1:27106176delT	ENST00000324856.7	+	20	6158	c.5787delT	c.(5785-5787)agtfs	p.S1930fs	ARID1A_ENST00000457599.2_Frame_Shift_Del_p.S1713fs|ARID1A_ENST00000374152.2_Frame_Shift_Del_p.S1547fs|ARID1A_ENST00000540690.1_Frame_Shift_Del_p.S258fs	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1930					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		GAGCTAAGAGTTCAGAGGCCA	0.532			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.S1929fs		Atlas-INDEL	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.5786delG						.						128	125	126					1																	27106176		2203	4300	6503	SO:0001589	frameshift_variant	8289	exon20			.	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.5787delT	chr1.hg19:g.27106176delT	ENSP00000320485:p.Ser1930fs	114.0	0.0		111.0	10.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Del	DEL	ENST00000324856.7	hg19	CCDS285.1																																																																																			.	.		0.532	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		-	27106176	T	-	27106176	7	5	316	1	0	1	0	1	0	0	0	0	913	1722	60	0	5865	0	ARID1A	1	27106176	Frame_Shift_Del	DEL	T	TCGA-KR-A7K8-01A-11D-A33K-10	1877065	27106176	222144445	2	44595										
RNF11	26994	hgsc.bcm.edu	37	chr1	51736890	51736890	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	ttctgccgtgcatgcacatcTatcacctggactgtatagat	8	11	3	1			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr1:51736890T>C	ENST00000242719.3	+	3	847	c.361T>C	c.(361-363)Tat>Cat	p.Y121H	RNF11_ENST00000494873.1_3'UTR	NM_014372.4	NP_055187.1	Q9Y3C5	RNF11_HUMAN	ring finger protein 11	121					protein autoubiquitination (GO:0051865)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	DNA binding (GO:0003677)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.0?(2)		large_intestine(1)	1						CATGCACATCTATCACCTGGA	0.473																																					p.Y121H		Atlas-SNP	.											.	RNF11	10	.	2	Whole gene deletion(2)	thyroid(1)|central_nervous_system(1)	c.T361C						.						244	202	216					1																	51736890		2203	4300	6503	SO:0001583	missense	26994	exon3			CACATCTATCACC	AB024703	CCDS556.1	1p32	2013-01-09			ENSG00000123091	ENSG00000123091		"RING-type (C3HC4) zinc fingers"	10056	protein-coding gene	gene with protein product		612598				10673045, 10810093	Standard	NM_014372		Approved	CGI-123, Sid1669p, MGC51169	uc001csi.4	Q9Y3C5	OTTHUMG00000008190	ENST00000242719.3:c.361T>C	chr1.hg19:g.51736890T>C	ENSP00000242719:p.Tyr121His	51.0	0.0		61.0	6.0	NM_014372	A8KAI2|Q5T7R8	Missense_Mutation	SNP	ENST00000242719.3	hg19	CCDS556.1	.	.	.	.	.	.	.	.	.	.	T	19.23	3.788012	0.70337	.	.	ENSG00000123091	ENST00000242719	T	0.45668	0.89	5.89	5.89	0.94794	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.000000	0.85682	D	0.000000	T	0.66587	0.2804	M	0.79123	2.44	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.70806	-0.4772	10	0.87932	D	0	-1.8925	16.3127	0.82898	0.0:0.0:0.0:1.0	.	121	Q9Y3C5	RNF11_HUMAN	H	121	ENSP00000242719:Y121H	ENSP00000242719:Y121H	Y	+	1	0	RNF11	51509478	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.004000	0.88535	2.246000	0.74042	0.533000	0.62120	TAT	.	.		0.473	RNF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022419.1	NM_014372		C	51736890	T	C	51736890	3	2	316	1	0	0	0	0	1	0	0	0	13439	1522	53	2	371	2	RNF11	1	51736890	Missense_Mutation	SNP	T	TCGA-KR-A7K8-01A-11D-A33K-10	24630714	51736890	197513731	3	44596										
TTN	7273	hgsc.bcm.edu	37	chr2	179614477	179614477	+	Intron	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	gagaattaacatccttaataTataattggtggctacaatta	6	5	0	1			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr2:179614477T>A	ENST00000591111.1	-	45	10585				TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Intron|TTN_ENST00000342992.6_Intron|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000360870.5_Missense_Mutation_p.Y4217F			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATCCTTAATATATAATTGGTG	0.373																																					p.Y4217F		Atlas-SNP	.											.	TTN	18412	.	0			c.A12650T						.						44	50	48					2																	179614477		2180	4284	6464	SO:0001627	intron_variant	7273	exon46			TTAATATATAATT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10360+3373A>T	chr2.hg19:g.179614477T>A		134.0	0.0		145.0	8.0	NM_133379	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	0.601	-0.829153	0.02734	.	.	ENSG00000155657	ENST00000360870	T	0.65916	-0.18	5.84	3.41	0.39046	.	.	.	.	.	T	0.26484	0.0647	N	0.01800	-0.715	0.58432	D	0.999999	B	0.10296	0.003	B	0.12156	0.007	T	0.04242	-1.0966	9	0.10902	T	0.67	.	1.9054	0.03276	0.1407:0.1402:0.1294:0.5897	.	4217	Q8WZ42-6	.	F	4217	ENSP00000354117:Y4217F	ENSP00000354117:Y4217F	Y	-	2	0	TTN	179322722	0.996000	0.38824	0.270000	0.24601	0.013000	0.08279	0.927000	0.28818	0.440000	0.26502	-0.261000	0.10672	TAT	.	.		0.373	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179614477	T	A	179614477	1	1	316	0	1	0	0	0	0	0	0	0	16750	1406	49	4		4	TTN	2	179614477	Intron	SNP	T	TCGA-KR-A7K8-01A-11D-A33K-10		179614477	63584896	4	44597										
RHBDD1	84236	hgsc.bcm.edu	37	chr2	227729638	227729638	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	tctctccccttcaccatgctGatgattggcatttgtatttc	6	12	2	2			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr2:227729638G>A	ENST00000341329.3	+	2	471	c.229G>A	c.(229-231)Gat>Aat	p.D77N	RHBDD1_ENST00000392062.2_Missense_Mutation_p.D77N	NM_032276.3	NP_115652.2	Q8TEB9	RHBL4_HUMAN	rhomboid domain containing 1	77					apoptotic process (GO:0006915)|cellular response to unfolded protein (GO:0034620)|cellular response to UV (GO:0034644)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|membrane protein intracellular domain proteolysis (GO:0031293)|membrane protein proteolysis (GO:0033619)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein processing (GO:0010954)|positive regulation of secretion (GO:0051047)|post-translational protein modification (GO:0043687)|spermatid differentiation (GO:0048515)	endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum quality control compartment (GO:0044322)|integral component of endoplasmic reticulum membrane (GO:0030176)|mitochondrion (GO:0005739)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)	p.D77N(1)		breast(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19		Renal(207;0.023)|all_lung(227;0.13)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;1.47e-11)|all cancers(144;1.52e-08)|Lung(261;0.0128)|LUSC - Lung squamous cell carcinoma(224;0.0175)		TCACCATGCTGATGATTGGCA	0.453																																					p.D77N		Atlas-SNP	.											RHBDD1,arm,malignant_melanoma,0,1	RHBDD1	34	.	1	Substitution - Missense(1)	skin(1)	c.G229A						.						171	159	163					2																	227729638		2203	4300	6503	SO:0001583	missense	84236	exon4			CATGCTGATGATT	AK074258	CCDS2464.1	2q36.3	2012-07-09			ENSG00000144468	ENSG00000144468			23081	protein-coding gene	gene with protein product						12838346	Standard	NM_032276		Approved	DKFZp547E052	uc002voi.3	Q8TEB9	OTTHUMG00000133178	ENST00000341329.3:c.229G>A	chr2.hg19:g.227729638G>A	ENSP00000344779:p.Asp77Asn	131.0	0.0		98.0	9.0	NM_001167608	Q495B9|Q53S43|Q5EBM8|Q6P5V8|Q8IV60|Q9H057	Missense_Mutation	SNP	ENST00000341329.3	hg19	CCDS2464.1	.	.	.	.	.	.	.	.	.	.	G	13.50	2.254607	0.39896	.	.	ENSG00000144468	ENST00000424132;ENST00000341329;ENST00000392062;ENST00000423616;ENST00000448992	T;T;T;T;T	0.13538	2.58;2.58;2.58;2.58;2.58	6.04	3.3	0.37823	Peptidase S54, rhomboid domain (1);	0.176196	0.64402	N	0.000012	T	0.30759	0.0775	L	0.59912	1.85	0.43617	D	0.995992	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.00822	-1.1552	10	0.20046	T	0.44	-13.515	14.614	0.68534	0.1711:0.0:0.8289:0.0	.	77;77	C9K011;Q8TEB9	.;RHBD1_HUMAN	N	77	ENSP00000400765:D77N;ENSP00000344779:D77N;ENSP00000375914:D77N;ENSP00000399694:D77N;ENSP00000388847:D77N	ENSP00000344779:D77N	D	+	1	0	RHBDD1	227437882	1.000000	0.71417	0.001000	0.08648	0.079000	0.17450	5.481000	0.66826	0.168000	0.19655	-2.010000	0.00438	GAT	.	.		0.453	RHBDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256885.2			A	227729638	G	A	227729638	3	1	316	1	0	0	0	0	1	0	0	0	13331	1290	45	3	231	3	RHBDD1	2	227729638	Missense_Mutation	SNP	G	TCGA-KR-A7K8-01A-11D-A33K-10	48115161	227729638	15469735	5	44598										
DGKD	8527	hgsc.bcm.edu	37	chr2	234299114	234299114	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	gaatccagtaccaaaaacgtCaacaacagttttacggtaag	7	9	1	0			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr2:234299114C>A	ENST00000264057.2	+	3	345	c.333C>A	c.(331-333)gtC>gtA	p.V111V	DGKD_ENST00000409813.3_Silent_p.V67V|AC019221.4_ENST00000442524.1_RNA	NM_152879.2	NP_690618.2	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa	111	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				blood coagulation (GO:0007596)|cell growth (GO:0016049)|diacylglycerol metabolic process (GO:0046339)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|multicellular organismal development (GO:0007275)|platelet activation (GO:0030168)|protein homooligomerization (GO:0051260)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein transport (GO:0015031)|response to organic substance (GO:0010033)|second-messenger-mediated signaling (GO:0019932)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol binding (GO:0019992)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(13)|lung(15)|ovary(1)|pancreas(1)|skin(1)	38		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Phosphatidylserine(DB00144)	CCAAAAACGTCAACAACAGTT	0.413																																					p.V111V		Atlas-SNP	.											.	DGKD	106	.	0			c.C333A						.						201	179	186					2																	234299114		2203	4300	6503	SO:0001819	synonymous_variant	8527	exon3			AAACGTCAACAAC	D63479	CCDS2504.1, CCDS46546.1	2q37	2013-01-10	2002-08-29		ENSG00000077044	ENSG00000077044		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	2851	protein-coding gene	gene with protein product	"diglyceride kinase"	601826	"diacylglycerol kinase, delta (130kD)"			8626538, 12810723	Standard	NM_003648		Approved	KIAA0145, DGKdelta	uc002vui.1	Q16760	OTTHUMG00000133290	ENST00000264057.2:c.333C>A	chr2.hg19:g.234299114C>A		91.0	0.0		85.0	7.0	NM_152879	Q14158|Q6PK55|Q8NG53	Silent	SNP	ENST00000264057.2	hg19	CCDS2504.1																																																																																			.	.		0.413	DGKD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257072.2	NM_003648		A	234299114	C	A	234299114	2	1	316	1	0	0	0	0	0	0	0	1	4469	813	29	3		3	DGKD	2	234299114	Silent	SNP	C	TCGA-KR-A7K8-01A-11D-A33K-10	6569476	234299114	8900259	6	44599										
CHCHD4	131474	hgsc.bcm.edu	37	chr3	14158003	14158003	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	tttcatgatcttctttggttAcaaatatgattcgatccttc	5	8	3	2			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr3:14158003A>G	ENST00000396914.3	-	2	225	c.44T>C	c.(43-45)gTa>gCa	p.V15A	CHCHD4_ENST00000295767.5_Missense_Mutation_p.V28A	NM_001098502.1	NP_001091972.1	Q8N4Q1	MIA40_HUMAN	coiled-coil-helix-coiled-coil-helix domain containing 4	15					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|protein import into mitochondrial intermembrane space (GO:0045041)|protein maturation by protein folding (GO:0022417)|protein targeting to mitochondrion (GO:0006626)	mitochondrial intermembrane space (GO:0005758)	protein disulfide oxidoreductase activity (GO:0015035)			kidney(1)|large_intestine(1)|lung(2)|prostate(1)	5						TTCTTTGGTTACAAATATGAT	0.463																																					p.V28A		Atlas-SNP	.											.	CHCHD4	8	.	0			c.T83C						.						204	182	189					3																	14158003		2203	4300	6503	SO:0001583	missense	131474	exon3			TTGGTTACAAATA	BC017082	CCDS2617.1, CCDS43054.1	3p25.1	2012-10-15			ENSG00000163528	ENSG00000163528		"Coiled-coil-helix-coiled-coil-helix domain containing"	26467	protein-coding gene	gene with protein product	"translocase of inner mitochondrial membrane 40 homolog (S. cerevisiae)", "mitochondrial intermembrane space import and assembly 40 homolog (S. cerevisiae)"	611077				22214851	Standard	NM_001098502		Approved	FLJ31709, TIMM40, MIA40	uc003byj.4	Q8N4Q1	OTTHUMG00000129805	ENST00000396914.3:c.44T>C	chr3.hg19:g.14158003A>G	ENSP00000380122:p.Val15Ala	107.0	0.0		75.0	17.0	NM_144636	A8K3Z9|Q96AI2|Q96MY6	Missense_Mutation	SNP	ENST00000396914.3	hg19	CCDS43054.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.956202	0.73902	.	.	ENSG00000163528	ENST00000295767;ENST00000396914	.	.	.	4.89	4.89	0.63831	.	0.000000	0.85682	D	0.000000	T	0.54143	0.1840	L	0.39397	1.21	0.80722	D	1	P;D	0.61697	0.952;0.99	P;P	0.57371	0.607;0.819	T	0.48246	-0.9052	9	0.19590	T	0.45	-34.5288	10.604	0.45384	0.9215:0.0:0.0785:0.0	.	15;28	Q8N4Q1;Q8N4Q1-2	MIA40_HUMAN;.	A	28;15	.	ENSP00000295767:V28A	V	-	2	0	CHCHD4	14133004	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	6.193000	0.72075	1.826000	0.53198	0.402000	0.26972	GTA	.	.		0.463	CHCHD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340423.1	NM_144636		G	14158003	A	G	14158003	3	3	316	1	0	0	0	0	1	0	0	0	3320	391	14	2	392	2	CHCHD4	3	14158003	Missense_Mutation	SNP	A	TCGA-KR-A7K8-01A-11D-A33K-10		14158003	183864427	7	44600										
FYCO1	79443	hgsc.bcm.edu	37	chr3	46008641	46008641	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	gctctcgagagccctaagctCtctgtgccgggcttctgcca	11	15	3	1			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr3:46008641C>A	ENST00000296137.2	-	8	2390	c.2185G>T	c.(2185-2187)Gag>Tag	p.E729*	FYCO1_ENST00000535325.1_Nonsense_Mutation_p.E729*	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	729					plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)			NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		GCCCTAAGCTCTCTGTGCCGG	0.612																																					p.E729X		Atlas-SNP	.											.	FYCO1	115	.	0			c.G2185T						.						83	87	86					3																	46008641		2203	4300	6503	SO:0001587	stop_gained	79443	exon8			TAAGCTCTCTGTG	AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"Zinc fingers, FYVE domain containing"	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.2185G>T	chr3.hg19:g.46008641C>A	ENSP00000296137:p.Glu729*	51.0	0.0		48.0	4.0	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Nonsense_Mutation	SNP	ENST00000296137.2	hg19	CCDS2734.1	.	.	.	.	.	.	.	.	.	.	C	37	6.490935	0.97612	.	.	ENSG00000163820	ENST00000296137;ENST00000535325	.	.	.	5.64	4.76	0.60689	.	0.315218	0.33772	N	0.004574	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.28530	T	0.3	-19.7616	15.1021	0.72288	0.0:0.8592:0.1407:0.0	.	.	.	.	X	729	.	ENSP00000296137:E729X	E	-	1	0	FYCO1	45983645	0.997000	0.39634	0.640000	0.29408	0.257000	0.26127	3.272000	0.51616	1.361000	0.45981	0.563000	0.77884	GAG	.	.		0.612	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513		A	46008641	C	A	46008641	4	1	316	1	0	0	0	0	0	1	0	0	6133	922	32	3	2295	3	FYCO1	3	46008641	Nonsense_Mutation	SNP	C	TCGA-KR-A7K8-01A-11D-A33K-10	31850638	46008641	152013789	8	44601										
CELSR3	1951	hgsc.bcm.edu	37	chr3	48691840	48691874	+	Frame_Shift_Del	DEL	GTTGGGGACACCTCCCAGAAGAAGAGGGCCCGTCA	GTTGGGGACACCTCCCAGAAGAAGAGGGCCCGTCA	-													0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	acggggaagttctcggggagGttggggacacctcccagaag					rs141878933		TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	GTTGGGGACACCTCCCAGAAGAAGAGGGCCCGTCA	GTTGGGGACACCTCCCAGAAGAAGAGGGCCCGTCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr3:48691840_48691874delGTTGGGGACACCTCCCAGAAGAAGAGGGCCCGTCA	ENST00000164024.4	-	7	5280_5314	c.5000_5034delTGACGGGCCCTCTTCTTCTGGGAGGTGTCCCCAAC	c.(4999-5034)ctgacgggccctcttcttctgggaggtgtccccaacfs	p.LTGPLLLGGVPN1667fs	CELSR3_ENST00000544264.1_Frame_Shift_Del_p.LTGPLLLGGVPN1667fs	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	1667	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		TCTCGGGGAGGTTGGGGACACCTCCCAGAAGAAGAGGGCCCGTCAGGTCCAGGGA	0.626																																					p.1667_1679del		Pindel	.											.	CELSR3	237	.	0			c.5001_5035del						.																																			SO:0001589	frameshift_variant	1951	exon7			.	AF231023	CCDS2775.1	3p21.31	2014-08-08	2013-02-18		ENSG00000008300	ENSG00000008300		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3230	protein-coding gene	gene with protein product	"flamingo homolog 1 (Drosophila)"	604264	"cadherin EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog"	EGFL1		9693030	Standard	NM_001407		Approved	MEGF2, HFMI1, FMI1, CDHF11	uc003cuf.1	Q9NYQ7	OTTHUMG00000133544	ENST00000164024.4:c.5000_5034delTGACGGGCCCTCTTCTTCTGGGAGGTGTCCCCAAC	chr3.hg19:g.48691840_48691874delGTTGGGGACACCTCCCAGAAGAAGAGGGCCCGTCA	ENSP00000164024:p.Leu1667fs	273.0	0.0		146.0	12.0	NM_001407	O75092	Frame_Shift_Del	DEL	ENST00000164024.4	hg19	CCDS2775.1																																																																																			.	.		0.626	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407		-	48691874	GTTGGGGACACCTCCCAGAAGAAGAGGGCCCGTCA	-	48691840	7	5	316	1	0	1	0	1	0	0	0	0	3225	1252	44	0	5020	0	CELSR3	3	48691840	Frame_Shift_Del	DEL	GTTGGGGACACCTCCCAGAAGAAGAGGGCCCGTCA	TCGA-KR-A7K8-01A-11D-A33K-10	2683199	48691840	149330590	9	44602										
LRIG1	26018	hgsc.bcm.edu	37	chr3	66431944	66431944	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	tcccttcagctttctccatcGctttccacggctctttgtga	6	15	3	1	rs201954431		TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr3:66431944G>A	ENST00000273261.3	-	17	3253	c.2729C>T	c.(2728-2730)gCg>gTg	p.A910V	SLC25A26_ENST00000536651.1_Intron|LRIG1_ENST00000496559.2_5'UTR|LRIG1_ENST00000383703.3_Missense_Mutation_p.A887V	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	910					innervation (GO:0060384)|otolith morphogenesis (GO:0032474)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)				NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		TTTCTCCATCGCTTTCCACGG	0.517																																					p.A910V		Atlas-SNP	.											.	LRIG1	138	.	0			c.C2729T						.	G	VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	135	129	131		2729	-6	0	3		131	0,8600		0,0,4300	yes	missense	LRIG1	NM_015541.2	64	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	910/1094	66431944	1,13005	2203	4300	6503	SO:0001583	missense	26018	exon17			TCCATCGCTTTCC	AB050468	CCDS33783.1	3p14	2013-01-14			ENSG00000144749	ENSG00000144749		"Immunoglobulin superfamily / I-set domain containing"	17360	protein-coding gene	gene with protein product	"ortholog of mouse integral membrane glycoprotein LIG-1", "leucine-rich repeat protein LRIG1"	608868				11414704, 12234026	Standard	NM_015541		Approved	LIG-1, DKFZP586O1624, LIG1	uc003dmx.3	Q96JA1	OTTHUMG00000158727	ENST00000273261.3:c.2729C>T	chr3.hg19:g.66431944G>A	ENSP00000273261:p.Ala910Val	94.0	0.0		91.0	4.0	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Missense_Mutation	SNP	ENST00000273261.3	hg19	CCDS33783.1	.	.	.	.	.	.	.	.	.	.	G	11.34	1.608442	0.28623	2.27E-4	0.0	ENSG00000144749	ENST00000273261;ENST00000383703;ENST00000383702	T;T	0.63417	-0.04;0.01	5.96	-5.96	0.02234	.	1.368680	0.04469	N	0.375714	T	0.30293	0.0760	N	0.01297	-0.9	0.09310	N	1	B;B;B	0.12013	0.005;0.005;0.002	B;B;B	0.09377	0.004;0.002;0.001	T	0.37174	-0.9717	10	0.13108	T	0.6	.	13.175	0.59621	0.1944:0.202:0.6036:0.0	.	887;910;910	Q96JA1-2;Q5XWD3;Q96JA1	.;.;LRIG1_HUMAN	V	910;887;813	ENSP00000273261:A910V;ENSP00000373208:A887V	ENSP00000273261:A910V	A	-	2	0	LRIG1	66514634	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.151000	0.10175	-1.444000	0.01950	-0.768000	0.03414	GCG	.	.		0.517	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541		A	66431944	G	A	66431944	3	1	316	1	0	0	0	0	1	0	0	0	8953	1087	38	1	564	1	LRIG1	3	66431944	Missense_Mutation	SNP	G	TCGA-KR-A7K8-01A-11D-A33K-10	17740104	66431944	131590486	10	44603										
CCDC50	152137	hgsc.bcm.edu	37	chr3	191107379	191107379	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	ggcatttctcaaaatcagagTcctctcataaaggtaagaag	8	8	3	2			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr3:191107379T>G	ENST00000392455.3	+	10	1487	c.889T>G	c.(889-891)Tcc>Gcc	p.S297A	CCDC50_ENST00000392456.3_Missense_Mutation_p.S473A	NM_174908.3	NP_777568.1	Q8IVM0	CCD50_HUMAN	coiled-coil domain containing 50	297						cytoplasm (GO:0005737)	ubiquitin protein ligase binding (GO:0031625)			endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|stomach(1)	23	all_cancers(143;8.88e-09)|Ovarian(172;0.103)|Breast(254;0.221)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000136)		AAAATCAGAGTCCTCTCATAA	0.388																																					p.S473A		Atlas-SNP	.											.	CCDC50	39	.	0			c.T1417G						.						162	162	162					3																	191107379		2203	4300	6503	SO:0001583	missense	152137	exon11			TCAGAGTCCTCTC	AJ416916	CCDS33912.1, CCDS33913.1	3q28	2010-12-24		2005-12-23	ENSG00000152492	ENSG00000152492			18111	protein-coding gene	gene with protein product		611051	"deafness, autosomal dominant 44"	C3orf6, DFNA44		16803894, 17503326	Standard	NM_178335		Approved	Ymer	uc003fsv.3	Q8IVM0	OTTHUMG00000156177	ENST00000392455.3:c.889T>G	chr3.hg19:g.191107379T>G	ENSP00000376249:p.Ser297Ala	152.0	0.0		173.0	12.0	NM_178335	Q86VH7	Missense_Mutation	SNP	ENST00000392455.3	hg19	CCDS33913.1	.	.	.	.	.	.	.	.	.	.	T	6.897	0.535063	0.13188	.	.	ENSG00000152492	ENST00000392455;ENST00000392456	T;T	0.34472	1.46;1.36	5.44	1.68	0.24146	.	0.503668	0.20997	N	0.081924	T	0.26048	0.0635	L	0.46741	1.465	0.23920	N	0.996462	B;B	0.25272	0.001;0.122	B;B	0.28305	0.003;0.088	T	0.15607	-1.0431	10	0.32370	T	0.25	.	3.3875	0.07277	0.1676:0.1806:0.0:0.6518	.	297;473	Q8IVM0;Q8IVM0-2	CCD50_HUMAN;.	A	297;473	ENSP00000376249:S297A;ENSP00000376250:S473A	ENSP00000376249:S297A	S	+	1	0	CCDC50	192590073	0.995000	0.38212	1.000000	0.80357	0.305000	0.27757	0.313000	0.19415	0.337000	0.23665	-0.503000	0.04515	TCC	.	.		0.388	CCDC50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343315.1	NM_174908		G	191107379	T	G	191107379	3	3	316	1	0	0	0	0	1	0	0	0	2822	1667	58	5	1459	5	CCDC50	3	191107379	Missense_Mutation	SNP	T	TCGA-KR-A7K8-01A-11D-A33K-10	124675435	191107379	6915051	11	44604										
GLRA3	8001	hgsc.bcm.edu	37	chr4	175564944	175564944	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	tgcccccagagacttaatctTgctgctgatgaatatcctca	7	12	2	3			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr4:175564944T>G	ENST00000274093.3	-	10	1890	c.1388A>C	c.(1387-1389)cAa>cCa	p.Q463P	GLRA3_ENST00000340217.5_Missense_Mutation_p.Q448P	NM_006529.2	NP_006520.2	O75311	GLRA3_HUMAN	glycine receptor, alpha 3	463					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glycine-gated chloride channel activity (GO:0016934)|glycine binding (GO:0016594)|transmitter-gated ion channel activity (GO:0022824)			endometrium(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	35		Prostate(90;0.00601)|Breast(14;0.0091)|Melanoma(52;0.00959)|Renal(120;0.0183)|all_neural(102;0.0891)|all_hematologic(60;0.107)		all cancers(43;4.99e-18)|Epithelial(43;1.18e-16)|OV - Ovarian serous cystadenocarcinoma(60;5.88e-09)|STAD - Stomach adenocarcinoma(60;0.00442)|GBM - Glioblastoma multiforme(59;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0421)	Glycine(DB00145)|Ivermectin(DB00602)|Lindane(DB00431)	GACTTAATCTTGCTGCTGATG	0.393																																					p.Q463P		Atlas-SNP	.											.	GLRA3	76	.	0			c.A1388C						.						102	110	107					4																	175564944		2203	4300	6503	SO:0001583	missense	8001	exon10			TAATCTTGCTGCT	AF017724	CCDS3822.1, CCDS43283.1	4q34.1	2012-02-07			ENSG00000145451	ENSG00000145451		"Ligand-gated ion channels / Glycine receptors"	4328	protein-coding gene	gene with protein product		600421				9677400	Standard	NM_001042543		Approved		uc003ity.1	O75311	OTTHUMG00000149816	ENST00000274093.3:c.1388A>C	chr4.hg19:g.175564944T>G	ENSP00000274093:p.Gln463Pro	77.0	0.0		101.0	13.0	NM_006529	D3DP44|O75816|Q5D0E3	Missense_Mutation	SNP	ENST00000274093.3	hg19	CCDS3822.1	.	.	.	.	.	.	.	.	.	.	T	14.61	2.588129	0.46110	.	.	ENSG00000145451	ENST00000274093;ENST00000340217	T;T	0.69306	-0.24;-0.39	5.87	4.69	0.59074	Neurotransmitter-gated ion-channel transmembrane domain (1);	0.260048	0.27664	N	0.018372	T	0.57681	0.2070	N	0.01874	-0.695	0.40139	D	0.976819	D;P	0.53462	0.96;0.932	D;P	0.64237	0.923;0.84	T	0.70263	-0.4920	10	0.87932	D	0	.	11.8396	0.52346	0.0:0.0684:0.0:0.9316	.	448;463	O75311-2;O75311	.;GLRA3_HUMAN	P	463;448	ENSP00000274093:Q463P;ENSP00000345284:Q448P	ENSP00000274093:Q463P	Q	-	2	0	GLRA3	175801519	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	2.967000	0.49216	1.047000	0.40274	0.482000	0.46254	CAA	.	.		0.393	GLRA3-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313427.1			G	175564944	T	G	175564944	3	3	316	1	0	0	0	0	1	0	0	0	6464	1812	63	5	10	5	GLRA3	4	175564944	Missense_Mutation	SNP	T	TCGA-KR-A7K8-01A-11D-A33K-10		175564944	15589332	12	44605										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13776635	13776635	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	gaacttcaaagctctgtttcGaaatttctcccccactggcg	7	13	3	0			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr5:13776635G>A	ENST00000265104.4	-	55	9390	c.9286C>T	c.(9286-9288)Cga>Tga	p.R3096*		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3096	AAA 4. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					GCTCTGTTTCGAAATTTCTCC	0.483									Kartagener syndrome																												p.R3096X		Atlas-SNP	.											DNAH5,caecum,carcinoma,+1,1	DNAH5	868	.	0			c.C9286T						.						97	91	93					5																	13776635		2203	4300	6503	SO:0001587	stop_gained	1767	exon55	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	TGTTTCGAAATTT	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.9286C>T	chr5.hg19:g.13776635G>A	ENSP00000265104:p.Arg3096*	231.0	0.0		244.0	25.0	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Nonsense_Mutation	SNP	ENST00000265104.4	hg19	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	G	52	18.969832	0.99913	.	.	ENSG00000039139	ENST00000265104	.	.	.	5.97	4.12	0.48240	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.937	0.64032	0.0:0.0:0.6006:0.3994	.	.	.	.	X	3096	.	ENSP00000265104:R3096X	R	-	1	2	DNAH5	13829635	1.000000	0.71417	0.996000	0.52242	0.995000	0.86356	3.116000	0.50399	0.791000	0.33826	0.655000	0.94253	CGA	.	.		0.483	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		A	13776635	G	A	13776635	4	1	316	1	0	0	0	0	0	1	0	0	4606	1066	37	1	4688	1	DNAH5	5	13776635	Nonsense_Mutation	SNP	G	TCGA-KR-A7K8-01A-11D-A33K-10		13776635	167138625	13	44606										
ZNF366	167465	hgsc.bcm.edu	37	chr5	71756473	71756473	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	tgaagagcttcccgcagtgcGtgcacgcgtgcggcttgatc	14	12	0	3			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr5:71756473G>A	ENST00000318442.5	-	2	1341	c.851C>T	c.(850-852)aCg>aTg	p.T284M		NM_152625.1	NP_689838.1	Q8N895	ZN366_HUMAN	zinc finger protein 366	284					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|estrogen receptor binding (GO:0030331)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	35		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)		CCCGCAGTGCGTGCACGCGTG	0.637																																					p.T284M		Atlas-SNP	.											ZNF366,colon,carcinoma,0,2	ZNF366	108	.	0			c.C851T						.						123	112	116					5																	71756473		2203	4300	6503	SO:0001583	missense	167465	exon2			CAGTGCGTGCACG	AK097115	CCDS4015.1	5q13.1	2013-01-08			ENSG00000178175	ENSG00000178175		"Zinc fingers, C2H2-type"	18316	protein-coding gene	gene with protein product		610159					Standard	NM_152625		Approved	FLJ39796	uc003kce.1	Q8N895	OTTHUMG00000100965	ENST00000318442.5:c.851C>T	chr5.hg19:g.71756473G>A	ENSP00000313158:p.Thr284Met	57.0	0.0		59.0	7.0	NM_152625	Q5HYI9|Q7RTV4	Missense_Mutation	SNP	ENST00000318442.5	hg19	CCDS4015.1	.	.	.	.	.	.	.	.	.	.	G	13.36	2.213632	0.39102	.	.	ENSG00000178175	ENST00000318442	T	0.77358	-1.09	5.79	0.231	0.15377	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.993471	0.08180	N	0.985683	T	0.81079	0.4748	L	0.43923	1.385	0.09310	N	1	D	0.53885	0.963	P	0.54210	0.745	T	0.74115	-0.3769	10	0.66056	D	0.02	-7.745	16.8323	0.85947	0.0:0.4978:0.4146:0.0876	.	284	Q8N895	ZN366_HUMAN	M	284	ENSP00000313158:T284M	ENSP00000313158:T284M	T	-	2	0	ZNF366	71792229	0.000000	0.05858	0.013000	0.15412	0.897000	0.52465	0.606000	0.24194	0.064000	0.16427	0.561000	0.74099	ACG	.	.		0.637	ZNF366-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218574.3			A	71756473	G	A	71756473	3	1	316	1	0	0	0	0	1	0	0	0	17885	1145	40	1	1399	1	ZNF366	5	71756473	Missense_Mutation	SNP	G	TCGA-KR-A7K8-01A-11D-A33K-10	57979838	71756473	109158787	14	44607										
IQGAP2	10788	hgsc.bcm.edu	37	chr5	75906955	75906955	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	ttagtgatgtggacccagccCatgcccagcactaccaggat	10	13	0	1			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr5:75906955C>T	ENST00000274364.6	+	13	1765	c.1468C>T	c.(1468-1470)Cat>Tat	p.H490Y	IQGAP2_ENST00000396234.3_Missense_Mutation_p.H43Y|CTD-2236F14.1_ENST00000511327.1_RNA|IQGAP2_ENST00000379730.3_Missense_Mutation_p.H49Y|IQGAP2_ENST00000502745.1_Missense_Mutation_p.H43Y	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	490					negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		GGACCCAGCCCATGCCCAGCA	0.408																																					p.H490Y		Atlas-SNP	.											.	IQGAP2	186	.	0			c.C1468T						.						133	134	133					5																	75906955		2203	4300	6503	SO:0001583	missense	10788	exon13			CCAGCCCATGCCC	U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.1468C>T	chr5.hg19:g.75906955C>T	ENSP00000274364:p.His490Tyr	108.0	0.0		74.0	10.0	NM_006633	A8K4V1|B7Z8A4|J3KR91	Missense_Mutation	SNP	ENST00000274364.6	hg19	CCDS34188.1	.	.	.	.	.	.	.	.	.	.	C	0.018	-1.475821	0.01035	.	.	ENSG00000145703	ENST00000274364;ENST00000379730;ENST00000514350;ENST00000505766;ENST00000514001;ENST00000396234;ENST00000545384;ENST00000509074;ENST00000502745	T;T;T;T;T;T;T;T	0.06218	3.33;3.33;3.33;3.33;3.33;3.33;3.33;3.33	5.8	-4.55	0.03441	.	1.197060	0.06071	N	0.660004	T	0.02767	0.0083	N	0.12182	0.205	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.08055	0.003;0.0;0.003;0.001	T	0.46303	-0.9201	10	0.02654	T	1	9.0892	7.3199	0.26521	0.2072:0.5359:0.0:0.2569	.	49;440;43;490	F5H7S7;E7EWC2;Q13576-2;Q13576	.;.;.;IQGA2_HUMAN	Y	490;49;463;440;43;43;43;43;43	ENSP00000274364:H490Y;ENSP00000442313:H49Y;ENSP00000423672:H463Y;ENSP00000421097:H440Y;ENSP00000422661:H43Y;ENSP00000379535:H43Y;ENSP00000425351:H43Y;ENSP00000426027:H43Y	ENSP00000274364:H490Y	H	+	1	0	IQGAP2	75942711	0.001000	0.12720	0.000000	0.03702	0.291000	0.27294	1.612000	0.36889	-0.455000	0.07054	-0.482000	0.04802	CAT	.	.		0.408	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633		T	75906955	C	T	75906955	3	4	316	1	0	0	0	0	1	0	0	0	7824	594	21	3	1518	3	IQGAP2	5	75906955	Missense_Mutation	SNP	C	TCGA-KR-A7K8-01A-11D-A33K-10	4150482	75906955	105008305	15	44608										
ADRB2	154	hgsc.bcm.edu	37	chr5	148206993	148206993	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	cttcacgaaccaagcctatgCcattgcctcttccatcgtgt	6	15	2	0			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr5:148206993C>T	ENST00000305988.4	+	1	838	c.599C>T	c.(598-600)gCc>gTc	p.A200V		NM_000024.5	NP_000015	P07550	ADRB2_HUMAN	adrenoceptor beta 2, surface	200	Agonist and antagonist binding.				activation of adenylate cyclase activity (GO:0007190)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|bone resorption (GO:0045453)|brown fat cell differentiation (GO:0050873)|cell surface receptor signaling pathway (GO:0007166)|desensitization of G-protein coupled receptor protein signaling pathway by arrestin (GO:0002032)|diet induced thermogenesis (GO:0002024)|endosome to lysosome transport (GO:0008333)|heat generation (GO:0031649)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of smooth muscle contraction (GO:0045986)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor-mediated endocytosis (GO:0006898)|regulation of sodium ion transport (GO:0002028)|regulation of vasodilation (GO:0042312)|response to cold (GO:0009409)|vasodilation by norepinephrine-epinephrine involved in regulation of systemic arterial blood pressure (GO:0002025)	apical plasma membrane (GO:0016324)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	beta2-adrenergic receptor activity (GO:0004941)|norepinephrine binding (GO:0051380)|potassium channel regulator activity (GO:0015459)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(1)|lung(8)|ovary(1)|prostate(3)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Acebutolol(DB01193)|Alprenolol(DB00866)|Amitriptyline(DB00321)|Amphetamine(DB00182)|Arbutamine(DB01102)|Arformoterol(DB01274)|Asenapine(DB06216)|Atenolol(DB00335)|Bambuterol(DB01408)|Betaxolol(DB00195)|Bethanidine(DB00217)|Bevantolol(DB01295)|Bisoprolol(DB00612)|Bopindolol(DB08807)|Bupranolol(DB08808)|Cabergoline(DB00248)|Carteolol(DB00521)|Carvedilol(DB01136)|Clenbuterol(DB01407)|Desipramine(DB01151)|Dipivefrin(DB00449)|Dobutamine(DB00841)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Fenoterol(DB01288)|Formoterol(DB00983)|Indacaterol(DB05039)|Isoetarine(DB00221)|Isoprenaline(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Mephentermine(DB01365)|Metipranolol(DB01214)|Metoprolol(DB00264)|Mirtazapine(DB00370)|Nadolol(DB01203)|Nebivolol(DB04861)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Orciprenaline(DB00816)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Phenoxybenzamine(DB00925)|Phenylpropanolamine(DB00397)|Pindolol(DB00960)|Pirbuterol(DB01291)|Procaterol(DB01366)|Propranolol(DB00571)|Pseudoephedrine(DB00852)|Ritodrine(DB00867)|Salbutamol(DB01001)|Salmeterol(DB00938)|Sotalol(DB00489)|Terbutaline(DB00871)|Timolol(DB00373)|Trimipramine(DB00726)	CAAGCCTATGCCATTGCCTCT	0.532																																					p.A200V		Atlas-SNP	.											.	ADRB2	42	.	0			c.C599T						.						310	260	277					5																	148206993		2203	4300	6503	SO:0001583	missense	154	exon1			CCTATGCCATTGC	AF022953	CCDS4292.1	5q31-q32	2012-08-08	2012-05-09		ENSG00000169252	ENSG00000169252		"GPCR / Class A : Adrenoceptors : beta"	286	protein-coding gene	gene with protein product		109690	"adrenergic, beta-2-, receptor, surface"	ADRB2R			Standard	NM_000024		Approved	ADRBR, BAR, B2AR	uc003lpr.2	P07550	OTTHUMG00000129933	ENST00000305988.4:c.599C>T	chr5.hg19:g.148206993C>T	ENSP00000305372:p.Ala200Val	59.0	0.0		55.0	13.0	NM_000024	B0LPE4|B2R7X2|O14823|O14824|O14825|O14826|Q4JG18|Q53GA6|Q6GMT4|Q6P4D8|Q8NEQ9|Q96EC3|Q9UCZ0|Q9UCZ1|Q9UCZ2|Q9UCZ3|Q9UH95|Q9UHA1|Q9UMZ5	Missense_Mutation	SNP	ENST00000305988.4	hg19	CCDS4292.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.898614	0.91962	.	.	ENSG00000169252	ENST00000305988	T	0.35421	1.31	5.65	5.65	0.86999	GPCR, rhodopsin-like superfamily (1);	0.053029	0.85682	D	0.000000	T	0.51244	0.1663	L	0.35593	1.075	0.80722	D	1	D	0.89917	1.0	D	0.67900	0.954	T	0.49854	-0.8895	10	0.87932	D	0	.	19.9142	0.97043	0.0:1.0:0.0:0.0	.	200	P07550	ADRB2_HUMAN	V	200	ENSP00000305372:A200V	ENSP00000305372:A200V	A	+	2	0	ADRB2	148187186	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.904000	0.69886	2.941000	0.99782	0.655000	0.94253	GCC	.	.		0.532	ADRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252189.1	NM_000024		T	148206993	C	T	148206993	3	4	316	1	0	0	0	0	1	0	0	0	341	739	26	3	601	3	ADRB2	5	148206993	Missense_Mutation	SNP	C	TCGA-KR-A7K8-01A-11D-A33K-10	72300038	148206993	32708267	16	44609										
HIST1H3C	8352	hgsc.bcm.edu	37	chr6	26045686	26045686	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	aagtctaccggcggcaaagcTccgcgcaagcagcttgctac	11	14	1	0			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr6:26045686T>A	ENST00000540144.1	+	1	48	c.48T>A	c.(46-48)gcT>gcA	p.A16A	HIST1H2BB_ENST00000357905.2_5'Flank	NM_003531.2	NP_003522.1	P68431	H31_HUMAN	histone cluster 1, H3c	16					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(1)|skin(1)	8						GCGGCAAAGCTCCGCGCAAGC	0.577																																					p.A16A		Atlas-SNP	.											.	HIST1H3C	34	.	0			c.T48A						.						40	43	42					6																	26045686		2202	4300	6502	SO:0001819	synonymous_variant	8352	exon1			CAAAGCTCCGCGC	X57128	CCDS4576.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000196532	ENSG00000278272		"Histones / Replication-dependent"	4768	protein-coding gene	gene with protein product		602812	"H3 histone family, member C", "histone 1, H3c"	H3FC		8227173, 9119399, 12408966	Standard	NM_003531		Approved	H3/c, H3.1	uc003nfv.3	P68431	OTTHUMG00000014416	ENST00000540144.1:c.48T>A	chr6.hg19:g.26045686T>A		113.0	0.0		122.0	13.0	NM_003531	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Silent	SNP	ENST00000540144.1	hg19	CCDS4576.1																																																																																			.	.		0.577	HIST1H3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040078.1	NM_003531		A	26045686	T	A	26045686	2	1	316	1	0	0	0	0	0	0	0	1	7166	1538	54	4		4	HIST1H3C	6	26045686	Silent	SNP	T	TCGA-KR-A7K8-01A-11D-A33K-10		26045686	145069381	17	44610										
ZNF311	282890	hgsc.bcm.edu	37	chr6	28963560	28963560	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	tcgttccccagtgtggattcTtatgtgtttggtgaggtctg	13	7	2	1			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr6:28963560T>G	ENST00000377179.3	-	7	1731	c.1219A>C	c.(1219-1221)Aga>Cga	p.R407R	ZNF311_ENST00000483450.1_5'UTR	NM_001010877.2	NP_001010877.2	Q5JNZ3	ZN311_HUMAN	zinc finger protein 311	407					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|skin(3)|upper_aerodigestive_tract(2)	28						GTGTGGATTCTTATGTGTTTG	0.517																																					p.R407R		Atlas-SNP	.											.	ZNF311	59	.	0			c.A1219C						.						85	80	82					6																	28963560		1510	2709	4219	SO:0001819	synonymous_variant	282890	exon7			GGATTCTTATGTG	AL833166	CCDS34357.1	6p21.33	2013-01-08			ENSG00000197935	ENSG00000197935		"Zinc fingers, C2H2-type", "-"	13847	protein-coding gene	gene with protein product							Standard	XM_006715067		Approved		uc003nlu.2	Q5JNZ3	OTTHUMG00000031292	ENST00000377179.3:c.1219A>C	chr6.hg19:g.28963560T>G		197.0	0.0		286.0	15.0	NM_001010877	A2BFK5|B0S7Y4|Q92971	Silent	SNP	ENST00000377179.3	hg19	CCDS34357.1																																																																																			.	.		0.517	ZNF311-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076631.3	XM_212581		G	28963560	T	G	28963560	2	3	316	1	0	0	0	0	0	0	0	1	17849	1617	56	5		5	ZNF311	6	28963560	Silent	SNP	T	TCGA-KR-A7K8-01A-11D-A33K-10	2917874	28963560	142151507	18	44611										
GSTA2	2939	hgsc.bcm.edu	37	chr6	52617735	52617735	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	ttgttcctcaggttgactaaAgggcagaagaaggatcattt	11	6	2	3			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr6:52617735A>C	ENST00000493422.1	-	5	486	c.331T>G	c.(331-333)Ttt>Gtt	p.F111V		NM_000846.4	NP_000837.3	P09210	GSTA2_HUMAN	glutathione S-transferase alpha 2	111	GST C-terminal.				epithelial cell differentiation (GO:0030855)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glutathione transferase activity (GO:0004364)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	Lung NSC(77;0.118)				Azathioprine(DB00993)|Busulfan(DB01008)|Chloroquine(DB00608)|Clofibrate(DB00636)|Ethacrynic acid(DB00903)|Glutathione(DB00143)|Vitamin E(DB00163)	GGTTGACTAAAGGGCAGAAGA	0.383																																					p.F111V		Atlas-SNP	.											.	GSTA2	33	.	0			c.T331G						.						213	200	205					6																	52617735		2203	4300	6503	SO:0001583	missense	2939	exon5			GACTAAAGGGCAG	AL109918	CCDS4944.1	6p12.2	2012-06-21	2008-11-26		ENSG00000244067	ENSG00000244067	2.5.1.18	"Glutathione S-transferases / Soluble"	4627	protein-coding gene	gene with protein product		138360	"glutathione S-transferase A2"	GST2			Standard	NM_000846		Approved		uc003pay.3	P09210	OTTHUMG00000016263	ENST00000493422.1:c.331T>G	chr6.hg19:g.52617735A>C	ENSP00000420168:p.Phe111Val	94.0	0.0		88.0	8.0	NM_000846	Q12759|Q16491|Q9NTY6	Missense_Mutation	SNP	ENST00000493422.1	hg19	CCDS4944.1	.	.	.	.	.	.	.	.	.	.	N	7.617	0.676038	0.14841	.	.	ENSG00000244067	ENST00000493422	T	0.10860	2.83	2.26	-4.51	0.03483	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);Glutathione S-transferase, C-terminal (1);	0.729488	0.12820	N	0.436484	T	0.02455	0.0075	M	0.67517	2.055	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.41016	-0.9532	10	0.46703	T	0.11	.	0.4985	0.00576	0.4261:0.1415:0.1522:0.2802	.	111	P09210	GSTA2_HUMAN	V	111	ENSP00000420168:F111V	ENSP00000420168:F111V	F	-	1	0	GSTA2	52725694	0.000000	0.05858	0.000000	0.03702	0.233000	0.25261	-3.848000	0.00351	-2.016000	0.00945	0.254000	0.18369	TTT	.	.		0.383	GSTA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043589.1	NM_000846		C	52617735	A	C	52617735	3	2	316	1	0	0	0	0	1	0	0	0	6840	72	3	5	349	5	GSTA2	6	52617735	Missense_Mutation	SNP	A	TCGA-KR-A7K8-01A-11D-A33K-10	23654175	52617735	118497332	19	44612										
TAAR2	9287	hgsc.bcm.edu	37	chr6	132938785	132938785	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	agatgtcatagccctctattCcatctgcataggcctctgag	8	12	4	2			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr6:132938785C>A	ENST00000367931.1	-	2	559	c.560G>T	c.(559-561)gGa>gTa	p.G187V	TAAR2_ENST00000275191.2_Missense_Mutation_p.G142V|TAAR2_ENST00000537809.1_Missense_Mutation_p.G142V			Q9P1P5	TAAR2_HUMAN	trace amine associated receptor 2	187					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|trace-amine receptor activity (GO:0001594)	p.G187E(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|skin(1)	23	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00608)|GBM - Glioblastoma multiforme(226;0.0151)		GCCCTCTATTCCATCTGCATA	0.463																																					p.G187V		Atlas-SNP	.											TAAR2,face,carcinoma,0,1	TAAR2	45	.	1	Substitution - Missense(1)	skin(1)	c.G560T						.						75	65	69					6																	132938785		2203	4299	6502	SO:0001583	missense	9287	exon2			TCTATTCCATCTG	AF112460	CCDS34541.1, CCDS5157.1	6q24	2012-08-08	2005-02-23	2005-02-24	ENSG00000146378	ENSG00000146378		"GPCR / Class A : Trace amine associated receptors"	4514	protein-coding gene	gene with protein product		604849	"G protein-coupled receptor 58"	GPR58		10684976, 15718104	Standard	NM_014626		Approved		uc003qdl.1	Q9P1P5	OTTHUMG00000015585	ENST00000367931.1:c.560G>T	chr6.hg19:g.132938785C>A	ENSP00000356908:p.Gly187Val	123.0	0.0		96.0	12.0	NM_001033080	Q5QD02|Q6NWS1|Q6NWS2|Q6NWS3	Missense_Mutation	SNP	ENST00000367931.1	hg19	CCDS34541.1	.	.	.	.	.	.	.	.	.	.	C	16.29	3.080470	0.55753	.	.	ENSG00000146378	ENST00000275191;ENST00000367931;ENST00000537809	T;T;T	0.72051	-0.62;-0.62;-0.62	6.0	6.0	0.97389	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.83330	0.5231	M	0.85373	2.75	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.85003	0.0901	10	0.72032	D	0.01	-31.393	15.5602	0.76237	0.0:0.9326:0.0:0.0674	.	187	Q9P1P5	TAAR2_HUMAN	V	142;187;142	ENSP00000275191:G142V;ENSP00000356908:G187V;ENSP00000441263:G142V	ENSP00000275191:G142V	G	-	2	0	TAAR2	132980478	0.947000	0.32204	0.961000	0.40146	0.540000	0.34992	2.348000	0.44045	2.846000	0.97976	0.650000	0.86243	GGA	.	.		0.463	TAAR2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390735.1	NM_014626		A	132938785	C	A	132938785	3	1	316	1	0	0	0	0	1	0	0	0	15505	855	30	3	499	3	TAAR2	6	132938785	Missense_Mutation	SNP	C	TCGA-KR-A7K8-01A-11D-A33K-10	80321050	132938785	38176282	20	44613										
ZC3H12D	340152	hgsc.bcm.edu	37	chr6	149771968	149771968	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	gagcgcgatgcgagcccgggCgcgcgcgtccccctcgtcgt	16	17	0	0			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr6:149771968C>T	ENST00000409806.3	-	6	1753	c.1435G>A	c.(1435-1437)Gcc>Acc	p.A479T	ZC3H12D_ENST00000389942.5_Missense_Mutation_p.A479T|ZC3H12D_ENST00000416573.2_3'UTR|ZC3H12D_ENST00000498662.1_5'Flank			A2A288	ZC12D_HUMAN	zinc finger CCCH-type containing 12D	479					negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|prostate(1)	6		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.23e-11)|GBM - Glioblastoma multiforme(68;0.0921)		CGAGCCCGGGCGCGCGCGTCC	0.721																																					p.A479T		Atlas-SNP	.											.	ZC3H12D	21	.	0			c.G1435A						.						7	13	12					6																	149771968		681	1580	2261	SO:0001583	missense	340152	exon6			CCCGGGCGCGCGC			6q25.1	2012-07-05	2005-06-30	2005-06-30	ENSG00000178199	ENSG00000178199		"Zinc fingers, CCCH-type domain containing"	21175	protein-coding gene	gene with protein product	"MCP induced protein 4"	611106	"chromosome 6 open reading frame 95"	C6orf95		18178554	Standard	NM_207360		Approved	dJ281H8.1, MCPIP4	uc010kid.3	A2A288	OTTHUMG00000015786	ENST00000409806.3:c.1435G>A	chr6.hg19:g.149771968C>T	ENSP00000386616:p.Ala479Thr	22.0	0.0		27.0	8.0	NM_207360	A1L178|B2RXF4|B7WNU7|B9ZZP9|B9ZZQ0|Q6ZRW2	Missense_Mutation	SNP	ENST00000409806.3	hg19		.	.	.	.	.	.	.	.	.	.	C	11.96	1.795999	0.31777	.	.	ENSG00000178199	ENST00000389942;ENST00000409806	T;T	0.34472	1.36;1.36	3.6	-7.2	0.01495	.	1.311170	0.05730	U	0.599408	T	0.03520	0.0101	N	0.03608	-0.345	0.09310	N	0.999998	B	0.06786	0.001	B	0.04013	0.001	T	0.24584	-1.0156	10	0.59425	D	0.04	.	1.3493	0.02169	0.2367:0.2469:0.3373:0.1791	.	479	A2A288	ZC12D_HUMAN	T	479	ENSP00000374592:A479T;ENSP00000386616:A479T	ENSP00000374592:A479T	A	-	1	0	ZC3H12D	149813661	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.073000	0.03430	-2.164000	0.00782	-0.254000	0.11334	GCC	.	.		0.721	ZC3H12D-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000286400.2	NM_207360		T	149771968	C	T	149771968	3	4	316	1	0	0	0	0	1	0	0	0	17579	768	27	1	152	1	ZC3H12D	6	149771968	Missense_Mutation	SNP	C	TCGA-KR-A7K8-01A-11D-A33K-10	16833183	149771968	21343099	21	44614										
ZBTB2	57621	hgsc.bcm.edu	37	chr6	151687673	151687673	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	tttgaagtcagctgggagagCtgtgaggcctcagggacctg	16	8	2	3			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr6:151687673C>A	ENST00000325144.4	-	3	668	c.528G>T	c.(526-528)caG>caT	p.Q176H		NM_020861.1	NP_065912.1	Q8N680	ZBTB2_HUMAN	zinc finger and BTB domain containing 2	176					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|large_intestine(2)|lung(6)|skin(1)	12			BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.63e-11)		GCTGGGAGAGCTGTGAGGCCT	0.562																																					p.Q176H		Atlas-SNP	.											.	ZBTB2	30	.	0			c.G528T						.						83	87	86					6																	151687673		2203	4300	6503	SO:0001583	missense	57621	exon3			GGAGAGCTGTGAG	BC020172	CCDS5231.1	6q25.1	2013-01-09			ENSG00000181472	ENSG00000181472		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	20868	protein-coding gene	gene with protein product						10819331	Standard	NM_020861		Approved	KIAA1483, ZNF437, bA351K16.2	uc003qoh.3	Q8N680	OTTHUMG00000015834	ENST00000325144.4:c.528G>T	chr6.hg19:g.151687673C>A	ENSP00000323183:p.Gln176His	89.0	0.0		77.0	15.0	NM_020861	A8K7C7|Q5SZ81|Q9P245	Missense_Mutation	SNP	ENST00000325144.4	hg19	CCDS5231.1	.	.	.	.	.	.	.	.	.	.	C	9.615	1.132176	0.21041	.	.	ENSG00000181472	ENST00000325144	T	0.05258	3.47	5.26	4.19	0.49359	.	0.404785	0.29273	N	0.012630	T	0.02230	0.0069	N	0.24115	0.695	0.42839	D	0.994044	B	0.20164	0.042	B	0.17433	0.018	T	0.35101	-0.9802	10	0.59425	D	0.04	-24.7215	11.2898	0.49244	0.0:0.8423:0.0:0.1577	.	176	Q8N680	ZBTB2_HUMAN	H	176	ENSP00000323183:Q176H	ENSP00000323183:Q176H	Q	-	3	2	ZBTB2	151729366	1.000000	0.71417	0.997000	0.53966	0.883000	0.51084	0.679000	0.25291	2.451000	0.82905	0.561000	0.74099	CAG	.	.		0.562	ZBTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042715.1	NM_020861		A	151687673	C	A	151687673	3	1	316	1	0	0	0	0	1	0	0	0	17543	796	28	3	1020	3	ZBTB2	6	151687673	Missense_Mutation	SNP	C	TCGA-KR-A7K8-01A-11D-A33K-10	1915705	151687673	19427394	22	44615										
PEG10	23089	hgsc.bcm.edu	37	chr7	94292809	94292810	+	5'UTR	DNP	AA	AA	CC													0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	ctcctcctccccctccccccAacaacaacaacaacaacaac							TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr7:94292809_94292810AA>CC	ENST00000482108.1	+	0	420_421				PEG10_ENST00000488574.1_5'UTR	NM_001040152.1|NM_001172438.1|NM_001184962.1	NP_001035242.1|NP_001165909.1|NP_001171891.1	Q86TG7	PEG10_HUMAN	paternally expressed 10						apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|placenta development (GO:0001890)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(9)|prostate(3)|skin(1)	21	all_cancers(62;8.26e-10)|all_epithelial(64;5.59e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			CCCTCCCCCcaacaacaacaac	0.589																																					p.N57H|p.N57T		Atlas-SNP	.											.	PEG10	36	.	0			c.A169C|c.A170C						.																																			SO:0001623	5_prime_UTR_variant	23089	exon2			CCCCCCAACAACA|CCCCCAACAACAA	AB049834	CCDS55126.1, CCDS75636.1, CCDS75637.1	7q21	2007-12-07			ENSG00000242265	ENSG00000242265			14005	protein-coding gene	gene with protein product		609810				11318613, 15716091, 16093683	Standard	NM_001172437		Approved	KIAA1051, HB-1, MEF3L, RGAG3, Mar2, Mart2	uc011kie.2	Q86TG7	OTTHUMG00000155578	Exception_encountered	chr7.hg19:g.94292809_94292810delinsCC		94.0	0.0		97.0|99.0	5.0|4.0	NM_001172438	Q96A68|Q9UPV1	Missense_Mutation	SNP	ENST00000482108.1	hg19	CCDS55126.1																																																																																			.	.		0.589	PEG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340751.1	NM_015068		CC	94292810	AA	CC	94292809	1	2	316	0	1	0	0	0	0	0	0	0	11728	130	5	5		5	PEG10	7	94292809	5'UTR	DNP	AA	TCGA-KR-A7K8-01A-11D-A33K-10		94292809	64845854	23	44616										
LHFPL3	375612	hgsc.bcm.edu	37	chr7	103969491	103969491	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	aacggcttctcccgggagctGacctgcaggggcagcttcac	13	14	2	1			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr7:103969491G>T	ENST00000401970.2	+	1	344	c.222G>T	c.(220-222)ctG>ctT	p.L74L	LHFPL3_ENST00000424859.1_Silent_p.L74L|LHFPL3_ENST00000543266.1_Silent_p.L88L|LHFPL3_ENST00000535008.1_Silent_p.L88L			Q86UP9	LHPL3_HUMAN	lipoma HMGIC fusion partner-like 3	88						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(6)	9						CCCGGGAGCTGACCTGCAGGG	0.617																																					p.L88L		Atlas-SNP	.											.	LHFPL3	24	.	0			c.G264T						.						46	53	51					7																	103969491		2019	4204	6223	SO:0001819	synonymous_variant	375612	exon1			GGAGCTGACCTGC	AY260763		7q22.2	2006-06-13			ENSG00000187416	ENSG00000187416			6589	protein-coding gene	gene with protein product		609719	"lipoma HMGIC fusion partner-like 4"	LHFPL4		10329012	Standard	NM_199000		Approved		uc003vce.3	Q86UP9	OTTHUMG00000157273	ENST00000401970.2:c.222G>T	chr7.hg19:g.103969491G>T		62.0	0.0		65.0	13.0	NM_199000	A1L383|A4D0Q5	Silent	SNP	ENST00000401970.2	hg19																																																																																				.	.		0.617	LHFPL3-002	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000348284.1	NM_199000		T	103969491	G	T	103969491	2	4	316	1	0	0	0	0	0	0	0	1	8775	1277	45	3		3	LHFPL3	7	103969491	Silent	SNP	G	TCGA-KR-A7K8-01A-11D-A33K-10	9676682	103969491	55169172	24	44617										
PENK	5179	hgsc.bcm.edu	37	chr8	57354357	57354357	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	accttttggctagcaaatggCtttcttccggtttgctattt	8	9	1	0			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr8:57354357C>T	ENST00000314922.3	-	2	354	c.278G>A	c.(277-279)aGc>aAc	p.S93N	PENK_ENST00000523274.1_5'UTR|PENK_ENST00000451791.2_Missense_Mutation_p.S93N	NM_006211.3	NP_006202.1	P01210	PENK_HUMAN	proenkephalin	93					aggressive behavior (GO:0002118)|behavioral fear response (GO:0001662)|locomotory behavior (GO:0007626)|neuropeptide signaling pathway (GO:0007218)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|startle response (GO:0001964)	extracellular region (GO:0005576)	neuropeptide hormone activity (GO:0005184)			central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(1)|lung(5)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	21		all_lung(136;0.229)	Epithelial(17;0.000873)|all cancers(17;0.0069)			TAGCAAATGGCTTTCTTCCGG	0.483																																					p.S93N		Atlas-SNP	.											.	PENK	59	.	0			c.G278A						.						107	104	105					8																	57354357		2203	4300	6503	SO:0001583	missense	5179	exon4			AAATGGCTTTCTT		CCDS6168.1	8q23-q24	2013-02-26				ENSG00000181195		"Endogenous ligands"	8831	protein-coding gene	gene with protein product	"preproenkephalin"	131330				6281660	Standard	NM_006211		Approved		uc003xsz.2	P01210		ENST00000314922.3:c.278G>A	chr8.hg19:g.57354357C>T	ENSP00000324248:p.Ser93Asn	91.0	0.0		81.0	10.0	NM_001135690	B2RC23|Q6FHC6|Q6FHE6	Missense_Mutation	SNP	ENST00000314922.3	hg19	CCDS6168.1	.	.	.	.	.	.	.	.	.	.	C	6.392	0.440467	0.12104	.	.	ENSG00000181195	ENST00000539312;ENST00000314922;ENST00000451791;ENST00000518974	T;T;T	0.43688	2.3;2.3;0.94	6.08	4.3	0.51218	.	0.376529	0.36002	N	0.002856	T	0.28962	0.0719	L	0.31926	0.97	0.40735	D	0.982786	B	0.06786	0.001	B	0.06405	0.002	T	0.07986	-1.0744	10	0.16896	T	0.51	-6.2633	9.8319	0.40948	0.0:0.771:0.0:0.229	.	93	P01210	PENK_HUMAN	N	93	ENSP00000324248:S93N;ENSP00000400894:S93N;ENSP00000428012:S93N	ENSP00000324248:S93N	S	-	2	0	PENK	57516911	0.001000	0.12720	0.499000	0.27577	0.749000	0.42624	-0.126000	0.10563	0.918000	0.36919	0.655000	0.94253	AGC	.	.		0.483	PENK-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378645.1			T	57354357	C	T	57354357	3	4	316	1	0	0	0	0	1	0	0	0	11736	797	28	3	529	3	PENK	8	57354357	Missense_Mutation	SNP	C	TCGA-KR-A7K8-01A-11D-A33K-10		57354357	89009665	25	44618										
TRPA1	8989	hgsc.bcm.edu	37	chr8	72975749	72975749	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	ggaacctgaaaatgcagcttGgtgaatagggaaacatcccc	11	9	0	2			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr8:72975749G>T	ENST00000262209.4	-	5	817	c.610C>A	c.(610-612)Caa>Aaa	p.Q204K		NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	204					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	AATGCAGCTTGGTGAATAGGG	0.343																																					p.Q204K		Atlas-SNP	.											TRPA1,NS,carcinoma,0,1	TRPA1	256	.	0			c.C610A						.						105	102	103					8																	72975749		2203	4300	6503	SO:0001583	missense	8989	exon5			CAGCTTGGTGAAT	Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	497	protein-coding gene	gene with protein product		604775	"ankyrin-like with transmembrane domains 1"	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.610C>A	chr8.hg19:g.72975749G>T	ENSP00000262209:p.Gln204Lys	58.0	0.0		85.0	7.0	NM_007332	A6NIN6	Missense_Mutation	SNP	ENST00000262209.4	hg19	CCDS34908.1	.	.	.	.	.	.	.	.	.	.	G	7.856	0.724951	0.15439	.	.	ENSG00000104321	ENST00000523582;ENST00000262209	T;T	0.64085	-0.08;2.44	5.46	4.54	0.55810	Ankyrin repeat-containing domain (3);	0.520658	0.22669	N	0.057092	T	0.52289	0.1725	L	0.51422	1.61	0.30999	N	0.720539	B	0.27823	0.19	B	0.26202	0.067	T	0.52931	-0.8509	10	0.29301	T	0.29	-5.112	9.3615	0.38199	0.0:0.1688:0.607:0.2243	.	204	O75762	TRPA1_HUMAN	K	56;204	ENSP00000428151:Q56K;ENSP00000262209:Q204K	ENSP00000262209:Q204K	Q	-	1	0	TRPA1	73138303	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.572000	0.45999	2.724000	0.93272	0.650000	0.86243	CAA	.	.		0.343	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332		T	72975749	G	T	72975749	3	4	316	1	0	0	0	0	1	0	0	0	16592	1357	47	3	2841	3	TRPA1	8	72975749	Missense_Mutation	SNP	G	TCGA-KR-A7K8-01A-11D-A33K-10	15621392	72975749	73388273	26	44619										
PMP2	5375	hgsc.bcm.edu	37	chr8	82357195	82357195	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	cacagtgggtttggccaaatTtcccagttttctggtggcta	11	9	1	0			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr8:82357195T>C	ENST00000256103.2	-	2	239	c.103A>G	c.(103-105)Aat>Gat	p.N35D	RP11-157I4.4_ENST00000524085.2_RNA|PMP2_ENST00000519260.1_Intron	NM_002677.3	NP_002668.1	P02689	MYP2_HUMAN	peripheral myelin protein 2	35					membrane organization (GO:0061024)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	cholesterol binding (GO:0015485)|fatty acid binding (GO:0005504)|transporter activity (GO:0005215)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)	6			Epithelial(68;0.186)			TTGGCCAAATTTCCCAGTTTT	0.398																																					p.N35D		Atlas-SNP	.											.	PMP2	21	.	0			c.A103G						.						101	97	98					8																	82357195		2203	4300	6503	SO:0001583	missense	5375	exon2			CCAAATTTCCCAG	X62167	CCDS6229.1	8q21.3-q22.1	2013-03-01			ENSG00000147588	ENSG00000147588		"Fatty acid binding protein family"	9117	protein-coding gene	gene with protein product		170715				1720307, 8288226	Standard	NM_002677		Approved	MP2, FABP8, M-FABP	uc003ycb.1	P02689	OTTHUMG00000164600	ENST00000256103.2:c.103A>G	chr8.hg19:g.82357195T>C	ENSP00000256103:p.Asn35Asp	82.0	0.0		104.0	22.0	NM_002677	Q6FHL4	Missense_Mutation	SNP	ENST00000256103.2	hg19	CCDS6229.1	.	.	.	.	.	.	.	.	.	.	T	15.47	2.844477	0.51164	.	.	ENSG00000147588	ENST00000256103	T	0.08546	3.08	6.16	5.01	0.66863	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.186077	0.56097	D	0.000027	T	0.13543	0.0328	M	0.82132	2.575	0.80722	D	1	B	0.21905	0.062	B	0.25884	0.064	T	0.01982	-1.1235	10	0.46703	T	0.11	.	8.404	0.32603	0.0:0.2159:0.0:0.7841	.	35	P02689	MYP2_HUMAN	D	35	ENSP00000256103:N35D	ENSP00000256103:N35D	N	-	1	0	PMP2	82519750	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.064000	0.41432	1.143000	0.42306	0.528000	0.53228	AAT	.	.		0.398	PMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379365.1	NM_002677		C	82357195	T	C	82357195	3	2	316	1	0	0	0	0	1	0	0	0	12147	1841	64	2	307	2	PMP2	8	82357195	Missense_Mutation	SNP	T	TCGA-KR-A7K8-01A-11D-A33K-10	9381446	82357195	64006827	27	44620										
CBWD1	55871	hgsc.bcm.edu	37	chr9	154795	154795	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	gcatctgccaaagcaacttgTctaaaatagcaaacagagaa	7	9	2	1	rs2785333	byFrequency	TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr9:154795T>C	ENST00000356521.4	-	8	664	c.576A>G	c.(574-576)agA>agG	p.R192R	CBWD1_ENST00000314367.10_Splice_Site_p.R156R|CBWD1_ENST00000382447.4_Splice_Site_p.R192R|CBWD1_ENST00000377447.3_Splice_Site_p.R192R|CBWD1_ENST00000377400.4_Intron	NM_018491.3	NP_060961.3	Q9BRT8	CBWD1_HUMAN	COBW domain containing 1	192							ATP binding (GO:0005524)			kidney(1)|lung(2)|ovary(1)|skin(1)	5	all_lung(41;0.218)	all_cancers(5;3.04e-16)|all_epithelial(5;4.68e-12)|all_lung(10;1.94e-10)|Lung NSC(10;3.61e-10)|Acute lymphoblastic leukemia(5;0.00439)|Breast(48;0.0148)|all_hematologic(5;0.024)|Prostate(43;0.122)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)		AAGCAACTTGTCTAAAATAGC	0.294													N|||	3941	0.786941	0.8306	0.7709	5008	,	,		15055	0.7232		0.7614	False		,,,				2504	0.8313				p.R192R		Atlas-SNP	.											.	CBWD1	24	.	0			c.A576G						.	C	,,	2060,592		826,408,92	51	68	62		468,576,576	1.3	1	9	dbSNP_100	62	3426,1104		1310,806,149	no	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	CBWD1	NM_001145355.1,NM_001145356.1,NM_018491.3	,,	2136,1214,241	CC,CT,TT		24.3709,22.3228,23.6146	,,	156/360,192/377,192/396	154795	5486,1696	1326	2265	3591	SO:0001630	splice_region_variant	55871	exon8			AACTTGTCTAAAA	AY343911	CCDS6438.1, CCDS47947.1, CCDS47948.1	9p24.3	2008-02-05			ENSG00000172785	ENSG00000172785			17134	protein-coding gene	gene with protein product		611078				15233989, 12421752	Standard	NM_018491		Approved		uc003zga.4	Q9BRT8	OTTHUMG00000019425	ENST00000356521.4:c.576-1A>G	chr9.hg19:g.154795T>C		0.0	0.0		5.0	5.0	NM_001145356	A2RU55|A8K3N3|B0AZR4|Q49AJ1|Q5VVK2|Q6VBU6|Q7Z5Z0|Q7Z652|Q9BY38|Q9NYD0	Silent	SNP	ENST00000356521.4	hg19	CCDS6438.1																																																																																			.	.		0.294	CBWD1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051463.1	NM_018491	Silent	C	154795	T	C	154795	5	2	316	1	0	0	0	0	0	0	1	0	2714	1681	58	2	643	2	CBWD1	9	154795	Splice_Site	SNP	T	TCGA-KR-A7K8-01A-11D-A33K-10		154795	141058636	28	44621										
TSC1	7248	hgsc.bcm.edu	37	chr9	135781136	135781136	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	gggctgtctttggcaatgccAcctcaaaaagatgatcatac	9	10	3	2			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr9:135781136A>G	ENST00000298552.3	-	15	2050	c.1829T>C	c.(1828-1830)gTg>gCg	p.V610A	TSC1_ENST00000545250.1_Missense_Mutation_p.V559A|TSC1_ENST00000440111.2_Missense_Mutation_p.V610A	NM_000368.4|NM_001162426.1|NM_001162427.1	NP_000359.1|NP_001155898.1|NP_001155899.1	Q92574	TSC1_HUMAN	tuberous sclerosis 1	610					activation of Rho GTPase activity (GO:0032862)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|insulin receptor signaling pathway (GO:0008286)|kidney development (GO:0001822)|myelination (GO:0042552)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of TOR signaling (GO:0032007)|negative regulation of translation (GO:0017148)|neural tube closure (GO:0001843)|positive regulation of focal adhesion assembly (GO:0051894)|potassium ion transport (GO:0006813)|protein heterooligomerization (GO:0051291)|protein stabilization (GO:0050821)|regulation of cell cycle (GO:0051726)|regulation of cell-matrix adhesion (GO:0001952)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of protein kinase activity (GO:0045859)|regulation of stress fiber assembly (GO:0051492)|regulation of translation (GO:0006417)|response to insulin (GO:0032868)|rRNA export from nucleus (GO:0006407)|synapse organization (GO:0050808)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|lamellipodium (GO:0030027)|membrane (GO:0016020)|protein complex (GO:0043234)|TSC1-TSC2 complex (GO:0033596)	chaperone binding (GO:0051087)|GTPase regulator activity (GO:0030695)|protein N-terminus binding (GO:0047485)	p.?(1)		NS(1)|bone(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(9)|lung(20)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	65				OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06)		TGGCAATGCCACCTCAAAAAG	0.498			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.V610A		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 1	9	9q34	7248	tuberous sclerosis 1 gene		"E, O"	.	TSC1	167	.	1	Unknown(1)	bone(1)	c.T1829C						.						111	100	104					9																	135781136		2203	4300	6503	SO:0001583	missense	7248	exon15	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	AATGCCACCTCAA	AF013168	CCDS6956.1, CCDS55350.1	9q34	2014-09-17			ENSG00000165699	ENSG00000165699			12362	protein-coding gene	gene with protein product		605284		TSC		9242607, 10806479	Standard	NM_000368		Approved	KIAA0243, LAM, hamartin	uc004cca.2	Q92574	OTTHUMG00000020844	ENST00000298552.3:c.1829T>C	chr9.hg19:g.135781136A>G	ENSP00000298552:p.Val610Ala	141.0	0.0		150.0	10.0	NM_000368	B7Z897|Q5VVN5	Missense_Mutation	SNP	ENST00000298552.3	hg19	CCDS6956.1	.	.	.	.	.	.	.	.	.	.	A	19.61	3.860222	0.71834	.	.	ENSG00000165699	ENST00000298552;ENST00000440111;ENST00000545250	D;D;D	0.88046	-2.33;-2.33;-2.33	5.94	5.94	0.96194	.	0.279923	0.39985	N	0.001201	D	0.83663	0.5303	L	0.54323	1.7	0.80722	D	1	B;B	0.33448	0.412;0.412	B;B	0.34038	0.174;0.174	T	0.80498	-0.1356	10	0.11794	T	0.64	-10.9031	15.5809	0.76439	1.0:0.0:0.0:0.0	.	559;610	B7Z897;Q92574	.;TSC1_HUMAN	A	610;610;559	ENSP00000298552:V610A;ENSP00000394524:V610A;ENSP00000444017:V559A	ENSP00000298552:V610A	V	-	2	0	TSC1	134770957	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.584000	0.67490	2.275000	0.75901	0.528000	0.53228	GTG	.	.		0.498	TSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054799.1			G	135781136	A	G	135781136	3	3	316	1	0	0	0	0	1	0	0	0	16620	159	6	2	1701	2	TSC1	9	135781136	Missense_Mutation	SNP	A	TCGA-KR-A7K8-01A-11D-A33K-10	135626341	135781136	5432295	29	44622										
ZNF33A	7581	hgsc.bcm.edu	37	chr10	38343571	38343571	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	tctgatgaatttaatgcctgTgggaaattgttactcaatat	8	5	2	2			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr10:38343571T>C	ENST00000458705.2	+	5	674	c.516T>C	c.(514-516)tgT>tgC	p.C172C	ZNF33A_ENST00000307441.9_Silent_p.C172C|ZNF33A_ENST00000432900.2_Silent_p.C179C|ZNF33A_ENST00000374618.3_Silent_p.C173C|ZNF33A_ENST00000469037.2_Intron			Q06730	ZN33A_HUMAN	zinc finger protein 33A	172					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(2)|large_intestine(8)|liver(2)|lung(27)|ovary(2)|prostate(1)|skin(2)	46						TTAATGCCTGTGGGAAATTGT	0.328																																					p.C173C		Atlas-SNP	.											.	ZNF33A	103	.	0			c.T519C						.						64	65	65					10																	38343571		2203	4299	6502	SO:0001819	synonymous_variant	7581	exon5			TGCCTGTGGGAAA	D31763	CCDS31182.1, CCDS60514.1, CCDS73088.1, CCDS73089.1	10p11.2	2013-01-08	2005-03-18		ENSG00000189180	ENSG00000189180		"Zinc fingers, C2H2-type", "-"	13096	protein-coding gene	gene with protein product	"zinc finger and ZAK associated protein with KRAB domain"	194521	"zinc finger protein 33a (KOX 31)", "zinc finger protein 11A"	ZNF33, ZNF11A		2014798, 8464732	Standard	NM_006974		Approved	KOX5, KOX31, KIAA0065, FLJ23404, ZZAPK	uc031pui.1	Q06730	OTTHUMG00000017983	ENST00000458705.2:c.516T>C	chr10.hg19:g.38343571T>C		84.0	0.0		55.0	11.0	NM_006954	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Silent	SNP	ENST00000458705.2	hg19	CCDS31182.1																																																																																			.	.		0.328	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974		C	38343571	T	C	38343571	2	2	316	1	0	0	0	0	0	0	0	1	17869	1702	59	2		2	ZNF33A	10	38343571	Silent	SNP	T	TCGA-KR-A7K8-01A-11D-A33K-10		38343571	97191176	30	44623										
SORBS1	10580	hgsc.bcm.edu	37	chr10	97197265	97197265	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	acctttgtcttgcccattgcTgccaggtgccaagccattca	8	14	2	0			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr10:97197265T>A	ENST00000361941.3	-	2	84	c.58A>T	c.(58-60)Agc>Tgc	p.S20C	SORBS1_ENST00000371246.2_Missense_Mutation_p.S20C|SORBS1_ENST00000371239.1_Missense_Mutation_p.S20C|SORBS1_ENST00000277982.5_Missense_Mutation_p.S20C|SORBS1_ENST00000371247.2_Missense_Mutation_p.S20C|SORBS1_ENST00000474353.2_5'UTR|SORBS1_ENST00000371245.3_Missense_Mutation_p.S20C|SORBS1_ENST00000353505.5_Missense_Mutation_p.S20C|SORBS1_ENST00000371227.4_Missense_Mutation_p.S20C|SORBS1_ENST00000393949.1_Missense_Mutation_p.S20C|SORBS1_ENST00000354106.3_Missense_Mutation_p.S20C|SORBS1_ENST00000306402.6_Missense_Mutation_p.S20C|SORBS1_ENST00000347291.4_Missense_Mutation_p.S20C|SORBS1_ENST00000371249.2_Missense_Mutation_p.S20C|SORBS1_ENST00000607232.1_Missense_Mutation_p.S20C|SORBS1_ENST00000371241.1_Missense_Mutation_p.S20C	NM_001034954.1	NP_001030126			sorbin and SH3 domain containing 1											NS(1)|breast(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(19)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		TGCCCATTGCTGCCAGGTGCC	0.498																																					p.S20C		Atlas-SNP	.											.	SORBS1	185	.	0			c.A58T						.						182	148	159					10																	97197265		2203	4300	6503	SO:0001583	missense	10580	exon2			CATTGCTGCCAGG	AF136381	CCDS7442.1, CCDS31252.1, CCDS31253.1, CCDS31254.1, CCDS31255.1, CCDS31256.1, CCDS73169.1	10q23.33	2011-07-25	2002-05-08		ENSG00000095637	ENSG00000095637			14565	protein-coding gene	gene with protein product	"c-Cbl-associated protein"	605264	"SH3-domain protein 5 (ponsin)"	SH3D5		10085297, 11001060	Standard	XM_005269405		Approved	FLJ12406, CAP, sh3p12, ponsin, KIAA1296	uc001kkp.3	Q9BX66	OTTHUMG00000018812	ENST00000361941.3:c.58A>T	chr10.hg19:g.97197265T>A	ENSP00000355136:p.Ser20Cys	189.0	0.0		148.0	11.0	NM_001034955		Missense_Mutation	SNP	ENST00000361941.3	hg19	CCDS31255.1	.	.	.	.	.	.	.	.	.	.	T	14.91	2.676251	0.47886	.	.	ENSG00000095637	ENST00000371245;ENST00000306402;ENST00000371249;ENST00000371247;ENST00000371227;ENST00000371246;ENST00000393949;ENST00000353505;ENST00000347291;ENST00000361941;ENST00000277982;ENST00000371241;ENST00000354106;ENST00000371239	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.19938	2.71;2.21;2.66;2.51;2.33;2.83;2.29;2.71;2.11;2.51;2.83;2.59;2.29;2.6	5.19	4.02	0.46733	.	0.166674	0.28821	N	0.014028	T	0.31482	0.0798	L	0.32530	0.975	0.20403	N	0.999905	P;P;D;D;D;D;D;D;D;D;D;D	0.76494	0.947;0.464;0.999;0.996;0.993;0.986;0.983;0.996;0.996;0.994;0.998;0.996	P;B;D;D;P;P;P;D;P;P;D;P	0.68621	0.541;0.112;0.957;0.937;0.9;0.849;0.9;0.959;0.849;0.759;0.959;0.849	T	0.05616	-1.0874	10	0.87932	D	0	-1.7903	9.9905	0.41868	0.0:0.0:0.1704:0.8296	.	20;20;20;20;20;20;20;20;20;20;20;20	B7Z9B7;B4DTX5;F2Z2S3;Q9BX66-11;Q9BX66-10;Q9BX66-9;Q9BX66-4;Q9BX66-8;Q9BX66-3;Q9BX66;Q9BX66-2;Q9BX66-6	.;.;.;.;.;.;.;.;.;SRBS1_HUMAN;.;.	C	20	ENSP00000360291:S20C;ENSP00000302556:S20C;ENSP00000360295:S20C;ENSP00000360293:S20C;ENSP00000360271:S20C;ENSP00000360292:S20C;ENSP00000377521:S20C;ENSP00000343998:S20C;ENSP00000277985:S20C;ENSP00000355136:S20C;ENSP00000277982:S20C;ENSP00000360285:S20C;ENSP00000277984:S20C;ENSP00000360283:S20C	ENSP00000277982:S20C	S	-	1	0	SORBS1	97187255	1.000000	0.71417	0.846000	0.33378	0.440000	0.31957	4.662000	0.61525	0.880000	0.35969	0.528000	0.53228	AGC	.	.		0.498	SORBS1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049517.1			A	97197265	T	A	97197265	3	1	316	1	0	0	0	0	1	0	0	0	14942	1580	55	4	4137	4	SORBS1	10	97197265	Missense_Mutation	SNP	T	TCGA-KR-A7K8-01A-11D-A33K-10	58853694	97197265	38337482	31	44624										
TSSC4	10078	hgsc.bcm.edu	37	chr11	2424029	2424029	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	tgtccccgatggggctgcctGgggaggaggattcaggtcct	17	10	1	0			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr11:2424029G>T	ENST00000333256.6	+	3	609	c.166G>T	c.(166-168)Ggg>Tgg	p.G56W	TSSC4_ENST00000380992.1_Intron|AC124057.5_ENST00000433035.1_RNA|TSSC4_ENST00000380996.5_Intron|TSSC4_ENST00000451491.2_Missense_Mutation_p.G56W			Q9Y5U2	TSSC4_HUMAN	tumor suppressing subtransferable candidate 4	56										endometrium(3)|large_intestine(1)|lung(4)	8		all_epithelial(84;0.000161)|Breast(177;0.000962)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|all_neural(188;0.0137)|Lung NSC(207;0.209)		BRCA - Breast invasive adenocarcinoma(625;0.00145)|LUSC - Lung squamous cell carcinoma(625;0.19)		GGGGCTGCCTGGGGAGGAGGA	0.637																																					p.G56W		Atlas-SNP	.											.	TSSC4	19	.	0			c.G166T						.						47	34	39					11																	2424029		2190	4286	6476	SO:0001583	missense	10078	exon2			CTGCCTGGGGAGG	AF125568	CCDS7735.1, CCDS73241.1	11p15.5	2008-02-05			ENSG00000184281	ENSG00000184281			12386	protein-coding gene	gene with protein product		603852				10072438	Standard	XM_005252722		Approved		uc001lwl.3	Q9Y5U2	OTTHUMG00000009895	ENST00000333256.6:c.166G>T	chr11.hg19:g.2424029G>T	ENSP00000331087:p.Gly56Trp	94.0	0.0		100.0	12.0	NM_005706	C9JS66|Q86VL2|Q9BRS6	Missense_Mutation	SNP	ENST00000333256.6	hg19	CCDS7735.1	.	.	.	.	.	.	.	.	.	.	G	12.24	1.878104	0.33162	.	.	ENSG00000184281	ENST00000333256;ENST00000437110;ENST00000435795;ENST00000485682;ENST00000496468;ENST00000451491	T;T;T;T;T;T	0.47177	2.43;1.44;0.85;0.85;1.44;2.43	2.78	0.535	0.17133	.	0.907565	0.08908	N	0.876244	T	0.42131	0.1189	L	0.57536	1.79	0.09310	N	0.999997	B	0.23735	0.09	B	0.18263	0.021	T	0.34153	-0.9840	9	.	.	.	-10.3048	10.1334	0.42693	0.0:0.0:0.6491:0.3509	.	56	Q9Y5U2	TSSC4_HUMAN	W	56	ENSP00000331087:G56W;ENSP00000396925:G56W;ENSP00000403475:G56W;ENSP00000431430:G56W;ENSP00000435013:G56W;ENSP00000411224:G56W	.	G	+	1	0	TSSC4	2380605	0.114000	0.22134	0.088000	0.20740	0.559000	0.35586	0.534000	0.23098	0.490000	0.27771	0.462000	0.41574	GGG	.	.		0.637	TSSC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027369.3	NM_005706		T	2424029	G	T	2424029	3	4	316	1	0	0	0	0	1	0	0	0	16682	1348	47	3	168	3	TSSC4	11	2424029	Missense_Mutation	SNP	G	TCGA-KR-A7K8-01A-11D-A33K-10		2424029	132582487	32	44625										
CLEC1A	51267	hgsc.bcm.edu	37	chr12	10228256	10228256	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	caagggctgcacctgtgtgcTtggaaaaaagccaattttat	10	8	0	0			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr12:10228256T>C	ENST00000315330.4	-	4	454		c.e4-2		CLEC1A_ENST00000420265.2_Splice_Site|CLEC1A_ENST00000457018.2_Splice_Site	NM_016511.2	NP_057595.2	Q8NC01	CLC1A_HUMAN	C-type lectin domain family 1, member A						cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	23						ACCTGTGTGCTTGGAAAAAAG	0.363																																					.		Atlas-SNP	.											.	CLEC1A	48	.	0			c.392-2A>G						.						102	96	98					12																	10228256		2203	4300	6503	SO:0001630	splice_region_variant	51267	exon5			GTGTGCTTGGAAA	AY358587	CCDS8612.1, CCDS73443.1	12p13.31	2005-02-09				ENSG00000150048		"C-type lectin domain containing"	24355	protein-coding gene	gene with protein product		606782				10671229, 11745369	Standard	XM_005253383		Approved	CLEC1, MGC34328	uc001qxb.3	Q8NC01		ENST00000315330.4:c.392-2A>G	chr12.hg19:g.10228256T>C		99.0	0.0		117.0	7.0	NM_016511	Q8IUW7|Q9NZH3	Splice_Site	SNP	ENST00000315330.4	hg19	CCDS8612.1	.	.	.	.	.	.	.	.	.	.	T	9.591	1.126268	0.20959	.	.	ENSG00000150048	ENST00000315330;ENST00000457018;ENST00000420265	.	.	.	5.06	5.06	0.68205	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.5034	0.50451	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	CLEC1A	10119523	0.944000	0.32072	0.882000	0.34594	0.086000	0.17979	3.752000	0.55172	2.040000	0.60383	0.533000	0.62120	.	.	.		0.363	CLEC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399924.1	NM_016511	Intron	C	10228256	T	C	10228256	5	2	316	1	0	0	0	0	0	0	1	0	3507	1623	56	2	464	2	CLEC1A	12	10228256	Splice_Site	SNP	T	TCGA-KR-A7K8-01A-11D-A33K-10		10228256	123623639	33	44626										
LOH12CR1	118426	hgsc.bcm.edu	37	chr12	12514204	12514204	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	gtggttgtagctcagggctcCcaggcctcacggaacgtcag	14	12	3	0			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr12:12514204C>T	ENST00000314565.4	+	2	454	c.123C>T	c.(121-123)tcC>tcT	p.S41S	LOH12CR1_ENST00000298571.6_Intron|LOH12CR1_ENST00000542728.1_Silent_p.S22S	NM_058169.3	NP_477517.1	Q969J3	L12R1_HUMAN	loss of heterozygosity, 12, chromosomal region 1	41			S -> C (in dbSNP:rs3741795).							kidney(1)|large_intestine(1)|lung(1)|ovary(1)	4		Prostate(47;0.0802)		BRCA - Breast invasive adenocarcinoma(232;0.0205)		CTCAGGGCTCCCAGGCCTCAC	0.463																																					p.S41S		Atlas-SNP	.											.	LOH12CR1	13	.	0			c.C123T						.						186	168	174					12																	12514204		2203	4300	6503	SO:0001819	synonymous_variant	118426	exon2			GGGCTCCCAGGCC	AY037865	CCDS8649.1, CCDS73448.1	12p12	2008-07-03			ENSG00000165714	ENSG00000165714			17950	protein-coding gene	gene with protein product						11896457, 15284860	Standard	XR_242885		Approved	LOH1CR12	uc001ral.2	Q969J3	OTTHUMG00000168542	ENST00000314565.4:c.123C>T	chr12.hg19:g.12514204C>T		162.0	0.0		148.0	12.0	NM_058169	Q96QS5	Silent	SNP	ENST00000314565.4	hg19	CCDS8649.1																																																																																			.	.		0.463	LOH12CR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400150.1			T	12514204	C	T	12514204	2	4	316	1	0	0	0	0	0	0	0	1	8900	610	22	3		3	LOH12CR1	12	12514204	Silent	SNP	C	TCGA-KR-A7K8-01A-11D-A33K-10	2285948	12514204	121337691	34	44627										
SETD8	387893	hgsc.bcm.edu	37	chr12	123880924	123880924	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	aacgcaacagaatcgcaaacTtacggatttctaccctgtcc	6	13	1	1	rs77198130		TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr12:123880924T>G	ENST00000402868.3	+	5	968	c.542T>G	c.(541-543)cTt>cGt	p.L181R	SETD8_ENST00000330479.4_Missense_Mutation_p.L181R|SETD8_ENST00000478781.2_3'UTR			Q9NQR1	SETD8_HUMAN	SET domain containing (lysine methyltransferase) 8	222					histone lysine methylation (GO:0034968)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine monomethylation (GO:0018026)|regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043516)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|urinary_tract(1)	13	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.00101)|Epithelial(86;0.00425)		AATCGCAAACTTACGGATTTC	0.502																																					p.L181R		Atlas-SNP	.											.	SETD8	35	.	0			c.T542G						.						84	84	84					12																	123880924		2203	4300	6503	SO:0001583	missense	387893	exon5			GCAAACTTACGGA	AY102937	CCDS9247.1	12q24.31	2011-07-01			ENSG00000183955	ENSG00000183955		"Chromatin-modifying enzymes / K-methyltransferases"	29489	protein-coding gene	gene with protein product		607240				15933070, 12086618, 12121615	Standard	NM_020382		Approved	SET8, SET07, PR-Set7, KMT5A	uc001uew.3	Q9NQR1	OTTHUMG00000150477	ENST00000402868.3:c.542T>G	chr12.hg19:g.123880924T>G	ENSP00000384629:p.Leu181Arg	50.0	0.0		34.0	8.0	NM_020382	A8K9D0|Q86W83|Q8TD09	Missense_Mutation	SNP	ENST00000402868.3	hg19	CCDS9247.1	.	.	.	.	.	.	.	.	.	.	T	25.1	4.601866	0.87055	.	.	ENSG00000183955	ENST00000402868;ENST00000330479;ENST00000437502	D;D	0.98531	-4.98;-4.98	5.84	5.84	0.93424	.	0.109289	0.64402	D	0.000007	D	0.98112	0.9377	L	0.48642	1.525	0.54753	D	0.999988	D;D	0.58970	0.984;0.973	P;P	0.59948	0.866;0.847	D	0.99357	1.0916	10	0.72032	D	0.01	-12.3499	16.2159	0.82217	0.0:0.0:0.0:1.0	.	222;181	Q9NQR1;Q9NQR1-2	SETD8_HUMAN;.	R	181;181;172	ENSP00000384629:L181R;ENSP00000332995:L181R	ENSP00000332995:L181R	L	+	2	0	SETD8	122446877	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	6.834000	0.75339	2.243000	0.73865	0.533000	0.62120	CTT	.	.		0.502	SETD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318263.1	NM_020382		G	123880924	T	G	123880924	3	3	316	1	0	0	0	0	1	0	0	0	14152	1609	56	5	560	5	SETD8	12	123880924	Missense_Mutation	SNP	T	TCGA-KR-A7K8-01A-11D-A33K-10	111366720	123880924	9970971	35	44628										
GAS6	2621	hgsc.bcm.edu	37	chr13	114537552	114537552	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	tgtccatgtcctgggacagcTtgaggcccccacgcccgtca	11	16	1	1			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr13:114537552T>C	ENST00000327773.6	-	8	952	c.806A>G	c.(805-807)aAg>aGg	p.K269R	GAS6_ENST00000450766.1_5'UTR|GAS6_ENST00000418959.3_5'Flank|GAS6_ENST00000355761.4_Missense_Mutation_p.K215R|GAS6-AS1_ENST00000458001.1_RNA|GAS6_ENST00000357389.3_Missense_Mutation_p.K269R	NM_000820.2	NP_000811.1	Q14393	GAS6_HUMAN	growth arrest-specific 6	269	EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				activation of protein kinase B activity (GO:0032148)|apoptotic cell clearance (GO:0043277)|B cell chemotaxis (GO:0035754)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell-substrate adhesion (GO:0031589)|cellular protein metabolic process (GO:0044267)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|cellular response to growth factor stimulus (GO:0071363)|cellular response to interferon-alpha (GO:0035457)|cellular response to starvation (GO:0009267)|cellular response to vitamin K (GO:0071307)|dendritic cell differentiation (GO:0097028)|enzyme linked receptor protein signaling pathway (GO:0007167)|extracellular matrix assembly (GO:0085029)|fusion of virus membrane with host plasma membrane (GO:0019064)|hematopoietic stem cell migration to bone marrow (GO:0097241)|leukocyte migration (GO:0050900)|macrophage cytokine production (GO:0010934)|negative regulation of apoptotic process (GO:0043066)|negative regulation of biomineral tissue development (GO:0070168)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-6 secretion (GO:1900165)|negative regulation of oligodendrocyte apoptotic process (GO:1900142)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of renal albumin absorption (GO:2000533)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|neuron migration (GO:0001764)|organ regeneration (GO:0031100)|peptidyl-glutamic acid carboxylation (GO:0017187)|peptidyl-serine phosphorylation (GO:0018105)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of gene expression (GO:0010628)|positive regulation of glomerular filtration (GO:0003104)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phagocytosis (GO:0050766)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of TOR signaling (GO:0032008)|post-translational protein modification (GO:0043687)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|protein targeting to plasma membrane (GO:0072661)|proteolysis (GO:0006508)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)|viral entry into host cell (GO:0046718)|viral genome replication (GO:0019079)	cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|platelet alpha granule lumen (GO:0031093)	binding, bridging (GO:0060090)|calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|phosphatidylserine binding (GO:0001786)|protein tyrosine kinase activator activity (GO:0030296)|receptor agonist activity (GO:0048018)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|voltage-gated calcium channel activity (GO:0005245)			central_nervous_system(4)|ovary(1)	5	Lung NSC(43;0.00976)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0176)|all_epithelial(44;0.0104)|all_lung(25;0.0249)|Lung NSC(25;0.0908)|Breast(118;0.188)				CTGGGACAGCTTGAGGCCCCC	0.697																																					p.K269R		Atlas-SNP	.											.	GAS6	75	.	0			c.A806G						.						31	28	29					13																	114537552		2172	4278	6450	SO:0001583	missense	2621	exon8			GACAGCTTGAGGC		CCDS45072.1	13q34	2008-07-18			ENSG00000183087	ENSG00000183087			4168	protein-coding gene	gene with protein product	"AXL stimulatory factor"	600441		AXLLG		8336730	Standard	NM_000820		Approved	AXSF, FLJ34709, DKFZp666G247	uc001vud.3	Q14393	OTTHUMG00000017395	ENST00000327773.6:c.806A>G	chr13.hg19:g.114537552T>C	ENSP00000331831:p.Lys269Arg	76.0	0.0		48.0	5.0	NM_000820	B3KRQ7|B3KVL4|E9PBL7|Q6IMN1|Q7Z7N3	Missense_Mutation	SNP	ENST00000327773.6	hg19	CCDS45072.1	.	.	.	.	.	.	.	.	.	.	T	15.35	2.809012	0.50421	.	.	ENSG00000183087	ENST00000357389;ENST00000355761;ENST00000327773	D;D;D	0.90504	-2.68;-2.22;-2.22	4.59	4.59	0.56863	.	.	.	.	.	T	0.80014	0.4546	N	0.04018	-0.295	0.80722	D	1	B	0.28713	0.22	B	0.29353	0.101	T	0.77520	-0.2557	9	0.33141	T	0.24	-27.3467	13.965	0.64202	0.0:0.0:0.0:1.0	.	269	Q14393-2	.	R	269;215;269	ENSP00000349962:K269R;ENSP00000348003:K215R;ENSP00000331831:K269R	ENSP00000331831:K269R	K	-	2	0	GAS6	113576391	0.989000	0.36119	1.000000	0.80357	0.440000	0.31957	2.433000	0.44793	1.696000	0.51158	0.374000	0.22700	AAG	.	.		0.697	GAS6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045946.2	NM_000820		C	114537552	T	C	114537552	3	2	316	1	0	0	0	0	1	0	0	0	6257	1609	56	2	1262	2	GAS6	13	114537552	Missense_Mutation	SNP	T	TCGA-KR-A7K8-01A-11D-A33K-10		114537552	632326	36	44629										
NIN	51199	hgsc.bcm.edu	37	chr14	51190328	51190328	+	IGR	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	gtcacttccagagctttcaaCaactgggcattttcaacata	6	11	3	1			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr14:51190328C>A	ENST00000382041.3	-	0	6496				NIN_ENST00000530997.2_Missense_Mutation_p.L2085F|NIN_ENST00000245441.5_Missense_Mutation_p.L2085F|RP11-248J18.3_ENST00000602615.1_RNA|NIN_ENST00000389868.3_3'UTR	NM_016350.4|NM_182946.1	NP_057434.4|NP_891991	Q8N4C6	NIN_HUMAN	ninein (GSK3B interacting protein)						centrosome localization (GO:0051642)|centrosome-templated microtubule nucleation (GO:0090222)|microtubule anchoring at centrosome (GO:0034454)	centriole (GO:0005814)|centrosome (GO:0005813)|microtubule (GO:0005874)|nucleolus (GO:0005730)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(13)|lung(16)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	71	all_epithelial(31;0.00244)|Breast(41;0.127)					GAGCTTTCAACAACTGGGCAT	0.433			T	PDGFRB	MPD																																p.L2085F		Atlas-SNP	.		Dom	yes		14	14q24	51199	ninein (GSK3B interacting protein)		L	.	NIN	475	.	0			c.G6255T						.						143	135	137					14																	51190328		1893	4116	6009	SO:0001628	intergenic_variant	51199	exon31			TTTCAACAACTGG	AF212162	CCDS32078.1, CCDS32079.1, CCDS32078.2	14q21-q22	2013-01-10			ENSG00000100503	ENSG00000100503		"EF-hand domain containing"	14906	protein-coding gene	gene with protein product		608684				11004522, 11162463	Standard	NM_020921		Approved		uc001wyi.3	Q8N4C6	OTTHUMG00000029569		chr14.hg19:g.51190328C>A		136.0	0.0		111.0	18.0	NM_020921	A6NDB8|B7WPA3|C9JSB6|C9JSG2|C9JXL2|Q5BKU3|Q6P0P6|Q9BWU6|Q9C012|Q9C013|Q9C014|Q9H5I6|Q9HAT7|Q9HBY5|Q9HCK7|Q9UH61	Missense_Mutation	SNP	ENST00000382041.3	hg19	CCDS32079.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.4|20.4	3.982684|3.982684	0.74474|0.74474	.|.	.|.	ENSG00000100503|ENSG00000100503	ENST00000245441;ENST00000311149|ENST00000530997	T|.	0.56941|.	0.43|.	5.92|5.92	3.02|3.02	0.34903|0.34903	.|.	0.079506|.	0.51477|.	N|.	0.000085|.	T|T	0.63733|0.63733	0.2536|0.2536	M|M	0.68317|0.68317	2.08|2.08	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	T|T	0.59085|0.59085	-0.7520|-0.7520	10|5	0.66056|.	D|.	0.02|.	-5.9259|-5.9259	10.2581|10.2581	0.43410|0.43410	0.0:0.7759:0.0:0.2241|0.0:0.7759:0.0:0.2241	.|.	2085|.	Q8N4C6-7|.	.|.	F|F	2085;2068|1576	ENSP00000245441:L2085F|.	ENSP00000245441:L2085F|.	L|V	-|-	3|1	2|0	NIN|NIN	50260078|50260078	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	1.008000|1.008000	0.29872|0.29872	0.358000|0.358000	0.24211|0.24211	-0.345000|-0.345000	0.07892|0.07892	TTG|GTT	.	.		0.433	NIN-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395207.2	NM_182946		A	51190328	C	A	51190328	1	1	316	0	1	0	0	0	0	0	0	0	10426	477	17	3		3	NIN	14	51190328	IGR	SNP	C	TCGA-KR-A7K8-01A-11D-A33K-10		51190328	56159212	37	44630										
PPP1R14D	54866	hgsc.bcm.edu	37	chr15	41120819	41120819	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	gggctgggagatgtgcaggaAgcagggcttgaagacagcat	18	6	0	3			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr15:41120819A>C	ENST00000299174.5	-	1	88	c.21T>G	c.(19-21)gcT>gcG	p.A7A	PPP1R14D_ENST00000427255.2_Silent_p.A7A	NM_017726.7	NP_060196.1	Q9NXH3	PP14D_HUMAN	protein phosphatase 1, regulatory (inhibitor) subunit 14D	7					regulation of phosphorylation (GO:0042325)	cytoplasm (GO:0005737)	protein phosphatase inhibitor activity (GO:0004864)			breast(1)|large_intestine(2)|lung(2)|skin(1)	6		all_cancers(109;6.29e-14)|all_epithelial(112;1.48e-11)|Lung NSC(122;5.77e-09)|all_lung(180;1.08e-07)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.88e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)		ATGTGCAGGAAGCAGGGCTTG	0.547																																					p.A7A		Atlas-SNP	.											.	PPP1R14D	8	.	0			c.T21G						.						95	83	87					15																	41120819		2203	4300	6503	SO:0001819	synonymous_variant	54866	exon1			GCAGGAAGCAGGG	AK000258	CCDS10066.1, CCDS45230.1	15q11.2-q14	2012-04-17			ENSG00000166143	ENSG00000166143		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14953	protein-coding gene	gene with protein product	"gut and brain phosphatase inhibitor 1", "PKC-dependent PP1 inhibitory protein"	613256				11948623	Standard	NM_017726		Approved	CPI17-like, FLJ20251, GBPI-1, MGC119014, MGC119016	uc001zmz.3	Q9NXH3	OTTHUMG00000130064	ENST00000299174.5:c.21T>G	chr15.hg19:g.41120819A>C		86.0	0.0		70.0	14.0	NM_017726	Q4V773	Silent	SNP	ENST00000299174.5	hg19	CCDS10066.1																																																																																			.	.		0.547	PPP1R14D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252355.2	NM_017726		C	41120819	A	C	41120819	2	2	316	1	0	0	0	0	0	0	0	1	12374	59	3	5		5	PPP1R14D	15	41120819	Silent	SNP	A	TCGA-KR-A7K8-01A-11D-A33K-10		41120819	61410573	38	44631										
WHAMM	123720	hgsc.bcm.edu	37	chr15	83481941	83481941	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	gaagcataccaggaattggtTaccgtggcaaccatgttctt	10	9	1	0			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr15:83481941T>A	ENST00000286760.4	+	2	795	c.696T>A	c.(694-696)gtT>gtA	p.V232V		NM_001080435.1	NP_001073904.1	Q8TF30	WHAMM_HUMAN	WAS protein homolog associated with actin, golgi membranes and microtubules	232	Mediates association with membranes. {ECO:0000269|PubMed:18614018}.				actin filament organization (GO:0007015)|actin filament reorganization (GO:0090527)|ER to Golgi vesicle-mediated transport (GO:0006888)|focal adhesion assembly (GO:0048041)|lamellipodium assembly (GO:0030032)|membrane tubulation (GO:0097320)|positive regulation of actin nucleation (GO:0051127)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum-Golgi intermediate compartment membrane (GO:0033116)|Golgi membrane (GO:0000139)	Arp2/3 complex binding (GO:0071933)|GTP-Rho binding (GO:0017049)|microtubule binding (GO:0008017)			endometrium(6)|large_intestine(5)|lung(1)|prostate(1)	13						AGGAATTGGTTACCGTGGCAA	0.393																																					p.V232V		Atlas-SNP	.											.	WHAMM	63	.	0			c.T696A						.						113	99	104					15																	83481941		1898	4129	6027	SO:0001819	synonymous_variant	123720	exon2			ATTGGTTACCGTG	AK126887	CCDS45333.1	15q25.2	2009-02-18	2009-02-18	2009-02-18	ENSG00000156232	ENSG00000156232			30493	protein-coding gene	gene with protein product		612393	"WAS protein homology region 2 domain containing 1"	WHDC1		11853319, 18226259, 18614018, 18812086	Standard	XM_005272422		Approved	KIAA1971	uc002bje.3	Q8TF30		ENST00000286760.4:c.696T>A	chr15.hg19:g.83481941T>A		260.0	0.0		192.0	32.0	NM_001080435	Q8N1J9	Silent	SNP	ENST00000286760.4	hg19	CCDS45333.1																																																																																			.	.		0.393	WHAMM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418463.1			A	83481941	T	A	83481941	2	1	316	1	0	0	0	0	0	0	0	1	17376	1741	61	4		4	WHAMM	15	83481941	Silent	SNP	T	TCGA-KR-A7K8-01A-11D-A33K-10	42361122	83481941	19049451	39	44632										
ACAN	176	hgsc.bcm.edu	37	chr15	89395101	89395101	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	tctggtgtggaggagtggatCgtgacccaagtggttcctgg	17	7	1	1			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr15:89395101C>A	ENST00000561243.1	+	10	2103	c.2103C>A	c.(2101-2103)atC>atA	p.I701I	ACAN_ENST00000559004.1_Silent_p.I701I|ACAN_ENST00000352105.7_Silent_p.I701I|ACAN_ENST00000439576.2_Silent_p.I701I			P16112	PGCA_HUMAN	aggrecan	700	KS.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			AGGAGTGGATCGTGACCCAAG	0.567																																					p.I701I		Atlas-SNP	.											.	ACAN	220	.	0			c.C2103A						.						52	68	63					15																	89395101		2080	4196	6276	SO:0001819	synonymous_variant	176	exon11			GTGGATCGTGACC	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	319	protein-coding gene	gene with protein product	"aggrecan proteoglycan"	155760	"chondroitin sulfate proteoglycan 1", "aggrecan 1"	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.2103C>A	chr15.hg19:g.89395101C>A		184.0	0.0		130.0	23.0	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Silent	SNP	ENST00000561243.1	hg19	CCDS53970.1																																																																																			.	.		0.567	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135		A	89395101	C	A	89395101	2	1	316	1	0	0	0	0	0	0	0	1	117	874	31	1		1	ACAN	15	89395101	Silent	SNP	C	TCGA-KR-A7K8-01A-11D-A33K-10	5913160	89395101	13136291	40	44633										
CCDC137	339230	hgsc.bcm.edu	37	chr17	79638802	79638802	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	agcggcgactagataaagtcCgacggaaaaaggaggaaaag	14	6	0	1			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr17:79638802C>T	ENST00000329214.8	+	4	929	c.526C>T	c.(526-528)Cga>Tga	p.R176*		NM_199287.2	NP_954981.1	Q6PK04	CC137_HUMAN	coiled-coil domain containing 137	176							poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(2)	12	all_neural(118;0.0878)|all_lung(278;0.23)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			AGATAAAGTCCGACGGAAAAA	0.577																																					p.R176X		Atlas-SNP	.											.	CCDC137	27	.	0			c.C526T						.						53	59	57					17																	79638802		1969	4158	6127	SO:0001587	stop_gained	339230	exon4			AAAGTCCGACGGA	BC009369	CCDS42400.1	17q25.3	2008-07-04				ENSG00000185298			33451	protein-coding gene	gene with protein product		614271					Standard	NM_199287		Approved	MGC16597	uc002kbc.4	Q6PK04		ENST00000329214.8:c.526C>T	chr17.hg19:g.79638802C>T	ENSP00000329360:p.Arg176*	95.0	0.0		124.0	26.0	NM_199287		Nonsense_Mutation	SNP	ENST00000329214.8	hg19	CCDS42400.1	.	.	.	.	.	.	.	.	.	.	C	35	5.584384	0.96578	.	.	ENSG00000185298	ENST00000329214	.	.	.	5.12	4.11	0.48088	.	0.401005	0.25820	N	0.028089	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.8525	14.0043	0.64453	0.1519:0.8481:0.0:0.0	.	.	.	.	X	176	.	ENSP00000329360:R176X	R	+	1	2	CCDC137	77249207	0.015000	0.18098	0.011000	0.14972	0.054000	0.15201	2.874000	0.48483	2.371000	0.80710	0.655000	0.94253	CGA	.	.		0.577	CCDC137-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440387.1			T	79638802	C	T	79638802	4	4	316	1	0	0	0	0	0	1	0	0	2773	644	23	1	540	1	CCDC137	17	79638802	Nonsense_Mutation	SNP	C	TCGA-KR-A7K8-01A-11D-A33K-10		79638802	1556408	41	44634										
PSMA8	143471	hgsc.bcm.edu	37	chr18	23772351	23772352	+	Frame_Shift_Ins	INS	-	-	A													0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	aaaaggaagaagcagagaagINSaaaaaatcaaagaaatctgt							TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr18:23772351_23772352insA	ENST00000308268.6	+	7	836_837	c.747_748insA	c.(748-750)aaafs	p.K250fs	PSMA8_ENST00000415576.2_Frame_Shift_Ins_p.K244fs|PSMA8_ENST00000343848.6_Frame_Shift_Ins_p.K206fs	NM_001025096.1|NM_144662.2	NP_001020267.1|NP_653263.2	Q8TAA3	PSA7L_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 8	250					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|proteasome core complex, alpha-subunit complex (GO:0019773)|spermatoproteasome complex (GO:1990111)	threonine-type endopeptidase activity (GO:0004298)	p.K249N(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|skin(2)	16	all_cancers(21;0.000585)|Lung NSC(5;0.00148)|all_lung(6;0.0038)|Ovarian(20;0.124)		OV - Ovarian serous cystadenocarcinoma(3;0.000324)|all cancers(3;0.000954)|LUSC - Lung squamous cell carcinoma(2;0.181)			AAGCAGAGAAGAAAAAATCAAA	0.302																																					p.K249fs		Atlas-Indel,Pindel	.											PSMA8,rectum,carcinoma,0,1	PSMA8	36	.	1	Substitution - Missense(1)	large_intestine(1)	c.747_748insA						.																																			SO:0001589	frameshift_variant	143471	exon7			.	BC047355	CCDS32808.1, CCDS45842.1, CCDS45843.1	18q11.2	2006-12-18				ENSG00000154611		"Proteasome (prosome, macropain) subunits"	22985	protein-coding gene	gene with protein product							Standard	XM_005258199		Approved	MGC26605, PSMA7L	uc002kvq.3	Q8TAA3		ENST00000308268.6:c.753dupA	chr18.hg19:g.23772357_23772357dupA	ENSP00000311121:p.Lys250fs	73.0	0.0		98.0	16.0	NM_144662	B0YJ75|Q8IVP4|Q8TA98|Q8TAA2	Frame_Shift_Ins	INS	ENST00000308268.6	hg19	CCDS32808.1																																																																																			.	.		0.302	PSMA8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000446255.1	NM_144662		A	23772352	-	A	23772351	7	5	316	1	0	1	1	0	0	0	0	0	12685	933	33	0	773	0	PSMA8	18	23772351	Frame_Shift_Ins	INS	-	TCGA-KR-A7K8-01A-11D-A33K-10		23772351	54304897	42	44635										
TMEM150B	284417	hgsc.bcm.edu	37	chr19	55824349	55824349	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	ggctaagagaccgaagagcgCgaacagcagcatggccacga	14	11	0	2			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr19:55824349C>T	ENST00000326652.4	-	8	762	c.580G>A	c.(580-582)Gcg>Acg	p.A194T	CTD-2105E13.14_ENST00000596786.1_RNA|TMEM150B_ENST00000438693.1_Missense_Mutation_p.A194T	NM_001282011.1	NP_001268940.1	A6NC51	T150B_HUMAN	transmembrane protein 150B	194						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(1)	3						CCGAAGAGCGCGAACAGCAGC	0.677																																					p.A194T		Atlas-SNP	.											.	TMEM150B	19	.	0			c.G580A						.						34	42	39					19																	55824349		2175	4271	6446	SO:0001583	missense	284417	exon8			AGAGCGCGAACAG	BC020862	CCDS42629.1	19q13.42	2009-06-12	2009-06-12	2009-06-12		ENSG00000180061			34415	protein-coding gene	gene with protein product			"transmembrane protein 224"	TMEM224			Standard	XM_005258812		Approved		uc010esw.1	A6NC51		ENST00000326652.4:c.580G>A	chr19.hg19:g.55824349C>T	ENSP00000320757:p.Ala194Thr	98.0	0.0		86.0	11.0	NM_001085488	B7ZW71	Missense_Mutation	SNP	ENST00000326652.4	hg19	CCDS42629.1	.	.	.	.	.	.	.	.	.	.	.	3.981	-0.006402	0.07773	.	.	ENSG00000180061	ENST00000326652;ENST00000438693	T;T	0.44482	0.92;0.92	4.55	-9.11	0.00711	.	3.398480	0.00628	N	0.000462	T	0.23727	0.0574	N	0.13098	0.295	0.09310	N	1	B	0.17465	0.022	B	0.06405	0.002	T	0.19910	-1.0291	10	0.21014	T	0.42	6.9623	11.427	0.50015	0.0:0.4132:0.4512:0.1356	.	194	A6NC51	T150B_HUMAN	T	194	ENSP00000320757:A194T;ENSP00000412658:A194T	ENSP00000320757:A194T	A	-	1	0	TMEM150B	60516161	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-5.438000	0.00122	-3.570000	0.00139	-0.350000	0.07774	GCG	.	.		0.677	TMEM150B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452685.1	NM_001085488		T	55824349	C	T	55824349	3	4	316	1	0	0	0	0	1	0	0	0	16083	768	27	1	125	1	TMEM150B	19	55824349	Missense_Mutation	SNP	C	TCGA-KR-A7K8-01A-11D-A33K-10		55824349	3304634	43	44636										
ZNF133	7692	hgsc.bcm.edu	37	chr20	18296766	18296766	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	cagcttcagccagaattcaaCcctcatctctcacaggcgga	7	15	5	1			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr20:18296766C>A	ENST00000316358.4	+	4	1368	c.1271C>A	c.(1270-1272)aCc>aAc	p.T424N	RP4-568F9.3_ENST00000436848.1_RNA|ZNF133_ENST00000401790.1_Missense_Mutation_p.T424N|ZNF133_ENST00000377671.3_Missense_Mutation_p.T423N|ZNF133_ENST00000535822.1_Missense_Mutation_p.T329N|ZNF133_ENST00000402618.2_Missense_Mutation_p.T361N|ZNF133_ENST00000462170.1_3'UTR|ZNF133_ENST00000396026.3_Missense_Mutation_p.T427N|ZNF133_ENST00000538547.1_Missense_Mutation_p.T329N	NM_001282998.1|NM_001282999.1|NM_001283000.1|NM_001283001.1|NM_001283008.1	NP_001269927.1|NP_001269928.1|NP_001269929.1|NP_001269930.1|NP_001269937.1	P52736	ZN133_HUMAN	zinc finger protein 133	424					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	26						CAGAATTCAACCCTCATCTCT	0.557																																					p.T423N		Atlas-SNP	.											.	ZNF133	63	.	0			c.C1268A						.						81	85	84					20																	18296766		2203	4300	6503	SO:0001583	missense	7692	exon4			ATTCAACCCTCAT	AK123005	CCDS13134.1, CCDS63234.1, CCDS63235.1, CCDS74703.1, CCDS74704.1	20p11.23	2013-01-08	2006-06-13		ENSG00000125846	ENSG00000125846		"Zinc fingers, C2H2-type", "-"	12917	protein-coding gene	gene with protein product		604075	"zinc finger protein 150 (pHZ-66)", "zinc finger protein 133 (clone pHZ-13)"	ZNF150		7557990, 7649249	Standard	XM_005260819		Approved	pHZ-13, pHZ-66	uc010gcs.3	P52736	OTTHUMG00000031965	ENST00000316358.4:c.1271C>A	chr20.hg19:g.18296766C>A	ENSP00000346090:p.Thr424Asn	55.0	0.0		45.0	7.0	NM_001083330	A8K5S4|B4DHU7|B4DIB8|B7ZAS1|F5H289|J3KQ11|J3KQJ0|Q53XU1|Q5JXV8|Q9BUV2|Q9H443	Missense_Mutation	SNP	ENST00000316358.4	hg19		.	.	.	.	.	.	.	.	.	.	C	1.761	-0.486844	0.04352	.	.	ENSG00000125846	ENST00000377671;ENST00000396026;ENST00000402618;ENST00000401790;ENST00000538547;ENST00000535822;ENST00000316358	T;T;T;T;T;T;T	0.07444	5.44;5.44;3.19;5.44;3.19;3.19;5.44	4.59	4.59	0.56863	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.51477	D	0.000098	T	0.03783	0.0107	N	0.12443	0.215	0.21822	N	0.999527	B;B;B;B	0.27679	0.089;0.185;0.014;0.014	B;B;B;B	0.22880	0.019;0.042;0.013;0.018	T	0.41197	-0.9522	10	0.02654	T	1	-19.7732	10.4126	0.44303	0.1945:0.8055:0.0:0.0	.	361;427;424;423	B4DIB8;B4DHU7;P52736;P52736-2	.;.;ZN133_HUMAN;.	N	423;427;361;424;329;329;424	ENSP00000366899:T423N;ENSP00000400897:T427N;ENSP00000385279:T361N;ENSP00000383945:T424N;ENSP00000442978:T329N;ENSP00000439427:T329N;ENSP00000346090:T424N	ENSP00000346090:T424N	T	+	2	0	ZNF133	18244766	0.000000	0.05858	1.000000	0.80357	0.978000	0.69477	-0.290000	0.08354	2.837000	0.97791	0.655000	0.94253	ACC	.	.		0.557	ZNF133-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000127616.1	NM_003434		A	18296766	C	A	18296766	3	1	316	1	0	0	0	0	1	0	0	0	17738	507	18	3	1278	3	ZNF133	20	18296766	Missense_Mutation	SNP	C	TCGA-KR-A7K8-01A-11D-A33K-10		18296766	44728754	44	44637										
ERG	2078	hgsc.bcm.edu	37	chr21	39755511	39755511	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	gggtgggcgtgataggagccCatgtacgggaggtctgaggg	21	6	1	2			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr21:39755511C>T	ENST00000417133.2	-	12	1460	c.1275G>A	c.(1273-1275)atG>atA	p.M425I	ERG_ENST00000442448.1_Missense_Mutation_p.M401I|ERG_ENST00000398919.2_Missense_Mutation_p.M425I|ERG_ENST00000398907.1_Missense_Mutation_p.M395I|ERG_ENST00000288319.7_Missense_Mutation_p.M418I|ERG_ENST00000398911.1_Missense_Mutation_p.M401I|ERG_ENST00000453032.2_Missense_Mutation_p.M326I|ERG_ENST00000398897.1_Missense_Mutation_p.M302I|ERG_ENST00000398910.1_Missense_Mutation_p.M402I|ERG_ENST00000398905.1_Missense_Mutation_p.M394I	NM_001136154.1|NM_001243432.1	NP_001129626.1|NP_001230361.1	Q12809	KCNH2_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog	0					cardiac muscle contraction (GO:0060048)|cellular response to drug (GO:0035690)|membrane depolarization during action potential (GO:0086010)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of potassium ion export (GO:1902303)|negative regulation of potassium ion transmembrane transport (GO:1901380)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|identical protein binding (GO:0042802)|inward rectifier potassium channel activity (GO:0005242)|phosphorelay sensor kinase activity (GO:0000155)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)		EWSR1/ERG(178)|NDRG1/ERG(5)|TMPRSS2/ERG(3582)|FUS/ERG(167)|SLC45A3/ERG(50)	lung(2)|ovary(1)|skin(1)	4		Prostate(19;3.6e-06)			Alfuzosin(DB00346)|Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Cisapride(DB00604)|Dofetilide(DB00204)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Halofantrine(DB01218)|Ibutilide(DB00308)|Imipramine(DB00458)|Miconazole(DB01110)|Pimozide(DB01100)|Prazosin(DB00457)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terazosin(DB01162)|Thioridazine(DB00679)|Verapamil(DB00661)	GATAGGAGCCCATGTACGGGA	0.602			T	"EWSR1, TMPRSS2, ELF4, FUS, HERPUD1, NDRG1"	"Ewing sarcoma, prostate, AML"																																p.M425I	Esophageal Squamous(130;336 1700 3010 3083 40589)	Atlas-SNP	.		Dom	yes		21	21q22.3	2078	v-ets erythroblastosis virus E26 oncogene like (avian)		"M, E, L"	.	ERG	78	.	0			c.G1275A						.						69	68	69					21																	39755511		2203	4300	6503	SO:0001583	missense	2078	exon12			GGAGCCCATGTAC		CCDS13657.1, CCDS13658.1, CCDS46648.1, CCDS46649.1, CCDS58789.1	21q22.3	2013-07-09	2013-07-09		ENSG00000157554	ENSG00000157554			3446	protein-coding gene	gene with protein product	"v-ets avian erythroblastosis virus E26 oncogene related", "transcriptional regulator ERG (transforming protein ERG)", "v-ets erythroblastosis virus E26 oncogene like", "TMPRSS2-ERG prostate cancer specific"	165080	"v-ets avian erythroblastosis virus E26 oncogene related"			3274086	Standard	NM_001136154		Approved	erg-3, p55	uc002yxa.3	P11308	OTTHUMG00000090767	ENST00000417133.2:c.1275G>A	chr21.hg19:g.39755511C>T	ENSP00000414150:p.Met425Ile	102.0	0.0		81.0	12.0	NM_001136154	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Missense_Mutation	SNP	ENST00000417133.2	hg19	CCDS46648.1	.	.	.	.	.	.	.	.	.	.	C	15.36	2.811913	0.50527	.	.	ENSG00000157554	ENST00000398905;ENST00000398907;ENST00000288319;ENST00000398897;ENST00000398911;ENST00000417133;ENST00000398910;ENST00000442448;ENST00000453032;ENST00000398919	T;T;T;T;T;T;T;T;T;T	0.53206	0.63;0.63;0.63;0.63;0.63;0.63;0.63;0.63;0.63;0.63	5.2	5.2	0.72013	.	0.144787	0.64402	D	0.000009	T	0.49983	0.1589	L	0.58428	1.81	0.80722	D	1	B;B;B;B	0.17667	0.0;0.001;0.023;0.0	B;B;B;B	0.25405	0.001;0.005;0.06;0.001	T	0.47209	-0.9135	10	0.46703	T	0.11	.	18.7596	0.91845	0.0:1.0:0.0:0.0	.	425;394;401;418	P11308;B5MDW0;P11308-1;P11308-4	ERG_HUMAN;.;.;.	I	394;395;418;302;401;425;402;401;326;425	ENSP00000381877:M394I;ENSP00000381879:M395I;ENSP00000288319:M418I;ENSP00000381871:M302I;ENSP00000381882:M401I;ENSP00000414150:M425I;ENSP00000381881:M402I;ENSP00000394694:M401I;ENSP00000396268:M326I;ENSP00000381891:M425I	ENSP00000288319:M418I	M	-	3	0	ERG	38677381	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.006000	0.70724	2.404000	0.81709	0.655000	0.94253	ATG	.	.		0.602	ERG-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207532.2	NM_182918		T	39755511	C	T	39755511	3	4	316	1	0	0	0	0	1	0	0	0	5224	594	21	3	189	3	ERG	21	39755511	Missense_Mutation	SNP	C	TCGA-KR-A7K8-01A-11D-A33K-10		39755511	8374384	45	44638										
RTN4R	65078	hgsc.bcm.edu	37	chr22	20229527	20229527	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	gggtgagtcattgatgtgccGtgggccagagccgttgcccg	17	10	1	3			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr22:20229527G>A	ENST00000043402.7	-	2	1567	c.1129C>T	c.(1129-1131)Cgg>Tgg	p.R377W	RTN4R_ENST00000469601.1_5'Flank	NM_023004.5	NP_075380.1	Q9BZR6	RTN4R_HUMAN	reticulon 4 receptor	377					axonogenesis (GO:0007409)|negative regulation of axonogenesis (GO:0050771)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of axonogenesis (GO:0050770)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			lung(1)|ovary(1)|prostate(1)	3	Colorectal(54;0.0993)					TTGATGTGCCGTGGGCCAGAG	0.687																																					p.R377W		Atlas-SNP	.											.	RTN4R	14	.	0			c.C1129T	GRCh37	CM086907	RTN4R	M		.						34	35	34					22																	20229527		2192	4272	6464	SO:0001583	missense	65078	exon2			TGTGCCGTGGGCC	AF283463	CCDS13777.1	22q11	2008-05-02			ENSG00000040608	ENSG00000040608			18601	protein-coding gene	gene with protein product		605566				11201742	Standard	NM_023004		Approved	NOGOR	uc002zrv.3	Q9BZR6	OTTHUMG00000150572	ENST00000043402.7:c.1129C>T	chr22.hg19:g.20229527G>A	ENSP00000043402:p.Arg377Trp	22.0	0.0		30.0	12.0	NM_023004	D3DX28	Missense_Mutation	SNP	ENST00000043402.7	hg19	CCDS13777.1	.	.	.	.	.	.	.	.	.	.	G	11.96	1.795123	0.31777	.	.	ENSG00000040608	ENST00000043402	T	0.63255	-0.03	3.84	-1.49	0.08718	.	.	.	.	.	T	0.59528	0.2200	N	0.22421	0.69	0.09310	N	1	D	0.89917	1.0	D	0.64687	0.928	T	0.52193	-0.8608	9	0.87932	D	0	.	6.3987	0.21626	0.0:0.1616:0.2918:0.5466	.	377	Q9BZR6	RTN4R_HUMAN	W	377	ENSP00000043402:R377W	ENSP00000043402:R377W	R	-	1	2	RTN4R	18609527	0.000000	0.05858	0.040000	0.18447	0.249000	0.25844	0.059000	0.14322	-0.007000	0.14345	0.313000	0.20887	CGG	.	.		0.687	RTN4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318950.2			A	20229527	G	A	20229527	3	1	316	1	0	0	0	0	1	0	0	0	13745	1144	40	1	296	1	RTN4R	22	20229527	Missense_Mutation	SNP	G	TCGA-KR-A7K8-01A-11D-A33K-10		20229527	31075039	46	44639										
THOC5	8563	hgsc.bcm.edu	37	chr22	29907254	29907254	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	gccaagggccacacagctccTtgtagcacacattgacttcg	9	14	0	1			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr22:29907254T>A	ENST00000490103.1	-	19	1951	c.1829A>T	c.(1828-1830)aAg>aTg	p.K610M	THOC5_ENST00000397871.1_Missense_Mutation_p.K610M|THOC5_ENST00000397873.2_Missense_Mutation_p.K610M|CTA-256D12.11_ENST00000411969.1_RNA|THOC5_ENST00000397872.1_Missense_Mutation_p.K610M	NM_003678.4	NP_003669.4	Q13769	THOC5_HUMAN	THO complex 5	610					blastocyst development (GO:0001824)|cell morphogenesis (GO:0000902)|monocyte differentiation (GO:0030224)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|negative regulation of DNA damage checkpoint (GO:2000002)|negative regulation of macrophage differentiation (GO:0045650)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|primitive hemopoiesis (GO:0060215)|regulation of mRNA export from nucleus (GO:0010793)|regulation of stem cell division (GO:2000035)|RNA splicing (GO:0008380)|stem cell division (GO:0017145)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	mRNA binding (GO:0003729)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(4)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						ACACAGCTCCTTGTAGCACAC	0.587																																					p.K610M		Atlas-SNP	.											.	THOC5	58	.	0			c.A1829T						.						102	86	91					22																	29907254		2203	4300	6503	SO:0001583	missense	8563	exon20			AGCTCCTTGTAGC	AB023200	CCDS13859.1	22q12	2013-02-11			ENSG00000100296	ENSG00000100296		"THO complex subunits"	19074	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 79"	612733	"chromosome 22 open reading frame 19"	C22orf19		11979277, 8242058, 10231032, 19015024, 18373705	Standard	NM_003678		Approved	PK1.3, KIAA0983, Fmip, fSAP79	uc003afs.3	Q13769	OTTHUMG00000151291	ENST00000490103.1:c.1829A>T	chr22.hg19:g.29907254T>A	ENSP00000420306:p.Lys610Met	51.0	0.0		60.0	8.0	NM_001002878	O60839|Q9UPZ5	Missense_Mutation	SNP	ENST00000490103.1	hg19	CCDS13859.1	.	.	.	.	.	.	.	.	.	.	T	14.94	2.684577	0.47991	.	.	ENSG00000100296	ENST00000490103;ENST00000397872;ENST00000397871;ENST00000397873	T;T;T;T	0.24350	1.86;1.86;1.86;1.86	6.05	3.57	0.40892	.	0.340144	0.38272	N	0.001743	T	0.22085	0.0532	L	0.47716	1.5	0.33191	D	0.550866	P	0.39624	0.681	B	0.37601	0.254	T	0.32981	-0.9886	10	0.45353	T	0.12	-30.2859	10.3983	0.44214	0.0:0.2017:0.0:0.7983	.	610	Q13769	THOC5_HUMAN	M	610	ENSP00000420306:K610M;ENSP00000380970:K610M;ENSP00000380969:K610M;ENSP00000380971:K610M	ENSP00000380969:K610M	K	-	2	0	THOC5	28237254	1.000000	0.71417	0.997000	0.53966	0.935000	0.57460	1.174000	0.31932	1.061000	0.40601	0.528000	0.53228	AAG	.	.		0.587	THOC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322097.1	NM_003678		A	29907254	T	A	29907254	3	1	316	1	0	0	0	0	1	0	0	0	15883	1609	56	4	230	4	THOC5	22	29907254	Missense_Mutation	SNP	T	TCGA-KR-A7K8-01A-11D-A33K-10	9677727	29907254	21397312	47	44640										
MYH9	4627	hgsc.bcm.edu	37	chr22	36700184	36700184	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	atgcggtacagattgctgtcGagctccagggcttttatcta	11	9	1	1			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chr22:36700184G>T	ENST00000216181.5	-	19	2477	c.2247C>A	c.(2245-2247)ctC>ctA	p.L749L		NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	749	Myosin motor.				actin cytoskeleton reorganization (GO:0031532)|actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|angiogenesis (GO:0001525)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood vessel endothelial cell migration (GO:0043534)|cytokinesis (GO:0000910)|establishment of meiotic spindle localization (GO:0051295)|establishment of T cell polarity (GO:0001768)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|meiotic spindle organization (GO:0000212)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte differentiation (GO:0030224)|myoblast fusion (GO:0007520)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of cell shape (GO:0008360)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|uropod organization (GO:0032796)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|actomyosin contractile ring (GO:0005826)|cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|cleavage furrow (GO:0032154)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|spindle (GO:0005819)|stress fiber (GO:0001725)|uropod (GO:0001931)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3)	86						GATTGCTGTCGAGCTCCAGGG	0.602			T	ALK	ALCL		"Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"		Hereditary Macrothrombocytopenia, MYH9-associated																												p.L749L		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"myosin, heavy polypeptide 9, non-muscle"	yes	L	.	MYH9	225	.	0			c.C2247A						.						63	58	60					22																	36700184		2203	4300	6503	SO:0001819	synonymous_variant	4627	exon19	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	GCTGTCGAGCTCC		CCDS13927.1	22q13.1	2014-09-17	2006-09-29		ENSG00000100345	ENSG00000100345		"Myosins / Myosin superfamily : Class II"	7579	protein-coding gene	gene with protein product	"nonmuscle myosin heavy chain II-A"	160775	"myosin, heavy polypeptide 9, non-muscle"	DFNA17		1860190, 11023810	Standard	NM_002473		Approved	NMMHCA, NMHC-II-A, MHA, FTNS, EPSTS	uc003apg.3	P35579	OTTHUMG00000030429	ENST00000216181.5:c.2247C>A	chr22.hg19:g.36700184G>T		119.0	0.0		103.0	16.0	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Silent	SNP	ENST00000216181.5	hg19	CCDS13927.1																																																																																			.	.		0.602	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473		T	36700184	G	T	36700184	2	4	316	1	0	0	0	0	0	0	0	1	10051	1045	37	1		1	MYH9	22	36700184	Silent	SNP	G	TCGA-KR-A7K8-01A-11D-A33K-10	6792930	36700184	14604382	48	44641										
CT45A5	441521	hgsc.bcm.edu	37	chrX	134947978	134947978	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0204081632653061	1	1	0.512365591397849	0	0.548963133640553	1	1	0	taatttcttgttggcttttgGgagaggaggctattcctctg	12	6	2	1			TCGA-KR-A7K8-01A-11D-A33K-10	TCGA-KR-A7K8-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4fc5ba8-74ba-4047-8857-5d6d6cbc978b	96ab975c-1da6-431f-a23b-cbfeaf1697dc	g.chrX:134947978G>C	ENST00000463085.2	-	3	436	c.347C>G	c.(346-348)cCc>cGc	p.P116R	CT45A4_ENST00000420087.2_Intron|CT45A5_ENST00000491480.1_Missense_Mutation_p.P116R|CT45A5_ENST00000370724.3_Missense_Mutation_p.P116R			Q6NSH3	CT455_HUMAN	cancer/testis antigen family 45, member A5	116										endometrium(1)|large_intestine(2)|lung(6)	9						TTGGCTTTTGGGAGAGGAGGC	0.423																																					p.P116R		Atlas-SNP	.											.	CT45A5	26	.	0			c.C347G						.						218	188	199					X																	134947978		2189	4274	6463	SO:0001583	missense	441521	exon3			CTTTTGGGAGAGG	AY743713	CCDS35406.1	Xq26.3	2009-03-12				ENSG00000269586			33270	protein-coding gene	gene with protein product	"cancer/testis antigen CT45-5"	300796				15905330	Standard	XM_006724759		Approved	CT45-5, CT45.5	uc022ces.1	Q6NSH3		ENST00000463085.2:c.347C>G	chrX.hg19:g.134947978G>C	ENSP00000424778:p.Pro116Arg	68.0	0.0		79.0	30.0	NM_001007551	A8K842|B7ZMC5	Missense_Mutation	SNP	ENST00000463085.2	hg19	CCDS35406.1	.	.	.	.	.	.	.	.	.	.	G	11.56	1.673820	0.29693	.	.	ENSG00000242284	ENST00000370724;ENST00000491480	T;T	0.50813	0.73;0.73	2.19	-3.9	0.04181	.	1.140670	0.06592	U	0.752189	T	0.35711	0.0941	L	0.36672	1.1	0.09310	N	1	D	0.53745	0.962	P	0.45099	0.469	T	0.33266	-0.9875	10	0.66056	D	0.02	-17.3663	3.8122	0.08801	0.0:0.1746:0.3242:0.5012	.	116	Q6NSH3	CT455_HUMAN	R	116	ENSP00000359759:P116R;ENSP00000425997:P116R	ENSP00000359759:P116R	P	-	2	0	CT45A5	134775644	0.005000	0.15991	0.000000	0.03702	0.004000	0.04260	1.590000	0.36654	-1.016000	0.03371	0.365000	0.22127	CCC	.	.		0.423	CT45A5-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472589.1	NM_001007551		C	134947978	G	C	134947978	3	2	316	1	0	0	0	0	1	0	0	0	3990	1232	43	4	234	4	CT45A5	23	134947978	Missense_Mutation	SNP	G	TCGA-KR-A7K8-01A-11D-A33K-10		134947978	20322582	49	44642										
KLHL17	339451	hgsc.bcm.edu	37	chr1	898282	898282	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gctgcgagggggccgggcctGtgctttttgctgtgggtatg	19	8	0	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr1:898282G>A	ENST00000338591.3	+	6	1134	c.1027G>A	c.(1027-1029)Gtg>Atg	p.V343M		NM_198317.2	NP_938073.1	Q6TDP4	KLH17_HUMAN	kelch-like family member 17	343	Interaction with F-actin. {ECO:0000250}.				actin cytoskeleton organization (GO:0030036)|brain development (GO:0007420)|protein ubiquitination (GO:0016567)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|dendrite cytoplasm (GO:0032839)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	protein complex scaffold (GO:0032947)			central_nervous_system(1)|kidney(2)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.52e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.59e-23)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.000469)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		GGCCGGGCCTGTGCTTTTTGC	0.682																																					p.V343M		Atlas-SNP	.											.	KLHL17	31	.	0			c.G1027A						.						17	24	22					1																	898282		2179	4284	6463	SO:0001583	missense	339451	exon6			GGGCCTGTGCTTT	AY423763	CCDS30550.1	1p36	2013-01-30	2013-01-30		ENSG00000187961	ENSG00000187961		"Kelch-like", "BTB/POZ domain containing"	24023	protein-coding gene	gene with protein product	"actinfilin"		"kelch-like 17 (Drosophila)"			12063253	Standard	NM_198317		Approved		uc001aca.2	Q6TDP4	OTTHUMG00000040721	ENST00000338591.3:c.1027G>A	chr1.hg19:g.898282G>A	ENSP00000343930:p.Val343Met	30.0	0.0		27.0	12.0	NM_198317	Q5SV94	Missense_Mutation	SNP	ENST00000338591.3	hg19	CCDS30550.1	.	.	.	.	.	.	.	.	.	.	G	9.763	1.170557	0.21621	.	.	ENSG00000187961	ENST00000338591;ENST00000455747;ENST00000540863	T	0.49139	0.79	5.42	5.42	0.78866	Galactose oxidase, beta-propeller (1);	0.778438	0.11747	N	0.533365	T	0.61714	0.2369	L	0.37750	1.13	0.80722	D	1	D;D	0.65815	0.994;0.995	D;P	0.65233	0.933;0.897	T	0.58629	-0.7603	10	0.48119	T	0.1	.	19.2666	0.93988	0.0:0.0:1.0:0.0	.	66;343	B4DDM9;Q6TDP4	.;KLH17_HUMAN	M	343;219;66	ENSP00000343930:V343M	ENSP00000343930:V343M	V	+	1	0	KLHL17	888145	1.000000	0.71417	0.993000	0.49108	0.150000	0.21749	7.389000	0.79806	2.568000	0.86640	0.442000	0.29010	GTG	.	.		0.682	KLHL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097875.3	NM_198317		A	898282	G	A	898282	3	1	317	1	0	0	0	0	1	0	0	0	8381	1377	48	3	1049	3	KLHL17	1	898282	Missense_Mutation	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10		898282	248352339	1	44643										
CCDC27	148870	hgsc.bcm.edu	37	chr1	3686347	3686347	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tgttgtccctttgctcacagCtcgagaggttaaggaataag	11	8	1	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr1:3686347C>A	ENST00000294600.2	+	11	1828	c.1744C>A	c.(1744-1746)Ctc>Atc	p.L582I		NM_152492.2	NP_689705.2	Q2M243	CCD27_HUMAN	coiled-coil domain containing 27	582										breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(2)|lung(17)|prostate(1)|skin(2)|urinary_tract(2)	36	all_cancers(77;0.0385)|Ovarian(185;0.0634)|Lung NSC(156;0.21)|all_lung(157;0.218)	all_epithelial(116;5.52e-17)|all_lung(118;1.04e-06)|Lung NSC(185;0.000214)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Lung SC(97;0.0367)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)		Epithelial(90;1.11e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.35e-22)|GBM - Glioblastoma multiforme(42;3.46e-16)|Colorectal(212;1.17e-05)|COAD - Colon adenocarcinoma(227;5.76e-05)|Kidney(185;0.00036)|BRCA - Breast invasive adenocarcinoma(365;0.000696)|KIRC - Kidney renal clear cell carcinoma(229;0.00558)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.203)		TTGCTCACAGCTCGAGAGGTT	0.517																																					p.L582I		Atlas-SNP	.											.	CCDC27	79	.	0			c.C1744A						.						163	126	139					1																	3686347		2203	4300	6503	SO:0001630	splice_region_variant	148870	exon11			TCACAGCTCGAGA		CCDS50.1	1p36.32	2008-02-05			ENSG00000162592	ENSG00000162592			26546	protein-coding gene	gene with protein product							Standard	NM_152492		Approved	FLJ32825	uc001akv.2	Q2M243	OTTHUMG00000003504	ENST00000294600.2:c.1744-1C>A	chr1.hg19:g.3686347C>A		74.0	0.0		74.0	26.0	NM_152492	Q5TBV3|Q96M50	Missense_Mutation	SNP	ENST00000294600.2	hg19	CCDS50.1	.	.	.	.	.	.	.	.	.	.	C	13.26	2.183952	0.38609	.	.	ENSG00000162592	ENST00000294600	T	0.27402	1.67	4.79	3.86	0.44501	.	0.463546	0.18117	N	0.151161	T	0.43366	0.1244	M	0.64997	1.995	0.25438	N	0.988122	D	0.62365	0.991	P	0.56563	0.801	T	0.23084	-1.0198	9	.	.	.	-3.1819	9.4366	0.38643	0.0:0.898:0.0:0.102	.	582	Q2M243	CCD27_HUMAN	I	582	ENSP00000294600:L582I	.	L	+	1	0	CCDC27	3676207	1.000000	0.71417	0.246000	0.24233	0.015000	0.08874	1.650000	0.37292	0.978000	0.38470	0.655000	0.94253	CTC	.	.		0.517	CCDC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009740.1	NM_152492	Missense_Mutation	A	3686347	C	A	3686347	5	1	317	1	0	0	0	0	0	0	1	0	2803	811	28	3	1786	3	CCDC27	1	3686347	Splice_Site	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	2788065	3686347	245564274	2	44644										
MFAP2	4237	hgsc.bcm.edu	37	chr1	17303663	17303663	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ggaacggcggcagcgggtccAggtcatactggccctgagcc	16	13	1	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr1:17303663A>G	ENST00000375535.3	-	3	357	c.68T>C	c.(67-69)cTg>cCg	p.L23P	MFAP2_ENST00000375534.3_Missense_Mutation_p.L22P|MFAP2_ENST00000438542.1_Missense_Mutation_p.L22P|RP1-37C10.3_ENST00000446261.1_RNA|MFAP2_ENST00000490075.1_5'UTR			P55001	MFAP2_HUMAN	microfibrillar-associated protein 2	23					extracellular matrix organization (GO:0030198)|platelet formation (GO:0030220)	extracellular region (GO:0005576)|microfibril (GO:0001527)				kidney(1)|lung(1)	2		Colorectal(325;3.46e-05)|Breast(348;0.000118)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000538)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|COAD - Colon adenocarcinoma(227;1.07e-05)|BRCA - Breast invasive adenocarcinoma(304;3.04e-05)|Kidney(64;0.000377)|KIRC - Kidney renal clear cell carcinoma(64;0.00544)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		CAGCGGGTCCAGGTCATACTG	0.652																																					p.L23P		Atlas-SNP	.											.	MFAP2	8	.	0			c.T68C						.						31	27	28					1																	17303663		2202	4299	6501	SO:0001583	missense	4237	exon3			GGGTCCAGGTCAT	BC015039	CCDS174.1, CCDS44071.1	1p36.1-p35	2008-02-05			ENSG00000117122	ENSG00000117122			7033	protein-coding gene	gene with protein product		156790				7759096	Standard	NM_017459		Approved	MAGP, MAGP-1	uc001azw.3	P55001	OTTHUMG00000002290	ENST00000375535.3:c.68T>C	chr1.hg19:g.17303663A>G	ENSP00000364685:p.Leu23Pro	91.0	0.0		76.0	4.0	NM_017459	Q53X60|Q5JXY0	Missense_Mutation	SNP	ENST00000375535.3	hg19	CCDS174.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.975008	0.74360	.	.	ENSG00000117122	ENST00000375535;ENST00000375534;ENST00000438542	.	.	.	4.33	4.33	0.51752	.	0.631968	0.12996	N	0.422047	T	0.62551	0.2437	L	0.36672	1.1	0.58432	D	0.999991	P;D	0.56287	0.911;0.975	P;P	0.59424	0.583;0.857	T	0.61720	-0.7005	9	0.66056	D	0.02	.	10.2049	0.43107	1.0:0.0:0.0:0.0	.	22;23	Q5JXY0;P55001	.;MFAP2_HUMAN	P	23;22;22	.	ENSP00000364684:L22P	L	-	2	0	MFAP2	17176250	0.935000	0.31712	0.991000	0.47740	0.932000	0.56968	1.747000	0.38298	1.733000	0.51620	0.379000	0.24179	CTG	.	.		0.652	MFAP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000006609.1	NM_002403		G	17303663	A	G	17303663	3	3	317	1	0	0	0	0	1	0	0	0	9523	188	7	2	511	2	MFAP2	1	17303663	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	13617316	17303663	231946958	3	44645										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27102066	27102066	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	acgacatggaggtttatttcAggaaccccggaggcatggcg	14	9	1	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr1:27102066A>T	ENST00000324856.7	+	19	5364		c.e19-1		ARID1A_ENST00000457599.2_Splice_Site|ARID1A_ENST00000374152.2_Splice_Site|ARID1A_ENST00000540690.1_Splice_Site	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)						androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		GGTTTATTTCAGGAACCCCGG	0.532			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																.		Atlas-SNP	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.4343-2A>T						.						56	50	52					1																	27102066		2203	4300	6503	SO:0001630	splice_region_variant	8289	exon19			TATTTCAGGAACC	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.4994-1A>T	chr1.hg19:g.27102066A>T		45.0	0.0		30.0	20.0	NM_139135	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Splice_Site	SNP	ENST00000324856.7	hg19	CCDS285.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.290461	0.80914	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000374152;ENST00000430799	.	.	.	4.9	4.9	0.64082	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.6916	0.69091	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ARID1A	26974653	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.971000	0.93419	2.065000	0.61736	0.533000	0.62120	.	.	.		0.532	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135	Intron	T	27102066	A	T	27102066	5	4	317	1	0	0	0	0	0	0	1	0	913	202	7	4	5066	4	ARID1A	1	27102066	Splice_Site	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	9798403	27102066	222148555	4	44646										
ZMYM4	9202	hgsc.bcm.edu	37	chr1	35884069	35884069	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ctgactgttggcaagaggaaAcgaaatgaagatgatgaggt	14	4	0	6			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr1:35884069A>G	ENST00000314607.6	+	29	4415	c.4335A>G	c.(4333-4335)aaA>aaG	p.K1445K	ZMYM4_ENST00000373297.2_Silent_p.K1356K	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	1445					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(16)|ovary(2)|prostate(3)|skin(2)	54		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				GCAAGAGGAAACGAAATGAAG	0.398																																					p.K1445K		Atlas-SNP	.											ZMYM4,NS,carcinoma,0,1	ZMYM4	143	.	0			c.A4335G						.						118	111	113					1																	35884069		2203	4300	6503	SO:0001819	synonymous_variant	9202	exon29			GAGGAAACGAAAT	AB007885	CCDS389.1	1p34-p32	2013-01-08	2005-12-19	2005-12-19	ENSG00000146463	ENSG00000146463		"Zinc fingers, MYM type"	13055	protein-coding gene	gene with protein product		613568	"zinc finger protein 262"	ZNF262		10449923	Standard	NM_005095		Approved	KIAA0425, ZNF198L3, MYM	uc001byt.3	Q5VZL5	OTTHUMG00000004241	ENST00000314607.6:c.4335A>G	chr1.hg19:g.35884069A>G		111.0	0.0		84.0	28.0	NM_005095	A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	Silent	SNP	ENST00000314607.6	hg19	CCDS389.1	.	.	.	.	.	.	.	.	.	.	A	9.726	1.160948	0.21538	.	.	ENSG00000146463	ENST00000457946	.	.	.	5.84	5.84	0.93424	.	.	.	.	.	T	0.62925	0.2468	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.62315	-0.6880	4	.	.	.	-15.3005	10.5374	0.45013	0.9282:0.0:0.0717:0.0	.	.	.	.	A	1104	.	.	T	+	1	0	ZMYM4	35656656	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.539000	0.45718	2.230000	0.72887	0.528000	0.53228	ACG	.	.		0.398	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012207.3	NM_005095		G	35884069	A	G	35884069	2	3	317	1	0	0	0	0	0	0	0	1	17717	40	2	2		2	ZMYM4	1	35884069	Silent	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	8782003	35884069	213366552	5	44647										
LEPRE1	64175	hgsc.bcm.edu	37	chr1	43218272	43218272	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	cgccgtccatcaccacccgcTgggaaccattcaggagtttg	10	15	2	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr1:43218272T>A	ENST00000296388.5	-	9	1460	c.1409A>T	c.(1408-1410)cAg>cTg	p.Q470L	LEPRE1_ENST00000397054.3_Missense_Mutation_p.Q470L|LEPRE1_ENST00000236040.4_Missense_Mutation_p.Q470L			Q32P28	P3H1_HUMAN	leucine proline-enriched proteoglycan (leprecan) 1	470					bone development (GO:0060348)|cell growth (GO:0016049)|chaperone-mediated protein folding (GO:0061077)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|negative regulation of post-translational protein modification (GO:1901874)|peptidyl-proline hydroxylation (GO:0019511)|protein folding (GO:0006457)|protein hydroxylation (GO:0018126)|protein stabilization (GO:0050821)|regulation of ossification (GO:0030278)|regulation of protein secretion (GO:0050708)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|macromolecular complex (GO:0032991)|membrane (GO:0016020)|nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-proline 3-dioxygenase activity (GO:0019797)|protein complex binding (GO:0032403)			large_intestine(2)|lung(15)|ovary(5)|prostate(1)|urinary_tract(3)	26	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	CACCACCCGCTGGGAACCATT	0.532																																					p.Q470L		Atlas-SNP	.											.	LEPRE1	130	.	0			c.A1409T						.						104	87	92					1																	43218272		2203	4300	6503	SO:0001583	missense	64175	exon9			ACCCGCTGGGAAC	AK027648	CCDS472.2, CCDS53307.1, CCDS57986.1	1p34.1	2014-09-17			ENSG00000117385	ENSG00000117385			19316	protein-coding gene	gene with protein product	"prolyl 3-hydroxylase 1", "growth suppressor 1"	610339				10951563	Standard	NM_022356		Approved	GROS1, P3H1, LEPRECAN, MGC117314	uc001chx.4	Q32P28	OTTHUMG00000007525	ENST00000296388.5:c.1409A>T	chr1.hg19:g.43218272T>A	ENSP00000296388:p.Gln470Leu	94.0	0.0		108.0	25.0	NM_001146289	Q7KZR4|Q96BR8|Q96SK8|Q96SL5|Q96SN3|Q9H6K3|Q9HC86|Q9HC87	Missense_Mutation	SNP	ENST00000296388.5	hg19	CCDS472.2	.	.	.	.	.	.	.	.	.	.	t	19.77	3.889529	0.72524	.	.	ENSG00000117385	ENST00000397054;ENST00000236040;ENST00000296388;ENST00000540027	T;T;T	0.63417	-0.04;-0.04;-0.04	4.96	4.96	0.65561	Prolyl 4-hydroxylase, alpha subunit (1);	0.055934	0.64402	D	0.000001	T	0.54919	0.1888	L	0.54323	1.7	0.51482	D	0.999928	B;B;P	0.34662	0.41;0.043;0.462	B;B;B	0.29663	0.103;0.025;0.105	T	0.60000	-0.7348	10	0.54805	T	0.06	-32.4245	12.6255	0.56628	0.0:0.0:0.0:1.0	.	470;335;470	Q32P28-3;B4DNM8;Q32P28	.;.;P3H1_HUMAN	L	470;470;470;335	ENSP00000380245:Q470L;ENSP00000236040:Q470L;ENSP00000296388:Q470L	ENSP00000236040:Q470L	Q	-	2	0	LEPRE1	42990859	1.000000	0.71417	1.000000	0.80357	0.630000	0.37929	7.523000	0.81856	2.097000	0.63578	0.375000	0.23000	CAG	.	.		0.532	LEPRE1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019790.2	NM_022356		A	43218272	T	A	43218272	3	1	317	1	0	0	0	0	1	0	0	0	8738	1580	55	4	848	4	LEPRE1	1	43218272	Missense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	7334203	43218272	206032349	6	44648										
RAP1A	5906	hgsc.bcm.edu	37	chr1	112247100	112247100	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ctgcaaagtcaaagatcaatGttaatgaggtaacctacaac	7	8	2	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr1:112247100G>A	ENST00000369709.3	+	6	639	c.460G>A	c.(460-462)Gtt>Att	p.V154I	RAP1A_ENST00000356415.1_Missense_Mutation_p.V154I|RAP1A_ENST00000545460.1_Missense_Mutation_p.V154I|RAP1A_ENST00000436150.2_Missense_Mutation_p.V154I|RAP1A_ENST00000494982.1_3'UTR	NM_002884.2	NP_002875.1	P62834	RAP1A_HUMAN	RAP1A, member of RAS oncogene family	154					activation of MAPKK activity (GO:0000186)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to nerve growth factor stimulus (GO:1990090)|energy reserve metabolic process (GO:0006112)|establishment of endothelial barrier (GO:0061028)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of vasculogenesis (GO:2001214)|protein transport (GO:0015031)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|guanyl-nucleotide exchange factor complex (GO:0032045)|late endosome (GO:0005770)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|protein complex binding (GO:0032403)|protein transporter activity (GO:0008565)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)			endometrium(1)|large_intestine(2)|lung(3)	6		all_cancers(81;6.79e-06)|all_epithelial(167;2.42e-05)|all_lung(203;0.000105)|Lung NSC(277;0.00021)		Lung(183;0.0183)|Colorectal(144;0.0418)|LUSC - Lung squamous cell carcinoma(189;0.0966)|all cancers(265;0.098)|Epithelial(280;0.0981)|COAD - Colon adenocarcinoma(174;0.141)		AAAGATCAATGTTAATGAGGT	0.383																																					p.V154I		Atlas-SNP	.											.	RAP1A	14	.	0			c.G460A						.						85	80	82					1																	112247100		2203	4300	6503	SO:0001583	missense	5906	exon7			ATCAATGTTAATG	BC014086	CCDS840.1	1p13.3	2014-05-09			ENSG00000116473	ENSG00000116473			9855	protein-coding gene	gene with protein product		179520				3143720	Standard	XM_006710803		Approved	KREV-1, SMGP21	uc001ebl.3	P62834	OTTHUMG00000011959	ENST00000369709.3:c.460G>A	chr1.hg19:g.112247100G>A	ENSP00000358723:p.Val154Ile	99.0	0.0		150.0	55.0	NM_001010935	P10113	Missense_Mutation	SNP	ENST00000369709.3	hg19	CCDS840.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.986864	0.74589	.	.	ENSG00000116473	ENST00000356415;ENST00000369709;ENST00000436150;ENST00000545460	T;T;T;T	0.80653	-1.4;-1.4;-1.4;-1.4	5.92	5.92	0.95590	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.68174	0.2972	L	0.31157	0.91	0.80722	D	1	B	0.17667	0.023	B	0.28232	0.087	T	0.63888	-0.6535	10	0.49607	T	0.09	.	19.9157	0.97061	0.0:0.0:1.0:0.0	.	154	P62834	RAP1A_HUMAN	I	154	ENSP00000348786:V154I;ENSP00000358723:V154I;ENSP00000394318:V154I;ENSP00000443009:V154I	ENSP00000348786:V154I	V	+	1	0	RAP1A	112048623	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.476000	0.97823	2.809000	0.96659	0.655000	0.94253	GTT	.	.		0.383	RAP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033071.1	NM_002884		A	112247100	G	A	112247100	3	1	317	1	0	0	0	0	1	0	0	0	13050	1377	48	3	478	3	RAP1A	1	112247100	Missense_Mutation	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	69028828	112247100	137003521	7	44649										
SV2A	9900	hgsc.bcm.edu	37	chr1	149879627	149879627	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	actgcccgcctcggtggatcTgattctccaacgtgaagtta	10	12	2	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr1:149879627T>A	ENST00000369146.3	-	9	2001	c.1511A>T	c.(1510-1512)cAg>cTg	p.Q504L	SV2A_ENST00000369145.1_Missense_Mutation_p.Q504L	NM_001278719.1|NM_014849.3	NP_001265648.1|NP_055664.3	Q7L0J3	SV2A_HUMAN	synaptic vesicle glycoprotein 2A	504					cellular calcium ion homeostasis (GO:0006874)|neurotransmitter transport (GO:0006836)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	protein kinase binding (GO:0019901)|receptor activity (GO:0004872)|transmembrane transporter activity (GO:0022857)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(16)|ovary(6)|pancreas(1)|prostate(8)|skin(2)|urinary_tract(2)	55	Breast(34;0.00769)|all_hematologic(923;0.127)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)		Levetiracetam(DB01202)	TCGGTGGATCTGATTCTCCAA	0.498																																					p.Q504L		Atlas-SNP	.											.	SV2A	123	.	0			c.A1511T						.						162	158	159					1																	149879627		2203	4300	6503	SO:0001583	missense	9900	exon9			TGGATCTGATTCT	AB018279	CCDS940.1	1q21.2	2008-02-05			ENSG00000159164	ENSG00000159164			20566	protein-coding gene	gene with protein product		185860				7681585, 10611374	Standard	NM_014849		Approved	SV2, KIAA0736	uc001etg.3	Q7L0J3	OTTHUMG00000012209	ENST00000369146.3:c.1511A>T	chr1.hg19:g.149879627T>A	ENSP00000358142:p.Gln504Leu	163.0	0.0		194.0	51.0	NM_014849	D3DUZ7|O94841|Q5QNX8|Q7Z3L6|Q8NBJ6|Q9BVZ9	Missense_Mutation	SNP	ENST00000369146.3	hg19	CCDS940.1	.	.	.	.	.	.	.	.	.	.	T	15.73	2.920403	0.52653	.	.	ENSG00000159164	ENST00000369146;ENST00000369145	T;T	0.39229	1.09;1.09	5.26	5.26	0.73747	Major facilitator superfamily domain (1);	0.163230	0.40728	N	0.001028	T	0.29850	0.0746	M	0.74467	2.265	0.80722	D	1	P	0.36027	0.533	B	0.36418	0.224	T	0.12451	-1.0547	10	0.25106	T	0.35	-15.2338	13.1692	0.59589	0.0:0.0:0.0:1.0	.	504	Q7L0J3	SV2A_HUMAN	L	504	ENSP00000358142:Q504L;ENSP00000358141:Q504L	ENSP00000358141:Q504L	Q	-	2	0	SV2A	148146251	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.868000	0.87116	2.213000	0.71641	0.454000	0.30748	CAG	.	.		0.498	SV2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033754.1			A	149879627	T	A	149879627	3	1	317	1	0	0	0	0	1	0	0	0	15432	1580	55	4	737	4	SV2A	1	149879627	Missense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	37632527	149879627	99370994	8	44650										
CRNN	49860	hgsc.bcm.edu	37	chr1	152382364	152382364	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tgggcctgtcctcccggtacTgtctctcctgcctcagggtt	11	15	2	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr1:152382364T>A	ENST00000271835.3	-	3	1256	c.1194A>T	c.(1192-1194)acA>acT	p.T398T	RP1-91G5.3_ENST00000411804.1_RNA	NM_016190.2	NP_057274.1	Q9UBG3	CRNN_HUMAN	cornulin	398					response to heat (GO:0009408)|single organismal cell-cell adhesion (GO:0016337)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(16)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTCCCGGTACTGTCTCTCCTG	0.612																																					p.T398T		Atlas-SNP	.											.	CRNN	78	.	0			c.A1194T						.						103	85	91					1																	152382364		2203	4300	6503	SO:0001819	synonymous_variant	49860	exon3			CGGTACTGTCTCT	AF077831	CCDS1010.1	1q21	2014-01-28	2005-06-13	2005-06-13	ENSG00000143536	ENSG00000143536		"EF-hand domain containing"	1230	protein-coding gene	gene with protein product		611312	"chromosome 1 open reading frame 10"	C1orf10		11056050, 15854041	Standard	NM_016190		Approved	SEP53	uc001ezx.2	Q9UBG3	OTTHUMG00000012383	ENST00000271835.3:c.1194A>T	chr1.hg19:g.152382364T>A		78.0	0.0		74.0	16.0	NM_016190	B2RE60|Q8N613	Silent	SNP	ENST00000271835.3	hg19	CCDS1010.1																																																																																			.	.		0.612	CRNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034503.1	NM_016190		A	152382364	T	A	152382364	2	1	317	1	0	0	0	0	0	0	0	1	3894	1567	55	4		4	CRNN	1	152382364	Silent	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	2502737	152382364	96868257	9	44651										
LENEP	55891	hgsc.bcm.edu	37	chr1	154966209	154966209	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tgggagggcttccagcggacCctgaaggaagtcgcctacat	14	11	0	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr1:154966209C>A	ENST00000392487.1	+	1	146	c.126C>A	c.(124-126)acC>acA	p.T42T				Q9Y5L5	LENEP_HUMAN	lens epithelial protein	42					multicellular organismal development (GO:0007275)		DNA binding (GO:0003677)			lung(2)	2	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			TCCAGCGGACCCTGAAGGAAG	0.602																																					p.T42T		Atlas-SNP	.											.	LENEP	6	.	0			c.C126A						.						85	82	83					1																	154966209		2203	4300	6503	SO:0001819	synonymous_variant	55891	exon1			GCGGACCCTGAAG	AF268478	CCDS1080.1	1q22.2	2008-02-05			ENSG00000163352	ENSG00000163352			14429	protein-coding gene	gene with protein product		607377				10655141, 11376938	Standard	NM_018655		Approved	LEP503	uc001fgi.3	Q9Y5L5	OTTHUMG00000037417	ENST00000392487.1:c.126C>A	chr1.hg19:g.154966209C>A		60.0	0.0		61.0	18.0	NM_018655	B5BUM1|Q5T1A4	Silent	SNP	ENST00000392487.1	hg19	CCDS1080.1																																																																																			.	.		0.602	LENEP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385609.2	NM_018655		A	154966209	C	A	154966209	2	1	317	1	0	0	0	0	0	0	0	1	8731	610	22	3		3	LENEP	1	154966209	Silent	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	2583845	154966209	94284412	10	44652										
DUSP27	92235	hgsc.bcm.edu	37	chr1	167096126	167096126	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	aacccctccgacgtcagcctGacagcctaccaggcctggaa	9	17	1	1	rs144793075		TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr1:167096126G>C	ENST00000361200.2	+	6	1924	c.1758G>C	c.(1756-1758)ctG>ctC	p.L586L	DUSP27_ENST00000271385.5_Silent_p.L586L|DUSP27_ENST00000443333.1_Silent_p.L586L|DUSP27_ENST00000485151.1_Intron			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	586					protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						ACGTCAGCCTGACAGCCTACC	0.592																																					p.L586L		Atlas-SNP	.											.	DUSP27	235	.	0			c.G1758C						.						45	45	45					1																	167096126		2203	4300	6503	SO:0001819	synonymous_variant	92235	exon5			CAGCCTGACAGCC	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.1758G>C	chr1.hg19:g.167096126G>C		92.0	0.0		111.0	38.0	NM_001080426	A0AUM4|Q9C074	Silent	SNP	ENST00000361200.2	hg19	CCDS30932.1																																																																																			.	G|1.000;T|0.000		0.592	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426		C	167096126	G	C	167096126	2	2	317	1	0	0	0	0	0	0	0	1	4826	1277	45	4		4	DUSP27	1	167096126	Silent	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	12129917	167096126	82154495	11	44653										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181701627	181701627	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ggccctcaacagagaggaggCgccgaccatgaacccgctca	12	15	2	2	rs374689888		TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr1:181701627C>A	ENST00000367573.2	+	20	2405	c.2405C>A	c.(2404-2406)gCg>gAg	p.A802E	CACNA1E_ENST00000367567.4_Missense_Mutation_p.A409E|CACNA1E_ENST00000360108.3_Missense_Mutation_p.A783E|CACNA1E_ENST00000526775.1_Missense_Mutation_p.A783E|CACNA1E_ENST00000357570.5_Missense_Mutation_p.A753E|CACNA1E_ENST00000367570.1_Missense_Mutation_p.A802E|CACNA1E_ENST00000358338.5_Missense_Mutation_p.A734E	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	802					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						AGAGAGGAGGCGCCGACCATG	0.657																																					p.A802E		Atlas-SNP	.											.	CACNA1E	778	.	0			c.C2405A						.						38	57	50					1																	181701627		1763	3295	5058	SO:0001583	missense	777	exon20			AGGAGGCGCCGAC	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.2405C>A	chr1.hg19:g.181701627C>A	ENSP00000356545:p.Ala802Glu	170.0	0.0		188.0	57.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	C	0.506	-0.868753	0.02570	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.96011	-3.81;-3.8;-3.81;-3.8;-3.88;-3.8;-3.81	3.82	3.82	0.43975	.	38.321500	0.00166	N	0.000000	D	0.92179	0.7520	N	0.03608	-0.345	0.35702	D	0.81569	D;D;D	0.63880	0.975;0.993;0.975	P;P;P	0.58013	0.686;0.831;0.686	D	0.84652	0.0701	10	0.02654	T	1	.	11.5128	0.50502	0.0:1.0:0.0:0.0	.	783;802;802	Q15878-2;Q15878;Q15878-3	.;CAC1E_HUMAN;.	E	802;783;753;734;409;783;802	ENSP00000356542:A802E;ENSP00000434814:A783E;ENSP00000350183:A753E;ENSP00000351101:A734E;ENSP00000356539:A409E;ENSP00000353222:A783E;ENSP00000356545:A802E	ENSP00000350183:A753E	A	+	2	0	CACNA1E	179968250	.	.	0.990000	0.47175	0.056000	0.15407	.	.	2.437000	0.82529	0.561000	0.74099	GCG	.	.		0.657	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		A	181701627	C	A	181701627	3	1	317	1	0	0	0	0	1	0	0	0	2544	768	27	1	2483	1	CACNA1E	1	181701627	Missense_Mutation	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	14605501	181701627	67548994	12	44654										
HHAT	55733	hgsc.bcm.edu	37	chr1	210591627	210591627	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tgtacatgcatgccatctacAgcagcatccccctcctggag	8	15	1	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr1:210591627A>T	ENST00000367010.1	+	7	1041	c.814A>T	c.(814-816)Agc>Tgc	p.S272C	HHAT_ENST00000391905.3_Missense_Mutation_p.S272C|HHAT_ENST00000537898.1_Missense_Mutation_p.S207C|HHAT_ENST00000261458.3_Missense_Mutation_p.S272C|HHAT_ENST00000413764.2_Missense_Mutation_p.S272C|HHAT_ENST00000308852.6_Missense_Mutation_p.S227C|HHAT_ENST00000545154.1_Missense_Mutation_p.S273C|HHAT_ENST00000545781.1_Missense_Mutation_p.S209C|HHAT_ENST00000541565.1_Missense_Mutation_p.S135C	NM_001170580.1	NP_001164051.1	Q5VTY9	HHAT_HUMAN	hedgehog acyltransferase	272					multicellular organismal development (GO:0007275)|protein palmitoylation (GO:0018345)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|palmitoyltransferase activity (GO:0016409)			breast(3)|central_nervous_system(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	27				OV - Ovarian serous cystadenocarcinoma(81;0.0136)|all cancers(67;0.161)|KIRC - Kidney renal clear cell carcinoma(1967;0.215)		TGCCATCTACAGCAGCATCCC	0.572																																					p.S273C		Atlas-SNP	.											.	HHAT	66	.	0			c.A817T						.						117	105	109					1																	210591627		2203	4300	6503	SO:0001583	missense	55733	exon6			ATCTACAGCAGCA	AK001586	CCDS1495.1, CCDS53471.1, CCDS53472.1, CCDS53473.1	1q32	2008-02-05			ENSG00000054392	ENSG00000054392			18270	protein-coding gene	gene with protein product		605743				11160356	Standard	NM_001170587		Approved	FLJ10724, MART-2, MART2, Skn, ski, rasp, sit, GUP2	uc009xcx.3	Q5VTY9	OTTHUMG00000036447	ENST00000367010.1:c.814A>T	chr1.hg19:g.210591627A>T	ENSP00000355977:p.Ser272Cys	173.0	0.0		186.0	47.0	NM_001170587	B7Z4D5|B7Z5I1|B7Z868|B7ZA75|D3DT91|F5H444|Q17RZ7|Q4G0K3|Q5CZ95|Q5TGI2|Q9NVH9|Q9Y3N8	Missense_Mutation	SNP	ENST00000367010.1	hg19	CCDS1495.1	.	.	.	.	.	.	.	.	.	.	A	12.78	2.041830	0.35989	.	.	ENSG00000054392	ENST00000413764;ENST00000541565;ENST00000545154;ENST00000537898;ENST00000391905;ENST00000545781;ENST00000261458;ENST00000308852;ENST00000367010;ENST00000426968	T;T;T;T;T;T;T;T;T;T	0.74737	-0.87;-0.87;-0.87;-0.87;-0.87;-0.87;-0.87;-0.87;-0.87;-0.87	5.1	-1.53	0.08611	.	0.313354	0.39475	N	0.001360	T	0.80618	0.4657	M	0.72118	2.19	0.38827	D	0.955751	D;D;D;D;D	0.76494	0.996;0.999;0.999;0.998;0.996	D;P;D;P;D	0.66979	0.948;0.894;0.947;0.907;0.94	T	0.79351	-0.1839	10	0.56958	D	0.05	-5.1928	10.1145	0.42583	0.6314:0.0:0.3686:0.0	.	227;273;135;207;272	B7Z2U8;F5H444;B7Z4D5;B7Z5I1;Q5VTY9	.;.;.;.;HHAT_HUMAN	C	272;135;273;207;272;209;272;227;272;144	ENSP00000416845:S272C;ENSP00000444995:S135C;ENSP00000438468:S273C;ENSP00000442625:S207C;ENSP00000375773:S272C;ENSP00000439229:S209C;ENSP00000261458:S272C;ENSP00000308628:S227C;ENSP00000355977:S272C;ENSP00000413399:S144C	ENSP00000261458:S272C	S	+	1	0	HHAT	208658250	0.996000	0.38824	0.991000	0.47740	0.095000	0.18619	0.583000	0.23849	-0.258000	0.09446	-0.475000	0.04921	AGC	.	.		0.572	HHAT-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088662.1	NM_018194		T	210591627	A	T	210591627	3	4	317	1	0	0	0	0	1	0	0	0	7098	188	7	4	934	4	HHAT	1	210591627	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	28890000	210591627	38658994	13	44655										
SIPA1L2	57568	hgsc.bcm.edu	37	chr1	232539296	232539296	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gctgcatatctgtcagggtgCagaaggatgccaccctctgg	13	11	3	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr1:232539296C>A	ENST00000366630.1	-	20	5196	c.4838G>T	c.(4837-4839)tGc>tTc	p.C1613F	SIPA1L2_ENST00000262861.4_Missense_Mutation_p.C1613F|SIPA1L2_ENST00000308942.4_Missense_Mutation_p.C669F			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	1613					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				TGTCAGGGTGCAGAAGGATGC	0.507																																					p.C1613F		Atlas-SNP	.											.	SIPA1L2	218	.	0			c.G4838T						.						53	56	55					1																	232539296		1942	4160	6102	SO:0001583	missense	57568	exon19			AGGGTGCAGAAGG	AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.4838G>T	chr1.hg19:g.232539296C>A	ENSP00000355589:p.Cys1613Phe	63.0	0.0		97.0	37.0	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	hg19	CCDS41474.1	.	.	.	.	.	.	.	.	.	.	C	11.66	1.705639	0.30232	.	.	ENSG00000116991	ENST00000366630;ENST00000262861;ENST00000308942	T;T;T	0.28069	1.63;1.63;1.63	5.04	5.04	0.67666	.	0.227351	0.45867	D	0.000322	T	0.22205	0.0535	N	0.12182	0.205	0.50467	D	0.99987	P;D	0.54964	0.662;0.969	B;P	0.47827	0.273;0.558	T	0.02457	-1.1156	10	0.07990	T	0.79	-10.1775	16.9133	0.86145	0.0:1.0:0.0:0.0	.	1613;669	Q9P2F8;Q9P2F8-2	SI1L2_HUMAN;.	F	1613;1613;669	ENSP00000355589:C1613F;ENSP00000262861:C1613F;ENSP00000309102:C669F	ENSP00000262861:C1613F	C	-	2	0	SIPA1L2	230605919	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.504000	0.73704	2.639000	0.89480	0.644000	0.83932	TGC	.	.		0.507	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839		A	232539296	C	A	232539296	3	1	317	1	0	0	0	0	1	0	0	0	14345	710	25	3	342	3	SIPA1L2	1	232539296	Missense_Mutation	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	21947669	232539296	16711325	14	44656										
FMN2	56776	hgsc.bcm.edu	37	chr1	240286488	240286488	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ttcatctgcagggcgaacgcTgttggagaagctgttcagcc	13	10	3	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr1:240286488T>C	ENST00000319653.9	+	2	1855	c.1625T>C	c.(1624-1626)cTg>cCg	p.L542P		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	542					cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			GGGCGAACGCTGTTGGAGAAG	0.552																																					p.L542P		Atlas-SNP	.											.	FMN2	451	.	0			c.T1625C						.						95	88	91					1																	240286488		2203	4300	6503	SO:0001583	missense	56776	exon2			GAACGCTGTTGGA	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.1625T>C	chr1.hg19:g.240286488T>C	ENSP00000318884:p.Leu542Pro	99.0	0.0		132.0	35.0	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	hg19	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	T	10.04	1.242496	0.22796	.	.	ENSG00000155816	ENST00000319653	T	0.80480	-1.38	5.57	5.57	0.84162	DEP domain (1);	0.000000	0.51477	D	0.000084	D	0.88676	0.6501	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.89811	0.3982	10	0.87932	D	0	.	16.0108	0.80402	0.0:0.0:0.0:1.0	.	542	Q9NZ56	FMN2_HUMAN	P	542	ENSP00000318884:L542P	ENSP00000318884:L542P	L	+	2	0	FMN2	238353111	1.000000	0.71417	0.828000	0.32881	0.364000	0.29643	6.950000	0.75977	2.242000	0.73789	0.482000	0.46254	CTG	.	.		0.552	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		C	240286488	T	C	240286488	3	2	317	1	0	0	0	0	1	0	0	0	5958	1580	55	2	1631	2	FMN2	1	240286488	Missense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	7747192	240286488	8964133	15	44657										
PLD5	200150	hgsc.bcm.edu	37	chr1	242264076	242264076	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gcattctctctttccagatcAaaaaatttctgtaagaaaaa	4	8	4	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr1:242264076A>G	ENST00000536534.2	-	9	1489	c.1248T>C	c.(1246-1248)ttT>ttC	p.F416F	PLD5_ENST00000442594.2_Silent_p.F324F|PLD5_ENST00000427495.1_Silent_p.F354F			Q8N7P1	PLD5_HUMAN	phospholipase D family, member 5	416						integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(22)|ovary(6)|skin(3)|urinary_tract(1)	55	Melanoma(84;0.242)		OV - Ovarian serous cystadenocarcinoma(106;0.0329)			TTTCCAGATCAAAAAATTTCT	0.378																																					p.F416F		Atlas-SNP	.											.	PLD5	216	.	0			c.T1248C						.						80	77	78					1																	242264076		2203	4300	6503	SO:0001819	synonymous_variant	200150	exon10			CAGATCAAAAAAT	AK098092	CCDS1621.1, CCDS1621.2, CCDS55692.1	1q43	2008-02-05			ENSG00000180287	ENSG00000180287			26879	protein-coding gene	gene with protein product							Standard	NM_001195811		Approved	FLJ40773	uc001hzn.2	Q8N7P1	OTTHUMG00000039867	ENST00000536534.2:c.1248T>C	chr1.hg19:g.242264076A>G		91.0	0.0		127.0	29.0	NM_152666	A1KXV0|B7Z324|Q494U9|Q8NB22	Silent	SNP	ENST00000536534.2	hg19	CCDS1621.2																																																																																			.	.		0.378	PLD5-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397213.2	NM_152666		G	242264076	A	G	242264076	2	3	317	1	0	0	0	0	0	0	0	1	12058	127	5	2		2	PLD5	1	242264076	Silent	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	1977588	242264076	6986545	16	44658										
EFCAB2	84288	hgsc.bcm.edu	37	chr1	245250660	245250660	+	Intron	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tgatggtgatagatgaaaatTaaatgttctaaagataattt	8	1	1	5			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr1:245250660T>A	ENST00000366522.2	+	7	922				EFCAB2_ENST00000447569.2_Intron|EFCAB2_ENST00000366523.1_Nonstop_Mutation_p.*163K|EFCAB2_ENST00000487845.1_Intron			Q5VUJ9	EFCB2_HUMAN	EF-hand calcium binding domain 2								calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|stomach(2)	13	all_cancers(71;2.93e-06)|all_epithelial(71;2.13e-05)|all_lung(81;0.0337)|Lung NSC(105;0.0472)|Ovarian(71;0.0584)|Breast(184;0.0716)|all_neural(11;0.0982)		OV - Ovarian serous cystadenocarcinoma(106;0.015)			AGATGAAAATTAAATGTTCTA	0.274																																					p.X163K		Atlas-SNP	.											.	EFCAB2	19	.	0			c.T487A						.						43	45	44					1																	245250660		2202	4294	6496	SO:0001627	intron_variant	84288	exon8			GAAAATTAAATGT	AB209286	CCDS31082.1, CCDS44341.1	1q44	2014-07-18			ENSG00000203666	ENSG00000203666		"EF-hand domain containing"	28166	protein-coding gene	gene with protein product	"dynein regulatory complex subunit 8"					23427265	Standard	NM_032328		Approved	MGC12458, DRC8, CFAP200	uc001ibc.2	Q5VUJ9	OTTHUMG00000040474	ENST00000366522.2:c.781+3670T>A	chr1.hg19:g.245250660T>A		221.0	0.0		339.0	79.0	NM_032328	B4DZE9|Q59G23|Q9BS36	Missense_Mutation	SNP	ENST00000366522.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	22.4|22.4	4.280193|4.280193	0.80692|0.80692	.|.	.|.	ENSG00000203666|ENSG00000203666	ENST00000366521|ENST00000366523	.|.	.|.	.|.	5.78|5.78	4.65|4.65	0.58169|0.58169	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	8.6474|8.6474	0.34013|0.34013	0.0:0.0861:0.0:0.9139|0.0:0.0861:0.0:0.9139	.|.	.|.	.|.	.|.	X|K	221|163	.|.	.|.	L|X	+|+	2|1	0|0	EFCAB2|EFCAB2	243317283|243317283	1.000000|1.000000	0.71417|0.71417	0.017000|0.017000	0.16124|0.16124	0.984000|0.984000	0.73092|0.73092	2.276000|2.276000	0.43408|0.43408	1.011000|1.011000	0.39340|0.39340	0.460000|0.460000	0.39030|0.39030	TTA|TAA	.	.		0.274	EFCAB2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000097407.2			A	245250660	T	A	245250660	1	1	317	0	1	0	0	0	0	0	0	0	4936	1767	61	4		4	EFCAB2	1	245250660	Intron	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	2986584	245250660	3999961	17	44659										
ROCK2	9475	hgsc.bcm.edu	37	chr2	11337476	11337476	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ggctctcttcagctatttgcTataagaaatttaattacaat	5	7	2	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr2:11337476T>A	ENST00000315872.6	-	27	3728		c.e27-2		ROCK2_ENST00000401753.1_Splice_Site	NM_004850.3	NP_004841.2	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein kinase 2						actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|neural tube closure (GO:0001843)|positive regulation of centrosome duplication (GO:0010825)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of circadian rhythm (GO:0042752)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|rhythmic process (GO:0048511)|smooth muscle contraction (GO:0006939)	centrosome (GO:0005813)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole centrosome (GO:0031616)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(6)|lung(10)|prostate(1)|skin(4)|stomach(3)|urinary_tract(2)	43	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)		AGCTATTTGCTATAAGAAATT	0.348																																					.		Atlas-SNP	.											.	ROCK2	224	.	0			c.3280-2A>T						.						70	65	66					2																	11337476		1852	4096	5948	SO:0001630	splice_region_variant	9475	exon28			ATTTGCTATAAGA	D87931	CCDS42654.1	2p24	2013-01-10			ENSG00000134318	ENSG00000134318	2.7.11.1	"Pleckstrin homology (PH) domain containing"	10252	protein-coding gene	gene with protein product		604002				9933571	Standard	NM_004850		Approved		uc002rbd.1	O75116	OTTHUMG00000149916	ENST00000315872.6:c.3280-2A>T	chr2.hg19:g.11337476T>A		215.0	0.0		219.0	61.0	NM_004850	Q53QZ0|Q53SJ7|Q9UQN5	Splice_Site	SNP	ENST00000315872.6	hg19	CCDS42654.1	.	.	.	.	.	.	.	.	.	.	T	17.67	3.446931	0.63178	.	.	ENSG00000134318	ENST00000315872;ENST00000401753;ENST00000399089	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0084	0.80380	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	ROCK2	11254927	1.000000	0.71417	0.926000	0.36857	0.675000	0.39556	7.849000	0.86908	2.180000	0.69256	0.460000	0.39030	.	.	.		0.348	ROCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313886.3		Intron	A	11337476	T	A	11337476	5	1	317	1	0	0	0	0	0	0	1	0	13533	1536	53	4	916	4	ROCK2	2	11337476	Splice_Site	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10		11337476	231861897	18	44660										
ATAD2B	54454	hgsc.bcm.edu	37	chr2	23980759	23980759	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ggatgattcatcattggtcaTagataagtctccagtctctt	8	8	5	2	rs201429059		TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr2:23980759T>C	ENST00000238789.5	-	25	3950	c.3607A>G	c.(3607-3609)Atg>Gtg	p.M1203V	ATAD2B_ENST00000474583.1_5'UTR	NM_001242338.1|NM_017552.2	NP_001229267.1|NP_060022.1	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B	1203						nucleus (GO:0005634)	ATP binding (GO:0005524)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCATTGGTCATAGATAAGTCT	0.448													T|||	1	0.000199681	0	0	5008	,	,		19034	0		0	False		,,,				2504	0.001				p.M1203V		Atlas-SNP	.											.	ATAD2B	110	.	0			c.A3607G						.	T	VAL/MET,VAL/MET	1,3919		0,1,1959	144	141	142		3592,3607	3.1	1	2		142	1,8289		0,1,4144	yes	missense,missense	ATAD2B	NM_001242338.1,NM_017552.2	21,21	0,2,6103	CC,CT,TT		0.0121,0.0255,0.0164	benign,benign	1198/1454,1203/1459	23980759	2,12208	1960	4145	6105	SO:0001583	missense	54454	exon25			TGGTCATAGATAA	AB033066	CCDS46227.1	2p24.1-p23.3	2010-04-21		2007-02-08	ENSG00000119778	ENSG00000119778		"ATPases / AAA-type"	29230	protein-coding gene	gene with protein product		615347					Standard	XM_005264372		Approved	KIAA1240	uc002rek.4	Q9ULI0	OTTHUMG00000151902	ENST00000238789.5:c.3607A>G	chr2.hg19:g.23980759T>C	ENSP00000238789:p.Met1203Val	111.0	0.0		162.0	49.0	NM_017552	B9ZVQ5|Q6ZNA6|Q8N9E7	Missense_Mutation	SNP	ENST00000238789.5	hg19	CCDS46227.1	.	.	.	.	.	.	.	.	.	.	T	5.775	0.327444	0.10956	2.55E-4	1.21E-4	ENSG00000119778	ENST00000238789;ENST00000546030	D	0.91124	-2.79	5.62	3.11	0.35812	.	0.625902	0.17751	N	0.163256	T	0.76343	0.3974	N	0.12182	0.205	0.29304	N	0.86848	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.62300	-0.6883	10	0.22706	T	0.39	.	1.8178	0.03104	0.1345:0.1453:0.1401:0.5801	.	1203;1198	Q9ULI0;Q9ULI0-2	ATD2B_HUMAN;.	V	1203;371	ENSP00000238789:M1203V	ENSP00000238789:M1203V	M	-	1	0	ATAD2B	23834263	0.981000	0.34729	1.000000	0.80357	0.993000	0.82548	0.954000	0.29175	1.084000	0.41184	0.460000	0.39030	ATG	.	.		0.448	ATAD2B-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324333.1	NM_017552		C	23980759	T	C	23980759	3	2	317	1	0	0	0	0	1	0	0	0	1072	1406	49	2	785	2	ATAD2B	2	23980759	Missense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	12643283	23980759	219218614	19	44661										
KCNK3	3777	hgsc.bcm.edu	37	chr2	26915803	26915803	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tgcaccttcacctacctgctGgtgggcgccgcggtcttcga	12	15	2	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr2:26915803G>T	ENST00000302909.3	+	1	185	c.60G>T	c.(58-60)ctG>ctT	p.L20L		NM_002246.2	NP_002237.1	O14649	KCNK3_HUMAN	potassium channel, subfamily K, member 3	20					brain development (GO:0007420)|cellular response to hypoxia (GO:0071456)|cellular response to zinc ion (GO:0071294)|cochlea development (GO:0090102)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|potassium ion transport (GO:0006813)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ion channel activity (GO:0005216)|open rectifier potassium channel activity (GO:0005252)|potassium channel activity (GO:0005267)|potassium ion leak channel activity (GO:0022841)|S100 protein binding (GO:0044548)			endometrium(3)|large_intestine(4)|lung(5)|ovary(1)|urinary_tract(1)	14	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Doxapram(DB00561)|Halothane(DB01159)	CCTACCTGCTGGTGGGCGCCG	0.751																																					p.L20L	GBM(80;1457 1631 27100 45946)	Atlas-SNP	.											.	KCNK3	43	.	0			c.G60T						.						6	7	7					2																	26915803		2130	4141	6271	SO:0001819	synonymous_variant	3777	exon1			CCTGCTGGTGGGC	AF006823	CCDS1727.1	2p23	2012-03-07			ENSG00000171303	ENSG00000171303		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6278	protein-coding gene	gene with protein product		603220				9312005, 9721223, 16382106	Standard	NM_002246		Approved	K2p3.1, TASK, TASK-1	uc002rhn.2	O14649	OTTHUMG00000125530	ENST00000302909.3:c.60G>T	chr2.hg19:g.26915803G>T		53.0	0.0		69.0	20.0	NM_002246	Q53SU2	Silent	SNP	ENST00000302909.3	hg19	CCDS1727.1																																																																																			.	.		0.751	KCNK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246861.2	NM_002246		T	26915803	G	T	26915803	2	4	317	1	0	0	0	0	0	0	0	1	8076	1335	47	3		3	KCNK3	2	26915803	Silent	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	2935044	26915803	216283570	20	44662										
AAK1	22848	hgsc.bcm.edu	37	chr2	69741794	69741794	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ctgctgctggtagaaattctGcattagctgctgttgagagc	12	8	1	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr2:69741794G>T	ENST00000409085.4	-	13	1961	c.1585C>A	c.(1585-1587)Cag>Aag	p.Q529K	AAK1_ENST00000406297.3_Missense_Mutation_p.Q529K|AAK1_ENST00000409068.1_Missense_Mutation_p.Q529K|RN7SL604P_ENST00000492589.2_RNA	NM_014911.3	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1	529	Gln-rich.				endocytosis (GO:0006897)|positive regulation of Notch signaling pathway (GO:0045747)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of clathrin-mediated endocytosis (GO:2000369)|regulation of protein localization (GO:0032880)	cell leading edge (GO:0031252)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extrinsic component of plasma membrane (GO:0019897)|terminal bouton (GO:0043195)	AP-2 adaptor complex binding (GO:0035612)|ATP binding (GO:0005524)|Notch binding (GO:0005112)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)	17						TAGAAATTCTGCATTAGCTGC	0.522																																					p.Q529K		Atlas-SNP	.											.	AAK1	121	.	0			c.C1585A						.						46	48	47					2																	69741794		2195	4300	6495	SO:0001583	missense	22848	exon13			AATTCTGCATTAG	AB028971	CCDS1893.2	2p13.3	2012-07-10			ENSG00000115977	ENSG00000115977			19679	protein-coding gene	gene with protein product						11877461, 12471243	Standard	NM_014911		Approved	KIAA1048, DKFZp686K16132	uc002sfp.2	Q2M2I8	OTTHUMG00000129648	ENST00000409085.4:c.1585C>A	chr2.hg19:g.69741794G>T	ENSP00000386456:p.Gln529Lys	65.0	0.0		73.0	5.0	NM_014911	Q4ZFZ3|Q53RX6|Q9UPV4	Missense_Mutation	SNP	ENST00000409085.4	hg19	CCDS1893.2	.	.	.	.	.	.	.	.	.	.	G	16.27	3.075907	0.55646	.	.	ENSG00000115977	ENST00000409068;ENST00000409085;ENST00000406297	T;T;T	0.36699	1.24;1.24;1.24	5.43	5.43	0.79202	.	0.426268	0.23708	N	0.045357	T	0.40595	0.1123	N	0.24115	0.695	0.35959	D	0.83448	P;P;P	0.52577	0.924;0.954;0.713	P;D;P	0.67900	0.9;0.954;0.761	T	0.08848	-1.0702	10	0.02654	T	1	-9.2741	16.0855	0.81045	0.0:0.0:1.0:0.0	.	529;529;529	B7ZLC4;Q2M2I8-2;Q2M2I8	.;.;AAK1_HUMAN	K	529	ENSP00000386342:Q529K;ENSP00000386456:Q529K;ENSP00000385181:Q529K	ENSP00000385181:Q529K	Q	-	1	0	AAK1	69595298	1.000000	0.71417	0.997000	0.53966	0.962000	0.63368	3.503000	0.53340	2.822000	0.97130	0.650000	0.86243	CAG	.	.		0.522	AAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251847.4	NM_014911		T	69741794	G	T	69741794	3	4	317	1	0	0	0	0	1	0	0	0	16	1328	46	3	1340	3	AAK1	2	69741794	Missense_Mutation	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	42825991	69741794	173457579	21	44663										
DNAH6	1768	hgsc.bcm.edu	37	chr2	84832704	84832704	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gtgtttatactgggcggcacAgatgacatacaggtgggtaa	14	6	0	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr2:84832704A>T	ENST00000237449.6	+	19	3170	c.3162A>T	c.(3160-3162)acA>acT	p.T1054T	DNAH6_ENST00000389394.3_Silent_p.T1054T|DNAH6_ENST00000398278.2_Silent_p.T1054T			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	1054	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						TGGGCGGCACAGATGACATAC	0.418																																					p.T1054T		Atlas-SNP	.											.	DNAH6	194	.	0			c.A3162T						.						157	132	140					2																	84832704		692	1591	2283	SO:0001819	synonymous_variant	1768	exon20			CGGCACAGATGAC	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.3162A>T	chr2.hg19:g.84832704A>T		191.0	0.0		202.0	71.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	hg19	CCDS46348.1																																																																																			.	.		0.418	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		T	84832704	A	T	84832704	2	4	317	1	0	0	0	0	0	0	0	1	4607	175	7	4		4	DNAH6	2	84832704	Silent	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	15090910	84832704	158366669	22	44664										
VWA3B	200403	hgsc.bcm.edu	37	chr2	98779401	98779401	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ccagatccagaggctggtggCcgagcctcccaagcccgacg	13	16	0	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr2:98779401C>T	ENST00000477737.1	+	8	1280	c.1076C>T	c.(1075-1077)gCc>gTc	p.A359V	VWA3B_ENST00000435344.1_Missense_Mutation_p.A359V|VWA3B_ENST00000451075.2_Missense_Mutation_p.A209V	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	359										NS(3)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						AGGCTGGTGGCCGAGCCTCCC	0.562																																					p.A359V		Atlas-SNP	.											.	VWA3B	138	.	0			c.C1076T						.						51	59	57					2																	98779401		2076	4228	6304	SO:0001583	missense	200403	exon8			TGGTGGCCGAGCC	AL832761	CCDS42718.1	2q11.2	2008-02-05			ENSG00000168658	ENSG00000168658			28385	protein-coding gene	gene with protein product						12477932	Standard	NM_144992		Approved	DKFZp686F2227, MGC26733	uc002syo.3	Q502W6	OTTHUMG00000153104	ENST00000477737.1:c.1076C>T	chr2.hg19:g.98779401C>T	ENSP00000417955:p.Ala359Val	49.0	0.0		65.0	21.0	NM_144992	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Missense_Mutation	SNP	ENST00000477737.1	hg19	CCDS42718.1	.	.	.	.	.	.	.	.	.	.	C	8.571	0.880069	0.17467	.	.	ENSG00000168658	ENST00000435344;ENST00000477737;ENST00000451075	T;T;T	0.22945	1.93;3.37;2.48	4.68	0.144	0.14824	.	0.974484	0.08412	N	0.949710	T	0.19565	0.0470	L	0.47716	1.5	0.09310	N	1	B;B;B	0.26318	0.146;0.085;0.029	B;B;B	0.19666	0.014;0.026;0.005	T	0.28038	-1.0056	10	0.31617	T	0.26	.	5.6348	0.17530	0.5569:0.3416:0.0:0.1015	.	209;359;359	B7Z7Q7;Q502W6;Q502W6-8	.;VWA3B_HUMAN;.	V	359;359;209	ENSP00000401959:A359V;ENSP00000417955:A359V;ENSP00000389463:A209V	ENSP00000411168:A359V	A	+	2	0	VWA3B	98145833	0.000000	0.05858	0.024000	0.17045	0.910000	0.53928	0.157000	0.16402	0.155000	0.19261	0.650000	0.86243	GCC	.	.		0.562	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992		T	98779401	C	T	98779401	3	4	317	1	0	0	0	0	1	0	0	0	17256	739	26	3	1102	3	VWA3B	2	98779401	Missense_Mutation	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	13946697	98779401	144419972	23	44665										
TGFBRAP1	9392	hgsc.bcm.edu	37	chr2	105890085	105890085	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	aggcaattgataatgtcgtcTggattaaaactgttcttctg	9	6	3	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr2:105890085T>A	ENST00000393359.2	-	9	2154	c.1728A>T	c.(1726-1728)ccA>ccT	p.P576P	TGFBRAP1_ENST00000258449.1_Silent_p.P576P			Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor associated protein 1	576					intracellular protein transport (GO:0006886)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|membrane (GO:0016020)	SMAD binding (GO:0046332)|small GTPase regulator activity (GO:0005083)|transforming growth factor beta receptor binding (GO:0005160)			central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	31						TAATGTCGTCTGGATTAAAAC	0.438																																					p.P576P	Esophageal Squamous(183;794 2019 9730 21801 48859)	Atlas-SNP	.											.	TGFBRAP1	70	.	0			c.A1728T						.						216	207	210					2																	105890085		2203	4300	6503	SO:0001819	synonymous_variant	9392	exon9			GTCGTCTGGATTA	AF022795	CCDS2067.1	2q12.1	2008-02-05			ENSG00000135966	ENSG00000135966			16836	protein-coding gene	gene with protein product		606237				9545258, 11278302	Standard	NM_001142621		Approved	TRAP-1, TRAP1	uc002tcr.4	Q8WUH2	OTTHUMG00000130809	ENST00000393359.2:c.1728A>T	chr2.hg19:g.105890085T>A		149.0	0.0		157.0	49.0	NM_004257	A8K5R7|D3DVJ8|O60466	Silent	SNP	ENST00000393359.2	hg19	CCDS2067.1																																																																																			.	.		0.438	TGFBRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253354.2	NM_004257		A	105890085	T	A	105890085	2	1	317	1	0	0	0	0	0	0	0	1	15839	1567	55	4		4	TGFBRAP1	2	105890085	Silent	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	7110684	105890085	137309288	24	44666										
MERTK	10461	hgsc.bcm.edu	37	chr2	112732991	112732991	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	agcattggtgtttcctgcatGaatgaaataggctggtctgc	12	7	1	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr2:112732991G>T	ENST00000295408.4	+	7	1343	c.1086G>T	c.(1084-1086)atG>atT	p.M362I	MERTK_ENST00000421804.2_Missense_Mutation_p.M362I|MERTK_ENST00000409780.1_Missense_Mutation_p.M186I			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase	362	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic cell clearance (GO:0043277)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|leukocyte migration (GO:0050900)|natural killer cell differentiation (GO:0001779)|negative regulation of lymphocyte activation (GO:0051250)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of phagocytosis (GO:0050766)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|retina development in camera-type eye (GO:0060041)|secretion by cell (GO:0032940)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|rhabdomere (GO:0016028)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(10)	46						TTTCCTGCATGAATGAAATAG	0.468																																					p.M362I		Atlas-SNP	.											.	MERTK	112	.	0			c.G1086T						.						140	134	136					2																	112732991		2203	4300	6503	SO:0001583	missense	10461	exon7			CTGCATGAATGAA	U08023	CCDS2094.1	2q14.1	2014-06-26	2014-06-26		ENSG00000153208	ENSG00000153208		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7027	protein-coding gene	gene with protein product		604705	"c-mer proto-oncogene tyrosine kinase"			8086340, 10343112	Standard	XM_005263565		Approved	mer, RP38	uc002thk.1	Q12866	OTTHUMG00000131278	ENST00000295408.4:c.1086G>T	chr2.hg19:g.112732991G>T	ENSP00000295408:p.Met362Ile	150.0	0.0		141.0	56.0	NM_006343	Q9HBB4	Missense_Mutation	SNP	ENST00000295408.4	hg19	CCDS2094.1	.	.	.	.	.	.	.	.	.	.	G	14.97	2.694470	0.48202	.	.	ENSG00000153208	ENST00000295408;ENST00000421804;ENST00000409780	T;T;T	0.55413	0.52;0.52;0.52	5.57	5.57	0.84162	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.239142	0.21365	U	0.075740	T	0.50939	0.1645	L	0.51422	1.61	0.32822	D	0.502865	B	0.24483	0.104	B	0.21917	0.037	T	0.56318	-0.7999	10	0.34782	T	0.22	-13.0059	19.1494	0.93482	0.0:0.0:1.0:0.0	.	362	Q12866	MERTK_HUMAN	I	362;362;186	ENSP00000295408:M362I;ENSP00000389152:M362I;ENSP00000387277:M186I	ENSP00000295408:M362I	M	+	3	0	MERTK	112449462	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	5.173000	0.65010	2.634000	0.89283	0.563000	0.77884	ATG	.	.		0.468	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254046.2			T	112732991	G	T	112732991	3	4	317	1	0	0	0	0	1	0	0	0	9488	1290	45	3	1112	3	MERTK	2	112732991	Missense_Mutation	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	6842906	112732991	130466382	25	44667										
DPP10	57628	hgsc.bcm.edu	37	chr2	116525912	116525912	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ctagagacggcagcaaattcTttatgacagtgcctgttaag	10	8	1	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr2:116525912T>A	ENST00000410059.1	+	13	1633	c.1153T>A	c.(1153-1155)Ttt>Att	p.F385I	DPP10_ENST00000393147.2_Missense_Mutation_p.F389I|DPP10_ENST00000310323.8_Missense_Mutation_p.F378I|DPP10_ENST00000409163.1_Missense_Mutation_p.F335I	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	385						integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						CAGCAAATTCTTTATGACAGT	0.443																																					p.F389I		Atlas-SNP	.											DPP10_ENST00000410059,NS,carcinoma,-1,2	DPP10	415	.	0			c.T1165A						.						143	137	139					2																	116525912		2203	4300	6503	SO:0001583	missense	57628	exon13			AAATTCTTTATGA	AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"dipeptidylpeptidase 10", "dipeptidyl-peptidase 10"			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.1153T>A	chr2.hg19:g.116525912T>A	ENSP00000386565:p.Phe385Ile	182.0	0.0		156.0	48.0	NM_001178034	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Missense_Mutation	SNP	ENST00000410059.1	hg19	CCDS46400.1	.	.	.	.	.	.	.	.	.	.	T	28.7	4.943034	0.92526	.	.	ENSG00000175497	ENST00000410059;ENST00000409163;ENST00000393147;ENST00000310323;ENST00000476155	T;T;T;T	0.31247	1.5;1.5;1.5;1.5	5.25	5.25	0.73442	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.43122	0.1233	L	0.31664	0.95	0.58432	D	0.999998	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.993;0.996;0.996;0.996	T	0.28776	-1.0033	10	0.45353	T	0.12	-15.5129	14.1307	0.65253	0.0:0.0:0.0:1.0	.	378;389;381;385	Q8N608-2;Q0GLB8;Q0GLB9;Q8N608	.;.;.;DPP10_HUMAN	I	385;335;389;378;335	ENSP00000386565:F385I;ENSP00000387038:F335I;ENSP00000376855:F389I;ENSP00000309066:F378I	ENSP00000309066:F378I	F	+	1	0	DPP10	116242382	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	6.898000	0.75676	2.199000	0.70637	0.533000	0.62120	TTT	.	.		0.443	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868		A	116525912	T	A	116525912	3	1	317	1	0	0	0	0	1	0	0	0	4729	1609	56	4	1374	4	DPP10	2	116525912	Missense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	3792921	116525912	126673461	26	44668										
IWS1	55677	hgsc.bcm.edu	37	chr2	128249666	128249666	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	cctggctcacactaggcagcTggggaacataaacacataca	9	12	1	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr2:128249666T>A	ENST00000295321.4	-	10	2189		c.e10-2		AC010976.2_ENST00000598065.1_RNA|AC010976.2_ENST00000599001.1_RNA|AC010976.2_ENST00000454503.2_RNA|AC010976.2_ENST00000595561.1_RNA|AC010976.2_ENST00000596439.1_RNA|IWS1_ENST00000455721.2_Splice_Site	NM_017969.2	NP_060439.2	Q96ST2	IWS1_HUMAN	IWS1 homolog (S. cerevisiae)						mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|regulation of histone H3-K36 trimethylation (GO:2001253)|regulation of histone H4 acetylation (GO:0090239)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(2)|kidney(6)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0735)		ACTAGGCAGCTGGGGAACATA	0.458																																					.		Atlas-SNP	.											.	IWS1	61	.	0			c.1930-2A>T						.						73	64	67					2																	128249666		2203	4300	6503	SO:0001630	splice_region_variant	55677	exon11			GGCAGCTGGGGAA	AK000868	CCDS2146.1	2q14.3	2006-03-17			ENSG00000163166	ENSG00000163166			25467	protein-coding gene	gene with protein product							Standard	NM_017969		Approved	DKFZp761G0123, FLJ10006, FLJ14655, FLJ32319	uc002ton.2	Q96ST2	OTTHUMG00000131527	ENST00000295321.4:c.1930-2A>T	chr2.hg19:g.128249666T>A		113.0	0.0		127.0	38.0	NM_017969	Q2TB65|Q6P157|Q8N3E8|Q96MI7|Q9NV97|Q9NWH8	Splice_Site	SNP	ENST00000295321.4	hg19	CCDS2146.1	.	.	.	.	.	.	.	.	.	.	T	26.5	4.743126	0.89663	.	.	ENSG00000163166	ENST00000295321;ENST00000433551	.	.	.	5.2	5.2	0.72013	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1355	0.72562	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	IWS1	127966136	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.789000	0.85783	1.969000	0.57287	0.456000	0.33151	.	.	.		0.458	IWS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254384.2	NM_017969	Intron	A	128249666	T	A	128249666	5	1	317	1	0	0	0	0	0	0	1	0	7940	1594	55	4	551	4	IWS1	2	128249666	Splice_Site	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	11723754	128249666	114949707	27	44669										
LCT	3938	hgsc.bcm.edu	37	chr2	136567010	136567010	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	aagcggtaggccttcaccttCaaagctcggagcatattcag	10	11	3	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr2:136567010C>T	ENST00000264162.2	-	8	2917	c.2907G>A	c.(2905-2907)ttG>ttA	p.L969L	Y_RNA_ENST00000363794.1_RNA	NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	969	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	CCTTCACCTTCAAAGCTCGGA	0.507																																					p.L969L		Atlas-SNP	.											.	LCT	309	.	0			c.G2907A						.						88	90	89					2																	136567010		2203	4300	6503	SO:0001819	synonymous_variant	3938	exon8			CACCTTCAAAGCT	X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.2907G>A	chr2.hg19:g.136567010C>T		108.0	0.0		81.0	18.0	NM_002299	Q4ZG58	Silent	SNP	ENST00000264162.2	hg19	CCDS2178.1																																																																																			.	.		0.507	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299		T	136567010	C	T	136567010	2	4	317	1	0	0	0	0	0	0	0	1	8702	825	29	3		3	LCT	2	136567010	Silent	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	8317344	136567010	106632363	28	44670										
PDE11A	50940	hgsc.bcm.edu	37	chr2	178494226	178494226	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tttggtgtagctcttcccacTtacttctgtttgtagctact	7	10	2	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr2:178494226T>A	ENST00000286063.6	-	20	3028	c.2711A>T	c.(2710-2712)aAg>aTg	p.K904M	PDE11A_ENST00000449286.2_Missense_Mutation_p.K546M|PDE11A_ENST00000358450.4_Missense_Mutation_p.K654M|PDE11A_ENST00000389683.3_Missense_Mutation_p.K460M|PDE11A_ENST00000450799.2_Missense_Mutation_p.K95M|PDE11A_ENST00000409504.1_Missense_Mutation_p.K546M	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	904	Catalytic. {ECO:0000250}.				blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|signal transduction (GO:0007165)	cytosol (GO:0005829)|perikaryon (GO:0043204)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)		Caffeine(DB00201)|Tadalafil(DB00820)	CTCTTCCCACTTACTTCTGTT	0.478									Primary Pigmented Nodular Adrenocortical Disease, Familial																												p.K904M		Atlas-SNP	.											.	PDE11A	283	.	0			c.A2711T						.						290	244	260					2																	178494226		2203	4300	6503	SO:0001583	missense	50940	exon20	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	TCCCACTTACTTC	AJ251509	CCDS33334.1, CCDS42785.1, CCDS42786.1, CCDS46459.1	2q31.3	2010-06-22			ENSG00000128655	ENSG00000128655	3.1.4.17	"Phosphodiesterases"	8773	protein-coding gene	gene with protein product		604961				10725373	Standard	NM_001077196		Approved		uc002ulq.3	Q9HCR9	OTTHUMG00000154188	ENST00000286063.6:c.2711A>T	chr2.hg19:g.178494226T>A	ENSP00000286063:p.Lys904Met	220.0	0.0		243.0	76.0	NM_016953	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	Missense_Mutation	SNP	ENST00000286063.6	hg19	CCDS33334.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.1|25.1	4.599654|4.599654	0.87055|0.87055	.|.	.|.	ENSG00000128655|ENSG00000128655	ENST00000286063;ENST00000358450;ENST00000450799;ENST00000409504;ENST00000389683;ENST00000449286|ENST00000436700	T;T;T;T;T;T|.	0.77098|.	-1.07;-1.07;-1.07;-1.07;-1.07;-1.07|.	5.62|5.62	5.62|5.62	0.85841|0.85841	5&apos (1);-cyclic nucleotide phosphodiesterase, catalytic domain (1);3&apos (1);|.	0.046341|.	0.85682|.	D|.	0.000000|.	T|.	0.48857|.	0.1523|.	N|N	0.14661|0.14661	0.345|0.345	0.58432|0.58432	D|D	0.999995|0.999995	D;D|.	0.64830|.	0.994;0.988|.	P;P|.	0.58873|.	0.847;0.635|.	T|.	0.46414|.	-0.9193|.	10|.	0.72032|.	D|.	0.01|.	.|.	15.8132|15.8132	0.78581|0.78581	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	654;904|.	Q9HCR9-2;Q9HCR9|.	.;PDE11_HUMAN|.	M|Y	904;654;95;546;460;546|106	ENSP00000286063:K904M;ENSP00000351232:K654M;ENSP00000387964:K95M;ENSP00000386539:K546M;ENSP00000374333:K460M;ENSP00000390599:K546M|.	ENSP00000286063:K904M|.	K|X	-|-	2|3	0|2	PDE11A|PDE11A	178202472|178202472	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.958000|0.958000	0.62258|0.62258	5.722000|5.722000	0.68485|0.68485	2.144000|2.144000	0.66660|0.66660	0.482000|0.482000	0.46254|0.46254	AAG|TAA	.	.		0.478	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2			A	178494226	T	A	178494226	3	1	317	1	0	0	0	0	1	0	0	0	11640	1609	56	4	94	4	PDE11A	2	178494226	Missense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	41927216	178494226	64705147	29	44671										
TTN	7273	hgsc.bcm.edu	37	chr2	179641996	179641996	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gggaaccttcctttatattgAcatttttcagtttttctaca	5	8	2	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr2:179641996A>G	ENST00000591111.1	-	27	4918	c.4694T>C	c.(4693-4695)gTc>gCc	p.V1565A	TTN_ENST00000360870.5_Missense_Mutation_p.V1565A|TTN_ENST00000342175.6_Missense_Mutation_p.V1519A|TTN_ENST00000359218.5_Missense_Mutation_p.V1519A|TTN_ENST00000460472.2_Missense_Mutation_p.V1519A|TTN-AS1_ENST00000584485.1_RNA|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V1565A|TTN-AS1_ENST00000585451.1_RNA|RP11-88L24.4_ENST00000582038.2_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.V1565A			Q8WZ42	TITIN_HUMAN	titin	12422	Ig-like 7.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTTTATATTGACATTTTTCAG	0.398																																					p.V1565A		Atlas-SNP	.											.	TTN	18412	.	0			c.T4694C						.						126	118	120					2																	179641996		2203	4300	6503	SO:0001583	missense	7273	exon27			ATATTGACATTTT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.4694T>C	chr2.hg19:g.179641996A>G	ENSP00000465570:p.Val1565Ala	76.0	0.0		99.0	22.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	8.113	0.779292	0.16120	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.70282	-0.47;-0.47;-0.47;-0.47;-0.47	5.9	5.9	0.94986	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.65873	0.2733	L	0.52011	1.625	0.28910	N	0.892782	B;B;B;B;B	0.34329	0.052;0.052;0.052;0.052;0.449	B;B;B;B;B	0.26094	0.055;0.055;0.055;0.055;0.066	T	0.67225	-0.5724	9	0.87932	D	0	.	16.3228	0.82958	1.0:0.0:0.0:0.0	.	1519;1519;1519;1565;1565	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	A	1565;1519;1519;1519;1519;1565	ENSP00000343764:V1565A;ENSP00000434586:V1519A;ENSP00000340554:V1519A;ENSP00000352154:V1519A;ENSP00000354117:V1565A	ENSP00000340554:V1519A	V	-	2	0	TTN	179350241	1.000000	0.71417	0.996000	0.52242	0.143000	0.21401	9.265000	0.95647	2.262000	0.75019	0.528000	0.53228	GTC	.	.		0.398	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179641996	A	G	179641996	3	3	317	1	0	0	0	0	1	0	0	0	16750	275	10	2	106638	2	TTN	2	179641996	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	1147770	179641996	63557377	30	44672										
NCKAP1	10787	hgsc.bcm.edu	37	chr2	183866687	183866687	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	caactgcctcttaccttgctAtggggtacaaattcttccat	6	12	2	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr2:183866687A>G	ENST00000361354.4	-	6	969	c.597T>C	c.(595-597)caT>caC	p.H199H	NCKAP1_ENST00000360982.2_Silent_p.H205H	NM_013436.3	NP_038464.1	Q9Y2A7	NCKP1_HUMAN	NCK-associated protein 1	199					apical protein localization (GO:0045176)|apoptotic process (GO:0006915)|basal protein localization (GO:0045175)|central nervous system development (GO:0007417)|embryonic body morphogenesis (GO:0010172)|embryonic foregut morphogenesis (GO:0048617)|embryonic heart tube development (GO:0035050)|endoderm development (GO:0007492)|establishment or maintenance of actin cytoskeleton polarity (GO:0030950)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|mesodermal cell migration (GO:0008078)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|paraxial mesoderm morphogenesis (GO:0048340)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|positive regulation of lamellipodium assembly (GO:0010592)|protein stabilization (GO:0050821)|Rac protein signal transduction (GO:0016601)|regulation of protein localization (GO:0032880)|somitogenesis (GO:0001756)|zygotic determination of anterior/posterior axis, embryo (GO:0007354)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|SCAR complex (GO:0031209)	protein complex binding (GO:0032403)			breast(3)|cervix(2)|endometrium(3)|kidney(4)|large_intestine(11)|lung(16)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			TTACCTTGCTATGGGGTACAA	0.383																																					p.H205H		Atlas-SNP	.											.	NCKAP1	105	.	0			c.T615C						.						138	127	131					2																	183866687		2203	4300	6503	SO:0001819	synonymous_variant	10787	exon7			CTTGCTATGGGGT	AB014509	CCDS2287.1, CCDS2288.1	2q32	2009-08-14			ENSG00000061676	ENSG00000061676			7666	protein-coding gene	gene with protein product		604891				10673335, 12181570, 9344857	Standard	NM_013436		Approved	Nap1, HEM2, NAP125	uc002upb.4	Q9Y2A7	OTTHUMG00000132623	ENST00000361354.4:c.597T>C	chr2.hg19:g.183866687A>G		252.0	0.0		283.0	77.0	NM_205842	O60329|Q53QN5|Q53S94|Q53Y35	Silent	SNP	ENST00000361354.4	hg19	CCDS2287.1																																																																																			.	.		0.383	NCKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255867.2	NM_205842		G	183866687	A	G	183866687	2	3	317	1	0	0	0	0	0	0	0	1	10230	446	16	2		2	NCKAP1	2	183866687	Silent	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	4224691	183866687	59332686	31	44673										
ZDBF2	57683	hgsc.bcm.edu	37	chr2	207176232	207176232	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tacacctgtgagagcatatgAtctgagaagctcatcttgtt	9	8	3	3			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr2:207176232A>T	ENST00000374423.3	+	5	7366	c.6980A>T	c.(6979-6981)gAt>gTt	p.D2327V		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	2327							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						AGAGCATATGATCTGAGAAGC	0.458																																					p.D2327V		Atlas-SNP	.											.	ZDBF2	531	.	0			c.A6980T						.						46	47	47					2																	207176232		1934	4147	6081	SO:0001583	missense	57683	exon5			CATATGATCTGAG	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"Zinc fingers, DBF-type"	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.6980A>T	chr2.hg19:g.207176232A>T	ENSP00000363545:p.Asp2327Val	309.0	0.0		289.0	74.0	NM_020923	Q6ZNP7|Q6ZSN8	Missense_Mutation	SNP	ENST00000374423.3	hg19	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	A	13.07	2.128475	0.37533	.	.	ENSG00000204186	ENST00000374423	T	0.50813	0.73	5.09	-10.2	0.00374	.	.	.	.	.	T	0.21468	0.0517	N	0.02011	-0.69	0.09310	N	0.999999	B	0.19706	0.038	B	0.19391	0.025	T	0.42327	-0.9458	9	0.62326	D	0.03	.	18.0918	0.89477	0.1267:0.7882:0.0:0.0851	.	2327	Q9HCK1	ZDBF2_HUMAN	V	2327	ENSP00000363545:D2327V	ENSP00000363545:D2327V	D	+	2	0	ZDBF2	206884477	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.575000	0.05861	-1.159000	0.02807	-0.435000	0.05868	GAT	.	.		0.458	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		T	207176232	A	T	207176232	3	4	317	1	0	0	0	0	1	0	0	0	17614	333	12	4	6990	4	ZDBF2	2	207176232	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	23309545	207176232	36023141	32	44674										
ANKMY1	51281	hgsc.bcm.edu	37	chr2	241463387	241463387	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	cgaggccatcttcagcaagcTgtgggactgggcgcttctct	13	12	3	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr2:241463387T>A	ENST00000272972.3	-	7	1694	c.1480A>T	c.(1480-1482)Agc>Tgc	p.S494C	ANKMY1_ENST00000401804.1_Missense_Mutation_p.S583C|ANKMY1_ENST00000373318.2_Missense_Mutation_p.S353C|ANKMY1_ENST00000373320.4_Missense_Mutation_p.S264C|ANKMY1_ENST00000361678.4_Missense_Mutation_p.S353C|ANKMY1_ENST00000391987.1_Missense_Mutation_p.S494C|ANKMY1_ENST00000462004.1_5'Flank|ANKMY1_ENST00000536462.1_Missense_Mutation_p.S306C|ANKMY1_ENST00000403283.1_Missense_Mutation_p.S432C|ANKMY1_ENST00000405523.3_Missense_Mutation_p.S353C|ANKMY1_ENST00000405002.1_Missense_Mutation_p.S264C|ANKMY1_ENST00000406958.1_Missense_Mutation_p.S255C	NM_016552.2	NP_057636.2	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1	494							metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	30		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.03e-30)|all cancers(36;4.78e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.45e-14)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.8e-06)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.01)|Colorectal(34;0.0101)|COAD - Colon adenocarcinoma(134;0.0476)		TTCAGCAAGCTGTGGGACTGG	0.592																																					p.S494C		Atlas-SNP	.											.	ANKMY1	112	.	0			c.A1480T						.						91	83	86					2																	241463387		2203	4300	6503	SO:0001583	missense	51281	exon7			GCAAGCTGTGGGA	AB034636	CCDS2535.1, CCDS2536.1, CCDS63184.1, CCDS63185.1, CCDS74681.1	2q37.3	2013-01-10			ENSG00000144504	ENSG00000144504		"Zinc fingers, MYND-type", "Ankyrin repeat domain containing"	20987	protein-coding gene	gene with protein product							Standard	XM_005247020		Approved	FLJ20499, ZMYND13	uc002vyz.1	Q9P2S6	OTTHUMG00000133355	ENST00000272972.3:c.1480A>T	chr2.hg19:g.241463387T>A	ENSP00000272972:p.Ser494Cys	63.0	0.0		63.0	18.0	NM_016552	B2RB78|Q4ZFV3|Q8IYX5|Q8NDK5|Q9H0V8|Q9NX10	Missense_Mutation	SNP	ENST00000272972.3	hg19	CCDS2536.1	.	.	.	.	.	.	.	.	.	.	T	15.22	2.769843	0.49680	.	.	ENSG00000144504	ENST00000373318;ENST00000406958;ENST00000272972;ENST00000361678;ENST00000391987;ENST00000373320;ENST00000403283;ENST00000401804;ENST00000536462;ENST00000405523;ENST00000405002	T;T;T;T;T;T;T;T;T;T;T	0.60424	2.65;3.48;0.19;1.96;0.19;4.12;2.2;0.21;1.76;1.82;2.06	4.06	2.89	0.33648	Ankyrin repeat-containing domain (1);	0.873356	0.09919	N	0.738663	T	0.61664	0.2365	L	0.34521	1.04	0.09310	N	1	D;D;D;D;D;D;D	0.89917	0.993;1.0;0.999;0.999;0.999;0.999;0.993	P;D;D;P;D;D;P	0.68353	0.72;0.957;0.935;0.907;0.948;0.947;0.72	T	0.46693	-0.9173	10	0.42905	T	0.14	-21.5812	6.4404	0.21847	0.0:0.1202:0.0:0.8798	.	494;306;264;353;255;353;494	Q4ZFV3;F5H558;Q9P2S6-4;Q6GPI0;B5MBY4;Q9P2S6-2;Q9P2S6	.;.;.;.;.;.;ANKY1_HUMAN	C	353;255;494;353;494;264;432;583;306;353;264	ENSP00000362415:S353C;ENSP00000384555:S255C;ENSP00000272972:S494C;ENSP00000355097:S353C;ENSP00000375847:S494C;ENSP00000362417:S264C;ENSP00000383968:S432C;ENSP00000385887:S583C;ENSP00000444707:S306C;ENSP00000385635:S353C;ENSP00000385145:S264C	ENSP00000272972:S494C	S	-	1	0	ANKMY1	241112060	0.000000	0.05858	0.008000	0.14137	0.019000	0.09904	-0.265000	0.08644	0.683000	0.31428	0.402000	0.26972	AGC	.	.		0.592	ANKMY1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257187.2	NM_017844		A	241463387	T	A	241463387	3	1	317	1	0	0	0	0	1	0	0	0	634	1580	55	4	1389	4	ANKMY1	2	241463387	Missense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	34287155	241463387	1735986	33	44675										
AGXT	189	hgsc.bcm.edu	37	chr2	241813413	241813413	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	aggcatcgacatcctgtactCgggctcccagaaggccctga	11	14	0	2	rs180177248		TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr2:241813413C>T	ENST00000307503.3	+	6	1001	c.614C>T	c.(613-615)tCg>tTg	p.S205L		NM_000030.2	NP_000021.1	P21549	SPYA_HUMAN	alanine-glyoxylate aminotransferase	205			S -> P (in HP1). {ECO:0000269|PubMed:2039493}.		cellular nitrogen compound metabolic process (GO:0034641)|glycine biosynthetic process, by transamination of glyoxylate (GO:0019265)|glyoxylate catabolic process (GO:0009436)|glyoxylate metabolic process (GO:0046487)|L-alanine catabolic process (GO:0042853)|L-cysteine catabolic process (GO:0019448)|oxalic acid secretion (GO:0046724)|pyruvate biosynthetic process (GO:0042866)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	alanine-glyoxylate transaminase activity (GO:0008453)|amino acid binding (GO:0016597)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|receptor binding (GO:0005102)|serine-pyruvate transaminase activity (GO:0004760)|transaminase activity (GO:0008483)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)	18		all_epithelial(40;1.61e-15)|Breast(86;2.35e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;8.14e-32)|all cancers(36;4.77e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;4.88e-06)|Lung(119;0.000452)|LUSC - Lung squamous cell carcinoma(224;0.00415)|Colorectal(34;0.021)|COAD - Colon adenocarcinoma(134;0.15)	Glycine(DB00145)|L-Alanine(DB00160)|L-Serine(DB00133)	ATCCTGTACTCGGGCTCCCAG	0.622																																					p.S205L		Atlas-SNP	.											.	AGXT	50	.	0			c.C614T						.						112	97	102					2																	241813413		2203	4300	6503	SO:0001583	missense	189	exon6			TGTACTCGGGCTC	D13368	CCDS2543.1	2q37.3	2008-02-05	2007-04-13		ENSG00000172482	ENSG00000172482	2.6.1.44, 2.6.1.51		341	protein-coding gene	gene with protein product	"oxalosis I", "primary hyperoxaluria type 1", "L-alanine: glyoxylate aminotransferase 1", "serine:pyruvate aminotransferase", "glycolicaciduria"	604285		SPAT		2039493, 2045108	Standard	NM_000030		Approved	AGXT1, PH1, AGT, SPT, AGT1	uc002waa.4	P21549	OTTHUMG00000133354	ENST00000307503.3:c.614C>T	chr2.hg19:g.241813413C>T	ENSP00000302620:p.Ser205Leu	41.0	0.0		45.0	22.0	NM_000030	Q53QU6	Missense_Mutation	SNP	ENST00000307503.3	hg19	CCDS2543.1	.	.	.	.	.	.	.	.	.	.	C	14.71	2.616531	0.46736	.	.	ENSG00000172482	ENST00000307503	D	0.86230	-2.09	4.1	4.1	0.47936	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	0.377799	0.29572	N	0.011764	D	0.94719	0.8296	M	0.91038	3.17	0.52501	D	0.999952	D	0.89917	1.0	D	0.87578	0.998	D	0.96145	0.9103	10	0.87932	D	0	-9.0683	16.6951	0.85333	0.0:1.0:0.0:0.0	.	205	P21549	SPYA_HUMAN	L	205	ENSP00000302620:S205L	ENSP00000302620:S205L	S	+	2	0	AGXT	241462086	0.998000	0.40836	0.213000	0.23690	0.006000	0.05464	4.052000	0.57420	2.008000	0.58898	0.579000	0.79373	TCG	.	.		0.622	AGXT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257186.1	NM_000030		T	241813413	C	T	241813413	3	4	317	1	0	0	0	0	1	0	0	0	404	893	31	1	636	1	AGXT	2	241813413	Missense_Mutation	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	350026	241813413	1385960	34	44676										
EAF1	85403	hgsc.bcm.edu	37	chr3	15475936	15475936	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	acgtcacagccaccaccaccTccaccacctatgccattcag	4	20	2	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr3:15475936T>G	ENST00000396842.2	+	4	842	c.417T>G	c.(415-417)ccT>ccG	p.P139P	RNU6-1024P_ENST00000384199.1_RNA|EAF1-AS1_ENST00000597949.1_RNA|EAF1_ENST00000432764.2_Silent_p.P38P	NM_033083.6	NP_149074.3	Q96JC9	EAF1_HUMAN	ELL associated factor 1	139	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ELL-EAF complex (GO:0032783)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|urinary_tract(1)	7						CACCACCACCTCCACCACCTA	0.537																																					p.P139P		Atlas-SNP	.											.	EAF1	16	.	0			c.T417G						.						276	253	260					3																	15475936		2203	4300	6503	SO:0001819	synonymous_variant	85403	exon4			ACCACCTCCACCA	AF272973	CCDS2626.1	3p25.1	2011-06-10			ENSG00000144597	ENSG00000144597			20907	protein-coding gene	gene with protein product		608315				11418481	Standard	NM_033083		Approved		uc003bzu.3	Q96JC9	OTTHUMG00000162544	ENST00000396842.2:c.417T>G	chr3.hg19:g.15475936T>G		97.0	0.0		75.0	29.0	NM_033083	B4E3F5|Q8IW10	Silent	SNP	ENST00000396842.2	hg19	CCDS2626.1																																																																																			.	.		0.537	EAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252100.4	NM_033083		G	15475936	T	G	15475936	2	3	317	1	0	0	0	0	0	0	0	1	4877	1538	54	5		5	EAF1	3	15475936	Silent	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10		15475936	182546494	35	44677										
KAT2B	8850	hgsc.bcm.edu	37	chr3	20156480	20156482	+	Splice_Site	TNP	GGT	GGT	TTG													0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gccagctaggcatccaaacaGgtaagtttccttttacatga							TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G|G|T	G|G|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr3:20156480_20156482GGT>TTG	ENST00000263754.4	+	7	1605	c.1150_1150GGT>TTG	c.(1150-1152)GGTgt>TTGgtgt	p.384_384G>LV		NM_003884.4	NP_003875.3	Q92831	KAT2B_HUMAN	K(lysine) acetyltransferase 2B	384					cell cycle arrest (GO:0007050)|cellular response to insulin stimulus (GO:0032869)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|histone H3-K9 acetylation (GO:0043970)|internal peptidyl-lysine acetylation (GO:0018393)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|Notch signaling pathway (GO:0007219)|peptidyl-lysine acetylation (GO:0018394)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein acetylation (GO:0006473)|regulation of protein ADP-ribosylation (GO:0010835)|rhythmic process (GO:0048511)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	A band (GO:0031672)|actomyosin (GO:0042641)|Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|I band (GO:0031674)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)	acetyltransferase activity (GO:0016407)|cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|histone acetyltransferase activity (GO:0004402)|histone deacetylase binding (GO:0042826)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	40						CATCCAAACAGGTAAGTTTCCTT	0.433																																					p.V384F|.|.		Atlas-SNP	.											.	KAT2B	73	.	0			c.G1150T|c.1150+1G>T|c.1150+2T>G						.																																			SO:0001630	splice_region_variant	8850	exon7			CAAACAGGTAAGT|AAACAGGTAAGTT|AACAGGTAAGTTT	U57316	CCDS2634.1	3p24	2011-07-01	2008-07-04	2008-07-04	ENSG00000114166	ENSG00000114166		"Chromatin-modifying enzymes / K-acetyltransferases"	8638	protein-coding gene	gene with protein product		602303	"p300/CBP-associated factor"	PCAF		8684459, 9722949	Standard	NM_003884		Approved	P/CAF, GCN5, GCN5L	uc003cbq.3	Q92831	OTTHUMG00000130481	ENST00000263754.4:c.1150+1GGT>TTG	chr3.hg19:g.20156480GGT>TTG		147.0|142.0|143.0	0.0		86.0|84.0|83.0	30.0	NM_003884	Q6NSK1	Missense_Mutation|Splice_Site|Splice_Site	SNP	ENST00000263754.4	hg19	CCDS2634.1																																																																																			.	.		0.433	KAT2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252880.1	NM_003884	Missense_Mutation	TTG	20156482	GGT	TTG	20156480	5	4	317	1	0	0	0	0	0	0	1	0	7991	1014	35	3	1176	3	KAT2B	3	20156480	Splice_Site	TNP	GGT	TCGA-LG-A6GG-01A-11D-A30V-10	4680544	20156480	177865950	36	44678										
DLEC1	9940	hgsc.bcm.edu	37	chr3	38158025	38158025	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gctggtgttttatgggccacCtttcccgctgcgggaccaag	13	12	0	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr3:38158025C>T	ENST00000308059.6	+	28	3959	c.3938C>T	c.(3937-3939)cCt>cTt	p.P1313L	DLEC1_ENST00000346219.3_Missense_Mutation_p.P1313L|DLEC1_ENST00000452631.2_Missense_Mutation_p.P1316L					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		TATGGGCCACCTTTCCCGCTG	0.607																																					p.P1313L		Atlas-SNP	.											.	DLEC1	278	.	0			c.C3938T						.						51	55	53					3																	38158025		1999	4158	6157	SO:0001583	missense	9940	exon28			GGCCACCTTTCCC	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"cilia and flagella associated protein 81"	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.3938C>T	chr3.hg19:g.38158025C>T	ENSP00000308597:p.Pro1313Leu	96.0	0.0		81.0	31.0	NM_007337		Missense_Mutation	SNP	ENST00000308059.6	hg19	CCDS2672.2	.	.	.	.	.	.	.	.	.	.	C	15.15	2.748585	0.49257	.	.	ENSG00000008226	ENST00000308059;ENST00000346219;ENST00000452631	T;T;T	0.08458	3.13;3.09;3.36	5.08	3.24	0.37175	.	0.222183	0.37809	N	0.001934	T	0.25044	0.0608	M	0.75264	2.295	0.58432	D	0.999994	D;D;D;D	0.89917	0.999;0.976;0.999;1.0	D;P;D;D	0.78314	0.984;0.629;0.984;0.991	T	0.00366	-1.1786	10	0.72032	D	0.01	-7.1893	9.1685	0.37065	0.0:0.7695:0.1482:0.0823	.	1316;1313;1313;1313	F8W6T4;B7ZW06;Q9Y238-3;Q9Y238	.;.;.;DLEC1_HUMAN	L	1313;1313;1316	ENSP00000308597:P1313L;ENSP00000315914:P1313L;ENSP00000410427:P1316L	ENSP00000308597:P1313L	P	+	2	0	DLEC1	38133029	0.000000	0.05858	0.528000	0.27938	0.235000	0.25334	0.484000	0.22308	0.512000	0.28257	0.462000	0.41574	CCT	.	.		0.607	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337		T	38158025	C	T	38158025	3	4	317	1	0	0	0	0	1	0	0	0	4554	681	24	3	4048	3	DLEC1	3	38158025	Missense_Mutation	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	18001545	38158025	159864405	37	44679										
SCAP	22937	hgsc.bcm.edu	37	chr3	47461017	47461017	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tagcttaggggcatcaggtgGgaagatggagaaggcagggt	19	4	1	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr3:47461017G>T	ENST00000265565.5	-	13	2153	c.1741C>A	c.(1741-1743)Cca>Aca	p.P581T	SCAP_ENST00000545718.1_Missense_Mutation_p.P189T|SCAP_ENST00000465628.1_5'Flank|SCAP_ENST00000441517.2_Missense_Mutation_p.P326T	NM_012235.2	NP_036367.2	Q12770	SCAP_HUMAN	SREBF chaperone	581					aging (GO:0007568)|cholesterol metabolic process (GO:0008203)|negative regulation of cholesterol biosynthetic process (GO:0045541)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|regulation of fatty acid biosynthetic process (GO:0042304)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)	unfolded protein binding (GO:0051082)			endometrium(4)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	26				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)		GCATCAGGTGGGAAGATGGAG	0.642																																					p.P581T	Pancreas(149;978 1908 29304 37806 46700)	Atlas-SNP	.											.	SCAP	88	.	0			c.C1741A						.						77	77	77					3																	47461017		2203	4300	6503	SO:0001583	missense	22937	exon13			CAGGTGGGAAGAT	BC020987	CCDS2755.2	3p21.31	2013-01-10			ENSG00000114650	ENSG00000114650		"WD repeat domain containing"	30634	protein-coding gene	gene with protein product	"SREBP cleavage activating protein"	601510				8898195, 8724849, 10570913	Standard	XM_005264967		Approved	KIAA0199	uc003crh.1	Q12770	OTTHUMG00000125539	ENST00000265565.5:c.1741C>A	chr3.hg19:g.47461017G>T	ENSP00000265565:p.Pro581Thr	128.0	0.0		97.0	35.0	NM_012235	Q8N2E0|Q8WUA1	Missense_Mutation	SNP	ENST00000265565.5	hg19	CCDS2755.2	.	.	.	.	.	.	.	.	.	.	G	17.36	3.370887	0.61624	.	.	ENSG00000114650	ENST00000360832;ENST00000265565;ENST00000441517;ENST00000545718	T;T;T	0.79749	-1.3;-1.25;0.88	4.33	3.43	0.39272	.	0.058060	0.64402	D	0.000001	T	0.81475	0.4830	L	0.60455	1.87	0.41946	D	0.990631	P;B	0.51653	0.947;0.021	P;B	0.49853	0.624;0.03	T	0.81600	-0.0859	10	0.44086	T	0.13	-4.3161	13.7526	0.62917	0.0:0.1555:0.8445:0.0	.	326;581	F8W921;Q12770	.;SCAP_HUMAN	T	208;581;326;189	ENSP00000265565:P581T;ENSP00000416847:P326T;ENSP00000438956:P189T	ENSP00000265565:P581T	P	-	1	0	SCAP	47436021	1.000000	0.71417	0.999000	0.59377	0.943000	0.58893	5.060000	0.64312	0.990000	0.38787	0.462000	0.41574	CCA	.	.		0.642	SCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246872.2	NM_012235		T	47461017	G	T	47461017	3	4	317	1	0	0	0	0	1	0	0	0	13892	1232	43	3	2142	3	SCAP	3	47461017	Missense_Mutation	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	9302992	47461017	150561413	38	44680										
PDZRN3	23024	hgsc.bcm.edu	37	chr3	73432795	73432795	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tgctgcttcctctcctccttGctccagtagcgccccatctt	6	18	2	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr3:73432795G>T	ENST00000263666.4	-	10	3036	c.2922C>A	c.(2920-2922)agC>agA	p.S974R	PDZRN3_ENST00000479530.1_Missense_Mutation_p.S691R|PDZRN3_ENST00000535920.1_Missense_Mutation_p.S696R|PDZRN3_ENST00000466780.1_Missense_Mutation_p.S631R|PDZRN3_ENST00000466348.1_5'Flank|PDZRN3_ENST00000462146.2_Missense_Mutation_p.S631R	NM_015009.1	NP_055824.1	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	974					neuromuscular junction development (GO:0007528)|protein ubiquitination (GO:0016567)	neuromuscular junction (GO:0031594)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(31)|ovary(4)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		TCTCCTCCTTGCTCCAGTAGC	0.642																																					p.S974R		Atlas-SNP	.											.	PDZRN3	196	.	0			c.C2922A						.						105	101	102					3																	73432795		2203	4300	6503	SO:0001583	missense	23024	exon10			CTCCTTGCTCCAG	AB029018	CCDS33789.1	3p14.1	2013-01-09	2008-08-14		ENSG00000121440	ENSG00000121440		"RING-type (C3HC4) zinc fingers"	17704	protein-coding gene	gene with protein product	"likely ortholog of mouse semaF cytoplasmic domain associated protein 3"	609729				10470851	Standard	XM_005264718		Approved	KIAA1095, SEMACAP3, LNX3	uc003dpl.1	Q9UPQ7	OTTHUMG00000158865	ENST00000263666.4:c.2922C>A	chr3.hg19:g.73432795G>T	ENSP00000263666:p.Ser974Arg	70.0	0.0		44.0	16.0	NM_015009	A7MCZ6|Q8N2N7|Q96CC2|Q9NSQ2	Missense_Mutation	SNP	ENST00000263666.4	hg19	CCDS33789.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	18.26|18.26|18.26	3.584098|3.584098|3.584098	0.65992|0.65992|0.65992	.|.|.	.|.|.	ENSG00000121440|ENSG00000121440|ENSG00000121440	ENST00000494559|ENST00000416926|ENST00000263666;ENST00000535920;ENST00000462146;ENST00000466780;ENST00000479530	.|.|T;T;T;T;T	.|.|0.75589	.|.|-0.95;-0.95;-0.95;-0.95;-0.95	5.53|5.53|5.53	4.63|4.63|4.63	0.57726|0.57726|0.57726	.|.|.	.|.|0.000000	.|.|0.85682	.|.|D	.|.|0.000000	D|D|D	0.83972|0.83972|0.83972	0.5370|0.5370|0.5370	M|M|M	0.75777|0.75777|0.75777	2.31|2.31|2.31	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|.|D;D;D;D	.|.|0.89917	.|.|0.999;1.0;0.998;0.999	.|.|D;D;D;D	.|.|0.85130	.|.|0.991;0.997;0.969;0.993	D|D|D	0.84852|0.84852|0.84852	0.0814|0.0814|0.0814	5|6|10	.|0.59425|0.87932	.|D|D	.|0.04|0	.|.|.	9.7339|9.7339|9.7339	0.40376|0.40376|0.40376	0.0747:0.0:0.7829:0.1423|0.0747:0.0:0.7829:0.1423|0.0747:0.0:0.7829:0.1423	.|.|.	.|.|696;691;691;974	.|.|F5H8I9;B7ZAG0;B7Z5X9;Q9UPQ7	.|.|.;.;.;PZRN3_HUMAN	E|K|R	290|694|974;696;631;631;691	.|.|ENSP00000263666:S974R;ENSP00000442026:S696R;ENSP00000418168:S631R;ENSP00000418484:S631R;ENSP00000418624:S691R	.|ENSP00000392657:Q694K|ENSP00000263666:S974R	A|Q|S	-|-|-	2|1|3	0|0|2	PDZRN3|PDZRN3|PDZRN3	73515485|73515485|73515485	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.984000|0.984000|0.984000	0.73092|0.73092|0.73092	7.519000|7.519000|7.519000	0.81809|0.81809|0.81809	1.254000|1.254000|1.254000	0.44035|0.44035|0.44035	0.563000|0.563000|0.563000	0.77884|0.77884|0.77884	GCA|CAA|AGC	.	.		0.642	PDZRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352460.1	XM_041363		T	73432795	G	T	73432795	3	4	317	1	0	0	0	0	1	0	0	0	11718	1310	46	3	282	3	PDZRN3	3	73432795	Missense_Mutation	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	25971778	73432795	124589635	39	44681										
PDZRN3	23024	hgsc.bcm.edu	37	chr3	73673351	73673351	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	agcgcagcgcggtcatctgcAgctcaagctgcgccgcggcc	14	16	3	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr3:73673351A>C	ENST00000263666.4	-	1	740	c.626T>G	c.(625-627)cTg>cGg	p.L209R	PDZRN3-AS1_ENST00000478988.1_RNA|PDZRN3-AS1_ENST00000608304.1_RNA|PDZRN3_ENST00000308537.4_Missense_Mutation_p.L209R|PDZRN3-AS1_ENST00000608743.1_RNA	NM_015009.1	NP_055824.1	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	209					neuromuscular junction development (GO:0007528)|protein ubiquitination (GO:0016567)	neuromuscular junction (GO:0031594)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(31)|ovary(4)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		GGTCATCTGCAGCTCAAGCTG	0.701																																					p.L209R		Atlas-SNP	.											.	PDZRN3	196	.	0			c.T626G						.						4	4	4					3																	73673351		1905	3829	5734	SO:0001583	missense	23024	exon1			ATCTGCAGCTCAA	AB029018	CCDS33789.1	3p14.1	2013-01-09	2008-08-14		ENSG00000121440	ENSG00000121440		"RING-type (C3HC4) zinc fingers"	17704	protein-coding gene	gene with protein product	"likely ortholog of mouse semaF cytoplasmic domain associated protein 3"	609729				10470851	Standard	XM_005264718		Approved	KIAA1095, SEMACAP3, LNX3	uc003dpl.1	Q9UPQ7	OTTHUMG00000158865	ENST00000263666.4:c.626T>G	chr3.hg19:g.73673351A>C	ENSP00000263666:p.Leu209Arg	24.0	0.0		15.0	7.0	NM_015009	A7MCZ6|Q8N2N7|Q96CC2|Q9NSQ2	Missense_Mutation	SNP	ENST00000263666.4	hg19	CCDS33789.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.549084	0.86127	.	.	ENSG00000121440	ENST00000263666;ENST00000416926;ENST00000308537	T;T	0.27720	1.65;1.65	5.04	5.04	0.67666	TRAF-like (1);	0.634448	0.14989	N	0.286781	T	0.51686	0.1689	L	0.59436	1.845	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	T	0.38779	-0.9645	10	0.33141	T	0.24	.	14.7898	0.69830	1.0:0.0:0.0:0.0	.	209	Q9UPQ7	PZRN3_HUMAN	R	209	ENSP00000263666:L209R;ENSP00000308831:L209R	ENSP00000263666:L209R	L	-	2	0	PDZRN3	73756041	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	6.816000	0.75247	1.870000	0.54199	0.477000	0.44152	CTG	.	.		0.701	PDZRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352460.1	XM_041363		C	73673351	A	C	73673351	3	2	317	1	0	0	0	0	1	0	0	0	11718	188	7	5	2614	5	PDZRN3	3	73673351	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	240556	73673351	124349079	40	44682										
OR5H1	26341	hgsc.bcm.edu	37	chr3	97851772	97851772	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gcttggatatcatccacagtGaccccaaagatgctgaataa	8	10	1	3			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr3:97851772G>T	ENST00000354565.2	+	1	231	c.231G>T	c.(229-231)gtG>gtT	p.V77V	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005338.1	NP_001005338.1	A6NKK0	OR5H1_HUMAN	olfactory receptor, family 5, subfamily H, member 1	77						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(7)|kidney(8)|large_intestine(3)|lung(13)|ovary(1)|skin(1)	34						CATCCACAGTGACCCCAAAGA	0.408																																					p.V77V		Atlas-SNP	.											.	OR5H1	71	.	0			c.G231T						.						77	78	77					3																	97851772		2203	4296	6499	SO:0001819	synonymous_variant	26341	exon1			CACAGTGACCCCA	X64988	CCDS33797.1	3q12.1	2012-08-09			ENSG00000231192	ENSG00000231192		"GPCR / Class A : Olfactory receptors"	8346	protein-coding gene	gene with protein product						1370859	Standard	NM_001005338		Approved	HTPCRX14, HSHTPCRX14	uc011bgt.2	A6NKK0	OTTHUMG00000160070	ENST00000354565.2:c.231G>T	chr3.hg19:g.97851772G>T		963.0	1.0		701.0	251.0	NM_001005338		Silent	SNP	ENST00000354565.2	hg19	CCDS33797.1																																																																																			.	.		0.408	OR5H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359100.2	NM_001005338		T	97851772	G	T	97851772	2	4	317	1	0	0	0	0	0	0	0	1	11168	1277	45	3		3	OR5H1	3	97851772	Silent	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	24178421	97851772	100170658	41	44683										
GPR156	165829	hgsc.bcm.edu	37	chr3	119886209	119886209	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	catggggcagcaggacttggGgcccggccagaaccagaagg	17	11	0	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr3:119886209G>C	ENST00000464295.1	-	10	2560	c.2115C>G	c.(2113-2115)gcC>gcG	p.A705A	GPR156_ENST00000315843.3_Silent_p.A705A|GPR156_ENST00000461057.1_Silent_p.A701A			Q8NFN8	GP156_HUMAN	G protein-coupled receptor 156	705						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled GABA receptor activity (GO:0004965)			breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|ovary(1)|prostate(1)|skin(1)	32				GBM - Glioblastoma multiforme(114;0.19)		CAGGACTTGGGGCCCGGCCAG	0.632																																					p.A705A		Atlas-SNP	.											.	GPR156	85	.	0			c.C2115G						.						43	46	45					3																	119886209		2203	4300	6503	SO:0001819	synonymous_variant	165829	exon9			ACTTGGGGCCCGG	AF488739	CCDS2997.1, CCDS54629.1	3q13.33	2012-08-21			ENSG00000175697	ENSG00000175697		"GPCR / Class C : Orphans"	20844	protein-coding gene	gene with protein product		610464				12591167	Standard	NM_153002		Approved	PGR28, GABABL	uc011bjf.2	Q8NFN8	OTTHUMG00000159406	ENST00000464295.1:c.2115C>G	chr3.hg19:g.119886209G>C		65.0	0.0		47.0	16.0	NM_153002	B7ZL66|E9PFZ4|Q14CM1|Q86SN6	Silent	SNP	ENST00000464295.1	hg19	CCDS2997.1																																																																																			.	.		0.632	GPR156-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355139.1	NM_153002		C	119886209	G	C	119886209	2	2	317	1	0	0	0	0	0	0	0	1	6669	1219	43	4		4	GPR156	3	119886209	Silent	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	22034437	119886209	78136221	42	44684										
FBXO40	51725	hgsc.bcm.edu	37	chr3	121341447	121341447	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ggatcactgtggaggacctgCccaaatcagatctcatcaag	10	11	4	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr3:121341447C>G	ENST00000338040.4	+	3	1585	c.1171C>G	c.(1171-1173)Ccc>Gcc	p.P391A		NM_016298.3	NP_057382.2	Q9UH90	FBX40_HUMAN	F-box protein 40	391					muscle cell differentiation (GO:0042692)	cytoplasm (GO:0005737)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(11)|lung(19)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	46				GBM - Glioblastoma multiforme(114;0.189)		GGAGGACCTGCCCAAATCAGA	0.483																																					p.P391A		Atlas-SNP	.											.	FBXO40	108	.	0			c.C1171G						.						119	110	113					3																	121341447		2203	4300	6503	SO:0001583	missense	51725	exon3			GACCTGCCCAAAT	AF204674	CCDS33835.1	3q21.1	2004-08-24			ENSG00000163833	ENSG00000163833		"F-boxes /  "other""	29816	protein-coding gene	gene with protein product		609107				10574462	Standard	NM_016298		Approved	KIAA1195, Fbx40	uc003eeg.2	Q9UH90	OTTHUMG00000159410	ENST00000338040.4:c.1171C>G	chr3.hg19:g.121341447C>G	ENSP00000337510:p.Pro391Ala	159.0	0.0		115.0	51.0	NM_016298	B2RAX7|Q32M70|Q9ULM5	Missense_Mutation	SNP	ENST00000338040.4	hg19	CCDS33835.1	.	.	.	.	.	.	.	.	.	.	C	18.17	3.564107	0.65651	.	.	ENSG00000163833	ENST00000338040	T	0.50277	0.75	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.67163	0.2864	M	0.66939	2.045	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.62613	-0.6817	10	0.33141	T	0.24	-18.5238	17.4071	0.87476	0.0:1.0:0.0:0.0	.	391	Q9UH90	FBX40_HUMAN	A	391	ENSP00000337510:P391A	ENSP00000337510:P391A	P	+	1	0	FBXO40	122824137	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.487000	0.81328	2.721000	0.93114	0.655000	0.94253	CCC	.	.		0.483	FBXO40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355158.1	NM_016298		G	121341447	C	G	121341447	3	3	317	1	0	0	0	0	1	0	0	0	5757	739	26	4	1177	4	FBXO40	3	121341447	Missense_Mutation	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	1455238	121341447	76680983	43	44685										
COL6A6	131873	hgsc.bcm.edu	37	chr3	130285713	130285713	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ccgttcagtatgctgacagcTgggacttggaatttgagatc	12	8	1	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr3:130285713T>A	ENST00000358511.6	+	4	1481	c.1450T>A	c.(1450-1452)Tgg>Agg	p.W484R	COL6A6_ENST00000453409.2_Missense_Mutation_p.W484R	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	484	Nonhelical region.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						TGCTGACAGCTGGGACTTGGA	0.478																																					p.W484R		Atlas-SNP	.											.	COL6A6	497	.	0			c.T1450A						.						127	128	128					3																	130285713		1919	4117	6036	SO:0001583	missense	131873	exon4			GACAGCTGGGACT	AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.1450T>A	chr3.hg19:g.130285713T>A	ENSP00000351310:p.Trp484Arg	129.0	0.0		90.0	36.0	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	hg19	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	T	10.44	1.351649	0.24512	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	T;T	0.77358	-1.09;-1.09	5.18	4.01	0.46588	von Willebrand factor, type A (3);	0.351095	0.25222	N	0.032223	T	0.53417	0.1795	N	0.08118	0	0.09310	N	1	B	0.17268	0.021	B	0.19391	0.025	T	0.33548	-0.9864	10	0.15952	T	0.53	.	6.4847	0.22083	0.0:0.2761:0.0:0.7239	.	484	A6NMZ7	CO6A6_HUMAN	R	484	ENSP00000351310:W484R;ENSP00000399236:W484R	ENSP00000351310:W484R	W	+	1	0	COL6A6	131768403	0.000000	0.05858	0.984000	0.44739	0.995000	0.86356	0.237000	0.17985	1.954000	0.56735	0.459000	0.35465	TGG	.	.		0.478	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		A	130285713	T	A	130285713	3	1	317	1	0	0	0	0	1	0	0	0	3705	1580	55	4	1464	4	COL6A6	3	130285713	Missense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	8944266	130285713	67736717	44	44686										
ACAP2	23527	hgsc.bcm.edu	37	chr3	195013010	195013010	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	atacccctaatacagcctgaAtaagtggtgtcgctttgttt	8	9	0	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr3:195013010A>T	ENST00000326793.6	-	19	2167	c.1937T>A	c.(1936-1938)aTt>aAt	p.I646N		NM_012287.5	NP_036419.3	Q15057	ACAP2_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	646					cellular response to nerve growth factor stimulus (GO:1990090)|protein localization to endosome (GO:0036010)|regulation of ARF GTPase activity (GO:0032312)	endosome membrane (GO:0010008)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	27						TACAGCCTGAATAAGTGGTGT	0.378																																					p.I646N		Atlas-SNP	.											.	ACAP2	72	.	0			c.T1937A						.						160	157	158					3																	195013010		2203	4300	6503	SO:0001583	missense	23527	exon19			GCCTGAATAAGTG		CCDS33924.1	3q29	2013-01-10	2008-09-22	2008-09-22	ENSG00000114331	ENSG00000114331		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16469	protein-coding gene	gene with protein product		607766	"centaurin, beta 2"	CENTB2		11050434, 11062263	Standard	NM_012287		Approved	KIAA0041, CNT-B2	uc003fun.4	Q15057	OTTHUMG00000155885	ENST00000326793.6:c.1937T>A	chr3.hg19:g.195013010A>T	ENSP00000324287:p.Ile646Asn	218.0	0.0		108.0	39.0	NM_012287	A8K2V4|Q8N5Z8|Q9UQR3	Missense_Mutation	SNP	ENST00000326793.6	hg19	CCDS33924.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.580179	0.86645	.	.	ENSG00000114331	ENST00000326793	T	0.64803	-0.12	5.75	5.75	0.90469	Ankyrin repeat-containing domain (3);	0.207707	0.49916	D	0.000132	T	0.67392	0.2888	N	0.25485	0.75	0.58432	D	0.999997	D	0.60160	0.987	D	0.63703	0.917	T	0.71133	-0.4681	10	0.66056	D	0.02	.	15.2475	0.73517	1.0:0.0:0.0:0.0	.	646	Q15057	ACAP2_HUMAN	N	646	ENSP00000324287:I646N	ENSP00000324287:I646N	I	-	2	0	ACAP2	196494299	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.737000	0.91562	2.201000	0.70794	0.533000	0.62120	ATT	.	.		0.378	ACAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342126.2	NM_012287		T	195013010	A	T	195013010	3	4	317	1	0	0	0	0	1	0	0	0	119	101	4	4	419	4	ACAP2	3	195013010	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	64727297	195013010	3009420	45	44687										
GAK	2580	hgsc.bcm.edu	37	chr4	887684	887684	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	atgaggctgtggaagaccgtGtactgcgtgtcgtgcggggg	19	7	0	2	rs140104121	byFrequency	TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr4:887684G>T	ENST00000314167.4	-	8	965	c.855C>A	c.(853-855)taC>taA	p.Y285*	GAK_ENST00000511163.1_Nonsense_Mutation_p.Y206*	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	285	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|cell development (GO:0048468)|clathrin coat disassembly (GO:0072318)|clathrin-mediated endocytosis (GO:0072583)|endoplasmic reticulum organization (GO:0007029)|epidermal cell differentiation (GO:0009913)|establishment of skin barrier (GO:0061436)|forebrain morphogenesis (GO:0048853)|Golgi organization (GO:0007030)|intrahepatic bile duct development (GO:0035622)|positive regulation of neural precursor cell proliferation (GO:2000179)	cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(16)|skin(7)|urinary_tract(2)	39				Colorectal(103;0.219)		GGAAGACCGTGTACTGCGTGT	0.612																																					p.Y285X		Atlas-SNP	.											.	GAK	104	.	0			c.C855A						.						113	80	91					4																	887684		2202	4300	6502	SO:0001587	stop_gained	2580	exon8			GACCGTGTACTGC	D88435	CCDS3340.1	4p16	2011-09-07			ENSG00000178950	ENSG00000178950		"Heat shock proteins / DNAJ (HSP40)"	4113	protein-coding gene	gene with protein product	"auxilin-2"	602052				9299234	Standard	NM_005255		Approved	DNAJC26	uc003gbm.4	O14976	OTTHUMG00000088301	ENST00000314167.4:c.855C>A	chr4.hg19:g.887684G>T	ENSP00000314499:p.Tyr285*	106.0	0.0		123.0	33.0	NM_005255	Q5U4P5|Q9BVY6	Nonsense_Mutation	SNP	ENST00000314167.4	hg19	CCDS3340.1	.	.	.	.	.	.	.	.	.	.	G	33	5.287891	0.95517	.	.	ENSG00000178950	ENST00000314167;ENST00000511163	.	.	.	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-34.2497	15.4704	0.75437	0.0:0.0:1.0:0.0	.	.	.	.	X	285;206	.	ENSP00000314499:Y285X	Y	-	3	2	GAK	877684	1.000000	0.71417	0.962000	0.40283	0.242000	0.25591	3.194000	0.51005	2.232000	0.73038	0.563000	0.77884	TAC	.	G|0.999;A|0.001		0.612	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239188.1	NM_005255		T	887684	G	T	887684	4	4	317	1	0	0	0	0	0	1	0	0	6203	1372	48	3	3164	3	GAK	4	887684	Nonsense_Mutation	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10		887684	190266592	46	44688										
RNF212	285498	hgsc.bcm.edu	37	chr4	1084625	1084625	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gtttttcttgaaattctaaaAtctgaaaagatcataggttt	6	4	4	3			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr4:1084625A>T	ENST00000433731.2	-	4	309	c.248T>A	c.(247-249)aTt>aAt	p.I83N	RNF212_ENST00000382968.5_Splice_Site_p.I83N			Q495C1	RN212_HUMAN	ring finger protein 212	83					chiasma assembly (GO:0051026)|meiotic gene conversion (GO:0006311)|protein sumoylation (GO:0016925)|reciprocal meiotic recombination (GO:0007131)	synaptonemal complex (GO:0000795)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	10			OV - Ovarian serous cystadenocarcinoma(23;0.0179)	UCEC - Uterine corpus endometrioid carcinoma (64;0.151)		AAATTCTAAAATCTGAAAAGA	0.423																																					p.I83N		Atlas-SNP	.											.	RNF212	69	.	0			c.T248A						.						91	87	88					4																	1084625		2202	4300	6502	SO:0001630	splice_region_variant	285498	exon4			TCTAAAATCTGAA	AK096160	CCDS3345.1, CCDS46996.1, CCDS54704.1	4p16.3	2013-02-27	2007-01-19	2007-01-19	ENSG00000178222	ENSG00000178222		"RING-type (C3HC4) zinc fingers"	27729	protein-coding gene	gene with protein product		612041	"hypothetical protein LOC285498"	LOC285498		23396135	Standard	NM_001131034		Approved	FLJ38841	uc003gcj.3	Q495C1	OTTHUMG00000118997	ENST00000433731.2:c.247-1T>A	chr4.hg19:g.1084625A>T		84.0	0.0		91.0	24.0	NM_194439	C9J8N0|Q495C0|Q86W82|Q8IY99|Q8N8U7	Missense_Mutation	SNP	ENST00000433731.2	hg19	CCDS46996.1	.	.	.	.	.	.	.	.	.	.	A	12.24	1.878848	0.33162	.	.	ENSG00000178222	ENST00000382968;ENST00000433731	D;D	0.98835	-5.17;-5.17	3.91	3.91	0.45181	.	.	.	.	.	D	0.97720	0.9252	L	0.53249	1.67	0.80722	D	1	D;P;P	0.54964	0.969;0.925;0.925	P;P;P	0.51701	0.648;0.677;0.556	D	0.97240	0.9890	9	0.66056	D	0.02	0.2099	9.3084	0.37889	1.0:0.0:0.0:0.0	.	83;83;83	Q495C1-2;Q495C1;Q495C1-5	.;RN212_HUMAN;.	N	83	ENSP00000372428:I83N;ENSP00000389709:I83N	ENSP00000372428:I83N	I	-	2	0	RNF212	1074625	1.000000	0.71417	0.851000	0.33527	0.056000	0.15407	3.989000	0.56958	1.782000	0.52362	0.172000	0.16884	ATT	.	.		0.423	RNF212-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359124.2	NM_194439	Missense_Mutation	T	1084625	A	T	1084625	5	4	317	1	0	0	0	0	0	0	1	0	13491	115	4	4	673	4	RNF212	4	1084625	Splice_Site	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	196941	1084625	190069651	47	44689										
ABLIM2	84448	hgsc.bcm.edu	37	chr4	8031435	8031435	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gtcggagtgtagcgcccgagGctaaccgacccagtggagct	15	12	0	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr4:8031435G>A	ENST00000341937.5	-	11	1180	c.1116C>T	c.(1114-1116)agC>agT	p.S372S	ABLIM2_ENST00000428004.2_Silent_p.S383S|ABLIM2_ENST00000361581.5_Silent_p.S372S|ABLIM2_ENST00000318888.4_Silent_p.S140S|ABLIM2_ENST00000447017.2_Silent_p.S372S|ABLIM2_ENST00000546334.1_Silent_p.S383S|ABLIM2_ENST00000515079.1_5'UTR|ABLIM2_ENST00000361737.5_Silent_p.S383S|ABLIM2_ENST00000505872.1_Silent_p.S372S|ABLIM2_ENST00000545242.1_Silent_p.S372S|ABLIM2_ENST00000514025.1_Silent_p.S140S|ABLIM2_ENST00000296372.8_Silent_p.S372S|ABLIM2_ENST00000407564.3_Silent_p.S372S	NM_001130084.1	NP_001123556.1	Q6H8Q1	ABLM2_HUMAN	actin binding LIM protein family, member 2	372					actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|myofibril (GO:0030016)	zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|pancreas(3)|prostate(2)|urinary_tract(1)	25						AGCGCCCGAGGCTAACCGACC	0.617																																					p.S383S		Atlas-SNP	.											.	ABLIM2	59	.	0			c.C1149T						.						36	48	44					4																	8031435		2010	4108	6118	SO:0001819	synonymous_variant	84448	exon12			CCCGAGGCTAACC	AB058711	CCDS47011.1, CCDS47012.1, CCDS47013.1, CCDS47014.1, CCDS47015.1, CCDS47016.1, CCDS54719.1, CCDS68669.1	4p16.1	2012-05-16			ENSG00000163995	ENSG00000163995			19195	protein-coding gene	gene with protein product		612544	"actin binding LIM protein 2"				Standard	NM_001130083		Approved	KIAA1808	uc003gkj.4	Q6H8Q1	OTTHUMG00000057427	ENST00000341937.5:c.1116C>T	chr4.hg19:g.8031435G>A		101.0	0.0		91.0	23.0	NM_001130087	E9PF39|Q08E71|Q19VH0|Q6H8Q0|Q6NX73|Q8N3C5|Q8N9E9|Q8N9G2|Q96JL7	Silent	SNP	ENST00000341937.5	hg19	CCDS47013.1																																																																																			.	.		0.617	ABLIM2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358862.2	NM_001130083		A	8031435	G	A	8031435	2	1	317	1	0	0	0	0	0	0	0	1	95	1194	42	3		3	ABLIM2	4	8031435	Silent	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	6946810	8031435	183122841	48	44690										
PCDH7	5099	hgsc.bcm.edu	37	chr4	30723268	30723268	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ggagtccggttccgagtaccTgaagatcgacaacctcactg	11	12	1	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr4:30723268T>A	ENST00000361762.2	+	1	1232	c.224T>A	c.(223-225)cTg>cAg	p.L75Q	PCDH7_ENST00000543491.1_Missense_Mutation_p.L75Q	NM_002589.2	NP_002580.2	O60245	PCDH7_HUMAN	protocadherin 7	75	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(8)|liver(1)|lung(26)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	55						TCCGAGTACCTGAAGATCGAC	0.632																																					p.L75Q		Atlas-SNP	.											.	PCDH7	215	.	0			c.T224A						.						67	57	60					4																	30723268		2203	4300	6503	SO:0001583	missense	5099	exon1			AGTACCTGAAGAT	AB006755	CCDS33971.1, CCDS75116.1	4p15	2014-06-13	2007-02-12			ENSG00000169851		"Cadherins / Protocadherins : Non-clustered"	8659	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 120"	602988	"BH-protocadherin (brain-heart)"			9615233	Standard	NM_002589		Approved	BH-Pcdh, PPP1R120	uc021xnd.1	O60245		ENST00000361762.2:c.224T>A	chr4.hg19:g.30723268T>A	ENSP00000355243:p.Leu75Gln	59.0	0.0		61.0	15.0	NM_032457	O60246|O60247|Q4W5C4	Missense_Mutation	SNP	ENST00000361762.2	hg19	CCDS33971.1	.	.	.	.	.	.	.	.	.	.	T	14.91	2.677695	0.47886	.	.	ENSG00000169851	ENST00000361762;ENST00000543491;ENST00000333135	T;T	0.40476	1.03;1.03	4.87	3.6	0.41247	Cadherin, N-terminal (1);Cadherin (3);	.	.	.	.	T	0.63414	0.2509	M	0.82433	2.59	0.42717	D	0.993668	D;D;D	0.71674	0.992;0.998;0.994	D;D;D	0.73708	0.967;0.967;0.981	T	0.68819	-0.5308	9	0.87932	D	0	.	10.154	0.42812	0.1494:0.0:0.0:0.8506	.	75;75;75	F5GWJ1;O60245-3;O60245	.;.;PCDH7_HUMAN	Q	75	ENSP00000355243:L75Q;ENSP00000441802:L75Q	ENSP00000330302:L75Q	L	+	2	0	PCDH7	30332366	1.000000	0.71417	1.000000	0.80357	0.506000	0.33950	5.735000	0.68587	1.828000	0.53243	0.254000	0.18369	CTG	.	.		0.632	PCDH7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360366.1	NM_032457, NM_002589		A	30723268	T	A	30723268	3	1	317	1	0	0	0	0	1	0	0	0	11525	1580	55	4	226	4	PCDH7	4	30723268	Missense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	22691833	30723268	160431008	49	44691										
HERC6	55008	hgsc.bcm.edu	37	chr4	89329771	89329771	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ggaatggatttcttccatggTaatagccaatacttacttta	7	7	1	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr4:89329771T>C	ENST00000264346.7	+	11	1427		c.e11+2		HERC6_ENST00000380265.5_Splice_Site	NM_017912.3	NP_060382.3	Q8IVU3	HERC6_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 6						hematopoietic progenitor cell differentiation (GO:0002244)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)	11		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000222)		TCTTCCATGGTAATAGCCAAT	0.368																																					.		Atlas-SNP	.											.	HERC6	104	.	0			c.1368+2T>C						.						68	60	62					4																	89329771		1839	4086	5925	SO:0001630	splice_region_variant	55008	exon11			CCATGGTAATAGC	AF336798	CCDS47098.1, CCDS54777.1	4q22	2012-02-23	2012-02-23		ENSG00000138642	ENSG00000138642			26072	protein-coding gene	gene with protein product		609249	"hect domain and RLD 6"				Standard	NM_001165136		Approved	FLJ20637	uc011cdi.2	Q8IVU3	OTTHUMG00000160983	ENST00000264346.7:c.1368+2T>C	chr4.hg19:g.89329771T>C		402.0	0.0		158.0	107.0	NM_017912	B4DIY5|Q5GC90|Q5GRH3|Q5HYM6|Q5JPB6|Q6PIF4|Q8NAN3|Q9NWS4	Splice_Site	SNP	ENST00000264346.7	hg19	CCDS47098.1	.	.	.	.	.	.	.	.	.	.	T	19.80	3.894310	0.72639	.	.	ENSG00000138642	ENST00000380265;ENST00000264346	.	.	.	4.19	3.0	0.34707	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.4534	0.21916	0.0:0.1123:0.0:0.8877	.	.	.	.	.	-1	.	.	.	+	.	.	HERC6	89548794	1.000000	0.71417	0.937000	0.37676	0.846000	0.48090	3.706000	0.54830	0.772000	0.33382	0.397000	0.26171	.	.	.		0.368	HERC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363259.2		Intron	C	89329771	T	C	89329771	5	2	317	1	0	0	0	0	0	0	1	0	7071	1652	57	2	1209	2	HERC6	4	89329771	Splice_Site	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	58606503	89329771	101824505	50	44692										
CFI	3426	hgsc.bcm.edu	37	chr4	110685711	110685711	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	actgttgaaacccaaggtcaAggcaggccacgttggcttcc	11	12	1	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr4:110685711A>C	ENST00000394634.2	-	3	671	c.464T>G	c.(463-465)cTt>cGt	p.L155R	CFI_ENST00000394635.3_Missense_Mutation_p.L155R|CFI_ENST00000512148.1_Missense_Mutation_p.L155R|CFI_ENST00000510800.1_Missense_Mutation_p.L155R	NM_000204.3	NP_000195	P05156	CFAI_HUMAN	complement factor I	155	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	metal ion binding (GO:0046872)|scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|skin(2)|stomach(1)	27		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000331)		CCCAAGGTCAAGGCAGGCCAC	0.418																																					p.L155R		Atlas-SNP	.											.	CFI	59	.	0			c.T464G						.						220	199	206					4																	110685711		2203	4300	6503	SO:0001583	missense	3426	exon3			AGGTCAAGGCAGG	J02770	CCDS34049.1	4q25	2014-09-17	2006-02-10	2006-02-10		ENSG00000205403	3.4.21.45	"Complement system"	5394	protein-coding gene	gene with protein product	"Konglutinogen-activating factor", "C3b-inactivator"	217030	"I factor (complement)"	IF		2956252	Standard	NM_000204		Approved	FI, C3b-INA, KAF	uc003hzr.4	P05156		ENST00000394634.2:c.464T>G	chr4.hg19:g.110685711A>C	ENSP00000378130:p.Leu155Arg	60.0	0.0		65.0	32.0	NM_000204	O60442	Missense_Mutation	SNP	ENST00000394634.2	hg19	CCDS34049.1	.	.	.	.	.	.	.	.	.	.	A	12.39	1.924959	0.34002	.	.	ENSG00000205403	ENST00000394635;ENST00000394634;ENST00000540104;ENST00000512148;ENST00000536228;ENST00000510800	T;T;T;T	0.26373	1.74;1.74;1.74;1.74	5.86	0.0617	0.14341	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	1.251480	0.05616	N	0.578929	T	0.06917	0.0176	N	0.00602	-1.34	0.09310	N	1	B;B;B	0.14012	0.002;0.007;0.009	B;B;B	0.15052	0.007;0.007;0.012	T	0.31779	-0.9931	10	0.17369	T	0.5	-0.8633	3.4879	0.07626	0.2996:0.4315:0.0717:0.1972	.	155;155;155	E7ETH0;G3XAM2;P05156	.;.;CFAI_HUMAN	R	155;155;155;155;137;155	ENSP00000378131:L155R;ENSP00000378130:L155R;ENSP00000427438:L155R;ENSP00000422009:L155R	ENSP00000378130:L155R	L	-	2	0	CFI	110905160	0.000000	0.05858	0.006000	0.13384	0.877000	0.50540	-1.324000	0.02690	0.428000	0.26173	0.533000	0.62120	CTT	.	.		0.418	CFI-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_000204		C	110685711	A	C	110685711	3	2	317	1	0	0	0	0	1	0	0	0	3291	72	3	5	1331	5	CFI	4	110685711	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	21355940	110685711	80468565	51	44693										
EGF	1950	hgsc.bcm.edu	37	chr4	110897334	110897334	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gcgatgccaagcagtctgtgAttgaaatggccaatctggat	12	8	2	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr4:110897334A>T	ENST00000265171.5	+	13	2441	c.1996A>T	c.(1996-1998)Att>Ttt	p.I666F	EGF_ENST00000509793.1_Missense_Mutation_p.I624F|EGF_ENST00000503392.1_Missense_Mutation_p.I666F	NM_001178130.1|NM_001963.4	NP_001171601.1|NP_001954.2	P01133	EGF_HUMAN	epidermal growth factor	666					activation of MAPKK activity (GO:0000186)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|branching morphogenesis of an epithelial tube (GO:0048754)|DNA replication (GO:0006260)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mammary gland alveolus development (GO:0060749)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of secretion (GO:0051048)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)|positive regulation of DNA binding (GO:0043388)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of calcium ion import (GO:0090279)|regulation of protein localization to cell surface (GO:2000008)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(1)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sucralfate(DB00364)	GCAGTCTGTGATTGAAATGGC	0.463																																					p.I666F		Atlas-SNP	.											.	EGF	113	.	0			c.A1996T						.						130	110	117					4																	110897334		2203	4300	6503	SO:0001583	missense	1950	exon13			TCTGTGATTGAAA	X04571	CCDS3689.1, CCDS54794.1, CCDS54795.1	4q25	2012-10-02	2010-05-11		ENSG00000138798	ENSG00000138798			3229	protein-coding gene	gene with protein product		131530	"epidermal growth factor (beta-urogastrone)"				Standard	NM_001963		Approved		uc003hzy.4	P01133	OTTHUMG00000132044	ENST00000265171.5:c.1996A>T	chr4.hg19:g.110897334A>T	ENSP00000265171:p.Ile666Phe	203.0	0.0		180.0	108.0	NM_001963	B4DRK7|E7EVD2|E9PBF0|Q52LZ6	Missense_Mutation	SNP	ENST00000265171.5	hg19	CCDS3689.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.086189	0.76642	.	.	ENSG00000138798	ENST00000509793;ENST00000265171;ENST00000503392	D;D;D	0.94687	-3.49;-3.49;-3.49	5.77	4.6	0.57074	Six-bladed beta-propeller, TolB-like (1);	0.221347	0.47093	D	0.000244	D	0.98015	0.9346	H	0.98005	4.125	0.53688	D	0.99997	D;D;D	0.76494	0.999;0.998;0.999	D;D;D	0.76575	0.988;0.984;0.988	D	0.98089	1.0408	10	0.87932	D	0	.	9.1427	0.36914	0.8654:0.0:0.1346:0.0	.	666;624;666	E7EVD2;P01133-2;P01133	.;.;EGF_HUMAN	F	624;666;666	ENSP00000424316:I624F;ENSP00000265171:I666F;ENSP00000421384:I666F	ENSP00000265171:I666F	I	+	1	0	EGF	111116783	0.908000	0.30866	0.996000	0.52242	0.998000	0.95712	0.526000	0.22971	2.199000	0.70637	0.533000	0.62120	ATT	.	.		0.463	EGF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255065.1			T	110897334	A	T	110897334	3	4	317	1	0	0	0	0	1	0	0	0	4964	333	12	4	2046	4	EGF	4	110897334	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	211623	110897334	80256942	52	44694										
USP53	54532	hgsc.bcm.edu	37	chr4	120189490	120189490	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ggatttggtgatcaggcaaaGcagagagaaaatcagaaatt	12	4	2	4			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr4:120189490G>A	ENST00000274030.6	+	14	2382	c.1203G>A	c.(1201-1203)aaG>aaA	p.K401K	USP53_ENST00000450251.1_Silent_p.K401K	NM_019050.2	NP_061923.2			ubiquitin specific peptidase 53											breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(5)|ovary(1)|pancreas(1)|skin(2)|stomach(1)	27						ATCAGGCAAAGCAGAGAGAAA	0.343																																					p.K401K		Atlas-SNP	.											.	USP53	69	.	0			c.G1203A						.						67	63	65					4																	120189490		1828	4089	5917	SO:0001819	synonymous_variant	54532	exon13			GGCAAAGCAGAGA	BC017382	CCDS43265.1	4q26	2010-05-12	2005-08-08		ENSG00000145390	ENSG00000145390		"Ubiquitin-specific peptidases"	29255	protein-coding gene	gene with protein product			"ubiquitin specific protease 53"			10718198, 14715245	Standard	NM_019050		Approved	KIAA1350	uc003ics.4	Q70EK8	OTTHUMG00000161331	ENST00000274030.6:c.1203G>A	chr4.hg19:g.120189490G>A		682.0	0.0		664.0	193.0	NM_019050		Silent	SNP	ENST00000274030.6	hg19	CCDS43265.1																																																																																			.	.		0.343	USP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364564.2	XM_052597		A	120189490	G	A	120189490	2	1	317	1	0	0	0	0	0	0	0	1	17099	962	34	3		3	USP53	4	120189490	Silent	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	9292156	120189490	70964786	53	44695										
TLL1	7092	hgsc.bcm.edu	37	chr4	166996136	166996136	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ggatttgtgctacatgacaaTaaacatgattgcaaggaagg	11	5	0	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr4:166996136T>A	ENST00000061240.2	+	17	2942	c.2295T>A	c.(2293-2295)aaT>aaA	p.N765K	TLL1_ENST00000507499.1_Missense_Mutation_p.N788K	NM_012464.4	NP_036596.3	O43897	TLL1_HUMAN	tolloid-like 1	765	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(21)|lung(26)|ovary(2)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		TACATGACAATAAACATGATT	0.403																																					p.N765K		Atlas-SNP	.											.	TLL1	194	.	0			c.T2295A						.						289	239	256					4																	166996136		2203	4300	6503	SO:0001583	missense	7092	exon17			TGACAATAAACAT	AF282732	CCDS3811.1, CCDS56342.1	4q32-q33	2008-07-29			ENSG00000038295	ENSG00000038295			11843	protein-coding gene	gene with protein product		606742				10516436	Standard	NM_012464		Approved		uc003irh.2	O43897	OTTHUMG00000161112	ENST00000061240.2:c.2295T>A	chr4.hg19:g.166996136T>A	ENSP00000061240:p.Asn765Lys	171.0	0.0		185.0	17.0	NM_012464	B2RMU2|Q96AN3|Q9NQS4	Missense_Mutation	SNP	ENST00000061240.2	hg19	CCDS3811.1	.	.	.	.	.	.	.	.	.	.	T	13.58	2.280481	0.40294	.	.	ENSG00000038295	ENST00000061240;ENST00000507499	D;D	0.96522	-4.04;-4.04	5.72	-1.6	0.08426	EGF-like region, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	U	0.000000	D	0.97241	0.9098	M	0.74258	2.255	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.85130	0.997;0.99	D	0.95944	0.8949	10	0.62326	D	0.03	.	13.255	0.60073	0.0:0.534:0.0:0.466	.	788;765	E9PD25;O43897	.;TLL1_HUMAN	K	765;788	ENSP00000061240:N765K;ENSP00000426082:N788K	ENSP00000061240:N765K	N	+	3	2	TLL1	167215586	0.942000	0.31987	0.996000	0.52242	0.007000	0.05969	0.081000	0.14823	-0.155000	0.11098	-0.924000	0.02725	AAT	.	.		0.403	TLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363821.1			A	166996136	T	A	166996136	3	1	317	1	0	0	0	0	1	0	0	0	15960	1403	49	4	2361	4	TLL1	4	166996136	Missense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	46806646	166996136	24158140	54	44696										
HMGB2	3148	hgsc.bcm.edu	37	chr4	174253236	174253236	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ttaaaggatagccatttattCttcatcttcatcctcttcct	3	11	5	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr4:174253236C>T	ENST00000296503.5	-	5	1498	c.625G>A	c.(625-627)Gaa>Aaa	p.E209K	HMGB2_ENST00000438704.2_Missense_Mutation_p.E209K|RP11-798M19.3_ENST00000507803.1_RNA|HMGB2_ENST00000446922.2_Missense_Mutation_p.E209K			P26583	HMGB2_HUMAN	high mobility group box 2	209	Asp/Glu-rich (acidic).				apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|base-excision repair, DNA ligation (GO:0006288)|cell chemotaxis (GO:0060326)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to lipopolysaccharide (GO:0071222)|chromatin organization (GO:0006325)|DNA ligation involved in DNA repair (GO:0051103)|DNA topological change (GO:0006265)|male gonad development (GO:0008584)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive chemotaxis (GO:0050918)|positive regulation of DNA binding (GO:0043388)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of nuclease activity (GO:0032075)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to steroid hormone (GO:0048545)|spermatid nucleus differentiation (GO:0007289)|V(D)J recombination (GO:0033151)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	chemoattractant activity (GO:0042056)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|RAGE receptor binding (GO:0050786)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription regulatory region DNA binding (GO:0044212)			endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|urinary_tract(3)	14		Prostate(90;0.0132)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_hematologic(60;0.107)|all_neural(102;0.122)		all cancers(43;9.58e-18)|Epithelial(43;3.75e-16)|OV - Ovarian serous cystadenocarcinoma(60;6.24e-09)|STAD - Stomach adenocarcinoma(60;0.00273)|GBM - Glioblastoma multiforme(59;0.0064)|LUSC - Lung squamous cell carcinoma(193;0.0903)|Kidney(143;0.249)		GCCATTTAttcttcatcttca	0.433																																					p.E209K		Atlas-SNP	.											.	HMGB2	24	.	0			c.G625A						.						429	360	383					4																	174253236		2203	4300	6503	SO:0001583	missense	3148	exon4			TTTATTCTTCATC		CCDS3816.1	4q31	2011-07-01	2011-04-05	2002-08-16	ENSG00000164104	ENSG00000164104		"High-mobility group / Canonical"	5000	protein-coding gene	gene with protein product		163906	"high-mobility group (nonhistone chromosomal) protein 2", "high-mobility group box 2"	HMG2		1754403	Standard	NM_002129		Approved		uc011ckc.1	P26583	OTTHUMG00000160799	ENST00000296503.5:c.625G>A	chr4.hg19:g.174253236C>T	ENSP00000296503:p.Glu209Lys	130.0	0.0		138.0	28.0	NM_001130689	B2R4K8|D3DP37|Q5U072	Missense_Mutation	SNP	ENST00000296503.5	hg19	CCDS3816.1	.	.	.	.	.	.	.	.	.	.	C	11.85	1.761225	0.31137	.	.	ENSG00000164104	ENST00000296503;ENST00000446922;ENST00000438704	D;D;D	0.95103	-3.61;-3.61;-3.61	6.05	6.05	0.98169	.	0.000000	0.64402	D	0.000013	D	0.94000	0.8078	N	0.08118	0	0.49483	D	0.999791	D	0.63880	0.993	D	0.68192	0.956	D	0.95381	0.8473	10	0.87932	D	0	.	20.2037	0.98272	0.0:1.0:0.0:0.0	.	209	P26583	HMGB2_HUMAN	K	209	ENSP00000296503:E209K;ENSP00000393448:E209K;ENSP00000404912:E209K	ENSP00000296503:E209K	E	-	1	0	HMGB2	174489811	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	5.111000	0.64628	2.866000	0.98385	0.650000	0.86243	GAA	.	.		0.433	HMGB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362362.1	NM_001130688		T	174253236	C	T	174253236	3	4	317	1	0	0	0	0	1	0	0	0	7235	922	32	3	8	3	HMGB2	4	174253236	Missense_Mutation	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	7257100	174253236	16901040	55	44697										
ZFP42	132625	hgsc.bcm.edu	37	chr4	188924650	188924650	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gaaagcgttcgttgagagctCaaaactaaagagacatttcc	9	8	1	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr4:188924650C>A	ENST00000326866.4	+	4	1097	c.689C>A	c.(688-690)tCa>tAa	p.S230*	ZFP42_ENST00000509524.1_Nonsense_Mutation_p.S230*	NM_174900.3	NP_777560.2	Q96MM3	ZFP42_HUMAN	ZFP42 zinc finger protein	230					female gonad development (GO:0008585)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|meiotic nuclear division (GO:0007126)|regulation of genetic imprinting (GO:2000653)|spermatid development (GO:0007286)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S230L(1)		breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(14;6.2e-52)|all_epithelial(14;7.36e-37)|all_lung(41;2.29e-15)|Lung NSC(41;6.7e-15)|Breast(6;1.53e-05)|Melanoma(20;3.01e-05)|Hepatocellular(41;0.00335)|all_hematologic(60;0.014)|Renal(120;0.0183)|Prostate(90;0.0421)|Colorectal(36;0.227)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-11)|BRCA - Breast invasive adenocarcinoma(30;4.21e-06)|GBM - Glioblastoma multiforme(59;8.93e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.157)		GTTGAGAGCTCAAAACTAAAG	0.493																																					p.S230X		Atlas-SNP	.											ZFP42,NS,carcinoma,0,2	ZFP42	87	.	1	Substitution - Missense(1)	lung(1)	c.C689A						.						116	122	120					4																	188924650		2203	4300	6503	SO:0001587	stop_gained	132625	exon4			AGAGCTCAAAACT	AK056719	CCDS3849.1	4q35.2	2014-09-04	2012-11-27		ENSG00000179059	ENSG00000179059		"Zinc fingers, C2H2-type"	30949	protein-coding gene	gene with protein product		614572	"zinc finger protein 42 homolog (mouse)", "zinc finger protein 42"			12110702	Standard	NM_174900		Approved	REX1, ZNF754	uc003izh.1	Q96MM3	OTTHUMG00000160235	ENST00000326866.4:c.689C>A	chr4.hg19:g.188924650C>A	ENSP00000317686:p.Ser230*	50.0	0.0		68.0	39.0	NM_174900	D3DP65|Q8WXE2	Nonsense_Mutation	SNP	ENST00000326866.4	hg19	CCDS3849.1	.	.	.	.	.	.	.	.	.	.	C	37	6.460024	0.97585	.	.	ENSG00000179059	ENST00000326866;ENST00000509524	.	.	.	4.39	3.52	0.40303	.	0.304578	0.31949	N	0.006809	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.5078	0.55991	0.0:0.8301:0.1699:0.0	.	.	.	.	X	230	.	ENSP00000317686:S230X	S	+	2	0	ZFP42	189161644	0.265000	0.24102	0.002000	0.10522	0.009000	0.06853	4.645000	0.61404	1.405000	0.46838	0.655000	0.94253	TCA	.	.		0.493	ZFP42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359794.1	NM_174900		A	188924650	C	A	188924650	4	1	317	1	0	0	0	0	0	1	0	0	17665	838	29	3	691	3	ZFP42	4	188924650	Nonsense_Mutation	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	14671414	188924650	2229626	56	44698										
MYO10	4651	hgsc.bcm.edu	37	chr5	16682120	16682120	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tgatgatcacaaacgagttgGgtctgagccacaagatgaga	12	7	2	5			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr5:16682120G>A	ENST00000513610.1	-	31	4503	c.4049C>T	c.(4048-4050)cCc>cTc	p.P1350L	MYO10_ENST00000274203.9_Missense_Mutation_p.P707L|MYO10_ENST00000505695.1_Missense_Mutation_p.P689L|MYO10_ENST00000515803.1_Missense_Mutation_p.P689L|MYO10_ENST00000427430.2_Missense_Mutation_p.P707L	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	1350					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						AAACGAGTTGGGTCTGAGCCA	0.567																																					p.P1350L		Atlas-SNP	.											.	MYO10	198	.	0			c.C4049T						.						115	115	115					5																	16682120		2128	4231	6359	SO:0001583	missense	4651	exon31			GAGTTGGGTCTGA	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"Myosins / Myosin superfamily : Class X", "Pleckstrin homology (PH) domain containing"	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.4049C>T	chr5.hg19:g.16682120G>A	ENSP00000421280:p.Pro1350Leu	27.0	0.0		37.0	8.0	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Missense_Mutation	SNP	ENST00000513610.1	hg19	CCDS54834.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.703432	0.88924	.	.	ENSG00000145555	ENST00000513610;ENST00000515803;ENST00000274203;ENST00000505695;ENST00000427430	T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18	5.82	5.82	0.92795	Pleckstrin homology-type (1);	.	.	.	.	T	0.80025	0.4548	M	0.74881	2.28	0.80722	D	1	D;D;D	0.89917	0.991;0.995;1.0	P;P;D	0.69142	0.778;0.645;0.962	T	0.81008	-0.1127	9	0.87932	D	0	.	20.1027	0.97880	0.0:0.0:1.0:0.0	.	229;990;1350	B4DIJ5;Q69YP8;Q9HD67	.;.;MYO10_HUMAN	L	1350;689;707;689;707	ENSP00000421280:P1350L;ENSP00000425051:P689L;ENSP00000274203:P707L;ENSP00000421170:P689L;ENSP00000391106:P707L	ENSP00000274203:P707L	P	-	2	0	MYO10	16735120	1.000000	0.71417	0.998000	0.56505	0.459000	0.32528	6.622000	0.74233	2.756000	0.94617	0.655000	0.94253	CCC	.	.		0.567	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		A	16682120	G	A	16682120	3	1	317	1	0	0	0	0	1	0	0	0	10071	1232	43	3	2171	3	MYO10	5	16682120	Missense_Mutation	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10		16682120	164233140	57	44699										
GPR98	84059	hgsc.bcm.edu	37	chr5	89925133	89925133	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	aggtgaacgatacttatcctTgagttttacaagactaggag	10	6	0	3			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr5:89925133T>C	ENST00000405460.2	+	9	1712	c.1616T>C	c.(1615-1617)tTg>tCg	p.L539S		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	539					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TACTTATCCTTGAGTTTTACA	0.408																																					p.L539S		Atlas-SNP	.											.	GPR98	605	.	0			c.T1616C						.						96	90	92					5																	89925133		1881	4113	5994	SO:0001583	missense	84059	exon9			TATCCTTGAGTTT	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.1616T>C	chr5.hg19:g.89925133T>C	ENSP00000384582:p.Leu539Ser	190.0	0.0		304.0	141.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.464819	0.84425	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000399043	T	0.40476	1.03	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	T	0.65678	0.2714	M	0.76002	2.32	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.69793	-0.5049	10	0.87932	D	0	.	15.9247	0.79606	0.0:0.0:0.0:1.0	.	539	Q8WXG9	GPR98_HUMAN	S	539	ENSP00000384582:L539S	ENSP00000296619:L539S	L	+	2	0	GPR98	89960889	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.463000	0.80869	2.165000	0.68154	0.533000	0.62120	TTG	.	.		0.408	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		C	89925133	T	C	89925133	3	2	317	1	0	0	0	0	1	0	0	0	6730	1821	63	2	1650	2	GPR98	5	89925133	Missense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	73243013	89925133	90990127	58	44700										
SEMA6A	57556	hgsc.bcm.edu	37	chr5	115783094	115783094	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ctcgcggctgccgcggctggGcttccgcttctgctgcagcg	15	16	1	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr5:115783094G>A	ENST00000343348.6	-	19	3095	c.2308C>T	c.(2308-2310)Ccc>Tcc	p.P770S	CTB-118N6.3_ENST00000512128.1_RNA|CTB-118N6.3_ENST00000508424.1_RNA|SEMA6A_ENST00000257414.8_Missense_Mutation_p.P787S|CTB-118N6.3_ENST00000510682.1_RNA|SEMA6A_ENST00000513137.1_Missense_Mutation_p.P197S|CTB-118N6.3_ENST00000514214.1_RNA|SEMA6A_ENST00000510263.1_Missense_Mutation_p.P770S|SEMA6A_ENST00000503865.1_Missense_Mutation_p.P149S|SEMA6A_ENST00000282394.6_Missense_Mutation_p.P247S|CTB-118N6.3_ENST00000508640.1_RNA	NM_020796.3	NP_065847	Q9H2E6	SEM6A_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	770					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|centrosome localization (GO:0051642)|cytoskeleton organization (GO:0007010)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|positive regulation of neuron migration (GO:2001224)|semaphorin-plexin signaling pathway (GO:0071526)	axon (GO:0030424)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31		all_cancers(142;0.00316)|all_epithelial(76;5.71e-05)|Prostate(80;0.00845)|Ovarian(225;0.0796)|Lung NSC(810;0.171)|all_lung(232;0.203)		OV - Ovarian serous cystadenocarcinoma(64;1.59e-08)|Epithelial(69;2e-08)|all cancers(49;5.7e-08)|COAD - Colon adenocarcinoma(49;0.151)		CCGCGGCTGGGCTTCCGCTTC	0.627																																					p.P770S		Atlas-SNP	.											.	SEMA6A	93	.	0			c.C2308T						.						51	62	59					5																	115783094		2089	4204	6293	SO:0001583	missense	57556	exon19			GGCTGGGCTTCCG	AB037789	CCDS47256.1, CCDS75288.1	5q23.1	2014-07-29			ENSG00000092421			"Semaphorins"	10738	protein-coding gene	gene with protein product	"sema VIa"	605885		SEMAQ		9204478, 10993894	Standard	XM_006714663		Approved	KIAA1368, SEMA6A1, SEMA, HT018	uc010jck.3	Q9H2E6	OTTHUMG00000162987	ENST00000343348.6:c.2308C>T	chr5.hg19:g.115783094G>A	ENSP00000345512:p.Pro770Ser	73.0	0.0		82.0	44.0	NM_020796	Q9P2H9	Missense_Mutation	SNP	ENST00000343348.6	hg19	CCDS47256.1	.	.	.	.	.	.	.	.	.	.	G	16.34	3.096092	0.56075	.	.	ENSG00000092421	ENST00000343348;ENST00000257414;ENST00000513137;ENST00000282394;ENST00000503865;ENST00000510263	T;T;T;T;T;T	0.47869	2.21;2.21;0.84;2.69;0.83;2.21	5.45	4.57	0.56435	.	0.115400	0.64402	D	0.000014	T	0.60996	0.2312	L	0.44542	1.39	0.58432	D	0.999999	D;D;D;D;D;D	0.89917	1.0;0.995;1.0;1.0;1.0;1.0	D;P;D;D;D;D	0.87578	0.998;0.844;0.998;0.998;0.998;0.998	T	0.60321	-0.7286	10	0.40728	T	0.16	.	15.8163	0.78604	0.0:0.1366:0.8634:0.0	.	149;770;314;787;247;197	E9PDV9;Q9H2E6;Q96SM8;Q9H2E6-2;E7ERF3;B3KU01	.;SEM6A_HUMAN;.;.;.;.	S	770;787;197;247;149;770	ENSP00000345512:P770S;ENSP00000257414:P787S;ENSP00000422997:P197S;ENSP00000282394:P247S;ENSP00000425364:P149S;ENSP00000424388:P770S	ENSP00000257414:P787S	P	-	1	0	SEMA6A	115810993	1.000000	0.71417	0.961000	0.40146	0.996000	0.88848	7.501000	0.81600	1.279000	0.44446	0.650000	0.86243	CCC	.	.		0.627	SEMA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371270.1	NM_020796		A	115783094	G	A	115783094	3	1	317	1	0	0	0	0	1	0	0	0	14054	1203	42	3	788	3	SEMA6A	5	115783094	Missense_Mutation	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	25857961	115783094	65132166	59	44701										
PCDHGB2	56103	hgsc.bcm.edu	37	chr5	140740665	140740665	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tacactctgagtatcgaagcAaaagatcctggagatctagc	9	9	2	3			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr5:140740665A>C	ENST00000522605.1	+	1	963	c.963A>C	c.(961-963)gcA>gcC	p.A321A	PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA4_ENST00000571252.1_Intron	NM_018923.2|NM_032096.1	NP_061746.1|NP_115267.1	Q9Y5G2	PCDGE_HUMAN	protocadherin gamma subfamily B, 2	321	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTATCGAAGCAAAAGATCCTG	0.378																																					p.A321A		Atlas-SNP	.											.	PCDHGB2	196	.	0			c.A963C						.						63	61	62					5																	140740665		1975	4158	6133	SO:0001819	synonymous_variant	56103	exon1			CGAAGCAAAAGAT	AF152331	CCDS54924.1, CCDS75332.1	5q31	2010-01-26				ENSG00000253910		"Cadherins / Protocadherins : Clustered"	8709	other	protocadherin		606300				10380929	Standard	NM_018923		Approved	PCDH-GAMMA-B2		Q9Y5G2		ENST00000522605.1:c.963A>C	chr5.hg19:g.140740665A>C		131.0	0.0		183.0	39.0	NM_018923	Q3MIJ3|Q9UN65	Silent	SNP	ENST00000522605.1	hg19	CCDS54924.1																																																																																			.	.		0.378	PCDHGB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374741.1	NM_018923		C	140740665	A	C	140740665	2	2	317	1	0	0	0	0	0	0	0	1	11572	117	5	5		5	PCDHGB2	5	140740665	Silent	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	24957571	140740665	40174595	60	44702										
PCDHGA8	9708	hgsc.bcm.edu	37	chr5	140773878	140773878	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	aggacacgctgcagggggcgCccctgtcctcgtatatctcc	12	15	1	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr5:140773878C>T	ENST00000398604.2	+	1	1498	c.1498C>T	c.(1498-1500)Ccc>Tcc	p.P500S	PCDHGB4_ENST00000519479.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_032088.1	NP_114477.1	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8	500	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			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)			GCAGGGGGCGCCCCTGTCCTC	0.567																																					p.P500S		Atlas-SNP	.											.	PCDHGA8	146	.	0			c.C1498T						.						46	53	50					5																	140773878		2164	4282	6446	SO:0001583	missense	9708	exon1			GGGGCGCCCCTGT	AF152515	CCDS47291.1, CCDS75338.1	5q31	2010-01-26			ENSG00000253767	ENSG00000253767		"Cadherins / Protocadherins : Clustered"	8706	other	protocadherin		606295				10380929	Standard	NM_014004		Approved	KIAA0327, PCDH-GAMMA-A8		Q9Y5G5	OTTHUMG00000164053	ENST00000398604.2:c.1498C>T	chr5.hg19:g.140773878C>T	ENSP00000381605:p.Pro500Ser	128.0	0.0		184.0	88.0	NM_014004	A7MCZ4|O15039	Missense_Mutation	SNP	ENST00000398604.2	hg19	CCDS47291.1	.	.	.	.	.	.	.	.	.	.	.	2.470	-0.322220	0.05350	.	.	ENSG00000253767	ENST00000398604	T	0.62941	-0.01	4.33	3.46	0.39613	Cadherin (4);Cadherin-like (1);	0.000000	0.31221	U	0.008030	T	0.54902	0.1887	L	0.56199	1.76	0.23126	N	0.998255	B;B	0.28400	0.107;0.21	B;B	0.34180	0.177;0.169	T	0.49781	-0.8903	10	0.41790	T	0.15	.	6.3579	0.21412	0.0:0.6755:0.1526:0.1719	.	500;500	Q9Y5G5;Q9Y5G5-2	PCDG8_HUMAN;.	S	500	ENSP00000381605:P500S	ENSP00000381605:P500S	P	+	1	0	PCDHGA8	140754062	0.177000	0.23109	0.019000	0.16419	0.008000	0.06430	0.914000	0.28624	1.139000	0.42245	-0.157000	0.13467	CCC	.	.		0.567	PCDHGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376972.1	NM_032088		T	140773878	C	T	140773878	3	4	317	1	0	0	0	0	1	0	0	0	11569	739	26	3	1500	3	PCDHGA8	5	140773878	Missense_Mutation	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	33213	140773878	40141382	61	44703										
FAM71B	153745	hgsc.bcm.edu	37	chr5	156590005	156590005	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tttccttgttttcattccagActtcagcactgggctgggaa	9	10	2	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr5:156590005A>T	ENST00000302938.4	-	2	1366	c.1271T>A	c.(1270-1272)gTc>gAc	p.V424D		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	424						nucleus (GO:0005634)				NS(3)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(32)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TTCATTCCAGACTTCAGCACT	0.512																																					p.V424D		Atlas-SNP	.											.	FAM71B	145	.	0			c.T1271A						.						113	112	112					5																	156590005		2203	4300	6503	SO:0001583	missense	153745	exon2			TTCCAGACTTCAG		CCDS4335.1	5q33.3	2005-08-09			ENSG00000170613	ENSG00000170613			28397	protein-coding gene	gene with protein product						12477932	Standard	NM_130899		Approved	MGC26988	uc003lwn.3	Q8TC56	OTTHUMG00000130246	ENST00000302938.4:c.1271T>A	chr5.hg19:g.156590005A>T	ENSP00000305596:p.Val424Asp	82.0	0.0		95.0	22.0	NM_130899	Q1EDD9|Q8TC64|Q96LY8	Missense_Mutation	SNP	ENST00000302938.4	hg19	CCDS4335.1	.	.	.	.	.	.	.	.	.	.	G	10.51	1.370628	0.24771	.	.	ENSG00000170613	ENST00000302938	T	0.17691	2.26	4.4	1.2	0.21068	.	1.426320	0.04613	N	0.400568	T	0.12008	0.0292	N	0.22421	0.69	0.09310	N	1	B	0.17667	0.023	B	0.15052	0.012	T	0.33137	-0.9880	10	0.54805	T	0.06	-0.0421	3.5692	0.07910	0.3561:0.1924:0.4515:0.0	.	424	Q8TC56	FA71B_HUMAN	D	424	ENSP00000305596:V424D	ENSP00000305596:V424D	V	-	2	0	FAM71B	156522583	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	-0.397000	0.07269	0.157000	0.19338	-0.215000	0.12644	GTC	.	.		0.512	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252570.2	NM_130899		T	156590005	A	T	156590005	3	4	317	1	0	0	0	0	1	0	0	0	5616	275	10	4	550	4	FAM71B	5	156590005	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	15816127	156590005	24325255	62	44704										
KIAA1191	57179	hgsc.bcm.edu	37	chr5	175774922	175774922	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ttttttgaaggtgctgccttAccagaatcgtacttctgaag	9	8	1	3			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr5:175774922A>C	ENST00000298569.4	-	8	1243		c.e8+1		KIAA1191_ENST00000393725.2_Splice_Site|KIAA1191_ENST00000393728.2_Splice_Site|RP11-843P14.2_ENST00000508187.1_RNA|KIAA1191_ENST00000510164.1_Splice_Site	NM_020444.3	NP_065177.2	Q96A73	P33MX_HUMAN	KIAA1191							cytoplasm (GO:0005737)	oxidoreductase activity (GO:0016491)			endometrium(1)|kidney(1)|lung(2)|ovary(1)|skin(1)	6	all_cancers(89;0.00575)|Renal(175;0.000269)|Lung NSC(126;0.0105)|all_lung(126;0.0168)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	Kidney(146;0.101)		GTGCTGCCTTACCAGAATCGT	0.458																																					.		Atlas-SNP	.											.	KIAA1191	12	.	0			c.709+2T>G						.						118	118	118					5																	175774922		2203	4300	6503	SO:0001630	splice_region_variant	57179	exon8			TGCCTTACCAGAA	BC010448	CCDS4399.1, CCDS43402.1, CCDS75373.1	5q35.2	2008-02-05			ENSG00000122203	ENSG00000122203			29209	protein-coding gene	gene with protein product						10574461, 10565538	Standard	XM_005265941		Approved	FLJ21022	uc003mdy.3	Q96A73	OTTHUMG00000130656	ENST00000298569.4:c.709+1T>G	chr5.hg19:g.175774922A>C		109.0	0.0		161.0	44.0	NM_001079685	B2RD69|B8K1S6|Q6IA24|Q8NDU3|Q9BRE5|Q9H7D5|Q9ULM9	Splice_Site	SNP	ENST00000298569.4	hg19	CCDS4399.1	.	.	.	.	.	.	.	.	.	.	A	10.36	1.327886	0.24080	.	.	ENSG00000122203	ENST00000298569;ENST00000393725;ENST00000510164	.	.	.	5.3	5.3	0.74995	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.7317	0.46100	0.9255:0.0:0.0745:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	KIAA1191	175707528	1.000000	0.71417	0.992000	0.48379	0.285000	0.27093	5.053000	0.64269	2.123000	0.65237	0.533000	0.62120	.	.	.		0.458	KIAA1191-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253146.2	NM_020444	Intron	C	175774922	A	C	175774922	5	2	317	1	0	0	0	0	0	0	1	0	8221	405	14	5	214	5	KIAA1191	5	175774922	Splice_Site	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	19184917	175774922	5140338	63	44705										
CDHR2	54825	hgsc.bcm.edu	37	chr5	176016107	176016107	+	Frame_Shift_Del	DEL	G	G	-													0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tagacttcatctctaaggacGgggccaccatccctttccag					rs373435992		TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr5:176016107delG	ENST00000510636.1	+	22	3206	c.2932delG	c.(2932-2934)gggfs	p.G978fs	CDHR2_ENST00000261944.5_Frame_Shift_Del_p.G978fs|CDHR2_ENST00000506348.1_Frame_Shift_Del_p.G978fs	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	978	Cadherin 9. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.G978W(1)		breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|liver(1)|lung(23)|ovary(3)|prostate(5)|skin(4)|urinary_tract(1)	56						CTCTAAGGACGGGGCCACCAT	0.577																																					p.D977fs		Atlas-Indel,Pindel	.											.	CDHR2	152	.	1	Substitution - Missense(1)	lung(1)	c.2931delC						.						227	218	221					5																	176016107		2203	4300	6503	SO:0001589	frameshift_variant	54825	exon22			.	AB047004	CCDS34297.1	5q35.2	2011-07-01	2010-01-25	2010-01-25		ENSG00000074276		"Cadherins / Cadherin-related"	18231	protein-coding gene	gene with protein product	"protocadherin LKC"		"protocadherin 24"	PCDH24		11082270, 12117771	Standard	NM_001171976		Approved	PC-LKC, FLJ20124, FLJ20383, PCLKC	uc003mem.2	Q9BYE9		ENST00000510636.1:c.2932delG	chr5.hg19:g.176016107delG	ENSP00000424565:p.Gly978fs	93.0	0.0		111.0	23.0	NM_001171976	A1L3U4|A6NC80|Q9NXP8	Frame_Shift_Del	DEL	ENST00000510636.1	hg19	CCDS34297.1																																																																																			.	.		0.577	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675		-	176016107	G	-	176016107	7	5	317	1	0	1	0	1	0	0	0	0	3121	1116	39	0	3014	0	CDHR2	5	176016107	Frame_Shift_Del	DEL	G	TCGA-LG-A6GG-01A-11D-A30V-10	241185	176016107	4899153	64	44706										
TRIM52	84851	hgsc.bcm.edu	37	chr5	180684462	180684462	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gctttcttgctctatctgaaGtattcccaccagagttgttt	7	10	3	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr5:180684462G>T	ENST00000327767.4	-	2	1151	c.847C>A	c.(847-849)Ctt>Att	p.L283I	CTC-338M12.4_ENST00000511331.1_RNA|AC008443.1_ENST00000599439.1_3'UTR|CTC-338M12.4_ENST00000505151.1_RNA|TRIM52_ENST00000514805.1_5'Flank|CTC-338M12.4_ENST00000417281.2_RNA|CTC-338M12.4_ENST00000506340.1_RNA	NM_032765.2	NP_116154.1	Q96A61	TRI52_HUMAN	tripartite motif containing 52	283					positive regulation of NF-kappaB transcription factor activity (GO:0051092)	intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(3)|skin(1)|stomach(1)	8	all_cancers(89;8.79e-06)|all_epithelial(37;1.13e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0654)	all_cancers(40;0.0106)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.0588)|all_lung(500;0.149)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.232)		TCTATCTGAAGTATTCCCACC	0.333																																					p.L283I		Atlas-SNP	.											.	TRIM52	20	.	0			c.C847A						.						129	114	119					5																	180684462		2201	4300	6501	SO:0001583	missense	84851	exon2			TCTGAAGTATTCC		CCDS4467.1	5q35.3	2013-01-09	2011-01-25		ENSG00000183718	ENSG00000183718		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19024	protein-coding gene	gene with protein product			"tripartite motif-containing 52"				Standard	NM_032765		Approved	RNF102	uc003mnp.3	Q96A61	OTTHUMG00000130964	ENST00000327767.4:c.847C>A	chr5.hg19:g.180684462G>T	ENSP00000332152:p.Leu283Ile	143.0	0.0		223.0	42.0	NM_032765		Missense_Mutation	SNP	ENST00000327767.4	hg19	CCDS4467.1	.	.	.	.	.	.	.	.	.	.	g	1.308	-0.602894	0.03744	.	.	ENSG00000183718	ENST00000327767	T	0.22743	1.94	2.24	0.374	0.16183	.	.	.	.	.	T	0.08537	0.0212	N	0.08118	0	0.09310	N	1	B	0.27192	0.171	B	0.15870	0.014	T	0.26677	-1.0096	9	0.52906	T	0.07	.	3.5641	0.07893	0.1607:0.2636:0.5757:0.0	.	283	Q96A61	TRI52_HUMAN	I	283	ENSP00000332152:L283I	ENSP00000332152:L283I	L	-	1	0	TRIM52	180617068	0.000000	0.05858	0.086000	0.20670	0.183000	0.23260	-0.421000	0.07053	0.062000	0.16340	0.561000	0.74099	CTT	.	.		0.333	TRIM52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253572.3	NM_032765		T	180684462	G	T	180684462	3	4	317	1	0	0	0	0	1	0	0	0	16542	1029	36	3	50	3	TRIM52	5	180684462	Missense_Mutation	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	4668355	180684462	230798	65	44707										
SLC17A3	10786	hgsc.bcm.edu	37	chr6	25850686	25850686	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	aagggaaggaaacatactcaCgtctctgatgttaacatggt	10	7	2	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr6:25850686C>T	ENST00000360657.3	-	7	1045		c.e7+1		SLC17A3_ENST00000361703.6_Splice_Site|SLC17A3_ENST00000397060.4_Splice_Site			O00476	NPT4_HUMAN	solute carrier family 17 (organic anion transporter), member 3						drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|glucose-6-phosphate transport (GO:0015760)|ion transmembrane transport (GO:0034220)|organic acid transport (GO:0015849)|organic anion transport (GO:0015711)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|regulation of anion transport (GO:0044070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|efflux transmembrane transporter activity (GO:0015562)|organic anion transmembrane transporter activity (GO:0008514)|sodium:phosphate symporter activity (GO:0005436)|toxin transporter activity (GO:0019534)|urate transmembrane transporter activity (GO:0015143)|voltage-gated anion channel activity (GO:0008308)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)	20						AACATACTCACGTCTCTGATG	0.403																																					.		Atlas-SNP	.											.	SLC17A3	95	.	0			c.759+1G>A						.						180	139	153					6																	25850686		2203	4300	6503	SO:0001630	splice_region_variant	10786	exon8			TACTCACGTCTCT	U90545	CCDS4566.2, CCDS47385.1	6p22.2	2013-07-18	2013-07-18		ENSG00000124564	ENSG00000124564		"Solute carriers"	10931	protein-coding gene	gene with protein product		611034	"solute carrier family 17 (sodium phosphate), member 3"			9149941	Standard	NM_006632		Approved	NPT4	uc003nfk.4	O00476	OTTHUMG00000014412	ENST00000360657.3:c.759+1G>A	chr6.hg19:g.25850686C>T		160.0	0.0		157.0	41.0	NM_006632	B7WNJ5|B7Z511|Q8WWC7|Q9H533	Splice_Site	SNP	ENST00000360657.3	hg19	CCDS4566.2	.	.	.	.	.	.	.	.	.	.	C	7.632	0.679015	0.14841	.	.	ENSG00000124564	ENST00000397060;ENST00000360657;ENST00000361703	.	.	.	3.53	2.66	0.31614	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.9028	0.24293	0.0:0.873:0.0:0.127	.	.	.	.	.	-1	.	.	.	-	.	.	SLC17A3	25958665	0.996000	0.38824	0.999000	0.59377	0.323000	0.28346	4.283000	0.58977	1.050000	0.40346	-0.237000	0.12165	.	.	.		0.403	SLC17A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040070.2		Intron	T	25850686	C	T	25850686	5	4	317	1	0	0	0	0	0	0	1	0	14433	550	19	1	522	1	SLC17A3	6	25850686	Splice_Site	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10		25850686	145264381	66	44708										
HIST1H2BE	8344	hgsc.bcm.edu	37	chr6	26184113	26184113	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	aagaaggacggcaagaagcgCaagcgcagccgcaaggagag	16	9	0	3			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr6:26184113C>G	ENST00000356530.3	+	1	156	c.90C>G	c.(88-90)cgC>cgG	p.R30R		NM_003523.2	NP_003514.2	P62807	H2B1C_HUMAN	histone cluster 1, H2be	30					antibacterial humoral response (GO:0019731)|chromatin organization (GO:0006325)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|nucleosome assembly (GO:0006334)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|large_intestine(2)|lung(1)	4						GCAAGAAGCGCAAGCGCAGCC	0.587																																					p.R30R		Atlas-SNP	.											.	HIST1H2BE	10	.	0			c.C90G						.						148	135	140					6																	26184113		2203	4300	6503	SO:0001819	synonymous_variant	8344	exon1			GAAGCGCAAGCGC	Z80780	CCDS4588.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000197697	ENSG00000274290		"Histones / Replication-dependent"	4753	protein-coding gene	gene with protein product		602805	"H2B histone family, member H", "histone 1, H2be"	H2BFH		9119399, 12408966	Standard	NM_003523		Approved	H2B/h, H2B.h	uc003ngt.3	P62807	OTTHUMG00000014427	ENST00000356530.3:c.90C>G	chr6.hg19:g.26184113C>G		148.0	0.0		160.0	42.0	NM_003523	P02278|Q3B872|Q4VB69|Q93078|Q93080	Silent	SNP	ENST00000356530.3	hg19	CCDS4588.1																																																																																			.	.		0.587	HIST1H2BE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040090.1	NM_003523		G	26184113	C	G	26184113	2	3	317	1	0	0	0	0	0	0	0	1	7153	697	25	4		4	HIST1H2BE	6	26184113	Silent	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	333427	26184113	144930954	67	44709										
FANCE	2178	hgsc.bcm.edu	37	chr6	35428340	35428340	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gctttgcagacagatcttggAgctgccctggaaggaggaaa	14	8	1	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr6:35428340A>G	ENST00000229769.2	+	8	1513	c.1328A>G	c.(1327-1329)gAg>gGg	p.E443G		NM_021922.2	NP_068741.1	Q9HB96	FANCE_HUMAN	Fanconi anemia, complementation group E	443					DNA repair (GO:0006281)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|ovary(1)|skin(2)	13						CAGATCTTGGAGCTGCCCTGG	0.562			"N, F, S"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.E443G		Atlas-SNP	.	yes	Rec		Fanconi anaemia E	6	6p21-p22	2178	"Fanconi anemia, complementation group E"		L	.	FANCE	45	.	0			c.A1328G						.						87	82	83					6																	35428340		2203	4300	6503	SO:0001583	missense	2178	exon8	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TCTTGGAGCTGCC	AF265210	CCDS4805.1	6p22-p21	2014-09-17			ENSG00000112039	ENSG00000112039		"Fanconi anemia, complementation groups"	3586	protein-coding gene	gene with protein product		613976		FACE		7662964, 11001585	Standard	XM_005248885		Approved	FAE	uc003oko.1	Q9HB96	OTTHUMG00000014565	ENST00000229769.2:c.1328A>G	chr6.hg19:g.35428340A>G	ENSP00000229769:p.Glu443Gly	76.0	0.0		109.0	32.0	NM_021922	A8K907|Q4ZGH2	Missense_Mutation	SNP	ENST00000229769.2	hg19	CCDS4805.1	.	.	.	.	.	.	.	.	.	.	A	14.89	2.670059	0.47677	.	.	ENSG00000112039	ENST00000229769	T	0.45276	0.9	4.97	4.97	0.65823	Fanconi Anaemia group E protein, C-terminal (1);	0.388525	0.29133	N	0.013059	T	0.32823	0.0842	L	0.55103	1.725	0.35519	D	0.801275	D	0.54601	0.967	P	0.49708	0.62	T	0.21314	-1.0249	10	0.37606	T	0.19	-8.5378	11.3467	0.49565	1.0:0.0:0.0:0.0	.	443	Q9HB96	FANCE_HUMAN	G	443	ENSP00000229769:E443G	ENSP00000229769:E443G	E	+	2	0	FANCE	35536318	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.236000	0.51336	1.988000	0.58038	0.533000	0.62120	GAG	.	.		0.562	FANCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040282.1			G	35428340	A	G	35428340	3	3	317	1	0	0	0	0	1	0	0	0	5674	304	11	2	1358	2	FANCE	6	35428340	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	9244227	35428340	135686727	68	44710										
MDGA1	266727	hgsc.bcm.edu	37	chr6	37611713	37611713	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tcgatgtctcgatgaacatgTagtagcctgcggggaatggg	15	7	1	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr6:37611713T>C	ENST00000434837.3	-	14	3586	c.2408A>G	c.(2407-2409)tAc>tGc	p.Y803C	MDGA1_ENST00000297153.7_Missense_Mutation_p.Y807C|MDGA1_ENST00000510077.1_5'Flank|MDGA1_ENST00000505425.1_Missense_Mutation_p.Y803C	NM_153487.3	NP_705691.1	Q8NFP4	MDGA1_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 1	803	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				brain development (GO:0007420)|cerebral cortex radially oriented cell migration (GO:0021799)|neuron migration (GO:0001764)|spinal cord association neuron differentiation (GO:0021527)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)				central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	38						GATGAACATGTAGTAGCCTGC	0.592																																					p.Y803C		Atlas-SNP	.											.	MDGA1	104	.	0			c.A2408G						.						49	53	52					6																	37611713		2043	4190	6233	SO:0001583	missense	266727	exon14			AACATGTAGTAGC	AF478693	CCDS47417.1	6p21	2013-01-29			ENSG00000112139	ENSG00000112139		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19267	protein-coding gene	gene with protein product		609626				15922729, 15019943	Standard	NM_153487		Approved	GPIM, MAMDC3	uc003onu.1	Q8NFP4	OTTHUMG00000014626	ENST00000434837.3:c.2408A>G	chr6.hg19:g.37611713T>C	ENSP00000402584:p.Tyr803Cys	63.0	0.0		76.0	20.0	NM_153487	A6NHG0|Q8NBE3	Missense_Mutation	SNP	ENST00000434837.3	hg19	CCDS47417.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.2|20.2	3.943199|3.943199	0.73672|0.73672	.|.	.|.	ENSG00000112139|ENSG00000112139	ENST00000418178|ENST00000434837;ENST00000297153;ENST00000505425	.|T;T;T	.|0.03982	.|3.74;3.74;3.74	5.8|5.8	5.8|5.8	0.92144|0.92144	.|Concanavalin A-like lectin/glucanase (1);MAM domain (3);	.|0.000000	.|0.45867	.|D	.|0.000322	T|T	0.24005|0.24005	0.0581|0.0581	H|H	0.95611|0.95611	3.695|3.695	0.46725|0.46725	D|D	0.999179|0.999179	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.83275	.|0.996;0.992	T|T	0.30357|0.30357	-0.9981|-0.9981	5|10	.|0.87932	.|D	.|0	.|.	13.8959|13.8959	0.63770|0.63770	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|803;803	.|Q8NFP4-2;Q8NFP4	.|.;MDGA1_HUMAN	A|C	113|803;807;803	.|ENSP00000402584:Y803C;ENSP00000297153:Y807C;ENSP00000422042:Y803C	.|ENSP00000297153:Y807C	T|Y	-|-	1|2	0|0	MDGA1|MDGA1	37719691|37719691	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.950000|0.950000	0.60333|0.60333	4.722000|4.722000	0.61958|0.61958	2.209000|2.209000	0.71365|0.71365	0.533000|0.533000	0.62120|0.62120	ACA|TAC	.	.		0.592	MDGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040419.3			C	37611713	T	C	37611713	3	2	317	1	0	0	0	0	1	0	0	0	9415	1638	57	2	475	2	MDGA1	6	37611713	Missense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	2183373	37611713	133503354	69	44711										
KIF6	221458	hgsc.bcm.edu	37	chr6	39311593	39311593	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	cactggcctcttggggatgcTggaggcaaccacgtgtcaca	13	12	2	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr6:39311593T>A	ENST00000287152.7	-	22	2416		c.e22-2		KIF6_ENST00000373216.3_Splice_Site|KIF6_ENST00000229913.5_Splice_Site|KIF6_ENST00000373215.3_Splice_Site|KIF6_ENST00000394362.1_Splice_Site|KIF6_ENST00000373213.4_Splice_Site|KIF6_ENST00000538893.1_Splice_Site|KIF6_ENST00000541946.1_Splice_Site	NM_145027.4	NP_659464.3	Q6ZMV9	KIF6_HUMAN	kinesin family member 6						ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|male germ cell nucleus (GO:0001673)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(16)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						TTGGGGATGCTGGAGGCAACC	0.493																																					.		Atlas-SNP	.											.	KIF6	233	.	0			c.2322-2A>T						.						135	97	110					6																	39311593		2203	4300	6503	SO:0001630	splice_region_variant	221458	exon23			GGATGCTGGAGGC	AL832634	CCDS4844.1, CCDS75449.1	6p21.2	2010-03-30			ENSG00000164627	ENSG00000164627		"Kinesins"	21202	protein-coding gene	gene with protein product		613919	"chromosome 6 open reading frame 102"	C6orf102			Standard	NM_145027		Approved	dJ1043E3.1, MGC33317, dJ137F1.4, dJ188D3.1, DKFZp451I2418	uc003oot.2	Q6ZMV9	OTTHUMG00000014648	ENST00000287152.7:c.2322-2A>T	chr6.hg19:g.39311593T>A		90.0	0.0		76.0	28.0	NM_145027	Q2MDE3|Q2MDE4|Q5T8J6|Q6ZWE3|Q86T87|Q8WTV4	Splice_Site	SNP	ENST00000287152.7	hg19	CCDS4844.1	.	.	.	.	.	.	.	.	.	.	T	11.79	1.743077	0.30865	.	.	ENSG00000164627	ENST00000287152;ENST00000458470;ENST00000394362;ENST00000373216;ENST00000373213;ENST00000229913;ENST00000373215;ENST00000538893;ENST00000541946	.	.	.	4.91	3.72	0.42706	.	.	.	.	.	.	.	.	.	.	.	0.29465	N	0.857503	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.6963	0.28596	0.0:0.1019:0.0:0.8981	.	.	.	.	.	-1	.	.	.	-	.	.	KIF6	39419571	0.990000	0.36364	0.213000	0.23690	0.091000	0.18340	2.047000	0.41269	1.817000	0.53016	0.379000	0.24179	.	.	.		0.493	KIF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040455.2	NM_145027	Intron	A	39311593	T	A	39311593	5	1	317	1	0	0	0	0	0	0	1	0	8317	1594	55	4	132	4	KIF6	6	39311593	Splice_Site	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	1699880	39311593	131803474	70	44712										
TRERF1	55809	hgsc.bcm.edu	37	chr6	42200563	42200563	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	aggggatggcacctcgggccTtggtcacctggttggtgccc	16	12	1	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr6:42200563T>C	ENST00000372922.4	-	17	3696	c.3134A>G	c.(3133-3135)aAg>aGg	p.K1045R	TRERF1_ENST00000354325.2_Missense_Mutation_p.K962R|TRERF1_ENST00000541110.1_Missense_Mutation_p.K1065R|TRERF1_ENST00000340840.2_Missense_Mutation_p.K974R|TRERF1_ENST00000372917.4_Missense_Mutation_p.K974R	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	1045	Interacts with CREBBP.				cholesterol catabolic process (GO:0006707)|homeostatic process (GO:0042592)|multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone biosynthetic process (GO:0046885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|steroid biosynthetic process (GO:0006694)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			ACCTCGGGCCTTGGTCACCTG	0.612																																					p.K1045R		Atlas-SNP	.											.	TRERF1	124	.	0			c.A3134G						.						43	37	39					6																	42200563		2203	4300	6503	SO:0001583	missense	55809	exon17			CGGGCCTTGGTCA	AF297872	CCDS4867.1, CCDS75455.1	6p21.1-p12.1	2012-09-25			ENSG00000124496	ENSG00000124496			18273	protein-coding gene	gene with protein product		610322	"breast cancer anti-estrogen resistance 2"	BCAR2		11349124	Standard	XM_005249223		Approved	TReP-132, HSA277276, RAPA, dJ139D8.5	uc003osd.2	Q96PN7	OTTHUMG00000014698	ENST00000372922.4:c.3134A>G	chr6.hg19:g.42200563T>C	ENSP00000362013:p.Lys1045Arg	36.0	0.0		56.0	12.0	NM_033502	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Missense_Mutation	SNP	ENST00000372922.4	hg19	CCDS4867.1	.	.	.	.	.	.	.	.	.	.	T	17.02	3.282926	0.59867	.	.	ENSG00000124496	ENST00000541110;ENST00000372917;ENST00000372922;ENST00000340840;ENST00000354325	T;T;T;T;T	0.31769	1.48;1.48;1.48;1.48;1.48	5.54	5.54	0.83059	.	0.224693	0.30999	N	0.008446	T	0.29850	0.0746	N	0.24115	0.695	0.37052	D	0.897636	D;D;D;D;P	0.71674	0.998;0.997;0.997;0.998;0.497	D;D;D;D;B	0.80764	0.994;0.985;0.985;0.994;0.242	T	0.12400	-1.0549	10	0.33141	T	0.24	-5.4772	15.7331	0.77822	0.0:0.0:0.0:1.0	.	962;1065;1045;801;813	Q96PN7-4;Q05GC8;Q96PN7;Q96PN7-2;Q96PN7-3	.;.;TREF1_HUMAN;.;.	R	1065;974;1045;974;962	ENSP00000439689:K1065R;ENSP00000362008:K974R;ENSP00000362013:K1045R;ENSP00000339438:K974R;ENSP00000346285:K962R	ENSP00000339438:K974R	K	-	2	0	TRERF1	42308541	1.000000	0.71417	0.994000	0.49952	0.994000	0.84299	5.505000	0.66981	2.123000	0.65237	0.477000	0.44152	AAG	.	.		0.612	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2	NM_033502		C	42200563	T	C	42200563	3	2	317	1	0	0	0	0	1	0	0	0	16490	1609	56	2	476	2	TRERF1	6	42200563	Missense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	2888970	42200563	128914504	71	44713										
C6orf138	442213	hgsc.bcm.edu	37	chr6	47846685	47846685	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ggatgctctttgagagggatAggggcctcagcttttccaac	13	9	2	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr6:47846685A>T	ENST00000339488.4	-	3	1928	c.1895T>A	c.(1894-1896)cTa>cAa	p.L632Q		NM_001013732.3	NP_001013754.3	Q6ZW05	PTHD4_HUMAN	patched domain containing 4	632						integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)										TGAGAGGGATAGGGGCCTCAG	0.478																																					p.L632Q		Atlas-SNP	.											.	.	.	.	0			c.T1895A						.						185	175	179					6																	47846685		2203	4300	6503	SO:0001583	missense	442213	exon3			AGGGATAGGGGCC		CCDS34473.2	6p12.3	2012-02-06	2012-02-06	2012-02-06	ENSG00000244694	ENSG00000244694			21345	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 138"	C6orf138			Standard	NM_001013732		Approved	dJ402H5.2, FLJ41841	uc011dwm.2	Q6ZW05	OTTHUMG00000150404	ENST00000339488.4:c.1895T>A	chr6.hg19:g.47846685A>T	ENSP00000341914:p.Leu632Gln	50.0	0.0		53.0	13.0	NM_001013732	B0QZ29|B4DRK3|Q5T884	Missense_Mutation	SNP	ENST00000339488.4	hg19	CCDS34473.2	.	.	.	.	.	.	.	.	.	.	A	17.30	3.353500	0.61293	.	.	ENSG00000244694	ENST00000339488	D	0.86097	-2.07	5.91	5.91	0.95273	.	0.000000	0.64402	D	0.000001	D	0.89918	0.6854	M	0.66939	2.045	0.80722	D	1	D	0.69078	0.997	D	0.79784	0.993	D	0.90563	0.4517	10	0.56958	D	0.05	.	16.35	0.83199	1.0:0.0:0.0:0.0	.	632	Q6ZW05	CF138_HUMAN	Q	632	ENSP00000341914:L632Q	ENSP00000341914:L632Q	L	-	2	0	C6orf138	47954644	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.270000	0.75569	0.528000	0.53228	CTA	.	.		0.478	PTCHD4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317987.2	NM_001013732		T	47846685	A	T	47846685	3	4	317	1	0	0	0	0	1	0	0	0	2334	420	15	4	649	4	C6orf138	6	47846685	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	5646122	47846685	123268382	72	44714										
PKHD1	5314	hgsc.bcm.edu	37	chr6	51923279	51923279	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	atgctctgcttccaggtagtAcatggctccacccaacagct	8	14	1	0	rs201989004		TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr6:51923279A>T	ENST00000371117.3	-	16	1629	c.1354T>A	c.(1354-1356)Tac>Aac	p.Y452N	PKHD1_ENST00000340994.4_Missense_Mutation_p.Y452N	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	452					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					TCCAGGTAGTACATGGCTCCA	0.557																																					p.Y452N		Atlas-SNP	.											.	PKHD1	927	.	0			c.T1354A						.						203	175	184					6																	51923279		2203	4300	6503	SO:0001583	missense	5314	exon16			GGTAGTACATGGC	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.1354T>A	chr6.hg19:g.51923279A>T	ENSP00000360158:p.Tyr452Asn	52.0	0.0		107.0	37.0	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	hg19	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.445970	0.84101	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.92545	-2.79;-3.06	5.94	5.94	0.96194	.	0.086604	0.50627	D	0.000120	D	0.95683	0.8596	M	0.83223	2.63	0.36492	D	0.868481	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	D	0.97014	0.9738	10	0.87932	D	0	.	15.5809	0.76439	1.0:0.0:0.0:0.0	.	452;452	P08F94-2;P08F94	.;PKHD1_HUMAN	N	452	ENSP00000360158:Y452N;ENSP00000341097:Y452N	ENSP00000341097:Y452N	Y	-	1	0	PKHD1	52031238	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.186000	0.72026	2.275000	0.75901	0.528000	0.53228	TAC	.	A|1.000;G|0.000		0.557	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		T	51923279	A	T	51923279	3	4	317	1	0	0	0	0	1	0	0	0	11980	391	14	4	11117	4	PKHD1	6	51923279	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	4076594	51923279	119191788	73	44715										
COL9A1	1297	hgsc.bcm.edu	37	chr6	70981793	70981793	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gtccaggaataccacggcccTaaaagagtacaataaaaatg	8	9	0	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr6:70981793T>A	ENST00000357250.6	-	13	1224		c.e13-2		COL9A1_ENST00000320755.7_Splice_Site|COL9A1_ENST00000489611.1_Splice_Site|COL9A1_ENST00000370499.4_Intron	NM_001851.4	NP_001842.3	P20849	CO9A1_HUMAN	collagen, type IX, alpha 1						axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|organ morphogenesis (GO:0009887)|tissue homeostasis (GO:0001894)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(44)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)	80						ACCACGGCCCTAAAAGAGTAC	0.323																																					.		Atlas-SNP	.											.	COL9A1	228	.	0			c.1066-2A>T						.						43	46	45					6																	70981793		2202	4299	6501	SO:0001630	splice_region_variant	1297	exon14			CGGCCCTAAAAGA		CCDS4971.1, CCDS47447.1	6q13	2013-05-07			ENSG00000112280	ENSG00000112280		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2217	protein-coding gene	gene with protein product		120210				1429648	Standard	NM_001851		Approved		uc003pfg.4	P20849	OTTHUMG00000014988	ENST00000357250.6:c.1066-2A>T	chr6.hg19:g.70981793T>A		393.0	0.0		388.0	113.0	NM_001851	Q13699|Q13700|Q5TF52|Q6P467|Q96BM8|Q99225|Q9H151|Q9H152|Q9Y6P2|Q9Y6P3	Splice_Site	SNP	ENST00000357250.6	hg19	CCDS4971.1	.	.	.	.	.	.	.	.	.	.	T	15.71	2.915352	0.52546	.	.	ENSG00000112280	ENST00000357250;ENST00000320755	.	.	.	6.01	4.79	0.61399	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.7159	0.46013	0.0:0.0:0.1594:0.8406	.	.	.	.	.	-1	.	.	.	-	.	.	COL9A1	71038514	1.000000	0.71417	0.958000	0.39756	0.756000	0.42949	2.968000	0.49224	2.307000	0.77673	0.528000	0.53228	.	.	.		0.323	COL9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041131.2		Intron	A	70981793	T	A	70981793	5	1	317	1	0	0	0	0	0	0	1	0	3709	1536	53	4	1805	4	COL9A1	6	70981793	Splice_Site	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	19058514	70981793	100133274	74	44716										
PHIP	55023	hgsc.bcm.edu	37	chr6	79688417	79688417	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ccattttcagttagttctccCacagccaatctctgacaaaa	4	13	3	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr6:79688417C>G	ENST00000275034.4	-	24	2948	c.2781G>C	c.(2779-2781)gtG>gtC	p.V927V	PHIP_ENST00000479165.1_5'UTR	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	927	Mediates interaction with IRS1. {ECO:0000250}.				cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		TTAGTTCTCCCACAGCCAATC	0.323																																					p.V927V		Atlas-SNP	.											.	PHIP	177	.	0			c.G2781C						.						71	68	69					6																	79688417		2203	4300	6503	SO:0001819	synonymous_variant	55023	exon24			TTCTCCCACAGCC	AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	15673	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 14"	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.2781G>C	chr6.hg19:g.79688417C>G		159.0	0.0		97.0	47.0	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000275034.4	hg19	CCDS4987.1																																																																																			.	.		0.323	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2			G	79688417	C	G	79688417	2	3	317	1	0	0	0	0	0	0	0	1	11851	581	21	4		4	PHIP	6	79688417	Silent	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	8706624	79688417	91426650	75	44717										
MDN1	23195	hgsc.bcm.edu	37	chr6	90388402	90388402	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ggcttctgaccgctgcttctCcttctctgcagagggttcca	10	14	3	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr6:90388402C>T	ENST00000369393.3	-	75	12443	c.12328G>A	c.(12328-12330)Gag>Aag	p.E4110K	MDN1_ENST00000428876.1_Missense_Mutation_p.E4110K|RP1-122O8.7_ENST00000438877.1_RNA			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	4110					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		CGCTGCTTCTCCTTCTCTGCA	0.478																																					p.E4110K		Atlas-SNP	.											.	MDN1	478	.	0			c.G12328A						.						150	137	142					6																	90388402		2203	4300	6503	SO:0001583	missense	23195	exon75			GCTTCTCCTTCTC	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.12328G>A	chr6.hg19:g.90388402C>T	ENSP00000358400:p.Glu4110Lys	121.0	0.0		107.0	35.0	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	hg19	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	C	16.68	3.189360	0.57909	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.03663	3.85;3.85	5.13	5.13	0.70059	.	0.061513	0.64402	D	0.000006	T	0.02970	0.0088	M	0.77616	2.38	0.58432	D	0.999992	B	0.32653	0.379	B	0.23716	0.048	T	0.17107	-1.0380	10	0.49607	T	0.09	.	12.9533	0.58413	0.0:0.922:0.0:0.078	.	4110	Q9NU22	MDN1_HUMAN	K	4110	ENSP00000358400:E4110K;ENSP00000413970:E4110K	ENSP00000358400:E4110K	E	-	1	0	MDN1	90445123	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	7.382000	0.79729	2.388000	0.81334	0.561000	0.74099	GAG	.	.		0.478	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			T	90388402	C	T	90388402	3	4	317	1	0	0	0	0	1	0	0	0	9424	864	30	3	4574	3	MDN1	6	90388402	Missense_Mutation	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	10699985	90388402	80726665	76	44718										
KLHL32	114792	hgsc.bcm.edu	37	chr6	97512550	97512550	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ggatgtgctagcagcgggcaGtcacctacagctgttggagc	15	10	1	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr6:97512550G>T	ENST00000369261.4	+	5	722	c.359G>T	c.(358-360)aGt>aTt	p.S120I	KLHL32_ENST00000536676.1_Missense_Mutation_p.S84I|KLHL32_ENST00000539200.1_Intron|KLHL32_ENST00000544166.1_5'UTR	NM_052904.3	NP_443136.2	Q96NJ5	KLH32_HUMAN	kelch-like family member 32	120										breast(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(13)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		all_cancers(76;1.19e-06)|Acute lymphoblastic leukemia(125;5.83e-10)|all_hematologic(75;3.67e-07)|all_epithelial(107;0.00778)|Colorectal(196;0.122)		BRCA - Breast invasive adenocarcinoma(108;0.0558)		GCAGCGGGCAGTCACCTACAG	0.428																																					p.S120I		Atlas-SNP	.											.	KLHL32	85	.	0			c.G359T						.						143	109	120					6																	97512550		2203	4300	6503	SO:0001583	missense	114792	exon5			CGGGCAGTCACCT	AB067487	CCDS5038.1, CCDS69154.1, CCDS69155.1, CCDS75495.1	6q16.3	2013-02-22	2013-02-22	2007-01-09	ENSG00000186231	ENSG00000186231		"Kelch-like", "BTB/POZ domain containing"	21221	protein-coding gene	gene with protein product			"BTB and kelch domain containing 5", "KIAA1900", "kelch-like 32 (Drosophila)"	BKLHD5, KIAA1900			Standard	NM_052904		Approved		uc010kcm.1	Q96NJ5	OTTHUMG00000015247	ENST00000369261.4:c.359G>T	chr6.hg19:g.97512550G>T	ENSP00000358265:p.Ser120Ile	94.0	0.0		92.0	33.0	NM_052904	B7Z346|B7Z4E2|E1P528|Q5THT0|Q96PY7	Missense_Mutation	SNP	ENST00000369261.4	hg19	CCDS5038.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.870181	0.91587	.	.	ENSG00000186231	ENST00000369255;ENST00000369261;ENST00000536676;ENST00000369254;ENST00000447886	T;T;T;T	0.68765	-0.35;1.73;-0.35;1.75	5.54	5.54	0.83059	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	T	0.73953	0.3653	L	0.48362	1.52	0.80722	D	1	D;D;D	0.71674	0.99;0.985;0.998	D;P;D	0.69142	0.962;0.897;0.941	T	0.74300	-0.3710	10	0.66056	D	0.02	.	19.6787	0.95950	0.0:0.0:1.0:0.0	.	84;120;120	B7Z346;Q96NJ5;Q6IQ08	.;KLH32_HUMAN;.	I	46;120;84;120;16	ENSP00000358265:S120I;ENSP00000440382:S84I;ENSP00000358258:S120I;ENSP00000389310:S16I	ENSP00000358258:S120I	S	+	2	0	KLHL32	97619271	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.722000	0.91452	2.890000	0.99128	0.650000	0.86243	AGT	.	.		0.428	KLHL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041570.1	NM_052904		T	97512550	G	T	97512550	3	4	317	1	0	0	0	0	1	0	0	0	8395	1029	36	3	373	3	KLHL32	6	97512550	Missense_Mutation	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	7124148	97512550	73602517	77	44719										
FBXL4	26235	hgsc.bcm.edu	37	chr6	99374696	99374696	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ggaactgaaatccactacttCtttggcatactggactacct	7	11	1	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr6:99374696C>A	ENST00000369244.2	-	4	597	c.169G>T	c.(169-171)Gaa>Taa	p.E57*	FBXL4_ENST00000229971.1_Nonsense_Mutation_p.E57*	NM_001278716.1	NP_001265645.1	Q9UKA2	FBXL4_HUMAN	F-box and leucine-rich repeat protein 4	57					ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(4)|prostate(3)|skin(2)	18		all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197)		BRCA - Breast invasive adenocarcinoma(108;0.0413)		TCCACTACTTCTTTGGCATAC	0.428																																					p.E57X		Atlas-SNP	.											.	FBXL4	54	.	0			c.G169T						.						239	213	222					6																	99374696		2203	4300	6503	SO:0001587	stop_gained	26235	exon3			CTACTTCTTTGGC	AF176699	CCDS5041.1	6q16.1-q16.3	2011-06-09			ENSG00000112234	ENSG00000112234		"F-boxes / Leucine-rich repeats"	13601	protein-coding gene	gene with protein product		605654				10531035	Standard	NM_012160		Approved	FBL4, FBL5	uc003ppf.1	Q9UKA2	OTTHUMG00000015259	ENST00000369244.2:c.169G>T	chr6.hg19:g.99374696C>A	ENSP00000358247:p.Glu57*	125.0	0.0		86.0	41.0	NM_012160	B2R7Q5|E1P530|O95919|Q5BJH0|Q9UJU0	Nonsense_Mutation	SNP	ENST00000369244.2	hg19	CCDS5041.1	.	.	.	.	.	.	.	.	.	.	C	39	7.637370	0.98403	.	.	ENSG00000112234	ENST00000369244;ENST00000229971	.	.	.	5.52	4.65	0.58169	.	0.044902	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	14.5366	0.67966	0.0:0.9294:0.0:0.0706	.	.	.	.	X	57	.	ENSP00000229971:E57X	E	-	1	0	FBXL4	99481417	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.587000	0.60991	1.466000	0.48025	0.650000	0.86243	GAA	.	.		0.428	FBXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041587.2			A	99374696	C	A	99374696	4	1	317	1	0	0	0	0	0	1	0	0	5729	922	32	3	1724	3	FBXL4	6	99374696	Nonsense_Mutation	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	1862146	99374696	71740371	78	44720										
PRDM1	639	hgsc.bcm.edu	37	chr6	106553643	106553643	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	cagcccaaagctacctcagcAgcgatggcagcccccagcag	10	17	1	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr6:106553643A>T	ENST00000369096.4	+	5	1842	c.1608A>T	c.(1606-1608)gcA>gcT	p.A536A	PRDM1_ENST00000369091.2_Silent_p.A500A|PRDM1_ENST00000369089.3_Silent_p.A402A	NM_001198.3	NP_001189.2	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain	536	Interaction with PIAS1.				cell fate commitment (GO:0045165)|eye photoreceptor cell development (GO:0042462)|germ cell development (GO:0007281)|intestinal epithelial cell development (GO:0060576)|maternal placenta development (GO:0001893)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gene expression (GO:0010628)|post-embryonic development (GO:0009791)|transcription, DNA-templated (GO:0006351)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(59)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(5)|urinary_tract(2)	94	Breast(9;0.022)	all_cancers(87;2.2e-31)|all_epithelial(87;2.03e-21)|Acute lymphoblastic leukemia(125;4.99e-11)|all_lung(197;7.55e-09)|all_hematologic(75;5.82e-08)|Lung NSC(302;1.28e-06)|Colorectal(196;0.0112)|Ovarian(999;0.0365)		all cancers(137;1.83e-46)|Epithelial(106;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(136;1.99e-20)|GBM - Glioblastoma multiforme(226;3.72e-11)|BRCA - Breast invasive adenocarcinoma(108;1.38e-05)		CTACCTCAGCAGCGATGGCAG	0.577			"D, N, Mis, F, S"		DLBCL																																p.A536A		Atlas-SNP	.		Rec	yes		6	6q21	639	"PR domain containing 1, with ZNF domain"		L	.	PRDM1	195	.	0			c.A1608T						.						42	46	45					6																	106553643		2203	4300	6503	SO:0001819	synonymous_variant	639	exon5			CTCAGCAGCGATG		CCDS5054.2, CCDS34505.1	6q21	2013-01-08			ENSG00000057657	ENSG00000057657		"Zinc fingers, C2H2-type"	9346	protein-coding gene	gene with protein product		603423		BLIMP1		1851123	Standard	NM_001198		Approved	PRDI-BF1	uc003prd.2	O75626	OTTHUMG00000015299	ENST00000369096.4:c.1608A>T	chr6.hg19:g.106553643A>T		161.0	0.0		122.0	48.0	NM_001198	B2REA6|E1P5E0|Q86WM7	Silent	SNP	ENST00000369096.4	hg19	CCDS5054.2																																																																																			.	.		0.577	PRDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041661.3			T	106553643	A	T	106553643	2	4	317	1	0	0	0	0	0	0	0	1	12462	175	7	4		4	PRDM1	6	106553643	Silent	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	7178947	106553643	64561424	79	44721										
REV3L	5980	hgsc.bcm.edu	37	chr6	111688372	111688372	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	aagcctttccagaagttttcTctgtatgattggtgtactat	8	7	1	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr6:111688372T>A	ENST00000358835.3	-	15	7073	c.6619A>T	c.(6619-6621)Aga>Tga	p.R2207*	REV3L_ENST00000435970.1_Nonsense_Mutation_p.R2129*|REV3L_ENST00000368805.1_Nonsense_Mutation_p.R2207*|REV3L_ENST00000368802.3_Nonsense_Mutation_p.R2207*			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	2207					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		AGAAGTTTTCTCTGTATGATT	0.408								DNA polymerases (catalytic subunits)																													p.R2207X		Atlas-SNP	.											.	REV3L	386	.	0			c.A6619T						.						98	97	97					6																	111688372		2203	4300	6503	SO:0001587	stop_gained	5980	exon14			GTTTTCTCTGTAT	AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"DNA polymerases"	9968	protein-coding gene	gene with protein product	"polymerase, DNA, zeta"	602776	"REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta", "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.6619A>T	chr6.hg19:g.111688372T>A	ENSP00000351697:p.Arg2207*	136.0	0.0		82.0	37.0	NM_002912	O43214|Q5TC33	Nonsense_Mutation	SNP	ENST00000358835.3	hg19	CCDS5091.2	.	.	.	.	.	.	.	.	.	.	T	31	5.066444	0.93898	.	.	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970;ENST00000543871	.	.	.	5.46	5.46	0.80206	.	0.074533	0.64402	D	0.000013	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.533	15.8257	0.78706	0.0:0.0:0.0:1.0	.	.	.	.	X	2207;2207;2207;2129;280	.	ENSP00000351697:R2207X	R	-	1	2	REV3L	111795065	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.085000	0.57657	2.188000	0.69820	0.533000	0.62120	AGA	.	.		0.408	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		A	111688372	T	A	111688372	4	1	317	1	0	0	0	0	0	1	0	0	13255	1559	54	4	2849	4	REV3L	6	111688372	Nonsense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	5134729	111688372	59426695	80	44722										
REV3L	5980	hgsc.bcm.edu	37	chr6	111693804	111693804	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	aaaataactgattacctgggCttttctggtacatcagaagg	9	7	2	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr6:111693804C>T	ENST00000358835.3	-	14	6208	c.5754G>A	c.(5752-5754)aaG>aaA	p.K1918K	REV3L_ENST00000435970.1_Silent_p.K1840K|REV3L_ENST00000368805.1_Silent_p.K1918K|REV3L_ENST00000368802.3_Silent_p.K1918K			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	1918					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		ATTACCTGGGCTTTTCTGGTA	0.348								DNA polymerases (catalytic subunits)																													p.K1918K		Atlas-SNP	.											.	REV3L	386	.	0			c.G5754A						.						75	79	78					6																	111693804		2203	4300	6503	SO:0001819	synonymous_variant	5980	exon13			CCTGGGCTTTTCT	AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"DNA polymerases"	9968	protein-coding gene	gene with protein product	"polymerase, DNA, zeta"	602776	"REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta", "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.5754G>A	chr6.hg19:g.111693804C>T		95.0	0.0		72.0	34.0	NM_002912	O43214|Q5TC33	Silent	SNP	ENST00000358835.3	hg19	CCDS5091.2																																																																																			.	.		0.348	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		T	111693804	C	T	111693804	2	4	317	1	0	0	0	0	0	0	0	1	13255	796	28	3		3	REV3L	6	111693804	Silent	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	5432	111693804	59421263	81	44723										
ROS1	6098	hgsc.bcm.edu	37	chr6	117686251	117686251	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ggtgctcgaagtgacagagaTgttttggggccctttcccca	13	10	0	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr6:117686251T>A	ENST00000368508.3	-	20	3288	c.3090A>T	c.(3088-3090)acA>acT	p.T1030T	GOPC_ENST00000467125.1_Intron|ROS1_ENST00000368507.3_Silent_p.T1025T	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	1030	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		GTGACAGAGATGTTTTGGGGC	0.398			T	"GOPC, SDC4, SLC34A2, EZR, LRIG3"	"glioblastoma, NSCLC"																																p.T1030T		Atlas-SNP	.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"O, E"	.	ROS1	728	.	0			c.A3090T						.						97	97	97					6																	117686251		2203	4300	6503	SO:0001819	synonymous_variant	6098	exon20			CAGAGATGTTTTG	M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"Fibronectin type III domain containing"	10261	protein-coding gene	gene with protein product		165020	"v-ros avian UR2 sarcoma virus oncogene homolog 1", "v-ros UR2 sarcoma virus oncogene homolog 1 (avian)", "c-ros oncogene 1 , receptor tyrosine kinase"			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.3090A>T	chr6.hg19:g.117686251T>A		144.0	0.0		97.0	42.0	NM_002944	Q15368|Q5TDB5	Silent	SNP	ENST00000368508.3	hg19	CCDS5116.1																																																																																			.	.		0.398	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1			A	117686251	T	A	117686251	2	1	317	1	0	0	0	0	0	0	0	1	13546	1451	51	4		4	ROS1	6	117686251	Silent	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	5992447	117686251	53428816	82	44724										
MED23	9439	hgsc.bcm.edu	37	chr6	131910712	131910712	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	acactggtcaacattcagcaGcatgtcataaaacgccacac	6	13	3	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr6:131910712G>T	ENST00000368068.3	-	28	4011	c.3832C>A	c.(3832-3834)Ctg>Atg	p.L1278M	MED23_ENST00000368060.3_Missense_Mutation_p.L1278M|MED23_ENST00000354577.4_Missense_Mutation_p.L1284M|MED23_ENST00000403834.3_Missense_Mutation_p.L1284M|MED23_ENST00000368058.1_Missense_Mutation_p.L1284M|MED23_ENST00000479213.1_5'UTR|MED23_ENST00000545957.1_Missense_Mutation_p.L919M	NM_004830.3	NP_004821.2	Q9ULK4	MED23_HUMAN	mediator complex subunit 23	1278					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(12)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	44	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608)		ACATTCAGCAGCATGTCATAA	0.378																																					p.L1284M		Atlas-SNP	.											.	MED23	112	.	0			c.C3850A						.						95	86	89					6																	131910712		2203	4300	6503	SO:0001583	missense	9439	exon29			TCAGCAGCATGTC	AF104255	CCDS5146.1, CCDS5147.1, CCDS59039.1	6q22.33-q24.1	2008-02-05	2007-08-08	2007-07-30	ENSG00000112282	ENSG00000112282			2372	protein-coding gene	gene with protein product		605042	"cofactor required for Sp1 transcriptional activation, subunit 3, 130kDa"	CRSP3		9989412	Standard	NM_004830		Approved	CRSP130, DRIP130, Sur2	uc003qcs.2	Q9ULK4	OTTHUMG00000015565	ENST00000368068.3:c.3832C>A	chr6.hg19:g.131910712G>T	ENSP00000357047:p.Leu1278Met	221.0	0.0		142.0	51.0	NM_015979	B9TX55|O95403|Q5JWT3|Q5JWT4|Q6P9H6|Q9H0J2|Q9NTT9|Q9NTU0|Q9Y5P7|Q9Y667	Missense_Mutation	SNP	ENST00000368068.3	hg19	CCDS5147.1	.	.	.	.	.	.	.	.	.	.	G	19.71	3.877552	0.72294	.	.	ENSG00000112282	ENST00000354577;ENST00000368068;ENST00000403834;ENST00000368060;ENST00000368058;ENST00000545957	T;T;T;T;T;T	0.79033	-1.23;-1.23;-1.23;-1.23;-1.23;-1.23	5.39	3.49	0.39957	.	0.000000	0.85682	D	0.000000	T	0.81074	0.4747	L	0.58810	1.83	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.83208	-0.0075	10	0.87932	D	0	-10.1418	13.7755	0.63050	0.0897:0.0:0.9103:0.0	.	1278;1284	Q9ULK4;Q9ULK4-3	MED23_HUMAN;.	M	1284;1278;1284;1278;1284;919	ENSP00000346588:L1284M;ENSP00000357047:L1278M;ENSP00000384536:L1284M;ENSP00000357039:L1278M;ENSP00000357037:L1284M;ENSP00000439977:L919M	ENSP00000346588:L1284M	L	-	1	2	MED23	131952405	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.659000	0.68010	0.519000	0.28406	0.591000	0.81541	CTG	.	.		0.378	MED23-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042215.1			T	131910712	G	T	131910712	3	4	317	1	0	0	0	0	1	0	0	0	9450	962	34	3	289	3	MED23	6	131910712	Missense_Mutation	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	14224461	131910712	39204355	83	44725										
AHI1	54806	hgsc.bcm.edu	37	chr6	135715921	135715921	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gaaaggggctcaccggtctgAgtgaaaccaaactgatgtag	13	8	2	3			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr6:135715921A>C	ENST00000367800.4	-	21	3318	c.3102T>G	c.(3100-3102)acT>acG	p.T1034T	AHI1_ENST00000457866.2_Silent_p.T1034T|AHI1_ENST00000417892.2_Silent_p.T388T|AHI1_ENST00000327035.6_Silent_p.T1034T	NM_001134830.1	NP_001128302.1	Q8N157	AHI1_HUMAN	Abelson helper integration site 1	1034					cellular protein localization (GO:0034613)|central nervous system development (GO:0007417)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|cloaca development (GO:0035844)|heart looping (GO:0001947)|hindbrain development (GO:0030902)|Kupffer's vesicle development (GO:0070121)|left/right axis specification (GO:0070986)|morphogenesis of a polarized epithelium (GO:0001738)|negative regulation of apoptotic process (GO:0043066)|otic vesicle development (GO:0071599)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of polarized epithelial cell differentiation (GO:0030862)|positive regulation of receptor internalization (GO:0002092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pronephric duct morphogenesis (GO:0039023)|pronephric nephron tubule morphogenesis (GO:0039008)|protein localization to organelle (GO:0033365)|regulation of behavior (GO:0050795)|retina layer formation (GO:0010842)|specification of axis polarity (GO:0065001)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vesicle targeting (GO:0006903)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|nonmotile primary cilium (GO:0031513)|photoreceptor outer segment (GO:0001750)|primary cilium (GO:0072372)|TCTN-B9D complex (GO:0036038)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(18)|ovary(1)	37	Breast(56;0.239)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00904)|OV - Ovarian serous cystadenocarcinoma(155;0.00991)		CACCGGTCTGAGTGAAACCAA	0.378																																					p.T1034T		Atlas-SNP	.											.	AHI1	81	.	0			c.T3102G						.						101	100	100					6																	135715921		1868	4106	5974	SO:0001819	synonymous_variant	54806	exon22			GGTCTGAGTGAAA	AJ459824	CCDS47483.1, CCDS47484.1	6q23.2	2013-01-10	2005-11-29		ENSG00000135541	ENSG00000135541		"WD repeat domain containing"	21575	protein-coding gene	gene with protein product	"Jouberin"	608894	"Abelson helper integration site"			15060101, 16240161	Standard	NM_017651		Approved	FLJ20069, ORF1, JBTS3	uc003qgj.3	Q8N157	OTTHUMG00000015631	ENST00000367800.4:c.3102T>G	chr6.hg19:g.135715921A>C		134.0	0.0		107.0	36.0	NM_001134832	E1P584|Q4FD35|Q504T3|Q5TCP9|Q6P098|Q6PIT6|Q8NDX0|Q9H0H2	Silent	SNP	ENST00000367800.4	hg19	CCDS47483.1	.	.	.	.	.	.	.	.	.	.	A	6.050	0.377504	0.11466	.	.	ENSG00000135541	ENST00000367799;ENST00000529865	.	.	.	5.6	4.39	0.52855	.	.	.	.	.	T	0.21881	0.0527	.	.	.	0.29387	N	0.862889	.	.	.	.	.	.	T	0.12785	-1.0534	4	.	.	.	0.0401	9.7582	0.40515	0.9194:0.0:0.0806:0.0	.	.	.	.	R	534;101	.	.	L	-	2	0	AHI1	135757614	0.420000	0.25457	0.319000	0.25293	0.712000	0.41017	1.199000	0.32235	1.008000	0.39264	0.533000	0.62120	CTC	.	.		0.378	AHI1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391948.1	NM_017651		C	135715921	A	C	135715921	2	2	317	1	0	0	0	0	0	0	0	1	413	291	11	5		5	AHI1	6	135715921	Silent	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	3805209	135715921	35399146	84	44726										
RBM16	22828	hgsc.bcm.edu	37	chr6	155145419	155145419	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gtttagtcccaccagcatttCctgtgtcgatgccggttcct	9	13	0	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr6:155145419C>A	ENST00000367178.3	+	17	2554	c.1978C>A	c.(1978-1980)Cct>Act	p.P660T	SCAF8_ENST00000367186.4_Missense_Mutation_p.P726T|SCAF8_ENST00000417268.1_Missense_Mutation_p.P660T|RNU6-824P_ENST00000363724.1_RNA	NM_014892.3	NP_055707.3	Q9UPN6	SCAF8_HUMAN	SR-related CTD-associated factor 8	660	Pro-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase core enzyme binding (GO:0043175)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(15)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	46						ACCAGCATTTCCTGTGTCGAT	0.473																																					p.P660T		Atlas-SNP	.											.	SCAF8	122	.	0			c.C1978A						.						195	190	192					6																	155145419		2203	4300	6503	SO:0001583	missense	22828	exon17			GCATTTCCTGTGT	AB029039	CCDS5247.1, CCDS69226.1, CCDS75541.1	6q25.1-q25.3	2013-02-12	2011-01-10	2011-01-10	ENSG00000213079	ENSG00000213079		"RNA binding motif (RRM) containing"	20959	protein-coding gene	gene with protein product			"RNA binding motif protein 16"	RBM16		10470851	Standard	NM_001286189		Approved	KIAA1116	uc003qpz.3	Q9UPN6	OTTHUMG00000015877	ENST00000367178.3:c.1978C>A	chr6.hg19:g.155145419C>A	ENSP00000356146:p.Pro660Thr	85.0	0.0		80.0	10.0	NM_014892	B7Z888|Q5TBU6|Q6NSK3|Q9BQN8|Q9BX43	Missense_Mutation	SNP	ENST00000367178.3	hg19	CCDS5247.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.667251	0.88348	.	.	ENSG00000213079	ENST00000367178;ENST00000417268;ENST00000367186	T;T;T	0.50548	0.79;0.79;0.74	5.27	5.27	0.74061	.	0.000000	0.64402	U	0.000001	T	0.50411	0.1614	L	0.37750	1.13	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.997;0.997;0.994;0.997	T	0.36286	-0.9754	10	0.23891	T	0.37	.	18.8836	0.92367	0.0:1.0:0.0:0.0	.	705;726;738;660	B7Z876;B7Z888;B7Z3A4;Q9UPN6	.;.;.;SCAF8_HUMAN	T	660;660;726	ENSP00000356146:P660T;ENSP00000413098:P660T;ENSP00000356154:P726T	ENSP00000356146:P660T	P	+	1	0	SCAF8	155187111	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.205000	0.77881	2.454000	0.82982	0.650000	0.86243	CCT	.	.		0.473	SCAF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042798.1	NM_014892		A	155145419	C	A	155145419	3	1	317	1	0	0	0	0	1	0	0	0	13133	855	30	3	2044	3	RBM16	6	155145419	Missense_Mutation	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	19429498	155145419	15969648	85	44727										
RPS6KA2	6196	hgsc.bcm.edu	37	chr6	166862319	166862319	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gtagccatcggtgaagtggaTgttgttcccgtgtaactgct	13	8	0	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr6:166862319T>A	ENST00000265678.4	-	14	1448	c.1225A>T	c.(1225-1227)Atc>Ttc	p.I409F	RPS6KA2_ENST00000481261.2_Missense_Mutation_p.I320F|RPS6KA2_ENST00000405189.3_Missense_Mutation_p.I320F|RPS6KA2_ENST00000510118.1_Missense_Mutation_p.I434F|RPS6KA2_ENST00000503859.1_Missense_Mutation_p.I417F	NM_021135.4	NP_066958.2	Q15349	KS6A2_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 2	409					axon guidance (GO:0007411)|brain renin-angiotensin system (GO:0002035)|cardiac muscle cell apoptotic process (GO:0010659)|cellular response to carbohydrate stimulus (GO:0071322)|heart contraction (GO:0060047)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of meiosis (GO:0045835)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oocyte maturation (GO:0001556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of gene expression (GO:0010628)|regulation of protein processing (GO:0070613)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|ribosomal protein S6 kinase activity (GO:0004711)	p.I409V(1)|p.I417V(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	45		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)		GTGAAGTGGATGTTGTTCCCG	0.557																																					p.I417F		Atlas-SNP	.											RPS6KA2_ENST00000503859,NS,carcinoma,0,2	RPS6KA2	212	.	2	Substitution - Missense(2)	lung(2)	c.A1249T						.						305	222	250					6																	166862319		2203	4300	6503	SO:0001583	missense	6196	exon15			AGTGGATGTTGTT	L07598	CCDS5294.1, CCDS34570.1	6q27	2011-04-05	2002-08-29		ENSG00000071242	ENSG00000071242			10431	protein-coding gene	gene with protein product		601685	"ribosomal protein S6 kinase, 90kD, polypeptide 2"			8141249	Standard	NM_001006932		Approved	RSK, RSK3, HU-2	uc003qvc.1	Q15349	OTTHUMG00000016007	ENST00000265678.4:c.1225A>T	chr6.hg19:g.166862319T>A	ENSP00000265678:p.Ile409Phe	78.0	0.0		49.0	25.0	NM_001006932	B3KTK9|Q15419|Q59GJ3|Q5TI68|Q96J38|Q9UJN5	Missense_Mutation	SNP	ENST00000265678.4	hg19	CCDS5294.1	.	.	.	.	.	.	.	.	.	.	T	5.617	0.298652	0.10622	.	.	ENSG00000071242	ENST00000265678;ENST00000510118;ENST00000503859;ENST00000481261;ENST00000405189	T;T;T;T;T	0.39406	1.08;1.08;1.08;1.08;1.08	4.39	-4.78	0.03209	Protein kinase-like domain (1);	0.436706	0.24485	N	0.038104	T	0.09862	0.0242	N	0.19112	0.55	0.35819	D	0.824425	B;B;B	0.23650	0.0;0.001;0.089	B;B;B	0.14023	0.002;0.007;0.01	T	0.08391	-1.0724	10	0.31617	T	0.26	.	13.1586	0.59533	0.0:0.6033:0.0:0.3967	.	434;417;409	F2Z2J1;Q15349-3;Q15349	.;.;KS6A2_HUMAN	F	409;434;417;320;320	ENSP00000265678:I409F;ENSP00000422435:I434F;ENSP00000427015:I417F;ENSP00000422484:I320F;ENSP00000386050:I320F	ENSP00000265678:I409F	I	-	1	0	RPS6KA2	166782309	0.002000	0.14202	0.574000	0.28523	0.989000	0.77384	-0.761000	0.04751	-1.168000	0.02776	-0.376000	0.06991	ATC	.	.		0.557	RPS6KA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043075.3	NM_021135		A	166862319	T	A	166862319	3	1	317	1	0	0	0	0	1	0	0	0	13666	1464	51	4	1008	4	RPS6KA2	6	166862319	Missense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	11716900	166862319	4252748	86	44728										
THBS2	7058	hgsc.bcm.edu	37	chr6	169639734	169639734	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	cattcgccttccacaaaggaTggactggcgcaggttgcagg	13	11	0	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr6:169639734T>C	ENST00000366787.3	-	8	1338	c.1089A>G	c.(1087-1089)ccA>ccG	p.P363P	XXyac-YX65C7_A.2_ENST00000444188.1_RNA	NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	363	VWFC. {ECO:0000255|PROSITE- ProRule:PRU00220}.				cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		CCACAAAGGATGGACTGGCGC	0.488																																					p.P363P	Esophageal Squamous(91;219 1934 18562 44706)	Atlas-SNP	.											.	THBS2	230	.	0			c.A1089G						.						81	60	67					6																	169639734		2201	4298	6499	SO:0001819	synonymous_variant	7058	exon8			AAAGGATGGACTG		CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.1089A>G	chr6.hg19:g.169639734T>C		58.0	0.0		41.0	17.0	NM_003247	A6H8N1|A7E232|Q5RI52	Silent	SNP	ENST00000366787.3	hg19	CCDS34574.1																																																																																			.	.		0.488	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247		C	169639734	T	C	169639734	2	2	317	1	0	0	0	0	0	0	0	1	15869	1451	51	2		2	THBS2	6	169639734	Silent	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	2777415	169639734	1475333	87	44729										
MAD1L1	8379	hgsc.bcm.edu	37	chr7	2252879	2252879	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	cccatggtctggtccagtctCtcccagctttgcagcttggc	10	15	2	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr7:2252879C>T	ENST00000406869.1	-	10	1511	c.954G>A	c.(952-954)gaG>gaA	p.E318E	MAD1L1_ENST00000402746.1_Silent_p.E226E|MAD1L1_ENST00000399654.2_Silent_p.E318E|MAD1L1_ENST00000265854.7_Silent_p.E318E|MAD1L1_ENST00000486340.1_5'UTR			Q9Y6D9	MD1L1_HUMAN	MAD1 mitotic arrest deficient-like 1 (yeast)	318					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|regulation of metaphase plate congression (GO:0090235)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|spindle (GO:0005819)				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)		GGTCCAGTCTCTCCCAGCTTT	0.557																																					p.E318E		Atlas-SNP	.											.	MAD1L1	81	.	0			c.G954A						.						81	94	90					7																	2252879		2065	4200	6265	SO:0001819	synonymous_variant	8379	exon10			CAGTCTCTCCCAG	U33822	CCDS43539.1	7p22	2013-01-17	2001-11-28		ENSG00000002822	ENSG00000002822			6762	protein-coding gene	gene with protein product		602686	"MAD1 (mitotic arrest deficient, yeast, homolog)-like 1"			10049595, 9546394	Standard	XM_005249876		Approved	HsMAD1, TXBP181, MAD1, PIG9, TP53I9	uc003slg.1	Q9Y6D9	OTTHUMG00000151493	ENST00000406869.1:c.954G>A	chr7.hg19:g.2252879C>T		46.0	0.0		49.0	19.0	NM_003550	B3KR41|Q13312|Q75MI0|Q86UM4|Q9UNH0	Silent	SNP	ENST00000406869.1	hg19	CCDS43539.1																																																																																			.	.		0.557	MAD1L1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322871.1	NM_003550		T	2252879	C	T	2252879	2	4	317	1	0	0	0	0	0	0	0	1	9156	912	32	3		3	MAD1L1	7	2252879	Silent	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10		2252879	156885784	88	44730										
CARD11	84433	hgsc.bcm.edu	37	chr7	2951897	2951897	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	agatgatggtctccgtcttcTgccttctgaggaactcatct	9	11	6	3			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr7:2951897T>C	ENST00000396946.4	-	23	3456	c.3053A>G	c.(3052-3054)cAg>cGg	p.Q1018R		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	1018	Guanylate kinase-like.				Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		CTCCGTCTTCTGCCTTCTGAG	0.587			Mis		DLBCL																																p.Q1018R		Atlas-SNP	.		Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	.	CARD11	339	.	0			c.A3053G						.						197	142	160					7																	2951897		2203	4300	6503	SO:0001583	missense	84433	exon23			GTCTTCTGCCTTC	AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"card-maguk protein 1", "bcl10-interacting maguk protein 3"	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.3053A>G	chr7.hg19:g.2951897T>C	ENSP00000380150:p.Gln1018Arg	84.0	0.0		108.0	43.0	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	hg19	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	T	14.67	2.604639	0.46423	.	.	ENSG00000198286	ENST00000396946	T	0.16324	2.35	4.62	4.62	0.57501	.	0.085870	0.48286	D	0.000193	T	0.12646	0.0307	L	0.35414	1.06	0.54753	D	0.999981	B	0.15930	0.015	B	0.10450	0.005	T	0.07908	-1.0748	10	0.11794	T	0.64	-37.6983	12.6016	0.56501	0.0:0.0:0.0:1.0	.	1018	Q9BXL7	CAR11_HUMAN	R	1018	ENSP00000380150:Q1018R	ENSP00000380150:Q1018R	Q	-	2	0	CARD11	2918423	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.968000	0.76086	1.723000	0.51488	0.482000	0.46254	CAG	.	.		0.587	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		C	2951897	T	C	2951897	3	2	317	1	0	0	0	0	1	0	0	0	2647	1580	55	2	423	2	CARD11	7	2951897	Missense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	699018	2951897	156186766	89	44731										
SLC29A4	222962	hgsc.bcm.edu	37	chr7	5336621	5336621	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	cctcacgaagctgctgctgcCcgacgagcgcgccagcacgc	12	18	1	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr7:5336621C>G	ENST00000396872.3	+	7	835	c.674C>G	c.(673-675)cCc>cGc	p.P225R	SLC29A4_ENST00000297195.4_Missense_Mutation_p.P225R|SLC29A4_ENST00000406453.3_Missense_Mutation_p.P211R			Q7RTT9	S29A4_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 4	225					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	nucleoside transmembrane transporter activity (GO:0005337)			breast(1)|cervix(2)|kidney(7)|large_intestine(1)|liver(1)|lung(7)|urinary_tract(1)	20		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0903)|OV - Ovarian serous cystadenocarcinoma(56;2.65e-15)	Metformin(DB00331)	CTGCTGCTGCCCGACGAGCGC	0.682																																					p.P225R		Atlas-SNP	.											.	SLC29A4	52	.	0			c.C674G						.						23	23	23					7																	5336621		2191	4254	6445	SO:0001583	missense	222962	exon7			TGCTGCCCGACGA	AK075422	CCDS5340.1, CCDS75561.1	7p22.2	2013-07-17	2013-07-17		ENSG00000164638	ENSG00000164638		"Solute carriers"	23097	protein-coding gene	gene with protein product		609149	"solute carrier family 29 (nucleoside transporters), member 4"			12838422	Standard	NM_153247		Approved	FLJ34923, ENT4	uc003soc.3	Q7RTT9	OTTHUMG00000023797	ENST00000396872.3:c.674C>G	chr7.hg19:g.5336621C>G	ENSP00000380081:p.Pro225Arg	34.0	0.0		46.0	10.0	NM_153247	Q6PJ08|Q86WY8|Q8NAR3|Q8NBM2	Missense_Mutation	SNP	ENST00000396872.3	hg19	CCDS5340.1	.	.	.	.	.	.	.	.	.	.	.	13.65	2.299093	0.40694	.	.	ENSG00000164638	ENST00000396872;ENST00000297195;ENST00000406453	T;T;T	0.63096	-0.02;-0.02;-0.02	3.45	3.45	0.39498	Major facilitator superfamily domain, general substrate transporter (1);	0.440030	0.24213	N	0.040514	T	0.59972	0.2233	L	0.58810	1.83	0.30794	N	0.740572	P;P	0.38078	0.617;0.584	B;B	0.40782	0.226;0.34	T	0.64041	-0.6500	10	0.33940	T	0.23	-16.3178	13.4531	0.61182	0.0:1.0:0.0:0.0	.	211;225	Q7RTT9-2;Q7RTT9	.;S29A4_HUMAN	R	225;225;211	ENSP00000380081:P225R;ENSP00000297195:P225R;ENSP00000385845:P211R	ENSP00000297195:P225R	P	+	2	0	SLC29A4	5303147	0.943000	0.32029	0.992000	0.48379	0.995000	0.86356	2.441000	0.44864	1.652000	0.50683	0.555000	0.69702	CCC	.	.		0.682	SLC29A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060118.6	NM_153247		G	5336621	C	G	5336621	3	3	317	1	0	0	0	0	1	0	0	0	14552	623	22	4	696	4	SLC29A4	7	5336621	Missense_Mutation	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	2384724	5336621	153802042	90	44732										
NPSR1	387129	hgsc.bcm.edu	37	chr7	34917718	34917718	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ctccgtcagctccaggaggcTgcgctaatgctctgccctca	10	16	3	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr7:34917718T>A	ENST00000359791.1	+	9	1184	c.1056T>A	c.(1054-1056)gcT>gcA	p.A352A	NPSR1_ENST00000531252.1_Silent_p.A341A	NM_207173.1	NP_997056.1	Q6W5P4	NPSR1_HUMAN	neuropeptide S receptor 1	0						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|vasopressin receptor activity (GO:0005000)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(7)	31					Halothane(DB01159)	TCCAGGAGGCTGCGCTAATGC	0.527																																					p.A352A		Atlas-SNP	.											.	NPSR1	134	.	0			c.T1056A						.						64	51	56					7																	34917718		2203	4300	6503	SO:0001819	synonymous_variant	387129	exon9			GGAGGCTGCGCTA	AY255536	CCDS5443.1, CCDS5444.1, CCDS75579.1, CCDS75580.1, CCDS75581.1	7p14.3	2012-08-08	2006-05-10	2006-05-10	ENSG00000187258	ENSG00000187258		"GPCR / Class A : Neuropeptide receptors : S"	23631	protein-coding gene	gene with protein product		608595	"G protein-coupled receptor 154"	GPR154		12679517, 15073379	Standard	NM_207173		Approved	PGR14, GPRA	uc003tei.1	Q6W5P4	OTTHUMG00000099383	ENST00000359791.1:c.1056T>A	chr7.hg19:g.34917718T>A		232.0	0.0		251.0	70.0	NM_207173	A2RTZ4|Q2XP58|Q56H76|Q56H77|Q56H78|Q6JSL4|Q6JSL5|Q6JSL6|Q6JSL7|Q6JSL8|Q6W5P3|Q6ZMB8	Silent	SNP	ENST00000359791.1	hg19	CCDS5443.1																																																																																			.	.		0.527	NPSR1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000216838.1	NM_207173		A	34917718	T	A	34917718	2	1	317	1	0	0	0	0	0	0	0	1	10609	1567	55	4		4	NPSR1	7	34917718	Silent	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	29581097	34917718	124220945	91	44733										
GPR141	353345	hgsc.bcm.edu	37	chr7	37780305	37780305	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tccacatgtacctcacgttcCtattctatgtggtgatcctg	7	12	2	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr7:37780305C>G	ENST00000447769.1	+	4	599	c.310C>G	c.(310-312)Cta>Gta	p.L104V	EPDR1_ENST00000476620.1_Intron|GPR141_ENST00000461610.1_Intron|GPR141_ENST00000334425.1_Missense_Mutation_p.L104V			Q7Z602	GP141_HUMAN	G protein-coupled receptor 141	104						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(13)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						CCTCACGTTCCTATTCTATGT	0.468																																					p.L104V		Atlas-SNP	.											.	GPR141	79	.	0			c.C310G						.						119	104	109					7																	37780305		2203	4300	6503	SO:0001583	missense	353345	exon1			ACGTTCCTATTCT	AY288420	CCDS5451.1	7p14.1	2012-08-21			ENSG00000187037	ENSG00000187037		"GPCR / Class A : Orphans"	19997	protein-coding gene	gene with protein product		609045				12679517, 14623098	Standard	NM_181791		Approved	PGR13	uc003tfm.1	Q7Z602	OTTHUMG00000102105	ENST00000447769.1:c.310C>G	chr7.hg19:g.37780305C>G	ENSP00000390410:p.Leu104Val	107.0	0.0		123.0	36.0	NM_181791	A4D1X7|Q0VAR5|Q86SP3	Missense_Mutation	SNP	ENST00000447769.1	hg19	CCDS5451.1	.	.	.	.	.	.	.	.	.	.	C	12.07	1.826144	0.32237	.	.	ENSG00000187037	ENST00000450180;ENST00000447769;ENST00000334425	T;T;T	0.40476	2.57;1.03;1.03	5.06	3.09	0.35607	GPCR, rhodopsin-like superfamily (1);	0.430924	0.23139	N	0.051490	T	0.36936	0.0985	L	0.48642	1.525	0.46981	D	0.999273	P	0.44776	0.843	P	0.44860	0.462	T	0.07290	-1.0780	10	0.23891	T	0.37	-11.164	9.6395	0.39831	0.1459:0.5702:0.2839:0.0	.	104	Q7Z602	GP141_HUMAN	V	104	ENSP00000396300:L104V;ENSP00000390410:L104V;ENSP00000334540:L104V	ENSP00000334540:L104V	L	+	1	2	GPR141	37746830	0.962000	0.33011	0.996000	0.52242	0.926000	0.56050	0.603000	0.24149	1.239000	0.43787	0.650000	0.86243	CTA	.	.		0.468	GPR141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219943.2	NM_181791		G	37780305	C	G	37780305	3	3	317	1	0	0	0	0	1	0	0	0	6657	680	24	4	312	4	GPR141	7	37780305	Missense_Mutation	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	2862587	37780305	121358358	92	44734										
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47886593	47886593	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	aaatgtactgtatagttcacTgccttagctaaatatctgtt	6	7	2	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr7:47886593T>A	ENST00000289672.2	-	32	5087	c.5037A>T	c.(5035-5037)gcA>gcT	p.A1679A		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	1679					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						TATAGTTCACTGCCTTAGCTA	0.403																																					p.A1679A		Atlas-SNP	.											.	PKD1L1	328	.	0			c.A5037T						.						109	103	105					7																	47886593		2203	4300	6503	SO:0001819	synonymous_variant	168507	exon32			GTTCACTGCCTTA	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"polycystin-1L1"	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.5037A>T	chr7.hg19:g.47886593T>A		313.0	0.0		327.0	114.0	NM_138295	Q6UWK1	Silent	SNP	ENST00000289672.2	hg19	CCDS34633.1																																																																																			.	.		0.403	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		A	47886593	T	A	47886593	2	1	317	1	0	0	0	0	0	0	0	1	11973	1567	55	4		4	PKD1L1	7	47886593	Silent	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	10106288	47886593	111252070	93	44735										
FZD9	8326	hgsc.bcm.edu	37	chr7	72849306	72849306	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ttcctactgctctactacttCggcatggccagctcgctctg	8	15	2	0	rs144961735		TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr7:72849306C>T	ENST00000344575.3	+	1	1198	c.969C>T	c.(967-969)ttC>ttT	p.F323F		NM_003508.2	NP_003499.1	O00144	FZD9_HUMAN	frizzled class receptor 9	323					B cell differentiation (GO:0030183)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|gonad development (GO:0008406)|learning or memory (GO:0007611)|nervous system development (GO:0007399)|neuroblast proliferation (GO:0007405)|vasculature development (GO:0001944)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(4)|prostate(2)|skin(1)	14		Lung NSC(55;0.0659)|all_lung(88;0.152)				TCTACTACTTCGGCATGGCCA	0.657																																					p.F323F	Pancreas(144;909 1878 36867 38226 39554)	Atlas-SNP	.											.	FZD9	51	.	0			c.C969T						.	C		2,4404	4.2+/-10.8	0,2,2201	94	84	87		969	3.3	1	7	dbSNP_134	87	0,8600		0,0,4300	no	coding-synonymous	FZD9	NM_003508.2		0,2,6501	TT,TC,CC		0.0,0.0454,0.0154		323/592	72849306	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	8326	exon1			CTACTTCGGCATG	U82169	CCDS5548.1	7q11.23	2014-01-29	2014-01-29		ENSG00000188763	ENSG00000188763		"GPCR / Class F : Frizzled receptors", "CD molecules"	4047	protein-coding gene	gene with protein product		601766	"frizzled (Drosophila) homolog 9", "frizzled homolog 9 (Drosophila)", "frizzled 9, seven transmembrane spanning receptor", "frizzled family receptor 9"			9147651, 10198163	Standard	NM_003508		Approved	FZD3, CD349	uc003tyb.3	O00144	OTTHUMG00000023051	ENST00000344575.3:c.969C>T	chr7.hg19:g.72849306C>T		54.0	0.0		59.0	18.0	NM_003508		Silent	SNP	ENST00000344575.3	hg19	CCDS5548.1																																																																																			.	C|1.000;T|0.000		0.657	FZD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252120.1			T	72849306	C	T	72849306	2	4	317	1	0	0	0	0	0	0	0	1	6145	883	31	1		1	FZD9	7	72849306	Silent	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	24962713	72849306	86289357	94	44736										
HIP1	3092	hgsc.bcm.edu	37	chr7	75176292	75176292	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tagaggccacgatgagcaccTgaatagcttgcatgaggctg	13	9	0	4			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr7:75176292T>A	ENST00000336926.6	-	25	2530	c.2504A>T	c.(2503-2505)cAg>cTg	p.Q835L	HIP1_ENST00000434438.2_Intron	NM_005338.5	NP_005329.3	O00291	HIP1_HUMAN	huntingtin interacting protein 1	835	I/LWEQ. {ECO:0000255|PROSITE- ProRule:PRU00292}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell differentiation (GO:0030154)|clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|positive regulation of receptor-mediated endocytosis (GO:0048260)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|phosphatidylinositol binding (GO:0035091)|structural constituent of cytoskeleton (GO:0005200)			breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						GATGAGCACCTGAATAGCTTG	0.547			T	PDGFRB	CMML																																p.Q835L		Atlas-SNP	.		Dom	yes		7	7q11.23	3092	huntingtin interacting protein 1		L	.	HIP1	91	.	0			c.A2504T						.						80	60	67					7																	75176292		2202	4298	6500	SO:0001583	missense	3092	exon25			AGCACCTGAATAG	AF052288	CCDS34669.1, CCDS59060.1	7q11.23	2008-07-18			ENSG00000127946	ENSG00000127946			4913	protein-coding gene	gene with protein product		601767				9140394, 9147654	Standard	NM_005338		Approved	ILWEQ	uc003uds.2	O00291	OTTHUMG00000156050	ENST00000336926.6:c.2504A>T	chr7.hg19:g.75176292T>A	ENSP00000336747:p.Gln835Leu	81.0	0.0		85.0	20.0	NM_005338	B4E3I7|E7ES17|O00328|Q2TB58|Q8TDL4	Missense_Mutation	SNP	ENST00000336926.6	hg19	CCDS34669.1	.	.	.	.	.	.	.	.	.	.	t	15.46	2.841478	0.51057	.	.	ENSG00000127946	ENST00000336926	T	0.28255	1.62	5.01	3.87	0.44632	I/LWEQ (4);	0.214476	0.49305	D	0.000143	T	0.25382	0.0617	L	0.42245	1.32	0.80722	D	1	B	0.13594	0.008	B	0.23275	0.045	T	0.04268	-1.0964	10	0.33141	T	0.24	-5.1368	9.2135	0.37333	0.0:0.0869:0.0:0.9131	.	835	O00291	HIP1_HUMAN	L	835	ENSP00000336747:Q835L	ENSP00000336747:Q835L	Q	-	2	0	HIP1	75014228	0.963000	0.33076	0.972000	0.41901	0.773000	0.43773	1.584000	0.36589	0.777000	0.33496	0.460000	0.39030	CAG	.	.		0.547	HIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342863.2	NM_005338		A	75176292	T	A	75176292	3	1	317	1	0	0	0	0	1	0	0	0	7123	1580	55	4	637	4	HIP1	7	75176292	Missense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	2326986	75176292	83962371	95	44737										
SEMA3A	10371	hgsc.bcm.edu	37	chr7	83675692	83675692	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ctgattgggtggtggtgcccAagagttcggaagatagcaaa	15	6	0	3	rs548421717		TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr7:83675692A>C	ENST00000265362.4	-	6	929	c.615T>G	c.(613-615)ctT>ctG	p.L205L	SEMA3A_ENST00000436949.1_Silent_p.L205L	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	205	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				apoptotic process (GO:0006915)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|dendrite morphogenesis (GO:0048813)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of epithelial cell migration (GO:0010633)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neural crest cell migration involved in sympathetic nervous system development (GO:1903045)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of male gonad development (GO:2000020)|positive regulation of neuron migration (GO:2001224)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of heart rate (GO:0002027)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sensory system development (GO:0048880)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular region (GO:0005576)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|neuropilin binding (GO:0038191)|receptor activity (GO:0004872)			breast(3)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						GGTGGTGCCCAAGAGTTCGGA	0.433																																					p.L205L		Atlas-SNP	.											.	SEMA3A	121	.	0			c.T615G						.						218	195	203					7																	83675692		2203	4300	6503	SO:0001819	synonymous_variant	10371	exon6			GTGCCCAAGAGTT	L26081	CCDS5599.1	7p12.1	2013-01-11			ENSG00000075213	ENSG00000075213		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10723	protein-coding gene	gene with protein product	"sema III"	603961		SEMAD		8269517, 7748561	Standard	NM_006080		Approved	SEMA1, SemD, coll-1, Hsema-I	uc003uhz.3	Q14563	OTTHUMG00000023443	ENST00000265362.4:c.615T>G	chr7.hg19:g.83675692A>C		157.0	0.0		219.0	66.0	NM_006080		Silent	SNP	ENST00000265362.4	hg19	CCDS5599.1																																																																																			.	.		0.433	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080		C	83675692	A	C	83675692	2	2	317	1	0	0	0	0	0	0	0	1	14039	117	5	5		5	SEMA3A	7	83675692	Silent	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	8499400	83675692	75462971	96	44738										
ARPC1A	10552	hgsc.bcm.edu	37	chr7	98955969	98955969	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gttcttgtgttcagggtctcGactctgaagacagagttcct	11	9	4	3			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr7:98955969G>T	ENST00000262942.5	+	7	844	c.720G>T	c.(718-720)tcG>tcT	p.S240S	ARPC1A_ENST00000432884.2_Silent_p.S193S|ARPC1A_ENST00000471960.1_3'UTR	NM_001190996.1|NM_006409.3	NP_001177925.1|NP_006400.2	Q92747	ARC1A_HUMAN	actin related protein 2/3 complex, subunit 1A, 41kDa	240					actin cytoskeleton organization (GO:0030036)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|regulation of actin filament polymerization (GO:0030833)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	actin binding (GO:0003779)	p.S240S(1)		endometrium(3)|large_intestine(5)|liver(2)|lung(7)|ovary(1)|prostate(1)	19	all_cancers(62;4.46e-09)|all_epithelial(64;3.44e-10)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0258)		STAD - Stomach adenocarcinoma(171;0.215)			TCAGGGTCTCGACTCTGAAGA	0.478																																					p.S240S		Atlas-SNP	.											ARPC1A,NS,carcinoma,0,2	ARPC1A	38	.	1	Substitution - coding silent(1)	prostate(1)	c.G720T						.						161	138	146					7																	98955969		2203	4300	6503	SO:0001819	synonymous_variant	10552	exon7			GGTCTCGACTCTG	Y08999	CCDS5660.1	7q22.1	2013-03-14	2002-08-29		ENSG00000241685	ENSG00000241685		"Actin related protein 2/3 complex subunits", "WD repeat domain containing"	703	protein-coding gene	gene with protein product	"actin binding protein (Schizosaccharomyces pombe sop2-like)", "SOP2-like protein"	604220	"actin related protein 2/3 complex, subunit 1A (41 kD)"			8978670, 9230079	Standard	NM_006409		Approved	SOP2Hs, SOP2L, Arc40	uc003upx.2	Q92747	OTTHUMG00000154553	ENST00000262942.5:c.720G>T	chr7.hg19:g.98955969G>T		92.0	0.0		79.0	4.0	NM_006409	A4D276|B4DLQ7|D6W5S1|Q7Z5U8|Q86WU5|Q8IXQ0	Silent	SNP	ENST00000262942.5	hg19	CCDS5660.1																																																																																			.	.		0.478	ARPC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335908.1	NM_006409		T	98955969	G	T	98955969	2	4	317	1	0	0	0	0	0	0	0	1	969	1045	37	1		1	ARPC1A	7	98955969	Silent	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	15280277	98955969	60182694	97	44739										
TRIM4	89122	hgsc.bcm.edu	37	chr7	99506413	99506413	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	aaaactccgtgctgattctcAttcgctgactctttatctta	5	11	3	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr7:99506413A>G	ENST00000355947.2	-	4	719	c.590T>C	c.(589-591)aTg>aCg	p.M197T	TRIM4_ENST00000349062.2_Missense_Mutation_p.M171T|TRIM4_ENST00000354241.5_Missense_Mutation_p.M171T	NM_033017.3	NP_148977.2	Q9C037	TRIM4_HUMAN	tripartite motif containing 4	197					protein trimerization (GO:0070206)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(1)	17	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)	Ovarian(593;0.238)				GCTGATTCTCATTCGCTGACT	0.428																																					p.M197T		Atlas-SNP	.											.	TRIM4	33	.	0			c.T590C						.						128	118	121					7																	99506413		2203	4300	6503	SO:0001583	missense	89122	exon4			ATTCTCATTCGCT	AF220023	CCDS5678.1, CCDS5679.1	7q22-q31.1	2013-01-09	2011-01-25		ENSG00000146833	ENSG00000146833		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16275	protein-coding gene	gene with protein product	"tripartite motif protein TRIM4", "tripartite motif protein 4"		"tripartite motif-containing 4"			11331580	Standard	NM_033017		Approved	RNF87	uc003use.3	Q9C037	OTTHUMG00000156648	ENST00000355947.2:c.590T>C	chr7.hg19:g.99506413A>G	ENSP00000348216:p.Met197Thr	88.0	0.0		99.0	30.0	NM_033017	A4D298|Q75MK1|Q96F06|Q9C036	Missense_Mutation	SNP	ENST00000355947.2	hg19	CCDS5679.1	.	.	.	.	.	.	.	.	.	.	A	3.136	-0.177375	0.06380	.	.	ENSG00000146833	ENST00000355947;ENST00000349062;ENST00000542799;ENST00000354241	T;T;T	0.04406	3.63;3.63;3.63	2.68	-5.36	0.02689	.	.	.	.	.	T	0.02767	0.0083	L	0.36672	1.1	0.09310	N	1	B;B;B	0.33073	0.002;0.358;0.396	B;B;B	0.29785	0.01;0.107;0.05	T	0.38672	-0.9650	9	0.27082	T	0.32	.	0.8981	0.01268	0.2544:0.3383:0.2405:0.1667	.	171;171;197	Q9C037-3;Q9C037-2;Q9C037	.;.;TRIM4_HUMAN	T	197;171;27;171	ENSP00000348216:M197T;ENSP00000275736:M171T;ENSP00000346186:M171T	ENSP00000275736:M171T	M	-	2	0	TRIM4	99344349	0.000000	0.05858	0.000000	0.03702	0.846000	0.48090	-0.143000	0.10296	-1.355000	0.02186	-0.263000	0.10527	ATG	.	.		0.428	TRIM4-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345050.1	NM_033017		G	99506413	A	G	99506413	3	3	317	1	0	0	0	0	1	0	0	0	16529	217	8	2	928	2	TRIM4	7	99506413	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	550444	99506413	59632250	98	44740										
DNAJC2	27000	hgsc.bcm.edu	37	chr7	102953436	102953436	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ttctttgtcctgccaggcacCgcttctgctattttttccca	6	14	2	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr7:102953436C>T	ENST00000379263.3	-	16	1999	c.1749G>A	c.(1747-1749)gcG>gcA	p.A583A	PMPCB_ENST00000420236.2_Intron|PMPCB_ENST00000249269.4_3'UTR|DNAJC2_ENST00000249270.7_Silent_p.A530A	NM_014377.1	NP_055192.1	Q99543	DNJC2_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 2	583	SANT 2. {ECO:0000255|PROSITE- ProRule:PRU00624}.				'de novo' cotranslational protein folding (GO:0051083)|chromatin modification (GO:0016568)|DNA replication (GO:0006260)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA biosynthetic process (GO:2000279)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone binding (GO:0042393)|Hsp70 protein binding (GO:0030544)|poly(A) RNA binding (GO:0044822)|ubiquitin binding (GO:0043130)			endometrium(1)|kidney(9)|large_intestine(6)|lung(4)|ovary(1)	21						TGCCAGGCACCGCTTCTGCTA	0.398																																					p.A583A		Atlas-SNP	.											.	DNAJC2	46	.	0			c.G1749A						.						276	256	262					7																	102953436		1862	4094	5956	SO:0001819	synonymous_variant	27000	exon16			AGGCACCGCTTCT	X98260	CCDS43628.1, CCDS47679.1	7q22-q32	2011-09-02	2008-07-01	2008-07-01	ENSG00000105821	ENSG00000105821		"Heat shock proteins / DNAJ (HSP40)"	13192	protein-coding gene	gene with protein product		605502	"zuotin related factor 1"	ZRF1		8885239	Standard	NM_001129887		Approved	MPP11, MPHOSPH11, ZUO1, zuotin	uc003vbo.3	Q99543	OTTHUMG00000157202	ENST00000379263.3:c.1749G>A	chr7.hg19:g.102953436C>T		181.0	0.0		154.0	57.0	NM_014377	A4VCI0|Q9BVX1	Silent	SNP	ENST00000379263.3	hg19	CCDS43628.1																																																																																			.	.		0.398	DNAJC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347891.1			T	102953436	C	T	102953436	2	4	317	1	0	0	0	0	0	0	0	1	4641	639	23	1		1	DNAJC2	7	102953436	Silent	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	3447023	102953436	56185227	99	44741										
DOCK4	9732	hgsc.bcm.edu	37	chr7	111575684	111575684	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	actcactctctgtgttacacCtatgaaaacattaacactct	3	12	3	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr7:111575684C>G	ENST00000437633.1	-	12	1234		c.e12-1		DOCK4_ENST00000428084.1_Splice_Site|DOCK4_ENST00000476846.1_Splice_Site	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4						cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				TGTGTTACACCTATGAAAACA	0.393																																					.		Atlas-SNP	.											DOCK4,NS,carcinoma,0,1	DOCK4	365	.	0			c.978-1G>C						.						216	212	213					7																	111575684		2049	4205	6254	SO:0001630	splice_region_variant	9732	exon13			TTACACCTATGAA		CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.978-1G>C	chr7.hg19:g.111575684C>G		207.0	0.0		207.0	55.0	NM_014705	O14584|O94824|Q8NB45	Splice_Site	SNP	ENST00000437633.1	hg19	CCDS47688.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.735794	0.89482	.	.	ENSG00000128512	ENST00000352877;ENST00000428084;ENST00000437633;ENST00000445943;ENST00000342288;ENST00000544250	.	.	.	5.78	5.78	0.91487	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.0137	0.97470	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DOCK4	111362920	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	7.396000	0.79891	2.734000	0.93682	0.563000	0.77884	.	.	.		0.393	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705	Intron	G	111575684	C	G	111575684	5	3	317	1	0	0	0	0	0	0	1	0	4691	695	24	4	5087	4	DOCK4	7	111575684	Splice_Site	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	8622248	111575684	47562979	100	44742										
ASB15	142685	hgsc.bcm.edu	37	chr7	123269106	123269106	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tgacgatgagaggaagactgCgctgtattttggcgtttcta	13	6	1	3			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr7:123269106C>T	ENST00000451558.1	+	12	1579	c.1058C>T	c.(1057-1059)gCg>gTg	p.A353V	ASB15_ENST00000434204.1_Missense_Mutation_p.A353V|ASB15_ENST00000451215.1_Missense_Mutation_p.A353V|ASB15_ENST00000275699.3_Missense_Mutation_p.A353V|ASB15_ENST00000540573.1_Missense_Mutation_p.A353V			Q8WXK1	ASB15_HUMAN	ankyrin repeat and SOCS box containing 15	353					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|kidney(1)|large_intestine(1)|lung(6)|skin(3)	12						AGGAAGACTGCGCTGTATTTT	0.443																																					p.A353V		Atlas-SNP	.											ASB15_ENST00000451558,NS,haematopoietic_neoplasm,0,1	ASB15	94	.	0			c.C1058T						.						168	152	158					7																	123269106		2203	4300	6503	SO:0001583	missense	142685	exon8			AGACTGCGCTGTA	AF403033	CCDS34742.1	7q31.31	2013-01-10	2011-01-25		ENSG00000146809	ENSG00000146809		"Ankyrin repeat domain containing"	19767	protein-coding gene	gene with protein product			"ankyrin repeat and SOCS box-containing 15"			12076535	Standard	XM_005250149		Approved	FLJ43370	uc003vkw.1	Q8WXK1	OTTHUMG00000157114	ENST00000451558.1:c.1058C>T	chr7.hg19:g.123269106C>T	ENSP00000397655:p.Ala353Val	214.0	2.0		235.0	70.0	NM_080928	Q3ZCP3|Q3ZCP5|Q68D37	Missense_Mutation	SNP	ENST00000451558.1	hg19	CCDS34742.1	.	.	.	.	.	.	.	.	.	.	C	33	5.210454	0.95069	.	.	ENSG00000146809	ENST00000451558;ENST00000434204;ENST00000451215;ENST00000540573;ENST00000542545;ENST00000275699	T;T;T;T;T	0.69175	-0.38;-0.38;-0.38;-0.38;-0.38	6.17	6.17	0.99709	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.80428	0.4621	M	0.63208	1.945	0.58432	D	0.999998	D	0.71674	0.998	D	0.64321	0.924	T	0.79060	-0.1958	10	0.59425	D	0.04	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	353	Q8WXK1	ASB15_HUMAN	V	353;353;353;353;142;353	ENSP00000397655:A353V;ENSP00000390963:A353V;ENSP00000416433:A353V;ENSP00000438643:A353V;ENSP00000275699:A353V	ENSP00000275699:A353V	A	+	2	0	ASB15	123056342	0.998000	0.40836	0.969000	0.41365	0.964000	0.63967	5.766000	0.68843	2.941000	0.99782	0.655000	0.94253	GCG	.	.		0.443	ASB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347493.1			T	123269106	C	T	123269106	3	4	317	1	0	0	0	0	1	0	0	0	1019	768	27	1	1084	1	ASB15	7	123269106	Missense_Mutation	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	11693422	123269106	35869557	101	44743										
CLCN1	1180	hgsc.bcm.edu	37	chr7	143043750	143043750	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	cacaaagaagaaaacaacccAggtgagaggagatgtgtttg	12	6	0	4	rs199610988	byFrequency	TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr7:143043750A>T	ENST00000343257.2	+	19	2450	c.2363A>T	c.(2362-2364)cAg>cTg	p.Q788L		NM_000083.2	NP_000074	P35523	CLCN1_HUMAN	chloride channel, voltage-sensitive 1	788					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|neuronal action potential propagation (GO:0019227)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	adenyl nucleotide binding (GO:0030554)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(4)|central_nervous_system(1)|endometrium(1)|large_intestine(11)|lung(26)|ovary(3)|prostate(2)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	58	Melanoma(164;0.205)					AAAACAACCCAGGTGAGAGGA	0.542																																					p.Q788L		Atlas-SNP	.											.	CLCN1	141	.	0			c.A2363T						.						80	79	80					7																	143043750		2203	4300	6503	SO:0001630	splice_region_variant	1180	exon19			CAACCCAGGTGAG	Z25884	CCDS5881.1	7q12	2012-09-26	2012-02-23		ENSG00000188037	ENSG00000188037		"Ion channels / Chloride channels : Voltage-sensitive"	2019	protein-coding gene	gene with protein product	"Thomsen disease, autosomal dominant"	118425	"chloride channel 1, skeletal muscle"			1379744	Standard	NM_000083		Approved	CLC1, ClC-1	uc003wcr.1	P35523	OTTHUMG00000152695	ENST00000343257.2:c.2364+1A>T	chr7.hg19:g.143043750A>T		31.0	0.0		40.0	10.0	NM_000083	A4D2H5|Q2M202	Missense_Mutation	SNP	ENST00000343257.2	hg19	CCDS5881.1	.	.	.	.	.	.	.	.	.	.	A	11.66	1.703664	0.30232	.	.	ENSG00000188037	ENST00000343257	D	0.85629	-2.01	4.49	4.49	0.54785	.	0.250077	0.29480	N	0.012040	D	0.83806	0.5334	M	0.75777	2.31	0.41610	D	0.988909	P	0.40970	0.734	B	0.39339	0.297	D	0.85181	0.1004	10	0.56958	D	0.05	.	10.4836	0.44708	1.0:0.0:0.0:0.0	.	788	P35523	CLCN1_HUMAN	L	788	ENSP00000339867:Q788L	ENSP00000339867:Q788L	Q	+	2	0	CLCN1	142753872	1.000000	0.71417	0.990000	0.47175	0.327000	0.28475	3.999000	0.57031	1.797000	0.52628	0.459000	0.35465	CAG	.	A|0.999;C|0.001		0.542	CLCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327420.1	NM_000083	Missense_Mutation	T	143043750	A	T	143043750	5	4	317	1	0	0	0	0	0	0	1	0	3464	202	7	4	2437	4	CLCN1	7	143043750	Splice_Site	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	19774644	143043750	16094913	102	44744										
NOBOX	135935	hgsc.bcm.edu	37	chr7	144096937	144096937	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ccatttttcgccacttggccCggcgattctggaaccacacc	8	16	1	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr7:144096937C>A	ENST00000467773.1	-	6	1066	c.1067G>T	c.(1066-1068)cGg>cTg	p.R356L	NOBOX_ENST00000483238.1_Missense_Mutation_p.R324L|NOBOX_ENST00000223140.5_Missense_Mutation_p.R239L	NM_001080413.3	NP_001073882.3	O60393	NOBOX_HUMAN	NOBOX oogenesis homeobox	356					oogenesis (GO:0048477)|ovarian follicle development (GO:0001541)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)	26	Melanoma(164;0.14)					CCACTTGGCCCGGCGATTCTG	0.542																																					p.R356L		Atlas-SNP	.											.	NOBOX	130	.	0			c.G1067T						.						78	82	80					7																	144096937		1955	4150	6105	SO:0001583	missense	135935	exon6			TTGGCCCGGCGAT			7q35	2011-06-20			ENSG00000106410	ENSG00000106410		"Homeoboxes / PRD class"	22448	protein-coding gene	gene with protein product	"newborn ovary homeobox-encoding gene"	610934				11804785, 16597639	Standard	NM_001080413		Approved	OG2, Og2x	uc022aoj.1	O60393	OTTHUMG00000158051	ENST00000467773.1:c.1067G>T	chr7.hg19:g.144096937C>A	ENSP00000419457:p.Arg356Leu	90.0	0.0		82.0	25.0	NM_001080413	A6NCD3|A8MZN5	Missense_Mutation	SNP	ENST00000467773.1	hg19		.	.	.	.	.	.	.	.	.	.	C	21.8	4.202985	0.79127	.	.	ENSG00000106410	ENST00000483238;ENST00000467773;ENST00000223140;ENST00000555556	D;D;D	0.99298	-5.5;-5.71;-5.5	5.55	4.67	0.58626	Homeodomain-related (1);Homeobox (2);	0.324668	0.29987	N	0.010695	D	0.99510	0.9825	M	0.93241	3.395	0.36537	D	0.87108	D	0.89917	1.0	D	0.91635	0.999	D	0.99552	1.0966	10	0.87932	D	0	-35.0972	12.3015	0.54876	0.0:0.918:0.0:0.082	.	356	O60393	NOBOX_HUMAN	L	324;356;239;113	ENSP00000419565:R324L;ENSP00000419457:R356L;ENSP00000223140:R239L	ENSP00000223140:R239L	R	-	2	0	NOBOX	143727870	1.000000	0.71417	0.990000	0.47175	0.993000	0.82548	5.277000	0.65586	1.352000	0.45808	0.650000	0.86243	CGG	.	.		0.542	NOBOX-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000350095.1	XM_001134420		A	144096937	C	A	144096937	3	1	317	1	0	0	0	0	1	0	0	0	10521	652	23	1	1028	1	NOBOX	7	144096937	Missense_Mutation	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	1053187	144096937	15041726	103	44745										
MLL3	58508	hgsc.bcm.edu	37	chr7	151873528	151873528	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tgcaggttttcctgtccccaGactgtggttaactgttgatt	10	9	0	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr7:151873528G>C	ENST00000262189.6	-	38	9228	c.9010C>G	c.(9010-9012)Ctg>Gtg	p.L3004V	KMT2C_ENST00000355193.2_Missense_Mutation_p.L3004V	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	3004					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										CCTGTCCCCAGACTGTGGTTA	0.463																																					p.L3004V		Atlas-SNP	.											.	MLL3	1564	.	0			c.C9010G						.						94	87	89					7																	151873528		2203	4300	6503	SO:0001583	missense	58508	exon38			TCCCCAGACTGTG	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.9010C>G	chr7.hg19:g.151873528G>C	ENSP00000262189:p.Leu3004Val	110.0	0.0		154.0	44.0	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	hg19	CCDS5931.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	2.806|2.806	-0.248006|-0.248006	0.05867|0.05867	.|.	.|.	ENSG00000055609|ENSG00000055609	ENST00000262189;ENST00000355193|ENST00000360104	D;D|D	0.83250|0.85702	-1.7;-1.7|-2.02	5.66|5.66	0.182|0.182	0.15077|0.15077	.|.	0.165520|.	0.27393|.	N|.	0.019566|.	T|T	0.68833|0.68833	0.3044|0.3044	N|N	0.11427|0.11427	0.14|0.14	0.09310|0.09310	N|N	0.99999|0.99999	B;B;B|.	0.02656|.	0.0;0.0;0.0|.	B;B;B|.	0.04013|.	0.0;0.0;0.001|.	T|T	0.59757|0.59757	-0.7394|-0.7394	10|7	0.33141|0.56958	T|D	0.24|0.05	.|.	3.3493|3.3493	0.07146|0.07146	0.5806:0.1219:0.0641:0.2333|0.5806:0.1219:0.0641:0.2333	.|.	3004;2065;3004|.	Q8NEZ4;Q8NEZ4-2;Q8NEZ4-3|.	MLL3_HUMAN;.;.|.	V|C	3004|509	ENSP00000262189:L3004V;ENSP00000347325:L3004V|ENSP00000353218:S509C	ENSP00000262189:L3004V|ENSP00000353218:S509C	L|S	-|-	1|2	2|0	MLL3|MLL3	151504461|151504461	0.992000|0.992000	0.36948|0.36948	0.025000|0.025000	0.17156|0.17156	0.773000|0.773000	0.43773|0.43773	2.254000|2.254000	0.43214|0.43214	-0.166000|-0.166000	0.10890|0.10890	-1.077000|-1.077000	0.02231|0.02231	CTG|TCT	.	.		0.463	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			C	151873528	G	C	151873528	3	2	317	1	0	0	0	0	1	0	0	0	9631	933	33	4	5813	4	MLL3	7	151873528	Missense_Mutation	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	7776591	151873528	7265135	104	44746										
ANK1	286	hgsc.bcm.edu	37	chr8	41547821	41547821	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	cgtacttcatcgccttgcgcAgaaacgacagggaccctccc	9	16	1	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr8:41547821A>T	ENST00000347528.4	-	33	4111	c.4028T>A	c.(4027-4029)cTg>cAg	p.L1343Q	ANK1_ENST00000396945.1_Missense_Mutation_p.L1343Q|ANK1_ENST00000265709.8_Missense_Mutation_p.L1384Q|ANK1_ENST00000396942.1_Missense_Mutation_p.L1343Q|ANK1_ENST00000352337.4_Missense_Mutation_p.L1343Q|ANK1_ENST00000379758.2_Missense_Mutation_p.L1343Q|ANK1_ENST00000289734.7_Missense_Mutation_p.L1343Q	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	1343	UPA domain. {ECO:0000250}.				axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			CGCCTTGCGCAGAAACGACAG	0.597																																					p.L1384Q		Atlas-SNP	.											.	ANK1	497	.	0			c.T4151A						.						133	111	119					8																	41547821		2203	4300	6503	SO:0001583	missense	286	exon34			TTGCGCAGAAACG	M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"Ankyrin repeat domain containing"	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.4028T>A	chr8.hg19:g.41547821A>T	ENSP00000339620:p.Leu1343Gln	107.0	0.0		79.0	37.0	NM_001142446	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Missense_Mutation	SNP	ENST00000347528.4	hg19	CCDS6119.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.495553	0.85069	.	.	ENSG00000029534	ENST00000347528;ENST00000289734;ENST00000379758;ENST00000396945;ENST00000396942;ENST00000352337;ENST00000265709;ENST00000358820	T;T;T;T;T;T;T	0.24151	1.87;1.87;1.87;1.87;1.87;1.87;1.87	5.08	5.08	0.68730	.	0.000000	0.64402	D	0.000002	T	0.48624	0.1510	M	0.65975	2.015	0.58432	D	0.999998	D;D;P;P;D;D	0.71674	0.996;0.985;0.956;0.956;0.996;0.998	D;P;P;P;D;D	0.72625	0.978;0.864;0.729;0.562;0.978;0.929	T	0.51387	-0.8712	10	0.87932	D	0	.	14.1776	0.65552	1.0:0.0:0.0:0.0	.	1384;1343;1343;1343;1343;659	P16157-21;P16157-4;P16157;P16157-5;P16157-3;B3KX39	.;.;ANK1_HUMAN;.;.;.	Q	1343;1343;1343;1343;1343;1343;1384;1343	ENSP00000339620:L1343Q;ENSP00000289734:L1343Q;ENSP00000369082:L1343Q;ENSP00000380149:L1343Q;ENSP00000380147:L1343Q;ENSP00000309131:L1343Q;ENSP00000265709:L1384Q	ENSP00000265709:L1384Q	L	-	2	0	ANK1	41666978	1.000000	0.71417	0.975000	0.42487	0.866000	0.49608	9.026000	0.93700	2.123000	0.65237	0.460000	0.39030	CTG	.	.		0.597	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475		T	41547821	A	T	41547821	3	4	317	1	0	0	0	0	1	0	0	0	620	188	7	4	1983	4	ANK1	8	41547821	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10		41547821	104816201	105	44747										
ST18	9705	hgsc.bcm.edu	37	chr8	53050033	53050033	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gccacttccatcacatcctgGtgttggacagctgagtcaat	9	12	2	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr8:53050033G>T	ENST00000276480.7	-	18	2862	c.2179C>A	c.(2179-2181)Cca>Aca	p.P727T		NM_014682.2	NP_055497.1	O60284	ST18_HUMAN	suppression of tumorigenicity 18, zinc finger	727					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(14)|lung(38)|ovary(4)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	85		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)				TCACATCCTGGTGTTGGACAG	0.463																																					p.P727T		Atlas-SNP	.											.	ST18	212	.	0			c.C2179A						.						160	129	139					8																	53050033		2203	4300	6503	SO:0001583	missense	9705	exon18			ATCCTGGTGTTGG	AB011107	CCDS6149.1	8q11.23	2014-03-24	2014-03-24	2002-12-13	ENSG00000147488	ENSG00000147488		"Zinc fingers, C2HC-type containing"	18695	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 3"		"zinc finger protein 387", "suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein)"	ZNF387		15489893	Standard	NM_014682		Approved	KIAA0535, ZC2HC10, NZF3	uc003xra.2	O60284	OTTHUMG00000164233	ENST00000276480.7:c.2179C>A	chr8.hg19:g.53050033G>T	ENSP00000276480:p.Pro727Thr	127.0	0.0		114.0	39.0	NM_014682	Q17RY1	Missense_Mutation	SNP	ENST00000276480.7	hg19	CCDS6149.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.968147	0.92855	.	.	ENSG00000147488	ENST00000276480	T	0.58060	0.36	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.78748	0.4332	M	0.88704	2.975	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.79564	-0.1751	10	0.49607	T	0.09	-13.7446	20.3052	0.98627	0.0:0.0:1.0:0.0	.	727	O60284	ST18_HUMAN	T	727	ENSP00000276480:P727T	ENSP00000276480:P727T	P	-	1	0	ST18	53212586	1.000000	0.71417	0.928000	0.36995	0.888000	0.51559	9.686000	0.98664	2.808000	0.96608	0.655000	0.94253	CCA	.	.		0.463	ST18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377867.1			T	53050033	G	T	53050033	3	4	317	1	0	0	0	0	1	0	0	0	15227	1261	44	3	1000	3	ST18	8	53050033	Missense_Mutation	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	11502212	53050033	93313989	106	44748										
RP1	6101	hgsc.bcm.edu	37	chr8	55533794	55533794	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tcagcacccctcggggcaggCacagcatcacgcgcctggag	13	16	2	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr8:55533794C>G	ENST00000220676.1	+	2	416	c.268C>G	c.(268-270)Cac>Gac	p.H90D		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	90	Doublecortin 1. {ECO:0000255|PROSITE- ProRule:PRU00072}.				axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			TCGGGGCAGGCACAGCATCAC	0.607																																					p.H90D	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.C268G						.						95	79	84					8																	55533794		2203	4300	6503	SO:0001583	missense	6101	exon2			GGCAGGCACAGCA	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.268C>G	chr8.hg19:g.55533794C>G	ENSP00000220676:p.His90Asp	104.0	0.0		58.0	32.0	NM_006269		Missense_Mutation	SNP	ENST00000220676.1	hg19	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	C	17.37	3.372261	0.61624	.	.	ENSG00000104237	ENST00000220676	D	0.92446	-3.04	5.34	5.34	0.76211	Doublecortin domain (5);	0.094927	0.46758	D	0.000277	D	0.95765	0.8622	M	0.70842	2.15	0.49483	D	0.999792	D	0.76494	0.999	D	0.73708	0.981	D	0.96064	0.9041	10	0.87932	D	0	-9.3041	19.0468	0.93022	0.0:1.0:0.0:0.0	.	90	P56715	RP1_HUMAN	D	90	ENSP00000220676:H90D	ENSP00000220676:H90D	H	+	1	0	RP1	55696347	1.000000	0.71417	0.997000	0.53966	0.332000	0.28634	5.911000	0.69939	2.498000	0.84270	0.650000	0.86243	CAC	.	.		0.607	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		G	55533794	C	G	55533794	3	3	317	1	0	0	0	0	1	0	0	0	13547	710	25	4	270	4	RP1	8	55533794	Missense_Mutation	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	2483761	55533794	90830228	107	44749										
CHD7	55636	hgsc.bcm.edu	37	chr8	61769252	61769252	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tttatcttgcctaatgtctcAacaccagtgtctgatgcctt	6	11	3	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr8:61769252A>G	ENST00000423902.2	+	34	7892	c.7413A>G	c.(7411-7413)tcA>tcG	p.S2471S	CHD7_ENST00000529472.1_3'UTR|CHD7_ENST00000524602.1_Intron	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	2471					adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			CTAATGTCTCAACACCAGTGT	0.433																																					p.S2471S		Atlas-SNP	.											.	CHD7	534	.	0			c.A7413G						.						176	169	171					8																	61769252		1889	4112	6001	SO:0001819	synonymous_variant	55636	exon34			TGTCTCAACACCA	AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"CHARGE association"	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.7413A>G	chr8.hg19:g.61769252A>G		153.0	0.0		140.0	70.0	NM_017780	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Silent	SNP	ENST00000423902.2	hg19	CCDS47865.1																																																																																			.	.		0.433	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762		G	61769252	A	G	61769252	2	3	317	1	0	0	0	0	0	0	0	1	3332	117	5	2		2	CHD7	8	61769252	Silent	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	6235458	61769252	84594770	108	44750										
PEX2	5828	hgsc.bcm.edu	37	chr8	77895734	77895734	+	Silent	SNP	A	A	T													0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tcactattaggtgcaccagtAagaggaatacaccatgaaga							TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr8:77895734A>T	ENST00000419564.2	-	4	1145	c.681T>A	c.(679-681)ctT>ctA	p.L227L	PEX2_ENST00000522527.1_Silent_p.L227L|PEX2_ENST00000520103.1_Silent_p.L227L|PEX2_ENST00000357039.4_Silent_p.L227L	NM_001172087.1	NP_001165558.1	P28328	PEX2_HUMAN	peroxisomal biogenesis factor 2	227					bile acid biosynthetic process (GO:0006699)|cholesterol homeostasis (GO:0042632)|fatty acid beta-oxidation (GO:0006635)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|peroxisome organization (GO:0007031)|protein destabilization (GO:0031648)|protein import into peroxisome matrix (GO:0016558)|regulation of cholesterol biosynthetic process (GO:0045540)|very long-chain fatty acid metabolic process (GO:0000038)	Cdc73/Paf1 complex (GO:0016593)|integral component of peroxisomal membrane (GO:0005779)|membrane (GO:0016020)|peroxisomal membrane (GO:0005778)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)	14						GTGCACCAGTAAGAGGAATAC	0.448																																					p.L227L		Atlas-SNP	.											.	PEX2	44	.	0			c.T681A						.						104	96	99					8																	77895734		2203	4300	6503	SO:0001819	synonymous_variant	5828	exon4			ACCAGTAAGAGGA	M86852	CCDS6221.1	8q21.11	2010-02-09	2010-01-25	2010-01-25		ENSG00000164751		"RING-type (C3HC4) zinc fingers"	9717	protein-coding gene	gene with protein product	"Zellweger syndrome", "peroxin 2"	170993	"peroxisomal membrane protein 3 (35kD, Zellweger syndrome)", "peroxisomal membrane protein 3, 35kDa"	PXMP3		1546315, 8858157	Standard	NM_000318		Approved	PMP35, PAF-1, RNF72, ZWS3	uc022awf.1	P28328		ENST00000419564.2:c.681T>A	chr8.hg19:g.77895734A>T		78.0	0.0		65.0	23.0	NM_000318	Q567S6|Q9BW41	Silent	SNP	ENST00000419564.2	hg19	CCDS6221.1																																																																																			.	.		0.448	PEX2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379122.1	NM_000318		T	77895734	A	T	77895734	2	4	317	1	0	0	0	0	0	0	0	1	11754	349	13	4		4	PEX2	8	77895734	Silent	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	16126482	77895734	68468288	109	44751	234	2								
PEX2	5828	hgsc.bcm.edu	37	chr8	77895736	77895737	+	Missense_Mutation	DNP	GA	GA	AT													0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	actattaggtgcaccagtaaGaggaatacaccatgaagaca							TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr8:77895736_77895737GA>AT	ENST00000419564.2	-	4	1142_1143	c.678_679TC>AT	c.(676-681)ccTCtt>ccATtt	p.L227F	PEX2_ENST00000522527.1_Missense_Mutation_p.L227F|PEX2_ENST00000520103.1_Missense_Mutation_p.L227F|PEX2_ENST00000357039.4_Missense_Mutation_p.L227F	NM_001172087.1	NP_001165558.1	P28328	PEX2_HUMAN	peroxisomal biogenesis factor 2	227					bile acid biosynthetic process (GO:0006699)|cholesterol homeostasis (GO:0042632)|fatty acid beta-oxidation (GO:0006635)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|peroxisome organization (GO:0007031)|protein destabilization (GO:0031648)|protein import into peroxisome matrix (GO:0016558)|regulation of cholesterol biosynthetic process (GO:0045540)|very long-chain fatty acid metabolic process (GO:0000038)	Cdc73/Paf1 complex (GO:0016593)|integral component of peroxisomal membrane (GO:0005779)|membrane (GO:0016020)|peroxisomal membrane (GO:0005778)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)	14						GCACCAGTAAGAGGAATACACC	0.45																																					p.L227F|p.P226P		Atlas-SNP	.											.	PEX2	44	.	0			c.C679T|c.T678A						.																																			SO:0001583	missense	5828	exon4			CAGTAAGAGGAAT|AGTAAGAGGAATA	M86852	CCDS6221.1	8q21.11	2010-02-09	2010-01-25	2010-01-25		ENSG00000164751		"RING-type (C3HC4) zinc fingers"	9717	protein-coding gene	gene with protein product	"Zellweger syndrome", "peroxin 2"	170993	"peroxisomal membrane protein 3 (35kD, Zellweger syndrome)", "peroxisomal membrane protein 3, 35kDa"	PXMP3		1546315, 8858157	Standard	NM_000318		Approved	PMP35, PAF-1, RNF72, ZWS3	uc022awf.1	P28328		ENST00000419564.2:c.678_679delinsAT	chr8.hg19:g.77895736_77895737delinsAT	ENSP00000400984:p.Leu227Phe	75.0	0.0		64.0|65.0	22.0|23.0	NM_000318	Q567S6|Q9BW41	Missense_Mutation|Silent	SNP	ENST00000419564.2	hg19	CCDS6221.1																																																																																			.	.		0.45	PEX2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379122.1	NM_000318		AT	77895737	GA	AT	77895736	3	1	317	1	0	0	0	0	1	0	0	0	11754	942	33	3	242	3	PEX2	8	77895736	Missense_Mutation	DNP	GA	TCGA-LG-A6GG-01A-11D-A30V-10	2	77895736	68468286	110	44752	234	2								
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110471959	110471959	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	cctgatggaactctgtttgaAgcaagagcagaagttggaat	12	6	1	4			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr8:110471959A>C	ENST00000378402.5	+	47	7244	c.7140A>C	c.(7138-7140)gaA>gaC	p.E2380D		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	2380					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			CTCTGTTTGAAGCAAGAGCAG	0.373										HNSCC(38;0.096)																											p.E2380D		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.A7140C						.						72	67	69					8																	110471959		1840	4083	5923	SO:0001583	missense	93035	exon47			GTTTGAAGCAAGA	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.7140A>C	chr8.hg19:g.110471959A>C	ENSP00000367655:p.Glu2380Asp	278.0	0.0		208.0	83.0	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	hg19	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	A	16.88	3.245453	0.59103	.	.	ENSG00000205038	ENST00000378402	D	0.93604	-3.25	5.24	1.35	0.21983	.	0.123125	0.53938	N	0.000058	D	0.82884	0.5134	N	0.12527	0.23	0.26600	N	0.973041	B	0.24258	0.1	B	0.22880	0.042	T	0.70605	-0.4826	10	0.28530	T	0.3	.	6.9475	0.24526	0.4623:0.4548:0.0829:0.0	.	2380	Q86WI1	PKHL1_HUMAN	D	2380	ENSP00000367655:E2380D	ENSP00000367655:E2380D	E	+	3	2	PKHD1L1	110541135	0.997000	0.39634	0.998000	0.56505	0.986000	0.74619	0.462000	0.21956	0.000000	0.14550	0.254000	0.18369	GAA	.	.		0.373	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		C	110471959	A	C	110471959	3	2	317	1	0	0	0	0	1	0	0	0	11981	69	3	5	7326	5	PKHD1L1	8	110471959	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	32576223	110471959	35892063	111	44753										
TSTA3	7264	hgsc.bcm.edu	37	chr8	144698802	144698802	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ggaagtccagctccatctgcTaccaccttctggatggcttt	9	13	2	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr8:144698802T>G	ENST00000425753.2	-	2	184	c.81A>C	c.(79-81)gtA>gtC	p.V27V	TSTA3_ENST00000529064.1_Silent_p.V27V	NM_003313.3	NP_003304.1	Q13630	FCL_HUMAN	tissue specific transplantation antigen P35B	27					'de novo' GDP-L-fucose biosynthetic process (GO:0042351)|cytolysis (GO:0019835)|GDP-mannose metabolic process (GO:0019673)|leukocyte cell-cell adhesion (GO:0007159)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	coenzyme binding (GO:0050662)|electron carrier activity (GO:0009055)|GDP-4-dehydro-D-rhamnose reductase activity (GO:0042356)|GDP-L-fucose synthase activity (GO:0050577)|isomerase activity (GO:0016853)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|skin(1)	9	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.17e-38)|Epithelial(56;7.17e-37)|all cancers(56;2.46e-32)|Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)			CTCCATCTGCTACCACCTTCT	0.562																																					p.V27V		Atlas-SNP	.											.	TSTA3	23	.	0			c.A81C						.						192	169	177					8																	144698802		2203	4300	6503	SO:0001819	synonymous_variant	7264	exon2			ATCTGCTACCACC	U58766	CCDS6408.1	8q24.3	2012-02-22			ENSG00000104522	ENSG00000104522	1.1.1.271	"Short chain dehydrogenase/reductase superfamily / Extended SDR fold"	12390	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 4E, member 1", "GDP-L-fucose synthase"	137020				7803801, 1348494, 19027726	Standard	NM_003313		Approved	FX, P35B, SDR4E1	uc003yzb.2	Q13630	OTTHUMG00000165159	ENST00000425753.2:c.81A>C	chr8.hg19:g.144698802T>G		83.0	0.0		95.0	43.0	NM_003313	B2R8Y7|D3DWK5|Q567Q9|Q9UDG7	Silent	SNP	ENST00000425753.2	hg19	CCDS6408.1																																																																																			.	.		0.562	TSTA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382263.1	NM_003313		G	144698802	T	G	144698802	2	3	317	1	0	0	0	0	0	0	0	1	16689	1509	53	5		5	TSTA3	8	144698802	Silent	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	34226843	144698802	1665220	112	44754										
CNTLN	54875	hgsc.bcm.edu	37	chr9	17309125	17309125	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ctatgctccggcaaagtgttActaatcttcaggatcagcta	8	10	3	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr9:17309125A>T	ENST00000380647.3	+	8	1300	c.1216A>T	c.(1216-1218)Act>Tct	p.T406S	CNTLN_ENST00000262360.5_Missense_Mutation_p.T406S|CNTLN_ENST00000425824.1_Missense_Mutation_p.T406S			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	406					centriole-centriole cohesion (GO:0010457)|protein localization to organelle (GO:0033365)	centriole (GO:0005814)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)|protein binding, bridging (GO:0030674)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(6)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53				GBM - Glioblastoma multiforme(50;6.14e-10)		GCAAAGTGTTACTAATCTTCA	0.323																																					p.T406S		Atlas-SNP	.											.	CNTLN	128	.	0			c.A1216T						.						49	47	48					9																	17309125		1834	4087	5921	SO:0001583	missense	54875	exon8			AGTGTTACTAATC	AK000283	CCDS43789.1, CCDS47953.1	9p22.2-p22.1	2008-11-11	2008-02-08	2008-02-08	ENSG00000044459	ENSG00000044459			23432	protein-coding gene	gene with protein product		611870	"chromosome 9 open reading frame 101", "chromosome 9 open reading frame 39"	C9orf101, C9orf39		18086554	Standard	XM_005251492		Approved	FLJ20276, bA340N12.1, OTTHUMG00000019597	uc003zmy.3	Q9NXG0	OTTHUMG00000019599	ENST00000380647.3:c.1216A>T	chr9.hg19:g.17309125A>T	ENSP00000370021:p.Thr406Ser	509.0	0.0		368.0	153.0	NM_017738	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Missense_Mutation	SNP	ENST00000380647.3	hg19	CCDS43789.1	.	.	.	.	.	.	.	.	.	.	A	10.27	1.304038	0.23736	.	.	ENSG00000044459	ENST00000380647;ENST00000425824;ENST00000262360	T;T;T	0.39229	1.09;1.09;1.09	5.66	-0.586	0.11694	.	.	.	.	.	T	0.16128	0.0388	N	0.08118	0	0.09310	N	1	B;B;B	0.09022	0.002;0.002;0.002	B;B;B	0.12837	0.008;0.008;0.008	T	0.31779	-0.9931	9	0.02654	T	1	.	5.6425	0.17572	0.555:0.1526:0.2923:0.0	.	406;406;406	Q9NXG0;C9J1F9;Q9NXG0-2	CNTLN_HUMAN;.;.	S	406	ENSP00000370021:T406S;ENSP00000392798:T406S;ENSP00000262360:T406S	ENSP00000262360:T406S	T	+	1	0	CNTLN	17299125	0.843000	0.29541	0.779000	0.31741	0.634000	0.38068	-0.008000	0.12788	0.153000	0.19213	-1.964000	0.00472	ACT	.	.		0.323	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738		T	17309125	A	T	17309125	3	4	317	1	0	0	0	0	1	0	0	0	3641	391	14	4	1276	4	CNTLN	9	17309125	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10		17309125	123904306	113	44755										
UBQLN1	29979	hgsc.bcm.edu	37	chr9	86284174	86284174	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gggggcagacaacatgttttGcatcagttgtgggttttcag	14	6	2	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr9:86284174G>T	ENST00000376395.4	-	7	1697	c.1174C>A	c.(1174-1176)Caa>Aaa	p.Q392K	UBQLN1_ENST00000257468.7_Missense_Mutation_p.Q392K	NM_013438.4|NM_053067.2	NP_038466.2|NP_444295.1	Q9UMX0	UBQL1_HUMAN	ubiquilin 1	392					cellular response to hypoxia (GO:0071456)|regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902175)|regulation of protein ubiquitination (GO:0031396)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|proteasome complex (GO:0000502)|protein complex (GO:0043234)	kinase binding (GO:0019900)			breast(4)|endometrium(2)|kidney(4)|large_intestine(6)|lung(10)|prostate(1)	27						AACATGTTTTGCATCAGTTGT	0.388																																					p.Q392K	Melanoma(186;1284 2073 12755 14558 18426)	Atlas-SNP	.											.	UBQLN1	49	.	0			c.C1174A						.						145	128	134					9																	86284174		2203	4300	6503	SO:0001583	missense	29979	exon7			TGTTTTGCATCAG	AF176069	CCDS6663.1, CCDS6664.1	9q22	2013-02-12			ENSG00000135018	ENSG00000135018		"Ubiquilin family"	12508	protein-coding gene	gene with protein product		605046				9303440, 10807547	Standard	NM_013438		Approved	DSK2, PLIC-1, XDRP1, DA41	uc004amv.3	Q9UMX0	OTTHUMG00000020104	ENST00000376395.4:c.1174C>A	chr9.hg19:g.86284174G>T	ENSP00000365576:p.Gln392Lys	117.0	0.0		87.0	32.0	NM_053067	Q5T6J5|Q5T6J9|Q8IXS9|Q8N2Q3|Q9H0T8|Q9H3R4|Q9HAZ5	Missense_Mutation	SNP	ENST00000376395.4	hg19	CCDS6663.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.6|22.6	4.317598|4.317598	0.81469|0.81469	.|.	.|.	ENSG00000135018|ENSG00000135018	ENST00000526134|ENST00000376395;ENST00000257468	.|T;T	.|0.54071	.|1.09;0.59	5.72|5.72	5.72|5.72	0.89469|0.89469	.|Heat shock chaperonin-binding (1);	.|0.077207	.|0.53938	.|D	.|0.000042	.|T	.|0.61438	.|0.2347	M|M	0.82823|0.82823	2.61|2.61	0.80722|0.80722	D|D	1|1	.|B;P	.|0.45348	.|0.354;0.856	.|B;B	.|0.42030	.|0.373;0.263	.|T	.|0.64563	.|-0.6378	.|10	.|0.34782	.|T	.|0.22	.|.	19.8548|19.8548	0.96752|0.96752	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|392;392	.|Q9UMX0-2;Q9UMX0	.|.;UBQL1_HUMAN	X|K	11|392	.|ENSP00000365576:Q392K;ENSP00000257468:Q392K	.|ENSP00000257468:Q392K	C|Q	-|-	3|1	2|0	UBQLN1|UBQLN1	85473994|85473994	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	9.471000|9.471000	0.97696|0.97696	2.687000|2.687000	0.91594|0.91594	0.655000|0.655000	0.94253|0.94253	TGC|CAA	.	.		0.388	UBQLN1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000052834.1	NM_013438		T	86284174	G	T	86284174	3	4	317	1	0	0	0	0	1	0	0	0	16911	1328	46	3	615	3	UBQLN1	9	86284174	Missense_Mutation	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	68975049	86284174	54929257	114	44756										
GARNL3	84253	hgsc.bcm.edu	37	chr9	130106562	130106562	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	atgtcttaccagagtcacccAagtcagcgcggaagaaagag	11	10	3	3			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr9:130106562A>G	ENST00000373387.4	+	15	1652	c.1300A>G	c.(1300-1302)Aag>Gag	p.K434E	GARNL3_ENST00000314904.5_Missense_Mutation_p.K434E|GARNL3_ENST00000435213.2_Missense_Mutation_p.K412E	NM_032293.4	NP_115669.3	Q5VVW2	GARL3_HUMAN	GTPase activating Rap/RanGAP domain-like 3	434					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)|small GTPase regulator activity (GO:0005083)			NS(1)|central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(24)|ovary(1)|skin(1)|urinary_tract(2)	41						AGAGTCACCCAAGTCAGCGCG	0.423																																					p.K434E		Atlas-SNP	.											.	GARNL3	83	.	0			c.A1300G						.						136	152	147					9																	130106562		2203	4300	6503	SO:0001583	missense	84253	exon15			TCACCCAAGTCAG	BC034983	CCDS6869.2, CCDS69663.1	9q34.13	2009-09-14	2004-08-09		ENSG00000136895	ENSG00000136895			25425	protein-coding gene	gene with protein product			"GTPase activating RANGAP domain-like 3"			11230166	Standard	NM_032293		Approved	DKFZp761J1523, bA356B19.1	uc011mae.2	Q5VVW2	OTTHUMG00000020700	ENST00000373387.4:c.1300A>G	chr9.hg19:g.130106562A>G	ENSP00000362485:p.Lys434Glu	230.0	0.0		178.0	79.0	NM_032293	B4DEP7|B7Z3Q6|Q8IYU1|Q8N951|Q8ND89|Q9BQH6	Missense_Mutation	SNP	ENST00000373387.4	hg19	CCDS6869.2	.	.	.	.	.	.	.	.	.	.	A	18.94	3.729582	0.69074	.	.	ENSG00000136895	ENST00000435213;ENST00000314904;ENST00000373387	D;D;D	0.87412	-2.24;-2.21;-2.25	5.58	5.58	0.84498	.	0.042704	0.85682	D	0.000000	T	0.81494	0.4834	L	0.44542	1.39	0.58432	D	0.99999	B;B;B	0.31769	0.339;0.224;0.013	B;B;B	0.24701	0.055;0.055;0.006	T	0.78863	-0.2036	9	.	.	.	.	14.5659	0.68176	1.0:0.0:0.0:0.0	.	434;412;375	Q5VVW2;B7Z3Q6;Q5VVW4	GARL3_HUMAN;.;.	E	412;434;434	ENSP00000396205:K412E;ENSP00000313970:K434E;ENSP00000362485:K434E	.	K	+	1	0	GARNL3	129146383	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.833000	0.92089	2.113000	0.64589	0.460000	0.39030	AAG	.	.		0.423	GARNL3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054151.3	NM_032293		G	130106562	A	G	130106562	3	3	317	1	0	0	0	0	1	0	0	0	6249	131	5	2	1358	2	GARNL3	9	130106562	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	43822388	130106562	11106869	115	44757										
NUP188	23511	hgsc.bcm.edu	37	chr9	131763862	131763862	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tgtgtgaggtagacgaggatGgtgactcctggctgcaggta	17	6	0	3			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr9:131763862G>A	ENST00000372577.2	+	35	3919	c.3898G>A	c.(3898-3900)Ggt>Agt	p.G1300S	RP11-167N5.5_ENST00000594418.1_lincRNA	NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	1300					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				breast(2)|central_nervous_system(3)|endometrium(6)|kidney(4)|large_intestine(9)|lung(20)|ovary(6)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	60						AGACGAGGATGGTGACTCCTG	0.582																																					p.G1300S		Atlas-SNP	.											.	NUP188	140	.	0			c.G3898A						.						69	60	63					9																	131763862		2203	4300	6503	SO:0001583	missense	23511	exon35			GAGGATGGTGACT	D79991	CCDS35156.1	9q34.13	2014-01-28	2004-03-19	2004-03-24	ENSG00000095319	ENSG00000095319			17859	protein-coding gene	gene with protein product		615587	"KIAA0169"	KIAA0169		11029043	Standard	NM_015354		Approved		uc004bws.2	Q5SRE5	OTTHUMG00000020768	ENST00000372577.2:c.3898G>A	chr9.hg19:g.131763862G>A	ENSP00000361658:p.Gly1300Ser	34.0	0.0		30.0	14.0	NM_015354	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Missense_Mutation	SNP	ENST00000372577.2	hg19	CCDS35156.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.324140	0.81580	.	.	ENSG00000095319	ENST00000356693;ENST00000372577	T	0.70164	-0.46	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	T	0.81192	0.4771	M	0.69823	2.125	0.80722	D	1	D;D	0.89917	0.996;1.0	P;D	0.87578	0.874;0.998	T	0.79813	-0.1645	10	0.38643	T	0.18	-13.5486	18.1417	0.89642	0.0:0.0:1.0:0.0	.	633;1300	E9PET9;Q5SRE5	.;NU188_HUMAN	S	1189;1300	ENSP00000361658:G1300S	ENSP00000349125:G1189S	G	+	1	0	NUP188	130803683	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.465000	0.97660	2.537000	0.85549	0.462000	0.41574	GGT	.	.		0.582	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2			A	131763862	G	A	131763862	3	1	317	1	0	0	0	0	1	0	0	0	10767	1348	47	3	4036	3	NUP188	9	131763862	Missense_Mutation	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	1657300	131763862	9449569	116	44758										
COBRA1	25920	hgsc.bcm.edu	37	chr9	140160781	140160781	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gctgagcccgtcctccctacAggacagccccgacctcctgc	9	20	0	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr9:140160781A>G	ENST00000343053.4	+	8	1336		c.e8-1			NM_015456.3	NP_056271.2	Q8WX92	NELFB_HUMAN	negative elongation factor complex member B						gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|NELF complex (GO:0032021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											TCCTCCCTACAGGACAGCCCC	0.642																																					.		Atlas-SNP	.											.	.	.	.	0			c.1000-2A>G						.						28	26	27					9																	140160781		2202	4283	6485	SO:0001630	splice_region_variant	25920	exon8			CCCTACAGGACAG	AF464935	CCDS7040.1	9q34	2013-01-31	2013-01-31	2013-01-31	ENSG00000188986	ENSG00000188986			24324	protein-coding gene	gene with protein product		611180	"cofactor of BRCA1"	COBRA1		11230166, 10574461, 17910036, 17659869	Standard	NM_015456		Approved	KIAA1182, NELF-B	uc004cmm.4	Q8WX92	OTTHUMG00000131778	ENST00000343053.4:c.1000-1A>G	chr9.hg19:g.140160781A>G		128.0	0.0		94.0	36.0	NM_015456	A2BFA3|Q96EW5|Q9H9R4|Q9ULN8|Q9Y3W0	Splice_Site	SNP	ENST00000343053.4	hg19	CCDS7040.1	.	.	.	.	.	.	.	.	.	.	A	14.48	2.548547	0.45383	.	.	ENSG00000188986	ENST00000343053	.	.	.	5.02	3.85	0.44370	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.2084	0.48784	0.8459:0.1541:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	COBRA1	139280602	1.000000	0.71417	0.860000	0.33809	0.492000	0.33523	9.044000	0.93805	0.827000	0.34685	0.402000	0.26972	.	.	.		0.642	NELFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254710.1	NM_015456	Intron	G	140160781	A	G	140160781	5	3	317	1	0	0	0	0	0	0	1	0	3657	202	7	2	1028	2	COBRA1	9	140160781	Splice_Site	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	8396919	140160781	1052650	117	44759										
ARMC3	219681	hgsc.bcm.edu	37	chr10	23244758	23244758	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gaggaaaataaaacaaccctCcttgaacttggagctgtgga	10	8	0	1	rs570281393		TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr10:23244758C>T	ENST00000298032.5	+	4	273	c.189C>T	c.(187-189)ctC>ctT	p.L63L	ARMC3_ENST00000464017.1_3'UTR|ARMC3_ENST00000409983.3_Silent_p.L63L|ARMC3_ENST00000376528.4_5'UTR|ARMC3_ENST00000409049.3_Silent_p.L63L	NM_173081.3	NP_775104.2	Q5W041	ARMC3_HUMAN	armadillo repeat containing 3	63						extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(24)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						AAACAACCCTCCTTGAACTTG	0.388													C|||	1	0.000199681	0	0	5008	,	,		19398	0		0	False		,,,				2504	0.001				p.L63L		Atlas-SNP	.											.	ARMC3	102	.	0			c.C189T						.						120	118	119					10																	23244758		2203	4300	6503	SO:0001819	synonymous_variant	219681	exon4			AACCCTCCTTGAA	AK057389	CCDS7142.1, CCDS60499.1, CCDS60500.1, CCDS73073.1	10p12.31	2013-02-14			ENSG00000165309	ENSG00000165309		"Armadillo repeat containing"	30964	protein-coding gene	gene with protein product	"cancer/testis antigen 81"	611226					Standard	XM_005252380		Approved	FLJ32827, CT81	uc001irm.4	Q5W041	OTTHUMG00000017811	ENST00000298032.5:c.189C>T	chr10.hg19:g.23244758C>T		213.0	0.0		171.0	88.0	NM_173081	A0PG76|A6NH64|B4DZL3|B7ZBN6|B7ZBN7|Q8IXS5|Q8N7B0|Q96M49	Silent	SNP	ENST00000298032.5	hg19	CCDS7142.1																																																																																			.	.		0.388	ARMC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047197.2	NM_173081		T	23244758	C	T	23244758	2	4	317	1	0	0	0	0	0	0	0	1	952	842	30	3		3	ARMC3	10	23244758	Silent	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10		23244758	112289989	118	44760										
SFTPA2	729238	hgsc.bcm.edu	37	chr10	81317058	81317058	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	acacactgctcttttccccgAcctgcaggctcccctcggta	7	18	1	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr10:81317058A>C	ENST00000372325.2	-	6	738	c.654T>G	c.(652-654)ggT>ggG	p.G218G	SFTPA2_ENST00000372327.5_Silent_p.G218G	NM_001098668.2	NP_001092138.1	Q8IWL1	SFPA2_HUMAN	surfactant protein A2	218	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				respiratory gaseous exchange (GO:0007585)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)			endometrium(1)|kidney(1)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	9	all_cancers(46;0.197)|Breast(12;0.000326)|Prostate(51;0.00985)|all_epithelial(25;0.0149)		Epithelial(14;0.00957)|all cancers(16;0.0179)|Colorectal(32;0.229)			CTTTTCCCCGACCTGCAGGCT	0.562									Pulmonary Fibrosis, Idiopathic																												p.G218G		Atlas-SNP	.											.	SFTPA2	19	.	0			c.T654G						.						234	223	227					10																	81317058		2203	4296	6499	SO:0001819	synonymous_variant	729238	exon6	Familial Cancer Database	Hamman-Rich syndrome, Fibrocystic Pulmonary Dysplasia	TCCCCGACCTGCA		CCDS41540.1	10q22.3	2012-11-02	2008-08-26			ENSG00000185303		"Collectins"	10799	protein-coding gene	gene with protein product	"surfactant, pulmonary-associated protein A2A"	178642	"surfactant, pulmonary-associated protein A2"				Standard	NM_001098668		Approved	SP-A2, COLEC5	uc001kal.4	Q8IWL1		ENST00000372325.2:c.654T>G	chr10.hg19:g.81317058A>C		455.0	1.0		322.0	261.0	NM_001098668	A4QPA7|B2RXI6|B2RXK9|C9J9I7|E3VLC6|E3VLC7|E3VLC8|E3VLC9|P07714|Q14DV3|Q5RIR8|Q5RIR9	Silent	SNP	ENST00000372325.2	hg19	CCDS41540.1																																																																																			.	.		0.562	SFTPA2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048961.1	NM_001098668		C	81317058	A	C	81317058	2	2	317	1	0	0	0	0	0	0	0	1	14205	262	10	5		5	SFTPA2	10	81317058	Silent	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	58072300	81317058	54217689	119	44761										
HPSE2	60495	hgsc.bcm.edu	37	chr10	100992230	100992230	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	agcgcagaaaggcgggcgaaAgtccccgggccagggtcacc	16	13	1	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr10:100992230A>T	ENST00000370552.3	-	2	382	c.323T>A	c.(322-324)cTt>cAt	p.L108H	HPSE2_ENST00000370546.1_Missense_Mutation_p.L108H|HPSE2_ENST00000404542.1_Missense_Mutation_p.L108H|HPSE2_ENST00000370549.1_Missense_Mutation_p.L108H	NM_021828.4	NP_068600.4	Q8WWQ2	HPSE2_HUMAN	heparanase 2 (inactive)	108					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	intracellular (GO:0005622)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	heparan sulfate proteoglycan binding (GO:0043395)|heparanase activity (GO:0030305)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	40				Epithelial(162;1.8e-09)|all cancers(201;4.72e-07)		GGCGGGCGAAAGTCCCCGGGC	0.642																																					p.L108H		Atlas-SNP	.											.	HPSE2	203	.	0			c.T323A						.						9	10	10					10																	100992230		2153	4206	6359	SO:0001583	missense	60495	exon2			GGCGAAAGTCCCC	AF282885	CCDS7477.1, CCDS53567.1, CCDS53568.1	10q23-q24	2014-05-09	2014-05-09		ENSG00000172987	ENSG00000172987			18374	protein-coding gene	gene with protein product		613469	"urofacial syndrome", "heparanase 2"	UFS		11027606, 20605132, 9199567, 20576607	Standard	NM_021828		Approved	HPA2, HPR2	uc001kpn.2	Q8WWQ2	OTTHUMG00000018880	ENST00000370552.3:c.323T>A	chr10.hg19:g.100992230A>T	ENSP00000359583:p.Leu108His	308.0	0.0		227.0	195.0	NM_001166246	Q5VUH4|Q5VUH5|Q5VUH6|Q8WWQ1|Q9HB37|Q9HB38|Q9HB39	Missense_Mutation	SNP	ENST00000370552.3	hg19	CCDS7477.1	.	.	.	.	.	.	.	.	.	.	A	15.35	2.806984	0.50421	.	.	ENSG00000172987	ENST00000370552;ENST00000370549;ENST00000370546;ENST00000404542	T;T;T;T	0.41065	1.01;1.01;1.01;1.01	5.27	4.11	0.48088	Glycoside hydrolase, superfamily (1);	0.000000	0.64402	D	0.000006	T	0.63212	0.2492	M	0.77486	2.375	0.29154	N	0.878202	B;D;D;D	0.89917	0.033;0.995;1.0;0.986	B;P;D;P	0.83275	0.04;0.847;0.996;0.62	T	0.62666	-0.6806	10	0.87932	D	0	-3.5153	11.1563	0.48489	0.8617:0.0:0.0:0.1383	.	108;108;108;108	Q8WWQ2-4;Q8WWQ2-2;Q8WWQ2-3;Q8WWQ2	.;.;.;HPSE2_HUMAN	H	108	ENSP00000359583:L108H;ENSP00000359580:L108H;ENSP00000359577:L108H;ENSP00000384384:L108H	ENSP00000359577:L108H	L	-	2	0	HPSE2	100982220	1.000000	0.71417	0.998000	0.56505	0.769000	0.43574	8.111000	0.89564	0.827000	0.34685	-0.333000	0.08304	CTT	.	.		0.642	HPSE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049789.1	NM_021828		T	100992230	A	T	100992230	3	4	317	1	0	0	0	0	1	0	0	0	7354	72	3	4	1537	4	HPSE2	10	100992230	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	19675172	100992230	34542517	120	44762										
DEAF1	10522	hgsc.bcm.edu	37	chr11	679715	679715	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ccctgcgaagacgtcgccctGggccggactctctgatatga	12	14	1	3			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr11:679715G>T	ENST00000382409.3	-	8	1583	c.1099C>A	c.(1099-1101)Cag>Aag	p.Q367K	RP11-754B17.1_ENST00000527799.1_RNA|DEAF1_ENST00000525904.1_5'UTR|DEAF1_ENST00000338675.6_Missense_Mutation_p.Q278K	NM_021008.2	NP_066288.2	O75398	DEAF1_HUMAN	DEAF1 transcription factor	367			Q -> H (in a primary colorectal cancer). {ECO:0000269|PubMed:11705868}.		anatomical structure morphogenesis (GO:0009653)|embryonic skeletal system development (GO:0048706)|germ cell development (GO:0007281)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|upper_aerodigestive_tract(1)	24		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;1.76e-27)|Epithelial(43;8.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.55e-21)|BRCA - Breast invasive adenocarcinoma(625;4.83e-05)|Lung(200;0.0259)|LUSC - Lung squamous cell carcinoma(625;0.075)		ACGTCGCCCTGGGCCGGACTC	0.642																																					p.Q367K		Atlas-SNP	.											.	DEAF1	47	.	0			c.C1099A						.						81	71	74					11																	679715		2203	4300	6503	SO:0001583	missense	10522	exon8			CGCCCTGGGCCGG	AF049460	CCDS31327.1	11p15.5	2013-01-10	2013-01-10		ENSG00000177030	ENSG00000177030		"Zinc fingers, MYND-type"	14677	protein-coding gene	gene with protein product		602635	"deformed epidermal autoregulatory factor 1 (Drosophila)"			9773984	Standard	XR_428838		Approved	NUDR, SPN, ZMYND5	uc001lqq.1	O75398	OTTHUMG00000165363	ENST00000382409.3:c.1099C>A	chr11.hg19:g.679715G>T	ENSP00000371846:p.Gln367Lys	27.0	0.0		29.0	5.0	NM_021008	A8K1F8|A8K5R8|C7T5V5|O15152|O75399|O75510|O75511|O75512|O75513|Q9UET1	Missense_Mutation	SNP	ENST00000382409.3	hg19	CCDS31327.1	.	.	.	.	.	.	.	.	.	.	G	15.98	2.993056	0.54041	.	.	ENSG00000177030	ENST00000382409;ENST00000338675;ENST00000359958;ENST00000388804	T	0.66099	-0.19	3.49	3.49	0.39957	.	0.273852	0.31061	N	0.008329	T	0.50137	0.1598	L	0.40543	1.245	0.40886	D	0.984035	B	0.23377	0.084	B	0.15870	0.014	T	0.48375	-0.9041	10	0.19147	T	0.46	-9.4207	14.3254	0.66515	0.0:0.0:1.0:0.0	.	367	O75398	DEAF1_HUMAN	K	367;278;353;290	ENSP00000371846:Q367K	ENSP00000341902:Q278K	Q	-	1	0	DEAF1	669715	1.000000	0.71417	0.984000	0.44739	0.741000	0.42261	6.803000	0.75180	1.975000	0.57531	0.557000	0.71058	CAG	.	.		0.642	DEAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383614.3	NM_021008		T	679715	G	T	679715	3	4	317	1	0	0	0	0	1	0	0	0	4382	1357	47	3	618	3	DEAF1	11	679715	Missense_Mutation	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10		679715	134326801	121	44763										
CDKN1C	1028	hgsc.bcm.edu	37	chr11	2906437	2906437	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gcggcagcgccccacctgcaCcgtctcgcggtagaacgcgg	14	17	1	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr11:2906437C>T	ENST00000414822.3	-	1	674	c.283G>A	c.(283-285)Gtg>Atg	p.V95M	CDKN1C_ENST00000430149.2_Missense_Mutation_p.V95M|CDKN1C_ENST00000380725.1_Missense_Mutation_p.V84M|CDKN1C_ENST00000440480.2_Missense_Mutation_p.V84M|CDKN1C_ENST00000313407.6_Missense_Mutation_p.V84M	NM_000076.2	NP_000067.1	P49918	CDN1C_HUMAN	cyclin-dependent kinase inhibitor 1C (p57, Kip2)	95					adrenal gland development (GO:0030325)|aging (GO:0007568)|camera-type eye development (GO:0043010)|cell cycle arrest (GO:0007050)|digestive system development (GO:0055123)|embryonic placenta morphogenesis (GO:0060669)|genetic imprinting (GO:0071514)|kidney development (GO:0001822)|multicellular organism growth (GO:0035264)|myeloid cell differentiation (GO:0030099)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of kinase activity (GO:0033673)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron maturation (GO:0042551)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|skeletal system development (GO:0001501)|uterus development (GO:0060065)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)			central_nervous_system(1)|lung(1)	2		all_epithelial(84;0.000187)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|Breast(177;0.00328)|all_neural(188;0.00681)|all_lung(207;0.157)|Lung NSC(207;0.216)		BRCA - Breast invasive adenocarcinoma(625;0.0025)|LUSC - Lung squamous cell carcinoma(625;0.19)		CCCACCTGCACCGTCTCGCGG	0.736																																					p.V95M	GBM(111;59 1151 2497 5746 16112 18241 29216)	Atlas-SNP	.											.	CDKN1C	4	.	0			c.G283A						.						8	6	7					11																	2906437		1997	3974	5971	SO:0001583	missense	1028	exon1			CCTGCACCGTCTC	D64137	CCDS7738.1, CCDS44519.1	11p15.5	2014-09-17	2004-02-13		ENSG00000129757	ENSG00000129757			1786	protein-coding gene	gene with protein product		600856	"Beckwith-Wiedemann syndrome"	BWCR, BWS		7729684	Standard	NM_000076		Approved	P57, KIP2	uc001lws.4	P49918	OTTHUMG00000010040	ENST00000414822.3:c.283G>A	chr11.hg19:g.2906437C>T	ENSP00000413720:p.Val95Met	52.0	0.0		54.0	17.0	NM_000076		Missense_Mutation	SNP	ENST00000414822.3	hg19	CCDS7738.1	.	.	.	.	.	.	.	.	.	.	c	18.27	3.586003	0.66105	.	.	ENSG00000129757	ENST00000380725;ENST00000414822;ENST00000440480;ENST00000313407;ENST00000430149	D;D;D;D;D	0.91464	-2.04;-2.51;-2.85;-2.85;-2.51	2.43	2.43	0.29744	.	.	.	.	.	D	0.92277	0.7550	L	0.61218	1.895	0.36664	D	0.878095	D;D	0.61080	0.989;0.989	P;D	0.69654	0.862;0.965	D	0.91945	0.5566	9	0.72032	D	0.01	.	5.3125	0.15837	0.1973:0.498:0.3046:0.0	.	84;95	A6NK88;P49918	.;CDN1C_HUMAN	M	84;95;84;84;95	ENSP00000370101:V84M;ENSP00000413720:V95M;ENSP00000411257:V84M;ENSP00000321019:V84M;ENSP00000411552:V95M	ENSP00000321019:V84M	V	-	1	0	CDKN1C	2863013	0.912000	0.30974	1.000000	0.80357	0.943000	0.58893	2.608000	0.46308	1.407000	0.46875	0.298000	0.19748	GTG	.	.		0.736	CDKN1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027774.2	NM_000076		T	2906437	C	T	2906437	3	4	317	1	0	0	0	0	1	0	0	0	3162	507	18	3	675	3	CDKN1C	11	2906437	Missense_Mutation	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	2226722	2906437	132100079	122	44764										
NUP98	4928	hgsc.bcm.edu	37	chr11	3721964	3721964	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	acatggacagtgctgtgtttTaatttgagctccagaggtgt	12	6	0	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr11:3721964T>A	ENST00000324932.7	-	24	4038	c.3618A>T	c.(3616-3618)ttA>ttT	p.L1206F	NUP98_ENST00000355260.3_Missense_Mutation_p.L1206F|NUP98_ENST00000359171.4_Missense_Mutation_p.L1206F	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	1223					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|DNA replication (GO:0006260)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore organization (GO:0006999)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nuclear pore outer ring (GO:0031080)|nucleoplasm (GO:0005654)	peptide binding (GO:0042277)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		TGCTGTGTTTTAATTTGAGCT	0.413			T	"HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"	AML																																p.L1206F		Atlas-SNP	.		Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	.	NUP98	149	.	0			c.A3618T						.						181	170	174					11																	3721964		2201	4298	6499	SO:0001583	missense	4928	exon24			GTGTTTTAATTTG	AF071076, AF231130, BC012906, BG773331	CCDS7746.1, CCDS31347.1, CCDS41605.1, CCDS41606.1	11p15	2008-02-26	2002-08-29		ENSG00000110713	ENSG00000110713			8068	protein-coding gene	gene with protein product		601021	"nucleoporin 98kD"			9166830	Standard	NM_139131		Approved	NUP96	uc001lyh.3	P52948	OTTHUMG00000011846	ENST00000324932.7:c.3618A>T	chr11.hg19:g.3721964T>A	ENSP00000316032:p.Leu1206Phe	120.0	0.0		139.0	34.0	NM_016320	Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Missense_Mutation	SNP	ENST00000324932.7	hg19	CCDS7746.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.47|18.47	3.631798|3.631798	0.67015|0.67015	.|.	.|.	ENSG00000110713|ENSG00000110713	ENST00000429801|ENST00000324932;ENST00000359171;ENST00000355260	.|.	.|.	.|.	5.4|5.4	-1.47|-1.47	0.08772|0.08772	.|.	.|0.000000	.|0.64402	.|D	.|0.000004	.|T	.|0.56673	.|0.2001	M|M	0.63843|0.63843	1.955|1.955	0.34501|0.34501	D|D	0.706095|0.706095	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.91635	.|0.999;0.999;0.999	.|T	.|0.60177	.|-0.7314	.|9	.|0.30078	.|T	.|0.28	-7.8161|-7.8161	1.5432|1.5432	0.02559|0.02559	0.1476:0.3349:0.2707:0.2468|0.1476:0.3349:0.2707:0.2468	.|.	.|1206;1206;1120	.|P52948-2;P52948-5;P52948-6	.|.;.;.	X|F	159|1206	.|.	.|ENSP00000316032:L1206F	K|L	-|-	1|3	0|2	NUP98|NUP98	3678540|3678540	0.796000|0.796000	0.28864|0.28864	0.999000|0.999000	0.59377|0.59377	0.972000|0.972000	0.66771|0.66771	-0.339000|-0.339000	0.07832|0.07832	0.038000|0.038000	0.15604|0.15604	-0.263000|-0.263000	0.10527|0.10527	AAA|TTA	.	.		0.413	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	NM_016320		A	3721964	T	A	3721964	3	1	317	1	0	0	0	0	1	0	0	0	10782	1751	61	4	1824	4	NUP98	11	3721964	Missense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	815527	3721964	131284552	123	44765										
OR51D1	390038	hgsc.bcm.edu	37	chr11	4661505	4661505	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	caagattggactatctgcccTgaccagggggtttgtattct	11	9	2	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr11:4661505T>A	ENST00000357605.2	+	1	561	c.485T>A	c.(484-486)cTg>cAg	p.L162Q		NM_001004751.2	NP_001004751.1	Q8NGF3	O51D1_HUMAN	olfactory receptor, family 51, subfamily D, member 1	162						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L162P(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|liver(2)|lung(14)|prostate(1)|skin(2)|urinary_tract(1)	27		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;2.74e-13)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|GBM - Glioblastoma multiforme(2;0.0841)|LUSC - Lung squamous cell carcinoma(625;0.19)		CTATCTGCCCTGACCAGGGGG	0.527																																					p.L162Q		Atlas-SNP	.											OR51D1,NS,carcinoma,0,1	OR51D1	49	.	1	Substitution - Missense(1)	lung(1)	c.T485A						.						220	191	201					11																	4661505		2201	4298	6499	SO:0001583	missense	390038	exon1			CTGCCCTGACCAG	AB065855	CCDS31357.1	11p15.4	2012-08-09			ENSG00000197428	ENSG00000197428		"GPCR / Class A : Olfactory receptors"	15193	protein-coding gene	gene with protein product							Standard	NM_001004751		Approved	OR51D1Q	uc010qyk.2	Q8NGF3	OTTHUMG00000165724	ENST00000357605.2:c.485T>A	chr11.hg19:g.4661505T>A	ENSP00000350222:p.Leu162Gln	66.0	0.0		69.0	24.0	NM_001004751	B9EIK4	Missense_Mutation	SNP	ENST00000357605.2	hg19	CCDS31357.1	.	.	.	.	.	.	.	.	.	.	T	12.29	1.893582	0.33442	.	.	ENSG00000197428	ENST00000357605	T	0.38887	1.11	4.4	4.4	0.53042	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35772	N	0.002987	T	0.64649	0.2617	M	0.81614	2.55	0.18873	N	0.999987	D	0.76494	0.999	D	0.77557	0.99	T	0.59473	-0.7448	10	0.87932	D	0	.	12.9235	0.58245	0.0:0.0:0.0:1.0	.	162	Q8NGF3	O51D1_HUMAN	Q	162	ENSP00000350222:L162Q	ENSP00000350222:L162Q	L	+	2	0	OR51D1	4618081	0.135000	0.22499	0.003000	0.11579	0.002000	0.02628	3.066000	0.50002	1.967000	0.57214	0.456000	0.33151	CTG	.	.		0.527	OR51D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385956.1	NM_001004751		A	4661505	T	A	4661505	3	1	317	1	0	0	0	0	1	0	0	0	11102	1580	55	4	487	4	OR51D1	11	4661505	Missense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	939541	4661505	130345011	124	44766										
OR51F1	256892	hgsc.bcm.edu	37	chr11	4790465	4790465	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	cttcaggggaggcaattctgAggacagagtgaataattaag	13	5	2	3			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr11:4790465A>C	ENST00000380383.1	-	1	703	c.704T>G	c.(703-705)cTc>cGc	p.L235R	MMP26_ENST00000477339.1_Intron|OR51F1_ENST00000343430.3_Missense_Mutation_p.L228R|MMP26_ENST00000380390.1_Intron			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	235						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	22		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.0778)		Epithelial(150;5.87e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0045)|LUSC - Lung squamous cell carcinoma(625;0.192)		GGCAATTCTGAGGACAGAGTG	0.463																																					p.L228R		Atlas-SNP	.											.	OR51F1	60	.	0			c.T683G						.						121	117	118					11																	4790465		2201	4298	6499	SO:0001583	missense	256892	exon1			ATTCTGAGGACAG	BK004771	CCDS31359.1	11p15.4	2012-08-09		2004-03-10	ENSG00000188069	ENSG00000188069		"GPCR / Class A : Olfactory receptors"	15196	protein-coding gene	gene with protein product				OR51F1P			Standard	NM_001004752		Approved		uc010qyl.2	A6NGY5	OTTHUMG00000066503	ENST00000380383.1:c.704T>G	chr11.hg19:g.4790465A>C	ENSP00000369744:p.Leu235Arg	167.0	0.0		185.0	56.0	NM_001004752		Missense_Mutation	SNP	ENST00000380383.1	hg19		.	.	.	.	.	.	.	.	.	.	A	11.25	1.583107	0.28268	.	.	ENSG00000188069	ENST00000343430;ENST00000380383	T;T	0.00316	8.13;8.13	5.24	5.24	0.73138	GPCR, rhodopsin-like superfamily (1);	0.294146	0.23065	N	0.052334	T	0.00936	0.0031	M	0.92604	3.325	0.09310	N	0.999992	D	0.76494	0.999	D	0.72338	0.977	T	0.25257	-1.0137	10	0.87932	D	0	.	14.0937	0.65006	1.0:0.0:0.0:0.0	.	235	A6NGY5	O51F1_HUMAN	R	228;235	ENSP00000345163:L228R;ENSP00000369744:L235R	ENSP00000345163:L228R	L	-	2	0	OR51F1	4747041	0.460000	0.25776	0.039000	0.18376	0.073000	0.16967	5.344000	0.65981	2.202000	0.70862	0.533000	0.62120	CTC	.	.		0.463	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752		C	4790465	A	C	4790465	3	2	317	1	0	0	0	0	1	0	0	0	11105	304	11	5	258	5	OR51F1	11	4790465	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	128960	4790465	130216051	125	44767										
CNGA4	1262	hgsc.bcm.edu	37	chr11	6261357	6261357	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	atctcgagtcgctacgttcgCacctggagtttcttcttgga	10	11	3	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr11:6261357C>T	ENST00000379936.2	+	4	448	c.333C>T	c.(331-333)cgC>cgT	p.R111R	CNGA4_ENST00000533426.1_Intron	NM_001037329.3	NP_001032406.1	Q8IV77	CNGA4_HUMAN	cyclic nucleotide gated channel alpha 4	111					phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sensory perception of smell (GO:0007608)	integral component of plasma membrane (GO:0005887)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			endometrium(2)|kidney(1)|large_intestine(9)|lung(24)|prostate(3)|skin(1)	40		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.04e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GCTACGTTCGCACCTGGAGTT	0.607																																					p.R111R		Atlas-SNP	.											.	CNGA4	96	.	0			c.C333T						.						133	125	128					11																	6261357		2201	4296	6497	SO:0001819	synonymous_variant	1262	exon4			CGTTCGCACCTGG	AK122736	CCDS31408.1	11p15.4	2011-07-05		2002-01-18		ENSG00000132259		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2152	protein-coding gene	gene with protein product		609472	"cyclic nucleotide gated channel beta 2"	CNCA2, CNGB2		11764791, 16382102	Standard	NM_001037329		Approved	OCNC2, OCNCb, CNG5	uc001mco.3	Q8IV77		ENST00000379936.2:c.333C>T	chr11.hg19:g.6261357C>T		75.0	0.0		75.0	23.0	NM_001037329		Silent	SNP	ENST00000379936.2	hg19	CCDS31408.1																																																																																			.	.		0.607	CNGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383765.2	NM_001037329		T	6261357	C	T	6261357	2	4	317	1	0	0	0	0	0	0	0	1	3601	697	25	3		3	CNGA4	11	6261357	Silent	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	1470892	6261357	128745159	126	44768										
CCKBR	887	hgsc.bcm.edu	37	chr11	6292577	6292577	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	cttgctgagctacgcctcggCctgtgtcaaccccctggtct	10	16	2	1	rs201876764		TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr11:6292577C>T	ENST00000334619.2	+	5	1341	c.1148C>T	c.(1147-1149)gCc>gTc	p.A383V	CCKBR_ENST00000525462.1_Missense_Mutation_p.A452V|CCKBR_ENST00000532715.1_Missense_Mutation_p.A299V	NM_176875.3	NP_795344.1	P32239	GASR_HUMAN	cholecystokinin B receptor	383					cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cholecystokinin signaling pathway (GO:0038188)|digestion (GO:0007586)|digestive tract development (GO:0048565)|feeding behavior (GO:0007631)|gastric acid secretion (GO:0001696)|gland development (GO:0048732)|metabolic process (GO:0008152)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|sensory perception (GO:0007600)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|cholecystokinin receptor activity (GO:0004951)|gastrin receptor activity (GO:0015054)|phosphatidylinositol phospholipase C activity (GO:0004435)|type B gastrin/cholecystokinin receptor binding (GO:0031741)			NS(2)|breast(2)|endometrium(4)|kidney(13)|large_intestine(10)|lung(22)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.139)	Pentagastrin(DB00183)	TACGCCTCGGCCTGTGTCAAC	0.632																																					p.A383V		Atlas-SNP	.											CCKBR_ENST00000525462,neck,malignant_melanoma,0,2	CCKBR	232	.	0			c.C1148T						.						129	108	115					11																	6292577		2201	4296	6497	SO:0001583	missense	887	exon5			CCTCGGCCTGTGT	D13305	CCDS7761.1	11p15.4	2012-08-10			ENSG00000110148	ENSG00000110148		"GPCR / Class A : Cholecystokinin receptors"	1571	protein-coding gene	gene with protein product		118445				1280419	Standard	NM_176875		Approved		uc001mcp.3	P32239	OTTHUMG00000133380	ENST00000334619.2:c.1148C>T	chr11.hg19:g.6292577C>T	ENSP00000335544:p.Ala383Val	94.0	0.0		97.0	30.0	NM_176875	A8K7P9|O75824|Q16144|Q92492|Q96LC6|Q9NYK7|Q9UBV1	Missense_Mutation	SNP	ENST00000334619.2	hg19	CCDS7761.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.928070	0.92389	.	.	ENSG00000110148	ENST00000334619;ENST00000532715;ENST00000525462	T;T;T	0.72835	-0.69;-0.69;-0.69	5.24	5.24	0.73138	GPCR, rhodopsin-like superfamily (1);	0.057241	0.64402	D	0.000001	D	0.86104	0.5853	M	0.86502	2.82	0.54753	D	0.999987	D;D	0.76494	0.999;0.998	D;D	0.74674	0.984;0.969	D	0.88527	0.3100	10	0.72032	D	0.01	.	17.3923	0.87435	0.0:1.0:0.0:0.0	.	452;383	P32239-2;P32239	.;GASR_HUMAN	V	383;299;452	ENSP00000335544:A383V;ENSP00000432079:A299V;ENSP00000435534:A452V	ENSP00000335544:A383V	A	+	2	0	CCKBR	6249153	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.770000	0.85390	2.425000	0.82216	0.557000	0.71058	GCC	.	.		0.632	CCKBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257230.2	NM_176875		T	6292577	C	T	6292577	3	4	317	1	0	0	0	0	1	0	0	0	2883	739	26	3	1166	3	CCKBR	11	6292577	Missense_Mutation	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	31220	6292577	128713939	127	44769										
OR5B12	390191	hgsc.bcm.edu	37	chr11	58207528	58207528	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	cccaaccagagtgatgaggtAgatgaaaaggaagactatga	12	6	0	7			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr11:58207528A>T	ENST00000302572.2	-	1	118	c.97T>A	c.(97-99)Tac>Aac	p.Y33N		NM_001004733.2	NP_001004733.1	Q96R08	OR5BC_HUMAN	olfactory receptor, family 5, subfamily B, member 12	33						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(6)|liver(1)|lung(28)|ovary(1)|prostate(3)|skin(1)	40	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				GTGATGAGGTAGATGAAAAGG	0.478																																					p.Y33N		Atlas-SNP	.											.	OR5B12	80	.	0			c.T97A						.						89	101	97					11																	58207528		2201	4295	6496	SO:0001583	missense	390191	exon1			TGAGGTAGATGAA	AB065851	CCDS31551.1	11q12.1	2012-08-09		2004-03-10	ENSG00000172362	ENSG00000172362		"GPCR / Class A : Olfactory receptors"	15432	protein-coding gene	gene with protein product				OR5B12P, OR5B16		12213199	Standard	NM_001004733		Approved	OST743	uc010rkh.2	Q96R08	OTTHUMG00000167543	ENST00000302572.2:c.97T>A	chr11.hg19:g.58207528A>T	ENSP00000306657:p.Tyr33Asn	160.0	0.0		155.0	40.0	NM_001004733	B2RNL2|Q6IEV5	Missense_Mutation	SNP	ENST00000302572.2	hg19	CCDS31551.1	.	.	.	.	.	.	.	.	.	.	A	11.22	1.573065	0.28092	.	.	ENSG00000172362	ENST00000302572	T	0.04654	3.58	4.74	4.74	0.60224	.	0.000000	0.39687	N	0.001298	T	0.36276	0.0961	H	0.98559	4.265	0.09310	N	0.999999	D	0.89917	1.0	D	0.83275	0.996	T	0.54944	-0.8217	10	0.87932	D	0	-6.4909	13.8357	0.63408	1.0:0.0:0.0:0.0	.	33	Q96R08	OR5BC_HUMAN	N	33	ENSP00000306657:Y33N	ENSP00000306657:Y33N	Y	-	1	0	OR5B12	57964104	1.000000	0.71417	0.336000	0.25522	0.015000	0.08874	5.916000	0.69981	2.118000	0.64928	0.459000	0.35465	TAC	.	.		0.478	OR5B12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394987.1	NM_001004733		T	58207528	A	T	58207528	3	4	317	1	0	0	0	0	1	0	0	0	11157	420	15	4	851	4	OR5B12	11	58207528	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	51914951	58207528	76798988	128	44770										
ZFP91	80829	hgsc.bcm.edu	37	chr11	58347078	58347078	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ccgtctccagttcagggcaaGaagagtccgcgactcctgtg	12	13	2	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr11:58347078G>A	ENST00000316059.6	+	1	495	c.324G>A	c.(322-324)aaG>aaA	p.K108K	LPXN_ENST00000528489.1_5'Flank|LPXN_ENST00000528954.1_5'Flank|ZFP91-CNTF_ENST00000389919.4_Silent_p.K108K	NM_001197051.1|NM_053023.4	NP_001183980.1|NP_444251.1	Q96JP5	ZFP91_HUMAN	ZFP91 zinc finger protein	108					activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein K63-linked ubiquitination (GO:0070534)	nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(4)|kidney(4)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	26		Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24)				TTCAGGGCAAGAAGAGTCCGC	0.677											OREG0020976	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K108K		Atlas-SNP	.											.	ZFP91	66	.	0			c.G324A						.						15	16	16					11																	58347078		1771	3606	5377	SO:0001819	synonymous_variant	80829	exon1			GGGCAAGAAGAGT	AB056107	CCDS31553.1	11q12	2012-11-27	2012-11-27		ENSG00000186660	ENSG00000186660		"Zinc fingers, C2H2-type"	14983	protein-coding gene	gene with protein product			"zinc finger protein homologous to Zfp91 in mouse", "zinc finger protein 91 homolog (mouse)"			12738986, 20682767	Standard	NM_053023		Approved	PZF, ZNF757	uc001nmx.4	Q96JP5	OTTHUMG00000137391	ENST00000316059.6:c.324G>A	chr11.hg19:g.58347078G>A		41.0	0.0	1030	47.0	12.0	NM_001197051	A6NHC4|A8MSG7|Q86V47|Q96JP4|Q96QA3	Silent	SNP	ENST00000316059.6	hg19	CCDS31553.1																																																																																			.	.		0.677	ZFP91-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268674.1	NM_053023		A	58347078	G	A	58347078	2	1	317	1	0	0	0	0	0	0	0	1	17670	933	33	3		3	ZFP91	11	58347078	Silent	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	139550	58347078	76659438	129	44771										
MYO7A	4647	hgsc.bcm.edu	37	chr11	76858873	76858873	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	atctctccgcagaacgcaacGcacatcaagcctatgcaccc	6	17	2	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr11:76858873G>A	ENST00000409709.3	+	4	434	c.162G>A	c.(160-162)acG>acA	p.T54T	MYO7A_ENST00000409893.1_Silent_p.T54T|MYO7A_ENST00000409619.2_Silent_p.T43T|MYO7A_ENST00000458637.2_Silent_p.T54T	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	54					actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						AGAACGCAACGCACATCAAGC	0.652																																					p.T54T		Atlas-SNP	.											.	MYO7A	164	.	0			c.G162A						.						36	40	39					11																	76858873		2133	4237	6370	SO:0001819	synonymous_variant	4647	exon4			CGCAACGCACATC	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"A-kinase anchor proteins", "Myosins / Myosin superfamily : Class VII"	7606	protein-coding gene	gene with protein product		276903	"myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.162G>A	chr11.hg19:g.76858873G>A		91.0	0.0		82.0	48.0	NM_001127179	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Silent	SNP	ENST00000409709.3	hg19	CCDS53683.1																																																																																			.	.		0.652	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260		A	76858873	G	A	76858873	2	1	317	1	0	0	0	0	0	0	0	1	10091	1074	38	1		1	MYO7A	11	76858873	Silent	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	18511795	76858873	58147643	130	44772										
NOX4	50507	hgsc.bcm.edu	37	chr11	89182674	89182674	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gcttttatccaacaatctccTggttctcctgcttggaacct	6	13	2	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr11:89182674T>A	ENST00000263317.4	-	4	521	c.283A>T	c.(283-285)Agg>Tgg	p.R95W	NOX4_ENST00000343727.5_Missense_Mutation_p.R71W|NOX4_ENST00000375979.3_Intron|NOX4_ENST00000542487.1_Missense_Mutation_p.R71W|NOX4_ENST00000534731.1_Missense_Mutation_p.R95W|NOX4_ENST00000413594.2_Missense_Mutation_p.R116W|NOX4_ENST00000532825.1_Missense_Mutation_p.R71W|NOX4_ENST00000528341.1_Missense_Mutation_p.R70W|NOX4_ENST00000531342.1_Intron|NOX4_ENST00000527626.1_Intron|NOX4_ENST00000527956.1_Missense_Mutation_p.R71W|NOX4_ENST00000424319.1_Missense_Mutation_p.R71W|NOX4_ENST00000525196.1_Missense_Mutation_p.R95W|NOX4_ENST00000535633.1_Missense_Mutation_p.R71W			Q9NPH5	NOX4_HUMAN	NADPH oxidase 4	95	Ferric oxidoreductase.				bone resorption (GO:0045453)|cardiac muscle cell differentiation (GO:0055007)|cell aging (GO:0007569)|cell morphogenesis (GO:0000902)|cellular response to cAMP (GO:0071320)|cellular response to gamma radiation (GO:0071480)|cellular response to glucose stimulus (GO:0071333)|cellular response to transforming growth factor beta stimulus (GO:0071560)|homocysteine metabolic process (GO:0050667)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|oxidation-reduction process (GO:0055114)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of stress fiber assembly (GO:0051496)|reactive oxygen species metabolic process (GO:0072593)|response to hypoxia (GO:0001666)|superoxide anion generation (GO:0042554)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|modified amino acid binding (GO:0072341)|NAD(P)H oxidase activity (GO:0016174)|nucleotide binding (GO:0000166)|oxygen sensor activity (GO:0019826)|superoxide-generating NADPH oxidase activity (GO:0016175)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(20)|ovary(2)|prostate(3)|skin(2)	44		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)				AACAATCTCCTGGTTCTCCTG	0.308																																					p.R95W		Atlas-SNP	.											.	NOX4	101	.	0			c.A283T						.						82	78	80					11																	89182674		2201	4295	6496	SO:0001583	missense	50507	exon4			ATCTCCTGGTTCT	AF254621	CCDS8285.1, CCDS44695.1, CCDS44696.1, CCDS73361.1, CCDS73362.1	11q14.2-q21	2008-02-05			ENSG00000086991	ENSG00000086991			7891	protein-coding gene	gene with protein product		605261					Standard	NM_001143837		Approved	KOX-1, KOX	uc001pct.3	Q9NPH5	OTTHUMG00000167298	ENST00000263317.4:c.283A>T	chr11.hg19:g.89182674T>A	ENSP00000263317:p.Arg95Trp	242.0	0.0		318.0	107.0	NM_001143836	A8K715|B7Z520|E7EMD7|Q5K3R4|Q5K3R5|Q5K3R6|Q5K3R8|Q7Z7G3|Q86V92	Missense_Mutation	SNP	ENST00000263317.4	hg19	CCDS8285.1	.	.	.	.	.	.	.	.	.	.	T	19.40	3.819687	0.71028	.	.	ENSG00000086991	ENST00000424319;ENST00000535633;ENST00000343727;ENST00000534731;ENST00000525196;ENST00000263317;ENST00000532825;ENST00000527956;ENST00000542487;ENST00000528341;ENST00000413594	D;D;D;D;D;D;D;D;D;D;D	0.91792	-2.91;-2.91;-2.91;-2.91;-2.91;-2.91;-2.91;-2.91;-2.91;-2.91;-2.91	5.42	4.28	0.50868	Flavoprotein transmembrane component (1);	0.000000	0.64402	D	0.000001	D	0.95329	0.8484	M	0.79343	2.45	0.49389	D	0.999788	D;D;D;D;D	0.89917	0.999;1.0;0.999;1.0;1.0	D;D;D;D;D	0.97110	0.989;1.0;0.996;0.998;0.999	D	0.94496	0.7705	9	.	.	.	-13.7512	11.7003	0.51567	0.0:0.0:0.1483:0.8517	.	71;70;95;95;95	E9PMY6;E9PPP2;E9PI95;Q9NPH5-6;Q9NPH5	.;.;.;.;NOX4_HUMAN	W	71;71;71;95;95;95;71;71;71;70;116	ENSP00000412446:R71W;ENSP00000440172:R71W;ENSP00000344747:R71W;ENSP00000436892:R95W;ENSP00000436716:R95W;ENSP00000263317:R95W;ENSP00000434924:R71W;ENSP00000433797:R71W;ENSP00000439373:R71W;ENSP00000436970:R70W;ENSP00000405705:R116W	.	R	-	1	2	NOX4	88822322	0.999000	0.42202	0.964000	0.40570	0.984000	0.73092	3.255000	0.51484	0.866000	0.35629	0.533000	0.62120	AGG	.	.		0.308	NOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394054.1	NM_016931		A	89182674	T	A	89182674	3	1	317	1	0	0	0	0	1	0	0	0	10567	1579	55	4	1513	4	NOX4	11	89182674	Missense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	12323801	89182674	45823842	131	44773										
SESN3	143686	hgsc.bcm.edu	37	chr11	94906456	94906456	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ttatggcacgaagagcataaAgaagttcagcttgcattcgt	10	7	1	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr11:94906456A>G	ENST00000536441.1	-	10	1778	c.1442T>C	c.(1441-1443)cTt>cCt	p.L481P	RP11-712B9.2_ENST00000534864.1_RNA|SESN3_ENST00000278499.2_Missense_Mutation_p.L342P|RP11-712B9.2_ENST00000534891.1_RNA	NM_001271594.1|NM_144665.2	NP_001258523.1|NP_653266.2	P58005	SESN3_HUMAN	sestrin 3	481					glucose homeostasis (GO:0042593)|regulation of protein kinase B signaling (GO:0051896)|regulation of response to reactive oxygen species (GO:1901031)|response to insulin (GO:0032868)	nucleus (GO:0005634)				endometrium(5)|large_intestine(6)|lung(3)|skin(1)|stomach(1)	16		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)		BRCA - Breast invasive adenocarcinoma(274;0.234)		AAGAGCATAAAGAAGTTCAGC	0.358																																					p.L481P		Atlas-SNP	.											.	SESN3	51	.	0			c.T1442C						.						110	95	100					11																	94906456		2201	4298	6499	SO:0001583	missense	143686	exon10			GCATAAAGAAGTT	AK096300	CCDS8303.1, CCDS60938.1	11q21	2005-09-18			ENSG00000149212	ENSG00000149212			23060	protein-coding gene	gene with protein product		607768				12607115	Standard	NM_144665		Approved	SEST3, MGC29667	uc001pfj.4	P58005	OTTHUMG00000167829	ENST00000536441.1:c.1442T>C	chr11.hg19:g.94906456A>G	ENSP00000441927:p.Leu481Pro	132.0	0.0		151.0	37.0	NM_144665	B7Z7P9|Q96AD1	Missense_Mutation	SNP	ENST00000536441.1	hg19	CCDS8303.1	.	.	.	.	.	.	.	.	.	.	A	12.60	1.986420	0.35036	.	.	ENSG00000149212	ENST00000536441;ENST00000278499	T;T	0.37915	1.17;1.17	5.37	5.37	0.77165	.	0.000000	0.64402	D	0.000003	T	0.66538	0.2799	M	0.89095	3.005	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.998;0.999	T	0.74352	-0.3693	10	0.87932	D	0	0.3648	15.3779	0.74625	1.0:0.0:0.0:0.0	.	342;481	B7Z7P9;P58005	.;SESN3_HUMAN	P	481;342	ENSP00000441927:L481P;ENSP00000278499:L342P	ENSP00000278499:L342P	L	-	2	0	SESN3	94546104	1.000000	0.71417	0.589000	0.28718	0.152000	0.21847	8.771000	0.91751	2.045000	0.60652	0.454000	0.30748	CTT	.	.		0.358	SESN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396475.3	NM_144665		G	94906456	A	G	94906456	3	3	317	1	0	0	0	0	1	0	0	0	14141	72	3	2	40	2	SESN3	11	94906456	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	5723782	94906456	40100060	132	44774										
PGR	5241	hgsc.bcm.edu	37	chr11	100999049	100999049	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ggcgggacagccgcggctccTcctccagccgccgcgccacc	13	21	0	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr11:100999049T>C	ENST00000325455.5	-	1	2206	c.753A>G	c.(751-753)ggA>ggG	p.G251G	PGR_ENST00000263463.5_Silent_p.G251G|PGR_ENST00000534013.1_Intron	NM_000926.4|NM_001202474.1|NM_001271162.1	NP_000917.3|NP_001189403.1|NP_001258091.1	P06401	PRGR_HUMAN	progesterone receptor	251	Modulating, Pro-Rich.				cell-cell signaling (GO:0007267)|epithelial cell maturation (GO:0002070)|gene expression (GO:0010467)|negative regulation of gene expression (GO:0010629)|ovulation from ovarian follicle (GO:0001542)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone receptor signaling pathway (GO:0050847)|regulation of epithelial cell proliferation (GO:0050678)|signal transduction (GO:0007165)|tertiary branching involved in mammary gland duct morphogenesis (GO:0060748)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mitochondrial outer membrane (GO:0005741)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|liver(1)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	36		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Allylestrenol(DB01431)|Danazol(DB01406)|Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluticasone Propionate(DB00588)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Megestrol acetate(DB00351)|Mifepristone(DB00834)|Norelgestromin(DB06713)|Norethindrone(DB00717)|Norgestimate(DB00957)|Progesterone(DB00396)|Spironolactone(DB00421)	CCGCGGCTCCTCCTCCAGCCG	0.711																																					p.G251G	Pancreas(124;2271 2354 21954 22882)	Atlas-SNP	.											.	PGR	115	.	0			c.A753G						.						4	6	6					11																	100999049		1965	4022	5987	SO:0001819	synonymous_variant	5241	exon1			GGCTCCTCCTCCA	M15716	CCDS8310.1, CCDS59229.1	11q22-q23	2013-01-16			ENSG00000082175	ENSG00000082175		"Nuclear hormone receptors"	8910	protein-coding gene	gene with protein product		607311					Standard	NM_000926		Approved	PR, NR3C3	uc001pgh.2	P06401	OTTHUMG00000167531	ENST00000325455.5:c.753A>G	chr11.hg19:g.100999049T>C		41.0	0.0		31.0	7.0	NM_000926	A7LQ08|A7X8B0|B4E3T0|Q8TDS3|Q9UPF7	Silent	SNP	ENST00000325455.5	hg19	CCDS8310.1																																																																																			.	.		0.711	PGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394934.1			C	100999049	T	C	100999049	2	2	317	1	0	0	0	0	0	0	0	1	11814	1538	54	2		2	PGR	11	100999049	Silent	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	6092593	100999049	34007467	133	44775										
PVRL1	5818	hgsc.bcm.edu	37	chr11	119508959	119508959	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ctgggtccaggtggacaaccTggaagagaaggcggtgagtg	18	7	0	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr11:119508959T>A	ENST00000341398.2	-	8	1227		c.e8-2		RP11-196E1.3_ENST00000532153.1_RNA|RP11-196E1.3_ENST00000601999.1_RNA	NM_203285.1	NP_976030.1	Q15223	PVRL1_HUMAN	poliovirus receptor-related 1 (herpesvirus entry mediator C)						adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|desmosome organization (GO:0002934)|enamel mineralization (GO:0070166)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|immune response (GO:0006955)|iron ion transport (GO:0006826)|lens morphogenesis in camera-type eye (GO:0002089)|regulation of synapse assembly (GO:0051963)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|viral entry into host cell (GO:0046718)	adherens junction (GO:0005912)|axon (GO:0030424)|cell-cell adherens junction (GO:0005913)|extracellular region (GO:0005576)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|coreceptor activity (GO:0015026)|protein homodimerization activity (GO:0042803)|virion binding (GO:0046790)|virus receptor activity (GO:0001618)			breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Breast(348;0.037)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.29e-05)		GTGGACAACCTGGAAGAGAAG	0.612																																					.		Atlas-SNP	.											.	PVRL1	133	.	0			c.1228-2A>T						.						45	42	43					11																	119508959		2199	4295	6494	SO:0001630	splice_region_variant	5818	exon9			ACAACCTGGAAGA	X76400	CCDS8425.1, CCDS8426.1, CCDS8427.1	11q23-q24	2013-01-29	2007-06-07		ENSG00000110400	ENSG00000110400		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9706	protein-coding gene	gene with protein product	"nectin"	600644		HVEC, ED4		7721102, 9616127	Standard	NM_203285		Approved	PRR, PRR1, PVRR1, SK-12, HIgR, CLPED1, CD111, OFC7	uc001pwv.3	Q15223	OTTHUMG00000166177	ENST00000341398.2:c.1228-2A>T	chr11.hg19:g.119508959T>A		35.0	0.0		50.0	9.0	NM_203285	O75465|Q2M3D3|Q9HBE6|Q9HBW2	Splice_Site	SNP	ENST00000341398.2	hg19	CCDS8425.1	.	.	.	.	.	.	.	.	.	.	T	6.210	0.406970	0.11754	.	.	ENSG00000110400	ENST00000341398	.	.	.	3.7	3.7	0.42460	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.9846	0.47514	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	PVRL1	119014169	0.996000	0.38824	0.525000	0.27900	0.072000	0.16883	4.511000	0.60462	1.901000	0.55032	0.482000	0.46254	.	.	.		0.612	PVRL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388230.1		Intron	A	119508959	T	A	119508959	5	1	317	1	0	0	0	0	0	0	1	0	12854	1594	55	4	154	4	PVRL1	11	119508959	Splice_Site	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	18509910	119508959	15497557	134	44776										
OR6M1	390261	hgsc.bcm.edu	37	chr11	123676307	123676307	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	cacatacacaaagatgttgcTcccgtgggcaatggagacaa	10	10	0	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr11:123676307T>A	ENST00000309154.2	-	1	788	c.751A>T	c.(751-753)Agc>Tgc	p.S251C		NM_001005325.1	NP_001005325.1	Q8NGM8	OR6M1_HUMAN	olfactory receptor, family 6, subfamily M, member 1	251						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|prostate(2)|skin(5)|urinary_tract(1)	29		Breast(109;0.0109)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.028)		AAGATGTTGCTCCCGTGGGCA	0.517																																					p.S251C		Atlas-SNP	.											.	OR6M1	60	.	0			c.A751T						.						102	89	93					11																	123676307		2202	4299	6501	SO:0001583	missense	390261	exon1			TGTTGCTCCCGTG	AB065762	CCDS31696.1	11q24.1	2012-08-09			ENSG00000196099	ENSG00000196099		"GPCR / Class A : Olfactory receptors"	14711	protein-coding gene	gene with protein product							Standard	NM_001005325		Approved		uc010rzz.2	Q8NGM8	OTTHUMG00000166012	ENST00000309154.2:c.751A>T	chr11.hg19:g.123676307T>A	ENSP00000311038:p.Ser251Cys	84.0	0.0		103.0	34.0	NM_001005325	B2RNK0|Q6IEW9|Q96R37	Missense_Mutation	SNP	ENST00000309154.2	hg19	CCDS31696.1	.	.	.	.	.	.	.	.	.	.	T	12.67	2.007547	0.35415	.	.	ENSG00000196099	ENST00000309154	T	0.00183	8.6	3.48	3.48	0.39840	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39615	U	0.001316	T	0.00300	0.0009	L	0.54863	1.705	0.09310	N	1	P	0.45126	0.851	P	0.52823	0.71	T	0.45308	-0.9270	10	0.87932	D	0	.	9.9694	0.41745	0.0:0.0:0.0:1.0	.	251	Q8NGM8	OR6M1_HUMAN	C	251	ENSP00000311038:S251C	ENSP00000311038:S251C	S	-	1	0	OR6M1	123181517	0.000000	0.05858	0.842000	0.33263	0.522000	0.34438	-0.608000	0.05641	1.432000	0.47375	0.533000	0.62120	AGC	.	.		0.517	OR6M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387437.1	NM_001005325		A	123676307	T	A	123676307	3	1	317	1	0	0	0	0	1	0	0	0	11214	1551	54	4	193	4	OR6M1	11	123676307	Missense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	4167348	123676307	11330209	135	44777										
ACAD8	27034	hgsc.bcm.edu	37	chr11	134131002	134131002	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ctgtgctgtccctgtggccaAcagaattgggagcgaggggc	16	10	0	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr11:134131002A>G	ENST00000281182.4	+	7	876	c.770A>G	c.(769-771)aAc>aGc	p.N257S	ACAD8_ENST00000537423.1_Missense_Mutation_p.N180S|ACAD8_ENST00000374752.4_Missense_Mutation_p.N130S|ACAD8_ENST00000524547.1_3'UTR|ACAD8_ENST00000543332.1_Missense_Mutation_p.N159S	NM_014384.2	NP_055199.1	Q9UKU7	ACAD8_HUMAN	acyl-CoA dehydrogenase family, member 8	257					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|lipid metabolic process (GO:0006629)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|valine catabolic process (GO:0006574)	mitochondrial matrix (GO:0005759)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)			endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	14	all_hematologic(175;0.127)	all_cancers(12;8e-23)|all_epithelial(12;2.59e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|all_neural(223;0.0189)|Medulloblastoma(222;0.0245)|Esophageal squamous(93;0.0559)		Epithelial(10;1.92e-10)|all cancers(11;2.26e-09)|BRCA - Breast invasive adenocarcinoma(10;8.73e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00154)|Lung(977;0.21)	Flavin adenine dinucleotide(DB03147)	CCTGTGGCCAACAGAATTGGG	0.577																																					p.N257S	GBM(65;238 1125 33403 41853 48889)	Atlas-SNP	.											.	ACAD8	33	.	0			c.A770G						.						64	59	60					11																	134131002		2201	4296	6497	SO:0001583	missense	27034	exon7			TGGCCAACAGAAT	AF126245	CCDS8498.1	11q25	2014-09-17	2010-04-30		ENSG00000151498	ENSG00000151498			87	protein-coding gene	gene with protein product		604773	"acyl-Coenzyme A dehydrogenase family, member 8"			10524212	Standard	NM_014384		Approved		uc001qhk.3	Q9UKU7	OTTHUMG00000167177	ENST00000281182.4:c.770A>G	chr11.hg19:g.134131002A>G	ENSP00000281182:p.Asn257Ser	112.0	0.0		119.0	29.0	NM_014384	B7Z5W4|Q6ZWP6|Q9BUS8	Missense_Mutation	SNP	ENST00000281182.4	hg19	CCDS8498.1	.	.	.	.	.	.	.	.	.	.	A	19.82	3.898592	0.72639	.	.	ENSG00000151498	ENST00000281182;ENST00000537423;ENST00000543332;ENST00000374752;ENST00000537915	D;D;D;D	0.99214	-5.57;-5.57;-5.57;-5.57	5.44	5.44	0.79542	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase/oxidase C-terminal (1);	0.040366	0.85682	D	0.000000	D	0.98868	0.9617	M	0.88704	2.975	0.80722	D	1	P;P;P	0.45902	0.509;0.782;0.868	B;B;B	0.42188	0.12;0.379;0.196	D	0.99616	1.0982	10	0.87932	D	0	.	15.4831	0.75542	1.0:0.0:0.0:0.0	.	180;130;257	B7Z5W4;Q6ZWP6;Q9UKU7	.;.;ACAD8_HUMAN	S	257;180;159;130;219	ENSP00000281182:N257S;ENSP00000443763:N180S;ENSP00000438302:N159S;ENSP00000363884:N130S	ENSP00000281182:N257S	N	+	2	0	ACAD8	133636212	1.000000	0.71417	1.000000	0.80357	0.832000	0.47134	7.448000	0.80631	2.069000	0.61940	0.459000	0.35465	AAC	.	.		0.577	ACAD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393607.1	NM_014384		G	134131002	A	G	134131002	3	3	317	1	0	0	0	0	1	0	0	0	110	43	2	2	796	2	ACAD8	11	134131002	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	10454695	134131002	875514	136	44778										
ERC1	23085	hgsc.bcm.edu	37	chr12	1192437	1192437	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	aggactggcgaaccttgtgtAgcagagctgacagaggagaa	15	7	0	4			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr12:1192437A>C	ENST00000397203.2	+	3	1183	c.777A>C	c.(775-777)gtA>gtC	p.V259V	ERC1_ENST00000360905.4_Silent_p.V259V|ERC1_ENST00000589028.1_Silent_p.V259V|ERC1_ENST00000546231.2_Silent_p.V259V|ERC1_ENST00000355446.5_Silent_p.V259V|ERC1_ENST00000543086.3_Silent_p.V259V			Q8IUD2	RB6I2_HUMAN	ELKS/RAB6-interacting/CAST family member 1	259					I-kappaB phosphorylation (GO:0007252)|multicellular organismal development (GO:0007275)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|IkappaB kinase complex (GO:0008385)|presynaptic membrane (GO:0042734)	leucine zipper domain binding (GO:0043522)			NS(1)|breast(2)|cervix(2)|endometrium(2)|large_intestine(8)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	38	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)			AACCTTGTGTAGCAGAGCTGA	0.512																																					p.V259V		Atlas-SNP	.											.	ERC1	95	.	0			c.A777C						.						89	81	84					12																	1192437		2203	4300	6503	SO:0001819	synonymous_variant	23085	exon3			TTGTGTAGCAGAG	AB015617	CCDS8508.1, CCDS53732.1	12p13.3	2008-02-05	2006-08-14	2006-08-14	ENSG00000082805	ENSG00000082805			17072	protein-coding gene	gene with protein product		607127	"RAB6 interacting protein 2"	RAB6IP2		10697956, 11929610	Standard	NM_178040		Approved	ELKS, KIAA1081, CAST2, MGC12974	uc001qjb.2	Q8IUD2	OTTHUMG00000130138	ENST00000397203.2:c.777A>C	chr12.hg19:g.1192437A>C		98.0	0.0		70.0	15.0	NM_178039	A2RU77|A7E295|D3DUP7|D3DUP8|Q6NVK2|Q8IUD3|Q8IUD4|Q8IUD5|Q8NAS1|Q9NXN5|Q9UIK7|Q9UPS1	Silent	SNP	ENST00000397203.2	hg19	CCDS8508.1																																																																																			.	.		0.512	ERC1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398380.2	NM_015064		C	1192437	A	C	1192437	2	2	317	1	0	0	0	0	0	0	0	1	5212	407	15	5		5	ERC1	12	1192437	Silent	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10		1192437	132659458	137	44779										
CACNA2D4	93589	hgsc.bcm.edu	37	chr12	1994036	1994036	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ttgcagaggcttccttgcttGgcctcttggaactgtgtagg	13	9	1	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr12:1994036G>T	ENST00000382722.5	-	11	1532	c.1170C>A	c.(1168-1170)gcC>gcA	p.A390A	CACNA2D4_ENST00000585732.1_Silent_p.A306A|CACNA2D4_ENST00000585708.1_Silent_p.A326A|CACNA2D4_ENST00000586184.1_Silent_p.A390A|CACNA2D4_ENST00000587995.1_Silent_p.A390A|CACNA2D4_ENST00000588077.1_Silent_p.A326A	NM_172364.4	NP_758952.4	Q7Z3S7	CA2D4_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 4	390	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				calcium ion transmembrane transport (GO:0070588)|detection of light stimulus involved in visual perception (GO:0050908)	voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			endometrium(3)|kidney(2)|large_intestine(1)|liver(1)|lung(27)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	39	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		TTCCTTGCTTGGCCTCTTGGA	0.617																																					p.A390A	Colon(2;101 179 21030 23310 28141)	Atlas-SNP	.											.	CACNA2D4	220	.	0			c.C1170A						.						43	49	47					12																	1994036		2079	4213	6292	SO:0001819	synonymous_variant	93589	exon11			TTGCTTGGCCTCT	AF516695	CCDS44785.1	12p13.33	2003-03-05			ENSG00000151062	ENSG00000151062		"Calcium channel subunits"	20202	protein-coding gene	gene with protein product		608171				12181424	Standard	NM_172364		Approved		uc021qsx.1	Q7Z3S7	OTTHUMG00000168111	ENST00000382722.5:c.1170C>A	chr12.hg19:g.1994036G>T		96.0	0.0		73.0	4.0	NM_172364	Q7Z3S8|Q86XZ5|Q8IZS9	Silent	SNP	ENST00000382722.5	hg19	CCDS44785.1																																																																																			.	.		0.617	CACNA2D4-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398230.2			T	1994036	G	T	1994036	2	4	317	1	0	0	0	0	0	0	0	1	2553	1335	47	3		3	CACNA2D4	12	1994036	Silent	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	801599	1994036	131857859	138	44780										
FKBP4	2288	hgsc.bcm.edu	37	chr12	2904411	2904411	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	aggacgaaggcgtgctgaagGtgaggggcggcggggcctgc	22	8	0	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr12:2904411G>A	ENST00000001008.4	+	1	292		c.e1+1		RP4-816N1.6_ENST00000547834.1_RNA|CBX3P4_ENST00000540428.1_RNA|RP4-816N1.7_ENST00000547042.1_RNA	NM_002014.3	NP_002005.1	Q02790	FKBP4_HUMAN	FK506 binding protein 4, 59kDa						androgen receptor signaling pathway (GO:0030521)|chaperone-mediated protein folding (GO:0061077)|copper ion transport (GO:0006825)|embryo implantation (GO:0007566)|male sex differentiation (GO:0046661)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)|negative regulation of neuron projection development (GO:0010977)|prostate gland development (GO:0030850)|protein complex localization (GO:0031503)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)|steroid hormone receptor complex assembly (GO:0006463)	axonal growth cone (GO:0044295)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|FK506 binding (GO:0005528)|GTP binding (GO:0005525)|heat shock protein binding (GO:0031072)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(1)	14			OV - Ovarian serous cystadenocarcinoma(31;0.00105)			CGTGCTGAAGGTGAGGGGCGG	0.771																																					.		Atlas-SNP	.											.	FKBP4	29	.	0			c.105+1G>A						.						16	17	16					12																	2904411		2186	4288	6474	SO:0001630	splice_region_variant	2288	exon1			CTGAAGGTGAGGG	M88279	CCDS8512.1	12p13.33	2013-01-10	2002-08-29		ENSG00000004478	ENSG00000004478		"Tetratricopeptide (TTC) repeat domain containing"	3720	protein-coding gene	gene with protein product		600611	"FK506-binding protein 4 (59kD)"			1279700	Standard	NM_002014		Approved	FKBP59, FKBP52	uc001qkz.3	Q02790	OTTHUMG00000090429	ENST00000001008.4:c.105+1G>A	chr12.hg19:g.2904411G>A		185.0	0.0		135.0	53.0	NM_002014	D3DUQ1|Q9UCP1|Q9UCV7	Splice_Site	SNP	ENST00000001008.4	hg19	CCDS8512.1	.	.	.	.	.	.	.	.	.	.	g	15.42	2.827631	0.50845	.	.	ENSG00000004478	ENST00000001008	.	.	.	4.28	3.35	0.38373	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.8563	0.52439	0.0:0.0:0.8233:0.1766	.	.	.	.	.	-1	.	.	.	+	.	.	FKBP4	2774672	1.000000	0.71417	0.398000	0.26321	0.452000	0.32318	7.851000	0.86920	0.744000	0.32741	0.298000	0.19748	.	.	.		0.771	FKBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206861.1		Intron	A	2904411	G	A	2904411	5	1	317	1	0	0	0	0	0	0	1	0	5918	1275	44	3	108	3	FKBP4	12	2904411	Splice_Site	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	910375	2904411	130947484	139	44781										
OR8S1	341568	hgsc.bcm.edu	37	chr12	48919696	48919696	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	cagaggaaaaccatttcagtAgagggctgcctggctcaggt	13	9	2	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr12:48919696A>G	ENST00000310194.1	+	1	282	c.282A>G	c.(280-282)gtA>gtG	p.V94V	OR8S1_ENST00000551654.1_Intron	NM_001005203.2	NP_001005203.2	Q8NH09	OR8S1_HUMAN	olfactory receptor, family 8, subfamily S, member 1	94						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|skin(4)	22						CCATTTCAGTAGAGGGCTGCC	0.522																																					p.V94V		Atlas-SNP	.											.	OR8S1	47	.	0			c.A282G						.						103	99	100					12																	48919696		2203	4300	6503	SO:0001819	synonymous_variant	341568	exon1			TTCAGTAGAGGGC		CCDS31789.1	12q13.2	2012-08-09				ENSG00000197376		"GPCR / Class A : Olfactory receptors"	19628	protein-coding gene	gene with protein product							Standard	NM_001005203		Approved		uc010slu.2	Q8NH09		ENST00000310194.1:c.282A>G	chr12.hg19:g.48919696A>G		98.0	0.0		69.0	29.0	NM_001005203		Silent	SNP	ENST00000310194.1	hg19	CCDS31789.1																																																																																			.	.		0.522	OR8S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406881.1			G	48919696	A	G	48919696	2	3	317	1	0	0	0	0	0	0	0	1	11255	407	15	2		2	OR8S1	12	48919696	Silent	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	46015285	48919696	84932199	140	44782										
KRT80	144501	hgsc.bcm.edu	37	chr12	52579367	52579367	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ggttgcgctgttccagggctTgcacctgggagagcaggaag	17	9	0	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr12:52579367T>A	ENST00000394815.2	-	2	402	c.305A>T	c.(304-306)cAa>cTa	p.Q102L	KRT80_ENST00000313234.5_Missense_Mutation_p.Q102L	NM_182507.2	NP_872313.2	Q6KB66	K2C80_HUMAN	keratin 80	102	Coil 1A.|Rod.					cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(2)|large_intestine(2)|lung(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.108)		TTCCAGGGCTTGCACCTGGGA	0.647																																					p.Q102L	GBM(178;2309 2916 15678 35873)	Atlas-SNP	.											.	KRT80	68	.	0			c.A305T						.						30	27	28					12																	52579367		2203	4300	6503	SO:0001583	missense	144501	exon2			AGGGCTTGCACCT	BX537567	CCDS8821.2, CCDS41784.1	12q13.13	2013-01-16			ENSG00000167767	ENSG00000167767		"-", "Intermediate filaments type II, keratins (basic)"	27056	protein-coding gene	gene with protein product		611161				16831889	Standard	NM_001081492		Approved	KB20	uc001rzx.3	Q6KB66	OTTHUMG00000150193	ENST00000394815.2:c.305A>T	chr12.hg19:g.52579367T>A	ENSP00000378292:p.Gln102Leu	16.0	0.0		14.0	6.0	NM_182507	Q6P1A5|Q7Z3Q0	Missense_Mutation	SNP	ENST00000394815.2	hg19	CCDS8821.2	.	.	.	.	.	.	.	.	.	.	T	17.35	3.367443	0.61513	.	.	ENSG00000167767	ENST00000313234;ENST00000394815	D;D	0.89123	-2.47;-2.47	5.08	1.48	0.22813	Filament (1);	0.000000	0.37955	N	0.001873	D	0.82857	0.5128	L	0.41492	1.28	0.34890	D	0.74539	P;P;P	0.46142	0.763;0.801;0.873	B;B;B	0.42361	0.229;0.339;0.385	T	0.82973	-0.0191	10	0.87932	D	0	.	8.0208	0.30408	0.0:0.4262:0.0:0.5738	.	102;102;39	Q6KB66-2;Q6KB66;Q6KB66-3	.;K2C80_HUMAN;.	L	102	ENSP00000369361:Q102L;ENSP00000378292:Q102L	ENSP00000369361:Q102L	Q	-	2	0	KRT80	50865634	0.824000	0.29247	0.332000	0.25469	0.656000	0.38851	1.342000	0.33919	0.097000	0.17492	-0.250000	0.11733	CAA	.	.		0.647	KRT80-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000316757.1	NM_182507		A	52579367	T	A	52579367	3	1	317	1	0	0	0	0	1	0	0	0	8503	1812	63	4	1120	4	KRT80	12	52579367	Missense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	3659671	52579367	81272528	141	44783										
KRT7	3855	hgsc.bcm.edu	37	chr12	52635357	52635357	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ggcatcatcgctgaggtcaaGgcgcagtatgaggagatggc	16	8	2	3			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr12:52635357G>T	ENST00000331817.5	+	5	978	c.795G>T	c.(793-795)aaG>aaT	p.K265N		NM_005556.3	NP_005547.3	P08729	K2C7_HUMAN	keratin 7	265	Coil 2.|Rod.				viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(2)|stomach(1)|urinary_tract(1)	14				BRCA - Breast invasive adenocarcinoma(357;0.105)	Primaquine(DB01087)	CTGAGGTCAAGGCGCAGTATG	0.597																																					p.K265N		Atlas-SNP	.											.	KRT7	48	.	0			c.G795T						.						93	83	86					12																	52635357		2203	4300	6503	SO:0001583	missense	3855	exon5			GGTCAAGGCGCAG		CCDS8822.1	12q13.13	2013-01-16			ENSG00000135480	ENSG00000135480		"-", "Intermediate filaments type II, keratins (basic)"	6445	protein-coding gene	gene with protein product	"keratin, type II cytoskeletal 7", "cytokeratin 7", "sarcolectin", "keratin, 55K type II cytoskeletal"	148059				1713141, 16831889	Standard	XR_245927		Approved	K7, CK7, K2C7, SCL	uc001saa.1	P08729	OTTHUMG00000169580	ENST00000331817.5:c.795G>T	chr12.hg19:g.52635357G>T	ENSP00000329243:p.Lys265Asn	85.0	0.0		57.0	22.0	NM_005556	Q92676|Q9BUD8|Q9Y3R7	Missense_Mutation	SNP	ENST00000331817.5	hg19	CCDS8822.1	.	.	.	.	.	.	.	.	.	.	G	11.84	1.759342	0.31137	.	.	ENSG00000135480	ENST00000331817;ENST00000422319;ENST00000551537	D	0.90133	-2.62	4.88	-3.07	0.05363	Prefoldin (1);Filament (1);	1.949080	0.02980	N	0.145483	D	0.96103	0.8730	H	0.97315	3.98	0.26908	N	0.966952	D;D	0.69078	0.996;0.997	D;D	0.70227	0.967;0.968	T	0.82961	-0.0197	10	0.87932	D	0	.	1.7895	0.03048	0.1863:0.2945:0.3215:0.1976	.	265;265	F8VZY5;P08729	.;K2C7_HUMAN	N	265;241;265	ENSP00000329243:K265N	ENSP00000329243:K265N	K	+	3	2	KRT7	50921624	0.229000	0.23729	0.074000	0.20217	0.095000	0.18619	-0.267000	0.08619	-0.468000	0.06922	-0.182000	0.12963	AAG	.	.		0.597	KRT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404897.1	NM_005556		T	52635357	G	T	52635357	3	4	317	1	0	0	0	0	1	0	0	0	8492	991	35	3	813	3	KRT7	12	52635357	Missense_Mutation	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	55990	52635357	81216538	142	44784										
KIF5A	3798	hgsc.bcm.edu	37	chr12	57963063	57963063	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gctatgttccatatcgtgacAgcaaaatgacaaggattctc	8	9	1	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr12:57963063A>T	ENST00000455537.2	+	10	1118	c.844A>T	c.(844-846)Agc>Tgc	p.S282C	KIF5A_ENST00000286452.5_Missense_Mutation_p.S193C	NM_004984.2	NP_004975.2	Q12840	KIF5A_HUMAN	kinesin family member 5A	282	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.|Microtubule-binding.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein localization (GO:0008104)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(32)|ovary(2)|prostate(2)|skin(2)	62						ATATCGTGACAGCAAAATGAC	0.448																																					p.S282C		Atlas-SNP	.											.	KIF5A	143	.	0			c.A844T						.						66	65	65					12																	57963063		2203	4300	6503	SO:0001583	missense	3798	exon10			CGTGACAGCAAAA	U06698	CCDS8945.1	12q13.13	2011-07-15	2004-02-13			ENSG00000155980		"Kinesins"	6323	protein-coding gene	gene with protein product		602821	"spastic paraplegia 10 (autosomal dominant)"	SPG10		9858832, 10441583, 16489470	Standard	NM_004984		Approved	D12S1889, NKHC, MY050	uc001sor.1	Q12840	OTTHUMG00000170143	ENST00000455537.2:c.844A>T	chr12.hg19:g.57963063A>T	ENSP00000408979:p.Ser282Cys	104.0	0.0		82.0	35.0	NM_004984	A6H8M5|Q4LE26	Missense_Mutation	SNP	ENST00000455537.2	hg19	CCDS8945.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.412656	0.83340	.	.	ENSG00000155980	ENST00000455537;ENST00000286452	D;D	0.86230	-2.09;-2.09	4.23	4.23	0.50019	Kinesin, motor domain (4);	0.000000	0.85682	D	0.000000	D	0.95379	0.8500	H	0.96805	3.885	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96440	0.9326	10	0.87932	D	0	.	12.76	0.57359	1.0:0.0:0.0:0.0	.	193;282	B7Z2M7;Q12840	.;KIF5A_HUMAN	C	282;193	ENSP00000408979:S282C;ENSP00000286452:S193C	ENSP00000286452:S193C	S	+	1	0	KIF5A	56249330	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.799000	0.91895	1.915000	0.55452	0.454000	0.30748	AGC	.	.		0.448	KIF5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407634.1	NM_004984		T	57963063	A	T	57963063	3	4	317	1	0	0	0	0	1	0	0	0	8314	188	7	4	882	4	KIF5A	12	57963063	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	5327706	57963063	75888832	143	44785										
ATP2B1	490	hgsc.bcm.edu	37	chr12	89998055	89998055	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	cacataactgctttaacaatGcttgtaaagttgtcatctgt	6	8	2	0	rs112647159		TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr12:89998055G>A	ENST00000428670.3	-	16	2967	c.2511C>T	c.(2509-2511)agC>agT	p.S837S	ATP2B1_ENST00000348959.3_Silent_p.S837S|ATP2B1_ENST00000393164.2_Silent_p.S580S|ATP2B1_ENST00000261173.2_Silent_p.S837S|ATP2B1_ENST00000359142.3_Silent_p.S837S			P20020	AT2B1_HUMAN	ATPase, Ca++ transporting, plasma membrane 1	837					blood coagulation (GO:0007596)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	45						CTTTAACAATGCTTGTAAAGT	0.348																																					p.S837S		Atlas-SNP	.											.	ATP2B1	191	.	0			c.C2511T						.						116	109	111					12																	89998055		2203	4300	6503	SO:0001819	synonymous_variant	490	exon15			AACAATGCTTGTA	J04027	CCDS9035.1, CCDS41817.1	12q21.33	2010-04-20			ENSG00000070961	ENSG00000070961	3.6.3.8	"ATPases / P-type"	814	protein-coding gene	gene with protein product	"plasma membrane calcium-transporting ATPase 1"	108731				1674727	Standard	NM_001682		Approved	PMCA1	uc001tbh.3	P20020		ENST00000428670.3:c.2511C>T	chr12.hg19:g.89998055G>A		187.0	0.0		135.0	56.0	NM_001001323	Q12992|Q12993|Q13819|Q13820|Q13821|Q16504|Q93082	Silent	SNP	ENST00000428670.3	hg19	CCDS9035.1																																																																																			.	G|0.500;A|0.500		0.348	ATP2B1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406653.1	NM_001682		A	89998055	G	A	89998055	2	1	317	1	0	0	0	0	0	0	0	1	1139	1310	46	3		3	ATP2B1	12	89998055	Silent	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	32034992	89998055	43853840	144	44786										
CRADD	8738	hgsc.bcm.edu	37	chr12	94243784	94243784	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tcccctcgcacatcctcaacAgctccccatcagaccggcag	6	20	2	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr12:94243784A>T	ENST00000542893.2	+	3	655	c.337A>T	c.(337-339)Agc>Tgc	p.S113C	CRADD_ENST00000541813.1_Intron|CRADD_ENST00000332896.3_Missense_Mutation_p.S113C|CRADD_ENST00000548330.1_3'UTR|CRADD_ENST00000548483.1_Intron			P78560	CRADD_HUMAN	CASP2 and RIPK1 domain containing adaptor with death domain	113					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to mechanical stimulus (GO:0071260)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|positive regulation of apoptotic signaling pathway (GO:2001235)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	death domain binding (GO:0070513)|protease binding (GO:0002020)|protein binding, bridging (GO:0030674)			endometrium(1)|large_intestine(5)|lung(1)|ovary(1)	8						CATCCTCAACAGCTCCCCATC	0.567																																					p.S113C		Atlas-SNP	.											.	CRADD	21	.	0			c.A337T						.						60	61	61					12																	94243784		2203	4300	6503	SO:0001583	missense	8738	exon3			CTCAACAGCTCCC	U84388	CCDS9048.1	12q21.33-q23.1	2008-08-04				ENSG00000169372			2340	protein-coding gene	gene with protein product	"RIP-associated ICH1/CED3-homologous protein with death domain"	603454				8985253, 9044836	Standard	NM_003805		Approved	RAIDD	uc001tda.3	P78560		ENST00000542893.2:c.337A>T	chr12.hg19:g.94243784A>T	ENSP00000439068:p.Ser113Cys	92.0	0.0		74.0	31.0	NM_003805	B7Z2Q5	Missense_Mutation	SNP	ENST00000542893.2	hg19	CCDS9048.1	.	.	.	.	.	.	.	.	.	.	A	16.76	3.212499	0.58452	.	.	ENSG00000169372	ENST00000332896;ENST00000542893	D;D	0.93712	-3.27;-3.27	5.86	4.65	0.58169	Death (1);DEATH-like (1);	0.297093	0.44097	D	0.000486	D	0.90665	0.7072	L	0.45581	1.43	0.80722	D	1	D	0.59357	0.985	B	0.43754	0.43	D	0.91248	0.5027	10	0.59425	D	0.04	-29.5476	12.7723	0.57427	0.8634:0.1366:0.0:0.0	.	113	P78560	CRADD_HUMAN	C	113	ENSP00000327647:S113C;ENSP00000439068:S113C	ENSP00000327647:S113C	S	+	1	0	CRADD	92767915	1.000000	0.71417	1.000000	0.80357	0.320000	0.28249	6.140000	0.71738	2.237000	0.73441	0.460000	0.39030	AGC	.	.		0.567	CRADD-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408515.1	NM_003805		T	94243784	A	T	94243784	3	4	317	1	0	0	0	0	1	0	0	0	3847	188	7	4	343	4	CRADD	12	94243784	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	4245729	94243784	39608111	145	44787										
TMCC3	57458	hgsc.bcm.edu	37	chr12	94972248	94972248	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	agctcctgcttcaggttggcTgtctcatgctgatgcaggtc	12	11	2	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr12:94972248T>A	ENST00000261226.4	-	3	1184	c.1053A>T	c.(1051-1053)acA>acT	p.T351T	TMCC3_ENST00000551457.1_Silent_p.T320T	NM_020698.2	NP_065749	Q9ULS5	TMCC3_HUMAN	transmembrane and coiled-coil domain family 3	351						integral component of membrane (GO:0016021)				NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	29						TCAGGTTGGCTGTCTCATGCT	0.562																																					p.T351T		Atlas-SNP	.											.	TMCC3	63	.	0			c.A1053T						.						92	76	82					12																	94972248		2203	4300	6503	SO:0001819	synonymous_variant	57458	exon3			GTTGGCTGTCTCA	AB032971	CCDS31877.1, CCDS73506.1	12q22	2005-01-21	2005-07-13			ENSG00000057704		"Transmembrane and coiled-coil domain containing"	29199	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 3"			10574461	Standard	XM_005269039		Approved	KIAA1145	uc001tdj.2	Q9ULS5	OTTHUMG00000170225	ENST00000261226.4:c.1053A>T	chr12.hg19:g.94972248T>A		88.0	0.0		52.0	31.0	NM_020698	Q8IWB2	Silent	SNP	ENST00000261226.4	hg19	CCDS31877.1																																																																																			.	.		0.562	TMCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408113.1	NM_020698		A	94972248	T	A	94972248	2	1	317	1	0	0	0	0	0	0	0	1	16009	1567	55	4		4	TMCC3	12	94972248	Silent	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	728464	94972248	38879647	146	44788										
C12orf52	84934	hgsc.bcm.edu	37	chr12	113629261	113629261	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gccaccacctacccccagggGtagccactcgccccgcccca	8	23	0	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr12:113629261G>T	ENST00000548278.1	+	4	1141	c.449G>T	c.(448-450)gGt>gTt	p.G150V	C12orf52_ENST00000549621.1_Missense_Mutation_p.G150V|RP11-545P7.4_ENST00000552525.1_RNA|C12orf52_ENST00000552495.1_Missense_Mutation_p.G174V	NM_032848.1	NP_116237.1	Q96K30	RITA1_HUMAN		150	Interaction with RBPJ/RBPSUH.				negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurogenesis (GO:0022008)|Notch signaling pathway (GO:0007219)|nuclear export (GO:0051168)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	tubulin binding (GO:0015631)			large_intestine(2)|lung(1)|prostate(1)|urinary_tract(1)	5						ACCCCCAGGGGTAGCCACTCG	0.682																																					p.G150V		Atlas-SNP	.											.	C12orf52	19	.	0			c.G449T						.																																			SO:0001583	missense	84934	exon4			CCAGGGGTAGCCA																												ENST00000548278.1:c.449G>T	chr12.hg19:g.113629261G>T	ENSP00000449841:p.Gly150Val	59.0	0.0		46.0	16.0	NM_032848	B3KVZ4|C9JIN1|F8VRG5|Q53GM3|Q96K25	Missense_Mutation	SNP	ENST00000548278.1	hg19	CCDS9166.1	.	.	.	.	.	.	.	.	.	.	G	10.97	1.500355	0.26861	.	.	ENSG00000139405	ENST00000549621;ENST00000548278;ENST00000552495;ENST00000436053;ENST00000299731;ENST00000266813	T;T;T	0.33865	1.41;1.41;1.39	4.6	-0.693	0.11298	.	0.482752	0.19095	N	0.122844	T	0.27832	0.0685	M	0.64997	1.995	0.30687	N	0.751767	B;B;B	0.22683	0.041;0.073;0.041	B;B;B	0.26864	0.074;0.074;0.074	T	0.24693	-1.0153	10	0.56958	D	0.05	-7.5702	0.7008	0.00907	0.2938:0.1666:0.3683:0.1713	.	150;174;150	Q96K30-2;F8VRG5;Q96K30	.;.;RITA_HUMAN	V	150;150;174;150;150;147	ENSP00000448289:G150V;ENSP00000449841:G150V;ENSP00000448680:G174V	ENSP00000266813:G147V	G	+	2	0	C12orf52	112113644	0.335000	0.24748	0.232000	0.24009	0.008000	0.06430	0.463000	0.21972	0.178000	0.19917	-0.961000	0.02630	GGT	.	.		0.682	C12orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405239.1			T	113629261	G	T	113629261	3	4	317	1	0	0	0	0	1	0	0	0	1699	1261	44	3	455	3	C12orf52	12	113629261	Missense_Mutation	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	18657013	113629261	20222634	147	44789										
NOS1	4842	hgsc.bcm.edu	37	chr12	117655927	117655927	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gttggtcacttcgtacgttcGcagggtgactccaaaaatat	10	9	1	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr12:117655927G>A	ENST00000338101.4	-	28	4319	c.4315C>T	c.(4315-4317)Cga>Tga	p.R1439*	NOS1_ENST00000317775.6_Nonsense_Mutation_p.R1405*|NOS1_ENST00000344089.3_3'UTR			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		TCGTACGTTCGCAGGGTGACT	0.478																																					p.R1439X	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											.	NOS1	240	.	0			c.C4315T						.						315	308	310					12																	117655927		1959	4156	6115	SO:0001587	stop_gained	4842	exon29			ACGTTCGCAGGGT		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.4315C>T	chr12.hg19:g.117655927G>A	ENSP00000337459:p.Arg1439*	179.0	0.0		144.0	43.0	NM_001204218		Nonsense_Mutation	SNP	ENST00000338101.4	hg19	CCDS55890.1	.	.	.	.	.	.	.	.	.	.	G	47	13.579327	0.99750	.	.	ENSG00000089250	ENST00000397605;ENST00000317775;ENST00000338101	.	.	.	4.57	0.385	0.16249	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.064	8.0152	0.30376	0.0748:0.0:0.3835:0.5417	.	.	.	.	X	1300;1405;1439	.	ENSP00000320758:R1405X	R	-	1	2	NOS1	116140310	1.000000	0.71417	0.449000	0.26957	0.723000	0.41478	4.243000	0.58721	-0.109000	0.12044	0.561000	0.74099	CGA	.	.		0.478	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1			A	117655927	G	A	117655927	4	1	317	1	0	0	0	0	0	1	0	0	10550	1095	38	1	99	1	NOS1	12	117655927	Nonsense_Mutation	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	4026666	117655927	16195968	148	44790										
RNF6	6049	hgsc.bcm.edu	37	chr13	26789149	26789149	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ctttggtttgtattcctcacTgtaacattacttctagcccc	5	12	2	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr13:26789149T>A	ENST00000381588.4	-	5	1622	c.870A>T	c.(868-870)acA>acT	p.T290T	RNF6_ENST00000399762.2_Intron|RNF6_ENST00000381570.3_Silent_p.T290T|RNF6_ENST00000346166.3_Silent_p.T290T|RNF6_ENST00000468480.1_Intron	NM_005977.3	NP_005968.1	Q9Y252	RNF6_HUMAN	ring finger protein (C3H2C3 type) 6	290					negative regulation of axon extension (GO:0030517)|positive regulation of transcription, DNA-templated (GO:0045893)|protein K27-linked ubiquitination (GO:0044314)|protein K48-linked ubiquitination (GO:0070936)|protein K6-linked ubiquitination (GO:0085020)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)	axon (GO:0030424)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|PML body (GO:0016605)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(1)|large_intestine(9)|lung(3)|ovary(2)|prostate(2)|skin(2)	23	Colorectal(5;0.000442)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.00893)|Epithelial(112;0.0481)|OV - Ovarian serous cystadenocarcinoma(117;0.148)|GBM - Glioblastoma multiforme(144;0.23)|Lung(94;0.245)		TATTCCTCACTGTAACATTAC	0.448																																					p.T290T		Atlas-SNP	.											.	RNF6	68	.	0			c.A870T						.						214	206	208					13																	26789149		2203	4300	6503	SO:0001819	synonymous_variant	6049	exon5			CCTCACTGTAACA	AJ010346	CCDS9316.1	13q12.2	2013-01-09			ENSG00000127870	ENSG00000127870		"RING-type (C3HC4) zinc fingers"	10069	protein-coding gene	gene with protein product	"RING-H2 protein RNF-6"	604242				10331950	Standard	NM_005977		Approved	DKFZp686P0776	uc001uqq.3	Q9Y252	OTTHUMG00000016614	ENST00000381588.4:c.870A>T	chr13.hg19:g.26789149T>A		127.0	0.0		105.0	38.0	NM_183043	B4DDP0|Q5W0H0|Q9BZP5|Q9UF41	Silent	SNP	ENST00000381588.4	hg19	CCDS9316.1																																																																																			.	.		0.448	RNF6-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044246.2	NM_005977		A	26789149	T	A	26789149	2	1	317	1	0	0	0	0	0	0	0	1	13513	1567	55	4		4	RNF6	13	26789149	Silent	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10		26789149	88380729	149	44791										
FLT1	2321	hgsc.bcm.edu	37	chr13	29008090	29008090	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ttggacatctatgattgtatTggctgcaagcataagagaga	11	5	1	3			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr13:29008090T>A	ENST00000282397.4	-	6	930	c.679A>T	c.(679-681)Aat>Tat	p.N227Y	FLT1_ENST00000541932.1_Missense_Mutation_p.N227Y|FLT1_ENST00000539099.1_Missense_Mutation_p.N227Y	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	227					blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	ATGATTGTATTGGCTGCAAGC	0.383																																					p.N227Y		Atlas-SNP	.											.	FLT1	393	.	0			c.A679T						.						120	122	121					13																	29008090		2203	4300	6503	SO:0001583	missense	2321	exon6			TTGTATTGGCTGC	AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3763	protein-coding gene	gene with protein product	"vascular endothelial growth factor receptor 1", "vascular permeability factor receptor"	165070	"fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.679A>T	chr13.hg19:g.29008090T>A	ENSP00000282397:p.Asn227Tyr	213.0	0.0		143.0	69.0	NM_002019	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Missense_Mutation	SNP	ENST00000282397.4	hg19	CCDS9330.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.091112	0.76756	.	.	ENSG00000102755	ENST00000282397;ENST00000541932;ENST00000539099	T;T;T	0.75260	-0.92;-0.31;-0.26	5.78	5.78	0.91487	Tyrosine-protein kinase, vascular endothelial growth factor receptor 1 (VEGFR1), N-terminal (1);	0.224825	0.44097	D	0.000495	T	0.77928	0.4204	L	0.41492	1.28	0.54753	D	0.999986	D;D;D;D	0.76494	0.999;0.999;0.992;0.994	D;D;D;D	0.72338	0.977;0.977;0.967;0.963	T	0.72516	-0.4269	10	0.02654	T	1	.	16.1141	0.81289	0.0:0.0:0.0:1.0	.	227;227;227;227	P17948-4;P17948-3;P17948-2;P17948	.;.;.;VGFR1_HUMAN	Y	227	ENSP00000282397:N227Y;ENSP00000437631:N227Y;ENSP00000442630:N227Y	ENSP00000282397:N227Y	N	-	1	0	FLT1	27906090	1.000000	0.71417	0.986000	0.45419	0.860000	0.49131	5.475000	0.66787	2.214000	0.71695	0.528000	0.53228	AAT	.	.		0.383	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1			A	29008090	T	A	29008090	3	1	317	1	0	0	0	0	1	0	0	0	5949	1812	63	4	3700	4	FLT1	13	29008090	Missense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	2218941	29008090	86161788	150	44792										
TPP2	7174	hgsc.bcm.edu	37	chr13	103288606	103288606	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tatgactacctcgttcagaaTacatcatttgctaataaatt	4	8	2	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr13:103288606T>A	ENST00000376065.4	+	13	1578	c.1542T>A	c.(1540-1542)aaT>aaA	p.N514K	TPP2_ENST00000376052.3_Missense_Mutation_p.N514K	NM_003291.2	NP_003282.2	P29144	TPP2_HUMAN	tripeptidyl peptidase II	514					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)|tripeptidyl-peptidase activity (GO:0008240)			breast(2)|endometrium(5)|kidney(2)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	52	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					TCGTTCAGAATACATCATTTG	0.363																																					p.N514K		Atlas-SNP	.											.	TPP2	124	.	0			c.T1542A						.						93	84	87					13																	103288606		2203	4300	6503	SO:0001583	missense	7174	exon13			TCAGAATACATCA	M55169	CCDS9502.1	13q32-q33	2008-02-05			ENSG00000134900	ENSG00000134900	3.4.14.10		12016	protein-coding gene	gene with protein product		190470				1670990	Standard	NM_003291		Approved		uc001vpi.4	P29144	OTTHUMG00000017305	ENST00000376065.4:c.1542T>A	chr13.hg19:g.103288606T>A	ENSP00000365233:p.Asn514Lys	204.0	0.0		167.0	61.0	NM_003291	Q5VZU8	Missense_Mutation	SNP	ENST00000376065.4	hg19	CCDS9502.1	.	.	.	.	.	.	.	.	.	.	T	15.62	2.886737	0.51908	.	.	ENSG00000134900	ENST00000376065;ENST00000376052	T;T	0.41065	1.01;1.01	5.96	-2.27	0.06846	.	0.183525	0.64402	D	0.000020	T	0.30634	0.0771	L	0.43923	1.385	0.49051	D	0.99974	B	0.26318	0.146	B	0.22152	0.038	T	0.10965	-1.0607	10	0.59425	D	0.04	.	11.5795	0.50883	0.0:0.4156:0.0:0.5844	.	514	P29144	TPP2_HUMAN	K	514	ENSP00000365233:N514K;ENSP00000365220:N514K	ENSP00000365220:N514K	N	+	3	2	TPP2	102086607	0.976000	0.34144	0.993000	0.49108	0.998000	0.95712	0.116000	0.15561	-0.276000	0.09206	0.533000	0.62120	AAT	.	.		0.363	TPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045683.2			A	103288606	T	A	103288606	3	1	317	1	0	0	0	0	1	0	0	0	16427	1403	49	4	1592	4	TPP2	13	103288606	Missense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	74280516	103288606	11881272	151	44793										
SLC7A8	23428	hgsc.bcm.edu	37	chr14	23635745	23635745	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	aagattccagagccgatgatGttccctgcatgaggcaccaa	10	11	0	4			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr14:23635745G>C	ENST00000316902.7	-	2	881	c.156C>G	c.(154-156)aaC>aaG	p.N52K	SLC7A8_ENST00000469263.1_Missense_Mutation_p.N52K	NM_012244.3	NP_036376.2	Q9UHI5	LAT2_HUMAN	solute carrier family 7 (amino acid transporter light chain, L system), member 8	52					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|metal ion homeostasis (GO:0055065)|neutral amino acid transport (GO:0015804)|organic cation transport (GO:0015695)|response to toxic substance (GO:0009636)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-amino acid transmembrane transporter activity (GO:0015179)|neutral amino acid transmembrane transporter activity (GO:0015175)|organic cation transmembrane transporter activity (GO:0015101)|peptide antigen binding (GO:0042605)|toxin transporter activity (GO:0019534)			autonomic_ganglia(1)|endometrium(6)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|skin(1)	24	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.00809)	L-Alanine(DB00160)|L-DOPA(DB01235)|L-Glutamine(DB00130)|L-Phenylalanine(DB00120)	AGCCGATGATGTTCCCTGCAT	0.532																																					p.N52K		Atlas-SNP	.											.	SLC7A8	54	.	0			c.C156G						.						133	131	132					14																	23635745		2203	4300	6503	SO:0001583	missense	23428	exon2			GATGATGTTCCCT	Y18483	CCDS9590.1, CCDS41924.1, CCDS58304.1, CCDS58305.1	14q11.2	2013-05-22	2011-07-12		ENSG00000092068	ENSG00000092068		"Solute carriers"	11066	protein-coding gene	gene with protein product		604235				10080183, 10391915	Standard	NM_001267036		Approved	LPI-PC1, LAT2	uc001wiz.4	Q9UHI5	OTTHUMG00000028720	ENST00000316902.7:c.156C>G	chr14.hg19:g.23635745G>C	ENSP00000320378:p.Asn52Lys	45.0	0.0		26.0	11.0	NM_012244	B2R8Q4|B4DKT4|B4DTV6|D3DS46|F2Z2J4|Q86U05|Q9UKQ6|Q9UKQ7|Q9UKQ8|Q9Y445	Missense_Mutation	SNP	ENST00000316902.7	hg19	CCDS9590.1	.	.	.	.	.	.	.	.	.	.	G	17.36	3.369677	0.61624	.	.	ENSG00000092068	ENST00000316902;ENST00000469263;ENST00000524758;ENST00000525062	D;D;D;D	0.94497	-2.52;-2.52;-2.73;-3.44	5.49	4.6	0.57074	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.96234	0.8772	M	0.71920	2.185	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.78314	0.985;0.991	D	0.96003	0.8995	10	0.72032	D	0.01	.	9.6422	0.39846	0.1611:0.0:0.8389:0.0	.	52;52	E9PLV9;Q9UHI5	.;LAT2_HUMAN	K	52	ENSP00000320378:N52K;ENSP00000435114:N52K;ENSP00000434352:N52K;ENSP00000436665:N52K	ENSP00000320378:N52K	N	-	3	2	SLC7A8	22705585	1.000000	0.71417	1.000000	0.80357	0.337000	0.28794	3.287000	0.51732	1.453000	0.47775	0.655000	0.94253	AAC	.	.		0.532	SLC7A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071718.3			C	23635745	G	C	23635745	3	2	317	1	0	0	0	0	1	0	0	0	14719	1368	48	4	1491	4	SLC7A8	14	23635745	Missense_Mutation	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10		23635745	83713795	152	44794										
HEATR4	399671	hgsc.bcm.edu	37	chr14	73989702	73989702	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ggtgtagacggtactgtgagCtgaagaagaccataggcaca	14	7	0	5			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr14:73989702C>A	ENST00000553558.1	-	3	476	c.155G>T	c.(154-156)aGc>aTc	p.S52I	HEATR4_ENST00000560393.1_Missense_Mutation_p.S5I|RP3-414A15.11_ENST00000553394.1_RNA|HEATR4_ENST00000334988.2_Missense_Mutation_p.S52I|RP3-414A15.2_ENST00000555972.2_RNA	NM_001220484.1	NP_001207413.1	Q86WZ0	HEAT4_HUMAN	HEAT repeat containing 4	52										breast(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00386)|OV - Ovarian serous cystadenocarcinoma(108;0.0719)		GTACTGTGAGCTGAAGAAGAC	0.527																																					p.S52I		Atlas-SNP	.											.	HEATR4	126	.	0			c.G155T						.						87	91	89					14																	73989702		2203	4300	6503	SO:0001583	missense	399671	exon2			TGTGAGCTGAAGA	BC047590	CCDS9815.1, CCDS9815.2	14q24.3	2013-09-20			ENSG00000187105	ENSG00000187105			16761	protein-coding gene	gene with protein product						15489334	Standard	NM_203309		Approved	MGC48595	uc021rwf.2	Q86WZ0	OTTHUMG00000171602	ENST00000553558.1:c.155G>T	chr14.hg19:g.73989702C>A	ENSP00000450444:p.Ser52Ile	125.0	0.0		86.0	36.0	NM_203309	B7Z7V9|E9KL41	Missense_Mutation	SNP	ENST00000553558.1	hg19	CCDS9815.2	.	.	.	.	.	.	.	.	.	.	C	15.96	2.985548	0.53934	.	.	ENSG00000187105	ENST00000553558;ENST00000334988;ENST00000556455	T;T	0.14766	2.48;2.48	5.6	2.76	0.32466	.	0.446203	0.21515	N	0.073318	T	0.14570	0.0352	L	0.34521	1.04	0.09310	N	1	D	0.55385	0.971	P	0.50440	0.641	T	0.05886	-1.0858	10	0.87932	D	0	-0.3005	7.4349	0.27150	0.0:0.7334:0.0:0.2666	.	52	Q86WZ0	HEAT4_HUMAN	I	52;5;52	ENSP00000450444:S52I;ENSP00000452407:S52I	ENSP00000335447:S5I	S	-	2	0	HEATR4	73059455	0.001000	0.12720	0.017000	0.16124	0.019000	0.09904	0.689000	0.25437	0.706000	0.31912	0.563000	0.77884	AGC	.	.		0.527	HEATR4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414422.2	NM_203309		A	73989702	C	A	73989702	3	1	317	1	0	0	0	0	1	0	0	0	7039	797	28	3	2989	3	HEATR4	14	73989702	Missense_Mutation	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	50353957	73989702	33359838	153	44795										
C14orf43	91748	hgsc.bcm.edu	37	chr14	74191982	74191982	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gagcccagctcaccagcttcTgcaccaggaagaaatccttc	8	15	2	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr14:74191982T>C	ENST00000286523.5	-	9	3349	c.2567A>G	c.(2566-2568)cAg>cGg	p.Q856R	ELMSAN1_ENST00000394071.2_Missense_Mutation_p.Q856R	NM_194278.3	NP_919254.2	Q6PJG2	EMSA1_HUMAN	ELM2 and Myb/SANT-like domain containing 1	856	SANT. {ECO:0000255|PROSITE- ProRule:PRU00624}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)										CACCAGCTTCTGCACCAGGAA	0.537																																					p.Q856R		Atlas-SNP	.											.	.	.	.	0			c.A2567G						.						148	139	142					14																	74191982		2203	4300	6503	SO:0001583	missense	91748	exon9			AGCTTCTGCACCA	BF971739	CCDS9819.1	14q24.3	2012-09-25	2012-09-25	2012-09-25	ENSG00000156030	ENSG00000156030			19853	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 117", "chromosome 14 open reading frame 43"	C14orf117, C14orf43			Standard	NM_194278		Approved	LSR68	uc001xou.3	Q6PJG2	OTTHUMG00000150359	ENST00000286523.5:c.2567A>G	chr14.hg19:g.74191982T>C	ENSP00000286523:p.Gln856Arg	63.0	0.0		51.0	20.0	NM_194278	Q6PK13|Q6PK59|Q6ZS23	Missense_Mutation	SNP	ENST00000286523.5	hg19	CCDS9819.1	.	.	.	.	.	.	.	.	.	.	T	29.9	5.041565	0.93685	.	.	ENSG00000156030	ENST00000394071;ENST00000286523;ENST00000423556;ENST00000435371	T;T;T;T	0.28895	1.59;1.59;1.59;1.59	5.94	5.94	0.96194	SANT domain, DNA binding (1);Homeodomain-like (1);SANT, eukarya (1);	0.000000	0.64402	D	0.000008	T	0.49236	0.1545	L	0.43923	1.385	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.80764	0.99;0.994	T	0.47275	-0.9130	10	0.66056	D	0.02	-22.5884	16.3979	0.83621	0.0:0.0:0.0:1.0	.	856;856	A0PJD3;Q6PJG2	.;CN043_HUMAN	R	856	ENSP00000377634:Q856R;ENSP00000286523:Q856R;ENSP00000407767:Q856R;ENSP00000402380:Q856R	ENSP00000286523:Q856R	Q	-	2	0	C14orf43	73261735	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.548000	0.82154	2.279000	0.76181	0.459000	0.35465	CAG	.	.		0.537	ELMSAN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317793.1	NM_194278		C	74191982	T	C	74191982	3	2	317	1	0	0	0	0	1	0	0	0	1776	1580	55	2	586	2	C14orf43	14	74191982	Missense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	202280	74191982	33157558	154	44796										
CPSF2	53981	hgsc.bcm.edu	37	chr14	92609350	92609350	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tctttccccccatgttaggtAgaatggatgagtgataaatt	9	7	1	3			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr14:92609350A>G	ENST00000298875.4	+	9	1137	c.852A>G	c.(850-852)gtA>gtG	p.V284V		NM_017437.2	NP_059133.1	Q9P2I0	CPSF2_HUMAN	cleavage and polyadenylation specific factor 2, 100kDa	284					gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)|mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	RNA binding (GO:0003723)			breast(2)|cervix(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	24		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.222)		CATGTTAGGTAGAATGGATGA	0.333																																					p.V284V	Ovarian(78;28 1788 18702 44111)	Atlas-SNP	.											.	CPSF2	63	.	0			c.A852G						.						82	77	79					14																	92609350		2203	4300	6503	SO:0001819	synonymous_variant	53981	exon9			TTAGGTAGAATGG	AB037788	CCDS9902.1	14q31.1	2008-07-28	2002-08-29			ENSG00000165934			2325	protein-coding gene	gene with protein product		606028	"cleavage and polyadenylation specific factor 2, 100kD subunit"			7969155, 11124543	Standard	NM_017437		Approved	KIAA1367	uc001yah.2	Q9P2I0		ENST00000298875.4:c.852A>G	chr14.hg19:g.92609350A>G		207.0	0.0		165.0	65.0	NM_017437	B3KME1|Q6NSJ1|Q9H3W7	Silent	SNP	ENST00000298875.4	hg19	CCDS9902.1																																																																																			.	.		0.333	CPSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412123.1			G	92609350	A	G	92609350	2	3	317	1	0	0	0	0	0	0	0	1	3827	407	15	2		2	CPSF2	14	92609350	Silent	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	18417368	92609350	14740190	155	44797										
PPP1R13B	23368	hgsc.bcm.edu	37	chr14	104206739	104206739	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gatgggcgtgagcttggtggGgctgagtggccgtggcaggc	22	7	0	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr14:104206739G>A	ENST00000202556.9	-	12	2296	c.2014C>T	c.(2014-2016)Ccc>Tcc	p.P672S	PPP1R13B_ENST00000555391.1_5'UTR|PPP1R13B_ENST00000423488.2_Missense_Mutation_p.P91S	NM_015316.2	NP_056131.2	Q96KQ4	ASPP1_HUMAN	protein phosphatase 1, regulatory subunit 13B	672	Pro-rich.				intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell cycle (GO:0045786)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(6)|kidney(2)|large_intestine(7)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.173)|all_epithelial(191;0.131)|Melanoma(154;0.155)				AGCTTGGTGGGGCTGAGTGGC	0.667																																					p.P672S		Atlas-SNP	.											.	PPP1R13B	72	.	0			c.C2014T						.						57	69	65					14																	104206739		2143	4241	6384	SO:0001583	missense	23368	exon12			TGGTGGGGCTGAG	AB018314	CCDS41997.1	14q32.33	2013-01-10	2011-10-04		ENSG00000088808	ENSG00000088808		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	14950	protein-coding gene	gene with protein product		606455	"protein phosphatase 1, regulatory (inhibitor) subunit 13B"			9872452	Standard	NM_015316		Approved	p53BP2-like, KIAA0771, p85, ASPP1	uc001yof.1	Q96KQ4	OTTHUMG00000171647	ENST00000202556.9:c.2014C>T	chr14.hg19:g.104206739G>A	ENSP00000202556:p.Pro672Ser	42.0	0.0		32.0	16.0	NM_015316	B2RMX5|O94870	Missense_Mutation	SNP	ENST00000202556.9	hg19	CCDS41997.1	.	.	.	.	.	.	.	.	.	.	G	35	5.515550	0.96402	.	.	ENSG00000088808	ENST00000202556;ENST00000423488;ENST00000380023	T;D	0.92099	-0.98;-2.97	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	D	0.95239	0.8456	L	0.54323	1.7	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.95107	0.8235	10	0.59425	D	0.04	.	19.5918	0.95518	0.0:0.0:1.0:0.0	.	672	Q96KQ4	ASPP1_HUMAN	S	672;91;539	ENSP00000202556:P672S;ENSP00000395213:P91S	ENSP00000202556:P672S	P	-	1	0	PPP1R13B	103276492	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.858000	0.99539	2.608000	0.88229	0.655000	0.94253	CCC	.	.		0.667	PPP1R13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414591.1	NM_015316		A	104206739	G	A	104206739	3	1	317	1	0	0	0	0	1	0	0	0	12369	1232	43	3	1282	3	PPP1R13B	14	104206739	Missense_Mutation	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	11597389	104206739	3142801	156	44798										
KIAA0284	283638	hgsc.bcm.edu	37	chr14	105349414	105349414	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gcaggacggggagctccacgGcttccgcgcccctgctgagc	15	16	0	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr14:105349414G>C	ENST00000414716.3	+	8	848	c.620G>C	c.(619-621)gGc>gCc	p.G207A	CEP170B_ENST00000418279.1_Missense_Mutation_p.G137A|CEP170B_ENST00000453495.1_Missense_Mutation_p.G208A|CEP170B_ENST00000556508.1_Missense_Mutation_p.G137A	NM_001112726.2	NP_001106197.1	Q9Y4F5	C170B_HUMAN	centrosomal protein 170B	207						cytoplasm (GO:0005737)|microtubule (GO:0005874)											GAGCTCCACGGCTTCCGCGCC	0.692																																					p.G207A		Atlas-SNP	.											.	.	.	.	0			c.G620C						.						6	8	8					14																	105349414		1908	4073	5981	SO:0001583	missense	283638	exon8			TCCACGGCTTCCG	AB006622	CCDS45175.1, CCDS45176.1, CCDS45176.2	14q32.33	2014-02-20	2012-11-30	2012-11-30	ENSG00000099814	ENSG00000099814			20362	protein-coding gene	gene with protein product	"Cep170-related"		"KIAA0284"	KIAA0284		23087211	Standard	NM_015005		Approved	FAM68C, Cep170R	uc010axb.4	Q9Y4F5	OTTHUMG00000170763	ENST00000414716.3:c.620G>C	chr14.hg19:g.105349414G>C	ENSP00000404151:p.Gly207Ala	56.0	0.0		25.0	13.0	NM_001112726	Q2KHR7|Q86TI7	Missense_Mutation	SNP	ENST00000414716.3	hg19	CCDS45175.1	.	.	.	.	.	.	.	.	.	.	g	10.57	1.388079	0.25118	.	.	ENSG00000099814	ENST00000556508;ENST00000414716;ENST00000453495;ENST00000418279	T;T;T;T	0.34275	1.37;1.37;1.37;1.37	3.25	2.33	0.28932	.	1.378270	0.04536	N	0.387270	T	0.31009	0.0783	L	0.48362	1.52	0.09310	N	1	B;B;B	0.26708	0.157;0.004;0.001	B;B;B	0.29785	0.107;0.003;0.003	T	0.26087	-1.0113	10	0.12103	T	0.63	-17.2276	5.2461	0.15498	0.1595:0.2094:0.6311:0.0	.	207;207;137	Q9Y4F5-2;Q9Y4F5;E9PFC1	.;K0284_HUMAN;.	A	137;207;208;137	ENSP00000451249:G137A;ENSP00000404151:G207A;ENSP00000407238:G208A;ENSP00000415006:G137A	ENSP00000404151:G207A	G	+	2	0	KIAA0284	104420459	0.039000	0.19947	0.014000	0.15608	0.144000	0.21451	2.394000	0.44450	0.667000	0.31107	0.401000	0.26515	GGC	.	.		0.692	CEP170B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000410289.2	NM_001112726		C	105349414	G	C	105349414	3	2	317	1	0	0	0	0	1	0	0	0	8175	1203	42	4	646	4	KIAA0284	14	105349414	Missense_Mutation	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	1142675	105349414	2000126	157	44799										
JMJD7-PLA2G4B	100137049	hgsc.bcm.edu	37	chr15	42139617	42139617	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	cagccccgaagagcagctccAgcctcgggagtgccacacct	11	17	0	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr15:42139617A>G	ENST00000452633.1	+	20	2382	c.2030A>G	c.(2029-2031)cAg>cGg	p.Q677R	PLA2G4B_ENST00000458483.1_Missense_Mutation_p.Q677R|JMJD7-PLA2G4B_ENST00000342159.4_Intron|PLA2G4B_ENST00000542534.2_Missense_Mutation_p.Q908R|JMJD7-PLA2G4B_ENST00000382448.4_Missense_Mutation_p.Q908R			P0C869	PA24B_HUMAN	phospholipase A2, group IVB (cytosolic)	677	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|arachidonic acid metabolic process (GO:0019369)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|parturition (GO:0007567)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular region (GO:0005576)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|calcium-dependent phospholipid binding (GO:0005544)|lysophospholipase activity (GO:0004622)						all_cancers(109;1.84e-13)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		all cancers(2;1.08e-30)|Epithelial(2;1.43e-22)|OV - Ovarian serous cystadenocarcinoma(18;1.13e-17)|GBM - Glioblastoma multiforme(94;9.77e-07)|Colorectal(2;0.0129)|COAD - Colon adenocarcinoma(120;0.0371)		GAGCAGCTCCAGCCTCGGGAG	0.682																																					p.Q908R		Atlas-SNP	.											.	JMJD7-PLA2G4B	90	.	0			c.A2723G						.						83	88	86					15																	42139617		2203	4300	6503	SO:0001583	missense	8681	exon24			AGCTCCAGCCTCG	AF065215	CCDS45241.1	15q11.2-q21.3	2010-08-17			ENSG00000243708	ENSG00000243708	3.1.1.4		9036	protein-coding gene	gene with protein product		606088				9705332	Standard	NM_001114633		Approved	cPLA2-beta, HsT16992		P0C869	OTTHUMG00000156809	ENST00000452633.1:c.2030A>G	chr15.hg19:g.42139617A>G	ENSP00000396045:p.Gln677Arg	60.0	0.0		42.0	16.0	NM_005090	B4DRT9|O95712|Q19KD5|Q19KD6|Q59GF9|Q8TB10|Q9UKV7	Missense_Mutation	SNP	ENST00000452633.1	hg19	CCDS45241.1	.	.	.	.	.	.	.	.	.	.	.	7.871	0.728059	0.15507	.	.	ENSG00000168970;ENSG00000168970;ENSG00000243708	ENST00000382448;ENST00000458483;ENST00000452633	T;T;T	0.14516	2.5;2.5;2.5	5.09	1.41	0.22369	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (2);	0.365883	0.25961	N	0.027181	T	0.08044	0.0201	.	.	.	0.24823	N	0.992572	B;B	0.11235	0.004;0.0	B;B	0.16722	0.016;0.001	T	0.24119	-1.0169	9	0.34782	T	0.22	-18.566	5.2293	0.15412	0.7037:0.0:0.1607:0.1356	.	677;908	P0C869;P0C869-6	PA24B_HUMAN;.	R	908;677;677	ENSP00000371886:Q908R;ENSP00000416610:Q677R;ENSP00000396045:Q677R	ENSP00000371886:Q908R	Q	+	2	0	JMJD7-PLA2G4B;PLA2G4B	39926909	0.357000	0.24938	0.757000	0.31301	0.027000	0.11550	0.383000	0.20651	0.896000	0.36366	-0.411000	0.06167	CAG	.	.		0.682	PLA2G4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000345969.1	NM_001114633		G	42139617	A	G	42139617	3	3	317	1	0	0	0	0	1	0	0	0	7964	188	7	2	2817	2	JMJD7-PLA2G4B	15	42139617	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10		42139617	60391775	158	44800										
SPTBN5	51332	hgsc.bcm.edu	37	chr15	42185565	42185565	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gggcctgtagcttgcgaatgTggcccgtctcgtactgagag	15	10	1	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr15:42185565T>C	ENST00000320955.6	-	2	358	c.131A>G	c.(130-132)cAc>cGc	p.H44R	RP11-23P13.6_ENST00000564432.2_RNA|RP11-23P13.6_ENST00000309874.2_RNA|RP11-23P13.6_ENST00000568861.1_RNA|RP11-23P13.7_ENST00000605942.1_lincRNA|RP11-23P13.6_ENST00000562920.1_RNA	NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	44	Actin-binding.				actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		CTTGCGAATGTGGCCCGTCTC	0.607																																					p.H9R		Atlas-SNP	.											.	SPTBN5	171	.	0			c.A26G						.						59	63	61					15																	42185565		2043	4192	6235	SO:0001583	missense	51332	exon2			CGAATGTGGCCCG	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"beta V spectrin"	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.131A>G	chr15.hg19:g.42185565T>C	ENSP00000317790:p.His44Arg	60.0	0.0		48.0	24.0	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	hg19		.	.	.	.	.	.	.	.	.	.	T	18.34	3.601563	0.66445	.	.	ENSG00000137877	ENST00000320955	D	0.95103	-3.61	5.32	2.91	0.33838	Calponin homology domain (1);	0.276491	0.30252	N	0.010049	D	0.85435	0.5696	N	0.17723	0.515	0.24630	N	0.993621	B	0.31599	0.33	B	0.28011	0.085	T	0.72377	-0.4312	10	0.02654	T	1	.	10.2877	0.43577	0.2631:0.0:0.0:0.7369	.	44	Q9NRC6	SPTN5_HUMAN	R	44	ENSP00000317790:H44R	ENSP00000317790:H44R	H	-	2	0	SPTBN5	39972857	0.987000	0.35691	0.355000	0.25773	0.841000	0.47740	2.138000	0.42140	0.292000	0.22492	0.533000	0.62120	CAC	.	.		0.607	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642		C	42185565	T	C	42185565	3	2	317	1	0	0	0	0	1	0	0	0	15137	1696	59	2	11161	2	SPTBN5	15	42185565	Missense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	45948	42185565	60345827	159	44801										
FSD2	123722	hgsc.bcm.edu	37	chr15	83437679	83437679	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tcagcctgggtcagctccacAgtgtacgagtccacaggatt	11	12	2	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr15:83437679A>G	ENST00000334574.8	-	9	1687	c.1506T>C	c.(1504-1506)acT>acC	p.T502T	FSD2_ENST00000541889.1_Silent_p.T457T			A1L4K1	FSD2_HUMAN	fibronectin type III and SPRY domain containing 2	502	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.									breast(2)|central_nervous_system(1)|large_intestine(5)|lung(10)	18						TCAGCTCCACAGTGTACGAGT	0.527																																					p.T502T		Atlas-SNP	.											.	FSD2	45	.	0			c.T1506C						.						50	54	52					15																	83437679		2011	4198	6209	SO:0001819	synonymous_variant	123722	exon9			CTCCACAGTGTAC	AK122875	CCDS45332.1, CCDS61738.1	15q25.2	2013-02-11	2006-01-11	2006-01-11		ENSG00000186628		"Fibronectin type III domain containing"	18024	protein-coding gene	gene with protein product			"SPRY domain containing 1"	SPRYD1			Standard	NM_001007122		Approved	RP11-127F21	uc002bjd.2	A1L4K1		ENST00000334574.8:c.1506T>C	chr15.hg19:g.83437679A>G		65.0	0.0		75.0	34.0	NM_001007122	B3KVG1|B7ZM02	Silent	SNP	ENST00000334574.8	hg19	CCDS45332.1																																																																																			.	.		0.527	FSD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418385.1	NM_001007122		G	83437679	A	G	83437679	2	3	317	1	0	0	0	0	0	0	0	1	6079	175	7	2		2	FSD2	15	83437679	Silent	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	41252114	83437679	19093713	160	44802										
MRPL46	26589	hgsc.bcm.edu	37	chr15	89008827	89008827	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	aggatcacaacctgttatgcGagctccaagtttgaactgta	9	9	1	1	rs146169028		TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr15:89008827G>C	ENST00000312475.4	-	2	447	c.406C>G	c.(406-408)Cgc>Ggc	p.R136G	MRPS11_ENST00000325844.4_5'Flank|MRPL46_ENST00000559538.1_5'Flank|MRPS11_ENST00000353598.6_5'Flank	NM_022163.3	NP_071446.2	Q9H2W6	RM46_HUMAN	mitochondrial ribosomal protein L46	136						mitochondrion (GO:0005739)|ribosome (GO:0005840)	hydrolase activity (GO:0016787)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)	5	Lung NSC(78;0.203)		BRCA - Breast invasive adenocarcinoma(143;0.188)			CCTGTTATGCGAGCTCCAAGT	0.438																																					p.R136G		Atlas-SNP	.											.	MRPL46	13	.	0			c.C406G						.						99	99	99					15																	89008827		2201	4299	6500	SO:0001583	missense	26589	exon2			TTATGCGAGCTCC	AF210056	CCDS10341.1	15q25.3	2012-10-08	2001-12-10	2001-12-14	ENSG00000259494	ENSG00000259494		"Mitochondrial ribosomal proteins / large subunits"	1192	protein-coding gene	gene with protein product		611851	"chromosome 15 open reading frame 4"	C15orf4		11761714, 11551941	Standard	NM_022163		Approved	LIECG2, P2ECSL	uc002bmj.2	Q9H2W6	OTTHUMG00000148683	ENST00000312475.4:c.406C>G	chr15.hg19:g.89008827G>C	ENSP00000312311:p.Arg136Gly	64.0	0.0		57.0	22.0	NM_022163	B2RD75|Q9HBU8	Missense_Mutation	SNP	ENST00000312475.4	hg19	CCDS10341.1	.	.	.	.	.	.	.	.	.	.	G	16.35	3.097527	0.56075	.	.	ENSG00000173867	ENST00000312475	T	0.69561	-0.41	4.87	4.87	0.63330	.	0.000000	0.85682	D	0.000000	D	0.84129	0.5404	M	0.87682	2.9	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.994;0.998	D	0.86288	0.1672	10	0.59425	D	0.04	.	17.5509	0.87875	0.0:0.0:1.0:0.0	.	51;136;67	Q8TER9;Q9H2W6;E9PCP9	.;RM46_HUMAN;.	G	136	ENSP00000312311:R136G	ENSP00000312311:R136G	R	-	1	0	MRPL46	86809831	1.000000	0.71417	0.998000	0.56505	0.509000	0.34042	3.125000	0.50469	2.683000	0.91414	0.655000	0.94253	CGC	.	G|1.000;A|0.000		0.438	MRPL46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309073.1	NM_022163		C	89008827	G	C	89008827	3	2	317	1	0	0	0	0	1	0	0	0	9819	1058	37	4	445	4	MRPL46	15	89008827	Missense_Mutation	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	5571148	89008827	13522565	161	44803										
ZNF174	7727	hgsc.bcm.edu	37	chr16	3458764	3458764	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gagagagaccctacacgtgcGgagagtgtggaaactgcttt	14	8	0	3			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr16:3458764G>A	ENST00000268655.4	+	3	1654	c.1069G>A	c.(1069-1071)Gga>Aga	p.G357R	ZNF174_ENST00000571936.1_Missense_Mutation_p.G357R	NM_003450.2	NP_003441.1	Q15697	ZN174_HUMAN	zinc finger protein 174	357					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription from RNA polymerase II promoter (GO:0006366)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			endometrium(2)|large_intestine(3)|lung(3)|prostate(2)|urinary_tract(2)	12						CTACACGTGCGGAGAGTGTGG	0.527																																					p.G357R		Atlas-SNP	.											.	ZNF174	32	.	0			c.G1069A						.						51	59	56					16																	3458764		2197	4300	6497	SO:0001583	missense	7727	exon3			ACGTGCGGAGAGT	U31248	CCDS10504.1, CCDS32380.1	16p13	2013-01-09			ENSG00000103343	ENSG00000103343		"-", "Zinc fingers, C2H2-type"	12963	protein-coding gene	gene with protein product		603900					Standard	NM_003450		Approved	ZSCAN8	uc002cvc.3	Q15697	OTTHUMG00000129358	ENST00000268655.4:c.1069G>A	chr16.hg19:g.3458764G>A	ENSP00000268655:p.Gly357Arg	134.0	0.0		77.0	33.0	NM_003450	Q53Y68|Q9BQ34	Missense_Mutation	SNP	ENST00000268655.4	hg19	CCDS10504.1	.	.	.	.	.	.	.	.	.	.	G	1.874	-0.459444	0.04508	.	.	ENSG00000103343	ENST00000268655	T	0.17691	2.26	4.72	3.76	0.43208	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.147725	0.31809	N	0.007025	T	0.11024	0.0269	N	0.13272	0.32	0.19300	N	0.999974	D	0.60575	0.988	P	0.47786	0.557	T	0.15178	-1.0446	10	0.17832	T	0.49	.	8.1977	0.31407	0.0:0.1734:0.6469:0.1797	.	357	Q15697	ZN174_HUMAN	R	357	ENSP00000268655:G357R	ENSP00000268655:G357R	G	+	1	0	ZNF174	3398765	0.000000	0.05858	0.065000	0.19835	0.027000	0.11550	-1.233000	0.02934	1.578000	0.49821	-0.176000	0.13171	GGA	.	.		0.527	ZNF174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251510.1	NM_003450		A	3458764	G	A	3458764	3	1	317	1	0	0	0	0	1	0	0	0	17759	1117	39	1	1163	1	ZNF174	16	3458764	Missense_Mutation	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10		3458764	86895989	162	44804										
SCNN1G	6340	hgsc.bcm.edu	37	chr16	23197855	23197855	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ctcagtttccatcaaagtccActtccggaagctggattttc	7	12	2	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr16:23197855A>T	ENST00000300061.2	+	2	406	c.263A>T	c.(262-264)cAc>cTc	p.H88L		NM_001039.3	NP_001030.2	P51170	SCNNG_HUMAN	sodium channel, non-voltage-gated 1, gamma subunit	88					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|sodium channel activity (GO:0005272)|WW domain binding (GO:0050699)			NS(2)|autonomic_ganglia(1)|breast(1)|cervix(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	34				GBM - Glioblastoma multiforme(48;0.0366)	Amiloride(DB00594)|Triamterene(DB00384)	ATCAAAGTCCACTTCCGGAAG	0.562																																					p.H88L		Atlas-SNP	.											.	SCNN1G	82	.	0			c.A263T						.						59	56	57					16																	23197855		2197	4300	6497	SO:0001583	missense	6340	exon2			AAGTCCACTTCCG	U48937	CCDS10608.1	16p12	2012-02-28	2012-02-28		ENSG00000166828	ENSG00000166828		"Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels"	10602	protein-coding gene	gene with protein product		600761	"sodium channel, nonvoltage-gated 1, gamma", "sodium channel, non-voltage-gated 1, gamma"			7490094	Standard	NM_001039		Approved	ENaCgamma, SCNEG	uc002dlm.1	P51170	OTTHUMG00000131609	ENST00000300061.2:c.263A>T	chr16.hg19:g.23197855A>T	ENSP00000300061:p.His88Leu	49.0	0.0		28.0	14.0	NM_001039	P78437|Q6PCC2|Q93023|Q93024|Q93025|Q93026|Q93027|Q96TD2	Missense_Mutation	SNP	ENST00000300061.2	hg19	CCDS10608.1	.	.	.	.	.	.	.	.	.	.	A	13.13	2.145201	0.37825	.	.	ENSG00000166828	ENST00000300061	T	0.62639	0.01	4.99	4.99	0.66335	.	0.501673	0.21372	N	0.075617	T	0.55641	0.1933	L	0.57536	1.79	0.34913	D	0.747655	P	0.35226	0.491	B	0.31946	0.138	T	0.69254	-0.5193	10	0.62326	D	0.03	-13.9998	9.8043	0.40783	0.8271:0.1729:0.0:0.0	.	88	P51170	SCNNG_HUMAN	L	88	ENSP00000300061:H88L	ENSP00000300061:H88L	H	+	2	0	SCNN1G	23105356	1.000000	0.71417	1.000000	0.80357	0.505000	0.33919	3.868000	0.56055	1.875000	0.54330	0.460000	0.39030	CAC	.	.		0.562	SCNN1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254496.1	NM_001039		T	23197855	A	T	23197855	3	4	317	1	0	0	0	0	1	0	0	0	13945	159	6	4	265	4	SCNN1G	16	23197855	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	19739091	23197855	67156898	163	44805										
SIAH1	6477	hgsc.bcm.edu	37	chr16	48395984	48395984	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	aaggcctaaactcacagagcTcttcatggtctgctttttct	7	11	5	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr16:48395984T>G	ENST00000380006.2	-	1	1809	c.356A>C	c.(355-357)gAg>gCg	p.E119A	SIAH1_ENST00000573005.1_5'Flank|SIAH1_ENST00000394725.2_Missense_Mutation_p.E119A|SIAH1_ENST00000356721.3_Missense_Mutation_p.E150A			Q8IUQ4	SIAH1_HUMAN	siah E3 ubiquitin protein ligase 1	119	SBD.				anatomical structure morphogenesis (GO:0009653)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cell cycle (GO:0007049)|nervous system development (GO:0007399)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein catabolic process (GO:0030163)|protein destabilization (GO:0031648)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|proteolysis (GO:0006508)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	beta-catenin destruction complex (GO:0030877)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ligase activity (GO:0016874)|protein C-terminus binding (GO:0008022)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(1)|ovary(1)|stomach(1)	7		all_cancers(37;0.157)|all_lung(18;0.11)|Breast(268;0.238)				CTCACAGAGCTCTTCATGGTC	0.468																																					p.E150A		Atlas-SNP	.											.	SIAH1	33	.	0			c.A449C						.						84	62	70					16																	48395984		2200	4300	6500	SO:0001583	missense	6477	exon2			CAGAGCTCTTCAT	U76247	CCDS10735.1, CCDS32444.1	16q12.1	2013-06-03	2012-02-23		ENSG00000196470	ENSG00000196470			10857	protein-coding gene	gene with protein product		602212	"seven in absentia homolog 1 (Drosophila)"			9403064, 9334332	Standard	NM_001006610		Approved	hSIAH1	uc002efo.1	Q8IUQ4	OTTHUMG00000175417	ENST00000380006.2:c.356A>C	chr16.hg19:g.48395984T>G	ENSP00000369343:p.Glu119Ala	136.0	0.0		88.0	37.0	NM_001006610	A0FKF3|O43269|Q49A58|Q92880	Missense_Mutation	SNP	ENST00000380006.2	hg19	CCDS10735.1	.	.	.	.	.	.	.	.	.	.	T	15.01	2.705885	0.48412	.	.	ENSG00000196470	ENST00000356721;ENST00000394725;ENST00000380006	T;T	0.27104	1.69;1.69	5.2	5.2	0.72013	Seven-in-absentia protein, TRAF-like domain (1);TRAF-like (1);Seven In Absentia Homolog-type (1);Zinc finger, SIAH-type (1);	0.000000	0.85682	U	0.000000	T	0.31358	0.0794	L	0.42245	1.32	0.80722	D	1	P;B	0.42757	0.789;0.049	P;B	0.47705	0.555;0.061	T	0.02009	-1.1230	10	0.30078	T	0.28	-19.9522	15.3506	0.74380	0.0:0.0:0.0:1.0	.	119;150	Q8IUQ4;Q8IUQ4-2	SIAH1_HUMAN;.	A	150;119;135	ENSP00000349156:E150A;ENSP00000378214:E119A	ENSP00000349156:E150A	E	-	2	0	SIAH1	46953485	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.997000	0.88414	2.094000	0.63399	0.533000	0.62120	GAG	.	.		0.468	SIAH1-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256842.12			G	48395984	T	G	48395984	3	3	317	1	0	0	0	0	1	0	0	0	14314	1551	54	5	496	5	SIAH1	16	48395984	Missense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	25198129	48395984	41958769	164	44806										
CDH11	1009	hgsc.bcm.edu	37	chr16	65016064	65016064	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	cttggggccaagaacataggGggctcatcagcatcttctac	11	11	4	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr16:65016064G>A	ENST00000268603.4	-	8	1755	c.1140C>T	c.(1138-1140)ccC>ccT	p.P380P	CDH11_ENST00000566827.1_Silent_p.P254P|CDH11_ENST00000394156.3_Silent_p.P380P	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	380	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		AGAACATAGGGGGCTCATCAG	0.527			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)																											p.P380P		Atlas-SNP	.		Dom	yes		16	16q22.1	1009	"cadherin 11, type 2, OB-cadherin (osteoblast)"		M	CDH11,colon,carcinoma,-1,1	CDH11	260	.	0			c.C1140T						.						165	138	147					16																	65016064		2203	4300	6503	SO:0001819	synonymous_variant	1009	exon8			CATAGGGGGCTCA	D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"Cadherins / Major cadherins"	1750	protein-coding gene	gene with protein product	"OB-Cadherin"	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.1140C>T	chr16.hg19:g.65016064G>A		125.0	0.0		58.0	43.0	NM_001797	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Silent	SNP	ENST00000268603.4	hg19	CCDS10803.1																																																																																			.	.		0.527	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664		A	65016064	G	A	65016064	2	1	317	1	0	0	0	0	0	0	0	1	3099	1219	43	3		3	CDH11	16	65016064	Silent	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	16620080	65016064	25338689	165	44807										
AARS	16	hgsc.bcm.edu	37	chr16	70299543	70299543	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	actggaaacccataggtgtcAtagaggagccaagcagtgtc	12	9	1	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr16:70299543A>G	ENST00000261772.8	-	10	1388	c.1245T>C	c.(1243-1245)taT>taC	p.Y415Y	AARS_ENST00000564359.1_5'Flank|RN7SL407P_ENST00000583724.1_RNA	NM_001605.2	NP_001596.2			alanyl-tRNA synthetase											breast(3)|cervix(2)|endometrium(5)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)	27		Ovarian(137;0.0365)		BRCA - Breast invasive adenocarcinoma(221;0.161)		CATAGGTGTCATAGAGGAGCC	0.517																																					p.Y415Y		Atlas-SNP	.											.	AARS	62	.	0			c.T1245C						.						96	93	94					16																	70299543		2198	4300	6498	SO:0001819	synonymous_variant	16	exon10			GGTGTCATAGAGG	D32050	CCDS32474.1	16q22.1	2014-09-17			ENSG00000090861	ENSG00000090861	6.1.1.7	"Aminoacyl tRNA synthetases / Class II"	20	protein-coding gene	gene with protein product	"alanine tRNA ligase 1, cytoplasmic"	601065				8595897	Standard	NM_001605		Approved		uc002eyn.1	P49588	OTTHUMG00000177042	ENST00000261772.8:c.1245T>C	chr16.hg19:g.70299543A>G		127.0	0.0		43.0	32.0	NM_001605		Silent	SNP	ENST00000261772.8	hg19	CCDS32474.1																																																																																			.	.		0.517	AARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435021.2	NM_001605		G	70299543	A	G	70299543	2	3	317	1	0	0	0	0	0	0	0	1	19	224	8	2		2	AARS	16	70299543	Silent	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	5283479	70299543	20055210	166	44808										
ACAP1	9744	hgsc.bcm.edu	37	chr17	7240643	7240643	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tttcccagagcctctattgaGctggtggaagccgaagtgtc	12	10	1	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr17:7240643G>T	ENST00000158762.3	+	2	272	c.66G>T	c.(64-66)gaG>gaT	p.E22D		NM_014716.3	NP_055531.1	Q15027	ACAP1_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 1	22	BAR.|Required for formation of endosomal tubules when overexpressed with PIP5K1C.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)	endosome (GO:0005768)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(3)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|prostate(3)|skin(1)|urinary_tract(1)	33						CCTCTATTGAGCTGGTGGAAG	0.582																																					p.E22D		Atlas-SNP	.											.	ACAP1	66	.	0			c.G66T						.						148	137	141					17																	7240643		2203	4300	6503	SO:0001583	missense	9744	exon2			TATTGAGCTGGTG	D30758	CCDS11101.1	17p13.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000072818	ENSG00000072818		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16467	protein-coding gene	gene with protein product		607763	"centaurin, beta 1"	CENTB1		11050434, 11062263	Standard	NM_014716		Approved	KIAA0050	uc002ggd.2	Q15027	OTTHUMG00000102199	ENST00000158762.3:c.66G>T	chr17.hg19:g.7240643G>T	ENSP00000158762:p.Glu22Asp	150.0	0.0		88.0	6.0	NM_014716	Q53XN9	Missense_Mutation	SNP	ENST00000158762.3	hg19	CCDS11101.1	.	.	.	.	.	.	.	.	.	.	G	12.58	1.981788	0.34942	.	.	ENSG00000072818	ENST00000158762	T	0.04758	3.56	5.49	2.38	0.29361	.	0.320128	0.32518	N	0.005983	T	0.09686	0.0238	L	0.35542	1.07	0.80722	D	1	D	0.69078	0.997	D	0.72625	0.978	T	0.28650	-1.0037	10	0.19147	T	0.46	.	9.658	0.39939	0.26:0.0:0.74:0.0	.	22	Q15027	ACAP1_HUMAN	D	22	ENSP00000158762:E22D	ENSP00000158762:E22D	E	+	3	2	ACAP1	7181367	0.780000	0.28664	0.773000	0.31616	0.324000	0.28378	0.158000	0.16422	0.026000	0.15269	-1.134000	0.01955	GAG	.	.		0.582	ACAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220049.4	NM_014716		T	7240643	G	T	7240643	3	4	317	1	0	0	0	0	1	0	0	0	118	962	34	3	72	3	ACAP1	17	7240643	Missense_Mutation	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10		7240643	73954567	167	44809										
MYH3	4621	hgsc.bcm.edu	37	chr17	10558329	10558329	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tcctctccttttctgacttcCggaggaaaggagcagctatg	10	11	2	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr17:10558329C>T	ENST00000583535.1	-	3	140	c.53G>A	c.(52-54)cGg>cAg	p.R18Q	MYH3_ENST00000226209.7_Missense_Mutation_p.R18Q	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	18					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						TTCTGACTTCCGGAGGAAAGG	0.527																																					p.R18Q		Atlas-SNP	.											.,1	MYH3	227	.	0			c.G53A						.						139	129	132					17																	10558329		2203	4300	6503	SO:0001583	missense	4621	exon3			GACTTCCGGAGGA		CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"Myosins / Myosin superfamily : Class II"	7573	protein-coding gene	gene with protein product	"myosin, skeletal, heavy chain, embryonic 1", "muscle embryonic myosin heavy chain 3"	160720	"myosin, heavy polypeptide 3, skeletal muscle, embryonic"			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.53G>A	chr17.hg19:g.10558329C>T	ENSP00000464317:p.Arg18Gln	111.0	0.0		47.0	2.0	NM_002470	Q15492	Missense_Mutation	SNP	ENST00000583535.1	hg19	CCDS11157.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.263469	0.80358	.	.	ENSG00000109063	ENST00000226209	D	0.86097	-2.07	5.14	5.14	0.70334	.	.	.	.	.	D	0.89787	0.6816	H	0.94385	3.53	0.46113	D	0.998879	P	0.50819	0.939	B	0.40375	0.327	D	0.92779	0.6239	9	0.62326	D	0.03	.	18.796	0.91994	0.0:1.0:0.0:0.0	.	18	P11055	MYH3_HUMAN	Q	18	ENSP00000226209:R18Q	ENSP00000226209:R18Q	R	-	2	0	MYH3	10499054	1.000000	0.71417	0.993000	0.49108	0.484000	0.33280	7.531000	0.81973	2.679000	0.91253	0.655000	0.94253	CGG	.	.		0.527	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470		T	10558329	C	T	10558329	3	4	317	1	0	0	0	0	1	0	0	0	10045	652	23	1	5925	1	MYH3	17	10558329	Missense_Mutation	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	3317686	10558329	70636881	168	44810										
TOP3A	7156	hgsc.bcm.edu	37	chr17	18193874	18193874	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ccagaggagccactgaccaaTgccatgcttctccatgaggg	11	13	1	3			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr17:18193874T>A	ENST00000321105.5	-	13	1808	c.1594A>T	c.(1594-1596)Att>Ttt	p.I532F	TOP3A_ENST00000542570.1_Missense_Mutation_p.I437F|TOP3A_ENST00000540524.1_Missense_Mutation_p.I62F	NM_004618.3	NP_004609.1	Q13472	TOP3A_HUMAN	topoisomerase (DNA) III alpha	532					DNA topological change (GO:0006265)|meiotic nuclear division (GO:0007126)	chromosome (GO:0005694)|nucleus (GO:0005634)|PML body (GO:0016605)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(2)|urinary_tract(1)	36						CACTGACCAATGCCATGCTTC	0.552																																					p.I532F		Atlas-SNP	.											.	TOP3A	85	.	0			c.A1594T						.						58	45	49					17																	18193874		2203	4300	6503	SO:0001583	missense	7156	exon13			GACCAATGCCATG	U43431	CCDS11194.1	17p12-p11.2	2014-02-18			ENSG00000177302	ENSG00000177302			11992	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 7"	601243		TOP3		9450867	Standard	NM_004618		Approved	ZGRF7	uc002gsx.1	Q13472	OTTHUMG00000059391	ENST00000321105.5:c.1594A>T	chr17.hg19:g.18193874T>A	ENSP00000321636:p.Ile532Phe	51.0	0.0		28.0	11.0	NM_004618	A8KA61|B4DK80|D3DXC7|Q13473	Missense_Mutation	SNP	ENST00000321105.5	hg19	CCDS11194.1	.	.	.	.	.	.	.	.	.	.	T	17.41	3.382966	0.61845	.	.	ENSG00000177302	ENST00000321105;ENST00000540524;ENST00000542570	T;T;T	0.37915	1.17;1.17;1.17	5.66	5.66	0.87406	DNA topoisomerase, type IA, core domain (1);DNA topoisomerase, type IA, central (1);DNA topoisomerase, type IA, DNA-binding (1);DNA topoisomerase, type IA, central region, subdomain 1 (1);	0.000000	0.85682	D	0.000000	T	0.75583	0.3869	H	0.98682	4.3	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.85866	0.1413	10	0.87932	D	0	.	15.8887	0.79273	0.0:0.0:0.0:1.0	.	437;532	B4DK80;Q13472	.;TOP3A_HUMAN	F	532;62;437	ENSP00000321636:I532F;ENSP00000446425:I62F;ENSP00000442336:I437F	ENSP00000321636:I532F	I	-	1	0	TOP3A	18134599	1.000000	0.71417	0.999000	0.59377	0.976000	0.68499	7.965000	0.87945	2.154000	0.67381	0.460000	0.39030	ATT	.	.		0.552	TOP3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132052.2			A	18193874	T	A	18193874	3	1	317	1	0	0	0	0	1	0	0	0	16382	1464	51	4	1439	4	TOP3A	17	18193874	Missense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	7635545	18193874	63001336	169	44811										
TBC1D28	254272	hgsc.bcm.edu	37	chr17	18541690	18541690	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gcaaaagtgacaacgcccggCcccgcaccgccaggggaatg	13	15	0	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr17:18541690C>T	ENST00000345096.4	-	7	1022	c.323G>A	c.(322-324)gGc>gAc	p.G108D	TBC1D28_ENST00000405044.1_Missense_Mutation_p.G108D			Q2M2D7	TBC28_HUMAN	TBC1 domain family, member 28	108	Rab-GAP TBC.						Rab GTPase activator activity (GO:0005097)			breast(1)|large_intestine(5)|lung(2)|ovary(1)	9						CAACGCCCGGCCCCGCACCGC	0.507																																					p.G108D		Atlas-SNP	.											.	TBC1D28	14	.	0			c.G323A						.						116	117	117					17																	18541690		1923	4127	6050	SO:0001583	missense	254272	exon8			GCCCGGCCCCGCA		CCDS42273.1	17p11.2	2008-10-27			ENSG00000189375	ENSG00000189375			26858	protein-coding gene	gene with protein product							Standard	NM_001039397		Approved	FLJ40244	uc002gud.2	Q2M2D7	OTTHUMG00000059054	ENST00000345096.4:c.323G>A	chr17.hg19:g.18541690C>T	ENSP00000339973:p.Gly108Asp	164.0	0.0		133.0	54.0	NM_001039397	Q2M2E1	Missense_Mutation	SNP	ENST00000345096.4	hg19	CCDS42273.1	.	.	.	.	.	.	.	.	.	.	N	11.40	1.626577	0.28978	.	.	ENSG00000189375	ENST00000345096;ENST00000405044	T;T	0.12672	2.66;2.66	0.185	0.185	0.15096	Rab-GAP/TBC domain (2);	0.064020	0.64402	U	0.000008	T	0.34803	0.0910	M	0.87547	2.89	0.09310	N	1	D	0.89917	1.0	D	0.75020	0.985	T	0.06058	-1.0848	9	0.66056	D	0.02	.	.	.	.	.	108	Q2M2D7	TBC28_HUMAN	D	108	ENSP00000339973:G108D;ENSP00000385821:G108D	ENSP00000339973:G108D	G	-	2	0	TBC1D28	18482415	0.853000	0.29707	0.001000	0.08648	0.001000	0.01503	2.423000	0.44705	0.293000	0.22520	0.298000	0.19748	GGC	.	.		0.507	TBC1D28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130672.2	NM_001039397		T	18541690	C	T	18541690	3	4	317	1	0	0	0	0	1	0	0	0	15632	739	26	3	321	3	TBC1D28	17	18541690	Missense_Mutation	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	347816	18541690	62653520	170	44812										
MAPK7	5598	hgsc.bcm.edu	37	chr17	19284705	19284705	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tccatgcaaggcgtgagggcAtccgccaacagatccgcttc	11	14	0	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr17:19284705A>T	ENST00000308406.5	+	4	1569	c.1183A>T	c.(1183-1185)Atc>Ttc	p.I395F	MAPK7_ENST00000299612.7_Missense_Mutation_p.I256F|MAPK7_ENST00000395604.3_Missense_Mutation_p.I395F|MAPK7_ENST00000395602.4_Missense_Mutation_p.I395F|MAPK7_ENST00000571657.1_Intron|MFAP4_ENST00000574313.2_5'Flank	NM_139033.2	NP_620602.2	Q13164	MK07_HUMAN	mitogen-activated protein kinase 7	395	Necessary for oligomerization. {ECO:0000250}.				cAMP-mediated signaling (GO:0019933)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to transforming growth factor beta stimulus (GO:0071560)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cAMP catabolic process (GO:0030821)|negative regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051344)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NFAT protein import into nucleus (GO:0051534)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of response to cytokine stimulus (GO:0060761)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|regulation of angiogenesis (GO:0045765)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|mitogen-activated protein kinase binding (GO:0051019)			autonomic_ganglia(1)|central_nervous_system(4)|endometrium(5)|kidney(2)|large_intestine(4)|lung(9)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	30	all_cancers(12;2.87e-05)|all_epithelial(12;0.00114)|Hepatocellular(7;0.00345)|Breast(13;0.206)					GCGTGAGGGCATCCGCCAACA	0.582																																					p.I395F		Atlas-SNP	.											.	MAPK7	72	.	0			c.A1183T						.						71	64	67					17																	19284705		2203	4300	6503	SO:0001583	missense	5598	exon4			GAGGGCATCCGCC	U25278	CCDS11206.1, CCDS11207.1	17p11.2	2011-06-09			ENSG00000166484	ENSG00000166484	2.7.11.24	"Mitogen-activated protein kinase cascade / Kinases"	6880	protein-coding gene	gene with protein product	"BMK1 kinase", "extracellular-signal-regulated kinase 5"	602521		PRKM7		10072598, 7759517	Standard	NM_139032		Approved	BMK1, ERK5	uc002gvp.3	Q13164	OTTHUMG00000059587	ENST00000308406.5:c.1183A>T	chr17.hg19:g.19284705A>T	ENSP00000311005:p.Ile395Phe	95.0	0.0		44.0	17.0	NM_002749	Q16634|Q59F50|Q6QLU7|Q7L4P4|Q969G1|Q96G51	Missense_Mutation	SNP	ENST00000308406.5	hg19	CCDS11206.1	.	.	.	.	.	.	.	.	.	.	A	12.03	1.814615	0.32053	.	.	ENSG00000166484	ENST00000308406;ENST00000299612;ENST00000395604;ENST00000395602	T;T;T;T	0.74209	-0.56;-0.82;-0.56;-0.56	4.31	4.31	0.51392	.	0.180267	0.47455	D	0.000232	T	0.69360	0.3102	N	0.25647	0.755	0.36006	D	0.837731	D	0.54772	0.968	P	0.50970	0.655	T	0.77960	-0.2391	10	0.66056	D	0.02	-12.697	11.4779	0.50308	1.0:0.0:0.0:0.0	.	395	Q13164	MK07_HUMAN	F	395;256;395;395	ENSP00000311005:I395F;ENSP00000299612:I256F;ENSP00000378968:I395F;ENSP00000378966:I395F	ENSP00000299612:I256F	I	+	1	0	MAPK7	19225298	0.998000	0.40836	1.000000	0.80357	0.925000	0.55904	3.866000	0.56040	1.808000	0.52836	0.459000	0.35465	ATC	.	.		0.582	MAPK7-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132506.1	NM_139033		T	19284705	A	T	19284705	3	4	317	1	0	0	0	0	1	0	0	0	9291	217	8	4	1193	4	MAPK7	17	19284705	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	743015	19284705	61910505	171	44813										
MLLT6	4302	hgsc.bcm.edu	37	chr17	36868254	36868254	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gcaccccacccaccacgagaGgggccagaagaaggtagaag	13	13	0	4			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr17:36868254G>C	ENST00000325718.7	+	7	798	c.707G>C	c.(706-708)aGg>aCg	p.R236T	MLLT6_ENST00000378137.5_Missense_Mutation_p.R236T	NM_005937.3	NP_005928	P55198	AF17_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6	236					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(3)|lung(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8	Breast(7;4.43e-21)					CACCACGAGAGGGGCCAGAAG	0.607			T	MLL	AL																																p.R236T		Atlas-SNP	.		Dom	yes		17	17q21	4302	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6 (AF17)"		L	.	MLLT6	80	.	0			c.G707C						.						103	104	104					17																	36868254		2203	4299	6502	SO:0001583	missense	4302	exon7			ACGAGAGGGGCCA		CCDS11327.1	17q21	2014-04-10	2001-11-28		ENSG00000108292	ENSG00000275023		"Zinc fingers, PHD-type"	7138	protein-coding gene	gene with protein product	"Myeloid/lymphoid or mixed-lineage leukemia, translocated to, 6", "trithorax homolog"	600328	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 6"			8058765	Standard	NM_005937		Approved	AF17, FLJ23480	uc002hqi.4	P55198	OTTHUMG00000188498	ENST00000325718.7:c.707G>C	chr17.hg19:g.36868254G>C	ENSP00000316426:p.Arg236Thr	181.0	0.0		121.0	55.0	NM_005937	Q59F28|Q96IU3|Q9H5F6|Q9UF49	Missense_Mutation	SNP	ENST00000325718.7	hg19	CCDS11327.1	.	.	.	.	.	.	.	.	.	.	g	12.88	2.070750	0.36566	.	.	ENSG00000108292	ENST00000325718;ENST00000378137	T;T	0.81163	-1.46;2.46	4.02	1.98	0.26296	.	0.672888	0.13450	N	0.387017	T	0.71143	0.3305	L	0.51422	1.61	0.29188	N	0.876062	B;B;B	0.29432	0.244;0.244;0.023	B;B;B	0.29785	0.107;0.107;0.021	T	0.58498	-0.7626	10	0.20519	T	0.43	.	6.4327	0.21807	0.2408:0.0:0.7592:0.0	.	236;236;236	E9PEP1;Q6P2C6;P55198	.;.;AF17_HUMAN	T	236	ENSP00000316426:R236T;ENSP00000367377:R236T	ENSP00000316426:R236T	R	+	2	0	MLLT6	34121780	1.000000	0.71417	0.994000	0.49952	0.914000	0.54420	1.327000	0.33746	0.335000	0.23614	0.472000	0.43445	AGG	.	.		0.607	MLLT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256799.1	NM_005937		C	36868254	G	C	36868254	3	2	317	1	0	0	0	0	1	0	0	0	9639	1000	35	4	733	4	MLLT6	17	36868254	Missense_Mutation	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	17583549	36868254	44326956	172	44814										
STAC2	342667	hgsc.bcm.edu	37	chr17	37371219	37371219	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ctcaccactgtcaccaggccCctcctcagagctgcggatgc	9	18	3	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr17:37371219C>A	ENST00000333461.5	-	6	1126	c.757G>T	c.(757-759)Ggg>Tgg	p.G253W		NM_198993.3	NP_945344.1	Q6ZMT1	STAC2_HUMAN	SH3 and cysteine rich domain 2	253					intracellular signal transduction (GO:0035556)		metal ion binding (GO:0046872)			NS(2)|endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|pancreas(1)|prostate(1)|skin(2)	17						TCACCAGGCCCCTCCTCAGAG	0.642																																					p.G253W		Atlas-SNP	.											.	STAC2	47	.	0			c.G757T						.						240	214	223					17																	37371219		2203	4300	6503	SO:0001583	missense	342667	exon6			CAGGCCCCTCCTC	AJ608762	CCDS11335.1	17q21.2	2012-11-19			ENSG00000141750	ENSG00000141750			23990	protein-coding gene	gene with protein product							Standard	NM_198993		Approved	24b2	uc002hrs.3	Q6ZMT1	OTTHUMG00000179039	ENST00000333461.5:c.757G>T	chr17.hg19:g.37371219C>A	ENSP00000327509:p.Gly253Trp	79.0	0.0		63.0	20.0	NM_198993	Q32MA3	Missense_Mutation	SNP	ENST00000333461.5	hg19	CCDS11335.1	.	.	.	.	.	.	.	.	.	.	c	17.71	3.455943	0.63401	.	.	ENSG00000141750	ENST00000333461	T	0.80909	-1.43	4.75	4.75	0.60458	.	0.615509	0.15526	N	0.257796	T	0.77631	0.4159	L	0.36672	1.1	0.26967	N	0.96568	D	0.57257	0.979	P	0.50231	0.635	T	0.70857	-0.4758	10	0.66056	D	0.02	-9.2732	9.2826	0.37737	0.0:0.9003:0.0:0.0997	.	253	Q6ZMT1	STAC2_HUMAN	W	253	ENSP00000327509:G253W	ENSP00000327509:G253W	G	-	1	0	STAC2	34624745	0.978000	0.34361	1.000000	0.80357	0.992000	0.81027	1.472000	0.35376	2.353000	0.79882	0.556000	0.70494	GGG	.	.		0.642	STAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444533.2	NM_198993		A	37371219	C	A	37371219	3	1	317	1	0	0	0	0	1	0	0	0	15255	623	22	3	502	3	STAC2	17	37371219	Missense_Mutation	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	502965	37371219	43823991	173	44815										
PLEKHM1	9842	hgsc.bcm.edu	37	chr17	43545720	43545720	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ctgaggtgctctctacaggcTgctgtaagtccagggggctg	15	10	1	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr17:43545720T>C	ENST00000430334.3	-	5	1296	c.1163A>G	c.(1162-1164)cAg>cGg	p.Q388R	PLEKHM1_ENST00000421073.2_Missense_Mutation_p.Q299R|RN7SL730P_ENST00000583727.1_RNA	NM_014798.2	NP_055613.1	Q9Y4G2	PKHM1_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 1	388					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(6)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26	Renal(3;0.0405)					CTCTACAGGCTGCTGTAAGTC	0.637																																					p.Q388R		Atlas-SNP	.											.	PLEKHM1	69	.	0			c.A1163G						.						23	24	24					17																	43545720		2203	4300	6503	SO:0001583	missense	9842	exon5			ACAGGCTGCTGTA	X85792	CCDS32671.1	17q21.31	2013-01-11				ENSG00000225190		"Pleckstrin homology (PH) domain containing"	29017	protein-coding gene	gene with protein product		611466				9205841, 12820725	Standard	NM_014798		Approved	KIAA0356	uc002ija.3	Q9Y4G2		ENST00000430334.3:c.1163A>G	chr17.hg19:g.43545720T>C	ENSP00000389913:p.Gln388Arg	174.0	0.0		118.0	39.0	NM_014798	Q6P2R5|Q8TEL9|Q9NPP5|Q9NYA0	Missense_Mutation	SNP	ENST00000430334.3	hg19	CCDS32671.1	.	.	.	.	.	.	.	.	.	.	T	6.266	0.417220	0.11870	.	.	ENSG00000225190	ENST00000430334;ENST00000446609;ENST00000421073	T;T	0.64803	-0.1;-0.12	4.45	2.06	0.26882	.	1.201540	0.05874	N	0.625103	T	0.55353	0.1915	L	0.51422	1.61	0.09310	N	1	B;B	0.31100	0.255;0.308	B;B	0.32393	0.145;0.101	T	0.36335	-0.9752	10	0.16896	T	0.51	.	8.557	0.33487	0.0:0.0:0.3831:0.6169	.	299;388	F8W648;Q9Y4G2	.;PKHM1_HUMAN	R	388;337;299	ENSP00000389913:Q388R;ENSP00000414352:Q299R	ENSP00000414352:Q299R	Q	-	2	0	PLEKHM1	40901503	0.001000	0.12720	0.028000	0.17463	0.050000	0.14768	-0.091000	0.11146	0.268000	0.21939	0.533000	0.62120	CAG	.	.		0.637	PLEKHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444659.1	NM_014798		C	43545720	T	C	43545720	3	2	317	1	0	0	0	0	1	0	0	0	12089	1580	55	2	2039	2	PLEKHM1	17	43545720	Missense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	6174501	43545720	37649490	174	44816										
C17orf47	284083	hgsc.bcm.edu	37	chr17	56620661	56620661	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gataggcagaatacttatgaAgagactcagggtctacccgt	11	8	2	3			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr17:56620661A>T	ENST00000321691.3	-	1	1068	c.887T>A	c.(886-888)cTt>cAt	p.L296H	SEPT4_ENST00000412945.3_5'Flank|RP11-112H10.4_ENST00000580769.1_RNA|SEPT4_ENST00000457347.2_5'Flank|RP11-112H10.4_ENST00000580589.1_RNA|RP11-112H10.4_ENST00000578022.1_RNA	NM_001038704.2	NP_001033793	Q8NEP4	CQ047_HUMAN	chromosome 17 open reading frame 47	296										NS(1)|breast(2)|endometrium(1)|kidney(4)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	24	Medulloblastoma(34;0.127)|all_neural(34;0.237)					ATACTTATGAAGAGACTCAGG	0.468																																					p.L296H		Atlas-SNP	.											.	C17orf47	59	.	0			c.T887A						.						87	80	82					17																	56620661		2203	4300	6503	SO:0001583	missense	284083	exon1			TTATGAAGAGACT		CCDS32691.1	17q23.2	2012-10-11			ENSG00000181013	ENSG00000181013			26844	protein-coding gene	gene with protein product							Standard	NM_001038704		Approved	FLJ40121	uc002iwq.2	Q8NEP4	OTTHUMG00000179244	ENST00000321691.3:c.887T>A	chr17.hg19:g.56620661A>T	ENSP00000354874:p.Leu296His	169.0	0.0		189.0	55.0	NM_001038704	Q8N821	Missense_Mutation	SNP	ENST00000321691.3	hg19	CCDS32691.1	.	.	.	.	.	.	.	.	.	.	A	15.16	2.751565	0.49257	.	.	ENSG00000181013	ENST00000321691	T	0.33216	1.42	4.9	-2.06	0.07298	.	1.925310	0.02226	N	0.064424	T	0.24470	0.0593	N	0.08118	0	0.09310	N	1	D	0.63046	0.992	P	0.54431	0.752	T	0.09751	-1.0660	10	0.38643	T	0.18	-3.0E-4	4.622	0.12460	0.3417:0.3329:0.3254:0.0	.	296	Q8NEP4	CQ047_HUMAN	H	296	ENSP00000354874:L296H	ENSP00000354874:L296H	L	-	2	0	C17orf47	53975660	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.315000	0.08081	-0.330000	0.08514	0.379000	0.24179	CTT	.	.		0.468	C17orf47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445443.1	NM_001038704		T	56620661	A	T	56620661	3	4	317	1	0	0	0	0	1	0	0	0	1860	72	3	4	833	4	C17orf47	17	56620661	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	13074941	56620661	24574549	175	44817										
BCAS3	54828	hgsc.bcm.edu	37	chr17	59445783	59445783	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	cctccatggagcacacggagGagggcctccgggagcgactt	15	13	0	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr17:59445783G>A	ENST00000390652.5	+	24	2597	c.2566G>A	c.(2566-2568)Gag>Aag	p.E856K	BCAS3_ENST00000585812.1_3'UTR|BCAS3_ENST00000588462.1_Missense_Mutation_p.E856K|BCAS3_ENST00000588874.1_Missense_Mutation_p.E612K|RP11-332H18.5_ENST00000585765.1_RNA|BCAS3_ENST00000407086.3_Missense_Mutation_p.E841K|BCAS3_ENST00000408905.3_Missense_Mutation_p.E841K|BCAS3_ENST00000585744.1_Missense_Mutation_p.E627K|BCAS3_ENST00000589222.1_Missense_Mutation_p.E841K	NM_001099432.1	NP_001092902.1			breast carcinoma amplified sequence 3											NS(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(24)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)			GCACACGGAGGAGGGCCTCCG	0.642																																					p.E856K		Atlas-SNP	.											.	BCAS3	90	.	0			c.G2566A						.						47	57	54					17																	59445783		2078	4205	6283	SO:0001583	missense	54828	exon24			ACGGAGGAGGGCC	AF361219	CCDS11626.1, CCDS45749.1	17q23.2	2013-06-25			ENSG00000141376	ENSG00000141376		"WD repeat domain containing"	14347	protein-coding gene	gene with protein product		607470				12378525	Standard	NM_017679		Approved	FLJ20128	uc002iyv.4	Q9H6U6	OTTHUMG00000180064	ENST00000390652.5:c.2566G>A	chr17.hg19:g.59445783G>A	ENSP00000375067:p.Glu856Lys	78.0	0.0		81.0	18.0	NM_001099432		Missense_Mutation	SNP	ENST00000390652.5	hg19	CCDS45749.1	.	.	.	.	.	.	.	.	.	.	G	12.31	1.901051	0.33535	.	.	ENSG00000141376	ENST00000390652;ENST00000407086;ENST00000408905	T;T;T	0.32023	1.48;1.49;1.47	5.92	4.95	0.65309	.	0.000000	0.85682	D	0.000000	T	0.38532	0.1044	N	0.24115	0.695	0.50313	D	0.999862	D;D;D;P;D	0.58268	0.974;0.982;0.974;0.956;0.974	D;P;D;D;D	0.70487	0.969;0.831;0.969;0.931;0.969	T	0.10989	-1.0606	10	0.10377	T	0.69	.	16.7192	0.85406	0.0:0.0:0.8698:0.1302	.	841;856;841;856;841	Q9H6U6-3;Q9H6U6-8;Q9H6U6-7;Q9H6U6;Q9H6U6-2	.;.;.;BCAS3_HUMAN;.	K	856;841;841	ENSP00000375067:E856K;ENSP00000385323:E841K;ENSP00000386173:E841K	ENSP00000375067:E856K	E	+	1	0	BCAS3	56800565	1.000000	0.71417	0.996000	0.52242	0.253000	0.25986	9.187000	0.94912	1.505000	0.48720	0.555000	0.69702	GAG	.	.		0.642	BCAS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449578.1	NM_017679		A	59445783	G	A	59445783	3	1	317	1	0	0	0	0	1	0	0	0	1352	1175	41	3	2656	3	BCAS3	17	59445783	Missense_Mutation	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	2825122	59445783	21749427	176	44818										
NPTX1	4884	hgsc.bcm.edu	37	chr17	78450179	78450179	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	agcgcgtcggcccgaaatccTgggccccggcgcccaggagg	16	16	0	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr17:78450179T>A	ENST00000306773.4	-	1	225	c.68A>T	c.(67-69)cAg>cTg	p.Q23L	NPTX1_ENST00000575212.1_Intron	NM_002522.3	NP_002513.2	Q15818	NPTX1_HUMAN	neuronal pentraxin I	23					axonogenesis involved in innervation (GO:0060385)|cellular response to glucose stimulus (GO:0071333)|cellular response to potassium ion (GO:0035865)|central nervous system development (GO:0007417)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial transport (GO:0006839)|synaptic transmission (GO:0007268)|transport (GO:0006810)	cytoplasmic vesicle (GO:0031410)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			kidney(1)|large_intestine(2)|liver(1)|lung(4)|prostate(2)|upper_aerodigestive_tract(1)	11	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0487)			CCCGAAATCCTGGGCCCCGGC	0.796																																					p.Q23L		Atlas-SNP	.											.	NPTX1	28	.	0			c.A68T						.						2	2	2					17																	78450179		1667	3278	4945	SO:0001583	missense	4884	exon1			AAATCCTGGGCCC	U61849	CCDS32762.1	17q25.3	2008-05-14				ENSG00000171246			7952	protein-coding gene	gene with protein product		602367				8884281	Standard	NM_002522		Approved		uc002jyp.1	Q15818		ENST00000306773.4:c.68A>T	chr17.hg19:g.78450179T>A	ENSP00000307549:p.Gln23Leu	32.0	0.0		40.0	13.0	NM_002522	B3KXH3|Q5FWE6	Missense_Mutation	SNP	ENST00000306773.4	hg19	CCDS32762.1	.	.	.	.	.	.	.	.	.	.	T	17.26	3.344305	0.61073	.	.	ENSG00000171246	ENST00000306773	T	0.10668	2.85	2.47	2.47	0.30058	.	0.000000	0.85682	U	0.000000	T	0.12178	0.0296	M	0.64997	1.995	0.53688	D	0.999977	P	0.37781	0.608	B	0.36666	0.23	T	0.04767	-1.0928	10	0.72032	D	0.01	.	9.2929	0.37797	0.0:0.0:0.0:1.0	.	23	Q15818	NPTX1_HUMAN	L	23	ENSP00000307549:Q23L	ENSP00000307549:Q23L	Q	-	2	0	NPTX1	76064774	1.000000	0.71417	0.999000	0.59377	0.982000	0.71751	1.772000	0.38552	1.003000	0.39130	0.254000	0.18369	CAG	.	.		0.796	NPTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438051.1			A	78450179	T	A	78450179	3	1	317	1	0	0	0	0	1	0	0	0	10611	1580	55	4	1250	4	NPTX1	17	78450179	Missense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	19004396	78450179	2745031	177	44819										
MC4R	4160	hgsc.bcm.edu	37	chr18	58039130	58039130	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tggtactggagagcatagaaGatagtaaagtacctgtccac	11	7	0	3	rs142925940		TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr18:58039130G>A	ENST00000299766.3	-	1	871	c.453C>T	c.(451-453)atC>atT	p.I151I		NM_005912.2	NP_005903.2	P32245	MC4R_HUMAN	melanocortin 4 receptor	151					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|diet induced thermogenesis (GO:0002024)|energy reserve metabolic process (GO:0006112)|feeding behavior (GO:0007631)|insulin secretion (GO:0030073)|negative regulation of feeding behavior (GO:2000252)|positive regulation of bone resorption (GO:0045780)|positive regulation of cAMP biosynthetic process (GO:0030819)|regulation of grooming behavior (GO:2000821)|response to insulin (GO:0032868)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	melanocortin receptor activity (GO:0004977)|melanocyte-stimulating hormone receptor activity (GO:0004980)|neuropeptide binding (GO:0042923)|peptide hormone binding (GO:0017046)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|kidney(1)|large_intestine(5)|liver(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	17		Colorectal(73;0.0946)				GAGCATAGAAGATAGTAAAGT	0.428																																					p.I151I		Atlas-SNP	.											.	MC4R	49	.	0			c.C453T						.	G		1,4405	2.1+/-5.4	0,1,2202	91	82	85		453	4.8	1	18	dbSNP_134	85	0,8600		0,0,4300	no	coding-synonymous	MC4R	NM_005912.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		151/333	58039130	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	4160	exon1			ATAGAAGATAGTA	AY236539	CCDS11976.1	18q22	2012-08-10			ENSG00000166603	ENSG00000166603		"GPCR / Class A : Melanocortin receptors"	6932	protein-coding gene	gene with protein product		155541				7949735, 9763669	Standard	NM_005912		Approved		uc002lie.1	P32245	OTTHUMG00000132766	ENST00000299766.3:c.453C>T	chr18.hg19:g.58039130G>A		99.0	0.0		63.0	20.0	NM_005912	B2RAC3|Q16317|Q3MIJ6	Silent	SNP	ENST00000299766.3	hg19	CCDS11976.1																																																																																			.	G|1.000;A|0.000		0.428	MC4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256139.1	NM_005912		A	58039130	G	A	58039130	2	1	317	1	0	0	0	0	0	0	0	1	9375	932	33	3		3	MC4R	18	58039130	Silent	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10		58039130	20038118	178	44820										
CDH7	1005	hgsc.bcm.edu	37	chr18	63530135	63530135	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ccctgatagccatactcgccTgtgtcttgacattattgggt	9	11	1	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr18:63530135T>A	ENST00000397968.2	+	11	2272	c.1846T>A	c.(1846-1848)Tgt>Agt	p.C616S	CDH7_ENST00000323011.3_Missense_Mutation_p.C616S|RP11-389J22.1_ENST00000581987.1_RNA|CDH7_ENST00000536984.2_Missense_Mutation_p.C616S	NM_004361.2	NP_004352.2	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2	616					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(43)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	80		Esophageal squamous(42;0.129)				CATACTCGCCTGTGTCTTGAC	0.507																																					p.C616S		Atlas-SNP	.											.	CDH7	362	.	0			c.T1846A						.						90	85	87					18																	63530135		2203	4300	6503	SO:0001583	missense	1005	exon11			CTCGCCTGTGTCT	AB035301	CCDS11993.1	18q22.1	2010-01-26			ENSG00000081138	ENSG00000081138		"Cadherins / Major cadherins"	1766	protein-coding gene	gene with protein product		605806				9615235	Standard	NM_033646		Approved		uc002ljz.3	Q9ULB5	OTTHUMG00000132800	ENST00000397968.2:c.1846T>A	chr18.hg19:g.63530135T>A	ENSP00000381058:p.Cys616Ser	99.0	0.0		64.0	28.0	NM_004361	Q9H157	Missense_Mutation	SNP	ENST00000397968.2	hg19	CCDS11993.1	.	.	.	.	.	.	.	.	.	.	T	16.94	3.261269	0.59431	.	.	ENSG00000081138	ENST00000323011;ENST00000536984;ENST00000397966;ENST00000397968	T;T;T	0.60299	0.2;0.51;0.2	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.74650	0.3744	M	0.72118	2.19	0.80722	D	1	D;D	0.76494	0.997;0.999	P;D	0.78314	0.858;0.991	T	0.77048	-0.2732	10	0.56958	D	0.05	.	15.3548	0.74418	0.0:0.0:0.0:1.0	.	616;616	F5H5X9;Q9ULB5	.;CADH7_HUMAN	S	616	ENSP00000319166:C616S;ENSP00000443030:C616S;ENSP00000381058:C616S	ENSP00000319166:C616S	C	+	1	0	CDH7	61681115	1.000000	0.71417	0.996000	0.52242	0.141000	0.21300	8.013000	0.88655	2.044000	0.60594	0.482000	0.46254	TGT	.	.		0.507	CDH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256217.2	NM_033646		A	63530135	T	A	63530135	3	1	317	1	0	0	0	0	1	0	0	0	3117	1580	55	4	1884	4	CDH7	18	63530135	Missense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	5491005	63530135	14547113	179	44821										
ABCA7	10347	hgsc.bcm.edu	37	chr19	1052055	1052055	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tggctccccactcttcctgcGccgtcacctgggctccggct	10	19	2	0	rs530537679		TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr19:1052055G>A	ENST00000263094.6	+	22	3308	c.3077G>A	c.(3076-3078)cGc>cAc	p.R1026H	ABCA7_ENST00000433129.1_Missense_Mutation_p.R1026H|ABCA7_ENST00000435683.2_Missense_Mutation_p.R888H	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1026	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTCTTCCTGCGCCGTCACCTG	0.672													G|||	1	0.000199681	0	0.0014	5008	,	,		10625	0		0	False		,,,				2504	0				p.R1026H		Atlas-SNP	.											.	ABCA7	174	.	0			c.G3077A						.						52	36	42					19																	1052055		2180	4281	6461	SO:0001583	missense	10347	exon22			TCCTGCGCCGTCA	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"ATP binding cassette transporters / subfamily A"	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.3077G>A	chr19.hg19:g.1052055G>A	ENSP00000263094:p.Arg1026His	61.0	0.0		49.0	21.0	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	hg19	CCDS12055.1	.	.	.	.	.	.	.	.	.	.	g	21.6	4.175052	0.78564	.	.	ENSG00000064687	ENST00000263094;ENST00000433129	D;D	0.90004	-2.6;-2.6	4.44	2.09	0.27110	ABC transporter-like (1);	.	.	.	.	D	0.91178	0.7221	M	0.68593	2.085	0.29532	N	0.852681	D;D	0.89917	0.999;1.0	D;D	0.65773	0.938;0.925	D	0.84058	0.0373	9	0.87932	D	0	.	4.2618	0.10744	0.5206:0.0:0.4794:0.0	.	888;1026	Q8IZY2-2;Q8IZY2	.;ABCA7_HUMAN	H	1026	ENSP00000263094:R1026H;ENSP00000414062:R1026H	ENSP00000263094:R1026H	R	+	2	0	ABCA7	1003055	1.000000	0.71417	0.558000	0.28319	0.848000	0.48234	6.230000	0.72301	0.855000	0.35359	0.550000	0.68814	CGC	.	.		0.672	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112		A	1052055	G	A	1052055	3	1	317	1	0	0	0	0	1	0	0	0	37	1087	38	1	3159	1	ABCA7	19	1052055	Missense_Mutation	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10		1052055	58076928	180	44822										
ZFR2	23217	hgsc.bcm.edu	37	chr19	3820200	3820200	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ctggagtggggcgctggcggGtgactccggcctgcccatga	18	12	0	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr19:3820200G>T	ENST00000262961.4	-	11	1730	c.1720C>A	c.(1720-1722)Ccc>Acc	p.P574T		NM_015174.1	NP_055989.1	Q9UPR6	ZFR2_HUMAN	zinc finger RNA binding protein 2	574	DZF. {ECO:0000255|PROSITE- ProRule:PRU01040}.						nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(5)|pancreas(1)|prostate(1)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00514)|STAD - Stomach adenocarcinoma(1328;0.19)		GCGCTGGCGGGTGACTCCGGC	0.716																																					p.P574T		Atlas-SNP	.											.	ZFR2	63	.	0			c.C1720A						.						12	16	14					19																	3820200		2088	4109	6197	SO:0001583	missense	23217	exon11			TGGCGGGTGACTC	AB029009	CCDS45921.1, CCDS45922.1	19p13.3	2012-10-05	2008-03-25	2008-03-25	ENSG00000105278	ENSG00000105278			29189	protein-coding gene	gene with protein product			"KIAA1086"	KIAA1086		10470851	Standard	NM_015174		Approved		uc002lyw.2	Q9UPR6	OTTHUMG00000180918	ENST00000262961.4:c.1720C>A	chr19.hg19:g.3820200G>T	ENSP00000262961:p.Pro574Thr	84.0	0.0		52.0	20.0	NM_015174		Missense_Mutation	SNP	ENST00000262961.4	hg19	CCDS45921.1	.	.	.	.	.	.	.	.	.	.	G	12.14	1.850101	0.32699	.	.	ENSG00000105278	ENST00000262961	T	0.09350	2.99	2.52	0.0452	0.14229	.	0.000000	0.64402	U	0.000005	T	0.18215	0.0437	M	0.82323	2.585	0.09310	N	0.999999	P	0.46784	0.884	P	0.48952	0.596	T	0.07404	-1.0774	10	0.66056	D	0.02	-8.7711	4.5513	0.12114	0.1491:0.4539:0.397:0.0	.	574	Q9UPR6	ZFR2_HUMAN	T	574	ENSP00000262961:P574T	ENSP00000262961:P574T	P	-	1	0	ZFR2	3771200	0.014000	0.17966	0.000000	0.03702	0.005000	0.04900	0.151000	0.16283	-0.037000	0.13646	0.491000	0.48974	CCC	.	.		0.716	ZFR2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453648.2	NM_015174		T	3820200	G	T	3820200	3	4	317	1	0	0	0	0	1	0	0	0	17675	1261	44	3	1135	3	ZFR2	19	3820200	Missense_Mutation	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	2768145	3820200	55308783	181	44823										
ZNF101	94039	hgsc.bcm.edu	37	chr19	19790802	19790802	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tgaaagagctcacactggagAaagaccttatgaatgtaata	9	6	1	5			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr19:19790802A>G	ENST00000592502.1	+	4	1114	c.1004A>G	c.(1003-1005)gAa>gGa	p.E335G	ZNF101_ENST00000444249.2_3'UTR|ZNF101_ENST00000415784.2_Missense_Mutation_p.E215G			Q8IZC7	ZN101_HUMAN	zinc finger protein 101	335					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(2)|prostate(1)	17						CACACTGGAGAAAGACCTTAT	0.373																																					p.E335G		Atlas-SNP	.											.	ZNF101	43	.	0			c.A1004G						.						57	56	56					19																	19790802		2203	4300	6503	SO:0001583	missense	94039	exon4			CTGGAGAAAGACC	AK097169	CCDS32971.1	19p13.11	2013-01-08	2004-02-10		ENSG00000181896	ENSG00000181896		"Zinc fingers, C2H2-type", "-"	12881	protein-coding gene	gene with protein product		603983	"zinc finger protein 101 (Y2)"			11441184	Standard	XM_005260165		Approved	HZF12, DKFZp570I0164	uc002nni.2	Q8IZC7	OTTHUMG00000167736	ENST00000592502.1:c.1004A>G	chr19.hg19:g.19790802A>G	ENSP00000468049:p.Glu335Gly	96.0	0.0		79.0	33.0	NM_033204	C9JU83|Q0VDG9	Missense_Mutation	SNP	ENST00000592502.1	hg19	CCDS32971.1	.	.	.	.	.	.	.	.	.	.	A	12.99	2.104672	0.37145	.	.	ENSG00000181896	ENST00000318110;ENST00000415440;ENST00000415784	T;T	0.27557	1.66;1.66	0.235	0.235	0.15431	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.32882	0.0844	M	0.83312	2.635	0.25011	N	0.991406	B	0.25312	0.123	B	0.27170	0.077	T	0.34153	-0.9840	8	.	.	.	.	4.8392	0.13481	0.9998:0.0:2.0E-4:0.0	.	335	Q8IZC7	ZN101_HUMAN	G	335;335;215	ENSP00000319716:E335G;ENSP00000400952:E215G	.	E	+	2	0	ZNF101	19651802	0.003000	0.15002	0.181000	0.23098	0.181000	0.23173	0.805000	0.27112	0.263000	0.21812	0.260000	0.18958	GAA	.	.		0.373	ZNF101-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460559.1	NM_033204		G	19790802	A	G	19790802	3	3	317	1	0	0	0	0	1	0	0	0	17729	246	9	2	1018	2	ZNF101	19	19790802	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	15970602	19790802	39338181	182	44824										
ZNF536	9745	hgsc.bcm.edu	37	chr19	31038966	31038967	+	Missense_Mutation	DNP	GG	GG	TT													0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	acggggctgggccgctgtctGggcaacccccaaatcaagac							TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr19:31038966_31038967GG>TT	ENST00000355537.3	+	4	2587_2588	c.2440_2441GG>TT	c.(2440-2442)GGg>TTg	p.G814L		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	814					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					GCCGCTGTCTGGGCAACCCCCA	0.574																																					p.G814W|p.G814V		Atlas-SNP	.											.|ZNF536,caecum,carcinoma,0,2	ZNF536	424	.	0			c.G2440T|c.G2441T						.																																			SO:0001583	missense	9745	exon4			CTGTCTGGGCAAC|TGTCTGGGCAACC		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"Zinc fingers, C2H2-type"	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		Exception_encountered	chr19.hg19:g.31038966_31038967delinsTT	ENSP00000347730:p.Gly814Leu	169.0	0.0		133.0|130.0	62.0|58.0	NM_014717	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	hg19	CCDS32984.1																																																																																			.	.		0.574	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		TT	31038967	GG	TT	31038966	3	4	317	1	0	0	0	0	1	0	0	0	17989	1348	47	3	2450	3	ZNF536	19	31038966	Missense_Mutation	DNP	GG	TCGA-LG-A6GG-01A-11D-A30V-10	11248164	31038966	28090017	183	44825										
TSHZ3	57616	hgsc.bcm.edu	37	chr19	31768760	31768760	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gggttccccgacttcgctgcTacatggggagggagtggccc	16	12	0	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr19:31768760T>G	ENST00000240587.4	-	2	2266	c.1939A>C	c.(1939-1941)Agc>Cgc	p.S647R		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	647					in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					ACTTCGCTGCTACATGGGGAG	0.617																																					p.S647R		Atlas-SNP	.											.	TSHZ3	549	.	0			c.A1939C						.						22	25	24					19																	31768760		2192	4283	6475	SO:0001583	missense	57616	exon2			CGCTGCTACATGG	AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	30700	protein-coding gene	gene with protein product	"teashirt 3"	614119	"zinc finger protein 537", "teashirt family zinc finger 3"	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.1939A>C	chr19.hg19:g.31768760T>G	ENSP00000240587:p.Ser647Arg	74.0	0.0		48.0	21.0	NM_020856	Q9H0G6|Q9P254	Missense_Mutation	SNP	ENST00000240587.4	hg19	CCDS12421.2	.	.	.	.	.	.	.	.	.	.	T	7.367	0.626095	0.14257	.	.	ENSG00000121297	ENST00000240587	T	0.44482	0.92	5.41	0.989	0.19802	.	0.221279	0.53938	D	0.000052	T	0.29976	0.0750	L	0.43152	1.355	0.43296	D	0.995287	B	0.06786	0.001	B	0.04013	0.001	T	0.08493	-1.0719	10	0.21540	T	0.41	-12.8003	9.2101	0.37313	0.0:0.3575:0.0:0.6425	.	647	Q63HK5	TSH3_HUMAN	R	647	ENSP00000240587:S647R	ENSP00000240587:S647R	S	-	1	0	TSHZ3	36460600	1.000000	0.71417	0.902000	0.35471	0.514000	0.34195	2.073000	0.41519	-0.172000	0.10779	0.477000	0.44152	AGC	.	.		0.617	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856		G	31768760	T	G	31768760	3	3	317	1	0	0	0	0	1	0	0	0	16640	1522	53	5	1310	5	TSHZ3	19	31768760	Missense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	729794	31768760	27360223	184	44826										
ARHGAP33	115703	hgsc.bcm.edu	37	chr19	36269405	36269405	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tccggagttacgatgactttCgttccctggatgcccacctc	9	14	0	1	rs374221923		TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr19:36269405C>T	ENST00000007510.4	+	5	454	c.310C>T	c.(310-312)Cgt>Tgt	p.R104C	ARHGAP33_ENST00000314737.5_Missense_Mutation_p.R104C|ARHGAP33_ENST00000221905.1_3'UTR|ARHGAP33_ENST00000378944.5_5'UTR			O14559	RHG33_HUMAN	Rho GTPase activating protein 33	104	PX; atypical.				protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|Rac GTPase activator activity (GO:0030675)			endometrium(7)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	37						CGATGACTTTCGTTCCCTGGA	0.652																																					p.R104C		Atlas-SNP	.											.	ARHGAP33	102	.	0			c.C310T						.	C	,CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	102	101	101		,310	5.3	1	19		101	0,8600		0,0,4300	no	utr-5,missense	ARHGAP33	NM_001172630.1,NM_052948.3	,180	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,probably-damaging	,104/1127	36269405	1,13005	2203	4300	6503	SO:0001583	missense	115703	exon5			GACTTTCGTTCCC	AY044864	CCDS12477.1, CCDS54254.1	19q13.13	2011-06-29	2010-02-19	2010-02-19		ENSG00000004777		"Rho GTPase activating proteins"	23085	protein-coding gene	gene with protein product		614902	"sorting nexin 26"	SNX26		12297274, 12461558	Standard	NM_052948		Approved	FLJ39019, TCGAP	uc002obs.2	O14559		ENST00000007510.4:c.310C>T	chr19.hg19:g.36269405C>T	ENSP00000007510:p.Arg104Cys	57.0	0.0		38.0	14.0	NM_052948	O14552|O14560|Q6ZSP6|Q96CP3|Q9NT23	Missense_Mutation	SNP	ENST00000007510.4	hg19		.	.	.	.	.	.	.	.	.	.	C	26.0	4.699052	0.88830	2.27E-4	0.0	ENSG00000004777	ENST00000007510;ENST00000314737;ENST00000221905	T;T;T	0.26660	1.72;1.72;1.72	5.34	5.34	0.76211	.	0.000000	0.64402	D	0.000004	T	0.43077	0.1231	L	0.38649	1.16	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.983	T	0.28618	-1.0038	10	0.59425	D	0.04	.	17.8148	0.88628	0.0:1.0:0.0:0.0	.	122;104	O14559-12;O14559-11	.;.	C	104;104;122	ENSP00000007510:R104C;ENSP00000320038:R104C;ENSP00000221905:R122C	ENSP00000007510:R104C	R	+	1	0	ARHGAP33	40961245	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	3.908000	0.56355	2.483000	0.83821	0.655000	0.94253	CGT	.	.		0.652	ARHGAP33-201	KNOWN	basic	protein_coding	protein_coding		NM_052948		T	36269405	C	T	36269405	3	4	317	1	0	0	0	0	1	0	0	0	882	884	31	1	328	1	ARHGAP33	19	36269405	Missense_Mutation	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	4500645	36269405	22859578	185	44827										
ZNF793	390927	hgsc.bcm.edu	37	chr19	38024278	38024278	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	aagcaccatggattggtgagGcagcatgcccgggctgccac	14	12	0	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr19:38024278G>A	ENST00000587143.1	+	5	446	c.211G>A	c.(211-213)Gca>Aca	p.A71T	ZNF793_ENST00000445217.1_Missense_Mutation_p.A71T|ZNF793_ENST00000589319.1_Missense_Mutation_p.A71T|ZNF793_ENST00000542455.1_Missense_Mutation_p.A71T|ZNF793_ENST00000588578.1_Missense_Mutation_p.A71T|ZNF793_ENST00000587986.1_Missense_Mutation_p.A71T			Q6ZN11	ZN793_HUMAN	zinc finger protein 793	71	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(2)|lung(1)	3			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GATTGGTGAGGCAGCATGCCC	0.512																																					p.A71T	Melanoma(44;400 1431 1499 19093)	Atlas-SNP	.											.	ZNF793	50	.	0			c.G211A						.						81	84	83					19																	38024278		1955	4146	6101	SO:0001583	missense	390927	exon7			GGTGAGGCAGCAT	AK131417	CCDS46062.1	19q13.12	2013-01-08				ENSG00000188227		"Zinc fingers, C2H2-type", "-"	33115	protein-coding gene	gene with protein product							Standard	NM_001013659		Approved		uc010efm.3	Q6ZN11		ENST00000587143.1:c.211G>A	chr19.hg19:g.38024278G>A	ENSP00000468605:p.Ala71Thr	135.0	0.0		128.0	60.0	NM_001013659	E9PGN4|Q7Z3Q9	Missense_Mutation	SNP	ENST00000587143.1	hg19	CCDS46062.1	.	.	.	.	.	.	.	.	.	.	G	5.232	0.228274	0.09916	.	.	ENSG00000188227	ENST00000542455;ENST00000418827;ENST00000445217;ENST00000322299	T;T	0.06294	3.32;3.32	3.46	2.38	0.29361	Krueppel-associated box (1);	0.816405	0.09992	N	0.729552	T	0.03827	0.0108	N	0.16833	0.445	0.09310	N	1	B;B	0.27498	0.18;0.018	B;B	0.19391	0.025;0.011	T	0.46219	-0.9207	10	0.15066	T	0.55	.	7.938	0.29941	0.0:0.0:0.7543:0.2457	.	71;71	Q6ZN11;E9PGN4	ZN793_HUMAN;.	T	71;71;71;70	ENSP00000444355:A71T;ENSP00000396402:A71T	ENSP00000318811:A70T	A	+	1	0	ZNF793	42716118	0.023000	0.18921	0.372000	0.25991	0.679000	0.39708	0.332000	0.19751	0.729000	0.32403	0.462000	0.41574	GCA	.	.		0.512	ZNF793-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458621.1	NM_001013659		A	38024278	G	A	38024278	3	1	317	1	0	0	0	0	1	0	0	0	18180	1203	42	3	221	3	ZNF793	19	38024278	Missense_Mutation	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	1754873	38024278	21104705	186	44828										
SERTAD3	29946	hgsc.bcm.edu	37	chr19	40947776	40947776	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gcagggcaggggcgggagccAggcgaagtgcagcctgcagc	20	11	0	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr19:40947776A>T	ENST00000322354.3	-	2	708	c.212T>A	c.(211-213)cTg>cAg	p.L71Q	SERTAD3_ENST00000392028.4_Missense_Mutation_p.L71Q|CTC-492K19.4_ENST00000599050.1_RNA|SERTAD3_ENST00000601217.1_5'Flank	NM_203344.2	NP_976219.1	Q9UJW9	SRTD3_HUMAN	SERTA domain containing 3	71	SERTA. {ECO:0000255|PROSITE- ProRule:PRU00396}.				negative regulation of cell growth (GO:0030308)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				kidney(1)|large_intestine(4)|lung(2)	7			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GGCGGGAGCCAGGCGAAGTGC	0.657																																					p.L71Q		Atlas-SNP	.											.	SERTAD3	21	.	0			c.T212A						.						26	22	23					19																	40947776		2203	4296	6499	SO:0001583	missense	29946	exon2			GGAGCCAGGCGAA	AF192529	CCDS12558.1	19q13.2	2008-02-05				ENSG00000167565			17931	protein-coding gene	gene with protein product	"RPA-binding trans-activator"	612125				10982866, 11331592	Standard	NM_013368		Approved	RBT1	uc002onv.4	Q9UJW9		ENST00000322354.3:c.212T>A	chr19.hg19:g.40947776A>T	ENSP00000325414:p.Leu71Gln	52.0	0.0		38.0	13.0	NM_013368	B3KQB3|Q96CQ2	Missense_Mutation	SNP	ENST00000322354.3	hg19	CCDS12558.1	.	.	.	.	.	.	.	.	.	.	A	6.459	0.452792	0.12283	.	.	ENSG00000167565	ENST00000322354;ENST00000392028	.	.	.	5.17	2.91	0.33838	.	0.665545	0.12590	N	0.455709	T	0.17195	0.0413	N	0.08118	0	0.09310	N	1	B	0.32968	0.392	B	0.30029	0.11	T	0.16482	-1.0401	9	0.21540	T	0.41	-10.9924	8.955	0.35812	0.6338:0.3662:0.0:0.0	.	71	Q9UJW9	SRTD3_HUMAN	Q	71	.	ENSP00000325414:L71Q	L	-	2	0	SERTAD3	45639616	0.789000	0.28775	0.010000	0.14722	0.904000	0.53231	1.294000	0.33365	0.783000	0.33636	0.533000	0.62120	CTG	.	.		0.657	SERTAD3-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462573.1	NM_013368		T	40947776	A	T	40947776	3	4	317	1	0	0	0	0	1	0	0	0	14137	188	7	4	382	4	SERTAD3	19	40947776	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	2923498	40947776	18181207	187	44829										
DMRTC2	63946	hgsc.bcm.edu	37	chr19	42353305	42353305	+	Frame_Shift_Del	DEL	C	C	-													0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tttctggagagccccaagggCcccctagccagccccgcacg							TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr19:42353305delC	ENST00000269945.3	+	6	787	c.736delC	c.(736-738)cccfs	p.P247fs	DMRTC2_ENST00000596827.1_Frame_Shift_Del_p.P247fs	NM_001040283.1	NP_001035373.1	Q8IXT2	DMRTD_HUMAN	DMRT-like family C2	247	Pro-rich.				male meiosis I (GO:0007141)|positive regulation of histone H3-K9 dimethylation (GO:1900111)|positive regulation of histone H3-K9 trimethylation (GO:1900114)|sex differentiation (GO:0007548)|spermatid nucleus elongation (GO:0007290)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|XY body (GO:0001741)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)	10						GCCCCAAGGGCCCCCTAGCCA	0.607																																					p.G245fs		Atlas-Indel,Pindel	.											.	DMRTC2	31	.	0			c.735delG						.						82	94	90					19																	42353305		2203	4300	6503	SO:0001589	frameshift_variant	63946	exon6			.	AJ291669	CCDS33034.1	19q13.2	2008-07-16				ENSG00000142025			13911	protein-coding gene	gene with protein product		614806				11863363	Standard	NM_001040283		Approved		uc002ors.3	Q8IXT2		ENST00000269945.3:c.736delC	chr19.hg19:g.42353305delC	ENSP00000269945:p.Pro247fs	62.0	0.0		65.0	29.0	NM_001040283	Q8N6Q2|Q96M39|Q96SD4	Frame_Shift_Del	DEL	ENST00000269945.3	hg19	CCDS33034.1																																																																																			.	.		0.607	DMRTC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463045.1	NM_001040283		-	42353305	C	-	42353305	7	5	317	1	0	1	0	1	0	0	0	0	4593	739	26	0	754	0	DMRTC2	19	42353305	Frame_Shift_Del	DEL	C	TCGA-LG-A6GG-01A-11D-A30V-10	1405529	42353305	16775678	188	44830										
ZNF233	353355	hgsc.bcm.edu	37	chr19	44778799	44778799	+	Frame_Shift_Del	DEL	G	G	-													0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ggctttagtaagagttcgttGtcttcagattcatcagagag					rs386809645|rs2884016	byFrequency	TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr19:44778799delG	ENST00000391958.2	+	5	2113	c.1986delG	c.(1984-1986)ttgfs	p.L662fs	ZNF233_ENST00000334152.1_Frame_Shift_Del_p.L644fs|ZNF233_ENST00000592581.1_3'UTR|ZNF235_ENST00000589799.1_Intron	NM_181756.2	NP_861421.2	A6NK53	ZN233_HUMAN	zinc finger protein 233	662					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(4)|skin(3)|urinary_tract(1)	20		Prostate(69;0.0435)|all_neural(266;0.226)				AGAGTTCGTTGTCTTCAGATT	0.413																																					p.L662fs		Atlas-INDEL	.											.	ZNF233	73	.	0			c.1985delT						.		,	1875,2387		595,685,851	69	77	74		,	-7.5	0	19	dbSNP_129	75	977,7273		67,843,3215	no	frameshift,frameshift	ZNF233	NM_181756.2,NM_001207005.1	,	662,1528,4066	A1A1,A1R,RR		11.8424,43.9934,22.7941	,	,	44778799	2852,9660	2203	4300	6503	SO:0001589	frameshift_variant	353355	exon5			.	AY166792	CCDS33047.1	19q13.31	2013-01-08				ENSG00000159915		"Zinc fingers, C2H2-type", "-"	30946	protein-coding gene	gene with protein product						12743021	Standard	NM_001207005		Approved	FLJ38032	uc021uvi.1	A6NK53		ENST00000391958.2:c.1986delG	chr19.hg19:g.44778799delG	ENSP00000375820:p.Leu662fs	73.0	0.0		37.0	21.0	NM_001207005	B2RN78|B2RN79|Q86WL8	Frame_Shift_Del	DEL	ENST00000391958.2	hg19	CCDS33047.1																																																																																			.	.		0.413	ZNF233-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000460737.1	NM_181756		-	44778799	G	-	44778799	7	5	317	1	0	1	0	1	0	0	0	0	17801	1368	48	0	2000	0	ZNF233	19	44778799	Frame_Shift_Del	DEL	G	TCGA-LG-A6GG-01A-11D-A30V-10	2425494	44778799	14350184	189	44831										
ZNF180	7733	hgsc.bcm.edu	37	chr19	44981527	44981527	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	aacaaggtgcgagctccggcTgaaggattttccacattcac	10	11	1	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr19:44981527T>G	ENST00000221327.4	-	5	1452	c.1171A>C	c.(1171-1173)Agc>Cgc	p.S391R	ZNF180_ENST00000592529.1_Missense_Mutation_p.S364R|ZNF180_ENST00000391956.4_Missense_Mutation_p.S366R|ZNF180_ENST00000585514.1_5'Flank|AC069278.4_ENST00000591684.1_lincRNA	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	391					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				GAGCTCCGGCTGAAGGATTTT	0.463																																					p.S391R	Esophageal Squamous(180;1353 2003 32862 46574 49854)	Atlas-SNP	.											.	ZNF180	103	.	0			c.A1171C						.						68	70	69					19																	44981527		2203	4300	6503	SO:0001583	missense	7733	exon5			TCCGGCTGAAGGA	AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"Zinc fingers, C2H2-type", "-"	12970	protein-coding gene	gene with protein product		606740	"zinc finger protein 180 (HHZ168)"				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8		ENST00000221327.4:c.1171A>C	chr19.hg19:g.44981527T>G	ENSP00000221327:p.Ser391Arg	93.0	0.0		82.0	37.0	NM_013256	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Missense_Mutation	SNP	ENST00000221327.4	hg19	CCDS12639.1	.	.	.	.	.	.	.	.	.	.	T	0.395	-0.921267	0.02396	.	.	ENSG00000167384	ENST00000221327;ENST00000391956	T;T	0.07567	3.18;3.18	5.47	0.616	0.17613	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.277746	0.25938	N	0.027321	T	0.05227	0.0139	N	0.26130	0.795	0.09310	N	0.999995	B;B;B	0.14012	0.008;0.009;0.009	B;B;B	0.11329	0.004;0.006;0.006	T	0.33240	-0.9876	10	0.44086	T	0.13	-2.6399	5.3941	0.16259	0.0959:0.0672:0.3717:0.4653	.	366;390;391	G5E9B8;Q58F03;Q9UJW8	.;.;ZN180_HUMAN	R	391;366	ENSP00000221327:S391R;ENSP00000375818:S366R	ENSP00000221327:S391R	S	-	1	0	ZNF180	49673367	0.073000	0.21202	0.802000	0.32245	0.000000	0.00434	0.849000	0.27723	-0.220000	0.09988	-2.613000	0.00159	AGC	.	.		0.463	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256		G	44981527	T	G	44981527	3	3	317	1	0	0	0	0	1	0	0	0	17763	1580	55	5	911	5	ZNF180	19	44981527	Missense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	202728	44981527	14147456	190	44832										
PTGIR	5739	hgsc.bcm.edu	37	chr19	47124692	47124692	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ctttcccacaggagcagaggGggcccttgggtccctcctcc	12	16	0	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr19:47124692G>A	ENST00000291294.2	-	3	1139	c.1006C>T	c.(1006-1008)Ccc>Tcc	p.P336S	PTGIR_ENST00000598865.1_Missense_Mutation_p.P124S|PTGIR_ENST00000594275.1_Missense_Mutation_p.P93S|PTGIR_ENST00000597185.1_Missense_Mutation_p.P65S	NM_000960.3	NP_000951.1	P43119	PI2R_HUMAN	prostaglandin I2 (prostacyclin) receptor (IP)	336					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of GTPase activity (GO:0043547)|response to lipopolysaccharide (GO:0032496)	cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	13		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000327)|all cancers(93;0.000641)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0331)	Dinoprost Tromethamine(DB01160)|Epoprostenol(DB01240)|Iloprost(DB01088)|Treprostinil(DB00374)	GGAGCAGAGGGGGCCCTTGGG	0.682																																					p.P336S		Atlas-SNP	.											.	PTGIR	31	.	0			c.C1006T						.						29	33	31					19																	47124692		2203	4300	6503	SO:0001583	missense	5739	exon3			CAGAGGGGGCCCT		CCDS12686.1	19q13.3	2012-08-08				ENSG00000160013		"GPCR / Class A : Prostanoid receptors"	9602	protein-coding gene	gene with protein product		600022				7759114	Standard	NM_000960		Approved	IP	uc002pex.3	P43119		ENST00000291294.2:c.1006C>T	chr19.hg19:g.47124692G>A	ENSP00000291294:p.Pro336Ser	146.0	0.0		104.0	49.0	NM_000960		Missense_Mutation	SNP	ENST00000291294.2	hg19	CCDS12686.1	.	.	.	.	.	.	.	.	.	.	G	16.52	3.147272	0.57151	.	.	ENSG00000160013	ENST00000291294	T	0.08458	3.09	4.91	1.34	0.21922	.	0.202762	0.31358	N	0.007797	T	0.04634	0.0126	L	0.29908	0.895	0.09310	N	1	B	0.32781	0.384	B	0.34180	0.177	T	0.36138	-0.9760	10	0.10111	T	0.7	-16.2334	4.1798	0.10369	0.2215:0.211:0.5675:0.0	.	336	P43119	PI2R_HUMAN	S	336	ENSP00000291294:P336S	ENSP00000291294:P336S	P	-	1	0	PTGIR	51816532	0.000000	0.05858	0.014000	0.15608	0.863000	0.49368	0.064000	0.14437	1.050000	0.40346	0.561000	0.74099	CCC	.	.		0.682	PTGIR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466581.1			A	47124692	G	A	47124692	3	1	317	1	0	0	0	0	1	0	0	0	12764	1232	43	3	158	3	PTGIR	19	47124692	Missense_Mutation	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	2143165	47124692	12004291	191	44833										
CACNG8	59283	hgsc.bcm.edu	37	chr19	54485674	54485674	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	agctcccgctccagcgagccGtcgccgtcgcgggacgcgtc	14	18	0	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr19:54485674G>T	ENST00000270458.2	+	4	952	c.849G>T	c.(847-849)ccG>ccT	p.P283P	MIR935_ENST00000401179.1_RNA	NM_031895.5	NP_114101	Q8WXS5	CCG8_HUMAN	calcium channel, voltage-dependent, gamma subunit 8	283	Gly-rich.				calcium ion transport (GO:0006816)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			kidney(1)|large_intestine(3)|lung(8)|urinary_tract(1)	13	all_cancers(19;0.0385)|all_epithelial(19;0.0207)|all_lung(19;0.145)|Lung NSC(19;0.168)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.162)		CCAGCGAGCCGTCGCCGTCGC	0.746																																					p.P283P		Atlas-SNP	.											.	CACNG8	29	.	0			c.G849T						.						1	2	1					19																	54485674		1088	2434	3522	SO:0001819	synonymous_variant	59283	exon4			CGAGCCGTCGCCG	AF288388	CCDS33104.1	19q13.4	2008-05-02			ENSG00000142408	ENSG00000142408		"Calcium channel subunits"	13628	protein-coding gene	gene with protein product		606900				11170751	Standard	NM_031895		Approved		uc002qcs.2	Q8WXS5	OTTHUMG00000064908	ENST00000270458.2:c.849G>T	chr19.hg19:g.54485674G>T		22.0	0.0		26.0	9.0	NM_031895	Q9BXT0|Q9BY23	Silent	SNP	ENST00000270458.2	hg19	CCDS33104.1																																																																																			.	.		0.746	CACNG8-001	KNOWN	non_ATG_start|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139361.3			T	54485674	G	T	54485674	2	4	317	1	0	0	0	0	0	0	0	1	2565	1132	40	1		1	CACNG8	19	54485674	Silent	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	7360982	54485674	4643309	192	44834										
ZNF773	374928	hgsc.bcm.edu	37	chr19	58018610	58018610	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	aacatcgaaaagttcacactGgagaaaaaccttttaagtgc	7	8	1	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr19:58018610G>C	ENST00000282292.4	+	4	1287	c.1147G>C	c.(1147-1149)Gga>Cga	p.G383R	ZNF773_ENST00000598770.1_Missense_Mutation_p.G382R|ZNF773_ENST00000593916.1_Intron|ZNF773_ENST00000599847.1_Intron	NM_198542.1	NP_940944.1	Q6PK81	ZN773_HUMAN	zinc finger protein 773	383					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	22		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0254)		AGTTCACACTGGAGAAAAACC	0.423																																					p.G383R		Atlas-SNP	.											.	ZNF773	62	.	0			c.G1147C						.						107	110	109					19																	58018610		2203	4300	6503	SO:0001583	missense	374928	exon4			CACACTGGAGAAA	BC005167	CCDS33134.1	19q13.43	2013-01-08	2006-12-15	2006-12-15		ENSG00000152439		"Zinc fingers, C2H2-type", "-"	30487	protein-coding gene	gene with protein product			"zinc finger protein 419B"	ZNF419B		12477932	Standard	NM_198542		Approved	MGC4728	uc002qox.3	Q6PK81		ENST00000282292.4:c.1147G>C	chr19.hg19:g.58018610G>C	ENSP00000282292:p.Gly383Arg	221.0	0.0		128.0	55.0	NM_198542	Q96DL8	Missense_Mutation	SNP	ENST00000282292.4	hg19	CCDS33134.1	.	.	.	.	.	.	.	.	.	.	G	14.65	2.599732	0.46318	.	.	ENSG00000152439	ENST00000282292	T	0.26223	1.75	1.09	1.09	0.20402	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.37517	0.1006	L	0.41632	1.29	0.35383	D	0.790063	D;D	0.89917	1.0;1.0	D;D	0.97110	0.99;1.0	T	0.49890	-0.8891	9	0.72032	D	0.01	.	9.7158	0.40274	0.0:0.0:1.0:0.0	.	382;383	Q6PK81-2;Q6PK81	.;ZN773_HUMAN	R	383	ENSP00000282292:G383R	ENSP00000282292:G383R	G	+	1	0	ZNF773	62710422	0.004000	0.15560	0.996000	0.52242	0.922000	0.55478	0.398000	0.20899	0.880000	0.35969	0.305000	0.20034	GGA	.	.		0.423	ZNF773-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466475.1	NM_198542		C	58018610	G	C	58018610	3	2	317	1	0	0	0	0	1	0	0	0	18161	1349	47	4	1161	4	ZNF773	19	58018610	Missense_Mutation	SNP	G	TCGA-LG-A6GG-01A-11D-A30V-10	3532936	58018610	1110373	193	44835										
CST9L	128821	hgsc.bcm.edu	37	chr20	23548859	23548859	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	gtcaccaacctgctccttccAggaattcaagatgtgcccca	7	15	2	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr20:23548859A>G	ENST00000376979.3	-	1	527	c.229T>C	c.(229-231)Tgg>Cgg	p.W77R		NM_080610.2	NP_542177.1	Q9H4G1	CST9L_HUMAN	cystatin 9-like	77						extracellular region (GO:0005576)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	8	Colorectal(13;0.0431)|Lung NSC(19;0.235)					TGCTCCTTCCAGGAATTCAAG	0.552																																					p.W77R		Atlas-SNP	.											.	CST9L	25	.	0			c.T229C						.						139	112	122					20																	23548859		2203	4300	6503	SO:0001583	missense	128821	exon1			CCTTCCAGGAATT		CCDS13157.1	20p11.21	2012-08-14	2008-03-06		ENSG00000101435	ENSG00000101435			16233	protein-coding gene	gene with protein product			"cystatin 9 (mouse)-like"			20565543	Standard	NM_080610		Approved	bA218C14.1, CTES7B	uc002wtk.4	Q9H4G1	OTTHUMG00000032073	ENST00000376979.3:c.229T>C	chr20.hg19:g.23548859A>G	ENSP00000366178:p.Trp77Arg	82.0	0.0		101.0	25.0	NM_080610	B2R5A1	Missense_Mutation	SNP	ENST00000376979.3	hg19	CCDS13157.1	.	.	.	.	.	.	.	.	.	.	A	6.704	0.498515	0.12762	.	.	ENSG00000101435	ENST00000376979	T	0.25749	1.78	1.75	0.617	0.17619	Proteinase inhibitor I25, cystatin (2);	1.252520	0.06139	N	0.672032	T	0.16769	0.0403	N	0.25992	0.78	0.09310	N	1	P	0.39181	0.663	B	0.39771	0.309	T	0.21008	-1.0258	10	0.21540	T	0.41	.	3.452	0.07502	0.7749:0.0:0.2251:0.0	.	77	Q9H4G1	CST9L_HUMAN	R	77	ENSP00000366178:W77R	ENSP00000366178:W77R	W	-	1	0	CST9L	23496859	0.000000	0.05858	0.001000	0.08648	0.065000	0.16274	-0.063000	0.11655	0.138000	0.18790	0.260000	0.18958	TGG	.	.		0.552	CST9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078338.1	NM_080610		G	23548859	A	G	23548859	3	3	317	1	0	0	0	0	1	0	0	0	3982	188	7	2	226	2	CST9L	20	23548859	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10		23548859	39476661	194	44836										
PLUNC	51297	hgsc.bcm.edu	37	chr20	31828158	31828158	+	Frame_Shift_Del	DEL	C	C	-													0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ccttggtgactgcacccattCccctggaagcctgcaaattt							TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr20:31828158delC	ENST00000354297.4	+	5	619	c.548delC	c.(547-549)tccfs	p.S183fs	BPIFA1_ENST00000375413.4_Frame_Shift_Del_p.S183fs|BPIFA1_ENST00000375422.2_Frame_Shift_Del_p.S183fs	NM_130852.2	NP_570913.1	Q9NP55	BPIA1_HUMAN	BPI fold containing family A, member 1	183					antibacterial humoral response (GO:0019731)|innate immune response (GO:0045087)|multicellular organismal water homeostasis (GO:0050891)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|regulation of liquid surface tension (GO:0050828)|regulation of sodium ion transmembrane transport (GO:1902305)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	lipid binding (GO:0008289)										TGCACCCATTCCCCTGGAAGC	0.537																																					p.S183fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.547delT						.						185	177	180					20																	31828158		2203	4300	6503	SO:0001589	frameshift_variant	51297	exon5			.	AB024937	CCDS13217.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000198183	ENSG00000198183		"BPI fold containing"	15749	protein-coding gene	gene with protein product		607412	"palate, lung and nasal epithelium carcinoma associated", "palate, lung and nasal epithelium associated"	PLUNC		11018263, 11251963, 21787333	Standard	NM_130852		Approved	LUNX, bA49G10.5, SPLUNC1	uc002wyv.3	Q9NP55	OTTHUMG00000032243	ENST00000354297.4:c.548delC	chr20.hg19:g.31828158delC	ENSP00000346251:p.Ser183fs	79.0	0.0		73.0	17.0	NM_130852	A8K9R3|E1P5M9|Q9NZT0	Frame_Shift_Del	DEL	ENST00000354297.4	hg19	CCDS13217.1																																																																																			.	.		0.537	BPIFA1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078667.2	NM_130852		-	31828158	C	-	31828158	7	5	317	1	0	1	0	1	0	0	0	0	12124	855	30	0	562	0	PLUNC	20	31828158	Frame_Shift_Del	DEL	C	TCGA-LG-A6GG-01A-11D-A30V-10	8279299	31828158	31197362	195	44837										
PTPRT	11122	hgsc.bcm.edu	37	chr20	40944529	40944529	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	caaagtagtgtagagaatcgAggctggaggcattccgatag	14	6	0	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr20:40944529A>T	ENST00000373187.1	-	12	1972	c.1973T>A	c.(1972-1974)cTc>cAc	p.L658H	PTPRT_ENST00000373193.3_Missense_Mutation_p.L658H|PTPRT_ENST00000373190.1_Missense_Mutation_p.L658H|PTPRT_ENST00000373184.1_Missense_Mutation_p.L658H|PTPRT_ENST00000373201.1_Missense_Mutation_p.L658H|PTPRT_ENST00000356100.2_Missense_Mutation_p.L658H|PTPRT_ENST00000373198.4_Missense_Mutation_p.L658H			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	658	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)			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)				TAGAGAATCGAGGCTGGAGGC	0.522																																					p.L658H		Atlas-SNP	.											.	PTPRT	372	.	0			c.T1973A						.						128	127	127					20																	40944529		2027	4166	6193	SO:0001583	missense	11122	exon12			GAATCGAGGCTGG	AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.1973T>A	chr20.hg19:g.40944529A>T	ENSP00000362283:p.Leu658His	172.0	0.0		180.0	63.0	NM_007050	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Missense_Mutation	SNP	ENST00000373187.1	hg19	CCDS42874.1	.	.	.	.	.	.	.	.	.	.	A	16.54	3.152474	0.57259	.	.	ENSG00000196090	ENST00000373190;ENST00000373187;ENST00000373193;ENST00000356100;ENST00000373198;ENST00000373184;ENST00000373201	T;T;T;T;T;T;T	0.36699	1.29;1.28;1.28;1.24;1.24;1.29;1.28	5.57	5.57	0.84162	.	0.138558	0.49305	D	0.000155	T	0.56688	0.2002	M	0.72118	2.19	0.54753	D	0.999988	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.984	T	0.53620	-0.8413	10	0.13853	T	0.58	.	15.7373	0.77856	1.0:0.0:0.0:0.0	.	658;658	O14522-1;O14522	.;PTPRT_HUMAN	H	658	ENSP00000362286:L658H;ENSP00000362283:L658H;ENSP00000362289:L658H;ENSP00000348408:L658H;ENSP00000362294:L658H;ENSP00000362280:L658H;ENSP00000362297:L658H	ENSP00000348408:L658H	L	-	2	0	PTPRT	40377943	0.991000	0.36638	0.847000	0.33407	0.936000	0.57629	4.056000	0.57448	2.120000	0.65058	0.460000	0.39030	CTC	.	.		0.522	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			T	40944529	A	T	40944529	3	4	317	1	0	0	0	0	1	0	0	0	12827	304	11	4	2493	4	PTPRT	20	40944529	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	9116371	40944529	22080991	196	44838										
TUBB1	81027	hgsc.bcm.edu	37	chr20	57599165	57599165	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ctatggggatctcaaccaccTagtgtccttgaccatgagcg	10	12	1	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr20:57599165T>A	ENST00000217133.1	+	4	952	c.683T>A	c.(682-684)cTa>cAa	p.L228Q		NM_030773.3	NP_110400.1	Q9H4B7	TBB1_HUMAN	tubulin, beta 1 class VI	228					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|protein polymerization (GO:0051258)|spindle assembly (GO:0051225)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|skin(2)	16	all_lung(29;0.00711)		Colorectal(105;0.109)		Cabazitaxel(DB06772)|Colchicine(DB01394)|Docetaxel(DB01248)|Paclitaxel(DB01229)|Vindesine(DB00309)	CTCAACCACCTAGTGTCCTTG	0.572																																					p.L228Q		Atlas-SNP	.											.	TUBB1	42	.	0			c.T683A						.						136	117	124					20																	57599165		2203	4300	6503	SO:0001583	missense	81027	exon4			ACCACCTAGTGTC	AJ292757	CCDS13475.1	20q13.32	2014-09-17	2011-10-10		ENSG00000101162	ENSG00000101162		"Tubulins"	16257	protein-coding gene	gene with protein product	"class VI beta-tubulin"	612901	"tubulin, beta 1"				Standard	NM_030773		Approved	dJ543J19.4	uc002yak.3	Q9H4B7	OTTHUMG00000032860	ENST00000217133.1:c.683T>A	chr20.hg19:g.57599165T>A	ENSP00000217133:p.Leu228Gln	85.0	0.0		101.0	27.0	NM_030773		Missense_Mutation	SNP	ENST00000217133.1	hg19	CCDS13475.1	.	.	.	.	.	.	.	.	.	.	T	19.29	3.798708	0.70567	.	.	ENSG00000101162	ENST00000217133	T	0.72051	-0.62	5.19	5.19	0.71726	Tubulin/FtsZ, GTPase domain (3);	0.000000	0.85682	D	0.000000	D	0.89347	0.6689	H	0.97659	4.05	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.92886	0.6327	10	0.87932	D	0	.	14.1922	0.65646	0.0:0.0:0.0:1.0	.	228	Q9H4B7	TBB1_HUMAN	Q	228	ENSP00000217133:L228Q	ENSP00000217133:L228Q	L	+	2	0	TUBB1	57032560	1.000000	0.71417	1.000000	0.80357	0.621000	0.37620	8.040000	0.89188	1.966000	0.57179	0.459000	0.35465	CTA	.	.		0.572	TUBB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079903.1	NM_030773		A	57599165	T	A	57599165	3	1	317	1	0	0	0	0	1	0	0	0	16768	1522	53	4	697	4	TUBB1	20	57599165	Missense_Mutation	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10	16654636	57599165	5426355	197	44839										
C21orf58	54058	hgsc.bcm.edu	37	chr21	47722400	47722400	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tgctgggggctaagcctaccTgcagggctgggggcagggcc	19	11	0	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr21:47722400T>A	ENST00000291691.7	-	7	1948	c.812A>T	c.(811-813)cAg>cTg	p.Q271L	C21orf58_ENST00000397682.3_Splice_Site_p.Q165L|C21orf58_ENST00000397683.1_Splice_Site_p.Q165L|C21orf58_ENST00000397680.1_Splice_Site_p.Q165L|C21orf58_ENST00000397679.1_Splice_Site_p.Q165L|C21orf58_ENST00000472607.1_5'UTR	NM_058180.3	NP_478060.2	P58505	CU058_HUMAN	chromosome 21 open reading frame 58	271										breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(1)|pancreas(1)	9	Breast(49;0.112)			Colorectal(79;0.239)		TAAGCCTACCTGCAGGGCTGG	0.572																																					p.Q271L		Atlas-SNP	.											.	C21orf58	25	.	0			c.A812T						.						25	23	24					21																	47722400		2203	4299	6502	SO:0001630	splice_region_variant	54058	exon7			CCTACCTGCAGGG		CCDS13735.1, CCDS68229.1	21q22.3	2008-07-07			ENSG00000160298	ENSG00000160298			1300	protein-coding gene	gene with protein product							Standard	XM_005261149		Approved		uc002zjf.3	P58505	OTTHUMG00000090634	ENST00000291691.7:c.813+1A>T	chr21.hg19:g.47722400T>A		163.0	0.0		81.0	57.0	NM_058180	B3KPI1	Missense_Mutation	SNP	ENST00000291691.7	hg19	CCDS13735.1	.	.	.	.	.	.	.	.	.	.	T	10.88	1.476108	0.26511	.	.	ENSG00000160298	ENST00000397683;ENST00000417060;ENST00000397682;ENST00000291691;ENST00000397679;ENST00000397680	T;T;T;T;T;T	0.46819	0.86;0.87;0.86;0.86;0.86;0.86	3.8	1.36	0.22044	.	1.397300	0.04488	N	0.378914	T	0.61286	0.2335	L	0.54323	1.7	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.78314	0.991;0.991;0.991	T	0.52034	-0.8629	10	0.41790	T	0.15	4.3196	5.1767	0.15139	0.0:0.1025:0.1822:0.7153	.	271;165;271	P58505;Q8N7N9;P58505-2	CU058_HUMAN;.;.	L	165;233;165;271;165;165	ENSP00000380799:Q165L;ENSP00000402356:Q233L;ENSP00000380798:Q165L;ENSP00000291691:Q271L;ENSP00000380796:Q165L;ENSP00000380797:Q165L	ENSP00000291691:Q271L	Q	-	2	0	C21orf58	46546828	1.000000	0.71417	0.973000	0.42090	0.065000	0.16274	4.404000	0.59735	0.284000	0.22305	0.379000	0.24179	CAG	.	.		0.572	C21orf58-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207283.1	NM_058180	Missense_Mutation	A	47722400	T	A	47722400	5	1	317	1	0	0	0	0	0	0	1	0	2131	1594	55	4	164	4	C21orf58	21	47722400	Splice_Site	SNP	T	TCGA-LG-A6GG-01A-11D-A30V-10		47722400	407495	198	44840										
TCN2	6948	hgsc.bcm.edu	37	chr22	31006953	31006953	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tggagcacttgaaccccagcAtctatgtgggcctacgcctc	10	14	1	1	rs556464879		TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chr22:31006953A>G	ENST00000215838.3	+	2	654	c.160A>G	c.(160-162)Atc>Gtc	p.I54V	TCN2_ENST00000405742.3_Missense_Mutation_p.I54V|TCN2_ENST00000407817.3_Missense_Mutation_p.I54V			P20062	TCO2_HUMAN	transcobalamin II	54					cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|cobalt ion transport (GO:0006824)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	cobalamin binding (GO:0031419)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|prostate(2)|urinary_tract(1)	22					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GAACCCCAGCATCTATGTGGG	0.557																																					p.I54V		Atlas-SNP	.											.	TCN2	44	.	0			c.A160G						.						196	183	187					22																	31006953		2203	4300	6503	SO:0001583	missense	6948	exon2			CCCAGCATCTATG		CCDS13881.1, CCDS54519.1	22q12.2	2014-09-17	2010-05-11		ENSG00000185339	ENSG00000185339			11653	protein-coding gene	gene with protein product	"macrocytic anemia"	613441	"transcobalamin II; macrocytic anemia"			1708393, 7742531	Standard	NM_000355		Approved	D22S676, D22S750, TC2	uc003aip.2	P20062	OTTHUMG00000151095	ENST00000215838.3:c.160A>G	chr22.hg19:g.31006953A>G	ENSP00000215838:p.Ile54Val	112.0	0.0		76.0	29.0	NM_001184726	Q96FD4|Q9BVI8|Q9UCI5|Q9UCI6|Q9UDM0	Missense_Mutation	SNP	ENST00000215838.3	hg19	CCDS13881.1	.	.	.	.	.	.	.	.	.	.	A	11.99	1.802737	0.31869	.	.	ENSG00000185339	ENST00000215838;ENST00000423350;ENST00000405742;ENST00000407817	T;T;T;T	0.41400	1.39;1.39;1.39;1.0	6.16	-1.24	0.09435	.	0.312746	0.39407	N	0.001362	T	0.19927	0.0479	N	0.17723	0.515	0.80722	D	1	B;B;B	0.12630	0.006;0.003;0.003	B;B;B	0.20184	0.028;0.021;0.021	T	0.17228	-1.0376	10	0.10377	T	0.69	-18.156	6.2067	0.20606	0.3659:0.3603:0.2738:0.0	.	54;54;54	Q96FD4;B5MBX2;P20062	.;.;TCO2_HUMAN	V	54	ENSP00000215838:I54V;ENSP00000411529:I54V;ENSP00000385914:I54V;ENSP00000384914:I54V	ENSP00000215838:I54V	I	+	1	0	TCN2	29336953	0.860000	0.29831	0.965000	0.40720	0.966000	0.64601	-0.187000	0.09656	-0.629000	0.05575	-0.280000	0.10049	ATC	.	.		0.557	TCN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321282.2	NM_000355		G	31006953	A	G	31006953	3	3	317	1	0	0	0	0	1	0	0	0	15722	217	8	2	166	2	TCN2	22	31006953	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10		31006953	20297613	199	44841										
PRDX4	10549	hgsc.bcm.edu	37	chrX	23693213	23693213	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ctgttgattcacagtttaccCatttggcctggtcagtatct	8	10	3	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chrX:23693213C>G	ENST00000379341.4	+	3	591	c.466C>G	c.(466-468)Cat>Gat	p.H156D	PRDX4_ENST00000495599.1_3'UTR|PRDX4_ENST00000379331.3_Missense_Mutation_p.H156D	NM_006406.1	NP_006397.1	Q13162	PRDX4_HUMAN	peroxiredoxin 4	156	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				4-hydroxyproline metabolic process (GO:0019471)|cell redox homeostasis (GO:0045454)|extracellular matrix organization (GO:0030198)|I-kappaB phosphorylation (GO:0007252)|male gonad development (GO:0008584)|negative regulation of male germ cell proliferation (GO:2000255)|protein maturation by protein folding (GO:0022417)|reactive oxygen species metabolic process (GO:0072593)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	thioredoxin peroxidase activity (GO:0008379)			lung(6)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	9						ACAGTTTACCCATTTGGCCTG	0.348																																					p.H156D		Atlas-SNP	.											.	PRDX4	17	.	0			c.C466G						.						149	129	136					X																	23693213		2203	4300	6503	SO:0001583	missense	10549	exon3			TTTACCCATTTGG	U25182	CCDS14206.1	Xp22.11	2012-09-20			ENSG00000123131	ENSG00000123131			17169	protein-coding gene	gene with protein product		300927				9388242	Standard	XM_005274438		Approved	AOE37-2	uc004dam.3	Q13162	OTTHUMG00000021253	ENST00000379341.4:c.466C>G	chrX.hg19:g.23693213C>G	ENSP00000368646:p.His156Asp	695.0	0.0		577.0	228.0	NM_006406	Q6FHT3	Missense_Mutation	SNP	ENST00000379341.4	hg19	CCDS14206.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.5|25.5	4.648807|4.648807	0.87958|0.87958	.|.	.|.	ENSG00000123131|ENSG00000123131	ENST00000379349;ENST00000379341;ENST00000379331|ENST00000439422	T;T;T|.	0.19532|.	2.14;2.14;2.14|.	5.84|5.84	5.84|5.84	0.93424|0.93424	Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant (1);Thioredoxin-like fold (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.92632|0.92632	0.7659|0.7659	H|H	0.99900|0.99900	4.915|4.915	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.85130|.	0.997|.	D|D	0.96221|0.96221	0.9160|0.9160	10|5	0.87932|.	D|.	0|.	-4.3105|-4.3105	18.7138|18.7138	0.91668|0.91668	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	156|.	Q13162|.	PRDX4_HUMAN|.	D|R	142;156;156|33	ENSP00000368654:H142D;ENSP00000368646:H156D;ENSP00000368635:H156D|.	ENSP00000368635:H156D|.	H|P	+|+	1|2	0|0	PRDX4|PRDX4	23603134|23603134	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	7.485000|7.485000	0.81204|0.81204	2.463000|2.463000	0.83235|0.83235	0.594000|0.594000	0.82650|0.82650	CAT|CCA	.	.		0.348	PRDX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056049.1	NM_006406		G	23693213	C	G	23693213	3	3	317	1	0	0	0	0	1	0	0	0	12479	594	21	4	476	4	PRDX4	23	23693213	Missense_Mutation	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10		23693213	131577347	200	44842										
PFKFB1	5207	hgsc.bcm.edu	37	chrX	54982655	54982655	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	ttctctttagaaagtcttccAgaaccttttcccggtcacag	6	12	3	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chrX:54982655A>C	ENST00000375006.3	-	7	639	c.569T>G	c.(568-570)cTg>cGg	p.L190R	PFKFB1_ENST00000374992.2_Intron|PFKFB1_ENST00000545676.1_Missense_Mutation_p.L125R	NM_002625.2	NP_002616.2	P16118	F261_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1	190	6-phosphofructo-2-kinase.				carbohydrate metabolic process (GO:0005975)|dephosphorylation (GO:0016311)|energy reserve metabolic process (GO:0006112)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|intracellular signal transduction (GO:0035556)|organ regeneration (GO:0031100)|positive regulation of glucokinase activity (GO:0033133)|response to cAMP (GO:0051591)|response to glucagon (GO:0033762)|response to glucocorticoid (GO:0051384)|response to insulin (GO:0032868)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase complex (GO:0043540)|cytosol (GO:0005829)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)|fructose-6-phosphate binding (GO:0070095)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(11)|ovary(1)	24						AAAGTCTTCCAGAACCTTTTC	0.483																																					p.L190R		Atlas-SNP	.											.	PFKFB1	64	.	0			c.T569G						.						97	83	87					X																	54982655		2203	4300	6503	SO:0001583	missense	5207	exon7			TCTTCCAGAACCT		CCDS14364.1, CCDS65273.1	Xp11.21	2012-07-13			ENSG00000158571	ENSG00000158571	2.7.1.105, 3.1.3.46		8872	protein-coding gene	gene with protein product		311790		PFRX		9119406	Standard	NM_002625		Approved		uc004dty.2	P16118	OTTHUMG00000021643	ENST00000375006.3:c.569T>G	chrX.hg19:g.54982655A>C	ENSP00000364145:p.Leu190Arg	120.0	0.0		78.0	9.0	NM_002625	B2RA88|B4DUN5|Q5JXS5|Q99951	Missense_Mutation	SNP	ENST00000375006.3	hg19	CCDS14364.1	.	.	.	.	.	.	.	.	.	.	A	14.00	2.405529	0.42715	.	.	ENSG00000158571	ENST00000375006;ENST00000545676	.	.	.	4.65	4.65	0.58169	6-phosphofructo-2-kinase (1);	0.197023	0.42964	D	0.000636	T	0.61726	0.2370	M	0.75150	2.29	0.80722	D	1	B;B	0.29115	0.233;0.06	B;B	0.28849	0.095;0.071	T	0.62369	-0.6869	9	0.38643	T	0.18	-8.3604	12.6988	0.57020	1.0:0.0:0.0:0.0	.	125;190	B4DUN5;P16118	.;F261_HUMAN	R	190;125	.	ENSP00000364145:L190R	L	-	2	0	PFKFB1	54999380	0.998000	0.40836	0.983000	0.44433	0.978000	0.69477	7.304000	0.78882	1.800000	0.52685	0.486000	0.48141	CTG	.	.		0.483	PFKFB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056847.1			C	54982655	A	C	54982655	3	2	317	1	0	0	0	0	1	0	0	0	11769	188	7	5	878	5	PFKFB1	23	54982655	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	31289442	54982655	100287905	201	44843										
DIAPH2	1730	hgsc.bcm.edu	37	chrX	95940062	95940062	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	acagggccggagaaagatggAgcagcccggggcggcggcgt	20	10	0	2			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chrX:95940062A>C	ENST00000324765.8	+	1	352	c.5A>C	c.(4-6)gAg>gCg	p.E2A	DIAPH2_ENST00000373061.3_Missense_Mutation_p.E2A|DIAPH2_ENST00000373054.4_Missense_Mutation_p.E2A|DIAPH2_ENST00000373049.4_Missense_Mutation_p.E2A|DIAPH2_ENST00000355827.4_Missense_Mutation_p.E2A			O60879	DIAP2_HUMAN	diaphanous-related formin 2	2					actin filament polymerization (GO:0030041)|cytokinesis (GO:0000910)|female gamete generation (GO:0007292)|multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)	endosome (GO:0005768)	receptor binding (GO:0005102)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	51						AGAAAGATGGAGCAGCCCGGG	0.711																																					p.E2A		Atlas-SNP	.											.	DIAPH2	148	.	0			c.A5C						.						11	14	13					X																	95940062		2022	3928	5950	SO:0001583	missense	1730	exon1			AGATGGAGCAGCC	Y15909	CCDS14467.1, CCDS14468.1	Xq22	2013-05-24	2013-05-24		ENSG00000147202	ENSG00000147202			2877	protein-coding gene	gene with protein product		300108	"diaphanous (Drosophila, homolog) 2", "diaphanous homolog 2 (Drosophila)"			9360932	Standard	NM_006729		Approved	POF, DIA, POF2, DIA2	uc004efu.4	O60879	OTTHUMG00000022689	ENST00000324765.8:c.5A>C	chrX.hg19:g.95940062A>C	ENSP00000321348:p.Glu2Ala	217.0	0.0		166.0	73.0	NM_007309	A6NG19|O60878|Q8WX06|Q8WX48|Q9UJL2	Missense_Mutation	SNP	ENST00000324765.8	hg19	CCDS14467.1	.	.	.	.	.	.	.	.	.	.	A	14.64	2.595429	0.46318	.	.	ENSG00000147202	ENST00000373061;ENST00000373054;ENST00000355827;ENST00000373049;ENST00000324765;ENST00000537885	D;D;D;D;D	0.82433	-1.55;-1.61;-1.5;-1.5;-1.55	3.63	3.63	0.41609	.	0.653709	0.12306	U	0.480680	D	0.83294	0.5223	N	0.22421	0.69	0.29630	N	0.845499	P;D;P	0.67145	0.956;0.996;0.88	P;D;P	0.73708	0.899;0.981;0.636	T	0.75671	-0.3237	10	0.87932	D	0	.	7.9505	0.30012	1.0:0.0:0.0:0.0	.	2;2;2	O60879;O60879-2;B7ZLJ0	DIAP2_HUMAN;.;.	A	2	ENSP00000362152:E2A;ENSP00000362145:E2A;ENSP00000348082:E2A;ENSP00000362140:E2A;ENSP00000321348:E2A	ENSP00000321348:E2A	E	+	2	0	DIAPH2	95826718	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.323000	0.52014	1.464000	0.47987	0.381000	0.24937	GAG	.	.		0.711	DIAPH2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058871.2	NM_006729, NM_007309		C	95940062	A	C	95940062	3	2	317	1	0	0	0	0	1	0	0	0	4521	304	11	5	7	5	DIAPH2	23	95940062	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	40957407	95940062	59330498	202	44844										
MAGEC2	51438	hgsc.bcm.edu	37	chrX	141291161	141291161	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	tgtgtttgcaaacacacagaAgtggtcagggcccacttcta	10	10	2	1			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chrX:141291161A>T	ENST00000247452.3	-	3	960	c.613T>A	c.(613-615)Ttc>Atc	p.F205I		NM_016249.3	NP_057333.1	Q9UBF1	MAGC2_HUMAN	melanoma antigen family C, 2	205	Interaction with TRIM28.|MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				cellular protein catabolic process (GO:0044257)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin protein ligase binding (GO:0031625)			NS(2)|breast(3)|endometrium(3)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)	47	Acute lymphoblastic leukemia(192;6.56e-05)					AACACACAGAAGTGGTCAGGG	0.478										HNSCC(46;0.14)																											p.F205I		Atlas-SNP	.											.	MAGEC2	102	.	0			c.T613A						.						111	104	106					X																	141291161		2203	4300	6503	SO:0001583	missense	51438	exon3			CACAGAAGTGGTC	AF116195	CCDS14678.1	Xq27	2009-03-25	2004-06-08	2004-06-09	ENSG00000046774	ENSG00000046774			13574	protein-coding gene	gene with protein product	"cancer/testis antigen 10"	300468	"melanoma antigen, family E, 1, cancer/testis specific"	MAGEE1		10699956	Standard	NM_016249		Approved	CT10, MAGE-C2	uc004fbu.2	Q9UBF1	OTTHUMG00000022574	ENST00000247452.3:c.613T>A	chrX.hg19:g.141291161A>T	ENSP00000354660:p.Phe205Ile	171.0	0.0		137.0	60.0	NM_016249	Q5JZ00|Q96D45|Q9P1M6|Q9P1M7	Missense_Mutation	SNP	ENST00000247452.3	hg19	CCDS14678.1	.	.	.	.	.	.	.	.	.	.	-	7.306	0.613952	0.14066	.	.	ENSG00000046774	ENST00000247452	T	0.04454	3.62	0.988	0.988	0.19796	.	2.722080	0.02290	U	0.070170	T	0.01940	0.0061	N	0.01219	-0.95	0.09310	N	1	B	0.22003	0.063	B	0.20955	0.032	T	0.39440	-0.9614	10	0.16896	T	0.51	.	3.916	0.09224	1.0:0.0:0.0:0.0	.	205	Q9UBF1	MAGC2_HUMAN	I	205	ENSP00000354660:F205I	ENSP00000354660:F205I	F	-	1	0	MAGEC2	141118827	0.000000	0.05858	0.010000	0.14722	0.091000	0.18340	-0.355000	0.07671	0.635000	0.30488	0.235000	0.17854	TTC	.	.		0.478	MAGEC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058611.1	NM_016249		T	141291161	A	T	141291161	3	4	317	1	0	0	0	0	1	0	0	0	9190	72	3	4	512	4	MAGEC2	23	141291161	Missense_Mutation	SNP	A	TCGA-LG-A6GG-01A-11D-A30V-10	45351099	141291161	13979399	203	44845										
GPR50	9248	hgsc.bcm.edu	37	chrX	150349506	150349506	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0344827586206897	7	1	0.98394495412844	0.98394495412844	0.98394495412844	0.361455108359133	1	0	cactggccaccatgtctctgCtggcagccactccaagtctg	9	16	2	0			TCGA-LG-A6GG-01A-11D-A30V-10	TCGA-LG-A6GG-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85af03fa-9e34-4b29-8897-d39a1b1773e2	b9ec4d89-18c3-4d18-b0cc-43cb9a086ec5	g.chrX:150349506C>A	ENST00000218316.3	+	2	1520	c.1451C>A	c.(1450-1452)gCt>gAt	p.A484D	AF003625.3_ENST00000602313.1_lincRNA	NM_004224.3	NP_004215.2	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	484	Pro-rich.				cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|identical protein binding (GO:0042802)|melatonin receptor activity (GO:0008502)			breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	38	Acute lymphoblastic leukemia(192;6.56e-05)					CATGTCTCTGCTGGCAGCCAC	0.567																																					p.A484D		Atlas-SNP	.											.	GPR50	195	.	0			c.C1451A						.						135	148	144					X																	150349506		2101	4205	6306	SO:0001583	missense	9248	exon2			TCTCTGCTGGCAG	U52219	CCDS44012.1	Xq28	2012-08-21			ENSG00000102195	ENSG00000102195		"GPCR / Class A : Orphans"	4506	protein-coding gene	gene with protein product		300207				9933574, 18400093	Standard	NM_004224		Approved	H9, Mel1c	uc010ntg.2	Q13585	OTTHUMG00000024166	ENST00000218316.3:c.1451C>A	chrX.hg19:g.150349506C>A	ENSP00000218316:p.Ala484Asp	81.0	0.0		57.0	22.0	NM_004224	Q0VGG3|Q3ZAR0	Missense_Mutation	SNP	ENST00000218316.3	hg19	CCDS44012.1	.	.	.	.	.	.	.	.	.	.	C	5.341	0.248297	0.10130	.	.	ENSG00000102195	ENST00000218316	T	0.75260	-0.92	3.32	0.578	0.17391	.	0.951679	0.08587	N	0.923590	T	0.53594	0.1806	N	0.19112	0.55	0.09310	N	1	P	0.44877	0.845	B	0.33750	0.169	T	0.45571	-0.9252	10	0.87932	D	0	-0.8327	6.7161	0.23304	0.0:0.6358:0.0:0.3642	.	484	Q13585	MTR1L_HUMAN	D	484	ENSP00000218316:A484D	ENSP00000218316:A484D	A	+	2	0	GPR50	150100164	0.000000	0.05858	0.000000	0.03702	0.150000	0.21749	0.417000	0.21214	0.000000	0.14550	0.529000	0.55759	GCT	.	.		0.567	GPR50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060874.1	NM_004224		A	150349506	C	A	150349506	3	1	317	1	0	0	0	0	1	0	0	0	6705	797	28	3	1457	3	GPR50	23	150349506	Missense_Mutation	SNP	C	TCGA-LG-A6GG-01A-11D-A30V-10	9058345	150349506	4921054	204	44846										
KIAA0754	643314	hgsc.bcm.edu	37	chr1	39876450	39876450	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	ttgcaagagaagaaggagtcCagttctgcattaacagaaag	11	6	1	3			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr1:39876450C>T	ENST00000530275.1	+	1	300	c.105C>T	c.(103-105)tcC>tcT	p.S35S	MACF1_ENST00000317713.7_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000372915.3_Intron|MACF1_ENST00000289893.4_Intron|MACF1_ENST00000564288.1_Intron|MACF1_ENST00000545844.1_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	35	13 X 13 AA approximate tandem repeat of P-T-S-P-A-A-A-V-P-T-P-E-E.									central_nervous_system(1)|large_intestine(6)|skin(1)	8	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			AGAAGGAGTCCAGTTCTGCAT	0.458																																					p.S171S		Atlas-SNP	.											.	KIAA0754	93	.	0			c.C513T						.						50	50	50					1																	39876450		1886	4108	5994	SO:0001819	synonymous_variant	643314	exon1			GGAGTCCAGTTCT			1p34.2	2009-07-09				ENSG00000255103			29111	protein-coding gene	gene with protein product						9872452	Standard	NM_015038		Approved		uc009vvt.1	O94854		ENST00000530275.1:c.105C>T	chr1.hg19:g.39876450C>T		241.0	1.0		159.0	109.0	NM_015038	E9PMC2|Q6ZSB2	Silent	SNP	ENST00000530275.1	hg19																																																																																				.	.		0.458	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1	NM_015038		T	39876450	C	T	39876450	2	4	318	1	0	0	0	0	0	0	0	1	8201	581	21	3		3	KIAA0754	1	39876450	Silent	SNP	C	TCGA-LG-A9QC-01A-11D-A36X-10		39876450	209374171	1	44847										
CEPT1	10390	hgsc.bcm.edu	37	chr1	111702018	111702018	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	acaggcacctctgtgggcatAtattgcttgtgcctgtggcc	12	11	1	0			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr1:111702018A>G	ENST00000545121.1	+	3	564	c.356A>G	c.(355-357)tAt>tGt	p.Y119C	CEPT1_ENST00000357172.4_Missense_Mutation_p.Y119C	NM_001007794.1	NP_001007795.1	Q9Y6K0	CEPT1_HUMAN	choline/ethanolamine phosphotransferase 1	119					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	diacylglycerol cholinephosphotransferase activity (GO:0004142)|ethanolaminephosphotransferase activity (GO:0004307)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)	8		all_cancers(81;2.27e-05)|all_epithelial(167;7.36e-06)|all_lung(203;0.00018)|Lung NSC(277;0.000359)		Lung(183;0.0173)|Colorectal(144;0.0375)|all cancers(265;0.0701)|LUSC - Lung squamous cell carcinoma(189;0.0888)|Epithelial(280;0.103)|COAD - Colon adenocarcinoma(174;0.141)	Choline(DB00122)	CTGTGGGCATATATTGCTTGT	0.408																																					p.Y119C		Atlas-SNP	.											.	CEPT1	25	.	0			c.A356G						.						181	182	181					1																	111702018		2203	4300	6503	SO:0001583	missense	10390	exon3			GGGCATATATTGC	AF068302	CCDS830.1	1p13	2010-07-08			ENSG00000134255	ENSG00000134255	2.7.8.1, 2.7.8.2		24289	protein-coding gene	gene with protein product						10191259, 12216837	Standard	XM_005270353		Approved		uc001eah.1	Q9Y6K0	OTTHUMG00000012357	ENST00000545121.1:c.356A>G	chr1.hg19:g.111702018A>G	ENSP00000441980:p.Tyr119Cys	82.0	0.0		52.0	4.0	NM_006090	Q69YJ9|Q9P0Y8	Missense_Mutation	SNP	ENST00000545121.1	hg19	CCDS830.1	.	.	.	.	.	.	.	.	.	.	A	18.44	3.623556	0.66901	.	.	ENSG00000134255	ENST00000545121;ENST00000357172	T;T	0.43294	0.95;0.95	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.52338	0.1728	M	0.67625	2.065	0.80722	D	1	D;B	0.89917	1.0;0.238	D;B	0.79108	0.992;0.316	T	0.55842	-0.8077	10	0.49607	T	0.09	-38.8014	13.131	0.59382	1.0:0.0:0.0:0.0	.	119;119	Q9Y6K0;B3KN25	CEPT1_HUMAN;.	C	119	ENSP00000441980:Y119C;ENSP00000349696:Y119C	ENSP00000349696:Y119C	Y	+	2	0	CEPT1	111503541	1.000000	0.71417	0.976000	0.42696	0.996000	0.88848	5.944000	0.70219	1.983000	0.57843	0.533000	0.62120	TAT	.	.		0.408	CEPT1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034462.2	NM_006090		G	111702018	A	G	111702018	3	3	318	1	0	0	0	0	1	0	0	0	3266	449	16	2	362	2	CEPT1	1	111702018	Missense_Mutation	SNP	A	TCGA-LG-A9QC-01A-11D-A36X-10	71825568	111702018	137548603	2	44848										
ZNF687	57592	hgsc.bcm.edu	37	chr1	151259173	151259173	+	Frame_Shift_Del	DEL	G	G	-													0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	gccctgaaccttccctcccaGgaactccccactctcctgct							TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr1:151259173delG	ENST00000368879.2	+	2	504	c.406delG	c.(406-408)ggafs	p.G136fs		NM_020832.1	NP_065883.1	Q8N1G0	ZN687_HUMAN	zinc finger protein 687	136	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(2)	32	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			TTCCCTCCCAGGAACTCCCCA	0.577																																					p.P135fs		Atlas-INDEL	.											.	ZNF687	94	.	0			c.405delA						.						73	77	75					1																	151259173		2203	4300	6503	SO:0001589	frameshift_variant	57592	exon2			.		CCDS992.1	1q21.2	2008-05-02			ENSG00000143373	ENSG00000143373			29277	protein-coding gene	gene with protein product		610568				10718198	Standard	NM_020832		Approved	KIAA1441	uc001exq.3	Q8N1G0	OTTHUMG00000012347	ENST00000368879.2:c.406delG	chr1.hg19:g.151259173delG	ENSP00000357874:p.Gly136fs	72.0	0.0		99.0	32.0	NM_020832	D3DV17|Q68DQ8|Q9H937|Q9P2A7	Frame_Shift_Del	DEL	ENST00000368879.2	hg19																																																																																				.	.		0.577	ZNF687-201	KNOWN	basic	protein_coding	protein_coding		NM_020832		-	151259173	G	-	151259173	7	5	318	1	0	1	0	1	0	0	0	0	18107	1001	35	0	408	0	ZNF687	1	151259173	Frame_Shift_Del	DEL	G	TCGA-LG-A9QC-01A-11D-A36X-10	39557155	151259173	97991448	3	44849										
KCNN3	3782	hgsc.bcm.edu	37	chr1	154842253	154842253	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	gctgctgctgaagctgcggaGgctgaggctgcagcgagggt	19	9	0	2			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr1:154842253G>T	ENST00000271915.4	-	1	503	c.188C>A	c.(187-189)cCt>cAt	p.P63H	KCNN3_ENST00000358505.2_5'Flank	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	63	Gln-rich.|Pro-rich.				potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	aagctgcggaggctgaggctg	0.697																																					p.P63H		Atlas-SNP	.											.	KCNN3	141	.	0			c.C188A						.						6	4	5					1																	154842253		1984	3925	5909	SO:0001583	missense	3782	exon1			TGCGGAGGCTGAG	AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.188C>A	chr1.hg19:g.154842253G>T	ENSP00000271915:p.Pro63His	56.0	0.0		105.0	15.0	NM_001204087	B1ANX0|O43517|Q86VF9|Q8WXG7	Missense_Mutation	SNP	ENST00000271915.4	hg19	CCDS30880.1	.	.	.	.	.	.	.	.	.	.	g	11.14	1.552427	0.27739	.	.	ENSG00000143603	ENST00000271915;ENST00000539103	T	0.56275	0.47	5.07	3.18	0.36537	.	1.727610	0.03258	N	0.182822	T	0.18551	0.0445	N	0.08118	0	0.80722	D	1	.	.	.	.	.	.	T	0.11372	-1.0590	8	0.33141	T	0.24	-4.1487	6.4327	0.21807	0.0918:0.0:0.7284:0.1798	.	.	.	.	H	63;158	ENSP00000271915:P63H	ENSP00000271915:P63H	P	-	2	0	KCNN3	153108877	0.863000	0.29885	1.000000	0.80357	0.998000	0.95712	1.873000	0.39558	0.823000	0.34589	0.563000	0.77884	CCT	.	.		0.697	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249		T	154842253	G	T	154842253	3	4	318	1	0	0	0	0	1	0	0	0	8089	1000	35	3	2061	3	KCNN3	1	154842253	Missense_Mutation	SNP	G	TCGA-LG-A9QC-01A-11D-A36X-10	3583080	154842253	94408368	4	44850										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228509374	228509374	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	ctgaccgatgggcggcaccaTcacatcgaccagcttgggga	13	13	1	1			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr1:228509374T>A	ENST00000422127.1	+	55	14876	c.14832T>A	c.(14830-14832)caT>caA	p.H4944Q	OBSCN_ENST00000366707.4_Missense_Mutation_p.H2578Q|OBSCN_ENST00000570156.2_Missense_Mutation_p.H5901Q|OBSCN_ENST00000284548.11_Missense_Mutation_p.H4944Q|OBSCN_ENST00000366709.4_Missense_Mutation_p.H2063Q	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4944	Ig-like 48.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GGCGGCACCATCACATCGACC	0.622																																					p.H5901Q		Atlas-SNP	.											.	OBSCN	2142	.	0			c.T17703A						.						57	61	59					1																	228509374		2176	4269	6445	SO:0001583	missense	84033	exon66			GCACCATCACATC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.14832T>A	chr1.hg19:g.228509374T>A	ENSP00000409493:p.His4944Gln	80.0	0.0		114.0	36.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.195810	0.78902	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28	5.34	2.44	0.29823	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.397790	0.25388	N	0.031021	T	0.66509	0.2796	L	0.39245	1.2	0.26246	N	0.978798	P;P	0.50819	0.939;0.925	P;P	0.55455	0.776;0.667	T	0.58589	-0.7610	10	0.56958	D	0.05	.	8.9103	0.35548	0.0:0.6285:0.0:0.3715	.	4944;4944	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	Q	4944;4944;2578;2063	ENSP00000284548:H4944Q;ENSP00000409493:H4944Q;ENSP00000355668:H2578Q;ENSP00000355670:H2063Q	ENSP00000284548:H4944Q	H	+	3	2	OBSCN	226575997	0.611000	0.26992	1.000000	0.80357	0.920000	0.55202	-0.192000	0.09587	0.244000	0.21351	-0.242000	0.12053	CAT	.	.		0.622	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228509374	T	A	228509374	3	1	318	1	0	0	0	0	1	0	0	0	10821	1432	50	4	15046	4	OBSCN	1	228509374	Missense_Mutation	SNP	T	TCGA-LG-A9QC-01A-11D-A36X-10	73667121	228509374	20741247	5	44851										
HS1BP3	64342	hgsc.bcm.edu	37	chr2	20838354	20838354	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	ttccctgtctgactgtctgtGccatccaggacagaggaatc	10	12	2	2	rs570622489		TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr2:20838354G>A	ENST00000304031.3	-	4	490	c.465C>T	c.(463-465)ggC>ggT	p.G155G	HS1BP3_ENST00000402541.1_Silent_p.G155G	NM_022460.3	NP_071905.3	Q53T59	H1BP3_HUMAN	HCLS1 binding protein 3	155							phosphatidylinositol binding (GO:0035091)			endometrium(4)|large_intestine(1)|lung(7)|ovary(1)|skin(2)	15	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GACTGTCTGTGCCATCCAGGA	0.562													G|||	1	0.000199681	0	0	5008	,	,		20765	0		0	False		,,,				2504	0.001				p.G155G		Atlas-SNP	.											.	HS1BP3	33	.	0			c.C465T						.						116	109	111					2																	20838354		2203	4300	6503	SO:0001819	synonymous_variant	64342	exon4			GTCTGTGCCATCC		CCDS1700.1	2p24.1	2006-08-15			ENSG00000118960	ENSG00000118960			24979	protein-coding gene	gene with protein product		609359				10590261, 15699368	Standard	NM_022460		Approved	HS1-BP3,FLJ14249	uc002rdw.1	Q53T59	OTTHUMG00000122099	ENST00000304031.3:c.465C>T	chr2.hg19:g.20838354G>A		62.0	0.0		69.0	30.0	NM_022460	B2RAW2|D6W529|Q86VC2|Q8N367	Silent	SNP	ENST00000304031.3	hg19	CCDS1700.1																																																																																			.	.		0.562	HS1BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242863.1	NM_022460		A	20838354	G	A	20838354	2	1	318	1	0	0	0	0	0	0	0	1	7370	1306	46	3		3	HS1BP3	2	20838354	Silent	SNP	G	TCGA-LG-A9QC-01A-11D-A36X-10		20838354	222361019	6	44852										
TMEM214	54867	hgsc.bcm.edu	37	chr2	27257068	27257068	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	aagaagcagccaaagaaggtGgcaactcctcccaaccaaaa	8	12	0	2			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr2:27257068G>A	ENST00000238788.9	+	2	347	c.285G>A	c.(283-285)gtG>gtA	p.V95V	TMEM214_ENST00000404032.3_Silent_p.V95V	NM_017727.4	NP_060197.4	Q6NUQ4	TM214_HUMAN	transmembrane protein 214	95					apoptotic process (GO:0006915)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)	18						CAAAGAAGGTGGCAACTCCTC	0.537																																					p.V95V		Atlas-SNP	.											.	TMEM214	41	.	0			c.G285A						.						57	60	59					2																	27257068		2016	4185	6201	SO:0001819	synonymous_variant	54867	exon2			GAAGGTGGCAACT		CCDS42664.1, CCDS46242.1	2p23.3	2013-06-19			ENSG00000119777	ENSG00000119777			25983	protein-coding gene	gene with protein product						23661706	Standard	NM_001083590		Approved	FLJ20254	uc002ria.4	Q6NUQ4	OTTHUMG00000151999	ENST00000238788.9:c.285G>A	chr2.hg19:g.27257068G>A		235.0	0.0		214.0	91.0	NM_017727	A6NNF2|B3KUI9|B5MCD8|D6W547|Q53SW1|Q69YH4|Q8NC45|Q8WZ37|Q9NXH2	Silent	SNP	ENST00000238788.9	hg19	CCDS42664.1																																																																																			.	.		0.537	TMEM214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324748.1	NM_017727		A	27257068	G	A	27257068	2	1	318	1	0	0	0	0	0	0	0	1	16152	1335	47	3		3	TMEM214	2	27257068	Silent	SNP	G	TCGA-LG-A9QC-01A-11D-A36X-10	6418714	27257068	215942305	7	44853										
CCDC104	112942	hgsc.bcm.edu	37	chr2	55771427	55771427	+	Frame_Shift_Del	DEL	G	G	-													0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	aagcagaagagagataagttGatgtccatgagaaaggatat							TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr2:55771427delG	ENST00000349456.4	+	9	997	c.849delG	c.(847-849)ttgfs	p.L283fs	CCDC104_ENST00000490934.1_3'UTR|CCDC104_ENST00000407816.3_Frame_Shift_Del_p.L254fs|CCDC104_ENST00000339012.3_Frame_Shift_Del_p.L308fs			Q96G28	CFA36_HUMAN		283										breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|liver(2)|lung(1)|ovary(2)	14			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			GAGATAAGTTGATGTCCATGA	0.413																																					p.L283X		Atlas-INDEL	.											.	CCDC104	35	.	0			c.848delT						.						81	77	78					2																	55771427		2203	4299	6502	SO:0001589	frameshift_variant	112942	exon9			.																												ENST00000349456.4:c.849delG	chr2.hg19:g.55771427delG	ENSP00000295117:p.Leu283fs	337.0	0.0		302.0	110.0	NM_080667	Q53SF0|Q53ST9|Q6UY34	Frame_Shift_Del	DEL	ENST00000349456.4	hg19	CCDS1854.2																																																																																			.	.		0.413	CCDC104-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319610.2			-	55771427	G	-	55771427	7	5	318	1	0	1	0	1	0	0	0	0	2741	1281	45	0	883	0	CCDC104	2	55771427	Frame_Shift_Del	DEL	G	TCGA-LG-A9QC-01A-11D-A36X-10	28514359	55771427	187427946	8	44854										
TGOLN2	10618	hgsc.bcm.edu	37	chr2	85554487	85554487	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	gctccggatgcgacttactaGtgctgtcttttgtggtctgc	12	10	2	0	rs553348456		TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr2:85554487G>C	ENST00000409232.3	-	2	429	c.368C>G	c.(367-369)aCt>aGt	p.T123S	TGOLN2_ENST00000377386.3_Missense_Mutation_p.T123S|TGOLN2_ENST00000444342.2_Missense_Mutation_p.T123S|TGOLN2_ENST00000282120.2_Intron|TGOLN2_ENST00000398263.2_Missense_Mutation_p.T123S|TGOLN2_ENST00000409015.1_Missense_Mutation_p.T123S			O43493	TGON2_HUMAN	trans-golgi network protein 2	123	14 X 14 AA tandem repeats.					Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)											CGACTTACTAGTGCTGTCTTT	0.582													G|||	1	0.000199681	0	0	5008	,	,		16933	0		0	False		,,,				2504	0.001				p.T123S		Atlas-SNP	.											.	TGOLN2	32	.	0			c.C368G						.						367	365	365					2																	85554487		1990	4161	6151	SO:0001583	missense	10618	exon2			TTACTAGTGCTGT	AF027515	CCDS46351.1, CCDS56126.1, CCDS56127.1	2p11.2	2012-06-25			ENSG00000152291	ENSG00000152291			15450	protein-coding gene	gene with protein product	"trans-Golgi network protein (46, 48, 51kD isoforms)"	603062				9422759, 21994457	Standard	NM_001206840		Approved	TGN51, TGN46, TGN48, TGN38, TTGN2	uc021vjw.1	O43493	OTTHUMG00000153017	ENST00000409232.3:c.368C>G	chr2.hg19:g.85554487G>C	ENSP00000386443:p.Thr123Ser	132.0	0.0		170.0	66.0	NM_001206841	B2R686|B8ZZ88|D6W5K3|F8WBK2|O15282|O43492|O43499|O43500|O43501|Q53G68|Q53GV2|Q6MZV1|Q6ZTM7|Q8N6T8|Q92760|Q96QL2	Missense_Mutation	SNP	ENST00000409232.3	hg19	CCDS56126.1	.	.	.	.	.	.	.	.	.	.	G	8.262	0.811324	0.16537	.	.	ENSG00000152291	ENST00000377386;ENST00000398263;ENST00000409232;ENST00000409015;ENST00000444342	T;T;T;T;T	0.10573	2.95;2.86;3.05;2.95;2.98	3.32	2.38	0.29361	.	.	.	.	.	T	0.05777	0.0151	N	0.14661	0.345	0.25516	N	0.987417	B;B;B;B	0.16396	0.017;0.017;0.003;0.017	B;B;B;B	0.12837	0.008;0.008;0.001;0.008	T	0.42565	-0.9444	9	0.10111	T	0.7	1.1236	9.4191	0.38539	0.0:0.0:0.776:0.224	.	123;123;123;123	O43493;O43493-5;O43493-4;O43493-2	TGON2_HUMAN;.;.;.	S	123	ENSP00000366603:T123S;ENSP00000381312:T123S;ENSP00000386443:T123S;ENSP00000387035:T123S;ENSP00000391190:T123S	ENSP00000366603:T123S	T	-	2	0	TGOLN2	85407998	0.005000	0.15991	0.001000	0.08648	0.003000	0.03518	1.359000	0.34113	0.719000	0.32188	0.380000	0.24917	ACT	.	.		0.582	TGOLN2-006	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000329045.2	NM_006464		C	85554487	G	C	85554487	3	2	318	1	0	0	0	0	1	0	0	0	15851	1029	36	4	957	4	TGOLN2	2	85554487	Missense_Mutation	SNP	G	TCGA-LG-A9QC-01A-11D-A36X-10	29783060	85554487	157644886	9	44855										
POLR1A	25885	hgsc.bcm.edu	37	chr2	86260785	86260785	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	cccccggggactcactcaccCgactcctccccaactcccca	5	24	2	0	rs78239085	byFrequency	TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr2:86260785C>G	ENST00000263857.6	-	28	4538	c.4160G>C	c.(4159-4161)cGg>cCg	p.R1387P	POLR1A_ENST00000409681.1_Splice_Site_p.R1387P			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	1387					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						CTCACTCACCCGACTCCTCCC	0.557																																					p.R1387P		Atlas-SNP	.											.	POLR1A	137	.	0			c.G4160C						.						75	80	79					2																	86260785		1929	4126	6055	SO:0001630	splice_region_variant	25885	exon28			CTCACCCGACTCC	AK025568	CCDS42706.1	2p11.2	2013-01-21			ENSG00000068654	ENSG00000068654		"RNA polymerase subunits"	17264	protein-coding gene	gene with protein product						9236775	Standard	NM_015425		Approved	DKFZP586M0122, FLJ21915, RPO1-4, RPA1	uc002sqs.3	O95602	OTTHUMG00000153165	ENST00000263857.6:c.4161+1G>C	chr2.hg19:g.86260785C>G		88.0	0.0		94.0	41.0	NM_015425	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Missense_Mutation	SNP	ENST00000263857.6	hg19	CCDS42706.1	.	.	.	.	.	.	.	.	.	.	C	9.348	1.064764	0.20067	.	.	ENSG00000068654	ENST00000263857;ENST00000409681	T;T	0.67698	-0.28;3.38	5.38	0.278	0.15673	RNA polymerase Rpb1, domain 5 (1);	0.752143	0.11949	N	0.513863	T	0.46249	0.1383	N	0.25647	0.755	0.29848	N	0.828664	B;B	0.11235	0.004;0.002	B;B	0.12837	0.008;0.005	T	0.32719	-0.9896	10	0.27785	T	0.31	-11.629	3.8346	0.08888	0.1601:0.4853:0.0:0.3546	.	753;1387	B7Z8X7;O95602	.;RPA1_HUMAN	P	1387	ENSP00000263857:R1387P;ENSP00000386300:R1387P	ENSP00000263857:R1387P	R	-	2	0	POLR1A	86114296	0.006000	0.16342	0.398000	0.26321	0.073000	0.16967	-0.714000	0.05002	-0.024000	0.13941	-0.258000	0.10820	CGG	.	C|0.978;T|0.022		0.557	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425	Missense_Mutation	G	86260785	C	G	86260785	5	3	318	1	0	0	0	0	0	0	1	0	12218	666	23	4	1030	4	POLR1A	2	86260785	Splice_Site	SNP	C	TCGA-LG-A9QC-01A-11D-A36X-10	706298	86260785	156938588	10	44856										
SCN9A	6335	hgsc.bcm.edu	37	chr2	167089924	167089924	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	ccgaagggatttaatggggcCaagatctgagtagccaagag	14	7	1	3			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr2:167089924C>T	ENST00000409435.1	-	20	3849	c.3850G>A	c.(3850-3852)Ggc>Agc	p.G1284S	AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Missense_Mutation_p.G1285S|SCN9A_ENST00000409672.1_Missense_Mutation_p.G1273S|SCN9A_ENST00000375387.4_Missense_Mutation_p.G1285S			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	1284					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TTAATGGGGCCAAGATCTGAG	0.338																																					p.G1273S		Atlas-SNP	.											.	SCN9A	296	.	0			c.G3817A						.						54	53	53					2																	167089924		1913	4159	6072	SO:0001583	missense	6335	exon21			TGGGGCCAAGATC	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10597	protein-coding gene	gene with protein product		603415	"sodium channel, voltage-gated, type IX, alpha polypeptide"			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.3850G>A	chr2.hg19:g.167089924C>T	ENSP00000386330:p.Gly1284Ser	75.0	0.0		97.0	25.0	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Missense_Mutation	SNP	ENST00000409435.1	hg19	CCDS46441.1	.	.	.	.	.	.	.	.	.	.	C	17.49	3.402923	0.62288	.	.	ENSG00000169432	ENST00000409672;ENST00000375387;ENST00000303354;ENST00000409435	D;D;D;D	0.97505	-4.41;-4.41;-4.41;-4.41	5.72	4.85	0.62838	.	0.177237	0.40554	N	0.001070	D	0.96241	0.8774	L	0.45352	1.415	0.35497	D	0.79944	P	0.37824	0.609	P	0.46917	0.531	D	0.99731	1.1012	10	0.56958	D	0.05	.	14.7226	0.69317	0.0:0.9306:0.0:0.0694	.	1273	E7EUN6	.	S	1273;1285;1285;1284	ENSP00000386306:G1273S;ENSP00000364536:G1285S;ENSP00000304748:G1285S;ENSP00000386330:G1284S	ENSP00000304748:G1285S	G	-	1	0	SCN9A	166798170	0.013000	0.17824	0.982000	0.44146	0.978000	0.69477	0.726000	0.25984	1.422000	0.47177	0.650000	0.86243	GGC	.	.		0.338	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977		T	167089924	C	T	167089924	3	4	318	1	0	0	0	0	1	0	0	0	13940	594	21	3	2144	3	SCN9A	2	167089924	Missense_Mutation	SNP	C	TCGA-LG-A9QC-01A-11D-A36X-10	80829139	167089924	76109449	11	44857										
LRP2	4036	hgsc.bcm.edu	37	chr2	170058314	170058314	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	agtcattgtagtaatcacagCggtaagagtattggacacat	10	6	2	1			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr2:170058314C>A	ENST00000263816.3	-	44	8561	c.8276G>T	c.(8275-8277)cGc>cTc	p.R2759L		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	2759	LDL-receptor class A 17. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	GTAATCACAGCGGTAAGAGTA	0.498																																					p.R2759L		Atlas-SNP	.											.	LRP2	751	.	0			c.G8276T						.						153	131	138					2																	170058314		2203	4300	6503	SO:0001583	missense	4036	exon44			TCACAGCGGTAAG		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.8276G>T	chr2.hg19:g.170058314C>A	ENSP00000263816:p.Arg2759Leu	61.0	0.0		46.0	17.0	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	hg19	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.022647	0.75275	.	.	ENSG00000081479	ENST00000263816	D	0.95622	-3.76	5.7	5.7	0.88788	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.95300	0.8475	N	0.25060	0.705	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.91926	0.5551	10	0.08837	T	0.75	.	19.8429	0.96697	0.0:1.0:0.0:0.0	.	2759	P98164	LRP2_HUMAN	L	2759	ENSP00000263816:R2759L	ENSP00000263816:R2759L	R	-	2	0	LRP2	169766560	1.000000	0.71417	0.991000	0.47740	0.309000	0.27889	7.701000	0.84566	2.685000	0.91497	0.650000	0.86243	CGC	.	.		0.498	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		A	170058314	C	A	170058314	3	1	318	1	0	0	0	0	1	0	0	0	8965	768	27	1	5835	1	LRP2	2	170058314	Missense_Mutation	SNP	C	TCGA-LG-A9QC-01A-11D-A36X-10	2968390	170058314	73141059	12	44858										
SLC4A3	6508	hgsc.bcm.edu	37	chr2	220500504	220500504	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	gatgtgaggcgccggtacccGcactaccccagtgacctgcg	13	15	0	2			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr2:220500504G>T	ENST00000358055.3	+	14	2594	c.2082G>T	c.(2080-2082)ccG>ccT	p.P694P	SLC4A3_ENST00000317151.3_Silent_p.P694P|SLC4A3_ENST00000273063.6_Silent_p.P721P|SLC4A3_ENST00000373760.2_Silent_p.P694P|SLC4A3_ENST00000373762.3_Silent_p.P721P			P48751	B3A3_HUMAN	solute carrier family 4 (anion exchanger), member 3	694					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	51		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GCCGGTACCCGCACTACCCCA	0.642																																					p.P721P		Atlas-SNP	.											.	SLC4A3	144	.	0			c.G2163T						.						35	35	35					2																	220500504		2203	4300	6503	SO:0001819	synonymous_variant	6508	exon14			GTACCCGCACTAC		CCDS2445.1, CCDS2446.1	2q35	2013-07-19	2013-07-19		ENSG00000114923	ENSG00000114923		"Solute carriers"	11029	protein-coding gene	gene with protein product	"Anion exchanger 3, neuronal"	106195	"solute carrier family 4, anion exchanger, member 3"			8001971	Standard	NM_005070		Approved	AE3, SLC2C	uc002vmo.4	P48751	OTTHUMG00000059238	ENST00000358055.3:c.2082G>T	chr2.hg19:g.220500504G>T		94.0	0.0		99.0	4.0	NM_201574	A6H8L2|A8K1Q9|B7ZVX6|B9EGD1|Q6YIQ9	Silent	SNP	ENST00000358055.3	hg19	CCDS2445.1																																																																																			.	.		0.642	SLC4A3-009	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316472.1	NM_005070		T	220500504	G	T	220500504	2	4	318	1	0	0	0	0	0	0	0	1	14670	1074	38	1		1	SLC4A3	2	220500504	Silent	SNP	G	TCGA-LG-A9QC-01A-11D-A36X-10	50442190	220500504	22698869	13	44859										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266105	41266105	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	cagtcttacctggactctggAatccattctggtgccactac	8	13	3	0	rs121913416		TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr3:41266105A>G	ENST00000349496.5	+	3	382	c.102A>G	c.(100-102)ggA>ggG	p.G34G	CTNNB1_ENST00000396185.3_Silent_p.G34G|CTNNB1_ENST00000405570.1_Silent_p.G34G|CTNNB1_ENST00000453024.1_Silent_p.G27G|CTNNB1_ENST00000396183.3_Silent_p.G34G	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	34			G -> E (in PTR). {ECO:0000269|PubMed:10192393}.|G -> R (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|G -> V (in hepatoblastoma; dbSNP:rs28931589). {ECO:0000269|PubMed:9927029}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.D32_H36>D(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.I35_T41del(1)|p.I35_G38del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.D32fs*9(1)|p.A5_T40del(1)|p.S29_H36del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.GIHS34?(1)|p.A5_I35del(1)|p.D32_H36del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TGGACTCTGGAATCCATTCTG	0.493		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.G34G	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,+1,1	CTNNB1	4904	.	133	Deletion - In frame(107)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(99)|large_intestine(19)|stomach(7)|small_intestine(2)|skin(2)|adrenal_gland(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)|pancreas(1)	c.A102G						.						93	78	83					3																	41266105		2203	4300	6503	SO:0001819	synonymous_variant	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	CTCTGGAATCCAT	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.102A>G	chr3.hg19:g.41266105A>G		154.0	1.0		33.0	15.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Silent	SNP	ENST00000349496.5	hg19	CCDS2694.1																																																																																			.	.		0.493	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266105	A	G	41266105	2	3	318	1	0	0	0	0	0	0	0	1	4018	233	9	2		2	CTNNB1	3	41266105	Silent	SNP	A	TCGA-LG-A9QC-01A-11D-A36X-10		41266105	156756325	14	44860										
PBRM1	55193	hgsc.bcm.edu	37	chr3	52598082	52598082	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	ttacctgaagtagtaaatttCatcatctaccactttagcag	5	9	3	1			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr3:52598082C>T	ENST00000296302.7	-	23	3860	c.3859G>A	c.(3859-3861)Gaa>Aaa	p.E1287K	PBRM1_ENST00000410007.1_Missense_Mutation_p.E1262K|PBRM1_ENST00000409767.1_Missense_Mutation_p.E1302K|PBRM1_ENST00000337303.4_Missense_Mutation_p.E1287K|PBRM1_ENST00000409114.3_Missense_Mutation_p.E1302K|PBRM1_ENST00000409057.1_Missense_Mutation_p.E1287K|PBRM1_ENST00000394830.3_Missense_Mutation_p.E1262K|SMIM4_ENST00000476842.1_Intron|PBRM1_ENST00000356770.4_Missense_Mutation_p.E1255K			Q86U86	PB1_HUMAN	polybromo 1	1287			E -> Q (found in a breast cancer cell line). {ECO:0000269|PubMed:21248752}.		chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TAGTAAATTTCATCATCTACC	0.358			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																p.E1262K		Atlas-SNP	.		Rec	yes		3	3p21	55193	polybromo 1		E	PBRM1_ENST00000296302,NS,carcinoma,+2,2	PBRM1	1252	.	0			c.G3784A						.						92	91	91					3																	52598082		2203	4300	6503	SO:0001583	missense	55193	exon24			AAATTTCATCATC	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.3859G>A	chr3.hg19:g.52598082C>T	ENSP00000296302:p.Glu1287Lys	54.0	1.0		37.0	26.0	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Missense_Mutation	SNP	ENST00000296302.7	hg19		.	.	.	.	.	.	.	.	.	.	C	22.5	4.292169	0.80914	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351	T;T;T;T;T;T;T;T;T	0.59638	0.26;0.88;0.25;0.27;0.26;0.86;0.71;0.29;0.28	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.75664	0.3880	M	0.69358	2.11	0.80722	D	1	D;D;D;D;D;D;D;D	0.76494	0.998;0.99;0.998;0.996;0.999;0.999;0.998;0.996	D;D;D;D;D;D;D;D	0.81914	0.991;0.961;0.986;0.987;0.995;0.994;0.991;0.987	T	0.78102	-0.2335	10	0.87932	D	0	-15.2979	19.0144	0.92888	0.0:1.0:0.0:0.0	.	1262;1262;1287;1302;1302;1287;1255;1287	Q86U86-9;Q86U86-4;Q86U86-2;Q86U86-8;Q86U86-7;Q86U86;Q86U86-3;Q86U86-5	.;.;.;.;.;PB1_HUMAN;.;.	K	1255;1262;1287;1287;1287;1262;1302;1302;1286	ENSP00000349213:E1255K;ENSP00000378307:E1262K;ENSP00000296302:E1287K;ENSP00000338302:E1287K;ENSP00000386593:E1287K;ENSP00000386529:E1262K;ENSP00000386643:E1302K;ENSP00000386601:E1302K;ENSP00000387775:E1286K	ENSP00000296302:E1287K	E	-	1	0	PBRM1	52573122	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.764000	0.85297	2.493000	0.84123	0.655000	0.94253	GAA	.	.		0.358	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165		T	52598082	C	T	52598082	3	4	318	1	0	0	0	0	1	0	0	0	11500	835	29	3	1073	3	PBRM1	3	52598082	Missense_Mutation	SNP	C	TCGA-LG-A9QC-01A-11D-A36X-10	11331977	52598082	145424348	15	44861										
C4orf37	285555	hgsc.bcm.edu	37	chr4	98902341	98902341	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	tctgtcctgatgtcctgtgtGaatcgaacagcactttgacc	9	11	1	3			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr4:98902341G>C	ENST00000295268.3	-	6	830	c.741C>G	c.(739-741)ttC>ttG	p.F247L		NM_174952.2	NP_777612.1	Q8N412	STPG2_HUMAN	sperm-tail PG-rich repeat containing 2	247																	TGTCCTGTGTGAATCGAACAG	0.383																																					p.F247L		Atlas-SNP	.											.	.	.	.	0			c.C741G						.						193	190	191					4																	98902341		2203	4300	6503	SO:0001583	missense	285555	exon6			CTGTGTGAATCGA	BC036870	CCDS3645.1	4q22.3-q23	2013-10-11	2012-07-30	2012-07-30	ENSG00000163116	ENSG00000163116			28712	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 37"	C4orf37		23031811	Standard	NM_174952		Approved	MGC46496	uc003htt.2	Q8N412	OTTHUMG00000131009	ENST00000295268.3:c.741C>G	chr4.hg19:g.98902341G>C	ENSP00000295268:p.Phe247Leu	78.0	0.0		39.0	6.0	NM_174952		Missense_Mutation	SNP	ENST00000295268.3	hg19	CCDS3645.1	.	.	.	.	.	.	.	.	.	.	G	17.25	3.341323	0.60963	.	.	ENSG00000163116	ENST00000295268	T	0.19394	2.15	5.58	2.92	0.33932	.	0.000000	0.85682	D	0.000000	T	0.43322	0.1242	M	0.78801	2.425	0.31353	N	0.682331	D	0.89917	1.0	D	0.87578	0.998	T	0.51148	-0.8742	10	0.87932	D	0	-19.3986	8.5742	0.33587	0.3068:0.0:0.6932:0.0	.	247	Q8N412	CD037_HUMAN	L	247	ENSP00000295268:F247L	ENSP00000295268:F247L	F	-	3	2	C4orf37	99121364	0.953000	0.32496	0.671000	0.29857	0.823000	0.46562	1.279000	0.33191	0.303000	0.22785	0.563000	0.77884	TTC	.	.		0.383	STPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253642.1	NM_174952		C	98902341	G	C	98902341	3	2	318	1	0	0	0	0	1	0	0	0	2269	1281	45	4	662	4	C4orf37	4	98902341	Missense_Mutation	SNP	G	TCGA-LG-A9QC-01A-11D-A36X-10		98902341	92251935	16	44862										
SKIV2L2	23517	hgsc.bcm.edu	37	chr5	54693274	54693274	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	ttttggtgcatctcctgtctGctatcagcagtgttaggctt	10	9	3	0			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr5:54693274G>T	ENST00000230640.5	+	20	2466	c.2212G>T	c.(2212-2214)Gct>Tct	p.A738S	SKIV2L2_ENST00000545714.1_Missense_Mutation_p.A637S	NM_015360.4	NP_056175.3	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2 (S. cerevisiae)	738					maturation of 5.8S rRNA (GO:0000460)|mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			NS(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|lung(12)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)				TCTCCTGTCTGCTATCAGCAG	0.363																																					p.A738S	Melanoma(2;92 134 23744 29976 33782)	Atlas-SNP	.											.	SKIV2L2	104	.	0			c.G2212T						.						164	155	158					5																	54693274		2203	4300	6503	SO:0001583	missense	23517	exon20			CTGTCTGCTATCA	D29641	CCDS3967.1	5q11.2	2008-11-25	2005-02-18	2005-02-18	ENSG00000039123	ENSG00000039123			18734	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 118"		"KIAA0052"	KIAA0052			Standard	NM_015360		Approved	Mtr4, Dob1, fSAP118	uc003jpy.4	P42285	OTTHUMG00000097019	ENST00000230640.5:c.2212G>T	chr5.hg19:g.54693274G>T	ENSP00000230640:p.Ala738Ser	82.0	0.0		83.0	4.0	NM_015360	Q2M386|Q6MZZ8|Q6P170|Q8N5R0|Q8TAG2	Missense_Mutation	SNP	ENST00000230640.5	hg19	CCDS3967.1	.	.	.	.	.	.	.	.	.	.	G	10.28	1.306643	0.23736	.	.	ENSG00000039123	ENST00000230640;ENST00000545714	T;T	0.29655	1.56;1.56	5.28	4.34	0.51931	.	0.161766	0.56097	D	0.000030	T	0.17492	0.0420	N	0.12961	0.28	0.52501	D	0.999956	B;B	0.12013	0.001;0.005	B;B	0.18871	0.006;0.023	T	0.05007	-1.0912	10	0.08179	T	0.78	-28.994	14.9965	0.71436	0.0:0.0:0.857:0.143	.	637;738	F5H7E2;P42285	.;SK2L2_HUMAN	S	738;637	ENSP00000230640:A738S;ENSP00000442583:A637S	ENSP00000230640:A738S	A	+	1	0	SKIV2L2	54729031	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.736000	0.62059	2.636000	0.89361	0.655000	0.94253	GCT	.	.		0.363	SKIV2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214108.1			T	54693274	G	T	54693274	3	4	318	1	0	0	0	0	1	0	0	0	14375	1319	46	3	2290	3	SKIV2L2	5	54693274	Missense_Mutation	SNP	G	TCGA-LG-A9QC-01A-11D-A36X-10		54693274	126221986	17	44863										
YTHDC2	64848	hgsc.bcm.edu	37	chr5	112891817	112891817	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	atttccaaagctagtgccatAcagcggaaaggcaggtaatg	11	8	0	0			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr5:112891817A>G	ENST00000161863.4	+	17	2415	c.2202A>G	c.(2200-2202)atA>atG	p.I734M	YTHDC2_ENST00000515883.1_Missense_Mutation_p.I734M	NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	734	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|positive regulation by host of viral genome replication (GO:0044829)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)	endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA polymerase binding (GO:0070063)|RNA-dependent ATPase activity (GO:0008186)			NS(2)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(13)|lung(10)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		CTAGTGCCATACAGCGGAAAG	0.289																																					p.I734M		Atlas-SNP	.											.	YTHDC2	118	.	0			c.A2202G						.						60	63	62					5																	112891817		2202	4287	6489	SO:0001583	missense	64848	exon17			TGCCATACAGCGG	AK000915	CCDS4113.1	5q22.3	2008-02-05			ENSG00000047188	ENSG00000047188			24721	protein-coding gene	gene with protein product						12477932	Standard	NM_022828		Approved	FLJ2194, FLJ10053, DKFZp564A186	uc003kqn.3	Q9H6S0	OTTHUMG00000128837	ENST00000161863.4:c.2202A>G	chr5.hg19:g.112891817A>G	ENSP00000161863:p.Ile734Met	168.0	0.0		276.0	63.0	NM_022828	B2RP66	Missense_Mutation	SNP	ENST00000161863.4	hg19	CCDS4113.1	.	.	.	.	.	.	.	.	.	.	A	12.75	2.032262	0.35893	.	.	ENSG00000047188	ENST00000161863;ENST00000515883;ENST00000511372	T;T	0.79454	-1.27;-1.27	4.89	2.55	0.30701	Helicase, C-terminal (3);	0.207171	0.42964	D	0.000630	T	0.61098	0.2320	N	0.26092	0.79	0.34411	D	0.696319	B	0.26876	0.162	B	0.25140	0.058	T	0.62383	-0.6866	10	0.51188	T	0.08	.	5.4887	0.16763	0.3278:0.4399:0.0:0.2322	.	734	Q9H6S0	YTDC2_HUMAN	M	734;734;644	ENSP00000161863:I734M;ENSP00000423101:I734M	ENSP00000161863:I734M	I	+	3	3	YTHDC2	112919716	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.357000	0.34090	0.706000	0.31912	0.524000	0.50904	ATA	.	.		0.289	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828		G	112891817	A	G	112891817	3	3	318	1	0	0	0	0	1	0	0	0	17512	381	14	2	2268	2	YTHDC2	5	112891817	Missense_Mutation	SNP	A	TCGA-LG-A9QC-01A-11D-A36X-10	58198543	112891817	68023443	18	44864										
RNF44	22838	hgsc.bcm.edu	37	chr5	175959076	175959076	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	cattcgggggctcccgccggCaggagccgaggctcggcgct	17	15	0	0			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr5:175959076C>A	ENST00000274811.4	-	3	750	c.226G>T	c.(226-228)Gcc>Tcc	p.A76S	RNF44_ENST00000509404.1_5'Flank|RNF44_ENST00000537487.1_5'UTR	NM_014901.4	NP_055716.1	Q7L0R7	RNF44_HUMAN	ring finger protein 44	76	Pro-rich.						zinc ion binding (GO:0008270)			endometrium(2)|lung(3)|prostate(1)|skin(1)|stomach(1)	8	all_cancers(89;0.0029)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTCCCGCCGGCAGGAGCCGAG	0.706																																					p.A76S		Atlas-SNP	.											.	RNF44	33	.	0			c.G226T						.						18	26	23					5																	175959076		2195	4292	6487	SO:0001583	missense	22838	exon3			CGCCGGCAGGAGC	AB029023	CCDS4404.1	5q35.3	2013-01-09			ENSG00000146083	ENSG00000146083		"RING-type (C3HC4) zinc fingers"	19180	protein-coding gene	gene with protein product						10470851	Standard	NM_014901		Approved	KIAA1100	uc003mek.1	Q7L0R7	OTTHUMG00000130664	ENST00000274811.4:c.226G>T	chr5.hg19:g.175959076C>A	ENSP00000274811:p.Ala76Ser	219.0	0.0		276.0	83.0	NM_014901	B4DYE0|Q8ND05|Q9UPQ2	Missense_Mutation	SNP	ENST00000274811.4	hg19	CCDS4404.1	.	.	.	.	.	.	.	.	.	.	C	15.77	2.932413	0.52866	.	.	ENSG00000146083	ENST00000274811	T	0.29142	1.58	3.98	3.98	0.46160	.	0.133306	0.49305	D	0.000149	T	0.15003	0.0362	N	0.08118	0	0.80722	D	1	B	0.17268	0.021	B	0.14023	0.01	T	0.05338	-1.0891	10	0.52906	T	0.07	-17.2002	7.9028	0.29744	0.0:0.7483:0.163:0.0887	.	76	Q7L0R7	RNF44_HUMAN	S	76	ENSP00000274811:A76S	ENSP00000274811:A76S	A	-	1	0	RNF44	175891682	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	0.874000	0.28065	2.223000	0.72356	0.561000	0.74099	GCC	.	.		0.706	RNF44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253156.2			A	175959076	C	A	175959076	3	1	318	1	0	0	0	0	1	0	0	0	13511	710	25	3	1108	3	RNF44	5	175959076	Missense_Mutation	SNP	C	TCGA-LG-A9QC-01A-11D-A36X-10	63067259	175959076	4956184	19	44865										
MYLK4	340156	hgsc.bcm.edu	37	chr6	2678490	2678490	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	gaagcttagagatgaactccTtggcctcctccgagatgtcc	10	12	0	3			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr6:2678490T>G	ENST00000274643.7	-	10	1346	c.1004A>C	c.(1003-1005)aAg>aCg	p.K335T	MYLK4_ENST00000268446.5_Missense_Mutation_p.K335T	NM_001012418.3	NP_001012418.2	Q86YV6	MYLK4_HUMAN	myosin light chain kinase family, member 4	335	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(10)|ovary(2)|skin(1)	23	Ovarian(93;0.0412)	all_hematologic(90;0.0897)				GATGAACTCCTTGGCCTCCTC	0.527																																					p.K335T		Atlas-SNP	.											.	MYLK4	74	.	0			c.A1004C						.						184	168	173					6																	2678490		2203	4300	6503	SO:0001583	missense	340156	exon10			AACTCCTTGGCCT		CCDS34330.1	6p25.2	2008-01-23			ENSG00000145949	ENSG00000145949			27972	protein-coding gene	gene with protein product	"caMLCK like"						Standard	NM_001012418		Approved	SgK085	uc003mty.4	Q86YV6	OTTHUMG00000014121	ENST00000274643.7:c.1004A>C	chr6.hg19:g.2678490T>G	ENSP00000274643:p.Lys335Thr	100.0	0.0		95.0	33.0	NM_001012418	A2RUC0|Q5TAW2	Missense_Mutation	SNP	ENST00000274643.7	hg19	CCDS34330.1	.	.	.	.	.	.	.	.	.	.	T	19.53	3.845492	0.71603	.	.	ENSG00000145949	ENST00000268446;ENST00000274643	T;T	0.68181	-0.31;-0.31	4.98	-1.76	0.08006	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.643019	0.13476	N	0.385077	T	0.69602	0.3129	M	0.70275	2.135	0.37270	D	0.907372	D	0.71674	0.998	D	0.77004	0.989	T	0.73107	-0.4087	10	0.87932	D	0	.	10.672	0.45764	0.0:0.2057:0.0:0.7943	.	335	Q86YV6	MYLK4_HUMAN	T	335	ENSP00000268446:K335T;ENSP00000274643:K335T	ENSP00000268446:K335T	K	-	2	0	MYLK4	2623489	1.000000	0.71417	0.840000	0.33206	0.899000	0.52679	2.185000	0.42584	-0.162000	0.10964	-0.290000	0.09829	AAG	.	.		0.527	MYLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039632.2	NM_001012418		G	2678490	T	G	2678490	3	3	318	1	0	0	0	0	1	0	0	0	10068	1609	56	5	174	5	MYLK4	6	2678490	Missense_Mutation	SNP	T	TCGA-LG-A9QC-01A-11D-A36X-10		2678490	168436577	20	44866										
REV3L	5980	hgsc.bcm.edu	37	chr6	111714108	111714108	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	tcatcttgttcccaccgaaaTaaagtatcagcaagagaatt	6	9	3	1			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr6:111714108T>C	ENST00000358835.3	-	6	1087	c.633A>G	c.(631-633)ttA>ttG	p.L211L	REV3L_ENST00000435970.1_Silent_p.L133L|REV3L_ENST00000368805.1_Silent_p.L211L|REV3L_ENST00000368802.3_Silent_p.L211L			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	211					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		CCCACCGAAATAAAGTATCAG	0.328								DNA polymerases (catalytic subunits)																													p.L211L		Atlas-SNP	.											.	REV3L	386	.	0			c.A633G						.						71	71	71					6																	111714108		2203	4298	6501	SO:0001819	synonymous_variant	5980	exon5			CCGAAATAAAGTA	AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"DNA polymerases"	9968	protein-coding gene	gene with protein product	"polymerase, DNA, zeta"	602776	"REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta", "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.633A>G	chr6.hg19:g.111714108T>C		91.0	0.0		69.0	29.0	NM_002912	O43214|Q5TC33	Silent	SNP	ENST00000358835.3	hg19	CCDS5091.2																																																																																			.	.		0.328	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		C	111714108	T	C	111714108	2	2	318	1	0	0	0	0	0	0	0	1	13255	1403	49	2		2	REV3L	6	111714108	Silent	SNP	T	TCGA-LG-A9QC-01A-11D-A36X-10	109035618	111714108	59400959	21	44867										
AMZ1	155185	hgsc.bcm.edu	37	chr7	2752261	2752261	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	ggtggctggccatgtgcatcCaggccctgcagcgggaagtg	17	11	0	0			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr7:2752261C>A	ENST00000312371.4	+	7	1614	c.1246C>A	c.(1246-1248)Cag>Aag	p.Q416K	AMZ1_ENST00000407112.1_3'UTR|AMZ1_ENST00000489665.1_Intron	NM_133463.1	NP_597720.1	Q400G9	AMZ1_HUMAN	archaelysin family metallopeptidase 1	416							metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	16		Ovarian(82;0.0779)		OV - Ovarian serous cystadenocarcinoma(56;5.03e-14)		CATGTGCATCCAGGCCCTGCA	0.687																																					p.Q416K		Atlas-SNP	.											.	AMZ1	41	.	0			c.C1246A						.						41	38	39					7																	2752261		2203	4298	6501	SO:0001583	missense	155185	exon7			TGCATCCAGGCCC	AB075830	CCDS34589.1, CCDS64582.1	7p22.3	2008-01-17			ENSG00000174945	ENSG00000174945			22231	protein-coding gene	gene with protein product	"archaemetzincin-1"	615168				15972818	Standard	NM_133463		Approved	KIAA1950	uc003smr.1	Q400G9	OTTHUMG00000152111	ENST00000312371.4:c.1246C>A	chr7.hg19:g.2752261C>A	ENSP00000308149:p.Gln416Lys	80.0	0.0		142.0	47.0	NM_133463	B3KRS0|Q8TF51	Missense_Mutation	SNP	ENST00000312371.4	hg19	CCDS34589.1	.	.	.	.	.	.	.	.	.	.	C	10.45	1.353370	0.24512	.	.	ENSG00000174945	ENST00000312371	T	0.21932	1.98	4.67	1.27	0.21489	.	0.963974	0.08503	N	0.936061	T	0.16769	0.0403	L	0.48642	1.525	0.80722	D	1	B	0.22003	0.063	B	0.19666	0.026	T	0.13656	-1.0501	10	0.13470	T	0.59	-27.5171	7.0815	0.25234	0.0:0.3477:0.5388:0.1135	.	416	Q400G9	AMZ1_HUMAN	K	416	ENSP00000308149:Q416K	ENSP00000308149:Q416K	Q	+	1	0	AMZ1	2718787	0.046000	0.20272	0.998000	0.56505	0.537000	0.34900	0.991000	0.29654	0.910000	0.36722	0.462000	0.41574	CAG	.	.		0.687	AMZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325244.1	NM_133463		A	2752261	C	A	2752261	3	1	318	1	0	0	0	0	1	0	0	0	596	595	21	3	1268	3	AMZ1	7	2752261	Missense_Mutation	SNP	C	TCGA-LG-A9QC-01A-11D-A36X-10		2752261	156386402	22	44868										
TXNDC3	51314	hgsc.bcm.edu	37	chr7	37903054	37903054	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	gttagtgaagaatcaccatgTgaaagtgttcgtaagtaaat	10	4	1	3			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr7:37903054T>C	ENST00000199447.4	+	8	816	c.444T>C	c.(442-444)tgT>tgC	p.C148C	NME8_ENST00000440017.1_Silent_p.C148C|EPDR1_ENST00000476620.1_Intron	NM_016616.4	NP_057700.3	Q8N427	TXND3_HUMAN	NME/NM23 family member 8	148					cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)|UTP biosynthetic process (GO:0006228)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)										AATCACCATGTGAAAGTGTTC	0.358																																					p.C148C		Atlas-SNP	.											.	.	.	.	0			c.T444C						.						105	110	108					7																	37903054		2203	4300	6503	SO:0001819	synonymous_variant	51314	exon8			ACCATGTGAAAGT	AF202051	CCDS5452.1	7p15.2	2012-05-18	2012-05-18	2012-05-18	ENSG00000086288	ENSG00000086288			16473	protein-coding gene	gene with protein product	"sperm-specific thioredoxin 2"	607421	"thioredoxin domain containing 3 (spermatozoa)"	TXNDC3		11737268, 11768308, 19852809	Standard	NM_016616		Approved	CILD6, SPTRX2, NM23-H8	uc003tfn.3	Q8N427	OTTHUMG00000023716	ENST00000199447.4:c.444T>C	chr7.hg19:g.37903054T>C		63.0	0.0		55.0	25.0	NM_016616	Q9NZH1	Silent	SNP	ENST00000199447.4	hg19	CCDS5452.1																																																																																			.	.		0.358	NME8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219946.1	NM_016616		C	37903054	T	C	37903054	2	2	318	1	0	0	0	0	0	0	0	1	16813	1702	59	2		2	TXNDC3	7	37903054	Silent	SNP	T	TCGA-LG-A9QC-01A-11D-A36X-10	35150793	37903054	121235609	23	44869										
HIPK2	28996	hgsc.bcm.edu	37	chr7	139281611	139281611	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	ggccacgtcgccccacccacAggtgaccgaggtgctgcagg	14	16	0	1			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr7:139281611A>T	ENST00000406875.3	-	12	2663	c.2569T>A	c.(2569-2571)Tgt>Agt	p.C857S	HIPK2_ENST00000428878.2_Missense_Mutation_p.C830S|HIPK2_ENST00000342645.6_Intron	NM_022740.4	NP_073577.3	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2	857	Interaction with CTBP1. {ECO:0000250}.|Interaction with HMGA1. {ECO:0000250}.|Interaction with POU4F1. {ECO:0000250}.|Interaction with TP53 and TP73.				adult walking behavior (GO:0007628)|anterior/posterior pattern specification (GO:0009952)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|erythrocyte differentiation (GO:0030218)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|retina layer formation (GO:0010842)|SMAD protein signal transduction (GO:0060395)|smoothened signaling pathway (GO:0007224)|transforming growth factor beta receptor signaling pathway (GO:0007179)|voluntary musculoskeletal movement (GO:0050882)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|virion binding (GO:0046790)			breast(4)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Melanoma(164;0.205)					CCCCACCCACAGGTGACCGAG	0.652																																					p.C857S		Atlas-SNP	.											.	HIPK2	192	.	0			c.T2569A						.						54	61	59					7																	139281611		2176	4275	6451	SO:0001583	missense	28996	exon12			ACCCACAGGTGAC	AF208291	CCDS75666.1, CCDS75667.1	7q32-q34	2004-01-29	2001-11-29		ENSG00000064393	ENSG00000064393			14402	protein-coding gene	gene with protein product		606868	"homeodomain-interacting protein kinase 2"			11120354	Standard	NM_001113239		Approved		uc003vvf.4	Q9H2X6	OTTHUMG00000157704	ENST00000406875.3:c.2569T>A	chr7.hg19:g.139281611A>T	ENSP00000385571:p.Cys857Ser	55.0	0.0		58.0	30.0	NM_022740	Q75MR7|Q8WWI4|Q9H2Y1	Missense_Mutation	SNP	ENST00000406875.3	hg19		.	.	.	.	.	.	.	.	.	.	A	7.417	0.635945	0.14386	.	.	ENSG00000064393	ENST00000406875;ENST00000428878	T;T	0.19394	2.15;2.15	5.49	5.49	0.81192	.	.	.	.	.	T	0.09686	0.0238	.	.	.	0.48632	D	0.999688	P;B	0.42827	0.791;0.218	B;B	0.29785	0.107;0.059	T	0.17561	-1.0365	8	0.07325	T	0.83	.	15.7597	0.78070	1.0:0.0:0.0:0.0	.	857;830	Q9H2X6;Q9H2X6-3	HIPK2_HUMAN;.	S	857;830	ENSP00000385571:C857S;ENSP00000413724:C830S	ENSP00000385571:C857S	C	-	1	0	HIPK2	138932151	1.000000	0.71417	1.000000	0.80357	0.765000	0.43378	5.350000	0.66016	2.304000	0.77564	0.528000	0.53228	TGT	.	.		0.652	HIPK2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000349430.3	NM_022740		T	139281611	A	T	139281611	3	4	318	1	0	0	0	0	1	0	0	0	7126	188	7	4	1043	4	HIPK2	7	139281611	Missense_Mutation	SNP	A	TCGA-LG-A9QC-01A-11D-A36X-10	101378557	139281611	19857052	24	44870										
ATP6V0E2	155066	hgsc.bcm.edu	37	chr7	149571165	149571165	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	gcgcccggccatgacggcgcActcattcgccctcccggtca	11	19	2	1			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr7:149571165A>G	ENST00000425642.2	+	1	34	c.11A>G	c.(10-12)cAc>cGc	p.H4R	ATP6V0E2_ENST00000479613.1_Missense_Mutation_p.H4R|ATP6V0E2-AS1_ENST00000461019.1_RNA|ATP6V0E2_ENST00000464662.1_Missense_Mutation_p.H4R|ATP6V0E2_ENST00000421974.2_Missense_Mutation_p.H53R|ATP6V0E2-AS1_ENST00000488315.1_RNA|ATP6V0E2_ENST00000606024.1_Missense_Mutation_p.H4R|ATP6V0E2_ENST00000456496.2_Missense_Mutation_p.H53R|ATP6V0E2-AS1_ENST00000464939.1_RNA			Q8NHE4	VA0E2_HUMAN	ATPase, H+ transporting V0 subunit e2	4					ATP hydrolysis coupled proton transport (GO:0015991)|cell growth (GO:0016049)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|vacuolar acidification (GO:0007035)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|phagocytic vesicle membrane (GO:0030670)|proton-transporting V-type ATPase, V0 domain (GO:0033179)	ATPase activity, coupled to transmembrane movement of ions (GO:0042625)|hydrogen ion transmembrane transporter activity (GO:0015078)			lung(1)	1			OV - Ovarian serous cystadenocarcinoma(82;0.00256)			ATGACGGCGCACTCATTCGCC	0.711																																					p.H53R		Atlas-SNP	.											.	ATP6V0E2	12	.	0			c.A158G						.						7	10	9					7																	149571165		1721	3443	5164	SO:0001583	missense	155066	exon1			CGGCGCACTCATT	AK057700	CCDS47742.1, CCDS55181.1	7q36.1	2010-04-21	2006-10-12	2006-10-12	ENSG00000171130	ENSG00000171130		"ATPases / V-type"	21723	protein-coding gene	gene with protein product		611019	"chromosome 7 open reading frame 32", "ATPase, H+ transporting V0 subunit E isoform 2-like (rat)"	C7orf32, ATP6V0E2L			Standard	XM_005249958		Approved		uc003wgs.3	Q8NHE4	OTTHUMG00000158094	ENST00000425642.2:c.11A>G	chr7.hg19:g.149571165A>G	ENSP00000396148:p.His4Arg	105.0	0.0		105.0	46.0	NM_001100592	A2T863|A2T8L7|B5MDP5|J3KQW7|Q6MZW1|Q75L47|Q7Z4R7|Q8N7I8	Missense_Mutation	SNP	ENST00000425642.2	hg19		.	.	.	.	.	.	.	.	.	.	A	26.7	4.762001	0.89932	.	.	ENSG00000171130	ENST00000421974;ENST00000456496;ENST00000425642;ENST00000479613	.	.	.	5.7	4.54	0.55810	.	.	.	.	.	T	0.54013	0.1832	N	0.19112	0.55	0.40088	D	0.976219	D;P;B	0.89917	1.0;0.748;0.17	D;P;B	0.69307	0.963;0.611;0.035	T	0.58423	-0.7639	8	0.72032	D	0.01	-5.9164	9.0551	0.36401	0.8362:0.0:0.0:0.1638	.	53;4;4	E9PAS2;Q8NHE4-3;Q8NHE4	.;.;VA0E2_HUMAN	R	53;53;4;4	.	ENSP00000411672:H53R	H	+	2	0	ATP6V0E2	149202098	1.000000	0.71417	0.999000	0.59377	0.964000	0.63967	3.626000	0.54245	0.970000	0.38263	0.460000	0.39030	CAC	.	.		0.711	ATP6V0E2-010	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470874.1	NM_145230		G	149571165	A	G	149571165	3	3	318	1	0	0	0	0	1	0	0	0	1176	159	6	2	160	2	ATP6V0E2	7	149571165	Missense_Mutation	SNP	A	TCGA-LG-A9QC-01A-11D-A36X-10	10289554	149571165	9567498	25	44871										
DLGAP2	9228	hgsc.bcm.edu	37	chr8	1616621	1616621	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	ggacgcctaccaggacagccGcgcacagaggatgtccccgt	13	15	0	1	rs200214556	byFrequency	TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr8:1616621G>A	ENST00000421627.2	+	6	1831	c.1697G>A	c.(1696-1698)cGc>cAc	p.R566H		NM_004745.3	NP_004736.2	Q9P1A6	DLGP2_HUMAN	discs, large (Drosophila) homolog-associated protein 2	645					neuron-neuron synaptic transmission (GO:0007270)	cell junction (GO:0030054)|neurofilament (GO:0005883)|postsynaptic membrane (GO:0045211)				breast(1)|endometrium(6)|lung(31)|prostate(3)	41		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)		CAGGACAGCCGCGCACAGAGG	0.672													G|||	3	0.000599042	8e-04	0	5008	,	,		14006	0		0	False		,,,				2504	0.002				p.R566H		Atlas-SNP	.											.	DLGAP2	292	.	0			c.G1697A						.	G	HIS/ARG	12,4090		0,12,2039	13	18	16		1697	5.3	1	8		16	0,8366		0,0,4183	yes	missense	DLGAP2	NM_004745.3	29	0,12,6222	AA,AG,GG		0.0,0.2925,0.0962	probably-damaging	566/976	1616621	12,12456	2051	4183	6234	SO:0001583	missense	9228	exon6			ACAGCCGCGCACA	AB000275	CCDS47760.1, CCDS75689.1	8p23	2007-12-06	2001-11-28		ENSG00000198010	ENSG00000198010			2906	protein-coding gene	gene with protein product		605438	"discs, large (Drosophila) homolog-associated protein 2"			9286858, 10854099	Standard	NM_004745		Approved	DAP-2	uc003wpl.4	Q9P1A6	OTTHUMG00000163599	ENST00000421627.2:c.1697G>A	chr8.hg19:g.1616621G>A	ENSP00000400258:p.Arg566His	217.0	0.0		138.0	6.0	NM_004745	A1QCF8|A1QCF9|A5D8Y2|O14488|O14664|Q9P1A7	Missense_Mutation	SNP	ENST00000421627.2	hg19	CCDS47760.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.4|25.4	4.633499|4.633499	0.87660|0.87660	0.002925|0.002925	0.0|0.0	ENSG00000198010|ENSG00000198010	ENST00000520901|ENST00000356067;ENST00000421627	.|T	.|0.22539	.|1.95	5.32|5.32	5.32|5.32	0.75619|0.75619	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.43344|0.43344	0.1243|0.1243	L|L	0.60455|0.60455	1.87|1.87	0.43435|0.43435	D|D	0.995607|0.995607	.|D;D	.|0.71674	.|0.998;0.992	.|D;P	.|0.64595	.|0.927;0.799	T|T	0.21895|0.21895	-1.0232|-1.0232	5|10	.|0.52906	.|T	.|0.07	-7.4578|-7.4578	19.0005|19.0005	0.92832|0.92832	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|645;645	.|Q9P1A6-2;Q9P1A6	.|.;DLGP2_HUMAN	T|H	583|611;566	.|ENSP00000400258:R566H	.|ENSP00000348366:R611H	A|R	+|+	1|2	0|0	DLGAP2|DLGAP2	1604028|1604028	1.000000|1.000000	0.71417|0.71417	0.986000|0.986000	0.45419|0.45419	0.958000|0.958000	0.62258|0.62258	6.266000|6.266000	0.72540|0.72540	2.483000|2.483000	0.83821|0.83821	0.655000|0.655000	0.94253|0.94253	GCG|CGC	.	.		0.672	DLGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374478.1	NM_004745		A	1616621	G	A	1616621	3	1	318	1	0	0	0	0	1	0	0	0	4562	1087	38	1	1715	1	DLGAP2	8	1616621	Missense_Mutation	SNP	G	TCGA-LG-A9QC-01A-11D-A36X-10		1616621	144747401	26	44872										
HR	55806	hgsc.bcm.edu	37	chr8	21984727	21984727	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	gctgcctgcccttttgagggCccggagccgagcaaccggcc	14	16	0	1			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr8:21984727C>A	ENST00000381418.4	-	3	2708	c.1228G>T	c.(1228-1230)Gcc>Tcc	p.A410S	HR_ENST00000312841.8_Missense_Mutation_p.A410S	NM_005144.4	NP_005135.2	O43593	HAIR_HUMAN	hair growth associated	410					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	27		Breast(100;0.000162)|Acute lymphoblastic leukemia(644;0.0775)|Prostate(55;0.116)		KIRC - Kidney renal clear cell carcinoma(542;1.19e-05)|BRCA - Breast invasive adenocarcinoma(99;3.56e-05)|Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)		CTTTTGAGGGCCCGGAGCCGA	0.657																																					p.A410S		Atlas-SNP	.											.	HR	71	.	0			c.G1228T						.						52	63	60					8																	21984727		2202	4297	6499	SO:0001583	missense	55806	exon3			TGAGGGCCCGGAG	AF039196	CCDS6022.1, CCDS6023.1	8p12	2012-12-07	2012-12-07		ENSG00000168453	ENSG00000168453			5172	protein-coding gene	gene with protein product		602302	"hairless (mouse) homolog", "hairless homolog (mouse)"	ALUNC		10051399, 9463324	Standard	NM_018411		Approved	AU	uc003xas.3	O43593	OTTHUMG00000097089	ENST00000381418.4:c.1228G>T	chr8.hg19:g.21984727C>A	ENSP00000370826:p.Ala410Ser	53.0	0.0		49.0	35.0	NM_018411	Q6GS30|Q96H33|Q9NPE1	Missense_Mutation	SNP	ENST00000381418.4	hg19	CCDS6022.1	.	.	.	.	.	.	.	.	.	.	C	11.83	1.755439	0.31046	.	.	ENSG00000168453	ENST00000381418;ENST00000312841	T;T	0.73363	-0.73;-0.74	5.63	-0.0146	0.13980	.	0.607709	0.15479	N	0.260191	T	0.50137	0.1598	N	0.20986	0.625	0.18873	N	0.999983	B;B	0.20671	0.047;0.028	B;B	0.21360	0.034;0.015	T	0.21621	-1.0240	10	0.13470	T	0.59	-3.5287	2.275	0.04100	0.1411:0.487:0.1244:0.2475	.	410;410	O43593-2;O43593	.;HAIR_HUMAN	S	410	ENSP00000370826:A410S;ENSP00000326765:A410S	ENSP00000326765:A410S	A	-	1	0	HR	22040672	0.134000	0.22483	0.373000	0.26003	0.813000	0.45954	0.268000	0.18571	0.056000	0.16144	-0.244000	0.11960	GCC	.	.		0.657	HR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214213.1			A	21984727	C	A	21984727	3	1	318	1	0	0	0	0	1	0	0	0	7356	739	26	3	2409	3	HR	8	21984727	Missense_Mutation	SNP	C	TCGA-LG-A9QC-01A-11D-A36X-10	20368106	21984727	124379295	27	44873										
JRK	8629	hgsc.bcm.edu	37	chr8	143746089	143746089	+	RNA	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	tggagtcttttctgaactccAcacacaacctctgctggcga	8	13	3	1	rs559317070|rs33951456		TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr8:143746089A>C	ENST00000507178.2	-	0	1721							O75564	JERKY_HUMAN	Jrk homolog (mouse)							nucleus (GO:0005634)	DNA binding (GO:0003677)					all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)				tctgaactccacacacaacct	0.682																																					.		Atlas-SNP	.											.	.	.	.	0			c.1388+1T>G						.						3	3	3					8																	143746089		1561	3375	4936			8629	exon3			AACTCCACACACA	AF072467	CCDS75796.1, CCDS75797.1	8q24.3	2014-03-28	2014-03-28			ENSG00000234616			6199	protein-coding gene	gene with protein product		603210	"jerky (mouse) homolog", "jerky homolog (mouse)"			9675132	Standard	NM_003724		Approved	JH8, jerky	uc003ywo.3	O75564			chr8.hg19:g.143746089A>C		5.0	0.0		8.0	4.0	NM_001077527	O75565	Splice_Site	SNP	ENST00000507178.2	hg19																																																																																				.	.		0.682	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724		C	143746089	A	C	143746089	1	2	318	0	1	0	0	0	0	0	0	0	7973	157	6	5		5	JRK	8	143746089	RNA	SNP	A	TCGA-LG-A9QC-01A-11D-A36X-10	121761362	143746089	2617933	28	44874										
CYP11B2	1585	hgsc.bcm.edu	37	chr8	143996509	143996509	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	gctggacgtccagggtcaggCtcccccgggcgttctgcagc	15	15	2	0			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr8:143996509C>T	ENST00000323110.2	-	3	550	c.548G>A	c.(547-549)aGc>aAc	p.S183N		NM_000498.3	NP_000489.3	P19099	C11B2_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 2	183					aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|mineralocorticoid biosynthetic process (GO:0006705)|potassium ion homeostasis (GO:0055075)|regulation of blood volume by renal aldosterone (GO:0002017)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	corticosterone 18-monooxygenase activity (GO:0047783)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(22)|ovary(3)|upper_aerodigestive_tract(3)	39	all_cancers(97;5.56e-11)|all_epithelial(106;2.49e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Eplerenone(DB00700)|Etomidate(DB00292)|Hydrocortisone(DB00741)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Spironolactone(DB00421)	CAGGGTCAGGCTCCCCCGGGC	0.642									Familial Hyperaldosteronism type I																												p.S183N		Atlas-SNP	.											.	CYP11B2	107	.	0			c.G548A						.						48	45	46					8																	143996509		2203	4296	6499	SO:0001583	missense	1585	exon3	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	GTCAGGCTCCCCC	X54741	CCDS6393.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000179142	ENSG00000179142	1.14.15.4	"Cytochrome P450s"	2592	protein-coding gene	gene with protein product	"steroid 11-beta-monooxygenase"	124080	"cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 2"	CYP11B		1303253	Standard	NM_000498		Approved	CYP11BL, CPN2, P-450C18, P450aldo, ALDOS	uc003yxk.1	P19099	OTTHUMG00000160254	ENST00000323110.2:c.548G>A	chr8.hg19:g.143996509C>T	ENSP00000325822:p.Ser183Asn	143.0	0.0		132.0	61.0	NM_000498	B0ZBE4|Q16726	Missense_Mutation	SNP	ENST00000323110.2	hg19	CCDS6393.1	.	.	.	.	.	.	.	.	.	.	.	13.74	2.327623	0.41197	.	.	ENSG00000179142	ENST00000323110	T	0.69040	-0.37	3.44	2.46	0.29980	.	0.340584	0.25117	N	0.033015	T	0.62490	0.2432	M	0.69523	2.12	0.31950	N	0.609855	P	0.36837	0.571	B	0.38921	0.285	T	0.67883	-0.5555	10	0.35671	T	0.21	.	8.8722	0.35323	0.0:0.6266:0.3734:0.0	.	183	P19099	C11B2_HUMAN	N	183	ENSP00000325822:S183N	ENSP00000325822:S183N	S	-	2	0	CYP11B2	143993511	0.001000	0.12720	0.793000	0.32043	0.175000	0.22909	0.364000	0.20325	1.910000	0.55303	0.561000	0.74099	AGC	.	.		0.642	CYP11B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359904.1			T	143996509	C	T	143996509	3	4	318	1	0	0	0	0	1	0	0	0	4148	797	28	3	991	3	CYP11B2	8	143996509	Missense_Mutation	SNP	C	TCGA-LG-A9QC-01A-11D-A36X-10	250420	143996509	2367513	29	44875										
C5	727	hgsc.bcm.edu	37	chr9	123777539	123777539	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	gaatttctttacaaggttcaTctggtttttttaaaaaaaga	6	4	3	1			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr9:123777539T>C	ENST00000223642.1	-	16	2026	c.1997A>G	c.(1996-1998)gAt>gGt	p.D666G		NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	666					activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cell surface receptor signaling pathway (GO:0007166)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukocyte migration involved in inflammatory response (GO:0002523)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of macrophage chemotaxis (GO:0010760)|negative regulation of norepinephrine secretion (GO:0010700)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of chemotaxis (GO:0050921)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|response to stress (GO:0006950)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)	chemokine activity (GO:0008009)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(14)|lung(5)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)|Intravenous Immunoglobulin(DB00028)	ACAAGGTTCATCTGGTTTTTT	0.294																																					p.D666G		Atlas-SNP	.											.	C5	124	.	0			c.A1997G						.						111	105	107					9																	123777539		2202	4295	6497	SO:0001630	splice_region_variant	727	exon16			GGTTCATCTGGTT	M57729	CCDS6826.1	9q33-q34	2014-09-17			ENSG00000106804	ENSG00000106804		"Complement system", "Endogenous ligands"	1331	protein-coding gene	gene with protein product	"prepro-C5", "C5a anaphylatoxin"	120900					Standard	NM_001735		Approved	CPAMD4, C5a, C5b	uc004bkv.3	P01031	OTTHUMG00000020579	ENST00000223642.1:c.1997-1A>G	chr9.hg19:g.123777539T>C		35.0	0.0		34.0	10.0	NM_001735	Q14CJ0|Q27I61	Missense_Mutation	SNP	ENST00000223642.1	hg19	CCDS6826.1	.	.	.	.	.	.	.	.	.	.	T	3.528	-0.096269	0.07010	.	.	ENSG00000106804	ENST00000223642;ENST00000430906	T	0.34072	1.38	5.95	4.81	0.61882	.	1.003860	0.08008	N	0.989950	T	0.34135	0.0887	L	0.53780	1.695	0.35623	D	0.809571	B;B	0.15141	0.003;0.012	B;B	0.13407	0.001;0.009	T	0.21965	-1.0230	10	0.18276	T	0.48	.	8.5955	0.33712	0.0:0.0861:0.0:0.9139	.	737;666	Q59GS8;P01031	.;CO5_HUMAN	G	666;737	ENSP00000223642:D666G	ENSP00000223642:D666G	D	-	2	0	C5	122817360	0.997000	0.39634	0.985000	0.45067	0.040000	0.13550	2.446000	0.44908	1.078000	0.41014	0.460000	0.39030	GAT	.	.		0.294	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735	Missense_Mutation	C	123777539	T	C	123777539	5	2	318	1	0	0	0	0	0	0	1	0	2282	1449	50	2	3137	2	C5	9	123777539	Splice_Site	SNP	T	TCGA-LG-A9QC-01A-11D-A36X-10		123777539	17435892	30	44876										
C9orf139	401563	hgsc.bcm.edu	37	chr9	139927656	139927656	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	tggtcccaggcgtggccagaCccagacgtcctggagatctc	13	14	1	3			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr9:139927656C>T	ENST00000314330.2	+	2	1655	c.141C>T	c.(139-141)gaC>gaT	p.D47D	FUT7_ENST00000314412.6_5'Flank	NM_207511.1	NP_997394.1	Q6ZV77	CI139_HUMAN	chromosome 9 open reading frame 139	47										cervix(1)|lung(2)	3	all_cancers(76;0.0893)	Myeloproliferative disorder(178;0.0821)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.99e-05)|Epithelial(140;0.000493)		CGTGGCCAGACCCAGACGTCC	0.562																																					p.D47D		Atlas-SNP	.											.	C9orf139	12	.	0			c.C141T						.						137	116	123					9																	139927656		2203	4297	6500	SO:0001819	synonymous_variant	401563	exon2			GCCAGACCCAGAC		CCDS7023.1	9q34.3	2008-02-05			ENSG00000180539	ENSG00000180539			31426	protein-coding gene	gene with protein product							Standard	NM_207511		Approved	FLJ36268, FLJ42909	uc004ckp.1	Q6ZV77	OTTHUMG00000020959	ENST00000314330.2:c.141C>T	chr9.hg19:g.139927656C>T		88.0	0.0		80.0	31.0	NM_207511	A2RUA3|B9EGW2|Q5SPY0|Q8N224	Silent	SNP	ENST00000314330.2	hg19	CCDS7023.1																																																																																			.	.		0.562	C9orf139-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055213.2	NM_207511		T	139927656	C	T	139927656	2	4	318	1	0	0	0	0	0	0	0	1	2461	506	18	3		3	C9orf139	9	139927656	Silent	SNP	C	TCGA-LG-A9QC-01A-11D-A36X-10	16150117	139927656	1285775	31	44877										
TTC18	118491	hgsc.bcm.edu	37	chr10	75071614	75071614	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	gtccttcaggattgtgacttAgagggggttcaccttccaaa	11	9	2	2			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr10:75071614A>T	ENST00000310715.3	-	12	1472	c.1352T>A	c.(1351-1353)cTa>cAa	p.L451Q	TTC18_ENST00000401621.2_Missense_Mutation_p.L451Q|TTC18_ENST00000493787.1_5'UTR|TTC18_ENST00000340329.3_Intron|TTC18_ENST00000355577.3_5'UTR|TTC18_ENST00000394865.1_Missense_Mutation_p.L451Q	NM_145170.3	NP_660153.3	Q5T0N1	TTC18_HUMAN		451						extracellular vesicular exosome (GO:0070062)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	Prostate(51;0.0119)					ATTGTGACTTAGAGGGGGTTC	0.373																																					p.L451Q		Atlas-SNP	.											.	TTC18	106	.	0			c.T1352A						.						160	172	168					10																	75071614		2203	4300	6503	SO:0001583	missense	118491	exon12			TGACTTAGAGGGG																												ENST00000310715.3:c.1352T>A	chr10.hg19:g.75071614A>T	ENSP00000310829:p.Leu451Gln	91.0	0.0		97.0	41.0	NM_145170	C9JIZ9|Q5T0M4|Q5T0M9|Q5T0N0|Q69YH9|Q8IYZ8|Q8N7D5|Q8NI30|Q8NI31	Missense_Mutation	SNP	ENST00000310715.3	hg19	CCDS7324.3	.	.	.	.	.	.	.	.	.	.	A	11.88	1.772145	0.31411	.	.	ENSG00000156042	ENST00000310715;ENST00000401621;ENST00000355577;ENST00000372928;ENST00000394865	D;D;D	0.93133	-3.17;-3.17;-3.17	4.72	2.35	0.29111	.	1.147620	0.06565	N	0.747447	D	0.90266	0.6956	L	0.28274	0.84	0.09310	N	1	P;P	0.47604	0.898;0.71	P;B	0.51355	0.667;0.372	T	0.79057	-0.1959	10	0.13853	T	0.58	-13.7468	6.2397	0.20783	0.7909:0.0:0.2091:0.0	.	451;451	Q5T0N1-2;Q5T0N1	.;TTC18_HUMAN	Q	451	ENSP00000310829:L451Q;ENSP00000384479:L451Q;ENSP00000378334:L451Q	ENSP00000310829:L451Q	L	-	2	0	TTC18	74741620	0.006000	0.16342	0.001000	0.08648	0.412000	0.31113	0.135000	0.15952	0.196000	0.20367	0.460000	0.39030	CTA	.	.		0.373	TTC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				T	75071614	A	T	75071614	3	4	318	1	0	0	0	0	1	0	0	0	16700	420	15	4	2081	4	TTC18	10	75071614	Missense_Mutation	SNP	A	TCGA-LG-A9QC-01A-11D-A36X-10		75071614	60463133	32	44878										
SYVN1	84447	hgsc.bcm.edu	37	chr11	64898172	64898173	+	In_Frame_Ins	INS	-	-	GGG													0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	gtggtggggggtggggggcaINSgggggtggcccctgatccgc							TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr11:64898172_64898173insGGG	ENST00000377190.3	-	11	1158_1159	c.1064_1065insCCC	c.(1063-1065)cct>ccCCCt	p.355_355P>PP	SYVN1_ENST00000307289.6_In_Frame_Ins_p.304_304P>PP|SYVN1_ENST00000526121.1_5'Flank|SYVN1_ENST00000294256.8_In_Frame_Ins_p.355_355P>PP|SYVN1_ENST00000526060.1_In_Frame_Ins_p.355_355P>PP	NM_172230.2	NP_757385.1	Q86TM6	SYVN1_HUMAN	synovial apoptosis inhibitor 1, synoviolin	355	Pro-rich.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|in utero embryonic development (GO:0001701)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22						GGTGGGGGGCAGGGGGTGGCCC	0.673																																					p.P355delinsPP		Atlas-INDEL	.											.	SYVN1	55	.	0			c.1065_1066insCCC						.																																			SO:0001652	inframe_insertion	84447	exon11			.	AB085847	CCDS8097.1, CCDS31605.1	11q13	2013-01-09			ENSG00000162298	ENSG00000162298		"RING-type (C3HC4) zinc fingers"	20738	protein-coding gene	gene with protein product	"HMG-coA reductase degradation 1 homolog (S. cerevisiae)"	608046				12975321	Standard	NM_032431		Approved	HRD1, DER3	uc001odb.3	Q86TM6		ENST00000377190.3:c.1062_1064dupCCC	chr11.hg19:g.64898173_64898175dupGGG	ENSP00000366395:p.Pro355dup	20.0	0.0		44.0	19.0	NM_032431	Q8N3K3|Q8N6E8|Q96JL5|Q96PK3	In_Frame_Ins	INS	ENST00000377190.3	hg19	CCDS31605.1																																																																																			.	.		0.673	SYVN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385274.1	NM_032431		GGG	64898173	-	GGG	64898172	7	5	318	1	0	1	1	0	0	0	0	0	15502	175	7	0	812	0	SYVN1	11	64898172	In_Frame_Ins	INS	-	TCGA-LG-A9QC-01A-11D-A36X-10		64898172	70108344	33	44879										
ERC1	23085	hgsc.bcm.edu	37	chr12	1192720	1192720	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	aaagccttttggagcagaagGaaaaagagaacagtatgttg	12	4	0	2			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr12:1192720G>A	ENST00000397203.2	+	3	1466	c.1060G>A	c.(1060-1062)Gaa>Aaa	p.E354K	ERC1_ENST00000589028.1_Missense_Mutation_p.E354K|ERC1_ENST00000360905.4_Missense_Mutation_p.E354K|ERC1_ENST00000543086.3_Missense_Mutation_p.E354K|ERC1_ENST00000546231.2_Missense_Mutation_p.E354K|ERC1_ENST00000355446.5_Missense_Mutation_p.E354K			Q8IUD2	RB6I2_HUMAN	ELKS/RAB6-interacting/CAST family member 1	354					I-kappaB phosphorylation (GO:0007252)|multicellular organismal development (GO:0007275)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|IkappaB kinase complex (GO:0008385)|presynaptic membrane (GO:0042734)	leucine zipper domain binding (GO:0043522)			NS(1)|breast(2)|cervix(2)|endometrium(2)|large_intestine(8)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	38	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)			GGAGCAGAAGGAAAAAGAGAA	0.418																																					p.E354K		Atlas-SNP	.											.	ERC1	95	.	0			c.G1060A						.						96	91	93					12																	1192720		2203	4300	6503	SO:0001583	missense	23085	exon3			CAGAAGGAAAAAG	AB015617	CCDS8508.1, CCDS53732.1	12p13.3	2008-02-05	2006-08-14	2006-08-14	ENSG00000082805	ENSG00000082805			17072	protein-coding gene	gene with protein product		607127	"RAB6 interacting protein 2"	RAB6IP2		10697956, 11929610	Standard	NM_178040		Approved	ELKS, KIAA1081, CAST2, MGC12974	uc001qjb.2	Q8IUD2	OTTHUMG00000130138	ENST00000397203.2:c.1060G>A	chr12.hg19:g.1192720G>A	ENSP00000380386:p.Glu354Lys	80.0	0.0		82.0	32.0	NM_178039	A2RU77|A7E295|D3DUP7|D3DUP8|Q6NVK2|Q8IUD3|Q8IUD4|Q8IUD5|Q8NAS1|Q9NXN5|Q9UIK7|Q9UPS1	Missense_Mutation	SNP	ENST00000397203.2	hg19	CCDS8508.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.294827	0.81025	.	.	ENSG00000082805	ENST00000347735;ENST00000397203;ENST00000454194;ENST00000537890;ENST00000543086;ENST00000542302;ENST00000546231;ENST00000355446;ENST00000360905;ENST00000440394;ENST00000538971	T;T;T;T;T;T;T;T	0.55052	0.54;0.54;0.54;0.54;0.54;0.54;0.54;0.54	5.56	5.56	0.83823	.	0.147026	0.64402	D	0.000009	T	0.58018	0.2093	L	0.52573	1.65	0.80722	D	1	P;B;P;P	0.45768	0.855;0.338;0.804;0.866	P;B;B;P	0.47430	0.547;0.115;0.229;0.489	T	0.54754	-0.8246	10	0.39692	T	0.17	-19.9041	19.8756	0.96869	0.0:0.0:1.0:0.0	.	130;354;354;354	F5H327;Q8IUD2-2;Q8IUD2-3;Q8IUD2	.;.;.;RB6I2_HUMAN	K	354;354;354;354;354;354;354;354;354;354;130	ENSP00000340054:E354K;ENSP00000380386:E354K;ENSP00000438546:E354K;ENSP00000445336:E354K;ENSP00000442739:E354K;ENSP00000347621:E354K;ENSP00000354158:E354K;ENSP00000410064:E354K	ENSP00000340054:E354K	E	+	1	0	ERC1	1062981	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	9.810000	0.99221	2.768000	0.95171	0.655000	0.94253	GAA	.	.		0.418	ERC1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398380.2	NM_015064		A	1192720	G	A	1192720	3	1	318	1	0	0	0	0	1	0	0	0	5212	1175	41	3	1066	3	ERC1	12	1192720	Missense_Mutation	SNP	G	TCGA-LG-A9QC-01A-11D-A36X-10		1192720	132659175	34	44880										
KLRC4	8302	hgsc.bcm.edu	37	chr12	10560370	10560370	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	atgtaatccactcctcaggaCaatggccacaatgacgtgct	8	12	1	1			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr12:10560370C>T	ENST00000309384.1	-	4	540	c.359G>A	c.(358-360)tGt>tAt	p.C120Y	KLRC4-KLRK1_ENST00000539300.1_Silent_p.L111L	NM_013431.2	NP_038459.1	O43908	NKG2F_HUMAN	killer cell lectin-like receptor subfamily C, member 4	120					cellular defense response (GO:0006968)	integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(1)|lung(1)	5						CTCCTCAGGACAATGGCCACA	0.323																																					p.C120Y		Atlas-SNP	.											.	KLRC4	23	.	0			c.G359A						.						146	146	146					12																	10560370		2203	4300	6503	SO:0001583	missense	8302	exon4			TCAGGACAATGGC	U96846	CCDS8624.1	12p13.2-p12.3	2008-08-05			ENSG00000183542	ENSG00000183542		"Killer cell lectin-like receptors"	6377	protein-coding gene	gene with protein product		602893				9598306	Standard	NM_013431		Approved	NKG2-F	uc001qye.3	O43908	OTTHUMG00000168575	ENST00000309384.1:c.359G>A	chr12.hg19:g.10560370C>T	ENSP00000310216:p.Cys120Tyr	232.0	0.0		181.0	75.0	NM_013431	O60851	Missense_Mutation	SNP	ENST00000309384.1	hg19	CCDS8624.1	.	.	.	.	.	.	.	.	.	.	C	14.89	2.669016	0.47677	.	.	ENSG00000183542	ENST00000309384	T	0.38887	1.11	4.1	4.1	0.47936	C-type lectin fold (1);C-type lectin-like (1);	0.124113	0.37623	N	0.002015	T	0.66127	0.2758	M	0.85041	2.73	0.36455	D	0.86631	D	0.89917	1.0	D	0.91635	0.999	T	0.76534	-0.2924	10	0.66056	D	0.02	.	12.5279	0.56098	0.0:1.0:0.0:0.0	.	120	O43908	NKG2F_HUMAN	Y	120	ENSP00000310216:C120Y	ENSP00000310216:C120Y	C	-	2	0	KLRC4	10451637	0.979000	0.34478	0.326000	0.25389	0.048000	0.14542	1.480000	0.35464	2.204000	0.70986	0.585000	0.79938	TGT	.	.		0.323	KLRC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400108.1	NM_013431		T	10560370	C	T	10560370	3	4	318	1	0	0	0	0	1	0	0	0	8427	478	17	3	121	3	KLRC4	12	10560370	Missense_Mutation	SNP	C	TCGA-LG-A9QC-01A-11D-A36X-10	9367650	10560370	123291525	35	44881										
RERG	85004	hgsc.bcm.edu	37	chr12	15262379	15262379	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	cacttcctcaaaacttcctcGgtcagtaatgtcgtagacca	6	13	2	1			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr12:15262379G>T	ENST00000256953.2	-	5	601	c.265C>A	c.(265-267)Cga>Aga	p.R89R	RERG_ENST00000546331.1_Silent_p.R70R|RERG_ENST00000538313.1_Silent_p.R89R|RERG_ENST00000536465.1_Silent_p.R89R|RERG-IT1_ENST00000539734.1_RNA	NM_032918.2	NP_116307.1	Q96A58	RERG_HUMAN	RAS-like, estrogen-regulated, growth inhibitor	89					negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|response to hormone (GO:0009725)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	estrogen receptor binding (GO:0030331)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.R89R(1)		NS(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	16						AAACTTCCTCGGTCAGTAATG	0.473																																					p.R89R		Atlas-SNP	.											.	RERG	30	.	1	Substitution - coding silent(1)	lung(1)	c.C265A						.						322	326	324					12																	15262379		2203	4300	6503	SO:0001819	synonymous_variant	85004	exon5			TTCCTCGGTCAGT	AF339750	CCDS8673.1, CCDS53753.1	12p13.1	2014-05-09			ENSG00000134533	ENSG00000134533			15980	protein-coding gene	gene with protein product		612664				11533059	Standard	NM_032918		Approved	MGC15754	uc001rct.3	Q96A58	OTTHUMG00000168745	ENST00000256953.2:c.265C>A	chr12.hg19:g.15262379G>T		130.0	0.0		113.0	5.0	NM_032918	B2R9R0|B4DI02	Silent	SNP	ENST00000256953.2	hg19	CCDS8673.1																																																																																			.	.		0.473	RERG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400882.1	NM_032918		T	15262379	G	T	15262379	2	4	318	1	0	0	0	0	0	0	0	1	13247	1124	39	1		1	RERG	12	15262379	Silent	SNP	G	TCGA-LG-A9QC-01A-11D-A36X-10	4702009	15262379	118589516	36	44882										
DCD	117159	hgsc.bcm.edu	37	chr12	55038527	55038527	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	gagtcaaggacgtctttaacGtcatggacggctcctaggac	12	10	3	0	rs373661792		TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr12:55038527G>A	ENST00000293371.6	-	5	492	c.303C>T	c.(301-303)gaC>gaT	p.D101D	DCD_ENST00000456047.2_3'UTR	NM_053283.2	NP_444513.1	P81605	DCD_HUMAN	dermcidin	101					defense response to bacterium (GO:0042742)|defense response to fungus (GO:0050832)|killing of cells of other organism (GO:0031640)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	peptidase activity (GO:0008233)|poly(A) RNA binding (GO:0044822)			large_intestine(2)|lung(2)|ovary(1)|skin(1)	6		Myeloproliferative disorder(1001;0.0255)				CGTCTTTAACGTCATGGACGG	0.468																																					p.D101D		Atlas-SNP	.											.	DCD	20	.	0			c.C303T						.	G		0,4406		0,0,2203	35	30	32		303	-3.1	0	12		32	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	DCD	NM_053283.2		0,1,6501	AA,AG,GG		0.0116,0.0,0.0077		101/111	55038527	1,13003	2203	4299	6502	SO:0001819	synonymous_variant	117159	exon5			TTTAACGTCATGG	AF144011	CCDS8884.1, CCDS73478.1	12q13.1	2008-08-04				ENSG00000161634			14669	protein-coding gene	gene with protein product	"proteolysis inducing factor", "preproteolysin", "diffusible survival/evasion peptide", "survival promoting peptide"	606634				11694882	Standard	XM_005268627		Approved	AIDD, PIF, DSEP, HCAP, DCD-1	uc001sgj.3	P81605	OTTHUMG00000169937	ENST00000293371.6:c.303C>T	chr12.hg19:g.55038527G>A		448.0	1.0		373.0	159.0	NM_053283	A5JHP2|A5JHP3|P58461|Q53YJ2	Silent	SNP	ENST00000293371.6	hg19	CCDS8884.1																																																																																			.	.		0.468	DCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406617.1	NM_053283		A	55038527	G	A	55038527	2	1	318	1	0	0	0	0	0	0	0	1	4285	1136	40	1		1	DCD	12	55038527	Silent	SNP	G	TCGA-LG-A9QC-01A-11D-A36X-10	39776148	55038527	78813368	37	44883										
C12orf51	283450	hgsc.bcm.edu	37	chr12	112673432	112673432	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	ctccagggtgggagctccacGtttccacagtcttctacgct	10	14	2	0	rs373022791		TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr12:112673432G>A	ENST00000430131.2	-	35	5480	c.4335C>T	c.(4333-4335)aaC>aaT	p.N1445N	HECTD4_ENST00000550722.1_Silent_p.N1721N|HECTD4_ENST00000377560.5_Silent_p.N1695N			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	1445					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										GGAGCTCCACGTTTCCACAGT	0.587																																					p.N1733N		Atlas-SNP	.											.	.	.	.	0			c.C5199T						.	G		0,3928		0,0,1964	50	52	51		5085	-10	0.1	12		51	1,8321		0,1,4160	no	coding-synonymous	C12orf51	NM_001109662.2		0,1,6124	AA,AG,GG		0.012,0.0,0.0082		1695/4247	112673432	1,12249	1964	4161	6125	SO:0001819	synonymous_variant	283450	exon36			CTCCACGTTTCCA	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 51"	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.4335C>T	chr12.hg19:g.112673432G>A		110.0	0.0		115.0	43.0	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Silent	SNP	ENST00000430131.2	hg19																																																																																				.	.		0.587	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		A	112673432	G	A	112673432	2	1	318	1	0	0	0	0	0	0	0	1	1698	1136	40	1		1	C12orf51	12	112673432	Silent	SNP	G	TCGA-LG-A9QC-01A-11D-A36X-10	57634905	112673432	21178463	38	44884										
GALNT9	50614	hgsc.bcm.edu	37	chr12	132685703	132685703	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	gggtgttgttgtagaccctcAtctccgggtacacgttctcc	11	12	3	1			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr12:132685703A>G	ENST00000328957.8	-	8	1366	c.1367T>C	c.(1366-1368)aTg>aCg	p.M456T	GALNT9_ENST00000535228.1_Missense_Mutation_p.M207T|GALNT9_ENST00000541995.1_Missense_Mutation_p.M90T|GALNT9_ENST00000397325.2_Missense_Mutation_p.M90T	NM_001122636.1	NP_001116108.1	Q9HCQ5	GALT9_HUMAN	polypeptide N-acetylgalactosaminyltransferase 9	456					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(1)|endometrium(1)|large_intestine(2)|lung(5)	9	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.49e-08)|Epithelial(86;3.55e-07)|all cancers(50;2.09e-05)		GTAGACCCTCATCTCCGGGTA	0.622																																					p.M456T	Colon(186;2147 2752 13553 41466)	Atlas-SNP	.											.	GALNT9	74	.	0			c.T1367C						.						79	95	89					12																	132685703		2138	4246	6384	SO:0001583	missense	50614	exon8			ACCCTCATCTCCG	AB040672	CCDS41866.1	12q24.33	2014-03-13	2014-03-13		ENSG00000182870	ENSG00000182870	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4131	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 9"	606251	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 9 (GalNAc-T9)"			10978536, 12407114	Standard	NM_021808		Approved	GALNAC-T9	uc001ukc.4	Q9HCQ5	OTTHUMG00000168256	ENST00000328957.8:c.1367T>C	chr12.hg19:g.132685703A>G	ENSP00000329846:p.Met456Thr	94.0	0.0		50.0	21.0	NM_001122636	Q52LR8|Q6NT54|Q8NFR1	Missense_Mutation	SNP	ENST00000328957.8	hg19		.	.	.	.	.	.	.	.	.	.	a	21.3	4.130097	0.77549	.	.	ENSG00000182870	ENST00000397325;ENST00000328957;ENST00000535228;ENST00000541995;ENST00000538356	T;T;T;T;T	0.71341	-0.56;-0.56;-0.56;-0.56;-0.56	4.39	4.39	0.52855	Ricin B-related lectin (1);	0.000000	0.85682	D	0.000000	T	0.80237	0.4586	M	0.63843	1.955	0.80722	D	1	D;D;D	0.63046	0.992;0.992;0.992	P;D;P	0.65573	0.882;0.936;0.882	T	0.81609	-0.0855	10	0.54805	T	0.06	.	13.5816	0.61907	1.0:0.0:0.0:0.0	.	207;456;313	B3KNR7;Q9HCQ5;B3KP58	.;GALT9_HUMAN;.	T	90;456;207;90;90	ENSP00000380488:M90T;ENSP00000329846:M456T;ENSP00000439745:M207T;ENSP00000440544:M90T;ENSP00000444709:M90T	ENSP00000329846:M456T	M	-	2	0	GALNT9	131251656	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	9.034000	0.93747	1.599000	0.50093	0.379000	0.24179	ATG	.	.		0.622	GALNT9-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000402967.1	NM_001122636		G	132685703	A	G	132685703	3	3	318	1	0	0	0	0	1	0	0	0	6228	217	8	2	460	2	GALNT9	12	132685703	Missense_Mutation	SNP	A	TCGA-LG-A9QC-01A-11D-A36X-10	20012271	132685703	1166192	39	44885										
NPAS3	64067	hgsc.bcm.edu	37	chr14	34269678	34269678	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	cctcaccccgcccggcgccgAcggcgcggccgcccgcaaga	13	22	1	1			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr14:34269678A>T	ENST00000356141.4	+	12	2165	c.2165A>T	c.(2164-2166)gAc>gTc	p.D722V	NPAS3_ENST00000357798.5_Missense_Mutation_p.D709V|NPAS3_ENST00000551492.1_Missense_Mutation_p.D727V|NPAS3_ENST00000346562.2_Missense_Mutation_p.D690V|NPAS3_ENST00000548645.1_Missense_Mutation_p.D692V			Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3	722	Gly-rich.				locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|positive regulation of transcription, DNA-templated (GO:0045893)|startle response (GO:0001964)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(4)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	40	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)		cccggcgccgacggcgcggcc	0.801																																					p.D722V		Atlas-SNP	.											.	NPAS3	266	.	0			c.A2165T						.						2	3	3					14																	34269678		915	2172	3087	SO:0001583	missense	64067	exon12			GCGCCGACGGCGC	AF164438	CCDS9645.1, CCDS53891.1, CCDS53892.1, CCDS55912.1	14q13.1	2013-08-23			ENSG00000151322	ENSG00000151322		"Basic helix-loop-helix proteins"	19311	protein-coding gene	gene with protein product		609430					Standard	NM_022123		Approved	MOP6, PASD6, bHLHe12	uc001wru.3	Q8IXF0	OTTHUMG00000140215	ENST00000356141.4:c.2165A>T	chr14.hg19:g.34269678A>T	ENSP00000348460:p.Asp722Val	37.0	0.0		42.0	16.0	NM_001164749	Q86US6|Q86US7|Q8IXF2|Q9BY81|Q9H323|Q9Y4L8	Missense_Mutation	SNP	ENST00000356141.4	hg19	CCDS53891.1	.	.	.	.	.	.	.	.	.	.	A	11.05	1.523546	0.27299	.	.	ENSG00000151322	ENST00000551634;ENST00000551492;ENST00000346562;ENST00000548645;ENST00000356141;ENST00000357798	T;T;T;T;T;T	0.07216	3.47;3.35;3.35;3.35;3.35;3.21	4.74	4.74	0.60224	.	0.125026	0.51477	D	0.000092	T	0.06005	0.0156	N	0.14661	0.345	0.80722	D	1	B;B;B;B	0.17038	0.02;0.012;0.02;0.02	B;B;B;B	0.21360	0.034;0.015;0.034;0.034	T	0.25779	-1.0122	10	0.72032	D	0.01	.	10.5429	0.45043	0.838:0.162:0.0:0.0	.	692;722;690;709	Q8IXF0-2;Q8IXF0;Q8IXF0-4;Q8IXF0-3	.;NPAS3_HUMAN;.;.	V	696;727;690;692;722;709	ENSP00000448373:D696V;ENSP00000450392:D727V;ENSP00000319610:D690V;ENSP00000448916:D692V;ENSP00000348460:D722V;ENSP00000350446:D709V	ENSP00000319610:D690V	D	+	2	0	NPAS3	33339429	1.000000	0.71417	0.994000	0.49952	0.663000	0.39108	6.102000	0.71486	1.977000	0.57605	0.454000	0.30748	GAC	.	.		0.801	NPAS3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276645.1			T	34269678	A	T	34269678	3	4	318	1	0	0	0	0	1	0	0	0	10573	275	10	4	2266	4	NPAS3	14	34269678	Missense_Mutation	SNP	A	TCGA-LG-A9QC-01A-11D-A36X-10		34269678	73079862	40	44886										
SFRS5	6430	hgsc.bcm.edu	37	chr14	70238105	70238106	+	Frame_Shift_Ins	INS	-	-	GTCTCCAGCATCTGTGG													0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	ggttcttcaagtagatctaaINSgtctccagcatctgtggatc							TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr14:70238105_70238106insGTCTCCAGCATCTGTGG	ENST00000553521.1	+	9	2199_2200	c.746_747insGTCTCCAGCATCTGTGG	c.(745-750)aagtctfs	p.-250fs	SRSF5_ENST00000553635.1_Frame_Shift_Ins_p.-247fs|SRSF5_ENST00000556587.1_3'UTR|SRSF5_ENST00000557154.1_Frame_Shift_Ins_p.-250fs|SRSF5_ENST00000394366.2_Frame_Shift_Ins_p.-250fs			Q13243	SRSF5_HUMAN	serine/arginine-rich splicing factor 5						gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|regulation of cell cycle (GO:0051726)|response to wounding (GO:0009611)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			large_intestine(1)|liver(1)	2						AGTAGATCTAAGTCTCCAGCAT	0.54																																					p.K249fs		Atlas-INDEL	.											.	SRSF5	45	.	0			c.746_747insGTCTCCAGCATCTGTGG						.																																			SO:0001589	frameshift_variant	6430	exon8			.	AF020307	CCDS32109.1	14q24	2013-02-12	2010-06-22	2010-06-22	ENSG00000100650	ENSG00000100650		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10787	protein-coding gene	gene with protein product	"SR splicing factor 5"	600914	"splicing factor, arginine/serine-rich 5"	SFRS5		7686911, 20516191	Standard	XM_005267998		Approved	SRP40, HRS	uc001xlp.3	Q13243		ENST00000553521.1:c.747_763dupGTCTCCAGCATCTGTGG	chr14.hg19:g.70238105_70238106insGTCTCCAGCATCTGTGG	ENSP00000452123:p.Ser250fs	114.0	0.0		92.0	18.0	NM_001039465	O14797|Q16662|Q49AD6|Q6FGE0	Frame_Shift_Ins	INS	ENST00000553521.1	hg19	CCDS32109.1																																																																																			.	.		0.54	SRSF5-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412456.1	NM_001039465		GTCTCCAGCATCTGTGG	70238106	-	GTCTCCAGCATCTGTGG	70238105	7	5	318	1	0	1	1	0	0	0	0	0	14195	72	3	0	772	0	SFRS5	14	70238105	Frame_Shift_Ins	INS	-	TCGA-LG-A9QC-01A-11D-A36X-10	35968427	70238105	37111435	41	44887										
SPATA7	55812	hgsc.bcm.edu	37	chr14	88857757	88857757	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	ctgtccttcccagatatggtCcaccgtgcctatttaaagga	8	12	0	1			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr14:88857757C>G	ENST00000393545.4	+	2	341	c.52C>G	c.(52-54)Cca>Gca	p.P18A	SPATA7_ENST00000045347.7_Missense_Mutation_p.P18A|SPATA7_ENST00000554102.1_3'UTR|SPATA7_ENST00000356583.5_Missense_Mutation_p.P18A|SPATA7_ENST00000556553.1_Missense_Mutation_p.P18A	NM_018418.4	NP_060888.2	Q9P0W8	SPAT7_HUMAN	spermatogenesis associated 7	18					response to stimulus (GO:0050896)|visual perception (GO:0007601)					cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)	18						CAGATATGGTCCACCGTGCCT	0.353																																					p.P18A		Atlas-SNP	.											.	SPATA7	58	.	0			c.C52G						.						87	79	82					14																	88857757		2203	4300	6503	SO:0001583	missense	55812	exon2			TATGGTCCACCGT	AF144487	CCDS9883.1, CCDS32132.1	14q31.3	2011-02-17				ENSG00000042317			20423	protein-coding gene	gene with protein product		609868	"Leber congenital amaurosis 3"	LCA3		9799089, 19268277	Standard	NM_018418		Approved	HSD3	uc001xwq.3	Q9P0W8		ENST00000393545.4:c.52C>G	chr14.hg19:g.88857757C>G	ENSP00000377176:p.Pro18Ala	72.0	0.0		69.0	28.0	NM_018418	Q5BKY5|Q8WX30|Q96HF3|Q9H0X0|Q9P0W7	Missense_Mutation	SNP	ENST00000393545.4	hg19	CCDS9883.1	.	.	.	.	.	.	.	.	.	.	C	9.058	0.993818	0.19043	.	.	ENSG00000042317	ENST00000556553;ENST00000393545;ENST00000356583;ENST00000553885;ENST00000045347	T;T;T;T;T	0.19105	2.17;2.17;2.17;2.17;2.17	4.97	1.03	0.20045	.	0.664046	0.14047	N	0.345003	T	0.12774	0.0310	L	0.38838	1.175	0.30610	N	0.759624	B;B	0.30281	0.129;0.275	B;B	0.26202	0.067;0.046	T	0.17048	-1.0382	10	0.45353	T	0.12	-1.7177	2.7024	0.05153	0.1501:0.5421:0.145:0.1628	.	18;18	Q9P0W8-2;Q9P0W8	.;SPAT7_HUMAN	A	18	ENSP00000451128:P18A;ENSP00000377176:P18A;ENSP00000348991:P18A;ENSP00000450606:P18A;ENSP00000045347:P18A	ENSP00000045347:P18A	P	+	1	0	SPATA7	87927510	0.999000	0.42202	0.298000	0.25002	0.956000	0.61745	0.795000	0.26972	-0.014000	0.14175	0.585000	0.79938	CCA	.	.		0.353	SPATA7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410172.1			G	88857757	C	G	88857757	3	3	318	1	0	0	0	0	1	0	0	0	15029	855	30	4	58	4	SPATA7	14	88857757	Missense_Mutation	SNP	C	TCGA-LG-A9QC-01A-11D-A36X-10	18619652	88857757	18491783	42	44888										
ADAMTSL3	57188	hgsc.bcm.edu	37	chr15	84639347	84639347	+	Frame_Shift_Del	DEL	G	G	-													0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	tgatgtgcagggatctaccaGggctccctcttgtaagatct							TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr15:84639347delG	ENST00000286744.5	+	20	2826	c.2602delG	c.(2602-2604)gggfs	p.G868fs	ADAMTSL3_ENST00000567716.1_3'UTR|ADAMTSL3_ENST00000567476.1_Frame_Shift_Del_p.G868fs	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	868	TSP type-1 7. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			GGATCTACCAGGGCTCCCTCT	0.522																																					p.P867fs		Atlas-INDEL	.											.	ADAMTSL3	290	.	0			c.2601delA						.						182	159	167					15																	84639347		2203	4300	6503	SO:0001589	frameshift_variant	57188	exon20			.	AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.2602delG	chr15.hg19:g.84639347delG	ENSP00000286744:p.Gly868fs	90.0	0.0		82.0	31.0	NM_207517	A1A566|A1A567|Q9ULI7	Frame_Shift_Del	DEL	ENST00000286744.5	hg19	CCDS10326.1																																																																																			.	.		0.522	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517		-	84639347	G	-	84639347	7	5	318	1	0	1	0	1	0	0	0	0	276	1000	35	0	2676	0	ADAMTSL3	15	84639347	Frame_Shift_Del	DEL	G	TCGA-LG-A9QC-01A-11D-A36X-10		84639347	17892045	43	44889										
IL21R	50615	hgsc.bcm.edu	37	chr16	27460045	27460045	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	gcccaagcccagcttctggcCgacagcccagaactcggggg	13	16	1	1	rs550842554		TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr16:27460045C>T	ENST00000337929.3	+	9	1531	c.1058C>T	c.(1057-1059)cCg>cTg	p.P353L	IL21R_ENST00000564089.1_Missense_Mutation_p.P353L|IL21R_ENST00000395754.4_Missense_Mutation_p.P353L|IL21R_ENST00000395755.1_Missense_Mutation_p.P353L|IL21R-AS1_ENST00000563191.1_RNA	NM_181078.2	NP_851564.1	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor	353					interleukin-21-mediated signaling pathway (GO:0038114)|natural killer cell activation (GO:0030101)	integral component of membrane (GO:0016021)	interleukin-21 receptor activity (GO:0001532)			breast(2)|large_intestine(3)|lung(1)|ovary(2)	8						AGCTTCTGGCCGACAGCCCAG	0.627			T	BCL6	NHL								C|||	1	0.000199681	8e-04	0	5008	,	,		19549	0		0	False		,,,				2504	0				p.P375L		Atlas-SNP	.		Dom	yes		16	16p11	50615	interleukin 21 receptor		L	.	IL21R	95	.	0			c.C1124T						.						49	49	49					16																	27460045		2197	4300	6497	SO:0001583	missense	50615	exon10			TCTGGCCGACAGC	AF254067	CCDS10630.1	16p11	2014-09-17			ENSG00000103522	ENSG00000103522		"Interleukins and interleukin receptors", "CD molecules"	6006	protein-coding gene	gene with protein product		605383				11081504	Standard	NM_181078		Approved	CD360	uc002dos.2	Q9HBE5	OTTHUMG00000131675	ENST00000337929.3:c.1058C>T	chr16.hg19:g.27460045C>T	ENSP00000338010:p.Pro353Leu	167.0	0.0		133.0	10.0	NM_181079	A8K9E8|D3DWF7|Q96HZ1|Q9HB91	Missense_Mutation	SNP	ENST00000337929.3	hg19	CCDS10630.1	.	.	.	.	.	.	.	.	.	.	C	8.579	0.881907	0.17467	.	.	ENSG00000103522	ENST00000337929;ENST00000395755;ENST00000395754	T;T;T	0.34072	1.38;1.38;1.38	3.56	0.452	0.16634	.	2.565700	0.01028	N	0.004085	T	0.24736	0.0600	L	0.38175	1.15	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.05699	-1.0869	10	0.10636	T	0.68	3.1814	1.662	0.02794	0.1526:0.346:0.3517:0.1497	.	353	Q9HBE5	IL21R_HUMAN	L	353	ENSP00000338010:P353L;ENSP00000379104:P353L;ENSP00000379103:P353L	ENSP00000338010:P353L	P	+	2	0	IL21R	27367546	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.039000	0.13884	0.137000	0.18759	0.561000	0.74099	CCG	.	.		0.627	IL21R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254578.2	NM_181078		T	27460045	C	T	27460045	3	4	318	1	0	0	0	0	1	0	0	0	7680	652	23	1	1088	1	IL21R	16	27460045	Missense_Mutation	SNP	C	TCGA-LG-A9QC-01A-11D-A36X-10		27460045	62894708	44	44890										
PLEKHG4	25894	hgsc.bcm.edu	37	chr16	67319052	67319052	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	cagaccagaggctggaggagGtgccctgccccaggcatccc	14	15	0	2			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr16:67319052G>A	ENST00000360461.5	+	12	4664	c.2129G>A	c.(2128-2130)gGt>gAt	p.G710D	PLEKHG4_ENST00000379344.3_Missense_Mutation_p.G710D|PLEKHG4_ENST00000450733.1_Missense_Mutation_p.G629D|PLEKHG4_ENST00000427155.2_Missense_Mutation_p.G710D	NM_001129727.1|NM_015432.3	NP_001123199.1|NP_056247.1	Q58EX7	PKHG4_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4	710							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)|Kidney(780;0.119)		GCTGGAGGAGGTGCCCTGCCC	0.642																																					p.G710D		Atlas-SNP	.											.	PLEKHG4	94	.	0			c.G2129A						.						21	22	22					16																	67319052		2193	4292	6485	SO:0001583	missense	25894	exon13			GAGGAGGTGCCCT	AK024475	CCDS32466.1, CCDS45512.1	16q22.1	2013-01-11						"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	24501	protein-coding gene	gene with protein product	"puratrophin-1"	609526	"spinocerebellar ataxia 4"	SCA4		16491300, 16001362	Standard	NM_015432		Approved	DKFZP434I216, ARHGEF44	uc010cef.3	Q58EX7		ENST00000360461.5:c.2129G>A	chr16.hg19:g.67319052G>A	ENSP00000353646:p.Gly710Asp	39.0	0.0		55.0	21.0	NM_001129728	Q4G0J8|Q4H485|Q56A69|Q9H7K4|Q9UFW0	Missense_Mutation	SNP	ENST00000360461.5	hg19	CCDS32466.1	.	.	.	.	.	.	.	.	.	.	G	9.051	0.992011	0.18966	.	.	ENSG00000196155	ENST00000360461;ENST00000427155;ENST00000379344;ENST00000450733	T;T;T;T	0.10005	2.92;2.92;2.92;2.96	4.34	2.34	0.29019	.	0.000000	0.34002	N	0.004357	T	0.06371	0.0164	L	0.34521	1.04	0.09310	N	1	B;B	0.30281	0.275;0.079	B;B	0.26202	0.067;0.021	T	0.37454	-0.9705	10	0.10636	T	0.68	.	7.4781	0.27390	0.2075:0.0:0.7925:0.0	.	629;710	Q58EX7-2;Q58EX7	.;PKHG4_HUMAN	D	710;710;710;629	ENSP00000353646:G710D;ENSP00000401118:G710D;ENSP00000368649:G710D;ENSP00000398030:G629D	ENSP00000353646:G710D	G	+	2	0	PLEKHG4	65876553	0.008000	0.16893	0.894000	0.35097	0.212000	0.24457	0.951000	0.29135	0.957000	0.37930	-0.258000	0.10820	GGT	.	.		0.642	PLEKHG4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421395.2	NM_015432		A	67319052	G	A	67319052	3	1	318	1	0	0	0	0	1	0	0	0	12080	1261	44	3	2175	3	PLEKHG4	16	67319052	Missense_Mutation	SNP	G	TCGA-LG-A9QC-01A-11D-A36X-10	39859007	67319052	23035701	45	44891										
TERF2IP	54386	hgsc.bcm.edu	37	chr16	75681935	75681948	+	Frame_Shift_Del	DEL	CCGTGTGCCGAGTG	CCGTGTGCCGAGTG	-													0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	catcctgcacggcggcggcaCcgtgtgccgagtgcaggagc							TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	CCGTGTGCCGAGTG	CCGTGTGCCGAGTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr16:75681935_75681948delCCGTGTGCCGAGTG	ENST00000300086.4	+	1	252_265	c.155_168delCCGTGTGCCGAGTG	c.(154-168)accgtgtgccgagtgfs	p.TVCRV52fs	KARS_ENST00000568378.1_5'Flank|KARS_ENST00000319410.5_5'Flank|KARS_ENST00000302445.3_5'Flank	NM_018975.3	NP_061848.2	Q9NYB0	TE2IP_HUMAN	telomeric repeat binding factor 2, interacting protein	52					negative regulation of DNA recombination at telomere (GO:0048239)|negative regulation of telomere maintenance (GO:0032205)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protection from non-homologous end joining at telomere (GO:0031848)|protein localization to chromosome, telomeric region (GO:0070198)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of transcription, DNA-templated (GO:0006355)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)|telomere maintenance via telomere lengthening (GO:0010833)|transcription, DNA-templated (GO:0006351)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear chromosome (GO:0000228)|nuclear chromosome, telomeric region (GO:0000784)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)	5						GGCGGCGGCACCGTGTGCCGAGTGCAGGAGCCCG	0.696																																					p.52_56del		Atlas-INDEL	.											.	TERF2IP	17	.	0			c.154_167del						.																																			SO:0001589	frameshift_variant	54386	exon1			.	AK000669	CCDS32491.1	16q23.1	2012-10-03			ENSG00000166848	ENSG00000166848			19246	protein-coding gene	gene with protein product		605061				10850490	Standard	NM_018975		Approved	RAP1	uc002fet.2	Q9NYB0	OTTHUMG00000177136	ENST00000300086.4:c.155_168delCCGTGTGCCGAGTG	chr16.hg19:g.75681935_75681948delCCGTGTGCCGAGTG	ENSP00000300086:p.Thr52fs	66.0	0.0		63.0	23.0	NM_018975	B4DQN4|Q4W4Y2|Q8WYZ3|Q9NWR2	Frame_Shift_Del	DEL	ENST00000300086.4	hg19	CCDS32491.1																																																																																			.	.		0.696	TERF2IP-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000435519.1	NM_018975		-	75681948	CCGTGTGCCGAGTG	-	75681935	7	5	318	1	0	1	0	1	0	0	0	0	15778	507	18	0	157	0	TERF2IP	16	75681935	Frame_Shift_Del	DEL	CCGTGTGCCGAGTG	TCGA-LG-A9QC-01A-11D-A36X-10	8362883	75681935	14672818	46	44892										
ZNF397	84307	hgsc.bcm.edu	37	chr18	32823230	32823230	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	taaagacacagctgaaatccTggaaaccatgcctttcccct	6	13	0	2			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr18:32823230T>A	ENST00000330501.7	+	3	682	c.529T>A	c.(529-531)Tgg>Agg	p.W177R	ZNF397_ENST00000592264.1_Missense_Mutation_p.W177R|ZNF397_ENST00000589420.1_3'UTR|ZNF397_ENST00000355632.4_Missense_Mutation_p.W177R|ZNF397_ENST00000261333.6_Missense_Mutation_p.W177R|ZNF397_ENST00000591206.1_Missense_Mutation_p.W177R|ZNF397_ENST00000585800.1_Missense_Mutation_p.W177R	NM_001135178.2	NP_001128650.1	Q8NF99	ZN397_HUMAN	zinc finger protein 397	177					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|large_intestine(3)|lung(5)|skin(1)	12						GCTGAAATCCTGGAAACCATG	0.458																																					p.W177R		Atlas-SNP	.											.	ZNF397	51	.	0			c.T529A						.						119	113	115					18																	32823230		2203	4300	6503	SO:0001583	missense	84307	exon3			AAATCCTGGAAAC	BC006172	CCDS32814.1, CCDS45852.1	18p12	2013-01-09	2003-07-22			ENSG00000186812		"-", "Zinc fingers, C2H2-type"	18818	protein-coding gene	gene with protein product		609601	"zinc finger protein 47"	ZNF47			Standard	NM_032347		Approved	ZSCAN15, MGC13250	uc010dmp.3	Q8NF99		ENST00000330501.7:c.529T>A	chr18.hg19:g.32823230T>A	ENSP00000331577:p.Trp177Arg	120.0	0.0		109.0	44.0	NM_032347	Q9BRM2	Missense_Mutation	SNP	ENST00000330501.7	hg19	CCDS45852.1	.	.	.	.	.	.	.	.	.	.	T	11.12	1.546111	0.27652	.	.	ENSG00000186812	ENST00000261333;ENST00000330501;ENST00000355632	T;T;T	0.06449	4.39;3.3;4.33	4.79	2.13	0.27403	.	.	.	.	.	T	0.04588	0.0125	L	0.34521	1.04	0.29832	N	0.829952	B;B;B;B	0.31459	0.014;0.001;0.324;0.324	B;B;B;B	0.31686	0.011;0.001;0.134;0.053	T	0.34079	-0.9843	9	0.17832	T	0.49	.	4.8934	0.13738	0.1884:0.0:0.1959:0.6157	.	177;177;177;177	Q96K65;Q8NF99;Q8NF99-2;Q8NF99-3	.;ZN397_HUMAN;.;.	R	177	ENSP00000261333:W177R;ENSP00000331577:W177R;ENSP00000347850:W177R	ENSP00000261333:W177R	W	+	1	0	ZNF397	31077228	0.992000	0.36948	0.998000	0.56505	0.976000	0.68499	0.959000	0.29240	0.887000	0.36136	0.477000	0.44152	TGG	.	.		0.458	ZNF397-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442398.1	NM_032347		A	32823230	T	A	32823230	3	1	318	1	0	0	0	0	1	0	0	0	17898	1580	55	4	535	4	ZNF397	18	32823230	Missense_Mutation	SNP	T	TCGA-LG-A9QC-01A-11D-A36X-10		32823230	45254018	47	44893										
DNMT1	1786	hgsc.bcm.edu	37	chr19	10248604	10248604	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	ccgttgtaggagatctccagTgccgaggctccattccgcac	11	14	1	1			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr19:10248604T>G	ENST00000340748.4	-	35	4384	c.4149A>C	c.(4147-4149)gcA>gcC	p.A1383A	DNMT1_ENST00000540357.1_Silent_p.A1383A|DNMT1_ENST00000359526.4_Silent_p.A1399A|DNMT1_ENST00000589538.1_5'Flank			P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1	1383	Catalytic.|Interaction with the PRC2/EED-EZH2 complex. {ECO:0000250}.|SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				cellular response to amino acid stimulus (GO:0071230)|chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|gene silencing (GO:0016458)|maintenance of DNA methylation (GO:0010216)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|regulation of cell proliferation (GO:0042127)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|replication fork (GO:0005657)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methyl-CpG binding (GO:0008327)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(5)|endometrium(8)|kidney(5)|large_intestine(21)|lung(11)|ovary(2)|pancreas(1)|prostate(10)|skin(5)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Procainamide(DB01035)	AGATCTCCAGTGCCGAGGCTC	0.617																																					p.A1399A		Atlas-SNP	.											.	DNMT1	148	.	0			c.A4197C						.						67	50	56					19																	10248604		2203	4300	6503	SO:0001819	synonymous_variant	1786	exon36			CTCCAGTGCCGAG	X63692	CCDS12228.1, CCDS45958.1	19p13.2	2014-09-17				ENSG00000130816	2.1.1.37		2976	protein-coding gene	gene with protein product		126375		DNMT		1594447	Standard	NM_001379		Approved	MCMT, CXXC9	uc010xlc.2	P26358		ENST00000340748.4:c.4149A>C	chr19.hg19:g.10248604T>G		56.0	0.0		99.0	39.0	NM_001130823	A0AV63|B7ZLW6|Q9UHG5|Q9ULA2|Q9UMZ6	Silent	SNP	ENST00000340748.4	hg19	CCDS12228.1																																																																																			.	.		0.617	DNMT1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451166.1	NM_001379		G	10248604	T	G	10248604	2	3	318	1	0	0	0	0	0	0	0	1	4677	1683	59	5		5	DNMT1	19	10248604	Silent	SNP	T	TCGA-LG-A9QC-01A-11D-A36X-10		10248604	48880379	48	44894										
IL12RB1	3594	hgsc.bcm.edu	37	chr19	18174687	18174687	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	tcctaccccctccactcaccGatgctgaagcgctggggctg	10	17	1	1			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr19:18174687G>A	ENST00000600835.2	-	14	1915	c.1617C>T	c.(1615-1617)atC>atT	p.I539I	IL12RB1_ENST00000593993.2_Splice_Site_p.I539I			P42701	I12R1_HUMAN	interleukin 12 receptor, beta 1	539	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-23-mediated signaling pathway (GO:0038155)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|interleukin-12 receptor complex (GO:0042022)|interleukin-23 receptor complex (GO:0072536)	cytokine receptor activity (GO:0004896)			endometrium(1)|kidney(1)|lung(3)|pancreas(1)|skin(2)	8						TCCACTCACCGATGCTGAAGC	0.622																																					p.I539I		Atlas-SNP	.											IL12RB1_ENST00000430026,colon,carcinoma,0,1	IL12RB1	92	.	0			c.C1617T						.						28	31	30					19																	18174687		2092	4225	6317	SO:0001630	splice_region_variant	3594	exon13			CTCACCGATGCTG	U03187	CCDS32957.1, CCDS54232.1	19p13.1	2014-09-17						"Interleukins and interleukin receptors", "CD molecules", "Fibronectin type III domain containing"	5971	protein-coding gene	gene with protein product		601604		IL12RB		9284929	Standard	XM_005259893		Approved	CD212	uc002nhw.1	P42701		ENST00000600835.2:c.1618+1C>T	chr19.hg19:g.18174687G>A		60.0	0.0		61.0	20.0	NM_005535	A8K308|B2RPF1|B7ZKK3|Q8N6Q7	Silent	SNP	ENST00000600835.2	hg19	CCDS54232.1																																																																																			.	.		0.622	IL12RB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466525.3		Silent	A	18174687	G	A	18174687	5	1	318	1	0	0	0	0	0	0	1	0	7635	1072	37	1	391	1	IL12RB1	19	18174687	Splice_Site	SNP	G	TCGA-LG-A9QC-01A-11D-A36X-10	7926083	18174687	40954296	49	44895										
LGALS7B	653499	hgsc.bcm.edu	37	chr19	39281456	39281456	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	gctcctggggccgcgaggagCgcgggccgggcgttcctttc	18	14	0	0			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr19:39281456C>T	ENST00000314980.4	+	3	239	c.223C>T	c.(223-225)Cgc>Tgc	p.R75C		NM_001042507.3	NP_001035972.1	P47929	LEG7_HUMAN	lectin, galactoside-binding, soluble, 7B	75	Beta-galactoside binding. {ECO:0000255}.|Galectin. {ECO:0000255|PROSITE- ProRule:PRU00639}.				apoptotic process (GO:0006915)|heterophilic cell-cell adhesion (GO:0007157)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	carbohydrate binding (GO:0030246)										CCGCGAGGAGCGCGGGCCGGG	0.677																																					p.R75C		Atlas-SNP	.											.	.	.	.	0			c.C223T						.						12	13	13					19																	39281456		2122	4201	6323	SO:0001583	missense	653499	exon3			GAGGAGCGCGGGC		CCDS42565.1	19q13.2	2011-08-04			ENSG00000178934	ENSG00000178934		"Lectins, galactoside-binding"	34447	protein-coding gene	gene with protein product	"galectin 7B"						Standard	NM_001042507		Approved	GAL7	uc002ojf.4	P47929		ENST00000314980.4:c.223C>T	chr19.hg19:g.39281456C>T	ENSP00000313571:p.Arg75Cys	358.0	0.0		381.0	122.0	NM_001042507	Q6IB87	Missense_Mutation	SNP	ENST00000314980.4	hg19	CCDS42565.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.324151	0.81580	.	.	ENSG00000178934	ENST00000314980	T	0.10382	2.88	4.07	3.04	0.35103	.	0.233245	0.30565	N	0.009343	T	0.19846	0.0477	.	.	.	0.50813	D	0.999892	.	.	.	.	.	.	T	0.00710	-1.1599	7	0.87932	D	0	-32.4222	8.7313	0.34501	0.0:0.8902:0.0:0.1098	.	.	.	.	C	75	ENSP00000313571:R75C	ENSP00000313571:R75C	R	+	1	0	LGALS7B	43973296	0.998000	0.40836	0.956000	0.39512	0.416000	0.31233	1.793000	0.38764	0.931000	0.37242	0.556000	0.70494	CGC	.	.		0.677	LGALS7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462638.1			T	39281456	C	T	39281456	3	4	318	1	0	0	0	0	1	0	0	0	8755	768	27	1	233	1	LGALS7B	19	39281456	Missense_Mutation	SNP	C	TCGA-LG-A9QC-01A-11D-A36X-10	21106769	39281456	19847527	50	44896										
SPTBN4	57731	hgsc.bcm.edu	37	chr19	41078287	41078287	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	tgctccaggcaaaagatgagGtgagatctggtcctttcctc	11	10	1	3			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr19:41078287G>T	ENST00000352632.3	+	35	7622		c.e35+1		SPTBN4_ENST00000392025.1_Splice_Site|SPTBN4_ENST00000598249.1_Splice_Site|SPTBN4_ENST00000593816.1_3'UTR			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4						actin filament capping (GO:0051693)|adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cardiac conduction (GO:0061337)|central nervous system projection neuron axonogenesis (GO:0021952)|clustering of voltage-gated sodium channels (GO:0045162)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization to plasma membrane (GO:0090002)|fertilization (GO:0009566)|negative regulation of heart rate (GO:0010459)|positive regulation of multicellular organism growth (GO:0040018)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of sodium ion transport (GO:0002028)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|axon hillock (GO:0043203)|axon initial segment (GO:0043194)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|nuclear matrix (GO:0016363)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|PML body (GO:0016605)|spectrin (GO:0008091)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phosphatase binding (GO:0019902)|phospholipid binding (GO:0005543)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			breast(4)|central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	73			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			AAAAGATGAGGTGAGATCTGG	0.577																																					.		Atlas-SNP	.											.	SPTBN4	213	.	0			c.7536+1G>T						.						194	162	173					19																	41078287		2203	4300	6503	SO:0001630	splice_region_variant	57731	exon35			GATGAGGTGAGAT	AF082075	CCDS12559.1, CCDS42569.1	19q13.13	2013-01-10				ENSG00000160460		"Pleckstrin homology (PH) domain containing"	14896	protein-coding gene	gene with protein product		606214				11086001	Standard	NM_020971		Approved	SPTBN3, KIAA1642	uc002onz.3	Q9H254		ENST00000352632.3:c.7536+1G>T	chr19.hg19:g.41078287G>T		74.0	0.0		79.0	20.0	NM_020971	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Splice_Site	SNP	ENST00000352632.3	hg19	CCDS12559.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.803551	0.90623	.	.	ENSG00000160460	ENST00000428507;ENST00000352632;ENST00000392025	.	.	.	5.59	5.59	0.84812	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.0785	0.86592	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SPTBN4	45770127	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.570000	0.98174	2.636000	0.89361	0.563000	0.77884	.	.	.		0.577	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2		Intron	T	41078287	G	T	41078287	5	4	318	1	0	0	0	0	0	0	1	0	15136	1275	44	3	7765	3	SPTBN4	19	41078287	Splice_Site	SNP	G	TCGA-LG-A9QC-01A-11D-A36X-10	1796831	41078287	18050696	51	44897										
NEFH	4744	hgsc.bcm.edu	37	chr22	29885570	29885570	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	ccaacgaaggaggaagcaaaGtcccctgagaaggccaagtc	12	11	0	1	rs200634512	byFrequency	TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr22:29885570G>T	ENST00000310624.6	+	4	1974	c.1941G>T	c.(1939-1941)aaG>aaT	p.K647N		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	653	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.			Missing (in Ref. 1; CAA33366 and 5; AC000035). {ECO:0000305}.	axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AGGAAGCAAAGTCCCCTGAGA	0.572																																					p.K647N		Atlas-SNP	.											.	NEFH	178	.	0			c.G1941T						.						89	96	94					22																	29885570		2203	4300	6503	SO:0001583	missense	4744	exon4			AGCAAAGTCCCCT		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1941G>T	chr22.hg19:g.29885570G>T	ENSP00000311997:p.Lys647Asn	195.0	0.0		209.0	32.0	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Missense_Mutation	SNP	ENST00000310624.6	hg19	CCDS13858.1	.	.	.	.	.	.	.	.	.	.	G	10.52	1.373873	0.24857	.	.	ENSG00000100285	ENST00000328842;ENST00000310624	D	0.84730	-1.89	4.77	-0.296	0.12824	.	0.000000	0.56097	D	0.000031	D	0.87237	0.6127	M	0.68593	2.085	0.42351	D	0.992376	D	0.64830	0.994	P	0.56278	0.795	D	0.86272	0.1662	10	0.87932	D	0	.	10.9944	0.47567	0.2639:0.0:0.7361:0.0	.	653	P12036	NFH_HUMAN	N	647	ENSP00000311997:K647N	ENSP00000311997:K647N	K	+	3	2	NEFH	28215570	0.071000	0.21146	0.748000	0.31131	0.198000	0.23893	-0.402000	0.07223	-0.019000	0.14055	0.591000	0.81541	AAG	.	G|0.999;C|0.001		0.572	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		T	29885570	G	T	29885570	3	4	318	1	0	0	0	0	1	0	0	0	10323	1020	36	3	1955	3	NEFH	22	29885570	Missense_Mutation	SNP	G	TCGA-LG-A9QC-01A-11D-A36X-10		29885570	21418996	52	44898			1	54		2	2	19	G		3.139815e-05
NEFH	4744	hgsc.bcm.edu	37	chr22	29885588	29885588	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	aagtcccctgagaaggccaaGtccccagagaaggaagaggc	13	11	0	3	rs200984527|rs267607533		TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr22:29885588G>T	ENST00000310624.6	+	4	1992	c.1959G>T	c.(1957-1959)aaG>aaT	p.K653N		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	659	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AGAAGGCCAAGTCCCCAGAGA	0.567																																					p.K653N		Atlas-SNP	.											.	NEFH	178	.	0			c.G1959T						.						85	93	90					22																	29885588		2203	4300	6503	SO:0001583	missense	4744	exon4			GGCCAAGTCCCCA		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1959G>T	chr22.hg19:g.29885588G>T	ENSP00000311997:p.Lys653Asn	215.0	0.0		236.0	24.0	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Missense_Mutation	SNP	ENST00000310624.6	hg19	CCDS13858.1	.	.	.	.	.	.	.	.	.	.	G	7.917	0.737766	0.15574	.	.	ENSG00000100285	ENST00000328842;ENST00000310624	D	0.84298	-1.83	4.41	-0.067	0.13762	.	0.000000	0.56097	D	0.000032	D	0.89121	0.6625	M	0.72894	2.215	0.33402	D	0.577433	D	0.62365	0.991	D	0.79108	0.992	D	0.88893	0.3347	10	0.87932	D	0	.	8.2741	0.31862	0.4205:0.0:0.5795:0.0	.	659	P12036	NFH_HUMAN	N	653	ENSP00000311997:K653N	ENSP00000311997:K653N	K	+	3	2	NEFH	28215588	0.000000	0.05858	0.660000	0.29694	0.058000	0.15608	-0.114000	0.10757	0.208000	0.20626	-0.469000	0.05056	AAG	.	.		0.567	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		T	29885588	G	T	29885588	3	4	318	1	0	0	0	0	1	0	0	0	10323	1020	36	3	1973	3	NEFH	22	29885588	Missense_Mutation	SNP	G	TCGA-LG-A9QC-01A-11D-A36X-10	18	29885588	21418978	53	44899			1	54		2	2	19	G		3.139815e-05
MYH9	4627	hgsc.bcm.edu	37	chr22	36702652	36702652	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.037037037037037	2	1	0.906796906796907	2.38034188034188	0.560080442433384	1	1	0	tccaggccgatgatgcggtcCactgtggagaccacagagaa	13	11	0	3			TCGA-LG-A9QC-01A-11D-A36X-10	TCGA-LG-A9QC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80c45b60-c7e2-456d-aa46-4fb7269b9181	d9d44786-28b8-44ec-b915-1e0bbc537b27	g.chr22:36702652C>T	ENST00000216181.5	-	16	2075	c.1845G>A	c.(1843-1845)gtG>gtA	p.V615V		NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	615	Myosin motor.				actin cytoskeleton reorganization (GO:0031532)|actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|angiogenesis (GO:0001525)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood vessel endothelial cell migration (GO:0043534)|cytokinesis (GO:0000910)|establishment of meiotic spindle localization (GO:0051295)|establishment of T cell polarity (GO:0001768)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|meiotic spindle organization (GO:0000212)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte differentiation (GO:0030224)|myoblast fusion (GO:0007520)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of cell shape (GO:0008360)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|uropod organization (GO:0032796)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|actomyosin contractile ring (GO:0005826)|cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|cleavage furrow (GO:0032154)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|spindle (GO:0005819)|stress fiber (GO:0001725)|uropod (GO:0001931)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3)	86						TGATGCGGTCCACTGTGGAGA	0.642			T	ALK	ALCL		"Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"		Hereditary Macrothrombocytopenia, MYH9-associated																												p.V615V		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"myosin, heavy polypeptide 9, non-muscle"	yes	L	.	MYH9	225	.	0			c.G1845A						.						30	28	28					22																	36702652		2203	4300	6503	SO:0001630	splice_region_variant	4627	exon16	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	GCGGTCCACTGTG		CCDS13927.1	22q13.1	2014-09-17	2006-09-29		ENSG00000100345	ENSG00000100345		"Myosins / Myosin superfamily : Class II"	7579	protein-coding gene	gene with protein product	"nonmuscle myosin heavy chain II-A"	160775	"myosin, heavy polypeptide 9, non-muscle"	DFNA17		1860190, 11023810	Standard	NM_002473		Approved	NMMHCA, NMHC-II-A, MHA, FTNS, EPSTS	uc003apg.3	P35579	OTTHUMG00000030429	ENST00000216181.5:c.1844-1G>A	chr22.hg19:g.36702652C>T		51.0	0.0		59.0	24.0	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Silent	SNP	ENST00000216181.5	hg19	CCDS13927.1																																																																																			.	.		0.642	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473	Silent	T	36702652	C	T	36702652	5	4	318	1	0	0	0	0	0	0	1	0	10051	608	21	3	4141	3	MYH9	22	36702652	Splice_Site	SNP	C	TCGA-LG-A9QC-01A-11D-A36X-10	6817064	36702652	14601914	54	44900										
RCAN3	11123	hgsc.bcm.edu	37	chr1	24859572	24859572	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	tgagcgtctcgctccctgcaGgtgcagatgtccggcgaagt	14	12	1	2			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr1:24859572G>A	ENST00000374395.4	+	4	682		c.e4-1		RCAN3_ENST00000538532.1_Splice_Site|RCAN3_ENST00000374393.2_Intron|RCAN3_ENST00000436717.2_Intron|RCAN3_ENST00000412742.2_Intron	NM_001251978.1|NM_001251979.1|NM_001251984.1	NP_001238907.1|NP_001238908.1|NP_001238913.1	Q9UKA8	RCAN3_HUMAN	RCAN family member 3						anatomical structure morphogenesis (GO:0009653)|calcium-mediated signaling (GO:0019722)		RNA binding (GO:0003723)|troponin I binding (GO:0031013)			central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)	7		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00473)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0427)|OV - Ovarian serous cystadenocarcinoma(117;1.13e-24)|Colorectal(126;6.09e-08)|COAD - Colon adenocarcinoma(152;3.33e-06)|GBM - Glioblastoma multiforme(114;0.000923)|BRCA - Breast invasive adenocarcinoma(304;0.0018)|KIRC - Kidney renal clear cell carcinoma(1967;0.00359)|STAD - Stomach adenocarcinoma(196;0.00493)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.14)		GCTCCCTGCAGGTGCAGATGT	0.527																																					.		Atlas-SNP	.											.	RCAN3	22	.	0			c.370-1G>A						.						48	42	44					1																	24859572		2203	4300	6503	SO:0001630	splice_region_variant	11123	exon4			CCTGCAGGTGCAG		CCDS254.1, CCDS57980.1, CCDS57981.1, CCDS57982.1, CCDS72730.1	1p35.3-p33	2008-02-05	2007-06-26	2007-06-26	ENSG00000117602	ENSG00000117602			3042	protein-coding gene	gene with protein product		605860	"Down syndrome critical region gene 1-like 2"	DSCR1L2		10756093	Standard	NM_001251984		Approved		uc001bjj.3	Q9UKA8	OTTHUMG00000003298	ENST00000374395.4:c.370-1G>A	chr1.hg19:g.24859572G>A		60.0	0.0		73.0	28.0	NM_001251979	A4GU14|A4LA69|E3VWE2|E5L4P0|E5L4P7|E7ENV1|E7EWD8|G1FI66|G1FLF0|Q5ECL3|Q5TGC6|Q9NUC8|Q9UKA7	Splice_Site	SNP	ENST00000374395.4	hg19	CCDS254.1	.	.	.	.	.	.	.	.	.	.	G	12.73	2.025331	0.35701	.	.	ENSG00000117602	ENST00000374395;ENST00000538532	.	.	.	5.08	5.08	0.68730	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.094	0.93242	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	RCAN3	24732159	1.000000	0.71417	0.996000	0.52242	0.225000	0.24961	7.307000	0.78920	2.822000	0.97130	0.558000	0.71614	.	.	.		0.527	RCAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009176.2		Intron	A	24859572	G	A	24859572	5	1	319	1	0	0	0	0	0	0	1	0	13185	1014	35	3	379	3	RCAN3	1	24859572	Splice_Site	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10		24859572	224391049	1	44901										
C1orf87	127795	hgsc.bcm.edu	37	chr1	60521079	60521079	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	tggtttctggtgcattgtttGggtttctgttttcaagctgt	12	5	3	0			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr1:60521079G>A	ENST00000371201.3	-	3	246	c.139C>T	c.(139-141)Caa>Taa	p.Q47*	C1orf87_ENST00000450089.2_Nonsense_Mutation_p.Q47*	NM_152377.2	NP_689590.1	Q8N0U7	CA087_HUMAN	chromosome 1 open reading frame 87	47							calcium ion binding (GO:0005509)			breast(2)|endometrium(2)|large_intestine(6)|lung(19)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33						TGCATTGTTTGGGTTTCTGTT	0.423																																					p.Q47X	NSCLC(75;811 1386 4923 13371 51772)	Atlas-SNP	.											.	C1orf87	55	.	0			c.C139T						.						266	223	237					1																	60521079		2203	4300	6503	SO:0001587	stop_gained	127795	exon3			TTGTTTGGGTTTC	AK124828	CCDS614.1	1p32.1	2014-04-03			ENSG00000162598	ENSG00000162598			28547	protein-coding gene	gene with protein product	"carcinoma-related EF-hand protein"					12477932	Standard	NM_152377		Approved	MGC34837, CREF	uc001czs.2	Q8N0U7	OTTHUMG00000008992	ENST00000371201.3:c.139C>T	chr1.hg19:g.60521079G>A	ENSP00000360244:p.Gln47*	135.0	0.0		126.0	37.0	NM_152377	Q6ZU07|Q8IVS0	Nonsense_Mutation	SNP	ENST00000371201.3	hg19	CCDS614.1	.	.	.	.	.	.	.	.	.	.	G	17.44	3.390081	0.61956	.	.	ENSG00000162598	ENST00000371201;ENST00000450089	.	.	.	4.66	4.66	0.58398	.	0.000000	0.46145	D	0.000313	.	.	.	.	.	.	0.58432	D	0.99999	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-12.6373	13.2382	0.59982	0.0:0.0:1.0:0.0	.	.	.	.	X	47	.	ENSP00000360244:Q47X	Q	-	1	0	C1orf87	60293667	0.216000	0.23585	0.039000	0.18376	0.013000	0.08279	2.188000	0.42612	2.563000	0.86464	0.591000	0.81541	CAA	.	.		0.423	C1orf87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024943.1	NM_152377		A	60521079	G	A	60521079	4	1	319	1	0	0	0	0	0	1	0	0	2066	1357	47	3	1541	3	C1orf87	1	60521079	Nonsense_Mutation	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10	35661507	60521079	188729542	2	44902										
JAK1	3716	hgsc.bcm.edu	37	chr1	65305399	65305399	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	tacctccactctcaggcttcAgagatttaacagccacctgc	6	15	2	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr1:65305399A>G	ENST00000342505.4	-	20	2977	c.2729T>C	c.(2728-2730)cTg>cCg	p.L910P	JAK1_ENST00000465376.1_5'Flank	NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	910	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	CTCAGGCTTCAGAGATTTAAC	0.478			Mis		ALL																																p.L910P		Atlas-SNP	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	JAK1,NS,carcinoma,0,2	JAK1	209	.	0			c.T2729C						.						150	138	142					1																	65305399		1917	4139	6056	SO:0001583	missense	3716	exon20			GGCTTCAGAGATT	M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.2729T>C	chr1.hg19:g.65305399A>G	ENSP00000343204:p.Leu910Pro	116.0	0.0		112.0	25.0	NM_002227	Q59GQ2|Q9UD26	Missense_Mutation	SNP	ENST00000342505.4	hg19	CCDS41346.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.517041	0.85495	.	.	ENSG00000162434	ENST00000342505	D	0.91351	-2.83	5.13	5.13	0.70059	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	D	0.94525	0.8237	M	0.79926	2.475	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95349	0.8445	9	0.87932	D	0	-3.8222	15.1086	0.72338	1.0:0.0:0.0:0.0	.	910	P23458	JAK1_HUMAN	P	910	ENSP00000343204:L910P	ENSP00000343204:L910P	L	-	2	0	JAK1	65077987	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.703000	0.91344	2.146000	0.66826	0.533000	0.62120	CTG	.	.		0.478	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227		G	65305399	A	G	65305399	3	3	319	1	0	0	0	0	1	0	0	0	7946	188	7	2	759	2	JAK1	1	65305399	Missense_Mutation	SNP	A	TCGA-LG-A9QD-01A-11D-A382-10	4784320	65305399	183945222	3	44903										
MCOLN3	55283	hgsc.bcm.edu	37	chr1	85510937	85510937	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	tgagttttcgcctcatctggTcttctaatagaagctcctca	7	11	5	2			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr1:85510937T>C	ENST00000370589.2	-	2	159	c.107A>G	c.(106-108)gAc>gGc	p.D36G	MCOLN3_ENST00000341115.4_Missense_Mutation_p.D36G|MCOLN3_ENST00000370587.1_Missense_Mutation_p.D36G|WDR63_ENST00000370596.1_Intron	NM_018298.10	NP_060768.8	Q8TDD5	MCLN3_HUMAN	mucolipin 3	36					auditory receptor cell differentiation (GO:0042491)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|locomotory behavior (GO:0007626)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(6)|kidney(3)|large_intestine(9)|lung(12)|prostate(3)|skin(1)	34				all cancers(265;0.00957)|Epithelial(280;0.0254)		CCTCATCTGGTCTTCTAATAG	0.413																																					p.D36G		Atlas-SNP	.											.	MCOLN3	74	.	0			c.A107G						.						72	71	71					1																	85510937		2203	4300	6503	SO:0001583	missense	55283	exon2			ATCTGGTCTTCTA	AF475085	CCDS701.1, CCDS58009.1	1p22.3	2011-12-16			ENSG00000055732	ENSG00000055732		"Voltage-gated ion channels / Transient receptor potential cation channels"	13358	protein-coding gene	gene with protein product		607400				16382100	Standard	NM_018298		Approved	TRPML3, FLJ11006, TRP-ML3	uc001dkp.3	Q8TDD5	OTTHUMG00000009955	ENST00000370589.2:c.107A>G	chr1.hg19:g.85510937T>C	ENSP00000359621:p.Asp36Gly	88.0	0.0		83.0	27.0	NM_001253693	Q5T4H5|Q5T4H6|Q9NV09	Missense_Mutation	SNP	ENST00000370589.2	hg19	CCDS701.1	.	.	.	.	.	.	.	.	.	.	T	17.41	3.381402	0.61845	.	.	ENSG00000055732	ENST00000370589;ENST00000302814;ENST00000370588;ENST00000341115;ENST00000370587	T;T;T	0.54479	0.57;0.57;0.57	5.55	5.55	0.83447	.	0.095153	0.64402	D	0.000001	T	0.46521	0.1397	M	0.74881	2.28	0.51233	D	0.999914	B;B;B	0.31174	0.311;0.122;0.043	B;B;B	0.34652	0.187;0.056;0.019	T	0.56177	-0.8022	10	0.72032	D	0.01	-5.9354	15.7034	0.77558	0.0:0.0:0.0:1.0	.	36;36;36	B1ANB7;Q8TDD5-2;Q8TDD5	.;.;MCLN3_HUMAN	G	36	ENSP00000359621:D36G;ENSP00000342698:D36G;ENSP00000359619:D36G	ENSP00000304843:D36G	D	-	2	0	MCOLN3	85283525	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	4.633000	0.61318	2.113000	0.64589	0.402000	0.26972	GAC	.	.		0.413	MCOLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027569.2	NM_018298		C	85510937	T	C	85510937	3	2	319	1	0	0	0	0	1	0	0	0	9406	1667	58	2	1602	2	MCOLN3	1	85510937	Missense_Mutation	SNP	T	TCGA-LG-A9QD-01A-11D-A382-10	20205538	85510937	163739684	4	44904										
CDC7	8317	hgsc.bcm.edu	37	chr1	91985781	91985781	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	gatgatttaactgctttggcCcaaattatgacaattagggg	10	6	0	2			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr1:91985781C>T	ENST00000428239.1	+	11	1534	c.1275C>T	c.(1273-1275)gcC>gcT	p.A425A	CDC7_ENST00000234626.6_Silent_p.A425A|CDC7_ENST00000430031.2_Silent_p.A397A	NM_001134420.1	NP_001127892.1	O00311	CDC7_HUMAN	cell division cycle 7	425	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle phase transition (GO:0044770)|cell division (GO:0051301)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|stomach(2)	23		all_lung(203;0.0165)|Lung NSC(277;0.0562)		all cancers(265;0.00108)|Epithelial(280;0.0184)|KIRC - Kidney renal clear cell carcinoma(1967;0.124)		CTGCTTTGGCCCAAATTATGA	0.358																																					p.A425A		Atlas-SNP	.											.	CDC7	74	.	0			c.C1275T						.						112	111	111					1																	91985781		2203	4300	6503	SO:0001819	synonymous_variant	8317	exon11			TTTGGCCCAAATT	AF015592	CCDS734.1	1p22	2013-01-17	2013-01-17	2003-07-23	ENSG00000097046	ENSG00000097046			1745	protein-coding gene	gene with protein product		603311	"CDC7 (cell division cycle 7, S. cerevisiae, homolog)-like 1", "CDC7 cell division cycle 7 (S. cerevisiae)", "cell division cycle 7 (S. cerevisiae)", "cell division cycle 7 homolog (S. cerevisiae)"	CDC7L1		9405610, 9250678	Standard	NM_003503		Approved	Hsk1, huCdc7, HsCdc7	uc001dof.3	O00311	OTTHUMG00000047810	ENST00000428239.1:c.1275C>T	chr1.hg19:g.91985781C>T		193.0	0.0		157.0	30.0	NM_001134419	D3DT31|O00558|Q5T5U5	Silent	SNP	ENST00000428239.1	hg19	CCDS734.1																																																																																			.	.		0.358	CDC7-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027928.1	NM_003503		T	91985781	C	T	91985781	2	4	319	1	0	0	0	0	0	0	0	1	3086	610	22	3		3	CDC7	1	91985781	Silent	SNP	C	TCGA-LG-A9QD-01A-11D-A382-10	6474844	91985781	157264840	5	44905										
LCE2D	353141	hgsc.bcm.edu	37	chr1	152636736	152636736	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	ttcctgctgtggtcccagctCtgggagctgctgtggtccca	13	13	1	0			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr1:152636736C>G	ENST00000368784.1	+	2	210	c.155C>G	c.(154-156)tCt>tGt	p.S52C		NM_178430.2	NP_848517.1	Q5TA82	LCE2D_HUMAN	late cornified envelope 2D	52	Cys-rich.				keratinization (GO:0031424)					large_intestine(1)|lung(7)|prostate(2)	10	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			GGTCCCAGCTCTGGGAGCTGC	0.647																																					p.S52C		Atlas-SNP	.											.	LCE2D	26	.	0			c.C155G						.						98	108	105					1																	152636736		2203	4300	6503	SO:0001583	missense	353141	exon2			CCAGCTCTGGGAG	BI670513	CCDS1018.1	1q21.3	2008-02-05	2004-10-11	2004-10-15	ENSG00000187223	ENSG00000187223		"Late cornified envelopes"	16518	protein-coding gene	gene with protein product		612612	"small proline rich-like (epidermal differentiation complex) 1A"	SPRL1A		11698679	Standard	NM_178430		Approved	LEP12	uc001fag.4	Q5TA82	OTTHUMG00000014400	ENST00000368784.1:c.155C>G	chr1.hg19:g.152636736C>G	ENSP00000357773:p.Ser52Cys	191.0	0.0		166.0	43.0	NM_178430	A1L4M8	Missense_Mutation	SNP	ENST00000368784.1	hg19	CCDS1018.1	.	.	.	.	.	.	.	.	.	.	C	0.745	-0.774942	0.02951	.	.	ENSG00000187223	ENST00000368784	T	0.05925	3.37	2.4	2.4	0.29515	.	.	.	.	.	T	0.11452	0.0279	M	0.78637	2.42	0.23198	N	0.998138	D	0.71674	0.998	D	0.69824	0.966	T	0.05386	-1.0888	9	0.87932	D	0	.	7.9554	0.30040	0.0:1.0:0.0:0.0	.	52	Q5TA82	LCE2D_HUMAN	C	52	ENSP00000357773:S52C	ENSP00000357773:S52C	S	+	2	0	LCE2D	150903360	0.329000	0.24696	0.942000	0.38095	0.053000	0.15095	1.805000	0.38883	1.157000	0.42530	0.305000	0.20034	TCT	.	.		0.647	LCE2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040058.1	NM_178430		G	152636736	C	G	152636736	3	3	319	1	0	0	0	0	1	0	0	0	8677	913	32	4	157	4	LCE2D	1	152636736	Missense_Mutation	SNP	C	TCGA-LG-A9QD-01A-11D-A382-10	60650955	152636736	96613885	6	44906										
S100A5	6276	hgsc.bcm.edu	37	chr1	153509857	153509857	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	actccttgaagtcgatctccTggtcgctgttcttgtccagg	10	12	2	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr1:153509857T>C	ENST00000368718.1	-	4	475	c.194A>G	c.(193-195)cAg>cGg	p.Q65R	BX470102.3_ENST00000420695.1_RNA|S100A6_ENST00000368720.2_5'Flank|S100A6_ENST00000496817.1_5'Flank|S100A6_ENST00000368719.4_5'Flank|S100A5_ENST00000359215.1_Missense_Mutation_p.Q83R|S100A5_ENST00000368717.2_Missense_Mutation_p.Q65R	NM_002962.1	NP_002953.2	P33763	S10A5_HUMAN	S100 calcium binding protein A5	65	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.					neuronal cell body (GO:0043025)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|copper ion binding (GO:0005507)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(1)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	4	all_lung(78;5.98e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			GTCGATCTCCTGGTCGCTGTT	0.547																																					p.Q65R		Atlas-SNP	.											.	S100A5	10	.	0			c.A194G						.						277	222	241					1																	153509857		2203	4300	6503	SO:0001583	missense	6276	exon4			ATCTCCTGGTCGC	Z18954	CCDS1041.1, CCDS1041.2	1q21	2013-01-10	2001-11-28		ENSG00000196420	ENSG00000196420		"S100 calcium binding proteins", "EF-hand domain containing"	10495	protein-coding gene	gene with protein product		176991	"S100 calcium-binding protein A5"	S100D		8341667	Standard	NM_002962		Approved		uc001fbx.3	P33763	OTTHUMG00000013547	ENST00000368718.1:c.194A>G	chr1.hg19:g.153509857T>C	ENSP00000357707:p.Gln65Arg	154.0	0.0		123.0	28.0	NM_002962	Q52LE7|Q5RHS3	Missense_Mutation	SNP	ENST00000368718.1	hg19	CCDS1041.2	.	.	.	.	.	.	.	.	.	.	T	13.10	2.135153	0.37728	.	.	ENSG00000196420	ENST00000368718;ENST00000359215;ENST00000368717	T;T;T	0.06218	3.33;3.33;3.33	4.4	0.752	0.18398	.	0.411381	0.27294	N	0.020034	T	0.01156	0.0038	.	.	.	0.27890	N	0.939378	B	0.02656	0.0	B	0.04013	0.001	T	0.46162	-0.9211	9	0.41790	T	0.15	.	2.6464	0.04985	0.1948:0.2144:0.0:0.5908	.	83	Q52LE7	.	R	65;83;65	ENSP00000357707:Q65R;ENSP00000352148:Q83R;ENSP00000357706:Q65R	ENSP00000352148:Q83R	Q	-	2	0	S100A5	151776481	0.878000	0.30173	1.000000	0.80357	0.843000	0.47879	0.043000	0.13971	0.277000	0.22141	-0.288000	0.09946	CAG	.	.		0.547	S100A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037719.1	NM_002962		C	153509857	T	C	153509857	3	2	319	1	0	0	0	0	1	0	0	0	13796	1580	55	2	88	2	S100A5	1	153509857	Missense_Mutation	SNP	T	TCGA-LG-A9QD-01A-11D-A382-10	873121	153509857	95740764	7	44907										
TNN	63923	hgsc.bcm.edu	37	chr1	175046704	175046704	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	cacacctacaagatcgatgtGcccaagtctgccttggttca	8	13	2	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr1:175046704G>A	ENST00000239462.4	+	2	263	c.150G>A	c.(148-150)gtG>gtA	p.V50V		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	50					axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		AGATCGATGTGCCCAAGTCTG	0.622																																					p.V50V		Atlas-SNP	.											.	TNN	297	.	0			c.G150A						.						90	63	72					1																	175046704		2203	4300	6503	SO:0001819	synonymous_variant	63923	exon2			CGATGTGCCCAAG	AK127044	CCDS30943.1	1q23-q24	2013-02-11			ENSG00000120332	ENSG00000120332		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	22942	protein-coding gene	gene with protein product							Standard	NM_022093		Approved		uc001gkl.1	Q9UQP3	OTTHUMG00000034882	ENST00000239462.4:c.150G>A	chr1.hg19:g.175046704G>A		168.0	0.0		131.0	29.0	NM_022093	B9EGP3|Q5R360	Silent	SNP	ENST00000239462.4	hg19	CCDS30943.1																																																																																			.	.		0.622	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527		A	175046704	G	A	175046704	2	1	319	1	0	0	0	0	0	0	0	1	16338	1306	46	3		3	TNN	1	175046704	Silent	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10	21536847	175046704	74203917	8	44908										
PTPRC	5788	hgsc.bcm.edu	37	chr1	198725152	198725152	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	ttgataatgaagtggacaaaGtaaagcaggatgctaattgt	11	3	0	2			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr1:198725152G>T	ENST00000367376.2	+	33	3928	c.3757G>T	c.(3757-3759)Gta>Tta	p.V1253L	PTPRC_ENST00000442510.2_Missense_Mutation_p.V1255L|PTPRC_ENST00000594404.1_Missense_Mutation_p.V1092L|PTPRC_ENST00000352140.3_Missense_Mutation_p.V1205L|PTPRC_ENST00000348564.6_Missense_Mutation_p.V1094L	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	1253					axon guidance (GO:0007411)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|bone marrow development (GO:0048539)|cell cycle phase transition (GO:0044770)|cell surface receptor signaling pathway (GO:0007166)|defense response to virus (GO:0051607)|dephosphorylation (GO:0016311)|hematopoietic progenitor cell differentiation (GO:0002244)|immunoglobulin biosynthetic process (GO:0002378)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of antigen receptor-mediated signaling pathway (GO:0050857)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of T cell proliferation (GO:0042102)|protein dephosphorylation (GO:0006470)|regulation of cell cycle (GO:0051726)|release of sequestered calcium ion into cytosol (GO:0051209)|stem cell development (GO:0048864)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			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						AGTGGACAAAGTAAAGCAGGA	0.428																																					p.V1255L		Atlas-SNP	.											.	PTPRC	229	.	0			c.G3763T						.						100	101	101					1																	198725152		2203	4300	6503	SO:0001583	missense	5788	exon33			GACAAAGTAAAGC	Y00062	CCDS1397.1, CCDS1398.1, CCDS44291.1, CCDS1397.2, CCDS1398.2, CCDS44291.2	1q31-q32	2014-09-17			ENSG00000081237	ENSG00000081237		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9666	protein-coding gene	gene with protein product		151460		CD45		2169617	Standard	NM_001267798		Approved	LCA, T200, GP180	uc001gur.2	P08575	OTTHUMG00000035702	ENST00000367376.2:c.3757G>T	chr1.hg19:g.198725152G>T	ENSP00000356346:p.Val1253Leu	374.0	0.0		340.0	99.0	NM_002838	A8K7W6|Q16614|Q9H0Y6	Missense_Mutation	SNP	ENST00000367376.2	hg19		.	.	.	.	.	.	.	.	.	.	G	4.452	0.083624	0.08533	.	.	ENSG00000081237	ENST00000367376;ENST00000352140;ENST00000442510;ENST00000348564	T	0.02369	4.32	5.7	0.392	0.16288	.	1.195290	0.06278	N	0.696855	T	0.01661	0.0053	N	0.08118	0	0.09310	N	1	B;B;B	0.19445	0.036;0.002;0.007	B;B;B	0.18263	0.021;0.002;0.005	T	0.48885	-0.8995	10	0.28530	T	0.3	.	2.5572	0.04763	0.1986:0.2627:0.3789:0.1598	.	1094;1205;1253	B1ALS3;E9PC28;P08575	.;.;PTPRC_HUMAN	L	1255;1205;1253;1092	ENSP00000193532:V1205L	ENSP00000306782:V1092L	V	+	1	0	PTPRC	196991775	0.000000	0.05858	0.005000	0.12908	0.087000	0.18053	-0.210000	0.09345	-0.164000	0.10927	0.557000	0.71058	GTA	.	.		0.428	PTPRC-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding				T	198725152	G	T	198725152	3	4	319	1	0	0	0	0	1	0	0	0	12812	1029	36	3	3894	3	PTPRC	1	198725152	Missense_Mutation	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10	23678448	198725152	50525469	9	44909										
IL24	11009	hgsc.bcm.edu	37	chr1	207073658	207073658	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	agcaagctcaggataacatcAcgagtgcccggctgctgcag	12	12	2	0			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr1:207073658A>T	ENST00000294984.2	+	4	533	c.259A>T	c.(259-261)Acg>Tcg	p.T87S	IL24_ENST00000391929.3_Missense_Mutation_p.T88S|IL24_ENST00000491169.1_3'UTR|IL24_ENST00000367093.3_Missense_Mutation_p.T88S	NM_001185156.1|NM_006850.3	NP_001172085.1|NP_006841.1	Q13007	IL24_HUMAN	interleukin 24	87					apoptotic process (GO:0006915)|cellular response to interleukin-4 (GO:0071353)|cellular response to lipopolysaccharide (GO:0071222)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|serine phosphorylation of STAT3 protein (GO:0033136)|wound healing (GO:0042060)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)				endometrium(4)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12	Breast(84;0.201)					GGATAACATCACGAGTGCCCG	0.547																																					p.T88S		Atlas-SNP	.											.	IL24	20	.	0			c.A262T						.						67	64	65					1																	207073658		2203	4300	6503	SO:0001583	missense	11009	exon4			AACATCACGAGTG	U16261	CCDS1471.1, CCDS53465.1, CCDS53466.1, CCDS73021.1	1q32	2011-07-15		2001-06-29	ENSG00000162892	ENSG00000162892		"Interleukins and interleukin receptors"	11346	protein-coding gene	gene with protein product	"melanoma differentiation association protein 7", "suppression of tumorigenicity 16 (melanoma differentiation)", "IL-4-induced secreted protein"	604136		ST16		8545104, 8799171	Standard	NM_001185156		Approved	mda-7, IL10B, Mob-5, C49A, FISP, IL-24	uc001heu.2	Q13007	OTTHUMG00000036459	ENST00000294984.2:c.259A>T	chr1.hg19:g.207073658A>T	ENSP00000294984:p.Thr87Ser	76.0	0.0		73.0	19.0	NM_001185156	Q2YHE5|Q53XZ7|Q5YLN8|Q96DB0|Q96KG4	Missense_Mutation	SNP	ENST00000294984.2	hg19	CCDS1471.1	.	.	.	.	.	.	.	.	.	.	A	7.035	0.561385	0.13498	.	.	ENSG00000162892	ENST00000391929;ENST00000294984;ENST00000367093	T;T;T	0.17528	2.27;2.27;2.27	4.3	4.3	0.51218	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.515737	0.20794	N	0.085568	T	0.08891	0.0220	.	.	.	0.09310	N	1	B;B;B	0.34329	0.361;0.449;0.184	B;B;B	0.34652	0.187;0.098;0.098	T	0.26744	-1.0094	9	0.09084	T	0.74	.	9.782	0.40653	1.0:0.0:0.0:0.0	.	88;88;87	Q2YHE5;Q53XZ7;Q13007	.;.;IL24_HUMAN	S	88;87;88	ENSP00000375795:T88S;ENSP00000294984:T87S;ENSP00000356060:T88S	ENSP00000294984:T87S	T	+	1	0	IL24	205140281	0.146000	0.22672	0.029000	0.17559	0.002000	0.02628	3.554000	0.53720	1.809000	0.52856	0.459000	0.35465	ACG	.	.		0.547	IL24-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000088680.2	NM_006850		T	207073658	A	T	207073658	3	4	319	1	0	0	0	0	1	0	0	0	7686	159	6	4	272	4	IL24	1	207073658	Missense_Mutation	SNP	A	TCGA-LG-A9QD-01A-11D-A382-10	8348506	207073658	42176963	10	44910										
ACTN2	88	hgsc.bcm.edu	37	chr1	236900515	236900515	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	atgagaggctagcgagtgagGtaaaggaaactggtgacctg	16	5	0	3			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr1:236900515G>T	ENST00000366578.4	+	9	1042		c.e9+1		ACTN2_ENST00000492634.1_Splice_Site|ACTN2_ENST00000546208.1_Intron|ACTN2_ENST00000542672.1_Splice_Site	NM_001103.2|NM_001278343.1	NP_001094.1|NP_001265272.1	P35609	ACTN2_HUMAN	actinin, alpha 2						blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|focal adhesion assembly (GO:0048041)|microspike assembly (GO:0030035)|muscle filament sliding (GO:0030049)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of protein localization to cell surface (GO:2000009)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein homotetramerization (GO:0051289)|regulation of apoptotic process (GO:0042981)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	actin filament (GO:0005884)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|cytoskeletal protein binding (GO:0008092)|FATZ binding (GO:0051373)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|protein dimerization activity (GO:0046983)|structural constituent of muscle (GO:0008307)|thyroid hormone receptor coactivator activity (GO:0030375)|titin binding (GO:0031432)|titin Z domain binding (GO:0070080)			endometrium(4)|kidney(2)|large_intestine(15)|lung(55)|ovary(4)|prostate(3)|skin(3)	86	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.00661)|Acute lymphoblastic leukemia(190;0.109)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00168)			AGCGAGTGAGGTAAAGGAAAC	0.468																																					.		Atlas-SNP	.											.	ACTN2	191	.	0			c.876+1G>T						.						105	92	97					1																	236900515		2203	4300	6503	SO:0001630	splice_region_variant	88	exon9			AGTGAGGTAAAGG	BC047901	CCDS1613.1, CCDS60455.1, CCDS73053.1	1q42-q43	2014-09-17			ENSG00000077522	ENSG00000077522		"EF-hand domain containing"	164	protein-coding gene	gene with protein product		102573				1339456	Standard	NM_001103		Approved		uc001hyf.2	P35609	OTTHUMG00000040059	ENST00000366578.4:c.876+1G>T	chr1.hg19:g.236900515G>T		135.0	0.0		110.0	38.0	NM_001103	B1ANE4|B2RCS5|Q86TF4|Q86TI8	Splice_Site	SNP	ENST00000366578.4	hg19	CCDS1613.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.646131	0.87958	.	.	ENSG00000077522	ENST00000542672;ENST00000366578;ENST00000545611	.	.	.	5.86	5.86	0.93980	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.1768	0.98178	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ACTN2	234967138	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.856000	0.99531	2.766000	0.95052	0.655000	0.94253	.	.	.		0.468	ACTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096628.1	NM_001103	Intron	T	236900515	G	T	236900515	5	4	319	1	0	0	0	0	0	0	1	0	205	1275	44	3	911	3	ACTN2	1	236900515	Splice_Site	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10	29826857	236900515	12350106	11	44911										
OR13G1	441933	hgsc.bcm.edu	37	chr1	247835685	247835685	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	tgcggatacggagaatagcaAcaatgataaaaccataggag	11	6	0	2			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr1:247835685A>G	ENST00000359688.2	-	1	680	c.659T>C	c.(658-660)gTt>gCt	p.V220A	RP11-634B7.4_ENST00000449298.1_RNA	NM_001005487.1	NP_001005487.1	Q8NGZ3	O13G1_HUMAN	olfactory receptor, family 13, subfamily G, member 1	220						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|kidney(1)|large_intestine(2)|lung(28)|skin(2)	35	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			GAGAATAGCAACAATGATAAA	0.443																																					p.V220A		Atlas-SNP	.											.	OR13G1	78	.	0			c.T659C						.						116	105	108					1																	247835685		2203	4300	6503	SO:0001583	missense	441933	exon1			ATAGCAACAATGA	AB065623	CCDS31094.1	1q44	2012-08-09			ENSG00000197437	ENSG00000197437		"GPCR / Class A : Olfactory receptors"	14999	protein-coding gene	gene with protein product		611677					Standard	NM_001005487		Approved		uc001idi.1	Q8NGZ3	OTTHUMG00000040212	ENST00000359688.2:c.659T>C	chr1.hg19:g.247835685A>G	ENSP00000352717:p.Val220Ala	155.0	0.0		131.0	32.0	NM_001005487	B2RN80|Q5T2T2|Q6IF86	Missense_Mutation	SNP	ENST00000359688.2	hg19	CCDS31094.1	.	.	.	.	.	.	.	.	.	.	A	0.026	-1.372834	0.01214	.	.	ENSG00000197437	ENST00000359688	T	0.37584	1.19	4.2	-2.46	0.06461	GPCR, rhodopsin-like superfamily (1);	0.519636	0.16050	N	0.232004	T	0.11324	0.0276	N	0.03084	-0.415	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.34502	-0.9826	10	0.07813	T	0.8	-0.256	7.1462	0.25585	0.3317:0.122:0.5463:0.0	.	220	Q8NGZ3	O13G1_HUMAN	A	220	ENSP00000352717:V220A	ENSP00000352717:V220A	V	-	2	0	OR13G1	245902308	0.000000	0.05858	0.000000	0.03702	0.253000	0.25986	-0.801000	0.04550	-0.326000	0.08564	-1.235000	0.01560	GTT	.	.		0.443	OR13G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096869.1	NM_001005487		G	247835685	A	G	247835685	3	3	319	1	0	0	0	0	1	0	0	0	10951	43	2	2	268	2	OR13G1	1	247835685	Missense_Mutation	SNP	A	TCGA-LG-A9QD-01A-11D-A382-10	10935170	247835685	1414936	12	44912										
APOB	338	hgsc.bcm.edu	37	chr2	21229990	21230013	+	In_Frame_Del	DEL	TCCAGGAATTTGAAAGGTCCTGGG	TCCAGGAATTTGAAAGGTCCTGGG	-													0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	ttgacaactggaacagtgtaTccaggaatttgaaaggtcct					rs372260836|rs368703055		TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	TCCAGGAATTTGAAAGGTCCTGGG	TCCAGGAATTTGAAAGGTCCTGGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr2:21229990_21230013delTCCAGGAATTTGAAAGGTCCTGGG	ENST00000233242.1	-	26	9854_9877	c.9727_9750delCCCAGGACCTTTCAAATTCCTGGA	c.(9727-9750)cccaggacctttcaaattcctggadel	p.PRTFQIPG3243del		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	3243					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GAACAGTGTATCCAGGAATTTGAAAGGTCCTGGGGAGCTCGTCG	0.388																																					p.3243_3251del		Atlas-INDEL	.											.	APOB	761	.	0			c.9728_9751del						.																																			SO:0001651	inframe_deletion	338	exon26			.	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.9727_9750delCCCAGGACCTTTCAAATTCCTGGA	chr2.hg19:g.21229990_21230013delTCCAGGAATTTGAAAGGTCCTGGG	ENSP00000233242:p.Pro3243_Gly3250del	180.0	0.0		99.0	13.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	In_Frame_Del	DEL	ENST00000233242.1	hg19	CCDS1703.1																																																																																			.	.		0.388	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			-	21230013	TCCAGGAATTTGAAAGGTCCTGGG	-	21229990	7	5	319	1	0	1	0	1	0	0	0	0	785	1422	50	0	3957	0	APOB	2	21229990	In_Frame_Del	DEL	TCCAGGAATTTGAAAGGTCCTGGG	TCGA-LG-A9QD-01A-11D-A382-10		21229990	221969383	13	44913			1	55		2	2	28	N	TCCAGGAATTTGAAAGGTCCTGGG_C	9.768e-05
APOB	338	hgsc.bcm.edu	37	chr2	21230017	21230017	+	Frame_Shift_Del	DEL	C	C	-													0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	atttgaaaggtcctggggagCtcgtcgtgagatttttcagc							TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr2:21230017delC	ENST00000233242.1	-	26	9850	c.9723delG	c.(9721-9723)gagfs	p.E3241fs		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	3241					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCCTGGGGAGCTCGTCGTGAG	0.378																																					p.L3242fs		Atlas-INDEL	.											.	APOB	761	.	0			c.9724delC						.						52	52	52					2																	21230017		2203	4300	6503	SO:0001589	frameshift_variant	338	exon26			.	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.9723delG	chr2.hg19:g.21230017delC	ENSP00000233242:p.Glu3241fs	170.0	0.0		99.0	13.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Frame_Shift_Del	DEL	ENST00000233242.1	hg19	CCDS1703.1																																																																																			.	.		0.378	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			-	21230017	C	-	21230017	7	5	319	1	0	1	0	1	0	0	0	0	785	796	28	0	3984	0	APOB	2	21230017	Frame_Shift_Del	DEL	C	TCGA-LG-A9QD-01A-11D-A382-10	27	21230017	221969356	14	44914			1	55		2	2	28	N	TCCAGGAATTTGAAAGGTCCTGGG_C	9.768e-05
MCEE	84693	hgsc.bcm.edu	37	chr2	71351621	71351621	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	acttgatccaagggctgtgaTgtggaagaagctcttactgt	12	7	1	3			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr2:71351621T>C	ENST00000244217.5	-	2	110	c.93A>G	c.(91-93)acA>acG	p.T31T	AC007881.1_ENST00000578636.1_RNA	NM_032601.3	NP_115990.3	Q96PE7	MCEE_HUMAN	methylmalonyl CoA epimerase	31					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|L-methylmalonyl-CoA metabolic process (GO:0046491)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	metal ion binding (GO:0046872)|methylmalonyl-CoA epimerase activity (GO:0004493)			kidney(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9						AGGGCTGTGATGTGGAAGAAG	0.448																																					p.T31T		Atlas-SNP	.											.	MCEE	19	.	0			c.A93G						.						106	115	112					2																	71351621		2203	4300	6503	SO:0001819	synonymous_variant	84693	exon2			CTGTGATGTGGAA	AF364547	CCDS1915.1	2p13.3	2011-05-12			ENSG00000124370	ENSG00000124370	5.1.99.1		16732	protein-coding gene	gene with protein product	"glyoxalase domain containing 2"	608419				16697227, 16752391, 16843692	Standard	NM_032601		Approved	GLOD2	uc002shs.2	Q96PE7	OTTHUMG00000129709	ENST00000244217.5:c.93A>G	chr2.hg19:g.71351621T>C		94.0	0.0		80.0	14.0	NM_032601	Q53TP1|Q8WW63	Silent	SNP	ENST00000244217.5	hg19	CCDS1915.1																																																																																			.	.		0.448	MCEE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251917.3	NM_032601		C	71351621	T	C	71351621	2	2	319	1	0	0	0	0	0	0	0	1	9386	1451	51	2		2	MCEE	2	71351621	Silent	SNP	T	TCGA-LG-A9QD-01A-11D-A382-10	50121604	71351621	171847752	15	44915										
CLASP1	23332	hgsc.bcm.edu	37	chr2	122165165	122165165	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	tacatcctcagtctgccgcaGataatggggaatgccaccat	9	12	2	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr2:122165165G>A	ENST00000263710.4	-	25	2940	c.2551C>T	c.(2551-2553)Ctg>Ttg	p.L851L	CLASP1_ENST00000397587.3_Silent_p.L831L|CLASP1_ENST00000409078.3_Silent_p.L823L|CLASP1_ENST00000545861.1_Silent_p.L598L|CLASP1_ENST00000541859.1_Silent_p.L584L|CLASP1_ENST00000541377.1_Silent_p.L829L|CLASP1_ENST00000455322.2_Silent_p.L823L	NM_015282.2	NP_056097.1	Q7Z460	CLAP1_HUMAN	cytoplasmic linker associated protein 1	851					axon guidance (GO:0007411)|cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|establishment or maintenance of cell polarity (GO:0007163)|exit from mitosis (GO:0010458)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)	cell cortex (GO:0005938)|centrosomal corona (GO:0031592)|centrosome (GO:0005813)|cortical microtubule cytoskeleton (GO:0030981)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|spindle microtubule (GO:0005876)	kinetochore binding (GO:0043515)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)	47	Renal(3;0.0496)					GTCTGCCGCAGATAATGGGGA	0.498																																					p.L851L		Atlas-SNP	.											.	CLASP1	135	.	0			c.C2551T						.						106	101	103					2																	122165165		1999	4174	6173	SO:0001819	synonymous_variant	23332	exon25			GCCGCAGATAATG	AB014522		2q14.2-q14.3	2013-01-18			ENSG00000074054	ENSG00000074054			17088	protein-coding gene	gene with protein product	"multiple asters 1"	605852				9734811, 10899121, 16914514	Standard	NM_015282		Approved	KIAA0622, MAST1	uc002tnc.3	Q7Z460	OTTHUMG00000153331	ENST00000263710.4:c.2551C>T	chr2.hg19:g.122165165G>A		209.0	0.0		183.0	42.0	NM_015282	B7ZLX3|O75118|Q2KHQ9|Q5H9P0|Q8N5B8|Q9BQT5	Silent	SNP	ENST00000263710.4	hg19																																																																																				.	.		0.498	CLASP1-201	KNOWN	basic	protein_coding	protein_coding		NM_015282		A	122165165	G	A	122165165	2	1	319	1	0	0	0	0	0	0	0	1	3456	933	33	3		3	CLASP1	2	122165165	Silent	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10	50813544	122165165	121034208	16	44916										
TTN	7273	hgsc.bcm.edu	37	chr2	179595433	179595433	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	gcttatgggatgtgacccagCcactatacattctaaatcaa	7	10	2	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr2:179595433C>T	ENST00000591111.1	-	59	17100	c.16876G>A	c.(16876-16878)Gct>Act	p.A5626T	TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.A5943T|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.A4699T|TTN-AS1_ENST00000582847.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12436	Ig-like 37.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGTGACCCAGCCACTATACAT	0.353																																					p.A5943T		Atlas-SNP	.											.	TTN	18412	.	0			c.G17827A						.						66	69	68					2																	179595433		1854	4109	5963	SO:0001583	missense	7273	exon61			ACCCAGCCACTAT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.16876G>A	chr2.hg19:g.179595433C>T	ENSP00000465570:p.Ala5626Thr	183.0	0.0		169.0	7.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	10.79	1.448667	0.26074	.	.	ENSG00000155657	ENST00000342992	T	0.65916	-0.18	5.86	4.98	0.66077	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.55893	0.1949	N	0.19112	0.55	0.80722	D	1	P	0.46859	0.885	P	0.48770	0.589	T	0.62096	-0.6926	9	0.87932	D	0	.	13.2588	0.60093	0.4327:0.5673:0.0:0.0	.	5626	Q8WZ42	TITIN_HUMAN	T	4699	ENSP00000343764:A4699T	ENSP00000343764:A4699T	A	-	1	0	TTN	179303678	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.511000	0.60462	1.449000	0.47699	0.563000	0.77884	GCT	.	.		0.353	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179595433	C	T	179595433	3	4	319	1	0	0	0	0	1	0	0	0	16750	739	26	3	86910	3	TTN	2	179595433	Missense_Mutation	SNP	C	TCGA-LG-A9QD-01A-11D-A382-10	57430268	179595433	63603940	17	44917										
TTN	7273	hgsc.bcm.edu	37	chr2	179634550	179634550	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	cttttcactcatctcaatttCcacaccattcttcagccaca	1	16	5	0			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr2:179634550C>T	ENST00000591111.1	-	37	8982	c.8758G>A	c.(8758-8760)Gaa>Aaa	p.E2920K	TTN_ENST00000359218.5_Missense_Mutation_p.E2874K|TTN_ENST00000342175.6_Missense_Mutation_p.E2874K|TTN_ENST00000589042.1_Missense_Mutation_p.E2920K|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.E2874K|TTN_ENST00000342992.6_Missense_Mutation_p.E2920K|TTN_ENST00000360870.5_Missense_Mutation_p.E2920K|TTN-AS1_ENST00000610005.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13250	Ig-like 16.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.E2920K(2)|p.E2874K(2)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATCTCAATTTCCACACCATTC	0.448																																					p.E2920K		Atlas-SNP	.											TTN_ENST00000360870,face,carcinoma,0,4	TTN	18412	.	4	Substitution - Missense(4)	skin(4)	c.G8758A						.						180	174	176					2																	179634550		2203	4300	6503	SO:0001583	missense	7273	exon37			CAATTTCCACACC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.8758G>A	chr2.hg19:g.179634550C>T	ENSP00000465570:p.Glu2920Lys	180.0	0.0		152.0	36.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	17.79	3.476683	0.63737	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24;-0.24	5.93	5.93	0.95920	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.82070	0.4957	M	0.67953	2.075	0.43902	D	0.99653	D;D;D;D;D	0.89917	0.999;0.999;0.999;0.999;1.0	D;D;D;D;D	0.87578	0.996;0.996;0.996;0.996;0.998	T	0.82327	-0.0512	9	0.87932	D	0	.	20.3363	0.98740	0.0:1.0:0.0:0.0	.	2874;2874;2874;2920;2920	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	K	2920;2874;2874;2874;2874;2920	ENSP00000343764:E2920K;ENSP00000434586:E2874K;ENSP00000340554:E2874K;ENSP00000352154:E2874K;ENSP00000354117:E2920K	ENSP00000340554:E2874K	E	-	1	0	TTN	179342795	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.818000	0.86416	2.814000	0.96858	0.563000	0.77884	GAA	.	.		0.448	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179634550	C	T	179634550	3	4	319	1	0	0	0	0	1	0	0	0	16750	864	30	3	102534	3	TTN	2	179634550	Missense_Mutation	SNP	C	TCGA-LG-A9QD-01A-11D-A382-10	39117	179634550	63564823	18	44918										
OSGEPL1	64172	hgsc.bcm.edu	37	chr2	190617705	190617705	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	tgcgacaccaccagatgcaaCctgaaggaattgagaaaacc	9	11	0	3			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr2:190617705C>A	ENST00000264151.5	-	6	1066	c.964G>T	c.(964-966)Gtt>Ttt	p.V322F	Y_RNA_ENST00000411317.1_RNA|OSGEPL1_ENST00000522700.1_Splice_Site_p.V322F|OSGEPL1_ENST00000519810.1_Splice_Site_p.V322F	NM_022353.2	NP_071748.2			O-sialoglycoprotein endopeptidase-like 1											large_intestine(2)|upper_aerodigestive_tract(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.00156)|Epithelial(96;0.0293)|all cancers(119;0.0831)			CCAGATGCAACCTGAAGGAAT	0.373																																					p.V322F		Atlas-SNP	.											.	OSGEPL1	19	.	0			c.G964T						.						58	53	54					2																	190617705		1855	4091	5946	SO:0001630	splice_region_variant	64172	exon6			ATGCAACCTGAAG	AJ295148	CCDS46472.1	2q32	2011-08-12			ENSG00000128694	ENSG00000128694			23075	protein-coding gene	gene with protein product						19578062	Standard	NM_022353		Approved	Qri7	uc002uqz.1	Q9H4B0	OTTHUMG00000164096	ENST00000264151.5:c.964-1G>T	chr2.hg19:g.190617705C>A		342.0	0.0		278.0	73.0	NM_022353		Missense_Mutation	SNP	ENST00000264151.5	hg19	CCDS46472.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.558937	0.86231	.	.	ENSG00000128694	ENST00000264151;ENST00000519810;ENST00000522700	T;T;T	0.23147	1.92;1.92;1.92	5.15	5.15	0.70609	Peptidase M22, glycoprotease (1);	0.057812	0.64402	D	0.000001	T	0.44201	0.1282	M	0.90309	3.105	0.80722	D	1	B	0.33477	0.413	B	0.36186	0.219	T	0.55309	-0.8161	10	0.87932	D	0	-27.5688	18.8073	0.92043	0.0:1.0:0.0:0.0	.	322	Q9H4B0	OSGP2_HUMAN	F	322	ENSP00000264151:V322F;ENSP00000428859:V322F;ENSP00000429697:V322F	ENSP00000264151:V322F	V	-	1	0	OSGEPL1	190325950	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	5.819000	0.69243	2.673000	0.90976	0.467000	0.42956	GTT	.	.		0.373	OSGEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377257.1	NM_022353	Missense_Mutation	A	190617705	C	A	190617705	5	1	319	1	0	0	0	0	0	0	1	0	11297	521	18	3	292	3	OSGEPL1	2	190617705	Splice_Site	SNP	C	TCGA-LG-A9QD-01A-11D-A382-10	10983155	190617705	52581668	19	44919										
CYP20A1	57404	hgsc.bcm.edu	37	chr2	204150447	204150447	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	gttactccagagaaaattgaGcagctcaggtaagaacacaa	9	8	1	3			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr2:204150447G>A	ENST00000356079.4	+	9	1086	c.963G>A	c.(961-963)gaG>gaA	p.E321E	CYP20A1_ENST00000461371.1_3'UTR|CYP20A1_ENST00000429815.2_Silent_p.E329E	NM_177538.2	NP_803882.1	Q6UW02	CP20A_HUMAN	cytochrome P450, family 20, subfamily A, polypeptide 1	321						integral component of membrane (GO:0016021)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)			cervix(1)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	11						AGAAAATTGAGCAGCTCAGGT	0.313																																					p.E321E		Atlas-SNP	.											.	CYP20A1	40	.	0			c.G963A						.						47	52	50					2																	204150447		2202	4295	6497	SO:0001819	synonymous_variant	57404	exon9			AATTGAGCAGCTC	AK021770	CCDS2357.1	2q33	2008-02-05			ENSG00000119004	ENSG00000119004		"Cytochrome P450s"	20576	protein-coding gene	gene with protein product							Standard	NM_177538		Approved	CYP-M	uc002uzv.4	Q6UW02	OTTHUMG00000132854	ENST00000356079.4:c.963G>A	chr2.hg19:g.204150447G>A		661.0	1.0		594.0	140.0	NM_177538	Q4ZG61|Q8N4Q8|Q8WWA9|Q9HC04	Silent	SNP	ENST00000356079.4	hg19	CCDS2357.1																																																																																			.	.		0.313	CYP20A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256328.3	NM_020674		A	204150447	G	A	204150447	2	1	319	1	0	0	0	0	0	0	0	1	4154	962	34	3		3	CYP20A1	2	204150447	Silent	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10	13532742	204150447	39048926	20	44920										
MAP2	4133	hgsc.bcm.edu	37	chr2	210558225	210558225	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	aaaggaaactgagctgaagcTtgaagaaaaaaccaccattt	8	7	0	4			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr2:210558225T>C	ENST00000360351.4	+	7	1837	c.1331T>C	c.(1330-1332)cTt>cCt	p.L444P	MAP2_ENST00000447185.1_Missense_Mutation_p.L440P|MAP2_ENST00000199940.6_Intron|MAP2_ENST00000361559.4_Intron|MAP2_ENST00000392194.1_Intron	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	444					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	GAGCTGAAGCTTGAAGAAAAA	0.433																																					p.L444P	Pancreas(27;423 979 28787 29963)	Atlas-SNP	.											.	MAP2	372	.	0			c.T1331C						.						67	69	68					2																	210558225		2203	4300	6503	SO:0001583	missense	4133	exon7			TGAAGCTTGAAGA		CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"A-kinase anchor proteins"	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.1331T>C	chr2.hg19:g.210558225T>C	ENSP00000353508:p.Leu444Pro	190.0	0.0		185.0	55.0	NM_002374	Q17S04|Q8IUX2|Q99975|Q99976	Missense_Mutation	SNP	ENST00000360351.4	hg19	CCDS2384.1	.	.	.	.	.	.	.	.	.	.	T	3.857	-0.030580	0.07543	.	.	ENSG00000078018	ENST00000360351;ENST00000445941;ENST00000447185	T;T;T	0.28666	1.6;1.6;1.6	5.5	-0.0118	0.13991	MAP2/Tau projection (1);	0.696719	0.13130	N	0.411549	T	0.13457	0.0326	N	0.14661	0.345	0.19300	N	0.99998	B;B	0.06786	0.001;0.001	B;B	0.06405	0.001;0.002	T	0.25950	-1.0117	10	0.21540	T	0.41	-0.0403	3.4151	0.07373	0.5958:0.1331:0.0:0.2711	.	440;444	P11137-3;P11137	.;MAP2_HUMAN	P	444;526;440	ENSP00000353508:L444P;ENSP00000409969:L526P;ENSP00000392164:L440P	ENSP00000353508:L444P	L	+	2	0	MAP2	210266470	0.000000	0.05858	0.011000	0.14972	0.696000	0.40369	0.100000	0.15231	0.018000	0.15052	0.528000	0.53228	CTT	.	.		0.433	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538		C	210558225	T	C	210558225	3	2	319	1	0	0	0	0	1	0	0	0	9244	1609	56	2	1345	2	MAP2	2	210558225	Missense_Mutation	SNP	T	TCGA-LG-A9QD-01A-11D-A382-10	6407778	210558225	32641148	21	44921										
ZNF142	7701	hgsc.bcm.edu	37	chr2	219513983	219513983	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	agtgggcagtggtgggccttTtcacccagctcccgcagcag	14	13	1	0			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr2:219513983T>G	ENST00000449707.1	-	6	1069	c.648A>C	c.(646-648)gaA>gaC	p.E216D	ZNF142_ENST00000411696.2_Missense_Mutation_p.E216D	NM_001105537.1	NP_001099007.1	P52746	ZN142_HUMAN	zinc finger protein 142	216					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(7)|endometrium(7)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38		Renal(207;0.0474)		Epithelial(149;5.21e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		GGTGGGCCTTTTCACCCAGCT	0.552											OREG0015202	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E216D	Colon(170;867 1942 8995 15834 18053)	Atlas-SNP	.											.	ZNF142	190	.	0			c.A648C						.						66	70	68					2																	219513983		2070	4206	6276	SO:0001583	missense	7701	exon6			GGCCTTTTCACCC	U09849	CCDS42817.1	2q35	2013-01-08	2006-06-13		ENSG00000115568	ENSG00000115568		"Zinc fingers, C2H2-type"	12927	protein-coding gene	gene with protein product		604083	"zinc finger protein 142 (clone pHZ-49)"				Standard	NM_001105537		Approved	KIAA0236, pHZ-49	uc002vin.4	P52746	OTTHUMG00000154736	ENST00000449707.1:c.648A>C	chr2.hg19:g.219513983T>G	ENSP00000408643:p.Glu216Asp	104.0	0.0	2259	82.0	20.0	NM_001105537	Q92510	Missense_Mutation	SNP	ENST00000449707.1	hg19	CCDS42817.1	.	.	.	.	.	.	.	.	.	.	T	14.46	2.543170	0.45280	.	.	ENSG00000115568	ENST00000449707;ENST00000411696	T;T	0.19806	2.12;2.12	5.22	3.41	0.39046	Zinc finger, C2H2 (1);	0.260739	0.43579	D	0.000555	T	0.19208	0.0461	L	0.46885	1.475	0.32133	N	0.586534	B;B	0.28971	0.229;0.073	B;B	0.26094	0.036;0.066	T	0.15954	-1.0419	10	0.62326	D	0.03	-1.2625	11.5163	0.50524	0.0:0.852:0.0:0.148	.	216;53	P52746;A8MWU9	ZN142_HUMAN;.	D	216	ENSP00000408643:E216D;ENSP00000398798:E216D	ENSP00000398798:E216D	E	-	3	2	ZNF142	219222227	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.864000	0.39469	0.875000	0.35847	-0.468000	0.05107	GAA	.	.		0.552	ZNF142-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336833.1	NM_005081		G	219513983	T	G	219513983	3	3	319	1	0	0	0	0	1	0	0	0	17746	1838	64	5	4435	5	ZNF142	2	219513983	Missense_Mutation	SNP	T	TCGA-LG-A9QD-01A-11D-A382-10	8955758	219513983	23685390	22	44922										
OBSL1	23363	hgsc.bcm.edu	37	chr2	220426656	220426656	+	Intron	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	ggggaagcgggaccagagccGccgggtcttcggctttttca	16	11	2	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr2:220426656G>C	ENST00000404537.1	-	8	3010				OBSL1_ENST00000289656.3_Missense_Mutation_p.R597G|OBSL1_ENST00000265318.4_Intron|OBSL1_ENST00000265317.5_5'Flank|RP11-256I23.2_ENST00000597192.1_RNA|OBSL1_ENST00000373876.1_Intron|OBSL1_ENST00000603926.1_Intron|OBSL1_ENST00000373873.4_Missense_Mutation_p.R1010G	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1						cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)						Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		gaccagagccgccgggtcttc	0.557																																					p.R1010G		Atlas-SNP	.											.	OBSL1	120	.	0			c.C3028G						.																																			SO:0001627	intron_variant	23363	exon9			AGAGCCGCCGGGT	BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.2953+467C>G	chr2.hg19:g.220426656G>C		164.0	0.0		109.0	5.0	NM_001173408	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Missense_Mutation	SNP	ENST00000404537.1	hg19	CCDS46520.1	.	.	.	.	.	.	.	.	.	.	G	14.73	2.621252	0.46736	.	.	ENSG00000124006	ENST00000373873;ENST00000289656	T;T	0.62105	0.05;0.73	3.96	2.99	0.34606	.	.	.	.	.	T	0.40719	0.1128	N	0.08118	0	0.80722	D	1	B;B	0.15141	0.005;0.012	B;B	0.21708	0.003;0.036	T	0.43261	-0.9402	9	0.72032	D	0.01	.	8.9484	0.35773	0.0:0.228:0.772:0.0	.	597;1010	A8MSZ8;O75147-2	.;.	G	1010;597	ENSP00000362980:R1010G;ENSP00000289656:R597G	ENSP00000289656:R597G	R	-	1	2	OBSL1	220134900	0.993000	0.37304	1.000000	0.80357	0.996000	0.88848	1.746000	0.38288	2.217000	0.71921	0.650000	0.86243	CGG	.	.		0.557	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1			C	220426656	G	C	220426656	1	2	319	0	1	0	0	0	0	0	0	0	10822	1086	38	4		4	OBSL1	2	220426656	Intron	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10	912673	220426656	22772717	23	44923										
COL4A4	1286	hgsc.bcm.edu	37	chr2	227942713	227942713	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	ggaaatcccagtcctgggggCcccacaggtcctgctttgcc	12	15	0	0			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr2:227942713C>T	ENST00000396625.3	-	25	2091	c.1884G>A	c.(1882-1884)ggG>ggA	p.G628G	COL4A4_ENST00000329662.7_Silent_p.G628G	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	628	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		GTCCTGGGGGCCCCACAGGTC	0.612																																					p.G628G		Atlas-SNP	.											.	COL4A4	215	.	0			c.G1884A						.						25	28	27					2																	227942713		1805	4071	5876	SO:0001819	synonymous_variant	1286	exon25			TGGGGGCCCCACA		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"Collagens"	2206	protein-coding gene	gene with protein product	"collagen of basement membrane, alpha-4 chain"	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.1884G>A	chr2.hg19:g.227942713C>T		185.0	0.0		172.0	57.0	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Silent	SNP	ENST00000396625.3	hg19	CCDS42828.1																																																																																			.	.		0.612	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092		T	227942713	C	T	227942713	2	4	319	1	0	0	0	0	0	0	0	1	3695	726	26	3		3	COL4A4	2	227942713	Silent	SNP	C	TCGA-LG-A9QD-01A-11D-A382-10	7516057	227942713	15256660	24	44924										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266137	41266137	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	tgccactaccacagctccttCtctgagtggtaaaggcaatc	8	13	1	1	rs121913409		TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr3:41266137C>T	ENST00000349496.5	+	3	414	c.134C>T	c.(133-135)tCt>tTt	p.S45F	CTNNB1_ENST00000396183.3_Missense_Mutation_p.S45F|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S45F|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S45F|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S38F	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	45			Missing (in colorectal cancer). {ECO:0000269|PubMed:9065402}.|S -> F (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> P (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S45F(384)|p.S45del(53)|p.A5_A80del(53)|p.S45C(19)|p.S45Y(17)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.S45_S47>C(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.S45_G48del(1)|p.Q28_Q61del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.S45_L46del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.P44_N51del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.S45fs*2(1)|p.T40_L46del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.S45E(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.T42_K49>Q(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		ACAGCTCCTTCTCTGAGTGGT	0.498	S45F(HCC15_LUNG)|S45F(LS180_LARGE_INTESTINE)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S45F	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,carcinoma,+1,2	CTNNB1	4904	.	601	Substitution - Missense(421)|Deletion - In frame(152)|Complex - deletion inframe(20)|Unknown(7)|Deletion - Frameshift(1)	soft_tissue(233)|liver(141)|large_intestine(85)|kidney(74)|endometrium(16)|skin(11)|adrenal_gland(9)|stomach(7)|biliary_tract(5)|ovary(4)|lung(3)|central_nervous_system(2)|cervix(2)|small_intestine(2)|haematopoietic_and_lymphoid_tissue(2)|urinary_tract(1)|pituitary(1)|prostate(1)|bone(1)|pancreas(1)	c.C134T						.						84	74	77					3																	41266137		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	CTCCTTCTCTGAG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.134C>T	chr3.hg19:g.41266137C>T	ENSP00000344456:p.Ser45Phe	171.0	0.0		152.0	49.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.569754	0.86439	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.68165	0.2971	M	0.65677	2.01	0.80722	D	1	D	0.67145	0.996	D	0.64687	0.928	T	0.68895	-0.5288	10	0.87932	D	0	-13.6823	20.2983	0.98569	0.0:1.0:0.0:0.0	.	45	P35222	CTNB1_HUMAN	F	38;45;45;45;45;38;45;45;45	ENSP00000400508:S38F;ENSP00000385604:S45F;ENSP00000412219:S45F;ENSP00000379486:S45F;ENSP00000344456:S45F;ENSP00000411226:S38F;ENSP00000379488:S45F;ENSP00000409302:S45F;ENSP00000401599:S45F	ENSP00000344456:S45F	S	+	2	0	CTNNB1	41241141	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.802000	0.96397	0.655000	0.94253	TCT	.	.		0.498	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41266137	C	T	41266137	3	4	319	1	0	0	0	0	1	0	0	0	4018	913	32	3	140	3	CTNNB1	3	41266137	Missense_Mutation	SNP	C	TCGA-LG-A9QD-01A-11D-A382-10		41266137	156756293	25	44925										
LIMD1	8994	hgsc.bcm.edu	37	chr3	45636572	45636572	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	cagcagcagctcctgcaggaGgagactctgcccagggggag	16	12	1	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr3:45636572G>T	ENST00000273317.4	+	1	222	c.201G>T	c.(199-201)gaG>gaT	p.E67D	AC099539.1_ENST00000516118.1_RNA|LIMD1_ENST00000465039.1_Intron|LIMD1_ENST00000440097.1_Missense_Mutation_p.E67D	NM_014240.2	NP_055055.1	Q9UGP4	LIMD1_HUMAN	LIM domains containing 1	67	Mediates nuclear export.				cell migration (GO:0016477)|cytoplasmic mRNA processing body assembly (GO:0033962)|cytoskeleton organization (GO:0007010)|gene silencing by miRNA (GO:0035195)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of hippo signaling (GO:0035331)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|phosphorylation (GO:0016310)|positive regulation of gene silencing by miRNA (GO:2000637)|regulation of cell shape (GO:0008360)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|RISC complex (GO:0016442)	transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(193;0.011)|KIRC - Kidney renal clear cell carcinoma(197;0.0264)|Kidney(197;0.0315)		TCCTGCAGGAGGAGACTCTGC	0.627																																					p.E67D		Atlas-SNP	.											.	LIMD1	34	.	0			c.G201T						.						21	24	23					3																	45636572		2203	4294	6497	SO:0001583	missense	8994	exon1			GCAGGAGGAGACT	AJ132408	CCDS2729.1	3p21.31	2008-02-01			ENSG00000144791	ENSG00000144791			6612	protein-coding gene	gene with protein product		604543				10647888	Standard	NM_014240		Approved		uc003coq.3	Q9UGP4	OTTHUMG00000133453	ENST00000273317.4:c.201G>T	chr3.hg19:g.45636572G>T	ENSP00000273317:p.Glu67Asp	91.0	0.0		80.0	4.0	NM_014240	Q17RQ1|Q9BQQ9|Q9NQ47	Missense_Mutation	SNP	ENST00000273317.4	hg19	CCDS2729.1	.	.	.	.	.	.	.	.	.	.	G	17.20	3.329531	0.60743	.	.	ENSG00000144791	ENST00000440097;ENST00000273317	T;T	0.61158	0.13;0.35	4.22	2.41	0.29592	.	0.871395	0.09993	N	0.729440	T	0.53578	0.1805	L	0.32530	0.975	0.35838	D	0.825869	D	0.53885	0.963	P	0.50570	0.644	T	0.52601	-0.8554	10	0.39692	T	0.17	.	8.9299	0.35663	0.1521:0.0:0.8479:0.0	.	67	Q9UGP4	LIMD1_HUMAN	D	67	ENSP00000394537:E67D;ENSP00000273317:E67D	ENSP00000273317:E67D	E	+	3	2	LIMD1	45611576	1.000000	0.71417	1.000000	0.80357	0.588000	0.36517	1.830000	0.39131	0.264000	0.21851	0.462000	0.41574	GAG	.	.		0.627	LIMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257327.1	NM_014240		T	45636572	G	T	45636572	3	4	319	1	0	0	0	0	1	0	0	0	8807	991	35	3	203	3	LIMD1	3	45636572	Missense_Mutation	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10	4370435	45636572	152385858	26	44926										
PLCXD2	257068	hgsc.bcm.edu	37	chr3	111394161	111394161	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	tgctcccccaaccccagcggGacaaagacatcatcggaggt	10	15	1	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr3:111394161G>A	ENST00000477665.1	+	1	393	c.69G>A	c.(67-69)ggG>ggA	p.G23G	PLCXD2_ENST00000393934.3_Silent_p.G23G|PLCXD2-AS1_ENST00000493131.1_RNA	NM_001185106.1	NP_001172035.1	Q0VAA5	PLCX2_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 2	23					lipid catabolic process (GO:0016042)		phosphoric diester hydrolase activity (GO:0008081)|signal transducer activity (GO:0004871)			endometrium(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)	17						ACCCCAGCGGGACAAAGACAT	0.577																																					p.G23G		Atlas-SNP	.											.	PLCXD2	36	.	0			c.G69A						.						146	131	136					3																	111394161		2203	4300	6503	SO:0001819	synonymous_variant	257068	exon1			CAGCGGGACAAAG	AK056141	CCDS2961.1, CCDS54619.1	3q13.2	2004-09-09			ENSG00000240891	ENSG00000240891			26462	protein-coding gene	gene with protein product							Standard	NM_001185106		Approved	FLJ31579	uc003dxz.3	Q0VAA5	OTTHUMG00000159279	ENST00000477665.1:c.69G>A	chr3.hg19:g.111394161G>A		181.0	0.0		184.0	40.0	NM_001185106	Q96N12	Silent	SNP	ENST00000477665.1	hg19	CCDS54619.1																																																																																			.	.		0.577	PLCXD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354322.1	NM_153268		A	111394161	G	A	111394161	2	1	319	1	0	0	0	0	0	0	0	1	12051	1161	41	3		3	PLCXD2	3	111394161	Silent	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10	65757589	111394161	86628269	27	44927										
PLXNA1	5361	hgsc.bcm.edu	37	chr3	126726697	126726697	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	actggtgcaaataccgccacGtgtgcacacacaacgtggct	10	13	0	0			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr3:126726697G>A	ENST00000393409.2	+	8	2053	c.2053G>A	c.(2053-2055)Gtg>Atg	p.V685M	PLXNA1_ENST00000251772.4_Missense_Mutation_p.V662M	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	685					axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)	p.V662M(1)		breast(3)|central_nervous_system(5)|endometrium(10)|kidney(5)|large_intestine(4)|lung(32)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	67				GBM - Glioblastoma multiforme(114;0.155)		ATACCGCCACGTGTGCACACA	0.627																																					p.V685M		Atlas-SNP	.											PLXNA1,NS,carcinoma,0,1	PLXNA1	185	.	1	Substitution - Missense(1)	lung(1)	c.G2053A						.						80	71	74					3																	126726697		2203	4299	6502	SO:0001583	missense	5361	exon8			CGCCACGTGTGCA	X87832	CCDS33847.1, CCDS33847.2	3q21.2	2006-12-19				ENSG00000114554		"Plexins"	9099	protein-coding gene	gene with protein product		601055		PLXN1		8570614	Standard	NM_032242		Approved	NOV	uc003ejg.3	Q9UIW2		ENST00000393409.2:c.2053G>A	chr3.hg19:g.126726697G>A	ENSP00000377061:p.Val685Met	71.0	0.0		71.0	12.0	NM_032242		Missense_Mutation	SNP	ENST00000393409.2	hg19	CCDS33847.2	.	.	.	.	.	.	.	.	.	.	G	9.487	1.099645	0.20552	.	.	ENSG00000114554	ENST00000393409;ENST00000251772	T;T	0.17854	2.25;2.25	3.63	2.74	0.32292	.	0.277746	0.25436	N	0.030698	T	0.09905	0.0243	N	0.20685	0.6	0.37780	D	0.926974	B	0.27823	0.19	B	0.29663	0.105	T	0.13176	-1.0519	10	0.45353	T	0.12	.	6.1876	0.20506	0.2381:0.0:0.7619:0.0	.	685	Q9UIW2	PLXA1_HUMAN	M	685;662	ENSP00000377061:V685M;ENSP00000251772:V662M	ENSP00000251772:V662M	V	+	1	0	PLXNA1	128209387	0.996000	0.38824	0.909000	0.35828	0.586000	0.36452	2.516000	0.45520	2.025000	0.59659	0.467000	0.42956	GTG	.	.		0.627	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356451.1	NM_032242		A	126726697	G	A	126726697	3	1	319	1	0	0	0	0	1	0	0	0	12128	1145	40	1	2083	1	PLXNA1	3	126726697	Missense_Mutation	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10	15332536	126726697	71295733	28	44928										
ALB	213	hgsc.bcm.edu	37	chr4	74282072	74282072	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	agtacaaattccagaatgcgTaagtaatttttattgactga	7	5	0	3	rs77232890		TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr4:74282072T>G	ENST00000503124.1	+	8	1046		c.e8+2		ALB_ENST00000509063.1_Splice_Site|ALB_ENST00000295897.4_Splice_Site|ALB_ENST00000505649.1_Splice_Site|ALB_ENST00000415165.2_Splice_Site|ALB_ENST00000401494.3_Splice_Site			Q8TES7	FBF1_HUMAN	albumin						apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CCAGAATGCGTAAGTAATTTT	0.294																																					.		Atlas-SNP	.											.	ALB	132	.	0			c.1289+2T>G						.						36	37	36					4																	74282072		2202	4298	6500	SO:0001630	splice_region_variant	213	exon10			AATGCGTAAGTAA	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.839+2T>G	chr4.hg19:g.74282072T>G		224.0	0.0		200.0	58.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Splice_Site	SNP	ENST00000503124.1	hg19		.	.	.	.	.	.	.	.	.	.	T	12.63	1.995730	0.35226	.	.	ENSG00000163631	ENST00000295897;ENST00000415165;ENST00000329326;ENST00000503124;ENST00000509063;ENST00000401494;ENST00000430202;ENST00000511370	.	.	.	5.74	5.74	0.90152	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8657	0.70412	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	ALB	74500936	1.000000	0.71417	0.615000	0.29064	0.275000	0.26752	4.513000	0.60476	2.198000	0.70561	0.482000	0.46254	.	.	.		0.294	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477	Intron	G	74282072	T	G	74282072	5	3	319	1	0	0	0	0	0	0	1	0	486	1652	57	5	1329	5	ALB	4	74282072	Splice_Site	SNP	T	TCGA-LG-A9QD-01A-11D-A382-10		74282072	116872204	29	44929										
ARHGAP10	79658	hgsc.bcm.edu	37	chr4	148796299	148796299	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	ctacctgtatgtccaggaaaAaagtaagaggccctccagca	9	11	0	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr4:148796299A>G	ENST00000336498.3	+	8	1069	c.830A>G	c.(829-831)aAa>aGa	p.K277R		NM_024605.3	NP_078881.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 10	0					establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			autonomic_ganglia(2)|endometrium(5)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		GTCCAGGAAAAAAGTAAGAGG	0.438																																					p.K277R		Atlas-SNP	.											.	ARHGAP10	92	.	0			c.A830G						.						67	65	66					4																	148796299		2203	4300	6503	SO:0001583	missense	79658	exon8			AGGAAAAAAGTAA	BC047914	CCDS34075.1	4q31.23	2013-09-20			ENSG00000071205	ENSG00000071205		"Rho GTPase activating proteins"	26099	protein-coding gene	gene with protein product		609746				8288572	Standard	NM_024605		Approved	FLJ20896, FLJ41791, GRAF2	uc003ilf.3	A1A4S6	OTTHUMG00000161460	ENST00000336498.3:c.830A>G	chr4.hg19:g.148796299A>G	ENSP00000336923:p.Lys277Arg	698.0	0.0		558.0	162.0	NM_024605	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000336498.3	hg19	CCDS34075.1	.	.	.	.	.	.	.	.	.	.	A	14.85	2.657178	0.47467	.	.	ENSG00000071205	ENST00000336498	T	0.04654	3.58	4.54	3.35	0.38373	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.507731	0.23636	N	0.046075	T	0.16938	0.0407	M	0.78637	2.42	0.80722	D	1	D	0.67145	0.996	P	0.62740	0.906	T	0.00269	-1.1861	10	0.56958	D	0.05	.	9.8819	0.41238	0.9174:0.0:0.0826:0.0	.	277	A1A4S6	RHG10_HUMAN	R	277	ENSP00000336923:K277R	ENSP00000336923:K277R	K	+	2	0	ARHGAP10	149015749	1.000000	0.71417	0.995000	0.50966	0.009000	0.06853	8.365000	0.90108	0.701000	0.31803	-0.323000	0.08544	AAA	.	.		0.438	ARHGAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365005.1	NM_024605		G	148796299	A	G	148796299	3	3	319	1	0	0	0	0	1	0	0	0	862	14	1	2	860	2	ARHGAP10	4	148796299	Missense_Mutation	SNP	A	TCGA-LG-A9QD-01A-11D-A382-10	74514227	148796299	42357977	30	44930										
FBXO8	26269	hgsc.bcm.edu	37	chr4	175183929	175183929	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	acttacccttgccagagaagTtcatcattcgcaaggtcctg	8	12	2	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr4:175183929T>G	ENST00000393674.2	-	2	1177	c.315A>C	c.(313-315)gaA>gaC	p.E105D	FBXO8_ENST00000503293.1_Missense_Mutation_p.E64D	NM_012180.2	NP_036312.2	Q9NRD0	FBX8_HUMAN	F-box protein 8	105	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell junction (GO:0030054)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|prostate(1)|urinary_tract(1)	14		Prostate(90;0.00201)|Melanoma(52;0.012)|Renal(120;0.0183)|all_neural(102;0.0887)|all_hematologic(60;0.107)		all cancers(43;7.29e-18)|Epithelial(43;1.85e-15)|OV - Ovarian serous cystadenocarcinoma(60;5.62e-09)|GBM - Glioblastoma multiforme(59;0.00115)|STAD - Stomach adenocarcinoma(60;0.00299)|LUSC - Lung squamous cell carcinoma(193;0.1)		GCCAGAGAAGTTCATCATTCG	0.383																																					p.E105D		Atlas-SNP	.											.	FBXO8	34	.	0			c.A315C						.						77	69	71					4																	175183929		2203	4300	6503	SO:0001583	missense	26269	exon2			GAGAAGTTCATCA	AF174596	CCDS3820.1	4q34.1	2008-02-05	2004-06-15			ENSG00000164117		"F-boxes /  "other""	13587	protein-coding gene	gene with protein product		605649	"F-box only protein 8"			10531035, 10531037	Standard	NM_012180		Approved	FBX8, FBS	uc003itp.3	Q9NRD0		ENST00000393674.2:c.315A>C	chr4.hg19:g.175183929T>G	ENSP00000377280:p.Glu105Asp	161.0	0.0		156.0	35.0	NM_012180	B2RB40|D3DP41|G5E9Z0|Q6UWN4|Q8IWE1|Q9NRP5|Q9UKC4	Missense_Mutation	SNP	ENST00000393674.2	hg19	CCDS3820.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.70|14.70	2.613258|2.613258	0.46631|0.46631	.|.	.|.	ENSG00000164117|ENSG00000164117	ENST00000393674;ENST00000503293;ENST00000513696|ENST00000296517	T;T;T|.	0.51817|.	0.69;0.69;0.69|.	5.63|5.63	-2.78|-2.78	0.05859|0.05859	F-box domain, cyclin-like (1);F-box domain, Skp2-like (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.33673|0.33673	0.0871|0.0871	N|N	0.05177|0.05177	-0.1|-0.1	0.45205|0.45205	D|D	0.998218|0.998218	B;B|.	0.24920|.	0.079;0.114|.	B;B|.	0.28139|.	0.086;0.057|.	T|T	0.15122|0.15122	-1.0448|-1.0448	10|6	0.42905|0.35671	T|T	0.14|0.21	.|.	12.951|12.951	0.58401|0.58401	0.0:0.5958:0.0:0.4042|0.0:0.5958:0.0:0.4042	.|.	64;105|.	G5E9Z0;Q9NRD0|.	.;FBX8_HUMAN|.	D|T	105;64;105|19	ENSP00000377280:E105D;ENSP00000422905:E64D;ENSP00000427506:E105D|.	ENSP00000377280:E105D|ENSP00000296517:N19T	E|N	-|-	3|2	2|0	FBXO8|FBXO8	175420504|175420504	0.772000|0.772000	0.28567|0.28567	0.996000|0.996000	0.52242|0.52242	0.971000|0.971000	0.66376|0.66376	-0.126000|-0.126000	0.10563|0.10563	-0.206000|-0.206000	0.10203|0.10203	0.383000|0.383000	0.25322|0.25322	GAA|AAC	.	.		0.383	FBXO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362085.2	NM_012180		G	175183929	T	G	175183929	3	3	319	1	0	0	0	0	1	0	0	0	5769	1722	60	5	664	5	FBXO8	4	175183929	Missense_Mutation	SNP	T	TCGA-LG-A9QD-01A-11D-A382-10	26387630	175183929	15970347	31	44931										
ACTBL2	345651	hgsc.bcm.edu	37	chr5	56777436	56777436	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	tctgtgaacgataggaggacCagcctcatcatattcctgct	9	11	3	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr5:56777436C>T	ENST00000423391.1	-	1	1200	c.1099G>A	c.(1099-1101)Ggt>Agt	p.G367S	CTD-2023N9.1_ENST00000506106.1_RNA|AC025470.1_ENST00000584598.1_RNA	NM_001017992.3	NP_001017992.1	Q562R1	ACTBL_HUMAN	actin, beta-like 2	367						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(3)|pancreas(1)|prostate(2)	28		Lung NSC(810;0.000135)|Prostate(74;0.055)|Breast(144;0.0707)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;4.24e-37)		ATAGGAGGACCAGCCTCATCA	0.468																																					p.G367S		Atlas-SNP	.											.	ACTBL2	65	.	0			c.G1099A						.						85	89	87					5																	56777436		2203	4300	6503	SO:0001583	missense	345651	exon1			GAGGACCAGCCTC		CCDS34163.1	5q11.2	2014-08-08			ENSG00000169067	ENSG00000169067			17780	protein-coding gene	gene with protein product		614835					Standard	NM_001017992		Approved	DKFZp686D0972	uc003jrm.3	Q562R1	OTTHUMG00000162330	ENST00000423391.1:c.1099G>A	chr5.hg19:g.56777436C>T	ENSP00000416706:p.Gly367Ser	139.0	0.0		92.0	19.0	NM_001017992	B2RPJ1|Q562R2|Q562S9|Q562X8	Missense_Mutation	SNP	ENST00000423391.1	hg19	CCDS34163.1	.	.	.	.	.	.	.	.	.	.	C	15.63	2.891235	0.52014	.	.	ENSG00000169067	ENST00000423391	T	0.63744	-0.06	4.98	4.11	0.48088	.	0.000000	0.64402	D	0.000004	D	0.86104	0.5853	H	0.98786	4.33	0.51767	D	0.999934	P	0.52577	0.954	D	0.68353	0.957	D	0.89781	0.3961	10	0.87932	D	0	.	11.5182	0.50536	0.0:0.912:0.0:0.088	.	367	Q562R1	ACTBL_HUMAN	S	367	ENSP00000416706:G367S	ENSP00000416706:G367S	G	-	1	0	ACTBL2	56813193	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.878000	0.69682	1.319000	0.45190	0.655000	0.94253	GGT	.	.		0.468	ACTBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368579.1	NM_001017992		T	56777436	C	T	56777436	3	4	319	1	0	0	0	0	1	0	0	0	194	594	21	3	35	3	ACTBL2	5	56777436	Missense_Mutation	SNP	C	TCGA-LG-A9QD-01A-11D-A382-10		56777436	124137824	32	44932										
PDE4D	5144	hgsc.bcm.edu	37	chr5	59284493	59284493	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	gacaagatagggttccattcCgcggaaagggtcttcctctt	11	10	2	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr5:59284493C>T	ENST00000502484.2	-	3	317	c.94G>A	c.(94-96)Gga>Aga	p.G32R	PDE4D_ENST00000546160.1_Missense_Mutation_p.G32R	NM_001165899.1	NP_001159371.1	Q08499	PDE4D_HUMAN	phosphodiesterase 4D, cAMP-specific	0					adrenergic receptor signaling pathway (GO:0071875)|adrenergic receptor signaling pathway involved in positive regulation of heart rate (GO:0086024)|aging (GO:0007568)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to lipopolysaccharide (GO:0071222)|establishment of endothelial barrier (GO:0061028)|multicellular organism growth (GO:0035264)|negative regulation of heart contraction (GO:0045822)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of relaxation of cardiac muscle (GO:1901898)|neutrophil chemotaxis (GO:0030593)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-5 production (GO:0032754)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of receptor activity (GO:0010469)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|smooth muscle contraction (GO:0006939)|T cell receptor signaling pathway (GO:0050852)	calcium channel complex (GO:0034704)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|ATPase binding (GO:0051117)|beta-2 adrenergic receptor binding (GO:0031698)|cAMP binding (GO:0030552)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|pancreas(1)	15		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Caffeine(DB00201)|Dyphylline(DB00651)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Roflumilast(DB01656)	GGTTCCATTCCGCGGAAAGGG	0.433																																					p.G32R		Atlas-SNP	.											.	PDE4D	345	.	0			c.G94A						.						144	134	137					5																	59284493		1568	3582	5150	SO:0001583	missense	5144	exon3			CCATTCCGCGGAA		CCDS47213.1, CCDS54858.1, CCDS54859.1, CCDS56369.1, CCDS56370.1, CCDS56371.1, CCDS56372.1, CCDS56373.1	5q12	2010-06-24	2010-06-24				3.1.4.17	"Phosphodiesterases"	8783	protein-coding gene	gene with protein product	"phosphodiesterase E3 dunce homolog (Drosophila)"	600129	"phosphodiesterase 4D, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E3)"	DPDE3			Standard	NM_006203		Approved		uc003jsa.2	Q08499		ENST00000502484.2:c.94G>A	chr5.hg19:g.59284493C>T	ENSP00000423094:p.Gly32Arg	1888.0	1.0		1507.0	439.0	NM_001165899	O43433|Q13549|Q13550|Q13551|Q7Z2L8|Q8IV84|Q8IVA9|Q8IVD2|Q8IVD3|Q96HL4|Q9HCX7	Missense_Mutation	SNP	ENST00000502484.2	hg19	CCDS54859.1	.	.	.	.	.	.	.	.	.	.	C	14.38	2.517810	0.44763	.	.	ENSG00000113448	ENST00000502484;ENST00000546160;ENST00000505507;ENST00000514552	T;T	0.68624	-0.34;-0.34	5.86	5.86	0.93980	.	.	.	.	.	D	0.82309	0.5009	.	.	.	0.32133	N	0.586447	D;P	0.89917	1.0;0.941	D;B	0.69479	0.964;0.232	T	0.83227	-0.0065	8	0.52906	T	0.07	.	20.1854	0.98212	0.0:1.0:0.0:0.0	.	32;32	D6RIG1;Q08499-11	.;.	R	32	ENSP00000423094:G32R;ENSP00000442734:G32R	ENSP00000423094:G32R	G	-	1	0	PDE4D	59320250	0.999000	0.42202	0.919000	0.36401	0.412000	0.31113	4.681000	0.61663	2.772000	0.95346	0.585000	0.79938	GGA	.	.		0.433	PDE4D-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368094.3			T	59284493	C	T	59284493	3	4	319	1	0	0	0	0	1	0	0	0	11651	661	23	1	2722	1	PDE4D	5	59284493	Missense_Mutation	SNP	C	TCGA-LG-A9QD-01A-11D-A382-10	2507057	59284493	121630767	33	44933										
PCDHGB3	56102	hgsc.bcm.edu	37	chr5	140751548	140751548	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	gagcagctgcgtgccttcgaGctcactctgcaggcccgcga	13	15	2	0			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr5:140751548G>A	ENST00000576222.1	+	1	1718	c.1587G>A	c.(1585-1587)gaG>gaA	p.E529E	PCDHGA2_ENST00000394576.2_Intron|PCDHGA6_ENST00000517434.1_5'Flank|PCDHGB2_ENST00000522605.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3	529	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGCCTTCGAGCTCACTCTGC	0.692																																					p.E529E		Atlas-SNP	.											.	PCDHGB3	168	.	0			c.G1587A						.						34	41	39					5																	140751548		2132	4233	6365	SO:0001819	synonymous_variant	56102	exon1			CTTCGAGCTCACT	AF152519	CCDS58980.1, CCDS75334.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8710	other	protocadherin		606301				10380929	Standard	NM_018924		Approved	PCDH-GAMMA-B3		Q9Y5G1		ENST00000576222.1:c.1587G>A	chr5.hg19:g.140751548G>A		110.0	0.0		90.0	25.0	NM_018924	A7E229|Q9Y5C7	Silent	SNP	ENST00000576222.1	hg19	CCDS58980.1																																																																																			.	.		0.692	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924		A	140751548	G	A	140751548	2	1	319	1	0	0	0	0	0	0	0	1	11573	962	34	3		3	PCDHGB3	5	140751548	Silent	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10	81467055	140751548	40163712	34	44934										
DUSP1	1843	hgsc.bcm.edu	37	chr5	172196041	172196041	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	tcgtccagcttgactcgattAgtcctcataaggtaagcaag	9	10	1	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr5:172196041A>G	ENST00000239223.3	-	4	1070	c.828T>C	c.(826-828)acT>acC	p.T276T	RP11-779O18.3_ENST00000523005.1_RNA	NM_004417.3	NP_004408.1	P28562	DUS1_HUMAN	dual specificity phosphatase 1	276	Tyrosine-protein phosphatase.				cellular response to hormone stimulus (GO:0032870)|endoderm formation (GO:0001706)|inactivation of MAPK activity (GO:0000188)|intracellular signal transduction (GO:0035556)|mitotic cell cycle arrest (GO:0071850)|negative regulation of apoptotic process (GO:0043066)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of meiotic cell cycle (GO:0051447)|peptidyl-threonine dephosphorylation (GO:0035970)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of apoptotic process (GO:0043065)|protein dephosphorylation (GO:0006470)|regulation of apoptotic process (GO:0042981)|regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to estradiol (GO:0032355)|response to glucocorticoid (GO:0051384)|response to hydrogen peroxide (GO:0042542)|response to light stimulus (GO:0009416)|response to oxidative stress (GO:0006979)|response to retinoic acid (GO:0032526)|response to testosterone (GO:0033574)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|protein tyrosine/threonine phosphatase activity (GO:0008330)			NS(1)|breast(2)|endometrium(1)|large_intestine(1)|liver(1)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	10	Renal(175;0.000159)|Lung NSC(126;0.00431)|all_lung(126;0.00729)	all_hematologic(541;4.11e-18)|Breast(839;0.00637)|Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|Ovarian(839;0.15)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)	GBM - Glioblastoma multiforme(465;0.0103)		TGACTCGATTAGTCCTCATAA	0.527																																					p.T276T		Atlas-SNP	.											.	DUSP1	27	.	0			c.T828C						.						83	79	80					5																	172196041		2203	4300	6503	SO:0001819	synonymous_variant	1843	exon4			TCGATTAGTCCTC	X68277	CCDS4380.1	5q35.1	2011-06-09			ENSG00000120129	ENSG00000120129		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3064	protein-coding gene	gene with protein product		600714		PTPN10		1406996, 7806236	Standard	NM_004417		Approved	HVH1, CL100, MKP-1	uc003mbv.2	P28562	OTTHUMG00000130523	ENST00000239223.3:c.828T>C	chr5.hg19:g.172196041A>G		89.0	0.0		93.0	8.0	NM_004417	D3DQL9|Q2V508	Silent	SNP	ENST00000239223.3	hg19	CCDS4380.1																																																																																			.	.		0.527	DUSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252943.3	NM_004417		G	172196041	A	G	172196041	2	3	319	1	0	0	0	0	0	0	0	1	4811	407	15	2		2	DUSP1	5	172196041	Silent	SNP	A	TCGA-LG-A9QD-01A-11D-A382-10	31444493	172196041	8719219	35	44935										
C6orf145	221749	hgsc.bcm.edu	37	chr6	3751735	3751735	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	gcgcacgaacatgttcacgaGcgacgtgccctcaaacaccg	10	15	2	0			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr6:3751735G>A	ENST00000380283.4	-	1	525	c.31C>T	c.(31-33)Ctc>Ttc	p.L11F	PXDC1_ENST00000477592.2_5'UTR|RP11-420L9.5_ENST00000603791.1_RNA	NM_183373.3	NP_899229.2	Q5TGL8	PXDC1_HUMAN	PX domain containing 1	11	PX.						phosphatidylinositol binding (GO:0035091)										ATGTTCACGAGCGACGTGCCC	0.721																																					p.L11F		Atlas-SNP	.											.	.	.	.	0			c.C31T						.						15	14	14					6																	3751735		2188	4279	6467	SO:0001583	missense	221749	exon1			TCACGAGCGACGT	AJ420534	CCDS4486.1	6p25.1	2011-11-25	2011-11-25	2011-11-25	ENSG00000168994	ENSG00000168994			21361	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 145"	C6orf145			Standard	NM_183373		Approved		uc003mvt.2	Q5TGL8	OTTHUMG00000014146	ENST00000380283.4:c.31C>T	chr6.hg19:g.3751735G>A	ENSP00000369636:p.Leu11Phe	154.0	0.0		106.0	30.0	NM_183373	A8K0N3|Q6PGP0|Q86XB7	Missense_Mutation	SNP	ENST00000380283.4	hg19	CCDS4486.1	.	.	.	.	.	.	.	.	.	.	G	17.51	3.408810	0.62399	.	.	ENSG00000168994	ENST00000380283	T	0.42513	0.97	3.33	2.42	0.29668	.	0.187054	0.36338	U	0.002649	T	0.30823	0.0777	M	0.63428	1.95	0.58432	D	0.999991	P	0.46395	0.877	P	0.45377	0.478	T	0.18903	-1.0322	10	0.66056	D	0.02	-5.6091	11.8787	0.52562	0.0:0.0:0.8235:0.1765	.	11	Q5TGL8	CF145_HUMAN	F	11	ENSP00000369636:L11F	ENSP00000369636:L11F	L	-	1	0	C6orf145	3696734	1.000000	0.71417	0.966000	0.40874	0.990000	0.78478	5.170000	0.64990	0.489000	0.27749	0.454000	0.30748	CTC	.	.		0.721	PXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039688.1	NM_183373		A	3751735	G	A	3751735	3	1	319	1	0	0	0	0	1	0	0	0	2336	971	34	3	684	3	C6orf145	6	3751735	Missense_Mutation	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10		3751735	167363332	36	44936										
COL12A1	1303	hgsc.bcm.edu	37	chr6	75902065	75902065	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	aaagggtaaattctttagtaGgcccatctggaaatataaaa	8	5	2	0			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr6:75902065G>A	ENST00000322507.8	-	4	506	c.197C>T	c.(196-198)cCt>cTt	p.P66L	COL12A1_ENST00000483888.2_Missense_Mutation_p.P66L|COL12A1_ENST00000345356.6_Intron|COL12A1_ENST00000416123.2_Missense_Mutation_p.P66L	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	66	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						TTCTTTAGTAGGCCCATCTGG	0.323																																					p.P66L		Atlas-SNP	.											.	COL12A1	385	.	0			c.C197T						.						85	74	78					6																	75902065		1804	4070	5874	SO:0001583	missense	1303	exon4			TTAGTAGGCCCAT	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.197C>T	chr6.hg19:g.75902065G>A	ENSP00000325146:p.Pro66Leu	111.0	0.0		85.0	20.0	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	hg19	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.780374	0.90195	.	.	ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000416123;ENST00000483888	T;T;T	0.56444	0.46;0.46;0.46	5.91	5.91	0.95273	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000001	T	0.62319	0.2418	L	0.50333	1.59	0.80722	D	1	D	0.71674	0.998	D	0.64877	0.93	T	0.60611	-0.7229	10	0.54805	T	0.06	.	20.3011	0.98612	0.0:0.0:1.0:0.0	.	66	Q99715	COCA1_HUMAN	L	66	ENSP00000325146:P66L;ENSP00000412864:P66L;ENSP00000421216:P66L	ENSP00000325146:P66L	P	-	2	0	COL12A1	75958785	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.647000	0.74354	2.804000	0.96469	0.650000	0.86243	CCT	.	.		0.323	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		A	75902065	G	A	75902065	3	1	319	1	0	0	0	0	1	0	0	0	3671	1000	35	3	9246	3	COL12A1	6	75902065	Missense_Mutation	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10	72150330	75902065	95213002	37	44937										
FAM46A	55603	hgsc.bcm.edu	37	chr6	82459733	82459733	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	tggttctgcaaataggactcCagttttctctgctgctctcc	8	12	3	0			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr6:82459733C>T	ENST00000320172.6	-	3	1322	c.1008G>A	c.(1006-1008)ctG>ctA	p.L336L	FAM46A_ENST00000369756.3_Silent_p.L417L|FAM46A_ENST00000369754.3_Silent_p.L355L	NM_017633.2	NP_060103.2	Q96IP4	FA46A_HUMAN	family with sequence similarity 46, member A	336					regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)		poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(5)|skin(1)|urinary_tract(1)	12		all_cancers(76;6.74e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000282)|all_epithelial(107;0.0104)		BRCA - Breast invasive adenocarcinoma(397;0.0428)		AATAGGACTCCAGTTTTCTCT	0.463																																					p.L336L		Atlas-SNP	.											.	FAM46A	37	.	0			c.G1008A						.						99	93	95					6																	82459733		2203	4300	6503	SO:0001819	synonymous_variant	55603	exon3			GGACTCCAGTTTT	AF350451	CCDS34489.1	6q14	2008-07-03	2004-08-19	2004-08-26	ENSG00000112773	ENSG00000112773			18345	protein-coding gene	gene with protein product		611357	"chromosome 6 open reading frame 37"	C6orf37		12054608, 17803723	Standard	NM_017633		Approved	FLJ20037	uc003pjg.3	Q96IP4	OTTHUMG00000015097	ENST00000320172.6:c.1008G>A	chr6.hg19:g.82459733C>T		147.0	0.0		114.0	32.0	NM_017633	A8K7U4|Q5TF86|Q8NFZ9|Q9BW32|Q9NXV5	Silent	SNP	ENST00000320172.6	hg19	CCDS34489.1																																																																																			.	.		0.463	FAM46A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041331.1			T	82459733	C	T	82459733	2	4	319	1	0	0	0	0	0	0	0	1	5573	581	21	3		3	FAM46A	6	82459733	Silent	SNP	C	TCGA-LG-A9QD-01A-11D-A382-10	6557668	82459733	88655334	38	44938										
ZNF292	23036	hgsc.bcm.edu	37	chr6	87943233	87943233	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	acatcatcaccaaatggaaaGttaatcgaagaggtgagtat	9	6	2	2			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr6:87943233G>T	ENST00000369577.3	+	5	772	c.729G>T	c.(727-729)aaG>aaT	p.K243N	ZNF292_ENST00000339907.4_Missense_Mutation_p.K238N	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	243						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		CAAATGGAAAGTTAATCGAAG	0.313																																					p.K243N		Atlas-SNP	.											.	ZNF292	479	.	0			c.G729T						.						139	134	135					6																	87943233		1846	4087	5933	SO:0001583	missense	23036	exon5			TGGAAAGTTAATC	AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"Zinc fingers, C2H2-type"	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.729G>T	chr6.hg19:g.87943233G>T	ENSP00000358590:p.Lys243Asn	199.0	0.0		175.0	39.0	NM_015021	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Missense_Mutation	SNP	ENST00000369577.3	hg19	CCDS47457.1	.	.	.	.	.	.	.	.	.	.	G	15.92	2.974420	0.53720	.	.	ENSG00000188994	ENST00000369577;ENST00000339907	T;T	0.07327	3.2;3.21	5.23	4.35	0.52113	.	0.158347	0.56097	D	0.000021	T	0.03263	0.0095	N	0.22421	0.69	0.36852	D	0.887929	P	0.44627	0.839	B	0.41088	0.347	T	0.44892	-0.9298	10	0.54805	T	0.06	.	14.0139	0.64513	0.0734:0.0:0.9266:0.0	.	243	O60281	ZN292_HUMAN	N	243;238	ENSP00000358590:K243N;ENSP00000342847:K238N	ENSP00000342847:K238N	K	+	3	2	ZNF292	87999952	1.000000	0.71417	0.998000	0.56505	0.913000	0.54294	3.397000	0.52572	1.332000	0.45431	0.460000	0.39030	AAG	.	.		0.313	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021		T	87943233	G	T	87943233	3	4	319	1	0	0	0	0	1	0	0	0	17841	1020	36	3	747	3	ZNF292	6	87943233	Missense_Mutation	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10	5483500	87943233	83171834	39	44939										
SFRS18	25957	hgsc.bcm.edu	37	chr6	99849338	99849338	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	cttgtttttctttttctttaTgctctttttttggttctaaa	4	6	4	0	rs544853512	byFrequency	TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr6:99849338T>C	ENST00000369239.5	-	12	1700	c.1496A>G	c.(1495-1497)cAt>cGt	p.H499R	PNISR_ENST00000438806.1_Missense_Mutation_p.H499R	NM_032870.2	NP_116259.2	Q8TF01	PNISR_HUMAN	PNN-interacting serine/arginine-rich protein	499						cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24						TTTTTCTTTATGCTCTTTTTT	0.378													T|||	2	0.000399361	0.0015	0	5008	,	,		19327	0		0	False		,,,				2504	0				p.H499R		Atlas-SNP	.											.	PNISR	74	.	0			c.A1496G						.						99	99	99					6																	99849338		2203	4300	6503	SO:0001583	missense	25957	exon11			TCTTTATGCTCTT	AK027759	CCDS5043.1	6q16.3	2011-06-06	2011-06-06	2011-06-06	ENSG00000132424	ENSG00000132424			21222	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 111", "splicing factor, arginine/serine-rich 18"	C6orf111, SFRS18		14578391	Standard	NM_032870		Approved	FLJ14752, bA98I9.2, DKFZp564B0769, SRrp130	uc021zdd.1	Q8TF01	OTTHUMG00000015262	ENST00000369239.5:c.1496A>G	chr6.hg19:g.99849338T>C	ENSP00000358242:p.His499Arg	99.0	0.0		90.0	21.0	NM_015491	A8K540|E1P5D2|Q5T064|Q5T065|Q6P2B4|Q6P2N4|Q6PJ93|Q6PK36|Q7Z640|Q8N2L1|Q8TF00|Q96K10|Q96SI3|Q96SM5|Q9P076|Q9P0C0|Q9Y4N3	Missense_Mutation	SNP	ENST00000369239.5	hg19	CCDS5043.1	.	.	.	.	.	.	.	.	.	.	T	4.946	0.175777	0.09391	.	.	ENSG00000132424	ENST00000369239;ENST00000438806	.	.	.	4.82	4.82	0.62117	.	0.343432	0.32120	N	0.006547	T	0.06325	0.0163	N	0.14661	0.345	0.28096	N	0.931621	B	0.19331	0.035	B	0.17098	0.017	T	0.22661	-1.0210	9	0.16420	T	0.52	.	3.9444	0.09343	0.1856:0.0999:0.0:0.7145	.	499	Q8TF01	PNISR_HUMAN	R	499	.	ENSP00000358242:H499R	H	-	2	0	PNISR	99956059	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.299000	0.43611	2.156000	0.67533	0.472000	0.43445	CAT	.	.		0.378	PNISR-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041598.1	NM_032870		C	99849338	T	C	99849338	3	2	319	1	0	0	0	0	1	0	0	0	14189	1464	51	2	925	2	SFRS18	6	99849338	Missense_Mutation	SNP	T	TCGA-LG-A9QD-01A-11D-A382-10	11906105	99849338	71265729	40	44940										
BEND3	57673	hgsc.bcm.edu	37	chr6	107390291	107390303	+	Frame_Shift_Del	DEL	GGATCTTGCAAAA	GGATCTTGCAAAA	-													0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	gaccaccagctcgtccaaggGgatcttgcaaaagtccttgc							TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	GGATCTTGCAAAA	GGATCTTGCAAAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr6:107390291_107390303delGGATCTTGCAAAA	ENST00000369042.1	-	4	2282_2294	c.2092_2104delTTTTGCAAGATCC	c.(2092-2106)ttttgcaagatccccfs	p.FCKIP698fs	BEND3_ENST00000429433.2_Frame_Shift_Del_p.FCKIP698fs			Q5T5X7	BEND3_HUMAN	BEN domain containing 3	698										central_nervous_system(1)|cervix(2)|endometrium(3)|large_intestine(7)|lung(10)|ovary(4)|prostate(3)	30						TCGTCCAAGGGGATCTTGCAAAAGTCCTTGCTG	0.615																																					p.698_702del		Atlas-INDEL	.											.	BEND3	70	.	0			c.2093_2105del						.																																			SO:0001589	frameshift_variant	57673	exon5			.	AB046773	CCDS34507.1	6q21	2012-11-22	2008-10-03	2008-10-03	ENSG00000178409	ENSG00000178409		"BEN domain containing"	23040	protein-coding gene	gene with protein product			"KIAA1553"	KIAA1553			Standard	NM_001080450		Approved		uc003prs.2	Q5T5X7	OTTHUMG00000015308	ENST00000369042.1:c.2092_2104delTTTTGCAAGATCC	chr6.hg19:g.107390291_107390303delGGATCTTGCAAAA	ENSP00000358038:p.Phe698fs	246.0	0.0		157.0	29.0	NM_001080450	A2RRH2|Q9HCL9	Frame_Shift_Del	DEL	ENST00000369042.1	hg19	CCDS34507.1																																																																																			.	.		0.615	BEND3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041686.1	NM_020913		-	107390303	GGATCTTGCAAAA	-	107390291	7	5	319	1	0	1	0	1	0	0	0	0	1399	1232	43	0	386	0	BEND3	6	107390291	Frame_Shift_Del	DEL	GGATCTTGCAAAA	TCGA-LG-A9QD-01A-11D-A382-10	7540953	107390291	63724776	41	44941										
TNFAIP3	7128	hgsc.bcm.edu	37	chr6	138202372	138202372	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	ccccccaagcagcgttgccgGgcccccgcctgtgatcattt	10	18	1	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr6:138202372G>T	ENST00000237289.4	+	9	2355	c.2289G>T	c.(2287-2289)cgG>cgT	p.R763R		NM_001270507.1|NM_001270508.1|NM_006290.3	NP_001257436.1|NP_001257437.1|NP_006281.1	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3	763	Interaction with TNIP1. {ECO:0000250}.|Required for lysosomal localization and for TRAF2 lysosomal degradation.|Sufficient for inhibitory activity of TNF-induced NF-kappa-B activity. {ECO:0000250}.				apoptotic process (GO:0006915)|B-1 B cell homeostasis (GO:0001922)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of B cell activation (GO:0050869)|negative regulation of bone resorption (GO:0045779)|negative regulation of CD40 signaling pathway (GO:2000349)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast proliferation (GO:0090291)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 3 signaling pathway (GO:0034140)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of protein catabolic process (GO:0045732)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked deubiquitination (GO:0070536)|protein oligomerization (GO:0051259)|regulation of defense response to virus by host (GO:0050691)|regulation of germinal center formation (GO:0002634)|regulation of vascular wound healing (GO:0061043)|response to molecule of bacterial origin (GO:0002237)|tolerance induction to lipopolysaccharide (GO:0072573)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|protease binding (GO:0002020)|protein self-association (GO:0043621)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.0?(25)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(196)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	225	Breast(32;0.135)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468)		AGCGTTGCCGGGCCCCCGCCT	0.607			"D, N, F"		"marginal zone B-cell lymphomas, Hodgkin's lymphoma, primary mediastinal B cell lymphoma"																																p.R763R	GBM(130;153 1739 22295 28918 47987)	Atlas-SNP	.		Rec	yes		6	6q23	7128	"tumor necrosis factor, alpha-induced protein 3"		L	.	TNFAIP3	340	.	25	Whole gene deletion(25)	haematopoietic_and_lymphoid_tissue(25)	c.G2289T						.						53	61	58					6																	138202372		2202	4299	6501	SO:0001819	synonymous_variant	7128	exon9			TTGCCGGGCCCCC	M59465	CCDS5187.1	6q23-q25	2013-01-21			ENSG00000118503	ENSG00000118503		"OTU domain containing"	11896	protein-coding gene	gene with protein product		191163				2118515	Standard	NM_006290		Approved	A20, OTUD7C	uc031spw.1	P21580	OTTHUMG00000015664	ENST00000237289.4:c.2289G>T	chr6.hg19:g.138202372G>T		166.0	0.0		143.0	40.0	NM_001270507	B2R767|E1P588|Q2HIX9|Q5VXQ7|Q9NSR6	Silent	SNP	ENST00000237289.4	hg19	CCDS5187.1																																																																																			.	.		0.607	TNFAIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042414.1			T	138202372	G	T	138202372	2	4	319	1	0	0	0	0	0	0	0	1	16289	1219	43	3		3	TNFAIP3	6	138202372	Silent	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10	30812081	138202372	32912695	42	44942										
REPS1	85021	hgsc.bcm.edu	37	chr6	139238740	139238740	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	gttctgggtcagaagtaaaaGagtctgaactactgtaacca	10	7	3	3			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr6:139238740G>C	ENST00000450536.2	-	13	2127	c.1553C>G	c.(1552-1554)tCt>tGt	p.S518C	REPS1_ENST00000258062.5_Missense_Mutation_p.S517C|REPS1_ENST00000367663.4_Missense_Mutation_p.S491C|REPS1_ENST00000409812.2_Intron|REPS1_ENST00000415951.2_Missense_Mutation_p.S491C			Q96D71	REPS1_HUMAN	RALBP1 associated Eps domain containing 1	518					receptor-mediated endocytosis (GO:0006898)	coated pit (GO:0005905)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|SH3 domain binding (GO:0017124)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(2)	19				GBM - Glioblastoma multiforme(68;0.000434)|OV - Ovarian serous cystadenocarcinoma(155;0.000548)		AGAAGTAAAAGAGTCTGAACT	0.338																																					p.S517C		Atlas-SNP	.											.	REPS1	58	.	0			c.C1550G						.						127	117	121					6																	139238740		2203	4300	6503	SO:0001583	missense	85021	exon13			GTAAAAGAGTCTG		CCDS5193.2, CCDS47488.1, CCDS69212.1, CCDS69213.1	6q24.1	2013-01-10			ENSG00000135597	ENSG00000135597		"EF-hand domain containing"	15578	protein-coding gene	gene with protein product		614825					Standard	XM_005267177		Approved		uc011edr.2	Q96D71	OTTHUMG00000015685	ENST00000450536.2:c.1553C>G	chr6.hg19:g.139238740G>C	ENSP00000392065:p.Ser518Cys	76.0	0.0		77.0	19.0	NM_031922	B7ZBZ8|B7ZBZ9|B7ZC00|J3KP76|Q5JWJ5|Q5JWJ6|Q5JWJ7|Q8NDR7|Q8WU62|Q9BXY9	Missense_Mutation	SNP	ENST00000450536.2	hg19		.	.	.	.	.	.	.	.	.	.	G	25.8	4.673845	0.88445	.	.	ENSG00000135597	ENST00000450536;ENST00000367663;ENST00000529597;ENST00000258062;ENST00000415951;ENST00000367668	T;T;T;T;T	0.35605	1.31;1.3;1.3;1.31;1.31	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	T	0.50034	0.1592	L	0.50333	1.59	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;0.997	D;D;D;P	0.85130	0.997;0.995;0.993;0.817	T	0.43294	-0.9400	10	0.62326	D	0.03	-18.0709	18.7754	0.91910	0.0:0.0:1.0:0.0	.	517;466;518;491	Q96D71-3;B2R7D3;Q96D71;E9PMG1	.;.;REPS1_HUMAN;.	C	518;491;476;517;491;466	ENSP00000392065:S518C;ENSP00000356635:S491C;ENSP00000434251:S476C;ENSP00000258062:S517C;ENSP00000397941:S491C	ENSP00000258062:S517C	S	-	2	0	REPS1	139280433	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.668000	0.74457	2.873000	0.98535	0.563000	0.77884	TCT	.	.		0.338	REPS1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000042447.3			C	139238740	G	C	139238740	3	2	319	1	0	0	0	0	1	0	0	0	13243	942	33	4	869	4	REPS1	6	139238740	Missense_Mutation	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10	1036368	139238740	31876327	43	44943										
SCIN	85477	hgsc.bcm.edu	37	chr7	12617696	12617696	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	ttcactgttttaggaaaggaGtgttcccaggatgaaagcac	11	7	1	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr7:12617696G>A	ENST00000297029.5	+	2	308	c.207G>A	c.(205-207)gaG>gaA	p.E69E		NM_001112706.2	NP_001106177.1	Q9Y6U3	ADSV_HUMAN	scinderin	69	Actin-severing. {ECO:0000255}.				actin filament capping (GO:0051693)|actin filament severing (GO:0051014)|actin nucleation (GO:0045010)|calcium ion-dependent exocytosis (GO:0017156)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of secretion (GO:0051047)|regulation of chondrocyte differentiation (GO:0032330)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	1-phosphatidylinositol binding (GO:0005545)|actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	17				UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		TAGGAAAGGAGTGTTCCCAGG	0.408																																					p.E69E		Atlas-SNP	.											.	SCIN	105	.	0			c.G207A						.						90	74	79					7																	12617696		692	1591	2283	SO:0001819	synonymous_variant	85477	exon2			AAAGGAGTGTTCC	AF276507	CCDS47545.1, CCDS47546.1	7p21.3	2006-04-25			ENSG00000006747	ENSG00000006747			21695	protein-coding gene	gene with protein product		613416					Standard	NM_033128		Approved	adseverin, KIAA1905	uc003ssn.4	Q9Y6U3	OTTHUMG00000152385	ENST00000297029.5:c.207G>A	chr7.hg19:g.12617696G>A		106.0	0.0		96.0	24.0	NM_001112706	A8K2U8|Q8NBZ6|Q8WU97|Q96JC7|Q96PY2	Silent	SNP	ENST00000297029.5	hg19	CCDS47545.1																																																																																			.	.		0.408	SCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326041.1	NM_033128		A	12617696	G	A	12617696	2	1	319	1	0	0	0	0	0	0	0	1	13920	1020	36	3		3	SCIN	7	12617696	Silent	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10		12617696	146520967	44	44944										
PLXNA4	91584	hgsc.bcm.edu	37	chr7	131883359	131883359	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	ctcccctcggatagtgacctTggtgcccccttcccgggggc	12	17	0	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr7:131883359T>C	ENST00000359827.3	-	13	3585	c.2623A>G	c.(2623-2625)Aag>Gag	p.K875E	PLXNA4_ENST00000321063.4_Missense_Mutation_p.K875E			Q9HCM2	PLXA4_HUMAN	plexin A4	875	IPT/TIG 1.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						ATAGTGACCTTGGTGCCCCCT	0.552																																					p.K875E		Atlas-SNP	.											.	PLXNA4	873	.	0			c.A2623G						.						68	70	69					7																	131883359		1885	4104	5989	SO:0001583	missense	91584	exon13			TGACCTTGGTGCC	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"Plexins"	9102	protein-coding gene	gene with protein product		604280	"plexin A4, A", "plexin A4, B"	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.2623A>G	chr7.hg19:g.131883359T>C	ENSP00000352882:p.Lys875Glu	73.0	0.0		68.0	18.0	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	hg19	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	T	17.53	3.412286	0.62511	.	.	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.76316	-1.01;-1.01	5.94	5.94	0.96194	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.109437	0.64402	D	0.000007	T	0.63390	0.2507	L	0.27053	0.805	0.38548	D	0.949382	B	0.26547	0.152	B	0.29440	0.102	T	0.59974	-0.7353	10	0.02654	T	1	.	12.8606	0.57911	0.0:0.0:0.1357:0.8643	.	875	Q9HCM2	PLXA4_HUMAN	E	875	ENSP00000323194:K875E;ENSP00000352882:K875E	ENSP00000323194:K875E	K	-	1	0	PLXNA4	131533899	0.893000	0.30496	1.000000	0.80357	0.999000	0.98932	2.260000	0.43267	2.275000	0.75901	0.528000	0.53228	AAG	.	.		0.552	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		C	131883359	T	C	131883359	3	2	319	1	0	0	0	0	1	0	0	0	12131	1821	63	2	3141	2	PLXNA4	7	131883359	Missense_Mutation	SNP	T	TCGA-LG-A9QD-01A-11D-A382-10	119265663	131883359	27255304	45	44945										
GALNTL5	168391	hgsc.bcm.edu	37	chr7	151704964	151704964	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	tacgtcggcattattttaatGaaattggacagtatgacaag	9	5	0	2			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr7:151704964G>T	ENST00000392800.2	+	7	1215	c.961G>T	c.(961-963)Gaa>Taa	p.E321*	GALNTL5_ENST00000483959.1_3'UTR|GALNTL5_ENST00000431418.2_Nonsense_Mutation_p.E321*	NM_145292.3	NP_660335.2	Q7Z4T8	GLTL5_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 5	321	Catalytic subdomain B.				spermatid development (GO:0007286)	endosome (GO:0005768)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(11)|ovary(2)|prostate(2)|skin(3)	32	all_neural(206;0.187)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00427)	UCEC - Uterine corpus endometrioid carcinoma (81;0.18)|BRCA - Breast invasive adenocarcinoma(188;0.166)		TTATTTTAATGAAATTGGACA	0.328																																					p.E321X		Atlas-SNP	.											GALNTL5,colon,carcinoma,0,1	GALNTL5	87	.	0			c.G961T						.						116	119	118					7																	151704964		2203	4300	6503	SO:0001587	stop_gained	168391	exon7			TTTAATGAAATTG	AF440400	CCDS5929.1	7q36.2	2014-03-13	2014-03-13	2004-07-28	ENSG00000106648	ENSG00000106648		"Glycosyltransferase family 2 domain containing"	21725	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase-like 5"	615133	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15", "UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 5"	GALNT15			Standard	NM_145292		Approved	GalNAc-T5L	uc003wkp.3	Q7Z4T8	OTTHUMG00000157306	ENST00000392800.2:c.961G>T	chr7.hg19:g.151704964G>T	ENSP00000376548:p.Glu321*	248.0	0.0		191.0	51.0	NM_145292	Q75KN2|Q75MD3|Q8NCV4|Q8WW05|Q9UDR9	Nonsense_Mutation	SNP	ENST00000392800.2	hg19	CCDS5929.1	.	.	.	.	.	.	.	.	.	.	G	36	5.943700	0.97128	.	.	ENSG00000106648	ENST00000431418;ENST00000392800	.	.	.	4.68	3.8	0.43715	.	0.788243	0.10557	N	0.660721	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	.	11.9562	0.52983	0.084:0.0:0.916:0.0	.	.	.	.	X	321	.	ENSP00000376548:E321X	E	+	1	0	GALNTL5	151335897	1.000000	0.71417	0.992000	0.48379	0.989000	0.77384	3.739000	0.55075	1.194000	0.43101	0.632000	0.83419	GAA	.	.		0.328	GALNTL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348395.1	NM_145292		T	151704964	G	T	151704964	4	4	319	1	0	0	0	0	0	1	0	0	6232	1291	45	3	983	3	GALNTL5	7	151704964	Nonsense_Mutation	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10	19821605	151704964	7433699	46	44946										
MLL3	58508	hgsc.bcm.edu	37	chr7	151944994	151944994	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	aaaatcaccctacctgtttgGaccgaggtctaccaggagaa	9	11	2	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr7:151944994G>T	ENST00000262189.6	-	14	2743	c.2525C>A	c.(2524-2526)tCc>tAc	p.S842Y	KMT2C_ENST00000355193.2_Missense_Mutation_p.S842Y	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	842					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										TACCTGTTTGGACCGAGGTCT	0.378																																					p.S842Y		Atlas-SNP	.											.	MLL3	1564	.	0			c.C2525A						.						114	104	107					7																	151944994		2203	4297	6500	SO:0001583	missense	58508	exon14			TGTTTGGACCGAG	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.2525C>A	chr7.hg19:g.151944994G>T	ENSP00000262189:p.Ser842Tyr	332.0	0.0		299.0	21.0	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	hg19	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	G	16.10	3.026519	0.54683	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.84070	-1.8;-1.8	5.67	5.67	0.87782	.	0.000000	0.44285	D	0.000478	D	0.85318	0.5669	N	0.22421	0.69	0.80722	D	1	D	0.71674	0.998	D	0.63488	0.915	D	0.85809	0.1378	10	0.48119	T	0.1	.	19.7692	0.96356	0.0:0.0:1.0:0.0	.	842	Q8NEZ4	MLL3_HUMAN	Y	842	ENSP00000262189:S842Y;ENSP00000347325:S842Y	ENSP00000262189:S842Y	S	-	2	0	MLL3	151575927	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.939000	0.75911	2.658000	0.90341	0.650000	0.86243	TCC	.	.		0.378	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			T	151944994	G	T	151944994	3	4	319	1	0	0	0	0	1	0	0	0	9631	1174	41	3	12394	3	MLL3	7	151944994	Missense_Mutation	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10	240030	151944994	7193669	47	44947										
C8orf41	80185	hgsc.bcm.edu	37	chr8	33360968	33360968	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	tgggccaagtatgttgcatgAgaagttttagggtttccaat	12	5	0	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr8:33360968A>C	ENST00000431156.2	-	6	1856	c.1238T>G	c.(1237-1239)cTc>cGc	p.L413R	TTI2_ENST00000519356.1_5'UTR|TTI2_ENST00000520636.1_Missense_Mutation_p.L382R|TTI2_ENST00000360742.5_Missense_Mutation_p.L413R	NM_001102401.2	NP_001095871.1	Q6NXR4	TTI2_HUMAN	TELO2 interacting protein 2	413																	ATGTTGCATGAGAAGTTTTAG	0.418																																					p.L413R		Atlas-SNP	.											.	.	.	.	0			c.T1238G						.						132	131	131					8																	33360968		2203	4300	6503	SO:0001583	missense	80185	exon6			TGCATGAGAAGTT	AK026916	CCDS6090.1	8p12	2011-11-10	2011-11-10	2011-09-22		ENSG00000129696			26262	protein-coding gene	gene with protein product		614426	"chromosome 8 open reading frame 41", "Tel2 interacting protein 2 homolog (S. pombe)"	C8orf41		20801936, 20810650	Standard	NM_025115		Approved	FLJ23263	uc003xjm.5	Q6NXR4		ENST00000431156.2:c.1238T>G	chr8.hg19:g.33360968A>C	ENSP00000411169:p.Leu413Arg	130.0	0.0		77.0	31.0	NM_001265581	D3DSV7|Q96IM2|Q9H5N4	Missense_Mutation	SNP	ENST00000431156.2	hg19	CCDS6090.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.378128	0.82682	.	.	ENSG00000129696	ENST00000360742;ENST00000431156;ENST00000522668;ENST00000520636	T;T;T	0.74421	-0.74;-0.74;-0.84	6.17	5.04	0.67666	.	0.437819	0.20832	N	0.084870	T	0.69593	0.3128	L	0.51422	1.61	0.80722	D	1	P;P	0.49961	0.93;0.93	P;P	0.48030	0.564;0.564	T	0.72633	-0.4234	10	0.66056	D	0.02	-5.7749	3.7509	0.08566	0.7161:0.0:0.2839:0.0	.	413;382	Q6NXR4;E5RIH5	TTI2_HUMAN;.	R	413;413;402;382	ENSP00000353971:L413R;ENSP00000411169:L413R;ENSP00000428401:L382R	ENSP00000353971:L413R	L	-	2	0	C8orf41	33480510	1.000000	0.71417	0.998000	0.56505	0.980000	0.70556	5.064000	0.64338	2.371000	0.80710	0.533000	0.62120	CTC	.	.		0.418	TTI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376555.1	NM_025115		C	33360968	A	C	33360968	3	2	319	1	0	0	0	0	1	0	0	0	2429	304	11	5	300	5	C8orf41	8	33360968	Missense_Mutation	SNP	A	TCGA-LG-A9QD-01A-11D-A382-10		33360968	113003054	48	44948										
MTFR1	9650	hgsc.bcm.edu	37	chr8	66617100	66617100	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	tgcgctctcgaaaatgaactTgctgctctcagagctcagat	9	11	3	3			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr8:66617100T>G	ENST00000262146.4	+	5	579	c.453T>G	c.(451-453)ctT>ctG	p.L151L	MTFR1_ENST00000517944.1_3'UTR|MTFR1_ENST00000458689.2_Silent_p.L118L	NM_014637.3	NP_055452.3	Q15390	MTFR1_HUMAN	mitochondrial fission regulator 1	151					aerobic respiration (GO:0009060)|mitochondrial fission (GO:0000266)|mitochondrion organization (GO:0007005)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(1)|pancreas(1)|urinary_tract(1)	11			Epithelial(68;0.0526)|BRCA - Breast invasive adenocarcinoma(89;0.156)|all cancers(69;0.171)|OV - Ovarian serous cystadenocarcinoma(28;0.194)			AAAATGAACTTGCTGCTCTCA	0.468																																					p.L151L		Atlas-SNP	.											.	MTFR1	26	.	0			c.T453G						.						34	35	34					8																	66617100		2203	4300	6503	SO:0001819	synonymous_variant	9650	exon5			TGAACTTGCTGCT		CCDS6182.1, CCDS55240.1	8q13.1	2012-11-30							29510	protein-coding gene	gene with protein product	"likely ortholog of chicken chondrocyte protein with a poly proline region"					7584026, 7584028, 15389597	Standard	NM_014637		Approved	CHPPR, KIAA0009, FAM54A2	uc003xvn.2	Q15390		ENST00000262146.4:c.453T>G	chr8.hg19:g.66617100T>G		213.0	0.0		339.0	200.0	NM_014637	E7EP84|Q6IB94|Q7Z669|Q86XH5|Q8IVD7	Silent	SNP	ENST00000262146.4	hg19	CCDS6182.1	.	.	.	.	.	.	.	.	.	.	T	10.57	1.387408	0.25031	.	.	ENSG00000066855	ENST00000518800	T	0.72835	-0.69	5.39	-1.92	0.07618	.	0.000000	0.85682	D	0.000000	T	0.67325	0.2881	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63492	-0.6625	7	0.87932	D	0	1.5451	2.8746	0.05627	0.1152:0.3252:0.1069:0.4528	.	.	.	.	W	109	ENSP00000430621:L109W	ENSP00000430621:L109W	L	+	2	0	MTFR1	66779654	0.030000	0.19436	0.999000	0.59377	0.990000	0.78478	-1.119000	0.03276	0.051000	0.15978	0.460000	0.39030	TTG	.	.		0.468	MTFR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378894.1	NM_014637		G	66617100	T	G	66617100	2	3	319	1	0	0	0	0	0	0	0	1	9934	1799	63	5		5	MTFR1	8	66617100	Silent	SNP	T	TCGA-LG-A9QD-01A-11D-A382-10	33256132	66617100	79746922	49	44949										
PRDM14	63978	hgsc.bcm.edu	37	chr8	70981937	70981937	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	gctgcggcctccagctgccgGaaaggttggaagtcttcctc	13	13	1	0			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr8:70981937G>A	ENST00000276594.2	-	2	360	c.159C>T	c.(157-159)ttC>ttT	p.F53F		NM_024504.3	NP_078780.1	Q9GZV8	PRD14_HUMAN	PR domain containing 14	53					cell fate specification (GO:0001708)|cell morphogenesis (GO:0000902)|fertilization (GO:0009566)|germ cell development (GO:0007281)|germ-line stem cell maintenance (GO:0030718)|histone H3-R26 methylation (GO:0034972)|homeostasis of number of cells within a tissue (GO:0048873)|inner cell mass cell fate commitment (GO:0001827)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|regulation of DNA methylation (GO:0044030)|regulation of gene expression, epigenetic (GO:0040029)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Breast(64;0.193)		Epithelial(68;0.00508)|all cancers(69;0.0259)|OV - Ovarian serous cystadenocarcinoma(28;0.0405)			CCAGCTGCCGGAAAGGTTGGA	0.662																																					p.F53F	NSCLC(129;99 1813 5906 40656 46114)	Atlas-SNP	.											.	PRDM14	102	.	0			c.C159T						.						11	11	11					8																	70981937		2185	4277	6462	SO:0001819	synonymous_variant	63978	exon2			CTGCCGGAAAGGT	AF319458	CCDS6206.1	8q13.3	2013-01-08			ENSG00000147596	ENSG00000147596		"Zinc fingers, C2H2-type"	14001	protein-coding gene	gene with protein product		611781					Standard	NM_024504		Approved		uc003xym.3	Q9GZV8	OTTHUMG00000150495	ENST00000276594.2:c.159C>T	chr8.hg19:g.70981937G>A		84.0	0.0		135.0	22.0	NM_024504	Q86UX9	Silent	SNP	ENST00000276594.2	hg19	CCDS6206.1																																																																																			.	.		0.662	PRDM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318505.1			A	70981937	G	A	70981937	2	1	319	1	0	0	0	0	0	0	0	1	12467	1165	41	3		3	PRDM14	8	70981937	Silent	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10	4364837	70981937	75382085	50	44950										
VPS13B	157680	hgsc.bcm.edu	37	chr8	100147862	100147862	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	tgtggtgacaatttgagtacGaaaggtttcacataccttac	9	7	1	2			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr8:100147862G>T	ENST00000358544.2	+	11	1575	c.1464G>T	c.(1462-1464)acG>acT	p.T488T	VPS13B_ENST00000355155.1_Silent_p.T488T|VPS13B_ENST00000357162.2_Silent_p.T488T|VPS13B_ENST00000395996.1_Silent_p.T488T	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	488					protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			ATTTGAGTACGAAAGGTTTCA	0.338																																					p.T488T	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											VPS13B_ENST00000357162,NS,carcinoma,0,2	VPS13B	811	.	0			c.G1464T						.						144	128	134					8																	100147862		2202	4299	6501	SO:0001819	synonymous_variant	157680	exon11			GAGTACGAAAGGT	AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.1464G>T	chr8.hg19:g.100147862G>T		149.0	1.0		227.0	142.0	NM_152564	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Silent	SNP	ENST00000358544.2	hg19	CCDS6280.1																																																																																			.	.		0.338	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		T	100147862	G	T	100147862	2	4	319	1	0	0	0	0	0	0	0	1	17205	1045	37	1		1	VPS13B	8	100147862	Silent	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10	29165925	100147862	46216160	51	44951										
RSPO2	340419	hgsc.bcm.edu	37	chr8	108970401	108970401	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	cactggctttttaacaatttGccgtgttctggtttccagac	8	10	1	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr8:108970401G>A	ENST00000276659.5	-	5	1143	c.523C>T	c.(523-525)Caa>Taa	p.Q175*	RSPO2_ENST00000517781.1_Nonsense_Mutation_p.Q111*|RSPO2_ENST00000517939.1_Nonsense_Mutation_p.Q108*|RSPO2_ENST00000378439.2_Nonsense_Mutation_p.Q111*	NM_178565.4	NP_848660.3	Q6UXX9	RSPO2_HUMAN	R-spondin 2	175	TSP type-1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				bone mineralization (GO:0030282)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|lung growth (GO:0060437)|osteoblast differentiation (GO:0001649)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|extracellular region (GO:0005576)	heparin binding (GO:0008201)|receptor binding (GO:0005102)		EIF3E/RSPO2(6)	haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	28			OV - Ovarian serous cystadenocarcinoma(57;1.55e-09)			TTAACAATTTGCCGTGTTCTG	0.443																																					p.Q175X		Atlas-SNP	.											.	RSPO2	65	.	0			c.C523T						.						250	229	236					8																	108970401		2203	4300	6503	SO:0001587	stop_gained	340419	exon5			CAATTTGCCGTGT	AK123023	CCDS6307.1, CCDS64953.1	8q23.1	2014-01-30	2011-06-29		ENSG00000147655	ENSG00000147655		"Endogenous ligands"	28583	protein-coding gene	gene with protein product		610575	"R-spondin 2 homolog (Xenopus laevis)"			15469841	Standard	NM_178565		Approved	MGC35555	uc003yms.3	Q6UXX9	OTTHUMG00000164893	ENST00000276659.5:c.523C>T	chr8.hg19:g.108970401G>A	ENSP00000276659:p.Gln175*	183.0	0.0		230.0	118.0	NM_178565	B3KVP0|Q4G0U4|Q8N6X6	Nonsense_Mutation	SNP	ENST00000276659.5	hg19	CCDS6307.1	.	.	.	.	.	.	.	.	.	.	G	41	8.907511	0.98998	.	.	ENSG00000147655	ENST00000517939;ENST00000517781;ENST00000378439;ENST00000276659;ENST00000521502	.	.	.	5.9	5.9	0.94986	.	0.049429	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10111	T	0.7	-5.2068	20.2723	0.98479	0.0:0.0:1.0:0.0	.	.	.	.	X	108;111;111;175;108	.	ENSP00000276659:Q175X	Q	-	1	0	RSPO2	109039577	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.444000	0.97578	2.793000	0.96121	0.563000	0.77884	CAA	.	.		0.443	RSPO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380830.1	NM_178565		A	108970401	G	A	108970401	4	1	319	1	0	0	0	0	0	1	0	0	13725	1328	46	3	216	3	RSPO2	8	108970401	Nonsense_Mutation	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10	8822539	108970401	37393621	52	44952										
ATAD2	29028	hgsc.bcm.edu	37	chr8	124373808	124373808	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	gccctattacgactccttttCctccgcctctcaaagtgctg	6	16	1	0			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr8:124373808C>G	ENST00000287394.5	-	9	1235	c.1128G>C	c.(1126-1128)agG>agC	p.R376S	ATAD2_ENST00000534257.1_5'UTR|ATAD2_ENST00000521903.1_5'UTR	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	376					ATP catabolic process (GO:0006200)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	48	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			GACTCCTTTTCCTCCGCCTCT	0.383																																					p.R376S		Atlas-SNP	.											.	ATAD2	160	.	0			c.G1128C						.						145	144	144					8																	124373808		2203	4300	6503	SO:0001583	missense	29028	exon9			CCTTTTCCTCCGC	BC019909	CCDS6343.1	8q24.13	2014-01-21		2007-02-08	ENSG00000156802	ENSG00000156802		"ATPases / AAA-type"	30123	protein-coding gene	gene with protein product		611941				12477932	Standard	NM_014109		Approved	PRO2000, DKFZp667N1320, MGC5254, MGC29843, CT137	uc003yqh.4	Q6PL18	OTTHUMG00000165090	ENST00000287394.5:c.1128G>C	chr8.hg19:g.124373808C>G	ENSP00000287394:p.Arg376Ser	87.0	0.0		130.0	6.0	NM_014109	Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	Missense_Mutation	SNP	ENST00000287394.5	hg19	CCDS6343.1	.	.	.	.	.	.	.	.	.	.	C	15.23	2.772672	0.49680	.	.	ENSG00000156802	ENST00000287394	D	0.92048	-2.96	5.59	-1.02	0.10135	.	0.276047	0.45606	D	0.000359	D	0.86535	0.5956	L	0.43923	1.385	0.80722	D	1	B;B	0.34264	0.382;0.446	B;B	0.35727	0.209;0.15	T	0.77186	-0.2680	10	0.22109	T	0.4	-12.1846	12.6492	0.56751	0.0:0.7707:0.0:0.2293	.	206;376	Q6PL18-2;Q6PL18	.;ATAD2_HUMAN	S	376	ENSP00000287394:R376S	ENSP00000287394:R376S	R	-	3	2	ATAD2	124442989	0.794000	0.28838	0.961000	0.40146	0.978000	0.69477	-0.016000	0.12613	-0.145000	0.11294	-0.290000	0.09829	AGG	.	.		0.383	ATAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381766.2	NM_014109		G	124373808	C	G	124373808	3	3	319	1	0	0	0	0	1	0	0	0	1071	854	30	4	3124	4	ATAD2	8	124373808	Missense_Mutation	SNP	C	TCGA-LG-A9QD-01A-11D-A382-10	15403407	124373808	21990214	53	44953										
TLN1	7094	hgsc.bcm.edu	37	chr9	35707195	35707195	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	ctgtctggatgagtcccccgGcactctctaacattgtcttg	9	13	3	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr9:35707195G>T	ENST00000314888.9	-	37	5182	c.4829C>A	c.(4828-4830)gCc>gAc	p.A1610D	TLN1_ENST00000540444.1_Missense_Mutation_p.A1610D|TLN1_ENST00000464379.1_Intron	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	1610	Interaction with SYNM.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			GAGTCCCCCGGCACTCTCTAA	0.647																																					p.A1610D		Atlas-SNP	.											.	TLN1	185	.	0			c.C4829A						.						43	51	48					9																	35707195		2203	4300	6503	SO:0001583	missense	7094	exon37			CCCCCGGCACTCT	AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.4829C>A	chr9.hg19:g.35707195G>T	ENSP00000316029:p.Ala1610Asp	53.0	0.0		45.0	9.0	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	hg19	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.190975	0.78789	.	.	ENSG00000137076	ENST00000314888;ENST00000540444	T;T	0.16196	2.36;2.36	5.69	5.69	0.88448	.	0.111909	0.64402	D	0.000007	T	0.21718	0.0523	N	0.24115	0.695	0.58432	D	0.999998	B	0.27264	0.173	B	0.40134	0.32	T	0.11251	-1.0595	10	0.66056	D	0.02	-10.7986	19.7999	0.96502	0.0:0.0:1.0:0.0	.	1610	Q9Y490	TLN1_HUMAN	D	1610	ENSP00000316029:A1610D;ENSP00000442981:A1610D	ENSP00000316029:A1610D	A	-	2	0	TLN1	35697195	1.000000	0.71417	0.989000	0.46669	0.951000	0.60555	9.754000	0.98908	2.691000	0.91804	0.561000	0.74099	GCC	.	.		0.647	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289		T	35707195	G	T	35707195	3	4	319	1	0	0	0	0	1	0	0	0	15962	1203	42	3	2880	3	TLN1	9	35707195	Missense_Mutation	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10		35707195	105506236	54	44954										
LMX1B	4010	hgsc.bcm.edu	37	chr9	129376817	129376817	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	gatgttggacggcatcaagaTggaggagcacgccctgcgcc	15	11	1	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr9:129376817T>C	ENST00000373474.4	+	1	96	c.89T>C	c.(88-90)aTg>aCg	p.M30T	RP11-123K19.1_ENST00000432418.1_RNA|LMX1B_ENST00000561065.1_Missense_Mutation_p.M7T|LMX1B_ENST00000526117.1_Missense_Mutation_p.M30T|RP11-123K19.1_ENST00000451449.2_RNA|RP11-123K19.1_ENST00000425370.1_RNA|LMX1B_ENST00000355497.5_Missense_Mutation_p.M30T|LMX1B_ENST00000425646.2_Missense_Mutation_p.M7T			O60663	LMX1B_HUMAN	LIM homeobox transcription factor 1, beta	30					cell proliferation (GO:0008283)|central nervous system neuron development (GO:0021954)|cerebellum morphogenesis (GO:0021587)|collagen fibril organization (GO:0030199)|dopaminergic neuron differentiation (GO:0071542)|dorsal/ventral pattern formation (GO:0009953)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|midbrain development (GO:0030901)|multicellular organismal development (GO:0007275)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|organ growth (GO:0035265)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|trabecular meshwork development (GO:0002930)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	15						GGCATCAAGATGGAGGAGCAC	0.697									Nail-Patella Syndrome																												p.M30T	Pancreas(110;1796 2278 18357 20466)	Atlas-SNP	.											.	LMX1B	86	.	0			c.T89C						.						20	19	19					9																	129376817		2197	4296	6493	SO:0001583	missense	4010	exon1	Familial Cancer Database	Osteo-Onychodysplasia, Turner-Kieser syndrome, Fong disease	TCAAGATGGAGGA	U77457	CCDS6866.1, CCDS6866.2, CCDS55342.1, CCDS55343.1	9q33.3	2011-06-20			ENSG00000136944	ENSG00000136944		"Homeoboxes / LIM class"	6654	protein-coding gene	gene with protein product		602575		NPS1		9441763, 9590287	Standard	NM_002316		Approved		uc004bqj.3	O60663	OTTHUMG00000020692	ENST00000373474.4:c.89T>C	chr9.hg19:g.129376817T>C	ENSP00000362573:p.Met30Thr	111.0	0.0		83.0	20.0	NM_001174146	F8W7W6|O75463|Q5JU95|Q6ISC9	Missense_Mutation	SNP	ENST00000373474.4	hg19	CCDS55342.1	.	.	.	.	.	.	.	.	.	.	t	14.60	2.585038	0.46110	.	.	ENSG00000136944	ENST00000526117;ENST00000373474;ENST00000355497;ENST00000425646	D;D;D;D	0.85556	-1.85;-1.83;-2.0;-1.91	3.04	3.04	0.35103	.	0.167683	0.51477	U	0.000092	T	0.75236	0.3822	L	0.29908	0.895	0.36961	D	0.893359	B;B;B	0.27679	0.116;0.116;0.185	B;B;B	0.29862	0.055;0.046;0.108	T	0.71856	-0.4466	10	0.23302	T	0.38	.	10.2391	0.43301	0.0:0.0:0.0:1.0	.	7;7;30	B7ZLH2;O60663;F8VYP0	.;LMX1B_HUMAN;.	T	30;30;30;7	ENSP00000436930:M30T;ENSP00000362573:M30T;ENSP00000347684:M30T;ENSP00000390923:M7T	ENSP00000347684:M30T	M	+	2	0	LMX1B	128416638	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.751000	0.62169	1.284000	0.44531	0.319000	0.21371	ATG	.	.		0.697	LMX1B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054123.2			C	129376817	T	C	129376817	3	2	319	1	0	0	0	0	1	0	0	0	8871	1464	51	2	91	2	LMX1B	9	129376817	Missense_Mutation	SNP	T	TCGA-LG-A9QD-01A-11D-A382-10	93669622	129376817	11836614	55	44955										
IDI1	22884	hgsc.bcm.edu	37	chr10	1094891	1094891	+	5'Flank	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	cgcgcaccgcccactggcccCgcccccgggccgcgcagcca	12	24	0	0			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr10:1094891C>A	ENST00000358220.1	+	0	0				IDI1_ENST00000381344.3_Missense_Mutation_p.R18L|IDI1_ENST00000491735.1_5'UTR			Q9Y2I8	WDR37_HUMAN	WD repeat domain 37											breast(2)|endometrium(2)|kidney(1)|lung(9)|prostate(2)|skin(1)	17		all_epithelial(10;0.0449)|Colorectal(49;0.142)		Epithelial(11;0.134)		CCACTggccccgcccccgggc	0.716																																					p.R18L		Atlas-SNP	.											.	IDI1	22	.	0			c.G53T						.						6	7	6					10																	1094891		2081	4102	6183	SO:0001631	upstream_gene_variant	3422	exon1			TGGCCCCGCCCCC	AB023199	CCDS7057.1	10p15.3	2013-01-09			ENSG00000047056	ENSG00000047056		"WD repeat domain containing"	31406	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_014023		Approved	KIAA0982	uc001igf.1	Q9Y2I8	OTTHUMG00000017540		chr10.hg19:g.1094891C>A	Exception_encountered	111.0	0.0		74.0	20.0	NM_004508	A8K976|D3DRQ7|Q5SW03|Q8WVG2|Q9NTJ6	Missense_Mutation	SNP	ENST00000358220.1	hg19	CCDS7057.1	.	.	.	.	.	.	.	.	.	.	C	16.58	3.162470	0.57368	.	.	ENSG00000067064	ENST00000381344	.	.	.	1.67	1.67	0.24075	.	0.429373	0.14188	U	0.335564	T	0.16428	0.0395	.	.	.	0.09310	N	1	B	0.26081	0.141	B	0.13407	0.009	T	0.19549	-1.0302	8	0.13108	T	0.6	.	6.9709	0.24648	0.0:1.0:0.0:0.0	.	18	Q13907-2	.	L	18	.	ENSP00000370748:R18L	R	-	2	0	IDI1	1084891	0.013000	0.17824	0.074000	0.20217	0.019000	0.09904	0.778000	0.26732	1.288000	0.44600	0.472000	0.43445	CGG	.	.		0.716	WDR37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046418.1	NM_014023		A	1094891	C	A	1094891	1	1	319	0	1	0	0	0	0	0	0	0	7508	652	23	1		1	IDI1	10	1094891	5'Flank	SNP	C	TCGA-LG-A9QD-01A-11D-A382-10		1094891	134439856	56	44956										
IL2RA	3559	hgsc.bcm.edu	37	chr10	6061870	6061870	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	caggaagtctcactctcaggAcggccttcggggcttgcctg	13	13	2	0			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr10:6061870A>G	ENST00000379959.3	-	5	791	c.618T>C	c.(616-618)cgT>cgC	p.R206R	IL2RA_ENST00000379954.1_Silent_p.R134R|IL2RA_ENST00000256876.6_Silent_p.R197R|SNORA14_ENST00000516113.1_RNA	NM_000417.2	NP_000408.1	P01589	IL2RA_HUMAN	interleukin 2 receptor, alpha	206					activation-induced cell death of T cells (GO:0006924)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-2-mediated signaling pathway (GO:0038110)|negative regulation of defense response to virus (GO:0050687)|negative regulation of immune response (GO:0050777)|negative regulation of inflammatory response (GO:0050728)|negative regulation of T cell proliferation (GO:0042130)|Notch signaling pathway (GO:0007219)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of T cell differentiation (GO:0045582)|regulation of T cell homeostatic proliferation (GO:0046013)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|interleukin-2 receptor activity (GO:0004911)			endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	17					Aldesleukin(DB00041)|Basiliximab(DB00074)|Daclizumab(DB00111)|Denileukin diftitox(DB00004)	CACTCTCAGGACGGCCTTCGG	0.592																																					p.R206R		Atlas-SNP	.											.	IL2RA	37	.	0			c.T618C						.						125	110	115					10																	6061870		2203	4300	6503	SO:0001819	synonymous_variant	3559	exon5			CTCAGGACGGCCT	X01057	CCDS7076.1	10p15-p14	2014-09-17			ENSG00000134460	ENSG00000134460		"Interleukins and interleukin receptors", "CD molecules"	6008	protein-coding gene	gene with protein product		147730	"insulin-dependent diabetes mellitus 10"	IL2R, IDDM10		3925551, 17676041	Standard	NM_000417		Approved	CD25	uc001iiz.2	P01589	OTTHUMG00000017616	ENST00000379959.3:c.618T>C	chr10.hg19:g.6061870A>G		60.0	0.0		65.0	16.0	NM_000417	Q5W007	Silent	SNP	ENST00000379959.3	hg19	CCDS7076.1																																																																																			.	.		0.592	IL2RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046627.1	NM_000417		G	6061870	A	G	6061870	2	3	319	1	0	0	0	0	0	0	0	1	7695	262	10	2		2	IL2RA	10	6061870	Silent	SNP	A	TCGA-LG-A9QD-01A-11D-A382-10	4966979	6061870	129472877	57	44957										
MYST4	23522	hgsc.bcm.edu	37	chr10	76789928	76789928	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	accccacccatgcagctggcTgaaatccccgagacgagcaa	9	16	0	2			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr10:76789928T>A	ENST00000287239.4	+	18	5835	c.5346T>A	c.(5344-5346)gcT>gcA	p.A1782A	KAT6B_ENST00000372714.1_Silent_p.A1490A|KAT6B_ENST00000372724.1_Silent_p.A1490A|KAT6B_ENST00000372711.1_Silent_p.A1599A|KAT6B_ENST00000372725.1_Silent_p.A1490A	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	1782	Interaction with RUNX1 and RUNX2.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										TGCAGCTGGCTGAAATCCCCG	0.592																																					p.A1782A		Atlas-SNP	.											.	.	.	.	0			c.T5346A						.						50	49	50					10																	76789928		2203	4300	6503	SO:0001819	synonymous_variant	23522	exon18			GCTGGCTGAAATC	AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	17582	protein-coding gene	gene with protein product	"MOZ-related factor"	605880	"MYST histone acetyltransferase (monocytic leukemia) 4"	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.5346T>A	chr10.hg19:g.76789928T>A		74.0	0.0		63.0	25.0	NM_012330	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Silent	SNP	ENST00000287239.4	hg19	CCDS7345.1																																																																																			.	.		0.592	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330		A	76789928	T	A	76789928	2	1	319	1	0	0	0	0	0	0	0	1	10114	1567	55	4		4	MYST4	10	76789928	Silent	SNP	T	TCGA-LG-A9QD-01A-11D-A382-10	70728058	76789928	58744819	58	44958										
CDHR1	92211	hgsc.bcm.edu	37	chr10	85970828	85970828	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	gttgtgatccagctcctggaCaccaatgacaatgtccccaa	8	13	0	2			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr10:85970828C>T	ENST00000372117.3	+	13	1495	c.1392C>T	c.(1390-1392)gaC>gaT	p.D464D	CDHR1_ENST00000440770.2_Intron|CDHR1_ENST00000332904.3_Silent_p.D464D	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1	464	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cellular process (GO:0009987)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						AGCTCCTGGACACCAATGACA	0.567																																					p.D464D		Atlas-SNP	.											.	CDHR1	122	.	0			c.C1392T						.						130	125	127					10																	85970828		2203	4300	6503	SO:0001819	synonymous_variant	92211	exon13			CCTGGACACCAAT	AB053448	CCDS7372.1, CCDS53548.1	10q23.1	2014-01-28	2010-01-25	2010-01-25	ENSG00000148600	ENSG00000148600		"Cadherins / Cadherin-related"	14550	protein-coding gene	gene with protein product		609502	"protocadherin 21"	PCDH21		11597768	Standard	NM_001171971		Approved	KIAA1775, CORD15, RP65	uc001kcv.3	Q96JP9	OTTHUMG00000018634	ENST00000372117.3:c.1392C>T	chr10.hg19:g.85970828C>T		155.0	0.0		132.0	33.0	NM_001171971	Q69YZ8|Q8IXY5	Silent	SNP	ENST00000372117.3	hg19	CCDS7372.1																																																																																			.	.		0.567	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100		T	85970828	C	T	85970828	2	4	319	1	0	0	0	0	0	0	0	1	3120	477	17	3		3	CDHR1	10	85970828	Silent	SNP	C	TCGA-LG-A9QD-01A-11D-A382-10	9180900	85970828	49563919	59	44959										
SLIT1	6585	hgsc.bcm.edu	37	chr10	98766260	98766260	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	ctgcaacgtgatgttggcccGtggccagttttgcaggtcag	14	10	1	1	rs546232285		TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr10:98766260G>A	ENST00000266058.4	-	32	3804	c.3559C>T	c.(3559-3561)Cgg>Tgg	p.R1187W	SLIT1_ENST00000371070.4_Missense_Mutation_p.R1187W|ARHGAP19-SLIT1_ENST00000453547.2_3'UTR	NM_003061.2	NP_003052.2	O75093	SLIT1_HUMAN	slit homolog 1 (Drosophila)	1187	Laminin G-like. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|dorsal/ventral axon guidance (GO:0033563)|establishment of nucleus localization (GO:0040023)|forebrain morphogenesis (GO:0048853)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of synapse assembly (GO:0051964)|retinal ganglion cell axon guidance (GO:0031290)|spinal cord development (GO:0021510)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(37)|ovary(5)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	78		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		ATGTTGGCCCGTGGCCAGTTT	0.592																																					p.R1187W		Atlas-SNP	.											SLIT1,colon,carcinoma,0,1	SLIT1	154	.	0			c.C3559T						.						61	45	51					10																	98766260		2203	4300	6503	SO:0001583	missense	6585	exon32			TGGCCCGTGGCCA	AB011537	CCDS7453.1	10q23.3-q24	2008-08-01	2001-11-28		ENSG00000187122	ENSG00000187122			11085	protein-coding gene	gene with protein product		603742	"slit (Drosophila) homolog 1"	SLIL1		9693030, 9813312	Standard	NM_003061		Approved	slit1, MEGF4, Slit-1, SLIT3	uc001kmw.2	O75093	OTTHUMG00000018843	ENST00000266058.4:c.3559C>T	chr10.hg19:g.98766260G>A	ENSP00000266058:p.Arg1187Trp	193.0	0.0		135.0	6.0	NM_003061	Q5T0V1|Q8WWZ2|Q9UIL7	Missense_Mutation	SNP	ENST00000266058.4	hg19	CCDS7453.1	.	.	.	.	.	.	.	.	.	.	G	18.42	3.620157	0.66787	.	.	ENSG00000187122	ENST00000266058;ENST00000371070	T;T	0.69926	-0.44;-0.44	4.93	1.92	0.25849	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);	0.059637	0.64402	D	0.000001	T	0.69557	0.3124	L	0.61036	1.89	0.80722	D	1	D	0.67145	0.996	P	0.49999	0.628	T	0.73069	-0.4099	10	0.87932	D	0	.	13.9426	0.64064	0.0:0.0:0.4775:0.5225	.	1187	O75093	SLIT1_HUMAN	W	1187	ENSP00000266058:R1187W;ENSP00000360109:R1187W	ENSP00000266058:R1187W	R	-	1	2	SLIT1	98756250	1.000000	0.71417	0.286000	0.24833	0.987000	0.75469	3.682000	0.54656	0.220000	0.20860	0.655000	0.94253	CGG	.	.		0.592	SLIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049636.1	NM_003061		A	98766260	G	A	98766260	3	1	319	1	0	0	0	0	1	0	0	0	14754	1144	40	1	1069	1	SLIT1	10	98766260	Missense_Mutation	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10	12795432	98766260	36768487	60	44960										
OR51A7	119687	hgsc.bcm.edu	37	chr11	4929013	4929013	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	tacagttctatcctcactagCaacagggttgctaaaatggg	9	9	2	0			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr11:4929013C>A	ENST00000359350.4	+	1	414	c.414C>A	c.(412-414)agC>agA	p.S138R	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001004749.1	NP_001004749.1	Q8NH64	O51A7_HUMAN	olfactory receptor, family 51, subfamily A, member 7	138						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(7)|lung(13)|ovary(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		TCCTCACTAGCAACAGGGTTG	0.378																																					p.S138R		Atlas-SNP	.											.	OR51A7	86	.	0			c.C414A						.						95	94	95					11																	4929013		2201	4298	6499	SO:0001583	missense	119687	exon1			CACTAGCAACAGG	AB065525	CCDS31364.1	11p15.4	2012-08-09			ENSG00000176895	ENSG00000176895		"GPCR / Class A : Olfactory receptors"	15188	protein-coding gene	gene with protein product							Standard	NM_001004749		Approved		uc010qyq.2	Q8NH64	OTTHUMG00000066502	ENST00000359350.4:c.414C>A	chr11.hg19:g.4929013C>A	ENSP00000352305:p.Ser138Arg	80.0	0.0		90.0	31.0	NM_001004749	Q6IFH8	Missense_Mutation	SNP	ENST00000359350.4	hg19	CCDS31364.1	.	.	.	.	.	.	.	.	.	.	C	12.47	1.948442	0.34377	.	.	ENSG00000176895	ENST00000359350;ENST00000545959;ENST00000544684	T	0.71222	-0.55	5.02	1.96	0.26148	GPCR, rhodopsin-like superfamily (1);	0.366598	0.23690	N	0.045532	T	0.59972	0.2233	L	0.37750	1.13	0.09310	N	1	P	0.46064	0.872	P	0.45794	0.493	T	0.53528	-0.8426	10	0.62326	D	0.03	.	5.4416	0.16511	0.0:0.5314:0.0:0.4686	.	138	Q8NH64	O51A7_HUMAN	R	138;138;127	ENSP00000352305:S138R	ENSP00000352305:S138R	S	+	3	2	OR51A7	4885589	0.000000	0.05858	0.112000	0.21494	0.814000	0.46013	-2.149000	0.01291	0.712000	0.32039	0.655000	0.94253	AGC	.	.		0.378	OR51A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142175.1	NM_001004749		A	4929013	C	A	4929013	3	1	319	1	0	0	0	0	1	0	0	0	11097	709	25	3	416	3	OR51A7	11	4929013	Missense_Mutation	SNP	C	TCGA-LG-A9QD-01A-11D-A382-10		4929013	130077503	61	44961										
CKAP5	9793	hgsc.bcm.edu	37	chr11	46817191	46817191	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	tcctggtttgggtgcagaaaTgtcctttgtgtccttatctc	10	9	1	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr11:46817191T>C	ENST00000529230.1	-	13	1649	c.1603A>G	c.(1603-1605)Att>Gtt	p.I535V	CKAP5_ENST00000415402.1_Missense_Mutation_p.I535V|CKAP5_ENST00000532321.1_5'Flank|CKAP5_ENST00000354558.3_Missense_Mutation_p.I535V|CKAP5_ENST00000312055.5_Missense_Mutation_p.I535V			Q14008	CKAP5_HUMAN	cytoskeleton associated protein 5	535					centrosome organization (GO:0051297)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|RNA transport (GO:0050658)|spindle organization (GO:0007051)	centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|protein complex (GO:0043234)|spindle pole (GO:0000922)				breast(1)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	43						GGTGCAGAAATGTCCTTTGTG	0.448																																					p.I535V	Ovarian(4;85 273 2202 4844 13323)	Atlas-SNP	.											.	CKAP5	134	.	0			c.A1603G						.						174	157	163					11																	46817191		2201	4299	6500	SO:0001583	missense	9793	exon13			CAGAAATGTCCTT		CCDS7924.1, CCDS31477.1	11p11.2	2006-09-20			ENSG00000175216	ENSG00000175216			28959	protein-coding gene	gene with protein product		611142				7788527, 8536682	Standard	NM_014756		Approved	ch-TOG, KIAA0097, TOG, TOGp	uc001ndi.2	Q14008	OTTHUMG00000166599	ENST00000529230.1:c.1603A>G	chr11.hg19:g.46817191T>C	ENSP00000432768:p.Ile535Val	151.0	0.0		112.0	30.0	NM_001008938	Q05D70|Q0VAX7|Q0VAX8|Q14668|Q2TA89|Q6NSH4	Missense_Mutation	SNP	ENST00000529230.1	hg19	CCDS31477.1	.	.	.	.	.	.	.	.	.	.	T	3.908	-0.020759	0.07634	.	.	ENSG00000175216	ENST00000529230;ENST00000415402;ENST00000312055;ENST00000354558	T;T;T;T	0.39056	1.1;1.11;1.1;1.1	5.32	-4.25	0.03766	.	1.260260	0.04970	N	0.463727	T	0.14787	0.0357	N	0.00729	-1.24	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.34104	-0.9842	10	0.12430	T	0.62	-19.6773	15.0038	0.71495	0.0:0.5931:0.0:0.4069	.	535;535;535	Q14008-3;Q14008-2;Q14008	.;.;CKAP5_HUMAN	V	535	ENSP00000432768:I535V;ENSP00000395302:I535V;ENSP00000310227:I535V;ENSP00000346566:I535V	ENSP00000310227:I535V	I	-	1	0	CKAP5	46773767	0.000000	0.05858	0.001000	0.08648	0.787000	0.44495	-0.585000	0.05794	-0.802000	0.04421	0.379000	0.24179	ATT	.	.		0.448	CKAP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390679.1	NM_014756		C	46817191	T	C	46817191	3	2	319	1	0	0	0	0	1	0	0	0	3447	1464	51	2	4623	2	CKAP5	11	46817191	Missense_Mutation	SNP	T	TCGA-LG-A9QD-01A-11D-A382-10	41888178	46817191	88189325	62	44962										
OR8H2	390151	hgsc.bcm.edu	37	chr11	55872871	55872871	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	atgttaccttctctcctcaaTggcccatgatcgctatgcag	7	13	2	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr11:55872871T>A	ENST00000313503.1	+	1	353	c.353T>A	c.(352-354)aTg>aAg	p.M118K		NM_001005200.1	NP_001005200.1	Q8N162	OR8H2_HUMAN	olfactory receptor, family 8, subfamily H, member 2	118						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(38)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	61	Esophageal squamous(21;0.00693)					CTCTCCTCAATGGCCCATGAT	0.458										HNSCC(53;0.14)																											p.M118K		Atlas-SNP	.											.	OR8H2	117	.	0			c.T353A						.						201	205	204					11																	55872871		2201	4296	6497	SO:0001583	missense	390151	exon1			CCTCAATGGCCCA	AB065657	CCDS31518.1	11q11	2012-08-09			ENSG00000181767	ENSG00000181767		"GPCR / Class A : Olfactory receptors"	15308	protein-coding gene	gene with protein product							Standard	NM_001005200		Approved		uc010riy.2	Q8N162	OTTHUMG00000166832	ENST00000313503.1:c.353T>A	chr11.hg19:g.55872871T>A	ENSP00000323982:p.Met118Lys	97.0	0.0		111.0	31.0	NM_001005200	Q6IFC1	Missense_Mutation	SNP	ENST00000313503.1	hg19	CCDS31518.1	.	.	.	.	.	.	.	.	.	.	t	13.17	2.157926	0.38119	.	.	ENSG00000181767	ENST00000313503	T	0.01159	5.25	3.58	2.43	0.29744	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000003	T	0.06872	0.0175	H	0.99454	4.575	0.39127	D	0.961784	P	0.49358	0.923	P	0.45794	0.493	T	0.04946	-1.0916	10	0.87932	D	0	.	9.1009	0.36667	0.0:0.0912:0.0:0.9088	.	118	Q8N162	OR8H2_HUMAN	K	118	ENSP00000323982:M118K	ENSP00000323982:M118K	M	+	2	0	OR8H2	55629447	1.000000	0.71417	0.741000	0.31004	0.011000	0.07611	5.802000	0.69122	0.535000	0.28714	-0.503000	0.04515	ATG	.	.		0.458	OR8H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391540.1	NM_001005200		A	55872871	T	A	55872871	3	1	319	1	0	0	0	0	1	0	0	0	11247	1464	51	4	355	4	OR8H2	11	55872871	Missense_Mutation	SNP	T	TCGA-LG-A9QD-01A-11D-A382-10	9055680	55872871	79133645	63	44963										
TIGD3	220359	hgsc.bcm.edu	37	chr11	65124368	65124368	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	ttcagcagcttcattcaagaAgggctggctcccggcaaaac	10	12	3	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr11:65124368A>G	ENST00000309880.5	+	2	1296	c.1089A>G	c.(1087-1089)gaA>gaG	p.E363E		NM_145719.2	NP_663771.1	Q6B0B8	TIGD3_HUMAN	tigger transposable element derived 3	363						nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(3)|large_intestine(1)|lung(9)|prostate(2)|skin(2)	17						TCATTCAAGAAGGGCTGGCTC	0.647																																					p.E363E		Atlas-SNP	.											.	TIGD3	32	.	0			c.A1089G						.						45	51	49					11																	65124368		2201	4296	6497	SO:0001819	synonymous_variant	220359	exon2			TCAAGAAGGGCTG		CCDS8101.1	11q13.1	2008-07-21				ENSG00000173825			18334	protein-coding gene	gene with protein product							Standard	NM_145719		Approved		uc001odo.4	Q6B0B8		ENST00000309880.5:c.1089A>G	chr11.hg19:g.65124368A>G		127.0	0.0		93.0	6.0	NM_145719		Silent	SNP	ENST00000309880.5	hg19	CCDS8101.1																																																																																			.	.		0.647	TIGD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387310.1	NM_145719		G	65124368	A	G	65124368	2	3	319	1	0	0	0	0	0	0	0	1	15912	69	3	2		2	TIGD3	11	65124368	Silent	SNP	A	TCGA-LG-A9QD-01A-11D-A382-10	9251497	65124368	69882148	64	44964										
CEP57	9702	hgsc.bcm.edu	37	chr11	95564320	95564320	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	taagaaagattttatgaaacTgagacctggagaaaaaagga	10	3	0	5	rs146538238		TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr11:95564320T>G	ENST00000325542.5	+	11	1641	c.1403T>G	c.(1402-1404)cTg>cGg	p.L468R	CEP57_ENST00000537677.1_Missense_Mutation_p.L441R|CEP57_ENST00000325486.5_Missense_Mutation_p.L442R|CEP57_ENST00000541150.1_Missense_Mutation_p.L459R	NM_001243776.1|NM_014679.4	NP_001230705.1|NP_055494.2	Q86XR8	CEP57_HUMAN	centrosomal protein 57kDa	468	Mediates interaction with microtubules. {ECO:0000250}.			L -> Q (in Ref. 3; BAA07654). {ECO:0000305}.	fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|mitotic cell cycle (GO:0000278)|protein homooligomerization (GO:0051260)|protein import into nucleus, translocation (GO:0000060)|spermatid development (GO:0007286)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	fibroblast growth factor binding (GO:0017134)|protein homodimerization activity (GO:0042803)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	13		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				TTTATGAAACTGAGACCTGGA	0.363									Mosaic Variegated Aneuploidy Syndrome																												p.L468R		Atlas-SNP	.											.	CEP57	40	.	0			c.T1403G						.						69	70	70					11																	95564320		2201	4297	6498	SO:0001583	missense	9702	exon11	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	TGAAACTGAGACC	D42054	CCDS8304.1, CCDS58166.1, CCDS58167.1	11q21	2014-09-17			ENSG00000166037	ENSG00000166037			30794	protein-coding gene	gene with protein product		607951				7788527	Standard	NM_014679		Approved	Translokin, TSP57, KIAA0092	uc001pfp.2	Q86XR8	OTTHUMG00000167740	ENST00000325542.5:c.1403T>G	chr11.hg19:g.95564320T>G	ENSP00000317902:p.Leu468Arg	507.0	1.0		404.0	110.0	NM_014679	A0PJH1|A8K5D0|B4DDP5|F5H5F7|Q14704|Q5JB46|Q8IXP0|Q9BVF9	Missense_Mutation	SNP	ENST00000325542.5	hg19	CCDS8304.1	.	.	.	.	.	.	.	.	.	.	T	0.052	-1.246817	0.01481	.	.	ENSG00000166037	ENST00000537677;ENST00000325542;ENST00000325486;ENST00000541150	T;T;T;T	0.29142	1.58;1.58;1.58;1.58	5.65	-1.99	0.07457	.	1.376700	0.04812	N	0.435324	T	0.14270	0.0345	N	0.08118	0	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.28554	-1.0040	10	0.87932	D	0	-16.6978	1.8248	0.03118	0.2623:0.1504:0.0955:0.4918	.	459;442;468	F5H5F7;Q86XR8-2;Q86XR8	.;.;CEP57_HUMAN	R	441;468;442;459	ENSP00000441392:L441R;ENSP00000317902:L468R;ENSP00000317487:L442R;ENSP00000443436:L459R	ENSP00000317487:L442R	L	+	2	0	CEP57	95203968	0.558000	0.26554	0.821000	0.32701	0.006000	0.05464	-0.192000	0.09587	-0.170000	0.10816	-0.263000	0.10527	CTG	.	T|1.000;A|0.000		0.363	CEP57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395983.1	NM_014679		G	95564320	T	G	95564320	3	3	319	1	0	0	0	0	1	0	0	0	3258	1580	55	5	1445	5	CEP57	11	95564320	Missense_Mutation	SNP	T	TCGA-LG-A9QD-01A-11D-A382-10	30439952	95564320	39442196	65	44965										
NPAT	4863	hgsc.bcm.edu	37	chr11	108047094	108047094	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	gatatatttttattattcttTgttttgcctgttaaaaaggg	7	3	1	0			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr11:108047094T>A	ENST00000278612.8	-	12	1116	c.1011A>T	c.(1009-1011)acA>acT	p.T337T	NPAT_ENST00000610253.1_5'UTR	NM_002519.2	NP_002510.2	Q14207	NPAT_HUMAN	nuclear protein, ataxia-telangiectasia locus	337	Mediates transcriptional activation.				positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|Gemini of coiled bodies (GO:0097504)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(21)|ovary(2)|prostate(2)|skin(5)	46		all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|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)		BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116)		TATTATTCTTTGTTTTGCCTG	0.294																																					p.T337T		Atlas-SNP	.											.	NPAT	124	.	0			c.A1011T						.						48	48	48					11																	108047094		1782	4045	5827	SO:0001819	synonymous_variant	4863	exon12			ATTCTTTGTTTTG	X97186	CCDS41710.1	11q22-q23	2008-02-01			ENSG00000149308	ENSG00000149308			7896	protein-coding gene	gene with protein product		601448				9205109	Standard	NM_002519		Approved	E14	uc001pjz.4	Q14207	OTTHUMG00000166385	ENST00000278612.8:c.1011A>T	chr11.hg19:g.108047094T>A		65.0	0.0		57.0	14.0	NM_002519	A8K1V5|A8K6M2|Q13632|Q14967|Q16580|Q86W55|Q8IWE9	Silent	SNP	ENST00000278612.8	hg19	CCDS41710.1																																																																																			.	.		0.294	NPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389506.2	NM_002519		A	108047094	T	A	108047094	2	1	319	1	0	0	0	0	0	0	0	1	10575	1799	63	4		4	NPAT	11	108047094	Silent	SNP	T	TCGA-LG-A9QD-01A-11D-A382-10	12482774	108047094	26959422	66	44966										
CCDC84	338657	hgsc.bcm.edu	37	chr11	118868995	118868995	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	gccgcaagcaccagcggcagCtgaaggaggctttggagagg	17	10	0	2			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr11:118868995C>G	ENST00000334418.1	+	1	144	c.88C>G	c.(88-90)Ctg>Gtg	p.L30V	RP11-110I1.12_ENST00000526453.1_lincRNA	NM_198489.1	NP_940891.1	Q86UT8	CCD84_HUMAN	coiled-coil domain containing 84	30										breast(1)|kidney(1)|large_intestine(1)|liver(1)|ovary(1)	5	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_neural(223;0.224)|all_hematologic(192;0.243)		BRCA - Breast invasive adenocarcinoma(274;7.72e-05)		CCAGCGGCAGCTGAAGGAGGC	0.672																																					p.L30V		Atlas-SNP	.											.	CCDC84	21	.	0			c.C88G						.						11	14	13					11																	118868995		2186	4278	6464	SO:0001583	missense	338657	exon1			CGGCAGCTGAAGG	AB094093	CCDS8405.1	11q23.3	2006-03-13			ENSG00000186166	ENSG00000186166			30460	protein-coding gene	gene with protein product							Standard	NM_198489		Approved	DLNB14	uc001pul.3	Q86UT8	OTTHUMG00000166348	ENST00000334418.1:c.88C>G	chr11.hg19:g.118868995C>G	ENSP00000334767:p.Leu30Val	178.0	0.0		148.0	48.0	NM_198489		Missense_Mutation	SNP	ENST00000334418.1	hg19	CCDS8405.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.212494	0.79240	.	.	ENSG00000186166	ENST00000334418	T	0.61510	0.1	5.12	3.96	0.45880	.	0.000000	0.85682	D	0.000000	T	0.66982	0.2845	L	0.52573	1.65	0.40548	D	0.981098	D	0.67145	0.996	D	0.80764	0.994	T	0.68591	-0.5368	10	0.72032	D	0.01	-13.3111	8.5707	0.33567	0.0:0.8579:0.0:0.1421	.	30	Q86UT8	CCD84_HUMAN	V	30	ENSP00000334767:L30V	ENSP00000334767:L30V	L	+	1	2	CCDC84	118374205	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	0.330000	0.19715	1.054000	0.40438	0.650000	0.86243	CTG	.	.		0.672	CCDC84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389315.1	NM_198489		G	118868995	C	G	118868995	3	3	319	1	0	0	0	0	1	0	0	0	2860	796	28	4	90	4	CCDC84	11	118868995	Missense_Mutation	SNP	C	TCGA-LG-A9QD-01A-11D-A382-10	10821901	118868995	16137521	67	44967										
C2CD2L	1798	hgsc.bcm.edu	37	chr11	118978593	118978593	+	5'UTR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	gggcccgcggggaccggggcCcgggacccgccttagccggg	20	16	0	0			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr11:118978593C>T	ENST00000409993.2	-	0	448				C2CD2L_ENST00000336702.3_Missense_Mutation_p.P48S			Q9H3H5	GPT_HUMAN	dolichyl-phosphate (UDP-N-acetylglucosamine) N-acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase)						cellular protein metabolic process (GO:0044267)|dolichol biosynthetic process (GO:0019408)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|protein oligomerization (GO:0051259)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	phospho-N-acetylmuramoyl-pentapeptide-transferase activity (GO:0008963)|transferase activity, transferring glycosyl groups (GO:0016757)|UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity (GO:0003975)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(2)	17	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.55e-05)		ggaccggggcccgggACCCGC	0.756																																					p.P48S		Atlas-SNP	.											.	C2CD2L	39	.	0			c.C142T						.						3	3	3					11																	118978593		1715	3431	5146	SO:0001623	5_prime_UTR_variant	9854	exon1			CGGGGCCCGGGAC	Z82022	CCDS8411.1	11q23.3	2007-12-14			ENSG00000172269	ENSG00000172269	2.7.8.15		2995	protein-coding gene	gene with protein product		191350		DPAGT2, DPAGT		8244387	Standard	NM_001382		Approved	GPT, D11S366, DGPT, ALG7, CDG-Ij	uc001pvi.3	Q9H3H5	OTTHUMG00000153533	ENST00000409993.2:c.-1104G>A	chr11.hg19:g.118978593C>T		93.0	0.0		57.0	9.0	NM_014807	O15216|Q86WV9|Q9BWE6	Missense_Mutation	SNP	ENST00000409993.2	hg19	CCDS8411.1	.	.	.	.	.	.	.	.	.	.	C	0.634	-0.815992	0.02776	.	.	ENSG00000172375	ENST00000336702	T	0.21191	2.02	4.46	-0.945	0.10388	.	0.910045	0.09321	N	0.818196	T	0.07143	0.0181	N	0.03608	-0.345	0.33311	D	0.566073	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44375	-0.9332	10	0.15066	T	0.55	-35.3607	4.1447	0.10210	0.0:0.4086:0.1727:0.4187	.	48;48	O14523;O14523-2	C2C2L_HUMAN;.	S	48	ENSP00000338885:P48S	ENSP00000338885:P48S	P	+	1	0	C2CD2L	118483803	0.000000	0.05858	0.017000	0.16124	0.105000	0.19272	-0.235000	0.09016	-0.384000	0.07845	-0.229000	0.12294	CCG	.	.		0.756	DPAGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331527.2	NM_001382		T	118978593	C	T	118978593	1	4	319	0	1	0	0	0	0	0	0	0	2155	623	22	3		3	C2CD2L	11	118978593	5'UTR	SNP	C	TCGA-LG-A9QD-01A-11D-A382-10	109598	118978593	16027923	68	44968										
SORL1	6653	hgsc.bcm.edu	37	chr11	121492888	121492888	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	cagtttcattatcagcacctGatgccttaaaaatcataaca	4	10	3	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr11:121492888G>A	ENST00000260197.7	+	45	6211	c.6082G>A	c.(6082-6084)Gat>Aat	p.D2028N	SORL1_ENST00000532694.1_Missense_Mutation_p.D874N|SORL1_ENST00000525532.1_Missense_Mutation_p.D972N|SORL1_ENST00000527934.1_Missense_Mutation_p.D643N|SORL1_ENST00000534286.1_Missense_Mutation_p.D938N	NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	2028	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell death (GO:0008219)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902960)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of neurofibrillary tangle assembly (GO:1902997)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of tau-protein kinase activity (GO:1902948)|positive regulation of choline O-acetyltransferase activity (GO:1902771)|positive regulation of early endosome to recycling endosome transport (GO:1902955)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|positive regulation of protein localization to early endosome (GO:1902966)|post-Golgi vesicle-mediated transport (GO:0006892)|protein maturation (GO:0051604)|protein retention in Golgi apparatus (GO:0045053)|protein targeting (GO:0006605)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|receptor-mediated endocytosis (GO:0006898)|regulation of smooth muscle cell migration (GO:0014910)|signal transduction (GO:0007165)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|nuclear envelope lumen (GO:0005641)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)|beta-amyloid binding (GO:0001540)|low-density lipoprotein particle binding (GO:0030169)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(2)|lung(34)|ovary(5)|pancreas(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(2)	91		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		ATCAGCACCTGATGCCTTAAA	0.333																																					p.D2028N		Atlas-SNP	.											.	SORL1	218	.	0			c.G6082A						.						119	118	118					11																	121492888		2201	4299	6500	SO:0001583	missense	6653	exon45			GCACCTGATGCCT	Y08110	CCDS8436.1	11q23.2-q24.4	2014-06-05	2011-01-25		ENSG00000137642	ENSG00000137642		"Fibronectin type III domain containing"	11185	protein-coding gene	gene with protein product	"LDLR relative with 11 ligand-binding repeats"	602005	"chromosome 11 open reading frame 32", "sortilin-related receptor, L(DLR class) A repeats-containing"	C11orf32		9157966, 8940146	Standard	NM_003105		Approved	gp250, LR11, LRP9, SorLA, SorLA-1	uc001pxx.3	Q92673	OTTHUMG00000166057	ENST00000260197.7:c.6082G>A	chr11.hg19:g.121492888G>A	ENSP00000260197:p.Asp2028Asn	82.0	0.0		88.0	18.0	NM_003105	B2RNX7|Q92856	Missense_Mutation	SNP	ENST00000260197.7	hg19	CCDS8436.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.180314	0.78677	.	.	ENSG00000137642	ENST00000260197;ENST00000525532;ENST00000532694;ENST00000534286;ENST00000527934	T;T;T;T;T	0.53423	0.62;0.62;0.62;0.62;0.62	5.6	5.6	0.85130	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.421091	0.24590	N	0.037236	T	0.41003	0.1140	N	0.14661	0.345	0.54753	D	0.999983	P;P	0.46395	0.877;0.651	P;B	0.45829	0.494;0.115	T	0.35025	-0.9805	10	0.44086	T	0.13	.	19.578	0.95452	0.0:0.0:1.0:0.0	.	643;2028	E9PKB0;Q92673	.;SORL_HUMAN	N	2028;972;874;938;643	ENSP00000260197:D2028N;ENSP00000434634:D972N;ENSP00000432131:D874N;ENSP00000436447:D938N;ENSP00000435405:D643N	ENSP00000260197:D2028N	D	+	1	0	SORL1	120998098	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.299000	0.78831	2.633000	0.89246	0.655000	0.94253	GAT	.	.		0.333	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2	NM_003105		A	121492888	G	A	121492888	3	1	319	1	0	0	0	0	1	0	0	0	14949	1290	45	3	6260	3	SORL1	11	121492888	Missense_Mutation	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10	2514295	121492888	13513628	69	44969										
KIAA0528	9847	hgsc.bcm.edu	37	chr12	22677545	22677545	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	attatcacagctctatagcaTtttggaatagacgttgctgt	8	7	2	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr12:22677545T>G	ENST00000333957.4	-	6	717	c.462A>C	c.(460-462)aaA>aaC	p.K154N	C2CD5_ENST00000396028.2_Missense_Mutation_p.K154N|C2CD5_ENST00000544930.1_5'UTR|C2CD5_ENST00000545552.1_Missense_Mutation_p.K154N|C2CD5_ENST00000542676.1_Missense_Mutation_p.K154N|C2CD5_ENST00000446597.1_Missense_Mutation_p.K154N|C2CD5_ENST00000540703.1_5'UTR|C2CD5_ENST00000536386.1_Missense_Mutation_p.K154N	NM_014802.1	NP_055617.1	Q86YS7	C2CD5_HUMAN	C2 calcium-dependent domain containing 5	154					cellular response to insulin stimulus (GO:0032869)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|intracellular protein transmembrane transport (GO:0065002)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)										CTCTATAGCATTTTGGAATAG	0.333																																					p.K154N		Atlas-SNP	.											.	.	.	.	0			c.A462C						.						101	93	96					12																	22677545		2203	4300	6503	SO:0001583	missense	9847	exon6			ATAGCATTTTGGA	AB011100	CCDS31758.1, CCDS66337.1, CCDS66338.1, CCDS66339.1, CCDS66340.1	12p12.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000111731	ENSG00000111731			29062	protein-coding gene	gene with protein product	"138 kDa C2 domain-containing phosphoprotein"		"KIAA0528"	KIAA0528		21907143	Standard	XM_005253538		Approved	CDP138	uc001rfq.3	Q86YS7	OTTHUMG00000169100	ENST00000333957.4:c.462A>C	chr12.hg19:g.22677545T>G	ENSP00000334229:p.Lys154Asn	105.0	0.0		96.0	32.0	NM_014802	B4DJ03|B4DRN7|B7ZLL0|F5H2A1|F5H5R1|O60280|Q17RY7|Q7Z619|Q86SU3	Missense_Mutation	SNP	ENST00000333957.4	hg19	CCDS31758.1	.	.	.	.	.	.	.	.	.	.	C	11.30	1.597367	0.28445	.	.	ENSG00000111731	ENST00000333957;ENST00000446597;ENST00000536386;ENST00000396028;ENST00000542676;ENST00000545552	T;T;T;T;T;T	0.51817	0.69;0.69;0.69;0.69;0.69;0.69	4.95	1.04	0.20106	.	0.059399	0.64402	D	0.000005	T	0.28797	0.0714	N	0.17474	0.49	0.80722	D	1	B;B;B;P;B	0.47762	0.356;0.032;0.029;0.9;0.017	B;B;B;B;B	0.42771	0.185;0.016;0.017;0.397;0.016	T	0.02539	-1.1144	10	0.25106	T	0.35	-17.8418	9.5055	0.39044	0.0:0.5872:0.0:0.4128	.	154;154;154;154;154	F5H2A1;B4DRN7;B7ZLL0;Q86YS7-2;Q86YS7	.;.;.;.;K0528_HUMAN	N	154	ENSP00000334229:K154N;ENSP00000388756:K154N;ENSP00000439392:K154N;ENSP00000379345:K154N;ENSP00000441951:K154N;ENSP00000443204:K154N	ENSP00000334229:K154N	K	-	3	2	KIAA0528	22568812	0.979000	0.34478	0.998000	0.56505	0.979000	0.70002	0.264000	0.18497	-0.052000	0.13311	-0.962000	0.02626	AAA	.	.		0.333	C2CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402257.1	NM_014802		G	22677545	T	G	22677545	3	3	319	1	0	0	0	0	1	0	0	0	8191	1490	52	5	2620	5	KIAA0528	12	22677545	Missense_Mutation	SNP	T	TCGA-LG-A9QD-01A-11D-A382-10		22677545	111174350	70	44970										
ERBB3	2065	hgsc.bcm.edu	37	chr12	56474108	56474108	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	agggcgaacgacgctctgcaGgtgctgggcttgcttttcag	15	10	2	0			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr12:56474108G>A	ENST00000267101.3	+	1	464	c.24G>A	c.(22-24)caG>caA	p.Q8Q	ERBB3_ENST00000415288.2_5'Flank|ERBB3_ENST00000450146.2_De_novo_Start_OutOfFrame|ERBB3_ENST00000411731.2_Silent_p.Q8Q	NM_001982.3	NP_001973.2	P21860	ERBB3_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3	8					cranial nerve development (GO:0021545)|endocardial cushion development (GO:0003197)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of cell adhesion (GO:0007162)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of secretion (GO:0051048)|negative regulation of signal transduction (GO:0009968)|neuron apoptotic process (GO:0051402)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell proliferation (GO:0042127)|Schwann cell differentiation (GO:0014037)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein tyrosine kinase activator activity (GO:0030296)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			ACGCTCTGCAGGTGCTGGGCT	0.687																																					p.Q8Q		Atlas-SNP	.											.	ERBB3	350	.	0			c.G24A						.						40	33	36					12																	56474108		2197	4285	6482	SO:0001819	synonymous_variant	2065	exon1			TCTGCAGGTGCTG	M34309	CCDS31833.1, CCDS44918.1	12q13	2013-07-09	2013-07-09			ENSG00000065361			3431	protein-coding gene	gene with protein product		190151	"lethal congenital contracture syndrome 2"	LCCS2			Standard	NM_001982		Approved	HER3	uc001sjh.3	P21860	OTTHUMG00000170140	ENST00000267101.3:c.24G>A	chr12.hg19:g.56474108G>A		138.0	0.0		136.0	54.0	NM_001982	A8K6L6|B4DIK7|B4DV32|E9PDT8|Q9BUD7	Silent	SNP	ENST00000267101.3	hg19	CCDS31833.1																																																																																			.	.		0.687	ERBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407619.3			A	56474108	G	A	56474108	2	1	319	1	0	0	0	0	0	0	0	1	5210	991	35	3		3	ERBB3	12	56474108	Silent	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10	33796563	56474108	77377787	71	44971										
IL31	386653	hgsc.bcm.edu	37	chr12	122657230	122657230	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	tgtttggcggctgggcgtcaGggctgagacacggcagcgtg	19	9	1	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr12:122657230G>A	ENST00000377035.1	-	3	250	c.224C>T	c.(223-225)cCt>cTt	p.P75L		NM_001014336.1	NP_001014358.1	Q6EBC2	IL31_HUMAN	interleukin 31	75					immune system process (GO:0002376)	extracellular space (GO:0005615)				central_nervous_system(2)|kidney(1)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	13	all_neural(191;0.0837)|Medulloblastoma(191;0.163)	Lung NSC(355;6.93e-05)|Breast(359;0.0544)		OV - Ovarian serous cystadenocarcinoma(86;3.27e-29)|Epithelial(86;4.86e-27)|BRCA - Breast invasive adenocarcinoma(302;0.223)		CTGGGCGTCAGGGCTGAGACA	0.512																																					p.P75L		Atlas-SNP	.											.	IL31	23	.	0			c.C224T						.						151	114	127					12																	122657230		2203	4300	6503	SO:0001583	missense	386653	exon3			GCGTCAGGGCTGA	AY499343	CCDS31919.1	12q24.31	2011-07-21			ENSG00000204671	ENSG00000204671		"Interleukins and interleukin receptors"	19372	protein-coding gene	gene with protein product		609509				15184896	Standard	NM_001014336		Approved	IL-31	uc001ubv.3	Q6EBC2	OTTHUMG00000168916	ENST00000377035.1:c.224C>T	chr12.hg19:g.122657230G>A	ENSP00000366234:p.Pro75Leu	154.0	0.0		130.0	40.0	NM_001014336	A2RUQ1	Missense_Mutation	SNP	ENST00000377035.1	hg19	CCDS31919.1	.	.	.	.	.	.	.	.	.	.	G	0.244	-1.011125	0.02095	.	.	ENSG00000204671	ENST00000377035	.	.	.	4.18	-1.03	0.10102	.	0.722199	0.12041	N	0.505035	T	0.12774	0.0310	N	0.04508	-0.205	0.09310	N	1	B	0.16603	0.018	B	0.14023	0.01	T	0.29305	-1.0016	9	0.15952	T	0.53	-1.3094	4.0412	0.09751	0.4512:0.1816:0.3672:0.0	.	75	Q6EBC2	IL31_HUMAN	L	75	.	ENSP00000366234:P75L	P	-	2	0	IL31	121223183	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.164000	0.16542	-0.185000	0.10550	0.563000	0.77884	CCT	.	.		0.512	IL31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401594.1	NM_001014336		A	122657230	G	A	122657230	3	1	319	1	0	0	0	0	1	0	0	0	7699	1000	35	3	274	3	IL31	12	122657230	Missense_Mutation	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10	66183122	122657230	11194665	72	44972										
UBC	7316	hgsc.bcm.edu	37	chr12	125397157	125397157	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	gtgatggtcttaccagtcagGgtcttcacgaagatctgcat	11	9	5	2			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr12:125397157G>A	ENST00000536769.1	-	1	2737	c.1161C>T	c.(1159-1161)acC>acT	p.T387T	UBC_ENST00000339647.5_Silent_p.T387T|UBC_ENST00000538617.1_Intron|UBC_ENST00000536661.1_5'Flank|MIR5188_ENST00000583467.1_RNA|UBC_ENST00000546120.1_Silent_p.T311T			P0CG48	UBC_HUMAN	ubiquitin C	387	Ubiquitin-like 6. {ECO:0000255|PROSITE- ProRule:PRU00214}.				activation of MAPK activity (GO:0000187)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protease binding (GO:0002020)			breast(3)|endometrium(4)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.17e-05)|Epithelial(86;0.000207)|all cancers(50;0.00308)		TACCAGTCAGGGTCTTCACGA	0.532																																					p.T387T		Atlas-SNP	.											.	UBC	79	.	0			c.C1161T						.						216	199	205					12																	125397157		2203	4296	6499	SO:0001819	synonymous_variant	7316	exon2			AGTCAGGGTCTTC		CCDS9260.1	12q24.3	2008-09-08			ENSG00000150991	ENSG00000150991			12468	protein-coding gene	gene with protein product	"polyubiquitin-C"	191340				1315303, 11872750	Standard	NM_021009		Approved		uc001ugs.4	P0CG48		ENST00000536769.1:c.1161C>T	chr12.hg19:g.125397157G>A		353.0	0.0		267.0	63.0	NM_021009	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	ENST00000536769.1	hg19	CCDS9260.1																																																																																			.	.		0.532	UBC-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400177.1	NM_021009		A	125397157	G	A	125397157	2	1	319	1	0	0	0	0	0	0	0	1	16857	1219	43	3		3	UBC	12	125397157	Silent	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10	2739927	125397157	8454738	73	44973										
DGKH	160851	hgsc.bcm.edu	37	chr13	42733407	42733407	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	tttttttttttttagtgtgtAaattcaaggctcacaaaaga	6	4	2	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr13:42733407A>G	ENST00000337343.4	+	6	649	c.628A>G	c.(628-630)Aaa>Gaa	p.K210E	DGKH_ENST00000261491.5_Missense_Mutation_p.K210E|DGKH_ENST00000538674.1_Intron|DGKH_ENST00000379274.2_Missense_Mutation_p.K74E|DGKH_ENST00000536612.1_Missense_Mutation_p.K74E|DGKH_ENST00000498255.2_3'UTR|DGKH_ENST00000540693.1_Missense_Mutation_p.K210E	NM_178009.3	NP_821077.1	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta	210					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(2)|endometrium(3)|kidney(5)|large_intestine(11)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		TTTAGTGTGTAAATTCAAGGC	0.343																																					p.K210E		Atlas-SNP	.											.	DGKH	106	.	0			c.A628G						.						48	43	45					13																	42733407		2203	4300	6503	SO:0001583	missense	160851	exon7			GTGTGTAAATTCA	AB078967	CCDS9381.1, CCDS9382.1, CCDS55898.1	13q13.3	2013-01-10			ENSG00000102780	ENSG00000102780		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	2854	protein-coding gene	gene with protein product		604071				8702685	Standard	XM_005266271		Approved	DGKeta	uc001uyl.2	Q86XP1	OTTHUMG00000016804	ENST00000337343.4:c.628A>G	chr13.hg19:g.42733407A>G	ENSP00000337572:p.Lys210Glu	68.0	0.0		39.0	12.0	NM_001204504	A2A2W7|A6NFX7|B4DZ34|Q5VZW0|Q6PI56|Q86XP2|Q8N3N0|Q8N7J9	Missense_Mutation	SNP	ENST00000337343.4	hg19	CCDS9381.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.398354	0.83120	.	.	ENSG00000102780	ENST00000540693;ENST00000337343;ENST00000261491;ENST00000379274;ENST00000536612	D;D;D;D;D	0.93426	-3.22;-3.22;-3.22;-3.22;-3.22	5.45	5.45	0.79879	Protein kinase C-like, phorbol ester/diacylglycerol binding (4);	0.000000	0.85682	D	0.000000	D	0.96463	0.8846	M	0.78344	2.41	0.80722	D	1	D;D;D	0.76494	0.994;0.999;0.998	D;D;D	0.80764	0.945;0.994;0.98	D	0.97039	0.9756	10	0.87932	D	0	.	15.5191	0.75851	1.0:0.0:0.0:0.0	.	74;210;210	Q86XP1-3;Q86XP1-2;Q86XP1	.;.;DGKH_HUMAN	E	210;210;210;74;74	ENSP00000440823:K210E;ENSP00000337572:K210E;ENSP00000261491:K210E;ENSP00000368576:K74E;ENSP00000445114:K74E	ENSP00000261491:K210E	K	+	1	0	DGKH	41631407	1.000000	0.71417	1.000000	0.80357	0.840000	0.47671	8.905000	0.92613	2.056000	0.61249	0.533000	0.62120	AAA	.	.		0.343	DGKH-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044699.2	NM_178009		G	42733407	A	G	42733407	3	3	319	1	0	0	0	0	1	0	0	0	4472	363	13	2	650	2	DGKH	13	42733407	Missense_Mutation	SNP	A	TCGA-LG-A9QD-01A-11D-A382-10		42733407	72436471	74	44974										
OR10G2	26534	hgsc.bcm.edu	37	chr14	22102423	22102423	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	acagttgtgtcagcacaggcCagtctcaatactgcgcggat	11	11	2	0			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr14:22102423C>T	ENST00000542433.1	-	1	673	c.576G>A	c.(574-576)ctG>ctA	p.L192L		NM_001005466.1	NP_001005466.1	Q8NGC3	O10G2_HUMAN	olfactory receptor, family 10, subfamily G, member 2	192						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|prostate(1)|skin(2)|stomach(2)	22	all_cancers(95;0.00113)	Acute lymphoblastic leukemia(2;0.0279)		GBM - Glioblastoma multiforme(265;0.0142)		CAGCACAGGCCAGTCTCAATA	0.527																																					p.L192L		Atlas-SNP	.											.	OR10G2	35	.	0			c.G576A						.						88	96	94					14																	22102423		2203	4300	6503	SO:0001819	synonymous_variant	26534	exon1			ACAGGCCAGTCTC		CCDS32047.1	14q11.2	2013-09-24			ENSG00000255582	ENSG00000255582		"GPCR / Class A : Olfactory receptors"	8170	protein-coding gene	gene with protein product						8188290	Standard	NM_001005466		Approved		uc010tmc.2	Q8NGC3	OTTHUMG00000168890	ENST00000542433.1:c.576G>A	chr14.hg19:g.22102423C>T		314.0	0.0		275.0	73.0	NM_001005466	B2RPD0	Silent	SNP	ENST00000542433.1	hg19	CCDS32047.1																																																																																			.	.		0.527	OR10G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401525.1			T	22102423	C	T	22102423	2	4	319	1	0	0	0	0	0	0	0	1	10908	581	21	3		3	OR10G2	14	22102423	Silent	SNP	C	TCGA-LG-A9QD-01A-11D-A382-10		22102423	85247117	75	44975										
DHRS1	115817	hgsc.bcm.edu	37	chr14	24760356	24760356	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	ggtcctcaccgtccacatccCgaaggccatagcgtcgagca	10	16	1	0	rs148282342		TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr14:24760356C>G	ENST00000288111.7	-	8	1070	c.794G>C	c.(793-795)cGg>cCg	p.R265P	DHRS1_ENST00000559088.1_5'UTR|DHRS1_ENST00000396813.1_Missense_Mutation_p.R265P	NM_001136050.2	NP_001129522.1	Q96LJ7	DHRS1_HUMAN	dehydrogenase/reductase (SDR family) member 1	265						endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)	oxidoreductase activity (GO:0016491)			cervix(1)|endometrium(1)|large_intestine(2)|lung(2)	6				GBM - Glioblastoma multiforme(265;2.81e-08)|OV - Ovarian serous cystadenocarcinoma(311;0.0442)		GTCCACATCCCGAAGGCCATA	0.607																																					p.R265P		Atlas-SNP	.											.	DHRS1	21	.	0			c.G794C						.						105	86	92					14																	24760356		2203	4300	6503	SO:0001583	missense	115817	exon8			ACATCCCGAAGGC	AK058159	CCDS9623.1	14q11.2	2011-09-14			ENSG00000157379	ENSG00000157379	1.1.-.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	16445	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 19C, member 1"	610410				12153138, 19027726	Standard	NM_138452		Approved	FLJ25430, MGC20204, SDR19C1	uc001wok.3	Q96LJ7	OTTHUMG00000029333	ENST00000288111.7:c.794G>C	chr14.hg19:g.24760356C>G	ENSP00000288111:p.Arg265Pro	94.0	0.0		91.0	34.0	NM_138452	D3DS71|Q8NDG3|Q96B59|Q96CQ5	Missense_Mutation	SNP	ENST00000288111.7	hg19	CCDS9623.1	.	.	.	.	.	.	.	.	.	.	C	11.19	1.566485	0.27915	.	.	ENSG00000157379	ENST00000288111;ENST00000396813	D;D	0.83591	-1.74;-1.74	5.24	-2.93	0.05598	.	0.768976	0.11801	N	0.528116	T	0.76357	0.3976	L	0.46157	1.445	0.19300	N	0.999973	B	0.32128	0.357	B	0.35607	0.206	T	0.65516	-0.6149	10	0.41790	T	0.15	-8.6692	11.3601	0.49638	0.0:0.2689:0.0:0.7311	.	265	Q96LJ7	DHRS1_HUMAN	P	265	ENSP00000288111:R265P;ENSP00000380027:R265P	ENSP00000288111:R265P	R	-	2	0	DHRS1	23830196	0.008000	0.16893	0.493000	0.27502	0.931000	0.56810	-0.361000	0.07612	-0.425000	0.07371	0.467000	0.42956	CGG	.	C|1.000;T|0.000		0.607	DHRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073168.4	NM_138452		G	24760356	C	G	24760356	3	3	319	1	0	0	0	0	1	0	0	0	4488	652	23	4	155	4	DHRS1	14	24760356	Missense_Mutation	SNP	C	TCGA-LG-A9QD-01A-11D-A382-10	2657933	24760356	82589184	76	44976										
SEL1L	6400	hgsc.bcm.edu	37	chr14	81943498	81943498	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	aggtcccaaaagctggtccaTatcaagttgggtgaacatat	10	8	1	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr14:81943498T>C	ENST00000336735.4	-	21	2319	c.2203A>G	c.(2203-2205)Atg>Gtg	p.M735V		NM_005065.5	NP_005056.3	Q9UBV2	SE1L1_HUMAN	sel-1 suppressor of lin-12-like (C. elegans)	735	Interaction with ERLEC1, OS9 and SYVN1.				Notch signaling pathway (GO:0007219)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	28				BRCA - Breast invasive adenocarcinoma(234;0.0299)		AGCTGGTCCATATCAAGTTGG	0.423																																					p.M735V		Atlas-SNP	.											.	SEL1L	67	.	0			c.A2203G						.						107	99	102					14																	81943498		2203	4300	6503	SO:0001583	missense	6400	exon21			GGTCCATATCAAG		CCDS9876.1, CCDS58333.1	14q31	2011-03-31	2001-11-28		ENSG00000071537	ENSG00000071537			10717	protein-coding gene	gene with protein product	"sel-1 suppressor of lin-12-like 1 (C. elegans)"	602329	"sel-1 (suppressor of lin-12, C.elegans)-like"			9417916, 10051412, 16331677	Standard	NM_005065		Approved	IBD2, SEL1L1	uc010tvv.2	Q9UBV2		ENST00000336735.4:c.2203A>G	chr14.hg19:g.81943498T>C	ENSP00000337053:p.Met735Val	136.0	0.0		134.0	41.0	NM_005065	Q6UWT6|Q9P1T9|Q9UHK7	Missense_Mutation	SNP	ENST00000336735.4	hg19	CCDS9876.1	.	.	.	.	.	.	.	.	.	.	T	12.92	2.083609	0.36758	.	.	ENSG00000071537	ENST00000336735	T	0.25912	1.77	6.17	5.01	0.66863	.	0.121175	0.85682	D	0.000000	T	0.25606	0.0623	L	0.58101	1.795	0.80722	D	1	B	0.18610	0.029	B	0.12837	0.008	T	0.04347	-1.0958	10	0.16896	T	0.51	.	13.556	0.61759	0.0:0.0:0.1299:0.8701	.	735	Q9UBV2	SE1L1_HUMAN	V	735	ENSP00000337053:M735V	ENSP00000337053:M735V	M	-	1	0	SEL1L	81013251	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	3.196000	0.51020	1.120000	0.41904	0.533000	0.62120	ATG	.	.		0.423	SEL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413325.1	NM_005065		C	81943498	T	C	81943498	3	2	319	1	0	0	0	0	1	0	0	0	14025	1406	49	2	185	2	SEL1L	14	81943498	Missense_Mutation	SNP	T	TCGA-LG-A9QD-01A-11D-A382-10	57183142	81943498	25406042	77	44977										
GABRG3	2567	hgsc.bcm.edu	37	chr15	27778000	27778000	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	ttcctgctctttaacctggtCtactgggttggatacctgta	9	10	2	0			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr15:27778000C>A	ENST00000333743.6	+	10	1631	c.1377C>A	c.(1375-1377)gtC>gtA	p.V459V	RP11-100M12.3_ENST00000556642.1_RNA	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	459					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(23)|skin(1)|upper_aerodigestive_tract(4)	42		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TTAACCTGGTCTACTGGGTTG	0.502																																					p.V459V	NSCLC(114;800 1656 7410 37729 45293)	Atlas-SNP	.											.	GABRG3	115	.	0			c.C1377A						.						54	54	54					15																	27778000		1941	4134	6075	SO:0001819	synonymous_variant	2567	exon10			CCTGGTCTACTGG		CCDS45195.1, CCDS59251.1	15q12	2012-06-22			ENSG00000182256	ENSG00000182256		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4088	protein-coding gene	gene with protein product	"GABA(G) receptor, gamma 3"	600233				7601451	Standard	NM_033223		Approved		uc001zbg.2	Q99928	OTTHUMG00000044462	ENST00000333743.6:c.1377C>A	chr15.hg19:g.27778000C>A		108.0	0.0		92.0	31.0	NM_033223	G3V594|Q9HD46|Q9NYT2	Silent	SNP	ENST00000333743.6	hg19	CCDS45195.1																																																																																			.	.		0.502	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2			A	27778000	C	A	27778000	2	1	319	1	0	0	0	0	0	0	0	1	6181	900	32	3		3	GABRG3	15	27778000	Silent	SNP	C	TCGA-LG-A9QD-01A-11D-A382-10		27778000	74753392	78	44978										
CA12	771	hgsc.bcm.edu	37	chr15	63632640	63632640	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	aatcccgggacgaatgcttcCtggcctagagagacatgttg	12	10	0	2			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr15:63632640C>T	ENST00000178638.3	-	7	1034	c.594G>A	c.(592-594)caG>caA	p.Q198Q	CA12_ENST00000344366.3_Silent_p.Q198Q|CA12_ENST00000422263.2_Silent_p.Q138Q	NM_001218.3	NP_001209.1	O43570	CAH12_HUMAN	carbonic anhydrase XII	198					bicarbonate transport (GO:0015701)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(2)	16					Benzthiazide(DB00562)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Zonisamide(DB00909)	CGAATGCTTCCTGGCCTAGAG	0.552																																					p.Q198Q		Atlas-SNP	.											.	CA12	33	.	0			c.G594A						.						81	70	74					15																	63632640		2203	4300	6503	SO:0001819	synonymous_variant	771	exon7			TGCTTCCTGGCCT	AF051882	CCDS10185.1, CCDS10186.1	15q22	2004-01-19			ENSG00000074410	ENSG00000074410		"Carbonic anhydrases"	1371	protein-coding gene	gene with protein product		603263				9636197	Standard	NM_001218		Approved	HsT18816	uc002amc.3	O43570	OTTHUMG00000132881	ENST00000178638.3:c.594G>A	chr15.hg19:g.63632640C>T		135.0	0.0		122.0	33.0	NM_206925	B2RE24|Q53YE5|Q9BWG2	Silent	SNP	ENST00000178638.3	hg19	CCDS10185.1																																																																																			.	.		0.552	CA12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256370.1	NM_001218		T	63632640	C	T	63632640	2	4	319	1	0	0	0	0	0	0	0	1	2515	680	24	3		3	CA12	15	63632640	Silent	SNP	C	TCGA-LG-A9QD-01A-11D-A382-10	35854640	63632640	38898752	79	44979										
LOXL1	4016	hgsc.bcm.edu	37	chr15	74219803	74219803	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	cctcggcgggggtcatctacCcctaccagccccgggcgcgc	13	19	2	0			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr15:74219803C>T	ENST00000261921.7	+	1	1005	c.679C>T	c.(679-681)Ccc>Tcc	p.P227S	LOXL1-AS1_ENST00000566675.1_RNA|LOXL1-AS1_ENST00000562965.1_RNA|LOXL1-AS1_ENST00000565756.1_RNA|LOXL1-AS1_ENST00000564194.1_RNA|LOXL1-AS1_ENST00000568229.1_RNA|LOXL1-AS1_ENST00000565416.1_RNA|LOXL1-AS1_ENST00000564963.1_RNA|LOXL1-AS1_ENST00000562130.1_RNA|LOXL1-AS1_ENST00000562739.1_RNA|LOXL1-AS1_ENST00000567257.1_RNA|LOXL1-AS1_ENST00000567644.1_RNA|LOXL1-AS1_ENST00000568087.1_RNA	NM_005576.2	NP_005567.2	Q08397	LOXL1_HUMAN	lysyl oxidase-like 1	227					extracellular matrix organization (GO:0030198)|oxidation-reduction process (GO:0055114)|protein deamination (GO:0018277)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	copper ion binding (GO:0005507)|oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor (GO:0016641)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10						ggTCATCTACCCCTACCAGCC	0.756																																					p.P227S		Atlas-SNP	.											.	LOXL1	25	.	0			c.C679T						.						2	3	2					15																	74219803		1032	2132	3164	SO:0001583	missense	4016	exon1			ATCTACCCCTACC	L21186	CCDS10253.1	15q24-q25	2008-07-18			ENSG00000129038	ENSG00000129038			6665	protein-coding gene	gene with protein product		153456				7689553	Standard	NM_005576		Approved	LOXL, LOL	uc002awc.1	Q08397	OTTHUMG00000137595	ENST00000261921.7:c.679C>T	chr15.hg19:g.74219803C>T	ENSP00000261921:p.Pro227Ser	109.0	0.0		79.0	14.0	NM_005576	Q6NUL3|Q96BW7	Missense_Mutation	SNP	ENST00000261921.7	hg19	CCDS10253.1	.	.	.	.	.	.	.	.	.	.	C	12.86	2.064728	0.36470	.	.	ENSG00000129038	ENST00000261921;ENST00000395162	T	0.27720	1.65	3.72	3.72	0.42706	.	1.163260	0.06428	N	0.723550	T	0.44030	0.1274	L	0.27053	0.805	0.27156	N	0.961285	D	0.89917	1.0	D	0.79108	0.992	T	0.40608	-0.9554	10	0.51188	T	0.08	.	10.9987	0.47591	0.0:1.0:0.0:0.0	.	227	Q08397	LOXL1_HUMAN	S	227;89	ENSP00000261921:P227S	ENSP00000261921:P227S	P	+	1	0	LOXL1	72006856	0.202000	0.23423	0.995000	0.50966	0.630000	0.37929	2.692000	0.47018	1.602000	0.50124	0.297000	0.19635	CCC	.	.		0.756	LOXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268995.2	NM_005576		T	74219803	C	T	74219803	3	4	319	1	0	0	0	0	1	0	0	0	8908	623	22	3	681	3	LOXL1	15	74219803	Missense_Mutation	SNP	C	TCGA-LG-A9QD-01A-11D-A382-10	10587163	74219803	28311589	80	44980										
ULK3	25989	hgsc.bcm.edu	37	chr15	75130667	75130667	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	caggtccagggcatcctgctCcccgccggcggcctcctcct	11	20	0	0			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr15:75130667C>A	ENST00000440863.2	-	12	1277	c.1186G>T	c.(1186-1188)Gag>Tag	p.E396*	ULK3_ENST00000569437.1_Nonsense_Mutation_p.E396*|ULK3_ENST00000568667.1_Nonsense_Mutation_p.E407*	NM_001099436.1	NP_001092906	Q6PHR2	ULK3_HUMAN	unc-51 like kinase 3	396	MIT 2.				autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|cellular senescence (GO:0090398)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of smoothened signaling pathway (GO:0045880)|protein autophosphorylation (GO:0046777)|regulation of autophagy (GO:0010506)	ATG1/UKL1 signaling complex (GO:0034273)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)	2						GCATCCTGCTCCCCGCCGGCG	0.687																																					p.E396X		Atlas-SNP	.											.	ULK3	30	.	0			c.G1186T						.						12	17	16					15																	75130667		1980	4120	6100	SO:0001587	stop_gained	25989	exon12			CCTGCTCCCCGCC	BC048289		15q24.1	2013-07-02	2013-07-02			ENSG00000140474			19703	protein-coding gene	gene with protein product		613472	"unc-51-like kinase 3 (C. elegans)"				Standard	XM_005254289		Approved	DKFZP434C131, FLJ90566	uc010bkf.1	Q6PHR2		ENST00000440863.2:c.1186G>T	chr15.hg19:g.75130667C>A	ENSP00000400312:p.Glu396*	208.0	0.0		142.0	36.0	NM_001099436	B2RXK3|B4DRQ7|D3DW68|Q9NPN5|Q9UFS4	Nonsense_Mutation	SNP	ENST00000440863.2	hg19	CCDS45305.1	.	.	.	.	.	.	.	.	.	.	C	34	5.300836	0.95601	.	.	ENSG00000140474	ENST00000440863;ENST00000418051	.	.	.	5.35	3.4	0.38934	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	-15.3133	8.1686	0.31241	0.0:0.614:0.3032:0.0828	.	.	.	.	X	396;407	.	ENSP00000393658:E407X	E	-	1	0	ULK3	72917720	0.944000	0.32072	0.935000	0.37517	0.567000	0.35839	2.239000	0.43079	1.210000	0.43336	0.555000	0.69702	GAG	.	.		0.687	ULK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421734.4	NM_015518		A	75130667	C	A	75130667	4	1	319	1	0	0	0	0	0	1	0	0	16992	864	30	3	252	3	ULK3	15	75130667	Nonsense_Mutation	SNP	C	TCGA-LG-A9QD-01A-11D-A382-10	910864	75130667	27400725	81	44981										
TMEM8A	58986	hgsc.bcm.edu	37	chr16	422023	422023	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	agttcctcccgatcgttcttGcagatctgatagtggcaggg	12	10	2	2			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr16:422023G>A	ENST00000431232.2	-	13	2440	c.2280C>T	c.(2278-2280)tgC>tgT	p.C760C	MRPL28_ENST00000199706.8_5'Flank|MRPL28_ENST00000389675.2_5'Flank|TMEM8A_ENST00000250930.3_Silent_p.C567C|MRPL28_ENST00000429738.1_5'Flank	NM_021259.2	NP_067082.2	Q9HCN3	TMM8A_HUMAN	transmembrane protein 8A	760					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)				central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	14						GATCGTTCTTGCAGATCTGAT	0.637																																					p.C760C		Atlas-SNP	.											.	TMEM8A	49	.	0			c.C2280T						.						75	78	77					16																	422023		2202	4300	6502	SO:0001819	synonymous_variant	58986	exon13			GTTCTTGCAGATC	AB045292	CCDS10407.1	16p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000129925	ENSG00000129925			17205	protein-coding gene	gene with protein product			"transmembrane protein 6", "transmembrane protein 8 (five membrane-spanning domains)"	TMEM6, TMEM8		11006113	Standard	NM_021259		Approved	M83	uc002cgu.4	Q9HCN3	OTTHUMG00000047996	ENST00000431232.2:c.2280C>T	chr16.hg19:g.422023G>A		93.0	0.0		49.0	12.0	NM_021259	D3DU49|Q4TT35|Q8WU24|Q96S25|Q9BR03|Q9BT97|Q9H7B9	Silent	SNP	ENST00000431232.2	hg19	CCDS10407.1	.	.	.	.	.	.	.	.	.	.	G	0.228	-1.023102	0.02061	.	.	ENSG00000129925	ENST00000424078	.	.	.	4.3	-1.8	0.07907	.	.	.	.	.	T	0.58566	0.2131	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55866	-0.8073	4	.	.	.	-0.2607	12.5035	0.55968	0.3895:0.0:0.6105:0.0	.	.	.	.	V	228	.	.	A	-	2	0	TMEM8A	362024	0.969000	0.33509	0.173000	0.22940	0.076000	0.17211	1.171000	0.31896	-0.422000	0.07405	-1.644000	0.00765	GCA	.	.		0.637	TMEM8A-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000109257.2	NM_021259		A	422023	G	A	422023	2	1	319	1	0	0	0	0	0	0	0	1	16229	1311	46	3		3	TMEM8A	16	422023	Silent	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10		422023	89932730	82	44982			2	56		2	2	16	G		5.426785e-05
TMEM8A	58986	hgsc.bcm.edu	37	chr16	422038	422038	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	ttcttgcagatctgatagtgGcaggggaatttctgcgagca	13	7	3	2			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr16:422038G>T	ENST00000431232.2	-	13	2425	c.2265C>A	c.(2263-2265)tgC>tgA	p.C755*	MRPL28_ENST00000199706.8_5'Flank|MRPL28_ENST00000389675.2_5'Flank|TMEM8A_ENST00000250930.3_Nonsense_Mutation_p.C562*|MRPL28_ENST00000429738.1_5'Flank	NM_021259.2	NP_067082.2	Q9HCN3	TMM8A_HUMAN	transmembrane protein 8A	755					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)				central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	14						TCTGATAGTGGCAGGGGAATT	0.632																																					p.C755X		Atlas-SNP	.											.	TMEM8A	49	.	0			c.C2265A						.						70	74	73					16																	422038		2202	4299	6501	SO:0001587	stop_gained	58986	exon13			ATAGTGGCAGGGG	AB045292	CCDS10407.1	16p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000129925	ENSG00000129925			17205	protein-coding gene	gene with protein product			"transmembrane protein 6", "transmembrane protein 8 (five membrane-spanning domains)"	TMEM6, TMEM8		11006113	Standard	NM_021259		Approved	M83	uc002cgu.4	Q9HCN3	OTTHUMG00000047996	ENST00000431232.2:c.2265C>A	chr16.hg19:g.422038G>T	ENSP00000401338:p.Cys755*	87.0	0.0		49.0	14.0	NM_021259	D3DU49|Q4TT35|Q8WU24|Q96S25|Q9BR03|Q9BT97|Q9H7B9	Nonsense_Mutation	SNP	ENST00000431232.2	hg19	CCDS10407.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	39|39	7.878713|7.878713	0.98539|0.98539	.|.	.|.	ENSG00000129925|ENSG00000129925	ENST00000424078|ENST00000431232;ENST00000250930;ENST00000382942	.|.	.|.	.|.	4.3|4.3	3.03|3.03	0.35002|0.35002	.|.	.|0.000000	.|0.64402	.|D	.|0.000004	T|.	0.26774|.	0.0655|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.14896|.	-1.0456|.	4|.	.|0.02654	.|T	.|1	-0.0764|-0.0764	6.6382|6.6382	0.22895|0.22895	0.3879:0.0:0.6121:0.0|0.3879:0.0:0.6121:0.0	.|.	.|.	.|.	.|.	D|X	223|755;562;243	.|.	.|ENSP00000250930:C562X	A|C	-|-	2|3	0|2	TMEM8A|TMEM8A	362039|362039	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.560000|0.560000	0.35617|0.35617	1.619000|1.619000	0.36965|0.36965	0.710000|0.710000	0.31997|0.31997	0.455000|0.455000	0.32223|0.32223	GCC|TGC	.	.		0.632	TMEM8A-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000109257.2	NM_021259		T	422038	G	T	422038	4	4	319	1	0	0	0	0	0	1	0	0	16229	1195	42	3	54	3	TMEM8A	16	422038	Nonsense_Mutation	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10	15	422038	89932715	83	44983			2	56		2	2	16	G		5.426785e-05
COQ7	10229	hgsc.bcm.edu	37	chr16	19083318	19083318	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	tagacaatatcagtcgggcaGctgtggatcgaataatccgg	12	8	1	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr16:19083318G>A	ENST00000321998.5	+	2	208	c.142G>A	c.(142-144)Gct>Act	p.A48T	COQ7_ENST00000544894.2_Missense_Mutation_p.A10T|COQ7_ENST00000569127.1_Missense_Mutation_p.A25T|COQ7_ENST00000568985.1_Missense_Mutation_p.A48T	NM_016138.4	NP_057222.2	Q99807	COQ7_HUMAN	coenzyme Q7 homolog, ubiquinone (yeast)	48	2 X approximate tandem repeats.				age-dependent response to oxidative stress (GO:0001306)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|in utero embryonic development (GO:0001701)|mitochondrial ATP synthesis coupled electron transport (GO:0042775)|mitochondrion morphogenesis (GO:0070584)|neural tube formation (GO:0001841)|neurogenesis (GO:0022008)|small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|large_intestine(1)|lung(3)|prostate(1)|skin(3)|urinary_tract(1)	10						CAGTCGGGCAGCTGTGGATCG	0.498											OREG0023656	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A48T		Atlas-SNP	.											.	COQ7	16	.	0			c.G142A						.						153	143	147					16																	19083318		2197	4300	6497	SO:0001583	missense	10229	exon2			CGGGCAGCTGTGG	U81276	CCDS10574.1, CCDS53993.1	16p12.3	2008-05-14	2001-11-28		ENSG00000167186	ENSG00000167186			2244	protein-coding gene	gene with protein product		601683	"coenzyme Q, 7 (rat, yeast) homolog"			9020081, 10373325	Standard	NM_016138		Approved	CLK-1, CAT5	uc002dfr.3	Q99807	OTTHUMG00000131455	ENST00000321998.5:c.142G>A	chr16.hg19:g.19083318G>A	ENSP00000322316:p.Ala48Thr	227.0	0.0	730	141.0	33.0	NM_016138	B2RDA9|Q9BTT7|Q9H0T5|Q9UEW5|Q9UNR5	Missense_Mutation	SNP	ENST00000321998.5	hg19	CCDS10574.1	.	.	.	.	.	.	.	.	.	.	G	11.52	1.664461	0.29604	.	.	ENSG00000167186	ENST00000321998;ENST00000544894	T;T	0.42513	0.97;0.97	5.74	1.19	0.21007	Ferritin/ribonucleotide reductase-like (1);	0.382154	0.34178	N	0.004190	T	0.19927	0.0479	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.002	T	0.19031	-1.0318	10	0.22706	T	0.39	-14.8787	10.3683	0.44038	0.3515:0.0:0.6485:0.0	.	25;48	Q49A71;Q99807	.;COQ7_HUMAN	T	48;10	ENSP00000322316:A48T;ENSP00000442923:A10T	ENSP00000322316:A48T	A	+	1	0	COQ7	18990819	0.000000	0.05858	0.006000	0.13384	0.787000	0.44495	-0.031000	0.12287	0.364000	0.24374	0.655000	0.94253	GCT	.	.		0.498	COQ7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254275.3	NM_016138		A	19083318	G	A	19083318	3	1	319	1	0	0	0	0	1	0	0	0	3752	971	34	3	148	3	COQ7	16	19083318	Missense_Mutation	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10	18661280	19083318	71271435	84	44984										
SRCAP	10847	hgsc.bcm.edu	37	chr16	30745076	30745076	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	tggatgctcaggcccaggacCgctgtcaccgaattggccag	13	13	2	0			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr16:30745076C>T	ENST00000262518.4	+	29	6836	c.6451C>T	c.(6451-6453)Cgc>Tgc	p.R2151C	SRCAP_ENST00000344771.4_Missense_Mutation_p.R1993C|SRCAP_ENST00000395059.2_Missense_Mutation_p.R2089C	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	2151	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			GGCCCAGGACCGCTGTCACCG	0.527																																					p.R2151C		Atlas-SNP	.											.	SRCAP	298	.	0			c.C6451T						.						117	119	118					16																	30745076		2197	4300	6497	SO:0001583	missense	10847	exon29			CAGGACCGCTGTC	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.6451C>T	chr16.hg19:g.30745076C>T	ENSP00000262518:p.Arg2151Cys	125.0	0.0		99.0	30.0	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	hg19	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	C	14.66	2.601669	0.46423	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	D;D;D	0.99150	-5.49;-5.49;-5.49	4.82	4.82	0.62117	Helicase, C-terminal (3);	0.000000	0.46145	D	0.000319	D	0.99625	0.9863	H	0.98901	4.365	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.97391	0.9989	10	0.87932	D	0	-7.7206	16.8447	0.85977	0.0:1.0:0.0:0.0	.	2089;2151	Q6ZRS2-2;Q6ZRS2	.;SRCAP_HUMAN	C	2151;2089;1993	ENSP00000262518:R2151C;ENSP00000378499:R2089C;ENSP00000343042:R1993C	ENSP00000262518:R2151C	R	+	1	0	SRCAP	30652577	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.184000	0.50926	2.485000	0.83878	0.563000	0.77884	CGC	.	.		0.527	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		T	30745076	C	T	30745076	3	4	319	1	0	0	0	0	1	0	0	0	15150	652	23	1	6557	1	SRCAP	16	30745076	Missense_Mutation	SNP	C	TCGA-LG-A9QD-01A-11D-A382-10	11661758	30745076	59609677	85	44985										
ITGAE	3682	hgsc.bcm.edu	37	chr17	3664397	3664397	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	ctgcctggctgtgttcacatCgtcttctccaccgccttctt	7	16	4	0	rs184355144		TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr17:3664397C>T	ENST00000263087.4	-	6	606	c.508G>A	c.(508-510)Gat>Aat	p.D170N		NM_002208.4	NP_002199.3	P38570	ITAE_HUMAN	integrin, alpha E (antigen CD103, human mucosal lymphocyte antigen 1; alpha polypeptide)	170	X-domain (extra domain).				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	external side of plasma membrane (GO:0009897)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	41				UCEC - Uterine corpus endometrioid carcinoma (3;0.0813)		GTGTTCACATCGTCTTCTCCA	0.542																																					p.D170N	NSCLC(182;635 2928 8995 38788)	Atlas-SNP	.											.	ITGAE	96	.	0			c.G508A						.						193	187	189					17																	3664397		2203	4300	6503	SO:0001583	missense	3682	exon6			TCACATCGTCTTC	L25851	CCDS32531.1	17p13	2010-03-23				ENSG00000083457		"CD molecules", "Integrins"	6147	protein-coding gene	gene with protein product		604682				8119947	Standard	NM_002208		Approved	CD103, HUMINAE	uc002fwo.4	P38570		ENST00000263087.4:c.508G>A	chr17.hg19:g.3664397C>T	ENSP00000263087:p.Asp170Asn	54.0	0.0		30.0	12.0	NM_002208	Q17RS6|Q9NZU9	Missense_Mutation	SNP	ENST00000263087.4	hg19	CCDS32531.1	.	.	.	.	.	.	.	.	.	.	C	5.593	0.294218	0.10567	.	.	ENSG00000083457	ENST00000263087	T	0.59502	0.26	2.63	-5.27	0.02763	.	.	.	.	.	T	0.35566	0.0936	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.15983	-1.0418	9	0.48119	T	0.1	.	5.4287	0.16440	0.0:0.5046:0.1682:0.3272	.	170	P38570	ITAE_HUMAN	N	170	ENSP00000263087:D170N	ENSP00000263087:D170N	D	-	1	0	ITGAE	3611146	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.556000	0.05992	-1.510000	0.01796	-0.693000	0.03709	GAT	.	C|1.000;G|0.000		0.542	ITGAE-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438169.1	NM_002208		T	3664397	C	T	3664397	3	4	319	1	0	0	0	0	1	0	0	0	7894	884	31	1	3135	1	ITGAE	17	3664397	Missense_Mutation	SNP	C	TCGA-LG-A9QD-01A-11D-A382-10		3664397	77530813	86	44986										
KCNJ16	3773	hgsc.bcm.edu	37	chr17	68129150	68129150	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	cccgagaaattctctggggcCataggtttaatgatgtcttg	11	8	2	2			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr17:68129150C>T	ENST00000589377.1	+	2	1085	c.922C>T	c.(922-924)Cat>Tat	p.H308Y	KCNJ16_ENST00000392671.1_Missense_Mutation_p.H308Y|KCNJ16_ENST00000586462.1_Missense_Mutation_p.H347Y|KCNJ16_ENST00000283936.1_Missense_Mutation_p.H308Y|KCNJ16_ENST00000585558.1_Missense_Mutation_p.H343Y|KCNJ16_ENST00000392670.1_Missense_Mutation_p.H308Y	NM_001270422.1	NP_001257351.1	Q9NPI9	KCJ16_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 16	308					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)			breast(3)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	32	Breast(10;2.96e-09)					TCTCTGGGGCCATAGGTTTAA	0.408																																					p.H308Y		Atlas-SNP	.											.	KCNJ16	72	.	0			c.C922T						.						72	76	75					17																	68129150		2203	4300	6503	SO:0001583	missense	3773	exon6			TGGGGCCATAGGT	AF153815	CCDS11687.1, CCDS74141.1	17q24.3	2011-07-05				ENSG00000153822		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6262	protein-coding gene	gene with protein product		605722				11240146, 16382105	Standard	NM_018658		Approved	Kir5.1, BIR9	uc002jio.4	Q9NPI9		ENST00000589377.1:c.922C>T	chr17.hg19:g.68129150C>T	ENSP00000465967:p.His308Tyr	135.0	0.0		136.0	29.0	NM_001270422		Missense_Mutation	SNP	ENST00000589377.1	hg19	CCDS11687.1	.	.	.	.	.	.	.	.	.	.	C	8.427	0.847662	0.17034	.	.	ENSG00000153822	ENST00000283936;ENST00000392671;ENST00000392670	D;D;D	0.94138	-3.36;-3.36;-3.36	5.78	5.78	0.91487	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (2);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.267267	0.43747	D	0.000525	D	0.84220	0.5424	N	0.11201	0.11	0.35913	D	0.831217	B;B	0.18968	0.032;0.006	B;B	0.18871	0.023;0.006	T	0.81223	-0.1030	9	.	.	.	.	10.4714	0.44640	0.0:0.8545:0.0:0.1455	.	308;308	A8K434;Q9NPI9	.;IRK16_HUMAN	Y	308	ENSP00000283936:H308Y;ENSP00000376439:H308Y;ENSP00000376438:H308Y	.	H	+	1	0	KCNJ16	65640745	0.999000	0.42202	0.377000	0.26055	0.102000	0.19082	3.957000	0.56730	2.722000	0.93159	0.650000	0.86243	CAT	.	.		0.408	KCNJ16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450880.1	NM_018658		T	68129150	C	T	68129150	3	4	319	1	0	0	0	0	1	0	0	0	8059	594	21	3	924	3	KCNJ16	17	68129150	Missense_Mutation	SNP	C	TCGA-LG-A9QD-01A-11D-A382-10	64464753	68129150	13066060	87	44987										
NOL4	8715	hgsc.bcm.edu	37	chr18	31432918	31432918	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	cggcattgatttcagttggaCtcagctggggtctggagttt	14	7	3	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr18:31432918C>T	ENST00000261592.5	-	11	2102	c.1805G>A	c.(1804-1806)aGt>aAt	p.S602N	NOL4_ENST00000535475.1_Missense_Mutation_p.S383N|NOL4_ENST00000269185.4_Missense_Mutation_p.S386N|NOL4_ENST00000535384.1_Missense_Mutation_p.S317N|NOL4_ENST00000589544.1_Missense_Mutation_p.S500N|NOL4_ENST00000538587.1_Missense_Mutation_p.S528N	NM_001198546.1|NM_003787.4	NP_001185475.1|NP_003778.2	O94818	NOL4_HUMAN	nucleolar protein 4	602						nucleolus (GO:0005730)	RNA binding (GO:0003723)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	51						TTCAGTTGGACTCAGCTGGGG	0.453																																					p.S602N		Atlas-SNP	.											.	NOL4	139	.	0			c.G1805A						.						110	97	102					18																	31432918		2203	4300	6503	SO:0001583	missense	8715	exon11			GTTGGACTCAGCT	AB017800	CCDS11907.2, CCDS56058.1, CCDS56059.1, CCDS59308.1	18q12	2010-05-04			ENSG00000101746	ENSG00000101746			7870	protein-coding gene	gene with protein product	"cancer/testis antigen 125"	603577				9813152	Standard	NM_003787		Approved	NOLP, HRIHFB2255, CT125	uc010dmi.3	O94818	OTTHUMG00000132291	ENST00000261592.5:c.1805G>A	chr18.hg19:g.31432918C>T	ENSP00000261592:p.Ser602Asn	68.0	0.0		82.0	24.0	NM_003787	B4DSQ0|B7Z3Z7|F5H1E3|Q6IBS2|Q9BWF1	Missense_Mutation	SNP	ENST00000261592.5	hg19	CCDS11907.2	.	.	.	.	.	.	.	.	.	.	C	10.84	1.464650	0.26335	.	.	ENSG00000101746	ENST00000261592;ENST00000269185;ENST00000535384;ENST00000535475;ENST00000538587	.	.	.	5.96	5.96	0.96718	.	0.058662	0.64402	D	0.000001	T	0.51753	0.1693	N	0.17312	0.475	0.45452	D	0.998421	B;B;B;B;P;B	0.44281	0.011;0.006;0.001;0.011;0.831;0.008	B;B;B;B;P;B	0.60541	0.017;0.007;0.008;0.017;0.876;0.028	T	0.44682	-0.9312	9	0.23302	T	0.38	-12.8717	10.7143	0.46002	0.0:0.8591:0.0:0.1409	.	317;528;602;317;500;383	B7Z3Z7;B4DSQ0;O94818;F5H1E3;O94818-2;B3KRF4	.;.;NOL4_HUMAN;.;.;.	N	602;386;317;383;528	.	ENSP00000261592:S602N	S	-	2	0	NOL4	29686916	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.721000	0.54941	2.814000	0.96858	0.655000	0.94253	AGT	.	.		0.453	NOL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255386.1	NM_003787		T	31432918	C	T	31432918	3	4	319	1	0	0	0	0	1	0	0	0	10533	565	20	3	115	3	NOL4	18	31432918	Missense_Mutation	SNP	C	TCGA-LG-A9QD-01A-11D-A382-10		31432918	46644330	88	44988										
KIAA1632	57724	hgsc.bcm.edu	37	chr18	43496496	43496496	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	gtgacctgttgtgtgacaccCtgagggacaccgctgtccaa	12	12	0	3			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr18:43496496C>T	ENST00000282041.5	-	18	3325	c.3291G>A	c.(3289-3291)caG>caA	p.Q1097Q	EPG5_ENST00000585906.1_5'UTR	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	1097					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)					NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						GTGTGACACCCTGAGGGACAC	0.547																																					p.Q1097Q		Atlas-SNP	.											.	EPG5	199	.	0			c.G3291A						.						68	71	70					18																	43496496		2082	4212	6294	SO:0001819	synonymous_variant	57724	exon18			GACACCCTGAGGG	AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"KIAA1632"	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.3291G>A	chr18.hg19:g.43496496C>T		106.0	0.0		52.0	18.0	NM_020964	A2BDF3|Q9H8C8	Silent	SNP	ENST00000282041.5	hg19	CCDS11926.2																																																																																			.	.		0.547	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		T	43496496	C	T	43496496	2	4	319	1	0	0	0	0	0	0	0	1	8258	680	24	3		3	KIAA1632	18	43496496	Silent	SNP	C	TCGA-LG-A9QD-01A-11D-A382-10	12063578	43496496	34580752	89	44989										
DCC	1630	hgsc.bcm.edu	37	chr18	50278724	50278724	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	tggctcaattattagtcggaCagcaaaagttgcagtagcag	11	7	1	0			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr18:50278724C>G	ENST00000442544.2	+	2	1008	c.392C>G	c.(391-393)aCa>aGa	p.T131R	DCC_ENST00000412726.1_5'UTR	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	131	Ig-like C2-type 1.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		ATTAGTCGGACAGCAAAAGTT	0.413																																					p.T131R		Atlas-SNP	.											.	DCC	360	.	0			c.C392G						.						108	101	103					18																	50278724		2203	4300	6503	SO:0001583	missense	1630	exon2			GTCGGACAGCAAA	X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2701	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 1"	120470	"deleted in colorectal carcinoma"			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.392C>G	chr18.hg19:g.50278724C>G	ENSP00000389140:p.Thr131Arg	173.0	0.0		128.0	33.0	NM_005215		Missense_Mutation	SNP	ENST00000442544.2	hg19	CCDS11952.1	.	.	.	.	.	.	.	.	.	.	C	12.33	1.907100	0.33628	.	.	ENSG00000187323	ENST00000442544;ENST00000304775	T	0.13196	2.61	5.06	5.06	0.68205	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.234953	0.33217	N	0.005159	T	0.30293	0.0760	L	0.48218	1.51	0.80722	D	1	D	0.67145	0.996	D	0.65443	0.935	T	0.01056	-1.1466	10	0.51188	T	0.08	.	17.2004	0.86904	0.0:1.0:0.0:0.0	.	131	P43146	DCC_HUMAN	R	131;64	ENSP00000389140:T131R	ENSP00000304146:T64R	T	+	2	0	DCC	48532722	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	3.738000	0.55067	2.354000	0.79902	0.655000	0.94253	ACA	.	.		0.413	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215		G	50278724	C	G	50278724	3	3	319	1	0	0	0	0	1	0	0	0	4284	478	17	4	398	4	DCC	18	50278724	Missense_Mutation	SNP	C	TCGA-LG-A9QD-01A-11D-A382-10	6782228	50278724	27798524	90	44990										
CNN2	1265	hgsc.bcm.edu	37	chr19	1036446	1036446	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	caaatgcgccagccagtcggGcatgactgcctacggcacga	12	14	0	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr19:1036446G>A	ENST00000263097.4	+	6	902	c.539G>A	c.(538-540)gGc>gAc	p.G180D	CNN2_ENST00000565096.2_Missense_Mutation_p.G169D|AC011558.5_ENST00000585757.1_RNA|CNN2_ENST00000348419.3_Missense_Mutation_p.G141D|CNN2_ENST00000606983.1_3'UTR|CNN2_ENST00000562958.2_Missense_Mutation_p.G201D	NM_004368.2	NP_004359.1	Q99439	CNN2_HUMAN	calponin 2	180					actomyosin structure organization (GO:0031032)|cellular response to mechanical stimulus (GO:0071260)|cytoskeleton organization (GO:0007010)|hemopoiesis (GO:0030097)|negative regulation of cell migration (GO:0030336)|negative regulation of phagocytosis (GO:0050765)|positive regulation of gene expression (GO:0010628)|regulation of actin filament-based process (GO:0032970)|regulation of cell proliferation (GO:0042127)|wound healing (GO:0042060)	cell-cell junction (GO:0005911)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|stress fiber (GO:0001725)	actin binding (GO:0003779)			endometrium(1)|large_intestine(2)|lung(3)|prostate(1)|skin(3)	10		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AGCCAGTCGGGCATGACTGCC	0.592																																					p.G180D		Atlas-SNP	.											.	CNN2	26	.	0			c.G539A						.						66	62	63					19																	1036446		2203	4300	6503	SO:0001583	missense	1265	exon6			AGTCGGGCATGAC	D83735	CCDS12053.1, CCDS12054.1	19p13.3	2011-02-18			ENSG00000064666	ENSG00000064666			2156	protein-coding gene	gene with protein product		602373				8889829	Standard	NM_004368		Approved		uc002lqu.3	Q99439		ENST00000263097.4:c.539G>A	chr19.hg19:g.1036446G>A	ENSP00000263097:p.Gly180Asp	171.0	0.0		91.0	29.0	NM_004368	A5D8U8|A6NFI4|D6W5X9|Q92578	Missense_Mutation	SNP	ENST00000263097.4	hg19	CCDS12053.1	.	.	.	.	.	.	.	.	.	.	g	23.9	4.473857	0.84640	.	.	ENSG00000064666	ENST00000263097;ENST00000348419;ENST00000442531	D;D	0.95307	-3.67;-3.67	4.18	4.18	0.49190	Calponin homology domain (1);	0.000000	0.85682	U	0.000000	D	0.98096	0.9372	H	0.96720	3.87	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.87578	0.993;0.997;0.998;0.992;0.989;0.992	D	0.99044	1.0825	10	0.87932	D	0	.	14.027	0.64592	0.0:0.0:1.0:0.0	.	201;169;155;141;180;180	B4DUT8;B4DDF4;B4DHU5;A6NFI4;Q99439;Q6FHE4	.;.;.;.;CNN2_HUMAN;.	D	180;141;159	ENSP00000263097:G180D;ENSP00000340129:G141D	ENSP00000263097:G180D	G	+	2	0	CNN2	987446	1.000000	0.71417	0.947000	0.38551	0.932000	0.56968	8.947000	0.93000	2.173000	0.68751	0.556000	0.70494	GGC	.	.		0.592	CNN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420293.3	NM_004368		A	1036446	G	A	1036446	3	1	319	1	0	0	0	0	1	0	0	0	3612	1203	42	3	561	3	CNN2	19	1036446	Missense_Mutation	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10		1036446	58092537	91	44991										
SLC1A6	6511	hgsc.bcm.edu	37	chr19	15064996	15064996	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	ctcgtagttgttaacttgagCaatgaagatggcagccaggg	13	7	0	3			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr19:15064996C>A	ENST00000221742.3	-	7	1322	c.1315G>T	c.(1315-1317)Gct>Tct	p.A439S	SLC1A6_ENST00000430939.2_Missense_Mutation_p.A375S|SLC1A6_ENST00000600144.1_Missense_Mutation_p.A361S	NM_005071.1	NP_005062.1	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6	439					aspartate transport (GO:0015810)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(8)|liver(1)|lung(12)|ovary(3)|pancreas(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42						TTAACTTGAGCAATGAAGATG	0.597																																					p.A439S		Atlas-SNP	.											.	SLC1A6	111	.	0			c.G1315T						.						89	79	82					19																	15064996		2203	4300	6503	SO:0001583	missense	6511	exon7			CTTGAGCAATGAA		CCDS12321.1, CCDS62578.1	19p13.12	2013-07-15			ENSG00000105143	ENSG00000105143		"Solute carriers"	10944	protein-coding gene	gene with protein product		600637				7791878	Standard	NM_005071		Approved	EAAT4	uc002naa.2	P48664	OTTHUMG00000183351	ENST00000221742.3:c.1315G>T	chr19.hg19:g.15064996C>A	ENSP00000221742:p.Ala439Ser	112.0	0.0		98.0	26.0	NM_005071	Q8N753	Missense_Mutation	SNP	ENST00000221742.3	hg19	CCDS12321.1	.	.	.	.	.	.	.	.	.	.	c	24.6	4.545485	0.86022	.	.	ENSG00000105143	ENST00000430939;ENST00000221742	T;T	0.66638	0.31;-0.22	4.46	4.46	0.54185	Sodium:dicarboxylate symporter, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.81297	0.4793	M	0.80332	2.49	0.80722	D	1	D;D	0.71674	0.99;0.998	D;D	0.69307	0.963;0.913	D	0.84307	0.0508	10	0.87932	D	0	-21.0269	14.9867	0.71353	0.0:1.0:0.0:0.0	.	375;439	E7EV13;P48664	.;EAA4_HUMAN	S	375;439	ENSP00000409386:A375S;ENSP00000221742:A439S	ENSP00000221742:A439S	A	-	1	0	SLC1A6	14925996	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	7.472000	0.80996	2.482000	0.83794	0.546000	0.68486	GCT	.	.		0.597	SLC1A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466283.1	NM_005071		A	15064996	C	A	15064996	3	1	319	1	0	0	0	0	1	0	0	0	14451	710	25	3	391	3	SLC1A6	19	15064996	Missense_Mutation	SNP	C	TCGA-LG-A9QD-01A-11D-A382-10	14028550	15064996	44063987	92	44992										
IFI30	10437	hgsc.bcm.edu	37	chr19	18288521	18288521	+	Splice_Site	DEL	A	A	-													0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	ccctgtcttgctttgtgcagAaacccttggaagatcagacc					rs202043324		TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr19:18288521delA	ENST00000407280.3	+	6	812	c.637delA	c.(637-639)aaa>aa	p.K213fs	PIK3R2_ENST00000593731.1_3'UTR	NM_006332.3	NP_006323.2	P13284	GILT_HUMAN	interferon, gamma-inducible protein 30	213					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of fibroblast proliferation (GO:0048147)|protein stabilization (GO:0050821)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	oxidoreductase activity, acting on a sulfur group of donors (GO:0016667)			endometrium(1)|kidney(2)|large_intestine(1)|stomach(1)	5						CTTTGTGCAGAAACCCTTGGA	0.572																																					.		Atlas-INDEL	.											.	IFI30	12	.	0			c.637-1A>-						.						72	70	71					19																	18288521		1952	4129	6081	SO:0001630	splice_region_variant	10437	exon6			.	J03909	CCDS46015.1	19p13.1	2008-07-16				ENSG00000216490			5398	protein-coding gene	gene with protein product	"gamma-interferon-inducible lysosomal thiol reductase", "interferon gamma-inducible protein 30 preproprotein"	604664				3136170, 10639150	Standard	NM_006332		Approved	IFI-30, GILT, IP30, MGC32056	uc002nic.1	P13284		ENST00000407280.3:c.637-1A>-	chr19.hg19:g.18288521delA		120.0	0.0		107.0	27.0	NM_006332	Q76MF9|Q8NEI4|Q8WU77|Q9UL08	Splice_Site	DEL	ENST00000407280.3	hg19	CCDS46015.1																																																																																			.	.		0.572	IFI30-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466396.3	NM_006332	Frame_Shift_Del	-	18288521	A	-	18288521	8	5	319	1	0	1	0	1	0	0	1	0	7524	260	9	0	659	0	IFI30	19	18288521	Splice_Site	DEL	A	TCGA-LG-A9QD-01A-11D-A382-10	3223525	18288521	40840462	93	44993										
ZNF254	9534	hgsc.bcm.edu	37	chr19	24270141	24270141	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	ccctagaagcctagaaatggTgagaatgccagtccgacatc	10	11	0	3			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr19:24270141T>C	ENST00000357002.4	+	1	145		c.e1+2		ZNF254_ENST00000339642.6_Splice_Site|ZNF254_ENST00000342944.6_Intron	NM_001278661.1|NM_001278662.1|NM_001278664.1|NM_001278677.1|NM_001278678.1|NM_203282.2	NP_001265590.1|NP_001265591.1|NP_001265593.1|NP_001265606.1|NP_001265607.1|NP_975011.3	O75437	ZN254_HUMAN	zinc finger protein 254						negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)						all_cancers(12;0.086)|all_lung(12;0.00528)|Lung NSC(12;0.00731)|all_epithelial(12;0.0186)				CTAGAAATGGTGAGAATGCCA	0.617																																					.		Atlas-SNP	.											.	ZNF254	88	.	0			c.30+2T>C						.						72	70	70					19																	24270141		2203	4300	6503	SO:0001630	splice_region_variant	9534	exon1			AAATGGTGAGAAT	AF054180	CCDS32983.1, CCDS62622.1, CCDS62623.1, CCDS74323.1, CCDS74324.1	19p13	2013-01-08				ENSG00000213096		"Zinc fingers, C2H2-type", "-"	13047	protein-coding gene	gene with protein product		604768	"zinc finger protein 539"	ZNF91L, ZNF539		9653160	Standard	NM_001278661		Approved	HD-ZNF1, BMZF-5	uc002nru.3	O75437		ENST00000357002.4:c.30+2T>C	chr19.hg19:g.24270141T>C		98.0	0.0		94.0	7.0	NM_203282	A4QPC0|Q86XL7	Splice_Site	SNP	ENST00000357002.4	hg19	CCDS32983.1	.	.	.	.	.	.	.	.	.	.	t	2.852	-0.238097	0.05944	.	.	ENSG00000213096	ENST00000357002;ENST00000392281;ENST00000339642	.	.	.	0.225	0.225	0.15325	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999992	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	-1	.	.	.	+	.	.	ZNF254	24061981	0.023000	0.18921	0.013000	0.15412	0.013000	0.08279	0.304000	0.19228	0.257000	0.21650	0.254000	0.18369	.	.	.		0.617	ZNF254-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466453.1	NM_004876	Intron	C	24270141	T	C	24270141	5	2	319	1	0	0	0	0	0	0	1	0	17813	1710	59	2	34	2	ZNF254	19	24270141	Splice_Site	SNP	T	TCGA-LG-A9QD-01A-11D-A382-10	5981620	24270141	34858842	94	44994										
C19orf2	8725	hgsc.bcm.edu	37	chr19	30505901	30505901	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	attccagaacgaaaggaagtTctgttggaagcatctgaaga	11	6	2	3			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr19:30505901T>G	ENST00000542441.2	+	11	1830	c.1533T>G	c.(1531-1533)gtT>gtG	p.V511V	URI1_ENST00000392271.1_Silent_p.V435V|URI1_ENST00000360605.4_Intron|URI1_ENST00000312051.6_Silent_p.V471V			O94763	RMP_HUMAN	URI1, prefoldin-like chaperone	511					cellular response to growth factor stimulus (GO:0071363)|cellular response to steroid hormone stimulus (GO:0071383)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of phosphatase activity (GO:0010923)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein folding (GO:0006457)|regulation of cell growth (GO:0001558)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to virus (GO:0009615)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, core complex (GO:0005665)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|prefoldin complex (GO:0016272)	chromatin binding (GO:0003682)|protein phosphatase inhibitor activity (GO:0004864)|RNA polymerase II transcription corepressor activity (GO:0001106)										GAAAGGAAGTTCTGTTGGAAG	0.433																																					p.V511V		Atlas-SNP	.											.	.	.	.	0			c.T1533G						.						119	119	119					19																	30505901		2203	4300	6503	SO:0001819	synonymous_variant	8725	exon11			GGAAGTTCTGTTG	AF091095	CCDS12420.1, CCDS58658.1	19q12	2012-04-17	2011-11-21	2011-11-21	ENSG00000105176	ENSG00000105176		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	13236	protein-coding gene	gene with protein product	"unconventional prefoldin RPB5 interactor", "RPB5-mediating protein", "protein phosphatase 1, regulatory subunit 19"	603494	"chromosome 19 open reading frame 2"	C19orf2		9878255, 9819440	Standard	NM_003796		Approved	RMP, NNX3, FLJ10575, URI, PPP1R19	uc002nsr.3	O94763		ENST00000542441.2:c.1533T>G	chr19.hg19:g.30505901T>G		193.0	0.0		145.0	38.0	NM_003796	A8K805|H7BY42|Q8TC23|Q9UNU3	Silent	SNP	ENST00000542441.2	hg19	CCDS12420.1																																																																																			.	.		0.433	URI1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439756.1	NM_134447		G	30505901	T	G	30505901	2	3	319	1	0	0	0	0	0	0	0	1	1913	1770	62	5		5	C19orf2	19	30505901	Silent	SNP	T	TCGA-LG-A9QD-01A-11D-A382-10	6235760	30505901	28623082	95	44995										
ZNF536	9745	hgsc.bcm.edu	37	chr19	30936438	30936438	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	cccgtgtccacaagcgggacCgcaagggcgaggaggatggg	18	11	0	0			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr19:30936438C>A	ENST00000355537.3	+	2	2116	c.1969C>A	c.(1969-1971)Cgc>Agc	p.R657S		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	657					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					CAAGCGGGACCGCAAGGGCGA	0.687																																					p.R657S		Atlas-SNP	.											.	ZNF536	424	.	0			c.C1969A						.						54	61	59					19																	30936438		2203	4300	6503	SO:0001583	missense	9745	exon2			CGGGACCGCAAGG		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"Zinc fingers, C2H2-type"	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.1969C>A	chr19.hg19:g.30936438C>A	ENSP00000347730:p.Arg657Ser	146.0	0.0		122.0	40.0	NM_014717	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	hg19	CCDS32984.1	.	.	.	.	.	.	.	.	.	.	C	14.12	2.441497	0.43326	.	.	ENSG00000198597	ENST00000355537	T	0.10573	2.86	5.42	4.31	0.51392	Zinc finger, C2H2 (1);	0.053940	0.64402	D	0.000003	T	0.16300	0.0392	N	0.24115	0.695	0.45822	D	0.998695	D;D	0.61697	0.99;0.99	P;P	0.59357	0.856;0.856	T	0.01212	-1.1417	10	0.87932	D	0	-41.0082	12.9214	0.58234	0.2828:0.7172:0.0:0.0	.	657;657	A7E228;O15090	.;ZN536_HUMAN	S	657	ENSP00000347730:R657S	ENSP00000347730:R657S	R	+	1	0	ZNF536	35628278	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	2.426000	0.44731	2.509000	0.84616	0.655000	0.94253	CGC	.	.		0.687	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		A	30936438	C	A	30936438	3	1	319	1	0	0	0	0	1	0	0	0	17989	652	23	1	1971	1	ZNF536	19	30936438	Missense_Mutation	SNP	C	TCGA-LG-A9QD-01A-11D-A382-10	430537	30936438	28192545	96	44996										
TSHZ3	57616	hgsc.bcm.edu	37	chr19	31770240	31770240	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	cagctgctgctgctgctactGctgctgctgctgctgccgtt	12	14	0	0			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr19:31770240G>A	ENST00000240587.4	-	2	786	c.459C>T	c.(457-459)agC>agT	p.S153S		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	153	Ser-rich.				in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					tgctgctactgctgctgctgc	0.612																																					p.S153S		Atlas-SNP	.											.	TSHZ3	549	.	0			c.C459T						.						39	44	42					19																	31770240		2183	4296	6479	SO:0001819	synonymous_variant	57616	exon2			GCTACTGCTGCTG	AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	30700	protein-coding gene	gene with protein product	"teashirt 3"	614119	"zinc finger protein 537", "teashirt family zinc finger 3"	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.459C>T	chr19.hg19:g.31770240G>A		153.0	0.0		148.0	6.0	NM_020856	Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	hg19	CCDS12421.2																																																																																			.	.		0.612	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856		A	31770240	G	A	31770240	2	1	319	1	0	0	0	0	0	0	0	1	16640	1310	46	3		3	TSHZ3	19	31770240	Silent	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10	833802	31770240	27358743	97	44997										
NUDT19	390916	hgsc.bcm.edu	37	chr19	33200280	33200280	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	tcttgttaactgctgatgggAtggtccatcttttaccaggt	10	8	2	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr19:33200280A>G	ENST00000397061.3	+	2	904	c.904A>G	c.(904-906)Atg>Gtg	p.M302V		NM_001105570.1	NP_001099040.1	A8MXV4	NUD19_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 19	302						mitochondrion (GO:0005739)|peroxisome (GO:0005777)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)			endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	8	Esophageal squamous(110;0.137)					TGCTGATGGGATGGTCCATCT	0.468																																					p.M302V		Atlas-SNP	.											.	NUDT19	15	.	0			c.A904G						.						139	126	130					19																	33200280		1965	4146	6111	SO:0001583	missense	390916	exon2			GATGGGATGGTCC		CCDS42543.1	19q13.11	2011-11-16			ENSG00000213965	ENSG00000213965		"Nudix motif containing"	32036	protein-coding gene	gene with protein product							Standard	NM_001105570		Approved	RP2	uc010edf.3	A8MXV4		ENST00000397061.3:c.904A>G	chr19.hg19:g.33200280A>G	ENSP00000380251:p.Met302Val	62.0	0.0		56.0	20.0	NM_001105570		Missense_Mutation	SNP	ENST00000397061.3	hg19	CCDS42543.1	.	.	.	.	.	.	.	.	.	.	A	2.187	-0.386224	0.04966	.	.	ENSG00000213965	ENST00000397061	T	0.39592	1.07	4.77	-3.36	0.04913	.	1.353990	0.05265	U	0.516445	T	0.25344	0.0616	L	0.36672	1.1	0.09310	N	1	B	0.16802	0.019	B	0.11329	0.006	T	0.12553	-1.0543	10	0.16420	T	0.52	-28.0466	1.0964	0.01674	0.3281:0.2809:0.2545:0.1365	.	302	A8MXV4	NUD19_HUMAN	V	302	ENSP00000380251:M302V	ENSP00000380251:M302V	M	+	1	0	NUDT19	37892120	0.000000	0.05858	0.000000	0.03702	0.056000	0.15407	-2.281000	0.01157	-1.162000	0.02797	0.482000	0.46254	ATG	.	.		0.468	NUDT19-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000450338.3	XM_372723		G	33200280	A	G	33200280	3	3	319	1	0	0	0	0	1	0	0	0	10745	333	12	2	910	2	NUDT19	19	33200280	Missense_Mutation	SNP	A	TCGA-LG-A9QD-01A-11D-A382-10	1430040	33200280	25928703	98	44998										
ATP4A	495	hgsc.bcm.edu	37	chr19	36042385	36042385	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	ggaaggcagagagacggcgcGtcttgcggatgaggacatcg	18	8	1	3			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr19:36042385G>T	ENST00000262623.3	-	19	2877	c.2849C>A	c.(2848-2850)aCg>aAg	p.T950K		NM_000704.2	NP_000695.2	P20648	ATP4A_HUMAN	ATPase, H+/K+ exchanging, alpha polypeptide	950					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|ion transmembrane transport (GO:0034220)|pH reduction (GO:0045851)|regulation of proton transport (GO:0010155)|response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|magnesium ion binding (GO:0000287)	p.T950K(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(26)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	53	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)	GAGACGGCGCGTCTTGCGGAT	0.597																																					p.T950K		Atlas-SNP	.											ATP4A,NS,carcinoma,0,1	ATP4A	123	.	1	Substitution - Missense(1)	lung(1)	c.C2849A						.						114	84	94					19																	36042385		2203	4300	6503	SO:0001583	missense	495	exon19			CGGCGCGTCTTGC		CCDS12467.1	19q13.1	2010-04-20			ENSG00000105675	ENSG00000105675	3.6.3.10	"ATPases / P-type"	819	protein-coding gene	gene with protein product	"gastric H,K-ATPase alpha subunit", "H(+)-K(+)-ATPase alpha subunit", "proton pump"	137216				1330887	Standard	NM_000704		Approved	ATP6A	uc002oal.1	P20648	OTTHUMG00000048106	ENST00000262623.3:c.2849C>A	chr19.hg19:g.36042385G>T	ENSP00000262623:p.Thr950Lys	102.0	0.0		69.0	5.0	NM_000704	O00738	Missense_Mutation	SNP	ENST00000262623.3	hg19	CCDS12467.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.207834	0.79240	.	.	ENSG00000105675	ENST00000262623	D	0.96073	-3.9	5.02	5.02	0.67125	ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type,  transmembrane domain (1);	0.000000	0.64402	D	0.000002	D	0.98327	0.9445	H	0.95004	3.61	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.99257	1.0889	10	0.87932	D	0	.	15.8627	0.79038	0.0:0.0:1.0:0.0	.	950	P20648	ATP4A_HUMAN	K	950	ENSP00000262623:T950K	ENSP00000262623:T950K	T	-	2	0	ATP4A	40734225	1.000000	0.71417	0.987000	0.45799	0.494000	0.33585	9.647000	0.98478	2.614000	0.88457	0.297000	0.19635	ACG	.	.		0.597	ATP4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109470.2	NM_000704		T	36042385	G	T	36042385	3	4	319	1	0	0	0	0	1	0	0	0	1145	1145	40	1	274	1	ATP4A	19	36042385	Missense_Mutation	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10	2842105	36042385	23086598	99	44999										
SLC23A2	9962	hgsc.bcm.edu	37	chr20	4842648	4842648	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	aaggacgagcccaaagaagaTcgaaaatccaagcacaaaga	9	9	0	3			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr20:4842648T>G	ENST00000379333.1	-	15	1962	c.1570A>C	c.(1570-1572)Atc>Ctc	p.I524L	SLC23A2_ENST00000338244.1_Missense_Mutation_p.I524L|SLC23A2_ENST00000424750.2_Missense_Mutation_p.I410L	NM_203327.1	NP_976072.1	Q9UGH3	S23A2_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 2	524					L-ascorbic acid metabolic process (GO:0019852)|L-ascorbic acid transport (GO:0015882)|molecular hydrogen transport (GO:0015993)|nucleobase transport (GO:0015851)|nucleobase-containing compound metabolic process (GO:0006139)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|transepithelial L-ascorbic acid transport (GO:0070904)|vitamin metabolic process (GO:0006766)|vitamin transmembrane transport (GO:0035461)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-ascorbate:sodium symporter activity (GO:0008520)|L-ascorbic acid transporter activity (GO:0015229)|nucleobase transmembrane transporter activity (GO:0015205)|sodium-dependent L-ascorbate transmembrane transporter activity (GO:0070890)|sodium-dependent multivitamin transmembrane transporter activity (GO:0008523)			endometrium(1)|kidney(3)|large_intestine(9)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						CCAAAGAAGATCGAAAATCCA	0.473																																					p.I524L		Atlas-SNP	.											.	SLC23A2	62	.	0			c.A1570C						.						101	101	101					20																	4842648		2203	4300	6503	SO:0001583	missense	9962	exon15			AGAAGATCGAAAA	AF058319	CCDS13085.1	20p13	2013-07-18	2013-07-18	2003-03-21	ENSG00000089057	ENSG00000089057		"Solute carriers"	10973	protein-coding gene	gene with protein product		603791	"solute carrier family 23 (nucleobase transporters), member 1"	SLC23A1		9804989, 10331392	Standard	NM_005116		Approved	SVCT2, KIAA0238, YSPL2	uc002wlh.1	Q9UGH3	OTTHUMG00000031793	ENST00000379333.1:c.1570A>C	chr20.hg19:g.4842648T>G	ENSP00000368637:p.Ile524Leu	210.0	0.0		169.0	38.0	NM_203327	B4DJZ1|Q8WWR4|Q92512|Q96D54|Q9UNU1|Q9UP85	Missense_Mutation	SNP	ENST00000379333.1	hg19	CCDS13085.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	8.114|8.114	0.779391|0.779391	0.16120|0.16120	.|.	.|.	ENSG00000089057|ENSG00000089057	ENST00000423430|ENST00000379333;ENST00000338244;ENST00000424750	.|T;T;T	.|0.12984	.|2.63;2.63;2.63	5.35|5.35	4.25|4.25	0.50352|0.50352	.|.	.|0.046508	.|0.85682	.|N	.|0.000000	T|T	0.06508|0.06508	0.0167|0.0167	N|N	0.04820|0.04820	-0.15|-0.15	0.52099|0.52099	D|D	0.999948|0.999948	.|B;B	.|0.25351	.|0.124;0.002	.|B;B	.|0.25614	.|0.062;0.01	T|T	0.36648|0.36648	-0.9739|-0.9739	5|10	.|0.18710	.|T	.|0.47	-21.4032|-21.4032	10.1054|10.1054	0.42530|0.42530	0.0:0.08:0.0:0.92|0.0:0.08:0.0:0.92	.|.	.|410;524	.|B4DJZ1;Q9UGH3	.|.;S23A2_HUMAN	A|L	280|524;524;410	.|ENSP00000368637:I524L;ENSP00000344322:I524L;ENSP00000406601:I410L	.|ENSP00000344322:I524L	D|I	-|-	2|1	0|0	SLC23A2|SLC23A2	4790648|4790648	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.986000|0.986000	0.74619|0.74619	7.698000|7.698000	0.84413|0.84413	0.975000|0.975000	0.38392|0.38392	0.379000|0.379000	0.24179|0.24179	GAT|ATC	.	.		0.473	SLC23A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077832.1			G	4842648	T	G	4842648	3	3	319	1	0	0	0	0	1	0	0	0	14478	1435	50	5	394	5	SLC23A2	20	4842648	Missense_Mutation	SNP	T	TCGA-LG-A9QD-01A-11D-A382-10		4842648	58182872	100	45000										
BPI	671	hgsc.bcm.edu	37	chr20	36954702	36954702	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	cccaacatgaagatacagatCcatgtctcagcctccacccc	5	17	1	3			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr20:36954702C>A	ENST00000262865.4	+	10	1130	c.1041C>A	c.(1039-1041)atC>atA	p.I347I	BPI_ENST00000489102.1_3'UTR|CTD-2308N23.2_ENST00000437016.1_RNA	NM_001725.2	NP_001716.2	P17213	BPI_HUMAN	bactericidal/permeability-increasing protein	347					defense response to bacterium (GO:0042742)|immune response (GO:0006955)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of macrophage activation (GO:0043031)|negative regulation of tumor necrosis factor production (GO:0032720)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	lipopolysaccharide binding (GO:0001530)			kidney(1)|large_intestine(6)|lung(15)|ovary(4)|prostate(2)|stomach(1)|urinary_tract(1)	30		Myeloproliferative disorder(115;0.00878)				AGATACAGATCCATGTCTCAG	0.542																																					p.I347I		Atlas-SNP	.											BPI,colon,carcinoma,0,1	BPI	67	.	0			c.C1041A						.						90	73	79					20																	36954702		2203	4300	6503	SO:0001819	synonymous_variant	671	exon10			ACAGATCCATGTC	J04739	CCDS13303.1	20q11.23	2011-08-16			ENSG00000101425	ENSG00000101425		"BPI fold containing"	1095	protein-coding gene	gene with protein product	"BPI fold containing family D, member 1"	109195				8432532	Standard	NM_001725		Approved	BPIFD1	uc002xia.2	P17213	OTTHUMG00000032441	ENST00000262865.4:c.1041C>A	chr20.hg19:g.36954702C>A		88.0	1.0		53.0	20.0	NM_001725	B2RCY2|Q1ZZU8|Q5JRW0|Q8IW58|Q9BYZ9|Q9H1L2|Q9H1M8|Q9H203|Q9UCT4|Q9UD65	Silent	SNP	ENST00000262865.4	hg19	CCDS13303.1	.	.	.	.	.	.	.	.	.	.	C	3.822	-0.037596	0.07497	.	.	ENSG00000101425	ENST00000417318	.	.	.	4.52	-4.15	0.03881	.	.	.	.	.	T	0.19846	0.0477	.	.	.	0.20764	N	0.99986	.	.	.	.	.	.	T	0.27502	-1.0072	4	.	.	.	-7.9026	3.5502	0.07843	0.1146:0.2877:0.4408:0.1569	.	.	.	.	Y	173	.	.	S	+	2	0	BPI	36388116	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.164000	0.03135	-0.859000	0.04105	-0.312000	0.09012	TCC	.	.		0.542	BPI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079157.2	NM_001725		A	36954702	C	A	36954702	2	1	319	1	0	0	0	0	0	0	0	1	1492	845	30	3		3	BPI	20	36954702	Silent	SNP	C	TCGA-LG-A9QD-01A-11D-A382-10	32112054	36954702	26070818	101	45001										
PLTP	5360	hgsc.bcm.edu	37	chr20	44531117	44531117	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	ctggacctcaggctggtctgGtgggaccagggcaatggtga	17	9	2	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr20:44531117G>T	ENST00000477313.1	-	10	1663	c.1069C>A	c.(1069-1071)Cca>Aca	p.P357T	PLTP_ENST00000420868.2_Missense_Mutation_p.P262T|PLTP_ENST00000372420.1_Missense_Mutation_p.P269T|PLTP_ENST00000354050.4_Missense_Mutation_p.P305T|PLTP_ENST00000542937.1_Missense_Mutation_p.P377T|PLTP_ENST00000372431.3_Missense_Mutation_p.P357T			P55058	PLTP_HUMAN	phospholipid transfer protein	357					lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|sperm motility (GO:0030317)|vitamin E biosynthetic process (GO:0010189)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	lipid binding (GO:0008289)			endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)	21		Myeloproliferative disorder(115;0.0122)				GGCTGGTCTGGTGGGACCAGG	0.632																																					p.P357T		Atlas-SNP	.											.	PLTP	49	.	0			c.C1069A						.						79	78	78					20																	44531117		2203	4300	6503	SO:0001583	missense	5360	exon11			GGTCTGGTGGGAC	L26232	CCDS13386.1, CCDS13387.1, CCDS56196.1, CCDS56197.1	20q13.12	2011-08-16			ENSG00000100979	ENSG00000100979		"BPI fold containing"	9093	protein-coding gene	gene with protein product	"BPI fold containing family E"	172425					Standard	NM_006227		Approved	BPIFE	uc002xqn.2	P55058	OTTHUMG00000033047	ENST00000477313.1:c.1069C>A	chr20.hg19:g.44531117G>T	ENSP00000417138:p.Pro357Thr	145.0	0.0		104.0	26.0	NM_006227	A8K006|B4DDD5|B4DRB4|E1P5N8|E7EV16|Q8WTT1|Q9BR07|Q9BSH8	Missense_Mutation	SNP	ENST00000477313.1	hg19	CCDS13386.1	.	.	.	.	.	.	.	.	.	.	G	11.99	1.803397	0.31869	.	.	ENSG00000100979	ENST00000372420;ENST00000372431;ENST00000354050;ENST00000477313;ENST00000542937;ENST00000420868	T;T;T;T;T;T	0.21932	1.98;1.98;1.98;1.98;1.98;1.98	5.28	2.15	0.27550	Lipid-binding serum glycoprotein, C-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	0.499266	0.23549	N	0.046984	T	0.13798	0.0334	N	0.22421	0.69	0.09310	N	1	P;P;P;P;P;P;P	0.40534	0.72;0.72;0.58;0.72;0.673;0.72;0.72	B;B;B;B;B;B;B	0.43867	0.342;0.342;0.363;0.342;0.178;0.342;0.434	T	0.09707	-1.0662	10	0.72032	D	0.01	-24.1366	2.5856	0.04829	0.2237:0.1228:0.5274:0.1261	.	262;262;269;357;305;357;377	E7EV16;B4DRB4;B4DDD5;Q53H91;P55058-2;P55058;B3KUE5	.;.;.;.;.;PLTP_HUMAN;.	T	269;357;305;357;377;262	ENSP00000361497:P269T;ENSP00000361508:P357T;ENSP00000335290:P305T;ENSP00000417138:P357T;ENSP00000440296:P377T;ENSP00000411671:P262T	ENSP00000335290:P305T	P	-	1	0	PLTP	43964524	0.026000	0.19158	0.006000	0.13384	0.699000	0.40488	0.629000	0.24538	0.752000	0.32923	0.655000	0.94253	CCA	.	.		0.632	PLTP-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354633.1	NM_006227		T	44531117	G	T	44531117	3	4	319	1	0	0	0	0	1	0	0	0	12123	1261	44	3	436	3	PLTP	20	44531117	Missense_Mutation	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10	7576415	44531117	18494403	102	45002										
DIDO1	11083	hgsc.bcm.edu	37	chr20	61525146	61525146	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	acatcctgtctggcttccacCatgtgggtgctgtctgggcg	13	12	2	0			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr20:61525146C>T	ENST00000266070.4	-	12	3298	c.2973G>A	c.(2971-2973)atG>atA	p.M991I	DIDO1_ENST00000395343.1_Missense_Mutation_p.M991I|DIDO1_ENST00000395335.2_Missense_Mutation_p.M991I|DIDO1_ENST00000395340.1_Missense_Mutation_p.M991I	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	991					apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					TGGCTTCCACCATGTGGGTGC	0.602																																					p.M991I	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											.	DIDO1	321	.	0			c.G2973A						.						108	92	98					20																	61525146		2203	4300	6503	SO:0001583	missense	11083	exon12			TTCCACCATGTGG	AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"Zinc fingers, PHD-type"	2680	protein-coding gene	gene with protein product		604140	"chromosome 20 open reading frame 158", "death associated transcription factor 1"	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.2973G>A	chr20.hg19:g.61525146C>T	ENSP00000266070:p.Met991Ile	84.0	0.0		72.0	30.0	NM_080797	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Missense_Mutation	SNP	ENST00000266070.4	hg19	CCDS33506.1	.	.	.	.	.	.	.	.	.	.	C	10.64	1.408173	0.25378	.	.	ENSG00000101191	ENST00000266070;ENST00000395343;ENST00000395340;ENST00000395335	T;T;T;T	0.11063	3.2;3.2;2.81;2.81	5.67	-11.3	0.00108	.	7.102440	0.01069	N	0.004784	T	0.04363	0.0120	N	0.08118	0	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.21109	-1.0255	10	0.26408	T	0.33	0.4447	7.0578	0.25109	0.3842:0.228:0.0:0.3877	.	991;991	Q9BTC0-1;Q9BTC0	.;DIDO1_HUMAN	I	991	ENSP00000266070:M991I;ENSP00000378752:M991I;ENSP00000378749:M991I;ENSP00000378744:M991I	ENSP00000266070:M991I	M	-	3	0	DIDO1	60995591	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.473000	0.00988	-2.432000	0.00556	-0.961000	0.02630	ATG	.	.		0.602	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796		T	61525146	C	T	61525146	3	4	319	1	0	0	0	0	1	0	0	0	4524	594	21	3	3798	3	DIDO1	20	61525146	Missense_Mutation	SNP	C	TCGA-LG-A9QD-01A-11D-A382-10	16994029	61525146	1500374	103	45003										
KRTAP6-1	337966	hgsc.bcm.edu	37	chr21	31986189	31986189	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	cacagaacccatagccagggGtgccatagtagtttccgtag	11	11	0	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr21:31986189G>A	ENST00000329122.2	-	1	60	c.35C>T	c.(34-36)aCc>aTc	p.T12I	KRTAP20-1_ENST00000334664.2_5'Flank	NM_181602.1	NP_853633.1	Q3LI64	KRA61_HUMAN	keratin associated protein 6-1	12						cytosol (GO:0005829)|intermediate filament (GO:0005882)				breast(2)|endometrium(1)|lung(7)	10						ATAGCCAGGGGTGCCATAGTA	0.562																																					p.T12I		Atlas-SNP	.											.	KRTAP6-1	21	.	0			c.C35T						.						203	195	198					21																	31986189		2203	4300	6503	SO:0001583	missense	337966	exon1			CCAGGGGTGCCAT	AP001708	CCDS13602.1	21q22.1	2006-03-13			ENSG00000184724	ENSG00000184724		"Keratin associated proteins"	18931	protein-coding gene	gene with protein product						12359730	Standard	NM_181602		Approved	KAP6.1, C21orf103	uc002yop.3	Q3LI64	OTTHUMG00000057788	ENST00000329122.2:c.35C>T	chr21.hg19:g.31986189G>A	ENSP00000332690:p.Thr12Ile	127.0	0.0		118.0	34.0	NM_181602		Missense_Mutation	SNP	ENST00000329122.2	hg19	CCDS13602.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	3.172|3.172	-0.169742|-0.169742	0.06461|0.06461	.|.	.|.	ENSG00000184724|ENSG00000184724	ENST00000399871|ENST00000329122	.|T	.|0.18338	.|2.22	5.03|5.03	0.972|0.972	0.19704|0.19704	.|.	.|0.813174	.|0.10260	.|U	.|0.696055	.|T	.|0.11922	.|0.0290	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|B	.|0.19817	.|0.039	.|B	.|0.19391	.|0.025	.|T	.|0.33599	.|-0.9862	.|9	.|0.87932	.|D	.|0	.|.	3.3924|3.3924	0.07294|0.07294	0.1369:0.5621:0.1376:0.1633|0.1369:0.5621:0.1376:0.1633	.|.	.|12	.|Q3LI64	.|KRA61_HUMAN	.|I	-1|12	.|ENSP00000332690:T12I	.|ENSP00000332690:T12I	.|T	-|-	.|2	.|0	KRTAP6-1|KRTAP6-1	30908060|30908060	0.012000|0.012000	0.17670|0.17670	0.016000|0.016000	0.15963|0.15963	0.319000|0.319000	0.28217|0.28217	0.082000|0.082000	0.14847|0.14847	0.411000|0.411000	0.25702|0.25702	-0.159000|-0.159000	0.13428|0.13428	.|ACC	.	.		0.562	KRTAP6-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128240.2	NM_181602		A	31986189	G	A	31986189	3	1	319	1	0	0	0	0	1	0	0	0	8578	1261	44	3	184	3	KRTAP6-1	21	31986189	Missense_Mutation	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10		31986189	16143706	104	45004										
KCNJ6	3763	hgsc.bcm.edu	37	chr21	38997477	38997477	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	ggcactaaactttggattcaTtctccaggtttgccacatca	7	11	3	0			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr21:38997477T>C	ENST00000609713.1	-	4	1845	c.1256A>G	c.(1255-1257)aAt>aGt	p.N419S	KCNJ6_ENST00000288309.6_Missense_Mutation_p.N419S	NM_002240.3	NP_002231.1	P48051	KCNJ6_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 6	419					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	G-protein activated inward rectifier potassium channel activity (GO:0015467)|inward rectifier potassium channel activity (GO:0005242)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	22					Halothane(DB01159)	TTTGGATTCATTCTCCAGGTT	0.443																																					p.N419S	Pancreas(48;379 1118 2936 19024 28214)	Atlas-SNP	.											.	KCNJ6	58	.	0			c.A1256G						.						207	197	200					21																	38997477		1892	4120	6012	SO:0001583	missense	3763	exon4			GATTCATTCTCCA	U24660	CCDS42927.1	21q22.1	2011-07-05			ENSG00000157542	ENSG00000157542		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6267	protein-coding gene	gene with protein product		600877		KCNJ7		7796919, 16382105	Standard	NM_002240		Approved	Kir3.2, GIRK2, KATP2, BIR1, hiGIRK2	uc002ywo.3	P48051	OTTHUMG00000086667	ENST00000609713.1:c.1256A>G	chr21.hg19:g.38997477T>C	ENSP00000477437:p.Asn419Ser	68.0	0.0		46.0	11.0	NM_002240	Q3MJ74|Q53WW6	Missense_Mutation	SNP	ENST00000609713.1	hg19	CCDS42927.1	.	.	.	.	.	.	.	.	.	.	T	4.367	0.067684	0.08436	.	.	ENSG00000157542	ENST00000400482;ENST00000288309	D;D	0.86956	-2.19;-2.19	5.77	3.44	0.39384	.	0.143577	0.64402	N	0.000007	T	0.64886	0.2639	N	0.02539	-0.55	0.38575	D	0.950038	B	0.06786	0.001	B	0.04013	0.001	T	0.54866	-0.8229	10	0.07990	T	0.79	.	8.1399	0.31078	0.0:0.2153:0.0:0.7847	.	419	P48051	IRK6_HUMAN	S	419	ENSP00000383330:N419S;ENSP00000288309:N419S	ENSP00000288309:N419S	N	-	2	0	KCNJ6	37919347	0.989000	0.36119	0.972000	0.41901	0.904000	0.53231	1.601000	0.36773	0.474000	0.27392	0.533000	0.62120	AAT	.	.		0.443	KCNJ6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194828.2	NM_002240		C	38997477	T	C	38997477	3	2	319	1	0	0	0	0	1	0	0	0	8064	1493	52	2	19	2	KCNJ6	21	38997477	Missense_Mutation	SNP	T	TCGA-LG-A9QD-01A-11D-A382-10	7011288	38997477	9132418	105	45005										
MYO18B	84700	hgsc.bcm.edu	37	chr22	26164310	26164310	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	caccaaccaaaaagactgtcCccttcaagaggggcgtgagg	11	12	1	3			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr22:26164310C>A	ENST00000407587.2	+	4	596	c.427C>A	c.(427-429)Ccc>Acc	p.P143T	MYO18B_ENST00000536101.1_Missense_Mutation_p.P143T|MYO18B_ENST00000335473.7_Missense_Mutation_p.P143T			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	143						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						AAAGACTGTCCCCTTCAAGAG	0.612																																					p.P143T		Atlas-SNP	.											.	MYO18B	322	.	0			c.C427A						.						35	40	38					22																	26164310		2032	4178	6210	SO:0001583	missense	84700	exon4			ACTGTCCCCTTCA	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.427C>A	chr22.hg19:g.26164310C>A	ENSP00000386096:p.Pro143Thr	231.0	0.0		172.0	47.0	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	hg19		.	.	.	.	.	.	.	.	.	.	C	14.08	2.428961	0.43122	.	.	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.93247	-3.16;-3.16;-3.19	4.9	3.81	0.43845	.	0.000000	0.36234	N	0.002707	D	0.95497	0.8537	M	0.65975	2.015	0.30538	N	0.766746	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.996;0.998;0.998	D	0.92534	0.6036	10	0.87932	D	0	.	11.7218	0.51688	0.0:0.8213:0.1787:0.0	.	143;143;143	Q8IUG5;F5GXR6;F5GYU7	MY18B_HUMAN;.;.	T	143	ENSP00000441229:P143T;ENSP00000334563:P143T;ENSP00000386096:P143T	ENSP00000334563:P143T	P	+	1	0	MYO18B	24494310	0.853000	0.29707	0.625000	0.29200	0.280000	0.26924	1.114000	0.31196	2.272000	0.75746	0.484000	0.47621	CCC	.	.		0.612	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		A	26164310	C	A	26164310	3	1	319	1	0	0	0	0	1	0	0	0	10075	623	22	3	437	3	MYO18B	22	26164310	Missense_Mutation	SNP	C	TCGA-LG-A9QD-01A-11D-A382-10		26164310	25140256	106	45006										
GGA1	26088	hgsc.bcm.edu	37	chr22	38012994	38012994	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	acaggagtgggaggcgatccAggccttgacggtgagaaggg	19	7	0	2			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr22:38012994A>T	ENST00000343632.4	+	3	580	c.194A>T	c.(193-195)cAg>cTg	p.Q65L	GGA1_ENST00000337437.4_Missense_Mutation_p.Q65L|GGA1_ENST00000414350.3_Missense_Mutation_p.Q65L|GGA1_ENST00000405147.3_Missense_Mutation_p.Q65L|GGA1_ENST00000381756.5_Missense_Mutation_p.Q65L|GGA1_ENST00000406772.1_De_novo_Start_OutOfFrame|GGA1_ENST00000325180.8_Missense_Mutation_p.Q65L	NM_001172687.1|NM_013365.4	NP_001166158.1|NP_037497.1	Q9UJY5	GGA1_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 1	65	VHS. {ECO:0000255|PROSITE- ProRule:PRU00218}.				intracellular protein transport (GO:0006886)|positive regulation of protein catabolic process (GO:0045732)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|urinary_tract(1)	10	Melanoma(58;0.0574)					GAGGCGATCCAGGCCTTGACG	0.642																																					p.Q65L		Atlas-SNP	.											.	GGA1	39	.	0			c.A194T						.						60	53	55					22																	38012994		2200	4297	6497	SO:0001583	missense	26088	exon3			CGATCCAGGCCTT	AF190862	CCDS13951.1, CCDS33643.1, CCDS54526.1	22q13.31	2010-02-12	2010-02-12		ENSG00000100083	ENSG00000100083			17842	protein-coding gene	gene with protein product		606004				10747088, 10747089, 16407204	Standard	NM_013365		Approved		uc003atc.3	Q9UJY5	OTTHUMG00000030985	ENST00000343632.4:c.194A>T	chr22.hg19:g.38012994A>T	ENSP00000341344:p.Gln65Leu	138.0	0.0		101.0	21.0	NM_001001560	A8K3D3|B0QYR7|Q5TG07|Q86YA9|Q8NCS6|Q9BW94|Q9UG00|Q9UGW0|Q9UGW1	Missense_Mutation	SNP	ENST00000343632.4	hg19	CCDS13951.1	.	.	.	.	.	.	.	.	.	.	A	33	5.203471	0.95033	.	.	ENSG00000100083	ENST00000414350;ENST00000343632;ENST00000381756;ENST00000405147;ENST00000325180;ENST00000337437;ENST00000449944	T;T;T;T;T;T;T	0.19669	2.13;2.13;2.13;2.13;2.13;2.13;2.13	5.43	5.43	0.79202	VHS subgroup (1);ENTH/VHS (2);VHS (2);	0.000000	0.85682	D	0.000000	T	0.36744	0.0978	L	0.56124	1.755	0.80722	D	1	D;D;B;D	0.89917	1.0;0.999;0.273;0.997	D;D;P;D	0.91635	0.999;0.995;0.457;0.996	T	0.18618	-1.0331	10	0.02654	T	1	-24.696	15.4889	0.75590	1.0:0.0:0.0:0.0	.	65;65;65;65	Q6IC75;Q86YA9;Q9UJY5;Q8NCS6	.;.;GGA1_HUMAN;.	L	65;65;65;65;65;65;57	ENSP00000414387:Q65L;ENSP00000341344:Q65L;ENSP00000371175:Q65L;ENSP00000384030:Q65L;ENSP00000321288:Q65L;ENSP00000338647:Q65L;ENSP00000390416:Q57L	ENSP00000321288:Q65L	Q	+	2	0	GGA1	36342940	1.000000	0.71417	0.996000	0.52242	0.961000	0.63080	9.070000	0.93974	2.062000	0.61559	0.528000	0.53228	CAG	.	.		0.642	GGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075873.3	NM_013365		T	38012994	A	T	38012994	3	4	319	1	0	0	0	0	1	0	0	0	6360	188	7	4	204	4	GGA1	22	38012994	Missense_Mutation	SNP	A	TCGA-LG-A9QD-01A-11D-A382-10	11848684	38012994	13291572	107	45007										
NCAPH2	29781	hgsc.bcm.edu	37	chr22	50961535	50961535	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	gagtggtgtccctttgcggaGctggtggctggccagccggc	18	11	0	0			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chr22:50961535G>T	ENST00000420993.2	+	19	1739	c.1617G>T	c.(1615-1617)gaG>gaT	p.E539D	CTA-384D8.36_ENST00000608319.1_RNA|NCAPH2_ENST00000299821.11_Missense_Mutation_p.E540D|NCAPH2_ENST00000395701.3_Missense_Mutation_p.E539D	NM_001185011.1|NM_152299.3	NP_001171940.1|NP_689512.2	Q6IBW4	CNDH2_HUMAN	non-SMC condensin II complex, subunit H2	539					chromosome condensation (GO:0030261)|mitotic cell cycle (GO:0000278)	chromosome (GO:0005694)|membrane (GO:0016020)|nucleoplasm (GO:0005654)				breast(1)|cervix(1)|endometrium(2)|kidney(3)|lung(10)|ovary(1)|prostate(2)|skin(3)|stomach(1)	24		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;0.212)		CCTTTGCGGAGCTGGTGGCTG	0.642																																					p.E540D		Atlas-SNP	.											.	NCAPH2	69	.	0			c.G1620T						.						58	45	49					22																	50961535		2202	4300	6502	SO:0001583	missense	29781	exon19			TGCGGAGCTGGTG	BC001937	CCDS14094.2, CCDS43038.1, CCDS54546.1	22q13.33	2008-02-04			ENSG00000025770	ENSG00000025770			25071	protein-coding gene	gene with protein product	"kleisin beta", "CAP-H2 subunit of the condensin II complex"	611230				10493829	Standard	NM_014551		Approved	384D8-2, hCAP-H2, CAP-H2	uc003blx.4	Q6IBW4	OTTHUMG00000150205	ENST00000420993.2:c.1617G>T	chr22.hg19:g.50961535G>T	ENSP00000410088:p.Glu539Asp	82.0	0.0		80.0	33.0	NM_001185011	B7WPH1|O43788|Q13391|Q96C14|Q96GJ0|Q9BQ71|Q9BUT3|Q9BVD1	Missense_Mutation	SNP	ENST00000420993.2	hg19	CCDS14094.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.95|11.95	1.791062|1.791062	0.31685|0.31685	.|.	.|.	ENSG00000025770|ENSG00000025770	ENST00000420993;ENST00000395701;ENST00000299821|ENST00000522304	.|.	.|.	.|.	4.79|4.79	-2.97|-2.97	0.05530|0.05530	.|.	0.979822|.	0.08392|.	N|.	0.952796|.	T|T	0.23965|0.23965	0.0580|0.0580	L|L	0.41824|0.41824	1.3|1.3	0.09310|0.09310	N|N	0.999991|0.999991	P;P;P|.	0.43938|.	0.787;0.787;0.822|.	B;B;B|.	0.40285|.	0.218;0.258;0.325|.	T|T	0.32955|0.32955	-0.9887|-0.9887	9|5	0.19147|.	T|.	0.46|.	-5.3658|-5.3658	0.6416|0.6416	0.00811|0.00811	0.2612:0.3148:0.2089:0.2151|0.2612:0.3148:0.2089:0.2151	.|.	540;517;539|.	Q6IBW4-4;Q6IBW4-2;Q6IBW4|.	.;.;CNDH2_HUMAN|.	D|I	539;539;540|75	.|.	ENSP00000299821:E540D|.	E|S	+|+	3|2	2|0	NCAPH2|NCAPH2	49308401|49308401	0.011000|0.011000	0.17503|0.17503	0.174000|0.174000	0.22961|0.22961	0.921000|0.921000	0.55340|0.55340	0.149000|0.149000	0.16243|0.16243	-0.054000|-0.054000	0.13266|0.13266	0.561000|0.561000	0.74099|0.74099	GAG|AGC	.	.		0.642	NCAPH2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317012.1	NM_152299		T	50961535	G	T	50961535	3	4	319	1	0	0	0	0	1	0	0	0	10219	962	34	3	1733	3	NCAPH2	22	50961535	Missense_Mutation	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10	12948541	50961535	343031	108	45008										
RBM10	8241	hgsc.bcm.edu	37	chrX	47028882	47028882	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	gactatgacgactcatctgaGgagcagagtgcggaggtgag	16	7	2	4			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chrX:47028882G>C	ENST00000377604.3	+	3	928	c.186G>C	c.(184-186)gaG>gaC	p.E62D	RBM10_ENST00000329236.7_Missense_Mutation_p.E62D|RBM10_ENST00000345781.6_Missense_Mutation_p.E62D	NM_001204467.1|NM_001204468.1|NM_005676.4	NP_001191396.1|NP_001191397.1|NP_005667.2	P98175	RBM10_HUMAN	RNA binding motif protein 10	62					3'-UTR-mediated mRNA stabilization (GO:0070935)|mRNA processing (GO:0006397)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	48						ACTCATCTGAGGAGCAGAGTG	0.647																																					p.E127D	Melanoma(171;120 2705 19495 39241)	Atlas-SNP	.											.	RBM10	117	.	0			c.G381C						.						63	41	49					X																	47028882		2203	4300	6503	SO:0001583	missense	8241	exon3			ATCTGAGGAGCAG	U35373	CCDS14274.1, CCDS56600.1, CCDS75969.1	Xp11.3	2014-06-09			ENSG00000182872	ENSG00000182872		"Zinc fingers, RAN-binding domain containing", "G patch domain containing", "RNA binding motif (RRM) containing"	9896	protein-coding gene	gene with protein product		300080				8590280, 8808293	Standard	NM_005676		Approved	DXS8237E, KIAA0122, GPATC9, ZRANB5, GPATCH9	uc004dhi.3	P98175	OTTHUMG00000021432	ENST00000377604.3:c.186G>C	chrX.hg19:g.47028882G>C	ENSP00000366829:p.Glu62Asp	68.0	0.0		41.0	26.0	NM_001204468	C4AM81|Q14136|Q5JRR2|Q9BTE4|Q9BTX0|Q9NTB1	Missense_Mutation	SNP	ENST00000377604.3	hg19	CCDS14274.1	.	.	.	.	.	.	.	.	.	.	G	11.58	1.680497	0.29872	.	.	ENSG00000182872	ENST00000377604;ENST00000329236;ENST00000345781	T;T;T	0.40476	1.03;2.15;2.39	4.65	-0.338	0.12651	.	0.260506	0.30714	N	0.009034	T	0.33206	0.0855	N	0.11560	0.145	0.30912	N	0.728979	B;D;D;B;D	0.61697	0.004;0.983;0.99;0.008;0.984	B;P;P;B;D	0.68192	0.009;0.621;0.789;0.009;0.956	T	0.39333	-0.9619	10	0.11485	T	0.65	-19.8756	7.7473	0.28877	0.5277:0.0:0.4723:0.0	.	62;127;62;62;62	P98175-3;Q7Z3D7;P98175-2;P98175-4;P98175	.;.;.;.;RBM10_HUMAN	D	62	ENSP00000366829:E62D;ENSP00000328848:E62D;ENSP00000329659:E62D	ENSP00000328848:E62D	E	+	3	2	RBM10	46913826	0.849000	0.29639	0.759000	0.31340	0.912000	0.54170	-0.155000	0.10115	-0.497000	0.06641	-0.322000	0.08575	GAG	.	.		0.647	RBM10-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056381.1	NM_005676		C	47028882	G	C	47028882	3	2	319	1	0	0	0	0	1	0	0	0	13126	991	35	4	192	4	RBM10	23	47028882	Missense_Mutation	SNP	G	TCGA-LG-A9QD-01A-11D-A382-10		47028882	108241678	109	45009										
DLG3	1741	hgsc.bcm.edu	37	chrX	69669569	69669569	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	ctgtgtgctgcgggtgaatgAggtggacgtgtcggaggtgg	21	5	0	2			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chrX:69669569A>C	ENST00000374360.3	+	4	796	c.563A>C	c.(562-564)gAg>gCg	p.E188A	DLG3_ENST00000194900.4_Missense_Mutation_p.E206A|DLG3_ENST00000374355.3_5'Flank|RNU4-81P_ENST00000363561.1_RNA	NM_021120.3	NP_066943.2	Q92796	DLG3_HUMAN	discs, large homolog 3 (Drosophila)	188	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				axon guidance (GO:0007411)|establishment of planar polarity (GO:0001736)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|negative regulation of cell proliferation (GO:0008285)|negative regulation of phosphatase activity (GO:0010923)|synaptic transmission (GO:0007268)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|extracellular space (GO:0005615)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)|tight junction (GO:0005923)	phosphatase binding (GO:0019902)			endometrium(4)|kidney(1)|large_intestine(10)|lung(5)|pancreas(1)|urinary_tract(1)	22	Renal(35;0.156)					CGGGTGAATGAGGTGGACGTG	0.662																																					p.E188A		Atlas-SNP	.											.	DLG3	100	.	0			c.A563C						.						73	48	56					X																	69669569		2203	4300	6503	SO:0001583	missense	1741	exon4			TGAATGAGGTGGA	U49089	CCDS14403.1, CCDS43967.1, CCDS55439.1	Xq13.1	2014-06-12	2008-12-15		ENSG00000082458	ENSG00000082458			2902	protein-coding gene	gene with protein product	"neuroendocrine-dlg", "protein phosphatase 1, regulatory subunit 82"	300189	"discs, large homolog 3 (neuroendocrine-dlg, Drosophila)"			9598320	Standard	NM_021120		Approved	NE-Dlg, SAP102, SAP-102, NEDLG, KIAA1232, MRX90, PPP1R82	uc004dyi.2	Q92796	OTTHUMG00000021778	ENST00000374360.3:c.563A>C	chrX.hg19:g.69669569A>C	ENSP00000363480:p.Glu188Ala	50.0	0.0		33.0	17.0	NM_021120	B4E0H1|D3DVU5|Q5JUW6|Q5JUW7|Q9ULI8	Missense_Mutation	SNP	ENST00000374360.3	hg19	CCDS14403.1	.	.	.	.	.	.	.	.	.	.	A	18.70	3.680362	0.68042	.	.	ENSG00000082458	ENST00000194900;ENST00000374360	T;T	0.27256	2.28;1.68	4.48	4.48	0.54585	PDZ/DHR/GLGF (4);	0.135579	0.47852	D	0.000204	T	0.28699	0.0711	L	0.31578	0.945	0.80722	D	1	P	0.37122	0.583	P	0.49332	0.607	T	0.05338	-1.0891	9	.	.	.	.	11.7928	0.52080	1.0:0.0:0.0:0.0	.	188	Q92796	DLG3_HUMAN	A	206;188	ENSP00000194900:E206A;ENSP00000363480:E188A	.	E	+	2	0	DLG3	69586294	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.618000	0.90932	1.658000	0.50742	0.356000	0.21956	GAG	.	.		0.662	DLG3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057074.2	NM_021120		C	69669569	A	C	69669569	3	2	319	1	0	0	0	0	1	0	0	0	4558	304	11	5	577	5	DLG3	23	69669569	Missense_Mutation	SNP	A	TCGA-LG-A9QD-01A-11D-A382-10	22640687	69669569	85600991	110	45010										
OR13H1	347468	hgsc.bcm.edu	37	chrX	130678861	130678861	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	cctaccctgaccaggacaagTttatctcagtgttttatgga	8	10	1	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chrX:130678861T>A	ENST00000338616.3	+	1	912	c.814T>A	c.(814-816)Ttt>Att	p.F272I		NM_001004486.1	NP_001004486.1	Q8NG92	O13H1_HUMAN	olfactory receptor, family 13, subfamily H, member 1	272						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	15	Acute lymphoblastic leukemia(192;0.000636)					CCAGGACAAGTTTATCTCAGT	0.433																																					p.F272I		Atlas-SNP	.											.	OR13H1	41	.	0			c.T814A						.						112	105	107					X																	130678861		2203	4300	6503	SO:0001583	missense	347468	exon1			GACAAGTTTATCT		CCDS35396.1	Xq26.2	2012-08-23			ENSG00000171054	ENSG00000171054		"GPCR / Class A : Olfactory receptors"	14755	protein-coding gene	gene with protein product							Standard	NM_001004486		Approved		uc011muw.2	Q8NG92	OTTHUMG00000022411	ENST00000338616.3:c.814T>A	chrX.hg19:g.130678861T>A	ENSP00000340748:p.Phe272Ile	281.0	1.0		246.0	134.0	NM_001004486	B2RNQ3|Q6IET8|Q96R12	Missense_Mutation	SNP	ENST00000338616.3	hg19	CCDS35396.1	.	.	.	.	.	.	.	.	.	.	T	3.841	-0.033882	0.07543	.	.	ENSG00000171054	ENST00000338616	T	0.00048	8.82	4.87	2.38	0.29361	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40640	U	0.001046	T	0.00039	0.0001	N	0.02213	-0.635	0.19300	N	0.999971	B	0.18863	0.031	B	0.13407	0.009	T	0.06162	-1.0842	10	0.20519	T	0.43	.	3.3027	0.06989	0.3731:0.0994:0.0:0.5275	.	272	Q8NG92	O13H1_HUMAN	I	272	ENSP00000340748:F272I	ENSP00000340748:F272I	F	+	1	0	OR13H1	130506542	0.000000	0.05858	0.379000	0.26080	0.911000	0.54048	-0.545000	0.06069	0.189000	0.20188	0.481000	0.45027	TTT	.	.		0.433	OR13H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058297.1			A	130678861	T	A	130678861	3	1	319	1	0	0	0	0	1	0	0	0	10952	1725	60	4	816	4	OR13H1	23	130678861	Missense_Mutation	SNP	T	TCGA-LG-A9QD-01A-11D-A382-10	61009292	130678861	24591699	111	45011										
IDS	3423	hgsc.bcm.edu	37	chrX	148564324	148564324	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0446428571428571	5	1	0.825	2.0625	0.589285714285714	1	1	0	tccaccttgggaatcattatAcatattgtgatcctgcaatg	7	9	1	1			TCGA-LG-A9QD-01A-11D-A382-10	TCGA-LG-A9QD-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5fcdf560-e18b-49e8-8a70-aad63a200d43	76fbd0ec-29e4-48fe-bfa2-438285845c0e	g.chrX:148564324A>G	ENST00000340855.6	-	9	1815	c.1606T>C	c.(1606-1608)Tat>Cat	p.Y536H	IDS_ENST00000422081.2_Missense_Mutation_p.Y325H|IDS_ENST00000541269.1_Missense_Mutation_p.Y325H|IDS_ENST00000537071.1_Missense_Mutation_p.Y139H	NM_000202.5|NM_001166550.1	NP_000193.1|NP_001160022.1	P22304	IDS_HUMAN	iduronate 2-sulfatase	536					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	lysosomal lumen (GO:0043202)	iduronate-2-sulfatase activity (GO:0004423)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(5)|large_intestine(2)|lung(8)|prostate(1)	20	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)					GAATCATTATACATATTGTGA	0.438																																					p.Y536H		Atlas-SNP	.											.	IDS	46	.	0			c.T1606C						.						86	74	78					X																	148564324		2203	4300	6503	SO:0001583	missense	3423	exon9			CATTATACATATT	M58342	CCDS14685.1, CCDS14686.1	Xq27.3-q28	2012-10-02	2008-08-01		ENSG00000010404	ENSG00000010404	3.1.6.13		5389	protein-coding gene	gene with protein product	"Hunter syndrome"	300823		SIDS			Standard	NM_006123		Approved		uc011mxe.2	P22304	OTTHUMG00000022615	ENST00000340855.6:c.1606T>C	chrX.hg19:g.148564324A>G	ENSP00000339801:p.Tyr536His	95.0	0.0		64.0	41.0	NM_000202	D3DWT4|Q14604|Q9BRM3	Missense_Mutation	SNP	ENST00000340855.6	hg19	CCDS14685.1	.	.	.	.	.	.	.	.	.	.	A	13.52	2.261526	0.39995	.	.	ENSG00000010404	ENST00000340855;ENST00000537071;ENST00000541269	D;D;D	0.99896	-7.6;-3.27;-7.6	5.77	4.62	0.57501	.	0.063724	0.64402	D	0.000004	D	0.99435	0.9800	M	0.69823	2.125	0.80722	D	1	B;B	0.28378	0.209;0.209	B;B	0.23419	0.046;0.046	D	0.99990	1.4245	10	0.17832	T	0.49	.	10.7906	0.46429	0.9254:0.0:0.0746:0.0	.	446;536	B4DGD7;P22304	.;IDS_HUMAN	H	536;139;325	ENSP00000339801:Y536H;ENSP00000440324:Y139H;ENSP00000441261:Y325H	ENSP00000339801:Y536H	Y	-	1	0	IDS	148372229	1.000000	0.71417	0.345000	0.25642	0.913000	0.54294	8.176000	0.89686	0.821000	0.34540	0.441000	0.28932	TAT	.	.		0.438	IDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058677.3			G	148564324	A	G	148564324	3	3	319	1	0	0	0	0	1	0	0	0	7512	391	14	2	50	2	IDS	23	148564324	Missense_Mutation	SNP	A	TCGA-LG-A9QD-01A-11D-A382-10	17885463	148564324	6706236	112	45012										
TNFRSF4	7293	hgsc.bcm.edu	37	chr1	1148033	1148033	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ctcacttggtccagggcttgCaggcctggttgtcgcctggg	15	12	1	0			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr1:1148033C>A	ENST00000379236.3	-	4	426	c.422G>T	c.(421-423)tGc>tTc	p.C141F	TNFRSF4_ENST00000453580.1_5'UTR	NM_003327.3	NP_003318.1	P43489	TNR4_HUMAN	tumor necrosis factor receptor superfamily, member 4	141					cellular defense response (GO:0006968)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of immunoglobulin secretion (GO:0051024)|regulation of apoptotic process (GO:0042981)|regulation of protein kinase activity (GO:0045859)|T cell proliferation (GO:0042098)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	tumor necrosis factor-activated receptor activity (GO:0005031)			large_intestine(1)|lung(2)|urinary_tract(1)	4	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;3.73e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.01e-21)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		CCAGGGCTTGCAGGCCTGGTT	0.706																																					p.C141F		Atlas-SNP	.											.	TNFRSF4	12	.	0			c.G422T						.						7	7	7					1																	1148033		2129	4208	6337	SO:0001583	missense	7293	exon4			GGCTTGCAGGCCT	X75962	CCDS11.1	1p36	2008-02-05			ENSG00000186827	ENSG00000186827		"Tumor necrosis factor receptor superfamily", "CD molecules"	11918	protein-coding gene	gene with protein product		600315		TXGP1L		7510240, 2828930	Standard	NM_003327		Approved	ACT35, OX40, CD134	uc001ade.3	P43489	OTTHUMG00000001415	ENST00000379236.3:c.422G>T	chr1.hg19:g.1148033C>A	ENSP00000368538:p.Cys141Phe	35.0	0.0		47.0	18.0	NM_003327	Q13663|Q2M312|Q5T7M0	Missense_Mutation	SNP	ENST00000379236.3	hg19	CCDS11.1	.	.	.	.	.	.	.	.	.	.	c	15.01	2.704974	0.48412	.	.	ENSG00000186827	ENST00000379236	T	0.41758	0.99	3.69	3.69	0.42338	TNFR/CD27/30/40/95 cysteine-rich region (1);	0.242450	0.33075	N	0.005301	T	0.67277	0.2876	M	0.85945	2.785	0.52099	D	0.999944	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.974	T	0.75204	-0.3400	10	0.87932	D	0	-20.1569	14.9756	0.71269	0.0:1.0:0.0:0.0	.	86;141	B1AME4;P43489	.;TNR4_HUMAN	F	141	ENSP00000368538:C141F	ENSP00000368538:C141F	C	-	2	0	TNFRSF4	1137896	0.995000	0.38212	0.998000	0.56505	0.535000	0.34838	2.644000	0.46613	2.081000	0.62600	0.472000	0.43445	TGC	.	.		0.706	TNFRSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004086.1			A	1148033	C	A	1148033	3	1	320	1	0	0	0	0	1	0	0	0	16312	710	25	3	427	3	TNFRSF4	1	1148033	Missense_Mutation	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10		1148033	248102588	1	45013										
KIAA1751	85452	hgsc.bcm.edu	37	chr1	1890603	1890603	+	IGR	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	cagtggaactgaaaactcgcCcgtctgagccaaaaatgaga	10	10	1	3			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr1:1890603C>G								TMEM52 (39891 upstream) : C1orf222 (28959 downstream)																							GAAAACTCGCCCGTCTGAGCC	0.438																																					p.G603R		Atlas-SNP	.											.	KIAA1751	92	.	0			c.G1807C						.						95	96	95					1																	1890603		1847	4100	5947	SO:0001628	intergenic_variant	85452	exon16			ACTCGCCCGTCTG																													chr1.hg19:g.1890603C>G		67.0	0.0		40.0	12.0	NM_001080484		Missense_Mutation	SNP		hg19		.	.	.	.	.	.	.	.	.	.	C	18.88	3.717694	0.68844	.	.	ENSG00000142609	ENST00000270720;ENST00000461752	.	.	.	4.72	4.72	0.59763	.	0.159217	0.39985	N	0.001214	T	0.80363	0.4609	M	0.82323	2.585	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.83505	0.0077	9	0.66056	D	0.02	-27.4137	15.5598	0.76234	0.0:1.0:0.0:0.0	.	603;603	Q9C0B2-2;Q9C0B2	.;K1751_HUMAN	R	603;50	.	ENSP00000270720:G603R	G	-	1	0	C1orf222	1880463	0.984000	0.35163	0.408000	0.26446	0.871000	0.50021	5.011000	0.64011	2.329000	0.79093	0.561000	0.74099	GGC	.	.	0	0.438									G	1890603	C	G	1890603	1	3	320	0	1	0	0	0	0	0	0	0	8265	623	22	4		4	KIAA1751	1	1890603	IGR	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	742570	1890603	247360018	2	45014										
PTCHD2	57540	hgsc.bcm.edu	37	chr1	11591710	11591710	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ctcccggggcagctgtcccaCggggcagtgggcgtcaggga	18	13	1	0			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr1:11591710C>T	ENST00000294484.6	+	17	3456	c.3318C>T	c.(3316-3318)caC>caT	p.H1106H	PTCHD2_ENST00000304391.6_5'Flank|PTCHD2_ENST00000389575.3_Silent_p.H1106H	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	1106					cholesterol homeostasis (GO:0042632)|regulation of lipid transport (GO:0032368)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hedgehog receptor activity (GO:0008158)			NS(3)|breast(2)|endometrium(9)|kidney(4)|large_intestine(5)|lung(34)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	76	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		AGCTGTCCCACGGGGCAGTGG	0.662																																					p.H1106H		Atlas-SNP	.											.	PTCHD2	193	.	0			c.C3318T						.						31	35	34					1																	11591710		2022	4168	6190	SO:0001819	synonymous_variant	57540	exon17			GTCCCACGGGGCA	AB037758	CCDS41247.1	1p36.22	2010-02-17			ENSG00000204624	ENSG00000204624			29251	protein-coding gene	gene with protein product		611251				15738394	Standard	NM_020780		Approved	KIAA1337, DISP3	uc001ash.4	Q9P2K9	OTTHUMG00000002074	ENST00000294484.6:c.3318C>T	chr1.hg19:g.11591710C>T		104.0	0.0		96.0	31.0	NM_020780	Q5VTU9|Q9UJD6	Silent	SNP	ENST00000294484.6	hg19	CCDS41247.1																																																																																			.	.		0.662	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561		T	11591710	C	T	11591710	2	4	320	1	0	0	0	0	0	0	0	1	12745	535	19	1		1	PTCHD2	1	11591710	Silent	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	9701107	11591710	237658911	3	45015										
EPHA8	2046	hgsc.bcm.edu	37	chr1	22902830	22902830	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	gctgggtcccccgagacggcGcccggcgcgtctatgctgag	16	15	1	2			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr1:22902830G>A	ENST00000166244.3	+	3	352	c.280G>A	c.(280-282)Gcc>Acc	p.A94T	EPHA8_ENST00000538803.1_Missense_Mutation_p.A94T|EPHA8_ENST00000374644.4_Missense_Mutation_p.A94T	NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8	94	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		CCGAGACGGCGCCCGGCGCGT	0.607																																					p.A94T		Atlas-SNP	.											.	EPHA8	221	.	0			c.G280A						.						60	61	61					1																	22902830		2203	4300	6503	SO:0001583	missense	2046	exon3			GACGGCGCCCGGC	BC038796	CCDS225.1, CCDS30626.1	1p36.12	2013-02-11	2004-10-28		ENSG00000070886	ENSG00000070886	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3391	protein-coding gene	gene with protein product		176945	"EphA8"	EEK		1648701	Standard	NM_001006943		Approved	Hek3	uc001bfx.1	P29322	OTTHUMG00000002892	ENST00000166244.3:c.280G>A	chr1.hg19:g.22902830G>A	ENSP00000166244:p.Ala94Thr	194.0	0.0		177.0	76.0	NM_020526	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Missense_Mutation	SNP	ENST00000166244.3	hg19	CCDS225.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.557296	0.86231	.	.	ENSG00000070886	ENST00000166244;ENST00000374644;ENST00000538803	T;T;T	0.15256	2.44;2.44;2.44	4.29	4.29	0.51040	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	T	0.46521	0.1397	M	0.84433	2.695	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.56013	-0.8049	10	0.87932	D	0	.	15.4668	0.75406	0.0:0.0:1.0:0.0	.	94;94	P29322;P29322-2	EPHA8_HUMAN;.	T	94	ENSP00000166244:A94T;ENSP00000363775:A94T;ENSP00000440274:A94T	ENSP00000166244:A94T	A	+	1	0	EPHA8	22775417	1.000000	0.71417	0.990000	0.47175	0.708000	0.40852	9.657000	0.98554	2.212000	0.71576	0.442000	0.29010	GCC	.	.		0.607	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526		A	22902830	G	A	22902830	3	1	320	1	0	0	0	0	1	0	0	0	5175	1087	38	1	290	1	EPHA8	1	22902830	Missense_Mutation	SNP	G	TCGA-MI-A75C-01A-11D-A32G-10	11311120	22902830	226347791	4	45016										
CD164L2	388611	hgsc.bcm.edu	37	chr1	27709145	27709145	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	gggctcccctcccaaagcctCgagctcctttacctggtagt	9	16	0	0			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr1:27709145C>T	ENST00000374030.1	-	2	241	c.101G>A	c.(100-102)cGa>cAa	p.R34Q	CD164L2_ENST00000374025.3_Missense_Mutation_p.R34Q|CD164L2_ENST00000374027.3_Missense_Mutation_p.R34Q			Q6UWJ8	C16L2_HUMAN	CD164 sialomucin-like 2	34						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;2.89e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00128)|KIRC - Kidney renal clear cell carcinoma(1967;0.00155)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		CCCAAAGCCTCGAGCTCCTTT	0.642																																					p.R34Q		Atlas-SNP	.											.	CD164L2	13	.	0			c.G101A						.						44	48	46					1																	27709145		2203	4299	6502	SO:0001583	missense	388611	exon2			AAGCCTCGAGCTC	AY358761	CCDS302.1	1p36.11	2008-02-05			ENSG00000174950	ENSG00000174950			32043	protein-coding gene	gene with protein product							Standard	XM_005245868		Approved		uc001boc.3	Q6UWJ8	OTTHUMG00000003395	ENST00000374030.1:c.101G>A	chr1.hg19:g.27709145C>T	ENSP00000363142:p.Arg34Gln	76.0	0.0		60.0	26.0	NM_207397	B2RPJ0|Q5JXD6	Missense_Mutation	SNP	ENST00000374030.1	hg19		.	.	.	.	.	.	.	.	.	.	C	20.3	3.968016	0.74131	.	.	ENSG00000174950	ENST00000374030;ENST00000374027;ENST00000374025	T;T;T	0.44083	0.93;0.93;0.93	4.64	-0.842	0.10748	.	1.028080	0.07785	N	0.954017	T	0.34019	0.0883	L	0.57536	1.79	0.26294	N	0.978071	B	0.16166	0.016	B	0.14578	0.011	T	0.39583	-0.9607	10	0.59425	D	0.04	-13.2005	1.751	0.02972	0.1489:0.3336:0.3314:0.1861	.	34	Q6UWJ8	C16L2_HUMAN	Q	34	ENSP00000363142:R34Q;ENSP00000363139:R34Q;ENSP00000363137:R34Q	ENSP00000363137:R34Q	R	-	2	0	CD164L2	27581732	0.467000	0.25831	0.887000	0.34795	0.943000	0.58893	0.090000	0.15025	-0.326000	0.08564	0.555000	0.69702	CGA	.	.		0.642	CD164L2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000009518.1	NM_207397		T	27709145	C	T	27709145	3	4	320	1	0	0	0	0	1	0	0	0	2972	884	31	1	436	1	CD164L2	1	27709145	Missense_Mutation	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	4806315	27709145	221541476	5	45017										
SESN2	83667	hgsc.bcm.edu	37	chr1	28595721	28595721	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	gggagagccgggctcggcgaGgccctcgagggcccagcgcc	19	15	0	1			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr1:28595721G>A	ENST00000253063.3	+	2	439	c.118G>A	c.(118-120)Ggc>Agc	p.G40S		NM_031459.4	NP_113647.1	P58004	SESN2_HUMAN	sestrin 2	40					autophagy (GO:0006914)|fatty acid beta-oxidation (GO:0006635)|glucose import (GO:0046323)|mitochondrial DNA metabolic process (GO:0032042)|protein kinase B signaling (GO:0043491)|regulation of cAMP-dependent protein kinase activity (GO:2000479)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of response to reactive oxygen species (GO:1901031)|response to glucose (GO:0009749)|response to insulin (GO:0032868)|triglyceride homeostasis (GO:0070328)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|endometrium(3)|large_intestine(5)|lung(7)|ovary(2)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	27		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;4.76e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;2.98e-22)|Colorectal(126;3.04e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00279)|STAD - Stomach adenocarcinoma(196;0.00303)|BRCA - Breast invasive adenocarcinoma(304;0.00595)|READ - Rectum adenocarcinoma(331;0.0649)		GGCTCGGCGAGGCCCTCGAGG	0.547																																					p.G40S		Atlas-SNP	.											.	SESN2	51	.	0			c.G118A						.						56	61	59					1																	28595721		2203	4300	6503	SO:0001583	missense	83667	exon2			CGGCGAGGCCCTC	AY123223	CCDS321.1	1p35.2	2008-02-05			ENSG00000130766	ENSG00000130766			20746	protein-coding gene	gene with protein product		607767				12607115, 12203114	Standard	NM_031459		Approved	SES2, DKFZp761M0212, HI95, SEST2	uc001bps.3	P58004	OTTHUMG00000003532	ENST00000253063.3:c.118G>A	chr1.hg19:g.28595721G>A	ENSP00000253063:p.Gly40Ser	50.0	0.0		30.0	9.0	NM_031459	Q5T7D0|Q96SI5	Missense_Mutation	SNP	ENST00000253063.3	hg19	CCDS321.1	.	.	.	.	.	.	.	.	.	.	G	12.22	1.872634	0.33069	.	.	ENSG00000130766	ENST00000253063	T	0.16324	2.35	4.85	2.88	0.33553	.	0.389236	0.25801	N	0.028211	T	0.06962	0.0177	N	0.08118	0	0.33998	D	0.649929	B	0.30068	0.267	B	0.25140	0.058	T	0.29941	-0.9995	10	0.12766	T	0.61	-25.8367	9.5877	0.39526	0.0768:0.2509:0.6723:0.0	.	40	P58004	SESN2_HUMAN	S	40	ENSP00000253063:G40S	ENSP00000253063:G40S	G	+	1	0	SESN2	28468308	0.547000	0.26465	0.998000	0.56505	0.890000	0.51754	0.685000	0.25378	1.282000	0.44496	-0.140000	0.14226	GGC	.	.		0.547	SESN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009840.1			A	28595721	G	A	28595721	3	1	320	1	0	0	0	0	1	0	0	0	14140	1000	35	3	124	3	SESN2	1	28595721	Missense_Mutation	SNP	G	TCGA-MI-A75C-01A-11D-A32G-10	886576	28595721	220654900	6	45018										
CC2D1B	200014	hgsc.bcm.edu	37	chr1	52830265	52830265	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ttggcctctggcctgagggcCcttccgaggtcttggccctg	14	14	2	1			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr1:52830265C>A	ENST00000371586.2	-	2	166	c.28G>T	c.(28-30)Ggc>Tgc	p.G10C	CC2D1B_ENST00000438831.1_5'UTR|CC2D1B_ENST00000284376.3_Missense_Mutation_p.G10C	NM_032449.2	NP_115825.1	Q5T0F9	C2D1B_HUMAN	coiled-coil and C2 domain containing 1B	10						nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(1)|large_intestine(6)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	27						GCCTGAGGGCCCTTCCGAGGT	0.587																																					p.G10C		Atlas-SNP	.											.	CC2D1B	73	.	0			c.G28T						.						43	38	40					1																	52830265		2203	4300	6503	SO:0001583	missense	200014	exon2			GAGGGCCCTTCCG	AB058739	CCDS30714.1	1p32.3	2008-02-05			ENSG00000154222	ENSG00000154222			29386	protein-coding gene	gene with protein product						11347906	Standard	NM_032449		Approved	KIAA1836	uc001ctq.2	Q5T0F9	OTTHUMG00000008102	ENST00000371586.2:c.28G>T	chr1.hg19:g.52830265C>A	ENSP00000360642:p.Gly10Cys	44.0	0.0		22.0	8.0	NM_032449	Q49AE8|Q5T0F8|Q5T0G0|Q6ZNQ1|Q96AP3|Q96I04|Q96JJ1	Missense_Mutation	SNP	ENST00000371586.2	hg19	CCDS30714.1	.	.	.	.	.	.	.	.	.	.	C	19.43	3.825864	0.71143	.	.	ENSG00000154222	ENST00000371586;ENST00000284376;ENST00000371575	T;T	0.26957	1.7;1.7	4.7	4.7	0.59300	.	0.299139	0.31279	N	0.007928	T	0.38585	0.1046	L	0.59436	1.845	0.80722	D	1	D	0.76494	0.999	D	0.64042	0.921	T	0.21348	-1.0248	10	0.54805	T	0.06	-13.354	5.5618	0.17148	0.0:0.7621:0.0:0.2379	.	10	Q5T0F9	C2D1B_HUMAN	C	10	ENSP00000360642:G10C;ENSP00000284376:G10C	ENSP00000284376:G10C	G	-	1	0	CC2D1B	52602853	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.668000	0.46816	2.439000	0.82584	0.591000	0.81541	GGC	.	.		0.587	CC2D1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000022189.1	NM_032449		A	52830265	C	A	52830265	3	1	320	1	0	0	0	0	1	0	0	0	2729	623	22	3	2640	3	CC2D1B	1	52830265	Missense_Mutation	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	24234544	52830265	196420356	7	45019										
PRKACB	5567	hgsc.bcm.edu	37	chr1	84662426	84662427	+	Splice_Site	INS	-	-	TA													0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ccatcaaggctatatccaggINStatgactttaacacattatg							TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr1:84662426_84662427insTA	ENST00000370689.2	+	6	810		c.e6+1		PRKACB_ENST00000394839.2_Splice_Site|PRKACB_ENST00000370680.1_Splice_Site|PRKACB_ENST00000370682.3_Splice_Site|PRKACB_ENST00000370688.3_Splice_Site|PRKACB_ENST00000370685.3_Splice_Site|PRKACB_ENST00000394838.2_Splice_Site	NM_001242862.1|NM_002731.2	NP_001229791.1|NP_002722.1	P22694	KAPCB_HUMAN	protein kinase, cAMP-dependent, catalytic, beta						activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|carbohydrate metabolic process (GO:0005975)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|negative regulation of meiotic cell cycle (GO:0051447)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|regulation of protein processing (GO:0070613)|response to clozapine (GO:0097338)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|triglyceride catabolic process (GO:0019433)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)|magnesium ion binding (GO:0000287)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(2)|kidney(1)|lung(11)|ovary(1)	16				all cancers(265;0.00536)|Epithelial(280;0.0161)|OV - Ovarian serous cystadenocarcinoma(397;0.141)		CTATATCCAGGTATGACTTTAA	0.351																																					.		Atlas-Indel,Pindel	.											.	PRKACB	174	.	0			c.546+1->TA						.																																			SO:0001630	splice_region_variant	5567	exon6			.	BC035058	CCDS691.1, CCDS692.1, CCDS693.1, CCDS55610.1, CCDS55611.1, CCDS72812.1, CCDS72813.1, CCDS72814.1, CCDS72815.1, CCDS72816.1	1p36.1	2012-10-02			ENSG00000142875	ENSG00000142875	2.7.11.1		9381	protein-coding gene	gene with protein product		176892					Standard	XM_005271016		Approved	PKACb	uc001djl.3	P22694	OTTHUMG00000009975	ENST00000370689.2:c.546+1->TA	chr1.hg19:g.84662427_84662428dupTA		155.0	0.0		125.0	51.0	NM_002731	B1APG4|B4DKB0|B4E2Q1|Q14VH1|Q59GC0|Q5BNE9|Q5BNF0|Q5BNF1|Q5BNF2|Q5BNF3|Q5CZ92|Q5T1K3|Q7Z3M1|Q8IYR5|Q8IZQ0|Q96B09	Splice_Site	INS	ENST00000370689.2	hg19	CCDS691.1																																																																																			.	.		0.351	PRKACB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027641.1	NM_182948	Intron	TA	84662427	-	TA	84662426	8	5	320	1	0	1	1	0	0	0	1	0	12510	1275	44	0	760	0	PRKACB	1	84662426	Splice_Site	INS	-	TCGA-MI-A75C-01A-11D-A32G-10	31832161	84662426	164588195	8	45020										
CHD1L	9557	hgsc.bcm.edu	37	chr1	146747921	146747921	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	gctgccgatgctgacctccaGgtatgatatgatatactgtt	10	9	0	3			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr1:146747921G>A	ENST00000369258.4	+	14	1559	c.1539G>A	c.(1537-1539)caG>caA	p.Q513Q	CHD1L_ENST00000431239.1_Splice_Site_p.Q419Q|CHD1L_ENST00000467213.1_3'UTR|CHD1L_ENST00000361293.5_Splice_Site_p.Q232Q|CHD1L_ENST00000369259.3_Splice_Site_p.Q309Q	NM_001256336.1|NM_004284.4|NM_024568.2	NP_001243265.1|NP_004275.4|NP_078844.2	Q86WJ1	CHD1L_HUMAN	chromodomain helicase DNA binding protein 1-like	513	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|nucleotide binding (GO:0000166)			breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(923;0.0487)					CTGACCTCCAGGTATGATATG	0.473																																					p.Q513Q		Atlas-SNP	.											.	CHD1L	72	.	0			c.G1539A						.						85	86	86					1																	146747921		2203	4300	6503	SO:0001630	splice_region_variant	9557	exon14			CCTCCAGGTATGA	AF054177	CCDS927.1, CCDS58021.1, CCDS58022.1, CCDS72882.1	1q21.1	2008-02-05			ENSG00000131778	ENSG00000131778			1916	protein-coding gene	gene with protein product		613039				9653160	Standard	NM_004284		Approved	ALC1	uc001epm.5	Q86WJ1	OTTHUMG00000150271	ENST00000369258.4:c.1539+1G>A	chr1.hg19:g.146747921G>A		73.0	0.0		66.0	22.0	NM_004284	A5YM64|B4DDE1|B5MDZ7|Q53EZ3|Q5VXX7|Q6DD94|Q6PK83|Q86XH3|Q96HF7|Q96SP3|Q9BVJ1|Q9NVV8	Silent	SNP	ENST00000369258.4	hg19	CCDS927.1																																																																																			.	.		0.473	CHD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040377.1	NM_004284	Silent	A	146747921	G	A	146747921	5	1	320	1	0	0	0	0	0	0	1	0	3326	1014	35	3	1593	3	CHD1L	1	146747921	Splice_Site	SNP	G	TCGA-MI-A75C-01A-11D-A32G-10	62085495	146747921	102502700	9	45021										
FLG2	388698	hgsc.bcm.edu	37	chr1	152323836	152323836	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ccatgtatagttccctgtctCccgtgaatggcagatcctga	9	12	1	3			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr1:152323836C>A	ENST00000388718.5	-	3	6498	c.6426G>T	c.(6424-6426)ggG>ggT	p.G2142G	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000445097.1_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	2142					establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TTCCCTGTCTCCCGTGAATGG	0.517																																					p.G2142G		Atlas-SNP	.											.	FLG2	431	.	0			c.G6426T						.						419	388	399					1																	152323836		2203	4300	6503	SO:0001819	synonymous_variant	388698	exon3			CTGTCTCCCGTGA	AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"EF-hand domain containing"	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.6426G>T	chr1.hg19:g.152323836C>A		129.0	0.0		188.0	32.0	NM_001014342	Q9H4U1	Silent	SNP	ENST00000388718.5	hg19	CCDS30861.1																																																																																			.	.		0.517	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		A	152323836	C	A	152323836	2	1	320	1	0	0	0	0	0	0	0	1	5931	842	30	3		3	FLG2	1	152323836	Silent	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	5575915	152323836	96926785	10	45022										
KIAA0907	22889	hgsc.bcm.edu	37	chr1	155891367	155891367	+	Nonsense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	gactgatagccattggatggAtaatatggtggttgaggagg	16	3	0	2			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr1:155891367A>C	ENST00000368321.3	-	10	1088	c.1065T>G	c.(1063-1065)taT>taG	p.Y355*	KIAA0907_ENST00000368319.3_Intron|KIAA0907_ENST00000368320.3_Nonsense_Mutation_p.Y355*|KIAA0907_ENST00000482337.1_Intron|SNORA42_ENST00000384744.1_RNA	NM_014949.2	NP_055764.2	Q7Z7F0	K0907_HUMAN	KIAA0907	355	Pro-rich.						RNA binding (GO:0003723)			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)			CATTGGATGGATAATATGGTG	0.488																																					p.Y355X		Atlas-SNP	.											.	KIAA0907	58	.	0			c.T1065G						.						125	122	123					1																	155891367		2203	4300	6503	SO:0001587	stop_gained	22889	exon10			GGATGGATAATAT	BC062637	CCDS30885.1	1q22	2012-11-30			ENSG00000132680	ENSG00000132680			29145	protein-coding gene	gene with protein product						10048485	Standard	NM_014949		Approved	BLOM7	uc001fmi.1	Q7Z7F0	OTTHUMG00000014103	ENST00000368321.3:c.1065T>G	chr1.hg19:g.155891367A>C	ENSP00000357304:p.Tyr355*	180.0	0.0		239.0	201.0	NM_014949	O94981|Q7L7Q2|Q7Z7E9|Q8TBQ0	Nonsense_Mutation	SNP	ENST00000368321.3	hg19	CCDS30885.1	.	.	.	.	.	.	.	.	.	.	A	29.1	4.978543	0.92982	.	.	ENSG00000132680	ENST00000368321;ENST00000368320	.	.	.	5.62	4.5	0.54988	.	0.125010	0.56097	D	0.000028	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.8562	4.8857	0.13701	0.7345:0.0:0.2655:0.0	.	.	.	.	X	355	.	ENSP00000357303:Y355X	Y	-	3	2	KIAA0907	154157991	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.440000	0.44855	2.136000	0.66102	0.402000	0.26972	TAT	.	.		0.488	KIAA0907-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039583.1	NM_014949		C	155891367	A	C	155891367	4	2	320	1	0	0	0	0	0	1	0	0	8208	340	12	5	799	5	KIAA0907	1	155891367	Nonsense_Mutation	SNP	A	TCGA-MI-A75C-01A-11D-A32G-10	3567531	155891367	93359254	11	45023										
FMO2	2327	hgsc.bcm.edu	37	chr1	171178027	171178027	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	gtgcgaagccagatttctgcTctctcttgttcaaagatcct	8	11	4	2			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr1:171178027T>A	ENST00000209929.7	+	9	1509	c.1351T>A	c.(1351-1353)Tct>Act	p.S451T	FMO2_ENST00000441535.1_Missense_Mutation_p.S451T|RP1-127D3.4_ENST00000445909.1_RNA|RP1-127D3.4_ENST00000445290.1_RNA|RP1-127D3.4_ENST00000422841.1_RNA|FMO2_ENST00000529935.1_3'UTR			P31512	FMO4_HUMAN	flavin containing monooxygenase 2 (non-functional)	449					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	22	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					AGATTTCTGCTCTCTCTTGTT	0.498																																					p.S451T		Atlas-SNP	.											.	FMO2	66	.	0			c.T1351A						.						210	203	205					1																	171178027		2203	4300	6503	SO:0001583	missense	2327	exon9			TTCTGCTCTCTCT	BC005894	CCDS1293.1	1q24.3	2011-08-04	2006-07-17		ENSG00000094963	ENSG00000094963			3770	protein-coding gene	gene with protein product		603955	"flavin containing monooxygenase 2"			1417778, 9804831	Standard	XR_426768		Approved		uc001ghk.1	Q99518	OTTHUMG00000035504	ENST00000209929.7:c.1351T>A	chr1.hg19:g.171178027T>A	ENSP00000209929:p.Ser451Thr	85.0	0.0		119.0	25.0	NM_001460	Q53XR0	Missense_Mutation	SNP	ENST00000209929.7	hg19	CCDS1293.1	.	.	.	.	.	.	.	.	.	.	T	2.843	-0.240102	0.05944	.	.	ENSG00000094963	ENST00000209929;ENST00000441535	T;T	0.56941	0.43;0.43	5.99	0.95	0.19572	.	0.562999	0.21084	N	0.080436	T	0.23766	0.0575	M	0.75777	2.31	0.09310	N	1	P	0.34699	0.464	B	0.36186	0.219	T	0.25082	-1.0142	10	0.22706	T	0.39	-6.2112	1.7888	0.03047	0.1247:0.1386:0.2591:0.4776	.	451	Q99518	FMO2_HUMAN	T	451	ENSP00000209929:S451T;ENSP00000405905:S451T	ENSP00000209929:S451T	S	+	1	0	FMO2	169444651	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-1.152000	0.03172	-0.079000	0.12707	-0.313000	0.08912	TCT	.	.		0.498	FMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086216.2	NM_001460		A	171178027	T	A	171178027	3	1	320	1	0	0	0	0	1	0	0	0	5963	1551	54	4	1381	4	FMO2	1	171178027	Missense_Mutation	SNP	T	TCGA-MI-A75C-01A-11D-A32G-10	15286660	171178027	78072594	12	45024										
ZNF695	57116	hgsc.bcm.edu	37	chr1	247150556	247150556	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	cttatgttgagtaaggtatgAaaaccaggtaaaagctttgc	10	5	0	2			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr1:247150556A>G	ENST00000339986.7	-	4	1408	c.1261T>C	c.(1261-1263)Tca>Cca	p.S421P	ZNF695_ENST00000487338.2_Intron|ZNF695_ENST00000498046.2_Intron	NM_020394.4	NP_065127	Q8IW36	ZN695_HUMAN	zinc finger protein 695	421					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(1)|large_intestine(1)|lung(9)|prostate(1)|urinary_tract(1)	13	all_cancers(71;4.01e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			GTAAGGTATGAAAACCAGGTA	0.368																																					p.S421P		Atlas-SNP	.											.	ZNF695	55	.	0			c.T1261C						.						49	53	52					1																	247150556		2125	4266	6391	SO:0001583	missense	57116	exon4			GGTATGAAAACCA		CCDS44344.1, CCDS55694.1	1q44	2013-01-08			ENSG00000197472	ENSG00000197472		"Zinc fingers, C2H2-type", "-"	30954	protein-coding gene	gene with protein product						12477932	Standard	NM_020394		Approved	SBZF3	uc009xgu.3	Q8IW36	OTTHUMG00000040707	ENST00000339986.7:c.1261T>C	chr1.hg19:g.247150556A>G	ENSP00000341236:p.Ser421Pro	34.0	0.0		59.0	15.0	NM_020394	Q5T0N9|Q5T0P1|Q5T0P3|Q7Z2W8|Q7Z648	Missense_Mutation	SNP	ENST00000339986.7	hg19	CCDS44344.1	.	.	.	.	.	.	.	.	.	.	A	10.66	1.412971	0.25465	.	.	ENSG00000197472	ENST00000339986	T	0.07908	3.15	0.642	0.642	0.17765	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08582	0.0213	M	0.84219	2.685	0.09310	N	1	P	0.50156	0.932	B	0.31290	0.127	T	0.35101	-0.9802	9	0.72032	D	0.01	.	3.4433	0.07472	0.5679:0.432:0.0:1.0E-4	.	421	Q8IW36	ZN695_HUMAN	P	421	ENSP00000341236:S421P	ENSP00000341236:S421P	S	-	1	0	ZNF695	245217179	0.000000	0.05858	0.001000	0.08648	0.219000	0.24729	0.720000	0.25896	0.534000	0.28695	0.172000	0.16884	TCA	.	.		0.368	ZNF695-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097823.5	NM_020394		G	247150556	A	G	247150556	3	3	320	1	0	0	0	0	1	0	0	0	18113	246	9	2	290	2	ZNF695	1	247150556	Missense_Mutation	SNP	A	TCGA-MI-A75C-01A-11D-A32G-10	75972529	247150556	2100065	13	45025										
OR2L13	284521	hgsc.bcm.edu	37	chr1	248263223	248263223	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ttcttctgcgatgtcccagcCatgttgcttcttgcctgtac	8	13	3	0			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr1:248263223C>T	ENST00000358120.2	+	2	691	c.546C>T	c.(544-546)gcC>gcT	p.A182A	OR2L13_ENST00000366478.2_Silent_p.A182A			Q8N349	OR2LD_HUMAN	olfactory receptor, family 2, subfamily L, member 13	182						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(12)|lung(32)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	59	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0132)			ATGTCCCAGCCATGTTGCTTC	0.453																																					p.A182A		Atlas-SNP	.											.	OR2L13	261	.	0			c.C546T						.						268	240	249					1																	248263223		2203	4300	6503	SO:0001819	synonymous_variant	284521	exon3			CCCAGCCATGTTG	BC028158	CCDS1637.1	1q44	2012-08-09			ENSG00000196071	ENSG00000196071		"GPCR / Class A : Olfactory receptors"	19578	protein-coding gene	gene with protein product				OR2L14			Standard	NM_175911		Approved		uc001ids.3	Q8N349	OTTHUMG00000040446	ENST00000358120.2:c.546C>T	chr1.hg19:g.248263223C>T		111.0	0.0		153.0	68.0	NM_175911	Q5VUR5	Silent	SNP	ENST00000358120.2	hg19	CCDS1637.1																																																																																			.	.		0.453	OR2L13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097342.1	NM_175911		T	248263223	C	T	248263223	2	4	320	1	0	0	0	0	0	0	0	1	11015	581	21	3		3	OR2L13	1	248263223	Silent	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	1112667	248263223	987398	14	45026										
OR2M3	127062	hgsc.bcm.edu	37	chr1	248366590	248366590	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	cctcatggacctcatgctcaTctgcaccaccgtacccaaga	6	17	4	1			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr1:248366590T>C	ENST00000456743.1	+	1	259	c.221T>C	c.(220-222)aTc>aCc	p.I74T		NM_001004689.1	NP_001004689.1	Q8NG83	OR2M3_HUMAN	olfactory receptor, family 2, subfamily M, member 3	74						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|large_intestine(4)|lung(33)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	50	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			CTCATGCTCATCTGCACCACC	0.517																																					p.I74T		Atlas-SNP	.											.	OR2M3	116	.	0			c.T221C						.						292	275	281					1																	248366590		2203	4300	6503	SO:0001583	missense	127062	exon1			TGCTCATCTGCAC		CCDS31107.1	1q44	2012-08-09		2004-03-10	ENSG00000228198	ENSG00000228198		"GPCR / Class A : Olfactory receptors"	8269	protein-coding gene	gene with protein product				OR2M6, OR2M3P			Standard	NM_001004689		Approved	OST003	uc010pzg.2	Q8NG83	OTTHUMG00000040459	ENST00000456743.1:c.221T>C	chr1.hg19:g.248366590T>C	ENSP00000389625:p.Ile74Thr	192.0	0.0		260.0	46.0	NM_001004689	B9EH06|Q6IEY0	Missense_Mutation	SNP	ENST00000456743.1	hg19	CCDS31107.1	.	.	.	.	.	.	.	.	.	.	T	10.28	1.306330	0.23736	.	.	ENSG00000228198	ENST00000456743	T	0.00601	6.29	2.44	1.3	0.21679	GPCR, rhodopsin-like superfamily (1);	0.543723	0.13772	U	0.363815	T	0.00412	0.0013	N	0.17312	0.475	0.09310	N	1	B	0.16802	0.019	B	0.18871	0.023	T	0.45920	-0.9228	10	0.38643	T	0.18	.	4.2878	0.10863	0.0:0.1266:0.2055:0.6679	.	74	Q8NG83	OR2M3_HUMAN	T	74	ENSP00000389625:I74T	ENSP00000389625:I74T	I	+	2	0	OR2M3	246433213	0.000000	0.05858	0.022000	0.16811	0.603000	0.37013	0.031000	0.13710	1.117000	0.41842	0.333000	0.21579	ATC	.	.		0.517	OR2M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097355.1	NM_001004689		C	248366590	T	C	248366590	3	2	320	1	0	0	0	0	1	0	0	0	11020	1435	50	2	223	2	OR2M3	1	248366590	Missense_Mutation	SNP	T	TCGA-MI-A75C-01A-11D-A32G-10	103367	248366590	884031	15	45027										
TPO	7173	hgsc.bcm.edu	37	chr2	1459934	1459934	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	tctgacctcctgatggcatgGggacaatacatcgaccacga	10	12	1	2			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr2:1459934G>A	ENST00000345913.4	+	7	790	c.699G>A	c.(697-699)tgG>tgA	p.W233*	TPO_ENST00000497517.2_Intron|TPO_ENST00000337415.3_Nonsense_Mutation_p.W233*|TPO_ENST00000382201.3_Nonsense_Mutation_p.W233*|TPO_ENST00000382198.1_Nonsense_Mutation_p.W233*|TPO_ENST00000346956.3_Nonsense_Mutation_p.W233*|TPO_ENST00000349624.3_Nonsense_Mutation_p.W233*|TPO_ENST00000329066.4_Nonsense_Mutation_p.W233*	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	233					cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	TGATGGCATGGGGACAATACA	0.527																																					p.W233X		Atlas-SNP	.											.	TPO	224	.	0			c.G699A						.						125	90	102					2																	1459934		2203	4300	6503	SO:0001587	stop_gained	7173	exon7			GGCATGGGGACAA		CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.699G>A	chr2.hg19:g.1459934G>A	ENSP00000318820:p.Trp233*	101.0	0.0		71.0	22.0	NM_175719	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Nonsense_Mutation	SNP	ENST00000345913.4	hg19	CCDS1643.1	.	.	.	.	.	.	.	.	.	.	G	32	5.180168	0.94846	.	.	ENSG00000115705	ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000329066;ENST00000382201;ENST00000382198;ENST00000422464	.	.	.	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-25.4484	18.7337	0.91746	0.0:0.0:1.0:0.0	.	.	.	.	X	233;233;233;233;233;233;233;162	.	ENSP00000329869:W233X	W	+	3	0	TPO	1438941	1.000000	0.71417	1.000000	0.80357	0.174000	0.22865	8.763000	0.91715	2.485000	0.83878	0.563000	0.77884	TGG	.	.		0.527	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547		A	1459934	G	A	1459934	4	1	320	1	0	0	0	0	0	1	0	0	16425	1241	43	3	721	3	TPO	2	1459934	Nonsense_Mutation	SNP	G	TCGA-MI-A75C-01A-11D-A32G-10		1459934	241739439	16	45028										
FAM179A	165186	hgsc.bcm.edu	37	chr2	29222109	29222109	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	aaccgtcacagctcctgcgtGgactcggacagctgggtggc	14	13	1	0			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr2:29222109G>T	ENST00000379558.4	+	4	553	c.202G>T	c.(202-204)Gga>Tga	p.G68*	FAM179A_ENST00000403861.2_Nonsense_Mutation_p.G68*	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	68										breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						GCTCCTGCGTGGACTCGGACA	0.617																																					p.G68X		Atlas-SNP	.											.	FAM179A	106	.	0			c.G202T						.						40	44	43					2																	29222109		2131	4240	6371	SO:0001587	stop_gained	165186	exon4			CTGCGTGGACTCG	AK125239, AK125744	CCDS1769.2	2p23.2	2008-10-30			ENSG00000189350	ENSG00000189350			33715	protein-coding gene	gene with protein product						16344560	Standard	NM_199280		Approved	FLJ43249, LOC165186	uc010ezl.3	Q6ZUX3	OTTHUMG00000128432	ENST00000379558.4:c.202G>T	chr2.hg19:g.29222109G>T	ENSP00000368876:p.Gly68*	78.0	0.0		58.0	15.0	NM_199280	Q6ZUF5	Nonsense_Mutation	SNP	ENST00000379558.4	hg19	CCDS1769.2	.	.	.	.	.	.	.	.	.	.	G	15.76	2.929203	0.52759	.	.	ENSG00000189350	ENST00000420297;ENST00000379558;ENST00000403861	.	.	.	5.51	3.36	0.38483	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	.	8.5104	0.33213	0.2071:0.0:0.7929:0.0	.	.	.	.	X	68	.	ENSP00000368876:G68X	G	+	1	0	FAM179A	29075613	0.295000	0.24389	0.009000	0.14445	0.022000	0.10575	2.135000	0.42112	1.324000	0.45282	0.478000	0.44815	GGA	.	.		0.617	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280		T	29222109	G	T	29222109	4	4	320	1	0	0	0	0	0	1	0	0	5510	1349	47	3	212	3	FAM179A	2	29222109	Nonsense_Mutation	SNP	G	TCGA-MI-A75C-01A-11D-A32G-10	27762175	29222109	213977264	17	45029										
C2orf71	388939	hgsc.bcm.edu	37	chr2	29295459	29295459	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	gtcctggtgcccacagggcaCagggacaaacttgatccttt	11	12	0	1			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr2:29295459C>A	ENST00000331664.5	-	1	1668	c.1669G>T	c.(1669-1671)Gtg>Ttg	p.V557L		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	557					response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						CCACAGGGCACAGGGACAAAC	0.597																																					p.V557L		Atlas-SNP	.											.	C2orf71	146	.	0			c.G1669T						.						45	49	47					2																	29295459		2009	4168	6177	SO:0001583	missense	388939	exon1			AGGGCACAGGGAC		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.1669G>T	chr2.hg19:g.29295459C>A	ENSP00000332809:p.Val557Leu	70.0	0.0		48.0	16.0	NM_001029883		Missense_Mutation	SNP	ENST00000331664.5	hg19	CCDS42669.1	.	.	.	.	.	.	.	.	.	.	C	9.414	1.081225	0.20309	.	.	ENSG00000179270	ENST00000331664	T	0.24350	1.86	5.17	1.12	0.20585	.	0.866213	0.10034	N	0.724349	T	0.17152	0.0412	L	0.33485	1.01	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.28235	-1.0050	10	0.40728	T	0.16	-0.6019	4.4834	0.11778	0.2635:0.4132:0.2548:0.0686	.	557	A6NGG8	CB071_HUMAN	L	557	ENSP00000332809:V557L	ENSP00000332809:V557L	V	-	1	0	C2orf71	29148963	0.000000	0.05858	0.167000	0.22817	0.861000	0.49209	0.011000	0.13264	-0.071000	0.12886	0.561000	0.74099	GTG	.	.		0.597	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883		A	29295459	C	A	29295459	3	1	320	1	0	0	0	0	1	0	0	0	2193	478	17	3	2205	3	C2orf71	2	29295459	Missense_Mutation	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	73350	29295459	213903914	18	45030										
REV1	51455	hgsc.bcm.edu	37	chr2	100046405	100046405	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ccacaatgatgaatctggtaTatctgctttaaaaataaaaa	5	6	2	2			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr2:100046405T>C	ENST00000258428.3	-	9	1672	c.1444A>G	c.(1444-1446)Ata>Gta	p.I482V	REV1_ENST00000393445.3_Missense_Mutation_p.I481V|REV1_ENST00000465835.1_5'UTR	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)	482	UmuC. {ECO:0000255|PROSITE- ProRule:PRU00216}.				DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|error-prone translesion synthesis (GO:0042276)|response to UV (GO:0009411)	nucleoplasm (GO:0005654)	damaged DNA binding (GO:0003684)|deoxycytidyl transferase activity (GO:0017125)|DNA-directed DNA polymerase activity (GO:0003887)|magnesium ion binding (GO:0000287)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(12)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GAATCTGGTATATCTGCttta	0.303								Direct reversal of damage																													p.I482V		Atlas-SNP	.											.	REV1	100	.	0			c.A1444G						.						57	54	55					2																	100046405		2203	4300	6503	SO:0001583	missense	51455	exon9			CTGGTATATCTGC	AF206019	CCDS2045.1, CCDS42722.1	2q11.1-q11.2	2012-05-18	2012-05-18	2006-11-07	ENSG00000135945	ENSG00000135945		"DNA polymerases"	14060	protein-coding gene	gene with protein product		606134	"REV1 (yeast homolog)- like", "REV1-like (yeast)", "REV1 homolog (S. cerevisiae)"	REV1L		10536157	Standard	XM_005263968		Approved		uc002tad.3	Q9UBZ9	OTTHUMG00000130636	ENST00000258428.3:c.1444A>G	chr2.hg19:g.100046405T>C	ENSP00000258428:p.Ile482Val	246.0	0.0		169.0	62.0	NM_016316	O95941|Q53SI7|Q9C0J4|Q9NUP2	Missense_Mutation	SNP	ENST00000258428.3	hg19	CCDS2045.1	.	.	.	.	.	.	.	.	.	.	T	3.157	-0.173004	0.06421	.	.	ENSG00000135945	ENST00000393445;ENST00000258428;ENST00000450415	T;T;T	0.42513	1.72;1.68;0.97	5.53	3.11	0.35812	DNA-repair protein, UmuC-like, N-terminal (1);DNA-repair protein, UmuC-like (1);	0.346611	0.31113	N	0.008222	T	0.20210	0.0486	N	0.12746	0.255	0.25954	N	0.982715	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	T	0.14337	-1.0476	10	0.25751	T	0.34	.	4.8658	0.13607	0.1371:0.1444:0.0:0.7185	.	482;481	Q9UBZ9;Q9UBZ9-2	REV1_HUMAN;.	V	481;482;119	ENSP00000377091:I481V;ENSP00000258428:I482V;ENSP00000414875:I119V	ENSP00000258428:I482V	I	-	1	0	REV1	99412837	1.000000	0.71417	0.799000	0.32177	0.086000	0.17979	1.617000	0.36943	0.365000	0.24400	-0.250000	0.11733	ATA	.	.		0.303	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253123.2	NM_016316		C	100046405	T	C	100046405	3	2	320	1	0	0	0	0	1	0	0	0	13254	1406	49	2	2371	2	REV1	2	100046405	Missense_Mutation	SNP	T	TCGA-MI-A75C-01A-11D-A32G-10	70750946	100046405	143152968	19	45031										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168102933	168102933	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	agatctgtaaagaaaggcatCttaattcaggaagatgaaaa	9	4	3	4			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr2:168102933C>T	ENST00000409195.1	+	9	5120	c.5031C>T	c.(5029-5031)atC>atT	p.I1677I	XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_Silent_p.I1455I|XIRP2_ENST00000295237.9_Silent_p.I1677I|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1502					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AGAAAGGCATCTTAATTCAGG	0.343																																					p.I1677I		Atlas-SNP	.											.	XIRP2	914	.	0			c.C5031T						.						93	88	90					2																	168102933		1859	4081	5940	SO:0001819	synonymous_variant	129446	exon9			AGGCATCTTAATT	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.5031C>T	chr2.hg19:g.168102933C>T		189.0	0.0		163.0	32.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent	SNP	ENST00000409195.1	hg19	CCDS42769.1																																																																																			.	.		0.343	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		T	168102933	C	T	168102933	2	4	320	1	0	0	0	0	0	0	0	1	17445	903	32	3		3	XIRP2	2	168102933	Silent	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	68056528	168102933	75096440	20	45032										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196866480	196866480	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	tgtaaagtcataagtgcagcAgcacagttgaaaaaagattc	9	6	1	2			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr2:196866480A>T	ENST00000312428.6	-	11	1192	c.1092T>A	c.(1090-1092)gcT>gcA	p.A364A	DNAH7_ENST00000410072.1_Silent_p.A364A	NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	364	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						TAAGTGCAGCAGCACAGTTGA	0.408																																					p.A364A		Atlas-SNP	.											.	DNAH7	512	.	0			c.T1092A						.						99	95	97					2																	196866480		1899	4111	6010	SO:0001819	synonymous_variant	56171	exon11			TGCAGCAGCACAG	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.1092T>A	chr2.hg19:g.196866480A>T		135.0	0.0		112.0	41.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Silent	SNP	ENST00000312428.6	hg19	CCDS42794.1																																																																																			.	.		0.408	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		T	196866480	A	T	196866480	2	4	320	1	0	0	0	0	0	0	0	1	4608	175	7	4		4	DNAH7	2	196866480	Silent	SNP	A	TCGA-MI-A75C-01A-11D-A32G-10	28763547	196866480	46332893	21	45033										
TRAK2	66008	hgsc.bcm.edu	37	chr2	202254174	202254174	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	tgggaatgagatagagcggcCccgtgtgtcattggcaatcc	14	9	1	2			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr2:202254174C>T	ENST00000332624.3	-	12	1674	c.1246G>A	c.(1246-1248)Ggc>Agc	p.G416S		NM_015049.2	NP_055864.2	O60296	TRAK2_HUMAN	trafficking protein, kinesin binding 2	416	Interaction with HGS. {ECO:0000250}.				protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|endosome (GO:0005768)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GABA receptor binding (GO:0050811)|receptor binding (GO:0005102)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	23						ATAGAGCGGCCCCGTGTGTCA	0.478																																					p.G416S		Atlas-SNP	.											.	TRAK2	62	.	0			c.G1246A						.						106	103	104					2																	202254174		2203	4300	6503	SO:0001583	missense	66008	exon12			AGCGGCCCCGTGT	AB038951	CCDS2347.1	2q33.1	2012-03-05	2005-12-13	2005-12-13	ENSG00000115993	ENSG00000115993			13206	protein-coding gene	gene with protein product	"gamma-aminobutyric acid(A) receptor-interacting factor", "milton homolog 2 (Drosophila)", "O-linked N-acetylglucosamine transferase interacting protein 98"	607334	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 3"	ALS2CR3		11161814, 16380713, 20230862	Standard	NM_015049		Approved	CALS-C, KIAA0549, GRIF-1, OIP98, MILT2	uc002uyb.4	O60296	OTTHUMG00000132822	ENST00000332624.3:c.1246G>A	chr2.hg19:g.202254174C>T	ENSP00000328875:p.Gly416Ser	47.0	0.0		60.0	14.0	NM_015049	E7EV21|Q8WVH7|Q96NS2|Q9C0K5|Q9C0K6	Missense_Mutation	SNP	ENST00000332624.3	hg19	CCDS2347.1	.	.	.	.	.	.	.	.	.	.	C	10.92	1.488016	0.26686	.	.	ENSG00000115993	ENST00000332624;ENST00000542292	T	0.41400	1.0	5.9	4.94	0.65067	Trafficking kinesin-binding protein domain (1);	0.302356	0.33327	N	0.005031	T	0.25754	0.0627	N	0.25144	0.715	0.80722	D	1	B	0.24092	0.097	B	0.23574	0.047	T	0.05869	-1.0859	10	0.08837	T	0.75	.	11.168	0.48554	0.1378:0.792:0.0:0.0703	.	416	O60296	TRAK2_HUMAN	S	416;322	ENSP00000328875:G416S	ENSP00000328875:G416S	G	-	1	0	TRAK2	201962419	0.061000	0.20836	0.910000	0.35882	0.649000	0.38597	0.249000	0.18216	2.788000	0.95919	0.650000	0.86243	GGC	.	.		0.478	TRAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256284.3	NM_015049		T	202254174	C	T	202254174	3	4	320	1	0	0	0	0	1	0	0	0	16465	623	22	3	1518	3	TRAK2	2	202254174	Missense_Mutation	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	5387694	202254174	40945199	22	45034										
FAM124B	79843	hgsc.bcm.edu	37	chr2	225266002	225266002	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	cttttgcaaggtcgcttctcTctgcaggatcatctcgtaga	9	11	4	1			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr2:225266002T>A	ENST00000409685.3	-	1	749	c.484A>T	c.(484-486)Aga>Tga	p.R162*	FAM124B_ENST00000389874.3_Nonsense_Mutation_p.R162*|FAM124B_ENST00000243806.2_Nonsense_Mutation_p.R162*	NM_001122779.1	NP_001116251.1	Q9H5Z6	F124B_HUMAN	family with sequence similarity 124B	162										endometrium(2)|large_intestine(2)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	16		Renal(207;0.0112)|all_lung(227;0.0126)|Lung NSC(271;0.0161)|all_hematologic(139;0.138)		Epithelial(121;4.4e-10)|all cancers(144;2.02e-07)|Lung(261;0.00766)|LUSC - Lung squamous cell carcinoma(224;0.00825)		GTCGCTTCTCTCTGCAGGATC	0.522																																					p.R162X		Atlas-SNP	.											.	FAM124B	71	.	0			c.A484T						.						89	84	86					2																	225266002		2203	4300	6503	SO:0001587	stop_gained	79843	exon1			CTTCTCTCTGCAG	AK075126	CCDS2461.1, CCDS46527.1	2q36.2	2008-02-05			ENSG00000124019	ENSG00000124019			26224	protein-coding gene	gene with protein product						12477932	Standard	NM_001122779		Approved	FLJ22746	uc002vnx.3	Q9H5Z6	OTTHUMG00000133168	ENST00000409685.3:c.484A>T	chr2.hg19:g.225266002T>A	ENSP00000386895:p.Arg162*	69.0	0.0		82.0	30.0	NM_024785	A6NNC7|Q8NBZ4|Q8TAV7	Nonsense_Mutation	SNP	ENST00000409685.3	hg19	CCDS46527.1	.	.	.	.	.	.	.	.	.	.	T	39	7.322505	0.98210	.	.	ENSG00000124019	ENST00000389874;ENST00000409685;ENST00000243806	.	.	.	5.64	1.74	0.24563	.	0.277697	0.39341	N	0.001382	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.8127	8.4307	0.32755	0.0:0.0666:0.3767:0.5566	.	.	.	.	X	162	.	ENSP00000243806:R162X	R	-	1	2	FAM124B	224974246	0.977000	0.34250	0.639000	0.29394	0.941000	0.58515	1.604000	0.36804	0.053000	0.16036	0.533000	0.62120	AGA	.	.		0.522	FAM124B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330873.1	NM_024785		A	225266002	T	A	225266002	4	1	320	1	0	0	0	0	0	1	0	0	5431	1559	54	4	982	4	FAM124B	2	225266002	Nonsense_Mutation	SNP	T	TCGA-MI-A75C-01A-11D-A32G-10	23011828	225266002	17933371	23	45035										
USP40	55230	hgsc.bcm.edu	37	chr2	234442150	234442150	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	gggggtctctgcaactgggaTttccgataaaacaacatgta	11	8	1	0			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr2:234442150T>C	ENST00000427112.2	-	10	1478	c.1443A>G	c.(1441-1443)aaA>aaG	p.K481K	USP40_ENST00000450966.1_Silent_p.K493K|USP40_ENST00000251722.6_Silent_p.K481K			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	481	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|endometrium(6)|kidney(5)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		GCAACTGGGATTTCCGATAAA	0.363																																					p.K493K		Atlas-SNP	.											.	USP40	174	.	0			c.A1479G						.						114	109	111					2																	234442150		1844	4084	5928	SO:0001819	synonymous_variant	55230	exon10			CTGGGATTTCCGA	AK001647	CCDS46547.1	2q37.1	2005-08-08	2005-08-08		ENSG00000085982	ENSG00000085982		"Ubiquitin-specific peptidases"	20069	protein-coding gene	gene with protein product		610570	"ubiquitin specific protease 40"			12838346	Standard	NM_018218		Approved	FLJ10785	uc010zmr.2	Q9NVE5	OTTHUMG00000153199	ENST00000427112.2:c.1443A>G	chr2.hg19:g.234442150T>C		123.0	0.0		107.0	26.0	NM_018218	Q6NX38|Q70EL0	Silent	SNP	ENST00000427112.2	hg19	CCDS46547.1																																																																																			.	.		0.363	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294		C	234442150	T	C	234442150	2	2	320	1	0	0	0	0	0	0	0	1	17087	1490	52	2		2	USP40	2	234442150	Silent	SNP	T	TCGA-MI-A75C-01A-11D-A32G-10	9176148	234442150	8757223	24	45036										
SRGAP3	9901	hgsc.bcm.edu	37	chr3	9101941	9101941	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	cagatcagagacatcatggaTgtagtatttgcttatagctg	10	6	2	2			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr3:9101941T>G	ENST00000383836.3	-	6	1202	c.775A>C	c.(775-777)Atc>Ctc	p.I259L	SRGAP3_ENST00000433332.3_5'UTR|SRGAP3_ENST00000360413.3_Missense_Mutation_p.I259L	NM_014850.3	NP_055665.1	O43295	SRGP3_HUMAN	SLIT-ROBO Rho GTPase activating protein 3	259	F-BAR domain.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)		SRGAP3/RAF1(6)	breast(1)|endometrium(2)|kidney(21)|large_intestine(7)|lung(13)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	54				OV - Ovarian serous cystadenocarcinoma(96;0.0563)		ACATCATGGATGTAGTATTTG	0.542			T	RAF1	pilocytic astrocytoma																																p.I259L		Atlas-SNP	.		Dom	yes		3	3p25.3	9901	SLIT-ROBO Rho GTPase activating protein 3		M	.	SRGAP3	146	.	0			c.A775C						.						202	176	184					3																	9101941		2203	4300	6503	SO:0001583	missense	9901	exon6			CATGGATGTAGTA	AB007871	CCDS2572.1, CCDS33689.1	3p25.3	2011-07-04	2004-11-12	2004-11-12	ENSG00000196220	ENSG00000196220		"Rho GTPase activating proteins"	19744	protein-coding gene	gene with protein product		606525	"SLIT-ROBO Rho GTPase activating protein 2"	SRGAP2		12195014	Standard	NM_014850		Approved	KIAA0411, MEGAP, WRP, ARHGAP14	uc003brf.2	O43295	OTTHUMG00000090589	ENST00000383836.3:c.775A>C	chr3.hg19:g.9101941T>G	ENSP00000373347:p.Ile259Leu	103.0	0.0		83.0	33.0	NM_014850	Q8IX13|Q8IZV8	Missense_Mutation	SNP	ENST00000383836.3	hg19	CCDS2572.1	.	.	.	.	.	.	.	.	.	.	T	17.72	3.460174	0.63401	.	.	ENSG00000196220	ENST00000383836;ENST00000360413;ENST00000544908	T;T	0.13420	2.59;2.59	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.13884	0.0336	L	0.46157	1.445	0.54753	D	0.999987	B;B;P;P	0.47106	0.296;0.026;0.89;0.606	B;B;B;B	0.40477	0.109;0.022;0.33;0.127	T	0.08953	-1.0697	10	0.21540	T	0.41	.	14.8468	0.70267	0.0:0.0:0.0:1.0	.	259;128;259;259	C7TPG7;Q9ULR4;O43295-2;O43295	.;.;.;SRGP2_HUMAN	L	259;259;139	ENSP00000373347:I259L;ENSP00000353587:I259L	ENSP00000353587:I259L	I	-	1	0	SRGAP3	9076941	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.810000	0.86072	1.992000	0.58205	0.377000	0.23210	ATC	.	.		0.542	SRGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207137.3			G	9101941	T	G	9101941	3	3	320	1	0	0	0	0	1	0	0	0	15162	1464	51	5	2627	5	SRGAP3	3	9101941	Missense_Mutation	SNP	T	TCGA-MI-A75C-01A-11D-A32G-10		9101941	188920489	25	45037										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41268766	41268766	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	gaggacctatacttacgaaaAactactgtggaccacaagca	8	10	0	0			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr3:41268766A>T	ENST00000349496.5	+	7	1284	c.1004A>T	c.(1003-1005)aAa>aTa	p.K335I	CTNNB1_ENST00000405570.1_Missense_Mutation_p.K335I|CTNNB1_ENST00000453024.1_Missense_Mutation_p.K328I|CTNNB1_ENST00000396185.3_Missense_Mutation_p.K335I|CTNNB1_ENST00000396183.3_Missense_Mutation_p.K335I	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	335					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.K335I(8)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		ACTTACGAAAAACTACTGTGG	0.383		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.K335I	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,colon,carcinoma,-1,11	CTNNB1	4904	.	8	Substitution - Missense(8)	liver(7)|kidney(1)	c.A1004T						.						110	108	109					3																	41268766		2203	4300	6503	SO:0001583	missense	1499	exon7	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	ACGAAAAACTACT	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.1004A>T	chr3.hg19:g.41268766A>T	ENSP00000344456:p.Lys335Ile	61.0	0.0		68.0	27.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	29.8	5.040885	0.93685	.	.	ENSG00000168036	ENST00000405570;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185	T;T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15;-0.15	5.5	5.5	0.81552	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.82148	0.4974	M	0.89287	3.02	0.80722	D	1	D;D	0.71674	0.995;0.998	D;D	0.75484	0.97;0.986	D	0.85830	0.1391	10	0.72032	D	0.01	-3.7939	15.5934	0.76558	1.0:0.0:0.0:0.0	.	263;335	B4DSW9;P35222	.;CTNB1_HUMAN	I	335;335;335;328;335	ENSP00000385604:K335I;ENSP00000379486:K335I;ENSP00000344456:K335I;ENSP00000411226:K328I;ENSP00000379488:K335I	ENSP00000344456:K335I	K	+	2	0	CTNNB1	41243770	1.000000	0.71417	0.998000	0.56505	0.968000	0.65278	9.339000	0.96797	2.094000	0.63399	0.482000	0.46254	AAA	.	.		0.383	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41268766	A	T	41268766	3	4	320	1	0	0	0	0	1	0	0	0	4018	14	1	4	1026	4	CTNNB1	3	41268766	Missense_Mutation	SNP	A	TCGA-MI-A75C-01A-11D-A32G-10	32166825	41268766	156753664	26	45038										
DTX3L	151636	hgsc.bcm.edu	37	chr3	122288501	122288501	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ggctggaaagaaattgaaagAgggtcatgaaacaccgatgg	14	5	1	4			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr3:122288501A>T	ENST00000296161.4	+	3	1754	c.1565A>T	c.(1564-1566)gAg>gTg	p.E522V	DTX3L_ENST00000383661.3_Intron	NM_138287.3	NP_612144.1	Q8TDB6	DTX3L_HUMAN	deltex 3 like, E3 ubiquitin ligase	522					cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|histone monoubiquitination (GO:0010390)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone binding (GO:0042393)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(114;0.0459)		AAATTGAAAGAGGGTCATGAA	0.463																																					p.E522V		Atlas-SNP	.											.	DTX3L	59	.	0			c.A1565T						.						87	88	88					3																	122288501		2203	4300	6503	SO:0001583	missense	151636	exon3			TGAAAGAGGGTCA		CCDS3015.1	3q21.1	2014-01-28	2014-01-28		ENSG00000163840	ENSG00000163840		"RING-type (C3HC4) zinc fingers"	30323	protein-coding gene	gene with protein product	"rhysin 2"	613143	"deltex 3-like (Drosophila)"			12670957, 22411408	Standard	NM_138287		Approved	BBAP	uc003efk.3	Q8TDB6	OTTHUMG00000159524	ENST00000296161.4:c.1565A>T	chr3.hg19:g.122288501A>T	ENSP00000296161:p.Glu522Val	100.0	0.0		68.0	4.0	NM_138287	B3KWH6|Q53ZZ3|Q5MJP7	Missense_Mutation	SNP	ENST00000296161.4	hg19	CCDS3015.1	.	.	.	.	.	.	.	.	.	.	A	10.73	1.431211	0.25726	.	.	ENSG00000163840	ENST00000296161	T	0.32515	1.45	5.25	1.19	0.21007	.	0.717658	0.12580	N	0.456485	T	0.26557	0.0649	M	0.63428	1.95	0.09310	N	1	B	0.18013	0.025	B	0.12837	0.008	T	0.30416	-0.9979	10	0.56958	D	0.05	-32.921	3.5652	0.07897	0.5826:0.0:0.1959:0.2215	.	522	Q8TDB6	DTX3L_HUMAN	V	522	ENSP00000296161:E522V	ENSP00000296161:E522V	E	+	2	0	DTX3L	123771191	0.000000	0.05858	0.001000	0.08648	0.089000	0.18198	0.154000	0.16343	0.344000	0.23847	0.533000	0.62120	GAG	.	.		0.463	DTX3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355966.1	NM_138287		T	122288501	A	T	122288501	3	4	320	1	0	0	0	0	1	0	0	0	4798	304	11	4	1575	4	DTX3L	3	122288501	Missense_Mutation	SNP	A	TCGA-MI-A75C-01A-11D-A32G-10	81019735	122288501	75733929	27	45039										
PCYT1A	5130	hgsc.bcm.edu	37	chr3	195975135	195975135	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	cgcttgcatcagagctcgggCgtgaccagagtgaaataagt	13	9	1	4			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr3:195975135C>A	ENST00000292823.2	-	5	449	c.277G>T	c.(277-279)Gcc>Tcc	p.A93S	PCYT1A_ENST00000419333.1_Missense_Mutation_p.A93S|PCYT1A_ENST00000431016.1_Missense_Mutation_p.A93S|RP11-447L10.1_ENST00000431391.1_3'UTR|AC069257.8_ENST00000608995.1_RNA|AC069257.8_ENST00000425275.1_RNA|PCYT1A_ENST00000491544.1_5'UTR	NM_005017.2	NP_005008.2	P49585	PCY1A_HUMAN	phosphate cytidylyltransferase 1, choline, alpha	93					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|glycogen granule (GO:0042587)	choline-phosphate cytidylyltransferase activity (GO:0004105)|lipid binding (GO:0008289)			cervix(1)|endometrium(3)|large_intestine(8)|lung(5)|ovary(1)	18	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.28e-24)|all cancers(36;1.01e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00259)	Choline(DB00122)|Lamivudine(DB00709)	AGAGCTCGGGCGTGACCAGAG	0.413																																					p.A93S		Atlas-SNP	.											.	PCYT1A	34	.	0			c.G277T						.						120	117	118					3																	195975135		2203	4300	6503	SO:0001583	missense	5130	exon5			CTCGGGCGTGACC	L28957	CCDS3315.1	3q29	2010-07-19	2005-09-05		ENSG00000161217	ENSG00000161217	2.7.7.15		8754	protein-coding gene	gene with protein product	"phosphate cytidylyltransferase 1, choline, alpha isoform"	123695	"phosphate cytidylyltransferase 1, choline, alpha isoform"	PCYT1		7918629	Standard	NM_005017		Approved	CT, CTPCT	uc003fwg.3	P49585	OTTHUMG00000155670	ENST00000292823.2:c.277G>T	chr3.hg19:g.195975135C>A	ENSP00000292823:p.Ala93Ser	80.0	0.0		63.0	26.0	NM_005017	A9LYK9|D3DXB1|Q86Y88	Missense_Mutation	SNP	ENST00000292823.2	hg19	CCDS3315.1	.	.	.	.	.	.	.	.	.	.	c	36	5.722870	0.96847	.	.	ENSG00000161217	ENST00000441879;ENST00000419333;ENST00000292823;ENST00000416798;ENST00000431016;ENST00000411591;ENST00000430755;ENST00000412869;ENST00000443555	D;D;D;D;D;D;D;D	0.96856	-4.15;-4.15;-4.15;-4.15;-4.15;-4.15;-4.15;-4.15	5.98	5.98	0.97165	Cytidylyltransferase (1);Rossmann-like alpha/beta/alpha sandwich fold (1);Cytidyltransferase-related (1);	0.000000	0.85682	D	0.000000	D	0.98362	0.9456	M	0.87758	2.905	0.80722	D	1	D	0.54601	0.967	D	0.68765	0.96	D	0.98794	1.0737	10	0.87932	D	0	-46.947	19.5104	0.95139	0.0:1.0:0.0:0.0	.	93	P49585	PCY1A_HUMAN	S	93;93;93;54;93;93;27;93;93	ENSP00000392397:A93S;ENSP00000390968:A93S;ENSP00000292823:A93S;ENSP00000394617:A93S;ENSP00000400430:A93S;ENSP00000402283:A27S;ENSP00000402015:A93S;ENSP00000393341:A93S	ENSP00000292823:A93S	A	-	1	0	PCYT1A	197459532	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.485000	0.81204	2.853000	0.98044	0.645000	0.84053	GCC	.	.		0.413	PCYT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341147.1	NM_005017		A	195975135	C	A	195975135	3	1	320	1	0	0	0	0	1	0	0	0	11619	768	27	1	850	1	PCYT1A	3	195975135	Missense_Mutation	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	73686634	195975135	2047295	28	45040										
ZNF595	152687	hgsc.bcm.edu	37	chr4	59395	59395	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	aatgtctggaccctgcccagCagaatttgtatagagatgtg	11	8	1	2			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr4:59395C>T	ENST00000509152.2	+	2	261	c.76C>T	c.(76-78)Cag>Tag	p.Q26*	ZNF595_ENST00000526473.2_Nonsense_Mutation_p.Q26*|ZNF595_ENST00000339368.6_3'UTR			Q8IYB9	ZN595_HUMAN	zinc finger protein 595	26	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(1)|large_intestine(1)|lung(11)|prostate(2)	20		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		CCCTGCCCAGCAGAATTTGTA	0.428																																					p.Q26X		Atlas-SNP	.											ZNF595,NS,carcinoma,0,1	.	.	.	0			c.C76T						.						369	402	391					4																	59395		2203	4300	6503	SO:0001587	stop_gained	255403	exon2			GCCCAGCAGAATT	BX537887	CCDS75075.1, CCDS75076.1, CCDS75077.1	4p16.3	2013-01-08				ENSG00000272602		"Zinc fingers, C2H2-type", "-"	27196	protein-coding gene	gene with protein product						12477932	Standard	NM_182524		Approved	FLJ31740		Q8IYB9		ENST00000509152.2:c.76C>T	chr4.hg19:g.59395C>T	ENSP00000434858:p.Gln26*	268.0	0.0		226.0	13.0	NM_001039127		Nonsense_Mutation	SNP	ENST00000509152.2	hg19		.	.	.	.	.	.	.	.	.	.	C	13.23	2.176256	0.38413	.	.	ENSG00000197701	ENST00000509152;ENST00000526473	.	.	.	1.26	-1.81	0.07882	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	.	2.1827	0.03879	0.4478:0.3171:0.0:0.235	.	.	.	.	X	26	.	ENSP00000434858:Q26X	Q	+	1	0	ZNF595	49395	0.480000	0.25933	0.019000	0.16419	0.037000	0.13140	-0.178000	0.09782	-0.157000	0.11059	0.484000	0.47621	CAG	.	.		0.428	ZNF595-004	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000357817.2	NM_182524		T	59395	C	T	59395	4	4	320	1	0	0	0	0	0	1	0	0	18040	711	25	3	82	3	ZNF595	4	59395	Nonsense_Mutation	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10		59395	191094881	29	45041										
FAM190A	401145	hgsc.bcm.edu	37	chr4	91389492	91389492	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	gagaagaaccagaatttcctGagccttccaaacagtgagtt	9	9	0	5			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr4:91389492G>A	ENST00000509176.1	+	5	1999	c.1711G>A	c.(1711-1713)Gag>Aag	p.E571K	CCSER1_ENST00000432775.2_Missense_Mutation_p.E571K|CCSER1_ENST00000333691.8_Missense_Mutation_p.E571K	NM_001145065.1	NP_001138537.1	Q9C0I3	CCSE1_HUMAN	coiled-coil serine-rich protein 1	571																	AGAATTTCCTGAGCCTTCCAA	0.343																																					p.E571K		Atlas-SNP	.											.	.	.	.	0			c.G1711A						.						73	70	71					4																	91389492		1820	4075	5895	SO:0001583	missense	401145	exon5			TTTCCTGAGCCTT		CCDS47099.1, CCDS47100.1	4q22.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184305	ENSG00000184305			29349	protein-coding gene	gene with protein product			"family with sequence similarity 190, member A"	FAM190A		11214970	Standard	NM_001145065		Approved	KIAA1680	uc003hsv.4	Q9C0I3	OTTHUMG00000160950	ENST00000509176.1:c.1711G>A	chr4.hg19:g.91389492G>A	ENSP00000425040:p.Glu571Lys	171.0	0.0		145.0	42.0	NM_001145065	Q4W5M0|Q86V57	Missense_Mutation	SNP	ENST00000509176.1	hg19	CCDS47099.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.277939	0.80692	.	.	ENSG00000184305	ENST00000509176;ENST00000432775;ENST00000333691;ENST00000458365	T;T;T	0.43294	1.51;0.95;1.51	4.63	4.63	0.57726	.	0.212785	0.40144	N	0.001178	T	0.37019	0.0988	N	0.17082	0.46	0.32536	N	0.534297	P;D	0.54207	0.782;0.965	B;P	0.50270	0.24;0.636	T	0.44467	-0.9326	10	0.37606	T	0.19	-17.1105	15.2528	0.73561	0.0:0.0:1.0:0.0	.	571;571	Q9C0I3-2;Q9C0I3	.;F190A_HUMAN	K	571	ENSP00000425040:E571K;ENSP00000389283:E571K;ENSP00000329482:E571K	ENSP00000329482:E571K	E	+	1	0	FAM190A	91608515	1.000000	0.71417	0.985000	0.45067	0.974000	0.67602	5.103000	0.64578	2.514000	0.84764	0.467000	0.42956	GAG	.	.		0.343	CCSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363109.3	NM_001145065		A	91389492	G	A	91389492	3	1	320	1	0	0	0	0	1	0	0	0	5526	1291	45	3	1725	3	FAM190A	4	91389492	Missense_Mutation	SNP	G	TCGA-MI-A75C-01A-11D-A32G-10	91330097	91389492	99764784	30	45042										
SFRP2	6423	hgsc.bcm.edu	37	chr4	154709533	154709533	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	cgctgctagcgagggggatgCaaaggtcgttgtcctggggg	19	8	0	0			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr4:154709533C>A	ENST00000274063.4	-	1	739	c.455G>T	c.(454-456)tGc>tTc	p.C152F		NM_003013.2	NP_003004.1	Q96HF1	SFRP2_HUMAN	secreted frizzled-related protein 2	152	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				bone morphogenesis (GO:0060349)|brain development (GO:0007420)|cardiac left ventricle morphogenesis (GO:0003214)|cell-cell signaling (GO:0007267)|cellular response to extracellular stimulus (GO:0031668)|cellular response to X-ray (GO:0071481)|chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|convergent extension involved in axis elongation (GO:0060028)|digestive tract morphogenesis (GO:0048546)|embryonic digit morphogenesis (GO:0042733)|gonad development (GO:0008406)|hematopoietic stem cell proliferation (GO:0071425)|male gonad development (GO:0008584)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dermatome development (GO:0061185)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of gene expression (GO:0010629)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of mesodermal cell fate specification (GO:0042662)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of planar cell polarity pathway involved in axis elongation (GO:2000041)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-anal tail morphogenesis (GO:0036342)|regulation of stem cell division (GO:2000035)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|sclerotome development (GO:0061056)|vasculature development (GO:0001944)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	endopeptidase activator activity (GO:0061133)|fibronectin binding (GO:0001968)|integrin binding (GO:0005178)|metalloenzyme activator activity (GO:0010577)|PDZ domain binding (GO:0030165)|receptor agonist activity (GO:0048018)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(1)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	16	all_hematologic(180;0.093)	Renal(120;0.117)				GAGGGGGATGCAAAGGTCGTT	0.657																																					p.C152F		Atlas-SNP	.											.	SFRP2	45	.	0			c.G455T						.						69	67	68					4																	154709533		2203	4300	6503	SO:0001583	missense	6423	exon1			GGGATGCAAAGGT	AF017986	CCDS34082.1	4q31.3	2008-08-29			ENSG00000145423	ENSG00000145423		"Secreted frizzled-related proteins"	10777	protein-coding gene	gene with protein product		604157				9391078	Standard	NM_003013		Approved	SARP1, SDF-5, FRP-2	uc003inv.1	Q96HF1	OTTHUMG00000161559	ENST00000274063.4:c.455G>T	chr4.hg19:g.154709533C>A	ENSP00000274063:p.Cys152Phe	60.0	0.0		57.0	25.0	NM_003013	B3KQR2|O14778|Q9HAP5	Missense_Mutation	SNP	ENST00000274063.4	hg19	CCDS34082.1	.	.	.	.	.	.	.	.	.	.	C	18.17	3.564531	0.65651	.	.	ENSG00000145423	ENST00000274063	D	0.93547	-3.24	5.1	5.1	0.69264	Frizzled domain (5);	0.000000	0.85682	D	0.000000	D	0.97860	0.9297	H	0.95574	3.69	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99013	1.0815	10	0.87932	D	0	.	18.8637	0.92282	0.0:1.0:0.0:0.0	.	152	Q96HF1	SFRP2_HUMAN	F	152	ENSP00000274063:C152F	ENSP00000274063:C152F	C	-	2	0	SFRP2	154928983	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.685000	0.84117	2.528000	0.85240	0.591000	0.81541	TGC	.	.		0.657	SFRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365296.1			A	154709533	C	A	154709533	3	1	320	1	0	0	0	0	1	0	0	0	14177	710	25	3	444	3	SFRP2	4	154709533	Missense_Mutation	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	63320041	154709533	36444743	31	45043										
STOX2	56977	hgsc.bcm.edu	37	chr4	184931082	184931082	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	taaaaagagtaggactcatcGgaagtcccatggaaagtctc	10	8	2	1			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr4:184931082G>A	ENST00000308497.4	+	3	2526	c.1091G>A	c.(1090-1092)cGg>cAg	p.R364Q	STOX2_ENST00000438269.1_Missense_Mutation_p.R364Q	NM_020225.1	NP_064610.1	Q9P2F5	STOX2_HUMAN	storkhead box 2	364					embryo development (GO:0009790)|maternal placenta development (GO:0001893)					breast(1)|endometrium(7)|lung(6)	14		all_lung(41;1.89e-12)|Lung NSC(41;3.48e-12)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|all_hematologic(60;0.027)|Prostate(90;0.0283)		all cancers(43;2.85e-26)|Epithelial(43;2.27e-22)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-10)|Colorectal(24;8.23e-06)|GBM - Glioblastoma multiforme(59;1.64e-05)|STAD - Stomach adenocarcinoma(60;3.6e-05)|COAD - Colon adenocarcinoma(29;4.37e-05)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.227)		AGGACTCATCGGAAGTCCCAT	0.517																																					p.R364Q		Atlas-SNP	.											.	STOX2	142	.	0			c.G1091A						.						33	32	32					4																	184931082		1898	4122	6020	SO:0001583	missense	56977	exon3			CTCATCGGAAGTC	AB037813	CCDS47167.1	4q35.1	2014-09-11			ENSG00000173320	ENSG00000173320			25450	protein-coding gene	gene with protein product							Standard	XM_005263142		Approved	DKFZp762K222	uc003ivz.1	Q9P2F5	OTTHUMG00000160618	ENST00000308497.4:c.1091G>A	chr4.hg19:g.184931082G>A	ENSP00000311257:p.Arg364Gln	89.0	0.0		47.0	21.0	NM_020225	A6H8U4|Q9NPS8	Missense_Mutation	SNP	ENST00000308497.4	hg19	CCDS47167.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.713573	0.89112	.	.	ENSG00000173320	ENST00000308497;ENST00000438269	T;T	0.80824	-0.42;-1.42	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.85423	0.5693	L	0.32530	0.975	0.80722	D	1	D;D	0.71674	0.991;0.998	P;D	0.66602	0.585;0.945	D	0.84479	0.0604	10	0.51188	T	0.08	-14.2328	20.8794	0.99867	0.0:0.0:1.0:0.0	.	364;364	Q9P2F5-2;Q9P2F5	.;STOX2_HUMAN	Q	364	ENSP00000311257:R364Q;ENSP00000390127:R364Q	ENSP00000311257:R364Q	R	+	2	0	STOX2	185168076	1.000000	0.71417	0.764000	0.31436	0.807000	0.45602	9.476000	0.97823	2.941000	0.99782	0.655000	0.94253	CGG	.	.		0.517	STOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361433.3	NM_020225		A	184931082	G	A	184931082	3	1	320	1	0	0	0	0	1	0	0	0	15335	1116	39	1	1101	1	STOX2	4	184931082	Missense_Mutation	SNP	G	TCGA-MI-A75C-01A-11D-A32G-10	30221549	184931082	6223194	32	45044										
VCAN	1462	hgsc.bcm.edu	37	chr5	82816091	82816091	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	atcgtacagaaatagaattgTttccttattctggtgataaa	7	5	1	3			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr5:82816091T>C	ENST00000265077.3	+	7	2531	c.1966T>C	c.(1966-1968)Ttt>Ctt	p.F656L	VCAN_ENST00000502527.2_Intron|VCAN_ENST00000343200.5_Intron|VCAN_ENST00000512590.2_Missense_Mutation_p.F608L|VCAN_ENST00000342785.4_Missense_Mutation_p.F656L	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	656	GAG-alpha (glucosaminoglycan attachment domain).				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	AATAGAATTGTTTCCTTATTC	0.358																																					p.F656L		Atlas-SNP	.											.	VCAN	498	.	0			c.T1966C						.						104	104	104					5																	82816091		2203	4299	6502	SO:0001583	missense	1462	exon7			GAATTGTTTCCTT	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.1966T>C	chr5.hg19:g.82816091T>C	ENSP00000265077:p.Phe656Leu	89.0	0.0		60.0	19.0	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	hg19	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	T	10.37	1.331274	0.24167	.	.	ENSG00000038427	ENST00000265077;ENST00000342785;ENST00000512590	T;T;T	0.17054	2.3;2.3;2.3	5.81	0.539	0.17156	.	0.427521	0.22294	N	0.061951	T	0.08846	0.0219	L	0.36672	1.1	0.19300	N	0.999971	B;B	0.26445	0.021;0.149	B;B	0.23716	0.013;0.048	T	0.28038	-1.0056	10	0.17369	T	0.5	.	0.8554	0.01181	0.1658:0.1772:0.1547:0.5024	.	656;656	P13611-3;P13611	.;CSPG2_HUMAN	L	656;656;608	ENSP00000265077:F656L;ENSP00000342768:F656L;ENSP00000425959:F608L	ENSP00000265077:F656L	F	+	1	0	VCAN	82851847	0.002000	0.14202	0.070000	0.20053	0.942000	0.58702	0.010000	0.13242	-0.125000	0.11703	0.533000	0.62120	TTT	.	.		0.358	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		C	82816091	T	C	82816091	3	2	320	1	0	0	0	0	1	0	0	0	17153	1725	60	2	1988	2	VCAN	5	82816091	Missense_Mutation	SNP	T	TCGA-MI-A75C-01A-11D-A32G-10		82816091	98099169	33	45045										
EPB41L4A	64097	hgsc.bcm.edu	37	chr5	111598279	111598279	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	cctcagaaggaatctgacccCtacacccagcacaaaaacaa	5	15	2	2			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr5:111598279C>T	ENST00000261486.5	-	7	831		c.e7-1			NM_022140.3	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte membrane protein band 4.1 like 4A							cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(2)|skin(1)	34		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		AATCTGACCCCTACACCCAGC	0.428																																					.		Atlas-SNP	.											.	EPB41L4A	130	.	0			c.555-1G>A						.						85	86	86					5																	111598279		1912	4111	6023	SO:0001630	splice_region_variant	64097	exon8			TGACCCCTACACC	AB030240	CCDS43350.1	5q21.3	2008-02-05			ENSG00000129595	ENSG00000129595			13278	protein-coding gene	gene with protein product		612141				10874211	Standard	XM_005272043		Approved	NBL4	uc003kpv.1	Q9HCS5	OTTHUMG00000162902	ENST00000261486.5:c.555-1G>A	chr5.hg19:g.111598279C>T		57.0	0.0		61.0	20.0	NM_022140	A4FUI6	Splice_Site	SNP	ENST00000261486.5	hg19	CCDS43350.1	.	.	.	.	.	.	.	.	.	.	C	17.03	3.284077	0.59867	.	.	ENSG00000129595	ENST00000261486	.	.	.	5.54	5.54	0.83059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.6127	0.91291	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	EPB41L4A	111626178	1.000000	0.71417	0.998000	0.56505	0.659000	0.38960	5.914000	0.69964	2.764000	0.94973	0.655000	0.94253	.	.	.		0.428	EPB41L4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370969.1		Intron	T	111598279	C	T	111598279	5	4	320	1	0	0	0	0	0	0	1	0	5157	695	24	3	1574	3	EPB41L4A	5	111598279	Splice_Site	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	28782188	111598279	69316981	34	45046										
SAR1B	51128	hgsc.bcm.edu	37	chr5	133945276	133945276	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	cttacatcaagttcttctttTgactctaacagcctttcgtg	5	11	4	1			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr5:133945276T>A	ENST00000402673.2	-	5	611	c.333A>T	c.(331-333)tcA>tcT	p.S111S	SAR1B_ENST00000502539.1_Silent_p.S43S|SAR1B_ENST00000507419.1_Silent_p.S43S|SAR1B_ENST00000439578.1_Silent_p.S111S|SAR1B_ENST00000509937.1_Silent_p.S43S	NM_016103.3	NP_057187.1	Q9Y6B6	SAR1B_HUMAN	secretion associated, Ras related GTPase 1B	111					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|GTP catabolic process (GO:0006184)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)			kidney(2)|lung(2)|urinary_tract(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GTTCTTCTTTTGACTCTAACA	0.393																																					p.S111S		Atlas-SNP	.											.	SAR1B	19	.	0			c.A333T						.						115	104	107					5																	133945276		2203	4300	6503	SO:0001819	synonymous_variant	51128	exon6			TTCTTTTGACTCT	AF092130	CCDS4177.1	5q31.1	2014-03-07	2014-03-07	2005-10-21	ENSG00000152700	ENSG00000152700			10535	protein-coding gene	gene with protein product		607690	"SAR1a gene homolog (S. cerevisiae) 2", "SAR1a gene homolog 2 (S. cerevisiae)", "SAR1 homolog B (S. cerevisiae)"	SARA2			Standard	NM_001033503		Approved		uc003kzr.3	Q9Y6B6	OTTHUMG00000129114	ENST00000402673.2:c.333A>T	chr5.hg19:g.133945276T>A		94.0	0.0		78.0	29.0	NM_001033503	D3DQA4|Q567T4	Silent	SNP	ENST00000402673.2	hg19	CCDS4177.1																																																																																			.	.		0.393	SAR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251158.2	NM_016103		A	133945276	T	A	133945276	2	1	320	1	0	0	0	0	0	0	0	1	13855	1799	63	4		4	SAR1B	5	133945276	Silent	SNP	T	TCGA-MI-A75C-01A-11D-A32G-10	22346997	133945276	46969984	35	45047										
HSPA9	3313	hgsc.bcm.edu	37	chr5	137902698	137902699	+	Missense_Mutation	DNP	TG	TG	GT													0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ttggtaactcacctctctctTgaactccttcacaatgtgcc					rs202180095|rs199831172		TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	T|G	T|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr5:137902698_137902699TG>GT	ENST00000297185.3	-	8	995_996	c.870_871CA>AC	c.(868-873)ttCAag>ttACag	p.290_291FK>LQ	HSPA9_ENST00000501917.2_5'Flank	NM_004134.6	NP_004125.3	P38646	GRP75_HUMAN	heat shock 70kDa protein 9 (mortalin)	290					cellular protein metabolic process (GO:0044267)|negative regulation of apoptotic process (GO:0043066)|protein export from nucleus (GO:0006611)|protein folding (GO:0006457)|protein targeting to mitochondrion (GO:0006626)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(1)|kidney(4)|large_intestine(8)|lung(12)|upper_aerodigestive_tract(1)	28			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			ACCTCTCTCTTGAACTCCTTCA	0.416																																					p.K291Q|p.F290L		Atlas-SNP	.											.	HSPA9	49	.	0			c.A871C|c.C870A						.																																			SO:0001583	missense	3313	exon8			CTCTCTTGAACTC|TCTCTTGAACTCC	L11066	CCDS4208.1	5q31.1	2011-09-02	2006-10-31	2006-10-31	ENSG00000113013	ENSG00000113013		"Heat shock proteins / HSP70"	5244	protein-coding gene	gene with protein product		600548	"heat shock 70kDa protein 9B (mortalin-2)"	HSPA9B		7684501	Standard	NM_004134		Approved	GRP75, PBP74, mot-2, mthsp75	uc003ldf.3	P38646	OTTHUMG00000129206	ENST00000297185.3:c.870_871delinsGT	chr5.hg19:g.137902698_137902699delinsGT	ENSP00000297185:p.F290_K291delinsLQ	209.0|211.0	0.0		172.0|174.0	16.0	NM_004134	B2RCM1|P30036|P31932|Q1HB43|Q53H23|Q6GU03|Q9BWB7|Q9UC56	Missense_Mutation	SNP	ENST00000297185.3	hg19	CCDS4208.1																																																																																			.	T|0.999;G|0.001|G|0.999;T|0.001		0.416	HSPA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251285.1	NM_004134		GT	137902699	TG	GT	137902698	3	3	320	1	0	0	0	0	1	0	0	0	7426	1821	63	5	1208	5	HSPA9	5	137902698	Missense_Mutation	DNP	TG	TCGA-MI-A75C-01A-11D-A32G-10	3957422	137902698	43012562	36	45048										
SOX30	11063	hgsc.bcm.edu	37	chr5	157053726	157053726	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ggaggccgactgtaagggcaTgtactgcagcagaaaaacac	13	9	0	1			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr5:157053726T>C	ENST00000265007.6	-	5	2225	c.1884A>G	c.(1882-1884)acA>acG	p.T628T	SOX30_ENST00000519442.1_Silent_p.T323T|SOX30_ENST00000311371.5_Missense_Mutation_p.H464R	NM_178424.1	NP_848511.1	O94993	SOX30_HUMAN	SRY (sex determining region Y)-box 30	628	Pro-rich.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to corticosteroid (GO:0031960)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	23	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TGTAAGGGCATGTACTGCAGC	0.433																																					p.H464R	Esophageal Squamous(31;525 799 19355 21125 41744)	Atlas-SNP	.											.	SOX30	67	.	0			c.A1391G						.						42	43	43					5																	157053726		2199	4293	6492	SO:0001819	synonymous_variant	11063	exon4			AGGGCATGTACTG	AB022083	CCDS4339.1, CCDS4340.1	5q33	2010-10-21			ENSG00000039600	ENSG00000039600		"SRY (sex determining region Y)-boxes"	30635	protein-coding gene	gene with protein product		606698				15019997, 11678506	Standard	NM_178424		Approved		uc003lxb.1	O94993	OTTHUMG00000130247	ENST00000265007.6:c.1884A>G	chr5.hg19:g.157053726T>C		39.0	0.0		48.0	17.0	NM_007017	O94995|Q8IYX6	Missense_Mutation	SNP	ENST00000265007.6	hg19	CCDS4339.1	.	.	.	.	.	.	.	.	.	.	T	5.009	0.187393	0.09547	.	.	ENSG00000039600	ENST00000311371	D	0.97575	-4.44	5.56	-8.43	0.00953	.	.	.	.	.	D	0.91382	0.7281	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.67821	-0.5571	8	0.52906	T	0.07	.	3.7413	0.08532	0.0889:0.2643:0.1751:0.4717	.	464	O94993-2	.	R	464	ENSP00000309343:H464R	ENSP00000309343:H464R	H	-	2	0	SOX30	156986304	0.070000	0.21116	0.581000	0.28614	0.301000	0.27625	-1.231000	0.02939	-1.599000	0.01605	-1.253000	0.01494	CAT	.	.		0.433	SOX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252571.2	NM_007017		C	157053726	T	C	157053726	2	2	320	1	0	0	0	0	0	0	0	1	14967	1464	51	2		2	SOX30	5	157053726	Silent	SNP	T	TCGA-MI-A75C-01A-11D-A32G-10	19151028	157053726	23861534	37	45049										
GABRA6	2559	hgsc.bcm.edu	37	chr5	161113294	161113294	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	acttctactcagaaaacgtcAgtcggatcctggacaacttg	8	11	3	1			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr5:161113294A>G	ENST00000274545.5	+	2	530	c.97A>G	c.(97-99)Agt>Ggt	p.S33G	GABRA6_ENST00000522269.1_3'UTR|RP11-348M17.2_ENST00000521984.1_RNA|GABRA6_ENST00000523217.1_Missense_Mutation_p.S33G			Q16445	GBRA6_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 6	33					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|liver(2)|lung(22)|ovary(7)|skin(6)|urinary_tract(2)	57	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	AGAAAACGTCAGTCGGATCCT	0.483										TCGA Ovarian(5;0.080)																											p.S33G		Atlas-SNP	.											.	GABRA6	139	.	0			c.A97G						.						112	113	112					5																	161113294		2203	4300	6503	SO:0001583	missense	2559	exon2			AACGTCAGTCGGA		CCDS4356.1	5q34	2012-06-22			ENSG00000145863	ENSG00000145863		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4080	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 6"	137143				8020978	Standard	NM_000811		Approved		uc003lyu.2	Q16445	OTTHUMG00000130351	ENST00000274545.5:c.97A>G	chr5.hg19:g.161113294A>G	ENSP00000274545:p.Ser33Gly	89.0	0.0		59.0	23.0	NM_000811	A8K096|Q4VAV2	Missense_Mutation	SNP	ENST00000274545.5	hg19	CCDS4356.1	.	.	.	.	.	.	.	.	.	.	A	17.98	3.521666	0.64747	.	.	ENSG00000145863	ENST00000274545;ENST00000523217	T;T	0.77750	-1.12;-1.12	5.63	5.63	0.86233	Neurotransmitter-gated ion-channel ligand-binding (3);	0.044841	0.85682	D	0.000000	T	0.81578	0.4852	M	0.72118	2.19	0.39704	D	0.971232	B	0.29955	0.263	B	0.42625	0.393	T	0.83144	-0.0107	10	0.87932	D	0	.	11.6013	0.51003	0.8668:0.0:0.0:0.1332	.	33	Q16445	GBRA6_HUMAN	G	33	ENSP00000274545:S33G;ENSP00000430527:S33G	ENSP00000274545:S33G	S	+	1	0	GABRA6	161045872	1.000000	0.71417	1.000000	0.80357	0.722000	0.41435	6.902000	0.75699	2.145000	0.66743	0.533000	0.62120	AGT	.	.		0.483	GABRA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252707.2			G	161113294	A	G	161113294	3	3	320	1	0	0	0	0	1	0	0	0	6173	188	7	2	103	2	GABRA6	5	161113294	Missense_Mutation	SNP	A	TCGA-MI-A75C-01A-11D-A32G-10	4059568	161113294	19801966	38	45050										
HIVEP1	3096	hgsc.bcm.edu	37	chr6	12120854	12120854	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ctcagaagaatgagcaagggGcaatgcagtcagcttctcat	11	9	3	3			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr6:12120854G>T	ENST00000379388.2	+	4	1158	c.826G>T	c.(826-828)Gca>Tca	p.A276S		NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	276					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				TGAGCAAGGGGCAATGCAGTC	0.448																																					p.A276S		Atlas-SNP	.											.	HIVEP1	242	.	0			c.G826T						.						113	105	107					6																	12120854		1944	4148	6092	SO:0001583	missense	3096	exon4			CAAGGGGCAATGC	J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"Zinc fingers, C2H2-type"	4920	protein-coding gene	gene with protein product		194540	"human immunodeficiency virus type I enhancer-binding protein 1", "zinc finger protein 40"	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.826G>T	chr6.hg19:g.12120854G>T	ENSP00000368698:p.Ala276Ser	102.0	0.0		82.0	36.0	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Missense_Mutation	SNP	ENST00000379388.2	hg19	CCDS43426.1	.	.	.	.	.	.	.	.	.	.	G	0.010	-1.754705	0.00663	.	.	ENSG00000095951	ENST00000379388	T	0.08546	3.08	5.17	-4.81	0.03180	.	0.806254	0.10135	N	0.711645	T	0.01287	0.0042	L	0.35414	1.06	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.47761	-0.9092	9	.	.	.	-1.0969	1.9728	0.03409	0.2448:0.4121:0.1564:0.1867	.	276	P15822	ZEP1_HUMAN	S	276	ENSP00000368698:A276S	.	A	+	1	0	HIVEP1	12228840	0.000000	0.05858	0.000000	0.03702	0.135000	0.20990	0.034000	0.13776	-0.837000	0.04223	-0.885000	0.02943	GCA	.	.		0.448	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114		T	12120854	G	T	12120854	3	4	320	1	0	0	0	0	1	0	0	0	7195	1203	42	3	836	3	HIVEP1	6	12120854	Missense_Mutation	SNP	G	TCGA-MI-A75C-01A-11D-A32G-10		12120854	158994213	39	45051										
MDC1	9656	hgsc.bcm.edu	37	chr6	30681730	30681731	+	Frame_Shift_Del	DEL	AG	AG	-													0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ctggcagagcaagtcagcaaAgagaatcaattcctggtccc							TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr6:30681730_30681731delAG	ENST00000376406.3	-	3	1013_1014	c.366_367delCT	c.(364-369)ctctttfs	p.F123fs	MDC1_ENST00000494654.1_5'Flank|MDC1-AS1_ENST00000442150.1_RNA|MDC1_ENST00000376405.2_Frame_Shift_Del_p.F123fs	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	123	Interaction with CHEK2.|Interaction with the MRN complex.				DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intra-S DNA damage checkpoint (GO:0031573)	chromosome (GO:0005694)|focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	FHA domain binding (GO:0070975)|protein C-terminus binding (GO:0008022)			breast(2)|kidney(1)|ovary(1)	4						AAGTCAGCAAAGAGAATCAATT	0.545								Other conserved DNA damage response genes																													p.123_123del		Atlas-Indel,Pindel	.											.	MDC1	218	.	0			c.367_368del						.																																			SO:0001589	frameshift_variant	9656	exon3			.	D79992	CCDS34384.1	6p21.3	2010-02-17	2009-06-12		ENSG00000137337	ENSG00000137337			21163	protein-coding gene	gene with protein product		607593				10975465, 12607005	Standard	NM_014641		Approved	NFBD1, KIAA0170, Em:AB023051.5	uc003nrg.4	Q14676	OTTHUMG00000031075	ENST00000376406.3:c.366_367delCT	chr6.hg19:g.30681732_30681733delAG	ENSP00000365588:p.Phe123fs	97.0	0.0		72.0	25.0	NM_014641	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Frame_Shift_Del	DEL	ENST00000376406.3	hg19	CCDS34384.1																																																																																			.	.		0.545	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641		-	30681731	AG	-	30681730	7	5	320	1	0	1	0	1	0	0	0	0	9412	72	3	0	5954	0	MDC1	6	30681730	Frame_Shift_Del	DEL	AG	TCGA-MI-A75C-01A-11D-A32G-10	18560876	30681730	140433337	40	45052										
SFRS13B	135295	hgsc.bcm.edu	37	chr6	89827583	89827583	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ctgatgaacagggaggtgttGgggggcctcgtgtagcgaga	19	6	0	3			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr6:89827583G>A	ENST00000452027.2	-	1	217	c.24C>T	c.(22-24)ccC>ccT	p.P8P		NM_080743.4	NP_542781.3	Q8WXF0	SRS12_HUMAN	serine/arginine-rich splicing factor 12	8					cytoplasmic transport (GO:0016482)|mRNA 5'-splice site recognition (GO:0000395)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|spliceosomal tri-snRNP complex assembly (GO:0000244)	nucleoplasm (GO:0005654)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RS domain binding (GO:0050733)|unfolded protein binding (GO:0051082)			autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(4)	8						GGGAGGTGTTGGGGGGCCTCG	0.711																																					p.P8P		Atlas-SNP	.											.	SRSF12	17	.	0			c.C24T						.						19	27	24					6																	89827583		2035	4179	6214	SO:0001819	synonymous_variant	135295	exon1			GGTGTTGGGGGGC	AF449428	CCDS47459.1	6q16.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000154548	ENSG00000154548		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	21220	protein-coding gene	gene with protein product	"splicing factor, arginine/serine-rich 19", "SR splicing factor 12"		"splicing factor, arginine/serine-rich 13B"	SFRS13B		11684676, 20516191	Standard	NM_080743		Approved	SRrp35, SFRS19	uc021zcq.1	Q8WXF0	OTTHUMG00000015192	ENST00000452027.2:c.24C>T	chr6.hg19:g.89827583G>A		76.0	0.0		98.0	43.0	NM_080743	B2RA22|Q5T7K0|Q8WW25	Silent	SNP	ENST00000452027.2	hg19	CCDS47459.1																																																																																			.	.		0.711	SRSF12-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041474.2	NM_080743		A	89827583	G	A	89827583	2	1	320	1	0	0	0	0	0	0	0	1	14184	1335	47	3		3	SFRS13B	6	89827583	Silent	SNP	G	TCGA-MI-A75C-01A-11D-A32G-10	59145853	89827583	81287484	41	45053										
ROS1	6098	hgsc.bcm.edu	37	chr6	117658467	117658619	+	Splice_Site	DEL	ATGAAGTTTTAACATGGTAAAACTCATTGTATTTCCACTAGAAAAAGAAGTCTCGATTAATATTTTTGTTTCTCTAAGAAAATATTCTTAAAACACAAAAATGTATAGGCTTATAGCAAGTGGTTAAAATTTAAGCATTCTTTTCTATTAAAG	ATGAAGTTTTAACATGGTAAAACTCATTGTATTTCCACTAGAAAAAGAAGTCTCGATTAATATTTTTGTTTCTCTAAGAAAATATTCTTAAAACACAAAAATGTATAGGCTTATAGCAAGTGGTTAAAATTTAAGCATTCTTTTCTATTAAAG	-													0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ataagcaggaccttggctgcAtgaagttttaacatggtaaa					rs573243428|rs200932342|rs150943500|rs143981354|rs112475836		TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	ATGAAGTTTTAACATGGTAAAACTCATTGTATTTCCACTAGAAAAAGAAGTCTCGATTAATATTTTTGTTTCTCTAAGAAAATATTCTTAAAACACAAAAATGTATAGGCTTATAGCAAGTGGTTAAAATTTAAGCATTCTTTTCTATTAAAG	ATGAAGTTTTAACATGGTAAAACTCATTGTATTTCCACTAGAAAAAGAAGTCTCGATTAATATTTTTGTTTCTCTAAGAAAATATTCTTAAAACACAAAAATGTATAGGCTTATAGCAAGTGGTTAAAATTTAAGCATTCTTTTCTATTAAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr6:117658467_117658619delATGAAGTTTTAACATGGTAAAACTCATTGTATTTCCACTAGAAAAAGAAGTCTCGATTAATATTTTTGTTTCTCTAAGAAAATATTCTTAAAACACAAAAATGTATAGGCTTATAGCAAGTGGTTAAAATTTAAGCATTCTTTTCTATTAAAG	ENST00000368508.3	-	31	5278_5314	c.5080_5116delCTTTAATAGAAAAGAATGCTTAAATTTTAACCACTTGCTATAAGCCTATACATTTTTGTGTTTTAAGAATATTTTCTTAGAGAAACAAAAATATTAATCGAGACTTCTTTTTCTAGTGGAAATACAATGAGTTTTACCATGTTAAAACTTCAT	c.(5080-5118)ctttaatagaaaagaatgcttaaattttaaccacttgct>ct	p.L**KRMLKF*PLA1694del	ROS1_ENST00000368507.3_Splice_Site_p.L**KRMLKF*PLA1688del|GOPC_ENST00000467125.1_Intron	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	1694	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		CCTTGGCTGCATGAAGTTTTAACATGGTAAAACTCATTGTATTTCCACTAGAAAAAGAAGTCTCGATTAATATTTTTGTTTCTCTAAGAAAATATTCTTAAAACACAAAAATGTATAGGCTTATAGCAAGTGGTTAAAATTTAAGCATTCTTTTCTATTAAAGAATAAGAACT	0.309			T	"GOPC, SDC4, SLC34A2, EZR, LRIG3"	"glioblastoma, NSCLC"																																p.1694_1706del		Pindel	.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"O, E"	.	ROS1	728	.	0			c.5080_5117del						.																																			SO:0001630	splice_region_variant	6098	exon31			.	M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"Fibronectin type III domain containing"	10261	protein-coding gene	gene with protein product		165020	"v-ros avian UR2 sarcoma virus oncogene homolog 1", "v-ros UR2 sarcoma virus oncogene homolog 1 (avian)", "c-ros oncogene 1 , receptor tyrosine kinase"			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.5080-1CTTTAATAGAAAAGAATGCTTAAATTTTAACCACTTGCTATAAGCCTATACATTTTTGTGTTTTAAGAATATTTTCTTAGAGAAACAAAAATATTAATCGAGACTTCTTTTTCTAGTGGAAATACAATGAGTTTTACCATGTTAAAACTTCAT>-	chr6.hg19:g.117658467_117658619delATGAAGTTTTAACATGGTAAAACTCATTGTATTTCCACTAGAAAAAGAAGTCTCGATTAATATTTTTGTTTCTCTAAGAAAATATTCTTAAAACACAAAAATGTATAGGCTTATAGCAAGTGGTTAAAATTTAAGCATTCTTTTCTATTAAAG		40.0	0.0		28.0	10.0	NM_002944	Q15368|Q5TDB5	Frame_Shift_Del	DEL	ENST00000368508.3	hg19	CCDS5116.1																																																																																			.	.		0.309	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1		In_Frame_Del	-	117658619	ATGAAGTTTTAACATGGTAAAACTCATTGTATTTCCACTAGAAAAAGAAGTCTCGATTAATATTTTTGTTTCTCTAAGAAAATATTCTTAAAACACAAAAATGTATAGGCTTATAGCAAGTGGTTAAAATTTAAGCATTCTTTTCTATTAAAG	-	117658467	8	5	320	1	0	1	0	1	0	0	1	0	13546	217	8	0	1979	0	ROS1	6	117658467	Splice_Site	DEL	ATGAAGTTTTAACATGGTAAAACTCATTGTATTTCCACTAGAAAAAGAAGTCTCGATTAATATTTTTGTTTCTCTAAGAAAATATTCTTAAAACACAAAAATGTATAGGCTTATAGCAAGTGGTTAAAATTTAAGCATTCTTTTCTATTAAAG	TCGA-MI-A75C-01A-11D-A32G-10	27830884	117658467	53456600	42	45054										
TIAM2	26230	hgsc.bcm.edu	37	chr6	155498070	155498070	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	gagttactgtagggatcaagCcagagcacagagtagaagat	13	6	1	4			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr6:155498070C>T	ENST00000461783.3	+	12	3755	c.2482C>T	c.(2482-2484)Cca>Tca	p.P828S	TIAM2_ENST00000318981.5_Missense_Mutation_p.P828S|TIAM2_ENST00000456144.1_Missense_Mutation_p.P828S|TIAM2_ENST00000529824.2_Missense_Mutation_p.P828S|TIAM2_ENST00000456877.2_Missense_Mutation_p.P140S|TIAM2_ENST00000528391.2_Missense_Mutation_p.P164S|TIAM2_ENST00000360366.4_Missense_Mutation_p.P852S|TIAM2_ENST00000367174.2_Missense_Mutation_p.P204S			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	828	RBD. {ECO:0000255|PROSITE- ProRule:PRU00262}.				apoptotic signaling pathway (GO:0097190)|cellular lipid metabolic process (GO:0044255)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(20)|lung(21)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	65		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		AGGGATCAAGCCAGAGCACAG	0.398																																					p.P828S		Atlas-SNP	.											.	TIAM2	161	.	0			c.C2482T						.						150	134	139					6																	155498070		2203	4300	6503	SO:0001583	missense	26230	exon9			ATCAAGCCAGAGC		CCDS34558.1, CCDS34559.1	6q25	2013-01-10			ENSG00000146426	ENSG00000146426		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11806	protein-coding gene	gene with protein product		604709				10512681	Standard	NM_012454		Approved	STEF	uc003qqe.3	Q8IVF5	OTTHUMG00000015880	ENST00000461783.3:c.2482C>T	chr6.hg19:g.155498070C>T	ENSP00000437188:p.Pro828Ser	71.0	0.0		72.0	30.0	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Missense_Mutation	SNP	ENST00000461783.3	hg19	CCDS34558.1	.	.	.	.	.	.	.	.	.	.	C	14.52	2.561315	0.45590	.	.	ENSG00000146426	ENST00000461783;ENST00000528928;ENST00000528535;ENST00000456144;ENST00000318981;ENST00000367174;ENST00000360366;ENST00000529824;ENST00000456877;ENST00000528391	T;T;T;T;T;T;T;T;T	0.05513	3.64;3.56;3.61;3.64;3.43;3.6;3.61;3.45;3.43	5.55	5.55	0.83447	Raf-like Ras-binding (2);	0.211686	0.42294	D	0.000721	T	0.03348	0.0097	L	0.48362	1.52	0.40816	D	0.983466	B;B;B;B	0.23058	0.079;0.023;0.048;0.013	B;B;B;B	0.19946	0.027;0.016;0.023;0.007	T	0.31052	-0.9957	10	0.39692	T	0.17	.	12.4036	0.55426	0.0:0.9225:0.0:0.0775	.	164;828;852;828	E9PKT1;Q8IVF5-2;Q8IVF5-5;Q8IVF5	.;.;.;TIAM2_HUMAN	S	828;1074;828;828;828;204;852;828;140;164	ENSP00000437188:P828S;ENSP00000434901:P828S;ENSP00000407746:P828S;ENSP00000327315:P828S;ENSP00000356142:P204S;ENSP00000353528:P852S;ENSP00000433348:P828S;ENSP00000407183:P140S;ENSP00000435335:P164S	ENSP00000327315:P828S	P	+	1	0	TIAM2	155539762	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	3.217000	0.51184	2.768000	0.95171	0.655000	0.94253	CCA	.	.		0.398	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454		T	155498070	C	T	155498070	3	4	320	1	0	0	0	0	1	0	0	0	15906	739	26	3	2508	3	TIAM2	6	155498070	Missense_Mutation	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	37839603	155498070	15616997	43	45055										
LAMB1	3912	hgsc.bcm.edu	37	chr7	107580787	107580787	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	tgtggcgtctcaatgcccctGgggtcacagtcacaggctag	13	12	3	0			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr7:107580787G>A	ENST00000222399.6	-	25	3638	c.3408C>T	c.(3406-3408)ccC>ccT	p.P1136P	LAMB1_ENST00000393561.1_Silent_p.P1160P|CTB-13F3.1_ENST00000608515.1_RNA	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	1136	Laminin EGF-like 13. {ECO:0000255|PROSITE-ProRule:PRU00460}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|neuron projection development (GO:0031175)|neuronal-glial interaction involved in cerebral cortex radial glia guided migration (GO:0021812)|odontogenesis (GO:0042476)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell proliferation (GO:0050679)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-2 complex (GO:0005607)|laminin-8 complex (GO:0043257)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)|structural molecule activity (GO:0005198)			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						CAATGCCCCTGGGGTCACAGT	0.522																																					p.P1136P		Atlas-SNP	.											LAMB1,right_upper_lobe,carcinoma,0,1	LAMB1	185	.	0			c.C3408T						.						60	53	56					7																	107580787		2203	4300	6503	SO:0001819	synonymous_variant	3912	exon25			GCCCCTGGGGTCA	M61916	CCDS5750.1	7q22	2013-03-01			ENSG00000091136	ENSG00000091136		"Laminins"	6486	protein-coding gene	gene with protein product		150240	"cutis laxa with marfanoid phenotype"	CLM		2563160, 2704655, 1864606	Standard	NM_002291		Approved		uc003vew.2	P07942	OTTHUMG00000149966	ENST00000222399.6:c.3408C>T	chr7.hg19:g.107580787G>A		34.0	0.0		42.0	18.0	NM_002291	Q14D91	Silent	SNP	ENST00000222399.6	hg19	CCDS5750.1																																																																																			.	.		0.522	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291		A	107580787	G	A	107580787	2	1	320	1	0	0	0	0	0	0	0	1	8619	1335	47	3		3	LAMB1	7	107580787	Silent	SNP	G	TCGA-MI-A75C-01A-11D-A32G-10		107580787	51557876	44	45056										
MLL3	58508	hgsc.bcm.edu	37	chr7	151945190	151945190	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ggaagacacatctgccttgcTtatgtctgctgatgatgaaa	10	8	2	4			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr7:151945190T>A	ENST00000262189.6	-	14	2547	c.2329A>T	c.(2329-2331)Agc>Tgc	p.S777C	KMT2C_ENST00000355193.2_Missense_Mutation_p.S777C	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	777					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.S777C(2)									TCTGCCTTGCTTATGTCTGCT	0.423																																					p.S777C		Atlas-SNP	.											MLL3_ENST00000355193,NS,carcinoma,0,2	MLL3	1564	.	2	Substitution - Missense(2)	lung(2)	c.A2329T						.						230	204	213					7																	151945190		2203	4300	6503	SO:0001583	missense	58508	exon14			CCTTGCTTATGTC	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.2329A>T	chr7.hg19:g.151945190T>A	ENSP00000262189:p.Ser777Cys	284.0	0.0		265.0	11.0	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	hg19	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	T	9.745	1.165912	0.21538	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.84442	-1.85;-1.85	5.68	2.04	0.26737	.	0.152963	0.33712	N	0.004631	T	0.74574	0.3734	N	0.19112	0.55	0.28561	N	0.911108	D	0.57257	0.979	P	0.46362	0.514	T	0.69822	-0.5041	10	0.72032	D	0.01	.	6.0078	0.19557	0.1219:0.1332:0.0:0.7449	.	777	Q8NEZ4	MLL3_HUMAN	C	777	ENSP00000262189:S777C;ENSP00000347325:S777C	ENSP00000262189:S777C	S	-	1	0	MLL3	151576123	0.058000	0.20735	0.099000	0.21106	0.065000	0.16274	1.463000	0.35277	0.106000	0.17784	-0.309000	0.09137	AGC	.	.		0.423	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			A	151945190	T	A	151945190	3	1	320	1	0	0	0	0	1	0	0	0	9631	1609	56	4	12590	4	MLL3	7	151945190	Missense_Mutation	SNP	T	TCGA-MI-A75C-01A-11D-A32G-10	44364403	151945190	7193473	45	45057										
STMN4	81551	hgsc.bcm.edu	37	chr8	27099966	27099966	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	tcggccaggaagcaggagcaGaacaaggacaccagcgggag	16	10	0	1			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr8:27099966G>A	ENST00000265770.7	-	3	193	c.57C>T	c.(55-57)ttC>ttT	p.F19F	STMN4_ENST00000519997.1_Silent_p.F10F|STMN4_ENST00000522908.1_Silent_p.F19F|STMN4_ENST00000350889.4_Silent_p.F19F|STMN4_ENST00000519614.1_Silent_p.F19F|STMN4_ENST00000523048.1_Silent_p.F19F			Q9H169	STMN4_HUMAN	stathmin-like 4	19					regulation of microtubule polymerization or depolymerization (GO:0031110)	cell projection (GO:0042995)|Golgi apparatus (GO:0005794)				endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)	11		Ovarian(32;0.00167)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0214)|Epithelial(17;9.82e-10)|Colorectal(74;0.142)	Lomustine(DB01206)	AGCAGGAGCAGAACAAGGACA	0.577																																					p.F19F		Atlas-SNP	.											.	STMN4	28	.	0			c.C57T						.						105	99	101					8																	27099966		2203	4300	6503	SO:0001819	synonymous_variant	81551	exon3			GGAGCAGAACAAG		CCDS6055.1, CCDS64851.1, CCDS64852.1, CCDS64854.1	8p21.2	2006-12-09			ENSG00000015592	ENSG00000015592			16078	protein-coding gene	gene with protein product						11230166	Standard	NM_001283054		Approved	RB3	uc003xfj.3	Q9H169	OTTHUMG00000099461	ENST00000265770.7:c.57C>T	chr8.hg19:g.27099966G>A		56.0	0.0		47.0	29.0	NM_030795	B7Z2Z7|B7Z4I9|D3DSS8|D3DSS9|G5EA16|Q2TAB9	Silent	SNP	ENST00000265770.7	hg19																																																																																				.	.		0.577	STMN4-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000375941.1	NM_030795		A	27099966	G	A	27099966	2	1	320	1	0	0	0	0	0	0	0	1	15326	933	33	3		3	STMN4	8	27099966	Silent	SNP	G	TCGA-MI-A75C-01A-11D-A32G-10		27099966	119264056	46	45058										
RP1	6101	hgsc.bcm.edu	37	chr8	55533949	55533949	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	gcgcactcaccgccccacccCgtagccgtcgctgctcccgg	10	22	1	0			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr8:55533949C>T	ENST00000220676.1	+	2	571	c.423C>T	c.(421-423)ccC>ccT	p.P141P		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	141					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			CGCCCCACCCCGTAGCCGTCG	0.697																																					p.P141P	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.C423T						.						28	34	32					8																	55533949		2193	4296	6489	SO:0001819	synonymous_variant	6101	exon2			CCACCCCGTAGCC	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.423C>T	chr8.hg19:g.55533949C>T		47.0	0.0		109.0	25.0	NM_006269		Silent	SNP	ENST00000220676.1	hg19	CCDS6160.1																																																																																			.	.		0.697	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		T	55533949	C	T	55533949	2	4	320	1	0	0	0	0	0	0	0	1	13547	639	23	1		1	RP1	8	55533949	Silent	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	28433983	55533949	90830073	47	45059										
HNF4G	3174	hgsc.bcm.edu	37	chr8	76471204	76471204	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	cacgtggcaaatgattgagcAaatacagtttgttaaacttt	8	6	0	2			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr8:76471204A>T	ENST00000354370.1	+	9	1184	c.914A>T	c.(913-915)cAa>cTa	p.Q305L	HNF4G_ENST00000396423.2_Missense_Mutation_p.Q342L			Q14541	HNF4G_HUMAN	hepatocyte nuclear factor 4, gamma	305					endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	37	Breast(64;0.0448)		BRCA - Breast invasive adenocarcinoma(89;0.161)			ATGATTGAGCAAATACAGTTT	0.413																																					p.Q342L		Atlas-SNP	.											.	HNF4G	111	.	0			c.A1025T						.						92	90	91					8																	76471204		2203	4300	6503	SO:0001583	missense	3174	exon8			TTGAGCAAATACA		CCDS6220.2	8q21-q22	2013-01-16			ENSG00000164749	ENSG00000164749		"Nuclear hormone receptors"	5026	protein-coding gene	gene with protein product		605966				8622695, 12220494	Standard	NM_004133		Approved	NR2A2	uc003yar.3	Q14541	OTTHUMG00000149920	ENST00000354370.1:c.914A>T	chr8.hg19:g.76471204A>T	ENSP00000346339:p.Gln305Leu	78.0	0.0		136.0	20.0	NM_004133	Q7Z2V9|Q9UH81|Q9UIS6	Missense_Mutation	SNP	ENST00000354370.1	hg19		.	.	.	.	.	.	.	.	.	.	A	29.3	4.994405	0.93167	.	.	ENSG00000164749	ENST00000354370;ENST00000396423	D;D	0.96745	-4.11;-4.11	5.52	5.52	0.82312	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (1);	0.000000	0.85682	D	0.000000	D	0.97281	0.9111	M	0.70787	2.145	0.80722	D	1	P;D	0.56521	0.898;0.976	B;P	0.58013	0.43;0.831	D	0.97878	1.0290	10	0.87932	D	0	.	15.6365	0.76958	1.0:0.0:0.0:0.0	.	342;305	F1D8Q4;Q14541	.;HNF4G_HUMAN	L	305;342	ENSP00000346339:Q305L;ENSP00000379701:Q342L	ENSP00000346339:Q305L	Q	+	2	0	HNF4G	76633759	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.281000	0.95811	2.093000	0.63338	0.533000	0.62120	CAA	.	.		0.413	HNF4G-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000313914.2	NM_004133		T	76471204	A	T	76471204	3	4	320	1	0	0	0	0	1	0	0	0	7263	130	5	4	1055	4	HNF4G	8	76471204	Missense_Mutation	SNP	A	TCGA-MI-A75C-01A-11D-A32G-10	20937255	76471204	69892818	48	45060										
POU5F1B	5462	hgsc.bcm.edu	37	chr8	128428177	128428199	+	Frame_Shift_Del	DEL	ATGGGGGGCGGAGCCGGGCTGGG	ATGGGGGGCGGAGCCGGGCTGGG	-													0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ggcggtgggggtgatgggccAtggggggcggagccgggctg					rs531267041|rs551358165		TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	ATGGGGGGCGGAGCCGGGCTGGG	ATGGGGGGCGGAGCCGGGCTGGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr8:128428177_128428199delATGGGGGGCGGAGCCGGGCTGGG	ENST00000465342.2	+	2	1223_1245	c.66_88delATGGGGGGCGGAGCCGGGCTGGG	c.(64-90)ccatggggggcggagccgggctgggttfs	p.WGAEPGWV23fs	POU5F1B_ENST00000391675.1_Frame_Shift_Del_p.WGAEPGWV23fs|CASC8_ENST00000502082.1_RNA|CASC8_ENST00000501396.1_RNA|CASC8_ENST00000523825.1_RNA			Q06416	P5F1B_HUMAN	POU class 5 homeobox 1B	23				WGA -> GGP (in Ref. 5; ADE48566/ ADE48597). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(1)|prostate(1)|urinary_tract(1)	3						GTGATGGGCCATGGGGGGCGGAGCCGGGCTGGGTTGATCCTCT	0.7																																					p.22_29del		Atlas-INDEL	.											.	POU5F1B	32	.	0			c.65_87del						.																																			SO:0001589	frameshift_variant	5462	exon1			.	AF268615	CCDS55274.1	8q24.21	2011-06-20	2009-04-15	2009-04-15	ENSG00000212993	ENSG00000212993		"Homeoboxes / POU class"	9223	protein-coding gene	gene with protein product		615739	"POU domain class 5, transcription factor 1 pseudogene 1", "POU class 5 homeobox 1 pseudogene 1"	OTF3P1, POU5F1P1		1408763	Standard	NM_001159542		Approved	OTF3C	uc003ysf.3	Q06416	OTTHUMG00000157807	ENST00000465342.2:c.66_88delATGGGGGGCGGAGCCGGGCTGGG	chr8.hg19:g.128428177_128428199delATGGGGGGCGGAGCCGGGCTGGG	ENSP00000419298:p.Trp23fs	56.0	0.0		76.0	10.0	NM_001159542	D5K9S4|D5K9S9|D5K9T0|D5K9T1|D5K9T3|D5K9U3|D5K9U6|D5K9V4|D5K9V6|D5K9W0|D5K9W2|D5K9W7|D5K9X2|D5K9X3|D5K9X5|D5K9X8|D5K9X9|E9LRB1|E9LRB2|E9LRH5|E9LRH6|E9LRH7|E9LRK4|E9LRK5|E9LRK7|E9LRK8|E9LRM7|E9LRM9|E9LRN2|E9LRN4|E9LRN5|E9LRP8|E9LRQ0|E9LRQ2|E9LRQ3|E9LRQ4|E9LRQ5|E9LRS3|Q2VIK6|Q9BZV7|Q9BZV9	Frame_Shift_Del	DEL	ENST00000465342.2	hg19	CCDS55274.1																																																																																			.	.		0.7	POU5F1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349649.2	NM_001159542		-	128428199	ATGGGGGGCGGAGCCGGGCTGGG	-	128428177	7	5	320	1	0	1	0	1	0	0	0	0	12291	204	8	0	68	0	POU5F1B	8	128428177	Frame_Shift_Del	DEL	ATGGGGGGCGGAGCCGGGCTGGG	TCGA-MI-A75C-01A-11D-A32G-10	51956973	128428177	17935845	49	45061										
CYP11B2	1585	hgsc.bcm.edu	37	chr8	143994269	143994269	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	gcaccaagtctgagctcaccActcgctccaaaaacagaccc	6	17	2	2			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr8:143994269A>G	ENST00000323110.2	-	7	1156	c.1154T>C	c.(1153-1155)gTg>gCg	p.V385A		NM_000498.3	NP_000489.3	P19099	C11B2_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 2	385					aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|mineralocorticoid biosynthetic process (GO:0006705)|potassium ion homeostasis (GO:0055075)|regulation of blood volume by renal aldosterone (GO:0002017)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	corticosterone 18-monooxygenase activity (GO:0047783)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(22)|ovary(3)|upper_aerodigestive_tract(3)	39	all_cancers(97;5.56e-11)|all_epithelial(106;2.49e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Eplerenone(DB00700)|Etomidate(DB00292)|Hydrocortisone(DB00741)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Spironolactone(DB00421)	TGAGCTCACCACTCGCTCCAA	0.592									Familial Hyperaldosteronism type I																												p.V385A		Atlas-SNP	.											.	CYP11B2	107	.	0			c.T1154C						.						84	76	79					8																	143994269		2203	4300	6503	SO:0001583	missense	1585	exon7	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	CTCACCACTCGCT	X54741	CCDS6393.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000179142	ENSG00000179142	1.14.15.4	"Cytochrome P450s"	2592	protein-coding gene	gene with protein product	"steroid 11-beta-monooxygenase"	124080	"cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 2"	CYP11B		1303253	Standard	NM_000498		Approved	CYP11BL, CPN2, P-450C18, P450aldo, ALDOS	uc003yxk.1	P19099	OTTHUMG00000160254	ENST00000323110.2:c.1154T>C	chr8.hg19:g.143994269A>G	ENSP00000325822:p.Val385Ala	68.0	0.0		131.0	20.0	NM_000498	B0ZBE4|Q16726	Missense_Mutation	SNP	ENST00000323110.2	hg19	CCDS6393.1	.	.	.	.	.	.	.	.	.	.	.	8.707	0.911008	0.17833	.	.	ENSG00000179142	ENST00000323110	T	0.68479	-0.33	2.96	-5.92	0.02261	.	4.047030	0.00738	N	0.000984	T	0.43656	0.1257	N	0.20357	0.565	0.09310	N	1	B	0.11235	0.004	B	0.20384	0.029	T	0.19031	-1.0318	10	0.23302	T	0.38	.	0.0342	0.00006	0.3101:0.2235:0.1884:0.278	rs28930074	385	P19099	C11B2_HUMAN	A	385	ENSP00000325822:V385A	ENSP00000325822:V385A	V	-	2	0	CYP11B2	143991271	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.492000	0.22435	-1.752000	0.01325	0.460000	0.39030	GTG	.	.		0.592	CYP11B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359904.1			G	143994269	A	G	143994269	3	3	320	1	0	0	0	0	1	0	0	0	4148	159	6	2	369	2	CYP11B2	8	143994269	Missense_Mutation	SNP	A	TCGA-MI-A75C-01A-11D-A32G-10	15566092	143994269	2369753	50	45062										
NFKBIL2	4796	hgsc.bcm.edu	37	chr8	145660436	145660436	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	agcacatcagggatgaggtcCtgtggggccagcagggcccc	16	12	1	1			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr8:145660436C>G	ENST00000409379.3	-	19	2999	c.2970G>C	c.(2968-2970)caG>caC	p.Q990H	AC084125.4_ENST00000442850.1_RNA|AC084125.4_ENST00000544423.1_RNA	NM_013432.4	NP_038460.4	Q96HA7	TONSL_HUMAN	tonsoku-like, DNA repair protein	990					cytoplasmic sequestering of transcription factor (GO:0042994)|double-strand break repair via homologous recombination (GO:0000724)|regulation of RNA biosynthetic process (GO:2001141)|replication fork processing (GO:0031297)	cytoplasm (GO:0005737)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	histone binding (GO:0042393)|transcription corepressor activity (GO:0003714)			biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|lung(14)|ovary(3)|prostate(1)|skin(1)	26						GGATGAGGTCCTGTGGGGCCA	0.706																																					p.Q990H		Atlas-SNP	.											.	TONSL	128	.	0			c.G2970C						.						20	22	21					8																	145660436		2201	4298	6499	SO:0001583	missense	4796	exon19			GAGGTCCTGTGGG		CCDS34968.2	8q24.3	2013-01-10	2010-12-02	2010-11-30	ENSG00000160949	ENSG00000160949		"Ankyrin repeat domain containing"	7801	protein-coding gene	gene with protein product		604546	"nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 2"	NFKBIL2		7738005, 11246458	Standard	NM_013432		Approved	IKBR	uc011llg.2	Q96HA7	OTTHUMG00000153122	ENST00000409379.3:c.2970G>C	chr8.hg19:g.145660436C>G	ENSP00000386239:p.Gln990His	59.0	0.0		106.0	26.0	NM_013432	B5MDP0|C9JKB1|C9JNV8|Q13006|Q9UGJ2	Missense_Mutation	SNP	ENST00000409379.3	hg19	CCDS34968.2	.	.	.	.	.	.	.	.	.	.	C	11.37	1.617331	0.28801	.	.	ENSG00000160949	ENST00000409379;ENST00000422691	T	0.44083	0.93	4.81	1.97	0.26223	.	0.069344	0.64402	D	0.000020	T	0.29620	0.0739	L	0.41824	1.3	0.46167	D	0.998906	B	0.18461	0.028	B	0.13407	0.009	T	0.06770	-1.0808	10	0.39692	T	0.17	-27.5114	7.156	0.25637	0.0:0.6178:0.0:0.3822	.	990	Q96HA7	TONSL_HUMAN	H	990;989	ENSP00000386239:Q990H	ENSP00000386239:Q990H	Q	-	3	2	TONSL	145631244	0.993000	0.37304	0.992000	0.48379	0.875000	0.50365	0.297000	0.19101	0.452000	0.26830	0.491000	0.48974	CAG	.	.		0.706	TONSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329668.2	NM_013432		G	145660436	C	G	145660436	3	3	320	1	0	0	0	0	1	0	0	0	10391	680	24	4	1198	4	NFKBIL2	8	145660436	Missense_Mutation	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	1666167	145660436	703586	51	45063										
TOPORS	10210	hgsc.bcm.edu	37	chr9	32543636	32543636	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	cacgttttaaccaggggactAatctgtgaaggcaagctgga	12	8	1	1			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr9:32543636A>G	ENST00000360538.2	-	3	1003	c.887T>C	c.(886-888)tTa>tCa	p.L296S	TOPORS_ENST00000379858.1_Missense_Mutation_p.L231S	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	296	Required for DNA-binding.				cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of apoptotic process (GO:0043066)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein localization to nucleus (GO:0034504)|protein monoubiquitination (GO:0006513)|protein sumoylation (GO:0016925)|regulation of cell proliferation (GO:0042127)|retina layer formation (GO:0010842)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|gamma-tubulin complex (GO:0000930)|midbody (GO:0030496)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|PML body (GO:0016605)|spindle pole (GO:0000922)|ubiquitin ligase complex (GO:0000151)	antigen binding (GO:0003823)|DNA binding (GO:0003677)|DNA topoisomerase binding (GO:0044547)|SUMO ligase activity (GO:0019789)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		CCAGGGGACTAATCTGTGAAG	0.403																																					p.L296S		Atlas-SNP	.											.	TOPORS	127	.	0			c.T887C						.						56	56	56					9																	32543636		2203	4299	6502	SO:0001583	missense	10210	exon3			GGGACTAATCTGT	AF098300	CCDS6527.1, CCDS56566.1	9p21	2013-01-09	2010-09-17		ENSG00000197579	ENSG00000197579		"RING-type (C3HC4) zinc fingers"	21653	protein-coding gene	gene with protein product		609507	"retinitis pigmentosa 31 (autosomal dominant)", "topoisomerase I binding, arginine/serine-rich"	RP31		10352183, 12083797, 17924349	Standard	NM_005802		Approved	TP53BPL, LUN	uc003zrb.3	Q9NS56	OTTHUMG00000019743	ENST00000360538.2:c.887T>C	chr9.hg19:g.32543636A>G	ENSP00000353735:p.Leu296Ser	31.0	0.0		35.0	9.0	NM_005802	O43273|Q6P987|Q9NS55|Q9UNR9	Missense_Mutation	SNP	ENST00000360538.2	hg19	CCDS6527.1	.	.	.	.	.	.	.	.	.	.	A	14.09	2.432275	0.43122	.	.	ENSG00000197579	ENST00000360538;ENST00000379858	T;T	0.35789	1.29;1.32	5.93	5.93	0.95920	.	0.000000	0.36066	N	0.002810	T	0.64216	0.2578	M	0.83312	2.635	0.50632	D	0.999885	D	0.89917	1.0	D	0.85130	0.997	T	0.69566	-0.5111	10	0.87932	D	0	-20.062	15.3592	0.74457	1.0:0.0:0.0:0.0	.	296	Q9NS56	TOPRS_HUMAN	S	296;231	ENSP00000353735:L296S;ENSP00000369187:L231S	ENSP00000353735:L296S	L	-	2	0	TOPORS	32533636	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.927000	0.92846	2.263000	0.75096	0.533000	0.62120	TTA	.	.		0.403	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802		G	32543636	A	G	32543636	3	3	320	1	0	0	0	0	1	0	0	0	16385	372	13	2	2254	2	TOPORS	9	32543636	Missense_Mutation	SNP	A	TCGA-MI-A75C-01A-11D-A32G-10		32543636	108669795	52	45064										
RECK	8434	hgsc.bcm.edu	37	chr9	36116999	36116999	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	caggtgcatacccaaaccacAggtctgcctgacgacttttg	9	13	1	1			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr9:36116999A>T	ENST00000377966.3	+	17	2644	c.2078A>T	c.(2077-2079)cAg>cTg	p.Q693L		NM_021111.2	NP_066934.1	O95980	RECK_HUMAN	reversion-inducing-cysteine-rich protein with kazal motifs	693					blood vessel maturation (GO:0001955)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)	anchored component of membrane (GO:0031225)|membrane (GO:0016020)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(7)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|pancreas(1)|skin(2)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(32;0.112)|STAD - Stomach adenocarcinoma(86;0.228)			CCCAAACCACAGGTCTGCCTG	0.498																																					p.Q693L		Atlas-SNP	.											.	RECK	73	.	0			c.A2078T						.						150	132	138					9																	36116999		2203	4300	6503	SO:0001583	missense	8434	exon17			AACCACAGGTCTG	E13833	CCDS6597.1	9p13.3	2008-05-15			ENSG00000122707	ENSG00000122707			11345	protein-coding gene	gene with protein product		605227		ST15		9789069	Standard	NM_021111		Approved	hRECK	uc003zyv.3	O95980	OTTHUMG00000019898	ENST00000377966.3:c.2078A>T	chr9.hg19:g.36116999A>T	ENSP00000367202:p.Gln693Leu	93.0	0.0		78.0	4.0	NM_021111	B2RNS1|Q5W0K6|Q8WX37	Missense_Mutation	SNP	ENST00000377966.3	hg19	CCDS6597.1	.	.	.	.	.	.	.	.	.	.	A	16.60	3.168416	0.57584	.	.	ENSG00000122707	ENST00000377966	T	0.45668	0.89	5.91	5.91	0.95273	.	0.068805	0.64402	D	0.000007	T	0.36880	0.0983	L	0.46157	1.445	0.41849	D	0.99016	P;P	0.35328	0.495;0.495	B;B	0.30716	0.119;0.119	T	0.27365	-1.0076	10	0.51188	T	0.08	-11.7409	14.3004	0.66346	1.0:0.0:0.0:0.0	.	693;693	A8K9D8;O95980	.;RECK_HUMAN	L	693	ENSP00000367202:Q693L	ENSP00000367202:Q693L	Q	+	2	0	RECK	36106999	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.193000	0.65120	2.254000	0.74563	0.533000	0.62120	CAG	.	.		0.498	RECK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052409.1			T	36116999	A	T	36116999	3	4	320	1	0	0	0	0	1	0	0	0	13215	188	7	4	2144	4	RECK	9	36116999	Missense_Mutation	SNP	A	TCGA-MI-A75C-01A-11D-A32G-10	3573363	36116999	105096432	53	45065										
ANXA1	301	hgsc.bcm.edu	37	chr9	75782426	75782426	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ctaacagtgaagtgcgccacAagcaaaccagctttctttgc	8	12	1	1			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr9:75782426A>T	ENST00000376911.1	+	10	1698	c.816A>T	c.(814-816)acA>acT	p.T272T	ANXA1_ENST00000257497.6_Silent_p.T272T			P04083	ANXA1_HUMAN	annexin A1	272					alpha-beta T cell differentiation (GO:0046632)|arachidonic acid secretion (GO:0050482)|cell surface receptor signaling pathway (GO:0007166)|cellular component movement (GO:0006928)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to hydrogen peroxide (GO:0070301)|endocrine pancreas development (GO:0031018)|estrous cycle phase (GO:0060206)|gliogenesis (GO:0042063)|hepatocyte differentiation (GO:0070365)|inflammatory response (GO:0006954)|insulin secretion (GO:0030073)|keratinocyte differentiation (GO:0030216)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of apoptotic process (GO:0043066)|negative regulation of catalytic activity (GO:0043086)|negative regulation of interleukin-8 secretion (GO:2000483)|neutrophil clearance (GO:0097350)|neutrophil homeostasis (GO:0001780)|peptide cross-linking (GO:0018149)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of neutrophil apoptotic process (GO:0033031)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of vesicle fusion (GO:0031340)|regulation of cell proliferation (GO:0042127)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to interleukin-1 (GO:0070555)|response to peptide hormone (GO:0043434)|response to X-ray (GO:0010165)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cilium (GO:0005929)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|phospholipase A2 inhibitor activity (GO:0019834)|phospholipid binding (GO:0005543)|protein binding, bridging (GO:0030674)|receptor binding (GO:0005102)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|large_intestine(1)|lung(5)	8		all_epithelial(88;2.54e-11)		OV - Ovarian serous cystadenocarcinoma(323;2.82e-06)|GBM - Glioblastoma multiforme(74;0.0325)	Amcinonide(DB00288)|Dexamethasone(DB01234)|Hydrocortisone(DB00741)	AGTGCGCCACAAGCAAACCAG	0.328																																					p.T272T		Atlas-SNP	.											.	ANXA1	27	.	0			c.A816T						.						109	107	107					9																	75782426		2203	4299	6502	SO:0001819	synonymous_variant	301	exon11			CGCCACAAGCAAA	X05908	CCDS6645.1	9q21.13	2013-02-25			ENSG00000135046	ENSG00000135046		"Annexins", "Endogenous ligands"	533	protein-coding gene	gene with protein product		151690		ANX1, LPC1		2936963	Standard	NM_000700		Approved		uc004ajf.1	P04083	OTTHUMG00000020016	ENST00000376911.1:c.816A>T	chr9.hg19:g.75782426A>T		150.0	0.0		123.0	9.0	NM_000700		Silent	SNP	ENST00000376911.1	hg19	CCDS6645.1																																																																																			.	.		0.328	ANXA1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052665.1	NM_000700		T	75782426	A	T	75782426	2	4	320	1	0	0	0	0	0	0	0	1	714	117	5	4		4	ANXA1	9	75782426	Silent	SNP	A	TCGA-MI-A75C-01A-11D-A32G-10	39665427	75782426	65431005	54	45066										
OR13C9	286362	hgsc.bcm.edu	37	chr9	107379836	107379836	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	tggaaatgattaatgagtaaGagataactatcaagagcagt	10	3	1	4			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr9:107379836G>T	ENST00000259362.1	-	1	649	c.650C>A	c.(649-651)tCt>tAt	p.S217Y		NM_001001956.1	NP_001001956.1	Q8NGT0	O13C9_HUMAN	olfactory receptor, family 13, subfamily C, member 9	217						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(6)|lung(9)|prostate(1)|skin(4)	22						TAATGAGTAAGAGATAACTAT	0.448																																					p.S217Y		Atlas-SNP	.											.	OR13C9	42	.	0			c.C650A						.						87	80	82					9																	107379836		2202	4300	6502	SO:0001583	missense	286362	exon1			GAGTAAGAGATAA		CCDS35093.1	9q31.1	2013-09-24			ENSG00000136839	ENSG00000136839		"GPCR / Class A : Olfactory receptors"	15104	protein-coding gene	gene with protein product							Standard	NM_001001956		Approved		uc011lvr.2	Q8NGT0	OTTHUMG00000020416	ENST00000259362.1:c.650C>A	chr9.hg19:g.107379836G>T	ENSP00000259362:p.Ser217Tyr	71.0	0.0		52.0	21.0	NM_001001956	Q6IFL2	Missense_Mutation	SNP	ENST00000259362.1	hg19	CCDS35093.1	.	.	.	.	.	.	.	.	.	.	G	15.38	2.817518	0.50633	.	.	ENSG00000136839	ENST00000259362	T	0.46063	0.88	4.46	4.46	0.54185	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47093	D	0.000260	T	0.78149	0.4238	H	0.98883	4.36	0.28238	N	0.925805	D	0.89917	1.0	D	0.87578	0.998	T	0.78959	-0.1998	10	0.87932	D	0	.	14.6428	0.68737	0.0:0.0:1.0:0.0	.	217	Q8NGT0	O13C9_HUMAN	Y	217	ENSP00000259362:S217Y	ENSP00000259362:S217Y	S	-	2	0	OR13C9	106419657	1.000000	0.71417	0.219000	0.23793	0.643000	0.38383	7.303000	0.78871	2.271000	0.75665	0.643000	0.83706	TCT	.	.		0.448	OR13C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053490.1			T	107379836	G	T	107379836	3	4	320	1	0	0	0	0	1	0	0	0	10948	942	33	3	309	3	OR13C9	9	107379836	Missense_Mutation	SNP	G	TCGA-MI-A75C-01A-11D-A32G-10	31597410	107379836	33833595	55	45067										
SEC16A	9919	hgsc.bcm.edu	37	chr9	139371483	139371483	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ggggatgctgctggggtgacCacaccgtcatgtgggttttg	17	8	1	1			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr9:139371483C>A	ENST00000371706.3	-	1	84	c.51G>T	c.(49-51)gtG>gtT	p.V17V	SEC16A_ENST00000290037.6_Silent_p.V17V|SEC16A_ENST00000313050.7_Silent_p.V195V|SEC16A_ENST00000431893.2_Silent_p.V17V			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	17					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|protein transport (GO:0015031)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)				breast(1)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(15)|lung(14)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)		CTGGGGTGACCACACCGTCAT	0.642																																					p.V195V		Atlas-SNP	.											.	SEC16A	249	.	0			c.G585T						.						59	66	63					9																	139371483		2105	4211	6316	SO:0001819	synonymous_variant	9919	exon3			GGTGACCACACCG	AK074565	CCDS55351.1, CCDS75936.1	9q34.3	2007-06-20	2007-06-20	2007-06-20	ENSG00000148396	ENSG00000148396			29006	protein-coding gene	gene with protein product		612854	"KIAA0310"	KIAA0310		9205841	Standard	NM_014866		Approved	p250	uc004chx.3	O15027	OTTHUMG00000020932	ENST00000371706.3:c.51G>T	chr9.hg19:g.139371483C>A		54.0	0.0		52.0	24.0	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Silent	SNP	ENST00000371706.3	hg19																																																																																				.	.		0.642	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459		A	139371483	C	A	139371483	2	1	320	1	0	0	0	0	0	0	0	1	14001	581	21	3		3	SEC16A	9	139371483	Silent	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	31991647	139371483	1841948	56	45068										
RBP3	5949	hgsc.bcm.edu	37	chr10	48390301	48390301	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	gatagtgtccacgtgcaggaTggtgttccctgggtgcaggt	16	8	0	0			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr10:48390301T>C	ENST00000224600.4	-	1	690	c.577A>G	c.(577-579)Atc>Gtc	p.I193V	AL731561.2_ENST00000581861.1_RNA	NM_002900.2	NP_002891.1	P10745	RET3_HUMAN	retinol binding protein 3, interstitial	193	4 X approximate tandem repeats.				lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transport (GO:0006810)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|interphotoreceptor matrix (GO:0033165)|vesicle (GO:0031982)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(30)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59					Vitamin A(DB00162)	ACGTGCAGGATGGTGTTCCCT	0.602																																					p.I193V		Atlas-SNP	.											.	RBP3	152	.	0			c.A577G						.						112	108	109					10																	48390301		2203	4300	6503	SO:0001583	missense	5949	exon1			GCAGGATGGTGTT	M22453	CCDS73119.1	10q11.2	2014-05-06	2001-11-28		ENSG00000107618	ENSG00000265203			9921	protein-coding gene	gene with protein product		180290	"retinol-binding protein 3, interstitial"				Standard	NM_002900		Approved	D10S64, D10S65, D10S66, RP66	uc001jez.3	P10745	OTTHUMG00000188321	ENST00000224600.4:c.577A>G	chr10.hg19:g.48390301T>C	ENSP00000224600:p.Ile193Val	159.0	0.0		121.0	6.0	NM_002900	Q0QD34|Q5VSR0|Q8IXN0	Missense_Mutation	SNP	ENST00000224600.4	hg19	CCDS7218.1	.	.	.	.	.	.	.	.	.	.	T	0.004	-2.249440	0.00268	.	.	ENSG00000107618	ENST00000224600	T	0.63580	-0.05	5.71	1.29	0.21616	Interphotoreceptor retinol-binding (2);	1.002030	0.08041	N	0.995104	T	0.24699	0.0599	N	0.00282	-1.705	0.09310	N	1	B	0.20550	0.046	B	0.34824	0.19	T	0.43572	-0.9383	10	0.02654	T	1	-38.3308	5.9919	0.19472	0.0:0.5154:0.143:0.3416	.	193	P10745	RET3_HUMAN	V	193	ENSP00000224600:I193V	ENSP00000224600:I193V	I	-	1	0	RBP3	48010307	0.000000	0.05858	0.009000	0.14445	0.350000	0.29205	0.105000	0.15333	0.355000	0.24131	-0.959000	0.02639	ATC	.	.		0.602	RBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047888.1	NM_002900		C	48390301	T	C	48390301	3	2	320	1	0	0	0	0	1	0	0	0	13172	1464	51	2	3182	2	RBP3	10	48390301	Missense_Mutation	SNP	T	TCGA-MI-A75C-01A-11D-A32G-10		48390301	87144446	57	45069										
PARG	8505	hgsc.bcm.edu	37	chr10	51040916	51040916	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	gtggccactgcagaaagattCtctgaagaaactccaggacg	11	10	1	4			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr10:51040916C>A	ENST00000402038.3	-	12	1124	c.1125G>T	c.(1123-1125)gaG>gaT	p.E375D	PARG_ENST00000492350.1_5'UTR	NM_003631.2	NP_003622.2	Q86W56	PARG_HUMAN	poly (ADP-ribose) glycohydrolase	860	A-domain.				carbohydrate metabolic process (GO:0005975)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	poly(ADP-ribose) glycohydrolase activity (GO:0004649)			endometrium(5)|kidney(2)|lung(1)|ovary(2)	10				Epithelial(53;0.213)		CAGAAAGATTCTCTGAAGAAA	0.453																																					p.E860D		Atlas-SNP	.											.	PARG	46	.	0			c.G2580T						.						74	70	71					10																	51040916		692	1591	2283	SO:0001583	missense	8505	exon16			AAGATTCTCTGAA	AF005043	CCDS73130.1	10q11.23	2012-04-20			ENSG00000227345	ENSG00000227345	3.2.1.143		8605	protein-coding gene	gene with protein product		603501				9115250, 10449915	Standard	NM_003631		Approved		uc001jif.3	Q86W56	OTTHUMG00000018201	ENST00000402038.3:c.1125G>T	chr10.hg19:g.51040916C>A	ENSP00000384408:p.Glu375Asp	199.0	0.0		150.0	44.0	NM_003631	A5YBK3|B2RC24|B4DIU5|B4DYR4|I6RUV3|Q6E4P6|Q6E4P7|Q7Z742|Q9Y4W7	Missense_Mutation	SNP	ENST00000402038.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.64|10.64	1.406817|1.406817	0.25378|0.25378	.|.	.|.	ENSG00000227345|ENSG00000227345	ENST00000402038|ENST00000432127	.|.	.|.	.|.	5.67|5.67	1.73|1.73	0.24493|0.24493	.|.	0.145331|.	0.64402|.	D|.	0.000010|.	T|T	0.24547|0.24547	0.0595|0.0595	N|N	0.16743|0.16743	0.435|0.435	.|.	.|.	.|.	P;P;B;P;B;B;P|.	0.45283|.	0.622;0.855;0.356;0.525;0.116;0.143;0.768|.	B;P;B;B;B;B;B|.	0.47015|.	0.146;0.534;0.084;0.124;0.062;0.084;0.415|.	T|T	0.30297|0.30297	-0.9983|-0.9983	8|4	0.19590|.	T|.	0.45|.	-13.7566|-13.7566	5.233|5.233	0.15432|0.15432	0.1307:0.4435:0.0:0.4258|0.1307:0.4435:0.0:0.4258	.|.	778;860;411;128;375;400;860|.	Q86W56-2;Q86W56;A5YBK3;B4DHS4;Q5SQP4;B4DX76;Q0MQR4|.	.;PARG_HUMAN;.;.;.;.;.|.	D|I	375|76	.|.	ENSP00000384408:E375D|.	E|R	-|-	3|2	2|0	PARG|PARG	50710922|50710922	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.897000|0.897000	0.52465|0.52465	0.964000|0.964000	0.29306|0.29306	0.064000|0.064000	0.16427|0.16427	-0.136000|-0.136000	0.14681|0.14681	GAG|AGA	.	.		0.453	PARG-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048011.2	NM_003631		A	51040916	C	A	51040916	3	1	320	1	0	0	0	0	1	0	0	0	11457	912	32	3	362	3	PARG	10	51040916	Missense_Mutation	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	2650615	51040916	84493831	58	45070										
COL13A1	1305	hgsc.bcm.edu	37	chr10	71688713	71688713	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	gggcctcctggtcttcctggGcaaattggcccacctggagc	13	14	1	0			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr10:71688713G>T	ENST00000398978.3	+	27	1902	c.1410G>T	c.(1408-1410)ggG>ggT	p.G470G	COL13A1_ENST00000522165.1_Silent_p.G451G|COL13A1_ENST00000354547.3_Silent_p.G448G|COL13A1_ENST00000398968.3_Silent_p.G451G|COL13A1_ENST00000517713.1_Silent_p.G448G|COL13A1_ENST00000398973.3_Silent_p.G470G|COL13A1_ENST00000398966.3_Silent_p.G448G|COL13A1_ENST00000520133.1_Silent_p.G419G|COL13A1_ENST00000398969.3_Silent_p.G413G|COL13A1_ENST00000357811.3_Silent_p.G448G|COL13A1_ENST00000520267.1_Silent_p.G413G|COL13A1_ENST00000398974.3_Silent_p.G458G|COL13A1_ENST00000356340.3_Silent_p.G470G|COL13A1_ENST00000398971.3_Silent_p.G470G|COL13A1_ENST00000398972.3_Silent_p.G470G|COL13A1_ENST00000398964.3_Silent_p.G441G	NM_001130103.1	NP_001123575.1			collagen, type XIII, alpha 1											endometrium(5)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	28						GTCTTCCTGGGCAAATTGGCC	0.557																																					p.G470G		Atlas-SNP	.											.	COL13A1	133	.	0			c.G1410T						.						61	65	64					10																	71688713		1852	4093	5945	SO:0001819	synonymous_variant	1305	exon27			TCCTGGGCAAATT	AJ293624	CCDS44419.1, CCDS44423.1, CCDS44424.1, CCDS44425.1, CCDS44427.1, CCDS44428.1, CCDS44423.2, CCDS44424.2, CCDS44425.2, CCDS44427.2, CCDS44428.2	10q22	2013-01-16			ENSG00000197467	ENSG00000197467		"Collagens"	2190	protein-coding gene	gene with protein product		120350					Standard	NM_001130103		Approved		uc001jql.3	Q5TAT6	OTTHUMG00000018394	ENST00000398978.3:c.1410G>T	chr10.hg19:g.71688713G>T		122.0	0.0		62.0	11.0	NM_001130103		Silent	SNP	ENST00000398978.3	hg19	CCDS44419.1	.	.	.	.	.	.	.	.	.	.	G	9.296	1.051945	0.19827	.	.	ENSG00000197467	ENST00000398975	D	0.99353	-5.77	4.84	2.44	0.29823	.	0.000000	0.56097	D	0.000038	D	0.98516	0.9505	.	.	.	0.80722	D	1	.	.	.	.	.	.	D	0.97779	1.0231	7	0.87932	D	0	-7.0981	4.2937	0.10890	0.2523:0.0:0.5322:0.2156	.	.	.	.	V	15	ENSP00000381947:G15V	ENSP00000381947:G15V	G	+	2	0	COL13A1	71358719	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	0.789000	0.26886	0.817000	0.34445	0.555000	0.69702	GGC	.	.		0.557	COL13A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048468.1	NM_005203		T	71688713	G	T	71688713	2	4	320	1	0	0	0	0	0	0	0	1	3672	1190	42	3		3	COL13A1	10	71688713	Silent	SNP	G	TCGA-MI-A75C-01A-11D-A32G-10	20647797	71688713	63846034	59	45071										
PI4K2A	55361	hgsc.bcm.edu	37	chr10	99400560	99400560	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	aacccccggactacaccttcCcgtcgggctcgggcgctcac	10	19	1	0			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr10:99400560C>T	ENST00000370631.3	+	1	118	c.61C>T	c.(61-63)Ccg>Tcg	p.P21S	PI4K2A_ENST00000555577.1_Intron|PI4K2A_ENST00000370649.3_Intron	NM_018425.2	NP_060895.1	Q9BTU6	P4K2A_HUMAN	phosphatidylinositol 4-kinase type 2 alpha	21					basophil degranulation (GO:0002561)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|early endosome membrane (GO:0031901)|endosome (GO:0005768)|exocytic vesicle (GO:0070382)|Golgi apparatus (GO:0005794)|growing cell tip (GO:0035838)|host cell presynaptic membrane (GO:0044231)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|presynaptic membrane (GO:0042734)|protein complex (GO:0043234)|synaptic vesicle membrane (GO:0030672)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|AP-3 adaptor complex binding (GO:0035651)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)			endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(1)	12		Colorectal(252;0.162)		Epithelial(162;1.24e-10)|all cancers(201;1.2e-08)		CTACACCTTCCCGTCGGGCTC	0.771																																					p.P21S		Atlas-SNP	.											.	PI4K2A	57	.	0			c.C61T						.						9	11	10					10																	99400560		2159	4249	6408	SO:0001583	missense	55361	exon1			ACCTTCCCGTCGG	AF070611	CCDS7469.1	10q24	2011-02-09			ENSG00000155252	ENSG00000155252			30031	protein-coding gene	gene with protein product		609763				11244087, 11279162	Standard	NM_018425		Approved	PI4KII, DKFZP761G1923, PIK42A	uc001kog.1	Q9BTU6	OTTHUMG00000018863	ENST00000370631.3:c.61C>T	chr10.hg19:g.99400560C>T	ENSP00000359665:p.Pro21Ser	35.0	0.0		44.0	18.0	NM_018425	D3DR59|Q9NSG8	Missense_Mutation	SNP	ENST00000370631.3	hg19	CCDS7469.1	.	.	.	.	.	.	.	.	.	.	C	15.82	2.947330	0.53186	.	.	ENSG00000155252	ENST00000370631	.	.	.	4.17	4.17	0.49024	.	0.270393	0.36234	N	0.002712	T	0.37732	0.1014	N	0.22421	0.69	0.80722	D	1	P	0.44627	0.839	B	0.38056	0.264	T	0.28004	-1.0057	9	0.30078	T	0.28	-6.8852	16.2281	0.82311	0.0:1.0:0.0:0.0	.	21	Q9BTU6	P4K2A_HUMAN	S	21	.	ENSP00000359665:P21S	P	+	1	0	PI4K2A	99390550	1.000000	0.71417	1.000000	0.80357	0.166000	0.22503	5.871000	0.69628	2.157000	0.67596	0.462000	0.41574	CCG	.	.		0.771	PI4K2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049735.1	NM_018425		T	99400560	C	T	99400560	3	4	320	1	0	0	0	0	1	0	0	0	11880	623	22	3	63	3	PI4K2A	10	99400560	Missense_Mutation	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	27711847	99400560	36134187	60	45072										
ADAM12	8038	hgsc.bcm.edu	37	chr10	127753560	127753560	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	agtccctgcacgctgttcctGcaggcttcagctggaaggag	13	12	1	0			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr10:127753560G>A	ENST00000368679.4	-	14	1742	c.1433C>T	c.(1432-1434)gCa>gTa	p.A478V	ADAM12_ENST00000368676.4_Missense_Mutation_p.A478V|ADAM12_ENST00000467145.1_5'UTR	NM_003474.4	NP_003465.3	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12	478	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				cell adhesion (GO:0007155)|epidermal growth factor receptor signaling pathway (GO:0007173)|myoblast fusion (GO:0007520)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(7)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)		CGCTGTTCCTGCAGGCTTCAG	0.612																																					p.A478V		Atlas-SNP	.											.	ADAM12	388	.	0			c.C1433T						.						57	56	56					10																	127753560		2203	4300	6503	SO:0001583	missense	8038	exon14			GTTCCTGCAGGCT	AF023476	CCDS7653.1, CCDS7654.1	10q26	2008-07-29	2008-07-29		ENSG00000148848	ENSG00000148848		"ADAM metallopeptidase domain containing"	190	protein-coding gene	gene with protein product	"meltrin alpha"	602714	"a disintegrin and metalloproteinase domain 12 (meltrin alpha)"			9417060, 18342566	Standard	NM_003474		Approved	MCMPMltna, MLTN	uc001ljk.2	O43184	OTTHUMG00000019243	ENST00000368679.4:c.1433C>T	chr10.hg19:g.127753560G>A	ENSP00000357668:p.Ala478Val	33.0	0.0		31.0	16.0	NM_021641	O60470|Q5JRP0|Q5JRP1|Q6P9E3|Q6UWB0	Missense_Mutation	SNP	ENST00000368679.4	hg19	CCDS7653.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.260318	0.80246	.	.	ENSG00000148848	ENST00000368679;ENST00000368676	T;T	0.12879	2.64;2.64	5.26	5.26	0.73747	Disintegrin, conserved site (1);Blood coagulation inhibitor, Disintegrin (6);	0.063944	0.64402	D	0.000008	T	0.43299	0.1241	M	0.85859	2.78	0.80722	D	1	D;D;D;D;D	0.71674	0.98;0.975;0.975;0.975;0.998	P;P;P;P;D	0.67900	0.893;0.828;0.828;0.828;0.954	T	0.45352	-0.9267	10	0.72032	D	0.01	.	19.0783	0.93171	0.0:0.0:1.0:0.0	.	475;475;478;475;478	A8K6G4;O43184-3;O43184-2;O43184-4;O43184	.;.;.;.;ADA12_HUMAN	V	478	ENSP00000357668:A478V;ENSP00000357665:A478V	ENSP00000357665:A478V	A	-	2	0	ADAM12	127743550	1.000000	0.71417	0.168000	0.22838	0.347000	0.29111	9.534000	0.98061	2.731000	0.93534	0.650000	0.86243	GCA	.	.		0.612	ADAM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050961.1			A	127753560	G	A	127753560	3	1	320	1	0	0	0	0	1	0	0	0	236	1319	46	3	1444	3	ADAM12	10	127753560	Missense_Mutation	SNP	G	TCGA-MI-A75C-01A-11D-A32G-10	28353000	127753560	7781187	61	45073										
PHRF1	57661	hgsc.bcm.edu	37	chr11	608998	608998	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	gcacaggcggcctcggtcccGtgagaagtggccgcagaccc	15	15	0	2			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr11:608998G>T	ENST00000264555.5	+	14	3670	c.3542G>T	c.(3541-3543)cGt>cTt	p.R1181L	PHRF1_ENST00000533464.1_Missense_Mutation_p.R1177L|PHRF1_ENST00000413872.2_Missense_Mutation_p.R1179L|PHRF1_ENST00000416188.2_Missense_Mutation_p.R1180L	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	1181	Arg-rich.				mRNA processing (GO:0006397)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)	RNA polymerase binding (GO:0070063)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|urinary_tract(2)	28						CCTCGGTCCCGTGAGAAGTGG	0.706																																					p.R1180L		Atlas-SNP	.											.	PHRF1	188	.	0			c.G3539T						.						7	9	9					11																	608998		2077	4169	6246	SO:0001583	missense	57661	exon14			GGTCCCGTGAGAA	BC004950	CCDS44507.1, CCDS65987.1, CCDS65988.1, CCDS65989.1	11p15.5	2014-06-13			ENSG00000070047	ENSG00000070047		"RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	24351	protein-coding gene	gene with protein product	"CTD binding SR like protein rA9", "protein phosphatase 1, regulatory subunit 125"	611780		RNF221			Standard	XM_005253027		Approved	KIAA1542, PPP1R125	uc010qwc.2	Q9P1Y6	OTTHUMG00000165141	ENST00000264555.5:c.3542G>T	chr11.hg19:g.608998G>T	ENSP00000264555:p.Arg1181Leu	35.0	0.0		25.0	11.0	NM_020901	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Missense_Mutation	SNP	ENST00000264555.5	hg19		.	.	.	.	.	.	.	.	.	.	G	10.66	1.413680	0.25465	.	.	ENSG00000070047	ENST00000264555;ENST00000413872;ENST00000416188;ENST00000533464	T;T;T;T	0.18657	2.2;2.2;2.2;2.2	5.19	0.0918	0.14469	.	2.028990	0.02544	N	0.094885	T	0.22437	0.0541	L	0.27053	0.805	0.09310	N	1	P;P;P;P	0.47191	0.826;0.891;0.891;0.826	B;P;P;B	0.46339	0.315;0.513;0.513;0.315	T	0.36648	-0.9739	10	0.62326	D	0.03	-1.9303	10.0174	0.42022	0.439:0.0:0.561:0.0	.	1177;1179;1180;1181	E9PJ24;F8WEF5;Q9P1Y6-3;Q9P1Y6	.;.;.;PHRF1_HUMAN	L	1181;1179;1180;1177	ENSP00000264555:R1181L;ENSP00000388589:R1179L;ENSP00000410626:R1180L;ENSP00000431870:R1177L	ENSP00000264555:R1181L	R	+	2	0	PHRF1	598998	0.090000	0.21635	0.031000	0.17742	0.036000	0.12997	0.993000	0.29680	-0.285000	0.09089	0.462000	0.41574	CGT	.	.		0.706	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901		T	608998	G	T	608998	3	4	320	1	0	0	0	0	1	0	0	0	11870	1145	40	1	3589	1	PHRF1	11	608998	Missense_Mutation	SNP	G	TCGA-MI-A75C-01A-11D-A32G-10		608998	134397518	62	45074										
AMPD3	272	hgsc.bcm.edu	37	chr11	10527413	10527413	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	gctatgaaatcagaagagatCaccgccttgaccaactaggt	9	10	2	4			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr11:10527413C>T	ENST00000396554.3	+	15	2654	c.2313C>T	c.(2311-2313)atC>atT	p.I771I	AMPD3_ENST00000444303.2_Silent_p.I603I	NM_000480.2	NP_000471.1	Q01432	AMPD3_HUMAN	adenosine monophosphate deaminase 3	762					ADP metabolic process (GO:0046031)|AMP catabolic process (GO:0006196)|ATP metabolic process (GO:0046034)|energy homeostasis (GO:0097009)|IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(3)|skin(1)	25				all cancers(16;1.14e-08)|Epithelial(150;2.83e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0291)		CAGAAGAGATCACCGCCTTGA	0.433																																					p.I771I		Atlas-SNP	.											.	AMPD3	68	.	0			c.C2313T						.						135	123	127					11																	10527413		2201	4294	6495	SO:0001819	synonymous_variant	272	exon15			AGAGATCACCGCC	M84722	CCDS7802.1, CCDS41617.1, CCDS44537.1, CCDS53601.1	11p15	2010-02-10	2010-02-10			ENSG00000133805	3.5.4.6		470	protein-coding gene	gene with protein product	"erythrocyte-specific AMP deaminase"	102772	"adenosine monophosphate deaminase (isoform E)"			1400401	Standard	NM_001172430		Approved		uc001min.1	Q01432		ENST00000396554.3:c.2313C>T	chr11.hg19:g.10527413C>T		45.0	0.0		36.0	15.0	NM_000480	A0AUX0|B7Z2S2|B7Z763|B7Z877	Silent	SNP	ENST00000396554.3	hg19	CCDS7802.1																																																																																			.	.		0.433	AMPD3-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385783.2	NM_000480		T	10527413	C	T	10527413	2	4	320	1	0	0	0	0	0	0	0	1	587	816	29	3		3	AMPD3	11	10527413	Silent	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	9918415	10527413	124479103	63	45075										
LRP4	4038	hgsc.bcm.edu	37	chr11	46921486	46921486	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	cagactccggatgcagtagcCattctggcagggaaactcgt	12	11	1	1			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr11:46921486C>T	ENST00000378623.1	-	4	600	c.358G>A	c.(358-360)Ggc>Agc	p.G120S		NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	120	LDL-receptor class A 3. {ECO:0000255|PROSITE-ProRule:PRU00124}.				dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			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)		ATGCAGTAGCCATTCTGGCAG	0.632																																					p.G120S		Atlas-SNP	.											.	LRP4	160	.	0			c.G358A						.						84	77	80					11																	46921486		2201	4299	6500	SO:0001583	missense	4038	exon4			AGTAGCCATTCTG	AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"Low density lipoprotein receptors"	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.358G>A	chr11.hg19:g.46921486C>T	ENSP00000367888:p.Gly120Ser	52.0	0.0		46.0	13.0	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Missense_Mutation	SNP	ENST00000378623.1	hg19	CCDS31478.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.682626	0.88542	.	.	ENSG00000134569	ENST00000378623;ENST00000534404	D;D	0.95980	-3.87;-3.07	5.33	4.42	0.53409	.	0.000000	0.85682	D	0.000000	D	0.97192	0.9082	M	0.73430	2.235	0.80722	D	1	B;D	0.76494	0.346;0.999	B;D	0.72982	0.212;0.979	D	0.97490	1.0053	10	0.62326	D	0.03	.	14.1484	0.65364	0.0:0.9276:0.0:0.0724	.	165;120	C9JRN7;O75096	.;LRP4_HUMAN	S	120;71	ENSP00000367888:G120S;ENSP00000434763:G71S	ENSP00000367888:G120S	G	-	1	0	LRP4	46878062	1.000000	0.71417	0.992000	0.48379	0.989000	0.77384	5.806000	0.69150	1.398000	0.46701	0.511000	0.50034	GGC	.	.		0.632	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334		T	46921486	C	T	46921486	3	4	320	1	0	0	0	0	1	0	0	0	8968	594	21	3	5499	3	LRP4	11	46921486	Missense_Mutation	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	36394073	46921486	88085030	64	45076										
OR5D18	219438	hgsc.bcm.edu	37	chr11	55587642	55587642	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	aacacaatcaatcacttcttCtgtgagttctcctcactact	3	13	6	1			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr11:55587642C>T	ENST00000333976.4	+	1	557	c.537C>T	c.(535-537)ttC>ttT	p.F179F		NM_001001952.1	NP_001001952.1	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D, member 18	179						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(3)|large_intestine(6)|lung(33)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		all_epithelial(135;0.208)				ATCACTTCTTCTGTGAGTTCT	0.428																																					p.F179F		Atlas-SNP	.											.	OR5D18	121	.	0			c.C537T						.						216	198	204					11																	55587642		2200	4296	6496	SO:0001819	synonymous_variant	219438	exon1			CTTCTTCTGTGAG	AB065781	CCDS31510.1	11q11	2012-08-09			ENSG00000186119	ENSG00000186119		"GPCR / Class A : Olfactory receptors"	15285	protein-coding gene	gene with protein product							Standard	NM_001001952		Approved		uc010rin.2	Q8NGL1	OTTHUMG00000166811	ENST00000333976.4:c.537C>T	chr11.hg19:g.55587642C>T		115.0	0.0		93.0	28.0	NM_001001952	Q6IF67|Q6IFD3|Q96RB3	Silent	SNP	ENST00000333976.4	hg19	CCDS31510.1																																																																																			.	.		0.428	OR5D18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391515.1	NM_001001952		T	55587642	C	T	55587642	2	4	320	1	0	0	0	0	0	0	0	1	11166	912	32	3		3	OR5D18	11	55587642	Silent	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	8666156	55587642	79418874	65	45077										
KAT5	10524	hgsc.bcm.edu	37	chr11	65484247	65484247	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	catgacagagtatgactgtaAgggcttccacatcgtgggct	12	9	0	3			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr11:65484247A>G	ENST00000377046.3	+	10	1312	c.1040A>G	c.(1039-1041)aAg>aGg	p.K347R	KAT5_ENST00000341318.4_Missense_Mutation_p.K380R|KAT5_ENST00000534650.1_Missense_Mutation_p.K136R|KAT5_ENST00000352980.4_Missense_Mutation_p.K295R|KAT5_ENST00000530446.1_Missense_Mutation_p.K328R	NM_006388.3	NP_006379.2	Q92993	KAT5_HUMAN	K(lysine) acetyltransferase 5	347	MYST-type HAT.				androgen receptor signaling pathway (GO:0030521)|cellular response to estradiol stimulus (GO:0071392)|chromatin organization (GO:0006325)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|double-strand break repair (GO:0006302)|histone acetylation (GO:0016573)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of growth (GO:0040008)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)|Swr1 complex (GO:0000812)|transcription factor complex (GO:0005667)	androgen receptor binding (GO:0050681)|histone acetyltransferase activity (GO:0004402)|metal ion binding (GO:0046872)|repressing transcription factor binding (GO:0070491)|transcription coactivator activity (GO:0003713)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)	21						TATGACTGTAAGGGCTTCCAC	0.522																																					p.K380R		Atlas-SNP	.											.	KAT5	36	.	0			c.A1139G						.						236	214	221					11																	65484247		2201	4297	6498	SO:0001583	missense	10524	exon9			ACTGTAAGGGCTT	U74667	CCDS8109.1, CCDS8110.1, CCDS31610.1, CCDS55771.1	11q13	2013-01-10	2008-07-04	2008-07-04	ENSG00000172977	ENSG00000172977		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing"	5275	protein-coding gene	gene with protein product	"Tat interacting protein, 60kDa", "K-acetyltransferase 5"	601409	"HIV-1 Tat interactive protein, 60kDa"	HTATIP		8607265	Standard	NM_006388		Approved	TIP60, PLIP, cPLA2, HTATIP1, ESA1, ZC2HC5	uc001ofk.3	Q92993	OTTHUMG00000166617	ENST00000377046.3:c.1040A>G	chr11.hg19:g.65484247A>G	ENSP00000366245:p.Lys347Arg	96.0	0.0		95.0	4.0	NM_182710	B4E3C7|C9JL99|O95624|Q13430|Q17RW5|Q561W3|Q6GSE8|Q9BWK7	Missense_Mutation	SNP	ENST00000377046.3	hg19	CCDS31610.1	.	.	.	.	.	.	.	.	.	.	A	10.87	1.471981	0.26423	.	.	ENSG00000172977	ENST00000377046;ENST00000352980;ENST00000341318;ENST00000530446;ENST00000534650	T;T;T;T	0.44083	0.93;0.93;0.94;0.93	5.58	5.58	0.84498	Acyl-CoA N-acyltransferase (2);MOZ/SAS-like protein (1);	0.000000	0.85682	D	0.000000	T	0.15955	0.0384	N	0.01522	-0.82	0.80722	D	1	B;B;B;B	0.06786	0.0;0.0;0.0;0.001	B;B;B;B	0.09377	0.004;0.002;0.001;0.002	T	0.18808	-1.0325	10	0.05721	T	0.95	-22.5859	13.7037	0.62624	1.0:0.0:0.0:0.0	.	328;380;295;347	B4E3C7;Q92993-3;Q92993-2;Q92993	.;.;.;KAT5_HUMAN	R	347;295;380;328;136	ENSP00000366245:K347R;ENSP00000344955:K295R;ENSP00000340330:K380R;ENSP00000434765:K328R	ENSP00000340330:K380R	K	+	2	0	KAT5	65240823	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	5.910000	0.69931	2.131000	0.65755	0.533000	0.62120	AAG	.	.		0.522	KAT5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390866.2	NM_006388		G	65484247	A	G	65484247	3	3	320	1	0	0	0	0	1	0	0	0	7992	72	3	2	1173	2	KAT5	11	65484247	Missense_Mutation	SNP	A	TCGA-MI-A75C-01A-11D-A32G-10	9896605	65484247	69522269	66	45078										
FADD	8772	hgsc.bcm.edu	37	chr11	70049616	70049616	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	gtgtcgtccagcctgtcgagCagcgagctgaccgagctcaa	13	13	1	1			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr11:70049616C>T	ENST00000301838.4	+	1	348	c.51C>T	c.(49-51)agC>agT	p.S17S	RP11-805J14.5_ENST00000526174.1_RNA	NM_003824.3	NP_003815.1	Q13158	FADD_HUMAN	Fas (TNFRSF6)-associated via death domain	17	DED. {ECO:0000255|PROSITE- ProRule:PRU00065}.				activation of cysteine-type endopeptidase activity (GO:0097202)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|innate immune response (GO:0045087)|lymph node development (GO:0048535)|motor neuron apoptotic process (GO:0097049)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic signaling pathway (GO:0097527)|negative regulation of activation-induced cell death of T cells (GO:0070236)|negative regulation of necroptotic process (GO:0060546)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of apoptotic process (GO:0043065)|positive regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation (GO:2000454)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of proteolysis (GO:0045862)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|protein heterooligomerization (GO:0051291)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRAIL-activated apoptotic signaling pathway (GO:0036462)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	CD95 death-inducing signaling complex (GO:0031265)|cell body (GO:0044297)|cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|ripoptosome (GO:0097342)	death effector domain binding (GO:0035877)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|tumor necrosis factor receptor superfamily binding (GO:0032813)			endometrium(1)|lung(4)|ovary(1)|pancreas(1)|urinary_tract(2)	9	Esophageal squamous(2;1.19e-45)		LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)			GCCTGTCGAGCAGCGAGCTGA	0.697																																					p.S17S		Atlas-SNP	.											.	FADD	14	.	0			c.C51T						.						13	12	12					11																	70049616		2186	4257	6443	SO:0001819	synonymous_variant	8772	exon1			GTCGAGCAGCGAG	U24231	CCDS8196.1	11q13.3	2014-09-17			ENSG00000168040	ENSG00000168040			3573	protein-coding gene	gene with protein product	"Fas-associating protein with death domain", "Fas-associating death domain-containing protein", "mediator of receptor-induced toxicity", "growth-inhibiting gene 3 protein"	602457				7536190, 7538907	Standard	NM_003824		Approved	MORT1, GIG3	uc001opm.2	Q13158	OTTHUMG00000167264	ENST00000301838.4:c.51C>T	chr11.hg19:g.70049616C>T		122.0	0.0		101.0	34.0	NM_003824	Q14866|Q6IBR4	Silent	SNP	ENST00000301838.4	hg19	CCDS8196.1																																																																																			.	.		0.697	FADD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393902.1	NM_003824		T	70049616	C	T	70049616	2	4	320	1	0	0	0	0	0	0	0	1	5369	709	25	3		3	FADD	11	70049616	Silent	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	4565369	70049616	64956900	67	45079										
TSKU	25987	hgsc.bcm.edu	37	chr11	76506706	76506706	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	tggccgtgagtggggcccagAcaacccggccatgcttcccc	13	16	0	2			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr11:76506706A>G	ENST00000527881.1	+	2	1072	c.46A>G	c.(46-48)Aca>Gca	p.T16A	TSKU_ENST00000333090.4_Missense_Mutation_p.T16A			Q8WUA8	TSK_HUMAN	tsukushi, small leucine rich proteoglycan	16					anterior commissure morphogenesis (GO:0021960)|ciliary body morphogenesis (GO:0061073)|corpus callosum morphogenesis (GO:0021540)|lateral ventricle development (GO:0021670)|negative regulation of Wnt signaling pathway (GO:0030178)|regulation of gene expression (GO:0010468)	extracellular space (GO:0005615)				NS(1)|large_intestine(4)|lung(6)|urinary_tract(1)	12	Ovarian(111;0.112)					TGGGGCCCAGACAACCCGGCC	0.632																																					p.T16A		Atlas-SNP	.											.	TSKU	26	.	0			c.A46G						.						40	44	42					11																	76506706		2200	4292	6492	SO:0001583	missense	25987	exon2			GCCCAGACAACCC	AK075476	CCDS8246.1	11q13.5	2012-12-05	2012-12-05	2006-11-21	ENSG00000182704	ENSG00000182704			28850	protein-coding gene	gene with protein product		608015	"leucine rich repeat containing 54", "tsukushin", "tsukushi small leucine rich proteoglycan homolog (Xenopus laevis)"	LRRC54		11085516, 19710929, 22880013	Standard	NM_001258210		Approved	E2IG4, TSK	uc031qcw.1	Q8WUA8		ENST00000527881.1:c.46A>G	chr11.hg19:g.76506706A>G	ENSP00000434847:p.Thr16Ala	36.0	0.0		29.0	10.0	NM_015516	B3KQT7|Q6UXK1|Q9UG10|Q9UJX9	Missense_Mutation	SNP	ENST00000527881.1	hg19	CCDS8246.1	.	.	.	.	.	.	.	.	.	.	A	5.577	0.291267	0.10567	.	.	ENSG00000182704	ENST00000533752;ENST00000333090;ENST00000439807;ENST00000525167;ENST00000527881	T;T;T	0.51817	0.69;1.53;1.53	5.14	1.11	0.20524	.	0.450566	0.25316	N	0.031552	T	0.16557	0.0398	N	0.04203	-0.255	0.29110	N	0.880902	B	0.02656	0.0	B	0.04013	0.001	T	0.29150	-1.0021	10	0.02654	T	1	-0.9992	4.7239	0.12931	0.5912:0.0:0.2692:0.1396	.	16	Q8WUA8	TSK_HUMAN	A	16	ENSP00000435133:T16A;ENSP00000332668:T16A;ENSP00000434847:T16A	ENSP00000332668:T16A	T	+	1	0	TSKU	76184354	0.810000	0.29049	0.901000	0.35422	0.482000	0.33219	1.277000	0.33167	0.303000	0.22785	0.533000	0.62120	ACA	.	.		0.632	TSKU-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382871.1	NM_015516		G	76506706	A	G	76506706	3	3	320	1	0	0	0	0	1	0	0	0	16642	275	10	2	48	2	TSKU	11	76506706	Missense_Mutation	SNP	A	TCGA-MI-A75C-01A-11D-A32G-10	6457090	76506706	58499810	68	45080										
DSCAML1	57453	hgsc.bcm.edu	37	chr11	117352790	117352790	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	cccagcggatgatgatgggcCgctcaccccgtgccgtgcag	14	15	1	2			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr11:117352790C>T	ENST00000321322.6	-	12	2628	c.2627G>A	c.(2626-2628)cGg>cAg	p.R876Q	DSCAML1_ENST00000527706.1_Missense_Mutation_p.R606Q	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	816	Ig-like C2-type 9.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		GATGATGGGCCGCTCACCCCG	0.642																																					p.R876Q		Atlas-SNP	.											.	DSCAML1	286	.	0			c.G2627A						.						153	108	123					11																	117352790		2201	4296	6497	SO:0001583	missense	57453	exon12			ATGGGCCGCTCAC		CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.2627G>A	chr11.hg19:g.117352790C>T	ENSP00000315465:p.Arg876Gln	107.0	0.0		81.0	28.0	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Missense_Mutation	SNP	ENST00000321322.6	hg19	CCDS8384.1	.	.	.	.	.	.	.	.	.	.	C	15.74	2.924106	0.52653	.	.	ENSG00000177103	ENST00000527706;ENST00000321322;ENST00000446508	T;T	0.66280	-0.2;-0.2	3.89	3.89	0.44902	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.37183	0.0994	N	0.02539	-0.55	0.37008	D	0.89557	B	0.21821	0.061	B	0.16289	0.015	T	0.35001	-0.9806	9	0.27082	T	0.32	.	16.1057	0.81220	0.0:1.0:0.0:0.0	.	816	Q8TD84	DSCL1_HUMAN	Q	606;876;583	ENSP00000434335:R606Q;ENSP00000315465:R876Q	ENSP00000315465:R876Q	R	-	2	0	DSCAML1	116858000	0.981000	0.34729	0.996000	0.52242	0.894000	0.52154	2.462000	0.45049	2.000000	0.58554	0.485000	0.47835	CGG	.	.		0.642	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693		T	117352790	C	T	117352790	3	4	320	1	0	0	0	0	1	0	0	0	4771	652	23	1	3802	1	DSCAML1	11	117352790	Missense_Mutation	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	40846084	117352790	17653726	69	45081										
BCL9L	283149	hgsc.bcm.edu	37	chr11	118769207	118769207	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	cacactgcgctgccgaagggGgtgggacaccatgaggttct	15	11	1	1			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr11:118769207G>T	ENST00000334801.3	-	8	5381	c.4417C>A	c.(4417-4419)Ccc>Acc	p.P1473T	BCL9L_ENST00000526143.1_5'UTR	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	1473					canonical Wnt signaling pathway (GO:0060070)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell morphogenesis (GO:0022604)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|transcription coactivator activity (GO:0003713)			NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		TGCCGAAGGGGGTGGGACACC	0.701																																					p.P1473T		Atlas-SNP	.											.	BCL9L	254	.	0			c.C4417A						.						22	25	24					11																	118769207		2198	4295	6493	SO:0001583	missense	283149	exon8			GAAGGGGGTGGGA	AB094091	CCDS8403.1	11q23.3	2012-06-06				ENSG00000186174			23688	protein-coding gene	gene with protein product		609004				12964048	Standard	NM_182557		Approved	DLNB11	uc001pug.3	Q86UU0		ENST00000334801.3:c.4417C>A	chr11.hg19:g.118769207G>T	ENSP00000335320:p.Pro1473Thr	83.0	0.0		62.0	28.0	NM_182557	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Missense_Mutation	SNP	ENST00000334801.3	hg19	CCDS8403.1	.	.	.	.	.	.	.	.	.	.	G	9.717	1.158604	0.21454	.	.	ENSG00000186174	ENST00000334801;ENST00000526143;ENST00000525300;ENST00000431085	T	0.63255	-0.03	3.98	3.98	0.46160	.	0.240053	0.22137	U	0.064119	T	0.45895	0.1365	N	0.22421	0.69	0.30303	N	0.789254	P;B	0.36535	0.557;0.436	B;B	0.27500	0.08;0.057	T	0.54423	-0.8296	10	0.48119	T	0.1	-4.1001	16.4076	0.83691	0.0:0.0:1.0:0.0	.	1468;1473	Q86UU0-2;Q86UU0	.;BCL9L_HUMAN	T	1473;1436;719;1428	ENSP00000335320:P1473T	ENSP00000335320:P1473T	P	-	1	0	BCL9L	118274417	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	2.725000	0.47294	1.909000	0.55274	0.305000	0.20034	CCC	.	.		0.701	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557		T	118769207	G	T	118769207	3	4	320	1	0	0	0	0	1	0	0	0	1382	1232	43	3	86	3	BCL9L	11	118769207	Missense_Mutation	SNP	G	TCGA-MI-A75C-01A-11D-A32G-10	1416417	118769207	16237309	70	45082										
CHD4	1108	hgsc.bcm.edu	37	chr12	6703766	6703778	+	Frame_Shift_Del	DEL	TCCACCTGTAGCA	TCCACCTGTAGCA	-													0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	atttgataggggtgcagggtTccacctgtagcatccaggta							TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	TCCACCTGTAGCA	TCCACCTGTAGCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr12:6703766_6703778delTCCACCTGTAGCA	ENST00000357008.2	-	15	2323_2335	c.2160_2172delTGCTACAGGTGGA	c.(2158-2172)gatgctacaggtggafs	p.DATGG720fs	CHD4_ENST00000544040.1_Frame_Shift_Del_p.DATGG713fs|CHD4_ENST00000309577.6_Frame_Shift_Del_p.DATGG720fs|CHD4_ENST00000544484.1_Frame_Shift_Del_p.DATGG717fs	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	720					ATP-dependent chromatin remodeling (GO:0043044)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|RNA polymerase II repressing transcription factor binding (GO:0001103)|zinc ion binding (GO:0008270)			central_nervous_system(2)	2						GGTGCAGGGTTCCACCTGTAGCATCCAGGTACT	0.54																																					p.721_725del	Colon(32;586 792 4568 16848 45314)	Atlas-Indel,Pindel	.											.	CHD4	539	.	0			c.2161_2173del						.																																			SO:0001589	frameshift_variant	1108	exon15			.	X86691	CCDS8552.1	12p13	2013-01-28				ENSG00000111642		"Zinc fingers, PHD-type"	1919	protein-coding gene	gene with protein product		603277				7575689, 8843877	Standard	XM_006718958		Approved	Mi-2b, Mi2-BETA	uc001qpo.3	Q14839		ENST00000357008.2:c.2160_2172delTGCTACAGGTGGA	chr12.hg19:g.6703766_6703778delTCCACCTGTAGCA	ENSP00000349508:p.Asp720fs	96.0	0.0		105.0	33.0	NM_001273	Q8IXZ5	Frame_Shift_Del	DEL	ENST00000357008.2	hg19	CCDS8552.1																																																																																			.	.		0.54	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001273		-	6703778	TCCACCTGTAGCA	-	6703766	7	5	320	1	0	1	0	1	0	0	0	0	3329	1770	62	0	3670	0	CHD4	12	6703766	Frame_Shift_Del	DEL	TCCACCTGTAGCA	TCGA-MI-A75C-01A-11D-A32G-10		6703766	127148129	71	45083										
PLEKHA5	54477	hgsc.bcm.edu	37	chr12	19436367	19436367	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ccttccactcatgacaagacAttaggacccggagcggagga	11	12	1	2	rs376638119		TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr12:19436367A>G	ENST00000299275.6	+	11	1455	c.1449A>G	c.(1447-1449)acA>acG	p.T483T	PLEKHA5_ENST00000317589.4_Silent_p.T483T|PLEKHA5_ENST00000543806.1_Silent_p.T375T|PLEKHA5_ENST00000429027.2_Silent_p.T489T|PLEKHA5_ENST00000539256.1_Silent_p.T241T|PLEKHA5_ENST00000424268.1_Silent_p.T375T|PLEKHA5_ENST00000538714.1_Silent_p.T483T|PLEKHA5_ENST00000355397.3_Silent_p.T483T|PLEKHA5_ENST00000359180.3_Silent_p.T483T|PLEKHA5_ENST00000510738.2_3'UTR|PLEKHA5_ENST00000309364.4_Silent_p.T483T	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5	483					reproductive system development (GO:0061458)	cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					ATGACAAGACATTAGGACCCG	0.493																																					p.T489T	Pancreas(196;329 2193 11246 14234 19524)	Atlas-SNP	.											.	PLEKHA5	198	.	0			c.A1467G						.	A	,	1,4405	2.1+/-5.4	0,1,2202	87	82	84		1449,1449	-7.3	0	12		84	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PLEKHA5	NM_001143821.2,NM_019012.5	,	0,1,6502	GG,GA,AA		0.0,0.0227,0.0077	,	483/1175,483/1117	19436367	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	54477	exon12			CAAGACATTAGGA	AF302150	CCDS8682.1, CCDS44840.1, CCDS44840.2, CCDS55809.1, CCDS58213.1, CCDS58214.1	12p12	2013-01-10			ENSG00000052126	ENSG00000052126		"Pleckstrin homology (PH) domain containing"	30036	protein-coding gene	gene with protein product		607770				11214970, 11001876	Standard	NM_001143821		Approved	PEPP2, KIAA1686, FLJ10667	uc031qgo.1	Q9HAU0	OTTHUMG00000167921	ENST00000299275.6:c.1449A>G	chr12.hg19:g.19436367A>G		57.0	0.0		66.0	36.0	NM_001256470	A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	Silent	SNP	ENST00000299275.6	hg19	CCDS8682.1																																																																																			.	.		0.493	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	NM_019012		G	19436367	A	G	19436367	2	3	320	1	0	0	0	0	0	0	0	1	12068	204	8	2		2	PLEKHA5	12	19436367	Silent	SNP	A	TCGA-MI-A75C-01A-11D-A32G-10	12732601	19436367	114415528	72	45084										
KRAS	3845	hgsc.bcm.edu	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	6	17	1	0	rs121913529		TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											p.G12D	Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	Atlas-SNP	.		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	KRAS_ENST00000256078,NS,adenocarcinoma,0,66	KRAS	30930	.	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	c.G35A						.						91	81	85					12																	25398284		2203	4300	6503	SO:0001583	missense	3845	exon2	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	ACGCCACCAGCTC	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>A	chr12.hg19:g.25398284C>T	ENSP00000256078:p.Gly12Asp	176.0	0.0		162.0	75.0	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	hg19	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT	.	.		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398284	C	T	25398284	3	4	320	1	0	0	0	0	1	0	0	0	8447	507	18	3	671	3	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	5961917	25398284	108453611	73	45085										
ARID2	196528	hgsc.bcm.edu	37	chr12	46123902	46123902	+	Frame_Shift_Del	DEL	T	T	-													0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ctctacaccagagtcactacTttaggcggattcgcgaaggt							TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr12:46123902delT	ENST00000334344.6	+	2	340	c.168delT	c.(166-168)actfs	p.T56fs	ARID2_ENST00000422737.1_5'UTR|LINC00938_ENST00000609803.1_lincRNA	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	56	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.				chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		GAGTCACTACTTTAGGCGGAT	0.537			"N, S, F"		hepatocellular carcinoma																																p.T56fs		Atlas-Indel,Pindel	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	311	.	0			c.167delC						.						82	83	83					12																	46123902		2203	4300	6503	SO:0001589	frameshift_variant	196528	exon2			.		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.168delT	chr12.hg19:g.46123902delT	ENSP00000335044:p.Thr56fs	114.0	0.0		110.0	46.0	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Frame_Shift_Del	DEL	ENST00000334344.6	hg19	CCDS31783.1																																																																																			.	.		0.537	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		-	46123902	T	-	46123902	7	5	320	1	0	1	0	1	0	0	0	0	915	1596	56	0	174	0	ARID2	12	46123902	Frame_Shift_Del	DEL	T	TCGA-MI-A75C-01A-11D-A32G-10	20725618	46123902	87727993	74	45086										
ARID2	196528	hgsc.bcm.edu	37	chr12	46246499	46246499	+	Frame_Shift_Del	DEL	A	A	-													0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	gaaacagtcgcaggaattccAaataaagtaggagttagaat							TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr12:46246499delA	ENST00000334344.6	+	15	4765	c.4593delA	c.(4591-4593)ccafs	p.P1531fs	ARID2_ENST00000444670.1_Frame_Shift_Del_p.P1141fs|ARID2_ENST00000457135.1_Frame_Shift_Del_p.P139fs|ARID2_ENST00000422737.1_Frame_Shift_Del_p.P1382fs|ARID2_ENST00000479608.1_3'UTR	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	1531					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		CAGGAATTCCAAATAAAGTAG	0.478			"N, S, F"		hepatocellular carcinoma																																p.P1531fs		Atlas-Indel,Pindel	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	311	.	0			c.4592delC						.						76	72	73					12																	46246499		2203	4300	6503	SO:0001589	frameshift_variant	196528	exon15			.		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.4593delA	chr12.hg19:g.46246499delA	ENSP00000335044:p.Pro1531fs	75.0	0.0		88.0	26.0	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Frame_Shift_Del	DEL	ENST00000334344.6	hg19	CCDS31783.1																																																																																			.	.		0.478	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		-	46246499	A	-	46246499	7	5	320	1	0	1	0	1	0	0	0	0	915	117	5	0	4651	0	ARID2	12	46246499	Frame_Shift_Del	DEL	A	TCGA-MI-A75C-01A-11D-A32G-10	122597	46246499	87605396	75	45087										
COPZ1	22818	hgsc.bcm.edu	37	chr12	54736037	54736037	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	aaggagcaaaaggcctttgaGaagaacattttcaacaagac	9	7	1	3			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr12:54736037G>T	ENST00000262061.2	+	3	172	c.135G>T	c.(133-135)gaG>gaT	p.E45D	COPZ1_ENST00000549043.1_Missense_Mutation_p.E53D|COPZ1_ENST00000552362.1_Missense_Mutation_p.E45D|COPZ1_ENST00000551779.1_Missense_Mutation_p.E45D|COPZ1_ENST00000548281.1_3'UTR|COPZ1_ENST00000552218.1_Missense_Mutation_p.E45D|COPZ1_ENST00000553231.1_Missense_Mutation_p.E22D|RN7SL744P_ENST00000577604.1_RNA|RP11-968A15.8_ENST00000553061.1_RNA|COPZ1_ENST00000549116.1_Intron|COPZ1_ENST00000455864.2_Missense_Mutation_p.E22D|COPZ1_ENST00000416254.2_Missense_Mutation_p.R25I|COPZ1_ENST00000548753.1_5'UTR	NM_001271734.1|NM_001271736.1|NM_016057.1	NP_001258663.1|NP_001258665.1|NP_057141.1	P61923	COPZ1_HUMAN	coatomer protein complex, subunit zeta 1	45					COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)				kidney(1)|lung(4)	5						AGGCCTTTGAGAAGAACATTT	0.502																																					p.E53D		Atlas-SNP	.											.	COPZ1	10	.	0			c.G159T						.						151	136	141					12																	54736037		2203	4300	6503	SO:0001583	missense	22818	exon3			CTTTGAGAAGAAC	AF151878	CCDS8877.1, CCDS61137.1, CCDS61138.1, CCDS61139.1	12q13.2-q13.3	2008-02-05		2003-07-23					2243	protein-coding gene	gene with protein product		615472	"coatomer protein complex, subunit zeta"	COPZ			Standard	NM_001271734		Approved	CGI-120	uc009znm.2	P61923		ENST00000262061.2:c.135G>T	chr12.hg19:g.54736037G>T	ENSP00000262061:p.Glu45Asp	113.0	0.0		89.0	31.0	NM_001271736	B4DDX8|B4DHZ0|F8VS17|F8VWL5|Q549N6|Q9Y3C3	Missense_Mutation	SNP	ENST00000262061.2	hg19	CCDS8877.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.57|19.57	3.852190|3.852190	0.71719|0.71719	.|.	.|.	ENSG00000111481|ENSG00000111481	ENST00000552848;ENST00000262061;ENST00000549043;ENST00000552218;ENST00000553231;ENST00000552362;ENST00000455864;ENST00000551779;ENST00000550713|ENST00000416254	.|.	.|.	.|.	5.12|5.12	3.31|3.31	0.37934|0.37934	Longin-like (1);AP complex, mu/sigma subunit (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.68375|0.68375	0.2994|0.2994	H|H	0.97023|0.97023	3.925|3.925	0.80722|0.80722	D|D	1|1	P;D;P|P	0.65815|0.36733	0.805;0.995;0.882|0.567	P;D;P|B	0.70016|0.34991	0.779;0.967;0.904|0.193	T|T	0.66567|0.66567	-0.5891|-0.5891	9|8	0.87932|0.23302	D|T	0|0.38	-0.9625|-0.9625	7.0527|7.0527	0.25081|0.25081	0.2694:0.0:0.7306:0.0|0.2694:0.0:0.7306:0.0	.|.	22;53;45|25	B4DDX8;F8VWL5;P61923|B4DHZ0	.;.;COPZ1_HUMAN|.	D|I	45;45;53;45;22;45;22;45;53|25	.|.	ENSP00000262061:E45D|ENSP00000388141:R25I	E|R	+|+	3|2	2|0	COPZ1|COPZ1	53022304|53022304	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	3.366000|3.366000	0.52343|0.52343	0.880000|0.880000	0.35969|0.35969	0.655000|0.655000	0.94253|0.94253	GAG|AGA	.	.		0.502	COPZ1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405753.1	NM_016057		T	54736037	G	T	54736037	3	4	320	1	0	0	0	0	1	0	0	0	3743	933	33	3	145	3	COPZ1	12	54736037	Missense_Mutation	SNP	G	TCGA-MI-A75C-01A-11D-A32G-10	8489538	54736037	79115858	76	45088										
PTPRB	5787	hgsc.bcm.edu	37	chr12	70953301	70953301	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	tctctgggcaaccactgcagCtcaaagtcgttgtagtctgt	10	11	3	0			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr12:70953301C>T	ENST00000261266.5	-	16	3911	c.3882G>A	c.(3880-3882)gaG>gaA	p.E1294E	PTPRB_ENST00000538708.1_Silent_p.E1204E|PTPRB_ENST00000551525.1_Silent_p.E1511E|PTPRB_ENST00000550857.1_Silent_p.E1204E|PTPRB_ENST00000550358.1_Silent_p.E1424E|PTPRB_ENST00000451516.2_Silent_p.E1204E|PTPRB_ENST00000334414.6_Silent_p.E1512E	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	1294	Fibronectin type-III 15. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			ACCACTGCAGCTCAAAGTCGT	0.498																																					p.E1512E		Atlas-SNP	.											.	PTPRB	676	.	0			c.G4536A						.						229	226	227					12																	70953301		1994	4170	6164	SO:0001819	synonymous_variant	5787	exon18			CTGCAGCTCAAAG	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.3882G>A	chr12.hg19:g.70953301C>T		155.0	0.0		173.0	47.0	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Silent	SNP	ENST00000261266.5	hg19	CCDS44944.1																																																																																			.	.		0.498	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1			T	70953301	C	T	70953301	2	4	320	1	0	0	0	0	0	0	0	1	12811	796	28	3		3	PTPRB	12	70953301	Silent	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	16217264	70953301	62898594	77	45089										
ALX1	8092	hgsc.bcm.edu	37	chr12	85677457	85677457	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ctcccgtgaaagggatgcaaGagaagggagagctggatgaa	16	6	0	4			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr12:85677457G>A	ENST00000316824.3	+	2	489	c.334G>A	c.(334-336)Gag>Aag	p.E112K		NM_006982.2	NP_008913.2	Q15699	ALX1_HUMAN	ALX homeobox 1	112					anterior/posterior pattern specification (GO:0009952)|brain development (GO:0007420)|cartilage condensation (GO:0001502)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|mesenchymal cell development (GO:0014031)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(16)|ovary(1)	26				GBM - Glioblastoma multiforme(134;0.134)		AGGGATGCAAGAGAAGGGAGA	0.483																																					p.E112K		Atlas-SNP	.											.	ALX1	61	.	0			c.G334A						.						119	112	114					12																	85677457		2203	4300	6503	SO:0001583	missense	8092	exon2			ATGCAAGAGAAGG	U31986	CCDS9028.1	12q21.31	2011-06-20	2007-07-26	2007-07-26		ENSG00000180318		"Homeoboxes / PRD class"	1494	protein-coding gene	gene with protein product		601527	"cartilage paired-class homeoprotein 1"	CART1		8756334, 7592751	Standard	NM_006982		Approved		uc001tae.4	Q15699	OTTHUMG00000169820	ENST00000316824.3:c.334G>A	chr12.hg19:g.85677457G>A	ENSP00000315417:p.Glu112Lys	120.0	0.0		120.0	41.0	NM_006982	Q546C8|Q96FH4	Missense_Mutation	SNP	ENST00000316824.3	hg19	CCDS9028.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.351348	0.82132	.	.	ENSG00000180318	ENST00000316824	D	0.92446	-3.04	5.62	5.62	0.85841	.	0.185627	0.56097	D	0.000024	D	0.86431	0.5931	N	0.14661	0.345	0.80722	D	1	B	0.19331	0.035	B	0.15484	0.013	T	0.80466	-0.1370	10	0.41790	T	0.15	.	20.0205	0.97499	0.0:0.0:1.0:0.0	.	112	Q15699	ALX1_HUMAN	K	112	ENSP00000315417:E112K	ENSP00000315417:E112K	E	+	1	0	ALX1	84201588	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.383000	0.73172	2.801000	0.96364	0.650000	0.86243	GAG	.	.		0.483	ALX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406072.1	NM_006982		A	85677457	G	A	85677457	3	1	320	1	0	0	0	0	1	0	0	0	556	943	33	3	340	3	ALX1	12	85677457	Missense_Mutation	SNP	G	TCGA-MI-A75C-01A-11D-A32G-10	14724156	85677457	48174438	78	45090										
EEA1	8411	hgsc.bcm.edu	37	chr12	93205145	93205145	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	tgactttccagctgactgcaAtgttcttgcttgtcttgtaa	8	9	2	2			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr12:93205145A>G	ENST00000322349.8	-	17	2373	c.2109T>C	c.(2107-2109)caT>caC	p.H703H		NM_003566.3	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1	703	Gln/Glu/Lys-rich.				early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|synaptic vesicle to endosome fusion (GO:0016189)|vesicle fusion (GO:0006906)	axonal spine (GO:0044308)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|recycling endosome (GO:0055037)|serine-pyruvate aminotransferase complex (GO:0005969)	1-phosphatidylinositol binding (GO:0005545)|calmodulin binding (GO:0005516)|GTP-dependent protein binding (GO:0030742)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(5)|large_intestine(11)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	36						GCTGACTGCAATGTTCTTGCT	0.333																																					p.H703H		Atlas-SNP	.											.	EEA1	104	.	0			c.T2109C						.						63	63	63					12																	93205145		2201	4300	6501	SO:0001819	synonymous_variant	8411	exon17			ACTGCAATGTTCT	L40157	CCDS31874.1	12q22	2007-02-23	2007-02-23			ENSG00000102189		"Zinc fingers, FYVE domain containing"	3185	protein-coding gene	gene with protein product		605070	"early endosome antigen 1, 162kD"			7768953, 9697774	Standard	NM_003566		Approved	ZFYVE2	uc001tck.3	Q15075	OTTHUMG00000170110	ENST00000322349.8:c.2109T>C	chr12.hg19:g.93205145A>G		54.0	0.0		62.0	38.0	NM_003566	Q14221	Silent	SNP	ENST00000322349.8	hg19	CCDS31874.1																																																																																			.	.		0.333	EEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407304.1	NM_003566		G	93205145	A	G	93205145	2	3	320	1	0	0	0	0	0	0	0	1	4923	98	4	2		2	EEA1	12	93205145	Silent	SNP	A	TCGA-MI-A75C-01A-11D-A32G-10	7527688	93205145	40646750	79	45091										
N4BP2L2	10443	hgsc.bcm.edu	37	chr13	33110720	33110720	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ttgtcctcctctgtcatttaTaccatttagaacatgtgcct	5	11	2	1	rs375163250		TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr13:33110720T>C	ENST00000267068.3	-	2	609	c.445A>G	c.(445-447)Ata>Gta	p.I149V	N4BP2L2_ENST00000399396.3_Intron|N4BP2L2_ENST00000504114.1_Intron|N4BP2L2_ENST00000446957.2_Missense_Mutation_p.I149V|N4BP2L2_ENST00000357505.6_Intron	NM_014887.2	NP_055702.1	Q92802	N42L2_HUMAN	NEDD4 binding protein 2-like 2	149					negative regulation of hematopoietic stem cell differentiation (GO:1902037)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of hematopoietic stem cell proliferation (GO:1902035)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptional repressor complex (GO:0017053)	enzyme binding (GO:0019899)|RNA polymerase II transcription corepressor activity (GO:0001106)			kidney(4)|large_intestine(3)|liver(1)|lung(6)|skin(1)|urinary_tract(1)	16		Lung SC(185;0.0262)		all cancers(112;9.5e-07)|Epithelial(112;5.07e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00196)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.243)		CTGTCATTTATACCATTTAGA	0.338																																					p.I149V		Atlas-SNP	.											.	N4BP2L2	90	.	0			c.A445G						.	T	VAL/ILE,	1,4405	2.1+/-5.4	0,1,2202	113	117	116		445,	-3	0	13		116	0,8600		0,0,4300	no	missense,intron	N4BP2L2	NM_014887.2,NM_033111.3	29,	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	,	149/584,	33110720	1,13005	2203	4300	6503	SO:0001583	missense	10443	exon2			CATTTATACCATT	U50532	CCDS9346.1, CCDS45024.1, CCDS61307.1	13q13.1	2010-12-02			ENSG00000244754	ENSG00000244754			26916	protein-coding gene	gene with protein product	"phosphonoformate immuno-associated protein 5"	615788				8812419	Standard	NM_014887		Approved	CG005, PFAAP5	uc010abe.1	Q92802	OTTHUMG00000016700	ENST00000267068.3:c.445A>G	chr13.hg19:g.33110720T>C	ENSP00000267068:p.Ile149Val	182.0	0.0		139.0	50.0	NM_014887	A3KME8	Missense_Mutation	SNP	ENST00000267068.3	hg19	CCDS9346.1	.	.	.	.	.	.	.	.	.	.	T	0.020	-1.436195	0.01108	2.27E-4	0.0	ENSG00000244754	ENST00000446957;ENST00000505213;ENST00000267068	T;T;T	0.41065	1.01;1.01;1.01	5.02	-3.03	0.05429	.	.	.	.	.	T	0.20007	0.0481	N	0.19112	0.55	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.36383	-0.9750	9	0.02654	T	1	-14.8072	8.7717	0.34735	0.1097:0.488:0.0:0.4023	.	149;149	D6R968;Q92802	.;N42L2_HUMAN	V	149	ENSP00000394239:I149V;ENSP00000423362:I149V;ENSP00000267068:I149V	ENSP00000267068:I149V	I	-	1	0	N4BP2L2	32008720	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	0.457000	0.21875	-0.454000	0.07066	0.460000	0.39030	ATA	.	.		0.338	N4BP2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044421.1	NM_014887		C	33110720	T	C	33110720	3	2	320	1	0	0	0	0	1	0	0	0	10121	1406	49	2	3187	2	N4BP2L2	13	33110720	Missense_Mutation	SNP	T	TCGA-MI-A75C-01A-11D-A32G-10		33110720	82059158	80	45092										
CARS2	79587	hgsc.bcm.edu	37	chr13	111335421	111335421	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	gctctccgactggaccagggAccacgccgaccaatttgcca	10	16	1	0			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr13:111335421A>C	ENST00000257347.4	-	6	695	c.632T>G	c.(631-633)gTc>gGc	p.V211G	CARS2_ENST00000535398.1_5'UTR	NM_024537.2	NP_078813.1	Q9HA77	SYCM_HUMAN	cysteinyl-tRNA synthetase 2, mitochondrial (putative)	211				LVGVVPGPVGEPADSDK -> IGRRGPWSSPETSGLLTS (in Ref. 4; BAB93499). {ECO:0000305}.	cysteinyl-tRNA aminoacylation (GO:0006423)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|cysteine-tRNA ligase activity (GO:0004817)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|prostate(4)|skin(1)	13	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.163)		L-Cysteine(DB00151)	TGGACCAGGGACCACGCCGAC	0.537																																					p.V211G		Atlas-SNP	.											.	CARS2	37	.	0			c.T632G						.						116	116	116					13																	111335421		2203	4300	6503	SO:0001583	missense	79587	exon6			CCAGGGACCACGC	BC007220	CCDS9514.1	13q34	2011-07-01	2007-02-22		ENSG00000134905	ENSG00000134905	6.1.1.16	"Aminoacyl tRNA synthetases / Class I"	25695	protein-coding gene	gene with protein product	"cysteine tRNA ligase 2, mitochondrial (putative)"	612800				15779907	Standard	NM_024537		Approved	FLJ12118	uc001vrd.2	Q9HA77	OTTHUMG00000017347	ENST00000257347.4:c.632T>G	chr13.hg19:g.111335421A>C	ENSP00000257347:p.Val211Gly	44.0	0.0		40.0	19.0	NM_024537	Q8NI84|Q96IV4	Missense_Mutation	SNP	ENST00000257347.4	hg19	CCDS9514.1	.	.	.	.	.	.	.	.	.	.	A	7.637	0.680045	0.14907	.	.	ENSG00000134905	ENST00000257347	T	0.29917	1.55	5.39	-7.39	0.01402	.	1.251980	0.05294	N	0.521770	T	0.15869	0.0382	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.19943	-1.0290	10	0.19147	T	0.46	-4.423	5.4535	0.16578	0.5509:0.1037:0.2597:0.0857	.	211	Q9HA77	SYCM_HUMAN	G	211	ENSP00000257347:V211G	ENSP00000257347:V211G	V	-	2	0	CARS2	110133422	0.000000	0.05858	0.000000	0.03702	0.128000	0.20619	-0.434000	0.06939	-1.409000	0.02038	-0.624000	0.04008	GTC	.	.		0.537	CARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045772.3	NM_024537		C	111335421	A	C	111335421	3	2	320	1	0	0	0	0	1	0	0	0	2660	275	10	5	1102	5	CARS2	13	111335421	Missense_Mutation	SNP	A	TCGA-MI-A75C-01A-11D-A32G-10	78224701	111335421	3834457	81	45093										
RIPK3	11035	hgsc.bcm.edu	37	chr14	24808429	24808429	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	tagtcaccagagccggcttgGgatcttggtcccagttcacc	11	13	3	1			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr14:24808429G>A	ENST00000216274.5	-	3	481	c.263C>T	c.(262-264)cCc>cTc	p.P88L	RP11-934B9.3_ENST00000555591.1_5'Flank|RIPK3_ENST00000554338.1_5'UTR	NM_006871.3	NP_006862.2	Q9Y572	RIPK3_HUMAN	receptor-interacting serine-threonine kinase 3	88	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|amyloid fibril formation (GO:1990000)|apoptotic signaling pathway (GO:0097190)|cellular protein modification process (GO:0006464)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|lymph node development (GO:0048535)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of ligase activity (GO:0051351)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phosphatase activity (GO:0010922)|positive regulation of protein deacetylation (GO:0090312)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of type I interferon production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of activated T cell proliferation (GO:0046006)|regulation of activation-induced cell death of T cells (GO:0070235)|regulation of adaptive immune response (GO:0002819)|regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation (GO:2000452)|regulation of interferon-gamma production (GO:0032649)|regulation of T cell mediated cytotoxicity (GO:0001914)|signal transduction (GO:0007165)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|NF-kappaB-inducing kinase activity (GO:0004704)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				GBM - Glioblastoma multiforme(265;0.0181)		AGCCGGCTTGGGATCTTGGTC	0.592																																					p.P88L	Pancreas(58;918 1191 4668 13304 15331)	Atlas-SNP	.											.	RIPK3	43	.	0			c.C263T						.						93	81	85					14																	24808429		2203	4300	6503	SO:0001583	missense	11035	exon3			GGCTTGGGATCTT	AF156884	CCDS9628.1	14q12	2006-05-15			ENSG00000129465	ENSG00000129465			10021	protein-coding gene	gene with protein product		605817				10339433, 10358032	Standard	NM_006871		Approved	RIP3	uc001wpb.3	Q9Y572	OTTHUMG00000029349	ENST00000216274.5:c.263C>T	chr14.hg19:g.24808429G>A	ENSP00000216274:p.Pro88Leu	50.0	0.0		57.0	26.0	NM_006871	B4DJL9|C4AM87|Q5J795|Q5J796|Q6P5Y1	Missense_Mutation	SNP	ENST00000216274.5	hg19	CCDS9628.1	.	.	.	.	.	.	.	.	.	.	G	5.317	0.243830	0.10077	.	.	ENSG00000129465	ENST00000216274	T	0.62639	0.01	4.69	-1.91	0.07641	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	1.081980	0.07194	N	0.856180	T	0.48095	0.1481	L	0.43923	1.385	0.09310	N	1	B;B	0.24132	0.008;0.098	B;B	0.25987	0.006;0.065	T	0.45026	-0.9289	10	0.56958	D	0.05	-0.336	1.2119	0.01906	0.2589:0.2936:0.3098:0.1377	.	88;88	B4DJZ5;Q9Y572	.;RIPK3_HUMAN	L	88	ENSP00000216274:P88L	ENSP00000216274:P88L	P	-	2	0	RIPK3	23878269	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.164000	0.09983	-0.218000	0.10018	-0.254000	0.11334	CCC	.	.		0.592	RIPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073203.4	NM_006871		A	24808429	G	A	24808429	3	1	320	1	0	0	0	0	1	0	0	0	13397	1232	43	3	1325	3	RIPK3	14	24808429	Missense_Mutation	SNP	G	TCGA-MI-A75C-01A-11D-A32G-10		24808429	82541111	82	45094										
TBPL2	22863	hgsc.bcm.edu	37	chr14	55881125	55881125	+	5'Flank	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ttttaaaaccttttagaataGgatagatgttttcaaatgct	6	4	1	2			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr14:55881125G>T	ENST00000247178.5	-	0	0				TBPL2_ENST00000247219.5_Missense_Mutation_p.P367H	NM_014924.4	NP_055739.2	Q6ZNE5	BAKOR_HUMAN	autophagy related 14						autophagic vacuole assembly (GO:0000045)|endosome to lysosome transport (GO:0008333)|positive regulation of autophagy (GO:0010508)	autophagic vacuole (GO:0005776)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|pre-autophagosomal structure membrane (GO:0034045)				central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(6)|prostate(2)	13						TTTTAGAATAGGATAGATGTT	0.318																																					p.P367H		Atlas-SNP	.											.	TBPL2	27	.	0			c.C1100A						.						79	81	80					14																	55881125		2202	4300	6502	SO:0001631	upstream_gene_variant	387332	exon7			AGAATAGGATAGA	AB020638	CCDS32087.1	14q22.2	2014-02-12	2012-06-06	2010-06-29	ENSG00000126775	ENSG00000126775			19962	protein-coding gene	gene with protein product	"Barkor", "beclin 1-associated autophagy-related key regulator"	613515	"KIAA0831", "ATG14 autophagy related 14 homolog (S. cerevisiae)"	KIAA0831		18843052	Standard	NM_014924		Approved	ATG14L	uc001xbx.2	Q6ZNE5	OTTHUMG00000172129		chr14.hg19:g.55881125G>T	Exception_encountered	97.0	0.0		39.0	16.0	NM_199047	A6NJE4|A8K9U5|B7ZWP5|O94920|Q32MK7|Q32MK8	Missense_Mutation	SNP	ENST00000247178.5	hg19	CCDS32087.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.273794	0.80580	.	.	ENSG00000182521	ENST00000247219	T	0.58060	0.36	5.34	5.34	0.76211	Transcription factor TFIID, C-terminal/DNA glycosylase, N-terminal (1);Beta2-adaptin/TATA-box binding, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.80660	0.4665	H	0.94620	3.56	0.80722	D	1	D	0.76494	0.999	D	0.73708	0.981	D	0.85789	0.1366	10	0.87932	D	0	-10.6571	18.2043	0.89850	0.0:0.0:1.0:0.0	.	367	Q6SJ96	TBPL2_HUMAN	H	367	ENSP00000247219:P367H	ENSP00000247219:P367H	P	-	2	0	TBPL2	54950878	1.000000	0.71417	1.000000	0.80357	0.770000	0.43624	8.686000	0.91250	2.775000	0.95449	0.655000	0.94253	CCT	.	.		0.318	ATG14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416992.1	NM_014924		T	55881125	G	T	55881125	1	4	320	0	1	0	0	0	0	0	0	0	15661	1000	35	3		3	TBPL2	14	55881125	5'Flank	SNP	G	TCGA-MI-A75C-01A-11D-A32G-10	31072696	55881125	51468415	83	45095										
ZFYVE26	23503	hgsc.bcm.edu	37	chr14	68274609	68274609	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	cgtcaggcacgtggcctactGcaccctgtgttaaggtctca	11	13	2	0			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr14:68274609G>A	ENST00000347230.4	-	5	530	c.392C>T	c.(391-393)gCa>gTa	p.A131V	ZFYVE26_ENST00000555452.1_Missense_Mutation_p.A131V	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	131					cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		GTGGCCTACTGCACCCTGTGT	0.537																																					p.A131V		Atlas-SNP	.											.	ZFYVE26	223	.	0			c.C392T						.						100	100	100					14																	68274609		2203	4299	6502	SO:0001583	missense	23503	exon5			CCTACTGCACCCT	AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"Zinc fingers, FYVE domain containing"	20761	protein-coding gene	gene with protein product	"spastizin", "FYVE-CENT"	612012	"spastic paraplegia 15 (complicated, autosomal recessive)"	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.392C>T	chr14.hg19:g.68274609G>A	ENSP00000251119:p.Ala131Val	89.0	0.0		62.0	27.0	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Missense_Mutation	SNP	ENST00000347230.4	hg19	CCDS9788.1	.	.	.	.	.	.	.	.	.	.	G	12.36	1.915620	0.33815	.	.	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000555452	T;T	0.27720	1.79;1.65	5.64	3.63	0.41609	.	1.383960	0.04182	N	0.326651	T	0.18383	0.0441	N	0.08118	0	0.09310	N	1	B;B;B	0.23442	0.085;0.02;0.012	B;B;B	0.21917	0.037;0.025;0.01	T	0.17471	-1.0368	10	0.28530	T	0.3	0.7986	7.4073	0.26998	0.0:0.1539:0.6081:0.2381	.	131;131;131	Q68DK2-4;G3V2D8;Q68DK2	.;.;ZFY26_HUMAN	V	131	ENSP00000251119:A131V;ENSP00000450603:A131V	ENSP00000251119:A131V	A	-	2	0	ZFYVE26	67344362	0.029000	0.19370	0.002000	0.10522	0.433000	0.31745	2.372000	0.44257	1.360000	0.45960	0.591000	0.81541	GCA	.	.		0.537	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346		A	68274609	G	A	68274609	3	1	320	1	0	0	0	0	1	0	0	0	17683	1319	46	3	7379	3	ZFYVE26	14	68274609	Missense_Mutation	SNP	G	TCGA-MI-A75C-01A-11D-A32G-10	12393484	68274609	39074931	84	45096										
ESRRB	2103	hgsc.bcm.edu	37	chr14	76905705	76905705	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ctgctgaacaggatgtcctcGgacgacaggcacctgggctc	13	13	0	1			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr14:76905705G>A	ENST00000509242.1	+	3	107	c.9G>A	c.(7-9)tcG>tcA	p.S3S	ESRRB_ENST00000556177.1_Silent_p.S3S|ESRRB_ENST00000380887.2_Silent_p.S3S|ESRRB_ENST00000261532.7_Silent_p.S3S|ESRRB_ENST00000507951.1_3'UTR	NM_004452.3	NP_004443.3	O95718	ERR2_HUMAN	estrogen-related receptor beta	3					gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|trophectodermal cell proliferation (GO:0001834)|trophectodermal cellular morphogenesis (GO:0001831)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding (GO:0043565)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(4)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(234;0.0213)		GGATGTCCTCGGACGACAGGC	0.657																																					p.S3S		Atlas-SNP	.											.	ESRRB	114	.	0			c.G9A						.						64	68	67					14																	76905705		2195	4284	6479	SO:0001819	synonymous_variant	2103	exon4			GTCCTCGGACGAC	X51417	CCDS9850.1, CCDS9850.2	14q24.3	2013-01-16				ENSG00000119715		"Nuclear hormone receptors"	3473	protein-coding gene	gene with protein product		602167	"deafness, autosomal recessive 35"	ESRL2, DFNB35		3267207, 9344655, 18179891	Standard	NM_004452		Approved	ERR2, ERRbeta, NR3B2, ERRb	uc001xsr.3	O95718		ENST00000509242.1:c.9G>A	chr14.hg19:g.76905705G>A		96.0	0.0		67.0	29.0	NM_004452	A2VDJ2|B6ZGU4|Q5F0P7|Q5F0P8|Q9HCB4	Silent	SNP	ENST00000509242.1	hg19	CCDS9850.2																																																																																			.	.		0.657	ESRRB-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360663.1			A	76905705	G	A	76905705	2	1	320	1	0	0	0	0	0	0	0	1	5263	1103	39	1		1	ESRRB	14	76905705	Silent	SNP	G	TCGA-MI-A75C-01A-11D-A32G-10	8631096	76905705	30443835	85	45097										
CCDC88C	440193	hgsc.bcm.edu	37	chr14	91779756	91779756	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	cagccggagggcctccaggtCccgccgcagcgcctggcgct	15	18	0	0			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr14:91779756C>G	ENST00000389857.6	-	15	2490	c.2404G>C	c.(2404-2406)Gac>Cac	p.D802H		NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	802					protein destabilization (GO:0031648)|protein homooligomerization (GO:0051260)|regulation of protein phosphorylation (GO:0001932)|Wnt signaling pathway (GO:0016055)		PDZ domain binding (GO:0030165)|protein self-association (GO:0043621)			central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(6)|pancreas(1)|urinary_tract(1)	24		all_cancers(154;0.0468)				GCCTCCAGGTCCCGCCGCAGC	0.672																																					p.D802H		Atlas-SNP	.											.	CCDC88C	192	.	0			c.G2404C						.						13	16	15					14																	91779756		2058	4195	6253	SO:0001583	missense	440193	exon15			CCAGGTCCCGCCG		CCDS45151.1	14q32.12	2014-07-30	2007-05-31	2007-05-31		ENSG00000015133			19967	protein-coding gene	gene with protein product	"Dvl-associating protein with a high frequency of leucine residues", "spinocerebellar ataxia 40"	611204	"KIAA1509"	KIAA1509		17185515, 25062847	Standard	NM_001080414		Approved	DAPLE, HkRP2, SCA40	uc010aty.3	Q9P219		ENST00000389857.6:c.2404G>C	chr14.hg19:g.91779756C>G	ENSP00000374507:p.Asp802His	23.0	0.0		26.0	10.0	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Missense_Mutation	SNP	ENST00000389857.6	hg19	CCDS45151.1	.	.	.	.	.	.	.	.	.	.	C	17.09	3.300824	0.60195	.	.	ENSG00000015133	ENST00000389857	T	0.14640	2.49	5.03	4.01	0.46588	.	0.262593	0.25552	U	0.029898	T	0.14700	0.0355	L	0.51422	1.61	0.80722	D	1	P	0.48016	0.904	P	0.47044	0.535	T	0.01545	-1.1328	10	0.66056	D	0.02	-27.7084	3.2625	0.06854	0.0:0.5971:0.0:0.4029	.	802	Q9P219	DAPLE_HUMAN	H	802	ENSP00000374507:D802H	ENSP00000374507:D802H	D	-	1	0	CCDC88C	90849509	0.972000	0.33761	0.997000	0.53966	0.985000	0.73830	2.818000	0.48041	2.338000	0.79540	0.561000	0.74099	GAC	.	.		0.672	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353		G	91779756	C	G	91779756	3	3	320	1	0	0	0	0	1	0	0	0	2867	855	30	4	3746	4	CCDC88C	14	91779756	Missense_Mutation	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	14874051	91779756	15569784	86	45098										
DICER1	23405	hgsc.bcm.edu	37	chr14	95574719	95574719	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ttgtggtatcttcaggaggaTagagcttccgccttctaaag	11	8	3	1	rs527568726		TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr14:95574719T>C	ENST00000526495.1	-	17	2669	c.2378A>G	c.(2377-2379)tAt>tGt	p.Y793C	DICER1_ENST00000393063.1_Missense_Mutation_p.Y793C|DICER1_ENST00000556045.1_5'Flank|DICER1_ENST00000343455.3_Missense_Mutation_p.Y793C|DICER1_ENST00000541352.1_Missense_Mutation_p.Y793C|DICER1_ENST00000527414.1_Missense_Mutation_p.Y793C			Q9UPY3	DICER_HUMAN	dicer 1, ribonuclease type III	793					angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac muscle cell development (GO:0055013)|cerebral cortex development (GO:0021987)|defense response to virus (GO:0051607)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|hair follicle cell proliferation (GO:0071335)|hair follicle morphogenesis (GO:0031069)|inner ear receptor cell development (GO:0060119)|intestinal epithelial cell development (GO:0060576)|lung development (GO:0030324)|mRNA stabilization (GO:0048255)|multicellular organism growth (GO:0035264)|negative regulation of Schwann cell proliferation (GO:0010626)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nerve development (GO:0021675)|neuron projection morphogenesis (GO:0048812)|olfactory bulb interneuron differentiation (GO:0021889)|peripheral nervous system myelin formation (GO:0032290)|positive regulation of gene expression (GO:0010628)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of myelination (GO:0031643)|positive regulation of Schwann cell differentiation (GO:0014040)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|production of siRNA involved in RNA interference (GO:0030422)|regulation of cell cycle (GO:0051726)|regulation of enamel mineralization (GO:0070173)|regulation of neuron differentiation (GO:0045664)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of viral genome replication (GO:0045069)|reproductive structure development (GO:0048608)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|spinal cord motor neuron differentiation (GO:0021522)|spindle assembly (GO:0051225)|spleen development (GO:0048536)|stem cell maintenance (GO:0019827)|targeting of mRNA for destruction involved in RNA interference (GO:0030423)|zygote asymmetric cell division (GO:0010070)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|growth cone (GO:0030426)|RISC complex (GO:0016442)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|ribonuclease III activity (GO:0004525)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(13)|kidney(3)|large_intestine(10)|lung(33)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	75		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)		TTCAGGAGGATAGAGCTTCCG	0.423			"Mis F, N"		"sex cord-stromal tumour, TGCT, embryonal rhadomyosarcoma"	pleuropulmonary blastoma			Familial Multinodular Goiter ;DICER 1 syndrome				T|||	1	0.000199681	8e-04	0	5008	,	,		18951	0		0	False		,,,				2504	0				p.Y793C		Atlas-SNP	.	yes	Rec	yes	Familial Pleuropulmonary Blastoma	14	14q32.13	23405	"dicer 1, ribonuclease type III "		"E, M, O"	.	DICER1	181	.	0			c.A2378G						.						168	159	162					14																	95574719		2203	4300	6503	SO:0001583	missense	23405	exon16	Familial Cancer Database	Adolescent Multinodular Goiter, incl. Multinodular Euthyroid Goiter & Non-Medullary Thyroid Cancer;incl. Pleuropulmonary Blastoma, Familial ; Cystic Nephroma, Familial	GGAGGATAGAGCT	AB028449	CCDS9931.1, CCDS55941.1	14q32.13	2014-09-17	2008-02-20		ENSG00000100697	ENSG00000100697			17098	protein-coding gene	gene with protein product	"dicer 1, double-stranded RNA-specific endoribonuclease"	606241	"Dicer1, Dcr-1 homolog (Drosophila)", "multinodular goitre 1"	MNG1		10051563, 10786632, 21205968	Standard	NM_177438		Approved	Dicer, KIAA0928, K12H4.8-LIKE, HERNA	uc001ydw.2	Q9UPY3	OTTHUMG00000166134	ENST00000526495.1:c.2378A>G	chr14.hg19:g.95574719T>C	ENSP00000437256:p.Tyr793Cys	78.0	0.0		69.0	21.0	NM_030621	A7E2D3|B3KRG4|E0AD28|O95943|Q9UQ02	Missense_Mutation	SNP	ENST00000526495.1	hg19	CCDS9931.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.061548	0.76187	.	.	ENSG00000100697	ENST00000343455;ENST00000526495;ENST00000393063;ENST00000527414;ENST00000541352	D;D;D;D;D	0.82803	-1.65;-1.65;-1.65;-1.65;-1.65	5.65	4.48	0.54585	.	0.056743	0.64402	D	0.000001	D	0.87533	0.6201	L	0.52905	1.665	0.80722	D	1	D	0.89917	1.0	D	0.69307	0.963	D	0.86843	0.2018	10	0.49607	T	0.09	-18.7645	12.1495	0.54042	0.1285:0.0:0.0:0.8715	.	793	Q9UPY3	DICER_HUMAN	C	793	ENSP00000343745:Y793C;ENSP00000437256:Y793C;ENSP00000376783:Y793C;ENSP00000435681:Y793C;ENSP00000444719:Y793C	ENSP00000343745:Y793C	Y	-	2	0	DICER1	94644472	1.000000	0.71417	0.973000	0.42090	0.967000	0.64934	7.771000	0.85420	1.037000	0.40024	0.533000	0.62120	TAT	.	.		0.423	DICER1-004	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387997.1			C	95574719	T	C	95574719	3	2	320	1	0	0	0	0	1	0	0	0	4523	1406	49	2	3442	2	DICER1	14	95574719	Missense_Mutation	SNP	T	TCGA-MI-A75C-01A-11D-A32G-10	3794963	95574719	11774821	87	45099										
BDKRB2	624	hgsc.bcm.edu	37	chr14	96707560	96707560	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	tggatacgctgcatcgcctcGgcatcctctccagctgccag	10	16	1	0			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr14:96707560G>A	ENST00000306005.3	+	3	1091	c.895G>A	c.(895-897)Ggc>Agc	p.G299S	BDKRB2_ENST00000542454.2_Missense_Mutation_p.G272S|RP11-404P21.8_ENST00000553811.1_Intron|BDKRB2_ENST00000539359.1_Missense_Mutation_p.G272S|BDKRB2_ENST00000554311.1_Missense_Mutation_p.G299S	NM_000623.3	NP_000614.1	P30411	BKRB2_HUMAN	bradykinin receptor B2	299					arachidonic acid secretion (GO:0050482)|blood circulation (GO:0008015)|cell surface receptor signaling pathway (GO:0007166)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|metabolic process (GO:0008152)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator (GO:1902239)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of vascular permeability (GO:0043114)|regulation of vasoconstriction (GO:0019229)|response to salt stress (GO:0009651)|smooth muscle contraction (GO:0006939)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vasoconstriction (GO:0042310)|vasodilation (GO:0042311)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bradykinin receptor activity (GO:0004947)|phosphatidylinositol phospholipase C activity (GO:0004435)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|type 1 angiotensin receptor binding (GO:0031702)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(5)|lung(7)|ovary(3)|skin(1)	24		all_cancers(154;0.0678)|Melanoma(154;0.155)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.226)	Icatibant(DB06196)	GCATCGCCTCGGCATCCTCTC	0.577																																					p.G299S		Atlas-SNP	.											.	BDKRB2	56	.	0			c.G895A						.						66	59	61					14																	96707560		2203	4300	6503	SO:0001583	missense	624	exon3			CGCCTCGGCATCC	S56772	CCDS9942.1	14q32.1-q32.2	2012-08-08				ENSG00000168398		"GPCR / Class A : Bradykinin receptors"	1030	protein-coding gene	gene with protein product		113503				7916737	Standard	NM_000623		Approved	BK-2	uc010avm.1	P30411		ENST00000306005.3:c.895G>A	chr14.hg19:g.96707560G>A	ENSP00000307713:p.Gly299Ser	43.0	0.0		52.0	20.0	NM_000623		Missense_Mutation	SNP	ENST00000306005.3	hg19	CCDS9942.1	.	.	.	.	.	.	.	.	.	.	G	0.232	-1.020393	0.02061	.	.	ENSG00000168398	ENST00000542454;ENST00000554311;ENST00000306005;ENST00000539359	T;T;T;T	0.70631	-0.5;-0.5;-0.5;-0.5	4.62	-5.69	0.02428	GPCR, rhodopsin-like superfamily (1);	1.913840	0.02342	N	0.075049	T	0.54464	0.1860	L	0.39245	1.2	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.23404	-1.0189	10	0.22109	T	0.4	-3.4146	3.1966	0.06635	0.3048:0.3955:0.201:0.0987	.	299	P30411	BKRB2_HUMAN	S	272;299;299;272	ENSP00000439459:G272S;ENSP00000450482:G299S;ENSP00000307713:G299S;ENSP00000438376:G272S	ENSP00000307713:G299S	G	+	1	0	BDKRB2	95777313	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-0.868000	0.04236	-1.006000	0.03412	-1.263000	0.01449	GGC	.	.		0.577	BDKRB2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413294.1			A	96707560	G	A	96707560	3	1	320	1	0	0	0	0	1	0	0	0	1393	1116	39	1	901	1	BDKRB2	14	96707560	Missense_Mutation	SNP	G	TCGA-MI-A75C-01A-11D-A32G-10	1132841	96707560	10641980	88	45100										
SNRPN	6638	hgsc.bcm.edu	37	chr15	25222974	25222974	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	agcagctgctgctgttgctgCgactgccagtattgctggag	14	10	0	0			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr15:25222974C>A	ENST00000400100.1	+	11	1360	c.470C>A	c.(469-471)gCg>gAg	p.A157E	SNURF_ENST00000338094.6_3'UTR|SNRPN_ENST00000346403.6_Missense_Mutation_p.A157E|SNRPN_ENST00000400098.1_Missense_Mutation_p.A157E|SNRPN_ENST00000390687.4_Missense_Mutation_p.A157E|SNHG14_ENST00000551631.2_RNA|SNRPN_ENST00000444203.2_Missense_Mutation_p.A161E|SNRPN_ENST00000577565.1_Missense_Mutation_p.A157E|SNRPN_ENST00000554227.2_Missense_Mutation_p.A161E|SNURF_ENST00000551312.2_Intron|SNRPN_ENST00000400097.1_Missense_Mutation_p.A157E	NM_022807.2	NP_073718.1	P63162	RSMN_HUMAN	small nuclear ribonucleoprotein polypeptide N	157					response to hormone (GO:0009725)|RNA splicing (GO:0008380)	small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U1 snRNP (GO:0005685)|U2 snRNP (GO:0005686)	RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(14)|ovary(1)|skin(2)	24		all_cancers(20;9.33e-22)|Breast(32;0.000625)		all cancers(64;3.38e-08)|Epithelial(43;3.45e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000207)|GBM - Glioblastoma multiforme(186;0.125)		GCTGTTGCTGCGACTGCCAGT	0.587									Prader-Willi syndrome																												p.A157E		Atlas-SNP	.											.	SNRPN	58	.	0			c.C470A						.						32	35	34					15																	25222974		1978	4184	6162	SO:0001583	missense	6638	exon11	Familial Cancer Database	Prader-Labhart-Willi syndrome	TTGCTGCGACTGC	L80005	CCDS10017.1	15q11.2	2013-07-16			ENSG00000128739	ENSG00000128739			11164	protein-coding gene	gene with protein product	"tissue-specific splicing protein", "SM protein N", "small nuclear ribonucleoprotein N"	182279	"Prader-Willi syndrome chromosome region"	PWCR		1533223	Standard	NM_022805		Approved	SMN, SM-D, HCERN3, SNRNP-N, SNURF-SNRPN, RT-LI	uc001ywt.1	P63162	OTTHUMG00000129180	ENST00000400100.1:c.470C>A	chr15.hg19:g.25222974C>A	ENSP00000382972:p.Ala157Glu	47.0	0.0		39.0	14.0	NM_022807	B3KVR1|P14648|P17135|Q0D2Q5	Missense_Mutation	SNP	ENST00000400100.1	hg19	CCDS10017.1	.	.	.	.	.	.	.	.	.	.	C	14.24	2.477692	0.44044	.	.	ENSG00000128739;ENSG00000128739;ENSG00000128739;ENSG00000128739;ENSG00000128739;ENSG00000128739;ENSG00000214265	ENST00000400100;ENST00000400098;ENST00000400097;ENST00000554227;ENST00000390687;ENST00000444203;ENST00000346403	T;T;T;T;T;T	0.43688	0.94;0.94;0.94;0.94;0.94;0.94	4.3	3.38	0.38709	.	0.167207	0.41097	D	0.000956	T	0.42653	0.1212	M	0.64997	1.995	0.80722	D	1	D;D	0.54397	0.966;0.966	P;P	0.45195	0.473;0.473	T	0.49163	-0.8968	10	0.87932	D	0	-13.5608	10.5289	0.44965	0.0:0.9041:0.0:0.0959	.	161;157	B3KVR1;P63162	.;RSMN_HUMAN	E	157;157;157;161;157;161;16	ENSP00000382972:A157E;ENSP00000382970:A157E;ENSP00000382969:A157E;ENSP00000452342:A161E;ENSP00000375105:A157E;ENSP00000408767:A161E	ENSP00000306223:A16E	A	+	2	0	SNRPN;SNURF	22774067	1.000000	0.71417	0.845000	0.33349	0.003000	0.03518	4.384000	0.59607	1.403000	0.46800	-0.142000	0.14014	GCG	.	.		0.587	SNRPN-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413849.10	NM_003097		A	25222974	C	A	25222974	3	1	320	1	0	0	0	0	1	0	0	0	14885	768	27	1	488	1	SNRPN	15	25222974	Missense_Mutation	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10		25222974	77308418	89	45101										
GLCE	26035	hgsc.bcm.edu	37	chr15	69560737	69560737	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	attgcttttaaagaaagagaTatatactatggcattgggcc	9	5	0	2			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr15:69560737T>C	ENST00000261858.2	+	5	1236	c.1008T>C	c.(1006-1008)gaT>gaC	p.D336D	GLCE_ENST00000559500.1_3'UTR|GLCE_ENST00000559420.2_Silent_p.D272D	NM_015554.1	NP_056369.1	O94923	GLCE_HUMAN	glucuronic acid epimerase	336					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)|small molecule metabolic process (GO:0044281)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	heparosan-N-sulfate-glucuronate 5-epimerase activity (GO:0047464)|racemase and epimerase activity, acting on carbohydrates and derivatives (GO:0016857)|UDP-glucuronate 5'-epimerase activity (GO:0050379)			NS(1)|breast(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	18						AAGAAAGAGATATATACTATG	0.433																																					p.D336D		Atlas-SNP	.											.	GLCE	48	.	0			c.T1008C						.						65	68	67					15																	69560737		2200	4298	6498	SO:0001819	synonymous_variant	26035	exon5			AAGAGATATATAC	AB020643	CCDS32277.1	15q23	2007-01-30	2007-01-30			ENSG00000138604	5.1.3.12		17855	protein-coding gene	gene with protein product	"heparan sulfate epimerase"	612134	"D-glucuronyl C5-epimerase", "UDP-glucuronic acid epimerase"			15853773	Standard	NM_015554		Approved	KIAA0836, HSEPI	uc002ary.1	O94923		ENST00000261858.2:c.1008T>C	chr15.hg19:g.69560737T>C		94.0	0.0		85.0	32.0	NM_015554	Q6GUQ2	Silent	SNP	ENST00000261858.2	hg19	CCDS32277.1																																																																																			.	.		0.433	GLCE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015554		C	69560737	T	C	69560737	2	2	320	1	0	0	0	0	0	0	0	1	6440	1403	49	2		2	GLCE	15	69560737	Silent	SNP	T	TCGA-MI-A75C-01A-11D-A32G-10	44337763	69560737	32970655	90	45102										
CHRNA3	1136	hgsc.bcm.edu	37	chr15	78894345	78894345	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ttgatgtcgtgtttgtagccTggggctttgatgatggccca	14	7	0	3			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr15:78894345T>A	ENST00000326828.5	-	5	1023	c.639A>T	c.(637-639)ccA>ccT	p.P213P	CHRNA3_ENST00000348639.3_Silent_p.P213P	NM_000743.4	NP_000734.2	P32297	ACHA3_HUMAN	cholinergic receptor, nicotinic, alpha 3 (neuronal)	213					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of dendrite morphogenesis (GO:0048814)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of membrane potential (GO:0042391)|regulation of smooth muscle contraction (GO:0006940)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18					Bupropion(DB01156)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Levomethadyl Acetate(DB01227)|Nicotine(DB00184)|Pentolinium(DB01090)|Varenicline(DB01273)	GTTTGTAGCCTGGGGCTTTGA	0.537																																					p.P213P		Atlas-SNP	.											.	CHRNA3	56	.	0			c.A639T						.						154	132	140					15																	78894345		2196	4293	6489	SO:0001819	synonymous_variant	1136	exon5			GTAGCCTGGGGCT		CCDS10305.1, CCDS53964.1	15q24	2012-02-11	2012-02-07		ENSG00000080644	ENSG00000080644		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1957	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 3 (neuronal)"	118503	"cholinergic receptor, nicotinic, alpha polypeptide 3"			2004777	Standard	NM_000743		Approved		uc002bec.3	P32297	OTTHUMG00000143863	ENST00000326828.5:c.639A>T	chr15.hg19:g.78894345T>A		111.0	0.0		94.0	4.0	NM_000743	Q15823|Q4KMN8|Q86U77|Q96RH3|Q99553|Q9BQ93|Q9BRR4	Silent	SNP	ENST00000326828.5	hg19	CCDS10305.1																																																																																			.	.		0.537	CHRNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290111.3			A	78894345	T	A	78894345	2	1	320	1	0	0	0	0	0	0	0	1	3386	1567	55	4		4	CHRNA3	15	78894345	Silent	SNP	T	TCGA-MI-A75C-01A-11D-A32G-10	9333608	78894345	23637047	91	45103										
ANPEP	290	hgsc.bcm.edu	37	chr15	90335706	90335706	+	Nonsense_Mutation	SNP	C	C	T													0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ttattattggggttctccatCcactgcttgaaaaggccaga							TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr15:90335706C>T	ENST00000300060.6	-	17	2650	c.2337G>A	c.(2335-2337)tgG>tgA	p.W779*		NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase	779	Metalloprotease.				angiogenesis (GO:0001525)|angiotensin maturation (GO:0002003)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|viral process (GO:0016032)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|receptor activity (GO:0004872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	57	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)|Icatibant(DB06196)	GGTTCTCCATCCACTGCTTGA	0.592																																					p.W779X	NSCLC(30;827 977 2459 19669 26125)	Atlas-SNP	.											.	ANPEP	124	.	0			c.G2337A						.						156	136	143					15																	90335706		2200	4299	6499	SO:0001587	stop_gained	290	exon17			CTCCATCCACTGC	M22324	CCDS10356.1	15q25-q26	2008-07-31	2008-07-31		ENSG00000166825	ENSG00000166825	3.4.11.2	"CD molecules"	500	protein-coding gene	gene with protein product	"aminopeptidase N", "aminopeptidase M", "microsomal aminopeptidase"	151530		CD13, PEPN		2428842, 1977688	Standard	NM_001150		Approved	LAP1, gp150, p150	uc002bop.4	P15144	OTTHUMG00000149814	ENST00000300060.6:c.2337G>A	chr15.hg19:g.90335706C>T	ENSP00000300060:p.Trp779*	126.0	0.0		95.0	33.0	NM_001150	Q16728|Q6GT90|Q8IUK3|Q8IVH3|Q9UCE0	Nonsense_Mutation	SNP	ENST00000300060.6	hg19	CCDS10356.1	.	.	.	.	.	.	.	.	.	.	C	42	9.233115	0.99108	.	.	ENSG00000166825	ENST00000300060	.	.	.	5.3	5.3	0.74995	.	0.142617	0.53938	D	0.000045	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.4527	0.83997	0.0:1.0:0.0:0.0	.	.	.	.	X	779	.	ENSP00000300060:W779X	W	-	3	0	ANPEP	88136710	1.000000	0.71417	0.997000	0.53966	0.456000	0.32438	7.683000	0.84093	2.490000	0.84030	0.555000	0.69702	TGG	.	.		0.592	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313425.1			T	90335706	C	T	90335706	4	4	320	1	0	0	0	0	0	1	0	0	710	856	30	3	586	3	ANPEP	15	90335706	Nonsense_Mutation	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	11441361	90335706	12195686	92	45104	235	2								
ANPEP	290	hgsc.bcm.edu	37	chr15	90335708	90335708	+	Missense_Mutation	SNP	A	A	C													0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	attattggggttctccatccActgcttgaaaaggccagaga							TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr15:90335708A>C	ENST00000300060.6	-	17	2648	c.2335T>G	c.(2335-2337)Tgg>Ggg	p.W779G		NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase	779	Metalloprotease.				angiogenesis (GO:0001525)|angiotensin maturation (GO:0002003)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|viral process (GO:0016032)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|receptor activity (GO:0004872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	57	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)|Icatibant(DB06196)	TTCTCCATCCACTGCTTGAAA	0.587																																					p.W779G	NSCLC(30;827 977 2459 19669 26125)	Atlas-SNP	.											.	ANPEP	124	.	0			c.T2335G						.						154	134	141					15																	90335708		2200	4299	6499	SO:0001583	missense	290	exon17			CCATCCACTGCTT	M22324	CCDS10356.1	15q25-q26	2008-07-31	2008-07-31		ENSG00000166825	ENSG00000166825	3.4.11.2	"CD molecules"	500	protein-coding gene	gene with protein product	"aminopeptidase N", "aminopeptidase M", "microsomal aminopeptidase"	151530		CD13, PEPN		2428842, 1977688	Standard	NM_001150		Approved	LAP1, gp150, p150	uc002bop.4	P15144	OTTHUMG00000149814	ENST00000300060.6:c.2335T>G	chr15.hg19:g.90335708A>C	ENSP00000300060:p.Trp779Gly	128.0	0.0		94.0	34.0	NM_001150	Q16728|Q6GT90|Q8IUK3|Q8IVH3|Q9UCE0	Missense_Mutation	SNP	ENST00000300060.6	hg19	CCDS10356.1	.	.	.	.	.	.	.	.	.	.	A	17.93	3.509527	0.64522	.	.	ENSG00000166825	ENST00000300060	T	0.06608	3.28	5.3	5.3	0.74995	.	0.142617	0.53938	D	0.000045	T	0.36908	0.0984	H	0.96301	3.8	0.58432	D	0.999997	D	0.89917	1.0	D	0.91635	0.999	T	0.53913	-0.8371	10	0.87932	D	0	.	13.1997	0.59761	1.0:0.0:0.0:0.0	.	779	P15144	AMPN_HUMAN	G	779	ENSP00000300060:W779G	ENSP00000300060:W779G	W	-	1	0	ANPEP	88136712	1.000000	0.71417	0.982000	0.44146	0.466000	0.32739	9.172000	0.94808	2.014000	0.59158	0.454000	0.30748	TGG	.	.		0.587	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313425.1			C	90335708	A	C	90335708	3	2	320	1	0	0	0	0	1	0	0	0	710	159	6	5	588	5	ANPEP	15	90335708	Missense_Mutation	SNP	A	TCGA-MI-A75C-01A-11D-A32G-10	2	90335708	12195684	93	45105	235	2								
PKD1	5310	hgsc.bcm.edu	37	chr16	2158624	2158624	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ctcccagcggtactcagtctGgtaggtgacgcagtcgcgca	13	13	2	1			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr16:2158624G>C	ENST00000262304.4	-	15	6752	c.6544C>G	c.(6544-6546)Cag>Gag	p.Q2182E	PKD1_ENST00000423118.1_Missense_Mutation_p.Q2182E|PKD1_ENST00000561991.1_5'Flank	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	2182	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						TACTCAGTCTGGTAGGTGACG	0.706																																					p.Q2182E		Atlas-SNP	.											.	PKD1	184	.	0			c.C6544G						.						21	17	18					16																	2158624		2138	4227	6365	SO:0001583	missense	5310	exon15			CAGTCTGGTAGGT	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"Voltage-gated ion channels / Transient receptor potential cation channels"	9008	protein-coding gene	gene with protein product	"polycystin 1", "transient receptor potential cation channel, subfamily P, member 1"	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.6544C>G	chr16.hg19:g.2158624G>C	ENSP00000262304:p.Gln2182Glu	53.0	0.0		46.0	16.0	NM_000296	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	hg19	CCDS32369.1	.	.	.	.	.	.	.	.	.	.	g	13.74	2.325879	0.41197	.	.	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101;ENST00000382481	T;T	0.69175	-0.38;-0.38	5.49	5.49	0.81192	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);Polycystin cation channel (1);	0.121954	0.56097	D	0.000031	T	0.75766	0.3894	M	0.68317	2.08	0.34664	D	0.722946	D;D	0.61080	0.989;0.968	P;P	0.58780	0.845;0.817	T	0.79212	-0.1896	10	0.26408	T	0.33	.	15.1	0.72266	0.0:0.0:0.8577:0.1423	.	2182;2182	P98161-3;P98161	.;PKD1_HUMAN	E	2182;2182;1533;461	ENSP00000262304:Q2182E;ENSP00000399501:Q2182E	ENSP00000262304:Q2182E	Q	-	1	0	PKD1	2098625	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	5.629000	0.67798	2.597000	0.87782	0.544000	0.68410	CAG	.	.		0.706	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			C	2158624	G	C	2158624	3	2	320	1	0	0	0	0	1	0	0	0	11972	1357	47	4	6495	4	PKD1	16	2158624	Missense_Mutation	SNP	G	TCGA-MI-A75C-01A-11D-A32G-10		2158624	88196129	94	45106										
PKMYT1	9088	hgsc.bcm.edu	37	chr16	3024301	3024301	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ctgccatgcaccacagcacaCcccaggcccgcggctgcctc	9	21	0	0			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr16:3024301C>T	ENST00000262300.8	-	6	1605	c.1097G>A	c.(1096-1098)gGt>gAt	p.G366D	PKMYT1_ENST00000431515.2_Missense_Mutation_p.G366D|PKMYT1_ENST00000574385.1_Missense_Mutation_p.G357D|PKMYT1_ENST00000574730.1_Missense_Mutation_p.G297D|PKMYT1_ENST00000440027.2_Missense_Mutation_p.G366D|PKMYT1_ENST00000573944.1_Missense_Mutation_p.G357D	NM_001258450.1|NM_004203.4|NM_182687.2	NP_001245379.1|NP_004194.3|NP_872629.1	Q99640	PMYT1_HUMAN	protein kinase, membrane associated tyrosine/threonine 1	366					G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	10						CCACAGCACACCCCAGGCCCG	0.706																																					p.G366D		Atlas-SNP	.											.	PKMYT1	23	.	0			c.G1097A						.						9	13	12					16																	3024301		2159	4255	6414	SO:0001583	missense	9088	exon6			AGCACACCCCAGG	AK097642	CCDS10486.1, CCDS45391.1, CCDS58414.1, CCDS58415.1	16p13.3	2014-06-13			ENSG00000127564	ENSG00000127564			29650	protein-coding gene	gene with protein product	"membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase", "protein phosphatase 1, regulatory subunit 126"	602474				9001210, 12606722	Standard	NM_004203		Approved	MYT1, PPP1R126	uc002csn.3	Q99640	OTTHUMG00000128975	ENST00000262300.8:c.1097G>A	chr16.hg19:g.3024301C>T	ENSP00000262300:p.Gly366Asp	117.0	0.0		105.0	35.0	NM_182687	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Missense_Mutation	SNP	ENST00000262300.8	hg19	CCDS10486.1	.	.	.	.	.	.	.	.	.	.	C	3.869	-0.028314	0.07589	.	.	ENSG00000127564	ENST00000431515;ENST00000262300;ENST00000440027;ENST00000402679;ENST00000382240	T;T;T;T	0.60548	0.18;0.27;0.23;1.9	5.36	0.757	0.18427	.	0.323813	0.34460	N	0.003948	T	0.32406	0.0828	N	0.24115	0.695	0.09310	N	1	B;B;B;P	0.34977	0.381;0.059;0.059;0.478	B;B;B;B	0.34489	0.184;0.024;0.024;0.122	T	0.26503	-1.0101	10	0.09338	T	0.73	-2.6839	5.1277	0.14894	0.0:0.5888:0.1563:0.2549	.	357;297;366;366	A6NHV6;B4DXD4;Q99640;F8W164	.;.;PMYT1_HUMAN;.	D	366;366;366;366;357	ENSP00000392855:G366D;ENSP00000262300:G366D;ENSP00000397739:G366D;ENSP00000371675:G357D	ENSP00000262300:G366D	G	-	2	0	PKMYT1	2964302	0.017000	0.18338	0.079000	0.20413	0.038000	0.13279	0.374000	0.20501	-0.094000	0.12374	0.650000	0.86243	GGT	.	.		0.706	PKMYT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250963.2	NM_004203		T	3024301	C	T	3024301	3	4	320	1	0	0	0	0	1	0	0	0	11987	507	18	3	456	3	PKMYT1	16	3024301	Missense_Mutation	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	865677	3024301	87330452	95	45107										
ZC3H7A	29066	hgsc.bcm.edu	37	chr16	11859416	11859416	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	agtaaggttaatctttccatTgccgccaaagaaagcctccc	7	12	1	1			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr16:11859416T>A	ENST00000396516.2	-	13	1845	c.1648A>T	c.(1648-1650)Aat>Tat	p.N550Y	ZC3H7A_ENST00000355758.4_Missense_Mutation_p.N550Y			Q8IWR0	Z3H7A_HUMAN	zinc finger CCCH-type containing 7A	550						nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(3)|kidney(5)|large_intestine(2)|liver(1)|lung(3)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(2)	25						ATCTTTCCATTGCCGCCAAAG	0.453																																					p.N550Y		Atlas-SNP	.											.	ZC3H7A	72	.	0			c.A1648T						.						96	95	96					16																	11859416		2197	4300	6497	SO:0001583	missense	29066	exon14			TTCCATTGCCGCC	AF161540	CCDS10550.1	16p13-p12	2013-01-11	2005-06-02	2005-06-08	ENSG00000122299	ENSG00000122299		"Zinc fingers, CCCH-type domain containing", "Tetratricopeptide (TTC) repeat domain containing"	30959	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 7", "zinc finger CCCH-type containing 7"	ZC3HDC7, ZC3H7		11042152	Standard	NM_014153		Approved	HSPC055, FLJ20318	uc002dbl.3	Q8IWR0	OTTHUMG00000129825	ENST00000396516.2:c.1648A>T	chr16.hg19:g.11859416T>A	ENSP00000379773:p.Asn550Tyr	59.0	0.0		38.0	13.0	NM_014153	D3DUG5|Q9NPE9	Missense_Mutation	SNP	ENST00000396516.2	hg19	CCDS10550.1	.	.	.	.	.	.	.	.	.	.	T	10.99	1.506772	0.26949	.	.	ENSG00000122299	ENST00000355758;ENST00000396516	T;T	0.10668	2.85;2.85	5.81	4.69	0.59074	.	0.342317	0.37393	N	0.002107	T	0.14700	0.0355	L	0.60455	1.87	0.80722	D	1	B;P	0.40376	0.178;0.715	B;B	0.40864	0.308;0.342	T	0.01013	-1.1481	10	0.56958	D	0.05	.	12.073	0.53628	0.0:0.0:0.2707:0.7293	.	271;550	Q9NXC8;Q8IWR0	.;Z3H7A_HUMAN	Y	550	ENSP00000347999:N550Y;ENSP00000379773:N550Y	ENSP00000347999:N550Y	N	-	1	0	ZC3H7A	11766917	1.000000	0.71417	0.971000	0.41717	0.373000	0.29922	2.264000	0.43302	0.979000	0.38497	0.533000	0.62120	AAT	.	.		0.453	ZC3H7A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437066.1	NM_014153		A	11859416	T	A	11859416	3	1	320	1	0	0	0	0	1	0	0	0	17587	1812	63	4	1307	4	ZC3H7A	16	11859416	Missense_Mutation	SNP	T	TCGA-MI-A75C-01A-11D-A32G-10	8835115	11859416	78495337	96	45108										
TEKT1	83659	hgsc.bcm.edu	37	chr17	6718550	6718550	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ttgttgttgagcgagaagcaGatatcatctatggtcagggc	13	6	3	3			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr17:6718550G>T	ENST00000338694.2	-	5	690	c.561C>A	c.(559-561)atC>atA	p.I187I	TEKT1_ENST00000535086.1_Silent_p.I41I	NM_053285.1	NP_444515.1	Q969V4	TEKT1_HUMAN	tektin 1	187						cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)		p.I187I(1)		NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)	20		Myeloproliferative disorder(207;0.0255)				GCGAGAAGCAGATATCATCTA	0.488																																					p.I187I		Atlas-SNP	.											TEKT1,NS,carcinoma,0,2	TEKT1	49	.	1	Substitution - coding silent(1)	lung(1)	c.C561A						.						238	214	222					17																	6718550		2203	4300	6503	SO:0001819	synonymous_variant	83659	exon5			GAAGCAGATATCA		CCDS11083.1	17p13.2	2011-05-23			ENSG00000167858	ENSG00000167858			15534	protein-coding gene	gene with protein product		609002				11606253	Standard	NM_053285		Approved		uc002gdt.3	Q969V4	OTTHUMG00000102063	ENST00000338694.2:c.561C>A	chr17.hg19:g.6718550G>T		158.0	0.0		122.0	6.0	NM_053285	D3DTM7	Silent	SNP	ENST00000338694.2	hg19	CCDS11083.1																																																																																			.	.		0.488	TEKT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219867.2	NM_053285		T	6718550	G	T	6718550	2	4	320	1	0	0	0	0	0	0	0	1	15767	932	33	3		3	TEKT1	17	6718550	Silent	SNP	G	TCGA-MI-A75C-01A-11D-A32G-10		6718550	74476660	97	45109										
PIGL	9487	hgsc.bcm.edu	37	chr17	16216896	16216896	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	gcagggggagtaagtggccaCagcaatcacattgctctgta	13	9	2	0			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr17:16216896C>A	ENST00000225609.5	+	4	479	c.462C>A	c.(460-462)caC>caA	p.H154Q	PIGL_ENST00000395844.4_Missense_Mutation_p.H154Q|PIGL_ENST00000498772.2_Missense_Mutation_p.H154Q|PIGL_ENST00000581006.1_Intron	NM_004278.3	NP_004269.1	Q9Y2B2	PIGL_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class L	154					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	N-acetylglucosaminylphosphatidylinositol deacetylase activity (GO:0000225)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|skin(1)	11				UCEC - Uterine corpus endometrioid carcinoma (92;0.0934)		TAAGTGGCCACAGCAATCACA	0.483																																					p.H154Q		Atlas-SNP	.											.	PIGL	16	.	0			c.C462A						.						239	205	216					17																	16216896		2203	4300	6503	SO:0001583	missense	9487	exon4			TGGCCACAGCAAT	AB017165	CCDS11176.1	17p12-p11.2	2013-02-26	2006-06-28		ENSG00000108474	ENSG00000108474	3.5.1.89	"Phosphatidylinositol glycan anchor biosynthesis"	8966	protein-coding gene	gene with protein product	"N-acetylglucosaminylphosphatidylinositol deacetylase"	605947	"phosphatidylinositol glycan, class L"			10085243	Standard	NM_004278		Approved		uc002gpv.3	Q9Y2B2	OTTHUMG00000059346	ENST00000225609.5:c.462C>A	chr17.hg19:g.16216896C>A	ENSP00000225609:p.His154Gln	99.0	0.0		74.0	29.0	NM_004278	A8KA67|B4DYN4	Missense_Mutation	SNP	ENST00000225609.5	hg19	CCDS11176.1	.	.	.	.	.	.	.	.	.	.	C	16.79	3.220892	0.58560	.	.	ENSG00000108474	ENST00000225609;ENST00000395844	D;D	0.86497	-2.13;-2.13	5.41	1.88	0.25563	Putative deacetylase LmbE-like domain (2);	0.000000	0.85682	D	0.000000	D	0.94503	0.8230	H	0.97214	3.96	0.48632	D	0.999681	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.92332	0.5874	10	0.87932	D	0	-24.8874	5.8218	0.18532	0.0:0.6384:0.0:0.3616	.	154;154	B4DYN4;Q9Y2B2	.;PIGL_HUMAN	Q	154	ENSP00000225609:H154Q;ENSP00000379185:H154Q	ENSP00000225609:H154Q	H	+	3	2	PIGL	16157621	0.976000	0.34144	0.999000	0.59377	0.656000	0.38851	0.510000	0.22723	0.785000	0.33685	-0.140000	0.14226	CAC	.	.		0.483	PIGL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131881.1			A	16216896	C	A	16216896	3	1	320	1	0	0	0	0	1	0	0	0	11900	477	17	3	476	3	PIGL	17	16216896	Missense_Mutation	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	9498346	16216896	64978314	98	45110										
KRT10	3858	hgsc.bcm.edu	37	chr17	38976377	38976377	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	cagtaatctcagatttatagCtggatatctgttcaatgtta	7	6	3	1			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr17:38976377C>G	ENST00000269576.5	-	5	1088	c.1079G>C	c.(1078-1080)aGc>aCc	p.S360T	TMEM99_ENST00000496847.1_Intron|TMEM99_ENST00000301665.3_Intron	NM_000421.3	NP_000412	P13645	K1C10_HUMAN	keratin 10	360	Coil 2.|Gly-rich.|Rod.				cellular response to calcium ion (GO:0071277)|keratinocyte differentiation (GO:0030216)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of epidermis (GO:0030280)			NS(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	11		Breast(137;0.000301)				AGATTTATAGCTGGATATCTG	0.353																																					p.S360T		Atlas-SNP	.											.	KRT10	56	.	0			c.G1079C						.						101	99	100					17																	38976377		2203	4300	6503	SO:0001583	missense	3858	exon5			TTATAGCTGGATA	J04029	CCDS11377.1	17q21.2	2013-06-20	2008-08-01		ENSG00000186395	ENSG00000186395		"-", "Intermediate filaments type I, keratins (acidic)"	6413	protein-coding gene	gene with protein product	"cytokeratin 10", "epidermolytic hyperkeratosis"	148080	"keratosis palmaris et plantaris"	KPP		2461420, 16831889	Standard	NM_000421		Approved	K10, CK10	uc002hvi.3	P13645	OTTHUMG00000133368	ENST00000269576.5:c.1079G>C	chr17.hg19:g.38976377C>G	ENSP00000269576:p.Ser360Thr	70.0	0.0		61.0	24.0	NM_000421	Q14664|Q8N175	Missense_Mutation	SNP	ENST00000269576.5	hg19	CCDS11377.1	.	.	.	.	.	.	.	.	.	.	C	17.27	3.346658	0.61073	.	.	ENSG00000186395	ENST00000269576	D	0.88975	-2.45	5.6	5.6	0.85130	Filament (1);	0.000000	0.43260	D	0.000590	D	0.83257	0.5215	N	0.12471	0.22	0.80722	D	1	B	0.17465	0.022	B	0.41174	0.349	T	0.76490	-0.2940	10	0.23302	T	0.38	.	10.1187	0.42607	0.0:0.8517:0.0:0.1483	.	360	P13645	K1C10_HUMAN	T	360	ENSP00000269576:S360T	ENSP00000269576:S360T	S	-	2	0	KRT10	36229903	0.000000	0.05858	0.999000	0.59377	0.957000	0.61999	0.515000	0.22801	2.655000	0.90218	0.655000	0.94253	AGC	.	.		0.353	KRT10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257875.1	NM_000421		G	38976377	C	G	38976377	3	3	320	1	0	0	0	0	1	0	0	0	8457	797	28	4	691	4	KRT10	17	38976377	Missense_Mutation	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	22759481	38976377	42218833	99	45111										
MRC2	9902	hgsc.bcm.edu	37	chr17	60742016	60742016	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ataccagcctccctgcccagCgctggaagtgggtctcccga	11	16	1	0			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr17:60742016C>A	ENST00000303375.5	+	2	628	c.226C>A	c.(226-228)Cgc>Agc	p.R76S	Y_RNA_ENST00000384652.1_RNA	NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	76	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				collagen catabolic process (GO:0030574)|endocytosis (GO:0006897)|osteoblast differentiation (GO:0001649)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|collagen binding (GO:0005518)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(11)|lung(28)|ovary(2)|prostate(1)|skin(3)	53						CCCTGCCCAGCGCTGGAAGTG	0.652																																					p.R76S		Atlas-SNP	.											.	MRC2	126	.	0			c.C226A						.						67	67	67					17																	60742016		2203	4300	6503	SO:0001583	missense	9902	exon2			GCCCAGCGCTGGA	AB014609	CCDS11634.1	17q23	2011-08-30				ENSG00000011028		"CD molecules", "C-type lectin domain containing"	16875	protein-coding gene	gene with protein product		612264				9734811, 8702911	Standard	NM_006039		Approved	KIAA0709, ENDO180, CLEC13E, CD280	uc002jad.4	Q9UBG0		ENST00000303375.5:c.226C>A	chr17.hg19:g.60742016C>A	ENSP00000307513:p.Arg76Ser	45.0	0.0		51.0	14.0	NM_006039	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	Missense_Mutation	SNP	ENST00000303375.5	hg19	CCDS11634.1	.	.	.	.	.	.	.	.	.	.	C	17.07	3.295546	0.60086	.	.	ENSG00000011028	ENST00000303375	T	0.31247	1.5	5.23	5.23	0.72850	Ricin B-related lectin (1);Ricin B lectin (2);	0.268277	0.40385	N	0.001120	T	0.21509	0.0518	L	0.29908	0.895	0.80722	D	1	P	0.38148	0.62	B	0.28849	0.095	T	0.05131	-1.0904	10	0.54805	T	0.06	-25.7213	14.5256	0.67887	0.1471:0.8529:0.0:0.0	.	76	Q9UBG0	MRC2_HUMAN	S	76	ENSP00000307513:R76S	ENSP00000307513:R76S	R	+	1	0	MRC2	58095748	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.369000	0.44231	2.450000	0.82876	0.561000	0.74099	CGC	.	.		0.652	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1			A	60742016	C	A	60742016	3	1	320	1	0	0	0	0	1	0	0	0	9767	768	27	1	232	1	MRC2	17	60742016	Missense_Mutation	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	21765639	60742016	20453194	100	45112										
GALK1	2584	hgsc.bcm.edu	37	chr17	73761055	73761055	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ccccgtgcagcccctcaccaTaggcagcaccaggccctggt	10	19	1	0			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr17:73761055T>C	ENST00000588479.1	-	1	737	c.163A>G	c.(163-165)Atg>Gtg	p.M55V	GALK1_ENST00000437911.1_Missense_Mutation_p.M85V|GALK1_ENST00000225614.2_Missense_Mutation_p.M55V			P51570	GALK1_HUMAN	galactokinase 1	55					carbohydrate metabolic process (GO:0005975)|galactitol metabolic process (GO:0019402)|galactose catabolic process (GO:0019388)|galactose metabolic process (GO:0006012)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)|galactokinase activity (GO:0004335)|galactose binding (GO:0005534)			endometrium(2)|large_intestine(1)|lung(1)|prostate(1)	5	all_cancers(13;1.5e-07)		all cancers(21;1.03e-06)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			CCCCTCACCATAGGCAGCACC	0.746																																					p.M55V		Atlas-SNP	.											.	GALK1	17	.	0			c.A163G						.						18	25	23					17																	73761055		2195	4287	6482	SO:0001583	missense	2584	exon1			TCACCATAGGCAG		CCDS11728.1	17q25.1	2013-09-19			ENSG00000108479	ENSG00000108479	2.7.1.6		4118	protein-coding gene	gene with protein product		604313		GALK		7670469	Standard	NM_000154		Approved		uc002jpk.3	P51570	OTTHUMG00000179832	ENST00000588479.1:c.163A>G	chr17.hg19:g.73761055T>C	ENSP00000465930:p.Met55Val	140.0	0.0		102.0	34.0	NM_000154	B2RC07|B4E1G6	Missense_Mutation	SNP	ENST00000588479.1	hg19	CCDS11728.1	.	.	.	.	.	.	.	.	.	.	T	17.06	3.292472	0.59976	.	.	ENSG00000108479	ENST00000225614;ENST00000437911;ENST00000375188	D;D	0.90504	-2.68;-2.68	4.47	4.47	0.54385	Ribosomal protein S5 domain 2-type fold (1);Galactokinase galactose-binding domain (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);	0.078972	0.85682	D	0.000000	D	0.94132	0.8118	M	0.77486	2.375	0.80722	D	1	D;D	0.63046	0.992;0.984	P;P	0.61201	0.852;0.885	D	0.94708	0.7889	10	0.66056	D	0.02	-15.9352	13.9259	0.63961	0.0:0.0:0.0:1.0	.	55;55	B4E1A8;P51570	.;GALK1_HUMAN	V	55;85;55	ENSP00000225614:M55V;ENSP00000406305:M85V	ENSP00000225614:M55V	M	-	1	0	GALK1	71272650	1.000000	0.71417	1.000000	0.80357	0.633000	0.38033	7.053000	0.76641	1.883000	0.54544	0.172000	0.16884	ATG	.	.		0.746	GALK1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448430.1			C	73761055	T	C	73761055	3	2	320	1	0	0	0	0	1	0	0	0	6211	1406	49	2	1047	2	GALK1	17	73761055	Missense_Mutation	SNP	T	TCGA-MI-A75C-01A-11D-A32G-10	13019039	73761055	7434155	101	45113										
HGS	9146	hgsc.bcm.edu	37	chr17	79661868	79661869	+	Missense_Mutation	DNP	GG	GG	TC													0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	tcgtcggcgcctctggctgaGgacatcgaccctgaggtaag							TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr17:79661868_79661869GG>TC	ENST00000329138.4	+	12	1095_1096	c.960_961GG>TC	c.(958-963)gaGGac>gaTCac	p.320_321ED>DH		NM_004712.4	NP_004703.1	O14964	HGS_HUMAN	hepatocyte growth factor-regulated tyrosine kinase substrate	320	Interaction with SNX1. {ECO:0000250}.				endosomal transport (GO:0016197)|endosome to lysosome transport (GO:0008333)|epidermal growth factor receptor signaling pathway (GO:0007173)|membrane invagination (GO:0010324)|membrane organization (GO:0061024)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of JAK-STAT cascade (GO:0046426)|positive regulation of gene expression (GO:0010628)|protein localization to membrane (GO:0072657)|protein targeting to lysosome (GO:0006622)|regulation of protein catabolic process (GO:0042176)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|secretory granule (GO:0030141)	metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			endometrium(2)|kidney(3)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12	all_neural(118;0.0878)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)			CTCTGGCTGAGGACATCGACCC	0.609																																					p.E320D|p.D321H		Atlas-SNP	.											.	HGS	54	.	0			c.G960T|c.G961C						.																																			SO:0001583	missense	9146	exon12			GGCTGAGGACATC|GCTGAGGACATCG	D84064	CCDS11784.1	17q25	2009-04-29				ENSG00000185359		"Zinc fingers, FYVE domain containing"	4897	protein-coding gene	gene with protein product		604375				9407053, 9630564	Standard	NM_004712		Approved	Hrs, ZFYVE8, Vps27	uc002kbg.3	O14964		Exception_encountered	chr17.hg19:g.79661868_79661869delinsTC	ENSP00000331201:p.E320_D321delinsDH	109.0|110.0	0.0		65.0|64.0	27.0	NM_004712	Q9NR36	Missense_Mutation	SNP	ENST00000329138.4	hg19	CCDS11784.1																																																																																			.	.		0.609	HGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440541.1	NM_004712		TC	79661869	GG	TC	79661868	3	4	320	1	0	0	0	0	1	0	0	0	7096	991	35	3	1006	3	HGS	17	79661868	Missense_Mutation	DNP	GG	TCGA-MI-A75C-01A-11D-A32G-10	5900813	79661868	1533342	102	45114										
ROCK1	6093	hgsc.bcm.edu	37	chr18	18586398	18586398	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	gcagctggtaataatctttgTctgtttgtgacttagaattc	9	6	2	2			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr18:18586398T>G	ENST00000399799.2	-	16	2739	c.1799A>C	c.(1798-1800)gAc>gCc	p.D600A		NM_005406.2	NP_005397.1	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein kinase 1	600	Interaction with FHOD1.				actin cytoskeleton organization (GO:0030036)|apical constriction (GO:0003383)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|bleb assembly (GO:0032060)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of focal adhesion assembly (GO:0051894)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(4)|central_nervous_system(1)|large_intestine(8)|lung(2)	16	Melanoma(1;0.165)					ATAATCTTTGTCTGTTTGTGA	0.378																																					p.D600A		Atlas-SNP	.											.	ROCK1	162	.	0			c.A1799C						.						143	136	139					18																	18586398		2203	4300	6503	SO:0001583	missense	6093	exon16			TCTTTGTCTGTTT		CCDS11870.2	18q11.2	2013-01-10			ENSG00000067900	ENSG00000067900	2.7.11.1	"Pleckstrin homology (PH) domain containing"	10251	protein-coding gene	gene with protein product		601702				8617235	Standard	NM_005406		Approved	p160ROCK	uc002kte.3	Q13464	OTTHUMG00000131723	ENST00000399799.2:c.1799A>C	chr18.hg19:g.18586398T>G	ENSP00000382697:p.Asp600Ala	75.0	0.0		46.0	19.0	NM_005406	B0YJ91|Q2KHM4|Q59GZ4	Missense_Mutation	SNP	ENST00000399799.2	hg19	CCDS11870.2	.	.	.	.	.	.	.	.	.	.	T	17.69	3.452443	0.63290	.	.	ENSG00000067900	ENST00000399799	T	0.65916	-0.18	5.44	5.44	0.79542	.	0.050567	0.85682	D	0.000000	T	0.47967	0.1474	N	0.19112	0.55	0.53688	D	0.999979	B	0.31174	0.311	B	0.26094	0.066	T	0.50906	-0.8772	10	0.52906	T	0.07	.	15.6661	0.77230	0.0:0.0:0.0:1.0	.	600	Q13464	ROCK1_HUMAN	A	600	ENSP00000382697:D600A	ENSP00000382697:D600A	D	-	2	0	ROCK1	16840396	1.000000	0.71417	0.999000	0.59377	0.946000	0.59487	7.525000	0.81892	2.285000	0.76669	0.533000	0.62120	GAC	.	.		0.378	ROCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254641.2	NM_005406		G	18586398	T	G	18586398	3	3	320	1	0	0	0	0	1	0	0	0	13532	1667	58	5	2337	5	ROCK1	18	18586398	Missense_Mutation	SNP	T	TCGA-MI-A75C-01A-11D-A32G-10		18586398	59490850	103	45115										
FHOD3	80206	hgsc.bcm.edu	37	chr18	34174853	34174853	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ggctgtcactgctgttgacaCgaaaagaggtgagtagtccc	13	9	1	3			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr18:34174853C>A	ENST00000359247.4	+	7	710	c.710C>A	c.(709-711)aCg>aAg	p.T237K	FHOD3_ENST00000590592.1_Missense_Mutation_p.T237K|FHOD3_ENST00000445677.1_Missense_Mutation_p.T237K|FHOD3_ENST00000591635.1_5'UTR|FHOD3_ENST00000257209.4_Missense_Mutation_p.T237K	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	237	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)				NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				GCTGTTGACACGAAAAGAGGT	0.502																																					p.T237K		Atlas-SNP	.											.	FHOD3	210	.	0			c.C710A						.						120	94	103					18																	34174853		2203	4300	6503	SO:0001583	missense	80206	exon7			TTGACACGAAAAG	AK091899	CCDS32816.1, CCDS62418.1, CCDS62419.1	18q12	2007-08-02				ENSG00000134775			26178	protein-coding gene	gene with protein product		609691				11214970	Standard	NM_025135		Approved	FHOS2, KIAA1695, FLJ22297, FLJ22717	uc021uiv.1	Q2V2M9		ENST00000359247.4:c.710C>A	chr18.hg19:g.34174853C>A	ENSP00000352186:p.Thr237Lys	101.0	0.0		100.0	39.0	NM_025135	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Missense_Mutation	SNP	ENST00000359247.4	hg19		.	.	.	.	.	.	.	.	.	.	C	8.245	0.807739	0.16467	.	.	ENSG00000134775	ENST00000257209;ENST00000359247;ENST00000445677	T;T;T	0.17054	2.3;2.3;2.3	5.3	5.3	0.74995	GTPase-binding/formin homology 3 (1);Armadillo-type fold (1);	0.421002	0.27406	N	0.019520	T	0.12263	0.0298	L	0.29908	0.895	0.24084	N	0.995939	P;P;B	0.43578	0.811;0.495;0.056	B;B;B	0.42319	0.383;0.148;0.117	T	0.15867	-1.0422	10	0.09843	T	0.71	.	10.3048	0.43674	0.0:0.9097:0.0:0.0903	.	237;237;237	Q2V2M9;Q2V2M9-3;E5F5Q0	FHOD3_HUMAN;.;.	K	237	ENSP00000257209:T237K;ENSP00000352186:T237K;ENSP00000411430:T237K	ENSP00000257209:T237K	T	+	2	0	FHOD3	32428851	0.063000	0.20901	0.995000	0.50966	0.163000	0.22366	0.524000	0.22940	2.625000	0.88918	0.655000	0.94253	ACG	.	.		0.502	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114		A	34174853	C	A	34174853	3	1	320	1	0	0	0	0	1	0	0	0	5891	536	19	1	736	1	FHOD3	18	34174853	Missense_Mutation	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	15588455	34174853	43902395	104	45116										
DSEL	92126	hgsc.bcm.edu	37	chr18	65179142	65179142	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	caccttccattcacaagcatCtacaaatgagtcgatttcca	4	13	2	1			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr18:65179142C>A	ENST00000310045.7	-	2	4207	c.2734G>T	c.(2734-2736)Gat>Tat	p.D912Y	CTD-2541J13.2_ENST00000583493.1_RNA|CTD-2541J13.2_ENST00000581951.1_RNA	NM_032160.2	NP_115536.1	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	902					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	isomerase activity (GO:0016853)|sulfotransferase activity (GO:0008146)			NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(25)|lung(23)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)				TCACAAGCATCTACAAATGAG	0.408																																					p.D912Y		Atlas-SNP	.											.	DSEL	196	.	0			c.G2734T						.						82	81	81					18																	65179142		2203	4300	6503	SO:0001583	missense	92126	exon2			AAGCATCTACAAA	AF480435	CCDS11995.1	18q22.1	2007-01-29	2007-01-29	2007-01-29	ENSG00000171451	ENSG00000171451			18144	protein-coding gene	gene with protein product		611125	"chromosome 18 open reading frame 4"	C18orf4		16505484	Standard	NM_032160		Approved	NCAG1, FLJ11477	uc002lke.1	Q8IZU8	OTTHUMG00000132804	ENST00000310045.7:c.2734G>T	chr18.hg19:g.65179142C>A	ENSP00000310565:p.Asp912Tyr	94.0	0.0		73.0	23.0	NM_032160	Q17RH1|Q6P5Z3	Missense_Mutation	SNP	ENST00000310045.7	hg19	CCDS11995.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.898842	0.91962	.	.	ENSG00000171451	ENST00000310045;ENST00000397964	T	0.24908	1.83	5.13	5.13	0.70059	Sulfotransferase domain (1);	0.320190	0.31010	N	0.008424	T	0.51822	0.1697	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.55263	-0.8168	10	0.87932	D	0	-22.1036	18.5756	0.91154	0.0:1.0:0.0:0.0	.	902	Q8IZU8	DSEL_HUMAN	Y	912;902	ENSP00000310565:D912Y	ENSP00000310565:D912Y	D	-	1	0	DSEL	63330122	1.000000	0.71417	0.844000	0.33320	0.950000	0.60333	7.717000	0.84732	2.384000	0.81235	0.563000	0.77884	GAT	.	.		0.408	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160		A	65179142	C	A	65179142	3	1	320	1	0	0	0	0	1	0	0	0	4777	913	32	3	938	3	DSEL	18	65179142	Missense_Mutation	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	31004289	65179142	12898106	105	45117										
MUC16	94025	hgsc.bcm.edu	37	chr19	9084547	9084547	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	cagatggagaggtggctgtaTttgtctctgttgtagatgtg	15	4	1	3			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr19:9084547T>G	ENST00000397910.4	-	1	7471	c.7268A>C	c.(7267-7269)aAt>aCt	p.N2423T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2423	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGTGGCTGTATTTGTCTCTGT	0.493																																					p.N2423T		Atlas-SNP	.											.	MUC16	4315	.	0			c.A7268C						.						84	87	86					19																	9084547		1970	4153	6123	SO:0001583	missense	94025	exon1			GCTGTATTTGTCT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.7268A>C	chr19.hg19:g.9084547T>G	ENSP00000381008:p.Asn2423Thr	183.0	0.0		93.0	6.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	3.290	-0.145088	0.06627	.	.	ENSG00000181143	ENST00000397910	T	0.02498	4.27	0.225	0.225	0.15325	.	.	.	.	.	T	0.03695	0.0105	N	0.08118	0	.	.	.	D	0.54772	0.968	P	0.59546	0.859	T	0.45745	-0.9240	7	0.87932	D	0	.	.	.	.	.	2423	B5ME49	.	T	2423	ENSP00000381008:N2423T	ENSP00000381008:N2423T	N	-	2	0	MUC16	8945547	0.003000	0.15002	0.359000	0.25824	0.361000	0.29550	-0.141000	0.10327	0.257000	0.21650	0.254000	0.18369	AAT	.	.		0.493	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	9084547	T	G	9084547	3	3	320	1	0	0	0	0	1	0	0	0	9982	1493	52	5	36591	5	MUC16	19	9084547	Missense_Mutation	SNP	T	TCGA-MI-A75C-01A-11D-A32G-10		9084547	50044436	106	45118										
RASAL3	64926	hgsc.bcm.edu	37	chr19	15569403	15569403	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	cagatccgcacatcccgctcGgcacccaggtccagttcaga	9	17	1	2			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr19:15569403G>T	ENST00000343625.7	-	7	811	c.726C>A	c.(724-726)gcC>gcA	p.A242A	RASAL3_ENST00000608577.1_5'Flank	NM_022904.1	NP_075055.1	Q86YV0	RASL3_HUMAN	RAS protein activator like 3	242	PH.				negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)	Ras GTPase activator activity (GO:0005099)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|skin(1)	18						CATCCCGCTCGGCACCCAGGT	0.637																																					p.A242A		Atlas-SNP	.											.	RASAL3	49	.	0			c.C726A						.						37	42	40					19																	15569403		2092	4221	6313	SO:0001819	synonymous_variant	64926	exon7			CCGCTCGGCACCC		CCDS46006.1	19p13.12	2008-12-18			ENSG00000105122	ENSG00000105122			26129	protein-coding gene	gene with protein product						12477932	Standard	NM_022904		Approved	FLJ21438	uc002nbe.2	Q86YV0		ENST00000343625.7:c.726C>A	chr19.hg19:g.15569403G>T		40.0	0.0		26.0	16.0	NM_022904	Q8N2T9|Q9H735	Silent	SNP	ENST00000343625.7	hg19	CCDS46006.1																																																																																			.	.		0.637	RASAL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461331.3	NM_022904		T	15569403	G	T	15569403	2	4	320	1	0	0	0	0	0	0	0	1	13080	1103	39	1		1	RASAL3	19	15569403	Silent	SNP	G	TCGA-MI-A75C-01A-11D-A32G-10	6484856	15569403	43559580	107	45119										
CD22	933	hgsc.bcm.edu	37	chr19	35832797	35832797	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ggtgaaggtccagcactcggGtgcctactggtgccagggga	17	10	0	1			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr19:35832797G>C	ENST00000085219.5	+	9	2030	c.1964G>C	c.(1963-1965)gGt>gCt	p.G655A	CD22_ENST00000536635.2_Missense_Mutation_p.G567A|CD22_ENST00000419549.2_Missense_Mutation_p.G483A|CD22_ENST00000544992.2_Missense_Mutation_p.G655A|CD22_ENST00000270311.6_Missense_Mutation_p.G535A|CD22_ENST00000341773.6_Missense_Mutation_p.G478A|CD22_ENST00000594250.1_Missense_Mutation_p.G478A	NM_001771.3	NP_001762.2	P20273	CD22_HUMAN	CD22 molecule	655	Ig-like C2-type 6.				cell adhesion (GO:0007155)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			breast(2)|endometrium(2)|kidney(3)|large_intestine(14)|lung(21)|ovary(5)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	54	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.83e-19)|OV - Ovarian serous cystadenocarcinoma(14;3.19e-18)|all cancers(14;3.41e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			CAGCACTCGGGTGCCTACTGG	0.587																																					p.G655A	Ovarian(42;1009 1133 23674 26041)	Atlas-SNP	.											.	CD22	129	.	0			c.G1964C						.						109	86	94					19																	35832797		2203	4300	6503	SO:0001583	missense	933	exon9			ACTCGGGTGCCTA	X52785	CCDS12457.1, CCDS54247.1, CCDS54248.1, CCDS54249.1, CCDS62634.1	19q13.1	2013-01-29	2006-03-28		ENSG00000012124	ENSG00000012124		"CD molecules", "Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1643	protein-coding gene	gene with protein product	"sialic acid binding Ig-like lectin 2"	107266	"CD22 antigen"			8496602, 1691828	Standard	NM_001185099		Approved	SIGLEC-2, SIGLEC2	uc010edt.3	P20273		ENST00000085219.5:c.1964G>C	chr19.hg19:g.35832797G>C	ENSP00000085219:p.Gly655Ala	84.0	0.0		66.0	25.0	NM_001185100	F5GYU4|F5H7U3|O95699|O95701|O95702|O95703|Q01665|Q32M46|Q92872|Q92873|Q9UQA6|Q9UQA7|Q9UQA8|Q9UQA9|Q9UQB0|Q9Y2A6	Missense_Mutation	SNP	ENST00000085219.5	hg19	CCDS12457.1	.	.	.	.	.	.	.	.	.	.	G	17.80	3.478467	0.63849	.	.	ENSG00000012124	ENST00000085219;ENST00000536635;ENST00000341773;ENST00000544992;ENST00000270311;ENST00000419549	T;T;T;T;T;T	0.21031	2.03;2.03;2.03;2.03;2.03;2.03	5.29	5.29	0.74685	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.000000	0.52532	D	0.000073	T	0.57755	0.2075	H	0.94222	3.51	0.26236	N	0.978942	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	T	0.62238	-0.6896	10	0.72032	D	0.01	.	14.4406	0.67314	0.0:0.0:1.0:0.0	.	483;655;567;655;478	Q32M46;F5GYU4;F5H7U3;P20273;P20273-2	.;.;.;CD22_HUMAN;.	A	655;567;478;655;535;483	ENSP00000085219:G655A;ENSP00000442279:G567A;ENSP00000339349:G478A;ENSP00000441237:G655A;ENSP00000270311:G535A;ENSP00000403822:G483A	ENSP00000085219:G655A	G	+	2	0	CD22	40524637	0.999000	0.42202	0.180000	0.23079	0.007000	0.05969	5.088000	0.64486	2.500000	0.84329	0.491000	0.48974	GGT	.	.		0.587	CD22-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466099.1	NM_001771		C	35832797	G	C	35832797	3	2	320	1	0	0	0	0	1	0	0	0	2987	1261	44	4	1994	4	CD22	19	35832797	Missense_Mutation	SNP	G	TCGA-MI-A75C-01A-11D-A32G-10	20263394	35832797	23296186	108	45120										
ZNF415	55786	hgsc.bcm.edu	37	chr19	53612297	53612297	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	acctcacactaaaggctttgCcacactctttacatgtgtaa	5	12	2	0			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr19:53612297C>G	ENST00000500065.4	-	4	1334	c.1001G>C	c.(1000-1002)gGc>gCc	p.G334A	ZNF415_ENST00000440291.1_Missense_Mutation_p.G321A|ZNF415_ENST00000601493.1_Missense_Mutation_p.G104A|ZNF415_ENST00000243643.4_Missense_Mutation_p.G334A|ZNF415_ENST00000597748.1_3'UTR|ZNF415_ENST00000455735.2_Missense_Mutation_p.G382A|ZNF415_ENST00000421033.1_Missense_Mutation_p.G346A|ZNF415_ENST00000597503.1_3'UTR|ZNF415_ENST00000594011.1_3'UTR|ZNF415_ENST00000448501.1_Missense_Mutation_p.G382A|ZNF415_ENST00000595193.1_3'UTR	NM_001136038.2	NP_001129510.2	Q09FC8	ZN415_HUMAN	zinc finger protein 415	382					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				GBM - Glioblastoma multiforme(134;0.0191)		AAAGGCTTTGCCACACTCTTT	0.403																																					p.G334A		Atlas-SNP	.											.	ZNF415	68	.	0			c.G1001C						.						85	78	81					19																	53612297		2203	4300	6503	SO:0001583	missense	55786	exon4			GCTTTGCCACACT	AK002053	CCDS12860.1, CCDS54313.1	19q13.42	2014-03-18			ENSG00000170954	ENSG00000170954		"Zinc fingers, C2H2-type", "-"	20636	protein-coding gene	gene with protein product						14702039	Standard	NM_001136038		Approved		uc002qaw.3	Q09FC8	OTTHUMG00000182865	ENST00000500065.4:c.1001G>C	chr19.hg19:g.53612297C>G	ENSP00000439435:p.Gly334Ala	45.0	0.0		39.0	12.0	NM_018355	F5H287|Q09FC7|Q09FC9|Q09FD0|Q6NSZ2|Q6P3S0|Q9NUR2	Missense_Mutation	SNP	ENST00000500065.4	hg19	CCDS54313.1	.	.	.	.	.	.	.	.	.	.	C	10.48	1.361411	0.24684	.	.	ENSG00000170954	ENST00000243643;ENST00000500065;ENST00000448501;ENST00000421033;ENST00000455735;ENST00000440291	T;T;T;T;T;T	0.21361	2.01;2.01;2.01;2.01;2.01;2.01	2.78	1.72	0.24424	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.40247	0.1109	M	0.70903	2.155	0.24520	N	0.994165	D;D;D;D;D;D	0.71674	0.998;0.997;0.998;0.998;0.998;0.998	P;D;D;D;P;D	0.76575	0.812;0.97;0.911;0.988;0.855;0.988	T	0.10590	-1.0623	9	0.72032	D	0.01	.	6.5532	0.22446	0.0:0.7444:0.0:0.2556	.	334;382;382;334;321;346	F5H287;B3KTG1;Q09FC8;Q09FC8-5;Q09FC8-4;Q09FC8-2	.;.;ZN415_HUMAN;.;.;.	A	334;334;382;346;382;321	ENSP00000243643:G334A;ENSP00000439435:G334A;ENSP00000396492:G382A;ENSP00000395055:G346A;ENSP00000388787:G382A;ENSP00000414601:G321A	ENSP00000243643:G334A	G	-	2	0	ZNF415	58304109	0.598000	0.26882	0.080000	0.20451	0.011000	0.07611	0.618000	0.24373	0.511000	0.28236	-0.339000	0.08088	GGC	.	.		0.403	ZNF415-025	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464043.1	NM_018355		G	53612297	C	G	53612297	3	3	320	1	0	0	0	0	1	0	0	0	17907	739	26	4	670	4	ZNF415	19	53612297	Missense_Mutation	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	17779500	53612297	5516686	109	45121										
ATRN	8455	hgsc.bcm.edu	37	chr20	3541522	3541522	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	gtcactgccctctctatggaTatataagcaatgtgcaggaa	9	9	2	0			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr20:3541522T>G	ENST00000262919.5	+	8	1485	c.1417T>G	c.(1417-1419)Tat>Gat	p.Y473D	ATRN_ENST00000446916.2_Missense_Mutation_p.Y473D	NM_139321.2	NP_647537.1	O75882	ATRN_HUMAN	attractin	473					cerebellum development (GO:0021549)|inflammatory response (GO:0006954)|myelination (GO:0042552)|pigmentation (GO:0043473)|regulation of multicellular organism growth (GO:0040014)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			breast(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	59						TCTCTATGGATATATAAGCAA	0.413																																					p.Y473D		Atlas-SNP	.											.	ATRN	118	.	0			c.T1417G						.						212	190	197					20																	3541522		2203	4300	6503	SO:0001583	missense	8455	exon8			TATGGATATATAA	AF034957	CCDS13053.1, CCDS13054.1	20p13	2008-07-02			ENSG00000088812	ENSG00000088812			885	protein-coding gene	gene with protein product	"mahogany protein"	603130				9736737, 8596018	Standard	NM_139321		Approved	DPPT-L, MGCA	uc002wim.2	O75882	OTTHUMG00000031746	ENST00000262919.5:c.1417T>G	chr20.hg19:g.3541522T>G	ENSP00000262919:p.Tyr473Asp	189.0	0.0		132.0	51.0	NM_139321	A8KAE5|O60295|O95414|Q3MIT3|Q5TDA2|Q5TDA4|Q5VYW3|Q9NTQ3|Q9NTQ4|Q9NU01|Q9NZ57|Q9NZ58|Q9UC75|Q9UDF5	Missense_Mutation	SNP	ENST00000262919.5	hg19	CCDS13053.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.132565	0.77662	.	.	ENSG00000088812	ENST00000262919;ENST00000446916;ENST00000340500	T;T	0.68181	3.23;-0.31	4.99	4.99	0.66335	Kelch-type beta propeller (1);	0.142166	0.49916	D	0.000123	T	0.82029	0.4948	M	0.79805	2.47	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.98;0.998	D	0.84958	0.0875	10	0.87932	D	0	-18.2912	14.4925	0.67660	0.0:0.0:0.0:1.0	.	473;473	O75882;O75882-2	ATRN_HUMAN;.	D	473;473;399	ENSP00000262919:Y473D;ENSP00000416587:Y473D	ENSP00000262919:Y473D	Y	+	1	0	ATRN	3489522	1.000000	0.71417	0.999000	0.59377	0.978000	0.69477	7.836000	0.86788	2.080000	0.62538	0.528000	0.53228	TAT	.	.		0.413	ATRN-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077740.2	NM_139321		G	3541522	T	G	3541522	3	3	320	1	0	0	0	0	1	0	0	0	1206	1406	49	5	1447	5	ATRN	20	3541522	Missense_Mutation	SNP	T	TCGA-MI-A75C-01A-11D-A32G-10		3541522	59483998	110	45122										
CBFA2T2	9139	hgsc.bcm.edu	37	chr20	32199083	32199084	+	In_Frame_Ins	INS	-	-	CAATGACAT													0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	accactctgcaacagtttggINScaatgacatctcccctgaga							TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr20:32199083_32199084insCAATGACAT	ENST00000346541.3	+	4	926_927	c.389_390insCAATGACAT	c.(388-393)ggcaat>ggCAATGACATcaat	p.131_132insDIN	CBFA2T2_ENST00000375279.2_In_Frame_Ins_p.131_132insDIN|CBFA2T2_ENST00000397798.2_In_Frame_Ins_p.102_103insDIN|CBFA2T2_ENST00000342704.6_In_Frame_Ins_p.122_123insDIN|CBFA2T2_ENST00000359606.3_In_Frame_Ins_p.141_142insDIN|CBFA2T2_ENST00000344201.3_In_Frame_Ins_p.102_103insDIN|CBFA2T2_ENST00000492345.1_In_Frame_Ins_p.102_103insDIN|CBFA2T2_ENST00000397800.1_In_Frame_Ins_p.102_103insDIN	NM_005093.3	NP_005084.1	O43439	MTG8R_HUMAN	core-binding factor, runt domain, alpha subunit 2; translocated to, 2	131	TAFH. {ECO:0000255|PROSITE- ProRule:PRU00440}.				epithelial cell differentiation (GO:0030855)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)	20						CAACAGTTTGGCAATGACATCT	0.495																																					p.G130delinsGNDI	Esophageal Squamous(174;142 1955 14837 21276 28041)	Atlas-Indel,Pindel	.											.	CBFA2T2	93	.	0			c.389_390insCAATGACAT						.																																			SO:0001652	inframe_insertion	9139	exon4			.	AF052210	CCDS13221.1, CCDS46590.1	20q11	2007-01-29			ENSG00000078699	ENSG00000078699		"Zinc fingers, MYND-type"	1536	protein-coding gene	gene with protein product		603672				9790752	Standard	XM_006723886		Approved	MTGR1, ZMYND3	uc002wze.1	O43439	OTTHUMG00000032261	ENST00000346541.3:c.390_398dupCAATGACAT	chr20.hg19:g.32199084_32199092dupCAATGACAT	ENSP00000262653:p.Asn131_Asp132insAspIleAsn	105.0	0.0		76.0	10.0	NM_005093	B2RAE6|F8W6D7|Q5TGE4|Q5TGE5|Q5TGE6|Q5TGE7|Q8IWF3|Q96B06|Q96L00|Q9H436|Q9UJP8|Q9UJP9|Q9UP24	In_Frame_Ins	INS	ENST00000346541.3	hg19	CCDS13221.1																																																																																			.	.		0.495	CBFA2T2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078708.2	NM_001032999		CAATGACAT	32199084	-	CAATGACAT	32199083	7	5	320	1	0	1	1	0	0	0	0	0	2699	1203	42	0	437	0	CBFA2T2	20	32199083	In_Frame_Ins	INS	-	TCGA-MI-A75C-01A-11D-A32G-10	28657561	32199083	30826437	111	45123										
ZNF217	7764	hgsc.bcm.edu	37	chr20	52198188	52198188	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ccttcttgtggaccctggagTgcaagaccagctggtggtag	14	10	1	1			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr20:52198188T>C	ENST00000371471.2	-	2	1603	c.1178A>G	c.(1177-1179)cAc>cGc	p.H393R	ZNF217_ENST00000302342.3_Missense_Mutation_p.H393R|ZNF217_ENST00000540425.1_5'Flank			O75362	ZN217_HUMAN	zinc finger protein 217	393					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			GACCCTGGAGTGCAAGACCAG	0.642																																					p.H393R		Atlas-SNP	.											.	ZNF217	227	.	0			c.A1178G						.						67	68	68					20																	52198188		2203	4300	6503	SO:0001583	missense	7764	exon1			CTGGAGTGCAAGA	AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"Zinc fingers, C2H2-type"	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.1178A>G	chr20.hg19:g.52198188T>C	ENSP00000360526:p.His393Arg	79.0	0.0		63.0	26.0	NM_006526	E1P5Y6|Q14DB8	Missense_Mutation	SNP	ENST00000371471.2	hg19	CCDS13443.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.559472	0.86335	.	.	ENSG00000171940	ENST00000371471;ENST00000302342	T;T	0.60548	0.18;0.18	5.7	5.7	0.88788	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.78868	0.4351	M	0.84585	2.705	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82637	-0.0359	10	0.87932	D	0	-40.9404	15.6258	0.76855	0.0:0.0:0.0:1.0	.	393	O75362	ZN217_HUMAN	R	393	ENSP00000360526:H393R;ENSP00000304308:H393R	ENSP00000304308:H393R	H	-	2	0	ZNF217	51631595	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.595000	0.82710	2.170000	0.68504	0.482000	0.46254	CAC	.	.		0.642	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526		C	52198188	T	C	52198188	3	2	320	1	0	0	0	0	1	0	0	0	17787	1696	59	2	1984	2	ZNF217	20	52198188	Missense_Mutation	SNP	T	TCGA-MI-A75C-01A-11D-A32G-10	19999105	52198188	10827332	112	45124										
ZNF831	128611	hgsc.bcm.edu	37	chr20	57766654	57766654	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	tctacaagcacaggcggacgCagacgcacctcaacaactcc	8	16	2	1			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr20:57766654C>T	ENST00000371030.2	+	1	580	c.580C>T	c.(580-582)Cag>Tag	p.Q194*		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	194							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					CAGGCGGACGCAGACGCACCT	0.662																																					p.Q194X		Atlas-SNP	.											.	ZNF831	287	.	0			c.C580T						.						47	55	52					20																	57766654		2054	4195	6249	SO:0001587	stop_gained	128611	exon1			CGGACGCAGACGC	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 174"	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.580C>T	chr20.hg19:g.57766654C>T	ENSP00000360069:p.Gln194*	49.0	0.0		26.0	9.0	NM_178457	Q5TDR4|Q8TCP0	Nonsense_Mutation	SNP	ENST00000371030.2	hg19	CCDS42894.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.698101	0.88830	.	.	ENSG00000124203	ENST00000371030	.	.	.	5.41	5.41	0.78517	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-11.7536	18.1834	0.89786	0.0:1.0:0.0:0.0	.	.	.	.	X	194	.	ENSP00000360069:Q194X	Q	+	1	0	ZNF831	57200049	1.000000	0.71417	1.000000	0.80357	0.087000	0.18053	7.755000	0.85180	2.538000	0.85594	0.561000	0.74099	CAG	.	.		0.662	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		T	57766654	C	T	57766654	4	4	320	1	0	0	0	0	0	1	0	0	18200	711	25	3	582	3	ZNF831	20	57766654	Nonsense_Mutation	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	5568466	57766654	5258866	113	45125										
ARFRP1	10139	hgsc.bcm.edu	37	chr20	62338416	62338416	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	gtccttctgaaacatgtactTgtacaagcccgacagcagcg	9	12	1	1			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr20:62338416T>C	ENST00000359715.5	-	1	594	c.28A>G	c.(28-30)Aag>Gag	p.K10E	ZGPAT_ENST00000357119.4_5'Flank|ARFRP1_ENST00000607873.1_Intron|ZGPAT_ENST00000328969.5_5'Flank|ZGPAT_ENST00000369967.3_5'Flank|ZGPAT_ENST00000448100.2_5'Flank|RP4-583P15.15_ENST00000490623.2_5'Flank|ARFRP1_ENST00000324228.2_Missense_Mutation_p.K10E|ARFRP1_ENST00000440854.1_Missense_Mutation_p.K10E|ZGPAT_ENST00000355969.6_5'Flank|ARFRP1_ENST00000609142.1_Missense_Mutation_p.K10E			Q13795	ARFRP_HUMAN	ADP-ribosylation factor related protein 1	10					gastrulation (GO:0007369)|Golgi to plasma membrane protein transport (GO:0043001)|GTP catabolic process (GO:0006184)|protein localization to Golgi apparatus (GO:0034067)|retrograde transport, endosome to Golgi (GO:0042147)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)	7	all_cancers(38;9.53e-13)|all_epithelial(29;2.64e-14)|Lung NSC(23;7e-10)|all_lung(23;2.53e-09)		Epithelial(9;4.09e-08)|all cancers(9;1.7e-07)|OV - Ovarian serous cystadenocarcinoma(5;0.0102)			AACATGTACTTGTACAAGCCC	0.607																																					p.K10E		Atlas-SNP	.											.	ARFRP1	17	.	0			c.A28G						.						200	121	148					20																	62338416		2203	4298	6501	SO:0001583	missense	10139	exon2			TGTACTTGTACAA	X91504	CCDS13533.1, CCDS46630.1, CCDS68172.1, CCDS68173.1	20q13.3	2014-05-09			ENSG00000101246	ENSG00000101246		"ADP-ribosylation factors"	662	protein-coding gene	gene with protein product		604699				8530503	Standard	NM_003224		Approved	ARP, Arp1, ARL18	uc031rup.1	Q13795	OTTHUMG00000032993	ENST00000359715.5:c.28A>G	chr20.hg19:g.62338416T>C	ENSP00000352746:p.Lys10Glu	60.0	0.0		49.0	20.0	NM_001134758	B7ZKX7|E1P5J9|Q6IBQ0	Missense_Mutation	SNP	ENST00000359715.5	hg19	CCDS13533.1	.	.	.	.	.	.	.	.	.	.	T	19.07	3.755360	0.69648	.	.	ENSG00000101246	ENST00000440854;ENST00000359715;ENST00000324228	T;T;T	0.63096	-0.02;-0.02;-0.02	4.79	4.79	0.61399	.	0.000000	0.85682	D	0.000000	T	0.64724	0.2624	M	0.75264	2.295	0.80722	D	1	B;B	0.31790	0.34;0.117	B;B	0.35278	0.199;0.152	T	0.68345	-0.5433	10	0.59425	D	0.04	-12.4031	13.4987	0.61440	0.0:0.0:0.0:1.0	.	10;10	B3KTR4;Q13795	.;ARFRP_HUMAN	E	10	ENSP00000403942:K10E;ENSP00000352746:K10E;ENSP00000326884:K10E	ENSP00000326884:K10E	K	-	1	0	ARFRP1	61808860	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.147000	0.77382	1.789000	0.52484	0.402000	0.26972	AAG	.	.		0.607	ARFRP1-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472024.1			C	62338416	T	C	62338416	3	2	320	1	0	0	0	0	1	0	0	0	856	1821	63	2	609	2	ARFRP1	20	62338416	Missense_Mutation	SNP	T	TCGA-MI-A75C-01A-11D-A32G-10	4571762	62338416	687104	114	45126										
CPT1B	1375	hgsc.bcm.edu	37	chr22	51014481	51014481	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	taccatgacataatagttgcTgttcaccatgagagggctcc	9	10	1	2	rs148070553		TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr22:51014481T>C	ENST00000360719.2	-	7	897	c.760A>G	c.(760-762)Agc>Ggc	p.S254G	CPT1B_ENST00000405237.3_Missense_Mutation_p.S254G|CHKB-CPT1B_ENST00000453634.1_3'UTR|CPT1B_ENST00000440709.1_Missense_Mutation_p.S254G|CPT1B_ENST00000457250.1_Missense_Mutation_p.S220G|CPT1B_ENST00000312108.7_Missense_Mutation_p.S254G|CPT1B_ENST00000434492.2_Missense_Mutation_p.S51G|CHKB-CPT1B_ENST00000452668.1_5'Flank|CPT1B_ENST00000395650.2_Missense_Mutation_p.S254G	NM_001145135.1|NM_152245.2	NP_001138607.1|NP_689451.1	Q92523	CPT1B_HUMAN	carnitine palmitoyltransferase 1B (muscle)	254					carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	carnitine O-palmitoyltransferase activity (GO:0004095)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22		all_cancers(38;8.8e-15)|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)		all cancers(3;3.56e-77)|OV - Ovarian serous cystadenocarcinoma(4;5.39e-74)|Epithelial(4;5.58e-70)|GBM - Glioblastoma multiforme(4;5.59e-08)|LUAD - Lung adenocarcinoma(64;0.0016)|Lung(4;0.00942)|BRCA - Breast invasive adenocarcinoma(115;0.207)		TAATAGTTGCTGTTCACCATG	0.587											OREG0026685	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S254G	Esophageal Squamous(170;988 1933 25577 30295 48163)	Atlas-SNP	.											.	CPT1B	61	.	0			c.A760G						.	T	GLY/SER,GLY/SER,GLY/SER,GLY/SER,GLY/SER,GLY/SER,GLY/SER	0,4406		0,0,2203	103	91	95		658,760,760,760,760,760,760	4.8	1	22	dbSNP_134	95	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense,missense	CPT1B	NM_001145134.1,NM_001145135.1,NM_001145136.1,NM_001145137.1,NM_004377.3,NM_152245.2,NM_152246.2	56,56,56,56,56,56,56	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	220/739,254/773,254/692,254/773,254/773,254/773,254/773	51014481	1,13005	2203	4300	6503	SO:0001583	missense	1375	exon7			AGTTGCTGTTCAC	U62733	CCDS14098.1, CCDS46734.1	22q13.33	2007-07-26			ENSG00000205560	ENSG00000205560			2329	protein-coding gene	gene with protein product		601987				9070950	Standard	NM_152245		Approved	M-CPT1, CPT1-M	uc003bmm.3	Q92523	OTTHUMG00000137390	ENST00000360719.2:c.760A>G	chr22.hg19:g.51014481T>C	ENSP00000353945:p.Ser254Gly	56.0	0.0	974	44.0	18.0	NM_001145135	B7Z4U4|B7Z5T8|E9PCP2|Q13389|Q99655|Q9BY90	Missense_Mutation	SNP	ENST00000360719.2	hg19	CCDS14098.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.031594	0.75504	0.0	1.16E-4	ENSG00000205560	ENST00000405237;ENST00000312108;ENST00000360719;ENST00000457250;ENST00000440709;ENST00000434492;ENST00000395650	D;D;D;D;D;D;D	0.91068	-2.78;-2.78;-2.78;-2.78;-2.78;-2.78;-2.78	4.81	4.81	0.61882	.	0.000000	0.85682	D	0.000000	D	0.95984	0.8692	M	0.92923	3.36	0.80722	D	1	D;P;D;D	0.89917	0.997;0.949;1.0;1.0	D;P;D;D	0.80764	0.994;0.833;0.992;0.99	D	0.96647	0.9478	10	0.87932	D	0	-34.0447	12.3354	0.55065	0.0:0.0:0.0:1.0	.	254;220;51;254	E9PCP2;B7Z4U4;A2RRE8;Q92523	.;.;.;CPT1B_HUMAN	G	254;254;254;220;254;51;254	ENSP00000385486:S254G;ENSP00000312189:S254G;ENSP00000353945:S254G;ENSP00000409342:S220G;ENSP00000414713:S254G;ENSP00000410966:S51G;ENSP00000379011:S254G	ENSP00000312189:S254G	S	-	1	0	CPT1B	49361347	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.368000	0.79567	2.024000	0.59613	0.459000	0.35465	AGC	.	T|1.000;C|0.000		0.587	CPT1B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317264.5	NM_152246		C	51014481	T	C	51014481	3	2	320	1	0	0	0	0	1	0	0	0	3834	1580	55	2	1610	2	CPT1B	22	51014481	Missense_Mutation	SNP	T	TCGA-MI-A75C-01A-11D-A32G-10		51014481	290085	115	45127										
ACR	49	hgsc.bcm.edu	37	chr22	51183204	51183204	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	ccggaatctacacggccaccTggccctatctgaactggatc	9	15	2	1			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chr22:51183204T>C	ENST00000216139.5	+	5	875	c.835T>C	c.(835-837)Tgg>Cgg	p.W279R	ACR_ENST00000527761.1_3'UTR|AC002056.5_ENST00000532913.1_RNA	NM_001097.2	NP_001088.2	P10323	ACRO_HUMAN	acrosin	279	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				acrosome matrix dispersal (GO:0002077)|acrosome reaction (GO:0007340)|activation of adenylate cyclase activity (GO:0007190)|binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|response to steroid hormone (GO:0048545)|single fertilization (GO:0007338)	acrosomal matrix (GO:0043159)|extracellular region (GO:0005576)|Golgi-associated vesicle (GO:0005798)|nucleus (GO:0005634)|protein complex (GO:0043234)	amidase activity (GO:0004040)|copper ion binding (GO:0005507)|DNA binding (GO:0003677)|drug binding (GO:0008144)|fucose binding (GO:0042806)|mannose binding (GO:0005537)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|skin(1)	7		all_cancers(38;8.8e-15)|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;1.1e-06)|LUAD - Lung adenocarcinoma(64;0.247)		CACGGCCACCTGGCCCTATCT	0.597																																					p.W279R		Atlas-SNP	.											.	ACR	28	.	0			c.T835C						.						15	16	16					22																	51183204		2195	4285	6480	SO:0001583	missense	49	exon5			GCCACCTGGCCCT	CR456366	CCDS14101.1	22q13.33	2012-10-23	2012-10-23		ENSG00000100312	ENSG00000100312	3.4.21.10		126	protein-coding gene	gene with protein product	"preproacrosin", "acrosin light and heavy chain prepropeptide"	102480				2298447, 12398221	Standard	NM_001097		Approved		uc003bnh.4	P10323	OTTHUMG00000150155	ENST00000216139.5:c.835T>C	chr22.hg19:g.51183204T>C	ENSP00000216139:p.Trp279Arg	176.0	0.0		171.0	64.0	NM_001097	Q6ICK2	Missense_Mutation	SNP	ENST00000216139.5	hg19	CCDS14101.1	.	.	.	.	.	.	.	.	.	.	T	13.96	2.391652	0.42410	.	.	ENSG00000100312	ENST00000216139	D	0.88201	-2.35	4.19	1.85	0.25348	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.382752	0.19487	N	0.113087	T	0.81269	0.4787	N	0.01493	-0.835	0.09310	N	1	D	0.89917	1.0	D	0.85130	0.997	T	0.69997	-0.4993	10	0.49607	T	0.09	-14.1835	4.5294	0.11997	0.3359:0.0:0.1731:0.4911	.	279	P10323	ACRO_HUMAN	R	279	ENSP00000216139:W279R	ENSP00000216139:W279R	W	+	1	0	ACR	49530070	0.997000	0.39634	0.603000	0.28903	0.948000	0.59901	1.858000	0.39408	0.629000	0.30376	0.254000	0.18369	TGG	.	.		0.597	ACR-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000316605.2	NM_001097		C	51183204	T	C	51183204	3	2	320	1	0	0	0	0	1	0	0	0	169	1580	55	2	853	2	ACR	22	51183204	Missense_Mutation	SNP	T	TCGA-MI-A75C-01A-11D-A32G-10	168723	51183204	121362	116	45128										
SHOX	6473	hgsc.bcm.edu	37	chrX	595367	595368	+	Frame_Shift_Del	DEL	AA	AA	-													0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	acgcagggatttatgaatgcAaagagaagcgcgaggacgtg							TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chrX:595367_595368delAA	ENST00000554971.1	+	2	383_384	c.292_293delAA	c.(292-294)aaafs	p.K98fs	SHOX_ENST00000381575.1_Frame_Shift_Del_p.K98fs|SHOX_ENST00000381578.1_Frame_Shift_Del_p.K98fs|SHOX_ENST00000334060.3_Frame_Shift_Del_p.K98fs			O15266	SHOX_HUMAN	short stature homeobox	98					skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|lung(9)|prostate(1)	13		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				TTATGAATGCAAAGAGAAGCGC	0.624																																					p.97_98del	Ovarian(95;18 1419 12424 14056 28266)	Atlas-Indel,Pindel	.											.	SHOX	31	.	0			c.291_292del						.																																			SO:0001589	frameshift_variant	6473	exon3			.	U82668	CCDS14106.1, CCDS14107.1	Xp22.33 and Yp11.32	2014-07-16			ENSG00000185960	ENSG00000185960		"Pseudoautosomal regions / PAR1", "Homeoboxes / PRD class"	10853	protein-coding gene	gene with protein product		312865, 400020				9259282, 9140395	Standard	XR_247282		Approved	PHOG, GCFX, SS, SHOXY	uc004cph.1	O15266	OTTHUMG00000021053	ENST00000554971.1:c.292_293delAA	chrX.hg19:g.595367_595368delAA	ENSP00000452016:p.Lys98fs	122.0	0.0		74.0	22.0	NM_000451	O00412|O00413|O15267	Frame_Shift_Del	DEL	ENST00000554971.1	hg19	CCDS14107.1																																																																																			.	.		0.624	SHOX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411999.3	NM_000451		-	595368	AA	-	595367	7	5	320	1	0	1	0	1	0	0	0	0	14303	131	5	0	298	0	SHOX	23	595367	Frame_Shift_Del	DEL	AA	TCGA-MI-A75C-01A-11D-A32G-10		595367	154675193	117	45129										
USP9X	8239	hgsc.bcm.edu	37	chrX	41002598	41002598	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	tgttgcgagatagtcttcatCagccacagtatgtagaaaag	10	7	3	2			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chrX:41002598C>G	ENST00000324545.8	+	10	1849	c.1216C>G	c.(1216-1218)Cag>Gag	p.Q406E	USP9X_ENST00000378308.2_Missense_Mutation_p.Q406E	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	406					axon extension (GO:0048675)|BMP signaling pathway (GO:0030509)|cerebellar cortex structural organization (GO:0021698)|chromosome segregation (GO:0007059)|female gamete generation (GO:0007292)|gene expression (GO:0010467)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|protein deubiquitination (GO:0016579)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)	co-SMAD binding (GO:0070410)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						TAGTCTTCATCAGCCACAGTA	0.353																																					p.Q406E	Ovarian(172;1807 2695 35459 49286)	Atlas-SNP	.											.	USP9X	385	.	0			c.C1216G						.						61	55	57					X																	41002598		1998	4200	6198	SO:0001583	missense	8239	exon10			CTTCATCAGCCAC	X98296	CCDS43930.1, CCDS55403.1	Xp11.4	2010-08-03	2006-02-14		ENSG00000124486	ENSG00000124486		"Ubiquitin-specific peptidases"	12632	protein-coding gene	gene with protein product		300072	"ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila)", "ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila)", "ubiquitin specific peptidase 9, X-linked (fat facets-like, Drosophila)"			8922996	Standard	NM_001039590		Approved	DFFRX, FAF	uc004dfb.3	Q93008	OTTHUMG00000021367	ENST00000324545.8:c.1216C>G	chrX.hg19:g.41002598C>G	ENSP00000316357:p.Gln406Glu	165.0	0.0		179.0	129.0	NM_001039591	O75550|Q8WWT3|Q8WX12	Missense_Mutation	SNP	ENST00000324545.8	hg19	CCDS43930.1	.	.	.	.	.	.	.	.	.	.	C	18.31	3.596387	0.66332	.	.	ENSG00000124486	ENST00000378308;ENST00000324545	T;T	0.75821	-0.97;-0.97	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.77164	0.4090	M	0.79475	2.455	0.80722	D	1	P;P	0.41910	0.607;0.764	B;B	0.39590	0.304;0.16	T	0.81865	-0.0736	10	0.72032	D	0.01	.	18.1174	0.89561	0.0:1.0:0.0:0.0	.	406;406	Q93008-1;Q93008	.;USP9X_HUMAN	E	406	ENSP00000367558:Q406E;ENSP00000316357:Q406E	ENSP00000316357:Q406E	Q	+	1	0	USP9X	40887542	1.000000	0.71417	1.000000	0.80357	0.845000	0.48019	7.442000	0.80503	2.304000	0.77564	0.415000	0.27848	CAG	.	.		0.353	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652		G	41002598	C	G	41002598	3	3	320	1	0	0	0	0	1	0	0	0	17105	827	29	4	1250	4	USP9X	23	41002598	Missense_Mutation	SNP	C	TCGA-MI-A75C-01A-11D-A32G-10	40407231	41002598	114267962	118	45130										
GPR174	84636	hgsc.bcm.edu	37	chrX	78427073	78427073	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0593220338983051	7	1	1.28859060402685	0.966442953020134	1.36439005132254	0.068649885583524	0.521678321678322	0	tgttatgatgaccattggcgAgttgattgggtttgtaactc	12	5	0	3			TCGA-MI-A75C-01A-11D-A32G-10	TCGA-MI-A75C-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea50cd47-c60a-4696-bd52-1e5fd735adad	95a91613-2d3d-4a43-a127-c826c46835e9	g.chrX:78427073A>G	ENST00000276077.1	+	1	605	c.569A>G	c.(568-570)gAg>gGg	p.E190G		NM_032553.1	NP_115942.1	Q9BXC1	GP174_HUMAN	G protein-coupled receptor 174	190						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.T187fs*3(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(19)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	38						ACCATTGGCGAGTTGATTGGG	0.453										HNSCC(63;0.18)																											p.E190G		Atlas-SNP	.											.	GPR174	79	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.A569G						.						114	103	107					X																	78427073		2203	4300	6503	SO:0001583	missense	84636	exon1			TTGGCGAGTTGAT	AF345567	CCDS14443.1	Xq13.3	2012-08-21			ENSG00000147138	ENSG00000147138		"GPCR / Class A : Orphans"	30245	protein-coding gene	gene with protein product		300903					Standard	NM_032553		Approved	FKSG79	uc004edg.1	Q9BXC1	OTTHUMG00000021898	ENST00000276077.1:c.569A>G	chrX.hg19:g.78427073A>G	ENSP00000276077:p.Glu190Gly	84.0	0.0		72.0	6.0	NM_032553	Q2M3F7	Missense_Mutation	SNP	ENST00000276077.1	hg19	CCDS14443.1	.	.	.	.	.	.	.	.	.	.	a	14.01	2.406348	0.42715	.	.	ENSG00000147138	ENST00000276077	T	0.71817	-0.6	5.08	5.08	0.68730	GPCR, rhodopsin-like superfamily (1);	0.055152	0.64402	D	0.000001	T	0.82019	0.4946	M	0.79011	2.435	0.58432	D	0.999997	D	0.76494	0.999	D	0.80764	0.994	T	0.80365	-0.1413	10	0.23302	T	0.38	.	12.6818	0.56926	1.0:0.0:0.0:0.0	.	190	Q9BXC1	GP174_HUMAN	G	190	ENSP00000276077:E190G	ENSP00000276077:E190G	E	+	2	0	GPR174	78313729	1.000000	0.71417	0.776000	0.31678	0.123000	0.20343	7.306000	0.78905	1.673000	0.50895	0.397000	0.26171	GAG	.	.		0.453	GPR174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057327.1	NM_032553		G	78427073	A	G	78427073	3	3	320	1	0	0	0	0	1	0	0	0	6680	304	11	2	571	2	GPR174	23	78427073	Missense_Mutation	SNP	A	TCGA-MI-A75C-01A-11D-A32G-10	37424475	78427073	76843487	119	45131										
STX12	23673	hgsc.bcm.edu	37	chr1	28099857	28099858	+	Frame_Shift_Ins	INS	-	-	C													0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	acatgtaccggaacccggggINSccctcggggccccagctccg							TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr1:28099857_28099858insC	ENST00000373943.4	+	1	164_165	c.39_40insC	c.(40-42)cccfs	p.P14fs	RP3-426I6.5_ENST00000602607.1_RNA|STX12_ENST00000468761.1_3'UTR	NM_177424.2	NP_803173.1	Q86Y82	STX12_HUMAN	syntaxin 12	14					cholesterol efflux (GO:0033344)|intracellular protein transport (GO:0006886)|protein stabilization (GO:0050821)|synaptic vesicle exocytosis (GO:0016079)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|phagocytic vesicle (GO:0045335)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)			breast(1)|central_nervous_system(1)|large_intestine(3)|lung(3)	8		Colorectal(325;3.46e-05)|all_lung(284;9.43e-05)|Lung NSC(340;0.000185)|Renal(390;0.00121)|Breast(348;0.0021)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;3.96e-24)|Colorectal(126;3.46e-08)|COAD - Colon adenocarcinoma(152;1.83e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00258)|KIRC - Kidney renal clear cell carcinoma(1967;0.00302)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0649)		GGAACCCGGGGCCCTCGGGGCC	0.653																																					p.G13fs	Ovarian(5;5 342 2097 9488 34083)	Atlas-INDEL	.											STX12,lower_third,carcinoma,0,1	STX12	26	.	0			c.39_40insC						.																																			SO:0001589	frameshift_variant	23673	exon1			.	BC046999	CCDS310.1	1p35.3	2008-05-14			ENSG00000117758	ENSG00000117758			11430	protein-coding gene	gene with protein product		606892				9507000	Standard	NM_177424		Approved	STX13, STX14	uc001bou.4	Q86Y82	OTTHUMG00000003730	ENST00000373943.4:c.42dupC	chr1.hg19:g.28099860_28099860dupC	ENSP00000363054:p.Pro14fs	209.0	0.0		204.0	12.0	NM_177424	B1AJQ7|O95564	Frame_Shift_Ins	INS	ENST00000373943.4	hg19	CCDS310.1																																																																																			.	.		0.653	STX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010519.1	NM_177424		C	28099858	-	C	28099857	7	5	321	1	0	1	1	0	0	0	0	0	15353	1190	42	0	41	0	STX12	1	28099857	Frame_Shift_Ins	INS	-	TCGA-MI-A75E-01A-11D-A32G-10		28099857	221150764	1	45132										
KIAA0319L	79932	hgsc.bcm.edu	37	chr1	35921730	35921730	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	gatggagttttggggcagggTgatcacttggttggggcctg	19	5	1	1			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr1:35921730T>C	ENST00000325722.3	-	10	1774	c.1540A>G	c.(1540-1542)Acc>Gcc	p.T514A	KIAA0319L_ENST00000485551.1_5'UTR|KIAA0319L_ENST00000373266.4_5'Flank	NM_024874.4	NP_079150.3	Q8IZA0	K319L_HUMAN	KIAA0319-like	514	PKD 3. {ECO:0000255|PROSITE- ProRule:PRU00151}.					cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(12)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	34		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TGGGGCAGGGTGATCACTTGG	0.532																																					p.T514A		Atlas-SNP	.											.	KIAA0319L	156	.	0			c.A1540G						.						203	199	200					1																	35921730		2203	4300	6503	SO:0001583	missense	79932	exon10			GCAGGGTGATCAC	AY163234	CCDS390.1	1p34.3	2008-10-24			ENSG00000142687	ENSG00000142687			30071	protein-coding gene	gene with protein product		613535				11347906	Standard	NM_024874		Approved	KIAA1837	uc001byx.3	Q8IZA0	OTTHUMG00000004370	ENST00000325722.3:c.1540A>G	chr1.hg19:g.35921730T>C	ENSP00000318406:p.Thr514Ala	139.0	0.0		120.0	16.0	NM_024874	B1AN13|D3DPR8|O95010|Q6PJJ7|Q7L1C9|Q8N2B3|Q8NDA0|Q8WY39|Q8WYZ5|Q96IC3|Q96JJ0|Q9BUW6|Q9H7V0	Missense_Mutation	SNP	ENST00000325722.3	hg19	CCDS390.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.023903	0.75390	.	.	ENSG00000142687	ENST00000325722;ENST00000426982;ENST00000440579	T;T;T	0.13196	2.61;2.61;2.61	5.59	5.59	0.84812	PKD/Chitinase domain (1);Fibronectin, type III (1);PKD/REJ-like protein (1);PKD domain (2);	0.107592	0.64402	D	0.000009	T	0.36386	0.0965	M	0.80332	2.49	0.80722	D	1	D;P	0.67145	0.996;0.924	P;P	0.61800	0.894;0.777	T	0.13335	-1.0513	10	0.42905	T	0.14	-12.8938	14.9413	0.70994	0.0:0.0:0.0:1.0	.	514;514	Q8IZA0-2;Q8IZA0	.;K319L_HUMAN	A	514	ENSP00000318406:T514A;ENSP00000395883:T514A;ENSP00000407576:T514A	ENSP00000318406:T514A	T	-	1	0	KIAA0319L	35694317	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.366000	0.73095	2.129000	0.65627	0.528000	0.53228	ACC	.	.		0.532	KIAA0319L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012684.2	NM_024874		C	35921730	T	C	35921730	3	2	321	1	0	0	0	0	1	0	0	0	8178	1696	59	2	1657	2	KIAA0319L	1	35921730	Missense_Mutation	SNP	T	TCGA-MI-A75E-01A-11D-A32G-10	7821873	35921730	213328891	2	45133										
EVI5	7813	hgsc.bcm.edu	37	chr1	93159906	93159906	+	Frame_Shift_Del	DEL	G	G	-													0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	cagttctgcctgattcatctGaagaagtgctaatcctacac							TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr1:93159906delG	ENST00000370331.1	-	8	1090	c.1081delC	c.(1081-1083)cagfs	p.Q361fs	EVI5_ENST00000543509.1_Frame_Shift_Del_p.Q361fs|EVI5_ENST00000540033.1_Frame_Shift_Del_p.Q361fs	NM_005665.4	NP_005656.4	O60447	EVI5_HUMAN	ecotropic viral integration site 5	361	Dimerization.|Interaction with alpha-tubulin, gamma- tubulin, BIRC5 and FBXO5.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|retrograde transport, endosome to Golgi (GO:0042147)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|prostate(1)|skin(1)	38		all_lung(203;0.00146)|Lung NSC(277;0.00565)|all_neural(321;0.185)|Melanoma(281;0.193)|Glioma(108;0.203)		Epithelial(280;8.09e-25)|OV - Ovarian serous cystadenocarcinoma(397;1.27e-22)|all cancers(265;1.74e-21)|GBM - Glioblastoma multiforme(16;0.00233)|BRCA - Breast invasive adenocarcinoma(282;0.211)		TGATTCATCTGAAGAAGTGCT	0.323																																					p.Q361fs		Atlas-Indel,Pindel	.											.	EVI5	94	.	0			c.1082delA						.						92	93	93					1																	93159906		2203	4300	6503	SO:0001589	frameshift_variant	7813	exon8			.	AF008915	CCDS30774.1	1p22	2013-07-09			ENSG00000067208	ENSG00000067208			3501	protein-coding gene	gene with protein product	"neuroblastoma stage 4S gene"	602942				9618176	Standard	XM_005271180		Approved	NB4S	uc001dox.3	O60447	OTTHUMG00000010895	ENST00000370331.1:c.1081delC	chr1.hg19:g.93159906delG	ENSP00000359356:p.Gln361fs	216.0	0.0		182.0	38.0	NM_005665	A6NKX8|B9A6J0|Q9H1Y9	Frame_Shift_Del	DEL	ENST00000370331.1	hg19	CCDS30774.1																																																																																			.	.		0.323	EVI5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030047.1	NM_005665		-	93159906	G	-	93159906	7	5	321	1	0	1	0	1	0	0	0	0	5291	1299	45	0	1395	0	EVI5	1	93159906	Frame_Shift_Del	DEL	G	TCGA-MI-A75E-01A-11D-A32G-10	57238176	93159906	156090715	3	45134										
STXBP3	6814	hgsc.bcm.edu	37	chr1	109340861	109340861	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	tatcaaagatattatggaggTaaaaatcattaaaatgtttt	6	2	2	1			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr1:109340861T>C	ENST00000370008.3	+	16	1499		c.e16+2			NM_007269.2	NP_009200.2	O00186	STXB3_HUMAN	syntaxin binding protein 3						blood coagulation (GO:0007596)|membrane organization (GO:0061024)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|neutrophil degranulation (GO:0043312)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein heterooligomerization (GO:0051291)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	syntaxin binding (GO:0019905)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(3)|urinary_tract(1)	13		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0386)|Lung(183;0.104)|COAD - Colon adenocarcinoma(174;0.137)|Epithelial(280;0.231)		ATTATGGAGGTAAAAATCATT	0.358																																					.		Atlas-SNP	.											.	STXBP3	44	.	0			c.1449+2T>C						.						74	80	78					1																	109340861		2203	4299	6502	SO:0001630	splice_region_variant	6814	exon16			TGGAGGTAAAAAT	D63506	CCDS790.1	1p13.3	2008-02-05			ENSG00000116266	ENSG00000116266			11446	protein-coding gene	gene with protein product		608339				10194441	Standard	NM_007269		Approved	UNC-18C	uc001dvy.3	O00186	OTTHUMG00000011122	ENST00000370008.3:c.1449+2T>C	chr1.hg19:g.109340861T>C		343.0	0.0		344.0	43.0	NM_007269	A8K269|A8K5K7|Q53FW1|Q86YJ3|Q9UPD7	Splice_Site	SNP	ENST00000370008.3	hg19	CCDS790.1	.	.	.	.	.	.	.	.	.	.	T	19.85	3.904031	0.72754	.	.	ENSG00000116266	ENST00000370008	.	.	.	5.52	5.52	0.82312	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.2063	0.65737	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	STXBP3	109142384	1.000000	0.71417	0.998000	0.56505	0.855000	0.48748	6.965000	0.76067	2.097000	0.63578	0.477000	0.44152	.	.	.		0.358	STXBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030591.1	NM_007269	Intron	C	109340861	T	C	109340861	5	2	321	1	0	0	0	0	0	0	1	0	15369	1652	57	2	1513	2	STXBP3	1	109340861	Splice_Site	SNP	T	TCGA-MI-A75E-01A-11D-A32G-10	16180955	109340861	139909760	4	45135										
MEF2D	4209	hgsc.bcm.edu	37	chr1	156450690	156450690	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	ggtacttgtcctccagcaggGggctctgttccagcgagtcc	13	13	1	0			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr1:156450690G>C	ENST00000348159.4	-	4	812	c.332C>G	c.(331-333)cCc>cGc	p.P111R	MEF2D_ENST00000360595.3_Missense_Mutation_p.P111R|MEF2D_ENST00000340875.5_Intron|MEF2D_ENST00000368240.2_Missense_Mutation_p.P111R|MEF2D_ENST00000353795.3_Intron|MEF2D_ENST00000464356.2_Intron	NM_005920.2	NP_005911.1	Q14814	MEF2D_HUMAN	myocyte enhancer factor 2D	111					adult heart development (GO:0007512)|apoptotic process (GO:0006915)|chondrocyte differentiation (GO:0002062)|endochondral ossification (GO:0001958)|muscle organ development (GO:0007517)|nervous system development (GO:0007399)|osteoblast differentiation (GO:0001649)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|histone deacetylase binding (GO:0042826)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	15	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CTCCAGCAGGGGGCTCTGTTC	0.667											OREG0013874	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P111R		Atlas-SNP	.											.	MEF2D	43	.	0			c.C332G						.						69	77	74					1																	156450690		2203	4300	6503	SO:0001583	missense	4209	exon4			AGCAGGGGGCTCT	BC054520	CCDS1143.1, CCDS60304.1	1q12-q23	2008-02-05	2007-04-24		ENSG00000116604	ENSG00000116604		"Myocyte enhancer factors"	6997	protein-coding gene	gene with protein product		600663				8269842	Standard	NM_005920		Approved		uc001fpb.4	Q14814	OTTHUMG00000033095	ENST00000348159.4:c.332C>G	chr1.hg19:g.156450690G>C	ENSP00000271555:p.Pro111Arg	45.0	0.0	1778	51.0	7.0	NM_005920	D3DVC0|Q14815|Q5T9U5|Q5T9U6	Missense_Mutation	SNP	ENST00000348159.4	hg19	CCDS1143.1	.	.	.	.	.	.	.	.	.	.	G	32	5.113501	0.94339	.	.	ENSG00000116604	ENST00000348159;ENST00000368240;ENST00000360595;ENST00000541336	T;T;T	0.68181	-0.31;-0.31;-0.31	5.08	5.08	0.68730	Holliday junction regulator protein family C-terminal repeat (1);	0.048511	0.85682	D	0.000000	T	0.80681	0.4669	M	0.85859	2.78	0.80722	D	1	D;D;P	0.62365	0.98;0.991;0.749	P;D;P	0.66716	0.876;0.946;0.856	D	0.83901	0.0290	10	0.87932	D	0	-21.1416	17.4126	0.87491	0.0:0.0:1.0:0.0	.	116;111;111	Q4LE66;Q14814;Q14814-4	.;MEF2D_HUMAN;.	R	111	ENSP00000271555:P111R;ENSP00000357223:P111R;ENSP00000353803:P111R	ENSP00000271555:P111R	P	-	2	0	MEF2D	154717314	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.466000	0.80914	2.529000	0.85273	0.561000	0.74099	CCC	.	.		0.667	MEF2D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080562.2	NM_005920		C	156450690	G	C	156450690	3	2	321	1	0	0	0	0	1	0	0	0	9467	1232	43	4	1269	4	MEF2D	1	156450690	Missense_Mutation	SNP	G	TCGA-MI-A75E-01A-11D-A32G-10	47109829	156450690	92799931	5	45136										
SLAMF8	56833	hgsc.bcm.edu	37	chr1	159802826	159802826	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	atggactttggtatggaaccAcacagcctcttcacagacgg	10	11	2	1			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr1:159802826A>G	ENST00000289707.5	+	3	677	c.528A>G	c.(526-528)ccA>ccG	p.P176P	SLAMF8_ENST00000471286.1_3'UTR|SLAMF8_ENST00000368104.4_Silent_p.P67P|C1orf204_ENST00000491974.1_5'Flank	NM_020125.2	NP_064510.1	Q9P0V8	SLAF8_HUMAN	SLAM family member 8	176	Ig-like C2-type.				cellular response to drug (GO:0035690)|defense response to bacterium (GO:0042742)|phagosome acidification (GO:0090383)|regulation of kinase activity (GO:0043549)|regulation of NAD(P)H oxidase activity (GO:0033860)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			endometrium(2)|large_intestine(4)|lung(6)	12	all_hematologic(112;0.0597)					GTATGGAACCACACAGCCTCT	0.547																																					p.P176P		Atlas-SNP	.											.	SLAMF8	30	.	0			c.A528G						.						139	125	130					1																	159802826		2203	4300	6503	SO:0001819	synonymous_variant	56833	exon3			GGAACCACACAGC	AF146761	CCDS1188.1	1q23.1	2013-01-11			ENSG00000158714	ENSG00000158714		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	21391	protein-coding gene	gene with protein product		606620				11313408	Standard	NM_020125		Approved	BLAME, SBBI42, CD353	uc001fue.4	Q9P0V8	OTTHUMG00000035433	ENST00000289707.5:c.528A>G	chr1.hg19:g.159802826A>G		64.0	0.0		65.0	7.0	NM_020125	Q32MC6|Q5VU15	Silent	SNP	ENST00000289707.5	hg19	CCDS1188.1																																																																																			.	.		0.547	SLAMF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085983.1	NM_020125		G	159802826	A	G	159802826	2	3	321	1	0	0	0	0	0	0	0	1	14385	146	6	2		2	SLAMF8	1	159802826	Silent	SNP	A	TCGA-MI-A75E-01A-11D-A32G-10	3352136	159802826	89447795	6	45137										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181741311	181741311	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	agaacgagaacgaacgctgcGgcaccgatctggcctacgtg	13	12	1	2			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr1:181741311G>A	ENST00000367573.2	+	37	5083	c.5083G>A	c.(5083-5085)Ggc>Agc	p.G1695S	CACNA1E_ENST00000360108.3_Missense_Mutation_p.G1676S|CACNA1E_ENST00000526775.1_Missense_Mutation_p.G1676S|CACNA1E_ENST00000358338.5_Missense_Mutation_p.G1627S|CACNA1E_ENST00000367570.1_Missense_Mutation_p.G1695S|CACNA1E_ENST00000367567.4_Missense_Mutation_p.G1302S|CACNA1E_ENST00000357570.5_Missense_Mutation_p.G1646S|RNA5SP70_ENST00000517168.1_RNA	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1695					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)	p.G1695S(2)		NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						CGAACGCTGCGGCACCGATCT	0.552																																					p.G1695S		Atlas-SNP	.											CACNA1E_ENST00000367573,NS,carcinoma,0,4	CACNA1E	778	.	2	Substitution - Missense(2)	cervix(2)	c.G5083A						.						203	204	204					1																	181741311		2187	4276	6463	SO:0001583	missense	777	exon37			CGCTGCGGCACCG	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.5083G>A	chr1.hg19:g.181741311G>A	ENSP00000356545:p.Gly1695Ser	81.0	1.0		111.0	17.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	G	37	6.146306	0.97324	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.98512	-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97	5.77	5.77	0.91146	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99187	0.9718	M	0.89840	3.065	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.989;1.0;0.999	D	0.99474	1.0946	10	0.87932	D	0	.	19.5857	0.95489	0.0:0.0:1.0:0.0	.	1676;1695;1695	Q15878-2;Q15878;Q15878-3	.;CAC1E_HUMAN;.	S	1695;1676;1646;1627;1302;1676;1695	ENSP00000356542:G1695S;ENSP00000434814:G1676S;ENSP00000350183:G1646S;ENSP00000351101:G1627S;ENSP00000356539:G1302S;ENSP00000353222:G1676S;ENSP00000356545:G1695S	ENSP00000350183:G1646S	G	+	1	0	CACNA1E	180007934	1.000000	0.71417	0.985000	0.45067	0.994000	0.84299	9.721000	0.98766	2.737000	0.93849	0.643000	0.83706	GGC	.	.		0.552	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		A	181741311	G	A	181741311	3	1	321	1	0	0	0	0	1	0	0	0	2544	1116	39	1	5229	1	CACNA1E	1	181741311	Missense_Mutation	SNP	G	TCGA-MI-A75E-01A-11D-A32G-10	21938485	181741311	67509310	7	45138										
TEDDM1	127670	hgsc.bcm.edu	37	chr1	182369506	182369506	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	aaccacataaaatgttaagaGggagccagtcactatcttta	7	8	2	1			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr1:182369506G>C	ENST00000367565.1	-	1	245	c.115C>G	c.(115-117)Ctc>Gtc	p.L39V		NM_172000.3	NP_741997.3	Q5T9Z0	TEDM1_HUMAN	transmembrane epididymal protein 1	39						integral component of membrane (GO:0016021)				haematopoietic_and_lymphoid_tissue(1)|lung(4)|ovary(2)	7						AATGTTAAGAGGGAGCCAGTC	0.473																																					p.L39V		Atlas-SNP	.											.	TEDDM1	32	.	0			c.C115G						.						148	127	134					1																	182369506		2203	4300	6503	SO:0001583	missense	127670	exon1			TTAAGAGGGAGCC	AJ515384	CCDS30953.1	1q25.3	2009-09-17		2005-08-09	ENSG00000203730	ENSG00000203730			30233	protein-coding gene	gene with protein product	"putative membrane protein HE9", "transmembrane protein 45C", "epididymal protein 9"						Standard	NM_172000		Approved	HE9, Epdd1, TMEM45C, EDDM9	uc001gpe.3	Q5T9Z0	OTTHUMG00000037398	ENST00000367565.1:c.115C>G	chr1.hg19:g.182369506G>C	ENSP00000356536:p.Leu39Val	102.0	0.0		121.0	15.0	NM_172000	Q8IVJ0	Missense_Mutation	SNP	ENST00000367565.1	hg19	CCDS30953.1	.	.	.	.	.	.	.	.	.	.	G	6.955	0.546171	0.13312	.	.	ENSG00000203730	ENST00000367565	T	0.48836	0.8	5.05	-10.1	0.00402	.	2.497220	0.01289	N	0.009955	T	0.25606	0.0623	N	0.25890	0.77	0.09310	N	1	B	0.15473	0.013	B	0.17433	0.018	T	0.10359	-1.0633	10	0.19590	T	0.45	-0.3392	2.5543	0.04756	0.1252:0.2266:0.2989:0.3493	.	39	Q5T9Z0	TEDM1_HUMAN	V	39	ENSP00000356536:L39V	ENSP00000356536:L39V	L	-	1	0	TEDDM1	180636129	0.000000	0.05858	0.000000	0.03702	0.056000	0.15407	-1.551000	0.02178	-1.921000	0.01068	-0.274000	0.10170	CTC	.	.		0.473	TEDDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091029.1	NM_172000		C	182369506	G	C	182369506	3	2	321	1	0	0	0	0	1	0	0	0	15764	1000	35	4	710	4	TEDDM1	1	182369506	Missense_Mutation	SNP	G	TCGA-MI-A75E-01A-11D-A32G-10	628195	182369506	66881115	8	45139										
C1orf14	81626	hgsc.bcm.edu	37	chr1	182872216	182872216	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	gtgctttttgaactgttactGgttctgaggttattacagtg	11	5	1	2			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr1:182872216G>A	ENST00000367547.3	-	9	1904	c.1668C>T	c.(1666-1668)acC>acT	p.T556T	SHCBP1L_ENST00000488956.1_5'UTR|SHCBP1L_ENST00000423786.1_Silent_p.T437T	NM_030933.2	NP_112195.2	Q9BZQ2	SHP1L_HUMAN	SHC SH2-domain binding protein 1-like	628										breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|pancreas(1)|prostate(1)|skin(2)	15						AACTGTTACTGGTTCTGAGGT	0.323																																					p.T556T		Atlas-SNP	.											.	SHCBP1L	64	.	0			c.C1668T						.						113	115	115					1																	182872216		2203	4298	6501	SO:0001819	synonymous_variant	81626	exon9			GTTACTGGTTCTG	AF288397	CCDS30955.1	1q25	2011-01-24	2011-01-24	2011-01-24	ENSG00000157060	ENSG00000157060			16788	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 14"	C1orf14		11318611	Standard	NM_030933		Approved		uc001gpu.3	Q9BZQ2	OTTHUMG00000035419	ENST00000367547.3:c.1668C>T	chr1.hg19:g.182872216G>A		82.0	0.0		83.0	19.0	NM_030933	Q4G195|Q9BZQ3|Q9H2B6	Silent	SNP	ENST00000367547.3	hg19	CCDS30955.1																																																																																			.	.		0.323	SHCBP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085956.1	NM_030933		A	182872216	G	A	182872216	2	1	321	1	0	0	0	0	0	0	0	1	2002	1335	47	3		3	C1orf14	1	182872216	Silent	SNP	G	TCGA-MI-A75E-01A-11D-A32G-10	502710	182872216	66378405	9	45140										
TP53BP2	7159	hgsc.bcm.edu	37	chr1	223983762	223983762	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	agaaggagctggcatgtcacTgttctctgtactggcattcc	11	10	2	1			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr1:223983762T>A	ENST00000343537.7	-	13	2770	c.2479A>T	c.(2479-2481)Agt>Tgt	p.S827C	TP53BP2_ENST00000498843.1_5'UTR|TP53BP2_ENST00000391878.2_Missense_Mutation_p.S698C|TP53BP2_ENST00000391879.2_Missense_Mutation_p.S60C	NM_001031685.2	NP_001026855.2	Q13625	ASPP2_HUMAN	tumor protein p53 binding protein 2	821	Pro-rich.				cell cycle (GO:0007049)|central nervous system development (GO:0007417)|embryo development ending in birth or egg hatching (GO:0009792)|heart development (GO:0007507)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell cycle (GO:0045786)|positive regulation of signal transduction (GO:0009967)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(2)	29				GBM - Glioblastoma multiforme(131;0.0958)		GGCATGTCACTGTTCTCTGTA	0.502																																					p.S827C		Atlas-SNP	.											.	TP53BP2	144	.	0			c.A2479T						.						124	122	122					1																	223983762		2203	4300	6503	SO:0001583	missense	7159	exon13			TGTCACTGTTCTC	U09582	CCDS1538.1, CCDS44319.1	1q41	2014-06-24	2014-06-24		ENSG00000143514	ENSG00000143514		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	12000	protein-coding gene	gene with protein product		602143	"tumor protein p53-binding protein, 2"			8668206, 8016121	Standard	NM_005426		Approved	PPP1R13A, ASPP2, 53BP2	uc010pvb.2	Q13625	OTTHUMG00000037379	ENST00000343537.7:c.2479A>T	chr1.hg19:g.223983762T>A	ENSP00000341957:p.Ser827Cys	60.0	0.0		96.0	14.0	NM_001031685	B4DG66|Q12892|Q86X75|Q96KQ3	Missense_Mutation	SNP	ENST00000343537.7	hg19	CCDS44319.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.32|12.32	1.901247|1.901247	0.33535|0.33535	.|.	.|.	ENSG00000143514|ENSG00000143514	ENST00000494100|ENST00000391878;ENST00000343537;ENST00000391879	.|T;T;T	.|0.50813	.|0.78;0.95;0.73	5.55|5.55	1.79|1.79	0.24919|0.24919	.|.	.|0.654370	.|0.17801	.|N	.|0.161563	T|T	0.39627|0.39627	0.1085|0.1085	L|L	0.56769|0.56769	1.78|1.78	0.09310|0.09310	N|N	0.999994|0.999994	.|P;P	.|0.45348	.|0.856;0.726	.|B;B	.|0.40101	.|0.319;0.156	T|T	0.25745|0.25745	-1.0123|-1.0123	5|10	.|0.51188	.|T	.|0.08	.|.	6.7368|6.7368	0.23413|0.23413	0.0:0.1363:0.1283:0.7354|0.0:0.1363:0.1283:0.7354	.|.	.|827;821	.|B4DG66;Q13625	.|.;ASPP2_HUMAN	L|C	160|698;827;60	.|ENSP00000375750:S698C;ENSP00000341957:S827C;ENSP00000375751:S60C	.|ENSP00000341957:S827C	Q|S	-|-	2|1	0|0	TP53BP2|TP53BP2	222050385|222050385	0.001000|0.001000	0.12720|0.12720	0.601000|0.601000	0.28877|0.28877	0.224000|0.224000	0.24922|0.24922	1.230000|1.230000	0.32612|0.32612	0.410000|0.410000	0.25675|0.25675	0.460000|0.460000	0.39030|0.39030	CAG|AGT	.	.		0.502	TP53BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090985.3	NM_001031685, NM_005426		A	223983762	T	A	223983762	3	1	321	1	0	0	0	0	1	0	0	0	16399	1580	55	4	949	4	TP53BP2	1	223983762	Missense_Mutation	SNP	T	TCGA-MI-A75E-01A-11D-A32G-10	41111546	223983762	25266859	10	45141										
KIF26B	55083	hgsc.bcm.edu	37	chr1	245849634	245849634	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	attccggcgtggcgtctaggGagtccttgctgcagcccgag	15	12	1	0			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr1:245849634G>A	ENST00000407071.2	+	12	3789	c.3349G>A	c.(3349-3351)Gag>Aag	p.E1117K	KIF26B_ENST00000366518.4_Missense_Mutation_p.E736K	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	1117					establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			GGCGTCTAGGGAGTCCTTGCT	0.617																																					p.E1117K		Atlas-SNP	.											.	KIF26B	343	.	0			c.G3349A						.						72	80	77					1																	245849634		1942	4144	6086	SO:0001583	missense	55083	exon12			TCTAGGGAGTCCT	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"Kinesins"	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.3349G>A	chr1.hg19:g.245849634G>A	ENSP00000385545:p.Glu1117Lys	58.0	0.0		74.0	8.0	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Missense_Mutation	SNP	ENST00000407071.2	hg19	CCDS44342.1	.	.	.	.	.	.	.	.	.	.	G	13.79	2.340931	0.41498	.	.	ENSG00000162849	ENST00000407071;ENST00000366518;ENST00000413001	T;T	0.78707	-1.2;-1.19	5.76	5.76	0.90799	.	.	.	.	.	T	0.79787	0.4506	M	0.77103	2.36	0.58432	D	0.999992	B;B	0.25719	0.06;0.132	B;B	0.18263	0.017;0.021	T	0.76277	-0.3018	9	0.46703	T	0.11	.	19.9554	0.97216	0.0:0.0:1.0:0.0	.	736;1117	B7WPD9;Q2KJY2	.;KI26B_HUMAN	K	1117;736;733	ENSP00000385545:E1117K;ENSP00000355475:E736K	ENSP00000355475:E736K	E	+	1	0	KIF26B	243916257	1.000000	0.71417	0.962000	0.40283	0.214000	0.24535	7.132000	0.77251	2.735000	0.93741	0.549000	0.68633	GAG	.	.		0.617	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354		A	245849634	G	A	245849634	3	1	321	1	0	0	0	0	1	0	0	0	8304	1175	41	3	3395	3	KIF26B	1	245849634	Missense_Mutation	SNP	G	TCGA-MI-A75E-01A-11D-A32G-10	21865872	245849634	3400987	11	45142										
OR2T12	127064	hgsc.bcm.edu	37	chr1	248458182	248458182	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	gagcaggtggcaaaggccttCttgcgggcttctgtagagcg	16	9	2	1			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr1:248458182C>T	ENST00000317996.1	-	1	698	c.699G>A	c.(697-699)aaG>aaA	p.K233K		NM_001004692.1	NP_001004692.1	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T, member 12	233						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(3)|large_intestine(3)|lung(25)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0201)			CAAAGGCCTTCTTGCGGGCTT	0.522																																					p.K233K		Atlas-SNP	.											.	OR2T12	113	.	0			c.G699A						.						93	89	90					1																	248458182		2203	4300	6503	SO:0001819	synonymous_variant	127064	exon1			GGCCTTCTTGCGG	BK004485	CCDS31110.1	1q44	2012-08-09			ENSG00000177201	ENSG00000177201		"GPCR / Class A : Olfactory receptors"	19592	protein-coding gene	gene with protein product							Standard	NM_001004692		Approved		uc010pzj.2	Q8NG77	OTTHUMG00000040457	ENST00000317996.1:c.699G>A	chr1.hg19:g.248458182C>T		290.0	0.0		343.0	55.0	NM_001004692		Silent	SNP	ENST00000317996.1	hg19	CCDS31110.1																																																																																			.	.		0.522	OR2T12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097353.1	NM_001004692		T	248458182	C	T	248458182	2	4	321	1	0	0	0	0	0	0	0	1	11028	912	32	3		3	OR2T12	1	248458182	Silent	SNP	C	TCGA-MI-A75E-01A-11D-A32G-10	2608548	248458182	792439	12	45143										
RSAD2	91543	hgsc.bcm.edu	37	chr2	7027257	7027257	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	tcaacgtggaagaggacatgAcggaacagatcaaagcacta	11	8	2	3			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr2:7027257A>G	ENST00000382040.3	+	3	836	c.700A>G	c.(700-702)Acg>Gcg	p.T234A	RSAD2_ENST00000541728.1_Missense_Mutation_p.T127A	NM_080657.4	NP_542388.2			radical S-adenosyl methionine domain containing 2											endometrium(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(1)	20	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			OV - Ovarian serous cystadenocarcinoma(76;0.191)		AGAGGACATGACGGAACAGAT	0.408																																					p.T234A		Atlas-SNP	.											.	RSAD2	38	.	0			c.A700G						.						83	76	78					2																	7027257		2203	4300	6503	SO:0001583	missense	91543	exon3			GACATGACGGAAC	AF442151	CCDS1656.1	2p25.2	2008-02-05			ENSG00000134321	ENSG00000134321			30908	protein-coding gene	gene with protein product		607810				11752458	Standard	NM_080657		Approved	cig5, viperin, vig1	uc002qyp.1	Q8WXG1	OTTHUMG00000090352	ENST00000382040.3:c.700A>G	chr2.hg19:g.7027257A>G	ENSP00000371471:p.Thr234Ala	81.0	0.0		86.0	13.0	NM_080657		Missense_Mutation	SNP	ENST00000382040.3	hg19	CCDS1656.1	.	.	.	.	.	.	.	.	.	.	A	8.642	0.896251	0.17686	.	.	ENSG00000134321	ENST00000382040;ENST00000541728	D;D	0.90900	-2.75;-2.75	5.79	4.62	0.57501	Elongator protein 3/MiaB/NifB (1);	0.982446	0.08333	N	0.962036	D	0.87720	0.6248	L	0.45137	1.4	0.26788	N	0.969454	B	0.10296	0.003	B	0.10450	0.005	T	0.73981	-0.3811	9	.	.	.	-7.8887	13.0855	0.59138	0.8659:0.1341:0.0:0.0	.	234	Q8WXG1	RSAD2_HUMAN	A	234;127	ENSP00000371471:T234A;ENSP00000440859:T127A	.	T	+	1	0	RSAD2	6944708	0.994000	0.37717	0.785000	0.31869	0.483000	0.33249	3.216000	0.51176	0.990000	0.38787	0.533000	0.62120	ACG	.	.		0.408	RSAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206724.2	NM_080657		G	7027257	A	G	7027257	3	3	321	1	0	0	0	0	1	0	0	0	13710	275	10	2	710	2	RSAD2	2	7027257	Missense_Mutation	SNP	A	TCGA-MI-A75E-01A-11D-A32G-10		7027257	236172116	13	45144										
C2orf63	130162	hgsc.bcm.edu	37	chr2	55407735	55407735	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	aaagaatagctttcttgtgcAggccacattcactgtagaca	8	9	2	2			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr2:55407735A>C	ENST00000401408.1	-	11	1640	c.1295T>G	c.(1294-1296)cTg>cGg	p.L432R	CLHC1_ENST00000494539.1_Intron|CLHC1_ENST00000406437.2_5'UTR|CLHC1_ENST00000406076.1_Missense_Mutation_p.L310R|CLHC1_ENST00000407122.1_Missense_Mutation_p.L432R	NM_152385.2	NP_689598.2	Q8NHS4	CLHC1_HUMAN	clathrin heavy chain linker domain containing 1	432																	TTTCTTGTGCAGGCCACATTC	0.448																																					p.L432R		Atlas-SNP	.											.	.	.	.	0			c.T1295G						.						129	116	120					2																	55407735		2203	4300	6503	SO:0001583	missense	130162	exon11			TTGTGCAGGCCAC		CCDS33201.1, CCDS46287.1	2p16.1	2012-08-03	2012-08-03	2012-08-03	ENSG00000162994	ENSG00000162994			26453	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 63"	C2orf63			Standard	NM_152385		Approved	FLJ31438	uc002ryi.2	Q8NHS4	OTTHUMG00000151918	ENST00000401408.1:c.1295T>G	chr2.hg19:g.55407735A>C	ENSP00000384869:p.Leu432Arg	80.0	0.0		68.0	13.0	NM_152385	B2RDV1|Q53R93|Q8N403	Missense_Mutation	SNP	ENST00000401408.1	hg19	CCDS33201.1	.	.	.	.	.	.	.	.	.	.	A	16.45	3.127453	0.56721	.	.	ENSG00000162994	ENST00000407122;ENST00000401408;ENST00000406076	T;T;T	0.46819	0.86;0.86;0.86	5.98	3.55	0.40652	Clathrin, heavy chain, linker (1);Armadillo-type fold (1);	0.370007	0.21640	N	0.071346	T	0.54464	0.1860	M	0.63428	1.95	0.24473	N	0.994384	D	0.63880	0.993	P	0.56398	0.797	T	0.48222	-0.9054	10	0.59425	D	0.04	-1.0667	6.1162	0.20127	0.7791:0.0:0.0773:0.1436	.	432	Q8NHS4	CB063_HUMAN	R	432;432;310	ENSP00000385778:L432R;ENSP00000384869:L432R;ENSP00000385512:L310R	ENSP00000384869:L432R	L	-	2	0	C2orf63	55261239	0.044000	0.20184	0.170000	0.22879	0.736000	0.42039	3.056000	0.49923	0.475000	0.27415	0.482000	0.46254	CTG	.	.		0.448	CLHC1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324412.4	NM_152385		C	55407735	A	C	55407735	3	2	321	1	0	0	0	0	1	0	0	0	2184	188	7	5	477	5	C2orf63	2	55407735	Missense_Mutation	SNP	A	TCGA-MI-A75E-01A-11D-A32G-10	48380478	55407735	187791638	14	45145										
C2orf3	6936	hgsc.bcm.edu	37	chr2	75897385	75897385	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	tgtcatctgtaaggagtccaTtccaaagaagaatattgcgg	10	7	2	2			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr2:75897385T>G	ENST00000321027.3	-	15	2115	c.1982A>C	c.(1981-1983)aAt>aCt	p.N661T	RP11-342K6.2_ENST00000604219.1_RNA|MRPL19_ENST00000358788.6_Intron|GCFC2_ENST00000541687.1_3'UTR|GCFC2_ENST00000409857.3_Missense_Mutation_p.N623T|MRPL19_ENST00000409374.1_Intron	NM_001201334.1|NM_003203.4	NP_001188263.1|NP_003194.3	P16383	GCFC2_HUMAN	GC-rich sequence DNA-binding factor 2	661					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)|U2-type post-mRNA release spliceosomal complex (GO:0071008)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)										AAGGAGTCCATTCCAAAGAAG	0.378																																					p.N661T		Atlas-SNP	.											.	.	.	.	0			c.A1982C						.						105	107	106					2																	75897385		2203	4300	6503	SO:0001583	missense	6936	exon15			AGTCCATTCCAAA	AB026911	CCDS1961.1, CCDS62943.1	2p12	2014-01-17	2011-11-24	2011-11-24	ENSG00000005436	ENSG00000005436			1317	protein-coding gene	gene with protein product	"GC binding factor"	189901	"transcription factor 9 (binds GC-rich sequences)", "chromosome 2 open reading frame 3"	TCF9, C2orf3		1370479, 2556218, 17309879, 24304693	Standard	NM_003203		Approved	DNABF, GCF	uc002sno.3	P16383	OTTHUMG00000129989	ENST00000321027.3:c.1982A>C	chr2.hg19:g.75897385T>G	ENSP00000318690:p.Asn661Thr	63.0	0.0		44.0	11.0	NM_003203	A4UHQ8|O95032|Q53TY0|Q6P2F2	Missense_Mutation	SNP	ENST00000321027.3	hg19	CCDS1961.1	.	.	.	.	.	.	.	.	.	.	T	9.421	1.082987	0.20309	.	.	ENSG00000005436	ENST00000321027;ENST00000409857;ENST00000427862	T;T;T	0.41400	1.0;1.0;1.0	4.65	2.14	0.27477	GC-rich sequence DNA-binding factor domain (1);	0.098090	0.64402	D	0.000002	T	0.30008	0.0751	L	0.51422	1.61	0.80722	D	1	P	0.38300	0.626	B	0.37650	0.255	T	0.05699	-1.0869	10	0.15952	T	0.53	-11.8751	5.0462	0.14485	0.0:0.0987:0.1836:0.7176	.	661	P16383	GCF_HUMAN	T	661;623;79	ENSP00000318690:N661T;ENSP00000386552:N623T;ENSP00000409340:N79T	ENSP00000318690:N661T	N	-	2	0	C2orf3	75750893	1.000000	0.71417	0.992000	0.48379	0.416000	0.31233	1.706000	0.37878	0.217000	0.20800	0.482000	0.46254	AAT	.	.		0.378	GCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252255.2	NM_003203		G	75897385	T	G	75897385	3	3	321	1	0	0	0	0	1	0	0	0	2164	1493	52	5	375	5	C2orf3	2	75897385	Missense_Mutation	SNP	T	TCGA-MI-A75E-01A-11D-A32G-10	20489650	75897385	167301988	15	45146										
CTNNA2	1496	hgsc.bcm.edu	37	chr2	80782957	80782957	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	atcaatgctgagatggagaaCtatgaagctggggtttatac	12	5	1	3			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr2:80782957C>G	ENST00000402739.4	+	11	1685	c.1680C>G	c.(1678-1680)aaC>aaG	p.N560K	CTNNA2_ENST00000540488.1_Missense_Mutation_p.N560K|CTNNA2_ENST00000343114.3_Missense_Mutation_p.N239K|CTNNA2_ENST00000496558.1_Missense_Mutation_p.N560K|CTNNA2_ENST00000466387.1_Missense_Mutation_p.N560K|CTNNA2_ENST00000541047.1_Missense_Mutation_p.N560K|CTNNA2_ENST00000361291.4_Missense_Mutation_p.N594K	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	560					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						AGATGGAGAACTATGAAGCTG	0.512																																					p.N560K		Atlas-SNP	.											.	CTNNA2	462	.	0			c.C1680G						.						147	139	142					2																	80782957		1899	4129	6028	SO:0001583	missense	1496	exon12			GGAGAACTATGAA		CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"cadherin-associated protein, related", "cancer/testis antigen 114"	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.1680C>G	chr2.hg19:g.80782957C>G	ENSP00000384638:p.Asn560Lys	87.0	0.0		78.0	9.0	NM_001164883	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Missense_Mutation	SNP	ENST00000402739.4	hg19		.	.	.	.	.	.	.	.	.	.	C	19.40	3.820310	0.71028	.	.	ENSG00000066032	ENST00000466387;ENST00000496558;ENST00000361291;ENST00000402739;ENST00000541047;ENST00000540488;ENST00000343114	T;T;T;T;T;T;T	0.50813	0.73;0.73;0.73;0.73;0.73;0.73;0.73	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.62648	0.2445	M	0.82433	2.59	0.58432	D	0.999991	D;D;D;D	0.67145	0.996;0.987;0.984;0.984	P;P;P;P	0.53760	0.55;0.734;0.713;0.62	T	0.66428	-0.5926	9	.	.	.	.	13.0806	0.59112	0.0:0.9265:0.0:0.0735	.	192;560;560;560	F6KRI5;P26232;P26232-3;P26232-2	.;CTNA2_HUMAN;.;.	K	560;560;594;560;560;560;239	ENSP00000418191:N560K;ENSP00000419295:N560K;ENSP00000355398:N594K;ENSP00000384638:N560K;ENSP00000444675:N560K;ENSP00000441705:N560K;ENSP00000341500:N239K	.	N	+	3	2	CTNNA2	80636468	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.352000	0.34033	2.765000	0.95021	0.650000	0.86243	AAC	.	.		0.512	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389		G	80782957	C	G	80782957	3	3	321	1	0	0	0	0	1	0	0	0	4015	564	20	4	1514	4	CTNNA2	2	80782957	Missense_Mutation	SNP	C	TCGA-MI-A75E-01A-11D-A32G-10	4885572	80782957	162416416	16	45147										
SLC9A4	389015	hgsc.bcm.edu	37	chr2	103120102	103120102	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	ctgcaattgagccactcatcGtcttcatgttcagctatttg	7	11	4	1	rs541859382		TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr2:103120102G>A	ENST00000295269.4	+	3	1373	c.916G>A	c.(916-918)Gtc>Atc	p.V306I		NM_001011552.3	NP_001011552.2	Q6AI14	SL9A4_HUMAN	solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4	306					epithelial cell development (GO:0002064)|gastric acid secretion (GO:0001696)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						GCCACTCATCGTCTTCATGTT	0.428																																					p.V306I		Atlas-SNP	.											.	SLC9A4	115	.	0			c.G916A						.						221	206	211					2																	103120102		2203	4300	6503	SO:0001583	missense	389015	exon3			CTCATCGTCTTCA		CCDS33264.1	2q12.1	2013-05-22	2012-03-22		ENSG00000180251	ENSG00000180251		"Solute carriers"	11077	protein-coding gene	gene with protein product		600531	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 4", "solute carrier family 9 (sodium/hydrogen exchanger), member 4"			8199403	Standard	NM_001011552		Approved	NHE4	uc002tbz.4	Q6AI14	OTTHUMG00000153093	ENST00000295269.4:c.916G>A	chr2.hg19:g.103120102G>A	ENSP00000295269:p.Val306Ile	113.0	0.0		113.0	18.0	NM_001011552	Q69YK0	Missense_Mutation	SNP	ENST00000295269.4	hg19	CCDS33264.1	.	.	.	.	.	.	.	.	.	.	G	19.69	3.874774	0.72180	.	.	ENSG00000180251	ENST00000295269	T	0.17528	2.27	5.61	5.61	0.85477	Cation/H+ exchanger (1);	0.052565	0.85682	D	0.000000	T	0.15825	0.0381	N	0.13272	0.32	0.44871	D	0.997886	D	0.55800	0.973	P	0.48270	0.572	T	0.08513	-1.0718	10	0.14656	T	0.56	.	20.0018	0.97417	0.0:0.0:1.0:0.0	.	306	Q6AI14	SL9A4_HUMAN	I	306	ENSP00000295269:V306I	ENSP00000295269:V306I	V	+	1	0	SLC9A4	102486534	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	4.413000	0.59795	2.793000	0.96121	0.655000	0.94253	GTC	.	.		0.428	SLC9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329498.1	NM_001011552.3		A	103120102	G	A	103120102	3	1	321	1	0	0	0	0	1	0	0	0	14731	1145	40	1	926	1	SLC9A4	2	103120102	Missense_Mutation	SNP	G	TCGA-MI-A75E-01A-11D-A32G-10	22337145	103120102	140079271	17	45148										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168107754	168107754	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	aattccactgatcacatggtGcccgacactgaaagttatga	8	10	1	3			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr2:168107754G>T	ENST00000409195.1	+	9	9941	c.9852G>T	c.(9850-9852)gtG>gtT	p.V3284V	XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_Silent_p.V3062V|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000295237.9_Silent_p.V3284V|XIRP2_ENST00000409756.2_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	3109					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						ATCACATGGTGCCCGACACTG	0.473																																					p.V3284V		Atlas-SNP	.											.	XIRP2	914	.	0			c.G9852T						.						94	94	94					2																	168107754		2019	4176	6195	SO:0001819	synonymous_variant	129446	exon9			CATGGTGCCCGAC	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.9852G>T	chr2.hg19:g.168107754G>T		108.0	0.0		81.0	22.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent	SNP	ENST00000409195.1	hg19	CCDS42769.1																																																																																			.	.		0.473	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		T	168107754	G	T	168107754	2	4	321	1	0	0	0	0	0	0	0	1	17445	1306	46	3		3	XIRP2	2	168107754	Silent	SNP	G	TCGA-MI-A75E-01A-11D-A32G-10	64987652	168107754	75091619	18	45149										
CERKL	375298	hgsc.bcm.edu	37	chr2	182412568	182412568	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	ccagatttgggagatccctgTgccctcctaaaagaaagaaa	9	10	0	4			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr2:182412568T>C	ENST00000339098.5	-	10	1217	c.1218A>G	c.(1216-1218)gcA>gcG	p.A406A	CERKL_ENST00000409440.3_Silent_p.A362A|CERKL_ENST00000374970.2_Silent_p.A311A|CERKL_ENST00000410087.3_Silent_p.A380A|CERKL_ENST00000374969.2_Silent_p.A267A|CERKL_ENST00000479558.1_5'UTR			Q49MI3	CERKL_HUMAN	ceramide kinase-like	406					negative regulation of apoptotic process (GO:0043066)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(13)|ovary(3)|skin(3)	32			OV - Ovarian serous cystadenocarcinoma(117;0.088)			GAGATCCCTGTGCCCTCCTAA	0.393																																					p.A406A		Atlas-SNP	.											.	CERKL	138	.	0			c.A1218G						.						121	130	127					2																	182412568		2203	4300	6503	SO:0001819	synonymous_variant	375298	exon10			TCCCTGTGCCCTC	BC020465	CCDS33340.1, CCDS33341.1, CCDS42789.1, CCDS46466.1, CCDS54425.1	2q31.3	2005-01-04			ENSG00000188452	ENSG00000188452			21699	protein-coding gene	gene with protein product			"retinitis pigmentosa 26 (autosomal recessive)"	RP26		14681825	Standard	NR_027689		Approved		uc002uny.3	Q49MI3	OTTHUMG00000154315	ENST00000339098.5:c.1218A>G	chr2.hg19:g.182412568T>C		106.0	0.0		116.0	12.0	NM_001030311	B2RPL2|B4DEY1|Q49MH9|Q49MI0|Q49MI1|Q49MI2|Q5DVJ2|Q5DVJ4|Q5DVJ5|Q6UZF6|Q6ZP59	Silent	SNP	ENST00000339098.5	hg19	CCDS42789.1																																																																																			.	.		0.393	CERKL-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334811.1			C	182412568	T	C	182412568	2	2	321	1	0	0	0	0	0	0	0	1	3270	1683	59	2		2	CERKL	2	182412568	Silent	SNP	T	TCGA-MI-A75E-01A-11D-A32G-10	14304814	182412568	60786805	19	45150										
BMPR2	659	hgsc.bcm.edu	37	chr2	203417602	203417602	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	tccaatgtctactgctatgcAgaatgaacggtaagacccta	8	10	1	3			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr2:203417602A>G	ENST00000374580.4	+	11	2116	c.1577A>G	c.(1576-1578)cAg>cGg	p.Q526R	BMPR2_ENST00000374574.2_Missense_Mutation_p.Q526R	NM_001204.6	NP_001195.2	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor, type II (serine/threonine kinase)	526					activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|brain development (GO:0007420)|cellular response to starvation (GO:0009267)|chondrocyte development (GO:0002063)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm formation (GO:0001707)|negative regulation of cell growth (GO:0030308)|negative regulation of chondrocyte proliferation (GO:1902731)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of vasoconstriction (GO:0045906)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of bone mineralization (GO:0030501)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|regulation of cell proliferation (GO:0042127)|regulation of lung blood pressure (GO:0014916)|retina vasculature development in camera-type eye (GO:0061298)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|venous blood vessel development (GO:0060841)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|fully spanning plasma membrane (GO:0044214)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	activin receptor activity, type II (GO:0016362)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(11)|lung(7)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	42						ACTGCTATGCAGAATGAACGG	0.403																																					p.Q526R		Atlas-SNP	.											.	BMPR2	142	.	0			c.A1577G						.						100	91	94					2																	203417602		2203	4300	6503	SO:0001583	missense	659	exon11			CTATGCAGAATGA	Z48923	CCDS33361.1	2q33-q34	2014-09-17			ENSG00000204217	ENSG00000204217			1078	protein-coding gene	gene with protein product		600799	"primary pulmonary hypertension 1"	PPH1		7791754	Standard	NM_001204		Approved	BRK-3, T-ALK, BMPR3, BMPR-II	uc002uzf.4	Q13873	OTTHUMG00000133617	ENST00000374580.4:c.1577A>G	chr2.hg19:g.203417602A>G	ENSP00000363708:p.Gln526Arg	47.0	0.0		59.0	4.0	NM_001204	Q13161|Q16569|Q4ZG08|Q53SA5|Q585T8	Missense_Mutation	SNP	ENST00000374580.4	hg19	CCDS33361.1	.	.	.	.	.	.	.	.	.	.	A	19.44	3.828817	0.71258	.	.	ENSG00000204217	ENST00000374580;ENST00000374574	D;D	0.89050	-2.46;-2.38	5.48	5.48	0.80851	.	0.052782	0.85682	D	0.000000	T	0.81814	0.4902	N	0.24115	0.695	0.80722	D	1	B;P	0.41475	0.421;0.751	B;B	0.36335	0.118;0.222	D	0.83948	0.0315	10	0.52906	T	0.07	.	15.5618	0.76256	1.0:0.0:0.0:0.0	.	526;526	Q13161;Q13873	.;BMPR2_HUMAN	R	526	ENSP00000363708:Q526R;ENSP00000363702:Q526R	ENSP00000363702:Q526R	Q	+	2	0	BMPR2	203125847	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.108000	0.94275	2.077000	0.62373	0.402000	0.26972	CAG	.	.		0.403	BMPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257743.1	NM_001204		G	203417602	A	G	203417602	3	3	321	1	0	0	0	0	1	0	0	0	1471	188	7	2	1619	2	BMPR2	2	203417602	Missense_Mutation	SNP	A	TCGA-MI-A75E-01A-11D-A32G-10	21005034	203417602	39781771	20	45151										
ALPP	250	hgsc.bcm.edu	37	chr2	233246210	233246210	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	ctgaaccctccaaccagggaGccccgagtatcggcagcagt	11	15	0	1			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr2:233246210G>A	ENST00000392027.2	+	11	1582	c.1313G>A	c.(1312-1314)aGc>aAc	p.S438N	AC068134.8_ENST00000441266.1_RNA|AC068134.8_ENST00000439072.1_RNA	NM_001632.3	NP_001623.3	P05187	PPB1_HUMAN	alkaline phosphatase, placental	438					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|endometrium(1)|kidney(4)|large_intestine(2)|liver(1)|lung(10)|ovary(2)	22		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)		CAACCAGGGAGCCCCGAGTAT	0.672																																					p.S438N		Atlas-SNP	.											.	ALPP	53	.	0			c.G1313A						.						24	28	27					2																	233246210		2201	4300	6501	SO:0001583	missense	250	exon11			CAGGGAGCCCCGA	M14169	CCDS2490.1	2q37.1	2010-06-24	2010-06-24		ENSG00000163283	ENSG00000163283	3.1.3.1		439	protein-coding gene	gene with protein product	"Regan isozyme"	171800	"alkaline phosphatase, placental (Regan isozyme)"			3001717, 3461452	Standard	XM_005246439		Approved		uc002vsq.3	P05187	OTTHUMG00000133255	ENST00000392027.2:c.1313G>A	chr2.hg19:g.233246210G>A	ENSP00000375881:p.Ser438Asn	195.0	0.0		211.0	41.0	NM_001632	P05188|P06861|Q53S78|Q96DB7	Missense_Mutation	SNP	ENST00000392027.2	hg19	CCDS2490.1	.	.	.	.	.	.	.	.	.	.	G	8.147	0.786429	0.16189	.	.	ENSG00000163283	ENST00000392027	D	0.95885	-3.84	1.79	-3.57	0.04612	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.716583	0.13422	N	0.389051	D	0.83399	0.5246	N	0.05330	-0.07	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.72633	-0.4234	10	0.31617	T	0.26	.	0.413	0.00444	0.3612:0.1883:0.2653:0.1852	.	438	P05187	PPB1_HUMAN	N	438	ENSP00000375881:S438N	ENSP00000375881:S438N	S	+	2	0	ALPP	232954454	0.000000	0.05858	0.006000	0.13384	0.296000	0.27459	-0.468000	0.06656	-0.960000	0.03613	0.305000	0.20034	AGC	.	.		0.672	ALPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257032.3	NM_001632		A	233246210	G	A	233246210	3	1	321	1	0	0	0	0	1	0	0	0	548	971	34	3	1355	3	ALPP	2	233246210	Missense_Mutation	SNP	G	TCGA-MI-A75E-01A-11D-A32G-10	29828608	233246210	9953163	21	45152										
ZNF385D	79750	hgsc.bcm.edu	37	chr3	21462713	21462713	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	tcctatttggaatttagtaaGgagcaaacagcacaggagtg	11	6	0	0			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr3:21462713G>A	ENST00000281523.2	-	8	1699	c.1181C>T	c.(1180-1182)cCt>cTt	p.P394L		NM_024697.2	NP_078973.1	Q9H6B1	Z385D_HUMAN	zinc finger protein 385D	394						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(1)|prostate(1)|skin(4)	46						AATTTAGTAAGGAGCAAACAG	0.438																																					p.P394L		Atlas-SNP	.											.	ZNF385D	93	.	0			c.C1181T						.						33	32	33					3																	21462713		2203	4300	6503	SO:0001583	missense	79750	exon8			TAGTAAGGAGCAA	BC007212	CCDS2636.1	3p24.3	2012-10-05	2007-12-06	2007-12-06	ENSG00000151789	ENSG00000151789			26191	protein-coding gene	gene with protein product			"zinc finger protein 659"	ZNF659		12477932	Standard	NM_024697		Approved	FLJ22419	uc003cce.3	Q9H6B1	OTTHUMG00000130484	ENST00000281523.2:c.1181C>T	chr3.hg19:g.21462713G>A	ENSP00000281523:p.Pro394Leu	41.0	0.0		54.0	6.0	NM_024697		Missense_Mutation	SNP	ENST00000281523.2	hg19	CCDS2636.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.130601	0.77549	.	.	ENSG00000151789	ENST00000281523	T	0.79247	-1.25	5.95	5.08	0.68730	.	0.000000	0.85682	D	0.000000	T	0.75391	0.3843	L	0.57536	1.79	0.80722	D	1	B	0.21225	0.053	B	0.17722	0.019	T	0.73603	-0.3930	10	0.87932	D	0	-29.7027	15.1365	0.72572	0.0677:0.0:0.9323:0.0	.	394	Q9H6B1	Z385D_HUMAN	L	394	ENSP00000281523:P394L	ENSP00000281523:P394L	P	-	2	0	ZNF385D	21437717	1.000000	0.71417	0.993000	0.49108	0.995000	0.86356	9.809000	0.99208	1.526000	0.49068	0.557000	0.71058	CCT	.	.		0.438	ZNF385D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252884.1	NM_024697		A	21462713	G	A	21462713	3	1	321	1	0	0	0	0	1	0	0	0	17893	1000	35	3	10	3	ZNF385D	3	21462713	Missense_Mutation	SNP	G	TCGA-MI-A75E-01A-11D-A32G-10		21462713	176559717	22	45153										
CELSR3	1951	hgsc.bcm.edu	37	chr3	48696462	48696462	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	gagtagaagaggtggtcggaGacatcggggtcataagctgg	18	5	1	3			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr3:48696462G>A	ENST00000164024.4	-	1	3886	c.3606C>T	c.(3604-3606)gtC>gtT	p.V1202V	CELSR3_ENST00000544264.1_Silent_p.V1202V	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	1202	Cadherin 9. {ECO:0000255|PROSITE- ProRule:PRU00043}.				axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		GGTGGTCGGAGACATCGGGGT	0.537																																					p.V1202V		Atlas-SNP	.											.	CELSR3	237	.	0			c.C3606T						.						95	88	90					3																	48696462		2203	4300	6503	SO:0001819	synonymous_variant	1951	exon1			GTCGGAGACATCG	AF231023	CCDS2775.1	3p21.31	2014-08-08	2013-02-18		ENSG00000008300	ENSG00000008300		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3230	protein-coding gene	gene with protein product	"flamingo homolog 1 (Drosophila)"	604264	"cadherin EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog"	EGFL1		9693030	Standard	NM_001407		Approved	MEGF2, HFMI1, FMI1, CDHF11	uc003cuf.1	Q9NYQ7	OTTHUMG00000133544	ENST00000164024.4:c.3606C>T	chr3.hg19:g.48696462G>A		71.0	0.0		69.0	12.0	NM_001407	O75092	Silent	SNP	ENST00000164024.4	hg19	CCDS2775.1																																																																																			.	.		0.537	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407		A	48696462	G	A	48696462	2	1	321	1	0	0	0	0	0	0	0	1	3225	929	33	3		3	CELSR3	3	48696462	Silent	SNP	G	TCGA-MI-A75E-01A-11D-A32G-10	27233749	48696462	149325968	23	45154										
FLNB	2317	hgsc.bcm.edu	37	chr3	58089691	58089691	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	ccttccttcccacagagggtCtggaggagctggtgaagcag	14	11	1	2			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr3:58089691C>T	ENST00000295956.4	+	10	1654	c.1489C>T	c.(1489-1491)Ctg>Ttg	p.L497L	FLNB_ENST00000490882.1_Silent_p.L497L|FLNB_ENST00000493452.1_Silent_p.L328L|FLNB_ENST00000358537.3_Silent_p.L497L|FLNB_ENST00000357272.4_Silent_p.L497L|FLNB_ENST00000348383.5_Silent_p.L497L|FLNB_ENST00000429972.2_Silent_p.L497L|FLNB_ENST00000419752.2_Silent_p.L328L	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	497					actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		CACAGAGGGTCTGGAGGAGCT	0.502																																					p.L497L		Atlas-SNP	.											.	FLNB	430	.	0			c.C1489T						.						93	96	95					3																	58089691		2203	4300	6503	SO:0001819	synonymous_variant	2317	exon10			GAGGGTCTGGAGG	AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"actin binding protein 278"	603381	"filamin B, beta (actin binding protein 278)", "Larsen syndrome 1 (autosomal dominant)"	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.1489C>T	chr3.hg19:g.58089691C>T		96.0	0.0		70.0	13.0	NM_001457	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Silent	SNP	ENST00000295956.4	hg19	CCDS2885.1																																																																																			.	.		0.502	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457		T	58089691	C	T	58089691	2	4	321	1	0	0	0	0	0	0	0	1	5942	912	32	3		3	FLNB	3	58089691	Silent	SNP	C	TCGA-MI-A75E-01A-11D-A32G-10	9393229	58089691	139932739	24	45155										
PRICKLE2	166336	hgsc.bcm.edu	37	chr3	64133075	64133075	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	ggtctacgtcggctgacagcCggttagaactcacttgcagc	12	12	2	2	rs372367565		TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr3:64133075C>A	ENST00000295902.6	-	7	1676	c.1091G>T	c.(1090-1092)cGg>cTg	p.R364L	PRICKLE2_ENST00000564377.1_Missense_Mutation_p.R420L	NM_198859.3	NP_942559.1	Q7Z3G6	PRIC2_HUMAN	prickle homolog 2 (Drosophila)	364					establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|neuron projection development (GO:0031175)	apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(9)|liver(1)|lung(10)|ovary(4)|prostate(2)|skin(2)|stomach(1)	32		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000971)|KIRC - Kidney renal clear cell carcinoma(15;0.00443)|Kidney(15;0.00497)		GGCTGACAGCCGGTTAGAACT	0.617																																					p.R364L		Atlas-SNP	.											.	PRICKLE2	88	.	0			c.G1091T						.						94	106	102					3																	64133075		2203	4300	6503	SO:0001583	missense	166336	exon7			GACAGCCGGTTAG	AK127839	CCDS2902.1	3p14.3	2006-09-12	2006-09-12		ENSG00000163637	ENSG00000163637			20340	protein-coding gene	gene with protein product		608501	"prickle-like 2 (Drosophila)"			12525887	Standard	NM_198859		Approved	DKFZp686D143	uc003dmf.3	Q7Z3G6	OTTHUMG00000158789	ENST00000295902.6:c.1091G>T	chr3.hg19:g.64133075C>A	ENSP00000295902:p.Arg364Leu	61.0	0.0		65.0	11.0	NM_198859	Q0VF44	Missense_Mutation	SNP	ENST00000295902.6	hg19	CCDS2902.1	.	.	.	.	.	.	.	.	.	.	C	9.873	1.199349	0.22121	.	.	ENSG00000163637	ENST00000295902	T	0.60171	0.21	6.08	4.24	0.50183	.	0.085246	0.48286	N	0.000189	T	0.68339	0.2990	L	0.53249	1.67	0.58432	D	0.999997	D	0.69078	0.997	P	0.60682	0.878	T	0.69049	-0.5248	10	0.49607	T	0.09	-17.0019	15.2738	0.73726	0.2786:0.7213:0.0:0.0	.	364	Q7Z3G6	PRIC2_HUMAN	L	364	ENSP00000295902:R364L	ENSP00000295902:R364L	R	-	2	0	PRICKLE2	64108115	0.997000	0.39634	0.992000	0.48379	0.001000	0.01503	6.157000	0.71846	0.843000	0.35070	-0.169000	0.13324	CGG	.	.		0.617	PRICKLE2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352219.1	NM_198859		A	64133075	C	A	64133075	3	1	321	1	0	0	0	0	1	0	0	0	12499	652	23	1	1451	1	PRICKLE2	3	64133075	Missense_Mutation	SNP	C	TCGA-MI-A75E-01A-11D-A32G-10	6043384	64133075	133889355	25	45156										
ADAMTS9	56999	hgsc.bcm.edu	37	chr3	64633684	64633684	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	ccggcagcctttgtgtactcCattgacgttattgcaccaga	9	12	0	2			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr3:64633684C>G	ENST00000498707.1	-	11	1984	c.1642G>C	c.(1642-1644)Gga>Cga	p.G548R	ADAMTS9_ENST00000295903.4_Missense_Mutation_p.G520R	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	548	Disintegrin.				glycoprotein catabolic process (GO:0006516)|multicellular organismal development (GO:0007275)|positive regulation of melanocyte differentiation (GO:0045636)|protein transport (GO:0015031)|proteolysis (GO:0006508)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(17)|liver(4)|lung(43)|ovary(3)|prostate(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	100		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		TTGTGTACTCCATTGACGTTA	0.498																																					p.G548R		Atlas-SNP	.											.	ADAMTS9	206	.	0			c.G1642C						.						152	136	141					3																	64633684		2203	4300	6503	SO:0001583	missense	56999	exon11			GTACTCCATTGAC	AF261918	CCDS2903.1	3p14.1	2008-05-15	2005-08-19		ENSG00000163638	ENSG00000163638		"ADAM metallopeptidases with thrombospondin type 1 motif"	13202	protein-coding gene	gene with protein product		605421	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 9"			10936055	Standard	NM_182920		Approved	KIAA1312	uc003dmg.3	Q9P2N4	OTTHUMG00000158722	ENST00000498707.1:c.1642G>C	chr3.hg19:g.64633684C>G	ENSP00000418735:p.Gly548Arg	22.0	0.0		35.0	7.0	NM_182920	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	Missense_Mutation	SNP	ENST00000498707.1	hg19	CCDS2903.1	.	.	.	.	.	.	.	.	.	.	C	13.31	2.200402	0.38905	.	.	ENSG00000163638	ENST00000295903;ENST00000498707	T;T	0.61158	0.14;0.13	5.89	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.56659	0.2000	L	0.49571	1.57	0.80722	D	1	B;B;P;B	0.35745	0.136;0.214;0.518;0.276	B;B;B;B	0.38755	0.242;0.159;0.281;0.157	T	0.56751	-0.7927	10	0.41790	T	0.15	.	16.8886	0.86082	0.0:0.8717:0.1283:0.0	.	520;548;548;548	B7ZVX9;Q9P2N4-2;Q9P2N4-1;Q9P2N4	.;.;.;ATS9_HUMAN	R	520;548	ENSP00000295903:G520R;ENSP00000418735:G548R	ENSP00000295903:G520R	G	-	1	0	ADAMTS9	64608724	1.000000	0.71417	0.971000	0.41717	0.327000	0.28475	4.633000	0.61318	1.456000	0.47831	0.585000	0.79938	GGA	.	.		0.498	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351891.1			G	64633684	C	G	64633684	3	3	321	1	0	0	0	0	1	0	0	0	273	603	21	4	4281	4	ADAMTS9	3	64633684	Missense_Mutation	SNP	C	TCGA-MI-A75E-01A-11D-A32G-10	500609	64633684	133388746	26	45157										
FRMD4B	23150	hgsc.bcm.edu	37	chr3	69246073	69246073	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	tgctttgcttccggtccaagTaaaactgatgctgactaatt	8	9	0	2			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr3:69246073T>C	ENST00000398540.3	-	13	1153	c.1070A>G	c.(1069-1071)tAc>tGc	p.Y357C	FRMD4B_ENST00000478263.1_Missense_Mutation_p.Y9C|FRMD4B_ENST00000542259.1_Missense_Mutation_p.Y303C	NM_015123.1	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B	357	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|ruffle (GO:0001726)				NS(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(2)	19		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)		CCGGTCCAAGTAAAACTGATG	0.413																																					p.Y357C		Atlas-SNP	.											.	FRMD4B	90	.	0			c.A1070G						.						102	97	99					3																	69246073		1886	4130	6016	SO:0001583	missense	23150	exon13			TCCAAGTAAAACT	AL832231	CCDS46863.1	3p14.2	2006-04-12			ENSG00000114541	ENSG00000114541			24886	protein-coding gene	gene with protein product						10231032, 11445584	Standard	XM_005264720		Approved	KIAA1013, GRSP1	uc003dnv.2	Q9Y2L6	OTTHUMG00000158772	ENST00000398540.3:c.1070A>G	chr3.hg19:g.69246073T>C	ENSP00000381549:p.Tyr357Cys	70.0	0.0		53.0	8.0	NM_015123	Q8TAI3	Missense_Mutation	SNP	ENST00000398540.3	hg19	CCDS46863.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.057826	0.76074	.	.	ENSG00000114541	ENST00000398540;ENST00000542259;ENST00000478263;ENST00000462512;ENST00000489817	D;D;D	0.86030	-2.06;-2.06;-2.06	5.9	5.9	0.94986	FERM, C-terminal PH-like domain (1);FERM domain (1);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	D	0.92371	0.7579	M	0.78801	2.425	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.93188	0.6580	10	0.87932	D	0	-15.3629	16.3217	0.82953	0.0:0.0:0.0:1.0	.	201;357	B4DHD5;Q9Y2L6	.;FRM4B_HUMAN	C	357;303;9;68;9	ENSP00000381549:Y357C;ENSP00000437658:Y303C;ENSP00000419869:Y68C	ENSP00000381549:Y357C	Y	-	2	0	FRMD4B	69328763	1.000000	0.71417	1.000000	0.80357	0.588000	0.36517	8.036000	0.88901	2.251000	0.74343	0.528000	0.53228	TAC	.	.		0.413	FRMD4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352111.1			C	69246073	T	C	69246073	3	2	321	1	0	0	0	0	1	0	0	0	6060	1638	57	2	2078	2	FRMD4B	3	69246073	Missense_Mutation	SNP	T	TCGA-MI-A75E-01A-11D-A32G-10	4612389	69246073	128776357	27	45158										
IL12A	3592	hgsc.bcm.edu	37	chr3	159710887	159710887	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	taaaaccagcacagtggaggCctgtttaccattggaattaa	9	8	0	0			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr3:159710887C>T	ENST00000305579.2	+	3	660	c.353C>T	c.(352-354)gCc>gTc	p.A118V	IL12A_ENST00000480787.1_Intron|IL12A_ENST00000466512.1_Missense_Mutation_p.A118V|IL12A-AS1_ENST00000497452.1_RNA	NM_000882.3	NP_000873.2	P29459	IL12A_HUMAN	interleukin 12A	84					cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|defense response to Gram-positive bacterium (GO:0050830)|defense response to protozoan (GO:0042832)|extrinsic apoptotic signaling pathway (GO:0097191)|immune response (GO:0006955)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cell adhesion (GO:0045785)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of mononuclear cell proliferation (GO:0032946)|positive regulation of natural killer cell activation (GO:0032816)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|positive regulation of NK T cell activation (GO:0051135)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat4 protein (GO:0042520)|response to lipopolysaccharide (GO:0032496)|response to UV-B (GO:0010224)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|interleukin-12 complex (GO:0043514)	interleukin-12 beta subunit binding (GO:0042163)|interleukin-12 receptor binding (GO:0005143)|interleukin-27 binding (GO:0045513)|protein heterodimerization activity (GO:0046982)			endometrium(3)|kidney(1)|large_intestine(1)|lung(4)	9			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			ACAGTGGAGGCCTGTTTACCA	0.378																																					p.A118V		Atlas-SNP	.											.	IL12A	23	.	0			c.C353T						.						81	89	86					3																	159710887		2203	4300	6503	SO:0001583	missense	3592	exon3			TGGAGGCCTGTTT	M65271	CCDS3187.1	3q25.33	2014-04-04	2014-04-04		ENSG00000168811	ENSG00000168811		"Interleukins and interleukin receptors"	5969	protein-coding gene	gene with protein product	"natural killer cell stimulatory factor 1, 35 kD subunit", "cytotoxic lymphocyte maturation factor 1, p35", "interleukin 12, p35", "IL-12, subunit p35", "NF cell stimulatory factor chain 1", "interleukin-12 alpha chain", "IL35 subunit"	161560	"interleukin 12A (natural killer cell stimulatory factor 1, cytotoxic lymphocyte maturation factor 1, p35)"	NKSF1		1673147	Standard	NM_000882		Approved	CLMF, IL-12A, p35, NFSK	uc003fcx.3	P29459	OTTHUMG00000158942	ENST00000305579.2:c.353C>T	chr3.hg19:g.159710887C>T	ENSP00000303231:p.Ala118Val	85.0	0.0		89.0	17.0	NM_000882	Q96QZ1	Missense_Mutation	SNP	ENST00000305579.2	hg19	CCDS3187.1	.	.	.	.	.	.	.	.	.	.	C	15.94	2.982038	0.53827	.	.	ENSG00000168811	ENST00000305579;ENST00000466512	.	.	.	5.66	4.76	0.60689	.	0.292876	0.37623	N	0.002019	T	0.70193	0.3196	M	0.78801	2.425	0.30689	N	0.751493	D	0.89917	1.0	D	0.87578	0.998	T	0.69595	-0.5103	9	0.38643	T	0.18	-12.8423	12.1144	0.53858	0.17:0.83:0.0:0.0	.	118	O60595	.	V	118	.	ENSP00000303231:A118V	A	+	2	0	IL12A	161193581	1.000000	0.71417	0.996000	0.52242	0.393000	0.30537	1.790000	0.38734	2.665000	0.90641	0.563000	0.77884	GCC	.	.		0.378	IL12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352602.2	NM_000882		T	159710887	C	T	159710887	3	4	321	1	0	0	0	0	1	0	0	0	7633	739	26	3	363	3	IL12A	3	159710887	Missense_Mutation	SNP	C	TCGA-MI-A75E-01A-11D-A32G-10	90464814	159710887	38311543	28	45159										
TBL1XR1	79718	hgsc.bcm.edu	37	chr3	176755936	176755936	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	caagagattgccagttgggtCccatttgatagcatttactt	9	8	0	2			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr3:176755936C>A	ENST00000430069.1	-	12	1331	c.1072G>T	c.(1072-1074)Gac>Tac	p.D358Y	TBL1XR1_ENST00000457928.2_Missense_Mutation_p.D358Y			Q9BZK7	TBL1R_HUMAN	transducin (beta)-like 1 X-linked receptor 1	358					canonical Wnt signaling pathway (GO:0060070)|cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|histone binding (GO:0042393)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(7)|liver(1)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	31	all_cancers(143;1.44e-17)|Ovarian(172;0.00163)|Breast(254;0.214)	Acute lymphoblastic leukemia(1;0.00599)|all_hematologic(1;0.0632)|Prostate(884;0.215)	OV - Ovarian serous cystadenocarcinoma(80;9.83e-31)			CCAGTTGGGTCCCATTTGATA	0.363																																					p.D358Y		Atlas-SNP	.											.	TBL1XR1	87	.	0			c.G1072T						.						88	84	85					3																	176755936		1867	4100	5967	SO:0001583	missense	79718	exon12			TTGGGTCCCATTT	AK022956	CCDS46961.1	3q26.33	2013-01-10	2008-01-17		ENSG00000177565	ENSG00000177565		"WD repeat domain containing"	29529	protein-coding gene	gene with protein product		608628	"transducin (beta)-like 1X-linked receptor 1"			11063877, 11931768	Standard	NM_024665		Approved	IRA1, FLJ12894, TBLR1, C21, DC42	uc003fix.4	Q9BZK7	OTTHUMG00000157140	ENST00000430069.1:c.1072G>T	chr3.hg19:g.176755936C>A	ENSP00000405574:p.Asp358Tyr	201.0	0.0		251.0	42.0	NM_024665	D3DNQ9|Q14DC3|Q9H2I1|Q9H9A1	Missense_Mutation	SNP	ENST00000430069.1	hg19	CCDS46961.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.799932	0.90538	.	.	ENSG00000177565	ENST00000430069;ENST00000457928;ENST00000536758	T;T	0.60920	0.15;0.15	5.48	5.48	0.80851	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.73877	0.3643	L	0.57536	1.79	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.75596	-0.3263	10	0.72032	D	0.01	-6.249	18.3369	0.90291	0.0:1.0:0.0:0.0	.	358	Q9BZK7	TBL1R_HUMAN	Y	358;358;220	ENSP00000405574:D358Y;ENSP00000413251:D358Y	ENSP00000405574:D358Y	D	-	1	0	TBL1XR1	178238630	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.741000	0.84997	2.581000	0.87130	0.585000	0.79938	GAC	.	.		0.363	TBL1XR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347587.3	NM_024665		A	176755936	C	A	176755936	3	1	321	1	0	0	0	0	1	0	0	0	15655	855	30	3	492	3	TBL1XR1	3	176755936	Missense_Mutation	SNP	C	TCGA-MI-A75E-01A-11D-A32G-10	17045049	176755936	21266494	29	45160										
LSG1	55341	hgsc.bcm.edu	37	chr3	194371616	194371616	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	agcagaaaggatattagtgaTacaggaggaacatgatctct	11	5	1	3			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr3:194371616T>C	ENST00000265245.5	-	10	1727	c.1413A>G	c.(1411-1413)gtA>gtG	p.V471V	AC046143.2_ENST00000582474.1_RNA	NM_018385.2	NP_060855.2	Q9H089	LSG1_HUMAN	large 60S subunit nuclear export GTPase 1	471					GTP catabolic process (GO:0006184)|nuclear export (GO:0051168)|protein transport (GO:0015031)|ribosome biogenesis (GO:0042254)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(3)|large_intestine(2)|lung(9)	16	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;4.34e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;7.55e-06)		ATATTAGTGATACAGGAGGAA	0.423																																					p.V471V		Atlas-SNP	.											.	LSG1	38	.	0			c.A1413G						.						98	96	97					3																	194371616		2203	4300	6503	SO:0001819	synonymous_variant	55341	exon10			TAGTGATACAGGA		CCDS33922.1	3q29	2013-08-21	2013-08-21		ENSG00000041802	ENSG00000041802			25652	protein-coding gene	gene with protein product		610780	"large subunit GTPase 1 homolog (S. cerevisiae)"			11230166	Standard	NM_018385		Approved	FLJ11301	uc003fui.3	Q9H089	OTTHUMG00000156021	ENST00000265245.5:c.1413A>G	chr3.hg19:g.194371616T>C		41.0	0.0		75.0	9.0	NM_018385	A0JLT4|A0PJK3|A6NI18|Q7L9H8|Q9NUK8	Silent	SNP	ENST00000265245.5	hg19	CCDS33922.1	.	.	.	.	.	.	.	.	.	.	T	0.084	-1.179348	0.01633	.	.	ENSG00000041802	ENST00000437613	.	.	.	5.63	-7.4	0.01397	.	.	.	.	.	T	0.44808	0.1311	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49513	-0.8932	4	.	.	.	.	6.0885	0.19980	0.1141:0.4991:0.1511:0.2358	.	.	.	.	C	205	.	.	Y	-	2	0	LSG1	195852905	0.963000	0.33076	0.001000	0.08648	0.029000	0.11900	0.026000	0.13599	-1.098000	0.03038	-0.899000	0.02877	TAT	.	.		0.423	LSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342740.1	NM_018385		C	194371616	T	C	194371616	2	2	321	1	0	0	0	0	0	0	0	1	9058	1393	49	2		2	LSG1	3	194371616	Silent	SNP	T	TCGA-MI-A75E-01A-11D-A32G-10	17615680	194371616	3650814	30	45161										
FGFR3	2261	hgsc.bcm.edu	37	chr4	1803246	1803246	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	gggagttccgcggcgagcacCgcattggaggcatcaaggtg	17	10	1	0			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr4:1803246C>T	ENST00000260795.2	+	4	700	c.598C>T	c.(598-600)Cgc>Tgc	p.R200C	FGFR3_ENST00000440486.2_Missense_Mutation_p.R200C|FGFR3_ENST00000412135.2_Missense_Mutation_p.R200C|FGFR3_ENST00000340107.4_Missense_Mutation_p.R200C|FGFR3_ENST00000481110.2_Missense_Mutation_p.R200C|FGFR3_ENST00000352904.1_Missense_Mutation_p.R200C			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	200	Ig-like C2-type 2.				alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)			NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	CGGCGAGCACCGCATTGGAGG	0.726		1	"Mis, T"	"IGH@, ETV6"	"bladder, MM, T-cell lymphoma"		"Hypochondroplasia, Thanatophoric dysplasia"		Saethre-Chotzen syndrome;Muenke syndrome																												p.R200C		Atlas-SNP	.		Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"L, E"	.	FGFR3	3320	.	0			c.C598T	GRCh37	CM066080	FGFR3	M		.						8	7	7					4																	1803246		2120	4173	6293	SO:0001583	missense	2261	exon5	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	GAGCACCGCATTG	M64347	CCDS3353.1, CCDS3354.1, CCDS54706.1	4p16.3	2013-01-11	2008-08-01		ENSG00000068078	ENSG00000068078		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3690	protein-coding gene	gene with protein product		134934	"achondroplasia, thanatophoric dwarfism"	ACH		1847508	Standard	NM_000142		Approved	CEK2, JTK4, CD333	uc003gdu.2	P22607	OTTHUMG00000121148	ENST00000260795.2:c.598C>T	chr4.hg19:g.1803246C>T	ENSP00000260795:p.Arg200Cys	50.0	0.0		46.0	10.0	NM_001163213	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Missense_Mutation	SNP	ENST00000260795.2	hg19	CCDS3353.1	.	.	.	.	.	.	.	.	.	.	c	14.51	2.557684	0.45590	.	.	ENSG00000068078	ENST00000481110;ENST00000340107;ENST00000440486;ENST00000412135;ENST00000260795;ENST00000352904;ENST00000507588	D;D;D;D;D;D;T	0.85702	-2.02;-2.02;-2.02;-2.02;-2.02;-2.02;-0.51	3.67	3.67	0.42095	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.129493	0.51477	D	0.000100	D	0.94138	0.8120	H	0.95884	3.735	0.25536	N	0.987225	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.991;0.999;0.998;0.999;1.0;0.999	D	0.87509	0.2438	10	0.87932	D	0	.	11.9344	0.52866	0.1868:0.8132:0.0:0.0	.	163;200;200;200;200;200	Q8NI15;P22607-2;P22607-4;P22607-3;P22607;F8W9L4	.;.;.;.;FGFR3_HUMAN;.	C	200;200;200;200;200;200;20	ENSP00000420533:R200C;ENSP00000339824:R200C;ENSP00000414914:R200C;ENSP00000412903:R200C;ENSP00000260795:R200C;ENSP00000231803:R200C;ENSP00000427289:R20C	ENSP00000260795:R200C	R	+	1	0	FGFR3	1773044	0.872000	0.30054	0.998000	0.56505	0.295000	0.27426	1.686000	0.37669	1.765000	0.52091	0.436000	0.28706	CGC	.	.		0.726	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142		T	1803246	C	T	1803246	3	4	321	1	0	0	0	0	1	0	0	0	5875	652	23	1	612	1	FGFR3	4	1803246	Missense_Mutation	SNP	C	TCGA-MI-A75E-01A-11D-A32G-10		1803246	189351030	31	45162										
HGFAC	3083	hgsc.bcm.edu	37	chr4	3449280	3449280	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	tcttcaaccgcacgacggacGtgacgcagaccttcggcatc	10	15	2	2	rs560293902		TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr4:3449280G>A	ENST00000382774.3	+	11	1532	c.1417G>A	c.(1417-1419)Gtg>Atg	p.V473M	HGFAC_ENST00000511533.1_Missense_Mutation_p.V480M	NM_001528.2	NP_001519.1	Q04756	HGFA_HUMAN	HGF activator	473	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|rough endoplasmic reticulum (GO:0005791)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		CACGACGGACGTGACGCAGAC	0.657																																					p.V473M		Atlas-SNP	.											HGFAC,colon,carcinoma,0,1	HGFAC	69	.	0			c.G1417A						.						195	171	179					4																	3449280		2203	4300	6503	SO:0001583	missense	3083	exon11			ACGGACGTGACGC	D14012	CCDS3369.1, CCDS75098.1	4p16	2008-02-07			ENSG00000109758	ENSG00000109758	3.4.21.-		4894	protein-coding gene	gene with protein product		604552				7683665, 8226803	Standard	XM_005247966		Approved	HGFAP, HGFA	uc003ghc.3	Q04756	OTTHUMG00000090281	ENST00000382774.3:c.1417G>A	chr4.hg19:g.3449280G>A	ENSP00000372224:p.Val473Met	245.0	0.0		267.0	43.0	NM_001528	Q14726|Q2M1W7|Q53X47	Missense_Mutation	SNP	ENST00000382774.3	hg19	CCDS3369.1	.	.	.	.	.	.	.	.	.	.	G	10.52	1.374241	0.24857	.	.	ENSG00000109758	ENST00000382774;ENST00000511533	D;D	0.88586	-2.4;-2.4	3.59	3.59	0.41128	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.326333	0.28940	N	0.013659	D	0.89487	0.6729	L	0.28115	0.83	0.40067	D	0.975964	D;P	0.89917	1.0;0.829	D;B	0.71870	0.975;0.171	D	0.89253	0.3592	10	0.38643	T	0.18	.	14.2846	0.66238	0.0:0.0:1.0:0.0	.	480;473	D6RAR4;Q04756	.;HGFA_HUMAN	M	473;480	ENSP00000372224:V473M;ENSP00000421801:V480M	ENSP00000372224:V473M	V	+	1	0	HGFAC	3419078	0.027000	0.19231	0.352000	0.25734	0.055000	0.15305	1.107000	0.31110	2.022000	0.59522	0.561000	0.74099	GTG	.	.		0.657	HGFAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206607.3			A	3449280	G	A	3449280	3	1	321	1	0	0	0	0	1	0	0	0	7095	1145	40	1	1459	1	HGFAC	4	3449280	Missense_Mutation	SNP	G	TCGA-MI-A75E-01A-11D-A32G-10	1646034	3449280	187704996	32	45163										
ENOPH1	58478	hgsc.bcm.edu	37	chr4	83372214	83372214	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	aggctgaagaggacgcccacCtggatggggctgttcctatc	14	11	0	2			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr4:83372214C>A	ENST00000273920.3	+	3	473	c.205C>A	c.(205-207)Ctg>Atg	p.L69M	ENOPH1_ENST00000509635.1_5'UTR	NM_021204.3	NP_067027.1			enolase-phosphatase 1											central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|skin(1)	13						GGACGCCCACCTGGATGGGGC	0.463																																					p.L69M		Atlas-SNP	.											.	ENOPH1	26	.	0			c.C205A						.						77	73	74					4																	83372214		2203	4300	6503	SO:0001583	missense	58478	exon3			GCCCACCTGGATG		CCDS3594.1, CCDS75154.1	4q21.3	2013-05-29			ENSG00000145293	ENSG00000145293	3.1.3.77		24599	protein-coding gene	gene with protein product	"Enolase-phosphatase E1", "acireductone synthase"					15843022	Standard	XM_005263168		Approved	MASA, E1, mtnC	uc003hmv.3	Q9UHY7	OTTHUMG00000130295	ENST00000273920.3:c.205C>A	chr4.hg19:g.83372214C>A	ENSP00000273920:p.Leu69Met	71.0	0.0		83.0	17.0	NM_021204		Missense_Mutation	SNP	ENST00000273920.3	hg19	CCDS3594.1	.	.	.	.	.	.	.	.	.	.	c	13.40	2.224668	0.39300	.	.	ENSG00000145293	ENST00000273920;ENST00000456931	.	.	.	5.36	4.5	0.54988	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);2,3-diketo-5-methylthio-1-phosphopentane phosphatase (1);	0.136231	0.50627	D	0.000112	T	0.42607	0.1210	L	0.31664	0.95	0.80722	D	1	B	0.30870	0.298	B	0.25291	0.059	T	0.35151	-0.9800	9	0.34782	T	0.22	-15.3012	12.5049	0.55975	0.0:0.867:0.0:0.133	.	69	Q9UHY7	ENOPH_HUMAN	M	69	.	ENSP00000273920:L69M	L	+	1	2	ENOPH1	83591238	1.000000	0.71417	1.000000	0.80357	0.693000	0.40251	1.432000	0.34936	2.673000	0.90976	0.650000	0.86243	CTG	.	.		0.463	ENOPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252638.2	NM_021204		A	83372214	C	A	83372214	3	1	321	1	0	0	0	0	1	0	0	0	5126	680	24	3	215	3	ENOPH1	4	83372214	Missense_Mutation	SNP	C	TCGA-MI-A75E-01A-11D-A32G-10	79922934	83372214	107782062	33	45164										
LARP1B	55132	hgsc.bcm.edu	37	chr4	128999091	128999091	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	aaacgtcagtgaggatgaggCtcagtcaagtaatcaacgta	11	7	4	2			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr4:128999091C>G	ENST00000326639.6	+	4	402	c.191C>G	c.(190-192)gCt>gGt	p.A64G	LARP1B_ENST00000427266.1_Missense_Mutation_p.A64G|LARP1B_ENST00000441387.1_Missense_Mutation_p.A64G|LARP1B_ENST00000512292.1_Missense_Mutation_p.A64G|LARP1B_ENST00000264584.5_Missense_Mutation_p.A64G|LARP1B_ENST00000394288.3_Missense_Mutation_p.A64G|LARP1B_ENST00000432347.2_Missense_Mutation_p.A64G|LARP1B_ENST00000354456.3_5'UTR	NM_018078.2	NP_060548.2	Q659C4	LAR1B_HUMAN	La ribonucleoprotein domain family, member 1B	64						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|lung(11)|ovary(1)|prostate(3)	34						GAGGATGAGGCTCAGTCAAGT	0.348																																					p.A64G		Atlas-SNP	.											.	LARP1B	120	.	0			c.C191G						.						124	118	120					4																	128999091		2203	4300	6503	SO:0001583	missense	55132	exon4			ATGAGGCTCAGTC		CCDS3738.1, CCDS47133.1, CCDS64057.1	4q28.2	2009-06-09	2009-06-09	2009-06-09	ENSG00000138709	ENSG00000138709		"La ribonucleoprotein domain containing"	24704	protein-coding gene	gene with protein product			"La ribonucleoprotein domain family, member 2"	LARP2		12045101	Standard	NM_018078		Approved	FLJ10378, DKFZp434K245, DKFZp686E0316	uc003iga.3	Q659C4	OTTHUMG00000133343	ENST00000326639.6:c.191C>G	chr4.hg19:g.128999091C>G	ENSP00000321997:p.Ala64Gly	302.0	0.0		289.0	48.0	NM_032239	Q2YDB6|Q4W599|Q4W5B2|Q659A0|Q6P5X2|Q7Z3F7|Q86VK7|Q8N6F4|Q8N7H4|Q8NAF2|Q9H5E7|Q9NW12	Missense_Mutation	SNP	ENST00000326639.6	hg19	CCDS3738.1	.	.	.	.	.	.	.	.	.	.	C	9.196	1.027280	0.19512	.	.	ENSG00000138709	ENST00000326639;ENST00000512292;ENST00000508819;ENST00000394288;ENST00000432347;ENST00000264584;ENST00000441387;ENST00000427266	T;T;T;T;T;T;T;T	0.47869	1.89;1.48;1.44;0.85;0.83;1.86;1.86;1.47	3.88	3.88	0.44766	.	0.217137	0.38778	N	0.001578	T	0.33556	0.0867	L	0.31664	0.95	0.80722	D	1	B;B;B;B	0.14805	0.003;0.005;0.005;0.011	B;B;B;B	0.16722	0.004;0.01;0.006;0.016	T	0.10965	-1.0607	10	0.22706	T	0.39	.	11.3929	0.49825	0.0:0.8165:0.1835:0.0	.	64;64;64;64	Q659C4;G3XAJ5;Q659C4-3;G3V0E9	LAR1B_HUMAN;.;.;.	G	64	ENSP00000321997:A64G;ENSP00000422850:A64G;ENSP00000427281:A64G;ENSP00000377829:A64G;ENSP00000390395:A64G;ENSP00000264584:A64G;ENSP00000396521:A64G;ENSP00000403586:A64G	ENSP00000264584:A64G	A	+	2	0	LARP1B	129218541	1.000000	0.71417	1.000000	0.80357	0.797000	0.45037	1.745000	0.38278	2.176000	0.68965	0.289000	0.19496	GCT	.	.		0.348	LARP1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257173.2	NM_018078		G	128999091	C	G	128999091	3	3	321	1	0	0	0	0	1	0	0	0	8638	797	28	4	197	4	LARP1B	4	128999091	Missense_Mutation	SNP	C	TCGA-MI-A75E-01A-11D-A32G-10	45626877	128999091	62155185	34	45165										
TLR3	7098	hgsc.bcm.edu	37	chr4	186998195	186998195	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	aatccagaaaattaaaaataAtccctttgtcaagcagaagg	6	7	1	2			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr4:186998195A>G	ENST00000296795.3	+	2	526	c.422A>G	c.(421-423)aAt>aGt	p.N141S		NM_003265.2	NP_003256.1	O15455	TLR3_HUMAN	toll-like receptor 3	141					activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to drug (GO:0035690)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|cellular response to interferon-gamma (GO:0071346)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|detection of virus (GO:0009597)|extrinsic apoptotic signaling pathway (GO:0097191)|hyperosmotic response (GO:0006972)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|microglial cell activation involved in immune response (GO:0002282)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic signaling pathway (GO:0097527)|negative regulation of osteoclast differentiation (GO:0045671)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of chemokine production (GO:0032722)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type III interferon production (GO:0034346)|response to exogenous dsRNA (GO:0043330)|signal transduction (GO:0007165)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	double-stranded RNA binding (GO:0003725)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(5)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	29		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.47e-11)|BRCA - Breast invasive adenocarcinoma(30;1.14e-05)|GBM - Glioblastoma multiforme(59;0.000107)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.16)		ATTAAAAATAATCCCTTTGTC	0.338																																					p.N141S		Atlas-SNP	.											.	TLR3	83	.	0			c.A422G						.						35	36	36					4																	186998195		2203	4300	6503	SO:0001583	missense	7098	exon2			AAAATAATCCCTT	U88879	CCDS3846.1	4q35	2014-09-17				ENSG00000164342		"CD molecules"	11849	protein-coding gene	gene with protein product		603029				9435236	Standard	NM_003265		Approved	CD283	uc003iyq.3	O15455		ENST00000296795.3:c.422A>G	chr4.hg19:g.186998195A>G	ENSP00000296795:p.Asn141Ser	101.0	0.0		137.0	24.0	NM_003265	B2RAI7|B7Z7K0|E6Y0F0|E6Y0F1|E9PGH4|Q4VAL2|Q504W0	Missense_Mutation	SNP	ENST00000296795.3	hg19	CCDS3846.1	.	.	.	.	.	.	.	.	.	.	A	10.28	1.306594	0.23736	.	.	ENSG00000164342	ENST00000296795;ENST00000513189;ENST00000542020	T;T	0.78707	0.53;-1.2	5.86	5.86	0.93980	.	0.380726	0.34676	N	0.003769	T	0.65780	0.2724	N	0.21617	0.685	0.80722	D	1	B	0.10296	0.003	B	0.15484	0.013	T	0.60999	-0.7151	10	0.14252	T	0.57	.	16.2668	0.82588	1.0:0.0:0.0:0.0	.	141	O15455	TLR3_HUMAN	S	141	ENSP00000296795:N141S;ENSP00000423386:N141S	ENSP00000296795:N141S	N	+	2	0	TLR3	187235189	0.989000	0.36119	0.656000	0.29637	0.075000	0.17131	7.133000	0.77259	2.240000	0.73641	0.533000	0.62120	AAT	.	.		0.338	TLR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360313.4			G	186998195	A	G	186998195	3	3	321	1	0	0	0	0	1	0	0	0	15967	101	4	2	424	2	TLR3	4	186998195	Missense_Mutation	SNP	A	TCGA-MI-A75E-01A-11D-A32G-10	57999104	186998195	4156081	35	45166										
SLC6A19	340024	hgsc.bcm.edu	37	chr5	1216776	1216776	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	tcattgggttccgcgccacaCagcgctacgacgactgcttc	10	15	1	0			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr5:1216776C>A	ENST00000304460.10	+	7	1047	c.991C>A	c.(991-993)Cag>Aag	p.Q331K		NM_001003841.2	NP_001003841.1	Q695T7	S6A19_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 19	331					amino acid transport (GO:0006865)|ion transport (GO:0006811)|response to nutrient (GO:0007584)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)|neutral amino acid transmembrane transporter activity (GO:0015175)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(25)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10)		Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			CCGCGCCACACAGCGCTACGA	0.612																																					p.Q331K		Atlas-SNP	.											.	SLC6A19	99	.	0			c.C991A						.						217	157	177					5																	1216776		2203	4300	6503	SO:0001583	missense	340024	exon7			GCCACACAGCGCT	AK096054	CCDS34130.1	5p15	2013-07-19			ENSG00000174358	ENSG00000174358		"Solute carriers"	27960	protein-coding gene	gene with protein product	"Hartnup disease"	608893					Standard	NM_001003841		Approved		uc003jbw.4	Q695T7	OTTHUMG00000161636	ENST00000304460.10:c.991C>A	chr5.hg19:g.1216776C>A	ENSP00000305302:p.Gln331Lys	58.0	0.0		62.0	9.0	NM_001003841	A8K446	Missense_Mutation	SNP	ENST00000304460.10	hg19	CCDS34130.1	.	.	.	.	.	.	.	.	.	.	C	3.838	-0.034445	0.07543	.	.	ENSG00000174358	ENST00000304460	T	0.73363	-0.74	4.61	2.75	0.32379	.	0.292824	0.36234	N	0.002716	T	0.55545	0.1927	N	0.17838	0.53	0.23376	N	0.997808	B	0.06786	0.001	B	0.13407	0.009	T	0.28202	-1.0051	10	0.05959	T	0.93	.	14.2262	0.65860	0.0:0.2986:0.7014:0.0	.	331	Q695T7	S6A19_HUMAN	K	331	ENSP00000305302:Q331K	ENSP00000305302:Q331K	Q	+	1	0	SLC6A19	1269776	0.998000	0.40836	0.249000	0.24280	0.006000	0.05464	2.621000	0.46418	0.349000	0.23975	-0.479000	0.04858	CAG	.	.		0.612	SLC6A19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365557.1	XM_291120		A	1216776	C	A	1216776	3	1	321	1	0	0	0	0	1	0	0	0	14697	479	17	3	1017	3	SLC6A19	5	1216776	Missense_Mutation	SNP	C	TCGA-MI-A75E-01A-11D-A32G-10		1216776	179698484	36	45167										
PDZD2	23037	hgsc.bcm.edu	37	chr5	32074465	32074465	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	tgtcaggatcaagtagcgcaCccaaattggaatacacagtc	9	10	2	0			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr5:32074465C>T	ENST00000438447.1	+	18	3641	c.3253C>T	c.(3253-3255)Ccc>Tcc	p.P1085S	PDZD2_ENST00000282493.3_Missense_Mutation_p.P1085S			O15018	PDZD2_HUMAN	PDZ domain containing 2	1085					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				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						AAGTAGCGCACCCAAATTGGA	0.592																																					p.P1085S		Atlas-SNP	.											.	PDZD2	306	.	0			c.C3253T						.						128	142	137					5																	32074465		2203	4300	6503	SO:0001583	missense	23037	exon17			AGCGCACCCAAAT	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"PDZ domain containing 3"	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.3253C>T	chr5.hg19:g.32074465C>T	ENSP00000402033:p.Pro1085Ser	67.0	0.0		59.0	10.0	NM_178140	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	hg19	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	C	16.34	3.097127	0.56075	.	.	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.41400	1.0;1.0	5.54	5.54	0.83059	.	0.163418	0.29383	N	0.012314	T	0.65165	0.2665	M	0.69823	2.125	0.53005	D	0.999961	P;D	0.89917	0.473;1.0	B;D	0.87578	0.069;0.998	T	0.67329	-0.5698	10	0.72032	D	0.01	.	16.9926	0.86358	0.0:1.0:0.0:0.0	.	911;1085	B4E3P2;O15018	.;PDZD2_HUMAN	S	1085;887;1085	ENSP00000402033:P1085S;ENSP00000282493:P1085S	ENSP00000282493:P1085S	P	+	1	0	PDZD2	32110222	0.998000	0.40836	0.937000	0.37676	0.012000	0.07955	5.260000	0.65490	2.603000	0.88011	0.467000	0.42956	CCC	.	.		0.592	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			T	32074465	C	T	32074465	3	4	321	1	0	0	0	0	1	0	0	0	11710	507	18	3	3319	3	PDZD2	5	32074465	Missense_Mutation	SNP	C	TCGA-MI-A75E-01A-11D-A32G-10	30857689	32074465	148840795	37	45168										
XRCC4	7518	hgsc.bcm.edu	37	chr5	82649043	82649043	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	agaaacagcagcccagaagaCctctttgatgagatttaaca	8	9	1	5			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr5:82649043C>T	ENST00000511817.1	+	8	1073	c.993C>T	c.(991-993)gaC>gaT	p.D331D	XRCC4_ENST00000338635.6_Silent_p.D331D|XRCC4_ENST00000396027.4_Silent_p.D329D|XRCC4_ENST00000282268.3_Silent_p.D329D			Q13426	XRCC4_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 4	331					cellular response to lithium ion (GO:0071285)|central nervous system development (GO:0007417)|DNA ligation involved in DNA repair (GO:0051103)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|immunoglobulin V(D)J recombination (GO:0033152)|in utero embryonic development (GO:0001701)|isotype switching (GO:0045190)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of ligase activity (GO:0051351)|positive regulation of neurogenesis (GO:0050769)|pro-B cell differentiation (GO:0002328)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytosol (GO:0005829)|DNA ligase IV complex (GO:0032807)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(2)|skin(3)	17		Lung NSC(167;0.00132)|all_lung(232;0.00154)|Ovarian(174;0.034)		OV - Ovarian serous cystadenocarcinoma(54;1.44e-38)|Epithelial(54;3.72e-33)|all cancers(79;9.22e-28)		GCCCAGAAGACCTCTTTGATG	0.358								Non-homologous end-joining																													p.D331D		Atlas-SNP	.											.	XRCC4	37	.	0			c.C993T						.						117	127	123					5																	82649043		2203	4300	6503	SO:0001819	synonymous_variant	7518	exon8			AGAAGACCTCTTT	AB017445	CCDS4058.1, CCDS4059.1	5q14.2	2008-02-05			ENSG00000152422	ENSG00000152422			12831	protein-coding gene	gene with protein product	"X-ray repair, complementing defective, repair in Chinese hamster", "DNA repair protein XRCC4"	194363				1697445, 7665175	Standard	NM_022406		Approved		uc003kib.3	Q13426	OTTHUMG00000131319	ENST00000511817.1:c.993C>T	chr5.hg19:g.82649043C>T		238.0	0.0		261.0	56.0	NM_022406	A8K3X4|Q9BS72|Q9UP94	Silent	SNP	ENST00000511817.1	hg19	CCDS4059.1																																																																																			.	.		0.358	XRCC4-003	NOVEL	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000369624.1	NM_022550		T	82649043	C	T	82649043	2	4	321	1	0	0	0	0	0	0	0	1	17470	506	18	3		3	XRCC4	5	82649043	Silent	SNP	C	TCGA-MI-A75E-01A-11D-A32G-10	50574578	82649043	98266217	38	45169										
PJA2	9867	hgsc.bcm.edu	37	chr5	108714881	108714881	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	caatgctgaaccacaagtggGaatttctgtttcactttttt	7	8	2	1	rs143063686		TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr5:108714881G>T	ENST00000361189.2	-	4	546	c.307C>A	c.(307-309)Ccc>Acc	p.P103T	PJA2_ENST00000361557.3_Missense_Mutation_p.P103T|PJA2_ENST00000511624.1_5'UTR	NM_014819.4	NP_055634.3	O43164	PJA2_HUMAN	praja ring finger 2, E3 ubiquitin protein ligase	103					long-term memory (GO:0007616)|protein ubiquitination (GO:0016567)|regulation of protein kinase A signaling (GO:0010738)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ligase activity (GO:0016874)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21		all_cancers(142;4.4e-06)|all_epithelial(76;8.17e-08)|Prostate(80;0.00676)|Lung NSC(167;0.0436)|Ovarian(225;0.0443)|all_lung(232;0.053)|Colorectal(57;0.0946)|Breast(839;0.151)		OV - Ovarian serous cystadenocarcinoma(64;3.46e-10)|Epithelial(69;6.02e-09)|COAD - Colon adenocarcinoma(37;0.224)		CCACAAGTGGGAATTTCTGTT	0.388																																					p.P103T		Atlas-SNP	.											.	PJA2	53	.	0			c.C307A						.						66	66	66					5																	108714881		2202	4300	6502	SO:0001583	missense	9867	exon4			AAGTGGGAATTTC	AB007898	CCDS4099.1	5q22.1	2013-01-09	2012-02-23	2003-06-05	ENSG00000198961	ENSG00000198961		"RING-type (C3HC4) zinc fingers"	17481	protein-coding gene	gene with protein product			"ring finger protein 131", "praja ring finger 2"	RNF131			Standard	NM_014819		Approved	KIAA0438, Neurodap1	uc003kos.4	O43164	OTTHUMG00000128750	ENST00000361189.2:c.307C>A	chr5.hg19:g.108714881G>T	ENSP00000354775:p.Pro103Thr	90.0	0.0		77.0	9.0	NM_014819	A8K6U4|D3DSZ5|Q68D49|Q8N1G5	Missense_Mutation	SNP	ENST00000361189.2	hg19	CCDS4099.1	.	.	.	.	.	.	.	.	.	.	G	9.715	1.158192	0.21454	.	.	ENSG00000198961	ENST00000361189;ENST00000361557	T;T	0.05996	3.36;3.36	6.16	0.21	0.15231	.	0.833028	0.11168	N	0.592392	T	0.10680	0.0261	M	0.63843	1.955	0.09310	N	0.999993	P	0.48640	0.913	P	0.47470	0.548	T	0.17868	-1.0355	10	0.87932	D	0	1.2813	6.9814	0.24706	0.3703:0.1067:0.523:0.0	.	103	O43164	PJA2_HUMAN	T	103	ENSP00000354775:P103T;ENSP00000355284:P103T	ENSP00000354775:P103T	P	-	1	0	PJA2	108742780	0.773000	0.28580	0.314000	0.25224	0.492000	0.33523	0.219000	0.17641	-0.252000	0.09528	-0.781000	0.03364	CCC	.	G|1.000;A|0.000		0.388	PJA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250663.1	NM_014819		T	108714881	G	T	108714881	3	4	321	1	0	0	0	0	1	0	0	0	11971	1174	41	3	1847	3	PJA2	5	108714881	Missense_Mutation	SNP	G	TCGA-MI-A75E-01A-11D-A32G-10	26065838	108714881	72200379	39	45170										
APC	324	hgsc.bcm.edu	37	chr5	112179045	112179045	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	agaatccagtgaaaaagcaaAaagtgaggatgaaaaacatg	10	4	0	4			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr5:112179045A>T	ENST00000457016.1	+	16	8134	c.7754A>T	c.(7753-7755)aAa>aTa	p.K2585I	APC_ENST00000257430.4_Missense_Mutation_p.K2585I|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Missense_Mutation_p.K2585I			P25054	APC_HUMAN	adenomatous polyposis coli	2585	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GAAAAAGCAAAAAGTGAGGAT	0.358		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											p.K2585I	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-SNP	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	.	APC	4158	.	1	Unknown(1)	skin(1)	c.A7754T						.						68	71	70					5																	112179045		2202	4300	6502	SO:0001583	missense	324	exon17	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	AAGCAAAAAGTGA	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.7754A>T	chr5.hg19:g.112179045A>T	ENSP00000413133:p.Lys2585Ile	61.0	0.0		53.0	7.0	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	hg19	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	17.17	3.322122	0.60634	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.91237	-2.81;-2.81;-2.81	5.97	5.97	0.96955	.	0.048040	0.85682	D	0.000000	D	0.90553	0.7039	L	0.27053	0.805	0.42088	D	0.991287	D;D	0.71674	0.998;0.998	P;P	0.59288	0.855;0.77	D	0.89941	0.4073	9	.	.	.	-28.1684	16.4473	0.83942	1.0:0.0:0.0:0.0	.	2587;2585	Q4LE70;P25054	.;APC_HUMAN	I	2585	ENSP00000413133:K2585I;ENSP00000257430:K2585I;ENSP00000427089:K2585I	.	K	+	2	0	APC	112206944	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.697000	0.74603	2.281000	0.76405	0.533000	0.62120	AAA	.	.		0.358	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112179045	A	T	112179045	3	4	321	1	0	0	0	0	1	0	0	0	763	14	1	4	7812	4	APC	5	112179045	Missense_Mutation	SNP	A	TCGA-MI-A75E-01A-11D-A32G-10	3464164	112179045	68736215	40	45171										
CEP120	153241	hgsc.bcm.edu	37	chr5	122725745	122725748	+	Frame_Shift_Del	DEL	AGTA	AGTA	-													0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	actgttggtgattttggcccAgtaagtgtcttctcctttat					rs376284108		TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	AGTA	AGTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr5:122725745_122725748delAGTA	ENST00000306467.5	-	8	1429_1432	c.1125_1128delTACT	c.(1123-1128)cttactfs	p.LT375fs	CEP120_ENST00000306481.6_Frame_Shift_Del_p.LT349fs|CEP120_ENST00000328236.5_Frame_Shift_Del_p.LT375fs			Q8N960	CE120_HUMAN	centrosomal protein 120kDa	375					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)|regulation of protein localization (GO:0032880)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	29						ATTTTGGCCCAGTAAGTGTCTTCT	0.387																																					p.376_377del		Atlas-Indel,Pindel	.											.	CEP120	72	.	0			c.1126_1129del						.																																			SO:0001589	frameshift_variant	153241	exon9			.	AK095646	CCDS4134.2, CCDS54890.1	5q23.2	2014-02-20	2008-08-14	2008-08-14	ENSG00000168944	ENSG00000168944			26690	protein-coding gene	gene with protein product		613446	"coiled-coil domain containing 100"	CCDC100		17920017	Standard	NM_153223		Approved	FLJ36090	uc003ktk.3	Q8N960	OTTHUMG00000128922	ENST00000306467.5:c.1125_1128delTACT	chr5.hg19:g.122725745_122725748delAGTA	ENSP00000303058:p.Leu375fs	142.0	0.0		153.0	26.0	NM_153223	Q6AI52|Q6AW89|Q8IWB5|Q8N9Y0|Q8NDE8	Frame_Shift_Del	DEL	ENST00000306467.5	hg19	CCDS4134.2																																																																																			.	.		0.387	CEP120-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250899.2	NM_153223		-	122725748	AGTA	-	122725745	7	5	321	1	0	1	0	1	0	0	0	0	3248	175	7	0	1884	0	CEP120	5	122725745	Frame_Shift_Del	DEL	AGTA	TCGA-MI-A75E-01A-11D-A32G-10	10546700	122725745	58189515	41	45172										
RAPGEF6	51735	hgsc.bcm.edu	37	chr5	130778169	130778169	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	gttgtttggccagctgacctCataggcactggagacatttc	11	10	1	2			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr5:130778169C>A	ENST00000509018.1	-	23	3688	c.3483G>T	c.(3481-3483)atG>atT	p.M1161I	CTC-432M15.3_ENST00000514667.1_Missense_Mutation_p.M1211I|RAPGEF6_ENST00000507093.1_Missense_Mutation_p.M1169I|RAPGEF6_ENST00000308008.6_Missense_Mutation_p.M1161I|RAPGEF6_ENST00000296859.6_Missense_Mutation_p.M1169I|RAPGEF6_ENST00000307984.5_Missense_Mutation_p.M1174I|RAPGEF6_ENST00000512052.1_Missense_Mutation_p.M884I	NM_001164386.1|NM_016340.5	NP_001157858.1|NP_057424.3	Q8TEU7	RPGF6_HUMAN	Rap guanine nucleotide exchange factor (GEF) 6	1161					positive regulation of GTPase activity (GO:0043547)|Ras protein signal transduction (GO:0007265)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP-dependent protein binding (GO:0030742)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		CAGCTGACCTCATAGGCACTG	0.448																																					p.M1174I	Melanoma(168;435 1955 13113 13877 23213)	Atlas-SNP	.											.	RAPGEF6	361	.	0			c.G3522T						.						187	173	178					5																	130778169		2203	4300	6503	SO:0001583	missense	51735	exon25			TGACCTCATAGGC	AF117947	CCDS34225.1, CCDS54897.1, CCDS54898.1, CCDS54899.1, CCDS54900.1	5q31.1	2008-02-05	2004-03-01	2004-03-02	ENSG00000158987	ENSG00000158987			20655	protein-coding gene	gene with protein product		610499	"PDZ domain containing guanine nucleotide exchange factor (GEF) 2"	PDZGEF2		11524421, 12095257	Standard	NM_016340		Approved	RA-GEF-2, PDZ-GEF2	uc010jdi.2	Q8TEU7	OTTHUMG00000162683	ENST00000509018.1:c.3483G>T	chr5.hg19:g.130778169C>A	ENSP00000421684:p.Met1161Ile	128.0	0.0		131.0	25.0	NM_001164387	A3KN82|A5PLL6|B7ZML2|E9PDV7|Q8NI21|Q8TEU6|Q96PC1	Missense_Mutation	SNP	ENST00000509018.1	hg19	CCDS34225.1	.	.	.	.	.	.	.	.	.	.	C	6.005	0.369283	0.11352	.	.	ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000217128	ENST00000509018;ENST00000307984;ENST00000507093;ENST00000296859;ENST00000358714;ENST00000512052;ENST00000308008;ENST00000514667	T;T;T;T;T;T;T	0.25085	2.02;1.92;1.92;2.02;1.82;1.82;2.11	5.84	4.98	0.66077	Ras guanine nucleotide exchange factor, domain (1);	0.469272	0.24745	N	0.035957	T	0.16854	0.0405	N	0.14661	0.345	0.80722	D	1	B;B;B;B;B;B;B	0.13145	0.001;0.001;0.007;0.002;0.004;0.002;0.001	B;B;B;B;B;B;B	0.19666	0.006;0.003;0.026;0.004;0.01;0.014;0.006	T	0.05517	-1.0880	10	0.21014	T	0.42	.	14.9361	0.70957	0.0:0.9315:0.0:0.0685	.	1169;1169;1161;884;1211;1174;1161	A3KN82;B7ZML2;Q8TEU7-2;D6RE77;E9PCH4;Q8TEU7-3;Q8TEU7	.;.;.;.;.;.;RPGF6_HUMAN	I	1161;1174;1169;1169;1174;884;1161;1211	ENSP00000421684:M1161I;ENSP00000309298:M1174I;ENSP00000426081:M1169I;ENSP00000296859:M1169I;ENSP00000426910:M884I;ENSP00000311419:M1161I;ENSP00000426948:M1211I	ENSP00000426948:M1211I	M	-	3	0	RAPGEF6;FNIP1	130806068	1.000000	0.71417	0.922000	0.36590	0.050000	0.14768	4.336000	0.59304	1.480000	0.48289	-0.253000	0.11424	ATG	.	.		0.448	RAPGEF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370059.1	NM_016340		A	130778169	C	A	130778169	3	1	321	1	0	0	0	0	1	0	0	0	13063	826	29	3	1781	3	RAPGEF6	5	130778169	Missense_Mutation	SNP	C	TCGA-MI-A75E-01A-11D-A32G-10	8052424	130778169	50137091	42	45173										
SPINK5	11005	hgsc.bcm.edu	37	chr5	147481371	147481371	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	gtagtgaataccgcaaatccAggaaaaacggacggcttttt	10	8	0	1			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr5:147481371A>T	ENST00000256084.7	+	15	1372	c.1330A>T	c.(1330-1332)Agg>Tgg	p.R444W	SPINK5_ENST00000359874.3_Missense_Mutation_p.R444W|SPINK5_ENST00000398454.1_Missense_Mutation_p.R444W	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	444	Kazal-like 7. {ECO:0000255|PROSITE- ProRule:PRU00798}.				anagen (GO:0042640)|epidermal cell differentiation (GO:0009913)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|hair cell differentiation (GO:0035315)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of proteolysis (GO:0045861)|negative regulation of serine-type peptidase activity (GO:1902572)|regulation of cell adhesion (GO:0030155)|regulation of T cell differentiation (GO:0045580)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(8)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCGCAAATCCAGGAAAAACGG	0.458																																					p.R444W		Atlas-SNP	.											.	SPINK5	245	.	0			c.A1330T						.						102	97	99					5																	147481371		1879	4109	5988	SO:0001583	missense	11005	exon15			AAATCCAGGAAAA	AJ228139	CCDS43382.1, CCDS47300.1, CCDS47301.1	5q31-q32	2014-09-17	2005-08-17		ENSG00000133710	ENSG00000133710		"Serine peptidase inhibitors, Kazal type"	15464	protein-coding gene	gene with protein product	"lymphoepithelial Kazal-type-related inhibitor"	605010	"serine protease inhibitor, Kazal type 5"			10419450	Standard	NM_001127698		Approved	VAKTI, LEKTI, LETKI, NETS, NS, FLJ21544, FLJ97536, FLJ97596, FLJ99794, DKFZp686K19184	uc003loy.2	Q9NQ38	OTTHUMG00000134305	ENST00000256084.7:c.1330A>T	chr5.hg19:g.147481371A>T	ENSP00000256084:p.Arg444Trp	93.0	0.0		92.0	9.0	NM_001127699	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Missense_Mutation	SNP	ENST00000256084.7	hg19	CCDS43382.1	.	.	.	.	.	.	.	.	.	.	A	9.490	1.100481	0.20552	.	.	ENSG00000133710	ENST00000398454;ENST00000359874;ENST00000508733;ENST00000256084	T;T;T;T	0.06687	3.27;3.27;3.27;3.27	3.99	-0.0887	0.13672	Proteinase inhibitor I1, Kazal (1);	0.878007	0.09732	N	0.763072	T	0.09069	0.0224	L	0.57536	1.79	0.09310	N	1	B;B;B;B	0.13145	0.002;0.007;0.002;0.007	B;B;B;B	0.17722	0.006;0.019;0.004;0.013	T	0.36768	-0.9734	10	0.66056	D	0.02	-0.8881	4.2672	0.10769	0.4664:0.1843:0.0:0.3492	.	425;444;444;444	B4DWS3;Q9NQ38-3;Q9NQ38;Q9NQ38-2	.;.;ISK5_HUMAN;.	W	444;444;425;444	ENSP00000381472:R444W;ENSP00000352936:R444W;ENSP00000421519:R425W;ENSP00000256084:R444W	ENSP00000256084:R444W	R	+	1	2	SPINK5	147461564	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.237000	0.08990	-0.012000	0.14223	0.528000	0.53228	AGG	.	.		0.458	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698		T	147481371	A	T	147481371	3	4	321	1	0	0	0	0	1	0	0	0	15077	179	7	4	1388	4	SPINK5	5	147481371	Missense_Mutation	SNP	A	TCGA-MI-A75E-01A-11D-A32G-10	16703202	147481371	33433889	43	45174										
TIMD4	91937	hgsc.bcm.edu	37	chr5	156375492	156375492	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	acacgtgggatgttgatgggAgatcccaaactttggactct	12	8	1	2			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr5:156375492A>T	ENST00000274532.2	-	5	835	c.779T>A	c.(778-780)cTc>cAc	p.L260H	TIMD4_ENST00000407087.3_Intron	NM_138379.2	NP_612388.2	Q96H15	TIMD4_HUMAN	T-cell immunoglobulin and mucin domain containing 4	260	Ser-rich.					integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(23)|ovary(2)|skin(2)	37	Renal(175;0.00488)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TGTTGATGGGAGATCCCAAAC	0.413																																					p.L260H		Atlas-SNP	.											.	TIMD4	94	.	0			c.T779A						.						73	62	66					5																	156375492		2203	4300	6503	SO:0001583	missense	91937	exon5			GATGGGAGATCCC	BC008988	CCDS4332.1, CCDS54943.1	5q33.3	2013-01-11			ENSG00000145850	ENSG00000145850		"Immunoglobulin superfamily / V-set domain containing"	25132	protein-coding gene	gene with protein product		610096				12477932	Standard	NM_001146726		Approved		uc003lwh.2	Q96H15	OTTHUMG00000130244	ENST00000274532.2:c.779T>A	chr5.hg19:g.156375492A>T	ENSP00000274532:p.Leu260His	74.0	0.0		80.0	12.0	NM_138379	B5MCL9	Missense_Mutation	SNP	ENST00000274532.2	hg19	CCDS4332.1	.	.	.	.	.	.	.	.	.	.	A	12.99	2.102577	0.37145	.	.	ENSG00000145850	ENST00000274532	T	0.26518	1.73	4.12	2.92	0.33932	.	1.052400	0.07506	N	0.908096	T	0.17492	0.0420	L	0.32530	0.975	0.09310	N	1	P	0.36974	0.576	B	0.27796	0.083	T	0.19484	-1.0304	10	0.62326	D	0.03	-5.9091	6.8157	0.23829	0.7931:0.0:0.0:0.2069	.	260	Q96H15	TIMD4_HUMAN	H	260	ENSP00000274532:L260H	ENSP00000274532:L260H	L	-	2	0	TIMD4	156308070	0.006000	0.16342	0.003000	0.11579	0.009000	0.06853	0.624000	0.24462	0.885000	0.36088	0.482000	0.46254	CTC	.	.		0.413	TIMD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252568.1	NM_138379		T	156375492	A	T	156375492	3	4	321	1	0	0	0	0	1	0	0	0	15918	304	11	4	377	4	TIMD4	5	156375492	Missense_Mutation	SNP	A	TCGA-MI-A75E-01A-11D-A32G-10	8894121	156375492	24539768	44	45175										
HIST1H1C	3006	hgsc.bcm.edu	37	chr6	26056228	26056229	+	Missense_Mutation	DNP	GC	GC	AA													0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	ctcttcttcggagttgcgccGccagccgccttcttgggctt							TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr6:26056228_26056229GC>AA	ENST00000343677.2	-	1	470_471	c.428_429GC>TT	c.(427-429)gGC>gTT	p.G143V		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	143					nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(4)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	34						GAGTTGCGCCGCCAGCCGCCTT	0.579																																					p.G143G|p.G143V		Atlas-SNP	.											.	HIST1H1C	80	.	0			c.C429T|c.G428T						.																																			SO:0001583	missense	3006	exon1			TGCGCCGCCAGCC|GCGCCGCCAGCCG	X57129	CCDS4577.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000187837	ENSG00000187837		"Histones / Replication-dependent"	4716	protein-coding gene	gene with protein product		142710	"H1 histone family, member 2", "histone 1, H1c"	H1F2		2759094, 12408966	Standard	NM_005319		Approved	H1.2, H1s-1, H1c	uc003nfw.3	P16403	OTTHUMG00000016140	ENST00000343677.2:c.428_429delinsAA	chr6.hg19:g.26056228_26056229delinsAA	ENSP00000339566:p.Gly143Val	93.0|94.0	0.0		95.0|94.0	18.0	NM_005319	A8K4I2	Silent|Missense_Mutation	SNP	ENST00000343677.2	hg19	CCDS4577.1																																																																																			.	.		0.579	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319		AA	26056229	GC	AA	26056228	3	1	321	1	0	0	0	0	1	0	0	0	7133	1074	38	1	216	1	HIST1H1C	6	26056228	Missense_Mutation	DNP	GC	TCGA-MI-A75E-01A-11D-A32G-10		26056228	145058839	45	45176										
DNAH8	1769	hgsc.bcm.edu	37	chr6	38775436	38775436	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	catcaattactagacagtctTcaaaaagctacacggttatc	5	10	3	1			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr6:38775436T>A	ENST00000359357.3	+	22	2804	c.2550T>A	c.(2548-2550)ctT>ctA	p.L850L	DNAH8_ENST00000449981.2_Silent_p.L1067L|DNAH8_ENST00000441566.1_Silent_p.L850L			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	850					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						TAGACAGTCTTCAAAAAGCTA	0.323																																					p.L1067L		Atlas-SNP	.											.	DNAH8	1239	.	0			c.T3201A						.						114	114	114					6																	38775436		2203	4298	6501	SO:0001819	synonymous_variant	1769	exon24			CAGTCTTCAAAAA	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.2550T>A	chr6.hg19:g.38775436T>A		101.0	0.0		122.0	28.0	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Silent	SNP	ENST00000359357.3	hg19																																																																																				.	.		0.323	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		A	38775436	T	A	38775436	2	1	321	1	0	0	0	0	0	0	0	1	4609	1770	62	4		4	DNAH8	6	38775436	Silent	SNP	T	TCGA-MI-A75E-01A-11D-A32G-10	12719208	38775436	132339631	46	45177										
ATG5	9474	hgsc.bcm.edu	37	chr6	106634468	106634468	+	Missense_Mutation	SNP	T	T	G													0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	aagaaaattatccgggtagcTcagatgttcactcagccact							TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr6:106634468T>G	ENST00000369076.3	-	8	1098	c.775A>C	c.(775-777)Agc>Cgc	p.S259R	ATG5_ENST00000343245.3_Missense_Mutation_p.S259R|ATG5_ENST00000369070.1_Missense_Mutation_p.S181R|ATG5_ENST00000475645.1_5'UTR|ATG5_ENST00000360666.4_3'UTR	NM_004849.2	NP_004840.1	Q9H1Y0	ATG5_HUMAN	autophagy related 5	259					apoptotic process (GO:0006915)|autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|blood vessel remodeling (GO:0001974)|heart contraction (GO:0060047)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of type I interferon production (GO:0032480)|negative stranded viral RNA replication (GO:0039689)|otolith development (GO:0048840)|post-translational protein modification (GO:0043687)|regulation of cilium assembly (GO:1902017)|regulation of cytokine secretion involved in immune response (GO:0002739)|response to drug (GO:0042493)|response to fungus (GO:0009620)|vasodilation (GO:0042311)|ventricular cardiac muscle cell development (GO:0055015)	autophagic vacuole (GO:0005776)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|membrane (GO:0016020)|pre-autophagosomal structure membrane (GO:0034045)				endometrium(1)|large_intestine(5)|lung(1)|prostate(1)	8	Breast(9;0.0296)	all_cancers(87;0.000301)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0612)|Lung NSC(302;0.216)	BRCA - Breast invasive adenocarcinoma(8;0.00802)	OV - Ovarian serous cystadenocarcinoma(136;0.128)|Epithelial(106;0.159)|all cancers(137;0.18)		TCCGGGTAGCTCAGATGTTCA	0.383																																					p.S259R		Atlas-SNP	.											.	ATG5	23	.	0			c.A775C						.						140	136	138					6																	106634468		2203	4300	6503	SO:0001583	missense	9474	exon8			GGTAGCTCAGATG	Y11588	CCDS5055.1, CCDS69159.1, CCDS75498.1	6q21	2014-02-12	2012-06-06	2005-09-11	ENSG00000057663	ENSG00000057663			589	protein-coding gene	gene with protein product		604261	"APG5 (autophagy 5, S. cerevisiae)-like", "APG5 autophagy 5-like (S. cerevisiae)", "ATG5 autophagy related 5 homolog (S. cerevisiae)"	APG5L		9563500, 11349150, 15778222	Standard	NM_001286111		Approved	ASP, APG5, hAPG5	uc003prf.3	Q9H1Y0	OTTHUMG00000016193	ENST00000369076.3:c.775A>C	chr6.hg19:g.106634468T>G	ENSP00000358072:p.Ser259Arg	44.0	0.0		40.0	12.0	NM_004849	O60875|Q5JVR2|Q68DI4|Q9H2B8|Q9HCZ7	Missense_Mutation	SNP	ENST00000369076.3	hg19	CCDS5055.1	.	.	.	.	.	.	.	.	.	.	T	19.92	3.916565	0.73098	.	.	ENSG00000057663	ENST00000369076;ENST00000343245;ENST00000369070	.	.	.	5.87	5.87	0.94306	.	0.086849	0.85682	D	0.000000	T	0.81805	0.4900	M	0.91459	3.21	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.995	T	0.82440	-0.0456	9	0.29301	T	0.29	-4.0816	16.2806	0.82678	0.0:0.0:0.0:1.0	.	181;259	Q9H1Y0-2;Q9H1Y0	.;ATG5_HUMAN	R	259;259;181	.	ENSP00000343313:S259R	S	-	1	0	ATG5	106741161	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.391000	0.79828	2.248000	0.74166	0.533000	0.62120	AGC	.	.		0.383	ATG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043476.1	NM_004849		G	106634468	T	G	106634468	3	3	321	1	0	0	0	0	1	0	0	0	1100	1551	54	5	56	5	ATG5	6	106634468	Missense_Mutation	SNP	T	TCGA-MI-A75E-01A-11D-A32G-10	67859032	106634468	64480599	47	45178	236	2								
ATG5	9474	hgsc.bcm.edu	37	chr6	106634473	106634473	+	Missense_Mutation	SNP	T	T	C													0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	aattatccgggtagctcagaTgttcactcagccactgcaga							TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr6:106634473T>C	ENST00000369076.3	-	8	1093	c.770A>G	c.(769-771)cAt>cGt	p.H257R	ATG5_ENST00000343245.3_Missense_Mutation_p.H257R|ATG5_ENST00000369070.1_Missense_Mutation_p.H179R|ATG5_ENST00000475645.1_5'UTR|ATG5_ENST00000360666.4_3'UTR	NM_004849.2	NP_004840.1	Q9H1Y0	ATG5_HUMAN	autophagy related 5	257					apoptotic process (GO:0006915)|autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|blood vessel remodeling (GO:0001974)|heart contraction (GO:0060047)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of type I interferon production (GO:0032480)|negative stranded viral RNA replication (GO:0039689)|otolith development (GO:0048840)|post-translational protein modification (GO:0043687)|regulation of cilium assembly (GO:1902017)|regulation of cytokine secretion involved in immune response (GO:0002739)|response to drug (GO:0042493)|response to fungus (GO:0009620)|vasodilation (GO:0042311)|ventricular cardiac muscle cell development (GO:0055015)	autophagic vacuole (GO:0005776)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|membrane (GO:0016020)|pre-autophagosomal structure membrane (GO:0034045)				endometrium(1)|large_intestine(5)|lung(1)|prostate(1)	8	Breast(9;0.0296)	all_cancers(87;0.000301)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0612)|Lung NSC(302;0.216)	BRCA - Breast invasive adenocarcinoma(8;0.00802)	OV - Ovarian serous cystadenocarcinoma(136;0.128)|Epithelial(106;0.159)|all cancers(137;0.18)		GTAGCTCAGATGTTCACTCAG	0.398																																					p.H257R		Atlas-SNP	.											.	ATG5	23	.	0			c.A770G						.						143	137	139					6																	106634473		2203	4300	6503	SO:0001583	missense	9474	exon8			CTCAGATGTTCAC	Y11588	CCDS5055.1, CCDS69159.1, CCDS75498.1	6q21	2014-02-12	2012-06-06	2005-09-11	ENSG00000057663	ENSG00000057663			589	protein-coding gene	gene with protein product		604261	"APG5 (autophagy 5, S. cerevisiae)-like", "APG5 autophagy 5-like (S. cerevisiae)", "ATG5 autophagy related 5 homolog (S. cerevisiae)"	APG5L		9563500, 11349150, 15778222	Standard	NM_001286111		Approved	ASP, APG5, hAPG5	uc003prf.3	Q9H1Y0	OTTHUMG00000016193	ENST00000369076.3:c.770A>G	chr6.hg19:g.106634473T>C	ENSP00000358072:p.His257Arg	44.0	0.0		40.0	12.0	NM_004849	O60875|Q5JVR2|Q68DI4|Q9H2B8|Q9HCZ7	Missense_Mutation	SNP	ENST00000369076.3	hg19	CCDS5055.1	.	.	.	.	.	.	.	.	.	.	T	18.63	3.664959	0.67700	.	.	ENSG00000057663	ENST00000369076;ENST00000343245;ENST00000369070	.	.	.	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.81607	0.4858	M	0.89904	3.07	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.79108	0.991;0.992	T	0.82902	-0.0227	9	0.37606	T	0.19	-8.934	16.2806	0.82678	0.0:0.0:0.0:1.0	.	179;257	Q9H1Y0-2;Q9H1Y0	.;ATG5_HUMAN	R	257;257;179	.	ENSP00000343313:H257R	H	-	2	0	ATG5	106741166	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.391000	0.79828	2.248000	0.74166	0.533000	0.62120	CAT	.	.		0.398	ATG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043476.1	NM_004849		C	106634473	T	C	106634473	3	2	321	1	0	0	0	0	1	0	0	0	1100	1464	51	2	61	2	ATG5	6	106634473	Missense_Mutation	SNP	T	TCGA-MI-A75E-01A-11D-A32G-10	5	106634473	64480594	48	45179	236	2								
REV3L	5980	hgsc.bcm.edu	37	chr6	111670435	111670435	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	acccacctcatttctcatgaTtctccaaagatttagtgtaa	4	11	3	2			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr6:111670435T>C	ENST00000358835.3	-	21	7859	c.7405A>G	c.(7405-7407)Atc>Gtc	p.I2469V	REV3L_ENST00000368802.3_Missense_Mutation_p.I2469V|REV3L_ENST00000368805.1_Missense_Mutation_p.I2469V|REV3L_ENST00000435970.1_Missense_Mutation_p.I2391V			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	2469					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		TTTCTCATGATTCTCCAAAGA	0.299								DNA polymerases (catalytic subunits)																													p.I2469V		Atlas-SNP	.											.	REV3L	386	.	0			c.A7405G						.						135	129	131					6																	111670435		2202	4298	6500	SO:0001583	missense	5980	exon20			TCATGATTCTCCA	AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"DNA polymerases"	9968	protein-coding gene	gene with protein product	"polymerase, DNA, zeta"	602776	"REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta", "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.7405A>G	chr6.hg19:g.111670435T>C	ENSP00000351697:p.Ile2469Val	111.0	0.0		88.0	16.0	NM_002912	O43214|Q5TC33	Missense_Mutation	SNP	ENST00000358835.3	hg19	CCDS5091.2	.	.	.	.	.	.	.	.	.	.	T	13.21	2.168802	0.38315	.	.	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970;ENST00000543871	T;T;T;T	0.07688	3.17;3.17;3.17;3.17	5.77	5.77	0.91146	DNA-directed DNA polymerase, family B, exonuclease domain (1);Ribonuclease H-like (1);	0.276070	0.35320	N	0.003291	T	0.03305	0.0096	L	0.33245	0.995	0.31509	N	0.66389	B	0.15930	0.015	B	0.23419	0.046	T	0.37174	-0.9717	10	0.22706	T	0.39	.	16.0836	0.81023	0.0:0.0:0.0:1.0	.	2469	O60673	DPOLZ_HUMAN	V	2469;2469;2469;2391;542	ENSP00000357792:I2469V;ENSP00000357795:I2469V;ENSP00000351697:I2469V;ENSP00000402003:I2391V	ENSP00000351697:I2469V	I	-	1	0	REV3L	111777128	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.619000	0.54196	2.196000	0.70406	0.528000	0.53228	ATC	.	.		0.299	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		C	111670435	T	C	111670435	3	2	321	1	0	0	0	0	1	0	0	0	13255	1493	52	2	2039	2	REV3L	6	111670435	Missense_Mutation	SNP	T	TCGA-MI-A75E-01A-11D-A32G-10	5035962	111670435	59444632	49	45180										
ZC3H12D	340152	hgsc.bcm.edu	37	chr6	149777857	149777857	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	ctcgatgaaccacttccactCggggttctcgctctgcaggt	10	14	2	1			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr6:149777857C>A	ENST00000409806.3	-	4	943	c.625G>T	c.(625-627)Gag>Tag	p.E209*	ZC3H12D_ENST00000416573.2_Nonsense_Mutation_p.E209*|ZC3H12D_ENST00000389942.5_Nonsense_Mutation_p.E209*|ZC3H12D_ENST00000542614.1_Nonsense_Mutation_p.E209*			A2A288	ZC12D_HUMAN	zinc finger CCCH-type containing 12D	209					negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|prostate(1)	6		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.23e-11)|GBM - Glioblastoma multiforme(68;0.0921)		CACTTCCACTCGGGGTTCTCG	0.642																																					p.E209X		Atlas-SNP	.											.	ZC3H12D	21	.	0			c.G625T						.						75	86	83					6																	149777857		2126	4260	6386	SO:0001587	stop_gained	340152	exon4			TCCACTCGGGGTT			6q25.1	2012-07-05	2005-06-30	2005-06-30	ENSG00000178199	ENSG00000178199		"Zinc fingers, CCCH-type domain containing"	21175	protein-coding gene	gene with protein product	"MCP induced protein 4"	611106	"chromosome 6 open reading frame 95"	C6orf95		18178554	Standard	NM_207360		Approved	dJ281H8.1, MCPIP4	uc010kid.3	A2A288	OTTHUMG00000015786	ENST00000409806.3:c.625G>T	chr6.hg19:g.149777857C>A	ENSP00000386616:p.Glu209*	50.0	0.0		35.0	7.0	NM_207360	A1L178|B2RXF4|B7WNU7|B9ZZP9|B9ZZQ0|Q6ZRW2	Nonsense_Mutation	SNP	ENST00000409806.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	39|39	7.863205|7.863205	0.98531|0.98531	.|.	.|.	ENSG00000178199|ENSG00000178199	ENST00000389942;ENST00000416573;ENST00000409806;ENST00000542614|ENST00000458251	.|.	.|.	.|.	4.84|4.84	4.84|4.84	0.62591|0.62591	.|.	0.069314|.	0.64402|.	D|.	0.000017|.	.|T	.|0.67942	.|0.2947	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.66791	.|-0.5834	.|3	0.87932|.	D|.	0|.	-23.8876|-23.8876	18.1465|18.1465	0.89656|0.89656	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|L	209|50	.|.	ENSP00000374592:E209X|.	E|R	-|-	1|2	0|0	ZC3H12D|ZC3H12D	149819550|149819550	0.995000|0.995000	0.38212|0.38212	0.994000|0.994000	0.49952|0.49952	0.998000|0.998000	0.95712|0.95712	3.052000|3.052000	0.49893|0.49893	2.526000|2.526000	0.85167|0.85167	0.561000|0.561000	0.74099|0.74099	GAG|CGA	.	.		0.642	ZC3H12D-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000286400.2	NM_207360		A	149777857	C	A	149777857	4	1	321	1	0	0	0	0	0	1	0	0	17579	893	31	1	970	1	ZC3H12D	6	149777857	Nonsense_Mutation	SNP	C	TCGA-MI-A75E-01A-11D-A32G-10	38107422	149777857	21337210	50	45181										
PHF10	55274	hgsc.bcm.edu	37	chr6	170116083	170116083	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	ataatggtctgtaattcgttGacgttctttttcttgtagaa	8	5	3	2	rs140258100		TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr6:170116083G>A	ENST00000339209.4	-	5	634	c.511C>T	c.(511-513)Caa>Taa	p.Q171*	PHF10_ENST00000366780.4_Nonsense_Mutation_p.Q169*|PHF10_ENST00000464779.1_5'Flank	NM_018288.3|NM_133325.2	NP_060758.2|NP_579866.2	Q8WUB8	PHF10_HUMAN	PHD finger protein 10	171	Essential to induce neural progenitor proliferation. {ECO:0000250}.|SAY.				nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	npBAF complex (GO:0071564)	zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|liver(3)|lung(4)|prostate(2)|urinary_tract(1)	14		Breast(66;5.08e-05)|Ovarian(120;0.208)		OV - Ovarian serous cystadenocarcinoma(33;1.4e-21)|BRCA - Breast invasive adenocarcinoma(81;1.4e-07)|GBM - Glioblastoma multiforme(31;0.00176)		GTAATTCGTTGACGTTCTTTT	0.333																																					p.Q171X		Atlas-SNP	.											.	PHF10	76	.	0			c.C511T						.						116	109	112					6																	170116083		2202	4300	6502	SO:0001587	stop_gained	55274	exon5			TTCGTTGACGTTC	AF338735	CCDS5308.2, CCDS5309.2	6q27	2014-05-13			ENSG00000130024	ENSG00000130024		"Zinc fingers, PHD-type"	18250	protein-coding gene	gene with protein product		613069				11827455	Standard	NM_018288		Approved	FLJ10975, XAP135, BAF45a	uc011egy.2	Q8WUB8	OTTHUMG00000016058	ENST00000339209.4:c.511C>T	chr6.hg19:g.170116083G>A	ENSP00000341805:p.Gln171*	238.0	0.0		175.0	30.0	NM_018288	Q2YDA3|Q53HG8|Q9BXD2|Q9NV26	Nonsense_Mutation	SNP	ENST00000339209.4	hg19	CCDS5308.2	.	.	.	.	.	.	.	.	.	.	G	35	5.494501	0.96339	.	.	ENSG00000130024	ENST00000366780;ENST00000339209	.	.	.	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.21540	T	0.41	-22.8934	19.3383	0.94329	0.0:0.0:1.0:0.0	.	.	.	.	X	169;171	.	ENSP00000341805:Q171X	Q	-	1	0	PHF10	169858008	1.000000	0.71417	0.829000	0.32907	0.868000	0.49771	7.306000	0.78905	2.807000	0.96579	0.650000	0.86243	CAA	.	G|1.000;C|0.000		0.333	PHF10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346732.1	NM_018288		A	170116083	G	A	170116083	4	1	321	1	0	0	0	0	0	1	0	0	11830	1299	45	3	1017	3	PHF10	6	170116083	Nonsense_Mutation	SNP	G	TCGA-MI-A75E-01A-11D-A32G-10	20338226	170116083	998984	51	45182										
SDK1	221935	hgsc.bcm.edu	37	chr7	3998620	3998620	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	ttcagctgaagtagaagaaaCtgtggacatcggatgtcaag	12	6	2	3			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr7:3998620C>T	ENST00000404826.2	+	8	1347	c.1208C>T	c.(1207-1209)aCt>aTt	p.T403I	SDK1_ENST00000389531.3_Missense_Mutation_p.T403I	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	403	Ig-like C2-type 4.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		GTAGAAGAAACTGTGGACATC	0.468																																					p.T403I		Atlas-SNP	.											.	SDK1	361	.	0			c.C1208T						.						122	120	121					7																	3998620		2203	4300	6503	SO:0001583	missense	221935	exon8			AAGAAACTGTGGA	AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19307	protein-coding gene	gene with protein product		607216	"sidekick homolog 1 (chicken)", "sidekick homolog 1, cell adhesion molecule (chicken)"			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.1208C>T	chr7.hg19:g.3998620C>T	ENSP00000385899:p.Thr403Ile	56.0	0.0		58.0	9.0	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	hg19	CCDS34590.1	.	.	.	.	.	.	.	.	.	.	C	5.957	0.360578	0.11296	.	.	ENSG00000146555	ENST00000404826;ENST00000389531	T;T	0.69306	-0.39;-0.39	5.35	3.48	0.39840	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.192456	0.33040	N	0.005348	T	0.61590	0.2359	M	0.70595	2.14	0.19300	N	0.999974	P	0.41524	0.753	B	0.41691	0.364	T	0.55023	-0.8205	10	0.37606	T	0.19	.	4.8625	0.13590	0.289:0.5132:0.1254:0.0723	.	403	Q7Z5N4	SDK1_HUMAN	I	403	ENSP00000385899:T403I;ENSP00000374182:T403I	ENSP00000374182:T403I	T	+	2	0	SDK1	3965146	0.000000	0.05858	0.485000	0.27403	0.276000	0.26787	0.129000	0.15830	0.696000	0.31696	0.655000	0.94253	ACT	.	.		0.468	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744		T	3998620	C	T	3998620	3	4	321	1	0	0	0	0	1	0	0	0	13983	565	20	3	1238	3	SDK1	7	3998620	Missense_Mutation	SNP	C	TCGA-MI-A75E-01A-11D-A32G-10		3998620	155140043	52	45183										
TMEM195	392636	hgsc.bcm.edu	37	chr7	15405237	15405237	+	Frame_Shift_Del	DEL	C	C	-													0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	gagagtttccataatagctgCcttgggtctgaaataaaatg							TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr7:15405237delC	ENST00000342526.3	-	12	1334	c.1165delG	c.(1165-1167)gcafs	p.A390fs		NM_001004320.1	NP_001004320.1	Q6ZNB7	ALKMO_HUMAN	alkylglycerol monooxygenase	390					ether lipid metabolic process (GO:0046485)|fatty acid biosynthetic process (GO:0006633)|membrane lipid metabolic process (GO:0006643)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glyceryl-ether monooxygenase activity (GO:0050479)|iron ion binding (GO:0005506)			breast(1)|kidney(1)|large_intestine(6)|liver(1)|lung(30)|prostate(1)|skin(2)	42						ATAATAGCTGCCTTGGGTCTG	0.353																																					p.A389fs		Atlas-Indel,Pindel	.											.	AGMO	98	.	0			c.1166delC						.						96	87	90					7																	15405237		2203	4300	6503	SO:0001589	frameshift_variant	392636	exon12			.		CCDS34604.1	7p21.1	2013-03-04	2011-01-31	2011-01-31	ENSG00000187546	ENSG00000187546	1.14.16.5	"Fatty acid hydroxylase domain containing"	33784	protein-coding gene	gene with protein product		613738	"transmembrane protein 195"	TMEM195		20643956	Standard	NM_001004320		Approved	FLJ16237	uc003stb.1	Q6ZNB7	OTTHUMG00000152387	ENST00000342526.3:c.1165delG	chr7.hg19:g.15405237delC	ENSP00000341662:p.Ala390fs	105.0	0.0		104.0	18.0	NM_001004320	A4D114|A6NCH5	Frame_Shift_Del	DEL	ENST00000342526.3	hg19	CCDS34604.1																																																																																			.	.		0.353	AGMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326049.2	NM_001004320		-	15405237	C	-	15405237	7	5	321	1	0	1	0	1	0	0	0	0	16132	739	26	0	180	0	TMEM195	7	15405237	Frame_Shift_Del	DEL	C	TCGA-MI-A75E-01A-11D-A32G-10	11406617	15405237	143733426	53	45184										
ABCB5	340273	hgsc.bcm.edu	37	chr7	20685483	20685484	+	Missense_Mutation	DNP	CC	CC	AG													0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	acagtcatagcctttagggcCcaggagaaagaacttcaaag					rs2074000	byFrequency	TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr7:20685483_20685484CC>AG	ENST00000404938.2	+	8	1435_1436	c.783_784CC>AG	c.(781-786)gcCCag>gcAGag	p.Q262E	ABCB5_ENST00000258738.6_5'Flank|ABCB5_ENST00000443026.2_5'Flank|ABCB5_ENST00000406935.1_5'Flank	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	262	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (GO:0002485)|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO:0002489)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|cell differentiation (GO:0030154)|compound eye corneal lens development (GO:0048058)|positive regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002591)|regulation of membrane potential (GO:0042391)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|efflux transmembrane transporter activity (GO:0015562)	p.A261A(1)		breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(1)|pancreas(1)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)	77						CCTTTAGGGCCCAGGAGAAAGA	0.406																																					p.A261A|p.Q262E		Atlas-SNP	.											.	ABCB5	357	.	1	Substitution - coding silent(1)	lung(1)	c.C783A|c.C784G						.																																			SO:0001583	missense	340273	exon8			TAGGGCCCAGGAG|AGGGCCCAGGAGA	U66692	CCDS5371.1, CCDS55090.1, CCDS55091.1, CCDS55092.1	7p14	2012-03-14			ENSG00000004846	ENSG00000004846		"ATP binding cassette transporters / subfamily B"	46	protein-coding gene	gene with protein product	"P-glycoprotein ABCB5", "ATP-binding cassette protein"	611785				8894702, 12960149	Standard	NM_001163942		Approved	EST422562, ABCB5beta, ABCB5alpha	uc010kuh.3	Q2M3G0	OTTHUMG00000094789	Exception_encountered	chr7.hg19:g.20685483_20685484delinsAG	ENSP00000384881:p.Gln262Glu	111.0|112.0	0.0		122.0|124.0	19.0	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Silent|Missense_Mutation	SNP	ENST00000404938.2	hg19	CCDS55090.1																																																																																			.	.|C|0.847;A|0.153		0.406	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559		AG	20685484	CC	AG	20685483	3	1	321	1	0	0	0	0	1	0	0	0	44	610	22	3	809	3	ABCB5	7	20685483	Missense_Mutation	DNP	CC	TCGA-MI-A75E-01A-11D-A32G-10	5280246	20685483	138453180	54	45185										
GLI3	2737	hgsc.bcm.edu	37	chr7	42005488	42005488	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	ctgggaggacagggggacgaGtggaagtttcgggactggcc	20	7	0	0	rs565428084		TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr7:42005488G>A	ENST00000395925.3	-	15	3267	c.3183C>T	c.(3181-3183)caC>caT	p.H1061H	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	1061					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						AGGGGGACGAGTGGAAGTTTC	0.642									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																												p.H1061H		Atlas-SNP	.											.	GLI3	312	.	0			c.C3183T						.						54	58	56					7																	42005488		2203	4300	6503	SO:0001819	synonymous_variant	2737	exon15	Familial Cancer Database	;	GGACGAGTGGAAG		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"Zinc fingers, C2H2-type"	4319	protein-coding gene	gene with protein product	"zinc finger protein GLI3", "oncogene GLI3", "DNA-binding protein"	165240	"Greig cephalopolysyndactyly syndrome", "GLI-Kruppel family member GLI3", "glioma-associated oncogene family zinc finger 3"	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.3183C>T	chr7.hg19:g.42005488G>A		65.0	0.0		74.0	9.0	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Silent	SNP	ENST00000395925.3	hg19	CCDS5465.1																																																																																			.	.		0.642	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168		A	42005488	G	A	42005488	2	1	321	1	0	0	0	0	0	0	0	1	6447	1020	36	3		3	GLI3	7	42005488	Silent	SNP	G	TCGA-MI-A75E-01A-11D-A32G-10	21320005	42005488	117133175	55	45186										
ZNF92	168374	hgsc.bcm.edu	37	chr7	64863556	64863556	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	agaaacctttcaaatgtaaaAaccgtggcaaatcattttgc	6	8	2	1			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr7:64863556A>G	ENST00000328747.7	+	4	728	c.529A>G	c.(529-531)Aac>Gac	p.N177D	ZNF92_ENST00000450302.2_Missense_Mutation_p.N108D|ZNF92_ENST00000357512.2_Missense_Mutation_p.N145D|ZNF92_ENST00000431504.1_Missense_Mutation_p.N101D	NM_152626.2	NP_689839.1	Q03936	ZNF92_HUMAN	zinc finger protein 92	177					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(3)|lung(4)|pancreas(1)|skin(1)|stomach(1)	13		Lung NSC(55;0.159)				CAAATGTAAAAACCGTGGCAA	0.289																																					p.N177D		Atlas-SNP	.											.	ZNF92	68	.	0			c.A529G						.						28	29	29					7																	64863556		2203	4294	6497	SO:0001583	missense	168374	exon4			TGTAAAAACCGTG	M61872	CCDS34646.1, CCDS47596.1, CCDS75608.1, CCDS75609.1	7q11.21	2013-01-08	2006-05-12		ENSG00000146757	ENSG00000146757		"Zinc fingers, C2H2-type", "-"	13168	protein-coding gene	gene with protein product		603974	"zinc finger protein 92 (HTF12)"			8467795	Standard	NM_001287533		Approved	HPF12, TF12	uc003ttz.3	Q03936	OTTHUMG00000156557	ENST00000328747.7:c.529A>G	chr7.hg19:g.64863556A>G	ENSP00000332595:p.Asn177Asp	50.0	0.0		53.0	12.0	NM_152626	A6NNF9|Q8N492|Q8NB35	Missense_Mutation	SNP	ENST00000328747.7	hg19	CCDS34646.1	.	.	.	.	.	.	.	.	.	.	A	3.731	-0.055490	0.07362	.	.	ENSG00000146757	ENST00000328747;ENST00000431504;ENST00000357512;ENST00000450302	T;T;T;T	0.27557	2.49;1.66;1.66;1.66	0.427	-0.759	0.11045	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12092	0.0294	N	0.03891	-0.335	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.11329	0.006;0.001	T	0.22138	-1.0225	9	0.56958	D	0.05	.	4.3551	0.11174	0.3764:0.0:0.6236:0.0	.	145;177	Q03936-3;Q03936	.;ZNF92_HUMAN	D	177;101;145;108	ENSP00000332595:N177D;ENSP00000400495:N101D;ENSP00000350113:N145D;ENSP00000396126:N108D	ENSP00000332595:N177D	N	+	1	0	ZNF92	64500991	0.001000	0.12720	0.020000	0.16555	0.019000	0.09904	0.105000	0.15333	-0.455000	0.07054	-0.456000	0.05471	AAC	.	.		0.289	ZNF92-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344589.2	NM_152626		G	64863556	A	G	64863556	3	3	321	1	0	0	0	0	1	0	0	0	18216	14	1	2	543	2	ZNF92	7	64863556	Missense_Mutation	SNP	A	TCGA-MI-A75E-01A-11D-A32G-10	22858068	64863556	94275107	56	45187										
MUC17	140453	hgsc.bcm.edu	37	chr7	100683668	100683668	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	aaagaagaactccattaacaAgtatgtctgtcagcaccatg	7	9	2	2			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr7:100683668A>T	ENST00000306151.4	+	3	9035	c.8971A>T	c.(8971-8973)Agt>Tgt	p.S2991C		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2991	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					TCCATTAACAAGTATGTCTGT	0.507																																					p.S2991C		Atlas-SNP	.											.	MUC17	804	.	0			c.A8971T						.						242	252	249					7																	100683668		2203	4300	6503	SO:0001583	missense	140453	exon3			TTAACAAGTATGT	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.8971A>T	chr7.hg19:g.100683668A>T	ENSP00000302716:p.Ser2991Cys	58.0	0.0		66.0	11.0	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	A	6.492	0.458991	0.12342	.	.	ENSG00000169876	ENST00000306151	T	0.02032	4.49	0.513	-0.665	0.11403	.	.	.	.	.	T	0.01940	0.0061	N	0.14661	0.345	0.09310	N	1	D	0.62365	0.991	P	0.49477	0.612	T	0.48490	-0.9031	9	0.38643	T	0.18	.	3.7701	0.08637	0.6255:0.0:0.3745:0.0	.	2991	Q685J3	MUC17_HUMAN	C	2991	ENSP00000302716:S2991C	ENSP00000302716:S2991C	S	+	1	0	MUC17	100470388	0.000000	0.05858	0.001000	0.08648	0.019000	0.09904	-0.252000	0.08806	-0.290000	0.09025	0.102000	0.15555	AGT	.	.		0.507	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		T	100683668	A	T	100683668	3	4	321	1	0	0	0	0	1	0	0	0	9983	72	3	4	8981	4	MUC17	7	100683668	Missense_Mutation	SNP	A	TCGA-MI-A75E-01A-11D-A32G-10	35820112	100683668	58454995	57	45188										
MUC17	140453	hgsc.bcm.edu	37	chr7	100695190	100695191	+	Frame_Shift_Ins	INS	-	-	A													0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	agcctggcttcagtgtctccINSaagaactgtaacctcggcaa							TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr7:100695190_100695191insA	ENST00000306151.4	+	9	13114_13115	c.13050_13051insA	c.(13051-13053)aagfs	p.K4351fs		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	4351					cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					TCAGTGTCTCCAAGAACTGTAA	0.574																																					p.S4350fs		Atlas-Indel,Pindel	.											.	MUC17	804	.	0			c.13050_13051insA						.																																			SO:0001589	frameshift_variant	140453	exon9			.	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.13052dupA	chr7.hg19:g.100695192_100695192dupA	ENSP00000302716:p.Lys4351fs	93.0	0.0		114.0	15.0	NM_001040105	O14761|Q685J2|Q8TDH7	Frame_Shift_Ins	INS	ENST00000306151.4	hg19	CCDS34711.1																																																																																			.	.		0.574	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		A	100695191	-	A	100695190	7	5	321	1	0	1	1	0	0	0	0	0	9983	581	21	0	13084	0	MUC17	7	100695190	Frame_Shift_Ins	INS	-	TCGA-MI-A75E-01A-11D-A32G-10	11522	100695190	58443473	58	45189										
CTTNBP2	83992	hgsc.bcm.edu	37	chr7	117385885	117385885	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	atttgctgaaatgttcttacCgctactaatgaacaggtcta	7	8	2	2			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr7:117385885C>A	ENST00000160373.3	-	14	3626	c.3535G>T	c.(3535-3537)Gct>Tct	p.A1179S		NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	1179					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)				breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		ATGTTCTTACCGCTACTAATG	0.408																																					p.A1179S		Atlas-SNP	.											.	CTTNBP2	200	.	0			c.G3535T						.						86	85	86					7																	117385885		2203	4300	6503	SO:0001630	splice_region_variant	83992	exon14			TCTTACCGCTACT		CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"Ankyrin repeat domain containing"	15679	protein-coding gene	gene with protein product		609772	"cortactin binding protein 2"	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.3535+1G>T	chr7.hg19:g.117385885C>A		71.0	0.0		66.0	7.0	NM_033427	O43389|Q7LG11|Q9C0A5	Missense_Mutation	SNP	ENST00000160373.3	hg19	CCDS5774.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.47|19.47	3.832792|3.832792	0.71258|0.71258	.|.	.|.	ENSG00000077063|ENSG00000077063	ENST00000160373|ENST00000446636	T|.	0.52057|.	0.68|.	5.87|5.87	4.98|4.98	0.66077|0.66077	.|.	0.048902|.	0.85682|.	D|.	0.000000|.	T|T	0.78253|0.78253	0.4254|0.4254	M|M	0.84082|0.84082	2.675|2.675	0.37380|0.37380	D|D	0.91201|0.91201	D|.	0.69078|.	0.997|.	P|.	0.61397|.	0.888|.	D|D	0.83610|0.83610	0.0133|0.0133	9|5	.|.	.|.	.|.	0.3876|0.3876	16.6019|16.6019	0.84818|0.84818	0.1314:0.8686:0.0:0.0|0.1314:0.8686:0.0:0.0	.|.	1179|.	Q8WZ74|.	CTTB2_HUMAN|.	S|L	1179|666	ENSP00000160373:A1179S|.	.|.	A|R	-|-	1|2	0|0	CTTNBP2|CTTNBP2	117173121|117173121	1.000000|1.000000	0.71417|0.71417	0.940000|0.940000	0.37924|0.37924	0.634000|0.634000	0.38068|0.38068	5.887000|5.887000	0.69751|0.69751	1.590000|1.590000	0.49995|0.49995	0.655000|0.655000	0.94253|0.94253	GCT|CGC	.	.		0.408	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427	Missense_Mutation	A	117385885	C	A	117385885	5	1	321	1	0	0	0	0	0	0	1	0	4047	666	23	1	1496	1	CTTNBP2	7	117385885	Splice_Site	SNP	C	TCGA-MI-A75E-01A-11D-A32G-10	16690695	117385885	41752778	59	45190										
PAX4	5078	hgsc.bcm.edu	37	chr7	127255566	127255566	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	ttcacaaagagccccccaagCtggttcatgctgctgatccc	8	15	2	2			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr7:127255566C>A	ENST00000341640.2	-	1	214	c.9G>T	c.(7-9)caG>caT	p.Q3H	PAX4_ENST00000338516.3_Missense_Mutation_p.Q11H|PAX4_ENST00000463946.1_5'UTR|PAX4_ENST00000378740.2_Missense_Mutation_p.Q3H	NM_006193.2	NP_006184.2	O43316	PAX4_HUMAN	paired box 4	11					cell differentiation (GO:0030154)|circadian rhythm (GO:0007623)|endocrine pancreas development (GO:0031018)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|positive regulation of cell differentiation (GO:0045597)|response to cAMP (GO:0051591)|response to drug (GO:0042493)|retina development in camera-type eye (GO:0060041)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)			cervix(1)|kidney(2)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35						GCCCCCCAAGCTGGTTCATGC	0.632																																					p.Q3H	Ovarian(113;737 1605 7858 27720 34092)	Atlas-SNP	.											.	PAX4	66	.	0			c.G9T						.						75	77	76					7																	127255566		2203	4300	6503	SO:0001583	missense	5078	exon1			CCCAAGCTGGTTC		CCDS5797.1	7q32.1	2011-06-20	2007-07-12		ENSG00000106331	ENSG00000106331		"Paired boxes", "Homeoboxes / PRD class"	8618	protein-coding gene	gene with protein product		167413	"paired box gene 4"				Standard	NM_006193		Approved	MODY9	uc010lld.1	O43316	OTTHUMG00000157562	ENST00000341640.2:c.9G>T	chr7.hg19:g.127255566C>A	ENSP00000339906:p.Gln3His	60.0	0.0		56.0	14.0	NM_006193	O95161|Q6B0H0	Missense_Mutation	SNP	ENST00000341640.2	hg19	CCDS5797.1	.	.	.	.	.	.	.	.	.	.	C	15.62	2.887875	0.52014	.	.	ENSG00000106331	ENST00000341640;ENST00000338516;ENST00000378740	D;D	0.99567	-6.18;-6.18	5.67	3.88	0.44766	Paired box protein, N-terminal (4);Winged helix-turn-helix transcription repressor DNA-binding (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99582	0.9849	M	0.91510	3.215	0.51767	D	0.999933	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.99204	1.0874	10	0.87932	D	0	.	7.7323	0.28793	0.0:0.7458:0.0:0.2542	.	3;11	O43316-4;O43316	.;PAX4_HUMAN	H	3;11;11	ENSP00000339906:Q3H;ENSP00000344297:Q11H	ENSP00000344297:Q11H	Q	-	3	2	PAX4	127042802	1.000000	0.71417	0.999000	0.59377	0.347000	0.29111	2.355000	0.44107	0.748000	0.32831	0.655000	0.94253	CAG	.	.		0.632	PAX4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349165.1			A	127255566	C	A	127255566	3	1	321	1	0	0	0	0	1	0	0	0	11490	796	28	3	1058	3	PAX4	7	127255566	Missense_Mutation	SNP	C	TCGA-MI-A75E-01A-11D-A32G-10	9869681	127255566	31883097	60	45191										
ATP6V1F	9296	hgsc.bcm.edu	37	chr7	128505594	128505594	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	ccaaggactccatcctgcgcAgggccaggggcatgttcact	12	14	1	0			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr7:128505594A>T	ENST00000249289.4	+	2	401	c.322A>T	c.(322-324)Agg>Tgg	p.R108W	RP11-309L24.4_ENST00000461420.1_lincRNA|ATP6V1F_ENST00000492758.1_Missense_Mutation_p.R136W|RP11-309L24.2_ENST00000469965.1_RNA	NM_004231.3	NP_004222.2	Q16864	VATF_HUMAN	ATPase, H+ transporting, lysosomal 14kDa, V1 subunit F	108					ATP catabolic process (GO:0006200)|ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	ATPase activity, uncoupled (GO:0042624)|hydrogen ion transmembrane transporter activity (GO:0015078)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			lung(1)|ovary(1)|prostate(1)	3						CATCCTGCGCAGGGCCAGGGG	0.652																																					p.R136W		Atlas-SNP	.											.	ATP6V1F	12	.	0			c.A406T						.						38	40	39					7																	128505594		2203	4300	6503	SO:0001583	missense	9296	exon3			CTGCGCAGGGCCA	D49400	CCDS5807.1, CCDS56511.1	7q32.1	2010-04-21	2002-08-29		ENSG00000128524	ENSG00000128524	3.6.3.14	"ATPases / V-type"	16832	protein-coding gene	gene with protein product		607160				8581736, 8621738	Standard	NM_004231		Approved	ATP6S14, VATF, Vma7	uc022all.1	Q16864	OTTHUMG00000158365	ENST00000249289.4:c.322A>T	chr7.hg19:g.128505594A>T	ENSP00000249289:p.Arg108Trp	55.0	0.0		66.0	9.0	NM_001198909	C9J2K4|Q6IBA8	Missense_Mutation	SNP	ENST00000249289.4	hg19	CCDS5807.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.009244	0.75046	.	.	ENSG00000128524	ENST00000249289;ENST00000492758	T;T	0.60299	0.25;0.2	5.02	2.68	0.31781	.	0.000000	0.85682	D	0.000000	T	0.81399	0.4814	H	0.96460	3.825	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.84788	0.0777	10	0.87932	D	0	-21.2484	11.162	0.48520	0.5948:0.4052:0.0:0.0	.	108	Q16864	VATF_HUMAN	W	108;136	ENSP00000249289:R108W;ENSP00000417378:R136W	ENSP00000249289:R108W	R	+	1	2	ATP6V1F	128292830	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	1.167000	0.31847	0.739000	0.32628	0.482000	0.46254	AGG	.	.		0.652	ATP6V1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350800.1	NM_004231		T	128505594	A	T	128505594	3	4	321	1	0	0	0	0	1	0	0	0	1185	179	7	4	328	4	ATP6V1F	7	128505594	Missense_Mutation	SNP	A	TCGA-MI-A75E-01A-11D-A32G-10	1250028	128505594	30633069	61	45192										
ABP1	26	hgsc.bcm.edu	37	chr7	150555959	150555959	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	tctggagcagacgcagtactCctgggagcgccaggcggcct	15	13	1	1			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr7:150555959C>T	ENST00000493429.1	+	5	2263	c.1679C>T	c.(1678-1680)tCc>tTc	p.S560F	AOC1_ENST00000480582.1_3'UTR|AOC1_ENST00000467291.1_Missense_Mutation_p.S560F|AOC1_ENST00000360937.4_Missense_Mutation_p.S560F|AOC1_ENST00000416793.2_Missense_Mutation_p.S560F			P19801	AOC1_HUMAN	amine oxidase, copper containing 1	560					amine metabolic process (GO:0009308)|cellular response to azide (GO:0097185)|cellular response to copper ion (GO:0071280)|cellular response to copper ion starvation (GO:0035874)|cellular response to heparin (GO:0071504)|cellular response to histamine (GO:0071420)|oxidation-reduction process (GO:0055114)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|diamine oxidase activity (GO:0052597)|drug binding (GO:0008144)|heparin binding (GO:0008201)|histamine oxidase activity (GO:0052598)|methylputrescine oxidase activity (GO:0052599)|primary amine oxidase activity (GO:0008131)|propane-1,3-diamine oxidase activity (GO:0052600)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|receptor activity (GO:0004872)|sodium channel activity (GO:0005272)|zinc ion binding (GO:0008270)									Amiloride(DB00594)	ACGCAGTACTCCTGGGAGCGC	0.592																																					p.S560F		Atlas-SNP	.											.	ABP1	92	.	0			c.C1679T						.						29	32	31					7																	150555959		1980	4167	6147	SO:0001583	missense	26	exon3			AGTACTCCTGGGA	AK092514	CCDS43679.1, CCDS64797.1	7q36.1	2013-06-19	2013-06-19	2013-06-19	ENSG00000002726	ENSG00000002726	1.4.3.22		80	protein-coding gene	gene with protein product	"diamine oxidase"	104610	"amiloride binding protein 1 (amine oxidase (copper-containing))"	ABP1		8182053	Standard	NM_001091		Approved	DAO	uc003wia.2	P19801	OTTHUMG00000158306	ENST00000493429.1:c.1679C>T	chr7.hg19:g.150555959C>T	ENSP00000418614:p.Ser560Phe	154.0	0.0		155.0	21.0	NM_001091	C9J690|Q16683|Q16684|Q56II4|Q6GU42	Missense_Mutation	SNP	ENST00000493429.1	hg19	CCDS43679.1	.	.	.	.	.	.	.	.	.	.	C	12.86	2.063367	0.36373	.	.	ENSG00000002726	ENST00000493429;ENST00000467291;ENST00000360937;ENST00000487631;ENST00000416793;ENST00000437714	T;T;T;T	0.03889	3.77;3.77;3.77;3.77	5.57	-7.02	0.01589	Copper amine oxidase, C-terminal (3);	1.413890	0.03680	N	0.245342	T	0.09818	0.0241	M	0.76002	2.32	0.09310	N	1	P;P	0.48694	0.598;0.914	P;P	0.51016	0.547;0.656	T	0.42103	-0.9471	10	0.66056	D	0.02	-33.5783	2.3574	0.04299	0.4927:0.1233:0.0879:0.2961	.	560;560	C9J690;P19801	.;ABP1_HUMAN	F	560;560;560;86;560;436	ENSP00000418614:S560F;ENSP00000418328:S560F;ENSP00000354193:S560F;ENSP00000411613:S560F	ENSP00000354193:S560F	S	+	2	0	ABP1	150186892	0.000000	0.05858	0.000000	0.03702	0.068000	0.16541	-0.791000	0.04599	-0.983000	0.03511	-0.314000	0.08810	TCC	.	.		0.592	AOC1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350628.1	NM_001091		T	150555959	C	T	150555959	3	4	321	1	0	0	0	0	1	0	0	0	98	855	30	3	1685	3	ABP1	7	150555959	Missense_Mutation	SNP	C	TCGA-MI-A75E-01A-11D-A32G-10	22050365	150555959	8582704	62	45193										
CHRNA2	1135	hgsc.bcm.edu	37	chr8	27321444	27321444	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	tagatggccgggggcacccaGtgcacagtgcccgtggagaa	16	11	0	2			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr8:27321444G>A	ENST00000520933.2	-	5	669	c.516C>T	c.(514-516)caC>caT	p.H172H	CHRNA2_ENST00000240132.2_Silent_p.H157H|CHRNA2_ENST00000407991.1_Silent_p.H172H			Q15822	ACHA2_HUMAN	cholinergic receptor, nicotinic, alpha 2 (neuronal)	172					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transport (GO:0006811)|protein heterooligomerization (GO:0051291)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|drug binding (GO:0008144)			breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	23		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0208)|Epithelial(17;2.77e-10)|Colorectal(74;0.136)	Atracurium(DB00732)|Biperiden(DB00810)|Carbachol(DB00411)|Cisatracurium Besylate(DB00565)|Decamethonium(DB01245)|Dextromethorphan(DB00514)|Doxacurium chloride(DB01135)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Mecamylamine(DB00657)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicotine(DB00184)|Pancuronium(DB01337)|Pipecuronium(DB01338)|Procaine(DB00721)|Rocuronium(DB00728)|Tubocurarine(DB01199)|Vecuronium(DB01339)	GGGGCACCCAGTGCACAGTGC	0.592																																					p.H172H		Atlas-SNP	.											.	CHRNA2	48	.	0			c.C516T						.						95	88	90					8																	27321444		2203	4300	6503	SO:0001819	synonymous_variant	1135	exon6			CACCCAGTGCACA	U62431	CCDS6059.1, CCDS64856.1	8p21	2012-02-11	2006-02-01		ENSG00000120903	ENSG00000120903		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1956	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 2 (neuronal)"	118502	"cholinergic receptor, nicotinic, alpha polypeptide 2 (neuronal)"			1505988	Standard	NM_000742		Approved		uc010lur.3	Q15822	OTTHUMG00000102083	ENST00000520933.2:c.516C>T	chr8.hg19:g.27321444G>A		75.0	0.0		74.0	10.0	NM_000742	A8KAX3|B4DK19|J3KMY9|Q9HAQ3	Silent	SNP	ENST00000520933.2	hg19	CCDS6059.1																																																																																			.	.		0.592	CHRNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376125.4			A	27321444	G	A	27321444	2	1	321	1	0	0	0	0	0	0	0	1	3385	1020	36	3		3	CHRNA2	8	27321444	Silent	SNP	G	TCGA-MI-A75E-01A-11D-A32G-10		27321444	119042578	63	45194										
NSMAF	8439	hgsc.bcm.edu	37	chr8	59536325	59536325	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	ggaacatccaattcaaaaacAtattccattttgccctaaca	3	11	1	0			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr8:59536325A>G	ENST00000038176.3	-	7	611	c.399T>C	c.(397-399)taT>taC	p.Y133Y	NSMAF_ENST00000519858.1_5'Flank|NSMAF_ENST00000427130.2_Silent_p.Y164Y	NM_003580.3	NP_003571.2	Q92636	FAN_HUMAN	neutral sphingomyelinase (N-SMase) activation associated factor	133					ceramide metabolic process (GO:0006672)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	receptor signaling protein activity (GO:0005057)|sphingomyelin phosphodiesterase activator activity (GO:0016230)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	38		all_lung(136;0.174)|Lung NSC(129;0.2)				ATTCAAAAACATATTCCATTT	0.403																																					p.Y164Y		Atlas-SNP	.											.	NSMAF	156	.	0			c.T492C						.						78	71	73					8																	59536325		2203	4300	6503	SO:0001819	synonymous_variant	8439	exon7			AAAAACATATTCC	X96586	CCDS6173.1, CCDS47864.1	8q12-q13	2013-01-10			ENSG00000035681	ENSG00000035681		"WD repeat domain containing"	8017	protein-coding gene	gene with protein product		603043				8808629, 10640829	Standard	NM_003580		Approved	FAN	uc011lee.2	Q92636	OTTHUMG00000164352	ENST00000038176.3:c.399T>C	chr8.hg19:g.59536325A>G		188.0	0.0		198.0	55.0	NM_001144772	B4DFB0|E9PCH0|Q8IW26	Silent	SNP	ENST00000038176.3	hg19	CCDS6173.1																																																																																			.	.		0.403	NSMAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378384.1	NM_003580		G	59536325	A	G	59536325	2	3	321	1	0	0	0	0	0	0	0	1	10683	224	8	2		2	NSMAF	8	59536325	Silent	SNP	A	TCGA-MI-A75E-01A-11D-A32G-10	32214881	59536325	86827697	64	45195										
ZNF510	22869	hgsc.bcm.edu	37	chr9	99522338	99522338	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	tcattaaaggcttttccaatTttattacattcaaaagcttg	4	7	2	0			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr9:99522338T>C	ENST00000375231.1	-	6	1424	c.774A>G	c.(772-774)aaA>aaG	p.K258K	ZNF510_ENST00000472201.1_5'Flank|ZNF510_ENST00000223428.4_Silent_p.K258K			Q9Y2H8	ZN510_HUMAN	zinc finger protein 510	258					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|stomach(1)|urinary_tract(1)	21		Acute lymphoblastic leukemia(62;0.0527)				CTTTTCCAATTTTATTACATT	0.303																																					p.K258K		Atlas-SNP	.											.	ZNF510	59	.	0			c.A774G						.						52	54	53					9																	99522338		2202	4300	6502	SO:0001819	synonymous_variant	22869	exon6			TCCAATTTTATTA	AB023189	CCDS35074.1	9q22.33	2013-01-08			ENSG00000081386	ENSG00000081386		"Zinc fingers, C2H2-type", "-"	29161	protein-coding gene	gene with protein product						10231032	Standard	XM_005251807		Approved	KIAA0972	uc004awn.1	Q9Y2H8	OTTHUMG00000020303	ENST00000375231.1:c.774A>G	chr9.hg19:g.99522338T>C		76.0	0.0		70.0	15.0	NM_014930	Q5SZP5	Silent	SNP	ENST00000375231.1	hg19	CCDS35074.1																																																																																			.	.		0.303	ZNF510-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053287.1	NM_014930		C	99522338	T	C	99522338	2	2	321	1	0	0	0	0	0	0	0	1	17969	1838	64	2		2	ZNF510	9	99522338	Silent	SNP	T	TCGA-MI-A75E-01A-11D-A32G-10		99522338	41691093	65	45196										
MYO3A	53904	hgsc.bcm.edu	37	chr10	26457744	26457744	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	tgtcagagcattcttgtgttCaagaagataccaaaaaatac	7	7	3	3			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr10:26457744C>T	ENST00000265944.5	+	28	3381	c.3215C>T	c.(3214-3216)tCa>tTa	p.S1072L	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	1072	IQ 1. {ECO:0000255|PROSITE- ProRule:PRU00116}.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						TTCTTGTGTTCAAGAAGATAC	0.328																																					p.S1072L		Atlas-SNP	.											.	MYO3A	371	.	0			c.C3215T						.						119	121	120					10																	26457744		2203	4300	6503	SO:0001583	missense	53904	exon28			TGTGTTCAAGAAG	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.3215C>T	chr10.hg19:g.26457744C>T	ENSP00000265944:p.Ser1072Leu	83.0	0.0		85.0	14.0	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	hg19	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	C	14.27	2.483989	0.44147	.	.	ENSG00000095777	ENST00000265944	T	0.70749	-0.51	5.63	5.63	0.86233	.	0.270481	0.36778	N	0.002406	T	0.57519	0.2059	N	0.14661	0.345	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.49606	-0.8922	10	0.27785	T	0.31	.	20.0499	0.97621	0.0:1.0:0.0:0.0	.	1072	Q8NEV4	MYO3A_HUMAN	L	1072	ENSP00000265944:S1072L	ENSP00000265944:S1072L	S	+	2	0	MYO3A	26497750	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.172000	0.58243	2.798000	0.96311	0.655000	0.94253	TCA	.	.		0.328	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		T	26457744	C	T	26457744	3	4	321	1	0	0	0	0	1	0	0	0	10085	838	29	3	3317	3	MYO3A	10	26457744	Missense_Mutation	SNP	C	TCGA-MI-A75E-01A-11D-A32G-10		26457744	109077003	66	45197										
RAB18	22931	hgsc.bcm.edu	37	chr10	27821473	27821473	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	gaggtttagaacattaactcCcagctattatagaggtgcac	9	8	0	2			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr10:27821473C>T	ENST00000356940.6	+	4	326	c.224C>T	c.(223-225)cCc>cTc	p.P75L	RAB18_ENST00000535776.1_Intron|RAB18_ENST00000375802.3_Intron|RAB18_ENST00000465772.1_3'UTR	NM_001256410.1|NM_001256415.1|NM_021252.4	NP_001243339.1|NP_001243344.1|NP_067075.1	Q9NP72	RAB18_HUMAN	RAB18, member RAS oncogene family	75					brain development (GO:0007420)|endoplasmic reticulum tubular network organization (GO:0071786)|eye development (GO:0001654)|GTP catabolic process (GO:0006184)|lipid particle organization (GO:0034389)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	endoplasmic reticulum tubular network (GO:0071782)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			kidney(1)|large_intestine(1)|lung(1)	3						ACATTAACTCCCAGCTATTAT	0.289																																					p.P104L		Atlas-SNP	.											.	RAB18	18	.	0			c.C311T						.						115	122	120					10																	27821473		2203	4296	6499	SO:0001583	missense	22931	exon5			TAACTCCCAGCTA	AJ277145	CCDS7155.1, CCDS58073.1, CCDS73080.1, CCDS73081.1	10p12	2011-03-07			ENSG00000099246	ENSG00000099246		"RAB, member RAS oncogene"	14244	protein-coding gene	gene with protein product		602207				10648831	Standard	NM_021252		Approved		uc001itw.4	Q9NP72	OTTHUMG00000017861	ENST00000356940.6:c.224C>T	chr10.hg19:g.27821473C>T	ENSP00000349415:p.Pro75Leu	32.0	0.0		51.0	9.0	NM_001256410	B3KMC7|B7Z333|D3DRW1|Q53FX8|Q56UN9|Q6FIH1	Missense_Mutation	SNP	ENST00000356940.6	hg19	CCDS7155.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.165748	0.78339	.	.	ENSG00000099246	ENST00000356940;ENST00000540268	T	0.77229	-1.08	5.93	5.03	0.67393	Small GTP-binding protein domain (1);	.	.	.	.	D	0.86360	0.5914	M	0.69185	2.1	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.97110	1.0;1.0;0.974	D	0.87625	0.2512	9	0.72032	D	0.01	.	13.9572	0.64157	0.0:0.9277:0.0:0.0723	.	75;104;75	B7Z4P9;Q56UN9;Q9NP72	.;.;RAB18_HUMAN	L	75;53	ENSP00000349415:P75L	ENSP00000349415:P75L	P	+	2	0	RAB18	27861479	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	7.216000	0.77974	1.497000	0.48584	0.655000	0.94253	CCC	.	.		0.289	RAB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047326.2	NM_021252		T	27821473	C	T	27821473	3	4	321	1	0	0	0	0	1	0	0	0	12918	623	22	3	238	3	RAB18	10	27821473	Missense_Mutation	SNP	C	TCGA-MI-A75E-01A-11D-A32G-10	1363729	27821473	107713274	67	45198										
RBP3	5949	hgsc.bcm.edu	37	chr10	48381913	48381913	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	tggggcccttccctacaggtGgtcctgcaggcctgggctcc	14	15	0	0			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr10:48381913G>A	ENST00000224600.4	-	4	3849	c.3736C>T	c.(3736-3738)Cac>Tac	p.H1246Y		NM_002900.2	NP_002891.1	P10745	RET3_HUMAN	retinol binding protein 3, interstitial	1246					lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transport (GO:0006810)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|interphotoreceptor matrix (GO:0033165)|vesicle (GO:0031982)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(30)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59					Vitamin A(DB00162)	CCCTACAGGTGGTCCTGCAGG	0.652																																					p.H1246Y		Atlas-SNP	.											.	RBP3	152	.	0			c.C3736T						.						28	25	26					10																	48381913		2203	4300	6503	SO:0001583	missense	5949	exon4			ACAGGTGGTCCTG	M22453	CCDS73119.1	10q11.2	2014-05-06	2001-11-28		ENSG00000107618	ENSG00000265203			9921	protein-coding gene	gene with protein product		180290	"retinol-binding protein 3, interstitial"				Standard	NM_002900		Approved	D10S64, D10S65, D10S66, RP66	uc001jez.3	P10745	OTTHUMG00000188321	ENST00000224600.4:c.3736C>T	chr10.hg19:g.48381913G>A	ENSP00000224600:p.His1246Tyr	58.0	0.0		34.0	6.0	NM_002900	Q0QD34|Q5VSR0|Q8IXN0	Missense_Mutation	SNP	ENST00000224600.4	hg19	CCDS7218.1	.	.	.	.	.	.	.	.	.	.	G	11.42	1.633097	0.29068	.	.	ENSG00000107618	ENST00000224600	T	0.63744	-0.06	4.41	0.911	0.19343	.	1.796310	0.03632	N	0.238040	T	0.41789	0.1174	N	0.08118	0	0.09310	N	1	B	0.24483	0.104	B	0.17433	0.018	T	0.39482	-0.9612	10	0.72032	D	0.01	.	5.3732	0.16150	0.4354:0.0:0.5645:0.0	.	1246	P10745	RET3_HUMAN	Y	1246	ENSP00000224600:H1246Y	ENSP00000224600:H1246Y	H	-	1	0	RBP3	48001919	0.013000	0.17824	0.003000	0.11579	0.012000	0.07955	0.584000	0.23864	0.421000	0.25980	0.561000	0.74099	CAC	.	.		0.652	RBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047888.1	NM_002900		A	48381913	G	A	48381913	3	1	321	1	0	0	0	0	1	0	0	0	13172	1348	47	3	11	3	RBP3	10	48381913	Missense_Mutation	SNP	G	TCGA-MI-A75E-01A-11D-A32G-10	20560440	48381913	87152834	68	45199										
CDH23	64072	hgsc.bcm.edu	37	chr10	73562794	73562794	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	tgaccaggatgaaggtcccaAtggagagttgacctactcac	11	10	1	4			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr10:73562794A>G	ENST00000224721.6	+	53	7642	c.7637A>G	c.(7636-7638)aAt>aGt	p.N2546S	CDH23_ENST00000398788.3_Missense_Mutation_p.N301S|CDH23_ENST00000475158.1_3'UTR	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	2541	Cadherin 24. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						GAAGGTCCCAATGGAGAGTTG	0.602																																					p.N2541S		Atlas-SNP	.											.	CDH23	365	.	0			c.A7622G						.						81	86	84					10																	73562794		1995	4165	6160	SO:0001583	missense	64072	exon52			GTCCCAATGGAGA	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"Cadherins / Cadherin-related"	13733	protein-coding gene	gene with protein product	"cadherin-related family member 23"	605516	"cadherin related 23", "cadherin-like 23"	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.7637A>G	chr10.hg19:g.73562794A>G	ENSP00000224721:p.Asn2546Ser	53.0	0.0		68.0	11.0	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	hg19		.	.	.	.	.	.	.	.	.	.	A	22.6	4.306651	0.81247	.	.	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000224721;ENST00000398788	T	0.60040	0.22	5.02	5.02	0.67125	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.78929	0.4361	M	0.86651	2.83	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.91635	0.999;0.981	T	0.83239	-0.0059	10	0.72032	D	0.01	.	15.0383	0.71767	1.0:0.0:0.0:0.0	.	2541;2541	E9PEX1;Q9H251	.;CAD23_HUMAN	S	2546;2541;2544;301	ENSP00000381768:N301S	ENSP00000224721:N2546S	N	+	2	0	CDH23	73232800	1.000000	0.71417	0.924000	0.36721	0.732000	0.41865	8.800000	0.91900	2.016000	0.59253	0.450000	0.29827	AAT	.	.		0.602	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836		G	73562794	A	G	73562794	3	3	321	1	0	0	0	0	1	0	0	0	3110	101	4	2	8177	2	CDH23	10	73562794	Missense_Mutation	SNP	A	TCGA-MI-A75E-01A-11D-A32G-10	25180881	73562794	61971953	69	45200										
ANXA7	310	hgsc.bcm.edu	37	chr10	75147452	75147452	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	gaaagaaaaacataccttgcCataggaggtcttaaatgctg	9	7	1	1			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr10:75147452C>T	ENST00000372921.5	-	7	684	c.628G>A	c.(628-630)Ggc>Agc	p.G210S	ANXA7_ENST00000535178.1_Missense_Mutation_p.G80S|ANXA7_ENST00000492380.1_5'UTR	NM_001156.3	NP_001147.1	P20073	ANXA7_HUMAN	annexin A7	232					autophagy (GO:0006914)|cell proliferation (GO:0008283)|cellular calcium ion homeostasis (GO:0006874)|cellular water homeostasis (GO:0009992)|epithelial cell differentiation (GO:0030855)|hemostasis (GO:0007599)|membrane fusion (GO:0061025)|negative regulation of gene expression (GO:0010629)|regulation of cell shape (GO:0008360)|response to calcium ion (GO:0051592)|response to organic cyclic compound (GO:0014070)|response to salt stress (GO:0009651)|social behavior (GO:0035176)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|integrin binding (GO:0005178)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	26	Prostate(51;0.0119)					CATACCTTGCCATAGGAGGTC	0.443																																					p.G232S		Atlas-SNP	.											.	ANXA7	50	.	0			c.G694A						.						192	185	187					10																	75147452		2203	4300	6503	SO:0001583	missense	310	exon8			CCTTGCCATAGGA	J04543	CCDS7325.1, CCDS7326.1	10q22.2	2005-11-09			ENSG00000138279	ENSG00000138279		"Annexins"	545	protein-coding gene	gene with protein product		186360		ANX7		7515686	Standard	NM_001156		Approved		uc001jtz.2	P20073	OTTHUMG00000018463	ENST00000372921.5:c.628G>A	chr10.hg19:g.75147452C>T	ENSP00000362012:p.Gly210Ser	103.0	0.0		109.0	19.0	NM_004034	Q5F2H3|Q5T0M6|Q5T0M7	Missense_Mutation	SNP	ENST00000372921.5	hg19	CCDS7325.1	.	.	.	.	.	.	.	.	.	.	C	33	5.271714	0.95429	.	.	ENSG00000138279	ENST00000372921;ENST00000372919;ENST00000535178	T;T;T	0.04917	3.53;3.53;3.53	5.7	5.7	0.88788	Annexin repeat, conserved site (1);	0.000000	0.64402	D	0.000001	T	0.28699	0.0711	M	0.79926	2.475	0.58432	D	0.999996	D;D;D;D;D	0.89917	0.996;1.0;1.0;0.997;1.0	D;D;D;D;D	0.91635	0.988;0.999;0.994;0.98;0.993	T	0.00688	-1.1609	10	0.72032	D	0.01	.	17.3321	0.87268	0.0:1.0:0.0:0.0	.	210;210;137;210;232	Q53HM8;B2R7L2;B4DWU2;P20073-2;P20073	.;.;.;.;ANXA7_HUMAN	S	210;232;80	ENSP00000362012:G210S;ENSP00000362010:G232S;ENSP00000442864:G80S	ENSP00000362010:G232S	G	-	1	0	ANXA7	74817458	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	6.022000	0.70839	2.683000	0.91414	0.650000	0.86243	GGC	.	.		0.443	ANXA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048646.2	NM_001156		T	75147452	C	T	75147452	3	4	321	1	0	0	0	0	1	0	0	0	723	594	21	3	800	3	ANXA7	10	75147452	Missense_Mutation	SNP	C	TCGA-MI-A75E-01A-11D-A32G-10	1584658	75147452	60387295	70	45201										
TRPM5	29850	hgsc.bcm.edu	37	chr11	2429133	2429133	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	gtgggtgggtggagcagttcAcacgggcttctggaaagcaa	17	7	2	0			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr11:2429133A>T	ENST00000155858.6	-	19	2800	c.2792T>A	c.(2791-2793)gTg>gAg	p.V931E	AC124057.5_ENST00000433035.1_RNA|TRPM5_ENST00000533060.1_Missense_Mutation_p.V931E|TRPM5_ENST00000452833.1_Missense_Mutation_p.V933E|TRPM5_ENST00000528453.1_Missense_Mutation_p.V931E	NM_014555.3	NP_055370.1			transient receptor potential cation channel, subfamily M, member 5											breast(1)|central_nervous_system(1)|endometrium(4)|liver(1)|lung(8)|ovary(2)|prostate(2)|skin(2)|urinary_tract(2)	23		Medulloblastoma(188;0.0049)|Breast(177;0.00586)|all_epithelial(84;0.0075)|Ovarian(85;0.0256)|all_neural(188;0.0311)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|LUSC - Lung squamous cell carcinoma(625;0.191)		GGAGCAGTTCACACGGGCTTC	0.627																																					p.V931E	NSCLC(1;49 61 17205 18850 43201)	Atlas-SNP	.											.	TRPM5	86	.	0			c.T2792A						.						108	95	100					11																	2429133		2202	4299	6501	SO:0001583	missense	29850	exon19			CAGTTCACACGGG	AF177473	CCDS31340.1	11p15.5	2011-12-14			ENSG00000070985	ENSG00000070985		"Voltage-gated ion channels / Transient receptor potential cation channels"	14323	protein-coding gene	gene with protein product		604600				10607831, 16382100	Standard	NM_014555		Approved	LTRPC5, MTR1	uc001lwm.4	Q9NZQ8	OTTHUMG00000009896	ENST00000155858.6:c.2792T>A	chr11.hg19:g.2429133A>T	ENSP00000155858:p.Val931Glu	97.0	0.0		117.0	16.0	NM_014555		Missense_Mutation	SNP	ENST00000155858.6	hg19	CCDS31340.1	.	.	.	.	.	.	.	.	.	.	A	9.329	1.060166	0.19987	.	.	ENSG00000070985	ENST00000533881;ENST00000155858;ENST00000452833;ENST00000533060;ENST00000528453	T;T;T;T;T	0.71341	-0.56;-0.56;-0.56;-0.56;-0.56	3.56	3.56	0.40772	Ion transport (1);	0.494629	0.19916	U	0.103196	T	0.34861	0.0912	N	0.01576	-0.805	0.33515	D	0.591694	B;B;B	0.34103	0.128;0.437;0.371	B;B;B	0.34093	0.03;0.175;0.064	T	0.45862	-0.9232	10	0.08837	T	0.75	-24.4573	5.1953	0.15233	0.7714:0.0:0.2286:0.0	.	931;933;931	E9PRW0;Q9NZQ8-2;Q9NZQ8	.;.;TRPM5_HUMAN	E	925;931;933;931;931	ENSP00000434383:V925E;ENSP00000155858:V931E;ENSP00000387965:V933E;ENSP00000434121:V931E;ENSP00000436809:V931E	ENSP00000155858:V931E	V	-	2	0	TRPM5	2385709	0.991000	0.36638	0.965000	0.40720	0.312000	0.27988	3.305000	0.51873	1.418000	0.47098	0.379000	0.24179	GTG	.	.		0.627	TRPM5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000027378.1	NM_014555		T	2429133	A	T	2429133	3	4	321	1	0	0	0	0	1	0	0	0	16604	159	6	4	729	4	TRPM5	11	2429133	Missense_Mutation	SNP	A	TCGA-MI-A75E-01A-11D-A32G-10		2429133	132577383	71	45202										
GRM5	2915	hgsc.bcm.edu	37	chr11	88241917	88241917	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	gggacggcggggtgagagccAccagctcctccaggtctggc	17	13	1	1			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr11:88241917A>T	ENST00000305447.4	-	9	3631	c.3482T>A	c.(3481-3483)gTg>gAg	p.V1161E	GRM5_ENST00000455756.2_Missense_Mutation_p.V1129E|GRM5_ENST00000305432.5_Missense_Mutation_p.V1129E|GRM5-AS1_ENST00000526448.1_RNA|GRM5_ENST00000418177.2_Missense_Mutation_p.V1161E|GRM5-AS1_ENST00000531994.1_RNA|GRM5_ENST00000393297.1_Intron	NM_001143831.2	NP_001137303.1	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5	1161					activation of MAPKKK activity (GO:0000185)|cognition (GO:0050890)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|learning (GO:0007612)|locomotory behavior (GO:0007626)|negative regulation of locomotion (GO:0040013)|phospholipase C-activating G-protein coupled glutamate receptor signaling pathway (GO:0007206)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(1)|breast(5)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(18)|lung(40)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)|Rufinamide(DB06201)	GGTGAGAGCCACCAGCTCCTC	0.741																																					p.V1161E		Atlas-SNP	.											.	GRM5	414	.	0			c.T3482A						.						7	8	8					11																	88241917		2136	4250	6386	SO:0001583	missense	2915	exon9			AGAGCCACCAGCT	D28538	CCDS8283.1, CCDS44694.1	11q14.3	2014-06-12			ENSG00000168959	ENSG00000168959		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4597	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 86"	604102				7908515	Standard	NM_001143831		Approved	MGLUR5, GPRC1E, mGlu5, PPP1R86	uc001pcq.3	P41594	OTTHUMG00000134306	ENST00000305447.4:c.3482T>A	chr11.hg19:g.88241917A>T	ENSP00000306138:p.Val1161Glu	34.0	0.0		60.0	7.0	NM_001143831	Q6J164	Missense_Mutation	SNP	ENST00000305447.4	hg19	CCDS44694.1	.	.	.	.	.	.	.	.	.	.	A	13.64	2.296780	0.40594	.	.	ENSG00000168959	ENST00000418177;ENST00000455756;ENST00000305432;ENST00000305447	D;D;D;D	0.88818	-2.41;-2.43;-2.43;-2.41	4.89	4.89	0.63831	.	0.213164	0.39407	N	0.001363	T	0.79452	0.4448	N	0.19112	0.55	0.34315	D	0.685952	B;B	0.32829	0.386;0.272	B;B	0.26770	0.073;0.027	T	0.81951	-0.0698	9	.	.	.	.	14.5655	0.68173	1.0:0.0:0.0:0.0	.	1129;1161	P41594-2;P41594	.;GRM5_HUMAN	E	1161;1129;1129;1161	ENSP00000402912:V1161E;ENSP00000405690:V1129E;ENSP00000305905:V1129E;ENSP00000306138:V1161E	.	V	-	2	0	GRM5	87881565	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	8.850000	0.92190	1.827000	0.53221	0.456000	0.33151	GTG	.	.		0.741	GRM5-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259226.1	NM_000842		T	88241917	A	T	88241917	3	4	321	1	0	0	0	0	1	0	0	0	6809	159	6	4	160	4	GRM5	11	88241917	Missense_Mutation	SNP	A	TCGA-MI-A75E-01A-11D-A32G-10	85812784	88241917	46764599	72	45203										
FAT3	120114	hgsc.bcm.edu	37	chr11	92495075	92495075	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	cagtcaaccatttgggtggtGgttcaggttctagatgaaaa	12	6	3	2			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr11:92495075G>T	ENST00000298047.6	+	4	3740	c.3723G>T	c.(3721-3723)gtG>gtT	p.V1241V	FAT3_ENST00000409404.2_Silent_p.V1241V|FAT3_ENST00000525166.1_Silent_p.V1091V|RP11-203F8.1_ENST00000529884.1_RNA			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	1241	Cadherin 11. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				TTTGGGTGGTGGTTCAGGTTC	0.458										TCGA Ovarian(4;0.039)																											p.V1241V		Atlas-SNP	.											.	FAT3	1822	.	0			c.G3723T						.						191	183	186					11																	92495075		1908	4123	6031	SO:0001819	synonymous_variant	120114	exon4			GGTGGTGGTTCAG	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.3723G>T	chr11.hg19:g.92495075G>T		64.0	0.0		77.0	12.0	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	hg19																																																																																				.	.		0.458	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		T	92495075	G	T	92495075	2	4	321	1	0	0	0	0	0	0	0	1	5699	1335	47	3		3	FAT3	11	92495075	Silent	SNP	G	TCGA-MI-A75E-01A-11D-A32G-10	4253158	92495075	42511441	73	45204										
CEP57	9702	hgsc.bcm.edu	37	chr11	95546100	95546100	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	tgtttgtatttggcagccatAttttctgctcttaagaatct	7	7	3	1			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr11:95546100A>G	ENST00000325542.5	+	3	445	c.207A>G	c.(205-207)atA>atG	p.I69M	CEP57_ENST00000537677.1_Missense_Mutation_p.I42M|CEP57_ENST00000541150.1_Missense_Mutation_p.I60M|CEP57_ENST00000536587.1_3'UTR|CEP57_ENST00000325486.5_Missense_Mutation_p.I69M|CEP57_ENST00000538658.1_Missense_Mutation_p.I69M	NM_001243776.1|NM_014679.4	NP_001230705.1|NP_055494.2	Q86XR8	CEP57_HUMAN	centrosomal protein 57kDa	69	centrosome localization domain (CLD). {ECO:0000250}.				fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|mitotic cell cycle (GO:0000278)|protein homooligomerization (GO:0051260)|protein import into nucleus, translocation (GO:0000060)|spermatid development (GO:0007286)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	fibroblast growth factor binding (GO:0017134)|protein homodimerization activity (GO:0042803)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	13		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				TGGCAGCCATATTTTCTGCTC	0.343									Mosaic Variegated Aneuploidy Syndrome																												p.I69M		Atlas-SNP	.											.	CEP57	40	.	0			c.A207G						.						89	92	91					11																	95546100		2201	4298	6499	SO:0001583	missense	9702	exon3	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	AGCCATATTTTCT	D42054	CCDS8304.1, CCDS58166.1, CCDS58167.1	11q21	2014-09-17			ENSG00000166037	ENSG00000166037			30794	protein-coding gene	gene with protein product		607951				7788527	Standard	NM_014679		Approved	Translokin, TSP57, KIAA0092	uc001pfp.2	Q86XR8	OTTHUMG00000167740	ENST00000325542.5:c.207A>G	chr11.hg19:g.95546100A>G	ENSP00000317902:p.Ile69Met	111.0	0.0		124.0	17.0	NM_001243777	A0PJH1|A8K5D0|B4DDP5|F5H5F7|Q14704|Q5JB46|Q8IXP0|Q9BVF9	Missense_Mutation	SNP	ENST00000325542.5	hg19	CCDS8304.1	.	.	.	.	.	.	.	.	.	.	A	17.64	3.440347	0.63067	.	.	ENSG00000166037	ENST00000537677;ENST00000325542;ENST00000325486;ENST00000544522;ENST00000541365;ENST00000538658;ENST00000541150	T;T;T;T;T;T;T	0.51325	0.71;0.71;0.71;0.71;0.71;0.71;0.71	5.98	0.698	0.18087	.	0.000000	0.85682	D	0.000000	T	0.58609	0.2134	L	0.56769	1.78	0.38707	D	0.953111	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.91635	0.997;0.982;0.999;0.997	T	0.58375	-0.7647	10	0.87932	D	0	-11.7024	7.8807	0.29621	0.4217:0.1194:0.0:0.459	.	60;69;69;69	F5H5F7;Q86XR8-2;Q86XR8;Q86XR8-3	.;.;CEP57_HUMAN;.	M	42;69;69;60;42;69;60	ENSP00000441392:I42M;ENSP00000317902:I69M;ENSP00000317487:I69M;ENSP00000438065:I60M;ENSP00000445821:I42M;ENSP00000445706:I69M;ENSP00000443436:I60M	ENSP00000317487:I69M	I	+	3	3	CEP57	95185748	1.000000	0.71417	0.997000	0.53966	0.949000	0.60115	0.942000	0.29017	-0.129000	0.11620	-0.468000	0.05107	ATA	.	.		0.343	CEP57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395983.1	NM_014679		G	95546100	A	G	95546100	3	3	321	1	0	0	0	0	1	0	0	0	3258	439	16	2	217	2	CEP57	11	95546100	Missense_Mutation	SNP	A	TCGA-MI-A75E-01A-11D-A32G-10	3051025	95546100	39460416	74	45205										
FAM55A	120400	hgsc.bcm.edu	37	chr11	114398621	114398621	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	tcatttcaactcccactttgGaccttcaaaaaaaaaataga	3	10	3	1			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr11:114398621G>T	ENST00000424269.1	-	3	835	c.836C>A	c.(835-837)tCc>tAc	p.S279Y	NXPE1_ENST00000251921.2_Missense_Mutation_p.S137Y|NXPE1_ENST00000536271.1_5'UTR|snoU13_ENST00000459372.1_RNA|NXPE1_ENST00000536312.1_Silent_p.V291V			Q8N323	NXPE1_HUMAN	neurexophilin and PC-esterase domain family, member 1	279						extracellular region (GO:0005576)											TCCCACTTTGGACCTTCAAAA	0.378																																					p.S137Y		Atlas-SNP	.											.	NXPE1	8	.	0			c.C410A						.						111	91	98					11																	114398621		2201	4296	6497	SO:0001583	missense	120400	exon4			ACTTTGGACCTTC	BC029049	CCDS8372.1	11q23.2	2012-06-14	2012-06-11	2012-06-11	ENSG00000095110	ENSG00000095110			28527	protein-coding gene	gene with protein product			"family with sequence similarity 55, member A"	FAM55A		12477932	Standard	NM_152315		Approved	MGC34290	uc001ppa.3	Q8N323	OTTHUMG00000168284	ENST00000424269.1:c.836C>A	chr11.hg19:g.114398621G>T	ENSP00000411690:p.Ser279Tyr	93.0	0.0		92.0	15.0	NM_152315	B0YJ13	Missense_Mutation	SNP	ENST00000424269.1	hg19		.	.	.	.	.	.	.	.	.	.	G	15.99	2.995531	0.54147	.	.	ENSG00000095110	ENST00000251921;ENST00000424269	T;T	0.15834	2.39;2.58	3.37	2.44	0.29823	.	0.431903	0.18735	N	0.132612	T	0.26195	0.0639	M	0.86953	2.85	0.30941	N	0.72587	.	.	.	.	.	.	T	0.34054	-0.9844	8	0.02654	T	1	.	10.107	0.42539	0.0:0.0:0.798:0.202	.	.	.	.	Y	137;279	ENSP00000251921:S137Y;ENSP00000411690:S279Y	ENSP00000251921:S137Y	S	-	2	0	FAM55A	113903831	1.000000	0.71417	0.999000	0.59377	0.427000	0.31564	1.319000	0.33655	0.964000	0.38108	-0.188000	0.12872	TCC	.	.		0.378	NXPE1-201	KNOWN	basic	protein_coding	protein_coding		NM_152315		T	114398621	G	T	114398621	3	4	321	1	0	0	0	0	1	0	0	0	5592	1174	41	3	819	3	FAM55A	11	114398621	Missense_Mutation	SNP	G	TCGA-MI-A75E-01A-11D-A32G-10	18852521	114398621	20607895	75	45206										
IL10RA	3587	hgsc.bcm.edu	37	chr11	117869720	117869720	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	agtagtggcagcagcaatagCacagacagcgggatctgcct	13	10	1	1			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr11:117869720C>T	ENST00000227752.3	+	7	1221	c.1101C>T	c.(1099-1101)agC>agT	p.S367S	IL10RA_ENST00000545409.1_Silent_p.S218S|IL10RA_ENST00000541785.1_Silent_p.S347S|IL10RA_ENST00000533700.1_3'UTR	NM_001558.3	NP_001549.2	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha	367					cytokine-mediated signaling pathway (GO:0019221)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-10 receptor activity (GO:0004920)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(2)|prostate(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.07e-05)|Epithelial(105;0.00108)		GCAGCAATAGCACAGACAGCG	0.652																																					p.S367S		Atlas-SNP	.											.	IL10RA	46	.	0			c.C1101T						.						29	31	31					11																	117869720		2200	4296	6496	SO:0001819	synonymous_variant	3587	exon7			CAATAGCACAGAC	U00672	CCDS8388.1	11q23	2014-09-17			ENSG00000110324	ENSG00000110324		"Interleukins and interleukin receptors", "CD molecules"	5964	protein-coding gene	gene with protein product		146933		IL10R		8120391	Standard	NR_026691		Approved	HIL-10R, CDW210A, CD210a, CD210	uc001prv.3	Q13651	OTTHUMG00000166523	ENST00000227752.3:c.1101C>T	chr11.hg19:g.117869720C>T		54.0	0.0		38.0	9.0	NM_001558	A8K6I0|B0YJ27	Silent	SNP	ENST00000227752.3	hg19	CCDS8388.1																																																																																			.	.		0.652	IL10RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390167.1			T	117869720	C	T	117869720	2	4	321	1	0	0	0	0	0	0	0	1	7629	709	25	3		3	IL10RA	11	117869720	Silent	SNP	C	TCGA-MI-A75E-01A-11D-A32G-10	3471099	117869720	17136796	76	45207										
PANX3	116337	hgsc.bcm.edu	37	chr11	124489603	124489603	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	tttgatctcctcagcagaaaGatgctaggatgtcccatcaa	8	10	3	3			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr11:124489603G>C	ENST00000284288.2	+	4	1018	c.951G>C	c.(949-951)aaG>aaC	p.K317N		NM_052959.2	NP_443191.1	Q96QZ0	PANX3_HUMAN	pannexin 3	317					cell-cell signaling (GO:0007267)|ion transport (GO:0006811)|protein hexamerization (GO:0034214)|transmembrane transport (GO:0055085)	gap junction (GO:0005921)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gap junction hemi-channel activity (GO:0055077)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(10)|prostate(2)|skin(2)|urinary_tract(1)	26	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0219)		TCAGCAGAAAGATGCTAGGAT	0.448																																					p.K317N		Atlas-SNP	.											.	PANX3	52	.	0			c.G951C						.						158	142	147					11																	124489603		2201	4299	6500	SO:0001583	missense	116337	exon4			CAGAAAGATGCTA	AF406650	CCDS8447.1	11q24.2	2011-12-02			ENSG00000154143	ENSG00000154143		"Ion channels / Pannexins"	20573	protein-coding gene	gene with protein product		608422					Standard	NM_052959		Approved	Px3	uc001qah.3	Q96QZ0	OTTHUMG00000165925	ENST00000284288.2:c.951G>C	chr11.hg19:g.124489603G>C	ENSP00000284288:p.Lys317Asn	125.0	0.0		124.0	22.0	NM_052959		Missense_Mutation	SNP	ENST00000284288.2	hg19	CCDS8447.1	.	.	.	.	.	.	.	.	.	.	G	15.52	2.856474	0.51376	.	.	ENSG00000154143	ENST00000284288	T	0.19669	2.13	5.5	-1.51	0.08664	.	0.096756	0.64402	D	0.000002	T	0.23649	0.0572	M	0.62723	1.935	0.32447	N	0.545887	D	0.60575	0.988	P	0.46479	0.518	T	0.42716	-0.9435	10	0.56958	D	0.05	-16.777	11.55	0.50715	0.4919:0.0:0.5081:0.0	.	317	Q96QZ0	PANX3_HUMAN	N	317	ENSP00000284288:K317N	ENSP00000284288:K317N	K	+	3	2	PANX3	123994813	1.000000	0.71417	0.994000	0.49952	0.959000	0.62525	0.578000	0.23773	-0.160000	0.11002	0.561000	0.74099	AAG	.	.		0.448	PANX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387064.1			C	124489603	G	C	124489603	3	2	321	1	0	0	0	0	1	0	0	0	11431	933	33	4	965	4	PANX3	11	124489603	Missense_Mutation	SNP	G	TCGA-MI-A75E-01A-11D-A32G-10	6619883	124489603	10516913	77	45208										
JAM3	83700	hgsc.bcm.edu	37	chr11	134014256	134014256	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	tcgaaatgaccgcaaggaaaTtgatgagattgtgatcgagt	12	5	0	4			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr11:134014256T>C	ENST00000299106.4	+	4	536	c.377T>C	c.(376-378)aTt>aCt	p.I126T	JAM3_ENST00000524969.1_3'UTR|JAM3_ENST00000441717.3_Intron|JAM3_ENST00000529443.2_Missense_Mutation_p.I171T			Q9BX67	JAM3_HUMAN	junctional adhesion molecule 3	126	Ig-like V-type.				adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|establishment of cell polarity (GO:0030010)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|myelination (GO:0042552)|myeloid progenitor cell differentiation (GO:0002318)|neutrophil homeostasis (GO:0001780)|regulation of actin cytoskeleton organization by cell-cell adhesion (GO:0090138)|regulation of neutrophil chemotaxis (GO:0090022)|spermatid development (GO:0007286)|transmission of nerve impulse (GO:0019226)	cell-cell contact zone (GO:0044291)|desmosome (GO:0030057)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|paranodal junction (GO:0033010)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	integrin binding (GO:0005178)			breast(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)	10	all_hematologic(175;0.127)	all_cancers(12;1.06e-21)|all_epithelial(12;3.37e-16)|all_lung(97;7.03e-06)|Lung NSC(97;1.67e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0506)|Esophageal squamous(93;0.0566)		Epithelial(10;1.55e-09)|BRCA - Breast invasive adenocarcinoma(10;1.35e-08)|all cancers(11;2.81e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00402)|Lung(977;0.245)		CGCAAGGAAATTGATGAGATT	0.473																																					p.I126T		Atlas-SNP	.											.	JAM3	41	.	0			c.T377C						.						186	152	163					11																	134014256		2201	4297	6498	SO:0001583	missense	83700	exon4			AGGAAATTGATGA	AF356518	CCDS8494.1, CCDS55799.1, CCDS8494.2	11q25	2013-01-29			ENSG00000166086	ENSG00000166086		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15532	protein-coding gene	gene with protein product		606871					Standard	NM_032801		Approved	JAM-C, JAMC	uc001qhb.3	Q9BX67	OTTHUMG00000167130	ENST00000299106.4:c.377T>C	chr11.hg19:g.134014256T>C	ENSP00000299106:p.Ile126Thr	65.0	0.0		64.0	7.0	NM_032801	B3KWG9|Q8WWL8|Q96FL1	Missense_Mutation	SNP	ENST00000299106.4	hg19	CCDS8494.2	.	.	.	.	.	.	.	.	.	.	T	16.22	3.061268	0.55432	.	.	ENSG00000166086	ENST00000299106	.	.	.	5.03	5.03	0.67393	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.326123	0.32372	N	0.006189	T	0.33904	0.0879	L	0.51422	1.61	0.27547	N	0.950611	P	0.40731	0.728	B	0.37833	0.259	T	0.21655	-1.0239	9	0.19590	T	0.45	.	10.2363	0.43286	0.0:0.0:0.1659:0.8341	.	126	Q9BX67	JAM3_HUMAN	T	171	.	ENSP00000299106:I171T	I	+	2	0	JAM3	133519466	0.986000	0.35501	1.000000	0.80357	0.856000	0.48823	3.980000	0.56895	1.905000	0.55150	0.459000	0.35465	ATT	.	.		0.473	JAM3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000393303.4	NM_032801		C	134014256	T	C	134014256	3	2	321	1	0	0	0	0	1	0	0	0	7953	1493	52	2	526	2	JAM3	11	134014256	Missense_Mutation	SNP	T	TCGA-MI-A75E-01A-11D-A32G-10	9524653	134014256	992260	78	45209										
CACNA1C	775	hgsc.bcm.edu	37	chr12	2794935	2794935	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	gatgacgaaaatcggcaactGacgctcccagaggaggacaa	12	10	0	3			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr12:2794935G>A	ENST00000347598.4	+	46	5751	c.5751G>A	c.(5749-5751)ctG>ctA	p.L1917L	CACNA1C_ENST00000335762.5_Silent_p.L1894L|CACNA1C_ENST00000399606.1_Silent_p.L1889L|CACNA1C_ENST00000406454.3_Silent_p.L1940L|CACNA1C_ENST00000399629.1_Silent_p.L1886L|CACNA1C_ENST00000399621.1_Silent_p.L1888L|CACNA1C_ENST00000399591.1_Silent_p.L1877L|CACNA1C_ENST00000399634.1_Silent_p.L1940L|CACNA1C_ENST00000399649.1_Silent_p.L1875L|CACNA1C_ENST00000399655.1_Silent_p.L1869L|CACNA1C_ENST00000399637.1_Silent_p.L1888L|CACNA1C_ENST00000399617.1_Silent_p.L1904L|CACNA1C_ENST00000399641.1_Silent_p.L1869L|CACNA1C_ENST00000399644.1_Silent_p.L1869L|CACNA1C_ENST00000399595.1_Silent_p.L1877L|CACNA1C_ENST00000399603.1_Silent_p.L1869L|CACNA1C-AS1_ENST00000501371.1_RNA|CACNA1C_ENST00000399601.1_Silent_p.L1869L|CACNA1C_ENST00000402845.3_Silent_p.L1888L|CACNA1C_ENST00000399638.1_Silent_p.L1897L|CACNA1C_ENST00000327702.7_Silent_p.L1904L|CACNA1C_ENST00000344100.3_Silent_p.L1910L|CACNA1C_ENST00000399597.1_Silent_p.L1869L	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	1952					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	ATCGGCAACTGACGCTCCCAG	0.587																																					p.L1952L		Atlas-SNP	.											.	CACNA1C	1023	.	0			c.G5856A						.						49	50	49					12																	2794935		2012	4159	6171	SO:0001819	synonymous_variant	775	exon47			GCAACTGACGCTC	AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.5751G>A	chr12.hg19:g.2794935G>A		129.0	0.0		125.0	22.0	NM_199460	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Silent	SNP	ENST00000347598.4	hg19	CCDS44788.1																																																																																			.	.		0.587	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719		A	2794935	G	A	2794935	2	1	321	1	0	0	0	0	0	0	0	1	2542	1277	45	3		3	CACNA1C	12	2794935	Silent	SNP	G	TCGA-MI-A75E-01A-11D-A32G-10		2794935	131056960	79	45210										
ABCC9	10060	hgsc.bcm.edu	37	chr12	21995268	21995268	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	ttagaggcaacccgaaagtaTttctggataaaataaaaggc	9	6	1	1			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr12:21995268T>G	ENST00000261201.4	-	27	3452	c.3453A>C	c.(3451-3453)aaA>aaC	p.K1151N	RP11-729I10.2_ENST00000539874.1_RNA|ABCC9_ENST00000261200.4_Missense_Mutation_p.K1151N|ABCC9_ENST00000345162.2_Missense_Mutation_p.K1115N	NM_005691.2	NP_005682.2	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	1151	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				defense response to virus (GO:0051607)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	ATP-sensitive potassium channel complex (GO:0008282)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcomere (GO:0030017)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|sulfonylurea receptor activity (GO:0008281)|transporter activity (GO:0005215)			NS(2)|breast(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|lung(56)|ovary(4)|pancreas(1)|prostate(4)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(5)	118					Adenosine triphosphate(DB00171)|Glyburide(DB01016)	CCCGAAAGTATTTCTGGATAA	0.448																																					p.K1151N		Atlas-SNP	.											.	ABCC9	411	.	0			c.A3453C						.						94	86	89					12																	21995268		2203	4300	6503	SO:0001583	missense	10060	exon27			AAAGTATTTCTGG	AF061323	CCDS8693.1, CCDS8694.1	12p12.1	2014-09-17			ENSG00000069431	ENSG00000069431		"ATP binding cassette transporters / subfamily C"	60	protein-coding gene	gene with protein product	"sulfonylurea receptor 2"	601439				9457174, 15034580	Standard	NM_020297		Approved	SUR2, CMD1O	uc001rfh.3	O60706	OTTHUMG00000169094	ENST00000261201.4:c.3453A>C	chr12.hg19:g.21995268T>G	ENSP00000261201:p.Lys1151Asn	49.0	0.0		54.0	13.0	NM_005691	O60707	Missense_Mutation	SNP	ENST00000261201.4	hg19	CCDS8694.1	.	.	.	.	.	.	.	.	.	.	T	18.39	3.614525	0.66672	.	.	ENSG00000069431	ENST00000261200;ENST00000544039;ENST00000261201;ENST00000345162	D;D;D;D	0.90133	-2.62;-2.62;-2.62;-2.62	5.15	3.99	0.46301	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.91432	0.7296	L	0.45228	1.405	0.48341	D	0.999631	D;P	0.59357	0.985;0.955	P;P	0.61477	0.889;0.649	D	0.90389	0.4394	10	0.49607	T	0.09	-21.0374	11.0283	0.47757	0.0:0.0732:0.0:0.9268	.	1151;1151	O60706;O60706-2	ABCC9_HUMAN;.	N	1151;778;1151;1115	ENSP00000261200:K1151N;ENSP00000440521:K778N;ENSP00000261201:K1151N;ENSP00000261202:K1115N	ENSP00000261200:K1151N	K	-	3	2	ABCC9	21886535	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	3.101000	0.50283	0.968000	0.38212	0.460000	0.39030	AAA	.	.		0.448	ABCC9-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402230.1	NM_005691		G	21995268	T	G	21995268	3	3	321	1	0	0	0	0	1	0	0	0	59	1490	52	5	1386	5	ABCC9	12	21995268	Missense_Mutation	SNP	T	TCGA-MI-A75E-01A-11D-A32G-10	19200333	21995268	111856627	80	45211										
SYT10	341359	hgsc.bcm.edu	37	chr12	33592330	33592330	+	Frame_Shift_Del	DEL	C	C	-													0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	tgctgcttccgccctggctgCccctgtcccgagggaagatg					rs561584640		TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr12:33592330delC	ENST00000228567.3	-	1	424	c.128delG	c.(127-129)ggcfs	p.G43fs	SYT10_ENST00000535526.1_5'UTR	NM_198992.3	NP_945343.1	Q6XYQ8	SYT10_HUMAN	synaptotagmin X	43					regulation of calcium ion-dependent exocytosis (GO:0017158)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(3)|skin(4)|urinary_tract(1)	42	Lung NSC(5;8.37e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0334)					GCCCTGGCTGCCCCTGTCCCG	0.682																																					p.G43fs		Atlas-Indel,Pindel	.											.	SYT10	109	.	0			c.129delC						.						106	104	105					12																	33592330		2203	4300	6503	SO:0001589	frameshift_variant	341359	exon1			.	AY198413	CCDS8732.1	12p11	2013-01-21			ENSG00000110975	ENSG00000110975		"Synaptotagmins"	19266	protein-coding gene	gene with protein product							Standard	NM_198992		Approved		uc001rll.1	Q6XYQ8	OTTHUMG00000169269	ENST00000228567.3:c.128delG	chr12.hg19:g.33592330delC	ENSP00000228567:p.Gly43fs	52.0	0.0		53.0	13.0	NM_198992	Q495U2	Frame_Shift_Del	DEL	ENST00000228567.3	hg19	CCDS8732.1																																																																																			.	.		0.682	SYT10-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403222.1	NM_198992		-	33592330	C	-	33592330	7	5	321	1	0	1	0	1	0	0	0	0	15481	739	26	0	1471	0	SYT10	12	33592330	Frame_Shift_Del	DEL	C	TCGA-MI-A75E-01A-11D-A32G-10	11597062	33592330	100259565	81	45212										
STAT2	6773	hgsc.bcm.edu	37	chr12	56742763	56742763	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	gagttgaggcctcggccaacAtaggaggagaactgccaact	13	10	0	2			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr12:56742763A>G	ENST00000314128.4	-	17	1544	c.1521T>C	c.(1519-1521)taT>taC	p.Y507Y	STAT2_ENST00000557235.1_Silent_p.Y503Y|STAT2_ENST00000556539.1_5'UTR			P52630	STAT2_HUMAN	signal transducer and activator of transcription 2, 113kDa	507					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|skin(3)	31						CTCGGCCAACATAGGAGGAGA	0.567																																					p.Y507Y		Atlas-SNP	.											.	STAT2	70	.	0			c.T1521C						.						71	72	72					12																	56742763		2203	4300	6503	SO:0001819	synonymous_variant	6773	exon17			GCCAACATAGGAG	BC051284	CCDS8917.1, CCDS55836.1	12q13.2	2013-02-14	2002-08-29			ENSG00000170581		"SH2 domain containing"	11363	protein-coding gene	gene with protein product		600556	"signal transducer and activator of transcription 2, 113kD"			7885841	Standard	NM_005419		Approved	STAT113	uc001slc.3	P52630		ENST00000314128.4:c.1521T>C	chr12.hg19:g.56742763A>G		27.0	0.0		43.0	6.0	NM_005419	B4DLC7|G3V2M6|Q16430|Q16431|Q9UDL4	Silent	SNP	ENST00000314128.4	hg19	CCDS8917.1																																																																																			.	.		0.567	STAT2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410277.1	NM_005419		G	56742763	A	G	56742763	2	3	321	1	0	0	0	0	0	0	0	1	15280	224	8	2		2	STAT2	12	56742763	Silent	SNP	A	TCGA-MI-A75E-01A-11D-A32G-10	23150433	56742763	77109132	82	45213										
MDM1	56890	hgsc.bcm.edu	37	chr12	68719226	68719226	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	catccattaagctacctgatTggctgcaaaagctggagcag	10	10	0	1	rs374381882		TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr12:68719226T>C	ENST00000303145.7	-	4	714	c.628A>G	c.(628-630)Aat>Gat	p.N210D	MDM1_ENST00000545724.1_5'UTR|MDM1_ENST00000411698.2_Intron|MDM1_ENST00000393543.3_3'UTR|MDM1_ENST00000430606.2_3'UTR|MDM1_ENST00000540418.1_5'UTR	NM_017440.4	NP_059136.2	Q8TC05	MDM1_HUMAN	Mdm1 nuclear protein homolog (mouse)	210					retina development in camera-type eye (GO:0060041)	nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|ovary(3)|pancreas(1)|prostate(2)|skin(7)	33			Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000174)		GCTACCTGATTGGCTGCAAAA	0.323																																					p.N210D		Atlas-SNP	.											.	MDM1	74	.	0			c.A628G						.	T	,,,ASP/ASN	1,4405	2.1+/-5.4	0,1,2202	118	130	126		,,,628	1.1	1	12		126	0,8600		0,0,4300	no	intron,utr-3,utr-3,missense	MDM1	NM_001205028.1,NM_001205029.1,NM_020128.2,NM_017440.4	,,,23	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	,,,benign	,,,210/715	68719226	1,13005	2203	4300	6503	SO:0001583	missense	56890	exon4			CCTGATTGGCTGC	AF007130	CCDS8983.1, CCDS44938.1, CCDS55841.1, CCDS55842.1	12q15	2008-04-14	2008-04-14			ENSG00000111554			29917	protein-coding gene	gene with protein product		613813	"Mdm4, transformed 3T3 cell double minute 1, p53 binding protein (mouse)"			8619474, 9110174	Standard	NM_017440		Approved		uc001stz.2	Q8TC05		ENST00000303145.7:c.628A>G	chr12.hg19:g.68719226T>C	ENSP00000302537:p.Asn210Asp	122.0	0.0		130.0	16.0	NM_017440	B4DM65|E7EPQ3|O43406|Q8WTV9|Q9NR04	Missense_Mutation	SNP	ENST00000303145.7	hg19	CCDS8983.1	.	.	.	.	.	.	.	.	.	.	T	9.255	1.041623	0.19748	2.27E-4	0.0	ENSG00000111554	ENST00000303145;ENST00000541686	T;T	0.20463	2.07;2.07	5.29	1.12	0.20585	.	0.499339	0.22696	N	0.056747	T	0.12774	0.0310	L	0.39898	1.24	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.12502	-1.0545	9	.	.	.	-7.1741	3.6246	0.08108	0.0:0.2096:0.4986:0.2918	.	210	Q8TC05	MDM1_HUMAN	D	210;205	ENSP00000302537:N210D;ENSP00000446000:N205D	.	N	-	1	0	MDM1	67005493	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	1.482000	0.35486	0.384000	0.24942	0.459000	0.35465	AAT	.	.		0.323	MDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402402.1	NM_020128		C	68719226	T	C	68719226	3	2	321	1	0	0	0	0	1	0	0	0	9421	1812	63	2	1560	2	MDM1	12	68719226	Missense_Mutation	SNP	T	TCGA-MI-A75E-01A-11D-A32G-10	11976463	68719226	65132669	83	45214										
SACS	26278	hgsc.bcm.edu	37	chr13	23911712	23911712	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	accaaaggatgcccctccaaGgaacaaggaatacatggagt	10	10	0	0			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr13:23911712G>T	ENST00000382292.3	-	9	6576	c.6303C>A	c.(6301-6303)tcC>tcA	p.S2101S	SACS_ENST00000402364.1_Silent_p.S1351S|SACS_ENST00000382298.3_Silent_p.S2101S			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	2101					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		GCCCCTCCAAGGAACAAGGAA	0.398																																					p.S2101S		Atlas-SNP	.											.	SACS	871	.	0			c.C6303A						.						61	61	61					13																	23911712		2203	4299	6502	SO:0001819	synonymous_variant	26278	exon10			CTCCAAGGAACAA	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.6303C>A	chr13.hg19:g.23911712G>T		57.0	0.0		62.0	12.0	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	hg19	CCDS9300.2																																																																																			.	.		0.398	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		T	23911712	G	T	23911712	2	4	321	1	0	0	0	0	0	0	0	1	13819	987	35	3		3	SACS	13	23911712	Silent	SNP	G	TCGA-MI-A75E-01A-11D-A32G-10		23911712	91258166	84	45215										
PABPC3	5042	hgsc.bcm.edu	37	chr13	25671982	25671982	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	ctccaggttggcatctgcccCtcctcaaaagcaaaagcaaa	7	14	2	0			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr13:25671982C>A	ENST00000281589.3	+	1	1683	c.1646C>A	c.(1645-1647)cCt>cAt	p.P549H		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	549	PABC. {ECO:0000255|PROSITE- ProRule:PRU00641}.				mRNA metabolic process (GO:0016071)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		GCATCTGCCCCTCCTCAAAAG	0.473																																					p.P549H		Atlas-SNP	.											.	PABPC3	129	.	0			c.C1646A						.						109	99	102					13																	25671982		2203	4300	6503	SO:0001583	missense	5042	exon1			CTGCCCCTCCTCA	AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"RNA binding motif (RRM) containing"	8556	protein-coding gene	gene with protein product	"testis PABP"	604680	"poly(A)-binding protein, cytoplasmic 3"	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	ENST00000281589.3:c.1646C>A	chr13.hg19:g.25671982C>A	ENSP00000281589:p.Pro549His	73.0	0.0		72.0	17.0	NM_030979	Q8NHV0|Q9H086	Missense_Mutation	SNP	ENST00000281589.3	hg19	CCDS9311.1	.	.	.	.	.	.	.	.	.	.	C	10.19	1.281984	0.23392	.	.	ENSG00000151846	ENST00000281589	T	0.48522	0.81	0.875	0.875	0.19130	Polyadenylate-binding protein/Hyperplastic disc protein (5);	0.135250	0.32161	U	0.006500	T	0.68485	0.3006	M	0.93283	3.4	0.51233	D	0.999919	D	0.56287	0.975	P	0.62298	0.9	T	0.71642	-0.4531	10	0.87932	D	0	.	7.5489	0.27783	0.0:1.0:0.0:0.0	.	549	Q9H361	PABP3_HUMAN	H	549	ENSP00000281589:P549H	ENSP00000281589:P549H	P	+	2	0	PABPC3	24569982	1.000000	0.71417	0.991000	0.47740	0.020000	0.10135	5.265000	0.65519	0.759000	0.33084	0.313000	0.20887	CCT	.	.		0.473	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979		A	25671982	C	A	25671982	3	1	321	1	0	0	0	0	1	0	0	0	11374	681	24	3	1648	3	PABPC3	13	25671982	Missense_Mutation	SNP	C	TCGA-MI-A75E-01A-11D-A32G-10	1760270	25671982	89497896	85	45216										
MYCBP2	23077	hgsc.bcm.edu	37	chr13	77750664	77750664	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	cactttgtcaagtctgatctCagctatatcactgggtgagt	9	9	4	2			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr13:77750664C>A	ENST00000544440.2	-	36	5343	c.5326G>T	c.(5326-5328)Gag>Tag	p.E1776*	MYCBP2_ENST00000360084.5_5'UTR|MYCBP2_ENST00000407578.2_Nonsense_Mutation_p.E1814*|MYCBP2_ENST00000357337.6_Nonsense_Mutation_p.E1776*					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		AGTCTGATCTCAGCTATATCA	0.378																																					p.E1814X		Atlas-SNP	.											.	MYCBP2	1029	.	0			c.G5440T						.						158	135	143					13																	77750664		2203	4300	6503	SO:0001587	stop_gained	23077	exon36			TGATCTCAGCTAT	AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"MYC binding protein 2"			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.5326G>T	chr13.hg19:g.77750664C>A	ENSP00000444596:p.Glu1776*	93.0	0.0		93.0	15.0	NM_015057		Nonsense_Mutation	SNP	ENST00000544440.2	hg19		.	.	.	.	.	.	.	.	.	.	C	46	12.823792	0.99699	.	.	ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440	.	.	.	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	19.0877	0.93212	0.0:1.0:0.0:0.0	.	.	.	.	X	1776;1814;1776	.	ENSP00000349892:E1776X	E	-	1	0	MYCBP2	76648665	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.818000	0.86416	2.593000	0.87608	0.655000	0.94253	GAG	.	.		0.378	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057		A	77750664	C	A	77750664	4	1	321	1	0	0	0	0	0	1	0	0	10027	835	29	3	8788	3	MYCBP2	13	77750664	Nonsense_Mutation	SNP	C	TCGA-MI-A75E-01A-11D-A32G-10	52078682	77750664	37419214	86	45217										
NYNRIN	57523	hgsc.bcm.edu	37	chr14	24878595	24878595	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	tcaaggggggctgacagatcAgtcagtacctggagctcaaa	13	9	4	2			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr14:24878595A>G	ENST00000382554.3	+	4	1913	c.1595A>G	c.(1594-1596)cAg>cGg	p.Q532R		NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	532					DNA integration (GO:0015074)	integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(8)|lung(21)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	56						CTGACAGATCAGTCAGTACCT	0.552																																					p.Q532R		Atlas-SNP	.											.	NYNRIN	120	.	0			c.A1595G						.						37	40	39					14																	24878595		2022	4178	6200	SO:0001583	missense	57523	exon4			CAGATCAGTCAGT	AB037726	CCDS45090.1	14q11.2	2009-10-14	2009-10-14	2009-10-14		ENSG00000205978			20165	protein-coding gene	gene with protein product	"Cousin of GIN1"		"KIAA1305"	KIAA1305		19561090, 17114934	Standard	NM_025081		Approved	FLJ11811, CGIN1	uc001wpf.4	Q9P2P1		ENST00000382554.3:c.1595A>G	chr14.hg19:g.24878595A>G	ENSP00000371994:p.Gln532Arg	52.0	0.0		54.0	6.0	NM_025081	Q6P153|Q86TR3|Q9HAC4	Missense_Mutation	SNP	ENST00000382554.3	hg19	CCDS45090.1	.	.	.	.	.	.	.	.	.	.	A	9.467	1.094695	0.20471	.	.	ENSG00000205978	ENST00000382554	T	0.11063	2.81	4.52	-4.39	0.03611	.	.	.	.	.	T	0.06962	0.0177	N	0.19112	0.55	0.09310	N	1	B	0.23650	0.089	B	0.24848	0.056	T	0.39840	-0.9594	9	0.66056	D	0.02	.	9.9308	0.41521	0.2162:0.6304:0.1534:0.0	.	532	Q9P2P1	NYNRI_HUMAN	R	532	ENSP00000371994:Q532R	ENSP00000371994:Q532R	Q	+	2	0	NYNRIN	23948435	0.815000	0.29118	0.000000	0.03702	0.002000	0.02628	0.922000	0.28734	-0.761000	0.04670	-2.124000	0.00347	CAG	.	.		0.552	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412939.1			G	24878595	A	G	24878595	3	3	321	1	0	0	0	0	1	0	0	0	10805	188	7	2	1605	2	NYNRIN	14	24878595	Missense_Mutation	SNP	A	TCGA-MI-A75E-01A-11D-A32G-10		24878595	82470945	87	45218										
NOVA1	4857	hgsc.bcm.edu	37	chr14	26949245	26949245	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	aatgctgactggttctgtctTggccacattttggggcattt	11	8	2	1			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr14:26949245T>C	ENST00000344429.5	-	3	388	c.385A>G	c.(385-387)Aag>Gag	p.K129E	NOVA1_ENST00000465357.2_Missense_Mutation_p.K129E|NOVA1_ENST00000547619.1_Missense_Mutation_p.K129E|NOVA1_ENST00000267422.7_Missense_Mutation_p.K7E|NOVA1_ENST00000539517.2_Missense_Mutation_p.K129E|NOVA1_ENST00000574031.1_Missense_Mutation_p.K129E	NM_006491.2	NP_006482.1	P51513	NOVA1_HUMAN	neuro-oncological ventral antigen 1	132					locomotory behavior (GO:0007626)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA metabolic process (GO:0051252)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(265;0.0135)		GGTTCTGTCTTGGCCACATTT	0.438																																					p.K129E		Atlas-SNP	.											.	NOVA1	146	.	0			c.A385G						.						206	171	183					14																	26949245		2203	4300	6503	SO:0001583	missense	4857	exon3			CTGTCTTGGCCAC	U04840	CCDS9635.1, CCDS32060.1, CCDS32061.1	14q12	2006-06-09			ENSG00000139910	ENSG00000139910			7886	protein-coding gene	gene with protein product		602157				8558240	Standard	NM_006489		Approved		uc001wpy.3	P51513	OTTHUMG00000029385	ENST00000344429.5:c.385A>G	chr14.hg19:g.26949245T>C	ENSP00000342387:p.Lys129Glu	104.0	0.0		85.0	14.0	NM_006489	A8K0S4|A8K4Q7|D3DS81|D3DS82|Q6B004	Missense_Mutation	SNP	ENST00000344429.5	hg19	CCDS9635.1	.	.	.	.	.	.	.	.	.	.	T	33	5.234573	0.95207	.	.	ENSG00000139910	ENST00000465357;ENST00000539517;ENST00000267422;ENST00000449198;ENST00000347476;ENST00000549146;ENST00000549571;ENST00000344429;ENST00000547619	T;T;T;T;T;T;T;T;T	0.50277	1.35;1.44;1.37;1.46;1.44;0.81;0.94;0.77;0.75	5.71	5.71	0.89125	.	0.000000	0.64402	D	0.000002	T	0.60702	0.2289	L	0.39245	1.2	0.58432	D	0.999994	D;D;P;D	0.67145	0.992;0.996;0.956;0.974	D;D;P;D	0.69824	0.966;0.936;0.899;0.953	T	0.63769	-0.6562	10	0.87932	D	0	-21.9861	15.9798	0.80097	0.0:0.0:0.0:1.0	.	129;132;129;129	P51513-2;P51513;D3DS81;P51513-4	.;NOVA1_HUMAN;.;.	E	129;129;7;88;7;7;92;129;129	ENSP00000447391:K129E;ENSP00000438875:K129E;ENSP00000267422:K7E;ENSP00000408914:K88E;ENSP00000299472:K7E;ENSP00000449113:K7E;ENSP00000449185:K92E;ENSP00000342387:K129E;ENSP00000448157:K129E	ENSP00000267422:K7E	K	-	1	0	NOVA1	26019085	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.013000	0.88655	2.169000	0.68431	0.477000	0.44152	AAG	.	.		0.438	NOVA1-001	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276557.1	NM_006491		C	26949245	T	C	26949245	3	2	321	1	0	0	0	0	1	0	0	0	10563	1821	63	2	1181	2	NOVA1	14	26949245	Missense_Mutation	SNP	T	TCGA-MI-A75E-01A-11D-A32G-10	2070650	26949245	80400295	88	45219										
SDCCAG1	9147	hgsc.bcm.edu	37	chr14	50251848	50251848	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	ctccaggagtaagtttcactTtatatctttaaaaaggaatt	6	6	2	0			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr14:50251848T>G	ENST00000298310.5	-	31	3484	c.3035A>C	c.(3034-3036)aAa>aCa	p.K1012T	NEMF_ENST00000546046.1_Missense_Mutation_p.K991T|NEMF_ENST00000382135.2_Missense_Mutation_p.K212T|NEMF_ENST00000556925.1_5'UTR|NEMF_ENST00000545773.1_Missense_Mutation_p.K970T			O60524	NEMF_HUMAN	nuclear export mediator factor	1012					nuclear export (GO:0051168)	nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(13)|liver(1)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	36						AAGTTTCACTTTATATCTTTA	0.284																																					p.K1012T		Atlas-SNP	.											.	NEMF	79	.	0			c.A3035C						.						49	50	50					14																	50251848		2202	4300	6502	SO:0001583	missense	9147	exon31			TTCACTTTATATC	AF039687	CCDS9694.1	14q21.3	2012-11-19	2011-01-31	2011-01-31	ENSG00000165525	ENSG00000165525			10663	protein-coding gene	gene with protein product		608378	"serologically defined colon cancer antigen 1"	SDCCAG1		9610721, 10575219	Standard	XR_429334		Approved	NY-CO-1, FLJ10051	uc001wxc.3	O60524	OTTHUMG00000170857	ENST00000298310.5:c.3035A>C	chr14.hg19:g.50251848T>G	ENSP00000298310:p.Lys1012Thr	79.0	0.0		86.0	21.0	NM_004713	A0JLQ3|B3KSK1|B4DDL3|B4DHA9|B4E3F3|Q32Q66|Q8WW70|Q9NWG1	Missense_Mutation	SNP	ENST00000298310.5	hg19	CCDS9694.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.053969	0.75960	.	.	ENSG00000165525	ENST00000298310;ENST00000545773;ENST00000382135;ENST00000546046;ENST00000555970	T;T;T;T	0.59772	0.26;0.26;0.24;0.31	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.81293	0.4792	M	0.91354	3.2	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.999;0.998;0.999	D	0.85741	0.1337	10	0.87932	D	0	-26.1922	16.1277	0.81406	0.0:0.0:0.0:1.0	.	991;987;970;1012;212	O60524-3;O60524-5;O60524-4;O60524;O60524-2	.;.;.;NEMF_HUMAN;.	T	1012;970;212;991;970	ENSP00000298310:K1012T;ENSP00000438309:K970T;ENSP00000441016:K991T;ENSP00000452540:K970T	ENSP00000298310:K1012T	K	-	2	0	NEMF	49321598	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	7.153000	0.77428	2.273000	0.75805	0.482000	0.46254	AAA	.	.		0.284	NEMF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410798.1	NM_004713		G	50251848	T	G	50251848	3	3	321	1	0	0	0	0	1	0	0	0	13972	1841	64	5	207	5	SDCCAG1	14	50251848	Missense_Mutation	SNP	T	TCGA-MI-A75E-01A-11D-A32G-10	23302603	50251848	57097692	89	45220										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64628942	64628942	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	acagctcgcaaacatcagcaTgtctggaaacaacctggcag	9	12	2	0			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr14:64628942T>C	ENST00000344113.4	+	88	16459	c.16247T>C	c.(16246-16248)aTg>aCg	p.M5416T	SYNE2_ENST00000357395.3_Missense_Mutation_p.M1801T|SYNE2_ENST00000394768.2_Missense_Mutation_p.M1801T|SYNE2_ENST00000554584.1_Missense_Mutation_p.M5333T|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000555002.1_Missense_Mutation_p.M2050T|SYNE2_ENST00000358025.3_Missense_Mutation_p.M5416T	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	5416					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		AACATCAGCATGTCTGGAAAC	0.537																																					p.M5416T		Atlas-SNP	.											.	SYNE2	577	.	0			c.T16247C						.						110	103	105					14																	64628942		2203	4300	6503	SO:0001583	missense	23224	exon88			TCAGCATGTCTGG	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.16247T>C	chr14.hg19:g.64628942T>C	ENSP00000341781:p.Met5416Thr	57.0	0.0		54.0	11.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	hg19	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	T	15.14	2.743982	0.49151	.	.	ENSG00000054654	ENST00000358025;ENST00000357395;ENST00000344113;ENST00000554584;ENST00000261678;ENST00000555002;ENST00000394768	T;T;T;T;T;T	0.55234	0.92;4.23;0.93;0.53;4.28;4.23	5.84	1.04	0.20106	.	0.367169	0.23581	N	0.046645	T	0.32010	0.0815	N	0.25890	0.77	0.80722	D	1	B;B;B;B;B	0.10296	0.0;0.001;0.001;0.0;0.003	B;B;B;B;B	0.06405	0.002;0.002;0.001;0.001;0.002	T	0.07214	-1.0784	10	0.13108	T	0.6	.	8.0715	0.30691	0.0:0.3142:0.0:0.6858	.	1801;5339;5333;5416;5416	Q8WXH0-7;F8WAA3;G3V5X4;Q8WXH0;Q8WXH0-2	.;.;.;SYNE2_HUMAN;.	T	5416;1801;5416;5333;5339;2050;1801	ENSP00000350719:M5416T;ENSP00000349969:M1801T;ENSP00000341781:M5416T;ENSP00000452570:M5333T;ENSP00000450831:M2050T;ENSP00000378249:M1801T	ENSP00000261678:M5339T	M	+	2	0	SYNE2	63698695	0.996000	0.38824	0.990000	0.47175	0.991000	0.79684	0.658000	0.24979	0.159000	0.19401	0.533000	0.62120	ATG	.	.		0.537	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		C	64628942	T	C	64628942	3	2	321	1	0	0	0	0	1	0	0	0	15461	1464	51	2	16593	2	SYNE2	14	64628942	Missense_Mutation	SNP	T	TCGA-MI-A75E-01A-11D-A32G-10	14377094	64628942	42720598	90	45221										
PCNX	22990	hgsc.bcm.edu	37	chr14	71444965	71444965	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	cattcctgtcagtctcctgaGggcagatacagtgctctaaa	9	11	3	2			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr14:71444965G>A	ENST00000304743.2	+	6	2357	c.1911G>A	c.(1909-1911)gaG>gaA	p.E637E	PCNX_ENST00000238570.5_Silent_p.E637E|PCNX_ENST00000439984.3_Silent_p.E637E	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	637						integral component of membrane (GO:0016021)				NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		AGTCTCCTGAGGGCAGATACA	0.468																																					p.E637E		Atlas-SNP	.											.	PCNX	198	.	0			c.G1911A						.						104	97	99					14																	71444965		2203	4300	6503	SO:0001819	synonymous_variant	22990	exon6			TCCTGAGGGCAGA	AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"pecanex-like 1 (Drosophila)"	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.1911G>A	chr14.hg19:g.71444965G>A		54.0	0.0		43.0	5.0	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Silent	SNP	ENST00000304743.2	hg19	CCDS9806.1																																																																																			.	.		0.468	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982		A	71444965	G	A	71444965	2	1	321	1	0	0	0	0	0	0	0	1	11600	991	35	3		3	PCNX	14	71444965	Silent	SNP	G	TCGA-MI-A75E-01A-11D-A32G-10	6816023	71444965	35904575	91	45222										
PSEN1	5663	hgsc.bcm.edu	37	chr14	73653618	73653618	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	tgctgttctttttttcattcAtttacttggggtaagttgtg	9	5	3	0			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr14:73653618A>G	ENST00000324501.5	+	6	810	c.538A>G	c.(538-540)Att>Gtt	p.I180V	PSEN1_ENST00000406768.1_Missense_Mutation_p.I88V|PSEN1_ENST00000357710.4_Missense_Mutation_p.I176V|PSEN1_ENST00000557511.1_Missense_Mutation_p.I180V|PSEN1_ENST00000261970.3_Missense_Mutation_p.I180V|PSEN1_ENST00000344094.3_Missense_Mutation_p.I180V|PSEN1_ENST00000394164.1_Missense_Mutation_p.I176V	NM_000021.3|NM_007318.2	NP_000012.1|NP_015557.2	P49768	PSN1_HUMAN	presenilin 1	180					activation of MAPKK activity (GO:0000186)|amyloid precursor protein catabolic process (GO:0042987)|anagen (GO:0042640)|autophagic vacuole assembly (GO:0000045)|beta-amyloid formation (GO:0034205)|beta-amyloid metabolic process (GO:0050435)|blood vessel development (GO:0001568)|brain morphogenesis (GO:0048854)|Cajal-Retzius cell differentiation (GO:0021870)|calcium ion transmembrane transport (GO:0070588)|canonical Wnt signaling pathway (GO:0060070)|cell fate specification (GO:0001708)|cellular response to DNA damage stimulus (GO:0006974)|cerebral cortex cell migration (GO:0021795)|choline transport (GO:0015871)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic limb morphogenesis (GO:0030326)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart looping (GO:0001947)|hematopoietic progenitor cell differentiation (GO:0002244)|intracellular signal transduction (GO:0035556)|L-glutamate transport (GO:0015813)|membrane protein ectodomain proteolysis (GO:0006509)|memory (GO:0007613)|mitochondrial transport (GO:0006839)|myeloid leukocyte differentiation (GO:0002573)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of axonogenesis (GO:0050771)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|neuron migration (GO:0001764)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|positive regulation of coagulation (GO:0050820)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of receptor recycling (GO:0001921)|post-embryonic development (GO:0009791)|protein glycosylation (GO:0006486)|protein processing (GO:0016485)|protein transport (GO:0015031)|regulation of phosphorylation (GO:0042325)|regulation of protein binding (GO:0043393)|regulation of resting membrane potential (GO:0060075)|regulation of synaptic plasticity (GO:0048167)|regulation of synaptic transmission, glutamatergic (GO:0051966)|response to oxidative stress (GO:0006979)|single organismal cell-cell adhesion (GO:0016337)|skeletal system morphogenesis (GO:0048705)|skin morphogenesis (GO:0043589)|smooth endoplasmic reticulum calcium ion homeostasis (GO:0051563)|somitogenesis (GO:0001756)|synaptic vesicle targeting (GO:0016080)|T cell activation involved in immune response (GO:0002286)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cell cortex (GO:0005938)|cell surface (GO:0009986)|centrosome (GO:0005813)|ciliary rootlet (GO:0035253)|cytoplasmic vesicle (GO:0031410)|dendritic shaft (GO:0043198)|endoplasmic reticulum (GO:0005783)|gamma-secretase complex (GO:0070765)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|kinetochore (GO:0000776)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nuclear outer membrane (GO:0005640)|perinuclear region of cytoplasm (GO:0048471)|rough endoplasmic reticulum (GO:0005791)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	aspartic-type endopeptidase activity (GO:0004190)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|calcium channel activity (GO:0005262)|endopeptidase activity (GO:0004175)|PDZ domain binding (GO:0030165)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.075)		TTTTTCATTCATTTACTTGGG	0.338																																					p.I180V		Atlas-SNP	.											.	PSEN1	38	.	0			c.A538G						.						205	198	201					14																	73653618		2203	4300	6503	SO:0001583	missense	5663	exon6			TCATTCATTTACT	AJ008005	CCDS9812.1, CCDS9813.1	14q24.3	2014-09-17	2008-07-28		ENSG00000080815	ENSG00000080815			9508	protein-coding gene	gene with protein product		104311	"Alzheimer disease 3"	AD3		1411576	Standard	NM_007318		Approved	FAD, S182, PS1	uc001xnr.3	P49768	OTTHUMG00000141279	ENST00000324501.5:c.538A>G	chr14.hg19:g.73653618A>G	ENSP00000326366:p.Ile180Val	155.0	0.0		141.0	26.0	NM_000021	B2R6D3|O95465|Q14762|Q15719|Q15720|Q96P33|Q9UIF0	Missense_Mutation	SNP	ENST00000324501.5	hg19	CCDS9812.1	.	.	.	.	.	.	.	.	.	.	A	16.31	3.086104	0.55861	.	.	ENSG00000080815	ENST00000324501;ENST00000357710;ENST00000261970;ENST00000344094;ENST00000394164;ENST00000557511;ENST00000406768	D;D;D;D;D;D;D	0.99541	-6.12;-6.12;-6.12;-6.12;-6.12;-6.12;-6.12	5.46	5.46	0.80206	.	0.092352	0.64402	D	0.000001	D	0.99184	0.9717	M	0.64676	1.99	0.80722	D	1	B;P	0.50369	0.393;0.934	B;P	0.50934	0.406;0.654	D	0.99201	1.0873	10	0.62326	D	0.03	-20.2897	15.8313	0.78752	1.0:0.0:0.0:0.0	.	176;180	P49768-2;P49768	.;PSN1_HUMAN	V	180;176;180;180;176;180;88	ENSP00000326366:I180V;ENSP00000350342:I176V;ENSP00000261970:I180V;ENSP00000339523:I180V;ENSP00000377719:I176V;ENSP00000451429:I180V;ENSP00000385948:I88V	ENSP00000261970:I180V	I	+	1	0	PSEN1	72723371	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	6.516000	0.73755	2.199000	0.70637	0.402000	0.26972	ATT	.	.		0.338	PSEN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280500.2			G	73653618	A	G	73653618	3	3	321	1	0	0	0	0	1	0	0	0	12662	217	8	2	552	2	PSEN1	14	73653618	Missense_Mutation	SNP	A	TCGA-MI-A75E-01A-11D-A32G-10	2208653	73653618	33695922	92	45223										
NRXN3	9369	hgsc.bcm.edu	37	chr14	79933569	79933569	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	tccttgcttttgcagctggcGctacgtacatctttgggaaa	10	10	1	0	rs373319691		TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr14:79933569G>A	ENST00000557594.1	+	2	1206	c.253G>A	c.(253-255)Gct>Act	p.A85T	NRXN3_ENST00000428277.2_Missense_Mutation_p.A85T|NRXN3_ENST00000335750.5_Missense_Mutation_p.A717T|NRXN3_ENST00000554719.1_Missense_Mutation_p.A717T|NRXN3_ENST00000281127.7_Missense_Mutation_p.A85T|NRXN3_ENST00000556003.1_3'UTR	NM_001272020.1	NP_001258949.1	Q9HDB5	NRX3B_HUMAN	neurexin 3	85	Laminin G-like. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|angiogenesis (GO:0001525)|learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(23)|lung(40)|ovary(3)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(9)|urinary_tract(1)	104		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		TGCAGCTGGCGCTACGTACAT	0.557																																					p.A717T		Atlas-SNP	.											.	NRXN3	342	.	0			c.G2149A						.						118	86	97					14																	79933569		2203	4300	6503	SO:0001583	missense	9369	exon13			GCTGGCGCTACGT	AB018286	CCDS9870.1, CCDS9871.1, CCDS45145.1, CCDS61515.1	14q31	2010-01-19				ENSG00000021645			8010	protein-coding gene	gene with protein product		600567	"chromosome 14 open reading frame 60"	C14orf60		11944992, 12379233	Standard	NM_004796		Approved	KIAA0743	uc001xun.4	Q9HDB5		ENST00000557594.1:c.253G>A	chr14.hg19:g.79933569G>A	ENSP00000451672:p.Ala85Thr	67.0	0.0		81.0	11.0	NM_004796	A5PKW8|A8MPU5|B3KPM7|Q6NUR0|Q8IUD8	Missense_Mutation	SNP	ENST00000557594.1	hg19		.	.	.	.	.	.	.	.	.	.	G	9.638	1.138311	0.21123	.	.	ENSG00000021645	ENST00000330071;ENST00000332068;ENST00000554719;ENST00000335750;ENST00000557594;ENST00000281127;ENST00000428277	T;T;T;T;T	0.78364	-1.17;-1.17;1.15;1.15;1.15	5.83	5.83	0.93111	Concanavalin A-like lectin/glucanase (1);Laminin G domain (1);	0.055635	0.64402	D	0.000001	T	0.47395	0.1443	N	0.00453	-1.485	0.54753	D	0.999986	B;B;B;B	0.26975	0.005;0.165;0.019;0.001	B;B;B;B	0.17979	0.006;0.02;0.005;0.001	T	0.57207	-0.7851	9	.	.	.	.	20.103	0.97881	0.0:0.0:1.0:0.0	.	85;85;85;717	Q9HDB5-4;Q9HDB5-2;Q9HDB5;Q9Y4C0-3	.;.;NRX3B_HUMAN;.	T	1090;1079;717;717;85;85;85	ENSP00000451648:A717T;ENSP00000338349:A717T;ENSP00000451672:A85T;ENSP00000281127:A85T;ENSP00000394426:A85T	.	A	+	1	0	NRXN3	79003322	1.000000	0.71417	0.994000	0.49952	0.957000	0.61999	5.980000	0.70516	2.738000	0.93877	0.655000	0.94253	GCT	.	.		0.557	NRXN3-004	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000413790.1	NM_001105250		A	79933569	G	A	79933569	3	1	321	1	0	0	0	0	1	0	0	0	10676	1087	38	1	2442	1	NRXN3	14	79933569	Missense_Mutation	SNP	G	TCGA-MI-A75E-01A-11D-A32G-10	6279951	79933569	27415971	93	45224										
CKMT1B	1159	hgsc.bcm.edu	37	chr15	43888719	43888719	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	gtttgaaagattctgccgagGcctcaaagaggttagagaag	13	6	2	4			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr15:43888719G>A	ENST00000441322.1	+	6	1226	c.866G>A	c.(865-867)gGc>gAc	p.G289D	CKMT1B_ENST00000450086.2_Missense_Mutation_p.G248D|CKMT1B_ENST00000300283.6_Missense_Mutation_p.G289D|CKMT1B_ENST00000413657.2_Missense_Mutation_p.G152D			P12532	KCRU_HUMAN	creatine kinase, mitochondrial 1B	289	Phosphagen kinase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00843}.				cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|creatine kinase activity (GO:0004111)			large_intestine(1)|lung(3)|skin(1)	5		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)	Creatine(DB00148)	TTCTGCCGAGGCCTCAAAGAG	0.443																																					p.G289D		Atlas-SNP	.											.	CKMT1B	10	.	0			c.G866A						.						93	105	101					15																	43888719		2148	4298	6446	SO:0001583	missense	1159	exon7			GCCGAGGCCTCAA	AK094322, J04469	CCDS10097.1	15q15	2005-04-15		2005-04-15	ENSG00000237289	ENSG00000237289	2.7.3.2		1995	protein-coding gene	gene with protein product		123290	"creatine kinase, mitochondrial 1 (ubiquitous)"	CKMT, CKMT1			Standard	XM_005254150		Approved	UMTCK	uc001zsc.3	P12532	OTTHUMG00000059900	ENST00000441322.1:c.866G>A	chr15.hg19:g.43888719G>A	ENSP00000413255:p.Gly289Asp	167.0	0.0		156.0	24.0	NM_020990	B4DIT8|B7ZA09|Q0VAM3|Q32NF6|Q53FC4	Missense_Mutation	SNP	ENST00000441322.1	hg19	CCDS10097.1	.	.	.	.	.	.	.	.	.	.	G	17.99	3.523754	0.64747	.	.	ENSG00000237289	ENST00000300283;ENST00000450086;ENST00000441322;ENST00000413657;ENST00000438947	T;T;T;T	0.12879	2.64;2.64;2.64;2.64	4.49	3.55	0.40652	ATP:guanido phosphotransferase, catalytic domain (2);Glutamine synthetase/guanido kinase, catalytic domain (1);	0.045722	0.85682	D	0.000000	T	0.54303	0.1850	H	0.98487	4.245	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;0.998;1.0	D;D;D;D;D;D;D	0.91635	0.996;0.999;0.999;0.999;0.999;0.99;0.999	T	0.75033	-0.3460	10	0.87932	D	0	-1.777	14.829	0.70135	0.0:0.145:0.855:0.0	.	289;248;248;227;320;130;289	F8WCN3;E9PCP8;B4DH34;B4DGR9;P12532-2;B4DJW9;P12532	.;.;.;.;.;.;KCRU_HUMAN	D	289;248;289;152;322	ENSP00000300283:G289D;ENSP00000389267:G248D;ENSP00000413255:G289D;ENSP00000390428:G152D	ENSP00000300283:G289D	G	+	2	0	CKMT1B	41676011	1.000000	0.71417	1.000000	0.80357	0.868000	0.49771	7.660000	0.83776	1.215000	0.43411	0.485000	0.47835	GGC	.	.		0.443	CKMT1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133147.2	NM_020990		A	43888719	G	A	43888719	3	1	321	1	0	0	0	0	1	0	0	0	3452	1203	42	3	888	3	CKMT1B	15	43888719	Missense_Mutation	SNP	G	TCGA-MI-A75E-01A-11D-A32G-10		43888719	58642673	94	45225										
SEMA6D	80031	hgsc.bcm.edu	37	chr15	48058317	48058317	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	cacaggtcttgtattgcatcTcgtgacccgtattgtggctg	11	10	2	1			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr15:48058317T>G	ENST00000316364.5	+	15	2023	c.1584T>G	c.(1582-1584)tcT>tcG	p.S528S	SEMA6D_ENST00000389433.2_Silent_p.S528S|SEMA6D_ENST00000537942.1_Silent_p.S528S|SEMA6D_ENST00000558816.1_Silent_p.S528S|SEMA6D_ENST00000358066.4_Silent_p.S528S|SEMA6D_ENST00000355997.3_Silent_p.S528S|SEMA6D_ENST00000389428.3_Silent_p.S528S|SEMA6D_ENST00000558014.1_Silent_p.S528S|SEMA6D_ENST00000536845.2_Silent_p.S528S|SEMA6D_ENST00000389432.2_Silent_p.S528S|SEMA6D_ENST00000354744.4_Silent_p.S528S	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	528	PSI.				axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		GTATTGCATCTCGTGACCCGT	0.438																																					p.S528S		Atlas-SNP	.											.	SEMA6D	322	.	0			c.T1584G						.						116	101	106					15																	48058317		2198	4297	6495	SO:0001819	synonymous_variant	80031	exon15			TGCATCTCGTGAC	AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"Semaphorins"	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.1584T>G	chr15.hg19:g.48058317T>G		113.0	0.0		108.0	23.0	NM_153617	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Silent	SNP	ENST00000316364.5	hg19	CCDS32225.1																																																																																			.	.		0.438	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966		G	48058317	T	G	48058317	2	3	321	1	0	0	0	0	0	0	0	1	14057	1538	54	5		5	SEMA6D	15	48058317	Silent	SNP	T	TCGA-MI-A75E-01A-11D-A32G-10	4169598	48058317	54473075	95	45226										
DIS3L	115752	hgsc.bcm.edu	37	chr15	66615033	66615052	+	Frame_Shift_Del	DEL	GATGCCAGTAAACACACCAG	GATGCCAGTAAACACACCAG	-													0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	tttctcatacagatgtgtgaGatgccagtaaacacaccaga					rs202123708|rs375573302		TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	GATGCCAGTAAACACACCAG	GATGCCAGTAAACACACCAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr15:66615033_66615052delGATGCCAGTAAACACACCAG	ENST00000319212.4	+	10	1385_1404	c.1335_1354delGATGCCAGTAAACACACCAG	c.(1333-1356)gagatgccagtaaacacaccagaafs	p.EMPVNTPE445fs	RP11-352G18.2_ENST00000565993.1_RNA|DIS3L_ENST00000441424.2_3'UTR|DIS3L_ENST00000319194.5_Frame_Shift_Del_p.EMPVNTPE362fs	NM_001143688.1	NP_001137160.1	Q8TF46	DI3L1_HUMAN	DIS3 like exosome 3'-5' exoribonuclease	445					RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA catabolic process (GO:0016075)	cytoplasmic exosome (RNase complex) (GO:0000177)	3'-5'-exoribonuclease activity (GO:0000175)|enzyme binding (GO:0019899)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						AGATGTGTGAGATGCCAGTAAACACACCAGAAAGTCCCTG	0.395																																					p.445_451del		Atlas-Indel,Pindel	.											DIS3L_ENST00000319212,NS,carcinoma,0,2	DIS3L	175	.	0			c.1334_1353del						.																																			SO:0001589	frameshift_variant	115752	exon10			.		CCDS10214.1, CCDS45286.1	15q22.31	2014-03-05	2014-03-05		ENSG00000166938	ENSG00000166938			28698	protein-coding gene	gene with protein product		614183	"DIS3 mitotic control homolog (S. cerevisiae)-like"			20531386	Standard	NM_001143688		Approved	MGC4562, FLJ38088, KIAA1955, DIS3L1	uc010ujm.2	Q8TF46	OTTHUMG00000133181	ENST00000319212.4:c.1335_1354delGATGCCAGTAAACACACCAG	chr15.hg19:g.66615033_66615052delGATGCCAGTAAACACACCAG	ENSP00000321711:p.Glu445fs	79.0	0.0		92.0	10.0	NM_001143688	Q8N1N8|Q8WTU9|Q96CM7	Frame_Shift_Del	DEL	ENST00000319212.4	hg19	CCDS45286.1																																																																																			.	.		0.395	DIS3L-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382792.2	NM_133375		-	66615052	GATGCCAGTAAACACACCAG	-	66615033	7	5	321	1	0	1	0	1	0	0	0	0	4538	933	33	0	1373	0	DIS3L	15	66615033	Frame_Shift_Del	DEL	GATGCCAGTAAACACACCAG	TCGA-MI-A75E-01A-11D-A32G-10	18556716	66615033	35916359	96	45227										
PRSS36	146547	hgsc.bcm.edu	37	chr16	31150725	31150725	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	catctggcacaggaggggcgGtgctgaggtcatctgcagag	17	9	3	2			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr16:31150725G>C	ENST00000268281.4	-	15	2360	c.2302C>G	c.(2302-2304)Ccg>Gcg	p.P768A	PRSS36_ENST00000569305.1_Missense_Mutation_p.P763A|PRSS36_ENST00000418068.2_Missense_Mutation_p.P665A	NM_001258290.1|NM_173502.4	NP_001245219.1|NP_775773.2	Q5K4E3	POLS2_HUMAN	protease, serine, 36	768	Peptidase S1 3. {ECO:0000255|PROSITE- ProRule:PRU00274}.					cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)	serine-type endopeptidase activity (GO:0004252)			kidney(2)|large_intestine(4)|lung(8)|ovary(3)	17						AGGAGGGGCGGTGCTGAGGTC	0.637																																					p.P768A		Atlas-SNP	.											.	PRSS36	50	.	0			c.C2302G						.						55	54	54					16																	31150725		2197	4300	6497	SO:0001583	missense	146547	exon15			GGGGCGGTGCTGA	AK075142	CCDS32436.1, CCDS58452.1, CCDS58453.1	16p11.2	2014-09-04			ENSG00000178226			"Serine peptidases / Serine peptidases"	26906	protein-coding gene	gene with protein product	"polyserase 2"	610560				15536082	Standard	NM_173502		Approved	FLJ90661	uc002ebd.4	Q5K4E3	OTTHUMG00000176751	ENST00000268281.4:c.2302C>G	chr16.hg19:g.31150725G>C	ENSP00000268281:p.Pro768Ala	103.0	0.0		84.0	16.0	NM_173502	A8K2P5|B4DW80|B7ZMK8|E7EX56|Q8NBY4	Missense_Mutation	SNP	ENST00000268281.4	hg19	CCDS32436.1	.	.	.	.	.	.	.	.	.	.	G	14.43	2.533163	0.45073	.	.	ENSG00000178226	ENST00000268281;ENST00000418068	D;D	0.91740	-2.35;-2.9	5.83	4.87	0.63330	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	D	0.92430	0.7597	L	0.27053	0.805	0.33715	D	0.616266	D;D;D	0.89917	0.997;1.0;1.0	D;D;D	0.87578	0.98;0.998;0.998	D	0.93282	0.6661	9	0.66056	D	0.02	.	11.3467	0.49565	0.0861:0.0:0.9139:0.0	.	665;763;768	E7EX56;B7ZMK8;Q5K4E3	.;.;POLS2_HUMAN	A	768;665	ENSP00000268281:P768A;ENSP00000407160:P665A	ENSP00000268281:P768A	P	-	1	0	PRSS36	31058226	0.553000	0.26513	0.989000	0.46669	0.028000	0.11728	1.324000	0.33712	2.755000	0.94549	0.561000	0.74099	CCG	.	.		0.637	PRSS36-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000433542.1	NM_173502		C	31150725	G	C	31150725	3	2	321	1	0	0	0	0	1	0	0	0	12637	1261	44	4	269	4	PRSS36	16	31150725	Missense_Mutation	SNP	G	TCGA-MI-A75E-01A-11D-A32G-10		31150725	59204028	97	45228										
SHCBP1	79801	hgsc.bcm.edu	37	chr16	46617445	46617445	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	taccttcagttccatcttcaGcattttcttgcaggtcagag	7	11	5	1			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr16:46617445G>C	ENST00000303383.3	-	12	1942	c.1676C>G	c.(1675-1677)gCt>gGt	p.A559G		NM_024745.4	NP_079021	Q8NEM2	SHCBP_HUMAN	SHC SH2-domain binding protein 1	559					fibroblast growth factor receptor signaling pathway (GO:0008543)|regulation of neural precursor cell proliferation (GO:2000177)					breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		all_cancers(37;0.00404)|all_epithelial(9;0.00527)|all_lung(18;0.0413)|Lung NSC(13;0.213)				TCCATCTTCAGCATTTTCTTG	0.313																																					p.A559G		Atlas-SNP	.											.	SHCBP1	54	.	0			c.C1676G						.						61	65	64					16																	46617445		2202	4298	6500	SO:0001583	missense	79801	exon12			TCTTCAGCATTTT	AK055931	CCDS10720.1	16q11	2008-02-05			ENSG00000171241	ENSG00000171241			29547	protein-coding gene	gene with protein product		611027				10086341	Standard	NM_024745		Approved	FLJ22009	uc002eec.4	Q8NEM2	OTTHUMG00000132540	ENST00000303383.3:c.1676C>G	chr16.hg19:g.46617445G>C	ENSP00000306473:p.Ala559Gly	342.0	0.0		320.0	34.0	NM_024745	Q96N60|Q9BVS0|Q9H6P6	Missense_Mutation	SNP	ENST00000303383.3	hg19	CCDS10720.1	.	.	.	.	.	.	.	.	.	.	G	5.568	0.289563	0.10567	.	.	ENSG00000171241	ENST00000303383	T	0.24723	1.84	3.85	-0.067	0.13762	.	1.065300	0.07195	N	0.856398	T	0.16041	0.0386	N	0.19112	0.55	0.09310	N	1	B	0.17038	0.02	B	0.19148	0.024	T	0.33574	-0.9863	10	0.62326	D	0.03	0.0779	5.348	0.16020	0.204:0.0:0.6454:0.1506	.	559	Q8NEM2	SHCBP_HUMAN	G	559	ENSP00000306473:A559G	ENSP00000306473:A559G	A	-	2	0	SHCBP1	45174946	0.523000	0.26274	0.058000	0.19502	0.302000	0.27658	1.296000	0.33389	-0.086000	0.12550	0.460000	0.39030	GCT	.	.		0.313	SHCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255740.1	NM_024745		C	46617445	G	C	46617445	3	2	321	1	0	0	0	0	1	0	0	0	14289	971	34	4	350	4	SHCBP1	16	46617445	Missense_Mutation	SNP	G	TCGA-MI-A75E-01A-11D-A32G-10	15466720	46617445	43737308	98	45229										
TNS4	84951	hgsc.bcm.edu	37	chr17	38638655	38638655	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	aggaagtgtcggatgaggtcAttgctgtcctcacctggaca	13	9	2	1			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr17:38638655A>G	ENST00000254051.6	-	7	1673	c.1515T>C	c.(1513-1515)aaT>aaC	p.N505N		NM_032865.5	NP_116254.4	Q8IZW8	TENS4_HUMAN	tensin 4	505	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				apoptotic process (GO:0006915)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	30		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(5;5.91e-05)			GGATGAGGTCATTGCTGTCCT	0.557																																					p.N505N		Atlas-SNP	.											.	TNS4	72	.	0			c.T1515C						.						92	85	87					17																	38638655		2203	4300	6503	SO:0001819	synonymous_variant	84951	exon7			GAGGTCATTGCTG	AF417488	CCDS11368.1	17q21.2	2013-02-14			ENSG00000131746	ENSG00000131746		"SH2 domain containing"	24352	protein-coding gene	gene with protein product	"C terminal tensin like"	608385				12154022, 12711115	Standard	NM_032865		Approved	CTEN	uc010cxb.3	Q8IZW8	OTTHUMG00000133330	ENST00000254051.6:c.1515T>C	chr17.hg19:g.38638655A>G		29.0	0.0		50.0	8.0	NM_032865	A6NMJ7|Q71RB7|Q8WV64|Q96JV4	Silent	SNP	ENST00000254051.6	hg19	CCDS11368.1																																																																																			.	.		0.557	TNS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257154.3	NM_032865		G	38638655	A	G	38638655	2	3	321	1	0	0	0	0	0	0	0	1	16360	214	8	2		2	TNS4	17	38638655	Silent	SNP	A	TCGA-MI-A75E-01A-11D-A32G-10		38638655	42556555	99	45230										
TBX4	9496	hgsc.bcm.edu	37	chr17	59557329	59557329	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	tgcgtgtggcccgactgcagAggtggggctgcgtagcctgg	19	10	0	1			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr17:59557329A>G	ENST00000240335.1	+	6	835	c.790A>G	c.(790-792)Agc>Ggc	p.S264G	TBX4_ENST00000589449.1_3'UTR|TBX4_ENST00000393853.4_Splice_Site_p.S264G	NM_018488.2	NP_060958.2	P57082	TBX4_HUMAN	T-box 4	264					angiogenesis (GO:0001525)|embryonic limb morphogenesis (GO:0030326)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(15)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						CCGACTGCAGAGGTGGGGCTG	0.587																																					p.S264G		Atlas-SNP	.											.	TBX4	69	.	0			c.A790G						.						68	72	70					17																	59557329		2203	4300	6503	SO:0001630	splice_region_variant	9496	exon6			CTGCAGAGGTGGG	AF188703	CCDS11629.1	17q21-q22	2005-10-11				ENSG00000121075		"T-boxes"	11603	protein-coding gene	gene with protein product		601719				10945475	Standard	NM_018488		Approved		uc002izi.3	P57082		ENST00000240335.1:c.791+1A>G	chr17.hg19:g.59557329A>G		65.0	0.0		79.0	10.0	NM_018488	A5PKU7|B2RMT1|B7ZLV3	Missense_Mutation	SNP	ENST00000240335.1	hg19	CCDS11629.1	.	.	.	.	.	.	.	.	.	.	A	16.85	3.236750	0.58886	.	.	ENSG00000121075	ENST00000393853;ENST00000240335	D;D	0.81908	-1.55;-1.55	5.43	5.43	0.79202	.	0.142496	0.64402	D	0.000003	D	0.85435	0.5696	L	0.38838	1.175	0.49582	D	0.999803	D;D	0.54964	0.969;0.969	D;D	0.63381	0.914;0.914	D	0.84586	0.0664	9	.	.	.	.	14.6668	0.68915	1.0:0.0:0.0:0.0	.	264;264	A5PKU7;P57082	.;TBX4_HUMAN	G	264	ENSP00000377435:S264G;ENSP00000240335:S264G	.	S	+	1	0	TBX4	56912111	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	5.682000	0.68182	2.049000	0.60858	0.459000	0.35465	AGC	.	.		0.587	TBX4-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449649.1	NM_018488	Missense_Mutation	G	59557329	A	G	59557329	5	3	321	1	0	0	0	0	0	0	1	0	15675	318	11	2	812	2	TBX4	17	59557329	Splice_Site	SNP	A	TCGA-MI-A75E-01A-11D-A32G-10	20918674	59557329	21637881	100	45231										
ANKRD30B	374860	hgsc.bcm.edu	37	chr18	14763926	14763926	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	gagaaattttcatggccagcAaaagaaagatctaggaagat	10	5	2	4			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr18:14763926A>C	ENST00000358984.4	+	7	1242	c.1062A>C	c.(1060-1062)gcA>gcC	p.A354A	ANKRD30B_ENST00000579292.1_Intron|ANKRD30B_ENST00000447268.2_Silent_p.A354A	NM_001145029.1	NP_001138501.1	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B	354										breast(3)|endometrium(4)|kidney(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	22						CATGGCCAGCAAAAGAAAGAT	0.378																																					p.A354A		Atlas-SNP	.											.	ANKRD30B	237	.	0			c.A1062C						.						66	58	61					18																	14763926		692	1591	2283	SO:0001819	synonymous_variant	374860	exon7			GCCAGCAAAAGAA	BC028407	CCDS54182.1	18p11.21	2013-01-10			ENSG00000180777	ENSG00000180777		"Ankyrin repeat domain containing"	24165	protein-coding gene	gene with protein product						11280766	Standard	NM_001145029		Approved	NY-BR-1.1	uc010dlo.2	Q9BXX2		ENST00000358984.4:c.1062A>C	chr18.hg19:g.14763926A>C		51.0	0.0		57.0	8.0	NM_001145029	B4DGP1|F8WAG3|Q4G175	Silent	SNP	ENST00000358984.4	hg19	CCDS54182.1																																																																																			.	.		0.378	ANKRD30B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443557.1	NM_001145029		C	14763926	A	C	14763926	2	2	321	1	0	0	0	0	0	0	0	1	659	117	5	5		5	ANKRD30B	18	14763926	Silent	SNP	A	TCGA-MI-A75E-01A-11D-A32G-10		14763926	63313322	101	45232										
SHC2	25759	hgsc.bcm.edu	37	chr19	430742	430742	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	gcatctcttagagaaggagaTgggccctggaaacagagcag	14	8	1	3			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr19:430742T>C	ENST00000264554.6	-	9	1115	c.1116A>G	c.(1114-1116)ccA>ccG	p.P372P		NM_012435.2	NP_036567.2	P98077	SHC2_HUMAN	SHC (Src homology 2 domain containing) transforming protein 2	372	CH1.				activation of MAPK activity (GO:0000187)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)	cytosol (GO:0005829)				endometrium(2)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	21		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GAGAAGGAGATGGGCCCTGGA	0.632																																					p.P372P		Atlas-SNP	.											.	SHC2	47	.	0			c.A1116G						.						57	68	65					19																	430742		1945	4137	6082	SO:0001819	synonymous_variant	25759	exon9			AGGAGATGGGCCC	AB001451	CCDS45891.1	19p13.3	2013-02-14				ENSG00000129946		"SH2 domain containing"	29869	protein-coding gene	gene with protein product	"neuronal Shc adaptor homolog"	605217				7527937, 9507002	Standard	NM_012435		Approved	SLI, SCK, SHCB	uc002loq.4	P98077		ENST00000264554.6:c.1116A>G	chr19.hg19:g.430742T>C		63.0	0.0		41.0	11.0	NM_012435	O60230|Q9NPL5|Q9UCX4	Silent	SNP	ENST00000264554.6	hg19	CCDS45891.1																																																																																			.	.		0.632	SHC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451840.3			C	430742	T	C	430742	2	2	321	1	0	0	0	0	0	0	0	1	14286	1451	51	2		2	SHC2	19	430742	Silent	SNP	T	TCGA-MI-A75E-01A-11D-A32G-10		430742	58698241	102	45233										
SLC44A2	57153	hgsc.bcm.edu	37	chr19	10742002	10742002	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	tcacgtacctgaatgctcgcAgctcccgggactttgagtac	10	13	1	2			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr19:10742002A>G	ENST00000335757.5	+	6	758	c.382A>G	c.(382-384)Agc>Ggc	p.S128G	SLC44A2_ENST00000407327.4_Missense_Mutation_p.S126G|SLC44A2_ENST00000586078.1_Missense_Mutation_p.S128G			Q8IWA5	CTL2_HUMAN	solute carrier family 44 (choline transporter), member 2	128					choline transport (GO:0015871)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	choline transmembrane transporter activity (GO:0015220)|signal transducer activity (GO:0004871)			NS(1)|breast(3)|endometrium(5)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	27			Epithelial(33;8.7e-06)|all cancers(31;2.77e-05)		Choline(DB00122)	GAATGCTCGCAGCTCCCGGGA	0.532																																					p.S128G		Atlas-SNP	.											.	SLC44A2	56	.	0			c.A382G						.						119	121	120					19																	10742002		2203	4300	6503	SO:0001583	missense	57153	exon6			GCTCGCAGCTCCC	AF070636	CCDS12245.1, CCDS54216.1	19p13.2	2014-08-12	2013-07-17		ENSG00000129353	ENSG00000129353		"Solute carriers"	17292	protein-coding gene	gene with protein product		606106				10677542, 15715662	Standard	NM_001145056		Approved	CTL2	uc002mpf.3	Q8IWA5	OTTHUMG00000180585	ENST00000335757.5:c.382A>G	chr19.hg19:g.10742002A>G	ENSP00000336888:p.Ser128Gly	49.0	0.0		57.0	9.0	NM_020428	B2RBB1|B3KNH3|B4DFJ0|F2Q9D7|Q658V1|Q658Z2|Q6PJV7|Q8N2F0|Q9NY68	Missense_Mutation	SNP	ENST00000335757.5	hg19	CCDS12245.1	.	.	.	.	.	.	.	.	.	.	A	5.402	0.259277	0.10239	.	.	ENSG00000129353	ENST00000407327;ENST00000335757;ENST00000380614	T;T	0.10005	2.92;2.92	4.71	-0.041	0.13869	.	0.976571	0.08374	N	0.955563	T	0.09113	0.0225	L	0.41492	1.28	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43718	-0.9374	10	0.20046	T	0.44	.	8.7421	0.34564	0.6438:0.0:0.3562:0.0	.	128;126	Q8IWA5;Q8IWA5-3	CTL2_HUMAN;.	G	126;128;128	ENSP00000385135:S126G;ENSP00000336888:S128G	ENSP00000336888:S128G	S	+	1	0	SLC44A2	10603002	0.000000	0.05858	0.000000	0.03702	0.704000	0.40688	-0.166000	0.09954	-0.221000	0.09973	0.374000	0.22700	AGC	.	.		0.532	SLC44A2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452045.1			G	10742002	A	G	10742002	3	3	321	1	0	0	0	0	1	0	0	0	14651	188	7	2	439	2	SLC44A2	19	10742002	Missense_Mutation	SNP	A	TCGA-MI-A75E-01A-11D-A32G-10	10311260	10742002	48386981	103	45234										
LPPR2	64748	hgsc.bcm.edu	37	chr19	11475082	11475082	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	gctgtgtctcctccagggccCcagccatgtgttcgtcgccc	11	17	1	0			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr19:11475082C>G	ENST00000591608.1	+	10	1264	c.1000C>G	c.(1000-1002)Cca>Gca	p.P334A	DKFZP761J1410_ENST00000251473.5_3'UTR																							CTCCAGGGCCCCAGCCATGTG	0.667																																					p.P334A		Atlas-SNP	.											.	LPPR2	21	.	0			c.C1000G						.						20	21	21					19																	11475082		2203	4300	6503	SO:0001583	missense	0	exon10			AGGGCCCCAGCCA																												ENST00000591608.1:c.1000C>G	chr19.hg19:g.11475082C>G	ENSP00000466898:p.Pro334Ala	29.0	0.0		27.0	10.0	NM_001170635		Missense_Mutation	SNP	ENST00000591608.1	hg19	CCDS59352.1																																																																																			.	.		0.667	DKFZP761J1410-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000458784.1			G	11475082	C	G	11475082	3	3	321	1	0	0	0	0	1	0	0	0	8934	623	22	4	1105	4	LPPR2	19	11475082	Missense_Mutation	SNP	C	TCGA-MI-A75E-01A-11D-A32G-10	733080	11475082	47653901	104	45235										
NOTCH3	4854	hgsc.bcm.edu	37	chr19	15292445	15292445	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	gcctccgtagcctggcgggcAggtgcaggtgaaggaggcca	18	11	0	1			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr19:15292445A>T	ENST00000263388.2	-	17	2809	c.2734T>A	c.(2734-2736)Tgc>Agc	p.C912S		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	912	EGF-like 23; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			CCTGGCGGGCAGGTGCAGGTG	0.692																																					p.C912S		Atlas-SNP	.											.	NOTCH3	340	.	0			c.T2734A						.						16	13	14					19																	15292445		2111	4110	6221	SO:0001583	missense	4854	exon17			GCGGGCAGGTGCA	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"Ankyrin repeat domain containing"	7883	protein-coding gene	gene with protein product		600276	"Notch (Drosophila) homolog 3", "Notch homolog 3 (Drosophila)"	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.2734T>A	chr19.hg19:g.15292445A>T	ENSP00000263388:p.Cys912Ser	101.0	0.0		94.0	17.0	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Missense_Mutation	SNP	ENST00000263388.2	hg19	CCDS12326.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.139544	0.77775	.	.	ENSG00000074181	ENST00000263388;ENST00000539383	D	0.96619	-4.07	5.45	5.45	0.79879	EGF-like region, conserved site (2);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.34879	N	0.003609	D	0.99004	0.9660	H	0.99249	4.485	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.99044	1.0825	10	0.87932	D	0	.	14.4883	0.67631	1.0:0.0:0.0:0.0	.	863;912	Q59FL3;Q9UM47	.;NOTC3_HUMAN	S	912;862	ENSP00000263388:C912S	ENSP00000263388:C912S	C	-	1	0	NOTCH3	15153445	1.000000	0.71417	1.000000	0.80357	0.383000	0.30230	6.249000	0.72427	2.077000	0.62373	0.459000	0.35465	TGC	.	.		0.692	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435		T	15292445	A	T	15292445	3	4	321	1	0	0	0	0	1	0	0	0	10559	188	7	4	4299	4	NOTCH3	19	15292445	Missense_Mutation	SNP	A	TCGA-MI-A75E-01A-11D-A32G-10	3817363	15292445	43836538	105	45236										
HSH2D	84941	hgsc.bcm.edu	37	chr19	16265269	16265269	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	actccaacgcagtggccgagGaagctgcctgcccggtgtct	13	14	1	0			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr19:16265269G>C	ENST00000253680.6	+	7	973	c.442G>C	c.(442-444)Gaa>Caa	p.E148Q	HSH2D_ENST00000588246.1_Missense_Mutation_p.E148Q|HSH2D_ENST00000397372.4_Missense_Mutation_p.E59Q|HSH2D_ENST00000593154.2_Missense_Mutation_p.E148Q			Q96JZ2	HSH2D_HUMAN	hematopoietic SH2 domain containing	148					negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of mitochondrial depolarization (GO:0051902)|positive regulation of signal transduction (GO:0009967)|T cell activation (GO:0042110)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				central_nervous_system(1)|kidney(1)|large_intestine(2)	4						AGTGGCCGAGGAAGCTGCCTG	0.617																																					p.E148Q		Atlas-SNP	.											.	HSH2D	16	.	0			c.G442C						.						21	25	24					19																	16265269		1954	4091	6045	SO:0001583	missense	84941	exon7			GCCGAGGAAGCTG	AK027792	CCDS74304.1	19p13.12	2013-02-14				ENSG00000196684		"SH2 domain containing"	24920	protein-coding gene	gene with protein product		608349				11700021	Standard	NM_032855		Approved	ALX, HSH2, FLJ14886	uc002ndp.4	Q96JZ2		ENST00000253680.6:c.442G>C	chr19.hg19:g.16265269G>C	ENSP00000253680:p.Glu148Gln	34.0	0.0		33.0	10.0	NM_032855	B5ME72|Q6ZNG7	Missense_Mutation	SNP	ENST00000253680.6	hg19		.	.	.	.	.	.	.	.	.	.	G	11.93	1.786974	0.31593	.	.	ENSG00000196684	ENST00000397372;ENST00000253680	T	0.48201	0.82	3.97	2.94	0.34122	.	1.229700	0.05981	N	0.644185	T	0.39517	0.1081	L	0.42245	1.32	0.09310	N	1	P;P	0.39883	0.693;0.567	B;B	0.35931	0.214;0.086	T	0.31586	-0.9938	10	0.45353	T	0.12	.	7.2638	0.26217	0.1178:0.0:0.8822:0.0	.	91;148	Q96JZ2-2;Q96JZ2	.;HSH2D_HUMAN	Q	59;148	ENSP00000253680:E148Q	ENSP00000253680:E148Q	E	+	1	0	HSH2D	16126269	0.791000	0.28800	0.027000	0.17364	0.034000	0.12701	2.273000	0.43381	1.278000	0.44430	0.591000	0.81541	GAA	.	.		0.617	HSH2D-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_032855		C	16265269	G	C	16265269	3	2	321	1	0	0	0	0	1	0	0	0	7409	1175	41	4	456	4	HSH2D	19	16265269	Missense_Mutation	SNP	G	TCGA-MI-A75E-01A-11D-A32G-10	972824	16265269	42863714	106	45237										
ZNF568	374900	hgsc.bcm.edu	37	chr19	37413702	37413702	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	caatcttcagtgatcagcaaTagctgtgtgacaatggagcg	11	8	3	2			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr19:37413702T>A	ENST00000333987.7	+	3	536	c.30T>A	c.(28-30)aaT>aaA	p.N10K	ZNF568_ENST00000455427.2_Intron|ZNF568_ENST00000427117.1_Missense_Mutation_p.N10K|ZNF568_ENST00000415168.1_Intron	NM_001204835.1|NM_198539.3	NP_001191764.1|NP_940941.2	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	10					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(9)|ovary(1)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TGATCAGCAATAGCTGTGTGA	0.507																																					p.N10K		Atlas-SNP	.											.	ZNF568	106	.	0			c.T30A						.						113	111	112					19																	37413702		1980	4157	6137	SO:0001583	missense	374900	exon3			CAGCAATAGCTGT	BX640681	CCDS42558.1, CCDS56092.1, CCDS56093.1, CCDS74351.1	19q13.12	2013-09-20			ENSG00000198453	ENSG00000198453		"Zinc fingers, C2H2-type", "-"	25392	protein-coding gene	gene with protein product							Standard	NM_198539		Approved	DKFZp686B0797	uc002ofc.3	Q3ZCX4	OTTHUMG00000048160	ENST00000333987.7:c.30T>A	chr19.hg19:g.37413702T>A	ENSP00000334685:p.Asn10Lys	47.0	0.0		53.0	9.0	NM_001204838	B4DS92|E7ER33|Q6N060|Q8NA64	Missense_Mutation	SNP	ENST00000333987.7	hg19	CCDS42558.1	.	.	.	.	.	.	.	.	.	.	T	11.54	1.670042	0.29693	.	.	ENSG00000198453	ENST00000427117;ENST00000333987;ENST00000444991	T;T;T	0.06068	5.89;3.58;3.35	3.05	-0.648	0.11464	.	.	.	.	.	T	0.02380	0.0073	N	0.08118	0	0.80722	D	1	B	0.09022	0.002	B	0.14023	0.01	T	0.47898	-0.9081	9	0.12103	T	0.63	.	3.0189	0.06069	0.0:0.2903:0.2341:0.4755	.	10	Q3ZCX4	ZN568_HUMAN	K	10	ENSP00000407012:N10K;ENSP00000334685:N10K;ENSP00000389794:N10K	ENSP00000334685:N10K	N	+	3	2	ZNF568	42105542	0.003000	0.15002	0.882000	0.34594	0.722000	0.41435	-0.658000	0.05329	-0.197000	0.10350	0.454000	0.30748	AAT	.	.		0.507	ZNF568-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109572.2	NM_198539		A	37413702	T	A	37413702	3	1	321	1	0	0	0	0	1	0	0	0	18014	1403	49	4	32	4	ZNF568	19	37413702	Missense_Mutation	SNP	T	TCGA-MI-A75E-01A-11D-A32G-10	21148433	37413702	21715281	107	45238										
PAK4	10298	hgsc.bcm.edu	37	chr19	39660216	39660216	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	gtttgggaagaggaagaagcGggtggagatctccgcgccgt	18	7	1	3			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr19:39660216G>A	ENST00000593690.1	+	4	450	c.23G>A	c.(22-24)cGg>cAg	p.R8Q	PAK4_ENST00000321944.4_Missense_Mutation_p.R8Q|PAK4_ENST00000358301.3_Missense_Mutation_p.R8Q|PAK4_ENST00000599386.1_Missense_Mutation_p.R8Q|PAK4_ENST00000599470.1_Missense_Mutation_p.R8Q|PAK4_ENST00000360442.3_Missense_Mutation_p.R8Q|PAK4_ENST00000435673.2_Missense_Mutation_p.R8Q	NM_001014831.2	NP_001014831.1	O96013	PAK4_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 4	8					apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|cytoskeleton organization (GO:0007010)|signal transduction (GO:0007165)	focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	13	all_cancers(60;1.03e-07)|all_epithelial(25;9.66e-08)|all_lung(34;1.58e-07)|Lung NSC(34;1.88e-07)|Ovarian(47;0.0454)		Epithelial(26;4.82e-25)|all cancers(26;2.94e-22)|Lung(45;0.000797)|LUSC - Lung squamous cell carcinoma(53;0.00113)			AGGAAGAAGCGGGTGGAGATC	0.657																																					p.R8Q		Atlas-SNP	.											.	PAK4	40	.	0			c.G23A						.						53	54	54					19																	39660216		2203	4300	6503	SO:0001583	missense	10298	exon2			AGAAGCGGGTGGA	AJ011855	CCDS12528.1, CCDS33019.1	19p11-q11	2008-06-17	2008-06-17						16059	protein-coding gene	gene with protein product		605451	"p21(CDKN1A)-activated kinase 4"			9822598, 10461188	Standard	NM_001014831		Approved		uc002okn.1	O96013		ENST00000593690.1:c.23G>A	chr19.hg19:g.39660216G>A	ENSP00000469413:p.Arg8Gln	109.0	0.0		102.0	19.0	NM_001014832	B4DGG6|Q8N4E1|Q8NCH5|Q8NDE3|Q9BU33|Q9ULS8	Missense_Mutation	SNP	ENST00000593690.1	hg19	CCDS12528.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.224710	0.79576	.	.	ENSG00000130669	ENST00000358301;ENST00000321944;ENST00000435673;ENST00000360442	T;T;T;T	0.74209	-0.82;-0.79;-0.82;-0.82	3.74	3.74	0.42951	.	0.000000	0.64402	U	0.000002	D	0.84266	0.5434	M	0.75447	2.3	0.50039	D	0.999849	D;D;D	0.76494	0.999;0.998;0.997	D;D;D	0.72982	0.96;0.979;0.953	D	0.86406	0.1745	10	0.72032	D	0.01	.	13.4054	0.60911	0.0:0.0:1.0:0.0	.	8;8;8	O96013-4;O96013-3;O96013	.;.;PAK4_HUMAN	Q	8	ENSP00000351049:R8Q;ENSP00000326864:R8Q;ENSP00000392753:R8Q;ENSP00000353625:R8Q	ENSP00000326864:R8Q	R	+	2	0	PAK4	44352056	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	9.474000	0.97718	2.067000	0.61834	0.479000	0.44913	CGG	.	.		0.657	PAK4-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463823.1			A	39660216	G	A	39660216	3	1	321	1	0	0	0	0	1	0	0	0	11412	1116	39	1	25	1	PAK4	19	39660216	Missense_Mutation	SNP	G	TCGA-MI-A75E-01A-11D-A32G-10	2246514	39660216	19468767	108	45239										
ARHGAP35	2909	hgsc.bcm.edu	37	chr19	47425519	47425519	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	agaggaggatcaggcatcccAgggttataaaggggacaatg	15	6	1	1			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr19:47425519A>T	ENST00000404338.3	+	1	3587	c.3587A>T	c.(3586-3588)cAg>cTg	p.Q1196L		NM_004491.4	NP_004482.4	Q9NRY4	RHG35_HUMAN	Rho GTPase activating protein 35	1196					axon guidance (GO:0007411)|camera-type eye development (GO:0043010)|forebrain development (GO:0030900)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular permeability (GO:0043116)|neural tube closure (GO:0001843)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|GTP binding (GO:0005525)|Rho GTPase activator activity (GO:0005100)|transcription corepressor activity (GO:0003714)										CAGGCATCCCAGGGTTATAAA	0.547																																					p.Q1196L		Atlas-SNP	.											.	.	.	.	0			c.A3587T						.						51	51	51					19																	47425519		1974	4173	6147	SO:0001583	missense	2909	exon1			CATCCCAGGGTTA	M73077	CCDS46127.1	19q13.32	2011-06-29	2011-06-07	2011-06-07	ENSG00000160007	ENSG00000160007		"Rho GTPase activating proteins"	4591	protein-coding gene	gene with protein product		605277	"glucocorticoid receptor DNA binding factor 1"	GRLF1		1894621, 20675588	Standard	NM_004491		Approved	GRF-1, p190ARhoGAP, P190A, KIAA1722, p190RhoGAP	uc010ekv.3	Q9NRY4		ENST00000404338.3:c.3587A>T	chr19.hg19:g.47425519A>T	ENSP00000385720:p.Gln1196Leu	60.0	0.0		41.0	5.0	NM_004491	A7E2A4|Q14452|Q9C0E1	Missense_Mutation	SNP	ENST00000404338.3	hg19	CCDS46127.1	.	.	.	.	.	.	.	.	.	.	A	13.16	2.154474	0.38021	.	.	ENSG00000160007	ENST00000317082;ENST00000404338	T	0.07444	3.19	5.6	4.52	0.55395	.	0.000000	0.64402	D	0.000002	T	0.06234	0.0161	N	0.22421	0.69	0.48830	D	0.999711	B	0.02656	0.0	B	0.04013	0.001	T	0.35151	-0.9800	10	0.27082	T	0.32	-30.6714	11.4825	0.50333	0.8498:0.1502:0.0:0.0	.	1196	Q9NRY4-2	.	L	1196	ENSP00000385720:Q1196L	ENSP00000324820:Q1196L	Q	+	2	0	ARHGAP35	52117359	0.951000	0.32395	1.000000	0.80357	0.987000	0.75469	1.958000	0.40402	2.136000	0.66102	0.533000	0.62120	CAG	.	.		0.547	ARHGAP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466652.1	NM_004491		T	47425519	A	T	47425519	3	4	321	1	0	0	0	0	1	0	0	0	6804	188	7	4	3589	4	ARHGAP35	19	47425519	Missense_Mutation	SNP	A	TCGA-MI-A75E-01A-11D-A32G-10	7765303	47425519	11703464	109	45240										
SEL1L2	80343	hgsc.bcm.edu	37	chr20	13830846	13830846	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	gacaaacttacattaaaaaaCaggatatcccggagcaaatg	7	8	0	0			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr20:13830846C>A	ENST00000284951.5	-	19	2012	c.1938G>T	c.(1936-1938)ctG>ctT	p.L646L	SEL1L2_ENST00000378072.5_Silent_p.L533L|SEL1L2_ENST00000486903.1_5'UTR			Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2 (C. elegans)	646						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	51						CATTAAAAAACAGGATATCCC	0.468																																					p.L533L		Atlas-SNP	.											.	SEL1L2	103	.	0			c.G1599T						.						79	75	76					20																	13830846		1909	4127	6036	SO:0001819	synonymous_variant	80343	exon17			AAAAAACAGGATA	AL137678	CCDS59443.1	20p12.1	2011-03-31	2006-11-24	2006-11-24	ENSG00000101251	ENSG00000101251			15897	protein-coding gene	gene with protein product		614289	"chromosome 20 open reading frame 50"	C20orf50			Standard	NM_001271539		Approved	DKFZp434C1826	uc010zrl.3	Q5TEA6	OTTHUMG00000031910	ENST00000284951.5:c.1938G>T	chr20.hg19:g.13830846C>A		50.0	0.0		62.0	14.0	NM_001271539	B4DXX5	Silent	SNP	ENST00000284951.5	hg19																																																																																				.	.		0.468	SEL1L2-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078067.3	NM_025229		A	13830846	C	A	13830846	2	1	321	1	0	0	0	0	0	0	0	1	14026	465	17	3		3	SEL1L2	20	13830846	Silent	SNP	C	TCGA-MI-A75E-01A-11D-A32G-10		13830846	49194674	110	45241										
C20orf152	140894	hgsc.bcm.edu	37	chr20	34568392	34568392	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	tctccccagggtcactttccTccaaaggccattcagatcat	6	15	4	1			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr20:34568392T>C	ENST00000373973.3	+	4	428	c.255T>C	c.(253-255)ccT>ccC	p.P85P	CNBD2_ENST00000538900.1_Silent_p.P85P|CNBD2_ENST00000349339.1_Silent_p.P85P			Q96M20	CNBD2_HUMAN	cyclic nucleotide binding domain containing 2	85																	GTCACTTTCCTCCAAAGGCCA	0.542																																					p.P85P		Atlas-SNP	.											.	.	.	.	0			c.T255C						.						89	76	80					20																	34568392		2203	4300	6503	SO:0001819	synonymous_variant	140894	exon4			CTTTCCTCCAAAG	AL359828	CCDS13270.1, CCDS56189.1	20q11.23	2012-11-15	2012-11-15	2012-11-15	ENSG00000149646	ENSG00000149646			16145	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 152", "cyclic nucleotide (cNMP) binding domain containing 1"	C20orf152, CNMPD1		11780052	Standard	NM_080834		Approved	dJ954P9.1	uc002xer.1	Q96M20	OTTHUMG00000032371	ENST00000373973.3:c.255T>C	chr20.hg19:g.34568392T>C		94.0	0.0		87.0	25.0	NM_080834	Q14C79|Q5JWY7|Q5T3S1|Q9BR36|Q9BWY5	Silent	SNP	ENST00000373973.3	hg19																																																																																				.	.		0.542	CNBD2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000078960.2	NM_080834		C	34568392	T	C	34568392	2	2	321	1	0	0	0	0	0	0	0	1	2094	1538	54	2		2	C20orf152	20	34568392	Silent	SNP	T	TCGA-MI-A75E-01A-11D-A32G-10	20737546	34568392	28457128	111	45242										
ZNFX1	57169	hgsc.bcm.edu	37	chr20	47864666	47864666	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	gctgttttatgctagttccaTacctcaggtttttgcggatg	10	8	1	0			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr20:47864666T>C	ENST00000396105.1	-	14	5141	c.4895A>G	c.(4894-4896)tAt>tGt	p.Y1632C	ZNFX1_ENST00000371752.1_Missense_Mutation_p.Y1632C|ZNFX1_ENST00000371754.4_Intron	NM_021035.2	NP_066363.1	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1	1632							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(8)|kidney(7)|large_intestine(15)|liver(1)|lung(17)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	60			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			GCTAGTTCCATACCTCAGGTT	0.488																																					p.Y1632C		Atlas-SNP	.											.	ZNFX1	194	.	0			c.A4895G						.						59	58	58					20																	47864666		2203	4300	6503	SO:0001583	missense	57169	exon14			GTTCCATACCTCA	AK022641	CCDS13417.1	20q13.13	2014-02-12			ENSG00000124201	ENSG00000124201			29271	protein-coding gene	gene with protein product						10718198	Standard	NM_021035		Approved	KIAA1404, FLJ11277	uc002xui.3	Q9P2E3	OTTHUMG00000032696	ENST00000396105.1:c.4895A>G	chr20.hg19:g.47864666T>C	ENSP00000379412:p.Tyr1632Cys	101.0	0.0		100.0	25.0	NM_021035	Q9BQM7|Q9BQM8|Q9H8C1|Q9H9S2|Q9NUM1|Q9NWW1	Missense_Mutation	SNP	ENST00000396105.1	hg19	CCDS13417.1	.	.	.	.	.	.	.	.	.	.	T	17.38	3.375618	0.61735	.	.	ENSG00000124201	ENST00000371752;ENST00000396105	T;T	0.58358	0.34;0.34	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	T	0.77942	0.4206	M	0.90369	3.11	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82686	-0.0334	10	0.87932	D	0	-19.4309	15.4003	0.74834	0.0:0.0:0.0:1.0	.	1632	Q9P2E3	ZNFX1_HUMAN	C	1632	ENSP00000360817:Y1632C;ENSP00000379412:Y1632C	ENSP00000360817:Y1632C	Y	-	2	0	ZNFX1	47298073	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	7.993000	0.88291	2.317000	0.78254	0.459000	0.35465	TAT	.	.		0.488	ZNFX1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079647.2	NM_021035		C	47864666	T	C	47864666	3	2	321	1	0	0	0	0	1	0	0	0	18220	1406	49	2	865	2	ZNFX1	20	47864666	Missense_Mutation	SNP	T	TCGA-MI-A75E-01A-11D-A32G-10	13296274	47864666	15160854	112	45243										
NKAIN4	128414	hgsc.bcm.edu	37	chr20	61880213	61880213	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	agaagcagatgatgaagacgTtccaggtgacccagacggct	13	9	0	7			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr20:61880213T>C	ENST00000370316.3	-	3	316	c.227A>G	c.(226-228)aAc>aGc	p.N76S	NKAIN4_ENST00000370307.2_Missense_Mutation_p.N14S|NKAIN4_ENST00000370313.1_Missense_Mutation_p.N14S|NKAIN4_ENST00000466885.1_5'Flank	NM_152864.3	NP_690603.3	Q8IVV8	NKAI4_HUMAN	Na+/K+ transporting ATPase interacting 4	76						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|lung(1)|ovary(1)	4	all_cancers(38;2.72e-09)					GATGAAGACGTTCCAGGTGAC	0.632																																					p.N76S		Atlas-SNP	.											.	NKAIN4	23	.	0			c.A227G						.						72	54	60					20																	61880213		2202	4300	6502	SO:0001583	missense	128414	exon3			AAGACGTTCCAGG	BC041812	CCDS13514.1	20q13.33	2007-10-04	2007-10-04	2007-10-04	ENSG00000101198	ENSG00000101198		"Na+/K+ transporting ATPase interacting"	16191	protein-coding gene	gene with protein product		612873	"chromosome 20 open reading frame 58"	C20orf58		17606467	Standard	NM_152864		Approved	bA261N11.2, FAM77A	uc002yek.3	Q8IVV8	OTTHUMG00000032959	ENST00000370316.3:c.227A>G	chr20.hg19:g.61880213T>C	ENSP00000359340:p.Asn76Ser	38.0	0.0		46.0	9.0	NM_152864	Q4VXQ6|Q9BQU8|Q9BQU9	Missense_Mutation	SNP	ENST00000370316.3	hg19	CCDS13514.1	.	.	.	.	.	.	.	.	.	.	T	15.90	2.968631	0.53614	.	.	ENSG00000101198	ENST00000370313;ENST00000370316;ENST00000370307;ENST00000370317	T;T;T;T	0.25579	1.79;1.79;1.79;1.79	3.44	3.44	0.39384	.	0.000000	0.85682	U	0.000000	T	0.53594	0.1806	M	0.87758	2.905	0.43199	D	0.995042	D;D	0.89917	0.999;1.0	D;D	0.87578	0.998;0.998	T	0.61471	-0.7056	10	0.87932	D	0	-9.841	11.5998	0.50995	0.0:0.0:0.0:1.0	.	14;76	A6NNM2;Q8IVV8	.;NKAI4_HUMAN	S	14;76;14;6	ENSP00000359336:N14S;ENSP00000359340:N76S;ENSP00000359330:N14S;ENSP00000359341:N6S	ENSP00000359330:N14S	N	-	2	0	NKAIN4	61350658	1.000000	0.71417	0.816000	0.32577	0.316000	0.28119	6.682000	0.74528	1.201000	0.43203	0.260000	0.18958	AAC	.	.		0.632	NKAIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080117.3	NM_152864		C	61880213	T	C	61880213	3	2	321	1	0	0	0	0	1	0	0	0	10447	1725	60	2	419	2	NKAIN4	20	61880213	Missense_Mutation	SNP	T	TCGA-MI-A75E-01A-11D-A32G-10	14015547	61880213	1145307	113	45244										
RFPL3	10738	hgsc.bcm.edu	37	chr22	32754310	32754310	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	tgctgttgctgttccatggtCtctcagaggaacaaaatcag	10	9	3	1			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr22:32754310C>T	ENST00000249007.4	+	1	457	c.252C>T	c.(250-252)gtC>gtT	p.V84V	RFPL3_ENST00000397468.1_Silent_p.V55V|RFPL3S_ENST00000461833.1_5'Flank|RFPL3_ENST00000382088.3_Silent_p.V55V	NM_001098535.1	NP_001092005.1	O75679	RFPL3_HUMAN	ret finger protein-like 3	84							zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|stomach(1)	15						GTTCCATGGTCTCTCAGAGGA	0.532																																					p.V84V		Atlas-SNP	.											.	RFPL3	91	.	0			c.C252T						.						128	119	122					22																	32754310		2203	4300	6503	SO:0001819	synonymous_variant	10738	exon1			CATGGTCTCTCAG	AJ010232	CCDS13904.1, CCDS43011.1	22q12	2006-04-25			ENSG00000128276	ENSG00000128276			9980	protein-coding gene	gene with protein product		605970				10508838	Standard	NM_006604		Approved		uc010gwn.3	O75679	OTTHUMG00000030290	ENST00000249007.4:c.252C>T	chr22.hg19:g.32754310C>T		119.0	0.0		137.0	25.0	NM_001098535	A2A279|Q6IC03|Q6IC04|Q6NSX3|Q8N5R4	Silent	SNP	ENST00000249007.4	hg19	CCDS43011.1																																																																																			.	.		0.532	RFPL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075172.3	NM_006604		T	32754310	C	T	32754310	2	4	321	1	0	0	0	0	0	0	0	1	13270	900	32	3		3	RFPL3	22	32754310	Silent	SNP	C	TCGA-MI-A75E-01A-11D-A32G-10		32754310	18550256	114	45245										
PICK1	9463	hgsc.bcm.edu	37	chr22	38469082	38469082	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	ccatcaagaagtacctggacGtgaagtttgagtacctggtg	12	8	1	3	rs199605777		TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chr22:38469082G>A	ENST00000404072.3	+	10	1113	c.766G>A	c.(766-768)Gtg>Atg	p.V256M	RP5-1039K5.13_ENST00000445483.1_RNA|PICK1_ENST00000356976.3_Missense_Mutation_p.V256M	NM_001039583.1|NM_001039584.1	NP_001034672.1|NP_001034673.1	Q9NRD5	PICK1_HUMAN	protein interacting with PRKCA 1	256	AH. {ECO:0000255|PROSITE- ProRule:PRU00294}.				ATP catabolic process (GO:0006200)|cellular response to decreased oxygen levels (GO:0036294)|cellular response to glucose starvation (GO:0042149)|dendritic spine maintenance (GO:0097062)|dendritic spine organization (GO:0097061)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|glial cell development (GO:0021782)|long term synaptic depression (GO:0060292)|monoamine transport (GO:0015844)|negative regulation of Arp2/3 complex-mediated actin nucleation (GO:0034316)|neuronal ion channel clustering (GO:0045161)|positive regulation of receptor internalization (GO:0002092)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|protein targeting (GO:0006605)|receptor clustering (GO:0043113)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endocytic vesicle membrane (GO:0030666)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	actin filament binding (GO:0051015)|Arp2/3 complex binding (GO:0071933)|ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein kinase C binding (GO:0005080)|receptor binding (GO:0005102)			cervix(1)|endometrium(3)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13	Melanoma(58;0.045)					GTACCTGGACGTGAAGTTTGA	0.582																																					p.V256M		Atlas-SNP	.											.	PICK1	30	.	0			c.G766A						.						193	153	166					22																	38469082		2203	4300	6503	SO:0001583	missense	9463	exon10			CTGGACGTGAAGT	AL049654	CCDS13965.1	22q13.1	2006-02-14	2006-02-14	2006-02-14	ENSG00000100151	ENSG00000100151			9394	protein-coding gene	gene with protein product		605926	"protein kinase C, alpha binding protein", "protein interacting with PRKCA"	PRKCABP		10340301, 10591208	Standard	XM_006724377		Approved	dJ1039K5, MGC15204	uc003aus.3	Q9NRD5	OTTHUMG00000151159	ENST00000404072.3:c.766G>A	chr22.hg19:g.38469082G>A	ENSP00000385205:p.Val256Met	110.0	0.0		120.0	18.0	NM_012407	B3KS52|O95906	Missense_Mutation	SNP	ENST00000404072.3	hg19	CCDS13965.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.641864	0.87859	.	.	ENSG00000100151	ENST00000404072;ENST00000356976	T;T	0.78246	-1.16;-1.16	5.64	5.64	0.86602	Arfaptin-like (3);	0.000000	0.85682	D	0.000000	D	0.87051	0.6081	M	0.66939	2.045	0.80722	D	1	D	0.76494	0.999	D	0.64877	0.93	D	0.87222	0.2254	10	0.72032	D	0.01	-35.3262	20.0957	0.97842	0.0:0.0:1.0:0.0	.	256	Q9NRD5	PICK1_HUMAN	M	256	ENSP00000385205:V256M;ENSP00000349465:V256M	ENSP00000349465:V256M	V	+	1	0	PICK1	36799028	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.205000	0.95048	2.837000	0.97791	0.655000	0.94253	GTG	.	G|0.999;A|0.001		0.582	PICK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321569.2	NM_012407		A	38469082	G	A	38469082	3	1	321	1	0	0	0	0	1	0	0	0	11890	1145	40	1	800	1	PICK1	22	38469082	Missense_Mutation	SNP	G	TCGA-MI-A75E-01A-11D-A32G-10	5714772	38469082	12835484	115	45246										
NAP1L2	4674	hgsc.bcm.edu	37	chrX	72433658	72433658	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	tctcttctccagtagcctcaAtgtcgtcctcctcctcctcc	4	19	3	0			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chrX:72433658A>G	ENST00000373517.3	-	1	1026	c.671T>C	c.(670-672)aTt>aCt	p.I224T	NAP1L2_ENST00000536638.1_Missense_Mutation_p.I82T	NM_021963.3	NP_068798.1	Q9ULW6	NP1L2_HUMAN	nucleosome assembly protein 1-like 2	224	Glu-rich (acidic).				nucleosome assembly (GO:0006334)|positive regulation of histone H3-K14 acetylation (GO:0071442)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of neuron differentiation (GO:0045666)|regulation of stem cell division (GO:2000035)	nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(12)|skin(3)	29	Renal(35;0.156)					AGTAGCCTCAATGTCGtcctc	0.423																																					p.I224T		Atlas-SNP	.											.	NAP1L2	77	.	0			c.T671C						.						70	54	59					X																	72433658		2203	4300	6503	SO:0001583	missense	4674	exon1			GCCTCAATGTCGT	AF136178	CCDS14423.1	Xq13	2008-02-05			ENSG00000186462	ENSG00000186462			7638	protein-coding gene	gene with protein product		300026				8789438	Standard	NM_021963		Approved	BPX, MGC26243	uc004ebi.3	Q9ULW6	OTTHUMG00000021827	ENST00000373517.3:c.671T>C	chrX.hg19:g.72433658A>G	ENSP00000362616:p.Ile224Thr	52.0	0.0		98.0	14.0	NM_021963	B2RE61|B4E161|Q8TAN6	Missense_Mutation	SNP	ENST00000373517.3	hg19	CCDS14423.1	.	.	.	.	.	.	.	.	.	.	a	0.004	-2.329258	0.00229	.	.	ENSG00000186462	ENST00000373517;ENST00000536638	T;T	0.40225	1.04;1.04	3.01	-5.44	0.02624	.	.	.	.	.	T	0.13586	0.0329	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.30268	-0.9984	9	0.14252	T	0.57	0.1061	7.0647	0.25145	0.3014:0.1413:0.5572:0.0	.	224	Q9ULW6	NP1L2_HUMAN	T	224;82	ENSP00000362616:I224T;ENSP00000441555:I82T	ENSP00000362616:I224T	I	-	2	0	NAP1L2	72350383	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	-2.003000	0.01463	-1.573000	0.01659	-0.453000	0.05500	ATT	.	.		0.423	NAP1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057225.1	NM_021963		G	72433658	A	G	72433658	3	3	321	1	0	0	0	0	1	0	0	0	10166	101	4	2	715	2	NAP1L2	23	72433658	Missense_Mutation	SNP	A	TCGA-MI-A75E-01A-11D-A32G-10		72433658	82836902	116	45247										
CXorf41	139212	hgsc.bcm.edu	37	chrX	106486408	106486408	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0775862068965517	9	1	1.39450549450549	1.18321678321678	1.46947890818859	0.0804953560371517	0.566505052865237	0	tttttttttaggaagctgttGataactcttcctgagctggt	9	6	1	2			TCGA-MI-A75E-01A-11D-A32G-10	TCGA-MI-A75E-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea65f8a8-708d-4880-9272-8bbb6f840341	08d2414c-c7d1-47bc-b387-9302d862a298	g.chrX:106486408G>C	ENST00000372453.3	+	7	587	c.525G>C	c.(523-525)ttG>ttC	p.L175F	PIH1D3_ENST00000535523.1_Missense_Mutation_p.L175F|PIH1D3_ENST00000336387.4_Missense_Mutation_p.L175F	NM_173494.1	NP_775765.1	Q9NQM4	PIHD3_HUMAN	PIH1 domain containing 3	175																	GGAAGCTGTTGATAACTCTTC	0.353																																					p.L175F		Atlas-SNP	.											.	.	.	.	0			c.G525C						.						97	96	97					X																	106486408		2203	4299	6502	SO:0001583	missense	139212	exon7			GCTGTTGATAACT	AL136112	CCDS14528.1	Xq22.3	2014-05-20	2012-07-18	2012-07-18	ENSG00000080572	ENSG00000080572			28570	protein-coding gene	gene with protein product	"sarcoma antigen NY-SAR-97"		"chromosome X open reading frame 41"	CXorf41		12601173, 24421334	Standard	NM_001169154		Approved	MGC35261, NYSAR97	uc004enc.3	Q9NQM4	OTTHUMG00000022160	ENST00000372453.3:c.525G>C	chrX.hg19:g.106486408G>C	ENSP00000361531:p.Leu175Phe	96.0	0.0		131.0	34.0	NM_173494	D3DUX5|Q86WE1	Missense_Mutation	SNP	ENST00000372453.3	hg19	CCDS14528.1	.	.	.	.	.	.	.	.	.	.	G	0.986	-0.695475	0.03279	.	.	ENSG00000080572	ENST00000372453;ENST00000535523;ENST00000336387	T;T;T	0.17691	2.26;2.26;2.26	5.03	2.03	0.26663	.	0.279934	0.28555	N	0.014928	T	0.30293	0.0760	M	0.73598	2.24	0.09310	N	1	D	0.61080	0.989	P	0.62298	0.9	T	0.05666	-1.0871	10	0.49607	T	0.09	0.3886	3.5279	0.07766	0.2619:0.2365:0.5015:0.0	.	175	Q9NQM4	CX041_HUMAN	F	175	ENSP00000361531:L175F;ENSP00000441930:L175F;ENSP00000337757:L175F	ENSP00000337757:L175F	L	+	3	2	CXorf41	106373064	0.257000	0.24022	0.030000	0.17652	0.016000	0.09150	0.586000	0.23894	0.874000	0.35823	0.544000	0.68410	TTG	.	.		0.353	PIH1D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057832.1	NM_173494		C	106486408	G	C	106486408	3	2	321	1	0	0	0	0	1	0	0	0	4112	1281	45	4	547	4	CXorf41	23	106486408	Missense_Mutation	SNP	G	TCGA-MI-A75E-01A-11D-A32G-10	34052750	106486408	48784152	117	45248										
TPRG1L	127262	hgsc.bcm.edu	37	chr1	3542442	3542442	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gaattccagtttccccctaaAtcgctcaacaagtaagcctg	6	13	1	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr1:3542442A>G	ENST00000378344.2	+	3	530	c.459A>G	c.(457-459)aaA>aaG	p.K153K	RP11-46F15.2_ENST00000435049.1_RNA|TPRG1L_ENST00000344579.5_Intron	NM_182752.3	NP_877429.2	Q5T0D9	TPRGL_HUMAN	tumor protein p63 regulated 1-like	153						cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|synaptic vesicle (GO:0008021)				endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|prostate(1)	8	all_cancers(77;0.0119)|all_epithelial(69;0.00481)|Ovarian(185;0.0634)|Lung NSC(156;0.162)|all_lung(157;0.172)	all_epithelial(116;7.37e-22)|all_lung(118;8.23e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.41e-38)|OV - Ovarian serous cystadenocarcinoma(86;3.83e-22)|GBM - Glioblastoma multiforme(42;4.77e-14)|Colorectal(212;1.12e-05)|COAD - Colon adenocarcinoma(227;5.61e-05)|Kidney(185;0.000351)|BRCA - Breast invasive adenocarcinoma(365;0.000688)|KIRC - Kidney renal clear cell carcinoma(229;0.00553)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.201)		TTCCCCCTAAATCGCTCAACA	0.502																																					p.K153K		Atlas-SNP	.											.	TPRG1L	24	.	0			c.A459G						.						65	61	63					1																	3542442		2203	4299	6502	SO:0001819	synonymous_variant	127262	exon3			CCCTAAATCGCTC	BC019034	CCDS47.1	1p36.32	2008-02-05	2008-01-16	2008-01-16	ENSG00000158109	ENSG00000158109			27007	protein-coding gene	gene with protein product		611460	"family with sequence similarity 79, member A"	FAM79A		12477932	Standard	NM_182752		Approved	RP11-46F15.3, FLJ21811	uc001akm.3	Q5T0D9	OTTHUMG00000000609	ENST00000378344.2:c.459A>G	chr1.hg19:g.3542442A>G		15.0	0.0		25.0	6.0	NM_182752	A8K1K4|Q8WV04	Silent	SNP	ENST00000378344.2	hg19	CCDS47.1																																																																																			.	.		0.502	TPRG1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001466.1	NM_182752		G	3542442	A	G	3542442	2	3	322	1	0	0	0	0	0	0	0	1	16434	98	4	2		2	TPRG1L	1	3542442	Silent	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10		3542442	245708179	1	45249										
LRRC47	57470	hgsc.bcm.edu	37	chr1	3712543	3712543	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	aagagctcggcgggaaaggaGtctaggcaattgccggtgag	17	7	1	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr1:3712543G>C	ENST00000378251.1	-	1	525	c.498C>G	c.(496-498)gaC>gaG	p.D166E		NM_020710.2	NP_065761.1	Q8N1G4	LRC47_HUMAN	leucine rich repeat containing 47	166							phenylalanine-tRNA ligase activity (GO:0004826)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|urinary_tract(1)	17	all_cancers(77;0.0375)|Ovarian(185;0.0634)|all_lung(157;0.208)|Lung NSC(156;0.21)	all_epithelial(116;1.34e-16)|all_lung(118;2.53e-06)|Lung NSC(185;0.00028)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.0743)|Ovarian(437;0.127)		Epithelial(90;5.49e-39)|OV - Ovarian serous cystadenocarcinoma(86;1.43e-22)|GBM - Glioblastoma multiforme(42;3.69e-16)|Colorectal(212;1.21e-05)|COAD - Colon adenocarcinoma(227;5.87e-05)|Kidney(185;0.000367)|BRCA - Breast invasive adenocarcinoma(365;0.000704)|KIRC - Kidney renal clear cell carcinoma(229;0.00567)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.124)		CGGGAAAGGAGTCTAGGCAAT	0.697																																					p.D166E		Atlas-SNP	.											.	LRRC47	42	.	0			c.C498G						.						13	12	12					1																	3712543		2166	4247	6413	SO:0001583	missense	57470	exon1			AAAGGAGTCTAGG	AB033011	CCDS51.1	1p36.32	2008-02-05			ENSG00000130764	ENSG00000130764			29207	protein-coding gene	gene with protein product						10574461	Standard	NM_020710		Approved	KIAA1185, RP1-286D6.3	uc001akx.1	Q8N1G4	OTTHUMG00000003506	ENST00000378251.1:c.498C>G	chr1.hg19:g.3712543G>C	ENSP00000367498:p.Asp166Glu	20.0	0.0		18.0	6.0	NM_020710	Q9ULN5	Missense_Mutation	SNP	ENST00000378251.1	hg19	CCDS51.1	.	.	.	.	.	.	.	.	.	.	G	1.088	-0.665020	0.03428	.	.	ENSG00000130764	ENST00000378251	T	0.08720	3.06	4.08	4.08	0.47627	.	0.634547	0.16442	N	0.214262	T	0.04452	0.0122	N	0.05608	-0.01	0.19300	N	0.999973	B	0.28820	0.224	B	0.28916	0.096	T	0.28170	-1.0052	10	0.02654	T	1	-27.7811	15.2691	0.73686	0.0:0.0:1.0:0.0	.	166	Q8N1G4	LRC47_HUMAN	E	166	ENSP00000367498:D166E	ENSP00000367498:D166E	D	-	3	2	LRRC47	3702403	0.000000	0.05858	0.992000	0.48379	0.228000	0.25075	0.236000	0.17967	1.817000	0.53016	0.561000	0.74099	GAC	.	.		0.697	LRRC47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009744.1	NM_020710		C	3712543	G	C	3712543	3	2	322	1	0	0	0	0	1	0	0	0	9013	1020	36	4	1281	4	LRRC47	1	3712543	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	170101	3712543	245538078	2	45250										
KIAA0562	9731	hgsc.bcm.edu	37	chr1	3740103	3740103	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cattccgtcagcaagtgctcCgtcagactggatatctcgac	9	13	3	1	rs374760299		TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr1:3740103C>G	ENST00000378230.3	-	19	2712	c.2388G>C	c.(2386-2388)acG>acC	p.T796T		NM_014704.3	NP_055519.1	O60308	CE104_HUMAN	centrosomal protein 104kDa	796						centriole (GO:0005814)	glutamate binding (GO:0016595)|glycine binding (GO:0016594)|thienylcyclohexylpiperidine binding (GO:0016596)			breast(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(14)|lung(8)|prostate(1)|skin(3)	39						GCAAGTGCTCCGTCAGACTGG	0.512																																					p.T796T		Atlas-SNP	.											.	CEP104	79	.	0			c.G2388C						.						156	143	148					1																	3740103		2203	4300	6503	SO:0001819	synonymous_variant	9731	exon19			GTGCTCCGTCAGA	AB011134	CCDS30571.1	1p36.32	2014-02-20	2011-05-06	2011-05-06	ENSG00000116198	ENSG00000116198			24866	protein-coding gene	gene with protein product	"glycine, glutamate, thienylcyclohexylpiperidine binding protein"		"KIAA0562"	KIAA0562		7488117, 21399614	Standard	NM_014704		Approved	GlyBP, RP1-286D6.4	uc001aky.2	O60308	OTTHUMG00000003507	ENST00000378230.3:c.2388G>C	chr1.hg19:g.3740103C>G		56.0	0.0		57.0	17.0	NM_014704	Q5JSQ3|Q5SR24|Q5SR25|Q6PKF5|Q86W32|Q86X14	Silent	SNP	ENST00000378230.3	hg19	CCDS30571.1	.	.	.	.	.	.	.	.	.	.	C	0.249	-1.007712	0.02112	.	.	ENSG00000116198	ENST00000438539	.	.	.	5.68	-11.4	0.00090	.	.	.	.	.	T	0.43277	0.1240	.	.	.	0.58432	D	0.999998	.	.	.	.	.	.	T	0.54523	-0.8281	4	.	.	.	.	7.484	0.27421	0.0754:0.1586:0.1497:0.6164	.	.	.	.	P	93	.	.	R	-	2	0	CEP104	3729963	0.000000	0.05858	0.179000	0.23059	0.086000	0.17979	-6.131000	0.00079	-2.525000	0.00495	-1.640000	0.00773	CGG	.	.		0.512	CEP104-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009747.3	NM_014704		G	3740103	C	G	3740103	2	3	322	1	0	0	0	0	0	0	0	1	8193	639	23	4		4	KIAA0562	1	3740103	Silent	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	27560	3740103	245510518	3	45251										
SLC2A5	6518	hgsc.bcm.edu	37	chr1	9117613	9117614	+	Nonsense_Mutation	DNP	CC	CC	AA													0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	caacgtcaaggggaagtcttCcatgaattcaccggtcctac							TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr1:9117613_9117614CC>AA	ENST00000377424.4	-	3	365_366	c.186_187GG>TT	c.(184-189)atGGaa>atTTaa	p.62_63ME>I*	SLC2A5_ENST00000535586.1_Intron|SLC2A5_ENST00000377414.3_Nonsense_Mutation_p.62_63ME>I*	NM_003039.2	NP_003030.1	P22732	GTR5_HUMAN	solute carrier family 2 (facilitated glucose/fructose transporter), member 5	62					carbohydrate metabolic process (GO:0005975)|cellular response to fructose stimulus (GO:0071332)|fructose transport (GO:0015755)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fructose transmembrane transporter activity (GO:0005353)|glucose transmembrane transporter activity (GO:0005355)			endometrium(6)|kidney(15)|large_intestine(6)|lung(4)|ovary(1)|pancreas(2)|prostate(1)|urinary_tract(1)	36	Ovarian(185;0.112)|all_lung(157;0.185)	all_epithelial(116;1.34e-15)|all_lung(118;9.46e-05)|Lung NSC(185;0.000172)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.00715)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;7.78e-07)|COAD - Colon adenocarcinoma(227;8.83e-05)|Kidney(185;0.000286)|KIRC - Kidney renal clear cell carcinoma(229;0.00103)|STAD - Stomach adenocarcinoma(132;0.0019)|BRCA - Breast invasive adenocarcinoma(304;0.00199)|READ - Rectum adenocarcinoma(331;0.0649)		GGGAAGTCTTCCATGAATTCAC	0.441																																					p.E63X|p.M62I		Atlas-SNP	.											.	SLC2A5	77	.	0			c.G187T|c.G186T						.																																			SO:0001587	stop_gained	6518	exon3			AGTCTTCCATGAA|GTCTTCCATGAAT	BC001820	CCDS99.1, CCDS44054.1	1p36.2	2013-05-22			ENSG00000142583	ENSG00000142583		"Solute carriers"	11010	protein-coding gene	gene with protein product		138230		GLUT5		9691177	Standard	NM_003039		Approved		uc001apo.3	P22732	OTTHUMG00000001771	ENST00000377424.4:c.186_187delinsAA	chr1.hg19:g.9117613_9117614delinsAA	ENSP00000366641:p.M62_E63delinsI*	70.0	0.0		75.0	26.0	NM_003039	Q14770|Q5T977|Q8IVB3	Nonsense_Mutation|Missense_Mutation	SNP	ENST00000377424.4	hg19	CCDS99.1																																																																																			.	.		0.441	SLC2A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004932.1	NM_003039		AA	9117614	CC	AA	9117613	4	1	322	1	0	0	0	0	0	1	0	0	14563	864	30	3	1522	3	SLC2A5	1	9117613	Nonsense_Mutation	DNP	CC	TCGA-MI-A75G-01A-11D-A32G-10	5377510	9117613	240133008	4	45252										
IPO13	9670	hgsc.bcm.edu	37	chr1	44422488	44422488	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cctggctctctcaggatgatAttctatcctttgaggcagag	10	10	3	3			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr1:44422488A>T	ENST00000372343.3	+	5	1773	c.1111A>T	c.(1111-1113)Att>Ttt	p.I371F	IPO13_ENST00000492152.1_3'UTR	NM_014652.3	NP_055467.3	O94829	IPO13_HUMAN	importin 13	371					protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0821)				TCAGGATGATATTCTATCCTT	0.542																																					p.I371F		Atlas-SNP	.											.	IPO13	86	.	0			c.A1111T						.						83	82	82					1																	44422488		2203	4300	6503	SO:0001583	missense	9670	exon5			GATGATATTCTAT	AB018267	CCDS503.1	1p34.1	2008-02-05			ENSG00000117408	ENSG00000117408		"Importins"	16853	protein-coding gene	gene with protein product		610411				9872452, 11447110	Standard	NM_014652		Approved	IMP13, KIAA0724, RANBP13	uc001ckx.3	O94829	OTTHUMG00000008297	ENST00000372343.3:c.1111A>T	chr1.hg19:g.44422488A>T	ENSP00000361418:p.Ile371Phe	31.0	0.0		38.0	19.0	NM_014652	D3DPY4|Q5T4X3|Q7LC04|Q96HS3|Q9H8N3|Q9UFR1	Missense_Mutation	SNP	ENST00000372343.3	hg19	CCDS503.1	.	.	.	.	.	.	.	.	.	.	A	15.47	2.842889	0.51057	.	.	ENSG00000117408	ENST00000372343	T	0.67345	-0.26	5.82	5.82	0.92795	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.60753	0.2293	L	0.44542	1.39	0.80722	D	1	P	0.42357	0.777	B	0.38500	0.275	T	0.63915	-0.6529	10	0.48119	T	0.1	-14.9255	16.1778	0.81874	1.0:0.0:0.0:0.0	.	371	O94829	IPO13_HUMAN	F	371	ENSP00000361418:I371F	ENSP00000361418:I371F	I	+	1	0	IPO13	44195075	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	8.970000	0.93415	2.225000	0.72522	0.459000	0.35465	ATT	.	.		0.542	IPO13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022846.1	NM_014652		T	44422488	A	T	44422488	3	4	322	1	0	0	0	0	1	0	0	0	7803	449	16	4	1129	4	IPO13	1	44422488	Missense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	35304875	44422488	204828133	5	45253										
KIAA0494	9813	hgsc.bcm.edu	37	chr1	47144177	47144177	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ctccaggaatgagtatcttcCatctccatcggaatcaaatg	7	11	3	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr1:47144177C>T	ENST00000371933.3	-	11	2420	c.1444G>A	c.(1444-1446)Gga>Aga	p.G482R	EFCAB14-AS1_ENST00000442839.1_RNA|EFCAB14-AS1_ENST00000418985.1_RNA|EFCAB14_ENST00000544071.1_Intron	NM_014774.2	NP_055589.1	O75071	EFC14_HUMAN	EF-hand calcium binding domain 14	482	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)										GAGTATCTTCCATCTCCATCG	0.448																																					p.G482R		Atlas-SNP	.											.	.	.	.	0			c.G1444A						.						117	111	113					1																	47144177		2203	4300	6503	SO:0001583	missense	9813	exon11			ATCTTCCATCTCC	AB007963	CCDS30706.1	1p33	2013-01-10	2012-11-29	2012-11-29	ENSG00000159658	ENSG00000159658		"EF-hand domain containing"	29051	protein-coding gene	gene with protein product			"KIAA0494"	KIAA0494		9455484	Standard	NM_014774		Approved		uc001cqk.4	O75071	OTTHUMG00000007992	ENST00000371933.3:c.1444G>A	chr1.hg19:g.47144177C>T	ENSP00000361001:p.Gly482Arg	41.0	0.0		60.0	19.0	NM_014774	D3DQ23|Q5SXB8	Missense_Mutation	SNP	ENST00000371933.3	hg19	CCDS30706.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.068198	0.76301	.	.	ENSG00000159658	ENST00000371933	T	0.25912	1.77	5.14	4.2	0.49525	EF-hand-like domain (1);	0.356104	0.29355	N	0.012381	T	0.42131	0.1189	L	0.47716	1.5	0.80722	D	1	D;B	0.89917	1.0;0.221	D;B	0.97110	1.0;0.074	T	0.15578	-1.0432	10	0.56958	D	0.05	-7.7213	12.5155	0.56030	0.0:0.921:0.0:0.079	.	274;482	B7Z3D1;O75071	.;K0494_HUMAN	R	482	ENSP00000361001:G482R	ENSP00000361001:G482R	G	-	1	0	KIAA0494	46916764	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.307000	0.51888	2.672000	0.90937	0.591000	0.81541	GGA	.	.		0.448	EFCAB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021931.1	NM_014774		T	47144177	C	T	47144177	3	4	322	1	0	0	0	0	1	0	0	0	8188	603	21	3	47	3	KIAA0494	1	47144177	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	2721689	47144177	202106444	6	45254										
CTH	1491	hgsc.bcm.edu	37	chr1	70881649	70881649	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tttttttcagggttttgaatAtagccgttctggaaatccca	8	7	2	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr1:70881649A>G	ENST00000370938.3	+	2	323	c.179A>G	c.(178-180)tAt>tGt	p.Y60C	CTH_ENST00000464926.1_3'UTR|CTH_ENST00000346806.2_Missense_Mutation_p.Y60C|CTH_ENST00000411986.2_Missense_Mutation_p.Y60C	NM_001902.5	NP_001893.2	Q96IQ7	VSIG2_HUMAN	cystathionine gamma-lyase	0	Ig-like V-type.					integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						GGTTTTGAATATAGCCGTTCT	0.383																																					p.Y60C		Atlas-SNP	.											.	CTH	48	.	0			c.A179G						.						85	92	89					1																	70881649		2203	4300	6503	SO:0001583	missense	1491	exon2			TTGAATATAGCCG	BC015807	CCDS650.1, CCDS651.1, CCDS53333.1	1p31.1	2014-06-24	2014-06-24		ENSG00000116761	ENSG00000116761	4.4.1.1		2501	protein-coding gene	gene with protein product		607657	"cystathionase (cystathionine gamma-lyase)"			1339280	Standard	NM_001902		Approved		uc001dfd.3	P32929	OTTHUMG00000009352	ENST00000370938.3:c.179A>G	chr1.hg19:g.70881649A>G	ENSP00000359976:p.Tyr60Cys	55.0	0.0		60.0	23.0	NM_153742	O95791|Q9NX42	Missense_Mutation	SNP	ENST00000370938.3	hg19	CCDS650.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.272207	0.80469	.	.	ENSG00000116761	ENST00000411986;ENST00000370938;ENST00000346806	D;D;D	0.94280	-1.97;-3.39;-1.97	5.55	5.55	0.83447	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.98280	0.9430	H	0.99590	4.645	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.99683	1.0999	10	0.87932	D	0	-3.6509	14.9772	0.71283	1.0:0.0:0.0:0.0	.	60;60;60	E9PDV0;P32929-2;P32929	.;.;CGL_HUMAN	C	60	ENSP00000413407:Y60C;ENSP00000359976:Y60C;ENSP00000311554:Y60C	ENSP00000311554:Y60C	Y	+	2	0	CTH	70654237	1.000000	0.71417	0.908000	0.35775	0.991000	0.79684	8.943000	0.92975	2.234000	0.73211	0.533000	0.62120	TAT	.	.		0.383	CTH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025918.1	NM_001902		G	70881649	A	G	70881649	3	3	322	1	0	0	0	0	1	0	0	0	4011	449	16	2	185	2	CTH	1	70881649	Missense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	23737472	70881649	178368972	7	45255										
FPGT	8790	hgsc.bcm.edu	37	chr1	74671023	74671023	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ggggcctgatgtttcagttgGggaaaactgcattattagtg	14	5	1	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr1:74671023G>A	ENST00000609362.1	+	4	1329	c.1292G>A	c.(1291-1293)gGg>gAg	p.G431E	FPGT-TNNI3K_ENST00000370899.3_Intron|FPGT-TNNI3K_ENST00000557284.2_Intron|FPGT_ENST00000370898.3_Missense_Mutation_p.G444E|FPGT_ENST00000524915.1_Intron|FPGT-TNNI3K_ENST00000533006.1_Intron|TNNI3K_ENST00000370891.2_Intron|FPGT-TNNI3K_ENST00000370893.1_Intron|FPGT_ENST00000370894.5_Missense_Mutation_p.G159R|FPGT-TNNI3K_ENST00000370895.1_Intron|FPGT_ENST00000534056.1_Missense_Mutation_p.G177E	NM_003838.4	NP_003829.3	O14772	FPGT_HUMAN	fucose-1-phosphate guanylyltransferase	431					fucose metabolic process (GO:0006004)	cytoplasm (GO:0005737)	catalytic activity (GO:0003824)|fucose-1-phosphate guanylyltransferase activity (GO:0047341)|GTP binding (GO:0005525)			breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	39						GTTTCAGTTGGGGAAAACTGC	0.413																																					p.G431E		Atlas-SNP	.											.	FPGT	77	.	0			c.G1292A						.						119	127	124					1																	74671023		2203	4300	6503	SO:0001583	missense	8790	exon4			CAGTTGGGGAAAA	AF017445	CCDS663.1, CCDS663.2	1p31.1	2013-09-24			ENSG00000254685	ENSG00000254685	2.7.7.30		3825	protein-coding gene	gene with protein product		603609				9804772	Standard	NM_003838		Approved	GFPP		O14772	OTTHUMG00000009571	ENST00000609362.1:c.1292G>A	chr1.hg19:g.74671023G>A	ENSP00000476680:p.Gly431Glu	129.0	0.0		137.0	28.0	NM_003838	A6NMH3|B4DRX2|B4E2Y7|E9PNQ2|Q8N5J7	Missense_Mutation	SNP	ENST00000609362.1	hg19	CCDS663.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.16|15.16	2.750374|2.750374	0.49257|0.49257	.|.	.|.	ENSG00000254685|ENSG00000254685	ENST00000370898;ENST00000534056|ENST00000370894	T;T|.	0.71579|.	-0.58;-0.58|.	5.72|5.72	3.85|3.85	0.44370|0.44370	L-fucokinase (1);|.	.|.	.|.	.|.	.|.	T|T	0.67683|0.67683	0.2919|0.2919	M|M	0.82630|0.82630	2.6|2.6	0.80722|0.80722	D|D	1|1	P;P;P|.	0.43169|.	0.513;0.719;0.8|.	B;B;P|.	0.48873|.	0.307;0.403;0.593|.	T|T	0.73033|0.73033	-0.4110|-0.4110	9|6	0.56958|0.87932	D|D	0.05|0	.|.	11.6377|11.6377	0.51213|0.51213	0.0668:0.1247:0.8085:0.0|0.0668:0.1247:0.8085:0.0	.|.	177;56;431|.	E9PNQ2;B4E2Y7;O14772|.	.;.;FPGT_HUMAN|.	E|R	431;177|159	ENSP00000359935:G431E;ENSP00000432819:G177E|.	ENSP00000359935:G431E|ENSP00000359931:G159R	G|G	+|+	2|1	0|0	TNNI3K|TNNI3K	74443611|74443611	1.000000|1.000000	0.71417|0.71417	0.930000|0.930000	0.37139|0.37139	0.432000|0.432000	0.31715|0.31715	5.424000|5.424000	0.66464|0.66464	0.761000|0.761000	0.33130|0.33130	0.655000|0.655000	0.94253|0.94253	GGG|GGG	.	.		0.413	FPGT-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	74671023	G	A	74671023	3	1	322	1	0	0	0	0	1	0	0	0	6045	1232	43	3	1306	3	FPGT	1	74671023	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	3789374	74671023	174579598	8	45256										
ST6GALNAC5	81849	hgsc.bcm.edu	37	chr1	77334301	77334301	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cagcagcagcagcagcagcaAcagcagcagcaggcgtcggc	14	14	0	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr1:77334301A>G	ENST00000477717.1	+	2	370	c.135A>G	c.(133-135)caA>caG	p.Q45Q	ST6GALNAC5_ENST00000496845.1_3'UTR	NM_030965.1	NP_112227.1	Q9BVH7	SIA7E_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	45	Poly-Gln.				glycosphingolipid biosynthetic process (GO:0006688)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	integral component of Golgi membrane (GO:0030173)	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity (GO:0001665)|sialyltransferase activity (GO:0008373)			endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	18						agcagcagcaacagcagcagc	0.716																																					p.Q45Q		Atlas-SNP	.											.	ST6GALNAC5	59	.	0			c.A135G						.						11	12	12					1																	77334301		2032	3963	5995	SO:0001819	synonymous_variant	81849	exon2			GCAGCAACAGCAG		CCDS673.1	1p31.1	2013-03-01	2005-02-07	2005-02-07	ENSG00000117069	ENSG00000117069		"Sialyltransferases"	19342	protein-coding gene	gene with protein product		610134	"sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) E"	SIAT7E		10521438, 10601645	Standard	NM_030965		Approved	MGC3184, ST6GalNAcV	uc001dhi.3	Q9BVH7	OTTHUMG00000009687	ENST00000477717.1:c.135A>G	chr1.hg19:g.77334301A>G		56.0	0.0		109.0	5.0	NM_030965	B1AK82	Silent	SNP	ENST00000477717.1	hg19	CCDS673.1																																																																																			.	.		0.716	ST6GALNAC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026692.2	NM_030965		G	77334301	A	G	77334301	2	3	322	1	0	0	0	0	0	0	0	1	15242	40	2	2		2	ST6GALNAC5	1	77334301	Silent	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	2663278	77334301	171916320	9	45257										
RAB25	57111	hgsc.bcm.edu	37	chr1	156039508	156039508	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	acctcagccctggactctacCaatgttgagctagcctttga	8	13	2	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr1:156039508C>G	ENST00000361084.5	+	4	721	c.480C>G	c.(478-480)acC>acG	p.T160T	RAB25_ENST00000487325.1_3'UTR	NM_020387.2	NP_065120.2	P57735	RAB25_HUMAN	RAB25, member RAS oncogene family	160					positive regulation of cell proliferation (GO:0008284)|protein transport (GO:0015031)|pseudopodium organization (GO:0031268)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	GTP binding (GO:0005525)|myosin V binding (GO:0031489)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	5	Hepatocellular(266;0.158)|all_neural(408;0.195)					TGGACTCTACCAATGTTGAGC	0.478																																					p.T160T		Atlas-SNP	.											.	RAB25	18	.	0			c.C480G						.						266	259	261					1																	156039508		1963	4143	6106	SO:0001819	synonymous_variant	57111	exon4			CTCTACCAATGTT	AF083124	CCDS41413.1	1q22	2008-07-03			ENSG00000132698	ENSG00000132698		"RAB, member RAS oncogene"	18238	protein-coding gene	gene with protein product		612942				11697911	Standard	NM_020387		Approved	CATX-8	uc001fnc.3	P57735	OTTHUMG00000017457	ENST00000361084.5:c.480C>G	chr1.hg19:g.156039508C>G		126.0	0.0		188.0	48.0	NM_020387	Q5VYA2|Q8NG24|Q96GB1|Q9BT12	Silent	SNP	ENST00000361084.5	hg19	CCDS41413.1																																																																																			.	.		0.478	RAB25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046185.1			G	156039508	C	G	156039508	2	3	322	1	0	0	0	0	0	0	0	1	12927	581	21	4		4	RAB25	1	156039508	Silent	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	78705207	156039508	93211113	10	45258										
CCT3	7203	hgsc.bcm.edu	37	chr1	156294772	156294772	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ccccaagataccttattttcTttagggtgctgatcatatca	6	10	3	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr1:156294772T>C	ENST00000295688.3	-	6	693	c.413A>G	c.(412-414)aAg>aGg	p.K138R	CCT3_ENST00000368259.2_Missense_Mutation_p.K100R|CCT3_ENST00000368261.3_Missense_Mutation_p.K93R|CCT3_ENST00000472765.2_Missense_Mutation_p.K93R	NM_005998.4	NP_005989.3	P49368	TCPG_HUMAN	chaperonin containing TCP1, subunit 3 (gamma)	138					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			endometrium(4)|large_intestine(1)|liver(1)|lung(11)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	22	Hepatocellular(266;0.158)					CCTTATTTTCTTTAGGGTGCT	0.498																																					p.K138R		Atlas-SNP	.											.	CCT3	61	.	0			c.A413G						.						111	94	100					1																	156294772		2203	4300	6503	SO:0001583	missense	7203	exon6			ATTTTCTTTAGGG	BC008019	CCDS1140.2, CCDS30888.1	1q23	2011-09-02			ENSG00000163468	ENSG00000163468		"Heat Shock Proteins / Chaperonins"	1616	protein-coding gene	gene with protein product		600114		TRIC5		8110840	Standard	NM_005998		Approved	Cctg	uc001fol.2	P49368	OTTHUMG00000024061	ENST00000295688.3:c.413A>G	chr1.hg19:g.156294772T>C	ENSP00000295688:p.Lys138Arg	37.0	0.0		41.0	26.0	NM_005998	A6NE14|Q5SZY1|Q9BR64	Missense_Mutation	SNP	ENST00000295688.3	hg19	CCDS1140.2	.	.	.	.	.	.	.	.	.	.	T	15.29	2.790312	0.50102	.	.	ENSG00000163468	ENST00000295688;ENST00000368259;ENST00000368261;ENST00000472765;ENST00000413555;ENST00000496684;ENST00000533194;ENST00000446905;ENST00000478640;ENST00000415548	T;T;T;T;T;T;T;T;T;T	0.78924	-1.22;-1.22;-1.22;-1.22;-1.22;-1.22;-1.22;-1.22;-1.22;-0.71	5.41	4.29	0.51040	.	0.111325	0.64402	D	0.000015	T	0.52338	0.1728	L	0.41906	1.305	0.36033	D	0.839533	B;B;B	0.12013	0.005;0.001;0.001	B;B;B	0.11329	0.005;0.006;0.004	T	0.52411	-0.8579	10	0.51188	T	0.08	-20.2897	8.2167	0.31516	0.0:0.0912:0.0:0.9088	.	100;137;138	P49368-2;E9PAQ6;P49368	.;.;TCPG_HUMAN	R	138;100;93;93;162;137;59;124;117;161	ENSP00000295688:K138R;ENSP00000357242:K100R;ENSP00000357244:K93R;ENSP00000431543:K93R;ENSP00000413308:K162R;ENSP00000434232:K137R;ENSP00000434481:K59R;ENSP00000388799:K124R;ENSP00000435026:K117R;ENSP00000413431:K161R	ENSP00000295688:K138R	K	-	2	0	CCT3	154561396	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	4.610000	0.61155	0.896000	0.36366	-0.443000	0.05667	AAG	.	.		0.498	CCT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060602.3	NM_005998		C	156294772	T	C	156294772	3	2	322	1	0	0	0	0	1	0	0	0	2956	1609	56	2	1260	2	CCT3	1	156294772	Missense_Mutation	SNP	T	TCGA-MI-A75G-01A-11D-A32G-10	255264	156294772	92955849	11	45259										
KLHDC9	126823	hgsc.bcm.edu	37	chr1	161068351	161068351	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ggtggccgtgcccccgggtcGggccgcaggctcaggctggg	20	14	1	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr1:161068351G>T	ENST00000368011.4	+	1	168	c.26G>T	c.(25-27)cGg>cTg	p.R9L	KLHDC9_ENST00000490724.2_Intron|PFDN2_ENST00000468311.1_5'Flank|KLHDC9_ENST00000392192.2_Missense_Mutation_p.R9L	NM_152366.4	NP_689579.3	Q8NEP7	KLDC9_HUMAN	kelch domain containing 9	9										lung(5)|upper_aerodigestive_tract(1)	6	all_cancers(52;1.28e-19)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			CCCCCGGGTCGGGCCGCAGGC	0.706																																					p.R9L		Atlas-SNP	.											.	KLHDC9	16	.	0			c.G26T						.						8	9	9					1																	161068351		2171	4230	6401	SO:0001583	missense	126823	exon1			CGGGTCGGGCCGC	BC022077	CCDS30919.1, CCDS41425.1	1q23.3	2008-02-05			ENSG00000162755	ENSG00000162755			28489	protein-coding gene	gene with protein product	"kelch/ankyrin repeat containing cyclin A1 interacting protein"					15159402	Standard	NM_152366		Approved	KARCA1	uc001fxr.3	Q8NEP7	OTTHUMG00000031479	ENST00000368011.4:c.26G>T	chr1.hg19:g.161068351G>T	ENSP00000356990:p.Arg9Leu	62.0	0.0		124.0	29.0	NM_001007255	Q5SY56|Q6NXT9|Q6PKN4|Q8N5E1|Q8NA16	Missense_Mutation	SNP	ENST00000368011.4	hg19	CCDS30919.1	.	.	.	.	.	.	.	.	.	.	G	11.48	1.651183	0.29336	.	.	ENSG00000162755	ENST00000368011;ENST00000392192	T;T	0.54071	1.79;0.59	3.28	0.271	0.15640	.	1.195530	0.06431	N	0.724182	T	0.12944	0.0314	N	0.14661	0.345	0.09310	N	1	B;B	0.23937	0.094;0.029	B;B	0.20767	0.031;0.008	T	0.21895	-1.0232	10	0.40728	T	0.16	-23.1162	3.3909	0.07289	0.2529:0.219:0.5281:0.0	.	9;9	Q8NEP7-2;Q8NEP7	.;KLDC9_HUMAN	L	9	ENSP00000356990:R9L;ENSP00000376030:R9L	ENSP00000356990:R9L	R	+	2	0	KLHDC9	159334975	0.000000	0.05858	0.001000	0.08648	0.744000	0.42396	-0.004000	0.12878	0.054000	0.16065	0.313000	0.20887	CGG	.	.		0.706	KLHDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077092.1	NM_152366		T	161068351	G	T	161068351	3	4	322	1	0	0	0	0	1	0	0	0	8373	1116	39	1	28	1	KLHDC9	1	161068351	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	4773579	161068351	88182270	12	45260										
SFT2D2	375035	hgsc.bcm.edu	37	chr1	168204373	168204373	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tgggaccagtgaaacagctgAagcgaatgtttgagcctact	12	8	0	3			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr1:168204373A>T	ENST00000271375.4	+	4	343	c.271A>T	c.(271-273)Aag>Tag	p.K91*	SFT2D2_ENST00000367829.1_Intron|SFT2D2_ENST00000471981.1_3'UTR|SFT2D2_ENST00000367825.3_Intron	NM_199344.2	NP_955376.1			SFT2 domain containing 2											lung(3)|skin(1)	4	all_hematologic(923;0.215)					GAAACAGCTGAAGCGAATGTT	0.458																																					p.K91X		Atlas-SNP	.											.	SFT2D2	10	.	0			c.A271T						.						380	369	373					1																	168204373		2203	4300	6503	SO:0001587	stop_gained	375035	exon4			CAGCTGAAGCGAA	AL035297	CCDS1271.1	1q24.2	2008-02-05			ENSG00000213064	ENSG00000213064			25140	protein-coding gene	gene with protein product							Standard	NM_199344		Approved	UNQ512, dJ747L4.C1.2	uc001gfi.4	O95562	OTTHUMG00000034650	ENST00000271375.4:c.271A>T	chr1.hg19:g.168204373A>T	ENSP00000271375:p.Lys91*	136.0	0.0		213.0	119.0	NM_199344		Nonsense_Mutation	SNP	ENST00000271375.4	hg19	CCDS1271.1	.	.	.	.	.	.	.	.	.	.	A	36	5.639031	0.96693	.	.	ENSG00000213064	ENST00000271375	.	.	.	5.04	5.04	0.67666	.	0.000000	0.85682	U	0.000000	.	.	.	.	.	.	0.80722	A	1.000000	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.8292	12.3349	0.55060	1.0:0.0:0.0:0.0	.	.	.	.	X	91	.	ENSP00000271375:K91X	K	+	1	0	SFT2D2	166470997	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.669000	0.68081	1.881000	0.54492	0.528000	0.53228	AAG	.	.		0.458	SFT2D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083827.2	NM_199344		T	168204373	A	T	168204373	4	4	322	1	0	0	0	0	0	1	0	0	14201	247	9	4	285	4	SFT2D2	1	168204373	Nonsense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	7136022	168204373	81046248	13	45261										
ASTN1	460	hgsc.bcm.edu	37	chr1	176905453	176905453	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gtggtacatcacagaccggaCcttccagtgctgcagcacag	11	13	1	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr1:176905453C>A	ENST00000367654.3	-	15	2666	c.2455G>T	c.(2455-2457)Gtc>Ttc	p.V819F	ASTN1_ENST00000361833.2_Missense_Mutation_p.V811F|ASTN1_ENST00000281881.3_5'UTR|ASTN1_ENST00000424564.2_Missense_Mutation_p.V811F|ASTN1_ENST00000367657.3_Missense_Mutation_p.V811F	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	819					locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						ACAGACCGGACCTTCCAGTGC	0.507																																					p.V811F		Atlas-SNP	.											.	ASTN1	314	.	0			c.G2431T						.						149	122	131					1																	176905453		2203	4300	6503	SO:0001583	missense	460	exon15			ACCGGACCTTCCA	AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"astrotactin"	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.2455G>T	chr1.hg19:g.176905453C>A	ENSP00000356626:p.Val819Phe	48.0	0.0		97.0	18.0	NM_004319	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Missense_Mutation	SNP	ENST00000367654.3	hg19		.	.	.	.	.	.	.	.	.	.	C	17.78	3.473128	0.63737	.	.	ENSG00000152092	ENST00000367657;ENST00000361833;ENST00000367654;ENST00000424564;ENST00000541808	T;T;T;T	0.52526	0.66;0.66;0.66;0.66	5.54	5.54	0.83059	Membrane attack complex component/perforin (MACPF) domain (1);	0.124914	0.53938	D	0.000049	T	0.47673	0.1458	L	0.42245	1.32	0.53005	D	0.999961	P;P;P	0.49090	0.919;0.815;0.815	B;B;B	0.43575	0.424;0.332;0.332	T	0.52837	-0.8522	10	0.87932	D	0	-34.3281	19.09	0.93223	0.0:1.0:0.0:0.0	.	819;811;811	O14525;O14525-2;B1AJS1	ASTN1_HUMAN;.;.	F	811;811;819;811;811	ENSP00000356629:V811F;ENSP00000354536:V811F;ENSP00000356626:V819F;ENSP00000395041:V811F	ENSP00000354536:V811F	V	-	1	0	ASTN1	175172076	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.505000	0.60421	2.613000	0.88420	0.650000	0.86243	GTC	.	.		0.507	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319		A	176905453	C	A	176905453	3	1	322	1	0	0	0	0	1	0	0	0	1064	507	18	3	1493	3	ASTN1	1	176905453	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	8701080	176905453	72345168	14	45262										
RASAL2	9462	hgsc.bcm.edu	37	chr1	178427346	178427346	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cccagcaatagcagcatggaAgatttcactaaacgtagcac	8	11	1	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr1:178427346A>G	ENST00000462775.1	+	12	2621	c.2496A>G	c.(2494-2496)gaA>gaG	p.E832E	RASAL2_ENST00000448150.3_Silent_p.E962E|RASAL2_ENST00000367649.3_Silent_p.E973E	NM_004841.3	NP_004832.1	Q9UJF2	NGAP_HUMAN	RAS protein activator like 2	832					negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Ras GTPase activator activity (GO:0005099)			biliary_tract(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(2)|lung(25)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54						GCAGCATGGAAGATTTCACTA	0.478																																					p.E973E		Atlas-SNP	.											.	RASAL2	334	.	0			c.A2919G						.						74	72	72					1																	178427346		2203	4300	6503	SO:0001819	synonymous_variant	9462	exon14			CATGGAAGATTTC	AF047711	CCDS1321.1, CCDS1322.1, CCDS1321.2	1q25	2013-01-10			ENSG00000075391	ENSG00000075391		"Pleckstrin homology (PH) domain containing"	9874	protein-coding gene	gene with protein product	"Ras GTPase activating protein-like", "Ras protein activator like 1"	606136				9877179	Standard	NM_004841		Approved	nGAP	uc001glq.3	Q9UJF2	OTTHUMG00000035022	ENST00000462775.1:c.2496A>G	chr1.hg19:g.178427346A>G		42.0	0.0		59.0	12.0	NM_170692	F8W755|O95174|Q2TB22|Q5TFU9	Silent	SNP	ENST00000462775.1	hg19	CCDS1322.1	.	.	.	.	.	.	.	.	.	.	A	6.268	0.417562	0.11870	.	.	ENSG00000075391	ENST00000433130	.	.	.	5.55	-2.64	0.06114	.	.	.	.	.	T	0.63141	0.2486	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61093	-0.7132	4	.	.	.	.	13.2065	0.59800	0.4135:0.0:0.5865:0.0	.	.	.	.	G	383	.	.	R	+	1	2	RASAL2	176693969	0.996000	0.38824	0.988000	0.46212	0.998000	0.95712	0.417000	0.21214	-0.500000	0.06614	0.533000	0.62120	AGA	.	.		0.478	RASAL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000084758.3	NM_170692		G	178427346	A	G	178427346	2	3	322	1	0	0	0	0	0	0	0	1	13079	69	3	2		2	RASAL2	1	178427346	Silent	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	1521893	178427346	70823275	15	45263										
LAMC2	3918	hgsc.bcm.edu	37	chr1	183209512	183209512	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	actcaacacattagacggccTcctgcatctgatgggtatgt	9	11	2	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr1:183209512T>A	ENST00000264144.4	+	22	3379	c.3314T>A	c.(3313-3315)cTc>cAc	p.L1105H	LAMC2_ENST00000461729.1_3'UTR|LAMC2_ENST00000493293.1_Missense_Mutation_p.L1105H	NM_005562.2	NP_005553.2	Q13753	LAMC2_HUMAN	laminin, gamma 2	1105	Domain II and I.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	cell cortex (GO:0005938)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-2 complex (GO:0005607)|laminin-5 complex (GO:0005610)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	heparin binding (GO:0008201)			breast(2)|endometrium(6)|kidney(8)|large_intestine(11)|lung(18)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55						TTAGACGGCCTCCTGCATCTG	0.507																																					p.L1105H		Atlas-SNP	.											.	LAMC2	113	.	0			c.T3314A						.						120	93	102					1																	183209512		2203	4300	6503	SO:0001583	missense	3918	exon22			ACGGCCTCCTGCA	Z15008	CCDS1352.1, CCDS44285.1	1q25-q31	2013-03-01	2002-08-29		ENSG00000058085	ENSG00000058085		"Laminins"	6493	protein-coding gene	gene with protein product		150292	"laminin, gamma 2 (nicein (100kD), kalinin (105kD), BM600 (100kD), Herlitz junctional epidermolysis bullosa))"	EBR2, LAMB2T, LAMNB2, EBR2A		1383240	Standard	NM_005562		Approved	nicein-100kDa, kalinin-105kDa, BM600-100kDa	uc001gqa.2	Q13753	OTTHUMG00000035520	ENST00000264144.4:c.3314T>A	chr1.hg19:g.183209512T>A	ENSP00000264144:p.Leu1105His	94.0	0.0		130.0	11.0	NM_005562	Q02536|Q02537|Q13752|Q14941|Q14DF7|Q2M1N2|Q5VYE8	Missense_Mutation	SNP	ENST00000264144.4	hg19	CCDS1352.1	.	.	.	.	.	.	.	.	.	.	T	15.02	2.709161	0.48517	.	.	ENSG00000058085	ENST00000493293;ENST00000264144	T;T	0.77489	1.97;-1.1	5.59	5.59	0.84812	.	0.321794	0.29522	N	0.011920	T	0.75997	0.3926	L	0.27053	0.805	0.44067	D	0.996816	D;D;D	0.60575	0.979;0.979;0.988	P;B;P	0.52758	0.514;0.41;0.708	T	0.79638	-0.1720	10	0.87932	D	0	.	14.3256	0.66518	0.0:0.0:0.0:1.0	.	1105;1105;1105	Q2M1N2;Q13753;Q13753-2	.;LAMC2_HUMAN;.	H	1105	ENSP00000432063:L1105H;ENSP00000264144:L1105H	ENSP00000264144:L1105H	L	+	2	0	LAMC2	181476135	1.000000	0.71417	0.988000	0.46212	0.025000	0.11179	4.621000	0.61233	2.119000	0.64992	0.533000	0.62120	CTC	.	.		0.507	LAMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086258.1	NM_005562		A	183209512	T	A	183209512	3	1	322	1	0	0	0	0	1	0	0	0	8624	1551	54	4	3400	4	LAMC2	1	183209512	Missense_Mutation	SNP	T	TCGA-MI-A75G-01A-11D-A32G-10	4782166	183209512	66041109	16	45264										
PIK3C2B	5287	hgsc.bcm.edu	37	chr1	204429747	204429747	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cgaatgtcaatgtcaaacttGcggcagtattggatgtactc	10	8	2	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr1:204429747G>C	ENST00000367187.3	-	7	1909	c.1353C>G	c.(1351-1353)cgC>cgG	p.R451R	PIK3C2B_ENST00000424712.2_Silent_p.R451R	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	451	PI3K-RBD. {ECO:0000255|PROSITE- ProRule:PRU00879}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			TGTCAAACTTGCGGCAGTATT	0.562																																					p.R451R		Atlas-SNP	.											.	PIK3C2B	142	.	0			c.C1353G						.						155	122	133					1																	204429747		2203	4300	6503	SO:0001819	synonymous_variant	5287	exon7			AAACTTGCGGCAG	Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"phosphoinositide-3-kinase, class 2, beta polypeptide"			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.1353C>G	chr1.hg19:g.204429747G>C		60.0	0.0		144.0	9.0	NM_002646	O95666|Q5SW99	Silent	SNP	ENST00000367187.3	hg19	CCDS1446.1																																																																																			.	.		0.562	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646		C	204429747	G	C	204429747	2	2	322	1	0	0	0	0	0	0	0	1	11919	1306	46	4		4	PIK3C2B	1	204429747	Silent	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	21220235	204429747	44820874	17	45265										
ENAH	55740	hgsc.bcm.edu	37	chr1	225707015	225707018	+	Frame_Shift_Del	DEL	TCTT	TCTT	-													0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tccagcctctctcgttcttgTctttcttgcctctcccgatc							TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	TCTT	TCTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr1:225707015_225707018delTCTT	ENST00000366844.3	-	5	1135_1138	c.684_687delAAGA	c.(682-687)gaaagafs	p.ER228fs	ENAH_ENST00000284563.6_Frame_Shift_Del_p.ER247fs|ENAH_ENST00000391874.2_5'UTR|ENAH_ENST00000366843.2_Frame_Shift_Del_p.ER228fs	NM_001008493.1|NM_018212.4	NP_001008493.1|NP_060682.2	Q8N8S7	ENAH_HUMAN	enabled homolog (Drosophila)	228					actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|intracellular transport (GO:0046907)|neural tube closure (GO:0001843)|T cell receptor signaling pathway (GO:0050852)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)|synapse (GO:0045202)	WW domain binding (GO:0050699)			NS(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23	Breast(184;0.206)			GBM - Glioblastoma multiforme(131;0.19)		CTCGTTCTTGTCTTTCTTGCCTCT	0.603																																					p.229_230del		Atlas-Indel,Pindel	.											.	ENAH	46	.	0			c.685_688del						.																																			SO:0001589	frameshift_variant	55740	exon5			.	AK001635	CCDS31040.1, CCDS31041.1	1q32.2	2013-08-06			ENSG00000154380	ENSG00000154380			18271	protein-coding gene	gene with protein product	"mammalian enabled"	609061				1420303	Standard	XM_005273182		Approved	FLJ10773, NDPP1, MENA	uc001hpc.1	Q8N8S7	OTTHUMG00000037742	ENST00000366844.3:c.684_687delAAGA	chr1.hg19:g.225707019_225707022delTCTT	ENSP00000355809:p.Glu228fs	54.0	0.0		93.0	22.0	NM_001008493	D0PQI2|Q502W5|Q5T5M7|Q5VTQ9|Q5VTR0|Q9NVF3|Q9UFB8	Frame_Shift_Del	DEL	ENST00000366844.3	hg19	CCDS31041.1																																																																																			.	.		0.603	ENAH-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000357426.2	NM_018212		-	225707018	TCTT	-	225707015	7	5	322	1	0	1	0	1	0	0	0	0	5113	1664	58	0	1132	0	ENAH	1	225707015	Frame_Shift_Del	DEL	TCTT	TCGA-MI-A75G-01A-11D-A32G-10	21277268	225707015	23543606	18	45266										
KIF26B	55083	hgsc.bcm.edu	37	chr1	245849630	245849630	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	aaggattccggcgtggcgtcTagggagtccttgctgcagcc	15	11	1	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr1:245849630T>C	ENST00000407071.2	+	12	3785	c.3345T>C	c.(3343-3345)tcT>tcC	p.S1115S	KIF26B_ENST00000366518.4_Silent_p.S734S	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	1115					establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			GCGTGGCGTCTAGGGAGTCCT	0.627																																					p.S1115S		Atlas-SNP	.											.	KIF26B	343	.	0			c.T3345C						.						69	77	74					1																	245849630		1942	4141	6083	SO:0001819	synonymous_variant	55083	exon12			GGCGTCTAGGGAG	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"Kinesins"	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.3345T>C	chr1.hg19:g.245849630T>C		68.0	0.0		98.0	29.0	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Silent	SNP	ENST00000407071.2	hg19	CCDS44342.1																																																																																			.	.		0.627	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354		C	245849630	T	C	245849630	2	2	322	1	0	0	0	0	0	0	0	1	8304	1509	53	2		2	KIF26B	1	245849630	Silent	SNP	T	TCGA-MI-A75G-01A-11D-A32G-10	20142615	245849630	3400991	19	45267										
OR2T1	26696	hgsc.bcm.edu	37	chr1	248569656	248569656	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gccacctttccttaattgacAtgatgtatatttccactatt	4	10	0	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr1:248569656A>G	ENST00000366474.1	+	1	361	c.361A>G	c.(361-363)Atg>Gtg	p.M121V		NM_030904.1	NP_112166.1	O43869	OR2T1_HUMAN	olfactory receptor, family 2, subfamily T, member 1	121						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(24)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	39	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CTTAATTGACATGATGTATAT	0.453																																					p.M121V		Atlas-SNP	.											.	OR2T1	89	.	0			c.A361G						.						181	169	173					1																	248569656		2203	4300	6503	SO:0001583	missense	26696	exon1			ATTGACATGATGT	U86215	CCDS31115.1	1q44	2012-08-09			ENSG00000175143	ENSG00000175143		"GPCR / Class A : Olfactory receptors"	8277	protein-coding gene	gene with protein product						9500546	Standard	NM_030904		Approved	OR1-25	uc010pzm.2	O43869	OTTHUMG00000040450	ENST00000366474.1:c.361A>G	chr1.hg19:g.248569656A>G	ENSP00000355430:p.Met121Val	61.0	0.0		83.0	32.0	NM_030904	Q6IEZ9	Missense_Mutation	SNP	ENST00000366474.1	hg19	CCDS31115.1	.	.	.	.	.	.	.	.	.	.	a	6.014	0.371053	0.11409	.	.	ENSG00000175143	ENST00000366474	T	0.02656	4.21	4.75	3.56	0.40772	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44688	U	0.000438	T	0.01627	0.0052	N	0.11313	0.125	0.29352	N	0.865306	B	0.17268	0.021	B	0.12156	0.007	T	0.34502	-0.9826	10	0.34782	T	0.22	.	4.9551	0.14035	0.7481:0.0:0.0887:0.1632	.	121	O43869	OR2T1_HUMAN	V	121	ENSP00000355430:M121V	ENSP00000355430:M121V	M	+	1	0	OR2T1	246636279	0.002000	0.14202	1.000000	0.80357	0.562000	0.35680	0.144000	0.16135	1.993000	0.58246	0.528000	0.53228	ATG	.	.		0.453	OR2T1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097346.2			G	248569656	A	G	248569656	3	3	322	1	0	0	0	0	1	0	0	0	11025	217	8	2	363	2	OR2T1	1	248569656	Missense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	2720026	248569656	680965	20	45268										
TPO	7173	hgsc.bcm.edu	37	chr2	1481040	1481040	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	accgtgtatggcagctccccGgccctagagaggcagctgcg	14	14	0	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr2:1481040G>T	ENST00000345913.4	+	8	1093	c.1002G>T	c.(1000-1002)ccG>ccT	p.P334P	TPO_ENST00000497517.2_Intron|TPO_ENST00000382201.3_Silent_p.P334P|TPO_ENST00000346956.3_Silent_p.P334P|TPO_ENST00000382198.1_Intron|TPO_ENST00000337415.3_Silent_p.P334P|TPO_ENST00000329066.4_Silent_p.P334P|TPO_ENST00000349624.3_Intron	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	334					cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	GCAGCTCCCCGGCCCTAGAGA	0.692																																					p.P334P		Atlas-SNP	.											.	TPO	224	.	0			c.G1002T						.						16	15	16					2																	1481040		2187	4283	6470	SO:0001819	synonymous_variant	7173	exon8			CTCCCCGGCCCTA		CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.1002G>T	chr2.hg19:g.1481040G>T		29.0	0.0		74.0	7.0	NM_175719	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Silent	SNP	ENST00000345913.4	hg19	CCDS1643.1																																																																																			.	.		0.692	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547		T	1481040	G	T	1481040	2	4	322	1	0	0	0	0	0	0	0	1	16425	1103	39	1		1	TPO	2	1481040	Silent	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10		1481040	241718333	21	45269										
CDKL4	344387	hgsc.bcm.edu	37	chr2	39414810	39414810	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ctgatgccatggaaaaacccGttacttttaaagattgattg	8	7	0	3	rs549348531		TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr2:39414810G>T	ENST00000395035.3	-	6	692	c.693C>A	c.(691-693)aaC>aaA	p.N231K	CDKL4_ENST00000378803.1_Missense_Mutation_p.N231K			Q5MAI5	CDKL4_HUMAN	cyclin-dependent kinase-like 4	231	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			breast(1)|large_intestine(2)|liver(1)|lung(7)|ovary(1)	12		all_hematologic(82;0.248)				GGAAAAACCCGTTACTTTTAA	0.328																																					p.N231K		Atlas-SNP	.											.	CDKL4	30	.	0			c.C693A						.						110	117	115					2																	39414810		2203	4300	6503	SO:0001583	missense	344387	exon6			AAACCCGTTACTT		CCDS33184.1	2p22.3	2011-11-04			ENSG00000205111	ENSG00000205111		"Cyclin-dependent kinases"	19287	protein-coding gene	gene with protein product							Standard	NM_001009565		Approved		uc002rrm.3	Q5MAI5	OTTHUMG00000133574	ENST00000395035.3:c.693C>A	chr2.hg19:g.39414810G>T	ENSP00000378476:p.Asn231Lys	58.0	0.0		77.0	37.0	NM_001009565	Q2NME9	Missense_Mutation	SNP	ENST00000395035.3	hg19		.	.	.	.	.	.	.	.	.	.	G	21.3	4.128485	0.77549	.	.	ENSG00000205111	ENST00000451199;ENST00000378803;ENST00000395035	T;T;T	0.72051	-0.62;0.98;0.98	5.15	5.15	0.70609	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000013	T	0.77772	0.4180	L	0.39085	1.19	0.58432	D	0.999995	D;D	0.89917	1.0;0.994	D;D	0.80764	0.994;0.969	T	0.78386	-0.2224	10	0.49607	T	0.09	-24.6347	16.1422	0.81534	0.0:0.0:1.0:0.0	.	231;231	Q2NME9;Q5MAI5	.;CDKL4_HUMAN	K	13;231;231	ENSP00000389833:N13K;ENSP00000368080:N231K;ENSP00000378476:N231K	ENSP00000368080:N231K	N	-	3	2	CDKL4	39268314	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	4.099000	0.57755	2.415000	0.81967	0.555000	0.69702	AAC	.	.		0.328	CDKL4-002	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000331655.1	XM_293029		T	39414810	G	T	39414810	3	4	322	1	0	0	0	0	1	0	0	0	3158	1136	40	1	266	1	CDKL4	2	39414810	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	37933770	39414810	203784563	22	45270										
THADA	63892	hgsc.bcm.edu	37	chr2	43819108	43819108	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tacctgtttaatataatggaTttgtgacactccatccgtga	7	8	0	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr2:43819108T>C	ENST00000405006.4	-	3	505	c.154A>G	c.(154-156)Atc>Gtc	p.I52V	THADA_ENST00000405975.2_Missense_Mutation_p.I52V|THADA_ENST00000403856.1_Missense_Mutation_p.I52V|THADA_ENST00000402360.2_Missense_Mutation_p.I52V|THADA_ENST00000404790.1_Missense_Mutation_p.I52V|THADA_ENST00000415080.2_5'UTR	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	52										breast(1)|endometrium(9)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	66		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				ATATAATGGATTTGTGACACT	0.318																																					p.I52V		Atlas-SNP	.											.	THADA	131	.	0			c.A154G						.						56	53	54					2																	43819108		1836	4070	5906	SO:0001583	missense	63892	exon3			AATGGATTTGTGA	AY149629	CCDS46268.1, CCDS62901.1, CCDS62902.1	2p21	2008-02-05			ENSG00000115970	ENSG00000115970			19217	protein-coding gene	gene with protein product		611800				12063398, 11214970	Standard	NM_022065		Approved	FLJ21877, KIAA1767, GITA	uc002rsx.4	Q6YHU6	OTTHUMG00000152398	ENST00000405006.4:c.154A>G	chr2.hg19:g.43819108T>C	ENSP00000385995:p.Ile52Val	99.0	0.0		128.0	62.0	NM_001083953	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Missense_Mutation	SNP	ENST00000405006.4	hg19	CCDS46268.1	.	.	.	.	.	.	.	.	.	.	T	18.21	3.573316	0.65765	.	.	ENSG00000115970	ENST00000405975;ENST00000356975;ENST00000405006;ENST00000402360;ENST00000404790;ENST00000403856	T;T;T;T;T	0.39056	2.54;2.54;1.18;1.15;1.1	4.86	4.86	0.63082	.	0.055295	0.64402	D	0.000002	T	0.60261	0.2255	M	0.63843	1.955	0.80722	D	1	D;D;D;D	0.69078	0.997;0.996;0.997;0.994	D;D;D;D	0.83275	0.993;0.99;0.996;0.978	T	0.61471	-0.7056	10	0.49607	T	0.09	.	13.1718	0.59602	0.0:0.0:0.0:1.0	.	52;52;52;52	B5MC89;Q8IY32;Q6YHU6-5;Q6YHU6	.;.;.;THADA_HUMAN	V	52	ENSP00000386088:I52V;ENSP00000385995:I52V;ENSP00000385441:I52V;ENSP00000384266:I52V;ENSP00000385469:I52V	ENSP00000349464:I52V	I	-	1	0	THADA	43672612	1.000000	0.71417	0.993000	0.49108	0.886000	0.51366	4.678000	0.61641	2.039000	0.60335	0.482000	0.46254	ATC	.	.		0.318	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326070.3	NM_022065		C	43819108	T	C	43819108	3	2	322	1	0	0	0	0	1	0	0	0	15855	1493	52	2	5851	2	THADA	2	43819108	Missense_Mutation	SNP	T	TCGA-MI-A75G-01A-11D-A32G-10	4404298	43819108	199380265	23	45271										
CNRIP1	25927	hgsc.bcm.edu	37	chr2	68546450	68546450	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tctggccgaagcgctgcccgTccaccttgtaaaagaccggg	12	14	1	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr2:68546450T>C	ENST00000263655.3	-	1	688	c.83A>G	c.(82-84)gAc>gGc	p.D28G	CNRIP1_ENST00000481714.1_5'UTR|CNRIP1_ENST00000409862.1_Missense_Mutation_p.D28G|CNRIP1_ENST00000409559.3_Missense_Mutation_p.D28G	NM_015463.2	NP_056278.1	Q96F85	CNRP1_HUMAN	cannabinoid receptor interacting protein 1	28										kidney(1)|large_intestine(5)|liver(1)|lung(1)|skin(1)	9						GCGCTGCCCGTCCACCTTGTA	0.632																																					p.D28G		Atlas-SNP	.											.	CNRIP1	45	.	0			c.A83G						.						47	36	40					2																	68546450		2175	4259	6434	SO:0001583	missense	25927	exon1			TGCCCGTCCACCT	AL110235	CCDS1886.1, CCDS46311.1	2p13	2008-02-05	2007-11-29	2007-11-29	ENSG00000119865	ENSG00000119865			24546	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 32"	C2orf32		12477932	Standard	NM_015463		Approved	DKFZP566K1924, CRIP1, CRIP1a, CRIP1b	uc002sek.4	Q96F85	OTTHUMG00000129565	ENST00000263655.3:c.83A>G	chr2.hg19:g.68546450T>C	ENSP00000263655:p.Asp28Gly	26.0	0.0		57.0	25.0	NM_001111101	B2R4D0|Q49AN4|Q9UFZ0	Missense_Mutation	SNP	ENST00000263655.3	hg19	CCDS1886.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.819973	0.90873	.	.	ENSG00000119865	ENST00000409559;ENST00000263655;ENST00000409862	.	.	.	4.83	4.83	0.62350	.	0.000000	0.85682	D	0.000000	T	0.74794	0.3763	L	0.57536	1.79	0.80722	D	1	D;P;D	0.89917	1.0;0.869;1.0	D;B;D	0.87578	0.998;0.38;0.998	T	0.77413	-0.2597	9	0.72032	D	0.01	-10.4549	13.1031	0.59231	0.0:0.0:0.0:1.0	.	28;28;28	B8ZZB8;Q96F85;Q96F85-2	.;CNRP1_HUMAN;.	G	28	.	ENSP00000263655:D28G	D	-	2	0	CNRIP1	68399954	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.212000	0.77941	2.018000	0.59344	0.402000	0.26972	GAC	.	.		0.632	CNRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251758.1	NM_015463		C	68546450	T	C	68546450	3	2	322	1	0	0	0	0	1	0	0	0	3635	1667	58	2	484	2	CNRIP1	2	68546450	Missense_Mutation	SNP	T	TCGA-MI-A75G-01A-11D-A32G-10	24727342	68546450	174652923	24	45272										
PLEK	5341	hgsc.bcm.edu	37	chr2	68613639	68613639	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gctggtcccatctaggtaacTgcgtcattgattggctggta	12	9	2	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr2:68613639T>A	ENST00000234313.7	+	5	657	c.478T>A	c.(478-480)Tgc>Agc	p.C160S		NM_002664.2	NP_002655.2	P08567	PLEK_HUMAN	pleckstrin	160	DEP. {ECO:0000255|PROSITE- ProRule:PRU00066}.				actin cytoskeleton reorganization (GO:0031532)|blood coagulation (GO:0007596)|cell projection organization (GO:0030030)|cortical actin cytoskeleton organization (GO:0030866)|hematopoietic progenitor cell differentiation (GO:0002244)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of calcium-mediated signaling (GO:0050849)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of inositol phosphate biosynthetic process (GO:0010920)|phosphatidylinositol metabolic process (GO:0046488)|phospholipase C-inhibiting G-protein coupled receptor signaling pathway (GO:0030845)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of inositol-polyphosphate 5-phosphatase activity (GO:0010925)|positive regulation of integrin activation (GO:0033625)|positive regulation of platelet activation (GO:0010572)|protein kinase C signaling (GO:0070528)|protein secretion by platelet (GO:0070560)|regulation of cell diameter (GO:0060305)|ruffle organization (GO:0031529)|thrombin receptor signaling pathway (GO:0070493)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|membrane (GO:0016020)|ruffle membrane (GO:0032587)	phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)			autonomic_ganglia(1)|endometrium(3)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	24		Ovarian(717;0.0129)		STAD - Stomach adenocarcinoma(1183;0.00159)|READ - Rectum adenocarcinoma(193;0.0419)		TCTAGGTAACTGCGTCATTGA	0.532																																					p.C160S		Atlas-SNP	.											.	PLEK	64	.	0			c.T478A						.						109	93	98					2																	68613639		2203	4300	6503	SO:0001583	missense	5341	exon5			GGTAACTGCGTCA	X07743	CCDS1887.1	2p13.3	2013-01-10			ENSG00000115956	ENSG00000115956		"Pleckstrin homology (PH) domain containing"	9070	protein-coding gene	gene with protein product		173570				2897630, 12054651	Standard	NM_002664		Approved	P47	uc002sen.4	P08567	OTTHUMG00000129562	ENST00000234313.7:c.478T>A	chr2.hg19:g.68613639T>A	ENSP00000234313:p.Cys160Ser	50.0	0.0		77.0	16.0	NM_002664	B2R9E8|Q53SU8|Q6FGM8|Q6FGQ1|Q8WV81	Missense_Mutation	SNP	ENST00000234313.7	hg19	CCDS1887.1	.	.	.	.	.	.	.	.	.	.	T	0.529	-0.858737	0.02610	.	.	ENSG00000115956	ENST00000234313	T	0.20598	2.06	5.23	4.02	0.46733	DEP domain (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.255160	0.46145	D	0.000303	T	0.13200	0.0320	L	0.28274	0.84	0.34774	D	0.734028	B;B	0.09022	0.002;0.001	B;B	0.08055	0.003;0.002	T	0.16748	-1.0392	10	0.07990	T	0.79	.	12.2787	0.54751	0.0:0.0:0.3339:0.6661	.	178;160	Q59GZ2;P08567	.;PLEK_HUMAN	S	160	ENSP00000234313:C160S	ENSP00000234313:C160S	C	+	1	0	PLEK	68467143	0.995000	0.38212	1.000000	0.80357	0.684000	0.39900	-0.260000	0.08708	0.727000	0.32360	0.533000	0.62120	TGC	.	.		0.532	PLEK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251755.1	NM_002664		A	68613639	T	A	68613639	3	1	322	1	0	0	0	0	1	0	0	0	12062	1580	55	4	496	4	PLEK	2	68613639	Missense_Mutation	SNP	T	TCGA-MI-A75G-01A-11D-A32G-10	67189	68613639	174585734	25	45273										
MYO7B	4648	hgsc.bcm.edu	37	chr2	128380906	128380906	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tcgctcacaagcagggcctcAgcgaccacctgggcttctcc	10	17	3	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr2:128380906A>T	ENST00000409816.2	+	27	3729	c.3697A>T	c.(3697-3699)Agc>Tgc	p.S1233C	MYO7B_ENST00000389524.4_Missense_Mutation_p.S1233C|RP11-286H15.1_ENST00000609697.1_RNA|MYO7B_ENST00000409090.1_Missense_Mutation_p.S86C|MYO7B_ENST00000428314.1_Missense_Mutation_p.S1233C			Q6PIF6	MYO7B_HUMAN	myosin VIIB	1233	FERM 1. {ECO:0000255|PROSITE- ProRule:PRU00084}.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		GCAGGGCCTCAGCGACCACCT	0.627																																					p.S1233C		Atlas-SNP	.											.	MYO7B	359	.	0			c.A3697T						.						54	63	60					2																	128380906		2142	4243	6385	SO:0001583	missense	4648	exon28			GGCCTCAGCGACC		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"Myosins / Myosin superfamily : Class VII"	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.3697A>T	chr2.hg19:g.128380906A>T	ENSP00000386461:p.Ser1233Cys	29.0	0.0		58.0	9.0	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	hg19	CCDS46405.1	.	.	.	.	.	.	.	.	.	.	.	15.82	2.947391	0.53186	.	.	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000272666;ENST00000409816;ENST00000437387;ENST00000409090	T;T;T;T;T	0.76060	-0.99;-0.99;-0.99;-0.99;-0.99	4.82	3.62	0.41486	Band 4.1 domain (1);FERM domain (1);	0.720633	0.13276	N	0.400116	T	0.70107	0.3186	L	0.53249	1.67	0.21967	N	0.999446	P	0.47604	0.898	B	0.42188	0.379	T	0.59731	-0.7399	10	0.56958	D	0.05	.	10.5338	0.44992	0.8369:0.163:0.0:0.0	.	1233	Q6PIF6	MYO7B_HUMAN	C	1233;1233;86;1233;86;86	ENSP00000374175:S1233C;ENSP00000415090:S1233C;ENSP00000386461:S1233C;ENSP00000404927:S86C;ENSP00000386850:S86C	ENSP00000272666:S86C	S	+	1	0	MYO7B	128097376	0.991000	0.36638	0.372000	0.25991	0.757000	0.42996	3.133000	0.50531	0.650000	0.30769	0.402000	0.26972	AGC	.	.		0.627	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001		T	128380906	A	T	128380906	3	4	322	1	0	0	0	0	1	0	0	0	10092	188	7	4	3803	4	MYO7B	2	128380906	Missense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	59767267	128380906	114818467	26	45274										
ARHGAP15	55843	hgsc.bcm.edu	37	chr2	144194492	144194492	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ctgtttccagccaaaggattCaagttgtccatcaagaaacc	7	11	2	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr2:144194492C>T	ENST00000295095.6	+	8	751	c.584C>T	c.(583-585)tCa>tTa	p.S195L	RP11-570L15.2_ENST00000546678.1_RNA|AC096558.1_ENST00000549032.1_RNA|AC096558.1_ENST00000550516.1_RNA|AC096558.1_ENST00000442794.1_RNA	NM_018460.3	NP_060930.3	Q53QZ3	RHG15_HUMAN	Rho GTPase activating protein 15	195					positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)			endometrium(1)|kidney(5)|large_intestine(8)|liver(2)|lung(15)|ovary(1)|skin(2)	34				BRCA - Breast invasive adenocarcinoma(221;0.151)		CCAAAGGATTCAAGTTGTCCA	0.343																																					p.S195L		Atlas-SNP	.											.	ARHGAP15	99	.	0			c.C584T						.						61	62	62					2																	144194492		2203	4300	6503	SO:0001583	missense	55843	exon8			AGGATTCAAGTTG	AY219338	CCDS2184.1	2q22.2-q22.3	2013-01-10			ENSG00000075884	ENSG00000075884		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	21030	protein-coding gene	gene with protein product		610578				12650940, 11042152	Standard	NM_018460		Approved	BM046	uc002tvm.4	Q53QZ3	OTTHUMG00000131845	ENST00000295095.6:c.584C>T	chr2.hg19:g.144194492C>T	ENSP00000295095:p.Ser195Leu	90.0	0.0		133.0	50.0	NM_018460	Q53R36|Q53RD7|Q53RT6|Q53SX9|Q584N9|Q6PJE6|Q86WP1|Q8IXX1|Q9NRL8|Q9NZ77|Q9NZ91	Missense_Mutation	SNP	ENST00000295095.6	hg19	CCDS2184.1	.	.	.	.	.	.	.	.	.	.	C	12.06	1.823683	0.32237	.	.	ENSG00000075884	ENST00000295095	T	0.79454	-1.27	5.55	4.59	0.56863	.	0.999584	0.08093	N	0.999003	T	0.59595	0.2205	N	0.08118	0	0.23700	N	0.997074	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.002	T	0.41179	-0.9523	10	0.23302	T	0.38	.	9.6244	0.39741	0.2313:0.6527:0.116:0.0	.	195;195	B4E0R3;Q53QZ3	.;RHG15_HUMAN	L	195	ENSP00000295095:S195L	ENSP00000295095:S195L	S	+	2	0	ARHGAP15	143910962	0.987000	0.35691	0.955000	0.39395	0.981000	0.71138	1.497000	0.35649	2.601000	0.87937	0.650000	0.86243	TCA	.	.		0.343	ARHGAP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254793.2	NM_018460		T	144194492	C	T	144194492	3	4	322	1	0	0	0	0	1	0	0	0	866	838	29	3	610	3	ARHGAP15	2	144194492	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	15813586	144194492	99004881	27	45275										
RIF1	55183	hgsc.bcm.edu	37	chr2	152322315	152322315	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	aaatactgagtatagtaaatCtgaagaaaaattagataaca	6	3	1	4			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr2:152322315C>T	ENST00000243326.5	+	29	6764	c.6281C>T	c.(6280-6282)tCt>tTt	p.S2094F	RIF1_ENST00000444746.2_Missense_Mutation_p.S2094F|RIF1_ENST00000430328.2_Missense_Mutation_p.S2094F|RIF1_ENST00000453091.2_Missense_Mutation_p.S2094F|RIF1_ENST00000428287.2_Missense_Mutation_p.S2094F			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		TATAGTAAATCTGAAGAAAAA	0.348																																					p.S2094F		Atlas-SNP	.											.	RIF1	244	.	0			c.C6281T						.						61	62	62					2																	152322315		2203	4300	6503	SO:0001583	missense	55183	exon30			GTAAATCTGAAGA	AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345			23207	protein-coding gene	gene with protein product		608952	"RAP1 interacting factor homolog (yeast)"			15342490, 15042697, 22850674	Standard	NM_018151		Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.6281C>T	chr2.hg19:g.152322315C>T	ENSP00000243326:p.Ser2094Phe	108.0	0.0		150.0	75.0	NM_018151	A0AVS0|Q9NS16	Missense_Mutation	SNP	ENST00000243326.5	hg19	CCDS2194.1	.	.	.	.	.	.	.	.	.	.	C	2.949	-0.217220	0.06101	.	.	ENSG00000080345	ENST00000444746;ENST00000453091;ENST00000428287;ENST00000243326;ENST00000430328	T;T;T;T;T	0.10382	2.88;2.88;2.88;2.88;2.88	4.87	-1.62	0.08372	.	1.348360	0.04637	N	0.404688	T	0.05686	0.0149	N	0.14661	0.345	0.09310	N	1	B;B	0.09022	0.001;0.002	B;B	0.08055	0.001;0.003	T	0.39272	-0.9622	10	0.09843	T	0.71	2.9121	6.1943	0.20542	0.0:0.3485:0.1354:0.5161	.	2094;2094	Q5UIP0;Q5UIP0-2	RIF1_HUMAN;.	F	2094	ENSP00000390181:S2094F;ENSP00000414615:S2094F;ENSP00000415691:S2094F;ENSP00000243326:S2094F;ENSP00000416123:S2094F	ENSP00000243326:S2094F	S	+	2	0	RIF1	152030561	0.416000	0.25424	0.000000	0.03702	0.020000	0.10135	0.432000	0.21461	-0.211000	0.10124	0.650000	0.86243	TCT	.	.		0.348	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3			T	152322315	C	T	152322315	3	4	322	1	0	0	0	0	1	0	0	0	13374	913	32	3	6395	3	RIF1	2	152322315	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	8127823	152322315	90877058	28	45276										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168106334	168106334	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	aagagaatttagcggatctgAcagagggaaacttccaggaa	12	6	1	3			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr2:168106334A>T	ENST00000409195.1	+	9	8521	c.8432A>T	c.(8431-8433)gAc>gTc	p.D2811V	XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.D2811V|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.D2589V	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2636					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AGCGGATCTGACAGAGGGAAA	0.398																																					p.D2811V		Atlas-SNP	.											.	XIRP2	914	.	0			c.A8432T						.						69	68	68					2																	168106334		1845	4095	5940	SO:0001583	missense	129446	exon9			GATCTGACAGAGG	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.8432A>T	chr2.hg19:g.168106334A>T	ENSP00000386840:p.Asp2811Val	102.0	0.0		131.0	55.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	hg19	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	A	3.299	-0.143332	0.06669	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273;ENST00000413534	T;T;T	0.02579	4.24;4.24;4.24	6.02	-4.86	0.03132	.	1.146790	0.06178	N	0.678890	T	0.02230	0.0069	N	0.25647	0.755	0.09310	N	0.999999	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.04013	0.0;0.001;0.001	T	0.48625	-0.9019	10	0.24483	T	0.36	0.0761	8.5414	0.33395	0.3836:0.0977:0.0:0.5187	.	2636;2636;2589	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	V	2811;2811;2589;225	ENSP00000386840:D2811V;ENSP00000295237:D2811V;ENSP00000387255:D2589V	ENSP00000295237:D2811V	D	+	2	0	XIRP2	167814580	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-0.002000	0.12924	-0.443000	0.07180	0.533000	0.62120	GAC	.	.		0.398	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		T	168106334	A	T	168106334	3	4	322	1	0	0	0	0	1	0	0	0	17445	275	10	4	8462	4	XIRP2	2	168106334	Missense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	15784019	168106334	75093039	29	45277										
PDE11A	50940	hgsc.bcm.edu	37	chr2	178634089	178634089	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	agcttttgaacatgttgcatGgtatgatagcacctgattca	9	7	1	3			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr2:178634089G>A	ENST00000286063.6	-	10	2067	c.1750C>T	c.(1750-1752)Cat>Tat	p.H584Y	PDE11A_ENST00000409504.1_Missense_Mutation_p.H226Y|PDE11A_ENST00000389683.3_Missense_Mutation_p.H140Y|PDE11A_ENST00000497003.1_5'UTR|PDE11A_ENST00000449286.2_Missense_Mutation_p.H226Y|PDE11A_ENST00000358450.4_Missense_Mutation_p.H334Y	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	584					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|signal transduction (GO:0007165)	cytosol (GO:0005829)|perikaryon (GO:0043204)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)		Caffeine(DB00201)|Tadalafil(DB00820)	CATGTTGCATGGTATGATAGC	0.338									Primary Pigmented Nodular Adrenocortical Disease, Familial																												p.H584Y		Atlas-SNP	.											.	PDE11A	283	.	0			c.C1750T						.						102	93	96					2																	178634089		2203	4300	6503	SO:0001583	missense	50940	exon10	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	TTGCATGGTATGA	AJ251509	CCDS33334.1, CCDS42785.1, CCDS42786.1, CCDS46459.1	2q31.3	2010-06-22			ENSG00000128655	ENSG00000128655	3.1.4.17	"Phosphodiesterases"	8773	protein-coding gene	gene with protein product		604961				10725373	Standard	NM_001077196		Approved		uc002ulq.3	Q9HCR9	OTTHUMG00000154188	ENST00000286063.6:c.1750C>T	chr2.hg19:g.178634089G>A	ENSP00000286063:p.His584Tyr	38.0	0.0		55.0	27.0	NM_016953	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	Missense_Mutation	SNP	ENST00000286063.6	hg19	CCDS33334.1	.	.	.	.	.	.	.	.	.	.	G	19.99	3.928267	0.73327	.	.	ENSG00000128655	ENST00000286063;ENST00000358450;ENST00000409504;ENST00000389683;ENST00000449286	T;T;T;T;T	0.69926	-0.44;-0.44;-0.44;-0.44;-0.44	5.73	5.73	0.89815	.	0.183052	0.64402	D	0.000017	D	0.84474	0.5480	M	0.88377	2.95	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.87578	0.997;0.998	D	0.86669	0.1909	10	0.87932	D	0	.	15.7604	0.78076	0.0:0.0:1.0:0.0	.	334;584	Q9HCR9-2;Q9HCR9	.;PDE11_HUMAN	Y	584;334;226;140;226	ENSP00000286063:H584Y;ENSP00000351232:H334Y;ENSP00000386539:H226Y;ENSP00000374333:H140Y;ENSP00000390599:H226Y	ENSP00000286063:H584Y	H	-	1	0	PDE11A	178342335	1.000000	0.71417	0.999000	0.59377	0.927000	0.56198	5.937000	0.70162	2.854000	0.98071	0.655000	0.94253	CAT	.	.		0.338	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2			A	178634089	G	A	178634089	3	1	322	1	0	0	0	0	1	0	0	0	11640	1348	47	3	1095	3	PDE11A	2	178634089	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	10527755	178634089	64565284	30	45278										
ZC3H15	55854	hgsc.bcm.edu	37	chr2	187351141	187351141	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gaaacaggctcaggccggggGcagcaaaaaggcggagcaaa	16	9	1	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr2:187351141G>A	ENST00000337859.6	+	1	259	c.32G>A	c.(31-33)gGc>gAc	p.G11D	ZC3H15_ENST00000544130.1_5'UTR	NM_018471.2	NP_060941.2	Q8WU90	ZC3HF_HUMAN	zinc finger CCCH-type containing 15	11					cytokine-mediated signaling pathway (GO:0019221)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|skin(1)	15			OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Epithelial(96;0.0922)|all cancers(119;0.233)			CAGGCCGGGGGCAGCAAAAAG	0.617																																					p.G11D		Atlas-SNP	.											.	ZC3H15	28	.	0			c.G32A						.						43	59	54					2																	187351141		1895	4094	5989	SO:0001583	missense	55854	exon1			CCGGGGGCAGCAA		CCDS42791.1	2q32.1	2012-07-05			ENSG00000065548	ENSG00000065548		"Zinc fingers, CCCH-type domain containing"	29528	protein-coding gene	gene with protein product	"likely ortholog of mouse immediate early response, erythropoietin 4"					10880228	Standard	NM_018471		Approved	LEREPO4	uc002upo.3	Q8WU90	OTTHUMG00000154251	ENST00000337859.6:c.32G>A	chr2.hg19:g.187351141G>A	ENSP00000338788:p.Gly11Asp	80.0	0.0		116.0	15.0	NM_018471	B4DMW2|D3DPG7|Q5QTQ4|Q8WZ06|Q9NUZ3|Q9NZ37|Q9P079	Missense_Mutation	SNP	ENST00000337859.6	hg19	CCDS42791.1	.	.	.	.	.	.	.	.	.	.	G	18.43	3.623283	0.66901	.	.	ENSG00000065548	ENST00000337859;ENST00000536434	T	0.61627	0.09	5.38	4.49	0.54785	.	0.260854	0.36167	N	0.002747	T	0.48484	0.1502	L	0.36672	1.1	0.80722	D	1	B	0.21520	0.057	B	0.29716	0.106	T	0.38067	-0.9678	10	0.27082	T	0.32	-1.9242	12.0046	0.53251	0.0:0.1744:0.8256:0.0	.	11	Q8WU90	ZC3HF_HUMAN	D	11	ENSP00000338788:G11D	ENSP00000338788:G11D	G	+	2	0	ZC3H15	187059386	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.054000	0.41335	1.230000	0.43646	0.655000	0.94253	GGC	.	.		0.617	ZC3H15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334547.2	NM_018471		A	187351141	G	A	187351141	3	1	322	1	0	0	0	0	1	0	0	0	17582	1203	42	3	34	3	ZC3H15	2	187351141	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	8717052	187351141	55848232	31	45279										
FAM171B	165215	hgsc.bcm.edu	37	chr2	187627500	187627500	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tagccaaaagagatagcaagActaacatctggaagaagcga	10	7	1	3			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr2:187627500A>G	ENST00000304698.5	+	8	2634	c.2431A>G	c.(2431-2433)Act>Gct	p.T811A		NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	811						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)			NS(1)|breast(6)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(22)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						AGATAGCAAGACTAACATCTG	0.458																																					p.T811A		Atlas-SNP	.											.	FAM171B	146	.	0			c.A2431G						.						78	76	77					2																	187627500		2203	4299	6502	SO:0001583	missense	165215	exon8			AGCAAGACTAACA	AF361495	CCDS33347.1	2q32.2	2008-06-16	2008-06-16	2008-06-16	ENSG00000144369	ENSG00000144369			29412	protein-coding gene	gene with protein product			"KIAA1946"	KIAA1946		11853319	Standard	NM_177454		Approved	FLJ34104	uc002ups.3	Q6P995	OTTHUMG00000154278	ENST00000304698.5:c.2431A>G	chr2.hg19:g.187627500A>G	ENSP00000304108:p.Thr811Ala	186.0	0.0		241.0	102.0	NM_177454	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	Missense_Mutation	SNP	ENST00000304698.5	hg19	CCDS33347.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.131662	0.77662	.	.	ENSG00000144369	ENST00000304698	T	0.30448	1.53	6.02	6.02	0.97574	.	0.128251	0.52532	D	0.000065	T	0.45175	0.1329	L	0.36672	1.1	0.52501	D	0.999956	D;D	0.63046	0.992;0.992	P;P	0.62740	0.906;0.906	T	0.37220	-0.9715	10	0.66056	D	0.02	-19.2732	16.5494	0.84464	1.0:0.0:0.0:0.0	.	811;812	Q6P995;A8K122	F171B_HUMAN;.	A	811	ENSP00000304108:T811A	ENSP00000304108:T811A	T	+	1	0	FAM171B	187335745	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.818000	0.55678	2.299000	0.77371	0.528000	0.53228	ACT	.	.		0.458	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1	NM_177454		G	187627500	A	G	187627500	3	3	322	1	0	0	0	0	1	0	0	0	5496	275	10	2	2461	2	FAM171B	2	187627500	Missense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	276359	187627500	55571873	32	45280										
FASTKD2	22868	hgsc.bcm.edu	37	chr2	207634821	207634821	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ttatatttcaataggaacgtAtcaatgagtgtgatgagata	9	3	2	3			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr2:207634821A>G	ENST00000236980.6	+	3	1132	c.784A>G	c.(784-786)Atc>Gtc	p.I262V	FASTKD2_ENST00000402774.3_Missense_Mutation_p.I262V|FASTKD2_ENST00000403094.3_Missense_Mutation_p.I262V	NM_014929.3	NP_055744.2	Q9NYY8	FAKD2_HUMAN	FAST kinase domains 2	262					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(2)	21				LUSC - Lung squamous cell carcinoma(261;0.0718)|Epithelial(149;0.119)|Lung(261;0.138)		ATAGGAACGTATCAATGAGTG	0.373																																					p.I262V		Atlas-SNP	.											.	FASTKD2	49	.	0			c.A784G						.						179	162	168					2																	207634821		2203	4300	6503	SO:0001583	missense	22868	exon3			GAACGTATCAATG	BC001544	CCDS2371.1	2q33.3	2008-02-05	2006-07-07	2006-07-07	ENSG00000118246	ENSG00000118246			29160	protein-coding gene	gene with protein product		612322	"KIAA0971"	KIAA0971			Standard	NM_014929		Approved		uc002vbx.3	Q9NYY8	OTTHUMG00000132917	ENST00000236980.6:c.784A>G	chr2.hg19:g.207634821A>G	ENSP00000236980:p.Ile262Val	70.0	0.0		100.0	45.0	NM_001136193	Q9NVX6|Q9Y2H7	Missense_Mutation	SNP	ENST00000236980.6	hg19	CCDS2371.1	.	.	.	.	.	.	.	.	.	.	A	13.09	2.133139	0.37630	.	.	ENSG00000118246	ENST00000236980;ENST00000402774;ENST00000403094	T;T;T	0.16324	2.35;2.35;2.35	5.57	5.57	0.84162	.	0.156953	0.42964	D	0.000635	T	0.24122	0.0584	M	0.72118	2.19	0.29664	N	0.843026	P;P	0.47106	0.89;0.495	P;B	0.47626	0.552;0.152	T	0.12372	-1.0550	10	0.15952	T	0.53	-18.0976	10.336	0.43850	0.721:0.279:0.0:0.0	.	262;262	Q9NYY8-2;Q9NYY8	.;FAKD2_HUMAN	V	262	ENSP00000236980:I262V;ENSP00000385990:I262V;ENSP00000384929:I262V	ENSP00000236980:I262V	I	+	1	0	FASTKD2	207343066	1.000000	0.71417	1.000000	0.80357	0.833000	0.47200	4.485000	0.60279	2.120000	0.65058	0.482000	0.46254	ATC	.	.		0.373	FASTKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256428.2	NM_014929		G	207634821	A	G	207634821	3	3	322	1	0	0	0	0	1	0	0	0	5694	449	16	2	790	2	FASTKD2	2	207634821	Missense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	20007321	207634821	35564552	33	45281										
CRYGD	1421	hgsc.bcm.edu	37	chr2	208986520	208986520	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cctcggtagttggacagctcGtagaggacccaggagccctc	13	13	0	1	rs398122948		TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr2:208986520G>T	ENST00000264376.4	-	3	429	c.402C>A	c.(400-402)taC>taA	p.Y134*		NM_006891.3	NP_008822.2	P07320	CRGD_HUMAN	crystallin, gamma D	134	Beta/gamma crystallin 'Greek key' 4. {ECO:0000255|PROSITE-ProRule:PRU00028}.				cellular response to reactive oxygen species (GO:0034614)|lens development in camera-type eye (GO:0002088)|lens fiber cell differentiation (GO:0070306)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	structural constituent of eye lens (GO:0005212)			breast(1)|endometrium(1)|lung(3)	5				LUSC - Lung squamous cell carcinoma(261;0.0703)|Epithelial(149;0.0858)|Lung(261;0.133)		TGGACAGCTCGTAGAGGACCC	0.582																																					p.Y134X		Atlas-SNP	.											CRYGD,NS,carcinoma,0,1	CRYGD	18	.	0			c.C402A	GRCh37	CM074129	CRYGD	M		.						100	93	95					2																	208986520		2203	4300	6503	SO:0001587	stop_gained	1421	exon3			CAGCTCGTAGAGG		CCDS2378.1	2q33.3	2013-02-14			ENSG00000118231	ENSG00000118231			2411	protein-coding gene	gene with protein product		123690		CRYG4			Standard	NM_006891		Approved		uc002vcn.4	P07320	OTTHUMG00000132944	ENST00000264376.4:c.402C>A	chr2.hg19:g.208986520G>T	ENSP00000264376:p.Tyr134*	80.0	0.0		98.0	48.0	NM_006891	Q17RF7|Q53R51|Q99681	Nonsense_Mutation	SNP	ENST00000264376.4	hg19	CCDS2378.1	.	.	.	.	.	.	.	.	.	.	G	15.38	2.816367	0.50527	.	.	ENSG00000118231	ENST00000264376	.	.	.	4.25	-8.5	0.00927	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.4563	0.90721	0.8722:0.0:0.1278:0.0	.	.	.	.	X	134	.	ENSP00000264376:Y134X	Y	-	3	2	CRYGD	208694765	0.001000	0.12720	0.391000	0.26233	0.965000	0.64279	-1.607000	0.02070	-2.415000	0.00568	-1.013000	0.02462	TAC	.	.		0.582	CRYGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256476.2	NM_006891		T	208986520	G	T	208986520	4	4	322	1	0	0	0	0	0	1	0	0	3919	1140	40	1	126	1	CRYGD	2	208986520	Nonsense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	1351699	208986520	34212853	34	45282										
SP140L	93349	hgsc.bcm.edu	37	chr2	231256927	231256927	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tgcgctgtggcgggtggcccCtacgacggctgatggaggta	18	10	0	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr2:231256927C>A	ENST00000415673.2	+	12	1176	c.1090C>A	c.(1090-1092)Cta>Ata	p.L364I	SP140L_ENST00000243810.6_Missense_Mutation_p.L364I|SP140L_ENST00000396563.4_Missense_Mutation_p.L329I|SP140L_ENST00000444636.1_Missense_Mutation_p.L364I	NM_138402.4	NP_612411.4	Q9H930	SP14L_HUMAN	SP140 nuclear body protein-like	364	SAND. {ECO:0000255|PROSITE- ProRule:PRU00185}.					nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|skin(1)	20						CGGGTGGCCCCTACGACGGCT	0.483																																					p.L364I		Atlas-SNP	.											.	SP140L	68	.	0			c.C1090A						.						80	94	89					2																	231256927		2056	4187	6243	SO:0001583	missense	93349	exon12			TGGCCCCTACGAC	BC004921	CCDS46538.1	2q37.1	2013-01-28			ENSG00000185404	ENSG00000185404		"Zinc fingers, PHD-type"	25105	protein-coding gene	gene with protein product						12477932	Standard	NM_138402		Approved		uc010fxm.1	Q9H930	OTTHUMG00000153730	ENST00000415673.2:c.1090C>A	chr2.hg19:g.231256927C>A	ENSP00000397911:p.Leu364Ile	106.0	0.0		110.0	53.0	NM_138402	Q2M375|Q4ZG65|Q9BSP3	Missense_Mutation	SNP	ENST00000415673.2	hg19	CCDS46538.1	.	.	.	.	.	.	.	.	.	.	C	13.87	2.365104	0.41902	.	.	ENSG00000185404	ENST00000444636;ENST00000415673;ENST00000243810;ENST00000396563	T;T;T;T	0.75367	-0.93;-0.93;-0.93;-0.93	3.44	2.54	0.30619	.	.	.	.	.	D	0.84871	0.5568	M	0.82716	2.605	0.09310	N	1	D;D	0.89917	1.0;0.982	D;D	0.91635	0.999;0.952	T	0.72168	-0.4372	9	0.87932	D	0	.	8.1663	0.31228	0.2388:0.7612:0.0:0.0	.	329;364	Q9H930-2;Q9H930-4	.;.	I	364;364;364;329	ENSP00000395195:L364I;ENSP00000397911:L364I;ENSP00000243810:L364I;ENSP00000379811:L329I	ENSP00000243810:L364I	L	+	1	2	SP140L	230965171	0.416000	0.25424	0.016000	0.15963	0.113000	0.19764	3.071000	0.50041	0.983000	0.38602	0.591000	0.81541	CTA	.	.		0.483	SP140L-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374538.1	NM_138402		A	231256927	C	A	231256927	3	1	322	1	0	0	0	0	1	0	0	0	14978	680	24	3	1136	3	SP140L	2	231256927	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	22270407	231256927	11942446	35	45283										
SAG	6295	hgsc.bcm.edu	37	chr2	234217900	234217900	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tatcttcaagaagatctcccGggacaaatcggtgagtggtg	12	8	3	3	rs371502229		TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr2:234217900G>T	ENST00000409110.1	+	2	295	c.65G>T	c.(64-66)cGg>cTg	p.R22L		NM_000541.4	NP_000532.2	P10523	ARRS_HUMAN	S-antigen; retina and pineal gland (arrestin)	22					cell surface receptor signaling pathway (GO:0007166)|negative regulation of catalytic activity (GO:0043086)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	cytosol (GO:0005829)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	protein phosphatase inhibitor activity (GO:0004864)			cervix(1)|kidney(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	9		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.018)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.054)		Epithelial(121;2.86e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00608)|Lung(119;0.00714)|GBM - Glioblastoma multiforme(43;0.207)		AAGATCTCCCGGGACAAATCG	0.443																																					p.R22L		Atlas-SNP	.											SAG_ENST00000409110,caecum,carcinoma,0,2	SAG	77	.	0			c.G65T						.						57	59	58					2																	234217900		1884	4118	6002	SO:0001583	missense	6295	exon2			TCTCCCGGGACAA		CCDS46545.1	2q37.1	2013-02-14			ENSG00000130561	ENSG00000130561			10521	protein-coding gene	gene with protein product	"arrestin 1"	181031				2249983	Standard	NM_000541		Approved	ARRESTIN, RP47	uc002vuh.2	P10523	OTTHUMG00000153213	ENST00000409110.1:c.65G>T	chr2.hg19:g.234217900G>T	ENSP00000386444:p.Arg22Leu	69.0	0.0		87.0	39.0	NM_000541	A0FDN6|Q53SV3|Q99858	Missense_Mutation	SNP	ENST00000409110.1	hg19	CCDS46545.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.059127	0.76074	.	.	ENSG00000130561	ENST00000252857;ENST00000447536;ENST00000409110;ENST00000415974;ENST00000478615	T;T;T	0.17370	2.28;2.28;2.28	4.46	4.46	0.54185	Arrestin, N-terminal (1);Immunoglobulin E-set (1);	0.236368	0.34959	N	0.003558	T	0.23965	0.0580	L	0.59436	1.845	0.80722	D	1	D	0.60160	0.987	P	0.46885	0.53	T	0.02190	-1.1198	10	0.62326	D	0.03	-14.1626	14.3198	0.66479	0.0:0.0:1.0:0.0	.	22	P10523	ARRS_HUMAN	L	22	ENSP00000408937:R22L;ENSP00000386444:R22L;ENSP00000409475:R22L	ENSP00000252857:R22L	R	+	2	0	SAG	233882639	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.418000	0.59828	2.484000	0.83849	0.555000	0.69702	CGG	.	.		0.443	SAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330126.1	NM_000541		T	234217900	G	T	234217900	3	4	322	1	0	0	0	0	1	0	0	0	13823	1116	39	1	67	1	SAG	2	234217900	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	2960973	234217900	8981473	36	45284										
C3orf20	84077	hgsc.bcm.edu	37	chr3	14745959	14745959	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cccgcaaaggagactctcagAccccgggtttacattaccct	8	15	1	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr3:14745959A>G	ENST00000253697.3	+	7	1446	c.994A>G	c.(994-996)Acc>Gcc	p.T332A	C3orf20_ENST00000412910.1_Missense_Mutation_p.T210A|C3orf20_ENST00000435614.1_Missense_Mutation_p.T210A|C3orf20_ENST00000495387.1_3'UTR	NM_032137.4	NP_115513.4	Q8ND61	CC020_HUMAN	chromosome 3 open reading frame 20	332						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(13)|lung(11)|ovary(4)|skin(2)	40						AGACTCTCAGACCCCGGGTTT	0.507																																					p.T332A		Atlas-SNP	.											.	C3orf20	109	.	0			c.A994G						.						150	160	157					3																	14745959		2203	4300	6503	SO:0001583	missense	84077	exon7			TCTCAGACCCCGG	AL136781	CCDS33706.1, CCDS54555.1	3p25.1	2011-01-25			ENSG00000131379	ENSG00000131379			25320	protein-coding gene	gene with protein product						11230166	Standard	NM_032137		Approved	DKFZP434N1817	uc003byy.3	Q8ND61	OTTHUMG00000155545	ENST00000253697.3:c.994A>G	chr3.hg19:g.14745959A>G	ENSP00000253697:p.Thr332Ala	119.0	0.0		205.0	30.0	NM_032137	Q7L0U6|Q8NCP2|Q9H0I7	Missense_Mutation	SNP	ENST00000253697.3	hg19	CCDS33706.1	.	.	.	.	.	.	.	.	.	.	A	8.343	0.829143	0.16749	.	.	ENSG00000131379	ENST00000253697;ENST00000435614;ENST00000412910	T;T;T	0.09350	3.28;2.99;2.99	3.43	-5.33	0.02713	.	1.818810	0.03725	N	0.252506	T	0.06826	0.0174	L	0.29908	0.895	0.09310	N	1	B	0.31817	0.341	B	0.28139	0.086	T	0.27938	-1.0059	10	0.30854	T	0.27	0.1437	5.0461	0.14485	0.3043:0.3146:0.3811:0.0	.	332	Q8ND61	CC020_HUMAN	A	332;210;210	ENSP00000253697:T332A;ENSP00000402933:T210A;ENSP00000396081:T210A	ENSP00000253697:T332A	T	+	1	0	C3orf20	14720963	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.700000	0.05081	-1.097000	0.03042	-0.334000	0.08254	ACC	.	.		0.507	C3orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340586.1	NM_032137		G	14745959	A	G	14745959	3	3	322	1	0	0	0	0	1	0	0	0	2215	275	10	2	1012	2	C3orf20	3	14745959	Missense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10		14745959	183276471	37	45285										
TRAK1	22906	hgsc.bcm.edu	37	chr3	42243973	42243973	+	Frame_Shift_Del	DEL	C	C	-													0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gggacgccgggcaccccaggCtcccacgacctggagacggc							TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr3:42243973delC	ENST00000327628.5	+	13	1873	c.1473delC	c.(1471-1473)ggcfs	p.G491fs	TRAK1_ENST00000341421.3_Frame_Shift_Del_p.G433fs|TRAK1_ENST00000449246.1_Frame_Shift_Del_p.G417fs|TRAK1_ENST00000396175.1_Frame_Shift_Del_p.G433fs|TRAK1_ENST00000487159.1_3'UTR	NM_001042646.2	NP_001036111.1	Q9UPV9	TRAK1_HUMAN	trafficking protein, kinesin binding 1	491	Interaction with HGS.				endosome to lysosome transport (GO:0008333)|protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	22						GCACCCCAGGCTCCCACGACC	0.637																																					p.G491fs	GBM(44;195 884 22595 31865 41850)	Atlas-INDEL	.											.	TRAK1	188	.	0			c.1472delG						.						25	34	31					3																	42243973		2203	4297	6500	SO:0001589	frameshift_variant	22906	exon13			.		CCDS2695.1, CCDS43072.1, CCDS58826.1, CCDS74922.1	3p22.1	2012-03-05			ENSG00000182606	ENSG00000182606			29947	protein-coding gene	gene with protein product	"OGT(O Glc NAc transferase) interacting protein 106 KDa", "O-linked N-acetylglucosamine transferase interacting protein 106", "milton homolog 1 (Drosophila)"	608112				10470851, 12435728, 16380713, 20230862	Standard	NM_014965		Approved	OIP106, KIAA1042, MILT1	uc003cky.4	Q9UPV9	OTTHUMG00000131795	ENST00000327628.5:c.1473delC	chr3.hg19:g.42243973delC	ENSP00000328998:p.Gly491fs	123.0	0.0		208.0	26.0	NM_001042646	E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	Frame_Shift_Del	DEL	ENST00000327628.5	hg19	CCDS43072.1																																																																																			.	.		0.637	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343413.1	NM_014965		-	42243973	C	-	42243973	7	5	322	1	0	1	0	1	0	0	0	0	16464	784	28	0	1639	0	TRAK1	3	42243973	Frame_Shift_Del	DEL	C	TCGA-MI-A75G-01A-11D-A32G-10	27498014	42243973	155778457	38	45286	237	2								
TRAK1	22906	hgsc.bcm.edu	37	chr3	42243975	42243976	+	Nonsense_Mutation	DNP	CC	CC	AA													0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gacgccgggcaccccaggctCccacgacctggagacggcgc							TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr3:42243975_42243976CC>AA	ENST00000327628.5	+	13	1875_1876	c.1475_1476CC>AA	c.(1474-1476)tCC>tAA	p.S492*	TRAK1_ENST00000341421.3_Nonsense_Mutation_p.S434*|TRAK1_ENST00000449246.1_Nonsense_Mutation_p.S418*|TRAK1_ENST00000396175.1_Nonsense_Mutation_p.S434*|TRAK1_ENST00000487159.1_3'UTR	NM_001042646.2	NP_001036111.1	Q9UPV9	TRAK1_HUMAN	trafficking protein, kinesin binding 1	492	Interaction with HGS.				endosome to lysosome transport (GO:0008333)|protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	22						ACCCCAGGCTCCCACGACCTGG	0.639																																					p.S492Y|p.S492S	GBM(44;195 884 22595 31865 41850)	Atlas-SNP	.											.	TRAK1	188	.	0			c.C1475A|c.C1476A						.																																			SO:0001587	stop_gained	22906	exon13			CAGGCTCCCACGA|AGGCTCCCACGAC		CCDS2695.1, CCDS43072.1, CCDS58826.1, CCDS74922.1	3p22.1	2012-03-05			ENSG00000182606	ENSG00000182606			29947	protein-coding gene	gene with protein product	"OGT(O Glc NAc transferase) interacting protein 106 KDa", "O-linked N-acetylglucosamine transferase interacting protein 106", "milton homolog 1 (Drosophila)"	608112				10470851, 12435728, 16380713, 20230862	Standard	NM_014965		Approved	OIP106, KIAA1042, MILT1	uc003cky.4	Q9UPV9	OTTHUMG00000131795	Exception_encountered	chr3.hg19:g.42243975_42243976delinsAA	ENSP00000328998:p.Ser492*	126.0|128.0	0.0		207.0|204.0	25.0|24.0	NM_001265608	E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	Missense_Mutation|Silent	SNP	ENST00000327628.5	hg19	CCDS43072.1																																																																																			.	.		0.639	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343413.1	NM_014965		AA	42243976	CC	AA	42243975	4	1	322	1	0	0	0	0	0	1	0	0	16464	855	30	3	1641	3	TRAK1	3	42243975	Nonsense_Mutation	DNP	CC	TCGA-MI-A75G-01A-11D-A32G-10	2	42243975	155778455	39	45287	237	2								
HHATL	57467	hgsc.bcm.edu	37	chr3	42735224	42735225	+	Missense_Mutation	DNP	AG	AG	TT													0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tgtcacaaggcccaagccacAgtgtggtgatggcaaatgtg					rs566301459		TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A|G	A|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr3:42735224_42735225AG>TT	ENST00000441594.1	-	10	1393_1394	c.1132_1133CT>AA	c.(1132-1134)CTg>AAg	p.L378K	HHATL_ENST00000310417.5_Missense_Mutation_p.L378K	NM_020707.3	NP_065758.3	Q9HCP6	HHATL_HUMAN	hedgehog acyltransferase-like	378					negative regulation of N-terminal protein palmitoylation (GO:0060262)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(3)|prostate(3)	19				KIRC - Kidney renal clear cell carcinoma(284;0.215)		CCCAAGCCACAGTGTGGTGATG	0.53																																					p.L378Q|p.L378M		Atlas-SNP	.											.	HHATL	49	.	0			c.T1133A|c.C1132A						.																																			SO:0001583	missense	57467	exon10			AGCCACAGTGTGG|GCCACAGTGTGGT	AB042554	CCDS2704.1	3p22	2009-10-06	2007-02-06	2007-02-06	ENSG00000010282	ENSG00000010282			13242	protein-coding gene	gene with protein product	"membrane bound O-acyltransferase domain containing 3"	608116	"chromosome 3 open reading frame 3", "GUP1, glycerol uptake/transporter homolog (yeast)"	C3orf3, GUP1		11374908	Standard	NM_020707		Approved	KIAA1173, OACT3, MSTP002, MBOAT3	uc003clx.3	Q9HCP6	OTTHUMG00000133043	ENST00000441594.1:c.1132_1133delinsTT	chr3.hg19:g.42735224_42735225delinsTT	ENSP00000405423:p.Leu378Lys	60.0|61.0	0.0		101.0|105.0	19.0|20.0	NM_020707	Q8TBG3|Q9ULP7	Missense_Mutation	SNP	ENST00000441594.1	hg19	CCDS2704.1																																																																																			.	.		0.53	HHATL-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343627.1	NM_020707		TT	42735225	AG	TT	42735224	3	4	322	1	0	0	0	0	1	0	0	0	7099	188	7	4	393	4	HHATL	3	42735224	Missense_Mutation	DNP	AG	TCGA-MI-A75G-01A-11D-A32G-10	491249	42735224	155287206	40	45288										
C3orf39	84892	hgsc.bcm.edu	37	chr3	43121653	43121653	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cctcacggctttgcaggataCgggcttgctcagcccggtcc	12	15	2	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr3:43121653C>T	ENST00000344697.2	-	2	1616	c.1271G>A	c.(1270-1272)cGt>cAt	p.R424H	POMGNT2_ENST00000441964.1_Missense_Mutation_p.R424H	NM_032806.5	NP_116195.2	Q8NAT1	PMGT2_HUMAN	protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-)	424					protein O-linked glycosylation (GO:0006493)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein O-GlcNAc transferase activity (GO:0097363)	p.R424H(1)									TTGCAGGATACGGGCTTGCTC	0.622																																					p.R424H		Atlas-SNP	.											C3orf39,colon,carcinoma,0,1	.	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1271A						.						41	40	40					3																	43121653		2203	4300	6503	SO:0001583	missense	84892	exon2			AGGATACGGGCTT	AK092147	CCDS2709.1	3p22.1	2014-07-15	2013-08-22	2013-08-22	ENSG00000144647	ENSG00000144647			25902	protein-coding gene	gene with protein product		614828	"chromosome 3 open reading frame 39", "glycosyltransferase-like domain containing 2"	C3orf39, GTDC2		12477932	Standard	NM_032806		Approved	FLJ14566, AGO61	uc003cmr.2	Q8NAT1	OTTHUMG00000133038	ENST00000344697.2:c.1271G>A	chr3.hg19:g.43121653C>T	ENSP00000344125:p.Arg424His	56.0	0.0		81.0	5.0	NM_032806	B3KWC3|Q96SY3	Missense_Mutation	SNP	ENST00000344697.2	hg19	CCDS2709.1	.	.	.	.	.	.	.	.	.	.	C	18.11	3.551883	0.65311	.	.	ENSG00000144647	ENST00000441964;ENST00000344697	T;T	0.78246	-1.16;-1.16	5.23	5.23	0.72850	.	0.054192	0.85682	D	0.000000	D	0.83216	0.5206	L	0.61387	1.9	0.80722	D	1	D	0.62365	0.991	P	0.54965	0.765	T	0.81703	-0.0812	10	0.33940	T	0.23	-12.0407	18.2115	0.89872	0.0:1.0:0.0:0.0	.	424	Q8NAT1	AGO61_HUMAN	H	424	ENSP00000408992:R424H;ENSP00000344125:R424H	ENSP00000344125:R424H	R	-	2	0	C3orf39	43096657	1.000000	0.71417	0.945000	0.38365	0.635000	0.38103	4.859000	0.62954	2.614000	0.88457	0.650000	0.86243	CGT	.	.		0.622	POMGNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256643.1	NM_032806		T	43121653	C	T	43121653	3	4	322	1	0	0	0	0	1	0	0	0	2231	536	19	1	475	1	C3orf39	3	43121653	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	386429	43121653	154900777	41	45289										
CCR3	1232	hgsc.bcm.edu	37	chr3	46307579	46307579	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gttggagagaggttccggaaGtacctgcgccacttcttcca	12	11	1	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr3:46307579G>T	ENST00000357422.2	+	4	1473	c.930G>T	c.(928-930)aaG>aaT	p.K310N	CCR3_ENST00000395942.2_Missense_Mutation_p.K310N|CCR3_ENST00000545097.1_Missense_Mutation_p.K331N|CCR3_ENST00000541018.1_Missense_Mutation_p.K310N|CCR3_ENST00000395940.2_Missense_Mutation_p.K310N			P51677	CCR3_HUMAN	chemokine (C-C motif) receptor 3	310					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell adhesion (GO:0007155)|cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|inflammatory response (GO:0006954)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell proliferation (GO:0001938)|viral process (GO:0016032)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(3)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(193;0.00119)|KIRC - Kidney renal clear cell carcinoma(197;0.0183)|Kidney(197;0.0216)		GGTTCCGGAAGTACCTGCGCC	0.547																																					p.K331N		Atlas-SNP	.											.	CCR3	52	.	0			c.G993T						.						110	91	97					3																	46307579		2203	4300	6503	SO:0001583	missense	1232	exon3			CCGGAAGTACCTG	AF247361	CCDS2738.1, CCDS54574.1	3p21.3	2012-08-08			ENSG00000183625	ENSG00000183625		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1604	protein-coding gene	gene with protein product		601268		CMKBR3			Standard	NM_178328		Approved	CC-CKR-3, CKR3, CD193	uc003cpk.2	P51677	OTTHUMG00000133484	ENST00000357422.2:c.930G>T	chr3.hg19:g.46307579G>T	ENSP00000350003:p.Lys310Asn	29.0	0.0		63.0	23.0	NM_178328	B3KVQ1|F5GWL6|Q15748|Q2YDB9|Q86WD2|Q8TDP6|Q9ULY8	Missense_Mutation	SNP	ENST00000357422.2	hg19	CCDS2738.1	.	.	.	.	.	.	.	.	.	.	G	4.694	0.129045	0.08981	.	.	ENSG00000183625	ENST00000357422;ENST00000545097;ENST00000541018;ENST00000395940;ENST00000395942	T;T;T;T;T	0.38240	1.15;1.15;1.15;1.15;1.15	5.55	0.627	0.17675	.	0.093240	0.45126	D	0.000390	T	0.29491	0.0735	M	0.62723	1.935	0.39195	D	0.963042	B;B	0.28636	0.218;0.054	B;B	0.37451	0.25;0.077	T	0.06661	-1.0814	10	0.12430	T	0.62	.	2.1353	0.03760	0.5229:0.1356:0.2045:0.1369	.	331;310	F5GWL6;P51677	.;CCR3_HUMAN	N	310;331;310;310;310	ENSP00000350003:K310N;ENSP00000441600:K331N;ENSP00000440097:K310N;ENSP00000379271:K310N;ENSP00000379273:K310N	ENSP00000350003:K310N	K	+	3	2	CCR3	46282583	0.021000	0.18746	0.602000	0.28890	0.330000	0.28571	0.113000	0.15499	0.175000	0.19841	-0.140000	0.14226	AAG	.	.		0.547	CCR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257380.2			T	46307579	G	T	46307579	3	4	322	1	0	0	0	0	1	0	0	0	2944	1020	36	3	999	3	CCR3	3	46307579	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	3185926	46307579	151714851	42	45290										
CCR2	729230	hgsc.bcm.edu	37	chr3	46400024	46400024	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gcaaacaatgtccagttttcTacagggagacagtggatgga	12	7	1	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr3:46400024T>C	ENST00000400888.2	+	1	980				CCR2_ENST00000292301.4_Intron|CCR2_ENST00000465202.1_3'UTR|CCR2_ENST00000445132.2_Missense_Mutation_p.Y336H			P41597	CCR2_HUMAN	chemokine (C-C motif) receptor 2						blood vessel remodeling (GO:0001974)|cellular calcium ion homeostasis (GO:0006874)|cellular defense response (GO:0006968)|cellular homeostasis (GO:0019725)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell chemotaxis (GO:0002407)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|JAK-STAT cascade (GO:0007259)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of angiogenesis (GO:0016525)|negative regulation of eosinophil degranulation (GO:0043310)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of astrocyte chemotaxis (GO:2000464)|positive regulation of CD8-positive, alpha-beta T cell extravasation (GO:2000451)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of immune complex clearance by monocytes and macrophages (GO:0090265)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of monocyte extravasation (GO:2000439)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of vascular endothelial growth factor production (GO:0010574)|response to wounding (GO:0009611)|T-helper 17 cell chemotaxis (GO:0035705)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|CCR2 chemokine receptor binding (GO:0031727)|chemokine receptor activity (GO:0004950)|protein homodimerization activity (GO:0042803)			breast(3)|endometrium(1)|large_intestine(1)|liver(2)|lung(7)	14				BRCA - Breast invasive adenocarcinoma(193;0.00114)|KIRC - Kidney renal clear cell carcinoma(197;0.0174)|Kidney(197;0.0206)		TCCAGTTTTCTACAGGGAGAC	0.483																																					p.Y336H		Atlas-SNP	.											.	CCR2	103	.	0			c.T1006C						.						70	63	65					3																	46400024		692	1591	2283	SO:0001627	intron_variant	729230	exon2			GTTTTCTACAGGG		CCDS43078.1, CCDS46813.1	3p21	2012-08-08			ENSG00000121807	ENSG00000121807		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1603	protein-coding gene	gene with protein product		601267		CMKBR2		8146186	Standard	NM_001123041		Approved	CC-CKR-2, CKR2, MCP-1-R, CD192, FLJ78302	uc003cpn.4	P41597	OTTHUMG00000156466	ENST00000400888.2:c.941+65T>C	chr3.hg19:g.46400024T>C		41.0	0.0		79.0	22.0	NM_001123396	A0AVQ3|B2RMT0|Q4VBL2	Missense_Mutation	SNP	ENST00000400888.2	hg19	CCDS43078.1	.	.	.	.	.	.	.	.	.	.	T	0.947	-0.707589	0.03230	.	.	ENSG00000121807	ENST00000445132	T	0.36520	1.25	4.91	3.73	0.42828	.	.	.	.	.	T	0.22859	0.0552	L	0.27053	0.805	0.51767	D	0.999936	B	0.02656	0.0	B	0.04013	0.001	T	0.05370	-1.0889	9	0.18276	T	0.48	.	9.817	0.40858	0.0:0.0834:0.0:0.9166	.	336	Q4VBL2	.	H	336	ENSP00000399285:Y336H	ENSP00000399285:Y336H	Y	+	1	0	CCR2	46375028	0.998000	0.40836	0.474000	0.27266	0.038000	0.13279	2.480000	0.45206	1.977000	0.57605	0.455000	0.32223	TAC	.	.		0.483	CCR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344292.1	NM_000647		C	46400024	T	C	46400024	1	2	322	0	1	0	0	0	0	0	0	0	2943	1522	53	2		2	CCR2	3	46400024	Intron	SNP	T	TCGA-MI-A75G-01A-11D-A32G-10	92445	46400024	151622406	43	45291										
LTF	4057	hgsc.bcm.edu	37	chr3	46480950	46480950	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ctgccagcttcaaatccttaGcccatgcctcattgttattt	5	13	2	0	rs149901533		TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr3:46480950G>T	ENST00000231751.4	-	15	2040	c.1745C>A	c.(1744-1746)gCt>gAt	p.A582D	LTF_ENST00000426532.2_Missense_Mutation_p.A538D|LTF_ENST00000493056.1_5'UTR|LTF_ENST00000417439.1_Missense_Mutation_p.A580D	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	582	Transferrin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00741}.				antibacterial humoral response (GO:0019731)|antifungal humoral response (GO:0019732)|bone morphogenesis (GO:0060349)|humoral immune response (GO:0006959)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|iron assimilation by chelation and transport (GO:0033214)|iron ion transport (GO:0006826)|negative regulation of apoptotic process (GO:0043066)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of osteoclast development (GO:2001205)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|negative regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000308)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of chondrocyte proliferation (GO:1902732)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|regulation of cytokine production (GO:0001817)|regulation of tumor necrosis factor production (GO:0032680)|response to host immune response (GO:0052572)|retina homeostasis (GO:0001895)|transcription, DNA-templated (GO:0006351)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|phagocytic vesicle lumen (GO:0097013)|secretory granule (GO:0030141)|specific granule (GO:0042581)	DNA binding (GO:0003677)|ferric iron binding (GO:0008199)|heparin binding (GO:0008201)|iron ion binding (GO:0005506)|protein serine/threonine kinase activator activity (GO:0043539)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	40				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)		CAAATCCTTAGCCCATGCCTC	0.542																																					p.A582D		Atlas-SNP	.											.	LTF	98	.	0			c.C1745A						.						90	81	84					3																	46480950		2203	4300	6503	SO:0001583	missense	4057	exon15			TCCTTAGCCCATG		CCDS33747.1, CCDS56251.1	3p21.31	2012-10-02			ENSG00000012223	ENSG00000012223			6720	protein-coding gene	gene with protein product		150210				17476971, 3356163	Standard	NM_001199149		Approved	HLF2	uc003cpq.3	P02788	OTTHUMG00000156325	ENST00000231751.4:c.1745C>A	chr3.hg19:g.46480950G>T	ENSP00000231751:p.Ala582Asp	66.0	0.0		130.0	37.0	NM_002343	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	Missense_Mutation	SNP	ENST00000231751.4	hg19	CCDS33747.1	.	.	.	.	.	.	.	.	.	.	G	19.18	3.777802	0.70107	.	.	ENSG00000012223	ENST00000231751;ENST00000426532;ENST00000417439;ENST00000443496	T;T;T;T	0.08807	3.05;3.05;3.05;3.05	5.16	5.16	0.70880	.	0.100111	0.64402	D	0.000002	T	0.45518	0.1346	H	0.97265	3.97	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.996;1.0;0.996	T	0.64127	-0.6480	10	0.87932	D	0	.	16.9598	0.86269	0.0:0.0:1.0:0.0	.	580;569;582	E7ER44;E7EQB2;P02788	.;.;TRFL_HUMAN	D	582;538;580;569	ENSP00000231751:A582D;ENSP00000405719:A538D;ENSP00000405546:A580D;ENSP00000397427:A569D	ENSP00000231751:A582D	A	-	2	0	LTF	46455954	1.000000	0.71417	0.972000	0.41901	0.378000	0.30076	8.052000	0.89448	2.790000	0.95986	0.655000	0.94253	GCT	.	G|1.000;A|0.000		0.542	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343		T	46480950	G	T	46480950	3	4	322	1	0	0	0	0	1	0	0	0	9088	971	34	3	399	3	LTF	3	46480950	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	80926	46480950	151541480	44	45292										
ALS2CL	259173	hgsc.bcm.edu	37	chr3	46730917	46730917	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gccgcagcagagctgcctccTcagggttgcacatggccagg	14	14	1	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr3:46730917T>A	ENST00000318962.4	-	2	97	c.14A>T	c.(13-15)gAg>gTg	p.E5V	ALS2CL_ENST00000415953.1_Missense_Mutation_p.E5V	NM_147129.3	NP_667340.2	Q60I27	AL2CL_HUMAN	ALS2 C-terminal like	5					endosome organization (GO:0007032)|protein localization (GO:0008104)	cytoplasmic membrane-bounded vesicle (GO:0016023)	GTPase activator activity (GO:0005096)|identical protein binding (GO:0042802)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|skin(3)|stomach(2)	29				BRCA - Breast invasive adenocarcinoma(193;0.000726)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)		AGCTGCCTCCTCAGGGTTGCA	0.632																																					p.E5V		Atlas-SNP	.											.	ALS2CL	78	.	0			c.A14T						.						32	30	30					3																	46730917		2202	4298	6500	SO:0001583	missense	259173	exon2			GCCTCCTCAGGGT	AK074118	CCDS2743.1, CCDS43080.1	3p21.31	2008-01-30			ENSG00000178038	ENSG00000178038			20605	protein-coding gene	gene with protein product		612402				15388334, 8889548, 17239822	Standard	NM_147129		Approved	FLJ36525, RN49018, DKFZp686I0110	uc003cqb.2	Q60I27	OTTHUMG00000128673	ENST00000318962.4:c.14A>T	chr3.hg19:g.46730917T>A	ENSP00000313670:p.Glu5Val	66.0	0.0		119.0	15.0	NM_001190707	Q32MA1|Q6AI56|Q6ZNC5|Q6ZNC7|Q6ZTL4|Q86YD2|Q8N9U1|Q8NAL7	Missense_Mutation	SNP	ENST00000318962.4	hg19	CCDS2743.1	.	.	.	.	.	.	.	.	.	.	T	18.06	3.538531	0.65085	.	.	ENSG00000178038	ENST00000318962;ENST00000415953	T;T	0.61040	0.14;0.14	4.81	3.62	0.41486	.	0.979255	0.08309	N	0.965720	T	0.64450	0.2599	L	0.32530	0.975	0.80722	D	1	D	0.76494	0.999	D	0.66084	0.941	T	0.56032	-0.8046	10	0.87932	D	0	.	8.5906	0.33686	0.0:0.0:0.1945:0.8055	.	5	Q60I27	AL2CL_HUMAN	V	5	ENSP00000313670:E5V;ENSP00000413223:E5V	ENSP00000313670:E5V	E	-	2	0	ALS2CL	46705921	0.956000	0.32656	0.919000	0.36401	0.824000	0.46624	2.200000	0.42724	0.929000	0.37192	0.460000	0.39030	GAG	.	.		0.632	ALS2CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250567.3	NM_147129		A	46730917	T	A	46730917	3	1	322	1	0	0	0	0	1	0	0	0	551	1551	54	4	2947	4	ALS2CL	3	46730917	Missense_Mutation	SNP	T	TCGA-MI-A75G-01A-11D-A32G-10	249967	46730917	151291513	45	45293										
CELSR3	1951	hgsc.bcm.edu	37	chr3	48686612	48686612	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tgaagaggtcgggctccagcCaaccctgggcctcatcacac	11	15	2	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr3:48686612C>A	ENST00000164024.4	-	17	6789	c.6509G>T	c.(6508-6510)tGg>tTg	p.W2170L	CELSR3_ENST00000544264.1_Missense_Mutation_p.W2175L	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	2170					axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		GGGCTCCAGCCAACCCTGGGC	0.602																																					p.W2170L		Atlas-SNP	.											.	CELSR3	237	.	0			c.G6509T						.						53	54	54					3																	48686612		2201	4299	6500	SO:0001583	missense	1951	exon17			TCCAGCCAACCCT	AF231023	CCDS2775.1	3p21.31	2014-08-08	2013-02-18		ENSG00000008300	ENSG00000008300		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3230	protein-coding gene	gene with protein product	"flamingo homolog 1 (Drosophila)"	604264	"cadherin EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog"	EGFL1		9693030	Standard	NM_001407		Approved	MEGF2, HFMI1, FMI1, CDHF11	uc003cuf.1	Q9NYQ7	OTTHUMG00000133544	ENST00000164024.4:c.6509G>T	chr3.hg19:g.48686612C>A	ENSP00000164024:p.Trp2170Leu	50.0	0.0		66.0	13.0	NM_001407	O75092	Missense_Mutation	SNP	ENST00000164024.4	hg19	CCDS2775.1	.	.	.	.	.	.	.	.	.	.	C	34	5.338415	0.95783	.	.	ENSG00000008300	ENST00000164024;ENST00000544264	T;T	0.59906	0.23;0.23	5.57	5.57	0.84162	GPCR, family 2, extracellular hormone receptor domain (3);	.	.	.	.	T	0.82250	0.4996	M	0.90870	3.155	0.80722	D	1	D;D	0.89917	0.988;1.0	D;D	0.91635	0.934;0.999	D	0.85894	0.1430	9	0.87932	D	0	.	19.5412	0.95275	0.0:1.0:0.0:0.0	.	2170;2240	Q9NYQ7;Q5Y190	CELR3_HUMAN;.	L	2170;2175	ENSP00000164024:W2170L;ENSP00000445694:W2175L	ENSP00000164024:W2170L	W	-	2	0	CELSR3	48661616	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.740000	0.55082	2.625000	0.88918	0.467000	0.42956	TGG	.	.		0.602	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407		A	48686612	C	A	48686612	3	1	322	1	0	0	0	0	1	0	0	0	3225	595	21	3	3505	3	CELSR3	3	48686612	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	1955695	48686612	149335818	46	45294										
TCTA	6988	hgsc.bcm.edu	37	chr3	49449889	49449889	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tcctggtctgggcaggccttGcaggctctgccggccacggt	15	14	2	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr3:49449889G>T	ENST00000273590.3	+	1	251	c.30G>T	c.(28-30)ttG>ttT	p.L10F	TCTA_ENST00000493381.1_3'UTR|RHOA_ENST00000422781.1_5'Flank|RHOA_ENST00000418115.1_5'Flank|RHOA_ENST00000454011.2_5'Flank|RHOA_ENST00000265538.3_5'UTR	NM_022171.2	NP_071503.1	P57738	TCTA_HUMAN	T-cell leukemia translocation altered	10						integral component of membrane (GO:0016021)				large_intestine(4)|lung(1)	5				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GGCAGGCCTTGCAGGCTCTGC	0.697																																					p.L10F		Atlas-SNP	.											.	TCTA	13	.	0			c.G30T						.						48	54	52					3																	49449889		2201	4297	6498	SO:0001583	missense	6988	exon1			GGCCTTGCAGGCT		CCDS2796.1	3p21	2012-02-27	2012-02-27		ENSG00000145022	ENSG00000145022			11692	protein-coding gene	gene with protein product		600690	"T-cell leukemia translocation altered gene"			7728759	Standard	NM_022171		Approved		uc003cwv.4	P57738	OTTHUMG00000156846	ENST00000273590.3:c.30G>T	chr3.hg19:g.49449889G>T	ENSP00000273590:p.Leu10Phe	48.0	0.0		46.0	12.0	NM_022171	B2R4I4|Q6I9U4|Q9BSB0	Missense_Mutation	SNP	ENST00000273590.3	hg19	CCDS2796.1	.	.	.	.	.	.	.	.	.	.	G	17.31	3.358352	0.61403	.	.	ENSG00000145022	ENST00000273590	.	.	.	5.18	5.18	0.71444	.	0.230121	0.37136	N	0.002221	T	0.42966	0.1226	N	0.14661	0.345	0.44555	D	0.997515	B	0.26809	0.16	B	0.30716	0.119	T	0.37150	-0.9718	9	0.41790	T	0.15	-4.3308	14.0669	0.64837	0.0:0.0:1.0:0.0	.	10	P57738	TCTA_HUMAN	F	10	.	ENSP00000273590:L10F	L	+	3	2	TCTA	49424893	1.000000	0.71417	0.997000	0.53966	0.457000	0.32468	2.407000	0.44565	2.695000	0.91970	0.555000	0.69702	TTG	.	.		0.697	TCTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346210.1	NM_022171		T	49449889	G	T	49449889	3	4	322	1	0	0	0	0	1	0	0	0	15731	1310	46	3	32	3	TCTA	3	49449889	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	763277	49449889	148572541	47	45295										
SLC38A3	10991	hgsc.bcm.edu	37	chr3	50256338	50256338	+	RNA	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tcacttgtatcaacctgctgGtcatctttgcccccaacatc	5	15	4	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr3:50256338G>T	ENST00000420502.1	+	0	1417									solute carrier family 38, member 3											breast(1)|cervix(1)|endometrium(1)|lung(3)	6				BRCA - Breast invasive adenocarcinoma(193;0.000275)|KIRC - Kidney renal clear cell carcinoma(197;0.00548)|Kidney(197;0.00615)		CAACCTGCTGGTCATCTTTGC	0.577																																					p.V422F		Atlas-SNP	.											.	SLC38A3	22	.	0			c.G1264T						.						81	82	81					3																	50256338		2065	4211	6276			10991	exon14			CTGCTGGTCATCT	U49082	CCDS74940.1	3p21.3	2013-05-22			ENSG00000188338	ENSG00000188338		"Solute carriers"	18044	protein-coding gene	gene with protein product		604437				10619430, 10823827	Standard	XM_006712954		Approved	G17, SN1	uc003cyn.4	Q99624	OTTHUMG00000156764		chr3.hg19:g.50256338G>T		36.0	0.0		69.0	13.0	NM_006841		Missense_Mutation	SNP	ENST00000420502.1	hg19																																																																																				.	.		0.577	SLC38A3-001	KNOWN	sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000345635.2	NM_006841		T	50256338	G	T	50256338	1	4	322	0	1	0	0	0	0	0	0	0	14620	1261	44	3		3	SLC38A3	3	50256338	RNA	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	806449	50256338	147766092	48	45296										
ROBO2	6092	hgsc.bcm.edu	37	chr3	77607255	77607255	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tttccgggtagagatccaagAgcaacaattcaagagcaagg	11	8	1	3			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr3:77607255A>T	ENST00000461745.1	+	9	2292	c.1392A>T	c.(1390-1392)agA>agT	p.R464S	ROBO2_ENST00000332191.8_Missense_Mutation_p.R464S|ROBO2_ENST00000487694.3_Missense_Mutation_p.R480S	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	464	Ig-like C2-type 5.				apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)			NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		GAGATCCAAGAGCAACAATTC	0.398																																					p.R464S		Atlas-SNP	.											.	ROBO2	527	.	0			c.A1392T						.						100	98	99					3																	77607255		1884	4122	6006	SO:0001583	missense	6092	exon9			TCCAAGAGCAACA	AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10250	protein-coding gene	gene with protein product		602431	"roundabout (axon guidance receptor, Drosophila) homolog 2"			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.1392A>T	chr3.hg19:g.77607255A>T	ENSP00000417164:p.Arg464Ser	89.0	0.0		170.0	11.0	NM_002942	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	hg19	CCDS43109.1	.	.	.	.	.	.	.	.	.	.	A	16.25	3.070312	0.55539	.	.	ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000343019;ENST00000461745;ENST00000332191;ENST00000398467	T;T;T	0.39229	1.09;1.09;1.09	5.68	4.5	0.54988	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.48286	D	0.000200	T	0.54319	0.1851	M	0.83223	2.63	0.43114	D	0.994827	P;P;P	0.50066	0.859;0.931;0.859	P;P;P	0.51777	0.679;0.646;0.679	T	0.71262	-0.4645	9	0.87932	D	0	.	8.1412	0.31084	0.7916:0.1357:0.0727:0.0	.	480;464;464	Q19AB5;F8W703;Q9HCK4	.;.;ROBO2_HUMAN	S	480;480;484;464;464;185	ENSP00000417335:R480S;ENSP00000417164:R464S;ENSP00000327536:R464S	ENSP00000327536:R464S	R	+	3	2	ROBO2	77689945	1.000000	0.71417	0.999000	0.59377	0.275000	0.26752	1.034000	0.30204	2.293000	0.77203	0.477000	0.44152	AGA	.	.		0.398	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		T	77607255	A	T	77607255	3	4	322	1	0	0	0	0	1	0	0	0	13529	301	11	4	1428	4	ROBO2	3	77607255	Missense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	27350917	77607255	120415175	49	45297										
FILIP1L	11259	hgsc.bcm.edu	37	chr3	99567271	99567272	+	Missense_Mutation	DNP	AG	AG	GT													0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ttatcctgcagtggtgctgaAgggctggcaggtctcacagg					rs36118713		TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A|G	A|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr3:99567271_99567272AG>GT	ENST00000354552.3	-	5	3718_3719	c.3248_3249CT>AC	c.(3247-3249)cCT>cAC	p.P1083H	FILIP1L_ENST00000471562.1_Missense_Mutation_p.P843H|CMSS1_ENST00000496116.1_Intron|FILIP1L_ENST00000383694.2_Missense_Mutation_p.P843H|FILIP1L_ENST00000331335.5_Missense_Mutation_p.P1083H|FILIP1L_ENST00000487087.1_Missense_Mutation_p.P659H|FILIP1L_ENST00000476723.1_Intron|CMSS1_ENST00000421999.2_Intron	NM_182909.2	NP_878913.2	Q4L180	FIL1L_HUMAN	filamin A interacting protein 1-like	1083						cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	35						GTGGTGCTGAAGGGCTGGCAGG	0.441																																					p.P1083P|p.P1083H		Atlas-SNP	.											.	FILIP1L	154	.	0			c.T3249C|c.C3248A						.																																			SO:0001583	missense	11259	exon5			TGCTGAAGGGCTG|GCTGAAGGGCTGG		CCDS43117.1, CCDS43118.1, CCDS43119.1, CCDS63700.1, CCDS74969.1	3q12.1	2011-10-21			ENSG00000168386	ENSG00000168386			24589	protein-coding gene	gene with protein product	"downregulated in ovarian cancer 1", "GPBP-interacting protein of 130 kDa"	612993				8314147, 15935955, 21832087	Standard	NM_001282793		Approved	DOC-1, GIP130	uc003dtm.3	Q4L180	OTTHUMG00000159055	ENST00000354552.3:c.3248_3249delinsGT	chr3.hg19:g.99567271_99567272delinsGT	ENSP00000346560:p.Pro1083His	149.0|150.0	0.0		228.0|227.0	38.0	NM_182909	B2CNV7|B2CNV8|Q13597|Q2YDY5|Q6KFX5|Q6KFX6|Q6KFX7|Q8IUM3|Q8N6Z0	Silent|Missense_Mutation	SNP	ENST00000354552.3	hg19	CCDS43117.1																																																																																			.	.		0.441	FILIP1L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353069.1	NM_014890		GT	99567272	AG	GT	99567271	3	3	322	1	0	0	0	0	1	0	0	0	5903	59	3	2	187	2	FILIP1L	3	99567271	Missense_Mutation	DNP	AG	TCGA-MI-A75G-01A-11D-A32G-10	21960016	99567271	98455159	50	45298										
TMPRSS7	344805	hgsc.bcm.edu	37	chr3	111780660	111780660	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tggctcctacatggatcatcAgacaatttttcgagtgccca	8	11	2	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr3:111780660A>T	ENST00000452346.2	+	11	1340	c.1337A>T	c.(1336-1338)cAg>cTg	p.Q446L	TMPRSS7_ENST00000419127.1_Missense_Mutation_p.Q320L			Q7RTY8	TMPS7_HUMAN	transmembrane protease, serine 7	446	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(2)|endometrium(6)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						ATGGATCATCAGACAATTTTT	0.483																																					p.Q320L		Atlas-SNP	.											.	TMPRSS7	126	.	0			c.A959T						.						127	129	128					3																	111780660		1929	4134	6063	SO:0001583	missense	344805	exon9			ATCATCAGACAAT	BN000125	CCDS43129.2	3q13.2	2010-04-13	2004-03-16		ENSG00000176040	ENSG00000176040		"Serine peptidases / Transmembrane"	30846	protein-coding gene	gene with protein product			"type II transmembrane serine protease 7"			12838346	Standard	NM_001042575		Approved		uc010hqb.2	Q7RTY8	OTTHUMG00000157148	ENST00000452346.2:c.1337A>T	chr3.hg19:g.111780660A>T	ENSP00000398236:p.Gln446Leu	71.0	0.0		122.0	35.0	NM_001042575	C9J8P7|E9PAS3|Q17RH4	Missense_Mutation	SNP	ENST00000452346.2	hg19		.	.	.	.	.	.	.	.	.	.	A	15.30	2.791297	0.50102	.	.	ENSG00000176040	ENST00000452346;ENST00000443106;ENST00000437906;ENST00000419127	T;T	0.32272	1.46;1.46	5.62	4.47	0.54385	CUB (1);	0.571239	0.18210	N	0.148215	T	0.20210	0.0486	L	0.36672	1.1	0.32112	N	0.589153	B;B	0.27625	0.183;0.066	B;B	0.27887	0.084;0.05	T	0.14392	-1.0474	10	0.19590	T	0.45	.	5.3101	0.15825	0.7307:0.1804:0.0889:0.0	.	446;320	Q7RTY8;Q7RTY8-2	TMPS7_HUMAN;.	L	446;434;420;320	ENSP00000398236:Q446L;ENSP00000411645:Q320L	ENSP00000411645:Q320L	Q	+	2	0	TMPRSS7	113263350	0.996000	0.38824	0.994000	0.49952	0.982000	0.71751	1.819000	0.39022	2.138000	0.66242	0.455000	0.32223	CAG	.	.		0.483	TMPRSS7-003	NOVEL	NAGNAG_splice_site|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000347592.2	XM_293599		T	111780660	A	T	111780660	3	4	322	1	0	0	0	0	1	0	0	0	16267	188	7	4	989	4	TMPRSS7	3	111780660	Missense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	12213389	111780660	86241770	51	45299										
GOLGB1	2804	hgsc.bcm.edu	37	chr3	121413069	121413069	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tttcaacttgagattgtctgCtaggacccttgctgcttcac	8	11	3	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr3:121413069C>A	ENST00000340645.5	-	13	6411	c.6286G>T	c.(6286-6288)Gca>Tca	p.A2096S	GOLGB1_ENST00000393667.3_Missense_Mutation_p.A2101S	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	2096					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		AGATTGTCTGCTAGGACCCTT	0.418																																					p.A2101S		Atlas-SNP	.											.	GOLGB1	319	.	0			c.G6301T						.						148	150	149					3																	121413069		2203	4300	6503	SO:0001583	missense	2804	exon13			TGTCTGCTAGGAC	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"macrogolgin", "golgi integral membrane protein 1"	602500	"golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1", "golgin B1, golgi integral membrane protein"			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.6286G>T	chr3.hg19:g.121413069C>A	ENSP00000341848:p.Ala2096Ser	42.0	0.0		67.0	9.0	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	hg19	CCDS3004.1	.	.	.	.	.	.	.	.	.	.	C	15.94	2.981711	0.53827	.	.	ENSG00000173230	ENST00000340645;ENST00000393667	T;T	0.17370	2.28;2.28	5.93	5.93	0.95920	.	0.000000	0.64402	D	0.000012	T	0.40767	0.1130	M	0.75264	2.295	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.996;0.999;0.999;0.99	T	0.13818	-1.0495	10	0.09843	T	0.71	.	17.8272	0.88669	0.0:1.0:0.0:0.0	.	2021;2101;2101;2096	F1T0J2;E7EP74;B2ZZ91;Q14789	.;.;.;GOGB1_HUMAN	S	2096;2101	ENSP00000341848:A2096S;ENSP00000377275:A2101S	ENSP00000341848:A2096S	A	-	1	0	GOLGB1	122895759	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.841000	0.55850	2.818000	0.97014	0.591000	0.81541	GCA	.	.		0.418	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		A	121413069	C	A	121413069	3	1	322	1	0	0	0	0	1	0	0	0	6573	797	28	3	3533	3	GOLGB1	3	121413069	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	9632409	121413069	76609361	52	45300										
ZXDC	79364	hgsc.bcm.edu	37	chr3	126194031	126194032	+	Frame_Shift_Ins	INS	-	-	T													0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cgtgcgactgcaggtgccgcINSttgagcttgtaggacgttgt							TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr3:126194031_126194032insT	ENST00000389709.3	-	1	730_731	c.677_678insA	c.(676-678)aagfs	p.K226fs	ZXDC_ENST00000336332.5_Frame_Shift_Ins_p.K226fs	NM_025112.4	NP_079388.3	Q2QGD7	ZXDC_HUMAN	ZXD family zinc finger C	226					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|LRR domain binding (GO:0030275)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|ovary(1)	17				GBM - Glioblastoma multiforme(114;0.155)		GCAGGTGCCGCTTGAGCTTGTA	0.634																																					p.K226fs		Atlas-Indel,Pindel	.											.	ZXDC	87	.	0			c.678_679insA						.																																			SO:0001589	frameshift_variant	79364	exon1			.	AK023923	CCDS43145.1, CCDS43146.1	3q21.3	2014-02-12			ENSG00000070476	ENSG00000070476		"Zinc fingers, C2H2-type"	28160	protein-coding gene	gene with protein product		615746				8619474, 9110174	Standard	XM_005247757		Approved	MGC11349, FLJ13861	uc003eiv.3	Q2QGD7	OTTHUMG00000162754	ENST00000389709.3:c.678dupA	chr3.hg19:g.126194033_126194033dupT	ENSP00000374359:p.Lys226fs	120.0	0.0		217.0	34.0	NM_025112	C5J0H9|Q6DKI8|Q7L3L1|Q8NAU2	Frame_Shift_Ins	INS	ENST00000389709.3	hg19	CCDS43145.1																																																																																			.	.		0.634	ZXDC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370327.2	NM_025112		T	126194032	-	T	126194031	7	5	322	1	0	1	1	0	0	0	0	0	18267	796	28	0	1944	0	ZXDC	3	126194031	Frame_Shift_Ins	INS	-	TCGA-MI-A75G-01A-11D-A32G-10	4780962	126194031	71828399	53	45301										
NMNAT3	349565	hgsc.bcm.edu	37	chr3	139297767	139297767	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tgctcactctcccaagggtcCacccggatccagtcggatgt	10	15	2	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr3:139297767C>T	ENST00000296202.7	-	4	621	c.240G>A	c.(238-240)gtG>gtA	p.V80V	NMNAT3_ENST00000413939.2_Intron|RP11-319G6.1_ENST00000515247.1_RNA|NMNAT3_ENST00000406824.1_5'UTR|NMNAT3_ENST00000507242.1_5'UTR|NMNAT3_ENST00000406164.1_Silent_p.V43V|RP11-319G6.1_ENST00000381790.3_RNA|NMNAT3_ENST00000512391.1_Silent_p.V80V|NMNAT3_ENST00000339837.5_Silent_p.V43V|NMNAT3_ENST00000511444.1_Silent_p.V43V			Q96T66	NMNA3_HUMAN	nicotinamide nucleotide adenylyltransferase 3	80					NAD biosynthetic process (GO:0009435)|NAD metabolic process (GO:0019674)|response to wounding (GO:0009611)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|nicotinamide-nucleotide adenylyltransferase activity (GO:0000309)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)			endometrium(2)|kidney(1)|large_intestine(2)|lung(4)	9						CCCAAGGGTCCACCCGGATCC	0.592																																					p.V43V		Atlas-SNP	.											.	NMNAT3	29	.	0			c.G129A						.						124	101	109					3																	139297767		2203	4300	6503	SO:0001819	synonymous_variant	349565	exon3			AGGGTCCACCCGG	AF345564	CCDS3111.1, CCDS56282.1	3q23	2013-09-20			ENSG00000163864	ENSG00000163864			20989	protein-coding gene	gene with protein product		608702				12574164	Standard	NM_178177		Approved	PNAT3	uc003etk.3	Q96T66	OTTHUMG00000159951	ENST00000296202.7:c.240G>A	chr3.hg19:g.139297767C>T		87.0	0.0		99.0	18.0	NM_178177	B3KVR6|D3DNF2|D3DNF3|Q8N4G1	Silent	SNP	ENST00000296202.7	hg19																																																																																				.	.		0.592	NMNAT3-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000358469.1	NM_178177		T	139297767	C	T	139297767	2	4	322	1	0	0	0	0	0	0	0	1	10509	581	21	3		3	NMNAT3	3	139297767	Silent	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	13103736	139297767	58724663	54	45302										
ATR	545	hgsc.bcm.edu	37	chr3	142217617	142217617	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ccatgttgtagattttccatCtgaaaaacaaatgaagagtc	7	7	1	4			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr3:142217617C>A	ENST00000350721.4	-	32	5502		c.e32-1		ATR_ENST00000383101.3_Splice_Site	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase						cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						GATTTTCCATCTGAAAAACAA	0.373								Other conserved DNA damage response genes																													.		Atlas-SNP	.											.	ATR	285	.	0			c.5381-1G>T						.						50	48	49					3																	142217617		2203	4299	6502	SO:0001630	splice_region_variant	545	exon33			TTCCATCTGAAAA	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.5381-1G>T	chr3.hg19:g.142217617C>A		110.0	0.0		142.0	42.0	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Splice_Site	SNP	ENST00000350721.4	hg19	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.078832	0.76528	.	.	ENSG00000175054	ENST00000350721;ENST00000383101	.	.	.	4.95	4.95	0.65309	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.1878	0.89797	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ATR	143700307	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.298000	0.78815	2.317000	0.78254	0.650000	0.86243	.	.	.		0.373	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184	Intron	A	142217617	C	A	142217617	5	1	322	1	0	0	0	0	0	0	1	0	1204	927	32	3	2618	3	ATR	3	142217617	Splice_Site	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	2919850	142217617	55804813	55	45303										
BOD1L	259282	hgsc.bcm.edu	37	chr4	13604910	13604910	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cactttgtatatgcattttcTtggtcaaggtgcttctatga	8	7	3	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr4:13604910T>C	ENST00000040738.5	-	10	3749	c.3614A>G	c.(3613-3615)aAg>aGg	p.K1205R		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	1205						nucleus (GO:0005634)	DNA binding (GO:0003677)										ATGCATTTTCTTGGTCAAGGT	0.413																																					p.K1205R		Atlas-SNP	.											.	.	.	.	0			c.A3614G						.						166	174	171					4																	13604910		2203	4300	6503	SO:0001583	missense	259282	exon10			ATTTTCTTGGTCA	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.3614A>G	chr4.hg19:g.13604910T>C	ENSP00000040738:p.Lys1205Arg	69.0	0.0		111.0	41.0	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	hg19	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	T	11.96	1.795466	0.31777	.	.	ENSG00000038219	ENST00000040738	T	0.14766	2.48	5.54	3.11	0.35812	.	0.268702	0.26887	N	0.021998	T	0.14227	0.0344	L	0.59436	1.845	0.26188	N	0.97963	B	0.25904	0.137	B	0.23852	0.049	T	0.15636	-1.0430	10	0.72032	D	0.01	-8.4431	8.4821	0.33049	0.0:0.1529:0.0:0.8471	.	1205	Q8NFC6	BOD1L_HUMAN	R	1205	ENSP00000040738:K1205R	ENSP00000040738:K1205R	K	-	2	0	BOD1L	13214008	1.000000	0.71417	0.991000	0.47740	0.078000	0.17371	1.821000	0.39041	0.403000	0.25479	-0.256000	0.11100	AAG	.	.		0.413	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		C	13604910	T	C	13604910	3	2	322	1	0	0	0	0	1	0	0	0	1483	1609	56	2	5609	2	BOD1L	4	13604910	Missense_Mutation	SNP	T	TCGA-MI-A75G-01A-11D-A32G-10		13604910	177549366	56	45304										
TMEM33	55161	hgsc.bcm.edu	37	chr4	41951403	41951403	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cgaagaaacccatattgtcgGtaagctgatgattattttag	9	6	0	3			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr4:41951403G>T	ENST00000504986.1	+	6	979		c.e6+1		TMEM33_ENST00000325094.5_Splice_Site|TMEM33_ENST00000513702.1_Splice_Site	NM_018126.2	NP_060596.2	P57088	TMM33_HUMAN	transmembrane protein 33							extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)				endometrium(1)|large_intestine(3)|lung(4)|ovary(1)	9						CATATTGTCGGTAAGCTGATG	0.318																																					.		Atlas-SNP	.											.	TMEM33	17	.	0			c.614+1G>T						.						111	113	113					4																	41951403		2203	4300	6503	SO:0001630	splice_region_variant	55161	exon6			TTGTCGGTAAGCT	BC000948	CCDS3464.1	4p14	2008-02-05			ENSG00000109133	ENSG00000109133			25541	protein-coding gene	gene with protein product						12477932	Standard	NM_018126		Approved	FLJ10525	uc003gwi.2	P57088	OTTHUMG00000099381	ENST00000504986.1:c.614+1G>T	chr4.hg19:g.41951403G>T		23.0	0.0		25.0	11.0	NM_018126	B3KSS8|Q9H953	Splice_Site	SNP	ENST00000504986.1	hg19	CCDS3464.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.445879	0.84101	.	.	ENSG00000109133	ENST00000504986;ENST00000508448;ENST00000513702;ENST00000325094;ENST00000513558	.	.	.	5.16	5.16	0.70880	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.6287	0.91350	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TMEM33	41646160	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.199000	0.95003	2.403000	0.81681	0.591000	0.81541	.	.	.		0.318	TMEM33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216834.2	NM_018126	Intron	T	41951403	G	T	41951403	5	4	322	1	0	0	0	0	0	0	1	0	16171	1275	44	3	637	3	TMEM33	4	41951403	Splice_Site	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	28346493	41951403	149202873	57	45305										
ATP8A1	10396	hgsc.bcm.edu	37	chr4	42571193	42571193	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cttaccattcatcaggagagCagccataatcctcaggttca	7	12	4	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr4:42571193C>T	ENST00000381668.5	-	15	1556	c.1325G>A	c.(1324-1326)tGc>tAc	p.C442Y	ATP8A1_ENST00000264449.10_Intron	NM_006095.2	NP_006086.1	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	442					cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	51					Phosphatidylserine(DB00144)	ATCAGGAGAGCAGCCATAATC	0.398																																					p.C442Y		Atlas-SNP	.											.	ATP8A1	206	.	0			c.G1325A						.						81	81	81					4																	42571193		2203	4300	6503	SO:0001583	missense	10396	exon15			GGAGAGCAGCCAT	AF067820	CCDS3466.1, CCDS47049.1	4p13	2010-04-20	2007-09-19		ENSG00000124406	ENSG00000124406		"ATPases / P-type"	13531	protein-coding gene	gene with protein product		609542	"ATPase, aminophospholipid transporter (APLT), Class I, type 8A, member 1"			10198212, 9548971	Standard	NM_006095		Approved	ATPIA	uc003gwr.2	Q9Y2Q0	OTTHUMG00000099403	ENST00000381668.5:c.1325G>A	chr4.hg19:g.42571193C>T	ENSP00000371084:p.Cys442Tyr	268.0	0.0		340.0	73.0	NM_006095	Q32M35|Q32M36|Q4W5J7|Q4W5P2	Missense_Mutation	SNP	ENST00000381668.5	hg19	CCDS3466.1	.	.	.	.	.	.	.	.	.	.	C	0.605	-0.827339	0.02734	.	.	ENSG00000124406	ENST00000381668	T	0.62498	0.02	5.5	4.53	0.55603	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.146330	0.47093	D	0.000259	T	0.19485	0.0468	N	0.00510	-1.415	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41288	-0.9517	10	0.07990	T	0.79	.	0.9765	0.01426	0.2304:0.3991:0.1881:0.1824	.	442	Q9Y2Q0	AT8A1_HUMAN	Y	442	ENSP00000371084:C442Y	ENSP00000371084:C442Y	C	-	2	0	ATP8A1	42265950	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.802000	0.27069	2.593000	0.87608	0.591000	0.81541	TGC	.	.		0.398	ATP8A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216861.2	NM_006095		T	42571193	C	T	42571193	3	4	322	1	0	0	0	0	1	0	0	0	1192	710	25	3	2261	3	ATP8A1	4	42571193	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	619790	42571193	148583083	58	45306										
ALB	213	hgsc.bcm.edu	37	chr4	74285252	74285252	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ttgagctcgtgaaacacaagCccaaggcaacaaaagagcaa	9	10	0	3			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr4:74285252C>T	ENST00000503124.1	+	11	1438	c.1231C>T	c.(1231-1233)Ccc>Tcc	p.P411S	ALB_ENST00000509063.1_Missense_Mutation_p.P561S|ALB_ENST00000401494.3_Missense_Mutation_p.P446S|ALB_ENST00000505649.1_3'UTR|ALB_ENST00000415165.2_Missense_Mutation_p.P369S|ALB_ENST00000295897.4_Missense_Mutation_p.P561S			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GAAACACAAGCCCAAGGCAAC	0.403																																					p.P561S		Atlas-SNP	.											.	ALB	132	.	0			c.C1681T						.						87	83	84					4																	74285252		2203	4300	6503	SO:0001583	missense	213	exon13			CACAAGCCCAAGG	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.1231C>T	chr4.hg19:g.74285252C>T	ENSP00000421027:p.Pro411Ser	30.0	0.0		30.0	15.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000503124.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.2|25.2	4.613772|4.613772	0.87359|0.87359	.|.	.|.	ENSG00000163631|ENSG00000163631	ENST00000511370|ENST00000295897;ENST00000415165;ENST00000329326;ENST00000503124;ENST00000509063;ENST00000401494;ENST00000430202	.|T;T;T;T;T	.|0.70749	.|-0.51;-0.51;-0.51;-0.51;-0.51	6.17|6.17	6.17|6.17	0.99709|0.99709	.|Serum albumin-like (1);Serum albumin, N-terminal (3);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.88299|0.88299	0.6399|0.6399	M|M	0.91406|0.91406	3.205|3.205	0.58432|0.58432	D|D	0.999999|0.999999	.|D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D	.|0.97110	.|0.999;1.0;1.0;0.999;0.999	D|D	0.89512|0.89512	0.3772|0.3772	5|10	.|0.87932	.|D	.|0	-24.0555|-24.0555	19.4432|19.4432	0.94831|0.94831	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|446;369;411;561;561	.|B7WNR0;C9JKR2;D6RHD5;A6NBZ8;P02768	.|.;.;.;.;ALBU_HUMAN	V|S	405|561;369;348;411;561;446;570	.|ENSP00000295897:P561S;ENSP00000401820:P369S;ENSP00000421027:P411S;ENSP00000422784:P561S;ENSP00000384695:P446S	.|ENSP00000295897:P561S	A|P	+|+	2|1	0|0	ALB|ALB	74504116|74504116	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.848000|0.848000	0.48234|0.48234	2.294000|2.294000	0.43567|0.43567	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	GCC|CCC	.	.		0.403	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		T	74285252	C	T	74285252	3	4	322	1	0	0	0	0	1	0	0	0	486	739	26	3	1731	3	ALB	4	74285252	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	31714059	74285252	116869024	59	45307										
DSPP	1834	hgsc.bcm.edu	37	chr4	88535128	88535128	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ccaggaaataaagttggacaCagcaatacaggtagtgacag	11	7	0	1	rs372553789		TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr4:88535128C>A	ENST00000282478.7	+	4	1347	c.1314C>A	c.(1312-1314)caC>caA	p.H438Q	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Missense_Mutation_p.H438Q			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	438					biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			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)		AAGTTGGACACAGCAATACAG	0.408																																					p.H438Q		Atlas-SNP	.											.	DSPP	174	.	0			c.C1314A						.						156	144	148					4																	88535128		1965	4165	6130	SO:0001583	missense	1834	exon5			TGGACACAGCAAT	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.1314C>A	chr4.hg19:g.88535128C>A	ENSP00000282478:p.His438Gln	145.0	0.0		191.0	28.0	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	hg19	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	C	6.618	0.482478	0.12581	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.91740	-2.9;-2.9	4.2	2.45	0.29901	.	0.481828	0.15504	N	0.258883	D	0.91543	0.7329	L	0.59436	1.845	0.25805	N	0.984467	D	0.57899	0.981	P	0.54140	0.743	T	0.83027	-0.0164	10	0.38643	T	0.18	-0.4613	6.3582	0.21412	0.0:0.7813:0.0:0.2187	.	438	Q9NZW4	DSPP_HUMAN	Q	438	ENSP00000382213:H438Q;ENSP00000282478:H438Q	ENSP00000282478:H438Q	H	+	3	2	DSPP	88754152	0.055000	0.20627	0.033000	0.17914	0.043000	0.13939	0.763000	0.26517	0.408000	0.25621	0.446000	0.29264	CAC	.	.		0.408	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		A	88535128	C	A	88535128	3	1	322	1	0	0	0	0	1	0	0	0	4784	477	17	3	1328	3	DSPP	4	88535128	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	14249876	88535128	102619148	60	45308										
DNAJB14	79982	hgsc.bcm.edu	37	chr4	100822217	100822218	+	Frame_Shift_Ins	INS	-	-	T													0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	taaagactggtaagccgctcINStaattctttacagttgtcca							TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr4:100822217_100822218insT	ENST00000442697.2	-	8	1261_1262	c.1107_1108insA	c.(1105-1110)ttagagfs	p.E370fs		NM_001031723.2|NM_001278310.1	NP_001026893.1|NP_001265239.1	Q8TBM8	DJB14_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 14	370						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				kidney(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	5				OV - Ovarian serous cystadenocarcinoma(123;4.59e-09)		GTAAGCCGCTCTAATTCTTTAC	0.366																																					p.E370fs		Atlas-Indel,Pindel	.											.	DNAJB14	25	.	0			c.1108_1109insA						.																																			SO:0001589	frameshift_variant	79982	exon8			.	BC022248	CCDS34035.1, CCDS75171.1	4q23	2011-09-02			ENSG00000164031	ENSG00000164031		"Heat shock proteins / DNAJ (HSP40)"	25881	protein-coding gene	gene with protein product							Standard	NM_001031723		Approved	FLJ14281	uc003hvl.4	Q8TBM8	OTTHUMG00000131049	ENST00000442697.2:c.1108dupA	chr4.hg19:g.100822218_100822218dupT	ENSP00000404381:p.Glu370fs	192.0	0.0		239.0	99.0	NM_001031723	Q6UXN1|Q7Z3P0|Q86TA7|Q86TM0|Q9GZU9	Frame_Shift_Ins	INS	ENST00000442697.2	hg19	CCDS34035.1																																																																																			.	.		0.366	DNAJB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253696.2	NM_001031723.2		T	100822218	-	T	100822217	7	5	322	1	0	1	1	0	0	0	0	0	4621	922	32	0	35	0	DNAJB14	4	100822217	Frame_Shift_Ins	INS	-	TCGA-MI-A75G-01A-11D-A32G-10	12287089	100822217	90332059	61	45309										
EGF	1950	hgsc.bcm.edu	37	chr4	110915962	110915962	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	aatagtgactctgaatgtccCctgtcccacgatgggtactg	10	11	1	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr4:110915962C>T	ENST00000265171.5	+	20	3376	c.2931C>T	c.(2929-2931)ccC>ccT	p.P977P	EGF_ENST00000509793.1_Silent_p.P935P|EGF_ENST00000503392.1_Silent_p.P936P|RNU6-35P_ENST00000384530.1_RNA	NM_001178130.1|NM_001963.4	NP_001171601.1|NP_001954.2	P01133	EGF_HUMAN	epidermal growth factor	977	EGF-like 9. {ECO:0000255|PROSITE- ProRule:PRU00076}.				activation of MAPKK activity (GO:0000186)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|branching morphogenesis of an epithelial tube (GO:0048754)|DNA replication (GO:0006260)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mammary gland alveolus development (GO:0060749)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of secretion (GO:0051048)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)|positive regulation of DNA binding (GO:0043388)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of calcium ion import (GO:0090279)|regulation of protein localization to cell surface (GO:2000008)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(1)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sucralfate(DB00364)	CTGAATGTCCCCTGTCCCACG	0.453																																					p.P977P		Atlas-SNP	.											.	EGF	113	.	0			c.C2931T						.						174	145	155					4																	110915962		2203	4300	6503	SO:0001819	synonymous_variant	1950	exon20			ATGTCCCCTGTCC	X04571	CCDS3689.1, CCDS54794.1, CCDS54795.1	4q25	2012-10-02	2010-05-11		ENSG00000138798	ENSG00000138798			3229	protein-coding gene	gene with protein product		131530	"epidermal growth factor (beta-urogastrone)"				Standard	NM_001963		Approved		uc003hzy.4	P01133	OTTHUMG00000132044	ENST00000265171.5:c.2931C>T	chr4.hg19:g.110915962C>T		42.0	0.0		62.0	19.0	NM_001963	B4DRK7|E7EVD2|E9PBF0|Q52LZ6	Silent	SNP	ENST00000265171.5	hg19	CCDS3689.1																																																																																			.	.		0.453	EGF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255065.1			T	110915962	C	T	110915962	2	4	322	1	0	0	0	0	0	0	0	1	4964	610	22	3		3	EGF	4	110915962	Silent	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	10093745	110915962	80238314	62	45310										
EDNRA	1909	hgsc.bcm.edu	37	chr4	148441067	148441067	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	atttctttgcaagctgttccCctttttgcagaagtcctcgg	8	11	1	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr4:148441067C>A	ENST00000324300.5	+	3	1000	c.485C>A	c.(484-486)cCc>cAc	p.P162H	EDNRA_ENST00000506066.1_Intron|EDNRA_ENST00000358556.4_Intron|EDNRA_ENST00000339690.5_Intron|EDNRA_ENST00000511804.1_5'UTR	NM_001957.3	NP_001948.1	P25101	EDNRA_HUMAN	endothelin receptor type A	162					activation of adenylate cyclase activity (GO:0007190)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|artery smooth muscle contraction (GO:0014824)|cell proliferation (GO:0008283)|cellular response to mechanical stimulus (GO:0071260)|endothelin receptor signaling pathway (GO:0086100)|enteric nervous system development (GO:0048484)|fibroblast proliferation (GO:0048144)|G-protein coupled receptor signaling pathway (GO:0007186)|glomerular filtration (GO:0003094)|glucose transport (GO:0015758)|head development (GO:0060322)|heart development (GO:0007507)|histamine secretion (GO:0001821)|in utero embryonic development (GO:0001701)|maternal process involved in parturition (GO:0060137)|metabolic process (GO:0008152)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cAMP biosynthetic process (GO:0030818)|neural crest cell development (GO:0014032)|patterning of blood vessels (GO:0001569)|penile erection (GO:0043084)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of inflammatory response (GO:0050729)|positive regulation of kidney development (GO:0090184)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of odontogenesis (GO:0042482)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of blood pressure (GO:0008217)|regulation of epithelial cell proliferation (GO:0050678)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to morphine (GO:0043278)|Rho protein signal transduction (GO:0007266)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|smooth muscle cell proliferation (GO:0048659)|smooth muscle contraction (GO:0006939)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)	endothelin receptor activity (GO:0004962)|phosphatidylinositol phospholipase C activity (GO:0004435)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(3)|ovary(1)	17	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.154)	Acetylsalicylic acid(DB00945)|Bosentan(DB00559)|MACITENTAN(DB08932)|Sitaxentan(DB06268)	AAGCTGTTCCCCTTTTTGCAG	0.502																																					p.P162H		Atlas-SNP	.											.	EDNRA	48	.	0			c.C485A						.						217	202	207					4																	148441067		2203	4300	6503	SO:0001583	missense	1909	exon3			TGTTCCCCTTTTT	D90348	CCDS3769.1, CCDS54810.1, CCDS58927.1	4q31.22	2013-09-20			ENSG00000151617	ENSG00000151617		"GPCR / Class A : Endothelin receptors"	3179	protein-coding gene	gene with protein product		131243				1659806	Standard	NM_001957		Approved		uc003iky.3	P25101	OTTHUMG00000161354	ENST00000324300.5:c.485C>A	chr4.hg19:g.148441067C>A	ENSP00000315011:p.Pro162His	75.0	0.0		112.0	53.0	NM_001957	B2R723|B4E2V6|B7Z9G6|D3DP03|E7ER36|O43441|Q16432|Q16433|Q8TBH2	Missense_Mutation	SNP	ENST00000324300.5	hg19	CCDS3769.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.821411	0.90873	.	.	ENSG00000151617	ENST00000394047;ENST00000324300	T	0.37058	1.22	5.48	5.48	0.80851	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.66616	0.2807	M	0.86268	2.805	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.71945	-0.4439	10	0.87932	D	0	-17.8311	18.9432	0.92612	0.0:1.0:0.0:0.0	.	162	P25101	EDNRA_HUMAN	H	162	ENSP00000315011:P162H	ENSP00000315011:P162H	P	+	2	0	EDNRA	148660517	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.060000	0.76692	2.572000	0.86782	0.591000	0.81541	CCC	.	.		0.502	EDNRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364635.1			A	148441067	C	A	148441067	3	1	322	1	0	0	0	0	1	0	0	0	4921	623	22	3	491	3	EDNRA	4	148441067	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	37525105	148441067	42713209	63	45311										
ADCY2	108	hgsc.bcm.edu	37	chr5	7707833	7707833	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tttcagacgtgttcacatttCttctgtcaccctggagcact	7	12	5	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr5:7707833C>A	ENST00000338316.4	+	9	1372	c.1283C>A	c.(1282-1284)tCt>tAt	p.S428Y	ADCY2_ENST00000537121.1_Missense_Mutation_p.S248Y|RP11-711G10.1_ENST00000514105.2_RNA	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	428					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						GTTCACATTTCTTCTGTCACC	0.388																																					p.S428Y		Atlas-SNP	.											.	ADCY2	337	.	0			c.C1283A						.						120	119	119					5																	7707833		2203	4300	6503	SO:0001583	missense	108	exon9			ACATTTCTTCTGT	AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"Adenylate cyclases"	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.1283C>A	chr5.hg19:g.7707833C>A	ENSP00000342952:p.Ser428Tyr	56.0	0.0		94.0	28.0	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Missense_Mutation	SNP	ENST00000338316.4	hg19	CCDS3872.2	.	.	.	.	.	.	.	.	.	.	C	32	5.127244	0.94473	.	.	ENSG00000078295	ENST00000338316;ENST00000541993;ENST00000537121	D;D	0.89552	-2.53;-2.53	5.49	5.49	0.81192	Adenylyl cyclase class-3/4/guanylyl cyclase (4);	0.177244	0.48767	D	0.000179	D	0.96349	0.8809	H	0.96301	3.8	0.48395	D	0.999645	D;P	0.61080	0.989;0.537	D;P	0.65140	0.932;0.797	D	0.97414	1.0004	10	0.87932	D	0	.	19.3671	0.94468	0.0:1.0:0.0:0.0	.	248;428	B7Z2C1;Q08462	.;ADCY2_HUMAN	Y	428;279;248	ENSP00000342952:S428Y;ENSP00000444803:S248Y	ENSP00000342952:S428Y	S	+	2	0	ADCY2	7760833	1.000000	0.71417	0.940000	0.37924	0.989000	0.77384	5.779000	0.68948	2.555000	0.86185	0.650000	0.86243	TCT	.	.		0.388	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546		A	7707833	C	A	7707833	3	1	322	1	0	0	0	0	1	0	0	0	294	913	32	3	1317	3	ADCY2	5	7707833	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10		7707833	173207427	64	45312										
C5orf22	55322	hgsc.bcm.edu	37	chr5	31538578	31538578	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ctgcctctactaactgtgacTcttcttcagaaggactggaa	8	11	4	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr5:31538578T>G	ENST00000325366.9	+	4	716	c.589T>G	c.(589-591)Tct>Gct	p.S197A	C5orf22_ENST00000355907.3_5'UTR	NM_018356.2	NP_060826.2	Q49AR2	CE022_HUMAN	chromosome 5 open reading frame 22	197										kidney(3)|large_intestine(2)|lung(10)|ovary(2)|skin(1)	18						TAACTGTGACTCTTCTTCAGA	0.433																																					p.S197A		Atlas-SNP	.											.	C5orf22	48	.	0			c.T589G						.						81	77	79					5																	31538578		2203	4300	6503	SO:0001583	missense	55322	exon4			TGTGACTCTTCTT	AK002055	CCDS3895.1	5p13.3	2012-02-22			ENSG00000082213	ENSG00000082213			25639	protein-coding gene	gene with protein product							Standard	NM_018356		Approved	FLJ11193	uc003jhj.4	Q49AR2	OTTHUMG00000131067	ENST00000325366.9:c.589T>G	chr5.hg19:g.31538578T>G	ENSP00000326879:p.Ser197Ala	133.0	0.0		176.0	56.0	NM_018356	Q8ND28|Q8WU61|Q9NUR1	Missense_Mutation	SNP	ENST00000325366.9	hg19	CCDS3895.1	.	.	.	.	.	.	.	.	.	.	T	10.79	1.450543	0.26074	.	.	ENSG00000082213	ENST00000325366	T	0.30714	1.52	5.2	4.05	0.47172	.	0.734400	0.13716	N	0.367778	T	0.33673	0.0871	M	0.67953	2.075	0.58432	D	0.999998	B	0.31125	0.309	B	0.31946	0.138	T	0.08351	-1.0726	10	0.48119	T	0.1	-3.7463	10.7368	0.46130	0.0:0.0737:0.0:0.9263	.	197	Q49AR2	CE022_HUMAN	A	197	ENSP00000326879:S197A	ENSP00000326879:S197A	S	+	1	0	C5orf22	31574335	0.000000	0.05858	0.003000	0.11579	0.337000	0.28794	0.327000	0.19663	1.004000	0.39156	0.533000	0.62120	TCT	.	.		0.433	C5orf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253726.2	NM_018356		G	31538578	T	G	31538578	3	3	322	1	0	0	0	0	1	0	0	0	2287	1551	54	5	603	5	C5orf22	5	31538578	Missense_Mutation	SNP	T	TCGA-MI-A75G-01A-11D-A32G-10	23830745	31538578	149376682	65	45313										
C5orf36	285600	hgsc.bcm.edu	37	chr5	93775731	93775731	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gtaaaagtccatcatgatgcAgtagggtttccagaagcaag	11	7	1	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr5:93775731A>T	ENST00000513200.3	-	13	2525	c.2453T>A	c.(2452-2454)cTg>cAg	p.L818Q	KIAA0825_ENST00000427991.2_Missense_Mutation_p.L818Q|KIAA0825_ENST00000312498.7_Missense_Mutation_p.L818Q	NM_001145678.1	NP_001139150.1	Q8IV33	K0825_HUMAN	KIAA0825	818										breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|pancreas(1)|prostate(1)|skin(1)	13						ATCATGATGCAGTAGGGTTTC	0.453																																					p.L818Q		Atlas-SNP	.											.	KIAA0825	172	.	0			c.T2453A						.						156	135	141					5																	93775731		692	1591	2283	SO:0001583	missense	285600	exon14			TGATGCAGTAGGG	BX648338	CCDS4070.1	5q15	2011-02-23	2011-02-23	2011-02-23	ENSG00000185261	ENSG00000185261			28532	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 36"	C5orf36		12477932	Standard	NM_173665		Approved	DKFZp686F0372, MGC34713	uc011cuk.2	Q8IV33	OTTHUMG00000131331	ENST00000513200.3:c.2453T>A	chr5.hg19:g.93775731A>T	ENSP00000424618:p.Leu818Gln	231.0	0.0		326.0	104.0	NM_001145678	O94914|Q6ZNN2	Missense_Mutation	SNP	ENST00000513200.3	hg19		.	.	.	.	.	.	.	.	.	.	A	18.22	3.575530	0.65878	.	.	ENSG00000185261	ENST00000513200;ENST00000427991;ENST00000312498	T;T;T	0.56444	0.46;0.46;0.47	5.55	5.55	0.83447	.	0.000000	0.50627	D	0.000101	T	0.71178	0.3309	M	0.68952	2.095	0.48341	D	0.999634	D	0.89917	1.0	D	0.91635	0.999	T	0.74659	-0.3591	10	0.87932	D	0	.	15.7041	0.77563	1.0:0.0:0.0:0.0	.	818	Q8IV33	K0825_HUMAN	Q	818	ENSP00000424618:L818Q;ENSP00000400288:L818Q;ENSP00000312205:L818Q	ENSP00000312205:L818Q	L	-	2	0	KIAA0825	93801487	1.000000	0.71417	0.453000	0.27007	0.814000	0.46013	7.077000	0.76814	2.105000	0.64084	0.383000	0.25322	CTG	.	.		0.453	KIAA0825-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000254102.5	NM_173665		T	93775731	A	T	93775731	3	4	322	1	0	0	0	0	1	0	0	0	2297	188	7	4	1406	4	C5orf36	5	93775731	Missense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	62237153	93775731	87139529	66	45314										
FBN2	2201	hgsc.bcm.edu	37	chr5	127685696	127685696	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	agccctcttgggcaagctgtAtctgtaacaacaacaggaca	9	11	2	0	rs183336575	byFrequency	TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr5:127685696A>G	ENST00000508053.1	-	28	3788	c.2814T>C	c.(2812-2814)gaT>gaC	p.D938D	FBN2_ENST00000262464.4_Splice_Site_p.D938D|FBN2_ENST00000508989.1_Splice_Site_p.D905D			P35556	FBN2_HUMAN	fibrillin 2	938	TB 4.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		GGCAAGCTGTATCTGTAACAA	0.353																																					p.D938D		Atlas-SNP	.											FBN2_ENST00000508053,NS,carcinoma,0,2	FBN2	858	.	0			c.T2814C						.						73	66	68					5																	127685696		2203	4300	6503	SO:0001630	splice_region_variant	2201	exon22			AGCTGTATCTGTA	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.2813-1T>C	chr5.hg19:g.127685696A>G		54.0	0.0		71.0	7.0	NM_001999	B4DU01|Q59ES6	Silent	SNP	ENST00000508053.1	hg19	CCDS34222.1																																																																																			.	A|1.000;C|0.000		0.353	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999	Silent	G	127685696	A	G	127685696	5	3	322	1	0	0	0	0	0	0	1	0	5711	463	16	2	6100	2	FBN2	5	127685696	Splice_Site	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	33909965	127685696	53229564	67	45315										
FBN2	2201	hgsc.bcm.edu	37	chr5	127704957	127704957	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cagcattcggacttggtcacTgcaccggggaaaggacgcac	13	12	1	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr5:127704957T>C	ENST00000508053.1	-	22	3140	c.2166A>G	c.(2164-2166)gcA>gcG	p.A722A	FBN2_ENST00000511489.1_5'UTR|Y_RNA_ENST00000384560.1_RNA|FBN2_ENST00000262464.4_Silent_p.A722A|FBN2_ENST00000508989.1_Silent_p.A689A			P35556	FBN2_HUMAN	fibrillin 2	722	TB 3.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		ACTTGGTCACTGCACCGGGGA	0.483																																					p.A722A		Atlas-SNP	.											.	FBN2	858	.	0			c.A2166G						.						179	143	155					5																	127704957		2203	4300	6503	SO:0001819	synonymous_variant	2201	exon16			GGTCACTGCACCG	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.2166A>G	chr5.hg19:g.127704957T>C		60.0	0.0		92.0	16.0	NM_001999	B4DU01|Q59ES6	Silent	SNP	ENST00000508053.1	hg19	CCDS34222.1																																																																																			.	.		0.483	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		C	127704957	T	C	127704957	2	2	322	1	0	0	0	0	0	0	0	1	5711	1567	55	2		2	FBN2	5	127704957	Silent	SNP	T	TCGA-MI-A75G-01A-11D-A32G-10	19261	127704957	53210303	68	45316										
CHSY3	337876	hgsc.bcm.edu	37	chr5	129520910	129520910	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	aatgaccctgatcccaatgaAgggagagttttccagaggtc	11	9	0	5			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr5:129520910A>T	ENST00000305031.4	+	3	2433	c.2075A>T	c.(2074-2076)aAg>aTg	p.K692M		NM_175856.4	NP_787052.3	Q70JA7	CHSS3_HUMAN	chondroitin sulfate synthase 3	692					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.136)		ATCCCAATGAAGGGAGAGTTT	0.443																																					p.K692M		Atlas-SNP	.											.	CHSY3	92	.	0			c.A2075T						.						80	74	76					5																	129520910		2203	4300	6503	SO:0001583	missense	337876	exon3			CAATGAAGGGAGA	AB086062	CCDS34223.1	5q13	2013-02-19			ENSG00000198108	ENSG00000198108	2.4.1.175, 2.4.1.226	"Beta 3-glycosyltransferases", "Beta 4-glycosyltransferases"	24293	protein-coding gene	gene with protein product		609963				12907687	Standard	XM_005271982		Approved	CSS3, CHSY-2	uc003kvd.3	Q70JA7	OTTHUMG00000163043	ENST00000305031.4:c.2075A>T	chr5.hg19:g.129520910A>T	ENSP00000302629:p.Lys692Met	93.0	0.0		135.0	12.0	NM_175856	B2RP97|Q76L22|Q86Y52	Missense_Mutation	SNP	ENST00000305031.4	hg19	CCDS34223.1	.	.	.	.	.	.	.	.	.	.	A	10.07	1.249908	0.22880	.	.	ENSG00000198108	ENST00000305031	T	0.36699	1.24	4.33	3.15	0.36227	.	0.341197	0.24713	N	0.036207	T	0.22205	0.0535	N	0.17082	0.46	0.31394	N	0.677447	B	0.25667	0.131	B	0.29440	0.102	T	0.19647	-1.0299	9	.	.	.	-2.2963	11.005	0.47629	0.4853:0.5147:0.0:0.0	.	692	Q70JA7	CHSS3_HUMAN	M	692	ENSP00000302629:K692M	.	K	+	2	0	CHSY3	129548809	0.993000	0.37304	0.985000	0.45067	0.901000	0.52897	3.551000	0.53698	0.966000	0.38159	0.528000	0.53228	AAG	.	.		0.443	CHSY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371453.1	NM_175856		T	129520910	A	T	129520910	3	4	322	1	0	0	0	0	1	0	0	0	3415	72	3	4	2085	4	CHSY3	5	129520910	Missense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	1815953	129520910	51394350	69	45317										
SLC4A9	83697	hgsc.bcm.edu	37	chr5	139740530	139740530	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gccttgtactgctggactgcCcagctcagagcctcctggag	12	14	1	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr5:139740530C>T	ENST00000230993.6	+	2	471	c.436C>T	c.(436-438)Cca>Tca	p.P146S	SLC4A9_ENST00000507527.1_Missense_Mutation_p.P146S|SLC4A9_ENST00000432095.2_Missense_Mutation_p.P122S|SLC4A9_ENST00000506757.2_Missense_Mutation_p.P122S|SLC4A9_ENST00000506545.1_Missense_Mutation_p.P122S	NM_001258428.1	NP_001245357.1	Q96Q91	B3A4_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 9	146					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)			endometrium(4)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCTGGACTGCCCAGCTCAGAG	0.652																																					p.P146S		Atlas-SNP	.											.	SLC4A9	125	.	0			c.C436T						.						11	13	12					5																	139740530		1926	4124	6050	SO:0001583	missense	83697	exon2			GACTGCCCAGCTC	AF313465	CCDS47278.1, CCDS58973.1, CCDS58974.1, CCDS58975.1	5q31.3	2013-05-22			ENSG00000113073	ENSG00000113073		"Solute carriers"	11035	protein-coding gene	gene with protein product		610207				11305939	Standard	NM_031467		Approved	AE4	uc003lfk.2	Q96Q91	OTTHUMG00000163352	ENST00000230993.6:c.436C>T	chr5.hg19:g.139740530C>T	ENSP00000230993:p.Pro146Ser	57.0	0.0		74.0	13.0	NM_001258428	B7ZL63|D3DQD4|D3DQD5|D3DQD6|E9PDK1|Q96RM5|Q9BXF2|Q9BXN3	Missense_Mutation	SNP	ENST00000230993.6	hg19	CCDS58973.1	.	.	.	.	.	.	.	.	.	.	C	14.04	2.416019	0.42817	.	.	ENSG00000113073	ENST00000230993;ENST00000506757;ENST00000432095;ENST00000506545;ENST00000507527	T;T;T;T;T	0.79141	-1.24;-1.24;-1.24;-1.24;-1.24	5.1	4.21	0.49690	Bicarbonate transporter, cytoplasmic (2);Phosphotransferase/anion transporter (1);	0.628911	0.15868	N	0.240649	T	0.70745	0.3259	L	0.43152	1.355	0.26578	N	0.973428	B;B;B;B	0.13145	0.005;0.007;0.001;0.004	B;B;B;B	0.20767	0.011;0.031;0.004;0.013	T	0.63161	-0.6699	10	0.48119	T	0.1	.	11.1849	0.48650	0.0:0.8146:0.1854:0.0	.	122;146;122;122	E9PDK1;Q96Q91;Q96Q91-2;Q96Q91-3	.;B3A4_HUMAN;.;.	S	146;122;122;122;146	ENSP00000230993:P146S;ENSP00000424424:P122S;ENSP00000410056:P122S;ENSP00000422855:P122S;ENSP00000427661:P146S	ENSP00000230993:P146S	P	+	1	0	SLC4A9	139720714	0.966000	0.33281	1.000000	0.80357	0.994000	0.84299	0.917000	0.28665	1.314000	0.45095	0.561000	0.74099	CCA	.	.		0.652	SLC4A9-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000372823.1	NM_031467		T	139740530	C	T	139740530	3	4	322	1	0	0	0	0	1	0	0	0	14675	623	22	3	370	3	SLC4A9	5	139740530	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	10219620	139740530	41174730	70	45318										
PCDH1	5097	hgsc.bcm.edu	37	chr5	141248170	141248170	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cctatggggctattctcagaTagttcggcctcataggaggg	13	9	2	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr5:141248170T>C	ENST00000394536.3	-	2	1006	c.867A>G	c.(865-867)ctA>ctG	p.L289L	PCDH1_ENST00000536585.1_Silent_p.L267L|PCDH1_ENST00000503492.1_Silent_p.L289L|PCDH1_ENST00000287008.3_Silent_p.L289L|PCDH1_ENST00000511044.1_5'Flank|PCDH1_ENST00000456271.1_Silent_p.L277L	NM_001278613.1|NM_001278615.1	NP_001265542.1|NP_001265544.1	Q08174	PCDH1_HUMAN	protocadherin 1	289	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell-cell signaling (GO:0007267)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(4)|lung(20)|ovary(5)|skin(3)|upper_aerodigestive_tract(1)	51		Lung NSC(810;0.027)|all_lung(500;0.0321)|all_hematologic(541;0.0433)|Prostate(461;0.0453)|Breast(839;0.128)|Lung SC(612;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;1.06e-05)		TATTCTCAGATAGTTCGGCCT	0.612																																					p.L289L	Ovarian(132;1609 1739 4190 14731 45037)	Atlas-SNP	.											.	PCDH1	119	.	0			c.A867G						.						37	39	39					5																	141248170		2203	4300	6503	SO:0001819	synonymous_variant	5097	exon2			CTCAGATAGTTCG	AK075233	CCDS4267.1, CCDS43375.1	5q31.3	2010-01-26	2007-02-12		ENSG00000156453	ENSG00000156453		"Cadherins / Protocadherins : Non-clustered"	8655	protein-coding gene	gene with protein product		603626	"protocadherin 1 (cadherin-like 1)"			8508762	Standard	NM_032420		Approved	pc42	uc003llp.3	Q08174	OTTHUMG00000129661	ENST00000394536.3:c.867A>G	chr5.hg19:g.141248170T>C		52.0	0.0		87.0	11.0	NM_032420	Q8IUP2	Silent	SNP	ENST00000394536.3	hg19	CCDS43375.1																																																																																			.	.		0.612	PCDH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251862.1	NM_032420		C	141248170	T	C	141248170	2	2	322	1	0	0	0	0	0	0	0	1	11515	1393	49	2		2	PCDH1	5	141248170	Silent	SNP	T	TCGA-MI-A75G-01A-11D-A32G-10	1507640	141248170	39667090	71	45319										
KCTD16	57528	hgsc.bcm.edu	37	chr5	143586687	143586687	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cccagatgaattctgccacaGtgactttgaagatgcctccc	8	13	1	5			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr5:143586687G>A	ENST00000507359.3	+	2	1501	c.410G>A	c.(409-411)aGt>aAt	p.S137N	KCTD16_ENST00000512467.1_Missense_Mutation_p.S137N	NM_020768.3	NP_065819.1	Q68DU8	KCD16_HUMAN	potassium channel tetramerization domain containing 16	137					protein homooligomerization (GO:0051260)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)				large_intestine(5)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	21		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)			TTCTGCCACAGTGACTTTGAA	0.527																																					p.S137N		Atlas-SNP	.											.	KCTD16	70	.	0			c.G410A						.						83	88	87					5																	143586687		2203	4300	6503	SO:0001583	missense	57528	exon3			GCCACAGTGACTT	AB037738	CCDS34260.1	5q32	2013-06-20	2013-06-20		ENSG00000183775	ENSG00000183775			29244	protein-coding gene	gene with protein product		613423	"potassium channel tetramerisation domain containing 16"			10718198	Standard	NM_020768		Approved	KIAA1317	uc003lnm.1	Q68DU8	OTTHUMG00000163172	ENST00000507359.3:c.410G>A	chr5.hg19:g.143586687G>A	ENSP00000426548:p.Ser137Asn	40.0	0.0		60.0	10.0	NM_020768	Q9P2M9	Missense_Mutation	SNP	ENST00000507359.3	hg19	CCDS34260.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.527374	0.85706	.	.	ENSG00000183775	ENST00000512467;ENST00000507359	T;T	0.49720	0.77;0.77	5.75	5.75	0.90469	BTB/POZ fold (1);	0.000000	0.85682	D	0.000000	T	0.62804	0.2458	M	0.77313	2.365	0.58432	D	0.999999	D	0.59767	0.986	P	0.50825	0.651	T	0.65492	-0.6155	10	0.51188	T	0.08	.	19.942	0.97168	0.0:0.0:1.0:0.0	.	137	Q68DU8	KCD16_HUMAN	N	137	ENSP00000424151:S137N;ENSP00000426548:S137N	ENSP00000426548:S137N	S	+	2	0	KCTD16	143566880	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.807000	0.99171	2.714000	0.92807	0.561000	0.74099	AGT	.	.		0.527	KCTD16-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371898.3	XM_098368		A	143586687	G	A	143586687	3	1	322	1	0	0	0	0	1	0	0	0	8112	1029	36	3	412	3	KCTD16	5	143586687	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	2338517	143586687	37328573	72	45320										
FBXO38	81545	hgsc.bcm.edu	37	chr5	147788727	147788727	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	actattgttctgggagcttgCaaaaatgctcttgaagtaga	10	6	2	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr5:147788727C>G	ENST00000340253.5	+	8	1077	c.909C>G	c.(907-909)tgC>tgG	p.C303W	FBXO38_ENST00000394370.3_Missense_Mutation_p.C303W|FBXO38_ENST00000296701.6_Missense_Mutation_p.C303W|FBXO38_ENST00000509699.2_3'UTR|FBXO38_ENST00000513826.1_Missense_Mutation_p.C303W			Q6PIJ6	FBX38_HUMAN	F-box protein 38	303					cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)			ATG4C/FBXO38(2)	NS(1)|breast(2)|endometrium(7)|kidney(5)|large_intestine(9)|lung(15)|ovary(5)|prostate(2)|skin(2)|stomach(2)|urinary_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGGAGCTTGCAAAAATGCTC	0.358																																					p.C303W		Atlas-SNP	.											.	FBXO38	115	.	0			c.C909G						.						245	239	241					5																	147788727		2203	4300	6503	SO:0001583	missense	81545	exon8			AGCTTGCAAAAAT	BC005873	CCDS43384.1, CCDS64285.1	5q33.1	2008-02-05			ENSG00000145868	ENSG00000145868		"F-boxes /  "other""	28844	protein-coding gene	gene with protein product		608533				12477932	Standard	NM_030793		Approved	MOKA, SP329, FLJ13962, Fbx38	uc003lpg.2	Q6PIJ6	OTTHUMG00000129929	ENST00000340253.5:c.909C>G	chr5.hg19:g.147788727C>G	ENSP00000342023:p.Cys303Trp	150.0	0.0		205.0	57.0	NM_001271723	Q6PK72|Q7Z2U0|Q86VN3|Q9BXY6|Q9H837|Q9HC40	Missense_Mutation	SNP	ENST00000340253.5	hg19		.	.	.	.	.	.	.	.	.	.	C	16.59	3.165088	0.57476	.	.	ENSG00000145868	ENST00000340253;ENST00000296701;ENST00000394370;ENST00000513826	T;T;T;T	0.21031	2.03;5.29;2.03;5.29	5.29	2.45	0.29901	.	0.000000	0.85682	D	0.000000	T	0.31104	0.0786	L	0.32530	0.975	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.85130	0.995;0.995;0.997	T	0.02004	-1.1231	10	0.87932	D	0	-10.7367	8.9713	0.35908	0.0:0.7435:0.0:0.2565	.	303;303;303	Q6PIJ6-3;Q6PIJ6-2;Q6PIJ6	.;.;FBX38_HUMAN	W	303	ENSP00000342023:C303W;ENSP00000296701:C303W;ENSP00000377895:C303W;ENSP00000426410:C303W	ENSP00000296701:C303W	C	+	3	2	FBXO38	147768920	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.645000	0.37238	0.277000	0.22141	-0.229000	0.12294	TGC	.	.		0.358	FBXO38-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000252185.2	NM_030793		G	147788727	C	G	147788727	3	3	322	1	0	0	0	0	1	0	0	0	5754	718	25	4	935	4	FBXO38	5	147788727	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	4202040	147788727	33126533	73	45321										
FAT2	2196	hgsc.bcm.edu	37	chr5	150925186	150925186	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tagacacagaattggaaagaGggcatgctctcataatccat	9	8	1	3			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr5:150925186G>T	ENST00000261800.5	-	9	5514	c.5502C>A	c.(5500-5502)ccC>ccA	p.P1834P		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	1834	Cadherin 16. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ATTGGAAAGAGGGCATGCTCT	0.428																																					p.P1834P		Atlas-SNP	.											.	FAT2	465	.	0			c.C5502A						.						67	71	70					5																	150925186		2203	4300	6503	SO:0001819	synonymous_variant	2196	exon9			GAAAGAGGGCATG	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.5502C>A	chr5.hg19:g.150925186G>T		73.0	0.0		129.0	26.0	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	hg19	CCDS4317.1																																																																																			.	.		0.428	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		T	150925186	G	T	150925186	2	4	322	1	0	0	0	0	0	0	0	1	5698	987	35	3		3	FAT2	5	150925186	Silent	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	3136459	150925186	29990074	74	45322										
ADAM19	8728	hgsc.bcm.edu	37	chr5	156934075	156934075	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gagactcaccatgttgactcCtccagactggtacacagagc	9	13	1	4			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr5:156934075C>T	ENST00000517905.1	-	10	1023	c.979G>A	c.(979-981)Gga>Aga	p.G327R	ADAM19_ENST00000430702.2_Missense_Mutation_p.G60R|ADAM19_ENST00000394020.1_Missense_Mutation_p.G329R|ADAM19_ENST00000257527.4_Missense_Mutation_p.G327R			Q9H013	ADA19_HUMAN	ADAM metallopeptidase domain 19	327	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				heart development (GO:0007507)|membrane protein ectodomain proteolysis (GO:0006509)	integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	Renal(175;0.00488)	Medulloblastoma(196;0.0359)|all_neural(177;0.14)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			ATGTTGACTCCTCCAGACTGG	0.562																																					p.G327R		Atlas-SNP	.											.	ADAM19	216	.	0			c.G979A						.						82	76	78					5																	156934075		2203	4300	6503	SO:0001583	missense	8728	exon10			TGACTCCTCCAGA	AF311317	CCDS4338.1	5q33.3	2010-06-24	2010-06-24		ENSG00000135074	ENSG00000135074		"ADAM metallopeptidase domain containing"	197	protein-coding gene	gene with protein product	"meltrin beta"	603640	"a disintegrin and metalloproteinase domain 19 (meltrin beta)"			9806848	Standard	NM_033274		Approved	MLTNB	uc003lwz.4	Q9H013	OTTHUMG00000130242	ENST00000517905.1:c.979G>A	chr5.hg19:g.156934075C>T	ENSP00000428654:p.Gly327Arg	100.0	0.0		139.0	32.0	NM_033274	Q9BZL5|Q9UHP2	Missense_Mutation	SNP	ENST00000517905.1	hg19		.	.	.	.	.	.	.	.	.	.	C	36	5.604250	0.96626	.	.	ENSG00000135074	ENST00000430702;ENST00000257527;ENST00000394020;ENST00000517905	T;T;T;T	0.70399	-0.48;-0.48;-0.48;-0.48	5.46	5.46	0.80206	.	0.000000	0.64402	D	0.000006	D	0.89171	0.6639	H	0.95004	3.61	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.91890	0.5523	10	0.87932	D	0	.	19.3107	0.94186	0.0:1.0:0.0:0.0	.	327;60	Q9H013-2;E9PD32	.;.	R	60;327;329;327	ENSP00000414088:G60R;ENSP00000257527:G327R;ENSP00000377588:G329R;ENSP00000428654:G327R	ENSP00000257527:G327R	G	-	1	0	ADAM19	156866653	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	7.770000	0.85390	2.561000	0.86390	0.650000	0.86243	GGA	.	.		0.562	ADAM19-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000373918.1	NM_033274		T	156934075	C	T	156934075	3	4	322	1	0	0	0	0	1	0	0	0	240	690	24	3	1833	3	ADAM19	5	156934075	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	6008889	156934075	23981185	75	45323										
GPRIN1	114787	hgsc.bcm.edu	37	chr5	176025588	176025588	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tttcccagagaaactggatcCaccttgcctgaagacatggg	10	11	0	3			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr5:176025588C>T	ENST00000303991.4	-	2	1425	c.1248G>A	c.(1246-1248)gtG>gtA	p.V416V		NM_052899.2	NP_443131.2	Q7Z2K8	GRIN1_HUMAN	G protein regulated inducer of neurite outgrowth 1	416					neuron projection development (GO:0031175)	cell projection (GO:0042995)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AAACTGGATCCACCTTGCCTG	0.532																																					p.V416V		Atlas-SNP	.											.	GPRIN1	77	.	0			c.G1248A						.						67	61	63					5																	176025588		2203	4300	6503	SO:0001819	synonymous_variant	114787	exon2			TGGATCCACCTTG	AB067480	CCDS4405.1	5q35.2	2008-02-05			ENSG00000169258	ENSG00000169258			24835	protein-coding gene	gene with protein product		611239				11572484	Standard	NM_052899		Approved	GRIN1, KIAA1893	uc003meo.1	Q7Z2K8	OTTHUMG00000130659	ENST00000303991.4:c.1248G>A	chr5.hg19:g.176025588C>T		63.0	0.0		81.0	27.0	NM_052899	C9JM70|Q8ND74|Q96PZ4	Silent	SNP	ENST00000303991.4	hg19	CCDS4405.1																																																																																			.	.		0.532	GPRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253149.1	NM_052899		T	176025588	C	T	176025588	2	4	322	1	0	0	0	0	0	0	0	1	6738	581	21	3		3	GPRIN1	5	176025588	Silent	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	19091513	176025588	4889672	76	45324										
HIST1H1C	3006	hgsc.bcm.edu	37	chr6	26056379	26056379	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cggtgcctttcgtttgcaccAgagtgcccttgctcaccagg	11	14	1	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr6:26056379A>G	ENST00000343677.2	-	1	320	c.278T>C	c.(277-279)cTg>cCg	p.L93P		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	93	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(4)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	34						CGTTTGCACCAGAGTGCCCTT	0.547																																					p.L93P		Atlas-SNP	.											.	HIST1H1C	80	.	0			c.T278C						.						109	114	113					6																	26056379		2203	4300	6503	SO:0001583	missense	3006	exon1			TGCACCAGAGTGC	X57129	CCDS4577.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000187837	ENSG00000187837		"Histones / Replication-dependent"	4716	protein-coding gene	gene with protein product		142710	"H1 histone family, member 2", "histone 1, H1c"	H1F2		2759094, 12408966	Standard	NM_005319		Approved	H1.2, H1s-1, H1c	uc003nfw.3	P16403	OTTHUMG00000016140	ENST00000343677.2:c.278T>C	chr6.hg19:g.26056379A>G	ENSP00000339566:p.Leu93Pro	65.0	0.0		129.0	60.0	NM_005319	A8K4I2	Missense_Mutation	SNP	ENST00000343677.2	hg19	CCDS4577.1	.	.	.	.	.	.	.	.	.	.	A	18.63	3.665582	0.67700	.	.	ENSG00000187837	ENST00000343677	T	0.56444	0.46	5.63	5.63	0.86233	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.64402	D	0.000002	T	0.79776	0.4504	H	0.99197	4.465	0.80722	D	1	P	0.50943	0.94	P	0.59643	0.861	D	0.88061	0.2794	10	0.87932	D	0	-12.168	15.3144	0.74062	1.0:0.0:0.0:0.0	.	93	P16403	H12_HUMAN	P	93	ENSP00000339566:L93P	ENSP00000339566:L93P	L	-	2	0	HIST1H1C	26164358	1.000000	0.71417	1.000000	0.80357	0.266000	0.26442	9.082000	0.94059	2.271000	0.75665	0.533000	0.62120	CTG	.	.		0.547	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319		G	26056379	A	G	26056379	3	3	322	1	0	0	0	0	1	0	0	0	7133	188	7	2	367	2	HIST1H1C	6	26056379	Missense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10		26056379	145058688	77	45325										
ZNF192	7745	hgsc.bcm.edu	37	chr6	28121655	28121655	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ctttcaatgggaacactggtCtcattcaacacctgagaatt	7	10	3	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr6:28121655C>G	ENST00000330236.6	+	6	1781	c.1597C>G	c.(1597-1599)Ctc>Gtc	p.L533V	ZKSCAN8_ENST00000457389.2_Missense_Mutation_p.L533V	NM_001278119.1|NM_001278121.1|NM_001278122.1|NM_006298.2	NP_001265048.1|NP_001265050.1|NP_001265051.1|NP_006289.2	Q15776	ZKSC8_HUMAN	zinc finger with KRAB and SCAN domains 8	533					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)										GAACACTGGTCTCATTCAACA	0.438																																					p.L533V		Atlas-SNP	.											.	.	.	.	0			c.C1597G						.						78	78	78					6																	28121655		2203	4300	6503	SO:0001583	missense	7745	exon6			ACTGGTCTCATTC		CCDS4645.1	6p21	2013-01-09	2013-01-09	2013-01-09	ENSG00000198315	ENSG00000198315		"Zinc fingers, C2H2-type", "-", "-", "-"	12983	protein-coding gene	gene with protein product		602240	"zinc finger protein 192"	ZNF192			Standard	NM_001278119		Approved	LD5-1, ZSCAN40	uc003nkn.2	Q15776	OTTHUMG00000014510	ENST00000330236.6:c.1597C>G	chr6.hg19:g.28121655C>G	ENSP00000332750:p.Leu533Val	49.0	0.0		76.0	31.0	NM_006298	A1L3D4|B4DYF1|Q4VAR1|Q4VAR2|Q4VAR3|Q9H4T1	Missense_Mutation	SNP	ENST00000330236.6	hg19	CCDS4645.1	.	.	.	.	.	.	.	.	.	.	C	16.12	3.034057	0.54896	.	.	ENSG00000198315	ENST00000330236;ENST00000457389	T;T	0.52983	0.64;0.64	5.85	5.85	0.93711	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.48767	D	0.000173	T	0.64204	0.2577	M	0.80746	2.51	0.80722	D	1	D	0.76494	0.999	D	0.75484	0.986	T	0.68337	-0.5435	10	0.87932	D	0	.	13.8457	0.63466	0.153:0.8469:0.0:0.0	.	533	Q15776	ZN192_HUMAN	V	533	ENSP00000332750:L533V;ENSP00000402948:L533V	ENSP00000332750:L533V	L	+	1	0	ZNF192	28229634	0.882000	0.30256	1.000000	0.80357	0.999000	0.98932	1.925000	0.40074	2.773000	0.95371	0.655000	0.94253	CTC	.	.		0.438	ZKSCAN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040178.2			G	28121655	C	G	28121655	3	3	322	1	0	0	0	0	1	0	0	0	17771	913	32	4	1615	4	ZNF192	6	28121655	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	2065276	28121655	142993412	78	45326										
DEF6	50619	hgsc.bcm.edu	37	chr6	35287441	35287441	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gtgaaagctcggcgagatgaAgaatctgtgcgaatcgctca	13	8	2	4			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr6:35287441A>C	ENST00000316637.5	+	8	1361	c.1356A>C	c.(1354-1356)gaA>gaC	p.E452D	DEF6_ENST00000542066.1_Missense_Mutation_p.E197D	NM_022047.3	NP_071330.3	Q9H4E7	DEFI6_HUMAN	differentially expressed in FDCP 6 homolog (mouse)	452	Glu-rich.					cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				cervix(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)	15						GGCGAGATGAAGAATCTGTGC	0.597																																					p.E452D		Atlas-SNP	.											.	DEF6	36	.	0			c.A1356C						.						68	70	69					6																	35287441		2203	4300	6503	SO:0001583	missense	50619	exon8			AGATGAAGAATCT	AJ276095	CCDS4802.1	6p21.33-p21.1	2013-01-10	2001-11-28		ENSG00000023892	ENSG00000023892		"Pleckstrin homology (PH) domain containing"	2760	protein-coding gene	gene with protein product	"SWAP-70-like adaptor protein of T cells"	610094	"differentially expressed in FDCP (mouse homolog) 6"			19251698	Standard	NM_022047		Approved	IBP, SLAT, SWAP70L	uc003okk.3	Q9H4E7	OTTHUMG00000014563	ENST00000316637.5:c.1356A>C	chr6.hg19:g.35287441A>C	ENSP00000319831:p.Glu452Asp	91.0	0.0		164.0	65.0	NM_022047	Q86VF4	Missense_Mutation	SNP	ENST00000316637.5	hg19	CCDS4802.1	.	.	.	.	.	.	.	.	.	.	G	18.57	3.653362	0.67472	.	.	ENSG00000023892	ENST00000542066;ENST00000316637	T;T	0.70516	-0.49;2.28	5.26	3.49	0.39957	.	0.000000	0.85682	D	0.000000	T	0.77110	0.4082	M	0.83012	2.62	0.58432	D	0.999996	D;D;D	0.71674	0.998;0.997;0.997	D;D;D	0.77557	0.99;0.978;0.978	T	0.78486	-0.2185	10	0.72032	D	0.01	-30.0273	8.3806	0.32468	0.3663:0.0:0.6337:0.0	.	197;452;452	F5H853;B2RBP7;Q9H4E7	.;.;DEFI6_HUMAN	D	197;452	ENSP00000442166:E197D;ENSP00000319831:E452D	ENSP00000319831:E452D	E	+	3	2	DEF6	35395419	1.000000	0.71417	1.000000	0.80357	0.760000	0.43138	2.228000	0.42981	0.379000	0.24794	-0.213000	0.12676	GAA	.	.		0.597	DEF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040276.1	NM_022047		C	35287441	A	C	35287441	3	2	322	1	0	0	0	0	1	0	0	0	4388	69	3	5	1386	5	DEF6	6	35287441	Missense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	7165786	35287441	135827626	79	45327										
BYSL	705	hgsc.bcm.edu	37	chr6	41889314	41889314	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gagaaaaatgcccaaattcaAggcggcccgtggggtggggg	17	8	1	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr6:41889314A>T	ENST00000230340.4	+	1	389	c.14A>T	c.(13-15)aAg>aTg	p.K5M	MED20_ENST00000467535.1_5'Flank|MED20_ENST00000265350.4_5'Flank|MED20_ENST00000409312.1_5'Flank|MED20_ENST00000409060.1_5'Flank	NM_004053.3	NP_004044.3	Q13895	BYST_HUMAN	bystin-like	5					cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|female pregnancy (GO:0007565)|maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)|trophectodermal cell differentiation (GO:0001829)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(5)|skin(1)	8	Colorectal(47;0.121)		STAD - Stomach adenocarcinoma(11;0.000204)|Epithelial(12;0.000473)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			CCCAAATTCAAGGCGGCCCGT	0.647											OREG0017436	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K5M		Atlas-SNP	.											.	BYSL	17	.	0			c.A14T						.						15	19	17					6																	41889314		2101	4225	6326	SO:0001583	missense	705	exon1			AATTCAAGGCGGC	L36720	CCDS34450.1	6p21.1	2008-08-29			ENSG00000112578	ENSG00000112578			1157	protein-coding gene	gene with protein product		603871				9925933, 17381424	Standard	NM_004053		Approved		uc003orl.3	Q13895	OTTHUMG00000014687	ENST00000230340.4:c.14A>T	chr6.hg19:g.41889314A>T	ENSP00000230340:p.Lys5Met	75.0	0.0	904	119.0	35.0	NM_004053	Q6P5W4|Q86W44|Q96IP8	Missense_Mutation	SNP	ENST00000230340.4	hg19	CCDS34450.1	.	.	.	.	.	.	.	.	.	.	A	14.83	2.653470	0.47362	.	.	ENSG00000112578	ENST00000230340	T	0.24151	1.87	4.87	4.87	0.63330	.	0.000000	0.85682	D	0.000000	T	0.40670	0.1126	M	0.80982	2.52	0.53688	D	0.999978	D	0.71674	0.998	P	0.60789	0.879	T	0.48055	-0.9068	10	0.87932	D	0	-21.834	14.3007	0.66346	1.0:0.0:0.0:0.0	.	5	Q13895	BYST_HUMAN	M	5	ENSP00000230340:K5M	ENSP00000230340:K5M	K	+	2	0	BYSL	41997292	1.000000	0.71417	0.109000	0.21407	0.054000	0.15201	4.722000	0.61958	2.036000	0.60181	0.533000	0.62120	AAG	.	.		0.647	BYSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040535.2			T	41889314	A	T	41889314	3	4	322	1	0	0	0	0	1	0	0	0	1578	72	3	4	16	4	BYSL	6	41889314	Missense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	6601873	41889314	129225753	80	45328										
MEP1A	4224	hgsc.bcm.edu	37	chr6	46787312	46787312	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	atgtgggacagaacatttccAttggccaaggatgtgcctat	11	8	0	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr6:46787312A>G	ENST00000230588.4	+	7	436	c.427A>G	c.(427-429)Att>Gtt	p.I143V		NM_005588.2	NP_005579.2	Q16819	MEP1A_HUMAN	meprin A, alpha (PABA peptide hydrolase)	143	Metalloprotease.				digestion (GO:0007586)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|meprin A complex (GO:0017090)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42			Lung(136;0.192)			GAACATTTCCATTGGCCAAGG	0.453																																					p.I143V		Atlas-SNP	.											.	MEP1A	93	.	0			c.A427G						.						159	141	147					6																	46787312		2203	4300	6503	SO:0001583	missense	4224	exon7			ATTTCCATTGGCC		CCDS4918.1	6p12-p11	2010-10-18			ENSG00000112818	ENSG00000112818	3.4.24.18		7015	protein-coding gene	gene with protein product		600388				7774936	Standard	NM_005588		Approved	PPHA	uc010jzh.1	Q16819	OTTHUMG00000014790	ENST00000230588.4:c.427A>G	chr6.hg19:g.46787312A>G	ENSP00000230588:p.Ile143Val	59.0	0.0		95.0	54.0	NM_005588	A2RRM4|B0AZP9|B2RCS2|Q8TDC9|Q9H1R1	Missense_Mutation	SNP	ENST00000230588.4	hg19	CCDS4918.1	.	.	.	.	.	.	.	.	.	.	A	17.05	3.288753	0.59976	.	.	ENSG00000112818	ENST00000230588	T	0.66995	-0.24	5.69	5.69	0.88448	Peptidase, metallopeptidase (1);Peptidase M12A, astacin (1);Metallopeptidase, catalytic domain (1);	0.061183	0.85682	D	0.000000	T	0.70456	0.3226	L	0.52759	1.655	0.53688	D	0.999978	D;D	0.63880	0.993;0.993	D;D	0.63381	0.914;0.914	T	0.73933	-0.3826	10	0.59425	D	0.04	-19.3152	15.9609	0.79930	1.0:0.0:0.0:0.0	.	171;143	B7ZL91;Q16819	.;MEP1A_HUMAN	V	143	ENSP00000230588:I143V	ENSP00000230588:I143V	I	+	1	0	MEP1A	46895271	0.973000	0.33851	1.000000	0.80357	0.466000	0.32739	2.478000	0.45189	2.162000	0.67917	0.528000	0.53228	ATT	.	.		0.453	MEP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040803.1	NM_005588		G	46787312	A	G	46787312	3	3	322	1	0	0	0	0	1	0	0	0	9484	217	8	2	453	2	MEP1A	6	46787312	Missense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	4897998	46787312	124327755	81	45329										
C6orf165	154313	hgsc.bcm.edu	37	chr6	88138481	88138481	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tactttcctgagagagtgatGcaatgtcatcttaatggagc	10	7	2	3			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr6:88138481G>T	ENST00000507897.1	+	9	1181	c.1098G>T	c.(1096-1098)atG>atT	p.M366I	C6ORF165_ENST00000369562.4_Missense_Mutation_p.M366I			Q8IYR0	CF165_HUMAN	chromosome 6 open reading frame 165	366										NS(1)|central_nervous_system(1)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0419)		AGAGAGTGATGCAATGTCATC	0.378																																					p.M366I		Atlas-SNP	.											.	C6orf165	116	.	0			c.G1098T						.						152	133	140					6																	88138481		2203	4300	6503	SO:0001583	missense	154313	exon9			AGTGATGCAATGT	BC035083	CCDS34498.1	6q15	2012-02-07			ENSG00000213204	ENSG00000213204			21405	protein-coding gene	gene with protein product							Standard	NM_001031743		Approved	FLJ25974, dJ382I10.1	uc003plv.3	Q8IYR0	OTTHUMG00000015173	ENST00000507897.1:c.1098G>T	chr6.hg19:g.88138481G>T	ENSP00000426769:p.Met366Ile	143.0	0.0		197.0	32.0	NM_001031743	A8K969|E1P507|Q8N9U4	Missense_Mutation	SNP	ENST00000507897.1	hg19	CCDS34498.1	.	.	.	.	.	.	.	.	.	.	G	0.239	-1.015397	0.02078	.	.	ENSG00000213204	ENST00000369562	T	0.27720	1.65	5.18	-0.553	0.11815	.	0.723121	0.14082	N	0.342647	T	0.03220	0.0094	N	0.05124	-0.11	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.38329	-0.9666	10	0.30854	T	0.27	.	0.7963	0.01067	0.3562:0.1176:0.2955:0.2306	.	366	Q8IYR0	CF165_HUMAN	I	366	ENSP00000358575:M366I	ENSP00000358575:M366I	M	+	3	0	C6orf165	88195200	0.001000	0.12720	0.009000	0.14445	0.003000	0.03518	-0.864000	0.04254	0.409000	0.25649	-0.355000	0.07637	ATG	.	.		0.378	C6orf165-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000470406.1	NM_178823		T	88138481	G	T	88138481	3	4	322	1	0	0	0	0	1	0	0	0	2343	1319	46	3	1128	3	C6orf165	6	88138481	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	41351169	88138481	82976586	82	45330										
EPHA7	2045	hgsc.bcm.edu	37	chr6	93969103	93969103	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	acacgctcaattttaatacaGgaggcatctagctccttggc	8	11	2	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr6:93969103G>A	ENST00000369303.4	-	10	2077	c.1893C>T	c.(1891-1893)tcC>tcT	p.S631S		NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	631					brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|ephrin receptor signaling pathway (GO:0048013)|negative chemotaxis (GO:0050919)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cell-cell adhesion (GO:0022407)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of protein autophosphorylation (GO:0031952)|retinal ganglion cell axon guidance (GO:0031290)	dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|chemorepellent activity (GO:0045499)|GPI-linked ephrin receptor activity (GO:0005004)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(1)|central_nervous_system(7)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|lung(43)|ovary(8)|pancreas(1)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(13)|urinary_tract(1)	112		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		TTTTAATACAGGAGGCATCTA	0.428																																					p.S631S		Atlas-SNP	.											.	EPHA7	251	.	0			c.C1893T						.						173	156	162					6																	93969103		2203	4300	6503	SO:0001819	synonymous_variant	2045	exon10			AATACAGGAGGCA	L36642	CCDS5031.1, CCDS75494.1	6q16.3	2013-02-11	2004-10-28		ENSG00000135333	ENSG00000135333		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3390	protein-coding gene	gene with protein product		602190	"EphA7"			9267020	Standard	NM_004440		Approved	Hek11	uc003poe.3	Q15375	OTTHUMG00000015228	ENST00000369303.4:c.1893C>T	chr6.hg19:g.93969103G>A		90.0	0.0		92.0	62.0	NM_004440	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Silent	SNP	ENST00000369303.4	hg19	CCDS5031.1																																																																																			.	.		0.428	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1			A	93969103	G	A	93969103	2	1	322	1	0	0	0	0	0	0	0	1	5174	987	35	3		3	EPHA7	6	93969103	Silent	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	5830622	93969103	77145964	83	45331										
CDC40	51362	hgsc.bcm.edu	37	chr6	110540596	110540596	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tatcaagatttacaaaccgaAaagtaccttattgtgtcaaa	5	7	2	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr6:110540596A>T	ENST00000368932.1	+	12	1221	c.1120A>T	c.(1120-1122)Aaa>Taa	p.K374*	CDC40_ENST00000307731.1_Nonsense_Mutation_p.K374*|CDC40_ENST00000368930.1_Nonsense_Mutation_p.K374*			O60508	PRP17_HUMAN	cell division cycle 40	374					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)	18		all_cancers(87;6.23e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488)		Epithelial(106;0.0221)|all cancers(137;0.0314)|OV - Ovarian serous cystadenocarcinoma(136;0.034)		TACAAACCGAAAAGTACCTTA	0.323																																					p.K374X		Atlas-SNP	.											.	CDC40	39	.	0			c.A1120T						.						135	130	131					6																	110540596		2203	4300	6503	SO:0001587	stop_gained	51362	exon11			AACCGAAAAGTAC	AF015044	CCDS5081.1	6q22.1	2013-01-17	2013-01-17		ENSG00000168438	ENSG00000168438		"WD repeat domain containing"	17350	protein-coding gene	gene with protein product		605585	"cell division cycle 40 homolog (yeast)", "cell division cycle 40 homolog (S. cerevisiae)"			9769104, 9830021	Standard	NM_015891		Approved	PRP17, EHB3, PRPF17, FLJ10564	uc003pua.3	O60508	OTTHUMG00000015358	ENST00000368932.1:c.1120A>T	chr6.hg19:g.110540596A>T	ENSP00000357928:p.Lys374*	99.0	0.0		115.0	18.0	NM_015891	B2RBC5|O75471|Q5SRN0|Q9UPG1	Nonsense_Mutation	SNP	ENST00000368932.1	hg19	CCDS5081.1	.	.	.	.	.	.	.	.	.	.	A	37	6.532367	0.97641	.	.	ENSG00000168438	ENST00000368932;ENST00000368933;ENST00000368930;ENST00000307731	.	.	.	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-24.5518	16.1773	0.81862	1.0:0.0:0.0:0.0	.	.	.	.	X	374	.	ENSP00000304370:K374X	K	+	1	0	CDC40	110647289	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	8.962000	0.93254	2.217000	0.71921	0.482000	0.46254	AAA	.	.		0.323	CDC40-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041791.1	NM_015891		T	110540596	A	T	110540596	4	4	322	1	0	0	0	0	0	1	0	0	3072	15	1	4	1162	4	CDC40	6	110540596	Nonsense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	16571493	110540596	60574471	84	45332										
LAMA2	3908	hgsc.bcm.edu	37	chr6	129588356	129588356	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cctgtgatgacgtcactggaGaatgcctggtaagtgctctc	12	10	2	3			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr6:129588356G>A	ENST00000421865.2	+	16	2363	c.2314G>A	c.(2314-2316)Gaa>Aaa	p.E772K		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	772	Laminin EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		CGTCACTGGAGAATGCCTGGT	0.502																																					p.E772K		Atlas-SNP	.											LAMA2,NS,carcinoma,0,1	LAMA2	481	.	0			c.G2314A						.						272	226	242					6																	129588356		2203	4300	6503	SO:0001583	missense	3908	exon16			ACTGGAGAATGCC	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"Laminins"	6482	protein-coding gene	gene with protein product	"merosin", "congenital muscular dystrophy"	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.2314G>A	chr6.hg19:g.129588356G>A	ENSP00000400365:p.Glu772Lys	67.0	0.0		69.0	9.0	NM_000426	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	hg19	CCDS5138.1	.	.	.	.	.	.	.	.	.	.	G	16.86	3.238393	0.58886	.	.	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865	T	0.61510	0.1	5.75	5.75	0.90469	EGF-like, laminin (3);	0.274054	0.36482	N	0.002569	T	0.42675	0.1213	L	0.33753	1.03	0.44366	D	0.997267	P;P	0.43231	0.801;0.801	B;B	0.43990	0.339;0.438	T	0.22521	-1.0214	10	0.25106	T	0.35	.	19.9525	0.97208	0.0:0.0:1.0:0.0	.	772;772	A6NF00;P24043	.;LAMA2_HUMAN	K	772	ENSP00000400365:E772K	ENSP00000346769:E772K	E	+	1	0	LAMA2	129630049	1.000000	0.71417	0.955000	0.39395	0.993000	0.82548	3.863000	0.56016	2.719000	0.93026	0.655000	0.94253	GAA	.	.		0.502	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			A	129588356	G	A	129588356	3	1	322	1	0	0	0	0	1	0	0	0	8615	943	33	3	2376	3	LAMA2	6	129588356	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	19047760	129588356	41526711	85	45333										
REPS1	85021	hgsc.bcm.edu	37	chr6	139265148	139265148	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ctacagttcgtactgttgtcTggtcctgtaatgaaacattt	8	8	1	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr6:139265148T>C	ENST00000450536.2	-	6	1332	c.758A>G	c.(757-759)cAg>cGg	p.Q253R	REPS1_ENST00000415951.2_Missense_Mutation_p.Q253R|REPS1_ENST00000258062.5_Missense_Mutation_p.Q253R|REPS1_ENST00000367663.4_Missense_Mutation_p.Q253R|REPS1_ENST00000409812.2_Missense_Mutation_p.Q253R			Q96D71	REPS1_HUMAN	RALBP1 associated Eps domain containing 1	253					receptor-mediated endocytosis (GO:0006898)	coated pit (GO:0005905)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|SH3 domain binding (GO:0017124)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(2)	19				GBM - Glioblastoma multiforme(68;0.000434)|OV - Ovarian serous cystadenocarcinoma(155;0.000548)		TACTGTTGTCTGGTCCTGTAA	0.358																																					p.Q253R		Atlas-SNP	.											.	REPS1	58	.	0			c.A758G						.						131	115	121					6																	139265148		2203	4300	6503	SO:0001583	missense	85021	exon6			GTTGTCTGGTCCT		CCDS5193.2, CCDS47488.1, CCDS69212.1, CCDS69213.1	6q24.1	2013-01-10			ENSG00000135597	ENSG00000135597		"EF-hand domain containing"	15578	protein-coding gene	gene with protein product		614825					Standard	XM_005267177		Approved		uc011edr.2	Q96D71	OTTHUMG00000015685	ENST00000450536.2:c.758A>G	chr6.hg19:g.139265148T>C	ENSP00000392065:p.Gln253Arg	92.0	0.0		106.0	65.0	NM_001128617	B7ZBZ8|B7ZBZ9|B7ZC00|J3KP76|Q5JWJ5|Q5JWJ6|Q5JWJ7|Q8NDR7|Q8WU62|Q9BXY9	Missense_Mutation	SNP	ENST00000450536.2	hg19		.	.	.	.	.	.	.	.	.	.	T	11.84	1.758179	0.31137	.	.	ENSG00000135597	ENST00000450536;ENST00000367663;ENST00000529597;ENST00000409812;ENST00000258062;ENST00000415951;ENST00000367668	T;T;T;T;T;T	0.35605	1.3;1.32;1.35;1.33;1.3;1.3	6.01	6.01	0.97437	.	0.155181	0.64402	D	0.000009	T	0.13329	0.0323	N	0.24115	0.695	0.43761	D	0.996278	B;P;B;P	0.41848	0.002;0.763;0.001;0.651	B;B;B;B	0.39027	0.006;0.288;0.002;0.15	T	0.05115	-1.0905	10	0.11182	T	0.66	-6.3368	16.5285	0.84344	0.0:0.0:0.0:1.0	.	253;253;253;253	Q96D71-3;Q96D71-2;Q96D71;E9PMG1	.;.;REPS1_HUMAN;.	R	253;253;239;253;253;253;201	ENSP00000392065:Q253R;ENSP00000356635:Q253R;ENSP00000434251:Q239R;ENSP00000386699:Q253R;ENSP00000258062:Q253R;ENSP00000397941:Q253R	ENSP00000258062:Q253R	Q	-	2	0	REPS1	139306841	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.674000	0.61612	2.307000	0.77673	0.528000	0.53228	CAG	.	.		0.358	REPS1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000042447.3			C	139265148	T	C	139265148	3	2	322	1	0	0	0	0	1	0	0	0	13243	1580	55	2	1692	2	REPS1	6	139265148	Missense_Mutation	SNP	T	TCGA-MI-A75G-01A-11D-A32G-10	9676792	139265148	31849919	86	45334										
RMND1	55005	hgsc.bcm.edu	37	chr6	151751308	151751308	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	attccaaaacacagcagctcCttccctgatttaaaaaaata	3	11	0	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr6:151751308C>T	ENST00000367303.4	-	5	816	c.694G>A	c.(694-696)Gga>Aga	p.G232R	RMND1_ENST00000336451.3_Missense_Mutation_p.G21R	NM_017909.2	NP_060379.2	Q9NWS8	RMND1_HUMAN	required for meiotic nuclear division 1 homolog (S. cerevisiae)	232					translation (GO:0006412)	mitochondrion (GO:0005739)				central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.146)	OV - Ovarian serous cystadenocarcinoma(155;6.8e-11)		ACAGCAGCTCCTTCCCTGATT	0.284																																					p.G232R		Atlas-SNP	.											.	RMND1	32	.	0			c.G694A						.						57	60	59					6																	151751308		2201	4290	6491	SO:0001583	missense	55005	exon5			CAGCTCCTTCCCT	AK000634	CCDS5232.1, CCDS75539.1	6q25.1	2008-02-05	2006-11-24	2006-11-24	ENSG00000155906	ENSG00000155906			21176	protein-coding gene	gene with protein product		614917	"chromosome 6 open reading frame 96"	C6orf96			Standard	NM_001271937		Approved	bA351K16.3, FLJ20627, RMD1	uc003qoi.3	Q9NWS8	OTTHUMG00000015837	ENST00000367303.4:c.694G>A	chr6.hg19:g.151751308C>T	ENSP00000356272:p.Gly232Arg	322.0	0.0		389.0	56.0	NM_017909	A8K8H4|Q0VDG6|Q5SZ48|Q5SZ83|Q6NSC5|Q96EN7	Missense_Mutation	SNP	ENST00000367303.4	hg19	CCDS5232.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.975121	0.74360	.	.	ENSG00000155906	ENST00000336451;ENST00000367303;ENST00000444024	D;D	0.97888	-4.59;-3.14	4.17	4.17	0.49024	.	0.000000	0.85682	D	0.000000	D	0.99105	0.9692	H	0.95504	3.68	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99208	1.0875	10	0.87932	D	0	-21.1437	16.6062	0.84830	0.0:1.0:0.0:0.0	.	232	Q9NWS8	RMND1_HUMAN	R	21;232;62	ENSP00000336683:G21R;ENSP00000356272:G232R	ENSP00000336683:G21R	G	-	1	0	RMND1	151793001	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	5.504000	0.66968	2.308000	0.77769	0.313000	0.20887	GGA	.	.		0.284	RMND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042718.2	NM_017909		T	151751308	C	T	151751308	3	4	322	1	0	0	0	0	1	0	0	0	13411	690	24	3	687	3	RMND1	6	151751308	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	12486160	151751308	19363759	87	45335										
WBSCR27	155368	hgsc.bcm.edu	37	chr7	73256365	73256365	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tacctggtcgtagtccggagCccagcggtcatagaaatgga	13	10	1	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr7:73256365C>A	ENST00000297873.4	-	2	155	c.106G>T	c.(106-108)Gct>Tct	p.A36S		NM_152559.2	NP_689772.2	Q8N6F8	WBS27_HUMAN	Williams Beuren syndrome chromosome region 27	36										NS(1)|central_nervous_system(1)|lung(2)|prostate(1)	5		Lung NSC(55;0.159)				TAGTCCGGAGCCCAGCGGTCA	0.627																																					p.A36S		Atlas-SNP	.											.	WBSCR27	21	.	0			c.G106T						.						62	57	59					7																	73256365		2203	4300	6503	SO:0001583	missense	155368	exon2			CCGGAGCCCAGCG	AF534110	CCDS5561.1	7q11.23	2004-07-05			ENSG00000165171	ENSG00000165171			19068	protein-coding gene	gene with protein product		612546					Standard	NM_152559		Approved		uc003tzj.2	Q8N6F8	OTTHUMG00000130033	ENST00000297873.4:c.106G>T	chr7.hg19:g.73256365C>A	ENSP00000297873:p.Ala36Ser	34.0	0.0		125.0	15.0	NM_152559		Missense_Mutation	SNP	ENST00000297873.4	hg19	CCDS5561.1	.	.	.	.	.	.	.	.	.	.	C	12.24	1.878739	0.33162	.	.	ENSG00000165171	ENST00000297873	T	0.72505	-0.66	4.57	2.74	0.32292	.	0.000000	0.85682	D	0.000000	T	0.79828	0.4513	M	0.71206	2.165	0.40776	D	0.983138	D;D	0.89917	0.976;1.0	P;D	0.70227	0.698;0.968	T	0.76465	-0.2949	10	0.38643	T	0.18	-0.1076	10.2754	0.43507	0.0:0.8158:0.0:0.1842	.	36;36	B4DWM3;Q8N6F8	.;WBS27_HUMAN	S	36	ENSP00000297873:A36S	ENSP00000297873:A36S	A	-	1	0	WBSCR27	72894301	1.000000	0.71417	0.673000	0.29887	0.002000	0.02628	1.924000	0.40065	0.147000	0.19030	-1.134000	0.01955	GCT	.	.		0.627	WBSCR27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252312.1	NM_152559		A	73256365	C	A	73256365	3	1	322	1	0	0	0	0	1	0	0	0	17281	739	26	3	651	3	WBSCR27	7	73256365	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10		73256365	85882298	88	45336										
HGF	3082	hgsc.bcm.edu	37	chr7	81374398	81374398	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tgattctgtatgatccatgaGacctcgataactctccccat	6	12	2	3			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr7:81374398G>T	ENST00000222390.5	-	6	890	c.664C>A	c.(664-666)Ctc>Atc	p.L222I	HGF_ENST00000444829.2_Missense_Mutation_p.L222I|HGF_ENST00000457544.2_Missense_Mutation_p.L217I|HGF_ENST00000453411.1_Missense_Mutation_p.L217I	NM_000601.4	NP_000592.3	P14210	HGF_HUMAN	hepatocyte growth factor (hepapoietin A; scatter factor)	222	Kringle 2. {ECO:0000255|PROSITE- ProRule:PRU00121}.				activation of MAPK activity (GO:0000187)|blood coagulation (GO:0007596)|cell chemotaxis (GO:0060326)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epithelial to mesenchymal transition (GO:0001837)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|hyaluronan metabolic process (GO:0030212)|liver development (GO:0001889)|mitotic nuclear division (GO:0007067)|myoblast proliferation (GO:0051450)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of hydrogen peroxide-mediated programmed cell death (GO:1901299)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|organ regeneration (GO:0031100)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of cell migration (GO:0030335)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	catalytic activity (GO:0003824)|chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|identical protein binding (GO:0042802)			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						TGATCCATGAGACCTCGATAA	0.393																																					p.L222I		Atlas-SNP	.											.	HGF	171	.	0			c.C664A						.						93	87	89					7																	81374398		2203	4300	6503	SO:0001583	missense	3082	exon6			CCATGAGACCTCG		CCDS5597.1, CCDS47626.1, CCDS47627.1, CCDS47628.1, CCDS47629.1	7q21.1	2009-09-11			ENSG00000019991	ENSG00000019991			4893	protein-coding gene	gene with protein product	"hepatopoietin A", "fibroblast-derived tumor cytotoxic factor", "scatter factor", "lung fibroblast-derived mitogen"	142409	"deafness, autosomal recessive 39"	DFNB39		1837206, 19576567	Standard	XM_006715956		Approved	SF, F-TCF, HGFB, HPTA	uc003uhl.3	P14210	OTTHUMG00000023804	ENST00000222390.5:c.664C>A	chr7.hg19:g.81374398G>T	ENSP00000222390:p.Leu222Ile	35.0	0.0		59.0	11.0	NM_000601	A1L3U6|Q02935|Q13494|Q14519|Q3KRB2|Q8TCE2|Q9BYL9|Q9BYM0|Q9UDU6	Missense_Mutation	SNP	ENST00000222390.5	hg19	CCDS5597.1	.	.	.	.	.	.	.	.	.	.	G	17.33	3.363000	0.61403	.	.	ENSG00000019991	ENST00000222390;ENST00000457544;ENST00000444829;ENST00000453411;ENST00000394769	T;T;T;T	0.62498	0.02;0.02;0.02;0.02	4.73	4.73	0.59995	Kringle (4);Kringle-like fold (1);	0.099613	0.64402	D	0.000001	T	0.41650	0.1168	N	0.03050	-0.425	0.80722	D	1	B;B;B;B	0.10296	0.0;0.001;0.001;0.003	B;B;B;B	0.22152	0.038;0.029;0.022;0.037	T	0.29792	-1.0000	10	0.33940	T	0.23	.	18.2555	0.90019	0.0:0.0:1.0:0.0	.	217;222;217;222	P14210-5;P14210-2;P14210-3;P14210	.;.;.;HGF_HUMAN	I	222;217;222;217;222	ENSP00000222390:L222I;ENSP00000391238:L217I;ENSP00000389854:L222I;ENSP00000408270:L217I	ENSP00000222390:L222I	L	-	1	0	HGF	81212334	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	8.772000	0.91757	2.609000	0.88269	0.655000	0.94253	CTC	.	.		0.393	HGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253315.2	NM_000601		T	81374398	G	T	81374398	3	4	322	1	0	0	0	0	1	0	0	0	7094	942	33	3	1586	3	HGF	7	81374398	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	8118033	81374398	77764265	89	45337										
ARPC1B	10095	hgsc.bcm.edu	37	chr7	98987539	98987539	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cgttcccaggtgggtttgcaAgcacatcaagaagcccatcc	10	13	1	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr7:98987539A>G	ENST00000451682.1	+	7	713	c.404A>G	c.(403-405)aAg>aGg	p.K135R	PDAP1_ENST00000496335.1_5'Flank|ARPC1B_ENST00000252725.5_Missense_Mutation_p.K135R			O15143	ARC1B_HUMAN	actin related protein 2/3 complex, subunit 1B, 41kDa	135					Arp2/3 complex-mediated actin nucleation (GO:0034314)|cellular component movement (GO:0006928)	actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|liver(2)|lung(1)	11	all_cancers(62;3.49e-09)|all_epithelial(64;2.57e-10)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			TGGGTTTGCAAGCACATCAAG	0.622																																					p.K135R		Atlas-SNP	.											.	ARPC1B	41	.	0			c.A404G						.						176	160	165					7																	98987539		2203	4300	6503	SO:0001583	missense	10095	exon5			TTTGCAAGCACAT	AF006084	CCDS5661.1	7q22.1	2013-03-14	2002-08-29		ENSG00000130429	ENSG00000130429		"Actin related protein 2/3 complex subunits", "WD repeat domain containing"	704	protein-coding gene	gene with protein product	"ARP2/3 protein complex subunit p41", "actin related protein 2/3 complex, subunit 1A (41 kD)"	604223	"actin related protein 2/3 complex, subunit 1B (41 kD)"			9230079, 9359840	Standard	NM_005720		Approved	ARC41, p40-ARC, p41-ARC	uc003upz.3	O15143	OTTHUMG00000154552	ENST00000451682.1:c.404A>G	chr7.hg19:g.98987539A>G	ENSP00000389631:p.Lys135Arg	52.0	0.0		151.0	30.0	NM_005720	Q9BU00	Missense_Mutation	SNP	ENST00000451682.1	hg19	CCDS5661.1	.	.	.	.	.	.	.	.	.	.	A	32	5.168347	0.94768	.	.	ENSG00000130429	ENST00000252725;ENST00000451682	T;T	0.63580	-0.05;-0.05	5.69	5.69	0.88448	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.043241	0.85682	D	0.000000	T	0.81702	0.4878	H	0.94808	3.585	0.80722	D	1	P;P	0.40553	0.721;0.721	P;P	0.52514	0.701;0.701	D	0.84915	0.0850	10	0.49607	T	0.09	-34.4296	15.6192	0.76793	1.0:0.0:0.0:0.0	.	135;135	A4D275;O15143	.;ARC1B_HUMAN	R	135	ENSP00000252725:K135R;ENSP00000389631:K135R	ENSP00000252725:K135R	K	+	2	0	ARPC1B	98825475	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	9.310000	0.96267	2.176000	0.68965	0.459000	0.35465	AAG	.	.		0.622	ARPC1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335894.1	NM_005720		G	98987539	A	G	98987539	3	3	322	1	0	0	0	0	1	0	0	0	970	72	3	2	418	2	ARPC1B	7	98987539	Missense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	17613141	98987539	60151124	90	45338										
ZNF498	221785	hgsc.bcm.edu	37	chr7	99226838	99226838	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tgggagcaaggaaaaggaggCaaaacccccacaggaagacc	13	10	0	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr7:99226838C>T	ENST00000394152.2	+	8	1157	c.830C>T	c.(829-831)gCa>gTa	p.A277V	ZSCAN25_ENST00000262941.6_Missense_Mutation_p.A205V|ZSCAN25_ENST00000466948.1_Intron|ZSCAN25_ENST00000334715.3_Missense_Mutation_p.A277V	NM_145115.2	NP_660090.2	Q6NSZ9	ZSC25_HUMAN	zinc finger and SCAN domain containing 25	277					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)										GAAAAGGAGGCAAAACCCCCA	0.552																																					p.A277V		Atlas-SNP	.											.	.	.	.	0			c.C830T						.						72	79	76					7																	99226838		2203	4300	6503	SO:0001583	missense	221785	exon8			AGGAGGCAAAACC	AK057030	CCDS5671.2	7q22.1	2013-01-09	2013-01-09	2013-01-09	ENSG00000197037	ENSG00000197037		"-", "Zinc fingers, C2H2-type"	21961	protein-coding gene	gene with protein product			"zinc finger protein 498"	ZNF498		11179890	Standard	XM_005250194		Approved	FLJ32468	uc003url.1	Q6NSZ9	OTTHUMG00000074055	ENST00000394152.2:c.830C>T	chr7.hg19:g.99226838C>T	ENSP00000377708:p.Ala277Val	58.0	0.0		117.0	27.0	NM_145115	A4D290|D6W5T5|Q14C82|Q14C99|Q5EBM9|Q6DJZ0|Q6N032|Q6ZML3	Missense_Mutation	SNP	ENST00000394152.2	hg19	CCDS5671.2	.	.	.	.	.	.	.	.	.	.	C	5.833	0.337936	0.11013	.	.	ENSG00000197037	ENST00000394152;ENST00000334715;ENST00000262941	T;T;T	0.08546	3.13;3.13;3.08	3.89	-0.099	0.13626	Krueppel-associated box (1);	0.823172	0.10196	N	0.704056	T	0.04952	0.0133	N	0.19112	0.55	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	T	0.47005	-0.9150	10	0.16896	T	0.51	-0.3209	7.6674	0.28439	0.0:0.5811:0.0:0.4189	.	205;277	Q6NSZ9-2;Q6NSZ9	.;ZN498_HUMAN	V	277;277;205	ENSP00000377708:A277V;ENSP00000334800:A277V;ENSP00000262941:A205V	ENSP00000262941:A205V	A	+	2	0	ZNF498	99064774	0.000000	0.05858	0.001000	0.08648	0.401000	0.30781	-1.281000	0.02802	-0.033000	0.13736	0.561000	0.74099	GCA	.	.		0.552	ZSCAN25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157203.4	NM_145115		T	99226838	C	T	99226838	3	4	322	1	0	0	0	0	1	0	0	0	17962	710	25	3	848	3	ZNF498	7	99226838	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	239299	99226838	59911825	91	45339										
MCM7	4176	hgsc.bcm.edu	37	chr7	99695002	99695002	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ccccatcagacagatgttgaTgttgcctggaggaagggaag	14	8	1	3			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr7:99695002T>C	ENST00000303887.5	-	10	1768	c.1123A>G	c.(1123-1125)Atc>Gtc	p.I375V	MCM7_ENST00000354230.3_Missense_Mutation_p.I199V|MCM7_ENST00000343023.6_Intron	NM_005916.3	NP_005907.3	P33993	MCM7_HUMAN	minichromosome maintenance complex component 7	375	MCM.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to epidermal growth factor stimulus (GO:0071364)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of phosphorylation (GO:0042325)|response to drug (GO:0042493)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|single-stranded DNA binding (GO:0003697)			endometrium(1)|kidney(5)|large_intestine(5)|lung(4)|ovary(1)|stomach(1)	17	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CAGATGTTGATGTTGCCTGGA	0.547																																					p.I375V		Atlas-SNP	.											.	MCM7	136	.	0			c.A1123G						.						114	96	102					7																	99695002		2203	4300	6503	SO:0001583	missense	4176	exon10			TGTTGATGTTGCC		CCDS5683.1, CCDS5684.1	7q21.3-q22.1	2014-06-12	2007-04-04		ENSG00000166508	ENSG00000166508			6950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 104"	600592	"minichromosome maintenance deficient (S. cerevisiae) 7", "MCM7 minichromosome maintenance deficient 7 (S. cerevisiae)"	MCM2		7842741	Standard	NM_005916		Approved	CDC47, PPP1R104	uc003usw.1	P33993	OTTHUMG00000154671	ENST00000303887.5:c.1123A>G	chr7.hg19:g.99695002T>C	ENSP00000307288:p.Ile375Val	37.0	0.0		96.0	21.0	NM_005916	A4D2A1|A4D2A2|E9PGN9|Q15076|Q96D34|Q96GL1	Missense_Mutation	SNP	ENST00000303887.5	hg19	CCDS5683.1	.	.	.	.	.	.	.	.	.	.	T	26.3	4.726663	0.89298	.	.	ENSG00000166508	ENST00000303887;ENST00000542483;ENST00000362082;ENST00000354230	T;T	0.10099	2.91;2.91	4.97	4.97	0.65823	ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	T	0.26919	0.0659	M	0.80982	2.52	0.80722	D	1	P	0.41848	0.763	P	0.51582	0.674	T	0.01294	-1.1393	10	0.52906	T	0.07	-20.3004	12.6646	0.56835	0.0:0.0:0.0:1.0	.	375	P33993	MCM7_HUMAN	V	375;312;268;199	ENSP00000307288:I375V;ENSP00000346171:I199V	ENSP00000307288:I375V	I	-	1	0	MCM7	99532938	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.708000	0.68377	2.083000	0.62718	0.533000	0.62120	ATC	.	.		0.547	MCM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336534.3			C	99695002	T	C	99695002	3	2	322	1	0	0	0	0	1	0	0	0	9401	1464	51	2	1060	2	MCM7	7	99695002	Missense_Mutation	SNP	T	TCGA-MI-A75G-01A-11D-A32G-10	468164	99695002	59443661	92	45340										
C7orf51	222950	hgsc.bcm.edu	37	chr7	100085812	100085812	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ccagagggccgagagtccagCcggaaggttcctccgcagaa	14	13	0	3	rs372170892		TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr7:100085812C>T	ENST00000300179.2	+	4	627	c.468C>T	c.(466-468)agC>agT	p.S156S	NYAP1_ENST00000423930.1_Silent_p.S156S|NYAP1_ENST00000454988.1_Silent_p.S99S	NM_173564.2	NP_775835.2	Q6ZVC0	NYAP1_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 1	156	Involved in CYFIP1- and NCKAP1-binding. {ECO:0000250}.				neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												GAGAGTCCAGCCGGAAGGTTC	0.597																																					p.S156S		Atlas-SNP	.											C7orf51,NS,carcinoma,0,1	.	.	.	0			c.C468T						.	C		0,4406		0,0,2203	111	126	121		468	4.4	1	7		121	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	C7orf51	NM_173564.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		156/842	100085812	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	222950	exon4			GTCCAGCCGGAAG	AK094857	CCDS5696.1	7q22.1	2011-11-30	2011-11-30	2011-11-30	ENSG00000166924	ENSG00000166924			22009	protein-coding gene	gene with protein product		615477	"chromosome 7 open reading frame 51", "KIAA1486-like"	C7orf51, KIAA1486L		21946561	Standard	NM_173564		Approved	FLJ37538	uc003uvd.2	Q6ZVC0	OTTHUMG00000155290	ENST00000300179.2:c.468C>T	chr7.hg19:g.100085812C>T		93.0	0.0		202.0	44.0	NM_173564	Q6U9Y3|Q8N1V0	Silent	SNP	ENST00000300179.2	hg19	CCDS5696.1																																																																																			.	.		0.597	NYAP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339335.2	NM_173564		T	100085812	C	T	100085812	2	4	322	1	0	0	0	0	0	0	0	1	2402	738	26	3		3	C7orf51	7	100085812	Silent	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	390810	100085812	59052851	93	45341										
FBXO24	26261	hgsc.bcm.edu	37	chr7	100190612	100190612	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	atcgtgctggttggtcaggaGacccagcgggctctactgct	14	11	2	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr7:100190612G>T	ENST00000241071.6	+	5	1087	c.765G>T	c.(763-765)gaG>gaT	p.E255D	FBXO24_ENST00000465843.1_Missense_Mutation_p.E241D|FBXO24_ENST00000427939.2_Missense_Mutation_p.E293D|PCOLCE-AS1_ENST00000442166.2_RNA|FBXO24_ENST00000360609.2_Missense_Mutation_p.E241D|PCOLCE-AS1_ENST00000544873.1_RNA|FBXO24_ENST00000468962.1_Missense_Mutation_p.E243D	NM_033506.2	NP_277041.1	O75426	FBX24_HUMAN	F-box protein 24	255					protein ubiquitination (GO:0016567)	ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|ovary(3)|skin(4)|urinary_tract(2)	28	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					TTGGTCAGGAGACCCAGCGGG	0.547																																					p.E293D		Atlas-SNP	.											.	FBXO24	125	.	0			c.G879T						.						79	64	69					7																	100190612		2203	4300	6503	SO:0001583	missense	26261	exon5			TCAGGAGACCCAG	AF174604	CCDS5698.1, CCDS5699.1, CCDS5699.2, CCDS55138.1	7q22	2005-10-07	2004-06-15		ENSG00000106336	ENSG00000106336		"F-boxes /  "other""	13595	protein-coding gene	gene with protein product		609097	"F-box only protein 24"			10531035, 10531037	Standard	NM_012172		Approved	FBX24	uc011kjz.1	O75426	OTTHUMG00000159543	ENST00000241071.6:c.765G>T	chr7.hg19:g.100190612G>T	ENSP00000241071:p.Glu255Asp	70.0	0.0		173.0	8.0	NM_012172	A4D2D4|B4DX91|B4DY42|Q9H0G1	Missense_Mutation	SNP	ENST00000241071.6	hg19	CCDS5698.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.691653	0.88735	.	.	ENSG00000106336	ENST00000241071;ENST00000360609;ENST00000465843;ENST00000468962;ENST00000427939	T;T;T;T;T	0.51574	2.33;0.7;0.7;2.33;2.31	5.74	5.74	0.90152	.	0.000000	0.64402	D	0.000004	T	0.50188	0.1601	N	0.08118	0	0.45390	D	0.998375	D;D;D;D	0.62365	0.991;0.991;0.991;0.99	P;P;P;D	0.72982	0.901;0.901;0.901;0.979	T	0.57365	-0.7824	10	0.46703	T	0.11	-31.9831	17.4859	0.87688	0.0:0.0:1.0:0.0	.	243;293;255;241	B4DY42;B4DX91;O75426;O75426-2	.;.;FBX24_HUMAN;.	D	255;241;241;243;293	ENSP00000241071:E255D;ENSP00000353821:E241D;ENSP00000419602:E241D;ENSP00000420239:E243D;ENSP00000416558:E293D	ENSP00000241071:E255D	E	+	3	2	FBXO24	100028548	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	4.450000	0.60041	2.740000	0.93945	0.558000	0.71614	GAG	.	.		0.547	FBXO24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356104.1			T	100190612	G	T	100190612	3	4	322	1	0	0	0	0	1	0	0	0	5743	933	33	3	940	3	FBXO24	7	100190612	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	104800	100190612	58948051	94	45342										
MOGAT3	346606	hgsc.bcm.edu	37	chr7	100839352	100839352	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ttcctcctcggtggggtggaGgcgctgggggacggggatgg	22	8	0	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr7:100839352G>A	ENST00000223114.4	-	7	1067	c.901C>T	c.(901-903)Ctc>Ttc	p.L301F	MOGAT3_ENST00000379423.3_Missense_Mutation_p.P233L|MOGAT3_ENST00000440203.2_Silent_p.A329A	NM_178176.2	NP_835470.1	Q86VF5	MOGT3_HUMAN	monoacylglycerol O-acyltransferase 3	301					glycerol metabolic process (GO:0006071)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	2-acylglycerol O-acyltransferase activity (GO:0003846)|diacylglycerol O-acyltransferase activity (GO:0004144)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(10)|ovary(3)	22	Lung NSC(181;0.168)|all_lung(186;0.215)					GTGGGGTGGAGGCGCTGGGGG	0.682																																					p.L301F		Atlas-SNP	.											.	MOGAT3	72	.	0			c.C901T						.						31	31	31					7																	100839352		2202	4300	6502	SO:0001583	missense	346606	exon7			GGTGGAGGCGCTG	AY229854	CCDS5714.1, CCDS75643.1	7q22	2012-09-06			ENSG00000106384	ENSG00000106384	2.3.1.20, 2.3.1.22		23249	protein-coding gene	gene with protein product		610184				12618427, 14970677	Standard	XM_005250309		Approved	DC7, MGAT3	uc003uyc.3	Q86VF5	OTTHUMG00000023328	ENST00000223114.4:c.901C>T	chr7.hg19:g.100839352G>A	ENSP00000223114:p.Leu301Phe	39.0	0.0		67.0	21.0	NM_178176	Q496A6|Q496A7|Q496A8|Q9UDW7	Missense_Mutation	SNP	ENST00000223114.4	hg19	CCDS5714.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.04|12.04	1.818533|1.818533	0.32145|0.32145	.|.	.|.	ENSG00000106384|ENSG00000106384	ENST00000223114|ENST00000379423	D|T	0.93763|0.29397	-3.28|1.57	5.02|5.02	0.732|0.732	0.18283|0.18283	.|.	1.147710|.	0.06542|.	N|.	0.743373|.	T|T	0.27454|0.27454	0.0674|0.0674	L|L	0.61218|0.61218	1.895|1.895	0.09310|0.09310	N|N	1|1	P|B	0.49696|0.25743	0.927|0.133	P|B	0.48952|0.25759	0.596|0.063	T|T	0.31081|0.31081	-0.9956|-0.9956	10|9	0.62326|0.62326	D|D	0.03|0.03	-9.5366|-9.5366	4.1772|4.1772	0.10358|0.10358	0.0844:0.272:0.4824:0.1612|0.0844:0.272:0.4824:0.1612	.|.	301|233	Q86VF5|Q86VF5-2	MOGT3_HUMAN|.	F|L	301|233	ENSP00000223114:L301F|ENSP00000368734:P233L	ENSP00000223114:L301F|ENSP00000368734:P233L	L|P	-|-	1|2	0|0	MOGAT3|MOGAT3	100626072|100626072	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.005000|0.005000	0.04900|0.04900	-0.007000|-0.007000	0.12810|0.12810	-0.164000|-0.164000	0.10927|0.10927	-0.145000|-0.145000	0.13849|0.13849	CTC|CCT	.	.		0.682	MOGAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059649.3	NM_178176		A	100839352	G	A	100839352	3	1	322	1	0	0	0	0	1	0	0	0	9705	1000	35	3	128	3	MOGAT3	7	100839352	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	648740	100839352	58299311	95	45343										
HBP1	26959	hgsc.bcm.edu	37	chr7	106820464	106820464	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cagtgtaatgagaatttgccAtcttcacctggatataactc	7	9	2	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr7:106820464A>G	ENST00000222574.4	+	2	312	c.126A>G	c.(124-126)ccA>ccG	p.P42P	HBP1_ENST00000468410.1_Silent_p.P42P|HBP1_ENST00000485846.1_Silent_p.P42P	NM_012257.3	NP_036389.2	O60381	HBP1_HUMAN	HMG-box transcription factor 1	42					cell cycle arrest (GO:0007050)|positive regulation of potassium ion transport (GO:0043268)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA binding (GO:0003723)			large_intestine(4)|lung(3)|prostate(1)|skin(2)	10						AGAATTTGCCATCTTCACCTG	0.378																																					p.P52P		Atlas-SNP	.											HBP1,NS,carcinoma,0,1	HBP1	31	.	0			c.A156G						.						144	139	141					7																	106820464		2203	4300	6503	SO:0001819	synonymous_variant	26959	exon2			TTTGCCATCTTCA	BC017069	CCDS5741.1	7q22-q31	2003-10-08			ENSG00000105856	ENSG00000105856			23200	protein-coding gene	gene with protein product						9030690, 11500377	Standard	NM_001244262		Approved		uc011klv.2	O60381	OTTHUMG00000157642	ENST00000222574.4:c.126A>G	chr7.hg19:g.106820464A>G		85.0	0.0		120.0	31.0	NM_001244262	B3KVB7|Q8TBM1|Q8TE93|Q96AJ2	Silent	SNP	ENST00000222574.4	hg19	CCDS5741.1																																																																																			.	.		0.378	HBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349297.1	NM_012257		G	106820464	A	G	106820464	2	3	322	1	0	0	0	0	0	0	0	1	6994	204	8	2		2	HBP1	7	106820464	Silent	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	5981112	106820464	52318199	96	45344										
RNF148	378925	hgsc.bcm.edu	37	chr7	122342607	122342620	+	Frame_Shift_Del	DEL	AGAATGATTCCCGA	AGAATGATTCCCGA	-													0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ccagacaccctttccagaggAgaatgattcccgaacactcc					rs544403291|rs142695415		TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	AGAATGATTCCCGA	AGAATGATTCCCGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr7:122342607_122342620delAGAATGATTCCCGA	ENST00000434824.1	-	1	401_414	c.185_198delTCGGGAATCATTCT	c.(184-198)ttcgggaatcattctfs	p.FGNHS62fs	RNF148_ENST00000447240.1_Intron|CADPS2_ENST00000313070.7_Intron|CADPS2_ENST00000334010.7_Intron|CADPS2_ENST00000412584.2_Intron|CADPS2_ENST00000449022.2_Intron	NM_198085.1	NP_932351.1	Q8N7C7	RN148_HUMAN	ring finger protein 148	62						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)	p.S66T(2)		endometrium(2)|kidney(1)|large_intestine(6)|lung(7)	16						TTTCCAGAGGAGAATGATTCCCGAACACTCCACT	0.467																																					p.62_67del		Atlas-Indel,Pindel	.											.	RNF148	71	.	2	Substitution - Missense(2)	lung(2)	c.186_199del						.																																			SO:0001589	frameshift_variant	378925	exon1			.	BC029264	CCDS47692.1	7q31.33	2013-01-09			ENSG00000235631	ENSG00000235631		"RING-type (C3HC4) zinc fingers"	22411	protein-coding gene	gene with protein product						8744354	Standard	NM_198085		Approved	MGC35222	uc003vkk.1	Q8N7C7	OTTHUMG00000157099	ENST00000434824.1:c.185_198delTCGGGAATCATTCT	chr7.hg19:g.122342607_122342620delAGAATGATTCCCGA	ENSP00000388207:p.Phe62fs	59.0	0.0		115.0	23.0	NM_198085	A4D0X4|Q8N308	Frame_Shift_Del	DEL	ENST00000434824.1	hg19	CCDS47692.1																																																																																			.	.		0.467	RNF148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347424.1	NM_198085		-	122342620	AGAATGATTCCCGA	-	122342607	7	5	322	1	0	1	0	1	0	0	0	0	13464	291	11	0	723	0	RNF148	7	122342607	Frame_Shift_Del	DEL	AGAATGATTCCCGA	TCGA-MI-A75G-01A-11D-A32G-10	15522143	122342607	36796056	97	45345										
PARP12	64761	hgsc.bcm.edu	37	chr7	139726111	139726111	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cagctgccgctcgtccacggCcttccctccgttctgcttct	8	19	2	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr7:139726111C>A	ENST00000263549.3	-	11	2539	c.1666G>T	c.(1666-1668)Gcc>Tcc	p.A556S		NM_022750.2	NP_073587.1	Q9H0J9	PAR12_HUMAN	poly (ADP-ribose) polymerase family, member 12	556	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.					nucleus (GO:0005634)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(1)	19	Melanoma(164;0.0142)					TCGTCCACGGCCTTCCCTCCG	0.582																																					p.A556S		Atlas-SNP	.											.	PARP12	59	.	0			c.G1666T						.						97	89	92					7																	139726111		2203	4300	6503	SO:0001583	missense	64761	exon11			CCACGGCCTTCCC	AL136766	CCDS5857.1	7q34	2014-01-28	2005-06-02	2005-06-02	ENSG00000059378	ENSG00000059378		"Zinc fingers, CCCH-type domain containing", "Poly (ADP-ribose) polymerases"	21919	protein-coding gene	gene with protein product		612481	"zinc finger CCCH-type domain containing 1"	ZC3HDC1		11230166, 12851707	Standard	NM_022750		Approved	FLJ22693, PARP-12, ZC3H1	uc003vvl.1	Q9H0J9	OTTHUMG00000157315	ENST00000263549.3:c.1666G>T	chr7.hg19:g.139726111C>A	ENSP00000263549:p.Ala556Ser	41.0	0.0		95.0	16.0	NM_022750	Q9H610|Q9NP36|Q9NTI3	Missense_Mutation	SNP	ENST00000263549.3	hg19	CCDS5857.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	c|c|c	7.093|7.093|7.093	0.572570|0.572570|0.572570	0.13623|0.13623|0.13623	.|.|.	.|.|.	ENSG00000059378|ENSG00000059378|ENSG00000059378	ENST00000263549|ENST00000489809|ENST00000484111	T|T|.	0.06142|0.53206|.	3.34|0.63|.	4.77|4.77|4.77	-0.402|-0.402|-0.402	0.12404|0.12404|0.12404	Poly(ADP-ribose) polymerase, catalytic domain (2);|.|.	1.698970|.|.	0.03082|.|.	N|.|.	0.158679|.|.	T|T|T	0.12433|0.12433|0.12433	0.0302|0.0302|0.0302	N|N|N	0.02286|0.02286|0.02286	-0.61|-0.61|-0.61	0.09310|0.09310|0.09310	N|N|N	1|1|1	B|.|.	0.09022|.|.	0.002|.|.	B|.|.	0.20184|.|.	0.028|.|.	T|T|T	0.30995|0.30995|0.30995	-0.9959|-0.9959|-0.9959	10|7|5	0.09590|0.31617|.	T|T|.	0.72|0.26|.	.|.|.	8.3507|8.3507|8.3507	0.32301|0.32301|0.32301	0.0:0.7035:0.1111:0.1854|0.0:0.7035:0.1111:0.1854|0.0:0.7035:0.1111:0.1854	.|.|.	556|.|.	Q9H0J9|.|.	PAR12_HUMAN|.|.	S|V|S	556|150|27	ENSP00000263549:A556S|ENSP00000417606:G150V|.	ENSP00000263549:A556S|ENSP00000417606:G150V|.	A|G|R	-|-|-	1|2|3	0|0|2	PARP12|PARP12|PARP12	139372580|139372580|139372580	0.000000|0.000000|0.000000	0.05858|0.05858|0.05858	0.000000|0.000000|0.000000	0.03702|0.03702|0.03702	0.722000|0.722000|0.722000	0.41435|0.41435|0.41435	-0.350000|-0.350000|-0.350000	0.07721|0.07721|0.07721	-0.430000|-0.430000|-0.430000	0.07318|0.07318|0.07318	0.461000|0.461000|0.461000	0.40582|0.40582|0.40582	GCC|GGC|AGG	.	.		0.582	PARP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348413.1	NM_022750		A	139726111	C	A	139726111	3	1	322	1	0	0	0	0	1	0	0	0	11466	739	26	3	447	3	PARP12	7	139726111	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	17383504	139726111	19412552	98	45346										
GIMAP6	474344	hgsc.bcm.edu	37	chr7	150327197	150327197	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cagctcttctgggggattctCctggggaatttgttcatatt	11	8	4	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr7:150327197C>A	ENST00000328902.5	-	2	250	c.34G>T	c.(34-36)Gag>Tag	p.E12*	GIMAP6_ENST00000493969.1_Nonsense_Mutation_p.E12*	NM_001244072.1|NM_024711.5	NP_001231001.1|NP_078987.3	Q6P9H5	GIMA6_HUMAN	GTPase, IMAP family member 6	12						cytosol (GO:0005829)	GTP binding (GO:0005525)			endometrium(4)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	29			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GGGGGATTCTCCTGGGGAATT	0.423																																					p.E12X		Atlas-SNP	.											.	GIMAP6	60	.	0			c.G34T						.						137	141	140					7																	150327197		2203	4300	6503	SO:0001587	stop_gained	474344	exon2			GATTCTCCTGGGG	AK026343	CCDS34778.1, CCDS59087.1, CCDS75676.1	7q36.1	2014-04-04			ENSG00000133561	ENSG00000133561		"GTPases, IMAP"	21918	protein-coding gene	gene with protein product	"immune-associated nucleotide-binding protein 6"					15474311	Standard	NM_001244072		Approved	FLJ22690, IAN6	uc022apv.1	Q6P9H5	OTTHUMG00000159137	ENST00000328902.5:c.34G>T	chr7.hg19:g.150327197C>A	ENSP00000330374:p.Glu12*	45.0	0.0		106.0	11.0	NM_001244072	C9J7B6|D3DWZ4|Q5ZPR6|Q9H612	Nonsense_Mutation	SNP	ENST00000328902.5	hg19	CCDS34778.1	.	.	.	.	.	.	.	.	.	.	c	15.28	2.786960	0.49997	.	.	ENSG00000133561	ENST00000328902;ENST00000477013;ENST00000493969	.	.	.	2.69	0.803	0.18691	.	.	.	.	.	.	.	.	.	.	.	0.52099	D	0.999947	.	.	.	.	.	.	.	.	.	.	0.19590	T	0.45	.	4.4641	0.11680	0.0:0.6578:0.0:0.3422	.	.	.	.	X	12	.	ENSP00000330374:E12X	E	-	1	0	GIMAP6	149958130	0.003000	0.15002	0.006000	0.13384	0.001000	0.01503	0.307000	0.19296	0.221000	0.20879	-0.265000	0.10407	GAG	.	.		0.423	GIMAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353457.1	NM_024711		A	150327197	C	A	150327197	4	1	322	1	0	0	0	0	0	1	0	0	6391	864	30	3	852	3	GIMAP6	7	150327197	Nonsense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	10601086	150327197	8811466	99	45347										
PRKAG2	51422	hgsc.bcm.edu	37	chr7	151254299	151254299	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cacggcggtcactccgtttcTgtctccttttgtttggcacc	9	14	3	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr7:151254299T>C	ENST00000287878.4	-	16	2202	c.1698A>G	c.(1696-1698)acA>acG	p.T566T	PRKAG2_ENST00000392801.2_Silent_p.T522T|PRKAG2_ENST00000492843.1_Silent_p.T442T|PRKAG2_ENST00000433631.2_Silent_p.T441T|PRKAG2_ENST00000418337.2_Silent_p.T325T	NM_016203.3	NP_057287.2	Q9UGJ0	AAKG2_HUMAN	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	566					ATP biosynthetic process (GO:0006754)|carnitine shuttle (GO:0006853)|cell cycle arrest (GO:0007050)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|glycogen metabolic process (GO:0005977)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase activity (GO:0045860)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of fatty acid metabolic process (GO:0019217)|regulation of fatty acid oxidation (GO:0046320)|regulation of glucose import (GO:0046324)|regulation of glycolytic process (GO:0006110)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)	ADP binding (GO:0043531)|AMP binding (GO:0016208)|ATP binding (GO:0005524)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|phosphorylase kinase regulator activity (GO:0008607)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|upper_aerodigestive_tract(1)	26	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)	Acetylsalicylic acid(DB00945)	ACTCCGTTTCTGTCTCCTTTT	0.498																																					p.T566T		Atlas-SNP	.											.	PRKAG2	86	.	0			c.A1698G						.						235	221	226					7																	151254299		2203	4300	6503	SO:0001819	synonymous_variant	51422	exon16			CGTTTCTGTCTCC	AF087875	CCDS5928.1, CCDS43683.1, CCDS47752.1	7q35-q36	2014-09-17			ENSG00000106617	ENSG00000106617			9386	protein-coding gene	gene with protein product	"AMPK gamma2"	602743				8557660, 8621499	Standard	NM_024429		Approved	AAKG, AAKG2, H91620p, WPWS, CMH6	uc003wkk.3	Q9UGJ0	OTTHUMG00000157324	ENST00000287878.4:c.1698A>G	chr7.hg19:g.151254299T>C		75.0	0.0		177.0	36.0	NM_016203	Q53Y07|Q6NUI0|Q75MP4|Q9NUZ9|Q9UDN8|Q9ULX8	Silent	SNP	ENST00000287878.4	hg19	CCDS5928.1																																																																																			.	.		0.498	PRKAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348440.2	NM_016203		C	151254299	T	C	151254299	2	2	322	1	0	0	0	0	0	0	0	1	12513	1567	55	2		2	PRKAG2	7	151254299	Silent	SNP	T	TCGA-MI-A75G-01A-11D-A32G-10	927102	151254299	7884364	100	45348										
UBE3C	9690	hgsc.bcm.edu	37	chr7	156974809	156974809	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ttttctttttcaggcaacaaGtttttacagccttcacagag	6	9	3	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr7:156974809G>C	ENST00000348165.5	+	8	1138	c.778G>C	c.(778-780)Gtt>Ctt	p.V260L	UBE3C_ENST00000389103.4_Missense_Mutation_p.V217L	NM_014671.2	NP_055486.2	Q15386	UBE3C_HUMAN	ubiquitin protein ligase E3C	260					protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(2)|endometrium(3)|kidney(16)|large_intestine(13)|lung(25)|ovary(2)|prostate(1)|urinary_tract(1)	63		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)		CAGGCAACAAGTTTTTACAGC	0.368																																					p.V260L		Atlas-SNP	.											.	UBE3C	124	.	0			c.G778C						.						71	76	75					7																	156974809		2203	4300	6503	SO:0001583	missense	9690	exon8			CAACAAGTTTTTA	AK127280	CCDS34789.1	7q36.3	2004-05-04			ENSG00000009335	ENSG00000009335			16803	protein-coding gene	gene with protein product		614454				7584026, 11278995	Standard	NM_014671		Approved	KIAA0010, KIAA10	uc010lqs.3	Q15386	OTTHUMG00000157239	ENST00000348165.5:c.778G>C	chr7.hg19:g.156974809G>C	ENSP00000309198:p.Val260Leu	76.0	0.0		148.0	24.0	NM_014671	A4D235|A6NCP3|Q8TC15|Q96CR4|Q9UDU3	Missense_Mutation	SNP	ENST00000348165.5	hg19	CCDS34789.1	.	.	.	.	.	.	.	.	.	.	G	15.64	2.894760	0.52121	.	.	ENSG00000009335	ENST00000348165;ENST00000389103	T	0.53423	0.62	5.08	4.07	0.47477	.	0.130780	0.56097	D	0.000040	T	0.40619	0.1124	M	0.62723	1.935	0.58432	D	0.999994	B;B;B	0.33739	0.085;0.422;0.251	B;B;B	0.37422	0.026;0.221;0.249	T	0.15838	-1.0423	10	0.13853	T	0.58	.	6.011	0.19575	0.2356:0.0:0.7644:0.0	.	260;260;217	Q15386;Q15386-2;Q15386-3	UBE3C_HUMAN;.;.	L	260;217	ENSP00000309198:V260L	ENSP00000309198:V260L	V	+	1	0	UBE3C	156667570	1.000000	0.71417	0.952000	0.39060	0.779000	0.44077	3.643000	0.54374	2.366000	0.80165	0.455000	0.32223	GTT	.	.		0.368	UBE3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348108.1	NM_014671		C	156974809	G	C	156974809	3	2	322	1	0	0	0	0	1	0	0	0	16896	1029	36	4	808	4	UBE3C	7	156974809	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	5720510	156974809	2163854	101	45349										
RP1L1	94137	hgsc.bcm.edu	37	chr8	10470654	10470654	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	atctccacggacaggctgccGtcctcattcatgcggacctt	9	15	3	0	rs200317816	byFrequency	TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr8:10470654G>A	ENST00000382483.3	-	4	1177	c.954C>T	c.(952-954)gaC>gaT	p.D318D		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	318					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		ACAGGCTGCCGTCCTCATTCA	0.662													G|||	39	0.00778754	0	0	5008	,	,		16661	0		0	False		,,,				2504	0.0399				p.D318D		Atlas-SNP	.											.	RP1L1	453	.	0			c.C954T						.	G		0,4274		0,0,2137	84	93	90		954	-10.9	0.2	8		90	3,8481		0,3,4239	no	coding-synonymous	RP1L1	NM_178857.5		0,3,6376	AA,AG,GG		0.0354,0.0,0.0235		318/2401	10470654	3,12755	2137	4242	6379	SO:0001819	synonymous_variant	94137	exon4			GCTGCCGTCCTCA	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.954C>T	chr8.hg19:g.10470654G>A		57.0	0.0		95.0	44.0	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	hg19	CCDS43708.1																																																																																			.	G|0.999;A|0.001		0.662	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			A	10470654	G	A	10470654	2	1	322	1	0	0	0	0	0	0	0	1	13548	1136	40	1		1	RP1L1	8	10470654	Silent	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10		10470654	135893368	102	45350										
CTSB	1508	hgsc.bcm.edu	37	chr8	11705647	11705647	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	agttccaagcttcagcaggaTagccaccattacagctgaaa	8	11	1	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr8:11705647T>C	ENST00000353047.6	-	6	714	c.461A>G	c.(460-462)tAt>tGt	p.Y154C	RP11-589N15.2_ENST00000602711.1_RNA|CTSB_ENST00000345125.3_Missense_Mutation_p.Y154C|CTSB_ENST00000531089.1_Missense_Mutation_p.Y154C|CTSB_ENST00000534510.1_Missense_Mutation_p.Y154C|CTSB_ENST00000525076.1_5'Flank|CTSB_ENST00000415599.2_3'UTR|CTSB_ENST00000530640.2_Missense_Mutation_p.Y154C|CTSB_ENST00000453527.2_Missense_Mutation_p.Y154C|CTSB_ENST00000434271.1_Missense_Mutation_p.Y154C|CTSB_ENST00000533455.1_Missense_Mutation_p.Y154C	NM_001908.3	NP_001899.1	P07858	CATB_HUMAN	cathepsin B	154					cellular response to thyroid hormone stimulus (GO:0097067)|collagen catabolic process (GO:0030574)|decidualization (GO:0046697)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of apoptotic process (GO:0042981)|regulation of catalytic activity (GO:0050790)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|perinuclear region of cytoplasm (GO:0048471)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|proteoglycan binding (GO:0043394)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(1)	16	all_epithelial(15;0.205)		STAD - Stomach adenocarcinoma(15;0.00546)	COAD - Colon adenocarcinoma(149;0.184)		TTCAGCAGGATAGCCACCATT	0.522																																					p.Y154C		Atlas-SNP	.											.	CTSB	24	.	0			c.A461G						.						93	90	91					8																	11705647		2203	4300	6503	SO:0001583	missense	1508	exon8			GCAGGATAGCCAC	M14221	CCDS5986.1	8p23.1	2012-10-02			ENSG00000164733	ENSG00000164733	3.4.22.1	"Cathepsins"	2527	protein-coding gene	gene with protein product		116810				8112600, 3463996	Standard	XM_006716244		Approved		uc003wuq.3	P07858	OTTHUMG00000090799	ENST00000353047.6:c.461A>G	chr8.hg19:g.11705647T>C	ENSP00000345672:p.Tyr154Cys	54.0	0.0		78.0	38.0	NM_147780	B3KQR5|B3KRR5|Q503A6|Q96D87	Missense_Mutation	SNP	ENST00000353047.6	hg19	CCDS5986.1	.	.	.	.	.	.	.	.	.	.	T	14.11	2.438647	0.43326	.	.	ENSG00000164733	ENST00000434271;ENST00000540571;ENST00000353047;ENST00000530640;ENST00000531089;ENST00000453527;ENST00000345125;ENST00000533455;ENST00000534510;ENST00000541328;ENST00000534636;ENST00000533572;ENST00000530296	D;D;D;D;D;D;D;D;D;D;D	0.84800	-1.9;-1.9;-1.9;-1.9;-1.9;-1.9;-1.9;-1.9;-1.9;-1.9;-1.9	5.14	2.58	0.30949	Peptidase C1A, papain C-terminal (2);	0.112402	0.64402	D	0.000007	D	0.92548	0.7633	M	0.92026	3.265	0.80722	D	1	D;B;B;D;D	0.89917	1.0;0.043;0.086;1.0;1.0	D;B;B;D;D	0.79108	0.992;0.113;0.091;0.978;0.985	D	0.92301	0.5849	10	0.72032	D	0.01	.	10.0057	0.41955	0.231:0.0:0.0:0.769	.	91;154;60;154;91	B3KUJ8;A8K2H4;B4DMY4;P07858;F5H2P9	.;.;.;CATB_HUMAN;.	C	154;91;154;154;154;154;154;154;154;60;154;154;154	ENSP00000415889:Y154C;ENSP00000345672:Y154C;ENSP00000435105:Y154C;ENSP00000433215:Y154C;ENSP00000409917:Y154C;ENSP00000342070:Y154C;ENSP00000432244:Y154C;ENSP00000434217:Y154C;ENSP00000436159:Y154C;ENSP00000433995:Y154C;ENSP00000435074:Y154C	ENSP00000342070:Y154C	Y	-	2	0	CTSB	11743056	0.993000	0.37304	0.998000	0.56505	0.359000	0.29487	1.174000	0.31932	0.789000	0.33779	0.459000	0.35465	TAT	.	.		0.522	CTSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207586.3	NM_147780		C	11705647	T	C	11705647	3	2	322	1	0	0	0	0	1	0	0	0	4032	1406	49	2	578	2	CTSB	8	11705647	Missense_Mutation	SNP	T	TCGA-MI-A75G-01A-11D-A32G-10	1234993	11705647	134658375	103	45351										
TUSC3	7991	hgsc.bcm.edu	37	chr8	15480657	15480657	+	Missense_Mutation	SNP	T	T	G													0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cgctcaatcttccgaatgaaTggtgataaattccgaaaatt							TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr8:15480657T>G	ENST00000503731.1	+	2	355	c.207T>G	c.(205-207)aaT>aaG	p.N69K	TUSC3_ENST00000382020.4_Missense_Mutation_p.N69K|TUSC3_ENST00000503191.1_3'UTR|TUSC3_ENST00000506802.1_Missense_Mutation_p.N69K|TUSC3_ENST00000509380.1_Missense_Mutation_p.N69K	NM_006765.3	NP_006756.2	Q13454	TUSC3_HUMAN	tumor suppressor candidate 3	69	Thioredoxin.				cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cognition (GO:0050890)|magnesium ion transport (GO:0015693)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|oligosaccharyltransferase complex (GO:0008250)	magnesium ion transmembrane transporter activity (GO:0015095)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(10)|ovary(2)	28				Colorectal(111;0.113)		TCCGAATGAATGGTGATAAAT	0.393																																					p.N69K		Atlas-SNP	.											.	TUSC3	98	.	0			c.T207G						.						81	81	81					8																	15480657		2203	4300	6503	SO:0001583	missense	7991	exon2			AATGAATGGTGAT	AK026149	CCDS5993.1, CCDS5994.1	8p22	2010-10-22			ENSG00000104723	ENSG00000104723			30242	protein-coding gene	gene with protein product	"oligosaccharyltransferase 3 homolog A (S. cerevisiae)"	601385				8661104, 10097140	Standard	NM_178234		Approved	MGC13453, N33, OST3A, MRT7	uc003wwt.3	Q13454	OTTHUMG00000094803	ENST00000503731.1:c.207T>G	chr8.hg19:g.15480657T>G	ENSP00000424544:p.Asn69Lys	66.0	0.0		93.0	34.0	NM_178234	A8MSM0|D3DSP2|Q14911|Q14912|Q96FW0	Missense_Mutation	SNP	ENST00000503731.1	hg19	CCDS5994.1	.	.	.	.	.	.	.	.	.	.	T	19.46	3.832711	0.71258	.	.	ENSG00000104723	ENST00000382020;ENST00000506802;ENST00000509380;ENST00000503731	T;T;T;T	0.41758	0.99;0.99;0.99;0.99	5.59	1.74	0.24563	Thioredoxin domain (1);Thioredoxin-like fold (2);	0.085998	0.85682	D	0.000000	T	0.62780	0.2456	M	0.85945	2.785	0.52099	D	0.999943	D;D;D;D;D;D	0.76494	0.969;0.998;0.989;0.999;0.994;0.999	D;D;D;D;D;D	0.83275	0.968;0.969;0.979;0.983;0.95;0.996	T	0.62426	-0.6857	10	0.51188	T	0.08	-22.2402	8.9569	0.35823	0.0:0.3572:0.0:0.6428	.	69;69;69;69;69;69	D6RDV0;D6RIY7;Q13454-2;Q13454;D6RA37;A8MSM0	.;.;.;TUSC3_HUMAN;.;.	K	69	ENSP00000371450:N69K;ENSP00000425777:N69K;ENSP00000423426:N69K;ENSP00000424544:N69K	ENSP00000221167:N69K	N	+	3	2	TUSC3	15525028	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.591000	0.23969	0.433000	0.26313	0.528000	0.53228	AAT	.	.		0.393	TUSC3-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365367.1	NM_006765		G	15480657	T	G	15480657	3	3	322	1	0	0	0	0	1	0	0	0	16793	1461	51	5	213	5	TUSC3	8	15480657	Missense_Mutation	SNP	T	TCGA-MI-A75G-01A-11D-A32G-10	3775010	15480657	130883365	104	45352	238	2								
TUSC3	7991	hgsc.bcm.edu	37	chr8	15480659	15480659	+	Missense_Mutation	SNP	G	G	T													0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ctcaatcttccgaatgaatgGtgataaattccgaaaattta							TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr8:15480659G>T	ENST00000503731.1	+	2	357	c.209G>T	c.(208-210)gGt>gTt	p.G70V	TUSC3_ENST00000382020.4_Missense_Mutation_p.G70V|TUSC3_ENST00000503191.1_3'UTR|TUSC3_ENST00000506802.1_Missense_Mutation_p.G70V|TUSC3_ENST00000509380.1_Missense_Mutation_p.G70V	NM_006765.3	NP_006756.2	Q13454	TUSC3_HUMAN	tumor suppressor candidate 3	70	Thioredoxin.				cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cognition (GO:0050890)|magnesium ion transport (GO:0015693)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|oligosaccharyltransferase complex (GO:0008250)	magnesium ion transmembrane transporter activity (GO:0015095)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(10)|ovary(2)	28				Colorectal(111;0.113)		CGAATGAATGGTGATAAATTC	0.403																																					p.G70V		Atlas-SNP	.											.	TUSC3	98	.	0			c.G209T						.						81	82	81					8																	15480659		2203	4300	6503	SO:0001583	missense	7991	exon2			TGAATGGTGATAA	AK026149	CCDS5993.1, CCDS5994.1	8p22	2010-10-22			ENSG00000104723	ENSG00000104723			30242	protein-coding gene	gene with protein product	"oligosaccharyltransferase 3 homolog A (S. cerevisiae)"	601385				8661104, 10097140	Standard	NM_178234		Approved	MGC13453, N33, OST3A, MRT7	uc003wwt.3	Q13454	OTTHUMG00000094803	ENST00000503731.1:c.209G>T	chr8.hg19:g.15480659G>T	ENSP00000424544:p.Gly70Val	67.0	0.0		91.0	33.0	NM_178234	A8MSM0|D3DSP2|Q14911|Q14912|Q96FW0	Missense_Mutation	SNP	ENST00000503731.1	hg19	CCDS5994.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.643729	0.87859	.	.	ENSG00000104723	ENST00000382020;ENST00000506802;ENST00000509380;ENST00000503731	T;T;T;T	0.41400	1.0;1.0;1.0;1.0	5.59	5.59	0.84812	Thioredoxin domain (1);Thioredoxin-like fold (2);	0.000000	0.85682	D	0.000000	T	0.67998	0.2953	M	0.80847	2.515	0.80722	D	1	D;P;D;P;P;D	0.89917	1.0;0.949;1.0;0.949;0.949;1.0	D;P;D;P;P;D	0.97110	0.999;0.837;0.998;0.771;0.837;1.0	T	0.67150	-0.5743	10	0.44086	T	0.13	-16.7342	18.9566	0.92661	0.0:0.0:1.0:0.0	.	70;70;70;70;70;70	D6RDV0;D6RIY7;Q13454-2;Q13454;D6RA37;A8MSM0	.;.;.;TUSC3_HUMAN;.;.	V	70	ENSP00000371450:G70V;ENSP00000425777:G70V;ENSP00000423426:G70V;ENSP00000424544:G70V	ENSP00000221167:G70V	G	+	2	0	TUSC3	15525030	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.476000	0.97823	2.804000	0.96469	0.650000	0.86243	GGT	.	.		0.403	TUSC3-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365367.1	NM_006765		T	15480659	G	T	15480659	3	4	322	1	0	0	0	0	1	0	0	0	16793	1261	44	3	215	3	TUSC3	8	15480659	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	2	15480659	130883363	105	45353	238	2								
MTMR7	9108	hgsc.bcm.edu	37	chr8	17228586	17228586	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	agggagatgtacacgtcgtgGcaatctctttcctgaggtat	12	8	1	2	rs368887856		TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr8:17228586G>T	ENST00000180173.5	-	3	304	c.270C>A	c.(268-270)tgC>tgA	p.C90*	MTMR7_ENST00000521857.1_Nonsense_Mutation_p.C90*	NM_004686.4	NP_004677.3	Q9Y216	MTMR7_HUMAN	myotubularin related protein 7	90					inositol phosphate dephosphorylation (GO:0046855)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|liver(1)|lung(8)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	32				Colorectal(111;0.112)		ACACGTCGTGGCAATCTCTTT	0.468																																					p.C90X		Atlas-SNP	.											MTMR7,NS,carcinoma,0,1	MTMR7	75	.	0			c.C270A						.	G	stop/CYS	0,4406		0,0,2203	154	139	144		270	4.3	1	8		144	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained	MTMR7	NM_004686.4		0,1,6502	TT,TG,GG		0.0116,0.0,0.0077		90/661	17228586	1,13005	2203	4300	6503	SO:0001587	stop_gained	9108	exon3			GTCGTGGCAATCT	AF073482	CCDS34851.1	8p22	2011-06-09			ENSG00000003987	ENSG00000003987		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7454	protein-coding gene	gene with protein product		603562				9736772, 12890864	Standard	NM_004686		Approved		uc003wxm.3	Q9Y216	OTTHUMG00000163771	ENST00000180173.5:c.270C>A	chr8.hg19:g.17228586G>T	ENSP00000180173:p.Cys90*	79.0	0.0		106.0	35.0	NM_004686	A1L4K9|B4DG87|Q68DX4	Nonsense_Mutation	SNP	ENST00000180173.5	hg19	CCDS34851.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.359020	0.82353	0.0	1.16E-4	ENSG00000003987	ENST00000180173;ENST00000521857	.	.	.	5.23	4.35	0.52113	.	0.135141	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.9859	0.64334	0.0736:0.0:0.9264:0.0	.	.	.	.	X	90	.	ENSP00000180173:C90X	C	-	3	2	MTMR7	17272957	1.000000	0.71417	0.998000	0.56505	0.515000	0.34225	1.678000	0.37586	1.326000	0.45319	0.655000	0.94253	TGC	.	.		0.468	MTMR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375311.1	NM_004686		T	17228586	G	T	17228586	4	4	322	1	0	0	0	0	0	1	0	0	9957	1195	42	3	1760	3	MTMR7	8	17228586	Nonsense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	1747927	17228586	129135436	106	45354										
CA8	767	hgsc.bcm.edu	37	chr8	61135274	61135274	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	acaccttcactgcaaggtggGatggtgagagagccttcata	12	9	2	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr8:61135274G>T	ENST00000317995.4	-	7	936	c.672C>A	c.(670-672)atC>atA	p.I224I	CA8_ENST00000528666.1_5'UTR	NM_004056.4	NP_004047.3	P35219	CAH8_HUMAN	carbonic anhydrase VIII	224					one-carbon metabolic process (GO:0006730)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasm (GO:0005737)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(5)|lung(6)|prostate(2)|skin(1)	16		all_cancers(86;0.172)|all_epithelial(80;0.0383)|all_lung(136;0.0413)|Lung NSC(129;0.0474)			Zonisamide(DB00909)	TGCAAGGTGGGATGGTGAGAG	0.463																																					p.I224I		Atlas-SNP	.											.	CA8	31	.	0			c.C672A						.						119	109	112					8																	61135274		2203	4300	6503	SO:0001819	synonymous_variant	767	exon7			AGGTGGGATGGTG	L04656	CCDS6174.1	8q12.1	2012-08-21			ENSG00000178538	ENSG00000178538		"Carbonic anhydrases"	1382	protein-coding gene	gene with protein product		114815		CALS		17219437	Standard	NM_004056		Approved	CARP	uc003xtz.1	P35219	OTTHUMG00000165325	ENST00000317995.4:c.672C>A	chr8.hg19:g.61135274G>T		62.0	0.0		69.0	28.0	NM_004056	A8K0A5|B3KQZ7|Q32MY2	Silent	SNP	ENST00000317995.4	hg19	CCDS6174.1																																																																																			.	.		0.463	CA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383445.1			T	61135274	G	T	61135274	2	4	322	1	0	0	0	0	0	0	0	1	2525	1164	41	3		3	CA8	8	61135274	Silent	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	43906688	61135274	85228748	107	45355										
EYA1	2138	hgsc.bcm.edu	37	chr8	72211880	72211880	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ctttttaaattacctgctgtGaactattaaatccagaggaa	6	7	0	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr8:72211880G>A	ENST00000340726.3	-	8	1271	c.632C>T	c.(631-633)tCa>tTa	p.S211L	EYA1_ENST00000388743.2_Missense_Mutation_p.S210L|EYA1_ENST00000388740.3_Missense_Mutation_p.S178L|EYA1_ENST00000303824.7_Missense_Mutation_p.S205L|EYA1_ENST00000388741.2_Missense_Mutation_p.S177L|EYA1_ENST00000419131.1_Missense_Mutation_p.S206L|EYA1_ENST00000388742.4_Missense_Mutation_p.S211L	NM_000503.4	NP_000494.2	Q99502	EYA1_HUMAN	EYA transcriptional coactivator and phosphatase 1	211					anatomical structure morphogenesis (GO:0009653)|aorta morphogenesis (GO:0035909)|branching involved in ureteric bud morphogenesis (GO:0001658)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|double-strand break repair (GO:0006302)|embryonic skeletal system morphogenesis (GO:0048704)|establishment of mitotic spindle orientation (GO:0000132)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|histone dephosphorylation (GO:0016576)|lung epithelial cell differentiation (GO:0060487)|metanephros development (GO:0001656)|middle ear morphogenesis (GO:0042474)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|neuron fate specification (GO:0048665)|otic vesicle morphogenesis (GO:0071600)|outer ear morphogenesis (GO:0042473)|outflow tract morphogenesis (GO:0003151)|pattern specification process (GO:0007389)|pharyngeal system development (GO:0060037)|positive regulation of DNA repair (GO:0045739)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of neuron differentiation (GO:0045664)|response to ionizing radiation (GO:0010212)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|striated muscle tissue development (GO:0014706)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)|RNA binding (GO:0003723)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(15)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	44	Breast(64;0.046)		Epithelial(68;0.0837)|all cancers(69;0.247)			TACCTGCTGTGAACTATTAAA	0.289																																					p.S211L		Atlas-SNP	.											.	EYA1	108	.	0			c.C632T	GRCh37	CM044880	EYA1	M		.						112	121	118					8																	72211880		2203	4299	6502	SO:0001583	missense	2138	exon8			TGCTGTGAACTAT	AJ000098	CCDS34906.1, CCDS34907.1, CCDS47873.1, CCDS75750.1	8q13.3	2014-06-19	2014-06-19		ENSG00000104313	ENSG00000104313		"Protein tyrosine phosphatases / Asp-based PTPs"	3519	protein-coding gene	gene with protein product		601653	"eyes absent (Drosophila) homolog 1", "eyes absent homolog 1 (Drosophila)"	BOR		9020840	Standard	XM_005251184		Approved		uc003xys.4	Q99502	OTTHUMG00000149894	ENST00000340726.3:c.632C>T	chr8.hg19:g.72211880G>A	ENSP00000342626:p.Ser211Leu	58.0	0.0		90.0	14.0	NM_000503	A6NHQ0|G5E9R4|Q0P516|Q8WX80	Missense_Mutation	SNP	ENST00000340726.3	hg19	CCDS34906.1	.	.	.	.	.	.	.	.	.	.	G	19.56	3.850367	0.71719	.	.	ENSG00000104313	ENST00000388742;ENST00000340726;ENST00000388744;ENST00000388740;ENST00000303824;ENST00000388741;ENST00000388743;ENST00000419131	D;D;D;D;D;D;D	0.82526	-1.62;-1.62;-1.62;-1.62;-1.62;-1.62;-1.62	5.56	5.56	0.83823	.	0.118168	0.64402	D	0.000019	D	0.82765	0.5108	L	0.57536	1.79	0.58432	D	0.999999	B;B;B;B;B	0.29805	0.091;0.257;0.125;0.18;0.053	B;B;B;B;B	0.31946	0.079;0.096;0.138;0.108;0.138	T	0.79962	-0.1582	10	0.44086	T	0.13	-14.3784	19.8772	0.96880	0.0:0.0:1.0:0.0	.	205;138;178;211;206	A6NCB9;Q0P517;Q99502-2;Q99502;G5E9R4	.;.;.;EYA1_HUMAN;.	L	211;211;179;178;205;177;210;206	ENSP00000373394:S211L;ENSP00000342626:S211L;ENSP00000373392:S178L;ENSP00000303221:S205L;ENSP00000373393:S177L;ENSP00000373395:S210L;ENSP00000410176:S206L	ENSP00000303221:S205L	S	-	2	0	EYA1	72374434	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.388000	0.97237	2.774000	0.95407	0.585000	0.79938	TCA	.	.		0.289	EYA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313788.2	NM_000503, NM_172060		A	72211880	G	A	72211880	3	1	322	1	0	0	0	0	1	0	0	0	5330	1294	45	3	1190	3	EYA1	8	72211880	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	11076606	72211880	74152142	108	45356										
CTHRC1	115908	hgsc.bcm.edu	37	chr8	104384015	104384015	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gcaaaaggcgcagctccggcAgagggaggtggtggacctgg	19	9	0	1	rs387907029		TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr8:104384015A>G	ENST00000330295.5	+	1	273	c.131A>G	c.(130-132)cAg>cGg	p.Q44R	CTHRC1_ENST00000415886.2_Missense_Mutation_p.Q44R|CTHRC1_ENST00000520337.1_5'Flank	NM_138455.3	NP_612464.1	Q96CG8	CTHR1_HUMAN	collagen triple helix repeat containing 1	44			Q -> P (found in patients with Barrett esophagus). {ECO:0000269|PubMed:21791690}.		cell migration (GO:0016477)|cochlea morphogenesis (GO:0090103)|establishment of planar polarity involved in neural tube closure (GO:0090177)|inner ear receptor stereocilium organization (GO:0060122)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|ossification involved in bone remodeling (GO:0043932)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein binding (GO:0032092)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	collagen trimer (GO:0005581)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)				endometrium(1)|large_intestine(5)|lung(4)|ovary(1)|urinary_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(57;2.79e-06)|STAD - Stomach adenocarcinoma(118;0.197)			CAGCTCCGGCAGAGGGAGGTG	0.741																																					p.Q44R		Atlas-SNP	.											.	CTHRC1	29	.	0			c.A131G						.						6	6	6					8																	104384015		1925	3776	5701	SO:0001583	missense	115908	exon1			TCCGGCAGAGGGA	BC014245	CCDS6299.1, CCDS59110.1	8q22.3	2008-08-07			ENSG00000164932	ENSG00000164932			18831	protein-coding gene	gene with protein product		610635				15618538	Standard	NM_138455		Approved		uc003ylk.4	Q96CG8	OTTHUMG00000164887	ENST00000330295.5:c.131A>G	chr8.hg19:g.104384015A>G	ENSP00000330523:p.Gln44Arg	96.0	0.0		158.0	40.0	NM_138455	G3V141|Q6UW91|Q8IX63	Missense_Mutation	SNP	ENST00000330295.5	hg19	CCDS6299.1	.	.	.	.	.	.	.	.	.	.	A	13.56	2.272285	0.40194	.	.	ENSG00000164932	ENST00000330295;ENST00000415886	T;T	0.78126	-1.15;-1.15	4.75	2.44	0.29823	.	0.749568	0.12285	N	0.482528	T	0.55893	0.1949	N	0.14661	0.345	0.80722	D	1	B;B	0.30326	0.276;0.02	B;B	0.20184	0.028;0.007	T	0.47032	-0.9148	10	0.33141	T	0.24	-1.6978	5.7962	0.18387	0.3646:0.5207:0.1147:0.0	.	44;44	E7EVQ5;Q96CG8	.;CTHR1_HUMAN	R	44	ENSP00000330523:Q44R;ENSP00000416045:Q44R	ENSP00000330523:Q44R	Q	+	2	0	CTHRC1	104453191	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	0.530000	0.23036	0.655000	0.30866	-0.406000	0.06334	CAG	.	.		0.741	CTHRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380792.1	NM_138455		G	104384015	A	G	104384015	3	3	322	1	0	0	0	0	1	0	0	0	4012	188	7	2	133	2	CTHRC1	8	104384015	Missense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	32172135	104384015	41980007	109	45357										
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110535606	110535606	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	actacacagaccttactcccCttagaacaggtgggtgcact	8	13	0	2	rs267601722		TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr8:110535606C>T	ENST00000378402.5	+	76	12579	c.12475C>T	c.(12475-12477)Ctt>Ttt	p.L4159F		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	4159					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			CCTTACTCCCCTTAGAACAGG	0.388										HNSCC(38;0.096)																											p.L4159F		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.C12475T						.						135	125	128					8																	110535606		1889	4116	6005	SO:0001583	missense	93035	exon76			ACTCCCCTTAGAA	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.12475C>T	chr8.hg19:g.110535606C>T	ENSP00000367655:p.Leu4159Phe	91.0	0.0		123.0	7.0	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	hg19	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	C	6.308	0.424906	0.11987	.	.	ENSG00000205038	ENST00000378402;ENST00000526472	D;D	0.85702	-2.02;-1.85	5.82	4.87	0.63330	.	0.898083	0.09506	N	0.793031	T	0.78848	0.4348	L	0.51422	1.61	0.21740	N	0.999568	P	0.40398	0.716	B	0.36186	0.219	T	0.66376	-0.5939	10	0.10111	T	0.7	.	10.4284	0.44391	0.2397:0.7603:0.0:0.0	.	4159	Q86WI1	PKHL1_HUMAN	F	4159;1087	ENSP00000367655:L4159F;ENSP00000437376:L1087F	ENSP00000367655:L4159F	L	+	1	0	PKHD1L1	110604782	0.187000	0.23238	0.996000	0.52242	0.742000	0.42306	0.551000	0.23361	2.751000	0.94390	0.650000	0.86243	CTT	.	.		0.388	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		T	110535606	C	T	110535606	3	4	322	1	0	0	0	0	1	0	0	0	11981	681	24	3	12777	3	PKHD1L1	8	110535606	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	6151591	110535606	35828416	110	45358										
POU5F1B	5462	hgsc.bcm.edu	37	chr8	128428491	128428491	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tgccgtgaagctggagaaggAgaagctagagcaaaacccgg	15	8	0	4			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr8:128428491A>G	ENST00000465342.2	+	2	1537	c.380A>G	c.(379-381)gAg>gGg	p.E127G	CASC8_ENST00000501396.1_RNA|POU5F1B_ENST00000391675.1_Missense_Mutation_p.E127G|CASC8_ENST00000523825.1_RNA|CASC8_ENST00000502082.1_RNA			Q06416	P5F1B_HUMAN	POU class 5 homeobox 1B	127					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(1)|prostate(1)|urinary_tract(1)	3						CTGGAGAAGGAGAAGCTAGAG	0.587																																					p.E127G		Atlas-SNP	.											.	POU5F1B	32	.	0			c.A380G						.						20	19	19					8																	128428491		692	1591	2283	SO:0001583	missense	5462	exon1			AGAAGGAGAAGCT	AF268615	CCDS55274.1	8q24.21	2011-06-20	2009-04-15	2009-04-15	ENSG00000212993	ENSG00000212993		"Homeoboxes / POU class"	9223	protein-coding gene	gene with protein product		615739	"POU domain class 5, transcription factor 1 pseudogene 1", "POU class 5 homeobox 1 pseudogene 1"	OTF3P1, POU5F1P1		1408763	Standard	NM_001159542		Approved	OTF3C	uc003ysf.3	Q06416	OTTHUMG00000157807	ENST00000465342.2:c.380A>G	chr8.hg19:g.128428491A>G	ENSP00000419298:p.Glu127Gly	32.0	0.0		73.0	34.0	NM_001159542	D5K9S4|D5K9S9|D5K9T0|D5K9T1|D5K9T3|D5K9U3|D5K9U6|D5K9V4|D5K9V6|D5K9W0|D5K9W2|D5K9W7|D5K9X2|D5K9X3|D5K9X5|D5K9X8|D5K9X9|E9LRB1|E9LRB2|E9LRH5|E9LRH6|E9LRH7|E9LRK4|E9LRK5|E9LRK7|E9LRK8|E9LRM7|E9LRM9|E9LRN2|E9LRN4|E9LRN5|E9LRP8|E9LRQ0|E9LRQ2|E9LRQ3|E9LRQ4|E9LRQ5|E9LRS3|Q2VIK6|Q9BZV7|Q9BZV9	Missense_Mutation	SNP	ENST00000465342.2	hg19	CCDS55274.1	.	.	.	.	.	.	.	.	.	.	A	12.25	1.881019	0.33255	.	.	ENSG00000212993	ENST00000465342;ENST00000391675	T;T	0.24151	1.87;1.87	1.59	0.214	0.15249	.	0.000000	0.42964	D	0.000633	T	0.31670	0.0804	L	0.59436	1.845	0.09310	N	1	D	0.69078	0.997	D	0.66847	0.947	T	0.22103	-1.0226	10	0.17369	T	0.5	.	1.5534	0.02580	0.4987:0.0:0.1968:0.3045	.	127	Q06416	P5F1B_HUMAN	G	127	ENSP00000419298:E127G;ENSP00000375557:E127G	ENSP00000375557:E127G	E	+	2	0	POU5F1B	128497673	0.023000	0.18921	0.000000	0.03702	0.110000	0.19582	1.216000	0.32443	0.059000	0.16252	0.102000	0.15555	GAG	.	.		0.587	POU5F1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349649.2	NM_001159542		G	128428491	A	G	128428491	3	3	322	1	0	0	0	0	1	0	0	0	12291	304	11	2	382	2	POU5F1B	8	128428491	Missense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	17892885	128428491	17935531	111	45359										
IFNA8	3445	hgsc.bcm.edu	37	chr9	21409382	21409382	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	caggaggagtttgatgataaAcagttccagaaggctcaagc	12	7	1	3			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr9:21409382A>G	ENST00000380205.1	+	1	237	c.207A>G	c.(205-207)aaA>aaG	p.K69K		NM_002170.3	NP_002161.2	P32881	IFNA8_HUMAN	interferon, alpha 8	69					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|cytokine receptor binding (GO:0005126)|type I interferon receptor binding (GO:0005132)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)	9				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.0174)		TTGATGATAAACAGTTCCAGA	0.488																																					p.K69K		Atlas-SNP	.											.	IFNA8	19	.	0			c.A207G						.						94	91	92					9																	21409382		2203	4300	6503	SO:0001819	synonymous_variant	3445	exon1			TGATAAACAGTTC		CCDS6507.1	9p22	2010-08-24			ENSG00000120242	ENSG00000120242		"Interferons"	5429	protein-coding gene	gene with protein product	"interferon alpha-B''", "interferon alpha type 201"	147568				1385305	Standard	NM_002170		Approved	IFN-alphaB	uc003zpc.1	P32881	OTTHUMG00000019677	ENST00000380205.1:c.207A>G	chr9.hg19:g.21409382A>G		70.0	0.0		73.0	38.0	NM_002170	P01565|P09236|Q5VWV7|Q5VYQ3	Silent	SNP	ENST00000380205.1	hg19	CCDS6507.1																																																																																			.	.		0.488	IFNA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051906.1	NM_002170		G	21409382	A	G	21409382	2	3	322	1	0	0	0	0	0	0	0	1	7552	40	2	2		2	IFNA8	9	21409382	Silent	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10		21409382	119804049	112	45360										
TPM2	7169	hgsc.bcm.edu	37	chr9	35685682	35685688	+	Frame_Shift_Del	DEL	CTTCTGC	CTTCTGC	-													0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gccttctcggcctcctccagCttctgcagggctgtagccag							TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	CTTCTGC	CTTCTGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr9:35685682_35685688delCTTCTGC	ENST00000360958.2	-	3	434_440	c.330_336delGCAGAAG	c.(328-336)ctgcagaagfs	p.LQK110fs	TPM2_ENST00000329305.2_Frame_Shift_Del_p.LQK110fs|TPM2_ENST00000378292.3_Frame_Shift_Del_p.LQK110fs|TPM2_ENST00000378300.5_Frame_Shift_Del_p.LQK110fs	NM_003289.3	NP_003280.2	P07951	TPM2_HUMAN	tropomyosin 2 (beta)	110					muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of ATPase activity (GO:0043462)	cytosol (GO:0005829)|muscle thin filament tropomyosin (GO:0005862)	actin binding (GO:0003779)|structural constituent of muscle (GO:0008307)			NS(1)|breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_epithelial(49;0.121)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			CCTCCTCCAGCTTCTGCAGGGCTGTAG	0.671																																					p.111_113del		Atlas-Indel,Pindel	.											.	TPM2	64	.	0			c.331_337del						.																																			SO:0001589	frameshift_variant	7169	exon3			.		CCDS6586.1, CCDS6587.1	9p13	2014-09-17	2003-12-02		ENSG00000198467	ENSG00000198467		"Tropomyosins"	12011	protein-coding gene	gene with protein product	"nemaline myopathy type 4"	190990	"arthrogryposis multiplex congenital, distal, type 1"	AMCD1		7606936	Standard	NM_003289		Approved	DA1, NEM4	uc003zxq.3	P07951	OTTHUMG00000019878	ENST00000360958.2:c.330_336delGCAGAAG	chr9.hg19:g.35685682_35685688delCTTCTGC	ENSP00000354219:p.Leu110fs	52.0	0.0		45.0	17.0	NM_213674	A6NM85|P06468|Q13894|Q53FM4|Q5TCU4|Q5TCU7|Q9UH67	Frame_Shift_Del	DEL	ENST00000360958.2	hg19	CCDS6587.1																																																																																			.	.		0.671	TPM2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052376.1	NM_003289		-	35685688	CTTCTGC	-	35685682	7	5	322	1	0	1	0	1	0	0	0	0	16421	796	28	0	713	0	TPM2	9	35685682	Frame_Shift_Del	DEL	CTTCTGC	TCGA-MI-A75G-01A-11D-A32G-10	14276300	35685682	105527749	113	45361										
FAM189A2	9413	hgsc.bcm.edu	37	chr9	72000833	72000833	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tgaggaccaggtcgaagagtGaccctgtgctccatccttct	11	12	1	3			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr9:72000833G>T	ENST00000257515.8	+	9	1246	c.826G>T	c.(826-828)Gac>Tac	p.D276Y	FAM189A2_ENST00000455972.1_Missense_Mutation_p.D276Y|FAM189A2_ENST00000377216.3_5'Flank|FAM189A2_ENST00000469179.1_3'UTR|FAM189A2_ENST00000303068.7_Missense_Mutation_p.D111Y	NM_004816.3	NP_004807.3	Q15884	F1892_HUMAN	family with sequence similarity 189, member A2	276						integral component of membrane (GO:0016021)				endometrium(3)|large_intestine(5)|liver(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	12						GTCGAAGAGTGACCCTGTGCT	0.562																																					p.D276Y		Atlas-SNP	.											.	FAM189A2	55	.	0			c.G826T						.						105	82	90					9																	72000833		2203	4300	6503	SO:0001583	missense	9413	exon9			AAGAGTGACCCTG	L27479	CCDS6629.1	9q21.11	2009-07-09	2009-07-09	2009-07-09	ENSG00000135063	ENSG00000135063			24820	protein-coding gene	gene with protein product		607710	"chromosome 9 open reading frame 61"	C9orf61		7951235	Standard	NM_004816		Approved	X123	uc010mon.1	Q15884	OTTHUMG00000019979	ENST00000257515.8:c.826G>T	chr9.hg19:g.72000833G>T	ENSP00000257515:p.Asp276Tyr	65.0	0.0		58.0	24.0	NM_004816	Q14CN5|Q5T6C8|Q5T6C9|Q6ZTX4|Q96N10	Missense_Mutation	SNP	ENST00000257515.8	hg19	CCDS6629.1	.	.	.	.	.	.	.	.	.	.	G	18.77	3.695658	0.68386	.	.	ENSG00000135063	ENST00000455972;ENST00000257515;ENST00000303068;ENST00000377225	T;T;T	0.47528	1.89;1.89;0.84	5.93	5.93	0.95920	.	0.247207	0.42682	D	0.000680	T	0.70369	0.3216	M	0.73962	2.25	0.58432	D	0.999996	D;D	0.89917	1.0;0.995	D;P	0.97110	1.0;0.867	T	0.71632	-0.4534	10	0.72032	D	0.01	-13.4037	18.1269	0.89589	0.0:0.0:1.0:0.0	.	111;276	F2Z2T9;Q15884	.;F1892_HUMAN	Y	276;276;111;275	ENSP00000395675:D276Y;ENSP00000257515:D276Y;ENSP00000304435:D111Y	ENSP00000257515:D276Y	D	+	1	0	FAM189A2	71190653	1.000000	0.71417	1.000000	0.80357	0.385000	0.30292	5.878000	0.69682	2.826000	0.97356	0.655000	0.94253	GAC	.	.		0.562	FAM189A2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052576.2	NM_004816		T	72000833	G	T	72000833	3	4	322	1	0	0	0	0	1	0	0	0	5521	1290	45	3	856	3	FAM189A2	9	72000833	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	36315151	72000833	69212598	114	45362										
VPS13A	23230	hgsc.bcm.edu	37	chr9	79973288	79973288	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cttagatccaaaatcagataCatggtgctgtatttcccttt	6	9	1	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr9:79973288C>G	ENST00000360280.3	+	57	8229	c.7969C>G	c.(7969-7971)Cat>Gat	p.H2657D	VPS13A_ENST00000376634.4_Missense_Mutation_p.H2657D|VPS13A_ENST00000357409.5_Missense_Mutation_p.H2657D|VPS13A_ENST00000376636.3_Missense_Mutation_p.H2618D	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	2657					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						AAATCAGATACATGGTGCTGT	0.318																																					p.H2657D		Atlas-SNP	.											.	VPS13A	735	.	0			c.C7969G						.						177	165	169					9																	79973288		2203	4300	6503	SO:0001583	missense	23230	exon57			CAGATACATGGTG	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"chorein"	605978	"chorea acanthocytosis", "vacuolar protein sorting 13A (yeast)"	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.7969C>G	chr9.hg19:g.79973288C>G	ENSP00000353422:p.His2657Asp	64.0	0.0		111.0	40.0	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	hg19	CCDS6655.1	.	.	.	.	.	.	.	.	.	.	C	10.74	1.434321	0.25813	.	.	ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409	T;T;T;T	0.76316	-1.01;-1.01;-1.01;-1.01	5.92	3.94	0.45596	.	0.459125	0.25050	N	0.033532	T	0.65729	0.2719	L	0.34521	1.04	0.80722	D	1	B;B;B;B	0.28636	0.0;0.139;0.218;0.218	B;B;B;B	0.23574	0.001;0.021;0.047;0.047	T	0.61579	-0.7034	9	.	.	.	.	13.3116	0.60384	0.2867:0.7133:0.0:0.0	.	2618;2657;2657;2657	Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4	.;VP13A_HUMAN;.;.	D	2657;2618;2657;2657	ENSP00000365821:H2657D;ENSP00000365823:H2618D;ENSP00000353422:H2657D;ENSP00000349985:H2657D	.	H	+	1	0	VPS13A	79163108	1.000000	0.71417	0.994000	0.49952	0.998000	0.95712	4.089000	0.57685	1.462000	0.47948	0.650000	0.86243	CAT	.	.		0.318	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		G	79973288	C	G	79973288	3	3	322	1	0	0	0	0	1	0	0	0	17204	478	17	4	8195	4	VPS13A	9	79973288	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	7972455	79973288	61240143	115	45363										
ZBTB43	23099	hgsc.bcm.edu	37	chr9	129595192	129595192	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	agtcctttgtcagaagctaaAtcatggcagtgaccaccagt	9	10	2	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr9:129595192A>G	ENST00000373464.4	+	3	668	c.404A>G	c.(403-405)aAt>aGt	p.N135S	ZBTB43_ENST00000373457.1_Missense_Mutation_p.N135S|ZBTB43_ENST00000449886.1_Missense_Mutation_p.N135S	NM_014007.3	NP_054726.1	O43298	ZBT43_HUMAN	zinc finger and BTB domain containing 43	135					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14						CAGAAGCTAAATCATGGCAGT	0.488																																					p.N135S		Atlas-SNP	.											.	ZBTB43	25	.	0			c.A404G						.						48	48	48					9																	129595192		2203	4300	6503	SO:0001583	missense	23099	exon2			AGCTAAATCATGG	AF049907	CCDS6867.1	9q33.3	2013-01-09	2006-04-12	2006-04-12	ENSG00000169155	ENSG00000169155		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	17908	protein-coding gene	gene with protein product			"zinc finger protein 297B"	ZNF297B			Standard	NM_014007		Approved	KIAA0414, ZNF-X, FLJ22470, ZBTB22B	uc010mxf.3	O43298	OTTHUMG00000020693	ENST00000373464.4:c.404A>G	chr9.hg19:g.129595192A>G	ENSP00000362563:p.Asn135Ser	66.0	0.0		64.0	22.0	NM_001135776	Q5JU96	Missense_Mutation	SNP	ENST00000373464.4	hg19	CCDS6867.1	.	.	.	.	.	.	.	.	.	.	A	2.002	-0.429247	0.04701	.	.	ENSG00000169155	ENST00000449886;ENST00000373464;ENST00000450858;ENST00000373457	T;T;T;T	0.56103	2.99;2.99;0.48;2.99	5.75	5.75	0.90469	.	0.055071	0.64402	D	0.000002	T	0.36717	0.0977	N	0.24115	0.695	0.34063	D	0.657497	B	0.33288	0.406	B	0.25884	0.064	T	0.48387	-0.9040	10	0.19147	T	0.46	.	16.3473	0.83146	1.0:0.0:0.0:0.0	.	135	O43298	ZBT43_HUMAN	S	135	ENSP00000390344:N135S;ENSP00000362563:N135S;ENSP00000412145:N135S;ENSP00000362556:N135S	ENSP00000362556:N135S	N	+	2	0	ZBTB43	128635013	0.987000	0.35691	0.963000	0.40424	0.989000	0.77384	3.573000	0.53856	2.320000	0.78422	0.528000	0.53228	AAT	.	.		0.488	ZBTB43-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054124.1	NM_001135776		G	129595192	A	G	129595192	3	3	322	1	0	0	0	0	1	0	0	0	17559	101	4	2	406	2	ZBTB43	9	129595192	Missense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	49621904	129595192	11618239	116	45364										
CUBN	8029	hgsc.bcm.edu	37	chr10	17157488	17157488	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	acctctccagcttgctctcgCattaaatcctcacagatgcc	5	16	3	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr10:17157488C>T	ENST00000377833.4	-	7	767	c.702G>A	c.(700-702)atG>atA	p.M234I		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	234					cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CTTGCTCTCGCATTAAATCCT	0.557																																					p.M234I		Atlas-SNP	.											.	CUBN	515	.	0			c.G702A						.						121	104	110					10																	17157488		2203	4300	6503	SO:0001583	missense	8029	exon7			CTCTCGCATTAAA	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.702G>A	chr10.hg19:g.17157488C>T	ENSP00000367064:p.Met234Ile	58.0	0.0		68.0	31.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	c	6.369	0.436163	0.12104	.	.	ENSG00000107611	ENST00000377833	D	0.86956	-2.19	5.53	-0.351	0.12602	Growth factor, receptor (1);Epidermal growth factor-like (1);	1.536280	0.04621	N	0.401988	T	0.73923	0.3649	N	0.03608	-0.345	0.27768	N	0.943599	B	0.02656	0.0	B	0.01281	0.0	T	0.60999	-0.7151	10	0.38643	T	0.18	.	11.7812	0.52016	0.0:0.4153:0.3798:0.2048	.	234	O60494	CUBN_HUMAN	I	234	ENSP00000367064:M234I	ENSP00000367064:M234I	M	-	3	0	CUBN	17197494	0.990000	0.36364	0.274000	0.24659	0.504000	0.33889	0.408000	0.21065	0.257000	0.21650	-0.123000	0.14984	ATG	.	.		0.557	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		T	17157488	C	T	17157488	3	4	322	1	0	0	0	0	1	0	0	0	4053	710	25	3	10413	3	CUBN	10	17157488	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10		17157488	118377259	117	45365										
GPR158	57512	hgsc.bcm.edu	37	chr10	25464991	25464991	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tcctccgcaccccacctggcCaacgccactctggagaccga	8	20	1	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr10:25464991C>T	ENST00000376351.3	+	1	1001	c.642C>T	c.(640-642)gcC>gcT	p.A214A	GPR158-AS1_ENST00000449643.1_RNA	NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	214					protein localization to plasma membrane (GO:0072659)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|cervix(1)|endometrium(9)|kidney(10)|large_intestine(20)|lung(56)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	119						CCCACCTGGCCAACGCCACTC	0.711																																					p.A214A		Atlas-SNP	.											.	GPR158	255	.	0			c.C642T						.						20	19	19					10																	25464991		2199	4298	6497	SO:0001819	synonymous_variant	57512	exon1			CCTGGCCAACGCC	AB032962	CCDS31166.1	10p12.31	2012-08-21			ENSG00000151025	ENSG00000151025		"GPCR / Class C : Orphans"	23689	protein-coding gene	gene with protein product		614573					Standard	NM_020752		Approved	KIAA1136	uc001isj.3	Q5T848	OTTHUMG00000017832	ENST00000376351.3:c.642C>T	chr10.hg19:g.25464991C>T		34.0	0.0		46.0	23.0	NM_020752	Q6QR81|Q9ULT3	Silent	SNP	ENST00000376351.3	hg19	CCDS31166.1																																																																																			.	.		0.711	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	XM_166110		T	25464991	C	T	25464991	2	4	322	1	0	0	0	0	0	0	0	1	6671	581	21	3		3	GPR158	10	25464991	Silent	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	8307503	25464991	110069756	118	45366										
KIAA1274	27143	hgsc.bcm.edu	37	chr10	72289050	72289050	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ggctcattacacgttgggccGgctctcggacaacacccctg	11	15	2	0	rs550643851		TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr10:72289050G>T	ENST00000263563.6	+	3	519	c.251G>T	c.(250-252)cGg>cTg	p.R84L		NM_014431.2	NP_055246.2	Q9ULE6	PALD_HUMAN	phosphatase domain containing, paladin 1	84						cytosol (GO:0005829)											ACGTTGGGCCGGCTCTCGGAC	0.602																																					p.R84L		Atlas-SNP	.											.	.	.	.	0			c.G251T						.						79	64	69					10																	72289050		2203	4300	6503	SO:0001583	missense	27143	exon3			TGGGCCGGCTCTC	AB033100	CCDS31215.1	10q22.2	2012-07-17	2012-07-17	2012-07-17	ENSG00000107719	ENSG00000107719			23530	protein-coding gene	gene with protein product		614656	"paladin", "KIAA1274"	PALD, KIAA1274			Standard	NM_014431		Approved		uc001jrd.4	Q9ULE6	OTTHUMG00000018411	ENST00000263563.6:c.251G>T	chr10.hg19:g.72289050G>T	ENSP00000263563:p.Arg84Leu	14.0	0.0		38.0	14.0	NM_014431	B2RMS1|B9EGC6|Q5JTK7|Q5JTK8	Missense_Mutation	SNP	ENST00000263563.6	hg19	CCDS31215.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.610557	0.87258	.	.	ENSG00000107719	ENST00000263563;ENST00000373214	T	0.29142	1.58	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.60051	0.2239	M	0.81942	2.565	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.65829	-0.6073	10	0.87932	D	0	-35.6225	18.3331	0.90277	0.0:0.0:1.0:0.0	.	84	Q9ULE6	PALD_HUMAN	L	84	ENSP00000263563:R84L	ENSP00000263563:R84L	R	+	2	0	KIAA1274	71959056	1.000000	0.71417	1.000000	0.80357	0.603000	0.37013	6.226000	0.72277	2.501000	0.84356	0.655000	0.94253	CGG	.	.		0.602	PALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048515.2	NM_014431		T	72289050	G	T	72289050	3	4	322	1	0	0	0	0	1	0	0	0	8229	1116	39	1	257	1	KIAA1274	10	72289050	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	46824059	72289050	63245697	119	45367										
PLCE1	51196	hgsc.bcm.edu	37	chr10	96006140	96006140	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gggccaccctggcattgataTacacactgtgtgtgttcaga	11	10	1	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr10:96006140T>C	ENST00000371380.3	+	7	3093	c.2858T>C	c.(2857-2859)aTa>aCa	p.I953T	PLCE1_ENST00000260766.3_Missense_Mutation_p.I953T|PLCE1_ENST00000371375.1_Missense_Mutation_p.I645T|PLCE1_ENST00000371385.3_Missense_Mutation_p.I645T			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1	953					activation of MAPK activity (GO:0000187)|calcium-mediated signaling (GO:0019722)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|diacylglycerol biosynthetic process (GO:0006651)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerulus development (GO:0032835)|heart development (GO:0007507)|inositol phosphate metabolic process (GO:0043647)|inositol phosphate-mediated signaling (GO:0048016)|lipid catabolic process (GO:0016042)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|phospholipid metabolic process (GO:0006644)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of GTPase activity (GO:0043547)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|Ras protein signal transduction (GO:0007265)|regulation of cell growth (GO:0001558)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of protein kinase activity (GO:0045859)|regulation of Ras protein signal transduction (GO:0046578)|regulation of smooth muscle contraction (GO:0006940)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)|guanyl-nucleotide exchange factor activity (GO:0005085)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|Ras GTPase binding (GO:0017016)|receptor signaling protein activity (GO:0005057)			liver(1)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	8		Colorectal(252;0.0458)				GGCATTGATATACACACTGTG	0.473																																					p.I953T		Atlas-SNP	.											.	PLCE1	543	.	0			c.T2858C						.						123	124	124					10																	96006140		1971	4161	6132	SO:0001583	missense	51196	exon8			TTGATATACACAC		CCDS41552.1, CCDS53555.1	10q23	2010-02-22			ENSG00000138193	ENSG00000138193	3.1.4.11		17175	protein-coding gene	gene with protein product	"nephrosis type 3"	608414				11022047, 11022048	Standard	NM_016341		Approved	KIAA1516, PLCE, NPHS3	uc001kjk.3	Q9P212	OTTHUMG00000018789	ENST00000371380.3:c.2858T>C	chr10.hg19:g.96006140T>C	ENSP00000360431:p.Ile953Thr	92.0	0.0		112.0	51.0	NM_016341	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Missense_Mutation	SNP	ENST00000371380.3	hg19	CCDS41552.1	.	.	.	.	.	.	.	.	.	.	T	16.77	3.215138	0.58452	.	.	ENSG00000138193	ENST00000260766;ENST00000371380;ENST00000371385;ENST00000371375	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	6.04	6.04	0.98038	.	0.237560	0.43579	D	0.000560	T	0.34803	0.0910	N	0.24115	0.695	0.40129	D	0.976695	B;B;B	0.25007	0.116;0.082;0.051	B;B;B	0.27380	0.034;0.079;0.012	T	0.19451	-1.0305	10	0.72032	D	0.01	.	16.6349	0.85050	0.0:0.0:0.0:1.0	.	953;645;953	B7ZM61;Q9P212-2;Q9P212	.;.;PLCE1_HUMAN	T	953;953;645;645	ENSP00000260766:I953T;ENSP00000360431:I953T;ENSP00000360438:I645T;ENSP00000360426:I645T	ENSP00000260766:I953T	I	+	2	0	PLCE1	95996130	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.803000	0.69129	2.330000	0.79161	0.477000	0.44152	ATA	.	.		0.473	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049469.3	NM_016341		C	96006140	T	C	96006140	3	2	322	1	0	0	0	0	1	0	0	0	12043	1406	49	2	3170	2	PLCE1	10	96006140	Missense_Mutation	SNP	T	TCGA-MI-A75G-01A-11D-A32G-10	23717090	96006140	39528607	120	45368										
BTBD16	118663	hgsc.bcm.edu	37	chr10	124090748	124090748	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cccagagtcatggctcgaccAggttacagtcaaccattacc	8	14	2	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr10:124090748A>T	ENST00000260723.4	+	12	1312	c.1061A>T	c.(1060-1062)cAg>cTg	p.Q354L	BTBD16_ENST00000368994.2_Missense_Mutation_p.Q355L	NM_144587.2	NP_653188.2	Q32M84	BTBDG_HUMAN	BTB (POZ) domain containing 16	354										breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(3)|skin(2)|stomach(1)|urinary_tract(1)	15		all_neural(114;0.107)|Lung NSC(174;0.175)|all_lung(145;0.222)|Breast(234;0.238)				TGGCTCGACCAGGTTACAGTC	0.463																																					p.Q354L		Atlas-SNP	.											.	BTBD16	44	.	0			c.A1061T						.						98	88	91					10																	124090748		2203	4300	6503	SO:0001583	missense	118663	exon12			TCGACCAGGTTAC	AK058088	CCDS31301.1	10q26.13	2013-01-24	2006-07-04	2006-07-04	ENSG00000138152	ENSG00000138152		"BTB/POZ domain containing"	26340	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 87"	C10orf87			Standard	NM_144587		Approved	FLJ25359, Em:AC061711.1	uc001lgc.1	Q32M84	OTTHUMG00000019182	ENST00000260723.4:c.1061A>T	chr10.hg19:g.124090748A>T	ENSP00000260723:p.Gln354Leu	62.0	0.0		81.0	18.0	NM_144587	A6NM63|Q4VXL1|Q96LN0	Missense_Mutation	SNP	ENST00000260723.4	hg19	CCDS31301.1	.	.	.	.	.	.	.	.	.	.	A	7.930	0.740456	0.15642	.	.	ENSG00000138152	ENST00000260723;ENST00000368994	T;T	0.17854	2.25;2.25	5.98	4.14	0.48551	.	0.281347	0.29791	N	0.011184	T	0.08492	0.0211	N	0.08118	0	0.09310	N	1	B;B	0.16603	0.018;0.018	B;B	0.15870	0.014;0.014	T	0.29181	-1.0020	10	0.31617	T	0.26	-24.1955	9.1282	0.36828	0.1671:0.0:0.8329:0.0	.	355;354	Q32M84-2;Q32M84	.;BTBDG_HUMAN	L	354;355	ENSP00000260723:Q354L;ENSP00000357990:Q355L	ENSP00000260723:Q354L	Q	+	2	0	BTBD16	124080738	0.880000	0.30214	0.009000	0.14445	0.026000	0.11368	1.678000	0.37586	0.881000	0.35993	-0.132000	0.14878	CAG	.	.		0.463	BTBD16-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050780.3	NM_144587		T	124090748	A	T	124090748	3	4	322	1	0	0	0	0	1	0	0	0	1543	188	7	4	1103	4	BTBD16	10	124090748	Missense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	28084608	124090748	11443999	121	45369										
MUC6	4588	hgsc.bcm.edu	37	chr11	1017897	1017897	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	aagtggccatctgtgcatggGtaggggtgatgactgtgtga	17	5	1	3			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr11:1017897G>T	ENST00000421673.2	-	31	4954	c.4904C>A	c.(4903-4905)aCc>aAc	p.T1635N		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1635	Approximate repeats.|Pro-rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CTGTGCATGGGTAGGGGTGAT	0.562																																					p.T1635N		Atlas-SNP	.											.	MUC6	408	.	0			c.C4904A						.						545	519	528					11																	1017897		2199	4295	6494	SO:0001583	missense	4588	exon31			GCATGGGTAGGGG	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"Mucins"	7517	protein-coding gene	gene with protein product		158374	"mucin 6, gastric"			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.4904C>A	chr11.hg19:g.1017897G>T	ENSP00000406861:p.Thr1635Asn	285.0	0.0		282.0	30.0	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	hg19	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	G	9.105	1.005047	0.19199	.	.	ENSG00000184956	ENST00000421673	T	0.27890	1.64	2.39	2.39	0.29439	.	.	.	.	.	T	0.45155	0.1328	L	0.56280	1.765	0.09310	N	1	D	0.76494	0.999	D	0.78314	0.991	T	0.12016	-1.0564	9	0.49607	T	0.09	.	6.8723	0.24127	0.0:0.0:0.7245:0.2755	.	1635	Q6W4X9	MUC6_HUMAN	N	1635	ENSP00000406861:T1635N	ENSP00000406861:T1635N	T	-	2	0	MUC6	1007897	0.000000	0.05858	0.023000	0.16930	0.017000	0.09413	0.259000	0.18405	1.293000	0.44690	0.297000	0.19635	ACC	.	.		0.562	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540		T	1017897	G	T	1017897	3	4	322	1	0	0	0	0	1	0	0	0	9989	1261	44	3	2427	3	MUC6	11	1017897	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10		1017897	133988619	122	45370										
MUC2	4583	hgsc.bcm.edu	37	chr11	1097846	1097847	+	Frame_Shift_Ins	INS	-	-	C													0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	agcgcccggccgtcactgtgINScccgggggcggtaaaacgac					rs201012212		TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr11:1097846_1097847insC	ENST00000441003.2	+	36	6966_6967	c.6939_6940insC	c.(6940-6942)cccfs	p.P2314fs	MUC2_ENST00000361558.6_3'UTR	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4676					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	CCGTCACTGTGCCCGGGGGCGG	0.673																																					p.V2309fs		Atlas-Indel,Pindel	.											.	MUC2	614	.	0			c.6927_6928insC						.																																			SO:0001589	frameshift_variant	4583	exon37			.	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.6942dupC	chr11.hg19:g.1097849_1097849dupC	ENSP00000415183:p.Pro2314fs	34.0	0.0		37.0	18.0	NM_002457	Q14878	Frame_Shift_Ins	INS	ENST00000441003.2	hg19																																																																																				.	.		0.673	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		C	1097847	-	C	1097846	7	5	322	1	0	1	1	0	0	0	0	0	9984	1306	46	0	7073	0	MUC2	11	1097846	Frame_Shift_Ins	INS	-	TCGA-MI-A75G-01A-11D-A32G-10	79949	1097846	133908670	123	45371										
MUC5B	727897	hgsc.bcm.edu	37	chr11	1248993	1248993	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gacccgctgcccttgccggcCggcaactgcacggacgaggt	14	16	0	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr11:1248993C>A	ENST00000529681.1	+	7	814	c.756C>A	c.(754-756)gcC>gcA	p.A252A	MUC5B_ENST00000447027.1_Silent_p.A252A	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	252	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CCTTGCCGGCCGGCAACTGCA	0.697																																					p.A252A		Atlas-SNP	.											.	MUC5B	473	.	0			c.C756A						.						11	13	13					11																	1248993		1842	3920	5762	SO:0001819	synonymous_variant	727897	exon7			GCCGGCCGGCAAC	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.756C>A	chr11.hg19:g.1248993C>A		57.0	0.0		56.0	15.0	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	hg19	CCDS44515.2																																																																																			.	.		0.697	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		A	1248993	C	A	1248993	2	1	322	1	0	0	0	0	0	0	0	1	9988	639	23	1		1	MUC5B	11	1248993	Silent	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	151147	1248993	133757523	124	45372										
BRSK2	9024	hgsc.bcm.edu	37	chr11	1464728	1464728	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gccgcccgcagggggctctgCccttcgacgatgacaacttg	13	15	1	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr11:1464728C>T	ENST00000528841.1	+	8	1027	c.643C>T	c.(643-645)Ccc>Tcc	p.P215S	BRSK2_ENST00000528710.1_Missense_Mutation_p.P155S|BRSK2_ENST00000382179.1_Missense_Mutation_p.P261S|BRSK2_ENST00000526678.1_Missense_Mutation_p.P215S|BRSK2_ENST00000308219.9_Missense_Mutation_p.P215S|BRSK2_ENST00000531197.1_Missense_Mutation_p.P215S|BRSK2_ENST00000544817.1_5'UTR|BRSK2_ENST00000308230.5_Missense_Mutation_p.P215S			Q8IWQ3	BRSK2_HUMAN	BR serine/threonine kinase 2	215	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|axonogenesis (GO:0007409)|establishment of cell polarity (GO:0030010)|exocytosis (GO:0006887)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mitotic nuclear division (GO:0007067)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			endometrium(4)|large_intestine(1)|lung(5)	10		all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00144)|Lung(200;0.0713)|LUSC - Lung squamous cell carcinoma(625;0.0842)		GGGGGCTCTGCCCTTCGACGA	0.677																																					p.P261S		Atlas-SNP	.											.	BRSK2	97	.	0			c.C781T						.						20	24	23					11																	1464728		2139	4266	6405	SO:0001583	missense	9024	exon8			GCTCTGCCCTTCG	AF020089	CCDS41590.1, CCDS58106.1, CCDS58107.1, CCDS58108.1, CCDS60696.1	11p15.5	2008-02-05	2003-09-11	2005-01-27	ENSG00000174672	ENSG00000174672			11405	protein-coding gene	gene with protein product	"serine/threonine kinase 29"	609236	"chromsosome 11 open reading frame 7"	C11orf7, STK29		9852686, 9929968	Standard	NM_001256629		Approved	PEN11B	uc001ltm.4	Q8IWQ3	OTTHUMG00000167089	ENST00000528841.1:c.643C>T	chr11.hg19:g.1464728C>T	ENSP00000432000:p.Pro215Ser	33.0	0.0		46.0	20.0	NM_001256630	B3KVE9|E9PLM7|O60843|O95099|Q5J5B4|Q6ZMQ4|Q8TB60	Missense_Mutation	SNP	ENST00000528841.1	hg19	CCDS58107.1	.	.	.	.	.	.	.	.	.	.	c	25.0	4.593626	0.86953	.	.	ENSG00000174672	ENST00000308219;ENST00000531197;ENST00000308230;ENST00000528841;ENST00000526678;ENST00000528710;ENST00000382179	T;T;T;T;T;T;T	0.39787	1.06;1.06;1.06;1.06;1.06;1.06;1.06	3.26	3.26	0.37387	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.137263	0.49305	U	0.000143	T	0.78528	0.4297	H	0.99104	4.43	0.80722	D	1	P;D;P;D;D	0.89917	0.915;1.0;0.852;0.996;0.995	P;D;P;D;P	0.85130	0.497;0.997;0.497;0.921;0.871	D	0.88435	0.3038	10	0.87932	D	0	.	15.048	0.71841	0.0:1.0:0.0:0.0	.	215;261;215;215;215	Q8IWQ3-4;Q8IWQ3-5;Q8IWQ3-3;Q8IWQ3;Q8IWQ3-2	.;.;.;BRSK2_HUMAN;.	S	215;215;215;215;215;155;261	ENSP00000310697:P215S;ENSP00000431152:P215S;ENSP00000310805:P215S;ENSP00000432000:P215S;ENSP00000433370:P215S;ENSP00000433235:P155S;ENSP00000371614:P261S	ENSP00000310697:P215S	P	+	1	0	BRSK2	1421304	1.000000	0.71417	1.000000	0.80357	0.810000	0.45777	7.043000	0.76572	1.835000	0.53391	0.306000	0.20318	CCC	.	.		0.677	BRSK2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393033.1	NM_003957		T	1464728	C	T	1464728	3	4	322	1	0	0	0	0	1	0	0	0	1526	739	26	3	673	3	BRSK2	11	1464728	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	215735	1464728	133541788	125	45373										
TRAF6	7189	hgsc.bcm.edu	37	chr11	36511424	36511424	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gtacttcgtggctgaaaaccCtccctccgaaggctacccat	8	15	0	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr11:36511424C>T	ENST00000526995.1	-	7	1779	c.1533G>A	c.(1531-1533)gaG>gaA	p.E511E	TRAF6_ENST00000348124.5_Silent_p.E511E|TRAF6_ENST00000529150.1_5'Flank	NM_004620.3	NP_004611.1	Q9Y4K3	TRAF6_HUMAN	TNF receptor-associated factor 6, E3 ubiquitin protein ligase	511					activation of MAPK activity (GO:0000187)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|activation of protein kinase activity (GO:0032147)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|apoptotic signaling pathway (GO:0097190)|bone resorption (GO:0045453)|cell development (GO:0048468)|cellular response to lipopolysaccharide (GO:0071222)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|JNK cascade (GO:0007254)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|protein autoubiquitination (GO:0051865)|protein complex assembly (GO:0006461)|protein K63-linked ubiquitination (GO:0070534)|protein polyubiquitination (GO:0000209)|regulation of immunoglobulin secretion (GO:0051023)|response to interleukin-1 (GO:0070555)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|lipid particle (GO:0005811)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	histone deacetylase binding (GO:0042826)|ligase activity (GO:0016874)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein kinase B binding (GO:0043422)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(13)|ovary(2)|pancreas(1)	27	all_lung(20;0.211)	all_hematologic(20;0.107)				GCTGAAAACCCTCCCTCCGAA	0.488																																					p.E511E		Atlas-SNP	.											.	TRAF6	56	.	0			c.G1533A						.						149	147	148					11																	36511424		2202	4298	6500	SO:0001819	synonymous_variant	7189	exon7			AAAACCCTCCCTC		CCDS7901.1	11p12	2013-01-09	2012-02-23		ENSG00000175104	ENSG00000175104		"RING-type (C3HC4) zinc fingers"	12036	protein-coding gene	gene with protein product		602355	"TNF receptor-associated factor 6"			8837778	Standard	NM_004620		Approved	RNF85	uc001mws.2	Q9Y4K3	OTTHUMG00000166391	ENST00000526995.1:c.1533G>A	chr11.hg19:g.36511424C>T		105.0	0.0		95.0	29.0	NM_004620	A6NKI7|A8KAB3|D3DR16|Q8NEH5	Silent	SNP	ENST00000526995.1	hg19	CCDS7901.1																																																																																			.	.		0.488	TRAF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389530.1	NM_145803		T	36511424	C	T	36511424	2	4	322	1	0	0	0	0	0	0	0	1	16460	680	24	3		3	TRAF6	11	36511424	Silent	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	35046696	36511424	98495092	126	45374										
OR4C15	81309	hgsc.bcm.edu	37	chr11	55322576	55322576	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tatctgcatcataaacttctCcttgttgcttgtctcctatg	5	11	4	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr11:55322576C>G	ENST00000314644.2	+	1	794	c.794C>G	c.(793-795)tCc>tGc	p.S265C		NM_001001920.1	NP_001001920.1	Q8NGM1	OR4CF_HUMAN	olfactory receptor, family 4, subfamily C, member 15	211						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(31)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(5)	56						ATAAACTTCTCCTTGTTGCTT	0.483										HNSCC(20;0.049)																											p.S265C		Atlas-SNP	.											OR4C15,NS,carcinoma,0,1	OR4C15	145	.	0			c.C794G						.						209	151	171					11																	55322576		2201	4296	6497	SO:0001583	missense	81309	exon1			ACTTCTCCTTGTT	BK004319	CCDS31501.1	11q11	2012-08-09			ENSG00000181939	ENSG00000181939		"GPCR / Class A : Olfactory receptors"	15171	protein-coding gene	gene with protein product							Standard	NM_001001920		Approved		uc010rig.2	Q8NGM1	OTTHUMG00000166714	ENST00000314644.2:c.794C>G	chr11.hg19:g.55322576C>G	ENSP00000324958:p.Ser265Cys	91.0	0.0		90.0	12.0	NM_001001920	Q6IFE2	Missense_Mutation	SNP	ENST00000314644.2	hg19	CCDS31501.1	.	.	.	.	.	.	.	.	.	.	C	12.06	1.824623	0.32237	.	.	ENSG00000181939	ENST00000314644	T	0.38401	1.14	4.8	2.88	0.33553	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.51856	0.1699	L	0.58428	1.81	0.09310	N	1	D	0.76494	0.999	D	0.69479	0.964	T	0.30650	-0.9971	9	0.62326	D	0.03	.	9.6211	0.39721	0.0:0.8208:0.0:0.1792	.	211	Q8NGM1	OR4CF_HUMAN	C	265	ENSP00000324958:S265C	ENSP00000324958:S265C	S	+	2	0	OR4C15	55079152	0.000000	0.05858	0.869000	0.34112	0.629000	0.37895	-1.043000	0.03535	1.241000	0.43820	0.385000	0.25706	TCC	.	.		0.483	OR4C15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391164.1	NM_001001920		G	55322576	C	G	55322576	3	3	322	1	0	0	0	0	1	0	0	0	11057	855	30	4	796	4	OR4C15	11	55322576	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	18811152	55322576	79683940	127	45375										
CNTN5	53942	hgsc.bcm.edu	37	chr11	99715953	99715953	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gtgtttagcaaccaacactgTggggagtattcttagtagag	12	6	1	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr11:99715953T>A	ENST00000524871.1	+	6	826	c.536T>A	c.(535-537)gTg>gAg	p.V179E	CNTN5_ENST00000418526.2_Missense_Mutation_p.V105E|CNTN5_ENST00000527185.1_Missense_Mutation_p.V179E|CNTN5_ENST00000279463.3_Missense_Mutation_p.V179E|CNTN5_ENST00000528682.1_Missense_Mutation_p.V179E	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	179	Ig-like C2-type 1.				cell adhesion (GO:0007155)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(12)|lung(38)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	81		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		ACCAACACTGTGGGGAGTATT	0.353																																					p.V179E		Atlas-SNP	.											.	CNTN5	324	.	0			c.T536A						.						141	133	135					11																	99715953		1827	4102	5929	SO:0001583	missense	53942	exon5			ACACTGTGGGGAG	AB013802	CCDS53696.1, CCDS53697.1, CCDS58168.1	11q22.1	2013-02-11			ENSG00000149972	ENSG00000149972		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2175	protein-coding gene	gene with protein product		607219					Standard	NM_014361		Approved	NB-2, hNB-2	uc021qpb.1	O94779	OTTHUMG00000167579	ENST00000524871.1:c.536T>A	chr11.hg19:g.99715953T>A	ENSP00000435637:p.Val179Glu	43.0	0.0		56.0	15.0	NM_001243270	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Missense_Mutation	SNP	ENST00000524871.1	hg19	CCDS53696.1	.	.	.	.	.	.	.	.	.	.	T	13.61	2.289515	0.40494	.	.	ENSG00000149972	ENST00000527185;ENST00000528682;ENST00000524871;ENST00000418526;ENST00000279463	T;T;T;T;T	0.69040	-0.37;-0.37;-0.37;-0.37;-0.37	5.8	5.8	0.92144	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.292191	0.38605	N	0.001640	T	0.60248	0.2254	L	0.31752	0.955	0.22552	N	0.998996	B;B;B	0.21606	0.058;0.037;0.058	B;B;B	0.31442	0.082;0.036;0.13	T	0.58329	-0.7655	10	0.59425	D	0.04	.	15.3151	0.74069	0.0:0.0:0.0:1.0	.	179;105;179	E9PKE8;O94779-2;O94779	.;.;CNTN5_HUMAN	E	179;179;179;105;179	ENSP00000433575:V179E;ENSP00000436185:V179E;ENSP00000435637:V179E;ENSP00000393229:V105E;ENSP00000279463:V179E	ENSP00000279463:V179E	V	+	2	0	CNTN5	99221163	1.000000	0.71417	0.916000	0.36221	0.281000	0.26958	4.751000	0.62169	2.216000	0.71823	0.528000	0.53228	GTG	.	.		0.353	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361		A	99715953	T	A	99715953	3	1	322	1	0	0	0	0	1	0	0	0	3646	1696	59	4	550	4	CNTN5	11	99715953	Missense_Mutation	SNP	T	TCGA-MI-A75G-01A-11D-A32G-10	44393377	99715953	35290563	128	45376										
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	102984322	102984322	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tttttcaagctgcgacctgaAgtaattactgatgagaatct	8	7	2	3			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr11:102984322A>G	ENST00000375735.2	+	2	396	c.252A>G	c.(250-252)gaA>gaG	p.E84E	DYNC2H1_ENST00000334267.7_Silent_p.E84E|DYNC2H1_ENST00000398093.3_Silent_p.E84E	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	84	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		TGCGACCTGAAGTAATTACTG	0.328																																					p.E84E		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.A252G						.						166	161	163					11																	102984322		1862	4106	5968	SO:0001819	synonymous_variant	79659	exon2			ACCTGAAGTAATT	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.252A>G	chr11.hg19:g.102984322A>G		135.0	0.0		224.0	9.0	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Silent	SNP	ENST00000375735.2	hg19	CCDS53701.1																																																																																			.	.		0.328	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		G	102984322	A	G	102984322	2	3	322	1	0	0	0	0	0	0	0	1	4848	69	3	2		2	DYNC2H1	11	102984322	Silent	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	3268369	102984322	32022194	129	45377										
DDI1	414301	hgsc.bcm.edu	37	chr11	103908253	103908253	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	atatagcgatagaagaggccCccgagagttttggacaagtg	13	7	0	3			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr11:103908253C>A	ENST00000302259.3	+	1	946	c.703C>A	c.(703-705)Ccc>Acc	p.P235T	PDGFD_ENST00000302251.5_Intron|PDGFD_ENST00000393158.2_Intron	NM_001001711.2	NP_001001711.1	Q8WTU0	DDI1_HUMAN	DNA-damage inducible 1 homolog 1 (S. cerevisiae)	235							aspartic-type endopeptidase activity (GO:0004190)			central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(12)|liver(2)|lung(21)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00648)|Melanoma(852;0.055)|all_neural(303;0.164)		BRCA - Breast invasive adenocarcinoma(274;0.00128)|Epithelial(105;0.0631)|all cancers(92;0.169)		AGAAGAGGCCCCCGAGAGTTT	0.478																																					p.P235T		Atlas-SNP	.											.	DDI1	222	.	0			c.C703A						.						114	127	123					11																	103908253		2202	4299	6501	SO:0001583	missense	414301	exon1			GAGGCCCCCGAGA		CCDS31660.1	11q22.3	2010-05-04	2010-05-04			ENSG00000170967			18961	protein-coding gene	gene with protein product			"DDI1, DNA-damage inducible 1, homolog 1 (S. cerevisiae)"				Standard	NM_001001711		Approved	FLJ36017	uc001phr.2	Q8WTU0		ENST00000302259.3:c.703C>A	chr11.hg19:g.103908253C>A	ENSP00000302805:p.Pro235Thr	76.0	0.0		102.0	58.0	NM_001001711	Q7Z4U6|Q8WTS3	Missense_Mutation	SNP	ENST00000302259.3	hg19	CCDS31660.1	.	.	.	.	.	.	.	.	.	.	C	17.09	3.299467	0.60195	.	.	ENSG00000170967	ENST00000302259	T	0.64438	-0.1	5.02	5.02	0.67125	Peptidase aspartic (1);Peptidase aspartic, eukaryotic predicted (1);	0.000000	0.85682	D	0.000000	D	0.84147	0.5408	M	0.93720	3.45	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	D	0.87908	0.2695	10	0.87932	D	0	-14.8119	16.2348	0.82365	0.0:1.0:0.0:0.0	.	235	Q8WTU0	DDI1_HUMAN	T	235	ENSP00000302805:P235T	ENSP00000302805:P235T	P	+	1	0	DDI1	103413463	1.000000	0.71417	0.121000	0.21740	0.460000	0.32559	7.133000	0.77259	2.781000	0.95711	0.655000	0.94253	CCC	.	.		0.478	DDI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387326.1	NM_001001711		A	103908253	C	A	103908253	3	1	322	1	0	0	0	0	1	0	0	0	4330	623	22	3	705	3	DDI1	11	103908253	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	923931	103908253	31098263	130	45378										
IL18	3606	hgsc.bcm.edu	37	chr11	112014513	112014513	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tatgatgtcactttttgtatCcttgatgttatcaggaggat	9	5	2	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr11:112014513C>T	ENST00000280357.7	-	6	607	c.388G>A	c.(388-390)Gat>Aat	p.D130N	SDHD_ENST00000532699.1_Intron|IL18_ENST00000528832.1_Missense_Mutation_p.D130N|IL18_ENST00000533858.1_5'UTR|IL18_ENST00000524595.1_Missense_Mutation_p.D126N	NM_001562.3	NP_001553.1	Q14116	IL18_HUMAN	interleukin 18	130					angiogenesis (GO:0001525)|cell-cell signaling (GO:0007267)|cellular response to organic cyclic compound (GO:0071407)|chemokine biosynthetic process (GO:0042033)|granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0042253)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma biosynthetic process (GO:0042095)|interleukin-13 biosynthetic process (GO:0042231)|interleukin-2 biosynthetic process (GO:0042094)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MAPK cascade (GO:0000165)|natural killer cell activation (GO:0030101)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of gene expression (GO:0010628)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of natural killer cell proliferation (GO:0032819)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NK T cell proliferation (GO:0051142)|positive regulation of tissue remodeling (GO:0034105)|regulation of cell adhesion (GO:0030155)|sleep (GO:0030431)|T-helper 1 type immune response (GO:0042088)|type 2 immune response (GO:0042092)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)						all_cancers(61;5.7e-14)|all_epithelial(67;3.4e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;6.72e-07)|Epithelial(105;8.15e-07)|all cancers(92;1.43e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.055)		CTTTTTGTATCCTTGATGTTA	0.313																																					p.D130N		Atlas-SNP	.											.	IL18	10	.	0			c.G388A						.						71	67	68					11																	112014513		1826	4074	5900	SO:0001583	missense	3606	exon6			TTGTATCCTTGAT	U90434	CCDS44731.1, CCDS58180.1	11q22.2-q22.3	2014-04-04	2014-04-04		ENSG00000150782	ENSG00000150782		"Interleukins and interleukin receptors"	5986	protein-coding gene	gene with protein product	"interferon-gamma-inducing factor"	600953	"interleukin 18 (interferon-gamma-inducing factor)"			7477296, 9693051	Standard	NM_001562		Approved	IGIF, IL1F4, IL-1g, IL-18	uc001pnb.2	Q14116	OTTHUMG00000167006	ENST00000280357.7:c.388G>A	chr11.hg19:g.112014513C>T	ENSP00000280357:p.Asp130Asn	60.0	0.0		81.0	44.0	NM_001562	O75599|Q6FGY3|Q6WWJ7	Missense_Mutation	SNP	ENST00000280357.7	hg19	CCDS44731.1	.	.	.	.	.	.	.	.	.	.	C	9.727	1.161296	0.21538	.	.	ENSG00000150782	ENST00000280357;ENST00000524595;ENST00000528832	T;T;T	0.16457	2.34;2.34;2.34	5.09	2.09	0.27110	.	0.685512	0.13612	N	0.375097	T	0.13030	0.0316	L	0.49126	1.545	0.09310	N	1	B;B;B	0.14012	0.003;0.002;0.009	B;B;B	0.22601	0.013;0.013;0.04	T	0.38308	-0.9667	10	0.11485	T	0.65	-15.9847	4.6568	0.12622	0.172:0.6441:0.0:0.1838	.	126;130;130	Q6WWJ7;Q14116;Q96KJ8	.;IL18_HUMAN;.	N	130;126;130	ENSP00000280357:D130N;ENSP00000434561:D126N;ENSP00000434161:D130N	ENSP00000280357:D130N	D	-	1	0	IL18	111519723	0.001000	0.12720	0.007000	0.13788	0.004000	0.04260	0.635000	0.24629	0.738000	0.32606	0.655000	0.94253	GAT	.	.		0.313	IL18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392409.1	NM_001562		T	112014513	C	T	112014513	3	4	322	1	0	0	0	0	1	0	0	0	7654	855	30	3	197	3	IL18	11	112014513	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	8106260	112014513	22992003	131	45379										
C11orf71	10179	hgsc.bcm.edu	37	chr11	114271008	114271008	+	5'UTR	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ggaagagcggtaggccacccTgctcctctgatcaccggagg	14	13	2	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr11:114271008T>A	ENST00000540163.1	+	0	257				RBM7_ENST00000545678.1_5'Flank|RBM7_ENST00000544582.1_5'Flank|RBM7_ENST00000541475.1_5'Flank|C11orf71_ENST00000325636.4_Missense_Mutation_p.R16W|RBM7_ENST00000375490.5_5'Flank|RP11-212D19.4_ENST00000544347.1_5'Flank			Q9Y580	RBM7_HUMAN	RNA binding motif protein 7						meiotic nuclear division (GO:0007126)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17		all_cancers(61;5.06e-12)|all_epithelial(67;5.3e-06)|all_hematologic(158;7.68e-05)|Acute lymphoblastic leukemia(157;0.000966)|Melanoma(852;0.00153)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Breast(348;0.0818)|Prostate(24;0.104)		BRCA - Breast invasive adenocarcinoma(274;2.56e-06)|Epithelial(105;4.17e-05)|all cancers(92;0.000348)		TAGGCCACCCTGCTCCTCTGA	0.602																																					p.R16W		Atlas-SNP	.											.	C11orf71	8	.	0			c.A46T						.						16	17	17					11																	114271008		2197	4287	6484	SO:0001623	5_prime_UTR_variant	54494	exon1			CCACCCTGCTCCT	AF156098	CCDS8370.1, CCDS66233.1, CCDS73395.1	11q23.1-q23.2	2013-02-12			ENSG00000076053	ENSG00000076053		"RNA binding motif (RRM) containing"	9904	protein-coding gene	gene with protein product		612413				12477932	Standard	NM_001286045		Approved		uc001pov.3	Q9Y580		ENST00000540163.1:c.-386T>A	chr11.hg19:g.114271008T>A		87.0	0.0		158.0	60.0	NM_001271562	B2R6K8|Q9NUT4	Missense_Mutation	SNP	ENST00000540163.1	hg19	CCDS8370.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.195879	0.78902	.	.	ENSG00000180425	ENST00000325636	.	.	.	5.1	-10.1	0.00402	.	0.159465	0.27375	N	0.019642	T	0.16257	0.0391	L	0.32530	0.975	0.18873	N	0.999987	B;B	0.31548	0.043;0.328	B;B	0.28011	0.035;0.085	T	0.03374	-1.1043	9	0.87932	D	0	-2.9015	5.425	0.16421	0.0956:0.205:0.5153:0.1841	.	16;16	Q6IPW1;Q6IPW1-2	CK071_HUMAN;.	W	16	.	ENSP00000325508:R16W	R	-	1	2	C11orf71	113776218	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.196000	0.00562	-1.895000	0.01104	-0.313000	0.08912	AGG	.	.		0.602	RBM7-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399010.1	NM_016090		A	114271008	T	A	114271008	1	1	322	0	1	0	0	0	0	0	0	0	1662	1579	55	4		4	C11orf71	11	114271008	5'UTR	SNP	T	TCGA-MI-A75G-01A-11D-A32G-10	2256495	114271008	20735508	132	45380										
HYOU1	10525	hgsc.bcm.edu	37	chr11	118922612	118922612	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	agcgcagctgcctggtacacTgcccccatggcggctgcttc	12	16	0	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr11:118922612T>A	ENST00000404233.3	-	12	1381	c.1257A>T	c.(1255-1257)gcA>gcT	p.A419A	HYOU1_ENST00000529972.1_Silent_p.A419A|HYOU1_ENST00000543287.1_Silent_p.A332A|HYOU1_ENST00000525859.1_Silent_p.A419A	NM_001130991.1|NM_006389.3	NP_001124463.1|NP_006380.1	Q9Y4L1	HYOU1_HUMAN	hypoxia up-regulated 1	419					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|response to ischemia (GO:0002931)|response to stress (GO:0006950)	endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(10)|prostate(1)|skin(2)	33	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.78e-05)		CCTGGTACACTGCCCCCATGG	0.582																																					p.A419A		Atlas-SNP	.											.	HYOU1	88	.	0			c.A1257T						.						87	83	84					11																	118922612		2200	4295	6495	SO:0001819	synonymous_variant	10525	exon12			GTACACTGCCCCC	U65785	CCDS8408.1	11q23.1-q23.3	2011-09-02			ENSG00000149428	ENSG00000149428		"Heat shock proteins / HSP70"	16931	protein-coding gene	gene with protein product	"glucose-regulated protein 170"	601746				9020069, 10037731	Standard	XM_005271390		Approved	ORP150, HSP12A, Grp170	uc001pux.3	Q9Y4L1	OTTHUMG00000166354	ENST00000404233.3:c.1257A>T	chr11.hg19:g.118922612T>A		64.0	0.0		104.0	33.0	NM_006389	A8C1Z0|B7Z909|Q2I204|Q53H25	Silent	SNP	ENST00000404233.3	hg19	CCDS8408.1																																																																																			.	.		0.582	HYOU1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389353.1	NM_006389		A	118922612	T	A	118922612	2	1	322	1	0	0	0	0	0	0	0	1	7479	1567	55	4		4	HYOU1	11	118922612	Silent	SNP	T	TCGA-MI-A75G-01A-11D-A32G-10	4651604	118922612	16083904	133	45381										
MRPL51	51258	hgsc.bcm.edu	37	chr12	6602118	6602118	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gggcgggagagtgagccttaTaccgatcaatctaggcacac	13	10	2	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr12:6602118T>C	ENST00000229238.3	-	2	561	c.100A>G	c.(100-102)Ata>Gta	p.I34V	MRPL51_ENST00000543703.1_Intron|MRPL51_ENST00000543164.1_5'UTR|NCAPD2_ENST00000315579.5_5'Flank|NCAPD2_ENST00000545962.1_5'Flank	NM_016497.3	NP_057581.2	Q4U2R6	RM51_HUMAN	mitochondrial ribosomal protein L51	34					translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrial ribosome (GO:0005761)	structural constituent of ribosome (GO:0003735)			kidney(2)|large_intestine(1)|lung(3)	6						GTGAGCCTTATACCGATCAAT	0.522																																					p.I34V		Atlas-SNP	.											.	MRPL51	17	.	0			c.A100G						.						83	87	85					12																	6602118		2203	4300	6503	SO:0001583	missense	51258	exon2			GCCTTATACCGAT	AB051355	CCDS8547.1	12p13.3-p13.1	2014-02-19	2002-01-07	2002-01-11		ENSG00000111639		"Mitochondrial ribosomal proteins / large subunits"	14044	protein-coding gene	gene with protein product		611855	"mitochondrial ribosomal protein 64"	MRP64		11551941, 11543634	Standard	NM_016497		Approved	CDA09, HSPC241, bMRP64	uc001qom.2	Q4U2R6		ENST00000229238.3:c.100A>G	chr12.hg19:g.6602118T>C	ENSP00000229238:p.Ile34Val	66.0	0.0		78.0	33.0	NM_016497	Q96Q57|Q9BQ36|Q9P0N7	Missense_Mutation	SNP	ENST00000229238.3	hg19	CCDS8547.1	.	.	.	.	.	.	.	.	.	.	T	1.391	-0.580802	0.03854	.	.	ENSG00000111639	ENST00000229238	T	0.40476	1.03	4.96	-0.0191	0.13961	.	0.314945	0.37623	N	0.002001	T	0.10423	0.0255	N	0.01576	-0.805	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.30765	-0.9967	10	0.02654	T	1	-22.4516	3.8453	0.08933	0.223:0.3883:0.0:0.3887	.	34	Q4U2R6	RM51_HUMAN	V	34	ENSP00000229238:I34V	ENSP00000229238:I34V	I	-	1	0	MRPL51	6472379	0.777000	0.28628	0.141000	0.22245	0.095000	0.18619	1.167000	0.31847	-0.014000	0.14175	-0.464000	0.05259	ATA	.	.		0.522	MRPL51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399956.1	NM_016497		C	6602118	T	C	6602118	3	2	322	1	0	0	0	0	1	0	0	0	9824	1406	49	2	294	2	MRPL51	12	6602118	Missense_Mutation	SNP	T	TCGA-MI-A75G-01A-11D-A32G-10		6602118	127249777	134	45382										
ANP32D	23519	hgsc.bcm.edu	37	chr12	48866816	48866816	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	agcttagaccttttcacttgCgaggtaaccaacctgaacaa	7	11	1	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr12:48866816C>T	ENST00000266594.1	+	1	369	c.369C>T	c.(367-369)tgC>tgT	p.C123C		NM_012404.2	NP_036536.2	O95626	AN32D_HUMAN	acidic (leucine-rich) nuclear phosphoprotein 32 family, member D	123						nuclear matrix (GO:0016363)				central_nervous_system(1)|large_intestine(2)|lung(3)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	9						TTTTCACTTGCGAGGTAACCA	0.438																																					p.C123C		Atlas-SNP	.											.	ANP32D	15	.	0			c.C369T						.						84	83	83					12																	48866816		2203	4300	6503	SO:0001819	synonymous_variant	23519	exon1			CACTTGCGAGGTA	U71084	CCDS31788.1	12q13.12	2008-08-04			ENSG00000139223	ENSG00000139223		"ANP32 acidic nuclear phosphoproteins"	16676	protein-coding gene	gene with protein product	"pp32 related 2"	606878				10086381, 10400610	Standard	NM_012404		Approved	PP32R2	uc010slt.2	O95626	OTTHUMG00000162681	ENST00000266594.1:c.369C>T	chr12.hg19:g.48866816C>T		77.0	0.0		81.0	28.0	NM_012404	Q6NTC4	Silent	SNP	ENST00000266594.1	hg19	CCDS31788.1																																																																																			.	.		0.438	ANP32D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370058.1	NM_012404		T	48866816	C	T	48866816	2	4	322	1	0	0	0	0	0	0	0	1	708	776	27	1		1	ANP32D	12	48866816	Silent	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	42264698	48866816	84985079	135	45383										
SLC4A8	9498	hgsc.bcm.edu	37	chr12	51864175	51864175	+	Splice_Site	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gatgactttttttcctctcaGagtgcaattgaatccttgtt	7	8	1	3			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr12:51864175G>T	ENST00000453097.2	+	13	1741		c.e13-1		SLC4A8_ENST00000546663.1_Splice_Site|SLC4A8_ENST00000394856.1_Splice_Site|SLC4A8_ENST00000514353.3_Splice_Site|SLC4A8_ENST00000358657.3_Splice_Site|SLC4A8_ENST00000535225.2_Splice_Site	NM_001039960.2|NM_001258401.2	NP_001035049.1|NP_001245330.1			solute carrier family 4, sodium bicarbonate cotransporter, member 8											NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(18)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(2)|urinary_tract(5)	55				BRCA - Breast invasive adenocarcinoma(357;0.15)		TTTCCTCTCAGAGTGCAATTG	0.478																																					.		Atlas-SNP	.											.	SLC4A8	292	.	0			c.1366-1G>T						.						190	169	176					12																	51864175		2203	4300	6503	SO:0001630	splice_region_variant	9498	exon13			CTCTCAGAGTGCA	AB018282	CCDS44890.1, CCDS58232.1, CCDS58233.1, CCDS73470.1	12q13.13	2013-05-22			ENSG00000050438	ENSG00000050438		"Solute carriers"	11034	protein-coding gene	gene with protein product		605024				11133997	Standard	NM_001039960		Approved	NBC3	uc001rys.2	Q2Y0W8	OTTHUMG00000169489	ENST00000453097.2:c.1525-1G>T	chr12.hg19:g.51864175G>T		84.0	0.0		90.0	34.0	NM_001258401		Splice_Site	SNP	ENST00000453097.2	hg19	CCDS44890.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.165795	0.78339	.	.	ENSG00000050438	ENST00000535225;ENST00000358657;ENST00000453097;ENST00000394856;ENST00000319957;ENST00000514353;ENST00000551071	.	.	.	5.36	5.36	0.76844	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.2369	0.89952	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC4A8	50150442	1.000000	0.71417	0.998000	0.56505	0.906000	0.53458	9.869000	0.99810	2.687000	0.91594	0.563000	0.77884	.	.	.		0.478	SLC4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404356.1	NM_004858	Intron	T	51864175	G	T	51864175	5	4	322	1	0	0	0	0	0	0	1	0	14674	956	33	3	1574	3	SLC4A8	12	51864175	Splice_Site	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	2997359	51864175	81987720	136	45384										
KRT83	3889	hgsc.bcm.edu	37	chr12	52715018	52715019	+	Missense_Mutation	DNP	GG	GG	CT													0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gagatgccgcggtagggggcGgcggtgatgcagcagcggct							TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr12:52715018_52715019GG>CT	ENST00000293670.3	-	1	163_164	c.101_102CC>AG	c.(100-102)gCC>gAG	p.A34E		NM_002282.3	NP_002273.3	P78385	KRT83_HUMAN	keratin 83	34	Head.				aging (GO:0007568)|epidermis development (GO:0008544)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(9)|prostate(1)|skin(4)|stomach(7)|upper_aerodigestive_tract(1)	32	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		GGTAGGGGGCGGCGGTGATGCA	0.693																																					p.A34A|p.A34D	GBM(41;747 834 12702 24089 39393)|Esophageal Squamous(97;805 1414 12559 28198 31861)	Atlas-SNP	.											.	KRT83	64	.	0			c.C102G|c.C101A						.																																			SO:0001583	missense	3889	exon1			GGGGGCGGCGGTG|GGGGCGGCGGTGA	X99141	CCDS8823.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000170523	ENSG00000170523		"-", "Intermediate filaments type II, keratins (basic)"	6460	protein-coding gene	gene with protein product	"hard keratin type II"	602765	"keratin, hair, basic, 3"	KRTHB3		9084137, 16831889	Standard	NM_002282		Approved	Hb-3	uc001saf.2	P78385	OTTHUMG00000169632	ENST00000293670.3:c.101_102delinsCT	chr12.hg19:g.52715018_52715019delinsCT	ENSP00000293670:p.Ala34Glu	44.0|41.0	0.0		103.0|102.0	26.0	NM_002282	A1A4S9|B2RC21|Q6NT21|Q9NSB3	Silent|Missense_Mutation	SNP	ENST00000293670.3	hg19	CCDS8823.1																																																																																			.	.		0.693	KRT83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405182.1	NM_002282		CT	52715019	GG	CT	52715018	3	2	322	1	0	0	0	0	1	0	0	0	8506	1103	39	4	1415	4	KRT83	12	52715018	Missense_Mutation	DNP	GG	TCGA-MI-A75G-01A-11D-A32G-10	850843	52715018	81136877	137	45385										
PDE1B	5153	hgsc.bcm.edu	37	chr12	54963367	54963367	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	acacctctgtgggccccactTactctactgcggttctcaac	7	16	3	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr12:54963367T>C	ENST00000243052.3	+	5	884	c.448T>C	c.(448-450)Tac>Cac	p.Y150H	PDE1B_ENST00000394277.3_3'UTR|PDE1B_ENST00000538346.1_Missense_Mutation_p.Y109H|PDE1B_ENST00000550620.1_Missense_Mutation_p.Y130H	NM_000924.3	NP_000915.1	Q01064	PDE1B_HUMAN	phosphodiesterase 1B, calmodulin-dependent	150					activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cGMP catabolic process (GO:0046069)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|monocyte differentiation (GO:0030224)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of dopamine metabolic process (GO:0042053)|regulation of neurotransmitter levels (GO:0001505)|response to amphetamine (GO:0001975)|serotonin metabolic process (GO:0042428)|signal transduction (GO:0007165)|visual learning (GO:0008542)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|calcium- and calmodulin-regulated 3',5'-cyclic-GMP phosphodiesterase activity (GO:0048101)|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)			endometrium(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(4)	31					Bepridil(DB01244)|Caffeine(DB00201)|Felodipine(DB01023)|Nicardipine(DB00622)	GGGCCCCACTTACTCTACTGC	0.507																																					p.Y150H		Atlas-SNP	.											.	PDE1B	76	.	0			c.T448C						.						141	115	124					12																	54963367		2203	4300	6503	SO:0001583	missense	5153	exon5			CCCACTTACTCTA	U56976	CCDS8882.1, CCDS53800.1, CCDS73477.1	12q13	2008-03-18				ENSG00000123360	3.1.4.17	"Phosphodiesterases"	8775	protein-coding gene	gene with protein product		171891		PDES1B		8855339, 9419816	Standard	NM_000924		Approved		uc001sgd.2	Q01064	OTTHUMG00000169844	ENST00000243052.3:c.448T>C	chr12.hg19:g.54963367T>C	ENSP00000243052:p.Tyr150His	90.0	0.0		111.0	47.0	NM_000924	Q92825|Q96KP3	Missense_Mutation	SNP	ENST00000243052.3	hg19	CCDS8882.1	.	.	.	.	.	.	.	.	.	.	T	16.42	3.116963	0.56505	.	.	ENSG00000123360	ENST00000243052;ENST00000538346;ENST00000550620	T;T;T	0.69926	-0.44;-0.4;-0.41	4.16	0.618	0.17624	5&apos (1);-cyclic nucleotide phosphodiesterase, catalytic domain (1);3&apos (1);	0.480321	0.21722	N	0.070103	T	0.73210	0.3558	M	0.67397	2.05	0.36352	D	0.860136	D;D	0.62365	0.991;0.984	D;P	0.67725	0.953;0.899	T	0.72181	-0.4368	10	0.37606	T	0.19	.	6.8959	0.24255	0.0:0.3464:0.0:0.6536	.	130;150	Q01064-2;Q01064	.;PDE1B_HUMAN	H	150;109;130	ENSP00000243052:Y150H;ENSP00000442559:Y109H;ENSP00000448519:Y130H	ENSP00000243052:Y150H	Y	+	1	0	PDE1B	53249634	0.971000	0.33674	0.780000	0.31762	0.694000	0.40290	0.357000	0.20199	0.097000	0.17492	0.533000	0.62120	TAC	.	.		0.507	PDE1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406203.1			C	54963367	T	C	54963367	3	2	322	1	0	0	0	0	1	0	0	0	11643	1754	61	2	519	2	PDE1B	12	54963367	Missense_Mutation	SNP	T	TCGA-MI-A75G-01A-11D-A32G-10	2248349	54963367	78888528	138	45386										
DCD	117159	hgsc.bcm.edu	37	chr12	55040905	55040905	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gaggaagagaaaggactcacGgttccccgatcctggggcag	15	10	1	1	rs552276383		TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr12:55040905G>T	ENST00000293371.6	-	2	286	c.97C>A	c.(97-99)Cct>Act	p.P33T	DCD_ENST00000456047.2_Splice_Site_p.P33T	NM_053283.2	NP_444513.1	P81605	DCD_HUMAN	dermcidin	33					defense response to bacterium (GO:0042742)|defense response to fungus (GO:0050832)|killing of cells of other organism (GO:0031640)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	peptidase activity (GO:0008233)|poly(A) RNA binding (GO:0044822)			large_intestine(2)|lung(2)|ovary(1)|skin(1)	6		Myeloproliferative disorder(1001;0.0255)				AAGGACTCACGGTTCCCCGAT	0.582																																					p.P33T		Atlas-SNP	.											.	DCD	20	.	0			c.C97A						.						53	35	41					12																	55040905		2188	4286	6474	SO:0001630	splice_region_variant	117159	exon2			ACTCACGGTTCCC	AF144011	CCDS8884.1, CCDS73478.1	12q13.1	2008-08-04				ENSG00000161634			14669	protein-coding gene	gene with protein product	"proteolysis inducing factor", "preproteolysin", "diffusible survival/evasion peptide", "survival promoting peptide"	606634				11694882	Standard	XM_005268627		Approved	AIDD, PIF, DSEP, HCAP, DCD-1	uc001sgj.3	P81605	OTTHUMG00000169937	ENST00000293371.6:c.97+1C>A	chr12.hg19:g.55040905G>T		29.0	0.0		33.0	5.0	NM_053283	A5JHP2|A5JHP3|P58461|Q53YJ2	Missense_Mutation	SNP	ENST00000293371.6	hg19	CCDS8884.1	.	.	.	.	.	.	.	.	.	.	G	4.087	0.014096	0.07959	.	.	ENSG00000161634	ENST00000293371;ENST00000456047	.	.	.	2.64	-2.13	0.07144	.	.	.	.	.	T	0.07863	0.0197	N	0.08118	0	0.09310	N	1	P;P	0.49696	0.927;0.927	B;B	0.36719	0.231;0.231	T	0.17501	-1.0367	7	.	.	.	.	1.1905	0.01864	0.1292:0.194:0.3144:0.3623	.	33;33	A5JHP3;P81605	.;DCD_HUMAN	T	33	.	.	P	-	1	0	DCD	53327172	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-2.294000	0.01144	-0.492000	0.06687	-0.311000	0.09066	CCT	.	.		0.582	DCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406617.1	NM_053283	Missense_Mutation	T	55040905	G	T	55040905	5	4	322	1	0	0	0	0	0	0	1	0	4285	1130	39	1	251	1	DCD	12	55040905	Splice_Site	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	77538	55040905	78810990	139	45387										
ERBB3	2065	hgsc.bcm.edu	37	chr12	56486836	56486836	+	Missense_Mutation	SNP	C	C	T													0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tgttttttccaatttgacaaCcattggaggcagaagcctct							TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr12:56486836C>T	ENST00000267101.3	+	11	1690	c.1250C>T	c.(1249-1251)aCc>aTc	p.T417I	ERBB3_ENST00000450146.2_Intron|ERBB3_ENST00000553131.1_5'Flank|ERBB3_ENST00000415288.2_Missense_Mutation_p.T358I	NM_001982.3	NP_001973.2	P21860	ERBB3_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3	417					cranial nerve development (GO:0021545)|endocardial cushion development (GO:0003197)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of cell adhesion (GO:0007162)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of secretion (GO:0051048)|negative regulation of signal transduction (GO:0009968)|neuron apoptotic process (GO:0051402)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell proliferation (GO:0042127)|Schwann cell differentiation (GO:0014037)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein tyrosine kinase activator activity (GO:0030296)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			AATTTGACAACCATTGGAGGC	0.478																																					p.T417I		Atlas-SNP	.											.	ERBB3	350	.	0			c.C1250T						.						74	73	73					12																	56486836		2203	4300	6503	SO:0001583	missense	2065	exon11			TGACAACCATTGG	M34309	CCDS31833.1, CCDS44918.1	12q13	2013-07-09	2013-07-09			ENSG00000065361			3431	protein-coding gene	gene with protein product		190151	"lethal congenital contracture syndrome 2"	LCCS2			Standard	NM_001982		Approved	HER3	uc001sjh.3	P21860	OTTHUMG00000170140	ENST00000267101.3:c.1250C>T	chr12.hg19:g.56486836C>T	ENSP00000267101:p.Thr417Ile	62.0	0.0		80.0	12.0	NM_001982	A8K6L6|B4DIK7|B4DV32|E9PDT8|Q9BUD7	Missense_Mutation	SNP	ENST00000267101.3	hg19	CCDS31833.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.970575	0.74246	.	.	ENSG00000065361	ENST00000267101;ENST00000415288	T;T	0.78126	-1.15;-1.15	5.06	5.06	0.68205	EGF receptor, L domain (1);	0.000000	0.64402	D	0.000003	T	0.75606	0.3872	L	0.33245	0.995	0.80722	D	1	P	0.40050	0.7	P	0.48840	0.592	T	0.69465	-0.5138	10	0.14252	T	0.57	.	17.3497	0.87320	0.0:1.0:0.0:0.0	.	417	P21860	ERBB3_HUMAN	I	417;358	ENSP00000267101:T417I;ENSP00000408340:T358I	ENSP00000267101:T417I	T	+	2	0	ERBB3	54773103	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.700000	0.54786	2.638000	0.89438	0.655000	0.94253	ACC	.	.		0.478	ERBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407619.3			T	56486836	C	T	56486836	3	4	322	1	0	0	0	0	1	0	0	0	5210	507	18	3	1423	3	ERBB3	12	56486836	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	1445931	56486836	77365059	140	45388	239	2								
ERBB3	2065	hgsc.bcm.edu	37	chr12	56486845	56486845	+	Missense_Mutation	SNP	G	G	T													0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	caatttgacaaccattggagGcagaagcctctacaagtgag							TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr12:56486845G>T	ENST00000267101.3	+	11	1699	c.1259G>T	c.(1258-1260)gGc>gTc	p.G420V	ERBB3_ENST00000450146.2_Intron|ERBB3_ENST00000553131.1_5'Flank|ERBB3_ENST00000415288.2_Missense_Mutation_p.G361V	NM_001982.3	NP_001973.2	P21860	ERBB3_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3	420					cranial nerve development (GO:0021545)|endocardial cushion development (GO:0003197)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of cell adhesion (GO:0007162)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of secretion (GO:0051048)|negative regulation of signal transduction (GO:0009968)|neuron apoptotic process (GO:0051402)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell proliferation (GO:0042127)|Schwann cell differentiation (GO:0014037)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein tyrosine kinase activator activity (GO:0030296)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			ACCATTGGAGGCAGAAGCCTC	0.468																																					p.G420V		Atlas-SNP	.											.	ERBB3	350	.	0			c.G1259T						.						61	61	61					12																	56486845		2203	4300	6503	SO:0001583	missense	2065	exon11			TTGGAGGCAGAAG	M34309	CCDS31833.1, CCDS44918.1	12q13	2013-07-09	2013-07-09			ENSG00000065361			3431	protein-coding gene	gene with protein product		190151	"lethal congenital contracture syndrome 2"	LCCS2			Standard	NM_001982		Approved	HER3	uc001sjh.3	P21860	OTTHUMG00000170140	ENST00000267101.3:c.1259G>T	chr12.hg19:g.56486845G>T	ENSP00000267101:p.Gly420Val	56.0	0.0		77.0	12.0	NM_001982	A8K6L6|B4DIK7|B4DV32|E9PDT8|Q9BUD7	Missense_Mutation	SNP	ENST00000267101.3	hg19	CCDS31833.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.755766	0.89843	.	.	ENSG00000065361	ENST00000267101;ENST00000415288	T;T	0.55052	0.54;0.54	5.06	5.06	0.68205	EGF receptor, L domain (1);	0.000000	0.64402	D	0.000003	T	0.81645	0.4866	H	0.96398	3.815	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87518	0.2444	10	0.87932	D	0	.	17.3497	0.87320	0.0:0.0:1.0:0.0	.	420	P21860	ERBB3_HUMAN	V	420;361	ENSP00000267101:G420V;ENSP00000408340:G361V	ENSP00000267101:G420V	G	+	2	0	ERBB3	54773112	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.256000	0.95535	2.638000	0.89438	0.655000	0.94253	GGC	.	.		0.468	ERBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407619.3			T	56486845	G	T	56486845	3	4	322	1	0	0	0	0	1	0	0	0	5210	1203	42	3	1432	3	ERBB3	12	56486845	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	9	56486845	77365050	141	45389	239	2								
LRP1	4035	hgsc.bcm.edu	37	chr12	57552232	57552232	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	atggcaagggccggccaggcAtcatccggggcatggatatg	16	10	1	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr12:57552232A>G	ENST00000243077.3	+	11	2075	c.1609A>G	c.(1609-1611)Atc>Gtc	p.I537V		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	537					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	CCGGCCAGGCATCATCCGGGG	0.592																																					p.I537V		Atlas-SNP	.											.	LRP1	428	.	0			c.A1609G						.						93	75	81					12																	57552232		2203	4300	6503	SO:0001583	missense	4035	exon11			CCAGGCATCATCC	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"CD molecules", "Low density lipoprotein receptors"	6692	protein-coding gene	gene with protein product		107770	"alpha-2-macroglobulin receptor"	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.1609A>G	chr12.hg19:g.57552232A>G	ENSP00000243077:p.Ile537Val	61.0	0.0		58.0	17.0	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	hg19	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	A	8.885	0.952583	0.18431	.	.	ENSG00000123384	ENST00000243077	T	0.29142	1.58	4.3	3.11	0.35812	Six-bladed beta-propeller, TolB-like (1);	0.083168	0.48767	D	0.000172	T	0.15003	0.0362	N	0.13098	0.295	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.07347	-1.0777	10	0.10377	T	0.69	.	9.4304	0.38606	0.8209:0.1791:0.0:0.0	.	537	Q07954	LRP1_HUMAN	V	537	ENSP00000243077:I537V	ENSP00000243077:I537V	I	+	1	0	LRP1	55838499	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.081000	0.57627	0.939000	0.37446	0.459000	0.35465	ATC	.	.		0.592	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		G	57552232	A	G	57552232	3	3	322	1	0	0	0	0	1	0	0	0	8960	217	8	2	1651	2	LRP1	12	57552232	Missense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	1065387	57552232	76299663	142	45390										
MARS	4141	hgsc.bcm.edu	37	chr12	57884114	57884114	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cggccttacctccaaaagcaGccccagcccagccccgctga	8	20	0	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr12:57884114G>T	ENST00000262027.5	+	6	749	c.615G>T	c.(613-615)caG>caT	p.Q205H	ARHGAP9_ENST00000393797.2_5'Flank|ARHGAP9_ENST00000550288.1_5'Flank|MARS_ENST00000315473.5_5'UTR|MARS_ENST00000447721.2_3'UTR	NM_004990.3	NP_004981.2	P56192	SYMC_HUMAN	methionyl-tRNA synthetase	205					gene expression (GO:0010467)|methionyl-tRNA aminoacylation (GO:0006431)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|methionine-tRNA ligase activity (GO:0004825)|tRNA binding (GO:0000049)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	33			GBM - Glioblastoma multiforme(3;4.27e-41)		L-Methionine(DB00134)	TCCAAAAGCAGCCCCAGCCCA	0.597																																					p.Q205H		Atlas-SNP	.											.	MARS	84	.	0			c.G615T						.						93	103	99					12																	57884114		2203	4300	6503	SO:0001583	missense	4141	exon6			AAAGCAGCCCCAG	X94754	CCDS8942.1	12q13.3	2014-05-06	2007-02-26		ENSG00000166986	ENSG00000166986	6.1.1.10	"Aminoacyl tRNA synthetases / Class I"	6898	protein-coding gene	gene with protein product	"methionine tRNA ligase 1, cytoplasmic"	156560				10448063, 24482476	Standard	NM_004990		Approved	MetRS, SPG70	uc001sog.3	P56192	OTTHUMG00000169996	ENST00000262027.5:c.615G>T	chr12.hg19:g.57884114G>T	ENSP00000262027:p.Gln205His	36.0	0.0		42.0	8.0	NM_004990	B3KVK7|Q14895|Q53H14|Q96A15|Q96BZ0|Q9NSE0	Missense_Mutation	SNP	ENST00000262027.5	hg19	CCDS8942.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.59|13.59	2.281463|2.281463	0.40394|0.40394	.|.	.|.	ENSG00000166986|ENSG00000166986	ENST00000262027|ENST00000552371	T|.	0.32515|.	1.45|.	4.44|4.44	3.54|3.54	0.40534|0.40534	.|.	0.216251|.	0.40064|.	N|.	0.001195|.	T|T	0.55033|0.55033	0.1895|0.1895	L|L	0.48642|0.48642	1.525|1.525	0.80722|0.80722	D|D	1|1	B;B|.	0.16396|.	0.017;0.009|.	B;B|.	0.15052|.	0.012;0.006|.	T|T	0.50759|0.50759	-0.8790|-0.8790	10|5	0.41790|.	T|.	0.15|.	-14.7929|-14.7929	7.4037|7.4037	0.26979|0.26979	0.0911:0.0:0.7422:0.1667|0.0911:0.0:0.7422:0.1667	.|.	78;205|.	B4E0E9;P56192|.	.;SYMC_HUMAN|.	H|I	205|77	ENSP00000262027:Q205H|.	ENSP00000262027:Q205H|.	Q|S	+|+	3|2	2|0	MARS|MARS	56170381|56170381	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	2.044000|2.044000	0.41241|0.41241	1.234000|1.234000	0.43709|0.43709	0.514000|0.514000	0.50259|0.50259	CAG|AGC	.	.		0.597	MARS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407014.1	NM_004990		T	57884114	G	T	57884114	3	4	322	1	0	0	0	0	1	0	0	0	9325	962	34	3	637	3	MARS	12	57884114	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	331882	57884114	75967781	143	45391										
C12orf64	283310	hgsc.bcm.edu	37	chr12	80762078	80762078	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	acatggaaaatggaacatcaGttgtatacgcggtatgtttc	10	6	1	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr12:80762078G>C	ENST00000547103.1	+	54	6547	c.6541G>C	c.(6541-6543)Gtt>Ctt	p.V2181L	OTOGL_ENST00000458043.2_Missense_Mutation_p.V2193L|OTOGL_ENST00000546620.1_Missense_Mutation_p.V212L			Q3ZCN5	OTOGL_HUMAN	otogelin-like	2181					L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						TGGAACATCAGTTGTATACGC	0.423																																					p.V2193L		Atlas-SNP	.											.	OTOGL	235	.	0			c.G6577C						.						136	119	125					12																	80762078		2203	4300	6503	SO:0001583	missense	283310	exon54			ACATCAGTTGTAT	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"chromosome 12 open reading frame 64"	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.6541G>C	chr12.hg19:g.80762078G>C	ENSP00000447211:p.Val2181Leu	55.0	0.0		60.0	17.0	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.14|11.14	1.549734|1.549734	0.27652|0.27652	.|.	.|.	ENSG00000165899|ENSG00000165899	ENST00000298820|ENST00000547103;ENST00000458043;ENST00000546620;ENST00000550182	.|T;T;T;T	.|0.42900	.|2.44;2.44;2.33;0.96	4.74|4.74	3.83|3.83	0.44106|0.44106	.|.	.|0.689513	.|0.13304	.|N	.|0.398006	T|T	0.30854|0.30854	0.0778|0.0778	L|L	0.42245|0.42245	1.32|1.32	0.24826|0.24826	N|N	0.992553|0.992553	.|B	.|0.30236	.|0.274	.|B	.|0.29353	.|0.101	T|T	0.18209|0.18209	-1.0344|-1.0344	5|10	.|0.15952	.|T	.|0.53	.|.	7.0272|7.0272	0.24946|0.24946	0.087:0.0:0.6063:0.3067|0.087:0.0:0.6063:0.3067	.|.	.|558	.|Q3ZCN5	.|OTOGL_HUMAN	H|L	600|2181;2193;212;210	.|ENSP00000447211:V2181L;ENSP00000400895:V2193L;ENSP00000449094:V212L;ENSP00000449641:V210L	.|ENSP00000400895:V2193L	Q|V	+|+	3|1	2|0	OTOGL|OTOGL	79286209|79286209	0.527000|0.527000	0.26306|0.26306	1.000000|1.000000	0.80357|0.80357	0.386000|0.386000	0.30323|0.30323	3.314000|3.314000	0.51943|0.51943	1.246000|1.246000	0.43901|0.43901	0.585000|0.585000	0.79938|0.79938	CAG|GTT	.	.		0.423	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591		C	80762078	G	C	80762078	3	2	322	1	0	0	0	0	1	0	0	0	1709	1029	36	4	6791	4	C12orf64	12	80762078	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	22877964	80762078	53089817	144	45392										
UTP20	27340	hgsc.bcm.edu	37	chr12	101750830	101750830	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ctcctatatgttttaaaagaAttacagactactcttgtccg	5	9	1	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr12:101750830A>C	ENST00000261637.4	+	43	5835	c.5661A>C	c.(5659-5661)gaA>gaC	p.E1887D	snoU13_ENST00000458958.1_RNA	NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	1887					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						TTTTAAAAGAATTACAGACTA	0.378																																					p.E1887D		Atlas-SNP	.											.	UTP20	222	.	0			c.A5661C						.						75	72	73					12																	101750830		2203	4300	6503	SO:0001583	missense	27340	exon43			AAAAGAATTACAG	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"down regulated in metastasis"	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.5661A>C	chr12.hg19:g.101750830A>C	ENSP00000261637:p.Glu1887Asp	64.0	0.0		77.0	11.0	NM_014503	Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	hg19	CCDS9081.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.349155	0.82132	.	.	ENSG00000120800	ENST00000261637	T	0.47177	0.85	5.79	-0.493	0.12038	Armadillo-type fold (1);	0.047730	0.85682	D	0.000000	T	0.57725	0.2073	L	0.61387	1.9	0.46981	D	0.999271	D	0.65815	0.995	D	0.67103	0.949	T	0.56068	-0.8040	10	0.48119	T	0.1	-24.176	9.6997	0.40178	0.4399:0.0:0.5601:0.0	.	1887	O75691	UTP20_HUMAN	D	1887	ENSP00000261637:E1887D	ENSP00000261637:E1887D	E	+	3	2	UTP20	100274961	1.000000	0.71417	0.982000	0.44146	0.953000	0.61014	0.754000	0.26390	0.107000	0.17824	0.533000	0.62120	GAA	.	.		0.378	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		C	101750830	A	C	101750830	3	2	322	1	0	0	0	0	1	0	0	0	17114	98	4	5	5831	5	UTP20	12	101750830	Missense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	20988752	101750830	32101065	145	45393										
STAB2	55576	hgsc.bcm.edu	37	chr12	104136187	104136187	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gtttcatctcttccagcctgCcctggaggaccagatgcccc	9	16	2	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr12:104136187C>T	ENST00000388887.2	+	56	6090	c.5886C>T	c.(5884-5886)tgC>tgT	p.C1962C		NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						TTCCAGCCTGCCCTGGAGGAC	0.542																																					p.C1962C		Atlas-SNP	.											.	STAB2	370	.	0			c.C5886T						.						111	101	104					12																	104136187		2203	4300	6503	SO:0001819	synonymous_variant	55576	exon56			AGCCTGCCCTGGA	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"hyaluronic acid receptor for endocytosis"	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.5886C>T	chr12.hg19:g.104136187C>T		53.0	0.0		67.0	27.0	NM_017564		Silent	SNP	ENST00000388887.2	hg19	CCDS31888.1																																																																																			.	.		0.542	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			T	104136187	C	T	104136187	2	4	322	1	0	0	0	0	0	0	0	1	15253	747	26	3		3	STAB2	12	104136187	Silent	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	2385357	104136187	29715708	146	45394										
PTPN11	5781	hgsc.bcm.edu	37	chr12	112910827	112910827	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	aaacaaaaacaaaaatagatAtaaaaacatcctgccctgta	3	8	0	1	rs121918456		TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr12:112910827A>G	ENST00000351677.2	+	7	1034	c.836A>G	c.(835-837)tAt>tGt	p.Y279C	PTPN11_ENST00000392597.1_Missense_Mutation_p.Y279C	NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	279	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.		Y -> C (in NS1 and LEOPARD1). {ECO:0000269|PubMed:11992261, ECO:0000269|PubMed:12058348, ECO:0000269|PubMed:12960218, ECO:0000269|PubMed:15121796, ECO:0000269|PubMed:15520399, ECO:0000269|PubMed:16679933}.|Y -> S (in LEOPARD1). {ECO:0000269|PubMed:15121796, ECO:0000269|PubMed:15520399}.		abortive mitotic cell cycle (GO:0033277)|activation of MAPK activity (GO:0000187)|atrioventricular canal development (GO:0036302)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage checkpoint (GO:0000077)|ephrin receptor signaling pathway (GO:0048013)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|genitalia development (GO:0048806)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|multicellular organismal reproductive process (GO:0048609)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cortisol secretion (GO:0051463)|negative regulation of growth hormone secretion (GO:0060125)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ growth (GO:0035265)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of hormone secretion (GO:0046887)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of multicellular organism growth (GO:0040014)|regulation of protein export from nucleus (GO:0046825)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	insulin receptor binding (GO:0005158)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3)	451						aaaaatagatataaaaacaTC	0.398			Mis		"JMML, AML, MDS"		Noonan Syndrome		Noonan syndrome																												p.Y279C		Atlas-SNP	.		Dom	yes		12	12q24.1	5781	"protein tyrosine phosphatase, non-receptor type 11"	yes	L	PTPN11,NS,carcinoma,0,1	PTPN11	623	.	0			c.A836G	GRCh37	CM021133|CM041069	PTPN11	M	rs121918456	.						56	61	60					12																	112910827		2202	4298	6500	SO:0001583	missense	5781	exon7	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	ATAGATATAAAAA	D13540	CCDS9163.1, CCDS58280.1	12q24.1	2014-09-17	2008-07-31		ENSG00000179295	ENSG00000179295		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor", "SH2 domain containing"	9644	protein-coding gene	gene with protein product		176876	"Noonan syndrome 1"	NS1		7894486, 1280823	Standard	NM_080601		Approved	BPTP3, SH-PTP2, SHP-2, PTP2C, SHP2	uc001ttx.3	Q06124	OTTHUMG00000134334	ENST00000351677.2:c.836A>G	chr12.hg19:g.112910827A>G	ENSP00000340944:p.Tyr279Cys	235.0	0.0		286.0	126.0	NM_080601	A8K1D9|Q96HD7	Missense_Mutation	SNP	ENST00000351677.2	hg19	CCDS9163.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.113664	0.77210	.	.	ENSG00000179295	ENST00000392597;ENST00000351677	D;D	0.99494	-6.01;-6.01	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	D	0.99594	0.9853	H	0.95114	3.625	0.80722	A	1	P;P	0.50819	0.939;0.846	P;P	0.57776	0.827;0.753	D	0.97782	1.0233	9	0.87932	D	0	.	15.2426	0.73482	1.0:0.0:0.0:0.0	.	279;279	Q06124-2;Q06124-3	.;.	C	279	ENSP00000376376:Y279C;ENSP00000340944:Y279C	ENSP00000340944:Y279C	Y	+	2	0	PTPN11	111395210	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.562000	0.90719	2.302000	0.77476	0.528000	0.53228	TAT	.	.		0.398	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259496.2			G	112910827	A	G	112910827	3	3	322	1	0	0	0	0	1	0	0	0	12793	449	16	2	862	2	PTPN11	12	112910827	Missense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	8774640	112910827	20941068	147	45395										
GCN1L1	10985	hgsc.bcm.edu	37	chr12	120594723	120594723	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	aaaaccacatcacctgtaagCgaggcgagcccgtcccgatc	9	15	1	0	rs201424442		TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr12:120594723C>T	ENST00000300648.6	-	27	3173	c.3161G>A	c.(3160-3162)cGc>cAc	p.R1054H	MIR4498_ENST00000577599.1_RNA	NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	1054					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CACCTGTAAGCGAGGCGAGCC	0.562													C|||	1	0.000199681	8e-04	0	5008	,	,		19196	0		0	False		,,,				2504	0				p.R1054H		Atlas-SNP	.											GCN1L1,NS,carcinoma,0,1	GCN1L1	207	.	0			c.G3161A						.	C	HIS/ARG	0,4226		0,0,2113	61	70	67		3161	2.7	1	12		67	1,8421		0,1,4210	yes	missense	GCN1L1	NM_006836.1	29	0,1,6323	TT,TC,CC		0.0119,0.0,0.0079	possibly-damaging	1054/2672	120594723	1,12647	2113	4211	6324	SO:0001583	missense	10985	exon27			TGTAAGCGAGGCG	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.3161G>A	chr12.hg19:g.120594723C>T	ENSP00000300648:p.Arg1054His	34.0	0.0		32.0	10.0	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Missense_Mutation	SNP	ENST00000300648.6	hg19	CCDS41847.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.611391	0.87258	0.0	1.19E-4	ENSG00000089154	ENST00000300648	T	0.37411	1.2	5.52	2.73	0.32206	Armadillo-like helical (1);Armadillo-type fold (1);	0.120029	0.64402	N	0.000015	T	0.37812	0.1017	L	0.49350	1.555	0.80722	D	1	D	0.65815	0.995	P	0.50934	0.654	T	0.08868	-1.0701	10	0.39692	T	0.17	.	8.6118	0.33806	0.0:0.71:0.0:0.29	.	1054	Q92616	GCN1L_HUMAN	H	1054	ENSP00000300648:R1054H	ENSP00000300648:R1054H	R	-	2	0	GCN1L1	119079106	1.000000	0.71417	0.992000	0.48379	0.877000	0.50540	2.516000	0.45520	0.695000	0.31675	0.591000	0.81541	CGC	.	.		0.562	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1			T	120594723	C	T	120594723	3	4	322	1	0	0	0	0	1	0	0	0	6307	768	27	1	4982	1	GCN1L1	12	120594723	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	7683896	120594723	13257172	148	45396										
SACS	26278	hgsc.bcm.edu	37	chr13	23905055	23905055	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ttttttcgttccgattctggAagcttccatgcttgctccac	7	12	1	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr13:23905055A>G	ENST00000382292.3	-	9	13233	c.12960T>C	c.(12958-12960)ctT>ctC	p.L4320L	SACS_ENST00000382298.3_Silent_p.L4320L|SACS_ENST00000402364.1_Silent_p.L3570L			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	4320	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		CCGATTCTGGAAGCTTCCATG	0.383																																					p.L4320L		Atlas-SNP	.											.	SACS	871	.	0			c.T12960C						.						116	126	123					13																	23905055		2203	4299	6502	SO:0001819	synonymous_variant	26278	exon10			TTCTGGAAGCTTC	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.12960T>C	chr13.hg19:g.23905055A>G		85.0	0.0		60.0	27.0	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	hg19	CCDS9300.2																																																																																			.	.		0.383	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		G	23905055	A	G	23905055	2	3	322	1	0	0	0	0	0	0	0	1	13819	233	9	2		2	SACS	13	23905055	Silent	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10		23905055	91264823	149	45397										
SACS	26278	hgsc.bcm.edu	37	chr13	23905368	23905368	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ttcctagaaaactagaattgTcagcatcttctctttcaact	4	10	4	2	rs550068559	byFrequency	TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr13:23905368T>C	ENST00000382292.3	-	9	12920	c.12647A>G	c.(12646-12648)gAc>gGc	p.D4216G	SACS_ENST00000382298.3_Missense_Mutation_p.D4216G|SACS_ENST00000402364.1_Missense_Mutation_p.D3466G			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	4216					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		ACTAGAATTGTCAGCATCTTC	0.343													T|||	2	0.000399361	0	0	5008	,	,		21397	0		0	False		,,,				2504	0.002				p.D4216G		Atlas-SNP	.											.	SACS	871	.	0			c.A12647G						.						50	53	52					13																	23905368		2203	4299	6502	SO:0001583	missense	26278	exon10			GAATTGTCAGCAT	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.12647A>G	chr13.hg19:g.23905368T>C	ENSP00000371729:p.Asp4216Gly	52.0	0.0		34.0	14.0	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	hg19	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	T	12.52	1.963518	0.34659	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.87729	-2.14;-2.29;-2.14	5.44	4.19	0.49359	.	0.142736	0.64402	D	0.000006	T	0.80412	0.4618	L	0.40543	1.245	0.46356	D	0.999002	B	0.32573	0.376	B	0.26770	0.073	T	0.81402	-0.0949	10	0.59425	D	0.04	.	12.1105	0.53836	0.0:0.0:0.1433:0.8567	.	4216	Q9NZJ4	SACS_HUMAN	G	4216;3466;4216	ENSP00000371729:D4216G;ENSP00000385844:D3466G;ENSP00000371735:D4216G	ENSP00000371729:D4216G	D	-	2	0	SACS	22803368	1.000000	0.71417	0.988000	0.46212	0.981000	0.71138	5.063000	0.64332	2.049000	0.60858	0.460000	0.39030	GAC	.	.		0.343	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		C	23905368	T	C	23905368	3	2	322	1	0	0	0	0	1	0	0	0	13819	1667	58	2	1096	2	SACS	13	23905368	Missense_Mutation	SNP	T	TCGA-MI-A75G-01A-11D-A32G-10	313	23905368	91264510	150	45398										
C13orf23	80209	hgsc.bcm.edu	37	chr13	39588511	39588511	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ctgctgatgctgatggatgaTtaattgccttgactggggat	13	6	0	4			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr13:39588511T>C	ENST00000352251.3	-	11	1711	c.878A>G	c.(877-879)aAt>aGt	p.N293S	PROSER1_ENST00000350125.3_Missense_Mutation_p.N271S|PROSER1_ENST00000484434.3_Intron	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	293	Pro-rich.																TGATGGATGATTAATTGCCTT	0.502																																					p.N293S		Atlas-SNP	.											.	.	.	.	0			c.A878G						.						112	93	99					13																	39588511		2203	4300	6503	SO:0001583	missense	80209	exon11			GGATGATTAATTG	AK022723	CCDS9368.2	13q13.2	2011-08-09	2011-08-09	2011-08-09	ENSG00000120685	ENSG00000120685			20291	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 23"	C13orf23			Standard	NM_025138		Approved	bA50D16.2, FLJ12661	uc001uwy.4	Q86XN7	OTTHUMG00000016764	ENST00000352251.3:c.878A>G	chr13.hg19:g.39588511T>C	ENSP00000332034:p.Asn293Ser	45.0	0.0		59.0	25.0	NM_025138	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	Missense_Mutation	SNP	ENST00000352251.3	hg19	CCDS9368.2	.	.	.	.	.	.	.	.	.	.	T	0.015	-1.568324	0.00895	.	.	ENSG00000120685	ENST00000352251;ENST00000350125	T;T	0.30981	1.51;1.51	4.52	-6.58	0.01836	.	.	.	.	.	T	0.12263	0.0298	N	0.11560	0.145	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.33343	-0.9872	8	.	.	.	-0.3502	8.0823	0.30752	0.0:0.4538:0.233:0.3132	.	271;293	A6NJ97;Q86XN7	.;PRSR1_HUMAN	S	293;271	ENSP00000332034:N293S;ENSP00000339123:N271S	.	N	-	2	0	PROSER1	38486511	0.050000	0.20438	0.000000	0.03702	0.000000	0.00434	-0.124000	0.10595	-1.559000	0.01688	-1.964000	0.00472	AAT	.	.		0.502	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5	NM_025138		C	39588511	T	C	39588511	3	2	322	1	0	0	0	0	1	0	0	0	1723	1493	52	2	1968	2	C13orf23	13	39588511	Missense_Mutation	SNP	T	TCGA-MI-A75G-01A-11D-A32G-10	15683143	39588511	75581367	151	45399										
NEK3	4752	hgsc.bcm.edu	37	chr13	52718081	52718081	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ggtgtgttatgcttcgaattTtttatttcttctaatacttc	6	6	2	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr13:52718081T>C	ENST00000400357.2	-	9	2139	c.846A>G	c.(844-846)aaA>aaG	p.K282K	NEK3_ENST00000339406.3_Silent_p.K282K|NEK3_ENST00000378101.2_Silent_p.K282K|NEK3_ENST00000452082.2_Silent_p.K303K			P51956	NEK3_HUMAN	NIMA-related kinase 3	282	Interaction with VAV2.				mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|stomach(2)	18		Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.034)|Hepatocellular(98;0.065)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.81e-08)		GCTTCGAATTTTTTATTTCTT	0.274																																					p.K282K		Atlas-SNP	.											.	NEK3	41	.	0			c.A846G						.						66	53	57					13																	52718081		1639	3684	5323	SO:0001819	synonymous_variant	4752	exon10			CGAATTTTTTATT	AK290259, BC019916	CCDS73576.1	13q14.2-q21.1	2014-07-17	2012-11-15		ENSG00000136098	ENSG00000136098	2.7.11.1		7746	protein-coding gene	gene with protein product	"serine/threonine-protein kinase NEK3", "phosphorylase B kinase kinase", "glycogen synthase A kinase", "hydroxyalkyl-protein kinase"	604044	"NIMA (never in mitosis gene a)-related kinase 3"			8274451, 7522034	Standard	NM_002498		Approved	HSPK36, MGC29949	uc010tgy.2	P51956	OTTHUMG00000016958	ENST00000400357.2:c.846A>G	chr13.hg19:g.52718081T>C		74.0	0.0		82.0	23.0	NM_002498	A8K2J4|Q5TAP2|Q8J023|Q8WUN5	Silent	SNP	ENST00000400357.2	hg19	CCDS53871.1																																																																																			.	.		0.274	NEK3-002	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045047.3			C	52718081	T	C	52718081	2	2	322	1	0	0	0	0	0	0	0	1	10334	1838	64	2		2	NEK3	13	52718081	Silent	SNP	T	TCGA-MI-A75G-01A-11D-A32G-10	13129570	52718081	62451797	152	45400										
PCDH9	5101	hgsc.bcm.edu	37	chr13	67800963	67800963	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cagttactgtaaaaatgaatCgttcttgttcttctctgtca	6	8	4	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr13:67800963C>T	ENST00000377865.2	-	1	1744	c.1610G>A	c.(1609-1611)cGa>cAa	p.R537Q	PCDH9_ENST00000544246.1_Missense_Mutation_p.R537Q|PCDH9_ENST00000456367.1_Missense_Mutation_p.R537Q|PCDH9_ENST00000377861.3_Missense_Mutation_p.R537Q|PCDH9_ENST00000328454.5_Missense_Mutation_p.R537Q			Q9HC56	PCDH9_HUMAN	protocadherin 9	537	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				forebrain development (GO:0030900)|homophilic cell adhesion (GO:0007156)	cell-cell contact zone (GO:0044291)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(33)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	103		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		AAAAATGAATCGTTCTTGTTC	0.463																																					p.R537Q		Atlas-SNP	.											.	PCDH9	252	.	0			c.G1610A						.						87	89	88					13																	67800963		2203	4300	6503	SO:0001583	missense	5101	exon2			ATGAATCGTTCTT	AF169692	CCDS9443.1, CCDS9444.1	13q21.32	2010-02-22			ENSG00000184226	ENSG00000184226		"Cadherins / Protocadherins : Non-clustered"	8661	protein-coding gene	gene with protein product		603581				9787079	Standard	NM_020403		Approved		uc001vik.3	Q9HC56	OTTHUMG00000017040	ENST00000377865.2:c.1610G>A	chr13.hg19:g.67800963C>T	ENSP00000367096:p.Arg537Gln	85.0	0.0		77.0	30.0	NM_203487	A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	Missense_Mutation	SNP	ENST00000377865.2	hg19	CCDS9444.1	.	.	.	.	.	.	.	.	.	.	C	17.09	3.299159	0.60195	.	.	ENSG00000184226	ENST00000544246;ENST00000377865;ENST00000456367;ENST00000328454;ENST00000377861	T;T;T;T;T	0.49432	0.78;0.78;0.78;0.78;0.78	6.08	6.08	0.98989	Cadherin (5);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.55768	0.1941	N	0.17838	0.53	0.58432	D	0.999994	D;D;D;D	0.65815	0.978;0.99;0.994;0.995	P;P;P;D	0.63283	0.821;0.806;0.859;0.913	T	0.57602	-0.7783	10	0.62326	D	0.03	.	20.6634	0.99662	0.0:1.0:0.0:0.0	.	537;537;537;537	B7ZM79;Q5VT82;Q9HC56-2;Q9HC56	.;.;.;PCDH9_HUMAN	Q	537	ENSP00000442186:R537Q;ENSP00000367096:R537Q;ENSP00000401699:R537Q;ENSP00000332060:R537Q;ENSP00000367092:R537Q	ENSP00000332060:R537Q	R	-	2	0	PCDH9	66698964	0.974000	0.33945	0.732000	0.30844	0.992000	0.81027	6.089000	0.71384	2.894000	0.99253	0.655000	0.94253	CGA	.	.		0.463	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1	NM_203487		T	67800963	C	T	67800963	3	4	322	1	0	0	0	0	1	0	0	0	11527	884	31	1	2119	1	PCDH9	13	67800963	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	15082882	67800963	47368915	153	45401										
TMCO3	55002	hgsc.bcm.edu	37	chr13	114201642	114201642	+	Frame_Shift_Del	DEL	C	C	-													0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cgtgttccccacgtttgtggCgtacgagctcacggtgctgg					rs576852684		TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr13:114201642delC	ENST00000434316.2	+	11	2077	c.1718delC	c.(1717-1719)gcgfs	p.A573fs	TMCO3_ENST00000375391.1_Intron	NM_017905.4	NP_060375.4	Q6UWJ1	TMCO3_HUMAN	transmembrane and coiled-coil domains 3	573						integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)			NS(1)|endometrium(4)|large_intestine(9)|liver(1)|lung(8)|prostate(1)|stomach(1)	25	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0145)|all_epithelial(44;0.00286)|all_lung(25;0.0273)|Breast(118;0.0411)|Lung NSC(25;0.0983)	all cancers(43;0.0317)			ACGTTTGTGGCGTACGAGCTC	0.582																																					p.A573fs		Atlas-INDEL	.											.	TMCO3	77	.	0			c.1717delG						.						251	165	194					13																	114201642		2203	4300	6503	SO:0001589	frameshift_variant	55002	exon11			.	BC012564	CCDS9537.1	13q34	2008-02-05	2005-07-22	2005-07-22	ENSG00000150403	ENSG00000150403			20329	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 11"	C13orf11			Standard	NM_017905		Approved	FLJ20623	uc001vtu.4	Q6UWJ1	OTTHUMG00000017389	ENST00000434316.2:c.1718delC	chr13.hg19:g.114201642delC	ENSP00000389399:p.Ala573fs	45.0	0.0		70.0	12.0	NM_017905	Q5JSB1|Q6NUN1|Q8NG29|Q8TCI6|Q96EA6|Q9NWT2	Frame_Shift_Del	DEL	ENST00000434316.2	hg19	CCDS9537.1																																																																																			.	.		0.582	TMCO3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045931.3	NM_017905		-	114201642	C	-	114201642	7	5	322	1	0	1	0	1	0	0	0	0	16012	768	27	0	1756	0	TMCO3	13	114201642	Frame_Shift_Del	DEL	C	TCGA-MI-A75G-01A-11D-A32G-10	46400679	114201642	968236	154	45402	240	2								
TMCO3	55002	hgsc.bcm.edu	37	chr13	114201644	114201644	+	Missense_Mutation	SNP	T	T	A													0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tgttccccacgtttgtggcgTacgagctcacggtgctggtg							TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr13:114201644T>A	ENST00000434316.2	+	11	2079	c.1720T>A	c.(1720-1722)Tac>Aac	p.Y574N	TMCO3_ENST00000375391.1_Intron	NM_017905.4	NP_060375.4	Q6UWJ1	TMCO3_HUMAN	transmembrane and coiled-coil domains 3	574						integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)			NS(1)|endometrium(4)|large_intestine(9)|liver(1)|lung(8)|prostate(1)|stomach(1)	25	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0145)|all_epithelial(44;0.00286)|all_lung(25;0.0273)|Breast(118;0.0411)|Lung NSC(25;0.0983)	all cancers(43;0.0317)			GTTTGTGGCGTACGAGCTCAC	0.582																																					p.Y574N		Atlas-SNP	.											.	TMCO3	77	.	0			c.T1720A						.						251	164	194					13																	114201644		2203	4300	6503	SO:0001583	missense	55002	exon11			GTGGCGTACGAGC	BC012564	CCDS9537.1	13q34	2008-02-05	2005-07-22	2005-07-22	ENSG00000150403	ENSG00000150403			20329	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 11"	C13orf11			Standard	NM_017905		Approved	FLJ20623	uc001vtu.4	Q6UWJ1	OTTHUMG00000017389	ENST00000434316.2:c.1720T>A	chr13.hg19:g.114201644T>A	ENSP00000389399:p.Tyr574Asn	47.0	0.0		71.0	13.0	NM_017905	Q5JSB1|Q6NUN1|Q8NG29|Q8TCI6|Q96EA6|Q9NWT2	Missense_Mutation	SNP	ENST00000434316.2	hg19	CCDS9537.1	.	.	.	.	.	.	.	.	.	.	T	7.341	0.620999	0.14193	.	.	ENSG00000150403	ENST00000434316	T	0.14516	2.5	4.78	3.56	0.40772	Cation/H+ exchanger (1);	0.220946	0.39834	N	0.001247	T	0.08980	0.0222	N	0.25647	0.755	0.80722	D	1	B	0.25206	0.12	B	0.24541	0.054	T	0.19976	-1.0289	10	0.13853	T	0.58	-15.8785	10.54	0.45026	0.0:0.0777:0.0:0.9223	.	574	Q6UWJ1	TMCO3_HUMAN	N	574	ENSP00000389399:Y574N	ENSP00000389399:Y574N	Y	+	1	0	TMCO3	113249645	1.000000	0.71417	0.005000	0.12908	0.083000	0.17756	5.908000	0.69916	0.668000	0.31126	0.374000	0.22700	TAC	.	.		0.582	TMCO3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045931.3	NM_017905		A	114201644	T	A	114201644	3	1	322	1	0	0	0	0	1	0	0	0	16012	1638	57	4	1758	4	TMCO3	13	114201644	Missense_Mutation	SNP	T	TCGA-MI-A75G-01A-11D-A32G-10	2	114201644	968234	155	45403	240	2								
OR4K17	390436	hgsc.bcm.edu	37	chr14	20585602	20585602	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cactcatactccatggtatgAgtgatcttttctttctctct	5	11	5	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr14:20585602A>T	ENST00000315543.4	+	1	37	c.37A>T	c.(37-39)Agt>Tgt	p.S13C		NM_001004715.1	NP_001004715.1	Q8NGC6	OR4KH_HUMAN	olfactory receptor, family 4, subfamily K, member 17	0						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(4)|lung(12)|pancreas(1)|skin(3)	21	all_cancers(95;0.00108)		Epithelial(56;7.58e-07)|all cancers(55;3.77e-06)	GBM - Glioblastoma multiforme(265;0.0144)		CCATGGTATGAGTGATCTTTT	0.368																																					p.S13C		Atlas-SNP	.											.	OR4K17	58	.	0			c.A37T						.						97	90	93					14																	20585602		2203	4300	6503	SO:0001583	missense	390436	exon1			GGTATGAGTGATC		CCDS32030.1	14q11.2	2013-09-23			ENSG00000176230	ENSG00000176230		"GPCR / Class A : Olfactory receptors"	15355	protein-coding gene	gene with protein product							Standard	NM_001004715		Approved		uc001vwo.1	Q8NGC6	OTTHUMG00000170783	ENST00000315543.4:c.37A>T	chr14.hg19:g.20585602A>T	ENSP00000319197:p.Ser13Cys	69.0	0.0		99.0	50.0	NM_001004715	Q6IF12	Missense_Mutation	SNP	ENST00000315543.4	hg19	CCDS32030.1	.	.	.	.	.	.	.	.	.	.	.	13.76	2.333352	0.41297	.	.	ENSG00000176230	ENST00000315543	T	0.28666	1.6	2.31	1.16	0.20824	.	.	.	.	.	T	0.26557	0.0649	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.22208	-1.0223	6	0.45353	T	0.12	.	5.5848	0.17269	0.8479:0.0:0.1521:0.0	.	.	.	.	C	13	ENSP00000319197:S13C	ENSP00000319197:S13C	S	+	1	0	OR4K17	19655442	0.002000	0.14202	0.000000	0.03702	0.044000	0.14063	1.020000	0.30027	0.322000	0.23283	0.164000	0.16699	AGT	.	.		0.368	OR4K17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410346.1			T	20585602	A	T	20585602	3	4	322	1	0	0	0	0	1	0	0	0	11080	304	11	4	39	4	OR4K17	14	20585602	Missense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10		20585602	86763938	156	45404										
RPGRIP1	57096	hgsc.bcm.edu	37	chr14	21770659	21770659	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	acttttagggccaagggacaGgctgagctacacagcccctc	11	13	0	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr14:21770659G>A	ENST00000400017.2	+	4	503	c.503G>A	c.(502-504)aGg>aAg	p.R168K	RPGRIP1_ENST00000556336.1_Missense_Mutation_p.R168K|RPGRIP1_ENST00000557771.1_Missense_Mutation_p.R168K|RPGRIP1_ENST00000206660.6_Missense_Mutation_p.R168K	NM_020366.3	NP_065099.3	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator interacting protein 1	168					eye photoreceptor cell development (GO:0042462)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	axoneme (GO:0005930)|nonmotile primary cilium (GO:0031513)				breast(3)|endometrium(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(4)|pancreas(1)|prostate(3)|stomach(1)	39	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)		CCAAGGGACAGGCTGAGCTAC	0.493																																					p.R168K		Atlas-SNP	.											.	RPGRIP1	213	.	0			c.G503A						.						48	48	48					14																	21770659		1956	4147	6103	SO:0001583	missense	57096	exon4			GGGACAGGCTGAG	AF227257	CCDS45080.1	14q11.2	2013-06-06			ENSG00000092200	ENSG00000092200			13436	protein-coding gene	gene with protein product		605446		RPGRIP		10958647, 10958648	Standard	NM_020366		Approved	RGI1, LCA6, CORD13	uc001wag.3	Q96KN7	OTTHUMG00000170758	ENST00000400017.2:c.503G>A	chr14.hg19:g.21770659G>A	ENSP00000382895:p.Arg168Lys	33.0	0.0		42.0	13.0	NM_020366	Q7Z2W6|Q8IXV5|Q96QA8|Q9HB94|Q9HB95|Q9HBK6|Q9NR40	Missense_Mutation	SNP	ENST00000400017.2	hg19	CCDS45080.1	.	.	.	.	.	.	.	.	.	.	G	16.04	3.008872	0.54361	.	.	ENSG00000092200	ENST00000556336;ENST00000557771;ENST00000400017;ENST00000206660	T;T;T;T	0.36340	1.26;1.26;1.26;1.26	4.96	4.96	0.65561	.	0.000000	0.85682	D	0.000000	T	0.31513	0.0799	L	0.58101	1.795	0.80722	D	1	P	0.43750	0.816	B	0.36766	0.232	T	0.11227	-1.0596	10	0.12766	T	0.61	-16.4631	15.2387	0.73452	0.0:0.0:1.0:0.0	.	168	Q96KN7	RPGR1_HUMAN	K	168	ENSP00000450445:R168K;ENSP00000451219:R168K;ENSP00000382895:R168K;ENSP00000206660:R168K	ENSP00000206660:R168K	R	+	2	0	RPGRIP1	20840499	0.939000	0.31865	0.023000	0.16930	0.733000	0.41908	4.513000	0.60476	2.582000	0.87167	0.650000	0.86243	AGG	.	.		0.493	RPGRIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410258.1	NM_020366		A	21770659	G	A	21770659	3	1	322	1	0	0	0	0	1	0	0	0	13564	1000	35	3	517	3	RPGRIP1	14	21770659	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	1185057	21770659	85578881	157	45405										
SALL2	6297	hgsc.bcm.edu	37	chr14	21991101	21991101	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ctccagagctgcctgggaggGaaaggcctggccacacactt	13	13	0	1	rs267603925		TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr14:21991101G>T	ENST00000327430.3	-	2	3055	c.2761C>A	c.(2761-2763)Ccc>Acc	p.P921T	SALL2_ENST00000317492.5_Intron|SALL2_ENST00000450879.2_Missense_Mutation_p.P784T|AE000658.22_ENST00000535893.1_RNA|SALL2_ENST00000538754.1_Intron	NM_005407.1	NP_005398.1	Q9Y467	SALL2_HUMAN	spalt-like transcription factor 2	921					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(12)|lung(12)|ovary(2)|skin(6)|urinary_tract(2)	43	all_cancers(95;0.000662)			GBM - Glioblastoma multiforme(265;0.0151)		GCCTGGGAGGGAAAGGCCTGG	0.602																																					p.P921T		Atlas-SNP	.											.	SALL2	95	.	0			c.C2761A						.						66	68	67					14																	21991101		2203	4300	6503	SO:0001583	missense	6297	exon2			GGGAGGGAAAGGC	AB002358	CCDS32045.1	14q11.1-q12.1	2013-10-17	2013-10-17		ENSG00000165821	ENSG00000165821		"Zinc fingers, C2H2-type"	10526	protein-coding gene	gene with protein product		602219	"sal (Drosophila)-like 2", "sal-like 2 (Drosophila)"			8975705	Standard	XM_005267983		Approved	KIAA0360, Hsal2, ZNF795	uc001wbe.3	Q9Y467	OTTHUMG00000168826	ENST00000327430.3:c.2761C>A	chr14.hg19:g.21991101G>T	ENSP00000333537:p.Pro921Thr	75.0	0.0		111.0	37.0	NM_005407	B2RMX6|B9EGK8|Q8N656|Q9Y4G1	Missense_Mutation	SNP	ENST00000327430.3	hg19	CCDS32045.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.05|11.05	1.524731|1.524731	0.27299|0.27299	.|.	.|.	ENSG00000165821|ENSG00000165821	ENST00000546363|ENST00000327430;ENST00000450879	T|T;T	0.38722|0.26810	1.12|1.71;1.71	4.69|4.69	3.76|3.76	0.43208|0.43208	.|Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.|0.000000	.|0.38837	.|N	.|0.001556	T|T	0.09113|0.09113	0.0225|0.0225	N|N	0.03281|0.03281	-0.365|-0.365	0.35584|0.35584	D|D	0.806488|0.806488	.|B;B;B;B	.|0.33694	.|0.421;0.421;0.281;0.281	.|B;B;B;B	.|0.30646	.|0.083;0.118;0.037;0.027	T|T	0.24621|0.24621	-1.0155|-1.0155	7|10	0.87932|0.21014	D|T	0|0.42	-22.7312|-22.7312	6.1929|6.1929	0.20534|0.20534	0.1001:0.1917:0.7082:0.0|0.1001:0.1917:0.7082:0.0	.|.	.|784;784;682;921	.|B4DK65;E7EW59;B4DFD9;Q9Y467	.|.;.;.;SALL2_HUMAN	L|T	779|921;784	ENSP00000440054:F779L|ENSP00000333537:P921T;ENSP00000396773:P784T	ENSP00000440054:F779L|ENSP00000333537:P921T	F|P	-|-	3|1	2|0	SALL2|SALL2	21060941|21060941	1.000000|1.000000	0.71417|0.71417	0.806000|0.806000	0.32338|0.32338	0.569000|0.569000	0.35902|0.35902	1.132000|1.132000	0.31418|0.31418	1.124000|1.124000	0.41980|0.41980	0.563000|0.563000	0.77884|0.77884	TTC|CCC	.	.		0.602	SALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401242.1	NM_005407		T	21991101	G	T	21991101	3	4	322	1	0	0	0	0	1	0	0	0	13826	1174	41	3	266	3	SALL2	14	21991101	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	220442	21991101	85358439	158	45406										
PCK2	5106	hgsc.bcm.edu	37	chr14	24572377	24572377	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ttggtgatctaggggtacccCtggtatacgaggccttcaac	12	10	2	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr14:24572377C>T	ENST00000216780.4	+	9	1649	c.1381C>T	c.(1381-1383)Ctg>Ttg	p.L461L	PCK2_ENST00000561286.1_Silent_p.L327L|PCK2_ENST00000559250.1_Silent_p.L473L|PCK2_ENST00000545054.2_Silent_p.L327L|PCK2_ENST00000558096.1_Intron|NRL_ENST00000561028.1_Intron	NM_004563.2	NP_004554.2	Q16822	PCKGM_HUMAN	phosphoenolpyruvate carboxykinase 2 (mitochondrial)	461					carbohydrate metabolic process (GO:0005975)|cellular response to glucose stimulus (GO:0071333)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|NADH oxidation (GO:0006116)|oxaloacetate metabolic process (GO:0006107)|positive regulation of insulin secretion (GO:0032024)|pyruvate metabolic process (GO:0006090)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|metal ion binding (GO:0046872)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)|phosphoenolpyruvate carboxykinase activity (GO:0004611)			breast(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	18				GBM - Glioblastoma multiforme(265;0.0184)		AGGGGTACCCCTGGTATACGA	0.557																																					p.L461L		Atlas-SNP	.											.	PCK2	66	.	0			c.C1381T						.						120	98	106					14																	24572377		2203	4300	6503	SO:0001819	synonymous_variant	5106	exon9			GTACCCCTGGTAT	AK129934	CCDS9609.1, CCDS41928.1	14q12	2006-06-09			ENSG00000100889	ENSG00000100889	4.1.1.32		8725	protein-coding gene	gene with protein product		614095				8645161, 9657976	Standard	XM_005267726		Approved	PEPCK, PEPCK2	uc001wlt.3	Q16822	OTTHUMG00000028791	ENST00000216780.4:c.1381C>T	chr14.hg19:g.24572377C>T		54.0	0.0		89.0	10.0	NM_004563	O43253|Q86U01|Q9BV62	Silent	SNP	ENST00000216780.4	hg19	CCDS9609.1																																																																																			.	.		0.557	PCK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071900.3	NM_001018073		T	24572377	C	T	24572377	2	4	322	1	0	0	0	0	0	0	0	1	11591	680	24	3		3	PCK2	14	24572377	Silent	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	2581276	24572377	82777163	159	45407										
NOVA1	4857	hgsc.bcm.edu	37	chr14	26949267	26949267	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gccacattttggggcatttcTcgaattttttctgcaatgaa	8	8	2	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr14:26949267T>G	ENST00000344429.5	-	3	366	c.363A>C	c.(361-363)cgA>cgC	p.R121R	NOVA1_ENST00000539517.2_Silent_p.R121R|NOVA1_ENST00000267422.7_5'UTR|NOVA1_ENST00000574031.1_Silent_p.R121R|NOVA1_ENST00000465357.2_Silent_p.R121R|NOVA1_ENST00000547619.1_Silent_p.R121R	NM_006491.2	NP_006482.1	P51513	NOVA1_HUMAN	neuro-oncological ventral antigen 1	124					locomotory behavior (GO:0007626)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA metabolic process (GO:0051252)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(265;0.0135)		GGGGCATTTCTCGAATTTTTT	0.443																																					p.R121R		Atlas-SNP	.											.	NOVA1	146	.	0			c.A363C						.						172	143	153					14																	26949267		2203	4300	6503	SO:0001819	synonymous_variant	4857	exon3			CATTTCTCGAATT	U04840	CCDS9635.1, CCDS32060.1, CCDS32061.1	14q12	2006-06-09			ENSG00000139910	ENSG00000139910			7886	protein-coding gene	gene with protein product		602157				8558240	Standard	NM_006489		Approved		uc001wpy.3	P51513	OTTHUMG00000029385	ENST00000344429.5:c.363A>C	chr14.hg19:g.26949267T>G		83.0	0.0		85.0	30.0	NM_006489	A8K0S4|A8K4Q7|D3DS81|D3DS82|Q6B004	Silent	SNP	ENST00000344429.5	hg19	CCDS9635.1																																																																																			.	.		0.443	NOVA1-001	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276557.1	NM_006491		G	26949267	T	G	26949267	2	3	322	1	0	0	0	0	0	0	0	1	10563	1538	54	5		5	NOVA1	14	26949267	Silent	SNP	T	TCGA-MI-A75G-01A-11D-A32G-10	2376890	26949267	80400273	160	45408										
C14orf4	64207	hgsc.bcm.edu	37	chr14	77493782	77493782	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tgctgctgctgctgctgctgCtgctgctgctgttgctgctg	14	12	0	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr14:77493782C>T	ENST00000238647.3	-	1	1252	c.354G>A	c.(352-354)caG>caA	p.Q118Q		NM_024496.3	NP_078772.1	Q9H1B7	I2BPL_HUMAN	interferon regulatory factor 2 binding protein-like	118	Poly-Gln.				development of secondary female sexual characteristics (GO:0046543)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	extracellular space (GO:0005615)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	11						gctgctgctgctgctgctgct	0.687																																					p.Q118Q		Atlas-SNP	.											.	IRF2BPL	40	.	0			c.G354A						.						3	2	2					14																	77493782		1199	2265	3464	SO:0001819	synonymous_variant	64207	exon1			CTGCTGCTGCTGC	AJ277365	CCDS9854.1	14q24.3	2011-02-23	2011-02-23	2011-02-23	ENSG00000119669	ENSG00000119669			14282	protein-coding gene	gene with protein product	"enhanced at puberty 1"	611720	"chromosome 14 open reading frame 4"	C14orf4		11095982, 17627301	Standard	NM_024496		Approved	EAP1, KIAA1865	uc001xsy.4	Q9H1B7		ENST00000238647.3:c.354G>A	chr14.hg19:g.77493782C>T		4.0	0.0		18.0	7.0	NM_024496	Q8NDQ2|Q96JG2|Q9H3I7	Silent	SNP	ENST00000238647.3	hg19	CCDS9854.1																																																																																			.	.		0.687	IRF2BPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414298.1	NM_024496		T	77493782	C	T	77493782	2	4	322	1	0	0	0	0	0	0	0	1	1775	796	28	3		3	C14orf4	14	77493782	Silent	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	50544515	77493782	29855758	161	45409										
ATG2B	55102	hgsc.bcm.edu	37	chr14	96781503	96781503	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tctcttacctgctcatgccaGctaagcccagaaggaagcat	8	13	2	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr14:96781503G>A	ENST00000359933.4	-	23	4523	c.3630C>T	c.(3628-3630)agC>agT	p.S1210S		NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	1210					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		GCTCATGCCAGCTAAGCCCAG	0.353																																					p.S1210S		Atlas-SNP	.											.	ATG2B	169	.	0			c.C3630T						.						37	36	36					14																	96781503		2203	4300	6503	SO:0001819	synonymous_variant	55102	exon23			ATGCCAGCTAAGC	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 103", "ATG2 autophagy related 2 homolog B (S. cerevisiae)"	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.3630C>T	chr14.hg19:g.96781503G>A		116.0	0.0		146.0	19.0	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Silent	SNP	ENST00000359933.4	hg19	CCDS9944.2																																																																																			.	.		0.353	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036		A	96781503	G	A	96781503	2	1	322	1	0	0	0	0	0	0	0	1	1094	962	34	3		3	ATG2B	14	96781503	Silent	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	19287721	96781503	10568037	162	45410										
PPP1R13B	23368	hgsc.bcm.edu	37	chr14	104205095	104205095	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gtgatggtggccggcgcagaCggcgttgtgcagtggggtga	21	7	0	3			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr14:104205095C>T	ENST00000202556.9	-	14	3067	c.2785G>A	c.(2785-2787)Gtc>Atc	p.V929I	PPP1R13B_ENST00000423488.2_Missense_Mutation_p.V348I|PPP1R13B_ENST00000555391.1_5'UTR	NM_015316.2	NP_056131.2	Q96KQ4	ASPP1_HUMAN	protein phosphatase 1, regulatory subunit 13B	929					intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell cycle (GO:0045786)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(6)|kidney(2)|large_intestine(7)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.173)|all_epithelial(191;0.131)|Melanoma(154;0.155)				CCGGCGCAGACGGCGTTGTGC	0.607																																					p.V929I		Atlas-SNP	.											.	PPP1R13B	72	.	0			c.G2785A						.						133	145	141					14																	104205095		2159	4263	6422	SO:0001583	missense	23368	exon14			CGCAGACGGCGTT	AB018314	CCDS41997.1	14q32.33	2013-01-10	2011-10-04		ENSG00000088808	ENSG00000088808		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	14950	protein-coding gene	gene with protein product		606455	"protein phosphatase 1, regulatory (inhibitor) subunit 13B"			9872452	Standard	NM_015316		Approved	p53BP2-like, KIAA0771, p85, ASPP1	uc001yof.1	Q96KQ4	OTTHUMG00000171647	ENST00000202556.9:c.2785G>A	chr14.hg19:g.104205095C>T	ENSP00000202556:p.Val929Ile	103.0	0.0		112.0	23.0	NM_015316	B2RMX5|O94870	Missense_Mutation	SNP	ENST00000202556.9	hg19	CCDS41997.1	.	.	.	.	.	.	.	.	.	.	C	35	5.425828	0.96131	.	.	ENSG00000088808	ENST00000202556;ENST00000423488	T;T	0.68181	-0.1;-0.31	5.25	5.25	0.73442	Src homology-3 domain (1);Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.77478	0.4136	L	0.54908	1.71	0.80722	D	1	D	0.59357	0.985	D	0.77004	0.989	T	0.69892	-0.5022	10	0.13853	T	0.58	.	19.0309	0.92957	0.0:1.0:0.0:0.0	.	929	Q96KQ4	ASPP1_HUMAN	I	929;348	ENSP00000202556:V929I;ENSP00000395213:V348I	ENSP00000202556:V929I	V	-	1	0	PPP1R13B	103274848	1.000000	0.71417	0.991000	0.47740	0.642000	0.38348	7.528000	0.81941	2.744000	0.94065	0.561000	0.74099	GTC	.	.		0.607	PPP1R13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414591.1	NM_015316		T	104205095	C	T	104205095	3	4	322	1	0	0	0	0	1	0	0	0	12369	536	19	1	503	1	PPP1R13B	14	104205095	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	7423592	104205095	3144445	163	45411										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105417167	105417167	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	agaagggggctgtatgctcaGgtcagtggccttgaggtccc	16	9	2	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr14:105417167G>T	ENST00000333244.5	-	7	4740	c.4621C>A	c.(4621-4623)Ctg>Atg	p.L1541M	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1541						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				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)			TGTATGCTCAGGTCAGTGGCC	0.652																																					p.L1541M		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C4621A						.						119	113	115					14																	105417167		1946	4089	6035	SO:0001583	missense	113146	exon7			TGCTCAGGTCAGT	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.4621C>A	chr14.hg19:g.105417167G>T	ENSP00000353114:p.Leu1541Met	145.0	0.0		151.0	13.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	hg19	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	g	15.28	2.786937	0.49997	.	.	ENSG00000185567	ENST00000333244	T	0.00995	5.46	4.16	-5.81	0.02340	.	.	.	.	.	T	0.01905	0.0060	L	0.52126	1.63	0.09310	N	1	D	0.57899	0.981	P	0.54026	0.74	T	0.08207	-1.0733	9	0.45353	T	0.12	-4.4575	11.3263	0.49450	0.0:0.5958:0.2201:0.1841	.	1541	Q8IVF2	AHNK2_HUMAN	M	1541	ENSP00000353114:L1541M	ENSP00000353114:L1541M	L	-	1	2	AHNAK2	104488212	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.997000	0.01470	-0.808000	0.04387	-0.333000	0.08304	CTG	.	.		0.652	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		T	105417167	G	T	105417167	3	4	322	1	0	0	0	0	1	0	0	0	415	991	35	3	12770	3	AHNAK2	14	105417167	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	1212072	105417167	1932373	164	45412										
MAGEL2	54551	hgsc.bcm.edu	37	chr15	23890418	23890418	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	agggcctctacacaggcaaaGggatcctgcagagcatatgg	13	10	1	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr15:23890418G>A	ENST00000532292.1	-	1	757	c.663C>T	c.(661-663)ccC>ccT	p.P221P		NM_019066.4	NP_061939.3	Q9UJ55	MAGL2_HUMAN	MAGE-like 2	104					Arp2/3 complex-mediated actin nucleation (GO:0034314)|protein K63-linked ubiquitination (GO:0070534)|retrograde transport, endosome to Golgi (GO:0042147)	endosome (GO:0005768)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;1.84e-06)|Epithelial(43;1.2e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)		CACAGGCAAAGGGATCCTGCA	0.567																																					p.P824P		Atlas-SNP	.											.	MAGEL2	108	.	0			c.C2472T						.						61	64	63					15																	23890418		2003	4181	6184	SO:0001819	synonymous_variant	54551	exon1			GGCAAAGGGATCC	AJ243531	CCDS73700.1	15q11-q12	2008-07-18				ENSG00000254585			6814	protein-coding gene	gene with protein product		605283		NDNL1		10556298	Standard	NM_019066		Approved	nM15	uc001ywj.4	Q9UJ55		ENST00000532292.1:c.663C>T	chr15.hg19:g.23890418G>A		74.0	0.0		86.0	23.0	NM_019066		Silent	SNP	ENST00000532292.1	hg19		.	.	.	.	.	.	.	.	.	.	G	8.708	0.911413	0.17833	.	.	ENSG00000254585	ENST00000532292	.	.	.	4.21	-6.13	0.02118	.	.	.	.	.	T	0.52613	0.1745	.	.	.	0.50313	D	0.999867	.	.	.	.	.	.	T	0.59467	-0.7449	5	0.87932	D	0	.	3.4447	0.07477	0.1023:0.2393:0.4503:0.2081	.	.	.	.	L	253	.	ENSP00000433433:P253L	P	-	2	0	MAGEL2	21441511	0.004000	0.15560	0.264000	0.24511	0.987000	0.75469	-1.972000	0.01502	-1.281000	0.02399	-0.188000	0.12872	CCT	.	.		0.567	MAGEL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395182.2	NM_019066		A	23890418	G	A	23890418	2	1	322	1	0	0	0	0	0	0	0	1	9198	987	35	3		3	MAGEL2	15	23890418	Silent	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10		23890418	78640974	165	45413										
GABRG3	2567	hgsc.bcm.edu	37	chr15	27271951	27271951	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	atgttaacagcattggtcctGtgtcatcaataaacatggta	8	7	2	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr15:27271951G>T	ENST00000333743.6	+	3	507	c.253G>T	c.(253-255)Gtg>Ttg	p.V85L	GABRG3_ENST00000555083.1_Missense_Mutation_p.V85L	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	85					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(23)|skin(1)|upper_aerodigestive_tract(4)	42		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CATTGGTCCTGTGTCATCAAT	0.378																																					p.V85L	NSCLC(114;800 1656 7410 37729 45293)	Atlas-SNP	.											.	GABRG3	115	.	0			c.G253T						.						118	109	112					15																	27271951		1922	4149	6071	SO:0001583	missense	2567	exon3			GGTCCTGTGTCAT		CCDS45195.1, CCDS59251.1	15q12	2012-06-22			ENSG00000182256	ENSG00000182256		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4088	protein-coding gene	gene with protein product	"GABA(G) receptor, gamma 3"	600233				7601451	Standard	NM_033223		Approved		uc001zbg.2	Q99928	OTTHUMG00000044462	ENST00000333743.6:c.253G>T	chr15.hg19:g.27271951G>T	ENSP00000331912:p.Val85Leu	143.0	0.0		150.0	50.0	NM_001270873	G3V594|Q9HD46|Q9NYT2	Missense_Mutation	SNP	ENST00000333743.6	hg19	CCDS45195.1	.	.	.	.	.	.	.	.	.	.	G	16.96	3.266090	0.59540	.	.	ENSG00000182256	ENST00000333743;ENST00000555083	D;D	0.82081	-1.57;-1.57	5.96	5.96	0.96718	Neurotransmitter-gated ion-channel ligand-binding (3);	0.079672	0.51477	D	0.000097	D	0.85323	0.5670	M	0.74467	2.265	0.53005	D	0.999966	B;P	0.35793	0.081;0.521	B;B	0.40410	0.1;0.328	D	0.86091	0.1550	10	0.87932	D	0	.	15.9083	0.79447	0.0:0.0:1.0:0.0	.	85;85	Q99928;G3V594	GBRG3_HUMAN;.	L	85	ENSP00000331912:V85L;ENSP00000452244:V85L	ENSP00000331912:V85L	V	+	1	0	GABRG3	24854697	1.000000	0.71417	0.989000	0.46669	0.657000	0.38888	7.057000	0.76669	2.814000	0.96858	0.655000	0.94253	GTG	.	.		0.378	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2			T	27271951	G	T	27271951	3	4	322	1	0	0	0	0	1	0	0	0	6181	1377	48	3	263	3	GABRG3	15	27271951	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	3381533	27271951	75259441	166	45414										
HERC2	8924	hgsc.bcm.edu	37	chr15	28422626	28422626	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ccacgaaaacacttttccatCgacagttaaagccgtcgcgt	7	13	0	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr15:28422626C>A	ENST00000261609.7	-	60	9301	c.9193G>T	c.(9193-9195)Gat>Tat	p.D3065Y		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		ACTTTTCCATCGACAGTTAAA	0.483																																					p.D3065Y		Atlas-SNP	.											.	HERC2	501	.	0			c.G9193T						.						90	79	83					15																	28422626		2203	4300	6503	SO:0001583	missense	8924	exon60			TTCCATCGACAGT	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.9193G>T	chr15.hg19:g.28422626C>A	ENSP00000261609:p.Asp3065Tyr	60.0	0.0		109.0	30.0	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	hg19	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.871615	0.91587	.	.	ENSG00000128731	ENST00000261609	D	0.89196	-2.48	5.79	5.79	0.91817	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.85682	D	0.000000	D	0.96150	0.8745	M	0.92923	3.36	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96468	0.9346	10	0.87932	D	0	.	20.0366	0.97561	0.0:1.0:0.0:0.0	.	3065	O95714	HERC2_HUMAN	Y	3065	ENSP00000261609:D3065Y	ENSP00000261609:D3065Y	D	-	1	0	HERC2	26096221	1.000000	0.71417	0.948000	0.38648	0.747000	0.42532	7.642000	0.83385	2.736000	0.93811	0.561000	0.74099	GAT	.	.		0.483	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		A	28422626	C	A	28422626	3	1	322	1	0	0	0	0	1	0	0	0	7067	884	31	1	5447	1	HERC2	15	28422626	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	1150675	28422626	74108766	167	45415										
RAD51	5888	hgsc.bcm.edu	37	chr15	40998470	40998470	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cagattactactggctccaaAgagcttgacaaactacttca	6	11	1	3			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr15:40998470A>T	ENST00000267868.3	+	4	589	c.321A>T	c.(319-321)aaA>aaT	p.K107N	RAD51_ENST00000423169.2_Missense_Mutation_p.K107N|RAD51_ENST00000532743.1_Intron|RAD51_ENST00000382643.3_Intron|RAD51_ENST00000557850.1_Intron	NM_002875.4	NP_002866.2	Q06609	RAD51_HUMAN	RAD51 recombinase	107					ATP catabolic process (GO:0006200)|cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to ionizing radiation (GO:0071479)|DNA recombinase assembly (GO:0000730)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA unwinding involved in DNA replication (GO:0006268)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|meiotic nuclear division (GO:0007126)|mitotic recombination (GO:0006312)|positive regulation of DNA ligation (GO:0051106)|protein homooligomerization (GO:0051260)|reciprocal meiotic recombination (GO:0007131)|regulation of double-strand break repair via homologous recombination (GO:0010569)	condensed chromosome (GO:0000793)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|lateral element (GO:0000800)|mitochondrion (GO:0005739)|nuclear chromosome (GO:0000228)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|PML body (GO:0016605)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA polymerase binding (GO:0070182)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|single-stranded DNA binding (GO:0003697)|single-stranded DNA-dependent ATPase activity (GO:0043142)			breast(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(1)|ovary(1)	9		all_cancers(109;1.19e-18)|all_epithelial(112;2.33e-15)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;1.45e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000421)|COAD - Colon adenocarcinoma(120;0.163)		CTGGCTCCAAAGAGCTTGACA	0.413								Homologous recombination																													p.K107N		Atlas-SNP	.											.	RAD51	19	.	0			c.A321T						.						70	67	68					15																	40998470		2203	4300	6503	SO:0001583	missense	5888	exon4			CTCCAAAGAGCTT	D13804	CCDS10062.1, CCDS53931.1, CCDS53932.1	15q15.1	2014-06-12	2013-07-02		ENSG00000051180	ENSG00000051180			9817	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 5"	179617	"RAD51 (S. cerevisiae) homolog (E coli RecA homolog)", "RAD51 homolog (RecA homolog, E. coli) (S. cerevisiae)", "RAD51 homolog (S. cerevisiae)"	RAD51A, RECA		8358431, 8479919	Standard	NM_002875		Approved	HsRad51, HsT16930, BRCC5	uc010bbx.3	Q06609	OTTHUMG00000130067	ENST00000267868.3:c.321A>T	chr15.hg19:g.40998470A>T	ENSP00000267868:p.Lys107Asn	234.0	0.0		337.0	108.0	NM_001164270	B0FXP0|B2R8T6|Q6FHX9|Q6ZNA8|Q9BV60	Missense_Mutation	SNP	ENST00000267868.3	hg19	CCDS10062.1	.	.	.	.	.	.	.	.	.	.	A	16.04	3.009313	0.54361	.	.	ENSG00000051180	ENST00000527860;ENST00000423169;ENST00000267868	T;T;T	0.43688	0.94;0.94;0.94	4.55	4.55	0.56014	DNA recombination/repair protein RecA/RadB, ATP-binding domain (1);DNA recombination and repair protein Rad51, C-terminal (1);	.	.	.	.	T	0.50137	0.1598	M	0.85630	2.765	0.80722	D	1	B;B	0.22800	0.075;0.029	B;B	0.23852	0.045;0.049	T	0.57087	-0.7871	9	0.72032	D	0.01	.	14.0465	0.64708	1.0:0.0:0.0:0.0	.	107;107	Q06609-3;Q06609	.;RAD51_HUMAN	N	107	ENSP00000432759:K107N;ENSP00000406602:K107N;ENSP00000267868:K107N	ENSP00000267868:K107N	K	+	3	2	RAD51	38785762	1.000000	0.71417	1.000000	0.80357	0.761000	0.43186	4.859000	0.62954	1.908000	0.55244	0.377000	0.23210	AAA	.	.		0.413	RAD51-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000252358.1	NM_002875, NM_133487		T	40998470	A	T	40998470	3	4	322	1	0	0	0	0	1	0	0	0	13000	69	3	4	456	4	RAD51	15	40998470	Missense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	12575844	40998470	61532922	168	45416										
CCPG1	9236	hgsc.bcm.edu	37	chr15	55651833	55651833	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	catcattatctacttcatatTccttcatgtttctaagataa	2	9	5	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr15:55651833T>A	ENST00000310958.6	-	8	2436	c.2138A>T	c.(2137-2139)gAa>gTa	p.E713V	CCPG1_ENST00000442196.3_Missense_Mutation_p.E713V|DYX1C1-CCPG1_ENST00000565113.1_RNA|CCPG1_ENST00000569205.1_Missense_Mutation_p.E713V|CCPG1_ENST00000425574.3_Missense_Mutation_p.E330V	NM_001204450.1|NM_001204451.1|NM_004748.4|NM_020739.3	NP_001191379.1|NP_001191380.1|NP_004739.3|NP_065790.2	Q9ULG6	CCPG1_HUMAN	cell cycle progression 1	713					cell cycle (GO:0007049)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001106)	integral component of membrane (GO:0016021)				autonomic_ganglia(1)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|stomach(3)	30				all cancers(107;0.0354)		TACTTCATATTCCTTCATGTT	0.338																																					p.E713V		Atlas-SNP	.											.	CCPG1	74	.	0			c.A2138T						.						58	56	57					15																	55651833		1806	4060	5866	SO:0001583	missense	9236	exon8			TCATATTCCTTCA	AF212228	CCDS42039.1, CCDS55966.1, CCDS55967.1	15q21.1	2011-04-20				ENSG00000260916			24227	protein-coding gene	gene with protein product		611326				9383053, 10574462	Standard	NM_004748		Approved	KIAA1254, CPR8	uc010bfk.2	Q9ULG6		ENST00000310958.6:c.2138A>T	chr15.hg19:g.55651833T>A	ENSP00000311656:p.Glu713Val	63.0	0.0		111.0	11.0	NM_020739	A0PJH3|A8K9T0|O14712|Q05DG4|Q5U5S7|Q8IYV8|Q9BY53|Q9HA17	Missense_Mutation	SNP	ENST00000310958.6	hg19	CCDS42039.1	.	.	.	.	.	.	.	.	.	.	T	19.96	3.922565	0.73213	.	.	ENSG00000256061	ENST00000310958;ENST00000442196;ENST00000425574	T;T;T	0.38722	3.63;3.63;1.12	5.83	5.83	0.93111	.	0.091451	0.64402	D	0.000001	T	0.60457	0.2270	M	0.65498	2.005	0.80722	D	1	D;D;D;D	0.59767	0.986;0.966;0.986;0.986	P;D;D;D	0.64237	0.875;0.923;0.92;0.92	T	0.59139	-0.7510	10	0.38643	T	0.18	.	15.3809	0.74654	0.0:0.0:0.0:1.0	.	713;330;713;569	A8K9T0;Q9ULG6-3;Q9ULG6;Q9ULG6-2	.;.;CCPG1_HUMAN;.	V	713;713;330	ENSP00000311656:E713V;ENSP00000403400:E713V;ENSP00000415128:E330V	ENSP00000311656:E713V	E	-	2	0	DYX1C1	53439125	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	5.791000	0.69045	2.240000	0.73641	0.528000	0.53228	GAA	.	.		0.338	CCPG1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419850.1	NM_004748		A	55651833	T	A	55651833	3	1	322	1	0	0	0	0	1	0	0	0	2940	1783	62	4	139	4	CCPG1	15	55651833	Missense_Mutation	SNP	T	TCGA-MI-A75G-01A-11D-A32G-10	14653363	55651833	46879559	169	45417										
DENND4A	10260	hgsc.bcm.edu	37	chr15	66031083	66031083	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gttaaaacaaaagtagaaaaTacaggcagagggtatttgct	10	4	0	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr15:66031083T>C	ENST00000431932.2	-	6	970	c.762A>G	c.(760-762)gtA>gtG	p.V254V	DENND4A_ENST00000443035.3_Silent_p.V254V	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	254	UDENN.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						AAGTAGAAAATACAGGCAGAG	0.348																																					p.V254V		Atlas-SNP	.											.	DENND4A	217	.	0			c.A762G						.						110	107	108					15																	66031083		1812	4074	5886	SO:0001819	synonymous_variant	10260	exon6			AGAAAATACAGGC	AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27				"DENN/MADD domain containing"	24321	protein-coding gene	gene with protein product		600382	"c-myc promoter binding protein"	MYCPBP		8056341, 12906859	Standard	NM_005848		Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.762A>G	chr15.hg19:g.66031083T>C		120.0	0.0		192.0	54.0	NM_001144823	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Silent	SNP	ENST00000431932.2	hg19	CCDS45285.1																																																																																			.	.		0.348	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848		C	66031083	T	C	66031083	2	2	322	1	0	0	0	0	0	0	0	1	4435	1393	49	2		2	DENND4A	15	66031083	Silent	SNP	T	TCGA-MI-A75G-01A-11D-A32G-10	10379250	66031083	36500309	170	45418										
DIS3L	115752	hgsc.bcm.edu	37	chr15	66621720	66621720	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ttgaggaattatgcagacatAtcaacaacagaaaccaagta	7	7	1	3			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr15:66621720A>G	ENST00000319212.4	+	14	2568	c.2518A>G	c.(2518-2520)Atc>Gtc	p.I840V	RP11-352G18.2_ENST00000565993.1_RNA|DIS3L_ENST00000319194.5_Missense_Mutation_p.I757V|DIS3L_ENST00000568874.1_3'UTR	NM_001143688.1	NP_001137160.1	Q8TF46	DI3L1_HUMAN	DIS3 like exosome 3'-5' exoribonuclease	840					RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA catabolic process (GO:0016075)	cytoplasmic exosome (RNase complex) (GO:0000177)	3'-5'-exoribonuclease activity (GO:0000175)|enzyme binding (GO:0019899)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						ATGCAGACATATCAACAACAG	0.353																																					p.I840V		Atlas-SNP	.											.	DIS3L	175	.	0			c.A2518G						.						56	57	56					15																	66621720		2201	4298	6499	SO:0001583	missense	115752	exon14			AGACATATCAACA		CCDS10214.1, CCDS45286.1	15q22.31	2014-03-05	2014-03-05		ENSG00000166938	ENSG00000166938			28698	protein-coding gene	gene with protein product		614183	"DIS3 mitotic control homolog (S. cerevisiae)-like"			20531386	Standard	NM_001143688		Approved	MGC4562, FLJ38088, KIAA1955, DIS3L1	uc010ujm.2	Q8TF46	OTTHUMG00000133181	ENST00000319212.4:c.2518A>G	chr15.hg19:g.66621720A>G	ENSP00000321711:p.Ile840Val	98.0	0.0		160.0	18.0	NM_001143688	Q8N1N8|Q8WTU9|Q96CM7	Missense_Mutation	SNP	ENST00000319212.4	hg19	CCDS45286.1	.	.	.	.	.	.	.	.	.	.	A	15.54	2.862715	0.51482	.	.	ENSG00000166938	ENST00000319194;ENST00000319212	T;T	0.44083	0.93;0.93	5.69	4.54	0.55810	.	0.142348	0.64402	D	0.000007	T	0.40322	0.1112	M	0.72118	2.19	0.80722	D	1	B	0.33103	0.397	B	0.31751	0.135	T	0.17961	-1.0352	10	0.18276	T	0.48	-12.4654	12.108	0.53823	0.8563:0.1437:0.0:0.0	.	840	Q8TF46	DI3L1_HUMAN	V	757;840	ENSP00000321583:I757V;ENSP00000321711:I840V	ENSP00000321583:I757V	I	+	1	0	DIS3L	64408774	1.000000	0.71417	0.994000	0.49952	0.998000	0.95712	5.483000	0.66838	1.050000	0.40346	0.533000	0.62120	ATC	.	.		0.353	DIS3L-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382792.2	NM_133375		G	66621720	A	G	66621720	3	3	322	1	0	0	0	0	1	0	0	0	4538	449	16	2	2572	2	DIS3L	15	66621720	Missense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	590637	66621720	35909672	171	45419										
THAP10	56906	hgsc.bcm.edu	37	chr15	71175115	71175115	+	Frame_Shift_Del	DEL	G	G	-													0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	catacccacactacggtgacGgggccttttcaaagaaattt					rs148723779		TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr15:71175115delG	ENST00000249861.4	-	2	1074	c.562delC	c.(562-564)cgtfs	p.R188fs	LRRC49_ENST00000544974.2_Intron	NM_020147.3	NP_064532.1	Q9P2Z0	THA10_HUMAN	THAP domain containing 10	188							DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|kidney(1)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	12						CTACGGTGACGGGGCCTTTTC	0.373																																					p.R188fs		Atlas-Indel,Pindel	.											THAP10,NS,carcinoma,0,1	THAP10	19	.	0			c.563delG						.						118	116	117					15																	71175115		2199	4297	6496	SO:0001589	frameshift_variant	56906	exon2			.	AL360202	CCDS10237.1	15q22.32	2013-01-25			ENSG00000129028	ENSG00000129028		"THAP (C2CH-type zinc finger) domain containing"	23193	protein-coding gene	gene with protein product		612538				12575992	Standard	NM_020147		Approved		uc002asv.3	Q9P2Z0	OTTHUMG00000133388	ENST00000249861.4:c.562delC	chr15.hg19:g.71175115delG	ENSP00000249861:p.Arg188fs	174.0	0.0		239.0	74.0	NM_020147	B2R8R0	Frame_Shift_Del	DEL	ENST00000249861.4	hg19	CCDS10237.1																																																																																			.	.		0.373	THAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257242.2	NM_020147		-	71175115	G	-	71175115	7	5	322	1	0	1	0	1	0	0	0	0	15857	1116	39	0	219	0	THAP10	15	71175115	Frame_Shift_Del	DEL	G	TCGA-MI-A75G-01A-11D-A32G-10	4553395	71175115	31356277	172	45420										
MAN2A2	4122	hgsc.bcm.edu	37	chr15	91450650	91450650	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ctgccaatttgatttcaaacGcctgcctggtgggcgcatca	10	12	2	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr15:91450650G>T	ENST00000559717.1	+	8	1580	c.1121G>T	c.(1120-1122)cGc>cTc	p.R374L	MAN2A2_ENST00000431652.2_5'UTR|MAN2A2_ENST00000360468.3_Missense_Mutation_p.R374L			P49641	MA2A2_HUMAN	mannosidase, alpha, class 2A, member 2	374					cellular protein metabolic process (GO:0044267)|mannose metabolic process (GO:0006013)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|lung(13)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)			GATTTCAAACGCCTGCCTGGT	0.557																																					p.R374L		Atlas-SNP	.											.	MAN2A2	99	.	0			c.G1121T						.						79	78	78					15																	91450650		2198	4298	6496	SO:0001583	missense	4122	exon7			TCAAACGCCTGCC	L28821	CCDS32332.1	15q25	2011-06-30			ENSG00000196547	ENSG00000196547			6825	protein-coding gene	gene with protein product		600988				8524845	Standard	NM_006122		Approved	MANA2X, HsT19662	uc002bqc.3	P49641		ENST00000559717.1:c.1121G>T	chr15.hg19:g.91450650G>T	ENSP00000452948:p.Arg374Leu	74.0	0.0		95.0	38.0	NM_006122	A6NH12|A8K1E8|Q13754	Missense_Mutation	SNP	ENST00000559717.1	hg19	CCDS32332.1	.	.	.	.	.	.	.	.	.	.	G	36	5.645149	0.96704	.	.	ENSG00000196547	ENST00000360468	T	0.23552	1.9	5.67	5.67	0.87782	Glycoside hydrolase/deacetylase, beta/alpha-barrel (1);Glycoside hydrolase, family 38, core (2);	0.000000	0.85682	D	0.000000	T	0.60894	0.2304	M	0.88704	2.975	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.997;0.999	T	0.67352	-0.5692	10	0.87932	D	0	-30.8742	19.8235	0.96607	0.0:0.0:1.0:0.0	.	44;374;374	B4DIK4;P49641-1;P49641	.;.;MA2A2_HUMAN	L	374	ENSP00000353655:R374L	ENSP00000353655:R374L	R	+	2	0	MAN2A2	89251654	1.000000	0.71417	0.996000	0.52242	0.946000	0.59487	9.869000	0.99810	2.696000	0.92011	0.456000	0.33151	CGC	.	.		0.557	MAN2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418246.5	NM_006122		T	91450650	G	T	91450650	3	4	322	1	0	0	0	0	1	0	0	0	9224	1087	38	1	1147	1	MAN2A2	15	91450650	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	20275535	91450650	11080742	173	45421										
NR2F2	7026	hgsc.bcm.edu	37	chr15	96875737	96875737	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gcaaccagtgccagtactgcCgcctcaaaaagtgcctcaaa	8	14	2	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr15:96875737C>A	ENST00000394166.3	+	1	1792	c.403C>A	c.(403-405)Cgc>Agc	p.R135S	NR2F2_ENST00000453270.2_5'Flank|NR2F2_ENST00000394171.2_5'Flank|NR2F2_ENST00000421109.2_Intron|MIR1469_ENST00000410719.1_RNA	NM_021005.3	NP_066285.1	P24468	COT2_HUMAN	nuclear receptor subfamily 2, group F, member 2	135	Interaction with ZFPM2. {ECO:0000250}.				anterior/posterior pattern specification (GO:0009952)|blood vessel morphogenesis (GO:0048514)|fertilization (GO:0009566)|forebrain development (GO:0030900)|intracellular receptor signaling pathway (GO:0030522)|limb development (GO:0060173)|lipid metabolic process (GO:0006629)|maternal placenta development (GO:0001893)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron migration (GO:0001764)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|radial pattern formation (GO:0009956)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription involved in lymphatic endothelial cell fate commitment (GO:0060849)|response to estradiol (GO:0032355)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|liver(2)|lung(3)|ovary(2)|urinary_tract(1)	17	Lung NSC(78;0.0186)|Melanoma(26;0.0195)|all_lung(78;0.0297)		OV - Ovarian serous cystadenocarcinoma(32;0.0856)			CCAGTACTGCCGCCTCAAAAA	0.607																																					p.R135S		Atlas-SNP	.											.	NR2F2	35	.	0			c.C403A						.						76	70	72					15																	96875737		2197	4298	6495	SO:0001583	missense	7026	exon1			TACTGCCGCCTCA	M64497	CCDS10375.1, CCDS45358.1, CCDS45359.1	15q26	2013-01-16			ENSG00000185551	ENSG00000185551		"Nuclear hormone receptors"	7976	protein-coding gene	gene with protein product		107773		ARP1, TFCOUP2		8530078, 11544252	Standard	NM_021005		Approved	COUP-TFII, COUPTFB, SVP40, NF-E3	uc010uri.2	P24468	OTTHUMG00000149848	ENST00000394166.3:c.403C>A	chr15.hg19:g.96875737C>A	ENSP00000377721:p.Arg135Ser	97.0	0.0		157.0	40.0	NM_021005	B4DQJ2|B6ZGU1|Q03754|Q3KQR7	Missense_Mutation	SNP	ENST00000394166.3	hg19	CCDS10375.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.934441	0.92458	.	.	ENSG00000185551	ENST00000394166	D	0.98585	-5.01	4.92	4.92	0.64577	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (4);	0.000000	0.64402	D	0.000001	D	0.99366	0.9777	H	0.97291	3.975	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98457	1.0594	10	0.87932	D	0	.	16.7089	0.85380	0.0:1.0:0.0:0.0	.	135	P24468	COT2_HUMAN	S	135	ENSP00000377721:R135S	ENSP00000377721:R135S	R	+	1	0	NR2F2	94676741	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.769000	0.85360	2.271000	0.75665	0.561000	0.74099	CGC	.	.		0.607	NR2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313534.1			A	96875737	C	A	96875737	3	1	322	1	0	0	0	0	1	0	0	0	10637	652	23	1	452	1	NR2F2	15	96875737	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	5425087	96875737	5655655	174	45422										
CREBBP	1387	hgsc.bcm.edu	37	chr16	3860606	3860606	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gggccaagggtaacttaccaTatttggcacgttggtgactg	13	8	0	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr16:3860606T>A	ENST00000262367.5	-	3	1782	c.973A>T	c.(973-975)Atg>Ttg	p.M325L	CREBBP_ENST00000382070.3_Missense_Mutation_p.M325L	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	325	Interaction with SRCAP.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		TAACTTACCATATTTGGCACG	0.468			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																														p.M325L		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP	546	.	0			c.A973T						.						183	170	174					16																	3860606		2197	4300	6497	SO:0001583	missense	1387	exon3			TTACCATATTTGG	U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.973A>T	chr16.hg19:g.3860606T>A	ENSP00000262367:p.Met325Leu	74.0	0.0		92.0	38.0	NM_001079846	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	hg19	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	T	12.99	2.103074	0.37145	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070	D;D	0.83992	-1.79;-1.77	5.28	5.28	0.74379	.	0.058309	0.64402	D	0.000001	T	0.78426	0.4281	L	0.45352	1.415	0.46542	D	0.999091	B;B	0.27450	0.112;0.179	B;B	0.28638	0.082;0.092	T	0.75260	-0.3380	10	0.35671	T	0.21	-18.2283	15.2145	0.73254	0.0:0.0:0.0:1.0	.	393;325	Q4LE28;Q92793	.;CBP_HUMAN	L	325;393;325	ENSP00000262367:M325L;ENSP00000371502:M325L	ENSP00000262367:M325L	M	-	1	0	CREBBP	3800607	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.382000	0.52463	1.993000	0.58246	0.460000	0.39030	ATG	.	.		0.468	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		A	3860606	T	A	3860606	3	1	322	1	0	0	0	0	1	0	0	0	3863	1406	49	4	6471	4	CREBBP	16	3860606	Missense_Mutation	SNP	T	TCGA-MI-A75G-01A-11D-A32G-10		3860606	86494147	175	45423										
RBBP6	5930	hgsc.bcm.edu	37	chr16	24583179	24583180	+	Frame_Shift_Ins	INS	-	-	T													0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	taacccaccagagacacaggINSttgaaaaagagcaaattact							TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr16:24583179_24583180insT	ENST00000319715.4	+	18	5224_5225	c.4792_4793insT	c.(4792-4794)gttfs	p.V1598fs	RBBP6_ENST00000348022.2_Frame_Shift_Ins_p.V1564fs|RBBP6_ENST00000381039.3_Frame_Shift_Ins_p.V758fs	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	1598					embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		AGAGACACAGGTTGAAAAAGAG	0.386																																					p.V1598fs		Atlas-Indel,Pindel	.											.	RBBP6	158	.	0			c.4792_4793insT						.																																			SO:0001589	frameshift_variant	5930	exon18			.		CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"proliferation potential-related protein"	600938	"retinoblastoma-binding protein 6"			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.4794dupT	chr16.hg19:g.24583181_24583181dupT	ENSP00000317872:p.Val1598fs	123.0	0.0		147.0	30.0	NM_006910	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Frame_Shift_Ins	INS	ENST00000319715.4	hg19	CCDS10621.1																																																																																			.	.		0.386	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910		T	24583180	-	T	24583179	7	5	322	1	0	1	1	0	0	0	0	0	13118	1261	44	0	4916	0	RBBP6	16	24583179	Frame_Shift_Ins	INS	-	TCGA-MI-A75G-01A-11D-A32G-10	20722573	24583179	65771574	176	45424										
CHD9	80205	hgsc.bcm.edu	37	chr16	53296958	53296958	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ttagatgatcccaacttctgGcaaaaatgggctaaaaaggc	9	8	1	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr16:53296958G>A	ENST00000398510.3	+	19	4356	c.4269G>A	c.(4267-4269)tgG>tgA	p.W1423*	CHD9_ENST00000447540.1_Nonsense_Mutation_p.W1423*|CHD9_ENST00000564845.1_Nonsense_Mutation_p.W1423*|CHD9_ENST00000566029.1_Nonsense_Mutation_p.W1423*			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	1423					cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				CCAACTTCTGGCAAAAATGGG	0.368																																					p.W1423X		Atlas-SNP	.											.	CHD9	203	.	0			c.G4269A						.						106	98	100					16																	53296958		1834	4091	5925	SO:0001587	stop_gained	80205	exon20			CTTCTGGCAAAAA	AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.4269G>A	chr16.hg19:g.53296958G>A	ENSP00000381522:p.Trp1423*	55.0	0.0		63.0	17.0	NM_025134	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Nonsense_Mutation	SNP	ENST00000398510.3	hg19		.	.	.	.	.	.	.	.	.	.	G	45	11.760148	0.99599	.	.	ENSG00000177200	ENST00000447540;ENST00000398510;ENST00000219084	.	.	.	5.42	5.42	0.78866	.	0.000000	0.51477	D	0.000098	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.7081	19.2231	0.93806	0.0:0.0:1.0:0.0	.	.	.	.	X	1423;1423;949	.	ENSP00000219084:W949X	W	+	3	0	CHD9	51854459	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.795000	0.99099	2.521000	0.84997	0.655000	0.94253	TGG	.	.		0.368	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134		A	53296958	G	A	53296958	4	1	322	1	0	0	0	0	0	1	0	0	3334	1212	42	3	4343	3	CHD9	16	53296958	Nonsense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	28713779	53296958	37057795	177	45425										
CNOT1	23019	hgsc.bcm.edu	37	chr16	58585618	58585629	+	In_Frame_Del	DEL	CCTGGGCCTGAG	CCTGGGCCTGAG	-													0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	aagaggagcttttgctggaaCctgggcctgagcctgggcct							TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	CCTGGGCCTGAG	CCTGGGCCTGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr16:58585618_58585629delCCTGGGCCTGAG	ENST00000317147.5	-	23	3397_3408	c.3065_3076delCTCAGGCCCAGG	c.(3064-3078)gctcaggcccaggtt>gtt	p.AQAQ1022del	CNOT1_ENST00000569732.1_5'UTR|CNOT1_ENST00000245138.4_5'Flank|CNOT1_ENST00000441024.2_In_Frame_Del_p.AQAQ1022del|CNOT1_ENST00000569240.1_In_Frame_Del_p.AQAQ1017del	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	1022					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		TTTGCTGGAAcctgggcctgagcctgggcctg	0.495																																					p.1022_1026del		Atlas-Indel,Pindel	.											.	CNOT1	359	.	0			c.3066_3077del						.																																			SO:0001651	inframe_deletion	23019	exon23			.	AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.3065_3076delCTCAGGCCCAGG	chr16.hg19:g.58585618_58585629delCCTGGGCCTGAG	ENSP00000320949:p.Ala1022_Gln1025del	50.0	0.0		57.0	19.0	NM_016284	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	In_Frame_Del	DEL	ENST00000317147.5	hg19	CCDS10799.1																																																																																			.	.		0.495	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284		-	58585629	CCTGGGCCTGAG	-	58585618	7	5	322	1	0	1	0	1	0	0	0	0	3619	507	18	0	4384	0	CNOT1	16	58585618	In_Frame_Del	DEL	CCTGGGCCTGAG	TCGA-MI-A75G-01A-11D-A32G-10	5288660	58585618	31769135	178	45426										
ADAMTS18	170692	hgsc.bcm.edu	37	chr16	77323232	77323232	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gaggtttctgatggagcagaCaacttgaggaaggccggcct	15	8	1	3			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr16:77323232C>T	ENST00000282849.5	-	22	3897	c.3479G>A	c.(3478-3480)tGt>tAt	p.C1160Y	RP11-538I12.3_ENST00000561672.1_RNA	NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	1160	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.				eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			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						ATGGAGCAGACAACTTGAGGA	0.542																																					p.C1160Y		Atlas-SNP	.											.	ADAMTS18	270	.	0			c.G3479A						.						114	120	118					16																	77323232		2198	4300	6498	SO:0001583	missense	170692	exon22			AGCAGACAACTTG	AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"ADAM metallopeptidases with thrombospondin type 1 motif"	17110	protein-coding gene	gene with protein product		607512	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.3479G>A	chr16.hg19:g.77323232C>T	ENSP00000282849:p.Cys1160Tyr	38.0	0.0		56.0	19.0	NM_199355	Q6P4R5|Q6ZWJ9	Missense_Mutation	SNP	ENST00000282849.5	hg19	CCDS10926.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.668611	0.88348	.	.	ENSG00000140873	ENST00000282849	T	0.69306	-0.39	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	D	0.91178	0.7221	H	0.99820	4.81	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94960	0.8107	10	0.87932	D	0	.	18.9804	0.92754	0.0:1.0:0.0:0.0	.	1160	Q8TE60	ATS18_HUMAN	Y	1160	ENSP00000282849:C1160Y	ENSP00000282849:C1160Y	C	-	2	0	ADAMTS18	75880733	1.000000	0.71417	0.936000	0.37596	0.830000	0.47004	7.461000	0.80834	2.740000	0.93945	0.557000	0.71058	TGT	.	.		0.542	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1			T	77323232	C	T	77323232	3	4	322	1	0	0	0	0	1	0	0	0	263	478	17	3	194	3	ADAMTS18	16	77323232	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	18737614	77323232	13031521	179	45427										
TP53	7157	hgsc.bcm.edu	37	chr17	7578271	7578271	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ttccttccactcggataagaTgctgaggaggggccagacct	12	11	0	3			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr17:7578271T>C	ENST00000269305.4	-	6	767	c.578A>G	c.(577-579)cAt>cGt	p.H193R	TP53_ENST00000574684.1_Intron|TP53_ENST00000413465.2_Missense_Mutation_p.H193R|TP53_ENST00000445888.2_Missense_Mutation_p.H193R|TP53_ENST00000420246.2_Missense_Mutation_p.H193R|TP53_ENST00000455263.2_Missense_Mutation_p.H193R|TP53_ENST00000359597.4_Missense_Mutation_p.H193R	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	193	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		H -> D (in sporadic cancers; somatic mutation).|H -> L (in sporadic cancers; somatic mutation).|H -> N (in sporadic cancers; somatic mutation).|H -> P (in sporadic cancers; somatic mutation).|H -> Q (in sporadic cancers; somatic mutation).|H -> R (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7887414}.|H -> Y (in sporadic cancers; somatic mutation).|QH -> HN (in a sporadic cancer; somatic mutation).|QH -> HY (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.H193R(80)|p.H193L(42)|p.H193P(18)|p.0?(8)|p.?(6)|p.H61R(4)|p.H100R(4)|p.H100L(4)|p.H61L(4)|p.A189_V197delAPPQHLIRV(4)|p.P191_E198>Q(3)|p.H193fs*16(3)|p.P191fs*53(2)|p.H61P(2)|p.H100P(2)|p.A189fs*53(1)|p.P191fs*6(1)|p.H193_I195delHLI(1)|p.P59_E66>Q(1)|p.P191fs*15(1)|p.P98_E105>Q(1)|p.H193_I195>AP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TCGGATAAGATGCTGAGGAGG	0.562		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.H193R	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,carcinoma,0,1	TP53	33396	.	193	Substitution - Missense(160)|Whole gene deletion(8)|Complex - deletion inframe(6)|Unknown(6)|Deletion - In frame(5)|Deletion - Frameshift(4)|Insertion - Frameshift(3)|Complex - frameshift(1)	lung(36)|upper_aerodigestive_tract(26)|ovary(20)|breast(18)|oesophagus(14)|haematopoietic_and_lymphoid_tissue(12)|endometrium(12)|biliary_tract(10)|liver(9)|stomach(7)|central_nervous_system(6)|large_intestine(6)|urinary_tract(5)|skin(5)|bone(4)|pancreas(2)|prostate(1)	c.A578G	GRCh37	CM083194|CM951225	TP53	M		.						97	87	90					17																	7578271		2203	4300	6503	SO:0001583	missense	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	ATAAGATGCTGAG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.578A>G	chr17.hg19:g.7578271T>C	ENSP00000269305:p.His193Arg	110.0	0.0		102.0	83.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	14.03	2.413611	0.42817	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99850	-7.16;-7.16;-7.16;-7.16;-7.16;-7.16;-7.16;-7.16	5.41	4.33	0.51752	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99825	0.9922	M	0.92738	3.34	0.58432	D	0.999992	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D	0.97536	1.0083	10	0.72032	D	0.01	-29.0766	9.707	0.40222	0.0:0.0827:0.0:0.9173	.	154;193;193;100;193;193;193	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	R	193;193;193;193;193;193;182;100;61;100;61	ENSP00000410739:H193R;ENSP00000352610:H193R;ENSP00000269305:H193R;ENSP00000398846:H193R;ENSP00000391127:H193R;ENSP00000391478:H193R;ENSP00000425104:H61R;ENSP00000423862:H100R	ENSP00000269305:H193R	H	-	2	0	TP53	7518996	1.000000	0.71417	0.814000	0.32528	0.023000	0.10783	7.996000	0.88334	1.001000	0.39076	-0.256000	0.11100	CAT	.	.		0.562	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7578271	T	C	7578271	3	2	322	1	0	0	0	0	1	0	0	0	16396	1464	51	2	716	2	TP53	17	7578271	Missense_Mutation	SNP	T	TCGA-MI-A75G-01A-11D-A32G-10		7578271	73616939	180	45428										
LGALS9	3965	hgsc.bcm.edu	37	chr17	25972916	25972916	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gtcatccacacagtgcagagCgcccctggacagatgttctc	10	14	2	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr17:25972916C>T	ENST00000395473.2	+	7	2074	c.606C>T	c.(604-606)agC>agT	p.S202S	LGALS9_ENST00000310394.5_Silent_p.S158S|LGALS9_ENST00000302228.5_Silent_p.S170S|LGALS9_ENST00000413914.2_Silent_p.S145S|LGALS9_ENST00000313648.6_Silent_p.S170S	NM_009587.2	NP_033665.1	O00182	LEG9_HUMAN	lectin, galactoside-binding, soluble, 9	202					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)|galactose binding (GO:0005534)|signal transducer activity (GO:0004871)			endometrium(3)|large_intestine(2)|lung(12)|skin(1)	18	Lung NSC(42;0.0103)		BRCA - Breast invasive adenocarcinoma(3;0.0141)	UCEC - Uterine corpus endometrioid carcinoma (53;0.155)		CAGTGCAGAGCGCCCCTGGAC	0.537																																					p.S202S	Melanoma(106;677 1527 28724 29571 46552)|Ovarian(193;263 2088 2118 29005 43023)	Atlas-SNP	.											.	LGALS9	29	.	0			c.C606T						.						51	50	50					17																	25972916		2202	4280	6482	SO:0001819	synonymous_variant	3965	exon7			GCAGAGCGCCCCT	AB006782	CCDS11222.1, CCDS32592.1	17q11.2	2013-03-28	2008-07-25		ENSG00000168961	ENSG00000168961		"Lectins, galactoside-binding"	6570	protein-coding gene	gene with protein product	"galectin 9"	601879				9045665	Standard	NM_009587		Approved	LGALS9A	uc002gzp.3	O00182	OTTHUMG00000179831	ENST00000395473.2:c.606C>T	chr17.hg19:g.25972916C>T		184.0	0.0		300.0	148.0	NM_009587	A7VJG6|O14532|O75028|Q3B8N1|Q53FQ0|Q9NQ58	Silent	SNP	ENST00000395473.2	hg19	CCDS11222.1																																																																																			.	.		0.537	LGALS9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255583.1	NM_009587		T	25972916	C	T	25972916	2	4	322	1	0	0	0	0	0	0	0	1	8757	767	27	1		1	LGALS9	17	25972916	Silent	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	18394645	25972916	55222294	181	45429										
CCL8	6355	hgsc.bcm.edu	37	chr17	32647344	32647344	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tgatcaataggaaaattcctAtccagaggctggagagctac	10	8	1	3			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr17:32647344A>G	ENST00000394620.1	+	2	599	c.133A>G	c.(133-135)Atc>Gtc	p.I45V		NM_005623.2	NP_005614.2	P80075	CCL8_HUMAN	chemokine (C-C motif) ligand 8	45					calcium ion transport (GO:0006816)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|exocytosis (GO:0006887)|immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of catalytic activity (GO:0043085)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	chemokine activity (GO:0008009)|heparin binding (GO:0008201)|phospholipase activator activity (GO:0016004)|protein kinase activity (GO:0004672)			NS(1)|endometrium(1)|large_intestine(1)|lung(1)	4		Ovarian(249;0.0443)|Breast(31;0.151)				GAAAATTCCTATCCAGAGGCT	0.443																																					p.I45V		Atlas-SNP	.											.	CCL8	12	.	0			c.A133G						.						86	73	78					17																	32647344		2203	4300	6503	SO:0001583	missense	6355	exon2			ATTCCTATCCAGA	X99886	CCDS11280.1	17q11.2	2013-02-25	2002-08-22	2002-08-23	ENSG00000108700	ENSG00000108700		"Chemokine ligands", "Endogenous ligands"	10635	protein-coding gene	gene with protein product		602283	"small inducible cytokine subfamily A (Cys-Cys), member 8 (monocyte chemotactic protein 2)"	SCYA8		9119400	Standard	NM_005623		Approved	MCP-2, HC14	uc002hib.3	P80075	OTTHUMG00000132883	ENST00000394620.1:c.133A>G	chr17.hg19:g.32647344A>G	ENSP00000378118:p.Ile45Val	54.0	0.0		38.0	29.0	NM_005623	A0AV77|P78388	Missense_Mutation	SNP	ENST00000394620.1	hg19	CCDS11280.1	.	.	.	.	.	.	.	.	.	.	A	3.904	-0.021432	0.07634	.	.	ENSG00000108700	ENST00000394620;ENST00000225840	.	.	.	5.62	-5.08	0.02929	CC chemokine, conserved site (1);Chemokine interleukin-8-like domain (3);	1.466460	0.04403	N	0.364669	T	0.14527	0.0351	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.14023	0.01	T	0.15093	-1.0449	8	0.13108	T	0.6	.	2.2282	0.03990	0.2052:0.2747:0.0767:0.4433	.	45	P80075	CCL8_HUMAN	V	55;45	.	ENSP00000225840:I45V	I	+	1	0	CCL8	29671457	0.000000	0.05858	0.002000	0.10522	0.011000	0.07611	-0.623000	0.05546	-0.479000	0.06813	-0.490000	0.04691	ATC	.	.		0.443	CCL8-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256376.2	NM_005623		G	32647344	A	G	32647344	3	3	322	1	0	0	0	0	1	0	0	0	2909	449	16	2	139	2	CCL8	17	32647344	Missense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	6674428	32647344	48547866	182	45430										
DCAKD	79877	hgsc.bcm.edu	37	chr17	43101864	43101864	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ctggcaatggcagcgagcccTgtgaggaccccaaacctcag	12	14	1	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr17:43101864T>C	ENST00000452796.2	-	4	888	c.633A>G	c.(631-633)acA>acG	p.T211T	DCAKD_ENST00000588499.1_Silent_p.T211T|DCAKD_ENST00000342350.5_Silent_p.T211T			Q8WVC6	DCAKD_HUMAN	dephospho-CoA kinase domain containing	211					coenzyme A biosynthetic process (GO:0015937)	membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|dephospho-CoA kinase activity (GO:0004140)			cervix(1)|endometrium(1)|large_intestine(1)|lung(2)|skin(1)	6		Prostate(33;0.155)				CAGCGAGCCCTGTGAGGACCC	0.627																																					p.T211T		Atlas-SNP	.											.	DCAKD	25	.	0			c.A633G						.						67	60	63					17																	43101864		2203	4300	6503	SO:0001819	synonymous_variant	79877	exon5			GAGCCCTGTGAGG	BC006546	CCDS11493.1	17q21.31	2005-12-20				ENSG00000172992			26238	protein-coding gene	gene with protein product							Standard	XM_005257688		Approved	FLJ22955	uc010daa.1	Q8WVC6		ENST00000452796.2:c.633A>G	chr17.hg19:g.43101864T>C		56.0	0.0		35.0	29.0	NM_001128631	A8K3Z0|D3DX60|D3DX62|Q9BR71|Q9H5W1	Silent	SNP	ENST00000452796.2	hg19	CCDS11493.1																																																																																			.	.		0.627	DCAKD-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449066.1	NM_024819		C	43101864	T	C	43101864	2	2	322	1	0	0	0	0	0	0	0	1	4281	1567	55	2		2	DCAKD	17	43101864	Silent	SNP	T	TCGA-MI-A75G-01A-11D-A32G-10	10454520	43101864	38093346	183	45431										
ABCC3	8714	hgsc.bcm.edu	37	chr17	48734481	48734481	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ggggtcctcattatcttctgGttcctgtgtgtggtctgcgc	13	10	4	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr17:48734481G>T	ENST00000285238.8	+	4	503	c.423G>T	c.(421-423)tgG>tgT	p.W141C	ABCC3_ENST00000427699.1_Missense_Mutation_p.W141C	NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	141					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33			BRCA - Breast invasive adenocarcinoma(22;3.05e-09)		Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Doxorubicin(DB00997)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indomethacin(DB00328)|Lamivudine(DB00709)|Leucovorin(DB00650)|Methotrexate(DB00563)|Metyrapone(DB01011)|Nifedipine(DB01115)|Omeprazole(DB00338)|Phenobarbital(DB01174)|Probenecid(DB01032)|Rifampicin(DB01045)|Sulfinpyrazone(DB01138)|Verapamil(DB00661)|Vincristine(DB00541)	TTATCTTCTGGTTCCTGTGTG	0.602																																					p.W141C		Atlas-SNP	.											.	ABCC3	138	.	0			c.G423T						.						178	148	158					17																	48734481		2203	4300	6503	SO:0001583	missense	8714	exon4			CTTCTGGTTCCTG	Y17151	CCDS32681.1, CCDS45739.1	17q21	2012-03-14			ENSG00000108846	ENSG00000108846		"ATP binding cassette transporters / subfamily C"	54	protein-coding gene	gene with protein product	"canalicular multispecific organic anion transporter 2"	604323				8894702, 9827529	Standard	NM_003786		Approved	MRP3, cMOAT2, EST90757, MLP2, MOAT-D	uc002isl.3	O15438	OTTHUMG00000162245	ENST00000285238.8:c.423G>T	chr17.hg19:g.48734481G>T	ENSP00000285238:p.Trp141Cys	56.0	0.0		107.0	13.0	NM_003786	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Missense_Mutation	SNP	ENST00000285238.8	hg19	CCDS32681.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.012708	0.75161	.	.	ENSG00000108846	ENST00000427699;ENST00000285238	T;T	0.46451	0.87;0.87	5.42	4.45	0.53987	.	0.167976	0.43110	D	0.000612	T	0.71771	0.3379	M	0.94063	3.49	0.80722	D	1	D;D	0.89917	0.997;1.0	P;D	0.83275	0.873;0.996	T	0.79446	-0.1800	10	0.87932	D	0	-4.2434	12.8436	0.57817	0.0802:0.0:0.9198:0.0	.	141;141	O15438;O15438-5	MRP3_HUMAN;.	C	141	ENSP00000395160:W141C;ENSP00000285238:W141C	ENSP00000285238:W141C	W	+	3	0	ABCC3	46089480	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.998000	0.93550	1.295000	0.44724	0.591000	0.81541	TGG	.	.		0.602	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038		T	48734481	G	T	48734481	3	4	322	1	0	0	0	0	1	0	0	0	54	1270	44	3	437	3	ABCC3	17	48734481	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	5632617	48734481	32460729	184	45432										
HELZ	9931	hgsc.bcm.edu	37	chr17	65144766	65144766	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cagggtaatgctcatagagtCggtcaagtaatgaaacgtga	12	6	2	3			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr17:65144766C>T	ENST00000358691.5	-	20	2706	c.2540G>A	c.(2539-2541)cGa>cAa	p.R847Q	HELZ_ENST00000580168.1_Missense_Mutation_p.R848Q	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	847						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					CTCATAGAGTCGGTCAAGTAA	0.458																																					p.R847Q		Atlas-SNP	.											.	HELZ	160	.	0			c.G2540A						.						232	227	229					17																	65144766		1898	4114	6012	SO:0001583	missense	9931	exon20			TAGAGTCGGTCAA	D29677	CCDS42374.1	17q24.2	2013-01-18			ENSG00000198265	ENSG00000198265		"Zinc fingers, CCCH-type domain containing"	16878	protein-coding gene	gene with protein product	"down-regulated in human cancers"	606699				10471385, 12691822	Standard	NM_014877		Approved	KIAA0054, HUMORF5, DHRC	uc002jfx.4	P42694	OTTHUMG00000179555	ENST00000358691.5:c.2540G>A	chr17.hg19:g.65144766C>T	ENSP00000351524:p.Arg847Gln	35.0	0.0		84.0	55.0	NM_014877	I6L9H4	Missense_Mutation	SNP	ENST00000358691.5	hg19	CCDS42374.1	.	.	.	.	.	.	.	.	.	.	C	19.24	3.788606	0.70337	.	.	ENSG00000198265	ENST00000358691	D	0.94793	-3.52	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	D	0.98432	0.9478	H	0.96720	3.87	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.99047	1.0826	10	0.87932	D	0	-12.4353	20.0585	0.97663	0.0:1.0:0.0:0.0	.	848;847	B7ZLW2;P42694	.;HELZ_HUMAN	Q	847	ENSP00000351524:R847Q	ENSP00000351524:R847Q	R	-	2	0	HELZ	62575228	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.046000	0.76592	2.812000	0.96745	0.557000	0.71058	CGA	.	.		0.458	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		T	65144766	C	T	65144766	3	4	322	1	0	0	0	0	1	0	0	0	7058	884	31	1	3344	1	HELZ	17	65144766	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	16410285	65144766	16050444	185	45433										
ITGB4	3691	hgsc.bcm.edu	37	chr17	73738729	73738730	+	Missense_Mutation	DNP	TC	TC	AG													0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cgtacgggtgcccctctttaTccggcctgaggatgacgacg							TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr17:73738729_73738730TC>AG	ENST00000200181.3	+	25	3036_3037	c.2849_2850TC>AG	c.(2848-2850)aTC>aAG	p.I950K	ITGB4_ENST00000579662.1_Missense_Mutation_p.I950K|ITGB4_ENST00000339591.3_Missense_Mutation_p.I950K|ITGB4_ENST00000449880.2_Missense_Mutation_p.I950K|ITGB4_ENST00000450894.3_Missense_Mutation_p.I950K|ITGB4_ENST00000584558.1_3'UTR	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	950					amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			CCCCTCTTTATCCGGCCTGAGG	0.663																																					p.I950N|p.I950M		Atlas-SNP	.											.	ITGB4	165	.	0			c.T2849A|c.C2850G						.																																			SO:0001583	missense	3691	exon25			TCTTTATCCGGCC|CTTTATCCGGCCT		CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"CD molecules", "Integrins", "Fibronectin type III domain containing"	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	Exception_encountered	chr17.hg19:g.73738729_73738730delinsAG	ENSP00000200181:p.Ile950Lys	85.0|86.0	0.0		144.0|143.0	24.0	NM_001005731	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Missense_Mutation	SNP	ENST00000200181.3	hg19	CCDS11727.1																																																																																			.	.		0.663	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1			AG	73738730	TC	AG	73738729	3	1	322	1	0	0	0	0	1	0	0	0	7906	1435	50	4	2943	4	ITGB4	17	73738729	Missense_Mutation	DNP	TC	TCGA-MI-A75G-01A-11D-A32G-10	8593963	73738729	7456481	186	45434										
TNRC6C	57690	hgsc.bcm.edu	37	chr17	76046694	76046694	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	aacgcgccacctgccgctgtGccagcaaacacaggttgggg	13	14	0	0	rs566391812		TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr17:76046694G>A	ENST00000588061.1	+	5	2278	c.1551G>A	c.(1549-1551)gtG>gtA	p.V517V	TNRC6C_ENST00000301624.4_Silent_p.V517V|TNRC6C_ENST00000544502.1_Silent_p.V517V|TNRC6C_ENST00000335749.4_Silent_p.V517V|TNRC6C_ENST00000588847.1_Silent_p.V517V|TNRC6C_ENST00000541771.1_Silent_p.V517V			Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C	517	Sufficient for interaction with argonaute family proteins.				embryonic hemopoiesis (GO:0035162)|endoderm formation (GO:0001706)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of gene silencing by miRNA (GO:0060964)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			CTGCCGCTGTGCCAGCAAACA	0.557																																					p.V517V		Atlas-SNP	.											.	TNRC6C	173	.	0			c.G1551A						.						62	72	69					17																	76046694		2028	4183	6211	SO:0001819	synonymous_variant	57690	exon4			CGCTGTGCCAGCA	AL834429	CCDS45798.1, CCDS45799.1	17q25.3	2012-10-04			ENSG00000078687	ENSG00000078687		"Trinucleotide (CAG) repeat containing"	29318	protein-coding gene	gene with protein product		610741					Standard	NM_018996		Approved	KIAA1582, FLJ20015	uc002juf.2	Q9HCJ0	OTTHUMG00000132642	ENST00000588061.1:c.1551G>A	chr17.hg19:g.76046694G>A		32.0	0.0		52.0	28.0	NM_018996	G3XAB8|Q86UE5|Q8N3D8|Q96MU9	Silent	SNP	ENST00000588061.1	hg19	CCDS45798.1																																																																																			.	.		0.557	TNRC6C-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395947.1	NM_018996		A	76046694	G	A	76046694	2	1	322	1	0	0	0	0	0	0	0	1	16357	1306	46	3		3	TNRC6C	17	76046694	Silent	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	2307965	76046694	5148516	187	45435										
COLEC12	81035	hgsc.bcm.edu	37	chr18	334785	334785	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ggctcattctgcagggccagGggcaccaccgctcctgatgg	14	14	2	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr18:334785G>A	ENST00000400256.3	-	6	1980	c.1773C>T	c.(1771-1773)ccC>ccT	p.P591P		NM_130386.2	NP_569057	Q5KU26	COL12_HUMAN	collectin sub-family member 12	591					carbohydrate mediated signaling (GO:0009756)|defense response (GO:0006952)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)|phagocytosis, recognition (GO:0006910)|protein homooligomerization (GO:0051260)|receptor-mediated endocytosis (GO:0006898)	collagen trimer (GO:0005581)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galactose binding (GO:0005534)|low-density lipoprotein particle binding (GO:0030169)|metal ion binding (GO:0046872)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	46		all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426)				GCAGGGCCAGGGGCACCACCG	0.682																																					p.P591P		Atlas-SNP	.											.	COLEC12	121	.	0			c.C1773T						.						37	34	35					18																	334785		2203	4300	6503	SO:0001819	synonymous_variant	81035	exon6			GGCCAGGGGCACC	AB038518	CCDS32782.1	18p11.32	2013-09-19			ENSG00000158270	ENSG00000158270		"Collectins"	16016	protein-coding gene	gene with protein product		607621				11162630	Standard	NM_130386		Approved	SRCL, CL-P1, SCARA4	uc002kkm.3	Q5KU26	OTTHUMG00000178145	ENST00000400256.3:c.1773C>T	chr18.hg19:g.334785G>A		87.0	0.0		97.0	19.0	NM_130386	Q6P9F2|Q8TCR2|Q8WZA4|Q9BY85|Q9BYH7	Silent	SNP	ENST00000400256.3	hg19	CCDS32782.1																																																																																			.	.		0.682	COLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440746.1			A	334785	G	A	334785	2	1	322	1	0	0	0	0	0	0	0	1	3714	1219	43	3		3	COLEC12	18	334785	Silent	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10		334785	77742463	188	45436										
PTPRM	5797	hgsc.bcm.edu	37	chr18	7888209	7888209	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ccactgcatcgattttcactAttttgtgtccagcaagagta	7	10	1	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr18:7888209A>T	ENST00000332175.8	+	3	1339	c.302A>T	c.(301-303)tAt>tTt	p.Y101F	PTPRM_ENST00000580170.1_Missense_Mutation_p.Y101F|PTPRM_ENST00000400053.4_Missense_Mutation_p.Y39F|PTPRM_ENST00000400060.4_Missense_Mutation_p.Y101F	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	101	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				GATTTTCACTATTTTGTGTCC	0.483																																					p.Y101F		Atlas-SNP	.											.	PTPRM	185	.	0			c.A302T						.						119	119	119					18																	7888209		2203	4300	6503	SO:0001583	missense	5797	exon3			TTCACTATTTTGT	X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.302A>T	chr18.hg19:g.7888209A>T	ENSP00000331418:p.Tyr101Phe	97.0	0.0		86.0	20.0	NM_001105244	A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	ENST00000332175.8	hg19	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	A	26.9	4.780820	0.90195	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053	T;T;T	0.03124	4.04;4.04;4.04	5.83	5.83	0.93111	Concanavalin A-like lectin/glucanase (1);MAM domain (5);	0.000000	0.85682	D	0.000000	T	0.07413	0.0187	M	0.73430	2.235	0.80722	D	1	B;B	0.11235	0.004;0.004	B;B	0.15484	0.013;0.013	T	0.04678	-1.0934	10	0.49607	T	0.09	.	11.9004	0.52680	0.8696:0.0:0.0:0.1304	.	101;101	A7MBN1;P28827	.;PTPRM_HUMAN	F	101;101;39	ENSP00000331418:Y101F;ENSP00000382933:Y101F;ENSP00000382927:Y39F	ENSP00000331418:Y101F	Y	+	2	0	PTPRM	7878209	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.062000	0.71155	2.236000	0.73375	0.533000	0.62120	TAT	.	.		0.483	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			T	7888209	A	T	7888209	3	4	322	1	0	0	0	0	1	0	0	0	12821	449	16	4	312	4	PTPRM	18	7888209	Missense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	7553424	7888209	70189039	189	45437										
MUC16	94025	hgsc.bcm.edu	37	chr19	9071326	9071326	+	Missense_Mutation	SNP	C	C	A													0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	caacacatctgtggttgtcaCcagaacagaagtaggaagtg							TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr19:9071326C>A	ENST00000397910.4	-	3	16323	c.16120G>T	c.(16120-16122)Gtg>Ttg	p.V5374L		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5376	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTGGTTGTCACCAGAACAGAA	0.512																																					p.V5374L		Atlas-SNP	.											.	MUC16	4315	.	0			c.G16120T						.						198	189	192					19																	9071326		2053	4203	6256	SO:0001583	missense	94025	exon3			TTGTCACCAGAAC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.16120G>T	chr19.hg19:g.9071326C>A	ENSP00000381008:p.Val5374Leu	66.0	0.0		105.0	21.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	4.525	0.097503	0.08681	.	.	ENSG00000181143	ENST00000397910	T	0.25579	1.79	2.39	-4.78	0.03209	.	.	.	.	.	T	0.10680	0.0261	N	0.12746	0.255	.	.	.	B	0.16603	0.018	B	0.12837	0.008	T	0.24584	-1.0156	8	0.87932	D	0	.	1.7129	0.02896	0.2868:0.1934:0.3935:0.1263	.	5374	B5ME49	.	L	5374	ENSP00000381008:V5374L	ENSP00000381008:V5374L	V	-	1	0	MUC16	8932326	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.813000	0.04491	-1.722000	0.01377	0.313000	0.20887	GTG	.	.		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9071326	C	A	9071326	3	1	322	1	0	0	0	0	1	0	0	0	9982	507	18	3	27731	3	MUC16	19	9071326	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10		9071326	50057657	190	45438	241	2								
MUC16	94025	hgsc.bcm.edu	37	chr19	9071328	9071328	+	Missense_Mutation	SNP	A	A	C													0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	acacatctgtggttgtcaccAgaacagaagtaggaagtgca							TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr19:9071328A>C	ENST00000397910.4	-	3	16321	c.16118T>G	c.(16117-16119)cTg>cGg	p.L5373R		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5375	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGTTGTCACCAGAACAGAAGT	0.517																																					p.L5373R		Atlas-SNP	.											.	MUC16	4315	.	0			c.T16118G						.						195	185	188					19																	9071328		2042	4204	6246	SO:0001583	missense	94025	exon3			GTCACCAGAACAG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.16118T>G	chr19.hg19:g.9071328A>C	ENSP00000381008:p.Leu5373Arg	69.0	0.0		107.0	21.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	a	1.276	-0.611833	0.03690	.	.	ENSG00000181143	ENST00000397910	T	0.24350	1.86	2.39	-4.52	0.03472	.	.	.	.	.	T	0.23133	0.0559	N	0.24115	0.695	.	.	.	P	0.49185	0.92	P	0.55391	0.775	T	0.30327	-0.9982	8	0.87932	D	0	.	5.4596	0.16610	0.2651:0.0:0.5533:0.1816	.	5373	B5ME49	.	R	5373	ENSP00000381008:L5373R	ENSP00000381008:L5373R	L	-	2	0	MUC16	8932328	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.534000	0.06150	-1.373000	0.02134	-2.546000	0.00178	CTG	.	.		0.517	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	9071328	A	C	9071328	3	2	322	1	0	0	0	0	1	0	0	0	9982	188	7	5	27733	5	MUC16	19	9071328	Missense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	2	9071328	50057655	191	45439	241	2								
SMARCA4	6597	hgsc.bcm.edu	37	chr19	11137010	11137010	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gcacttggggttcactggcgGcattgtccaagggtgagaag	16	8	1	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr19:11137010G>T	ENST00000429416.3	+	24	3484	c.3203G>T	c.(3202-3204)gGc>gTc	p.G1068V	SMARCA4_ENST00000541122.2_Missense_Mutation_p.G1068V|SMARCA4_ENST00000590574.1_Missense_Mutation_p.G1068V|SMARCA4_ENST00000450717.3_Missense_Mutation_p.G1068V|SMARCA4_ENST00000444061.3_Missense_Mutation_p.G1068V|SMARCA4_ENST00000413806.3_Missense_Mutation_p.G1068V|SMARCA4_ENST00000344626.4_Missense_Mutation_p.G1068V|SMARCA4_ENST00000358026.2_Missense_Mutation_p.G1068V|SMARCA4_ENST00000589677.1_Missense_Mutation_p.G1068V	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	1068					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				TTCACTGGCGGCATTGTCCAA	0.592			"F, N, Mis"		NSCLC																																p.G1068V		Atlas-SNP	.		Rec	yes		19	19p13.2	6597	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"		E	SMARCA4_ENST00000358026,NS,carcinoma,0,2	SMARCA4	502	.	1	Unknown(1)	lung(1)	c.G3203T						.						81	69	73					19																	11137010		2203	4300	6503	SO:0001583	missense	6597	exon23			CTGGCGGCATTGT	D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"SNF2-like 4", "global transcription activator homologous sequence", "sucrose nonfermenting-like 4", "mitotic growth and transcription activator", "BRM/SWI2-related gene 1", "homeotic gene regulator", "nuclear protein GRB1", "brahma protein-like 1", "ATP-dependent helicase SMARCA4"	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.3203G>T	chr19.hg19:g.11137010G>T	ENSP00000395654:p.Gly1068Val	87.0	0.0		102.0	11.0	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	hg19	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	G	15.03	2.712237	0.48517	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	T;T;T;T;T;T;T	0.74421	-0.84;-0.84;-0.84;-0.84;-0.84;-0.84;-0.84	4.49	4.49	0.54785	.	0.060357	0.64402	D	0.000003	T	0.79747	0.4499	M	0.83012	2.62	0.80722	D	1	B;P;B;B;B;B;B;B	0.45396	0.446;0.857;0.446;0.151;0.446;0.134;0.151;0.151	B;P;B;B;B;B;B;B	0.44811	0.272;0.461;0.272;0.13;0.272;0.094;0.185;0.185	D	0.84758	0.0760	10	0.87932	D	0	-29.5641	16.1707	0.81812	0.0:0.0:1.0:0.0	.	1068;1068;1068;1068;1068;288;1068;1068	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;A7E2E1;P51532	.;.;.;.;.;.;.;SMCA4_HUMAN	V	1068;1068;1132;1068;1068;1068;1068;1068	ENSP00000395654:G1068V;ENSP00000350720:G1068V;ENSP00000343896:G1068V;ENSP00000445036:G1068V;ENSP00000392837:G1068V;ENSP00000397783:G1068V;ENSP00000414727:G1068V	ENSP00000343896:G1068V	G	+	2	0	SMARCA4	10998010	1.000000	0.71417	0.998000	0.56505	0.519000	0.34347	9.104000	0.94239	2.351000	0.79841	0.555000	0.69702	GGC	.	.		0.592	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		T	11137010	G	T	11137010	3	4	322	1	0	0	0	0	1	0	0	0	14785	1203	42	3	3289	3	SMARCA4	19	11137010	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	2065682	11137010	47991973	192	45440										
SAMD1	646457	hgsc.bcm.edu	37	chr19	14199510	14199510	+	5'Flank	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tggaaagctgtcgcctgctcCgggaatccagcctcagtaaa	11	12	1	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr19:14199510C>T	ENST00000548523.1	-	0	0				C19orf67_ENST00000547589.1_5'Flank|PRKACA_ENST00000350356.3_5'Flank|SAMD1_ENST00000541938.1_5'Flank|SAMD1_ENST00000533683.2_Silent_p.P371P	NM_001277378.1	NP_001264307.1	A6NJJ6	CS067_HUMAN	chromosome 19 open reading frame 67											central_nervous_system(1)	1						TCGCCTGCTCCGGGAATCCAG	0.567																																					p.P371P		Atlas-SNP	.											.	SAMD1	27	.	0			c.G1113A						.						51	56	54					19																	14199510		2012	4170	6182	SO:0001631	upstream_gene_variant	90378	exon4			CTGCTCCGGGAAT		CCDS59360.1	19p13.12	2008-07-02			ENSG00000188032	ENSG00000188032			34354	protein-coding gene	gene with protein product							Standard	NM_001277378		Approved		uc031rjr.1	A6NJJ6			chr19.hg19:g.14199510C>T	Exception_encountered	68.0	0.0		93.0	21.0	NM_138352		Silent	SNP	ENST00000548523.1	hg19	CCDS59360.1																																																																																			.	.		0.567	C19orf67-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000403368.1	XM_929382		T	14199510	C	T	14199510	1	4	322	0	1	0	0	0	0	0	0	0	13829	639	23	1		1	SAMD1	19	14199510	5'Flank	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	3062500	14199510	44929473	193	45441										
PDE4C	5143	hgsc.bcm.edu	37	chr19	18321780	18321780	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gggtaagtccccagggtctgGgccggcttcaggggacagga	18	10	2	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr19:18321780G>C	ENST00000355502.3	-	19	2969	c.2098C>G	c.(2098-2100)Cca>Gca	p.P700A	PDE4C_ENST00000262805.12_Missense_Mutation_p.P668A|PDE4C_ENST00000447275.3_Missense_Mutation_p.P594A|PDE4C_ENST00000539010.1_Missense_Mutation_p.P469A|PDE4C_ENST00000598111.2_Missense_Mutation_p.P415A|PDE4C_ENST00000594465.3_Missense_Mutation_p.P700A|AC068499.10_ENST00000599416.2_RNA|PDE4C_ENST00000594617.3_Missense_Mutation_p.P700A|PDE4C_ENST00000597297.1_Missense_Mutation_p.P470A|AC068499.10_ENST00000594805.3_RNA			Q08493	PDE4C_HUMAN	phosphodiesterase 4C, cAMP-specific	700					cAMP catabolic process (GO:0006198)|signal transduction (GO:0007165)	cytosol (GO:0005829)|extracellular space (GO:0005615)|primary cilium (GO:0072372)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	33					Caffeine(DB00201)|Dyphylline(DB00651)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Roflumilast(DB01656)	CCAGGGTCTGGGCCGGCTTCA	0.587																																					p.P700A		Atlas-SNP	.											.	PDE4C	80	.	0			c.C2098G						.						98	78	85					19																	18321780		2203	4300	6503	SO:0001583	missense	5143	exon16			GGTCTGGGCCGGC		CCDS12373.1, CCDS42523.1, CCDS46016.1	19p13.11	2010-06-24	2010-06-24			ENSG00000105650	3.1.4.17	"Phosphodiesterases"	8782	protein-coding gene	gene with protein product	"phosphodiesterase E1 dunce homolog (Drosophila)"	600128	"phosphodiesterase 4C, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E1)"	DPDE1			Standard	NM_001098818		Approved		uc002nik.4	Q08493		ENST00000355502.3:c.2098C>G	chr19.hg19:g.18321780G>C	ENSP00000347689:p.Pro700Ala	77.0	0.0		89.0	34.0	NM_000923	B3KTC4|Q9UN44|Q9UN45|Q9UN46|Q9UPJ6	Missense_Mutation	SNP	ENST00000355502.3	hg19	CCDS12373.1	.	.	.	.	.	.	.	.	.	.	G	8.024	0.760210	0.15914	.	.	ENSG00000105650	ENST00000536045;ENST00000355502;ENST00000536507;ENST00000262805;ENST00000447275;ENST00000545961;ENST00000336173;ENST00000539010;ENST00000543547	T;T;T;T	0.69806	-0.43;-0.41;-0.39;-0.11	3.85	0.201	0.15186	.	3.221270	0.00682	N	0.000687	T	0.52500	0.1738	L	0.40543	1.245	0.09310	N	1	B;B;B;B	0.22683	0.043;0.073;0.043;0.003	B;B;B;B	0.21708	0.01;0.036;0.027;0.003	T	0.19484	-1.0304	10	0.07644	T	0.81	.	3.5148	0.07721	0.2269:0.0:0.5773:0.1957	.	700;668;506;415	Q08493;Q08493-3;O43850;O76104	PDE4C_HUMAN;.;.;.	A	779;700;688;668;594;506;414;469;809	ENSP00000347689:P700A;ENSP00000262805:P668A;ENSP00000402091:P594A;ENSP00000439470:P469A	ENSP00000262805:P668A	P	-	1	0	PDE4C	18182780	0.001000	0.12720	0.001000	0.08648	0.000000	0.00434	0.913000	0.28611	0.317000	0.23160	-0.263000	0.10527	CCA	.	.		0.587	PDE4C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466295.1			C	18321780	G	C	18321780	3	2	322	1	0	0	0	0	1	0	0	0	11650	1232	43	4	44	4	PDE4C	19	18321780	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	4122270	18321780	40807203	194	45442										
GATAD2A	54815	hgsc.bcm.edu	37	chr19	19612809	19612809	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ccggcgtaagttggcgttccGctcaggagaggcccgcgact	15	13	1	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr19:19612809G>T	ENST00000360315.3	+	10	1844	c.1532G>T	c.(1531-1533)cGc>cTc	p.R511L	GATAD2A_ENST00000537887.1_Missense_Mutation_p.R140L|GATAD2A_ENST00000358713.3_Missense_Mutation_p.R511L|GATAD2A_ENST00000429563.2_Intron|GATAD2A_ENST00000404158.1_Missense_Mutation_p.R512L|GATAD2A_ENST00000252577.5_Intron	NM_017660.3	NP_060130.3	Q86YP4	P66A_HUMAN	GATA zinc finger domain containing 2A	511					anterior neuropore closure (GO:0021506)|blood vessel development (GO:0001568)|DNA methylation (GO:0006306)|embryonic body morphogenesis (GO:0010172)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|neural fold formation (GO:0001842)|programmed cell death (GO:0012501)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|NuRD complex (GO:0016581)	protein binding, bridging (GO:0030674)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	13						TTGGCGTTCCGCTCAGGAGAG	0.667																																					p.R511L		Atlas-SNP	.											.	GATAD2A	81	.	0			c.G1532T						.						59	61	60					19																	19612809		2203	4300	6503	SO:0001583	missense	54815	exon10			CGTTCCGCTCAGG	AL390164	CCDS12402.2	19p13.11	2013-01-25			ENSG00000167491	ENSG00000167491		"GATA zinc finger domain containing"	29989	protein-coding gene	gene with protein product	"p66 alpha"	614997				12183469	Standard	NM_017660		Approved	p66alpha	uc010xqt.2	Q86YP4	OTTHUMG00000152541	ENST00000360315.3:c.1532G>T	chr19.hg19:g.19612809G>T	ENSP00000353463:p.Arg511Leu	27.0	0.0		36.0	5.0	NM_017660	B5MC40|Q7L3J2|Q96F28|Q9NPU2|Q9NXS1	Missense_Mutation	SNP	ENST00000360315.3	hg19	CCDS12402.2	.	.	.	.	.	.	.	.	.	.	G	10.40	1.340155	0.24339	.	.	ENSG00000167491	ENST00000360315;ENST00000537887;ENST00000404158;ENST00000358713	T;T	0.33216	1.42;1.42	4.78	3.72	0.42706	.	0.396523	0.27991	N	0.017026	T	0.19366	0.0465	N	0.25647	0.755	0.31349	N	0.682731	B;B	0.10296	0.003;0.001	B;B	0.08055	0.003;0.002	T	0.07083	-1.0791	10	0.27082	T	0.32	-23.8315	9.5191	0.39124	0.1046:0.0:0.8954:0.0	.	531;511	B5MC40;Q86YP4	.;P66A_HUMAN	L	511;140;531;511	ENSP00000353463:R511L;ENSP00000351552:R511L	ENSP00000351552:R511L	R	+	2	0	GATAD2A	19473809	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.859000	0.48364	2.370000	0.80446	0.585000	0.79938	CGC	.	.		0.667	GATAD2A-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326671.4	NM_017660		T	19612809	G	T	19612809	3	4	322	1	0	0	0	0	1	0	0	0	6268	1087	38	1	1566	1	GATAD2A	19	19612809	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	1291029	19612809	39516174	195	45443										
ZNF257	113835	hgsc.bcm.edu	37	chr19	22271140	22271141	+	Frame_Shift_Del	DEL	TA	TA	-													0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cgacataagagaattcatatTagagagaattcccacaaatg							TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	TA	TA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr19:22271140_22271141delTA	ENST00000594947.1	+	4	732_733	c.588_589delTA	c.(586-591)attagafs	p.IR196fs	ZNF257_ENST00000600162.1_3'UTR	NM_033468.2	NP_258429.2	Q9Y2Q1	ZN257_HUMAN	zinc finger protein 257	196					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|lung(4)	6		all_lung(12;0.0961)|Lung NSC(12;0.103)				GAATTCATATTAGAGAGAATTC	0.361																																					p.196_196del		Atlas-Indel,Pindel	.											.	ZNF257	156	.	0			c.587_588del						.																																			SO:0001589	frameshift_variant	113835	exon4			.	AF070651	CCDS46030.1	19p12	2014-02-14			ENSG00000197134	ENSG00000197134		"Zinc fingers, C2H2-type", "-"	13498	protein-coding gene	gene with protein product		606957				10585455	Standard	NM_033468		Approved	BMZF-4	uc010ecx.3	Q9Y2Q1	OTTHUMG00000182927	ENST00000594947.1:c.588_589delTA	chr19.hg19:g.22271140_22271141delTA	ENSP00000470209:p.Ile196fs	23.0	0.0		40.0	14.0	NM_033468	B3KPS4|E9PG34|Q8NE34	Frame_Shift_Del	DEL	ENST00000594947.1	hg19	CCDS46030.1																																																																																			.	.		0.361	ZNF257-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464382.1			-	22271141	TA	-	22271140	7	5	322	1	0	1	0	1	0	0	0	0	17815	1742	61	0	602	0	ZNF257	19	22271140	Frame_Shift_Del	DEL	TA	TCGA-MI-A75G-01A-11D-A32G-10	2658331	22271140	36857843	196	45444										
MAG	4099	hgsc.bcm.edu	37	chr19	35800910	35800919	+	Frame_Shift_Del	DEL	GAGCGAGCGG	GAGCGAGCGG	-													0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cgcaatgtgaccgtgaacgaGagcgagcgggagttcgtgta					rs201311667		TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	GAGCGAGCGG	GAGCGAGCGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr19:35800910_35800919delGAGCGAGCGG	ENST00000392213.3	+	8	1524_1533	c.1365_1374delGAGCGAGCGG	c.(1363-1374)gagagcgagcggfs	p.ESER455fs	MAG_ENST00000361922.4_Frame_Shift_Del_p.ESER455fs|MAG_ENST00000537831.2_Frame_Shift_Del_p.ESER430fs|MAG_ENST00000593348.1_3'UTR	NM_002361.3	NP_002352.1	P20916	MAG_HUMAN	myelin associated glycoprotein	455	Ig-like C2-type 4.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)|negative regulation of axonogenesis (GO:0050771)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of axonogenesis (GO:0050770)|substantia nigra development (GO:0021762)	integral component of membrane (GO:0016021)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)	carbohydrate binding (GO:0030246)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(10)|lung(11)|skin(2)|upper_aerodigestive_tract(2)	34	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)	Renal(1328;0.242)	Epithelial(14;3.14e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.5e-18)|all cancers(14;1.5e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			CCGTGAACGAGAGCGAGCGGGAGTTCGTGT	0.69																																					p.455_458del		Atlas-Indel,Pindel	.											.	MAG	172	.	0			c.1364_1373del						.																																			SO:0001589	frameshift_variant	4099	exon8			.	M29273	CCDS12455.1, CCDS12456.1, CCDS56090.1	19q13.1	2013-01-29			ENSG00000105695	ENSG00000105695		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6783	protein-coding gene	gene with protein product	"sialic acid binding Ig-like lectin 4A"	159460		GMA		2476987, 8432525	Standard	NM_080600		Approved	SIGLEC4A, SIGLEC-4A, S-MAG	uc002nyy.2	P20916		ENST00000392213.3:c.1365_1374delGAGCGAGCGG	chr19.hg19:g.35800910_35800919delGAGCGAGCGG	ENSP00000376048:p.Glu455fs	52.0	0.0		54.0	23.0	NM_080600	B7Z2E5|F5GYC0|Q567S4	Frame_Shift_Del	DEL	ENST00000392213.3	hg19	CCDS12455.1																																																																																			.	.		0.69	MAG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000466071.1	NM_080600		-	35800919	GAGCGAGCGG	-	35800910	7	5	322	1	0	1	0	1	0	0	0	0	9171	933	33	0	1387	0	MAG	19	35800910	Frame_Shift_Del	DEL	GAGCGAGCGG	TCGA-MI-A75G-01A-11D-A32G-10	13529770	35800910	23328073	197	45445										
KRTDAP	388533	hgsc.bcm.edu	37	chr19	35978347	35978347	+	Frame_Shift_Del	DEL	T	T	-													0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tggtcactgggcatcaggagTtgcgctcctcagtcctttca							TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr19:35978347delT	ENST00000338897.3	-	6	371	c.283delA	c.(283-285)actfs	p.T95fs	KRTDAP_ENST00000484218.2_Frame_Shift_Del_p.T81fs|KRTDAP_ENST00000479340.1_5'UTR	NM_207392.2	NP_997275.1	P60985	KTDAP_HUMAN	keratinocyte differentiation-associated protein	95					cell differentiation (GO:0030154)	extracellular region (GO:0005576)				breast(1)|lung(4)|prostate(1)	6	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			GCATCAGGAGTTGCGCTCCTC	0.547																																					p.T95fs		Atlas-Indel,Pindel	.											.	KRTDAP	9	.	0			c.284delC						.						126	121	123					19																	35978347		2203	4300	6503	SO:0001589	frameshift_variant	388533	exon6			.	AA297512	CCDS12462.1, CCDS59377.1	19q13.12	2013-06-20			ENSG00000188508	ENSG00000188508			16313	protein-coding gene	gene with protein product						11054531	Standard	NM_207392		Approved	KDAP, UNQ467	uc002nzh.3	P60985	OTTHUMG00000155449	ENST00000338897.3:c.283delA	chr19.hg19:g.35978347delT	ENSP00000339251:p.Thr95fs	50.0	0.0		83.0	19.0	NM_207392	A1L4D7	Frame_Shift_Del	DEL	ENST00000338897.3	hg19	CCDS12462.1																																																																																			.	.		0.547	KRTDAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340164.1			-	35978347	T	-	35978347	7	5	322	1	0	1	0	1	0	0	0	0	8589	1725	60	0	20	0	KRTDAP	19	35978347	Frame_Shift_Del	DEL	T	TCGA-MI-A75G-01A-11D-A32G-10	177437	35978347	23150636	198	45446										
FCGBP	8857	hgsc.bcm.edu	37	chr19	40364247	40364247	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ctcgcccagtgggtagtagcGgccatcatggaggcagccac	14	13	1	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr19:40364247G>A	ENST00000221347.6	-	31	14402	c.14395C>T	c.(14395-14397)Cgc>Tgc	p.R4799C		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4799						extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GGGTAGTAGCGGCCATCATGG	0.657																																					p.R4799C		Atlas-SNP	.											.	FCGBP	416	.	0			c.C14395T						.						43	44	44					19																	40364247		2199	4297	6496	SO:0001583	missense	8857	exon31			AGTAGCGGCCATC	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.14395C>T	chr19.hg19:g.40364247G>A	ENSP00000221347:p.Arg4799Cys	38.0	0.0		89.0	21.0	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	hg19	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	G	11.03	1.518025	0.27211	.	.	ENSG00000090920	ENST00000221347	T	0.05025	3.51	4.86	4.86	0.63082	.	0.780127	0.11686	U	0.539392	T	0.26340	0.0643	M	0.85462	2.755	0.41668	D	0.989225	D	0.89917	1.0	D	0.63033	0.91	T	0.00708	-1.1600	10	0.59425	D	0.04	.	12.2542	0.54615	0.0:0.0:0.8297:0.1702	.	4799	Q9Y6R7	FCGBP_HUMAN	C	4799	ENSP00000221347:R4799C	ENSP00000221347:R4799C	R	-	1	0	FCGBP	45056087	0.000000	0.05858	0.501000	0.27601	0.096000	0.18686	0.645000	0.24782	2.417000	0.82017	0.313000	0.20887	CGC	.	.		0.657	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		A	40364247	G	A	40364247	3	1	322	1	0	0	0	0	1	0	0	0	5786	1116	39	1	1846	1	FCGBP	19	40364247	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	4385900	40364247	18764736	199	45447										
PSG3	5671	hgsc.bcm.edu	37	chr19	43237165	43237165	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	aagctcacagcctccatgtcCtccctggggtataagttgct	9	13	1	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr19:43237165C>A	ENST00000327495.5	-	3	664	c.480G>T	c.(478-480)gaG>gaT	p.E160D	PSG3_ENST00000490592.1_5'Flank|PSG3_ENST00000595140.1_Missense_Mutation_p.E160D	NM_021016.3	NP_066296.2	Q16557	PSG3_HUMAN	pregnancy specific beta-1-glycoprotein 3	160	Ig-like C2-type 1.				defense response (GO:0006952)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	36		Prostate(69;0.00682)				CCTCCATGTCCTCCCTGGGGT	0.542																																					p.E160D		Atlas-SNP	.											.	PSG3	82	.	0			c.G480T						.						202	199	200					19																	43237165		2203	4300	6503	SO:0001583	missense	5671	exon3			CATGTCCTCCCTG		CCDS12611.1	19q13.2	2013-01-29			ENSG00000221826	ENSG00000221826		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9520	protein-coding gene	gene with protein product		176392				2341148	Standard	NM_021016		Approved		uc002oue.3	Q16557	OTTHUMG00000151120	ENST00000327495.5:c.480G>T	chr19.hg19:g.43237165C>A	ENSP00000332215:p.Glu160Asp	47.0	0.0		62.0	22.0	NM_021016	Q08265|Q9BRW2|Q9UPL4|Q9UQ77	Missense_Mutation	SNP	ENST00000327495.5	hg19	CCDS12611.1	.	.	.	.	.	.	.	.	.	.	-	11.75	1.731758	0.30684	.	.	ENSG00000221826	ENST00000327495	T	0.12672	2.66	1.59	0.424	0.16468	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.36496	0.0969	M	0.89968	3.075	0.09310	N	1	D;P	0.63880	0.993;0.798	D;P	0.70935	0.971;0.797	T	0.12630	-1.0540	9	0.87932	D	0	.	4.0653	0.09857	0.0:0.7552:0.0:0.2448	.	138;160	Q08266;Q16557	.;PSG3_HUMAN	D	160	ENSP00000332215:E160D	ENSP00000332215:E160D	E	-	3	2	PSG3	47929005	0.001000	0.12720	0.003000	0.11579	0.006000	0.05464	-0.169000	0.09911	0.021000	0.15133	0.393000	0.25936	GAG	.	.		0.542	PSG3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321423.2	NM_021016		A	43237165	C	A	43237165	3	1	322	1	0	0	0	0	1	0	0	0	12668	680	24	3	822	3	PSG3	19	43237165	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	2872918	43237165	15891818	200	45448										
FUT1	2523	hgsc.bcm.edu	37	chr19	49253497	49253497	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tgcattaatgcccacccactCgggcaggaaggccgcctccg	11	16	0	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr19:49253497C>A	ENST00000310160.3	-	4	2016	c.1042G>T	c.(1042-1044)Gag>Tag	p.E348*	FUT1_ENST00000601931.1_5'Flank	NM_000148.3	NP_000139.1	P19526	FUT1_HUMAN	fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase, H blood group)	348			E -> K (in para-Bombay allele H5; dbSNP:rs56131151). {ECO:0000269|PubMed:9226185}.		carbohydrate metabolic process (GO:0005975)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	fucosyltransferase activity (GO:0008417)|galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(3)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	17		all_lung(116;1.7e-06)|all_epithelial(76;3.52e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000135)|all cancers(93;0.000354)|Epithelial(262;0.0191)|GBM - Glioblastoma multiforme(486;0.0222)		CCCACCCACTCGGGCAGGAAG	0.552																																					p.E348X		Atlas-SNP	.											.	FUT1	44	.	0			c.G1042T	GRCh37	CM970544	FUT1	M	rs56131151	.																																			SO:0001587	stop_gained	2523	exon4			CCCACTCGGGCAG		CCDS12733.1	19q13.33	2014-07-19	2006-01-19		ENSG00000174951	ENSG00000174951	2.4.1.69	"Blood group antigens", "Fucosyltransferases"	4012	protein-coding gene	gene with protein product		211100	"fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase, Bombay phenotype included)", "fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase)"	H, HSC			Standard	NM_000148		Approved		uc002pkk.3	P19526		ENST00000310160.3:c.1042G>T	chr19.hg19:g.49253497C>A	ENSP00000312021:p.Glu348*	21.0	0.0		47.0	18.0	NM_000148	O14505|O14506|O14507	Nonsense_Mutation	SNP	ENST00000310160.3	hg19	CCDS12733.1	.	.	.	.	.	.	.	.	.	.	C	45	11.366407	0.99551	.	.	ENSG00000174951	ENST00000310160;ENST00000539428	.	.	.	4.69	3.61	0.41365	.	0.202037	0.34652	N	0.003797	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-6.5371	12.6485	0.56748	0.0:0.8321:0.1679:0.0	.	.	.	.	X	348;338	.	ENSP00000312021:E348X	E	-	1	0	FUT1	53945309	0.690000	0.27699	0.860000	0.33809	0.708000	0.40852	1.042000	0.30303	1.290000	0.44636	0.561000	0.74099	GAG	.	.		0.552	FUT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466194.1	NM_000148		A	49253497	C	A	49253497	4	1	322	1	0	0	0	0	0	1	0	0	6109	893	31	1	59	1	FUT1	19	49253497	Nonsense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	6016332	49253497	9875486	201	45449										
TRPM4	54795	hgsc.bcm.edu	37	chr19	49686109	49686109	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gctgaggatgctgctggggaAgatgtgcgcgccgaggtacc	18	9	0	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr19:49686109A>T	ENST00000252826.5	+	11	1664	c.1538A>T	c.(1537-1539)aAg>aTg	p.K513M	TRPM4_ENST00000427978.2_Missense_Mutation_p.K513M|TRPM4_ENST00000355712.5_Missense_Mutation_p.K159M	NM_017636.3	NP_060106.2	Q8TD43	TRPM4_HUMAN	transient receptor potential cation channel, subfamily M, member 4	513					calcium ion transmembrane transport (GO:0070588)|cardiac conduction (GO:0061337)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|protein sumoylation (GO:0016925)|regulation of membrane potential (GO:0042391)|regulation of T cell cytokine production (GO:0002724)|transmembrane transport (GO:0055085)|vasoconstriction (GO:0042310)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)			breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(18)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	49		all_lung(116;8.54e-05)|Lung NSC(112;0.000139)|all_neural(266;0.0506)|Ovarian(192;0.15)		all cancers(93;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000222)|GBM - Glioblastoma multiforme(486;0.00339)|Epithelial(262;0.00751)		CTGCTGGGGAAGATGTGCGCG	0.716																																					p.K513M		Atlas-SNP	.											.	TRPM4	119	.	0			c.A1538T						.						13	16	15					19																	49686109		2189	4284	6473	SO:0001583	missense	54795	exon11			TGGGGAAGATGTG	AK000048	CCDS33073.1, CCDS56098.1	19q13.3	2011-12-14				ENSG00000130529		"Voltage-gated ion channels / Transient receptor potential cation channels"	17993	protein-coding gene	gene with protein product		606936				11535825, 16382100	Standard	NM_017636		Approved	FLJ20041	uc002pmw.3	Q8TD43		ENST00000252826.5:c.1538A>T	chr19.hg19:g.49686109A>T	ENSP00000252826:p.Lys513Met	55.0	0.0		69.0	15.0	NM_001195227	A2RU25|Q7Z5D9|Q96L84|Q9NXV1	Missense_Mutation	SNP	ENST00000252826.5	hg19	CCDS33073.1	.	.	.	.	.	.	.	.	.	.	a	13.26	2.185144	0.38609	.	.	ENSG00000130529	ENST00000252826;ENST00000427978;ENST00000355712	T;T;T	0.63744	-0.06;-0.06;-0.06	4.03	2.92	0.33932	.	4.180590	0.01703	U	0.027296	T	0.68897	0.3051	L	0.55481	1.735	0.09310	N	1	P;P;P;P	0.50943	0.94;0.785;0.785;0.874	P;P;B;P	0.50378	0.533;0.639;0.444;0.461	T	0.55464	-0.8137	10	0.87932	D	0	-9.5923	8.8871	0.35409	0.8139:0.186:0.0:0.0	.	159;339;513;513	B4DIX5;Q8TD43-2;Q8TD43-3;Q8TD43	.;.;.;TRPM4_HUMAN	M	513;513;159	ENSP00000252826:K513M;ENSP00000407492:K513M;ENSP00000347944:K159M	ENSP00000252826:K513M	K	+	2	0	TRPM4	54377921	1.000000	0.71417	0.276000	0.24689	0.213000	0.24496	3.238000	0.51352	1.625000	0.50366	0.358000	0.22013	AAG	.	.		0.716	TRPM4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465543.2	NM_017636		T	49686109	A	T	49686109	3	4	322	1	0	0	0	0	1	0	0	0	16603	72	3	4	1580	4	TRPM4	19	49686109	Missense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	432612	49686109	9442874	202	45450										
ATF5	22809	hgsc.bcm.edu	37	chr19	50436140	50436141	+	Frame_Shift_Del	DEL	AA	AA	-													0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gaggggaccgcaagcaaaagAagagagaccagaacaagtcg							TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr19:50436140_50436141delAA	ENST00000423777.2	+	3	1017_1018	c.640_641delAA	c.(640-642)aagfs	p.K214fs	CTC-326K19.6_ENST00000451973.1_Intron|ATF5_ENST00000595125.1_Frame_Shift_Del_p.K214fs|MIR4751_ENST00000578027.1_RNA	NM_001193646.1	NP_001180575.1	Q9Y2D1	ATF5_HUMAN	activating transcription factor 5	214	Basic motif. {ECO:0000255|PROSITE- ProRule:PRU00978}.|Interaction with PTP4A1. {ECO:0000250}.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of astrocyte differentiation (GO:0048712)|olfactory bulb interneuron development (GO:0021891)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|transcription corepressor activity (GO:0003714)			NS(1)|endometrium(2)|large_intestine(1)|skin(3)	7		all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17)		GBM - Glioblastoma multiforme(134;0.00221)|OV - Ovarian serous cystadenocarcinoma(262;0.017)	Pseudoephedrine(DB00852)	CAAGCAAAAGAAGAGAGACCAG	0.673																																					p.213_214del	GBM(48;768 989 9196 9511 26329)	Atlas-Indel,Pindel	.											.	ATF5	27	.	0			c.639_640del						.																																			SO:0001589	frameshift_variant	22809	exon4			.	AF101388	CCDS12789.1	19q13.33	2013-09-20			ENSG00000169136	ENSG00000169136		"basic leucine zipper proteins"	790	protein-coding gene	gene with protein product		606398				10373550	Standard	NM_012068		Approved		uc002prd.3	Q9Y2D1	OTTHUMG00000183065	ENST00000423777.2:c.640_641delAA	chr19.hg19:g.50436140_50436141delAA	ENSP00000396954:p.Lys214fs	75.0	0.0		109.0	66.0	NM_012068	B3KND3|Q9BSA1|Q9UNQ3	Frame_Shift_Del	DEL	ENST00000423777.2	hg19	CCDS12789.1																																																																																			.	.		0.673	ATF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464915.2			-	50436141	AA	-	50436140	7	5	322	1	0	1	0	1	0	0	0	0	1083	247	9	0	646	0	ATF5	19	50436140	Frame_Shift_Del	DEL	AA	TCGA-MI-A75G-01A-11D-A32G-10	750031	50436140	8692843	203	45451										
C19orf75	284369	hgsc.bcm.edu	37	chr19	51770635	51770635	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ttatttccttagagtgaaacAtatcagaaagaagcaggcga	9	6	1	4			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr19:51770635A>G	ENST00000316401.7	+	5	800	c.419A>G	c.(418-420)cAt>cGt	p.H140R	CTD-3187F8.2_ENST00000597569.1_RNA|SIGLECL1_ENST00000593968.1_3'UTR|SIGLECL1_ENST00000597824.1_Missense_Mutation_p.H46R	NM_173635.1	NP_775906.1	Q96PQ1	SIG12_HUMAN	SIGLEC family like 1	504	Ig-like V-type 1.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)										AGAGTGAAACATATCAGAAAG	0.458																																					p.H140R		Atlas-SNP	.											.	.	.	.	0			c.A419G						.						124	127	126					19																	51770635		2203	4300	6503	SO:0001583	missense	284369	exon5			TGAAACATATCAG	AK097554	CCDS12827.1	19q13.33	2013-03-20	2012-07-20	2012-07-20	ENSG00000179213	ENSG00000179213			26856	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 75", "sialic acid binding Ig-like lectin 23, pseudogene", "sialic acid binding Ig-like lectin, pseudogene 7"	C19orf75, SIGLEC23P, SIGLECP7			Standard	NM_173635		Approved	FLJ40235	uc002pwb.1	Q8N7X8	OTTHUMG00000182881	ENST00000316401.7:c.419A>G	chr19.hg19:g.51770635A>G	ENSP00000321249:p.His140Arg	9.0	0.0		13.0	7.0	NM_173635	Q8IYH7	Missense_Mutation	SNP	ENST00000316401.7	hg19	CCDS12827.1	.	.	.	.	.	.	.	.	.	.	A	4.357	0.065714	0.08388	.	.	ENSG00000179213	ENST00000316401	T	0.29917	1.55	3.49	0.0143	0.14099	.	1.722310	0.03364	N	0.197990	T	0.14184	0.0343	N	0.08118	0	0.09310	N	1	B;B	0.18013	0.025;0.009	B;B	0.18263	0.021;0.011	T	0.13575	-1.0504	10	0.24483	T	0.36	-1.7619	0.668	0.00854	0.4651:0.201:0.1212:0.2127	.	46;140	B7ZLS6;Q8N7X8	.;CS075_HUMAN	R	140	ENSP00000321249:H140R	ENSP00000321249:H140R	H	+	2	0	C19orf75	56462447	0.013000	0.17824	0.034000	0.17996	0.832000	0.47134	-0.050000	0.11904	-0.091000	0.12440	0.528000	0.53228	CAT	.	.		0.458	SIGLECL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464161.2	NM_173635		G	51770635	A	G	51770635	3	3	322	1	0	0	0	0	1	0	0	0	1951	217	8	2	433	2	C19orf75	19	51770635	Missense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10	1334495	51770635	7358348	204	45452										
ZNF468	90333	hgsc.bcm.edu	37	chr19	53344538	53344538	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tgccagatatgaattatatgCgaaagcctcatcacaaacct	6	10	2	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr19:53344538C>T	ENST00000595646.1	-	4	1129	c.1009G>A	c.(1009-1011)Gca>Aca	p.A337T	ZNF28_ENST00000594602.1_Intron|ZNF468_ENST00000390651.4_Missense_Mutation_p.A284T|ZNF468_ENST00000243639.4_3'UTR|ZNF468_ENST00000396409.4_Missense_Mutation_p.A284T			Q5VIY5	ZN468_HUMAN	zinc finger protein 468	337					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|stomach(3)|urinary_tract(1)	23				GBM - Glioblastoma multiforme(134;0.0358)		GAATTATATGCGAAAGCCTCA	0.363																																					p.A337T		Atlas-SNP	.											ZNF468,NS,carcinoma,0,1	ZNF468	46	.	0			c.G1009A						.						125	129	127					19																	53344538		2203	4300	6503	SO:0001583	missense	90333	exon4			TATATGCGAAAGC	AK023558	CCDS33094.1, CCDS62781.1	19q13.41	2013-01-08				ENSG00000204604		"Zinc fingers, C2H2-type", "-"	33105	protein-coding gene	gene with protein product						16144304	Standard	NM_001277120		Approved		uc002qaf.3	Q5VIY5		ENST00000595646.1:c.1009G>A	chr19.hg19:g.53344538C>T	ENSP00000470381:p.Ala337Thr	42.0	0.0		61.0	23.0	NM_001008801	A8MV20|Q5CZB8|Q5VIY4|Q68DI7	Missense_Mutation	SNP	ENST00000595646.1	hg19	CCDS33094.1	.	.	.	.	.	.	.	.	.	.	-	4.573	0.106515	0.08780	.	.	ENSG00000204604	ENST00000243639;ENST00000396409;ENST00000390651;ENST00000393865	T;T	0.07567	3.18;3.18	1.99	0.889	0.19212	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03915	0.0110	N	0.12182	0.205	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.45323	-0.9269	9	0.25106	T	0.35	.	3.3498	0.07149	0.0:0.1646:0.2323:0.6031	.	337	Q5VIY5	ZN468_HUMAN	T	337;284;284;87	ENSP00000379690:A284T;ENSP00000445669:A284T	ENSP00000243639:A337T	A	-	1	0	ZNF468	58036350	0.552000	0.26505	0.000000	0.03702	0.000000	0.00434	0.652000	0.24888	0.039000	0.15632	-0.373000	0.07131	GCA	.	.		0.363	ZNF468-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463098.1	NM_001008801		T	53344538	C	T	53344538	3	4	322	1	0	0	0	0	1	0	0	0	17943	768	27	1	563	1	ZNF468	19	53344538	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	1573903	53344538	5784445	205	45453										
ZNF845	91664	hgsc.bcm.edu	37	chr19	53848860	53848860	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tacagggacgtgatgctggaGaattataggaacctggtctc	13	7	1	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr19:53848860G>A	ENST00000595091.1	+	4	336	c.117G>A	c.(115-117)gaG>gaA	p.E39E	ZNF845_ENST00000458035.1_Silent_p.E39E			Q96IR2	ZN845_HUMAN	zinc finger protein 845	39	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						TGATGCTGGAGAATTATAGGA	0.463																																					p.E39E		Atlas-SNP	.											.	ZNF845	101	.	0			c.G117A						.						58	65	63					19																	53848860		692	1589	2281	SO:0001819	synonymous_variant	91664	exon3			GCTGGAGAATTAT	BC007307	CCDS46170.1	19q13.42	2013-01-08			ENSG00000213799	ENSG00000213799		"Zinc fingers, C2H2-type", "-"	25112	protein-coding gene	gene with protein product							Standard	NM_138374		Approved		uc010ydv.1	Q96IR2		ENST00000595091.1:c.117G>A	chr19.hg19:g.53848860G>A		31.0	0.0		59.0	29.0	NM_138374		Silent	SNP	ENST00000595091.1	hg19	CCDS46170.1																																																																																			.	.		0.463	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908		A	53848860	G	A	53848860	2	1	322	1	0	0	0	0	0	0	0	1	18206	933	33	3		3	ZNF845	19	53848860	Silent	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	504322	53848860	5280123	206	45454										
NLRP9	338321	hgsc.bcm.edu	37	chr19	56223244	56223244	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	catcagcatccaaggcaatcCagtcgaggttcaggctcctc	9	14	2	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr19:56223244C>G	ENST00000332836.2	-	8	2792	c.2765G>C	c.(2764-2766)tGg>tCg	p.W922S	CTD-2611O12.8_ENST00000596293.1_RNA|CTD-2611O12.7_ENST00000597680.1_RNA	NM_176820.2	NP_789790.2	Q7RTR0	NALP9_HUMAN	NLR family, pyrin domain containing 9	922						cytoplasm (GO:0005737)	ATP binding (GO:0005524)			NS(2)|breast(5)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(15)|lung(21)|ovary(2)|prostate(3)|skin(7)|urinary_tract(3)	74		Colorectal(82;0.000133)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.123)		CAAGGCAATCCAGTCGAGGTT	0.582																																					p.W922S		Atlas-SNP	.											.	NLRP9	163	.	0			c.G2765C						.						106	82	90					19																	56223244		2202	4299	6501	SO:0001583	missense	338321	exon8			GCAATCCAGTCGA	AY154464	CCDS12934.1	19q13.43	2006-12-08	2006-12-08	2006-12-08				"Nucleotide-binding domain and leucine rich repeat containing"	22941	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 9"	609663	"NACHT, leucine rich repeat and PYD containing 9"	NALP9		12563287	Standard	NM_176820		Approved	NOD6, PAN12, CLR19.1	uc002qly.3	Q7RTR0		ENST00000332836.2:c.2765G>C	chr19.hg19:g.56223244C>G	ENSP00000331857:p.Trp922Ser	88.0	0.0		154.0	53.0	NM_176820	B2RN12|Q86W27	Missense_Mutation	SNP	ENST00000332836.2	hg19	CCDS12934.1	.	.	.	.	.	.	.	.	.	.	C	7.371	0.626916	0.14257	.	.	ENSG00000185792	ENST00000332836;ENST00000333452	T	0.39997	1.05	3.09	-0.538	0.11868	.	.	.	.	.	T	0.25269	0.0614	L	0.31371	0.925	0.09310	N	1	P	0.38863	0.65	B	0.39660	0.306	T	0.18999	-1.0319	9	0.08837	T	0.75	.	6.3517	0.21379	0.1993:0.4121:0.3886:0.0	.	922	Q7RTR0	NALP9_HUMAN	S	922	ENSP00000331857:W922S	ENSP00000331857:W922S	W	-	2	0	NLRP9	60915056	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.817000	0.04472	0.017000	0.15025	-0.171000	0.13296	TGG	.	.		0.582	NLRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453653.1	NM_176820		G	56223244	C	G	56223244	3	3	322	1	0	0	0	0	1	0	0	0	10493	595	21	4	218	4	NLRP9	19	56223244	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	2374384	56223244	2905739	207	45455										
ZNF586	54807	hgsc.bcm.edu	37	chr19	58290644	58290644	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	acacaggaggattcacactgGagagaggccttatgagtgca	13	8	1	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr19:58290644G>T	ENST00000396154.2	+	3	862	c.689G>T	c.(688-690)gGa>gTa	p.G230V	ZNF586_ENST00000599802.1_Intron|ZNF586_ENST00000598885.1_Intron|ZNF586_ENST00000598183.1_Intron|ZNF586_ENST00000396150.4_Nonsense_Mutation_p.E188*|ZNF586_ENST00000391702.3_Missense_Mutation_p.G187V	NM_017652.3	NP_060122.2	Q9NXT0	ZN586_HUMAN	zinc finger protein 586	230					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(2)|prostate(1)	15		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		ATTCACACTGGAGAGAGGCCT	0.423																																					p.E188X		Atlas-SNP	.											.	ZNF586	31	.	0			c.G562T						.						107	113	111					19																	58290644		2200	4300	6500	SO:0001583	missense	54807	exon2			ACACTGGAGAGAG	AK095993	CCDS42640.1, CCDS56107.1, CCDS56108.1	19q13.43	2013-01-08				ENSG00000083828		"Zinc fingers, C2H2-type", "-"	25949	protein-coding gene	gene with protein product						12477932	Standard	NM_017652		Approved	FLJ20070	uc002qqd.3	Q9NXT0		ENST00000396154.2:c.689G>T	chr19.hg19:g.58290644G>T	ENSP00000379458:p.Gly230Val	37.0	0.0		52.0	12.0	NM_001077426	A0JLV8|A8MY63|B3KTS9|E7ERT1|G3XAH3	Nonsense_Mutation	SNP	ENST00000396154.2	hg19	CCDS42640.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.12|16.12	3.032181|3.032181	0.54790|0.54790	.|.	.|.	ENSG00000083828|ENSG00000083828	ENST00000396150|ENST00000449441;ENST00000391702;ENST00000396154	.|T;T	.|0.01599	.|4.74;4.74	1.59|1.59	1.59|1.59	0.23543|0.23543	.|Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.|.	.|.	.|.	.|.	.|T	.|0.09818	.|0.0241	M|M	0.85299|0.85299	2.745|2.745	0.48087|0.48087	D|D	0.999589|0.999589	.|D	.|0.89917	.|1.0	.|D	.|0.91635	.|0.999	.|T	.|0.01743	.|-1.1283	.|9	0.28530|0.87932	T|D	0.3|0	.|.	10.1074|10.1074	0.42541|0.42541	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|230	.|Q9NXT0	.|ZN586_HUMAN	X|V	188|230;187;230	.|ENSP00000375583:G187V;ENSP00000379458:G230V	ENSP00000379454:E188X|ENSP00000375583:G187V	E|G	+|+	1|2	0|0	ZNF586|ZNF586	62982456|62982456	0.805000|0.805000	0.28982|0.28982	0.094000|0.094000	0.20943|0.20943	0.048000|0.048000	0.14542|0.14542	2.114000|2.114000	0.41911|0.41911	0.837000|0.837000	0.34925|0.34925	0.609000|0.609000	0.83330|0.83330	GAG|GGA	.	.		0.423	ZNF586-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466825.2	NM_017652		T	58290644	G	T	58290644	3	4	322	1	0	0	0	0	1	0	0	0	18034	1174	41	3	699	3	ZNF586	19	58290644	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	2067400	58290644	838339	208	45456										
PLCB4	5332	hgsc.bcm.edu	37	chr20	9319611	9319611	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tctggaagggcggatagtttGtgtctgcagtggcacagatc	15	7	2	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr20:9319611G>C	ENST00000378493.1	+	4	311	c.296G>C	c.(295-297)tGt>tCt	p.C99S	PLCB4_ENST00000414679.2_Missense_Mutation_p.C99S|PLCB4_ENST00000378473.3_Missense_Mutation_p.C99S|PLCB4_ENST00000492632.1_3'UTR|PLCB4_ENST00000378501.2_Missense_Mutation_p.C99S|PLCB4_ENST00000278655.4_Missense_Mutation_p.C99S|PLCB4_ENST00000334005.3_Missense_Mutation_p.C99S			Q15147	PLCB4_HUMAN	phospholipase C, beta 4	99					inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|smooth endoplasmic reticulum (GO:0005790)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(2)|breast(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(11)|liver(4)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(19)|upper_aerodigestive_tract(1)	87						CGGATAGTTTGTGTCTGCAGT	0.408																																					p.C99S		Atlas-SNP	.											PLCB4,NS,carcinoma,0,1	PLCB4	204	.	0			c.G296C						.						159	143	149					20																	9319611		2203	4300	6503	SO:0001583	missense	5332	exon5			TAGTTTGTGTCTG		CCDS13104.1, CCDS13105.1, CCDS54447.1	20p12	2008-03-18			ENSG00000101333	ENSG00000101333	3.1.4.11		9059	protein-coding gene	gene with protein product		600810				8530101	Standard	NM_000933		Approved		uc021wam.1	Q15147	OTTHUMG00000031853	ENST00000378493.1:c.296G>C	chr20.hg19:g.9319611G>C	ENSP00000367754:p.Cys99Ser	57.0	0.0		88.0	27.0	NM_182797	B7ZLK6|E2QRH8|Q17R56|Q5JYS8|Q5JYS9|Q5JYT0|Q5JYT3|Q5JYT4|Q9BQW5|Q9BQW6|Q9BQW8|Q9UJQ2	Missense_Mutation	SNP	ENST00000378493.1	hg19	CCDS13105.1	.	.	.	.	.	.	.	.	.	.	G	15.68	2.903745	0.52333	.	.	ENSG00000101333	ENST00000407043;ENST00000441846;ENST00000334005;ENST00000378473;ENST00000278655;ENST00000378493;ENST00000378501	T;T;T;T;T;T;T	0.39229	1.09;1.09;1.09;1.09;1.09;1.09;1.09	5.57	5.57	0.84162	Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	T	0.55289	0.1911	L	0.29908	0.895	0.80722	D	1	B;D;B	0.57899	0.429;0.981;0.253	B;D;B	0.69824	0.183;0.966;0.115	T	0.57087	-0.7871	10	0.66056	D	0.02	.	19.5465	0.95299	0.0:0.0:1.0:0.0	.	99;99;99	E2QRH8;Q15147;Q15147-4	.;PLCB4_HUMAN;.	S	99	ENSP00000385805:C99S;ENSP00000412982:C99S;ENSP00000334105:C99S;ENSP00000367734:C99S;ENSP00000278655:C99S;ENSP00000367754:C99S;ENSP00000367762:C99S	ENSP00000278655:C99S	C	+	2	0	PLCB4	9267611	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.818000	0.91991	2.643000	0.89663	0.591000	0.81541	TGT	.	.		0.408	PLCB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077948.2			C	9319611	G	C	9319611	3	2	322	1	0	0	0	0	1	0	0	0	12039	1377	48	4	310	4	PLCB4	20	9319611	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10		9319611	53705909	209	45457										
ZNF337	26152	hgsc.bcm.edu	37	chr20	25656381	25656381	+	Missense_Mutation	SNP	G	G	T													0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	acaatccctgcagaaaaaacGtttctcacccaagtgtgccc							TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr20:25656381G>T	ENST00000376436.1	-	4	2082	c.1543C>A	c.(1543-1545)Cgt>Agt	p.R515S	ZNF337_ENST00000538750.1_Missense_Mutation_p.R483S|RP4-694B14.5_ENST00000414393.1_RNA|RP4-694B14.5_ENST00000439498.1_RNA|ZNF337_ENST00000252979.5_Missense_Mutation_p.R515S|RP4-694B14.5_ENST00000428254.1_RNA|RP4-694B14.5_ENST00000455791.1_RNA|ZNF337_ENST00000481610.1_5'Flank|RP4-694B14.5_ENST00000421829.1_RNA			Q9Y3M9	ZN337_HUMAN	zinc finger protein 337	515					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						CAGAAAAAACGTTTCTCACCC	0.507																																					p.R515S		Atlas-SNP	.											.	ZNF337	65	.	0			c.C1543A						.						91	89	90					20																	25656381		2203	4300	6503	SO:0001583	missense	26152	exon5			AAAAACGTTTCTC		CCDS13174.1	20p11.1	2013-09-20			ENSG00000130684	ENSG00000130684		"Zinc fingers, C2H2-type", "-"	15809	protein-coding gene	gene with protein product							Standard	XM_005260702		Approved	dJ694B14.1	uc002wuz.3	Q9Y3M9	OTTHUMG00000032131	ENST00000376436.1:c.1543C>A	chr20.hg19:g.25656381G>T	ENSP00000365619:p.Arg515Ser	72.0	0.0		97.0	30.0	NM_015655	B4DSM2|Q9Y3Y5	Missense_Mutation	SNP	ENST00000376436.1	hg19	CCDS13174.1	.	.	.	.	.	.	.	.	.	.	.	19.05	3.752857	0.69648	.	.	ENSG00000130684	ENST00000376436;ENST00000252979;ENST00000376412;ENST00000538750	T;T;T	0.07444	3.19;3.19;3.19	1.29	1.29	0.21616	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05686	0.0149	N	0.21194	0.64	0.09310	N	0.999996	B;B	0.29835	0.258;0.258	B;B	0.24541	0.054;0.054	T	0.35151	-0.9800	9	0.51188	T	0.08	.	8.5422	0.33399	0.0:0.0:1.0:0.0	.	483;515	B4DSM2;Q9Y3M9	.;ZN337_HUMAN	S	515;515;515;483	ENSP00000365619:R515S;ENSP00000252979:R515S;ENSP00000442181:R483S	ENSP00000252979:R515S	R	-	1	0	ZNF337	25604381	0.736000	0.28164	0.001000	0.08648	0.812000	0.45895	4.548000	0.60718	1.011000	0.39340	0.298000	0.19748	CGT	.	.		0.507	ZNF337-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078454.1			T	25656381	G	T	25656381	3	4	322	1	0	0	0	0	1	0	0	0	17868	1145	40	1	716	1	ZNF337	20	25656381	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	16336770	25656381	37369139	210	45458	242	2								
ZNF337	26152	hgsc.bcm.edu	37	chr20	25656385	25656385	+	Missense_Mutation	SNP	C	C	G													0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tccctgcagaaaaaacgtttCtcacccaagtgtgccctcag					rs190880125	byFrequency	TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr20:25656385C>G	ENST00000376436.1	-	4	2078	c.1539G>C	c.(1537-1539)gaG>gaC	p.E513D	ZNF337_ENST00000538750.1_Missense_Mutation_p.E481D|RP4-694B14.5_ENST00000414393.1_RNA|RP4-694B14.5_ENST00000439498.1_RNA|ZNF337_ENST00000252979.5_Missense_Mutation_p.E513D|RP4-694B14.5_ENST00000428254.1_RNA|RP4-694B14.5_ENST00000455791.1_RNA|ZNF337_ENST00000481610.1_5'Flank|RP4-694B14.5_ENST00000421829.1_RNA			Q9Y3M9	ZN337_HUMAN	zinc finger protein 337	513					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						AAAAACGTTTCTCACCCAAGT	0.512																																					p.E513D		Atlas-SNP	.											.	ZNF337	65	.	0			c.G1539C						.						91	89	90					20																	25656385		2203	4300	6503	SO:0001583	missense	26152	exon5			ACGTTTCTCACCC		CCDS13174.1	20p11.1	2013-09-20			ENSG00000130684	ENSG00000130684		"Zinc fingers, C2H2-type", "-"	15809	protein-coding gene	gene with protein product							Standard	XM_005260702		Approved	dJ694B14.1	uc002wuz.3	Q9Y3M9	OTTHUMG00000032131	ENST00000376436.1:c.1539G>C	chr20.hg19:g.25656385C>G	ENSP00000365619:p.Glu513Asp	71.0	0.0		95.0	30.0	NM_015655	B4DSM2|Q9Y3Y5	Missense_Mutation	SNP	ENST00000376436.1	hg19	CCDS13174.1	.	.	.	.	.	.	.	.	.	.	.	15.63	2.891801	0.52014	.	.	ENSG00000130684	ENST00000376436;ENST00000252979;ENST00000376412;ENST00000538750	T;T;T	0.11277	2.79;2.79;2.79	1.29	-1.02	0.10135	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10465	0.0256	L	0.47016	1.485	0.23923	N	0.996452	P;P	0.52170	0.951;0.797	B;B	0.44278	0.445;0.365	T	0.19516	-1.0303	9	0.66056	D	0.02	.	5.5727	0.17206	0.0:0.6433:0.0:0.3567	.	481;513	B4DSM2;Q9Y3M9	.;ZN337_HUMAN	D	513;513;513;481	ENSP00000365619:E513D;ENSP00000252979:E513D;ENSP00000442181:E481D	ENSP00000252979:E513D	E	-	3	2	ZNF337	25604385	1.000000	0.71417	0.002000	0.10522	0.823000	0.46562	0.700000	0.25601	-0.298000	0.08921	0.298000	0.19748	GAG	.	C|0.999;T|0.001		0.512	ZNF337-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078454.1			G	25656385	C	G	25656385	3	3	322	1	0	0	0	0	1	0	0	0	17868	912	32	4	720	4	ZNF337	20	25656385	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	4	25656385	37369135	211	45459	242	2								
RALGAPB	57148	hgsc.bcm.edu	37	chr20	37191272	37191272	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	agatgtgggcagacaccctgGttggactgggcatgtttcta	14	8	1	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr20:37191272G>A	ENST00000262879.6	+	24	3913	c.3629G>A	c.(3628-3630)gGt>gAt	p.G1210D	RALGAPB_ENST00000397042.3_Missense_Mutation_p.G1206D|RALGAPB_ENST00000397038.1_Missense_Mutation_p.G988D|RALGAPB_ENST00000397040.1_Missense_Mutation_p.G1210D			Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit (non-catalytic)	1210	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)|Ral protein signal transduction (GO:0032484)|regulation of exocyst localization (GO:0060178)		protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(29)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						AGACACCCTGGTTGGACTGGG	0.423																																					p.G1210D		Atlas-SNP	.											.	RALGAPB	134	.	0			c.G3629A						.						184	161	169					20																	37191272		2203	4300	6503	SO:0001583	missense	57148	exon24			ACCCTGGTTGGAC	AB033045	CCDS13305.1, CCDS63272.1	20q11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000170471	ENSG00000170471			29221	protein-coding gene	gene with protein product			"KIAA1219"	KIAA1219		19520869	Standard	XM_005260462		Approved	DKFZp781M2411, RalGAPbeta	uc002xiw.3	Q86X10	OTTHUMG00000140270	ENST00000262879.6:c.3629G>A	chr20.hg19:g.37191272G>A	ENSP00000262879:p.Gly1210Asp	124.0	0.0		217.0	29.0	NM_020336	A2A2E8|A2A2E9|Q5TG31|Q8N3D1|Q8WWC0|Q9H3X8|Q9UJR1|Q9ULK1|Q9Y3G9	Missense_Mutation	SNP	ENST00000262879.6	hg19	CCDS13305.1	.	.	.	.	.	.	.	.	.	.	G	33	5.267402	0.95399	.	.	ENSG00000170471	ENST00000262879;ENST00000397042;ENST00000397038;ENST00000397040;ENST00000438490	D;D;D;D;D	0.94758	-3.51;-3.51;-3.51;-3.51;-3.51	5.79	5.79	0.91817	Rap/ran-GAP (1);	0.000000	0.85682	D	0.000000	D	0.97356	0.9135	M	0.76838	2.35	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.97501	1.0060	10	0.87932	D	0	.	20.0498	0.97621	0.0:0.0:1.0:0.0	.	1206;1210	A2A2E9;Q86X10	.;RLGPB_HUMAN	D	1210;1206;988;1210;1038	ENSP00000262879:G1210D;ENSP00000380235:G1206D;ENSP00000380231:G988D;ENSP00000380233:G1210D;ENSP00000416646:G1038D	ENSP00000262879:G1210D	G	+	2	0	RALGAPB	36624686	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.476000	0.97823	2.753000	0.94483	0.557000	0.71058	GGT	.	.		0.423	RALGAPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079191.1	NM_020336		A	37191272	G	A	37191272	3	1	322	1	0	0	0	0	1	0	0	0	13030	1261	44	3	3719	3	RALGAPB	20	37191272	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	11534887	37191272	25834248	212	45460										
MMP9	4318	hgsc.bcm.edu	37	chr20	44642129	44642129	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tgcaacgtgaacatcttcgaCgccatcgcggagattgggaa	12	10	1	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr20:44642129C>A	ENST00000372330.3	+	9	1585	c.1566C>A	c.(1564-1566)gaC>gaA	p.D522E	RP11-465L10.10_ENST00000535913.1_RNA	NM_004994.2	NP_004985.2	P14780	MMP9_HUMAN	matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)	522					collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|macrophage differentiation (GO:0030225)|negative regulation of cation channel activity (GO:2001258)|ossification (GO:0001503)|positive regulation of apoptotic process (GO:0043065)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of receptor binding (GO:1900122)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)|identical protein binding (GO:0042802)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|large_intestine(14)|liver(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(3)	46		Myeloproliferative disorder(115;0.0122)			Captopril(DB01197)|Glucosamine(DB01296)|Marimastat(DB00786)|Minocycline(DB01017)	ACATCTTCGACGCCATCGCGG	0.627											OREG0025990	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D522E		Atlas-SNP	.											.	MMP9	84	.	0			c.C1566A						.						28	30	30					20																	44642129		2203	4300	6503	SO:0001583	missense	4318	exon9			CTTCGACGCCATC		CCDS13390.1	20q12-q13	2008-01-07	2005-08-08		ENSG00000100985	ENSG00000100985	3.4.24.35		7176	protein-coding gene	gene with protein product		120361	"matrix metalloproteinase 9 (gelatinase B, 92kD gelatinase, 92kD type IV collagenase)", "matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)"	CLG4B		2158484	Standard	NM_004994		Approved		uc002xqz.3	P14780	OTTHUMG00000033044	ENST00000372330.3:c.1566C>A	chr20.hg19:g.44642129C>A	ENSP00000361405:p.Asp522Glu	61.0	0.0	925	119.0	8.0	NM_004994	B2R7V9|Q3LR70|Q8N725|Q9H4Z1|Q9UCJ9|Q9UCL1|Q9UDK2	Missense_Mutation	SNP	ENST00000372330.3	hg19	CCDS13390.1	.	.	.	.	.	.	.	.	.	.	C	16.07	3.017836	0.54576	.	.	ENSG00000100985	ENST00000372330	T	0.08370	3.1	4.9	-6.62	0.01813	Hemopexin/matrixin (2);	0.000000	0.85682	D	0.000000	T	0.33702	0.0872	H	0.95611	3.695	0.48901	D	0.999729	D	0.89917	1.0	D	0.91635	0.999	T	0.56709	-0.7934	10	0.49607	T	0.09	.	16.1145	0.81295	0.0:0.2294:0.0:0.7706	.	522	P14780	MMP9_HUMAN	E	522	ENSP00000361405:D522E	ENSP00000361405:D522E	D	+	3	2	MMP9	44075536	0.000000	0.05858	0.338000	0.25549	0.261000	0.26267	-2.798000	0.00762	-1.439000	0.01962	-0.136000	0.14681	GAC	.	.		0.627	MMP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080337.1			A	44642129	C	A	44642129	3	1	322	1	0	0	0	0	1	0	0	0	9678	535	19	1	1600	1	MMP9	20	44642129	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	7450857	44642129	18383391	213	45461										
FAM65C	140876	hgsc.bcm.edu	37	chr20	49221275	49221275	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	atagaaaacttgcccgtgggGctgggtgacaccaggaagct	14	9	0	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr20:49221275G>C	ENST00000327979.2	-	12	1392	c.981C>G	c.(979-981)agC>agG	p.S327R	FAM65C_ENST00000045083.2_Missense_Mutation_p.S327R|FAM65C_ENST00000535356.1_Missense_Mutation_p.S331R			Q96MK2	FA65C_HUMAN	family with sequence similarity 65, member C	327										endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|liver(1)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TGCCCGTGGGGCTGGGTGACA	0.597																																					p.S327R		Atlas-SNP	.											.	FAM65C	87	.	0			c.C981G						.						43	42	43					20																	49221275		2203	4300	6503	SO:0001583	missense	140876	exon12			CGTGGGGCTGGGT	AL133230	CCDS13431.2	20q13.13	2011-11-24	2008-06-13	2008-06-13	ENSG00000042062	ENSG00000042062			16168	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 175", "chromosome 20 open reading frame 176"	C20orf175, C20orf176			Standard	XM_005260294		Approved	dJ530I15.2, dJ530I15.3	uc002xvm.3	Q96MK2	OTTHUMG00000032724	ENST00000327979.2:c.981C>G	chr20.hg19:g.49221275G>C	ENSP00000332663:p.Ser327Arg	34.0	0.0		86.0	12.0	NM_080829	Q5QPB6|Q9NQQ2	Missense_Mutation	SNP	ENST00000327979.2	hg19	CCDS13431.2	.	.	.	.	.	.	.	.	.	.	G	16.99	3.273776	0.59649	.	.	ENSG00000042062	ENST00000327979;ENST00000045083;ENST00000535356	T;T;T	0.02158	4.42;4.42;4.42	3.95	-0.174	0.13319	.	0.342469	0.30723	N	0.009005	T	0.04137	0.0115	L	0.39898	1.24	0.32027	N	0.599977	D;D	0.71674	0.998;0.995	P;P	0.60541	0.876;0.836	T	0.32455	-0.9906	10	0.59425	D	0.04	-27.2238	3.7886	0.08710	0.2285:0.0:0.416:0.3555	.	331;327	F5H0X2;Q96MK2	.;FA65C_HUMAN	R	327;327;331	ENSP00000332663:S327R;ENSP00000045083:S327R;ENSP00000439802:S331R	ENSP00000045083:S327R	S	-	3	2	FAM65C	48654682	0.981000	0.34729	0.994000	0.49952	0.816000	0.46133	0.132000	0.15891	0.243000	0.21327	0.561000	0.74099	AGC	.	.		0.597	FAM65C-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257962.1			C	49221275	G	C	49221275	3	2	322	1	0	0	0	0	1	0	0	0	5609	1194	42	4	1903	4	FAM65C	20	49221275	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	4579146	49221275	13804245	214	45462										
GNAS	2778	hgsc.bcm.edu	37	chr20	57428390	57428390	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	atatcccccctgaaatcgggGaacagcccgagcaaccacct	8	16	0	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr20:57428390G>A	ENST00000371100.4	+	1	622	c.70G>A	c.(70-72)Gaa>Aaa	p.E24K	GNAS_ENST00000306120.3_5'Flank|GNAS_ENST00000371102.4_Missense_Mutation_p.E24K|GNAS_ENST00000371098.2_Intron|GNAS_ENST00000371075.3_Intron|GNAS_ENST00000313949.7_Intron|GNAS-AS1_ENST00000424094.2_RNA|GNAS-AS1_ENST00000598163.1_RNA|GNAS_ENST00000371099.2_Missense_Mutation_p.E24K|GNAS_ENST00000464624.2_3'UTR	NM_001077490.1|NM_080425.2	NP_001070958.1|NP_536350.2	P63092	GNAS2_HUMAN	GNAS complex locus	0					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|bone development (GO:0060348)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|cognition (GO:0050890)|developmental growth (GO:0048589)|energy reserve metabolic process (GO:0006112)|hair follicle placode formation (GO:0060789)|intracellular transport (GO:0046907)|platelet aggregation (GO:0070527)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of insulin secretion (GO:0050796)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intrinsic component of membrane (GO:0031224)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	adenylate cyclase activity (GO:0004016)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			adrenal_gland(12)|autonomic_ganglia(1)|biliary_tract(5)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(37)|liver(9)|lung(9)|ovary(16)|pancreas(56)|parathyroid(5)|pituitary(228)|prostate(2)|small_intestine(1)|stomach(1)|testis(2)|thyroid(35)|upper_aerodigestive_tract(3)|urinary_tract(1)	441	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			TGAAATCGGGGAACAGCCCGA	0.602			Mis		pituitary adenoma		"McCune-Albright syndrome; pseudohypoparathyroidism, type IA"			TSP Lung(22;0.16)																											p.E24K	Colon(117;935 1597 6045 8307 46442)	Atlas-SNP	.		Dom	yes		20	20q13.2	2778	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	yes	E	.	GNAS	867	.	0			c.G70A						.						22	26	25					20																	57428390		692	1591	2283	SO:0001583	missense	2778	exon1			ATCGGGGAACAGC	M21142	CCDS13471.1, CCDS13472.1, CCDS42892.1, CCDS46622.1, CCDS46623.1, CCDS46624.1	20q13.2-q13.3	2010-03-01	2001-12-19	2001-12-20	ENSG00000087460	ENSG00000087460			4392	protein-coding gene	gene with protein product	"secretogranin VI"	139320	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	GNAS1			Standard	NM_000516		Approved	NESP55, NESP, GNASXL, GPSA, SCG6	uc002xzw.3	O95467	OTTHUMG00000033069	ENST00000371100.4:c.70G>A	chr20.hg19:g.57428390G>A	ENSP00000360141:p.Glu24Lys	68.0	0.0		126.0	11.0	NM_080425	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Missense_Mutation	SNP	ENST00000371100.4	hg19	CCDS46622.1	.	.	.	.	.	.	.	.	.	.	G	15.17	2.752578	0.49362	.	.	ENSG00000087460	ENST00000371099;ENST00000371100;ENST00000371102	D;D	0.90900	-2.75;-2.74	4.36	2.21	0.28008	.	.	.	.	.	D	0.86410	0.5926	L	0.57536	1.79	0.80722	D	1	P	0.43024	0.798	B	0.36289	0.221	D	0.84091	0.0390	9	0.72032	D	0.01	.	10.7614	0.46266	0.0:0.3739:0.6261:0.0	.	24	Q5JWF2	GNAS1_HUMAN	K	24	ENSP00000360141:E24K;ENSP00000360143:E24K	ENSP00000360140:E24K	E	+	1	0	GNAS	56861785	0.656000	0.27385	0.682000	0.30024	0.865000	0.49528	0.783000	0.26802	0.455000	0.26910	0.563000	0.77884	GAA	.	.		0.602	GNAS-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080417.3	NM_000516		A	57428390	G	A	57428390	3	1	322	1	0	0	0	0	1	0	0	0	6518	1175	41	3	814	3	GNAS	20	57428390	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	8207115	57428390	5597130	215	45463										
ZNF831	128611	hgsc.bcm.edu	37	chr20	57766370	57766370	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ccctgtgctgcagcctgaagGgcctggccccacccaggtgg	14	16	0	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr20:57766370G>T	ENST00000371030.2	+	1	296	c.296G>T	c.(295-297)gGg>gTg	p.G99V		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	99	Pro-rich.						metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					CAGCCTGAAGGGCCTGGCCCC	0.721																																					p.G99V		Atlas-SNP	.											.	ZNF831	287	.	0			c.G296T						.						8	10	10					20																	57766370		1979	4115	6094	SO:0001583	missense	128611	exon1			CTGAAGGGCCTGG	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 174"	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.296G>T	chr20.hg19:g.57766370G>T	ENSP00000360069:p.Gly99Val	26.0	0.0		55.0	11.0	NM_178457	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	hg19	CCDS42894.1	.	.	.	.	.	.	.	.	.	.	G	15.17	2.753907	0.49362	.	.	ENSG00000124203	ENST00000371030	T	0.05513	3.43	5.67	4.72	0.59763	.	.	.	.	.	T	0.13500	0.0327	L	0.27053	0.805	0.09310	N	0.999999	D	0.89917	1.0	D	0.69307	0.963	T	0.10109	-1.0644	9	0.87932	D	0	-15.7075	11.4179	0.49962	0.0822:0.0:0.9178:0.0	.	99	Q5JPB2	ZN831_HUMAN	V	99	ENSP00000360069:G99V	ENSP00000360069:G99V	G	+	2	0	ZNF831	57199765	0.962000	0.33011	0.253000	0.24343	0.921000	0.55340	1.828000	0.39111	2.677000	0.91161	0.561000	0.74099	GGG	.	.		0.721	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		T	57766370	G	T	57766370	3	4	322	1	0	0	0	0	1	0	0	0	18200	1232	43	3	298	3	ZNF831	20	57766370	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	337980	57766370	5259150	216	45464										
OSBPL2	9885	hgsc.bcm.edu	37	chr20	60835074	60835074	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tcttctggggaattttcagaGgcaaatcagaaagtcacggg	12	7	5	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr20:60835074G>A	ENST00000313733.3	+	3	277	c.75G>A	c.(73-75)gaG>gaA	p.E25E	OSBPL2_ENST00000358053.2_Splice_Site_p.E13E|OSBPL2_ENST00000439951.2_Intron	NM_144498.1	NP_653081.1	Q9H1P3	OSBL2_HUMAN	oxysterol binding protein-like 2	25					lipid transport (GO:0006869)		cholesterol binding (GO:0015485)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	17	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;1.33e-06)			AATTTTCAGAGGCAAATCAGA	0.423																																					p.E25E		Atlas-SNP	.											.	OSBPL2	51	.	0			c.G75A						.						94	98	97					20																	60835074		2203	4300	6503	SO:0001819	synonymous_variant	9885	exon3			TTCAGAGGCAAAT	AB018315	CCDS13494.1, CCDS13495.1, CCDS63323.1	20q13.3	2008-08-01	2001-11-28		ENSG00000130703	ENSG00000130703		"Oxysterol binding proteins"	15761	protein-coding gene	gene with protein product		606731	"oxysterol-binding protein-like 2"			10588946, 11861666	Standard	NM_144498		Approved	KIAA0772, ORP-2	uc002yck.1	Q9H1P3	OTTHUMG00000032909	ENST00000313733.3:c.75G>A	chr20.hg19:g.60835074G>A		42.0	0.0		103.0	9.0	NM_144498	A8K736|Q6IBT0|Q9BZB1|Q9Y4B8	Silent	SNP	ENST00000313733.3	hg19	CCDS13495.1																																																																																			.	.		0.423	OSBPL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080021.1	NM_014835		A	60835074	G	A	60835074	2	1	322	1	0	0	0	0	0	0	0	1	11287	1014	35	3		3	OSBPL2	20	60835074	Silent	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	3068704	60835074	2190446	217	45465										
C21orf59	56683	hgsc.bcm.edu	37	chr21	33975557	33975557	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tcttctcagctccttggctgCccaccacagctgcgcctctg	8	18	3	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr21:33975557C>A	ENST00000290155.3	-	5	1202	c.580G>T	c.(580-582)Gca>Tca	p.A194S	C21orf59_ENST00000540881.1_Missense_Mutation_p.A138S|C21orf59_ENST00000382549.4_Missense_Mutation_p.A194S|AP000275.65_ENST00000553001.1_Missense_Mutation_p.A194S	NM_021254.2	NP_067077.1	P57076	CU059_HUMAN	chromosome 21 open reading frame 59	194						cytosol (GO:0005829)|nucleus (GO:0005634)				endometrium(2)|large_intestine(1)|prostate(1)|skin(1)	5						TCCTTGGCTGCCCACCACAGC	0.512																																					p.A194S		Atlas-SNP	.											.	C21orf59	11	.	0			c.G580T						.						122	108	113					21																	33975557		2203	4300	6503	SO:0001583	missense	56683	exon5			TGGCTGCCCACCA	AF282851	CCDS13617.1	21q22.11	2014-02-03	2003-07-22		ENSG00000159079	ENSG00000159079			1301	protein-coding gene	gene with protein product		615494	"chromosome 21 open reading frame 48"	C21orf48		24094744	Standard	NM_021254		Approved	FLJ20467, FBB18, CILD26	uc002yqc.3	P57076	OTTHUMG00000179510	ENST00000290155.3:c.580G>T	chr21.hg19:g.33975557C>A	ENSP00000290155:p.Ala194Ser	74.0	0.0		101.0	26.0	NM_021254	Q53FH0	Missense_Mutation	SNP	ENST00000290155.3	hg19	CCDS13617.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.0|23.0	4.358422|4.358422	0.82243|0.82243	.|.	.|.	ENSG00000159079|ENSG00000159079	ENST00000553001;ENST00000440966;ENST00000382549;ENST00000290155;ENST00000543202;ENST00000540881;ENST00000458138|ENST00000425336	.|.	.|.	.|.	5.28|5.28	5.28|5.28	0.74379|0.74379	.|.	0.048668|.	0.85682|.	D|.	0.000000|.	T|T	0.69106|0.69106	0.3074|0.3074	L|L	0.45581|0.45581	1.43|1.43	0.80722|0.80722	D|D	1|1	B;B;B;B;B;P;B|.	0.42908|.	0.167;0.017;0.055;0.055;0.044;0.793;0.056|.	B;B;B;B;B;B;B|.	0.43508|.	0.05;0.04;0.095;0.204;0.084;0.422;0.113|.	T|T	0.64875|0.64875	-0.6304|-0.6304	9|5	0.27082|.	T|.	0.32|.	-30.3542|-30.3542	19.2812|19.2812	0.94053|0.94053	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	138;194;194;194;194;75;194|.	F5GXV2;Q53FH0;C9J818;P57076;D3DSE6;Q8N9H5;Q96NJ2|.	.;.;.;CU059_HUMAN;.;.;.|.	S|V	194;194;194;194;194;138;177|41	.|.	ENSP00000290155:A194S|.	A|G	-|-	1|2	0|0	C21orf59|C21orf59	32897428|32897428	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.982000|0.982000	0.71751|0.71751	7.722000|7.722000	0.84778|0.84778	2.621000|2.621000	0.88768|0.88768	0.563000|0.563000	0.77884|0.77884	GCA|GGC	.	.		0.512	C21orf59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139431.1	NM_021254		A	33975557	C	A	33975557	3	1	322	1	0	0	0	0	1	0	0	0	2132	739	26	3	304	3	C21orf59	21	33975557	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10		33975557	14154338	218	45466										
PRDM15	63977	hgsc.bcm.edu	37	chr21	43248679	43248679	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	aaacacatctcacattggaaCgtcttgtcatctgtccagag	7	11	4	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr21:43248679C>A	ENST00000269844.3	-	19	2585	c.2475G>T	c.(2473-2475)acG>acT	p.T825T	PRDM15_ENST00000538201.1_Silent_p.T479T|PRDM15_ENST00000447207.2_Silent_p.T459T|PRDM15_ENST00000422911.1_Silent_p.T516T|PRDM15_ENST00000398548.1_Silent_p.T496T	NM_022115.3	NP_071398.3	P57071	PRD15_HUMAN	PR domain containing 15	825					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(3)|skin(2)|stomach(2)|urinary_tract(1)	43						CACATTGGAACGTCTTGTCAT	0.478																																					p.T825T		Atlas-SNP	.											.	PRDM15	110	.	0			c.G2475T						.						410	347	368					21																	43248679		2203	4300	6503	SO:0001819	synonymous_variant	63977	exon19			TTGGAACGTCTTG	AF276513	CCDS13676.1, CCDS42932.1, CCDS63370.1	21q22.3	2013-01-08	2002-07-31		ENSG00000141956	ENSG00000141956		"Zinc fingers, C2H2-type"	13999	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 83"	ZNF298, C21orf83		12036297, 12036298	Standard	NM_022115		Approved		uc002yzq.1	P57071	OTTHUMG00000086781	ENST00000269844.3:c.2475G>T	chr21.hg19:g.43248679C>A		38.0	0.0		58.0	9.0	NM_022115	E9PDJ6|E9PF37|E9PGL3|Q4W8S0|Q4W8S3|Q4W8S4|Q4W8S5|Q8N0X3|Q8NEX0|Q9NQV3	Silent	SNP	ENST00000269844.3	hg19	CCDS13676.1																																																																																			.	.		0.478	PRDM15-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022115		A	43248679	C	A	43248679	2	1	322	1	0	0	0	0	0	0	0	1	12468	523	19	1		1	PRDM15	21	43248679	Silent	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	9273122	43248679	4881216	219	45467										
ADARB1	104	hgsc.bcm.edu	37	chr21	46604970	46604970	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cggggtgctgcaaggggagcGgctgctcaccatgtcctgca	16	12	1	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr21:46604970G>A	ENST00000360697.3	+	7	1664	c.1649G>A	c.(1648-1650)cGg>cAg	p.R550Q	ADARB1_ENST00000389863.4_Missense_Mutation_p.R550Q|ADARB1_ENST00000437626.1_3'UTR|ADARB1_ENST00000348831.4_Missense_Mutation_p.R510Q|ADARB1_ENST00000539173.1_Missense_Mutation_p.R550Q			P78563	RED1_HUMAN	adenosine deaminase, RNA-specific, B1	550	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				adenosine to inosine editing (GO:0006382)|base conversion or substitution editing (GO:0016553)|defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|positive regulation of viral genome replication (GO:0045070)|regulation of cell cycle (GO:0051726)|RNA processing (GO:0006396)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|double-stranded RNA adenosine deaminase activity (GO:0003726)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|kidney(1)|large_intestine(3)|lung(8)|skin(1)	17				Colorectal(79;0.115)		CAAGGGGAGCGGCTGCTCACC	0.592																																					p.R550Q		Atlas-SNP	.											.	ADARB1	81	.	0			c.G1649A						.						117	109	112					21																	46604970		2203	4300	6503	SO:0001583	missense	104	exon9			GGGAGCGGCTGCT	U76420	CCDS33589.1, CCDS33590.1, CCDS42970.1	21q22.3	2012-03-22	2010-06-24		ENSG00000197381	ENSG00000197381	3.5.-.-		226	protein-coding gene	gene with protein product	"RED1 homolog (rat)"	601218	"adenosine deaminase, RNA-specific, B1 (homolog of rat RED1)"			9143496, 14759252	Standard	NR_027672		Approved	ADAR2, DRADA2, ADAR2g, DRABA2, RED1, hRED1, ADAR2a-L1, ADAR2a-L2, ADAR2a-L3, ADAR2a, ADAR2b, ADAR2c, ADAR2d	uc002zgy.2	P78563	OTTHUMG00000090295	ENST00000360697.3:c.1649G>A	chr21.hg19:g.46604970G>A	ENSP00000353920:p.Arg550Gln	42.0	0.0		60.0	20.0	NM_015834	A6NFK8|A6NJ84|C3TTQ1|C3TTQ2|C9JUP4|G5E9B4|O00395|O00465|O00691|O00692|P78555|Q4AE79|Q6P0M9|Q8NFD1	Missense_Mutation	SNP	ENST00000360697.3	hg19	CCDS33589.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.745115	0.89663	.	.	ENSG00000197381	ENST00000539173;ENST00000539917;ENST00000389863;ENST00000348831;ENST00000360697	D;D;D;D	0.93953	-3.32;-3.32;-3.32;-3.32	5.42	5.42	0.78866	Adenosine deaminase/editase (3);	0.000000	0.85682	D	0.000000	D	0.95626	0.8578	M	0.66378	2.025	0.80722	D	1	D;B;D;B	0.64830	0.994;0.191;0.981;0.446	D;B;P;B	0.65323	0.934;0.027;0.451;0.099	D	0.94109	0.7369	10	0.30078	T	0.28	-52.417	17.0803	0.86597	0.0:0.0:1.0:0.0	.	550;510;538;550	P78563;Q4AE77;G5E9B4;P78563-3	RED1_HUMAN;.;.;.	Q	550;550;550;510;550	ENSP00000441897:R550Q;ENSP00000374513:R550Q;ENSP00000015877:R510Q;ENSP00000353920:R550Q	ENSP00000015877:R510Q	R	+	2	0	ADARB1	45429398	1.000000	0.71417	0.996000	0.52242	0.963000	0.63663	7.566000	0.82347	2.712000	0.92718	0.563000	0.77884	CGG	.	.		0.592	ADARB1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206648.2	NM_015833		A	46604970	G	A	46604970	3	1	322	1	0	0	0	0	1	0	0	0	282	1116	39	1	1675	1	ADARB1	21	46604970	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	3356291	46604970	1524925	220	45468										
COL6A1	1291	hgsc.bcm.edu	37	chr21	47423312	47423312	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ccccgccccgcagtcacgttCtcctccccggctgacatcac	7	22	3	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr21:47423312C>G	ENST00000361866.3	+	35	2586	c.2472C>G	c.(2470-2472)ttC>ttG	p.F824L	COL6A1_ENST00000498614.1_3'UTR	NM_001848.2	NP_001839.2	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1	824	C-terminal globular domain.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)|protein heterotrimerization (GO:0070208)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)	platelet-derived growth factor binding (GO:0048407)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)		CAGTCACGTTCTCCTCCCCGG	0.682																																					p.F824L		Atlas-SNP	.											COL6A1,NS,neuroblastoma,0,1	COL6A1	101	.	0			c.C2472G						.						24	28	27					21																	47423312		2173	4216	6389	SO:0001583	missense	1291	exon35			CACGTTCTCCTCC	M20776	CCDS13727.1	21q22.3	2014-09-17			ENSG00000142156	ENSG00000142156		"Collagens"	2211	protein-coding gene	gene with protein product		120220					Standard	XM_006723964		Approved		uc002zhu.1	P12109	OTTHUMG00000090440	ENST00000361866.3:c.2472C>G	chr21.hg19:g.47423312C>G	ENSP00000355180:p.Phe824Leu	8.0	0.0		19.0	6.0	NM_001848	O00117|O00118|Q14040|Q14041|Q16258|Q7Z645|Q9BSA8	Missense_Mutation	SNP	ENST00000361866.3	hg19	CCDS13727.1	.	.	.	.	.	.	.	.	.	.	C	4.367	0.067702	0.08436	.	.	ENSG00000142156	ENST00000361866	T	0.77229	-1.08	4.84	3.03	0.35002	.	0.000000	0.85682	D	0.000000	T	0.64638	0.2616	N	0.19112	0.55	0.42148	D	0.991547	D	0.56521	0.976	P	0.46659	0.523	T	0.58679	-0.7594	10	0.25106	T	0.35	-22.8897	9.3631	0.38208	0.0:0.7033:0.0:0.2967	.	824	P12109	CO6A1_HUMAN	L	824	ENSP00000355180:F824L	ENSP00000355180:F824L	F	+	3	2	COL6A1	46247740	0.327000	0.24678	0.989000	0.46669	0.431000	0.31685	0.790000	0.26900	0.471000	0.27319	-0.347000	0.07816	TTC	.	.		0.682	COL6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206877.1	NM_001848		G	47423312	C	G	47423312	3	3	322	1	0	0	0	0	1	0	0	0	3701	912	32	4	2610	4	COL6A1	21	47423312	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	818342	47423312	706583	221	45469										
DGCR14	8220	hgsc.bcm.edu	37	chr22	19132075	19132075	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gctcgtcgcagccccagcctCtcccgcctcgcgcttcctcg	9	22	1	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr22:19132075C>T	ENST00000252137.6	-	1	122	c.79G>A	c.(79-81)Gag>Aag	p.E27K		NM_022719.2	NP_073210.1	Q96DF8	DGC14_HUMAN	DiGeorge syndrome critical region gene 14	27					mRNA splicing, via spliceosome (GO:0000398)|nervous system development (GO:0007399)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)	16	Colorectal(54;0.0993)					GCCCCAGCCTCTCCCGCCTCG	0.672																																					p.E27K		Atlas-SNP	.											.	DGCR14	43	.	0			c.G79A						.						18	18	18					22																	19132075		2169	4247	6416	SO:0001583	missense	8220	exon1			CAGCCTCTCCCGC	L77566	CCDS13756.1	22q11.21	2007-02-20			ENSG00000100056	ENSG00000100056			16817	protein-coding gene	gene with protein product		601755	"DiGeorge syndrome critical region gene 13"	DGCR13		8776594, 9063747	Standard	NM_022719		Approved	DGSI, Es2el, ES2, DGS-H	uc002zou.3	Q96DF8	OTTHUMG00000150119	ENST00000252137.6:c.79G>A	chr22.hg19:g.19132075C>T	ENSP00000252137:p.Glu27Lys	57.0	0.0		74.0	35.0	NM_022719	Q49AH7|Q9BTZ4	Missense_Mutation	SNP	ENST00000252137.6	hg19	CCDS13756.1	.	.	.	.	.	.	.	.	.	.	C	17.16	3.318200	0.60524	.	.	ENSG00000100056	ENST00000252137	T	0.22134	1.97	3.61	2.59	0.31030	.	1.145130	0.06431	N	0.724232	T	0.10337	0.0253	N	0.08118	0	0.09310	N	1	B	0.11235	0.004	B	0.12156	0.007	T	0.21655	-1.0239	10	0.06494	T	0.89	-4.5033	8.8938	0.35451	0.0:0.8891:0.0:0.1109	.	27	Q96DF8	DGC14_HUMAN	K	27	ENSP00000252137:E27K	ENSP00000252137:E27K	E	-	1	0	DGCR14	17512075	0.000000	0.05858	0.004000	0.12327	0.622000	0.37654	0.137000	0.15995	1.110000	0.41699	0.467000	0.42956	GAG	.	.		0.672	DGCR14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316432.2			T	19132075	C	T	19132075	3	4	322	1	0	0	0	0	1	0	0	0	4462	922	32	3	1391	3	DGCR14	22	19132075	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10		19132075	32172491	222	45470										
SCUBE1	80274	hgsc.bcm.edu	37	chr22	43608519	43608519	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	aagcagccggtgcgcccgggCtcaggctggtacgtgcccac	15	15	1	0			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr22:43608519C>T	ENST00000360835.4	-	17	2259	c.2133G>A	c.(2131-2133)gaG>gaA	p.E711E	Z82214.3_ENST00000420269.1_RNA	NM_173050.3	NP_766638.2	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1	711					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|post-embryonic development (GO:0009791)|protein homooligomerization (GO:0051260)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extrinsic component of plasma membrane (GO:0019897)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(4)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_neural(38;0.0414)|Ovarian(80;0.07)				TGCGCCCGGGCTCAGGCTGGT	0.642																																					p.E711E		Atlas-SNP	.											.	SCUBE1	105	.	0			c.G2133A						.						47	40	42					22																	43608519		2170	4252	6422	SO:0001819	synonymous_variant	80274	exon17			CCCGGGCTCAGGC		CCDS14048.1	22q13	2008-07-01			ENSG00000159307	ENSG00000159307			13441	protein-coding gene	gene with protein product		611746				11087664	Standard	NM_173050		Approved		uc003bdt.2	Q8IWY4	OTTHUMG00000150679	ENST00000360835.4:c.2133G>A	chr22.hg19:g.43608519C>T		59.0	0.0		64.0	8.0	NM_173050	Q5R336	Silent	SNP	ENST00000360835.4	hg19	CCDS14048.1																																																																																			.	.		0.642	SCUBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319582.3	NM_173050		T	43608519	C	T	43608519	2	4	322	1	0	0	0	0	0	0	0	1	13959	796	28	3		3	SCUBE1	22	43608519	Silent	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	24476444	43608519	7696047	223	45471										
NCAPH2	29781	hgsc.bcm.edu	37	chr22	50961497	50961497	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	atggggaccagctggtctcaCggttcccccagctcaatgag	12	13	2	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chr22:50961497C>A	ENST00000420993.2	+	19	1701	c.1579C>A	c.(1579-1581)Cgg>Agg	p.R527R	NCAPH2_ENST00000299821.11_Silent_p.R528R|NCAPH2_ENST00000395701.3_Silent_p.R527R|CTA-384D8.36_ENST00000608319.1_RNA	NM_001185011.1|NM_152299.3	NP_001171940.1|NP_689512.2	Q6IBW4	CNDH2_HUMAN	non-SMC condensin II complex, subunit H2	527					chromosome condensation (GO:0030261)|mitotic cell cycle (GO:0000278)	chromosome (GO:0005694)|membrane (GO:0016020)|nucleoplasm (GO:0005654)				breast(1)|cervix(1)|endometrium(2)|kidney(3)|lung(10)|ovary(1)|prostate(2)|skin(3)|stomach(1)	24		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;0.212)		GCTGGTCTCACGGTTCCCCCA	0.637																																					p.R528R		Atlas-SNP	.											.	NCAPH2	69	.	0			c.C1582A						.						64	45	52					22																	50961497		2203	4300	6503	SO:0001819	synonymous_variant	29781	exon19			GTCTCACGGTTCC	BC001937	CCDS14094.2, CCDS43038.1, CCDS54546.1	22q13.33	2008-02-04			ENSG00000025770	ENSG00000025770			25071	protein-coding gene	gene with protein product	"kleisin beta", "CAP-H2 subunit of the condensin II complex"	611230				10493829	Standard	NM_014551		Approved	384D8-2, hCAP-H2, CAP-H2	uc003blx.4	Q6IBW4	OTTHUMG00000150205	ENST00000420993.2:c.1579C>A	chr22.hg19:g.50961497C>A		29.0	0.0		45.0	13.0	NM_001185011	B7WPH1|O43788|Q13391|Q96C14|Q96GJ0|Q9BQ71|Q9BUT3|Q9BVD1	Silent	SNP	ENST00000420993.2	hg19	CCDS14094.2																																																																																			.	.		0.637	NCAPH2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317012.1	NM_152299		A	50961497	C	A	50961497	2	1	322	1	0	0	0	0	0	0	0	1	10219	527	19	1		1	NCAPH2	22	50961497	Silent	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	7352978	50961497	343069	224	45472										
CRLF2	64109	hgsc.bcm.edu	37	chrX	1327776	1327776	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	acggtttctaaattgaagtaGatgatctgaatctgtactcc	8	7	3	4			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chrX:1327776G>C	ENST00000381567.3	-	2	104	c.105C>G	c.(103-105)atC>atG	p.I35M	CRLF2_ENST00000381566.1_Missense_Mutation_p.I35M|CRLF2_ENST00000467626.1_5'UTR	NM_022148.2	NP_071431.2	Q9HC73	CRLF2_HUMAN	cytokine receptor-like factor 2	35					immunoglobulin secretion involved in immune response (GO:0002380)|inflammatory response (GO:0006954)|T-helper 2 cell cytokine production (GO:0035745)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(10)|lung(9)	20		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				AATTGAAGTAGATGATCTGAA	0.408			"Mis, T"	"P2RY8, IGH@"	"B-ALL, Downs associated ALL"																																p.I35M		Atlas-SNP	.		Dom	yes		"X,Y"	Xp22.3; Yp11.3	64109	cytokine receptor-like factor 2		L	.	CRLF2	24	.	0			c.C105G						.						242	239	240					X																	1327776		1912	4119	6031	SO:0001583	missense	64109	exon2			GAAGTAGATGATC	AF142570	CCDS75944.1, CCDS75945.1	Xp22.3 and Yp11.3	2011-10-07			ENSG00000205755	ENSG00000205755		"Pseudoautosomal regions / PAR1"	14281	protein-coding gene	gene with protein product		300357, 400023				11237741, 11474172	Standard	NM_022148		Approved	CRL2, TSLPR	uc004cpk.2	Q9HC73	OTTHUMG00000067432	ENST00000381567.3:c.105C>G	chrX.hg19:g.1327776G>C	ENSP00000370979:p.Ile35Met	385.0	0.0		460.0	65.0	NM_022148	Q9H5R3	Missense_Mutation	SNP	ENST00000381567.3	hg19		.	.	.	.	.	.	.	.	.	.	.	8.173	0.792207	0.16258	.	.	ENSG00000205755	ENST00000381567;ENST00000400841;ENST00000381566	D;D;D	0.95307	-3.67;-3.67;-3.67	0.52	0.52	0.17040	Fibronectin, type III (1);	0.658638	0.13278	U	0.399941	D	0.96043	0.8711	.	.	.	0.09310	N	1	D	0.76494	0.999	D	0.74023	0.982	D	0.88888	0.3344	8	0.72032	D	0.01	.	.	.	.	.	35	Q9HC73	CRLF2_HUMAN	M	35	ENSP00000370979:I35M;ENSP00000383641:I35M;ENSP00000370978:I35M	ENSP00000370978:I35M	I	-	3	3	CRLF2	1287776	0.941000	0.31946	0.194000	0.23346	0.144000	0.21451	1.469000	0.35343	0.551000	0.29008	0.068000	0.15388	ATC	.	.		0.408	CRLF2-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_022148		C	1327776	G	C	1327776	3	2	322	1	0	0	0	0	1	0	0	0	3889	932	33	4	688	4	CRLF2	23	1327776	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10		1327776	153942784	225	45473										
RGN	9104	hgsc.bcm.edu	37	chrX	46949222	46949222	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	cagttcttgagcggcaccagGgggccctgtactccctcttt	11	14	2	1			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chrX:46949222G>T	ENST00000352078.4	+	4	739	c.394G>T	c.(394-396)Ggg>Tgg	p.G132W	RNU6-1189P_ENST00000383958.1_RNA|RGN_ENST00000457380.1_Intron|RGN_ENST00000397180.1_Missense_Mutation_p.G132W|RGN_ENST00000336169.3_Missense_Mutation_p.G132W	NM_004683.4	NP_004674.1	Q15493	RGN_HUMAN	regucalcin	132					cellular calcium ion homeostasis (GO:0006874)|L-ascorbic acid biosynthetic process (GO:0019853)|positive regulation of ATPase activity (GO:0032781)|regulation of calcium-mediated signaling (GO:0050848)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|enzyme regulator activity (GO:0030234)|gluconolactonase activity (GO:0004341)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(2)|skin(1)|urinary_tract(1)	9						GCGGCACCAGGGGGCCCTGTA	0.507																																					p.G132W		Atlas-SNP	.											.	RGN	18	.	0			c.G394T						.						93	79	84					X																	46949222		2203	4300	6503	SO:0001583	missense	9104	exon4			CACCAGGGGGCCC	D31815	CCDS14272.1, CCDS75968.1	Xp11.3	2014-03-14	2013-04-26		ENSG00000130988	ENSG00000130988	3.1.1.17		9989	protein-coding gene	gene with protein product	"senescence marker protein-30", "gluconolactonase"	300212	"regucalcin (senescence marker protein-30)"			7548213	Standard	NM_152869		Approved	SMP30, RC	uc004dha.1	Q15493	OTTHUMG00000021435	ENST00000352078.4:c.394G>T	chrX.hg19:g.46949222G>T	ENSP00000253303:p.Gly132Trp	43.0	0.0		55.0	7.0	NM_004683	A4FTW1|A8K271|Q53FC9|Q5JRR5	Missense_Mutation	SNP	ENST00000352078.4	hg19	CCDS14272.1	.	.	.	.	.	.	.	.	.	.	G	13.35	2.210029	0.39003	.	.	ENSG00000130988	ENST00000397180;ENST00000352078;ENST00000336169	T;T;T	0.44482	0.92;0.92;0.92	5.5	4.62	0.57501	SMP-30/Gluconolaconase/LRE-like region (1);Six-bladed beta-propeller, TolB-like (1);	0.106384	0.64402	D	0.000005	T	0.75867	0.3908	H	0.96916	3.905	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.84372	0.0544	10	0.87932	D	0	-23.9076	14.7556	0.69560	0.0:0.0:0.8545:0.1455	.	132	Q15493	RGN_HUMAN	W	132	ENSP00000380365:G132W;ENSP00000253303:G132W;ENSP00000338400:G132W	ENSP00000338400:G132W	G	+	1	0	RGN	46834166	1.000000	0.71417	0.817000	0.32601	0.013000	0.08279	6.331000	0.72929	1.050000	0.40346	0.594000	0.82650	GGG	.	.		0.507	RGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056385.1	NM_004683		T	46949222	G	T	46949222	3	4	322	1	0	0	0	0	1	0	0	0	13297	1232	43	3	404	3	RGN	23	46949222	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	45621446	46949222	108321338	226	45474										
BRWD3	254065	hgsc.bcm.edu	37	chrX	79937564	79937576	+	Frame_Shift_Del	DEL	AACTTCATTTGTT	AACTTCATTTGTT	-													0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	tctggtcatttttaggctgcAacttcatttgtttctgcttc							TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	AACTTCATTTGTT	AACTTCATTTGTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chrX:79937564_79937576delAACTTCATTTGTT	ENST00000373275.4	-	39	4631_4643	c.4415_4427delAACAAATGAAGTT	c.(4414-4428)aaacaaatgaagttgfs	p.KQMKL1472fs	BRWD3_ENST00000473691.1_5'UTR	NM_153252.4	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	1472					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)					breast(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(39)|ovary(4)|prostate(2)|skin(3)	87						TTTAGGCTGCAACTTCATTTGTTTCTGCTTCCC	0.357																																					p.1472_1476del		Atlas-Indel,Pindel	.											.	BRWD3	251	.	0			c.4416_4428del						.																																			SO:0001589	frameshift_variant	254065	exon39			.		CCDS14447.1	Xq21.1	2013-01-09			ENSG00000165288	ENSG00000165288		"WD repeat domain containing"	17342	protein-coding gene	gene with protein product		300553				15543602, 16094372	Standard	NM_153252		Approved	FLJ38568, MRX93	uc004edt.3	Q6RI45	OTTHUMG00000021908	ENST00000373275.4:c.4415_4427delAACAAATGAAGTT	chrX.hg19:g.79937564_79937576delAACTTCATTTGTT	ENSP00000362372:p.Lys1472fs	40.0	0.0		80.0	13.0	NM_153252	C9IZ39|C9J3F3|Q2T9J6|Q5JRN1|Q6RI37|Q6RI42|Q6RI44|Q8N916	Frame_Shift_Del	DEL	ENST00000373275.4	hg19	CCDS14447.1																																																																																			.	.		0.357	BRWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057344.1	NM_153252		-	79937576	AACTTCATTTGTT	-	79937564	7	5	322	1	0	1	0	1	0	0	0	0	1528	131	5	0	993	0	BRWD3	23	79937564	Frame_Shift_Del	DEL	AACTTCATTTGTT	TCGA-MI-A75G-01A-11D-A32G-10	32988342	79937564	75332996	227	45475										
HNRNPH2	3188	hgsc.bcm.edu	37	chrX	100668006	100668006	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ctcatgaagatgctgtggcaGctatggcaaaagacaaagct	11	8	1	3			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chrX:100668006G>T	ENST00000316594.5	+	2	1108	c.1030G>T	c.(1030-1032)Gct>Tct	p.A344S		NM_001032393.2|NM_001199973.1|NM_001199974.1|NM_019597.4	NP_001027565.1|NP_001186902.1|NP_001186903.1|NP_062543.1	P55795	HNRH2_HUMAN	heterogeneous nuclear ribonucleoprotein H2 (H')	344	2 X 16 AA Gly-rich approximate repeats.|RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|large_intestine(2)|lung(6)|skin(1)	12						TGCTGTGGCAGCTATGGCAAA	0.438																																					p.A344S		Atlas-SNP	.											.	HNRNPH2	50	.	0			c.G1030T						.						111	99	103					X																	100668006		2203	4300	6503	SO:0001583	missense	3188	exon2			GTGGCAGCTATGG	U01923	CCDS14485.1	Xq22	2013-02-12		2008-04-18	ENSG00000126945	ENSG00000126945		"RNA binding motif (RRM) containing"	5042	protein-coding gene	gene with protein product		300610		HNRPH2		7499401	Standard	NM_019597		Approved	hnRNPH', FTP3, HNRPH'	uc004ehn.3	P55795	OTTHUMG00000022029	ENST00000316594.5:c.1030G>T	chrX.hg19:g.100668006G>T	ENSP00000361927:p.Ala344Ser	75.0	0.0		111.0	45.0	NM_001032393	A1L400|Q9HHA7	Missense_Mutation	SNP	ENST00000316594.5	hg19	CCDS14485.1	.	.	.	.	.	.	.	.	.	.	G	17.94	3.512140	0.64522	.	.	ENSG00000126945	ENST00000457902;ENST00000316594	T	0.59906	0.23	4.62	4.62	0.57501	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.79034	0.4378	M	0.93720	3.45	0.80722	D	1	B	0.24426	0.103	P	0.46796	0.527	T	0.82074	-0.0637	10	0.87932	D	0	-18.5968	14.0571	0.64776	0.0:0.0:1.0:0.0	.	344	P55795	HNRH2_HUMAN	S	299;344	ENSP00000361927:A344S	ENSP00000361927:A344S	A	+	1	0	HNRNPH2	100554662	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.562000	0.98145	2.281000	0.76405	0.513000	0.50165	GCT	.	.		0.438	HNRNPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057556.1	NM_019597		T	100668006	G	T	100668006	3	4	322	1	0	0	0	0	1	0	0	0	7276	971	34	3	1032	3	HNRNPH2	23	100668006	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	20730442	100668006	54602554	228	45476										
ZNF280C	55609	hgsc.bcm.edu	37	chrX	129350034	129350035	+	Frame_Shift_Ins	INS	-	-	A													0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	aaccgaaaggtgcagttggtINSaattttgactggagaggtcc							TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chrX:129350034_129350035insA	ENST00000370978.4	-	14	1721_1722	c.1568_1569insT	c.(1567-1569)ttafs	p.L523fs		NM_017666.4	NP_060136.1	Q8ND82	Z280C_HUMAN	zinc finger protein 280C	523					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(4)|large_intestine(9)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	26						GTGCAGTTGGTAATTTTGACTG	0.376																																					p.L523fs		Atlas-Indel,Pindel	.											.	ZNF280C	63	.	0			c.1569_1570insT						.																																			SO:0001589	frameshift_variant	55609	exon14			.	AL834333	CCDS14622.1	Xq25	2008-05-02	2007-09-20	2007-09-20	ENSG00000056277	ENSG00000056277			25955	protein-coding gene	gene with protein product			"suppressor of hairy wing homolog 3 (Drosophila)"	SUHW3		12477932	Standard	NM_017666		Approved	FLJ20095, ZNF633	uc004evm.3	Q8ND82	OTTHUMG00000022393	ENST00000370978.4:c.1569dupT	chrX.hg19:g.129350036_129350036dupA	ENSP00000360017:p.Leu523fs	37.0	0.0		61.0	28.0	NM_017666	A8K2V8|Q9NXR3	Frame_Shift_Ins	INS	ENST00000370978.4	hg19	CCDS14622.1																																																																																			.	.		0.376	ZNF280C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058251.1	NM_017666		A	129350035	-	A	129350034	7	5	322	1	0	1	1	0	0	0	0	0	17831	1635	57	0	668	0	ZNF280C	23	129350034	Frame_Shift_Ins	INS	-	TCGA-MI-A75G-01A-11D-A32G-10	28682028	129350034	25920526	229	45477										
MAGEA11	4110	hgsc.bcm.edu	37	chrX	148798282	148798282	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	gcaggtgcccggcactgatcCtgcatgctatgagttcctgt	12	12	0	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chrX:148798282C>T	ENST00000355220.5	+	5	1238	c.1136C>T	c.(1135-1137)cCt>cTt	p.P379L	MAGEA11_ENST00000333104.4_Missense_Mutation_p.P350L	NM_005366.4	NP_005357.2	P43364	MAGAB_HUMAN	melanoma antigen family A, 11	379	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.P379H(1)		cervix(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(2)|skin(1)	9	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)					GGCACTGATCCTGCATGCTAT	0.557																																					p.P379L		Atlas-SNP	.											.	MAGEA11	86	.	1	Substitution - Missense(1)	lung(1)	c.C1136T						.						120	112	115					X																	148798282		2203	4300	6503	SO:0001583	missense	4110	exon5			CTGATCCTGCATG		CCDS48180.1	Xq28	2009-03-13			ENSG00000185247	ENSG00000185247			6798	protein-coding gene	gene with protein product	"MAGE-11 antigen", "melanoma-associated antigen 11", "cancer/testis antigen family 1, member 11"	300344		MAGE11		8575766	Standard	NM_001011544		Approved	MAGE-11, MAGEA-11, MGC10511, CT1.11	uc004fdq.3	P43364	OTTHUMG00000022633	ENST00000355220.5:c.1136C>T	chrX.hg19:g.148798282C>T	ENSP00000347358:p.Pro379Leu	47.0	0.0		123.0	68.0	NM_005366	Q5ETU4|Q6ZRZ5	Missense_Mutation	SNP	ENST00000355220.5	hg19	CCDS48180.1	.	.	.	.	.	.	.	.	.	.	N	15.55	2.867745	0.51588	.	.	ENSG00000185247	ENST00000333104;ENST00000355220	T;T	0.06371	3.31;3.31	0.909	0.909	0.19332	.	.	.	.	.	T	0.22704	0.0548	M	0.89214	3.015	0.09310	N	0.999999	D;D	0.59357	0.981;0.985	D;D	0.66602	0.945;0.945	T	0.04255	-1.0965	8	.	.	.	.	4.8361	0.13466	0.0:1.0:0.0:0.0	.	350;379	G5E962;P43364	.;MAGAB_HUMAN	L	350;379	ENSP00000328177:P350L;ENSP00000347358:P379L	.	P	+	2	0	MAGEA11	148576123	0.037000	0.19845	0.003000	0.11579	0.810000	0.45777	1.737000	0.38197	0.721000	0.32231	0.377000	0.23210	CCT	.	.		0.557	MAGEA11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058725.4	NM_005366		T	148798282	C	T	148798282	3	4	322	1	0	0	0	0	1	0	0	0	9174	681	24	3	1163	3	MAGEA11	23	148798282	Missense_Mutation	SNP	C	TCGA-MI-A75G-01A-11D-A32G-10	19448248	148798282	6472278	230	45478										
MTM1	4534	hgsc.bcm.edu	37	chrX	149818234	149818234	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	atgatgcatatcataacgccGaacttttcttcttagacatt	5	9	3	2			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chrX:149818234G>A	ENST00000370396.2	+	10	967	c.913G>A	c.(913-915)Gaa>Aaa	p.E305K	MTM1_ENST00000542741.1_Missense_Mutation_p.E210K|MTM1_ENST00000306167.7_3'UTR|MTM1_ENST00000543350.1_Missense_Mutation_p.E190K|MTM1_ENST00000413012.2_Missense_Mutation_p.E268K	NM_000252.2	NP_000243.1	Q13496	MTM1_HUMAN	myotubularin 1	305	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				endosome to lysosome transport (GO:0008333)|intermediate filament organization (GO:0045109)|mitochondrion distribution (GO:0048311)|mitochondrion morphogenesis (GO:0070584)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|protein transport (GO:0015031)|regulation of vacuole organization (GO:0044088)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|late endosome (GO:0005770)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	intermediate filament binding (GO:0019215)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|liver(1)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Acute lymphoblastic leukemia(192;6.56e-05)					TCATAACGCCGAACTTTTCTT	0.323																																					p.E305K		Atlas-SNP	.											.	MTM1	89	.	0			c.G913A						.						117	108	111					X																	149818234		2203	4298	6501	SO:0001583	missense	4534	exon10			AACGCCGAACTTT	U46024	CCDS14694.1	Xq27.3-q28	2014-09-17			ENSG00000171100	ENSG00000171100		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7448	protein-coding gene	gene with protein product		300415	"myotubular myopathy 1"				Standard	NM_000252		Approved		uc004fef.4	Q13496	OTTHUMG00000024158	ENST00000370396.2:c.913G>A	chrX.hg19:g.149818234G>A	ENSP00000359423:p.Glu305Lys	62.0	0.0		149.0	10.0	NM_000252	A6NDB1|B7Z491|F2Z330|Q8NEL1	Missense_Mutation	SNP	ENST00000370396.2	hg19	CCDS14694.1	.	.	.	.	.	.	.	.	.	.	G	18.71	3.681730	0.68042	.	.	ENSG00000171100	ENST00000370396;ENST00000542741;ENST00000543350;ENST00000413012	D;D;D;D	0.89939	-2.59;-2.59;-2.59;-2.59	5.83	4.97	0.65823	Myotubularin phosphatase domain (1);Myotubularin-related (1);	0.000000	0.85682	D	0.000000	D	0.91102	0.7199	L	0.52126	1.63	0.51482	D	0.999924	D;D	0.56968	0.978;0.973	P;P	0.58077	0.832;0.592	D	0.91623	0.5312	10	0.87932	D	0	.	14.1344	0.65276	0.0738:0.0:0.9262:0.0	.	268;305	B7Z491;Q13496	.;MTM1_HUMAN	K	305;210;190;268	ENSP00000359423:E305K;ENSP00000444015:E210K;ENSP00000439784:E190K;ENSP00000389157:E268K	ENSP00000359423:E305K	E	+	1	0	MTM1	149568892	1.000000	0.71417	0.819000	0.32651	0.872000	0.50106	9.822000	0.99363	1.227000	0.43598	-0.198000	0.12761	GAA	.	.		0.323	MTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060847.3	NM_000252		A	149818234	G	A	149818234	3	1	322	1	0	0	0	0	1	0	0	0	9946	1059	37	1	947	1	MTM1	23	149818234	Missense_Mutation	SNP	G	TCGA-MI-A75G-01A-11D-A32G-10	1019952	149818234	5452326	231	45479										
PCDH11Y	83259	hgsc.bcm.edu	37	chrY	4967403	4967403	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0398230088495575	9	1	0.899061477935251	1.36732266435986	0.76761974139501	0.426986506746627	1	0	ctttgtaagcattattgatcAgaatgacaatagcccagttt	7	7	1	3			TCGA-MI-A75G-01A-11D-A32G-10	TCGA-MI-A75G-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	451ee39d-272a-47c5-9b55-cc1613bb6d2e	5d7b05ce-69de-4444-9baf-bb330ccce549	g.chrY:4967403A>G	ENST00000333703.4	+	5	2264	c.1751A>G	c.(1750-1752)cAg>cGg	p.Q584R	PCDH11Y_ENST00000362095.5_Missense_Mutation_p.Q595R|PCDH11Y_ENST00000215473.6_Missense_Mutation_p.Q595R	NM_001278619.1|NM_032971.2	NP_001265548.1|NP_116753.1	Q9BZA8	PC11Y_HUMAN	protocadherin 11 Y-linked	595	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|kidney(2)|large_intestine(7)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						ATTATTGATCAGAATGACAAT	0.368																																					p.Q595R		Atlas-SNP	.											.	PCDH11Y	163	.	0			c.A1784G						.						50	42	44					Y																	4967403		698	2094	2792	SO:0001583	missense	83259	exon2			TTGATCAGAATGA	AF332217	CCDS14776.1, CCDS14777.1, CCDS76066.1	Yp11.2	2010-01-26	2002-05-22	2002-05-24	ENSG00000099715	ENSG00000099715		"Cadherins / Protocadherins : Non-clustered"	15813	protein-coding gene	gene with protein product		400022	"protocadherin 22"	PCDH22		10644456, 11003707	Standard	NM_032971		Approved	PCDHY	uc004fqo.3	Q9BZA8	OTTHUMG00000035105	ENST00000333703.4:c.1751A>G	chrY.hg19:g.4967403A>G	ENSP00000330552:p.Gln584Arg	89.0	0.0		112.0	18.0	NM_032972	Q70LR6|Q70LR8|Q70LS0|Q70LS1|Q70LS2|Q70LS3|Q70LS4|Q70LS5|Q8WY34|Q9BZA9|Q9H4E1	Missense_Mutation	SNP	ENST00000333703.4	hg19	CCDS14776.1																																																																																			.	.		0.368	PCDH11Y-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084979.2	NM_032973		G	4967403	A	G	4967403	3	3	322	1	0	0	0	0	1	0	0	0	11518	188	7	2	1826	2	PCDH11Y	24	4967403	Missense_Mutation	SNP	A	TCGA-MI-A75G-01A-11D-A32G-10		4967403	54406163	232	45480										
PTPRU	10076	hgsc.bcm.edu	37	chr1	29609329	29609329	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	tacttcggggccgaactggcGgccagcagtctacctgaggc	14	13	1	1	rs142462225		TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr1:29609329G>C	ENST00000345512.3	+	12	2139	c.2010G>C	c.(2008-2010)gcG>gcC	p.A670A	PTPRU_ENST00000323874.8_Silent_p.A670A|PTPRU_ENST00000373779.3_Silent_p.A670A|PTPRU_ENST00000415600.2_3'UTR|PTPRU_ENST00000428026.2_Silent_p.A670A|PTPRU_ENST00000356870.3_Silent_p.A670A|PTPRU_ENST00000460170.2_Silent_p.A670A	NM_005704.4	NP_005695.3	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	670	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|homotypic cell-cell adhesion (GO:0034109)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|organ regeneration (GO:0031100)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|response to glucocorticoid (GO:0051384)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(26)|ovary(1)|prostate(3)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	79		Colorectal(325;0.000399)|Lung NSC(340;0.00953)|all_lung(284;0.0112)|Breast(348;0.0126)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;6.99e-07)|COAD - Colon adenocarcinoma(152;3.18e-05)|STAD - Stomach adenocarcinoma(196;0.0234)|READ - Rectum adenocarcinoma(331;0.0686)|BRCA - Breast invasive adenocarcinoma(304;0.0871)		CCGAACTGGCGGCCAGCAGTC	0.637																																					p.A670A		Atlas-SNP	.											.	PTPRU	374	.	0			c.G2010C						.						63	64	64					1																	29609329		2203	4300	6503	SO:0001819	synonymous_variant	10076	exon12			ACTGGCGGCCAGC	U71075	CCDS334.1, CCDS335.1, CCDS44098.1, CCDS44098.2, CCDS53290.1	1p35.3	2013-02-11			ENSG00000060656	ENSG00000060656		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9683	protein-coding gene	gene with protein product	"pi R-PTP-Psi"	602454				8700514, 9434160	Standard	NM_133178		Approved	PTPRO, hPTP-J, PCP-2, FMI, PTP	uc001bru.3	Q92729	OTTHUMG00000003699	ENST00000345512.3:c.2010G>C	chr1.hg19:g.29609329G>C		63.0	0.0		60.0	21.0	NM_001195001	A6H8L1|O00197|P78399|Q59HA4|Q5SYU4|Q5SYU5|Q92735|Q92850	Silent	SNP	ENST00000345512.3	hg19	CCDS334.1																																																																																			.	G|1.000;A|0.000		0.637	PTPRU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010447.1			C	29609329	G	C	29609329	2	2	323	1	0	0	0	0	0	0	0	1	12828	1103	39	4		4	PTPRU	1	29609329	Silent	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10		29609329	219641292	1	45481										
STK40	83931	hgsc.bcm.edu	37	chr1	36809505	36809505	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	gcctccaggacgtcggcggcGgccaggcgctgctgggggtc	19	14	0	0	rs575567942	byFrequency	TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr1:36809505G>A	ENST00000373129.3	-	10	1366	c.960C>T	c.(958-960)gcC>gcT	p.A320A	STK40_ENST00000373132.3_Silent_p.A320A|STK40_ENST00000373130.3_Silent_p.A325A|STK40_ENST00000359297.2_Silent_p.A320A	NM_032017.1	NP_114406.1	Q8N2I9	STK40_HUMAN	serine/threonine kinase 40	320	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				glycogen metabolic process (GO:0005977)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|regulation of gene expression (GO:0010468)|regulation of MAPK cascade (GO:0043408)|respiratory system process (GO:0003016)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)|stomach(1)	13		Myeloproliferative disorder(586;0.0393)				CGTCGGCGGCGGCCAGGCGCT	0.642													G|||	7	0.00139776	0	0	5008	,	,		19335	0		0	False		,,,				2504	0.0072				p.A320A		Atlas-SNP	.											.	STK40	53	.	0			c.C960T						.						28	30	29					1																	36809505		2202	4296	6498	SO:0001819	synonymous_variant	83931	exon10			GGCGGCGGCCAGG	BC008344	CCDS407.1, CCDS60089.1	1p34.3	2008-02-05			ENSG00000196182	ENSG00000196182			21373	protein-coding gene	gene with protein product		609437					Standard	NM_032017		Approved	MGC4796, SgK495	uc001cak.1	Q8N2I9	OTTHUMG00000008238	ENST00000373129.3:c.960C>T	chr1.hg19:g.36809505G>A		95.0	0.0		86.0	33.0	NM_032017	D3DPS8|Q5VTK8|Q5VTK9|Q6ZMN1|Q8N2J8|Q8N3I6|Q96HN6|Q96I44|Q9BSA3|Q9H7H6	Silent	SNP	ENST00000373129.3	hg19	CCDS407.1																																																																																			.	.		0.642	STK40-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022592.1	NM_032017		A	36809505	G	A	36809505	2	1	323	1	0	0	0	0	0	0	0	1	15322	1103	39	1		1	STK40	1	36809505	Silent	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10	7200176	36809505	212441116	2	45482										
ZMPSTE24	10269	hgsc.bcm.edu	37	chr1	40735691	40735691	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	gcaatcaagaaatttgttgtGactcagtgtattttgttgcc	9	6	2	2			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr1:40735691G>T	ENST00000372759.3	+	5	684	c.519G>T	c.(517-519)gtG>gtT	p.V173V		NM_005857.4	NP_005848.2	O75844	FACE1_HUMAN	zinc metallopeptidase STE24	173					CAAX-box protein processing (GO:0071586)|nuclear envelope organization (GO:0006998)|prenylated protein catabolic process (GO:0030327)|proteolysis (GO:0006508)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|metalloexopeptidase activity (GO:0008235)			endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|prostate(1)|skin(1)	16	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;6.3e-18)			AATTTGTTGTGACTCAGTGTA	0.338																																					p.V173V		Atlas-SNP	.											.	ZMPSTE24	50	.	0			c.G519T						.						190	196	194					1																	40735691		2203	4300	6503	SO:0001819	synonymous_variant	10269	exon5			TGTTGTGACTCAG	Y13834	CCDS449.1	1p34	2014-09-17	2012-12-10		ENSG00000084073	ENSG00000084073	3.4.24.84		12877	protein-coding gene	gene with protein product	"Hutchinson-Gilford progeria syndrome", "CAAX prenyl protease 1 homolog"	606480	"zinc metalloproteinase (STE24 homolog, yeast)", "zinc metallopeptidase (STE24 homolog, yeast)", "zinc metallopeptidase STE24 homolog (S. cerevisiae)"			10373325, 9700155, 16671095	Standard	NM_005857		Approved	FACE-1, Ste24p, STE24, HGPS, PRO1	uc001cfg.4	O75844	OTTHUMG00000005762	ENST00000372759.3:c.519G>T	chr1.hg19:g.40735691G>T		208.0	0.0		208.0	60.0	NM_005857	B3KQI7|D3DPU7|Q8NDZ8|Q9UBQ2	Silent	SNP	ENST00000372759.3	hg19	CCDS449.1																																																																																			.	.		0.338	ZMPSTE24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015766.1			T	40735691	G	T	40735691	2	4	323	1	0	0	0	0	0	0	0	1	17713	1277	45	3		3	ZMPSTE24	1	40735691	Silent	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10	3926186	40735691	208514930	3	45483										
MCOLN2	255231	hgsc.bcm.edu	37	chr1	85403450	85403450	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	ctacacaccttgtcatggtaTggtcctaagacaatccagcc	7	13	1	1			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr1:85403450T>G	ENST00000370608.3	-	11	1390	c.1323A>C	c.(1321-1323)ccA>ccC	p.P441P	MCOLN2_ENST00000531325.1_5'UTR|MCOLN2_ENST00000284027.5_Silent_p.P413P	NM_153259.2	NP_694991.2	Q8IZK6	MCLN2_HUMAN	mucolipin 2	441					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)	18				all cancers(265;0.0111)|Epithelial(280;0.0263)|OV - Ovarian serous cystadenocarcinoma(397;0.217)		TGTCATGGTATGGTCCTAAGA	0.478																																					p.P441P		Atlas-SNP	.											.	MCOLN2	60	.	0			c.A1323C						.						99	84	89					1																	85403450		2203	4300	6503	SO:0001819	synonymous_variant	255231	exon11			ATGGTATGGTCCT	AK094010	CCDS30762.1	1p22	2011-12-16			ENSG00000153898	ENSG00000153898		"Voltage-gated ion channels / Transient receptor potential cation channels"	13357	protein-coding gene	gene with protein product		607399				16382100	Standard	XM_005270719		Approved	TRPML2, FLJ36691, TRP-ML2	uc001dkm.3	Q8IZK6	OTTHUMG00000009954	ENST00000370608.3:c.1323A>C	chr1.hg19:g.85403450T>G		82.0	0.0		77.0	26.0	NM_153259	A6NI99|Q2M3I6|Q5TAG5|Q8N9R3	Silent	SNP	ENST00000370608.3	hg19	CCDS30762.1																																																																																			.	.		0.478	MCOLN2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027567.2	NM_153259		G	85403450	T	G	85403450	2	3	323	1	0	0	0	0	0	0	0	1	9405	1451	51	5		5	MCOLN2	1	85403450	Silent	SNP	T	TCGA-MI-A75H-01A-11D-A32G-10	44667759	85403450	163847171	4	45484										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103428289	103428289	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	gccaggatgcccacgttcccCtattggaccagtctcaccgg	10	16	1	0			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr1:103428289C>T	ENST00000370096.3	-	39	3256	c.2944G>A	c.(2944-2946)Ggg>Agg	p.G982R	COL11A1_ENST00000353414.4_Missense_Mutation_p.G943R|COL11A1_ENST00000358392.2_Missense_Mutation_p.G994R|COL11A1_ENST00000512756.1_Missense_Mutation_p.G866R	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	982	Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		CCACGTTCCCCTATTGGACCA	0.458																																					p.G994R		Atlas-SNP	.											.	COL11A1	972	.	0			c.G2980A						.						90	88	88					1																	103428289		2203	4300	6503	SO:0001583	missense	1301	exon39			GTTCCCCTATTGG	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.2944G>A	chr1.hg19:g.103428289C>T	ENSP00000359114:p.Gly982Arg	195.0	0.0		186.0	57.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	hg19	CCDS778.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.336260	0.81801	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000370090;ENST00000512756	D;D;D;D	0.99429	-5.89;-5.89;-5.89;-5.89	5.67	5.67	0.87782	.	0.056693	0.64402	D	0.000001	D	0.99834	0.9925	H	0.98883	4.36	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.997;1.0;1.0;0.999;0.999	D	0.96751	0.9554	10	0.87932	D	0	.	19.7741	0.96385	0.0:1.0:0.0:0.0	.	866;943;994;982;202	E9PCU0;P12107-3;P12107-2;P12107;F5H5Z5	.;.;.;COBA1_HUMAN;.	R	982;994;943;202;866	ENSP00000359114:G982R;ENSP00000351163:G994R;ENSP00000302551:G943R;ENSP00000426533:G866R	ENSP00000302551:G943R	G	-	1	0	COL11A1	103200877	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.719000	0.84751	2.673000	0.90976	0.557000	0.71058	GGG	.	.		0.458	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		T	103428289	C	T	103428289	3	4	323	1	0	0	0	0	1	0	0	0	3669	681	24	3	2592	3	COL11A1	1	103428289	Missense_Mutation	SNP	C	TCGA-MI-A75H-01A-11D-A32G-10	18024839	103428289	145822332	5	45485										
MOV10	4343	hgsc.bcm.edu	37	chr1	113231596	113231596	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	ggcttctcctccatgctgtaTggaatgaagattgcaaatct	9	9	2	2			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr1:113231596T>C	ENST00000413052.2	+	3	567	c.177T>C	c.(175-177)taT>taC	p.Y59Y	MOV10_ENST00000468624.1_3'UTR|MOV10_ENST00000369644.1_Silent_p.Y3Y|MOV10_ENST00000357443.2_Silent_p.Y59Y|MOV10_ENST00000369645.1_Silent_p.Y59Y	NM_001130079.1|NM_020963.3	NP_001123551.1|NP_066014.1	Q9HCE1	MOV10_HUMAN	Mov10 RISC complex RNA helicase	59					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(3)	38	Lung SC(450;0.246)	all_cancers(81;3.31e-11)|all_epithelial(167;5.69e-10)|all_lung(203;3.73e-05)|Breast(1374;0.000525)|Lung NSC(69;0.000954)|Ovarian(761;0.0367)|Lung SC(238;0.114)		OV - Ovarian serous cystadenocarcinoma(397;3.99e-67)|all cancers(265;1e-62)|Epithelial(280;4.78e-61)|Lung(183;0.0234)|Colorectal(144;0.0686)|READ - Rectum adenocarcinoma(129;0.0929)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|BRCA - Breast invasive adenocarcinoma(282;0.24)		CCATGCTGTATGGAATGAAGA	0.602																																					p.Y59Y		Atlas-SNP	.											.	MOV10	74	.	0			c.T177C						.						76	84	81					1																	113231596		2203	4300	6503	SO:0001819	synonymous_variant	4343	exon3			GCTGTATGGAATG	AL833353	CCDS853.1, CCDS65615.1	1p13.2	2014-07-02	2014-07-02		ENSG00000155363	ENSG00000155363			7200	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 113"	610742	"Mov10 (Moloney leukemia virus 10, mouse) homolog", "Mov10, Moloney leukemia virus 10, homolog (mouse)"			12226669	Standard	NM_001286072		Approved	gb110, MGC2948, fSAP113	uc001eck.3	Q9HCE1	OTTHUMG00000011906	ENST00000413052.2:c.177T>C	chr1.hg19:g.113231596T>C		105.0	0.0		104.0	32.0	NM_020963	Q5JR03|Q8TEF0|Q9BSY3|Q9BUJ9	Silent	SNP	ENST00000413052.2	hg19	CCDS853.1																																																																																			.	.		0.602	MOV10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032906.1	NM_020963		C	113231596	T	C	113231596	2	2	323	1	0	0	0	0	0	0	0	1	9727	1471	51	2		2	MOV10	1	113231596	Silent	SNP	T	TCGA-MI-A75H-01A-11D-A32G-10	9803307	113231596	136019025	6	45486										
ADAMTSL4	54507	hgsc.bcm.edu	37	chr1	150531864	150531864	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	tctccgagcaactgttctcaCctccccaggccccctgccct	6	21	2	0			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr1:150531864C>G	ENST00000369038.2	+	15	3066	c.2865C>G	c.(2863-2865)caC>caG	p.H955Q	ADAMTSL4_ENST00000271643.4_Missense_Mutation_p.H955Q|ADAMTSL4_ENST00000369039.5_Missense_Mutation_p.H978Q|RP11-54A4.2_ENST00000442435.2_RNA			Q6UY14	ATL4_HUMAN	ADAMTS-like 4	955	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.				apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|positive regulation of apoptotic process (GO:0043065)	interstitial matrix (GO:0005614)	metalloendopeptidase activity (GO:0004222)|protease binding (GO:0002020)			breast(1)|cervix(1)|endometrium(6)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(3)	32	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			ACTGTTCTCACCTCCCCAGGC	0.612											OREG0013787	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.H955Q		Atlas-SNP	.											.	ADAMTSL4	101	.	0			c.C2865G						.						101	78	86					1																	150531864		2203	4300	6503	SO:0001583	missense	54507	exon17			TTCTCACCTCCCC	BC027478	CCDS955.1, CCDS30852.1, CCDS72908.1	1q21.2	2008-02-05	2005-12-01	2005-12-01	ENSG00000143382	ENSG00000143382			19706	protein-coding gene	gene with protein product		610113	"thrombospondin repeat containing 1"	TSRC1		12706885	Standard	NM_019032		Approved	DKFZP434K1772	uc001eux.3	Q6UY14	OTTHUMG00000034863	ENST00000369038.2:c.2865C>G	chr1.hg19:g.150531864C>G	ENSP00000358034:p.His955Gln	75.0	0.0	1733	97.0	18.0	NM_019032	B2RTT0|F8WAD0|Q5T5F7|Q6IPM6|Q8N643|Q9HBS6	Missense_Mutation	SNP	ENST00000369038.2	hg19	CCDS955.1	.	.	.	.	.	.	.	.	.	.	C	17.98	3.520478	0.64747	.	.	ENSG00000143382	ENST00000271643;ENST00000369039;ENST00000369038	T;T;T	0.60424	0.19;0.19;0.19	5.52	4.41	0.53225	.	.	.	.	.	T	0.49098	0.1537	N	0.26130	0.795	0.41225	D	0.986533	D;D;D	0.89917	1.0;0.961;1.0	D;P;D	0.91635	0.999;0.835;0.998	T	0.44574	-0.9319	9	0.29301	T	0.29	.	8.4415	0.32818	0.0:0.8175:0.0:0.1825	.	916;978;955	B7ZMJ3;F8WAD0;Q6UY14	.;.;ATL4_HUMAN	Q	955;978;955	ENSP00000271643:H955Q;ENSP00000358035:H978Q;ENSP00000358034:H955Q	ENSP00000271643:H955Q	H	+	3	2	ADAMTSL4	148798488	0.009000	0.17119	1.000000	0.80357	0.858000	0.48976	0.111000	0.15458	2.584000	0.87258	0.462000	0.41574	CAC	.	.		0.612	ADAMTSL4-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084395.4	NM_019032		G	150531864	C	G	150531864	3	3	323	1	0	0	0	0	1	0	0	0	277	506	18	4	2998	4	ADAMTSL4	1	150531864	Missense_Mutation	SNP	C	TCGA-MI-A75H-01A-11D-A32G-10	37300268	150531864	98718757	7	45487										
SCNM1	79005	hgsc.bcm.edu	37	chr1	151139457	151139457	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	accggtactggacaccctggCcatgctgactgcccaccgtg	11	16	0	1	rs587766695		TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr1:151139457C>T	ENST00000368905.4	+	3	281	c.170C>T	c.(169-171)gCc>gTc	p.A57V	SCNM1_ENST00000461862.1_3'UTR|LYSMD1_ENST00000368908.5_5'Flank|LYSMD1_ENST00000440902.2_5'Flank	NM_001204856.1|NM_024041.3	NP_001191785.1|NP_076946.1	Q9BWG6	SCNM1_HUMAN	sodium channel modifier 1	57					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	17	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			GACACCCTGGCCATGCTGACT	0.572													C|||	1	0.000199681	0	0	5008	,	,		18765	0		0	False		,,,				2504	0.001				p.A57V		Atlas-SNP	.											.	SCNM1	22	.	0			c.C170T						.						85	71	76					1																	151139457		2203	4300	6503	SO:0001583	missense	79005	exon3			CCCTGGCCATGCT	BC000264	CCDS987.1, CCDS55636.1	1q21.3	2012-03-13			ENSG00000163156	ENSG00000163156			23136	protein-coding gene	gene with protein product		608095				12920299	Standard	NM_024041		Approved	MGC3180	uc001ewz.3	Q9BWG6	OTTHUMG00000012258	ENST00000368905.4:c.170C>T	chr1.hg19:g.151139457C>T	ENSP00000357901:p.Ala57Val	67.0	0.0		80.0	20.0	NM_024041	B4DWR1|Q5JR74	Missense_Mutation	SNP	ENST00000368905.4	hg19	CCDS987.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.154406	0.78114	.	.	ENSG00000163156	ENST00000368905;ENST00000368902	.	.	.	5.81	5.81	0.92471	.	0.106317	0.64402	D	0.000009	T	0.15349	0.0370	L	0.29908	0.895	0.25115	N	0.990681	P;P	0.42296	0.775;0.617	B;B	0.39660	0.306;0.242	T	0.07028	-1.0794	9	0.46703	T	0.11	-2.7374	12.5078	0.55991	0.1667:0.8333:0.0:0.0	.	57;57	B4DWR1;Q9BWG6	.;SCNM1_HUMAN	V	57;22	.	ENSP00000357898:A22V	A	+	2	0	SCNM1	149406081	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.576000	0.60915	2.748000	0.94277	0.462000	0.41574	GCC	.	.		0.572	SCNM1-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034064.2	NM_024041		T	151139457	C	T	151139457	3	4	323	1	0	0	0	0	1	0	0	0	13941	739	26	3	180	3	SCNM1	1	151139457	Missense_Mutation	SNP	C	TCGA-MI-A75H-01A-11D-A32G-10	607593	151139457	98111164	8	45488										
LCE5A	254910	hgsc.bcm.edu	37	chr1	152484038	152484038	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	gccagcagagccagcagcagTgccagcctcctcccaaatgt	10	16	0	1			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr1:152484038T>C	ENST00000334269.2	+	2	204	c.28T>C	c.(28-30)Tgc>Cgc	p.C10R	CRCT1_ENST00000368790.3_5'Flank	NM_178438.4	NP_848525.1	Q5TCM9	LCE5A_HUMAN	late cornified envelope 5A	10	Cys-rich.				keratinization (GO:0031424)					lung(3)|ovary(1)|prostate(3)	7	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCAGCAGCAGTGCCAGCCTCC	0.517																																					p.C10R		Atlas-SNP	.											.	LCE5A	15	.	0			c.T28C						.						83	79	80					1																	152484038		2203	4300	6503	SO:0001583	missense	254910	exon2			CAGCAGTGCCAGC	BI670518	CCDS1011.1	1q21.3	2008-02-05	2004-10-11	2004-10-15	ENSG00000186207	ENSG00000186207		"Late cornified envelopes"	16614	protein-coding gene	gene with protein product		612619	"small proline rich-like (epidermal differentiation complex) 5A"	SPRL5A		11698679	Standard	NM_178438		Approved	LEP18	uc001ezy.3	Q5TCM9	OTTHUMG00000014401	ENST00000334269.2:c.28T>C	chr1.hg19:g.152484038T>C	ENSP00000333952:p.Cys10Arg	90.0	0.0		106.0	35.0	NM_178438		Missense_Mutation	SNP	ENST00000334269.2	hg19	CCDS1011.1	.	.	.	.	.	.	.	.	.	.	T	11.78	1.740932	0.30865	.	.	ENSG00000186207	ENST00000334269	T	0.05649	3.41	5.28	5.28	0.74379	.	.	.	.	.	T	0.17959	0.0431	M	0.87180	2.865	0.45621	D	0.99855	D	0.69078	0.997	D	0.66497	0.944	T	0.00950	-1.1503	9	0.87932	D	0	-16.4346	11.5291	0.50597	0.0:0.0:0.0:1.0	.	10	Q5TCM9	LCE5A_HUMAN	R	10	ENSP00000333952:C10R	ENSP00000333952:C10R	C	+	1	0	LCE5A	150750662	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.129000	0.42055	2.215000	0.71742	0.491000	0.48974	TGC	.	.		0.517	LCE5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040059.1	NM_178438		C	152484038	T	C	152484038	3	2	323	1	0	0	0	0	1	0	0	0	8684	1696	59	2	30	2	LCE5A	1	152484038	Missense_Mutation	SNP	T	TCGA-MI-A75H-01A-11D-A32G-10	1344581	152484038	96766583	9	45489										
APCS	325	hgsc.bcm.edu	37	chr1	159558103	159558103	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	gagttggagagtatagtctaTacattggaagacacaaagtt	11	4	1	2			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr1:159558103T>C	ENST00000255040.2	+	2	374	c.277T>C	c.(277-279)Tac>Cac	p.Y93H		NM_001639.3	NP_001630.1	P02743	SAMP_HUMAN	amyloid P component, serum	93	Pentaxin.				acute-phase response (GO:0006953)|chaperone-mediated protein complex assembly (GO:0051131)|innate immune response (GO:0045087)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of exo-alpha-sialidase activity (GO:1903016)|negative regulation of glycoprotein metabolic process (GO:1903019)|negative regulation of monocyte differentiation (GO:0045656)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral process (GO:0048525)|negative regulation of wound healing (GO:0061045)|protein folding (GO:0006457)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|complement component C1q binding (GO:0001849)|unfolded protein binding (GO:0051082)|virion binding (GO:0046790)			breast(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(2)	20	all_hematologic(112;0.0429)					GTATAGTCTATACATTGGAAG	0.433																																					p.Y93H		Atlas-SNP	.											.	APCS	48	.	0			c.T277C						.						93	93	93					1																	159558103		2203	4300	6503	SO:0001583	missense	325	exon2			AGTCTATACATTG		CCDS1186.1	1q21-q23	2012-10-02			ENSG00000132703	ENSG00000132703			584	protein-coding gene	gene with protein product	"pentaxin-related", "9.5S alpha-1-glycoprotein"	104770				2987268	Standard	NM_001639		Approved	SAP, PTX2, MGC88159	uc001ftv.3	P02743	OTTHUMG00000022741	ENST00000255040.2:c.277T>C	chr1.hg19:g.159558103T>C	ENSP00000255040:p.Tyr93His	52.0	0.0		73.0	18.0	NM_001639		Missense_Mutation	SNP	ENST00000255040.2	hg19	CCDS1186.1	.	.	.	.	.	.	.	.	.	.	T	5.452	0.268503	0.10349	.	.	ENSG00000132703	ENST00000255040	T	0.07216	3.21	4.25	-0.876	0.10624	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.475016	0.24048	N	0.042031	T	0.01627	0.0052	L	0.38733	1.17	0.09310	N	0.999993	B	0.14012	0.009	B	0.24848	0.056	T	0.46162	-0.9211	10	0.25106	T	0.35	-3.283	4.0745	0.09897	0.1461:0.2556:0.0:0.5983	.	93	P02743	SAMP_HUMAN	H	93	ENSP00000255040:Y93H	ENSP00000255040:Y93H	Y	+	1	0	APCS	157824727	0.000000	0.05858	0.003000	0.11579	0.012000	0.07955	-0.050000	0.11904	-0.270000	0.09285	-0.301000	0.09380	TAC	.	.		0.433	APCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059024.2	NM_001639		C	159558103	T	C	159558103	3	2	323	1	0	0	0	0	1	0	0	0	767	1406	49	2	283	2	APCS	1	159558103	Missense_Mutation	SNP	T	TCGA-MI-A75H-01A-11D-A32G-10	7074065	159558103	89692518	10	45490										
DNM3	26052	hgsc.bcm.edu	37	chr1	172017769	172017769	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	caggacagggttgtttactcCagacatggcatttgaagcga	12	8	0	2			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr1:172017769C>A	ENST00000355305.5	+	10	1371	c.1214C>A	c.(1213-1215)cCa>cAa	p.P405Q	DNM3_ENST00000367733.2_Missense_Mutation_p.P405Q|DNM3_ENST00000367731.1_Missense_Mutation_p.P405Q|DNM3_ENST00000358155.4_Missense_Mutation_p.P405Q|DNM3_ENST00000520906.1_Missense_Mutation_p.P405Q			Q9UQ16	DYN3_HUMAN	dynamin 3	405					endocytosis (GO:0006897)|filopodium assembly (GO:0046847)|GTP catabolic process (GO:0006184)|synapse assembly (GO:0007416)	dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(16)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						TTGTTTACTCCAGACATGGCA	0.343																																					p.P405Q		Atlas-SNP	.											.	DNM3	85	.	0			c.C1214A						.						97	92	94					1																	172017769		1850	4088	5938	SO:0001583	missense	26052	exon10			TTACTCCAGACAT	AL136712	CCDS44276.1, CCDS60356.1	1q24.1	2013-01-10			ENSG00000197959	ENSG00000197959		"Pleckstrin homology (PH) domain containing"	29125	protein-coding gene	gene with protein product	"Dyna III"	611445				10048485	Standard	NM_015569		Approved	KIAA0820	uc001gie.4	Q9UQ16	OTTHUMG00000034913	ENST00000355305.5:c.1214C>A	chr1.hg19:g.172017769C>A	ENSP00000347457:p.Pro405Gln	190.0	0.0		229.0	100.0	NM_001136127	A9Z1Y1|O14982|O95555|Q1MTM8|Q5W129|Q6P2G1|Q9H0P3|Q9H548|Q9NQ68|Q9NQN6	Missense_Mutation	SNP	ENST00000355305.5	hg19		.	.	.	.	.	.	.	.	.	.	c	26.2	4.712336	0.89112	.	.	ENSG00000197959	ENST00000359070;ENST00000358155;ENST00000367733;ENST00000355305;ENST00000367731;ENST00000520906;ENST00000523513	T;T;T;T;T;T	0.74947	-0.89;-0.89;-0.89;-0.89;-0.89;-0.89	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	D	0.90246	0.6950	H	0.96111	3.77	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	D	0.92811	0.6264	10	0.87932	D	0	.	18.6647	0.91485	0.0:1.0:0.0:0.0	.	405;405;405;405	E5RHK8;Q9UQ16-2;Q9UQ16-3;Q6P2G1	.;.;.;.	Q	405;405;405;405;405;405;295	ENSP00000350876:P405Q;ENSP00000356707:P405Q;ENSP00000347457:P405Q;ENSP00000356705:P405Q;ENSP00000429701:P405Q;ENSP00000429416:P295Q	ENSP00000347457:P405Q	P	+	2	0	DNM3	170284392	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.773000	0.85462	2.640000	0.89533	0.558000	0.71614	CCA	.	.		0.343	DNM3-003	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000084531.1	NM_015569		A	172017769	C	A	172017769	3	1	323	1	0	0	0	0	1	0	0	0	4675	594	21	3	1252	3	DNM3	1	172017769	Missense_Mutation	SNP	C	TCGA-MI-A75H-01A-11D-A32G-10	12459666	172017769	77232852	11	45491										
PRSS38	339501	hgsc.bcm.edu	37	chr1	228004984	228004984	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	ggccggcaaccacacccagtGgtatgaggtgaacagggtga	15	10	0	3			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr1:228004984G>T	ENST00000366757.3	+	3	410	c.386G>T	c.(385-387)tGg>tTg	p.W129L		NM_183062.2	NP_898885.1	A1L453	PRS38_HUMAN	protease, serine, 38	129	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23						CACACCCAGTGGTATGAGGTG	0.537																																					p.W129L		Atlas-SNP	.											.	PRSS38	55	.	0			c.G386T						.						165	132	143					1																	228004984		2203	4300	6503	SO:0001583	missense	339501	exon3			CCCAGTGGTATGA		CCDS1563.1	1q42.13	2010-05-07			ENSG00000185888	ENSG00000185888		"Serine peptidases / Serine peptidases"	29625	protein-coding gene	gene with protein product	"marapsin 2"					12838346	Standard	NM_183062		Approved	MPN2	uc001hrh.3	A1L453	OTTHUMG00000037701	ENST00000366757.3:c.386G>T	chr1.hg19:g.228004984G>T	ENSP00000355719:p.Trp129Leu	71.0	0.0		84.0	40.0	NM_183062	Q7RTY6	Missense_Mutation	SNP	ENST00000366757.3	hg19	CCDS1563.1	.	.	.	.	.	.	.	.	.	.	G	15.33	2.801307	0.50315	.	.	ENSG00000185888	ENST00000366757	D	0.87729	-2.29	4.34	3.43	0.39272	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.182364	0.27331	N	0.019856	T	0.69450	0.3112	N	0.00190	-1.885	0.37097	D	0.899738	D	0.63046	0.992	P	0.61397	0.888	T	0.70543	-0.4843	10	0.12430	T	0.62	.	8.443	0.32826	0.1046:0.0:0.8954:0.0	.	129	A1L453	PRS38_HUMAN	L	129	ENSP00000355719:W129L	ENSP00000355719:W129L	W	+	2	0	PRSS38	226071607	0.996000	0.38824	0.998000	0.56505	0.804000	0.45430	1.004000	0.29822	1.429000	0.47314	0.655000	0.94253	TGG	.	.		0.537	PRSS38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091981.1	NM_183062		T	228004984	G	T	228004984	3	4	323	1	0	0	0	0	1	0	0	0	12639	1357	47	3	396	3	PRSS38	1	228004984	Missense_Mutation	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10	55987215	228004984	21245637	12	45492										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228481978	228481978	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	ggaaggggcatgagaccctcAgagatggggacagacacagc	16	9	1	3			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr1:228481978A>G	ENST00000422127.1	+	42	11301	c.11257A>G	c.(11257-11259)Aga>Gga	p.R3753G	OBSCN_ENST00000366707.4_Missense_Mutation_p.R872G|OBSCN_ENST00000284548.11_Missense_Mutation_p.R3753G|OBSCN_ENST00000359599.6_Missense_Mutation_p.R2600G|OBSCN_ENST00000570156.2_Missense_Mutation_p.R4182G|RP5-1139B12.4_ENST00000602778.1_RNA|OBSCN_ENST00000366709.4_Missense_Mutation_p.R872G	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3753	Ig-like 38.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				TGAGACCCTCAGAGATGGGGA	0.632																																					p.R4182G		Atlas-SNP	.											.	OBSCN	2142	.	0			c.A12544G						.						148	154	152					1																	228481978		2143	4235	6378	SO:0001583	missense	84033	exon47			ACCCTCAGAGATG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.11257A>G	chr1.hg19:g.228481978A>G	ENSP00000409493:p.Arg3753Gly	145.0	0.0		127.0	36.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	A	12.80	2.045657	0.36085	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709;ENST00000359599	T;T;T;T;T	0.68331	-0.32;-0.32;-0.32;-0.32;-0.32	4.98	3.83	0.44106	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.623093	0.14761	N	0.299976	T	0.63058	0.2479	M	0.62088	1.915	0.09310	N	1	B;B	0.14805	0.011;0.003	B;B	0.23018	0.043;0.04	T	0.51553	-0.8691	10	0.22706	T	0.39	.	12.974	0.58527	0.8566:0.1434:0.0:0.0	.	3753;3753	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	G	3753;3753;872;872;2600	ENSP00000284548:R3753G;ENSP00000409493:R3753G;ENSP00000355668:R872G;ENSP00000355670:R872G;ENSP00000352613:R2600G	ENSP00000284548:R3753G	R	+	1	2	OBSCN	226548601	0.000000	0.05858	0.809000	0.32408	0.186000	0.23388	0.749000	0.26320	2.110000	0.64415	0.416000	0.27883	AGA	.	.		0.632	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		G	228481978	A	G	228481978	3	3	323	1	0	0	0	0	1	0	0	0	10821	180	7	2	11419	2	OBSCN	1	228481978	Missense_Mutation	SNP	A	TCGA-MI-A75H-01A-11D-A32G-10	476994	228481978	20768643	13	45493										
MBD5	55777	hgsc.bcm.edu	37	chr2	149227546	149227546	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	cagtctcaaatggatagttcTgcagttcctaaacctggacc	8	11	2	0			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr2:149227546T>C	ENST00000407073.1	+	9	3031	c.2034T>C	c.(2032-2034)tcT>tcC	p.S678S	MBD5_ENST00000404807.1_Silent_p.S678S	NM_018328.4	NP_060798.2	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	678					glucose homeostasis (GO:0042593)|nervous system development (GO:0007399)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|regulation of multicellular organism growth (GO:0040014)|single-organism behavior (GO:0044708)	chromocenter (GO:0010369)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(16)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	62				BRCA - Breast invasive adenocarcinoma(221;0.0569)		TGGATAGTTCTGCAGTTCCTA	0.438																																					p.S678S		Atlas-SNP	.											.	MBD5	164	.	0			c.T2034C						.						109	107	107					2																	149227546		2203	4300	6503	SO:0001819	synonymous_variant	55777	exon9			TAGTTCTGCAGTT	AB040894	CCDS33302.1	2q23.2	2009-04-17			ENSG00000204406	ENSG00000204406			20444	protein-coding gene	gene with protein product		611472				12529184	Standard	NM_018328		Approved	FLJ11113, KIAA1461	uc002twm.4	Q9P267	OTTHUMG00000150440	ENST00000407073.1:c.2034T>C	chr2.hg19:g.149227546T>C		61.0	0.0		58.0	13.0	NM_018328	A5HMQ4|A7E2B1|Q53SR1|Q9NUV6	Silent	SNP	ENST00000407073.1	hg19	CCDS33302.1	.	.	.	.	.	.	.	.	.	.	T	2.720	-0.266769	0.05754	.	.	ENSG00000204406	ENST00000416015	.	.	.	4.84	3.69	0.42338	.	.	.	.	.	T	0.59142	0.2172	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55231	-0.8173	4	.	.	.	-3.8456	9.2701	0.37666	0.0:0.082:0.0:0.918	.	.	.	.	P	418	.	.	L	+	2	0	MBD5	148944016	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.124000	0.31320	0.994000	0.38892	0.533000	0.62120	CTG	.	.		0.438	MBD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318111.2			C	149227546	T	C	149227546	2	2	323	1	0	0	0	0	0	0	0	1	9356	1567	55	2		2	MBD5	2	149227546	Silent	SNP	T	TCGA-MI-A75H-01A-11D-A32G-10		149227546	93971827	14	45494										
PKP4	8502	hgsc.bcm.edu	37	chr2	159526346	159526346	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	tctgcacgaggtcaccagcaAaaacatggagaacgcaaaag	10	10	2	1			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr2:159526346A>G	ENST00000389759.3	+	17	2955	c.2843A>G	c.(2842-2844)aAa>aGa	p.K948R	AC005042.4_ENST00000342892.4_RNA|PKP4_ENST00000389757.3_Missense_Mutation_p.K948R	NM_003628.3	NP_003619.2	Q99569	PKP4_HUMAN	plakophilin 4	948					cell-cell junction assembly (GO:0007043)|cell-cell signaling (GO:0007267)|positive regulation of cytokinesis (GO:0032467)|positive regulation of gene expression (GO:0010628)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell adhesion (GO:0030155)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|desmosome (GO:0030057)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)				breast(2)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(21)|ovary(6)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	61						GTCACCAGCAAAAACATGGAG	0.592										HNSCC(62;0.18)																											p.K948R		Atlas-SNP	.											.	PKP4	133	.	0			c.A2843G						.						50	50	50					2																	159526346		2203	4300	6503	SO:0001583	missense	8502	exon17			CCAGCAAAAACAT	X81889	CCDS33305.1, CCDS33306.1	2q24.1	2013-02-14			ENSG00000144283	ENSG00000144283		"Armadillo repeat containing"	9026	protein-coding gene	gene with protein product		604276				9342840, 8937994	Standard	NM_003628		Approved	p0071	uc002tzv.3	Q99569	OTTHUMG00000153969	ENST00000389759.3:c.2843A>G	chr2.hg19:g.159526346A>G	ENSP00000374409:p.Lys948Arg	157.0	0.0		139.0	44.0	NM_001005476	Q86W91	Missense_Mutation	SNP	ENST00000389759.3	hg19	CCDS33305.1	.	.	.	.	.	.	.	.	.	.	A	17.48	3.401250	0.62288	.	.	ENSG00000144283	ENST00000389757;ENST00000389759	T;T	0.50813	0.73;0.73	6.06	6.06	0.98353	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.41581	0.1165	L	0.33245	0.995	0.58432	D	0.999999	B;B;B	0.22276	0.011;0.067;0.053	B;B;B	0.23574	0.01;0.047;0.021	T	0.19549	-1.0302	10	0.46703	T	0.11	-15.8661	16.6127	0.84892	1.0:0.0:0.0:0.0	.	903;948;948	Q4W5T8;Q99569-2;Q99569	.;.;PKP4_HUMAN	R	948	ENSP00000374407:K948R;ENSP00000374409:K948R	ENSP00000374407:K948R	K	+	2	0	PKP4	159234592	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	6.187000	0.72039	2.322000	0.78497	0.528000	0.53228	AAA	.	.		0.592	PKP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333250.1			G	159526346	A	G	159526346	3	3	323	1	0	0	0	0	1	0	0	0	11996	14	1	2	2905	2	PKP4	2	159526346	Missense_Mutation	SNP	A	TCGA-MI-A75H-01A-11D-A32G-10	10298800	159526346	83673027	15	45495										
CSRNP3	80034	hgsc.bcm.edu	37	chr2	166533005	166533005	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	tgaaaaagattgacgtggaaGaaaagcacgaactccgagcc	11	8	0	4			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr2:166533005G>A	ENST00000342316.4	+	4	864	c.592G>A	c.(592-594)Gaa>Aaa	p.E198K	CSRNP3_ENST00000409420.1_Missense_Mutation_p.E230K|CSRNP3_ENST00000314499.7_Missense_Mutation_p.E198K	NM_024969.3	NP_079245.2	Q8WYN3	CSRN3_HUMAN	cysteine-serine-rich nuclear protein 3	198					apoptotic process (GO:0006915)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|cervix(1)|endometrium(1)|large_intestine(9)|lung(15)|ovary(3)|skin(2)	33						TGACGTGGAAGAAAAGCACGA	0.527																																					p.E198K		Atlas-SNP	.											.	CSRNP3	73	.	0			c.G592A						.						111	112	112					2																	166533005		2203	4300	6503	SO:0001583	missense	80034	exon6			GTGGAAGAAAAGC	AB063300	CCDS2225.1	2q24.3	2012-04-17	2009-01-07	2009-01-07	ENSG00000178662	ENSG00000178662		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	30729	protein-coding gene	gene with protein product	"TGF beta induced apotosis protein 2", "protein phosphatase 1, regulatory subunit 73"		"family with sequence similarity 130, member A2"	FAM130A2		17726538	Standard	NM_024969		Approved	FLJ32093, TAIP-2, PPP1R73	uc002udg.3	Q8WYN3	OTTHUMG00000132145	ENST00000342316.4:c.592G>A	chr2.hg19:g.166533005G>A	ENSP00000344042:p.Glu198Lys	91.0	0.0		87.0	29.0	NM_001172173	B3KPR4|Q53SG0|Q6ZTX3|Q9HAF9	Missense_Mutation	SNP	ENST00000342316.4	hg19	CCDS2225.1	.	.	.	.	.	.	.	.	.	.	G	29.5	5.012413	0.93346	.	.	ENSG00000178662	ENST00000421875;ENST00000431452;ENST00000314499;ENST00000342316;ENST00000409420	T;T;T;T	0.15952	2.38;2.38;2.38;2.38	5.77	5.77	0.91146	.	0.111898	0.64402	D	0.000014	T	0.48960	0.1529	M	0.84683	2.71	0.80722	D	1	D	0.67145	0.996	D	0.77557	0.99	T	0.46176	-0.9210	10	0.51188	T	0.08	-17.1053	19.3504	0.94381	0.0:0.0:1.0:0.0	.	198	Q8WYN3	CSRN3_HUMAN	K	198;205;198;198;230	ENSP00000412081:E198K;ENSP00000318258:E198K;ENSP00000344042:E198K;ENSP00000387195:E230K	ENSP00000318258:E198K	E	+	1	0	CSRNP3	166241251	1.000000	0.71417	0.998000	0.56505	0.965000	0.64279	9.813000	0.99286	2.885000	0.99019	0.655000	0.94253	GAA	.	.		0.527	CSRNP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255191.2	NM_024969		A	166533005	G	A	166533005	3	1	323	1	0	0	0	0	1	0	0	0	3967	943	33	3	602	3	CSRNP3	2	166533005	Missense_Mutation	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10	7006659	166533005	76666368	16	45496										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168115372	168115372	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	gaatctgaaaagacttattcGaggaatgtactagcaatggc	10	6	1	2	rs371997749		TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr2:168115372G>A	ENST00000409728.1	+	11	2504	c.2415G>A	c.(2413-2415)tcG>tcA	p.S805S	XIRP2_ENST00000409273.1_3'UTR|XIRP2_ENST00000409195.1_3'UTR|XIRP2_ENST00000409756.2_Silent_p.S772S|XIRP2_ENST00000409605.1_Silent_p.S550S|XIRP2_ENST00000420519.1_Silent_p.S805S|XIRP2_ENST00000409043.1_Silent_p.S772S|XIRP2_ENST00000295237.9_3'UTR	NM_001199143.1	NP_001186072.1	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	94					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AGACTTATTCGAGGAATGTAC	0.413																																					p.S805S		Atlas-SNP	.											.	XIRP2	914	.	0			c.G2415A						.	G	,,,,	0,3678		0,0,1839	41	40	40		2316,2415,,1650,	-11.3	0	2		40	1,8185		0,1,4092	no	coding-synonymous,coding-synonymous,utr-3,coding-synonymous,utr-3	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199144.1,NM_001199145.1,NM_152381.5	,,,,	0,1,5931	AA,AG,GG		0.0122,0.0,0.0084	,,,,	772/939,805/972,,550/717,	168115372	1,11863	1839	4093	5932	SO:0001819	synonymous_variant	129446	exon11			TTATTCGAGGAAT	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409728.1:c.2415G>A	chr2.hg19:g.168115372G>A		138.0	0.0		143.0	47.0	NM_001199143	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent	SNP	ENST00000409728.1	hg19	CCDS56143.1																																																																																			.	.		0.413	XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333552.1	NM_152381		A	168115372	G	A	168115372	2	1	323	1	0	0	0	0	0	0	0	1	17445	1045	37	1		1	XIRP2	2	168115372	Silent	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10	1582367	168115372	75084001	17	45497										
LRP2	4036	hgsc.bcm.edu	37	chr2	170072882	170072882	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	agatgtgccatccatgttagCactggcgatcttggcaggaa	12	9	1	1			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr2:170072882C>T	ENST00000263816.3	-	35	5992	c.5707G>A	c.(5707-5709)Gct>Act	p.A1903T		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1903					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	TCCATGTTAGCACTGGCGATC	0.483																																					p.A1903T		Atlas-SNP	.											.	LRP2	751	.	0			c.G5707A						.						142	129	134					2																	170072882		2203	4300	6503	SO:0001583	missense	4036	exon35			TGTTAGCACTGGC		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.5707G>A	chr2.hg19:g.170072882C>T	ENSP00000263816:p.Ala1903Thr	140.0	0.0		144.0	44.0	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	hg19	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	C	36	5.695859	0.96802	.	.	ENSG00000081479	ENST00000263816	D	0.91464	-2.85	5.73	5.73	0.89815	Six-bladed beta-propeller, TolB-like (1);	0.107962	0.64402	D	0.000006	D	0.96716	0.8928	M	0.92604	3.325	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96940	0.9687	10	0.66056	D	0.02	.	19.8961	0.96958	0.0:1.0:0.0:0.0	.	1903	P98164	LRP2_HUMAN	T	1903	ENSP00000263816:A1903T	ENSP00000263816:A1903T	A	-	1	0	LRP2	169781128	1.000000	0.71417	0.996000	0.52242	0.920000	0.55202	6.081000	0.71309	2.699000	0.92147	0.655000	0.94253	GCT	.	.		0.483	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		T	170072882	C	T	170072882	3	4	323	1	0	0	0	0	1	0	0	0	8965	710	25	3	8440	3	LRP2	2	170072882	Missense_Mutation	SNP	C	TCGA-MI-A75H-01A-11D-A32G-10	1957510	170072882	73126491	18	45498										
TTN	7273	hgsc.bcm.edu	37	chr2	179432581	179432581	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	ccattattggttctggggttCctggtgggtcacagggatct	14	8	3	0			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr2:179432581C>T	ENST00000591111.1	-	276	73579	c.73355G>A	c.(73354-73356)gGa>gAa	p.G24452E	TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.G17220E|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.G26093E|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.G17153E|TTN_ENST00000460472.2_Missense_Mutation_p.G17028E|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.G23525E			Q8WZ42	TITIN_HUMAN	titin	24452	Fibronectin type-III 78. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTCTGGGGTTCCTGGTGGGTC	0.403																																					p.G26093E		Atlas-SNP	.											.	TTN	18412	.	0			c.G78278A						.						187	178	181					2																	179432581		1877	4112	5989	SO:0001583	missense	7273	exon326			GGGGTTCCTGGTG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.73355G>A	chr2.hg19:g.179432581C>T	ENSP00000465570:p.Gly24452Glu	120.0	0.0		112.0	40.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	13.86	2.362576	0.41902	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.55930	0.49;0.49;0.49;0.49	5.58	5.58	0.84498	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.74419	0.3714	M	0.74546	2.27	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	T	0.76697	-0.2864	9	0.87932	D	0	.	19.5644	0.95388	0.0:1.0:0.0:0.0	.	17028;17153;17220;24452	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	E	23525;17028;17220;17153;17026	ENSP00000343764:G23525E;ENSP00000434586:G17028E;ENSP00000340554:G17220E;ENSP00000352154:G17153E	ENSP00000340554:G17220E	G	-	2	0	TTN	179140827	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.770000	0.85390	2.615000	0.88500	0.555000	0.69702	GGA	.	.		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179432581	C	T	179432581	3	4	323	1	0	0	0	0	1	0	0	0	16750	855	30	3	29849	3	TTN	2	179432581	Missense_Mutation	SNP	C	TCGA-MI-A75H-01A-11D-A32G-10	9359699	179432581	63766792	19	45499										
TTN	7273	hgsc.bcm.edu	37	chr2	179554080	179554080	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	tttcctttcttcaggaacttTcttctttggtatttctggca	6	9	5	0			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr2:179554080T>G	ENST00000591111.1	-	122	31221	c.30997A>C	c.(30997-30999)Aaa>Caa	p.K10333Q	TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.K10650Q|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.K9406Q			Q8WZ42	TITIN_HUMAN	titin	0	Glu-rich.|Pro-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCAGGAACTTTCTTCTTTGGT	0.368																																					p.K10650Q		Atlas-SNP	.											.	TTN	18412	.	0			c.A31948C						.						127	123	124					2																	179554080		1835	4086	5921	SO:0001583	missense	7273	exon124			GAACTTTCTTCTT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.30997A>C	chr2.hg19:g.179554080T>G	ENSP00000465570:p.Lys10333Gln	106.0	0.0		106.0	35.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	10.68	1.418144	0.25552	.	.	ENSG00000155657	ENST00000342992;ENST00000414766;ENST00000473181	T;T	0.64618	-0.11;-0.11	5.08	3.92	0.45320	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.48059	0.1479	L	0.36672	1.1	0.80722	D	1	B;B	0.20671	0.047;0.032	B;B	0.21917	0.025;0.037	T	0.53683	-0.8404	9	0.87932	D	0	.	4.5138	0.11924	0.0:0.15:0.3344:0.5156	.	10333;10333	Q8WZ42;Q8WZ42-5	TITIN_HUMAN;.	Q	9406;528;133	ENSP00000343764:K9406Q;ENSP00000401501:K528Q	ENSP00000343764:K9406Q	K	-	1	0	TTN	179262325	0.000000	0.05858	1.000000	0.80357	0.769000	0.43574	-0.763000	0.04740	2.048000	0.60808	0.482000	0.46254	AAA	.	.		0.368	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179554080	T	G	179554080	3	3	323	1	0	0	0	0	1	0	0	0	16750	1792	62	5	72537	5	TTN	2	179554080	Missense_Mutation	SNP	T	TCGA-MI-A75H-01A-11D-A32G-10	121499	179554080	63645293	20	45500										
TTN	7273	hgsc.bcm.edu	37	chr2	179614607	179614607	+	Intron	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	acattcaagaatgatggaatCcccttctctacacctggcat	6	12	2	2			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr2:179614607C>A	ENST00000591111.1	-	45	10585				TTN_ENST00000360870.5_Missense_Mutation_p.D4174Y|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000589042.1_Intron|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000578746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Intron			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATGATGGAATCCCCTTCTCTA	0.373																																					p.D4174Y		Atlas-SNP	.											.	TTN	18412	.	0			c.G12520T						.						67	72	70					2																	179614607		2202	4298	6500	SO:0001627	intron_variant	7273	exon46			TGGAATCCCCTTC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10360+3243G>T	chr2.hg19:g.179614607C>A		154.0	0.0		151.0	59.0	NM_133379	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	16.50	3.139506	0.56936	.	.	ENSG00000155657	ENST00000360870	T	0.47177	0.85	5.77	4.89	0.63831	.	.	.	.	.	T	0.53481	0.1799	L	0.53617	1.68	0.53688	D	0.999979	P	0.52692	0.955	P	0.50537	0.643	T	0.57808	-0.7747	9	0.66056	D	0.02	.	13.9172	0.63905	0.0:0.926:0.0:0.074	.	4174	Q8WZ42-6	.	Y	4174	ENSP00000354117:D4174Y	ENSP00000354117:D4174Y	D	-	1	0	TTN	179322852	0.907000	0.30839	0.643000	0.29450	0.967000	0.64934	2.205000	0.42770	1.417000	0.47077	0.655000	0.94253	GAT	.	.		0.373	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179614607	C	A	179614607	1	1	323	0	1	0	0	0	0	0	0	0	16750	855	30	3		3	TTN	2	179614607	Intron	SNP	C	TCGA-MI-A75H-01A-11D-A32G-10	60527	179614607	63584766	21	45501										
GLB1L	79411	hgsc.bcm.edu	37	chr2	220102300	220102300	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	aaaattggaaatgttttggaGtagaatgtggggccagaagg	15	2	0	2	rs183755555	byFrequency	TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr2:220102300G>T	ENST00000295759.7	-	16	1936	c.1623C>A	c.(1621-1623)taC>taA	p.Y541*	GLB1L_ENST00000356283.3_Nonsense_Mutation_p.Y451*|GLB1L_ENST00000497855.1_5'UTR|GLB1L_ENST00000409640.1_Nonsense_Mutation_p.Y451*|GLB1L_ENST00000392089.2_Nonsense_Mutation_p.Y541*			Q6UWU2	GLB1L_HUMAN	galactosidase, beta 1-like	541					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	beta-galactosidase activity (GO:0004565)			breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22		all_lung(227;1.19e-05)|Lung NSC(271;2.76e-05)|Medulloblastoma(418;0.0208)|Esophageal squamous(248;0.0559)		Epithelial(149;1.3e-11)|all cancers(144;2.07e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		ATGTTTTGGAGTAGAATGTGG	0.463																																					p.Y541X		Atlas-SNP	.											.	GLB1L	52	.	0			c.C1623A						.						81	83	82					2																	220102300		2203	4300	6503	SO:0001587	stop_gained	79411	exon16			TTTGGAGTAGAAT		CCDS2437.1, CCDS74657.1	2q36.1	2008-02-05			ENSG00000163521	ENSG00000163521			28129	protein-coding gene	gene with protein product						12975309	Standard	XM_005246850		Approved	MGC10771	uc002vkm.3	Q6UWU2	OTTHUMG00000133133	ENST00000295759.7:c.1623C>A	chr2.hg19:g.220102300G>T	ENSP00000295759:p.Tyr541*	113.0	0.0		119.0	35.0	NM_024506	Q96DR0	Nonsense_Mutation	SNP	ENST00000295759.7	hg19	CCDS2437.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.462781	0.84425	.	.	ENSG00000163521	ENST00000295759;ENST00000409640;ENST00000392089;ENST00000356283	.	.	.	5.09	3.96	0.45880	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.2932	7.9902	0.30235	0.2227:0.0:0.7773:0.0	.	.	.	.	X	541;451;541;451	.	ENSP00000295759:Y541X	Y	-	3	2	GLB1L	219810544	1.000000	0.71417	1.000000	0.80357	0.823000	0.46562	2.674000	0.46867	1.023000	0.39654	0.655000	0.94253	TAC	.	G|0.999;A|0.001		0.463	GLB1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256822.2	NM_024506		T	220102300	G	T	220102300	4	4	323	1	0	0	0	0	0	1	0	0	6436	1024	36	3	349	3	GLB1L	2	220102300	Nonsense_Mutation	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10	40487693	220102300	23097073	22	45502										
GMPPA	29926	hgsc.bcm.edu	37	chr2	220370193	220370193	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	tccccagttcagccctctacGcctcccgcctctacctgagc	6	21	3	1			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr2:220370193G>A	ENST00000358215.3	+	9	1138	c.769G>A	c.(769-771)Gcc>Acc	p.A257T	AC053503.11_ENST00000429882.1_RNA|GMPPA_ENST00000373908.1_Missense_Mutation_p.A257T|GMPPA_ENST00000373917.3_Missense_Mutation_p.A257T|GMPPA_ENST00000313597.5_Missense_Mutation_p.A257T|GMPPA_ENST00000341142.3_Missense_Mutation_p.A257T	NM_205847.2	NP_995319.1	Q96IJ6	GMPPA_HUMAN	GDP-mannose pyrophosphorylase A	257					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotidyltransferase activity (GO:0016779)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(6)|prostate(1)|skin(1)	20		Renal(207;0.0183)		Epithelial(149;3.82e-10)|all cancers(144;6.25e-08)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00807)|READ - Rectum adenocarcinoma(5;0.148)		AGCCCTCTACGCCTCCCGCCT	0.672																																					p.A257T		Atlas-SNP	.											.	GMPPA	50	.	0			c.G769A						.						28	32	31					2																	220370193		2197	4292	6489	SO:0001583	missense	29926	exon9			CTCTACGCCTCCC	AF135422	CCDS2441.1	2q36.1	2008-02-05			ENSG00000144591	ENSG00000144591			22923	protein-coding gene	gene with protein product		615495					Standard	NM_205847		Approved		uc002vlr.3	Q96IJ6	OTTHUMG00000058922	ENST00000358215.3:c.769G>A	chr2.hg19:g.220370193G>A	ENSP00000350949:p.Ala257Thr	82.0	0.0		72.0	17.0	NM_205847	A6NJ74|A8K3Q6|B3KMT4|Q53GI0|Q9NWC3|Q9Y5P5	Missense_Mutation	SNP	ENST00000358215.3	hg19	CCDS2441.1	.	.	.	.	.	.	.	.	.	.	g	24.9	4.581802	0.86748	.	.	ENSG00000144591	ENST00000313597;ENST00000373917;ENST00000358215;ENST00000373908;ENST00000435316;ENST00000341142	D;D;D;D;T;D	0.95788	-3.81;-3.81;-3.81;-3.81;1.42;-3.81	4.9	3.96	0.45880	.	0.178411	0.47852	D	0.000205	D	0.97711	0.9249	M	0.87381	2.88	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.989	D	0.98335	1.0535	10	0.87932	D	0	-14.9034	14.2816	0.66216	0.0:0.1498:0.8502:0.0	.	257;257	Q96IJ6-2;Q96IJ6	.;GMPPA_HUMAN	T	257;257;257;257;222;257	ENSP00000315925:A257T;ENSP00000363027:A257T;ENSP00000350949:A257T;ENSP00000363016:A257T;ENSP00000411060:A222T;ENSP00000340760:A257T	ENSP00000315925:A257T	A	+	1	0	GMPPA	220078437	1.000000	0.71417	0.998000	0.56505	0.916000	0.54674	6.037000	0.70956	2.253000	0.74438	0.651000	0.88453	GCC	.	.		0.672	GMPPA-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130230.1	NM_013335		A	220370193	G	A	220370193	3	1	323	1	0	0	0	0	1	0	0	0	6502	1087	38	1	799	1	GMPPA	2	220370193	Missense_Mutation	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10	267893	220370193	22829180	23	45503										
OBSL1	23363	hgsc.bcm.edu	37	chr2	220422736	220422736	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	tccagaccacgggggcgccaGcccgggacagttcacagctc	13	16	1	1	rs373804245		TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr2:220422736G>A	ENST00000404537.1	-	11	3655	c.3599C>T	c.(3598-3600)gCt>gTt	p.A1200V	OBSL1_ENST00000373876.1_Missense_Mutation_p.A1200V|OBSL1_ENST00000603926.1_Missense_Mutation_p.A1200V|OBSL1_ENST00000265318.4_Missense_Mutation_p.A1108V|RP11-256I23.2_ENST00000597192.1_RNA|OBSL1_ENST00000265317.5_Missense_Mutation_p.A191V	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	1200	Ig-like 10.				cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)						Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		GGGGGCGCCAGCCCGGGACAG	0.677																																					p.A1200V		Atlas-SNP	.											.	OBSL1	120	.	0			c.C3599T						.						16	18	17					2																	220422736		1939	4129	6068	SO:0001583	missense	23363	exon11			GCGCCAGCCCGGG	BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.3599C>T	chr2.hg19:g.220422736G>A	ENSP00000385636:p.Ala1200Val	47.0	0.0		46.0	12.0	NM_001173431	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Missense_Mutation	SNP	ENST00000404537.1	hg19	CCDS46520.1	.	.	.	.	.	.	.	.	.	.	G	16.73	3.203130	0.58234	.	.	ENSG00000124006	ENST00000265318;ENST00000404537;ENST00000373876;ENST00000265317	T;T;T;T	0.04862	3.54;3.54;3.54;3.54	4.16	4.16	0.48862	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.17280	0.0415	L	0.56280	1.765	0.31969	N	0.607378	D;D;D;D	0.69078	0.987;0.987;0.993;0.997	D;P;D;D	0.73380	0.964;0.867;0.963;0.98	T	0.02821	-1.1106	9	0.27785	T	0.31	.	11.1464	0.48432	0.0:0.0:0.8158:0.1842	.	99;1201;1200;191	B7Z5P5;A4KVA4;O75147;E7ER99	.;.;OBSL1_HUMAN;.	V	1108;1200;1200;191	ENSP00000265318:A1108V;ENSP00000385636:A1200V;ENSP00000362983:A1200V;ENSP00000265317:A191V	ENSP00000265317:A191V	A	-	2	0	OBSL1	220130980	0.003000	0.15002	0.859000	0.33776	0.464000	0.32679	1.363000	0.34159	2.061000	0.61500	0.313000	0.20887	GCT	.	.		0.677	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1			A	220422736	G	A	220422736	3	1	323	1	0	0	0	0	1	0	0	0	10822	971	34	3	2158	3	OBSL1	2	220422736	Missense_Mutation	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10	52543	220422736	22776637	24	45504										
ALPPL2	251	hgsc.bcm.edu	37	chr2	233274441	233274441	+	Frame_Shift_Del	DEL	C	C	-													0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	gtcatggccttcgccgcctgCctggagccctacaccgcctg							TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr2:233274441delC	ENST00000295453.3	+	11	1510	c.1458delC	c.(1456-1458)tgcfs	p.C486fs		NM_031313.2	NP_112603.2	P10696	PPBN_HUMAN	alkaline phosphatase, placental-like 2	486					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|metal ion binding (GO:0046872)			breast(2)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(1)	13		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)	Amifostine(DB01143)	TCGCCGCCTGCCTGGAGCCCT	0.746																																					p.C486fs		Atlas-INDEL	.											.	ALPPL2	36	.	0			c.1457delG						.						12	16	15					2																	233274441		2186	4256	6442	SO:0001589	frameshift_variant	251	exon11			.	J04948	CCDS2491.1	2q37	2008-05-20			ENSG00000163286	ENSG00000163286			441	protein-coding gene	gene with protein product		171810					Standard	NM_031313		Approved		uc002vss.4	P10696	OTTHUMG00000133257	ENST00000295453.3:c.1458delC	chr2.hg19:g.233274441delC	ENSP00000295453:p.Cys486fs	28.0	0.0		41.0	15.0	NM_031313	A8KAF2|Q16727|Q53S81|Q96CM1	Frame_Shift_Del	DEL	ENST00000295453.3	hg19	CCDS2491.1																																																																																			.	.		0.746	ALPPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257034.2	NM_031313		-	233274441	C	-	233274441	7	5	323	1	0	1	0	1	0	0	0	0	549	747	26	0	1500	0	ALPPL2	2	233274441	Frame_Shift_Del	DEL	C	TCGA-MI-A75H-01A-11D-A32G-10	12851705	233274441	9924932	25	45505										
FANCD2	2177	hgsc.bcm.edu	37	chr3	10102063	10102063	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	gattattggtgctgtgaccaTggctggcatcatggcggcag	15	8	1	1			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr3:10102063T>C	ENST00000419585.1	+	19	1903	c.1742T>C	c.(1741-1743)aTg>aCg	p.M581T	FANCD2_ENST00000287647.3_Missense_Mutation_p.M581T|FANCD2_ENST00000383806.1_Missense_Mutation_p.M581T|FANCD2_ENST00000383807.1_Missense_Mutation_p.M581T			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2	581					DNA repair (GO:0006281)|gamete generation (GO:0007276)|response to gamma radiation (GO:0010332)|synapsis (GO:0007129)	condensed chromosome (GO:0000793)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA polymerase binding (GO:0070182)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	51				OV - Ovarian serous cystadenocarcinoma(96;0.148)		GCTGTGACCATGGCTGGCATC	0.438			"D, Mis, N, F"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.M581T		Atlas-SNP	.	yes	Rec		Fanconi anaemia D2	3	3p26	2177	"Fanconi anemia, complementation group D2"		L	.	FANCD2	253	.	0			c.T1742C						.						121	99	107					3																	10102063		2203	4300	6503	SO:0001583	missense	2177	exon19	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TGACCATGGCTGG	AF340183	CCDS2595.1, CCDS33696.1	3p25.3	2014-09-17		2001-10-05	ENSG00000144554	ENSG00000144554		"Fanconi anemia, complementation groups"	3585	protein-coding gene	gene with protein product		613984		FACD, FANCD		7581463, 11239453, 18475298	Standard	XM_005264946		Approved	FAD, FA-D2	uc003buw.3	Q9BXW9	OTTHUMG00000128670	ENST00000419585.1:c.1742T>C	chr3.hg19:g.10102063T>C	ENSP00000398754:p.Met581Thr	61.0	0.0		64.0	26.0	NM_001018115	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	Missense_Mutation	SNP	ENST00000419585.1	hg19	CCDS33696.1	.	.	.	.	.	.	.	.	.	.	T	19.22	3.784934	0.70222	.	.	ENSG00000144554	ENST00000287647;ENST00000383807;ENST00000383806;ENST00000419585	T;T;T;T	0.56444	0.46;0.46;0.46;0.46	5.43	5.43	0.79202	.	0.079031	0.85682	D	0.000000	T	0.67088	0.2856	M	0.68952	2.095	0.46749	D	0.999181	D;D	0.67145	0.996;0.991	D;P	0.64042	0.921;0.857	T	0.66548	-0.5896	10	0.36615	T	0.2	.	13.5743	0.61864	0.0:0.0:0.0:1.0	.	581;581	Q9BXW9-2;Q9BXW9	.;FACD2_HUMAN	T	581	ENSP00000287647:M581T;ENSP00000373318:M581T;ENSP00000373317:M581T;ENSP00000398754:M581T	ENSP00000287647:M581T	M	+	2	0	FANCD2	10077063	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	7.965000	0.87945	2.089000	0.63090	0.372000	0.22366	ATG	.	.		0.438	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339873.1			C	10102063	T	C	10102063	3	2	323	1	0	0	0	0	1	0	0	0	5673	1464	51	2	1812	2	FANCD2	3	10102063	Missense_Mutation	SNP	T	TCGA-MI-A75H-01A-11D-A32G-10		10102063	187920367	26	45506										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266098	41266098	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	gcagcaacagtcttacctggActctggaatccattctggtg	10	11	3	0	rs121913396|rs121913416		TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr3:41266098A>T	ENST00000349496.5	+	3	375	c.95A>T	c.(94-96)gAc>gTc	p.D32V	CTNNB1_ENST00000453024.1_Missense_Mutation_p.D25V|CTNNB1_ENST00000396183.3_Missense_Mutation_p.D32V|CTNNB1_ENST00000396185.3_Missense_Mutation_p.D32V|CTNNB1_ENST00000405570.1_Missense_Mutation_p.D32V	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	32			D -> A (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|D -> G (in PTR and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629}.|D -> Y (in PTR, hepatoblastoma and hepatocellular carcinoma; dbSNP:rs28931588). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:11703283, ECO:0000269|PubMed:9927029}.|Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.D32G(65)|p.A5_A80del(53)|p.D32V(33)|p.D32A(16)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.WQQQSYLD25?(5)|p.W25_D32del(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.S29_H36del(1)|p.D32del(1)|p.M14_S45del(1)|p.Q28_D32>H(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.D32fs*9(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TCTTACCTGGACTCTGGAATC	0.483	D32V(HEC265_ENDOMETRIUM)|D32V(HEC6_ENDOMETRIUM)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.D32V	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,+1,128	CTNNB1	4904	.	260	Deletion - In frame(120)|Substitution - Missense(114)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(154)|large_intestine(24)|pancreas(19)|central_nervous_system(16)|stomach(14)|endometrium(7)|skin(7)|ovary(4)|prostate(3)|pituitary(3)|small_intestine(2)|NS(2)|adrenal_gland(1)|soft_tissue(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)	c.A95T						.						92	77	82					3																	41266098		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	ACCTGGACTCTGG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.95A>T	chr3.hg19:g.41266098A>T	ENSP00000344456:p.Asp32Val	183.0	1.0		179.0	61.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.184569	0.78677	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.50001	0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.70037	0.3178	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.74325	-0.3702	10	0.87932	D	0	0.3843	16.0676	0.80897	1.0:0.0:0.0:0.0	.	32	P35222	CTNB1_HUMAN	V	25;32;32;32;32;25;32;32;32	ENSP00000400508:D25V;ENSP00000385604:D32V;ENSP00000412219:D32V;ENSP00000379486:D32V;ENSP00000344456:D32V;ENSP00000411226:D25V;ENSP00000379488:D32V;ENSP00000409302:D32V;ENSP00000401599:D32V	ENSP00000344456:D32V	D	+	2	0	CTNNB1	41241102	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.201000	0.70794	0.533000	0.62120	GAC	.	.		0.483	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41266098	A	T	41266098	3	4	323	1	0	0	0	0	1	0	0	0	4018	275	10	4	101	4	CTNNB1	3	41266098	Missense_Mutation	SNP	A	TCGA-MI-A75H-01A-11D-A32G-10	31164035	41266098	156756332	27	45507										
ZNF502	91392	hgsc.bcm.edu	37	chr3	44762400	44762400	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	acaagcctgctctggagcagGatgtctgtaaaattgactca	10	9	3	1			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr3:44762400G>A	ENST00000296091.4	+	4	347	c.91G>A	c.(91-93)Gat>Aat	p.D31N	ZNF502_ENST00000436624.2_Missense_Mutation_p.D31N|ZNF502_ENST00000449836.1_Missense_Mutation_p.D31N	NM_001134440.1|NM_001282880.1|NM_033210.4	NP_001127912.1|NP_001269809.1|NP_149987.2	Q8TBZ5	ZN502_HUMAN	zinc finger protein 502	31					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(4)|large_intestine(8)|lung(4)|prostate(1)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.00855)|KIRC - Kidney renal clear cell carcinoma(197;0.0471)|Kidney(197;0.0589)		TCTGGAGCAGGATGTCTGTAA	0.423																																					p.D31N		Atlas-SNP	.											.	ZNF502	58	.	0			c.G91A						.						64	68	67					3																	44762400		2203	4300	6503	SO:0001583	missense	91392	exon4			GAGCAGGATGTCT	AK022577	CCDS2719.1	3p21.32	2013-01-08			ENSG00000196653	ENSG00000196653		"Zinc fingers, C2H2-type"	23718	protein-coding gene	gene with protein product							Standard	NM_033210		Approved	FLJ14855, FLJ12515	uc003cnt.3	Q8TBZ5	OTTHUMG00000133086	ENST00000296091.4:c.91G>A	chr3.hg19:g.44762400G>A	ENSP00000296091:p.Asp31Asn	107.0	0.0		100.0	36.0	NM_001134440		Missense_Mutation	SNP	ENST00000296091.4	hg19	CCDS2719.1	.	.	.	.	.	.	.	.	.	.	G	8.359	0.832743	0.16820	.	.	ENSG00000196653	ENST00000449836;ENST00000296091;ENST00000436624;ENST00000427783;ENST00000411443	T;T;T;T	0.55588	3.17;3.17;3.17;0.51	4.41	1.6	0.23607	.	.	.	.	.	T	0.26774	0.0655	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.20874	-1.0262	9	0.17832	T	0.49	-0.8579	5.797	0.18392	0.1845:0.1613:0.6542:0.0	.	31	Q8TBZ5	ZN502_HUMAN	N	31	ENSP00000397390:D31N;ENSP00000296091:D31N;ENSP00000406469:D31N;ENSP00000401717:D31N	ENSP00000296091:D31N	D	+	1	0	ZNF502	44737404	0.000000	0.05858	0.027000	0.17364	0.015000	0.08874	0.066000	0.14489	0.230000	0.21059	-0.176000	0.13171	GAT	.	.		0.423	ZNF502-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256744.4	NM_033210		A	44762400	G	A	44762400	3	1	323	1	0	0	0	0	1	0	0	0	17965	1174	41	3	97	3	ZNF502	3	44762400	Missense_Mutation	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10	3496302	44762400	153260030	28	45508										
CLEC3B	7123	hgsc.bcm.edu	37	chr3	45077186	45077186	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	acctgcgccagagcgtgggcAacgaggccgagatctggctg	16	12	1	2			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr3:45077186A>T	ENST00000296130.4	+	3	559	c.379A>T	c.(379-381)Aac>Tac	p.N127Y	CLEC3B_ENST00000490386.1_3'UTR|RNU5B-3P_ENST00000516601.1_RNA|CLEC3B_ENST00000428034.1_Missense_Mutation_p.N85Y	NM_003278.2	NP_003269.2	P05452	TETN_HUMAN	C-type lectin domain family 3, member B	127	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				bone mineralization (GO:0030282)|cellular response to organic substance (GO:0071310)|cellular response to transforming growth factor beta stimulus (GO:0071560)|ossification (GO:0001503)|positive regulation of plasminogen activation (GO:0010756)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|granular component (GO:0001652)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|heparin binding (GO:0008201)|kringle domain binding (GO:0036143)			endometrium(1)|lung(3)	4				BRCA - Breast invasive adenocarcinoma(193;0.00863)|KIRC - Kidney renal clear cell carcinoma(197;0.0475)|Kidney(197;0.0595)	Tenecteplase(DB00031)	GAGCGTGGGCAACGAGGCCGA	0.677																																					p.N127Y	GBM(139;1487 3263 30871)	Atlas-SNP	.											.	CLEC3B	15	.	0			c.A379T						.						45	44	44					3																	45077186		2203	4300	6503	SO:0001583	missense	7123	exon3			GTGGGCAACGAGG		CCDS2726.1	3p22-p21.3	2010-04-27	2005-02-09	2005-02-09	ENSG00000163815	ENSG00000163815		"C-type lectin domain containing"	11891	protein-coding gene	gene with protein product		187520	"tetranectin (plasminogen binding protein)"	TNA			Standard	NM_003278		Approved	TN	uc003cok.4	P05452	OTTHUMG00000133087	ENST00000296130.4:c.379A>T	chr3.hg19:g.45077186A>T	ENSP00000296130:p.Asn127Tyr	52.0	0.0		46.0	19.0	NM_003278	Q6FGX6	Missense_Mutation	SNP	ENST00000296130.4	hg19	CCDS2726.1	.	.	.	.	.	.	.	.	.	.	A	15.26	2.780926	0.49891	.	.	ENSG00000163815	ENST00000296130;ENST00000428034	T;T	0.19394	2.15;2.15	4.53	-3.85	0.04243	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	1.573510	0.03288	N	0.187173	T	0.18341	0.0440	L	0.38531	1.155	0.09310	N	0.999998	P	0.42039	0.769	B	0.43754	0.43	T	0.25398	-1.0133	10	0.48119	T	0.1	-0.2591	4.4848	0.11785	0.6316:0.0915:0.1079:0.169	.	127	P05452	TETN_HUMAN	Y	127;85	ENSP00000296130:N127Y;ENSP00000396013:N85Y	ENSP00000296130:N127Y	N	+	1	0	CLEC3B	45052190	0.000000	0.05858	0.091000	0.20842	0.835000	0.47333	-1.159000	0.03150	-0.568000	0.06038	-0.366000	0.07423	AAC	.	.		0.677	CLEC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256745.1	NM_003278		T	45077186	A	T	45077186	3	4	323	1	0	0	0	0	1	0	0	0	3513	130	5	4	389	4	CLEC3B	3	45077186	Missense_Mutation	SNP	A	TCGA-MI-A75H-01A-11D-A32G-10	314786	45077186	152945244	29	45509										
SLMAP	7871	hgsc.bcm.edu	37	chr3	57898307	57898307	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	aagaaggtgagagctgagctTgagcggtggcggaaagcagc	18	6	0	4			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr3:57898307T>A	ENST00000428312.1	+	18	1942	c.1848T>A	c.(1846-1848)ctT>ctA	p.L616L	SLMAP_ENST00000472546.1_3'UTR|SLMAP_ENST00000442599.2_Silent_p.L84L|SLMAP_ENST00000295952.3_Silent_p.L599L|SLMAP_ENST00000494088.1_Silent_p.L109L|SLMAP_ENST00000295951.3_Silent_p.L599L|SLMAP_ENST00000449503.2_Silent_p.L578L|SLMAP_ENST00000495364.1_Silent_p.L150L|SLMAP_ENST00000416870.1_Silent_p.L109L			Q14BN4	SLMAP_HUMAN	sarcolemma associated protein	616					muscle contraction (GO:0006936)	cytoskeleton (GO:0005856)|integral component of plasma membrane (GO:0005887)|smooth endoplasmic reticulum (GO:0005790)				endometrium(5)|kidney(1)|large_intestine(3)|lung(7)|urinary_tract(2)	18				BRCA - Breast invasive adenocarcinoma(55;0.000271)|KIRC - Kidney renal clear cell carcinoma(284;0.0602)|Kidney(284;0.0754)|OV - Ovarian serous cystadenocarcinoma(275;0.182)		GAGCTGAGCTTGAGCGGTGGC	0.463																																					p.L599L		Atlas-SNP	.											.	SLMAP	46	.	0			c.T1797A						.						86	88	88					3																	57898307		2203	4300	6503	SO:0001819	synonymous_variant	7871	exon17			TGAGCTTGAGCGG	AF100750	CCDS33774.1	3p21.2-p14.3	2008-07-18			ENSG00000163681	ENSG00000163681			16643	protein-coding gene	gene with protein product	"Sarcolemmal-associated protein"	602701				9405447, 11042152	Standard	NM_007159		Approved	SLAP, KIAA1601	uc003djd.1	Q14BN4	OTTHUMG00000133764	ENST00000428312.1:c.1848T>A	chr3.hg19:g.57898307T>A		53.0	0.0		40.0	18.0	NM_007159	Q14C95|Q6AI54|Q6UXC9|Q6ZVQ8|Q8NCW9|Q9H297|Q9HCH1|Q9Y681	Silent	SNP	ENST00000428312.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	10.40|10.40	1.339658|1.339658	0.24339|0.24339	.|.	.|.	ENSG00000163681|ENSG00000163681	ENST00000417128|ENST00000416658;ENST00000438794	.|.	.|.	.|.	5.18|5.18	0.879|0.879	0.19155|0.19155	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|.	.|.	.|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.02654|.	T|.	1|.	-4.2163|-4.2163	10.3039|10.3039	0.43670|0.43670	0.0:0.0748:0.5269:0.3983|0.0:0.0748:0.5269:0.3983	.|.	.|.	.|.	.|.	X|R	200|224;154	.|.	ENSP00000412829:L200X|.	L|X	+|+	2|1	0|0	SLMAP|SLMAP	57873347|57873347	0.913000|0.913000	0.31002|0.31002	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	-0.397000|-0.397000	0.07269|0.07269	0.352000|0.352000	0.24053|0.24053	0.459000|0.459000	0.35465|0.35465	TTG|TGA	.	.		0.463	SLMAP-013	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351584.1	NM_007159		A	57898307	T	A	57898307	2	1	323	1	0	0	0	0	0	0	0	1	14764	1799	63	4		4	SLMAP	3	57898307	Silent	SNP	T	TCGA-MI-A75H-01A-11D-A32G-10	12821121	57898307	140124123	30	45510										
MECOM	2122	hgsc.bcm.edu	37	chr3	168838896	168838896	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	ttgtgttgtttgaggcccgaCgaagtggcaaacgttttgcc	13	8	0	1	rs185054275	byFrequency	TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr3:168838896C>A	ENST00000464456.1	-	6	1716	c.516G>T	c.(514-516)tcG>tcT	p.S172S	MECOM_ENST00000460814.1_Silent_p.S172S|MECOM_ENST00000392736.3_Silent_p.S172S|MECOM_ENST00000433243.2_Silent_p.S173S|MECOM_ENST00000264674.3_Silent_p.S237S|MECOM_ENST00000472280.1_Silent_p.S173S|MECOM_ENST00000468789.1_Silent_p.S172S|MECOM_ENST00000494292.1_Silent_p.S360S	NM_001164000.1	NP_001157472.1	Q13465	MDS1_HUMAN	MDS1 and EVI1 complex locus	0					regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	85						TGAGGCCCGACGAAGTGGCAA	0.552																																					p.S360S		Atlas-SNP	.											.	MECOM	216	.	0			c.G1080T						.						183	164	171					3																	168838896		2203	4300	6503	SO:0001819	synonymous_variant	2122	exon7			GCCCGACGAAGTG	S82592, AF164154	CCDS3205.1, CCDS54669.1, CCDS54670.1	3q26.2	2013-01-08	2009-08-07	2009-08-07	ENSG00000085276	ENSG00000085276		"Zinc fingers, C2H2-type"	3498	protein-coding gene	gene with protein product		165215	"myelodysplasia syndrome 1", "ecotropic viral integration site 1"	MDS1, EVI1		2115646, 8171026, 8643684	Standard	NM_001105077		Approved	MDS1-EVI1, PRDM3	uc011bpj.1	Q03112	OTTHUMG00000158596	ENST00000464456.1:c.516G>T	chr3.hg19:g.168838896C>A		81.0	0.0		68.0	30.0	NM_004991	Q13466|Q6FH90	Silent	SNP	ENST00000464456.1	hg19	CCDS54669.1																																																																																			.	C|0.999;T|0.001		0.552	MECOM-020	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351519.1	NM_005241, NM_004991		A	168838896	C	A	168838896	2	1	323	1	0	0	0	0	0	0	0	1	9431	523	19	1		1	MECOM	3	168838896	Silent	SNP	C	TCGA-MI-A75H-01A-11D-A32G-10	110940589	168838896	29183534	31	45511										
LRRC31	79782	hgsc.bcm.edu	37	chr3	169565966	169565966	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	ctcagcctcagcacttgaagAgacatggaaagctttagtgt	10	9	2	2			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr3:169565966A>T	ENST00000316428.5	-	8	1326	c.1269T>A	c.(1267-1269)tcT>tcA	p.S423S	LRRC31_ENST00000523069.1_Silent_p.S423S|LRRC31_ENST00000264676.5_Silent_p.S367S	NM_001277127.1|NM_024727.2	NP_001264056.1|NP_079003.2	Q6UY01	LRC31_HUMAN	leucine rich repeat containing 31	423										cervix(3)|endometrium(3)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	31	all_cancers(22;2.76e-22)|all_epithelial(15;4.73e-27)|all_lung(20;9.24e-17)|Lung NSC(18;3.85e-16)|Ovarian(172;0.000223)|Breast(254;0.197)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00943)			GCACTTGAAGAGACATGGAAA	0.498																																					p.S423S		Atlas-SNP	.											.	LRRC31	66	.	0			c.G1269A						.						78	81	80					3																	169565966		2050	4197	6247	SO:0001819	synonymous_variant	79782	exon8			TTGAAGAGACATG	AK026912	CCDS43167.1, CCDS63832.1, CCDS63833.1	3q26.2	2005-01-24			ENSG00000114248	ENSG00000114248			26261	protein-coding gene	gene with protein product						12975309	Standard	NM_001277127		Approved	FLJ23259	uc003fgc.2	Q6UY01	OTTHUMG00000164421	ENST00000316428.5:c.1269T>A	chr3.hg19:g.169565966A>T		65.0	0.0		48.0	24.0	NM_024727	B7ZL44|E5RJA9|Q17RA3|Q8N848|Q9H5N5|V9HW14	Silent	SNP	ENST00000316428.5	hg19	CCDS43167.1																																																																																			.	.		0.498	LRRC31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378699.1	NM_024727		T	169565966	A	T	169565966	2	4	323	1	0	0	0	0	0	0	0	1	8995	291	11	4		4	LRRC31	3	169565966	Silent	SNP	A	TCGA-MI-A75H-01A-11D-A32G-10	727070	169565966	28456464	32	45512										
ATP8A1	10396	hgsc.bcm.edu	37	chr4	42583637	42583637	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	tttcatagagaaaaatttcaCctgcatcagcttggtgtcat	7	8	4	1			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr4:42583637C>A	ENST00000381668.5	-	10	1066		c.e10+1		ATP8A1_ENST00000264449.10_Splice_Site	NM_006095.2	NP_006086.1	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1						cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	51					Phosphatidylserine(DB00144)	AAAAATTTCACCTGCATCAGC	0.438																																					.		Atlas-SNP	.											.	ATP8A1	206	.	0			c.834+1G>T						.						121	110	114					4																	42583637		2203	4300	6503	SO:0001630	splice_region_variant	10396	exon11			ATTTCACCTGCAT	AF067820	CCDS3466.1, CCDS47049.1	4p13	2010-04-20	2007-09-19		ENSG00000124406	ENSG00000124406		"ATPases / P-type"	13531	protein-coding gene	gene with protein product		609542	"ATPase, aminophospholipid transporter (APLT), Class I, type 8A, member 1"			10198212, 9548971	Standard	NM_006095		Approved	ATPIA	uc003gwr.2	Q9Y2Q0	OTTHUMG00000099403	ENST00000381668.5:c.834+1G>T	chr4.hg19:g.42583637C>A		70.0	0.0		65.0	30.0	NM_001105529	Q32M35|Q32M36|Q4W5J7|Q4W5P2	Splice_Site	SNP	ENST00000381668.5	hg19	CCDS3466.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.581908	0.86748	.	.	ENSG00000124406	ENST00000381668;ENST00000264449	.	.	.	5.92	5.92	0.95590	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.3151	0.98650	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ATP8A1	42278394	1.000000	0.71417	0.995000	0.50966	0.909000	0.53808	7.818000	0.86416	2.809000	0.96659	0.467000	0.42956	.	.	.		0.438	ATP8A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216861.2	NM_006095	Intron	A	42583637	C	A	42583637	5	1	323	1	0	0	0	0	0	0	1	0	1192	521	18	3	2771	3	ATP8A1	4	42583637	Splice_Site	SNP	C	TCGA-MI-A75H-01A-11D-A32G-10		42583637	148570639	33	45513										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79391155	79391155	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	atgacagcagcacctcagccGttccgagtagacatcctccc	8	16	1	2	rs546503799	byFrequency	TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr4:79391155G>A	ENST00000264895.6	+	51	7721	c.7281G>A	c.(7279-7281)ccG>ccA	p.P2427P		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	2427					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						CACCTCAGCCGTTCCGAGTAG	0.522													g|||	2	0.000399361	0.0015	0	5008	,	,		21392	0		0	False		,,,				2504	0				p.P2427P		Atlas-SNP	.											.	FRAS1	779	.	0			c.G7281A						.						76	77	77					4																	79391155		2021	4188	6209	SO:0001819	synonymous_variant	80144	exon51			TCAGCCGTTCCGA	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.7281G>A	chr4.hg19:g.79391155G>A		82.0	0.0		67.0	22.0	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000264895.6	hg19	CCDS54771.1	.	.	.	.	.	.	.	.	.	.	g	0.425	-0.906168	0.02453	.	.	ENSG00000138759	ENST00000512123	.	.	.	5.52	-1.97	0.07503	.	.	.	.	.	T	0.42381	0.1200	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.27971	-1.0058	4	.	.	.	.	3.6592	0.08232	0.284:0.0847:0.4717:0.1596	.	.	.	.	I	656	.	.	V	+	1	0	FRAS1	79610179	1.000000	0.71417	0.655000	0.29622	0.000000	0.00434	0.780000	0.26760	-0.421000	0.07416	-2.299000	0.00261	GTT	.	.		0.522	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	79391155	G	A	79391155	2	1	323	1	0	0	0	0	0	0	0	1	6050	1132	40	1		1	FRAS1	4	79391155	Silent	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10	36807518	79391155	111763121	34	45514										
C4orf37	285555	hgsc.bcm.edu	37	chr4	98902423	98902423	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	tgagagcagttcgaggttcaTtatatgtgccaggagccggg	15	7	1	1			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr4:98902423T>A	ENST00000295268.3	-	6	748	c.659A>T	c.(658-660)aAt>aTt	p.N220I		NM_174952.2	NP_777612.1	Q8N412	STPG2_HUMAN	sperm-tail PG-rich repeat containing 2	220																	TCGAGGTTCATTATATGTGCC	0.378																																					p.N220I		Atlas-SNP	.											.	.	.	.	0			c.A659T						.						122	121	121					4																	98902423		2203	4300	6503	SO:0001583	missense	285555	exon6			GGTTCATTATATG	BC036870	CCDS3645.1	4q22.3-q23	2013-10-11	2012-07-30	2012-07-30	ENSG00000163116	ENSG00000163116			28712	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 37"	C4orf37		23031811	Standard	NM_174952		Approved	MGC46496	uc003htt.2	Q8N412	OTTHUMG00000131009	ENST00000295268.3:c.659A>T	chr4.hg19:g.98902423T>A	ENSP00000295268:p.Asn220Ile	125.0	0.0		83.0	28.0	NM_174952		Missense_Mutation	SNP	ENST00000295268.3	hg19	CCDS3645.1	.	.	.	.	.	.	.	.	.	.	T	14.81	2.646291	0.47258	.	.	ENSG00000163116	ENST00000295268	T	0.13657	2.57	5.58	5.58	0.84498	.	0.339492	0.29707	N	0.011413	T	0.34048	0.0884	M	0.61703	1.905	0.35258	D	0.779367	D	0.62365	0.991	D	0.66847	0.947	T	0.46091	-0.9216	10	0.87932	D	0	-26.004	14.7372	0.69424	0.0:0.0:0.0:1.0	.	220	Q8N412	CD037_HUMAN	I	220	ENSP00000295268:N220I	ENSP00000295268:N220I	N	-	2	0	C4orf37	99121446	1.000000	0.71417	0.567000	0.28434	0.140000	0.21249	3.460000	0.53028	2.118000	0.64928	0.460000	0.39030	AAT	.	.		0.378	STPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253642.1	NM_174952		A	98902423	T	A	98902423	3	1	323	1	0	0	0	0	1	0	0	0	2269	1493	52	4	744	4	C4orf37	4	98902423	Missense_Mutation	SNP	T	TCGA-MI-A75H-01A-11D-A32G-10	19511268	98902423	92251853	35	45515										
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123128393	123128393	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	ctaatcaacacaattggatcGactgttctactaaacaacag	5	10	2	0			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr4:123128393G>A	ENST00000264501.4	+	16	2000	c.1627G>A	c.(1627-1629)Gac>Aac	p.D543N	KIAA1109_ENST00000388738.3_Missense_Mutation_p.D543N|KIAA1109_ENST00000495260.1_3'UTR|KIAA1109_ENST00000455637.1_Missense_Mutation_p.D543N			Q2LD37	K1109_HUMAN	KIAA1109	543					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						CAATTGGATCGACTGTTCTAC	0.299																																					p.D543N		Atlas-SNP	.											.	KIAA1109	424	.	0			c.G1627A						.						95	87	89					4																	123128393		1815	4075	5890	SO:0001583	missense	84162	exon14			TGGATCGACTGTT	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.1627G>A	chr4.hg19:g.123128393G>A	ENSP00000264501:p.Asp543Asn	207.0	0.0		165.0	40.0	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	34|34	5.316664|5.316664	0.95682|0.95682	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637|ENST00000424425	T;T;T|.	0.28666|.	2.2;2.2;1.6|.	5.67|5.67	5.67|5.67	0.87782|0.87782	.|.	0.996761|.	0.08123|.	N|.	0.994407|.	T|T	0.73377|0.73377	0.3579|0.3579	L|L	0.60455|0.60455	1.87|1.87	0.80722|0.80722	D|D	1|1	D|.	0.62365|.	0.991|.	P|.	0.49953|.	0.627|.	T|T	0.69840|0.69840	-0.5036|-0.5036	10|5	0.40728|.	T|.	0.16|.	.|.	19.7657|19.7657	0.96340|0.96340	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	543|.	Q2LD37|.	K1109_HUMAN|.	N|Q	543|375	ENSP00000264501:D543N;ENSP00000373390:D543N;ENSP00000389925:D543N|.	ENSP00000264501:D543N|.	D|R	+|+	1|2	0|0	KIAA1109|KIAA1109	123347843|123347843	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.979000|0.979000	0.70002|0.70002	9.394000|9.394000	0.97261|0.97261	2.649000|2.649000	0.89929|0.89929	0.655000|0.655000	0.94253|0.94253	GAC|CGA	.	.		0.299	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		A	123128393	G	A	123128393	3	1	323	1	0	0	0	0	1	0	0	0	8217	1058	37	1	1681	1	KIAA1109	4	123128393	Missense_Mutation	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10	24225970	123128393	68025883	36	45516										
BBS12	166379	hgsc.bcm.edu	37	chr4	123664403	123664404	+	Frame_Shift_Ins	INS	-	-	CAGG													0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	cagaggctgcaggagcagtaINScaggtggcctacattacaca							TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr4:123664403_123664404insCAGG	ENST00000314218.3	+	2	1549_1550	c.1356_1357insCAGG	c.(1357-1359)cagfs	p.-453fs	BBS12_ENST00000542236.1_Frame_Shift_Ins_p.-453fs	NM_152618.2	NP_689831.2	Q6ZW61	BBS12_HUMAN	Bardet-Biedl syndrome 12						cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|eating behavior (GO:0042755)|intraciliary transport (GO:0042073)|negative regulation of fat cell differentiation (GO:0045599)|photoreceptor cell maintenance (GO:0045494)	cilium (GO:0005929)	ATP binding (GO:0005524)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|prostate(4)	21						CAGGAGCAGTACAGGTGGCCTA	0.485									Bardet-Biedl syndrome																												p.V452fs		Atlas-Indel,Pindel	.											.	BBS12	63	.	0			c.1356_1357insCAGG						.																																			SO:0001589	frameshift_variant	166379	exon3	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	.	AK123553	CCDS3728.1	4q27	2014-06-17	2006-12-13	2006-12-13	ENSG00000181004	ENSG00000181004		"Heat Shock Proteins / Chaperonins"	26648	protein-coding gene	gene with protein product		610683	"chromosome 4 open reading frame 24"	C4orf24		17160889	Standard	NM_001178007		Approved	FLJ35630, FLJ41559	uc003ieu.3	Q6ZW61	OTTHUMG00000133070	ENST00000314218.3:c.1357_1360dupCAGG	chr4.hg19:g.123664404_123664407dupCAGG	ENSP00000319062:p.Gln453fs	119.0	0.0		85.0	24.0	NM_001178007	D3DNX5|Q7Z342|Q7Z482|Q8NAB8	Frame_Shift_Ins	INS	ENST00000314218.3	hg19	CCDS3728.1																																																																																			.	.		0.485	BBS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256710.1	NM_152618		CAGG	123664404	-	CAGG	123664403	7	5	323	1	0	1	1	0	0	0	0	0	1337	378	14	0	1358	0	BBS12	4	123664403	Frame_Shift_Ins	INS	-	TCGA-MI-A75H-01A-11D-A32G-10	536010	123664403	67489873	37	45517										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155157921	155157921	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	tgacaagctcatggctagcaCttgcttctctgtccagactg	9	12	2	2			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr4:155157921C>T	ENST00000357232.4	-	25	6517	c.6518G>A	c.(6517-6519)aGt>aAt	p.S2173N		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2173	Cadherin 19. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		ATGGCTAGCACTTGCTTCTCT	0.413																																					p.S2173N		Atlas-SNP	.											.	DCHS2	594	.	0			c.G6518A						.						70	69	69					4																	155157921		2203	4300	6503	SO:0001583	missense	54798	exon25			CTAGCACTTGCTT	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.6518G>A	chr4.hg19:g.155157921C>T	ENSP00000349768:p.Ser2173Asn	68.0	0.0		69.0	29.0	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	hg19	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	C	6.862	0.528390	0.13127	.	.	ENSG00000197410	ENST00000357232	T	0.51071	0.72	6.04	-0.489	0.12052	Cadherin (4);Cadherin-like (1);	1.482230	0.03819	N	0.267165	T	0.31199	0.0789	N	0.20986	0.625	0.09310	N	1	P	0.39920	0.695	B	0.40134	0.32	T	0.12041	-1.0563	10	0.11485	T	0.65	.	4.5108	0.11910	0.199:0.3225:0.3946:0.0839	.	2173	Q6V1P9	PCD23_HUMAN	N	2173	ENSP00000349768:S2173N	ENSP00000349768:S2173N	S	-	2	0	DCHS2	155377371	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.058000	0.11750	-0.066000	0.12998	-0.344000	0.07964	AGT	.	.		0.413	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		T	155157921	C	T	155157921	3	4	323	1	0	0	0	0	1	0	0	0	4290	565	20	3	2236	3	DCHS2	4	155157921	Missense_Mutation	SNP	C	TCGA-MI-A75H-01A-11D-A32G-10	31493518	155157921	35996355	38	45518										
FGA	2243	hgsc.bcm.edu	37	chr4	155507134	155507134	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	agaaccatcttcggaggtcaCcacttctttggtaacttctt	7	11	4	1			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr4:155507134C>T	ENST00000302053.3	-	5	1525	c.1447G>A	c.(1447-1449)Gtg>Atg	p.V483M	FGA_ENST00000403106.3_Missense_Mutation_p.V483M	NM_000508.3	NP_000499.1	P02671	FIBA_HUMAN	fibrinogen alpha chain	483					blood coagulation (GO:0007596)|blood coagulation, common pathway (GO:0072377)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|extracellular matrix organization (GO:0030198)|negative regulation of blood coagulation, common pathway (GO:2000261)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	structural molecule activity (GO:0005198)			NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	73	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)	TCGGAGGTCACCACTTCTTTG	0.498																																					p.V483M	NSCLC(143;340 1922 20892 22370 48145)	Atlas-SNP	.											.	FGA	179	.	0			c.G1447A						.						164	161	162					4																	155507134		2203	4300	6503	SO:0001583	missense	2243	exon5			AGGTCACCACTTC		CCDS3787.1, CCDS47152.1	4q28	2014-09-17			ENSG00000171560	ENSG00000171560		"Fibrinogen C domain containing", "Endogenous ligands"	3661	protein-coding gene	gene with protein product		134820	"fibrinogen, A alpha polypeptide"				Standard	NM_000508		Approved		uc003iod.1	P02671	OTTHUMG00000150330	ENST00000302053.3:c.1447G>A	chr4.hg19:g.155507134C>T	ENSP00000306361:p.Val483Met	140.0	0.0		100.0	33.0	NM_000508	A8K3E4|D3DP14|D3DP15|Q4QQH7|Q9BX62|Q9UCH2	Missense_Mutation	SNP	ENST00000302053.3	hg19	CCDS3787.1	.	.	.	.	.	.	.	.	.	.	C	12.59	1.983464	0.35036	.	.	ENSG00000171560	ENST00000302053;ENST00000403106	T;T	0.61510	0.1;0.1	5.99	-0.172	0.13327	Fibrinogen alpha C domain (1);	40.022400	0.00166	N	0.000000	T	0.67924	0.2945	L	0.52759	1.655	0.09310	N	1	P;D	0.76494	0.89;0.999	B;D	0.75020	0.337;0.985	T	0.49835	-0.8897	10	0.40728	T	0.16	.	4.6302	0.12498	0.2186:0.3407:0.0:0.4407	.	483;483	P02671-2;P02671	.;FIBA_HUMAN	M	483	ENSP00000306361:V483M;ENSP00000385981:V483M	ENSP00000306361:V483M	V	-	1	0	FGA	155726584	0.000000	0.05858	0.156000	0.22583	0.375000	0.29983	-0.559000	0.05971	0.127000	0.18452	0.655000	0.94253	GTG	.	.		0.498	FGA-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317593.1	NM_000508		T	155507134	C	T	155507134	3	4	323	1	0	0	0	0	1	0	0	0	5838	507	18	3	1205	3	FGA	4	155507134	Missense_Mutation	SNP	C	TCGA-MI-A75H-01A-11D-A32G-10	349213	155507134	35647142	39	45519										
NUP155	9631	hgsc.bcm.edu	37	chr5	37351407	37351407	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	taggaagagaatataaaggaTctggaagcaactgcattcca	10	6	1	1			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr5:37351407T>C	ENST00000231498.3	-	6	811	c.608A>G	c.(607-609)gAt>gGt	p.D203G	NUP155_ENST00000513532.1_Missense_Mutation_p.D203G|NUP155_ENST00000381843.2_Missense_Mutation_p.D144G	NM_153485.1	NP_705618.1	O75694	NU155_HUMAN	nucleoporin 155kDa	203					atrial cardiac muscle cell action potential (GO:0086014)|carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear envelope organization (GO:0006998)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			endometrium(1)|kidney(16)|large_intestine(5)|lung(29)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	62	all_lung(31;0.000137)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			ATATAAAGGATCTGGAAGCAA	0.338																																					p.D203G		Atlas-SNP	.											.	NUP155	116	.	0			c.A608G						.						77	77	77					5																	37351407		2203	4298	6501	SO:0001583	missense	9631	exon6			AAAGGATCTGGAA	AJ007558	CCDS3921.1, CCDS43310.1, CCDS64142.1	5p13.1	2008-02-05	2002-08-29		ENSG00000113569	ENSG00000113569			8063	protein-coding gene	gene with protein product		606694	"nucleoporin 155kD"			10191094	Standard	NM_153485		Approved	KIAA0791, N155	uc003jku.1	O75694	OTTHUMG00000090803	ENST00000231498.3:c.608A>G	chr5.hg19:g.37351407T>C	ENSP00000231498:p.Asp203Gly	170.0	0.0		123.0	39.0	NM_153485	Q9UBE9|Q9UFL5	Missense_Mutation	SNP	ENST00000231498.3	hg19	CCDS3921.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.597253	0.87055	.	.	ENSG00000113569	ENST00000231498;ENST00000381843;ENST00000434056;ENST00000513532	T;T;T	0.35421	1.31;1.31;1.31	5.83	5.83	0.93111	Nucleoporin, Nup133/Nup155-like, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.59797	0.2220	M	0.78049	2.395	0.80722	D	1	D;D	0.76494	0.996;0.999	D;D	0.71870	0.93;0.975	T	0.57625	-0.7779	10	0.23891	T	0.37	-3.9675	16.2041	0.82108	0.0:0.0:0.0:1.0	.	203;203	E9PF10;O75694	.;NU155_HUMAN	G	203;144;165;203	ENSP00000231498:D203G;ENSP00000371265:D144G;ENSP00000422019:D203G	ENSP00000231498:D203G	D	-	2	0	NUP155	37387164	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.541000	0.82084	2.219000	0.72066	0.533000	0.62120	GAT	.	.		0.338	NUP155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207593.2	NM_153485, NM_004298		C	37351407	T	C	37351407	3	2	323	1	0	0	0	0	1	0	0	0	10765	1435	50	2	3687	2	NUP155	5	37351407	Missense_Mutation	SNP	T	TCGA-MI-A75H-01A-11D-A32G-10		37351407	143563853	40	45520										
ERAP2	64167	hgsc.bcm.edu	37	chr5	96232185	96232185	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	cgactcaaatacaggaaatgTttgatgaagtttcctataac	7	7	1	2			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr5:96232185T>C	ENST00000437043.3	+	8	2059	c.1348T>C	c.(1348-1350)Ttt>Ctt	p.F450L	ERAP2_ENST00000379904.4_Missense_Mutation_p.F405L|CTD-2260A17.2_ENST00000501338.1_Intron|ERAP2_ENST00000515095.1_3'UTR	NM_001130140.1|NM_022350.3	NP_001123612.1|NP_071745.1	Q6P179	ERAP2_HUMAN	endoplasmic reticulum aminopeptidase 2	450					antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|regulation of blood pressure (GO:0008217)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24		all_cancers(142;0.000311)|all_epithelial(76;1.54e-06)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0596)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0703)		ACAGGAAATGTTTGATGAAGT	0.368																																					p.F450L		Atlas-SNP	.											.	ERAP2	77	.	0			c.T1348C						.						69	72	71					5																	96232185		2203	4300	6503	SO:0001583	missense	64167	exon8			GAAATGTTTGATG	AF191545	CCDS4086.1	5q15	2007-11-21			ENSG00000164308	ENSG00000164308			29499	protein-coding gene	gene with protein product	"leukocyte-derived arginine aminopeptidase"	609497				12799365, 15908954	Standard	NM_022350		Approved	L-RAP, LRAP	uc003kmt.3	Q6P179	OTTHUMG00000128718	ENST00000437043.3:c.1348T>C	chr5.hg19:g.96232185T>C	ENSP00000400376:p.Phe450Leu	233.0	0.0		200.0	63.0	NM_001130140	Q7Z5K1|Q8TD32|Q8WVJ4|Q9HBX2	Missense_Mutation	SNP	ENST00000437043.3	hg19	CCDS4086.1	.	.	.	.	.	.	.	.	.	.	T	28.3	4.909124	0.92107	.	.	ENSG00000164308	ENST00000437043;ENST00000510373;ENST00000513084;ENST00000379904	T;T;T;T	0.09538	2.97;2.97;2.97;2.97	5.36	4.16	0.48862	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.39009	0.1062	M	0.91561	3.22	0.80722	D	1	D;D	0.76494	0.999;0.996	D;D	0.83275	0.993;0.996	T	0.41945	-0.9480	10	0.87932	D	0	.	10.8578	0.46808	0.1417:0.0:0.0:0.8583	.	405;450	Q6P179-3;Q6P179	.;ERAP2_HUMAN	L	450;450;450;405	ENSP00000400376:F450L;ENSP00000421175:F450L;ENSP00000421849:F450L;ENSP00000369235:F405L	ENSP00000369235:F405L	F	+	1	0	ERAP2	96257941	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	5.684000	0.68197	0.932000	0.37266	0.460000	0.39030	TTT	.	.		0.368	ERAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250623.2	NM_022350		C	96232185	T	C	96232185	3	2	323	1	0	0	0	0	1	0	0	0	5206	1725	60	2	1374	2	ERAP2	5	96232185	Missense_Mutation	SNP	T	TCGA-MI-A75H-01A-11D-A32G-10	58880778	96232185	84683075	41	45521										
PCDHGB1	56104	hgsc.bcm.edu	37	chr5	140730776	140730776	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	gatatgtgttgagtgtggaaGctaaggatggaggagtacac	16	3	0	1			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr5:140730776G>T	ENST00000523390.1	+	1	949	c.949G>T	c.(949-951)Gct>Tct	p.A317S	PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018922.2|NM_032095.1	NP_061745.1|NP_115266.1	Q9Y5G3	PCDGD_HUMAN	protocadherin gamma subfamily B, 1	317	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAGTGTGGAAGCTAAGGATGG	0.418																																					p.A317S		Atlas-SNP	.											.	PCDHGB1	198	.	0			c.G949T						.						105	106	106					5																	140730776		1966	4173	6139	SO:0001583	missense	56104	exon1			GTGGAAGCTAAGG	AF152517	CCDS54923.1, CCDS75330.1	5q31	2010-01-26				ENSG00000254221		"Cadherins / Protocadherins : Clustered"	8708	other	protocadherin	"protocadherin gamma subfamily B, 1, isoform 2"	606299				10380929	Standard	NM_018922		Approved	PCDH-GAMMA-B1		Q9Y5G3		ENST00000523390.1:c.949G>T	chr5.hg19:g.140730776G>T	ENSP00000429273:p.Ala317Ser	106.0	0.0		84.0	4.0	NM_018922	Q3SY75|Q9Y5C8	Missense_Mutation	SNP	ENST00000523390.1	hg19	CCDS54923.1	.	.	.	.	.	.	.	.	.	.	.	18.14	3.557170	0.65425	.	.	ENSG00000254221	ENST00000523390	T	0.58652	0.32	5.43	5.43	0.79202	Cadherin (5);Cadherin-like (1);	.	.	.	.	D	0.84674	0.5524	H	0.96916	3.905	0.37380	D	0.91198	D;D	0.76494	0.999;0.999	D;D	0.73380	0.967;0.98	D	0.90993	0.4836	9	0.87932	D	0	.	19.2045	0.93724	0.0:0.0:1.0:0.0	.	317;317	Q9Y5G3-2;Q9Y5G3	.;PCDGD_HUMAN	S	317	ENSP00000429273:A317S	ENSP00000429273:A317S	A	+	1	0	PCDHGB1	140710960	1.000000	0.71417	1.000000	0.80357	0.518000	0.34316	9.692000	0.98682	2.706000	0.92434	0.563000	0.77884	GCT	.	.		0.418	PCDHGB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374740.1	NM_018922		T	140730776	G	T	140730776	3	4	323	1	0	0	0	0	1	0	0	0	11571	971	34	3	951	3	PCDHGB1	5	140730776	Missense_Mutation	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10	44498591	140730776	40184484	42	45522										
ARSI	340075	hgsc.bcm.edu	37	chr5	149677632	149677632	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	atgacactgttgttgtagaaAccgtagcgcttgagggccca	12	9	0	3			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr5:149677632A>G	ENST00000328668.7	-	2	1434	c.855T>C	c.(853-855)ggT>ggC	p.G285G		NM_001012301.2	NP_001012301.1	Q5FYB1	ARSI_HUMAN	arylsulfatase family, member I	285					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	23			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGTTGTAGAAACCGTAGCGCT	0.592																																					p.G285G		Atlas-SNP	.											.	ARSI	65	.	0			c.T855C						.						38	32	34					5																	149677632		2203	4300	6503	SO:0001819	synonymous_variant	340075	exon2			GTAGAAACCGTAG	AY875937	CCDS34275.1	5q32	2014-03-03	2006-03-07			ENSG00000183876		"Arylsulfatase family"	32521	protein-coding gene	gene with protein product		610009	"arylsulfatase I"			16174644, 24482476	Standard	NM_001012301		Approved	FLJ16069, SPG66	uc003lrv.2	Q5FYB1		ENST00000328668.7:c.855T>C	chr5.hg19:g.149677632A>G		80.0	0.0		64.0	27.0	NM_001012301	A1L3B0|B3KV22|B7XD03	Silent	SNP	ENST00000328668.7	hg19	CCDS34275.1																																																																																			.	.		0.592	ARSI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373681.1	NM_001012301		G	149677632	A	G	149677632	2	3	323	1	0	0	0	0	0	0	0	1	994	30	2	2		2	ARSI	5	149677632	Silent	SNP	A	TCGA-MI-A75H-01A-11D-A32G-10	8946856	149677632	31237628	43	45523										
GABRA6	2559	hgsc.bcm.edu	37	chr5	161118965	161118965	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	agggatcaccactgttttaaCtatgaccactttgagcatca	7	10	2	2			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr5:161118965C>A	ENST00000274545.5	+	8	1278	c.845C>A	c.(844-846)aCt>aAt	p.T282N	RP11-348M17.2_ENST00000521984.1_RNA|GABRA6_ENST00000523217.1_Missense_Mutation_p.T272N			Q16445	GBRA6_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 6	282					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|liver(2)|lung(22)|ovary(7)|skin(6)|urinary_tract(2)	57	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	ACTGTTTTAACTATGACCACT	0.398										TCGA Ovarian(5;0.080)																											p.T282N		Atlas-SNP	.											.	GABRA6	139	.	0			c.C845A						.						125	122	123					5																	161118965		2203	4300	6503	SO:0001583	missense	2559	exon8			TTTTAACTATGAC		CCDS4356.1	5q34	2012-06-22			ENSG00000145863	ENSG00000145863		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4080	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 6"	137143				8020978	Standard	NM_000811		Approved		uc003lyu.2	Q16445	OTTHUMG00000130351	ENST00000274545.5:c.845C>A	chr5.hg19:g.161118965C>A	ENSP00000274545:p.Thr282Asn	63.0	0.0		71.0	25.0	NM_000811	A8K096|Q4VAV2	Missense_Mutation	SNP	ENST00000274545.5	hg19	CCDS4356.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.593394	0.86953	.	.	ENSG00000145863	ENST00000274545;ENST00000523217	D;D	0.87887	-2.31;-2.31	5.32	5.32	0.75619	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.95468	0.8528	M	0.93978	3.48	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.96464	0.9343	10	0.87932	D	0	.	18.9984	0.92822	0.0:1.0:0.0:0.0	.	282	Q16445	GBRA6_HUMAN	N	282;272	ENSP00000274545:T282N;ENSP00000430527:T272N	ENSP00000274545:T282N	T	+	2	0	GABRA6	161051543	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.726000	0.84824	2.468000	0.83385	0.650000	0.86243	ACT	.	.		0.398	GABRA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252707.2			A	161118965	C	A	161118965	3	1	323	1	0	0	0	0	1	0	0	0	6173	565	20	3	875	3	GABRA6	5	161118965	Missense_Mutation	SNP	C	TCGA-MI-A75H-01A-11D-A32G-10	11441333	161118965	19796295	44	45524										
KCNIP1	30820	hgsc.bcm.edu	37	chr5	170160865	170160865	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	ggacaaaaataaagatggcaTcgtaactttagatgaatttc	8	5	0	3			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr5:170160865T>C	ENST00000411494.1	+	8	599	c.599T>C	c.(598-600)aTc>aCc	p.I200T	KCNIP1_ENST00000434108.1_Missense_Mutation_p.I214T|KCNIP1_ENST00000328939.4_Missense_Mutation_p.I189T|KCNIP1_ENST00000377360.4_Missense_Mutation_p.I198T|KCNIP1_ENST00000390656.4_Missense_Mutation_p.I189T|KCNIP1_ENST00000520740.1_Missense_Mutation_p.I161T			Q9NZI2	KCIP1_HUMAN	Kv channel interacting protein 1	200	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.				detection of calcium ion (GO:0005513)|positive regulation of action potential (GO:0045760)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|potassium channel complex (GO:0034705)	calcium ion binding (GO:0005509)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|voltage-gated ion channel activity (GO:0005244)			autonomic_ganglia(1)|large_intestine(7)|lung(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	18	Renal(175;0.000159)|Lung NSC(126;0.0191)|all_lung(126;0.0297)	Medulloblastoma(196;0.0109)|all_neural(177;0.0177)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			AAAGATGGCATCGTAACTTTA	0.423																																					p.I200T		Atlas-SNP	.											.	KCNIP1	66	.	0			c.T599C						.						118	113	114					5																	170160865		2203	4300	6503	SO:0001583	missense	30820	exon8			ATGGCATCGTAAC	AF199597	CCDS34285.1, CCDS34286.1, CCDS4374.1, CCDS64312.1, CCDS64313.1	5q35	2013-01-10			ENSG00000182132	ENSG00000182132		"EF-hand domain containing"	15521	protein-coding gene	gene with protein product		604660				10676964	Standard	NM_001278339		Approved	KCHIP1	uc003map.3	Q9NZI2	OTTHUMG00000130442	ENST00000411494.1:c.599T>C	chr5.hg19:g.170160865T>C	ENSP00000395323:p.Ile200Thr	46.0	0.0		45.0	11.0	NM_001034837	B7Z7B4|Q3YAD0|Q3YAD1|Q3YAD2|Q3YAD3|Q5U822	Missense_Mutation	SNP	ENST00000411494.1	hg19	CCDS34286.1	.	.	.	.	.	.	.	.	.	.	T	17.29	3.352419	0.61293	.	.	ENSG00000182132	ENST00000377360;ENST00000328939;ENST00000390656;ENST00000520740;ENST00000434108;ENST00000411494	T;T;T;T;T;T	0.70399	-0.48;-0.48;-0.48;-0.48;-0.48;-0.48	5.66	5.66	0.87406	EF-hand-like domain (1);	0.102292	0.64402	D	0.000003	T	0.63920	0.2552	L	0.39898	1.24	0.51767	D	0.999934	B;B;B;B	0.33512	0.259;0.152;0.415;0.262	B;B;B;B	0.36766	0.232;0.177;0.118;0.074	T	0.61505	-0.7049	9	.	.	.	.	13.863	0.63573	0.0:0.0:0.0:1.0	.	214;189;200;198	Q3YAD0;Q3YAD2;Q9NZI2;Q3YAD3	.;.;KCIP1_HUMAN;.	T	198;189;189;161;214;200	ENSP00000366577:I198T;ENSP00000329686:I189T;ENSP00000375071:I189T;ENSP00000431102:I161T;ENSP00000414886:I214T;ENSP00000395323:I200T	.	I	+	2	0	KCNIP1	170093443	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.680000	0.84062	2.156000	0.67533	0.528000	0.53228	ATC	.	.		0.423	KCNIP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000371760.1			C	170160865	T	C	170160865	3	2	323	1	0	0	0	0	1	0	0	0	8048	1435	50	2	721	2	KCNIP1	5	170160865	Missense_Mutation	SNP	T	TCGA-MI-A75H-01A-11D-A32G-10	9041900	170160865	10754395	45	45525										
HNRNPAB	85007	hgsc.bcm.edu	37	chr5	177637219	177637219	+	Intron	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	gctacgggcctggctatggcGgctacgactactcgccctat	12	14	0	0	rs115721462	byFrequency	TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr5:177637219G>T	ENST00000308158.5	-	13	1619				HNRNPAB_ENST00000358344.3_Missense_Mutation_p.G292C|HNRNPAB_ENST00000504898.1_Missense_Mutation_p.G292C|PHYKPL_ENST00000481811.1_Intron|HNRNPAB_ENST00000355836.5_Intron|HNRNPAB_ENST00000506259.1_Intron|HNRNPAB_ENST00000506339.1_Missense_Mutation_p.G287C|HNRNPAB_ENST00000514633.1_Intron|HNRNPAB_ENST00000515193.1_Intron	NM_153373.2	NP_699204.1	Q8IUZ5	AT2L2_HUMAN	5-phosphohydroxy-L-lysine phospho-lyase							mitochondrion (GO:0005739)	lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)									L-Alanine(DB00160)	TGGCTATGGCGGCTACGACTA	0.622																																					p.G292C		Atlas-SNP	.											.	HNRNPAB	24	.	0			c.G874T						.						62	63	63					5																	177637219		2203	4300	6503	SO:0001627	intron_variant	3182	exon7			TATGGCGGCTACG	BC037567	CCDS4434.1	5q35.3	2013-06-12	2013-06-12	2013-06-12	ENSG00000175309	ENSG00000175309	4.2.3.134		28249	protein-coding gene	gene with protein product	"5-phosphonooxy-L-lysine phospho-lyase"	614683	"alanine-glyoxylate aminotransferase 2-like 2"	AGXT2L2		22241472	Standard	NM_153373		Approved	MGC15875	uc003miz.3	Q8IUZ5	OTTHUMG00000130892	ENST00000308158.5:c.1351-1303C>A	chr5.hg19:g.177637219G>T		78.0	0.0		52.0	18.0	NM_031266	A8K7P6|B3KN36|D3DWP9|Q8WYS6|Q96HW8	Missense_Mutation	SNP	ENST00000308158.5	hg19	CCDS4434.1	.	.	.	.	.	.	.	.	.	.	G	13.89	2.372661	0.42003	.	.	ENSG00000197451	ENST00000358344;ENST00000506339;ENST00000504898	D;D;D	0.95756	-3.8;-3.8;-3.8	5.97	5.97	0.96955	.	0.343069	0.34580	N	0.003849	D	0.97514	0.9186	M	0.88512	2.96	0.80722	D	1	D	0.76494	0.999	D	0.63597	0.916	D	0.97506	1.0063	10	0.72032	D	0.01	.	11.2195	0.48846	0.0825:0.0:0.9175:0.0	.	292	Q99729-2	.	C	292;287;292	ENSP00000351108:G292C;ENSP00000422501:G287C;ENSP00000425031:G292C	ENSP00000351108:G292C	G	+	1	0	HNRNPAB	177569825	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.354000	0.52254	2.828000	0.97474	0.655000	0.94253	GGC	.	G|0.999;A|0.001		0.622	PHYKPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253477.1	NM_032921		T	177637219	G	T	177637219	1	4	323	0	1	0	0	0	0	0	0	0	7270	1116	39	1		1	HNRNPAB	5	177637219	Intron	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10	7476354	177637219	3278041	46	45526										
PHF10	55274	hgsc.bcm.edu	37	chr6	170114882	170114882	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	agagccactgggtaagaactGacctttgttcgctctgttgg	12	9	1	3			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr6:170114882G>T	ENST00000339209.4	-	7	873	c.750C>A	c.(748-750)gtC>gtA	p.V250V	PHF10_ENST00000366780.4_Silent_p.V248V|PHF10_ENST00000464779.1_5'Flank	NM_018288.3|NM_133325.2	NP_060758.2|NP_579866.2	Q8WUB8	PHF10_HUMAN	PHD finger protein 10	250	SAY.				nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	npBAF complex (GO:0071564)	zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|liver(3)|lung(4)|prostate(2)|urinary_tract(1)	14		Breast(66;5.08e-05)|Ovarian(120;0.208)		OV - Ovarian serous cystadenocarcinoma(33;1.4e-21)|BRCA - Breast invasive adenocarcinoma(81;1.4e-07)|GBM - Glioblastoma multiforme(31;0.00176)		GGTAAGAACTGACCTTTGTTC	0.418																																					p.V250V		Atlas-SNP	.											.	PHF10	76	.	0			c.C750A						.						189	180	183					6																	170114882		2203	4300	6503	SO:0001819	synonymous_variant	55274	exon7			AGAACTGACCTTT	AF338735	CCDS5308.2, CCDS5309.2	6q27	2014-05-13			ENSG00000130024	ENSG00000130024		"Zinc fingers, PHD-type"	18250	protein-coding gene	gene with protein product		613069				11827455	Standard	NM_018288		Approved	FLJ10975, XAP135, BAF45a	uc011egy.2	Q8WUB8	OTTHUMG00000016058	ENST00000339209.4:c.750C>A	chr6.hg19:g.170114882G>T		126.0	0.0		76.0	38.0	NM_018288	Q2YDA3|Q53HG8|Q9BXD2|Q9NV26	Silent	SNP	ENST00000339209.4	hg19	CCDS5308.2																																																																																			.	.		0.418	PHF10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346732.1	NM_018288		T	170114882	G	T	170114882	2	4	323	1	0	0	0	0	0	0	0	1	11830	1277	45	3		3	PHF10	6	170114882	Silent	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10		170114882	1000185	47	45527										
CPVL	54504	hgsc.bcm.edu	37	chr7	29160618	29160618	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	agggagcgaaacagcccatcAcaggggccaggcatcaacag	13	12	2	0			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr7:29160618A>G	ENST00000409850.1	-	6	706	c.60T>C	c.(58-60)tgT>tgC	p.C20C	CPVL_ENST00000396276.3_Silent_p.C20C|CPVL_ENST00000265394.5_Silent_p.C20C|CPVL_ENST00000488891.2_5'UTR			Q9H3G5	CPVL_HUMAN	carboxypeptidase, vitellogenic-like	20						extracellular vesicular exosome (GO:0070062)	serine-type carboxypeptidase activity (GO:0004185)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(1)	28						ACAGCCCATCACAGGGGCCAG	0.483																																					p.C20C		Atlas-SNP	.											.	CPVL	60	.	0			c.T60C						.						90	83	86					7																	29160618		2203	4300	6503	SO:0001819	synonymous_variant	54504	exon2			CCCATCACAGGGG	AF106704	CCDS5419.1	7p15.1	2012-02-10			ENSG00000106066	ENSG00000106066			14399	protein-coding gene	gene with protein product	"carboxypeptidase WUG", "vitellogenic carboxypeptidase-like protein", "CP-Mac carboxypeptidase"	609780				11401439	Standard	XM_005249786		Approved		uc003szw.3	Q9H3G5	OTTHUMG00000023669	ENST00000409850.1:c.60T>C	chr7.hg19:g.29160618A>G		144.0	0.0		105.0	34.0	NM_019029	A4D1A4|Q6UX20|Q8NBL7|Q96AR7|Q9HB41	Silent	SNP	ENST00000409850.1	hg19	CCDS5419.1																																																																																			.	.		0.483	CPVL-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328305.1	NM_019029		G	29160618	A	G	29160618	2	3	323	1	0	0	0	0	0	0	0	1	3837	157	6	2		2	CPVL	7	29160618	Silent	SNP	A	TCGA-MI-A75H-01A-11D-A32G-10		29160618	129978045	48	45528										
BMPER	168667	hgsc.bcm.edu	37	chr7	34192707	34192707	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	ctccttctctttttcagccaCccagtgtaagcatggtgctg	8	13	2	0	rs143727756		TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr7:34192707C>T	ENST00000297161.2	+	16	2254	c.1880C>T	c.(1879-1881)aCc>aTc	p.T627I	BMPER_ENST00000426693.1_Missense_Mutation_p.T627I	NM_133468.4	NP_597725.1	Q8N8U9	BMPER_HUMAN	BMP binding endothelial regulator	627					blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|endothelial cell activation (GO:0042118)|inner ear development (GO:0048839)|negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of endothelial cell migration (GO:0010594)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|ureteric bud development (GO:0001657)	extracellular space (GO:0005615)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(24)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						TTTTCAGCCACCCAGTGTAAG	0.493																																					p.T627I		Atlas-SNP	.											.	BMPER	131	.	0			c.C1880T						.	C	ILE/THR	0,4406		0,0,2203	190	176	181		1880	6	1	7	dbSNP_134	181	1,8599	1.2+/-3.3	0,1,4299	no	missense	BMPER	NM_133468.3	89	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	627/686	34192707	1,13005	2203	4300	6503	SO:0001583	missense	168667	exon16			CAGCCACCCAGTG		CCDS5442.1	7p14.3	2009-02-18			ENSG00000164619	ENSG00000164619			24154	protein-coding gene	gene with protein product	"crossveinless-2"	608699				12897139, 14766204	Standard	NM_133468		Approved	Cv2, CRIM3	uc011kap.2	Q8N8U9	OTTHUMG00000128675	ENST00000297161.2:c.1880C>T	chr7.hg19:g.34192707C>T	ENSP00000297161:p.Thr627Ile	84.0	0.0		97.0	37.0	NM_133468	A8K1P8|Q8TF36	Missense_Mutation	SNP	ENST00000297161.2	hg19	CCDS5442.1	.	.	.	.	.	.	.	.	.	.	C	12.80	2.045654	0.36085	0.0	1.16E-4	ENSG00000164619	ENST00000297161;ENST00000426693	T;T	0.78816	-1.21;-1.21	6.04	6.04	0.98038	Protease inhibitor I8, cysteine-rich trypsin inhibitor-like (1);	0.091322	0.85682	D	0.000000	T	0.67951	0.2948	L	0.35723	1.085	0.53688	D	0.999973	B	0.23442	0.085	B	0.17979	0.02	T	0.61461	-0.7058	10	0.22109	T	0.4	.	13.7479	0.62887	0.0:0.9302:0.0:0.0698	.	627	Q8N8U9	BMPER_HUMAN	I	627	ENSP00000297161:T627I;ENSP00000393950:T627I	ENSP00000297161:T627I	T	+	2	0	BMPER	34159232	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.699000	0.61796	2.873000	0.98535	0.563000	0.77884	ACC	.	C|1.000;T|0.000		0.493	BMPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250570.2	NM_133468		T	34192707	C	T	34192707	3	4	323	1	0	0	0	0	1	0	0	0	1468	507	18	3	1938	3	BMPER	7	34192707	Missense_Mutation	SNP	C	TCGA-MI-A75H-01A-11D-A32G-10	5032089	34192707	124945956	49	45529										
AMPH	273	hgsc.bcm.edu	37	chr7	38670937	38670937	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	ttcttggcgaagatgcccgtCttgatgtcggccatggctgc	13	11	2	2			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr7:38670937C>A	ENST00000356264.2	-	1	230	c.15G>T	c.(13-15)aaG>aaT	p.K5N	AMPH_ENST00000325590.5_Missense_Mutation_p.K5N|AMPH_ENST00000428293.2_Missense_Mutation_p.K5N	NM_001635.3	NP_001626.1	P49418	AMPH_HUMAN	amphiphysin	5					endocytosis (GO:0006897)|learning (GO:0007612)|synaptic transmission (GO:0007268)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|leading edge membrane (GO:0031256)|synaptic vesicle (GO:0008021)	phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|kidney(3)|large_intestine(12)|liver(3)|lung(27)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)	62						AGATGCCCGTCTTGATGTCGG	0.741																																					p.K5N		Atlas-SNP	.											.	AMPH	157	.	0			c.G15T						.						13	10	11					7																	38670937		2169	4254	6423	SO:0001583	missense	273	exon1			GCCCGTCTTGATG		CCDS5456.1, CCDS47574.1	7p14-p13	2007-06-19	2007-06-19		ENSG00000078053	ENSG00000078053			471	protein-coding gene	gene with protein product		600418	"amphiphysin (Stiff-Mann syndrome with breast cancer 128kD autoantigen)", "amphiphysin (Stiff-Man syndrome with breast cancer 128kDa autoantigen)"			8245793	Standard	NM_139316		Approved		uc003tgu.3	P49418	OTTHUMG00000023725	ENST00000356264.2:c.15G>T	chr7.hg19:g.38670937C>A	ENSP00000348602:p.Lys5Asn	30.0	0.0		46.0	17.0	NM_139316	A4D1X8|A4D1X9|O43538|Q75MJ8|Q75MK5|Q75MM3|Q8N4G0	Missense_Mutation	SNP	ENST00000356264.2	hg19	CCDS5456.1	.	.	.	.	.	.	.	.	.	.	C	18.35	3.603794	0.66445	.	.	ENSG00000078053	ENST00000325590;ENST00000356264;ENST00000428293;ENST00000544070	T;T;T	0.62498	0.05;0.02;0.04	4.35	3.46	0.39613	.	0.000000	0.64402	D	0.000001	T	0.50701	0.1631	L	0.29908	0.895	0.48288	D	0.999625	P;D	0.53619	0.873;0.961	P;P	0.47206	0.466;0.541	T	0.44559	-0.9320	10	0.39692	T	0.17	-16.3014	7.0348	0.24987	0.1734:0.737:0.0:0.0896	.	5;5	P49418-2;P49418	.;AMPH_HUMAN	N	5	ENSP00000317441:K5N;ENSP00000348602:K5N;ENSP00000390734:K5N	ENSP00000317441:K5N	K	-	3	2	AMPH	38637462	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.497000	0.35649	0.786000	0.33708	0.467000	0.42956	AAG	.	.		0.741	AMPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226953.2	NM_001635		A	38670937	C	A	38670937	3	1	323	1	0	0	0	0	1	0	0	0	588	912	32	3	2156	3	AMPH	7	38670937	Missense_Mutation	SNP	C	TCGA-MI-A75H-01A-11D-A32G-10	4478230	38670937	120467726	50	45530										
CDK13	8621	hgsc.bcm.edu	37	chr7	40027408	40027408	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	gcagaagcagcgaaagctgcAgaagcaactaaggctgctga	13	9	0	3			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr7:40027408A>C	ENST00000181839.4	+	2	2027	c.1422A>C	c.(1420-1422)gcA>gcC	p.A474A	CDK13_ENST00000340829.5_Silent_p.A474A	NM_003718.4|NM_031267.3	NP_003709.3|NP_112557.2	Q14004	CDK13_HUMAN	cyclin-dependent kinase 13	474					alternative mRNA splicing, via spliceosome (GO:0000380)|hemopoiesis (GO:0030097)|multicellular organismal development (GO:0007275)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|positive regulation of cell proliferation (GO:0008284)|regulation of mitosis (GO:0007088)|viral process (GO:0016032)	cyclin K-CDK13 complex (GO:0002945)|extracellular space (GO:0005615)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(2)|prostate(2)|skin(5)|stomach(2)|urinary_tract(1)	49						cgaaagctgcagaagcaacTA	0.512																																					p.A474A		Atlas-SNP	.											.	CDK13	114	.	0			c.A1422C						.						36	37	37					7																	40027408		2203	4300	6503	SO:0001819	synonymous_variant	8621	exon2			AGCTGCAGAAGCA	M80629	CCDS5461.1, CCDS5462.1	7p14.1	2011-11-08	2009-12-16	2009-12-16	ENSG00000065883	ENSG00000065883		"Cyclin-dependent kinases"	1733	protein-coding gene	gene with protein product	"cholinesterase-related cell division controller"	603309	"cell division cycle 2-like 5 (cholinesterase-related cell division controller)"	CDC2L5		1731328, 19884882	Standard	NM_003718		Approved	CHED, CDC2L, KIAA1791	uc003thh.4	Q14004	OTTHUMG00000023726	ENST00000181839.4:c.1422A>C	chr7.hg19:g.40027408A>C		105.0	0.0		99.0	40.0	NM_003718	Q53G78|Q6DKQ9|Q75MH4|Q75MH5|Q96JN4|Q9H4A0|Q9H4A1|Q9UDR4	Silent	SNP	ENST00000181839.4	hg19	CCDS5461.1																																																																																			.	.		0.512	CDK13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250726.2	NM_003718		C	40027408	A	C	40027408	2	2	323	1	0	0	0	0	0	0	0	1	3131	175	7	5		5	CDK13	7	40027408	Silent	SNP	A	TCGA-MI-A75H-01A-11D-A32G-10	1356471	40027408	119111255	51	45531										
CAMK2B	816	hgsc.bcm.edu	37	chr7	44281927	44281927	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	aggagtgacggtgtcccactCaggggacgggaactgcagaa	16	9	1	2			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr7:44281927C>A	ENST00000395749.2	-	10	785	c.709G>T	c.(709-711)Gag>Tag	p.E237*	CAMK2B_ENST00000258682.6_Nonsense_Mutation_p.E237*|CAMK2B_ENST00000346990.4_Nonsense_Mutation_p.E237*|CAMK2B_ENST00000350811.3_Nonsense_Mutation_p.E237*|CAMK2B_ENST00000395747.2_Nonsense_Mutation_p.E237*|CAMK2B_ENST00000347193.4_Nonsense_Mutation_p.E237*|CAMK2B_ENST00000440254.2_Nonsense_Mutation_p.E237*|CAMK2B_ENST00000502837.2_Nonsense_Mutation_p.E108*|CAMK2B_ENST00000353625.4_Nonsense_Mutation_p.E237*|CAMK2B_ENST00000358707.3_Nonsense_Mutation_p.E237*|CAMK2B_ENST00000457475.1_Nonsense_Mutation_p.E237*	NM_001220.4	NP_001211.3	Q13554	KCC2B_HUMAN	calcium/calmodulin-dependent protein kinase II beta	237	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of meiosis involved in egg activation (GO:0060466)|calcium ion transport (GO:0006816)|cytokine-mediated signaling pathway (GO:0019221)|G1/S transition of mitotic cell cycle (GO:0000082)|inhibitory G-protein coupled receptor phosphorylation (GO:0002030)|interferon-gamma-mediated signaling pathway (GO:0060333)|neuromuscular process controlling balance (GO:0050885)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of neuron projection development (GO:0010976)|positive regulation of synapse maturation (GO:0090129)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of calcium ion transport (GO:0051924)|regulation of dendritic spine development (GO:0060998)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of skeletal muscle adaptation (GO:0014733)|regulation of synapse structural plasticity (GO:0051823)|regulation of synaptic transmission, cholinergic (GO:0032222)|response to cadmium ion (GO:0046686)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)	18						GTGTCCCACTCAGGGGACGGG	0.607																																					p.E237X		Atlas-SNP	.											CAMK2B,right_upper_lobe,carcinoma,0,1	CAMK2B	56	.	0			c.G709T						.						129	125	126					7																	44281927		2203	4300	6503	SO:0001587	stop_gained	816	exon10			CCCACTCAGGGGA	U50358	CCDS5483.1, CCDS5484.1, CCDS5485.1, CCDS5486.1, CCDS5487.1, CCDS5488.1, CCDS5489.1, CCDS43573.1	7p14.3-p14.1	2008-10-30	2008-10-30		ENSG00000058404	ENSG00000058404			1461	protein-coding gene	gene with protein product	"CaM-kinase II beta chain", "calcium/calmodulin-dependent protein kinase type II beta chain", "CaM kinase II beta subunit", "proline rich calmodulin-dependent protein kinase"	607707	"calcium/calmodulin-dependent protein kinase (CaM kinase) II beta"	CAMKB			Standard	NM_172079		Approved	CAM2, CAMK2	uc003tkq.2	Q13554	OTTHUMG00000023491	ENST00000395749.2:c.709G>T	chr7.hg19:g.44281927C>A	ENSP00000379098:p.Glu237*	75.0	0.0		67.0	28.0	NM_172081	A4D2K0|A4D2K1|A4D2K2|A4D2K3|A4D2K4|A4D2K5|A4D2K6|O95437|O95438|O95599|Q9UGH7|Q9UGH8|Q9UGH9|Q9UNX0|Q9UNX7|Q9UP00|Q9Y5N4|Q9Y6F4	Nonsense_Mutation	SNP	ENST00000395749.2	hg19	CCDS5483.1	.	.	.	.	.	.	.	.	.	.	C	36	5.863704	0.97043	.	.	ENSG00000058404	ENST00000350811;ENST00000457475;ENST00000395749;ENST00000502837;ENST00000440254;ENST00000358707;ENST00000353625;ENST00000347193;ENST00000346990;ENST00000258682;ENST00000395747	.	.	.	4.39	4.39	0.52855	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	16.7614	0.85513	0.0:1.0:0.0:0.0	.	.	.	.	X	237;237;237;108;237;237;237;237;237;237;237	.	ENSP00000258682:E237X	E	-	1	0	CAMK2B	44248452	1.000000	0.71417	0.968000	0.41197	0.447000	0.32167	5.775000	0.68915	2.277000	0.76020	0.563000	0.77884	GAG	.	.		0.607	CAMK2B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251138.2	NM_172084		A	44281927	C	A	44281927	4	1	323	1	0	0	0	0	0	1	0	0	2602	835	29	3	1350	3	CAMK2B	7	44281927	Nonsense_Mutation	SNP	C	TCGA-MI-A75H-01A-11D-A32G-10	4254519	44281927	114856736	52	45532										
DDC	1644	hgsc.bcm.edu	37	chr7	50595913	50595913	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	gcacgcatggcgaagttgccAtctgaggggatggcttttaa	14	8	1	1			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr7:50595913A>T	ENST00000444124.2	-	6	836	c.636T>A	c.(634-636)gaT>gaA	p.D212E	DDC_ENST00000380984.4_Missense_Mutation_p.D212E|DDC_ENST00000357936.5_Missense_Mutation_p.D212E|DDC_ENST00000489162.1_5'UTR|DDC_ENST00000431062.1_Intron|DDC_ENST00000426377.1_Missense_Mutation_p.D134E	NM_001082971.1	NP_001076440	P20711	DDC_HUMAN	dopa decarboxylase (aromatic L-amino acid decarboxylase)	212					catecholamine biosynthetic process (GO:0042423)|cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to alkaloid (GO:0071312)|cellular response to drug (GO:0035690)|cellular response to growth factor stimulus (GO:0071363)|circadian rhythm (GO:0007623)|dopamine biosynthetic process (GO:0042416)|indolalkylamine biosynthetic process (GO:0046219)|isoquinoline alkaloid metabolic process (GO:0033076)|multicellular organismal aging (GO:0010259)|phytoalexin metabolic process (GO:0052314)|response to pyrethroid (GO:0046684)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)|synaptic vesicle amine transport (GO:0015842)	axon (GO:0030424)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|synaptic vesicle (GO:0008021)	amino acid binding (GO:0016597)|aromatic-L-amino-acid decarboxylase activity (GO:0004058)|enzyme binding (GO:0019899)|L-dopa decarboxylase activity (GO:0036468)|pyridoxal phosphate binding (GO:0030170)			breast(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(23)|ovary(4)|skin(2)|stomach(1)	40	Glioma(55;0.08)|all_neural(89;0.245)				Amantadine(DB00915)|Carbidopa(DB00190)|Cycloserine(DB00260)|Droxidopa(DB06262)|Flupentixol(DB00875)|L-DOPA(DB01235)|L-Tryptophan(DB00150)|Methyldopa(DB00968)	CGAAGTTGCCATCTGAGGGGA	0.522																																					p.D212E		Atlas-SNP	.											.	DDC	100	.	0			c.T636A						.						107	106	106					7																	50595913		2203	4300	6503	SO:0001583	missense	1644	exon6			GTTGCCATCTGAG		CCDS5511.1, CCDS56485.1, CCDS56486.1, CCDS56487.1, CCDS75598.1, CCDS75599.1	7p12.1	2012-08-30			ENSG00000132437	ENSG00000132437	4.1.1.28		2719	protein-coding gene	gene with protein product		107930				1612608	Standard	NM_001082971		Approved	AADC	uc003tpf.4	P20711	OTTHUMG00000023353	ENST00000444124.2:c.636T>A	chr7.hg19:g.50595913A>T	ENSP00000403644:p.Asp212Glu	79.0	0.0		81.0	28.0	NM_001082971	C9IYA0|E7ER62|E7EU95|Q16723|Q5W5T9|Q75MJ6	Missense_Mutation	SNP	ENST00000444124.2	hg19	CCDS5511.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.84|14.84	2.654103|2.654103	0.47362|0.47362	.|.	.|.	ENSG00000132437|ENSG00000132437	ENST00000357936;ENST00000426377;ENST00000444124;ENST00000380984|ENST00000430300	T;T;T;T|.	0.52057|.	0.68;0.68;0.68;0.68|.	6.06|6.06	-0.553|-0.553	0.11815|0.11815	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.56337|0.56337	0.1978|0.1978	L|L	0.52364|0.52364	1.645|1.645	0.48632|0.48632	D|D	0.999688|0.999688	D;D|.	0.61080|.	0.989;0.989|.	D;D|.	0.70716|.	0.97;0.97|.	T|T	0.49744|0.49744	-0.8907|-0.8907	10|5	0.39692|.	T|.	0.17|.	7.1068|7.1068	10.374|10.374	0.44071|0.44071	0.6711:0.0:0.3289:0.0|0.6711:0.0:0.3289:0.0	.|.	212;212|.	Q53Y41;P20711|.	.;DDC_HUMAN|.	E|K	212;134;212;212|93	ENSP00000350616:D212E;ENSP00000395069:D134E;ENSP00000403644:D212E;ENSP00000370371:D212E|.	ENSP00000350616:D212E|.	D|M	-|-	3|2	2|0	DDC|DDC	50563407|50563407	0.968000|0.968000	0.33430|0.33430	0.918000|0.918000	0.36340|0.36340	0.367000|0.367000	0.29736|0.29736	0.469000|0.469000	0.22067|0.22067	-0.302000|-0.302000	0.08869|0.08869	-0.297000|-0.297000	0.09499|0.09499	GAT|ATG	.	.		0.522	DDC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342593.1			T	50595913	A	T	50595913	3	4	323	1	0	0	0	0	1	0	0	0	4327	214	8	4	842	4	DDC	7	50595913	Missense_Mutation	SNP	A	TCGA-MI-A75H-01A-11D-A32G-10	6313986	50595913	108542750	53	45533										
HIP1	3092	hgsc.bcm.edu	37	chr7	75368213	75368213	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	gcagtgggttgggcacctgcTtcatggagctggccatccga	15	11	1	0			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr7:75368213T>G	ENST00000336926.6	-	1	52	c.26A>C	c.(25-27)aAg>aCg	p.K9T	HIP1_ENST00000434438.2_Missense_Mutation_p.K9T|HIP1_ENST00000479835.1_5'UTR	NM_005338.5	NP_005329.3	O00291	HIP1_HUMAN	huntingtin interacting protein 1	9					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell differentiation (GO:0030154)|clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|positive regulation of receptor-mediated endocytosis (GO:0048260)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|phosphatidylinositol binding (GO:0035091)|structural constituent of cytoskeleton (GO:0005200)			breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						GGGCACCTGCTTCATGGAGCT	0.746			T	PDGFRB	CMML																																p.K9T		Atlas-SNP	.		Dom	yes		7	7q11.23	3092	huntingtin interacting protein 1		L	.	HIP1	91	.	0			c.A26C						.						5	6	6					7																	75368213		2075	4086	6161	SO:0001583	missense	3092	exon1			ACCTGCTTCATGG	AF052288	CCDS34669.1, CCDS59060.1	7q11.23	2008-07-18			ENSG00000127946	ENSG00000127946			4913	protein-coding gene	gene with protein product		601767				9140394, 9147654	Standard	NM_005338		Approved	ILWEQ	uc003uds.2	O00291	OTTHUMG00000156050	ENST00000336926.6:c.26A>C	chr7.hg19:g.75368213T>G	ENSP00000336747:p.Lys9Thr	45.0	0.0		31.0	14.0	NM_005338	B4E3I7|E7ES17|O00328|Q2TB58|Q8TDL4	Missense_Mutation	SNP	ENST00000336926.6	hg19	CCDS34669.1	.	.	.	.	.	.	.	.	.	.	T	16.22	3.060300	0.55432	.	.	ENSG00000127946	ENST00000336926;ENST00000434438	T;T	0.15487	2.63;2.42	4.96	4.96	0.65561	.	0.244954	0.26470	U	0.024198	T	0.08358	0.0208	N	0.08118	0	0.32133	N	0.586516	B	0.33694	0.421	B	0.26969	0.075	T	0.08680	-1.0710	10	0.48119	T	0.1	-26.5628	10.9991	0.47593	0.0:0.0:0.0:1.0	.	9	O00291	HIP1_HUMAN	T	9	ENSP00000336747:K9T;ENSP00000410300:K9T	ENSP00000336747:K9T	K	-	2	0	HIP1	75206149	1.000000	0.71417	1.000000	0.80357	0.682000	0.39822	1.884000	0.39668	1.845000	0.53610	0.377000	0.23210	AAG	.	.		0.746	HIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342863.2	NM_005338		G	75368213	T	G	75368213	3	3	323	1	0	0	0	0	1	0	0	0	7123	1609	56	5	3211	5	HIP1	7	75368213	Missense_Mutation	SNP	T	TCGA-MI-A75H-01A-11D-A32G-10	24772300	75368213	83770450	54	45534										
GIMAP5	55340	hgsc.bcm.edu	37	chr7	150440117	150440117	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	gttgtgcagcatacttttttTcattatttttctgttcatct	5	7	4	0			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr7:150440117T>C	ENST00000358647.3	+	3	1257	c.890T>C	c.(889-891)tTc>tCc	p.F297S	GIMAP5_ENST00000479556.1_3'UTR	NM_018384.4	NP_060854.2	Q96F15	GIMA5_HUMAN	GTPase, IMAP family member 5	297					myeloid dendritic cell differentiation (GO:0043011)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of T cell activation (GO:0050868)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0032831)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of membrane potential (GO:0045838)|positive regulation of natural killer cell cytokine production (GO:0002729)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|regulation of mitochondrial membrane permeability (GO:0046902)|T cell differentiation (GO:0030217)|T cell homeostasis (GO:0043029)|temperature homeostasis (GO:0001659)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)|mitochondrial outer membrane (GO:0005741)	GTP binding (GO:0005525)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|urinary_tract(2)	19			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		ATACTTTTTTTCATTATTTTT	0.363																																					p.F501S		Atlas-SNP	.											.	.	.	.	0			c.T1502C						.						46	41	43					7																	150440117		2202	4297	6499	SO:0001583	missense	0	exon6			TTTTTTTCATTAT	AK002158	CCDS5907.1	7q36.1	2014-04-04	2004-10-29	2004-10-30	ENSG00000196329	ENSG00000196329		"GTPases, IMAP"	18005	protein-coding gene	gene with protein product	"immune-associated nucleotide-binding protein 5"	608086	"immune associated nucleotide 4 like 1 (mouse)"	IAN4L1			Standard	NM_018384		Approved	HIMAP3, IAN5		Q96F15	OTTHUMG00000157542	ENST00000358647.3:c.890T>C	chr7.hg19:g.150440117T>C	ENSP00000351473:p.Phe297Ser	80.0	0.0		51.0	12.0	NM_001199577	D3DWZ5|Q6IA75|Q96NE4|Q9NUK9	Missense_Mutation	SNP	ENST00000358647.3	hg19	CCDS5907.1	.	.	.	.	.	.	.	.	.	.	T	6.582	0.475673	0.12521	.	.	ENSG00000196329	ENST00000358647;ENST00000447239	T	0.05580	3.42	3.65	3.65	0.41850	.	1.790210	0.02812	N	0.124450	T	0.07324	0.0185	L	0.29908	0.895	0.09310	N	1	B	0.22604	0.072	B	0.12156	0.007	T	0.24261	-1.0165	10	0.48119	T	0.1	.	8.5889	0.33674	0.0:0.0:0.0:1.0	.	297	Q96F15	GIMA5_HUMAN	S	297;333	ENSP00000351473:F297S	ENSP00000351473:F297S	F	+	2	0	GIMAP5	150071050	0.003000	0.15002	0.001000	0.08648	0.002000	0.02628	1.409000	0.34680	1.540000	0.49301	0.332000	0.21555	TTC	.	.		0.363	GIMAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349108.2	NM_018384		C	150440117	T	C	150440117	3	2	323	1	0	0	0	0	1	0	0	0	6390	1783	62	2	896	2	GIMAP5	7	150440117	Missense_Mutation	SNP	T	TCGA-MI-A75H-01A-11D-A32G-10	75071904	150440117	8698546	55	45535										
MLL3	58508	hgsc.bcm.edu	37	chr7	151860694	151860694	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	gcattctaacagggctagtaTggccagaaataactgttgtg	11	7	1	1			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr7:151860694T>G	ENST00000262189.6	-	43	10186	c.9968A>C	c.(9967-9969)cAt>cCt	p.H3323P	KMT2C_ENST00000355193.2_Missense_Mutation_p.H3323P	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	3323	Gln-rich.|Pro-rich.				histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										AGGGCTAGTATGGCCAGAAAT	0.552																																					p.H3323P		Atlas-SNP	.											.	MLL3	1564	.	0			c.A9968C						.						124	109	115					7																	151860694		2203	4300	6503	SO:0001583	missense	58508	exon43			CTAGTATGGCCAG	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.9968A>C	chr7.hg19:g.151860694T>G	ENSP00000262189:p.His3323Pro	187.0	0.0		158.0	56.0	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	hg19	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	T	8.240	0.806598	0.16467	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.83673	-1.75;-1.74	5.28	5.28	0.74379	.	0.154227	0.30365	N	0.009789	T	0.80919	0.4716	L	0.44542	1.39	0.80722	D	1	B;B;P	0.41265	0.026;0.066;0.744	B;B;B	0.44044	0.004;0.024;0.439	T	0.80113	-0.1518	10	0.35671	T	0.21	.	15.2352	0.73422	0.0:0.0:0.0:1.0	.	3323;2384;3323	Q8NEZ4;Q8NEZ4-2;Q8NEZ4-3	MLL3_HUMAN;.;.	P	3323	ENSP00000262189:H3323P;ENSP00000347325:H3323P	ENSP00000262189:H3323P	H	-	2	0	MLL3	151491627	1.000000	0.71417	0.652000	0.29579	0.226000	0.24999	5.501000	0.66950	1.997000	0.58415	0.533000	0.62120	CAT	.	.		0.552	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			G	151860694	T	G	151860694	3	3	323	1	0	0	0	0	1	0	0	0	9631	1464	51	5	4835	5	MLL3	7	151860694	Missense_Mutation	SNP	T	TCGA-MI-A75H-01A-11D-A32G-10	1420577	151860694	7277969	56	45536										
DPP6	1804	hgsc.bcm.edu	37	chr7	154593130	154593130	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	atcagagccatcccccagggAggacgagggaaattctatca	11	11	3	1			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr7:154593130A>T	ENST00000377770.3	+	13	1506	c.1365A>T	c.(1363-1365)ggA>ggT	p.G455G	DPP6_ENST00000404039.1_Silent_p.G391G|DPP6_ENST00000427557.1_Silent_p.G348G|DPP6_ENST00000332007.3_Silent_p.G393G			P42658	DPP6_HUMAN	dipeptidyl-peptidase 6	455					cell death (GO:0008219)|neuronal action potential (GO:0019228)|positive regulation of potassium ion transmembrane transport (GO:1901381)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(3)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(35)|pancreas(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	71	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			TCCCCCAGGGAGGACGAGGGA	0.522																																					p.G455G	NSCLC(125;1384 1783 2490 7422 34254)	Atlas-SNP	.											.	DPP6	383	.	0			c.A1365T						.						58	55	56					7																	154593130		1931	4118	6049	SO:0001819	synonymous_variant	1804	exon13			CCAGGGAGGACGA	M96859	CCDS75682.1, CCDS75683.1, CCDS75684.1	7q36.2	2006-08-07	2006-01-12		ENSG00000130226	ENSG00000130226			3010	protein-coding gene	gene with protein product		126141	"dipeptidylpeptidase VI", "dipeptidylpeptidase 6"			1729689	Standard	XM_006715871		Approved	DPPX	uc003wlk.3	P42658	OTTHUMG00000151511	ENST00000377770.3:c.1365A>T	chr7.hg19:g.154593130A>T		55.0	0.0		70.0	15.0	NM_130797		Silent	SNP	ENST00000377770.3	hg19																																																																																				.	.		0.522	DPP6-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322932.1	NM_130797		T	154593130	A	T	154593130	2	4	323	1	0	0	0	0	0	0	0	1	4732	291	11	4		4	DPP6	7	154593130	Silent	SNP	A	TCGA-MI-A75H-01A-11D-A32G-10	2732436	154593130	4545533	57	45537										
EXTL3	2137	hgsc.bcm.edu	37	chr8	28575255	28575255	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	cccccaccgttcaggcaaggCggctggaactgaccccaaca	10	17	1	1	rs200494893		TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr8:28575255C>T	ENST00000220562.4	+	3	2581	c.1679C>T	c.(1678-1680)gCg>gTg	p.A560V	EXTL3_ENST00000523149.1_Missense_Mutation_p.A176V|EXTL3_ENST00000519886.1_Intron	NM_001440.2	NP_001431.1	O43909	EXTL3_HUMAN	exostosin-like glycosyltransferase 3	560					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|positive regulation of cell growth (GO:0030307)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0001888)|metal ion binding (GO:0046872)	p.A560V(1)		biliary_tract(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(8)|ovary(1)|prostate(2)|skin(2)|soft_tissue(1)|urinary_tract(1)	36		Ovarian(32;0.069)		KIRC - Kidney renal clear cell carcinoma(542;0.107)|Kidney(114;0.129)|Colorectal(74;0.228)		TCAGGCAAGGCGGCTGGAACT	0.617													C|||	1	0.000199681	0	0.0014	5008	,	,		16582	0		0	False		,,,				2504	0				p.A560V		Atlas-SNP	.											EXTL3,caecum,carcinoma,0,1	EXTL3	83	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1679T						.	C	VAL/ALA	0,4406		0,0,2203	45	43	44		1679	5.9	1	8		44	2,8598	2.2+/-6.3	0,2,4298	yes	missense	EXTL3	NM_001440.2	64	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	560/920	28575255	2,13004	2203	4300	6503	SO:0001583	missense	2137	exon3			GCAAGGCGGCTGG	U76188	CCDS6070.1	8p22-p12	2013-03-01	2013-03-01		ENSG00000012232	ENSG00000012232	2.4.1.223	"Exostosin glycosyltransferase family"	3518	protein-coding gene	gene with protein product	"REG receptor", "glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase"	605744	"exostoses (multiple)-like 3"			9479495, 9450183, 11257457	Standard	NM_001440		Approved	botv, REGR	uc003xgz.2	O43909	OTTHUMG00000102146	ENST00000220562.4:c.1679C>T	chr8.hg19:g.28575255C>T	ENSP00000220562:p.Ala560Val	78.0	0.0		35.0	16.0	NM_001440	D3DST8|O00225|Q53XT3	Missense_Mutation	SNP	ENST00000220562.4	hg19	CCDS6070.1	.	.	.	.	.	.	.	.	.	.	C	3.404	-0.121681	0.06838	0.0	2.33E-4	ENSG00000012232	ENST00000523149;ENST00000220562	D;D	0.95272	-3.27;-3.66	5.95	5.95	0.96441	.	0.187488	0.47455	D	0.000230	D	0.88905	0.6564	N	0.14661	0.345	0.48632	D	0.999686	B	0.28512	0.214	B	0.13407	0.009	D	0.84690	0.0722	10	0.27082	T	0.32	-23.8028	20.3748	0.98911	0.0:1.0:0.0:0.0	.	560	O43909	EXTL3_HUMAN	V	176;560	ENSP00000428691:A176V;ENSP00000220562:A560V	ENSP00000220562:A560V	A	+	2	0	EXTL3	28631174	1.000000	0.71417	0.973000	0.42090	0.583000	0.36354	4.950000	0.63603	2.817000	0.96982	0.563000	0.77884	GCG	.	C|0.999;T|0.001		0.617	EXTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219987.3	NM_001440		T	28575255	C	T	28575255	3	4	323	1	0	0	0	0	1	0	0	0	5329	768	27	1	1681	1	EXTL3	8	28575255	Missense_Mutation	SNP	C	TCGA-MI-A75H-01A-11D-A32G-10		28575255	117788767	58	45538										
SULF1	23213	hgsc.bcm.edu	37	chr8	70551048	70551048	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	taatggagctcagaagctgtCaaggatataagcagtgcaac	11	7	2	1			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr8:70551048C>T	ENST00000260128.4	+	21	3223	c.2506C>T	c.(2506-2508)Caa>Taa	p.Q836*	SULF1_ENST00000419716.3_Nonsense_Mutation_p.Q836*|SULF1_ENST00000458141.2_Nonsense_Mutation_p.Q836*|SULF1_ENST00000402687.4_Nonsense_Mutation_p.Q836*|SULF1_ENST00000521946.1_3'UTR	NM_015170.2	NP_055985.2	Q8IWU6	SULF1_HUMAN	sulfatase 1	836					apoptotic process (GO:0006915)|bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of prostatic bud formation (GO:0060686)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|central_nervous_system(3)|endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)			CAGAAGCTGTCAAGGATATAA	0.383																																					p.Q836X		Atlas-SNP	.											.	SULF1	153	.	0			c.C2506T						.						94	82	86					8																	70551048		2203	4300	6503	SO:0001587	stop_gained	23213	exon21			AGCTGTCAAGGAT	AB029000	CCDS6204.1	8q13.2	2014-09-11			ENSG00000137573	ENSG00000137573			20391	protein-coding gene	gene with protein product		610012				12368295	Standard	NM_015170		Approved	KIAA1077, SULF-1	uc003xyd.2	Q8IWU6	OTTHUMG00000164466	ENST00000260128.4:c.2506C>T	chr8.hg19:g.70551048C>T	ENSP00000260128:p.Gln836*	205.0	0.0		333.0	72.0	NM_001128205	Q86YV8|Q8NCA2|Q9UPS5	Nonsense_Mutation	SNP	ENST00000260128.4	hg19	CCDS6204.1	.	.	.	.	.	.	.	.	.	.	C	48	14.004790	0.99774	.	.	ENSG00000137573	ENST00000458141;ENST00000260128;ENST00000402687;ENST00000419716	.	.	.	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.3457	0.94362	0.0:1.0:0.0:0.0	.	.	.	.	X	836	.	ENSP00000260128:Q836X	Q	+	1	0	SULF1	70713602	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.748000	0.85085	2.645000	0.89757	0.650000	0.86243	CAA	.	.		0.383	SULF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378885.2	NM_015170		T	70551048	C	T	70551048	4	4	323	1	0	0	0	0	0	1	0	0	15385	827	29	3	2572	3	SULF1	8	70551048	Nonsense_Mutation	SNP	C	TCGA-MI-A75H-01A-11D-A32G-10	41975793	70551048	75812974	59	45539										
TERF1	7013	hgsc.bcm.edu	37	chr8	73944310	73944310	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	cttttcttatctaagttgcaAcatggaacccagcaacaaga	6	10	2	1			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr8:73944310A>G	ENST00000276603.5	+	8	1004	c.981A>G	c.(979-981)caA>caG	p.Q327Q	TERF1_ENST00000276602.6_Silent_p.Q307Q|TERF1_ENST00000520783.1_3'UTR	NM_017489.2	NP_059523.2	P54274	TERF1_HUMAN	telomeric repeat binding factor (NIMA-interacting) 1	327	Interaction with RLIM.				age-dependent telomere shortening (GO:0001309)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of DNA replication (GO:0008156)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via semi-conservative replication (GO:0032214)|negative regulation of telomere maintenance via telomerase (GO:0032211)|positive regulation of apoptotic process (GO:0043065)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of mitosis (GO:0045840)|positive regulation of mitotic cell cycle (GO:0045931)|protein homooligomerization (GO:0051260)|response to drug (GO:0042493)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)|telomere maintenance via telomere shortening (GO:0010834)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nuclear telomere cap complex (GO:0000783)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|double-stranded telomeric DNA binding (GO:0003691)|microtubule binding (GO:0008017)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|telomeric DNA binding (GO:0042162)			central_nervous_system(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	9	Breast(64;0.218)		Epithelial(68;0.0984)			CTAAGTTGCAACATGGAACCC	0.353																																					p.Q327Q		Atlas-SNP	.											.	TERF1	48	.	0			c.A981G						.						81	76	78					8																	73944310		2203	4300	6503	SO:0001819	synonymous_variant	7013	exon8			GTTGCAACATGGA	U74382	CCDS6210.1, CCDS6211.1	8q21.11	2011-05-24			ENSG00000147601	ENSG00000147601			11728	protein-coding gene	gene with protein product		600951		TRBF1		9391075	Standard	NM_003218		Approved	PIN2, TRF1, TRF	uc003xzd.2	P54274	OTTHUMG00000164522	ENST00000276603.5:c.981A>G	chr8.hg19:g.73944310A>G		116.0	0.0		180.0	106.0	NM_017489	A7XP29|Q15553|Q8NHT6|Q93029	Silent	SNP	ENST00000276603.5	hg19	CCDS6211.1																																																																																			.	.		0.353	TERF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379093.1	NM_017489		G	73944310	A	G	73944310	2	3	323	1	0	0	0	0	0	0	0	1	15776	40	2	2		2	TERF1	8	73944310	Silent	SNP	A	TCGA-MI-A75H-01A-11D-A32G-10	3393262	73944310	72419712	60	45540										
ARHGAP39	80728	hgsc.bcm.edu	37	chr8	145780976	145780976	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	agctggccgtccgcactgtaAtcccggtaaatctcatagtc	9	13	1	0			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr8:145780976A>T	ENST00000276826.5	-	3	765	c.564T>A	c.(562-564)gaT>gaA	p.D188E	ARHGAP39_ENST00000540274.1_Missense_Mutation_p.D188E|ARHGAP39_ENST00000377307.2_Missense_Mutation_p.D188E			Q9C0H5	RHG39_HUMAN	Rho GTPase activating protein 39	188					axon guidance (GO:0007411)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	22						CCGCACTGTAATCCCGGTAAA	0.478																																					p.D188E		Atlas-SNP	.											.	ARHGAP39	80	.	0			c.T564A						.						147	126	133					8																	145780976		2203	4300	6503	SO:0001583	missense	80728	exon5			ACTGTAATCCCGG		CCDS34971.1	8q24.3	2011-06-29			ENSG00000147799	ENSG00000147799		"Rho GTPase activating proteins"	29351	protein-coding gene	gene with protein product	"RhoGAP93B homolog (Drosophila)", "crossGAP homolog (Drosophila)"	615880				15755809	Standard	XM_005272344		Approved	KIAA1688, Vilse, CrGAP	uc003zds.1	Q9C0H5	OTTHUMG00000165182	ENST00000276826.5:c.564T>A	chr8.hg19:g.145780976A>T	ENSP00000276826:p.Asp188Glu	101.0	0.0		129.0	25.0	NM_025251	B4E1I1	Missense_Mutation	SNP	ENST00000276826.5	hg19		.	.	.	.	.	.	.	.	.	.	A	12.87	2.068451	0.36470	.	.	ENSG00000147799	ENST00000276826;ENST00000377307;ENST00000540274	T;T;T	0.21932	1.98;1.98;1.98	4.74	-0.936	0.10419	.	0.223982	0.37053	N	0.002273	T	0.11922	0.0290	L	0.47716	1.5	0.24093	N	0.995906	B;P	0.36837	0.435;0.571	B;B	0.31101	0.057;0.124	T	0.18241	-1.0343	10	0.28530	T	0.3	-6.549	4.3736	0.11260	0.4575:0.1789:0.3636:0.0	.	188;188	Q9C0H5;Q9C0H5-2	RHG39_HUMAN;.	E	188	ENSP00000276826:D188E;ENSP00000366522:D188E;ENSP00000445075:D188E	ENSP00000276826:D188E	D	-	3	2	ARHGAP39	145751784	1.000000	0.71417	0.515000	0.27774	0.916000	0.54674	1.341000	0.33907	-0.293000	0.08986	0.533000	0.62120	GAT	.	.		0.478	ARHGAP39-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382509.1			T	145780976	A	T	145780976	3	4	323	1	0	0	0	0	1	0	0	0	884	98	4	4	2816	4	ARHGAP39	8	145780976	Missense_Mutation	SNP	A	TCGA-MI-A75H-01A-11D-A32G-10	71836666	145780976	583046	61	45541										
KCNV2	169522	hgsc.bcm.edu	37	chr9	2718181	2718181	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	actacgaggagcagacagacGaatacttcttcgaccgcgac	10	12	1	2	rs140256288		TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr9:2718181G>A	ENST00000382082.3	+	1	680	c.442G>A	c.(442-444)Gaa>Aaa	p.E148K		NM_133497.3	NP_598004.1	Q8TDN2	KCNV2_HUMAN	potassium channel, subfamily V, member 2	148					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(2)	35				GBM - Glioblastoma multiforme(50;0.0257)		GCAGACAGACGAATACTTCTT	0.657																																					p.E148K		Atlas-SNP	.											.	KCNV2	72	.	0			c.G442A	GRCh37	CM080425	KCNV2	M	rs140256288	.	G	LYS/GLU	2,4402		0,2,2200	24	22	23		442	5.1	0.2	9	dbSNP_134	23	0,8596		0,0,4298	no	missense	KCNV2	NM_133497.3	56	0,2,6498	AA,AG,GG		0.0,0.0454,0.0154	probably-damaging	148/546	2718181	2,12998	2202	4298	6500	SO:0001583	missense	169522	exon1			ACAGACGAATACT	AF348983	CCDS6447.1	9p24.2	2011-07-05			ENSG00000168263	ENSG00000168263		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	19698	protein-coding gene	gene with protein product		607604				12060745, 16382104	Standard	NM_133497		Approved	Kv8.2	uc003zho.2	Q8TDN2	OTTHUMG00000019449	ENST00000382082.3:c.442G>A	chr9.hg19:g.2718181G>A	ENSP00000371514:p.Glu148Lys	163.0	0.0		113.0	38.0	NM_133497	Q5T6X0	Missense_Mutation	SNP	ENST00000382082.3	hg19	CCDS6447.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.327786	0.81690	4.54E-4	0.0	ENSG00000168263	ENST00000423608;ENST00000382082	T	0.79454	-1.27	5.07	5.07	0.68467	BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.055998	0.64402	D	0.000001	D	0.92358	0.7575	H	0.97023	3.925	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.94993	0.8136	10	0.87932	D	0	.	18.4533	0.90711	0.0:0.0:1.0:0.0	.	148	Q8TDN2	KCNV2_HUMAN	K	148	ENSP00000371514:E148K	ENSP00000371514:E148K	E	+	1	0	KCNV2	2708181	1.000000	0.71417	0.245000	0.24217	0.616000	0.37450	7.995000	0.88328	2.352000	0.79861	0.462000	0.41574	GAA	.	G|1.000;A|0.000		0.657	KCNV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051528.1	NM_133497		A	2718181	G	A	2718181	3	1	323	1	0	0	0	0	1	0	0	0	8104	1059	37	1	444	1	KCNV2	9	2718181	Missense_Mutation	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10		2718181	138495250	62	45542										
CNTFR	1271	hgsc.bcm.edu	37	chr9	34552230	34552230	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	atggggacgctgaccaagaaGggtgccgagggtcccccgcc	16	13	0	2			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr9:34552230G>T	ENST00000378980.3	-	9	1340	c.1047C>A	c.(1045-1047)ccC>ccA	p.P349P	CNTFR_ENST00000351266.4_Silent_p.P349P	NM_001207011.1|NM_147164.2	NP_001193940.1|NP_671693.1	P26992	CNTFR_HUMAN	ciliary neurotrophic factor receptor	349					brainstem development (GO:0003360)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)|positive regulation of cell proliferation (GO:0008284)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|skeletal muscle organ development (GO:0060538)|suckling behavior (GO:0001967)	anchored component of membrane (GO:0031225)|CNTFR-CLCF1 complex (GO:0097059)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|cytokine binding (GO:0019955)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(4)|skin(1)	15	all_epithelial(49;0.0899)		STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.00494)		TGACCAAGAAGGGTGCCGAGG	0.667																																					p.P349P		Atlas-SNP	.											.	CNTFR	46	.	0			c.C1047A						.						18	22	20					9																	34552230		2169	4260	6429	SO:0001819	synonymous_variant	1271	exon9			CAAGAAGGGTGCC	M73238	CCDS6558.1	9p13	2013-02-11			ENSG00000122756	ENSG00000122756		"Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2170	protein-coding gene	gene with protein product		118946				1648265	Standard	NM_001842		Approved		uc003zuq.2	P26992	OTTHUMG00000019821	ENST00000378980.3:c.1047C>A	chr9.hg19:g.34552230G>T		32.0	0.0		23.0	10.0	NM_147164	Q5U050	Silent	SNP	ENST00000378980.3	hg19	CCDS6558.1																																																																																			.	.		0.667	CNTFR-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052176.1			T	34552230	G	T	34552230	2	4	323	1	0	0	0	0	0	0	0	1	3640	987	35	3		3	CNTFR	9	34552230	Silent	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10	31834049	34552230	106661201	63	45543										
TRPM6	140803	hgsc.bcm.edu	37	chr9	77442785	77442785	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	cccacggtcccatcatcagaCaggatgaagtgcgagtgcat	11	12	2	2			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr9:77442785C>T	ENST00000360774.1	-	7	987	c.750G>A	c.(748-750)ctG>ctA	p.L250L	TRPM6_ENST00000451710.3_Silent_p.L250L|TRPM6_ENST00000361255.3_Silent_p.L245L|TRPM6_ENST00000483186.1_5'UTR|TRPM6_ENST00000376871.3_Silent_p.L250L|TRPM6_ENST00000359047.2_Silent_p.L250L|TRPM6_ENST00000449912.2_Silent_p.L245L|TRPM6_ENST00000376872.3_Silent_p.L250L|TRPM6_ENST00000376864.4_Silent_p.L250L	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	250					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						CATCATCAGACAGGATGAAGT	0.502																																					p.L250L		Atlas-SNP	.											.	TRPM6	377	.	0			c.G750A						.						186	163	171					9																	77442785		2203	4300	6503	SO:0001819	synonymous_variant	140803	exon7			ATCAGACAGGATG	AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"Voltage-gated ion channels / Transient receptor potential cation channels"	17995	protein-coding gene	gene with protein product		607009	"hypomagnesemia, secondary hypocalcemia"	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.750G>A	chr9.hg19:g.77442785C>T		111.0	0.0		85.0	28.0	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Silent	SNP	ENST00000360774.1	hg19	CCDS6647.1																																																																																			.	.		0.502	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662		T	77442785	C	T	77442785	2	4	323	1	0	0	0	0	0	0	0	1	16605	465	17	3		3	TRPM6	9	77442785	Silent	SNP	C	TCGA-MI-A75H-01A-11D-A32G-10	42890555	77442785	63770646	64	45544										
GAPVD1	26130	hgsc.bcm.edu	37	chr9	128064751	128064751	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	ccaaacaagctaattgagagGttctctccatctcagcagga	8	11	2	1			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr9:128064751G>T	ENST00000495955.1	+	5	965	c.675G>T	c.(673-675)agG>agT	p.R225S	GAPVD1_ENST00000297933.6_Missense_Mutation_p.R225S|GAPVD1_ENST00000394083.2_Missense_Mutation_p.R225S|GAPVD1_ENST00000265956.4_Missense_Mutation_p.R225S|RNU6-1020P_ENST00000363684.1_RNA|GAPVD1_ENST00000394104.2_Missense_Mutation_p.R225S|GAPVD1_ENST00000394105.2_Missense_Mutation_p.R225S|GAPVD1_ENST00000470056.1_Missense_Mutation_p.R225S|GAPVD1_ENST00000312123.9_Missense_Mutation_p.R225S|GAPVD1_ENST00000394084.1_Missense_Mutation_p.R225S			Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1	225	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|regulation of protein transport (GO:0051223)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	GTPase activating protein binding (GO:0032794)|GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						TAATTGAGAGGTTCTCTCCAT	0.423																																					p.R225S		Atlas-SNP	.											.	GAPVD1	124	.	0			c.G675T						.						60	56	57					9																	128064751		2203	4300	6503	SO:0001583	missense	26130	exon3			TGAGAGGTTCTCT		CCDS65130.1, CCDS65131.1, CCDS65132.1	9q34.11	2008-02-05			ENSG00000165219	ENSG00000165219			23375	protein-coding gene	gene with protein product		611714					Standard	XM_005251901		Approved	DKFZP434C212, KIAA1521	uc004bpr.3	Q14C86	OTTHUMG00000020678	ENST00000495955.1:c.675G>T	chr9.hg19:g.128064751G>T	ENSP00000419063:p.Arg225Ser	55.0	0.0		54.0	25.0	NM_015635	A8MYK3|B0QZ62|B0QZ63|B0QZ64|Q14C76|Q2Q1W1|Q8ND92|Q8WU86|Q96CZ4|Q9NXQ1|Q9P207|Q9Y4N0	Missense_Mutation	SNP	ENST00000495955.1	hg19		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	16.99|16.99|16.99	3.273672|3.273672|3.273672	0.59649|0.59649|0.59649	.|.|.	.|.|.	ENSG00000165219|ENSG00000165219|ENSG00000165219	ENST00000431329|ENST00000394084;ENST00000470056;ENST00000394105;ENST00000394104;ENST00000265956;ENST00000394083;ENST00000495955;ENST00000467750;ENST00000297933;ENST00000312123|ENST00000436712	.|T;T;T;T;T;T;T;T;T;T|.	.|0.79749|.	.|-1.3;-1.3;-1.3;-1.3;-1.3;-1.3;-1.3;-1.3;-1.3;-1.3|.	6.03|6.03|6.03	-1.11|-1.11|-1.11	0.09840|0.09840|0.09840	.|Rho GTPase activation protein (1);Ras GTPase-activating protein (3);|.	.|0.045406|.	.|0.85682|.	.|D|.	.|0.000000|.	T|T|T	0.50905|0.50905|0.50905	0.1643|0.1643|0.1643	L|L|L	0.37630|0.37630|0.37630	1.12|1.12|1.12	0.54753|0.54753|0.54753	D|D|D	0.999984|0.999984|0.999984	.|D;D;B;D;D;D;P|.	.|0.64830|.	.|0.992;0.994;0.218;0.981;0.981;0.992;0.94|.	.|D;D;B;D;D;D;P|.	.|0.75020|.	.|0.974;0.985;0.059;0.962;0.962;0.974;0.897|.	T|T|T	0.36089|0.36089|0.36089	-0.9762|-0.9762|-0.9762	5|10|5	.|0.35671|.	.|T|.	.|0.21|.	.|.|.	11.8016|11.8016|11.8016	0.52130|0.52130|0.52130	0.5301:0.0:0.4699:0.0|0.5301:0.0:0.4699:0.0|0.5301:0.0:0.4699:0.0	.|.|.	.|225;225;225;225;225;225;225|.	.|Q14C86-5;Q14C86;Q14C86-3;Q14C86-4;Q14C86-2;Q14C86-6;B0QZ65|.	.|.;GAPD1_HUMAN;.;.;.;.;.|.	V|S|F	88|225|56	.|ENSP00000377646:R225S;ENSP00000419767:R225S;ENSP00000377665:R225S;ENSP00000377664:R225S;ENSP00000265956:R225S;ENSP00000377645:R225S;ENSP00000419063:R225S;ENSP00000418747:R225S;ENSP00000297933:R225S;ENSP00000309582:R225S|.	.|ENSP00000265956:R225S|.	G|R|V	+|+|+	2|3|1	0|2|0	GAPVD1|GAPVD1|GAPVD1	127104572|127104572|127104572	0.999000|0.999000|0.999000	0.42202|0.42202|0.42202	0.975000|0.975000|0.975000	0.42487|0.42487|0.42487	0.992000|0.992000|0.992000	0.81027|0.81027|0.81027	0.524000|0.524000|0.524000	0.22940|0.22940|0.22940	-0.508000|-0.508000|-0.508000	0.06540|0.06540|0.06540	-0.150000|-0.150000|-0.150000	0.13652|0.13652|0.13652	GGT|AGG|GTT	.	.		0.423	GAPVD1-014	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000355644.1			T	128064751	G	T	128064751	3	4	323	1	0	0	0	0	1	0	0	0	6247	1252	44	3	681	3	GAPVD1	9	128064751	Missense_Mutation	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10	50621966	128064751	13148680	65	45545										
TET1	80312	hgsc.bcm.edu	37	chr10	70333914	70333914	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	agaccaactgtggtgaatgcActtactgcaagaacagaaag	10	8	0	4			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr10:70333914A>G	ENST00000373644.4	+	2	2028	c.1819A>G	c.(1819-1821)Act>Gct	p.T607A		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	607	Sufficient for binding to genomic CpG islands.				chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						TGGTGAATGCACTTACTGCAA	0.438																																					p.T607A		Atlas-SNP	.											.	TET1	255	.	0			c.A1819G						.						89	95	93					10																	70333914		2203	4300	6503	SO:0001583	missense	80312	exon2			GAATGCACTTACT	AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"leukemia-associated protein with a CXXC domain", "ten-eleven translocation-1"	607790	"CXXC zinc finger 6", "tet oncogene 1"	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.1819A>G	chr10.hg19:g.70333914A>G	ENSP00000362748:p.Thr607Ala	44.0	0.0		37.0	14.0	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	hg19	CCDS7281.1	.	.	.	.	.	.	.	.	.	.	A	18.03	3.531756	0.64972	.	.	ENSG00000138336	ENST00000373644	T	0.07114	3.22	5.27	4.12	0.48240	Zinc finger, CXXC-type (2);	0.401888	0.21188	N	0.078690	T	0.06690	0.0171	N	0.05078	-0.115	0.29792	N	0.833118	P	0.52463	0.953	P	0.49752	0.621	T	0.07385	-1.0775	10	0.54805	T	0.06	.	9.9056	0.41375	0.9207:0.0:0.0793:0.0	.	607	Q8NFU7	TET1_HUMAN	A	607	ENSP00000362748:T607A	ENSP00000362748:T607A	T	+	1	0	TET1	70003920	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.158000	0.77470	1.985000	0.57927	0.383000	0.25322	ACT	.	.		0.438	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		G	70333914	A	G	70333914	3	3	323	1	0	0	0	0	1	0	0	0	15784	159	6	2	1821	2	TET1	10	70333914	Missense_Mutation	SNP	A	TCGA-MI-A75H-01A-11D-A32G-10		70333914	65200833	66	45546										
HTRA1	5654	hgsc.bcm.edu	37	chr10	124273831	124273831	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	tggtggtccgcaggggtaatGaagatatcatgatcacagtg	14	6	2	3			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr10:124273831G>A	ENST00000368984.3	+	9	1527	c.1399G>A	c.(1399-1401)Gaa>Aaa	p.E467K		NM_002775.4	NP_002766.1	Q92743	HTRA1_HUMAN	HtrA serine peptidase 1	467	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(1)|kidney(1)|large_intestine(8)|lung(7)	17		all_neural(114;0.0765)|Lung NSC(174;0.133)|all_lung(145;0.163)|Breast(234;0.238)				CAGGGGTAATGAAGATATCAT	0.498																																					p.E467K		Atlas-SNP	.											.	HTRA1	40	.	0			c.G1399A						.						170	151	157					10																	124273831		2203	4300	6503	SO:0001583	missense	5654	exon9			GGTAATGAAGATA	AF097709	CCDS7630.1	10q26.3	2014-01-28	2005-08-18	2005-08-18	ENSG00000166033	ENSG00000166033		"Serine peptidases / Serine peptidases"	9476	protein-coding gene	gene with protein product		602194	"protease, serine, 11 (IGF binding)"	PRSS11		8977104	Standard	NM_002775		Approved	HtrA, IGFBP5-protease, ARMD7	uc001lgj.2	Q92743	OTTHUMG00000019186	ENST00000368984.3:c.1399G>A	chr10.hg19:g.124273831G>A	ENSP00000357980:p.Glu467Lys	114.0	0.0		110.0	28.0	NM_002775	D3DRE4|Q9UNS5	Missense_Mutation	SNP	ENST00000368984.3	hg19	CCDS7630.1	.	.	.	.	.	.	.	.	.	.	G	14.59	2.581644	0.46006	.	.	ENSG00000166033	ENST00000368984;ENST00000435263;ENST00000420892	D;D	0.82255	-1.59;-1.59	5.48	5.48	0.80851	PDZ/DHR/GLGF (1);	0.000000	0.85682	D	0.000000	T	0.81083	0.4749	L	0.45470	1.425	0.80722	D	1	B	0.26902	0.163	B	0.30716	0.119	T	0.76399	-0.2973	10	0.33141	T	0.24	-7.8902	19.387	0.94560	0.0:0.0:1.0:0.0	.	467	Q92743	HTRA1_HUMAN	K	467;434;208	ENSP00000357980:E467K;ENSP00000412676:E208K	ENSP00000357980:E467K	E	+	1	0	HTRA1	124263821	1.000000	0.71417	0.984000	0.44739	0.165000	0.22458	9.270000	0.95690	2.572000	0.86782	0.655000	0.94253	GAA	.	.		0.498	HTRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128327.1	NM_002775		A	124273831	G	A	124273831	3	1	323	1	0	0	0	0	1	0	0	0	7462	1291	45	3	1433	3	HTRA1	10	124273831	Missense_Mutation	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10	53939917	124273831	11260916	67	45547										
OR52B4	143496	hgsc.bcm.edu	37	chr11	4388835	4388835	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	gtggcaagcatctggagaagGcatgtggaagacagcatgga	16	6	1	2	rs200224336		TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr11:4388835G>A	ENST00000408920.2	-	1	781	c.691C>T	c.(691-693)Cct>Tct	p.P231S		NM_001005161.3	NP_001005161.2	Q8NGK2	O52B4_HUMAN	olfactory receptor, family 52, subfamily B, member 4	231					cognition (GO:0050890)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|endometrium(2)|kidney(3)|large_intestine(7)|lung(15)|skin(2)	31		Medulloblastoma(188;0.0075)|Breast(177;0.0249)|all_neural(188;0.0577)		Epithelial(150;1.57e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0826)|LUSC - Lung squamous cell carcinoma(625;0.19)		TCTGGAGAAGGCATGTGGAAG	0.428																																					p.P231S		Atlas-SNP	.											.	OR52B4	56	.	0			c.C691T						.						115	118	117					11																	4388835		2057	4206	6263	SO:0001583	missense	143496	exon1			GAGAAGGCATGTG	AB065792	CCDS41609.1	11p15.4	2012-08-09			ENSG00000221996	ENSG00000221996		"GPCR / Class A : Olfactory receptors"	15209	protein-coding gene	gene with protein product							Standard	NM_001005161		Approved		uc010qye.2	Q8NGK2	OTTHUMG00000154222	ENST00000408920.2:c.691C>T	chr11.hg19:g.4388835G>A	ENSP00000386160:p.Pro231Ser	91.0	0.0		73.0	31.0	NM_001005161	A6NP68|Q6IFK6	Missense_Mutation	SNP	ENST00000408920.2	hg19	CCDS41609.1	.	.	.	.	.	.	.	.	.	.	G	9.252	1.041090	0.19669	.	.	ENSG00000221996	ENST00000408920	T	0.36878	1.23	5.27	2.22	0.28083	GPCR, rhodopsin-like superfamily (1);	0.193036	0.25052	N	0.033505	T	0.34978	0.0916	L	0.52266	1.64	0.09310	N	1	P	0.41673	0.759	P	0.48304	0.573	T	0.08391	-1.0724	10	0.30078	T	0.28	.	5.455	0.16586	0.0805:0.1412:0.6325:0.1458	.	231	Q8NGK2	O52B4_HUMAN	S	231	ENSP00000386160:P231S	ENSP00000386160:P231S	P	-	1	0	OR52B4	4345411	0.000000	0.05858	0.062000	0.19696	0.004000	0.04260	0.048000	0.14078	0.735000	0.32537	0.561000	0.74099	CCT	.	G|0.999;A|0.001		0.428	OR52B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334449.3	NM_001005161		A	4388835	G	A	4388835	3	1	323	1	0	0	0	0	1	0	0	0	11121	1203	42	3	257	3	OR52B4	11	4388835	Missense_Mutation	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10		4388835	130617681	68	45548										
STK33	65975	hgsc.bcm.edu	37	chr11	8457664	8457664	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	cttctcttctgagcttgccaAaaagggtggttctccacgta	9	11	3	1			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr11:8457664A>G	ENST00000447869.1	-	9	1888	c.970T>C	c.(970-972)Ttg>Ctg	p.L324L	STK33_ENST00000396672.1_Silent_p.L324L|STK33_ENST00000534493.1_Silent_p.L283L|STK33_ENST00000358872.3_Silent_p.L137L|STK33_ENST00000315204.1_Silent_p.L324L|STK33_ENST00000396673.1_Silent_p.L324L|STK33_ENST00000473980.1_5'UTR			Q9BYT3	STK33_HUMAN	serine/threonine kinase 33	324	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|skin(3)	23				Epithelial(150;2.13e-06)|BRCA - Breast invasive adenocarcinoma(625;0.239)		GAGCTTGCCAAAAAGGGTGGT	0.323																																					p.L324L		Atlas-SNP	.											.	STK33	147	.	0			c.T970C						.						46	42	44					11																	8457664		2201	4296	6497	SO:0001819	synonymous_variant	65975	exon11			TTGCCAAAAAGGG	AJ303380	CCDS7789.1, CCDS73253.1, CCDS73254.1	11p15.3	2010-03-10			ENSG00000130413	ENSG00000130413			14568	protein-coding gene	gene with protein product		607670				11738831	Standard	NM_030906		Approved		uc001mgj.1	Q9BYT3	OTTHUMG00000140275	ENST00000447869.1:c.970T>C	chr11.hg19:g.8457664A>G		123.0	0.0		88.0	32.0	NM_030906	Q658S6|Q8NEF5	Silent	SNP	ENST00000447869.1	hg19	CCDS7789.1																																																																																			.	.		0.323	STK33-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276819.2	NM_030906		G	8457664	A	G	8457664	2	3	323	1	0	0	0	0	0	0	0	1	15315	11	1	2		2	STK33	11	8457664	Silent	SNP	A	TCGA-MI-A75H-01A-11D-A32G-10	4068829	8457664	126548852	69	45549										
SBF2	81846	hgsc.bcm.edu	37	chr11	9868632	9868632	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	acaactgtctgctcacccacTgtaaatagacaggacacagc	7	13	2	1			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr11:9868632T>C	ENST00000256190.8	-	23	2944		c.e23-2		RP11-1H15.2_ENST00000533659.1_RNA	NM_030962.3	NP_112224.1	Q86WG5	MTMRD_HUMAN	SET binding factor 2						cell death (GO:0008219)|myelination (GO:0042552)|positive regulation of Rab GTPase activity (GO:0032851)|protein tetramerization (GO:0051262)	membrane (GO:0016020)|vacuolar membrane (GO:0005774)	phosphatase activity (GO:0016791)|phosphatase regulator activity (GO:0019208)|phosphatidylinositol binding (GO:0035091)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(4)|endometrium(8)|kidney(2)|large_intestine(8)|lung(16)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)		GCTCACCCACTGTAAATAGAC	0.438																																					.		Atlas-SNP	.											.	SBF2	146	.	0			c.2807-2A>G						.						153	134	140					11																	9868632		2201	4294	6495	SO:0001630	splice_region_variant	81846	exon24			ACCCACTGTAAAT	AB051553	CCDS31427.1	11p15.3	2014-09-17	2004-11-12	2004-11-12	ENSG00000133812	ENSG00000133812		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins", "DENN/MADD domain containing", "Pleckstrin homology (PH) domain containing"	2135	protein-coding gene	gene with protein product	"myotubularin related 13"	607697	"Charcot-Marie-Tooth neuropathy 4B2 (autosomal recessive, with myelin outfolding)", "DENN/MADD domain containing 7B"	CMT4B2		10644431	Standard	NM_030962		Approved	KIAA1766, MTMR13, DENND7B	uc001mib.2	Q86WG5	OTTHUMG00000165890	ENST00000256190.8:c.2807-2A>G	chr11.hg19:g.9868632T>C		195.0	0.0		159.0	52.0	NM_030962	Q3MJF0|Q68DQ3|Q6P459|Q6PJD1|Q7Z325|Q7Z621|Q86VE2|Q96FE2|Q9C097	Splice_Site	SNP	ENST00000256190.8	hg19	CCDS31427.1	.	.	.	.	.	.	.	.	.	.	T	17.23	3.337280	0.60963	.	.	ENSG00000133812	ENST00000256190	.	.	.	6.03	6.03	0.97812	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5582	0.84512	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	SBF2	9825208	1.000000	0.71417	0.984000	0.44739	0.502000	0.33828	7.798000	0.85924	2.308000	0.77769	0.533000	0.62120	.	.	.		0.438	SBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386911.2	NM_030962	Intron	C	9868632	T	C	9868632	5	2	323	1	0	0	0	0	0	0	1	0	13874	1594	55	2	2816	2	SBF2	11	9868632	Splice_Site	SNP	T	TCGA-MI-A75H-01A-11D-A32G-10	1410968	9868632	125137884	70	45550										
SAAL1	113174	hgsc.bcm.edu	37	chr11	18105155	18105155	+	Frame_Shift_Del	DEL	T	T	-													0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	agattttcaagtggaaatcaTcttgggttaaatcagtcctt							TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr11:18105155delT	ENST00000524803.1	-	10	1215	c.1166delA	c.(1165-1167)gatfs	p.D390fs	SAAL1_ENST00000300013.4_Frame_Shift_Del_p.D389fs|SAAL1_ENST00000529318.1_Frame_Shift_Del_p.D392fs			Q96ER3	SAAL1_HUMAN	serum amyloid A-like 1	390										breast(2)|large_intestine(5)|lung(8)	15						GTGGAAATCATCTTGGGTTAA	0.338																																					p.D389fs		Atlas-Indel,Pindel	.											.	SAAL1	34	.	0			c.1167delT						.						120	120	120					11																	18105155		2199	4293	6492	SO:0001589	frameshift_variant	113174	exon10			.	AK123457	CCDS31439.1	11p15.1	2005-10-28			ENSG00000166788	ENSG00000166788			25158	protein-coding gene	gene with protein product							Standard	NM_138421		Approved	FLJ41463	uc001mnq.3	Q96ER3	OTTHUMG00000166428	ENST00000524803.1:c.1166delA	chr11.hg19:g.18105155delT	ENSP00000432487:p.Asp390fs	193.0	0.0		199.0	66.0	NM_138421	A6NH05	Frame_Shift_Del	DEL	ENST00000524803.1	hg19	CCDS31439.1																																																																																			.	.		0.338	SAAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389728.1	NM_138421		-	18105155	T	-	18105155	7	5	323	1	0	1	0	1	0	0	0	0	13816	1435	50	0	270	0	SAAL1	11	18105155	Frame_Shift_Del	DEL	T	TCGA-MI-A75H-01A-11D-A32G-10	8236523	18105155	116901361	71	45551										
NRXN2	9379	hgsc.bcm.edu	37	chr11	64375122	64375122	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	ctcggtggttcattttgcccGccggcaggttgggggccggg	18	11	1	0			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr11:64375122G>T	ENST00000377551.1	-	22	4896	c.4685C>A	c.(4684-4686)gCg>gAg	p.A1562E	NRXN2_ENST00000301894.2_Missense_Mutation_p.A516E|NRXN2_ENST00000377559.3_Missense_Mutation_p.A1492E|NRXN2_ENST00000409571.1_Missense_Mutation_p.A1555E|NRXN2_ENST00000265459.6_Missense_Mutation_p.A1562E			Q9P2S2	NRX2A_HUMAN	neurexin 2	1562					adult behavior (GO:0030534)|gephyrin clustering (GO:0097116)|neuroligin clustering (GO:0097118)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	calcium channel regulator activity (GO:0005246)|cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|neuroligin family protein binding (GO:0097109)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	71						CATTTTGCCCGCCGGCAGGTT	0.741																																					p.A1562E		Atlas-SNP	.											NRXN2_ENST00000301894,caecum,carcinoma,0,2	NRXN2	247	.	0			c.C4685A						.						5	7	6					11																	64375122		2014	4000	6014	SO:0001583	missense	9379	exon23			TTGCCCGCCGGCA		CCDS8077.1, CCDS31597.1, CCDS8078.1	11q13	2008-07-18			ENSG00000110076	ENSG00000110076			8009	protein-coding gene	gene with protein product	"neurexin II"	600566				1621094	Standard	NM_015080		Approved		uc021qkw.1	P58401	OTTHUMG00000045214	ENST00000377551.1:c.4685C>A	chr11.hg19:g.64375122G>T	ENSP00000366774:p.Ala1562Glu	32.0	0.0		32.0	2.0	NM_015080	A7E2C1|Q9Y2D6	Missense_Mutation	SNP	ENST00000377551.1	hg19	CCDS8077.1	.	.	.	.	.	.	.	.	.	.	G	12.87	2.068258	0.36470	.	.	ENSG00000110076	ENST00000301894;ENST00000377551;ENST00000377559;ENST00000265459;ENST00000345863;ENST00000409571	T;T;T;T;T	0.68331	0.28;-0.29;-0.32;-0.29;-0.19	3.41	2.48	0.30137	.	0.000000	0.42053	U	0.000779	T	0.76421	0.3985	M	0.65498	2.005	0.51767	D	0.999932	P;P;D;D	0.89917	0.761;0.68;1.0;1.0	B;B;D;D	0.97110	0.251;0.35;0.997;1.0	T	0.75903	-0.3153	10	0.72032	D	0.01	.	8.4335	0.32773	0.1221:0.0:0.8779:0.0	.	1492;1562;1308;516	Q9P2S2-2;Q9P2S2;E7EV67;P58401	.;NRX2A_HUMAN;.;NRX2B_HUMAN	E	516;1562;1492;1562;1492;1555	ENSP00000301894:A516E;ENSP00000366774:A1562E;ENSP00000366782:A1492E;ENSP00000265459:A1562E;ENSP00000386416:A1555E	ENSP00000265459:A1562E	A	-	2	0	NRXN2	64131698	1.000000	0.71417	0.951000	0.38953	0.337000	0.28794	7.230000	0.78097	0.773000	0.33404	0.313000	0.20887	GCG	.	.		0.741	NRXN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104967.3	NM_015080		T	64375122	G	T	64375122	3	4	323	1	0	0	0	0	1	0	0	0	10675	1087	38	1	457	1	NRXN2	11	64375122	Missense_Mutation	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10	46269967	64375122	70631394	72	45552										
ODZ4	26011	hgsc.bcm.edu	37	chr11	78413217	78413217	+	Frame_Shift_Del	DEL	G	G	-													0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	atcagtctcagcaatatacaGgaccccattgtgtgaaacag					rs374057696		TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr11:78413217delG	ENST00000278550.7	-	28	4903	c.4441delC	c.(4441-4443)ctgfs	p.L1481fs		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	1481					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										GCAATATACAGGACCCCATTG	0.557																																					p.L1481fs		Pindel	.											.	.	.	.	0			c.4442delT						.						62	64	63					11																	78413217		2030	4189	6219	SO:0001589	frameshift_variant	26011	exon28			.	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"odz, odd Oz/ten-m homolog 4 (Drosophila)"	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.4441delC	chr11.hg19:g.78413217delG	ENSP00000278550:p.Leu1481fs	79.0	0.0		83.0	21.0	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Frame_Shift_Del	DEL	ENST00000278550.7	hg19	CCDS44688.1																																																																																			.	.		0.557	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			-	78413217	G	-	78413217	7	5	323	1	0	1	0	1	0	0	0	0	10846	991	35	0	3896	0	ODZ4	11	78413217	Frame_Shift_Del	DEL	G	TCGA-MI-A75H-01A-11D-A32G-10	14038095	78413217	56593299	73	45553										
TRPC6	7225	hgsc.bcm.edu	37	chr11	101375213	101375213	+	Frame_Shift_Del	DEL	C	C	-													0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	aatagctagaagcaaagcatCcccaactcgagagaggtttt							TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr11:101375213delC	ENST00000344327.3	-	2	911	c.487delG	c.(487-489)gatfs	p.D163fs	TRPC6_ENST00000526713.1_5'Flank|TRPC6_ENST00000532133.1_Frame_Shift_Del_p.D163fs|TRPC6_ENST00000360497.4_Frame_Shift_Del_p.D163fs|TRPC6_ENST00000348423.4_Frame_Shift_Del_p.D163fs	NM_004621.5	NP_004612.2	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel, subfamily C, member 6	163					aging (GO:0007568)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|ion transmembrane transport (GO:0034220)|platelet activation (GO:0030168)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ion transmembrane transporter activity (GO:0032414)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(14)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)		BRCA - Breast invasive adenocarcinoma(274;0.0442)		AGCAAAGCATCCCCAACTCGA	0.463																																					p.D163fs	Colon(166;1315 1927 11094 12848 34731)	Atlas-Indel,Pindel	.											.	TRPC6	132	.	0			c.488delA						.						63	63	63					11																	101375213		2203	4299	6502	SO:0001589	frameshift_variant	7225	exon2			.	AJ006276	CCDS8311.1	11q22.1	2014-02-04				ENSG00000137672		"Voltage-gated ion channels / Transient receptor potential cation channels"	12338	protein-coding gene	gene with protein product		603652	"focal segmental glomerulosclerosis 2"	FSGS2		9925922, 16382100, 15879175	Standard	NM_004621		Approved	TRP6	uc001pgk.4	Q9Y210		ENST00000344327.3:c.487delG	chr11.hg19:g.101375213delC	ENSP00000340913:p.Asp163fs	67.0	0.0		69.0	21.0	NM_004621	Q52M59|Q9HCW3|Q9NQA8|Q9NQA9	Frame_Shift_Del	DEL	ENST00000344327.3	hg19	CCDS8311.1																																																																																			.	.		0.463	TRPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394770.1	NM_004621		-	101375213	C	-	101375213	7	5	323	1	0	1	0	1	0	0	0	0	16598	855	30	0	2356	0	TRPC6	11	101375213	Frame_Shift_Del	DEL	C	TCGA-MI-A75H-01A-11D-A32G-10	22961996	101375213	33631303	74	45554										
KCNA1	3736	hgsc.bcm.edu	37	chr12	5020766	5020766	+	Frame_Shift_Del	DEL	C	C	-													0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	aaacgcatgcgctacttcgaCcccctgaggaacgagtactt							TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr12:5020766delC	ENST00000382545.3	+	2	1329	c.222delC	c.(220-222)gacfs	p.D74fs	KCNA1_ENST00000543874.2_Intron	NM_000217.2	NP_000208.2	Q09470	KCNA1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 1 (episodic ataxia with myokymia)	74					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|dendrite (GO:0030425)|juxtaparanode region of axon (GO:0044224)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|potassium ion transmembrane transporter activity (GO:0015079)			NS(1)|breast(3)|cervix(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(23)|ovary(3)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63					Amitriptyline(DB00321)|Dalfampridine(DB06637)|Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Nifedipine(DB01115)|Sevoflurane(DB01236)	GCTACTTCGACCCCCTGAGGA	0.632																																					p.D74fs		Atlas-Indel,Pindel	.											.	KCNA1	112	.	0			c.221delA						.						67	68	67					12																	5020766		2203	4300	6503	SO:0001589	frameshift_variant	3736	exon2			.	L02750	CCDS8535.1	12p13	2012-07-05			ENSG00000111262	ENSG00000111262		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6218	protein-coding gene	gene with protein product		176260		AEMK		1349297, 8821794, 16382104	Standard	NM_000217		Approved	Kv1.1, RBK1, HUK1, MBK1	uc001qnh.3	Q09470	OTTHUMG00000044398	ENST00000382545.3:c.222delC	chr12.hg19:g.5020766delC	ENSP00000371985:p.Asp74fs	61.0	0.0		64.0	22.0	NM_000217	A6NM83|Q3MIQ9	Frame_Shift_Del	DEL	ENST00000382545.3	hg19	CCDS8535.1																																																																																			.	.		0.632	KCNA1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103343.2	NM_000217		-	5020766	C	-	5020766	7	5	323	1	0	1	0	1	0	0	0	0	8010	506	18	0	224	0	KCNA1	12	5020766	Frame_Shift_Del	DEL	C	TCGA-MI-A75H-01A-11D-A32G-10		5020766	128831129	75	45555										
AICDA	57379	hgsc.bcm.edu	37	chr12	8759514	8759514	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	ggatgtagcactgtcacgccTcttcactacgtagcacaggt	10	12	3	0			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr12:8759514T>A	ENST00000229335.6	-	2	206	c.103A>T	c.(103-105)Agg>Tgg	p.R35W	AICDA_ENST00000537228.1_Missense_Mutation_p.R35W	NM_020661.2	NP_065712.1	Q9GZX7	AICDA_HUMAN	activation-induced cytidine deaminase	35					B cell differentiation (GO:0030183)|cellular response to lipopolysaccharide (GO:0071222)|DNA demethylation (GO:0080111)|isotype switching (GO:0045190)|mRNA processing (GO:0006397)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|somatic diversification of immunoglobulins (GO:0016445)|somatic hypermutation of immunoglobulin genes (GO:0016446)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cytidine deaminase activity (GO:0004126)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(4)|ovary(2)|pancreas(1)	16	Lung SC(5;0.184)					CTGTCACGCCTCTTCACTACG	0.463																																					p.R35W	GBM(62;896 1067 5527 26594 30137)	Atlas-SNP	.											.	AICDA	37	.	0			c.A103T						.						90	86	88					12																	8759514		1971	4148	6119	SO:0001583	missense	57379	exon2			CACGCCTCTTCAC	AB040430	CCDS41747.1	12p13	2014-09-17			ENSG00000111732	ENSG00000111732		"Apolipoprotein B mRNA editing enzymes"	13203	protein-coding gene	gene with protein product		605257					Standard	NM_020661		Approved	HIGM2, CDA2, ARP2, AID	uc001qur.2	Q9GZX7	OTTHUMG00000168676	ENST00000229335.6:c.103A>T	chr12.hg19:g.8759514T>A	ENSP00000229335:p.Arg35Trp	81.0	0.0		47.0	14.0	NM_020661	Q6QJ81|Q8NFC1	Missense_Mutation	SNP	ENST00000229335.6	hg19	CCDS41747.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.48|19.48	3.834909|3.834909	0.71373|0.71373	.|.	.|.	ENSG00000111732|ENSG00000111732	ENST00000543081;ENST00000544516;ENST00000545512|ENST00000229335;ENST00000537228	.|D;D	.|0.85088	.|-1.94;-1.94	5.36|5.36	2.31|2.31	0.28768|0.28768	.|APOBEC-like, N-terminal (1);	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	D|D	0.86560|0.86560	0.5962|0.5962	L|L	0.41236|0.41236	1.265|1.265	0.58432|0.58432	D|D	0.999998|0.999998	.|D;D;D	.|0.64830	.|0.99;0.994;0.99	.|P;P;P	.|0.60345	.|0.873;0.873;0.873	D|D	0.85691|0.85691	0.1307|0.1307	6|10	.|0.72032	.|D	.|0.01	-21.6095|-21.6095	13.1484|13.1484	0.59477|0.59477	0.0:0.0:0.5278:0.4722|0.0:0.0:0.5278:0.4722	.|.	.|35;35;35	.|Q9GZX7;Q6QJ80;Q6QJ81	.|AICDA_HUMAN;.;.	S|W	33|35	.|ENSP00000229335:R35W;ENSP00000445691:R35W	.|ENSP00000229335:R35W	R|R	-|-	3|1	2|2	AICDA|AICDA	8650781|8650781	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.943000|0.943000	0.58893|0.58893	2.452000|2.452000	0.44961|0.44961	0.151000|0.151000	0.19162|0.19162	0.383000|0.383000	0.25322|0.25322	AGA|AGG	.	.		0.463	AICDA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400575.1	NM_020661		A	8759514	T	A	8759514	3	1	323	1	0	0	0	0	1	0	0	0	422	1550	54	4	509	4	AICDA	12	8759514	Missense_Mutation	SNP	T	TCGA-MI-A75H-01A-11D-A32G-10	3738748	8759514	125092381	76	45556										
BIN2	51411	hgsc.bcm.edu	37	chr12	51693401	51693401	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	tttgttttaccttggcagtcTtggcctcatctttcttcttg	7	10	5	0			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr12:51693401T>A	ENST00000267012.4	-	6	567	c.506A>T	c.(505-507)aAg>aTg	p.K169M	BIN2_ENST00000452142.2_Missense_Mutation_p.K137M|BIN2_ENST00000544402.1_Missense_Mutation_p.K143M|BIN2_ENST00000604560.1_Missense_Mutation_p.K142M	NM_016293.2	NP_057377.2	Q9UBW5	BIN2_HUMAN	bridging integrator 2	169	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				cell chemotaxis (GO:0060326)|membrane tubulation (GO:0097320)|phagocytosis, engulfment (GO:0006911)|podosome assembly (GO:0071800)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|podosome (GO:0002102)	phospholipid binding (GO:0005543)			NS(2)|breast(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(3)	31						CTTGGCAGTCTTGGCCTCATC	0.517																																					p.K169M		Atlas-SNP	.											.	BIN2	58	.	0			c.A506T						.						144	146	146					12																	51693401		2203	4300	6503	SO:0001583	missense	51411	exon6			GCAGTCTTGGCCT	AF146531	CCDS8811.1	12q13.13	2012-01-23			ENSG00000110934	ENSG00000110934			1053	protein-coding gene	gene with protein product		605936				10903846	Standard	XM_005268957		Approved	BRAP-1	uc001ryg.3	Q9UBW5		ENST00000267012.4:c.506A>T	chr12.hg19:g.51693401T>A	ENSP00000267012:p.Lys169Met	58.0	0.0		40.0	13.0	NM_016293	Q86VV0|Q9NWK4|Q9UKN4	Missense_Mutation	SNP	ENST00000267012.4	hg19	CCDS8811.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.238883	0.79800	.	.	ENSG00000110934	ENST00000452142;ENST00000267012;ENST00000544402	T;T;T	0.65916	-0.18;-0.18;-0.18	4.87	4.87	0.63330	BAR (3);	0.000000	0.85682	D	0.000000	T	0.80105	0.4562	M	0.85859	2.78	0.54753	D	0.999987	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.993;0.996;0.994	D	0.83437	0.0041	10	0.87932	D	0	-16.4707	12.761	0.57363	0.0:0.0:0.0:1.0	.	143;137;169	F5H0W4;Q9UBW5-2;Q9UBW5	.;.;BIN2_HUMAN	M	137;169;143	ENSP00000410217:K137M;ENSP00000267012:K169M;ENSP00000445874:K143M	ENSP00000267012:K169M	K	-	2	0	BIN2	49979668	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	4.431000	0.59915	2.180000	0.69256	0.533000	0.62120	AAG	.	.		0.517	BIN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000469800.1			A	51693401	T	A	51693401	3	1	323	1	0	0	0	0	1	0	0	0	1433	1609	56	4	1223	4	BIN2	12	51693401	Missense_Mutation	SNP	T	TCGA-MI-A75H-01A-11D-A32G-10	42933887	51693401	82158494	77	45557										
TSPAN31	6302	hgsc.bcm.edu	37	chr12	58140038	58140038	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	ggctattaaccgaagcaaacAggtaagacagtaccctttca	8	10	1	1			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr12:58140038A>C	ENST00000257910.3	+	3	585	c.311A>C	c.(310-312)cAg>cCg	p.Q104P	TSPAN31_ENST00000547992.1_Intron|TSPAN31_ENST00000547472.1_Intron|CDK4_ENST00000551888.1_5'Flank|TSPAN31_ENST00000553221.1_3'UTR	NM_005981.3	NP_005972.1	Q12999	TSN31_HUMAN	tetraspanin 31	104					positive regulation of cell proliferation (GO:0008284)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				endometrium(1)|kidney(1)|lung(5)	7	all_cancers(7;4.96e-69)|Lung NSC(6;5.5e-25)|all_lung(6;3.87e-23)|all_epithelial(6;1.66e-15)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)		GBM - Glioblastoma multiforme(5;4.21e-120)|all cancers(5;3.75e-83)|BRCA - Breast invasive adenocarcinoma(9;0.0294)			CGAAGCAAACAGGTAAGACAG	0.403																																					p.Q104P		Atlas-SNP	.											.	TSPAN31	20	.	0			c.A311C						.						213	192	199					12																	58140038		2202	4300	6502	SO:0001630	splice_region_variant	6302	exon3			GCAAACAGGTAAG		CCDS8952.1	12q13-q14	2013-02-14	2005-08-16	2005-08-16		ENSG00000135452		"Tetraspanins"	10539	protein-coding gene	gene with protein product		181035	"sarcoma amplified sequence"	SAS			Standard	NM_005981		Approved		uc001spt.3	Q12999		ENST00000257910.3:c.312+1A>C	chr12.hg19:g.58140038A>C		134.0	0.0		118.0	40.0	NM_005981	O00577|Q53X76	Missense_Mutation	SNP	ENST00000257910.3	hg19	CCDS8952.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.446890	0.84101	.	.	ENSG00000135452	ENST00000257910;ENST00000552816;ENST00000548167	T	0.79352	-1.26	4.82	4.82	0.62117	.	0.000000	0.85682	D	0.000000	D	0.88058	0.6335	M	0.84948	2.725	0.80722	D	1	D	0.69078	0.997	D	0.81914	0.995	D	0.88178	0.2869	10	0.39692	T	0.17	-2.103	13.804	0.63218	1.0:0.0:0.0:0.0	.	104	Q12999	TSN31_HUMAN	P	104;26;26	ENSP00000257910:Q104P	ENSP00000257910:Q104P	Q	+	2	0	TSPAN31	56426305	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	8.356000	0.90085	2.152000	0.67230	0.455000	0.32223	CAG	.	.		0.403	TSPAN31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408778.1		Missense_Mutation	C	58140038	A	C	58140038	5	2	323	1	0	0	0	0	0	0	1	0	16661	202	7	5	321	5	TSPAN31	12	58140038	Splice_Site	SNP	A	TCGA-MI-A75H-01A-11D-A32G-10	6446637	58140038	75711857	78	45558										
LRRIQ1	84125	hgsc.bcm.edu	37	chr12	85450884	85450884	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	gttagaagaaagagacctgtGaaatgcccagccaacatgac	10	9	0	5			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr12:85450884G>A	ENST00000393217.2	+	8	2374	c.2313G>A	c.(2311-2313)gtG>gtA	p.V771V		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	771										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		AGAGACCTGTGAAATGCCCAG	0.358																																					p.V771V		Atlas-SNP	.											LRRIQ1_ENST00000393217,NS,carcinoma,0,2	LRRIQ1	512	.	0			c.G2313A						.						110	126	120					12																	85450884		2203	4300	6503	SO:0001819	synonymous_variant	84125	exon8			ACCTGTGAAATGC	AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.2313G>A	chr12.hg19:g.85450884G>A		193.0	0.0		155.0	61.0	NM_001079910	Q567P4|Q9BS17|Q9HA36	Silent	SNP	ENST00000393217.2	hg19	CCDS41816.1																																																																																			.	.		0.358	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165		A	85450884	G	A	85450884	2	1	323	1	0	0	0	0	0	0	0	1	9038	1277	45	3		3	LRRIQ1	12	85450884	Silent	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10	27310846	85450884	48401011	79	45559										
UHRF1BP1L	23074	hgsc.bcm.edu	37	chr12	100452950	100452950	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	tcatcccttcataatctatcCaaaattgagaaaagtacaca	3	10	3	1			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr12:100452950C>T	ENST00000279907.7	-	14	2317	c.2105G>A	c.(2104-2106)tGg>tAg	p.W702*	UHRF1BP1L_ENST00000545232.2_Nonsense_Mutation_p.W352*	NM_015054.1	NP_055869.1	A0JNW5	UH1BL_HUMAN	UHRF1 binding protein 1-like	702										breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(21)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	50						ATAATCTATCCAAAATTGAGA	0.358																																					p.W702X		Atlas-SNP	.											.	UHRF1BP1L	144	.	0			c.G2105A						.						77	84	81					12																	100452950		2203	4300	6503	SO:0001587	stop_gained	23074	exon14			TCTATCCAAAATT		CCDS31882.1, CCDS31883.1	12q23.1	2011-04-15	2008-08-15		ENSG00000111647	ENSG00000111647			29102	protein-coding gene	gene with protein product							Standard	XM_005268737		Approved	KIAA0701	uc001tgq.3	A0JNW5	OTTHUMG00000170195	ENST00000279907.7:c.2105G>A	chr12.hg19:g.100452950C>T	ENSP00000279907:p.Trp702*	135.0	0.0		135.0	46.0	NM_015054	A0PJE5|O75183|Q8NDL1|Q96C30|Q9BTS5|Q9H0F1	Nonsense_Mutation	SNP	ENST00000279907.7	hg19	CCDS31882.1	.	.	.	.	.	.	.	.	.	.	C	38	7.178588	0.98118	.	.	ENSG00000111647	ENST00000279907;ENST00000545232	.	.	.	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.22706	T	0.39	-4.5418	20.0118	0.97458	0.0:1.0:0.0:0.0	.	.	.	.	X	702;352	.	ENSP00000279907:W702X	W	-	2	0	UHRF1BP1L	98977081	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.625000	0.83145	2.742000	0.94016	0.650000	0.86243	TGG	.	.		0.358	UHRF1BP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407875.1	NM_001006947		T	100452950	C	T	100452950	4	4	323	1	0	0	0	0	0	1	0	0	16984	595	21	3	2321	3	UHRF1BP1L	12	100452950	Nonsense_Mutation	SNP	C	TCGA-MI-A75H-01A-11D-A32G-10	15002066	100452950	33398945	80	45560										
TMEM132B	114795	hgsc.bcm.edu	37	chr12	126068404	126068404	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	ctctcctgtttaggacaccgAggttttgaacactgccattc	8	12	1	1			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr12:126068404A>T	ENST00000299308.3	+	5	1294	c.1286A>T	c.(1285-1287)gAg>gTg	p.E429V		NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	429						integral component of membrane (GO:0016021)				NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		TAGGACACCGAGGTTTTGAAC	0.547																																					p.E429V		Atlas-SNP	.											.	TMEM132B	207	.	0			c.A1286T						.						221	217	218					12																	126068404		1981	4130	6111	SO:0001583	missense	114795	exon5			ACACCGAGGTTTT	AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.1286A>T	chr12.hg19:g.126068404A>T	ENSP00000299308:p.Glu429Val	43.0	0.0		45.0	15.0	NM_052907	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Missense_Mutation	SNP	ENST00000299308.3	hg19	CCDS41859.1	.	.	.	.	.	.	.	.	.	.	A	16.47	3.132318	0.56828	.	.	ENSG00000139364	ENST00000299308	T	0.17854	2.25	4.83	4.83	0.62350	.	0.000000	0.37219	U	0.002196	T	0.41811	0.1175	M	0.76574	2.34	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.39881	-0.9592	10	0.87932	D	0	.	13.3917	0.60827	1.0:0.0:0.0:0.0	.	429	Q14DG7	T132B_HUMAN	V	429	ENSP00000299308:E429V	ENSP00000299308:E429V	E	+	2	0	TMEM132B	124634357	1.000000	0.71417	0.994000	0.49952	0.126000	0.20510	7.988000	0.88194	1.800000	0.52685	0.533000	0.62120	GAG	.	.		0.547	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907		T	126068404	A	T	126068404	3	4	323	1	0	0	0	0	1	0	0	0	16061	304	11	4	1304	4	TMEM132B	12	126068404	Missense_Mutation	SNP	A	TCGA-MI-A75H-01A-11D-A32G-10	25615454	126068404	7783491	81	45561										
NOC4L	79050	hgsc.bcm.edu	37	chr12	132636050	132636050	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	cacctccccgcctacctggtGgccgccttcgccaagcggct	10	20	0	0	rs375514217		TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr12:132636050G>A	ENST00000330579.1	+	12	1136	c.1095G>A	c.(1093-1095)gtG>gtA	p.V365V	NOC4L_ENST00000538784.1_5'UTR|NOC4L_ENST00000535343.1_3'UTR	NM_024078.1	NP_076983.1	Q9BVI4	NOC4L_HUMAN	nucleolar complex associated 4 homolog (S. cerevisiae)	365					rRNA processing (GO:0006364)	integral component of membrane (GO:0016021)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(2)|large_intestine(1)|lung(7)|skin(2)	14	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.2e-08)|Epithelial(86;3.34e-07)|all cancers(50;1.97e-05)		CCTACCTGGTGGCCGCCTTCG	0.721																																					p.V365V		Atlas-SNP	.											.	NOC4L	31	.	0			c.G1095A						.	G		0,4358		0,0,2179	14	17	16		1095	1.3	1	12		16	1,8553		0,1,4276	no	coding-synonymous	NOC4L	NM_024078.1		0,1,6455	AA,AG,GG		0.0117,0.0,0.0077		365/517	132636050	1,12911	2179	4277	6456	SO:0001819	synonymous_variant	79050	exon12			CCTGGTGGCCGCC		CCDS9277.1	12q24.33	2011-08-12			ENSG00000184967	ENSG00000184967			28461	protein-coding gene	gene with protein product		612819				12446671	Standard	NM_024078		Approved	MGC3162, NET49, UTP19	uc001ujz.1	Q9BVI4	OTTHUMG00000168260	ENST00000330579.1:c.1095G>A	chr12.hg19:g.132636050G>A		26.0	0.0		23.0	11.0	NM_024078	Q8N2S5|Q96I14	Silent	SNP	ENST00000330579.1	hg19	CCDS9277.1																																																																																			.	.		0.721	NOC4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398999.1	NM_024078		A	132636050	G	A	132636050	2	1	323	1	0	0	0	0	0	0	0	1	10524	1335	47	3		3	NOC4L	12	132636050	Silent	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10	6567646	132636050	1215845	82	45562										
NALCN	259232	hgsc.bcm.edu	37	chr13	101735199	101735199	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	gtgaaaacaactgacattgtTgccaaaggtacggtcaccgg	11	9	1	2			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr13:101735199T>G	ENST00000251127.6	-	33	3807	c.3726A>C	c.(3724-3726)gcA>gcC	p.A1242A		NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	1242					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					CTGACATTGTTGCCAAAGGTA	0.507																																					p.A1242A		Atlas-SNP	.											.	NALCN	431	.	0			c.A3726C						.						129	117	121					13																	101735199		2203	4300	6503	SO:0001819	synonymous_variant	259232	exon33			CATTGTTGCCAAA	AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"Ion channels / Sodium leak channels, non-selective"	19082	protein-coding gene	gene with protein product		611549	"voltage gated channel like 1"	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.3726A>C	chr13.hg19:g.101735199T>G		66.0	0.0		73.0	32.0	NM_052867	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Silent	SNP	ENST00000251127.6	hg19	CCDS9498.1																																																																																			.	.		0.507	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867		G	101735199	T	G	101735199	2	3	323	1	0	0	0	0	0	0	0	1	10157	1799	63	5		5	NALCN	13	101735199	Silent	SNP	T	TCGA-MI-A75H-01A-11D-A32G-10		101735199	13434679	83	45563										
FAM179B	23116	hgsc.bcm.edu	37	chr14	45521641	45521641	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	tttttcaaatactcacaggtAttatggtcgaaagatgctgt	8	6	2	1			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr14:45521641A>G	ENST00000361577.3	+	14	4371	c.4157A>G	c.(4156-4158)tAt>tGt	p.Y1386C	FAM179B_ENST00000361462.2_Missense_Mutation_p.Y1439C|FAM179B_ENST00000382233.2_3'UTR	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	1386										endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						ACTCACAGGTATTATGGTCGA	0.318																																					p.Y1386C		Atlas-SNP	.											.	FAM179B	115	.	0			c.A4157G						.						54	54	54					14																	45521641		2202	4295	6497	SO:0001583	missense	23116	exon14			ACAGGTATTATGG	AB007883	CCDS9681.1	14q21.3	2008-07-21	2008-07-21	2008-07-21	ENSG00000198718	ENSG00000198718			19959	protein-coding gene	gene with protein product			"KIAA0423"	KIAA0423			Standard	XM_005267451		Approved		uc001wvv.3	Q9Y4F4	OTTHUMG00000140264	ENST00000361577.3:c.4157A>G	chr14.hg19:g.45521641A>G	ENSP00000355045:p.Tyr1386Cys	75.0	0.0		53.0	17.0	NM_015091	Q68D66|Q6PG27	Missense_Mutation	SNP	ENST00000361577.3	hg19	CCDS9681.1	.	.	.	.	.	.	.	.	.	.	A	14.98	2.698372	0.48307	.	.	ENSG00000198718	ENST00000361577;ENST00000361462	T;T	0.23147	1.92;1.92	4.92	3.77	0.43336	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.46347	0.1388	M	0.70275	2.135	0.80722	D	1	D;D	0.89917	0.964;1.0	P;D	0.91635	0.757;0.999	T	0.36866	-0.9730	10	0.54805	T	0.06	-11.5931	9.2229	0.37388	0.7109:0.0:0.0:0.289	.	1439;1386	G3XAE9;Q9Y4F4	.;F179B_HUMAN	C	1386;1439	ENSP00000355045:Y1386C;ENSP00000354917:Y1439C	ENSP00000354917:Y1439C	Y	+	2	0	FAM179B	44591391	1.000000	0.71417	1.000000	0.80357	0.723000	0.41478	4.595000	0.61048	0.812000	0.34326	-0.757000	0.03467	TAT	.	.		0.318	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781		G	45521641	A	G	45521641	3	3	323	1	0	0	0	0	1	0	0	0	5511	449	16	2	4211	2	FAM179B	14	45521641	Missense_Mutation	SNP	A	TCGA-MI-A75H-01A-11D-A32G-10		45521641	61827899	84	45564										
PYGL	5836	hgsc.bcm.edu	37	chr14	51390766	51390766	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	caggcagcatgaattctgggCgggacttctcccaagggttt	13	10	2	1			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr14:51390766C>A	ENST00000216392.7	-	5	913	c.581G>T	c.(580-582)cGc>cTc	p.R194L	PYGL_ENST00000532462.1_Missense_Mutation_p.R194L|PYGL_ENST00000544180.2_Missense_Mutation_p.R160L	NM_002863.4	NP_002854.3	P06737	PYGL_HUMAN	phosphorylase, glycogen, liver	194					5-phosphoribose 1-diphosphate biosynthetic process (GO:0006015)|carbohydrate metabolic process (GO:0005975)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|necroptotic process (GO:0070266)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	AMP binding (GO:0016208)|ATP binding (GO:0005524)|bile acid binding (GO:0032052)|drug binding (GO:0008144)|glucose binding (GO:0005536)|glycogen phosphorylase activity (GO:0008184)|protein homodimerization activity (GO:0042803)|purine nucleobase binding (GO:0002060)|pyridoxal phosphate binding (GO:0030170)|vitamin binding (GO:0019842)	p.R194L(1)		NS(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)|skin(3)	25	all_epithelial(31;0.00825)|Breast(41;0.148)				Adenosine monophosphate(DB00131)	GAATTCTGGGCGGGACTTCTC	0.438																																					p.R194L		Atlas-SNP	.											PYGL,NS,carcinoma,0,1	PYGL	77	.	1	Substitution - Missense(1)	lung(1)	c.G581T						.						153	142	146					14																	51390766		2203	4300	6503	SO:0001583	missense	5836	exon5			TCTGGGCGGGACT		CCDS32080.1, CCDS53894.1	14q11.2-q24.3	2013-03-01	2008-07-31		ENSG00000100504	ENSG00000100504	2.4.1.1	"Glycogen phosphorylases"	9725	protein-coding gene	gene with protein product	"Hers disease", "glycogen storage disease type VI", "glycogen phosphorylase, liver form"	613741	"phosphorylase, glycogen; liver"			2877458	Standard	NM_002863		Approved		uc001wyu.3	P06737	OTTHUMG00000166596	ENST00000216392.7:c.581G>T	chr14.hg19:g.51390766C>A	ENSP00000216392:p.Arg194Leu	140.0	0.0		110.0	34.0	NM_002863	A6NDQ4|B4DUB7|F5H816|O60567|O60752|O60913|Q501V9|Q641R5|Q96G82	Missense_Mutation	SNP	ENST00000216392.7	hg19	CCDS32080.1	.	.	.	.	.	.	.	.	.	.	C	36	5.804547	0.96967	.	.	ENSG00000100504	ENST00000532462;ENST00000544180;ENST00000216392	D;D;D	0.94417	-3.42;-3.42;-3.42	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.98570	0.9522	H	0.98068	4.14	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.996	D	0.98903	1.0777	10	0.72032	D	0.01	-17.3855	19.8676	0.96824	0.0:1.0:0.0:0.0	.	160;216;194	F5H816;Q6P1L4;P06737	.;.;PYGL_HUMAN	L	194;160;194	ENSP00000431657:R194L;ENSP00000443787:R160L;ENSP00000216392:R194L	ENSP00000216392:R194L	R	-	2	0	PYGL	50460516	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.776000	0.85560	2.941000	0.99782	0.655000	0.94253	CGC	.	.		0.438	PYGL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390654.3	NM_002863		A	51390766	C	A	51390766	3	1	323	1	0	0	0	0	1	0	0	0	12876	768	27	1	2026	1	PYGL	14	51390766	Missense_Mutation	SNP	C	TCGA-MI-A75H-01A-11D-A32G-10	5869125	51390766	55958774	85	45565										
SFRS5	6430	hgsc.bcm.edu	37	chr14	70237967	70237967	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	ttcctctaggtctcgtagccGatcccgttcccgtagtcgca	9	15	2	0			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr14:70237967G>T	ENST00000553521.1	+	9	2061	c.608G>T	c.(607-609)cGa>cTa	p.R203L	SRSF5_ENST00000557154.1_Missense_Mutation_p.R203L|SRSF5_ENST00000556587.1_3'UTR|SRSF5_ENST00000553635.1_Missense_Mutation_p.R200L|SRSF5_ENST00000394366.2_Missense_Mutation_p.R203L			Q13243	SRSF5_HUMAN	serine/arginine-rich splicing factor 5	203	Arg/Ser-rich (RS domain).				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|regulation of cell cycle (GO:0051726)|response to wounding (GO:0009611)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			large_intestine(1)|liver(1)	2						TCTCGTAGCCGATCCCGTTCC	0.522																																					p.R203L		Atlas-SNP	.											SRSF5_ENST00000553521,NS,carcinoma,0,1	SRSF5	45	.	0			c.G608T						.						86	94	91					14																	70237967		2203	4300	6503	SO:0001583	missense	6430	exon8			GTAGCCGATCCCG	AF020307	CCDS32109.1	14q24	2013-02-12	2010-06-22	2010-06-22	ENSG00000100650	ENSG00000100650		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10787	protein-coding gene	gene with protein product	"SR splicing factor 5"	600914	"splicing factor, arginine/serine-rich 5"	SFRS5		7686911, 20516191	Standard	XM_005267998		Approved	SRP40, HRS	uc001xlp.3	Q13243		ENST00000553521.1:c.608G>T	chr14.hg19:g.70237967G>T	ENSP00000452123:p.Arg203Leu	64.0	0.0		65.0	3.0	NM_001039465	O14797|Q16662|Q49AD6|Q6FGE0	Missense_Mutation	SNP	ENST00000553521.1	hg19	CCDS32109.1	.	.	.	.	.	.	.	.	.	.	G	19.22	3.785719	0.70337	.	.	ENSG00000100650	ENST00000553521;ENST00000394366;ENST00000557154;ENST00000553635	T;T;T;T	0.10960	2.82;2.82;2.82;2.82	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.35711	0.0941	M	0.82323	2.585	0.80722	D	1	D;D	0.56968	0.978;0.962	P;P	0.59487	0.858;0.726	T	0.05037	-1.0910	10	0.52906	T	0.07	.	20.0022	0.97423	0.0:0.0:1.0:0.0	.	200;203	Q13243-3;Q13243	.;SRSF5_HUMAN	L	203;203;203;200	ENSP00000452123:R203L;ENSP00000377892:R203L;ENSP00000451088:R203L;ENSP00000451391:R200L	ENSP00000377892:R203L	R	+	2	0	SRSF5	69307720	1.000000	0.71417	0.997000	0.53966	0.855000	0.48748	6.731000	0.74785	2.738000	0.93877	0.655000	0.94253	CGA	.	.		0.522	SRSF5-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412456.1	NM_001039465		T	70237967	G	T	70237967	3	4	323	1	0	0	0	0	1	0	0	0	14195	1058	37	1	634	1	SFRS5	14	70237967	Missense_Mutation	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10	18847201	70237967	37111573	86	45566										
SEL1L	6400	hgsc.bcm.edu	37	chr14	81965951	81965953	+	Splice_Site	DEL	ACC	ACC	-													0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	aataaagttttaatagtattAcctttgcctgacttgaatta							TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	ACC	ACC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr14:81965951_81965953delACC	ENST00000336735.4	-	7	947_948	c.831_832delGGT	c.(829-834)aaggtc>aatc	p.277_278KV>N	SEL1L_ENST00000555824.1_Splice_Site_p.277_278KV>N	NM_005065.5	NP_005056.3	Q9UBV2	SE1L1_HUMAN	sel-1 suppressor of lin-12-like (C. elegans)	277	Interaction with ERLEC1, OS9 and SYVN1.				Notch signaling pathway (GO:0007219)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	28				BRCA - Breast invasive adenocarcinoma(234;0.0299)		TAATAGTATTACCTTTGCCTGAC	0.33																																					.		Atlas-INDEL	.											.	SEL1L	67	.	0			.						.																																			SO:0001630	splice_region_variant	6400	.			.		CCDS9876.1, CCDS58333.1	14q31	2011-03-31	2001-11-28		ENSG00000071537	ENSG00000071537			10717	protein-coding gene	gene with protein product	"sel-1 suppressor of lin-12-like 1 (C. elegans)"	602329	"sel-1 (suppressor of lin-12, C.elegans)-like"			9417916, 10051412, 16331677	Standard	NM_005065		Approved	IBD2, SEL1L1	uc010tvv.2	Q9UBV2		ENST00000336735.4:c.831+1GGT>-	chr14.hg19:g.81965951_81965953delACC		209.0	0.0		149.0	30.0	.	Q6UWT6|Q9P1T9|Q9UHK7	Splice_Site	DEL	ENST00000336735.4	hg19	CCDS9876.1																																																																																			.	.		0.33	SEL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413325.1	NM_005065	In_Frame_Del	-	81965953	ACC	-	81965951	8	5	323	1	0	1	0	1	0	0	1	0	14025	405	14	0	1611	0	SEL1L	14	81965951	Splice_Site	DEL	ACC	TCGA-MI-A75H-01A-11D-A32G-10	11727984	81965951	25383589	87	45567										
GALC	2581	hgsc.bcm.edu	37	chr14	88411981	88411981	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	ggttgagaacttggcgtagcGtgaagtgatgctcgccaggg	17	7	0	3	rs200960659		TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr14:88411981G>A	ENST00000261304.2	-	14	1692	c.1586C>T	c.(1585-1587)aCg>aTg	p.T529M	GALC_ENST00000393568.4_Missense_Mutation_p.T506M|GALC_ENST00000393569.2_Missense_Mutation_p.T503M|GALC_ENST00000544807.2_Missense_Mutation_p.T473M	NM_000153.3|NM_001201401.1	NP_000144.2|NP_001188330.1	P54803	GALC_HUMAN	galactosylceramidase	529			T -> M (in GLD; infantile).		carbohydrate metabolic process (GO:0005975)|galactosylceramide catabolic process (GO:0006683)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	galactosylceramidase activity (GO:0004336)			endometrium(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						TTGGCGTAGCGTGAAGTGATG	0.408																																					p.T529M		Atlas-SNP	.											.	GALC	48	.	0			c.C1586T	GRCh37	CM970565	GALC	M		.	G	MET/THR,MET/THR,MET/THR	1,3749		0,1,1874	121	117	118		1586,1517,1508	5.5	1	14		118	2,8188		0,2,4093	yes	missense,missense,missense	GALC	NM_000153.3,NM_001201401.1,NM_001201402.1	81,81,81	0,3,5967	AA,AG,GG		0.0244,0.0267,0.0251	probably-damaging,probably-damaging,probably-damaging	529/686,506/663,503/660	88411981	3,11937	1875	4095	5970	SO:0001583	missense	2581	exon14			CGTAGCGTGAAGT	L23116	CCDS9878.2, CCDS55936.1, CCDS55937.1	14q31	2009-01-06	2005-11-29		ENSG00000054983	ENSG00000054983	3.2.1.46		4115	protein-coding gene	gene with protein product	"Krabbe disease"	606890	"galactosylceramidase (Krabbe disease)"				Standard	NM_000153		Approved		uc001xvt.3	P54803	OTTHUMG00000028646	ENST00000261304.2:c.1586C>T	chr14.hg19:g.88411981G>A	ENSP00000261304:p.Thr529Met	139.0	0.0		139.0	46.0	NM_000153	B4DKE8|B4DYN1|B4DZJ8|B7Z7Z2|J3KN25|J3KPP8|Q8J030	Missense_Mutation	SNP	ENST00000261304.2	hg19	CCDS9878.2	.	.	.	.	.	.	.	.	.	.	G	16.89	3.246310	0.59103	2.67E-4	2.44E-4	ENSG00000054983	ENST00000261304;ENST00000544807;ENST00000393569;ENST00000539620;ENST00000393568	D;D;D;D	0.94613	-3.47;-3.47;-3.47;-3.47	5.5	5.5	0.81552	.	0.043428	0.85682	D	0.000000	D	0.97745	0.9260	M	0.88842	2.985	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.81914	0.995;0.995;0.995;0.995	D	0.97840	1.0268	10	0.59425	D	0.04	-16.3314	19.7586	0.96304	0.0:0.0:1.0:0.0	.	473;506;503;529	P54803-5;E7EPA4;P54803-4;P54803	.;.;.;GALC_HUMAN	M	529;473;503;318;506	ENSP00000261304:T529M;ENSP00000437513:T473M;ENSP00000377199:T503M;ENSP00000377198:T506M	ENSP00000261304:T529M	T	-	2	0	GALC	87481734	1.000000	0.71417	0.959000	0.39883	0.026000	0.11368	9.634000	0.98435	2.754000	0.94517	0.585000	0.79938	ACG	.	.		0.408	GALC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071559.2			A	88411981	G	A	88411981	3	1	323	1	0	0	0	0	1	0	0	0	6209	1145	40	1	487	1	GALC	14	88411981	Missense_Mutation	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10	6446030	88411981	18937559	88	45568										
RYR3	6263	hgsc.bcm.edu	37	chr15	33872221	33872221	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	catcaccctgcctatagaagAagtcctgcagaccctacagg	8	14	1	3			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr15:33872221A>G	ENST00000389232.4	+	13	1383	c.1313A>G	c.(1312-1314)gAa>gGa	p.E438G	RYR3_ENST00000415757.3_Missense_Mutation_p.E438G	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	438					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			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)		CCTATAGAAGAAGTCCTGCAG	0.537																																					p.E438G		Atlas-SNP	.											.	RYR3	760	.	0			c.A1313G						.						60	61	61					15																	33872221		2003	4169	6172	SO:0001583	missense	6263	exon13			TAGAAGAAGTCCT		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.1313A>G	chr15.hg19:g.33872221A>G	ENSP00000373884:p.Glu438Gly	167.0	0.0		134.0	41.0	NM_001243996	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	hg19	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	A	10.07	1.250511	0.22880	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D;D	0.88896	-2.44;-2.44	5.15	5.15	0.70609	Intracellular calcium-release channel (1);	0.057558	0.64402	D	0.000002	T	0.76343	0.3974	N	0.08118	0	0.48696	D	0.999695	P;P	0.38677	0.617;0.642	B;B	0.37144	0.242;0.182	T	0.76318	-0.3003	10	0.29301	T	0.29	.	10.3987	0.44216	0.8542:0.0:0.0:0.1458	.	438;438	Q15413-2;Q15413	.;RYR3_HUMAN	G	438	ENSP00000373884:E438G;ENSP00000399610:E438G	ENSP00000354735:E438G	E	+	2	0	RYR3	31659513	1.000000	0.71417	1.000000	0.80357	0.509000	0.34042	4.891000	0.63185	2.160000	0.67779	0.533000	0.62120	GAA	.	.		0.537	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			G	33872221	A	G	33872221	3	3	323	1	0	0	0	0	1	0	0	0	13785	246	9	2	1363	2	RYR3	15	33872221	Missense_Mutation	SNP	A	TCGA-MI-A75H-01A-11D-A32G-10		33872221	68659171	89	45569										
TMEM87A	25963	hgsc.bcm.edu	37	chr15	42519078	42519078	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	gagaacagcaagcgccagatGgcatcgtctacccacagctc	10	14	1	2			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr15:42519078G>A	ENST00000389834.4	-	15	1593	c.1329C>T	c.(1327-1329)gcC>gcT	p.A443A	TMEM87A_ENST00000448392.1_Silent_p.A382A|RP11-546B15.1_ENST00000563846.1_RNA	NM_015497.3	NP_056312.2	Q8NBN3	TM87A_HUMAN	transmembrane protein 87A	443						integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(4)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	24		all_cancers(109;4.28e-16)|all_epithelial(112;1.04e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;1.03e-06)		AGCGCCAGATGGCATCGTCTA	0.468																																					p.A443A		Atlas-SNP	.											.	TMEM87A	56	.	0			c.C1329T						.						132	120	124					15																	42519078		2203	4299	6502	SO:0001819	synonymous_variant	25963	exon15			CCAGATGGCATCG	AF132733	CCDS32205.1, CCDS45243.1, CCDS66742.1	15q15.1	2005-10-30				ENSG00000103978			24522	protein-coding gene	gene with protein product						12477932	Standard	XM_005254287		Approved	DKFZP564G2022	uc021sjr.1	Q8NBN3		ENST00000389834.4:c.1329C>T	chr15.hg19:g.42519078G>A		54.0	0.0		45.0	14.0	NM_015497	Q6NT77|Q8NCA4|Q9BS46|Q9P103|Q9Y3Y7	Silent	SNP	ENST00000389834.4	hg19	CCDS32205.1																																																																																			.	.		0.468	TMEM87A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420482.2	NM_015497		A	42519078	G	A	42519078	2	1	323	1	0	0	0	0	0	0	0	1	16225	1335	47	3		3	TMEM87A	15	42519078	Silent	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10	8646857	42519078	60012314	90	45570										
KIAA1199	57214	hgsc.bcm.edu	37	chr15	81235392	81235392	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	gagcttcaggaactccattcTgcaaggcataccatggcagc	10	12	2	0			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr15:81235392T>G	ENST00000394685.3	+	28	4225	c.3806T>G	c.(3805-3807)cTg>cGg	p.L1269R	RP11-351M8.2_ENST00000560873.1_RNA|KIAA1199_ENST00000220244.3_Missense_Mutation_p.L1269R|KIAA1199_ENST00000356249.5_Missense_Mutation_p.L1269R			Q8WUJ3	CEMIP_HUMAN		1269					hyaluronan catabolic process (GO:0030214)|positive regulation of cell migration (GO:0030335)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase C activity (GO:1900020)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|sensory perception of sound (GO:0007605)	clathrin-coated vesicle membrane (GO:0030665)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	clathrin heavy chain binding (GO:0032050)|ER retention sequence binding (GO:0046923)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						AACTCCATTCTGCAAGGCATA	0.562																																					p.L1269R		Atlas-SNP	.											.	KIAA1199	118	.	0			c.T3806G						.						380	351	361					15																	81235392		2203	4300	6503	SO:0001583	missense	57214	exon27			CCATTCTGCAAGG																												ENST00000394685.3:c.3806T>G	chr15.hg19:g.81235392T>G	ENSP00000378177:p.Leu1269Arg	107.0	0.0		99.0	34.0	NM_018689	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Missense_Mutation	SNP	ENST00000394685.3	hg19	CCDS10315.1	.	.	.	.	.	.	.	.	.	.	T	15.90	2.969270	0.53614	.	.	ENSG00000103888	ENST00000220244;ENST00000394685;ENST00000356249	T;T;T	0.66638	-0.22;-0.22;-0.22	5.41	5.41	0.78517	.	0.000000	0.64402	D	0.000016	T	0.79770	0.4503	M	0.71581	2.175	0.52099	D	0.99994	D	0.76494	0.999	D	0.87578	0.998	T	0.77354	-0.2619	10	0.24483	T	0.36	-16.7876	15.4306	0.75092	0.0:0.0:0.0:1.0	.	1269	Q8WUJ3	K1199_HUMAN	R	1269	ENSP00000220244:L1269R;ENSP00000378177:L1269R;ENSP00000348583:L1269R	ENSP00000220244:L1269R	L	+	2	0	KIAA1199	79022447	1.000000	0.71417	0.987000	0.45799	0.149000	0.21700	6.762000	0.74950	2.039000	0.60335	0.482000	0.46254	CTG	.	.		0.562	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1			G	81235392	T	G	81235392	3	3	323	1	0	0	0	0	1	0	0	0	8222	1580	55	5	3908	5	KIAA1199	15	81235392	Missense_Mutation	SNP	T	TCGA-MI-A75H-01A-11D-A32G-10	38716314	81235392	21296000	91	45571										
C15orf42	90381	hgsc.bcm.edu	37	chr15	90159653	90159653	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	taggttatcacaaactgctgActaagagtgtggccgagact	11	8	1	3			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr15:90159653A>T	ENST00000268138.7	+	16	2992	c.2887A>T	c.(2887-2889)Act>Tct	p.T963S	TICRR_ENST00000560985.1_Missense_Mutation_p.T962S|KIF7_ENST00000558928.1_Intron			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	963					cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|formation of translation preinitiation complex (GO:0001731)|mitotic DNA replication checkpoint (GO:0033314)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)	chromatin binding (GO:0003682)										CAAACTGCTGACTAAGAGTGT	0.453																																					p.T963S		Atlas-SNP	.											.	.	.	.	0			c.A2887T						.						62	63	63					15																	90159653		1971	4150	6121	SO:0001583	missense	90381	exon16			CTGCTGACTAAGA	AK123612	CCDS10352.2	15q26.1	2012-07-11	2012-07-11	2012-07-11	ENSG00000140534	ENSG00000140534			28704	protein-coding gene	gene with protein product	"TOPBP1-interacting replication-stimulating protein", "SLD3 homolog (S. cerevisiae)"	613298	"chromosome 15 open reading frame 42"	C15orf42		20116089, 20080954	Standard	NM_152259		Approved	MGC45866, FLJ41618, Treslin, SLD3	uc002boe.3	Q7Z2Z1	OTTHUMG00000149648	ENST00000268138.7:c.2887A>T	chr15.hg19:g.90159653A>T	ENSP00000268138:p.Thr963Ser	94.0	0.0		56.0	20.0	NM_152259	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Missense_Mutation	SNP	ENST00000268138.7	hg19	CCDS10352.2	.	.	.	.	.	.	.	.	.	.	A	26.0	4.697531	0.88830	.	.	ENSG00000140534	ENST00000268138	T	0.31510	1.49	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.51058	0.1652	L	0.57536	1.79	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.44205	-0.9343	10	0.36615	T	0.2	-21.6679	14.3845	0.66934	1.0:0.0:0.0:0.0	.	963	Q7Z2Z1	TICRR_HUMAN	S	963	ENSP00000268138:T963S	ENSP00000268138:T963S	T	+	1	0	C15orf42	87960657	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.892000	0.87324	2.211000	0.71520	0.533000	0.62120	ACT	.	.		0.453	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259		T	90159653	A	T	90159653	3	4	323	1	0	0	0	0	1	0	0	0	1798	275	10	4	2949	4	C15orf42	15	90159653	Missense_Mutation	SNP	A	TCGA-MI-A75H-01A-11D-A32G-10	8924261	90159653	12371739	92	45572										
MLST8	64223	hgsc.bcm.edu	37	chr16	2256124	2256124	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	cacggtgggcagtgacccggTcatcctggccactgcaggct	14	14	1	1			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr16:2256124T>C	ENST00000569417.1	+	2	392	c.38T>C	c.(37-39)gTc>gCc	p.V13A	MLST8_ENST00000561651.1_3'UTR|MLST8_ENST00000301725.7_Missense_Mutation_p.V32A|MLST8_ENST00000565250.1_Missense_Mutation_p.V13A|MLST8_ENST00000397124.1_Missense_Mutation_p.V13A|MLST8_ENST00000301724.10_Missense_Mutation_p.V13A|MLST8_ENST00000382450.4_Missense_Mutation_p.V13A|MLST8_ENST00000564088.1_Missense_Mutation_p.V13A|AC009065.3_ENST00000517149.1_RNA	NM_022372.4	NP_071767.3	Q9BVC4	LST8_HUMAN	MTOR associated protein, LST8 homolog (S. cerevisiae)	13					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of TOR signaling (GO:0032008)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of Rac GTPase activity (GO:0032314)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|cytosol (GO:0005829)				large_intestine(3)|lung(2)|skin(1)	6						AGTGACCCGGTCATCCTGGCC	0.657																																					p.V13A		Atlas-SNP	.											.	MLST8	60	.	0			c.T38C						.						60	66	64					16																	2256124		2072	4204	6276	SO:0001583	missense	64223	exon2			ACCCGGTCATCCT		CCDS10462.2, CCDS58409.1	16p13.3	2013-01-09			ENSG00000167965	ENSG00000167965		"WD repeat domain containing"	24825	protein-coding gene	gene with protein product	"G protein beta subunit like"	612190				12477932	Standard	NM_022372		Approved	Lst8, Pop3, GBL, GbetaL	uc002cpc.3	Q9BVC4	OTTHUMG00000128827	ENST00000569417.1:c.38T>C	chr16.hg19:g.2256124T>C	ENSP00000456405:p.Val13Ala	57.0	0.0		38.0	15.0	NM_001199174	B3KMM4|B4DY00|D3DU88|Q5M800|Q86Y18|Q8WUI5|Q9HA66|Q9UJV6	Missense_Mutation	SNP	ENST00000569417.1	hg19	CCDS10462.2	.	.	.	.	.	.	.	.	.	.	T	17.84	3.487233	0.63962	.	.	ENSG00000167965	ENST00000382450;ENST00000301724;ENST00000397124;ENST00000301725	T;T;T;T	0.68624	1.11;-0.12;1.11;-0.34	5.11	5.11	0.69529	WD40/YVTN repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.70762	0.3261	L	0.37561	1.115	0.80722	D	1	D;P;P	0.76494	0.999;0.954;0.776	D;D;P	0.80764	0.994;0.954;0.536	T	0.65380	-0.6182	10	0.10636	T	0.68	-61.3119	13.7076	0.62648	0.0:0.0:0.0:1.0	.	13;32;13	B4E2R3;Q9BVC4-4;Q9BVC4	.;.;LST8_HUMAN	A	13;13;13;32	ENSP00000371888:V13A;ENSP00000301724:V13A;ENSP00000380313:V13A;ENSP00000301725:V32A	ENSP00000301724:V13A	V	+	2	0	MLST8	2196125	1.000000	0.71417	0.997000	0.53966	0.971000	0.66376	5.876000	0.69667	1.919000	0.55581	0.358000	0.22013	GTC	.	.		0.657	MLST8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250763.2	NM_022372		C	2256124	T	C	2256124	3	2	323	1	0	0	0	0	1	0	0	0	9643	1667	58	2	40	2	MLST8	16	2256124	Missense_Mutation	SNP	T	TCGA-MI-A75H-01A-11D-A32G-10		2256124	88098629	93	45573										
NLRP1	22861	hgsc.bcm.edu	37	chr17	5462324	5462325	+	Frame_Shift_Ins	INS	-	-	A													0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	ggtctctgagctggggtcccINSaatggctgagcttggagagc							TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr17:5462324_5462325insA	ENST00000572272.1	-	4	1690_1691	c.1691_1692insT	c.(1690-1692)ttgfs	p.L564fs	NLRP1_ENST00000262467.5_Frame_Shift_Ins_p.L564fs|NLRP1_ENST00000571307.1_5'UTR|NLRP1_ENST00000269280.4_Frame_Shift_Ins_p.L564fs|NLRP1_ENST00000577119.1_Frame_Shift_Ins_p.L564fs|NLRP1_ENST00000354411.3_Frame_Shift_Ins_p.L564fs|NLRP1_ENST00000345221.3_Frame_Shift_Ins_p.L564fs			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	564	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of inflammatory response (GO:0050727)|response to muramyl dipeptide (GO:0032495)	cytosol (GO:0005829)|intracellular (GO:0005622)|NLRP1 inflammasome complex (GO:0072558)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(17)|liver(5)|lung(17)|ovary(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Colorectal(1115;3.48e-05)				GCTGGGGTCCCAATGGCTGAGC	0.525																																					p.L564fs		Atlas-Indel,Pindel	.											.	NLRP1	358	.	0			c.1692_1693insT						.																																			SO:0001589	frameshift_variant	22861	exon4			.	AB023143	CCDS32537.1, CCDS42244.1, CCDS42245.1, CCDS42246.1, CCDS58508.1	17p13	2014-01-29	2006-12-08	2006-12-08	ENSG00000091592	ENSG00000091592		"Nucleotide-binding domain and leucine rich repeat containing"	14374	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 1"	606636	"NACHT, leucine rich repeat and PYD (pyrin domain) containing 1", "systemic lupus erythematosus, vitiligo-related 1"	NALP1, SLEV1		8781126, 12563287, 17377159	Standard	NM_033006		Approved	KIAA0926, DKFZp586O1822, CARD7, NAC, CLR17.1, DEFCAP, VAMAS1	uc002gci.3	Q9C000		ENST00000572272.1:c.1692dupT	chr17.hg19:g.5462326_5462326dupA	ENSP00000460475:p.Leu564fs	137.0	0.0		109.0	39.0	NM_014922	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Frame_Shift_Ins	INS	ENST00000572272.1	hg19	CCDS42246.1																																																																																			.	.		0.525	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004		A	5462325	-	A	5462324	7	5	323	1	0	1	1	0	0	0	0	0	10480	593	21	0	2860	0	NLRP1	17	5462324	Frame_Shift_Ins	INS	-	TCGA-MI-A75H-01A-11D-A32G-10		5462324	75732886	94	45574										
MYH1	4619	hgsc.bcm.edu	37	chr17	10408576	10408576	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	gggccagcttctcatctcgcAtctcctctaggagccccaga	9	16	4	1			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr17:10408576A>G	ENST00000226207.5	-	21	2433	c.2339T>C	c.(2338-2340)aTg>aCg	p.M780T	RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	780	Myosin motor.				muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						CTCATCTCGCATCTCCTCTAG	0.463																																					p.M780T		Atlas-SNP	.											.	MYH1	403	.	0			c.T2339C						.						71	72	72					17																	10408576		2203	4300	6503	SO:0001583	missense	4619	exon21			TCTCGCATCTCCT		CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"Myosins / Myosin superfamily : Class II"	7567	protein-coding gene	gene with protein product	"myosin heavy chain IIx/d"	160730	"myosin, heavy polypeptide 1, skeletal muscle, adult"			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.2339T>C	chr17.hg19:g.10408576A>G	ENSP00000226207:p.Met780Thr	116.0	0.0		121.0	39.0	NM_005963	Q14CA4|Q9Y622	Missense_Mutation	SNP	ENST00000226207.5	hg19	CCDS11155.1	.	.	.	.	.	.	.	.	.	.	A	18.98	3.737275	0.69304	.	.	ENSG00000109061	ENST00000226207	D	0.93247	-3.19	5.47	5.47	0.80525	Myosin head, motor domain (1);	0.000000	0.52532	U	0.000072	D	0.94218	0.8144	M	0.81179	2.53	0.58432	D	0.999999	P	0.41475	0.751	B	0.43445	0.42	D	0.94940	0.8090	10	0.87932	D	0	.	15.8518	0.78937	1.0:0.0:0.0:0.0	.	780	P12882	MYH1_HUMAN	T	780	ENSP00000226207:M780T	ENSP00000226207:M780T	M	-	2	0	MYH1	10349301	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.085000	0.94083	2.216000	0.71823	0.528000	0.53228	ATG	.	.		0.463	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963		G	10408576	A	G	10408576	3	3	323	1	0	0	0	0	1	0	0	0	10038	217	8	2	3560	2	MYH1	17	10408576	Missense_Mutation	SNP	A	TCGA-MI-A75H-01A-11D-A32G-10	4946252	10408576	70786634	95	45575										
CDRT1	374286	hgsc.bcm.edu	37	chr17	15508540	15508541	+	Frame_Shift_Del	DEL	AT	AT	-													0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	gtctttggactcctcacctgAtacttaggtcatagctcccg							TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr17:15508540_15508541delAT	ENST00000395906.3	-	7	1428_1429	c.1429_1430delAT	c.(1429-1431)atcfs	p.I477fs	RP11-385D13.1_ENST00000455584.2_Frame_Shift_Del_p.I787fs	NM_006382.3	NP_006373.2	O95170	CDRT1_HUMAN	CMT1A duplicated region transcript 1	477										endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	10				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(2;1.36e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0541)		TCCTCACCTGATACTTAGGTCA	0.51																																					p.477_477del		Atlas-Indel,Pindel	.											.	CDRT1	83	.	0			c.1430_1431del						.																																			SO:0001589	frameshift_variant	374286	exon7			.	U65652	CCDS45619.1, CCDS73996.1	17p11	2013-01-10			ENSG00000241322	ENSG00000241322		"F-boxes / WD-40 domains", "WD repeat domain containing"	14379	protein-coding gene	gene with protein product		604596	"F-box and WD repeat domain containing 10 pseudogene 1", "F-box and WD-40 domain protein 10 pseudogene 1"	FBXW10P1		9787083, 11381029	Standard	NM_006382		Approved	HREP, SM25H2, FBXW10B		O95170	OTTHUMG00000059074	ENST00000395906.3:c.1429_1430delAT	chr17.hg19:g.15508540_15508541delAT	ENSP00000379242:p.Ile477fs	378.0	0.0		347.0	140.0	NM_006382	O43848|O95611	Frame_Shift_Del	DEL	ENST00000395906.3	hg19	CCDS45619.1																																																																																			.	.		0.51	CDRT1-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448127.1	NM_006382		-	15508541	AT	-	15508540	7	5	323	1	0	1	0	1	0	0	0	0	3176	333	12	0	852	0	CDRT1	17	15508540	Frame_Shift_Del	DEL	AT	TCGA-MI-A75H-01A-11D-A32G-10	5099964	15508540	65686670	96	45576										
FAM83G	644815	hgsc.bcm.edu	37	chr17	18874756	18874756	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	ctaccgcccgtcctggccttTaggtgcttcgactgagacag	11	14	0	1			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr17:18874756T>C	ENST00000388995.6	-	6	2611	c.2388A>G	c.(2386-2388)ctA>ctG	p.L796L	SLC5A10_ENST00000395645.3_Intron|SLC5A10_ENST00000317977.6_Intron|SLC5A10_ENST00000395643.2_Intron|SLC5A10_ENST00000395642.1_Intron|SLC5A10_ENST00000395647.2_Intron|FAM83G_ENST00000345041.4_Silent_p.L796L|FAM83G_ENST00000585154.2_Silent_p.L796L|SLC5A10_ENST00000417251.2_Intron			A6ND36	FA83G_HUMAN	family with sequence similarity 83, member G	796					BMP signaling pathway (GO:0030509)	cytosol (GO:0005829)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(3)|stomach(1)	22						TCCTGGCCTTTAGGTGCTTCG	0.622																																					p.L796L		Atlas-SNP	.											.	FAM83G	51	.	0			c.A2388G						.						71	85	80					17																	18874756		2084	4190	6274	SO:0001819	synonymous_variant	644815	exon6			GGCCTTTAGGTGC	AK123558	CCDS42276.1	17p11.2	2014-05-01	2006-03-22		ENSG00000188522	ENSG00000188522			32554	protein-coding gene	gene with protein product	"protein associated with SMAD1"	615886				24554596	Standard	NM_001039999		Approved	FLJ41564, PAWS1	uc002guw.3	A6ND36	OTTHUMG00000059411	ENST00000388995.6:c.2388A>G	chr17.hg19:g.18874756T>C		60.0	0.0		57.0	12.0	NM_001039999	Q3KQZ4|Q6ZW60	Silent	SNP	ENST00000388995.6	hg19	CCDS42276.1																																																																																			.	.		0.622	FAM83G-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253108.4			C	18874756	T	C	18874756	2	2	323	1	0	0	0	0	0	0	0	1	5647	1741	61	2		2	FAM83G	17	18874756	Silent	SNP	T	TCGA-MI-A75H-01A-11D-A32G-10	3366216	18874756	62320454	97	45577										
KRTAP1-5	83895	hgsc.bcm.edu	37	chr17	39183121	39183122	+	Missense_Mutation	DNP	CC	CC	AA													0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	agctgatgccaccaccaatgCcacagccagttccgcaggag							TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr17:39183121_39183122CC>AA	ENST00000361883.5	-	1	332_333	c.286_287GG>TT	c.(286-288)GGc>TTc	p.G96F		NM_031957.1	NP_114163.1	Q9BYS1	KRA15_HUMAN	keratin associated protein 1-5	96	15 X 5 AA repeats of C-C-[QEPVRC]- [TPIVLE]-[SRHVP].					keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(2)|kidney(1)|lung(9)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	17		Breast(137;0.00043)	STAD - Stomach adenocarcinoma(17;0.000371)			ACCACCAATGCCACAGCCAGTT	0.634																																					p.G96V|p.G96C		Atlas-SNP	.											.	KRTAP1-5	33	.	0			c.G287T|c.G286T						.																																			SO:0001583	missense	83895	exon1			CCAATGCCACAGC|CAATGCCACAGCC	AJ406928	CCDS42321.1	17q21.2	2013-06-25			ENSG00000221852	ENSG00000221852		"Keratin associated proteins"	16777	protein-coding gene	gene with protein product		608822				11279113	Standard	NM_031957		Approved	KAP1.5	uc002hvu.3	Q9BYS1	OTTHUMG00000133587	ENST00000361883.5:c.286_287delinsAA	chr17.hg19:g.39183121_39183122delinsAA	ENSP00000355302:p.Gly96Phe	52.0|51.0	0.0		56.0|55.0	21.0	NM_031957	A6NJW6|A6NLZ6|B6ZDR1|Q52LP6	Missense_Mutation	SNP	ENST00000361883.5	hg19	CCDS42321.1																																																																																			.	.		0.634	KRTAP1-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257691.1			AA	39183122	CC	AA	39183121	3	1	323	1	0	0	0	0	1	0	0	0	8513	739	26	3	241	3	KRTAP1-5	17	39183121	Missense_Mutation	DNP	CC	TCGA-MI-A75H-01A-11D-A32G-10	20308365	39183121	42012089	98	45578										
SOST	50964	hgsc.bcm.edu	37	chr17	41832903	41832903	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	gcgcgcgcggcgcctcaccaCcgggacacagcagctgcacg	14	18	1	0			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr17:41832903C>T	ENST00000301691.2	-	2	495	c.449G>A	c.(448-450)gGt>gAt	p.G150D		NM_025237.2	NP_079513.1	Q9BQB4	SOST_HUMAN	sclerostin	150	CTCK.				cellular response to parathyroid hormone stimulus (GO:0071374)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000054)|ossification (GO:0001503)|positive regulation of transcription, DNA-templated (GO:0045893)|response to mechanical stimulus (GO:0009612)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|transcription factor binding (GO:0008134)			large_intestine(2)|lung(3)|prostate(1)	6		Breast(137;0.00725)		UCEC - Uterine corpus endometrioid carcinoma (308;0.177)|BRCA - Breast invasive adenocarcinoma(366;0.0741)		CGCCTCACCACCGGGACACAG	0.706																																					p.G150D		Atlas-SNP	.											.	SOST	19	.	0			c.G449A						.						12	14	13					17																	41832903		2030	4075	6105	SO:0001583	missense	50964	exon2			TCACCACCGGGAC	AF326736	CCDS11468.1	17q12-q21	2014-06-28	2010-04-28			ENSG00000167941			13771	protein-coding gene	gene with protein product		605740	"sclerosteosis"			11179006, 11181578	Standard	NM_025237		Approved	VBCH	uc002iec.1	Q9BQB4		ENST00000301691.2:c.449G>A	chr17.hg19:g.41832903C>T	ENSP00000301691:p.Gly150Asp	4.0	0.0		12.0	5.0	NM_025237	Q495N9	Missense_Mutation	SNP	ENST00000301691.2	hg19	CCDS11468.1	.	.	.	.	.	.	.	.	.	.	C	0.091	-1.166612	0.01660	.	.	ENSG00000167941	ENST00000301691	T	0.73363	-0.74	5.09	4.11	0.48088	.	0.345899	0.30374	N	0.009780	T	0.42017	0.1184	N	0.08118	0	0.09310	N	1	P	0.35684	0.515	B	0.29267	0.1	T	0.47911	-0.9080	10	0.02654	T	1	-9.8443	5.0409	0.14458	0.2022:0.6687:0.0:0.1291	.	150	Q9BQB4	SOST_HUMAN	D	150	ENSP00000301691:G150D	ENSP00000301691:G150D	G	-	2	0	SOST	39188429	0.048000	0.20356	0.133000	0.22050	0.336000	0.28762	1.943000	0.40253	1.130000	0.42092	0.655000	0.94253	GGT	.	.		0.706	SOST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453502.1	NM_025237		T	41832903	C	T	41832903	3	4	323	1	0	0	0	0	1	0	0	0	14953	507	18	3	196	3	SOST	17	41832903	Missense_Mutation	SNP	C	TCGA-MI-A75H-01A-11D-A32G-10	2649782	41832903	39362307	99	45579										
CRHR1	1394	hgsc.bcm.edu	37	chr17	43911988	43911988	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	gtgctcctccctgtgcccacAggtccgttctgccatccgga	10	17	1	0			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr17:43911988A>T	ENST00000398285.3	+	14	1194		c.e14-1		CRHR1_ENST00000352855.5_Splice_Site|CRHR1_ENST00000577353.1_Splice_Site|CRHR1_ENST00000339069.5_Splice_Site|CRHR1_ENST00000314537.5_Splice_Site|CRHR1_ENST00000293493.7_Splice_Site	NM_001145146.1	NP_001138618.1	P34998	CRFR1_HUMAN	corticotropin releasing hormone receptor 1						activation of adenylate cyclase activity (GO:0007190)|adrenal gland development (GO:0030325)|behavioral response to cocaine (GO:0048148)|behavioral response to ethanol (GO:0048149)|behavioral response to pain (GO:0048266)|cellular response to corticotropin-releasing hormone stimulus (GO:0071376)|corticotropin secretion (GO:0051458)|epithelial cell differentiation (GO:0030855)|fear response (GO:0042596)|female pregnancy (GO:0007565)|general adaptation syndrome, behavioral process (GO:0051867)|hypothalamus development (GO:0021854)|immune response (GO:0006955)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of feeding behavior (GO:2000252)|negative regulation of neuron death (GO:1901215)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|neuropeptide signaling pathway (GO:0007218)|parturition (GO:0007567)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mast cell degranulation (GO:0043306)|regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010578)|regulation of corticosterone secretion (GO:2000852)|response to hypoxia (GO:0001666)|response to immobilization stress (GO:0035902)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|vesicle (GO:0031982)	corticotrophin-releasing factor receptor activity (GO:0015056)|corticotropin-releasing hormone binding (GO:0051424)|corticotropin-releasing hormone receptor activity (GO:0043404)			NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(15)|pancreas(1)|skin(1)	24	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.161)		CTGTGCCCACAGGTCCGTTCT	0.677																																					.	Ovarian(110;57 1568 10207 38216 49865)	Atlas-SNP	.											.	CRHR1	48	.	0			c.583-2A>T						.						42	50	47					17																	43911988		2172	4259	6431	SO:0001630	splice_region_variant	1394	exon15			GCCCACAGGTCCG	L23332	CCDS42350.1, CCDS45712.1, CCDS45713.1, CCDS45714.1	17q12-q22	2012-08-14			ENSG00000120088	ENSG00000120088		"GPCR / Class B : Corticotropin-releasing factor receptors"	2357	protein-coding gene	gene with protein product	"corticotropin-releasing factor receptor"	122561		CRHR		7590738	Standard	NM_004382		Approved	CRF-R, CRF1	uc010dap.3	P34998		ENST00000398285.3:c.1195-1A>T	chr17.hg19:g.43911988A>T		22.0	0.0		23.0	4.0	NM_001256299	B4DIE9|Q13008|Q4QRJ1|Q9UK64	Splice_Site	SNP	ENST00000398285.3	hg19	CCDS45712.1	.	.	.	.	.	.	.	.	.	.	A	19.84	3.901957	0.72754	.	.	ENSG00000120088	ENST00000293493;ENST00000339069;ENST00000398285;ENST00000314537;ENST00000347197;ENST00000352855;ENST00000535778	.	.	.	5.24	5.24	0.73138	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.1022	0.59226	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CRHR1	41267769	1.000000	0.71417	1.000000	0.80357	0.730000	0.41778	9.314000	0.96306	1.985000	0.57927	0.454000	0.30748	.	.	.		0.677	CRHR1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000441241.3		Intron	T	43911988	A	T	43911988	5	4	323	1	0	0	0	0	0	0	1	0	3873	202	7	4	1247	4	CRHR1	17	43911988	Splice_Site	SNP	A	TCGA-MI-A75H-01A-11D-A32G-10	2079085	43911988	37283222	100	45580										
CA10	56934	hgsc.bcm.edu	37	chr17	50235089	50235089	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	ttcggcgcgtcccgtacctgAtatgcagacgatgaaattgg	12	10	0	3			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr17:50235089A>G	ENST00000285273.4	-	2	1169	c.58T>C	c.(58-60)Tca>Cca	p.S20P	CA10_ENST00000442502.2_Missense_Mutation_p.S20P|CA10_ENST00000340813.6_5'UTR|CA10_ENST00000451037.2_Missense_Mutation_p.S20P|CA10_ENST00000570565.1_Intron	NM_001082533.1	NP_001076002.1	Q9NS85	CAH10_HUMAN	carbonic anhydrase X	20					brain development (GO:0007420)					cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(21)|ovary(1)|skin(3)|stomach(2)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(22;4.74e-06)		Zonisamide(DB00909)	CCCGTACCTGATATGCAGACG	0.488																																					p.S20P		Atlas-SNP	.											.	CA10	84	.	0			c.T58C						.						133	124	127					17																	50235089		2203	4300	6503	SO:0001583	missense	56934	exon2			TACCTGATATGCA	AF288385	CCDS32684.1	17q21	2012-08-21			ENSG00000154975	ENSG00000154975		"Carbonic anhydrases"	1369	protein-coding gene	gene with protein product		604642				8673298, 9921901	Standard	NM_020178		Approved	CARPX, CA-RPX, HUCEP-15	uc002itx.4	Q9NS85	OTTHUMG00000177544	ENST00000285273.4:c.58T>C	chr17.hg19:g.50235089A>G	ENSP00000285273:p.Ser20Pro	109.0	0.0		78.0	32.0	NM_001082534	B2R7J0|B4DGL6	Missense_Mutation	SNP	ENST00000285273.4	hg19	CCDS32684.1	.	.	.	.	.	.	.	.	.	.	A	13.29	2.193883	0.38707	.	.	ENSG00000154975	ENST00000442502;ENST00000285273;ENST00000451037	T;T;T	0.26660	1.72;1.72;1.72	5.32	5.32	0.75619	.	.	.	.	.	T	0.25306	0.0615	N	0.14661	0.345	0.80722	D	1	P	0.45531	0.86	P	0.52217	0.693	T	0.04454	-1.0950	8	.	.	.	.	14.6182	0.68565	1.0:0.0:0.0:0.0	.	20	Q9NS85	CAH10_HUMAN	P	20	ENSP00000390666:S20P;ENSP00000285273:S20P;ENSP00000405388:S20P	.	S	-	1	0	CA10	47590088	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.553000	0.73918	2.233000	0.73108	0.533000	0.62120	TCA	.	.		0.488	CA10-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000437480.1	NM_020178		G	50235089	A	G	50235089	3	3	323	1	0	0	0	0	1	0	0	0	2513	333	12	2	964	2	CA10	17	50235089	Missense_Mutation	SNP	A	TCGA-MI-A75H-01A-11D-A32G-10	6323101	50235089	30960121	101	45581										
AMZ2	51321	hgsc.bcm.edu	37	chr17	66246521	66246521	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	attggatcacctcccaccctGaggctccccaagactttgaa	7	15	1	3			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr17:66246521G>T	ENST00000359904.3	+	2	1325	c.193G>T	c.(193-195)Gag>Tag	p.E65*	AMZ2_ENST00000577273.1_Nonsense_Mutation_p.E65*|RP11-147L13.2_ENST00000577698.1_RNA|AMZ2_ENST00000392720.2_Nonsense_Mutation_p.E65*|AMZ2_ENST00000585050.1_3'UTR|AMZ2_ENST00000577985.1_Nonsense_Mutation_p.E65*|AMZ2_ENST00000359783.4_Nonsense_Mutation_p.E65*|AMZ2_ENST00000580753.1_Nonsense_Mutation_p.E65*|AMZ2_ENST00000577866.1_Nonsense_Mutation_p.E65*	NM_016627.4	NP_057711.3	Q86W34	AMZ2_HUMAN	archaelysin family metallopeptidase 2	65							metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	9	all_cancers(12;1.12e-09)		BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)			CTCCCACCCTGAGGCTCCCCA	0.458																																					p.E65X		Atlas-SNP	.											.	AMZ2	15	.	0			c.G193T						.						115	113	114					17																	66246521		2203	4300	6503	SO:0001587	stop_gained	51321	exon2			CACCCTGAGGCTC	CR609550	CCDS11674.1, CCDS32714.1	17q24.2	2010-04-08			ENSG00000196704	ENSG00000196704			28041	protein-coding gene	gene with protein product	"archaemetzincin-2"	615169				15972818	Standard	XM_005257436		Approved		uc002jgr.1	Q86W34		ENST00000359904.3:c.193G>T	chr17.hg19:g.66246521G>T	ENSP00000352976:p.Glu65*	115.0	0.0		108.0	19.0	NM_001033574	A6NLD9|B3KR44|Q5XKF1|Q9NZE2	Nonsense_Mutation	SNP	ENST00000359904.3	hg19	CCDS11674.1	.	.	.	.	.	.	.	.	.	.	G	32	5.111274	0.94339	.	.	ENSG00000196704	ENST00000359904;ENST00000359783;ENST00000392720	.	.	.	3.58	1.54	0.23209	.	0.000000	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	-16.8236	7.6032	0.28087	0.2284:0.0:0.7716:0.0	.	.	.	.	X	65	.	ENSP00000352831:E65X	E	+	1	0	AMZ2	63758116	1.000000	0.71417	0.928000	0.36995	0.936000	0.57629	6.075000	0.71261	0.832000	0.34804	0.306000	0.20318	GAG	.	.		0.458	AMZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448261.1	NM_016627		T	66246521	G	T	66246521	4	4	323	1	0	0	0	0	0	1	0	0	597	1291	45	3	195	3	AMZ2	17	66246521	Nonsense_Mutation	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10	16011432	66246521	14948689	102	45582										
ASPSCR1	79058	hgsc.bcm.edu	37	chr17	79974909	79974909	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	tgctgaggagggggcgctggTcccccctgagcccatcccag	15	15	0	2			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr17:79974909T>A	ENST00000306739.4	+	15	1665	c.1568T>A	c.(1567-1569)gTc>gAc	p.V523D	STRA13_ENST00000583767.1_5'Flank|ASPSCR1_ENST00000580534.1_Missense_Mutation_p.V471D|ASPSCR1_ENST00000306729.7_Missense_Mutation_p.V617D|ASPSCR1_ENST00000582404.1_3'UTR	NM_024083.3	NP_076988.1	Q9BZE9	ASPC1_HUMAN	alveolar soft part sarcoma chromosome region, candidate 1	523					glucose homeostasis (GO:0042593)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|regulation of glucose import (GO:0046324)	cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)			ASPSCR1/TFE3(167)	breast(2)|large_intestine(2)	4	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)			GGGGCGCTGGTCCCCCCTGAG	0.692			T	TFE3	alveolar soft part sarcoma																																p.V617D		Atlas-SNP	.		Dom	yes		17	17q25	79058	"alveolar soft part sarcoma chromosome region, candidate 1"		M	.	ASPSCR1	27	.	0			c.T1850A						.						21	25	24					17																	79974909		2199	4293	6492	SO:0001583	missense	79058	exon16			CGCTGGTCCCCCC	AF324219	CCDS11796.1, CCDS58611.1	17q25	2011-06-28				ENSG00000169696		"UBX domain containing"	13825	protein-coding gene	gene with protein product	"UBX domain protein 9"	606236				11244503, 10506710	Standard	NM_024083		Approved	ASPS, ASPL, UBXD9, UBXN9	uc002kcy.3	Q9BZE9		ENST00000306739.4:c.1568T>A	chr17.hg19:g.79974909T>A	ENSP00000302176:p.Val523Asp	54.0	0.0		33.0	14.0	NM_001251888	A8K3K9|Q7Z6N7|Q8WV59|Q96LS5|Q96M40	Missense_Mutation	SNP	ENST00000306739.4	hg19	CCDS11796.1	.	.	.	.	.	.	.	.	.	.	T	8.209	0.799968	0.16397	.	.	ENSG00000169696	ENST00000306739;ENST00000306729	T;T	0.21543	2.02;2.0	3.78	-2.34	0.06704	.	0.441437	0.19705	N	0.107954	T	0.06280	0.0162	N	0.08118	0	0.09310	N	1	B;P;B	0.39535	0.012;0.677;0.093	B;B;B	0.36719	0.012;0.231;0.06	T	0.25257	-1.0137	9	.	.	.	-2.1265	0.6568	0.00835	0.2611:0.1285:0.3451:0.2654	.	471;617;523	Q9BZE9-3;Q9BZE9-2;Q9BZE9	.;.;ASPC1_HUMAN	D	523;617	ENSP00000302176:V523D;ENSP00000306625:V617D	.	V	+	2	0	ASPSCR1	77568198	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-0.074000	0.11450	-0.312000	0.08741	-0.408000	0.06270	GTC	.	.		0.692	ASPSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441972.1	NM_024083		A	79974909	T	A	79974909	3	1	323	1	0	0	0	0	1	0	0	0	1059	1667	58	4	1626	4	ASPSCR1	17	79974909	Missense_Mutation	SNP	T	TCGA-MI-A75H-01A-11D-A32G-10	13728388	79974909	1220301	103	45583										
POTEC	388468	hgsc.bcm.edu	37	chr18	14511960	14511960	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	aacatgctgttttcacgcaaGagatcttcttctttcttatg	6	9	5	1			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr18:14511960G>A	ENST00000358970.5	-	11	1565	c.1566C>T	c.(1564-1566)ctC>ctT	p.L522L		NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	522										NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						TTTCACGCAAGAGATCTTCTT	0.343																																					p.L522L		Atlas-SNP	.											.	POTEC	129	.	0			c.C1566T						.						78	59	64					18																	14511960		692	1591	2283	SO:0001819	synonymous_variant	388468	exon11			ACGCAAGAGATCT	BX649118	CCDS45835.1	18p11.21	2013-01-10	2008-11-26	2008-11-26	ENSG00000183206	ENSG00000183206		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	33894	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 6"		"ANKRD26-like family B, member 2"	A26B2			Standard	NM_001137671		Approved	POTE18, POTE-18, DKFZp686J0529, CT104.6	uc010dln.3	B2RU33	OTTHUMG00000162963	ENST00000358970.5:c.1566C>T	chr18.hg19:g.14511960G>A		756.0	0.0		608.0	183.0	NM_001137671		Silent	SNP	ENST00000358970.5	hg19	CCDS45835.1																																																																																			.	.		0.343	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269		A	14511960	G	A	14511960	2	1	323	1	0	0	0	0	0	0	0	1	12271	929	33	3		3	POTEC	18	14511960	Silent	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10		14511960	63565288	104	45584										
LMAN1	3998	hgsc.bcm.edu	37	chr18	57021788	57021788	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	gatttgtccattgttgcctaTaattactatagcaggattat	7	6	0	0	rs139797136		TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr18:57021788T>A	ENST00000251047.5	-	4	1219	c.502A>T	c.(502-504)Ata>Tta	p.I168L	LMAN1_ENST00000587940.1_5'Flank	NM_005570.3	NP_005561.1	P49257	LMAN1_HUMAN	lectin, mannose-binding, 1	168	L-type lectin-like. {ECO:0000255|PROSITE- ProRule:PRU00658}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum organization (GO:0007029)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|positive regulation of organelle organization (GO:0010638)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)	endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|ER to Golgi transport vesicle membrane (GO:0012507)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|sarcomere (GO:0030017)	mannose binding (GO:0005537)|metal ion binding (GO:0046872)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	16		Colorectal(73;0.0946)			Antihemophilic Factor(DB00025)	TTGTTGCCTATAATTACTATA	0.284																																					p.I168L		Atlas-SNP	.											.	LMAN1	57	.	0			c.A502T						.						76	71	73					18																	57021788		2201	4294	6495	SO:0001583	missense	3998	exon4			TGCCTATAATTAC	X71661	CCDS11974.1	18q21.3-q22	2014-09-17	2002-08-30		ENSG00000074695	ENSG00000074695			6631	protein-coding gene	gene with protein product	"endoplasmic reticulum-golgi intermediate compartment protein 53"	601567	"coagulation factor V-factor VIII combined deficiency"	F5F8D		9546392, 8854877	Standard	NM_005570		Approved	MR60, ERGIC-53, ERGIC53, gp58, MCFD1, FMFD1	uc002lhz.3	P49257	OTTHUMG00000132758	ENST00000251047.5:c.502A>T	chr18.hg19:g.57021788T>A	ENSP00000251047:p.Ile168Leu	76.0	0.0		77.0	24.0	NM_005570	Q12895|Q8N5I7|Q9UQG1|Q9UQG2|Q9UQG3|Q9UQG4|Q9UQG5|Q9UQG6|Q9UQG7|Q9UQG8|Q9UQG9|Q9UQH0|Q9UQH1|Q9UQH2	Missense_Mutation	SNP	ENST00000251047.5	hg19	CCDS11974.1	.	.	.	.	.	.	.	.	.	.	T	16.34	3.096881	0.56075	.	.	ENSG00000074695	ENST00000251047	T	0.62639	0.01	5.6	0.66	0.17868	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.232980	0.42172	D	0.000745	T	0.43122	0.1233	N	0.17800	0.525	0.40219	D	0.977712	B;B	0.02656	0.0;0.0	B;B	0.20955	0.032;0.023	T	0.14035	-1.0487	10	0.32370	T	0.25	-5.6707	10.2186	0.43184	0.0:0.5154:0.0:0.4846	.	168;168	B4DVV0;P49257	.;LMAN1_HUMAN	L	168	ENSP00000251047:I168L	ENSP00000251047:I168L	I	-	1	0	LMAN1	55172768	1.000000	0.71417	0.987000	0.45799	0.999000	0.98932	1.955000	0.40372	-0.104000	0.12154	0.533000	0.62120	ATA	.	T|1.000;C|0.000		0.284	LMAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256129.2	NM_005570		A	57021788	T	A	57021788	3	1	323	1	0	0	0	0	1	0	0	0	8845	1406	49	4	1070	4	LMAN1	18	57021788	Missense_Mutation	SNP	T	TCGA-MI-A75H-01A-11D-A32G-10	42509828	57021788	21055460	105	45585										
ELANE	1991	hgsc.bcm.edu	37	chr19	855988	855988	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	gcagccccttggtctgcaacGggctaatccacggaattgcc	11	14	1	0	rs140880838	byFrequency	TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr19:855988G>T	ENST00000590230.1	+	6	769	c.628G>T	c.(628-630)Ggg>Tgg	p.G210W	ELANE_ENST00000263621.1_Missense_Mutation_p.G210W			P08246	ELNE_HUMAN	elastase, neutrophil expressed	210	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		G -> V (in SCN1). {ECO:0000269|PubMed:11001877}.|G -> W (in CH). {ECO:0000269|PubMed:23463630}.		acute inflammatory response to antigenic stimulus (GO:0002438)|cellular calcium ion homeostasis (GO:0006874)|collagen catabolic process (GO:0030574)|defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|negative regulation of chemokine biosynthetic process (GO:0045079)|negative regulation of chemotaxis (GO:0050922)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-8 biosynthetic process (GO:0045415)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neutrophil mediated killing of fungus (GO:0070947)|phagocytosis (GO:0006909)|positive regulation of immune response (GO:0050778)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein catabolic process (GO:0030163)|proteolysis (GO:0006508)|response to lipopolysaccharide (GO:0032496)|response to UV (GO:0009411)|response to yeast (GO:0001878)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|secretory granule (GO:0030141)|transcriptional repressor complex (GO:0017053)	cytokine binding (GO:0019955)|endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|peptidase activity (GO:0008233)|protease binding (GO:0002020)|RNA polymerase II transcription corepressor activity (GO:0001106)|serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(1)|lung(4)|pancreas(1)	13					Alpha-1-proteinase inhibitor(DB00058)|Filgrastim(DB00099)|Pegfilgrastim(DB00019)	GGTCTGCAACGGGCTAATCCA	0.657																																					p.G210W		Atlas-SNP	.											.	ELANE	27	.	0			c.G628T						.						50	55	53					19																	855988		2203	4300	6503	SO:0001583	missense	1991	exon5			TGCAACGGGCTAA		CCDS12045.1	19p13.3	2014-09-17	2009-05-05	2009-05-05	ENSG00000197561	ENSG00000197561	3.4.21.37		3309	protein-coding gene	gene with protein product	"neutrophil elastase", "leukocyte elastase", "medullasin"	130130	"elastase 2, neutrophil"	ELA2		2902087	Standard	XM_005259517		Approved	NE, HNE, HLE	uc002lqb.3	P08246		ENST00000590230.1:c.628G>T	chr19.hg19:g.855988G>T	ENSP00000466090:p.Gly210Trp	62.0	0.0		67.0	4.0	NM_001972	P09649|Q6B0D9|Q6LDP5	Missense_Mutation	SNP	ENST00000590230.1	hg19	CCDS12045.1	.	.	.	.	.	.	.	.	.	.	G	12.02	1.812663	0.32053	.	.	ENSG00000197561	ENST00000263621	D	0.89343	-2.5	4.46	2.3	0.28687	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.497520	0.15369	U	0.265980	D	0.91270	0.7248	M	0.64676	1.99	0.31710	N	0.639576	D	0.89917	1.0	D	0.97110	1.0	D	0.86499	0.1802	10	0.27785	T	0.31	.	6.6446	0.22929	0.2337:0.0:0.7663:0.0	.	210	P08246	ELNE_HUMAN	W	210	ENSP00000263621:G210W	ENSP00000263621:G210W	G	+	1	0	ELANE	806988	0.969000	0.33509	0.621000	0.29145	0.019000	0.09904	2.894000	0.48640	0.430000	0.26230	0.462000	0.41574	GGG	.	G|1.000;A|0.000		0.657	ELANE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457890.2	NM_001972		T	855988	G	T	855988	3	4	323	1	0	0	0	0	1	0	0	0	5050	1116	39	1	646	1	ELANE	19	855988	Missense_Mutation	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10		855988	58272995	106	45586										
MLLT1	4298	hgsc.bcm.edu	37	chr19	6226990	6226990	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	gccttccgcctcactaacctTggagccgtgggatggtttgg	13	12	1	0			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr19:6226990T>A	ENST00000252674.7	-	5	707	c.544A>T	c.(544-546)Aag>Tag	p.K182*		NM_005934.3	NP_005925.2	Q03111	ENL_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 1	182					negative regulation of protein kinase activity (GO:0006469)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	DNA binding (GO:0003677)			endometrium(3)|kidney(3)|large_intestine(2)|lung(5)|prostate(2)|skin(2)	17						TCACTAACCTTGGAGCCGTGG	0.662			T	MLL	AL																																p.K182X		Atlas-SNP	.		Dom	yes		19	19p13.3	4298	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 1 (ENL)"		L	.	MLLT1	47	.	0			c.A544T						.						171	141	151					19																	6226990		2203	4300	6503	SO:0001587	stop_gained	4298	exon5			TAACCTTGGAGCC		CCDS12160.1	19p13.3	2012-10-04	2001-11-28		ENSG00000130382	ENSG00000130382			7134	protein-coding gene	gene with protein product		159556	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 1"				Standard	XM_005259561		Approved	ENL, LTG19, YEATS1	uc002mek.3	Q03111	OTTHUMG00000180757	ENST00000252674.7:c.544A>T	chr19.hg19:g.6226990T>A	ENSP00000252674:p.Lys182*	132.0	0.0		110.0	28.0	NM_005934	Q14768	Nonsense_Mutation	SNP	ENST00000252674.7	hg19	CCDS12160.1	.	.	.	.	.	.	.	.	.	.	T	39	7.388274	0.98252	.	.	ENSG00000130382	ENST00000252674	.	.	.	4.85	4.85	0.62838	.	0.106292	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.2253	13.2805	0.60212	0.0:0.0:0.0:1.0	.	.	.	.	X	182	.	ENSP00000252674:K182X	K	-	1	0	MLLT1	6177990	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.891000	0.87319	1.808000	0.52836	0.402000	0.26972	AAG	.	.		0.662	MLLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452909.1	NM_005934		A	6226990	T	A	6226990	4	1	323	1	0	0	0	0	0	1	0	0	9634	1821	63	4	1167	4	MLLT1	19	6226990	Nonsense_Mutation	SNP	T	TCGA-MI-A75H-01A-11D-A32G-10	5371002	6226990	52901993	107	45587										
MUC16	94025	hgsc.bcm.edu	37	chr19	9072822	9072822	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	tcttagaggatttaggtattGatctggaaattgtggtgtct	12	3	3	2			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr19:9072822G>T	ENST00000397910.4	-	3	14827	c.14624C>A	c.(14623-14625)tCa>tAa	p.S4875*		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4877	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TTTAGGTATTGATCTGGAAAT	0.458																																					p.S4875X		Atlas-SNP	.											.	MUC16	4315	.	0			c.C14624A						.						224	211	215					19																	9072822		2029	4199	6228	SO:0001587	stop_gained	94025	exon3			GGTATTGATCTGG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.14624C>A	chr19.hg19:g.9072822G>T	ENSP00000381008:p.Ser4875*	295.0	0.0		267.0	93.0	NM_024690	Q6ZQW5|Q96RK2	Nonsense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	55	24.314818	0.99960	.	.	ENSG00000181143	ENST00000397910	.	.	.	2.4	-1.2	0.09554	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	2.0647	0.03600	0.3242:0.0:0.4179:0.2578	.	.	.	.	X	4875	.	ENSP00000381008:S4875X	S	-	2	0	MUC16	8933822	0.016000	0.18221	0.000000	0.03702	0.060000	0.15804	1.989000	0.40707	-0.182000	0.10602	0.298000	0.19748	TCA	.	.		0.458	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9072822	G	T	9072822	4	4	323	1	0	0	0	0	0	1	0	0	9982	1294	45	3	29227	3	MUC16	19	9072822	Nonsense_Mutation	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10	2845832	9072822	50056161	108	45588										
MUC16	94025	hgsc.bcm.edu	37	chr19	9085379	9085379	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	agaagttatggccattggaaGagggacttcagagctgatac	13	6	1	4			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr19:9085379G>A	ENST00000397910.4	-	1	6639	c.6436C>T	c.(6436-6438)Ctt>Ttt	p.L2146F		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2146	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.L2146V(2)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GCCATTGGAAGAGGGACTTCA	0.498																																					p.L2146F		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,0,2	MUC16	4315	.	2	Substitution - Missense(2)	lung(2)	c.C6436T						.						73	71	72					19																	9085379		1912	4127	6039	SO:0001583	missense	94025	exon1			TTGGAAGAGGGAC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.6436C>T	chr19.hg19:g.9085379G>A	ENSP00000381008:p.Leu2146Phe	93.0	0.0		83.0	29.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	0.104	-1.148522	0.01714	.	.	ENSG00000181143	ENST00000397910	T	0.03124	4.04	0.235	-0.47	0.12131	.	.	.	.	.	T	0.01940	0.0061	N	0.08118	0	.	.	.	B	0.09022	0.002	B	0.04013	0.001	T	0.42916	-0.9423	7	0.87932	D	0	.	.	.	.	.	2146	B5ME49	.	F	2146	ENSP00000381008:L2146F	ENSP00000381008:L2146F	L	-	1	0	MUC16	8946379	0.003000	0.15002	0.001000	0.08648	0.001000	0.01503	-0.144000	0.10280	-0.671000	0.05274	-0.657000	0.03884	CTT	.	.		0.498	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9085379	G	A	9085379	3	1	323	1	0	0	0	0	1	0	0	0	9982	942	33	3	37423	3	MUC16	19	9085379	Missense_Mutation	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10	12557	9085379	50043604	109	45589										
NOTCH3	4854	hgsc.bcm.edu	37	chr19	15280956	15280956	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	gtctgtggccacctcccccaTcaggctctcacccttggcca	8	19	3	0			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr19:15280956T>A	ENST00000263388.2	-	28	5215	c.5140A>T	c.(5140-5142)Atg>Ttg	p.M1714L		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	1714					forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			ACCTCCCCCATCAGGCTCTCA	0.627																																					p.M1714L		Atlas-SNP	.											.	NOTCH3	340	.	0			c.A5140T						.						41	30	34					19																	15280956		2203	4300	6503	SO:0001583	missense	4854	exon28			CCCCCATCAGGCT	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"Ankyrin repeat domain containing"	7883	protein-coding gene	gene with protein product		600276	"Notch (Drosophila) homolog 3", "Notch homolog 3 (Drosophila)"	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.5140A>T	chr19.hg19:g.15280956T>A	ENSP00000263388:p.Met1714Leu	95.0	0.0		72.0	29.0	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Missense_Mutation	SNP	ENST00000263388.2	hg19	CCDS12326.1	.	.	.	.	.	.	.	.	.	.	T	10.70	1.423401	0.25639	.	.	ENSG00000074181	ENST00000263388	T	0.81247	-1.47	5.22	4.19	0.49359	.	0.000000	0.38897	N	0.001526	T	0.60366	0.2263	N	0.04994	-0.135	0.32242	N	0.572649	B	0.06786	0.001	B	0.06405	0.002	T	0.59123	-0.7513	10	0.25106	T	0.35	.	10.6684	0.45745	0.1435:0.0:0.0:0.8564	.	1714	Q9UM47	NOTC3_HUMAN	L	1714	ENSP00000263388:M1714L	ENSP00000263388:M1714L	M	-	1	0	NOTCH3	15141956	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.323000	0.43823	0.978000	0.38470	0.482000	0.46254	ATG	.	.		0.627	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435		A	15280956	T	A	15280956	3	1	323	1	0	0	0	0	1	0	0	0	10559	1435	50	4	1849	4	NOTCH3	19	15280956	Missense_Mutation	SNP	T	TCGA-MI-A75H-01A-11D-A32G-10	6195577	15280956	43848027	110	45590										
KIAA1683	80726	hgsc.bcm.edu	37	chr19	18375495	18375495	+	Intron	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	gctcgccccgggacagggctCgggacagggtcaggcgcagc	18	14	1	0			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr19:18375495C>A	ENST00000600328.3	-	3	2810				KIAA1683_ENST00000392413.4_Missense_Mutation_p.R952L|KIAA1683_ENST00000600359.3_Intron			Q9H0B3	K1683_HUMAN	KIAA1683							mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						GGACAGGGCTCGGGACAGGGT	0.647																																					p.R952L		Atlas-SNP	.											.	KIAA1683	190	.	0			c.G2855T						.						36	37	36					19																	18375495		692	1591	2283	SO:0001627	intron_variant	80726	exon3			AGGGCTCGGGACA	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.2616+238G>T	chr19.hg19:g.18375495C>A		49.0	0.0		58.0	16.0	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Missense_Mutation	SNP	ENST00000600328.3	hg19	CCDS32958.1	.	.	.	.	.	.	.	.	.	.	C	12.57	1.978593	0.34942	.	.	ENSG00000130518	ENST00000392413	T	0.04758	3.56	4.67	1.39	0.22231	.	.	.	.	.	T	0.04588	0.0125	N	0.14661	0.345	0.09310	N	0.999999	D	0.53151	0.958	P	0.49451	0.611	T	0.42799	-0.9430	9	0.54805	T	0.06	.	6.0889	0.19983	0.0:0.6772:0.0:0.3228	.	952	E9PDE0	.	L	952	ENSP00000376213:R952L	ENSP00000376213:R952L	R	-	2	0	KIAA1683	18236495	0.000000	0.05858	0.003000	0.11579	0.081000	0.17604	0.270000	0.18607	0.419000	0.25927	-0.474000	0.04947	CGA	.	.		0.647	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3			A	18375495	C	A	18375495	1	1	323	0	1	0	0	0	0	0	0	0	8260	884	31	1		1	KIAA1683	19	18375495	Intron	SNP	C	TCGA-MI-A75H-01A-11D-A32G-10	3094539	18375495	40753488	111	45591										
HAPLN4	404037	hgsc.bcm.edu	37	chr19	19369444	19369444	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	ccgccccctgcactcccggtCccccccaggccgccgcaggg	11	24	0	0			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr19:19369444C>T	ENST00000291481.7	-	4	768	c.705G>A	c.(703-705)ggG>ggA	p.G235G	AC138430.4_ENST00000586064.2_RNA	NM_023002.2	NP_075378.1	Q86UW8	HPLN4_HUMAN	hyaluronan and proteoglycan link protein 4	235	Link 1. {ECO:0000255|PROSITE- ProRule:PRU00323, ECO:0000305}.				cell adhesion (GO:0007155)	proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|pancreas(1)|prostate(1)	16			Epithelial(12;0.00575)		Hyaluronan(DB08818)	CACTCCCGGTCCCCCCCAGGC	0.711																																					p.G235G		Atlas-SNP	.											HAPLN4,NS,malignant_melanoma,-1,1	HAPLN4	44	.	0			c.G705A						.						23	24	23					19																	19369444		2202	4298	6500	SO:0001819	synonymous_variant	404037	exon4			CCCGGTCCCCCCC	AB107883	CCDS12398.1	19p13.1	2013-01-11						"Immunoglobulin superfamily / V-set domain containing"	31357	protein-coding gene	gene with protein product	"brain link protein 2"					12663660	Standard	NM_023002		Approved	BRAL2, KIAA1926	uc002nmb.3	Q86UW8		ENST00000291481.7:c.705G>A	chr19.hg19:g.19369444C>T		42.0	0.0		48.0	21.0	NM_023002	A5PKW5|Q96PW2	Silent	SNP	ENST00000291481.7	hg19	CCDS12398.1																																																																																			.	.		0.711	HAPLN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460117.2	NM_023002		T	19369444	C	T	19369444	2	4	323	1	0	0	0	0	0	0	0	1	6966	842	30	3		3	HAPLN4	19	19369444	Silent	SNP	C	TCGA-MI-A75H-01A-11D-A32G-10	993949	19369444	39759539	112	45592										
ZNF737	100129842	hgsc.bcm.edu	37	chr19	20736517	20736517	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	tattaaagtttttctcaccaAggaagaccaggtttctgtag	8	7	2	1			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr19:20736517A>G	ENST00000427401.4	-	2	222	c.128T>C	c.(127-129)cTt>cCt	p.L43P	CTC-513N18.7_ENST00000595094.1_lincRNA|ZNF737_ENST00000596797.1_Missense_Mutation_p.L43P	NM_001159293.1	NP_001152765.1	O75373	ZN737_HUMAN	zinc finger protein 737	43	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|kidney(1)|lung(7)|ovary(1)|stomach(1)|urinary_tract(1)	13						TTTCTCACCAAGGAAGACCAG	0.333																																					p.L43P		Atlas-SNP	.											.	ZNF737	50	.	0			c.T128C						.						58	52	54					19																	20736517		692	1591	2283	SO:0001583	missense	100129842	exon2			TCACCAAGGAAGA	BC015765	CCDS54238.1	19p12	2013-01-08						"Zinc fingers, C2H2-type", "-"	32468	protein-coding gene	gene with protein product		603984					Standard	NM_001159293		Approved	ZNF102	uc002npa.3	O75373		ENST00000427401.4:c.128T>C	chr19.hg19:g.20736517A>G	ENSP00000395733:p.Leu43Pro	442.0	0.0		399.0	162.0	NM_001159293	C9JHM3	Missense_Mutation	SNP	ENST00000427401.4	hg19	CCDS54238.1	.	.	.	.	.	.	.	.	.	.	a	9.912	1.209746	0.22289	.	.	ENSG00000237440	ENST00000427401	T	0.02837	4.14	0.819	0.819	0.18785	.	.	.	.	.	T	0.20901	0.0503	H	0.98721	4.31	0.53688	D	0.999974	D	0.76494	0.999	D	0.73380	0.98	T	0.00491	-1.1708	9	0.87932	D	0	.	3.7374	0.08515	1.0:0.0:0.0:0.0	.	43	C9JHM3	.	P	43	ENSP00000395733:L43P	ENSP00000395733:L43P	L	-	2	0	ZNF737	20528357	0.968000	0.33430	0.623000	0.29173	0.623000	0.37688	1.610000	0.36869	0.165000	0.19558	0.163000	0.16589	CTT	.	.		0.333	ZNF737-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447844.2	NM_145289		G	20736517	A	G	20736517	3	3	323	1	0	0	0	0	1	0	0	0	18141	72	3	2	1494	2	ZNF737	19	20736517	Missense_Mutation	SNP	A	TCGA-MI-A75H-01A-11D-A32G-10	1367073	20736517	38392466	113	45593										
ZNF536	9745	hgsc.bcm.edu	37	chr19	30935240	30935240	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	gtggcccacccggtgccctcGcccaagcctgccagcgtgca	12	19	0	0			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr19:30935240G>A	ENST00000355537.3	+	2	918	c.771G>A	c.(769-771)tcG>tcA	p.S257S		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	257					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					CGGTGCCCTCGCCCAAGCCTG	0.726																																					p.S257S		Atlas-SNP	.											.	ZNF536	424	.	0			c.G771A						.						6	7	7					19																	30935240		2041	4038	6079	SO:0001819	synonymous_variant	9745	exon2			GCCCTCGCCCAAG		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"Zinc fingers, C2H2-type"	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.771G>A	chr19.hg19:g.30935240G>A		7.0	0.0		11.0	5.0	NM_014717	A2RU18	Silent	SNP	ENST00000355537.3	hg19	CCDS32984.1																																																																																			.	.		0.726	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		A	30935240	G	A	30935240	2	1	323	1	0	0	0	0	0	0	0	1	17989	1074	38	1		1	ZNF536	19	30935240	Silent	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10	10198723	30935240	28193743	114	45594										
SIGLEC9	27180	hgsc.bcm.edu	37	chr19	51633221	51633221	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	agcttctgcccgctcctcagTgggggaaggagagctccagt	14	12	2	1	rs377533277		TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr19:51633221T>C	ENST00000250360.3	+	7	1344	c.1277T>C	c.(1276-1278)gTg>gCg	p.V426A	SIGLEC9_ENST00000440804.3_Intron	NM_014441.2	NP_055256.1	Q9Y336	SIGL9_HUMAN	sialic acid binding Ig-like lectin 9	426					cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(3)|lung(25)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	45		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.000826)|OV - Ovarian serous cystadenocarcinoma(262;0.00295)		CGCTCCTCAGTGGGGGAAGGA	0.617																																					p.V426A		Atlas-SNP	.											.	SIGLEC9	85	.	0			c.T1277C						.						66	68	68					19																	51633221		2203	4300	6503	SO:0001583	missense	27180	exon7			CCTCAGTGGGGGA	AF135027	CCDS12825.1, CCDS56100.1	19q13.3-q13.4	2013-01-29			ENSG00000129450	ENSG00000129450		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10878	protein-coding gene	gene with protein product		605640				10903842	Standard	NM_014441		Approved	CD329	uc002pvu.3	Q9Y336		ENST00000250360.3:c.1277T>C	chr19.hg19:g.51633221T>C	ENSP00000250360:p.Val426Ala	76.0	0.0		138.0	29.0	NM_014441	Q6GTU4|Q9BYI9	Missense_Mutation	SNP	ENST00000250360.3	hg19	CCDS12825.1	.	.	.	.	.	.	.	.	.	.	.	0.026	-1.374328	0.01214	.	.	ENSG00000129450	ENST00000250360	T	0.04406	3.63	1.68	-3.36	0.04913	.	.	.	.	.	T	0.01592	0.0051	N	0.08118	0	0.09310	N	1	B	0.12630	0.006	B	0.13407	0.009	T	0.45116	-0.9283	9	0.02654	T	1	.	0.6084	0.00757	0.1948:0.3204:0.2742:0.2107	.	426	Q9Y336	SIGL9_HUMAN	A	426	ENSP00000250360:V426A	ENSP00000250360:V426A	V	+	2	0	SIGLEC9	56325033	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.773000	0.04689	-0.757000	0.04697	-0.505000	0.04504	GTG	.	.		0.617	SIGLEC9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464224.1	NM_014441		C	51633221	T	C	51633221	3	2	323	1	0	0	0	0	1	0	0	0	14330	1696	59	2	1303	2	SIGLEC9	19	51633221	Missense_Mutation	SNP	T	TCGA-MI-A75H-01A-11D-A32G-10	20697981	51633221	7495762	115	45595										
ZNF845	91664	hgsc.bcm.edu	37	chr19	53854549	53854549	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	ttactcacacaaaagcaggaAgtacacatgagagaaaaatc	7	8	1	2			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr19:53854549A>T	ENST00000595091.1	+	5	840	c.621A>T	c.(619-621)gaA>gaT	p.E207D	ZNF845_ENST00000458035.1_Missense_Mutation_p.E207D			Q96IR2	ZN845_HUMAN	zinc finger protein 845	207					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						AAAAGCAGGAAGTACACATGA	0.353																																					p.E207D		Atlas-SNP	.											.	ZNF845	101	.	0			c.A621T						.						62	47	51					19																	53854549		692	1591	2283	SO:0001583	missense	91664	exon4			GCAGGAAGTACAC	BC007307	CCDS46170.1	19q13.42	2013-01-08			ENSG00000213799	ENSG00000213799		"Zinc fingers, C2H2-type", "-"	25112	protein-coding gene	gene with protein product							Standard	NM_138374		Approved		uc010ydv.1	Q96IR2		ENST00000595091.1:c.621A>T	chr19.hg19:g.53854549A>T	ENSP00000470005:p.Glu207Asp	172.0	0.0		194.0	35.0	NM_138374		Missense_Mutation	SNP	ENST00000595091.1	hg19	CCDS46170.1	.	.	.	.	.	.	.	.	.	.	A	12.52	1.962186	0.34659	.	.	ENSG00000213799	ENST00000458035;ENST00000427984	T	0.28454	1.61	1.5	0.452	0.16634	.	.	.	.	.	T	0.25044	0.0608	L	0.50333	1.59	0.09310	N	1	B	0.21309	0.054	B	0.20184	0.028	T	0.25537	-1.0129	9	0.48119	T	0.1	.	5.7115	0.17937	0.8385:0.0:0.1615:0.0	.	207	Q96IR2	ZN845_HUMAN	D	207	ENSP00000388311:E207D	ENSP00000412086:E207D	E	+	3	2	ZNF845	58546361	0.000000	0.05858	0.001000	0.08648	0.346000	0.29079	-2.079000	0.01369	0.075000	0.16796	0.172000	0.16884	GAA	.	.		0.353	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908		T	53854549	A	T	53854549	3	4	323	1	0	0	0	0	1	0	0	0	18206	69	3	4	631	4	ZNF845	19	53854549	Missense_Mutation	SNP	A	TCGA-MI-A75H-01A-11D-A32G-10	2221328	53854549	5274434	116	45596										
ZNF845	91664	hgsc.bcm.edu	37	chr19	53856524	53856524	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	acaagtgtagtgaatgtggcAaggtttttaatagaaaagca	11	3	0	2			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr19:53856524A>T	ENST00000595091.1	+	5	2815	c.2596A>T	c.(2596-2598)Aag>Tag	p.K866*	ZNF845_ENST00000458035.1_Nonsense_Mutation_p.K866*			Q96IR2	ZN845_HUMAN	zinc finger protein 845	866					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						TGAATGTGGCAAGGTTTTTAA	0.368																																					p.K866X		Atlas-SNP	.											.	ZNF845	101	.	0			c.A2596T						.						41	38	39					19																	53856524		692	1591	2283	SO:0001587	stop_gained	91664	exon4			TGTGGCAAGGTTT	BC007307	CCDS46170.1	19q13.42	2013-01-08			ENSG00000213799	ENSG00000213799		"Zinc fingers, C2H2-type", "-"	25112	protein-coding gene	gene with protein product							Standard	NM_138374		Approved		uc010ydv.1	Q96IR2		ENST00000595091.1:c.2596A>T	chr19.hg19:g.53856524A>T	ENSP00000470005:p.Lys866*	86.0	0.0		173.0	37.0	NM_138374		Nonsense_Mutation	SNP	ENST00000595091.1	hg19	CCDS46170.1	.	.	.	.	.	.	.	.	.	.	A	35	5.523278	0.96431	.	.	ENSG00000213799	ENST00000458035;ENST00000427984	.	.	.	2.07	0.986	0.19784	.	.	.	.	.	.	.	.	.	.	.	0.48452	D	0.999652	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.0713	0.19891	0.8554:0.0:0.1446:0.0	.	.	.	.	X	866;782	.	ENSP00000412086:K782X	K	+	1	0	ZNF845	58548336	0.119000	0.22226	0.000000	0.03702	0.017000	0.09413	2.116000	0.41930	0.069000	0.16605	0.378000	0.23410	AAG	.	.		0.368	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908		T	53856524	A	T	53856524	4	4	323	1	0	0	0	0	0	1	0	0	18206	131	5	4	2606	4	ZNF845	19	53856524	Nonsense_Mutation	SNP	A	TCGA-MI-A75H-01A-11D-A32G-10	1975	53856524	5272459	117	45597										
KIR2DL3	3804	hgsc.bcm.edu	37	chr19	55263136	55263136	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	tgcatgttctgattgggaccTcagtggtcatcatcctcttc	9	11	5	1			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr19:55263136T>A	ENST00000342376.3	+	6	782	c.751T>A	c.(751-753)Tca>Aca	p.S251T	KIR3DL1_ENST00000538269.1_Intron|KIR3DL1_ENST00000541392.1_Intron|CTB-61M7.1_ENST00000400864.3_RNA|KIR3DL1_ENST00000402254.2_Intron|KIR2DL4_ENST00000396284.2_Intron|KIR2DL3_ENST00000434419.2_Intron	NM_015868.2	NP_056952.2	P43628	KI2L3_HUMAN	killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail, 3	251					immune response (GO:0006955)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|large_intestine(1)|lung(11)|ovary(3)|pancreas(1)|skin(2)|urinary_tract(1)	21				GBM - Glioblastoma multiforme(193;0.0192)		GATTGGGACCTCAGTGGtcat	0.468																																					p.S251T		Atlas-SNP	.											.	KIR2DL3	68	.	0			c.T751A						.						173	147	156					19																	55263136		1424	2573	3997	SO:0001583	missense	3804	exon6			GGGACCTCAGTGG	L41268	CCDS33107.1	19q13.4	2013-01-29				ENSG00000243772		"Killer cell immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6331	protein-coding gene	gene with protein product		604938				7749980, 8662091	Standard	XM_006725426		Approved	cl-6, nkat2, nkat2a, nkat2b, p58, CD158B2		P43628	OTTHUMG00000065887	ENST00000342376.3:c.751T>A	chr19.hg19:g.55263136T>A	ENSP00000342215:p.Ser251Thr	22.0	0.0		14.0	7.0	NM_015868	O43472|P78402|Q14944|Q14945|Q9UM51|Q9UQ70	Missense_Mutation	SNP	ENST00000342376.3	hg19	CCDS33107.1	.	.	.	.	.	.	.	.	.	.	T	7.003	0.555186	0.13436	.	.	ENSG00000243772	ENST00000342376	T	0.00492	7.01	0.635	0.635	0.17723	.	.	.	.	.	T	0.02156	0.0067	M	0.94142	3.5	0.09310	N	1	D;P;D;D	0.69078	0.972;0.877;0.997;0.997	P;D;D;D	0.69654	0.776;0.916;0.965;0.965	T	0.20107	-1.0285	8	0.87932	D	0	.	.	.	.	.	251;153;251;251	E3NZD7;P43628-2;P43628;E3NZD8	.;.;KI2L3_HUMAN;.	T	251	ENSP00000342215:S251T	ENSP00000342215:S251T	S	+	1	0	KIR2DL3	59954948	0.003000	0.15002	0.002000	0.10522	0.013000	0.08279	1.475000	0.35409	0.516000	0.28340	0.248000	0.18094	TCA	.	.		0.468	KIR2DL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000141150.1			A	55263136	T	A	55263136	3	1	323	1	0	0	0	0	1	0	0	0	8326	1551	54	4	773	4	KIR2DL3	19	55263136	Missense_Mutation	SNP	T	TCGA-MI-A75H-01A-11D-A32G-10	1406612	55263136	3865847	118	45598										
ZNF417	147687	hgsc.bcm.edu	37	chr19	58419943	58419943	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	aggcctttctcctgtgtgaaCtctgatgatgaaggagggta	13	7	2	4			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr19:58419943C>T	ENST00000312026.5	-	3	1867	c.1703G>A	c.(1702-1704)aGt>aAt	p.S568N	CTD-2583A14.9_ENST00000602124.1_Intron|ZNF417_ENST00000536263.1_Missense_Mutation_p.S369N|ZNF417_ENST00000595559.1_Missense_Mutation_p.S567N	NM_152475.2	NP_689688.2	Q8TAU3	ZN417_HUMAN	zinc finger protein 417	568					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|stomach(3)|upper_aerodigestive_tract(1)	18		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0151)		CCTGTGTGAACTCTGATGATG	0.423																																					p.S568N		Atlas-SNP	.											.	ZNF417	44	.	0			c.G1703A						.						76	78	77					19																	58419943		2203	4297	6500	SO:0001583	missense	147687	exon3			TGTGAACTCTGAT	BC025783	CCDS12965.1, CCDS74469.1	19q13.43	2013-01-08				ENSG00000173480		"Zinc fingers, C2H2-type", "-"	20646	protein-coding gene	gene with protein product							Standard	NM_152475		Approved	MGC34079	uc002qqq.3	Q8TAU3		ENST00000312026.5:c.1703G>A	chr19.hg19:g.58419943C>T	ENSP00000311319:p.Ser568Asn	185.0	0.0		346.0	67.0	NM_152475	B4DEU1	Missense_Mutation	SNP	ENST00000312026.5	hg19	CCDS12965.1	.	.	.	.	.	.	.	.	.	.	.	10.07	1.249834	0.22880	.	.	ENSG00000173480	ENST00000312026;ENST00000536263	T;T	0.06687	3.4;3.27	2.65	-2.31	0.06765	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06050	0.0157	L	0.28274	0.84	0.09310	N	1	B	0.14438	0.01	B	0.12156	0.007	T	0.38265	-0.9669	9	0.87932	D	0	.	8.291	0.31958	0.0:0.5528:0.0:0.4472	.	568	Q8TAU3	ZN417_HUMAN	N	568;369	ENSP00000311319:S568N;ENSP00000442760:S369N	ENSP00000311319:S568N	S	-	2	0	ZNF417	63111755	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-1.066000	0.03454	-0.328000	0.08539	0.461000	0.40582	AGT	.	.		0.423	ZNF417-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466860.1	NM_152475		T	58419943	C	T	58419943	3	4	323	1	0	0	0	0	1	0	0	0	17909	565	20	3	28	3	ZNF417	19	58419943	Missense_Mutation	SNP	C	TCGA-MI-A75H-01A-11D-A32G-10	3156807	58419943	709040	119	45599										
ZBP1	81030	hgsc.bcm.edu	37	chr20	56179629	56179629	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	gccccacgtgaggctgtgcaCtaaatcccacctccccacca	7	19	0	1			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr20:56179629C>T	ENST00000371173.3	-	8	1467	c.1290G>A	c.(1288-1290)taG>taA	p.*430*	ZBP1_ENST00000340462.4_Silent_p.*407*|ZBP1_ENST00000395822.3_Silent_p.*355*	NM_001160417.1|NM_030776.2	NP_001153889.1|NP_110403.2	Q9H171	ZBP1_HUMAN	Z-DNA binding protein 1	0					innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|left-handed Z-DNA binding (GO:0003692)|RNA binding (GO:0003723)			large_intestine(11)|lung(8)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	27	Lung NSC(12;0.000545)|all_lung(29;0.00195)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;7.87e-13)|Epithelial(14;3.26e-09)|all cancers(14;3.62e-08)			AGGCTGTGCACTAAATCCCAC	0.562																																					p.X430X		Atlas-SNP	.											.	ZBP1	65	.	0			c.G1290A						.						91	82	85					20																	56179629		2203	4300	6503	SO:0001819	synonymous_variant	81030	exon8			TGTGCACTAAATC	AJ300575	CCDS13461.1, CCDS54477.1, CCDS54478.1	20q13.31	2009-08-21	2002-07-25	2002-07-26	ENSG00000124256	ENSG00000124256			16176	protein-coding gene	gene with protein product	"DNA-dependent activator of IRFs"	606750	"chromosome 20 open reading frame 183"	C20orf183		11842111	Standard	NM_030776		Approved	dJ718J7.3, DLM1, DLM-1, DAI	uc002xyo.3	Q9H171	OTTHUMG00000032824	ENST00000371173.3:c.1290G>A	chr20.hg19:g.56179629C>T		50.0	0.0		50.0	12.0	NM_030776	A2A2F7|B3KVA1|F5GYT1|Q5JY39|Q9BYW4	Silent	SNP	ENST00000371173.3	hg19	CCDS13461.1																																																																																			.	.		0.562	ZBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079849.1	NM_030776		T	56179629	C	T	56179629	2	4	323	1	0	0	0	0	0	0	0	1	17536	576	20	3		3	ZBP1	20	56179629	Silent	SNP	C	TCGA-MI-A75H-01A-11D-A32G-10		56179629	6845891	120	45600										
PPDPF	79144	hgsc.bcm.edu	37	chr20	62153144	62153144	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	acctccccaggcctccagcaGcatgaccgcctgtggcctgg	11	18	0	1			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr20:62153144G>A	ENST00000370179.3	+	4	453	c.257G>A	c.(256-258)aGc>aAc	p.S86N	PPDPF_ENST00000370177.1_Missense_Mutation_p.S112N|PPDPF_ENST00000473620.1_3'UTR	NM_024299.2	NP_077275.1	Q9H3Y8	PPDPF_HUMAN	pancreatic progenitor cell differentiation and proliferation factor	86					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)					kidney(1)|lung(2)|ovary(1)	4						GCCTCCAGCAGCATGACCGCC	0.672																																					p.S86N		Atlas-SNP	.											.	PPDPF	6	.	0			c.G257A						.						27	28	28					20																	62153144		2200	4299	6499	SO:0001583	missense	79144	exon4			CCAGCAGCATGAC	AL121829	CCDS13523.1	20q13.33	2013-07-23	2013-07-23	2009-06-04	ENSG00000125534	ENSG00000125534			16142	protein-coding gene	gene with protein product	"exocrine differentiation and proliferation factor"		"chromosome 20 open reading frame 149", "pancreatic progenitor cell differentiation and proliferation factor homolog (zebrafish)"	C20orf149			Standard	NM_024299		Approved	dJ697K14.9, exdpf	uc002yff.3	Q9H3Y8	OTTHUMG00000032978	ENST00000370179.3:c.257G>A	chr20.hg19:g.62153144G>A	ENSP00000359198:p.Ser86Asn	51.0	0.0		52.0	21.0	NM_024299	E1P5J2|Q4VXP1|Q9H3Y7	Missense_Mutation	SNP	ENST00000370179.3	hg19	CCDS13523.1	.	.	.	.	.	.	.	.	.	.	.	0.017	-1.501254	0.01001	.	.	ENSG00000125534	ENST00000370179;ENST00000370177	.	.	.	4.38	3.43	0.39272	.	0.702747	0.14155	N	0.337752	T	0.36026	0.0952	L	0.29908	0.895	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.21348	-1.0248	9	0.37606	T	0.19	-1.3352	11.9002	0.52680	0.0865:0.0:0.9135:0.0	.	86	Q9H3Y8	PPDPF_HUMAN	N	86;112	.	ENSP00000359196:S112N	S	+	2	0	PPDPF	61623588	0.001000	0.12720	0.003000	0.11579	0.013000	0.08279	0.691000	0.25467	0.837000	0.34925	-0.145000	0.13849	AGC	.	.		0.672	PPDPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080149.1			A	62153144	G	A	62153144	3	1	323	1	0	0	0	0	1	0	0	0	12315	971	34	3	267	3	PPDPF	20	62153144	Missense_Mutation	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10	5973515	62153144	872376	121	45601										
TPTE	7179	hgsc.bcm.edu	37	chr21	10942966	10942966	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	tgtcttttttgatgaaacagAtgaaaaattcttaacagaat	6	4	2	5			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr21:10942966A>T	ENST00000361285.4	-	12	950	c.621T>A	c.(619-621)caT>caA	p.H207Q	TPTE_ENST00000415664.2_5'UTR|TPTE_ENST00000298232.7_Missense_Mutation_p.H189Q|TPTE_ENST00000342420.5_Missense_Mutation_p.H169Q	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	207					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		GATGAAACAGATGAAAAATTC	0.318																																					p.H207Q		Atlas-SNP	.											.	TPTE	513	.	0			c.T621A						.						87	81	83					21																	10942966		2203	4299	6502	SO:0001583	missense	7179	exon12			AAACAGATGAAAA	AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	12023	protein-coding gene	gene with protein product	"PTEN-related tyrosine phosphatase", "cancer/testis antigen 44"	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.621T>A	chr21.hg19:g.10942966A>T	ENSP00000355208:p.His207Gln	695.0	0.0		572.0	99.0	NM_199261	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Missense_Mutation	SNP	ENST00000361285.4	hg19	CCDS13560.2	.	.	.	.	.	.	.	.	.	.	.	0.723	-0.782935	0.02907	.	.	ENSG00000166157	ENST00000298232;ENST00000361285;ENST00000342420	D;D;D	0.97404	-4.37;-4.37;-4.37	2.07	-0.677	0.11357	Ion transport (1);	0.250767	0.35708	N	0.003023	D	0.92977	0.7765	L	0.51422	1.61	0.23156	N	0.998209	B;B;B	0.32862	0.12;0.2;0.387	B;B;B	0.35813	0.112;0.112;0.211	D	0.85531	0.1209	10	0.30854	T	0.27	-21.1403	3.6276	0.08119	0.5657:0.22:0.0:0.2143	.	169;189;207	P56180-3;P56180-2;P56180	.;.;TPTE_HUMAN	Q	189;207;169	ENSP00000298232:H189Q;ENSP00000355208:H207Q;ENSP00000344441:H169Q	ENSP00000298232:H189Q	H	-	3	2	TPTE	9964837	0.825000	0.29262	0.243000	0.24186	0.026000	0.11368	-0.312000	0.08113	-0.144000	0.11314	0.163000	0.16589	CAT	.	.		0.318	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1			T	10942966	A	T	10942966	3	4	323	1	0	0	0	0	1	0	0	0	16445	330	12	4	1086	4	TPTE	21	10942966	Missense_Mutation	SNP	A	TCGA-MI-A75H-01A-11D-A32G-10		10942966	37186929	122	45602										
SHANK3	85358	hgsc.bcm.edu	37	chr22	51113571	51113571	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	ctccaggacgcgctcaactaTgggcttttccagccgccctc	9	17	1	0			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chr22:51113571T>C	ENST00000414786.2	+	2	386	c.159T>C	c.(157-159)taT>taC	p.Y53Y	SHANK3_ENST00000445220.2_Silent_p.Y53Y|SHANK3_ENST00000262795.3_Silent_p.Y53Y			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	53	Intramolecular interaction with the ANK repeats. {ECO:0000250}.				adult behavior (GO:0030534)|alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|brain morphogenesis (GO:0048854)|dendritic spine morphogenesis (GO:0060997)|guanylate kinase-associated protein clustering (GO:0097117)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell volume (GO:0045794)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glutamate receptor signaling pathway (GO:1900451)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse structural plasticity (GO:0051835)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density assembly (GO:0097107)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of long term synaptic depression (GO:1900452)|regulation of long-term synaptic potentiation (GO:1900271)|social behavior (GO:0035176)|striatal medium spiny neuron differentiation (GO:0021773)|synapse assembly (GO:0007416)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)	8		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)		CGCTCAACTATGGGCTTTTCC	0.711																																					p.Y53Y		Atlas-SNP	.											.	SHANK3	96	.	0			c.T159C						.						6	7	7					22																	51113571		1811	3906	5717	SO:0001819	synonymous_variant	85358	exon2			CAACTATGGGCTT	AB051437		22q13.3	2013-11-14			ENSG00000251322	ENSG00000251322		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	14294	protein-coding gene	gene with protein product	"proline rich synapse associated protein 2", "shank postsynaptic density protein"	606230				11258795, 11431708, 10806096, 17173049	Standard	NM_033517		Approved	SPANK-2, prosap2, KIAA1650, PSAP2	uc031ryd.1	Q9BYB0	OTTHUMG00000150169	ENST00000414786.2:c.159T>C	chr22.hg19:g.51113571T>C		29.0	0.0		32.0	24.0	NM_033517	D7UT47|Q8TET3	Silent	SNP	ENST00000414786.2	hg19																																																																																				.	.		0.711	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420		C	51113571	T	C	51113571	2	2	323	1	0	0	0	0	0	0	0	1	14281	1471	51	2		2	SHANK3	22	51113571	Silent	SNP	T	TCGA-MI-A75H-01A-11D-A32G-10		51113571	190995	123	45603										
SSX1	6756	hgsc.bcm.edu	37	chrX	48125757	48125757	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	aacatgcctggacccacagaCtgcgtgagagaaagcagctg	12	11	0	3			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chrX:48125757C>A	ENST00000376919.3	+	7	638	c.502C>A	c.(502-504)Ctg>Atg	p.L168M		NM_001278691.1|NM_005635.2	NP_001265620.1|NP_005626.1	Q16384	SSX1_HUMAN	synovial sarcoma, X breakpoint 1	168					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|transcription corepressor activity (GO:0003714)		SS18/SSX1(1169)|SS18L1/SSX1(2)	endometrium(2)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	9						GACCCACAGACTGCGTGAGAG	0.498			T	SS18	synovial sarcoma																																p.L168M	Esophageal Squamous(175;994 1982 2214 6527 18857)	Atlas-SNP	.		Dom	yes		X	Xp11.23-p11.22	6756	"synovial sarcoma, X breakpoint 1"		M	.	SSX1	27	.	0			c.C502A						.						289	281	284					X																	48125757		1511	2706	4217	SO:0001583	missense	6756	exon7			CACAGACTGCGTG	BC001003	CCDS14290.1	Xp11.23	2009-03-12			ENSG00000126752	ENSG00000126752			11335	protein-coding gene	gene with protein product	"cancer/testis antigen family 5, member 1"	312820				7655467	Standard	NM_005635		Approved	CT5.1	uc004djb.1	Q16384	OTTHUMG00000021488	ENST00000376919.3:c.502C>A	chrX.hg19:g.48125757C>A	ENSP00000366118:p.Leu168Met	238.0	0.0		216.0	170.0	NM_005635	A3KN76|Q08AJ2|Q5JQ64	Missense_Mutation	SNP	ENST00000376919.3	hg19	CCDS14290.1	.	.	.	.	.	.	.	.	.	.	N	11.26	1.587650	0.28268	.	.	ENSG00000126752	ENST00000376919	T	0.19806	2.12	2.39	-1.68	0.08212	SSXRD motif (1);	0.211314	0.23727	N	0.045164	T	0.34337	0.0894	L	0.61218	1.895	0.09310	N	1	D	0.69078	0.997	D	0.79108	0.992	T	0.14615	-1.0466	10	0.87932	D	0	.	6.4281	0.21780	0.0:0.338:0.0:0.662	.	168	Q16384	SSX1_HUMAN	M	168	ENSP00000366118:L168M	ENSP00000366118:L168M	L	+	1	2	SSX1	48010701	0.004000	0.15560	0.000000	0.03702	0.031000	0.12232	-0.573000	0.05874	-0.651000	0.05415	0.380000	0.24917	CTG	.	.		0.498	SSX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056485.1	NM_005635		A	48125757	C	A	48125757	3	1	323	1	0	0	0	0	1	0	0	0	15218	564	20	3	524	3	SSX1	23	48125757	Missense_Mutation	SNP	C	TCGA-MI-A75H-01A-11D-A32G-10		48125757	107144803	124	45604										
ZXDA	7789	hgsc.bcm.edu	37	chrX	57936473	57936473	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	gcccgcggggttcgcgccgcTctcgtccccctggagccccg	14	20	1	0			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chrX:57936473T>G	ENST00000358697.4	-	1	594	c.382A>C	c.(382-384)Agc>Cgc	p.S128R		NM_007156.4	NP_009087.1	P98168	ZXDA_HUMAN	zinc finger, X-linked, duplicated A	128					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(9)|kidney(1)|large_intestine(7)|lung(13)|ovary(2)|prostate(2)|skin(1)	37						TTCGCGCCGCTCTCGTCCCCC	0.786																																					p.S128R		Atlas-SNP	.											.	ZXDA	70	.	0			c.A382C						.						4	5	4					X																	57936473		1900	3614	5514	SO:0001583	missense	7789	exon1			CGCCGCTCTCGTC	L14787	CCDS14376.1	Xp11.21	2013-01-08			ENSG00000198205	ENSG00000198205		"Zinc fingers, C2H2-type"	13198	protein-coding gene	gene with protein product	"zinc finger protein 896"	300235				8268913	Standard	NM_007156		Approved	ZNF896	uc004dve.3	P98168	OTTHUMG00000021688	ENST00000358697.4:c.382A>C	chrX.hg19:g.57936473T>G	ENSP00000351530:p.Ser128Arg	8.0	0.0		9.0	8.0	NM_007156	Q9UJP7	Missense_Mutation	SNP	ENST00000358697.4	hg19	CCDS14376.1	.	.	.	.	.	.	.	.	.	.	.	7.693	0.691444	0.15039	.	.	ENSG00000198205	ENST00000358697	T	0.49720	0.77	3.98	-1.53	0.08611	.	1.037060	0.07616	N	0.926158	T	0.33323	0.0859	L	0.40543	1.245	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.23833	-1.0177	9	.	.	.	.	5.1565	0.15038	0.0:0.3586:0.3706:0.2708	.	128	P98168	ZXDA_HUMAN	R	128	ENSP00000351530:S128R	.	S	-	1	0	ZXDA	57953198	0.000000	0.05858	0.004000	0.12327	0.044000	0.14063	-1.923000	0.01567	-0.178000	0.10672	0.235000	0.17854	AGC	.	.		0.786	ZXDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056925.1	NM_007156		G	57936473	T	G	57936473	3	3	323	1	0	0	0	0	1	0	0	0	18265	1551	54	5	2021	5	ZXDA	23	57936473	Missense_Mutation	SNP	T	TCGA-MI-A75H-01A-11D-A32G-10	9810716	57936473	97334087	125	45605										
NAP1L2	4674	hgsc.bcm.edu	37	chrX	72434298	72434298	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	ctcttcttgactggattctgAcagctccttgcggttctctg	9	12	4	2			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chrX:72434298A>G	ENST00000373517.3	-	1	386	c.31T>C	c.(31-33)Tca>Cca	p.S11P	NAP1L2_ENST00000536638.1_Intron	NM_021963.3	NP_068798.1	Q9ULW6	NP1L2_HUMAN	nucleosome assembly protein 1-like 2	11					nucleosome assembly (GO:0006334)|positive regulation of histone H3-K14 acetylation (GO:0071442)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of neuron differentiation (GO:0045666)|regulation of stem cell division (GO:2000035)	nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(12)|skin(3)	29	Renal(35;0.156)					CTGGATTCTGACAGCTCCTTG	0.547																																					p.S11P		Atlas-SNP	.											.	NAP1L2	77	.	0			c.T31C						.						53	58	56					X																	72434298		2179	4190	6369	SO:0001583	missense	4674	exon1			ATTCTGACAGCTC	AF136178	CCDS14423.1	Xq13	2008-02-05			ENSG00000186462	ENSG00000186462			7638	protein-coding gene	gene with protein product		300026				8789438	Standard	NM_021963		Approved	BPX, MGC26243	uc004ebi.3	Q9ULW6	OTTHUMG00000021827	ENST00000373517.3:c.31T>C	chrX.hg19:g.72434298A>G	ENSP00000362616:p.Ser11Pro	135.0	0.0		119.0	86.0	NM_021963	B2RE61|B4E161|Q8TAN6	Missense_Mutation	SNP	ENST00000373517.3	hg19	CCDS14423.1	.	.	.	.	.	.	.	.	.	.	a	3.261	-0.151099	0.06585	.	.	ENSG00000186462	ENST00000373517	T	0.32515	1.45	2.94	2.94	0.34122	.	1.336430	0.06283	U	0.697753	T	0.16854	0.0405	N	0.14661	0.345	0.23425	N	0.9977	P	0.38078	0.617	B	0.31614	0.133	T	0.12604	-1.0541	10	0.37606	T	0.19	-8.3847	6.7261	0.23357	1.0:0.0:0.0:0.0	.	11	Q9ULW6	NP1L2_HUMAN	P	11	ENSP00000362616:S11P	ENSP00000362616:S11P	S	-	1	0	NAP1L2	72351023	0.983000	0.35010	0.236000	0.24074	0.152000	0.21847	3.022000	0.49659	1.390000	0.46547	0.441000	0.28932	TCA	.	.		0.547	NAP1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057225.1	NM_021963		G	72434298	A	G	72434298	3	3	323	1	0	0	0	0	1	0	0	0	10166	275	10	2	1355	2	NAP1L2	23	72434298	Missense_Mutation	SNP	A	TCGA-MI-A75H-01A-11D-A32G-10	14497825	72434298	82836262	126	45606										
KLHL4	56062	hgsc.bcm.edu	37	chrX	86877345	86877345	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	catgctctaatgcagtgggtGgggcatgatgtgcagaatag	15	6	1	2			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chrX:86877345G>T	ENST00000373119.4	+	5	1204	c.1059G>T	c.(1057-1059)gtG>gtT	p.V353V	KLHL4_ENST00000373114.4_Silent_p.V353V	NM_019117.4	NP_061990.2	Q9C0H6	KLHL4_HUMAN	kelch-like family member 4	353						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(29)|ovary(2)|prostate(1)|skin(1)	67						TGCAGTGGGTGGGGCATGATG	0.443																																					p.V353V		Atlas-SNP	.											.	KLHL4	263	.	0			c.G1059T						.						157	129	138					X																	86877345		2203	4300	6503	SO:0001819	synonymous_variant	56062	exon5			GTGGGTGGGGCAT	AF284765	CCDS14456.1, CCDS14457.1	Xq21.3	2013-01-30	2013-01-30		ENSG00000102271	ENSG00000102271		"Kelch-like", "BTB/POZ domain containing"	6355	protein-coding gene	gene with protein product		300348	"kelch (Drosophila)-like 4", "kelch-like 4 (Drosophila)"			11401425	Standard	NM_019117		Approved	KIAA1687, DKELCHL, KHL4	uc004efa.2	Q9C0H6	OTTHUMG00000021946	ENST00000373119.4:c.1059G>T	chrX.hg19:g.86877345G>T		173.0	1.0		122.0	83.0	NM_019117	B2RTW2|Q9Y3J5	Silent	SNP	ENST00000373119.4	hg19	CCDS14457.1																																																																																			.	.		0.443	KLHL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057413.1			T	86877345	G	T	86877345	2	4	323	1	0	0	0	0	0	0	0	1	8400	1335	47	3		3	KLHL4	23	86877345	Silent	SNP	G	TCGA-MI-A75H-01A-11D-A32G-10	14443047	86877345	68393215	127	45607										
IL9R	3581	hgsc.bcm.edu	37	chrX	155233487	155233487	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.046875	6	1	1.26821654481229	0	1.34068606165871	0.0137299771167048	0.256064073226545	0	ctgggagggagcaggtcagcCtggtggacccggagtacctg	18	10	1	0			TCGA-MI-A75H-01A-11D-A32G-10	TCGA-MI-A75H-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2f0c1405-3730-4b0c-a6c4-679e1bd0c6cf	9804bf31-f0fd-4531-bca1-3ac172fc2b29	g.chrX:155233487C>T	ENST00000244174.5	+	4	579	c.400C>T	c.(400-402)Ctg>Ttg	p.L134L	IL9R_ENST00000369423.2_Silent_p.A178A|IL9R_ENST00000424344.3_Silent_p.L113L|IL9R_ENST00000540897.1_Silent_p.A168A	NM_002186.2	NP_002177.2	Q01113	IL9R_HUMAN	interleukin 9 receptor	134					cell proliferation (GO:0008283)|positive regulation of cell growth (GO:0030307)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	interleukin-9 receptor activity (GO:0004919)			NS(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(12)|upper_aerodigestive_tract(1)	23	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					GCAGGTCAGCCTGGTGGACCC	0.617																																					p.A178A		Atlas-SNP	.											.	IL9R	73	.	0			c.C534T						.						108	99	102					X																	155233487		2203	4296	6499	SO:0001819	synonymous_variant	3581	exon5			GTCAGCCTGGTGG	M84747	CCDS14771.4, CCDS59180.1	Xq28 and Yq12	2008-02-05			ENSG00000124334	ENSG00000124334		"Pseudoautosomal regions / PAR2", "Interleukins and interleukin receptors", "CD molecules"	6030	protein-coding gene	gene with protein product		300007				1376929, 8666384	Standard	NM_002186		Approved	CD129	uc004fnv.1	Q01113	OTTHUMG00000022720	ENST00000244174.5:c.400C>T	chrX.hg19:g.155233487C>T		113.0	0.0		121.0	38.0	NM_176786	B9ZVT0|Q14634|Q8WWU1|Q96TF0	Silent	SNP	ENST00000244174.5	hg19	CCDS14771.4																																																																																			.	.		0.617	IL9R-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058981.1	NM_002186		T	155233487	C	T	155233487	2	4	323	1	0	0	0	0	0	0	0	1	7717	680	24	3		3	IL9R	23	155233487	Silent	SNP	C	TCGA-MI-A75H-01A-11D-A32G-10	68356142	155233487	37073	128	45608										
PTCHD2	57540	hgsc.bcm.edu	37	chr1	11574466	11574466	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	gcaaagtccaggttctctatGgggggacagacctgtttgac	13	9	1	2			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr1:11574466G>T	ENST00000294484.6	+	4	1474	c.1336G>T	c.(1336-1338)Ggg>Tgg	p.G446W	PTCHD2_ENST00000389575.3_Missense_Mutation_p.G446W	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	446					cholesterol homeostasis (GO:0042632)|regulation of lipid transport (GO:0032368)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hedgehog receptor activity (GO:0008158)			NS(3)|breast(2)|endometrium(9)|kidney(4)|large_intestine(5)|lung(34)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	76	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		GGTTCTCTATGGGGGGACAGA	0.512																																					p.G446W		Atlas-SNP	.											.	PTCHD2	193	.	0			c.G1336T						.						130	128	129					1																	11574466		1981	4166	6147	SO:0001583	missense	57540	exon4			CTCTATGGGGGGA	AB037758	CCDS41247.1	1p36.22	2010-02-17			ENSG00000204624	ENSG00000204624			29251	protein-coding gene	gene with protein product		611251				15738394	Standard	NM_020780		Approved	KIAA1337, DISP3	uc001ash.4	Q9P2K9	OTTHUMG00000002074	ENST00000294484.6:c.1336G>T	chr1.hg19:g.11574466G>T	ENSP00000294484:p.Gly446Trp	61.0	0.0		41.0	13.0	NM_020780	Q5VTU9|Q9UJD6	Missense_Mutation	SNP	ENST00000294484.6	hg19	CCDS41247.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.031930	0.75504	.	.	ENSG00000204624	ENST00000294484;ENST00000389575	D;D	0.96459	-4.02;-4.02	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	D	0.97318	0.9123	L	0.52573	1.65	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97697	1.0182	10	0.54805	T	0.06	-33.4867	17.7404	0.88405	0.0:0.0:1.0:0.0	.	446	Q9P2K9	PTHD2_HUMAN	W	446	ENSP00000294484:G446W;ENSP00000374226:G446W	ENSP00000294484:G446W	G	+	1	0	PTCHD2	11497053	1.000000	0.71417	0.761000	0.31378	0.743000	0.42351	9.391000	0.97249	2.490000	0.84030	0.655000	0.94253	GGG	.	.		0.512	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561		T	11574466	G	T	11574466	3	4	324	1	0	0	0	0	1	0	0	0	12745	1348	47	3	1346	3	PTCHD2	1	11574466	Missense_Mutation	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10		11574466	237676155	1	45609										
PADI4	23569	hgsc.bcm.edu	37	chr1	17690059	17690059	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	agcacctgggcatccccaagCccttcgggcccgtcatcaac	9	18	2	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr1:17690059C>A	ENST00000375448.4	+	16	1827	c.1801C>A	c.(1801-1803)Ccc>Acc	p.P601T		NM_012387.2	NP_036519.2	Q9UM07	PADI4_HUMAN	peptidyl arginine deiminase, type IV	601					cellular protein modification process (GO:0006464)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|histone citrullination (GO:0036414)|histone H3-R26 citrullination (GO:0036413)|innate immune response (GO:0045087)|nucleosome assembly (GO:0006334)|protein citrullination (GO:0018101)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	arginine deiminase activity (GO:0016990)|calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(13)|ovary(2)|skin(2)|urinary_tract(3)	26		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000338)|Lung NSC(340;0.00042)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00537)|BRCA - Breast invasive adenocarcinoma(304;8.54e-06)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(64;0.000223)|KIRC - Kidney renal clear cell carcinoma(64;0.00313)|STAD - Stomach adenocarcinoma(196;0.00707)|READ - Rectum adenocarcinoma(331;0.0689)|Lung(427;0.199)	L-Citrulline(DB00155)	CATCCCCAAGCCCTTCGGGCC	0.622																																					p.P601T		Atlas-SNP	.											.	PADI4	70	.	0			c.C1801A						.						41	39	40					1																	17690059		2203	4300	6503	SO:0001583	missense	23569	exon16			CCCAAGCCCTTCG	AB017919	CCDS180.1	1p36.13	2014-06-06	2003-02-12		ENSG00000159339	ENSG00000159339	3.5.3.15	"Peptidyl arginine deiminases"	18368	protein-coding gene	gene with protein product		605347	"peptidyl arginine deiminase, type V"	PADI5		10488123	Standard	NM_012387		Approved	PAD, PDI5, PDI4	uc001baj.2	Q9UM07	OTTHUMG00000002371	ENST00000375448.4:c.1801C>A	chr1.hg19:g.17690059C>A	ENSP00000364597:p.Pro601Thr	84.0	0.0		114.0	50.0	NM_012387	A8K392|B2RBW0|Q5VTZ8|Q70SX4	Missense_Mutation	SNP	ENST00000375448.4	hg19	CCDS180.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.189475	0.78789	.	.	ENSG00000159339	ENST00000375448	T	0.58060	0.36	5.03	4.12	0.48240	Protein-arginine deiminase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.79936	0.4532	H	0.96365	3.81	0.42729	D	0.9937	D	0.89917	1.0	D	0.83275	0.996	D	0.85769	0.1354	10	0.87932	D	0	-30.2633	12.5475	0.56208	0.0:0.918:0.0:0.082	.	601	Q9UM07	PADI4_HUMAN	T	601	ENSP00000364597:P601T	ENSP00000364597:P601T	P	+	1	0	PADI4	17562646	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.588000	0.82629	1.258000	0.44101	0.561000	0.74099	CCC	.	.		0.622	PADI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006799.1	NM_012387		A	17690059	C	A	17690059	3	1	324	1	0	0	0	0	1	0	0	0	11389	739	26	3	1863	3	PADI4	1	17690059	Missense_Mutation	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	6115593	17690059	231560562	2	45610										
PTCH2	8643	hgsc.bcm.edu	37	chr1	45292375	45292375	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	gatggcctccacaaagtctgCagtcttctggaggccacgca	11	13	3	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr1:45292375C>T	ENST00000372192.3	-	18	2891	c.2761G>A	c.(2761-2763)Gca>Aca	p.A921T	PTCH2_ENST00000447098.2_Missense_Mutation_p.A921T	NM_003738.4	NP_003729.3	Q9Y6C5	PTC2_HUMAN	patched 2	921					epidermis development (GO:0008544)|hair cycle (GO:0042633)|negative regulation of smoothened signaling pathway (GO:0045879)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|smoothened binding (GO:0005119)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(19)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	50	Acute lymphoblastic leukemia(166;0.155)					ACAAAGTCTGCAGTCTTCTGG	0.677									Basal Cell Nevus syndrome																												p.A921T		Atlas-SNP	.											.	PTCH2	96	.	0			c.G2761A						.						16	20	19					1																	45292375		2199	4286	6485	SO:0001583	missense	8643	exon18	Familial Cancer Database	Gorlin syndrome, Gorlin-Golz syndrome, Naevoid Basal Cell Carcinoma syndrome, NBCCS	AGTCTGCAGTCTT	AF091501	CCDS516.1, CCDS53312.1	1p34.1	2010-06-24	2010-06-24		ENSG00000117425	ENSG00000117425			9586	protein-coding gene	gene with protein product		603673	"patched (Drosophila) homolog 2", "patched homolog 2 (Drosophila)"			9811851, 9931336	Standard	NM_003738		Approved		uc010olf.2	Q9Y6C5	OTTHUMG00000008490	ENST00000372192.3:c.2761G>A	chr1.hg19:g.45292375C>T	ENSP00000361266:p.Ala921Thr	34.0	0.0		29.0	8.0	NM_001166292	O95341|O95856|Q53Z57|Q5QP87|Q6UX14	Missense_Mutation	SNP	ENST00000372192.3	hg19	CCDS516.1	.	.	.	.	.	.	.	.	.	.	C	12.91	2.078411	0.36662	.	.	ENSG00000117425	ENST00000447098;ENST00000372192	D;D	0.85013	-1.93;-1.93	3.89	3.89	0.44902	.	0.281434	0.25720	N	0.028757	T	0.75649	0.3878	N	0.17723	0.515	0.33295	D	0.564053	B;B	0.27166	0.024;0.17	B;B	0.32211	0.025;0.142	T	0.78858	-0.2038	10	0.39692	T	0.17	-8.7297	11.8824	0.52583	0.2929:0.7071:0.0:0.0	.	921;921	Q9Y6C5-2;Q9Y6C5	.;PTC2_HUMAN	T	921	ENSP00000389703:A921T;ENSP00000361266:A921T	ENSP00000361266:A921T	A	-	1	0	PTCH2	45064962	0.850000	0.29656	0.999000	0.59377	0.998000	0.95712	1.531000	0.36018	2.462000	0.83206	0.563000	0.77884	GCA	.	.		0.677	PTCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023428.4	NM_003738		T	45292375	C	T	45292375	3	4	324	1	0	0	0	0	1	0	0	0	12743	710	25	3	890	3	PTCH2	1	45292375	Missense_Mutation	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	27602316	45292375	203958246	3	45611										
INADL	10207	hgsc.bcm.edu	37	chr1	62341008	62341008	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ttgacgacctggaaaatcttAattcattagcaaaaactagt	6	7	2	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr1:62341008A>C	ENST00000371158.2	+	21	3043	c.2929A>C	c.(2929-2931)Aat>Cat	p.N977H	INADL_ENST00000316485.6_Missense_Mutation_p.N977H	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	977					cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						GGAAAATCTTAATTCATTAGC	0.333																																					p.N977H		Atlas-SNP	.											.	INADL	179	.	0			c.A2929C						.						99	100	100					1																	62341008		2203	4300	6503	SO:0001583	missense	10207	exon21			AATCTTAATTCAT	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.2929A>C	chr1.hg19:g.62341008A>C	ENSP00000360200:p.Asn977His	406.0	0.0		392.0	144.0	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	hg19	CCDS617.2	.	.	.	.	.	.	.	.	.	.	A	8.259	0.810814	0.16537	.	.	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000255202	T;T	0.12361	2.81;2.69	5.16	-3.31	0.04988	.	0.781774	0.11837	N	0.524613	T	0.05593	0.0147	N	0.13043	0.29	0.09310	N	1	B;B;B	0.09022	0.002;0.001;0.001	B;B;B	0.06405	0.002;0.001;0.002	T	0.43766	-0.9371	10	0.13470	T	0.59	.	6.009	0.19565	0.2557:0.4629:0.2814:0.0	.	977;977;977	F8W8T2;Q8NI35;Q8NI35-4	.;INADL_HUMAN;.	H	977	ENSP00000360200:N977H;ENSP00000326199:N977H	ENSP00000255202:N977H	N	+	1	0	INADL	62113596	0.026000	0.19158	0.686000	0.30086	0.979000	0.70002	-0.009000	0.12765	-0.439000	0.07222	-0.262000	0.10625	AAT	.	.		0.333	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		C	62341008	A	C	62341008	3	2	324	1	0	0	0	0	1	0	0	0	7740	362	13	5	3007	5	INADL	1	62341008	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	17048633	62341008	186909613	4	45612										
FOXD3	27022	hgsc.bcm.edu	37	chr1	63788839	63788839	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	gggcgacgacgggctggaagAgaaggacagcgacgcaggtt	19	8	0	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr1:63788839A>G	ENST00000371116.2	+	1	110	c.110A>G	c.(109-111)gAg>gGg	p.E37G	RP4-792G4.2_ENST00000426393.1_RNA|RP4-792G4.2_ENST00000431294.1_RNA|RP4-792G4.2_ENST00000449386.1_RNA|RP4-792G4.2_ENST00000427268.1_RNA|RP4-792G4.2_ENST00000418244.1_RNA	NM_012183.2	NP_036315.1	Q9UJU5	FOXD3_HUMAN	forkhead box D3	37					embryonic placenta development (GO:0001892)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|trophectodermal cell differentiation (GO:0001829)	nuclear chromatin (GO:0000790)	double-stranded DNA binding (GO:0003690)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|lung(2)|upper_aerodigestive_tract(1)	5						GGGCTGGAAGAGAAGGACAGC	0.731																																					p.E37G	Pancreas(68;276 1750 11966 31252)	Atlas-SNP	.											.	FOXD3	15	.	0			c.A110G						.						23	21	22					1																	63788839		2169	4263	6432	SO:0001583	missense	27022	exon1			TGGAAGAGAAGGA	AF197560	CCDS624.1	1p31.3	2008-04-10			ENSG00000187140	ENSG00000187140		"Forkhead boxes"	3804	protein-coding gene	gene with protein product		611539				8499623	Standard	NM_012183		Approved	Genesis, HFH2	uc001dax.2	Q9UJU5	OTTHUMG00000009141	ENST00000371116.2:c.110A>G	chr1.hg19:g.63788839A>G	ENSP00000360157:p.Glu37Gly	10.0	0.0		20.0	7.0	NM_012183	Q9BYM2|Q9UDD1	Missense_Mutation	SNP	ENST00000371116.2	hg19	CCDS624.1	.	.	.	.	.	.	.	.	.	.	A	14.58	2.577013	0.45902	.	.	ENSG00000187140	ENST00000371116	D	0.94232	-3.38	3.01	3.01	0.34805	.	.	.	.	.	T	0.72859	0.3513	N	0.12182	0.205	0.32214	N	0.576097	P	0.39480	0.675	B	0.30943	0.122	T	0.65788	-0.6083	9	0.22109	T	0.4	.	11.0679	0.47987	1.0:0.0:0.0:0.0	.	37	Q9UJU5	FOXD3_HUMAN	G	37	ENSP00000360157:E37G	ENSP00000360157:E37G	E	+	2	0	FOXD3	63561427	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	2.940000	0.49003	1.618000	0.50286	0.374000	0.22700	GAG	.	.		0.731	FOXD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025331.1			G	63788839	A	G	63788839	3	3	324	1	0	0	0	0	1	0	0	0	6006	304	11	2	112	2	FOXD3	1	63788839	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	1447831	63788839	185461782	5	45613										
LHX8	431707	hgsc.bcm.edu	37	chr1	75608866	75608866	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	tctactgactgggtccggagAgccaaggggaatgtctatca	13	9	3	2			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr1:75608866A>G	ENST00000294638.5	+	6	1117	c.453A>G	c.(451-453)agA>agG	p.R151R	LHX8_ENST00000356261.3_Silent_p.R141R	NM_001001933.1	NP_001001933.1	Q68G74	LHX8_HUMAN	LIM homeobox 8	151	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				female gonad development (GO:0008585)|forebrain neuron development (GO:0021884)|learning or memory (GO:0007611)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	female germ cell nucleus (GO:0001674)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(18)|ovary(3)|urinary_tract(1)	30						GGGTCCGGAGAGCCAAGGGGA	0.463																																					p.R151R		Atlas-SNP	.											.	LHX8	73	.	0			c.A453G						.						123	116	118					1																	75608866		2203	4299	6502	SO:0001819	synonymous_variant	431707	exon6			CCGGAGAGCCAAG	AB050476	CCDS30756.1, CCDS58008.1	1p31.1	2011-06-20			ENSG00000162624	ENSG00000162624		"Homeoboxes / LIM class"	28838	protein-coding gene	gene with protein product		604425				9598319	Standard	NM_001256114		Approved	Lhx7	uc031pmx.1	Q68G74	OTTHUMG00000009692	ENST00000294638.5:c.453A>G	chr1.hg19:g.75608866A>G		76.0	0.0		97.0	27.0	NM_001001933	E9PGE3	Silent	SNP	ENST00000294638.5	hg19	CCDS30756.1																																																																																			.	.		0.463	LHX8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026700.1	NM_001001933		G	75608866	A	G	75608866	2	3	324	1	0	0	0	0	0	0	0	1	8785	301	11	2		2	LHX8	1	75608866	Silent	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	11820027	75608866	173641755	6	45614										
SSX2IP	117178	hgsc.bcm.edu	37	chr1	85121516	85121516	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ctacaattgtttaaaataccTccaatcccaggcgaatagcg	6	11	0	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr1:85121516T>A	ENST00000342203.3	-	11	1651	c.1388A>T	c.(1387-1389)gAg>gTg	p.E463V	SSX2IP_ENST00000603677.1_Intron|SSX2IP_ENST00000437941.2_Splice_Site_p.E436V|SSX2IP_ENST00000370612.4_Splice_Site_p.E463V|SSX2IP_ENST00000605755.1_Splice_Site_p.E436V	NM_001166293.1|NM_001166294.1|NM_014021.3	NP_001159765.1|NP_001159766.1|NP_054740.3	Q9Y2D8	ADIP_HUMAN	synovial sarcoma, X breakpoint 2 interacting protein	463					cell adhesion (GO:0007155)|centrosome organization (GO:0051297)|regulation of cell motility (GO:2000145)|regulation of Rac protein signal transduction (GO:0035020)	cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|centriolar satellite (GO:0034451)|nucleus (GO:0005634)|protein complex (GO:0043234)				endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|urinary_tract(1)	19				all cancers(265;0.0053)|Epithelial(280;0.0214)|OV - Ovarian serous cystadenocarcinoma(397;0.173)		TTAAAATACCTCCAATCCCAG	0.403																																					p.E463V		Atlas-SNP	.											.	SSX2IP	53	.	0			c.A1388T						.						69	70	69					1																	85121516		2203	4300	6503	SO:0001630	splice_region_variant	117178	exon12			AATACCTCCAATC		CCDS699.1, CCDS53337.1	1p22.3	2008-02-05			ENSG00000117155	ENSG00000117155			16509	protein-coding gene	gene with protein product		608690					Standard	NM_014021		Approved		uc001dkj.3	Q9Y2D8	OTTHUMG00000009926	ENST00000342203.3:c.1389+1A>T	chr1.hg19:g.85121516T>A		73.0	0.0		61.0	25.0	NM_001166417	A8K8W0|B4DFE3|D3DT13|J3KR02|Q6P2P8|Q6ULS1|Q7L168|Q9UIX0	Missense_Mutation	SNP	ENST00000342203.3	hg19	CCDS699.1	.	.	.	.	.	.	.	.	.	.	T	28.0	4.883401	0.91740	.	.	ENSG00000117155	ENST00000342203;ENST00000437941;ENST00000544699;ENST00000370612	T;T	0.68181	-0.3;-0.31	5.6	5.6	0.85130	.	0.047070	0.85682	D	0.000000	T	0.74245	0.3691	L	0.57536	1.79	0.58432	D	0.999999	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.72625	0.978;0.952;0.952	T	0.78231	-0.2284	10	0.87932	D	0	-0.6233	15.774	0.78193	0.0:0.0:0.0:1.0	.	459;463;436	F5H549;Q9Y2D8;B4DFE3	.;ADIP_HUMAN;.	V	463;436;459;463	ENSP00000340279:E463V;ENSP00000412781:E436V	ENSP00000340279:E463V	E	-	2	0	SSX2IP	84894104	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.407000	0.80029	2.139000	0.66308	0.482000	0.46254	GAG	.	.		0.403	SSX2IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027469.1	NM_014021	Missense_Mutation	A	85121516	T	A	85121516	5	1	324	1	0	0	0	0	0	0	1	0	15219	1565	54	4	472	4	SSX2IP	1	85121516	Splice_Site	SNP	T	TCGA-MI-A75I-01A-11D-A32G-10	9512650	85121516	164129105	7	45615										
CLCA2	9635	hgsc.bcm.edu	37	chr1	86913417	86913417	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	cactgccacagttgagccagAgactggagatcctgttacgc	11	12	0	3			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr1:86913417A>T	ENST00000370565.4	+	11	2102	c.1940A>T	c.(1939-1941)gAg>gTg	p.E647V		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	647					cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)			NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		GTTGAGCCAGAGACTGGAGAT	0.433																																					p.E647V	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											.	CLCA2	102	.	0			c.A1940T						.						83	80	81					1																	86913417		2203	4300	6503	SO:0001583	missense	9635	exon11			AGCCAGAGACTGG		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"chloride channel, calcium activated, family member 2", "chloride channel regulator 2"				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.1940A>T	chr1.hg19:g.86913417A>T	ENSP00000359596:p.Glu647Val	37.0	0.0		38.0	11.0	NM_006536	A8K2T3|Q9Y6N2	Missense_Mutation	SNP	ENST00000370565.4	hg19	CCDS708.1	.	.	.	.	.	.	.	.	.	.	A	3.324	-0.138179	0.06669	.	.	ENSG00000137975	ENST00000370565	T	0.31510	1.49	5.72	4.6	0.57074	Domain of unknown function DUF1973 (1);	0.252260	0.37623	N	0.002012	T	0.09555	0.0235	L	0.46670	1.46	0.09310	N	1	B	0.24186	0.099	B	0.27608	0.081	T	0.22695	-1.0209	10	0.32370	T	0.25	-9.1903	3.3521	0.07156	0.6491:0.1413:0.0739:0.1358	.	647	Q9UQC9	CLCA2_HUMAN	V	647	ENSP00000359596:E647V	ENSP00000359596:E647V	E	+	2	0	CLCA2	86686005	0.993000	0.37304	0.657000	0.29651	0.017000	0.09413	2.602000	0.46257	1.018000	0.39521	0.533000	0.62120	GAG	.	.		0.433	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536		T	86913417	A	T	86913417	3	4	324	1	0	0	0	0	1	0	0	0	3460	304	11	4	1982	4	CLCA2	1	86913417	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	1791901	86913417	162337204	8	45616										
CD1E	913	hgsc.bcm.edu	37	chr1	158325807	158325807	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	acatggtatctccgagcaacCctggatgtggcggctgggga	15	10	1	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr1:158325807C>A	ENST00000368167.3	+	4	1055	c.816C>A	c.(814-816)acC>acA	p.T272T	CD1E_ENST00000452291.2_Silent_p.T83T|CD1E_ENST00000368154.1_Intron|CD1E_ENST00000368161.3_Intron|CD1E_ENST00000368165.3_Silent_p.T182T|CD1E_ENST00000434258.1_Silent_p.T270T|CD1E_ENST00000368157.1_Intron|CD1E_ENST00000368155.3_Intron|CD1E_ENST00000444681.2_Silent_p.T173T|CD1E_ENST00000368166.3_Silent_p.T83T|CD1E_ENST00000368160.3_Silent_p.T272T|CD1E_ENST00000368163.3_Intron|CD1E_ENST00000368156.1_Silent_p.T182T|CD1E_ENST00000368164.3_Intron	NM_030893.3	NP_112155.2	P15812	CD1E_HUMAN	CD1e molecule	272	Ig-like.				antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(27)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|urinary_tract(1)	49	all_hematologic(112;0.0378)					TCCGAGCAACCCTGGATGTGG	0.612																																					p.T272T		Atlas-SNP	.											.	CD1E	129	.	0			c.C816A						.						97	97	97					1																	158325807		2203	4300	6503	SO:0001819	synonymous_variant	913	exon4			AGCAACCCTGGAT	AJ289111	CCDS41417.1, CCDS41418.1, CCDS41419.1, CCDS41420.1, CCDS41421.1, CCDS41422.1, CCDS53387.1, CCDS53388.1, CCDS53389.1, CCDS53390.1, CCDS53384.1, CCDS53385.1, CCDS53386.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158488	ENSG00000158488		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	1638	protein-coding gene	gene with protein product		188411	"CD1E antigen, e polypeptide", "CD1e antigen"			10948205	Standard	NM_001042585		Approved		uc001fse.3	P15812	OTTHUMG00000017515	ENST00000368167.3:c.816C>A	chr1.hg19:g.158325807C>A		89.0	0.0		111.0	28.0	NM_030893	B4DZV3|E7EP01|Q5TDJ9|Q5TDK3|Q5TDK4|Q5TDK5|Q5TDK6|Q5TDK8|Q5TDL1|Q712E4|Q712E5|Q712E6|Q712E7|Q712E8|Q712E9|Q712F0|Q712F1|Q712F2|Q712F3|Q712F4|Q712F5|Q96TD0|Q96TD1|Q9UMM1|Q9Y5M3	Silent	SNP	ENST00000368167.3	hg19	CCDS41417.1																																																																																			.	.		0.612	CD1E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046353.3	NM_030893		A	158325807	C	A	158325807	2	1	324	1	0	0	0	0	0	0	0	1	2980	610	22	3		3	CD1E	1	158325807	Silent	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	71412390	158325807	90924814	9	45617										
USP21	27005	hgsc.bcm.edu	37	chr1	161132173	161132173	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ggaggccgagcccaagagctCactgaaggtggggcaacaac	15	11	1	2			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr1:161132173C>T	ENST00000289865.8	+	4	995	c.774C>T	c.(772-774)ctC>ctT	p.L258L	USP21_ENST00000368002.3_Silent_p.L258L|USP21_ENST00000368001.1_Silent_p.L258L	NM_012475.4	NP_036607.3	Q9UK80	UBP21_HUMAN	ubiquitin specific peptidase 21	258	USP.				histone deubiquitination (GO:0016578)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	cysteine-type peptidase activity (GO:0008234)|metal ion binding (GO:0046872)|NEDD8-specific protease activity (GO:0019784)|transcription coactivator activity (GO:0003713)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(10)|ovary(3)|prostate(3)	29	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			CCCAAGAGCTCACTGAAGGTG	0.592																																					p.L258L		Atlas-SNP	.											.	USP21	63	.	0			c.C774T						.						53	56	55					1																	161132173		2203	4300	6503	SO:0001819	synonymous_variant	27005	exon4			AGAGCTCACTGAA	AF177758	CCDS30920.1	1q22	2008-04-11	2005-08-08		ENSG00000143258	ENSG00000143258		"Ubiquitin-specific peptidases"	12620	protein-coding gene	gene with protein product		604729	"ubiquitin specific protease 21"	USP23		12838346, 10799498	Standard	XM_006711273		Approved	USP16	uc010pkd.2	Q9UK80	OTTHUMG00000033154	ENST00000289865.8:c.774C>T	chr1.hg19:g.161132173C>T		120.0	0.0		148.0	51.0	NM_012475	Q59H60|Q5BKT5|Q5VTW9|Q5VTX0|Q9BTV1|Q9HBS2|Q9NYN4	Silent	SNP	ENST00000289865.8	hg19	CCDS30920.1																																																																																			.	.		0.592	USP21-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080801.1			T	161132173	C	T	161132173	2	4	324	1	0	0	0	0	0	0	0	1	17068	813	29	3		3	USP21	1	161132173	Silent	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	2806366	161132173	88118448	10	45618										
ATF6	22926	hgsc.bcm.edu	37	chr1	161762113	161762114	+	Frame_Shift_Ins	INS	-	-	A													0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	gtttacaacctgcacccactINSaaaggtacctgagcagaatt							TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr1:161762113_161762114insA	ENST00000367942.3	+	6	751_752	c.684_685insA	c.(685-687)aaafs	p.K229fs		NM_007348.3	NP_031374.2	P18850	ATF6A_HUMAN	activating transcription factor 6	229					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response (GO:0006990)|protein folding (GO:0006457)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to stress (GO:0006950)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(14)|ovary(3)|skin(1)|stomach(1)	34	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.00953)		Pseudoephedrine(DB00852)	CTGCACCCACTAAAGGTACCTG	0.391																																					p.T228fs		Atlas-Indel,Pindel	.											.	ATF6	84	.	0			c.684_685insA						.																																			SO:0001589	frameshift_variant	22926	exon6			.	AB015856	CCDS1235.1	1q22-q23	2013-01-10			ENSG00000118217	ENSG00000118217		"basic leucine zipper proteins"	791	protein-coding gene	gene with protein product	"activating transcription factor 6 alpha"	605537				9837962, 9271374, 11256944	Standard	NM_007348		Approved	ATF6A	uc001gbs.3	P18850	OTTHUMG00000023961	ENST00000367942.3:c.687dupA	chr1.hg19:g.161762116_161762116dupA	ENSP00000356919:p.Lys229fs	30.0	0.0		32.0	11.0	NM_007348	O15139|Q5VW62|Q6IPB5|Q9UEC9	Frame_Shift_Ins	INS	ENST00000367942.3	hg19	CCDS1235.1																																																																																			.	.		0.391	ATF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060304.2	NM_007348		A	161762114	-	A	161762113	7	5	324	1	0	1	1	0	0	0	0	0	1084	1509	53	0	706	0	ATF6	1	161762113	Frame_Shift_Ins	INS	-	TCGA-MI-A75I-01A-11D-A32G-10	629940	161762113	87488508	11	45619										
LHX9	56956	hgsc.bcm.edu	37	chr1	197887089	197887089	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	gcagatccaagactgaggccCgtctggccaaaggcgcccag	13	14	1	3			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr1:197887089C>T	ENST00000367387.4	+	1	561	c.136C>T	c.(136-138)Cgt>Tgt	p.R46C	LHX9_ENST00000367391.1_Missense_Mutation_p.R37C|LHX9_ENST00000367390.3_Missense_Mutation_p.R37C|LHX9_ENST00000337020.2_Missense_Mutation_p.R46C|LHX9_ENST00000606127.1_3'UTR|LHX9_ENST00000561173.1_Missense_Mutation_p.R52C	NM_020204.2	NP_064589.2	Q9NQ69	LHX9_HUMAN	LIM homeobox 9	46					cell proliferation (GO:0008283)|female gonad development (GO:0008585)|gonad morphogenesis (GO:0035262)|male gonad development (GO:0008584)|motor neuron axon guidance (GO:0008045)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			endometrium(8)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(2)|skin(1)|stomach(1)	35						GACTGAGGCCCGTCTGGCCAA	0.662																																					p.R46C		Atlas-SNP	.											.	LHX9	144	.	0			c.C136T						.						70	73	72					1																	197887089		2203	4300	6503	SO:0001583	missense	56956	exon1			GAGGCCCGTCTGG	AJ277915	CCDS1393.1, CCDS30962.1	1q31.1	2011-06-20			ENSG00000143355	ENSG00000143355		"Homeoboxes / LIM class"	14222	protein-coding gene	gene with protein product		606066					Standard	NM_020204		Approved		uc001guk.1	Q9NQ69	OTTHUMG00000035656	ENST00000367387.4:c.136C>T	chr1.hg19:g.197887089C>T	ENSP00000356357:p.Arg46Cys	81.0	0.0		111.0	29.0	NM_020204	Q5VUE2|Q5VUE3|Q5VUE6|Q86UH2|Q9BYU6|Q9NQ70	Missense_Mutation	SNP	ENST00000367387.4	hg19	CCDS1393.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.915957	0.92178	.	.	ENSG00000143355	ENST00000367391;ENST00000367390;ENST00000367388;ENST00000337020;ENST00000367387	T;D;T;D	0.88431	0.59;-2.37;0.5;-2.38	5.06	5.06	0.68205	.	0.000000	0.85682	D	0.000000	D	0.91506	0.7318	L	0.44542	1.39	0.80722	D	1	D;D;D	0.63880	0.989;0.989;0.993	P;P;P	0.61275	0.676;0.781;0.886	D	0.92281	0.5833	10	0.66056	D	0.02	.	17.7666	0.88480	0.0:1.0:0.0:0.0	.	46;37;37	Q9NQ69;Q9NQ69-3;Q9NQ69-2	LHX9_HUMAN;.;.	C	37;37;89;46;46	ENSP00000356361:R37C;ENSP00000356360:R37C;ENSP00000337969:R46C;ENSP00000356357:R46C	ENSP00000337969:R46C	R	+	1	0	LHX9	196153712	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.215000	0.77966	2.506000	0.84524	0.655000	0.94253	CGT	.	.		0.662	LHX9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086547.2	NM_020204		T	197887089	C	T	197887089	3	4	324	1	0	0	0	0	1	0	0	0	8786	652	23	1	170	1	LHX9	1	197887089	Missense_Mutation	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	36124976	197887089	51363532	12	45620										
IPO9	55705	hgsc.bcm.edu	37	chr1	201817700	201817700	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ggagacttaaatgccgtccaTggagccatgcgtgtgctgac	13	10	0	2			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr1:201817700T>C	ENST00000361565.4	+	4	561	c.492T>C	c.(490-492)caT>caC	p.H164H	IPO9_ENST00000464348.1_3'UTR	NM_018085.4	NP_060555.2	Q96P70	IPO9_HUMAN	importin 9	164					protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	histone binding (GO:0042393)|protein transporter activity (GO:0008565)			cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	38						ATGCCGTCCATGGAGCCATGC	0.517																																					p.H164H		Atlas-SNP	.											.	IPO9	98	.	0			c.T492C						.						133	107	116					1																	201817700		2203	4300	6503	SO:0001819	synonymous_variant	55705	exon4			CGTCCATGGAGCC	AF410465	CCDS1415.1	1q31.3	2008-02-05			ENSG00000198700	ENSG00000198700		"Importins"	19425	protein-coding gene	gene with protein product						11823430, 10574461	Standard	NM_018085		Approved	Imp9, FLJ10402	uc001gwz.3	Q96P70	OTTHUMG00000035805	ENST00000361565.4:c.492T>C	chr1.hg19:g.201817700T>C		98.0	0.0		105.0	26.0	NM_018085	B1ASV5|Q8N1Y1|Q8N3I2|Q8NCG9|Q96SU6|Q9NW01|Q9P0A8|Q9ULM8	Silent	SNP	ENST00000361565.4	hg19	CCDS1415.1																																																																																			.	.		0.517	IPO9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087088.1	NM_018085		C	201817700	T	C	201817700	2	2	324	1	0	0	0	0	0	0	0	1	7808	1461	51	2		2	IPO9	1	201817700	Silent	SNP	T	TCGA-MI-A75I-01A-11D-A32G-10	3930611	201817700	47432921	13	45621										
PLEKHA6	22874	hgsc.bcm.edu	37	chr1	204210871	204210871	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	tgcctggtgggcacaaggctGatgtctctgggggtgtccag	17	9	1	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr1:204210871G>A	ENST00000272203.3	-	16	2560	c.2244C>T	c.(2242-2244)atC>atT	p.I748I	PLEKHA6_ENST00000414478.1_Silent_p.I768I	NM_014935.4	NP_055750.2	Q9Y2H5	PKHA6_HUMAN	pleckstrin homology domain containing, family A member 6	748								p.I748I(1)		breast(2)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_cancers(21;0.0222)|Breast(84;0.179)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.229)			GCACAAGGCTGATGTCTCTGG	0.532																																					p.I748I		Atlas-SNP	.											PLEKHA6,NS,carcinoma,0,1	PLEKHA6	115	.	1	Substitution - coding silent(1)	lung(1)	c.C2244T						.						128	121	124					1																	204210871		2203	4300	6503	SO:0001819	synonymous_variant	22874	exon16			AAGGCTGATGTCT	AB023186	CCDS1444.1	1q32	2013-01-10			ENSG00000143850	ENSG00000143850		"Pleckstrin homology (PH) domain containing"	17053	protein-coding gene	gene with protein product		607771				11001876	Standard	NM_014935		Approved	PEPP3, KIAA0969	uc001hau.4	Q9Y2H5	OTTHUMG00000036057	ENST00000272203.3:c.2244C>T	chr1.hg19:g.204210871G>A		95.0	0.0		100.0	33.0	NM_014935	A7MD51|Q5VTI6	Silent	SNP	ENST00000272203.3	hg19	CCDS1444.1																																																																																			.	.		0.532	PLEKHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087889.3	NM_014935		A	204210871	G	A	204210871	2	1	324	1	0	0	0	0	0	0	0	1	12069	1280	45	3		3	PLEKHA6	1	204210871	Silent	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10	2393171	204210871	45039750	14	45622										
CNTN2	6900	hgsc.bcm.edu	37	chr1	205041085	205041085	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	cctccttcagatccgctactGgaaagctggggacaaagaag	11	11	1	2			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr1:205041085G>T	ENST00000331830.4	+	20	2839	c.2555G>T	c.(2554-2556)tGg>tTg	p.W852L		NM_005076.3	NP_005067.1	Q02246	CNTN2_HUMAN	contactin 2 (axonal)	852	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|central nervous system myelination (GO:0022010)|cerebral cortex GABAergic interneuron migration (GO:0021853)|clustering of voltage-gated potassium channels (GO:0045163)|establishment of protein localization to juxtaparanode region of axon (GO:0071206)|learning (GO:0007612)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|positive regulation of protein processing (GO:0010954)|presynaptic membrane organization (GO:0097090)|receptor internalization (GO:0031623)|regulation of astrocyte differentiation (GO:0048710)|regulation of axon diameter (GO:0031133)|regulation of neuronal synaptic plasticity (GO:0048168)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|juxtaparanode region of axon (GO:0044224)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated potassium channel complex (GO:0008076)	carbohydrate binding (GO:0030246)|identical protein binding (GO:0042802)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(11)|lung(23)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	54	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			ATCCGCTACTGGAAAGCTGGG	0.612																																					p.W852L	Melanoma(183;2548 2817 37099 41192)	Atlas-SNP	.											.	CNTN2	116	.	0			c.G2555T						.						56	54	54					1																	205041085		2203	4300	6503	SO:0001583	missense	6900	exon20			GCTACTGGAAAGC	X67734	CCDS1449.1	1q32.1	2013-02-11			ENSG00000184144	ENSG00000184144		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2172	protein-coding gene	gene with protein product		190197		TAX, AXT		8307567, 8586965	Standard	NM_005076		Approved	TAG-1, TAX1	uc001hbr.3	Q02246	OTTHUMG00000037105	ENST00000331830.4:c.2555G>T	chr1.hg19:g.205041085G>T	ENSP00000330633:p.Trp852Leu	39.0	0.0		52.0	20.0	NM_005076	P78432|Q5T054	Missense_Mutation	SNP	ENST00000331830.4	hg19	CCDS1449.1	.	.	.	.	.	.	.	.	.	.	G	32	5.137740	0.94517	.	.	ENSG00000184144	ENST00000331830	T	0.56941	0.43	5.46	5.46	0.80206	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.46145	D	0.000312	T	0.70962	0.3284	L	0.58810	1.83	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.73036	-0.4109	10	0.87932	D	0	.	18.9039	0.92453	0.0:0.0:1.0:0.0	.	852;743	Q02246;Q68DA2	CNTN2_HUMAN;.	L	852	ENSP00000330633:W852L	ENSP00000330633:W852L	W	+	2	0	CNTN2	203307708	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.531000	0.98054	2.570000	0.86706	0.655000	0.94253	TGG	.	.		0.612	CNTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090080.3	NM_005076		T	205041085	G	T	205041085	3	4	324	1	0	0	0	0	1	0	0	0	3643	1357	47	3	2629	3	CNTN2	1	205041085	Missense_Mutation	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10	830214	205041085	44209536	15	45623										
CR2	1380	hgsc.bcm.edu	37	chr1	207644213	207644213	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	tggtgggagaagaatccataCagtgtacctctgagggggtg	16	6	1	3			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr1:207644213C>G	ENST00000367058.3	+	7	1543	c.1354C>G	c.(1354-1356)Cag>Gag	p.Q452E	CR2_ENST00000458541.2_Missense_Mutation_p.Q452E|CR2_ENST00000367059.3_Missense_Mutation_p.Q452E|CR2_ENST00000367057.3_Missense_Mutation_p.Q452E	NM_001877.4	NP_001868.2	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus) receptor 2	452	Sushi 7. {ECO:0000255|PROSITE- ProRule:PRU00302}.				B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|complement activation, classical pathway (GO:0006958)|immune response (GO:0006955)|innate immune response (GO:0045087)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	complement binding (GO:0001848)|complement receptor activity (GO:0004875)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|breast(3)|endometrium(4)|kidney(3)|large_intestine(12)|lung(26)|ovary(1)|pancreas(1)|prostate(1)|skin(12)|upper_aerodigestive_tract(3)|urinary_tract(1)	69						AGAATCCATACAGTGTACCTC	0.463																																					p.Q452E		Atlas-SNP	.											.	CR2	164	.	0			c.C1354G						.						68	69	68					1																	207644213		2203	4300	6503	SO:0001583	missense	1380	exon7			TCCATACAGTGTA	M26004	CCDS1478.1, CCDS31007.1	1q32	2014-09-17			ENSG00000117322	ENSG00000117322		"CD molecules", "Complement system"	2336	protein-coding gene	gene with protein product		120650					Standard	NM_001006658		Approved	CD21	uc001hfv.3	P20023	OTTHUMG00000036307	ENST00000367058.3:c.1354C>G	chr1.hg19:g.207644213C>G	ENSP00000356025:p.Gln452Glu	70.0	0.0		96.0	24.0	NM_001006658	C9JHD2|Q13866|Q14212|Q53EL2|Q5BKT9|Q5SR46|Q5SR48	Missense_Mutation	SNP	ENST00000367058.3	hg19	CCDS1478.1	.	.	.	.	.	.	.	.	.	.	C	11.74	1.728734	0.30593	.	.	ENSG00000117322	ENST00000367058;ENST00000367057;ENST00000367059;ENST00000458541	T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07	4.57	4.57	0.56435	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.44414	0.1292	N	0.10664	0.02	0.21290	N	0.999731	B;B;B	0.23377	0.084;0.015;0.015	B;B;B	0.29524	0.103;0.028;0.026	T	0.27606	-1.0069	9	0.25751	T	0.34	.	13.6005	0.62015	0.0:1.0:0.0:0.0	.	452;452;452	Q5SR47;P20023;P20023-3	.;CR2_HUMAN;.	E	452	ENSP00000356025:Q452E;ENSP00000356024:Q452E;ENSP00000356026:Q452E;ENSP00000404222:Q452E	ENSP00000356024:Q452E	Q	+	1	0	CR2	205710836	0.003000	0.15002	0.858000	0.33744	0.664000	0.39144	0.533000	0.23082	2.473000	0.83533	0.655000	0.94253	CAG	.	.		0.463	CR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000088274.1	NM_001877		G	207644213	C	G	207644213	3	3	324	1	0	0	0	0	1	0	0	0	3844	479	17	4	1380	4	CR2	1	207644213	Missense_Mutation	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	2603128	207644213	41606408	16	45624										
KCNK2	3776	hgsc.bcm.edu	37	chr1	215259976	215259976	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	cagaagcaaacattcatatcCcaacattcctgtgtcaattc	4	12	2	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr1:215259976C>G	ENST00000444842.2	+	2	462	c.312C>G	c.(310-312)tcC>tcG	p.S104S	KCNK2_ENST00000391894.2_Silent_p.S89S|KCNK2_ENST00000391895.2_Silent_p.S100S	NM_001017425.2|NM_014217.3	NP_001017425.2|NP_055032.1	O95069	KCNK2_HUMAN	potassium channel, subfamily K, member 2	104					G-protein coupled receptor signaling pathway (GO:0007186)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	outward rectifier potassium channel activity (GO:0015271)|potassium channel inhibitor activity (GO:0019870)|potassium ion leak channel activity (GO:0022841)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|upper_aerodigestive_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(81;0.0399)|all cancers(67;0.0556)|GBM - Glioblastoma multiforme(131;0.068)	Dofetilide(DB00204)|Dronedarone(DB04855)	CATTCATATCCCAACATTCCT	0.458																																					p.S104S		Atlas-SNP	.											.	KCNK2	135	.	0			c.C312G						.						169	156	160					1																	215259976		2203	4300	6503	SO:0001819	synonymous_variant	3776	exon2			CATATCCCAACAT	AF004711	CCDS31024.1, CCDS41466.1, CCDS41467.1	1q41	2012-03-07			ENSG00000082482	ENSG00000082482		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6277	protein-coding gene	gene with protein product		603219				9721223, 16382106	Standard	NM_001017424		Approved	K2p2.1, TREK-1	uc001hkr.4	O95069	OTTHUMG00000037017	ENST00000444842.2:c.312C>G	chr1.hg19:g.215259976C>G		60.0	0.0		96.0	24.0	NM_001017425	A1Z1V3|A8K618|B2RCS4|B7ZL56|D3DTA5|Q5DP47|Q5DP48|Q9NRT2|Q9UNE3	Silent	SNP	ENST00000444842.2	hg19	CCDS41467.1																																																																																			.	.		0.458	KCNK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089856.2	NM_014217		G	215259976	C	G	215259976	2	3	324	1	0	0	0	0	0	0	0	1	8075	610	22	4		4	KCNK2	1	215259976	Silent	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	7615763	215259976	33990645	17	45625										
TGFB2	7042	hgsc.bcm.edu	37	chr1	218607497	218607497	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	agttgtgaaaacaagagcagAaggcgaatggctctccttcg	12	8	1	3			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr1:218607497A>T	ENST00000366930.4	+	3	1051	c.584A>T	c.(583-585)gAa>gTa	p.E195V	TGFB2_ENST00000366929.4_Missense_Mutation_p.E223V|TGFB2_ENST00000479322.1_3'UTR	NM_003238.3	NP_003229.1	P61812	TGFB2_HUMAN	transforming growth factor, beta 2	195					activation of protein kinase activity (GO:0032147)|angiogenesis (GO:0001525)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell proliferation (GO:0060038)|cardioblast differentiation (GO:0010002)|cartilage condensation (GO:0001502)|catagen (GO:0042637)|cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|collagen fibril organization (GO:0030199)|dopamine biosynthetic process (GO:0042416)|embryo development (GO:0009790)|embryonic digestive tract development (GO:0048566)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|face morphogenesis (GO:0060325)|generation of neurons (GO:0048699)|glial cell migration (GO:0008347)|hair follicle development (GO:0001942)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hemopoiesis (GO:0030097)|menstrual cycle phase (GO:0022601)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of immune response (GO:0050777)|negative regulation of macrophage cytokine production (GO:0010936)|neuron development (GO:0048666)|neuron fate commitment (GO:0048663)|neutrophil chemotaxis (GO:0030593)|odontogenesis (GO:0042476)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of activation-induced cell death of T cells (GO:0070237)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of catagen (GO:0051795)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of gene expression (GO:0010628)|positive regulation of heart contraction (GO:0045823)|positive regulation of immune response (GO:0050778)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of ossification (GO:0045778)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein secretion (GO:0050714)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein phosphorylation (GO:0006468)|regulation of transforming growth factor beta2 production (GO:0032909)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to progesterone (GO:0032570)|response to wounding (GO:0009611)|salivary gland morphogenesis (GO:0007435)|signal transduction by phosphorylation (GO:0023014)|SMAD protein import into nucleus (GO:0007184)|somatic stem cell division (GO:0048103)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	axon (GO:0030424)|endosome (GO:0005768)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|platelet alpha granule lumen (GO:0031093)	beta-amyloid binding (GO:0001540)|cytokine activity (GO:0005125)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta receptor binding (GO:0005160)|type II transforming growth factor beta receptor binding (GO:0005114)			breast(1)|endometrium(1)|large_intestine(11)|lung(15)|upper_aerodigestive_tract(2)|urinary_tract(1)	31				all cancers(67;0.0459)|OV - Ovarian serous cystadenocarcinoma(81;0.049)|GBM - Glioblastoma multiforme(131;0.0776)		ACAAGAGCAGAAGGCGAATGG	0.438																																					p.E223V		Atlas-SNP	.											.	TGFB2	102	.	0			c.A668T						.						180	165	170					1																	218607497		2203	4300	6503	SO:0001583	missense	7042	exon4			GAGCAGAAGGCGA	M19154	CCDS1521.1, CCDS44318.1	1q41	2014-01-30			ENSG00000092969	ENSG00000092969		"Endogenous ligands"	11768	protein-coding gene	gene with protein product	"prepro-transforming growth factor beta-2"	190220					Standard	NM_003238		Approved		uc001hln.3	P61812	OTTHUMG00000039521	ENST00000366930.4:c.584A>T	chr1.hg19:g.218607497A>T	ENSP00000355897:p.Glu195Val	124.0	0.0		161.0	72.0	NM_001135599	B4DKC5|P08112|Q15579|Q15581|Q4VAV9	Missense_Mutation	SNP	ENST00000366930.4	hg19	CCDS1521.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.712924	0.89112	.	.	ENSG00000092969	ENST00000366930;ENST00000366929	T;T	0.76578	-0.88;-1.03	5.91	5.91	0.95273	Transforming growth factor-beta, N-terminal (1);	0.044771	0.85682	D	0.000000	T	0.72471	0.3464	L	0.49350	1.555	0.80722	D	1	B;P	0.37731	0.337;0.607	B;B	0.33121	0.133;0.158	T	0.73626	-0.3923	10	0.44086	T	0.13	.	16.3512	0.83208	1.0:0.0:0.0:0.0	.	223;195	P61812-2;P61812	.;TGFB2_HUMAN	V	195;223	ENSP00000355897:E195V;ENSP00000355896:E223V	ENSP00000355896:E223V	E	+	2	0	TGFB2	216674120	1.000000	0.71417	0.996000	0.52242	0.966000	0.64601	8.904000	0.92590	2.266000	0.75297	0.533000	0.62120	GAA	.	.		0.438	TGFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095359.2	NM_003238		T	218607497	A	T	218607497	3	4	324	1	0	0	0	0	1	0	0	0	15833	246	9	4	682	4	TGFB2	1	218607497	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	3347521	218607497	30643124	18	45626										
LPIN1	23175	hgsc.bcm.edu	37	chr2	11922631	11922631	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ggattctccttccaggaaaaGaggtaccaaggctggggctt	13	9	1	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr2:11922631G>C	ENST00000256720.2	+	7	1247	c.1154G>C	c.(1153-1155)aGa>aCa	p.R385T	LPIN1_ENST00000396099.1_Missense_Mutation_p.R427T|LPIN1_ENST00000396097.1_Missense_Mutation_p.R115T|LPIN1_ENST00000449576.2_Missense_Mutation_p.R470T|LPIN1_ENST00000425416.2_Missense_Mutation_p.R391T|LPIN1_ENST00000396098.1_Missense_Mutation_p.R427T	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	385					cellular lipid metabolic process (GO:0044255)|fatty acid catabolic process (GO:0009062)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)|triglyceride mobilization (GO:0006642)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(15)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	45	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		TCCAGGAAAAGAGGTACCAAG	0.522																																					p.R470T		Atlas-SNP	.											.	LPIN1	99	.	0			c.G1409C						.						50	54	53					2																	11922631		2203	4300	6503	SO:0001583	missense	23175	exon9			GGAAAAGAGGTAC	D80010	CCDS1682.1, CCDS58699.1, CCDS58700.1, CCDS58701.1	2p25.1	2008-05-23			ENSG00000134324	ENSG00000134324			13345	protein-coding gene	gene with protein product		605518				11138012, 8724849, 16950137	Standard	NM_145693		Approved	KIAA0188	uc010yjm.3	Q14693	OTTHUMG00000119082	ENST00000256720.2:c.1154G>C	chr2.hg19:g.11922631G>C	ENSP00000256720:p.Arg385Thr	68.0	0.0		70.0	21.0	NM_001261428	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Missense_Mutation	SNP	ENST00000256720.2	hg19	CCDS1682.1	.	.	.	.	.	.	.	.	.	.	g	12.36	1.914167	0.33815	.	.	ENSG00000134324	ENST00000449576;ENST00000396098;ENST00000396099;ENST00000425416;ENST00000256720;ENST00000396097	T;T;T;T;T;T	0.69175	-0.38;-0.38;-0.38;-0.38;-0.38;-0.38	5.28	2.86	0.33363	.	0.091406	0.85682	D	0.000000	T	0.49440	0.1557	N	0.17723	0.515	0.80722	D	1	B;B;B	0.17038	0.015;0.02;0.006	B;B;B	0.22753	0.041;0.024;0.024	T	0.42032	-0.9475	10	0.38643	T	0.18	-14.5035	10.48	0.44687	0.8592:0.0:0.1408:0.0	.	470;385;427	F5GY24;Q14693;A8MU38	.;LPIN1_HUMAN;.	T	470;427;427;391;385;115	ENSP00000397908:R470T;ENSP00000379405:R427T;ENSP00000379406:R427T;ENSP00000401522:R391T;ENSP00000256720:R385T;ENSP00000379404:R115T	ENSP00000256720:R385T	R	+	2	0	LPIN1	11840082	1.000000	0.71417	0.992000	0.48379	0.448000	0.32197	3.092000	0.50207	0.949000	0.37715	-0.285000	0.09966	AGA	.	.		0.522	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693		C	11922631	G	C	11922631	3	2	324	1	0	0	0	0	1	0	0	0	8927	942	33	4	1176	4	LPIN1	2	11922631	Missense_Mutation	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10		11922631	231276742	19	45627										
ATAD2B	54454	hgsc.bcm.edu	37	chr2	24011501	24011501	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	agacctcttcatactgtattCtaaagatacatttaacctac	3	10	3	2			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr2:24011501C>A	ENST00000238789.5	-	20	3000	c.2657G>T	c.(2656-2658)aGa>aTa	p.R886I	ATAD2B_ENST00000474583.1_5'UTR	NM_001242338.1|NM_017552.2	NP_001229267.1|NP_060022.1	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B	886						nucleus (GO:0005634)	ATP binding (GO:0005524)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ATACTGTATTCTAAAGATACA	0.303																																					p.R886I		Atlas-SNP	.											.	ATAD2B	110	.	0			c.G2657T						.						66	58	60					2																	24011501		1799	4065	5864	SO:0001583	missense	54454	exon20			TGTATTCTAAAGA	AB033066	CCDS46227.1	2p24.1-p23.3	2010-04-21		2007-02-08	ENSG00000119778	ENSG00000119778		"ATPases / AAA-type"	29230	protein-coding gene	gene with protein product		615347					Standard	XM_005264372		Approved	KIAA1240	uc002rek.4	Q9ULI0	OTTHUMG00000151902	ENST00000238789.5:c.2657G>T	chr2.hg19:g.24011501C>A	ENSP00000238789:p.Arg886Ile	120.0	0.0		99.0	36.0	NM_001242338	B9ZVQ5|Q6ZNA6|Q8N9E7	Missense_Mutation	SNP	ENST00000238789.5	hg19	CCDS46227.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.72|10.72	1.428684|1.428684	0.25726|0.25726	.|.	.|.	ENSG00000119778|ENSG00000119778	ENST00000381024|ENST00000238789;ENST00000546030	.|D	.|0.91894	.|-2.93	5.52|5.52	5.52|5.52	0.82312|0.82312	.|.	.|3.143910	.|0.00678	.|N	.|0.000666	.|D	.|0.90242	.|0.6949	L|L	0.36672|0.36672	1.1|1.1	0.80722|0.80722	D|D	1|1	.|B;B	.|0.25609	.|0.08;0.13	.|B;B	.|0.22386	.|0.017;0.039	.|T	.|0.63897	.|-0.6533	.|10	.|0.37606	.|T	.|0.19	.|.	14.0477|14.0477	0.64714|0.64714	0.0:0.9278:0.0:0.0722|0.0:0.9278:0.0:0.0722	.|.	.|886;886	.|Q9ULI0;Q9ULI0-2	.|ATD2B_HUMAN;.	X|I	167|886;54	.|ENSP00000238789:R886I	.|ENSP00000238789:R886I	E|R	-|-	1|2	0|0	ATAD2B|ATAD2B	23865005|23865005	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	3.841000|3.841000	0.55850|0.55850	2.760000|2.760000	0.94817|0.94817	0.655000|0.655000	0.94253|0.94253	GAA|AGA	.	.		0.303	ATAD2B-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324333.1	NM_017552		A	24011501	C	A	24011501	3	1	324	1	0	0	0	0	1	0	0	0	1072	913	32	3	1755	3	ATAD2B	2	24011501	Missense_Mutation	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	12088870	24011501	219187872	20	45628										
POMC	5443	hgsc.bcm.edu	37	chr2	25384341	25384341	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ggaagtgctccatggagtagGagcgcttgccctcgcgcggg	17	11	0	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr2:25384341G>A	ENST00000405623.1	-	3	868	c.413C>T	c.(412-414)tCc>tTc	p.S138F	POMC_ENST00000395826.2_Missense_Mutation_p.S138F|POMC_ENST00000264708.3_Missense_Mutation_p.S138F|RP11-509E16.1_ENST00000567599.1_lincRNA|POMC_ENST00000380794.1_Missense_Mutation_p.S138F			P01189	COLI_HUMAN	proopiomelanocortin	138					cell-cell signaling (GO:0007267)|cellular pigmentation (GO:0033059)|cellular protein metabolic process (GO:0044267)|generation of precursor metabolites and energy (GO:0006091)|glucose homeostasis (GO:0042593)|negative regulation of tumor necrosis factor production (GO:0032720)|neuropeptide signaling pathway (GO:0007218)|peptide hormone processing (GO:0016486)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of appetite (GO:0032098)|regulation of blood pressure (GO:0008217)|regulation of corticosterone secretion (GO:2000852)|regulation of glycogen metabolic process (GO:0070873)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|peroxisomal matrix (GO:0005782)|secretory granule (GO:0030141)|secretory granule lumen (GO:0034774)	G-protein coupled receptor binding (GO:0001664)|hormone activity (GO:0005179)|receptor binding (GO:0005102)|type 1 melanocortin receptor binding (GO:0070996)|type 3 melanocortin receptor binding (GO:0031781)|type 4 melanocortin receptor binding (GO:0031782)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(5)|ovary(1)	12	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Loperamide(DB00836)	CATGGAGTAGGAGCGCTTGCC	0.726																																					p.S138F	Colon(110;1515 1566 8452 10082 43216)	Atlas-SNP	.											.	POMC	33	.	0			c.C413T						.						9	11	10					2																	25384341		2169	4251	6420	SO:0001583	missense	5443	exon4			GAGTAGGAGCGCT		CCDS1717.1	2p23	2013-02-25	2008-07-31		ENSG00000115138	ENSG00000115138		"Endogenous ligands"	9201	protein-coding gene	gene with protein product	"adrenocorticotropin", "beta-lipotropin", "alpha-melanocyte stimulating hormone", "beta-melanocyte stimulating hormone", "beta-endorphin", "adrenocorticotropic hormone", "opiomelanocortin prepropeptide"	176830				6254047, 9620771	Standard	NM_001035256		Approved	MSH, POC, CLIP, ACTH, NPP, LPH	uc002rfz.1	P01189	OTTHUMG00000094764	ENST00000405623.1:c.413C>T	chr2.hg19:g.25384341G>A	ENSP00000384092:p.Ser138Phe	12.0	0.0		30.0	16.0	NM_001035256	P78442|Q53T23|Q9UD39|Q9UD40	Missense_Mutation	SNP	ENST00000405623.1	hg19	CCDS1717.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.944546	0.92593	.	.	ENSG00000115138	ENST00000380794;ENST00000405623;ENST00000264708;ENST00000395826;ENST00000449220	D;D;D;D;D	0.86230	-2.09;-2.09;-2.09;-2.09;-2.09	5.16	5.16	0.70880	Pro-opiomelanocortin/corticotropin, ACTH, central region (1);	0.055164	0.85682	D	0.000000	D	0.93874	0.8040	M	0.83312	2.635	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94692	0.7875	10	0.87932	D	0	-17.1067	17.2372	0.87002	0.0:0.0:1.0:0.0	.	138	P01189	COLI_HUMAN	F	138	ENSP00000370171:S138F;ENSP00000384092:S138F;ENSP00000264708:S138F;ENSP00000379170:S138F;ENSP00000387993:S138F	ENSP00000264708:S138F	S	-	2	0	POMC	25237845	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.343000	0.97047	2.409000	0.81822	0.462000	0.41574	TCC	.	.		0.726	POMC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211573.3	NM_001035256		A	25384341	G	A	25384341	3	1	324	1	0	0	0	0	1	0	0	0	12251	1174	41	3	394	3	POMC	2	25384341	Missense_Mutation	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10	1372840	25384341	217815032	21	45629										
KCNG3	170850	hgsc.bcm.edu	37	chr2	42720469	42720469	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ggtcgaagaagtactcgttgCgctcgcggtcgtagtcgtcg	15	10	0	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr2:42720469C>A	ENST00000306078.1	-	1	768	c.173G>T	c.(172-174)cGc>cTc	p.R58L	MTA3_ENST00000405592.1_5'Flank|KCNG3_ENST00000394973.4_Missense_Mutation_p.R58L	NM_133329.5|NM_172344.2	NP_579875.1|NP_758847.1	Q8TAE7	KCNG3_HUMAN	potassium voltage-gated channel, subfamily G, member 3	58					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			central_nervous_system(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(2)	6						GTACTCGTTGCGCTCGCGGTC	0.692																																					p.R58L		Atlas-SNP	.											.	KCNG3	19	.	0			c.G173T						.						33	30	31					2																	42720469		2196	4297	6493	SO:0001583	missense	170850	exon1			TCGTTGCGCTCGC	AB070604	CCDS1809.1, CCDS42674.1	2p21	2011-07-05			ENSG00000171126	ENSG00000171126		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18306	protein-coding gene	gene with protein product		606767				11852086, 16382104	Standard	NM_133329		Approved	Kv6.3	uc002rsn.3	Q8TAE7	OTTHUMG00000128604	ENST00000306078.1:c.173G>T	chr2.hg19:g.42720469C>A	ENSP00000304127:p.Arg58Leu	9.0	0.0		24.0	8.0	NM_172344	Q53SC1	Missense_Mutation	SNP	ENST00000306078.1	hg19	CCDS1809.1	.	.	.	.	.	.	.	.	.	.	C	19.46	3.832483	0.71258	.	.	ENSG00000171126	ENST00000306078;ENST00000394973	T;T	0.76968	-1.06;-1.06	3.31	3.31	0.37934	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.000000	0.85682	D	0.000000	D	0.83473	0.5262	L	0.52011	1.625	0.49389	D	0.999784	D;D	0.69078	0.997;0.996	D;D	0.81914	0.995;0.992	T	0.83064	-0.0146	10	0.37606	T	0.19	.	14.7779	0.69743	0.0:1.0:0.0:0.0	.	58;58	Q8TAE7;Q8TAE7-2	KCNG3_HUMAN;.	L	58	ENSP00000304127:R58L;ENSP00000378424:R58L	ENSP00000304127:R58L	R	-	2	0	KCNG3	42573973	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.875000	0.48491	1.666000	0.50821	0.462000	0.41574	CGC	.	.		0.692	KCNG3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250464.2	NM_172344		A	42720469	C	A	42720469	3	1	324	1	0	0	0	0	1	0	0	0	8038	768	27	1	1145	1	KCNG3	2	42720469	Missense_Mutation	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	17336128	42720469	200478904	22	45630										
MAT2A	4144	hgsc.bcm.edu	37	chr2	85770059	85770059	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ggagtttctcatccattatcTatctccattttccattatgg	5	10	3	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr2:85770059T>C	ENST00000306434.3	+	8	1110	c.987T>C	c.(985-987)tcT>tcC	p.S329S	MAT2A_ENST00000409017.1_Silent_p.S266S	NM_005911.5	NP_005902.1	P31153	METK2_HUMAN	methionine adenosyltransferase II, alpha	329					cellular nitrogen compound metabolic process (GO:0034641)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|S-adenosylmethionine biosynthetic process (GO:0006556)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|methionine adenosyltransferase complex (GO:0048269)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methionine adenosyltransferase activity (GO:0004478)			breast(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	9					L-Methionine(DB00134)|S-Adenosylmethionine(DB00118)	ATCCATTATCTATCTCCATTT	0.388																																					p.S329S		Atlas-SNP	.											.	MAT2A	23	.	0			c.T987C						.						192	195	194					2																	85770059		2203	4300	6503	SO:0001819	synonymous_variant	4144	exon8			ATTATCTATCTCC		CCDS1977.1	2p11.2	2008-06-03			ENSG00000168906	ENSG00000168906			6904	protein-coding gene	gene with protein product		601468				1426236, 9703951	Standard	NM_005911		Approved	SAMS2, MATA2, MATII	uc002spr.3	P31153	OTTHUMG00000130174	ENST00000306434.3:c.987T>C	chr2.hg19:g.85770059T>C		181.0	0.0		172.0	57.0	NM_005911	A8K511|B4DN45|D6W5L1|Q53SP5	Silent	SNP	ENST00000306434.3	hg19	CCDS1977.1																																																																																			.	.		0.388	MAT2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252491.2	NM_005911		C	85770059	T	C	85770059	2	2	324	1	0	0	0	0	0	0	0	1	9339	1509	53	2		2	MAT2A	2	85770059	Silent	SNP	T	TCGA-MI-A75I-01A-11D-A32G-10	43049590	85770059	157429314	23	45631										
GLI2	2736	hgsc.bcm.edu	37	chr2	121747847	121747847	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	actactacggccagatccacAtgtacgaacaggatggaggc	11	11	0	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr2:121747847A>T	ENST00000452319.1	+	14	4417	c.4357A>T	c.(4357-4359)Atg>Ttg	p.M1453L	GLI2_ENST00000314490.11_Intron|GLI2_ENST00000361492.4_Missense_Mutation_p.M1453L					GLI family zinc finger 2											NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				CCAGATCCACATGTACGAACA	0.657																																					p.M1453L		Atlas-SNP	.											.	GLI2	187	.	0			c.A4357T						.						59	63	62					2																	121747847		2203	4300	6503	SO:0001583	missense	2736	exon13			ATCCACATGTACG		CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"Zinc fingers, C2H2-type"	4318	protein-coding gene	gene with protein product	"tax-responsive element-2 holding protein", "tax helper protein 1", "tax helper protein 2"	165230	"GLI-Kruppel family member GLI2", "glioma-associated oncogene family zinc finger 2"			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.4357A>T	chr2.hg19:g.121747847A>T	ENSP00000390436:p.Met1453Leu	96.0	0.0		99.0	38.0	NM_005270		Missense_Mutation	SNP	ENST00000452319.1	hg19	CCDS33283.1	.	.	.	.	.	.	.	.	.	.	A	19.48	3.835069	0.71373	.	.	ENSG00000074047	ENST00000452319;ENST00000361492	T;T	0.16897	2.31;2.31	4.89	4.89	0.63831	.	0.042036	0.85682	D	0.000000	T	0.28962	0.0719	M	0.77820	2.39	0.80722	D	1	P;P	0.50528	0.675;0.936	B;P	0.46585	0.202;0.521	T	0.10314	-1.0635	9	.	.	.	.	14.6681	0.68924	1.0:0.0:0.0:0.0	.	1453;1108	P10070;P10070-2	GLI2_HUMAN;.	L	1453	ENSP00000390436:M1453L;ENSP00000354586:M1453L	.	M	+	1	0	GLI2	121464317	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	5.771000	0.68881	2.050000	0.60909	0.454000	0.30748	ATG	.	.		0.657	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270		T	121747847	A	T	121747847	3	4	324	1	0	0	0	0	1	0	0	0	6446	217	8	4	4407	4	GLI2	2	121747847	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	35977788	121747847	121451526	24	45632										
FAM123C	205147	hgsc.bcm.edu	37	chr2	131520150	131520150	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	acctattccacattcggagaAacaagactgaggacttggcc	9	11	0	3			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr2:131520150A>G	ENST00000423981.1	+	2	615	c.505A>G	c.(505-507)Aac>Gac	p.N169D	AMER3_ENST00000321420.4_Missense_Mutation_p.N169D	NM_001105193.1|NM_001105194.1|NM_001105195.1|NM_152698.2	NP_001098663.1|NP_001098664.1|NP_001098665.1|NP_689911.2	Q8N944	AMER3_HUMAN	APC membrane recruitment protein 3	169					Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	lipid binding (GO:0008289)										CATTCGGAGAAACAAGACTGA	0.607																																					p.N169D		Atlas-SNP	.											.	.	.	.	0			c.A505G						.						56	59	58					2																	131520150		2199	4294	6493	SO:0001583	missense	205147	exon2			CGGAGAAACAAGA	AK095696	CCDS2164.1	2q21.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000178171	ENSG00000178171		"-"	26771	protein-coding gene	gene with protein product			"family with sequence similarity 123C"	FAM123C		20843316	Standard	NM_001105195		Approved	FLJ38377	uc002trw.2	Q8N944	OTTHUMG00000131637	ENST00000423981.1:c.505A>G	chr2.hg19:g.131520150A>G	ENSP00000392700:p.Asn169Asp	28.0	0.0		32.0	10.0	NM_152698	B7ZLH6	Missense_Mutation	SNP	ENST00000423981.1	hg19	CCDS2164.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.033216	0.75504	.	.	ENSG00000178171	ENST00000321420;ENST00000458606;ENST00000423981	T;T;T	0.17370	2.28;2.28;2.28	5.1	5.1	0.69264	.	0.396710	0.27349	N	0.019775	T	0.22627	0.0546	L	0.29908	0.895	0.25782	N	0.984715	P	0.51240	0.943	P	0.54544	0.755	T	0.05084	-1.0907	10	0.37606	T	0.19	.	13.1336	0.59397	1.0:0.0:0.0:0.0	.	169	Q8N944	F123C_HUMAN	D	169	ENSP00000314914:N169D;ENSP00000389242:N169D;ENSP00000392700:N169D	ENSP00000314914:N169D	N	+	1	0	FAM123C	131236620	1.000000	0.71417	0.986000	0.45419	0.858000	0.48976	7.161000	0.77505	2.043000	0.60533	0.459000	0.35465	AAC	.	.		0.607	AMER3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254531.3	NM_152698		G	131520150	A	G	131520150	3	3	324	1	0	0	0	0	1	0	0	0	5429	14	1	2	507	2	FAM123C	2	131520150	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	9772303	131520150	111679223	25	45633										
FMNL2	114793	hgsc.bcm.edu	37	chr2	153471456	153471456	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	aggagctctactggaagatgCtgaaactaagaatgctgcct	11	8	1	3			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr2:153471456C>A	ENST00000288670.9	+	12	1521	c.1154C>A	c.(1153-1155)gCt>gAt	p.A385D		NM_052905.3	NP_443137.2	Q96PY5	FMNL2_HUMAN	formin-like 2	385	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				cortical actin cytoskeleton organization (GO:0030866)|cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)				central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(2)|lung(3)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	23						CTGGAAGATGCTGAAACTAAG	0.408																																					p.A385D		Atlas-SNP	.											.	FMNL2	75	.	0			c.C1154A						.						103	104	104					2																	153471456		1971	4163	6134	SO:0001583	missense	114793	exon12			AAGATGCTGAAAC	AB067489	CCDS46429.1	2q23.3	2008-02-05	2003-12-02	2003-12-03	ENSG00000157827	ENSG00000157827			18267	protein-coding gene	gene with protein product			"formin homology 2 domain containing 2"	FHOD2			Standard	XM_005246263		Approved	KIAA1902	uc002tye.3	Q96PY5	OTTHUMG00000154035	ENST00000288670.9:c.1154C>A	chr2.hg19:g.153471456C>A	ENSP00000288670:p.Ala385Asp	92.0	0.0		90.0	40.0	NM_052905	B2RZH5|Q14CC9|Q4ZG52|Q8N3E0	Missense_Mutation	SNP	ENST00000288670.9	hg19	CCDS46429.1	.	.	.	.	.	.	.	.	.	.	C	34	5.374161	0.95923	.	.	ENSG00000157827	ENST00000288670	T	0.22539	1.95	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.47673	0.1458	M	0.73319	2.225	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.23868	-1.0176	10	0.33940	T	0.23	.	19.419	0.94713	0.0:1.0:0.0:0.0	.	385	Q96PY5-3	.	D	385	ENSP00000288670:A385D	ENSP00000288670:A385D	A	+	2	0	FMNL2	153179702	1.000000	0.71417	0.996000	0.52242	0.987000	0.75469	7.776000	0.85560	2.665000	0.90641	0.650000	0.86243	GCT	.	.		0.408	FMNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333582.2	NM_052905		A	153471456	C	A	153471456	3	1	324	1	0	0	0	0	1	0	0	0	5960	797	28	3	1200	3	FMNL2	2	153471456	Missense_Mutation	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	21951306	153471456	89727917	26	45634										
ERMN	57471	hgsc.bcm.edu	37	chr2	158177872	158177872	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ggatattgtattgtatctggAataagcatttctggagatat	10	3	2	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr2:158177872A>G	ENST00000410096.1	-	3	1057	c.766T>C	c.(766-768)Tcc>Ccc	p.S256P	ERMN_ENST00000397283.2_Missense_Mutation_p.S269P|ERMN_ENST00000420719.2_Missense_Mutation_p.S236P|ERMN_ENST00000535935.1_Missense_Mutation_p.S150P	NM_020711.1	NP_065762.1	Q8TAM6	ERMIN_HUMAN	ermin, ERM-like protein	256					actin filament organization (GO:0007015)|morphogenesis of a branching structure (GO:0001763)|regulation of cell projection organization (GO:0031344)|regulation of cell shape (GO:0008360)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|internode region of axon (GO:0033269)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|paranode region of axon (GO:0033270)				endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	12						TTGTATCTGGAATAAGCATTT	0.413																																					p.S269P		Atlas-SNP	.											.	ERMN	31	.	0			c.T805C						.						160	157	158					2																	158177872		1947	4135	6082	SO:0001583	missense	57471	exon4			ATCTGGAATAAGC	AB033015	CCDS42764.1, CCDS46431.1	2q24	2008-02-05	2008-01-15	2008-01-15	ENSG00000136541	ENSG00000136541			29208	protein-coding gene	gene with protein product	"juxtanodin", "ermin"	610072	"KIAA1189"	KIAA1189		16051705, 16421295	Standard	NM_020711		Approved	JN, ERMIN	uc002tzi.3	Q8TAM6	OTTHUMG00000153843	ENST00000410096.1:c.766T>C	chr2.hg19:g.158177872A>G	ENSP00000387047:p.Ser256Pro	130.0	0.0		102.0	5.0	NM_001009959	B4DKA6|Q9ULN1	Missense_Mutation	SNP	ENST00000410096.1	hg19	CCDS46431.1	.	.	.	.	.	.	.	.	.	.	A	13.29	2.192325	0.38707	.	.	ENSG00000136541	ENST00000410096;ENST00000397283;ENST00000535935;ENST00000420719	D;D;D;D	0.88741	-2.42;-2.42;-2.42;-2.42	6.07	4.91	0.64330	.	0.110120	0.41396	D	0.000897	D	0.91123	0.7205	L	0.36672	1.1	0.36994	D	0.894939	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79784	0.993;0.99;0.99	D	0.93138	0.6539	10	0.87932	D	0	-52.8423	13.2643	0.60125	0.8674:0.1326:0.0:0.0	.	236;269;256	B4DIZ1;Q8TAM6-2;Q8TAM6	.;.;ERMIN_HUMAN	P	256;269;150;236	ENSP00000387047:S256P;ENSP00000380453:S269P;ENSP00000438397:S150P;ENSP00000410646:S236P	ENSP00000380453:S269P	S	-	1	0	ERMN	157886118	1.000000	0.71417	0.994000	0.49952	0.207000	0.24258	2.288000	0.43514	1.094000	0.41399	-0.316000	0.08728	TCC	.	.		0.413	ERMN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332659.1	NM_001009959		G	158177872	A	G	158177872	3	3	324	1	0	0	0	0	1	0	0	0	5237	246	9	2	92	2	ERMN	2	158177872	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	4706416	158177872	85021501	27	45635										
TBR1	10716	hgsc.bcm.edu	37	chr2	162273138	162273138	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	acaattttcctgactccaagGactcaccaggggacgtccag	9	13	1	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr2:162273138G>A	ENST00000389554.3	+	1	534	c.217G>A	c.(217-219)Gac>Aac	p.D73N	TBR1_ENST00000410035.1_5'Flank	NM_006593.2	NP_006584.1	Q16650	TBR1_HUMAN	T-box, brain, 1	73					axon guidance (GO:0007411)|brain development (GO:0007420)|hindbrain development (GO:0030902)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of neuron projection development (GO:0010975)|specification of organ identity (GO:0010092)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|prostate(1)|skin(3)	30						TGACTCCAAGGACTCACCAGG	0.493																																					p.D73N		Atlas-SNP	.											.	TBR1	59	.	0			c.G217A						.						89	97	94					2																	162273138		2203	4300	6503	SO:0001583	missense	10716	exon1			TCCAAGGACTCAC	U49250	CCDS33310.1	2q24.2	2011-06-13			ENSG00000136535	ENSG00000136535		"T-boxes"	11590	protein-coding gene	gene with protein product		604616				7619531	Standard	NM_006593		Approved		uc002ubw.1	Q16650	OTTHUMG00000153888	ENST00000389554.3:c.217G>A	chr2.hg19:g.162273138G>A	ENSP00000374205:p.Asp73Asn	62.0	0.0		64.0	28.0	NM_006593	B0AZS4|B2R6G5|Q14DC5|Q53TH0|Q56A81	Missense_Mutation	SNP	ENST00000389554.3	hg19	CCDS33310.1	.	.	.	.	.	.	.	.	.	.	G	15.17	2.753740	0.49362	.	.	ENSG00000136535	ENST00000389554	D	0.87412	-2.25	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	D	0.90532	0.7033	L	0.44542	1.39	0.80722	D	1	D	0.63880	0.993	D	0.74674	0.984	D	0.87829	0.2643	10	0.27082	T	0.32	.	17.8745	0.88821	0.0:0.0:1.0:0.0	.	73	Q16650	TBR1_HUMAN	N	73	ENSP00000374205:D73N	ENSP00000374205:D73N	D	+	1	0	TBR1	161981384	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.161000	0.71868	2.803000	0.96430	0.655000	0.94253	GAC	.	.		0.493	TBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332845.1	NM_006593		A	162273138	G	A	162273138	3	1	324	1	0	0	0	0	1	0	0	0	15662	1174	41	3	219	3	TBR1	2	162273138	Missense_Mutation	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10	4095266	162273138	80926235	28	45636										
LRP2	4036	hgsc.bcm.edu	37	chr2	170003385	170003385	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	gttggccaaccaaggtcctcGaaaaccaggatgttgcggtc	12	11	0	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr2:170003385G>T	ENST00000263816.3	-	69	12960	c.12675C>A	c.(12673-12675)ttC>ttA	p.F4225L		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	4225					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.F4225F(1)		biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	CAAGGTCCTCGAAAACCAGGA	0.438																																					p.F4225L		Atlas-SNP	.											LRP2,colon,carcinoma,0,1	LRP2	751	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C12675A						.						105	86	93					2																	170003385		2203	4300	6503	SO:0001583	missense	4036	exon69			GTCCTCGAAAACC		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.12675C>A	chr2.hg19:g.170003385G>T	ENSP00000263816:p.Phe4225Leu	153.0	0.0		149.0	49.0	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	hg19	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	G	4.926	0.172110	0.09391	.	.	ENSG00000081479	ENST00000263816	D	0.95821	-3.82	5.38	-10.8	0.00216	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.665589	0.16485	N	0.212355	D	0.85526	0.5717	N	0.24115	0.695	0.09310	N	0.999998	B	0.21905	0.062	B	0.29077	0.098	T	0.71948	-0.4438	10	0.31617	T	0.26	.	2.8995	0.05701	0.5481:0.1319:0.1151:0.2049	.	4225	P98164	LRP2_HUMAN	L	4225	ENSP00000263816:F4225L	ENSP00000263816:F4225L	F	-	3	2	LRP2	169711631	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.136000	0.00288	-3.144000	0.00232	-1.069000	0.02264	TTC	.	.		0.438	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		T	170003385	G	T	170003385	3	4	324	1	0	0	0	0	1	0	0	0	8965	1049	37	1	1336	1	LRP2	2	170003385	Missense_Mutation	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10	7730247	170003385	73195988	29	45637										
TTN	7273	hgsc.bcm.edu	37	chr2	179479034	179479034	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	tagaagacatgactcattggTtacatctgtgatgtcaaagg	10	6	3	4			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr2:179479034T>C	ENST00000591111.1	-	212	44391	c.44167A>G	c.(44167-44169)Acc>Gcc	p.T14723A	RP11-171I2.4_ENST00000605334.1_lincRNA|TTN_ENST00000342175.6_Missense_Mutation_p.T7491A|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.T7424A|TTN_ENST00000460472.2_Missense_Mutation_p.T7299A|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.T16364A|TTN_ENST00000342992.6_Missense_Mutation_p.T13796A			Q8WZ42	TITIN_HUMAN	titin	14723	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GACTCATTGGTTACATCTGTG	0.398																																					p.T16364A		Atlas-SNP	.											.	TTN	18412	.	0			c.A49090G						.						92	85	88					2																	179479034		1969	4163	6132	SO:0001583	missense	7273	exon262			CATTGGTTACATC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.44167A>G	chr2.hg19:g.179479034T>C	ENSP00000465570:p.Thr14723Ala	133.0	0.0		140.0	46.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	14.28	2.487645	0.44249	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.60299	0.2;0.2;0.2;0.2	5.55	5.55	0.83447	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.76898	0.4052	M	0.79123	2.44	0.58432	D	0.999996	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.83275	0.996;0.996;0.996;0.996	T	0.80216	-0.1474	9	0.87932	D	0	.	15.9963	0.80250	0.0:0.0:0.0:1.0	.	7299;7424;7491;14723	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	A	13796;7299;7491;7424;7299	ENSP00000343764:T13796A;ENSP00000434586:T7299A;ENSP00000340554:T7491A;ENSP00000352154:T7424A	ENSP00000340554:T7491A	T	-	1	0	TTN	179187279	1.000000	0.71417	0.996000	0.52242	0.997000	0.91878	6.206000	0.72154	2.234000	0.73211	0.533000	0.62120	ACC	.	.		0.398	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179479034	T	C	179479034	3	2	324	1	0	0	0	0	1	0	0	0	16750	1725	60	2	59007	2	TTN	2	179479034	Missense_Mutation	SNP	T	TCGA-MI-A75I-01A-11D-A32G-10	9475649	179479034	63720339	30	45638										
TTN	7273	hgsc.bcm.edu	37	chr2	179489420	179489420	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	agtggctccctcttcgaccgTctggtcctcaagaggcttag	11	13	3	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr2:179489420T>C	ENST00000591111.1	-	192	39888	c.39664A>G	c.(39664-39666)Acg>Gcg	p.T13222A	TTN_ENST00000342175.6_Missense_Mutation_p.T5990A|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.T5923A|TTN_ENST00000460472.2_Missense_Mutation_p.T5798A|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.T14863A|TTN_ENST00000342992.6_Missense_Mutation_p.T12295A			Q8WZ42	TITIN_HUMAN	titin	13222	Ig-like 88.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCTTCGACCGTCTGGTCCTCA	0.453																																					p.T14863A		Atlas-SNP	.											.	TTN	18412	.	0			c.A44587G						.						58	58	58					2																	179489420		1830	4087	5917	SO:0001583	missense	7273	exon242			CGACCGTCTGGTC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.39664A>G	chr2.hg19:g.179489420T>C	ENSP00000465570:p.Thr13222Ala	87.0	0.0		91.0	33.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	14.75	2.629254	0.46944	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24	5.82	4.65	0.58169	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.67211	0.2869	L	0.58101	1.795	0.45762	D	0.998659	D;D;D;P	0.53151	0.958;0.958;0.958;0.919	P;P;P;P	0.46172	0.506;0.506;0.506;0.506	T	0.70651	-0.4813	9	0.87932	D	0	.	13.1241	0.59344	0.0:0.0:0.1338:0.8662	.	5798;5923;5990;13222	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	A	12295;5798;5990;5923;5798	ENSP00000343764:T12295A;ENSP00000434586:T5798A;ENSP00000340554:T5990A;ENSP00000352154:T5923A	ENSP00000340554:T5990A	T	-	1	0	TTN	179197665	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.991000	0.88244	1.016000	0.39470	0.528000	0.53228	ACG	.	.		0.453	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179489420	T	C	179489420	3	2	324	1	0	0	0	0	1	0	0	0	16750	1667	58	2	63590	2	TTN	2	179489420	Missense_Mutation	SNP	T	TCGA-MI-A75I-01A-11D-A32G-10	10386	179489420	63709953	31	45639										
SF3B1	23451	hgsc.bcm.edu	37	chr2	198266711	198266711	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ggtaattggtggatttacctTtcctctgtgttggcggatac	12	7	1	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr2:198266711T>G	ENST00000335508.6	-	15	2312	c.2221A>C	c.(2221-2223)Aag>Cag	p.K741Q	SNORA4_ENST00000365564.1_RNA|SF3B1_ENST00000462613.1_5'Flank	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	741					anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)			NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			GGATTTACCTTTCCTCTGTGT	0.353			Mis		myelodysplastic syndrome																																p.K741Q		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	.	SF3B1	1038	.	0			c.A2221C						.						89	84	86					2																	198266711		2203	4300	6503	SO:0001583	missense	23451	exon15			TTACCTTTCCTCT	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"splicing factor 3b, subunit 1, 155kD"			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.2221A>C	chr2.hg19:g.198266711T>G	ENSP00000335321:p.Lys741Gln	155.0	0.0		169.0	60.0	NM_012433	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	hg19	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.789531	0.90367	.	.	ENSG00000115524	ENST00000335508	T	0.65732	-0.17	5.71	5.71	0.89125	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.85678	0.5752	H	0.96175	3.78	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	D	0.90320	0.4344	10	0.87932	D	0	.	15.9781	0.80086	0.0:0.0:0.0:1.0	.	741	O75533	SF3B1_HUMAN	Q	741	ENSP00000335321:K741Q	ENSP00000335321:K741Q	K	-	1	0	SF3B1	197974956	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	7.566000	0.82347	2.171000	0.68590	0.533000	0.62120	AAG	.	.		0.353	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			G	198266711	T	G	198266711	3	3	324	1	0	0	0	0	1	0	0	0	14164	1850	64	5	1737	5	SF3B1	2	198266711	Missense_Mutation	SNP	T	TCGA-MI-A75I-01A-11D-A32G-10	18777291	198266711	44932662	32	45640										
SPEG	10290	hgsc.bcm.edu	37	chr2	220336992	220336992	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ggcgccccgcaggtggtggcTgtgacggggaggatggtcac	20	10	1	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr2:220336992T>C	ENST00000312358.7	+	15	4011	c.3879T>C	c.(3877-3879)gcT>gcC	p.A1293A	SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	1293	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		AGGTGGTGGCTGTGACGGGGA	0.652																																					p.A1293A		Atlas-SNP	.											.	SPEG	272	.	0			c.T3879C						.						51	56	54					2																	220336992		1984	4150	6134	SO:0001819	synonymous_variant	10290	exon15			GGTGGCTGTGACG	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"Immunoglobulin superfamily / I-set domain containing"	16901	protein-coding gene	gene with protein product		615950	"aortic preferentially expressed gene 1"	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.3879T>C	chr2.hg19:g.220336992T>C		33.0	0.0		28.0	11.0	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Silent	SNP	ENST00000312358.7	hg19	CCDS42824.1																																																																																			.	.		0.652	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		C	220336992	T	C	220336992	2	2	324	1	0	0	0	0	0	0	0	1	15051	1567	55	2		2	SPEG	2	220336992	Silent	SNP	T	TCGA-MI-A75I-01A-11D-A32G-10	22070281	220336992	22862381	33	45641										
ANO7	50636	hgsc.bcm.edu	37	chr2	242148731	242148731	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	gttcgaccacggcggcaccgTgttcttcagcttgttcatgg	12	12	3	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr2:242148731T>C	ENST00000274979.8	+	12	1374	c.1271T>C	c.(1270-1272)gTg>gCg	p.V424A	ANO7_ENST00000402430.3_Missense_Mutation_p.V423A	NM_001001891.3	NP_001001891.2	Q6IWH7	ANO7_HUMAN	anoctamin 7	424					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(14)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	32						GGCGGCACCGTGTTCTTCAGC	0.647																																					p.V424A		Atlas-SNP	.											.	ANO7	136	.	0			c.T1271C						.						29	24	26					2																	242148731		2187	4278	6465	SO:0001583	missense	50636	exon12			GCACCGTGTTCTT	AY617079	CCDS33423.1, CCDS46563.1	2q37.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000146205	ENSG00000146205		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	31677	protein-coding gene	gene with protein product		605096	"transmembrane protein 16G"	PCANAP5, TMEM16G		14981236, 15375614, 24692353	Standard	NM_001001891		Approved	NGEP, PCANAP5L, IPCA-5	uc002wax.2	Q6IWH7	OTTHUMG00000151702	ENST00000274979.8:c.1271T>C	chr2.hg19:g.242148731T>C	ENSP00000274979:p.Val424Ala	24.0	0.0		32.0	7.0	NM_001001891	Q6IWH6	Missense_Mutation	SNP	ENST00000274979.8	hg19	CCDS33423.1	.	.	.	.	.	.	.	.	.	.	T	15.59	2.877334	0.51801	.	.	ENSG00000146205	ENST00000274979;ENST00000402430	T;T	0.68765	-0.35;-0.35	3.33	3.33	0.38152	.	0.208574	0.31156	N	0.008150	T	0.80711	0.4675	M	0.84219	2.685	0.40986	D	0.984815	D	0.89917	1.0	D	0.80764	0.994	T	0.83168	-0.0095	10	0.87932	D	0	.	10.6969	0.45905	0.0:0.0:0.0:1.0	.	424	Q6IWH7	ANO7_HUMAN	A	424;423	ENSP00000274979:V424A;ENSP00000385418:V423A	ENSP00000274979:V424A	V	+	2	0	ANO7	241797404	0.999000	0.42202	0.187000	0.23214	0.169000	0.22640	6.510000	0.73729	1.149000	0.42402	0.260000	0.18958	GTG	.	.		0.647	ANO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323509.1	NM_001001891		C	242148731	T	C	242148731	3	2	324	1	0	0	0	0	1	0	0	0	702	1696	59	2	1389	2	ANO7	2	242148731	Missense_Mutation	SNP	T	TCGA-MI-A75I-01A-11D-A32G-10	21811739	242148731	1050642	34	45642										
ATG4B	23192	hgsc.bcm.edu	37	chr2	242590731	242590731	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	agactttggtttacatacagGaaaaactttccagccattgg	8	8	0	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr2:242590731G>A	ENST00000404914.3	+	3	268	c.165G>A	c.(163-165)agG>agA	p.R55R	ATG4B_ENST00000405546.3_Silent_p.R55R|ATG4B_ENST00000396411.3_5'UTR|ATG4B_ENST00000491867.1_3'UTR|ATG4B_ENST00000402096.1_5'UTR|ATG4B_ENST00000474739.2_Missense_Mutation_p.G11E	NM_013325.4|NM_178326.2	NP_037457.3|NP_847896.1	Q9Y4P1	ATG4B_HUMAN	autophagy related 4B, cysteine peptidase	55					autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|positive regulation of autophagy (GO:0010508)|positive regulation of protein catabolic process (GO:0045732)|protein transport (GO:0015031)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	cysteine-type peptidase activity (GO:0008234)|endopeptidase activity (GO:0004175)			breast(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;2.44e-33)|all cancers(36;5.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.75e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0848)		TTACATACAGGAAAAACTTTC	0.373																																					p.R55R	Melanoma(78;458 1323 6342 12171 39523)	Atlas-SNP	.											.	ATG4B	35	.	0			c.G165A						.						109	99	102					2																	242590731		1862	4094	5956	SO:0001819	synonymous_variant	23192	exon3			ATACAGGAAAAAC	AB023160	CCDS46564.1, CCDS46565.1	2q37.3	2014-02-12	2012-06-06	2005-09-11	ENSG00000168397	ENSG00000168397			20790	protein-coding gene	gene with protein product		611338	"APG4 autophagy 4 homolog B (S. cerevisiae)", "ATG4 autophagy related 4 homolog B (S. cerevisiae)"	APG4B		12446702	Standard	NM_013325		Approved	Apg4B, KIAA0943, DKFZp586D1822, AUTL1	uc002wbv.3	Q9Y4P1	OTTHUMG00000151514	ENST00000404914.3:c.165G>A	chr2.hg19:g.242590731G>A		83.0	0.0		78.0	21.0	NM_178326	B7WNK2|Q53NU4|Q6ZUV8|Q8WYM9|Q96K07|Q96K96|Q96SZ1|Q9Y2F2	Silent	SNP	ENST00000404914.3	hg19	CCDS46564.1	.	.	.	.	.	.	.	.	.	.	G	13.77	2.336973	0.41398	.	.	ENSG00000168397	ENST00000474739	T	0.47177	0.85	5.36	4.48	0.54585	.	.	.	.	.	T	0.30978	0.0782	.	.	.	0.80722	D	1	B	0.21309	0.054	B	0.19666	0.026	T	0.08576	-1.0715	7	.	.	.	-21.0015	7.4735	0.27363	0.2532:0.0:0.7468:0.0	.	11	F5H7P2	.	E	11	ENSP00000442378:G11E	.	G	+	2	0	ATG4B	242239404	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.128000	0.42045	1.274000	0.44362	0.561000	0.74099	GGA	.	.		0.373	ATG4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322967.3	NM_013325		A	242590731	G	A	242590731	2	1	324	1	0	0	0	0	0	0	0	1	1097	1165	41	3		3	ATG4B	2	242590731	Silent	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10	442000	242590731	608642	35	45643										
CLASP2	23122	hgsc.bcm.edu	37	chr3	33638205	33638205	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	aggaaaggaagttcttaccaTccagcttgtcagaagtatcc	9	9	2	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr3:33638205T>C	ENST00000468888.2	-	19	1995	c.1949A>G	c.(1948-1950)gAt>gGt	p.D650G	CLASP2_ENST00000307312.7_Missense_Mutation_p.D138G|CLASP2_ENST00000539981.1_Missense_Mutation_p.D401G|CLASP2_ENST00000461133.3_Missense_Mutation_p.D416G|CLASP2_ENST00000399362.4_Missense_Mutation_p.D649G|CLASP2_ENST00000480013.1_Missense_Mutation_p.D416G|CLASP2_ENST00000359576.5_Missense_Mutation_p.D649G			O75122	CLAP2_HUMAN	cytoplasmic linker associated protein 2	416					axon guidance (GO:0007411)|establishment or maintenance of cell polarity (GO:0007163)|fucosylation (GO:0036065)|microtubule anchoring (GO:0034453)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)|regulation of microtubule polymerization or depolymerization (GO:0031110)|regulation of microtubule-based process (GO:0032886)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)|microtubule plus-end binding (GO:0051010)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	48						GTTCTTACCATCCAGCTTGTC	0.289																																					p.D650G		Atlas-SNP	.											.	CLASP2	138	.	0			c.A1949G						.						20	20	20					3																	33638205		1797	4050	5847	SO:0001583	missense	23122	exon19			TTACCATCCAGCT	AB014527		3p24.3	2013-01-18			ENSG00000163539	ENSG00000163539			17078	protein-coding gene	gene with protein product		605853				9734811, 10899121	Standard	NM_015097		Approved	KIAA0627	uc021wvc.1	O75122	OTTHUMG00000156489	ENST00000468888.2:c.1949A>G	chr3.hg19:g.33638205T>C	ENSP00000419974:p.Asp650Gly	334.0	0.0		358.0	134.0	NM_015097	Q7L8F6|Q8N6R6|Q9BQT3|Q9BQT4|Q9H7A3|Q9NSZ2	Missense_Mutation	SNP	ENST00000468888.2	hg19		.	.	.	.	.	.	.	.	.	.	T	15.15	2.747666	0.49257	.	.	ENSG00000163539	ENST00000468888;ENST00000399362;ENST00000359576;ENST00000307312;ENST00000539981;ENST00000480013;ENST00000461133	T;T;T	0.18174	2.23;2.23;2.24	5.72	5.72	0.89469	Armadillo-type fold (1);	0.379923	0.24470	N	0.038249	T	0.29817	0.0745	L	0.29908	0.895	0.44736	D	0.997737	D;D	0.67145	0.993;0.996	D;D	0.76071	0.971;0.987	T	0.01688	-1.1295	10	0.36615	T	0.2	-8.177	14.8667	0.70422	0.0:0.0:0.0:1.0	.	416;649	O75122;F5H604	CLAP2_HUMAN;.	G	650;649;649;138;401;416;416	ENSP00000419974:D650G;ENSP00000382297:D649G;ENSP00000352581:D649G	ENSP00000304743:D138G	D	-	2	0	CLASP2	33613209	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.779000	0.75057	2.304000	0.77564	0.528000	0.53228	GAT	.	.		0.289	CLASP2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000344320.4	NM_001207044		C	33638205	T	C	33638205	3	2	324	1	0	0	0	0	1	0	0	0	3457	1435	50	2	2654	2	CLASP2	3	33638205	Missense_Mutation	SNP	T	TCGA-MI-A75I-01A-11D-A32G-10		33638205	164384225	36	45644										
RHOA	387	hgsc.bcm.edu	37	chr3	49400013	49400013	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	accaggatgatgggcacgttGggacagaaatgcttgacttc	13	8	0	3			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr3:49400013G>A	ENST00000418115.1	-	4	708	c.324C>T	c.(322-324)ccC>ccT	p.P108P	RHOA_ENST00000422781.1_Silent_p.P108P|RHOA-IT1_ENST00000428083.1_RNA|RHOA_ENST00000454011.2_Missense_Mutation_p.P68L	NM_001664.2	NP_001655.1	P61586	RHOA_HUMAN	ras homolog family member A	108					actin cytoskeleton organization (GO:0030036)|androgen receptor signaling pathway (GO:0030521)|apical junction assembly (GO:0043297)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cerebral cortex cell migration (GO:0021795)|cleavage furrow formation (GO:0036089)|forebrain radial glial cell differentiation (GO:0021861)|negative chemotaxis (GO:0050919)|negative regulation of axonogenesis (GO:0050771)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of intracellular steroid hormone receptor signaling pathway (GO:0033144)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron differentiation (GO:0045665)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification involved in bone maturation (GO:0043931)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of axonogenesis (GO:0050772)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytokinesis (GO:0032467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of podosome assembly (GO:0071803)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of translation (GO:0045727)|positive regulation of vasoconstriction (GO:0045907)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion transport (GO:0051924)|regulation of cell migration (GO:0030334)|regulation of dendrite development (GO:0050773)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of osteoblast proliferation (GO:0033688)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|Rho protein signal transduction (GO:0007266)|skeletal muscle tissue development (GO:0007519)|small GTPase mediated signal transduction (GO:0007264)|spindle assembly involved in mitosis (GO:0090307)|stress fiber assembly (GO:0043149)|stress-activated protein kinase signaling cascade (GO:0031098)|substantia nigra development (GO:0021762)|trabecula morphogenesis (GO:0061383)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	apical junction complex (GO:0043296)|axon (GO:0030424)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin binding (GO:0017022)			cervix(1)|kidney(1)|large_intestine(5)|lung(1)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	12				BRCA - Breast invasive adenocarcinoma(193;8.58e-05)|Kidney(197;0.0023)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		TGGGCACGTTGGGACAGAAAT	0.458																																					p.P108P		Atlas-SNP	.											.	RHOA	46	.	0			c.C324T						.						122	110	114					3																	49400013		2203	4300	6503	SO:0001819	synonymous_variant	387	exon4			CACGTTGGGACAG	BC001360	CCDS2795.1	3p21.3	2012-02-27	2012-02-27	2004-03-23	ENSG00000067560	ENSG00000067560			667	protein-coding gene	gene with protein product		165390	"ras homolog gene family, member A"	ARH12, ARHA		9605859	Standard	NM_001664		Approved	RhoA, Rho12, RHOH12	uc003cwu.3	P61586	OTTHUMG00000156838	ENST00000418115.1:c.324C>T	chr3.hg19:g.49400013G>A		120.0	0.0		110.0	39.0	NM_001664	P06749|Q53HM4|Q5U024|Q9UDJ0|Q9UEJ4	Silent	SNP	ENST00000418115.1	hg19	CCDS2795.1	.	.	.	.	.	.	.	.	.	.	G	13.83	2.353734	0.41700	.	.	ENSG00000067560	ENST00000454011	T	0.22336	1.96	6.07	1.83	0.25207	.	0.235349	0.44688	N	0.000427	T	0.28665	0.0710	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.03840	-1.0999	7	0.87932	D	0	.	5.738	0.18077	0.0692:0.1168:0.5609:0.2532	.	.	.	.	L	68	ENSP00000394483:P68L	ENSP00000394483:P68L	P	-	2	0	RHOA	49375017	1.000000	0.71417	0.990000	0.47175	0.971000	0.66376	1.788000	0.38714	0.814000	0.34374	0.655000	0.94253	CCA	.	.		0.458	RHOA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346157.3	NM_001664		A	49400013	G	A	49400013	2	1	324	1	0	0	0	0	0	0	0	1	13346	1335	47	3		3	RHOA	3	49400013	Silent	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10	15761808	49400013	148622417	37	45645										
GPR62	118442	hgsc.bcm.edu	37	chr3	51990739	51990739	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ttggcaggagggcggagcccCgcataccaggggccacctga	16	13	0	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr3:51990739C>A	ENST00000322241.4	+	1	1410	c.1071C>A	c.(1069-1071)ccC>ccA	p.P357P		NM_080865.3	NP_543141.3	Q9BZJ7	GPR62_HUMAN	G protein-coupled receptor 62	357						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			endometrium(1)|kidney(1)|large_intestine(1)|ovary(1)|upper_aerodigestive_tract(1)	5				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		GGCGGAGCCCCGCATACCAGG	0.647																																					p.P357P		Atlas-SNP	.											.	GPR62	13	.	0			c.C1071A						.						16	21	19					3																	51990739		2181	4277	6458	SO:0001819	synonymous_variant	118442	exon1			GAGCCCCGCATAC	AF317653	CCDS2838.1	3p21.1	2012-08-21			ENSG00000180929	ENSG00000180929		"GPCR / Class A : Orphans"	13301	protein-coding gene	gene with protein product		606917				11165367	Standard	NM_080865		Approved		uc003dca.4	Q9BZJ7	OTTHUMG00000157367	ENST00000322241.4:c.1071C>A	chr3.hg19:g.51990739C>A		96.0	0.0		130.0	44.0	NM_080865	F1DAM4|Q5KU27	Silent	SNP	ENST00000322241.4	hg19	CCDS2838.1																																																																																			.	.		0.647	GPR62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348611.1			A	51990739	C	A	51990739	2	1	324	1	0	0	0	0	0	0	0	1	6711	639	23	1		1	GPR62	3	51990739	Silent	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	2590726	51990739	146031691	38	45646										
EPHA6	285220	hgsc.bcm.edu	37	chr3	97185271	97185271	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	tatattccataggactctccAtttcaagtgacaaaactgta	5	9	2	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr3:97185271A>C	ENST00000514100.1	+	4	257	c.15A>C	c.(13-15)ccA>ccC	p.P5P	EPHA6_ENST00000502694.1_Silent_p.P5P|EPHA6_ENST00000389672.5_Intron|EPHA6_ENST00000442602.2_Intron	NM_001278300.1	NP_001265229.1	Q9UF33	EPHA6_HUMAN	EPH receptor A6	0						integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(2)|lung(60)|ovary(3)|skin(11)|stomach(5)|upper_aerodigestive_tract(2)	101						aggactctccatttcaagtga	0.413																																					p.P5P		Atlas-SNP	.											.	EPHA6	439	.	0			c.A15C						.						113	107	109					3																	97185271		1854	4102	5956	SO:0001819	synonymous_variant	285220	exon5			CTCTCCATTTCAA	AK092565	CCDS46876.1, CCDS54616.1, CCDS63697.1	3q12.1	2013-02-11	2004-10-28		ENSG00000080224	ENSG00000080224		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	19296	protein-coding gene	gene with protein product		600066				12471243	Standard	NM_001080448		Approved	FLJ35246	uc010how.1	Q9UF33	OTTHUMG00000159208	ENST00000514100.1:c.15A>C	chr3.hg19:g.97185271A>C		67.0	0.0		68.0	30.0	NM_173655	D6RAL5	Silent	SNP	ENST00000514100.1	hg19																																																																																				.	.		0.413	EPHA6-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000359997.1	NM_001080448		C	97185271	A	C	97185271	2	2	324	1	0	0	0	0	0	0	0	1	5173	204	8	5		5	EPHA6	3	97185271	Silent	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	45194532	97185271	100837159	39	45647										
IGSF11	152404	hgsc.bcm.edu	37	chr3	118647489	118647489	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	gagacattggtagctggcatGgtgcctgtaaatcctaccct	11	10	0	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr3:118647489G>A	ENST00000393775.2	-	3	596	c.291C>T	c.(289-291)acC>acT	p.T97T	IGSF11_ENST00000425327.2_Silent_p.T96T|IGSF11_ENST00000489689.1_Silent_p.T97T|IGSF11_ENST00000491903.1_Silent_p.T97T|IGSF11_ENST00000354673.2_Silent_p.T96T|IGSF11_ENST00000441144.2_Silent_p.T96T|IGSF11_ENST00000459718.1_5'UTR	NM_001015887.1	NP_001015887.1	Q5DX21	IGS11_HUMAN	immunoglobulin superfamily, member 11	97	Ig-like V-type.				cell adhesion (GO:0007155)|regulation of growth (GO:0040008)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						TAGCTGGCATGGTGCCTGTAA	0.473																																					p.T97T		Atlas-SNP	.											.	IGSF11	122	.	0			c.C291T						.						94	85	88					3																	118647489		2203	4300	6503	SO:0001819	synonymous_variant	152404	exon3			TGGCATGGTGCCT	AB079879	CCDS2983.1, CCDS46891.1	3q21.2	2013-01-11			ENSG00000144847	ENSG00000144847		"Immunoglobulin superfamily / I-set domain containing"	16669	protein-coding gene	gene with protein product	"cancer/testis antigen 119"	608351				12207903	Standard	XM_006713516		Approved	BT-IgSF, MGC35227, Igsf13, VSIG3, CT119	uc003ebw.3	Q5DX21	OTTHUMG00000159387	ENST00000393775.2:c.291C>T	chr3.hg19:g.118647489G>A		53.0	0.0		73.0	21.0	NM_001015887	C9JZN0|Q8N4F1|Q8N7T8|Q8NDD2	Silent	SNP	ENST00000393775.2	hg19	CCDS46891.1																																																																																			.	.		0.473	IGSF11-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355075.2			A	118647489	G	A	118647489	2	1	324	1	0	0	0	0	0	0	0	1	7607	1335	47	3		3	IGSF11	3	118647489	Silent	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10	21462218	118647489	79374941	40	45648										
GPR156	165829	hgsc.bcm.edu	37	chr3	119885965	119885965	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ttcccaggaagccagcccccCagtaggctcagggtcagtgt	12	14	2	0	rs375340933		TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr3:119885965C>A	ENST00000464295.1	-	10	2804	c.2359G>T	c.(2359-2361)Ggg>Tgg	p.G787W	GPR156_ENST00000315843.3_Missense_Mutation_p.G787W|GPR156_ENST00000461057.1_Missense_Mutation_p.G783W			Q8NFN8	GP156_HUMAN	G protein-coupled receptor 156	787						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled GABA receptor activity (GO:0004965)			breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|ovary(1)|prostate(1)|skin(1)	32				GBM - Glioblastoma multiforme(114;0.19)		GCCAGCCCCCCAGTAGGCTCA	0.547																																					p.G787W		Atlas-SNP	.											.	GPR156	85	.	0			c.G2359T						.	C	TRP/GLY,TRP/GLY	0,4406		0,0,2203	140	158	152		2347,2359	-3.7	0	3		152	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	GPR156	NM_001168271.1,NM_153002.2	184,184	0,1,6502	AA,AC,CC		0.0116,0.0,0.0077	benign,benign	783/811,787/815	119885965	1,13005	2203	4300	6503	SO:0001583	missense	165829	exon9			GCCCCCCAGTAGG	AF488739	CCDS2997.1, CCDS54629.1	3q13.33	2012-08-21			ENSG00000175697	ENSG00000175697		"GPCR / Class C : Orphans"	20844	protein-coding gene	gene with protein product		610464				12591167	Standard	NM_153002		Approved	PGR28, GABABL	uc011bjf.2	Q8NFN8	OTTHUMG00000159406	ENST00000464295.1:c.2359G>T	chr3.hg19:g.119885965C>A	ENSP00000417261:p.Gly787Trp	57.0	0.0		80.0	31.0	NM_153002	B7ZL66|E9PFZ4|Q14CM1|Q86SN6	Missense_Mutation	SNP	ENST00000464295.1	hg19	CCDS2997.1	.	.	.	.	.	.	.	.	.	.	C	7.348	0.622294	0.14193	0.0	1.16E-4	ENSG00000175697	ENST00000464295;ENST00000315843;ENST00000461057	T;T;T	0.24723	1.84;1.84;1.84	4.95	-3.71	0.04424	.	1.884040	0.02330	N	0.073800	T	0.12987	0.0315	N	0.19112	0.55	0.09310	N	1	P;P	0.47106	0.89;0.89	B;B	0.39185	0.293;0.293	T	0.13737	-1.0498	9	.	.	.	6.8521	1.6275	0.02726	0.1158:0.2889:0.2166:0.3787	.	783;787	E9PFZ4;Q8NFN8	.;GP156_HUMAN	W	787;787;783	ENSP00000417261:G787W;ENSP00000324553:G787W;ENSP00000418758:G783W	.	G	-	1	0	GPR156	121368655	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-0.279000	0.08479	-0.481000	0.06792	-0.345000	0.07892	GGG	.	.		0.547	GPR156-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355139.1	NM_153002		A	119885965	C	A	119885965	3	1	324	1	0	0	0	0	1	0	0	0	6669	594	21	3	89	3	GPR156	3	119885965	Missense_Mutation	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	1238476	119885965	78136465	41	45649										
FAM194A	131831	hgsc.bcm.edu	37	chr3	150421522	150421523	+	In_Frame_Ins	INS	-	-	CCTCCT													0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	caccaactcctcctccaccaINScctcctcctcctcctcctcc					rs372003402		TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr3:150421522_150421523insCCTCCT	ENST00000295910.6	-	1	215_216	c.163_164insAGGAGG	c.(163-165)gtg>gAGGAGGtg	p.54_55insEE	FAM194A_ENST00000491361.1_Intron|RP11-103G8.2_ENST00000471093.1_RNA|RP11-103G8.2_ENST00000475393.1_RNA	NM_152394.3	NP_689607.2														NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						ctcctccaccacctcctcctcc	0.604																																					p.V55delinsEEV		Atlas-INDEL	.											.	FAM194A	91	.	0			c.164_165insAGGAGG						.																																			SO:0001652	inframe_insertion	131831	exon1			.																												ENST00000295910.6:c.158_163dupAGGAGG	chr3.hg19:g.150421523_150421528dupCCTCCT	ENSP00000295910:p.Glu53_Glu54dup	33.0	0.0		40.0	14.0	NM_152394		In_Frame_Ins	INS	ENST00000295910.6	hg19	CCDS3151.2																																																																																			.	.		0.604	FAM194A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257666.1			CCTCCT	150421523	-	CCTCCT	150421522	7	5	324	1	0	1	1	0	0	0	0	0	5531	159	6	0	1883	0	FAM194A	3	150421522	In_Frame_Ins	INS	-	TCGA-MI-A75I-01A-11D-A32G-10	30535557	150421522	47600908	42	45650										
MRPL47	57129	hgsc.bcm.edu	37	chr3	179310438	179310438	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	gtgcttgtgctcacctgagaAaatggtccacataaggcaag	11	9	1	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr3:179310438A>C	ENST00000476781.1	-	6	652	c.623T>G	c.(622-624)tTt>tGt	p.F208C	MRPL47_ENST00000392659.2_Missense_Mutation_p.F98C|MRPL47_ENST00000259038.2_Missense_Mutation_p.F188C	NM_020409.2	NP_065142.2	Q9HD33	RM47_HUMAN	mitochondrial ribosomal protein L47	208					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)	structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(1)|large_intestine(3)|lung(4)|skin(1)|stomach(1)	11	all_cancers(143;9.62e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.18)			TCACCTGAGAAAATGGTCCAC	0.363																																					p.F208C		Atlas-SNP	.											.	MRPL47	31	.	0			c.T623G						.						103	91	95					3																	179310438		2203	4300	6503	SO:0001583	missense	57129	exon6			CTGAGAAAATGGT	AF285120	CCDS3232.1, CCDS3233.1	3q26.33	2012-11-14			ENSG00000136522	ENSG00000136522		"Mitochondrial ribosomal proteins / large subunits"	16652	protein-coding gene	gene with protein product	"nasopharyngeal carcinoma metastasis-related 1"	611852				11551941	Standard	NM_177988		Approved	CGI-204, NCM1	uc003fjz.3	Q9HD33	OTTHUMG00000157784	ENST00000476781.1:c.623T>G	chr3.hg19:g.179310438A>C	ENSP00000417602:p.Phe208Cys	57.0	0.0		78.0	27.0	NM_020409	Q6XRG1|Q8N5D1	Missense_Mutation	SNP	ENST00000476781.1	hg19	CCDS3232.1	.	.	.	.	.	.	.	.	.	.	A	18.08	3.544265	0.65198	.	.	ENSG00000136522	ENST00000476781;ENST00000259038;ENST00000392659	T;T;T	0.57436	0.93;1.04;0.4	5.96	5.96	0.96718	.	0.190645	0.49916	D	0.000126	T	0.70579	0.3240	M	0.69823	2.125	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.70487	0.969;0.931	T	0.73978	-0.3812	10	0.87932	D	0	-24.3422	13.9716	0.64245	1.0:0.0:0.0:0.0	.	188;208	Q9HD33-2;Q9HD33	.;RM47_HUMAN	C	208;188;98	ENSP00000417602:F208C;ENSP00000259038:F188C;ENSP00000376427:F98C	ENSP00000259038:F188C	F	-	2	0	MRPL47	180793132	1.000000	0.71417	0.121000	0.21740	0.384000	0.30261	5.148000	0.64857	2.285000	0.76669	0.533000	0.62120	TTT	.	.		0.363	MRPL47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349623.1	NM_020409		C	179310438	A	C	179310438	3	2	324	1	0	0	0	0	1	0	0	0	9820	14	1	5	137	5	MRPL47	3	179310438	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	28888916	179310438	18711992	43	45651										
IQCG	84223	hgsc.bcm.edu	37	chr3	197670818	197670818	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	tttctatgtctgtttctttaGgtattccttcttcttctacg	5	9	6	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr3:197670818G>A	ENST00000265239.6	-	4	537	c.113C>T	c.(112-114)cCt>cTt	p.P38L	IQCG_ENST00000455191.1_Missense_Mutation_p.P38L|IQCG_ENST00000480302.1_5'UTR|IQCG_ENST00000453254.1_Missense_Mutation_p.P38L	NM_032263.3	NP_115639.1	Q9H095	IQCG_HUMAN	IQ motif containing G	38						extracellular vesicular exosome (GO:0070062)				autonomic_ganglia(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;7.19e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.149)		TGTTTCTTTAGGTATTCCTTC	0.488																																					p.P38L		Atlas-SNP	.											.	IQCG	44	.	0			c.C113T						.						152	145	148					3																	197670818		2203	4300	6503	SO:0001583	missense	84223	exon4			TCTTTAGGTATTC	AL136889	CCDS3331.1	3q29	2014-07-18			ENSG00000114473	ENSG00000114473			25251	protein-coding gene	gene with protein product	"dynein regulatory complex subunit 9"	612477				11230166, 23427265, 24362311	Standard	NM_032263		Approved	DKFZp434B227, DRC9, CFAP122	uc003fyo.3	Q9H095	OTTHUMG00000155408	ENST00000265239.6:c.113C>T	chr3.hg19:g.197670818G>A	ENSP00000265239:p.Pro38Leu	107.0	0.0		79.0	33.0	NM_032263	Q9BST2|Q9HAG8	Missense_Mutation	SNP	ENST00000265239.6	hg19	CCDS3331.1	.	.	.	.	.	.	.	.	.	.	G	8.892	0.954337	0.18431	.	.	ENSG00000114473	ENST00000265239;ENST00000455191;ENST00000453254;ENST00000416896;ENST00000452735	T;T;T;T	0.44881	0.91;0.91;0.91;0.94	3.79	-1.73	0.08081	.	2.329850	0.01678	N	0.025997	T	0.25344	0.0616	L	0.36672	1.1	0.09310	N	1	B;B	0.30406	0.278;0.016	B;B	0.25759	0.063;0.007	T	0.03193	-1.1062	10	0.09843	T	0.71	6.5902	0.7161	0.00932	0.1996:0.1538:0.333:0.3136	.	38;38	C9JKX8;Q9H095	.;IQCG_HUMAN	L	38;38;38;19;38	ENSP00000265239:P38L;ENSP00000407736:P38L;ENSP00000389897:P38L;ENSP00000406411:P19L	ENSP00000265239:P38L	P	-	2	0	IQCG	199155215	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.160000	0.03147	-0.284000	0.09102	-0.331000	0.08364	CCT	.	.		0.488	IQCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339730.1	NM_032263		A	197670818	G	A	197670818	3	1	324	1	0	0	0	0	1	0	0	0	7819	1000	35	3	1254	3	IQCG	3	197670818	Missense_Mutation	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10	18360380	197670818	351612	44	45652										
BOD1L	259282	hgsc.bcm.edu	37	chr4	13610294	13610294	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	aagtccacactactcctgccTagaaaagaagcaatcaataa	5	11	1	2			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr4:13610294T>C	ENST00000040738.5	-	8	1739		c.e8-2			NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1							nucleus (GO:0005634)	DNA binding (GO:0003677)										TACTCCTGCCTAGAAAAGAAG	0.299																																					.		Atlas-SNP	.											.	.	.	.	0			c.1604-2A>G						.						39	36	37					4																	13610294		2200	4296	6496	SO:0001630	splice_region_variant	259282	exon9			CCTGCCTAGAAAA	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.1604-2A>G	chr4.hg19:g.13610294T>C		83.0	0.0		83.0	36.0	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Splice_Site	SNP	ENST00000040738.5	hg19	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	T	12.58	1.979184	0.34942	.	.	ENSG00000038219	ENST00000040738	.	.	.	5.63	5.63	0.86233	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4085	0.67099	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	BOD1L	13219392	1.000000	0.71417	0.936000	0.37596	0.364000	0.29643	4.060000	0.57477	2.152000	0.67230	0.528000	0.53228	.	.	.		0.299	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894	Intron	C	13610294	T	C	13610294	5	2	324	1	0	0	0	0	0	0	1	0	1483	1536	53	2	7629	2	BOD1L	4	13610294	Splice_Site	SNP	T	TCGA-MI-A75I-01A-11D-A32G-10		13610294	177543982	45	45653										
KDR	3791	hgsc.bcm.edu	37	chr4	55963911	55963911	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	gcttcaatcacttggccaaaGgcaccacggccaagaggctt	10	13	2	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr4:55963911G>C	ENST00000263923.4	-	18	2827	c.2532C>G	c.(2530-2532)gcC>gcG	p.A844A		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	844	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CTTGGCCAAAGGCACCACGGC	0.418			Mis		"NSCLC, angiosarcoma"					TSP Lung(20;0.16)																											p.A844A		Atlas-SNP	.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	.	KDR	307	.	0			c.C2532G						.						113	102	106					4																	55963911		2203	4300	6503	SO:0001819	synonymous_variant	3791	exon18			GCCAAAGGCACCA	AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.2532C>G	chr4.hg19:g.55963911G>C		47.0	0.0		63.0	20.0	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Silent	SNP	ENST00000263923.4	hg19	CCDS3497.1																																																																																			.	.		0.418	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1			C	55963911	G	C	55963911	2	2	324	1	0	0	0	0	0	0	0	1	8148	987	35	4		4	KDR	4	55963911	Silent	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10	42353617	55963911	135190365	46	45654										
FAM190A	401145	hgsc.bcm.edu	37	chr4	91645123	91645123	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	tcctgttagtcctcttactgAagagccagtgcctttcaagg	9	11	2	2			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr4:91645123A>T	ENST00000509176.1	+	7	2279	c.1991A>T	c.(1990-1992)gAa>gTa	p.E664V	CCSER1_ENST00000333691.8_Missense_Mutation_p.E664V|CCSER1_ENST00000504150.1_3'UTR|CCSER1_ENST00000432775.2_Missense_Mutation_p.E664V	NM_001145065.1	NP_001138537.1	Q9C0I3	CCSE1_HUMAN	coiled-coil serine-rich protein 1	664																	CCTCTTACTGAAGAGCCAGTG	0.333																																					p.E664V		Atlas-SNP	.											.	.	.	.	0			c.A1991T						.						30	28	28					4																	91645123		1831	4084	5915	SO:0001583	missense	401145	exon7			TTACTGAAGAGCC		CCDS47099.1, CCDS47100.1	4q22.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184305	ENSG00000184305			29349	protein-coding gene	gene with protein product			"family with sequence similarity 190, member A"	FAM190A		11214970	Standard	NM_001145065		Approved	KIAA1680	uc003hsv.4	Q9C0I3	OTTHUMG00000160950	ENST00000509176.1:c.1991A>T	chr4.hg19:g.91645123A>T	ENSP00000425040:p.Glu664Val	360.0	0.0		349.0	135.0	NM_001145065	Q4W5M0|Q86V57	Missense_Mutation	SNP	ENST00000509176.1	hg19	CCDS47099.1	.	.	.	.	.	.	.	.	.	.	A	17.20	3.328131	0.60743	.	.	ENSG00000184305	ENST00000509176;ENST00000432775;ENST00000333691;ENST00000458365;ENST00000503421	T;T;T	0.54279	1.22;0.58;1.22	4.63	4.63	0.57726	.	0.200481	0.41194	D	0.000938	T	0.59878	0.2226	L	0.60455	1.87	0.32985	D	0.524207	D;D	0.61080	0.989;0.989	P;P	0.53518	0.728;0.728	T	0.73350	-0.4010	10	0.87932	D	0	-14.8246	12.2264	0.54463	1.0:0.0:0.0:0.0	.	664;664	Q9C0I3-2;Q9C0I3	.;F190A_HUMAN	V	664;664;664;664;17	ENSP00000425040:E664V;ENSP00000389283:E664V;ENSP00000329482:E664V	ENSP00000329482:E664V	E	+	2	0	FAM190A	91864146	1.000000	0.71417	0.987000	0.45799	0.747000	0.42532	4.856000	0.62932	2.026000	0.59711	0.454000	0.30748	GAA	.	.		0.333	CCSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363109.3	NM_001145065		T	91645123	A	T	91645123	3	4	324	1	0	0	0	0	1	0	0	0	5526	246	9	4	2013	4	FAM190A	4	91645123	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	35681212	91645123	99509153	47	45655										
ADH1A	124	hgsc.bcm.edu	37	chr4	100205700	100205700	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	gagaaggtgctgatgccaagGaagtggtggatgggcttcct	17	6	0	2			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr4:100205700G>T	ENST00000209668.2	-	5	536	c.423C>A	c.(421-423)ttC>ttA	p.F141L	RP11-696N14.1_ENST00000500358.2_RNA|ADH1A_ENST00000511656.1_5'Flank	NM_000667.3	NP_000658.1	P07327	ADH1A_HUMAN	alcohol dehydrogenase 1A (class I), alpha polypeptide	141					alcohol metabolic process (GO:0006066)|drug metabolic process (GO:0017144)|ethanol oxidation (GO:0006069)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(1)	25				OV - Ovarian serous cystadenocarcinoma(123;9.56e-08)	Ethanol(DB00898)|Fomepizole(DB01213)	TGATGCCAAGGAAGTGGTGGA	0.517																																					p.F141L		Atlas-SNP	.											.	ADH1A	49	.	0			c.C423A						.						90	86	88					4																	100205700		2203	4300	6503	SO:0001583	missense	124	exon5			GCCAAGGAAGTGG	M12963	CCDS3648.1	4q23	2009-12-04			ENSG00000187758	ENSG00000187758	1.1.1.1	"Alcohol dehydrogenases"	249	protein-coding gene	gene with protein product		103700		ADH1		3006456	Standard	NM_000667		Approved		uc003hur.2	P07327	OTTHUMG00000131026	ENST00000209668.2:c.423C>A	chr4.hg19:g.100205700G>T	ENSP00000209668:p.Phe141Leu	112.0	0.0		139.0	32.0	NM_000667	A8K3E3|Q17R68	Missense_Mutation	SNP	ENST00000209668.2	hg19	CCDS3648.1	.	.	.	.	.	.	.	.	.	.	G	9.770	1.172558	0.21704	.	.	ENSG00000187758	ENST00000209668	T	0.03441	3.93	2.59	0.673	0.17941	GroES-like (1);Alcohol dehydrogenase GroES-like (1);	0.048449	0.85682	N	0.000000	T	0.11836	0.0288	M	0.69358	2.11	0.41767	D	0.989742	D	0.89917	1.0	D	0.97110	1.0	T	0.01504	-1.1338	10	0.87932	D	0	-9.2382	6.7327	0.23393	0.4393:0.0:0.5607:0.0	.	141	P07327	ADH1A_HUMAN	L	141	ENSP00000209668:F141L	ENSP00000209668:F141L	F	-	3	2	ADH1A	100424723	0.000000	0.05858	0.437000	0.26809	0.029000	0.11900	-0.320000	0.08028	0.364000	0.24374	0.460000	0.39030	TTC	.	.		0.517	ADH1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253669.1	NM_000667		T	100205700	G	T	100205700	3	4	324	1	0	0	0	0	1	0	0	0	307	1165	41	3	724	3	ADH1A	4	100205700	Missense_Mutation	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10	8560577	100205700	90948576	48	45656										
MTTP	4547	hgsc.bcm.edu	37	chr4	100532577	100532577	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	agtaacctgaacatctttcaGtacattgggaaggctggtct	10	8	3	1	rs369415595		TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr4:100532577G>A	ENST00000265517.5	+	14	2159	c.1956G>A	c.(1954-1956)caG>caA	p.Q652Q	MTTP_ENST00000511045.1_Silent_p.Q679Q|RP11-766F14.1_ENST00000508578.1_RNA|MTTP_ENST00000457717.1_Silent_p.Q652Q			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	652	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.				cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|protein lipidation (GO:0006497)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|microvillus membrane (GO:0031528)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)	lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(14)|lung(19)|ovary(4)|prostate(5)|skin(1)|urinary_tract(1)	57				OV - Ovarian serous cystadenocarcinoma(123;6.04e-09)	Hesperetin(DB01094)|Lomitapide(DB08827)	ACATCTTTCAGTACATTGGGA	0.438																																					p.Q652Q		Atlas-SNP	.											.	MTTP	127	.	0			c.G1956A						.	G		1,4405	2.1+/-5.4	0,1,2202	174	159	164		1956	5.6	1	4		164	0,8600		0,0,4300	no	coding-synonymous	MTTP	NM_000253.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		652/895	100532577	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	4547	exon15			CTTTCAGTACATT		CCDS3651.1, CCDS75169.1	4q24	2008-02-05	2005-11-04	2005-11-04	ENSG00000138823	ENSG00000138823			7467	protein-coding gene	gene with protein product		157147	"microsomal triglyceride transfer protein (large polypeptide, 88kD)", "microsomal triglyceride transfer protein (large polypeptide, 88kDa)"	MTP		8111381	Standard	XM_005263025		Approved	ABL	uc003hvc.4	P55157	OTTHUMG00000131023	ENST00000265517.5:c.1956G>A	chr4.hg19:g.100532577G>A		153.0	0.0		150.0	57.0	NM_000253	A8K428|Q08AM4|Q6P5T3	Silent	SNP	ENST00000265517.5	hg19	CCDS3651.1																																																																																			.	.		0.438	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3			A	100532577	G	A	100532577	2	1	324	1	0	0	0	0	0	0	0	1	9973	1020	36	3		3	MTTP	4	100532577	Silent	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10	326877	100532577	90621699	49	45657										
H2AFZ	3015	hgsc.bcm.edu	37	chr4	100870052	100870052	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	caagtgacgaggggtaatacGctttacctttaagtcttttg	10	7	1	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr4:100870052G>A	ENST00000296417.5	-	4	458	c.241C>T	c.(241-243)Cgt>Tgt	p.R81C	RP11-15B17.1_ENST00000507494.1_RNA|RP11-15B17.1_ENST00000501976.2_RNA|H2AFZ_ENST00000529158.1_5'UTR|DNAJB14_ENST00000442697.2_5'Flank|RP11-15B17.1_ENST00000514624.1_RNA|DNAJB14_ENST00000471738.1_5'Flank	NM_002106.3	NP_002097.1	P0C0S5	H2AZ_HUMAN	H2A histone family, member Z	81					cellular response to estradiol stimulus (GO:0071392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	extracellular vesicular exosome (GO:0070062)|nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|nucleosomal DNA binding (GO:0031492)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)			breast(1)|endometrium(3)|lung(1)	5				OV - Ovarian serous cystadenocarcinoma(123;2.32e-08)		GGGGTAATACGCTTTACCTTT	0.418											OREG0016271	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R81C		Atlas-SNP	.											H2AFZ,NS,carcinoma,0,1	H2AFZ	13	.	0			c.C241T						.						93	88	90					4																	100870052		2203	4300	6503	SO:0001583	missense	3015	exon4			TAATACGCTTTAC	X52317	CCDS3654.1	4q23	2011-01-27			ENSG00000164032	ENSG00000164032		"Histones / Replication-independent"	4741	protein-coding gene	gene with protein product		142763		H2AZ		1697587	Standard	XM_005262971		Approved	H2A.Z	uc003hvo.1	P0C0S5	OTTHUMG00000131048	ENST00000296417.5:c.241C>T	chr4.hg19:g.100870052G>A	ENSP00000296417:p.Arg81Cys	173.0	1.0	1354	167.0	50.0	NM_002106	B2RD56|P17317|Q6I9U0	Missense_Mutation	SNP	ENST00000296417.5	hg19	CCDS3654.1	.	.	.	.	.	.	.	.	.	.	G	17.20	3.329373	0.60743	.	.	ENSG00000164032	ENST00000296417	T	0.69561	-0.41	4.74	4.74	0.60224	Histone-fold (2);Histone core (1);Histone H2A (2);	0.000000	0.85682	D	0.000000	T	0.79335	0.4428	H	0.97315	3.98	0.80722	D	1	B	0.25312	0.123	B	0.16722	0.016	T	0.82824	-0.0266	10	0.62326	D	0.03	-12.0973	17.7576	0.88453	0.0:0.0:1.0:0.0	.	81	P0C0S5	H2AZ_HUMAN	C	81	ENSP00000296417:R81C	ENSP00000296417:R81C	R	-	1	0	H2AFZ	101089075	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.910000	0.92685	2.187000	0.69744	0.655000	0.94253	CGT	.	.		0.418	H2AFZ-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000253695.1	NM_002106		A	100870052	G	A	100870052	3	1	324	1	0	0	0	0	1	0	0	0	6940	1087	38	1	153	1	H2AFZ	4	100870052	Missense_Mutation	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10	337475	100870052	90284224	50	45658										
GUCY1B3	2983	hgsc.bcm.edu	37	chr4	156724875	156724875	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	acctggccttggacatgatgGaaattgctggccaggttcaa	12	9	1	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr4:156724875G>T	ENST00000264424.8	+	11	1595	c.1513G>T	c.(1513-1515)Gaa>Taa	p.E505*	GUCY1B3_ENST00000505154.1_Nonsense_Mutation_p.E437*|GUCY1B3_ENST00000502959.1_Nonsense_Mutation_p.E527*|GUCY1B3_ENST00000513437.1_Nonsense_Mutation_p.E437*|GUCY1B3_ENST00000507146.1_Nonsense_Mutation_p.E480*|GUCY1B3_ENST00000505764.1_Nonsense_Mutation_p.E485*|GUCY1B3_ENST00000503520.1_Nonsense_Mutation_p.E472*	NM_000857.2	NP_000848.1	Q02153	GCYB1_HUMAN	guanylate cyclase 1, soluble, beta 3	505	Guanylate cyclase. {ECO:0000255|PROSITE- ProRule:PRU00099}.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|nitric oxide mediated signal transduction (GO:0007263)	cytoplasm (GO:0005737)|guanylate cyclase complex, soluble (GO:0008074)|intracellular membrane-bounded organelle (GO:0043231)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)			NS(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.148)		GGACATGATGGAAATTGCTGG	0.423																																					p.E505X		Atlas-SNP	.											.	GUCY1B3	65	.	0			c.G1513T						.						76	78	78					4																	156724875		1950	4158	6108	SO:0001587	stop_gained	2983	exon11			ATGATGGAAATTG	AF020340	CCDS47154.1, CCDS75203.1	4q31.3-q33	2008-03-18			ENSG00000061918	ENSG00000061918	4.6.1.2		4687	protein-coding gene	gene with protein product		139397		GUC1B3		1352257	Standard	XM_005262959		Approved	GC-SB3, GC-S-beta-1	uc003ipc.3	Q02153	OTTHUMG00000161698	ENST00000264424.8:c.1513G>T	chr4.hg19:g.156724875G>T	ENSP00000264424:p.Glu505*	48.0	0.0		59.0	22.0	NM_000857	B7Z426|Q86WY5	Nonsense_Mutation	SNP	ENST00000264424.8	hg19	CCDS47154.1	.	.	.	.	.	.	.	.	.	.	G	38	6.988580	0.97983	.	.	ENSG00000061918	ENST00000505154;ENST00000502959;ENST00000505764;ENST00000507146;ENST00000264424;ENST00000503520;ENST00000513437	.	.	.	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	.	20.0018	0.97417	0.0:0.0:1.0:0.0	.	.	.	.	X	437;527;485;480;505;472;437	.	ENSP00000264424:E505X	E	+	1	0	GUCY1B3	156944325	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.805000	0.99149	2.793000	0.96121	0.655000	0.94253	GAA	.	.		0.423	GUCY1B3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365770.2			T	156724875	G	T	156724875	4	4	324	1	0	0	0	0	0	1	0	0	6904	1175	41	3	1555	3	GUCY1B3	4	156724875	Nonsense_Mutation	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10	55854823	156724875	34429401	51	45659										
GRIA2	2891	hgsc.bcm.edu	37	chr4	158281153	158281153	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	gggtggctagagtgcggaagTccaaagggaaatatgcctac	15	7	0	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr4:158281153T>C	ENST00000264426.9	+	13	2428	c.2149T>C	c.(2149-2151)Tcc>Ccc	p.S717P	GRIA2_ENST00000393815.2_Missense_Mutation_p.S670P|GRIA2_ENST00000449365.1_Missense_Mutation_p.S670P|GRIA2_ENST00000296526.7_Missense_Mutation_p.S717P|GRIA2_ENST00000507898.1_Missense_Mutation_p.S670P|AC079233.1_ENST00000578227.1_RNA	NM_001083619.1	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2	717					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(2)|lung(32)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	79	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	AGTGCGGAAGTCCAAAGGGAA	0.493																																					p.S717P		Atlas-SNP	.											.	GRIA2	358	.	0			c.T2149C						.						139	132	134					4																	158281153		2203	4300	6503	SO:0001583	missense	2891	exon13			CGGAAGTCCAAAG		CCDS3797.1, CCDS43274.1, CCDS43275.1	4q32.1	2012-08-29			ENSG00000120251	ENSG00000120251		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4572	protein-coding gene	gene with protein product		138247		GLUR2		1311100	Standard	NM_001083619		Approved	GluA2, GLURB	uc003ipl.4	P42262	OTTHUMG00000133836	ENST00000264426.9:c.2149T>C	chr4.hg19:g.158281153T>C	ENSP00000264426:p.Ser717Pro	91.0	0.0		89.0	24.0	NM_000826	A8MT92|I6L997|Q96FP6	Missense_Mutation	SNP	ENST00000264426.9	hg19	CCDS43274.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.04|19.04	3.750399|3.750399	0.69533|0.69533	.|.	.|.	ENSG00000120251|ENSG00000120251	ENST00000507898;ENST00000393815;ENST00000296526;ENST00000264426;ENST00000449365|ENST00000510854	T;T;T;T;T|.	0.38887|.	1.11;1.11;1.11;1.11;1.11|.	5.69|5.69	5.69|5.69	0.88448|0.88448	Ionotropic glutamate receptor (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.79941|0.79941	0.4533|0.4533	M|M	0.86343|0.86343	2.81|2.81	0.80722|0.80722	D|D	1|1	D;D;D;D;D|.	0.89917|.	1.0;0.98;0.998;0.992;0.963|.	D;P;D;P;P|.	0.81914|.	0.995;0.732;0.966;0.854;0.773|.	T|T	0.82739|0.82739	-0.0308|-0.0308	10|5	0.87932|.	D|.	0|.	.|.	15.9526|15.9526	0.79855|0.79855	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	745;717;717;717;670|.	Q59F93;P42262-3;P42262;P42262-2;A8MT92|.	.;.;GRIA2_HUMAN;.;.|.	P|A	670;670;717;717;670|47	ENSP00000426845:S670P;ENSP00000377403:S670P;ENSP00000296526:S717P;ENSP00000264426:S717P;ENSP00000389837:S670P|.	ENSP00000264426:S717P|.	S|V	+|+	1|2	0|0	GRIA2|GRIA2	158500603|158500603	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.995000|0.995000	0.86356|0.86356	8.040000|8.040000	0.89188|0.89188	2.168000|2.168000	0.68352|0.68352	0.533000|0.533000	0.62120|0.62120	TCC|GTC	.	.		0.493	GRIA2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000258367.2			C	158281153	T	C	158281153	3	2	324	1	0	0	0	0	1	0	0	0	6777	1667	58	2	2199	2	GRIA2	4	158281153	Missense_Mutation	SNP	T	TCGA-MI-A75I-01A-11D-A32G-10	1556278	158281153	32873123	52	45660										
C4orf45	152940	hgsc.bcm.edu	37	chr4	159956201	159956201	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ttacctgtaaaaatcatttgTtttcccacagtagtagatgt	6	7	1	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr4:159956201T>G	ENST00000434826.2	-	1	132	c.48A>C	c.(46-48)aaA>aaC	p.K16N	C4orf45_ENST00000508011.1_Intron	NM_152543.2	NP_689756.2	Q96LM5	CD045_HUMAN	chromosome 4 open reading frame 45	16										large_intestine(2)|lung(3)	5						AAATCATTTGTTTTCCCACAG	0.328																																					p.K16N		Atlas-SNP	.											.	C4orf45	8	.	0			c.A48C						.						107	102	103					4																	159956201		1830	4085	5915	SO:0001583	missense	152940	exon1			CATTTGTTTTCCC		CCDS47156.1	4q32.1	2012-03-02			ENSG00000164123	ENSG00000164123			26342	protein-coding gene	gene with protein product							Standard	NM_152543		Approved	FLJ25371	uc003iqf.1	Q96LM5	OTTHUMG00000161988	ENST00000434826.2:c.48A>C	chr4.hg19:g.159956201T>G	ENSP00000412215:p.Lys16Asn	82.0	0.0		87.0	33.0	NM_152543	A8MPU3|C9J0T8	Missense_Mutation	SNP	ENST00000434826.2	hg19	CCDS47156.1	.	.	.	.	.	.	.	.	.	.	T	14.32	2.498974	0.44455	.	.	ENSG00000164123	ENST00000434826	T	0.17054	2.3	5.4	-1.42	0.08913	.	0.651684	0.14766	N	0.299718	T	0.26159	0.0638	L	0.57536	1.79	0.09310	N	0.999993	D	0.61697	0.99	P	0.57152	0.814	T	0.10870	-1.0611	9	.	.	.	-15.1744	9.2284	0.37421	0.0:0.4775:0.0:0.5225	.	16	Q96LM5	CD045_HUMAN	N	16	ENSP00000412215:K16N	.	K	-	3	2	C4orf45	160175651	0.704000	0.27836	0.243000	0.24186	0.772000	0.43724	-0.425000	0.07017	-0.372000	0.07992	0.533000	0.62120	AAA	.	.		0.328	C4orf45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366636.1	NM_152543		G	159956201	T	G	159956201	3	3	324	1	0	0	0	0	1	0	0	0	2275	1722	60	5	532	5	C4orf45	4	159956201	Missense_Mutation	SNP	T	TCGA-MI-A75I-01A-11D-A32G-10	1675048	159956201	31198075	53	45661										
C5orf55	116349	hgsc.bcm.edu	37	chr5	442609	442609	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	cctctgcagcgcggcccagtGacccacattcattctccaag	8	17	3	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr5:442609G>A	ENST00000408966.2	-	1	649	c.329C>T	c.(328-330)tCa>tTa	p.S110L	EXOC3_ENST00000512944.1_5'Flank	NM_138464.2	NP_612473.1	Q8N2X6	CE055_HUMAN	chromosome 5 open reading frame 55	110						extracellular region (GO:0005576)				large_intestine(1)|lung(2)	3						GCGGCCCAGTGACCCACATTC	0.642																																					p.S110L		Atlas-SNP	.											.	C5orf55	11	.	0			c.C329T						.						39	43	41					5																	442609		1906	4122	6028	SO:0001583	missense	116349	exon1			CCCAGTGACCCAC	BC014011	CCDS43298.1	5p15.33	2012-02-24			ENSG00000221990	ENSG00000221990			25175	protein-coding gene	gene with protein product						12477932	Standard	NM_138464		Approved		uc010ita.3	Q8N2X6	OTTHUMG00000162235	ENST00000408966.2:c.329C>T	chr5.hg19:g.442609G>A	ENSP00000386139:p.Ser110Leu	19.0	0.0		37.0	16.0	NM_138464	Q96CR9	Missense_Mutation	SNP	ENST00000408966.2	hg19	CCDS43298.1	.	.	.	.	.	.	.	.	.	.	G	7.018	0.558114	0.13436	.	.	ENSG00000221990	ENST00000408966	T	0.38401	1.14	0.849	-0.208	0.13185	.	.	.	.	.	T	0.16727	0.0402	N	0.08118	0	0.09310	N	1	B	0.12630	0.006	B	0.08055	0.003	T	0.19877	-1.0292	9	0.87932	D	0	.	4.5407	0.12056	0.0:0.5635:0.4365:0.0	.	110	Q8N2X6	CE055_HUMAN	L	110	ENSP00000386139:S110L	ENSP00000386139:S110L	S	-	2	0	C5orf55	495609	0.000000	0.05858	0.000000	0.03702	0.267000	0.26476	-0.139000	0.10358	-0.106000	0.12110	0.205000	0.17691	TCA	.	.		0.642	C5orf55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368033.1	NM_138464		A	442609	G	A	442609	3	1	324	1	0	0	0	0	1	0	0	0	2313	1294	45	3	34	3	C5orf55	5	442609	Missense_Mutation	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10		442609	180472651	54	45662										
ACOT12	134526	hgsc.bcm.edu	37	chr5	80640019	80640019	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	gcgtgcaatagctccccgatAgcgtctgaaatcatccttta	8	12	2	1	rs533220517		TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr5:80640019A>C	ENST00000307624.3	-	9	968	c.940T>G	c.(940-942)Tat>Gat	p.Y314D	ACOT12_ENST00000508234.1_5'UTR	NM_130767.2	NP_570123.1	Q8WYK0	ACO12_HUMAN	acyl-CoA thioesterase 12	314					acetyl-CoA metabolic process (GO:0006084)|acyl-CoA metabolic process (GO:0006637)|fatty acid metabolic process (GO:0006631)|pyruvate metabolic process (GO:0006090)	cytosol (GO:0005829)	acetyl-CoA hydrolase activity (GO:0003986)|ATP binding (GO:0005524)|carboxylic ester hydrolase activity (GO:0052689)|lipid binding (GO:0008289)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)	23		Lung NSC(167;0.0176)|all_lung(232;0.0205)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;1.37e-45)|Epithelial(54;1.25e-39)|all cancers(79;5.01e-34)		GCTCCCCGATAGCGTCTGAAA	0.328													A|||	1	0.000199681	0	0	5008	,	,		17862	0		0	False		,,,				2504	0.001				p.Y314D		Atlas-SNP	.											.	ACOT12	57	.	0			c.T940G						.						65	67	66					5																	80640019		2203	4300	6503	SO:0001583	missense	134526	exon9			CCCGATAGCGTCT	AB078619	CCDS4055.1	5q14.1	2011-09-13			ENSG00000172497	ENSG00000172497		"Acyl CoA thioesterases", "StAR-related lipid transfer (START) domain containing"	24436	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 15"	614315				16103133, 16940157	Standard	NM_130767		Approved	Cach, THEAL, STARD15	uc003khl.4	Q8WYK0	OTTHUMG00000131305	ENST00000307624.3:c.940T>G	chr5.hg19:g.80640019A>C	ENSP00000303246:p.Tyr314Asp	155.0	0.0		196.0	51.0	NM_130767	B3KVK9|Q5FWE9	Missense_Mutation	SNP	ENST00000307624.3	hg19	CCDS4055.1	.	.	.	.	.	.	.	.	.	.	A	17.93	3.509989	0.64522	.	.	ENSG00000172497	ENST00000307624	T	0.34072	1.38	5.45	5.45	0.79879	.	0.073069	0.56097	D	0.000038	T	0.62575	0.2439	M	0.89287	3.02	0.80722	D	1	D	0.63046	0.992	P	0.62184	0.899	T	0.69602	-0.5101	10	0.59425	D	0.04	-23.7265	13.3403	0.60540	1.0:0.0:0.0:0.0	.	314	Q8WYK0	ACO12_HUMAN	D	314	ENSP00000303246:Y314D	ENSP00000303246:Y314D	Y	-	1	0	ACOT12	80675775	0.993000	0.37304	0.640000	0.29408	0.878000	0.50629	7.166000	0.77553	2.201000	0.70794	0.533000	0.62120	TAT	.	.		0.328	ACOT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254074.1	NM_130767		C	80640019	A	C	80640019	3	2	324	1	0	0	0	0	1	0	0	0	150	420	15	5	755	5	ACOT12	5	80640019	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	80197410	80640019	100275241	55	45663										
MEF2C	4208	hgsc.bcm.edu	37	chr5	88057132	88057132	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	tgtcacagccattaaggcccTtctttctcaacgtctgaaat	6	12	4	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr5:88057132T>C	ENST00000437473.2	-	4	689	c.272A>G	c.(271-273)aAg>aGg	p.K91R	MEF2C_ENST00000503554.1_5'UTR|MEF2C_ENST00000504921.2_Missense_Mutation_p.K91R|MEF2C_ENST00000514015.1_Missense_Mutation_p.K91R|MEF2C_ENST00000424173.2_Intron|MEF2C_ENST00000508569.1_Missense_Mutation_p.K91R|MEF2C_ENST00000510942.1_Missense_Mutation_p.K91R|MEF2C_ENST00000506554.1_Missense_Mutation_p.K91R|MEF2C_ENST00000539796.1_Intron|MEF2C_ENST00000340208.5_Missense_Mutation_p.K91R|MEF2C_ENST00000514028.1_Missense_Mutation_p.K91R	NM_001193350.1|NM_002397.4	NP_001180279.1|NP_002388.2	Q06413	MEF2C_HUMAN	myocyte enhancer factor 2C	91					apoptotic process (GO:0006915)|B cell homeostasis (GO:0001782)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac ventricle formation (GO:0003211)|cartilage morphogenesis (GO:0060536)|cell morphogenesis involved in neuron differentiation (GO:0048667)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|cellular response to fluid shear stress (GO:0071498)|cellular response to glucose stimulus (GO:0071333)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to parathyroid hormone stimulus (GO:0071374)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cellular response to trichostatin A (GO:0035984)|chondrocyte differentiation (GO:0002062)|dentate gyrus development (GO:0021542)|embryonic viscerocranium morphogenesis (GO:0048703)|endochondral ossification (GO:0001958)|epithelial cell proliferation involved in renal tubule morphogenesis (GO:2001013)|germinal center formation (GO:0002467)|glomerulus morphogenesis (GO:0072102)|heart development (GO:0007507)|heart looping (GO:0001947)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|MAPK cascade (GO:0000165)|melanocyte differentiation (GO:0030318)|monocyte differentiation (GO:0030224)|muscle cell differentiation (GO:0042692)|muscle cell fate determination (GO:0007521)|muscle organ development (GO:0007517)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|myotube differentiation (GO:0014902)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of gene expression (GO:0010629)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of ossification (GO:0030279)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nephron tubule epithelial cell differentiation (GO:0072160)|nervous system development (GO:0007399)|neural crest cell differentiation (GO:0014033)|neuron development (GO:0048666)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|osteoblast differentiation (GO:0001649)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|platelet formation (GO:0030220)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of behavioral fear response (GO:2000987)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation in bone marrow (GO:0071864)|positive regulation of gene expression (GO:0010628)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of skeletal muscle cell differentiation (GO:2001016)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|primary heart field specification (GO:0003138)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of dendritic spine development (GO:0060998)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of germinal center formation (GO:0002634)|regulation of megakaryocyte differentiation (GO:0045652)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuron apoptotic process (GO:0043523)|regulation of neurotransmitter secretion (GO:0046928)|regulation of sarcomere organization (GO:0060297)|regulation of synapse assembly (GO:0051963)|regulation of synaptic activity (GO:0060025)|regulation of synaptic plasticity (GO:0048167)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of transcription, DNA-templated (GO:0006355)|renal tubule morphogenesis (GO:0061333)|response to ischemia (GO:0002931)|response to virus (GO:0009615)|response to vitamin E (GO:0033197)|secondary heart field specification (GO:0003139)|sinoatrial valve morphogenesis (GO:0003185)|skeletal muscle tissue development (GO:0007519)|smooth muscle cell differentiation (GO:0051145)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ventricular cardiac muscle cell differentiation (GO:0055012)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|sarcomere (GO:0030017)	activating transcription factor binding (GO:0033613)|AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|miRNA binding (GO:0035198)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	40		all_cancers(142;6.67e-05)|all_epithelial(76;7.77e-07)|Lung NSC(167;0.00566)|all_lung(232;0.00732)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;1.04e-33)|Epithelial(54;1.6e-28)|all cancers(79;2.9e-25)		ATTAAGGCCCTTCTTTCTCAA	0.448										HNSCC(66;0.2)																											p.K91R		Atlas-SNP	.											.	MEF2C	184	.	0			c.A272G						.						95	94	94					5																	88057132		1867	4100	5967	SO:0001583	missense	4208	exon4			AGGCCCTTCTTTC	AL833268	CCDS47244.1, CCDS47245.1, CCDS54877.1, CCDS54878.1	5q14.3	2013-07-03	2007-04-24		ENSG00000081189	ENSG00000081189		"Myocyte enhancer factors"	6996	protein-coding gene	gene with protein product		600662				8455629	Standard	NM_002397		Approved		uc003kjl.3	Q06413	OTTHUMG00000162634	ENST00000437473.2:c.272A>G	chr5.hg19:g.88057132T>C	ENSP00000396219:p.Lys91Arg	63.0	0.0		82.0	5.0	NM_001193350	C9JMZ0|D7F7N5|F8W7V7	Missense_Mutation	SNP	ENST00000437473.2	hg19	CCDS47245.1	.	.	.	.	.	.	.	.	.	.	T	33	5.194313	0.94960	.	.	ENSG00000081189	ENST00000340208;ENST00000504921;ENST00000514028;ENST00000437473;ENST00000510942;ENST00000506554;ENST00000508569;ENST00000514015;ENST00000502983;ENST00000508610;ENST00000502831	T;T;T;T;T;T;T;T;D;D;D	0.87334	0.02;-0.16;-0.16;-0.16;-0.17;-0.5;-0.49;-0.45;-2.24;-2.2;-1.81	5.93	5.93	0.95920	Transcription factor, MADS-box (1);	0.000000	0.85682	D	0.000000	D	0.93831	0.8027	M	0.82193	2.58	0.80722	D	1	D;D;D	0.89917	0.974;0.995;1.0	D;D;D	0.80764	0.953;0.994;0.982	D	0.94541	0.7745	10	0.87932	D	0	-6.944	16.3756	0.83387	0.0:0.0:0.0:1.0	.	91;91;91	F8W7V7;Q06413;Q06413-2	.;MEF2C_HUMAN;.	R	91	ENSP00000340874:K91R;ENSP00000421925:K91R;ENSP00000426665:K91R;ENSP00000396219:K91R;ENSP00000422390:K91R;ENSP00000425636:K91R;ENSP00000423597:K91R;ENSP00000424606:K91R;ENSP00000427163:K91R;ENSP00000426442:K91R;ENSP00000427286:K91R	ENSP00000340874:K91R	K	-	2	0	MEF2C	88092888	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.698000	0.84413	2.270000	0.75569	0.460000	0.39030	AAG	.	.		0.448	MEF2C-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000369817.1	NM_002397		C	88057132	T	C	88057132	3	2	324	1	0	0	0	0	1	0	0	0	9466	1609	56	2	1323	2	MEF2C	5	88057132	Missense_Mutation	SNP	T	TCGA-MI-A75I-01A-11D-A32G-10	7417113	88057132	92858128	56	45664										
TRIM36	55521	hgsc.bcm.edu	37	chr5	114506870	114506870	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	tcgctgtggcaagttccgtcGtcttcccacagccctgtctg	10	15	2	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr5:114506870G>A	ENST00000282369.3	-	2	185				TRIM36_ENST00000379618.2_Missense_Mutation_p.T38M|TRIM36_ENST00000515104.1_5'Flank|TRIM36_ENST00000513154.1_5'Flank|TRIM36_ENST00000514154.1_Intron	NM_018700.3	NP_061170.2	Q9NQ86	TRI36_HUMAN	tripartite motif containing 36						acrosome reaction (GO:0007340)|regulation of cell cycle (GO:0051726)	acrosomal vesicle (GO:0001669)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	37		all_cancers(142;0.00133)|all_epithelial(76;2.41e-05)|Prostate(80;0.00955)|Ovarian(225;0.0443)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;3.62e-08)|Epithelial(69;7.69e-08)|all cancers(49;9.33e-06)		AAGTTCCGTCGTCTTCCCACA	0.463																																					p.T38M		Atlas-SNP	.											.	TRIM36	126	.	0			c.C113T						.						145	155	152					5																	114506870		2202	4300	6502	SO:0001627	intron_variant	55521	exon2			TCCGTCGTCTTCC	AJ272269	CCDS4115.1, CCDS34211.1, CCDS34212.1, CCDS75287.1	5q22	2013-02-11	2011-01-25		ENSG00000152503	ENSG00000152503		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Fibronectin type III domain containing"	16280	protein-coding gene	gene with protein product	"zinc-binding protein Rbcc728", "tripartite motif protein 36", "RING finger protein 98"	609317	"tripartite motif-containing 36"			11331580	Standard	XM_005272031		Approved	RBCC728, RNF98, HAPRIN	uc003kqs.3	Q9NQ86	OTTHUMG00000128892	ENST00000282369.3:c.64-7421C>T	chr5.hg19:g.114506870G>A		94.0	0.0		129.0	56.0	NM_001017397	A1L3Z1|A6NDD0|B7Z3V4|B7ZAV7|E9PFI8|Q0P5Z9	Missense_Mutation	SNP	ENST00000282369.3	hg19	CCDS4115.1	.	.	.	.	.	.	.	.	.	.	G	13.01	2.109292	0.37242	.	.	ENSG00000152503	ENST00000379618	.	.	.	2.81	-0.166	0.13351	.	.	.	.	.	T	0.26304	0.0642	.	.	.	0.09310	N	1	B	0.28584	0.216	B	0.13407	0.009	T	0.17531	-1.0366	7	0.87932	D	0	.	5.2455	0.15494	0.4427:0.0:0.5573:0.0	.	38	Q0P5Z9	.	M	38	.	ENSP00000368938:T38M	T	-	2	0	TRIM36	114534769	0.001000	0.12720	0.000000	0.03702	0.865000	0.49528	1.031000	0.30165	-0.053000	0.13289	0.650000	0.86243	ACG	.	.		0.463	TRIM36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250854.2	NM_018700		A	114506870	G	A	114506870	1	1	324	0	1	0	0	0	0	0	0	0	16525	1145	40	1		1	TRIM36	5	114506870	Intron	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10	26449738	114506870	66408390	57	45665										
CXCL14	9547	hgsc.bcm.edu	37	chr5	134914414	134914414	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	cccgcactcaccgtccacacGcgcggtgtacagcgccagca	10	19	1	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr5:134914414G>A	ENST00000337225.5	-	1	555	c.91C>T	c.(91-93)Cgt>Tgt	p.R31C	CTC-321K16.1_ENST00000509372.1_RNA|CXCL14_ENST00000512158.1_Missense_Mutation_p.R19C|CTC-321K16.1_ENST00000514446.1_RNA	NM_004887.4	NP_004878.2	O95715	CXL14_HUMAN	chemokine (C-X-C motif) ligand 14	31					cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|chemotaxis (GO:0006935)|immune response (GO:0006955)|inner ear development (GO:0048839)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)	chemokine activity (GO:0008009)			large_intestine(2)|lung(2)|prostate(1)|skin(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CCGTCCACACGCGCGGTGTAC	0.697																																					p.R31C		Atlas-SNP	.											.	CXCL14	13	.	0			c.C91T						.						10	9	9					5																	134914414		2016	3979	5995	SO:0001583	missense	9547	exon1			CCACACGCGCGGT	AF073957	CCDS4188.1	5q31	2010-04-30	2002-08-22	2002-08-23	ENSG00000145824	ENSG00000145824			10640	protein-coding gene	gene with protein product	"breast and kidney"	604186	"small inducible cytokine subfamily B (Cys-X-Cys), member 14 (BRAK)"	SCYB14		10049774	Standard	NM_004887		Approved	BRAK, NJAC, bolekine, Kec, MIP-2g, BMAC, KS1	uc003lay.3	O95715	OTTHUMG00000129139	ENST00000337225.5:c.91C>T	chr5.hg19:g.134914414G>A	ENSP00000337065:p.Arg31Cys	40.0	0.0		57.0	32.0	NM_004887	B3KQU8|Q6UW97|Q86U69|Q9BTR1|Q9NS21	Missense_Mutation	SNP	ENST00000337225.5	hg19	CCDS4188.1	.	.	.	.	.	.	.	.	.	.	G	14.28	2.488725	0.44249	.	.	ENSG00000145824	ENST00000337225;ENST00000512158	.	.	.	4.67	2.78	0.32641	Chemokine interleukin-8-like domain (1);	0.586313	0.19383	N	0.115618	T	0.28333	0.0700	L	0.36672	1.1	0.09310	N	0.999994	D	0.61697	0.99	P	0.44946	0.465	T	0.09818	-1.0657	9	0.52906	T	0.07	1.6211	6.7845	0.23665	0.0:0.3784:0.397:0.2246	.	31	O95715	CXL14_HUMAN	C	31;19	.	ENSP00000337065:R31C	R	-	1	0	CXCL14	134942313	1.000000	0.71417	0.996000	0.52242	0.868000	0.49771	1.825000	0.39081	0.934000	0.37316	0.563000	0.77884	CGT	.	.		0.697	CXCL14-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_004887		A	134914414	G	A	134914414	3	1	324	1	0	0	0	0	1	0	0	0	4084	1087	38	1	260	1	CXCL14	5	134914414	Missense_Mutation	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10	20407544	134914414	46000846	58	45666										
PCDHA7	56141	hgsc.bcm.edu	37	chr5	140215935	140215935	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	gcttgtgaaggaccacggggAgccctcgctgacagccacag	14	13	0	2			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr5:140215935A>T	ENST00000525929.1	+	1	1967	c.1967A>T	c.(1966-1968)gAg>gTg	p.E656V	PCDHA2_ENST00000526136.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA7_ENST00000378125.3_Missense_Mutation_p.E656V|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000504120.2_Intron	NM_018910.2	NP_061733.1	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7	656	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|biliary_tract(1)|breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GACCACGGGGAGCCCTCGCTG	0.662																																					p.E656V	NSCLC(160;258 2013 5070 22440 28951)	Atlas-SNP	.											.	PCDHA7	367	.	0			c.A1967T						.						59	63	62					5																	140215935		2203	4298	6501	SO:0001583	missense	56141	exon1			ACGGGGAGCCCTC	AF152485	CCDS54918.1	5q31	2010-11-26				ENSG00000204963		"Cadherins / Protocadherins : Clustered"	8673	other	complex locus constituent	"KIAA0345-like 7", "ortholog to mouse CNR4"	606313		CNRS4		10380929, 10662547	Standard	NM_018910		Approved	CNR4, CRNR4		Q9UN72		ENST00000525929.1:c.1967A>T	chr5.hg19:g.140215935A>T	ENSP00000436426:p.Glu656Val	54.0	0.0		78.0	39.0	NM_031852	O75282	Missense_Mutation	SNP	ENST00000525929.1	hg19	CCDS54918.1	.	.	.	.	.	.	.	.	.	.	A	15.30	2.791206	0.50102	.	.	ENSG00000204963	ENST00000525929;ENST00000378125	T;T	0.53206	0.63;0.63	3.57	3.57	0.40892	Cadherin (4);Cadherin-like (1);	0.000000	0.31936	U	0.006824	T	0.57110	0.2031	L	0.53249	1.67	0.23572	N	0.997388	P;P	0.52316	0.93;0.952	P;P	0.57244	0.816;0.772	T	0.51872	-0.8650	10	0.87932	D	0	.	12.5944	0.56461	1.0:0.0:0.0:0.0	.	656;656	Q9UN72-2;Q9UN72	.;PCDA7_HUMAN	V	656	ENSP00000436426:E656V;ENSP00000367365:E656V	ENSP00000367365:E656V	E	+	2	0	PCDHA7	140196119	0.011000	0.17503	0.929000	0.37066	0.374000	0.29953	2.440000	0.44855	1.603000	0.50134	0.379000	0.24179	GAG	.	.		0.662	PCDHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372887.2	NM_018910		T	140215935	A	T	140215935	3	4	324	1	0	0	0	0	1	0	0	0	11538	304	11	4	1969	4	PCDHA7	5	140215935	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	5301521	140215935	40699325	59	45667										
ARHGEF37	389337	hgsc.bcm.edu	37	chr5	148996303	148996303	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ggacgtgaacaccaatatcaAtgagtacaagatgcgcaagg	11	8	1	3			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr5:148996303A>G	ENST00000333677.6	+	5	795	c.632A>G	c.(631-633)aAt>aGt	p.N211S		NM_001001669.2	NP_001001669.2	A1IGU5	ARH37_HUMAN	Rho guanine nucleotide exchange factor (GEF) 37	211	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.					cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(5)|lung(6)|ovary(1)|prostate(2)|stomach(3)	17						ACCAATATCAATGAGTACAAG	0.473																																					p.N211S		Atlas-SNP	.											.	ARHGEF37	45	.	0			c.A632G						.						115	107	110					5																	148996303		1963	4164	6127	SO:0001583	missense	389337	exon5			ATATCAATGAGTA	BC041325	CCDS43385.1	5q33.1	2012-07-24			ENSG00000183111	ENSG00000183111		"Rho guanine nucleotide exchange factors"	34430	protein-coding gene	gene with protein product							Standard	XM_005268448		Approved	FLJ41603	uc003lra.1	A1IGU5	OTTHUMG00000163491	ENST00000333677.6:c.632A>G	chr5.hg19:g.148996303A>G	ENSP00000328083:p.Asn211Ser	109.0	0.0		146.0	33.0	NM_001001669	Q6ZW51	Missense_Mutation	SNP	ENST00000333677.6	hg19	CCDS43385.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.555867	0.86231	.	.	ENSG00000183111	ENST00000333677	T	0.75589	-0.95	5.42	5.42	0.78866	Dbl homology (DH) domain (5);	0.000000	0.85682	D	0.000000	D	0.88618	0.6485	M	0.90309	3.105	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.91018	0.4855	10	0.87932	D	0	-6.5827	15.7747	0.78204	1.0:0.0:0.0:0.0	.	211	A1IGU5	ARH37_HUMAN	S	211	ENSP00000328083:N211S	ENSP00000328083:N211S	N	+	2	0	ARHGEF37	148976496	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	8.825000	0.92029	2.194000	0.70268	0.533000	0.62120	AAT	.	.		0.473	ARHGEF37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373763.1	NM_001001669		G	148996303	A	G	148996303	3	3	324	1	0	0	0	0	1	0	0	0	906	101	4	2	646	2	ARHGEF37	5	148996303	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	8780368	148996303	31918957	60	45668										
ODZ2	57451	hgsc.bcm.edu	37	chr5	167645700	167645700	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ttttcaacgctgatggcatcCaccaatacactgtgagcctg	8	12	1	2			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr5:167645700C>G	ENST00000518659.1	+	23	4843	c.4804C>G	c.(4804-4806)Cac>Gac	p.H1602D	TENM2_ENST00000519204.1_Missense_Mutation_p.H1481D|TENM2_ENST00000545108.1_Missense_Mutation_p.H1601D|TENM2_ENST00000403607.2_Missense_Mutation_p.H1426D|TENM2_ENST00000520394.1_Missense_Mutation_p.H1363D	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	1602					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										TGATGGCATCCACCAATACAC	0.453																																					p.H1593D		Atlas-SNP	.											.	.	.	.	0			c.C4777G						.						118	115	116					5																	167645700		2013	4190	6203	SO:0001583	missense	57451	exon23			GGCATCCACCAAT	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"odz, odd Oz/ten-m homolog 2 (Drosophila)"	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.4804C>G	chr5.hg19:g.167645700C>G	ENSP00000429430:p.His1602Asp	105.0	0.0		186.0	36.0	NM_001122679	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	hg19		.	.	.	.	.	.	.	.	.	.	C	21.2	4.115501	0.77323	.	.	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	T;T;T;T;T	0.56444	1.63;0.46;1.63;1.63;1.63	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.78168	0.4241	M	0.87617	2.895	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.984	D;D;D	0.75484	0.986;0.968;0.964	T	0.80821	-0.1211	10	0.87932	D	0	.	20.1577	0.98120	0.0:1.0:0.0:0.0	.	1601;1602;1363	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	D	1602;1601;1481;1363;1426	ENSP00000429430:H1602D;ENSP00000438635:H1601D;ENSP00000428964:H1481D;ENSP00000427874:H1363D;ENSP00000384905:H1426D	ENSP00000384905:H1426D	H	+	1	0	ODZ2	167578278	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.818000	0.86416	2.767000	0.95098	0.655000	0.94253	CAC	.	.		0.453	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		G	167645700	C	G	167645700	3	3	324	1	0	0	0	0	1	0	0	0	10844	594	21	4	4867	4	ODZ2	5	167645700	Missense_Mutation	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	18649397	167645700	13269560	61	45669										
DSP	1832	hgsc.bcm.edu	37	chr6	7571705	7571705	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	atcagaaatagccaaggctcAgagatgtttggagatgatga	12	5	2	5			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr6:7571705A>T	ENST00000379802.3	+	14	2132	c.1791A>T	c.(1789-1791)tcA>tcT	p.S597S	DSP_ENST00000418664.2_Silent_p.S597S	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	597	Globular 1.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		GCCAAGGCTCAGAGATGTTTG	0.473																																					p.S597S		Atlas-SNP	.											.	DSP	306	.	0			c.A1791T						.						224	215	218					6																	7571705		2203	4300	6503	SO:0001819	synonymous_variant	1832	exon14			AGGCTCAGAGATG	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"desmoplakin (DPI, DPII)"			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.1791A>T	chr6.hg19:g.7571705A>T		85.0	0.0		173.0	43.0	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Silent	SNP	ENST00000379802.3	hg19	CCDS4501.1																																																																																			.	.		0.473	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		T	7571705	A	T	7571705	2	4	324	1	0	0	0	0	0	0	0	1	4783	175	7	4		4	DSP	6	7571705	Silent	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10		7571705	163543362	62	45670										
JARID2	3720	hgsc.bcm.edu	37	chr6	15496837	15496837	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	agtcgccccccaagaagatgAaaggggcggctggccccgcc	14	15	0	3			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr6:15496837A>G	ENST00000341776.2	+	7	1625	c.1381A>G	c.(1381-1383)Aaa>Gaa	p.K461E	JARID2_ENST00000541660.1_Missense_Mutation_p.K423E|JARID2_ENST00000397311.3_Missense_Mutation_p.K289E	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	461					central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	59	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				CAAGAAGATGAAAGGGGCGGC	0.677																																					p.K461E		Atlas-SNP	.											.	JARID2	135	.	0			c.A1381G						.						9	13	12					6																	15496837		2140	4204	6344	SO:0001583	missense	3720	exon7			AAGATGAAAGGGG	U57592	CCDS4533.1, CCDS58996.1	6p24-p23	2008-02-05	2006-10-06	2004-01-30	ENSG00000008083	ENSG00000008083			6196	protein-coding gene	gene with protein product		601594	"jumonji (mouse) homolog", "Jumonji, AT rich interactive domain 2"	JMJ		8894700	Standard	NM_001267040		Approved		uc003nbj.4	Q92833	OTTHUMG00000014293	ENST00000341776.2:c.1381A>G	chr6.hg19:g.15496837A>G	ENSP00000341280:p.Lys461Glu	12.0	0.0		67.0	15.0	NM_004973	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Missense_Mutation	SNP	ENST00000341776.2	hg19	CCDS4533.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.124946	0.77436	.	.	ENSG00000008083	ENST00000538175;ENST00000341776;ENST00000397311;ENST00000541660	D;D;D	0.89552	-1.88;-1.88;-2.53	5.54	5.54	0.83059	.	0.046492	0.85682	D	0.000000	D	0.83631	0.5296	L	0.34521	1.04	0.44937	D	0.997954	D;D;B	0.62365	0.972;0.991;0.39	P;P;B	0.51550	0.673;0.556;0.108	T	0.83218	-0.0070	10	0.29301	T	0.29	-13.3442	15.6626	0.77199	1.0:0.0:0.0:0.0	.	423;325;461	F5H590;B7Z7X9;Q92833	.;.;JARD2_HUMAN	E	325;461;289;423	ENSP00000341280:K461E;ENSP00000380478:K289E;ENSP00000444623:K423E	ENSP00000341280:K461E	K	+	1	0	JARID2	15604816	1.000000	0.71417	0.999000	0.59377	0.676000	0.39594	4.011000	0.57124	2.095000	0.63458	0.533000	0.62120	AAA	.	.		0.677	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973		G	15496837	A	G	15496837	3	3	324	1	0	0	0	0	1	0	0	0	7954	247	9	2	1407	2	JARID2	6	15496837	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	7925132	15496837	155618230	63	45671										
BTN3A1	11119	hgsc.bcm.edu	37	chr6	26409957	26409957	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	atgaagcaagaacaaagcacAagaggtagctgaccttggga	12	7	0	4			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr6:26409957A>G	ENST00000289361.6	+	5	1280	c.912A>G	c.(910-912)acA>acG	p.T304T	BTN3A1_ENST00000476549.2_Silent_p.T304T|BTN3A1_ENST00000414912.2_Silent_p.T252T|BTN3A1_ENST00000425234.2_Silent_p.T304T	NM_001145008.1|NM_001145009.1|NM_007048.5	NP_001138480.1|NP_001138481.1|NP_008979.3	O00481	BT3A1_HUMAN	butyrophilin, subfamily 3, member A1	304					activated T cell proliferation (GO:0050798)|cytokine secretion (GO:0050663)|interferon-gamma secretion (GO:0072643)|T cell receptor signaling pathway (GO:0050852)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28						AACAAAGCACAAGAGGTAGCT	0.493																																					p.T304T		Atlas-SNP	.											.	BTN3A1	80	.	0			c.A912G						.						152	164	160					6																	26409957		2203	4300	6503	SO:0001819	synonymous_variant	11119	exon5			AAGCACAAGAGGT	U90552	CCDS4608.1, CCDS4609.1, CCDS47388.1, CCDS47389.1	6p22.1	2014-01-14			ENSG00000026950	ENSG00000026950		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Butyrophilins"	1138	protein-coding gene	gene with protein product		613593				9149941	Standard	NM_007048		Approved	BT3.1, BTF5, CD277, BTN3.1	uc003nhv.3	O00481	OTTHUMG00000014449	ENST00000289361.6:c.912A>G	chr6.hg19:g.26409957A>G		20.0	0.0		48.0	9.0	NM_007048	A2A278|A8K2C8|B4DIQ1|B4DRM2|E9PGB4|E9PHG8|Q0P515|Q147X5|Q53F15|Q99420|Q9HCY1	Silent	SNP	ENST00000289361.6	hg19	CCDS4608.1																																																																																			.	.		0.493	BTN3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040112.3			G	26409957	A	G	26409957	2	3	324	1	0	0	0	0	0	0	0	1	1564	117	5	2		2	BTN3A1	6	26409957	Silent	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	10913120	26409957	144705110	64	45672										
GABBR1	2550	hgsc.bcm.edu	37	chr6	29572726	29572726	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ggctgcatcctgctggctggAcagaatcatggtgacaggag	15	9	1	2			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr6:29572726A>G	ENST00000377034.4	-	21	2814	c.2479T>C	c.(2479-2481)Tcc>Ccc	p.S827P	GABBR1_ENST00000377012.4_Missense_Mutation_p.S710P|GABBR1_ENST00000355973.3_Missense_Mutation_p.S710P|GABBR1_ENST00000376977.3_3'UTR|GABBR1_ENST00000377016.4_Missense_Mutation_p.S765P	NM_001470.2	NP_001461.1	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 1	827					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	G-protein coupled GABA receptor activity (GO:0004965)			endometrium(3)|kidney(1)|large_intestine(13)|liver(1)|lung(16)|ovary(5)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47					Baclofen(DB00181)|Progabide(DB00837)|Vigabatrin(DB01080)	TGCTGGCTGGACAGAATCATG	0.507																																					p.S827P		Atlas-SNP	.											.	GABBR1	95	.	0			c.T2479C						.						103	70	82					6																	29572726		1511	2709	4220	SO:0001583	missense	2550	exon21			GGCTGGACAGAAT	Y11044	CCDS4663.1, CCDS4664.1, CCDS4665.1	6p21.3	2012-08-29			ENSG00000204681	ENSG00000204681		"GABA receptors", "GPCR / Class C : GABA(B) receptors"	4070	protein-coding gene	gene with protein product	"GABA-B receptor"	603540				9753614, 9798068	Standard	NM_001470		Approved	hGB1a, GPRC3A	uc003nmt.4	Q9UBS5	OTTHUMG00000031095	ENST00000377034.4:c.2479T>C	chr6.hg19:g.29572726A>G	ENSP00000366233:p.Ser827Pro	48.0	0.0		74.0	27.0	NM_001470	B0UXY7|O95375|O95468|O95975|O96022|Q5STL4|Q5SUJ8|Q5SUL3|Q71SG6|Q86W60|Q9UQQ0	Missense_Mutation	SNP	ENST00000377034.4	hg19	CCDS4663.1	.	.	.	.	.	.	.	.	.	.	A	19.90	3.912876	0.72983	.	.	ENSG00000204681	ENST00000355973;ENST00000377016;ENST00000377012;ENST00000377034	D;D;D;D	0.88431	-2.38;-2.38;-2.38;-2.38	5.16	3.97	0.46021	GPCR, family 3, C-terminal (2);	0.130213	0.52532	D	0.000061	D	0.88872	0.6555	L	0.55213	1.73	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.83275	0.996;0.996;0.996	D	0.88419	0.3027	10	0.51188	T	0.08	-18.1341	7.7623	0.28959	0.6622:0.0:0.0:0.3377	.	765;827;710	Q9UBS5-3;Q9UBS5;Q5SUJ9	.;GABR1_HUMAN;.	P	710;765;710;827	ENSP00000348248:S710P;ENSP00000366215:S765P;ENSP00000366211:S710P;ENSP00000366233:S827P	ENSP00000348248:S710P	S	-	1	0	GABBR1	29680705	0.985000	0.35326	0.998000	0.56505	0.999000	0.98932	2.509000	0.45459	0.954000	0.37851	0.533000	0.62120	TCC	.	.		0.507	GABBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076141.3			G	29572726	A	G	29572726	3	3	324	1	0	0	0	0	1	0	0	0	6163	275	10	2	418	2	GABBR1	6	29572726	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	3162769	29572726	141542341	65	45673										
TTBK1	84630	hgsc.bcm.edu	37	chr6	43214466	43214466	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	gggaggggagcaggccgacaTcctgccggccaactacgtgg	17	12	0	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr6:43214466T>C	ENST00000259750.4	+	2	151	c.68T>C	c.(67-69)aTc>aCc	p.I23T	TTBK1_ENST00000304139.5_5'Flank	NM_032538.1	NP_115927.1	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	23					substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(10)|liver(1)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)			CAGGCCGACATCCTGCCGGCC	0.677																																					p.I23T		Atlas-SNP	.											.	TTBK1	124	.	0			c.T68C						.						44	40	41					6																	43214466		2203	4300	6503	SO:0001583	missense	84630	exon2			CCGACATCCTGCC	AB058758	CCDS34455.1	6p21.1	2008-02-05			ENSG00000146216	ENSG00000146216			19140	protein-coding gene	gene with protein product						11347906	Standard	XM_006715229		Approved	KIAA1855	uc003ouq.1	Q5TCY1	OTTHUMG00000014725	ENST00000259750.4:c.68T>C	chr6.hg19:g.43214466T>C	ENSP00000259750:p.Ile23Thr	113.0	0.0		206.0	24.0	NM_032538	A2A2U5|Q2L6C6|Q6ZNH0|Q8N444|Q96JH2	Missense_Mutation	SNP	ENST00000259750.4	hg19	CCDS34455.1	.	.	.	.	.	.	.	.	.	.	T	29.0	4.967280	0.92855	.	.	ENSG00000146216	ENST00000259750	T	0.56275	0.47	4.62	4.62	0.57501	.	0.000000	0.64402	D	0.000001	T	0.47303	0.1438	L	0.29908	0.895	0.80722	D	1	D	0.69078	0.997	P	0.61477	0.889	T	0.55945	-0.8060	10	0.87932	D	0	.	13.0392	0.58889	0.0:0.0:0.0:1.0	.	23	Q5TCY1	TTBK1_HUMAN	T	23	ENSP00000259750:I23T	ENSP00000259750:I23T	I	+	2	0	TTBK1	43322444	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.593000	0.82686	1.709000	0.51313	0.533000	0.62120	ATC	.	.		0.677	TTBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040584.3			C	43214466	T	C	43214466	3	2	324	1	0	0	0	0	1	0	0	0	16691	1435	50	2	70	2	TTBK1	6	43214466	Missense_Mutation	SNP	T	TCGA-MI-A75I-01A-11D-A32G-10	13641740	43214466	127900601	66	45674										
PLA2G7	7941	hgsc.bcm.edu	37	chr6	46682256	46682256	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	tatttttcaccaggcctcagAggggaattccagtttgcagg	11	9	2	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr6:46682256A>T	ENST00000274793.7	-	5	607	c.411T>A	c.(409-411)ccT>ccA	p.P137P	PLA2G7_ENST00000541026.1_Silent_p.P10P|PLA2G7_ENST00000538237.1_Silent_p.P92P|PLA2G7_ENST00000537365.1_Silent_p.P137P	NM_005084.3	NP_005075.3	Q13093	PAFA_HUMAN	phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)	137					cellular protein metabolic process (GO:0044267)|lipid catabolic process (GO:0016042)|lipid oxidation (GO:0034440)|low-density lipoprotein particle remodeling (GO:0034374)|plasma lipoprotein particle oxidation (GO:0034441)|positive regulation of inflammatory response (GO:0050729)|positive regulation of monocyte chemotaxis (GO:0090026)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|low-density lipoprotein particle (GO:0034362)	1-alkyl-2-acetylglycerophosphocholine esterase activity (GO:0003847)|calcium-independent phospholipase A2 activity (GO:0047499)|phospholipid binding (GO:0005543)			endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|skin(1)|soft_tissue(1)	14			Lung(136;0.192)			CAGGCCTCAGAGGGGAATTCC	0.388																																					p.P137P		Atlas-SNP	.											.	PLA2G7	49	.	0			c.T411A						.						104	102	103					6																	46682256		2203	4300	6503	SO:0001819	synonymous_variant	7941	exon5			CCTCAGAGGGGAA	U20157	CCDS4917.1	6p21.2-p12	2008-09-19			ENSG00000146070	ENSG00000146070	3.1.1.4		9040	protein-coding gene	gene with protein product		601690				7700381, 8624782	Standard	NM_005084		Approved	PAFAH, LDL-PLA2	uc021zae.1	Q13093	OTTHUMG00000014789	ENST00000274793.7:c.411T>A	chr6.hg19:g.46682256A>T		58.0	0.0		121.0	23.0	NM_005084	A5HTT5|Q15692|Q5VTT1|Q8IVA2	Silent	SNP	ENST00000274793.7	hg19	CCDS4917.1																																																																																			.	.		0.388	PLA2G7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040802.1			T	46682256	A	T	46682256	2	4	324	1	0	0	0	0	0	0	0	1	12018	291	11	4		4	PLA2G7	6	46682256	Silent	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	3467790	46682256	124432811	67	45675										
PRDM1	639	hgsc.bcm.edu	37	chr6	106536266	106536266	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	tgatggcggtacttcggttcAggcggaggcatccttaccaa	13	10	1	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr6:106536266A>T	ENST00000369096.4	+	2	467	c.233A>T	c.(232-234)cAg>cTg	p.Q78L	PRDM1_ENST00000369091.2_Missense_Mutation_p.Q42L	NM_001198.3	NP_001189.2	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain	78					cell fate commitment (GO:0045165)|eye photoreceptor cell development (GO:0042462)|germ cell development (GO:0007281)|intestinal epithelial cell development (GO:0060576)|maternal placenta development (GO:0001893)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gene expression (GO:0010628)|post-embryonic development (GO:0009791)|transcription, DNA-templated (GO:0006351)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q42fs*23(2)|p.?(1)		NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(59)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(5)|urinary_tract(2)	94	Breast(9;0.022)	all_cancers(87;2.2e-31)|all_epithelial(87;2.03e-21)|Acute lymphoblastic leukemia(125;4.99e-11)|all_lung(197;7.55e-09)|all_hematologic(75;5.82e-08)|Lung NSC(302;1.28e-06)|Colorectal(196;0.0112)|Ovarian(999;0.0365)		all cancers(137;1.83e-46)|Epithelial(106;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(136;1.99e-20)|GBM - Glioblastoma multiforme(226;3.72e-11)|BRCA - Breast invasive adenocarcinoma(108;1.38e-05)		ACTTCGGTTCAGGCGGAGGCA	0.493			"D, N, Mis, F, S"		DLBCL																																p.Q78L		Atlas-SNP	.		Rec	yes		6	6q21	639	"PR domain containing 1, with ZNF domain"		L	.,1	PRDM1	195	.	3	Deletion - Frameshift(2)|Unknown(1)	haematopoietic_and_lymphoid_tissue(3)	c.A233T						.						201	178	186					6																	106536266		2203	4300	6503	SO:0001583	missense	639	exon2			CGGTTCAGGCGGA		CCDS5054.2, CCDS34505.1	6q21	2013-01-08			ENSG00000057657	ENSG00000057657		"Zinc fingers, C2H2-type"	9346	protein-coding gene	gene with protein product		603423		BLIMP1		1851123	Standard	NM_001198		Approved	PRDI-BF1	uc003prd.2	O75626	OTTHUMG00000015299	ENST00000369096.4:c.233A>T	chr6.hg19:g.106536266A>T	ENSP00000358092:p.Gln78Leu	76.0	0.0		73.0	33.0	NM_001198	B2REA6|E1P5E0|Q86WM7	Missense_Mutation	SNP	ENST00000369096.4	hg19	CCDS5054.2	.	.	.	.	.	.	.	.	.	.	A	15.75	2.924727	0.52653	.	.	ENSG00000057657	ENST00000369091;ENST00000369096;ENST00000456278;ENST00000424894	T;T;T	0.50001	3.24;3.23;0.76	5.8	5.8	0.92144	.	0.060966	0.64402	D	0.000004	T	0.39462	0.1079	M	0.62723	1.935	0.80722	D	1	D	0.53462	0.96	B	0.43082	0.407	T	0.49194	-0.8965	10	0.72032	D	0.01	-29.8017	16.1606	0.81704	1.0:0.0:0.0:0.0	.	78	O75626	PRDM1_HUMAN	L	42;78;42;42	ENSP00000358087:Q42L;ENSP00000358092:Q78L;ENSP00000395566:Q42L	ENSP00000358087:Q42L	Q	+	2	0	PRDM1	106642959	1.000000	0.71417	0.997000	0.53966	0.584000	0.36387	6.919000	0.75793	2.227000	0.72691	0.460000	0.39030	CAG	.	.		0.493	PRDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041661.3			T	106536266	A	T	106536266	3	4	324	1	0	0	0	0	1	0	0	0	12462	188	7	4	239	4	PRDM1	6	106536266	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	59854010	106536266	64578801	68	45676										
RADIL	55698	hgsc.bcm.edu	37	chr7	4854972	4854972	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	caggagagcttctggaagaaGtgctctccagccgccccgaa	12	13	2	2			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr7:4854972G>C	ENST00000399583.3	-	9	2263	c.2076C>G	c.(2074-2076)caC>caG	p.H692Q	RADIL_ENST00000536091.1_3'UTR|RADIL_ENST00000538469.1_Missense_Mutation_p.H452Q	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	692	Dilute. {ECO:0000255|PROSITE- ProRule:PRU00503}.				multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		TCTGGAAGAAGTGCTCTCCAG	0.687																																					p.H692Q		Atlas-SNP	.											.	RADIL	110	.	0			c.C2076G						.						7	9	9					7																	4854972		1850	4031	5881	SO:0001583	missense	55698	exon9			GAAGAAGTGCTCT	AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.2076C>G	chr7.hg19:g.4854972G>C	ENSP00000382492:p.His692Gln	42.0	0.0		46.0	17.0	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	hg19	CCDS43544.1	.	.	.	.	.	.	.	.	.	.	G	6.428	0.447035	0.12223	.	.	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000544486;ENST00000538469	T;T	0.05855	3.46;3.38	5.74	1.74	0.24563	Dilute (1);Dil domain (1);	0.727630	0.13634	N	0.373482	T	0.02083	0.0065	N	0.01482	-0.84	0.80722	D	1	B	0.10296	0.003	B	0.10450	0.005	T	0.45469	-0.9259	10	0.13470	T	0.59	-12.5832	7.1312	0.25502	0.0:0.3576:0.3083:0.3341	.	692	Q96JH8	RADIL_HUMAN	Q	692;663;426;452	ENSP00000382492:H692Q;ENSP00000442966:H452Q	ENSP00000320946:H663Q	H	-	3	2	RADIL	4821498	0.226000	0.23696	0.938000	0.37757	0.484000	0.33280	0.289000	0.18957	0.734000	0.32515	0.655000	0.94253	CAC	.	.		0.687	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059		C	4854972	G	C	4854972	3	2	324	1	0	0	0	0	1	0	0	0	13012	1020	36	4	1179	4	RADIL	7	4854972	Missense_Mutation	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10		4854972	154283691	69	45677										
AHR	196	hgsc.bcm.edu	37	chr7	17379497	17379497	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	agacttacatgggatcagtcAagagttcccctacaaatctg	8	10	3	2			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr7:17379497A>G	ENST00000242057.4	+	10	2691	c.2048A>G	c.(2047-2049)cAa>cGa	p.Q683R		NM_001621.4	NP_001612.1	P35869	AHR_HUMAN	aryl hydrocarbon receptor	683					apoptotic process (GO:0006915)|blood vessel development (GO:0001568)|cell cycle (GO:0007049)|circadian regulation of gene expression (GO:0032922)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|regulation of B cell proliferation (GO:0030888)|regulation of gene expression (GO:0010468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to toxic substance (GO:0009636)|response to xenobiotic stimulus (GO:0009410)|transcription from RNA polymerase II promoter (GO:0006366)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosolic aryl hydrocarbon receptor complex (GO:0034752)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|Hsp90 protein binding (GO:0051879)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(11)|ovary(1)|pancreas(1)|urinary_tract(3)	33	Lung NSC(10;0.0392)|all_lung(11;0.0754)				Atorvastatin(DB01076)|Flutamide(DB00499)|Ginseng(DB01404)|Leflunomide(DB01097)|Mexiletine(DB00379)|Nimodipine(DB00393)	GGGATCAGTCAAGAGTTCCCC	0.373																																					p.Q683R		Atlas-SNP	.											.	AHR	89	.	0			c.A2048G						.						117	113	114					7																	17379497		2203	4300	6503	SO:0001583	missense	196	exon10			TCAGTCAAGAGTT	L19872	CCDS5366.1	7p15	2013-05-21			ENSG00000106546	ENSG00000106546		"Basic helix-loop-helix proteins"	348	protein-coding gene	gene with protein product		600253				8125016	Standard	NM_001621		Approved	bHLHe76	uc011jxz.1	P35869	OTTHUMG00000149967	ENST00000242057.4:c.2048A>G	chr7.hg19:g.17379497A>G	ENSP00000242057:p.Gln683Arg	71.0	0.0		52.0	19.0	NM_001621	A4D130|Q13728|Q13803|Q13804	Missense_Mutation	SNP	ENST00000242057.4	hg19	CCDS5366.1	.	.	.	.	.	.	.	.	.	.	A	7.358	0.624283	0.14193	.	.	ENSG00000106546	ENST00000242057	T	0.49432	0.78	5.9	3.33	0.38152	.	0.644386	0.15487	N	0.259768	T	0.46737	0.1408	M	0.70275	2.135	0.09310	N	1	B	0.33413	0.411	B	0.27608	0.081	T	0.40079	-0.9582	10	0.46703	T	0.11	.	14.7511	0.69528	0.718:0.282:0.0:0.0	.	683	P35869	AHR_HUMAN	R	683	ENSP00000242057:Q683R	ENSP00000242057:Q683R	Q	+	2	0	AHR	17346022	0.005000	0.15991	0.342000	0.25602	0.230000	0.25150	2.026000	0.41069	1.021000	0.39600	0.528000	0.53228	CAA	.	.		0.373	AHR-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314620.2	NM_001621		G	17379497	A	G	17379497	3	3	324	1	0	0	0	0	1	0	0	0	416	130	5	2	2086	2	AHR	7	17379497	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	12524525	17379497	141759166	70	45678										
STK31	56164	hgsc.bcm.edu	37	chr7	23825118	23825118	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	actctggtggtctccttacaAtgagcttggaacgagatctt	10	9	3	2			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr7:23825118A>G	ENST00000355870.3	+	18	2289	c.2170A>G	c.(2170-2172)Atg>Gtg	p.M724V	STK31_ENST00000405627.3_3'UTR|STK31_ENST00000428484.1_Missense_Mutation_p.M701V|STK31_ENST00000433467.2_Missense_Mutation_p.M724V|STK31_ENST00000354639.3_Missense_Mutation_p.M701V	NM_031414.4	NP_113602.2	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31	724	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					acrosomal vesicle (GO:0001669)	ATP binding (GO:0005524)|hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(31)|ovary(2)|prostate(1)|skin(7)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						TCTCCTTACAATGAGCTTGGA	0.403																																					p.M724V		Atlas-SNP	.											.	STK31	175	.	0			c.A2170G						.						193	184	187					7																	23825118		2203	4300	6503	SO:0001583	missense	56164	exon18			CTTACAATGAGCT	AF285599	CCDS5386.1, CCDS43556.1, CCDS59049.1	7p15.3	2014-04-23			ENSG00000196335	ENSG00000196335		"Tudor domain containing"	11407	protein-coding gene	gene with protein product		605790				11279525	Standard	NM_031414		Approved	TDRD8, SgK396	uc003sws.5	Q9BXU1	OTTHUMG00000023053	ENST00000355870.3:c.2170A>G	chr7.hg19:g.23825118A>G	ENSP00000348132:p.Met724Val	100.0	0.0		90.0	21.0	NM_031414	B4DZ06|B7WPP5|C9J4F9|Q6PCD3|Q9BXH8	Missense_Mutation	SNP	ENST00000355870.3	hg19	CCDS5386.1	.	.	.	.	.	.	.	.	.	.	A	0.890	-0.725800	0.03158	.	.	ENSG00000196335	ENST00000355870;ENST00000433467;ENST00000354639;ENST00000428484	T;T;T;T	0.68331	-0.32;1.41;-0.32;-0.32	5.24	-0.0559	0.13807	Protein kinase, catalytic domain (1);	0.596299	0.18382	N	0.142927	T	0.39572	0.1083	L	0.31294	0.92	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.19418	-1.0306	10	0.02654	T	1	-4.5115	1.7963	0.03062	0.2572:0.3743:0.2397:0.1288	.	724;724	B4DZ06;Q9BXU1	.;STK31_HUMAN	V	724;724;701;701	ENSP00000348132:M724V;ENSP00000411852:M724V;ENSP00000346660:M701V;ENSP00000406146:M701V	ENSP00000346660:M701V	M	+	1	0	STK31	23791643	0.052000	0.20516	0.995000	0.50966	0.982000	0.71751	0.116000	0.15561	0.371000	0.24564	0.528000	0.53228	ATG	.	.		0.403	STK31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214036.2	NM_031414		G	23825118	A	G	23825118	3	3	324	1	0	0	0	0	1	0	0	0	15311	101	4	2	2240	2	STK31	7	23825118	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	6445621	23825118	135313545	71	45679										
MAGI2	9863	hgsc.bcm.edu	37	chr7	79082460	79082460	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	agcagctcctccgacaccaaTttgctgccgctctcataggc	8	16	1	0	rs373785355		TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr7:79082460T>G	ENST00000354212.4	-	1	430	c.177A>C	c.(175-177)aaA>aaC	p.K59N	MAGI2-AS3_ENST00000451809.1_RNA|MAGI2_ENST00000419488.1_Missense_Mutation_p.K59N|MAGI2-AS3_ENST00000414797.1_RNA|MAGI2-AS3_ENST00000429408.1_RNA|MAGI2-AS3_ENST00000448195.1_RNA|MAGI2-AS3_ENST00000424477.1_RNA|MAGI2-AS3_ENST00000446159.1_RNA|MAGI2-AS3_ENST00000422093.1_RNA|MAGI2_ENST00000522391.1_Missense_Mutation_p.K59N|MAGI2-AS3_ENST00000426835.1_RNA	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	59	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|glomerular visceral epithelial cell development (GO:0072015)|mitotic cell cycle arrest (GO:0071850)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase B signaling (GO:0051898)|nerve growth factor signaling pathway (GO:0038180)|planar cell polarity pathway involved in axis elongation (GO:0003402)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of receptor internalization (GO:0002092)|protein heterooligomerization (GO:0051291)|receptor clustering (GO:0043113)|SMAD protein signal transduction (GO:0060395)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|late endosome (GO:0005770)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)|synapse (GO:0045202)|tight junction (GO:0005923)	beta-1 adrenergic receptor binding (GO:0031697)|phosphatase binding (GO:0019902)|receptor signaling complex scaffold activity (GO:0030159)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|type II activin receptor binding (GO:0070699)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(37)|ovary(5)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(3)	84		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				CCGACACCAATTTGCTGCCGC	0.642																																					p.K59N		Atlas-SNP	.											.	MAGI2	246	.	0			c.A177C						.						57	62	60					7																	79082460		2203	4300	6503	SO:0001583	missense	9863	exon1			CACCAATTTGCTG	AB014605	CCDS5594.1, CCDS75623.1	7q21	2005-08-09			ENSG00000187391	ENSG00000187391			18957	protein-coding gene	gene with protein product		606382				10681527, 9734811	Standard	XM_005250725		Approved	AIP1, ARIP1, KIAA0705, ACVRIP1, MAGI-2	uc003ugx.3	Q86UL8	OTTHUMG00000130697	ENST00000354212.4:c.177A>C	chr7.hg19:g.79082460T>G	ENSP00000346151:p.Lys59Asn	72.0	0.0		79.0	22.0	NM_012301	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Missense_Mutation	SNP	ENST00000354212.4	hg19	CCDS5594.1	.	.	.	.	.	.	.	.	.	.	C	18.39	3.613838	0.66672	.	.	ENSG00000187391	ENST00000419488;ENST00000354212;ENST00000536298;ENST00000522391	T;T;T	0.11712	2.86;2.86;2.75	5.39	5.39	0.77823	PDZ/DHR/GLGF (4);	.	.	.	.	T	0.26919	0.0659	L	0.58101	1.795	0.80722	D	1	D;P	0.67145	0.996;0.896	D;P	0.65010	0.931;0.673	T	0.00643	-1.1630	9	0.46703	T	0.11	.	13.4339	0.61073	0.0:0.9241:0.0:0.0759	.	59;59	Q86UL8-2;Q86UL8	.;MAGI2_HUMAN	N	59	ENSP00000405766:K59N;ENSP00000346151:K59N;ENSP00000428389:K59N	ENSP00000346151:K59N	K	-	3	2	MAGI2	78920396	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.976000	0.40579	1.279000	0.44446	-0.320000	0.08662	AAA	.	.		0.642	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301		G	79082460	T	G	79082460	3	3	324	1	0	0	0	0	1	0	0	0	9200	1490	52	5	4278	5	MAGI2	7	79082460	Missense_Mutation	SNP	T	TCGA-MI-A75I-01A-11D-A32G-10	55257342	79082460	80056203	72	45680										
AKAP9	10142	hgsc.bcm.edu	37	chr7	91669986	91669986	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ttttttttttttactattaaAgattcatgatgagatttcag	5	3	2	3			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr7:91669986A>C	ENST00000359028.2	+	19	4953		c.e19-1		AKAP9_ENST00000358100.2_Splice_Site|AKAP9_ENST00000356239.3_Splice_Site			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9						G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TTACTATTAAAGATTCATGAT	0.294			T	BRAF	papillary thyroid																																.		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.4693-2A>C						.						29	29	29					7																	91669986		2202	4300	6502	SO:0001630	splice_region_variant	10142	exon18			TATTAAAGATTCA	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	379	protein-coding gene	gene with protein product	"A-kinase anchoring protein 450", "AKAP9-BRAF fusion protein", "AKAP120-like protein", "centrosome- and golgi-localized protein kinase N-associated protein", "protein kinase A anchoring protein 9", "A-kinase anchor protein, 350kDa", "protein phosphatase 1, regulatory subunit 45", "yotiao"	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.4729-1A>C	chr7.hg19:g.91669986A>C		91.0	0.0		86.0	34.0	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Splice_Site	SNP	ENST00000359028.2	hg19		.	.	.	.	.	.	.	.	.	.	A	9.334	1.061236	0.19987	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394565	.	.	.	4.23	4.23	0.50019	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.8334	0.29355	0.9014:0.0:0.0986:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	AKAP9	91507922	1.000000	0.71417	0.224000	0.23877	0.075000	0.17131	5.412000	0.66392	1.895000	0.54865	0.477000	0.44152	.	.	.		0.294	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	Intron	C	91669986	A	C	91669986	5	2	324	1	0	0	0	0	0	0	1	0	459	86	3	5	4761	5	AKAP9	7	91669986	Splice_Site	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	12587526	91669986	67468677	73	45681										
MUC17	140453	hgsc.bcm.edu	37	chr7	100683826	100683826	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ccaatctcaactcctagtgaAggaagtactccattaacaag	6	11	1	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr7:100683826A>T	ENST00000306151.4	+	3	9193	c.9129A>T	c.(9127-9129)gaA>gaT	p.E3043D		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	3043	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					CTCCTAGTGAAGGAAGTACTC	0.512																																					p.E3043D		Atlas-SNP	.											.	MUC17	804	.	0			c.A9129T						.						268	280	276					7																	100683826		2203	4300	6503	SO:0001583	missense	140453	exon3			TAGTGAAGGAAGT	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.9129A>T	chr7.hg19:g.100683826A>T	ENSP00000302716:p.Glu3043Asp	50.0	0.0		46.0	21.0	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	a	7.902	0.734560	0.15574	.	.	ENSG00000169876	ENST00000306151	T	0.01821	4.62	0.664	-0.833	0.10782	.	.	.	.	.	T	0.01730	0.0055	N	0.19112	0.55	0.09310	N	1	P	0.46578	0.88	P	0.50270	0.636	T	0.44452	-0.9327	9	0.13108	T	0.6	.	4.2429	0.10658	0.7458:0.0:0.2542:0.0	.	3043	Q685J3	MUC17_HUMAN	D	3043	ENSP00000302716:E3043D	ENSP00000302716:E3043D	E	+	3	2	MUC17	100470546	0.000000	0.05858	0.001000	0.08648	0.020000	0.10135	-2.974000	0.00666	-0.294000	0.08973	0.102000	0.15555	GAA	.	.		0.512	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		T	100683826	A	T	100683826	3	4	324	1	0	0	0	0	1	0	0	0	9983	69	3	4	9139	4	MUC17	7	100683826	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	9013840	100683826	58454837	74	45682										
DENND2A	27147	hgsc.bcm.edu	37	chr7	140221816	140221816	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	cacgctcgcccgacgtcaggAacaaagagtagtgtcccaca	10	14	1	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr7:140221816A>G	ENST00000275884.6	-	17	3167	c.2750T>C	c.(2749-2751)tTc>tCc	p.F917S	DENND2A_ENST00000537639.1_Missense_Mutation_p.F917S|DENND2A_ENST00000496613.1_Missense_Mutation_p.F917S			Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	917	dDENN. {ECO:0000255|PROSITE- ProRule:PRU00306}.				positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(22)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49	Melanoma(164;0.00956)					CGACGTCAGGAACAAAGAGTA	0.587																																					p.F917S		Atlas-SNP	.											.	DENND2A	132	.	0			c.T2750C						.						60	64	63					7																	140221816		2036	4189	6225	SO:0001583	missense	27147	exon16			GTCAGGAACAAAG	AB033103	CCDS43659.1	7q34	2012-10-03	2005-08-17	2005-08-17	ENSG00000146966	ENSG00000146966		"DENN/MADD domain containing"	22212	protein-coding gene	gene with protein product			"KIAA1277"	KIAA1277			Standard	NM_015689		Approved	FAM31D	uc010lnj.3	Q9ULE3	OTTHUMG00000157411	ENST00000275884.6:c.2750T>C	chr7.hg19:g.140221816A>G	ENSP00000275884:p.Phe917Ser	66.0	0.0		77.0	29.0	NM_015689	C9JUI3|Q1RMD5|Q86XY0	Missense_Mutation	SNP	ENST00000275884.6	hg19	CCDS43659.1	.	.	.	.	.	.	.	.	.	.	A	14.85	2.659085	0.47467	.	.	ENSG00000146966	ENST00000275884;ENST00000537639;ENST00000496613	T;T;T	0.54279	0.58;0.58;0.58	5.26	5.26	0.73747	dDENN (3);	0.000000	0.64402	D	0.000012	T	0.55752	0.1940	M	0.67953	2.075	0.50632	D	0.999885	B	0.19935	0.04	B	0.30716	0.119	T	0.54649	-0.8262	10	0.40728	T	0.16	-18.5382	15.2034	0.73159	1.0:0.0:0.0:0.0	.	917	Q9ULE3	DEN2A_HUMAN	S	917	ENSP00000275884:F917S;ENSP00000442245:F917S;ENSP00000419654:F917S	ENSP00000275884:F917S	F	-	2	0	DENND2A	139868285	1.000000	0.71417	1.000000	0.80357	0.855000	0.48748	6.980000	0.76160	1.989000	0.58080	0.455000	0.32223	TTC	.	.		0.587	DENND2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348742.1	NM_015689		G	140221816	A	G	140221816	3	3	324	1	0	0	0	0	1	0	0	0	4431	246	9	2	291	2	DENND2A	7	140221816	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	39537990	140221816	18916847	75	45683										
ZNF398	57541	hgsc.bcm.edu	37	chr7	148876417	148876417	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	cacaagagcgccctttctccTgccctcagtgtggcattgac	9	15	2	2			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr7:148876417T>C	ENST00000475153.1	+	6	1720	c.1453T>C	c.(1453-1455)Tgc>Cgc	p.C485R	ZNF398_ENST00000491174.1_Missense_Mutation_p.C314R|ZNF398_ENST00000335901.4_Missense_Mutation_p.C314R|ZNF398_ENST00000426851.2_Missense_Mutation_p.C314R|ZNF398_ENST00000540950.1_Missense_Mutation_p.C490R|ZNF398_ENST00000483892.1_Missense_Mutation_p.C314R|ZNF398_ENST00000420008.2_Missense_Mutation_p.C314R			Q8TD17	ZN398_HUMAN	zinc finger protein 398	485					positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(14)|ovary(1)	25	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00143)			CCCTTTCTCCTGCCCTCAGTG	0.607																																					p.C485R		Atlas-SNP	.											.	ZNF398	54	.	0			c.T1453C						.						59	52	54					7																	148876417		2203	4300	6503	SO:0001583	missense	57541	exon6			TTCTCCTGCCCTC	AB037760	CCDS5894.1, CCDS47739.1	7q35	2013-01-08			ENSG00000197024	ENSG00000197024		"Zinc fingers, C2H2-type", "-"	18373	protein-coding gene	gene with protein product						11779858	Standard	NM_170686		Approved	ZER6, KIAA1339, P51, P71	uc003wfl.3	Q8TD17	OTTHUMG00000158970	ENST00000475153.1:c.1453T>C	chr7.hg19:g.148876417T>C	ENSP00000420418:p.Cys485Arg	41.0	0.0		39.0	12.0	NM_170686	A8K384|B4E377|Q8TD18|Q9P2K7|Q9UDV8	Missense_Mutation	SNP	ENST00000475153.1	hg19	CCDS5894.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.094345	0.76870	.	.	ENSG00000197024	ENST00000426851;ENST00000420008;ENST00000475153;ENST00000483892;ENST00000491174;ENST00000540950;ENST00000335901	T;T;T;T;T;T;T	0.40225	1.04;1.04;1.04;1.04;1.04;1.04;1.04	5.18	5.18	0.71444	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.56097	D	0.000033	T	0.74366	0.3707	H	0.96398	3.815	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.82760	-0.0298	10	0.87932	D	0	-22.0993	12.9978	0.58657	0.0:0.0:0.0:1.0	.	490;485	B4DXA9;Q8TD17	.;ZN398_HUMAN	R	314;314;485;314;314;490;314	ENSP00000389972:C314R;ENSP00000416751:C314R;ENSP00000420418:C485R;ENSP00000418564:C314R;ENSP00000419391:C314R;ENSP00000439340:C490R;ENSP00000338984:C314R	ENSP00000338984:C314R	C	+	1	0	ZNF398	148507350	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.823000	0.86660	1.958000	0.56883	0.528000	0.53228	TGC	.	.		0.607	ZNF398-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352722.2			C	148876417	T	C	148876417	3	2	324	1	0	0	0	0	1	0	0	0	17900	1580	55	2	1475	2	ZNF398	7	148876417	Missense_Mutation	SNP	T	TCGA-MI-A75I-01A-11D-A32G-10	8654601	148876417	10262246	76	45684										
AGAP3	116988	hgsc.bcm.edu	37	chr7	150817090	150817090	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ttaggccacgaatggcggcgGcagcgccttcagcgactact	13	13	1	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr7:150817090G>T	ENST00000463381.1	+	8	798	c.302G>T	c.(301-303)gGc>gTc	p.G101V	AGAP3_ENST00000397238.2_Missense_Mutation_p.G329V|AGAP3_ENST00000335367.3_Missense_Mutation_p.G509V|AGAP3_ENST00000473312.1_Missense_Mutation_p.G329V|AGAP3_ENST00000479901.1_Intron	NM_001281300.1	NP_001268229.1	Q96P47	AGAP3_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 3	293	Small GTPase-like.				cellular response to reactive oxygen species (GO:0034614)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein import into nucleus, translocation (GO:0000060)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|liver(2)|lung(9)|ovary(2)|prostate(3)|urinary_tract(1)	28						AATGGCGGCGGCAGCGCCTTC	0.682																																					p.G329V		Atlas-SNP	.											.	AGAP3	121	.	0			c.G986T						.						25	34	31					7																	150817090		2098	4222	6320	SO:0001583	missense	116988	exon8			GCGGCGGCAGCGC	AF413079	CCDS43681.1, CCDS55185.1, CCDS64802.1	7q36.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000133612	ENSG00000133612		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16923	protein-coding gene	gene with protein product			"centaurin, gamma 3"	CENTG3			Standard	NM_001042535		Approved		uc003wjg.1	Q96P47	OTTHUMG00000158724	ENST00000463381.1:c.302G>T	chr7.hg19:g.150817090G>T	ENSP00000418016:p.Gly101Val	49.0	0.0		38.0	16.0	NM_001042535	B3KNZ8|E9PAL8|Q59EN0|Q96RK3	Missense_Mutation	SNP	ENST00000463381.1	hg19		.	.	.	.	.	.	.	.	.	.	g	20.7	4.027970	0.75390	.	.	ENSG00000133612	ENST00000463381;ENST00000473312;ENST00000397238;ENST00000335355;ENST00000335367;ENST00000468796	T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54	3.61	3.61	0.41365	.	0.621363	0.14897	U	0.292007	T	0.32912	0.0845	M	0.68593	2.085	0.80722	D	1	B;B;B;B	0.33940	0.029;0.433;0.047;0.226	B;B;B;B	0.36845	0.017;0.234;0.022;0.093	T	0.07712	-1.0758	10	0.16420	T	0.52	.	12.8158	0.57665	0.0:0.0:1.0:0.0	.	509;329;329;101	E7ESL9;Q96P47-4;E9PAL8;B3KNZ8	.;.;.;.	V	101;329;329;293;509;94	ENSP00000418016:G101V;ENSP00000418921:G329V;ENSP00000380413:G329V;ENSP00000335589:G509V;ENSP00000418159:G94V	ENSP00000334157:G293V	G	+	2	0	AGAP3	150448023	1.000000	0.71417	0.995000	0.50966	0.939000	0.58152	3.550000	0.53691	1.853000	0.53794	0.306000	0.20318	GGC	.	.		0.682	AGAP3-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000351909.2	NM_031946		T	150817090	G	T	150817090	3	4	324	1	0	0	0	0	1	0	0	0	369	1203	42	3	1016	3	AGAP3	7	150817090	Missense_Mutation	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10	1940673	150817090	8321573	77	45685										
RP1	6101	hgsc.bcm.edu	37	chr8	55534100	55534100	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	agcacctgacagaggtcatgCagcgccctgtggtcaagctg	13	12	2	2			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr8:55534100C>A	ENST00000220676.1	+	2	722	c.574C>A	c.(574-576)Cag>Aag	p.Q192K		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	192	Doublecortin 2. {ECO:0000255|PROSITE- ProRule:PRU00072}.				axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			AGAGGTCATGCAGCGCCCTGT	0.582																																					p.Q192K	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.C574A						.						121	124	123					8																	55534100		2203	4300	6503	SO:0001583	missense	6101	exon2			GTCATGCAGCGCC	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.574C>A	chr8.hg19:g.55534100C>A	ENSP00000220676:p.Gln192Lys	61.0	0.0		92.0	44.0	NM_006269		Missense_Mutation	SNP	ENST00000220676.1	hg19	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.071221	0.76301	.	.	ENSG00000104237	ENST00000427058;ENST00000220676	D	0.91351	-2.83	5.14	4.25	0.50352	Doublecortin domain (5);	0.606668	0.14844	N	0.295121	D	0.91523	0.7323	M	0.76002	2.32	0.47659	D	0.999482	B;P	0.37061	0.006;0.58	B;B	0.41723	0.013;0.365	D	0.90186	0.4246	10	0.51188	T	0.08	2.4733	14.9386	0.70975	0.1441:0.8559:0.0:0.0	.	2;192	E7EVW9;P56715	.;RP1_HUMAN	K	2;192	ENSP00000220676:Q192K	ENSP00000220676:Q192K	Q	+	1	0	RP1	55696653	1.000000	0.71417	0.735000	0.30896	0.563000	0.35712	3.944000	0.56629	1.145000	0.42336	0.650000	0.86243	CAG	.	.		0.582	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		A	55534100	C	A	55534100	3	1	324	1	0	0	0	0	1	0	0	0	13547	711	25	3	576	3	RP1	8	55534100	Missense_Mutation	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10		55534100	90829922	78	45686										
LRRCC1	85444	hgsc.bcm.edu	37	chr8	86048194	86048194	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	tggggacatgagctggcacaAcaaggtaaaattctcagatt	11	7	1	2			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr8:86048194A>G	ENST00000360375.3	+	14	2474	c.2325A>G	c.(2323-2325)caA>caG	p.Q775Q	LRRCC1_ENST00000414626.2_Silent_p.Q755Q	NM_033402.4	NP_208325.3	Q9C099	LRCC1_HUMAN	leucine rich repeat and coiled-coil centrosomal protein 1	775					mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(4)|kidney(9)|large_intestine(7)|lung(16)|skin(1)|upper_aerodigestive_tract(2)	43						AGCTGGCACAACAAGGTAAAA	0.373																																					p.Q775Q		Atlas-SNP	.											.	LRRCC1	212	.	0			c.A2325G						.						83	82	82					8																	86048194		1832	4091	5923	SO:0001819	synonymous_variant	85444	exon14			GGCACAACAAGGT	BC030701	CCDS43750.1	8q21.2	2012-04-10	2012-04-10		ENSG00000133739	ENSG00000133739			29373	protein-coding gene	gene with protein product	"centrosomal leucine-rich repeat and coiled-coil containing protein", "variable number of flagella 1 homolog (Chlamydomonas)"		"leucine rich repeat and coiled-coil domain containing 1"			11214970, 18728398	Standard	NM_033402		Approved	KIAA1764, CLERC, VFL1	uc003ycw.3	Q9C099	OTTHUMG00000164784	ENST00000360375.3:c.2325A>G	chr8.hg19:g.86048194A>G		133.0	0.0		235.0	39.0	NM_033402	B4DYX6|B5RI11|Q8N768|Q96DK7|Q96N01	Silent	SNP	ENST00000360375.3	hg19	CCDS43750.1																																																																																			.	.		0.373	LRRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380267.1	NM_033402		G	86048194	A	G	86048194	2	3	324	1	0	0	0	0	0	0	0	1	9035	40	2	2		2	LRRCC1	8	86048194	Silent	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	30514094	86048194	60315828	79	45687										
MMP16	4325	hgsc.bcm.edu	37	chr8	89053953	89053953	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ttgaggatggatcttggataTccaggttctaccttgagtat	11	6	2	2			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr8:89053953T>A	ENST00000286614.6	-	10	1841	c.1560A>T	c.(1558-1560)ggA>ggT	p.G520G		NM_005941.4	NP_005932.2	P51512	MMP16_HUMAN	matrix metallopeptidase 16 (membrane-inserted)	520					chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)	Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(51)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	81					Marimastat(DB00786)	ATCTTGGATATCCAGGTTCTA	0.423																																					p.G520G		Atlas-SNP	.											.	MMP16	176	.	0			c.A1560T						.						233	196	209					8																	89053953		2203	4300	6503	SO:0001819	synonymous_variant	4325	exon10			TGGATATCCAGGT	D85511	CCDS6246.1	8q21	2009-01-09	2005-08-08		ENSG00000156103	ENSG00000156103			7162	protein-coding gene	gene with protein product		602262	"matrix metalloproteinase 16 (membrane-inserted)", "chromosome 8 open reading frame 57"	C8orf57		7559440	Standard	NM_005941		Approved	MT3-MMP, DKFZp761D112	uc003yeb.4	P51512	OTTHUMG00000163769	ENST00000286614.6:c.1560A>T	chr8.hg19:g.89053953T>A		106.0	0.0		152.0	65.0	NM_005941	B2RAN7|Q14824|Q52H48	Silent	SNP	ENST00000286614.6	hg19	CCDS6246.1																																																																																			.	.		0.423	MMP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375304.2	NM_005941		A	89053953	T	A	89053953	2	1	324	1	0	0	0	0	0	0	0	1	9664	1422	50	4		4	MMP16	8	89053953	Silent	SNP	T	TCGA-MI-A75I-01A-11D-A32G-10	3005759	89053953	57310069	80	45688										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113314168	113314168	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	caatcttatttccatttggaGgtgtaggtagttctccacag	9	8	2	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr8:113314168G>T	ENST00000297405.5	-	53	8538	c.8294C>A	c.(8293-8295)cCt>cAt	p.P2765H	CSMD3_ENST00000352409.3_Missense_Mutation_p.P2695H|CSMD3_ENST00000455883.2_Missense_Mutation_p.P2596H|CSMD3_ENST00000343508.3_Missense_Mutation_p.P2725H	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2765	Sushi 17. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TCCATTTGGAGGTGTAGGTAG	0.368										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.P2765H		Atlas-SNP	.											.	CSMD3	2325	.	0			c.C8294A						.						97	98	98					8																	113314168		2203	4300	6503	SO:0001583	missense	114788	exon53			TTTGGAGGTGTAG	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.8294C>A	chr8.hg19:g.113314168G>T	ENSP00000297405:p.Pro2765His	41.0	0.0		104.0	17.0	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.310624	0.81358	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17;-0.17	5.59	5.59	0.84812	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.64402	D	0.000001	D	0.87022	0.6074	H	0.97940	4.11	0.58432	D	0.999994	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.991;0.995;0.996	D	0.87451	0.2401	10	0.23302	T	0.38	.	19.9636	0.97259	0.0:0.0:1.0:0.0	.	2596;2765;2725	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	H	2725;2765;2035;2596;2695	ENSP00000345799:P2725H;ENSP00000297405:P2765H;ENSP00000341558:P2035H;ENSP00000412263:P2596H;ENSP00000343124:P2695H	ENSP00000297405:P2765H	P	-	2	0	CSMD3	113383344	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.811000	0.86092	2.795000	0.96236	0.637000	0.83480	CCT	.	.		0.368	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	113314168	G	T	113314168	3	4	324	1	0	0	0	0	1	0	0	0	3948	1000	35	3	2905	3	CSMD3	8	113314168	Missense_Mutation	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10	24260215	113314168	33049854	81	45689										
ARC	23237	hgsc.bcm.edu	37	chr8	143695326	143695326	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	gacccagcgctccaggttggCgatggtctcctggcagcggc	15	14	1	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr8:143695326C>G	ENST00000356613.2	-	1	1507	c.307G>C	c.(307-309)Gcc>Ccc	p.A103P	ARC_ENST00000581404.1_5'Flank	NM_015193.4	NP_056008.1	O60936	NOL3_HUMAN	activity-regulated cytoskeleton-associated protein	0					apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of gene expression (GO:0010468)|response to hypoxia (GO:0001666)|response to injury involved in regulation of muscle adaptation (GO:0014876)|RNA splicing (GO:0008380)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|sarcoplasm (GO:0016528)	identical protein binding (GO:0042802)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(3)|upper_aerodigestive_tract(1)	13	all_cancers(97;3.55e-12)|all_epithelial(106;1.03e-08)|Lung NSC(106;0.000353)|all_lung(105;0.00092)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;0.0279)				TCCAGGTTGGCGATGGTCTCC	0.672																																					p.A103P		Atlas-SNP	.											.	ARC	34	.	0			c.G307C						.						36	30	32					8																	143695326		2203	4299	6502	SO:0001583	missense	23237	exon1			GGTTGGCGATGGT	AF193421	CCDS34950.1	8q24.3	2008-08-01			ENSG00000198576	ENSG00000198576			648	protein-coding gene	gene with protein product		612461				10970730, 17466953	Standard	NM_015193		Approved	KIAA0278, Arg3.1	uc003ywn.2	Q7LC44	OTTHUMG00000134310	ENST00000356613.2:c.307G>C	chr8.hg19:g.143695326C>G	ENSP00000349022:p.Ala103Pro	20.0	0.0		38.0	6.0	NM_015193	B4DFL0|O60937	Missense_Mutation	SNP	ENST00000356613.2	hg19	CCDS34950.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.197187	0.79015	.	.	ENSG00000198576	ENST00000356613	T	0.31247	1.5	4.46	4.46	0.54185	.	0.108387	0.39083	U	0.001467	T	0.41003	0.1140	L	0.27053	0.805	0.37958	D	0.932866	D	0.76494	0.999	D	0.63703	0.917	T	0.50750	-0.8791	10	0.72032	D	0.01	.	16.0761	0.80969	0.0:1.0:0.0:0.0	.	103	Q7LC44	ARC_HUMAN	P	103	ENSP00000349022:A103P	ENSP00000349022:A103P	A	-	1	0	ARC	143692328	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.107000	0.50329	2.027000	0.59764	0.563000	0.77884	GCC	.	.		0.672	ARC-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259274.2			G	143695326	C	G	143695326	3	3	324	1	0	0	0	0	1	0	0	0	841	768	27	4	887	4	ARC	8	143695326	Missense_Mutation	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	30381158	143695326	2668696	82	45690										
RECK	8434	hgsc.bcm.edu	37	chr9	36122844	36122844	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	gaagcctgcaataaagaagcAgagaagattgagtcccttat	10	7	0	4			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr9:36122844A>G	ENST00000377966.3	+	21	3284	c.2718A>G	c.(2716-2718)gcA>gcG	p.A906A		NM_021111.2	NP_066934.1	O95980	RECK_HUMAN	reversion-inducing-cysteine-rich protein with kazal motifs	906					blood vessel maturation (GO:0001955)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)	anchored component of membrane (GO:0031225)|membrane (GO:0016020)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(7)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|pancreas(1)|skin(2)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(32;0.112)|STAD - Stomach adenocarcinoma(86;0.228)			ATAAAGAAGCAGAGAAGATTG	0.463																																					p.A906A		Atlas-SNP	.											.	RECK	73	.	0			c.A2718G						.						125	124	124					9																	36122844		2203	4300	6503	SO:0001819	synonymous_variant	8434	exon21			AGAAGCAGAGAAG	E13833	CCDS6597.1	9p13.3	2008-05-15			ENSG00000122707	ENSG00000122707			11345	protein-coding gene	gene with protein product		605227		ST15		9789069	Standard	NM_021111		Approved	hRECK	uc003zyv.3	O95980	OTTHUMG00000019898	ENST00000377966.3:c.2718A>G	chr9.hg19:g.36122844A>G		65.0	0.0		46.0	23.0	NM_021111	B2RNS1|Q5W0K6|Q8WX37	Silent	SNP	ENST00000377966.3	hg19	CCDS6597.1																																																																																			.	.		0.463	RECK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052409.1			G	36122844	A	G	36122844	2	3	324	1	0	0	0	0	0	0	0	1	13215	175	7	2		2	RECK	9	36122844	Silent	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10		36122844	105090587	83	45691										
TRPM6	140803	hgsc.bcm.edu	37	chr9	77397736	77397736	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	aaagctcagcaggactatggCcatgatgatcacaatataga	9	8	2	3			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr9:77397736C>G	ENST00000360774.1	-	22	3190	c.2953G>C	c.(2953-2955)Gcc>Ccc	p.A985P	TRPM6_ENST00000449912.2_Missense_Mutation_p.A980P|TRPM6_ENST00000451710.3_Missense_Mutation_p.A985P|TRPM6_ENST00000376871.3_Intron|TRPM6_ENST00000376864.4_Missense_Mutation_p.A985P|TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000361255.3_Missense_Mutation_p.A980P	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	985					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						AGGACTATGGCCATGATGATC	0.428																																					p.A985P		Atlas-SNP	.											.	TRPM6	377	.	0			c.G2953C						.						110	96	101					9																	77397736		2203	4300	6503	SO:0001583	missense	140803	exon22			CTATGGCCATGAT	AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"Voltage-gated ion channels / Transient receptor potential cation channels"	17995	protein-coding gene	gene with protein product		607009	"hypomagnesemia, secondary hypocalcemia"	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.2953G>C	chr9.hg19:g.77397736C>G	ENSP00000354006:p.Ala985Pro	105.0	0.0		59.0	38.0	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	ENST00000360774.1	hg19	CCDS6647.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.844254	0.91197	.	.	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000449912;ENST00000361255;ENST00000376864;ENST00000312449;ENST00000448641	T;T;T;T;T	0.11063	2.81;2.81;2.81;2.81;2.81	5.71	5.71	0.89125	Ion transport (1);	0.000000	0.85682	D	0.000000	T	0.42268	0.1195	M	0.88377	2.95	0.80722	D	1	P;P;D	0.76494	0.648;0.91;0.999	P;P;D	0.75484	0.482;0.737;0.986	T	0.37126	-0.9719	10	0.46703	T	0.11	.	19.8632	0.96793	0.0:1.0:0.0:0.0	.	648;985;980	F5H7D1;Q9BX84;Q9BX84-3	.;TRPM6_HUMAN;.	P	985;985;980;980;985;648;648	ENSP00000354006:A985P;ENSP00000407341:A985P;ENSP00000396672:A980P;ENSP00000354962:A980P;ENSP00000366060:A985P	ENSP00000309693:A648P	A	-	1	0	TRPM6	76587556	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	3.867000	0.56047	2.704000	0.92352	0.561000	0.74099	GCC	.	.		0.428	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662		G	77397736	C	G	77397736	3	3	324	1	0	0	0	0	1	0	0	0	16605	739	26	4	3187	4	TRPM6	9	77397736	Missense_Mutation	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	41274892	77397736	63815695	84	45692										
TUBB8	347688	hgsc.bcm.edu	37	chr10	93331	93331	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	agtaactgctgttcttatctTgaatgttgaacatttgttca	7	6	3	2			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr10:93331T>C	ENST00000309812.4	-	4	1063	c.1001A>G	c.(1000-1002)cAa>cGa	p.Q334R	TUBB8_ENST00000447903.2_Missense_Mutation_p.Q262R|TUBB8_ENST00000413237.3_5'Flank	NM_177987.2	NP_817124.1	Q3ZCM7	TBB8_HUMAN	tubulin, beta 8 class VIII	334					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(12)|ovary(2)|prostate(3)|skin(3)|stomach(1)	32		all_cancers(4;0.00131)|all_lung(4;0.000777)|Lung NSC(4;0.0043)|all_epithelial(10;0.0154)|Colorectal(49;0.235)		Epithelial(11;0.00341)|all cancers(11;0.00922)|OV - Ovarian serous cystadenocarcinoma(14;0.0508)|Lung(33;0.132)		GTTCTTATCTTGAATGTTGAA	0.547																																					p.Q334R	Pancreas(192;2041 3010 9013 18103)	Atlas-SNP	.											.	TUBB8	62	.	0			c.A1001G						.						81	90	87					10																	93331		2203	4298	6501	SO:0001583	missense	347688	exon4			TTATCTTGAATGT	AF355127	CCDS7051.1	10p15.3	2014-05-06			ENSG00000173876			"Tubulins"	20773	protein-coding gene	gene with protein product	"class VIII beta-tubulin"						Standard	NM_177987		Approved	bA631M21.2	uc001ifi.2	Q3ZCM7	OTTHUMG00000174803	ENST00000309812.4:c.1001A>G	chr10.hg19:g.93331T>C	ENSP00000311042:p.Gln334Arg	100.0	0.0		95.0	7.0	NM_177987	Q5SQX9|Q8WZ78	Missense_Mutation	SNP	ENST00000309812.4	hg19	CCDS7051.1	.	.	.	.	.	.	.	.	.	.	T	6.433	0.448038	0.12223	.	.	ENSG00000173876	ENST00000447903;ENST00000272035;ENST00000440680;ENST00000328974	D	0.82619	-1.63	.	.	.	Tubulin/FtsZ, 2-layer sandwich domain (3);Tubulin/FtsZ, C-terminal (1);	0.000000	0.56097	U	0.000029	D	0.89259	0.6664	M	0.93197	3.39	0.31442	N	0.67189	B;B	0.23990	0.002;0.095	B;P	0.46237	0.003;0.508	D	0.86973	0.2099	9	0.87932	D	0	.	4.5487	0.12098	0.0:6.0E-4:0.0:0.9994	.	297;334	C9JAA5;Q3ZCM7	.;TBB8_HUMAN	R	262;300;297;334	ENSP00000403895:Q262R	ENSP00000272035:Q300R	Q	-	2	0	RP11-631M21.2	83331	1.000000	0.71417	0.144000	0.22314	0.145000	0.21501	5.418000	0.66429	0.103000	0.17682	0.102000	0.15555	CAA	.	.		0.547	TUBB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467795.1	NM_177987		C	93331	T	C	93331	3	2	324	1	0	0	0	0	1	0	0	0	16776	1812	63	2	337	2	TUBB8	10	93331	Missense_Mutation	SNP	T	TCGA-MI-A75I-01A-11D-A32G-10		93331	135441416	85	45693										
DIP2C	22982	hgsc.bcm.edu	37	chr10	329266	329266	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	gaaccccaagtagcctgtgcGtgcccagatggtctgggtgt	14	11	1	1	rs534481067		TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr10:329266G>T	ENST00000280886.6	-	35	4327	c.4240C>A	c.(4240-4242)Cgc>Agc	p.R1414S	RNA5SP298_ENST00000364991.1_RNA	NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	1414						nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(8)|endometrium(6)|kidney(10)|large_intestine(13)|lung(26)|ovary(3)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	81		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		TAGCCTGTGCGTGCCCAGATG	0.547																																					p.R1414S		Atlas-SNP	.											DIP2C,rectum,adenoma,0,1	DIP2C	195	.	0			c.C4240A						.						120	114	116					10																	329266		2203	4300	6503	SO:0001583	missense	22982	exon35			CTGTGCGTGCCCA	BC035216	CCDS7054.1	10p15.3	2006-01-13	2006-01-13	2006-01-13	ENSG00000151240	ENSG00000151240			29150	protein-coding gene	gene with protein product		611380	"KIAA0934"	KIAA0934			Standard	NM_014974		Approved		uc001ifp.3	Q9Y2E4	OTTHUMG00000017532	ENST00000280886.6:c.4240C>A	chr10.hg19:g.329266G>T	ENSP00000280886:p.Arg1414Ser	69.0	0.0		100.0	37.0	NM_014974	B4DPI5|Q5SS78	Missense_Mutation	SNP	ENST00000280886.6	hg19	CCDS7054.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.055110	0.75960	.	.	ENSG00000151240	ENST00000280886;ENST00000535541	T	0.50277	0.75	5.92	4.06	0.47325	AMP-dependent synthetase/ligase (1);	0.064948	0.64402	N	0.000005	T	0.65523	0.2699	M	0.76574	2.34	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	T	0.67146	-0.5744	10	0.87932	D	0	-14.0495	10.1202	0.42616	0.0643:0.0:0.6908:0.2449	.	1414	Q9Y2E4	DIP2C_HUMAN	S	1414;339	ENSP00000280886:R1414S	ENSP00000280886:R1414S	R	-	1	0	DIP2C	319266	1.000000	0.71417	0.337000	0.25536	0.981000	0.71138	3.432000	0.52824	0.828000	0.34709	0.549000	0.68633	CGC	.	.		0.547	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974		T	329266	G	T	329266	3	4	324	1	0	0	0	0	1	0	0	0	4531	1145	40	1	442	1	DIP2C	10	329266	Missense_Mutation	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10	235935	329266	135205481	86	45694										
SPAG6	9576	hgsc.bcm.edu	37	chr10	22678098	22678098	+	Frame_Shift_Del	DEL	C	C	-													0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ccatcgcttagctttcacagCtggtagttaacgcaggaggg							TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr10:22678098delC	ENST00000376624.3	+	7	1004	c.862delC	c.(862-864)ctgfs	p.L288fs	RP11-301N24.3_ENST00000422675.1_RNA|SPAG6_ENST00000538630.1_Frame_Shift_Del_p.L263fs|SPAG6_ENST00000376601.1_Intron|SPAG6_ENST00000376603.2_Frame_Shift_Del_p.L364fs|SPAG6_ENST00000313311.6_Frame_Shift_Del_p.L288fs	NM_001253855.1|NM_012443.3	NP_001240784.1|NP_036575.1	O75602	SPAG6_HUMAN	sperm associated antigen 6	288					cell projection organization (GO:0030030)|spermatid development (GO:0007286)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|motile cilium (GO:0031514)|nucleus (GO:0005634)				breast(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|prostate(1)|skin(2)	27						GCTTTCACAGCTGGTAGTTAA	0.463																																					p.Q287fs		Atlas-INDEL	.											.	SPAG6	90	.	0			c.861delG						.						148	126	133					10																	22678098		2203	4300	6503	SO:0001589	frameshift_variant	9576	exon7			.	AF079363	CCDS7139.1, CCDS7140.1, CCDS58071.1, CCDS73072.1	10p12.31	2014-01-21			ENSG00000077327	ENSG00000077327		"Armadillo repeat containing"	11215	protein-coding gene	gene with protein product	"axoneme central apparatus protein"	605730				10493827	Standard	NM_012443		Approved	Repro-SA-1, pf16, CT141	uc001iri.3	O75602	OTTHUMG00000017808	ENST00000376624.3:c.862delC	chr10.hg19:g.22678098delC	ENSP00000365811:p.Leu288fs	73.0	0.0		107.0	37.0	NM_172242	A8K1I8|B4DXZ4|Q5VUX5|Q5VUX6|Q5VUX7|Q6FI74|Q8NHQ6	Frame_Shift_Del	DEL	ENST00000376624.3	hg19	CCDS7139.1																																																																																			.	.		0.463	SPAG6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047187.1			-	22678098	C	-	22678098	7	5	324	1	0	1	0	1	0	0	0	0	14997	796	28	0	888	0	SPAG6	10	22678098	Frame_Shift_Del	DEL	C	TCGA-MI-A75I-01A-11D-A32G-10	22348832	22678098	112856649	87	45695										
ENTPD1	953	hgsc.bcm.edu	37	chr10	97602202	97602202	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	tgattccaaggtcccagcacCaagagacacccgtttacctg	8	14	0	2			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr10:97602202C>A	ENST00000371205.4	+	4	647	c.364C>A	c.(364-366)Caa>Aaa	p.Q122K	ENTPD1_ENST00000490659.1_3'UTR|ENTPD1_ENST00000371207.3_Missense_Mutation_p.Q134K|ENTPD1_ENST00000453258.2_Missense_Mutation_p.Q129K|RP11-429G19.3_ENST00000433113.1_RNA|ENTPD1_ENST00000371203.5_Intron|ENTPD1_ENST00000543964.1_Missense_Mutation_p.Q14K|ENTPD1_ENST00000539125.1_Intron|ENTPD1-AS1_ENST00000416301.1_RNA			P49961	ENTP1_HUMAN	ectonucleoside triphosphate diphosphohydrolase 1	122					ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|purine ribonucleoside diphosphate catabolic process (GO:0009181)	basal lamina (GO:0005605)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|nucleoside-diphosphatase activity (GO:0017110)|nucleoside-triphosphatase activity (GO:0017111)			cervix(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(3)|prostate(1)|skin(1)	16		Colorectal(252;0.0821)		Epithelial(162;1.31e-07)|all cancers(201;5.33e-06)		GTCCCAGCACCAAGAGACACC	0.488																																					p.Q134K		Atlas-SNP	.											.	ENTPD1	44	.	0			c.C400A						.						87	89	88					10																	97602202		2203	4300	6503	SO:0001583	missense	953	exon4			CAGCACCAAGAGA	S73813	CCDS7444.1, CCDS53556.1, CCDS53557.1, CCDS53558.1, CCDS41554.1	10q24.1	2014-03-03			ENSG00000138185	ENSG00000138185		"CD molecules"	3363	protein-coding gene	gene with protein product		601752		CD39		9226376, 24482476	Standard	NM_001098175		Approved	NTPDase-1, ATPDase, SPG64	uc010qoj.2	P49961	OTTHUMG00000018818	ENST00000371205.4:c.364C>A	chr10.hg19:g.97602202C>A	ENSP00000360248:p.Gln122Lys	129.0	0.0		135.0	52.0	NM_001164178	A9Z1X8|B4DWB9|B4E1X1|B7Z599|G3XAF6|Q5T561|Q5T562|Q86VV3|Q9UQQ9|Q9Y3Q9	Missense_Mutation	SNP	ENST00000371205.4	hg19	CCDS7444.1	.	.	.	.	.	.	.	.	.	.	C	8.851	0.944604	0.18356	.	.	ENSG00000138185	ENST00000453258;ENST00000371206;ENST00000371207;ENST00000543964;ENST00000371205	T;T;T;T	0.10960	2.82;2.82;2.82;2.82	5.26	1.29	0.21616	.	1.485950	0.03397	N	0.202833	T	0.05593	0.0147	N	0.16708	0.43	0.09310	N	1	B;B;B;B;B	0.14012	0.009;0.007;0.007;0.009;0.004	B;B;B;B;B	0.16722	0.016;0.009;0.006;0.016;0.012	T	0.28681	-1.0036	10	0.02654	T	1	5.5126	1.3911	0.02250	0.3172:0.3784:0.1376:0.1668	.	134;134;129;122;129	B4DWB9;G3XAF6;P49961-2;P49961;P49961-3	.;.;.;ENTP1_HUMAN;.	K	129;129;134;14;122	ENSP00000390955:Q129K;ENSP00000360250:Q134K;ENSP00000442968:Q14K;ENSP00000360248:Q122K	ENSP00000360248:Q122K	Q	+	1	0	ENTPD1	97592192	0.000000	0.05858	0.000000	0.03702	0.932000	0.56968	-0.252000	0.08806	0.073000	0.16731	0.591000	0.81541	CAA	.	.		0.488	ENTPD1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049566.1	NM_001776		A	97602202	C	A	97602202	3	1	324	1	0	0	0	0	1	0	0	0	5140	595	21	3	475	3	ENTPD1	10	97602202	Missense_Mutation	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	74924104	97602202	37932545	88	45696										
ZRANB1	54764	hgsc.bcm.edu	37	chr10	126631850	126631850	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	aaacaggatgaaaaagactgAttggctcttcctcaatgctt	8	8	2	3			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr10:126631850A>T	ENST00000359653.4	+	1	1159	c.788A>T	c.(787-789)gAt>gTt	p.D263V	RP11-298J20.3_ENST00000449984.1_RNA|RP11-298J20.4_ENST00000508096.1_RNA	NM_017580.2	NP_060050.2	Q9UGI0	ZRAN1_HUMAN	zinc finger, RAN-binding domain containing 1	263					cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|positive regulation of Wnt signaling pathway (GO:0030177)|protein deubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0071947)|protein K29-linked deubiquitination (GO:0035523)|protein K33-linked deubiquitination (GO:1990168)|protein K63-linked deubiquitination (GO:0070536)|regulation of cell morphogenesis (GO:0022604)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	K63-linked polyubiquitin binding (GO:0070530)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(2)|lung(3)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	23		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.172)		Colorectal(40;0.113)|COAD - Colon adenocarcinoma(40;0.119)		AAAAAGACTGATTGGCTCTTC	0.388																																					p.D263V		Atlas-SNP	.											.	ZRANB1	60	.	0			c.A788T						.						39	43	42					10																	126631850		2202	4300	6502	SO:0001583	missense	54764	exon1			AGACTGATTGGCT	AJ252060	CCDS7642.1	10q26.12	2014-02-24			ENSG00000019995	ENSG00000019995		"Zinc fingers, RAN-binding domain containing", "OTU domain containing"	18224	protein-coding gene	gene with protein product		611749				11463333	Standard	NM_017580		Approved	TRABID	uc001lic.3	Q9UGI0	OTTHUMG00000019223	ENST00000359653.4:c.788A>T	chr10.hg19:g.126631850A>T	ENSP00000352676:p.Asp263Val	38.0	0.0		42.0	15.0	NM_017580	B4DZ98|D3DRF4|Q5SQP6|Q69YK3	Missense_Mutation	SNP	ENST00000359653.4	hg19	CCDS7642.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.961583	0.74016	.	.	ENSG00000019995	ENST00000359653	T	0.23950	1.88	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.51975	0.1706	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.57106	-0.7868	10	0.87932	D	0	-25.7875	15.1999	0.73126	1.0:0.0:0.0:0.0	.	263	Q9UGI0	ZRAN1_HUMAN	V	263	ENSP00000352676:D263V	ENSP00000352676:D263V	D	+	2	0	ZRANB1	126621840	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	8.962000	0.93254	1.986000	0.57962	0.460000	0.39030	GAT	.	.		0.388	ZRANB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050898.1	NM_017580		T	126631850	A	T	126631850	3	4	324	1	0	0	0	0	1	0	0	0	18237	333	12	4	790	4	ZRANB1	10	126631850	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	29029648	126631850	8902897	89	45697										
KRTAP5-2	440021	hgsc.bcm.edu	37	chr11	1619366	1619366	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	gcagcccccacagccagagcCacagcccccacggccggagc	11	21	0	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr11:1619366C>T	ENST00000412090.1	-	1	158	c.115G>A	c.(115-117)Ggc>Agc	p.G39S	KRTAP5-AS1_ENST00000534077.1_RNA|KRTAP5-AS1_ENST00000524947.1_RNA|KRTAP5-AS1_ENST00000532922.1_RNA|KRTAP5-AS1_ENST00000424148.1_RNA	NM_001004325.1	NP_001004325.1	Q701N4	KRA52_HUMAN	keratin associated protein 5-2	39						keratin filament (GO:0045095)				large_intestine(1)|lung(2)|skin(1)	4		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		CAGCCAGAGCCACAGCCCCCA	0.687																																					p.G39S		Atlas-SNP	.											.	KRTAP5-2	38	.	0			c.G115A						.						31	39	37					11																	1619366		2168	4223	6391	SO:0001583	missense	440021	exon1			CAGAGCCACAGCC	AB126071	CCDS31331.1	11p15.5	2008-02-05				ENSG00000205867		"Keratin associated proteins"	23597	protein-coding gene	gene with protein product						15144888	Standard	NM_001004325		Approved	KRTAP5.2, KRTAP5-8	uc001ltv.3	Q701N4		ENST00000412090.1:c.115G>A	chr11.hg19:g.1619366C>T	ENSP00000400041:p.Gly39Ser	40.0	0.0		38.0	13.0	NM_001004325	A9JTZ1	Missense_Mutation	SNP	ENST00000412090.1	hg19	CCDS31331.1	.	.	.	.	.	.	.	.	.	.	-	11.16	1.555745	0.27827	.	.	ENSG00000205867	ENST00000412090	T	0.00995	5.46	.	.	.	.	.	.	.	.	T	0.00998	0.0033	L	0.42245	1.32	0.20873	N	0.999838	.	.	.	.	.	.	T	0.46373	-0.9196	5	0.12103	T	0.63	.	.	.	.	.	39	Q701N4	KRA52_HUMAN	S	39	ENSP00000400041:G39S	ENSP00000400041:G39S	G	-	1	0	KRTAP5-2	1575942	0.003000	0.15002	0.677000	0.29947	0.648000	0.38561	-0.350000	0.07721	0.000000	0.14550	0.000000	0.15137	GGC	.	.		0.687	KRTAP5-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384775.1	NM_001004325		T	1619366	C	T	1619366	3	4	324	1	0	0	0	0	1	0	0	0	8570	594	21	3	422	3	KRTAP5-2	11	1619366	Missense_Mutation	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10		1619366	133387150	90	45698										
OR8K3	219473	hgsc.bcm.edu	37	chr11	56085886	56085886	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	tgcattgttcctcatgatctAtgtgatctcagtgatgggca	10	8	3	3			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr11:56085886A>G	ENST00000312711.1	+	1	104	c.104A>G	c.(103-105)tAt>tGt	p.Y35C		NM_001005202.1	NP_001005202.1	Q8NH51	OR8K3_HUMAN	olfactory receptor, family 8, subfamily K, member 3	35						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(2)|endometrium(3)|large_intestine(6)|liver(2)|lung(15)|ovary(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	40	Esophageal squamous(21;0.00448)					CTCATGATCTATGTGATCTCA	0.433																																					p.Y35C		Atlas-SNP	.											.	OR8K3	92	.	0			c.A104G						.						210	191	198					11																	56085886		2201	4296	6497	SO:0001583	missense	219473	exon1			TGATCTATGTGAT	AB065541	CCDS31527.1	11q11	2012-08-09			ENSG00000181689	ENSG00000181689		"GPCR / Class A : Olfactory receptors"	15313	protein-coding gene	gene with protein product							Standard	NM_001005202		Approved		uc010rjf.2	Q8NH51	OTTHUMG00000166855	ENST00000312711.1:c.104A>G	chr11.hg19:g.56085886A>G	ENSP00000323555:p.Tyr35Cys	80.0	0.0		67.0	36.0	NM_001005202	Q6IFC4	Missense_Mutation	SNP	ENST00000312711.1	hg19	CCDS31527.1	.	.	.	.	.	.	.	.	.	.	A	11.13	1.546716	0.27652	.	.	ENSG00000181689	ENST00000312711	T	0.04706	3.57	4.65	3.5	0.40072	.	0.000000	0.56097	D	0.000039	T	0.11793	0.0287	M	0.86864	2.845	0.39941	D	0.974415	P	0.45531	0.86	B	0.43360	0.417	T	0.03325	-1.1048	10	0.87932	D	0	.	10.6838	0.45830	0.839:0.161:0.0:0.0	.	35	Q8NH51	OR8K3_HUMAN	C	35	ENSP00000323555:Y35C	ENSP00000323555:Y35C	Y	+	2	0	OR8K3	55842462	1.000000	0.71417	0.681000	0.30009	0.007000	0.05969	6.008000	0.70739	0.890000	0.36211	-0.337000	0.08149	TAT	.	.		0.433	OR8K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391602.1	NM_001005202		G	56085886	A	G	56085886	3	3	324	1	0	0	0	0	1	0	0	0	11253	449	16	2	106	2	OR8K3	11	56085886	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	54466520	56085886	78920630	91	45699										
ODZ4	26011	hgsc.bcm.edu	37	chr11	78369307	78369307	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ctctgctgctcgcgggcccaCgcttggcgcacggctctctg	13	17	2	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr11:78369307C>G	ENST00000278550.7	-	34	8568	c.8106G>C	c.(8104-8106)gcG>gcC	p.A2702A		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	2702					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)	p.A2702A(2)									CGCGGGCCCACGCTTGGCGCA	0.672																																					p.A2702A		Atlas-SNP	.											ODZ4_ENST00000278550,colon,carcinoma,0,2	.	.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G8106C						.						40	45	44					11																	78369307		2031	4185	6216	SO:0001819	synonymous_variant	26011	exon34			GGCCCACGCTTGG	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"odz, odd Oz/ten-m homolog 4 (Drosophila)"	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.8106G>C	chr11.hg19:g.78369307C>G		44.0	0.0		69.0	28.0	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Silent	SNP	ENST00000278550.7	hg19	CCDS44688.1																																																																																			.	.		0.672	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			G	78369307	C	G	78369307	2	3	324	1	0	0	0	0	0	0	0	1	10846	523	19	4		4	ODZ4	11	78369307	Silent	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	22283421	78369307	56637209	92	45700										
FAT3	120114	hgsc.bcm.edu	37	chr11	92616284	92616284	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	cagtggggacggccgcaacgTctaccaggaggtggggcccc	17	13	1	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr11:92616284T>C	ENST00000298047.6	+	23	12679	c.12662T>C	c.(12661-12663)gTc>gCc	p.V4221A	FAT3_ENST00000409404.2_Missense_Mutation_p.V4221A|FAT3_ENST00000533797.1_Missense_Mutation_p.V556A|FAT3_ENST00000525166.1_Missense_Mutation_p.V4071A			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	4221					homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				GGCCGCAACGTCTACCAGGAG	0.652										TCGA Ovarian(4;0.039)																											p.V4221A		Atlas-SNP	.											.	FAT3	1822	.	0			c.T12662C						.						57	71	66					11																	92616284		1959	4130	6089	SO:0001583	missense	120114	exon23			GCAACGTCTACCA	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.12662T>C	chr11.hg19:g.92616284T>C	ENSP00000298047:p.Val4221Ala	31.0	0.0		46.0	13.0	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	hg19		.	.	.	.	.	.	.	.	.	.	T	15.28	2.787965	0.49997	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166;ENST00000533797	T;T;T;D	0.85629	-0.87;-0.87;-0.88;-2.01	5.85	3.54	0.40534	.	.	.	.	.	T	0.73179	0.3554	N	0.19112	0.55	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.62248	-0.6894	9	0.30078	T	0.28	.	10.1022	0.42511	0.0:0.1355:0.0:0.8645	.	4221;4221	Q8TDW7-3;Q8TDW7	.;FAT3_HUMAN	A	4221;4221;4071;556	ENSP00000298047:V4221A;ENSP00000387040:V4221A;ENSP00000432586:V4071A;ENSP00000436399:V556A	ENSP00000298047:V4221A	V	+	2	0	FAT3	92255932	1.000000	0.71417	0.932000	0.37286	0.874000	0.50279	4.058000	0.57463	0.477000	0.27464	0.533000	0.62120	GTC	.	.		0.652	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		C	92616284	T	C	92616284	3	2	324	1	0	0	0	0	1	0	0	0	5699	1667	58	2	12752	2	FAT3	11	92616284	Missense_Mutation	SNP	T	TCGA-MI-A75I-01A-11D-A32G-10	14246977	92616284	42390232	93	45701										
PKNOX2	63876	hgsc.bcm.edu	37	chr11	125267956	125267956	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	cctccatcaaccttcactcaCaggtaacacccagagctggg	7	16	3	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr11:125267956C>G	ENST00000298282.9	+	7	857	c.586C>G	c.(586-588)Cag>Gag	p.Q196E	PKNOX2_ENST00000542175.1_Missense_Mutation_p.Q132E|PKNOX2_ENST00000530517.1_3'UTR	NM_022062.2	NP_071345.2	Q96KN3	PKNX2_HUMAN	PBX/knotted 1 homeobox 2	196					regulation of transcription from RNA polymerase II promoter (GO:0006357)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(14)|ovary(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	29		Breast(109;0.00234)|all_lung(97;0.0191)|Lung NSC(97;0.0196)|Medulloblastoma(222;0.0447)|all_neural(223;0.116)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.117)		CCTTCACTCACAGGTAACACC	0.587																																					p.Q196E		Atlas-SNP	.											.	PKNOX2	60	.	0			c.C586G						.						60	65	63					11																	125267956		1919	4121	6040	SO:0001583	missense	63876	exon7			CACTCACAGGTAA	AK023136	CCDS41730.1	11q24.2	2014-09-04			ENSG00000165495	ENSG00000165495		"Homeoboxes / TALE class"	16714	protein-coding gene	gene with protein product		613066				11549286	Standard	NM_022062		Approved		uc001qbu.3	Q96KN3	OTTHUMG00000165884	ENST00000298282.9:c.586C>G	chr11.hg19:g.125267956C>G	ENSP00000298282:p.Gln196Glu	68.0	0.0		89.0	30.0	NM_022062	B7Z5I5|F5GZ15|Q63HL6|Q86XD1	Missense_Mutation	SNP	ENST00000298282.9	hg19	CCDS41730.1	.	.	.	.	.	.	.	.	.	.	C	16.00	2.997762	0.54147	.	.	ENSG00000165495	ENST00000530517;ENST00000531116;ENST00000298282;ENST00000542175;ENST00000535518	D;D;D;D	0.84298	-1.83;-1.83;-1.82;-1.8	5.52	5.52	0.82312	.	0.120567	0.56097	D	0.000025	T	0.73481	0.3592	N	0.14661	0.345	0.80722	D	1	B;B	0.10296	0.003;0.001	B;B	0.13407	0.009;0.001	T	0.68622	-0.5360	10	0.02654	T	1	-10.6274	19.8721	0.96854	0.0:1.0:0.0:0.0	.	132;196	F5GZ15;Q96KN3	.;PKNX2_HUMAN	E	167;167;196;132;184	ENSP00000434732:Q167E;ENSP00000433971:Q167E;ENSP00000298282:Q196E;ENSP00000441470:Q132E	ENSP00000298282:Q196E	Q	+	1	0	PKNOX2	124773166	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.250000	0.78287	2.772000	0.95346	0.644000	0.83932	CAG	.	.		0.587	PKNOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386866.3			G	125267956	C	G	125267956	3	3	324	1	0	0	0	0	1	0	0	0	11992	479	17	4	600	4	PKNOX2	11	125267956	Missense_Mutation	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	32651672	125267956	9738560	94	45702										
NTM	50863	hgsc.bcm.edu	37	chr11	132205003	132205003	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ggcaggctgcgtctggctgcTgcctcttctggtcttgcacc	13	14	4	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr11:132205003T>A	ENST00000374786.1	+	7	1477	c.998T>A	c.(997-999)cTg>cAg	p.L333Q	NTM_ENST00000474900.1_3'UTR|NTM_ENST00000374791.3_Missense_Mutation_p.L333Q|NTM_ENST00000427481.2_Missense_Mutation_p.L335Q|NTM_ENST00000425719.2_Missense_Mutation_p.L344Q|NTM_ENST00000539799.1_Missense_Mutation_p.L344Q	NM_001144058.1|NM_016522.2	NP_001137530.1|NP_057606.1	Q9P121	NTRI_HUMAN	neurotrimin	333					cell adhesion (GO:0007155)|neuron recognition (GO:0008038)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(9)|lung(30)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	56						GTCTGGCTGCTGCCTCTTCTG	0.612																																					p.L344Q		Atlas-SNP	.											.	NTM	253	.	0			c.T1031A						.						100	98	99					11																	132205003		2201	4297	6498	SO:0001583	missense	50863	exon8			GGCTGCTGCCTCT	AF126426	CCDS8491.1, CCDS41733.1, CCDS44777.1, CCDS44778.1	11q25	2013-01-11			ENSG00000182667	ENSG00000182667		"Immunoglobulin superfamily / I-set domain containing"	17941	protein-coding gene	gene with protein product	"neurotrimin", "IgLON family member 2"	607938				7891157	Standard	NM_001048209		Approved	HNT, NTRI, IGLON2	uc001qgq.3	Q9P121	OTTHUMG00000066364	ENST00000374786.1:c.998T>A	chr11.hg19:g.132205003T>A	ENSP00000363918:p.Leu333Gln	29.0	0.0		35.0	20.0	NM_001144058	A0MTT2|Q6UXJ3|Q86VJ9	Missense_Mutation	SNP	ENST00000374786.1	hg19	CCDS8491.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.77|15.77	2.932567|2.932567	0.52866|0.52866	.|.	.|.	ENSG00000182667|ENSG00000182667	ENST00000457381|ENST00000374791;ENST00000539799;ENST00000427481;ENST00000374786;ENST00000425719	.|T;T;T;T;T	.|0.62639	.|0.05;0.07;0.01;0.08;0.06	5.13|5.13	5.13|5.13	0.70059|0.70059	.|.	.|0.350658	.|0.26963	.|N	.|0.021608	T|T	0.64800|0.64800	0.2631|0.2631	L|L	0.46157|0.46157	1.445|1.445	0.35227|0.35227	D|D	0.776546|0.776546	.|P;P;P;D;P;D	.|0.59357	.|0.835;0.944;0.725;0.967;0.944;0.985	.|P;P;B;P;B;P	.|0.51385	.|0.514;0.462;0.26;0.587;0.383;0.668	T|T	0.76052|0.76052	-0.3100|-0.3100	5|10	.|0.66056	.|D	.|0.02	-5.9966|-5.9966	13.2101|13.2101	0.59819|0.59819	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|344;335;292;344;333;333	.|B7Z1Z5;B7Z1I4;B7Z1H3;Q9P121-4;Q9P121;Q9P121-2	.|.;.;.;.;NTRI_HUMAN;.	S|Q	108|333;344;335;333;344	.|ENSP00000363923:L333Q;ENSP00000437668:L344Q;ENSP00000416320:L335Q;ENSP00000363918:L333Q;ENSP00000396722:L344Q	.|ENSP00000363918:L333Q	C|L	+|+	1|2	0|0	NTM|NTM	131710213|131710213	1.000000|1.000000	0.71417|0.71417	0.988000|0.988000	0.46212|0.46212	0.734000|0.734000	0.41952|0.41952	4.711000|4.711000	0.61881|0.61881	1.940000|1.940000	0.56252|0.56252	0.528000|0.528000	0.53228|0.53228	TGC|CTG	.	.		0.612	NTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141937.1	NM_016522		A	132205003	T	A	132205003	3	1	324	1	0	0	0	0	1	0	0	0	10708	1580	55	4	1164	4	NTM	11	132205003	Missense_Mutation	SNP	T	TCGA-MI-A75I-01A-11D-A32G-10	6937047	132205003	2801513	95	45703										
OPCML	4978	hgsc.bcm.edu	37	chr11	132526997	132526997	+	Frame_Shift_Del	DEL	G	G	-													0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	cttaccttgcactattaggtGaacccgggacgttttgggat							TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr11:132526997delG	ENST00000331898.7	-	2	963	c.385delC	c.(385-387)cacfs	p.H129fs	OPCML_ENST00000374778.4_Frame_Shift_Del_p.H88fs|OPCML_ENST00000541867.1_Frame_Shift_Del_p.H129fs|OPCML_ENST00000529038.1_5'UTR|OPCML_ENST00000524381.1_Frame_Shift_Del_p.H122fs	NM_002545.3	NP_002536.1	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion molecule-like	129					cell adhesion (GO:0007155)|neuron recognition (GO:0008038)|opioid receptor signaling pathway (GO:0038003)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	opioid receptor activity (GO:0004985)			endometrium(5)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|skin(2)|urinary_tract(8)	47	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		ACTATTAGGTGAACCCGGGAC	0.507																																					p.H129fs		Atlas-Indel,Pindel	.											.	OPCML	166	.	0			c.386delA						.						162	142	149					11																	132526997		2201	4297	6498	SO:0001589	frameshift_variant	4978	exon2			.	BX537377	CCDS8492.1, CCDS31722.1	11q25	2013-01-11	2001-11-28		ENSG00000183715	ENSG00000183715		"Immunoglobulin superfamily / I-set domain containing"	8143	protein-coding gene	gene with protein product	"IgLON family member 1"	600632	"opioid-binding protein/cell adhesion molecule-like"			8244387	Standard	XM_005271578		Approved	OPCM, OBCAM, IGLON1	uc001qgs.3	Q14982	OTTHUMG00000163658	ENST00000331898.7:c.385delC	chr11.hg19:g.132526997delG	ENSP00000330862:p.His129fs	135.0	0.0		147.0	45.0	NM_002545	B2CZX2|B7ZLQ1|Q17RN7|Q7Z3W6	Frame_Shift_Del	DEL	ENST00000331898.7	hg19	CCDS8492.1																																																																																			.	.		0.507	OPCML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374689.3	NM_001012393		-	132526997	G	-	132526997	7	5	324	1	0	1	0	1	0	0	0	0	10883	1290	45	0	676	0	OPCML	11	132526997	Frame_Shift_Del	DEL	G	TCGA-MI-A75I-01A-11D-A32G-10	321994	132526997	2479519	96	45704										
NCAPD3	23310	hgsc.bcm.edu	37	chr11	134076627	134076627	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	atggaaaacacaactgatgaCctagaagagaaaagaaaatt	8	5	0	5			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr11:134076627C>A	ENST00000534548.2	-	8	947	c.883G>T	c.(883-885)Gtc>Ttc	p.V295F		NM_015261.2	NP_056076.1	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3	295					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	germinal vesicle (GO:0042585)|membrane (GO:0016020)|nuclear condensin complex (GO:0000799)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)	methylated histone binding (GO:0035064)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)		CAACTGATGACCTAGAAGAGA	0.408																																					p.V295F		Atlas-SNP	.											.	NCAPD3	141	.	0			c.G883T						.						96	93	94					11																	134076627		2201	4297	6498	SO:0001630	splice_region_variant	23310	exon8			TGATGACCTAGAA	AK124878	CCDS31723.1	11q25	2008-02-04			ENSG00000151503	ENSG00000151503			28952	protein-coding gene	gene with protein product		609276				7584044, 8619474, 14532007	Standard	NM_015261		Approved	hCAP-D3, CAP-D3, hHCP-6, KIAA0056, FLJ42888, hcp-6	uc001qhd.1	P42695	OTTHUMG00000167172	ENST00000534548.2:c.883-1G>T	chr11.hg19:g.134076627C>A		70.0	0.0		81.0	43.0	NM_015261	A6NFS2|Q4KMQ9	Missense_Mutation	SNP	ENST00000534548.2	hg19	CCDS31723.1	.	.	.	.	.	.	.	.	.	.	C	11.10	1.540500	0.27563	.	.	ENSG00000151503	ENST00000534548	T	0.04706	3.57	5.68	2.81	0.32909	Armadillo-type fold (1);	0.269957	0.39909	N	0.001235	T	0.05181	0.0138	L	0.60455	1.87	0.80722	D	1	P	0.35383	0.498	B	0.29716	0.106	T	0.33574	-0.9863	10	0.59425	D	0.04	-20.1388	6.2882	0.21045	0.0:0.5599:0.0:0.4401	.	295	P42695	CNDD3_HUMAN	F	295	ENSP00000433681:V295F	ENSP00000431612:V295F	V	-	1	0	NCAPD3	133581837	0.991000	0.36638	0.998000	0.56505	0.182000	0.23217	0.627000	0.24506	0.885000	0.36088	-0.216000	0.12614	GTC	.	.		0.408	NCAPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393575.2	NM_015261	Missense_Mutation	A	134076627	C	A	134076627	5	1	324	1	0	0	0	0	0	0	1	0	10215	521	18	3	3725	3	NCAPD3	11	134076627	Splice_Site	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	1549630	134076627	929889	97	45705										
NECAP1	25977	hgsc.bcm.edu	37	chr12	8242584	8242584	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ggactggtcgcctccgaatcActtcaaaagggaagactgcc	11	12	2	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr12:8242584A>T	ENST00000339754.5	+	2	226	c.148A>T	c.(148-150)Act>Tct	p.T50S		NM_015509.3	NP_056324.2	Q8NC96	NECP1_HUMAN	NECAP endocytosis associated 1	50					endocytosis (GO:0006897)|protein transport (GO:0015031)	clathrin vesicle coat (GO:0030125)|coated pit (GO:0005905)|plasma membrane (GO:0005886)				cervix(1)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10				Kidney(36;0.0915)		CCTCCGAATCACTTCAAAAGG	0.438																																					p.T50S		Atlas-SNP	.											.	NECAP1	21	.	0			c.A148T						.						109	115	113					12																	8242584		2203	4300	6503	SO:0001583	missense	25977	exon2			CGAATCACTTCAA	AK074923	CCDS8589.1	12p13.31	2012-05-02			ENSG00000089818	ENSG00000089818			24539	protein-coding gene	gene with protein product		611623				14555962, 15494011	Standard	NM_015509		Approved	DKFZP566B183	uc001qtx.2	Q8NC96	OTTHUMG00000168568	ENST00000339754.5:c.148A>T	chr12.hg19:g.8242584A>T	ENSP00000341737:p.Thr50Ser	76.0	0.0		52.0	22.0	NM_015509	Q2NL73|Q5XG95|Q6NWY6|Q8N153|Q8NCB0|Q9BU52|Q9Y407	Missense_Mutation	SNP	ENST00000339754.5	hg19	CCDS8589.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.568954	0.86439	.	.	ENSG00000089818	ENST00000545179;ENST00000339754	T	0.43688	0.94	4.63	4.63	0.57726	.	0.000000	0.85682	D	0.000000	T	0.53578	0.1805	M	0.77616	2.38	0.80722	D	1	B	0.30021	0.265	B	0.42555	0.391	T	0.58515	-0.7623	10	0.54805	T	0.06	.	12.312	0.54933	1.0:0.0:0.0:0.0	.	50	Q8NC96	NECP1_HUMAN	S	50	ENSP00000341737:T50S	ENSP00000341737:T50S	T	+	1	0	NECAP1	8133851	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.521000	0.90569	2.067000	0.61834	0.533000	0.62120	ACT	.	.		0.438	NECAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400244.1	NM_015509		T	8242584	A	T	8242584	3	4	324	1	0	0	0	0	1	0	0	0	10316	159	6	4	154	4	NECAP1	12	8242584	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10		8242584	125609311	98	45706										
OVCH1	341350	hgsc.bcm.edu	37	chr12	29628110	29628110	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ttgaagtgatggtcaacattCcacaaagtttagctgaaaaa	8	6	1	3			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr12:29628110C>A	ENST00000318184.5	-	14	1483	c.1484G>T	c.(1483-1485)gGa>gTa	p.G495V	OVCH1-AS1_ENST00000549411.1_Intron|OVCH1-AS1_ENST00000551108.1_Intron	NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	495	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.					extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					GGTCAACATTCCACAAAGTTT	0.289																																					p.G495V		Atlas-SNP	.											.	OVCH1	195	.	0			c.G1484T						.						31	28	29					12																	29628110		1799	4064	5863	SO:0001583	missense	341350	exon14			AACATTCCACAAA	BN000128		12p11.23	2012-11-08			ENSG00000187950	ENSG00000187950			23080	protein-coding gene	gene with protein product						12838346	Standard	NM_183378		Approved	OVCH	uc001rix.1	Q7RTY7	OTTHUMG00000167741	ENST00000318184.5:c.1484G>T	chr12.hg19:g.29628110C>A	ENSP00000326708:p.Gly495Val	135.0	0.0		143.0	42.0	NM_183378		Missense_Mutation	SNP	ENST00000318184.5	hg19		.	.	.	.	.	.	.	.	.	.	C	11.94	1.787481	0.31593	.	.	ENSG00000187950	ENST00000318184	T	0.65178	-0.14	2.59	0.643	0.17770	CUB (5);	.	.	.	.	T	0.81927	0.4926	H	0.97158	3.95	0.37988	D	0.933822	D	0.76494	0.999	D	0.72338	0.977	T	0.80910	-0.1171	9	0.87932	D	0	.	6.376	0.21507	0.0:0.6972:0.1878:0.115	.	495	Q7RTY7	OVCH1_HUMAN	V	495	ENSP00000326708:G495V	ENSP00000326708:G495V	G	-	2	0	OVCH1	29519377	0.620000	0.27068	0.111000	0.21465	0.365000	0.29674	0.772000	0.26647	0.156000	0.19299	0.467000	0.42956	GGA	.	.		0.289	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378		A	29628110	C	A	29628110	3	1	324	1	0	0	0	0	1	0	0	0	11332	855	30	3	1980	3	OVCH1	12	29628110	Missense_Mutation	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	21385526	29628110	104223785	99	45707										
CCDC65	85478	hgsc.bcm.edu	37	chr12	49298898	49298898	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	taaggacaatgtcatcaaggTaggcactctttccaaggaaa	9	8	3	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr12:49298898T>C	ENST00000320516.4	+	2	488		c.e2+2		CCDC65_ENST00000266984.5_Splice_Site|RP11-302B13.5_ENST00000398092.4_Intron	NM_033124.4	NP_149115.2	Q8IXS2	CCD65_HUMAN	coiled-coil domain containing 65											breast(1)|large_intestine(4)|lung(7)|ovary(1)|skin(2)	15						GTCATCAAGGTAGGCACTCTT	0.458																																					.		Atlas-SNP	.											.	CCDC65	41	.	0			c.300+2T>C						.						149	126	134					12																	49298898		2203	4300	6503	SO:0001630	splice_region_variant	85478	exon2			TCAAGGTAGGCAC		CCDS8772.1	12q13.12	2014-07-18			ENSG00000139537	ENSG00000139537			29937	protein-coding gene	gene with protein product		611088				17089017, 21700706	Standard	NM_033124		Approved	NYD-SP28, FLJ35732, FAP250, CILD27	uc001rso.3	Q8IXS2		ENST00000320516.4:c.300+2T>C	chr12.hg19:g.49298898T>C		52.0	0.0		37.0	18.0	NM_033124	A6NJG5|B2RBE2|Q8N7G4|Q8NA91|Q96JA0	Splice_Site	SNP	ENST00000320516.4	hg19	CCDS8772.1	.	.	.	.	.	.	.	.	.	.	T	16.17	3.047002	0.55110	.	.	ENSG00000139537	ENST00000266984;ENST00000552942;ENST00000320516	.	.	.	4.7	3.57	0.40892	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.6655	0.34118	0.0:0.0962:0.0:0.9038	.	.	.	.	.	-1	.	.	.	+	.	.	CCDC65	47585165	0.999000	0.42202	0.831000	0.32960	0.939000	0.58152	3.172000	0.50832	0.957000	0.37930	0.482000	0.46254	.	.	.		0.458	CCDC65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408922.1	NM_033124	Intron	C	49298898	T	C	49298898	5	2	324	1	0	0	0	0	0	0	1	0	2839	1652	57	2	308	2	CCDC65	12	49298898	Splice_Site	SNP	T	TCGA-MI-A75I-01A-11D-A32G-10	19670788	49298898	84552997	100	45708										
HOXC8	3224	hgsc.bcm.edu	37	chr12	54403335	54403335	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ggagacgcctccaaattctaTggctacgaggcgctccccag	11	14	1	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr12:54403335T>C	ENST00000040584.4	+	1	504	c.267T>C	c.(265-267)taT>taC	p.Y89Y	RP11-834C11.12_ENST00000513209.1_Intron	NM_022658.3	NP_073149.1	P31273	HXC8_HUMAN	homeobox C8	89					anterior/posterior pattern specification (GO:0009952)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(3)	8						CCAAATTCTATGGCTACGAGG	0.567																																					p.Y89Y	GBM(197;701 2226 7002 18822 41696)	Atlas-SNP	.											.	HOXC8	15	.	0			c.T267C						.						121	130	127					12																	54403335		2203	4300	6503	SO:0001819	synonymous_variant	3224	exon1			ATTCTATGGCTAC	X99680	CCDS8870.1	12q13.13	2011-06-20	2005-12-22			ENSG00000037965		"Homeoboxes / ANTP class : HOXL subclass"	5129	protein-coding gene	gene with protein product		142970	"homeo box C8"	HOX3, HOX3A		1973146, 1358459	Standard	NM_022658		Approved		uc001ser.3	P31273		ENST00000040584.4:c.267T>C	chr12.hg19:g.54403335T>C		65.0	0.0		66.0	22.0	NM_022658	A8K4J4|O15221|O15362	Silent	SNP	ENST00000040584.4	hg19	CCDS8870.1																																																																																			.	.		0.567	HOXC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358957.2			C	54403335	T	C	54403335	2	2	324	1	0	0	0	0	0	0	0	1	7325	1471	51	2		2	HOXC8	12	54403335	Silent	SNP	T	TCGA-MI-A75I-01A-11D-A32G-10	5104437	54403335	79448560	101	45709										
GLS2	27165	hgsc.bcm.edu	37	chr12	56868406	56868406	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	gtgttgcgcactgcttcagcActcagcacactctcgcctgt	9	15	3	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr12:56868406A>G	ENST00000311966.4	-	12	1424	c.1146T>C	c.(1144-1146)agT>agC	p.S382S	GLS2_ENST00000476991.1_5'UTR	NM_013267.2	NP_037399.2	Q9UI32	GLSL_HUMAN	glutaminase 2 (liver, mitochondrial)	382					cellular amino acid biosynthetic process (GO:0008652)|cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate secretion (GO:0014047)|glutamine metabolic process (GO:0006541)|neurotransmitter secretion (GO:0007269)|reactive oxygen species metabolic process (GO:0072593)|regulation of apoptotic process (GO:0042981)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	glutaminase activity (GO:0004359)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	13					L-Glutamine(DB00130)	CTGCTTCAGCACTCAGCACAC	0.567																																					p.S382S		Atlas-SNP	.											.	GLS2	42	.	0			c.T1146C						.						139	124	129					12																	56868406		2203	4300	6503	SO:0001819	synonymous_variant	27165	exon12			TTCAGCACTCAGC		CCDS8921.1, CCDS73482.1	12q13	2013-01-10			ENSG00000135423	ENSG00000135423		"Ankyrin repeat domain containing"	29570	protein-coding gene	gene with protein product		606365				11130979, 10620514	Standard	NM_013267		Approved	GA, GLS, LGA, hLGA	uc001slj.3	Q9UI32	OTTHUMG00000140379	ENST00000311966.4:c.1146T>C	chr12.hg19:g.56868406A>G		25.0	0.0		28.0	10.0	NM_013267	B7Z8Q9|Q8IX91|Q9NYY2|Q9UI31	Silent	SNP	ENST00000311966.4	hg19	CCDS8921.1																																																																																			.	.		0.567	GLS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277113.1	NM_013267		G	56868406	A	G	56868406	2	3	324	1	0	0	0	0	0	0	0	1	6472	156	6	2		2	GLS2	12	56868406	Silent	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	2465071	56868406	76983489	102	45710										
LRP1	4035	hgsc.bcm.edu	37	chr12	57603645	57603645	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	tttaccatcagcacaagcagCccgaaggtgggggcagaggg	15	10	1	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr12:57603645C>T	ENST00000243077.3	+	80	12899	c.12433C>T	c.(12433-12435)Ccc>Tcc	p.P4145S		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	4145					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	GCACAAGCAGCCCGAAGGTGG	0.627																																					p.P4145S		Atlas-SNP	.											.	LRP1	428	.	0			c.C12433T						.						39	41	40					12																	57603645		2203	4300	6503	SO:0001583	missense	4035	exon80			AAGCAGCCCGAAG	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"CD molecules", "Low density lipoprotein receptors"	6692	protein-coding gene	gene with protein product		107770	"alpha-2-macroglobulin receptor"	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.12433C>T	chr12.hg19:g.57603645C>T	ENSP00000243077:p.Pro4145Ser	28.0	0.0		26.0	10.0	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	hg19	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	C	13.30	2.196055	0.38806	.	.	ENSG00000123384	ENST00000243077	T	0.32753	1.44	4.45	4.45	0.53987	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.000000	0.64402	D	0.000002	T	0.51466	0.1676	M	0.61703	1.905	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.41875	-0.9484	10	0.27785	T	0.31	.	16.3785	0.83418	0.0:1.0:0.0:0.0	.	4145	Q07954	LRP1_HUMAN	S	4145	ENSP00000243077:P4145S	ENSP00000243077:P4145S	P	+	1	0	LRP1	55889912	1.000000	0.71417	1.000000	0.80357	0.861000	0.49209	7.332000	0.79203	2.486000	0.83907	0.557000	0.71058	CCC	.	.		0.627	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		T	57603645	C	T	57603645	3	4	324	1	0	0	0	0	1	0	0	0	8960	739	26	3	12751	3	LRP1	12	57603645	Missense_Mutation	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	735239	57603645	76248250	103	45711										
MDM1	56890	hgsc.bcm.edu	37	chr12	68715374	68715374	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	agtcttttaattccatctctGcttccaattttaaacgatcg	4	10	2	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr12:68715374G>A	ENST00000303145.7	-	6	922	c.836C>T	c.(835-837)gCa>gTa	p.A279V	MDM1_ENST00000540418.1_5'UTR|MDM1_ENST00000411698.2_Missense_Mutation_p.A234V	NM_017440.4	NP_059136.2	Q8TC05	MDM1_HUMAN	Mdm1 nuclear protein homolog (mouse)	279					retina development in camera-type eye (GO:0060041)	nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|ovary(3)|pancreas(1)|prostate(2)|skin(7)	33			Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000174)		TTCCATCTCTGCTTCCAATTT	0.313																																					p.A279V		Atlas-SNP	.											.	MDM1	74	.	0			c.C836T						.						138	138	138					12																	68715374		2203	4300	6503	SO:0001583	missense	56890	exon6			ATCTCTGCTTCCA	AF007130	CCDS8983.1, CCDS44938.1, CCDS55841.1, CCDS55842.1	12q15	2008-04-14	2008-04-14			ENSG00000111554			29917	protein-coding gene	gene with protein product		613813	"Mdm4, transformed 3T3 cell double minute 1, p53 binding protein (mouse)"			8619474, 9110174	Standard	NM_017440		Approved		uc001stz.2	Q8TC05		ENST00000303145.7:c.836C>T	chr12.hg19:g.68715374G>A	ENSP00000302537:p.Ala279Val	73.0	0.0		89.0	20.0	NM_017440	B4DM65|E7EPQ3|O43406|Q8WTV9|Q9NR04	Missense_Mutation	SNP	ENST00000303145.7	hg19	CCDS8983.1	.	.	.	.	.	.	.	.	.	.	G	9.452	1.090738	0.20471	.	.	ENSG00000111554	ENST00000303145;ENST00000411698;ENST00000541686	T;T;T	0.20598	2.06;2.06;2.06	4.49	1.48	0.22813	.	0.814921	0.11178	N	0.591255	T	0.11281	0.0275	N	0.22421	0.69	0.80722	D	1	B;B	0.10296	0.002;0.003	B;B	0.14578	0.011;0.01	T	0.20806	-1.0264	9	.	.	.	-0.5526	2.964	0.05902	0.1044:0.1786:0.5329:0.1841	.	234;279	E7EPQ3;Q8TC05	.;MDM1_HUMAN	V	279;234;274	ENSP00000302537:A279V;ENSP00000391006:A234V;ENSP00000446000:A274V	.	A	-	2	0	MDM1	67001641	0.997000	0.39634	0.999000	0.59377	0.830000	0.47004	0.268000	0.18571	0.187000	0.20147	-0.314000	0.08810	GCA	.	.		0.313	MDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402402.1	NM_020128		A	68715374	G	A	68715374	3	1	324	1	0	0	0	0	1	0	0	0	9421	1319	46	3	1344	3	MDM1	12	68715374	Missense_Mutation	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10	11111729	68715374	65136521	104	45712										
C12orf42	374470	hgsc.bcm.edu	37	chr12	103762676	103762676	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ttaatttacctggaaaattcAgaaagtgtagactacgaaat	7	5	1	2			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr12:103762676A>T	ENST00000378113.2	-	4	473	c.248T>A	c.(247-249)cTg>cAg	p.L83Q	C12orf42_ENST00000315192.8_Missense_Mutation_p.L83Q|C12orf42_ENST00000548883.1_Missense_Mutation_p.L83Q|C12orf42_ENST00000548789.1_5'UTR|C12orf42_ENST00000548048.1_Missense_Mutation_p.L16Q	NM_001099336.1	NP_001092806.1	Q96LP6	CL042_HUMAN	chromosome 12 open reading frame 42	83										NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)	22						TGGAAAATTCAGAAAGTGTAG	0.348																																					p.L83Q		Atlas-SNP	.											.	C12orf42	50	.	0			c.T248A						.						39	38	38					12																	103762676		1801	4062	5863	SO:0001583	missense	374470	exon4			AAATTCAGAAAGT	AK058052	CCDS44963.1	12q23.2	2012-05-30			ENSG00000179088	ENSG00000179088			24729	protein-coding gene	gene with protein product							Standard	NM_001099336		Approved	FLJ25323	uc001tjt.2	Q96LP6	OTTHUMG00000169988	ENST00000378113.2:c.248T>A	chr12.hg19:g.103762676A>T	ENSP00000367353:p.Leu83Gln	256.0	0.0		242.0	72.0	NM_001099336	Q49A64|Q4G0S2	Missense_Mutation	SNP	ENST00000378113.2	hg19	CCDS44963.1	.	.	.	.	.	.	.	.	.	.	A	13.77	2.336666	0.41398	.	.	ENSG00000179088	ENST00000315192;ENST00000548883;ENST00000548048;ENST00000378113;ENST00000552578	T;T;T;T;T	0.60920	0.15;0.87;0.29;0.87;0.86	4.07	2.94	0.34122	.	.	.	.	.	T	0.58538	0.2129	L	0.27053	0.805	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.60424	-0.7266	9	0.87932	D	0	-1.9286	5.4022	0.16303	0.875:0.0:0.125:0.0	.	83	Q96LP6	CL042_HUMAN	Q	83;83;16;83;83	ENSP00000324984:L83Q;ENSP00000447908:L83Q;ENSP00000449362:L16Q;ENSP00000367353:L83Q;ENSP00000447795:L83Q	ENSP00000324984:L83Q	L	-	2	0	C12orf42	102286806	0.004000	0.15560	0.035000	0.18076	0.003000	0.03518	0.486000	0.22340	1.786000	0.52430	0.533000	0.62120	CTG	.	.		0.348	C12orf42-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406754.1	NM_198521		T	103762676	A	T	103762676	3	4	324	1	0	0	0	0	1	0	0	0	1690	188	7	4	846	4	C12orf42	12	103762676	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	35047302	103762676	30089219	105	45713										
WSCD2	9671	hgsc.bcm.edu	37	chr12	108589818	108589818	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	gctgtccttcttgggtgacaTgcatctgggcagaggtttcc	13	10	2	2			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr12:108589818T>C	ENST00000332082.4	+	3	1027	c.209T>C	c.(208-210)aTg>aCg	p.M70T	WSCD2_ENST00000549903.1_Missense_Mutation_p.M70T|WSCD2_ENST00000547525.1_Missense_Mutation_p.M70T|WSCD2_ENST00000261400.3_Missense_Mutation_p.M70T			Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	70						integral component of membrane (GO:0016021)				breast(4)|endometrium(3)|kidney(1)|large_intestine(16)|liver(2)|lung(23)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	57						TTGGGTGACATGCATCTGGGC	0.617																																					p.M70T		Atlas-SNP	.											.	WSCD2	125	.	0			c.T209C						.						145	146	146					12																	108589818		2068	4218	6286	SO:0001583	missense	9671	exon2			GTGACATGCATCT		CCDS41828.1	12q23.3	2008-02-05				ENSG00000075035			29117	protein-coding gene	gene with protein product							Standard	NM_014653		Approved	KIAA0789	uc001tms.3	Q2TBF2		ENST00000332082.4:c.209T>C	chr12.hg19:g.108589818T>C	ENSP00000331933:p.Met70Thr	63.0	0.0		48.0	17.0	NM_014653	B2RN48|B4DES1|Q8IY35|Q9Y4B7	Missense_Mutation	SNP	ENST00000332082.4	hg19	CCDS41828.1	.	.	.	.	.	.	.	.	.	.	T	2.380	-0.342269	0.05243	.	.	ENSG00000075035	ENST00000547525;ENST00000261400;ENST00000332082;ENST00000549903	T;T;T;T	0.28666	1.61;1.6;1.61;1.6	5.74	3.38	0.38709	.	1.460410	0.03933	N	0.285650	T	0.12220	0.0297	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30707	-0.9969	10	0.11794	T	0.64	-4.6756	4.7924	0.13256	0.0:0.1995:0.1587:0.6419	.	70	Q2TBF2	WSCD2_HUMAN	T	70	ENSP00000448047:M70T;ENSP00000261400:M70T;ENSP00000331933:M70T;ENSP00000447272:M70T	ENSP00000261400:M70T	M	+	2	0	WSCD2	107113948	0.988000	0.35896	0.930000	0.37139	0.465000	0.32709	2.021000	0.41020	0.968000	0.38212	0.533000	0.62120	ATG	.	.		0.617	WSCD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405554.1	NM_014653		C	108589818	T	C	108589818	3	2	324	1	0	0	0	0	1	0	0	0	17422	1464	51	2	211	2	WSCD2	12	108589818	Missense_Mutation	SNP	T	TCGA-MI-A75I-01A-11D-A32G-10	4827142	108589818	25262077	106	45714										
IFT88	8100	hgsc.bcm.edu	37	chr13	21175874	21175874	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	atgcagaatattggagttacAtttattcaggctggtcagta	10	5	2	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr13:21175874A>G	ENST00000319980.6	+	14	1197	c.870A>G	c.(868-870)acA>acG	p.T290T	IFT88_ENST00000537103.1_Silent_p.T262T|IFT88_ENST00000382778.4_Silent_p.T290T|IFT88_ENST00000351808.5_Silent_p.T281T	NM_175605.3	NP_783195.2	Q13099	IFT88_HUMAN	intraflagellar transport 88	290					anterior/posterior pattern specification (GO:0009952)|cardiac muscle cell differentiation (GO:0055007)|cardiac septum morphogenesis (GO:0060411)|cilium morphogenesis (GO:0060271)|cochlea development (GO:0090102)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|embryonic digit morphogenesis (GO:0042733)|epidermal stem cell homeostasis (GO:0036334)|epidermis development (GO:0008544)|epithelial cell morphogenesis (GO:0003382)|eye development (GO:0001654)|forebrain morphogenesis (GO:0048853)|heart formation (GO:0060914)|inner ear receptor stereocilium organization (GO:0060122)|kidney development (GO:0001822)|liver development (GO:0001889)|lung vasculature development (GO:0060426)|negative regulation of epithelial cell proliferation (GO:0050680)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|pancreas development (GO:0031016)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|protein localization (GO:0008104)|regulation of autophagic vacuole assembly (GO:2000785)|regulation of cilium assembly (GO:1902017)|regulation of fat cell differentiation (GO:0045598)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|regulation of protein processing (GO:0070613)|regulation of smoothened signaling pathway (GO:0008589)|response to fluid shear stress (GO:0034405)|smoothened signaling pathway (GO:0007224)|sperm axoneme assembly (GO:0007288)|spermatid nucleus elongation (GO:0007290)|spinal cord dorsal/ventral patterning (GO:0021513)|telencephalon development (GO:0021537)	acrosomal membrane (GO:0002080)|apical part of cell (GO:0045177)|axonemal basal plate (GO:0097541)|centriole (GO:0005814)|ciliary basal body (GO:0036064)|ciliary base (GO:0097546)|ciliary tip (GO:0097542)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|kinocilium (GO:0060091)|motile cilium (GO:0031514)|motile primary cilium (GO:0031512)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	27		all_cancers(29;5.79e-25)|all_epithelial(30;2.57e-20)|all_lung(29;3.13e-16)|Lung SC(185;0.0262)|Ovarian(182;0.0825)|Hepatocellular(188;0.244)		all cancers(112;0.000667)|Epithelial(112;0.00119)|OV - Ovarian serous cystadenocarcinoma(117;0.0141)|Lung(94;0.0183)|LUSC - Lung squamous cell carcinoma(192;0.0528)		TTGGAGTTACATTTATTCAGG	0.338																																					p.T290T		Atlas-SNP	.											.	IFT88	83	.	0			c.A870G						.						71	71	71					13																	21175874		2203	4300	6503	SO:0001819	synonymous_variant	8100	exon14			AGTTACATTTATT	AK058172	CCDS31944.1, CCDS31945.1	13q12.1	2014-07-03	2014-07-03	2005-11-02	ENSG00000032742	ENSG00000032742		"Intraflagellar transport homologs", "Tetratricopeptide (TTC) repeat domain containing"	20606	protein-coding gene	gene with protein product	"polaris homolog"	600595	"tetratricopeptide repeat domain 10", "intraflagellar transport 88 homolog (Chlamydomonas)"	TTC10		7633404	Standard	XM_005266546		Approved	hTg737, Tg737, D13S1056E, MGC26259	uc001uni.3	Q13099	OTTHUMG00000016517	ENST00000319980.6:c.870A>G	chr13.hg19:g.21175874A>G		208.0	0.0		180.0	53.0	NM_175605	A2A491|B4DUS2|Q5SZJ6|Q8N719	Silent	SNP	ENST00000319980.6	hg19	CCDS31944.1																																																																																			.	.		0.338	IFT88-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044075.3	NM_006531		G	21175874	A	G	21175874	2	3	324	1	0	0	0	0	0	0	0	1	7575	204	8	2		2	IFT88	13	21175874	Silent	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10		21175874	93994004	107	45715										
COL4A2	1284	hgsc.bcm.edu	37	chr13	111090978	111090978	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ctcctagggcatttccttgaAgggagaagaaggaatcatgg	13	7	1	3			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr13:111090978A>C	ENST00000360467.5	+	15	1181	c.875A>C	c.(874-876)aAg>aCg	p.K292T		NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	292	Triple-helical region.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	extracellular matrix structural constituent (GO:0005201)			NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	80	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			ATTTCCTTGAAGGGAGAAGAA	0.547																																					p.K292T		Atlas-SNP	.											.	COL4A2	178	.	0			c.A875C						.						146	148	147					13																	111090978		1892	4121	6013	SO:0001583	missense	1284	exon15			CCTTGAAGGGAGA	AK025912	CCDS41907.1	13q34	2013-09-05			ENSG00000134871	ENSG00000134871		"Collagens"	2203	protein-coding gene	gene with protein product	"canstatin", "collagen type IV alpha 2"	120090				2439508, 3025878	Standard	NM_001846		Approved	FLJ22259, DKFZp686I14213	uc001vqx.3	P08572	OTTHUMG00000017344	ENST00000360467.5:c.875A>C	chr13.hg19:g.111090978A>C	ENSP00000353654:p.Lys292Thr	114.0	0.0		119.0	40.0	NM_001846	Q14052|Q548C3|Q5VZA9|Q66K23	Missense_Mutation	SNP	ENST00000360467.5	hg19	CCDS41907.1	.	.	.	.	.	.	.	.	.	.	A	10.23	1.294103	0.23564	.	.	ENSG00000134871	ENST00000360467;ENST00000257309	D	0.96619	-4.07	4.52	3.34	0.38264	.	0.155857	0.28504	N	0.015105	D	0.96602	0.8891	M	0.82056	2.57	0.37765	D	0.926489	D	0.63046	0.992	P	0.56865	0.808	D	0.95966	0.8966	10	0.45353	T	0.12	.	6.2121	0.20636	0.8868:0.0:0.1132:0.0	.	292	P08572	CO4A2_HUMAN	T	292	ENSP00000353654:K292T	ENSP00000257309:K292T	K	+	2	0	COL4A2	109888979	0.999000	0.42202	0.956000	0.39512	0.326000	0.28443	1.776000	0.38594	1.807000	0.52817	0.455000	0.32223	AAG	.	.		0.547	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846		C	111090978	A	C	111090978	3	2	324	1	0	0	0	0	1	0	0	0	3692	72	3	5	929	5	COL4A2	13	111090978	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	89915104	111090978	4078900	108	45716										
SRP54	6729	hgsc.bcm.edu	37	chr14	35492189	35492189	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	caaagagtagcaagaggatcGggtgtatcaacaagagatgt	13	5	1	3			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr14:35492189G>C	ENST00000556994.1	+	15	1627	c.1230G>C	c.(1228-1230)tcG>tcC	p.S410S	SRP54_ENST00000555557.1_Silent_p.S346S|SRP54_ENST00000216774.6_Silent_p.S410S|SRP54_ENST00000546080.1_Silent_p.S361S			P61011	SRP54_HUMAN	signal recognition particle 54kDa	410	M-domain.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|protein targeting to ER (GO:0045047)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition (GO:0006617)|SRP-dependent cotranslational protein targeting to membrane, translocation (GO:0006616)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|drug binding (GO:0008144)|endoplasmic reticulum signal peptide binding (GO:0030942)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|ribonucleoprotein complex binding (GO:0043021)	p.S410S(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	14	Breast(36;0.0545)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;2.48e-05)|Lung(238;3.13e-05)|Epithelial(34;0.0314)|all cancers(34;0.0797)|BRCA - Breast invasive adenocarcinoma(188;0.243)	GBM - Glioblastoma multiforme(112;0.0396)		CAAGAGGATCGGGTGTATCAA	0.393																																					p.S410S		Atlas-SNP	.											SRP54,rectum,carcinoma,0,1	SRP54	38	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1230C						.						106	98	101					14																	35492189		2203	4300	6503	SO:0001819	synonymous_variant	6729	exon14			AGGATCGGGTGTA	X86373	CCDS9652.1, CCDS53893.1	14q13.2	2014-06-02	2002-08-29		ENSG00000100883	ENSG00000100883			11301	protein-coding gene	gene with protein product		604857	"signal recognition particle 54kD"			8722571	Standard	NM_003136		Approved		uc001wso.3	P61011	OTTHUMG00000140214	ENST00000556994.1:c.1230G>C	chr14.hg19:g.35492189G>C		77.0	0.0		70.0	24.0	NM_003136	B2R759|B4DUW6|P13624	Silent	SNP	ENST00000556994.1	hg19	CCDS9652.1																																																																																			.	.		0.393	SRP54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276643.2	NM_003136		C	35492189	G	C	35492189	2	2	324	1	0	0	0	0	0	0	0	1	15170	1103	39	4		4	SRP54	14	35492189	Silent	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10		35492189	71857351	109	45717										
MTA1	9112	hgsc.bcm.edu	37	chr14	105931048	105931048	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	agcccggagcagcgggagccCcaagtttgccatgaagacca	13	13	0	2			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr14:105931048C>G	ENST00000331320.7	+	15	1596	c.1382C>G	c.(1381-1383)cCc>cGc	p.P461R	MTA1_ENST00000435036.2_5'UTR|MTA1_ENST00000406191.1_Missense_Mutation_p.P461R|MTA1_ENST00000405646.1_Missense_Mutation_p.P444R	NM_001203258.1|NM_004689.3	NP_001190187.1|NP_004680.2	Q13330	MTA1_HUMAN	metastasis associated 1	461					circadian regulation of gene expression (GO:0032922)|double-strand break repair (GO:0006302)|entrainment of circadian clock by photoperiod (GO:0043153)|locomotor rhythm (GO:0045475)|positive regulation of protein autoubiquitination (GO:1902499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of gene expression, epigenetic (GO:0040029)|regulation of inflammatory response (GO:0050727)|response to ionizing radiation (GO:0010212)|response to lipopolysaccharide (GO:0032496)|secretory granule organization (GO:0033363)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|microtubule (GO:0005874)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|stomach(1)	14		all_cancers(154;0.0293)|all_epithelial(191;0.128)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00897)|Epithelial(46;0.026)	Epithelial(152;0.19)		AGCGGGAGCCCCAAGTTTGCC	0.701																																					p.P461R		Atlas-SNP	.											.	MTA1	61	.	0			c.C1382G						.						28	23	25					14																	105931048		2196	4297	6493	SO:0001583	missense	9112	exon15			GGAGCCCCAAGTT	U35113	CCDS32169.1, CCDS55954.1	14q32.33	2013-01-25			ENSG00000182979	ENSG00000182979		"GATA zinc finger domain containing"	7410	protein-coding gene	gene with protein product		603526				8083195, 7607577	Standard	NM_004689		Approved		uc001yqx.3	Q13330	OTTHUMG00000150362	ENST00000331320.7:c.1382C>G	chr14.hg19:g.105931048C>G	ENSP00000333633:p.Pro461Arg	49.0	0.0		81.0	24.0	NM_004689	A5PLK4|Q86SW2|Q8NFI8|Q96GI8	Missense_Mutation	SNP	ENST00000331320.7	hg19	CCDS32169.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.829771	0.91036	.	.	ENSG00000182979	ENST00000414153;ENST00000331320;ENST00000406191;ENST00000405646;ENST00000434050	T;T;T;T	0.35048	1.35;1.33;1.35;1.36	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	T	0.60818	0.2298	M	0.77486	2.375	0.80722	D	1	D;B	0.67145	0.996;0.378	D;B	0.68621	0.959;0.127	T	0.63607	-0.6599	10	0.48119	T	0.1	-31.1175	16.8714	0.86041	0.0:1.0:0.0:0.0	.	253;461	Q59FW1;Q13330	.;MTA1_HUMAN	R	370;461;461;444;253	ENSP00000333633:P461R;ENSP00000385702:P461R;ENSP00000384180:P444R;ENSP00000394106:P253R	ENSP00000333633:P461R	P	+	2	0	MTA1	105002093	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	4.790000	0.62453	2.332000	0.79248	0.462000	0.41574	CCC	.	.		0.701	MTA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317849.15			G	105931048	C	G	105931048	3	3	324	1	0	0	0	0	1	0	0	0	9917	623	22	4	1440	4	MTA1	14	105931048	Missense_Mutation	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	70438859	105931048	1418492	110	45718										
TJP1	7082	hgsc.bcm.edu	37	chr15	30010589	30010589	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	cattgctggatcttcctcttCttcggtttgagttgggggtg	13	8	3	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr15:30010589C>A	ENST00000346128.6	-	21	4231	c.3757G>T	c.(3757-3759)Gaa>Taa	p.E1253*	TJP1_ENST00000356107.6_Nonsense_Mutation_p.E1253*|TJP1_ENST00000545208.2_Nonsense_Mutation_p.E1173*|TJP1_ENST00000400011.2_Nonsense_Mutation_p.E1177*	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	1253					apoptotic process (GO:0006915)|blastocyst formation (GO:0001825)|cell-cell junction assembly (GO:0007043)|cell-cell signaling involved in cell-cell junction organization (GO:1901350)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to glucose stimulus (GO:0071333)|hippo signaling (GO:0035329)|membrane organization (GO:0061024)|negative regulation of vascular permeability (GO:0043116)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to magnetism (GO:0071000)|sensory perception of sound (GO:0007605)	apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gap junction (GO:0005921)|intercalated disc (GO:0014704)|intercellular canaliculus (GO:0046581)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(4)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(1)	68		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)		TCTTCCTCTTCTTCGGTTTGA	0.473																																					p.E1253X	Melanoma(77;681 1843 6309 6570)	Atlas-SNP	.											.	TJP1	140	.	0			c.G3757T						.						111	108	109					15																	30010589		1998	4188	6186	SO:0001587	stop_gained	7082	exon21			CCTCTTCTTCGGT		CCDS42007.1, CCDS45199.1, CCDS73702.1	15q13	2012-07-12	2012-07-12		ENSG00000104067	ENSG00000104067			11827	protein-coding gene	gene with protein product	"zona occludens 1", "tight junction protein ZO-1"	601009				8825647	Standard	XM_005254616		Approved	ZO-1, MGC133289, DKFZp686M05161	uc001zcr.3	Q07157	OTTHUMG00000137397	ENST00000346128.6:c.3757G>T	chr15.hg19:g.30010589C>A	ENSP00000281537:p.Glu1253*	75.0	0.0		93.0	29.0	NM_003257	B4E3K1|Q2NKP3|Q4ZGJ6	Nonsense_Mutation	SNP	ENST00000346128.6	hg19	CCDS42007.1	.	.	.	.	.	.	.	.	.	.	C	41	9.080969	0.99059	.	.	ENSG00000104067	ENST00000346128;ENST00000400011;ENST00000545208;ENST00000400007;ENST00000356107	.	.	.	5.91	5.91	0.95273	.	0.411863	0.29106	N	0.013135	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	20.3057	0.98631	0.0:1.0:0.0:0.0	.	.	.	.	X	1253;1177;1253;1173;1173	.	ENSP00000281537:E1253X	E	-	1	0	TJP1	27797881	0.995000	0.38212	0.202000	0.23494	0.875000	0.50365	4.832000	0.62759	2.791000	0.96007	0.655000	0.94253	GAA	.	.		0.473	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257		A	30010589	C	A	30010589	4	1	324	1	0	0	0	0	0	1	0	0	15944	922	32	3	1521	3	TJP1	15	30010589	Nonsense_Mutation	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10		30010589	72520803	111	45719										
FBN1	2200	hgsc.bcm.edu	37	chr15	48764821	48764821	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	cggtatcctcctggtgcattGaggcactggccattgccaca	11	13	0	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr15:48764821G>A	ENST00000316623.5	-	35	4718	c.4263C>T	c.(4261-4263)ctC>ctT	p.L1421L		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	1421	EGF-like 24; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		CTGGTGCATTGAGGCACTGGC	0.542																																					p.L1421L		Atlas-SNP	.											.	FBN1	310	.	0			c.C4263T						.						133	123	127					15																	48764821		2198	4296	6494	SO:0001819	synonymous_variant	2200	exon35			TGCATTGAGGCAC	X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.4263C>T	chr15.hg19:g.48764821G>A		57.0	0.0		67.0	17.0	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Silent	SNP	ENST00000316623.5	hg19	CCDS32232.1																																																																																			.	.		0.542	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			A	48764821	G	A	48764821	2	1	324	1	0	0	0	0	0	0	0	1	5710	1277	45	3		3	FBN1	15	48764821	Silent	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10	18754232	48764821	53766571	112	45720										
PRTG	283659	hgsc.bcm.edu	37	chr15	55912922	55912922	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	actttttcttagagttgtttTtaattataggaccatagcta	6	5	1	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr15:55912922T>C	ENST00000389286.4	-	19	3184	c.3137A>G	c.(3136-3138)aAa>aGa	p.K1046R		NM_173814.4	NP_776175.2			protogenin											breast(1)|endometrium(6)|kidney(4)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)		AGAGTTGTTTTTAATTATAGG	0.333																																					p.K1046R		Atlas-SNP	.											.	PRTG	110	.	0			c.A3137G						.						57	57	57					15																	55912922		1785	4048	5833	SO:0001583	missense	283659	exon19			TTGTTTTTAATTA	AK098622	CCDS42040.1	15q21.3	2013-02-11	2010-06-24		ENSG00000166450	ENSG00000166450		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	26373	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 5"	613261	"protogenin homolog (Gallus gallus)"				Standard	NM_173814		Approved	FLJ25756, IGDCC5	uc002adg.3	Q2VWP7		ENST00000389286.4:c.3137A>G	chr15.hg19:g.55912922T>C	ENSP00000373937:p.Lys1046Arg	107.0	0.0		133.0	42.0	NM_173814		Missense_Mutation	SNP	ENST00000389286.4	hg19	CCDS42040.1	.	.	.	.	.	.	.	.	.	.	T	17.26	3.345095	0.61073	.	.	ENSG00000166450	ENST00000389286	T	0.51817	0.69	5.91	5.91	0.95273	.	0.366829	0.32204	N	0.006434	T	0.41971	0.1182	L	0.57536	1.79	0.80722	D	1	P	0.35328	0.495	B	0.27170	0.077	T	0.31081	-0.9956	10	0.20519	T	0.43	-24.7769	15.5264	0.75910	0.0:0.0:0.0:1.0	.	1046	Q2VWP7	PRTG_HUMAN	R	1046	ENSP00000373937:K1046R	ENSP00000373937:K1046R	K	-	2	0	PRTG	53700214	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.463000	0.53050	2.261000	0.74972	0.533000	0.62120	AAA	.	.		0.333	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814		C	55912922	T	C	55912922	3	2	324	1	0	0	0	0	1	0	0	0	12650	1841	64	2	323	2	PRTG	15	55912922	Missense_Mutation	SNP	T	TCGA-MI-A75I-01A-11D-A32G-10	7148101	55912922	46618470	113	45721										
RASGRF1	5923	hgsc.bcm.edu	37	chr15	79327481	79327481	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ctgactactcacccaggaccAgcgtgggccagctggagatg	13	13	1	2			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr15:79327481A>T	ENST00000419573.3	-	6	1224	c.950T>A	c.(949-951)cTg>cAg	p.L317Q	RASGRF1_ENST00000558480.2_Missense_Mutation_p.L317Q|RASGRF1_ENST00000560334.1_5'UTR	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	317	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						ACCCAGGACCAGCGTGGGCCA	0.567																																					p.L317Q		Atlas-SNP	.											.	RASGRF1	168	.	0			c.T950A						.						26	27	27					15																	79327481		2196	4293	6489	SO:0001583	missense	5923	exon6			AGGACCAGCGTGG	M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.950T>A	chr15.hg19:g.79327481A>T	ENSP00000405963:p.Leu317Gln	48.0	0.0		45.0	21.0	NM_001145648	F8VPA5|H0YKF2|J3KQP9|Q16027	Missense_Mutation	SNP	ENST00000419573.3	hg19	CCDS10309.1	.	.	.	.	.	.	.	.	.	.	A	19.39	3.817900	0.71028	.	.	ENSG00000058335	ENST00000419573;ENST00000394741	T	0.67523	-0.27	4.95	4.95	0.65309	Dbl homology (DH) domain (5);	0.000000	0.64402	D	0.000018	T	0.74703	0.3751	L	0.49699	1.58	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.999;0.999;0.998	T	0.70835	-0.4764	10	0.22109	T	0.4	.	12.6038	0.56511	1.0:0.0:0.0:0.0	.	317;317;317;317	A8K270;Q8IUU5;Q13972;F8VPA5	.;.;RGRF1_HUMAN;.	Q	317	ENSP00000405963:L317Q	ENSP00000378224:L317Q	L	-	2	0	RASGRF1	77114536	0.984000	0.35163	0.995000	0.50966	0.585000	0.36419	8.941000	0.92964	2.069000	0.61940	0.397000	0.26171	CTG	.	.		0.567	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891		T	79327481	A	T	79327481	3	4	324	1	0	0	0	0	1	0	0	0	13087	188	7	4	2963	4	RASGRF1	15	79327481	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	23414559	79327481	23203911	114	45722										
RASGRF1	5923	hgsc.bcm.edu	37	chr15	79339166	79339166	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	cggccatccgcagcgggcgcAggaaattgttgacaaggatg	15	10	0	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr15:79339166A>C	ENST00000419573.3	-	5	1074	c.800T>G	c.(799-801)cTg>cGg	p.L267R	RASGRF1_ENST00000558480.2_Missense_Mutation_p.L267R|RASGRF1_ENST00000560334.1_5'UTR	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	267	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						CAGCGGGCGCAGGAAATTGTT	0.587																																					p.L267R		Atlas-SNP	.											.	RASGRF1	168	.	0			c.T800G						.						135	108	117					15																	79339166		2196	4293	6489	SO:0001583	missense	5923	exon5			GGGCGCAGGAAAT	M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.800T>G	chr15.hg19:g.79339166A>C	ENSP00000405963:p.Leu267Arg	38.0	0.0		46.0	20.0	NM_001145648	F8VPA5|H0YKF2|J3KQP9|Q16027	Missense_Mutation	SNP	ENST00000419573.3	hg19	CCDS10309.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.020733	0.75275	.	.	ENSG00000058335	ENST00000419573;ENST00000394741	T	0.64991	-0.13	4.03	4.03	0.46877	Dbl homology (DH) domain (5);	0.000000	0.56097	D	0.000022	T	0.75722	0.3888	M	0.77820	2.39	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	T	0.74118	-0.3768	10	0.26408	T	0.33	.	10.9558	0.47356	1.0:0.0:0.0:0.0	.	267;267;267;267	A8K270;Q8IUU5;Q13972;F8VPA5	.;.;RGRF1_HUMAN;.	R	267	ENSP00000405963:L267R	ENSP00000378224:L267R	L	-	2	0	RASGRF1	77126221	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	8.873000	0.92357	1.684000	0.51022	0.533000	0.62120	CTG	.	.		0.587	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891		C	79339166	A	C	79339166	3	2	324	1	0	0	0	0	1	0	0	0	13087	188	7	5	3117	5	RASGRF1	15	79339166	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	11685	79339166	23192226	115	45723										
TM6SF1	53346	hgsc.bcm.edu	37	chr15	83795555	83795555	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	gccgattatatacgcaatttCaagagccctatctaaaggat	7	9	2	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr15:83795555C>T	ENST00000322019.9	+	8	1031	c.757C>T	c.(757-759)Caa>Taa	p.Q253*	TM6SF1_ENST00000565774.1_Intron|TM6SF1_ENST00000379386.4_Nonsense_Mutation_p.Q256*|TM6SF1_ENST00000379390.6_Intron			Q9BZW5	TM6S1_HUMAN	transmembrane 6 superfamily member 1	253						integral component of membrane (GO:0016021)				endometrium(1)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	15						TACGCAATTTCAAGAGCCCTA	0.318																																					p.Q253X		Atlas-SNP	.											.	TM6SF1	38	.	0			c.C757T						.						152	161	158					15																	83795555		2203	4300	6503	SO:0001587	stop_gained	53346	exon8			CAATTTCAAGAGC	AF255922	CCDS10323.1, CCDS45338.1	15q24-q26	2003-04-04			ENSG00000136404	ENSG00000136404			11860	protein-coding gene	gene with protein product		606562				11124529	Standard	NM_001144903		Approved		uc002bjp.3	Q9BZW5	OTTHUMG00000147365	ENST00000322019.9:c.757C>T	chr15.hg19:g.83795555C>T	ENSP00000317000:p.Gln253*	62.0	0.0		98.0	40.0	NM_023003	A8K7T5|H3BU56|Q4U0U5	Nonsense_Mutation	SNP	ENST00000322019.9	hg19	CCDS10323.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.936493	0.73442	.	.	ENSG00000136404	ENST00000322019;ENST00000379386	.	.	.	6.02	5.09	0.68999	.	0.244039	0.43579	D	0.000549	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-2.1509	17.1485	0.86772	0.0:0.8736:0.1264:0.0	.	.	.	.	X	253;256	.	ENSP00000317000:Q253X	Q	+	1	0	TM6SF1	81586559	1.000000	0.71417	0.963000	0.40424	0.477000	0.33069	3.733000	0.55029	1.522000	0.49001	0.655000	0.94253	CAA	.	.		0.318	TM6SF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000304009.1	NM_023003		T	83795555	C	T	83795555	4	4	324	1	0	0	0	0	0	1	0	0	15987	827	29	3	787	3	TM6SF1	15	83795555	Nonsense_Mutation	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	4456389	83795555	18735837	116	45724										
TSC2	7249	hgsc.bcm.edu	37	chr16	2122984	2122984	+	Splice_Site	DEL	G	G	-													0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	tacctggacaaaaccaaacaGgtaggaggtcagagcaggac					rs137854116|rs137854250		TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr16:2122984delG	ENST00000219476.3	+	21	2985	c.2355delG	c.(2353-2355)cag>ca	p.Q785fs	TSC2_ENST00000350773.4_Splice_Site_p.Q785fs|TSC2_ENST00000401874.2_Splice_Site_p.Q785fs|TSC2_ENST00000568454.1_Splice_Site_p.Q796fs|TSC2_ENST00000439673.2_Splice_Site_p.Q748fs|TSC2_ENST00000382538.6_Splice_Site_p.Q736fs|TSC2_ENST00000353929.4_Splice_Site_p.Q785fs	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	785					acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				AAACCAAACAGGTAGGAGGTC	0.547			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.Q785fs		Atlas-Indel,Pindel	.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"E, O"	.	TSC2	364	.	0			c.2354delA						.						46	44	45					16																	2122984		2198	4300	6498	SO:0001630	splice_region_variant	7249	exon21	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	.	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 160"	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.2355+1G>-	chr16.hg19:g.2122984delG		35.0	0.0		36.0	15.0	NM_001114382	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Frame_Shift_Del	DEL	ENST00000219476.3	hg19	CCDS10458.1																																																																																			.	.		0.547	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548	Frame_Shift_Del	-	2122984	G	-	2122984	8	5	324	1	0	1	0	1	0	0	1	0	16621	1014	35	0	2433	0	TSC2	16	2122984	Splice_Site	DEL	G	TCGA-MI-A75I-01A-11D-A32G-10		2122984	88231769	117	45725										
ACSM2B	348158	hgsc.bcm.edu	37	chr16	20554485	20554485	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	gttaatgatatcatctgcccGtcccataaactggaaatacc	6	11	2	1	rs143500332		TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr16:20554485G>A	ENST00000329697.6	-	11	1549	c.1381C>T	c.(1381-1383)Cgg>Tgg	p.R461W	ACSM2B_ENST00000565322.1_Missense_Mutation_p.R382W|ACSM2B_ENST00000565232.1_Missense_Mutation_p.R461W|ACSM2B_ENST00000567288.1_5'Flank|ACSM2B_ENST00000567001.1_Missense_Mutation_p.R461W	NM_001105069.1	NP_001098539.1	Q68CK6	ACS2B_HUMAN	acyl-CoA synthetase medium-chain family member 2B	461					fatty acid metabolic process (GO:0006631)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(4)|lung(33)|ovary(1)|prostate(1)|skin(5)	57						TCATCTGCCCGTCCCATAAAC	0.502																																					p.R461W		Atlas-SNP	.											.	ACSM2B	121	.	0			c.C1381T						.	G	TRP/ARG,TRP/ARG	1,4399	2.1+/-5.4	0,1,2199	337	355	349		1381,1381	-0.7	0	16	dbSNP_134	349	1,8597	1.2+/-3.3	0,1,4298	no	missense,missense	ACSM2B	NM_001105069.1,NM_182617.3	101,101	0,2,6497	AA,AG,GG		0.0116,0.0227,0.0154	probably-damaging,probably-damaging	461/578,461/578	20554485	2,12996	2200	4299	6499	SO:0001583	missense	348158	exon12			CTGCCCGTCCCAT	AY160217	CCDS10586.1	16p12.3	2014-08-08	2007-06-20	2007-06-20	ENSG00000066813	ENSG00000066813		"Acyl-CoA synthetase family"	30931	protein-coding gene	gene with protein product	"xenobiotic/medium chain fatty acid:CoA ligase"	614359	"acyl-CoA synthetase medium-chain family member 2"	ACSM2		12616642	Standard	NM_182617		Approved	HXMA, HYST1046	uc002dhk.4	Q68CK6	OTTHUMG00000131555	ENST00000329697.6:c.1381C>T	chr16.hg19:g.20554485G>A	ENSP00000327453:p.Arg461Trp	263.0	0.0		155.0	47.0	NM_182617	Q86YT1	Missense_Mutation	SNP	ENST00000329697.6	hg19	CCDS10586.1	.	.	.	.	.	.	.	.	.	.	G	10.98	1.504327	0.26949	2.27E-4	1.16E-4	ENSG00000066813	ENST00000329697	D	0.83163	-1.69	3.1	-0.684	0.11331	AMP-dependent synthetase/ligase (1);	0.200461	0.23734	N	0.045098	D	0.91064	0.7188	H	0.94582	3.555	0.20489	N	0.999897	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.81750	-0.0790	10	0.87932	D	0	-7.7757	6.4757	0.22034	0.0:0.1372:0.2742:0.5886	.	461;461	A8K051;Q68CK6	.;ACS2B_HUMAN	W	461	ENSP00000327453:R461W	ENSP00000327453:R461W	R	-	1	2	ACSM2B	20461986	0.000000	0.05858	0.012000	0.15200	0.150000	0.21749	-0.157000	0.10085	0.137000	0.18759	0.508000	0.49915	CGG	.	G|1.000;A|0.000		0.502	ACSM2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254417.2	NM_182617		A	20554485	G	A	20554485	3	1	324	1	0	0	0	0	1	0	0	0	184	1144	40	1	368	1	ACSM2B	16	20554485	Missense_Mutation	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10	18431501	20554485	69800268	118	45726										
CDH11	1009	hgsc.bcm.edu	37	chr16	65025685	65025685	+	Frame_Shift_Del	DEL	G	G	-													0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	acttactctgcggaaactttGgtgggttgtcattgacatcg							TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr16:65025685delG	ENST00000268603.4	-	6	1412	c.797delC	c.(796-798)ccafs	p.P266fs	CDH11_ENST00000566827.1_Frame_Shift_Del_p.P140fs|CDH11_ENST00000394156.3_Frame_Shift_Del_p.P266fs	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	266	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		CGGAAACTTTGGTGGGTTGTC	0.517			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)																											p.P266fs		Atlas-INDEL	.		Dom	yes		16	16q22.1	1009	"cadherin 11, type 2, OB-cadherin (osteoblast)"		M	.	CDH11	260	.	0			c.798delA						.						269	189	216					16																	65025685		2203	4300	6503	SO:0001589	frameshift_variant	1009	exon6			.	D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"Cadherins / Major cadherins"	1750	protein-coding gene	gene with protein product	"OB-Cadherin"	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.797delC	chr16.hg19:g.65025685delG	ENSP00000268603:p.Pro266fs	78.0	0.0		50.0	22.0	NM_001797	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Frame_Shift_Del	DEL	ENST00000268603.4	hg19	CCDS10803.1																																																																																			.	.		0.517	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664		-	65025685	G	-	65025685	7	5	324	1	0	1	0	1	0	0	0	0	3099	1348	47	0	1625	0	CDH11	16	65025685	Frame_Shift_Del	DEL	G	TCGA-MI-A75I-01A-11D-A32G-10	44471200	65025685	25329068	119	45727										
CAMKK1	84254	hgsc.bcm.edu	37	chr17	3779538	3779538	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ttcccactgaagctctggccGgaatcagaaatggcctcggg	12	12	2	2	rs560406629	byFrequency	TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr17:3779538G>T	ENST00000348335.2	-	10	1123	c.975C>A	c.(973-975)tcC>tcA	p.S325S	CAMKK1_ENST00000381769.2_Silent_p.S352S|CAMKK1_ENST00000158166.5_Silent_p.S363S|CAMKK1_ENST00000381771.2_Silent_p.S363S	NM_032294.2	NP_115670.1	Q8N5S9	KKCC1_HUMAN	calcium/calmodulin-dependent protein kinase kinase 1, alpha	325	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				synaptic transmission (GO:0007268)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)	11				LUAD - Lung adenocarcinoma(2;2.11e-05)|Lung(3;0.0176)		AGCTCTGGCCGGAATCAGAAA	0.622																																					p.S363S		Atlas-SNP	.											.	CAMKK1	70	.	0			c.C1089A						.						48	44	46					17																	3779538		2203	4300	6503	SO:0001819	synonymous_variant	84254	exon11			CTGGCCGGAATCA	AL136576	CCDS11038.1, CCDS11039.1	17p13.3	2004-02-18			ENSG00000004660	ENSG00000004660			1469	protein-coding gene	gene with protein product		611411				11230166	Standard	NM_172207		Approved	DKFZp761M0423, CAMKKA, MGC34095	uc002fwt.3	Q8N5S9	OTTHUMG00000090725	ENST00000348335.2:c.975C>A	chr17.hg19:g.3779538G>T		47.0	0.0		38.0	23.0	NM_172207	Q9BQH3	Silent	SNP	ENST00000348335.2	hg19	CCDS11038.1																																																																																			.	.		0.622	CAMKK1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207456.1	NM_032294, NM_172206, NM_172207		T	3779538	G	T	3779538	2	4	324	1	0	0	0	0	0	0	0	1	2608	1103	39	1		1	CAMKK1	17	3779538	Silent	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10		3779538	77415672	120	45728										
KIF1C	10749	hgsc.bcm.edu	37	chr17	4905414	4905414	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	gtgctcagctatcctactctGtggaggtaagcccgggtctt	12	11	3	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr17:4905414G>A	ENST00000320785.5	+	6	781	c.424G>A	c.(424-426)Gtg>Atg	p.V142M		NM_006612.5	NP_006603.2	O43896	KIF1C_HUMAN	kinesin family member 1C	142	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(4)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|skin(1)|urinary_tract(3)	30						ATCCTACTCTGTGGAGGTAAG	0.577																																					p.V142M	Melanoma(96;1023 1447 10250 19259 33730)	Atlas-SNP	.											.	KIF1C	70	.	0			c.G424A						.						98	86	90					17																	4905414		2203	4300	6503	SO:0001583	missense	10749	exon6			TACTCTGTGGAGG	U91329	CCDS11065.1	17p13.2	2014-03-03			ENSG00000129250	ENSG00000129250		"Kinesins"	6317	protein-coding gene	gene with protein product		603060	"spastic ataxia 2 (autosomal recessive)"	SAX2		9685376, 24319291, 24482476	Standard	NM_006612		Approved	SPAX2, SPG58	uc002gan.2	O43896	OTTHUMG00000099451	ENST00000320785.5:c.424G>A	chr17.hg19:g.4905414G>A	ENSP00000320821:p.Val142Met	76.0	0.0		43.0	20.0	NM_006612	D3DTL6|O75186|Q5U618	Missense_Mutation	SNP	ENST00000320785.5	hg19	CCDS11065.1	.	.	.	.	.	.	.	.	.	.	G	32	5.161251	0.94727	.	.	ENSG00000129250	ENST00000320785	T	0.78364	-1.17	5.45	5.45	0.79879	Kinesin, motor domain (4);	.	.	.	.	D	0.89280	0.6670	M	0.84683	2.71	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	D	0.90129	0.4205	9	0.62326	D	0.03	.	17.1494	0.86774	0.0:0.0:1.0:0.0	.	142	O43896	KIF1C_HUMAN	M	142	ENSP00000320821:V142M	ENSP00000320821:V142M	V	+	1	0	KIF1C	4846138	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.625000	0.98406	2.740000	0.93945	0.561000	0.74099	GTG	.	.		0.577	KIF1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216916.1			A	4905414	G	A	4905414	3	1	324	1	0	0	0	0	1	0	0	0	8294	1377	48	3	438	3	KIF1C	17	4905414	Missense_Mutation	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10	1125876	4905414	76289796	121	45729										
TP53	7157	hgsc.bcm.edu	37	chr17	7578457	7578457	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	gcttgtagatggccatggcgCggacgcgggtgccgggcggg	21	10	0	1	rs587782144		TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr17:7578457C>T	ENST00000269305.4	-	5	662	c.473G>A	c.(472-474)cGc>cAc	p.R158H	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.R158H|TP53_ENST00000413465.2_Missense_Mutation_p.R158H|TP53_ENST00000445888.2_Missense_Mutation_p.R158H|TP53_ENST00000455263.2_Missense_Mutation_p.R158H|TP53_ENST00000420246.2_Missense_Mutation_p.R158H	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	158	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		R -> C (in sporadic cancers; somatic mutation).|R -> F (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in a sporadic cancer; somatic mutation).|R -> S (in sporadic cancers; somatic mutation).|R -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R158L(77)|p.R158H(74)|p.R158P(9)|p.R65L(8)|p.0?(8)|p.R26L(8)|p.R158fs(6)|p.R158fs*11(6)|p.R65H(5)|p.R26H(5)|p.R158_A159insX(4)|p.R65fs(2)|p.R158_A159delRA(2)|p.R156_I162delRVRAMAI(2)|p.V157fs*9(2)|p.P153fs*22(2)|p.R26fs(2)|p.V157fs*22(2)|p.V157_C176del20(1)|p.R156_A161delRVRAMA(1)|p.R158F(1)|p.P151_V173del23(1)|p.R156_R158delRVR(1)|p.R156fs*18(1)|p.R26fs*11(1)|p.R156_A161del(1)|p.V157_M160delVRAM(1)|p.V157_R158delVR(1)|p.S149fs*72(1)|p.A159fs*21(1)|p.T155_A161delTRVRAMA(1)|p.G154fs*22(1)|p.R65fs*11(1)|p.R156fs*20(1)|p.R158C(1)|p.V157_I162delVRAMAI(1)|p.V157fs*21(1)|p.R158fs*8(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGCCATGGCGCGGACGCGGGT	0.627		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.R158H	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,adenocarcinoma,0,2	TP53	33396	.	244	Substitution - Missense(188)|Deletion - Frameshift(19)|Deletion - In frame(13)|Complex(10)|Whole gene deletion(8)|Insertion - In frame(4)|Complex - frameshift(2)	lung(78)|central_nervous_system(33)|oesophagus(20)|haematopoietic_and_lymphoid_tissue(19)|large_intestine(18)|upper_aerodigestive_tract(12)|stomach(12)|urinary_tract(9)|prostate(7)|kidney(6)|liver(6)|breast(5)|bone(4)|soft_tissue(3)|ovary(3)|pancreas(3)|thyroid(2)|biliary_tract(2)|vulva(1)|thymus(1)	c.G473A	GRCh37	CM994513	TP53	M		.						49	51	50					17																	7578457		2203	4300	6503	SO:0001583	missense	7157	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	ATGGCGCGGACGC	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.473G>A	chr17.hg19:g.7578457C>T	ENSP00000269305:p.Arg158His	60.0	1.0		41.0	18.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	13.67	2.306299	0.40795	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793	D;D;D;D;D;D;D;D;D	0.99868	-7.32;-7.32;-7.32;-7.32;-7.32;-7.32;-7.32;-7.32;-7.32	5.59	4.63	0.57726	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.110116	0.64402	D	0.000010	D	0.99809	0.9917	M	0.77486	2.375	0.58432	D	0.999999	D;P;D;D;P;P;D	0.89917	0.998;0.631;0.984;0.982;0.831;0.48;1.0	P;B;P;P;P;B;D	0.97110	0.907;0.274;0.76;0.751;0.516;0.242;1.0	D	0.96738	0.9544	10	0.87932	D	0	-10.4795	12.6491	0.56751	0.0:0.9196:0.0:0.0804	.	119;158;158;65;158;158;158	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	H	158;158;158;158;158;158;147;65;26;65;26;158	ENSP00000410739:R158H;ENSP00000352610:R158H;ENSP00000269305:R158H;ENSP00000398846:R158H;ENSP00000391127:R158H;ENSP00000391478:R158H;ENSP00000425104:R26H;ENSP00000423862:R65H;ENSP00000424104:R158H	ENSP00000269305:R158H	R	-	2	0	TP53	7519182	1.000000	0.71417	0.034000	0.17996	0.175000	0.22909	7.775000	0.85489	1.514000	0.48869	-0.140000	0.14226	CGC	.	.		0.627	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7578457	C	T	7578457	3	4	324	1	0	0	0	0	1	0	0	0	16396	768	27	1	825	1	TP53	17	7578457	Missense_Mutation	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	2673043	7578457	73616753	122	45730										
MYO18A	399687	hgsc.bcm.edu	37	chr17	27420004	27420004	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	cagccgcttctctgactcaaAgtcccgccggttcacctggg	10	16	3	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr17:27420004A>C	ENST00000527372.1	-	33	5122	c.4942T>G	c.(4942-4944)Ttt>Gtt	p.F1648V	MYO18A_ENST00000354329.4_Missense_Mutation_p.F1648V|MYO18A_ENST00000533112.1_Missense_Mutation_p.F1611V|TIAF1_ENST00000408971.2_5'Flank|MYO18A_ENST00000529578.1_5'Flank|MYO18A_ENST00000531253.1_Missense_Mutation_p.F1648V	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	1648					actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			TCTGACTCAAAGTCCCGCCGG	0.627																																					p.F1648V	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-SNP	.											.	MYO18A	217	.	0			c.T4942G						.						37	46	43					17																	27420004		2066	4201	6267	SO:0001583	missense	399687	exon33			ACTCAAAGTCCCG	D86970	CCDS45641.1, CCDS45642.1	17q11.2	2011-09-27			ENSG00000196535	ENSG00000196535		"Myosins / Myosin superfamily : Class XVIII"	31104	protein-coding gene	gene with protein product		610067				12761286	Standard	NM_078471		Approved	KIAA0216, MysPDZ	uc002hdt.1	Q92614	OTTHUMG00000166360	ENST00000527372.1:c.4942T>G	chr17.hg19:g.27420004A>C	ENSP00000437073:p.Phe1648Val	37.0	0.0		36.0	9.0	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Missense_Mutation	SNP	ENST00000527372.1	hg19	CCDS45642.1	.	.	.	.	.	.	.	.	.	.	a	10.11	1.261465	0.23051	.	.	ENSG00000196535	ENST00000354329;ENST00000359450;ENST00000533112;ENST00000531253;ENST00000527372;ENST00000529799;ENST00000540575;ENST00000458428	T;D;T;T	0.87729	-1.06;-2.29;-1.06;-1.06	4.57	2.27	0.28462	Myosin tail (1);	0.443166	0.26432	N	0.024411	T	0.69566	0.3125	N	0.10645	0.015	0.31133	N	0.707455	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.0;0.0	T	0.59075	-0.7522	10	0.19147	T	0.46	.	7.2518	0.26154	0.777:0.1456:0.0775:0.0	.	1251;1611;1648;1648	F8W6Y3;Q92614-3;Q92614-4;Q92614	.;.;.;MY18A_HUMAN	V	1648;1611;1611;1648;1648;544;544;1251	ENSP00000346291:F1648V;ENSP00000435932:F1611V;ENSP00000434228:F1648V;ENSP00000437073:F1648V	ENSP00000346291:F1648V	F	-	1	0	MYO18A	24444130	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	1.356000	0.34079	0.245000	0.21373	0.378000	0.23410	TTT	.	.		0.627	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471		C	27420004	A	C	27420004	3	2	324	1	0	0	0	0	1	0	0	0	10074	72	3	5	1262	5	MYO18A	17	27420004	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	19841547	27420004	53775206	123	45731										
LRRC37B	114659	hgsc.bcm.edu	37	chr17	30348372	30348372	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	cctgctcccccagcagccccGggggactttgattacctggg	12	16	0	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr17:30348372G>T	ENST00000341671.7	+	1	212	c.207G>T	c.(205-207)ccG>ccT	p.P69P	LRRC37B_ENST00000584368.1_Silent_p.P81P|LRRC37B_ENST00000394713.3_Silent_p.P69P|LRRC37B_ENST00000543378.2_Intron|LRRC37B_ENST00000327564.7_Silent_p.P96P	NM_052888.2	NP_443120.2	Q96QE4	LR37B_HUMAN	leucine rich repeat containing 37B	69						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)		p.P69P(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	29		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.111)|Ovarian(249;0.182)|Breast(31;0.244)				CAGCAGCCCCGGGGGACTTTG	0.592																																					p.P69P		Atlas-SNP	.											.	LRRC37B	67	.	1	Substitution - coding silent(1)	lung(1)	c.G207T						.						51	62	58					17																	30348372		2203	4298	6501	SO:0001819	synonymous_variant	114659	exon1			AGCCCCGGGGGAC	AJ314647	CCDS32609.1	17q11.2	2006-11-29		2005-08-09	ENSG00000185158	ENSG00000185158			29070	protein-coding gene	gene with protein product	"KIAA0563-related"					11468690, 10843809	Standard	NM_052888		Approved		uc002hgu.3	Q96QE4	OTTHUMG00000132785	ENST00000341671.7:c.207G>T	chr17.hg19:g.30348372G>T		67.0	0.0		87.0	6.0	NM_052888	Q17RC9|Q5YKG6	Silent	SNP	ENST00000341671.7	hg19	CCDS32609.1																																																																																			.	.		0.592	LRRC37B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446508.1	NM_052888		T	30348372	G	T	30348372	2	4	324	1	0	0	0	0	0	0	0	1	9003	1103	39	1		1	LRRC37B	17	30348372	Silent	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10	2928368	30348372	50846838	124	45732										
HOXB7	3217	hgsc.bcm.edu	37	chr17	46685380	46685380	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ccgccgccgcgtcaggtagcGattgtagtgaaattctttct	11	11	3	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr17:46685380G>A	ENST00000239165.7	-	2	576	c.478C>T	c.(478-480)Cgc>Tgc	p.R160C	HOXB-AS3_ENST00000494420.1_RNA|HOXB-AS3_ENST00000466037.2_RNA|HOXB-AS3_ENST00000491264.1_RNA|HOXB-AS3_ENST00000467155.2_RNA|HOXB-AS3_ENST00000487849.3_RNA|HOXB7_ENST00000567101.2_5'UTR	NM_004502.3	NP_004493.3	P09629	HXB7_HUMAN	homeobox B7	160					anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|multicellular organismal development (GO:0007275)|myeloid cell differentiation (GO:0030099)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R160C(1)		NS(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	8						GTCAGGTAGCGATTGTAGTGA	0.557																																					p.R160C		Atlas-SNP	.											HOXB7,colon,carcinoma,0,1	HOXB7	15	.	1	Substitution - Missense(1)	large_intestine(1)	c.C478T						.						92	92	92					17																	46685380		2203	4300	6503	SO:0001583	missense	3217	exon2			GGTAGCGATTGTA		CCDS11532.1	17q21.32	2013-05-22	2005-12-22					"Homeoboxes / ANTP class : HOXL subclass"	5118	protein-coding gene	gene with protein product		142962	"homeo box B7"	HOX2, HOX2C		1973146, 1358459	Standard	NM_004502		Approved		uc002inv.3	P09629	OTTHUMG00000170231	ENST00000239165.7:c.478C>T	chr17.hg19:g.46685380G>A	ENSP00000239165:p.Arg160Cys	66.0	0.0		105.0	24.0	NM_004502	A8K3N8|Q15957|Q53FN3|Q96BQ6	Missense_Mutation	SNP	ENST00000239165.7	hg19	CCDS11532.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.137468	0.77775	.	.	ENSG00000120087	ENST00000239165	D	0.96745	-4.11	4.58	4.58	0.56647	Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.98425	0.9476	M	0.91818	3.245	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	D	0.99671	1.0996	10	0.87932	D	0	.	17.1969	0.86895	0.0:0.0:1.0:0.0	.	160	P09629	HXB7_HUMAN	C	160	ENSP00000239165:R160C	ENSP00000239165:R160C	R	-	1	0	HOXB7	44040379	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	4.496000	0.60360	2.357000	0.79964	0.563000	0.77884	CGC	.	.		0.557	HOXB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358097.3			A	46685380	G	A	46685380	3	1	324	1	0	0	0	0	1	0	0	0	7315	1058	37	1	179	1	HOXB7	17	46685380	Missense_Mutation	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10	16337008	46685380	34509830	125	45733										
MPO	4353	hgsc.bcm.edu	37	chr17	56348028	56348028	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	acctggcctctaggaggcttCcctccaggaagccaggttca	11	14	2	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr17:56348028C>G	ENST00000225275.3	-	12	2403	c.2227G>C	c.(2227-2229)Gaa>Caa	p.E743Q	MPO_ENST00000340482.3_Missense_Mutation_p.E775Q	NM_000250.1	NP_000241.1	P05164	PERM_HUMAN	myeloperoxidase	743					aging (GO:0007568)|defense response (GO:0006952)|defense response to fungus (GO:0050832)|hydrogen peroxide catabolic process (GO:0042744)|hypochlorous acid biosynthetic process (GO:0002149)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of apoptotic process (GO:0043066)|negative regulation of growth of symbiont in host (GO:0044130)|oxidation-reduction process (GO:0055114)|removal of superoxide radicals (GO:0019430)|respiratory burst involved in defense response (GO:0002679)|response to food (GO:0032094)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|response to oxidative stress (GO:0006979)|response to yeast (GO:0001878)	azurophil granule (GO:0042582)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|secretory granule (GO:0030141)	chromatin binding (GO:0003682)|heme binding (GO:0020037)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(13)|ovary(2)|pancreas(1)|skin(4)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	46					Aminosalicylic Acid(DB00233)|Bivalirudin(DB00006)|Calcipotriol(DB02300)|Carboplatin(DB00958)|Cefaclor(DB00833)|Cefdinir(DB00535)|Cisplatin(DB00515)|Cysteamine(DB00847)|Dapsone(DB00250)|Enoxaparin(DB01225)|Human Serum Albumin(DB00062)|L-Carnitine(DB00583)|Melatonin(DB01065)|Mesalazine(DB00244)|Nabumetone(DB00461)|Octreotide(DB00104)|Oxaliplatin(DB00526)|Propylthiouracil(DB00550)|Ticlopidine(DB00208)|Tolmetin(DB00500)	TAGGAGGCTTCCCTCCAGGAA	0.552																																					p.E743Q		Atlas-SNP	.											.	MPO	114	.	0			c.G2227C						.						82	72	75					17																	56348028		2203	4300	6503	SO:0001583	missense	4353	exon12			AGGCTTCCCTCCA		CCDS11604.1	17q21.3-q23	2014-09-17				ENSG00000005381	1.11.1.7		7218	protein-coding gene	gene with protein product		606989					Standard	NM_000250		Approved		uc002ivu.1	P05164		ENST00000225275.3:c.2227G>C	chr17.hg19:g.56348028C>G	ENSP00000225275:p.Glu743Gln	80.0	0.0		104.0	23.0	NM_000250	A1L4B8|Q14862|Q4PJH5|Q9UCL7	Missense_Mutation	SNP	ENST00000225275.3	hg19	CCDS11604.1	.	.	.	.	.	.	.	.	.	.	C	13.61	2.289674	0.40494	.	.	ENSG00000005381	ENST00000340482;ENST00000225275	T;T	0.76448	-1.02;-1.02	5.46	-4.67	0.03319	.	0.942914	0.08962	N	0.868576	T	0.72003	0.3407	M	0.75777	2.31	0.21256	N	0.999746	B	0.02656	0.0	B	0.01281	0.0	T	0.63120	-0.6708	10	0.62326	D	0.03	-0.4993	7.4074	0.26998	0.0:0.244:0.4089:0.3471	.	743	P05164	PERM_HUMAN	Q	775;743	ENSP00000344419:E775Q;ENSP00000225275:E743Q	ENSP00000225275:E743Q	E	-	1	0	MPO	53703027	0.002000	0.14202	0.011000	0.14972	0.063000	0.16089	-0.074000	0.11450	-0.708000	0.05015	-0.150000	0.13652	GAA	.	.		0.552	MPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443971.1			G	56348028	C	G	56348028	3	3	324	1	0	0	0	0	1	0	0	0	9741	864	30	4	14	4	MPO	17	56348028	Missense_Mutation	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	9662648	56348028	24847182	126	45734										
TBX2	6909	hgsc.bcm.edu	37	chr17	59485645	59485645	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	agcactagcctcctcaccacCgggctggcctctgagggctc	11	17	2	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr17:59485645C>T	ENST00000240328.3	+	7	2198	c.1917C>T	c.(1915-1917)acC>acT	p.T639T	RP11-332H18.4_ENST00000592009.1_RNA	NM_005994.3	NP_005985.3	Q13207	TBX2_HUMAN	T-box 2	639					aorta morphogenesis (GO:0035909)|atrioventricular canal development (GO:0036302)|cardiac muscle tissue development (GO:0048738)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|developmental growth involved in morphogenesis (GO:0060560)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|endocardial cushion morphogenesis (GO:0003203)|mammary placode formation (GO:0060596)|muscle cell fate determination (GO:0007521)|negative regulation of cardiac chamber formation (GO:1901211)|negative regulation of heart looping (GO:1901208)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|outflow tract septum morphogenesis (GO:0003148)|palate development (GO:0060021)|pharynx development (GO:0060465)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|lung(7)|ovary(1)	9						TCCTCACCACCGGGCTGGCCT	0.697																																					p.T639T	GBM(3;187 253 11467 14965 23079)	Atlas-SNP	.											.	TBX2	30	.	0			c.C1917T						.						23	20	21					17																	59485645		2193	4296	6489	SO:0001819	synonymous_variant	6909	exon7			CACCACCGGGCTG	AB209378	CCDS11627.2	17q23.2	2012-01-23			ENSG00000121068	ENSG00000121068		"T-boxes"	11597	protein-coding gene	gene with protein product		600747				8530034	Standard	NM_005994		Approved		uc010wox.2	Q13207	OTTHUMG00000156986	ENST00000240328.3:c.1917C>T	chr17.hg19:g.59485645C>T		96.0	0.0		187.0	54.0	NM_005994	Q16424|Q7Z647	Silent	SNP	ENST00000240328.3	hg19	CCDS11627.2																																																																																			.	.		0.697	TBX2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346977.2	NM_005994		T	59485645	C	T	59485645	2	4	324	1	0	0	0	0	0	0	0	1	15670	639	23	1		1	TBX2	17	59485645	Silent	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	3137617	59485645	21709565	127	45735										
FASN	2194	hgsc.bcm.edu	37	chr17	80040839	80040839	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	acgagcttctgcaccccacgCtgtatcagccactgcgccaa	8	17	2	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr17:80040839C>T	ENST00000306749.2	-	33	5936	c.5718G>A	c.(5716-5718)caG>caA	p.Q1906Q	FASN_ENST00000579758.1_5'UTR	NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	1906	Beta-ketoacyl reductase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	GCACCCCACGCTGTATCAGCC	0.647																																					p.Q1906Q	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.G5718A						.						85	71	75					17																	80040839		2200	4298	6498	SO:0001819	synonymous_variant	2194	exon33			CCCACGCTGTATC	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.5718G>A	chr17.hg19:g.80040839C>T		40.0	0.0		68.0	21.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Silent	SNP	ENST00000306749.2	hg19	CCDS11801.1																																																																																			.	.		0.647	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		T	80040839	C	T	80040839	2	4	324	1	0	0	0	0	0	0	0	1	5691	796	28	3		3	FASN	17	80040839	Silent	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	20555194	80040839	1154371	128	45736										
TBCD	6904	hgsc.bcm.edu	37	chr17	80851463	80851463	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	tgatattttgaccacagctgActattttgccgtcggtaaca	8	9	0	3			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr17:80851463A>T	ENST00000355528.4	+	17	1734	c.1604A>T	c.(1603-1605)gAc>gTc	p.D535V	TBCD_ENST00000397466.2_Missense_Mutation_p.D149V|TBCD_ENST00000539345.2_Missense_Mutation_p.D535V	NM_005993.4	NP_005984.3	Q9BTW9	TBCD_HUMAN	tubulin folding cofactor D	535					'de novo' posttranslational protein folding (GO:0051084)|adherens junction assembly (GO:0034333)|cellular protein metabolic process (GO:0044267)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of microtubule polymerization (GO:0031115)|positive regulation of GTPase activity (GO:0043547)|post-chaperonin tubulin folding pathway (GO:0007023)|protein folding (GO:0006457)|tight junction assembly (GO:0070830)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|tight junction (GO:0005923)	beta-tubulin binding (GO:0048487)|chaperone binding (GO:0051087)|GTPase activator activity (GO:0005096)					Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)			ACCACAGCTGACTATTTTGCC	0.358																																					p.D535V		Atlas-SNP	.											.	TBCD	94	.	0			c.A1604T						.						118	102	107					17																	80851463		1852	4091	5943	SO:0001583	missense	6904	exon17			CAGCTGACTATTT	BC003094	CCDS45818.1	17q25.3	2006-11-21	2006-11-21			ENSG00000141556			11581	protein-coding gene	gene with protein product		604649	"tubulin-specific chaperone d"				Standard	NM_005993		Approved		uc002kfz.3	Q9BTW9		ENST00000355528.4:c.1604A>T	chr17.hg19:g.80851463A>T	ENSP00000347719:p.Asp535Val	312.0	0.0		430.0	231.0	NM_005993	O95458|Q7L8K1|Q8IXP6|Q8NAX0|Q8WYH4|Q96E74|Q9UF82|Q9UG46|Q9Y2J3	Missense_Mutation	SNP	ENST00000355528.4	hg19	CCDS45818.1	.	.	.	.	.	.	.	.	.	.	A	11.04	1.522378	0.27211	.	.	ENSG00000141556	ENST00000355528;ENST00000334614;ENST00000397466;ENST00000536182	T;T	0.66280	-0.2;-0.2	4.64	4.64	0.57946	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.81221	0.4777	M	0.90870	3.155	0.80722	D	1	P;P;P	0.48230	0.576;0.701;0.907	B;B;P	0.62491	0.194;0.356;0.903	D	0.84864	0.0821	9	.	.	.	.	13.2094	0.59815	1.0:0.0:0.0:0.0	.	535;535;535	Q9BTW9;Q9BTW9-4;F5H8C7	TBCD_HUMAN;.;.	V	535;286;149;535	ENSP00000347719:D535V;ENSP00000380608:D149V	.	D	+	2	0	TBCD	78444752	1.000000	0.71417	0.984000	0.44739	0.062000	0.15995	7.034000	0.76511	1.710000	0.51325	0.421000	0.28195	GAC	.	.		0.358	TBCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439415.1	NM_005993		T	80851463	A	T	80851463	3	4	324	1	0	0	0	0	1	0	0	0	15648	275	10	4	1670	4	TBCD	17	80851463	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	810624	80851463	343747	129	45737										
LAMA1	284217	hgsc.bcm.edu	37	chr18	7033066	7033066	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	caggtcgatggcattagagcTggctatgtccagagagacgg	15	8	0	3			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr18:7033066T>A	ENST00000389658.3	-	15	2173	c.2080A>T	c.(2080-2082)Agc>Tgc	p.S694C		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	694	Laminin IV type A 1. {ECO:0000255|PROSITE-ProRule:PRU00458}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				GCATTAGAGCTGGCTATGTCC	0.517																																					p.S694C		Atlas-SNP	.											.	LAMA1	458	.	0			c.A2080T						.						101	75	84					18																	7033066		2203	4300	6503	SO:0001583	missense	284217	exon15			TAGAGCTGGCTAT	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.2080A>T	chr18.hg19:g.7033066T>A	ENSP00000374309:p.Ser694Cys	51.0	0.0		36.0	11.0	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	hg19	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	T	13.22	2.170955	0.38315	.	.	ENSG00000101680	ENST00000389658	T	0.37915	1.17	6.07	4.85	0.62838	Laminin B type IV (2);Laminin B, subgroup (1);	0.410765	0.26907	N	0.021900	T	0.50154	0.1599	M	0.64404	1.975	0.24761	N	0.992922	D	0.71674	0.998	P	0.62813	0.907	T	0.44667	-0.9313	10	0.56958	D	0.05	.	8.3534	0.32316	0.1308:0.0:0.1367:0.7325	.	694	P25391	LAMA1_HUMAN	C	694	ENSP00000374309:S694C	ENSP00000374309:S694C	S	-	1	0	LAMA1	7023066	0.027000	0.19231	0.300000	0.25030	0.085000	0.17905	1.467000	0.35321	2.326000	0.78906	0.533000	0.62120	AGC	.	.		0.517	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		A	7033066	T	A	7033066	3	1	324	1	0	0	0	0	1	0	0	0	8614	1580	55	4	7343	4	LAMA1	18	7033066	Missense_Mutation	SNP	T	TCGA-MI-A75I-01A-11D-A32G-10		7033066	71044182	130	45738										
TXNDC2	84203	hgsc.bcm.edu	37	chr18	9886946	9886946	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	caagtcctcagcaaaacccaTccagcccaagctgggcaata	7	15	1	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr18:9886946T>C	ENST00000306084.6	+	2	669	c.470T>C	c.(469-471)aTc>aCc	p.I157T	TXNDC2_ENST00000536353.2_Missense_Mutation_p.I90T|TXNDC2_ENST00000357775.5_Missense_Mutation_p.I90T	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN	thioredoxin domain containing 2 (spermatozoa)	157	22 X 15 AA approximate tandem repeat of Q-P-K-X-G-D-I-P-K-S-[PS]-E-[KE]-X-I.				cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|glycerol ether metabolic process (GO:0006662)|multicellular organismal development (GO:0007275)|oxidation-reduction process (GO:0055114)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)	nutrient reservoir activity (GO:0045735)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)|thioredoxin-disulfide reductase activity (GO:0004791)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|skin(7)|urinary_tract(1)	31						GCAAAACCCATCCAGCCCAAG	0.542																																					p.I157T		Atlas-SNP	.											.	TXNDC2	168	.	0			c.T470C						.						128	135	133					18																	9886946		2203	4300	6503	SO:0001583	missense	84203	exon2			AACCCATCCAGCC	AF080095	CCDS11846.1, CCDS42414.1	18p11.31-p11.2	2009-03-11	2009-03-11	2007-08-16	ENSG00000168454	ENSG00000168454			16470	protein-coding gene	gene with protein product	"sperm-specific thioredoxin 1"					11230166, 11399755	Standard	NM_001098529		Approved	SPTRX1	uc002koi.4	Q86VQ3	OTTHUMG00000131602	ENST00000306084.6:c.470T>C	chr18.hg19:g.9886946T>C	ENSP00000304908:p.Ile157Thr	139.0	0.0		140.0	55.0	NM_001098529	A5YM73|Q8N7U4|Q96RX3|Q9H0L8	Missense_Mutation	SNP	ENST00000306084.6	hg19	CCDS42414.1	.	.	.	.	.	.	.	.	.	.	t	2.155	-0.393672	0.04899	.	.	ENSG00000168454	ENST00000536353;ENST00000357775;ENST00000306084;ENST00000426718	T;T;T	0.55234	1.58;0.53;0.53	2.72	-5.45	0.02616	.	0.692875	0.11934	N	0.515413	T	0.37210	0.0995	L	0.33245	0.995	0.09310	N	1	P	0.51791	0.948	P	0.48063	0.565	T	0.23868	-1.0176	9	.	.	.	.	3.7672	0.08627	0.4109:0.3183:0.0:0.2708	.	157	Q86VQ3	TXND2_HUMAN	T	90;90;157;157	ENSP00000437393:I90T;ENSP00000350419:I90T;ENSP00000304908:I157T	.	I	+	2	0	TXNDC2	9876946	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.998000	0.01469	-1.801000	0.01245	-0.680000	0.03767	ATC	.	.		0.542	TXNDC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254487.1			C	9886946	T	C	9886946	3	2	324	1	0	0	0	0	1	0	0	0	16812	1435	50	2	476	2	TXNDC2	18	9886946	Missense_Mutation	SNP	T	TCGA-MI-A75I-01A-11D-A32G-10	2853880	9886946	68190302	131	45739										
C18orf34	374864	hgsc.bcm.edu	37	chr18	30554599	30554599	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	tgaagaggaccaccagtttgAagtgctcctgccacagtgtg	12	10	0	3			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr18:30554599A>T	ENST00000383096.3	-	22	2617	c.2435T>A	c.(2434-2436)tTc>tAc	p.F812Y	CCDC178_ENST00000579916.1_Missense_Mutation_p.F132Y|CCDC178_ENST00000300227.8_Missense_Mutation_p.F774Y|CCDC178_ENST00000406524.2_Missense_Mutation_p.F836Y|CCDC178_ENST00000579947.1_Missense_Mutation_p.F812Y|CCDC178_ENST00000581852.1_Missense_Mutation_p.F17Y|CCDC178_ENST00000403303.1_Missense_Mutation_p.F812Y|CCDC178_ENST00000583930.1_Missense_Mutation_p.F836Y|CCDC178_ENST00000402325.1_Missense_Mutation_p.F762Y			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178	812																	CACCAGTTTGAAGTGCTCCTG	0.498																																					p.F812Y		Atlas-SNP	.											.	.	.	.	0			c.T2435A						.						56	50	52					18																	30554599		2203	4300	6503	SO:0001583	missense	374864	exon21			AGTTTGAAGTGCT	AK126038	CCDS11906.1, CCDS42424.1	18q12.1	2012-10-15	2012-10-15	2012-10-15	ENSG00000166960	ENSG00000166960			29588	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 34"	C18orf34			Standard	NM_198995		Approved	FLJ44050	uc002kxn.2	Q5BJE1	OTTHUMG00000132279	ENST00000383096.3:c.2435T>A	chr18.hg19:g.30554599A>T	ENSP00000372576:p.Phe812Tyr	45.0	0.0		67.0	34.0	NM_001105528	A6NDC6|J3KS92|Q6ZP67|Q6ZU20	Missense_Mutation	SNP	ENST00000383096.3	hg19	CCDS42424.1	.	.	.	.	.	.	.	.	.	.	A	11.51	1.661105	0.29515	.	.	ENSG00000166960	ENST00000403303;ENST00000383096;ENST00000300227;ENST00000406524;ENST00000402325	T;T;T;T;T	0.26957	1.86;1.86;1.98;1.7;1.7	5.5	5.5	0.81552	.	.	.	.	.	T	0.36853	0.0982	L	0.43152	1.355	0.30875	N	0.732087	D;D;D;D;D;D	0.76494	0.999;0.996;0.999;0.999;0.999;0.999	D;P;D;D;D;D	0.67548	0.952;0.892;0.935;0.952;0.952;0.952	T	0.09862	-1.0655	9	0.08381	T	0.77	-10.9787	12.7018	0.57038	0.8629:0.1371:0.0:0.0	.	836;812;762;812;774;812	F8W7A7;A1L4G8;Q5BJE1-3;B5MD75;Q5BJE1-2;Q5BJE1	.;.;.;.;.;CR034_HUMAN	Y	812;812;774;836;762	ENSP00000385591:F812Y;ENSP00000372576:F812Y;ENSP00000300227:F774Y;ENSP00000385867:F836Y;ENSP00000385234:F762Y	ENSP00000300227:F774Y	F	-	2	0	C18orf34	28808597	1.000000	0.71417	0.990000	0.47175	0.968000	0.65278	5.669000	0.68081	2.084000	0.62774	0.460000	0.39030	TTC	.	.		0.498	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255373.2	NM_198995		T	30554599	A	T	30554599	3	4	324	1	0	0	0	0	1	0	0	0	1904	246	9	4	176	4	C18orf34	18	30554599	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	20667653	30554599	47522649	132	45740										
DIRAS1	148252	hgsc.bcm.edu	37	chr19	2717599	2717599	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	tggacaggcgctgcatggccGggaactggtggctgccggtg	19	10	0	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr19:2717599G>C	ENST00000323469.4	-	2	389	c.206C>G	c.(205-207)cCg>cGg	p.P69R	DIRAS1_ENST00000585334.1_Missense_Mutation_p.P69R	NM_145173.3	NP_660156.1	O95057	DIRA1_HUMAN	DIRAS family, GTP-binding RAS-like 1	69					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			kidney(1)|lung(2)|ovary(2)|prostate(1)	6				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTGCATGGCCGGGAACTGGTG	0.622																																					p.P69R		Atlas-SNP	.											DIRAS1,bladder,carcinoma,0,1	DIRAS1	26	.	0			c.C206G						.						77	63	68					19																	2717599		2203	4299	6502	SO:0001583	missense	148252	exon2			ATGGCCGGGAACT	BC030660	CCDS12092.1	19p13.3	2014-05-09				ENSG00000176490			19127	protein-coding gene	gene with protein product		607862				12107278	Standard	NM_145173		Approved	Di-Ras1, GBTS1, RIG	uc002lwf.3	O95057		ENST00000323469.4:c.206C>G	chr19.hg19:g.2717599G>C	ENSP00000325836:p.Pro69Arg	31.0	0.0		38.0	15.0	NM_145173		Missense_Mutation	SNP	ENST00000323469.4	hg19	CCDS12092.1	.	.	.	.	.	.	.	.	.	.	G	17.79	3.475625	0.63737	.	.	ENSG00000176490	ENST00000323469	T	0.74947	-0.89	4.07	4.07	0.47477	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.69106	0.3074	N	0.03268	-0.37	0.80722	D	1	D	0.67145	0.996	D	0.69307	0.963	T	0.76545	-0.2920	10	0.52906	T	0.07	.	13.7485	0.62890	0.0:0.0:1.0:0.0	.	69	O95057	DIRA1_HUMAN	R	69	ENSP00000325836:P69R	ENSP00000325836:P69R	P	-	2	0	DIRAS1	2668599	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.502000	0.97981	1.813000	0.52934	0.549000	0.68633	CCG	.	.		0.622	DIRAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451350.1			C	2717599	G	C	2717599	3	2	324	1	0	0	0	0	1	0	0	0	4532	1116	39	4	394	4	DIRAS1	19	2717599	Missense_Mutation	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10		2717599	56411384	133	45741										
ZNF266	10781	hgsc.bcm.edu	37	chr19	9525003	9525003	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	gtgagtttgtatacgcacagCaaggtctgtggagtgaataa	13	5	1	2			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr19:9525003C>T	ENST00000592904.1	-	5	2674	c.598G>A	c.(598-600)Gct>Act	p.A200T	ZNF266_ENST00000592292.1_Missense_Mutation_p.A200T|ZNF266_ENST00000588933.1_Missense_Mutation_p.A200T|ZNF266_ENST00000361451.2_Missense_Mutation_p.A200T|ZNF266_ENST00000361151.1_Missense_Mutation_p.A200T|ZNF266_ENST00000588221.1_Missense_Mutation_p.A200T|ZNF266_ENST00000590306.1_Missense_Mutation_p.A200T			Q14584	ZN266_HUMAN	zinc finger protein 266	200					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(2)|large_intestine(11)|lung(8)|ovary(1)|skin(2)|stomach(1)	28						ATACGCACAGCAAGGTCTGTG	0.398																																					p.A200T		Atlas-SNP	.											.	ZNF266	65	.	0			c.G598A						.						89	83	85					19																	9525003		2203	4300	6503	SO:0001583	missense	10781	exon11			GCACAGCAAGGTC	X78924	CCDS12213.1	19p13.2	2013-01-08				ENSG00000174652		"Zinc fingers, C2H2-type"	13059	protein-coding gene	gene with protein product		604751				7865130	Standard	NM_006631		Approved	HZF1	uc002mlo.4	Q14584		ENST00000592904.1:c.598G>A	chr19.hg19:g.9525003C>T	ENSP00000466714:p.Ala200Thr	67.0	0.0		73.0	25.0	NM_001271314	A0AV90|A4FU85|Q6IQ07|Q6U8A5|Q8IVG3|Q8WVX1|Q96SX9	Missense_Mutation	SNP	ENST00000592904.1	hg19	CCDS12213.1	.	.	.	.	.	.	.	.	.	.	C	11.38	1.623003	0.28889	.	.	ENSG00000174652	ENST00000361451;ENST00000361151	T;T	0.14516	2.5;2.5	2.91	-5.82	0.02333	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03136	0.0092	N	0.03304	-0.355	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.24512	-1.0158	9	0.02654	T	1	.	0.9292	0.01331	0.2737:0.1037:0.2726:0.3501	.	200	Q14584	ZN266_HUMAN	T	200	ENSP00000354680:A200T;ENSP00000355047:A200T	ENSP00000355047:A200T	A	-	1	0	ZNF266	9386003	0.000000	0.05858	0.000000	0.03702	0.058000	0.15608	-1.207000	0.03008	-4.054000	0.00078	-0.226000	0.12346	GCT	.	.		0.398	ZNF266-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449033.1			T	9525003	C	T	9525003	3	4	324	1	0	0	0	0	1	0	0	0	17820	710	25	3	1055	3	ZNF266	19	9525003	Missense_Mutation	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	6807404	9525003	49603980	134	45742										
ZNF653	115950	hgsc.bcm.edu	37	chr19	11598499	11598499	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ctgctgggttggagcacagcGgggtaccctgctcggccagg	17	12	0	0	rs377200586		TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr19:11598499G>A	ENST00000293771.5	-	4	915	c.779C>T	c.(778-780)cCg>cTg	p.P260L	CTC-398G3.6_ENST00000585656.1_Intron	NM_138783.3	NP_620138.2	Q96CK0	ZN653_HUMAN	zinc finger protein 653	260					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	17						GGAGCACAGCGGGGTACCCTG	0.672																																					p.P260L	Pancreas(83;980 1446 4542 6441 43352)	Atlas-SNP	.											.	ZNF653	48	.	0			c.C779T						.	G	LEU/PRO	0,4406		0,0,2203	45	45	45		779	3.4	0.1	19		45	1,8595		0,1,4297	no	missense	ZNF653	NM_138783.3	98	0,1,6500	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	260/616	11598499	1,13001	2203	4298	6501	SO:0001583	missense	115950	exon4			CACAGCGGGGTAC	AY072704	CCDS12261.1	19p13.2	2013-01-08						"Zinc fingers, C2H2-type"	25196	protein-coding gene	gene with protein product		611371				12477932	Standard	NM_138783		Approved	Zip67	uc002mrz.2	Q96CK0		ENST00000293771.5:c.779C>T	chr19.hg19:g.11598499G>A	ENSP00000293771:p.Pro260Leu	119.0	0.0		144.0	55.0	NM_138783	Q96AS7	Missense_Mutation	SNP	ENST00000293771.5	hg19	CCDS12261.1	.	.	.	.	.	.	.	.	.	.	G	6.224	0.409514	0.11812	0.0	1.16E-4	ENSG00000161914	ENST00000293771	T	0.10668	2.85	4.49	3.44	0.39384	.	0.850722	0.10371	N	0.682878	T	0.05364	0.0142	N	0.14661	0.345	0.09310	N	0.999992	P	0.43352	0.804	B	0.25614	0.062	T	0.29671	-1.0004	10	0.87932	D	0	-11.0558	9.5582	0.39353	0.0:0.1548:0.6852:0.16	.	260	Q96CK0	ZN653_HUMAN	L	260	ENSP00000293771:P260L	ENSP00000293771:P260L	P	-	2	0	ZNF653	11459499	0.098000	0.21812	0.079000	0.20413	0.227000	0.25037	1.649000	0.37281	1.002000	0.39104	-0.304000	0.09214	CCG	.	.		0.672	ZNF653-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458836.2	NM_138783		A	11598499	G	A	11598499	3	1	324	1	0	0	0	0	1	0	0	0	18081	1116	39	1	1092	1	ZNF653	19	11598499	Missense_Mutation	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10	2073496	11598499	47530484	135	45743										
CACNA1A	773	hgsc.bcm.edu	37	chr19	13365942	13365942	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	acgatggtgttgagggcgatCatggccatgatcgtgtactc	14	8	1	2			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr19:13365942C>T	ENST00000360228.5	-	29	4721	c.4722G>A	c.(4720-4722)atG>atA	p.M1574I	CACNA1A_ENST00000573710.2_Missense_Mutation_p.M1575I|CACNA1A_ENST00000574822.1_5'Flank	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	1575					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	TGAGGGCGATCATGGCCATGA	0.567																																					p.M1575I		Atlas-SNP	.											.	CACNA1A	715	.	0			c.G4725A						.						90	100	97					19																	13365942		2126	4241	6367	SO:0001583	missense	773	exon29			GGCGATCATGGCC	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.4722G>A	chr19.hg19:g.13365942C>T	ENSP00000353362:p.Met1574Ile	26.0	0.0		24.0	9.0	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	hg19	CCDS45998.1	.	.	.	.	.	.	.	.	.	.	C	14.65	2.599304	0.46318	.	.	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084;ENST00000445042	D	0.97279	-4.32	4.8	4.8	0.61643	.	0.111141	0.56097	D	0.000025	D	0.95306	0.8477	L	0.57536	1.79	0.46725	D	0.99917	P;P;B;B	0.40431	0.594;0.717;0.278;0.377	B;B;B;B	0.38985	0.15;0.287;0.057;0.103	D	0.95475	0.8555	10	0.72032	D	0.01	.	12.5949	0.56463	0.0:0.8325:0.1675:0.0	.	1575;1578;1574;1575	O00555;E9PD31;Q9NS88;E7EVF2	CAC1A_HUMAN;.;.;.	I	1574;1578;1575;1575;191	ENSP00000353362:M1574I	ENSP00000317661:M1575I	M	-	3	0	CACNA1A	13226942	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.778000	0.55371	2.227000	0.72691	0.650000	0.86243	ATG	.	.		0.567	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		T	13365942	C	T	13365942	3	4	324	1	0	0	0	0	1	0	0	0	2540	826	29	3	2976	3	CACNA1A	19	13365942	Missense_Mutation	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	1767443	13365942	45763041	136	45744										
CALR3	125972	hgsc.bcm.edu	37	chr19	16601349	16601349	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	tttgaagcgtgcagagatggCatagaatcggccattctgag	13	7	1	4			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr19:16601349C>T	ENST00000269881.3	-	3	288	c.226G>A	c.(226-228)Gcc>Acc	p.A76T	CTD-3222D19.2_ENST00000409035.1_Intron	NM_145046.4	NP_659483.2	Q96L12	CALR3_HUMAN	calreticulin 3	76	N-domain.				cell differentiation (GO:0030154)|protein folding (GO:0006457)|spermatogenesis (GO:0007283)	endoplasmic reticulum (GO:0005783)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|prostate(1)|skin(1)	15						GCAGAGATGGCATAGAATCGG	0.443																																					p.A76T		Atlas-SNP	.											.	CALR3	41	.	0			c.G226A						.						154	145	148					19																	16601349		2203	4300	6503	SO:0001583	missense	125972	exon3			AGATGGCATAGAA	AK058084	CCDS12344.1	19p13.11	2014-09-17				ENSG00000269058			20407	protein-coding gene	gene with protein product	"cancer/testis antigen 93", "calsperin"	611414				12384296	Standard	NM_145046		Approved	CRT2, FLJ25355, MGC26577, CT93	uc002ned.3	Q96L12		ENST00000269881.3:c.226G>A	chr19.hg19:g.16601349C>T	ENSP00000269881:p.Ala76Thr	93.0	0.0		92.0	30.0	NM_145046	D9N574|Q96LN3	Missense_Mutation	SNP	ENST00000269881.3	hg19	CCDS12344.1	.	.	.	.	.	.	.	.	.	.	C	35	5.558203	0.96514	.	.	ENSG00000141979	ENST00000269881	T	0.54675	0.56	5.79	5.79	0.91817	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.81814	0.4902	H	0.95328	3.655	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.86641	0.1892	10	0.87932	D	0	-38.5102	18.6591	0.91465	0.0:1.0:0.0:0.0	.	76	Q96L12	CALR3_HUMAN	T	76	ENSP00000269881:A76T	ENSP00000269881:A76T	A	-	1	0	CALR3	16462349	1.000000	0.71417	0.990000	0.47175	0.986000	0.74619	7.494000	0.81503	2.756000	0.94617	0.644000	0.83932	GCC	.	.		0.443	CALR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461089.1	NM_145046		T	16601349	C	T	16601349	3	4	324	1	0	0	0	0	1	0	0	0	2595	710	25	3	956	3	CALR3	19	16601349	Missense_Mutation	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	3235407	16601349	42527634	137	45745										
MAG	4099	hgsc.bcm.edu	37	chr19	35786342	35786342	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	tcacggcactgcctctgttcTggattatgatttcaggtaac	9	10	4	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr19:35786342T>C	ENST00000392213.3	+	3	190	c.31T>C	c.(31-33)Tgg>Cgg	p.W11R	MAG_ENST00000597035.1_Missense_Mutation_p.W11R|MAG_ENST00000361922.4_Missense_Mutation_p.W11R|MAG_ENST00000537831.2_Intron	NM_002361.3	NP_002352.1	P20916	MAG_HUMAN	myelin associated glycoprotein	11					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)|negative regulation of axonogenesis (GO:0050771)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of axonogenesis (GO:0050770)|substantia nigra development (GO:0021762)	integral component of membrane (GO:0016021)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)	carbohydrate binding (GO:0030246)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(10)|lung(11)|skin(2)|upper_aerodigestive_tract(2)	34	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)	Renal(1328;0.242)	Epithelial(14;3.14e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.5e-18)|all cancers(14;1.5e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			GCCTCTGTTCTGGATTATGAT	0.577																																					p.W11R		Atlas-SNP	.											.	MAG	172	.	0			c.T31C						.						222	218	219					19																	35786342		2203	4300	6503	SO:0001583	missense	4099	exon3			CTGTTCTGGATTA	M29273	CCDS12455.1, CCDS12456.1, CCDS56090.1	19q13.1	2013-01-29			ENSG00000105695	ENSG00000105695		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6783	protein-coding gene	gene with protein product	"sialic acid binding Ig-like lectin 4A"	159460		GMA		2476987, 8432525	Standard	NM_080600		Approved	SIGLEC4A, SIGLEC-4A, S-MAG	uc002nyy.2	P20916		ENST00000392213.3:c.31T>C	chr19.hg19:g.35786342T>C	ENSP00000376048:p.Trp11Arg	65.0	0.0		59.0	21.0	NM_080600	B7Z2E5|F5GYC0|Q567S4	Missense_Mutation	SNP	ENST00000392213.3	hg19	CCDS12455.1	.	.	.	.	.	.	.	.	.	.	T	18.98	3.737928	0.69304	.	.	ENSG00000105695	ENST00000262624;ENST00000361922;ENST00000392213	T;T	0.66460	-0.05;-0.21	5.7	5.7	0.88788	.	0.161847	0.40908	D	0.000989	T	0.77831	0.4189	M	0.61703	1.905	0.80722	D	1	D;D;D	0.71674	0.99;0.99;0.998	D;D;D	0.81914	0.969;0.969;0.995	T	0.76865	-0.2801	10	0.37606	T	0.19	.	12.3464	0.55124	0.0:0.0:0.0:1.0	.	48;11;11	Q59GD9;P20916;Q567S4	.;MAG_HUMAN;.	R	48;11;11	ENSP00000355234:W11R;ENSP00000376048:W11R	ENSP00000262624:W48R	W	+	1	0	MAG	40478182	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	3.640000	0.54350	2.176000	0.68965	0.374000	0.22700	TGG	.	.		0.577	MAG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000466071.1	NM_080600		C	35786342	T	C	35786342	3	2	324	1	0	0	0	0	1	0	0	0	9171	1580	55	2	33	2	MAG	19	35786342	Missense_Mutation	SNP	T	TCGA-MI-A75I-01A-11D-A32G-10	19184993	35786342	23342641	138	45746										
COX6B1	1340	hgsc.bcm.edu	37	chr19	36142167	36142167	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	tggcggaagacatggagaccAaaatcaagaactacaagacc	10	9	1	4			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr19:36142167A>G	ENST00000592141.1	+	2	287	c.22A>G	c.(22-24)Aaa>Gaa	p.K8E	COX6B1_ENST00000246554.3_Missense_Mutation_p.K8E|COX6B1_ENST00000392201.1_Missense_Mutation_p.K8E			P14854	CX6B1_HUMAN	cytochrome c oxidase subunit VIb polypeptide 1 (ubiquitous)	8					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	cytochrome-c oxidase activity (GO:0004129)			lung(6)|prostate(1)|stomach(1)	8	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CATGGAGACCAAAATCAAGAA	0.567																																					p.K8E		Atlas-SNP	.											.	COX6B1	20	.	0			c.A22G						.						96	82	87					19																	36142167		2203	4300	6503	SO:0001583	missense	1340	exon2			GAGACCAAAATCA	BC001015	CCDS12469.1	19q13.1	2011-07-04	2010-01-07	2004-08-12	ENSG00000126267	ENSG00000126267	1.9.3.1	"Mitochondrial respiratory chain complex / Complex IV"	2280	protein-coding gene	gene with protein product		124089	"cytochrome c oxidase subunit Vib", "cytochrome c oxidase subunit Vib polypeptide 1 (ubiquitous)"	COX6B		1650756	Standard	NM_001863		Approved	COXG	uc002oav.3	P14854	OTTHUMG00000048112	ENST00000592141.1:c.22A>G	chr19.hg19:g.36142167A>G	ENSP00000466818:p.Lys8Glu	70.0	0.0		79.0	19.0	NM_001863	B2R5C9|Q6IBL4	Missense_Mutation	SNP	ENST00000592141.1	hg19	CCDS12469.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.019076	0.75275	.	.	ENSG00000126267	ENST00000246554;ENST00000392201	D	0.83163	-1.69	5.31	5.31	0.75309	.	0.056377	0.64402	D	0.000002	D	0.85784	0.5777	.	.	.	0.52099	D	0.99994	D	0.62365	0.991	P	0.58928	0.848	T	0.83142	-0.0108	9	0.21540	T	0.41	-38.4036	11.6541	0.51306	1.0:0.0:0.0:0.0	.	8	P14854	CX6B1_HUMAN	E	8;25	ENSP00000246554:K8E	ENSP00000246554:K8E	K	+	1	0	COX6B1	40834007	1.000000	0.71417	0.999000	0.59377	0.709000	0.40893	8.116000	0.89574	2.017000	0.59298	0.523000	0.50628	AAA	.	.		0.567	COX6B1-004	KNOWN	alternative_5_UTR|upstream_ATG|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000459068.3	NM_001863		G	36142167	A	G	36142167	3	3	324	1	0	0	0	0	1	0	0	0	3778	131	5	2	24	2	COX6B1	19	36142167	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	355825	36142167	22986816	139	45747										
ZNF571	51276	hgsc.bcm.edu	37	chr19	38056846	38056846	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ttcagagcatttttctatatTatgattttcctcatgttgaa	5	6	3	3			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr19:38056846T>A	ENST00000328550.2	-	4	583	c.484A>T	c.(484-486)Aat>Tat	p.N162Y	ZNF571_ENST00000358744.3_Missense_Mutation_p.N162Y|ZNF571-AS1_ENST00000586013.1_RNA|ZNF571-AS1_ENST00000589802.1_RNA|ZNF571_ENST00000593133.1_Missense_Mutation_p.N162Y|ZNF571-AS1_ENST00000591430.1_RNA|ZNF571-AS1_ENST00000585578.1_RNA|ZNF571-AS1_ENST00000589750.1_RNA|ZNF571-AS1_ENST00000590838.1_RNA|ZNF571_ENST00000451802.2_Missense_Mutation_p.N162Y|ZNF571-AS1_ENST00000586139.1_RNA|ZNF571-AS1_ENST00000587121.1_RNA|ZNF571_ENST00000590751.1_Intron|ZNF540_ENST00000592533.1_Intron|ZNF571-AS1_ENST00000592392.1_RNA			Q7Z3V5	ZN571_HUMAN	zinc finger protein 571	162					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|large_intestine(6)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	25			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TTTTCTATATTATGATTTTCC	0.353																																					p.N162Y		Atlas-SNP	.											.	ZNF571	54	.	0			c.A484T						.						85	86	86					19																	38056846		2203	4300	6503	SO:0001583	missense	51276	exon4			CTATATTATGATT	AF161544	CCDS12505.1	19q13.12	2013-09-20			ENSG00000180479	ENSG00000180479		"Zinc fingers, C2H2-type", "-"	25000	protein-coding gene	gene with protein product						11042152	Standard	XM_005258977		Approved	HSPC059	uc002ogt.3	Q7Z3V5	OTTHUMG00000182016	ENST00000328550.2:c.484A>T	chr19.hg19:g.38056846T>A	ENSP00000333660:p.Asn162Tyr	65.0	0.0		79.0	29.0	NM_016536	Q2HIY0|Q3ZCU3|Q9NZX7	Missense_Mutation	SNP	ENST00000328550.2	hg19	CCDS12505.1	.	.	.	.	.	.	.	.	.	.	T	16.07	3.017389	0.54576	.	.	ENSG00000180479	ENST00000328550;ENST00000451802;ENST00000358744	T;T;T	0.35605	1.3;1.3;1.3	3.45	1.02	0.19986	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.43545	0.1252	L	0.52126	1.63	0.21499	N	0.999667	P	0.51537	0.946	P	0.56163	0.793	T	0.28586	-1.0039	9	0.87932	D	0	.	7.3936	0.26923	0.4228:0.0:0.0:0.5772	.	162	Q7Z3V5	ZN571_HUMAN	Y	162	ENSP00000333660:N162Y;ENSP00000392638:N162Y;ENSP00000351594:N162Y	ENSP00000333660:N162Y	N	-	1	0	ZNF571	42748686	0.001000	0.12720	0.004000	0.12327	0.405000	0.30901	-0.115000	0.10741	-0.120000	0.11809	0.260000	0.18958	AAT	.	.		0.353	ZNF571-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458669.1	NM_016536		A	38056846	T	A	38056846	3	1	324	1	0	0	0	0	1	0	0	0	18018	1754	61	4	1349	4	ZNF571	19	38056846	Missense_Mutation	SNP	T	TCGA-MI-A75I-01A-11D-A32G-10	1914679	38056846	21072137	140	45748										
DEDD2	162989	hgsc.bcm.edu	37	chr19	42713936	42713936	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ggcccctctccgccgccgtcTggcaccaccactgggccggc	12	21	2	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr19:42713936T>A	ENST00000595337.1	-	4	592	c.505A>T	c.(505-507)Aga>Tga	p.R169*	DEDD2_ENST00000598727.1_Nonsense_Mutation_p.R169*|DEDD2_ENST00000596251.1_Nonsense_Mutation_p.R169*|DEDD2_ENST00000336034.4_Nonsense_Mutation_p.R164*|DEDD2_ENST00000593804.1_5'UTR	NM_001270614.1	NP_001257543.1	Q8WXF8	DEDD2_HUMAN	death effector domain containing 2	169					apoptotic nuclear changes (GO:0030262)|cellular homeostasis (GO:0019725)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|RNA processing (GO:0006396)|rRNA catabolic process (GO:0016075)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)	DNA binding (GO:0003677)|receptor signaling complex scaffold activity (GO:0030159)			endometrium(1)|large_intestine(1)|ovary(1)|prostate(2)	5		Prostate(69;0.0704)				CGCCGCCGTCTGGCACCACCA	0.667																																					p.R169X		Atlas-SNP	.											.	DEDD2	16	.	0			c.A505T						.						23	26	25					19																	42713936		2191	4276	6467	SO:0001587	stop_gained	162989	exon4			GCCGTCTGGCACC	AY125488	CCDS12597.1, CCDS59391.1	19q13.31	2008-02-05				ENSG00000160570			24450	protein-coding gene	gene with protein product						11965497, 12235123	Standard	NM_133328		Approved	FLAME-3	uc031rkv.1	Q8WXF8		ENST00000595337.1:c.505A>T	chr19.hg19:g.42713936T>A	ENSP00000470082:p.Arg169*	26.0	0.0		37.0	11.0	NM_133328	Q8NBR2|Q8NES1|Q8TAA8|Q96D35	Nonsense_Mutation	SNP	ENST00000595337.1	hg19	CCDS12597.1	.	.	.	.	.	.	.	.	.	.	T	28.1	4.892140	0.91889	.	.	ENSG00000160570	ENST00000336034	.	.	.	3.81	0.099	0.14501	.	0.260060	0.31660	N	0.007262	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.428	12.0896	0.53717	0.0:0.0:0.7078:0.2922	.	.	.	.	X	169	.	ENSP00000336972:R169X	R	-	1	2	DEDD2	47405776	0.997000	0.39634	0.988000	0.46212	0.961000	0.63080	0.651000	0.24873	-0.036000	0.13669	0.383000	0.25322	AGA	.	.		0.667	DEDD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463508.1	NM_133328		A	42713936	T	A	42713936	4	1	324	1	0	0	0	0	0	1	0	0	4387	1588	55	4	483	4	DEDD2	19	42713936	Nonsense_Mutation	SNP	T	TCGA-MI-A75I-01A-11D-A32G-10	4657090	42713936	16415047	141	45749										
ZNF468	90333	hgsc.bcm.edu	37	chr19	53352366	53352366	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	agacgaggttcctataattcTccagcatcacgtccctgtat	7	12	2	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr19:53352366T>G	ENST00000595646.1	-	3	236	c.116A>C	c.(115-117)gAg>gCg	p.E39A	ZNF468_ENST00000390651.4_5'UTR|ZNF468_ENST00000243639.4_Missense_Mutation_p.E39A|ZNF28_ENST00000594602.1_Intron|ZNF468_ENST00000396409.4_5'UTR			Q5VIY5	ZN468_HUMAN	zinc finger protein 468	39	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|stomach(3)|urinary_tract(1)	23				GBM - Glioblastoma multiforme(134;0.0358)		CCTATAATTCTCCAGCATCAC	0.488																																					p.E39A		Atlas-SNP	.											.	ZNF468	46	.	0			c.A116C						.						143	144	144					19																	53352366		2203	4300	6503	SO:0001583	missense	90333	exon3			TAATTCTCCAGCA	AK023558	CCDS33094.1, CCDS62781.1	19q13.41	2013-01-08				ENSG00000204604		"Zinc fingers, C2H2-type", "-"	33105	protein-coding gene	gene with protein product						16144304	Standard	NM_001277120		Approved		uc002qaf.3	Q5VIY5		ENST00000595646.1:c.116A>C	chr19.hg19:g.53352366T>G	ENSP00000470381:p.Glu39Ala	13.0	0.0		17.0	7.0	NM_001008801	A8MV20|Q5CZB8|Q5VIY4|Q68DI7	Missense_Mutation	SNP	ENST00000595646.1	hg19	CCDS33094.1	.	.	.	.	.	.	.	.	.	.	-	15.60	2.881197	0.51801	.	.	ENSG00000204604	ENST00000243639	T	0.04317	3.65	1.99	1.99	0.26369	Krueppel-associated box (4);	.	.	.	.	T	0.31606	0.0802	H	0.98487	4.245	0.80722	D	1	D	0.62365	0.991	D	0.77004	0.989	T	0.37572	-0.9700	9	0.87932	D	0	.	8.7623	0.34683	0.0:0.0:0.0:1.0	.	39	Q5VIY5	ZN468_HUMAN	A	39	ENSP00000243639:E39A	ENSP00000243639:E39A	E	-	2	0	ZNF468	58044178	0.997000	0.39634	0.981000	0.43875	0.755000	0.42902	1.160000	0.31761	0.915000	0.36847	0.409000	0.27619	GAG	.	.		0.488	ZNF468-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463098.1	NM_001008801		G	53352366	T	G	53352366	3	3	324	1	0	0	0	0	1	0	0	0	17943	1551	54	5	1460	5	ZNF468	19	53352366	Missense_Mutation	SNP	T	TCGA-MI-A75I-01A-11D-A32G-10	10638430	53352366	5776617	142	45750										
KIR2DL1	3811	hgsc.bcm.edu	37	chr19	55284949	55284949	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	tcattggagaacaccatgatGgggtctccaaggccaacttc	10	11	2	2			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr19:55284949G>A	ENST00000538269.1	+	2	61				KIR3DL1_ENST00000541392.1_Intron|KIR2DL1_ENST00000291633.7_Missense_Mutation_p.G79R|KIR2DL3_ENST00000434419.2_Intron|KIR2DL1_ENST00000336077.6_Missense_Mutation_p.G79R|KIR2DL4_ENST00000396284.2_Intron|KIR3DL1_ENST00000402254.2_Intron|CTB-61M7.1_ENST00000400864.3_RNA			P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1						immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		ACACCATGATGGGGTCTCCAA	0.517																																					p.G79R		Atlas-SNP	.											.	KIR2DL1	46	.	0			c.G235A						.						155	140	145					19																	55284949		2176	4207	6383	SO:0001627	intron_variant	3802	exon3			CATGATGGGGTCT	L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"Killer cell immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000538269.1:c.35-44040G>A	chr19.hg19:g.55284949G>A		33.0	0.0		26.0	21.0	NM_014218	O43473|Q14946|Q16541	Missense_Mutation	SNP	ENST00000538269.1	hg19		.	.	.	.	.	.	.	.	.	.	G	5.498	0.276940	0.10403	.	.	ENSG00000125498	ENST00000336077;ENST00000291633	T;T	0.19938	2.11;2.11	1.24	0.151	0.14888	.	.	.	.	.	T	0.24044	0.0582	M	0.78801	2.425	0.09310	N	1	B;B	0.30068	0.015;0.267	B;B	0.34242	0.018;0.178	T	0.36890	-0.9729	9	0.87932	D	0	.	3.2536	0.06823	0.2988:0.0:0.7012:0.0	.	79;79	Q6IST4;Q6H2H3	.;.	R	79	ENSP00000336769:G79R;ENSP00000291633:G79R	ENSP00000291633:G79R	G	+	1	0	KIR2DL1	59976761	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-0.203000	0.09438	0.098000	0.17522	0.398000	0.26397	GGG	.	.		0.517	KIR3DL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_013289		A	55284949	G	A	55284949	1	1	324	0	1	0	0	0	0	0	0	0	8325	1348	47	3		3	KIR2DL1	19	55284949	Intron	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10	1932583	55284949	3844034	143	45751										
FERMT1	55612	hgsc.bcm.edu	37	chr20	6057861	6057861	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	tttgtggaacaagtcctcatCgagtgtttcattctggtcct	9	9	3	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr20:6057861C>T	ENST00000217289.4	-	15	2781	c.1993G>A	c.(1993-1995)Gat>Aat	p.D665N	FERMT1_ENST00000536936.1_Missense_Mutation_p.D408N|FERMT1_ENST00000478194.1_5'UTR	NM_017671.4	NP_060141.3	Q9BQL6	FERM1_HUMAN	fermitin family member 1	665					cell adhesion (GO:0007155)|establishment of epithelial cell polarity (GO:0090162)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	17						AAGTCCTCATCGAGTGTTTCA	0.537											OREG0025763	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D665N		Atlas-SNP	.											.	FERMT1	106	.	0			c.G1993A						.						103	95	98					20																	6057861		2203	4300	6503	SO:0001583	missense	55612	exon15			CCTCATCGAGTGT	AK000123	CCDS13098.1	20p12.3	2013-01-10	2010-06-24	2007-12-14	ENSG00000101311	ENSG00000101311		"Fermitins", "Pleckstrin homology (PH) domain containing"	15889	protein-coding gene	gene with protein product	"kindlin-1", "kinderlin"	607900	"chromosome 20 open reading frame 42", "fermitin family homolog 1 (Drosophila)"	C20orf42		12697302, 12789646	Standard	NM_017671		Approved	FLJ20116, URP1, KIND1, UNC112A	uc002wmr.3	Q9BQL6	OTTHUMG00000031826	ENST00000217289.4:c.1993G>A	chr20.hg19:g.6057861C>T	ENSP00000217289:p.Asp665Asn	56.0	0.0	631	74.0	30.0	NM_017671	D3DW10|Q8IX34|Q8IYH2|Q9NWM2|Q9NXQ3	Missense_Mutation	SNP	ENST00000217289.4	hg19	CCDS13098.1	.	.	.	.	.	.	.	.	.	.	C	14.67	2.606196	0.46527	.	.	ENSG00000101311	ENST00000217289;ENST00000536936	T;T	0.51574	0.7;0.7	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.46151	0.1378	N	0.24115	0.695	0.80722	D	1	D	0.65815	0.995	P	0.54499	0.754	T	0.19976	-1.0289	10	0.06236	T	0.91	-4.5069	20.0027	0.97425	0.0:1.0:0.0:0.0	.	665	Q9BQL6	FERM1_HUMAN	N	665;408	ENSP00000217289:D665N;ENSP00000441063:D408N	ENSP00000217289:D665N	D	-	1	0	FERMT1	6005861	1.000000	0.71417	0.123000	0.21794	0.843000	0.47879	5.995000	0.70631	2.733000	0.93635	0.655000	0.94253	GAT	.	.		0.537	FERMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077908.2	NM_017671		T	6057861	C	T	6057861	3	4	324	1	0	0	0	0	1	0	0	0	5825	884	31	1	44	1	FERMT1	20	6057861	Missense_Mutation	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10		6057861	56967659	144	45752										
PAK7	57144	hgsc.bcm.edu	37	chr20	9546703	9546703	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ccctggggtctcctgggctgAccaccagctgcagggccgcc	14	17	1	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr20:9546703A>G	ENST00000378429.3	-	6	1865	c.1319T>C	c.(1318-1320)gTc>gCc	p.V440A	PAK7_ENST00000378423.1_Missense_Mutation_p.V440A|PAK7_ENST00000353224.5_Missense_Mutation_p.V440A	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	440	Linker.				apoptotic process (GO:0006915)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|learning (GO:0007612)|locomotory behavior (GO:0007626)|memory (GO:0007613)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(44)|ovary(2)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)	81			COAD - Colon adenocarcinoma(9;0.194)			TCCTGGGCTGACCACCAGCTG	0.612																																					p.V440A		Atlas-SNP	.											.	PAK7	194	.	0			c.T1319C						.						108	105	106					20																	9546703		2203	4300	6503	SO:0001583	missense	57144	exon5			GGGCTGACCACCA	AB033090	CCDS13107.1	20p12	2008-06-17	2008-06-17		ENSG00000101349	ENSG00000101349			15916	protein-coding gene	gene with protein product		608038	"p21(CDKN1A)-activated kinase 7"			11756552, 10574462	Standard	NM_020341		Approved	KIAA1264, PAK5	uc002wnk.2	Q9P286	OTTHUMG00000031857	ENST00000378429.3:c.1319T>C	chr20.hg19:g.9546703A>G	ENSP00000367686:p.Val440Ala	73.0	0.0		59.0	18.0	NM_177990	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Missense_Mutation	SNP	ENST00000378429.3	hg19	CCDS13107.1	.	.	.	.	.	.	.	.	.	.	A	27.0	4.790751	0.90367	.	.	ENSG00000101349	ENST00000378429;ENST00000353224;ENST00000378423;ENST00000439520	T;T;T	0.74947	-0.89;-0.89;-0.89	5.66	5.66	0.87406	Protein kinase-like domain (1);	0.109198	0.64402	D	0.000008	D	0.85423	0.5693	M	0.78049	2.395	0.80722	D	1	D;D	0.57257	0.979;0.979	D;D	0.66497	0.944;0.944	D	0.86088	0.1548	9	.	.	.	.	15.9044	0.79412	1.0:0.0:0.0:0.0	.	440;440	B0AZM9;Q9P286	.;PAK7_HUMAN	A	440;440;440;388	ENSP00000367686:V440A;ENSP00000322957:V440A;ENSP00000367679:V440A	.	V	-	2	0	PAK7	9494703	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.339000	0.96797	2.144000	0.66660	0.477000	0.44152	GTC	.	.		0.612	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1			G	9546703	A	G	9546703	3	3	324	1	0	0	0	0	1	0	0	0	11414	275	10	2	864	2	PAK7	20	9546703	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	3488842	9546703	53478817	145	45753										
CDK5RAP1	51654	hgsc.bcm.edu	37	chr20	31967440	31967440	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	tgcactgttgaactggacctCcgaattgtcccgaaaactat	8	11	0	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr20:31967440C>G	ENST00000357886.4	-	9	1129	c.976G>C	c.(976-978)Gag>Cag	p.E326Q	CDK5RAP1_ENST00000477105.1_5'UTR|CDK5RAP1_ENST00000339269.5_Intron|CDK5RAP1_ENST00000346416.2_Missense_Mutation_p.E312Q|CDK5RAP1_ENST00000473997.1_Missense_Mutation_p.E222Q|CDK5RAP1_ENST00000544843.1_Missense_Mutation_p.E312Q			Q96SZ6	CK5P1_HUMAN	CDK5 regulatory subunit associated protein 1	326					brain development (GO:0007420)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|regulation of neuron differentiation (GO:0045664)|tRNA modification (GO:0006400)	cytoplasm (GO:0005737)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|transferase activity (GO:0016740)			endometrium(2)|kidney(2)|large_intestine(3)|lung(12)|ovary(3)|skin(3)|urinary_tract(1)	26						AACTGGACCTCCGAATTGTCC	0.413																																					p.E312Q		Atlas-SNP	.											.	CDK5RAP1	62	.	0			c.G934C						.						124	122	122					20																	31967440		2203	4300	6503	SO:0001583	missense	51654	exon8			GGACCTCCGAATT	AF152097	CCDS13219.1, CCDS63255.1	20q11.21	2012-09-20	2002-07-22	2002-07-26	ENSG00000101391	ENSG00000101391			15880	protein-coding gene	gene with protein product		608200	"chromosome 20 open reading frame 34"	C20orf34		10721722, 11882646, 15329498	Standard	NM_016408		Approved	CGI-05, HSPC167, C42	uc002wyy.4	Q96SZ6	OTTHUMG00000032256	ENST00000357886.4:c.976G>C	chr20.hg19:g.31967440C>G	ENSP00000350558:p.Glu326Gln	90.0	0.0		107.0	44.0	NM_016408	A8K7R0|Q5QP46|Q5QP47|Q5QP48|Q675N4|Q675N5|Q9BVG6|Q9BWZ5|Q9H859|Q9NZZ9|Q9Y3F0	Missense_Mutation	SNP	ENST00000357886.4	hg19		.	.	.	.	.	.	.	.	.	.	C	9.765	1.171176	0.21621	.	.	ENSG00000101391	ENST00000346416;ENST00000357886;ENST00000452723;ENST00000544843	.	.	.	5.37	4.41	0.53225	Elongator protein 3/MiaB/NifB (1);Radical SAM, alpha/beta horseshoe (1);Radical SAM (1);	0.270973	0.41823	D	0.000815	T	0.30792	0.0776	L	0.35793	1.09	0.22562	N	0.998984	B;B;B;B;B	0.33777	0.425;0.203;0.203;0.169;0.066	B;B;B;B;B	0.36289	0.221;0.221;0.221;0.141;0.048	T	0.12502	-1.0545	9	0.31617	T	0.26	-21.9306	7.1777	0.25755	0.1691:0.7441:0.0:0.0868	.	326;312;312;312;222	Q96SZ6;Q675N5;Q53H36;Q96SZ6-3;Q96SZ6-2	CK5P1_HUMAN;.;.;.;.	Q	312;326;222;312	.	ENSP00000217372:E312Q	E	-	1	0	CDK5RAP1	31431101	0.974000	0.33945	0.940000	0.37924	0.274000	0.26718	2.884000	0.48562	2.786000	0.95864	0.561000	0.74099	GAG	.	.		0.413	CDK5RAP1-011	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000078697.1	NM_016408		G	31967440	C	G	31967440	3	3	324	1	0	0	0	0	1	0	0	0	3147	864	30	4	857	4	CDK5RAP1	20	31967440	Missense_Mutation	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	22420737	31967440	31058080	146	45754										
PREX1	57580	hgsc.bcm.edu	37	chr20	47267445	47267445	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	caggcacctcctggtagcagGcaatcctctggccaatgctc	10	15	1	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr20:47267445G>A	ENST00000371941.3	-	23	2826	c.2804C>T	c.(2803-2805)gCc>gTc	p.A935V	PREX1_ENST00000396220.1_Missense_Mutation_p.A935V	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	935					actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			CTGGTAGCAGGCAATCCTCTG	0.577																																					p.A935V		Atlas-SNP	.											.	PREX1	441	.	0			c.C2804T						.						94	72	80					20																	47267445		2203	4300	6503	SO:0001583	missense	57580	exon23			TAGCAGGCAATCC	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.2804C>T	chr20.hg19:g.47267445G>A	ENSP00000361009:p.Ala935Val	48.0	0.0		44.0	14.0	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	hg19	CCDS13410.1	.	.	.	.	.	.	.	.	.	.	G	14.39	2.520809	0.44866	.	.	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.38887	1.11;1.11	5.11	-2.99	0.05497	.	0.415430	0.19788	U	0.106048	T	0.27798	0.0684	L	0.36672	1.1	0.09310	N	1	B;B	0.33940	0.077;0.433	B;B	0.36244	0.066;0.22	T	0.32640	-0.9899	10	0.15066	T	0.55	.	11.5706	0.50832	0.0:0.4454:0.326:0.2287	.	935;232	Q8TCU6;Q8TCU6-2	PREX1_HUMAN;.	V	935	ENSP00000361009:A935V;ENSP00000379522:A935V	ENSP00000361009:A935V	A	-	2	0	PREX1	46700852	0.000000	0.05858	0.017000	0.16124	0.908000	0.53690	0.130000	0.15850	-0.433000	0.07286	0.462000	0.41574	GCC	.	.		0.577	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		A	47267445	G	A	47267445	3	1	324	1	0	0	0	0	1	0	0	0	12488	1203	42	3	2247	3	PREX1	20	47267445	Missense_Mutation	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10	15300005	47267445	15758075	147	45755										
BAGE2	85319	hgsc.bcm.edu	37	chr21	11049620	11049620	+	RNA	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	gcacagtttgcatcttccttCgctataattaacagtaaaac	5	10	1	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr21:11049620C>T	ENST00000470054.1	-	0	488							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		CATCTTCCTTCGCTATAATTA	0.373																																					p.R94Q		Atlas-SNP	.											.	.	.	.	0			c.G281A						.						138	98	111					21																	11049620		692	1591	2283			85318	exon4			TTCCTTCGCTATA	AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"cancer/testis antigen family 2, member 2"					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		chr21.hg19:g.11049620C>T		545.0	0.0		551.0	31.0	NM_182481	A8K925|Q08ER0	Missense_Mutation	SNP	ENST00000470054.1	hg19																																																																																				.	.		0.373	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482		T	11049620	C	T	11049620	1	4	324	0	1	0	0	0	0	0	0	0	1292	898	31	1		1	BAGE2	21	11049620	RNA	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10		11049620	37080275	148	45756										
USP25	29761	hgsc.bcm.edu	37	chr21	17250204	17250204	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	atcatgaatgagtttattgtCccatttttgccattattact	5	7	1	2			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr21:17250204C>T	ENST00000285679.6	+	23	3258	c.2889C>T	c.(2887-2889)gtC>gtT	p.V963V	USP25_ENST00000285681.2_Silent_p.V995V|USP25_ENST00000351097.5_Silent_p.V358V|USP25_ENST00000400183.2_Silent_p.V1033V	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	963					cellular protein modification process (GO:0006464)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|proteolysis (GO:0006508)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|SUMO binding (GO:0032183)|ubiquitin-specific protease activity (GO:0004843)			breast(4)|endometrium(6)|kidney(2)|large_intestine(13)|liver(5)|lung(14)|ovary(4)|prostate(1)|skin(1)|urinary_tract(2)	52				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)		AGTTTATTGTCCCATTTTTGC	0.363																																					p.V963V		Atlas-SNP	.											.	USP25	156	.	0			c.C2889T						.						121	121	121					21																	17250204		2203	4300	6503	SO:0001819	synonymous_variant	29761	exon23			TATTGTCCCATTT	AF170562	CCDS33515.1, CCDS63336.1, CCDS63337.1	21q11.2	2011-02-24	2005-08-08		ENSG00000155313	ENSG00000155313		"Ubiquitin-specific peptidases"	12624	protein-coding gene	gene with protein product		604736	"ubiquitin specific protease 25"			12838346, 10612803	Standard	NM_013396		Approved	USP21	uc002yjy.1	Q9UHP3	OTTHUMG00000074343	ENST00000285679.6:c.2889C>T	chr21.hg19:g.17250204C>T		170.0	0.0		167.0	59.0	NM_013396	C0LSZ0|Q6DHZ9|Q9H9W1	Silent	SNP	ENST00000285679.6	hg19	CCDS33515.1																																																																																			.	.		0.363	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1			T	17250204	C	T	17250204	2	4	324	1	0	0	0	0	0	0	0	1	17071	842	30	3		3	USP25	21	17250204	Silent	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	6200584	17250204	30879691	149	45757										
ADAMTS1	9510	hgsc.bcm.edu	37	chr21	28210528	28210528	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	ccattgttcctggatcccctCtggttccgctgtttcacttc	7	15	2	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr21:28210528C>T	ENST00000284984.3	-	9	2728	c.2274G>A	c.(2272-2274)caG>caA	p.Q758Q		NM_006988.3	NP_008919.3	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 1	758	Spacer.				heart trabecula formation (GO:0060347)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|negative regulation of cell proliferation (GO:0008285)|ovulation from ovarian follicle (GO:0001542)	basement membrane (GO:0005604)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)	heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(20)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	42		Breast(209;0.000962)		Lung(58;0.215)		TGGATCCCCTCTGGTTCCGCT	0.448																																					p.Q758Q		Atlas-SNP	.											.	ADAMTS1	131	.	0			c.G2274A						.						90	72	78					21																	28210528		2203	4300	6503	SO:0001819	synonymous_variant	9510	exon9			TCCCCTCTGGTTC	AF060152	CCDS33524.1	21q21.3	2008-05-14	2005-08-19		ENSG00000154734	ENSG00000154734		"ADAM metallopeptidases with thrombospondin type 1 motif"	217	protein-coding gene	gene with protein product		605174	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 1"			10438512	Standard	NM_006988		Approved	C3-C5, METH1, KIAA1346	uc002ymf.3	Q9UHI8	OTTHUMG00000078688	ENST00000284984.3:c.2274G>A	chr21.hg19:g.28210528C>T		64.0	0.0		68.0	29.0	NM_006988	D3DSD5|Q9NSJ8|Q9P2K0|Q9UH83|Q9UP80	Silent	SNP	ENST00000284984.3	hg19	CCDS33524.1																																																																																			.	.		0.448	ADAMTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171650.2			T	28210528	C	T	28210528	2	4	324	1	0	0	0	0	0	0	0	1	255	912	32	3		3	ADAMTS1	21	28210528	Silent	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	10960324	28210528	19919367	150	45758										
C2CD2	25966	hgsc.bcm.edu	37	chr21	43332526	43332526	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	aacaggatcgttcagctgcaCgacgcacactgcattaatgt	9	11	1	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr21:43332526C>A	ENST00000380486.3	-	7	1109	c.868G>T	c.(868-870)Gtg>Ttg	p.V290L	C2CD2_ENST00000329623.7_Missense_Mutation_p.V135L	NM_015500.1	NP_056315.1	Q9Y426	CU025_HUMAN	C2 calcium-dependent domain containing 2	290	C2.					cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|ovary(3)|prostate(1)|stomach(1)	15						TTCAGCTGCACGACGCACACT	0.433																																					p.V290L		Atlas-SNP	.											.	C2CD2	47	.	0			c.G868T						.						84	61	69					21																	43332526		2203	4300	6503	SO:0001583	missense	25966	exon7			GCTGCACGACGCA	AB047784	CCDS13677.1, CCDS42933.1	21q22.3	2008-11-24	2007-10-17	2007-10-17	ENSG00000157617	ENSG00000157617			1266	protein-coding gene	gene with protein product	"TMEM24-like"		"chromosome 21 open reading frame 25"	C21orf25		15289880	Standard	NM_015500		Approved	TMEM24L, DKFZP586F0422, C21orf258	uc002yzw.3	Q9Y426	OTTHUMG00000086779	ENST00000380486.3:c.868G>T	chr21.hg19:g.43332526C>A	ENSP00000369853:p.Val290Leu	46.0	0.0		48.0	20.0	NM_015500	Q5R2V7|Q6AHX8|Q9NSE6	Missense_Mutation	SNP	ENST00000380486.3	hg19	CCDS42933.1	.	.	.	.	.	.	.	.	.	.	C	10.98	1.504031	0.26949	.	.	ENSG00000157617	ENST00000329623;ENST00000380486	T;T	0.71579	-0.58;-0.58	5.29	2.33	0.28932	C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.421745	0.26915	N	0.021860	T	0.54351	0.1853	L	0.32530	0.975	0.09310	N	1	B;B	0.22346	0.068;0.025	B;B	0.25405	0.057;0.06	T	0.35895	-0.9770	10	0.21014	T	0.42	-5.3501	7.6487	0.28336	0.0:0.5982:0.2689:0.1328	.	135;290	Q6P6D1;Q9Y426	.;CU025_HUMAN	L	135;290	ENSP00000329302:V135L;ENSP00000369853:V290L	ENSP00000329302:V135L	V	-	1	0	C2CD2	42205595	0.000000	0.05858	0.001000	0.08648	0.022000	0.10575	0.080000	0.14802	0.658000	0.30925	0.655000	0.94253	GTG	.	.		0.433	C2CD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195228.2	NM_015500		A	43332526	C	A	43332526	3	1	324	1	0	0	0	0	1	0	0	0	2154	536	19	1	1254	1	C2CD2	21	43332526	Missense_Mutation	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	15121998	43332526	4797369	151	45759										
APOBEC3B	9582	hgsc.bcm.edu	37	chr22	39388141	39388141	+	Frame_Shift_Del	DEL	G	G	-													0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	agccctgagtgggaggctgcGggccattctccaggtgaggg							TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chr22:39388141delG	ENST00000333467.3	+	7	1166	c.1121delG	c.(1120-1122)cggfs	p.R374fs	APOBEC3B_ENST00000402182.3_Frame_Shift_Del_p.R374fs|APOBEC3B_ENST00000407298.3_Frame_Shift_Del_p.R349fs|APOBEC3B-AS1_ENST00000513758.2_RNA	NM_001270411.1|NM_004900.4	NP_001257340.1|NP_004891	Q9UH17	ABC3B_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B	374					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|negative regulation of transposition (GO:0010529)	nucleus (GO:0005634)	deoxycytidine deaminase activity (GO:0047844)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	13	Melanoma(58;0.04)					GGGAGGCTGCGGGCCATTCTC	0.647																																					p.R374fs		Atlas-INDEL	.											APOBEC3B,colon,carcinoma,-1,1	APOBEC3B	32	.	0			c.1120delC						.						76	64	68					22																	39388141		2198	4282	6480	SO:0001589	frameshift_variant	9582	exon7			.	AK024854	CCDS13982.1, CCDS58807.1	22q13.1-q13.2	2008-05-15			ENSG00000179750	ENSG00000179750		"Apolipoprotein B mRNA editing enzymes"	17352	protein-coding gene	gene with protein product	"phorbolin 3"	607110				11863358, 10469298	Standard	NM_004900		Approved	PHRBNL, FLJ21201	uc003awo.2	Q9UH17	OTTHUMG00000151085	ENST00000333467.3:c.1121delG	chr22.hg19:g.39388141delG	ENSP00000327459:p.Arg374fs	77.0	0.0		91.0	20.0	NM_004900	B0QYD2|O95618|Q20WL1|Q5IFJ4|Q7Z2N3|Q7Z6D6|Q9UE74	Frame_Shift_Del	DEL	ENST00000333467.3	hg19	CCDS13982.1																																																																																			.	.		0.647	APOBEC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321233.1	NM_004900		-	39388141	G	-	39388141	7	5	324	1	0	1	0	1	0	0	0	0	790	1116	39	0	1147	0	APOBEC3B	22	39388141	Frame_Shift_Del	DEL	G	TCGA-MI-A75I-01A-11D-A32G-10		39388141	11916425	152	45760										
MAGEB4	4115	hgsc.bcm.edu	37	chrX	30260451	30260451	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	aggagcctcagagagagccaCccaccacctctgctgctgca	10	16	2	2			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chrX:30260451C>A	ENST00000378982.2	+	1	395	c.199C>A	c.(199-201)Ccc>Acc	p.P67T	MAGEB1_ENST00000378981.3_5'Flank|MAGEB1_ENST00000397550.1_5'Flank	NM_002367.3	NP_002358.1	O15481	MAGB4_HUMAN	melanoma antigen family B, 4	67										breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	27						GAGAGAGCCACCCACCACCTC	0.527																																					p.P67T		Atlas-SNP	.											.	MAGEB4	75	.	0			c.C199A						.						54	50	51					X																	30260451		2202	4300	6502	SO:0001583	missense	4115	exon1			GAGCCACCCACCA		CCDS14221.1	Xp21.3	2009-03-17			ENSG00000120289	ENSG00000120289			6811	protein-coding gene	gene with protein product	"melanoma-associated antigen B4", "cancer/testis antigen family 3, member 6"	300153				9441743	Standard	NM_002367		Approved	MGC33144, CT3.6	uc004dcb.3	O15481	OTTHUMG00000021321	ENST00000378982.2:c.199C>A	chrX.hg19:g.30260451C>A	ENSP00000368266:p.Pro67Thr	58.0	0.0		64.0	45.0	NM_002367	B2R9G0|Q6FHH4|Q8IZ00	Missense_Mutation	SNP	ENST00000378982.2	hg19	CCDS14221.1	.	.	.	.	.	.	.	.	.	.	C	2.143	-0.396447	0.04899	.	.	ENSG00000120289	ENST00000378982	T	0.03831	3.79	3.37	0.0494	0.14289	Melanoma associated antigen, MAGE, N-terminal (1);	.	.	.	.	T	0.02767	0.0083	N	0.16862	0.45	0.09310	N	1	B	0.21381	0.055	B	0.21360	0.034	T	0.47328	-0.9126	9	0.27082	T	0.32	.	3.7193	0.08450	0.0:0.485:0.2789:0.2361	.	67	O15481	MAGB4_HUMAN	T	67	ENSP00000368266:P67T	ENSP00000368266:P67T	P	+	1	0	MAGEB4	30170372	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.960000	0.03849	-0.111000	0.12001	0.544000	0.68410	CCC	.	.		0.527	MAGEB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056159.1	NM_002367		A	30260451	C	A	30260451	3	1	324	1	0	0	0	0	1	0	0	0	9187	507	18	3	201	3	MAGEB4	23	30260451	Missense_Mutation	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10		30260451	125010109	153	45761										
KDM6A	7403	hgsc.bcm.edu	37	chrX	44870266	44870266	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	attataatgcatttcagtggTaagttgacataaaaccagta	7	5	1	1			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chrX:44870266T>G	ENST00000377967.4	+	5	484		c.e5+2		KDM6A_ENST00000536777.1_Splice_Site|KDM6A_ENST00000543216.1_Splice_Site|KDM6A_ENST00000382899.4_Splice_Site	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A						canonical Wnt signaling pathway (GO:0060070)|heart morphogenesis (GO:0003007)|histone H3-K4 methylation (GO:0051568)|in utero embryonic development (GO:0001701)|mesodermal cell differentiation (GO:0048333)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|regulation of gene expression (GO:0010468)|respiratory system process (GO:0003016)|somite rostral/caudal axis specification (GO:0032525)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	p.0(12)|p.0?(6)|p.?(1)		NS(1)|breast(7)|central_nervous_system(27)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(24)|kidney(24)|large_intestine(9)|liver(1)|lung(21)|oesophagus(11)|pancreas(2)|prostate(5)|skin(1)|soft_tissue(1)|urinary_tract(29)	170						ATTTCAGTGGTAAGTTGACAT	0.318			"D, N, F, S"		"renal, oesophageal SCC, MM"																																.	Colon(129;1273 1667 15230 27352 52914)	Atlas-SNP	.		Rec	yes		X	Xp11.2	7403	"lysine (K)-specific demethylase 6A, UTX"		"E, L"	.	KDM6A	274	.	19	No detectable mRNA/protein(12)|Whole gene deletion(6)|Unknown(1)	haematopoietic_and_lymphoid_tissue(11)|oesophagus(4)|breast(2)|pancreas(2)	c.443+2T>G						.						119	99	105					X																	44870266		2203	4293	6496	SO:0001630	splice_region_variant	7403	exon5			CAGTGGTAAGTTG	AF000992	CCDS14265.1	Xp11.2	2014-09-17	2009-04-17	2009-04-17	ENSG00000147050	ENSG00000147050		"Chromatin-modifying enzymes / K-demethylases", "Tetratricopeptide (TTC) repeat domain containing"	12637	protein-coding gene	gene with protein product		300128	"ubiquitously transcribed tetratricopeptide repeat, X chromosome"	UTX		9499428, 9381176	Standard	XM_005272655		Approved		uc004dge.4	O15550	OTTHUMG00000021402	ENST00000377967.4:c.443+2T>G	chrX.hg19:g.44870266T>G		49.0	0.0		40.0	26.0	NM_021140	Q52LL9|Q5JVQ7	Splice_Site	SNP	ENST00000377967.4	hg19	CCDS14265.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.431190	0.83776	.	.	ENSG00000147050	ENST00000377967;ENST00000536777;ENST00000382899;ENST00000543216;ENST00000542299	.	.	.	5.6	5.6	0.85130	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7731	0.69693	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	KDM6A	44755210	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	7.501000	0.81600	1.870000	0.54199	0.412000	0.27726	.	.	.		0.318	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056324.1	NM_021140	Intron	G	44870266	T	G	44870266	5	3	324	1	0	0	0	0	0	0	1	0	8146	1652	57	5	463	5	KDM6A	23	44870266	Splice_Site	SNP	T	TCGA-MI-A75I-01A-11D-A32G-10	14609815	44870266	110400294	154	45762										
KIF4A	24137	hgsc.bcm.edu	37	chrX	69595074	69595074	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	gttgagtgagcgccgccgcaAacgtctccaggagctggagg	16	11	1	2			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chrX:69595074A>G	ENST00000374403.3	+	17	1881	c.1799A>G	c.(1798-1800)aAa>aGa	p.K600R	KIF4A_ENST00000374388.3_Missense_Mutation_p.K600R	NM_012310.4	NP_036442.3	O95239	KIF4A_HUMAN	kinesin family member 4A	600				K -> E (in Ref. 3; CAB75427). {ECO:0000305}.	anterograde axon cargo transport (GO:0008089)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|organelle organization (GO:0006996)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(6)|endometrium(9)|kidney(3)|large_intestine(8)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	51						CGCCGCCGCAAACGTCTCCAG	0.473																																					p.K600R		Atlas-SNP	.											.	KIF4A	118	.	0			c.A1799G						.						70	61	64					X																	69595074		2203	4300	6503	SO:0001583	missense	24137	exon17			GCCGCAAACGTCT	AF179308	CCDS14401.1	Xq13.1	2008-08-11			ENSG00000090889	ENSG00000090889		"Kinesins"	13339	protein-coding gene	gene with protein product	"chromokinesin"	300521				10773663	Standard	NM_012310		Approved	KIF4-G1, KIF4, HSA271784, FLJ12530, FLJ12655, FLJ14204, FLJ20631	uc004dyg.3	O95239	OTTHUMG00000021775	ENST00000374403.3:c.1799A>G	chrX.hg19:g.69595074A>G	ENSP00000363524:p.Lys600Arg	62.0	0.0		70.0	54.0	NM_012310	B2R7V5|D3DVU4|Q86TN3|Q86XX7|Q9NNY6|Q9NY24|Q9UMW3	Missense_Mutation	SNP	ENST00000374403.3	hg19	CCDS14401.1	.	.	.	.	.	.	.	.	.	.	A	16.38	3.107412	0.56291	.	.	ENSG00000090889	ENST00000374388;ENST00000374403	T;T	0.70749	1.86;-0.51	5.53	4.38	0.52667	.	0.000000	0.64402	D	0.000009	T	0.69788	0.3150	L	0.61387	1.9	0.58432	D	0.999998	B;B	0.28291	0.049;0.206	B;B	0.36989	0.024;0.238	T	0.67654	-0.5615	10	0.54805	T	0.06	.	9.5477	0.39291	0.9181:0.0:0.0819:0.0	.	600;600	O95239;O95239-2	KIF4A_HUMAN;.	R	600	ENSP00000363509:K600R;ENSP00000363524:K600R	ENSP00000363509:K600R	K	+	2	0	KIF4A	69511799	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.624000	0.61254	0.900000	0.36469	0.486000	0.48141	AAA	.	.		0.473	KIF4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057068.1	NM_012310		G	69595074	A	G	69595074	3	3	324	1	0	0	0	0	1	0	0	0	8312	14	1	2	1861	2	KIF4A	23	69595074	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	24724808	69595074	85675486	155	45763										
CXCR3	2833	hgsc.bcm.edu	37	chrX	70836903	70836903	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	agctgatgcaggccagcaggAgggctcctgcgtagaagttg	16	9	0	2			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chrX:70836903A>T	ENST00000373693.3	-	2	486	c.419T>A	c.(418-420)cTc>cAc	p.L140H	CXCR3_ENST00000373691.4_Missense_Mutation_p.L187H	NM_001504.1	NP_001495.1	P49682	CXCR3_HUMAN	chemokine (C-X-C motif) receptor 3	140					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|calcium-mediated signaling (GO:0019722)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cellular component movement (GO:0006928)|chemokine (C-C motif) ligand 11 production (GO:0071954)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of execution phase of apoptosis (GO:1900118)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cAMP metabolic process (GO:0030816)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemotaxis (GO:0050921)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of leukocyte migration (GO:0002685)|T cell chemotaxis (GO:0010818)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-X-C chemokine binding (GO:0019958)|C-X-C chemokine receptor activity (GO:0016494)|chemokine binding (GO:0019956)|chemokine receptor activity (GO:0004950)|receptor activity (GO:0004872)			breast(1)|central_nervous_system(2)|large_intestine(2)|lung(3)|ovary(2)	10	Renal(35;0.156)					GGCCAGCAGGAGGGCTCCTGC	0.642																																					p.L187H		Atlas-SNP	.											.	CXCR3	57	.	0			c.T560A						.						23	21	22					X																	70836903		2203	4298	6501	SO:0001583	missense	2833	exon2			AGCAGGAGGGCTC	U32674	CCDS14416.1, CCDS48135.1	Xq13	2012-08-08	2002-08-22	2002-08-23	ENSG00000186810	ENSG00000186810		"CD molecules", "GPCR / Class A : Chemokine receptors : C-X-C motif"	4540	protein-coding gene	gene with protein product		300574	"G protein-coupled receptor 9"	GPR9		8666380, 9064356	Standard	NM_001142797		Approved	CKR-L2, CMKAR3, IP10-R, MigR, CD183	uc011mpx.2	P49682	OTTHUMG00000033326	ENST00000373693.3:c.419T>A	chrX.hg19:g.70836903A>T	ENSP00000362797:p.Leu140His	28.0	0.0		17.0	13.0	NM_001142797	B2R982|O15185|Q7Z710|Q9P2T4|Q9P2T5	Missense_Mutation	SNP	ENST00000373693.3	hg19	CCDS14416.1	.	.	.	.	.	.	.	.	.	.	A	15.19	2.760641	0.49468	.	.	ENSG00000186810	ENST00000373691;ENST00000373693;ENST00000373687	T;T	0.42900	0.96;0.96	5.44	5.44	0.79542	GPCR, rhodopsin-like superfamily (1);	0.208085	0.40554	N	0.001072	T	0.64560	0.2609	M	0.89214	3.015	0.26427	N	0.976003	D;P	0.61080	0.989;0.635	P;P	0.58721	0.844;0.465	T	0.65504	-0.6152	10	0.87932	D	0	.	12.1786	0.54199	1.0:0.0:0.0:0.0	.	187;140	P49682-2;P49682	.;CXCR3_HUMAN	H	187;140;140	ENSP00000362795:L187H;ENSP00000362797:L140H	ENSP00000362791:L140H	L	-	2	0	CXCR3	70753628	1.000000	0.71417	1.000000	0.80357	0.381000	0.30169	7.064000	0.76721	2.006000	0.58801	0.481000	0.45027	CTC	.	.		0.642	CXCR3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144141.1			T	70836903	A	T	70836903	3	4	324	1	0	0	0	0	1	0	0	0	4094	304	11	4	691	4	CXCR3	23	70836903	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	1241829	70836903	84433657	156	45764										
ESX1	80712	hgsc.bcm.edu	37	chrX	103495144	103495144	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	tgggcggcccgggtggcacaCgcgccatgggcggcccgggt	20	14	0	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chrX:103495144C>G	ENST00000372588.4	-	4	1069	c.986G>C	c.(985-987)cGt>cCt	p.R329P		NM_153448.3	NP_703149.1	Q8N693	ESX1_HUMAN	ESX homeobox 1	329	15 X 9 AA tandem repeats of P-P-x-x-P-x- P-P-x.				labyrinthine layer blood vessel development (GO:0060716)|labyrinthine layer morphogenesis (GO:0060713)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding (GO:0043565)			endometrium(2)|large_intestine(10)|lung(12)|ovary(1)|skin(2)	27						GGGTGGCACACGCGCCATGGG	0.811													c|||	23	0.00609272	0.0023	0.0058	3775	,	,		6672	0.0109		0.005	False		,,,				2504	0				p.R329P	Pancreas(200;1705 2227 25194 28471 45274)	Atlas-SNP	.											.	ESX1	57	.	0			c.G986C						.						1	2	1					X																	103495144		387	991	1378	SO:0001583	missense	80712	exon4			GGCACACGCGCCA	AL049631	CCDS14516.1	Xq22.2	2011-06-20	2007-07-11	2006-02-08	ENSG00000123576	ENSG00000123576		"Homeoboxes / PRD class"	14865	protein-coding gene	gene with protein product		300154	"extraembryonic, spermatogenesis, homeobox 1 homolog (mouse)"	ESX1L		11374906, 17242862	Standard	NM_153448		Approved	ESXR1	uc004ely.3	Q8N693	OTTHUMG00000022125	ENST00000372588.4:c.986G>C	chrX.hg19:g.103495144C>G	ENSP00000361669:p.Arg329Pro	1.0	0.0		20.0	7.0	NM_153448	B0QYU3|Q7Z6K7	Missense_Mutation	SNP	ENST00000372588.4	hg19	CCDS14516.1	.	.	.	.	.	.	.	.	.	.	c	0.976	-0.698559	0.03279	.	.	ENSG00000123576	ENST00000372588	T	0.72167	-0.63	1.26	-2.51	0.06365	.	.	.	.	.	T	0.39759	0.1090	N	0.02721	-0.515	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.08310	-1.0728	9	0.29301	T	0.29	.	5.5584	0.17129	0.1773:0.2094:0.6133:0.0	.	329	Q8N693	ESX1_HUMAN	P	329	ENSP00000361669:R329P	ENSP00000361669:R329P	R	-	2	0	ESX1	103381800	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.121000	0.15667	-2.202000	0.00745	-2.756000	0.00123	CGT	.	.		0.811	ESX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057763.2	NM_153448		G	103495144	C	G	103495144	3	3	324	1	0	0	0	0	1	0	0	0	5265	536	19	4	238	4	ESX1	23	103495144	Missense_Mutation	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	32658241	103495144	51775416	157	45765										
RGAG1	57529	hgsc.bcm.edu	37	chrX	109695556	109695556	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	cagcacagatgaaagccatgActtctggagcaatgtccacc	9	12	1	3			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chrX:109695556A>G	ENST00000465301.2	+	3	1957	c.1711A>G	c.(1711-1713)Act>Gct	p.T571A	RGAG1_ENST00000540313.1_Missense_Mutation_p.T571A	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	571										NS(1)|autonomic_ganglia(1)|breast(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	73						GAAAGCCATGACTTCTGGAGC	0.507																																					p.T571A		Atlas-SNP	.											.	RGAG1	168	.	0			c.A1711G						.						120	103	109					X																	109695556		2203	4300	6503	SO:0001583	missense	57529	exon3			GCCATGACTTCTG	AY121804	CCDS14552.1	Xq23	2008-02-05			ENSG00000243978	ENSG00000243978			29245	protein-coding gene	gene with protein product						10718198, 15716091, 16093683	Standard	NM_020769		Approved	KIAA1318, Mart9, Mar9	uc004eor.2	Q8NET4	OTTHUMG00000022196	ENST00000465301.2:c.1711A>G	chrX.hg19:g.109695556A>G	ENSP00000419786:p.Thr571Ala	70.0	0.0		63.0	6.0	NM_020769	Q9P2M8	Missense_Mutation	SNP	ENST00000465301.2	hg19	CCDS14552.1	.	.	.	.	.	.	.	.	.	.	A	0.001	-3.374027	0.00015	.	.	ENSG00000243978	ENST00000465301;ENST00000540313	T;T	0.39056	1.1;1.1	3.47	0.536	0.17138	.	1.004580	0.08028	N	0.993029	T	0.11965	0.0291	N	0.00859	-1.14	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.26189	-1.0110	9	.	.	.	-3.9872	2.627	0.04932	0.4001:0.0:0.3834:0.2164	.	571	Q8NET4	RGAG1_HUMAN	A	571	ENSP00000419786:T571A;ENSP00000441452:T571A	.	T	+	1	0	RGAG1	109582212	0.001000	0.12720	0.001000	0.08648	0.014000	0.08584	0.212000	0.17497	-0.009000	0.14296	-1.386000	0.01163	ACT	.	.		0.507	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	NM_020769		G	109695556	A	G	109695556	3	3	324	1	0	0	0	0	1	0	0	0	13289	275	10	2	1713	2	RGAG1	23	109695556	Missense_Mutation	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	6200412	109695556	45575004	158	45766										
AFF2	2334	hgsc.bcm.edu	37	chrX	148072845	148072845	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	gactgtgttggctgcgcatcGatgcccacttgttgtagtgg	14	9	0	0	rs149966195		TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chrX:148072845G>C	ENST00000370460.2	+	21	4398	c.3919G>C	c.(3919-3921)Gat>Cat	p.D1307H	AFF2_ENST00000342251.3_Missense_Mutation_p.D1274H|AFF2_ENST00000370457.5_Missense_Mutation_p.D1272H|AFF2_ENST00000286437.5_Missense_Mutation_p.D948H	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	1307					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)	p.D1307N(2)|p.D948N(1)		breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					GCTGCGCATCGATGCCCACTT	0.552																																					p.D1307H		Atlas-SNP	.											.	AFF2	679	.	3	Substitution - Missense(3)	endometrium(3)	c.G3919C						.						236	157	184					X																	148072845		2203	4300	6503	SO:0001583	missense	2334	exon21			CGCATCGATGCCC	U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"fragile X mental retardation 2"	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.3919G>C	chrX.hg19:g.148072845G>C	ENSP00000359489:p.Asp1307His	28.0	0.0		34.0	25.0	NM_002025	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Missense_Mutation	SNP	ENST00000370460.2	hg19	CCDS14684.1	.	.	.	.	.	.	.	.	.	.	G	19.08	3.758870	0.69763	.	.	ENSG00000155966	ENST00000370460;ENST00000370457;ENST00000342251;ENST00000286437	T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18	5.46	5.46	0.80206	.	0.066769	0.56097	D	0.000029	T	0.77974	0.4211	M	0.62723	1.935	0.41587	D	0.988773	P;D;D;D;D;D	0.76494	0.883;0.999;0.997;0.999;0.999;0.999	P;D;D;D;D;D	0.87578	0.778;0.998;0.994;0.964;0.964;0.979	T	0.79470	-0.1790	10	0.56958	D	0.05	.	18.3753	0.90433	0.0:0.0:1.0:0.0	.	948;1272;1272;1268;1297;1307	B4DXD5;P51816-6;P51816-3;P51816-2;P51816-5;P51816	.;.;.;.;.;AFF2_HUMAN	H	1307;1272;1274;948	ENSP00000359489:D1307H;ENSP00000359486:D1272H;ENSP00000345459:D1274H;ENSP00000286437:D948H	ENSP00000286437:D948H	D	+	1	0	AFF2	147880551	1.000000	0.71417	0.995000	0.50966	0.836000	0.47400	7.871000	0.87180	2.279000	0.76181	0.594000	0.82650	GAT	.	G|1.000;A|0.000		0.552	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025		C	148072845	G	C	148072845	3	2	324	1	0	0	0	0	1	0	0	0	357	1058	37	4	4056	4	AFF2	23	148072845	Missense_Mutation	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10	38377289	148072845	7197715	159	45767										
PLXNA3	55558	hgsc.bcm.edu	37	chrX	153698841	153698841	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	acagtgttcagcacagcccaCcggggctcggccctgcccct	11	18	1	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chrX:153698841C>A	ENST00000369682.3	+	30	5218	c.5043C>A	c.(5041-5043)caC>caA	p.H1681Q	PLXNA3_ENST00000493546.1_3'UTR	NM_017514.3	NP_059984.3	P51805	PLXA3_HUMAN	plexin A3	1681					axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|hippocampus development (GO:0021766)|multicellular organismal development (GO:0007275)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|positive regulation of cytoskeleton organization (GO:0051495)|pyramidal neuron development (GO:0021860)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|trigeminal nerve structural organization (GO:0021637)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	48	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GCACAGCCCACCGGGGCTCGG	0.622																																					p.H1681Q		Atlas-SNP	.											.	PLXNA3	156	.	0			c.C5043A						.						77	71	73					X																	153698841		2202	4300	6502	SO:0001583	missense	55558	exon30			AGCCCACCGGGGC	X74609	CCDS14752.1	Xq28	2008-02-05			ENSG00000130827	ENSG00000130827		"Plexins"	9101	protein-coding gene	gene with protein product		300022		PLXN4		8248200, 8733135	Standard	NM_017514		Approved	SEX, XAP-6, 6.3, Plxn3	uc004flm.3	P51805	OTTHUMG00000033290	ENST00000369682.3:c.5043C>A	chrX.hg19:g.153698841C>A	ENSP00000358696:p.His1681Gln	105.0	0.0		94.0	68.0	NM_017514	Q5HY36	Missense_Mutation	SNP	ENST00000369682.3	hg19	CCDS14752.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.401486	0.83120	.	.	ENSG00000130827	ENST00000369682	T	0.17691	2.26	5.0	4.14	0.48551	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.32496	0.0831	M	0.62088	1.915	0.58432	D	0.999999	P	0.40144	0.704	P	0.53760	0.734	T	0.03043	-1.1079	10	0.72032	D	0.01	.	11.5616	0.50780	0.0:0.9089:0.0:0.0911	.	1681	P51805	PLXA3_HUMAN	Q	1681	ENSP00000358696:H1681Q	ENSP00000358696:H1681Q	H	+	3	2	PLXNA3	153352035	1.000000	0.71417	0.993000	0.49108	0.901000	0.52897	1.229000	0.32600	0.898000	0.36418	0.529000	0.55759	CAC	.	.		0.622	PLXNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081634.1	NM_017514		A	153698841	C	A	153698841	3	1	324	1	0	0	0	0	1	0	0	0	12130	506	18	3	5157	3	PLXNA3	23	153698841	Missense_Mutation	SNP	C	TCGA-MI-A75I-01A-11D-A32G-10	5625996	153698841	1571719	160	45768										
DDX3Y	8653	hgsc.bcm.edu	37	chrY	15024659	15024659	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	atttgatgatcgtggacggaGtgactatgatggtattggca	14	4	0	4			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chrY:15024659G>T	ENST00000336079.3	+	5	408	c.302G>T	c.(301-303)aGt>aTt	p.S101I	DDX3Y_ENST00000360160.4_Missense_Mutation_p.S101I	NM_001122665.1|NM_004660.3	NP_001116137.1|NP_004651.2	O15523	DDX3Y_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 3, Y-linked	101						cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)|RNA binding (GO:0003723)			kidney(1)|liver(2)|lung(1)|upper_aerodigestive_tract(1)	5						CGTGGACGGAGTGACTATGAT	0.433																																					p.S101I		Atlas-SNP	.											.	DDX3Y	13	.	0			c.G302T						.						127	124	124					Y																	15024659		631	1994	2625	SO:0001583	missense	8653	exon5			GACGGAGTGACTA	AF000984	CCDS14782.1	Yq11	2013-07-16	2013-07-16	2003-06-20	ENSG00000067048	ENSG00000067048		"DEAD-boxes"	2699	protein-coding gene	gene with protein product		400010	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide, Y chromosome", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, Y-linked"	DBY		9381176	Standard	NM_004660		Approved		uc004fsv.2	O15523	OTTHUMG00000036324	ENST00000336079.3:c.302G>T	chrY.hg19:g.15024659G>T	ENSP00000336725:p.Ser101Ile	97.0	0.0		109.0	85.0	NM_004660	B4DK29|B4DXX7|Q8IYV7	Missense_Mutation	SNP	ENST00000336079.3	hg19	CCDS14782.1																																																																																			.	.		0.433	DDX3Y-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088407.1	NM_004660		T	15024659	G	T	15024659	3	4	324	1	0	0	0	0	1	0	0	0	4361	1029	36	3	320	3	DDX3Y	24	15024659	Missense_Mutation	SNP	G	TCGA-MI-A75I-01A-11D-A32G-10		15024659	44348907	161	45769										
NLGN4Y	22829	hgsc.bcm.edu	37	chrY	16941900	16941900	+	3'UTR	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0493827160493827	8	1	1.1717419921018	0.456634746922025	1.5094315245478	0.0197666110978804	0.288546119938488	0	agttcctcaactacgacatcAtgctgggcgtcaaccaaggg	10	12	3	0			TCGA-MI-A75I-01A-11D-A32G-10	TCGA-MI-A75I-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c9dad44d-b8c3-40f4-83ee-da8c82890611	dc087f7d-68c4-44c3-aa12-a62a8bf3c9a3	g.chrY:16941900A>G	ENST00000476359.1	+	0	1647							Q8NFZ3	NLGNY_HUMAN	neuroligin 4, Y-linked						learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)			large_intestine(3)|lung(7)|prostate(2)|skin(2)	14						CTACGACATCATGCTGGGCGT	0.582																																					p.M368V		Atlas-SNP	.											.	NLGN4Y	44	.	0			c.A1102G						.																																			SO:0001624	3_prime_UTR_variant	22829	exon5			GACATCATGCTGG		CCDS14788.1, CCDS55553.1, CCDS56619.1	Yq11.221	2013-09-20	2004-05-21		ENSG00000165246	ENSG00000165246			15529	protein-coding gene	gene with protein product		400028	"neuroligin 4, Y linked"			10231032	Standard	NM_014893		Approved	KIAA0951	uc004ftg.2	Q8NFZ3	OTTHUMG00000036618	ENST00000476359.1:c.*1644A>G	chrY.hg19:g.16941900A>G		188.0	1.0		199.0	107.0	NM_014893	F5H6W0|Q14D08|Q7Z3T5|Q8N5B6|Q9Y2F8	Missense_Mutation	SNP	ENST00000476359.1	hg19																																																																																				.	.		0.582	NLGN4Y-004	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000089064.2	NM_014893		G	16941900	A	G	16941900	1	3	324	0	1	0	0	0	0	0	0	0	10474	217	8	2		2	NLGN4Y	24	16941900	3'UTR	SNP	A	TCGA-MI-A75I-01A-11D-A32G-10	1917241	16941900	42431666	162	45770										
LZIC	84328	hgsc.bcm.edu	37	chr1	9995639	9995639	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.153846153846154	4	1	1.84868421052632	1.47894736842105	2.01674641148325	0.485714285714286	1	0	aaattcacttagttgctccaGagtttcctttttggtttctt	6	8	2	1			TCGA-MR-A520-01A-11D-A25V-10	TCGA-MR-A520-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	352fbbb4-88a5-4354-b1fa-3a01da3fbfa7	64b28729-b106-4b33-994d-f1710478466c	g.chr1:9995639G>C	ENST00000377223.1	-	4	395	c.148C>G	c.(148-150)Ctg>Gtg	p.L50V	LZIC_ENST00000377213.1_Missense_Mutation_p.L50V|LZIC_ENST00000541052.1_Missense_Mutation_p.L71V|LZIC_ENST00000400903.2_Missense_Mutation_p.L50V	NM_032368.3	NP_115744.2	Q8WZA0	LZIC_HUMAN	leucine zipper and CTNNBIP1 domain containing	50					response to ionizing radiation (GO:0010212)					breast(1)|endometrium(2)|large_intestine(2)|lung(1)|skin(1)	7		all_lung(284;0.000407)|Renal(390;0.000469)|Lung NSC(185;0.000577)|Colorectal(325;0.0062)|Breast(348;0.00686)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.29e-08)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;0.000242)|BRCA - Breast invasive adenocarcinoma(304;0.000299)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|STAD - Stomach adenocarcinoma(132;0.00842)|READ - Rectum adenocarcinoma(331;0.0419)		AGTTGCTCCAGAGTTTCCTTT	0.328																																					p.L50V		Atlas-SNP	.											.	LZIC	11	.	0			c.C148G						.						149	155	153					1																	9995639		2203	4299	6502	SO:0001583	missense	84328	exon3			GCTCCAGAGTTTC	AB060688	CCDS107.1	1p36.22	2008-02-05			ENSG00000162441	ENSG00000162441			17497	protein-coding gene	gene with protein product		610458				11712074	Standard	NM_032368		Approved	MGC15436	uc001aqm.3	Q8WZA0	OTTHUMG00000001804	ENST00000377223.1:c.148C>G	chr1.hg19:g.9995639G>C	ENSP00000366430:p.Leu50Val	70.0	0.0		78.0	28.0	NM_032368	B2R6F0|B4E2N0|Q96IU1	Missense_Mutation	SNP	ENST00000377223.1	hg19	CCDS107.1	.	.	.	.	.	.	.	.	.	.	G	12.78	2.039200	0.35989	.	.	ENSG00000162441	ENST00000377223;ENST00000400903;ENST00000541052;ENST00000377213	T;T;T;T	0.31510	1.49;1.49;1.49;1.49	5.63	3.39	0.38822	.	0.000000	0.64402	D	0.000001	T	0.20981	0.0505	L	0.33137	0.985	0.49130	D	0.999754	B;B	0.28512	0.214;0.087	B;B	0.20767	0.031;0.018	T	0.05037	-1.0910	9	.	.	.	.	12.5259	0.56085	0.1618:0.0:0.8382:0.0	.	71;50	B4E2N0;Q8WZA0	.;LZIC_HUMAN	V	50;50;71;50	ENSP00000366430:L50V;ENSP00000383695:L50V;ENSP00000437432:L71V;ENSP00000366418:L50V	.	L	-	1	2	LZIC	9918226	0.345000	0.24835	1.000000	0.80357	0.996000	0.88848	0.746000	0.26275	1.350000	0.45770	0.491000	0.48974	CTG	.	.		0.328	LZIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005037.1	NM_032368		C	9995639	G	C	9995639	3	2	325	1	0	0	0	0	1	0	0	0	9144	933	33	4	444	4	LZIC	1	9995639	Missense_Mutation	SNP	G	TCGA-MR-A520-01A-11D-A25V-10		9995639	239254982	1	45771										
RSC1A1	6248	hgsc.bcm.edu	37	chr1	15988085	15988085	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.153846153846154	4	1	1.84868421052632	1.47894736842105	2.01674641148325	0.485714285714286	1	0	ccaccattgatttttcctgcCacagatattgaccgcattct	5	13	1	3			TCGA-MR-A520-01A-11D-A25V-10	TCGA-MR-A520-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	352fbbb4-88a5-4354-b1fa-3a01da3fbfa7	64b28729-b106-4b33-994d-f1710478466c	g.chr1:15988085C>G	ENST00000345034.1	+	1	1722	c.1722C>G	c.(1720-1722)gcC>gcG	p.A574A	DDI2_ENST00000480945.1_3'UTR	NM_006511.1	NP_006502.1	Q92681	RSCA1_HUMAN	regulatory solute carrier protein, family 1, member 1	574	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.				intestinal absorption (GO:0050892)|negative regulation of transport (GO:0051051)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	brush border (GO:0005903)|cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ion channel inhibitor activity (GO:0008200)			kidney(1)|large_intestine(3)|lung(6)|ovary(1)	11		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00276)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.73e-07)|COAD - Colon adenocarcinoma(227;3.49e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000114)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TTTTTCCTGCCACAGATATTG	0.473																																					p.A574A		Atlas-SNP	.											.	RSC1A1	29	.	0			c.C1722G						.						220	200	207					1																	15988085		2203	4300	6503	SO:0001819	synonymous_variant	6248	exon1			TCCTGCCACAGAT	BN000122, X82877	CCDS161.1	1p36.1	1998-08-25			ENSG00000215695	ENSG00000215695			10458	protein-coding gene	gene with protein product		601966					Standard	NM_006511		Approved	RS1	uc010obn.2	Q92681	OTTHUMG00000067830	ENST00000345034.1:c.1722C>G	chr1.hg19:g.15988085C>G		239.0	0.0		250.0	79.0	NM_006511	B2RBP5	Silent	SNP	ENST00000345034.1	hg19	CCDS161.1																																																																																			.	.		0.473	RSC1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145500.1	NM_006511		G	15988085	C	G	15988085	2	3	325	1	0	0	0	0	0	0	0	1	13713	581	21	4		4	RSC1A1	1	15988085	Silent	SNP	C	TCGA-MR-A520-01A-11D-A25V-10	5992446	15988085	233262536	2	45772										
DDOST	1650	hgsc.bcm.edu	37	chr1	20980769	20980769	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.153846153846154	4	1	1.84868421052632	1.47894736842105	2.01674641148325	0.485714285714286	1	0	gagttgaagaaggagtcgctGaagaagtcgagggagccgct	17	6	0	4			TCGA-MR-A520-01A-11D-A25V-10	TCGA-MR-A520-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	352fbbb4-88a5-4354-b1fa-3a01da3fbfa7	64b28729-b106-4b33-994d-f1710478466c	g.chr1:20980769G>A	ENST00000375048.3	-	7	897	c.792C>T	c.(790-792)ttC>ttT	p.F264F	PINK1-AS_ENST00000451424.1_RNA|DDOST_ENST00000415136.2_Silent_p.F227F|DDOST_ENST00000602624.2_Silent_p.F247F	NM_005216.4	NP_005207	P39656	OST48_HUMAN	dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit (non-catalytic)	264					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|innate immune response (GO:0045087)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|response to cytokine (GO:0034097)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|T cell activation (GO:0042110)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)|protein complex (GO:0043234)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)|skin(1)	13		all_lung(284;2.98e-05)|Lung NSC(340;3.25e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.17e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000141)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.00046)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		AGGAGTCGCTGAAGAAGTCGA	0.632																																					p.F264F		Atlas-SNP	.											.	DDOST	30	.	0			c.C792T						.						38	35	36					1																	20980769		2164	4216	6380	SO:0001819	synonymous_variant	1650	exon7			GTCGCTGAAGAAG	D29643	CCDS212.1	1p36.1	2013-03-06	2013-03-06		ENSG00000244038	ENSG00000244038	2.4.1.119		2728	protein-coding gene	gene with protein product	"oligosaccharyltransferase subunit 48"	602202	"dolichyl-diphosphooligosaccharide-protein glycosyltransferase", "dolichyl-diphosphooligosaccharide--protein glycosyltransferase"			9367678	Standard	NM_005216		Approved	OST, KIAA0115, OST48, WBP1	uc001bdo.1	P39656	OTTHUMG00000002844	ENST00000375048.3:c.792C>T	chr1.hg19:g.20980769G>A		128.0	0.0		153.0	48.0	NM_005216	B2RDQ4|B4DJE3|B4DLI2|O43244|Q5VWA5|Q8NI93|Q9BUI2	Silent	SNP	ENST00000375048.3	hg19	CCDS212.1																																																																																			.	.		0.632	DDOST-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007961.2	NM_005216		A	20980769	G	A	20980769	2	1	325	1	0	0	0	0	0	0	0	1	4337	1281	45	3		3	DDOST	1	20980769	Silent	SNP	G	TCGA-MR-A520-01A-11D-A25V-10	4992684	20980769	228269852	3	45773										
AHDC1	27245	hgsc.bcm.edu	37	chr1	27875598	27875598	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.153846153846154	4	1	1.84868421052632	1.47894736842105	2.01674641148325	0.485714285714286	1	0	tgtgggcgctgctgggtgagGcagggaggctgttgccactg	20	8	0	1			TCGA-MR-A520-01A-11D-A25V-10	TCGA-MR-A520-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	352fbbb4-88a5-4354-b1fa-3a01da3fbfa7	64b28729-b106-4b33-994d-f1710478466c	g.chr1:27875598G>T	ENST00000247087.5	-	5	3625	c.3029C>A	c.(3028-3030)gCc>gAc	p.A1010D	AHDC1_ENST00000374011.2_Missense_Mutation_p.A1010D			Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	1010							DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)		GCTGGGTGAGGCAGGGAGGCT	0.647																																					p.A1010D		Atlas-SNP	.											.	AHDC1	98	.	0			c.C3029A						.						28	30	30					1																	27875598		2203	4298	6501	SO:0001583	missense	27245	exon6			GGTGAGGCAGGGA	AK125431	CCDS30652.1	1p36.13	2008-02-05			ENSG00000126705	ENSG00000126705			25230	protein-coding gene	gene with protein product		615790				8619474, 9110174	Standard	XM_005245848		Approved	DJ159A19.3, RP1-159A19.1	uc009vsy.3	Q5TGY3	OTTHUMG00000003398	ENST00000247087.5:c.3029C>A	chr1.hg19:g.27875598G>T	ENSP00000247087:p.Ala1010Asp	27.0	0.0		37.0	4.0	NM_001029882	Q5TGY4|Q6PJK1|Q6ZUQ6|Q99769|Q9NUF5	Missense_Mutation	SNP	ENST00000247087.5	hg19	CCDS30652.1	.	.	.	.	.	.	.	.	.	.	G	13.78	2.339478	0.41398	.	.	ENSG00000126705	ENST00000247087;ENST00000374011	T;T	0.52754	0.65;0.65	5.79	5.79	0.91817	.	0.094954	0.42053	D	0.000777	T	0.44787	0.1310	N	0.19112	0.55	0.36409	D	0.863591	P	0.46784	0.884	P	0.47206	0.541	T	0.55885	-0.8070	10	0.87932	D	0	-12.2488	18.7978	0.92003	0.0:0.0:1.0:0.0	.	1010	Q5TGY3	AHDC1_HUMAN	D	1010	ENSP00000247087:A1010D;ENSP00000363123:A1010D	ENSP00000247087:A1010D	A	-	2	0	AHDC1	27748185	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	4.791000	0.62460	2.735000	0.93741	0.655000	0.94253	GCC	.	.		0.647	AHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009523.3			T	27875598	G	T	27875598	3	4	325	1	0	0	0	0	1	0	0	0	412	1203	42	3	1786	3	AHDC1	1	27875598	Missense_Mutation	SNP	G	TCGA-MR-A520-01A-11D-A25V-10	6894829	27875598	221375023	4	45774										
TMEM61	199964	hgsc.bcm.edu	37	chr1	55452005	55452005	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.153846153846154	4	1	1.84868421052632	1.47894736842105	2.01674641148325	0.485714285714286	1	0	tggcctgctgctgctcattgGcctgctgtggtccgtcaagg	14	12	2	0			TCGA-MR-A520-01A-11D-A25V-10	TCGA-MR-A520-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	352fbbb4-88a5-4354-b1fa-3a01da3fbfa7	64b28729-b106-4b33-994d-f1710478466c	g.chr1:55452005G>A	ENST00000371268.3	+	2	525	c.251G>A	c.(250-252)gGc>gAc	p.G84D	RP11-12C17.2_ENST00000436960.1_RNA	NM_182532.1	NP_872338.1	Q8N0U2	TMM61_HUMAN	transmembrane protein 61	84						integral component of membrane (GO:0016021)				endometrium(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	4						CTGCTCATTGGCCTGCTGTGG	0.652																																					p.G84D		Atlas-SNP	.											.	TMEM61	22	.	0			c.G251A						.						93	93	93					1																	55452005		2203	4300	6503	SO:0001583	missense	199964	exon2			TCATTGGCCTGCT	BC029775	CCDS601.1	1p32.3	2008-02-05			ENSG00000143001	ENSG00000143001			27296	protein-coding gene	gene with protein product						12477932	Standard	NM_182532		Approved		uc001cyd.3	Q8N0U2	OTTHUMG00000009991	ENST00000371268.3:c.251G>A	chr1.hg19:g.55452005G>A	ENSP00000360315:p.Gly84Asp	72.0	0.0		125.0	36.0	NM_182532		Missense_Mutation	SNP	ENST00000371268.3	hg19	CCDS601.1	.	.	.	.	.	.	.	.	.	.	G	15.10	2.732199	0.48939	.	.	ENSG00000143001	ENST00000371268	T	0.62105	0.05	4.8	3.89	0.44902	.	0.000000	0.53938	D	0.000050	T	0.67813	0.2933	L	0.32530	0.975	0.29843	N	0.829037	D	0.89917	1.0	D	0.78314	0.991	T	0.66352	-0.5945	10	0.87932	D	0	-20.7621	11.2898	0.49244	0.0855:0.0:0.9145:0.0	.	84	Q8N0U2	TMM61_HUMAN	D	84	ENSP00000360315:G84D	ENSP00000360315:G84D	G	+	2	0	TMEM61	55224593	1.000000	0.71417	0.953000	0.39169	0.209000	0.24338	5.568000	0.67385	1.241000	0.43820	0.655000	0.94253	GGC	.	.		0.652	TMEM61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027683.1	NM_182532		A	55452005	G	A	55452005	3	1	325	1	0	0	0	0	1	0	0	0	16203	1203	42	3	257	3	TMEM61	1	55452005	Missense_Mutation	SNP	G	TCGA-MR-A520-01A-11D-A25V-10	27576407	55452005	193798616	5	45775										
ARHGAP29	9411	hgsc.bcm.edu	37	chr1	94654393	94654393	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.153846153846154	4	1	1.84868421052632	1.47894736842105	2.01674641148325	0.485714285714286	1	0	agacttaaatatagatgtacCtggacttatagattctgaat	7	5	1	4			TCGA-MR-A520-01A-11D-A25V-10	TCGA-MR-A520-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	352fbbb4-88a5-4354-b1fa-3a01da3fbfa7	64b28729-b106-4b33-994d-f1710478466c	g.chr1:94654393C>T	ENST00000260526.6	-	15	1863	c.1681G>A	c.(1681-1683)Gga>Aga	p.G561R	ARHGAP29_ENST00000482481.1_5'UTR	NM_004815.3	NP_004806.3	Q52LW3	RHG29_HUMAN	Rho GTPase activating protein 29	561					positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|Rho GTPase activator activity (GO:0005100)			NS(1)|breast(5)|endometrium(6)|kidney(2)|large_intestine(9)|lung(19)|ovary(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_lung(203;0.000732)|Lung NSC(277;0.00328)		all cancers(265;0.0187)|Epithelial(280;0.159)		ATAGATGTACCTGGACTTATA	0.353																																					p.G561R		Atlas-SNP	.											.	ARHGAP29	132	.	0			c.G1681A						.						73	74	74					1																	94654393		2203	4299	6502	SO:0001630	splice_region_variant	9411	exon15			ATGTACCTGGACT		CCDS748.1	1p22.1	2011-06-29			ENSG00000137962	ENSG00000137962		"Rho GTPase activating proteins"	30207	protein-coding gene	gene with protein product		610496				9305890	Standard	NM_004815		Approved	PARG1	uc001dqj.4	Q52LW3	OTTHUMG00000010643	ENST00000260526.6:c.1681+1G>A	chr1.hg19:g.94654393C>T		234.0	0.0		215.0	9.0	NM_004815	O15463|Q59H86|Q5VYZ0|Q6NVX2|Q8TBI6	Missense_Mutation	SNP	ENST00000260526.6	hg19	CCDS748.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.904241	0.92035	.	.	ENSG00000137962	ENST00000260526	T	0.27104	1.69	5.64	5.64	0.86602	.	0.000000	0.37530	N	0.002042	T	0.39860	0.1094	L	0.54323	1.7	0.80722	D	1	D;D	0.89917	1.0;0.989	D;P	0.81914	0.995;0.762	T	0.01371	-1.1372	9	.	.	.	-25.9961	18.8715	0.92317	0.0:1.0:0.0:0.0	.	561;561	F8VWZ8;Q52LW3	.;RHG29_HUMAN	R	561	ENSP00000260526:G561R	.	G	-	1	0	ARHGAP29	94426981	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	6.550000	0.73905	2.937000	0.99478	0.650000	0.86243	GGA	.	.		0.353	ARHGAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029376.2	NM_004815	Missense_Mutation	T	94654393	C	T	94654393	5	4	325	1	0	0	0	0	0	0	1	0	878	695	24	3	2140	3	ARHGAP29	1	94654393	Splice_Site	SNP	C	TCGA-MR-A520-01A-11D-A25V-10	39202388	94654393	154596228	6	45776										
GJA8	2703	hgsc.bcm.edu	37	chr1	147380477	147380477	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.153846153846154	4	1	1.84868421052632	1.47894736842105	2.01674641148325	0.485714285714286	1	0	ccagggcagcgtcaagaagaGcagcggcagcaaaggcacta	14	11	1	2			TCGA-MR-A520-01A-11D-A25V-10	TCGA-MR-A520-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	352fbbb4-88a5-4354-b1fa-3a01da3fbfa7	64b28729-b106-4b33-994d-f1710478466c	g.chr1:147380477G>A	ENST00000369235.1	+	1	395	c.395G>A	c.(394-396)aGc>aAc	p.S132N	GJA8_ENST00000240986.4_Missense_Mutation_p.S132N			P48165	CXA8_HUMAN	gap junction protein, alpha 8, 50kDa	132					cell-cell signaling (GO:0007267)|lens development in camera-type eye (GO:0002088)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of plasma membrane (GO:0005887)	channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)	37	all_hematologic(923;0.0276)					GTCAAGAAGAGCAGCGGCAGC	0.622																																					p.S132N	Melanoma(76;1255 1795 8195 52096)	Atlas-SNP	.											.	GJA8	108	.	0			c.G395A						.						58	67	64					1																	147380477		2203	4300	6503	SO:0001583	missense	2703	exon2			AGAAGAGCAGCGG	U34802	CCDS30834.1	1q21.1	2008-02-05	2007-01-16		ENSG00000121634	ENSG00000121634		"Ion channels / Gap junction proteins (connexins)"	4281	protein-coding gene	gene with protein product	"connexin 50"	600897	"gap junction protein, alpha 8, 50kD (connexin 50)", "gap junction protein, alpha 8, 50kDa (connexin 50)"	CAE1, CZP1, CAE		9497259, 7796604	Standard	NM_005267		Approved	CX50	uc001epu.2	P48165	OTTHUMG00000024085	ENST00000369235.1:c.395G>A	chr1.hg19:g.147380477G>A	ENSP00000358238:p.Ser132Asn	52.0	0.0		53.0	11.0	NM_005267	A7L5M5|Q5VVN9|Q9NP25	Missense_Mutation	SNP	ENST00000369235.1	hg19	CCDS30834.1	.	.	.	.	.	.	.	.	.	.	g	6.216	0.408009	0.11754	.	.	ENSG00000121634	ENST00000240986;ENST00000369235	D;D	0.97529	-4.42;-4.42	4.72	4.72	0.59763	.	1.187530	0.06334	N	0.706773	D	0.90438	0.7006	L	0.36672	1.1	0.30088	N	0.808548	B	0.02656	0.0	B	0.06405	0.002	T	0.80027	-0.1554	10	0.21014	T	0.42	.	11.1292	0.48336	0.0:0.1876:0.8124:0.0	.	132	P48165	CXA8_HUMAN	N	132	ENSP00000240986:S132N;ENSP00000358238:S132N	ENSP00000240986:S132N	S	+	2	0	GJA8	145847101	1.000000	0.71417	0.993000	0.49108	0.311000	0.27955	2.809000	0.47971	2.151000	0.67156	0.436000	0.28706	AGC	.	.		0.622	GJA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060647.1	NM_005267		A	147380477	G	A	147380477	3	1	325	1	0	0	0	0	1	0	0	0	6413	971	34	3	397	3	GJA8	1	147380477	Missense_Mutation	SNP	G	TCGA-MR-A520-01A-11D-A25V-10	52726084	147380477	101870144	7	45777										
CELF3	11189	hgsc.bcm.edu	37	chr1	151679692	151679692	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.153846153846154	4	1	1.84868421052632	1.47894736842105	2.01674641148325	0.485714285714286	1	0	cagtgggctgggtgggcaccGggctgtagccgttgacgccc	18	12	0	1			TCGA-MR-A520-01A-11D-A25V-10	TCGA-MR-A520-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	352fbbb4-88a5-4354-b1fa-3a01da3fbfa7	64b28729-b106-4b33-994d-f1710478466c	g.chr1:151679692G>T	ENST00000290583.4	-	8	1644	c.851C>A	c.(850-852)cCg>cAg	p.P284Q	CELF3_ENST00000470688.1_5'UTR|RP11-98D18.1_ENST00000457548.1_RNA|CELF3_ENST00000392706.3_Missense_Mutation_p.P101Q|CELF3_ENST00000290585.4_Intron	NM_001172648.1|NM_007185.4	NP_001166119.1|NP_009116.3	Q5SZQ8	CELF3_HUMAN	CUGBP, Elav-like family member 3	284				P -> Q (in Ref. 5; AAH52491). {ECO:0000305}.	mRNA splicing, via spliceosome (GO:0000398)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	21						GGTGGGCACCGGGCTGTAGCC	0.677																																					p.P284Q		Atlas-SNP	.											.	CELF3	49	.	0			c.C851A						.						23	23	23					1																	151679692		2169	4263	6432	SO:0001583	missense	11189	exon8			GGCACCGGGCTGT	U80759	CCDS1002.1, CCDS53367.1	1q21	2013-02-12	2010-02-19	2010-02-19	ENSG00000159409	ENSG00000159409		"Trinucleotide (CAG) repeat containing", "RNA binding motif (RRM) containing"	11967	protein-coding gene	gene with protein product	"expanded repeat domain, CAG/CTG 4", "CAG repeat domain", "CUG-BP and ETR-3 like factor 3"	612678	"trinucleotide repeat containing 4"	TNRC4		9225980	Standard	XM_005244859		Approved	CAGH4, BRUNOL1, ERDA4, MGC57297	uc001eys.2	Q5SZQ8	OTTHUMG00000013064	ENST00000290583.4:c.851C>A	chr1.hg19:g.151679692G>T	ENSP00000290583:p.Pro284Gln	75.0	0.0		97.0	4.0	NM_007185	B7ZKK6|O15414|Q499Y6|Q5SZQ7|Q6NVK0|Q8IZ98|Q9BZC2|Q9HB30	Missense_Mutation	SNP	ENST00000290583.4	hg19	CCDS1002.1	.	.	.	.	.	.	.	.	.	.	.	13.69	2.313326	0.40996	.	.	ENSG00000159409	ENST00000290583;ENST00000392706	T;T	0.15834	2.39;3.48	3.86	3.86	0.44501	.	0.362099	0.25558	N	0.029855	T	0.11196	0.0273	L	0.34521	1.04	0.41768	D	0.989759	P;B;B;B	0.49307	0.922;0.33;0.389;0.3	P;B;B;B	0.51895	0.683;0.265;0.159;0.227	T	0.03784	-1.1004	10	0.37606	T	0.19	-13.192	10.711	0.45984	0.0:0.1945:0.8055:0.0	.	101;284;284;283	B4DQL3;Q5SZQ8-2;Q5SZQ8;Q5SZQ8-3	.;.;CELF3_HUMAN;.	Q	284;101	ENSP00000290583:P284Q;ENSP00000376470:P101Q	ENSP00000290583:P284Q	P	-	2	0	CELF3	149946316	0.861000	0.29849	0.985000	0.45067	0.938000	0.57974	1.654000	0.37334	2.008000	0.58898	0.555000	0.69702	CCG	.	.		0.677	CELF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036663.2	NM_007185		T	151679692	G	T	151679692	3	4	325	1	0	0	0	0	1	0	0	0	3219	1116	39	1	566	1	CELF3	1	151679692	Missense_Mutation	SNP	G	TCGA-MR-A520-01A-11D-A25V-10	4299215	151679692	97570929	8	45778										
IGFN1	91156	hgsc.bcm.edu	37	chr1	201196307	201196307	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.153846153846154	4	1	1.84868421052632	1.47894736842105	2.01674641148325	0.485714285714286	1	0	tgagaacacgctgggccaggCagtcagcactgccaccctca	11	15	2	1	rs543665080		TCGA-MR-A520-01A-11D-A25V-10	TCGA-MR-A520-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	352fbbb4-88a5-4354-b1fa-3a01da3fbfa7	64b28729-b106-4b33-994d-f1710478466c	g.chr1:201196307C>A	ENST00000335211.4	+	23	11214	c.11084C>A	c.(11083-11085)gCa>gAa	p.A3695E	IGFN1_ENST00000295591.8_3'UTR	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	1238						nucleus (GO:0005634)|Z disc (GO:0030018)				autonomic_ganglia(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						CTGGGCCAGGCAGTCAGCACT	0.632													C|||	1	0.000199681	8e-04	0	5008	,	,		15052	0		0	False		,,,				2504	0				p.A3695E		Atlas-SNP	.											.	IGFN1	220	.	0			c.C11084A						.						36	22	27					1																	201196307		2201	4299	6500	SO:0001583	missense	91156	exon23			GCCAGGCAGTCAG	AY245430	CCDS53455.1	1q32.1	2013-02-11			ENSG00000163395	ENSG00000163395		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	24607	protein-coding gene	gene with protein product							Standard	NM_001164586		Approved	DKFZp434B1231, EEF1A2BP1	uc001gwc.3	Q86VF2	OTTHUMG00000035728	ENST00000335211.4:c.11084C>A	chr1.hg19:g.201196307C>A	ENSP00000334714:p.Ala3695Glu	106.0	0.0		127.0	6.0	NM_001164586	F8WAI1|Q9NT72	Missense_Mutation	SNP	ENST00000335211.4	hg19	CCDS53455.1	.	.	.	.	.	.	.	.	.	.	C	15.94	2.981139	0.53827	.	.	ENSG00000163395	ENST00000335211	T	0.67865	-0.29	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	T	0.81795	0.4898	M	0.77103	2.36	0.80722	D	1	D	0.69078	0.997	D	0.77557	0.99	D	0.84135	0.0414	10	0.72032	D	0.01	.	15.8823	0.79213	0.0:1.0:0.0:0.0	.	3695	F8WAI1	.	E	3695	ENSP00000334714:A3695E	ENSP00000334714:A3695E	A	+	2	0	IGFN1	199462930	0.948000	0.32251	0.947000	0.38551	0.140000	0.21249	2.084000	0.41625	2.430000	0.82344	0.655000	0.94253	GCA	.	.		0.632	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275		A	201196307	C	A	201196307	3	1	325	1	0	0	0	0	1	0	0	0	7599	710	25	3	11170	3	IGFN1	1	201196307	Missense_Mutation	SNP	C	TCGA-MR-A520-01A-11D-A25V-10	49516615	201196307	48054314	9	45779										
LYG2	254773	hgsc.bcm.edu	37	chr2	99861811	99861811	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.153846153846154	4	1	1.84868421052632	1.47894736842105	2.01674641148325	0.485714285714286	1	0	ttccctggagatgatggctgCgatgacagcagggtccacgc	14	11	0	3			TCGA-MR-A520-01A-11D-A25V-10	TCGA-MR-A520-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	352fbbb4-88a5-4354-b1fa-3a01da3fbfa7	64b28729-b106-4b33-994d-f1710478466c	g.chr2:99861811C>T	ENST00000409238.1	-	3	315	c.295G>A	c.(295-297)Gca>Aca	p.A99T	LYG2_ENST00000333017.2_Missense_Mutation_p.A99T|LYG2_ENST00000409679.1_Missense_Mutation_p.A99T|LYG2_ENST00000423800.1_Missense_Mutation_p.A99T			Q86SG7	LYG2_HUMAN	lysozyme G-like 2	99					cell wall macromolecule catabolic process (GO:0016998)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)	lysozyme activity (GO:0003796)			large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(1)|stomach(1)	12						ATGATGGCTGCGATGACAGCA	0.498																																					p.A99T		Atlas-SNP	.											LYG2,NS,carcinoma,0,2	LYG2	26	.	0			c.G295A						.						115	103	107					2																	99861811		2203	4300	6503	SO:0001583	missense	254773	exon4			TGGCTGCGATGAC	AF323919	CCDS2042.1	2q11.2	2008-02-05			ENSG00000185674	ENSG00000185674			29615	protein-coding gene	gene with protein product						8889548, 12574869	Standard	NM_175735		Approved	LYGH	uc002szw.1	Q86SG7	OTTHUMG00000130643	ENST00000409238.1:c.295G>A	chr2.hg19:g.99861811C>T	ENSP00000386939:p.Ala99Thr	49.0	0.0		62.0	3.0	NM_175735	Q496G2|Q53RW0	Missense_Mutation	SNP	ENST00000409238.1	hg19	CCDS2042.1	.	.	.	.	.	.	.	.	.	.	C	18.78	3.697377	0.68386	.	.	ENSG00000185674	ENST00000409238;ENST00000333017;ENST00000409679;ENST00000423306	.	.	.	5.78	5.78	0.91487	Lytic transglycosylase-like, catalytic (1);Lysozyme-like domain (1);	0.000000	0.64402	D	0.000007	T	0.81113	0.4755	M	0.84585	2.705	0.52501	D	0.999953	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.998;0.999	T	0.82500	-0.0426	8	.	.	.	-20.2617	15.5051	0.75731	0.0:1.0:0.0:0.0	.	99;99;99	Q496G2;C9J4J0;Q86SG7	.;.;LYG2_HUMAN	T	99	.	.	A	-	1	0	LYG2	99228243	1.000000	0.71417	0.951000	0.38953	0.128000	0.20619	5.656000	0.67988	2.745000	0.94114	0.555000	0.69702	GCA	.	.		0.498	LYG2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330307.1	NM_175735		T	99861811	C	T	99861811	3	4	325	1	0	0	0	0	1	0	0	0	9114	768	27	1	355	1	LYG2	2	99861811	Missense_Mutation	SNP	C	TCGA-MR-A520-01A-11D-A25V-10		99861811	143337562	10	45780										
FAM190A	401145	hgsc.bcm.edu	37	chr4	91230460	91230460	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.153846153846154	4	1	1.84868421052632	1.47894736842105	2.01674641148325	0.485714285714286	1	0	ttcattaccggaaacctctgCtgctaatcagaaggaagtgt	9	9	3	1			TCGA-MR-A520-01A-11D-A25V-10	TCGA-MR-A520-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	352fbbb4-88a5-4354-b1fa-3a01da3fbfa7	64b28729-b106-4b33-994d-f1710478466c	g.chr4:91230460C>T	ENST00000509176.1	+	2	1313	c.1025C>T	c.(1024-1026)gCt>gTt	p.A342V	CCSER1_ENST00000333691.8_Missense_Mutation_p.A342V|CCSER1_ENST00000432775.2_Missense_Mutation_p.A342V	NM_001145065.1	NP_001138537.1	Q9C0I3	CCSE1_HUMAN	coiled-coil serine-rich protein 1	342																	GAAACCTCTGCTGCTAATCAG	0.423																																					p.A342V		Atlas-SNP	.											.	.	.	.	0			c.C1025T						.						100	93	95					4																	91230460		1858	4105	5963	SO:0001583	missense	401145	exon2			CCTCTGCTGCTAA		CCDS47099.1, CCDS47100.1	4q22.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184305	ENSG00000184305			29349	protein-coding gene	gene with protein product			"family with sequence similarity 190, member A"	FAM190A		11214970	Standard	NM_001145065		Approved	KIAA1680	uc003hsv.4	Q9C0I3	OTTHUMG00000160950	ENST00000509176.1:c.1025C>T	chr4.hg19:g.91230460C>T	ENSP00000425040:p.Ala342Val	191.0	0.0		217.0	70.0	NM_001145065	Q4W5M0|Q86V57	Missense_Mutation	SNP	ENST00000509176.1	hg19	CCDS47099.1	.	.	.	.	.	.	.	.	.	.	C	13.79	2.340894	0.41498	.	.	ENSG00000184305	ENST00000509176;ENST00000432775;ENST00000333691;ENST00000458365	T;T;T	0.51325	1.23;0.71;1.23	4.73	3.89	0.44902	.	0.315828	0.30510	N	0.009475	T	0.34366	0.0895	L	0.43152	1.355	0.27462	N	0.953121	B;B;B	0.28783	0.222;0.192;0.192	B;B;B	0.27262	0.046;0.043;0.078	T	0.31194	-0.9952	10	0.52906	T	0.07	-25.062	3.7418	0.08533	0.1341:0.583:0.1304:0.1524	.	342;342;342	Q9C0I3-2;Q9C0I3;E7EUW0	.;F190A_HUMAN;.	V	342	ENSP00000425040:A342V;ENSP00000389283:A342V;ENSP00000329482:A342V	ENSP00000329482:A342V	A	+	2	0	FAM190A	91449483	1.000000	0.71417	1.000000	0.80357	0.853000	0.48598	1.463000	0.35277	1.317000	0.45149	-0.216000	0.12614	GCT	.	.		0.423	CCSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363109.3	NM_001145065		T	91230460	C	T	91230460	3	4	325	1	0	0	0	0	1	0	0	0	5526	797	28	3	1027	3	FAM190A	4	91230460	Missense_Mutation	SNP	C	TCGA-MR-A520-01A-11D-A25V-10		91230460	99923816	11	45781										
COL11A2	1302	hgsc.bcm.edu	37	chr6	33154431	33154431	+	Frame_Shift_Del	DEL	C	C	-													0.153846153846154	4	1	1.84868421052632	1.47894736842105	2.01674641148325	0.485714285714286	1	0	tggggttcctgattttgtggCctgtgaagtcttgatggttg							TCGA-MR-A520-01A-11D-A25V-10	TCGA-MR-A520-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	352fbbb4-88a5-4354-b1fa-3a01da3fbfa7	64b28729-b106-4b33-994d-f1710478466c	g.chr6:33154431delC	ENST00000374708.4	-	5	1029	c.771delG	c.(769-771)aggfs	p.R257fs	COL11A2_ENST00000357486.1_Frame_Shift_Del_p.R257fs|COL11A2_ENST00000395197.1_Frame_Shift_Del_p.R257fs|COL11A2_ENST00000374714.1_Frame_Shift_Del_p.R257fs|COL11A2_ENST00000341947.2_Frame_Shift_Del_p.R257fs|COL11A2_ENST00000374713.1_Frame_Shift_Del_p.R257fs|COL11A2_ENST00000361917.1_Frame_Shift_Del_p.R257fs|COL11A2_ENST00000395194.1_Frame_Shift_Del_p.R257fs|COL11A2_ENST00000374712.1_Frame_Shift_Del_p.R257fs	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	257	Nonhelical region.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						GATTTTGTGGCCTGTGAAGTC	0.587																																					p.P258fs	Melanoma(1;90 116 3946 5341 17093)	Pindel	.											.	COL11A2	124	.	0			c.772delC						.						213	206	208					6																	33154431		2203	4300	6503	SO:0001589	frameshift_variant	1302	exon5			.	U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"Collagens"	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000374708.4:c.771delG	chr6.hg19:g.33154431delC	ENSP00000363840:p.Arg257fs	275.0	0.0		324.0	52.0	NM_080679	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Frame_Shift_Del	DEL	ENST00000374708.4	hg19	CCDS43452.1																																																																																			.	.		0.587	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2			-	33154431	C	-	33154431	7	5	325	1	0	1	0	1	0	0	0	0	3670	738	26	0	4762	0	COL11A2	6	33154431	Frame_Shift_Del	DEL	C	TCGA-MR-A520-01A-11D-A25V-10		33154431	137960636	12	45782										
TOX	9760	hgsc.bcm.edu	37	chr8	59852023	59852023	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.153846153846154	4	1	1.84868421052632	1.47894736842105	2.01674641148325	0.485714285714286	1	0	tcaacttcattcaggtgcacCagcgagtggtctgggaggga	14	9	4	0			TCGA-MR-A520-01A-11D-A25V-10	TCGA-MR-A520-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	352fbbb4-88a5-4354-b1fa-3a01da3fbfa7	64b28729-b106-4b33-994d-f1710478466c	g.chr8:59852023C>T	ENST00000361421.1	-	3	469	c.249G>A	c.(247-249)ctG>ctA	p.L83L		NM_014729.2	NP_055544.1	O94900	TOX_HUMAN	thymocyte selection-associated high mobility group box	83						nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(13)|prostate(1)|skin(2)|stomach(1)	33		all_cancers(86;0.165)|Myeloproliferative disorder(644;0.00452)|all_lung(136;0.036)|Lung NSC(129;0.0464)|all_epithelial(80;0.0607)				TCAGGTGCACCAGCGAGTGGT	0.488																																					p.L83L	Pancreas(161;610 1969 17913 21374 22725)	Atlas-SNP	.											.	TOX	83	.	0			c.G249A						.						136	118	124					8																	59852023		2203	4300	6503	SO:0001819	synonymous_variant	9760	exon3			GTGCACCAGCGAG		CCDS34897.1	8q12.2-q12.3	2009-04-17			ENSG00000198846	ENSG00000198846			18988	protein-coding gene	gene with protein product		606863				9872452, 11850626	Standard	NM_014729		Approved	KIAA0808, TOX1	uc003xtw.1	O94900	OTTHUMG00000164331	ENST00000361421.1:c.249G>A	chr8.hg19:g.59852023C>T		209.0	0.0		213.0	11.0	NM_014729	Q96AV5	Silent	SNP	ENST00000361421.1	hg19	CCDS34897.1																																																																																			.	.		0.488	TOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378307.1	NM_014729		T	59852023	C	T	59852023	2	4	325	1	0	0	0	0	0	0	0	1	16392	581	21	3		3	TOX	8	59852023	Silent	SNP	C	TCGA-MR-A520-01A-11D-A25V-10		59852023	86511999	13	45783										
UCN3	114131	hgsc.bcm.edu	37	chr10	5416093	5416093	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.153846153846154	4	1	1.84868421052632	1.47894736842105	2.01674641148325	0.485714285714286	1	0	catgaacctcctcttcaacaTcgccaaggccaagaacctgc	6	16	2	2			TCGA-MR-A520-01A-11D-A25V-10	TCGA-MR-A520-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	352fbbb4-88a5-4354-b1fa-3a01da3fbfa7	64b28729-b106-4b33-994d-f1710478466c	g.chr10:5416093T>C	ENST00000380433.3	+	2	638	c.410T>C	c.(409-411)aTc>aCc	p.I137T		NM_053049.2	NP_444277.2	Q969E3	UCN3_HUMAN	urocortin 3	137					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|digestion (GO:0007586)|positive regulation of insulin secretion (GO:0032024)|positive regulation of membrane potential (GO:0045838)|response to corticosterone (GO:0051412)|response to glucose (GO:0009749)|response to immobilization stress (GO:0035902)|response to starvation (GO:0042594)	axon terminus (GO:0043679)|extracellular space (GO:0005615)|varicosity (GO:0043196)				endometrium(1)|large_intestine(1)	2						CTCTTCAACATCGCCAAGGCC	0.627																																					p.I137T		Atlas-SNP	.											.	UCN3	13	.	0			c.T410C						.						58	60	59					10																	5416093		2203	4300	6503	SO:0001583	missense	114131	exon2			TCAACATCGCCAA	AF361943	CCDS7065.1	10p15.1	2013-02-28	2012-10-17		ENSG00000178473	ENSG00000178473		"Endogenous ligands"	17781	protein-coding gene	gene with protein product	"stresscopin", "prepro-urocortin 3"	605901				11416224	Standard	NM_053049		Approved	UCNIII, SPC	uc001ihx.1	Q969E3	OTTHUMG00000017594	ENST00000380433.3:c.410T>C	chr10.hg19:g.5416093T>C	ENSP00000369798:p.Ile137Thr	66.0	0.0		66.0	4.0	NM_053049	Q496H2|Q5SR91	Missense_Mutation	SNP	ENST00000380433.3	hg19	CCDS7065.1	.	.	.	.	.	.	.	.	.	.	T	18.73	3.686176	0.68157	.	.	ENSG00000178473	ENST00000380433	T	0.37915	1.17	5.49	5.49	0.81192	.	0.070278	0.56097	D	0.000023	T	0.53530	0.1802	L	0.51422	1.61	0.46376	D	0.999011	D	0.71674	0.998	D	0.69824	0.966	T	0.55817	-0.8081	10	0.72032	D	0.01	-21.5148	14.395	0.67005	0.0:0.0:0.0:1.0	.	137	Q969E3	UCN3_HUMAN	T	137	ENSP00000369798:I137T	ENSP00000369798:I137T	I	+	2	0	UCN3	5406093	1.000000	0.71417	0.956000	0.39512	0.737000	0.42083	7.470000	0.80973	2.096000	0.63516	0.402000	0.26972	ATC	.	.		0.627	UCN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046547.1	NM_053049		C	5416093	T	C	5416093	3	2	325	1	0	0	0	0	1	0	0	0	16944	1435	50	2	412	2	UCN3	10	5416093	Missense_Mutation	SNP	T	TCGA-MR-A520-01A-11D-A25V-10		5416093	130118654	14	45784										
KIAA1279	26128	hgsc.bcm.edu	37	chr10	70775430	70775430	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.153846153846154	4	1	1.84868421052632	1.47894736842105	2.01674641148325	0.485714285714286	1	0	tgaactgtgtgatgccatctCtgcagtagaagagaaagtga	12	6	1	5			TCGA-MR-A520-01A-11D-A25V-10	TCGA-MR-A520-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	352fbbb4-88a5-4354-b1fa-3a01da3fbfa7	64b28729-b106-4b33-994d-f1710478466c	g.chr10:70775430C>T	ENST00000361983.4	+	7	1226	c.1124C>T	c.(1123-1125)tCt>tTt	p.S375F		NM_015634.3	NP_056449.1	Q96EK5	KBP_HUMAN	KIAA1279	375					cell differentiation (GO:0030154)|mitochondrial transport (GO:0006839)|nervous system development (GO:0007399)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)	kinesin binding (GO:0019894)			breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	14						GATGCCATCTCTGCAGTAGAA	0.413																																					p.S375F		Atlas-SNP	.											.	KIAA1279	35	.	0			c.C1124T						.						119	112	115					10																	70775430		2203	4300	6503	SO:0001583	missense	26128	exon7			CCATCTCTGCAGT	BC012180	CCDS7284.1	10q22.1	2008-02-05			ENSG00000198954	ENSG00000198954			23419	protein-coding gene	gene with protein product		609367					Standard	NM_015634		Approved	DKFZP586B0923, TTC20	uc001joy.3	Q96EK5	OTTHUMG00000018363	ENST00000361983.4:c.1124C>T	chr10.hg19:g.70775430C>T	ENSP00000354848:p.Ser375Phe	94.0	0.0		95.0	37.0	NM_015634	A8K5M8|Q9BR89|Q9ULE1|Q9Y428	Missense_Mutation	SNP	ENST00000361983.4	hg19	CCDS7284.1	.	.	.	.	.	.	.	.	.	.	C	13.71	2.317605	0.40996	.	.	ENSG00000198954	ENST00000361983	T	0.48836	0.8	5.51	4.38	0.52667	.	0.351400	0.32819	N	0.005605	T	0.26231	0.0640	N	0.14661	0.345	0.33903	D	0.638776	P	0.42649	0.786	B	0.40329	0.326	T	0.34502	-0.9826	10	0.54805	T	0.06	-20.501	2.826	0.05485	0.283:0.5395:0.0:0.1775	.	375	Q96EK5	KBP_HUMAN	F	375	ENSP00000354848:S375F	ENSP00000354848:S375F	S	+	2	0	KIAA1279	70445436	0.980000	0.34600	1.000000	0.80357	0.997000	0.91878	2.115000	0.41921	2.763000	0.94921	0.650000	0.86243	TCT	.	.		0.413	KIAA1279-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048370.1	NM_015634		T	70775430	C	T	70775430	3	4	325	1	0	0	0	0	1	0	0	0	8230	913	32	3	1150	3	KIAA1279	10	70775430	Missense_Mutation	SNP	C	TCGA-MR-A520-01A-11D-A25V-10	65359337	70775430	64759317	15	45785										
HTR7	3363	hgsc.bcm.edu	37	chr10	92616999	92616999	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.153846153846154	4	1	1.84868421052632	1.47894736842105	2.01674641148325	0.485714285714286	1	0	aaagatccacttgcccccgaTgaggtcggtgacgctgacga	12	12	0	4			TCGA-MR-A520-01A-11D-A25V-10	TCGA-MR-A520-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	352fbbb4-88a5-4354-b1fa-3a01da3fbfa7	64b28729-b106-4b33-994d-f1710478466c	g.chr10:92616999T>C	ENST00000336152.3	-	1	456	c.430A>G	c.(430-432)Atc>Gtc	p.I144V	HTR7_ENST00000371719.2_Missense_Mutation_p.I144V|HTR7_ENST00000371721.3_Missense_Mutation_p.I144V|HTR7_ENST00000277874.6_Missense_Mutation_p.I144V	NM_019859.3	NP_062873.1	P34969	5HT7R_HUMAN	5-hydroxytryptamine (serotonin) receptor 7, adenylate cyclase-coupled	144					blood circulation (GO:0008015)|circadian rhythm (GO:0007623)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|serotonin receptor signaling pathway (GO:0007210)|smooth muscle contraction (GO:0006939)|synaptic transmission (GO:0007268)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin receptor activity (GO:0004993)			NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30					Amisulpride(DB06288)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Clozapine(DB00363)|Dopamine(DB00988)|Eletriptan(DB00216)|Epinastine(DB00751)|Ergoloid mesylate(DB01049)|Iloperidone(DB04946)|Imipramine(DB00458)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Methysergide(DB00247)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Quetiapine(DB01224)|Ziprasidone(DB00246)	TTGCCCCCGATGAGGTCGGTG	0.597																																					p.I144V		Atlas-SNP	.											.	HTR7	122	.	0			c.A430G						.						66	58	61					10																	92616999		2203	4300	6503	SO:0001583	missense	3363	exon1			CCCCGATGAGGTC	BC047526	CCDS7408.1, CCDS7409.1, CCDS7410.1	10q21-q24	2012-08-08	2012-02-03		ENSG00000148680	ENSG00000148680		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5302	protein-coding gene	gene with protein product		182137	"5-hydroxytryptamine (serotonin) receptor 7 (adenylate cyclase-coupled)"			8226867	Standard	NM_000872		Approved	5-HT7	uc001kha.3	P34969	OTTHUMG00000018732	ENST00000336152.3:c.430A>G	chr10.hg19:g.92616999T>C	ENSP00000337949:p.Ile144Val	223.0	0.0		306.0	79.0	NM_019860	B5BUP6|P78336|P78372|P78516|Q5VX01|Q5VX02|Q5VX03	Missense_Mutation	SNP	ENST00000336152.3	hg19	CCDS7408.1	.	.	.	.	.	.	.	.	.	.	T	12.26	1.883669	0.33255	.	.	ENSG00000148680	ENST00000336152;ENST00000277874;ENST00000371719;ENST00000371721	T;T;T;T	0.19250	2.16;2.16;2.16;2.16	4.97	4.97	0.65823	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.10551	0.0258	N	0.10945	0.07	0.50171	D	0.99985	B;B	0.21821	0.061;0.035	B;B	0.20767	0.031;0.016	T	0.07121	-1.0789	10	0.02654	T	1	.	14.6436	0.68742	0.0:0.0:0.0:1.0	.	144;144	P34969;P34969-2	5HT7R_HUMAN;.	V	144	ENSP00000337949:I144V;ENSP00000277874:I144V;ENSP00000360784:I144V;ENSP00000360786:I144V	ENSP00000277874:I144V	I	-	1	0	HTR7	92606979	0.998000	0.40836	1.000000	0.80357	0.996000	0.88848	2.895000	0.48648	1.872000	0.54250	0.460000	0.39030	ATC	.	.		0.597	HTR7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049343.1	NM_000872		C	92616999	T	C	92616999	3	2	325	1	0	0	0	0	1	0	0	0	7461	1464	51	2	1029	2	HTR7	10	92616999	Missense_Mutation	SNP	T	TCGA-MR-A520-01A-11D-A25V-10	21841569	92616999	42917748	16	45786										
MYOF	26509	hgsc.bcm.edu	37	chr10	95109596	95109596	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.153846153846154	4	1	1.84868421052632	1.47894736842105	2.01674641148325	0.485714285714286	1	0	agagaacagaacttggaaagTtgggtgtcttcttaaggttt	12	4	2	2			TCGA-MR-A520-01A-11D-A25V-10	TCGA-MR-A520-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	352fbbb4-88a5-4354-b1fa-3a01da3fbfa7	64b28729-b106-4b33-994d-f1710478466c	g.chr10:95109596T>C	ENST00000359263.4	-	36	4051	c.4052A>G	c.(4051-4053)aAc>aGc	p.N1351S	MYOF_ENST00000358334.5_Missense_Mutation_p.N1338S|MYOF_ENST00000371502.4_Missense_Mutation_p.N1351S|MYOF_ENST00000371501.4_Missense_Mutation_p.N1351S	NM_013451.3	NP_038479.1	Q9NZM1	MYOF_HUMAN	myoferlin	1351					blood circulation (GO:0008015)|cellular response to heat (GO:0034605)|muscle contraction (GO:0006936)|plasma membrane repair (GO:0001778)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)	caveola (GO:0005901)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)			NS(2)|autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(7)|large_intestine(15)|lung(14)|ovary(4)|prostate(4)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						ACTTGGAAAGTTGGGTGTCTT	0.453																																					p.N1351S		Atlas-SNP	.											.	MYOF	177	.	0			c.A4052G						.						110	109	109					10																	95109596		1894	4118	6012	SO:0001583	missense	26509	exon36			GGAAAGTTGGGTG	AB033033	CCDS41550.1, CCDS41551.1	10q24	2014-06-27	2008-11-26	2008-11-26	ENSG00000138119	ENSG00000138119			3656	protein-coding gene	gene with protein product	"fer-1-like family member 3"	604603	"fer-1 (C.elegans)-like 3 (myoferlin)", "fer-1-like 3, myoferlin (C. elegans)"	FER1L3		10607832, 10995573, 17702744	Standard	NM_013451		Approved	KIAA1207	uc001kin.3	Q9NZM1	OTTHUMG00000018772	ENST00000359263.4:c.4052A>G	chr10.hg19:g.95109596T>C	ENSP00000352208:p.Asn1351Ser	177.0	0.0		209.0	59.0	NM_013451	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	Missense_Mutation	SNP	ENST00000359263.4	hg19	CCDS41551.1	.	.	.	.	.	.	.	.	.	.	T	25.8	4.675819	0.88445	.	.	ENSG00000138119	ENST00000358334;ENST00000359263;ENST00000371501;ENST00000371502	T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22	5.53	5.53	0.82687	C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.83312	0.5227	M	0.89353	3.025	0.58432	D	0.999999	D;D	0.64830	0.994;0.972	D;P	0.63877	0.919;0.721	D	0.86513	0.1811	10	0.62326	D	0.03	-27.4168	15.6595	0.77174	0.0:0.0:0.0:1.0	.	1338;1351	Q9NZM1-6;Q9NZM1	.;MYOF_HUMAN	S	1338;1351;1351;1351	ENSP00000351094:N1338S;ENSP00000352208:N1351S;ENSP00000360556:N1351S;ENSP00000360557:N1351S	ENSP00000351094:N1338S	N	-	2	0	MYOF	95099586	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.985000	0.88162	2.102000	0.63906	0.459000	0.35465	AAC	.	.		0.453	MYOF-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049423.2	NM_013451		C	95109596	T	C	95109596	3	2	325	1	0	0	0	0	1	0	0	0	10098	1725	60	2	2209	2	MYOF	10	95109596	Missense_Mutation	SNP	T	TCGA-MR-A520-01A-11D-A25V-10	2492597	95109596	40425151	17	45787										
OR5J2	282775	hgsc.bcm.edu	37	chr11	55944717	55944717	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.153846153846154	4	1	1.84868421052632	1.47894736842105	2.01674641148325	0.485714285714286	1	0	ttctccggagtcattgccatGgccaccttcttgactgtgat	9	12	3	2			TCGA-MR-A520-01A-11D-A25V-10	TCGA-MR-A520-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	352fbbb4-88a5-4354-b1fa-3a01da3fbfa7	64b28729-b106-4b33-994d-f1710478466c	g.chr11:55944717G>C	ENST00000312298.1	+	1	624	c.624G>C	c.(622-624)atG>atC	p.M208I		NM_001005492.1	NP_001005492.1	Q8NH18	OR5J2_HUMAN	olfactory receptor, family 5, subfamily J, member 2	208						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.M208I(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	44	Esophageal squamous(21;0.00693)					TCATTGCCATGGCCACCTTCT	0.478																																					p.M208I		Atlas-SNP	.											OR5J2,NS,carcinoma,0,1	OR5J2	98	.	1	Substitution - Missense(1)	lung(1)	c.G624C						.						168	128	141					11																	55944717		2201	4296	6497	SO:0001583	missense	282775	exon1			TGCCATGGCCACC	AB065595	CCDS31522.1	11q11	2012-08-09			ENSG00000174957	ENSG00000174957		"GPCR / Class A : Olfactory receptors"	19612	protein-coding gene	gene with protein product							Standard	NM_001005492		Approved		uc010rjb.2	Q8NH18	OTTHUMG00000166835	ENST00000312298.1:c.624G>C	chr11.hg19:g.55944717G>C	ENSP00000310788:p.Met208Ile	308.0	1.0		309.0	96.0	NM_001005492	Q6IEU5	Missense_Mutation	SNP	ENST00000312298.1	hg19	CCDS31522.1	.	.	.	.	.	.	.	.	.	.	G	0.004	-2.301242	0.00243	.	.	ENSG00000174957	ENST00000312298	T	0.34275	1.37	4.55	0.121	0.14695	GPCR, rhodopsin-like superfamily (1);	0.615899	0.15672	N	0.250346	T	0.12305	0.0299	N	0.05441	-0.05	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.32268	-0.9913	10	0.02654	T	1	.	4.0132	0.09632	0.1572:0.1288:0.5818:0.1322	.	208	Q8NH18	OR5J2_HUMAN	I	208	ENSP00000310788:M208I	ENSP00000310788:M208I	M	+	3	0	OR5J2	55701293	0.000000	0.05858	0.007000	0.13788	0.003000	0.03518	-0.947000	0.03901	0.461000	0.27071	0.591000	0.81541	ATG	.	.		0.478	OR5J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391544.1	NM_001005492		C	55944717	G	C	55944717	3	2	325	1	0	0	0	0	1	0	0	0	11174	1348	47	4	626	4	OR5J2	11	55944717	Missense_Mutation	SNP	G	TCGA-MR-A520-01A-11D-A25V-10		55944717	79061799	18	45788										
FAT3	120114	hgsc.bcm.edu	37	chr11	92533065	92533065	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.153846153846154	4	1	1.84868421052632	1.47894736842105	2.01674641148325	0.485714285714286	1	0	agcctacatacaatacaacaCtatcagaagcatctcttatt	3	11	2	1			TCGA-MR-A520-01A-11D-A25V-10	TCGA-MR-A520-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	352fbbb4-88a5-4354-b1fa-3a01da3fbfa7	64b28729-b106-4b33-994d-f1710478466c	g.chr11:92533065C>G	ENST00000298047.6	+	9	6903	c.6886C>G	c.(6886-6888)Cta>Gta	p.L2296V	FAT3_ENST00000525166.1_Missense_Mutation_p.L2146V|FAT3_ENST00000409404.2_Missense_Mutation_p.L2296V			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	2296	Cadherin 21. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				CAATACAACACTATCAGAAGC	0.403										TCGA Ovarian(4;0.039)																											p.L2296V		Atlas-SNP	.											.	FAT3	1822	.	0			c.C6886G						.						94	84	87					11																	92533065		1900	4119	6019	SO:0001583	missense	120114	exon9			ACAACACTATCAG	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.6886C>G	chr11.hg19:g.92533065C>G	ENSP00000298047:p.Leu2296Val	159.0	0.0		145.0	12.0	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	hg19		.	.	.	.	.	.	.	.	.	.	C	7.659	0.684550	0.14973	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.45276	0.9;0.9;0.9	5.8	1.1	0.20463	.	.	.	.	.	T	0.29126	0.0724	N	0.12961	0.28	0.80722	D	1	D	0.58268	0.982	P	0.51193	0.662	T	0.03673	-1.1014	9	0.09843	T	0.71	.	10.3138	0.43725	0.0:0.4573:0.0:0.5427	.	2296	Q8TDW7-3	.	V	2296;2296;2146	ENSP00000298047:L2296V;ENSP00000387040:L2296V;ENSP00000432586:L2146V	ENSP00000298047:L2296V	L	+	1	2	FAT3	92172713	0.017000	0.18338	0.832000	0.32986	0.986000	0.74619	0.152000	0.16302	0.154000	0.19237	-0.312000	0.09012	CTA	.	.		0.403	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		G	92533065	C	G	92533065	3	3	325	1	0	0	0	0	1	0	0	0	5699	564	20	4	6920	4	FAT3	11	92533065	Missense_Mutation	SNP	C	TCGA-MR-A520-01A-11D-A25V-10	36588348	92533065	42473451	19	45789										
ZNF423	23090	hgsc.bcm.edu	37	chr16	49671020	49671020	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.153846153846154	4	1	1.84868421052632	1.47894736842105	2.01674641148325	0.485714285714286	1	0	gtggtcatgtaatgcactgtCaggtgctgcaggagggactc	15	8	2	0			TCGA-MR-A520-01A-11D-A25V-10	TCGA-MR-A520-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	352fbbb4-88a5-4354-b1fa-3a01da3fbfa7	64b28729-b106-4b33-994d-f1710478466c	g.chr16:49671020C>T	ENST00000561648.1	-	4	2096	c.2043G>A	c.(2041-2043)ctG>ctA	p.L681L	ZNF423_ENST00000563137.2_Silent_p.L621L|ZNF423_ENST00000567169.1_Silent_p.L564L|ZNF423_ENST00000535559.1_Silent_p.L564L|ZNF423_ENST00000562520.1_Silent_p.L621L|ZNF423_ENST00000562871.1_Silent_p.L621L|ZNF423_ENST00000262383.2_Silent_p.L681L	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	681					cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				AATGCACTGTCAGGTGCTGCA	0.582																																					p.L681L		Atlas-SNP	.											.	ZNF423	463	.	0			c.G2043A						.						70	67	68					16																	49671020		2198	4300	6498	SO:0001819	synonymous_variant	23090	exon4			CACTGTCAGGTGC	AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"Zinc fingers, C2H2-type"	16762	protein-coding gene	gene with protein product	"OLF-1/EBF associated zinc finger gene", " Smad- and Olf-interacting zinc finger protein", "early B-cell factor associated zinc finger protein"	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.2043G>A	chr16.hg19:g.49671020C>T		182.0	0.0		249.0	77.0	NM_015069	O94860|Q76N04|Q9NZ13	Silent	SNP	ENST00000561648.1	hg19	CCDS32445.1																																																																																			.	.		0.582	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069		T	49671020	C	T	49671020	2	4	325	1	0	0	0	0	0	0	0	1	17913	813	29	3		3	ZNF423	16	49671020	Silent	SNP	C	TCGA-MR-A520-01A-11D-A25V-10		49671020	40683733	20	45790										
LDHD	84937	hgsc.bcm.edu	37	chr16	75146313	75146313	+	IGR	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.153846153846154	4	1	1.84868421052632	1.47894736842105	2.01674641148325	0.485714285714286	1	0	tagcacggccttgagctgccGcatggtctccacgcccacgg	12	16	1	1			TCGA-MR-A520-01A-11D-A25V-10	TCGA-MR-A520-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	352fbbb4-88a5-4354-b1fa-3a01da3fbfa7	64b28729-b106-4b33-994d-f1710478466c	g.chr16:75146313G>T	ENST00000335325.4	+	0	4620				RP11-252E2.1_ENST00000499110.1_RNA|LDHD_ENST00000450168.2_Silent_p.R466R|LDHD_ENST00000300051.4_Silent_p.R489R	NM_032268.4	NP_115644.1	Q8ND25	ZNRF1_HUMAN	zinc and ring finger 1, E3 ubiquitin protein ligase						proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|lysosome (GO:0005764)|membrane (GO:0016020)|synapse (GO:0045202)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)	1						TTGAGCTGCCGCATGGTCTCC	0.637																																					p.R489R		Atlas-SNP	.											.	LDHD	34	.	0			c.C1465A						.						33	34	34					16																	75146313		2198	4300	6498	SO:0001628	intergenic_variant	197257	exon11			GCTGCCGCATGGT	AF378524	CCDS10912.1	16q22.3	2013-01-09	2012-02-23		ENSG00000186187	ENSG00000186187		"RING-type (C3HC4) zinc fingers"	18452	protein-coding gene	gene with protein product		612060	"zinc and ring finger 1"				Standard	NM_032268		Approved	nin283, FLJ14846, DKFZp434E229	uc002fdl.1	Q8ND25	OTTHUMG00000137606		chr16.hg19:g.75146313G>T		93.0	0.0		99.0	4.0	NM_153486	D3DUJ9|Q9H083	Silent	SNP	ENST00000335325.4	hg19	CCDS10912.1																																																																																			.	.		0.637	ZNRF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269020.2			T	75146313	G	T	75146313	1	4	325	0	1	0	0	0	0	0	0	0	8712	1086	38	1		1	LDHD	16	75146313	IGR	SNP	G	TCGA-MR-A520-01A-11D-A25V-10	25475293	75146313	15208440	21	45791										
SGSH	6448	hgsc.bcm.edu	37	chr17	78188902	78188902	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.153846153846154	4	1	1.84868421052632	1.47894736842105	2.01674641148325	0.485714285714286	1	0	tcgaaggagttgaagtggtgCacgtcctggtgcagcccgta	15	9	0	1			TCGA-MR-A520-01A-11D-A25V-10	TCGA-MR-A520-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	352fbbb4-88a5-4354-b1fa-3a01da3fbfa7	64b28729-b106-4b33-994d-f1710478466c	g.chr17:78188902C>T	ENST00000326317.6	-	3	371	c.285G>A	c.(283-285)gtG>gtA	p.V95V	SGSH_ENST00000572208.1_5'UTR|SGSH_ENST00000534910.1_Intron|SGSH_ENST00000570923.1_Missense_Mutation_p.C107Y	NM_000199.3	NP_000190.1	P51688	SPHM_HUMAN	N-sulfoglucosamine sulfohydrolase	95					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|proteoglycan metabolic process (GO:0006029)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	catalytic activity (GO:0003824)|metal ion binding (GO:0046872)|N-sulfoglucosamine sulfohydrolase activity (GO:0016250)|sulfuric ester hydrolase activity (GO:0008484)			central_nervous_system(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			TGAAGTGGTGCACGTCCTGGT	0.667																																					p.V95V		Atlas-SNP	.											.	SGSH	27	.	0			c.G285A						.						80	66	71					17																	78188902		2201	4300	6501	SO:0001819	synonymous_variant	6448	exon3			GTGGTGCACGTCC	BC047318	CCDS11770.1	17q25.3	2011-11-08	2008-07-31			ENSG00000181523	3.10.1.1		10818	protein-coding gene	gene with protein product	"sulfamidase", "mucopolysaccharidosis type IIIA"	605270				7493035	Standard	NM_000199		Approved	HSS, MPS3A, SFMD	uc002jxz.4	P51688		ENST00000326317.6:c.285G>A	chr17.hg19:g.78188902C>T		17.0	0.0		55.0	4.0	NM_000199	A8K5E2	Silent	SNP	ENST00000326317.6	hg19	CCDS11770.1	.	.	.	.	.	.	.	.	.	.	C	15.66	2.900547	0.52227	.	.	ENSG00000181523	ENST00000535808	.	.	.	3.82	2.85	0.33270	.	.	.	.	.	T	0.46927	0.1418	.	.	.	0.80722	D	1	B	0.21225	0.053	B	0.15484	0.013	T	0.46428	-0.9192	7	0.87932	D	0	-11.5594	8.7412	0.34558	0.0:0.632:0.25:0.1181	.	107	B7Z9A6	.	Y	107	.	ENSP00000443457:C107Y	C	-	2	0	SGSH	75803497	0.941000	0.31946	0.994000	0.49952	0.977000	0.68977	0.064000	0.14437	0.807000	0.34208	0.563000	0.77884	TGC	.	.		0.667	SGSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437695.1	NM_000199		T	78188902	C	T	78188902	2	4	325	1	0	0	0	0	0	0	0	1	14236	697	25	3		3	SGSH	17	78188902	Silent	SNP	C	TCGA-MR-A520-01A-11D-A25V-10		78188902	3006308	22	45792										
LRFN1	57622	hgsc.bcm.edu	37	chr19	39804840	39804840	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.153846153846154	4	1	1.84868421052632	1.47894736842105	2.01674641148325	0.485714285714286	1	0	cacacctccacgggcgccgtCgcttccccagcagcattgga	10	18	0	0			TCGA-MR-A520-01A-11D-A25V-10	TCGA-MR-A520-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	352fbbb4-88a5-4354-b1fa-3a01da3fbfa7	64b28729-b106-4b33-994d-f1710478466c	g.chr19:39804840C>T	ENST00000248668.4	-	1	1136	c.1137G>A	c.(1135-1137)gcG>gcA	p.A379A	CTC-246B18.8_ENST00000601911.1_RNA	NM_020862.1	NP_065913.1	Q9P244	LRFN1_HUMAN	leucine rich repeat and fibronectin type III domain containing 1	379	Ig-like.					cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				central_nervous_system(2)|cervix(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	18	all_cancers(60;1.85e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;1.96e-27)|all cancers(26;2.05e-24)|Lung(45;0.000278)|LUSC - Lung squamous cell carcinoma(53;0.000335)			CGGGCGCCGTCGCTTCCCCAG	0.687																																					p.A379A		Atlas-SNP	.											.	LRFN1	59	.	0			c.G1137A						.						25	31	29					19																	39804840		2176	4269	6445	SO:0001819	synonymous_variant	57622	exon1			CGCCGTCGCTTCC	BC014678	CCDS46071.1	19q13.2	2013-02-11				ENSG00000128011		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	29290	protein-coding gene	gene with protein product		612807				10819331, 16828986	Standard	NM_020862		Approved	KIAA1484, SALM2	uc002okw.2	Q9P244		ENST00000248668.4:c.1137G>A	chr19.hg19:g.39804840C>T		30.0	0.0		50.0	20.0	NM_020862	Q8TBS9	Silent	SNP	ENST00000248668.4	hg19	CCDS46071.1																																																																																			.	.		0.687	LRFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463835.1	NM_020862		T	39804840	C	T	39804840	2	4	325	1	0	0	0	0	0	0	0	1	8946	871	31	1		1	LRFN1	19	39804840	Silent	SNP	C	TCGA-MR-A520-01A-11D-A25V-10		39804840	19324143	23	45793										
SHANK3	85358	hgsc.bcm.edu	37	chr22	51160334	51160334	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.153846153846154	4	1	1.84868421052632	1.47894736842105	2.01674641148325	0.485714285714286	1	0	tgcagccgactctggggtggAggaggctgacacacgcagct	16	11	1	1			TCGA-MR-A520-01A-11D-A25V-10	TCGA-MR-A520-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	352fbbb4-88a5-4354-b1fa-3a01da3fbfa7	64b28729-b106-4b33-994d-f1710478466c	g.chr22:51160334A>T	ENST00000414786.2	+	21	4258	c.4031A>T	c.(4030-4032)gAg>gTg	p.E1344V	SHANK3_ENST00000445220.2_Missense_Mutation_p.E1360V|SHANK3_ENST00000262795.3_Missense_Mutation_p.E1374V			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	1358	Pro-rich.				adult behavior (GO:0030534)|alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|brain morphogenesis (GO:0048854)|dendritic spine morphogenesis (GO:0060997)|guanylate kinase-associated protein clustering (GO:0097117)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell volume (GO:0045794)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glutamate receptor signaling pathway (GO:1900451)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse structural plasticity (GO:0051835)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density assembly (GO:0097107)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of long term synaptic depression (GO:1900452)|regulation of long-term synaptic potentiation (GO:1900271)|social behavior (GO:0035176)|striatal medium spiny neuron differentiation (GO:0021773)|synapse assembly (GO:0007416)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)	8		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)		TCTGGGGTGGAGGAGGCTGAC	0.697																																					p.E1344V		Atlas-SNP	.											.	SHANK3	96	.	0			c.A4031T						.						14	16	15					22																	51160334		2007	4097	6104	SO:0001583	missense	85358	exon21			GGGTGGAGGAGGC	AB051437		22q13.3	2013-11-14			ENSG00000251322	ENSG00000251322		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	14294	protein-coding gene	gene with protein product	"proline rich synapse associated protein 2", "shank postsynaptic density protein"	606230				11258795, 11431708, 10806096, 17173049	Standard	NM_033517		Approved	SPANK-2, prosap2, KIAA1650, PSAP2	uc031ryd.1	Q9BYB0	OTTHUMG00000150169	ENST00000414786.2:c.4031A>T	chr22.hg19:g.51160334A>T	ENSP00000464552:p.Glu1344Val	46.0	0.0		68.0	11.0	NM_033517	D7UT47|Q8TET3	Missense_Mutation	SNP	ENST00000414786.2	hg19		.	.	.	.	.	.	.	.	.	.	A	18.15	3.559285	0.65538	.	.	ENSG00000251322	ENST00000262795;ENST00000445220	T;T	0.20738	2.05;2.05	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	T	0.49012	0.1532	M	0.83603	2.65	0.36862	D	0.888442	D;P;D	0.76494	0.998;0.808;0.999	D;B;D	0.83275	0.994;0.225;0.996	T	0.62793	-0.6779	10	0.87932	D	0	.	12.8612	0.57913	1.0:0.0:0.0:0.0	.	1358;1359;1374	D7UT47;Q9BYB0;F2Z3L0	.;SHAN3_HUMAN;.	V	1374;1360	ENSP00000442518:E1374V;ENSP00000446078:E1360V	ENSP00000442518:E1374V	E	+	2	0	SHANK3	49507200	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	8.610000	0.90902	1.928000	0.55862	0.379000	0.24179	GAG	.	.		0.697	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420		T	51160334	A	T	51160334	3	4	325	1	0	0	0	0	1	0	0	0	14281	304	11	4	4207	4	SHANK3	22	51160334	Missense_Mutation	SNP	A	TCGA-MR-A520-01A-11D-A25V-10		51160334	144232	24	45794										
SLC9A6	10479	hgsc.bcm.edu	37	chrX	135122263	135122263	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.153846153846154	4	1	1.84868421052632	1.47894736842105	2.01674641148325	0.485714285714286	1	0	agcctctgctgacccacagcGggcctccgctgacaacaaca	9	17	1	2			TCGA-MR-A520-01A-11D-A25V-10	TCGA-MR-A520-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	352fbbb4-88a5-4354-b1fa-3a01da3fbfa7	64b28729-b106-4b33-994d-f1710478466c	g.chrX:135122263G>C	ENST00000370698.3	+	15	1695	c.1660G>C	c.(1660-1662)Ggg>Cgg	p.G554R	SLC9A6_ENST00000370695.4_Missense_Mutation_p.G586R|SLC9A6_ENST00000370701.1_Missense_Mutation_p.G534R	NM_006359.2	NP_006350.1	Q92581	SL9A6_HUMAN	solute carrier family 9, subfamily A (NHE6, cation proton antiporter 6), member 6	554					axon extension (GO:0048675)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|dendrite extension (GO:0097484)|dendritic spine development (GO:0060996)|ion transport (GO:0006811)|neuron projection morphogenesis (GO:0048812)|regulation of neurotrophin TRK receptor signaling pathway (GO:0051386)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon terminus (GO:0043679)|axonal spine (GO:0044308)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome membrane (GO:0031901)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)|synapse (GO:0045202)	sodium:proton antiporter activity (GO:0015385)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(18)|ovary(2)|upper_aerodigestive_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					GACCCACAGCGGGCCTCCGCT	0.502																																					p.G586R		Atlas-SNP	.											.	SLC9A6	64	.	0			c.G1756C						.						46	39	41					X																	135122263		2203	4300	6503	SO:0001583	missense	10479	exon15			CACAGCGGGCCTC	AF030409	CCDS14654.1, CCDS44003.1, CCDS55504.1	Xq26.3	2013-05-22	2012-03-22		ENSG00000198689	ENSG00000198689		"Solute carriers"	11079	protein-coding gene	gene with protein product		300231	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 6", "solute carrier family 9 (sodium/hydrogen exchanger), member 6"			9507001	Standard	NM_001042537		Approved	NHE6, KIAA0267	uc004ezk.3	Q92581	OTTHUMG00000022498	ENST00000370698.3:c.1660G>C	chrX.hg19:g.135122263G>C	ENSP00000359732:p.Gly554Arg	118.0	0.0		151.0	96.0	NM_001042537	A6NIQ9|A8K160|B4DU30|B7ZAE0|Q3ZCW7|Q5JPP8|Q5JPP9|Q86VS0	Missense_Mutation	SNP	ENST00000370698.3	hg19	CCDS14654.1	.	.	.	.	.	.	.	.	.	.	G	19.17	3.776063	0.70107	.	.	ENSG00000198689	ENST00000370701;ENST00000370698;ENST00000370695	T;T;T	0.69685	-0.42;-0.42;-0.42	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.76241	0.3960	L	0.45698	1.435	0.80722	D	1	D;P	0.89917	1.0;0.838	D;B	0.97110	1.0;0.446	T	0.71080	-0.4696	10	0.19147	T	0.46	.	17.4825	0.87677	0.0:0.0:1.0:0.0	.	586;554	Q92581-2;Q92581	.;SL9A6_HUMAN	R	534;554;586	ENSP00000359735:G534R;ENSP00000359732:G554R;ENSP00000359729:G586R	ENSP00000359729:G586R	G	+	1	0	SLC9A6	134949929	1.000000	0.71417	0.869000	0.34112	0.742000	0.42306	9.404000	0.97306	2.343000	0.79666	0.513000	0.50165	GGG	.	.		0.502	SLC9A6-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058450.1	NM_006359		C	135122263	G	C	135122263	3	2	325	1	0	0	0	0	1	0	0	0	14733	1116	39	4	1814	4	SLC9A6	23	135122263	Missense_Mutation	SNP	G	TCGA-MR-A520-01A-11D-A25V-10		135122263	20148297	25	45795										
CXorf1	9142	hgsc.bcm.edu	37	chrX	144909486	144909486	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.153846153846154	4	1	1.84868421052632	1.47894736842105	2.01674641148325	0.485714285714286	1	0	gcctacagaatgcagtctccCagggccctgccaagaacata	9	14	1	2			TCGA-MR-A520-01A-11D-A25V-10	TCGA-MR-A520-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	352fbbb4-88a5-4354-b1fa-3a01da3fbfa7	64b28729-b106-4b33-994d-f1710478466c	g.chrX:144909486C>A	ENST00000408967.2	+	1	559	c.291C>A	c.(289-291)ccC>ccA	p.P97P		NM_004709.2	NP_004700.1	O96002	TM257_HUMAN	transmembrane protein 257	97						integral component of membrane (GO:0016021)											TGCAGTCTCCCAGGGCCCTGC	0.413																																					p.P97P		Atlas-SNP	.											.	.	.	.	0			c.C291A						.						52	49	50					X																	144909486		2203	4300	6503	SO:0001819	synonymous_variant	9142	exon1			GTCTCCCAGGGCC	Y08902	CCDS14681.1	Xq27.3	2012-12-03	2012-12-03	2012-12-03	ENSG00000221870	ENSG00000221870			2562	protein-coding gene	gene with protein product		300565	"chromosome X open reading frame 1"	CXorf1		9881668	Standard	NM_004709		Approved		uc004fch.3	O96002	OTTHUMG00000159605	ENST00000408967.2:c.291C>A	chrX.hg19:g.144909486C>A		107.0	0.0		124.0	68.0	NM_004709	Q14CW0	Silent	SNP	ENST00000408967.2	hg19	CCDS14681.1																																																																																			.	.		0.413	TMEM257-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356465.1	NM_004709		A	144909486	C	A	144909486	2	1	325	1	0	0	0	0	0	0	0	1	4102	581	21	3		3	CXorf1	23	144909486	Silent	SNP	C	TCGA-MR-A520-01A-11D-A25V-10	9787223	144909486	10361074	26	45796										
RNF220	55182	hgsc.bcm.edu	37	chr1	45111132	45111132	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	2	1	1.47692307692308	8.12307692307692	0	0.4	1	0	gcaagcaggaggccatgcagAagacctgcaagaacagcgac	13	11	0	3			TCGA-MR-A8JO-01A-12D-A35Z-10	TCGA-MR-A8JO-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66a02e7c-ba44-4552-b8c9-3161a5b2c0e0	de1fdde4-5d17-43bb-a055-456bace72e84	g.chr1:45111132A>G	ENST00000355387.2	+	12	1867	c.1417A>G	c.(1417-1419)Aag>Gag	p.K473E	RNF220_ENST00000361799.2_Missense_Mutation_p.K473E|RNF220_ENST00000372247.2_Missense_Mutation_p.K473E|TMEM53_ENST00000372243.3_Missense_Mutation_p.F63S|TMEM53_ENST00000372242.3_Missense_Mutation_p.F153S|TMEM53_ENST00000372244.3_Silent_p.L22L|RNF220_ENST00000443020.2_Missense_Mutation_p.K260E|RNF220_ENST00000480686.1_3'UTR			Q5VTB9	RN220_HUMAN	ring finger protein 220	473					protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(1)|large_intestine(3)|lung(13)|ovary(2)|skin(2)|urinary_tract(2)	29						GGCCATGCAGAAGACCTGCAA	0.587																																					p.K473E		Atlas-SNP	.											.	RNF220	56	.	0			c.A1417G						.						111	94	100					1																	45111132		2203	4300	6503	SO:0001583	missense	55182	exon12			ATGCAGAAGACCT	AK056424	CCDS510.1	1p34.1	2008-06-13	2008-06-13	2008-06-13	ENSG00000187147	ENSG00000187147		"RING-type (C3HC4) zinc fingers"	25552	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 164"	C1orf164		11042152	Standard	NM_018150		Approved	FLJ10597	uc001clv.1	Q5VTB9	OTTHUMG00000007697	ENST00000355387.2:c.1417A>G	chr1.hg19:g.45111132A>G	ENSP00000347548:p.Lys473Glu	144.0	0.0		126.0	31.0	NM_018150	B3KPJ3|B4DLZ9|E9PCS1|Q4KMX2|Q9NVP6	Missense_Mutation	SNP	ENST00000355387.2	hg19	CCDS510.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.47|14.47	2.545819|2.545819	0.45280|0.45280	.|.	.|.	ENSG00000126106|ENSG00000187147	ENST00000372243;ENST00000372242|ENST00000355387;ENST00000361799;ENST00000453887;ENST00000372247;ENST00000443020;ENST00000440132;ENST00000335497;ENST00000372248	.|D;D;D;D;D;D	.|0.88124	.|-2.34;-2.34;-2.34;-2.34;-2.34;-2.34	5.84|5.84	5.84|5.84	0.93424|0.93424	.|.	.|0.058799	.|0.64402	.|D	.|0.000003	T|T	0.71643|0.71643	0.3364|0.3364	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	D|P;P;B;P;B	0.62365|0.36315	0.991|0.547;0.547;0.172;0.483;0.034	P|B;B;B;B;B	0.62089|0.30316	0.898|0.114;0.114;0.039;0.058;0.017	T|T	0.73930|0.73930	-0.3827|-0.3827	8|10	0.14656|0.07990	T|T	0.56|0.79	.|.	16.2163|16.2163	0.82224|0.82224	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	63|215;260;152;190;473	Q5TDE6|B4DJE2;B4DLZ9;D3DPZ1;C9JJY2;Q5VTB9	.|.;.;.;.;RN220_HUMAN	S|E	63;153|473;473;473;473;260;189;215;216	.|ENSP00000347548:K473E;ENSP00000354872:K473E;ENSP00000361321:K473E;ENSP00000414640:K260E;ENSP00000388533:K189E;ENSP00000335580:K215E	ENSP00000361316:F153S|ENSP00000335580:K215E	F|K	-|+	2|1	0|0	TMEM53|RNF220	44883719|44883719	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	6.336000|6.336000	0.72954|0.72954	2.235000|2.235000	0.73313|0.73313	0.459000|0.459000	0.35465|0.35465	TTC|AAG	.	.		0.587	RNF220-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000020683.4	NM_018150		G	45111132	A	G	45111132	3	3	326	1	0	0	0	0	1	0	0	0	13498	247	9	2	1459	2	RNF220	1	45111132	Missense_Mutation	SNP	A	TCGA-MR-A8JO-01A-12D-A35Z-10		45111132	204139489	1	45797										
PCSK9	255738	hgsc.bcm.edu	37	chr1	55521763	55521763	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	2	1	1.47692307692308	8.12307692307692	0	0.4	1	0	tacagccgcgtcctcaacgcCgcctgccagcgcctggcgag	12	18	1	0			TCGA-MR-A8JO-01A-12D-A35Z-10	TCGA-MR-A8JO-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66a02e7c-ba44-4552-b8c9-3161a5b2c0e0	de1fdde4-5d17-43bb-a055-456bace72e84	g.chr1:55521763C>T	ENST00000302118.5	+	6	1187	c.897C>T	c.(895-897)gcC>gcT	p.A299A	PCSK9_ENST00000543384.1_Silent_p.A99A|PCSK9_ENST00000490692.1_3'UTR	NM_174936.3	NP_777596.2	Q8NBP7	PCSK9_HUMAN	proprotein convertase subtilisin/kexin type 9	299	Peptidase S8.				apoptotic process (GO:0006915)|cellular response to insulin stimulus (GO:0032869)|cellular response to starvation (GO:0009267)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|kidney development (GO:0001822)|lipoprotein metabolic process (GO:0042157)|liver development (GO:0001889)|low-density lipoprotein particle receptor catabolic process (GO:0032802)|lysosomal transport (GO:0007041)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|negative regulation of receptor recycling (GO:0001920)|neurogenesis (GO:0022008)|neuron differentiation (GO:0030182)|phospholipid metabolic process (GO:0006644)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of receptor internalization (GO:0002092)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)|regulation of neuron apoptotic process (GO:0043523)|regulation of receptor activity (GO:0010469)|triglyceride metabolic process (GO:0006641)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	apolipoprotein binding (GO:0034185)|apolipoprotein receptor binding (GO:0034190)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein particle receptor binding (GO:0050750)|poly(A) RNA binding (GO:0044822)|protein self-association (GO:0043621)|serine-type endopeptidase activity (GO:0004252)|sodium channel inhibitor activity (GO:0019871)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor binding (GO:0070326)	p.A299A(1)		NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(1)|liver(2)|lung(4)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	32						TCCTCAACGCCGCCTGCCAGC	0.692																																					p.A299A	Pancreas(137;1454 1827 5886 22361 42375)	Atlas-SNP	.											PCSK9,NS,carcinoma,0,1	PCSK9	76	.	1	Substitution - coding silent(1)	prostate(1)	c.C897T						.						13	15	14					1																	55521763		2192	4288	6480	SO:0001819	synonymous_variant	255738	exon6			CAACGCCGCCTGC	AX207686	CCDS603.1	1p34.1-p32	2014-09-17	2003-05-13		ENSG00000169174	ENSG00000169174			20001	protein-coding gene	gene with protein product		607786	"hypercholesterolemia, autosomal dominant 3"	HCHOLA3		12552133, 12730697	Standard	NM_174936		Approved	NARC-1, FH3	uc001cyf.2	Q8NBP7	OTTHUMG00000008136	ENST00000302118.5:c.897C>T	chr1.hg19:g.55521763C>T		156.0	0.0		151.0	7.0	NM_174936	A8T640|C0JYY9|Q5PSM5|Q5SZQ2	Silent	SNP	ENST00000302118.5	hg19	CCDS603.1																																																																																			.	.		0.692	PCSK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022280.1	NM_174936		T	55521763	C	T	55521763	2	4	326	1	0	0	0	0	0	0	0	1	11615	639	23	1		1	PCSK9	1	55521763	Silent	SNP	C	TCGA-MR-A8JO-01A-12D-A35Z-10	10410631	55521763	193728858	2	45798										
ATP1A1	476	hgsc.bcm.edu	37	chr1	116940569	116940569	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	2	1	1.47692307692308	8.12307692307692	0	0.4	1	0	ggacatgacctccgagcagcTggatgacattttgaagtacc	11	10	0	3			TCGA-MR-A8JO-01A-12D-A35Z-10	TCGA-MR-A8JO-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66a02e7c-ba44-4552-b8c9-3161a5b2c0e0	de1fdde4-5d17-43bb-a055-456bace72e84	g.chr1:116940569T>C	ENST00000295598.5	+	15	2285	c.2033T>C	c.(2032-2034)cTg>cCg	p.L678P	ATP1A1_ENST00000369496.4_Missense_Mutation_p.L647P|ATP1A1_ENST00000537345.1_Missense_Mutation_p.L678P	NM_000701.7	NP_000692.2	P05023	AT1A1_HUMAN	ATPase, Na+/K+ transporting, alpha 1 polypeptide	678					ATP biosynthetic process (GO:0006754)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|membrane hyperpolarization (GO:0060081)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of glucocorticoid biosynthetic process (GO:0031947)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart contraction (GO:0045823)|positive regulation of striated muscle contraction (GO:0045989)|potassium ion import (GO:0010107)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of sodium ion transport (GO:0002028)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|chaperone binding (GO:0051087)|phosphatase activity (GO:0016791)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(2)|breast(2)|cervix(3)|endometrium(2)|kidney(5)|large_intestine(9)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47	Lung SC(450;0.225)	all_cancers(81;1.28e-06)|all_epithelial(167;3.48e-07)|all_lung(203;2.64e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0164)|LUSC - Lung squamous cell carcinoma(189;0.0548)|Colorectal(144;0.0825)|COAD - Colon adenocarcinoma(174;0.127)|all cancers(265;0.24)	Acetyldigitoxin(DB00511)|Almitrine(DB01430)|Aluminium(DB01370)|Bepridil(DB01244)|Bretylium(DB01158)|Ciclopirox(DB01188)|Deslanoside(DB01078)|Diazoxide(DB01119)|Digitoxin(DB01396)|Digoxin(DB00390)|Ethacrynic acid(DB00903)|Hydroflumethiazide(DB00774)|Ouabain(DB01092)|Trichlormethiazide(DB01021)	TCCGAGCAGCTGGATGACATT	0.483																																					p.L678P		Atlas-SNP	.											.	ATP1A1	87	.	0			c.T2033C						.						159	139	146					1																	116940569		2203	4300	6503	SO:0001583	missense	476	exon15			AGCAGCTGGATGA	D00099	CCDS887.1, CCDS53351.1, CCDS53352.1	1p13	2012-10-22			ENSG00000163399	ENSG00000163399	3.6.3.9	"ATPases / P-type"	799	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-1", "sodium pump subunit alpha-1", "sodium-potassium ATPase catalytic subunit alpha-1"	182310					Standard	NM_000701		Approved		uc001ege.3	P05023	OTTHUMG00000012109	ENST00000295598.5:c.2033T>C	chr1.hg19:g.116940569T>C	ENSP00000295598:p.Leu678Pro	80.0	0.0		56.0	10.0	NM_001160233	B2RBR6|B7Z2T5|B7Z3U6|F5H3A1|Q16689|Q6LDM4|Q9UCN1|Q9UJ20|Q9UJ21	Missense_Mutation	SNP	ENST00000295598.5	hg19	CCDS887.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.495271	0.85069	.	.	ENSG00000163399	ENST00000295598;ENST00000537345;ENST00000369496	D;D;D	0.96396	-4.0;-4.0;-4.0	5.15	5.15	0.70609	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type,  transmembrane domain (1);	0.156884	0.44902	D	0.000412	D	0.98535	0.9511	H	0.94771	3.58	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.996;0.998	D	0.99808	1.1039	10	0.87932	D	0	.	15.1447	0.72641	0.0:0.0:0.0:1.0	.	678;678	F5H3A1;P05023	.;AT1A1_HUMAN	P	678;678;647	ENSP00000295598:L678P;ENSP00000445306:L678P;ENSP00000358508:L647P	ENSP00000295598:L678P	L	+	2	0	ATP1A1	116742092	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.868000	0.87116	2.159000	0.67721	0.533000	0.62120	CTG	.	.		0.483	ATP1A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033481.5	NM_001160233		C	116940569	T	C	116940569	3	2	326	1	0	0	0	0	1	0	0	0	1128	1580	55	2	2107	2	ATP1A1	1	116940569	Missense_Mutation	SNP	T	TCGA-MR-A8JO-01A-12D-A35Z-10	61418806	116940569	132310052	3	45799										
TBX19	9095	hgsc.bcm.edu	37	chr1	168274288	168274288	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	2	1	1.47692307692308	8.12307692307692	0	0.4	1	0	tccagatggagtgtgcacagCaggaaactccaattaccagt	10	10	0	1			TCGA-MR-A8JO-01A-12D-A35Z-10	TCGA-MR-A8JO-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66a02e7c-ba44-4552-b8c9-3161a5b2c0e0	de1fdde4-5d17-43bb-a055-456bace72e84	g.chr1:168274288C>T	ENST00000367821.3	+	6	821	c.770C>T	c.(769-771)gCa>gTa	p.A257V		NM_005149.2	NP_005140.1	O60806	TBX19_HUMAN	T-box 19	257					anatomical structure morphogenesis (GO:0009653)|cell fate commitment (GO:0045165)|pituitary gland development (GO:0021983)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	enhancer sequence-specific DNA binding (GO:0001158)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|liver(1)|lung(11)|prostate(2)|skin(2)|urinary_tract(1)	34	all_hematologic(923;0.215)					GTGTGCACAGCAGGAAACTCC	0.527																																					p.A257V		Atlas-SNP	.											.	TBX19	68	.	0			c.C770T						.						162	147	152					1																	168274288		2203	4300	6503	SO:0001583	missense	9095	exon6			GCACAGCAGGAAA	AJ010277	CCDS1272.1	1q23-q24	2008-02-05			ENSG00000143178	ENSG00000143178		"T-boxes"	11596	protein-coding gene	gene with protein product	"TBS 19"	604614				9888994	Standard	NM_005149		Approved	dj747L4.1, TPIT	uc001gfl.3	O60806	OTTHUMG00000034648	ENST00000367821.3:c.770C>T	chr1.hg19:g.168274288C>T	ENSP00000356795:p.Ala257Val	68.0	0.0		71.0	12.0	NM_005149	Q52M53	Missense_Mutation	SNP	ENST00000367821.3	hg19	CCDS1272.1	.	.	.	.	.	.	.	.	.	.	C	14.00	2.403448	0.42613	.	.	ENSG00000143178	ENST00000367821	D	0.83419	-1.72	5.84	5.84	0.93424	.	0.467241	0.20894	N	0.083775	T	0.72495	0.3467	L	0.50333	1.59	0.33927	D	0.641639	B	0.26081	0.141	B	0.25759	0.063	T	0.68769	-0.5321	9	0.30854	T	0.27	.	17.9282	0.88990	0.0:1.0:0.0:0.0	.	257	O60806	TBX19_HUMAN	V	257	ENSP00000356795:A257V	ENSP00000356795:A257V	A	+	2	0	TBX19	166540912	0.391000	0.25221	0.112000	0.21494	0.113000	0.19764	4.102000	0.57776	2.760000	0.94817	0.655000	0.94253	GCA	.	.		0.527	TBX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083825.1	NM_005149		T	168274288	C	T	168274288	3	4	326	1	0	0	0	0	1	0	0	0	15669	710	25	3	792	3	TBX19	1	168274288	Missense_Mutation	SNP	C	TCGA-MR-A8JO-01A-12D-A35Z-10	51333719	168274288	80976333	4	45800										
ZRANB3	84083	hgsc.bcm.edu	37	chr2	136071142	136071142	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	2	1	1.47692307692308	8.12307692307692	0	0.4	1	0	tgaatttggagttctcattaTtttttcccactcttcaaagc	5	9	3	1			TCGA-MR-A8JO-01A-12D-A35Z-10	TCGA-MR-A8JO-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66a02e7c-ba44-4552-b8c9-3161a5b2c0e0	de1fdde4-5d17-43bb-a055-456bace72e84	g.chr2:136071142T>A	ENST00000264159.6	-	8	999	c.883A>T	c.(883-885)Ata>Tta	p.I295L	ZRANB3_ENST00000536680.1_Missense_Mutation_p.I295L|ZRANB3_ENST00000401392.1_Missense_Mutation_p.I295L	NM_032143.2	NP_115519.2	Q5FWF4	ZRAB3_HUMAN	zinc finger, RAN-binding domain containing 3	295	DNA annealing helicase activity.				cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|DNA rewinding (GO:0036292)|DNA strand renaturation (GO:0000733)|negative regulation of DNA recombination (GO:0045910)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to UV (GO:0009411)	nuclear replication fork (GO:0043596)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|endodeoxyribonuclease activity (GO:0004520)|helicase activity (GO:0004386)|K63-linked polyubiquitin binding (GO:0070530)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|upper_aerodigestive_tract(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.135)		GTTCTCATTATTTTTTCCCAC	0.378																																					p.I295L		Atlas-SNP	.											.	ZRANB3	109	.	0			c.A883T						.						142	133	136					2																	136071142		1850	4087	5937	SO:0001583	missense	84083	exon8			TCATTATTTTTTC	AL136824	CCDS46419.1, CCDS67963.1, CCDS74580.1	2q21.3	2013-05-13			ENSG00000121988	ENSG00000121988		"Zinc fingers, RAN-binding domain containing"	25249	protein-coding gene	gene with protein product						11230166	Standard	XM_005263809		Approved	DKFZP434B1727	uc002tum.3	Q5FWF4	OTTHUMG00000150475	ENST00000264159.6:c.883A>T	chr2.hg19:g.136071142T>A	ENSP00000264159:p.Ile295Leu	87.0	0.0		86.0	21.0	NM_032143	B3KYA1|B4E375|B5MDI3|D3DP76|E9PBP0|Q53SM1|Q6P2C4|Q8N1P4|Q9H0E8	Missense_Mutation	SNP	ENST00000264159.6	hg19	CCDS46419.1	.	.	.	.	.	.	.	.	.	.	T	1.552	-0.538912	0.04053	.	.	ENSG00000121988	ENST00000401392;ENST00000264159;ENST00000536680;ENST00000397448	D;D;D	0.90324	-2.65;-2.65;-2.63	5.56	3.06	0.35304	SNF2-related (1);	0.079119	0.51477	N	0.000081	T	0.66257	0.2771	N	0.00894	-1.105	0.28753	N	0.901347	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.60535	-0.7244	10	0.02654	T	1	-17.3694	5.3255	0.15905	0.7272:0.0:0.1406:0.1322	.	235;295;295	E9PBP0;Q5FWF4;Q5FWF4-3	.;ZRAB3_HUMAN;.	L	295;295;295;235	ENSP00000383979:I295L;ENSP00000264159:I295L;ENSP00000441320:I295L	ENSP00000264159:I295L	I	-	1	0	ZRANB3	135787612	1.000000	0.71417	1.000000	0.80357	0.556000	0.35491	2.420000	0.44679	0.365000	0.24400	-0.878000	0.02970	ATA	.	.		0.378	ZRANB3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318254.1	NM_032143		A	136071142	T	A	136071142	3	1	326	1	0	0	0	0	1	0	0	0	18239	1493	52	4	2412	4	ZRANB3	2	136071142	Missense_Mutation	SNP	T	TCGA-MR-A8JO-01A-12D-A35Z-10		136071142	107128231	5	45801										
STAB1	23166	hgsc.bcm.edu	37	chr3	52550761	52550761	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0714285714285714	2	1	1.47692307692308	8.12307692307692	0	0.4	1	0	cgcctgtgctgcgggatactCcggcaatggcatcttctgtt	12	12	2	0			TCGA-MR-A8JO-01A-12D-A35Z-10	TCGA-MR-A8JO-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66a02e7c-ba44-4552-b8c9-3161a5b2c0e0	de1fdde4-5d17-43bb-a055-456bace72e84	g.chr3:52550761C>A	ENST00000321725.6	+	41	4416	c.4340C>A	c.(4339-4341)tCc>tAc	p.S1447Y		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	1447	EGF-like 10. {ECO:0000255|PROSITE- ProRule:PRU00076, ECO:0000305}.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)			breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		GCGGGATACTCCGGCAATGGC	0.642																																					p.S1447Y		Atlas-SNP	.											.	STAB1	178	.	0			c.C4340A						.						22	25	24					3																	52550761		2201	4300	6501	SO:0001583	missense	23166	exon41			GATACTCCGGCAA	AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"MS-1 antigen", "fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1", "common lymphatic endothelial and vascular endothelial receptor-1"	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.4340C>A	chr3.hg19:g.52550761C>A	ENSP00000312946:p.Ser1447Tyr	154.0	0.0		164.0	34.0	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Missense_Mutation	SNP	ENST00000321725.6	hg19	CCDS33768.1	.	.	.	.	.	.	.	.	.	.	C	12.78	2.040206	0.35989	.	.	ENSG00000010327	ENST00000321725	D	0.85773	-2.03	4.51	3.62	0.41486	Epidermal growth factor-like (1);EGF-like region, conserved site (1);Epidermal growth factor-like, type 3 (1);	0.512387	0.19202	N	0.120170	D	0.87168	0.6110	L	0.58583	1.82	0.09310	N	1	D	0.69078	0.997	P	0.59221	0.854	T	0.78119	-0.2328	10	0.66056	D	0.02	.	7.7906	0.29119	0.0:0.8864:0.0:0.1136	.	1447	Q9NY15	STAB1_HUMAN	Y	1447	ENSP00000312946:S1447Y	ENSP00000312946:S1447Y	S	+	2	0	STAB1	52525801	0.017000	0.18338	0.334000	0.25495	0.024000	0.10985	1.264000	0.33015	2.222000	0.72286	0.462000	0.41574	TCC	.	.		0.642	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136		A	52550761	C	A	52550761	3	1	326	1	0	0	0	0	1	0	0	0	15252	855	30	3	4502	3	STAB1	3	52550761	Missense_Mutation	SNP	C	TCGA-MR-A8JO-01A-12D-A35Z-10		52550761	145471669	6	45802										
N4BP2	55728	hgsc.bcm.edu	37	chr4	40098980	40098980	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	2	1	1.47692307692308	8.12307692307692	0	0.4	1	0	aatgccaaggagaaggaaaaAtcttgggggaaatccttttc	11	6	1	1			TCGA-MR-A8JO-01A-12D-A35Z-10	TCGA-MR-A8JO-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66a02e7c-ba44-4552-b8c9-3161a5b2c0e0	de1fdde4-5d17-43bb-a055-456bace72e84	g.chr4:40098980A>G	ENST00000261435.6	+	3	436	c.20A>G	c.(19-21)aAt>aGt	p.N7S		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	7					nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|endonuclease activity (GO:0004519)			breast(4)|endometrium(3)|kidney(12)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	60						AGAAGGAAAAATCTTGGGGGA	0.398																																					p.N7S		Atlas-SNP	.											.	N4BP2	166	.	0			c.A20G						.						102	103	102					4																	40098980		2203	4300	6503	SO:0001583	missense	55728	exon3			GGAAAAATCTTGG	AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"BCL-3 binding protein"					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.20A>G	chr4.hg19:g.40098980A>G	ENSP00000261435:p.Asn7Ser	114.0	0.0		73.0	9.0	NM_018177	A0AVR3|Q9NVK2|Q9P2D4	Missense_Mutation	SNP	ENST00000261435.6	hg19	CCDS3457.1	.	.	.	.	.	.	.	.	.	.	A	13.44	2.238601	0.39598	.	.	ENSG00000078177	ENST00000261435	T	0.20332	2.08	4.96	4.96	0.65561	.	0.351137	0.20830	N	0.084909	T	0.20170	0.0485	N	0.08118	0	0.29253	N	0.871855	D	0.56968	0.978	P	0.58210	0.835	T	0.04440	-1.0951	10	0.52906	T	0.07	.	9.8828	0.41245	0.8282:0.1718:0.0:0.0	.	7	Q86UW6	N4BP2_HUMAN	S	7	ENSP00000261435:N7S	ENSP00000261435:N7S	N	+	2	0	N4BP2	39775375	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	2.214000	0.42853	1.851000	0.53745	0.460000	0.39030	AAT	.	.		0.398	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177		G	40098980	A	G	40098980	3	3	326	1	0	0	0	0	1	0	0	0	10119	101	4	2	22	2	N4BP2	4	40098980	Missense_Mutation	SNP	A	TCGA-MR-A8JO-01A-12D-A35Z-10		40098980	151055296	7	45803										
REST	5978	hgsc.bcm.edu	37	chr4	57797085	57797085	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	2	1	1.47692307692308	8.12307692307692	0	0.4	1	0	gtacttgctcacatggagctGcctcctcccatggagactgc	10	14	1	1			TCGA-MR-A8JO-01A-12D-A35Z-10	TCGA-MR-A8JO-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66a02e7c-ba44-4552-b8c9-3161a5b2c0e0	de1fdde4-5d17-43bb-a055-456bace72e84	g.chr4:57797085G>A	ENST00000309042.7	+	4	2375	c.2061G>A	c.(2059-2061)ctG>ctA	p.L687L		NM_001193508.1|NM_005612.4	NP_001180437.1|NP_005603.3	Q13127	REST_HUMAN	RE1-silencing transcription factor	687	Pro-rich.				cardiac muscle cell myoblast differentiation (GO:0060379)|cellular response to drug (GO:0035690)|cellular response to electrical stimulus (GO:0071257)|cellular response to glucocorticoid stimulus (GO:0071385)|hematopoietic progenitor cell differentiation (GO:0002244)|histone H4 deacetylation (GO:0070933)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of amniotic stem cell differentiation (GO:2000798)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of dense core granule biogenesis (GO:2000706)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of mesenchymal stem cell differentiation (GO:2000740)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transmembrane transport (GO:0071805)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|outward rectifier potassium channel activity (GO:0015271)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	50	Glioma(25;0.08)|all_neural(26;0.181)					ACATGGAGCTGCCTCCTCCCA	0.602																																					p.L687L		Atlas-SNP	.											.	REST	104	.	0			c.G2061A						.						78	80	79					4																	57797085		2203	4300	6503	SO:0001819	synonymous_variant	5978	exon4			GGAGCTGCCTCCT	U13879	CCDS3509.1	4q12	2008-02-05			ENSG00000084093	ENSG00000084093			9966	protein-coding gene	gene with protein product		600571				7871435, 7697725	Standard	NM_005612		Approved	NRSF, XBR	uc003hci.3	Q13127	OTTHUMG00000128770	ENST00000309042.7:c.2061G>A	chr4.hg19:g.57797085G>A		108.0	0.0		92.0	4.0	NM_001193508	A2RUE0|B9EGJ0|Q12956|Q12957|Q13134|Q59ER1|Q8IWI3	Silent	SNP	ENST00000309042.7	hg19	CCDS3509.1																																																																																			.	.		0.602	REST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250691.2	NM_005612		A	57797085	G	A	57797085	2	1	326	1	0	0	0	0	0	0	0	1	13249	1306	46	3		3	REST	4	57797085	Silent	SNP	G	TCGA-MR-A8JO-01A-12D-A35Z-10	17698105	57797085	133357191	8	45804										
FGA	2243	hgsc.bcm.edu	37	chr4	155507560	155507560	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	2	1	1.47692307692308	8.12307692307692	0	0.4	1	0	ttggtttccagtacttccagTtccagagctcccagagttcc	8	13	0	2			TCGA-MR-A8JO-01A-12D-A35Z-10	TCGA-MR-A8JO-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66a02e7c-ba44-4552-b8c9-3161a5b2c0e0	de1fdde4-5d17-43bb-a055-456bace72e84	g.chr4:155507560T>G	ENST00000302053.3	-	5	1099	c.1021A>C	c.(1021-1023)Act>Cct	p.T341P	FGA_ENST00000403106.3_Missense_Mutation_p.T341P	NM_000508.3	NP_000499.1	P02671	FIBA_HUMAN	fibrinogen alpha chain	341					blood coagulation (GO:0007596)|blood coagulation, common pathway (GO:0072377)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|extracellular matrix organization (GO:0030198)|negative regulation of blood coagulation, common pathway (GO:2000261)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	structural molecule activity (GO:0005198)			NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	73	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)	GTACTTCCAGTTCCAGAGCTC	0.587																																					p.T341P	NSCLC(143;340 1922 20892 22370 48145)	Atlas-SNP	.											.	FGA	179	.	0			c.A1021C						.						89	94	92					4																	155507560		2203	4300	6503	SO:0001583	missense	2243	exon5			TTCCAGTTCCAGA		CCDS3787.1, CCDS47152.1	4q28	2014-09-17			ENSG00000171560	ENSG00000171560		"Fibrinogen C domain containing", "Endogenous ligands"	3661	protein-coding gene	gene with protein product		134820	"fibrinogen, A alpha polypeptide"				Standard	NM_000508		Approved		uc003iod.1	P02671	OTTHUMG00000150330	ENST00000302053.3:c.1021A>C	chr4.hg19:g.155507560T>G	ENSP00000306361:p.Thr341Pro	155.0	0.0		101.0	6.0	NM_000508	A8K3E4|D3DP14|D3DP15|Q4QQH7|Q9BX62|Q9UCH2	Missense_Mutation	SNP	ENST00000302053.3	hg19	CCDS3787.1	.	.	.	.	.	.	.	.	.	.	T	1.216	-0.628422	0.03610	.	.	ENSG00000171560	ENST00000302053;ENST00000403106	T;T	0.79940	-1.32;-1.32	5.0	-9.99	0.00435	.	3.070920	0.01435	N	0.014886	T	0.40222	0.1108	N	0.00260	-1.75	0.09310	N	1	B;B	0.12630	0.0;0.006	B;B	0.08055	0.0;0.003	T	0.53592	-0.8417	10	0.31617	T	0.26	.	3.293	0.06956	0.5603:0.171:0.0957:0.173	.	341;341	P02671-2;P02671	.;FIBA_HUMAN	P	341	ENSP00000306361:T341P;ENSP00000385981:T341P	ENSP00000306361:T341P	T	-	1	0	FGA	155727010	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.587000	0.00422	-2.390000	0.00586	-1.626000	0.00786	ACT	.	.		0.587	FGA-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317593.1	NM_000508		G	155507560	T	G	155507560	3	3	326	1	0	0	0	0	1	0	0	0	5838	1725	60	5	1631	5	FGA	4	155507560	Missense_Mutation	SNP	T	TCGA-MR-A8JO-01A-12D-A35Z-10	97710475	155507560	35646716	9	45805										
SPINK5	11005	hgsc.bcm.edu	37	chr5	147477477	147477477	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0714285714285714	2	1	1.47692307692308	8.12307692307692	0	0.4	1	0	gcaaagaatggaatacttttCtgtaccagagaaaatgaccc	8	8	1	3			TCGA-MR-A8JO-01A-12D-A35Z-10	TCGA-MR-A8JO-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66a02e7c-ba44-4552-b8c9-3161a5b2c0e0	de1fdde4-5d17-43bb-a055-456bace72e84	g.chr5:147477477C>G	ENST00000256084.7	+	11	972	c.930C>G	c.(928-930)ttC>ttG	p.F310L	SPINK5_ENST00000476608.1_3'UTR|SPINK5_ENST00000359874.3_Missense_Mutation_p.F310L|SPINK5_ENST00000398454.1_Missense_Mutation_p.F310L	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	310	Kazal-like 5. {ECO:0000255|PROSITE- ProRule:PRU00798}.				anagen (GO:0042640)|epidermal cell differentiation (GO:0009913)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|hair cell differentiation (GO:0035315)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of proteolysis (GO:0045861)|negative regulation of serine-type peptidase activity (GO:1902572)|regulation of cell adhesion (GO:0030155)|regulation of T cell differentiation (GO:0045580)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(8)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAATACTTTTCTGTACCAGAG	0.353																																					p.F310L		Atlas-SNP	.											.	SPINK5	245	.	0			c.C930G						.						114	102	106					5																	147477477		1834	4094	5928	SO:0001583	missense	11005	exon11			ACTTTTCTGTACC	AJ228139	CCDS43382.1, CCDS47300.1, CCDS47301.1	5q31-q32	2014-09-17	2005-08-17		ENSG00000133710	ENSG00000133710		"Serine peptidase inhibitors, Kazal type"	15464	protein-coding gene	gene with protein product	"lymphoepithelial Kazal-type-related inhibitor"	605010	"serine protease inhibitor, Kazal type 5"			10419450	Standard	NM_001127698		Approved	VAKTI, LEKTI, LETKI, NETS, NS, FLJ21544, FLJ97536, FLJ97596, FLJ99794, DKFZp686K19184	uc003loy.2	Q9NQ38	OTTHUMG00000134305	ENST00000256084.7:c.930C>G	chr5.hg19:g.147477477C>G	ENSP00000256084:p.Phe310Leu	92.0	0.0		95.0	14.0	NM_001127699	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Missense_Mutation	SNP	ENST00000256084.7	hg19	CCDS43382.1	.	.	.	.	.	.	.	.	.	.	C	15.66	2.900516	0.52227	.	.	ENSG00000133710	ENST00000398454;ENST00000359874;ENST00000508733;ENST00000256084	T;T;T;T	0.06068	3.35;3.35;3.35;3.35	5.58	4.71	0.59529	Proteinase inhibitor I1, Kazal (1);	0.273097	0.26499	N	0.024030	T	0.16981	0.0408	M	0.67700	2.07	0.29827	N	0.830321	P;P;P;D	0.53885	0.919;0.951;0.919;0.963	P;P;P;P	0.60886	0.489;0.82;0.665;0.88	T	0.03287	-1.1052	10	0.23891	T	0.37	-1.7647	10.4951	0.44772	0.0:0.9105:0.0:0.0895	.	291;310;310;310	B4DWS3;Q9NQ38-3;Q9NQ38;Q9NQ38-2	.;.;ISK5_HUMAN;.	L	310;310;291;310	ENSP00000381472:F310L;ENSP00000352936:F310L;ENSP00000421519:F291L;ENSP00000256084:F310L	ENSP00000256084:F310L	F	+	3	2	SPINK5	147457670	0.995000	0.38212	0.989000	0.46669	0.202000	0.24057	1.383000	0.34385	1.503000	0.48686	0.655000	0.94253	TTC	.	.		0.353	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698		G	147477477	C	G	147477477	3	3	326	1	0	0	0	0	1	0	0	0	15077	912	32	4	972	4	SPINK5	5	147477477	Missense_Mutation	SNP	C	TCGA-MR-A8JO-01A-12D-A35Z-10		147477477	33437783	10	45806										
GABBR1	2550	hgsc.bcm.edu	37	chr6	29599274	29599274	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	2	1	1.47692307692308	8.12307692307692	0	0.4	1	0	ccccccggcacacatactcaAtctcatagtccactggcagg	7	17	2	0			TCGA-MR-A8JO-01A-12D-A35Z-10	TCGA-MR-A8JO-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66a02e7c-ba44-4552-b8c9-3161a5b2c0e0	de1fdde4-5d17-43bb-a055-456bace72e84	g.chr6:29599274A>T	ENST00000377034.4	-	3	523	c.188T>A	c.(187-189)aTt>aAt	p.I63N	GABBR1_ENST00000377016.4_Missense_Mutation_p.I63N|GABBR1_ENST00000376977.3_Missense_Mutation_p.I63N	NM_001470.2	NP_001461.1	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 1	63	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	G-protein coupled GABA receptor activity (GO:0004965)			endometrium(3)|kidney(1)|large_intestine(13)|liver(1)|lung(16)|ovary(5)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47					Baclofen(DB00181)|Progabide(DB00837)|Vigabatrin(DB01080)	CACATACTCAATCTCATAGTC	0.627																																					p.I63N		Atlas-SNP	.											.	GABBR1	95	.	0			c.T188A						.						95	101	99					6																	29599274		2203	4300	6503	SO:0001583	missense	2550	exon3			TACTCAATCTCAT	Y11044	CCDS4663.1, CCDS4664.1, CCDS4665.1	6p21.3	2012-08-29			ENSG00000204681	ENSG00000204681		"GABA receptors", "GPCR / Class C : GABA(B) receptors"	4070	protein-coding gene	gene with protein product	"GABA-B receptor"	603540				9753614, 9798068	Standard	NM_001470		Approved	hGB1a, GPRC3A	uc003nmt.4	Q9UBS5	OTTHUMG00000031095	ENST00000377034.4:c.188T>A	chr6.hg19:g.29599274A>T	ENSP00000366233:p.Ile63Asn	107.0	0.0		105.0	9.0	NM_021904	B0UXY7|O95375|O95468|O95975|O96022|Q5STL4|Q5SUJ8|Q5SUL3|Q71SG6|Q86W60|Q9UQQ0	Missense_Mutation	SNP	ENST00000377034.4	hg19	CCDS4663.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.713704	0.89112	.	.	ENSG00000204681	ENST00000376977;ENST00000377016;ENST00000377034;ENST00000462632;ENST00000476670	T;D;T;T;T	0.88277	-0.35;-2.36;-0.35;-0.35;-0.35	4.49	4.49	0.54785	Complement control module (2);Sushi/SCR/CCP (2);	0.137056	0.46442	D	0.000296	D	0.86527	0.5954	N	0.19112	0.55	0.53688	D	0.999973	D;D;D	0.76494	0.997;0.995;0.999	D;D;D	0.83275	0.994;0.989;0.996	D	0.89538	0.3790	10	0.87932	D	0	-43.0741	11.8141	0.52199	1.0:0.0:0.0:0.0	.	63;63;63	Q9UBS5-5;Q9UBS5-3;Q9UBS5	.;.;GABR1_HUMAN	N	63;63;63;63;68	ENSP00000366176:I63N;ENSP00000366215:I63N;ENSP00000366233:I63N;ENSP00000419755:I63N;ENSP00000417332:I68N	ENSP00000366176:I63N	I	-	2	0	GABBR1	29707253	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.499000	0.90494	1.680000	0.50976	0.374000	0.22700	ATT	.	.		0.627	GABBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076141.3			T	29599274	A	T	29599274	3	4	326	1	0	0	0	0	1	0	0	0	6163	101	4	4	2926	4	GABBR1	6	29599274	Missense_Mutation	SNP	A	TCGA-MR-A8JO-01A-12D-A35Z-10		29599274	141515793	11	45807										
ELOVL5	60481	hgsc.bcm.edu	37	chr6	53134002	53134003	+	Missense_Mutation	DNP	CC	CC	AA													0.0714285714285714	2	1	1.47692307692308	8.12307692307692	0	0.4	1	0	ggtgtgtccattcacagcagCcatggacccattctggtggt							TCGA-MR-A8JO-01A-12D-A35Z-10	TCGA-MR-A8JO-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66a02e7c-ba44-4552-b8c9-3161a5b2c0e0	de1fdde4-5d17-43bb-a055-456bace72e84	g.chr6:53134002_53134003CC>AA	ENST00000542638.1	-	8	1269_1270	c.822_823GG>TT	c.(820-825)atGGct>atTTct	p.274_275MA>IS	ELOVL5_ENST00000541407.1_Missense_Mutation_p.301_302MA>IS|ELOVL5_ENST00000304434.6_Missense_Mutation_p.274_275MA>IS|ELOVL5_ENST00000370918.4_Missense_Mutation_p.264_265MA>IS			Q9NYP7	ELOV5_HUMAN	ELOVL fatty acid elongase 5	274					alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|fatty acid elongation, monounsaturated fatty acid (GO:0034625)|fatty acid elongation, polyunsaturated fatty acid (GO:0034626)|linoleic acid metabolic process (GO:0043651)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|unsaturated fatty acid biosynthetic process (GO:0006636)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid biosynthetic process (GO:0042761)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	fatty acid elongase activity (GO:0009922)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	7	Lung NSC(77;0.116)					TTCACAGCAGCCATGGACCCAT	0.485																																					p.A302S|p.M301I		Atlas-SNP	.											.	ELOVL5	25	.	0			c.G904T|c.G903T						.																																			SO:0001583	missense	60481	exon9			CAGCAGCCATGGA|AGCAGCCATGGAC	AF052129	CCDS4951.1, CCDS56433.1, CCDS56434.1, CCDS75470.1	6p21.1-p12.1	2014-07-30	2011-05-25		ENSG00000012660	ENSG00000012660			21308	protein-coding gene	gene with protein product		611805	"ELOVL family member 5, elongation of long chain fatty acids (FEN1/Elo2, SUR4/Elo3-like, yeast)", "spinocerebellar ataxia 38"	SCA38		10970790, 25065913	Standard	NM_021814		Approved	HELO1, dJ483K16.1	uc011dwx.2	Q9NYP7	OTTHUMG00000016249	ENST00000542638.1:c.822_823delinsAA	chr6.hg19:g.53134002_53134003delinsAA	ENSP00000440728:p.M274_A275delinsIS	116.0|115.0	0.0		99.0	5.0	NM_001242828	B4DZJ2|F6SH78|Q59EL3|Q5TGH5|Q6NXE7|Q7L2S5|Q8NCG4|Q9UI22	Missense_Mutation	SNP	ENST00000542638.1	hg19	CCDS4951.1																																																																																			.	.		0.485	ELOVL5-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043566.1	NM_021814		AA	53134003	CC	AA	53134002	3	1	326	1	0	0	0	0	1	0	0	0	5079	739	26	3	80	3	ELOVL5	6	53134002	Missense_Mutation	DNP	CC	TCGA-MR-A8JO-01A-12D-A35Z-10	23534728	53134002	117981065	12	45808										
TSGA14	95681	hgsc.bcm.edu	37	chr7	130067812	130067812	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	2	1	1.47692307692308	8.12307692307692	0	0.4	1	0	tcaccagtgtccagtcttgaTttgatatgctggtatcttgg	10	8	3	2			TCGA-MR-A8JO-01A-12D-A35Z-10	TCGA-MR-A8JO-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66a02e7c-ba44-4552-b8c9-3161a5b2c0e0	de1fdde4-5d17-43bb-a055-456bace72e84	g.chr7:130067812T>C	ENST00000223208.5	-	2	351	c.81A>G	c.(79-81)aaA>aaG	p.K27K	CEP41_ENST00000489512.1_Silent_p.K27K|CEP41_ENST00000343969.5_Silent_p.K27K|CEP41_ENST00000495702.1_5'UTR|CEP41_ENST00000541543.1_Silent_p.K27K	NM_001257158.1|NM_018718.2	NP_001244087.1|NP_061188.1	Q9BYV8	CEP41_HUMAN	centrosomal protein 41kDa	27					cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein polyglutamylation (GO:0018095)|protein transport (GO:0015031)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|membrane (GO:0016020)|primary cilium (GO:0072372)											CCAGTCTTGATTTGATATGCT	0.303																																					p.K27K		Atlas-SNP	.											.	.	.	.	0			c.A81G						.						85	84	84					7																	130067812		2203	4300	6503	SO:0001819	synonymous_variant	95681	exon2			TCTTGATTTGATA	AJ278890	CCDS5821.1, CCDS59078.1, CCDS59079.1, CCDS59080.1	7q32	2014-02-20	2011-10-04	2011-10-04	ENSG00000106477	ENSG00000106477			12370	protein-coding gene	gene with protein product		610523	"testis specific, 14"	TSGA14		14654843, 22246503	Standard	NM_018718		Approved	DKFZp762H1311, FLJ22445, JBTS15	uc003vpz.4	Q9BYV8	OTTHUMG00000157823	ENST00000223208.5:c.81A>G	chr7.hg19:g.130067812T>C		55.0	0.0		41.0	9.0	NM_001257159	A4D1M0|B4DQ35|F5H0V6|Q7Z496|Q86TM1|Q8NFU8|Q9H6A3|Q9NPV3	Silent	SNP	ENST00000223208.5	hg19	CCDS5821.1																																																																																			.	.		0.303	CEP41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349702.2	NM_018718		C	130067812	T	C	130067812	2	2	326	1	0	0	0	0	0	0	0	1	16635	1490	52	2		2	TSGA14	7	130067812	Silent	SNP	T	TCGA-MR-A8JO-01A-12D-A35Z-10		130067812	29070851	13	45809										
DPP6	1804	hgsc.bcm.edu	37	chr7	154667656	154667656	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0714285714285714	2	1	1.47692307692308	8.12307692307692	0	0.4	1	0	agagtgtggctgagaagttcGaggtgagctgggagacggtg	20	4	0	4			TCGA-MR-A8JO-01A-12D-A35Z-10	TCGA-MR-A8JO-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66a02e7c-ba44-4552-b8c9-3161a5b2c0e0	de1fdde4-5d17-43bb-a055-456bace72e84	g.chr7:154667656G>A	ENST00000377770.3	+	20	2065	c.1924G>A	c.(1924-1926)Gag>Aag	p.E642K	DPP6_ENST00000332007.3_Missense_Mutation_p.E580K|DPP6_ENST00000404039.1_Missense_Mutation_p.E578K|DPP6_ENST00000427557.1_Missense_Mutation_p.E535K			P42658	DPP6_HUMAN	dipeptidyl-peptidase 6	642					cell death (GO:0008219)|neuronal action potential (GO:0019228)|positive regulation of potassium ion transmembrane transport (GO:1901381)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(3)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(35)|pancreas(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	71	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			TGAGAAGTTCGAGGTGAGCTG	0.652																																					p.E642K	NSCLC(125;1384 1783 2490 7422 34254)	Atlas-SNP	.											.	DPP6	383	.	0			c.G1924A						.						29	36	34					7																	154667656		2085	4202	6287	SO:0001583	missense	1804	exon20			AAGTTCGAGGTGA	M96859	CCDS75682.1, CCDS75683.1, CCDS75684.1	7q36.2	2006-08-07	2006-01-12		ENSG00000130226	ENSG00000130226			3010	protein-coding gene	gene with protein product		126141	"dipeptidylpeptidase VI", "dipeptidylpeptidase 6"			1729689	Standard	XM_006715871		Approved	DPPX	uc003wlk.3	P42658	OTTHUMG00000151511	ENST00000377770.3:c.1924G>A	chr7.hg19:g.154667656G>A	ENSP00000367001:p.Glu642Lys	95.0	0.0		88.0	26.0	NM_130797		Missense_Mutation	SNP	ENST00000377770.3	hg19		.	.	.	.	.	.	.	.	.	.	G	7.357	0.624011	0.14193	.	.	ENSG00000130226	ENST00000404039;ENST00000377770;ENST00000332007;ENST00000427557	T;T;T;T	0.29397	1.57;1.57;1.57;1.57	4.92	0.591	0.17465	Peptidase S9, prolyl oligopeptidase, catalytic domain (1);	0.379656	0.30235	N	0.010097	T	0.12050	0.0293	N	0.04090	-0.28	0.37317	D	0.909407	B;B;B;B	0.26635	0.042;0.027;0.155;0.033	B;B;B;B	0.21360	0.017;0.005;0.034;0.014	T	0.19844	-1.0293	10	0.18710	T	0.47	-10.5252	10.8215	0.46608	0.0744:0.5189:0.4066:0.0	.	535;580;642;578	E9PDL2;P42658-2;P42658;E9PF59	.;.;DPP6_HUMAN;.	K	578;642;580;535	ENSP00000385578:E578K;ENSP00000367001:E642K;ENSP00000328226:E580K;ENSP00000397303:E535K	ENSP00000328226:E580K	E	+	1	0	DPP6	154298589	0.622000	0.27085	0.883000	0.34634	0.448000	0.32197	1.592000	0.36676	0.092000	0.17331	-0.450000	0.05554	GAG	.	.		0.652	DPP6-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322932.1	NM_130797		A	154667656	G	A	154667656	3	1	326	1	0	0	0	0	1	0	0	0	4732	1059	37	1	2118	1	DPP6	7	154667656	Missense_Mutation	SNP	G	TCGA-MR-A8JO-01A-12D-A35Z-10	24599844	154667656	4471007	14	45810										
DPP6	1804	hgsc.bcm.edu	37	chr7	154677362	154677362	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	2	1	1.47692307692308	8.12307692307692	0	0.4	1	0	ggattacggtggctacctgaGcacctacatcctcccagcaa	9	14	0	1			TCGA-MR-A8JO-01A-12D-A35Z-10	TCGA-MR-A8JO-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66a02e7c-ba44-4552-b8c9-3161a5b2c0e0	de1fdde4-5d17-43bb-a055-456bace72e84	g.chr7:154677362G>A	ENST00000377770.3	+	22	2294	c.2153G>A	c.(2152-2154)aGc>aAc	p.S718N	DPP6_ENST00000332007.3_Missense_Mutation_p.S656N|DPP6_ENST00000404039.1_Missense_Mutation_p.S654N|DPP6_ENST00000427557.1_Missense_Mutation_p.S611N			P42658	DPP6_HUMAN	dipeptidyl-peptidase 6	718					cell death (GO:0008219)|neuronal action potential (GO:0019228)|positive regulation of potassium ion transmembrane transport (GO:1901381)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(3)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(35)|pancreas(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	71	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			GGCTACCTGAGCACCTACATC	0.522																																					p.S718N	NSCLC(125;1384 1783 2490 7422 34254)	Atlas-SNP	.											.	DPP6	383	.	0			c.G2153A						.						52	57	55					7																	154677362		2051	4195	6246	SO:0001583	missense	1804	exon22			ACCTGAGCACCTA	M96859	CCDS75682.1, CCDS75683.1, CCDS75684.1	7q36.2	2006-08-07	2006-01-12		ENSG00000130226	ENSG00000130226			3010	protein-coding gene	gene with protein product		126141	"dipeptidylpeptidase VI", "dipeptidylpeptidase 6"			1729689	Standard	XM_006715871		Approved	DPPX	uc003wlk.3	P42658	OTTHUMG00000151511	ENST00000377770.3:c.2153G>A	chr7.hg19:g.154677362G>A	ENSP00000367001:p.Ser718Asn	96.0	0.0		95.0	24.0	NM_130797		Missense_Mutation	SNP	ENST00000377770.3	hg19		.	.	.	.	.	.	.	.	.	.	G	16.23	3.064730	0.55432	.	.	ENSG00000130226	ENST00000404039;ENST00000377770;ENST00000332007;ENST00000427557	T;T;T;T	0.48201	0.82;0.82;0.82;0.82	5.42	5.42	0.78866	Peptidase S9, prolyl oligopeptidase, catalytic domain (1);	0.131587	0.64402	D	0.000001	T	0.70202	0.3197	M	0.86028	2.79	0.52501	D	0.999951	P;P;D;D	0.57571	0.891;0.952;0.98;0.961	P;P;P;P	0.58660	0.83;0.756;0.843;0.843	T	0.75625	-0.3253	10	0.72032	D	0.01	-33.19	19.2472	0.93906	0.0:0.0:1.0:0.0	.	611;656;718;654	E9PDL2;P42658-2;P42658;E9PF59	.;.;DPP6_HUMAN;.	N	654;718;656;611	ENSP00000385578:S654N;ENSP00000367001:S718N;ENSP00000328226:S656N;ENSP00000397303:S611N	ENSP00000328226:S656N	S	+	2	0	DPP6	154308295	1.000000	0.71417	1.000000	0.80357	0.297000	0.27493	5.875000	0.69660	2.543000	0.85770	0.585000	0.79938	AGC	.	.		0.522	DPP6-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322932.1	NM_130797		A	154677362	G	A	154677362	3	1	326	1	0	0	0	0	1	0	0	0	4732	971	34	3	2355	3	DPP6	7	154677362	Missense_Mutation	SNP	G	TCGA-MR-A8JO-01A-12D-A35Z-10	9706	154677362	4461301	15	45811										
COL5A1	1289	hgsc.bcm.edu	37	chr9	137696861	137696861	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	2	1	1.47692307692308	8.12307692307692	0	0.4	1	0	cctccctgggaaagatggccCtccaggattacgtggtttcc	11	13	0	1	rs377125301		TCGA-MR-A8JO-01A-12D-A35Z-10	TCGA-MR-A8JO-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66a02e7c-ba44-4552-b8c9-3161a5b2c0e0	de1fdde4-5d17-43bb-a055-456bace72e84	g.chr9:137696861C>T	ENST00000371817.3	+	40	3569	c.3155C>T	c.(3154-3156)cCt>cTt	p.P1052L		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	1052	Triple-helical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		AAAGATGGCCCTCCAGGATTA	0.617																																					p.P1052L		Atlas-SNP	.											.	COL5A1	323	.	0			c.C3155T						.	C	LEU/PRO	0,4406		0,0,2203	57	52	54		3155	5.1	0.8	9		54	1,8599	1.2+/-3.3	0,1,4299	no	missense	COL5A1	NM_000093.3	98	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	1052/1839	137696861	1,13005	2203	4300	6503	SO:0001583	missense	1289	exon40			ATGGCCCTCCAGG	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"Collagens"	2209	protein-coding gene	gene with protein product	"alpha 1 type V collagen"	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.3155C>T	chr9.hg19:g.137696861C>T	ENSP00000360882:p.Pro1052Leu	90.0	0.0		80.0	13.0	NM_000093	Q15094|Q5SUX4	Missense_Mutation	SNP	ENST00000371817.3	hg19	CCDS6982.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.142536	0.77888	0.0	1.16E-4	ENSG00000130635	ENST00000371817	D	0.96685	-4.09	5.12	5.12	0.69794	.	0.070617	0.64402	U	0.000017	D	0.96867	0.8977	L	0.35341	1.055	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.98074	1.0400	10	0.87932	D	0	.	18.5537	0.91075	0.0:1.0:0.0:0.0	.	1052	P20908	CO5A1_HUMAN	L	1052	ENSP00000360882:P1052L	ENSP00000360882:P1052L	P	+	2	0	COL5A1	136836682	1.000000	0.71417	0.780000	0.31762	0.982000	0.71751	7.683000	0.84093	2.390000	0.81377	0.446000	0.29264	CCT	.	.		0.617	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093		T	137696861	C	T	137696861	3	4	326	1	0	0	0	0	1	0	0	0	3698	681	24	3	3313	3	COL5A1	9	137696861	Missense_Mutation	SNP	C	TCGA-MR-A8JO-01A-12D-A35Z-10		137696861	3516570	16	45812										
OR5M8	219484	hgsc.bcm.edu	37	chr11	56257944	56257944	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0714285714285714	2	1	1.47692307692308	8.12307692307692	0	0.4	1	0	atcttcattgacagctctttGattaatgcttcttttacatt	4	8	4	2			TCGA-MR-A8JO-01A-12D-A35Z-10	TCGA-MR-A8JO-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66a02e7c-ba44-4552-b8c9-3161a5b2c0e0	de1fdde4-5d17-43bb-a055-456bace72e84	g.chr11:56257944G>C	ENST00000327216.2	-	1	927	c.903C>G	c.(901-903)atC>atG	p.I301M		NM_001005282.1	NP_001005282.1	Q8NGP6	OR5M8_HUMAN	olfactory receptor, family 5, subfamily M, member 8	301						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(22)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	Esophageal squamous(21;0.00352)					ACAGCTCTTTGATTAATGCTT	0.303																																					p.I301M		Atlas-SNP	.											.	OR5M8	74	.	0			c.C903G						.						33	36	35					11																	56257944		2195	4290	6485	SO:0001583	missense	219484	exon1			CTCTTTGATTAAT	AB065744	CCDS31533.1	11q11	2012-08-09			ENSG00000181371	ENSG00000181371		"GPCR / Class A : Olfactory receptors"	14846	protein-coding gene	gene with protein product							Standard	NM_001005282		Approved		uc001nix.1	Q8NGP6	OTTHUMG00000166877	ENST00000327216.2:c.903C>G	chr11.hg19:g.56257944G>C	ENSP00000323354:p.Ile301Met	168.0	0.0		113.0	7.0	NM_001005282	B2RNM5|Q6IEW3|Q96RB8	Missense_Mutation	SNP	ENST00000327216.2	hg19	CCDS31533.1	.	.	.	.	.	.	.	.	.	.	G	7.597	0.671886	0.14776	.	.	ENSG00000181371	ENST00000327216	T	0.37752	1.18	4.13	1.99	0.26369	.	0.979946	0.08257	U	0.973645	T	0.23688	0.0573	N	0.11756	0.17	0.09310	N	1	B	0.11235	0.004	B	0.09377	0.004	T	0.26258	-1.0108	10	0.56958	D	0.05	-0.9483	11.4296	0.50032	0.0:0.5168:0.4832:0.0	.	301	Q8NGP6	OR5M8_HUMAN	M	301	ENSP00000323354:I301M	ENSP00000323354:I301M	I	-	3	3	OR5M8	56014520	0.000000	0.05858	0.011000	0.14972	0.031000	0.12232	-0.551000	0.06027	0.846000	0.35142	0.632000	0.83419	ATC	.	.		0.303	OR5M8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391641.1	NM_001005282		C	56257944	G	C	56257944	3	2	326	1	0	0	0	0	1	0	0	0	11185	1280	45	4	36	4	OR5M8	11	56257944	Missense_Mutation	SNP	G	TCGA-MR-A8JO-01A-12D-A35Z-10		56257944	78748572	17	45813										
SMTNL1	219537	hgsc.bcm.edu	37	chr11	57310235	57310235	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	2	1	1.47692307692308	8.12307692307692	0	0.4	1	0	accaaaggcacagctggaaaGgccatcaatgaggggcctcc	12	12	1	1			TCGA-MR-A8JO-01A-12D-A35Z-10	TCGA-MR-A8JO-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66a02e7c-ba44-4552-b8c9-3161a5b2c0e0	de1fdde4-5d17-43bb-a055-456bace72e84	g.chr11:57310235G>A	ENST00000399154.2	+	1	120	c.120G>A	c.(118-120)aaG>aaA	p.K40K	SMTNL1_ENST00000457912.1_Silent_p.K58K|SMTNL1_ENST00000527972.1_Silent_p.K40K			A8MU46	SMTL1_HUMAN	smoothelin-like 1	40					negative regulation of vasodilation (GO:0045908)|positive regulation of vasoconstriction (GO:0045907)	contractile fiber (GO:0043292)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|large_intestine(1)|lung(4)|ovary(1)	8						CAGCTGGAAAGGCCATCAATG	0.592																																					p.K40K		Atlas-SNP	.											.	SMTNL1	68	.	0			c.G120A						.						39	45	43					11																	57310235		1999	4160	6159	SO:0001819	synonymous_variant	219537	exon1			TGGAAAGGCCATC	BX116227		11q12.1	2006-02-02				ENSG00000214872			32394	protein-coding gene	gene with protein product	"calponin homology-associated smooth muscle protein"	613664				15327999	Standard	NM_001105565		Approved	CHASM	uc021qjh.1	A8MU46		ENST00000399154.2:c.120G>A	chr11.hg19:g.57310235G>A		251.0	0.0		178.0	28.0	NM_001105565		Silent	SNP	ENST00000399154.2	hg19																																																																																				.	.		0.592	SMTNL1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_166203		A	57310235	G	A	57310235	2	1	326	1	0	0	0	0	0	0	0	1	14830	991	35	3		3	SMTNL1	11	57310235	Silent	SNP	G	TCGA-MR-A8JO-01A-12D-A35Z-10	1052291	57310235	77696281	18	45814										
OSBP	5007	hgsc.bcm.edu	37	chr11	59369293	59369293	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	2	1	1.47692307692308	8.12307692307692	0	0.4	1	0	actatgggtctgggctaacaTgaggaaatctctgcaggcct	12	9	2	1	rs370601390		TCGA-MR-A8JO-01A-12D-A35Z-10	TCGA-MR-A8JO-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66a02e7c-ba44-4552-b8c9-3161a5b2c0e0	de1fdde4-5d17-43bb-a055-456bace72e84	g.chr11:59369293T>C	ENST00000263847.1	-	4	1320	c.841A>G	c.(841-843)Atg>Gtg	p.M281V		NM_002556.2	NP_002547.1	P22059	OSBP1_HUMAN	oxysterol binding protein	281					lipid transport (GO:0006869)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	oxysterol binding (GO:0008142)			NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		all_epithelial(135;0.000236)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)		TGGGCTAACATGAGGAAATCT	0.488																																					p.M281V		Atlas-SNP	.											.	OSBP	57	.	0			c.A841G						.						87	84	85					11																	59369293		2201	4295	6496	SO:0001583	missense	5007	exon4			CTAACATGAGGAA	AF185696	CCDS7974.1	11q12-q13	2013-01-10			ENSG00000110048	ENSG00000110048		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	8503	protein-coding gene	gene with protein product		167040					Standard	NM_002556		Approved	OSBP1	uc001noc.1	P22059	OTTHUMG00000167422	ENST00000263847.1:c.841A>G	chr11.hg19:g.59369293T>C	ENSP00000263847:p.Met281Val	121.0	0.0		85.0	15.0	NM_002556	Q6P524	Missense_Mutation	SNP	ENST00000263847.1	hg19	CCDS7974.1	.	.	.	.	.	.	.	.	.	.	T	11.48	1.651694	0.29336	.	.	ENSG00000110048	ENST00000263847	D	0.86297	-2.1	6.07	-0.197	0.13228	.	0.591766	0.20846	N	0.084603	T	0.72078	0.3416	N	0.22421	0.69	0.22675	N	0.998868	B	0.02656	0.0	B	0.04013	0.001	T	0.56486	-0.7971	10	0.34782	T	0.22	-5.2994	2.9018	0.05708	0.1138:0.3481:0.1173:0.4208	.	281	P22059	OSBP1_HUMAN	V	281	ENSP00000263847:M281V	ENSP00000263847:M281V	M	-	1	0	OSBP	59125869	0.000000	0.05858	0.988000	0.46212	0.998000	0.95712	-1.489000	0.02306	-0.052000	0.13311	0.533000	0.62120	ATG	.	.		0.488	OSBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394555.1			C	59369293	T	C	59369293	3	2	326	1	0	0	0	0	1	0	0	0	11282	1464	51	2	1626	2	OSBP	11	59369293	Missense_Mutation	SNP	T	TCGA-MR-A8JO-01A-12D-A35Z-10	2059058	59369293	75637223	19	45815										
CCND2	894	hgsc.bcm.edu	37	chr12	4385334	4385334	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	2	1	1.47692307692308	8.12307692307692	0	0.4	1	0	agagaccagcccgctgaccgCggagaagctgtgcatttaca	12	12	0	3			TCGA-MR-A8JO-01A-12D-A35Z-10	TCGA-MR-A8JO-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66a02e7c-ba44-4552-b8c9-3161a5b2c0e0	de1fdde4-5d17-43bb-a055-456bace72e84	g.chr12:4385334C>A	ENST00000261254.3	+	2	628	c.359C>A	c.(358-360)gCg>gAg	p.A120E	RP11-264F23.4_ENST00000537370.1_RNA|RP11-264F23.3_ENST00000539135.1_RNA	NM_001759.3	NP_001750.1	P30279	CCND2_HUMAN	cyclin D2	120	Cyclin N-terminal.				cell cycle (GO:0007049)|cell division (GO:0051301)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of protein phosphorylation (GO:0001934)	chromatin (GO:0000785)|cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	17			all cancers(3;4.15e-10)|GBM - Glioblastoma multiforme(3;6.34e-05)|Colorectal(7;0.00245)|OV - Ovarian serous cystadenocarcinoma(31;0.00301)|COAD - Colon adenocarcinoma(12;0.0264)|STAD - Stomach adenocarcinoma(119;0.206)			CCGCTGACCGCGGAGAAGCTG	0.582			T	IGL@	"NHL,CLL"																																p.A120E		Atlas-SNP	.		Dom	yes		12	12p13	894	cyclin D2		L	.	CCND2	50	.	0			c.C359A						.						65	55	59					12																	4385334		2203	4300	6503	SO:0001583	missense	894	exon2			TGACCGCGGAGAA	AF518005	CCDS8524.1	12p13	2008-08-04			ENSG00000118971	ENSG00000118971			1583	protein-coding gene	gene with protein product	"G1/S-specific cyclin D2"	123833				1386335	Standard	NM_001759		Approved		uc001qmo.3	P30279	OTTHUMG00000168123	ENST00000261254.3:c.359C>A	chr12.hg19:g.4385334C>A	ENSP00000261254:p.Ala120Glu	78.0	0.0		67.0	7.0	NM_001759	A8K531|Q13955|Q5U035	Missense_Mutation	SNP	ENST00000261254.3	hg19	CCDS8524.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.984438	0.93044	.	.	ENSG00000118971	ENST00000261254	T	0.11821	2.74	5.15	5.15	0.70609	Cyclin, N-terminal (1);Cyclin-like (3);	0.049681	0.85682	D	0.000000	T	0.48822	0.1521	M	0.92367	3.3	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.61662	-0.7017	10	0.66056	D	0.02	.	17.6727	0.88223	0.0:1.0:0.0:0.0	.	120	P30279	CCND2_HUMAN	E	120	ENSP00000261254:A120E	ENSP00000261254:A120E	A	+	2	0	CCND2	4255595	1.000000	0.71417	0.119000	0.21687	0.967000	0.64934	6.018000	0.70811	2.432000	0.82394	0.555000	0.69702	GCG	.	.		0.582	CCND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398287.1	NM_001759		A	4385334	C	A	4385334	3	1	326	1	0	0	0	0	1	0	0	0	2919	768	27	1	365	1	CCND2	12	4385334	Missense_Mutation	SNP	C	TCGA-MR-A8JO-01A-12D-A35Z-10		4385334	129466561	20	45816										
STARD13	90627	hgsc.bcm.edu	37	chr13	33704163	33704163	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	2	1	1.47692307692308	8.12307692307692	0	0.4	1	0	tccagcatgaccgggttgtcTgtacagcactggcccggctg	13	13	1	1			TCGA-MR-A8JO-01A-12D-A35Z-10	TCGA-MR-A8JO-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66a02e7c-ba44-4552-b8c9-3161a5b2c0e0	de1fdde4-5d17-43bb-a055-456bace72e84	g.chr13:33704163T>C	ENST00000336934.5	-	5	767	c.651A>G	c.(649-651)acA>acG	p.T217T	STARD13_ENST00000255486.4_Silent_p.T209T|STARD13_ENST00000399365.3_Silent_p.T99T	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	217					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	40	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		CCGGGTTGTCTGTACAGCACT	0.622																																					p.T217T		Atlas-SNP	.											.	STARD13	100	.	0			c.A651G						.						41	44	43					13																	33704163		2203	4300	6503	SO:0001819	synonymous_variant	90627	exon5			GTTGTCTGTACAG	AL049801	CCDS9348.1, CCDS9349.1, CCDS9350.1	13q13.1	2013-08-13	2007-08-16		ENSG00000133121	ENSG00000133121		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	19164	protein-coding gene	gene with protein product		609866	"START domain containing 13", "long intergenic non-protein coding RNA 464"	LINC00464		8812419	Standard	NM_178006		Approved	GT650, DLC2, ARHGAP37	uc001uuw.3	Q9Y3M8	OTTHUMG00000016708	ENST00000336934.5:c.651A>G	chr13.hg19:g.33704163T>C		52.0	0.0		40.0	8.0	NM_178006	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Silent	SNP	ENST00000336934.5	hg19	CCDS9348.1																																																																																			.	.		0.622	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2	NM_001243466		C	33704163	T	C	33704163	2	2	326	1	0	0	0	0	0	0	0	1	15271	1567	55	2		2	STARD13	13	33704163	Silent	SNP	T	TCGA-MR-A8JO-01A-12D-A35Z-10		33704163	81465715	21	45817										
THBS1	7057	hgsc.bcm.edu	37	chr15	39874936	39874936	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	2	1	1.47692307692308	8.12307692307692	0	0.4	1	0	tccgcatcgcaaaggggggcGtcaatgacaatttccaggtg	13	10	1	1			TCGA-MR-A8JO-01A-12D-A35Z-10	TCGA-MR-A8JO-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66a02e7c-ba44-4552-b8c9-3161a5b2c0e0	de1fdde4-5d17-43bb-a055-456bace72e84	g.chr15:39874936G>A	ENST00000260356.5	+	3	775	c.610G>A	c.(610-612)Gtc>Atc	p.V204I		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	204	Laminin G-like.				activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		AAAGGGGGGCGTCAATGACAA	0.562																																					p.V204I		Atlas-SNP	.											.	THBS1	106	.	0			c.G610A						.						37	35	36					15																	39874936		2200	4296	6496	SO:0001583	missense	7057	exon3			GGGGGCGTCAATG		CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"thrombospondin-1p180"	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.610G>A	chr15.hg19:g.39874936G>A	ENSP00000260356:p.Val204Ile	39.0	0.0		34.0	5.0	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Missense_Mutation	SNP	ENST00000260356.5	hg19	CCDS32194.1	.	.	.	.	.	.	.	.	.	.	G	14.30	2.494400	0.44352	.	.	ENSG00000137801	ENST00000260356	T	0.02177	4.41	5.56	4.62	0.57501	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G, thrombospondin-type, N-terminal (1);	0.000000	0.32802	N	0.005635	T	0.02571	0.0078	L	0.34521	1.04	0.43667	D	0.996095	B	0.20887	0.049	B	0.10450	0.005	T	0.54523	-0.8281	10	0.20046	T	0.44	-19.6668	15.5318	0.75970	0.0:0.1384:0.8616:0.0	.	204	P07996	TSP1_HUMAN	I	204	ENSP00000260356:V204I	ENSP00000260356:V204I	V	+	1	0	THBS1	37662228	1.000000	0.71417	0.936000	0.37596	0.986000	0.74619	5.330000	0.65899	1.533000	0.49186	0.655000	0.94253	GTC	.	.		0.562	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246		A	39874936	G	A	39874936	3	1	326	1	0	0	0	0	1	0	0	0	15868	1145	40	1	616	1	THBS1	15	39874936	Missense_Mutation	SNP	G	TCGA-MR-A8JO-01A-12D-A35Z-10		39874936	62656456	22	45818										
BAHD1	22893	hgsc.bcm.edu	37	chr15	40758269	40758270	+	Frame_Shift_Ins	INS	-	-	T													0.0714285714285714	2	1	1.47692307692308	8.12307692307692	0	0.4	1	0	acacggaccctgagctggtgINSttcctttgccgccatgtcta							TCGA-MR-A8JO-01A-12D-A35Z-10	TCGA-MR-A8JO-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66a02e7c-ba44-4552-b8c9-3161a5b2c0e0	de1fdde4-5d17-43bb-a055-456bace72e84	g.chr15:40758269_40758270insT	ENST00000416165.1	+	7	2354_2355	c.2283_2284insT	c.(2284-2286)ttcfs	p.F762fs	RP11-64K12.8_ENST00000559730.1_RNA|BAHD1_ENST00000560846.1_Frame_Shift_Ins_p.F759fs|BAHD1_ENST00000561234.1_Frame_Shift_Ins_p.F761fs	NM_014952.3	NP_055767.3	Q8TBE0	BAHD1_HUMAN	bromo adjacent homology domain containing 1	762	BAH. {ECO:0000255|PROSITE- ProRule:PRU00370}.				heterochromatin assembly (GO:0031507)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|chromosome (GO:0005694)	chromatin binding (GO:0003682)			NS(1)|endometrium(6)|kidney(3)|large_intestine(3)|lung(10)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	28		all_cancers(109;8.28e-19)|all_epithelial(112;2.64e-15)|Lung NSC(122;5.14e-11)|all_lung(180;1.27e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.46e-06)|BRCA - Breast invasive adenocarcinoma(123;0.08)		CTGAGCTGGTGTTCCTTTGCCG	0.624																																					p.V761fs		Atlas-INDEL	.											.	BAHD1	68	.	0			c.2283_2284insT						.																																			SO:0001589	frameshift_variant	22893	exon7			.	AL833923	CCDS10058.1, CCDS73705.1	15q14	2005-11-10			ENSG00000140320	ENSG00000140320			29153	protein-coding gene	gene with protein product		613880				10231032	Standard	XM_005254229		Approved	KIAA0945	uc001zlu.2	Q8TBE0	OTTHUMG00000129982	ENST00000416165.1:c.2285dupT	chr15.hg19:g.40758271_40758271dupT	ENSP00000396976:p.Phe762fs	162.0	0.0		142.0	34.0	NM_014952	Q8NDF7|Q9Y2F4	Frame_Shift_Ins	INS	ENST00000416165.1	hg19	CCDS10058.1																																																																																			.	.		0.624	BAHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252248.1	NM_014952		T	40758270	-	T	40758269	7	5	326	1	0	1	1	0	0	0	0	0	1297	1364	48	0	2305	0	BAHD1	15	40758269	Frame_Shift_Ins	INS	-	TCGA-MR-A8JO-01A-12D-A35Z-10	883333	40758269	61773123	23	45819										
ARL6IP1	23204	hgsc.bcm.edu	37	chr16	18804626	18804626	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	2	1	1.47692307692308	8.12307692307692	0	0.4	1	0	gtttgtttatctccctcttgGccattccaatgtacttcaaa	5	11	3	0			TCGA-MR-A8JO-01A-12D-A35Z-10	TCGA-MR-A8JO-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66a02e7c-ba44-4552-b8c9-3161a5b2c0e0	de1fdde4-5d17-43bb-a055-456bace72e84	g.chr16:18804626G>T	ENST00000304414.7	-	6	771	c.560C>A	c.(559-561)gCc>gAc	p.A187D	RPS15A_ENST00000322989.4_5'Flank|ARL6IP1_ENST00000546206.2_Missense_Mutation_p.A158D|ARL6IP1_ENST00000562819.1_Missense_Mutation_p.A72D|RP11-1035H13.3_ENST00000567078.2_Intron|RPS15A_ENST00000563390.1_5'Flank	NM_015161.1	NP_055976.1	Q15041	AR6P1_HUMAN	ADP-ribosylation factor-like 6 interacting protein 1	187					cell death (GO:0008219)|cotranslational protein targeting to membrane (GO:0006613)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|Sec61 translocon complex (GO:0005784)				breast(1)|large_intestine(2)|lung(6)|pancreas(1)|prostate(1)	11						CTCCCTCTTGGCCATTCCAAT	0.373																																					p.A187D		Atlas-SNP	.											.	ARL6IP1	23	.	0			c.C560A						.						82	80	80					16																	18804626		2197	4300	6497	SO:0001583	missense	23204	exon6			CTCTTGGCCATTC	BC010281	CCDS10572.1	16p12-p11.2	2014-03-12	2006-09-26	2006-09-26	ENSG00000170540	ENSG00000170540			697	protein-coding gene	gene with protein product		607669	"ADP-ribosylation factor-like 6 interacting protein"	ARL6IP		24482476	Standard	NM_015161		Approved	AIP1, ARMER, KIAA0069, SPG61	uc002dfl.1	Q15041	OTTHUMG00000131367	ENST00000304414.7:c.560C>A	chr16.hg19:g.18804626G>T	ENSP00000306788:p.Ala187Asp	169.0	0.0		139.0	6.0	NM_015161		Missense_Mutation	SNP	ENST00000304414.7	hg19	CCDS10572.1	.	.	.	.	.	.	.	.	.	.	N	17.82	3.483534	0.63962	.	.	ENSG00000170540	ENST00000304414;ENST00000545430;ENST00000546206	T;T	0.54479	0.57;0.57	5.36	5.36	0.76844	.	0.051556	0.85682	D	0.000000	T	0.54838	0.1883	M	0.62723	1.935	0.44539	D	0.997494	P	0.44946	0.846	B	0.43623	0.425	T	0.61078	-0.7135	10	0.72032	D	0.01	-8.532	14.6457	0.68759	0.0:0.1455:0.8545:0.0	.	187	Q15041	AR6P1_HUMAN	D	187;139;158	ENSP00000306788:A187D;ENSP00000440048:A158D	ENSP00000306788:A187D	A	-	2	0	ARL6IP1	18712127	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.826000	0.86716	2.669000	0.90835	0.591000	0.81541	GCC	.	.		0.373	ARL6IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254156.2	NM_015161		T	18804626	G	T	18804626	3	4	326	1	0	0	0	0	1	0	0	0	942	1203	42	3	55	3	ARL6IP1	16	18804626	Missense_Mutation	SNP	G	TCGA-MR-A8JO-01A-12D-A35Z-10		18804626	71550127	24	45820										
PPM1D	8493	hgsc.bcm.edu	37	chr17	58740434	58740434	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0714285714285714	2	1	1.47692307692308	8.12307692307692	0	0.4	1	0	ttcgtagcaatgccttctcaGagaattttttagaggtttca	8	7	2	2			TCGA-MR-A8JO-01A-12D-A35Z-10	TCGA-MR-A8JO-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66a02e7c-ba44-4552-b8c9-3161a5b2c0e0	de1fdde4-5d17-43bb-a055-456bace72e84	g.chr17:58740434G>T	ENST00000305921.3	+	6	1571	c.1339G>T	c.(1339-1341)Gag>Tag	p.E447*	RNU6-623P_ENST00000363143.1_RNA	NM_003620.3	NP_003611.1	O15297	PPM1D_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1D	447					G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of cell proliferation (GO:0008285)|peptidyl-threonine dephosphorylation (GO:0035970)|protein dephosphorylation (GO:0006470)|response to bacterium (GO:0009617)|response to radiation (GO:0009314)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)	p.E447K(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	15	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;6.75e-12)|all cancers(12;1.96e-10)			TGCCTTCTCAGAGAATTTTTT	0.433											OREG0031485	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.E447X		Atlas-SNP	.											PPM1D,scalp,carcinoma,0,1	PPM1D	50	.	1	Substitution - Missense(1)	skin(1)	c.G1339T						.						100	100	100					17																	58740434		2203	4300	6503	SO:0001587	stop_gained	8493	exon6			TTCTCAGAGAATT	U78305	CCDS11625.1	17q23.3	2014-09-17	2010-03-05		ENSG00000170836	ENSG00000170836		"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	9277	protein-coding gene	gene with protein product	"wild-type p53-induced phosphatase 1", "protein phosphatase 2C, delta isoform"	605100	"protein phosphatase 1D magnesium-dependent, delta isoform"			9177166	Standard	NM_003620		Approved	Wip1, PP2C-DELTA	uc002iyt.2	O15297		ENST00000305921.3:c.1339G>T	chr17.hg19:g.58740434G>T	ENSP00000306682:p.Glu447*	122.0	0.0	1033	102.0	18.0	NM_003620	Q53XP4|Q6P991|Q8IVR6	Nonsense_Mutation	SNP	ENST00000305921.3	hg19	CCDS11625.1	.	.	.	.	.	.	.	.	.	.	G	39	7.352756	0.98231	.	.	ENSG00000170836	ENST00000305921	.	.	.	6.08	6.08	0.98989	.	0.219106	0.48286	D	0.000199	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	-23.029	9.6637	0.39972	0.0698:0.0:0.7885:0.1417	.	.	.	.	X	447	.	ENSP00000306682:E447X	E	+	1	0	PPM1D	56095216	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.741000	0.62095	2.894000	0.99253	0.591000	0.81541	GAG	.	.		0.433	PPM1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449474.1	NM_003620		T	58740434	G	T	58740434	4	4	326	1	0	0	0	0	0	1	0	0	12349	943	33	3	1361	3	PPM1D	17	58740434	Nonsense_Mutation	SNP	G	TCGA-MR-A8JO-01A-12D-A35Z-10		58740434	22454776	25	45821										
MED13	9969	hgsc.bcm.edu	37	chr17	60059776	60059777	+	Nonsense_Mutation	DNP	GC	GC	TT													0.0714285714285714	2	1	1.47692307692308	8.12307692307692	0	0.4	1	0	aagggtgaaaataaattagtGcactgatcttgtagcaataa							TCGA-MR-A8JO-01A-12D-A35Z-10	TCGA-MR-A8JO-10A-01D-A35Z-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66a02e7c-ba44-4552-b8c9-3161a5b2c0e0	de1fdde4-5d17-43bb-a055-456bace72e84	g.chr17:60059776_60059777GC>TT	ENST00000397786.2	-	16	3663_3664	c.3587_3588GC>AA	c.(3586-3588)tGC>tAA	p.C1196*		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	1196					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						ATAAATTAGTGCACTGATCTTG	0.391																																					p.C1196X|p.C1196Y		Atlas-SNP	.											.	MED13	181	.	0			c.C3588A|c.G3587A						.																																			SO:0001587	stop_gained	9969	exon16			ATTAGTGCACTGA|TTAGTGCACTGAT	AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"thyroid hormone receptor associated protein 1"	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.3587_3588delinsTT	chr17.hg19:g.60059776_60059777delinsTT	ENSP00000380888:p.Cys1196*	151.0|150.0	0.0		104.0|102.0	11.0	NM_005121	B2RU05|O60334	Nonsense_Mutation|Missense_Mutation	SNP	ENST00000397786.2	hg19	CCDS42366.1																																																																																			.	.		0.391	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121		TT	60059777	GC	TT	60059776	4	4	326	1	0	0	0	0	0	1	0	0	9439	1311	46	3	2996	3	MED13	17	60059776	Nonsense_Mutation	DNP	GC	TCGA-MR-A8JO-01A-12D-A35Z-10	1319342	60059776	21135434	26	45822										
ZFP28	140612	hgsc.bcm.edu	37	chr19	57065959	57065959	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	2	1	1.47692307692308	8.12307692307692	0	0.4	1	0	aaaagcttttaggcagaataTacaccttgccagtcatttaa	6	8	1	1			TCGA-MR-A8JO-01A-12D-A35Z-10	TCGA-MR-A8JO-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66a02e7c-ba44-4552-b8c9-3161a5b2c0e0	de1fdde4-5d17-43bb-a055-456bace72e84	g.chr19:57065959T>C	ENST00000301318.3	+	8	1876	c.1805T>C	c.(1804-1806)aTa>aCa	p.I602T	AC007228.11_ENST00000596587.1_RNA	NM_020828.1	NP_065879.1	Q8NHY6	ZFP28_HUMAN	ZFP28 zinc finger protein	602					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(6)|ovary(1)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	35		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0302)		AGGCAGAATATACACCTTGCC	0.433																																					p.I602T	Ovarian(124;554 1662 19430 21141 52494)	Atlas-SNP	.											.	ZFP28	99	.	0			c.T1805C						.						94	103	100					19																	57065959		2203	4300	6503	SO:0001583	missense	140612	exon8			AGAATATACACCT		CCDS12946.1	19q13.43	2013-01-08	2012-11-27			ENSG00000196867		"Zinc fingers, C2H2-type", "-"	17801	protein-coding gene	gene with protein product			"zinc finger protein 28 homolog (mouse)"				Standard	NM_020828		Approved	KIAA1431, mkr5	uc002qnj.3	Q8NHY6		ENST00000301318.3:c.1805T>C	chr19.hg19:g.57065959T>C	ENSP00000301318:p.Ile602Thr	174.0	0.0		148.0	25.0	NM_020828	A0JNV6|K7ES88|Q8NHU8|Q9BY30|Q9P2B6	Missense_Mutation	SNP	ENST00000301318.3	hg19	CCDS12946.1	.	.	.	.	.	.	.	.	.	.	T	6.026	0.373232	0.11409	.	.	ENSG00000196867	ENST00000301318	T	0.07216	3.21	4.12	3.1	0.35709	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.130039	0.34435	N	0.003971	T	0.02047	0.0064	N	0.01800	-0.715	0.09310	N	1	P	0.36027	0.533	B	0.27076	0.076	T	0.34354	-0.9832	10	0.41790	T	0.15	.	1.1688	0.01821	0.1839:0.1052:0.1917:0.5192	.	602	Q8NHY6	ZFP28_HUMAN	T	602	ENSP00000301318:I602T	ENSP00000301318:I602T	I	+	2	0	ZFP28	61757771	0.000000	0.05858	0.948000	0.38648	0.783000	0.44284	-1.213000	0.02991	1.852000	0.53769	0.454000	0.30748	ATA	.	.		0.433	ZFP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458409.1	NM_020828		C	57065959	T	C	57065959	3	2	326	1	0	0	0	0	1	0	0	0	17657	1406	49	2	1835	2	ZFP28	19	57065959	Missense_Mutation	SNP	T	TCGA-MR-A8JO-01A-12D-A35Z-10		57065959	2063024	27	45823										
CHRNA4	1137	hgsc.bcm.edu	37	chr20	61981058	61981058	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0714285714285714	2	1	1.47692307692308	8.12307692307692	0	0.4	1	0	tgcaatgtactggacgccctCcaccgcccgggtcagggccg	13	16	1	0			TCGA-MR-A8JO-01A-12D-A35Z-10	TCGA-MR-A8JO-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	66a02e7c-ba44-4552-b8c9-3161a5b2c0e0	de1fdde4-5d17-43bb-a055-456bace72e84	g.chr20:61981058C>T	ENST00000370263.4	-	5	1926	c.1705G>A	c.(1705-1707)Gag>Aag	p.E569K	CHRNA4_ENST00000463705.1_5'UTR	NM_000744.6|NM_001256573.1	NP_000735.1|NP_001243502.1	P43681	ACHA4_HUMAN	cholinergic receptor, nicotinic, alpha 4 (neuronal)	569					action potential (GO:0001508)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cognition (GO:0050890)|DNA repair (GO:0006281)|exploration behavior (GO:0035640)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|neurological system process (GO:0050877)|regulation of dopamine secretion (GO:0014059)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of membrane potential (GO:0042391)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(19)|prostate(3)|skin(3)|soft_tissue(1)	33	all_cancers(38;1.71e-10)				Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273)	TGGACGCCCTCCACCGCCCGG	0.682																																					p.E569K		Atlas-SNP	.											.	CHRNA4	98	.	0			c.G1705A						.						43	51	48					20																	61981058		2201	4300	6501	SO:0001583	missense	1137	exon5			CGCCCTCCACCGC		CCDS13517.1	20q13.33	2013-09-20	2012-02-07		ENSG00000101204	ENSG00000101204		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1958	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 4 (neuronal)"	118504	"cholinergic receptor, nicotinic, alpha polypeptide 4"	EBN, EBN1		1505988	Standard	NM_000744		Approved	BFNC	uc002yes.3	P43681	OTTHUMG00000033080	ENST00000370263.4:c.1705G>A	chr20.hg19:g.61981058C>T	ENSP00000359285:p.Glu569Lys	132.0	0.0		106.0	10.0	NM_000744	Q4JGR7|Q4VAQ5|Q4VAQ6	Missense_Mutation	SNP	ENST00000370263.4	hg19	CCDS13517.1	.	.	.	.	.	.	.	.	.	.	C	19.62	3.861238	0.71949	.	.	ENSG00000101204	ENST00000370258;ENST00000370263;ENST00000539366	T	0.71341	-0.56	4.72	4.72	0.59763	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.350601	0.32671	N	0.005785	T	0.80199	0.4579	M	0.66378	2.025	0.80722	D	1	P;D	0.56746	0.949;0.977	P;P	0.57425	0.777;0.82	T	0.81951	-0.0698	10	0.51188	T	0.08	.	17.668	0.88208	0.0:1.0:0.0:0.0	.	498;569	Q4VAQ5;P43681	.;ACHA4_HUMAN	K	475;569;498	ENSP00000359285:E569K	ENSP00000359280:E475K	E	-	1	0	CHRNA4	61451502	1.000000	0.71417	0.914000	0.36105	0.249000	0.25844	5.770000	0.68873	2.176000	0.68965	0.491000	0.48974	GAG	.	.		0.682	CHRNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080508.3			T	61981058	C	T	61981058	3	4	326	1	0	0	0	0	1	0	0	0	3387	864	30	3	186	3	CHRNA4	20	61981058	Missense_Mutation	SNP	C	TCGA-MR-A8JO-01A-12D-A35Z-10		61981058	1044462	28	45824										
TNFRSF8	943	hgsc.bcm.edu	37	chr1	12175637	12175637	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	tcatctgtgtcccttagatgAccttgtggagaagacgccat	10	10	2	4			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr1:12175637A>C	ENST00000263932.2	+	8	1019	c.797A>C	c.(796-798)gAc>gCc	p.D266A	TNFRSF8_ENST00000417814.2_Missense_Mutation_p.D155A	NM_001243.3|NM_001281430.1	NP_001234.2|NP_001268359.1	P28908	TNR8_HUMAN	tumor necrosis factor receptor superfamily, member 8	266					cellular response to mechanical stimulus (GO:0071260)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of TRAIL biosynthetic process (GO:0045556)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	27	Ovarian(185;0.249)	Lung NSC(185;8.71e-05)|all_lung(284;9.89e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Brentuximab vedotin(DB08870)	CCCTTAGATGACCTTGTGGAG	0.577																																					p.D266A		Atlas-SNP	.											.	TNFRSF8	70	.	0			c.A797C						.						157	134	141					1																	12175637		2203	4300	6503	SO:0001583	missense	943	exon8			TAGATGACCTTGT	M83554	CCDS144.1, CCDS59989.1	1p36	2008-02-05			ENSG00000120949	ENSG00000120949		"Tumor necrosis factor receptor superfamily", "CD molecules"	11923	protein-coding gene	gene with protein product		153243		CD30, D1S166E		1330892, 1310894	Standard	XM_006711049		Approved	KI-1	uc001atq.3	P28908	OTTHUMG00000001827	ENST00000263932.2:c.797A>C	chr1.hg19:g.12175637A>C	ENSP00000263932:p.Asp266Ala	100.0	0.0		103.0	34.0	NM_001243	B1AN79|B9EGD9|D3YTD8|Q6P4D9	Missense_Mutation	SNP	ENST00000263932.2	hg19	CCDS144.1	.	.	.	.	.	.	.	.	.	.	A	8.631	0.893756	0.17613	.	.	ENSG00000120949	ENST00000263932;ENST00000417814	D;D	0.91351	-2.83;-2.83	3.83	1.51	0.23008	TNFR/CD27/30/40/95 cysteine-rich region (3);	4.245900	0.00520	N	0.000187	D	0.92341	0.7570	M	0.63843	1.955	0.25715	N	0.98543	P;P	0.52316	0.916;0.952	P;P	0.56127	0.491;0.792	T	0.76143	-0.3067	10	0.29301	T	0.29	-10.2473	5.0616	0.14560	0.738:0.0:0.262:0.0	.	155;266	D3YTD8;P28908	.;TNR8_HUMAN	A	266;155	ENSP00000263932:D266A;ENSP00000390650:D155A	ENSP00000263932:D266A	D	+	2	0	TNFRSF8	12098224	1.000000	0.71417	0.836000	0.33094	0.025000	0.11179	2.222000	0.42926	0.206000	0.20587	0.383000	0.25322	GAC	.	.		0.577	TNFRSF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005130.1			C	12175637	A	C	12175637	3	2	327	1	0	0	0	0	1	0	0	0	16314	275	10	5	827	5	TNFRSF8	1	12175637	Missense_Mutation	SNP	A	TCGA-NI-A4U2-01A-11D-A28X-10		12175637	237074984	1	45825										
LRP8	7804	hgsc.bcm.edu	37	chr1	53727742	53727742	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	tctccttacaggactcacctCaaacacagctatcccaaaag	4	15	3	0			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr1:53727742C>G	ENST00000306052.6	-	12	2013	c.1912G>C	c.(1912-1914)Gag>Cag	p.E638Q	LRP8_ENST00000347547.2_Missense_Mutation_p.E468Q|LRP8_ENST00000354412.3_Missense_Mutation_p.E509Q|LRP8_ENST00000465675.1_Missense_Mutation_p.E191Q|LRP8_ENST00000460214.1_5'UTR|LRP8_ENST00000371454.2_Missense_Mutation_p.E638Q	NM_004631.4	NP_004622.2	Q14114	LRP8_HUMAN	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	638					ammon gyrus development (GO:0021541)|blood coagulation (GO:0007596)|cellular response to cholesterol (GO:0071397)|cellular response to growth factor stimulus (GO:0071363)|cytokine-mediated signaling pathway (GO:0019221)|endocytosis (GO:0006897)|layer formation in cerebral cortex (GO:0021819)|lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phototransduction, visible light (GO:0007603)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendrite development (GO:1900006)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|proteolysis (GO:0006508)|receptor-mediated endocytosis (GO:0006898)|reelin-mediated signaling pathway (GO:0038026)|regulation of synaptic transmission (GO:0050804)|response to drug (GO:0042493)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)	caveola (GO:0005901)|dendrite (GO:0030425)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|high-density lipoprotein particle binding (GO:0008035)|reelin receptor activity (GO:0038025)|transmembrane signaling receptor activity (GO:0004888)|very-low-density lipoprotein particle receptor activity (GO:0030229)			endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(2)|skin(1)	21						GGACTCACCTCAAACACAGCT	0.488																																					p.E638Q		Atlas-SNP	.											.	LRP8	58	.	0			c.G1912C						.						85	77	80					1																	53727742		2203	4300	6503	SO:0001583	missense	7804	exon12			TCACCTCAAACAC	D50678	CCDS578.1, CCDS579.1, CCDS580.1, CCDS30720.1	1p32.3	2013-05-29			ENSG00000157193	ENSG00000157193		"Low density lipoprotein receptors"	6700	protein-coding gene	gene with protein product		602600				8626535, 9079678	Standard	NM_004631		Approved	APOER2, MCI1, LRP-8, HSZ75190	uc001cvi.2	Q14114	OTTHUMG00000008924	ENST00000306052.6:c.1912G>C	chr1.hg19:g.53727742C>G	ENSP00000303634:p.Glu638Gln	205.0	0.0		211.0	76.0	NM_004631	B1AMT6|B1AMT7|B1AMT8|O14968|Q86V27|Q99876|Q9BR78	Missense_Mutation	SNP	ENST00000306052.6	hg19	CCDS578.1	.	.	.	.	.	.	.	.	.	.	C	33	5.239332	0.95240	.	.	ENSG00000157193	ENST00000306052;ENST00000371454;ENST00000465675;ENST00000354412;ENST00000347547	D;D;D;D;D	0.91792	-2.91;-2.91;-2.91;-2.91;-2.91	6.16	6.16	0.99307	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	.	.	.	.	D	0.96728	0.8932	M	0.84773	2.715	0.80722	D	1	D;D;D;D;D;D	0.76494	0.995;0.997;0.991;0.999;0.997;0.995	D;D;D;D;D;D	0.80764	0.911;0.987;0.97;0.994;0.973;0.911	D	0.96343	0.9252	9	0.87932	D	0	.	20.8598	0.99761	0.0:1.0:0.0:0.0	.	191;509;468;638;638;191	B3KU40;Q14114-2;Q14114-4;Q14114-3;Q14114;E9PP15	.;.;.;.;LRP8_HUMAN;.	Q	638;638;191;509;468	ENSP00000303634:E638Q;ENSP00000360509:E638Q;ENSP00000437009:E191Q;ENSP00000346391:E509Q;ENSP00000334522:E468Q	ENSP00000303634:E638Q	E	-	1	0	LRP8	53500330	1.000000	0.71417	1.000000	0.80357	0.848000	0.48234	7.745000	0.85046	2.937000	0.99478	0.650000	0.86243	GAG	.	.		0.488	LRP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000024699.1	NM_004631		G	53727742	C	G	53727742	3	3	327	1	0	0	0	0	1	0	0	0	8972	835	29	4	1011	4	LRP8	1	53727742	Missense_Mutation	SNP	C	TCGA-NI-A4U2-01A-11D-A28X-10	41552105	53727742	195522879	2	45826										
IL12RB2	3595	hgsc.bcm.edu	37	chr1	67833556	67833556	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	aaactcagagggcatggacaAcattctggtgacttggcagc	12	9	2	2			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr1:67833556A>G	ENST00000262345.1	+	10	1947	c.1307A>G	c.(1306-1308)aAc>aGc	p.N436S	IL12RB2_ENST00000541374.1_Missense_Mutation_p.N436S|IL12RB2_ENST00000371000.1_Missense_Mutation_p.N436S|IL12RB2_ENST00000544434.1_Missense_Mutation_p.N436S	NM_001559.2	NP_001550.1	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2	436	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma production (GO:0032609)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interferon-gamma production (GO:0032729)|response to lipopolysaccharide (GO:0032496)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(21)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	45						GGCATGGACAACATTCTGGTG	0.517																																					p.N436S		Atlas-SNP	.											.	IL12RB2	94	.	0			c.A1307G						.						130	121	124					1																	67833556		2203	4300	6503	SO:0001583	missense	3595	exon10			TGGACAACATTCT	U64198	CCDS638.1, CCDS58006.1, CCDS58007.1, CCDS72805.1	1p31.3-p31.2	2014-07-15			ENSG00000081985	ENSG00000081985		"Interleukins and interleukin receptors", "Fibronectin type III domain containing"	5972	protein-coding gene	gene with protein product		601642				9284929, 8943050	Standard	NM_001559		Approved		uc001ddu.3	Q99665	OTTHUMG00000009094	ENST00000262345.1:c.1307A>G	chr1.hg19:g.67833556A>G	ENSP00000262345:p.Asn436Ser	140.0	0.0		159.0	39.0	NM_001559	B1AN98|B7ZKL9|F5H7L6|Q2M3V3	Missense_Mutation	SNP	ENST00000262345.1	hg19	CCDS638.1	.	.	.	.	.	.	.	.	.	.	A	3.044	-0.196926	0.06259	.	.	ENSG00000081985	ENST00000262345;ENST00000371000;ENST00000541374;ENST00000544434	T;T;T;T	0.46451	0.87;0.87;0.87;0.87	5.02	-9.72	0.00515	Long hematopoietin receptor, Gp130 family 2, conserved site (1);Fibronectin, type III (4);Immunoglobulin-like fold (1);	1.498590	0.03717	N	0.251221	T	0.06096	0.0158	N	0.14661	0.345	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.09377	0.004;0.001;0.003;0.003	T	0.17684	-1.0361	10	0.02654	T	1	0.1314	14.3573	0.66745	0.6539:0.0:0.3461:0.0	.	436;436;436;436	B4DGA4;F5H7L6;Q99665-2;Q99665	.;.;.;I12R2_HUMAN	S	436	ENSP00000262345:N436S;ENSP00000360039:N436S;ENSP00000445276:N436S;ENSP00000442443:N436S	ENSP00000262345:N436S	N	+	2	0	IL12RB2	67606144	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.742000	0.01835	-2.245000	0.00705	-0.798000	0.03219	AAC	.	.		0.517	IL12RB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025202.2	NM_001559		G	67833556	A	G	67833556	3	3	327	1	0	0	0	0	1	0	0	0	7636	43	2	2	1341	2	IL12RB2	1	67833556	Missense_Mutation	SNP	A	TCGA-NI-A4U2-01A-11D-A28X-10	14105814	67833556	181417065	3	45827										
CTSK	1513	hgsc.bcm.edu	37	chr1	150778408	150778408	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	tggggctctaccttcccattCtgggatataaagggtgtcat	11	9	3	0			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr1:150778408C>A	ENST00000271651.3	-	4	438	c.328G>T	c.(328-330)Gaa>Taa	p.E110*	CTSK_ENST00000480670.1_5'UTR	NM_000396.3	NP_000387.1	P43235	CATK_HUMAN	cathepsin K	110					bone resorption (GO:0045453)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|intramembranous ossification (GO:0001957)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|fibronectin binding (GO:0001968)|proteoglycan binding (GO:0043394)			cervix(1)|endometrium(1)|lung(4)|skin(1)	7	all_cancers(9;2.32e-51)|all_epithelial(9;3.89e-42)|all_lung(15;4.59e-35)|Lung NSC(24;1.7e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Colorectal(459;0.171)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0485)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211)			CCTTCCCATTCTGGGATATAA	0.448																																					p.E110X		Atlas-SNP	.											.	CTSK	27	.	0			c.G328T						.						122	117	119					1																	150778408		2203	4300	6503	SO:0001587	stop_gained	1513	exon4			CCCATTCTGGGAT	BC016058	CCDS969.1	1q21	2008-02-05	2006-12-05		ENSG00000143387	ENSG00000143387		"Cathepsins"	2536	protein-coding gene	gene with protein product		601105	"cathepsin K (pycnodysostosis)"	CTSO2, CTSO, PYCD		7818555	Standard	NM_000396		Approved	PKND	uc001evp.2	P43235	OTTHUMG00000035008	ENST00000271651.3:c.328G>T	chr1.hg19:g.150778408C>A	ENSP00000271651:p.Glu110*	204.0	0.0		134.0	59.0	NM_000396	Q6FHS6	Nonsense_Mutation	SNP	ENST00000271651.3	hg19	CCDS969.1	.	.	.	.	.	.	.	.	.	.	C	14.62	2.590290	0.46214	.	.	ENSG00000143387	ENST00000271651;ENST00000443913	.	.	.	5.52	4.59	0.56863	.	0.251846	0.44285	D	0.000478	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	.	13.7444	0.62865	0.1551:0.8449:0.0:0.0	.	.	.	.	X	110;169	.	ENSP00000271651:E110X	E	-	1	0	CTSK	149045032	0.874000	0.30092	0.980000	0.43619	0.023000	0.10783	1.766000	0.38491	1.440000	0.47531	0.655000	0.94253	GAA	.	.		0.448	CTSK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084732.1	NM_000396		A	150778408	C	A	150778408	4	1	327	1	0	0	0	0	0	1	0	0	4039	922	32	3	681	3	CTSK	1	150778408	Nonsense_Mutation	SNP	C	TCGA-NI-A4U2-01A-11D-A28X-10	82944852	150778408	98472213	4	45828										
CHRNB2	1141	hgsc.bcm.edu	37	chr1	154543798	154543798	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	agcacttcccatttgaccagCagaactgcaccatgaagttc	7	13	0	3			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr1:154543798C>A	ENST00000368476.3	+	5	763	c.499C>A	c.(499-501)Cag>Aag	p.Q167K		NM_000748.2	NP_000739.1	P17787	ACHB2_HUMAN	cholinergic receptor, nicotinic, beta 2 (neuronal)	167					action potential (GO:0001508)|associative learning (GO:0008306)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|central nervous system projection neuron axonogenesis (GO:0021952)|cognition (GO:0050890)|conditioned taste aversion (GO:0001661)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|lateral geniculate nucleus development (GO:0021771)|learning (GO:0007612)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|memory (GO:0007613)|negative regulation of action potential (GO:0045759)|neurological system process (GO:0050877)|optic nerve morphogenesis (GO:0021631)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|protein heterooligomerization (GO:0051291)|regulation of circadian sleep/wake cycle, non-REM sleep (GO:0045188)|regulation of circadian sleep/wake cycle, REM sleep (GO:0042320)|regulation of dendrite morphogenesis (GO:0048814)|regulation of dopamine metabolic process (GO:0042053)|regulation of dopamine secretion (GO:0014059)|regulation of synapse assembly (GO:0051963)|regulation of synaptic transmission, dopaminergic (GO:0032225)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|sensory perception of pain (GO:0019233)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)|social behavior (GO:0035176)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)|vestibulocochlear nerve development (GO:0021562)|visual learning (GO:0008542)|visual perception (GO:0007601)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|drug binding (GO:0008144)|ligand-gated ion channel activity (GO:0015276)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(12)|skin(1)|urinary_tract(3)	28	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)		Dextromethorphan(DB00514)|Galantamine(DB00674)|Nicotine(DB00184)	ATTTGACCAGCAGAACTGCAC	0.542																																					p.Q167K		Atlas-SNP	.											.	CHRNB2	74	.	0			c.C499A						.						133	109	117					1																	154543798		2203	4300	6503	SO:0001583	missense	1141	exon5			GACCAGCAGAACT	U62437	CCDS1070.1	1q21.3	2012-02-11	2006-02-01		ENSG00000160716	ENSG00000160716		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1962	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, beta 2 (neuronal)"	118507	"cholinergic receptor, nicotinic, beta polypeptide 2 (neuronal)"			1505988	Standard	NM_000748		Approved		uc001ffg.3	P17787	OTTHUMG00000037262	ENST00000368476.3:c.499C>A	chr1.hg19:g.154543798C>A	ENSP00000357461:p.Gln167Lys	274.0	0.0		278.0	16.0	NM_000748	Q9UEH9	Missense_Mutation	SNP	ENST00000368476.3	hg19	CCDS1070.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.631225	0.87660	.	.	ENSG00000160716	ENST00000368476	D	0.84660	-1.88	4.38	4.38	0.52667	Neurotransmitter-gated ion-channel ligand-binding (3);Neurotransmitter-gated ion-channel, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.94857	0.8338	H	0.97918	4.105	0.80722	D	1	D	0.65815	0.995	D	0.70227	0.968	D	0.96834	0.9613	10	0.87932	D	0	.	16.7273	0.85426	0.0:1.0:0.0:0.0	.	167	P17787	ACHB2_HUMAN	K	167	ENSP00000357461:Q167K	ENSP00000357461:Q167K	Q	+	1	0	CHRNB2	152810422	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.616000	0.83018	2.238000	0.73509	0.563000	0.77884	CAG	.	.		0.542	CHRNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090697.1	NM_000748		A	154543798	C	A	154543798	3	1	327	1	0	0	0	0	1	0	0	0	3393	711	25	3	517	3	CHRNB2	1	154543798	Missense_Mutation	SNP	C	TCGA-NI-A4U2-01A-11D-A28X-10	3765390	154543798	94706823	5	45829										
RUSC1	23623	hgsc.bcm.edu	37	chr1	155295430	155295430	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	cccgctgagcagcagccgtaGccgcttccatgcctttatcc	9	17	0	1			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr1:155295430G>C	ENST00000368352.5	+	6	1932	c.1781G>C	c.(1780-1782)aGc>aCc	p.S594T	RUSC1_ENST00000462780.1_3'UTR|RUSC1_ENST00000368354.3_Missense_Mutation_p.S594T|RUSC1_ENST00000368349.4_Missense_Mutation_p.S125T|RUSC1_ENST00000368347.4_Missense_Mutation_p.S184T|RUSC1_ENST00000292254.4_Missense_Mutation_p.S125T|RUSC1-AS1_ENST00000450199.1_RNA|RUSC1-AS1_ENST00000443642.1_RNA	NM_001105203.1	NP_001098673.1	Q9BVN2	RUSC1_HUMAN	RUN and SH3 domain containing 1	594	Interaction with TRAF6.|RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.				positive regulation of signal transduction (GO:0009967)|protein polyubiquitination (GO:0000209)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(2)|skin(1)|urinary_tract(1)	21	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;1.55e-10)|all cancers(21;4.15e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)			AGCAGCCGTAGCCGCTTCCAT	0.622											OREG0013860	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S594T		Atlas-SNP	.											.	RUSC1	85	.	0			c.G1781C						.						57	59	58					1																	155295430		2203	4300	6503	SO:0001583	missense	23623	exon6			GCCGTAGCCGCTT	AB026894	CCDS1112.1, CCDS41410.1, CCDS41411.1, CCDS41412.1	1q21-q22	2011-04-28			ENSG00000160753	ENSG00000160753			17153	protein-coding gene	gene with protein product						10760598	Standard	NM_001105203		Approved	NESCA	uc001fkj.2	Q9BVN2	OTTHUMG00000013910	ENST00000368352.5:c.1781G>C	chr1.hg19:g.155295430G>C	ENSP00000357336:p.Ser594Thr	110.0	0.0	1769	118.0	37.0	NM_001105203	B3KWM9|Q5T9U9|Q5T9V0|Q5T9V1|Q5T9V2|Q9UPY4|Q9Y4T5	Missense_Mutation	SNP	ENST00000368352.5	hg19	CCDS41410.1	.	.	.	.	.	.	.	.	.	.	G	15.98	2.991347	0.54041	.	.	ENSG00000160753	ENST00000368354;ENST00000368352;ENST00000368347;ENST00000368349;ENST00000292254	T;T;T;T;T	0.11495	2.77;2.77;2.77;2.77;2.77	4.34	4.34	0.51931	RUN (2);	0.218004	0.34435	N	0.003961	T	0.03178	0.0093	N	0.03608	-0.345	0.09310	N	0.999998	P;P;B;P;D;P	0.53885	0.89;0.55;0.369;0.605;0.963;0.823	P;B;B;B;P;P	0.54401	0.707;0.254;0.237;0.37;0.751;0.564	T	0.40308	-0.9570	10	0.26408	T	0.33	-24.7239	9.096	0.36640	0.1409:0.0:0.8591:0.0	.	92;125;125;184;199;594	B4DQB8;Q9BVN2-2;B3KWM9;Q5T9V0;Q9BT86;Q9BVN2	.;.;.;.;.;RUSC1_HUMAN	T	594;594;184;125;125	ENSP00000357338:S594T;ENSP00000357336:S594T;ENSP00000357331:S184T;ENSP00000357333:S125T;ENSP00000292254:S125T	ENSP00000292254:S125T	S	+	2	0	RUSC1	153562054	1.000000	0.71417	0.775000	0.31657	0.774000	0.43823	2.703000	0.47110	2.393000	0.81446	0.655000	0.94253	AGC	.	.		0.622	RUSC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039071.1			C	155295430	G	C	155295430	3	2	327	1	0	0	0	0	1	0	0	0	13765	971	34	4	1930	4	RUSC1	1	155295430	Missense_Mutation	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10	751632	155295430	93955191	6	45830										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181452992	181452992	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	cggcctcggggcaggcggccGcctacaagcagacgaaagca	15	14	0	1			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr1:181452992G>T	ENST00000367573.2	+	1	112	c.112G>T	c.(112-114)Gcc>Tcc	p.A38S	CACNA1E_ENST00000526775.1_Missense_Mutation_p.A38S|CACNA1E_ENST00000367567.4_5'UTR|CACNA1E_ENST00000357570.5_5'UTR|CACNA1E_ENST00000360108.3_Missense_Mutation_p.A38S|CACNA1E_ENST00000367570.1_Missense_Mutation_p.A38S|CACNA1E_ENST00000358338.5_5'UTR	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	38					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						GCAGGCGGCCGCCTACAAGCA	0.652																																					p.A38S		Atlas-SNP	.											CACNA1E_ENST00000367573,colon,carcinoma,0,2	CACNA1E	778	.	0			c.G112T						.						51	59	56					1																	181452992		1883	4084	5967	SO:0001583	missense	777	exon1			GCGGCCGCCTACA	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.112G>T	chr1.hg19:g.181452992G>T	ENSP00000356545:p.Ala38Ser	202.0	1.0		198.0	79.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	G	18.73	3.687429	0.68157	.	.	ENSG00000198216	ENST00000524607;ENST00000367570;ENST00000526775;ENST00000360108;ENST00000367573	D;D;D;D;D	0.97186	-4.28;-3.93;-3.9;-3.9;-3.93	5.67	4.76	0.60689	.	0.000000	0.64402	D	0.000002	D	0.92561	0.7637	N	0.17082	0.46	0.80722	D	1	B	0.15473	0.013	B	0.17098	0.017	D	0.88852	0.3320	10	0.35671	T	0.21	.	12.6171	0.56584	0.0805:0.0:0.9195:0.0	.	38	Q15878-3	.	S	38	ENSP00000432038:A38S;ENSP00000356542:A38S;ENSP00000434814:A38S;ENSP00000353222:A38S;ENSP00000356545:A38S	ENSP00000353222:A38S	A	+	1	0	CACNA1E	179719615	0.994000	0.37717	1.000000	0.80357	0.997000	0.91878	3.071000	0.50041	1.393000	0.46605	0.561000	0.74099	GCC	.	.		0.652	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		T	181452992	G	T	181452992	3	4	327	1	0	0	0	0	1	0	0	0	2544	1087	38	1	114	1	CACNA1E	1	181452992	Missense_Mutation	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10	26157562	181452992	67797629	7	45831										
TRAF5	7188	hgsc.bcm.edu	37	chr1	211545809	211545809	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	gttgcagtggccattcaggcAgagggtgaccctgatgcttc	14	10	1	3			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr1:211545809A>G	ENST00000261464.5	+	11	1493	c.1439A>G	c.(1438-1440)cAg>cGg	p.Q480R	TRAF5_ENST00000427925.2_Missense_Mutation_p.Q374R|TRAF5_ENST00000336184.2_Missense_Mutation_p.Q480R|TRAF5_ENST00000367004.3_Missense_Mutation_p.Q480R	NM_001033910.2	NP_001029082.1	O00463	TRAF5_HUMAN	TNF receptor-associated factor 5	480	Interaction with EIF2AK2/PKR.|MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.				apoptotic process (GO:0006915)|positive regulation of cell proliferation (GO:0008284)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	CD40 receptor complex (GO:0035631)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)	signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				OV - Ovarian serous cystadenocarcinoma(81;0.00946)|all cancers(67;0.0808)|Epithelial(68;0.144)		CCATTCAGGCAGAGGGTGACC	0.517																																					p.Q480R		Atlas-SNP	.											.	TRAF5	64	.	0			c.A1439G						.						103	92	95					1																	211545809		2203	4300	6503	SO:0001583	missense	7188	exon11			TCAGGCAGAGGGT	AB000509	CCDS1497.1	1q32	2008-02-05			ENSG00000082512	ENSG00000082512		"RING-type (C3HC4) zinc fingers"	12035	protein-coding gene	gene with protein product		602356				9126477	Standard	NM_001033910		Approved	RNF84	uc001hii.3	O00463	OTTHUMG00000036997	ENST00000261464.5:c.1439A>G	chr1.hg19:g.211545809A>G	ENSP00000261464:p.Gln480Arg	74.0	0.0		81.0	25.0	NM_004619	B4DIS9|B4E0A2|Q6FHY1	Missense_Mutation	SNP	ENST00000261464.5	hg19	CCDS1497.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.638128	0.87760	.	.	ENSG00000082512	ENST00000336184;ENST00000427925;ENST00000261464;ENST00000367004	T;T;T;T	0.41400	1.0;1.0;1.0;1.0	5.51	5.51	0.81932	TRAF-type (1);TRAF-like (1);MATH (3);	0.000000	0.85682	D	0.000000	T	0.58750	0.2144	L	0.56280	1.765	0.58432	D	0.999992	D;D;D	0.89917	0.994;1.0;0.997	D;D;D	0.91635	0.988;0.999;0.995	T	0.53136	-0.8481	10	0.23891	T	0.37	-23.8815	15.907	0.79439	1.0:0.0:0.0:0.0	.	374;491;480	F5H1P7;B4E0A2;O00463	.;.;TRAF5_HUMAN	R	480;374;480;480	ENSP00000336825:Q480R;ENSP00000389891:Q374R;ENSP00000261464:Q480R;ENSP00000355971:Q480R	ENSP00000261464:Q480R	Q	+	2	0	TRAF5	209612432	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.946000	0.92992	2.210000	0.71456	0.528000	0.53228	CAG	.	.		0.517	TRAF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089825.1	NM_004619		G	211545809	A	G	211545809	3	3	327	1	0	0	0	0	1	0	0	0	16459	188	7	2	1477	2	TRAF5	1	211545809	Missense_Mutation	SNP	A	TCGA-NI-A4U2-01A-11D-A28X-10	30092817	211545809	37704812	8	45832										
EPRS	2058	hgsc.bcm.edu	37	chr1	220193425	220193425	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	cgactatattcccaaatataTggttttcttatgcctaaagc	5	9	1	0			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr1:220193425T>C	ENST00000366923.3	-	10	1523	c.1254A>G	c.(1252-1254)ccA>ccG	p.P418P		NM_004446.2	NP_004437.2	P07814	SYEP_HUMAN	glutamyl-prolyl-tRNA synthetase	418	Glutamate--tRNA ligase.				cellular response to interferon-gamma (GO:0071346)|gene expression (GO:0010467)|glutamyl-tRNA aminoacylation (GO:0006424)|negative regulation of translation (GO:0017148)|prolyl-tRNA aminoacylation (GO:0006433)|protein complex assembly (GO:0006461)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|GAIT complex (GO:0097452)|membrane (GO:0016020)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|glutamate-tRNA ligase activity (GO:0004818)|proline-tRNA ligase activity (GO:0004827)|RNA stem-loop binding (GO:0035613)			breast(2)|endometrium(11)|kidney(2)|large_intestine(13)|lung(24)|ovary(1)|prostate(3)|skin(2)|stomach(2)|urinary_tract(3)	63				GBM - Glioblastoma multiforme(131;0.0735)	L-Proline(DB00172)	CCCAAATATATGGTTTTCTTA	0.388																																					p.P418P		Atlas-SNP	.											.	EPRS	140	.	0			c.A1254G						.						166	160	162					1																	220193425		2203	4300	6503	SO:0001819	synonymous_variant	2058	exon10			AATATATGGTTTT	X54326	CCDS31027.1	1q41	2011-07-01			ENSG00000136628	ENSG00000136628	6.1.1.15, 6.1.1.17	"Aminoacyl tRNA synthetases / Class I", "Aminoacyl tRNA synthetases / Class II"	3418	protein-coding gene	gene with protein product	"glutamate tRNA ligase", "proline tRNA ligase"	138295		QPRS, QARS		1988429	Standard	NM_004446		Approved	EARS, PARS, GLUPRORS	uc001hly.1	P07814	OTTHUMG00000037433	ENST00000366923.3:c.1254A>G	chr1.hg19:g.220193425T>C		140.0	0.0		102.0	23.0	NM_004446	A0AVA9|B9EGH3|Q05BP6|Q05DF8|Q5DSM1|Q5H9S5|Q6PD57|Q86X73	Silent	SNP	ENST00000366923.3	hg19	CCDS31027.1																																																																																			.	.		0.388	EPRS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091133.2	NM_004446		C	220193425	T	C	220193425	2	2	327	1	0	0	0	0	0	0	0	1	5193	1451	51	2		2	EPRS	1	220193425	Silent	SNP	T	TCGA-NI-A4U2-01A-11D-A28X-10	8647616	220193425	29057196	9	45833										
WDR43	23160	hgsc.bcm.edu	37	chr2	29129433	29129433	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	gtggaatggaacgtacagacAtgcaaagtaaagtggtgagt	14	4	0	2			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr2:29129433A>G	ENST00000407426.3	+	3	527	c.471A>G	c.(469-471)acA>acG	p.T157T		NM_015131.1	NP_055946.1	Q15061	WDR43_HUMAN	WD repeat domain 43	157						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	20	Acute lymphoblastic leukemia(172;0.155)					ACGTACAGACATGCAAAGTAA	0.388																																					p.T157T		Atlas-SNP	.											.	WDR43	38	.	0			c.A471G						.						94	91	92					2																	29129433		1998	4178	6176	SO:0001819	synonymous_variant	23160	exon3			ACAGACATGCAAA	D87716	CCDS46251.1	2p23.3	2013-01-09			ENSG00000163811	ENSG00000163811		"WD repeat domain containing"	28945	protein-coding gene	gene with protein product	"UTP5, small subunit (SSU) processome component, homolog (yeast)"					7584026, 7584028, 17699751	Standard	NM_015131		Approved	KIAA0007, NET12, UTP5	uc002rmo.2	Q15061	OTTHUMG00000152015	ENST00000407426.3:c.471A>G	chr2.hg19:g.29129433A>G		98.0	0.0		85.0	24.0	NM_015131	Q15395|Q92577	Silent	SNP	ENST00000407426.3	hg19	CCDS46251.1																																																																																			.	.		0.388	WDR43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324865.1	XM_087089		G	29129433	A	G	29129433	2	3	327	1	0	0	0	0	0	0	0	1	17310	204	8	2		2	WDR43	2	29129433	Silent	SNP	A	TCGA-NI-A4U2-01A-11D-A28X-10		29129433	214069940	10	45834										
PEX13	5194	hgsc.bcm.edu	37	chr2	61258823	61258823	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	acccagtagatttgttcagcAagctgaagaaagcagcaggg	12	8	1	3			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr2:61258823A>C	ENST00000295030.5	+	2	400	c.362A>C	c.(361-363)cAa>cCa	p.Q121P	PEX13_ENST00000472678.1_3'UTR	NM_002618.3	NP_002609.1	Q92968	PEX13_HUMAN	peroxisomal biogenesis factor 13	121					cerebral cortex cell migration (GO:0021795)|fatty acid alpha-oxidation (GO:0001561)|locomotory behavior (GO:0007626)|microtubule-based peroxisome localization (GO:0060152)|neuron migration (GO:0001764)|protein import into peroxisome matrix, docking (GO:0016560)|suckling behavior (GO:0001967)	integral component of peroxisomal membrane (GO:0005779)|membrane (GO:0016020)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)				endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10			LUSC - Lung squamous cell carcinoma(5;2.05e-06)|Lung(5;3.13e-05)|Epithelial(17;0.114)			TTTGTTCAGCAAGCTGAAGAA	0.443																																					p.Q121P		Atlas-SNP	.											.	PEX13	27	.	0			c.A362C						.						142	136	138					2																	61258823		2203	4300	6503	SO:0001583	missense	5194	exon2			TTCAGCAAGCTGA	U71374	CCDS1866.1	2p16.1	2008-08-26	2008-08-26		ENSG00000162928	ENSG00000162928			8855	protein-coding gene	gene with protein product		601789	"peroxisome biogenesis factor 13"			9878256	Standard	NM_002618		Approved		uc002sau.4	Q92968	OTTHUMG00000129422	ENST00000295030.5:c.362A>C	chr2.hg19:g.61258823A>C	ENSP00000295030:p.Gln121Pro	94.0	0.0		138.0	36.0	NM_002618	B2RCS1	Missense_Mutation	SNP	ENST00000295030.5	hg19	CCDS1866.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.056146	0.76074	.	.	ENSG00000162928	ENST00000295030	T	0.78126	-1.15	5.85	5.85	0.93711	Peroxin 13, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.85146	0.5630	L	0.60455	1.87	0.80722	D	1	D	0.71674	0.998	D	0.68621	0.959	D	0.83751	0.0209	10	0.33940	T	0.23	-10.22	16.2375	0.82384	1.0:0.0:0.0:0.0	.	121	Q92968	PEX13_HUMAN	P	121	ENSP00000295030:Q121P	ENSP00000295030:Q121P	Q	+	2	0	PEX13	61112327	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.865000	0.69583	2.222000	0.72286	0.533000	0.62120	CAA	.	.		0.443	PEX13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251581.3	NM_002618		C	61258823	A	C	61258823	3	2	327	1	0	0	0	0	1	0	0	0	11750	130	5	5	368	5	PEX13	2	61258823	Missense_Mutation	SNP	A	TCGA-NI-A4U2-01A-11D-A28X-10	32129390	61258823	181940550	11	45835										
USP34	9736	hgsc.bcm.edu	37	chr2	61441759	61441760	+	In_Frame_Ins	INS	-	-	GACCTTGTT													0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	cacgggttgggatgtgcaaaINSgaccttgttgaccggaacat							TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr2:61441759_61441760insGACCTTGTT	ENST00000398571.2	-	68	8193_8194	c.8117_8118insAACAAGGTC	c.(8116-8118)tct>tcAACAAGGTCt	p.2706_2706S>STRS	USP34_ENST00000472689.1_Intron	NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	2706					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			GGATGTGCAAAGACCTTGTTGA	0.46																																					p.S2706delinsSTRS		Atlas-Indel,Pindel	.											.	USP34	334	.	0			c.8118_8119insAACAAGGTC						.																																			SO:0001652	inframe_insertion	9736	exon68			.	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"Ubiquitin-specific peptidases"	20066	protein-coding gene	gene with protein product		615295	"ubiquitin specific protease 34"			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.8109_8117dupAACAAGGTC	chr2.hg19:g.61441760_61441768dupGACCTTGTT	ENSP00000381577:p.ThrArgSer2706dup	236.0	0.0		267.0	21.0	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	In_Frame_Ins	INS	ENST00000398571.2	hg19	CCDS42686.1																																																																																			.	.		0.46	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			GACCTTGTT	61441760	-	GACCTTGTT	61441759	7	5	327	1	0	1	1	0	0	0	0	0	17080	59	3	0	2574	0	USP34	2	61441759	In_Frame_Ins	INS	-	TCGA-NI-A4U2-01A-11D-A28X-10	182936	61441759	181757614	12	45836										
OTX1	5013	hgsc.bcm.edu	37	chr2	63283430	63283430	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	gactataaggaccaagcctcAtggcggttccaggtcttgtg	12	10	2	0			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr2:63283430A>T	ENST00000282549.2	+	5	1320	c.1044A>T	c.(1042-1044)tcA>tcT	p.S348S	OTX1_ENST00000366671.3_Silent_p.S348S	NM_014562.3	NP_055377.1	P32242	OTX1_HUMAN	orthodenticle homeobox 1	348					anterior/posterior pattern specification (GO:0009952)|diencephalon morphogenesis (GO:0048852)|inner ear morphogenesis (GO:0042472)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|pancreas(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	20	Lung NSC(7;0.121)|all_lung(7;0.211)					ACCAAGCCTCATGGCGGTTCC	0.582																																					p.S348S		Atlas-SNP	.											.	OTX1	49	.	0			c.A1044T						.						44	46	46					2																	63283430		2203	4300	6503	SO:0001819	synonymous_variant	5013	exon5			AGCCTCATGGCGG		CCDS1873.1	2p15	2011-06-20	2007-02-15		ENSG00000115507	ENSG00000115507		"Homeoboxes / PRD class"	8521	protein-coding gene	gene with protein product		600036	"orthodenticle (Drosophila) homolog 1", "orthodenticle homolog 1 (Drosophila)"			7959790	Standard	NM_001199770		Approved		uc002scd.3	P32242	OTTHUMG00000129454	ENST00000282549.2:c.1044A>T	chr2.hg19:g.63283430A>T		153.0	0.0		157.0	54.0	NM_014562	A6NHA2|B3KTJ4|Q53TG6	Silent	SNP	ENST00000282549.2	hg19	CCDS1873.1																																																																																			.	.		0.582	OTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251617.1			T	63283430	A	T	63283430	2	4	327	1	0	0	0	0	0	0	0	1	11329	204	8	4		4	OTX1	2	63283430	Silent	SNP	A	TCGA-NI-A4U2-01A-11D-A28X-10	1841671	63283430	179915943	13	45837										
MRPL53	116540	hgsc.bcm.edu	37	chr2	74699251	74699251	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	gtctctttggcgctgtcagcGaccagtatcagcgcccggct	12	14	3	0			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr2:74699251G>A	ENST00000258105.7	-	3	995	c.334C>T	c.(334-336)Cgc>Tgc	p.R112C	MRPL53_ENST00000409710.1_3'UTR	NM_053050.4	NP_444278.1	Q96EL3	RM53_HUMAN	mitochondrial ribosomal protein L53	112						mitochondrion (GO:0005739)|ribosome (GO:0005840)				central_nervous_system(1)|large_intestine(2)|lung(1)|urinary_tract(1)	5						CGCTGTCAGCGACCAGTATCA	0.552																																					p.R112C		Atlas-SNP	.											.	MRPL53	13	.	0			c.C334T						.						45	51	49					2																	74699251		2196	4298	6494	SO:0001583	missense	116540	exon3			GTCAGCGACCAGT	BC012163	CCDS1944.1	2p13.1	2012-09-13			ENSG00000204822	ENSG00000204822		"Mitochondrial ribosomal proteins / large subunits"	16684	protein-coding gene	gene with protein product		611857				11551941	Standard	NM_053050		Approved		uc002sln.3	Q96EL3	OTTHUMG00000129961	ENST00000258105.7:c.334C>T	chr2.hg19:g.74699251G>A	ENSP00000258105:p.Arg112Cys	138.0	0.0		120.0	10.0	NM_053050		Missense_Mutation	SNP	ENST00000258105.7	hg19	CCDS1944.1	.	.	.	.	.	.	.	.	.	.	G	16.69	3.193251	0.58017	.	.	ENSG00000204822	ENST00000258105	T	0.53640	0.61	4.13	-1.01	0.10169	.	0.000000	0.50627	D	0.000115	T	0.26340	0.0643	L	0.29908	0.895	0.09310	N	0.999992	B	0.09022	0.002	B	0.04013	0.001	T	0.13575	-1.0504	10	0.87932	D	0	.	0.8064	0.01084	0.2903:0.1616:0.3822:0.1658	.	112	Q96EL3	RM53_HUMAN	C	112	ENSP00000258105:R112C	ENSP00000258105:R112C	R	-	1	0	MRPL53	74552759	0.510000	0.26171	0.000000	0.03702	0.007000	0.05969	2.273000	0.43381	-0.198000	0.10333	-0.149000	0.13747	CGC	.	.		0.552	MRPL53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252225.2	NM_053050		A	74699251	G	A	74699251	3	1	327	1	0	0	0	0	1	0	0	0	9826	1058	37	1	8	1	MRPL53	2	74699251	Missense_Mutation	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10	11415821	74699251	168500122	14	45838										
NCKAP5	344148	hgsc.bcm.edu	37	chr2	133489528	133489528	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	cagcgtcctctggggagtctGgctggcataggtagcgtcct	15	11	2	0			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr2:133489528G>T	ENST00000409261.1	-	17	5598	c.5225C>A	c.(5224-5226)cCa>cAa	p.P1742Q	NCKAP5_ENST00000405974.3_Missense_Mutation_p.P423Q|NCKAP5_ENST00000473859.1_5'UTR|NCKAP5_ENST00000409213.1_Missense_Mutation_p.P423Q|NCKAP5_ENST00000317721.6_Missense_Mutation_p.P1742Q	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	1742										NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						TGGGGAGTCTGGCTGGCATAG	0.557																																					p.P1742Q		Atlas-SNP	.											.	NCKAP5	322	.	0			c.C5225A						.						84	93	90					2																	133489528		2079	4212	6291	SO:0001583	missense	344148	exon17			GAGTCTGGCTGGC	AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"Nck associated protein 5", "peripheral clock protein"	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.5225C>A	chr2.hg19:g.133489528G>T	ENSP00000387128:p.Pro1742Gln	236.0	0.0		220.0	72.0	NM_207363	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	hg19	CCDS46418.1	.	.	.	.	.	.	.	.	.	.	G	4.664	0.123478	0.08931	.	.	ENSG00000176771	ENST00000409261;ENST00000409213;ENST00000317721;ENST00000405974;ENST00000537661	T;T;T;T	0.44083	2.98;0.93;2.98;0.93	5.2	3.35	0.38373	.	0.641465	0.11643	N	0.543605	T	0.19644	0.0472	N	0.04880	-0.145	0.20926	N	0.999821	B;B	0.20052	0.006;0.041	B;B	0.20384	0.004;0.029	T	0.29058	-1.0024	10	0.14252	T	0.57	.	6.5747	0.22560	0.0859:0.0:0.5052:0.4089	.	423;1742	O14513-2;O14513	.;NCKP5_HUMAN	Q	1742;423;1742;423;423	ENSP00000387128:P1742Q;ENSP00000386952:P423Q;ENSP00000380603:P1742Q;ENSP00000385692:P423Q	ENSP00000380603:P1742Q	P	-	2	0	NCKAP5	133205998	1.000000	0.71417	0.217000	0.23759	0.340000	0.28889	2.882000	0.48546	0.733000	0.32492	0.655000	0.94253	CCA	.	.		0.557	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481		T	133489528	G	T	133489528	3	4	327	1	0	0	0	0	1	0	0	0	10232	1348	47	3	520	3	NCKAP5	2	133489528	Missense_Mutation	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10	58790277	133489528	109709845	15	45839										
LRP2	4036	hgsc.bcm.edu	37	chr2	170055351	170055351	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	cagtcattgtctccgtcacaCaaataaacgcgaggaataca	7	11	3	0	rs80338749		TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr2:170055351C>T	ENST00000263816.3	-	45	8808	c.8523G>A	c.(8521-8523)ttG>ttA	p.L2841L		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	2841	LDL-receptor class A 19. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	CTCCGTCACACAAATAAACGC	0.373																																					p.L2841L		Atlas-SNP	.											.	LRP2	751	.	0			c.G8523A						.						128	121	123					2																	170055351		2203	4300	6503	SO:0001819	synonymous_variant	4036	exon45			GTCACACAAATAA		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.8523G>A	chr2.hg19:g.170055351C>T		89.0	0.0		94.0	27.0	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	hg19	CCDS2232.1																																																																																			.	.		0.373	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		T	170055351	C	T	170055351	2	4	327	1	0	0	0	0	0	0	0	1	8965	477	17	3		3	LRP2	2	170055351	Silent	SNP	C	TCGA-NI-A4U2-01A-11D-A28X-10	36565823	170055351	73144022	16	45840										
MYO3B	140469	hgsc.bcm.edu	37	chr2	171260757	171260757	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	cacaatccatttccctccagAtggaatatcagaatgaaggc	7	11	1	3			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr2:171260757A>T	ENST00000408978.4	+	20	2421	c.2278A>T	c.(2278-2280)Atg>Ttg	p.M760L	MYO3B_ENST00000409044.3_Splice_Site_p.M760L|MYO3B_ENST00000334231.6_Splice_Site_p.M769L|MYO3B_ENST00000602629.1_3'UTR	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	760	Myosin motor.				peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						TTCCCTCCAGATGGAATATCA	0.498																																					p.M760L		Atlas-SNP	.											.	MYO3B	320	.	0			c.A2278T						.						161	152	155					2																	171260757		1903	4118	6021	SO:0001630	splice_region_variant	140469	exon20			CTCCAGATGGAAT		CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"Myosins / Myosin superfamily : Class III"	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.2278-1A>T	chr2.hg19:g.171260757A>T		94.0	0.0		88.0	28.0	NM_001083615	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Missense_Mutation	SNP	ENST00000408978.4	hg19	CCDS42773.1	.	.	.	.	.	.	.	.	.	.	A	12.32	1.902040	0.33628	.	.	ENSG00000071909	ENST00000409044;ENST00000408978;ENST00000317915;ENST00000484338;ENST00000334231	T;T;T;T	0.70869	-0.52;-0.52;-0.52;-0.52	5.47	1.64	0.23874	Myosin head, motor domain (2);	0.194685	0.64402	D	0.000003	T	0.45677	0.1354	N	0.08118	0	0.40675	D	0.982253	B;B;B	0.16603	0.007;0.007;0.018	B;B;B	0.19946	0.015;0.016;0.027	T	0.13442	-1.0509	9	.	.	.	.	9.7715	0.40591	0.7998:0.0:0.2002:0.0	.	760;760;760	Q8WXR4-5;Q8WXR4-4;Q8WXR4	.;.;MYO3B_HUMAN	L	760;760;759;769;769	ENSP00000386497:M760L;ENSP00000386213:M760L;ENSP00000446237:M769L;ENSP00000335100:M769L	.	M	+	1	0	MYO3B	170969003	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	2.201000	0.42734	0.097000	0.17492	0.533000	0.62120	ATG	.	.		0.498	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1		Missense_Mutation	T	171260757	A	T	171260757	5	4	327	1	0	0	0	0	0	0	1	0	10086	347	12	4	2356	4	MYO3B	2	171260757	Splice_Site	SNP	A	TCGA-NI-A4U2-01A-11D-A28X-10	1205406	171260757	71938616	17	45841										
HNRNPA3	220988	hgsc.bcm.edu	37	chr2	178081416	178081416	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	tattaaaggtcgtggaggtgGatctggcaattttatgggtc	14	4	1	0			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr2:178081416G>T	ENST00000392524.2	+	6	893	c.656G>T	c.(655-657)gGa>gTa	p.G219V	HNRNPA3_ENST00000411529.2_Missense_Mutation_p.G197V|HNRNPA3_ENST00000435711.1_Missense_Mutation_p.G219V			P51991	ROA3_HUMAN	heterogeneous nuclear ribonucleoprotein A3	219	Gly-rich.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|urinary_tract(1)	16						CGTGGAGGTGGATCTGGCAAT	0.463																																					p.G219V		Atlas-SNP	.											.	HNRNPA3	42	.	0			c.G656T						.						140	143	142					2																	178081416		2203	4300	6503	SO:0001583	missense	220988	exon6			GAGGTGGATCTGG	AF517524	CCDS2273.1	2q31.2	2013-02-12		2008-04-18	ENSG00000170144	ENSG00000170144		"RNA binding motif (RRM) containing"	24941	protein-coding gene	gene with protein product		605372		HNRPA3		11886857, 15776420	Standard	XM_005246380		Approved		uc002ulc.1	P51991	OTTHUMG00000132529	ENST00000392524.2:c.656G>T	chr2.hg19:g.178081416G>T	ENSP00000376309:p.Gly219Val	148.0	0.0		111.0	31.0	NM_194247	D3DPF4|Q53RW7|Q6URK5	Missense_Mutation	SNP	ENST00000392524.2	hg19	CCDS2273.1	.	.	.	.	.	.	.	.	.	.	G	16.93	3.257085	0.59321	.	.	ENSG00000170144	ENST00000392524;ENST00000411529;ENST00000416446;ENST00000420139;ENST00000435711;ENST00000432457	D;D;D;D	0.90732	-2.72;-2.72;-2.72;-2.72	4.42	4.42	0.53409	.	0.000000	0.46442	D	0.000296	D	0.91818	0.7411	M	0.91249	3.19	0.80722	D	1	B;B	0.34015	0.232;0.435	B;B	0.27170	0.077;0.077	D	0.92471	0.5985	10	0.45353	T	0.12	.	17.3931	0.87437	0.0:0.0:1.0:0.0	.	197;219	B4DDB6;P51991	.;ROA3_HUMAN	V	219;197;197;197;219;27	ENSP00000376309:G219V;ENSP00000408487:G197V;ENSP00000416340:G219V;ENSP00000400688:G27V	ENSP00000376309:G219V	G	+	2	0	HNRNPA3	177789662	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.215000	0.77966	2.197000	0.70478	0.551000	0.68910	GGA	.	.		0.463	HNRNPA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255729.3	NM_194247		T	178081416	G	T	178081416	3	4	327	1	0	0	0	0	1	0	0	0	7269	1174	41	3	678	3	HNRNPA3	2	178081416	Missense_Mutation	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10	6820659	178081416	65117957	18	45842										
OSBPL6	114880	hgsc.bcm.edu	37	chr2	179201097	179201097	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	gcctccctgcaacgtgcacaActggccagagtaaagtggca	11	13	0	1			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr2:179201097A>G	ENST00000190611.4	+	9	1103	c.727A>G	c.(727-729)Act>Gct	p.T243A	OSBPL6_ENST00000359685.3_Missense_Mutation_p.T243A|OSBPL6_ENST00000357080.4_Missense_Mutation_p.T243A|OSBPL6_ENST00000409045.3_Missense_Mutation_p.T243A|OSBPL6_ENST00000409631.1_Missense_Mutation_p.T243A|OSBPL6_ENST00000392505.2_Missense_Mutation_p.T243A|OSBPL6_ENST00000315022.2_Missense_Mutation_p.T222A	NM_032523.3	NP_115912.1	Q9BZF3	OSBL6_HUMAN	oxysterol binding protein-like 6	243					lipid transport (GO:0006869)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(18)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			AACGTGCACAACTGGCCAGAG	0.507																																					p.T243A		Atlas-SNP	.											.	OSBPL6	178	.	0			c.A727G						.						185	182	183					2																	179201097		2203	4300	6503	SO:0001583	missense	114880	exon9			TGCACAACTGGCC	AF392448	CCDS2277.1, CCDS2278.1, CCDS56150.1, CCDS56151.1, CCDS56152.1	2q32.1	2008-05-27			ENSG00000079156	ENSG00000079156		"Oxysterol binding proteins"	16388	protein-coding gene	gene with protein product	"OSBP-related protein 6"	606734				11483621	Standard	NM_001201480		Approved	ORP6	uc002uly.3	Q9BZF3	OTTHUMG00000132579	ENST00000190611.4:c.727A>G	chr2.hg19:g.179201097A>G	ENSP00000190611:p.Thr243Ala	136.0	0.0		112.0	39.0	NM_001201482	B4DTW1|C4AMC0|C4AME4|D3DPF6|D3DPF7|Q4ZG68|Q53T68|Q59H61|Q7Z4Q1|Q86V84|Q8N9T0|Q96SR1	Missense_Mutation	SNP	ENST00000190611.4	hg19	CCDS2277.1	.	.	.	.	.	.	.	.	.	.	A	10.69	1.421029	0.25639	.	.	ENSG00000079156	ENST00000392505;ENST00000359685;ENST00000361154;ENST00000357080;ENST00000409045;ENST00000190611;ENST00000409631;ENST00000315022	T;T;T;T;T;T;T	0.11277	2.81;2.81;2.79;2.81;2.8;2.81;2.81	5.57	4.34	0.51931	.	0.161156	0.56097	D	0.000034	T	0.06645	0.0170	N	0.22421	0.69	0.33897	D	0.638003	B;B;B;B;B;B	0.24721	0.0;0.023;0.008;0.11;0.055;0.038	B;B;B;B;B;B	0.22880	0.002;0.042;0.009;0.041;0.012;0.02	T	0.12578	-1.0542	10	0.07175	T	0.84	-13.5516	11.7903	0.52065	0.8686:0.0:0.0:0.1314	.	243;222;243;243;243;243	Q9BZF3-4;Q9BZF3-3;Q9BZF3-2;Q9BZF3-5;Q9BZF3;Q86V84	.;.;.;.;OSBL6_HUMAN;.	A	243;243;28;243;243;243;243;222	ENSP00000376293:T243A;ENSP00000352713:T243A;ENSP00000349591:T243A;ENSP00000387248:T243A;ENSP00000190611:T243A;ENSP00000386885:T243A;ENSP00000318723:T222A	ENSP00000190611:T243A	T	+	1	0	OSBPL6	178909343	0.998000	0.40836	0.056000	0.19401	0.308000	0.27856	6.532000	0.73825	2.244000	0.73946	0.533000	0.62120	ACT	.	.		0.507	OSBPL6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334393.2	NM_032523		G	179201097	A	G	179201097	3	3	327	1	0	0	0	0	1	0	0	0	11290	43	2	2	796	2	OSBPL6	2	179201097	Missense_Mutation	SNP	A	TCGA-NI-A4U2-01A-11D-A28X-10	1119681	179201097	63998276	19	45843										
TTN	7273	hgsc.bcm.edu	37	chr2	179579150	179579150	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	tgttttctgaataagaaatcCatatgttgtcactttctcta	5	7	3	2			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr2:179579150C>T	ENST00000591111.1	-	89	25624	c.25400G>A	c.(25399-25401)tGg>tAg	p.W8467*	TTN_ENST00000342992.6_Nonsense_Mutation_p.W7540*|TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000359218.5_Intron|TTN_ENST00000589042.1_Nonsense_Mutation_p.W8784*|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589830.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12635	Ig-like 67.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATAAGAAATCCATATGTTGTC	0.408																																					p.W8784X		Atlas-SNP	.											.	TTN	18412	.	0			c.G26351A						.						88	83	85					2																	179579150		1854	4093	5947	SO:0001587	stop_gained	7273	exon91			GAAATCCATATGT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.25400G>A	chr2.hg19:g.179579150C>T	ENSP00000465570:p.Trp8467*	61.0	0.0		70.0	11.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Nonsense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	59	36.689866	0.99983	.	.	ENSG00000155657	ENST00000342992	.	.	.	5.96	5.96	0.96718	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	20.422	0.99049	0.0:1.0:0.0:0.0	.	.	.	.	X	7540	.	ENSP00000343764:W7540X	W	-	2	0	TTN	179287395	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.253000	0.32886	2.832000	0.97577	0.655000	0.94253	TGG	.	.		0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179579150	C	T	179579150	4	4	327	1	0	0	0	0	0	1	0	0	16750	595	21	3	78266	3	TTN	2	179579150	Nonsense_Mutation	SNP	C	TCGA-NI-A4U2-01A-11D-A28X-10	378053	179579150	63620223	20	45844										
FAM119A	151194	hgsc.bcm.edu	37	chr2	208478154	208478154	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	gctacttttcgatccgtgatAgtcacatgagcacctacaat	7	11	1	2			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr2:208478154A>T	ENST00000411432.1	-	4	489	c.273T>A	c.(271-273)acT>acA	p.T91T	METTL21A_ENST00000426075.1_Silent_p.T91T|METTL21A_ENST00000432416.1_Intron|METTL21A_ENST00000458426.1_Intron|METTL21A_ENST00000448007.2_Silent_p.T91T|METTL21A_ENST00000272839.3_Silent_p.T109T|METTL21A_ENST00000425132.1_Intron|METTL21A_ENST00000477919.1_5'Flank|METTL21A_ENST00000406927.2_Silent_p.T91T|METTL21A_ENST00000448823.2_3'UTR|METTL21A_ENST00000442521.1_Silent_p.T91T	NM_001127395.1	NP_001120867.1	Q8WXB1	MT21A_HUMAN	methyltransferase like 21A	91					peptidyl-lysine methylation (GO:0018022)|protein methylation (GO:0006479)	cytoplasm (GO:0005737)	ATPase binding (GO:0051117)|Hsp70 protein binding (GO:0030544)|protein-lysine N-methyltransferase activity (GO:0016279)			endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|stomach(1)	10						GATCCGTGATAGTCACATGAG	0.378																																					p.T91T		Atlas-SNP	.											.	METTL21A	24	.	0			c.T273A						.						68	61	63					2																	208478154		2203	4300	6503	SO:0001819	synonymous_variant	151194	exon4			CGTGATAGTCACA	AK093812, AF455817	CCDS2376.1	2q33.3	2013-09-30	2011-03-03	2011-03-03	ENSG00000144401	ENSG00000144401			30476	protein-coding gene	gene with protein product	"Hepatocellular carcinoma-associated antigen 557b", "heat shock protein 70kDa lysine (K) methyltransferase"	615257	"family with sequence similarity 119, member A"	FAM119A		23921388	Standard	NM_145280		Approved	LOC151194, HCA557b, HSPA-KMT	uc010fuk.1	Q8WXB1	OTTHUMG00000132934	ENST00000411432.1:c.273T>A	chr2.hg19:g.208478154A>T		26.0	0.0		19.0	5.0	NM_145280	Q53RV0|Q8N1Z9|Q96GH6	Silent	SNP	ENST00000411432.1	hg19	CCDS2376.1																																																																																			.	.		0.378	METTL21A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337044.1	NM_145280		T	208478154	A	T	208478154	2	4	327	1	0	0	0	0	0	0	0	1	5418	407	15	4		4	FAM119A	2	208478154	Silent	SNP	A	TCGA-NI-A4U2-01A-11D-A28X-10	28899004	208478154	34721219	21	45845										
TRPM8	79054	hgsc.bcm.edu	37	chr2	234894478	234894478	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	acatgttatccaccaacatcCtgctggtcaacctgctggtc	7	14	1	0			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr2:234894478C>T	ENST00000324695.4	+	21	2948	c.2908C>T	c.(2908-2910)Ctg>Ttg	p.L970L	TRPM8_ENST00000433712.2_Silent_p.L548L	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8	970					calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|protein homotetramerization (GO:0051289)|protein homotrimerization (GO:0070207)|response to cold (GO:0009409)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(2)|lung(27)|prostate(2)|skin(7)|stomach(2)	66		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)	CACCAACATCCTGCTGGTCAA	0.577																																					p.L970L		Atlas-SNP	.											.	TRPM8	146	.	0			c.C2908T						.						129	87	101					2																	234894478		2203	4300	6503	SO:0001819	synonymous_variant	79054	exon21			AACATCCTGCTGG	AC005538	CCDS33407.1	2q37	2011-12-14			ENSG00000144481	ENSG00000144481		"Voltage-gated ion channels / Transient receptor potential cation channels"	17961	protein-coding gene	gene with protein product		606678				16382100	Standard	NM_024080		Approved		uc002vvh.3	Q7Z2W7	OTTHUMG00000059129	ENST00000324695.4:c.2908C>T	chr2.hg19:g.234894478C>T		251.0	0.0		208.0	84.0	NM_024080	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Silent	SNP	ENST00000324695.4	hg19	CCDS33407.1																																																																																			.	.		0.577	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080		T	234894478	C	T	234894478	2	4	327	1	0	0	0	0	0	0	0	1	16607	680	24	3		3	TRPM8	2	234894478	Silent	SNP	C	TCGA-NI-A4U2-01A-11D-A28X-10	26416324	234894478	8304895	22	45846										
TOP2B	7155	hgsc.bcm.edu	37	chr3	25668275	25668275	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	agactaacctctggtaagccAtgtagcctacgctgtctccg	9	13	2	1			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr3:25668275A>T	ENST00000264331.4	-	17	2096	c.2097T>A	c.(2095-2097)caT>caA	p.H699Q	TOP2B_ENST00000435706.2_Missense_Mutation_p.H694Q	NM_001068.2	NP_001059.2	Q02880	TOP2B_HUMAN	topoisomerase (DNA) II beta 180kDa	699					ATP catabolic process (GO:0006200)|axonogenesis (GO:0007409)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|forebrain development (GO:0030900)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|neuron migration (GO:0001764)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein kinase C binding (GO:0005080)			breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|skin(2)|stomach(1)	36					Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Etoposide(DB00773)	CTGGTAAGCCATGTAGCCTAC	0.383																																					p.H694Q		Atlas-SNP	.											.	TOP2B	98	.	0			c.T2082A						.						69	70	70					3																	25668275		2203	4299	6502	SO:0001583	missense	7155	exon17			TAAGCCATGTAGC	X68060	CCDS46776.1	3p24.2	2012-08-30	2002-08-29		ENSG00000077097	ENSG00000077097	5.99.1.3		11990	protein-coding gene	gene with protein product		126431	"topoisomerase (DNA) II beta (180kD)"			1309226, 1333583	Standard	NM_001068		Approved		uc003cdj.3	Q02880	OTTHUMG00000155596	ENST00000264331.4:c.2097T>A	chr3.hg19:g.25668275A>T	ENSP00000264331:p.His699Gln	66.0	0.0		74.0	4.0	NM_001068	Q13600|Q9UMG8|Q9UQP8	Missense_Mutation	SNP	ENST00000264331.4	hg19		.	.	.	.	.	.	.	.	.	.	A	10.34	1.324066	0.24080	.	.	ENSG00000077097	ENST00000435706;ENST00000264331;ENST00000424225	T;T	0.42131	0.98;0.98	5.4	3.0	0.34707	.	0.000000	0.85682	D	0.000000	T	0.23451	0.0567	N	0.16656	0.425	0.80722	D	1	B	0.21688	0.059	B	0.17433	0.018	T	0.04664	-1.0935	10	0.21014	T	0.42	.	8.7808	0.34789	0.7131:0.0:0.2869:0.0	.	694	Q02880-2	.	Q	694;699;694	ENSP00000396704:H694Q;ENSP00000264331:H699Q	ENSP00000264331:H699Q	H	-	3	2	TOP2B	25643279	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	2.018000	0.40991	0.433000	0.26313	-0.379000	0.06801	CAT	.	.		0.383	TOP2B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding				T	25668275	A	T	25668275	3	4	327	1	0	0	0	0	1	0	0	0	16381	214	8	4	2863	4	TOP2B	3	25668275	Missense_Mutation	SNP	A	TCGA-NI-A4U2-01A-11D-A28X-10		25668275	172354155	23	45847										
MST1	63891	hgsc.bcm.edu	37	chr3	49724207	49724207	+	5'Flank	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	gccgtcaggattccggcaatAgttgtcgtccagaccttggt	12	11	1	1			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr3:49724207A>G	ENST00000327697.6	+	0	0				MST1_ENST00000545762.1_3'UTR|AC099668.5_ENST00000563780.1_RNA|RNF123_ENST00000432042.1_5'Flank|MST1_ENST00000383728.3_Missense_Mutation_p.Y178H|MST1_ENST00000494828.2_5'UTR|MST1_ENST00000449682.2_Missense_Mutation_p.Y253H	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123						protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		TTCCGGCAATAGTTGTCGTCC	0.627																																					p.Y253H		Atlas-SNP	.											.	MST1	84	.	0			c.T757C						.						9	11	11					3																	49724207		2139	4203	6342	SO:0001631	upstream_gene_variant	4485	exon7			GGCAATAGTTGTC	AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"RING-type (C3HC4) zinc fingers"	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891		chr3.hg19:g.49724207A>G	Exception_encountered	425.0	0.0		436.0	74.0	NM_020998	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Missense_Mutation	SNP	ENST00000327697.6	hg19	CCDS33758.1	.	.	.	.	.	.	.	.	.	.	A	35	5.430667	0.96150	.	.	ENSG00000173531	ENST00000449682;ENST00000383728	T;T	0.75704	-0.96;-0.96	5.75	5.75	0.90469	Kringle (5);Kringle-like fold (1);Kringle, conserved site (1);	0.478958	0.15547	N	0.256612	D	0.89979	0.6872	M	0.93420	3.415	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.994	D	0.91709	0.5380	10	0.87932	D	0	.	16.0663	0.80878	1.0:0.0:0.0:0.0	.	239;253	P26927;G3XAK1	HGFL_HUMAN;.	H	253;178	ENSP00000414287:Y253H;ENSP00000373234:Y178H	ENSP00000373234:Y178H	Y	-	1	0	MST1	49699211	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.046000	0.93817	2.201000	0.70794	0.533000	0.62120	TAT	.	.		0.627	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064		G	49724207	A	G	49724207	1	3	327	0	1	0	0	0	0	0	0	0	9899	420	15	2		2	MST1	3	49724207	5'Flank	SNP	A	TCGA-NI-A4U2-01A-11D-A28X-10	24055932	49724207	148298223	24	45848										
GNAI2	2771	hgsc.bcm.edu	37	chr3	50273847	50273847	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	caagaacctgcgggaggacgGagagaaggcggcgcgggagg	21	8	0	2			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr3:50273847G>T	ENST00000313601.6	+	1	464	c.80G>T	c.(79-81)gGa>gTa	p.G27V	GNAI2_ENST00000440628.1_5'Flank|GNAI2_ENST00000491100.1_Intron|GNAI2_ENST00000536647.1_5'UTR|GNAI2_ENST00000422163.1_Intron	NM_002070.2	NP_002061.1	P04899	GNAI2_HUMAN	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 2	27					activation of MAPKK activity (GO:0000186)|adenosine receptor signaling pathway (GO:0001973)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of synaptic transmission (GO:0050805)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|regulation of calcium ion transport (GO:0051924)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|membrane (GO:0016020)|membrane raft (GO:0045121)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|liver(2)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	16				BRCA - Breast invasive adenocarcinoma(193;0.000288)|KIRC - Kidney renal clear cell carcinoma(197;0.00571)|Kidney(197;0.00651)		CGGGAGGACGGAGAGAAGGCG	0.667																																					p.G27V		Atlas-SNP	.											.	GNAI2	42	.	0			c.G80T						.						86	87	87					3																	50273847		2202	4300	6502	SO:0001583	missense	2771	exon1			AGGACGGAGAGAA	X04828	CCDS2813.1, CCDS54587.1, CCDS63642.1, CCDS63644.1	3p21.31	2010-08-27			ENSG00000114353	ENSG00000114353			4385	protein-coding gene	gene with protein product	"GTP-binding regulatory protein Gi alpha-2 chain"	139360		GNAI2B		3100330, 1733849	Standard	NM_001166425		Approved	GIP	uc003cyq.1	P04899	OTTHUMG00000156940	ENST00000313601.6:c.80G>T	chr3.hg19:g.50273847G>T	ENSP00000312999:p.Gly27Val	99.0	0.0		118.0	41.0	NM_002070	B3KTZ0|B4DYA0|B4E2X5|Q6B6N3|Q8IZ71	Missense_Mutation	SNP	ENST00000313601.6	hg19	CCDS2813.1	.	.	.	.	.	.	.	.	.	.	G	35	5.591748	0.96590	.	.	ENSG00000114353	ENST00000313601;ENST00000540560	D	0.88277	-2.36	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	D	0.93530	0.7935	M	0.89478	3.035	0.80722	D	1	P	0.43542	0.81	P	0.50825	0.651	D	0.94677	0.7862	10	0.87932	D	0	.	16.2417	0.82411	0.0:0.0:1.0:0.0	.	27	P04899	GNAI2_HUMAN	V	27	ENSP00000312999:G27V	ENSP00000312999:G27V	G	+	2	0	GNAI2	50248851	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.227000	0.95236	2.413000	0.81919	0.650000	0.86243	GGA	.	.		0.667	GNAI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346688.1	NM_002070		T	50273847	G	T	50273847	3	4	327	1	0	0	0	0	1	0	0	0	6513	1174	41	3	82	3	GNAI2	3	50273847	Missense_Mutation	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10	549640	50273847	147748583	25	45849										
CACNA2D2	9254	hgsc.bcm.edu	37	chr3	50415488	50415488	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	gcacctgcttggcctccttgCctgccagcaccatgggcctg	11	17	0	0			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr3:50415488C>T	ENST00000479441.1	-	15	1429	c.1430G>A	c.(1429-1431)gGc>gAc	p.G477D	CACNA2D2_ENST00000424201.2_Missense_Mutation_p.G477D|CACNA2D2_ENST00000435965.1_Missense_Mutation_p.G477D|CACNA2D2_ENST00000266039.3_Missense_Mutation_p.G477D|CACNA2D2_ENST00000429770.1_Missense_Mutation_p.G477D|CACNA2D2_ENST00000395083.1_Missense_Mutation_p.G477D|CACNA2D2_ENST00000423994.2_Missense_Mutation_p.G477D|CACNA2D2_ENST00000360963.3_Missense_Mutation_p.G408D			Q9NY47	CA2D2_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 2	477					energy reserve metabolic process (GO:0006112)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|positive regulation of organ growth (GO:0046622)|regulation of insulin secretion (GO:0050796)|regulation of multicellular organism growth (GO:0040014)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|cervix(1)|endometrium(4)|large_intestine(4)|lung(8)|ovary(2)|prostate(4)|skin(4)|urinary_tract(1)	31				BRCA - Breast invasive adenocarcinoma(193;0.000365)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)	Amiodarone(DB01118)|Bepridil(DB01244)|Felodipine(DB01023)|Gabapentin(DB00996)|Isradipine(DB00270)|Nitrendipine(DB01054)|Spironolactone(DB00421)	GGCCTCCTTGCCTGCCAGCAC	0.612																																					p.G477D		Atlas-SNP	.											.	CACNA2D2	82	.	0			c.G1430A						.						106	93	98					3																	50415488		2203	4300	6503	SO:0001583	missense	9254	exon15			TCCTTGCCTGCCA	AF040709	CCDS33763.1, CCDS54588.1, CCDS63647.1	3p21.3	2004-02-27			ENSG00000007402	ENSG00000007402		"Calcium channel subunits"	1400	protein-coding gene	gene with protein product	"gene 26"	607082					Standard	XM_005265581		Approved	KIAA0558	uc003daq.3	Q9NY47	OTTHUMG00000156887	ENST00000479441.1:c.1430G>A	chr3.hg19:g.50415488C>T	ENSP00000418081:p.Gly477Asp	113.0	0.0		134.0	32.0	NM_001174051	A7MD15|Q9NY48|Q9UEW0|Q9Y268	Missense_Mutation	SNP	ENST00000479441.1	hg19	CCDS54588.1	.	.	.	.	.	.	.	.	.	.	C	18.45	3.627259	0.66901	.	.	ENSG00000007402	ENST00000423994;ENST00000429770;ENST00000266039;ENST00000360963;ENST00000435965;ENST00000395083;ENST00000424201;ENST00000479441	T;T;T;T;T;T;T;T	0.06687	3.28;3.27;3.27;3.28;3.28;3.27;3.27;3.28	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.12902	0.0313	L	0.36672	1.1	0.52501	D	0.999955	B;B	0.27013	0.051;0.166	B;B	0.37943	0.042;0.261	T	0.13176	-1.0519	10	0.40728	T	0.16	-21.7662	19.0208	0.92915	0.0:1.0:0.0:0.0	.	477;477	Q9NY47;Q9NY47-2	CA2D2_HUMAN;.	D	477;477;477;408;477;477;477;477	ENSP00000407393:G477D;ENSP00000404631:G477D;ENSP00000266039:G477D;ENSP00000354228:G408D;ENSP00000390526:G477D;ENSP00000378519:G477D;ENSP00000390329:G477D;ENSP00000418081:G477D	ENSP00000266039:G477D	G	-	2	0	CACNA2D2	50390492	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.002000	0.70693	2.492000	0.84095	0.585000	0.79938	GGC	.	.		0.612	CACNA2D2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346457.1	NM_006030		T	50415488	C	T	50415488	3	4	327	1	0	0	0	0	1	0	0	0	2551	739	26	3	2128	3	CACNA2D2	3	50415488	Missense_Mutation	SNP	C	TCGA-NI-A4U2-01A-11D-A28X-10	141641	50415488	147606942	26	45850										
TMPRSS7	344805	hgsc.bcm.edu	37	chr3	111785275	111785275	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	ctgcaataccagctccttcaGgcagcatggccctctcatct	7	16	3	0			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr3:111785275G>A	ENST00000452346.2	+	13	1595	c.1592G>A	c.(1591-1593)aGg>aAg	p.R531K	TMPRSS7_ENST00000419127.1_Missense_Mutation_p.R405K			Q7RTY8	TMPS7_HUMAN	transmembrane protease, serine 7	531	LDL-receptor class A 2. {ECO:0000255|PROSITE-ProRule:PRU00124}.				proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(2)|endometrium(6)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						AGCTCCTTCAGGCAGCATGGC	0.512																																					p.R405K		Atlas-SNP	.											.	TMPRSS7	126	.	0			c.G1214A						.						104	104	104					3																	111785275		1968	4164	6132	SO:0001583	missense	344805	exon11			CCTTCAGGCAGCA	BN000125	CCDS43129.2	3q13.2	2010-04-13	2004-03-16		ENSG00000176040	ENSG00000176040		"Serine peptidases / Transmembrane"	30846	protein-coding gene	gene with protein product			"type II transmembrane serine protease 7"			12838346	Standard	NM_001042575		Approved		uc010hqb.2	Q7RTY8	OTTHUMG00000157148	ENST00000452346.2:c.1592G>A	chr3.hg19:g.111785275G>A	ENSP00000398236:p.Arg531Lys	79.0	0.0		80.0	36.0	NM_001042575	C9J8P7|E9PAS3|Q17RH4	Missense_Mutation	SNP	ENST00000452346.2	hg19		.	.	.	.	.	.	.	.	.	.	G	3.696	-0.062452	0.07273	.	.	ENSG00000176040	ENST00000452346;ENST00000443106;ENST00000437906;ENST00000419127	T;T	0.58652	0.32;0.32	5.67	3.81	0.43845	.	0.698068	0.14485	N	0.316738	T	0.35885	0.0947	N	0.22421	0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.24977	-1.0145	10	0.06099	T	0.92	.	7.6679	0.28443	0.0868:0.0:0.7474:0.1658	.	531;405	Q7RTY8;Q7RTY8-2	TMPS7_HUMAN;.	K	531;519;505;405	ENSP00000398236:R531K;ENSP00000411645:R405K	ENSP00000411645:R405K	R	+	2	0	TMPRSS7	113267965	0.126000	0.22350	0.809000	0.32408	0.867000	0.49689	0.872000	0.28037	1.484000	0.48361	0.655000	0.94253	AGG	.	.		0.512	TMPRSS7-003	NOVEL	NAGNAG_splice_site|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000347592.2	XM_293599		A	111785275	G	A	111785275	3	1	327	1	0	0	0	0	1	0	0	0	16267	1000	35	3	1252	3	TMPRSS7	3	111785275	Missense_Mutation	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10	61369787	111785275	86237155	27	45851										
NR1I2	8856	hgsc.bcm.edu	37	chr3	119526207	119526207	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	cgcagatgaggaagtcggagGtccccaaatctgccgtgtat	13	10	1	2			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr3:119526207G>T	ENST00000337940.4	+	2	275	c.227G>T	c.(226-228)gGt>gTt	p.G76V	NR1I2_ENST00000393716.2_Missense_Mutation_p.G37V|NR1I2_ENST00000466380.1_Missense_Mutation_p.G37V	NM_022002.2	NP_071285.1	O75469	NR1I2_HUMAN	nuclear receptor subfamily 1, group I, member 2	37					drug export (GO:0046618)|exogenous drug catabolic process (GO:0042738)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|steroid metabolic process (GO:0008202)|transcription initiation from RNA polymerase II promoter (GO:0006367)|xenobiotic metabolic process (GO:0006805)|xenobiotic transport (GO:0042908)	nucleoplasm (GO:0005654)	drug binding (GO:0008144)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(2)|prostate(2)|skin(3)	23				GBM - Glioblastoma multiforme(114;0.175)	Docetaxel(DB01248)|Erlotinib(DB00530)|Estradiol(DB00783)|Ethinyl Estradiol(DB00977)|Paclitaxel(DB01229)|Rifampicin(DB01045)|Rifaximin(DB01220)|Rilpivirine(DB08864)|Vitamin E(DB00163)	GAAGTCGGAGGTCCCCAAATC	0.502																																					p.G76V		Atlas-SNP	.											.	NR1I2	44	.	0			c.G227T						.						152	141	145					3																	119526207		2203	4300	6503	SO:0001583	missense	8856	exon2			TCGGAGGTCCCCA	AF061056	CCDS2995.1, CCDS43136.1, CCDS54627.1	3q12-q13.3	2013-03-25			ENSG00000144852	ENSG00000144852		"Nuclear hormone receptors"	7968	protein-coding gene	gene with protein product	"pregnane X receptor", "orphan nuclear receptor PXR"	603065				9727070, 9770465	Standard	NM_003889		Approved	ONR1, PXR, BXR, SXR, PAR2	uc003edk.3	O75469	OTTHUMG00000159400	ENST00000337940.4:c.227G>T	chr3.hg19:g.119526207G>T	ENSP00000336528:p.Gly76Val	166.0	0.0		171.0	50.0	NM_022002	Q006P5|Q008C8|Q96AC7|Q9UJ22|Q9UJ23|Q9UJ24|Q9UJ25|Q9UJ26|Q9UJ27|Q9UNW4	Missense_Mutation	SNP	ENST00000337940.4	hg19	CCDS2995.1	.	.	.	.	.	.	.	.	.	.	G	12.09	1.834346	0.32421	.	.	ENSG00000144852	ENST00000393716;ENST00000466380;ENST00000337940	D;D;D	0.91843	-2.89;-2.8;-2.92	4.21	3.24	0.37175	.	0.513929	0.17668	N	0.166070	T	0.81950	0.4931	N	0.19112	0.55	0.51233	D	0.999918	B;B	0.19445	0.015;0.036	B;B	0.16289	0.011;0.015	T	0.74856	-0.3522	10	0.25106	T	0.35	.	4.908	0.13807	0.2439:0.0:0.7561:0.0	.	76;60	F1D8P9;O75469-6	.;.	V	37;37;76	ENSP00000377319:G37V;ENSP00000420297:G37V;ENSP00000336528:G76V	ENSP00000336528:G76V	G	+	2	0	NR1I2	121008897	0.699000	0.27786	0.529000	0.27951	0.304000	0.27724	1.042000	0.30303	2.167000	0.68274	0.591000	0.81541	GGT	.	.		0.502	NR1I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355126.1			T	119526207	G	T	119526207	3	4	327	1	0	0	0	0	1	0	0	0	10629	1261	44	3	233	3	NR1I2	3	119526207	Missense_Mutation	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10	7740932	119526207	78496223	28	45852										
KCNMB3	27094	hgsc.bcm.edu	37	chr3	178968887	178968887	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	gttcagagcttggtgaaaagTccatctaaataagctaaagt	9	6	2	2			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr3:178968887T>C	ENST00000314235.5	-	1	516	c.5A>G	c.(4-6)gAc>gGc	p.D2G	KCNMB3_ENST00000485523.1_Intron|KCNMB3_ENST00000497599.1_Intron|KCNMB3_ENST00000392685.2_5'UTR|KCNMB3_ENST00000349697.2_Intron	NM_014407.3	NP_055222.3	Q9NPA1	KCMB3_HUMAN	potassium large conductance calcium-activated channel, subfamily M beta member 3	2					action potential (GO:0001508)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|neuronal action potential (GO:0019228)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|potassium channel regulator activity (GO:0015459)			NS(1)|large_intestine(1)|lung(2)|stomach(1)	5	all_cancers(143;5.6e-17)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;2.41e-27)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.03)		Miconazole(DB01110)|Procaine(DB00721)	TGGTGAAAAGTCCATCTAAAT	0.398																																					p.D2G		Atlas-SNP	.											.	KCNMB3	46	.	0			c.A5G						.						117	115	116					3																	178968887		2203	4300	6503	SO:0001583	missense	27094	exon1			GAAAAGTCCATCT	AF139471	CCDS3225.1, CCDS3226.1, CCDS43172.1, CCDS43173.1, CCDS54683.1	3q26.3-q27	2010-09-30			ENSG00000171121	ENSG00000171121		"Potassium channels"	6287	protein-coding gene	gene with protein product		605222		KCNMB2, KCNMBL		10585773	Standard	NM_001163677		Approved		uc003fjm.3	Q9NPA1	OTTHUMG00000157337	ENST00000314235.5:c.5A>G	chr3.hg19:g.178968887T>C	ENSP00000319370:p.Asp2Gly	122.0	0.0		101.0	26.0	NM_014407	B7Z9C9|D3DNR2|E9PER5|Q9NPG7|Q9NRM9|Q9UHN3	Missense_Mutation	SNP	ENST00000314235.5	hg19	CCDS3226.1	.	.	.	.	.	.	.	.	.	.	T	17.52	3.408948	0.62399	.	.	ENSG00000171121	ENST00000314235	T	0.11821	2.74	4.68	-0.481	0.12082	.	3.420860	0.01121	N	0.005798	T	0.07863	0.0197	N	0.08118	0	0.09310	N	0.999999	B	0.06786	0.001	B	0.04013	0.001	T	0.35251	-0.9796	10	0.87932	D	0	.	4.1753	0.10349	0.0:0.2055:0.3848:0.4097	.	2	Q9NPA1	KCMB3_HUMAN	G	2	ENSP00000319370:D2G	ENSP00000319370:D2G	D	-	2	0	KCNMB3	180451581	0.001000	0.12720	0.001000	0.08648	0.058000	0.15608	-0.070000	0.11523	0.050000	0.15949	0.533000	0.62120	GAC	.	.		0.398	KCNMB3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000348484.1			C	178968887	T	C	178968887	3	2	327	1	0	0	0	0	1	0	0	0	8085	1667	58	2	979	2	KCNMB3	3	178968887	Missense_Mutation	SNP	T	TCGA-NI-A4U2-01A-11D-A28X-10	59442680	178968887	19053543	29	45853										
PEX5L	51555	hgsc.bcm.edu	37	chr3	179537706	179537706	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	cttggttctcagatatccagTtcctccgagccatttcttcc	6	14	2	1			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr3:179537706T>A	ENST00000467460.1	-	9	1211	c.881A>T	c.(880-882)aAc>aTc	p.N294I	PEX5L_ENST00000465751.1_Missense_Mutation_p.N270I|PEX5L_ENST00000467440.2_5'UTR|PEX5L_ENST00000468741.1_Missense_Mutation_p.N102I|PEX5L_ENST00000392649.3_Missense_Mutation_p.N186I|PEX5L_ENST00000476138.1_Missense_Mutation_p.N251I|PEX5L_ENST00000485199.1_Missense_Mutation_p.N259I|PEX5L_ENST00000263962.8_Missense_Mutation_p.N292I|PEX5L_ENST00000472994.1_Missense_Mutation_p.N235I|PEX5L_ENST00000464614.1_Missense_Mutation_p.N186I	NM_001256751.1|NM_016559.2	NP_001243680.1|NP_057643.1	Q8IYB4	PEX5R_HUMAN	peroxisomal biogenesis factor 5-like	294					maintenance of protein location (GO:0045185)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome matrix, docking (GO:0016560)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of membrane potential (GO:0042391)	cytosol (GO:0005829)|dendrite (GO:0030425)|peroxisomal membrane (GO:0005778)|receptor complex (GO:0043235)	peroxisome matrix targeting signal-1 binding (GO:0005052)|peroxisome targeting sequence binding (GO:0000268)|small GTPase binding (GO:0031267)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(23)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	all_cancers(143;3.94e-14)|Ovarian(172;0.0338)|Breast(254;0.183)		OV - Ovarian serous cystadenocarcinoma(80;1.75e-26)|GBM - Glioblastoma multiforme(14;0.000518)			AGATATCCAGTTCCTCCGAGC	0.428																																					p.N294I		Atlas-SNP	.											.	PEX5L	104	.	0			c.A881T						.						236	207	217					3																	179537706		2203	4300	6503	SO:0001583	missense	51555	exon9			ATCCAGTTCCTCC	AJ245503	CCDS3236.1, CCDS58861.1, CCDS58862.1, CCDS58863.1, CCDS58864.1, CCDS58865.1, CCDS58866.1, CCDS58867.1	3q27.1	2013-01-10			ENSG00000114757	ENSG00000114757		"Tetratricopeptide (TTC) repeat domain containing"	30024	protein-coding gene	gene with protein product		611058				11463335	Standard	NM_016559		Approved	PEX5R, PXR2	uc003fki.2	Q8IYB4	OTTHUMG00000157363	ENST00000467460.1:c.881A>T	chr3.hg19:g.179537706T>A	ENSP00000419975:p.Asn294Ile	188.0	0.0		182.0	57.0	NM_016559	B7Z2A5|B7Z305|B7Z318|B7Z5Z5|B7Z8P2|E7EUV8|E7EUZ0|E9PEC1|E9PH97|Q9NQD1|Q9P2U3|Q9P2U4	Missense_Mutation	SNP	ENST00000467460.1	hg19	CCDS3236.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.642853	0.87859	.	.	ENSG00000114757	ENST00000467460;ENST00000263962;ENST00000485199;ENST00000382596;ENST00000392649;ENST00000468741;ENST00000476138;ENST00000467440;ENST00000472994;ENST00000464614;ENST00000465751	D;D;D;D;D;D;D;D;D	0.88664	-2.41;-2.41;-2.39;-2.35;-2.36;-2.4;-2.4;-2.35;-2.4	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	D	0.93106	0.7805	L	0.57536	1.79	0.80722	D	1	D;D;D;D;D;D	0.89917	0.998;0.998;0.982;1.0;0.999;0.999	D;D;P;D;D;D	0.91635	0.991;0.987;0.776;0.999;0.998;0.997	D	0.93820	0.7118	10	0.87932	D	0	-23.8923	15.2627	0.73637	0.0:0.0:0.0:1.0	.	235;270;186;292;259;294	E7EUZ0;E9PH97;E9PEC1;Q8IYB4-2;Q8IYB4-3;Q8IYB4	.;.;.;.;.;PEX5R_HUMAN	I	294;292;259;292;186;102;251;182;235;186;270	ENSP00000419975:N294I;ENSP00000263962:N292I;ENSP00000418440:N259I;ENSP00000376420:N186I;ENSP00000418665:N102I;ENSP00000420555:N251I;ENSP00000418054:N235I;ENSP00000417270:N186I;ENSP00000419348:N270I	ENSP00000263962:N292I	N	-	2	0	PEX5L	181020400	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.684000	0.68197	2.096000	0.63516	0.533000	0.62120	AAC	.	.		0.428	PEX5L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348577.1	NM_016559		A	179537706	T	A	179537706	3	1	327	1	0	0	0	0	1	0	0	0	11758	1725	60	4	1027	4	PEX5L	3	179537706	Missense_Mutation	SNP	T	TCGA-NI-A4U2-01A-11D-A28X-10	568819	179537706	18484724	30	45854										
TLR1	7096	hgsc.bcm.edu	37	chr4	38799346	38799346	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	gtctccaactcagtaaggtgCccacaattttcaaaaaccgt	6	12	3	0			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr4:38799346C>T	ENST00000502213.2	-	3	1336	c.1107G>A	c.(1105-1107)ggG>ggA	p.G369G	TLR1_ENST00000308979.2_Silent_p.G369G			Q15399	TLR1_HUMAN	toll-like receptor 1	369					cellular response to triacyl bacterial lipopeptide (GO:0071727)|detection of triacyl bacterial lipopeptide (GO:0042495)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|toll-like receptor 1 signaling pathway (GO:0034130)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)	protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(2)	28						CAGTAAGGTGCCCACAATTTT	0.373																																					p.G369G	GBM(5;216 373 40795 46382)	Atlas-SNP	.											.	TLR1	70	.	0			c.G1107A						.						44	46	45					4																	38799346		2203	4300	6503	SO:0001819	synonymous_variant	7096	exon4			AAGGTGCCCACAA	U88540	CCDS33973.1	4p14	2008-02-05				ENSG00000174125		"CD molecules"	11847	protein-coding gene	gene with protein product		601194				9435236, 7584026	Standard	NM_003263		Approved	rsc786, KIAA0012, CD281	uc003gtl.3	Q15399		ENST00000502213.2:c.1107G>A	chr4.hg19:g.38799346C>T		38.0	0.0		32.0	5.0	NM_003263	D1CS39|D1CS41|O15452|Q32MK3|Q32MK4|Q9UG90	Silent	SNP	ENST00000502213.2	hg19	CCDS33973.1																																																																																			.	.		0.373	TLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360510.3			T	38799346	C	T	38799346	2	4	327	1	0	0	0	0	0	0	0	1	15964	726	26	3		3	TLR1	4	38799346	Silent	SNP	C	TCGA-NI-A4U2-01A-11D-A28X-10		38799346	152354930	31	45855										
IBSP	3381	hgsc.bcm.edu	37	chr4	88732684	88732684	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	gcagaaaacggcaacggcagCagcggaggagacaatggaga	16	8	0	3			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr4:88732684C>T	ENST00000226284.5	+	7	643	c.576C>T	c.(574-576)agC>agT	p.S192S		NM_004967.3	NP_004958.2	P21815	SIAL_HUMAN	integrin-binding sialoprotein	192					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|cellular response to growth factor stimulus (GO:0071363)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|membrane-bounded vesicle (GO:0031988)				breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(10)	21		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000333)|COAD - Colon adenocarcinoma(81;0.154)		GCAACGGCAGCAGCGGAGGAG	0.522																																					p.S192S		Atlas-SNP	.											.	IBSP	53	.	0			c.C576T						.						146	133	137					4																	88732684		2203	4300	6503	SO:0001819	synonymous_variant	3381	exon7			CGGCAGCAGCGGA		CCDS3624.1	4q21.1	2008-07-28	2008-07-28		ENSG00000029559	ENSG00000029559			5341	protein-coding gene	gene with protein product	"bone sialoprotein", "bone sialoprotein II"	147563				8406493	Standard	NM_004967		Approved	BSP, SP-II, BSP-II	uc003hqx.4	P21815	OTTHUMG00000130600	ENST00000226284.5:c.576C>T	chr4.hg19:g.88732684C>T		240.0	0.0		238.0	79.0	NM_004967		Silent	SNP	ENST00000226284.5	hg19	CCDS3624.1																																																																																			.	.		0.522	IBSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253050.2			T	88732684	C	T	88732684	2	4	327	1	0	0	0	0	0	0	0	1	7484	709	25	3		3	IBSP	4	88732684	Silent	SNP	C	TCGA-NI-A4U2-01A-11D-A28X-10	49933338	88732684	102421592	32	45856										
TBC1D9	23158	hgsc.bcm.edu	37	chr4	141543975	141543975	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	ctccccaatctccagcaggaGgctggtcactgctgccgtgg	12	15	2	0			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr4:141543975G>A	ENST00000442267.2	-	21	3249	c.3175C>T	c.(3175-3177)Ctc>Ttc	p.L1059F		NM_015130.2	NP_055945.2	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)	1059							calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	31	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				TCCAGCAGGAGGCTGGTCACT	0.602																																					p.L1059F		Atlas-SNP	.											.	TBC1D9	198	.	0			c.C3175T						.						27	28	27					4																	141543975		2047	4197	6244	SO:0001583	missense	23158	exon21			GCAGGAGGCTGGT	AB020689	CCDS47136.1	4q31.1	2013-01-10	2006-07-12		ENSG00000109436	ENSG00000109436		"EF-hand domain containing"	21710	protein-coding gene	gene with protein product			"TBC1 domain family, member 9"			12970790	Standard	NM_015130		Approved	KIAA0882, MDR1	uc010ioj.3	Q6ZT07	OTTHUMG00000161405	ENST00000442267.2:c.3175C>T	chr4.hg19:g.141543975G>A	ENSP00000411197:p.Leu1059Phe	38.0	0.0		43.0	26.0	NM_015130	A6H8U8|D3DNZ1|O94958	Missense_Mutation	SNP	ENST00000442267.2	hg19	CCDS47136.1	.	.	.	.	.	.	.	.	.	.	G	18.50	3.637256	0.67130	.	.	ENSG00000109436	ENST00000442267	T	0.65916	-0.18	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.74846	0.3770	M	0.76574	2.34	0.58432	D	0.999998	D	0.89917	1.0	D	0.80764	0.994	T	0.77319	-0.2632	10	0.87932	D	0	.	6.8792	0.24163	0.2146:0.0:0.7854:0.0	.	1059	Q6ZT07	TBCD9_HUMAN	F	1059	ENSP00000411197:L1059F	ENSP00000411197:L1059F	L	-	1	0	TBC1D9	141763425	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.690000	0.61731	2.461000	0.83175	0.655000	0.94253	CTC	.	.		0.602	TBC1D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364806.1	NM_015130		A	141543975	G	A	141543975	3	1	327	1	0	0	0	0	1	0	0	0	15642	1000	35	3	629	3	TBC1D9	4	141543975	Missense_Mutation	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10	52811291	141543975	49610301	33	45857										
ARFIP1	27236	hgsc.bcm.edu	37	chr4	153750843	153750843	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	ttccagtgactagtaatggaGaagttgatgactctcgtgaa	11	6	1	5			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr4:153750843G>A	ENST00000451320.2	+	2	222	c.58G>A	c.(58-60)Gaa>Aaa	p.E20K	ARFIP1_ENST00000356064.3_Missense_Mutation_p.E20K|ARFIP1_ENST00000429148.2_Missense_Mutation_p.E20K|ARFIP1_ENST00000353617.2_Missense_Mutation_p.E20K|ARFIP1_ENST00000405727.2_Missense_Mutation_p.E20K			P53367	ARFP1_HUMAN	ADP-ribosylation factor interacting protein 1	20					intracellular protein transport (GO:0006886)|regulation of protein secretion (GO:0050708)	cytosol (GO:0005829)|Golgi membrane (GO:0000139)			ARFIP1/FHDC1(2)	cervix(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|urinary_tract(1)	14	all_hematologic(180;0.093)					TAGTAATGGAGAAGTTGATGA	0.358																																					p.E20K		Atlas-SNP	.											ARFIP1_ENST00000451320,NS,carcinoma,0,2	ARFIP1	69	.	0			c.G58A						.						138	147	144					4																	153750843		2203	4300	6503	SO:0001583	missense	27236	exon2			AATGGAGAAGTTG	U52521	CCDS3780.1, CCDS34080.1	4q31.3	2008-08-01	2008-08-01			ENSG00000164144			21496	protein-coding gene	gene with protein product	"arfaptin 1"	605928				9038142, 10413101	Standard	NM_001025595		Approved	HSU52521	uc003imz.3	P53367		ENST00000451320.2:c.58G>A	chr4.hg19:g.153750843G>A	ENSP00000395083:p.Glu20Lys	77.0	0.0		40.0	11.0	NM_001025593	Q2M2X4|Q3SYL4|Q9Y2X6	Missense_Mutation	SNP	ENST00000451320.2	hg19	CCDS34080.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.016254	0.75161	.	.	ENSG00000164144	ENST00000451320;ENST00000429148;ENST00000353617;ENST00000405727;ENST00000356064	T;T;T;T	0.79653	-1.27;-1.27;-1.29;-1.29	5.65	5.65	0.86999	.	0.101764	0.64402	D	0.000003	D	0.85911	0.5807	L	0.46157	1.445	0.48762	D	0.999702	P;B;B	0.51057	0.941;0.026;0.191	P;B;B	0.60415	0.874;0.04;0.073	D	0.86316	0.1689	10	0.62326	D	0.03	-17.8338	18.4954	0.90863	0.0:0.0:1.0:0.0	.	20;20;20	B4DS69;Q2M2X4;P53367	.;.;ARFP1_HUMAN	K	20	ENSP00000395083:E20K;ENSP00000296557:E20K;ENSP00000384189:E20K;ENSP00000348360:E20K	ENSP00000296557:E20K	E	+	1	0	ARFIP1	153970293	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.222000	0.58580	2.654000	0.90174	0.557000	0.71058	GAA	.	.		0.358	ARFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365032.1	NM_014447		A	153750843	G	A	153750843	3	1	327	1	0	0	0	0	1	0	0	0	854	943	33	3	60	3	ARFIP1	4	153750843	Missense_Mutation	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10	12206868	153750843	37403433	34	45858										
HMGCR	3156	hgsc.bcm.edu	37	chr5	74651016	74651017	+	In_Frame_Ins	INS	-	-	CAAGAC													0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	ttgtcttgtggccagcaccaINSatagaggctgcagagcaata							TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr5:74651016_74651017insCAAGAC	ENST00000287936.4	+	13	1855_1856	c.1699_1700insCAAGAC	c.(1699-1701)aat>aCAAGACat	p.567_567N>TRH	HMGCR_ENST00000343975.5_Intron|HMGCR_ENST00000511206.1_In_Frame_Ins_p.567_567N>TRH	NM_000859.2	NP_000850.1	P04035	HMDH_HUMAN	3-hydroxy-3-methylglutaryl-CoA reductase	567	Catalytic.				aging (GO:0007568)|cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|coenzyme A metabolic process (GO:0015936)|isoprenoid biosynthetic process (GO:0008299)|myoblast differentiation (GO:0045445)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of striated muscle cell apoptotic process (GO:0010664)|negative regulation of vasodilation (GO:0045908)|negative regulation of wound healing (GO:0061045)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein tetramerization (GO:0051262)|response to ethanol (GO:0045471)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|ubiquinone metabolic process (GO:0006743)|visual learning (GO:0008542)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|peroxisomal membrane (GO:0005778)	coenzyme binding (GO:0050662)|hydroxymethylglutaryl-CoA reductase (NADPH) activity (GO:0004420)|hydroxymethylglutaryl-CoA reductase activity (GO:0042282)|NADPH binding (GO:0070402)			breast(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	20		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;2.24e-54)	Atorvastatin(DB01076)|Fluvastatin(DB01095)|Lovastatin(DB00227)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rosuvastatin(DB01098)|Simvastatin(DB00641)	GGCCAGCACCAATAGAGGCTGC	0.406																																					p.N567delinsTRH		Atlas-INDEL	.											.	HMGCR	53	.	0			c.1699_1700insCAAGAC						.																																			SO:0001652	inframe_insertion	3156	exon13			.		CCDS4027.1, CCDS47234.1	5q13.3-q14	2012-10-02	2010-04-30		ENSG00000113161	ENSG00000113161	1.1.1.88, 1.1.1.34		5006	protein-coding gene	gene with protein product	"hydroxymethylglutaryl-CoA reductase", "3-hydroxy-3-methylglutaryl CoA reductase (NADPH)"	142910	"3-hydroxy-3-methylglutaryl-Coenzyme A reductase"				Standard	NM_000859		Approved		uc003kdp.3	P04035	OTTHUMG00000102069	Exception_encountered	chr5.hg19:g.74651016_74651017insCAAGAC	ENSP00000287936:p.Asn567delinsThrArgHis	112.0	0.0		107.0	21.0	NM_000859	B7Z3Y9|Q8N190	In_Frame_Ins	INS	ENST00000287936.4	hg19	CCDS4027.1																																																																																			.	.		0.406	HMGCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219877.2			CAAGAC	74651017	-	CAAGAC	74651016	7	5	327	1	0	1	1	0	0	0	0	0	7240	130	5	0	1745	0	HMGCR	5	74651016	In_Frame_Ins	INS	-	TCGA-NI-A4U2-01A-11D-A28X-10		74651016	106264244	35	45859	243	3								
HMGCR	3156	hgsc.bcm.edu	37	chr5	74651018	74651018	+	Frame_Shift_Del	DEL	T	T	-													0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	tgtcttgtggccagcaccaaTagaggctgcagagcaatagg							TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr5:74651018delT	ENST00000287936.4	+	13	1857	c.1701delT	c.(1699-1701)aatfs	p.N567fs	HMGCR_ENST00000343975.5_Intron|HMGCR_ENST00000511206.1_Frame_Shift_Del_p.N567fs	NM_000859.2	NP_000850.1	P04035	HMDH_HUMAN	3-hydroxy-3-methylglutaryl-CoA reductase	567	Catalytic.				aging (GO:0007568)|cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|coenzyme A metabolic process (GO:0015936)|isoprenoid biosynthetic process (GO:0008299)|myoblast differentiation (GO:0045445)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of striated muscle cell apoptotic process (GO:0010664)|negative regulation of vasodilation (GO:0045908)|negative regulation of wound healing (GO:0061045)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein tetramerization (GO:0051262)|response to ethanol (GO:0045471)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|ubiquinone metabolic process (GO:0006743)|visual learning (GO:0008542)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|peroxisomal membrane (GO:0005778)	coenzyme binding (GO:0050662)|hydroxymethylglutaryl-CoA reductase (NADPH) activity (GO:0004420)|hydroxymethylglutaryl-CoA reductase activity (GO:0042282)|NADPH binding (GO:0070402)			breast(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	20		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;2.24e-54)	Atorvastatin(DB01076)|Fluvastatin(DB01095)|Lovastatin(DB00227)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rosuvastatin(DB01098)|Simvastatin(DB00641)	CCAGCACCAATAGAGGCTGCA	0.413																																					p.N567fs		Atlas-INDEL	.											.	HMGCR	53	.	0			c.1700delA						.						59	56	57					5																	74651018		2203	4300	6503	SO:0001589	frameshift_variant	3156	exon13			.		CCDS4027.1, CCDS47234.1	5q13.3-q14	2012-10-02	2010-04-30		ENSG00000113161	ENSG00000113161	1.1.1.88, 1.1.1.34		5006	protein-coding gene	gene with protein product	"hydroxymethylglutaryl-CoA reductase", "3-hydroxy-3-methylglutaryl CoA reductase (NADPH)"	142910	"3-hydroxy-3-methylglutaryl-Coenzyme A reductase"				Standard	NM_000859		Approved		uc003kdp.3	P04035	OTTHUMG00000102069	ENST00000287936.4:c.1701delT	chr5.hg19:g.74651018delT	ENSP00000287936:p.Asn567fs	108.0	0.0		106.0	21.0	NM_000859	B7Z3Y9|Q8N190	Frame_Shift_Del	DEL	ENST00000287936.4	hg19	CCDS4027.1																																																																																			.	.		0.413	HMGCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219877.2			-	74651018	T	-	74651018	7	5	327	1	0	1	0	1	0	0	0	0	7240	1403	49	0	1747	0	HMGCR	5	74651018	Frame_Shift_Del	DEL	T	TCGA-NI-A4U2-01A-11D-A28X-10	2	74651018	106264242	36	45860	243	3								
HMGCR	3156	hgsc.bcm.edu	37	chr5	74651021	74651022	+	Frame_Shift_Ins	INS	-	-	CAAGA													0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	ttgtggccagcaccaatagaINSggctgcagagcaataggtgt							TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr5:74651021_74651022insCAAGA	ENST00000287936.4	+	13	1860_1861	c.1704_1705insCAAGA	c.(1705-1707)ggcfs	p.G569fs	HMGCR_ENST00000343975.5_Intron|HMGCR_ENST00000511206.1_Frame_Shift_Ins_p.G569fs	NM_000859.2	NP_000850.1	P04035	HMDH_HUMAN	3-hydroxy-3-methylglutaryl-CoA reductase	569	Catalytic.				aging (GO:0007568)|cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|coenzyme A metabolic process (GO:0015936)|isoprenoid biosynthetic process (GO:0008299)|myoblast differentiation (GO:0045445)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of striated muscle cell apoptotic process (GO:0010664)|negative regulation of vasodilation (GO:0045908)|negative regulation of wound healing (GO:0061045)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein tetramerization (GO:0051262)|response to ethanol (GO:0045471)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|ubiquinone metabolic process (GO:0006743)|visual learning (GO:0008542)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|peroxisomal membrane (GO:0005778)	coenzyme binding (GO:0050662)|hydroxymethylglutaryl-CoA reductase (NADPH) activity (GO:0004420)|hydroxymethylglutaryl-CoA reductase activity (GO:0042282)|NADPH binding (GO:0070402)			breast(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	20		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;2.24e-54)	Atorvastatin(DB01076)|Fluvastatin(DB01095)|Lovastatin(DB00227)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rosuvastatin(DB01098)|Simvastatin(DB00641)	GCACCAATAGAGGCTGCAGAGC	0.406																																					p.R568fs		Pindel	.											.	HMGCR	53	.	0			c.1704_1705insCAAGA						.																																			SO:0001589	frameshift_variant	3156	exon13			.		CCDS4027.1, CCDS47234.1	5q13.3-q14	2012-10-02	2010-04-30		ENSG00000113161	ENSG00000113161	1.1.1.88, 1.1.1.34		5006	protein-coding gene	gene with protein product	"hydroxymethylglutaryl-CoA reductase", "3-hydroxy-3-methylglutaryl CoA reductase (NADPH)"	142910	"3-hydroxy-3-methylglutaryl-Coenzyme A reductase"				Standard	NM_000859		Approved		uc003kdp.3	P04035	OTTHUMG00000102069	Exception_encountered	chr5.hg19:g.74651021_74651022insCAAGA	ENSP00000287936:p.Gly569fs	107.0	0.0		107.0	16.0	NM_000859	B7Z3Y9|Q8N190	Frame_Shift_Ins	INS	ENST00000287936.4	hg19	CCDS4027.1																																																																																			.	.		0.406	HMGCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219877.2			CAAGA	74651022	-	CAAGA	74651021	7	5	327	1	0	1	1	0	0	0	0	0	7240	301	11	0	1750	0	HMGCR	5	74651021	Frame_Shift_Ins	INS	-	TCGA-NI-A4U2-01A-11D-A28X-10	3	74651021	106264239	37	45861	243	3								
CHD1	1105	hgsc.bcm.edu	37	chr5	98229286	98229286	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	ttcatcaacacctataaatgCccaatttagacctccaagga	4	12	2	1			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr5:98229286C>A	ENST00000284049.3	-	13	1974	c.1825G>T	c.(1825-1827)Gca>Tca	p.A609S		NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	609	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	49		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	CCTATAAATGCCCAATTTAGA	0.328																																					p.A609S		Atlas-SNP	.											.	CHD1	137	.	0			c.G1825T						.						82	92	88					5																	98229286		2203	4300	6503	SO:0001583	missense	1105	exon13			TAAATGCCCAATT	AF006513	CCDS34204.1	5q15-q21	2008-07-18			ENSG00000153922	ENSG00000153922			1915	protein-coding gene	gene with protein product		602118				8460153, 9326634	Standard	XM_005271866		Approved		uc003knf.3	O14646	OTTHUMG00000162744	ENST00000284049.3:c.1825G>T	chr5.hg19:g.98229286C>A	ENSP00000284049:p.Ala609Ser	107.0	0.0		71.0	4.0	NM_001270	Q17RZ3	Missense_Mutation	SNP	ENST00000284049.3	hg19	CCDS34204.1	.	.	.	.	.	.	.	.	.	.	C	29.7	5.025195	0.93518	.	.	ENSG00000153922	ENST00000284049	D	0.92858	-3.12	5.41	5.41	0.78517	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.33346	U	0.005016	D	0.89476	0.6726	N	0.11870	0.19	0.80722	D	1	P	0.42123	0.771	P	0.48488	0.579	D	0.91279	0.5050	10	0.72032	D	0.01	.	19.1964	0.93690	0.0:1.0:0.0:0.0	.	609	O14646	CHD1_HUMAN	S	609	ENSP00000284049:A609S	ENSP00000284049:A609S	A	-	1	0	CHD1	98257186	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.792000	0.85828	2.547000	0.85894	0.555000	0.69702	GCA	.	.		0.328	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270		A	98229286	C	A	98229286	3	1	327	1	0	0	0	0	1	0	0	0	3325	739	26	3	3399	3	CHD1	5	98229286	Missense_Mutation	SNP	C	TCGA-NI-A4U2-01A-11D-A28X-10	23578265	98229286	82685974	38	45862										
PPIP5K2	23262	hgsc.bcm.edu	37	chr5	102469329	102469329	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	aaactggcctttatgtgattGtcttatttctttccattcta	5	8	3	1			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr5:102469329G>T	ENST00000358359.3	+	3	796	c.287G>T	c.(286-288)tGt>tTt	p.C96F	PPIP5K2_ENST00000321521.9_Missense_Mutation_p.C96F|PPIP5K2_ENST00000414217.1_Missense_Mutation_p.C96F|PPIP5K2_ENST00000513500.1_3'UTR	NM_001276277.1	NP_001263206.1	O43314	VIP2_HUMAN	diphosphoinositol pentakisphosphate kinase 2	96					inositol metabolic process (GO:0006020)|inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	acid phosphatase activity (GO:0003993)|ATP binding (GO:0005524)|diphosphoinositol-pentakisphosphate kinase activity (GO:0033857)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol-1,3,4,5,6-pentakisphosphate kinase activity (GO:0000827)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						TTATGTGATTGTCTTATTTCT	0.328																																					p.C96F		Atlas-SNP	.											.	PPIP5K2	98	.	0			c.G287T						.						90	94	92					5																	102469329		2202	4300	6502	SO:0001583	missense	23262	exon2			GTGATTGTCTTAT	AB007893	CCDS34207.1, CCDS64212.1, CCDS75283.1	5q21.1	2014-05-06	2010-01-26	2010-01-26	ENSG00000145725	ENSG00000145725	2.7.4.24		29035	protein-coding gene	gene with protein product		611648	"histidine acid phosphatase domain containing 1"	HISPPD1		9455477, 17690096, 18981179	Standard	NM_001276277		Approved	KIAA0433, VIP2	uc003koe.4	O43314	OTTHUMG00000181461	ENST00000358359.3:c.287G>T	chr5.hg19:g.102469329G>T	ENSP00000351126:p.Cys96Phe	61.0	0.0		40.0	14.0	NM_015216	A1NI53|A6NGS8|Q8TB50	Missense_Mutation	SNP	ENST00000358359.3	hg19		.	.	.	.	.	.	.	.	.	.	G	17.19	3.327354	0.60743	.	.	ENSG00000145725	ENST00000321521;ENST00000358359;ENST00000451606;ENST00000414217;ENST00000507310	T;T;T	0.15139	2.46;2.45;2.46	5.17	4.31	0.51392	.	0.000000	0.85682	D	0.000000	T	0.33876	0.0878	L	0.49350	1.555	0.80722	D	1	P;D	0.89917	0.93;1.0	P;D	0.65987	0.452;0.94	T	0.08391	-1.0724	10	0.87932	D	0	.	13.9491	0.64104	0.0738:0.0:0.9262:0.0	.	96;96	O43314-2;O43314	.;VIP2_HUMAN	F	96;96;96;96;26	ENSP00000313070:C96F;ENSP00000351126:C96F;ENSP00000416016:C96F	ENSP00000313070:C96F	C	+	2	0	PPIP5K2	102497228	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.420000	0.97426	1.322000	0.45245	0.491000	0.48974	TGT	.	.		0.328	PPIP5K2-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000370487.1	NM_015216		T	102469329	G	T	102469329	3	4	327	1	0	0	0	0	1	0	0	0	12345	1377	48	3	293	3	PPIP5K2	5	102469329	Missense_Mutation	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10	4240043	102469329	78445931	39	45863										
PCDHB11	56125	hgsc.bcm.edu	37	chr5	140579644	140579644	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	gaggagctctgcggttccatCgagccttgcgtgctacattt	12	11	1	0	rs377046428		TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr5:140579644C>T	ENST00000354757.3	+	1	297	c.297C>T	c.(295-297)atC>atT	p.I99I	PCDHB11_ENST00000536699.1_Intron	NM_018931.2	NP_061754.1	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11	99	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.I99I(1)		NS(2)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GCGGTTCCATCGAGCCTTGCG	0.453																																					p.I99I		Atlas-SNP	.											PCDHB11,colon,carcinoma,0,1	PCDHB11	162	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C297T						.	C		0,4406		0,0,2203	120	131	127		297	-5.6	0	5		127	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PCDHB11	NM_018931.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		99/798	140579644	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	56125	exon1			TTCCATCGAGCCT	AF152490	CCDS4253.1	5q31	2010-01-26			ENSG00000197479	ENSG00000197479		"Cadherins / Protocadherins : Clustered"	8682	other	protocadherin	"cadherin ME2"	606337				10380929	Standard	NM_018931		Approved	PCDH-BETA11, ME2	uc003liy.3	Q9Y5F2	OTTHUMG00000129618	ENST00000354757.3:c.297C>T	chr5.hg19:g.140579644C>T		109.0	0.0		96.0	5.0	NM_018931	B4DSF7|Q2M223	Silent	SNP	ENST00000354757.3	hg19	CCDS4253.1																																																																																			.	.		0.453	PCDHB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251813.1	NM_018931		T	140579644	C	T	140579644	2	4	327	1	0	0	0	0	0	0	0	1	11545	874	31	1		1	PCDHB11	5	140579644	Silent	SNP	C	TCGA-NI-A4U2-01A-11D-A28X-10	38110315	140579644	40335616	40	45864										
C1QTNF2	114898	hgsc.bcm.edu	37	chr5	159781851	159781851	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	ggaaagcccattcgtcccatCattcctgagggccctggggc	12	14	1	1			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr5:159781851C>T	ENST00000393975.3	-	2	306	c.303G>A	c.(301-303)atG>atA	p.M101I		NM_031908.4	NP_114114.2	Q9BXJ5	C1QT2_HUMAN	C1q and tumor necrosis factor related protein 2	56	Collagen-like.				activation of MAPK activity (GO:0000187)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|protein heterotrimerization (GO:0070208)|protein homooligomerization (GO:0051260)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)				breast(2)|endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|skin(3)	13	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TTCGTCCCATCATTCCTGAGG	0.667																																					p.M101I		Atlas-SNP	.											.	C1QTNF2	33	.	0			c.G303A						.						25	22	23					5																	159781851		2203	4299	6502	SO:0001583	missense	114898	exon2			TCCCATCATTCCT	AF329836	CCDS4351.2	5q33.3	2008-05-15			ENSG00000145861	ENSG00000145861			14325	protein-coding gene	gene with protein product							Standard	XM_005265815		Approved	CTRP2	uc003lyd.3	Q9BXJ5	OTTHUMG00000130323	ENST00000393975.3:c.303G>A	chr5.hg19:g.159781851C>T	ENSP00000377545:p.Met101Ile	66.0	0.0		80.0	29.0	NM_031908		Missense_Mutation	SNP	ENST00000393975.3	hg19	CCDS4351.2	.	.	.	.	.	.	.	.	.	.	C	11.71	1.719452	0.30503	.	.	ENSG00000145861	ENST00000393975	D	0.91295	-2.82	5.16	4.29	0.51040	.	0.553935	0.20174	N	0.097675	T	0.80924	0.4717	N	0.20881	0.62	0.22127	N	0.999342	B	0.11235	0.004	B	0.15870	0.014	T	0.65372	-0.6184	10	0.25751	T	0.34	.	4.9414	0.13967	0.1702:0.6538:0.0:0.176	.	56	Q9BXJ5	C1QT2_HUMAN	I	101	ENSP00000377545:M101I	ENSP00000377545:M101I	M	-	3	0	C1QTNF2	159714429	0.685000	0.27652	1.000000	0.80357	0.962000	0.63368	-0.038000	0.12144	1.157000	0.42530	0.313000	0.20887	ATG	.	.		0.667	C1QTNF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252672.2			T	159781851	C	T	159781851	3	4	327	1	0	0	0	0	1	0	0	0	1965	826	29	3	697	3	C1QTNF2	5	159781851	Missense_Mutation	SNP	C	TCGA-NI-A4U2-01A-11D-A28X-10	19202207	159781851	21133409	41	45865										
AGPAT1	10554	hgsc.bcm.edu	37	chr6	32138303	32138303	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	tcctgccagccagcaggccaGcccggcagagccagcccaca	11	19	0	1			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr6:32138303G>A	ENST00000395499.1	-	4	988	c.409C>T	c.(409-411)Ctg>Ttg	p.L137L	AGPAT1_ENST00000336984.6_Silent_p.L137L|AGPAT1_ENST00000412465.2_Silent_p.L25L|PPT2-EGFL8_ENST00000422437.1_3'UTR|AGPAT1_ENST00000490711.1_Intron|AGPAT1_ENST00000395496.1_Silent_p.L137L|AGPAT1_ENST00000395497.1_Silent_p.L137L|AGPAT1_ENST00000375104.2_Silent_p.L137L|AGPAT1_ENST00000375107.3_Silent_p.L137L			Q99943	PLCA_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 1	137					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of cellular metabolic process (GO:0031325)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			central_nervous_system(1)|large_intestine(3)|lung(6)|ovary(2)	12						CAGCAGGCCAGCCCGGCAGAG	0.652																																					p.L137L		Atlas-SNP	.											.	AGPAT1	22	.	0			c.C409T						.						70	77	75					6																	32138303		1510	2708	4218	SO:0001819	synonymous_variant	10554	exon4			AGGCCAGCCCGGC	U56417	CCDS4744.1	6p21.3	2013-02-05	2013-02-05		ENSG00000204310	ENSG00000204310	2.3.1.51	"1-acylglycerol-3-phosphate O-acyltransferases"	324	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, alpha"	603099	"1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha)"			9461603, 9291118	Standard	NM_032741		Approved	LPAAT-alpha	uc003oae.3	Q99943	OTTHUMG00000031210	ENST00000395499.1:c.409C>T	chr6.hg19:g.32138303G>A		114.0	0.0		124.0	36.0	NM_006411	A2BFI5|Q5BL03	Silent	SNP	ENST00000395499.1	hg19	CCDS4744.1																																																																																			.	.		0.652	AGPAT1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268941.1	NM_006411		A	32138303	G	A	32138303	2	1	327	1	0	0	0	0	0	0	0	1	386	962	34	3		3	AGPAT1	6	32138303	Silent	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10		32138303	138976764	42	45866										
FOXP4	116113	hgsc.bcm.edu	37	chr6	41566660	41566660	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	tggaggaggagctgccgggaGaagaactgtcctaagggcct	17	8	0	2			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr6:41566660G>A	ENST00000307972.4	+	16	2041	c.2029G>A	c.(2029-2031)Gaa>Aaa	p.E677K	FOXP4_ENST00000373063.3_Missense_Mutation_p.E664K|FOXP4_ENST00000373057.3_Missense_Mutation_p.E675K|MIR4641_ENST00000578353.1_RNA|FOXP4_ENST00000373060.1_Missense_Mutation_p.E677K|FOXP4_ENST00000409208.1_Missense_Mutation_p.E665K			Q8IVH2	FOXP4_HUMAN	forkhead box P4	677					embryonic foregut morphogenesis (GO:0048617)|heart development (GO:0007507)|lung secretory cell differentiation (GO:0061140)|negative regulation of lung goblet cell differentiation (GO:1901250)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	16	Ovarian(28;0.0327)|Colorectal(47;0.196)					GCTGCCGGGAGAAGAACTGTC	0.692																																					p.E677K		Atlas-SNP	.											.	FOXP4	83	.	0			c.G2029A						.						25	30	28					6																	41566660		2203	4298	6501	SO:0001583	missense	116113	exon17			CCGGGAGAAGAAC	AB080747	CCDS4856.1, CCDS34447.1, CCDS34448.1	6p21.1	2008-02-05			ENSG00000137166	ENSG00000137166		"Forkhead boxes"	20842	protein-coding gene	gene with protein product		608924					Standard	XM_006714991		Approved	FLJ40908	uc003oql.3	Q8IVH2	OTTHUMG00000014679	ENST00000307972.4:c.2029G>A	chr6.hg19:g.41566660G>A	ENSP00000309823:p.Glu677Lys	275.0	0.0		258.0	89.0	NM_001012426	Q5W098|Q7Z7F8|Q8IW55|Q96E19	Missense_Mutation	SNP	ENST00000307972.4	hg19	CCDS34447.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.271378	0.80469	.	.	ENSG00000137166	ENST00000373060;ENST00000373063;ENST00000409208;ENST00000373057;ENST00000307972	D;D;D;D;D	0.91945	-2.92;-2.93;-2.94;-2.92;-2.92	4.36	4.36	0.52297	.	0.135315	0.46442	D	0.000292	D	0.93822	0.8024	L	0.60455	1.87	0.58432	D	0.999999	D;D;D	0.63880	0.993;0.993;0.993	D;D;D	0.68192	0.956;0.956;0.956	D	0.94431	0.7649	10	0.87932	D	0	.	15.206	0.73180	0.0:0.0:1.0:0.0	.	664;675;677	Q8IW55;Q7Z7F8;Q8IVH2	.;.;FOXP4_HUMAN	K	677;664;665;675;677	ENSP00000362151:E677K;ENSP00000362154:E664K;ENSP00000386958:E665K;ENSP00000362148:E675K;ENSP00000309823:E677K	ENSP00000309823:E677K	E	+	1	0	FOXP4	41674638	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	6.578000	0.74032	2.435000	0.82474	0.462000	0.41574	GAA	.	.		0.692	FOXP4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000106767.1	NM_138457		A	41566660	G	A	41566660	3	1	327	1	0	0	0	0	1	0	0	0	6037	943	33	3	2091	3	FOXP4	6	41566660	Missense_Mutation	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10	9428357	41566660	129548407	43	45867										
LGSN	51557	hgsc.bcm.edu	37	chr6	63990465	63990465	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	gagctgctcagttccagaagTgctgcagaacatgtttttct	10	9	2	2			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr6:63990465T>C	ENST00000370657.4	-	4	1024	c.991A>G	c.(991-993)Act>Gct	p.T331A	LGSN_ENST00000370658.5_Silent_p.A190A			Q5TDP6	LGSN_HUMAN	lengsin, lens protein with glutamine synthetase domain	331					glutamine biosynthetic process (GO:0006542)	plasma membrane (GO:0005886)	glutamate-ammonia ligase activity (GO:0004356)			NS(1)|endometrium(2)|large_intestine(5)|lung(16)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						GTTCCAGAAGTGCTGCAGAAC	0.473																																					p.T331A		Atlas-SNP	.											.	LGSN	82	.	0			c.A991G						.						87	88	88					6																	63990465		2203	4300	6503	SO:0001583	missense	51557	exon4			CAGAAGTGCTGCA	AF242388	CCDS4964.1, CCDS55027.1	6q12	2013-09-19	2008-09-19	2008-09-19	ENSG00000146166	ENSG00000146166			21016	protein-coding gene	gene with protein product		611470	"glutamate-ammonia ligase (glutamine synthetase) domain containing 1"	GLULD1		12107412	Standard	NM_016571		Approved	LGS	uc003peh.3	Q5TDP6	OTTHUMG00000014946	ENST00000370657.4:c.991A>G	chr6.hg19:g.63990465T>C	ENSP00000359691:p.Thr331Ala	67.0	0.0		51.0	25.0	NM_016571	A1L421|Q0PVN9|Q0PVP0|Q9NYJ0	Missense_Mutation	SNP	ENST00000370657.4	hg19	CCDS4964.1	.	.	.	.	.	.	.	.	.	.	T	0.017	-1.487866	0.01018	.	.	ENSG00000146166	ENST00000370657	D	0.85171	-1.95	5.62	-0.412	0.12367	Glutamine synthetase, catalytic domain (1);Glutamine synthetase/guanido kinase, catalytic domain (1);	0.452483	0.29616	N	0.011657	T	0.59224	0.2178	.	.	.	0.09310	N	0.999992	B	0.02656	0.0	B	0.01281	0.0	T	0.55661	-0.8106	9	0.38643	T	0.18	-6.7024	10.7564	0.46239	0.0:0.7178:0.0:0.2822	.	331	Q5TDP6	LGSN_HUMAN	A	331	ENSP00000359691:T331A	ENSP00000359691:T331A	T	-	1	0	LGSN	64048424	0.367000	0.25023	0.007000	0.13788	0.001000	0.01503	1.721000	0.38032	-0.030000	0.13804	-0.250000	0.11733	ACT	.	.		0.473	LGSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041076.2	NM_016571		C	63990465	T	C	63990465	3	2	327	1	0	0	0	0	1	0	0	0	8768	1696	59	2	542	2	LGSN	6	63990465	Missense_Mutation	SNP	T	TCGA-NI-A4U2-01A-11D-A28X-10	22423805	63990465	107124602	44	45868										
PGM3	5238	hgsc.bcm.edu	37	chr6	83888466	83888466	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	tacaacaccaatattcaaacTttctccaatctagacaaaaa	1	11	3	1			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr6:83888466T>G	ENST00000283977.4	-	7	838	c.712A>C	c.(712-714)Agt>Cgt	p.S238R	PGM3_ENST00000513973.1_Missense_Mutation_p.S319R|PGM3_ENST00000512866.1_Missense_Mutation_p.S319R|PGM3_ENST00000506587.1_Missense_Mutation_p.S347R					phosphoglucomutase 3											NS(1)|breast(1)|endometrium(2)|large_intestine(4)|lung(6)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	18		all_cancers(76;0.000504)|Acute lymphoblastic leukemia(125;3.85e-06)|all_hematologic(105;0.0017)|all_epithelial(107;0.068)		BRCA - Breast invasive adenocarcinoma(397;0.0478)		ATATTCAAACTTTCTCCAATC	0.318																																					p.S347R		Atlas-SNP	.											.	PGM3	39	.	0			c.A1039C						.						109	97	101					6																	83888466		2203	4299	6502	SO:0001583	missense	5238	exon9			TCAAACTTTCTCC	BC001258	CCDS4997.1, CCDS56435.1, CCDS56436.1, CCDS75487.1	6q14.1-q15	2012-10-02			ENSG00000013375	ENSG00000013375	5.4.2.3		8907	protein-coding gene	gene with protein product	"acetylglucosamine phosphomutase"	172100				12174217, 10721701	Standard	NM_001199917		Approved	AGM1, DKFZP434B187, PAGM	uc011dyz.2	O95394	OTTHUMG00000015110	ENST00000283977.4:c.712A>C	chr6.hg19:g.83888466T>G	ENSP00000283977:p.Ser238Arg	109.0	0.0		85.0	32.0	NM_001199917		Missense_Mutation	SNP	ENST00000283977.4	hg19		.	.	.	.	.	.	.	.	.	.	T	11.77	1.737001	0.30774	.	.	ENSG00000013375	ENST00000513973;ENST00000512866;ENST00000283977;ENST00000506587	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	5.87	3.51	0.40186	Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III (2);	0.488846	0.26387	N	0.024664	T	0.10594	0.0259	N	0.20357	0.565	0.40017	D	0.975362	B;B;B	0.26935	0.164;0.002;0.072	B;B;B	0.24269	0.052;0.007;0.032	T	0.09100	-1.0690	10	0.16420	T	0.52	-53.103	9.8444	0.41017	0.0:0.139:0.0:0.861	.	347;347;319	E9PF86;B4DX94;O95394	.;.;AGM1_HUMAN	R	319;319;238;347	ENSP00000424874:S319R;ENSP00000421565:S319R;ENSP00000283977:S238R;ENSP00000425809:S347R	ENSP00000283977:S238R	S	-	1	0	PGM3	83945185	0.213000	0.23551	0.510000	0.27712	0.861000	0.49209	0.526000	0.22971	0.492000	0.27815	0.528000	0.53228	AGT	.	.		0.318	PGM3-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000366385.2	NM_015599		G	83888466	T	G	83888466	3	3	327	1	0	0	0	0	1	0	0	0	11809	1609	56	5	697	5	PGM3	6	83888466	Missense_Mutation	SNP	T	TCGA-NI-A4U2-01A-11D-A28X-10	19898001	83888466	87226601	45	45869										
KIAA0408	9729	hgsc.bcm.edu	37	chr6	127768213	127768213	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	tttctaagtgggctactgctCtctgctactgaggagctaca	10	10	2	1			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr6:127768213C>T	ENST00000483725.3	-	5	1587	c.1251G>A	c.(1249-1251)gaG>gaA	p.E417E	SOGA3_ENST00000481848.2_3'UTR|SOGA3_ENST00000556132.1_3'UTR	NM_014702.4	NP_055517.3	Q6ZU52	K0408_HUMAN	KIAA0408	417										endometrium(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|skin(1)	28				GBM - Glioblastoma multiforme(226;0.0217)|all cancers(137;0.13)		GGCTACTGCTCTCTGCTACTG	0.413																																					p.E417E		Atlas-SNP	.											.	KIAA0408	61	.	0			c.G1251A						.						67	69	68					6																	127768213		2202	4300	6502	SO:0001819	synonymous_variant	9729	exon5			ACTGCTCTCTGCT	AB007868	CCDS34531.1	6q22.33	2012-11-29			ENSG00000189367	ENSG00000189367			21636	protein-coding gene	gene with protein product							Standard	NM_014702		Approved		uc011ebs.2	Q6ZU52	OTTHUMG00000166439	ENST00000483725.3:c.1251G>A	chr6.hg19:g.127768213C>T		66.0	0.0		36.0	5.0	NM_014702	B3KRE5|E1P573|O43158|Q5TF20|Q7L2M2	Silent	SNP	ENST00000483725.3	hg19	CCDS34531.1																																																																																			.	.		0.413	KIAA0408-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042145.3	NM_014702		T	127768213	C	T	127768213	2	4	327	1	0	0	0	0	0	0	0	1	8183	912	32	3		3	KIAA0408	6	127768213	Silent	SNP	C	TCGA-NI-A4U2-01A-11D-A28X-10	43879747	127768213	43346854	46	45870										
ZDHHC4	55146	hgsc.bcm.edu	37	chr7	6621814	6621814	+	Frame_Shift_Del	DEL	T	T	-													0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	ggagttgtccttgcattaccTtcttctgccctatctgctgc					rs183719718	byFrequency	TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr7:6621814delT	ENST00000396706.2	+	5	745	c.302delT	c.(301-303)cttfs	p.L103fs	AC079742.4_ENST00000434951.1_RNA|ZDHHC4_ENST00000396707.2_Frame_Shift_Del_p.L103fs|ZDHHC4_ENST00000396709.1_Frame_Shift_Del_p.L103fs|ZDHHC4_ENST00000405731.3_Frame_Shift_Del_p.L103fs|ZDHHC4_ENST00000396713.2_Frame_Shift_Del_p.L103fs|ZDHHC4_ENST00000335965.6_Frame_Shift_Del_p.L103fs			Q9NPG8	ZDHC4_HUMAN	zinc finger, DHHC-type containing 4	103						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.1)		TTGCATTACCTTCTTCTGCCC	0.468																																					p.L101fs		Atlas-Indel,Pindel	.											.	ZDHHC4	36	.	0			c.301delC						.						328	288	301					7																	6621814		2203	4300	6503	SO:0001589	frameshift_variant	55146	exon5			.	AF201931	CCDS5352.1	7p22.1	2011-01-11			ENSG00000136247	ENSG00000136247		"Zinc fingers, DHHC-type"	18471	protein-coding gene	gene with protein product							Standard	NM_018106		Approved	FLJ10479, ZNF374	uc003sqj.3	Q9NPG8	OTTHUMG00000023579	ENST00000396706.2:c.302delT	chr7.hg19:g.6621814delT	ENSP00000379934:p.Leu103fs	171.0	0.0		167.0	61.0	NM_018106	A4D2N9|Q53EV7|Q6FIB5|Q9H0R9	Frame_Shift_Del	DEL	ENST00000396706.2	hg19	CCDS5352.1																																																																																			.	.		0.468	ZDHHC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207477.3	NM_018106		-	6621814	T	-	6621814	7	5	327	1	0	1	0	1	0	0	0	0	17632	1609	56	0	312	0	ZDHHC4	7	6621814	Frame_Shift_Del	DEL	T	TCGA-NI-A4U2-01A-11D-A28X-10		6621814	152516849	47	45871										
PLXNA4	91584	hgsc.bcm.edu	37	chr7	131833385	131833385	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	atcctgcaagatcatccttgCcccacttccttgtcgccact	5	17	1	1			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr7:131833385C>T	ENST00000359827.3	-	26	5643	c.4681G>A	c.(4681-4683)Gca>Aca	p.A1561T	PLXNA4_ENST00000321063.4_Missense_Mutation_p.A1561T			Q9HCM2	PLXA4_HUMAN	plexin A4	1561					anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						ATCATCCTTGCCCCACTTCCT	0.537																																					p.A1561T		Atlas-SNP	.											PLXNA4_ENST00000359827,right_upper_lobe,carcinoma,0,2	PLXNA4	873	.	0			c.G4681A						.						133	131	132					7																	131833385		2156	4288	6444	SO:0001583	missense	91584	exon26			TCCTTGCCCCACT	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"Plexins"	9102	protein-coding gene	gene with protein product		604280	"plexin A4, A", "plexin A4, B"	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.4681G>A	chr7.hg19:g.131833385C>T	ENSP00000352882:p.Ala1561Thr	109.0	0.0		151.0	49.0	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	hg19	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	C	17.96	3.516951	0.64634	.	.	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.11712	2.75;2.75	4.62	4.62	0.57501	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.286062	0.38959	N	0.001516	T	0.11750	0.0286	L	0.33753	1.03	0.41275	D	0.986873	P	0.39665	0.682	B	0.39503	0.301	T	0.08249	-1.0731	10	0.49607	T	0.09	.	17.6545	0.88174	0.0:1.0:0.0:0.0	.	1561	Q9HCM2	PLXA4_HUMAN	T	1561	ENSP00000323194:A1561T;ENSP00000352882:A1561T	ENSP00000323194:A1561T	A	-	1	0	PLXNA4	131483925	0.998000	0.40836	0.963000	0.40424	0.940000	0.58332	3.815000	0.55651	2.401000	0.81631	0.561000	0.74099	GCA	.	.		0.537	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		T	131833385	C	T	131833385	3	4	327	1	0	0	0	0	1	0	0	0	12131	739	26	3	1031	3	PLXNA4	7	131833385	Missense_Mutation	SNP	C	TCGA-NI-A4U2-01A-11D-A28X-10	125211571	131833385	27305278	48	45872										
NRG1	3084	hgsc.bcm.edu	37	chr8	32621590	32621590	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	tatgaaacgacccaagagtaCgagccagcccaagagcctgt	10	12	0	3	rs576124928		TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr8:32621590C>T	ENST00000405005.3	+	12	1593	c.1593C>T	c.(1591-1593)taC>taT	p.Y531Y	NRG1_ENST00000519301.1_Silent_p.Y481Y|RP11-1002K11.1_ENST00000607314.1_lincRNA|NRG1_ENST00000539990.1_Silent_p.Y374Y|NRG1_ENST00000287842.3_Silent_p.Y528Y|NRG1_ENST00000287845.5_Silent_p.Y502Y|NRG1_ENST00000338921.4_Silent_p.Y539Y|NRG1_ENST00000341377.5_3'UTR|NRG1_ENST00000356819.4_Silent_p.Y536Y			Q02297	NRG1_HUMAN	neuregulin 1	531					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell myoblast differentiation (GO:0060379)|cell communication (GO:0007154)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cellular protein complex disassembly (GO:0043624)|embryo development (GO:0009790)|endocardial cell differentiation (GO:0060956)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell fate commitment (GO:0021781)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|mammary gland development (GO:0030879)|MAPK cascade (GO:0000165)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of secretion (GO:0051048)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|neural crest cell development (GO:0014032)|neuron fate commitment (GO:0048663)|neurotransmitter receptor metabolic process (GO:0045213)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|synapse assembly (GO:0007416)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular trabecula myocardium morphogenesis (GO:0003222)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|ErbB-3 class receptor binding (GO:0043125)|growth factor activity (GO:0008083)|protein tyrosine kinase activator activity (GO:0030296)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(1)|skin(1)	39		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		CCCAAGAGTACGAGCCAGCCC	0.547													C|||	1	0.000199681	8e-04	0	5008	,	,		16851	0		0	False		,,,				2504	0				p.Y536Y		Atlas-SNP	.											.	NRG1	260	.	0			c.C1608T						.						59	54	56					8																	32621590		2203	4300	6503	SO:0001819	synonymous_variant	3084	exon13			AGAGTACGAGCCA	L12261	CCDS6084.1, CCDS6085.1, CCDS6086.1, CCDS6087.1, CCDS47836.1, CCDS55218.1, CCDS55219.1, CCDS75727.1	8p21-p12	2014-06-23			ENSG00000157168	ENSG00000157168		"Immunoglobulin superfamily / I-set domain containing"	7997	protein-coding gene	gene with protein product		142445	"NRG1 intronic transcript 2 (non-protein coding)"	HGL, NRG1-IT2		1350381, 8095334	Standard	NM_013962		Approved	HRG, NDF, GGF	uc003xiu.2	Q02297	OTTHUMG00000163918	ENST00000405005.3:c.1593C>T	chr8.hg19:g.32621590C>T		114.0	0.0		106.0	29.0	NM_013956	A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	Silent	SNP	ENST00000405005.3	hg19	CCDS6085.1																																																																																			.	.		0.547	NRG1-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472504.1			T	32621590	C	T	32621590	2	4	327	1	0	0	0	0	0	0	0	1	10656	547	19	1		1	NRG1	8	32621590	Silent	SNP	C	TCGA-NI-A4U2-01A-11D-A28X-10		32621590	113742432	49	45873										
PRDM14	63978	hgsc.bcm.edu	37	chr8	70981670	70981670	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	aaagtgtcaggtccacaacaCgggccactctcgttgtcgcc	10	14	2	0			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr8:70981670C>T	ENST00000276594.2	-	2	627	c.426G>A	c.(424-426)ccG>ccA	p.P142P		NM_024504.3	NP_078780.1	Q9GZV8	PRD14_HUMAN	PR domain containing 14	142					cell fate specification (GO:0001708)|cell morphogenesis (GO:0000902)|fertilization (GO:0009566)|germ cell development (GO:0007281)|germ-line stem cell maintenance (GO:0030718)|histone H3-R26 methylation (GO:0034972)|homeostasis of number of cells within a tissue (GO:0048873)|inner cell mass cell fate commitment (GO:0001827)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|regulation of DNA methylation (GO:0044030)|regulation of gene expression, epigenetic (GO:0040029)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Breast(64;0.193)		Epithelial(68;0.00508)|all cancers(69;0.0259)|OV - Ovarian serous cystadenocarcinoma(28;0.0405)			GTCCACAACACGGGCCACTCT	0.592																																					p.P142P	NSCLC(129;99 1813 5906 40656 46114)	Atlas-SNP	.											.	PRDM14	102	.	0			c.G426A						.						54	51	52					8																	70981670		2203	4300	6503	SO:0001819	synonymous_variant	63978	exon2			ACAACACGGGCCA	AF319458	CCDS6206.1	8q13.3	2013-01-08			ENSG00000147596	ENSG00000147596		"Zinc fingers, C2H2-type"	14001	protein-coding gene	gene with protein product		611781					Standard	NM_024504		Approved		uc003xym.3	Q9GZV8	OTTHUMG00000150495	ENST00000276594.2:c.426G>A	chr8.hg19:g.70981670C>T		150.0	0.0		147.0	12.0	NM_024504	Q86UX9	Silent	SNP	ENST00000276594.2	hg19	CCDS6206.1																																																																																			.	.		0.592	PRDM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318505.1			T	70981670	C	T	70981670	2	4	327	1	0	0	0	0	0	0	0	1	12467	523	19	1		1	PRDM14	8	70981670	Silent	SNP	C	TCGA-NI-A4U2-01A-11D-A28X-10	38360080	70981670	75382352	50	45874										
CNTLN	54875	hgsc.bcm.edu	37	chr9	17394764	17394764	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	cagtgagctggagacagaagTcacttccctgaggagacaag	13	9	1	5			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr9:17394764T>C	ENST00000380647.3	+	15	2396	c.2312T>C	c.(2311-2313)gTc>gCc	p.V771A	CNTLN_ENST00000425824.1_Missense_Mutation_p.V771A|CNTLN_ENST00000262360.5_Missense_Mutation_p.V771A			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	771					centriole-centriole cohesion (GO:0010457)|protein localization to organelle (GO:0033365)	centriole (GO:0005814)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)|protein binding, bridging (GO:0030674)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(6)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53				GBM - Glioblastoma multiforme(50;6.14e-10)		GAGACAGAAGTCACTTCCCTG	0.398																																					p.V771A		Atlas-SNP	.											.	CNTLN	128	.	0			c.T2312C						.						84	84	84					9																	17394764		1933	4150	6083	SO:0001583	missense	54875	exon15			CAGAAGTCACTTC	AK000283	CCDS43789.1, CCDS47953.1	9p22.2-p22.1	2008-11-11	2008-02-08	2008-02-08	ENSG00000044459	ENSG00000044459			23432	protein-coding gene	gene with protein product		611870	"chromosome 9 open reading frame 101", "chromosome 9 open reading frame 39"	C9orf101, C9orf39		18086554	Standard	XM_005251492		Approved	FLJ20276, bA340N12.1, OTTHUMG00000019597	uc003zmy.3	Q9NXG0	OTTHUMG00000019599	ENST00000380647.3:c.2312T>C	chr9.hg19:g.17394764T>C	ENSP00000370021:p.Val771Ala	142.0	0.0		96.0	33.0	NM_017738	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Missense_Mutation	SNP	ENST00000380647.3	hg19	CCDS43789.1	.	.	.	.	.	.	.	.	.	.	T	8.423	0.846840	0.17034	.	.	ENSG00000044459	ENST00000380647;ENST00000425824;ENST00000262360	T;T;T	0.20200	2.09;2.09;2.35	5.77	5.77	0.91146	.	.	.	.	.	T	0.15522	0.0374	L	0.34521	1.04	0.30276	N	0.791744	P;P;P	0.46784	0.607;0.884;0.884	B;B;B	0.39503	0.224;0.301;0.301	T	0.04811	-1.0925	9	0.18710	T	0.47	.	11.1671	0.48550	0.0:0.0734:0.0:0.9266	.	771;771;771	Q9NXG0;C9J1F9;Q9NXG0-2	CNTLN_HUMAN;.;.	A	771	ENSP00000370021:V771A;ENSP00000392798:V771A;ENSP00000262360:V771A	ENSP00000262360:V771A	V	+	2	0	CNTLN	17384764	1.000000	0.71417	1.000000	0.80357	0.381000	0.30169	3.291000	0.51764	2.201000	0.70794	0.528000	0.53228	GTC	.	.		0.398	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738		C	17394764	T	C	17394764	3	2	327	1	0	0	0	0	1	0	0	0	3641	1667	58	2	2400	2	CNTLN	9	17394764	Missense_Mutation	SNP	T	TCGA-NI-A4U2-01A-11D-A28X-10		17394764	123818667	51	45875										
FRMD3	257019	hgsc.bcm.edu	37	chr9	85863364	85863364	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	gggggatcttcatactcccgGgctgccttcactggggagct	14	12	3	0			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr9:85863364G>A	ENST00000304195.3	-	14	1469	c.1263C>T	c.(1261-1263)gcC>gcT	p.A421A	FRMD3_ENST00000328788.1_Silent_p.A78A|FRMD3_ENST00000376434.1_Silent_p.A227A|FRMD3_ENST00000465485.1_5'UTR|FRMD3_ENST00000376438.1_Silent_p.A421A	NM_001244960.1|NM_174938.5	NP_001231889.1|NP_777598.3	A2A2Y4	FRMD3_HUMAN	FERM domain containing 3	421						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(1)|upper_aerodigestive_tract(1)	30						CATACTCCCGGGCTGCCTTCA	0.433																																					p.A421A		Atlas-SNP	.											.	FRMD3	96	.	0			c.C1263T						.						71	71	71					9																	85863364		1845	4102	5947	SO:0001819	synonymous_variant	257019	exon14			CTCCCGGGCTGCC	AK094281	CCDS43840.1, CCDS59131.1, CCDS59132.1, CCDS59133.1, CCDS75852.1	9q21.33	2008-02-05			ENSG00000172159	ENSG00000172159			24125	protein-coding gene	gene with protein product		607619				12601556	Standard	NM_174938		Approved	EPB41L4O, MGC20553	uc004ams.2	A2A2Y4	OTTHUMG00000020103	ENST00000304195.3:c.1263C>T	chr9.hg19:g.85863364G>A		36.0	0.0		40.0	14.0	NM_174938	A8MQB0|B4DN14|Q53EP2|Q5JV59|Q5VZA1|Q86WP8|Q8IZ44|Q8N3Y5|Q8N9L2	Silent	SNP	ENST00000304195.3	hg19	CCDS43840.1																																																																																			.	.		0.433	FRMD3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157355.1	NM_174938		A	85863364	G	A	85863364	2	1	327	1	0	0	0	0	0	0	0	1	6058	1219	43	3		3	FRMD3	9	85863364	Silent	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10	68468600	85863364	55350067	52	45876										
KIAA1529	100499483	hgsc.bcm.edu	37	chr9	100105674	100105674	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	atactatgaggacatggagtCcttcacaatctccagtggaa	9	9	2	1			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr9:100105674C>G	ENST00000357054.1	+	33	3811	c.2876C>G	c.(2875-2877)tCc>tGc	p.S959C	CCDC180_ENST00000395220.1_3'UTR|CCDC180_ENST00000529487.1_Missense_Mutation_p.S820C|CCDC180_ENST00000460482.2_3'UTR|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000375202.2_Missense_Mutation_p.S820C|CCDC180_ENST00000411667.2_Missense_Mutation_p.S817C			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	959						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											GACATGGAGTCCTTCACAATC	0.423																																					p.S820C		Atlas-SNP	.											.	.	.	.	0			c.C2459G						.						141	124	130					9																	100105674		2203	4300	6503	SO:0001583	missense	0	exon19			TGGAGTCCTTCAC	AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"Behcet's Disease Associated Gene 1"		"KIAA1529", "chromosome 9 open reading frame 174"	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.2876C>G	chr9.hg19:g.100105674C>G	ENSP00000349562:p.Ser959Cys	83.0	0.0		108.0	6.0	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Missense_Mutation	SNP	ENST00000357054.1	hg19		.	.	.	.	.	.	.	.	.	.	C	16.48	3.135348	0.56828	.	.	ENSG00000197816	ENST00000357054;ENST00000375202;ENST00000411667;ENST00000541524;ENST00000529487	T;T;T;T	0.13089	2.99;3.0;2.62;3.0	5.49	-0.913	0.10500	.	0.874303	0.09928	N	0.737591	T	0.15696	0.0378	N	0.19112	0.55	0.24518	N	0.994177	D;D;D	0.67145	0.995;0.996;0.995	P;P;P	0.61592	0.847;0.891;0.847	T	0.22836	-1.0205	10	0.56958	D	0.05	-2.8289	5.534	0.17001	0.0:0.3408:0.1489:0.5103	.	843;959;959	Q86Y65;B7ZMG3;Q9P1Z9	.;.;CI174_HUMAN	C	959;820;817;843;820	ENSP00000349562:S959C;ENSP00000364348:S820C;ENSP00000414000:S817C;ENSP00000434727:S820C	ENSP00000349562:S959C	S	+	2	0	C9orf174	99145495	0.797000	0.28877	0.994000	0.49952	0.776000	0.43924	-0.341000	0.07811	-0.129000	0.11620	-0.140000	0.14226	TCC	.	.		0.423	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893		G	100105674	C	G	100105674	3	3	327	1	0	0	0	0	1	0	0	0	8249	855	30	4	2962	4	KIAA1529	9	100105674	Missense_Mutation	SNP	C	TCGA-NI-A4U2-01A-11D-A28X-10	14242310	100105674	41107757	53	45877										
TGFBR1	7046	hgsc.bcm.edu	37	chr9	101908774	101908774	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	aaattttttttaggtacatgGcccctgaagttctcgatgat	8	7	1	2			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr9:101908774G>A	ENST00000374994.4	+	7	1255	c.1138G>A	c.(1138-1140)Gcc>Acc	p.A380T	TGFBR1_ENST00000550253.1_Missense_Mutation_p.A311T|RNA5SP290_ENST00000517133.1_RNA|TGFBR1_ENST00000374990.2_Missense_Mutation_p.A303T|TGFBR1_ENST00000552516.1_Missense_Mutation_p.A384T	NM_004612.2	NP_004603.1	P36897	TGFR1_HUMAN	transforming growth factor, beta receptor 1	380	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|angiogenesis (GO:0001525)|anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|artery morphogenesis (GO:0048844)|blastocyst development (GO:0001824)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen fibril organization (GO:0030199)|embryonic cranial skeleton morphogenesis (GO:0048701)|endothelial cell migration (GO:0043542)|epithelial to mesenchymal transition (GO:0001837)|extracellular structure organization (GO:0043062)|germ cell migration (GO:0008354)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|mesenchymal cell differentiation (GO:0048762)|negative regulation of apoptotic process (GO:0043066)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|parathyroid gland development (GO:0060017)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|pharyngeal system development (GO:0060037)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|regulation of protein binding (GO:0043393)|regulation of protein ubiquitination (GO:0031396)|regulation of transcription, DNA-templated (GO:0006355)|response to cholesterol (GO:0070723)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|skeletal system morphogenesis (GO:0048705)|thymus development (GO:0048538)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	endosome (GO:0005768)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|tight junction (GO:0005923)|transforming growth factor beta receptor homodimeric complex (GO:0070022)	ATP binding (GO:0005524)|I-SMAD binding (GO:0070411)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type I (GO:0005025)|transforming growth factor beta-activated receptor activity (GO:0005024)|type II transforming growth factor beta receptor binding (GO:0005114)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	27		Acute lymphoblastic leukemia(62;0.0559)				TAGGTACATGGCCCCTGAAGT	0.363																																					p.A380T		Atlas-SNP	.											.	TGFBR1	70	.	0			c.G1138A						.						172	175	174					9																	101908774		2203	4300	6503	SO:0001583	missense	7046	exon7			TACATGGCCCCTG		CCDS6738.1, CCDS47998.1	9q22	2014-01-30	2008-07-31		ENSG00000106799	ENSG00000106799			11772	protein-coding gene	gene with protein product	"activin A receptor type II-like kinase, 53kDa"	190181	"transforming growth factor, beta receptor I (activin A receptor type II-like kinase, 53kD)", "multiple self-healing squamous epithelioma"	MSSE, ESS1		1319842, 8530052, 21358634	Standard	NM_001130916		Approved	ALK-5, ACVRLK4	uc004azc.3	P36897	OTTHUMG00000020353	ENST00000374994.4:c.1138G>A	chr9.hg19:g.101908774G>A	ENSP00000364133:p.Ala380Thr	77.0	0.0		45.0	9.0	NM_004612	Q6IR47|Q706C0|Q706C1	Missense_Mutation	SNP	ENST00000374994.4	hg19	CCDS6738.1	.	.	.	.	.	.	.	.	.	.	G	34	5.352851	0.95830	.	.	ENSG00000106799	ENST00000374994;ENST00000540092;ENST00000374990;ENST00000552516;ENST00000550253	D;D;D;D	0.97455	-4.39;-4.39;-4.39;-4.39	5.43	5.43	0.79202	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.99187	0.9718	H	0.98314	4.2	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.984;0.999	D	0.98883	1.0770	10	0.87932	D	0	.	18.3871	0.90470	0.0:0.0:1.0:0.0	.	303;380	P36897-3;P36897	.;TGFR1_HUMAN	T	380;342;303;384;311	ENSP00000364133:A380T;ENSP00000364129:A303T;ENSP00000447297:A384T;ENSP00000450052:A311T	ENSP00000364129:A303T	A	+	1	0	TGFBR1	100948595	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.810000	0.99221	2.708000	0.92522	0.467000	0.42956	GCC	.	.		0.363	TGFBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053390.3			A	101908774	G	A	101908774	3	1	327	1	0	0	0	0	1	0	0	0	15836	1203	42	3	1164	3	TGFBR1	9	101908774	Missense_Mutation	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10	1803100	101908774	39304657	54	45878										
EXD3	54932	hgsc.bcm.edu	37	chr9	140247082	140247082	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	cggcgctcacctcccctggaGcctgaaccggcggagttcca	12	17	1	1			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr9:140247082G>T	ENST00000340951.4	-	11	1222	c.1027C>A	c.(1027-1029)Ctc>Atc	p.L343I	EXD3_ENST00000342129.4_Missense_Mutation_p.L23I	NM_017820.3	NP_060290.3	Q9NX53	MUT7B_HUMAN	exonuclease 3'-5' domain containing 3	0										NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)	12						CTCCCCTGGAGCCTGAACCGG	0.701																																					p.L343I		Atlas-SNP	.											.	EXD3	86	.	0			c.C1027A						.						4	6	6					9																	140247082		1738	3751	5489	SO:0001583	missense	54932	exon11			CCTGGAGCCTGAA		CCDS48066.1, CCDS75942.1	9q34.3	2009-03-04			ENSG00000187609	ENSG00000187609			26023	protein-coding gene	gene with protein product							Standard	XM_005266093		Approved	LOC54932, FLJ20433, mut-7	uc004cmp.2	Q8N9H8	OTTHUMG00000156149	ENST00000340951.4:c.1027C>A	chr9.hg19:g.140247082G>T	ENSP00000340474:p.Leu343Ile	53.0	0.0		65.0	4.0	NM_017820	Q6P1M1|Q8IXT8	Missense_Mutation	SNP	ENST00000340951.4	hg19	CCDS48066.1	.	.	.	.	.	.	.	.	.	.	G	7.327	0.618228	0.14129	.	.	ENSG00000187609	ENST00000342129;ENST00000340951	T;T	0.66460	-0.21;0.59	3.69	0.263	0.15602	.	0.735839	0.12406	N	0.471684	T	0.51024	0.1650	L	0.53249	1.67	0.09310	N	1	P;B	0.35745	0.518;0.158	B;B	0.32533	0.147;0.018	T	0.37478	-0.9704	10	0.30854	T	0.27	.	1.741	0.02952	0.1129:0.1746:0.3572:0.3554	.	23;343	Q8N9H8-3;Q8N9H8	.;MUT7_HUMAN	I	23;343	ENSP00000343705:L23I;ENSP00000340474:L343I	ENSP00000340474:L343I	L	-	1	0	EXD3	139366903	0.003000	0.15002	0.009000	0.14445	0.001000	0.01503	-0.126000	0.10563	0.163000	0.19507	-0.350000	0.07774	CTC	.	.		0.701	EXD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343182.1	NM_017820		T	140247082	G	T	140247082	3	4	327	1	0	0	0	0	1	0	0	0	5301	971	34	3	1651	3	EXD3	9	140247082	Missense_Mutation	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10	38338308	140247082	966349	55	45879										
AKR1E2	83592	hgsc.bcm.edu	37	chr10	4879675	4879675	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	tggaggacctggtgatcaccGggctggtgaagaacatcggg	17	8	1	3			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr10:4879675G>A	ENST00000298375.7	+	5	555	c.484G>A	c.(484-486)Ggg>Agg	p.G162R	AKR1E2_ENST00000525281.1_3'UTR|AKR1E2_ENST00000532248.1_Missense_Mutation_p.G162R|AKR1E2_ENST00000334019.4_Missense_Mutation_p.G162R|AKR1E2_ENST00000345253.5_Intron	NM_001040177.2	NP_001035267.1	Q96JD6	AKCL2_HUMAN	aldo-keto reductase family 1, member E2	162						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	1,5-anhydro-D-fructose reductase activity (GO:0050571)			NS(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)	15						GGTGATCACCGGGCTGGTGAA	0.507																																					p.G162R	NSCLC(43;343 1097 20371 28813 45509)	Atlas-SNP	.											.	AKR1E2	30	.	0			c.G484A						.						101	95	97					10																	4879675		2203	4300	6503	SO:0001583	missense	83592	exon5			ATCACCGGGCTGG	AB040820	CCDS31134.1, CCDS59210.1, CCDS59209.1	10p15.2	2009-09-09	2009-09-09	2009-09-09	ENSG00000165568	ENSG00000165568		"Aldo-keto reductases"	23437	protein-coding gene	gene with protein product			"aldo-keto reductase family 1, member C-like 2"	AKRDC1, AKR1CL2			Standard	NM_001271021		Approved	MGC10612	uc001ihi.4	Q96JD6	OTTHUMG00000017577	ENST00000298375.7:c.484G>A	chr10.hg19:g.4879675G>A	ENSP00000298375:p.Gly162Arg	92.0	0.0		108.0	41.0	NM_001040177	Q86Z16|Q86Z17|Q86Z18|Q9BU71	Missense_Mutation	SNP	ENST00000298375.7	hg19	CCDS31134.1	.	.	.	.	.	.	.	.	.	.	G	14.37	2.513869	0.44763	.	.	ENSG00000165568	ENST00000462718;ENST00000533295;ENST00000298375;ENST00000532248;ENST00000334019	D;T;T;T	0.87809	-2.3;-0.72;-0.72;-0.72	4.2	3.27	0.37495	Aldo/keto reductase, conserved site (1);NADP-dependent oxidoreductase domain (3);	0.000000	0.85682	D	0.000000	D	0.94578	0.8253	H	0.94222	3.51	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.95052	0.8188	10	0.72032	D	0.01	.	11.5482	0.50706	0.0:0.0:0.8199:0.1801	.	123;162;162;162	B7Z7K2;Q96JD6-2;Q96JD6;Q96JD6-3	.;.;AKCL2_HUMAN;.	R	58;166;162;162;162	ENSP00000435436:G166R;ENSP00000298375:G162R;ENSP00000432947:G162R;ENSP00000335034:G162R	ENSP00000298375:G162R	G	+	1	0	AKR1E2	4869675	1.000000	0.71417	0.557000	0.28306	0.012000	0.07955	6.848000	0.75409	1.314000	0.45095	0.455000	0.32223	GGG	.	.		0.507	AKR1E2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046520.4	NM_031436		A	4879675	G	A	4879675	3	1	327	1	0	0	0	0	1	0	0	0	474	1116	39	1	502	1	AKR1E2	10	4879675	Missense_Mutation	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10		4879675	130655072	56	45880										
ADAM12	8038	hgsc.bcm.edu	37	chr10	127760045	127760046	+	Splice_Site	DNP	CC	CC	AA													0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	tgttctgggaatggttcttaCctctggctccccacagtcac							TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr10:127760045_127760046CC>AA	ENST00000368679.4	-	12	1641_1642	c.1332_1333GG>TT	c.(1330-1335)gaGGaa>gaTTaa	p.444_445EE>D*	ADAM12_ENST00000467145.1_5'Flank|ADAM12_ENST00000368676.4_Splice_Site_p.444_445EE>D*	NM_003474.4	NP_003465.3	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12	444	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				cell adhesion (GO:0007155)|epidermal growth factor receptor signaling pathway (GO:0007173)|myoblast fusion (GO:0007520)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(7)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)		ATGGTTCTTACCTCTGGCTCCC	0.5																																					.|p.E444D		Atlas-SNP	.											.	ADAM12	388	.	0			c.1332+1G>T|c.G1332T						.																																			SO:0001630	splice_region_variant	8038	exon13|exon12			TTCTTACCTCTGG|TCTTACCTCTGGC	AF023476	CCDS7653.1, CCDS7654.1	10q26	2008-07-29	2008-07-29		ENSG00000148848	ENSG00000148848		"ADAM metallopeptidase domain containing"	190	protein-coding gene	gene with protein product	"meltrin alpha"	602714	"a disintegrin and metalloproteinase domain 12 (meltrin alpha)"			9417060, 18342566	Standard	NM_003474		Approved	MCMPMltna, MLTN	uc001ljk.2	O43184	OTTHUMG00000019243	ENST00000368679.4:c.1332_1333delinsAA	chr10.hg19:g.127760045_127760046delinsAA		210.0|211.0	0.0		95.0|96.0	47.0	NM_003474|NM_021641	O60470|Q5JRP0|Q5JRP1|Q6P9E3|Q6UWB0	Splice_Site|Missense_Mutation	SNP	ENST00000368679.4	hg19	CCDS7653.1																																																																																			.	.		0.5	ADAM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050961.1		Nonsense_Mutation	AA	127760046	CC	AA	127760045	5	1	327	1	0	0	0	0	0	0	1	0	236	521	18	3	1552	3	ADAM12	10	127760045	Splice_Site	DNP	CC	TCGA-NI-A4U2-01A-11D-A28X-10	122880370	127760045	7774702	57	45881										
MUC2	4583	hgsc.bcm.edu	37	chr11	1095258	1095258	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	ccaacacccacgccctccaaGtcgacgcccacgccttccaa	5	22	0	0			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr11:1095258G>A	ENST00000441003.2	+	32	6105	c.6078G>A	c.(6076-6078)aaG>aaA	p.K2026K	MUC2_ENST00000333592.6_3'UTR|MUC2_ENST00000361558.6_Silent_p.K164K	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4388					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	CGCCCTCCAAGTCGACGCCCA	0.612																																					p.K2022K		Atlas-SNP	.											.	MUC2	614	.	0			c.G6066A						.						77	99	92					11																	1095258		2130	4223	6353	SO:0001819	synonymous_variant	4583	exon33			CTCCAAGTCGACG	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.6078G>A	chr11.hg19:g.1095258G>A		153.0	0.0		169.0	19.0	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	hg19																																																																																				.	.		0.612	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		A	1095258	G	A	1095258	2	1	327	1	0	0	0	0	0	0	0	1	9984	1020	36	3		3	MUC2	11	1095258	Silent	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10		1095258	133911258	58	45882										
NUP98	4928	hgsc.bcm.edu	37	chr11	3707425	3707425	+	Splice_Site	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	gctggttgagatcataatgtCtgcaaagaacgtgttgagag	13	5	2	3			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr11:3707425C>G	ENST00000324932.7	-	29	4875		c.e29-1		NUP98_ENST00000355260.3_Intron|NUP98_ENST00000359171.4_Intron	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa						carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|DNA replication (GO:0006260)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore organization (GO:0006999)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nuclear pore outer ring (GO:0031080)|nucleoplasm (GO:0005654)	peptide binding (GO:0042277)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		ATCATAATGTCTGCAAAGAAC	0.483			T	"HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"	AML																																.		Atlas-SNP	.		Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	.	NUP98	149	.	0			c.4455-1G>C						.						79	67	71					11																	3707425		2201	4298	6499	SO:0001630	splice_region_variant	4928	exon30			TAATGTCTGCAAA	AF071076, AF231130, BC012906, BG773331	CCDS7746.1, CCDS31347.1, CCDS41605.1, CCDS41606.1	11p15	2008-02-26	2002-08-29		ENSG00000110713	ENSG00000110713			8068	protein-coding gene	gene with protein product		601021	"nucleoporin 98kD"			9166830	Standard	NM_139131		Approved	NUP96	uc001lyh.3	P52948	OTTHUMG00000011846	ENST00000324932.7:c.4455-1G>C	chr11.hg19:g.3707425C>G		110.0	0.0		109.0	38.0	NM_016320	Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Splice_Site	SNP	ENST00000324932.7	hg19	CCDS7746.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.472871	0.84640	.	.	ENSG00000110713	ENST00000324932;ENST00000429801	.	.	.	5.59	5.59	0.84812	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.9921	0.92796	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NUP98	3664001	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	7.575000	0.82447	2.805000	0.96524	0.650000	0.86243	.	.	.		0.483	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	NM_016320	Intron	G	3707425	C	G	3707425	5	3	327	1	0	0	0	0	0	0	1	0	10782	927	32	4	968	4	NUP98	11	3707425	Splice_Site	SNP	C	TCGA-NI-A4U2-01A-11D-A28X-10	2612167	3707425	131299091	59	45883										
IPO7	10527	hgsc.bcm.edu	37	chr11	9450696	9450696	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	tagagaaatgcctgtgaaagTggaagctgccattgcccttc	11	9	0	2			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr11:9450696T>A	ENST00000379719.3	+	14	1686	c.1544T>A	c.(1543-1545)gTg>gAg	p.V515E	CTD-2371O3.2_ENST00000531111.1_RNA|SNORA23_ENST00000365128.1_RNA	NM_006391.2	NP_006382.1	O95373	IPO7_HUMAN	importin 7	515					innate immune response (GO:0045087)|protein import into nucleus (GO:0006606)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	Ran GTPase binding (GO:0008536)|small GTPase regulator activity (GO:0005083)|transporter activity (GO:0005215)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(12)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				all cancers(16;8.29e-09)|Epithelial(150;4.76e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0217)		CCTGTGAAAGTGGAAGCTGCC	0.388																																					p.V515E		Atlas-SNP	.											.	IPO7	72	.	0			c.T1544A						.						85	82	83					11																	9450696		2201	4293	6494	SO:0001583	missense	10527	exon14			TGAAAGTGGAAGC	AF098799	CCDS31425.1	11p15.3	2010-12-02	2003-03-11	2003-03-14	ENSG00000205339	ENSG00000205339		"Importins"	9852	protein-coding gene	gene with protein product		605586	"RAN binding protein 7"	RANBP7		9214382	Standard	NM_006391		Approved	Imp7	uc001mho.3	O95373	OTTHUMG00000165753	ENST00000379719.3:c.1544T>A	chr11.hg19:g.9450696T>A	ENSP00000369042:p.Val515Glu	156.0	0.0		119.0	31.0	NM_006391	A6NNM5|B2R786|Q1RMF7|Q9H177|Q9NTE3	Missense_Mutation	SNP	ENST00000379719.3	hg19	CCDS31425.1	.	.	.	.	.	.	.	.	.	.	T	28.7	4.941537	0.92526	.	.	ENSG00000205339	ENST00000379719	T	0.65549	-0.16	5.95	5.95	0.96441	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.82226	0.4991	M	0.87381	2.88	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85406	0.1134	10	0.87932	D	0	.	16.4237	0.83790	0.0:0.0:0.0:1.0	.	515	O95373	IPO7_HUMAN	E	515	ENSP00000369042:V515E	ENSP00000369042:V515E	V	+	2	0	IPO7	9407272	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.040000	0.89188	2.279000	0.76181	0.533000	0.62120	GTG	.	.		0.388	IPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386022.1	NM_006391		A	9450696	T	A	9450696	3	1	327	1	0	0	0	0	1	0	0	0	7806	1696	59	4	1598	4	IPO7	11	9450696	Missense_Mutation	SNP	T	TCGA-NI-A4U2-01A-11D-A28X-10	5743271	9450696	125555820	60	45884										
CTR9	9646	hgsc.bcm.edu	37	chr11	10796824	10796824	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	ccaaaccaaaaaaacgacgtCcaccaaaagcagagaagaaa	6	11	0	2			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr11:10796824C>A	ENST00000361367.2	+	23	3382	c.2956C>A	c.(2956-2958)Cca>Aca	p.P986T		NM_014633.3	NP_055448.1	Q6PD62	CTR9_HUMAN	CTR9, Paf1/RNA polymerase II complex component	986	Lys-rich.				cellular response to lipopolysaccharide (GO:0071222)|endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone H3-K4 trimethylation (GO:0080182)|histone monoubiquitination (GO:0010390)|interleukin-6-mediated signaling pathway (GO:0070102)|JAK-STAT cascade (GO:0007259)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K79 methylation (GO:2001162)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|transcriptionally active chromatin (GO:0035327)				breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(12)|ovary(2)|pancreas(1)|stomach(1)	40				all cancers(16;1.64e-07)|Epithelial(150;2.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		AAAACGACGTCCACCAAAAGC	0.383																																					p.P986T		Atlas-SNP	.											.	CTR9	94	.	0			c.C2956A						.						110	103	106					11																	10796824		2201	4294	6495	SO:0001583	missense	9646	exon23			CGACGTCCACCAA	D63875	CCDS7805.1	11p15.3	2013-07-03	2013-07-03	2006-05-22	ENSG00000198730	ENSG00000198730		"Tetratricopeptide (TTC) repeat domain containing"	16850	protein-coding gene	gene with protein product		609366	"SH2 domain binding protein 1 (tetratricopeptide repeat containing)", "Ctr9, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)"	SH2BP1		8590280, 8636124	Standard	NM_014633		Approved	KIAA0155, TSBP, p150TSP	uc001mja.3	Q6PD62	OTTHUMG00000165789	ENST00000361367.2:c.2956C>A	chr11.hg19:g.10796824C>A	ENSP00000355013:p.Pro986Thr	66.0	0.0		46.0	20.0	NM_014633	D3DQV8|Q15015	Missense_Mutation	SNP	ENST00000361367.2	hg19	CCDS7805.1	.	.	.	.	.	.	.	.	.	.	C	1.046	-0.677318	0.03378	.	.	ENSG00000198730	ENST00000361367	T	0.40476	1.03	5.55	1.37	0.22104	.	0.267927	0.43747	N	0.000540	T	0.22437	0.0541	N	0.14661	0.345	0.09310	N	0.999995	B	0.02656	0.0	B	0.01281	0.0	T	0.16719	-1.0393	10	0.25751	T	0.34	-0.1623	9.6251	0.39746	0.3591:0.5773:0.0:0.0636	.	986	Q6PD62	CTR9_HUMAN	T	986	ENSP00000355013:P986T	ENSP00000355013:P986T	P	+	1	0	CTR9	10753400	0.027000	0.19231	0.339000	0.25562	0.025000	0.11179	0.815000	0.27253	0.276000	0.22118	-0.244000	0.11960	CCA	.	.		0.383	CTR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386215.1	NM_014633		A	10796824	C	A	10796824	3	1	327	1	0	0	0	0	1	0	0	0	4026	855	30	3	3046	3	CTR9	11	10796824	Missense_Mutation	SNP	C	TCGA-NI-A4U2-01A-11D-A28X-10	1346128	10796824	124209692	61	45885										
ARHGAP20	57569	hgsc.bcm.edu	37	chr11	110477435	110477435	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	tgtcaggagtgcagagtctcGaagatggctcattttaattc	11	7	3	2			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr11:110477435G>A	ENST00000260283.4	-	10	1098	c.814C>T	c.(814-816)Cga>Tga	p.R272*	ARHGAP20_ENST00000527598.1_Nonsense_Mutation_p.R236*|ARHGAP20_ENST00000524756.1_Nonsense_Mutation_p.R249*|ARHGAP20_ENST00000528829.1_Nonsense_Mutation_p.R236*|ARHGAP20_ENST00000357139.3_Nonsense_Mutation_p.R246*|ARHGAP20_ENST00000533353.1_Nonsense_Mutation_p.R246*	NM_020809.3	NP_065860.2	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20	272	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(18)|lung(13)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	60		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;3.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|all cancers(92;0.000147)|OV - Ovarian serous cystadenocarcinoma(223;0.0475)		GCAGAGTCTCGAAGATGGCTC	0.483																																					p.R272X		Atlas-SNP	.											.	ARHGAP20	150	.	0			c.C814T						.						154	156	155					11																	110477435		2201	4298	6499	SO:0001587	stop_gained	57569	exon10			AGTCTCGAAGATG	AB037812	CCDS31673.1, CCDS58175.1, CCDS58176.1, CCDS58177.1	11q23.2	2011-06-29			ENSG00000137727	ENSG00000137727		"Rho GTPase activating proteins"	18357	protein-coding gene	gene with protein product		609568				14532992	Standard	NM_020809		Approved	KIAA1391	uc001pkz.2	Q9P2F6	OTTHUMG00000166590	ENST00000260283.4:c.814C>T	chr11.hg19:g.110477435G>A	ENSP00000260283:p.Arg272*	72.0	0.0		55.0	12.0	NM_020809	A8K8C5|B0YIW7|B0YIW8|Q6RJU1|Q6RJU2|Q6RJU3|Q6RJU5|Q8IXS1	Nonsense_Mutation	SNP	ENST00000260283.4	hg19	CCDS31673.1	.	.	.	.	.	.	.	.	.	.	G	38	7.177823	0.98114	.	.	ENSG00000137727	ENST00000260283;ENST00000357139;ENST00000524756;ENST00000528829;ENST00000533353;ENST00000527598	.	.	.	5.41	4.48	0.54585	.	0.058925	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.3081	0.82856	0.0:0.1326:0.8673:0.0	.	.	.	.	X	272;246;249;236;246;236	.	ENSP00000260283:R272X	R	-	1	2	ARHGAP20	109982645	1.000000	0.71417	0.997000	0.53966	0.642000	0.38348	4.177000	0.58276	1.367000	0.46095	0.650000	0.86243	CGA	.	.		0.483	ARHGAP20-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390628.1	NM_020809		A	110477435	G	A	110477435	4	1	327	1	0	0	0	0	0	1	0	0	870	1066	37	1	2789	1	ARHGAP20	11	110477435	Nonsense_Mutation	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10	99680611	110477435	24529081	62	45886										
BCO2	83875	hgsc.bcm.edu	37	chr11	112064703	112064703	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	aagtggacattgaaactctgGaaaaaacagaaaaggtaaag	10	4	1	2	rs556041453		TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr11:112064703G>T	ENST00000357685.5	+	4	754	c.619G>T	c.(619-621)Gaa>Taa	p.E207*	BCO2_ENST00000526088.1_Nonsense_Mutation_p.E173*|BCO2_ENST00000532593.1_Nonsense_Mutation_p.E102*|AP002884.3_ENST00000532612.1_Intron|BCO2_ENST00000393032.2_Nonsense_Mutation_p.E173*|BCO2_ENST00000531169.1_Nonsense_Mutation_p.E173*|BCO2_ENST00000438022.1_Nonsense_Mutation_p.E173*|BCO2_ENST00000361053.4_Intron			Q9BYV7	BCDO2_HUMAN	beta-carotene oxygenase 2	207					carotene catabolic process (GO:0016121)|carotene metabolic process (GO:0016119)|carotenoid metabolic process (GO:0016116)|oxidation-reduction process (GO:0055114)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of reactive oxygen species metabolic process (GO:2000377)|retinal metabolic process (GO:0042574)|retinoic acid metabolic process (GO:0042573)	intracellular (GO:0005622)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			NS(1)|breast(1)|kidney(3)|large_intestine(1)|lung(9)|skin(1)	16						TGAAACTCTGGAAAAAACAGA	0.318																																					p.E207X	GBM(177;1916 2099 21049 29541 39946)	Atlas-SNP	.											.	BCO2	44	.	0			c.G619T						.						74	71	72					11																	112064703		2201	4297	6498	SO:0001587	stop_gained	83875	exon4			ACTCTGGAAAAAA	AJ290393	CCDS8358.2, CCDS41716.1, CCDS58181.1, CCDS58182.1, CCDS58183.1	11q23.1	2014-05-12	2008-04-15	2008-04-15	ENSG00000197580	ENSG00000197580	1.13.11.71		18503	protein-coding gene	gene with protein product	"beta-carotene 9',10' oxygenase", "carotenoid-9',10'-cleaving dioxygenase"	611740	"beta-carotene dioxygenase 2"	BCDO2		11278918, 15983114, 15949678	Standard	NM_031938		Approved	FLJ34464, B-DIOX-II	uc001pnf.3	Q9BYV7	OTTHUMG00000167155	ENST00000357685.5:c.619G>T	chr11.hg19:g.112064703G>T	ENSP00000350314:p.Glu207*	71.0	0.0		68.0	16.0	NM_031938	B0YIX5|B4DNC3|E9PBI8|E9PJJ1|Q8IUS0|Q96JC8|Q96JY5	Nonsense_Mutation	SNP	ENST00000357685.5	hg19	CCDS8358.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	34|34	5.372167|5.372167	0.95923|0.95923	.|.	.|.	ENSG00000197580|ENSG00000197580	ENST00000357685;ENST00000393032;ENST00000438022;ENST00000526088;ENST00000532593;ENST00000531169|ENST00000530677	.|.	.|.	.|.	5.07|5.07	4.15|4.15	0.48705|0.48705	.|.	0.217660|.	0.46758|.	D|.	0.000269|.	.|T	.|0.66396	.|0.2785	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.71873	.|-0.4461	.|3	0.72032|.	D|.	0.01|.	-14.2432|-14.2432	15.3094|15.3094	0.74019|0.74019	0.0:0.1493:0.8507:0.0|0.0:0.1493:0.8507:0.0	.|.	.|.	.|.	.|.	X|V	207;173;173;173;102;173|105	.|.	ENSP00000350314:E207X|.	E|G	+|+	1|2	0|0	BCO2|BCO2	111569913|111569913	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.940000|0.940000	0.58332|0.58332	4.305000|4.305000	0.59110|0.59110	1.106000|1.106000	0.41623|0.41623	0.563000|0.563000	0.77884|0.77884	GAA|GGA	.	.		0.318	BCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256570.3	NM_001037290		T	112064703	G	T	112064703	4	4	327	1	0	0	0	0	0	1	0	0	1385	1175	41	3	633	3	BCO2	11	112064703	Nonsense_Mutation	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10	1587268	112064703	22941813	63	45887										
USP2	9099	hgsc.bcm.edu	37	chr11	119228275	119228275	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	gtgagcttgctggttcggatCctggattctgagaaccgctt	13	9	1	2			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr11:119228275C>T	ENST00000260187.2	-	11	1821	c.1527G>A	c.(1525-1527)agG>agA	p.R509R	USP2_ENST00000455332.2_Silent_p.R266R|USP2_ENST00000525735.1_Silent_p.R300R	NM_004205.4	NP_004196.4	O75604	UBP2_HUMAN	ubiquitin specific peptidase 2	509	USP.				cell cycle (GO:0007049)|muscle organ development (GO:0007517)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of skeletal muscle tissue development (GO:0048643)|protein deubiquitination (GO:0016579)|protein stabilization (GO:0050821)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell cortex (GO:0005938)|centrosome (GO:0005813)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cyclin binding (GO:0030332)|cysteine-type endopeptidase activity (GO:0004197)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	24		all_hematologic(192;4.65e-05)|Breast(348;0.0101)|all_neural(223;0.0218)|Medulloblastoma(222;0.0425)|Renal(330;0.157)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.000513)|Colorectal(284;0.0116)|Lung(307;0.0853)|LUSC - Lung squamous cell carcinoma(976;0.0889)		tggttcggatcctggattctg	0.463																																					p.R509R		Atlas-SNP	.											.	USP2	71	.	0			c.G1527A						.						79	80	80					11																	119228275		2199	4295	6494	SO:0001819	synonymous_variant	9099	exon11			TCGGATCCTGGAT	AF079564	CCDS8422.1, CCDS8423.1, CCDS58189.1	11q23.3	2008-02-05	2005-08-08			ENSG00000036672		"Ubiquitin-specific peptidases"	12618	protein-coding gene	gene with protein product		604725	"ubiquitin specific protease 2"			12838346	Standard	NM_004205		Approved	UBP41	uc001pwm.4	O75604		ENST00000260187.2:c.1527G>A	chr11.hg19:g.119228275C>T		115.0	0.0		132.0	50.0	NM_004205	B0YJB8|E9PPM2|Q8IUM2|Q8IW04|Q96MB9|Q9BQ21	Silent	SNP	ENST00000260187.2	hg19	CCDS8422.1																																																																																			.	.		0.463	USP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388361.2	NM_171997		T	119228275	C	T	119228275	2	4	327	1	0	0	0	0	0	0	0	1	17066	854	30	3		3	USP2	11	119228275	Silent	SNP	C	TCGA-NI-A4U2-01A-11D-A28X-10	7163572	119228275	15778241	64	45888										
NANOG	79923	hgsc.bcm.edu	37	chr12	7945627	7945627	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	tcccaaaggcaaacaacccaCttctgcagagaagagtgtcg	9	12	1	2			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr12:7945627C>T	ENST00000229307.4	+	2	452	c.233C>T	c.(232-234)aCt>aTt	p.T78I	NANOG_ENST00000526286.1_Missense_Mutation_p.T78I	NM_024865.2	NP_079141.2	Q9H9S0	NANOG_HUMAN	Nanog homeobox	78					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|embryo development (GO:0009790)|embryonic pattern specification (GO:0009880)|endodermal cell fate specification (GO:0001714)|gonad development (GO:0008406)|mesodermal cell fate commitment (GO:0001710)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell fate commitment (GO:0010454)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell differentiation (GO:0045595)|regulation of gene expression (GO:0010468)|regulation of transcription, DNA-templated (GO:0006355)|response to retinoic acid (GO:0032526)|somatic stem cell maintenance (GO:0035019)|stem cell division (GO:0017145)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enhancer sequence-specific DNA binding (GO:0001158)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	14				Kidney(36;0.0872)		AAACAACCCACTTCTGCAGAG	0.473																																					p.T78I		Atlas-SNP	.											.	NANOG	30	.	0			c.C233T						.						83	77	79					12																	7945627		2202	4295	6497	SO:0001583	missense	79923	exon2			AACCCACTTCTGC	AB093576	CCDS31736.1, CCDS73436.1	12p13.31	2011-06-20			ENSG00000111704	ENSG00000111704		"Homeoboxes / ANTP class : NKL subclass"	20857	protein-coding gene	gene with protein product		607937				12787505, 12787504	Standard	XM_005253484		Approved	FLJ12581, FLJ40451	uc009zfy.1	Q9H9S0		ENST00000229307.4:c.233C>T	chr12.hg19:g.7945627C>T	ENSP00000229307:p.Thr78Ile	194.0	0.0		134.0	62.0	NM_024865	D3DUU4|Q2TTG0|Q6JZS5	Missense_Mutation	SNP	ENST00000229307.4	hg19	CCDS31736.1	.	.	.	.	.	.	.	.	.	.	.	13.57	2.275830	0.40294	.	.	ENSG00000111704	ENST00000541267;ENST00000229307;ENST00000526286	D;D;D	0.91686	-2.88;-2.89;-2.88	4.42	-2.41	0.06562	Homeodomain-related (1);	2.536840	0.01075	N	0.004894	D	0.85566	0.5726	L	0.29908	0.895	0.09310	N	1	P	0.43885	0.82	B	0.42555	0.391	T	0.75566	-0.3273	10	0.39692	T	0.17	5.0072	0.335	0.00325	0.274:0.3064:0.1421:0.2775	.	78	Q9H9S0	NANOG_HUMAN	I	54;78;78	ENSP00000444434:T54I;ENSP00000229307:T78I;ENSP00000435288:T78I	ENSP00000229307:T78I	T	+	2	0	NANOG	7836894	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.390000	0.07332	-0.829000	0.04268	0.456000	0.33151	ACT	.	.		0.473	NANOG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387480.2	NM_024865		T	7945627	C	T	7945627	3	4	327	1	0	0	0	0	1	0	0	0	10159	565	20	3	239	3	NANOG	12	7945627	Missense_Mutation	SNP	C	TCGA-NI-A4U2-01A-11D-A28X-10		7945627	125906268	65	45889										
OR9K2	441639	hgsc.bcm.edu	37	chr12	55524128	55524128	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	agcatgacatttactttatcTttttgcgcttctcgggctgt	8	9	2	1			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr12:55524128T>C	ENST00000305377.5	+	1	664	c.576T>C	c.(574-576)tcT>tcC	p.S192S		NM_001005243.1	NP_001005243.1	Q8NGE7	OR9K2_HUMAN	olfactory receptor, family 9, subfamily K, member 2	192						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S192S(1)		NS(2)|breast(3)|central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(2)	31						TTACTTTATCTTTTTGCGCTT	0.408																																					p.S192S		Atlas-SNP	.											OR9K2,NS,carcinoma,0,1	OR9K2	63	.	1	Substitution - coding silent(1)	lung(1)	c.T576C						.						153	141	145					12																	55524128		2203	4300	6503	SO:0001819	synonymous_variant	441639	exon1			TTTATCTTTTTGC	BK004326	CCDS31814.1	12q13.2	2012-08-09						"GPCR / Class A : Olfactory receptors"	15339	protein-coding gene	gene with protein product							Standard	NM_001005243		Approved		uc010spe.2	Q8NGE7	OTTHUMG00000169827	ENST00000305377.5:c.576T>C	chr12.hg19:g.55524128T>C		107.0	1.0		96.0	33.0	NM_001005243	B9EH19|Q6IFD6	Silent	SNP	ENST00000305377.5	hg19	CCDS31814.1																																																																																			.	.		0.408	OR9K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406105.1			C	55524128	T	C	55524128	2	2	327	1	0	0	0	0	0	0	0	1	11263	1596	56	2		2	OR9K2	12	55524128	Silent	SNP	T	TCGA-NI-A4U2-01A-11D-A28X-10	47578501	55524128	78327767	66	45890										
TMBIM4	51643	hgsc.bcm.edu	37	chr12	66531753	66531753	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	cttttaattactttttattaActgcttccagaaaccgtaac	3	9	0	1			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr12:66531753A>C	ENST00000358230.3	-	7	824	c.704T>G	c.(703-705)gTt>gGt	p.V235G	TMBIM4_ENST00000539652.1_3'UTR|TMBIM4_ENST00000556010.1_3'UTR|TMBIM4_ENST00000542724.1_Missense_Mutation_p.V204G|TMBIM4_ENST00000286424.7_Missense_Mutation_p.V282G|TMBIM4_ENST00000398033.4_3'UTR|TMBIM4_ENST00000544599.1_Missense_Mutation_p.V58G	NM_016056.2	NP_057140.2	Q9HC24	LFG4_HUMAN	transmembrane BAX inhibitor motif containing 4	235					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|regulation of calcium-mediated signaling (GO:0050848)	Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(4)|ovary(1)|prostate(2)	9				GBM - Glioblastoma multiforme(28;0.0745)		CTTTTTATTAACTGCTTCCAG	0.333																																					p.V235G		Atlas-SNP	.											.	TMBIM4	47	.	0			c.T704G						.						94	89	90					12																	66531753		1844	4084	5928	SO:0001583	missense	51643	exon7			TTATTAACTGCTT	AF113127	CCDS41805.1, CCDS61187.1, CCDS73493.1	12q14.3	2014-05-09			ENSG00000155957	ENSG00000155957			24257	protein-coding gene	gene with protein product						11042152, 10810093	Standard	NM_001282609		Approved	CGI-119, S1R, ZPRO, LFG4, GAAP	uc001stc.3	Q9HC24	OTTHUMG00000168973	ENST00000358230.3:c.704T>G	chr12.hg19:g.66531753A>C	ENSP00000350965:p.Val235Gly	55.0	0.0		51.0	16.0	NM_016056	Q542Z6|Q9UHY5|Q9Y3C2	Missense_Mutation	SNP	ENST00000358230.3	hg19	CCDS41805.1	.	.	.	.	.	.	.	.	.	.	A	11.84	1.758419	0.31137	.	.	ENSG00000155957	ENST00000358230;ENST00000544599;ENST00000286424;ENST00000539427;ENST00000542724	T;T;T	0.48522	1.42;1.4;0.81	5.87	3.53	0.40419	.	0.272984	0.33005	N	0.005381	T	0.21509	0.0518	N	0.02708	-0.52	0.80722	D	1	B;B;B	0.09022	0.002;0.001;0.001	B;B;B	0.18263	0.021;0.005;0.002	T	0.04065	-1.0980	9	.	.	.	-10.7337	10.4472	0.44501	0.8687:0.0:0.1313:0.0	.	282;204;235	G3XAA5;G3V1M2;Q9HC24	.;.;TMBI4_HUMAN	G	235;58;282;280;204	ENSP00000350965:V235G;ENSP00000286424:V282G;ENSP00000441291:V204G	.	V	-	2	0	TMBIM4	64818020	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.386000	0.59620	0.571000	0.29365	0.533000	0.62120	GTT	.	.		0.333	TMBIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401832.2	NM_016056		C	66531753	A	C	66531753	3	2	327	1	0	0	0	0	1	0	0	0	15997	43	2	5	16	5	TMBIM4	12	66531753	Missense_Mutation	SNP	A	TCGA-NI-A4U2-01A-11D-A28X-10	11007625	66531753	67320142	67	45891										
LRRIQ1	84125	hgsc.bcm.edu	37	chr12	85518185	85518185	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	aaatattagtatgtcagaagAgagaagacagcaaggcaagc	11	5	1	4			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr12:85518185A>T	ENST00000393217.2	+	17	3956	c.3895A>T	c.(3895-3897)Aga>Tga	p.R1299*		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	1299										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		ATGTCAGAAGAGAGAAGACAG	0.413																																					p.R1299X		Atlas-SNP	.											.	LRRIQ1	512	.	0			c.A3895T						.						165	178	173					12																	85518185		2203	4300	6503	SO:0001587	stop_gained	84125	exon17			CAGAAGAGAGAAG	AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.3895A>T	chr12.hg19:g.85518185A>T	ENSP00000376910:p.Arg1299*	76.0	0.0		78.0	27.0	NM_001079910	Q567P4|Q9BS17|Q9HA36	Nonsense_Mutation	SNP	ENST00000393217.2	hg19	CCDS41816.1	.	.	.	.	.	.	.	.	.	.	A	38	7.261921	0.98171	.	.	ENSG00000133640	ENST00000256007;ENST00000378580;ENST00000393217	.	.	.	5.39	5.39	0.77823	.	1.220000	0.06013	N	0.649856	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.5212	0.44920	0.8562:0.0:0.0:0.1438	.	.	.	.	X	1299;1274;1299	.	ENSP00000256007:R1299X	R	+	1	2	LRRIQ1	84042316	0.017000	0.18338	0.002000	0.10522	0.011000	0.07611	1.182000	0.32029	2.043000	0.60533	0.482000	0.46254	AGA	.	.		0.413	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165		T	85518185	A	T	85518185	4	4	327	1	0	0	0	0	0	1	0	0	9038	296	11	4	3957	4	LRRIQ1	12	85518185	Nonsense_Mutation	SNP	A	TCGA-NI-A4U2-01A-11D-A28X-10	18986432	85518185	48333710	68	45892										
LRRIQ1	84125	hgsc.bcm.edu	37	chr12	85554390	85554390	+	Splice_Site	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	tttcttattcgttttgtttaGattccactgtgcgtctagcc	7	9	2	1			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr12:85554390G>C	ENST00000393217.2	+	24	4781		c.e24-1		LRRIQ1_ENST00000528777.3_Splice_Site	NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1											breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		GTTTTGTTTAGATTCCACTGT	0.343																																					.		Atlas-SNP	.											.	LRRIQ1	512	.	0			c.4721-1G>C						.						113	102	105					12																	85554390		1822	4093	5915	SO:0001630	splice_region_variant	84125	exon24			TGTTTAGATTCCA	AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.4721-1G>C	chr12.hg19:g.85554390G>C		50.0	0.0		52.0	23.0	NM_001079910	Q567P4|Q9BS17|Q9HA36	Splice_Site	SNP	ENST00000393217.2	hg19	CCDS41816.1	.	.	.	.	.	.	.	.	.	.	G	10.74	1.436600	0.25813	.	.	ENSG00000133640	ENST00000393217	.	.	.	4.76	3.86	0.44501	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4921	0.67657	0.0:0.0:0.8517:0.1483	.	.	.	.	.	-1	.	.	.	+	.	.	LRRIQ1	84078521	1.000000	0.71417	0.995000	0.50966	0.417000	0.31264	4.755000	0.62198	1.083000	0.41159	0.650000	0.86243	.	.	.		0.343	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165	Intron	C	85554390	G	C	85554390	5	2	327	1	0	0	0	0	0	0	1	0	9038	956	33	4	4814	4	LRRIQ1	12	85554390	Splice_Site	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10	36205	85554390	48297505	69	45893										
HNF1A	6927	hgsc.bcm.edu	37	chr12	121431983	121431983	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	gcagggcggaatgcatccagAgaggggtgtccccatcacag	15	11	1	1			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr12:121431983A>G	ENST00000257555.6	+	4	956	c.730A>G	c.(730-732)Aga>Gga	p.R244G	HNF1A_ENST00000541395.1_Missense_Mutation_p.R244G|HNF1A_ENST00000544413.1_Missense_Mutation_p.R244G|HNF1A_ENST00000400024.2_Missense_Mutation_p.R244G|HNF1A_ENST00000402929.1_Missense_Mutation_p.R244G|HNF1A_ENST00000538626.1_Intron|HNF1A_ENST00000543427.1_Missense_Mutation_p.R127G			P20823	HNF1A_HUMAN	HNF1 homeobox A	244			R -> G (in a hepatic adenoma sample; somatic mutation; expected to interfere with DNA binding). {ECO:0000269|PubMed:12355088}.		glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.R244G(2)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					ATGCATCCAGAGAGGGGTGTC	0.602									Hepatic Adenoma, Familial Clustering of																												p.R244G		Atlas-SNP	.											HNF1A,NS,other,0,2	HNF1A	302	.	2	Substitution - Missense(2)	liver(2)	c.A730G						.						34	35	35					12																	121431983		2203	4300	6503	SO:0001583	missense	6927	exon4	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	ATCCAGAGAGGGG	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100		"Homeoboxes / HNF class"	11621	protein-coding gene	gene with protein product		142410	"transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor"	MODY3, TCF1		1535333, 7795649	Standard	NM_000545		Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	ENST00000257555.6:c.730A>G	chr12.hg19:g.121431983A>G	ENSP00000257555:p.Arg244Gly	150.0	1.0		163.0	46.0	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Missense_Mutation	SNP	ENST00000257555.6	hg19	CCDS9209.1	.	.	.	.	.	.	.	.	.	.	A	35	5.423542	0.96111	.	.	ENSG00000135100	ENST00000257555;ENST00000535125;ENST00000543536;ENST00000544680;ENST00000537424;ENST00000543427;ENST00000545458;ENST00000541395;ENST00000340577;ENST00000344370;ENST00000544413	D;D;D;D	0.95622	-3.76;-3.76;-3.76;-3.76	4.84	4.84	0.62591	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.97151	0.9069	M	0.70595	2.14	0.54753	D	0.999986	D;D;D;D	0.89917	1.0;1.0;1.0;0.998	D;D;D;D	0.85130	0.997;0.995;0.994;0.969	D	0.97740	1.0208	10	0.87932	D	0	-35.8616	13.6279	0.62178	1.0:0.0:0.0:0.0	.	244;244;244;244	F5H0K0;P20823;E7EUQ4;E7EMR0	.;HNF1A_HUMAN;.;.	G	244;244;244;244;244;127;244;244;244;244;244	ENSP00000257555:R244G;ENSP00000439721:R127G;ENSP00000443112:R244G;ENSP00000438804:R244G	ENSP00000257555:R244G	R	+	1	2	HNF1A	119916366	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	2.421000	0.44688	1.820000	0.53075	0.335000	0.21663	AGA	.	.		0.602	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545		G	121431983	A	G	121431983	3	3	327	1	0	0	0	0	1	0	0	0	7260	296	11	2	744	2	HNF1A	12	121431983	Missense_Mutation	SNP	A	TCGA-NI-A4U2-01A-11D-A28X-10	35877593	121431983	12419912	70	45894										
HNF1A	6927	hgsc.bcm.edu	37	chr12	121434162	121434162	+	Silent	SNP	G	G	T													0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	tctacacccctccaccaagtGtcccccacgggcctggagcc							TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr12:121434162G>T	ENST00000257555.6	+	5	1279	c.1053G>T	c.(1051-1053)gtG>gtT	p.V351V	HNF1A_ENST00000541395.1_Silent_p.V351V|HNF1A_ENST00000544413.1_Silent_p.V351V|HNF1A_ENST00000400024.2_Silent_p.V351V|HNF1A_ENST00000402929.1_Silent_p.V351V|HNF1A_ENST00000538626.1_Intron|HNF1A_ENST00000543427.1_Silent_p.V234V			P20823	HNF1A_HUMAN	HNF1 homeobox A	351					glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					TCCACCAAGTGTCCCCCACGG	0.582									Hepatic Adenoma, Familial Clustering of																												p.V351V		Atlas-SNP	.											.	HNF1A	302	.	0			c.G1053T	GRCh37	CD064655	HNF1A	D		.						107	95	99					12																	121434162		2203	4300	6503	SO:0001819	synonymous_variant	6927	exon5	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	CCAAGTGTCCCCC	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100		"Homeoboxes / HNF class"	11621	protein-coding gene	gene with protein product		142410	"transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor"	MODY3, TCF1		1535333, 7795649	Standard	NM_000545		Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	ENST00000257555.6:c.1053G>T	chr12.hg19:g.121434162G>T		168.0	0.0		142.0	33.0	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Silent	SNP	ENST00000257555.6	hg19	CCDS9209.1																																																																																			.	.		0.582	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545		T	121434162	G	T	121434162	2	4	327	1	0	0	0	0	0	0	0	1	7260	1364	48	3		3	HNF1A	12	121434162	Silent	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10	2179	121434162	12417733	71	45895	244	3								
HNF1A	6927	hgsc.bcm.edu	37	chr12	121434164	121434164	+	Missense_Mutation	SNP	C	C	T													0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	tacacccctccaccaagtgtCccccacgggcctggagccca					rs151344538		TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr12:121434164C>T	ENST00000257555.6	+	5	1281	c.1055C>T	c.(1054-1056)tCc>tTc	p.S352F	HNF1A_ENST00000541395.1_Missense_Mutation_p.S352F|HNF1A_ENST00000544413.1_Missense_Mutation_p.S352F|HNF1A_ENST00000400024.2_Missense_Mutation_p.S352F|HNF1A_ENST00000402929.1_Missense_Mutation_p.S352F|HNF1A_ENST00000538626.1_Intron|HNF1A_ENST00000543427.1_Missense_Mutation_p.S235F			P20823	HNF1A_HUMAN	HNF1 homeobox A	352					glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CACCAAGTGTCCCCCACGGGC	0.587									Hepatic Adenoma, Familial Clustering of																												p.S352F		Atlas-SNP	.											.	HNF1A	302	.	0			c.C1055T						.						106	95	98					12																	121434164		2203	4300	6503	SO:0001583	missense	6927	exon5	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	AAGTGTCCCCCAC	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100		"Homeoboxes / HNF class"	11621	protein-coding gene	gene with protein product		142410	"transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor"	MODY3, TCF1		1535333, 7795649	Standard	NM_000545		Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	ENST00000257555.6:c.1055C>T	chr12.hg19:g.121434164C>T	ENSP00000257555:p.Ser352Phe	167.0	0.0		141.0	29.0	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Missense_Mutation	SNP	ENST00000257555.6	hg19	CCDS9209.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.934898	0.73442	.	.	ENSG00000135100	ENST00000257555;ENST00000543536;ENST00000544680;ENST00000537424;ENST00000543427;ENST00000545458;ENST00000541395;ENST00000340577;ENST00000344370;ENST00000544413	D;D;D;D	0.98862	-5.19;-5.19;-5.19;-5.19	5.06	5.06	0.68205	Hepatocyte nuclear factor 1, beta isoform, C-terminal (1);	0.000000	0.64402	D	0.000002	D	0.99017	0.9664	M	0.74647	2.275	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.965	D;D;D;P	0.97110	1.0;1.0;1.0;0.734	D	0.99873	1.1099	10	0.87932	D	0	-20.899	17.4803	0.87671	0.0:1.0:0.0:0.0	.	352;352;352;352	F5H0K0;P20823;E7EUQ4;E7EMR0	.;HNF1A_HUMAN;.;.	F	352;352;352;352;235;352;352;352;352;352	ENSP00000257555:S352F;ENSP00000439721:S235F;ENSP00000443112:S352F;ENSP00000438804:S352F	ENSP00000257555:S352F	S	+	2	0	HNF1A	119918547	0.996000	0.38824	1.000000	0.80357	0.993000	0.82548	2.980000	0.49321	2.373000	0.80994	0.638000	0.83543	TCC	.	.		0.587	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545		T	121434164	C	T	121434164	3	4	327	1	0	0	0	0	1	0	0	0	7260	855	30	3	1073	3	HNF1A	12	121434164	Missense_Mutation	SNP	C	TCGA-NI-A4U2-01A-11D-A28X-10	2	121434164	12417731	72	45896	244	3								
HNF1A	6927	hgsc.bcm.edu	37	chr12	121434166	121434166	+	Frame_Shift_Del	DEL	C	C	-													0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	cacccctccaccaagtgtccCccacgggcctggagcccagc							TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr12:121434166delC	ENST00000257555.6	+	5	1283	c.1057delC	c.(1057-1059)cccfs	p.P353fs	HNF1A_ENST00000541395.1_Frame_Shift_Del_p.P353fs|HNF1A_ENST00000544413.1_Frame_Shift_Del_p.P353fs|HNF1A_ENST00000400024.2_Frame_Shift_Del_p.P353fs|HNF1A_ENST00000402929.1_Frame_Shift_Del_p.P353fs|HNF1A_ENST00000538626.1_Intron|HNF1A_ENST00000543427.1_Frame_Shift_Del_p.P236fs			P20823	HNF1A_HUMAN	HNF1 homeobox A	353					glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CCAAGTGTCCCCCACGGGCCT	0.582									Hepatic Adenoma, Familial Clustering of																												p.S352fs		Pindel	.											.	HNF1A	302	.	0			c.1056delC						.						103	93	97					12																	121434166		2203	4300	6503	SO:0001589	frameshift_variant	6927	exon5	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	.	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100		"Homeoboxes / HNF class"	11621	protein-coding gene	gene with protein product		142410	"transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor"	MODY3, TCF1		1535333, 7795649	Standard	NM_000545		Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	ENST00000257555.6:c.1057delC	chr12.hg19:g.121434166delC	ENSP00000257555:p.Pro353fs	168.0	0.0		139.0	21.0	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Frame_Shift_Del	DEL	ENST00000257555.6	hg19	CCDS9209.1																																																																																			.	.		0.582	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545		-	121434166	C	-	121434166	7	5	327	1	0	1	0	1	0	0	0	0	7260	623	22	0	1075	0	HNF1A	12	121434166	Frame_Shift_Del	DEL	C	TCGA-NI-A4U2-01A-11D-A28X-10	2	121434166	12417729	73	45897	244	3								
CPB2	1361	hgsc.bcm.edu	37	chr13	46638821	46638821	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	caaagttcctattcaggtctGttccgatgcaatgattgttc	8	9	2	1			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr13:46638821G>A	ENST00000181383.4	-	8	774	c.758C>T	c.(757-759)aCa>aTa	p.T253I	CPB2_ENST00000439329.3_Missense_Mutation_p.T216I|CPB2-AS1_ENST00000415033.2_RNA|CPB2-AS1_ENST00000606351.1_RNA|CPB2-AS1_ENST00000606243.1_RNA|CPB2-AS1_ENST00000606991.1_RNA	NM_001872.3	NP_001863.3	Q96IY4	CBPB2_HUMAN	carboxypeptidase B2 (plasma)	253					blood coagulation (GO:0007596)|cellular response to glucose stimulus (GO:0071333)|fibrinolysis (GO:0042730)|liver regeneration (GO:0097421)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of plasminogen activation (GO:0010757)|positive regulation of extracellular matrix constituent secretion (GO:0003331)|proteolysis (GO:0006508)|response to drug (GO:0042493)|response to heat (GO:0009408)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|cervix(1)|large_intestine(3)|liver(1)|lung(9)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21		Lung NSC(96;4.21e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|all_neural(104;0.235)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.44e-05)		ATTCAGGTCTGTTCCGATGCA	0.418																																					p.T253I		Atlas-SNP	.											.	CPB2	60	.	0			c.C758T						.						187	155	166					13																	46638821		2203	4300	6503	SO:0001583	missense	1361	exon8			AGGTCTGTTCCGA	M75106	CCDS9401.1, CCDS73568.1	13q14.11	2012-02-10	2007-02-21		ENSG00000080618	ENSG00000080618			2300	protein-coding gene	gene with protein product	"thrombin-activatable fibrinolysis inhibitor", "carboxypeptidase U", "plasma carboxypeptidase B", "carboxypeptidase R"	603101	"carboxypeptidase B2 (plasma, carboxypeptidase U)"			1939207, 1427879	Standard	NM_001278541		Approved	CPU, PCPB, TAFI	uc001vaw.3	Q96IY4	OTTHUMG00000016867	ENST00000181383.4:c.758C>T	chr13.hg19:g.46638821G>A	ENSP00000181383:p.Thr253Ile	160.0	0.0		145.0	50.0	NM_001872	A8K464|Q15114|Q5T9K1|Q5T9K2|Q9P2Y6	Missense_Mutation	SNP	ENST00000181383.4	hg19	CCDS9401.1	.	.	.	.	.	.	.	.	.	.	G	19.01	3.744899	0.69418	.	.	ENSG00000080618	ENST00000181383;ENST00000439329	T;T	0.28454	1.61;2.87	5.66	5.66	0.87406	Peptidase M14, carboxypeptidase A (3);	0.156175	0.64402	D	0.000018	T	0.55386	0.1917	M	0.65498	2.005	0.47778	D	0.99951	D;D	0.71674	0.99;0.998	P;D	0.68483	0.891;0.958	T	0.55598	-0.8116	10	0.66056	D	0.02	.	18.74	0.91770	0.0:0.0:1.0:0.0	.	216;253	Q96IY4-2;Q96IY4	.;CBPB2_HUMAN	I	253;216	ENSP00000181383:T253I;ENSP00000400714:T216I	ENSP00000181383:T253I	T	-	2	0	CPB2	45536822	1.000000	0.71417	1.000000	0.80357	0.841000	0.47740	4.447000	0.60020	2.662000	0.90505	0.650000	0.86243	ACA	.	.		0.418	CPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044803.2	NM_001872		A	46638821	G	A	46638821	3	1	327	1	0	0	0	0	1	0	0	0	3799	1377	48	3	529	3	CPB2	13	46638821	Missense_Mutation	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10		46638821	68531057	74	45898										
KLHL1	57626	hgsc.bcm.edu	37	chr13	70293586	70293586	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	ataaagaaaaccgtcacatgTggccactccgacaccccctc	6	16	1	1			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr13:70293586T>C	ENST00000377844.4	-	9	2689	c.1930A>G	c.(1930-1932)Aca>Gca	p.T644A	KLHL1_ENST00000545028.1_Missense_Mutation_p.T451A	NM_020866.2	NP_065917.1	Q9NR64	KLHL1_HUMAN	kelch-like family member 1	644					actin cytoskeleton organization (GO:0030036)|adult walking behavior (GO:0007628)|cerebellar Purkinje cell layer development (GO:0021680)|dendrite development (GO:0016358)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	actin binding (GO:0003779)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(56)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	84		Breast(118;0.000162)		COAD - Colon adenocarcinoma(199;0.000193)|GBM - Glioblastoma multiforme(99;0.000211)		CCGTCACATGTGGCCACTCCG	0.453																																					p.T644A		Atlas-SNP	.											.	KLHL1	164	.	0			c.A1930G						.						135	119	124					13																	70293586		2203	4300	6503	SO:0001583	missense	57626	exon9			CACATGTGGCCAC	AB040923	CCDS9445.1, CCDS73582.1	13q21	2013-01-30	2013-01-30		ENSG00000150361	ENSG00000150361		"Kelch-like", "BTB/POZ domain containing"	6352	protein-coding gene	gene with protein product	"Kelch-like protein 1", "Mayven-related protein 2"	605332	"kelch (Drosophila)-like 1", "kelch-like 1 (Drosophila)"			10888605	Standard	NM_020866		Approved	KIAA1490, MRP2, FLJ30047	uc001vip.3	Q9NR64	OTTHUMG00000017056	ENST00000377844.4:c.1930A>G	chr13.hg19:g.70293586T>C	ENSP00000367075:p.Thr644Ala	146.0	0.0		130.0	32.0	NM_020866	A8K5X0|Q5VZ64|Q9H4X4|Q9NR65|Q9P238	Missense_Mutation	SNP	ENST00000377844.4	hg19	CCDS9445.1	.	.	.	.	.	.	.	.	.	.	T	16.15	3.042209	0.55003	.	.	ENSG00000150361	ENST00000377844;ENST00000545028	T;T	0.77358	-1.09;-1.09	5.68	5.68	0.88126	Galactose oxidase, beta-propeller (1);	0.095038	0.46145	N	0.000305	T	0.60741	0.2292	N	0.01649	-0.78	0.42107	D	0.991367	B;B	0.28128	0.201;0.106	B;B	0.37346	0.247;0.085	T	0.66172	-0.5990	10	0.49607	T	0.09	.	15.9251	0.79609	0.0:0.0:0.0:1.0	.	644;644	Q8TBJ7;Q9NR64	.;KLHL1_HUMAN	A	644;451	ENSP00000367075:T644A;ENSP00000439602:T451A	ENSP00000367075:T644A	T	-	1	0	KLHL1	69191587	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	6.289000	0.72696	2.156000	0.67533	0.459000	0.35465	ACA	.	.		0.453	KLHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045231.3	NM_020866		C	70293586	T	C	70293586	3	2	327	1	0	0	0	0	1	0	0	0	8374	1696	59	2	328	2	KLHL1	13	70293586	Missense_Mutation	SNP	T	TCGA-NI-A4U2-01A-11D-A28X-10	23654765	70293586	44876292	75	45899										
LMO7	4008	hgsc.bcm.edu	37	chr13	76429476	76429476	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	catgatcatcgagtccctggGtctttgttatcatttgcatt	8	9	3	1			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr13:76429476G>A	ENST00000321797.8	+	27	4764	c.4043G>A	c.(4042-4044)gGt>gAt	p.G1348D	LMO7_ENST00000341547.4_Missense_Mutation_p.G1299D|LMO7_ENST00000357063.3_Intron|LMO7_ENST00000377534.3_Intron|LMO7_ENST00000526202.1_Missense_Mutation_p.G1225D|LMO7_ENST00000465261.2_Intron			Q8WWI1	LMO7_HUMAN	LIM domain 7	1633					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(20)|lung(15)|ovary(2)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		GAGTCCCTGGGTCTTTGTTAT	0.493																																					p.G1299D		Atlas-SNP	.											.	LMO7	334	.	0			c.G3896A						.						146	121	129					13																	76429476		2203	4300	6503	SO:0001583	missense	4008	exon28			CCCTGGGTCTTTG	AF092557	CCDS9454.1, CCDS53876.1	13q22.2	2008-02-05	2004-06-15		ENSG00000136153	ENSG00000136153			6646	protein-coding gene	gene with protein product	"F-box only protein 20"	604362	"LIM domain only 7"	FBXO20		9826547, 10531035	Standard	NM_005358		Approved	FBX20, KIAA0858	uc021rkq.1	Q8WWI1	OTTHUMG00000017093	ENST00000321797.8:c.4043G>A	chr13.hg19:g.76429476G>A	ENSP00000317802:p.Gly1348Asp	176.0	0.0		166.0	49.0	NM_005358	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Missense_Mutation	SNP	ENST00000321797.8	hg19		.	.	.	.	.	.	.	.	.	.	G	32	5.117643	0.94385	.	.	ENSG00000136153	ENST00000341547;ENST00000321797;ENST00000526202	D;D;D	0.87256	-2.23;-2.23;-2.23	5.99	5.99	0.97316	.	0.159223	0.56097	D	0.000033	D	0.92811	0.7714	L	0.56396	1.775	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92382	0.5914	10	0.66056	D	0.02	-23.5131	20.4777	0.99188	0.0:0.0:1.0:0.0	.	1225;1299	E9PMS6;Q8WWI1-3	.;.	D	1299;1348;1225	ENSP00000342112:G1299D;ENSP00000317802:G1348D;ENSP00000431129:G1225D	ENSP00000317802:G1348D	G	+	2	0	LMO7	75327477	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.476000	0.97823	2.840000	0.97914	0.655000	0.94253	GGT	.	.		0.493	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3	NM_005358		A	76429476	G	A	76429476	3	1	327	1	0	0	0	0	1	0	0	0	8864	1261	44	3	5016	3	LMO7	13	76429476	Missense_Mutation	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10	6135890	76429476	38740402	76	45900										
FBXL3	26224	hgsc.bcm.edu	37	chr13	77589641	77589641	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	agagatggatcatctactggAgtatcatctatcttaagcga	9	7	5	1			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr13:77589641A>T	ENST00000355619.5	-	4	870	c.546T>A	c.(544-546)acT>acA	p.T182T	FBXL3_ENST00000477982.1_5'UTR	NM_012158.2	NP_036290.1	Q9UKT7	FBXL3_HUMAN	F-box and leucine-rich repeat protein 3	182					entrainment of circadian clock by photoperiod (GO:0043153)|protein destabilization (GO:0031648)|protein ubiquitination (GO:0016567)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	cytosol (GO:0005829)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|urinary_tract(1)	16		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.218)		GBM - Glioblastoma multiforme(99;0.0521)		CATCTACTGGAGTATCATCTA	0.393																																					p.T182T		Atlas-SNP	.											.	FBXL3	46	.	0			c.T546A						.						135	121	125					13																	77589641		2203	4300	6503	SO:0001819	synonymous_variant	26224	exon4			TACTGGAGTATCA	AF129532	CCDS9457.1	13q22	2011-06-09	2004-07-20	2004-07-21	ENSG00000005812	ENSG00000005812		"F-boxes / Leucine-rich repeats"	13599	protein-coding gene	gene with protein product		605653	"F-box and leucine-rich repeat protein 3A"	FBXL3A		10531035, 10828603	Standard	NM_012158		Approved	FBL3, FBL3A	uc001vkd.3	Q9UKT7	OTTHUMG00000017099	ENST00000355619.5:c.546T>A	chr13.hg19:g.77589641A>T		147.0	0.0		109.0	38.0	NM_012158	B2RB04|Q9P122	Silent	SNP	ENST00000355619.5	hg19	CCDS9457.1																																																																																			.	.		0.393	FBXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045312.3			T	77589641	A	T	77589641	2	4	327	1	0	0	0	0	0	0	0	1	5728	291	11	4		4	FBXL3	13	77589641	Silent	SNP	A	TCGA-NI-A4U2-01A-11D-A28X-10	1160165	77589641	37580237	77	45901										
IRS2	8660	hgsc.bcm.edu	37	chr13	110437992	110437992	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	gaccaggtcggtgagcgcgcGgtaccagccctcctgctcct	13	16	0	1			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr13:110437992G>A	ENST00000375856.3	-	1	923	c.409C>T	c.(409-411)Cgc>Tgc	p.R137C		NM_003749.2	NP_003740.2	Q9Y4H2	IRS2_HUMAN	insulin receptor substrate 2	137	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				brain development (GO:0007420)|cell proliferation (GO:0008283)|cellular response to glucose stimulus (GO:0071333)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid homeostasis (GO:0055088)|mammary gland development (GO:0030879)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of kinase activity (GO:0033673)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin secretion (GO:0032024)|positive regulation of mesenchymal cell proliferation (GO:0002053)|regulation of lipid metabolic process (GO:0019216)|response to glucose (GO:0009749)|signal transduction (GO:0007165)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	19	all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155)	Breast(118;0.159)	all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147)			GTGAGCGCGCGGTACCAGCCC	0.756																																					p.R137C	Melanoma(100;613 2409 40847)	Atlas-SNP	.											.	IRS2	44	.	0			c.C409T						.						16	13	14					13																	110437992		2186	4284	6470	SO:0001583	missense	8660	exon1			GCGCGCGGTACCA	AB000732	CCDS9510.1	13q34	2013-01-10			ENSG00000185950	ENSG00000185950		"Pleckstrin homology (PH) domain containing"	6126	protein-coding gene	gene with protein product		600797				9312143	Standard	NM_003749		Approved		uc001vqv.3	Q9Y4H2	OTTHUMG00000017338	ENST00000375856.3:c.409C>T	chr13.hg19:g.110437992G>A	ENSP00000365016:p.Arg137Cys	30.0	0.0		39.0	12.0	NM_003749	Q96RR2|Q9BZG0|Q9Y6I5	Missense_Mutation	SNP	ENST00000375856.3	hg19	CCDS9510.1	.	.	.	.	.	.	.	.	.	.	g	20.7	4.031136	0.75504	.	.	ENSG00000185950	ENST00000375856	T	0.76316	-1.01	3.39	3.39	0.38822	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.083411	0.49916	U	0.000137	D	0.86289	0.5897	M	0.73598	2.24	0.45366	D	0.998351	D	0.89917	1.0	D	0.74674	0.984	D	0.88089	0.2812	10	0.66056	D	0.02	-11.841	13.7503	0.62904	0.0:0.0:1.0:0.0	.	137	Q9Y4H2	IRS2_HUMAN	C	137	ENSP00000365016:R137C	ENSP00000365016:R137C	R	-	1	0	IRS2	109235993	0.991000	0.36638	1.000000	0.80357	0.992000	0.81027	1.617000	0.36943	1.747000	0.51819	0.487000	0.48397	CGC	.	.		0.756	IRS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045755.1	NM_003749		A	110437992	G	A	110437992	3	1	327	1	0	0	0	0	1	0	0	0	7850	1116	39	1	3615	1	IRS2	13	110437992	Missense_Mutation	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10	32848351	110437992	4731886	78	45902										
NDN	4692	hgsc.bcm.edu	37	chr15	23931535	23931535	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	taaagaccctggccaggaacTccatgatttgcatcttggtg	10	10	1	2			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr15:23931535T>C	ENST00000331837.4	-	1	915	c.830A>G	c.(829-831)gAg>gGg	p.E277G		NM_002487.2	NP_002478.1	Q99608	NECD_HUMAN	necdin, melanoma antigen (MAGE) family member	277	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				axon extension (GO:0048675)|axonal fasciculation (GO:0007413)|central nervous system development (GO:0007417)|genetic imprinting (GO:0071514)|glial cell migration (GO:0008347)|multicellular organismal homeostasis (GO:0048871)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|post-embryonic development (GO:0009791)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|respiratory system process (GO:0003016)|sensory perception of pain (GO:0019233)|transcription, DNA-templated (GO:0006351)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|skin(1)	39		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;8.37e-11)|Epithelial(43;9.29e-10)|BRCA - Breast invasive adenocarcinoma(123;0.00179)|GBM - Glioblastoma multiforme(186;0.018)|Lung(196;0.153)		GGCCAGGAACTCCATGATTTG	0.592									Prader-Willi syndrome																												p.E277G		Atlas-SNP	.											.	NDN	79	.	0			c.A830G						.						30	33	32					15																	23931535		2202	4300	6502	SO:0001583	missense	4692	exon1	Familial Cancer Database	Prader-Labhart-Willi syndrome	AGGAACTCCATGA	U35139	CCDS10014.1	15q11-q12	2012-12-07	2012-12-07		ENSG00000182636	ENSG00000182636			7675	protein-coding gene	gene with protein product	"Prader-Willi syndrome chromosome region"	602117	"necdin (mouse) homolog", "necdin homolog (mouse)"			9302265	Standard	NM_002487		Approved	HsT16328, PWCR	uc001ywk.3	Q99608	OTTHUMG00000129161	ENST00000331837.4:c.830A>G	chr15.hg19:g.23931535T>C	ENSP00000332643:p.Glu277Gly	69.0	0.0		52.0	12.0	NM_002487	B2R6Z5	Missense_Mutation	SNP	ENST00000331837.4	hg19	CCDS10014.1	.	.	.	.	.	.	.	.	.	.	T	14.06	2.422619	0.43020	.	.	ENSG00000182636	ENST00000331837	T	0.03065	4.06	3.5	3.5	0.40072	.	0.285984	0.32190	N	0.006443	T	0.05456	0.0144	M	0.64567	1.98	0.43494	D	0.995736	B	0.16396	0.017	B	0.14578	0.011	T	0.14035	-1.0487	10	0.87932	D	0	.	8.7038	0.34343	0.0:0.0:0.0:1.0	.	277	Q99608	NECD_HUMAN	G	277	ENSP00000332643:E277G	ENSP00000332643:E277G	E	-	2	0	NDN	21482628	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.254000	0.32897	1.832000	0.53329	0.459000	0.35465	GAG	.	.		0.592	NDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251226.2	NM_002487		C	23931535	T	C	23931535	3	2	327	1	0	0	0	0	1	0	0	0	10256	1551	54	2	139	2	NDN	15	23931535	Missense_Mutation	SNP	T	TCGA-NI-A4U2-01A-11D-A28X-10		23931535	78599857	79	45903										
UNC13C	440279	hgsc.bcm.edu	37	chr15	54590037	54590037	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	acagataagtcagctgtatcTggggccatacgattgaaaat	10	7	2	2			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr15:54590037T>A	ENST00000260323.11	+	11	4017	c.4017T>A	c.(4015-4017)tcT>tcA	p.S1339S	UNC13C_ENST00000545554.1_Silent_p.S1339S|UNC13C_ENST00000537900.1_Silent_p.S1337S	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	1339					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		CAGCTGTATCTGGGGCCATAC	0.363																																					p.S1339S		Atlas-SNP	.											.	UNC13C	674	.	0			c.T4017A						.						64	63	63					15																	54590037		1856	4088	5944	SO:0001819	synonymous_variant	440279	exon10			TGTATCTGGGGCC	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.4017T>A	chr15.hg19:g.54590037T>A		291.0	0.0		276.0	81.0	NM_001080534	Q0P613|Q8ND48|Q96NP3	Silent	SNP	ENST00000260323.11	hg19	CCDS45264.1																																																																																			.	.		0.363	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		A	54590037	T	A	54590037	2	1	327	1	0	0	0	0	0	0	0	1	17001	1567	55	4		4	UNC13C	15	54590037	Silent	SNP	T	TCGA-NI-A4U2-01A-11D-A28X-10	30658502	54590037	47941355	80	45904										
UNKL	64718	hgsc.bcm.edu	37	chr16	1417163	1417179	+	Intron	DEL	CCGATGTCCCCACAGCC	CCGATGTCCCCACAGCC	-													0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	gcttcggcaggggaatggtgCcgatgtccccacagccccgc					rs372155593|rs529314659|rs557591189|rs149887709		TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	CCGATGTCCCCACAGCC	CCGATGTCCCCACAGCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr16:1417163_1417179delCCGATGTCCCCACAGCC	ENST00000389221.4	-	14	1887				UNKL_ENST00000403703.1_Frame_Shift_Del_p.GCGDIG153fs|UNKL_ENST00000402641.2_Frame_Shift_Del_p.GCGDIG153fs|UNKL_ENST00000391893.2_Frame_Shift_Del_p.GCGDIG150fs|UNKL_ENST00000508903.2_Frame_Shift_Del_p.GCGDIG654fs|UNKL_ENST00000397464.1_Intron|UNKL_ENST00000248104.7_Frame_Shift_Del_p.GCGDIG150fs	NM_001193388.1	NP_001180317	Q9H9P5	UNKL_HUMAN	unkempt family zinc finger-like						protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.I157I(1)		autonomic_ganglia(1)|endometrium(1)|large_intestine(1)|lung(1)	4		Hepatocellular(780;0.0893)				GGGAATGGTGCCGATGTCCCCACAGCCCCGCAGCCCC	0.691																																					p.153_158del		Atlas-Indel,Pindel	.											.	UNKL	46	.	1	Substitution - coding silent(1)	lung(1)	c.458_474del						.																																			SO:0001627	intron_variant	64718	exon5			.	BC011924	CCDS32359.1, CCDS53980.1, CCDS61787.1	16p13.3	2014-03-10	2013-10-17		ENSG00000059145	ENSG00000059145		"Zinc fingers, CCCH-type domain containing"	14184	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 28", "unkempt homolog (Drosophila)-like"	C16orf28		20148946	Standard	NM_001193389		Approved	ZC3HDC5L, ZC3H5L, FLJ23360	uc031qup.1	Q9H9P5	OTTHUMG00000128553	ENST00000389221.4:c.1887+63GGCTGTGGGGACATCGG>-	chr16.hg19:g.1417163_1417179delCCGATGTCCCCACAGCC		128.0	0.0		144.0	10.0	NM_023076	B0QYN6|B1GXI8|Q96EV1|Q96RZ1|Q9BWL5|Q9H5K0|Q9UJJ8	Frame_Shift_Del	DEL	ENST00000389221.4	hg19	CCDS53981.1																																																																																			.	.		0.691	UNKL-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001037125		-	1417179	CCGATGTCCCCACAGCC	-	1417163	6	5	327	0	1	1	0	1	0	0	0	0	17016	739	26	0		0	UNKL	16	1417163	Intron	DEL	CCGATGTCCCCACAGCC	TCGA-NI-A4U2-01A-11D-A28X-10		1417163	88937590	81	45905										
GTF3C1	2975	hgsc.bcm.edu	37	chr16	27549250	27549250	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	cagcttcccagcatcaacccTggaggaaaagaggagccatg	11	12	1	1			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr16:27549250T>A	ENST00000356183.4	-	4	624		c.e4-2		GTF3C1_ENST00000561623.1_Splice_Site	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa						5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						GCATCAACCCTGGAGGAAAAG	0.448																																					.		Atlas-SNP	.											.	GTF3C1	210	.	0			c.609-2A>T						.						64	63	63					16																	27549250		2197	4300	6497	SO:0001630	splice_region_variant	2975	exon5			CAACCCTGGAGGA	U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"General transcription factors"	4664	protein-coding gene	gene with protein product		603246	"general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.609-2A>T	chr16.hg19:g.27549250T>A		71.0	0.0		79.0	26.0	NM_001520	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Splice_Site	SNP	ENST00000356183.4	hg19	CCDS32414.1	.	.	.	.	.	.	.	.	.	.	T	17.55	3.416940	0.62511	.	.	ENSG00000077235	ENST00000356183;ENST00000388971	.	.	.	5.69	5.69	0.88448	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.6229	0.76820	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	GTF3C1	27456751	1.000000	0.71417	0.975000	0.42487	0.517000	0.34286	7.421000	0.80204	2.164000	0.68074	0.460000	0.39030	.	.	.		0.448	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520	Intron	A	27549250	T	A	27549250	5	1	327	1	0	0	0	0	0	0	1	0	6881	1594	55	4	5858	4	GTF3C1	16	27549250	Splice_Site	SNP	T	TCGA-NI-A4U2-01A-11D-A28X-10	26132087	27549250	62805503	82	45906										
VPS35	55737	hgsc.bcm.edu	37	chr16	46716005	46716005	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	agatacaaagttcatagtaaCtctttggtgataacatagaa	7	5	2	3			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr16:46716005C>G	ENST00000299138.7	-	3	243	c.185G>C	c.(184-186)aGt>aCt	p.S62T		NM_018206.4	NP_060676.2	Q96QK1	VPS35_HUMAN	vacuolar protein sorting 35 homolog (S. cerevisiae)	62					cell death (GO:0008219)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|retromer complex (GO:0030904)				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(11)|pancreas(1)|prostate(1)|urinary_tract(1)	23		all_cancers(37;7.65e-05)|all_epithelial(9;0.000154)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				TTCATAGTAACTCTTTGGTGA	0.333																																					p.S62T		Atlas-SNP	.											.	VPS35	49	.	0			c.G185C						.						102	95	97					16																	46716005		2203	4299	6502	SO:0001583	missense	55737	exon3			TAGTAACTCTTTG	AF175265	CCDS10721.1	16q12	2012-06-27	2006-12-19		ENSG00000069329	ENSG00000069329		"Parkinson disease"	13487	protein-coding gene	gene with protein product		601501	"vacuolar protein sorting 35 (yeast homolog)", "vacuolar protein sorting 35 (yeast)"			11112353, 21763482	Standard	NM_018206		Approved	FLJ10752, MEM3, PARK17	uc002eef.4	Q96QK1	OTTHUMG00000132542	ENST00000299138.7:c.185G>C	chr16.hg19:g.46716005C>G	ENSP00000299138:p.Ser62Thr	214.0	0.0		156.0	10.0	NM_018206	Q561W2|Q9H016|Q9H096|Q9H4P3|Q9H8J0|Q9NRS7|Q9NVG2|Q9NX80|Q9NZK2	Missense_Mutation	SNP	ENST00000299138.7	hg19	CCDS10721.1	.	.	.	.	.	.	.	.	.	.	.	13.61	2.288658	0.40494	.	.	ENSG00000069329	ENST00000299138	T	0.42900	0.96	4.88	4.88	0.63580	.	0.084158	0.85682	D	0.000000	T	0.41096	0.1144	L	0.43152	1.355	0.80722	D	1	P	0.35383	0.498	B	0.40506	0.331	T	0.15122	-1.0448	10	0.14252	T	0.57	-5.5078	18.4459	0.90683	0.0:1.0:0.0:0.0	.	62	Q96QK1	VPS35_HUMAN	T	62	ENSP00000299138:S62T	ENSP00000299138:S62T	S	-	2	0	VPS35	45273506	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.818000	0.86416	2.405000	0.81733	0.551000	0.68910	AGT	.	.		0.333	VPS35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255742.3			G	46716005	C	G	46716005	3	3	327	1	0	0	0	0	1	0	0	0	17218	565	20	4	2265	4	VPS35	16	46716005	Missense_Mutation	SNP	C	TCGA-NI-A4U2-01A-11D-A28X-10	19166755	46716005	43638748	83	45907										
DVL2	1856	hgsc.bcm.edu	37	chr17	7131298	7131298	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	tccctgagtgtcactcacttCgggggagagtgaaataggcc	13	10	2	3			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr17:7131298C>A	ENST00000005340.5	-	10	1382	c.1100G>T	c.(1099-1101)cGa>cTa	p.R367L	DVL2_ENST00000575458.1_Missense_Mutation_p.R361L|DVL2_ENST00000574642.1_5'Flank	NM_004422.2	NP_004413.1	O14641	DVL2_HUMAN	dishevelled segment polarity protein 2	367					canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration in hindbrain (GO:0021535)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|convergent extension involved in neural plate elongation (GO:0022007)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hippo signaling (GO:0035329)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|segment specification (GO:0007379)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|clathrin-coated endocytic vesicle (GO:0045334)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|identical protein binding (GO:0042802)			breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(7)|skin(1)	25						TCACTCACTTCGGGGGAGAGT	0.642																																					p.R367L		Atlas-SNP	.											.	DVL2	49	.	0			c.G1100T						.						37	38	37					17																	7131298		2203	4300	6503	SO:0001583	missense	1856	exon10			TCACTTCGGGGGA	BC014844	CCDS11091.1	17p13.1	2013-05-22	2013-05-22		ENSG00000004975	ENSG00000004975		"Dishevelled homologs"	3086	protein-coding gene	gene with protein product		602151	"dishevelled 2 (homologous to Drosophila dsh)", "dishevelled, dsh homolog 2 (Drosophila)"			8662242	Standard	NM_004422		Approved		uc002gez.1	O14641	OTTHUMG00000102155	ENST00000005340.5:c.1100G>T	chr17.hg19:g.7131298C>A	ENSP00000005340:p.Arg367Leu	187.0	0.0		97.0	51.0	NM_004422	D3DTN3|Q53XM0	Missense_Mutation	SNP	ENST00000005340.5	hg19	CCDS11091.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.719943	0.89205	.	.	ENSG00000004975	ENST00000005340	T	0.06371	3.31	4.89	4.89	0.63831	PDZ/DHR/GLGF (1);	0.065725	0.64402	D	0.000007	T	0.30448	0.0765	M	0.91459	3.21	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.71870	0.975;0.975	T	0.12760	-1.0535	10	0.59425	D	0.04	-17.7923	13.4054	0.60911	0.0:1.0:0.0:0.0	.	361;367	B4DLQ0;O14641	.;DVL2_HUMAN	L	367	ENSP00000005340:R367L	ENSP00000005340:R367L	R	-	2	0	DVL2	7072022	1.000000	0.71417	0.995000	0.50966	0.679000	0.39708	7.651000	0.83577	2.552000	0.86080	0.655000	0.94253	CGA	.	.		0.642	DVL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219999.2	NM_004422		A	7131298	C	A	7131298	3	1	327	1	0	0	0	0	1	0	0	0	4838	884	31	1	1134	1	DVL2	17	7131298	Missense_Mutation	SNP	C	TCGA-NI-A4U2-01A-11D-A28X-10		7131298	74063912	84	45908										
KIAA0100	9703	hgsc.bcm.edu	37	chr17	26948494	26948494	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	cagagtccagactacgctgcCggtgctcctcgatattcttc	9	14	1	2			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr17:26948494C>A	ENST00000528896.2	-	27	5056	c.4982G>T	c.(4981-4983)cGg>cTg	p.R1661L	KIAA0100_ENST00000544884.1_Missense_Mutation_p.R1518L|KIAA0100_ENST00000579924.2_5'Flank|KIAA0100_ENST00000389003.3_Missense_Mutation_p.R1518L	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	1661						extracellular region (GO:0005576)				breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68	Lung NSC(42;0.00431)					ACTACGCTGCCGGTGCTCCTC	0.562																																					p.R1661L		Atlas-SNP	.											.	KIAA0100	175	.	0			c.G4982T						.						86	79	81					17																	26948494		2203	4300	6503	SO:0001583	missense	9703	exon27			CGCTGCCGGTGCT	D43947	CCDS32595.1	17q11.2	2012-11-29			ENSG00000007202	ENSG00000007202			28960	protein-coding gene	gene with protein product	"cancer/testis antigen 101", "breast cancer overexpressed gene 1"	610664				16289875	Standard	NM_014680		Approved	DKFZp686M0843, MGC111488, BCOX1, CT101, BCOX	uc002hbu.3	Q14667	OTTHUMG00000166587	ENST00000528896.2:c.4982G>T	chr17.hg19:g.26948494C>A	ENSP00000436773:p.Arg1661Leu	83.0	0.0		69.0	21.0	NM_014680	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Missense_Mutation	SNP	ENST00000528896.2	hg19	CCDS32595.1	.	.	.	.	.	.	.	.	.	.	C	15.06	2.719966	0.48728	.	.	ENSG00000007202	ENST00000005905;ENST00000389003;ENST00000528896;ENST00000544884	T;T	0.23552	1.9;1.9	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.31358	0.0794	N	0.08118	0	0.80722	D	1	D	0.63880	0.993	D	0.74023	0.982	T	0.21724	-1.0237	10	0.26408	T	0.33	.	18.2554	0.90017	0.0:1.0:0.0:0.0	.	1661	Q14667	K0100_HUMAN	L	1661;1631;1661;1518	ENSP00000436773:R1661L;ENSP00000446443:R1518L	ENSP00000005905:R1661L	R	-	2	0	KIAA0100	23972621	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.277000	0.78572	2.826000	0.97356	0.491000	0.48974	CGG	.	.		0.562	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680		A	26948494	C	A	26948494	3	1	327	1	0	0	0	0	1	0	0	0	8163	652	23	1	1777	1	KIAA0100	17	26948494	Missense_Mutation	SNP	C	TCGA-NI-A4U2-01A-11D-A28X-10	19817196	26948494	54246716	85	45909										
ABCA6	23460	hgsc.bcm.edu	37	chr17	67080447	67080447	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	ctatgcccgtagatggttcaTccaggagcaagacaggtgag	13	9	1	3			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr17:67080447T>C	ENST00000284425.2	-	34	4484	c.4310A>G	c.(4309-4311)gAt>gGt	p.D1437G	ABCA6_ENST00000446604.2_5'UTR	NM_080284.2	NP_525023.2	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 6	1437	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(6)|endometrium(5)|kidney(17)|large_intestine(18)|lung(20)|ovary(3)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	82	Breast(10;5.65e-12)					AGATGGTTCATCCAGGAGCAA	0.517																																					p.D1437G		Atlas-SNP	.											.	ABCA6	210	.	0			c.A4310G						.						121	113	116					17																	67080447		2203	4300	6503	SO:0001583	missense	23460	exon34			GGTTCATCCAGGA	U66680	CCDS11683.1	17q21	2012-03-14			ENSG00000154262	ENSG00000154262		"ATP binding cassette transporters / subfamily A"	36	protein-coding gene	gene with protein product		612504				8894702	Standard	NM_080284		Approved	EST155051	uc002jhw.1	Q8N139		ENST00000284425.2:c.4310A>G	chr17.hg19:g.67080447T>C	ENSP00000284425:p.Asp1437Gly	109.0	0.0		114.0	29.0	NM_080284	Q6NSH9|Q8N856|Q8WWZ6	Missense_Mutation	SNP	ENST00000284425.2	hg19	CCDS11683.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.075929	0.76415	.	.	ENSG00000154262	ENST00000284425;ENST00000446604	D	0.99695	-6.43	5.18	5.18	0.71444	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.52532	D	0.000074	D	0.99862	0.9935	H	0.99312	4.51	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96409	0.9303	10	0.87932	D	0	.	14.3635	0.66789	0.0:0.0:0.0:1.0	.	1437	Q8N139	ABCA6_HUMAN	G	1437;297	ENSP00000284425:D1437G	ENSP00000284425:D1437G	D	-	2	0	ABCA6	64592042	1.000000	0.71417	1.000000	0.80357	0.582000	0.36321	7.229000	0.78088	2.171000	0.68590	0.533000	0.62120	GAT	.	.		0.517	ABCA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450463.1	NM_080284		C	67080447	T	C	67080447	3	2	327	1	0	0	0	0	1	0	0	0	36	1435	50	2	567	2	ABCA6	17	67080447	Missense_Mutation	SNP	T	TCGA-NI-A4U2-01A-11D-A28X-10	40131953	67080447	14114763	86	45910										
SLC26A11	284129	hgsc.bcm.edu	37	chr17	78220002	78220002	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	gcaccccggcggggggcctgGtgacgggtaaggccccccat	17	15	0	1			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr17:78220002G>A	ENST00000361193.3	+	12	1427	c.1147G>A	c.(1147-1149)Gtg>Atg	p.V383M	SLC26A11_ENST00000546047.2_Missense_Mutation_p.V383M|SLC26A11_ENST00000411502.3_Missense_Mutation_p.V383M|SLC26A11_ENST00000572725.1_Missense_Mutation_p.V383M	NM_001166347.1|NM_173626.3	NP_001159819.1|NP_775897.3			solute carrier family 26 (anion exchanger), member 11											central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(7)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	28	all_neural(118;0.0538)		OV - Ovarian serous cystadenocarcinoma(97;0.0344)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			GGGGGGCCTGGTGACGGGTAA	0.672																																					p.V383M		Atlas-SNP	.											.	SLC26A11	60	.	0			c.G1147A						.						42	51	48					17																	78220002		2201	4293	6494	SO:0001583	missense	284129	exon12			GGCCTGGTGACGG		CCDS11771.2	17q25	2013-07-18	2013-07-18		ENSG00000181045	ENSG00000181045		"Solute carriers"	14471	protein-coding gene	gene with protein product		610117	"solute carrier family 26, member 11"				Standard	NM_001166347		Approved		uc010dhv.2	Q86WA9	OTTHUMG00000133419	ENST00000361193.3:c.1147G>A	chr17.hg19:g.78220002G>A	ENSP00000355384:p.Val383Met	53.0	0.0		69.0	20.0	NM_173626		Missense_Mutation	SNP	ENST00000361193.3	hg19	CCDS11771.2	.	.	.	.	.	.	.	.	.	.	G	9.672	1.147078	0.21288	.	.	ENSG00000181045	ENST00000411502;ENST00000546047;ENST00000361193	D;D;D	0.94184	-3.37;-3.37;-3.37	4.12	3.12	0.35913	Sulphate transporter (1);	0.230563	0.45126	N	0.000389	D	0.92341	0.7570	M	0.77820	2.39	0.43852	D	0.996449	B	0.33448	0.412	B	0.39503	0.301	D	0.89902	0.4045	10	0.48119	T	0.1	-29.6563	7.1222	0.25450	0.1045:0.1875:0.7079:0.0	.	383	Q86WA9	S2611_HUMAN	M	383	ENSP00000403998:V383M;ENSP00000440724:V383M;ENSP00000355384:V383M	ENSP00000355384:V383M	V	+	1	0	SLC26A11	75834597	1.000000	0.71417	1.000000	0.80357	0.228000	0.25075	0.773000	0.26661	1.022000	0.39626	0.491000	0.48974	GTG	.	.		0.672	SLC26A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257281.1			A	78220002	G	A	78220002	3	1	327	1	0	0	0	0	1	0	0	0	14531	1261	44	3	1185	3	SLC26A11	17	78220002	Missense_Mutation	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10	11139555	78220002	2975208	87	45911										
NDUFV2	4729	hgsc.bcm.edu	37	chr18	9102767	9102767	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	cttctccgcggcgctccgggCccgggcggctggcctcaccg	15	19	2	0			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr18:9102767C>T	ENST00000318388.6	+	1	140	c.26C>T	c.(25-27)gCc>gTc	p.A9V	RP11-21J18.1_ENST00000579126.1_RNA|NDUFV2_ENST00000400033.1_5'Flank|NDUFV2_ENST00000497577.2_Missense_Mutation_p.A9V	NM_021074.4	NP_066552.2	P19404	NDUV2_HUMAN	NADH dehydrogenase (ubiquinone) flavoprotein 2, 24kDa	9					cardiac muscle tissue development (GO:0048738)|cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|nervous system development (GO:0007399)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|lung(4)|ovary(1)|stomach(1)	7						GCGCTCCGGGCCCGGGCGGCT	0.706																																					p.A9V		Atlas-SNP	.											.	NDUFV2	17	.	0			c.C26T						.						6	8	7					18																	9102767		2125	4156	6281	SO:0001583	missense	4729	exon1			TCCGGGCCCGGGC	X84421	CCDS11842.1	18p11.22	2011-07-04	2002-08-29		ENSG00000178127	ENSG00000178127	1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7717	protein-coding gene	gene with protein product	"complex I 24kDa subunit", "NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial"	600532	"NADH dehydrogenase (ubiquinone) flavoprotein 2 (24kD)"			9763677, 7607668	Standard	NM_021074		Approved	CI-24k	uc002knu.3	P19404	OTTHUMG00000131593	ENST00000318388.6:c.26C>T	chr18.hg19:g.9102767C>T	ENSP00000327268:p.Ala9Val	20.0	0.0		33.0	16.0	NM_021074	Q9BV41	Missense_Mutation	SNP	ENST00000318388.6	hg19	CCDS11842.1	.	.	.	.	.	.	.	.	.	.	C	7.170	0.587450	0.13812	.	.	ENSG00000178127	ENST00000318388	T	0.46819	0.86	4.7	2.89	0.33648	.	.	.	.	.	T	0.30070	0.0753	N	0.22421	0.69	0.26272	N	0.978407	B	0.14438	0.01	B	0.09377	0.004	T	0.17745	-1.0359	9	0.33940	T	0.23	.	5.7902	0.18357	0.1899:0.7112:0.0:0.0988	.	9	P19404	NDUV2_HUMAN	V	9	ENSP00000327268:A9V	ENSP00000327268:A9V	A	+	2	0	NDUFV2	9092767	0.833000	0.29383	0.066000	0.19879	0.005000	0.04900	1.158000	0.31737	0.565000	0.29255	-0.150000	0.13652	GCC	.	.		0.706	NDUFV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254475.2	NM_021074		T	9102767	C	T	9102767	3	4	327	1	0	0	0	0	1	0	0	0	10309	739	26	3	28	3	NDUFV2	18	9102767	Missense_Mutation	SNP	C	TCGA-NI-A4U2-01A-11D-A28X-10		9102767	68974481	88	45912										
FZR1	51343	hgsc.bcm.edu	37	chr19	3522996	3522996	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	ccctgcctcgccatggaccaGgactatgagcggcgcctgct	12	16	0	1			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr19:3522996G>A	ENST00000395095.3	+	1	9	c.9G>A	c.(7-9)caG>caA	p.Q3Q	FZR1_ENST00000313639.8_Silent_p.Q3Q|SNORD38_ENST00000516599.1_RNA|FZR1_ENST00000441788.2_Silent_p.Q3Q	NM_001136198.1	NP_001129670.1	Q9UM11	FZR_HUMAN	fizzy/cell division cycle 20 related 1 (Drosophila)	3					activation of anaphase-promoting complex activity (GO:0051488)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|DNA repair (GO:0006281)|G2 DNA damage checkpoint (GO:0031572)|lens fiber cell differentiation (GO:0070306)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of cell aging (GO:0090344)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of meiosis (GO:0040020)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(1)|kidney(4)|liver(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(2)	13				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00253)|STAD - Stomach adenocarcinoma(1328;0.18)		CCATGGACCAGGACTATGAGC	0.692																																					p.Q3Q		Atlas-SNP	.											.	FZR1	42	.	0			c.G9A						.						70	72	72					19																	3522996		2203	4297	6500	SO:0001819	synonymous_variant	51343	exon1			GGACCAGGACTAT	AF083810	CCDS12109.1, CCDS45916.1, CCDS45917.1	19p13.3	2013-01-10				ENSG00000105325		"WD repeat domain containing"	24824	protein-coding gene	gene with protein product		603619				9734353, 11003657	Standard	NM_016263		Approved	HCDH1, CDH1, HCDH, FZR, FZR2, KIAA1242, CDC20C	uc010dtk.2	Q9UM11		ENST00000395095.3:c.9G>A	chr19.hg19:g.3522996G>A		164.0	0.0		202.0	66.0	NM_001136197	O75869|Q86U66|Q96NW8|Q9UI96|Q9ULH8|Q9UM10|Q9UNQ1|Q9Y2T8	Silent	SNP	ENST00000395095.3	hg19	CCDS45916.1																																																																																			.	.		0.692	FZR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452869.2	NM_016263		A	3522996	G	A	3522996	2	1	327	1	0	0	0	0	0	0	0	1	6146	991	35	3		3	FZR1	19	3522996	Silent	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10		3522996	55605987	89	45913										
ZNF558	148156	hgsc.bcm.edu	37	chr19	8932718	8932718	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	agctcattaaccagctctccGccctgtgtgtgtcctttttg	8	13	2	0			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr19:8932718G>A	ENST00000601372.1	-	6	792	c.81C>T	c.(79-81)ggC>ggT	p.G27G	ZNF558_ENST00000444186.2_5'Flank|ZNF558_ENST00000301475.1_Silent_p.G27G|CTD-2529P6.3_ENST00000594006.1_RNA|ZNF558_ENST00000599938.1_5'Flank			Q96NG5	ZN558_HUMAN	zinc finger protein 558	27					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	15						CCAGCTCTCCGCCCTGTGTGT	0.512																																					p.G27G		Atlas-SNP	.											ZNF558,NS,carcinoma,0,2	ZNF558	43	.	0			c.C81T						.						196	174	182					19																	8932718		2203	4300	6503	SO:0001819	synonymous_variant	148156	exon2			CTCTCCGCCCTGT	AK055494	CCDS12208.1	19p13.2	2013-09-20			ENSG00000167785	ENSG00000167785		"Zinc fingers, C2H2-type", "-"	26422	protein-coding gene	gene with protein product							Standard	NM_144693		Approved	FLJ30932	uc002mkn.1	Q96NG5	OTTHUMG00000182196	ENST00000601372.1:c.81C>T	chr19.hg19:g.8932718G>A		217.0	1.0		191.0	77.0	NM_144693	A8K5F0|B7Z798	Silent	SNP	ENST00000601372.1	hg19	CCDS12208.1																																																																																			.	.		0.512	ZNF558-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459955.2	NM_144693		A	8932718	G	A	8932718	2	1	327	1	0	0	0	0	0	0	0	1	18004	1074	38	1		1	ZNF558	19	8932718	Silent	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10	5409722	8932718	50196265	90	45914										
SCN1B	6324	hgsc.bcm.edu	37	chr19	35523452	35523452	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	tgtcctcagcctgcgggggcTgcgtggaggtggactcggag	19	10	1	0			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr19:35523452T>A	ENST00000262631.5	+	2	198	c.61T>A	c.(61-63)Tgc>Agc	p.C21S	SCN1B_ENST00000415950.3_Missense_Mutation_p.C21S|SCN1B_ENST00000596348.1_3'UTR|SCN1B_ENST00000595652.1_Missense_Mutation_p.C21S	NM_001037.4	NP_001028.1	Q07699	SCN1B_HUMAN	sodium channel, voltage-gated, type I, beta subunit	21					axon guidance (GO:0007411)|cardiac conduction (GO:0061337)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|corticospinal neuron axon guidance (GO:0021966)|locomotion (GO:0040011)|membrane depolarization (GO:0051899)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane depolarization during Purkinje myocyte cell action potential (GO:0086047)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to pyrethroid (GO:0046684)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	extracellular region (GO:0005576)|intercalated disc (GO:0014704)|node of Ranvier (GO:0033268)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	sodium channel inhibitor activity (GO:0019871)|sodium channel regulator activity (GO:0017080)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)|voltage-gated sodium channel activity involved in Purkinje myocyte action potential (GO:0086062)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(3)	11	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)		Valproic Acid(DB00313)|Zonisamide(DB00909)	CTGCGGGGGCTGCGTGGAGGT	0.597																																					p.C21S		Atlas-SNP	.											.	SCN1B	32	.	0			c.T61A						.						90	90	90					19																	35523452		2203	4300	6503	SO:0001583	missense	6324	exon2			GGGGGCTGCGTGG		CCDS12441.1, CCDS46047.1	19q13.12	2014-09-17	2012-02-28		ENSG00000105711	ENSG00000105711		"Sodium channels", "Voltage-gated ion channels / Sodium channels", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10586	protein-coding gene	gene with protein product		600235	"sodium channel, voltage-gated, type I, beta polypeptide", "sodium channel, voltage-gated, type I, beta"			8394762	Standard	NM_001037		Approved		uc002nxo.2	Q07699	OTTHUMG00000182472	ENST00000262631.5:c.61T>A	chr19.hg19:g.35523452T>A	ENSP00000262631:p.Cys21Ser	87.0	0.0		80.0	19.0	NM_001037	Q5TZZ4|Q6TN97	Missense_Mutation	SNP	ENST00000262631.5	hg19	CCDS12441.1	.	.	.	.	.	.	.	.	.	.	T	15.18	2.756207	0.49362	.	.	ENSG00000105711	ENST00000262631;ENST00000415950	D;D	0.98044	-4.68;-2.33	3.72	3.72	0.42706	.	0.000000	0.85682	D	0.000000	D	0.97676	0.9238	L	0.59436	1.845	0.58432	D	0.999997	D;D;D	0.76494	0.981;0.981;0.999	D;D;D	0.83275	0.95;0.95;0.996	D	0.96414	0.9306	10	0.33940	T	0.23	-27.6615	8.7296	0.34491	0.0:0.0:0.0:1.0	.	21;21;21	B4DI92;Q07699;Q07699-2	.;SCN1B_HUMAN;.	S	21	ENSP00000262631:C21S;ENSP00000396915:C21S	ENSP00000262631:C21S	C	+	1	0	SCN1B	40215292	1.000000	0.71417	0.996000	0.52242	0.556000	0.35491	6.970000	0.76099	1.557000	0.49525	0.460000	0.39030	TGC	.	.		0.597	SCN1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461567.1			A	35523452	T	A	35523452	3	1	327	1	0	0	0	0	1	0	0	0	13930	1580	55	4	67	4	SCN1B	19	35523452	Missense_Mutation	SNP	T	TCGA-NI-A4U2-01A-11D-A28X-10	26590734	35523452	23605531	91	45915										
PLA2G4C	8605	hgsc.bcm.edu	37	chr19	48565344	48565344	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	gagtgggaagggagtgttgaTggctaaaccagcatccacca	14	8	0	1			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr19:48565344T>C	ENST00000599921.1	-	14	1525	c.1168A>G	c.(1168-1170)Atc>Gtc	p.I390V	PLA2G4C_ENST00000413144.2_Missense_Mutation_p.I390V|CTD-2265M8.2_ENST00000596552.1_RNA|CTD-2265M8.2_ENST00000601548.1_RNA|PLA2G4C_ENST00000354276.3_Missense_Mutation_p.I390V|CTD-2265M8.2_ENST00000601950.1_RNA|PLA2G4C_ENST00000596510.1_5'UTR|PLA2G4C_ENST00000599111.1_Missense_Mutation_p.I400V			Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC (cytosolic, calcium-independent)	390	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid metabolic process (GO:0019369)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|parturition (GO:0007567)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(12)|lung(13)|ovary(2)|prostate(1)|skin(3)	38		all_cancers(25;2.84e-05)|all_lung(116;4.62e-05)|Lung NSC(112;7.61e-05)|all_epithelial(76;0.000192)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;8.09e-05)|all cancers(93;0.000517)|Epithelial(262;0.0135)|GBM - Glioblastoma multiforme(486;0.0717)		GGAGTGTTGATGGCTAAACCA	0.572																																					p.I400V		Atlas-SNP	.											.	PLA2G4C	76	.	0			c.A1198G						.						88	69	76					19																	48565344		2203	4300	6503	SO:0001583	missense	8605	exon14			TGTTGATGGCTAA	AF065214	CCDS12710.1, CCDS54286.1, CCDS59403.1	19q13.3	2008-09-19					3.1.1.4		9037	protein-coding gene	gene with protein product		603602				9705332	Standard	NM_003706		Approved	cPLA2-gamma	uc002phx.3	Q9UP65		ENST00000599921.1:c.1168A>G	chr19.hg19:g.48565344T>C	ENSP00000469473:p.Ile390Val	162.0	0.0		147.0	43.0	NM_001159322	B2RB71|B4DI40|O75457|Q6IBI8|Q9UG68	Missense_Mutation	SNP	ENST00000599921.1	hg19	CCDS12710.1	.	.	.	.	.	.	.	.	.	.	T	13.54	2.268688	0.40095	.	.	ENSG00000105499	ENST00000354276;ENST00000413144	T;T	0.17370	2.28;2.28	2.79	2.79	0.32731	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (2);	0.372534	0.21783	U	0.069161	T	0.13500	0.0327	L	0.44542	1.39	0.22457	N	0.999084	B;B	0.27117	0.104;0.168	B;B	0.26969	0.059;0.075	T	0.15983	-1.0418	10	0.39692	T	0.17	-8.6609	7.4822	0.27411	0.0:0.0:0.0:1.0	.	400;390	B4DI40;Q9UP65	.;PA24C_HUMAN	V	390	ENSP00000346228:I390V;ENSP00000400036:I390V	ENSP00000346228:I390V	I	-	1	0	PLA2G4C	53257156	1.000000	0.71417	0.999000	0.59377	0.281000	0.26958	3.354000	0.52254	1.045000	0.40225	0.333000	0.21579	ATC	.	.		0.572	PLA2G4C-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465551.1			C	48565344	T	C	48565344	3	2	327	1	0	0	0	0	1	0	0	0	12012	1464	51	2	477	2	PLA2G4C	19	48565344	Missense_Mutation	SNP	T	TCGA-NI-A4U2-01A-11D-A28X-10	13041892	48565344	10563639	92	45916										
SHANK1	50944	hgsc.bcm.edu	37	chr19	51171701	51171701	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	gcctcggtgctgctgccctgGctgctgcggccgctgctact	14	16	0	0			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr19:51171701G>A	ENST00000293441.1	-	22	3534	c.3516C>T	c.(3514-3516)agC>agT	p.S1172S	SHANK1_ENST00000359082.3_Silent_p.S1163S|SYT3_ENST00000544769.1_5'Flank|SHANK1_ENST00000391813.1_Silent_p.S559S|SHANK1_ENST00000391814.1_Silent_p.S1180S	NM_016148.2	NP_057232.2	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	1172					adult behavior (GO:0030534)|associative learning (GO:0008306)|cytoskeletal anchoring at plasma membrane (GO:0007016)|dendritic spine morphogenesis (GO:0060997)|determination of affect (GO:0050894)|habituation (GO:0046959)|long-term memory (GO:0007616)|negative regulation of actin filament bundle assembly (GO:0032232)|neuromuscular process controlling balance (GO:0050885)|olfactory behavior (GO:0042048)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|protein complex assembly (GO:0006461)|protein localization to synapse (GO:0035418)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|righting reflex (GO:0060013)|social behavior (GO:0035176)|synapse maturation (GO:0060074)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|excitatory synapse (GO:0060076)|intracellular (GO:0005622)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ankyrin repeat binding (GO:0071532)|GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|somatostatin receptor binding (GO:0031877)			breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	64		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)		TGCTGCCCTGGCTGCTGCGGC	0.761																																					p.S1172S		Atlas-SNP	.											.	SHANK1	210	.	0			c.C3516T						.						18	19	19					19																	51171701		1537	3337	4874	SO:0001819	synonymous_variant	50944	exon22			GCCCTGGCTGCTG	AF163302	CCDS12799.1	19q13.3	2013-01-10			ENSG00000161681	ENSG00000161681		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	15474	protein-coding gene	gene with protein product	"somatostatin receptor-interacting protein"	604999				10551867	Standard	NM_016148		Approved	SSTRIP, SPANK-1, synamon	uc002psx.1	Q9Y566	OTTHUMG00000137380	ENST00000293441.1:c.3516C>T	chr19.hg19:g.51171701G>A		18.0	0.0		15.0	6.0	NM_016148	A8MXP5|B7WNY6|Q9NYW9	Silent	SNP	ENST00000293441.1	hg19	CCDS12799.1																																																																																			.	.		0.761	SHANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268071.1	NM_016148		A	51171701	G	A	51171701	2	1	327	1	0	0	0	0	0	0	0	1	14279	1194	42	3		3	SHANK1	19	51171701	Silent	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10	2606357	51171701	7957282	93	45917										
ZNF480	147657	hgsc.bcm.edu	37	chr19	52817496	52817496	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	agagggctttatacaaggatGtgatgttggagaactacagg	14	4	0	3			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr19:52817496G>T	ENST00000595962.1	+	3	229	c.163G>T	c.(163-165)Gtg>Ttg	p.V55L	CTD-2525I3.6_ENST00000594379.1_RNA|ZNF480_ENST00000490272.1_Intron|ZNF480_ENST00000334564.7_Missense_Mutation_p.V55L|ZNF480_ENST00000335090.6_Intron	NM_144684.2	NP_653285.2	Q8WV37	ZN480_HUMAN	zinc finger protein 480	55	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	12				GBM - Glioblastoma multiforme(134;0.00212)|OV - Ovarian serous cystadenocarcinoma(262;0.00369)		ATACAAGGATGTGATGTTGGA	0.507																																					p.V55L		Atlas-SNP	.											.	ZNF480	123	.	0			c.G163T						.						138	123	128					19																	52817496		2203	4300	6503	SO:0001583	missense	147657	exon3			AAGGATGTGATGT	AY512662	CCDS12850.2, CCDS74437.1	19q13.41	2013-01-08			ENSG00000198464	ENSG00000198464		"Zinc fingers, C2H2-type", "-"	23305	protein-coding gene	gene with protein product		613910				15219843	Standard	XM_005258525		Approved	MGC32104	uc010ydl.2	Q8WV37	OTTHUMG00000157507	ENST00000595962.1:c.163G>T	chr19.hg19:g.52817496G>T	ENSP00000471754:p.Val55Leu	63.0	0.0		67.0	18.0	NM_144684	Q5JPG9|Q6P0Q4|Q8N1M5	Missense_Mutation	SNP	ENST00000595962.1	hg19	CCDS12850.2	.	.	.	.	.	.	.	.	.	.	G	9.983	1.228670	0.22542	.	.	ENSG00000198464	ENST00000354515;ENST00000468240;ENST00000334564	T;T	0.03801	3.8;3.8	2.04	0.919	0.19392	Krueppel-associated box (4);	.	.	.	.	T	0.29914	0.0748	H	0.97940	4.11	0.20489	N	0.999899	P;D	0.63046	0.842;0.992	B;D	0.77004	0.201;0.989	T	0.07654	-1.0761	9	0.87932	D	0	.	6.3975	0.21620	0.1717:0.0:0.8283:0.0	.	55;55	F8WEZ9;Q8WV37	.;ZN480_HUMAN	L	77;55;55	ENSP00000417424:V55L;ENSP00000334164:V55L	ENSP00000334164:V55L	V	+	1	0	ZNF480	57509308	0.983000	0.35010	0.253000	0.24343	0.046000	0.14306	2.017000	0.40981	0.178000	0.19917	0.508000	0.49915	GTG	.	.		0.507	ZNF480-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349001.3	NM_144684		T	52817496	G	T	52817496	3	4	327	1	0	0	0	0	1	0	0	0	17950	1377	48	3	169	3	ZNF480	19	52817496	Missense_Mutation	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10	1645795	52817496	6311487	94	45918										
C20orf71	128861	hgsc.bcm.edu	37	chr20	31814775	31814775	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	aaatcctcgggcagctggatGtgaaactgttgaaaagcctc	11	9	0	2			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr20:31814775G>A	ENST00000375454.3	+	6	871	c.661G>A	c.(661-663)Gtg>Atg	p.V221M	BPIFA3_ENST00000490499.1_3'UTR|BPIFA3_ENST00000375452.3_Missense_Mutation_p.V185M	NM_178466.3	NP_848561.2	Q9BQP9	BPIA3_HUMAN	BPI fold containing family A, member 3	221						extracellular region (GO:0005576)	lipid binding (GO:0008289)										GCAGCTGGATGTGAAACTGTT	0.537																																					p.V221M		Atlas-SNP	.											.	.	.	.	0			c.G661A						.						139	132	135					20																	31814775		2203	4300	6503	SO:0001583	missense	128861	exon6			CTGGATGTGAAAC		CCDS13216.2, CCDS42865.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000131059	ENSG00000131059		"BPI fold containing"	16204	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 71"	C20orf71		11971875, 21787333	Standard	XR_244132		Approved	bA49G10.4, SPLUNC3	uc002wyr.3	Q9BQP9	OTTHUMG00000032245	ENST00000375454.3:c.661G>A	chr20.hg19:g.31814775G>A	ENSP00000364603:p.Val221Met	134.0	0.0		105.0	18.0	NM_178466	Q5JWG8|Q6NZ38	Missense_Mutation	SNP	ENST00000375454.3	hg19	CCDS13216.2	.	.	.	.	.	.	.	.	.	.	G	17.52	3.409226	0.62399	.	.	ENSG00000131059	ENST00000375454;ENST00000375452	T;T	0.04654	3.58;3.58	4.02	4.02	0.46733	.	0.000000	0.41194	D	0.000931	T	0.11537	0.0281	L	0.29908	0.895	0.31907	N	0.615221	D;D	0.89917	1.0;0.998	D;D	0.91635	0.999;0.995	T	0.00870	-1.1533	10	0.72032	D	0.01	-21.3752	11.9596	0.53001	0.0:0.0:1.0:0.0	.	185;221	Q9BQP9-2;Q9BQP9	.;BPIA3_HUMAN	M	221;185	ENSP00000364603:V221M;ENSP00000364601:V185M	ENSP00000364601:V185M	V	+	1	0	BPIFA3	31278436	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	3.665000	0.54532	2.538000	0.85594	0.462000	0.41574	GTG	.	.		0.537	BPIFA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078672.1	NM_178466		A	31814775	G	A	31814775	3	1	327	1	0	0	0	0	1	0	0	0	2119	1377	48	3	683	3	C20orf71	20	31814775	Missense_Mutation	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10		31814775	31210745	95	45919										
EPB41L1	2036	hgsc.bcm.edu	37	chr20	34773213	34773213	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	cgcttcgcccctaaccagacCcgggagctggaggagaggat	14	13	0	2			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr20:34773213C>T	ENST00000338074.2	+	7	902	c.741C>T	c.(739-741)acC>acT	p.T247T	EPB41L1_ENST00000441639.1_Silent_p.T185T|EPB41L1_ENST00000373950.2_Silent_p.T150T|EPB41L1_ENST00000202028.5_Silent_p.T185T|EPB41L1_ENST00000373946.3_Silent_p.T216T|EPB41L1_ENST00000373941.1_Silent_p.T247T	NM_001258329.1|NM_012156.2	NP_001245258.1|NP_036288.2	Q9H4G0	E41L1_HUMAN	erythrocyte membrane protein band 4.1-like 1	247	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cortical actin cytoskeleton organization (GO:0030866)|synaptic transmission (GO:0007268)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(10)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	37	Breast(12;0.0239)					CTAACCAGACCCGGGAGCTGG	0.592																																					p.T247T		Atlas-SNP	.											.	EPB41L1	111	.	0			c.C741T						.						48	46	47					20																	34773213		2203	4300	6503	SO:0001819	synonymous_variant	2036	exon8			CCAGACCCGGGAG	AB002336	CCDS13271.1, CCDS13272.1, CCDS58771.1	20q11.2-q12	2003-03-17			ENSG00000088367	ENSG00000088367			3378	protein-coding gene	gene with protein product		602879				9570967, 9828140	Standard	NM_012156		Approved	KIAA0338	uc002xfb.3	Q9H4G0	OTTHUMG00000032378	ENST00000338074.2:c.741C>T	chr20.hg19:g.34773213C>T		93.0	0.0		86.0	13.0	NM_001258329	O15046|Q4VXM6|Q4VXM7|Q4VXM8|Q4VXN4|Q6ZT61|Q8IUU7|Q96CV5|Q96L65	Silent	SNP	ENST00000338074.2	hg19	CCDS13271.1																																																																																			.	.		0.592	EPB41L1-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078978.3	NM_012156		T	34773213	C	T	34773213	2	4	327	1	0	0	0	0	0	0	0	1	5154	610	22	3		3	EPB41L1	20	34773213	Silent	SNP	C	TCGA-NI-A4U2-01A-11D-A28X-10	2958438	34773213	28252307	96	45920										
ZSWIM1	90204	hgsc.bcm.edu	37	chr20	44511883	44511883	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	gaaagttgtatacactcctgAgcaactgcatccctccagcc	7	14	0	1			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr20:44511883A>C	ENST00000372523.1	+	2	747	c.652A>C	c.(652-654)Agc>Cgc	p.S218R	ZSWIM1_ENST00000372520.1_Missense_Mutation_p.S218R	NM_080603.4	NP_542170.3	Q9BR11	ZSWM1_HUMAN	zinc finger, SWIM-type containing 1	218						nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	13		Myeloproliferative disorder(115;0.028)				TACACTCCTGAGCAACTGCAT	0.597																																					p.S218R		Atlas-SNP	.											.	ZSWIM1	35	.	0			c.A652C						.						50	48	49					20																	44511883		2203	4300	6503	SO:0001583	missense	90204	exon2			CTCCTGAGCAACT	AL008726	CCDS13382.2	20q13.12	2013-09-20	2003-12-17	2003-12-19	ENSG00000168612	ENSG00000168612		"Zinc fingers, SWIM-type"	16155	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 162"	C20orf162			Standard	NM_080603		Approved	dJ337O18.5	uc010ghi.3	Q9BR11	OTTHUMG00000074023	ENST00000372523.1:c.652A>C	chr20.hg19:g.44511883A>C	ENSP00000361601:p.Ser218Arg	80.0	0.0		74.0	20.0	NM_080603	Q5JZH2|Q9BR12|Q9BV30	Missense_Mutation	SNP	ENST00000372523.1	hg19	CCDS13382.2	.	.	.	.	.	.	.	.	.	.	A	1.243	-0.620919	0.03636	.	.	ENSG00000168612	ENST00000372523;ENST00000372520	T;T	0.24151	1.87;1.87	5.37	4.28	0.50868	.	0.328871	0.25439	U	0.030673	T	0.15089	0.0364	L	0.27053	0.805	0.26265	N	0.978518	B	0.26876	0.162	B	0.24006	0.05	T	0.24012	-1.0172	10	0.09084	T	0.74	-11.2214	9.9652	0.41721	0.924:0.0:0.076:0.0	.	218	Q9BR11	ZSWM1_HUMAN	R	218	ENSP00000361601:S218R;ENSP00000361598:S218R	ENSP00000361598:S218R	S	+	1	0	ZSWIM1	43945290	1.000000	0.71417	0.992000	0.48379	0.122000	0.20287	2.852000	0.48310	1.060000	0.40578	0.528000	0.53228	AGC	.	.		0.597	ZSWIM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157064.2	NM_080603		C	44511883	A	C	44511883	3	2	327	1	0	0	0	0	1	0	0	0	18255	304	11	5	654	5	ZSWIM1	20	44511883	Missense_Mutation	SNP	A	TCGA-NI-A4U2-01A-11D-A28X-10	9738670	44511883	18513637	97	45921										
RFPL2	10739	hgsc.bcm.edu	37	chr22	32589248	32589248	+	Intron	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	gcctgttagttgtgacaagtGacaaccttttcatgcataga	9	8	1	3			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chr22:32589248G>A	ENST00000400237.1	-	4	1201				RFPL2_ENST00000489846.1_5'UTR|RFPL2_ENST00000248980.4_Missense_Mutation_p.S5L|RFPL2_ENST00000400236.3_Intron|RFPL2_ENST00000248983.4_Intron			O75678	RFPL2_HUMAN	ret finger protein-like 2								zinc ion binding (GO:0008270)			endometrium(2)|kidney(4)|large_intestine(3)|lung(9)|ovary(1)|skin(2)	21						TGTGACAAGTGACAACCTTTT	0.468																																					p.S5L		Atlas-SNP	.											.	RFPL2	81	.	0			c.C14T						.						53	60	58					22																	32589248		1323	2305	3628	SO:0001627	intron_variant	10739	exon1			ACAAGTGACAACC	AJ010231	CCDS43009.1, CCDS46694.1, CCDS43009.2	22q12.3	2008-06-12				ENSG00000128253		"RING-type (C3HC4) zinc fingers"	9979	protein-coding gene	gene with protein product		605969				10508838	Standard	NM_001098527		Approved	RNF79	uc003amg.3	O75678		ENST00000400237.1:c.266-69C>T	chr22.hg19:g.32589248G>A		217.0	0.0		211.0	106.0	NM_006605		Missense_Mutation	SNP	ENST00000400237.1	hg19	CCDS43009.2	.	.	.	.	.	.	.	.	.	.	G	3.137	-0.177170	0.06380	.	.	ENSG00000128253	ENST00000248980	T	0.54071	0.59	0.628	-1.26	0.09376	.	.	.	.	.	T	0.30070	0.0753	N	0.22421	0.69	0.09310	N	1	B	0.19817	0.039	B	0.18263	0.021	T	0.15896	-1.0421	7	.	.	.	.	.	.	.	.	5	O75678-3	.	L	5	ENSP00000248980:S5L	.	S	-	2	0	RFPL2	30919248	0.033000	0.19621	0.004000	0.12327	0.011000	0.07611	-0.582000	0.05814	-0.961000	0.03609	-0.693000	0.03709	TCA	.	.		0.468	RFPL2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075262.2	NM_006605		A	32589248	G	A	32589248	1	1	327	0	1	0	0	0	0	0	0	0	13269	1294	45	3		3	RFPL2	22	32589248	Intron	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10		32589248	18715318	98	45922										
CLCN5	1184	hgsc.bcm.edu	37	chrX	49854827	49854827	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	cataatgtttgaactgactgGtggcttagaatacatcgtgc	10	7	0	3			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chrX:49854827G>T	ENST00000307367.2	+	10	1880	c.1589G>T	c.(1588-1590)gGt>gTt	p.G530V	CLCN5_ENST00000376108.3_Missense_Mutation_p.G530V|CLCN5_ENST00000376088.3_Missense_Mutation_p.G600V|CLCN5_ENST00000376091.3_Missense_Mutation_p.G600V			P51795	CLCN5_HUMAN	chloride channel, voltage-sensitive 5	530					chloride transmembrane transport (GO:1902476)|endocytosis (GO:0006897)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(8)|ovary(2)|skin(1)	30	Ovarian(276;0.236)					GAACTGACTGGTGGCTTAGAA	0.498																																					p.G600V		Atlas-SNP	.											.	CLCN5	137	.	0			c.G1799T						.						181	165	171					X																	49854827		2203	4300	6503	SO:0001583	missense	1184	exon13			TGACTGGTGGCTT	X91906	CCDS14328.1, CCDS48115.1, CCDS69763.1	Xp11.23-p11.22	2012-09-26	2012-02-23		ENSG00000171365	ENSG00000171365		"Ion channels / Chloride channels : Voltage-sensitive"	2023	protein-coding gene	gene with protein product	"Dent disease"	300008	"nephrolithiasis 2, X-linked", "nephrolithiasis 1 (X-linked)", "chloride channel 5"	NPHL2, NPHL1		7874126, 8111383, 8099916, 8559248, 9602200	Standard	NM_001272102		Approved	DENTS, XLRH, hClC-K2, hCIC-K2, CLC5, XRN, ClC-5	uc004doq.1	P51795	OTTHUMG00000021514	ENST00000307367.2:c.1589G>T	chrX.hg19:g.49854827G>T	ENSP00000304257:p.Gly530Val	66.0	0.0		49.0	29.0	NM_001127898	A1L475|B3KPN6|Q5JQD5|Q7RTN8	Missense_Mutation	SNP	ENST00000307367.2	hg19	CCDS14328.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.455589	0.84209	.	.	ENSG00000171365	ENST00000376088;ENST00000450422;ENST00000376091;ENST00000376108;ENST00000307367	D;D;D;D	0.95069	-3.6;-3.6;-3.6;-3.6	5.79	5.79	0.91817	Chloride channel, core (2);	0.000000	0.85682	D	0.000000	D	0.98416	0.9473	H	0.97682	4.055	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.99723	1.1010	10	0.87932	D	0	-2.6316	17.6718	0.88220	0.0:0.0:1.0:0.0	.	530;600	P51795;P51795-2	CLCN5_HUMAN;.	V	600;432;600;530;530	ENSP00000365256:G600V;ENSP00000365259:G600V;ENSP00000365276:G530V;ENSP00000304257:G530V	ENSP00000304257:G530V	G	+	2	0	CLCN5	49741567	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.705000	0.98719	2.445000	0.82738	0.600000	0.82982	GGT	.	.		0.498	CLCN5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056544.1			T	49854827	G	T	49854827	3	4	327	1	0	0	0	0	1	0	0	0	3468	1261	44	3	1841	3	CLCN5	23	49854827	Missense_Mutation	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10		49854827	105415733	99	45923										
FAM46D	169966	hgsc.bcm.edu	37	chrX	79698451	79698451	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	acagaaattggtcaaggtttGcaatgggcatgattgttgga	13	4	1	2			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chrX:79698451G>A	ENST00000308293.5	+	3	652	c.413G>A	c.(412-414)tGc>tAc	p.C138Y	FAM46D_ENST00000538312.1_Missense_Mutation_p.C138Y	NM_152630.4	NP_689843.1	Q8NEK8	FA46D_HUMAN	family with sequence similarity 46, member D	138										kidney(1)|large_intestine(6)|liver(3)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23						GTCAAGGTTTGCAATGGGCAT	0.378																																					p.C138Y		Atlas-SNP	.											.	FAM46D	69	.	0			c.G413A						.						119	114	116					X																	79698451		2203	4298	6501	SO:0001583	missense	169966	exon5			AGGTTTGCAATGG	BX537938	CCDS14446.1	Xq21.1	2009-08-18			ENSG00000174016	ENSG00000174016			28399	protein-coding gene	gene with protein product	"cancer/testis antigen 112"					12477932	Standard	NM_152630		Approved	MGC26999, CT1.26, CT112	uc004edl.1	Q8NEK8	OTTHUMG00000021902	ENST00000308293.5:c.413G>A	chrX.hg19:g.79698451G>A	ENSP00000308575:p.Cys138Tyr	80.0	0.0		49.0	7.0	NM_001170574	B2R9Q6|Q7Z3F6|Q8NHU1	Missense_Mutation	SNP	ENST00000308293.5	hg19	CCDS14446.1	.	.	.	.	.	.	.	.	.	.	G	0.250	-1.007247	0.02112	.	.	ENSG00000174016	ENST00000538312;ENST00000308293	T;T	0.24723	1.84;1.84	4.38	3.48	0.39840	Domain of unknown function DUF1693 (1);	0.123552	0.56097	D	0.000027	T	0.19886	0.0478	L	0.58101	1.795	0.33804	D	0.627047	P	0.34864	0.473	B	0.31812	0.136	T	0.12041	-1.0563	10	0.08179	T	0.78	-7.5637	9.7805	0.40645	0.0:0.4204:0.5796:0.0	.	138	Q8NEK8	FA46D_HUMAN	Y	138	ENSP00000443410:C138Y;ENSP00000308575:C138Y	ENSP00000308575:C138Y	C	+	2	0	FAM46D	79585107	1.000000	0.71417	1.000000	0.80357	0.037000	0.13140	2.639000	0.46570	2.025000	0.59659	0.538000	0.68166	TGC	.	.		0.378	FAM46D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057338.1	NM_152630		A	79698451	G	A	79698451	3	1	327	1	0	0	0	0	1	0	0	0	5576	1319	46	3	415	3	FAM46D	23	79698451	Missense_Mutation	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10	29843624	79698451	75572109	100	45924										
SLC25A5	292	hgsc.bcm.edu	37	chrX	118603838	118603838	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	tgtggacaagagaacccagtTttggctctactttgcaggga	12	8	1	1			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chrX:118603838T>G	ENST00000317881.8	+	2	442	c.326T>G	c.(325-327)tTt>tGt	p.F109C	SLC25A5-AS1_ENST00000446986.1_RNA|SLC25A5_ENST00000460013.1_3'UTR	NM_001152.4	NP_001143.2	P05141	ADT2_HUMAN	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 5	109					adenine transport (GO:0015853)|chromosome segregation (GO:0007059)|energy reserve metabolic process (GO:0006112)|negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901029)|positive regulation of cell proliferation (GO:0008284)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|MMXD complex (GO:0071817)|nucleus (GO:0005634)	adenine transmembrane transporter activity (GO:0015207)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|stomach(2)	12					Clodronate(DB00720)	AGAACCCAGTTTTGGCTCTAC	0.517																																					p.F109C		Atlas-SNP	.											.	SLC25A5	33	.	0			c.T326G						.						105	105	105					X																	118603838		2203	4300	6503	SO:0001583	missense	292	exon2			CCCAGTTTTGGCT	BC068199	CCDS14578.1	Xq24	2013-08-09			ENSG00000005022	ENSG00000005022		"Solute carriers"	10991	protein-coding gene	gene with protein product		300150		ANT2		2168878, 2829183	Standard	NM_001152		Approved	T2, 2F1, T3	uc004erh.4	P05141	OTTHUMG00000022715	ENST00000317881.8:c.326T>G	chrX.hg19:g.118603838T>G	ENSP00000360671:p.Phe109Cys	80.0	0.0		104.0	11.0	NM_001152	B2RCV1|O43350	Missense_Mutation	SNP	ENST00000317881.8	hg19	CCDS14578.1	.	.	.	.	.	.	.	.	.	.	T	17.63	3.436537	0.62955	.	.	ENSG00000005022	ENST00000317881	T	0.78595	-1.19	4.35	4.35	0.52113	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.87736	0.6252	M	0.85299	2.745	0.58432	D	0.999998	D	0.76494	0.999	D	0.71414	0.973	D	0.89459	0.3735	10	0.87932	D	0	.	12.0671	0.53594	0.0:0.0:0.0:1.0	.	109	P05141	ADT2_HUMAN	C	109	ENSP00000360671:F109C	ENSP00000360671:F109C	F	+	2	0	SLC25A5	118487866	1.000000	0.71417	0.997000	0.53966	0.988000	0.76386	7.635000	0.83286	1.685000	0.51034	0.430000	0.28490	TTT	.	.		0.517	SLC25A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058952.2	NM_001152		G	118603838	T	G	118603838	3	3	327	1	0	0	0	0	1	0	0	0	14527	1841	64	5	332	5	SLC25A5	23	118603838	Missense_Mutation	SNP	T	TCGA-NI-A4U2-01A-11D-A28X-10	38905387	118603838	36666722	101	45925										
XPNPEP2	7512	hgsc.bcm.edu	37	chrX	128876095	128876095	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	ggcttctagcttgtgcctggGgccacacaaagccagtggac	13	12	1	0			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chrX:128876095G>T	ENST00000371106.3	+	2	253	c.61G>T	c.(61-63)Ggc>Tgc	p.G21C	XPNPEP2_ENST00000371105.3_Missense_Mutation_p.G21C	NM_003399.5	NP_003390.4	O43895	XPP2_HUMAN	X-prolyl aminopeptidase (aminopeptidase P) 2, membrane-bound	21						anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			endometrium(3)|kidney(3)|large_intestine(5)|liver(1)|lung(20)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	37						TTGTGCCTGGGGCCACACAAA	0.637																																					p.G21C		Atlas-SNP	.											.	XPNPEP2	84	.	0			c.G61T						.						52	46	48					X																	128876095		2203	4300	6503	SO:0001583	missense	7512	exon2			GCCTGGGGCCACA	U90724	CCDS14613.1	Xq25	2008-02-05			ENSG00000122121	ENSG00000122121	3.4.11.9		12823	protein-coding gene	gene with protein product		300145				9375790, 9628831	Standard	NM_003399		Approved		uc004eut.1	O43895	OTTHUMG00000022373	ENST00000371106.3:c.61G>T	chrX.hg19:g.128876095G>T	ENSP00000360147:p.Gly21Cys	48.0	0.0		58.0	4.0	NM_003399	A0AV16|O75994	Missense_Mutation	SNP	ENST00000371106.3	hg19	CCDS14613.1	.	.	.	.	.	.	.	.	.	.	G	15.50	2.850939	0.51270	.	.	ENSG00000122121	ENST00000371105;ENST00000371106	T	0.75367	-0.93	5.35	4.4	0.53042	.	0.145984	0.64402	D	0.000012	T	0.72011	0.3408	L	0.32530	0.975	0.30260	N	0.793254	D;D	0.71674	0.998;0.994	P;P	0.57371	0.797;0.819	T	0.70876	-0.4753	10	0.87932	D	0	-6.6377	5.5858	0.17274	0.1988:0.0:0.8012:0.0	.	21;21	B4DV70;O43895	.;XPP2_HUMAN	C	21	ENSP00000360147:G21C	ENSP00000360146:G21C	G	+	1	0	XPNPEP2	128703776	1.000000	0.71417	0.951000	0.38953	0.532000	0.34746	1.594000	0.36697	0.932000	0.37266	0.594000	0.82650	GGC	.	.		0.637	XPNPEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058210.1	NM_003399		T	128876095	G	T	128876095	3	4	327	1	0	0	0	0	1	0	0	0	17458	1232	43	3	67	3	XPNPEP2	23	128876095	Missense_Mutation	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10	10272257	128876095	26394465	102	45926										
BCORL1	63035	hgsc.bcm.edu	37	chrX	129149866	129149866	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	ccagcacagagcgcccacagCttggaagccaggtggatctg	13	13	1	1			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chrX:129149866C>G	ENST00000218147.7	+	4	3315	c.3118C>G	c.(3118-3120)Ctt>Gtt	p.L1040V	BCORL1_ENST00000303743.5_Missense_Mutation_p.L1040V|BCORL1_ENST00000359304.2_Missense_Mutation_p.L1040V|BCORL1_ENST00000540052.1_Missense_Mutation_p.L1040V			Q5H9F3	BCORL_HUMAN	BCL6 corepressor-like 1	1040					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|liver(3)|lung(30)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	75						GCGCCCACAGCTTGGAAGCCA	0.582																																					p.L1040V		Atlas-SNP	.											.	BCORL1	213	.	0			c.C3118G						.						71	61	65					X																	129149866		2203	4300	6503	SO:0001583	missense	63035	exon3			CCACAGCTTGGAA	AL136450	CCDS14616.1	Xq25-q26.1	2014-09-17	2010-06-10		ENSG00000085185	ENSG00000085185		"Ankyrin repeat domain containing"	25657	protein-coding gene	gene with protein product		300688	"chromosome X open reading frame 10", "BCL6 co-repressor-like 1"	CXorf10			Standard	NM_021946		Approved	FLJ11362	uc022cdu.1	Q5H9F3	OTTHUMG00000022379	ENST00000218147.7:c.3118C>G	chrX.hg19:g.129149866C>G	ENSP00000218147:p.Leu1040Val	101.0	0.0		129.0	81.0	NM_021946	B5MDQ8|Q5H9F2|Q5H9F4|Q6ZVE0|Q8TEN3|Q9Y528	Missense_Mutation	SNP	ENST00000218147.7	hg19	CCDS14616.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.207|9.207	1.029862|1.029862	0.19512|0.19512	.|.	.|.	ENSG00000085185|ENSG00000085185	ENST00000441294|ENST00000218147;ENST00000303743;ENST00000359304;ENST00000540052;ENST00000456822	.|T;T;T;T;T	.|0.41758	.|1.0;1.37;0.99;1.0;1.44	5.05|5.05	4.18|4.18	0.49190|0.49190	.|.	.|0.000000	.|0.32868	.|N	.|0.005546	T|T	0.30070|0.30070	0.0753|0.0753	N|N	0.24115|0.24115	0.695|0.695	0.24437|0.24437	N|N	0.994542|0.994542	.|P;P	.|0.45474	.|0.859;0.801	.|P;B	.|0.47673	.|0.554;0.275	T|T	0.09509|0.09509	-1.0671|-1.0671	5|10	.|0.30854	.|T	.|0.27	-12.9564|-12.9564	4.3872|4.3872	0.11323|0.11323	0.0:0.6334:0.0:0.3666|0.0:0.6334:0.0:0.3666	.|.	.|1040;1040	.|Q5H9F3-2;Q5H9F3	.|.;BCORL_HUMAN	G|V	475|1040;1040;1040;1040;640	.|ENSP00000218147:L1040V;ENSP00000307541:L1040V;ENSP00000352253:L1040V;ENSP00000437775:L1040V;ENSP00000399483:L640V	.|ENSP00000218147:L1040V	A|L	+|+	2|1	0|0	BCORL1|BCORL1	128977547|128977547	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.418000|0.418000	0.31294|0.31294	2.400000|2.400000	0.44504|0.44504	2.097000|2.097000	0.63578|0.63578	0.529000|0.529000	0.55759|0.55759	GCT|CTT	.	.		0.582	BCORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058223.1	NM_021946		G	129149866	C	G	129149866	3	3	327	1	0	0	0	0	1	0	0	0	1387	797	28	4	3128	4	BCORL1	23	129149866	Missense_Mutation	SNP	C	TCGA-NI-A4U2-01A-11D-A28X-10	273771	129149866	26120694	103	45927										
IGSF1	3547	hgsc.bcm.edu	37	chrX	130408573	130408573	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	tggagagattattctcttacCtgctgcccccaccagctcca	7	15	1	1			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chrX:130408573C>T	ENST00000361420.3	-	18	3830	c.3751G>A	c.(3751-3753)Ggg>Agg	p.G1251R	IGSF1_ENST00000467244.1_5'Flank|IGSF1_ENST00000370903.3_Splice_Site_p.G1256R|IGSF1_ENST00000370910.1_Splice_Site_p.G1242R|IGSF1_ENST00000370904.1_Splice_Site_p.G1242R			Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1	1251					regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	coreceptor activity (GO:0015026)|inhibin binding (GO:0034711)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|liver(1)|lung(37)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)	78						ATTCTCTTACCTGCTGCCCCC	0.552																																					p.G1256R		Atlas-SNP	.											.	IGSF1	231	.	0			c.G3766A						.						109	100	103					X																	130408573		2203	4300	6503	SO:0001630	splice_region_variant	3547	exon18			TCTTACCTGCTGC	AF034198	CCDS14629.1, CCDS14630.1, CCDS55490.1, CCDS55491.1	Xq25	2013-01-11			ENSG00000147255	ENSG00000147255		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5948	protein-coding gene	gene with protein product		300137				9521868, 9729118	Standard	NM_001555		Approved	KIAA0364, IGDC1, IGCD1, INHBP, MGC75490, PGSF2	uc004ewe.4	Q8N6C5	OTTHUMG00000022406	ENST00000361420.3:c.3751+1G>A	chrX.hg19:g.130408573C>T		60.0	0.0		29.0	5.0	NM_001170961	B5MEG2|H9KV64|O15070|Q9NTC8	Missense_Mutation	SNP	ENST00000361420.3	hg19	CCDS14629.1	.	.	.	.	.	.	.	.	.	.	C	15.47	2.843851	0.51164	.	.	ENSG00000147255	ENST00000370910;ENST00000361420;ENST00000370904;ENST00000370903	T;T;T;T	0.00705	5.82;5.82;5.82;5.81	5.42	5.42	0.78866	.	0.000000	0.48767	D	0.000176	T	0.02767	0.0083	L	0.48642	1.525	0.38767	D	0.954455	D;D;D	0.89917	0.958;1.0;1.0	P;D;D	0.87578	0.903;0.997;0.998	T	0.66221	-0.5978	9	.	.	.	.	13.7754	0.63050	0.0:1.0:0.0:0.0	.	1242;695;1251	Q8N6C5-2;C9JP68;Q8N6C5	.;.;IGSF1_HUMAN	R	1242;1251;1242;1256	ENSP00000359947:G1242R;ENSP00000355010:G1251R;ENSP00000359941:G1242R;ENSP00000359940:G1256R	.	G	-	1	0	IGSF1	130236254	1.000000	0.71417	1.000000	0.80357	0.855000	0.48748	2.509000	0.45459	2.410000	0.81850	0.594000	0.82650	GGG	.	.		0.552	IGSF1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058288.1		Missense_Mutation	T	130408573	C	T	130408573	5	4	327	1	0	0	0	0	0	0	1	0	7605	695	24	3	271	3	IGSF1	23	130408573	Splice_Site	SNP	C	TCGA-NI-A4U2-01A-11D-A28X-10	1258707	130408573	24861987	104	45928										
SLC9A6	10479	hgsc.bcm.edu	37	chrX	135106598	135106598	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	gtgttttttaccgtgtgggtAtttggtggtggcaccactgc	14	7	0	0			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chrX:135106598A>G	ENST00000370698.3	+	12	1511	c.1476A>G	c.(1474-1476)gtA>gtG	p.V492V	SLC9A6_ENST00000370701.1_Silent_p.V472V|SLC9A6_ENST00000370695.4_Silent_p.V524V	NM_006359.2	NP_006350.1	Q92581	SL9A6_HUMAN	solute carrier family 9, subfamily A (NHE6, cation proton antiporter 6), member 6	492					axon extension (GO:0048675)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|dendrite extension (GO:0097484)|dendritic spine development (GO:0060996)|ion transport (GO:0006811)|neuron projection morphogenesis (GO:0048812)|regulation of neurotrophin TRK receptor signaling pathway (GO:0051386)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon terminus (GO:0043679)|axonal spine (GO:0044308)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome membrane (GO:0031901)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)|synapse (GO:0045202)	sodium:proton antiporter activity (GO:0015385)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(18)|ovary(2)|upper_aerodigestive_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					CCGTGTGGGTATTTGGTGGTG	0.408																																					p.V524V		Atlas-SNP	.											.	SLC9A6	64	.	0			c.A1572G						.						286	207	234					X																	135106598		2203	4300	6503	SO:0001819	synonymous_variant	10479	exon12			GTGGGTATTTGGT	AF030409	CCDS14654.1, CCDS44003.1, CCDS55504.1	Xq26.3	2013-05-22	2012-03-22		ENSG00000198689	ENSG00000198689		"Solute carriers"	11079	protein-coding gene	gene with protein product		300231	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 6", "solute carrier family 9 (sodium/hydrogen exchanger), member 6"			9507001	Standard	NM_001042537		Approved	NHE6, KIAA0267	uc004ezk.3	Q92581	OTTHUMG00000022498	ENST00000370698.3:c.1476A>G	chrX.hg19:g.135106598A>G		106.0	0.0		93.0	54.0	NM_001042537	A6NIQ9|A8K160|B4DU30|B7ZAE0|Q3ZCW7|Q5JPP8|Q5JPP9|Q86VS0	Silent	SNP	ENST00000370698.3	hg19	CCDS14654.1																																																																																			.	.		0.408	SLC9A6-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058450.1	NM_006359		G	135106598	A	G	135106598	2	3	327	1	0	0	0	0	0	0	0	1	14733	436	16	2		2	SLC9A6	23	135106598	Silent	SNP	A	TCGA-NI-A4U2-01A-11D-A28X-10	4698025	135106598	20163962	105	45929										
GAB3	139716	hgsc.bcm.edu	37	chrX	153940659	153940659	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0784313725490196	8	1	1.38183048553544	3.40522512506948	1.018657088696	0.637186343068696	1	0	ggcggggaggtggagtgttgGacataatgtctagttctttt	16	4	2	0			TCGA-NI-A4U2-01A-11D-A28X-10	TCGA-NI-A4U2-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa0d37a-b560-4a23-bc45-a3118eb5883a	3f6c5637-3042-4e1e-95c6-189ca0e5719e	g.chrX:153940659G>A	ENST00000369575.3	-	4	942	c.911C>T	c.(910-912)tCc>tTc	p.S304F	GAB3_ENST00000496390.1_Intron|GAB3_ENST00000424127.2_Missense_Mutation_p.S305F	NM_001081573.1|NM_080612.2	NP_001075042.1|NP_542179.1	Q8WWW8	GAB3_HUMAN	GRB2-associated binding protein 3	304					macrophage differentiation (GO:0030225)					NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)	25	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					TGGAGTGTTGGACATAATGTC	0.488																																					p.S305F		Atlas-SNP	.											.	GAB3	73	.	0			c.C914T						.						139	127	131					X																	153940659		2203	4300	6503	SO:0001583	missense	139716	exon4			GTGTTGGACATAA	AY057989	CCDS14760.1, CCDS48198.1, CCDS65357.1	Xq28	2013-01-10			ENSG00000160219	ENSG00000160219		"Pleckstrin homology (PH) domain containing"	17515	protein-coding gene	gene with protein product	"DOS/Gab family member 3", "Gab3 scaffolding protein"	300482				11739737	Standard	XM_005274648		Approved		uc004fmk.1	Q8WWW8	OTTHUMG00000024245	ENST00000369575.3:c.911C>T	chrX.hg19:g.153940659G>A	ENSP00000358588:p.Ser304Phe	95.0	0.0		130.0	95.0	NM_001081573	A6NHF8|E9PB44	Missense_Mutation	SNP	ENST00000369575.3	hg19	CCDS14760.1	.	.	.	.	.	.	.	.	.	.	G	10.83	1.461877	0.26248	.	.	ENSG00000160219	ENST00000369575;ENST00000369568;ENST00000424127	T;T;T	0.21932	1.98;1.98;1.98	5.63	1.8	0.24995	.	0.378282	0.28376	N	0.015571	T	0.22936	0.0554	M	0.72118	2.19	0.09310	N	1	P;P;P	0.46395	0.877;0.877;0.877	P;P;P	0.45037	0.467;0.467;0.467	T	0.16364	-1.0405	10	0.54805	T	0.06	-0.1214	3.4229	0.07400	0.1424:0.1349:0.5809:0.1418	.	305;305;304	A6NHF8;E9PB44;Q8WWW8	.;.;GAB3_HUMAN	F	304;305;305	ENSP00000358588:S304F;ENSP00000358581:S305F;ENSP00000399588:S305F	ENSP00000358581:S305F	S	-	2	0	GAB3	153593853	0.022000	0.18835	0.000000	0.03702	0.489000	0.33432	0.867000	0.27968	-0.070000	0.12908	0.506000	0.49869	TCC	.	.		0.488	GAB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061192.2	NM_001081573		A	153940659	G	A	153940659	3	1	327	1	0	0	0	0	1	0	0	0	6158	1174	41	3	877	3	GAB3	23	153940659	Missense_Mutation	SNP	G	TCGA-NI-A4U2-01A-11D-A28X-10	18834061	153940659	1329901	106	45930										
YTHDF2	51441	hgsc.bcm.edu	37	chr1	29070165	29070165	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	gtttacttacttttcagtgtCaacggcagtggacacttctg	9	9	3	0			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr1:29070165C>T	ENST00000373812.3	+	4	1745	c.1383C>T	c.(1381-1383)gtC>gtT	p.V461V	YTHDF2_ENST00000542507.1_Silent_p.V461V|YTHDF2_ENST00000478283.1_3'UTR|YTHDF2_ENST00000541996.1_Silent_p.V411V	NM_016258.2	NP_057342.2	Q9Y5A9	YTHD2_HUMAN	YTH domain family, member 2	461	Interaction with m6A-containing mRNAs.|YTH. {ECO:0000255|PROSITE- ProRule:PRU00225}.				humoral immune response (GO:0006959)|regulation of mRNA stability (GO:0043488)	cytoplasmic mRNA processing body (GO:0000932)	N6-methyladenosine-containing RNA binding (GO:1990247)|poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Colorectal(325;3.46e-05)|Lung NSC(340;0.000601)|all_lung(284;0.000771)|Breast(348;0.00502)|Renal(390;0.00758)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;5.46e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0221)|KIRC - Kidney renal clear cell carcinoma(1967;0.0296)|READ - Rectum adenocarcinoma(331;0.0649)		TTTTCAGTGTCAACGGCAGTG	0.483																																					p.V461V		Atlas-SNP	.											.	YTHDF2	47	.	0			c.C1383T						.						64	63	63					1																	29070165		1912	4131	6043	SO:0001819	synonymous_variant	51441	exon4			CAGTGTCAACGGC	AF155095	CCDS41296.1, CCDS53287.1	1p35	2008-02-05	2004-11-16		ENSG00000198492	ENSG00000198492			31675	protein-coding gene	gene with protein product		610640	"YTH domain family 2"			10508479	Standard	NM_016258		Approved	HGRG8, NY-REN-2	uc021okf.1	Q9Y5A9	OTTHUMG00000003648	ENST00000373812.3:c.1383C>T	chr1.hg19:g.29070165C>T		356.0	0.0		302.0	55.0	NM_016258	A6NKG4|A8K966|B4E1G7|D3DPM8|Q5VSZ9|Q8TDH0|Q9BUJ5	Silent	SNP	ENST00000373812.3	hg19	CCDS41296.1																																																																																			.	.		0.483	YTHDF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010335.1	NM_016258		T	29070165	C	T	29070165	2	4	328	1	0	0	0	0	0	0	0	1	17514	813	29	3		3	YTHDF2	1	29070165	Silent	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10		29070165	220180456	1	45931										
MACF1	23499	hgsc.bcm.edu	37	chr1	39909144	39909144	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	ggcttccacagtgaaattgaAgatttcctcttggaacttac	8	9	1	3			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr1:39909144A>T	ENST00000372915.3	+	78	19113	c.19026A>T	c.(19024-19026)gaA>gaT	p.E6342D	MACF1_ENST00000567887.1_Missense_Mutation_p.E6480D|MACF1_ENST00000564288.1_Missense_Mutation_p.E6443D|MACF1_ENST00000289893.4_Missense_Mutation_p.E4886D|MACF1_ENST00000539005.1_Missense_Mutation_p.E4254D|MACF1_ENST00000317713.7_Missense_Mutation_p.E4384D|MACF1_ENST00000545844.1_Missense_Mutation_p.E4384D|MACF1_ENST00000361689.2_Missense_Mutation_p.E4384D			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	6342					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			GTGAAATTGAAGATTTCCTCT	0.408																																					p.E4384D		Atlas-SNP	.											.	MACF1	909	.	0			c.A13152T						.						85	88	87					1																	39909144		2203	4300	6503	SO:0001583	missense	23499	exon76			AATTGAAGATTTC	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.19026A>T	chr1.hg19:g.39909144A>T	ENSP00000362006:p.Glu6342Asp	55.0	0.0		42.0	28.0	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.54|18.54	3.645261|3.645261	0.67358|0.67358	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893|ENST00000372925	T;T;T;T;T;T|.	0.47528|.	1.39;0.84;1.39;1.39;1.39;0.84|.	6.16|6.16	6.16|6.16	0.99307|0.99307	.|.	0.000000|.	0.64402|.	D|.	0.000005|.	T|.	0.63896|.	0.2550|.	M|M	0.66939|0.66939	2.045|2.045	0.80722|0.80722	D|D	1|1	P;D|.	0.62365|.	0.709;0.991|.	B;P|.	0.59595|.	0.338;0.86|.	T|.	0.65421|.	-0.6172|.	10|.	0.59425|.	D|.	0.04|.	.|.	7.6753|7.6753	0.28481|0.28481	0.7893:0.1416:0.0691:0.0|0.7893:0.1416:0.0691:0.0	.|.	6342;4384|.	Q9UPN3;F8W8Q1|.	MACF1_HUMAN;.|.	D|X	4384;6342;4384;4384;4254;4886|3388	ENSP00000439537:E4384D;ENSP00000362006:E6342D;ENSP00000354573:E4384D;ENSP00000313438:E4384D;ENSP00000444364:E4254D;ENSP00000289893:E4886D|.	ENSP00000289893:E4886D|.	E|R	+|+	3|1	2|2	MACF1|MACF1	39681731|39681731	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	3.051000|3.051000	0.49885|0.49885	2.367000|2.367000	0.80283|0.80283	0.528000|0.528000	0.53228|0.53228	GAA|AGA	.	.		0.408	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		T	39909144	A	T	39909144	3	4	328	1	0	0	0	0	1	0	0	0	9153	69	3	4	19601	4	MACF1	1	39909144	Missense_Mutation	SNP	A	TCGA-NI-A8LF-01A-11D-A35Z-10	10838979	39909144	209341477	2	45932										
SEMA6C	10500	hgsc.bcm.edu	37	chr1	151111134	151111134	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	tgcggcacacagggctgaatGagttcgttccacaggcaagg	14	10	0	2			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr1:151111134G>T	ENST00000341697.3	-	7	2119	c.428C>A	c.(427-429)tCa>tAa	p.S143*				Q9H3T2	SEM6C_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C	143	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	28	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			AGGGCTGAATGAGTTCGTTCC	0.527																																					p.S143X		Atlas-SNP	.											.	SEMA6C	70	.	0			c.C428A						.						94	86	89					1																	151111134		2203	4300	6503	SO:0001587	stop_gained	10500	exon7			CTGAATGAGTTCG	AF339154	CCDS984.1, CCDS53363.1, CCDS53364.1	1q21.2	2008-02-05			ENSG00000143434	ENSG00000143434		"Semaphorins"	10740	protein-coding gene	gene with protein product	"m-Sema Y2"	609294				12110693	Standard	NM_030913		Approved	KIAA1869	uc001ewv.3	Q9H3T2	OTTHUMG00000012261	ENST00000341697.3:c.428C>A	chr1.hg19:g.151111134G>T	ENSP00000344148:p.Ser143*	203.0	0.0		205.0	29.0	NM_001178061	D3DV15|Q5JR71|Q5JR72|Q5JR73|Q8WXT8|Q8WXT9|Q8WXU0|Q96JF8	Nonsense_Mutation	SNP	ENST00000341697.3	hg19	CCDS984.1	.	.	.	.	.	.	.	.	.	.	G	38	7.054255	0.98032	.	.	ENSG00000143434	ENST00000368914;ENST00000368912;ENST00000368913;ENST00000341697;ENST00000392792	.	.	.	5.06	5.06	0.68205	.	0.063943	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	.	15.9776	0.80083	0.0:0.0:1.0:0.0	.	.	.	.	X	143	.	ENSP00000344148:S143X	S	-	2	0	SEMA6C	149377758	1.000000	0.71417	0.978000	0.43139	0.939000	0.58152	9.101000	0.94219	2.642000	0.89623	0.561000	0.74099	TCA	.	.		0.527	SEMA6C-004	KNOWN	alternative_5_UTR|mRNA_start_NF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034074.1	NM_030913		T	151111134	G	T	151111134	4	4	328	1	0	0	0	0	0	1	0	0	14056	1294	45	3	2516	3	SEMA6C	1	151111134	Nonsense_Mutation	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10	111201990	151111134	98139487	3	45933										
FCRL5	83416	hgsc.bcm.edu	37	chr1	157488260	157488260	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	ggatgatccgtacttctgagTaaaccacattttctcctcta	6	11	3	2			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr1:157488260T>C	ENST00000361835.3	-	15	2928	c.2771A>G	c.(2770-2772)tAc>tGc	p.Y924C	FCRL5_ENST00000461387.1_5'UTR|FCRL5_ENST00000356953.4_Missense_Mutation_p.Y924C	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	924					negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(45)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	85	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)				TACTTCTGAGTAAACCACATT	0.438																																					p.Y924C		Atlas-SNP	.											.	FCRL5	177	.	0			c.A2771G						.						218	203	208					1																	157488260		2203	4300	6503	SO:0001583	missense	83416	exon15			TCTGAGTAAACCA	AF369794	CCDS1165.1	1q21	2013-01-11			ENSG00000143297	ENSG00000143297		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18508	protein-coding gene	gene with protein product		605877				11027651, 11290337	Standard	NM_031281		Approved	FCRH5, IRTA2, BXMAS1, CD307e	uc009wsm.3	Q96RD9	OTTHUMG00000017481	ENST00000361835.3:c.2771A>G	chr1.hg19:g.157488260T>C	ENSP00000354691:p.Tyr924Cys	105.0	0.0		113.0	27.0	NM_031281	A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Missense_Mutation	SNP	ENST00000361835.3	hg19	CCDS1165.1	.	.	.	.	.	.	.	.	.	.	T	13.49	2.252872	0.39797	.	.	ENSG00000143297	ENST00000361835;ENST00000356953	T;T	0.57595	0.39;0.4	5.04	5.04	0.67666	.	515.203000	0.00166	N	0.000000	T	0.67277	0.2876	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.52313	-0.8592	9	0.72032	D	0.01	.	11.0693	0.47993	0.0:0.0:0.0:1.0	.	924	Q96RD9	FCRL5_HUMAN	C	924	ENSP00000354691:Y924C;ENSP00000349434:Y924C	ENSP00000349434:Y924C	Y	-	2	0	FCRL5	155754884	0.969000	0.33509	0.963000	0.40424	0.107000	0.19398	3.093000	0.50217	2.108000	0.64289	0.533000	0.62120	TAC	.	.		0.438	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1	NM_031281		C	157488260	T	C	157488260	3	2	328	1	0	0	0	0	1	0	0	0	5806	1638	57	2	174	2	FCRL5	1	157488260	Missense_Mutation	SNP	T	TCGA-NI-A8LF-01A-11D-A35Z-10	6377126	157488260	91762361	4	45934										
CENPF	1063	hgsc.bcm.edu	37	chr1	214818024	214818024	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	tgctcagcaggacctcaatcTagacattgagaaaataactg	8	9	3	2			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr1:214818024T>C	ENST00000366955.3	+	13	5279	c.5111T>C	c.(5110-5112)cTa>cCa	p.L1704P		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	1800					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		GACCTCAATCTAGACATTGAG	0.428																																					p.L1704P	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.T5111C						.						69	68	69					1																	214818024		2203	4300	6503	SO:0001583	missense	1063	exon13			TCAATCTAGACAT	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.5111T>C	chr1.hg19:g.214818024T>C	ENSP00000355922:p.Leu1704Pro	276.0	0.0		254.0	99.0	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	hg19	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	T	9.826	1.187201	0.21870	.	.	ENSG00000117724	ENST00000366955	T	0.03920	3.76	5.04	1.25	0.21368	.	0.000000	0.30528	N	0.009422	T	0.06371	0.0164	M	0.68317	2.08	0.20307	N	0.999915	P	0.50943	0.94	P	0.44990	0.466	T	0.29058	-1.0024	10	0.66056	D	0.02	.	1.8429	0.03153	0.1734:0.0913:0.1611:0.5741	.	1800	P49454	CENPF_HUMAN	P	1704	ENSP00000355922:L1704P	ENSP00000355922:L1704P	L	+	2	0	CENPF	212884647	0.001000	0.12720	0.001000	0.08648	0.006000	0.05464	0.556000	0.23438	0.352000	0.24053	0.496000	0.49642	CTA	.	.		0.428	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		C	214818024	T	C	214818024	3	2	328	1	0	0	0	0	1	0	0	0	3233	1522	53	2	5157	2	CENPF	1	214818024	Missense_Mutation	SNP	T	TCGA-NI-A8LF-01A-11D-A35Z-10	57329764	214818024	34432597	5	45935										
NUP133	55746	hgsc.bcm.edu	37	chr1	229601263	229601263	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	atgactagcagcctgcagcaTatcctggaaaaaaagttaat	8	8	0	1			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr1:229601263T>A	ENST00000261396.3	-	17	2294	c.2203A>T	c.(2203-2205)Atg>Ttg	p.M735L	NUP133_ENST00000537506.1_Missense_Mutation_p.M719L	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	735					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore organization (GO:0006999)|paraxial mesoderm development (GO:0048339)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)			NS(1)|breast(7)|endometrium(1)|kidney(6)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(4)	56	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				GCCTGCAGCATATCCTGGAAA	0.338																																					p.M735L		Atlas-SNP	.											.	NUP133	111	.	0			c.A2203T						.						129	129	129					1																	229601263		2202	4299	6501	SO:0001583	missense	55746	exon17			GCAGCATATCCTG		CCDS1579.1	1q42.13	2008-02-05	2002-08-29		ENSG00000069248	ENSG00000069248			18016	protein-coding gene	gene with protein product		607613	"nucleoporin 133kD"			11684705	Standard	NM_018230		Approved	FLJ10814	uc001htn.3	Q8WUM0	OTTHUMG00000039462	ENST00000261396.3:c.2203A>T	chr1.hg19:g.229601263T>A	ENSP00000261396:p.Met735Leu	59.0	0.0		56.0	18.0	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Missense_Mutation	SNP	ENST00000261396.3	hg19	CCDS1579.1	.	.	.	.	.	.	.	.	.	.	T	15.56	2.869923	0.51588	.	.	ENSG00000069248	ENST00000366681;ENST00000261396;ENST00000366679;ENST00000537506	T;T;T	0.25250	2.0;1.81;2.01	5.88	5.88	0.94601	Nucleoporin, Nup133/Nup155-like, C-terminal (1);	0.108239	0.85682	D	0.000000	T	0.31638	0.0803	M	0.72894	2.215	0.52501	D	0.999955	B	0.19445	0.036	B	0.27608	0.081	T	0.08186	-1.0734	10	0.21540	T	0.41	-24.8757	14.5382	0.67976	0.0:0.0:0.0:1.0	.	735	Q8WUM0	NU133_HUMAN	L	735;735;735;719	ENSP00000261396:M735L;ENSP00000355640:M735L;ENSP00000443496:M719L	ENSP00000261396:M735L	M	-	1	0	NUP133	227667886	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	3.465000	0.53064	2.243000	0.73865	0.528000	0.53228	ATG	.	.		0.338	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230		A	229601263	T	A	229601263	3	1	328	1	0	0	0	0	1	0	0	0	10763	1406	49	4	1307	4	NUP133	1	229601263	Missense_Mutation	SNP	T	TCGA-NI-A8LF-01A-11D-A35Z-10	14783239	229601263	19649358	6	45936										
ABCB10	23456	hgsc.bcm.edu	37	chr1	229667460	229667460	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	ccagtcctttcatcagctccGagtagaaagagctcagacct	8	13	3	3	rs139689788		TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr1:229667460G>A	ENST00000344517.4	-	7	1400	c.1358C>T	c.(1357-1359)tCg>tTg	p.S453L		NM_012089.2	NP_036221.2	Q9NRK6	ABCBA_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 10	453	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of mitochondrial membrane (GO:0032592)|mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)	31	Breast(184;0.143)|Ovarian(103;0.249)	Prostate(94;0.167)				CATCAGCTCCGAGTAGAAAGA	0.542																																					p.S453L		Atlas-SNP	.											ABCB10,caecum,carcinoma,0,1	ABCB10	71	.	0			c.C1358T						.	G	LEU/SER	1,4405	2.1+/-5.4	0,1,2202	55	60	58		1358	6	1	1	dbSNP_134	58	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ABCB10	NM_012089.2	145	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	probably-damaging	453/739	229667460	2,13004	2203	4300	6503	SO:0001583	missense	23456	exon7			AGCTCCGAGTAGA	U18237	CCDS1580.1	1q32	2012-03-14			ENSG00000135776	ENSG00000135776		"ATP binding cassette transporters / subfamily B"	41	protein-coding gene	gene with protein product	"ATP-binding cassette sub-family B member 10, mitochondrial", "ATP-binding cassette transporter 10", "ABC transporter 10 protein", "mitochondrial ATP-binding cassette 2"	605454				7766993	Standard	NM_012089		Approved	EST20237, M-ABC2, MTABC2	uc001htp.4	Q9NRK6	OTTHUMG00000039471	ENST00000344517.4:c.1358C>T	chr1.hg19:g.229667460G>A	ENSP00000355637:p.Ser453Leu	158.0	1.0		103.0	18.0	NM_012089	Q13040|Q6P1Q8|Q9H3V0	Missense_Mutation	SNP	ENST00000344517.4	hg19	CCDS1580.1	.	.	.	.	.	.	.	.	.	.	G	35	5.541785	0.96474	2.27E-4	1.16E-4	ENSG00000135776	ENST00000344517	T	0.80653	-1.4	5.96	5.96	0.96718	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);	0.000000	0.85682	D	0.000000	D	0.82710	0.5096	M	0.79805	2.47	0.80722	D	1	P	0.51351	0.944	B	0.39503	0.301	D	0.85866	0.1413	10	0.72032	D	0.01	-16.8627	20.4043	0.99006	0.0:0.0:1.0:0.0	.	453	Q9NRK6	ABCBA_HUMAN	L	453	ENSP00000355637:S453L	ENSP00000355637:S453L	S	-	2	0	ABCB10	227734083	1.000000	0.71417	0.967000	0.41034	0.963000	0.63663	9.407000	0.97325	2.823000	0.97156	0.650000	0.86243	TCG	.	G|1.000;A|0.000		0.542	ABCB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095240.1	NM_012089		A	229667460	G	A	229667460	3	1	328	1	0	0	0	0	1	0	0	0	41	1059	37	1	886	1	ABCB10	1	229667460	Missense_Mutation	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10	66197	229667460	19583161	7	45937										
GNPAT	8443	hgsc.bcm.edu	37	chr1	231408132	231408132	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	tcttccttccaggaaacacaCtaaaggtaaagtgcttacaa	6	10	1	0			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr1:231408132C>G	ENST00000366647.4	+	11	1766	c.1597C>G	c.(1597-1599)Cta>Gta	p.L533V	GNPAT_ENST00000366646.3_Missense_Mutation_p.L472V	NM_014236.3	NP_055051.1	O15228	GNPAT_HUMAN	glyceronephosphate O-acyltransferase	533					cellular lipid metabolic process (GO:0044255)|cerebellum morphogenesis (GO:0021587)|ether lipid biosynthetic process (GO:0008611)|glycerophospholipid biosynthetic process (GO:0046474)|membrane organization (GO:0061024)|paranodal junction assembly (GO:0030913)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to fatty acid (GO:0070542)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)|synapse assembly (GO:0007416)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	glycerone-phosphate O-acyltransferase activity (GO:0016287)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	23	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)				AGGAAACACACTAAAGGTAAA	0.403																																					p.L533V		Atlas-SNP	.											.	GNPAT	73	.	0			c.C1597G						.						200	186	191					1																	231408132		2203	4300	6503	SO:0001583	missense	8443	exon11			AACACACTAAAGG	AF043937	CCDS1592.1	1q42	2008-02-05			ENSG00000116906	ENSG00000116906	2.3.1.42		4416	protein-coding gene	gene with protein product		602744				9459311, 9536089	Standard	NM_014236		Approved	DHAPAT, DAPAT, DAP-AT	uc001hup.4	O15228	OTTHUMG00000038024	ENST00000366647.4:c.1597C>G	chr1.hg19:g.231408132C>G	ENSP00000355607:p.Leu533Val	91.0	0.0		69.0	5.0	NM_014236	B4DNM9|Q5TBH7|Q9BWC2	Missense_Mutation	SNP	ENST00000366647.4	hg19	CCDS1592.1	.	.	.	.	.	.	.	.	.	.	C	1.005	-0.689837	0.03328	.	.	ENSG00000116906	ENST00000366647;ENST00000366646;ENST00000416000	T;T;T	0.63096	-0.02;-0.01;-0.02	4.71	-5.7	0.02421	.	1.030390	0.07678	N	0.936573	T	0.43700	0.1259	L	0.33485	1.01	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.23261	-1.0193	10	0.30854	T	0.27	-16.7215	7.0632	0.25137	0.1704:0.166:0.5403:0.1234	.	472;533	B4DNM9;O15228	.;GNPAT_HUMAN	V	533;472;523	ENSP00000355607:L533V;ENSP00000355606:L472V;ENSP00000411640:L523V	ENSP00000355606:L472V	L	+	1	2	GNPAT	229474755	0.020000	0.18652	0.001000	0.08648	0.854000	0.48673	-0.241000	0.08940	-1.325000	0.02269	-1.126000	0.01995	CTA	.	.		0.403	GNPAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092871.1			G	231408132	C	G	231408132	3	3	328	1	0	0	0	0	1	0	0	0	6549	564	20	4	1639	4	GNPAT	1	231408132	Missense_Mutation	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10	1740672	231408132	17842489	8	45938										
DISC1	27185	hgsc.bcm.edu	37	chr1	231829897	231829897	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	ggcaccagattgcctgacagGcttagctggccgtgtggccc	14	13	0	2			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr1:231829897G>A	ENST00000602281.1	+	2	446	c.393G>A	c.(391-393)agG>agA	p.R131R	DISC1_ENST00000317586.4_Silent_p.R131R|DISC1_ENST00000537876.1_Silent_p.R131R|DISC1_ENST00000366637.3_5'UTR|DISC1_ENST00000602873.1_Intron|DISC1_ENST00000539444.1_Silent_p.R131R|DISC1_ENST00000535983.1_Silent_p.R131R|TSNAX-DISC1_ENST00000602962.1_3'UTR|DISC1_ENST00000439617.2_Silent_p.R131R|DISC1_ENST00000366633.3_Silent_p.R131R|DISC1_ENST00000366636.4_Silent_p.R131R	NM_001164542.1|NM_001164544.1	NP_001158014.1|NP_001158016.1	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1	131	Interaction with MAP1A.				canonical Wnt signaling pathway (GO:0060070)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cerebral cortex radially oriented cell migration (GO:0021799)|microtubule cytoskeleton organization (GO:0000226)|mitochondrial calcium ion homeostasis (GO:0051560)|neuron migration (GO:0001764)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neuron projection development (GO:0010975)|regulation of synapse maturation (GO:0090128)|TOR signaling (GO:0031929)	cell junction (GO:0030054)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|postsynaptic membrane (GO:0045211)				breast(1)|cervix(1)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	15		all_cancers(173;0.0208)|Prostate(94;0.0975)				TGCCTGACAGGCTTAGCTGGC	0.602																																					p.R131R		Atlas-SNP	.											.	DISC1	207	.	0			c.G393A						.						42	41	41					1																	231829897		2203	4300	6503	SO:0001819	synonymous_variant	27185	exon2			TGACAGGCTTAGC	AF222980	CCDS31055.1, CCDS31056.1, CCDS53482.1, CCDS53483.1, CCDS53484.1, CCDS59205.1, CCDS59206.1, CCDS59207.1	1q42.1	2008-02-05			ENSG00000162946	ENSG00000162946			2888	protein-coding gene	gene with protein product		605210				10814723	Standard	NM_001164550		Approved		uc010pxh.2	Q9NRI5	OTTHUMG00000037835	ENST00000602281.1:c.393G>A	chr1.hg19:g.231829897G>A		58.0	0.0		46.0	18.0	NM_001164541	A6NLH2|C4P091|C4P095|C4P0A1|C4P0A3|C4P0B3|C4P0B6|C4P0C1|C9J6D0|O75045|Q5VT44|Q5VT45|Q8IXJ0|Q8IXJ1|Q9BX19|Q9NRI3|Q9NRI4	Silent	SNP	ENST00000602281.1	hg19	CCDS59205.1																																																																																			.	.		0.602	DISC1-019	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467451.1	NM_018662		A	231829897	G	A	231829897	2	1	328	1	0	0	0	0	0	0	0	1	4540	1194	42	3		3	DISC1	1	231829897	Silent	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10	421765	231829897	17420724	9	45939										
FAM161A	84140	hgsc.bcm.edu	37	chr2	62069387	62069387	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	agccttcaactcttctacttTcttgaaatactcctcattag	3	12	5	1			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr2:62069387T>G	ENST00000405894.3	-	2	393	c.292A>C	c.(292-294)Aaa>Caa	p.K98Q	FAM161A_ENST00000404929.1_Missense_Mutation_p.K98Q	NM_032180.2	NP_115556.2	Q3B820	F161A_HUMAN	family with sequence similarity 161, member A	98					cilium assembly (GO:0042384)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(5)|large_intestine(8)|lung(4)|ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TCTTCTACTTTCTTGAAATAC	0.398																																					p.K98Q		Atlas-SNP	.											.	FAM161A	200	.	0			c.A292C						.						73	66	68					2																	62069387		1838	4085	5923	SO:0001583	missense	84140	exon2			CTACTTTCTTGAA		CCDS42687.2, CCDS56120.1	2p15	2011-03-15			ENSG00000170264	ENSG00000170264			25808	protein-coding gene	gene with protein product		613596	"retinitis pigmentosa 28 (autosomal recessive)"	RP28		10507729, 20705278, 20705279	Standard	NM_032180		Approved	FLJ13305	uc002sbm.4	Q3B820	OTTHUMG00000152165	ENST00000405894.3:c.292A>C	chr2.hg19:g.62069387T>G	ENSP00000385893:p.Lys98Gln	80.0	0.0		78.0	31.0	NM_032180	B4DJV7|Q9H8R2	Missense_Mutation	SNP	ENST00000405894.3	hg19	CCDS42687.2	.	.	.	.	.	.	.	.	.	.	T	18.05	3.537587	0.65085	.	.	ENSG00000170264	ENST00000404929;ENST00000405894	T;T	0.66815	-0.23;-0.23	5.95	5.95	0.96441	.	.	.	.	.	T	0.74261	0.3693	L	0.46157	1.445	0.30066	N	0.810514	D;D	0.71674	0.959;0.998	P;D	0.63113	0.631;0.911	T	0.71404	-0.4603	9	0.35671	T	0.21	-8.4	13.8073	0.63240	0.0:0.0:0.0:1.0	.	98;98	Q3B820;Q3B820-3	F161A_HUMAN;.	Q	98	ENSP00000385158:K98Q;ENSP00000385893:K98Q	ENSP00000385158:K98Q	K	-	1	0	FAM161A	61922891	1.000000	0.71417	1.000000	0.80357	0.735000	0.41995	5.099000	0.64554	2.279000	0.76181	0.533000	0.62120	AAA	.	.		0.398	FAM161A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325537.2	NM_032180		G	62069387	T	G	62069387	3	3	328	1	0	0	0	0	1	0	0	0	5477	1792	62	5	1710	5	FAM161A	2	62069387	Missense_Mutation	SNP	T	TCGA-NI-A8LF-01A-11D-A35Z-10		62069387	181129986	10	45940										
SAP130	79595	hgsc.bcm.edu	37	chr2	128757662	128757662	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	ctgaaggaatggtgttggttGccaaaataggtgctactgtg	14	5	0	1			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr2:128757662G>A	ENST00000259235.3	-	9	1283	c.1154C>T	c.(1153-1155)gCa>gTa	p.A385V	SAP130_ENST00000357702.5_Missense_Mutation_p.A385V|SAP130_ENST00000259234.6_Missense_Mutation_p.A359V	NM_024545.3	NP_078821.2	Q9H0E3	SP130_HUMAN	Sin3A-associated protein, 130kDa	385					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|STAGA complex (GO:0030914)	transcription coactivator activity (GO:0003713)			NS(4)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(2)	45	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0771)		GGTGTTGGTTGCCAAAATAGG	0.483																																					p.A385V		Atlas-SNP	.											.	SAP130	169	.	0			c.C1154T						.						140	139	139					2																	128757662		2203	4300	6503	SO:0001583	missense	79595	exon9			TTGGTTGCCAAAA	BC017453	CCDS2153.1, CCDS54397.1	2q14.3	2008-02-05	2006-02-02		ENSG00000136715	ENSG00000136715			29813	protein-coding gene	gene with protein product		609697	"sin3A-associated protein, 130kDa"			11230166, 12724404	Standard	NM_001145928		Approved	FLJ12761	uc010fmd.2	Q9H0E3	OTTHUMG00000131571	ENST00000259235.3:c.1154C>T	chr2.hg19:g.128757662G>A	ENSP00000259235:p.Ala385Val	166.0	0.0		118.0	26.0	NM_001145928	B7ZLM3|C9K0X9|Q4ZFV4|Q53T46|Q8WVW4|Q9H9G8	Missense_Mutation	SNP	ENST00000259235.3	hg19	CCDS2153.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.213174	0.79352	.	.	ENSG00000136715	ENST00000357702;ENST00000259235;ENST00000259234	.	.	.	5.58	5.58	0.84498	.	0.095244	0.64402	D	0.000001	T	0.62768	0.2455	N	0.14661	0.345	0.80722	D	1	B;D;D;D	0.89917	0.42;1.0;0.998;0.996	B;D;D;D	0.85130	0.143;0.997;0.994;0.99	T	0.62704	-0.6798	9	0.30854	T	0.27	-18.7903	19.5825	0.95473	0.0:0.0:1.0:0.0	.	385;358;385;23	B7ZLM3;Q96DP1;Q9H0E3;B3KRT9	.;.;SP130_HUMAN;.	V	385;385;359	.	ENSP00000259234:A359V	A	-	2	0	SAP130	128474132	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.014000	0.93635	2.624000	0.88883	0.655000	0.94253	GCA	.	.		0.483	SAP130-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254436.3	NM_024545		A	128757662	G	A	128757662	3	1	328	1	0	0	0	0	1	0	0	0	13846	1319	46	3	2149	3	SAP130	2	128757662	Missense_Mutation	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10	66688275	128757662	114441711	11	45941										
LRP1B	53353	hgsc.bcm.edu	37	chr2	142012194	142012194	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	tactgacaattcagctgttgGcaattggataacagttctgt	9	7	2	1			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr2:142012194G>A	ENST00000389484.3	-	4	1331	c.360C>T	c.(358-360)tgC>tgT	p.C120C		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	120	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TCAGCTGTTGGCAATTGGATA	0.318										TSP Lung(27;0.18)																											p.C120C	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.C360T						.						116	103	107					2																	142012194		2201	4297	6498	SO:0001819	synonymous_variant	53353	exon4			CTGTTGGCAATTG	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.360C>T	chr2.hg19:g.142012194G>A		64.0	0.0		57.0	12.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	hg19	CCDS2182.1																																																																																			.	.		0.318	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		A	142012194	G	A	142012194	2	1	328	1	0	0	0	0	0	0	0	1	8964	1195	42	3		3	LRP1B	2	142012194	Silent	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10	13254532	142012194	101187179	12	45942										
SCRN3	79634	hgsc.bcm.edu	37	chr2	175289262	175289262	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	acaactattggataccagttCaccaacatttgaacttgaag	6	9	1	2			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr2:175289262C>T	ENST00000272732.6	+	7	1059	c.977C>T	c.(976-978)tCa>tTa	p.S326L	SCRN3_ENST00000548921.1_3'UTR|SCRN3_ENST00000409673.3_Missense_Mutation_p.S319L	NM_001193528.1|NM_024583.4	NP_001180457.1|NP_078859.2	Q0VDG4	SCRN3_HUMAN	secernin 3	326							dipeptidase activity (GO:0016805)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|urinary_tract(3)	13			OV - Ovarian serous cystadenocarcinoma(117;0.229)			GATACCAGTTCACCAACATTT	0.318																																					p.S326L		Atlas-SNP	.											.	SCRN3	76	.	0			c.C977T						.						70	67	68					2																	175289262		2203	4300	6503	SO:0001583	missense	79634	exon7			CCAGTTCACCAAC	AF279776	CCDS2258.1, CCDS54420.1	2q31	2008-02-05			ENSG00000144306	ENSG00000144306			30382	protein-coding gene	gene with protein product		614967				12221138	Standard	NM_024583		Approved	FLJ23142	uc002uiq.3	Q0VDG4	OTTHUMG00000132332	ENST00000272732.6:c.977C>T	chr2.hg19:g.175289262C>T	ENSP00000272732:p.Ser326Leu	342.0	0.0		257.0	119.0	NM_024583	B4DI11|C9JPC1|D3DPE0|Q7L1C5|Q9H5R5	Missense_Mutation	SNP	ENST00000272732.6	hg19	CCDS2258.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.322743	0.81580	.	.	ENSG00000144306	ENST00000409673;ENST00000272732	T;T	0.13778	2.56;2.62	4.91	4.91	0.64330	.	0.000000	0.85682	D	0.000000	T	0.43634	0.1256	M	0.85373	2.75	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.81914	0.995;0.994	T	0.50398	-0.8833	10	0.59425	D	0.04	-7.4432	18.1068	0.89523	0.0:1.0:0.0:0.0	.	319;326	B4DI11;Q0VDG4	.;SCRN3_HUMAN	L	319;326	ENSP00000387142:S319L;ENSP00000272732:S326L	ENSP00000272732:S326L	S	+	2	0	SCRN3	174997508	1.000000	0.71417	0.995000	0.50966	0.525000	0.34531	7.238000	0.78173	2.281000	0.76405	0.555000	0.69702	TCA	.	.		0.318	SCRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255451.2	NM_024583		T	175289262	C	T	175289262	3	4	328	1	0	0	0	0	1	0	0	0	13955	838	29	3	999	3	SCRN3	2	175289262	Missense_Mutation	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10	33277068	175289262	67910111	13	45943										
TTN	7273	hgsc.bcm.edu	37	chr2	179448455	179448455	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	tctaggccagtagctgtgtaCtcttcctggggaatctggtg	13	9	3	0			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr2:179448455C>A	ENST00000591111.1	-	262	60755	c.60531G>T	c.(60529-60531)gaG>gaT	p.E20177D	TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.E12945D|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586831.1_RNA|RP11-171I2.2_ENST00000603521.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.E12878D|TTN_ENST00000460472.2_Missense_Mutation_p.E12753D|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.E21818D|TTN_ENST00000342992.6_Missense_Mutation_p.E19250D|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	20177	Fibronectin type-III 46. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TAGCTGTGTACTCTTCCTGGG	0.463																																					p.E21818D		Atlas-SNP	.											.	TTN	18412	.	0			c.G65454T						.						69	67	67					2																	179448455		1894	4112	6006	SO:0001583	missense	7273	exon312			TGTGTACTCTTCC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.60531G>T	chr2.hg19:g.179448455C>A	ENSP00000465570:p.Glu20177Asp	125.0	0.0		106.0	20.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	14.09	2.431502	0.43122	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.58210	0.35;0.35;0.35;0.35	6.02	3.22	0.36961	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.54711	0.1875	L	0.55834	1.745	0.46222	D	0.998936	P;P;P;P	0.48503	0.704;0.704;0.704;0.911	B;B;B;P	0.49752	0.388;0.388;0.388;0.621	T	0.57260	-0.7842	9	0.87932	D	0	.	10.0919	0.42451	0.0:0.6767:0.0:0.3233	.	12753;12878;12945;20177	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	D	19250;12753;12945;12878;12751	ENSP00000343764:E19250D;ENSP00000434586:E12753D;ENSP00000340554:E12945D;ENSP00000352154:E12878D	ENSP00000340554:E12945D	E	-	3	2	TTN	179156701	0.985000	0.35326	1.000000	0.80357	0.998000	0.95712	0.208000	0.17415	0.867000	0.35654	0.655000	0.94253	GAG	.	.		0.463	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179448455	C	A	179448455	3	1	328	1	0	0	0	0	1	0	0	0	16750	564	20	3	42729	3	TTN	2	179448455	Missense_Mutation	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10	4159193	179448455	63750918	14	45944										
AOX1	316	hgsc.bcm.edu	37	chr2	201462230	201462230	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	cagaattcatcctgttcaggTgaggatgtgcctcttcctta	9	10	3	2			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr2:201462230T>G	ENST00000374700.2	+	4	550		c.e4+2			NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1						inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)			breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	CCTGTTCAGGTGAGGATGTGC	0.517																																					.		Atlas-SNP	.											.	AOX1	152	.	0			c.309+2T>G						.						130	110	117					2																	201462230		2203	4300	6503	SO:0001630	splice_region_variant	316	exon4			TTCAGGTGAGGAT	AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356			553	protein-coding gene	gene with protein product		602841				7570184	Standard	NM_001159		Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	ENST00000374700.2:c.309+2T>G	chr2.hg19:g.201462230T>G		53.0	0.0		34.0	6.0	NM_001159	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	Splice_Site	SNP	ENST00000374700.2	hg19	CCDS33360.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.347637	0.82022	.	.	ENSG00000138356	ENST00000374700;ENST00000454629	.	.	.	4.96	4.96	0.65561	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4513	0.67386	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	AOX1	201170475	1.000000	0.71417	0.999000	0.59377	0.987000	0.75469	6.897000	0.75671	2.075000	0.62263	0.533000	0.62120	.	.	.		0.517	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335844.1	NM_001159	Intron	G	201462230	T	G	201462230	5	3	328	1	0	0	0	0	0	0	1	0	729	1710	59	5	325	5	AOX1	2	201462230	Splice_Site	SNP	T	TCGA-NI-A8LF-01A-11D-A35Z-10	22013775	201462230	41737143	15	45945										
ABCA12	26154	hgsc.bcm.edu	37	chr2	215840618	215840618	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	aaggcccatggcagtggtaaCaaagacgatggggaggataa	15	6	0	1			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr2:215840618C>A	ENST00000272895.7	-	34	5491	c.5272G>T	c.(5272-5274)Gtt>Ttt	p.V1758F	ABCA12_ENST00000389661.4_Missense_Mutation_p.V1440F	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1758					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		GCAGTGGTAACAAAGACGATG	0.498																																					p.V1758F	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											.	ABCA12	368	.	0			c.G5272T						.						171	158	162					2																	215840618		2203	4300	6503	SO:0001583	missense	26154	exon34			TGGTAACAAAGAC	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.5272G>T	chr2.hg19:g.215840618C>A	ENSP00000272895:p.Val1758Phe	209.0	0.0		179.0	36.0	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	hg19	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.784689	0.90282	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.91180	-2.8;-2.8	5.73	5.73	0.89815	.	0.000000	0.64402	D	0.000013	D	0.96222	0.8768	M	0.87547	2.89	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.993;0.997	D	0.96145	0.9103	10	0.87932	D	0	.	20.27	0.98469	0.0:1.0:0.0:0.0	.	1758;1440	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	F	1758;1440	ENSP00000272895:V1758F;ENSP00000374312:V1440F	ENSP00000272895:V1758F	V	-	1	0	ABCA12	215548863	1.000000	0.71417	0.983000	0.44433	0.946000	0.59487	6.039000	0.70972	2.854000	0.98071	0.655000	0.94253	GTT	.	.		0.498	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		A	215840618	C	A	215840618	3	1	328	1	0	0	0	0	1	0	0	0	30	478	17	3	2595	3	ABCA12	2	215840618	Missense_Mutation	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10	14378388	215840618	27358755	16	45946										
SCN10A	6336	hgsc.bcm.edu	37	chr3	38830494	38830494	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	gtcatgcacacacaattaacCaaaatagtgaccgtaataaa	5	9	1	1			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr3:38830494C>T	ENST00000449082.2	-	3	422	c.423G>A	c.(421-423)ttG>ttA	p.L141L		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	141					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	CACAATTAACCAAAATAGTGA	0.388																																					p.L141L		Atlas-SNP	.											.	SCN10A	359	.	0			c.G423A						.						137	126	130					3																	38830494		2203	4300	6503	SO:0001819	synonymous_variant	6336	exon3			ATTAACCAAAATA	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10582	protein-coding gene	gene with protein product		604427	"sodium channel, voltage-gated, type X, alpha polypeptide"			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.423G>A	chr3.hg19:g.38830494C>T		114.0	0.0		135.0	17.0	NM_006514	A6NDQ1	Silent	SNP	ENST00000449082.2	hg19	CCDS33736.1																																																																																			.	.		0.388	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		T	38830494	C	T	38830494	2	4	328	1	0	0	0	0	0	0	0	1	13927	593	21	3		3	SCN10A	3	38830494	Silent	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10		38830494	159191936	17	45947										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266136	41266136	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	gtgccactaccacagctcctTctctgagtggtaaaggcaat	9	12	1	1	rs121913407		TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr3:41266136T>C	ENST00000349496.5	+	3	413	c.133T>C	c.(133-135)Tct>Cct	p.S45P	CTNNB1_ENST00000453024.1_Missense_Mutation_p.S38P|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S45P|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S45P|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S45P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	45			Missing (in colorectal cancer). {ECO:0000269|PubMed:9065402}.|S -> F (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> P (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S45P(168)|p.A5_A80del(53)|p.S45del(50)|p.S45A(11)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.S45_G48del(1)|p.Q28_Q61del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.S45_L46del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.P44_N51del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.T40_L46del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.S45E(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.S45T(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.T42_K49>Q(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CACAGCTCCTTCTCTGAGTGG	0.502		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S45P	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,carcinoma,0,1	CTNNB1	4904	.	355	Substitution - Missense(181)|Deletion - In frame(149)|Complex - deletion inframe(18)|Unknown(7)	liver(151)|kidney(53)|soft_tissue(47)|large_intestine(37)|adrenal_gland(28)|endometrium(9)|stomach(7)|skin(6)|pituitary(3)|prostate(3)|thyroid(2)|small_intestine(2)|bone(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)	c.T133C						.						84	74	78					3																	41266136		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	GCTCCTTCTCTGA	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.133T>C	chr3.hg19:g.41266136T>C	ENSP00000344456:p.Ser45Pro	147.0	0.0		168.0	86.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.440246	0.83993	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.65903	0.2736	M	0.65677	2.01	0.80722	D	1	D	0.60575	0.988	P	0.62649	0.905	T	0.69083	-0.5239	10	0.87932	D	0	-13.6823	16.3453	0.83126	0.0:0.0:0.0:1.0	.	45	P35222	CTNB1_HUMAN	P	38;45;45;45;45;38;45;45;45	ENSP00000400508:S38P;ENSP00000385604:S45P;ENSP00000412219:S45P;ENSP00000379486:S45P;ENSP00000344456:S45P;ENSP00000411226:S38P;ENSP00000379488:S45P;ENSP00000409302:S45P;ENSP00000401599:S45P	ENSP00000344456:S45P	S	+	1	0	CTNNB1	41241140	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.261000	0.74972	0.533000	0.62120	TCT	.	.		0.502	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266136	T	C	41266136	3	2	328	1	0	0	0	0	1	0	0	0	4018	1783	62	2	139	2	CTNNB1	3	41266136	Missense_Mutation	SNP	T	TCGA-NI-A8LF-01A-11D-A35Z-10	2435642	41266136	156756294	18	45948										
ZBTB11	27107	hgsc.bcm.edu	37	chr3	101370476	101370476	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	tgacatggcgttttagagatCgggcatcagcccaagctact	11	10	1	2			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr3:101370476C>A	ENST00000312938.4	-	11	3276	c.2696G>T	c.(2695-2697)cGa>cTa	p.R899L		NM_014415.3	NP_055230.2	O95625	ZBT11_HUMAN	zinc finger and BTB domain containing 11	899					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						TTTTAGAGATCGGGCATCAGC	0.433																																					p.R899L		Atlas-SNP	.											.	ZBTB11	77	.	0			c.G2696T						.						83	84	83					3																	101370476		2203	4300	6503	SO:0001583	missense	27107	exon11			AGAGATCGGGCAT	U69274	CCDS2943.1	3q12.3	2013-01-09			ENSG00000066422	ENSG00000066422		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	16740	protein-coding gene	gene with protein product							Standard	NM_014415		Approved	ZNF-U69274, ZNF913	uc003dve.4	O95625	OTTHUMG00000159133	ENST00000312938.4:c.2696G>T	chr3.hg19:g.101370476C>A	ENSP00000326200:p.Arg899Leu	66.0	0.0		72.0	32.0	NM_014415	Q2NKP9	Missense_Mutation	SNP	ENST00000312938.4	hg19	CCDS2943.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.727218	0.89390	.	.	ENSG00000066422	ENST00000312938	T	0.07567	3.18	5.81	4.92	0.64577	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.11793	0.0287	N	0.25286	0.73	0.80722	D	1	P	0.51653	0.947	P	0.50590	0.645	T	0.06162	-1.0842	10	0.49607	T	0.09	-8.654	16.6963	0.85336	0.0:0.8703:0.1296:0.0	.	899	O95625	ZBT11_HUMAN	L	899	ENSP00000326200:R899L	ENSP00000326200:R899L	R	-	2	0	ZBTB11	102853166	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.434000	0.80377	1.423000	0.47198	0.555000	0.69702	CGA	.	.		0.433	ZBTB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353441.2	NM_014415		A	101370476	C	A	101370476	3	1	328	1	0	0	0	0	1	0	0	0	17539	884	31	1	469	1	ZBTB11	3	101370476	Missense_Mutation	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10	60104340	101370476	96651954	19	45949										
KBTBD12	166348	hgsc.bcm.edu	37	chr3	127642047	127642047	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	atttccttgccacagactggTcctggctgcatttagccctt	8	13	0	1			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr3:127642047T>A	ENST00000405109.1	+	2	610	c.143T>A	c.(142-144)gTc>gAc	p.V48D	KBTBD12_ENST00000407609.3_Intron|KBTBD12_ENST00000343941.4_5'Flank|KBTBD12_ENST00000405256.1_Missense_Mutation_p.V48D			Q3ZCT8	KBTBC_HUMAN	kelch repeat and BTB (POZ) domain containing 12	48	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.									endometrium(1)|large_intestine(6)|lung(5)|ovary(1)	13						CACAGACTGGTCCTGGCTGCA	0.378																																					p.V48D		Atlas-SNP	.											.	KBTBD12	41	.	0			c.T143A						.						93	90	91					3																	127642047		1922	4142	6064	SO:0001583	missense	166348	exon1			GACTGGTCCTGGC		CCDS33848.2	3q21.3	2013-01-08	2009-10-01	2009-10-01	ENSG00000187715	ENSG00000187715		"BTB/POZ domain containing"	25731	protein-coding gene	gene with protein product			"kelch domain containing 6"	KLHDC6			Standard	NM_207335		Approved	FLJ46299	uc010hsr.3	Q3ZCT8	OTTHUMG00000150508	ENST00000405109.1:c.143T>A	chr3.hg19:g.127642047T>A	ENSP00000385957:p.Val48Asp	323.0	0.0		286.0	52.0	NM_207335	B5MCC6|Q6ZRK1	Missense_Mutation	SNP	ENST00000405109.1	hg19	CCDS33848.2	.	.	.	.	.	.	.	.	.	.	T	21.4	4.142710	0.77888	.	.	ENSG00000187715	ENST00000405109;ENST00000405256	T;T	0.74106	-0.81;-0.81	5.7	5.7	0.88788	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	.	.	.	.	D	0.90796	0.7110	H	0.97516	4.02	0.80722	D	1	D	0.67145	0.996	D	0.68039	0.955	D	0.93986	0.7262	9	0.87932	D	0	.	15.9694	0.80001	0.0:0.0:0.0:1.0	.	48	Q3ZCT8	KBTBC_HUMAN	D	48	ENSP00000385957:V48D;ENSP00000385879:V48D	ENSP00000385957:V48D	V	+	2	0	KBTBD12	129124737	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.698000	0.84413	2.177000	0.69029	0.377000	0.23210	GTC	.	.		0.378	KBTBD12-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318682.1	NM_207335		A	127642047	T	A	127642047	3	1	328	1	0	0	0	0	1	0	0	0	8000	1667	58	4	145	4	KBTBD12	3	127642047	Missense_Mutation	SNP	T	TCGA-NI-A8LF-01A-11D-A35Z-10	26271571	127642047	70380383	20	45950										
MAGEF1	64110	hgsc.bcm.edu	37	chr3	184429511	184429511	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	tcctccttggggcgctcctgCgaggcggtcggggcccgggt	18	14	0	0			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr3:184429511C>T	ENST00000317897.3	-	1	325	c.99G>A	c.(97-99)tcG>tcA	p.S33S		NM_022149.4	NP_071432.2	Q9HAY2	MAGF1_HUMAN	melanoma antigen family F, 1	33						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(2)|urinary_tract(1)	11	all_cancers(143;4.61e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;5.64e-35)|OV - Ovarian serous cystadenocarcinoma(80;2.56e-22)			GGCGCTCCTGCGAGGCGGTCG	0.726																																					p.S33S		Atlas-SNP	.											MAGEF1,colon,carcinoma,0,1	MAGEF1	27	.	0			c.G99A						.						9	12	11					3																	184429511		2132	4200	6332	SO:0001819	synonymous_variant	64110	exon1			CTCCTGCGAGGCG	AF295378	CCDS3269.1	3q13	2008-02-05			ENSG00000177383	ENSG00000177383			29639	protein-coding gene	gene with protein product		609267				11313144	Standard	NM_022149		Approved		uc003fpa.3	Q9HAY2	OTTHUMG00000156712	ENST00000317897.3:c.99G>A	chr3.hg19:g.184429511C>T		151.0	1.0		93.0	45.0	NM_022149	Q9H215	Silent	SNP	ENST00000317897.3	hg19	CCDS3269.1																																																																																			.	.		0.726	MAGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345417.1	NM_022149		T	184429511	C	T	184429511	2	4	328	1	0	0	0	0	0	0	0	1	9196	755	27	1		1	MAGEF1	3	184429511	Silent	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10	56787464	184429511	13592919	21	45951										
EVC2	132884	hgsc.bcm.edu	37	chr4	5633652	5633652	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	tggaaaacagccagctgtctGtgagctttggcaaagtcttc	11	9	2	1			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr4:5633652G>A	ENST00000344408.5	-	11	1631	c.1578C>T	c.(1576-1578)caC>caT	p.H526H	EVC2_ENST00000344938.1_Silent_p.H526H|EVC2_ENST00000310917.2_Silent_p.H446H	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	526					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						CCAGCTGTCTGTGAGCTTTGG	0.463																																					p.H526H		Atlas-SNP	.											.	EVC2	202	.	0			c.C1578T						.						106	108	107					4																	5633652		2203	4300	6503	SO:0001819	synonymous_variant	132884	exon11			CTGTCTGTGAGCT	AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.1578C>T	chr4.hg19:g.5633652G>A		142.0	0.0		73.0	12.0	NM_147127	Q86YT3|Q86YT4|Q8NG49	Silent	SNP	ENST00000344408.5	hg19	CCDS3382.2																																																																																			.	.		0.463	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127		A	5633652	G	A	5633652	2	1	328	1	0	0	0	0	0	0	0	1	5288	1368	48	3		3	EVC2	4	5633652	Silent	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10		5633652	185520624	22	45952										
WDR19	57728	hgsc.bcm.edu	37	chr4	39254852	39254852	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	ggatcacctcaataatcctgAaaaagctgtcaatattgtta	6	8	3	1			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr4:39254852A>G	ENST00000399820.3	+	25	2970	c.2816A>G	c.(2815-2817)gAa>gGa	p.E939G	WDR19_ENST00000288634.7_Missense_Mutation_p.E779G	NM_025132.3	NP_079408.3	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19	939					ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium assembly (GO:0042384)|digestive system development (GO:0055123)|ear morphogenesis (GO:0042471)|embryonic camera-type eye development (GO:0031076)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|intraciliary retrograde transport (GO:0035721)|myotome development (GO:0061055)|neurological system process (GO:0050877)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|motile cilium (GO:0031514)|nonmotile primary cilium (GO:0031513)|photoreceptor connecting cilium (GO:0032391)				large_intestine(1)	1						AATAATCCTGAAAAAGCTGTC	0.353																																					p.E939G		Atlas-SNP	.											.	WDR19	96	.	0			c.A2816G						.						71	69	70					4																	39254852		1826	4102	5928	SO:0001583	missense	57728	exon25			ATCCTGAAAAAGC	AB046858, AY029257	CCDS47042.1	4p14	2014-02-21			ENSG00000157796	ENSG00000157796		"WD repeat domain containing", "Intraflagellar transport homologs"	18340	protein-coding gene	gene with protein product	"intraflagellar transport 144 homolog (Chlamydomonas)"	608151				12906858, 22019273	Standard	XM_005262658		Approved	Pwdmp, KIAA1638, FLJ23127, ORF26, DYF-2, Oseg6, IFT144, NPHP13	uc003gtv.3	Q8NEZ3	OTTHUMG00000160466	ENST00000399820.3:c.2816A>G	chr4.hg19:g.39254852A>G	ENSP00000382717:p.Glu939Gly	135.0	0.0		88.0	24.0	NM_025132	B5MEF2|Q8N5B4|Q9H5S0|Q9HCD4	Missense_Mutation	SNP	ENST00000399820.3	hg19	CCDS47042.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.682521	0.88542	.	.	ENSG00000157796	ENST00000399820;ENST00000288634	T;T	0.79247	-1.25;-1.25	5.49	5.49	0.81192	Tetratricopeptide-like helical (1);	0.044980	0.85682	D	0.000000	T	0.80944	0.4721	M	0.85197	2.74	0.80722	D	1	P	0.35011	0.48	B	0.35312	0.2	T	0.82667	-0.0344	10	0.54805	T	0.06	-27.2414	15.5954	0.76574	1.0:0.0:0.0:0.0	.	939	Q8NEZ3	WDR19_HUMAN	G	939;779	ENSP00000382717:E939G;ENSP00000288634:E779G	ENSP00000288634:E779G	E	+	2	0	WDR19	38931247	1.000000	0.71417	0.890000	0.34922	0.930000	0.56654	9.296000	0.96104	2.075000	0.62263	0.528000	0.53228	GAA	.	.		0.353	WDR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360689.1			G	39254852	A	G	39254852	3	3	328	1	0	0	0	0	1	0	0	0	17294	246	9	2	2914	2	WDR19	4	39254852	Missense_Mutation	SNP	A	TCGA-NI-A8LF-01A-11D-A35Z-10	33621200	39254852	151899424	23	45953										
OCIAD2	132299	hgsc.bcm.edu	37	chr4	48901944	48901944	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	ttggacaaaacaacaggctcTgtaaggaaagttatatggtg	11	5	1	0			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr4:48901944T>C	ENST00000508632.1	-	3	299		c.e3-2		OCIAD2_ENST00000508069.2_Intron|OCIAD2_ENST00000273860.4_Splice_Site	NM_001014446.1	NP_001014446.1	Q56VL3	OCAD2_HUMAN	OCIA domain containing 2							endosome (GO:0005768)|mitochondrial inner membrane (GO:0005743)				kidney(1)|lung(3)|skin(1)|urinary_tract(1)	6						CAACAGGCTCTGTAAGGAAAG	0.408																																					.		Atlas-SNP	.											.	OCIAD2	16	.	0			c.67-2A>G						.						134	128	130					4																	48901944		2203	4300	6503	SO:0001630	splice_region_variant	132299	exon4			AGGCTCTGTAAGG	BC032808	CCDS3485.1, CCDS33981.1	4p12	2013-10-11			ENSG00000145247	ENSG00000145247			28685	protein-coding gene	gene with protein product						17054434	Standard	NM_001286774		Approved	MGC45416	uc003gyt.3	Q56VL3	OTTHUMG00000128626	ENST00000508632.1:c.67-2A>G	chr4.hg19:g.48901944T>C		109.0	0.0		77.0	11.0	NM_152398	B4DPE7|Q8N544	Splice_Site	SNP	ENST00000508632.1	hg19	CCDS33981.1	.	.	.	.	.	.	.	.	.	.	T	11.65	1.701698	0.30142	.	.	ENSG00000145247	ENST00000508632;ENST00000273860;ENST00000381464	.	.	.	4.74	4.74	0.60224	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.792	0.46438	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	OCIAD2	48596701	1.000000	0.71417	1.000000	0.80357	0.288000	0.27193	3.901000	0.56303	2.111000	0.64477	0.379000	0.24179	.	.	.		0.408	OCIAD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361984.5	NM_152398	Intron	C	48901944	T	C	48901944	5	2	328	1	0	0	0	0	0	0	1	0	10827	1594	55	2	419	2	OCIAD2	4	48901944	Splice_Site	SNP	T	TCGA-NI-A8LF-01A-11D-A35Z-10	9647092	48901944	142252332	24	45954										
LPHN3	23284	hgsc.bcm.edu	37	chr4	62936333	62936333	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	acacagaagatctccagtcaCcccatagagactctctctat	5	14	4	3	rs146722627		TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr4:62936333C>G	ENST00000514591.1	+	25	4446	c.4117C>G	c.(4117-4119)Ccc>Gcc	p.P1373A	RP11-84A1.3_ENST00000509461.1_RNA|RP11-84A1.3_ENST00000504135.1_RNA|LPHN3_ENST00000512091.2_3'UTR|LPHN3_ENST00000511324.1_3'UTR|LPHN3_ENST00000507625.1_Missense_Mutation_p.P1432A|RP11-84A1.3_ENST00000506704.1_RNA|LPHN3_ENST00000506720.1_Missense_Mutation_p.P1484A|LPHN3_ENST00000507164.1_3'UTR|LPHN3_ENST00000506746.1_Missense_Mutation_p.P1475A|LPHN3_ENST00000509896.1_3'UTR|LPHN3_ENST00000506700.1_3'UTR|LPHN3_ENST00000514157.1_3'UTR|LPHN3_ENST00000514996.1_Missense_Mutation_p.P1407A|LPHN3_ENST00000504896.1_3'UTR|LPHN3_ENST00000508946.1_Missense_Mutation_p.P1416A|LPHN3_ENST00000545650.1_Missense_Mutation_p.P1373A|LPHN3_ENST00000508693.1_3'UTR			Q9HAR2	LPHN3_HUMAN	latrophilin 3	1351					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						TCTCCAGTCACCCCATAGAGA	0.567																																					p.P1373A		Atlas-SNP	.											.	LPHN3	800	.	0			c.C4117G						.						53	52	52					4																	62936333		692	1591	2283	SO:0001583	missense	23284	exon23			CAGTCACCCCATA	AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"-", "GPCR / Class B : Orphans"	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.4117C>G	chr4.hg19:g.62936333C>G	ENSP00000422533:p.Pro1373Ala	165.0	0.0		129.0	34.0	NM_015236	E9PE04|O94867|Q9NWK5	Missense_Mutation	SNP	ENST00000514591.1	hg19	CCDS54768.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.35|14.35	2.508538|2.508538	0.44660|0.44660	.|.	.|.	ENSG00000150471|ENSG00000150471	ENST00000514591;ENST00000545650;ENST00000295349;ENST00000507625;ENST00000508946;ENST00000506720;ENST00000506746;ENST00000514996|ENST00000502815	D;D;D;T;T;T;T|.	0.83755|.	-1.69;-1.69;-1.76;-1.22;-1.27;-1.29;-1.24|.	5.39|5.39	5.39|5.39	0.77823|0.77823	GPCR, family 2, latrophilin, C-terminal (1);|.	0.177067|.	0.50627|.	D|.	0.000103|.	T|T	0.75975|0.75975	0.3923|0.3923	M|M	0.69823|0.69823	2.125|2.125	0.58432|0.58432	D|D	0.999998|0.999998	P;P|.	0.42078|.	0.77;0.77|.	B;B|.	0.42112|.	0.376;0.376|.	T|T	0.74731|0.74731	-0.3566|-0.3566	10|5	0.87932|.	D|.	0|.	.|.	19.1541|19.1541	0.93503|0.93503	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1373;1351|.	E9PE04;Q9HAR2|.	.;LPHN3_HUMAN|.	A|S	1373;1373;1351;1432;1416;1484;1475;1407|821	ENSP00000422533:P1373A;ENSP00000439831:P1373A;ENSP00000421372:P1432A;ENSP00000421627:P1416A;ENSP00000420931:P1484A;ENSP00000425884:P1475A;ENSP00000424258:P1407A|.	ENSP00000295349:P1351A|.	P|T	+|+	1|2	0|0	LPHN3|LPHN3	62618928|62618928	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.929000|0.929000	0.56500|0.56500	6.763000|6.763000	0.74955|0.74955	2.535000|2.535000	0.85469|0.85469	0.591000|0.591000	0.81541|0.81541	CCC|ACC	.	C|1.000;T|0.000		0.567	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1			G	62936333	C	G	62936333	3	3	328	1	0	0	0	0	1	0	0	0	8926	507	18	4	4207	4	LPHN3	4	62936333	Missense_Mutation	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10	14034389	62936333	128217943	25	45955										
GSTCD	79807	hgsc.bcm.edu	37	chr4	106638934	106638934	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	ttgcttagttgtcaccaaagAggtgagtagagatagttcac	11	6	2	3			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr4:106638934A>T	ENST00000515279.1	+	2	384	c.164A>T	c.(163-165)gAg>gTg	p.E55V	GSTCD_ENST00000394728.3_Missense_Mutation_p.E55V|GSTCD_ENST00000507281.1_Splice_Site_p.E55V|GSTCD_ENST00000394730.3_Splice_Site_p.E55V|GSTCD_ENST00000360505.5_Missense_Mutation_p.E55V|GSTCD_ENST00000515255.1_Intron			Q8NEC7	GSTCD_HUMAN	glutathione S-transferase, C-terminal domain containing	55						extracellular vesicular exosome (GO:0070062)				breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(2)|ovary(1)|skin(1)	14		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.15e-07)|READ - Rectum adenocarcinoma(30;0.139)		GTCACCAAAGAGGTGAGTAGA	0.368																																					p.E55V		Atlas-SNP	.											.	GSTCD	69	.	0			c.A164T						.						94	92	93					4																	106638934		2203	4300	6503	SO:0001583	missense	79807	exon2			CCAAAGAGGTGAG	BC032942	CCDS3672.2, CCDS43257.1	4q24	2008-02-05	2006-05-09		ENSG00000138780	ENSG00000138780			25806	protein-coding gene	gene with protein product		615912	"Glutathione S-transferase, C-terminal domain containing"			12477932	Standard	NM_001031720		Approved	FLJ13273	uc003hxz.4	Q8NEC7	OTTHUMG00000131211	ENST00000515279.1:c.164A>T	chr4.hg19:g.106638934A>T	ENSP00000422354:p.Glu55Val	267.0	0.0		260.0	91.0	NM_024751	A8K8J0|A8MVD3|H9KV97|Q9H8S3	Missense_Mutation	SNP	ENST00000515279.1	hg19	CCDS43257.1	.	.	.	.	.	.	.	.	.	.	A	15.61	2.885516	0.51908	.	.	ENSG00000138780	ENST00000394730;ENST00000507281;ENST00000515279;ENST00000360505;ENST00000510865;ENST00000509336;ENST00000394728	.	.	.	5.71	3.37	0.38596	.	0.216488	0.42294	D	0.000724	T	0.50000	0.1590	M	0.65975	2.015	0.09310	N	1	P;P	0.52842	0.956;0.946	P;P	0.54499	0.575;0.754	T	0.38265	-0.9669	9	0.51188	T	0.08	-6.647	8.5481	0.33435	0.806:0.0:0.194:0.0	.	55;55	Q8NEC7;D6RCC9	GSTCD_HUMAN;.	V	55	.	ENSP00000353695:E55V	E	+	2	0	GSTCD	106858383	0.958000	0.32768	0.401000	0.26359	0.888000	0.51559	1.643000	0.37217	2.187000	0.69744	0.533000	0.62120	GAG	.	.		0.368	GSTCD-006	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363981.1	NM_024751		T	106638934	A	T	106638934	3	4	328	1	0	0	0	0	1	0	0	0	6844	318	11	4	166	4	GSTCD	4	106638934	Missense_Mutation	SNP	A	TCGA-NI-A8LF-01A-11D-A35Z-10	43702601	106638934	84515342	26	45956										
PITX2	5308	hgsc.bcm.edu	37	chr4	111543517	111543517	+	Intron	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	agccagaaccgaagccatggCtaacggctggggatggtgac	15	10	0	2			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr4:111543517C>A	ENST00000354925.2	-	6	1890				PITX2_ENST00000557119.2_Missense_Mutation_p.A34S|PITX2_ENST00000394595.3_Intron|PITX2_ENST00000306732.3_Missense_Mutation_p.A34S|PITX2_ENST00000556049.1_5'Flank|PITX2_ENST00000355080.5_Intron|PITX2_ENST00000394598.2_Intron	NM_001204397.1	NP_001191326.1	Q99697	PITX2_HUMAN	paired-like homeodomain 2						atrial cardiac muscle tissue morphogenesis (GO:0055009)|atrioventricular valve development (GO:0003171)|camera-type eye development (GO:0043010)|cardiac neural crest cell migration involved in outflow tract morphogenesis (GO:0003253)|cell proliferation involved in outflow tract morphogenesis (GO:0061325)|deltoid tuberosity development (GO:0035993)|determination of left/right symmetry (GO:0007368)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic hindlimb morphogenesis (GO:0035116)|endodermal digestive tract morphogenesis (GO:0061031)|extraocular skeletal muscle development (GO:0002074)|female gonad development (GO:0008585)|hair cell differentiation (GO:0035315)|hypothalamus cell migration (GO:0021855)|in utero embryonic development (GO:0001701)|iris morphogenesis (GO:0061072)|left lung morphogenesis (GO:0060460)|left/right axis specification (GO:0070986)|male gonad development (GO:0008584)|myoblast fusion (GO:0007520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|odontogenesis (GO:0042476)|odontogenesis of dentin-containing tooth (GO:0042475)|patterning of blood vessels (GO:0001569)|positive regulation of DNA binding (GO:0043388)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prolactin secreting cell differentiation (GO:0060127)|pulmonary myocardium development (GO:0003350)|pulmonary vein morphogenesis (GO:0060577)|regulation of cell migration (GO:0030334)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to hormone (GO:0009725)|response to vitamin A (GO:0033189)|somatotropin secreting cell differentiation (GO:0060126)|spleen development (GO:0048536)|subthalamic nucleus development (GO:0021763)|superior vena cava morphogenesis (GO:0060578)|vascular smooth muscle cell differentiation (GO:0035886)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell development (GO:0055015)|ventricular septum morphogenesis (GO:0060412)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin DNA binding (GO:0031490)|phosphoprotein binding (GO:0051219)|protein homodimerization activity (GO:0042803)|ribonucleoprotein complex binding (GO:0043021)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|endometrium(3)|large_intestine(1)|lung(5)	10		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00222)		GAAGCCATGGCTAACGGCTGG	0.642																																					p.A34S		Atlas-SNP	.											.	PITX2	73	.	0			c.G100T						.						24	25	24					4																	111543517		2199	4297	6496	SO:0001627	intron_variant	5308	exon1			CCATGGCTAACGG	U69961	CCDS3692.1, CCDS3693.1, CCDS3694.1	4q25	2011-06-20	2007-07-12		ENSG00000164093	ENSG00000164093		"Homeoboxes / PRD class"	9005	protein-coding gene	gene with protein product		601542	"paired-like homeodomain transcription factor 2"	IRID2, IHG2, RIEG, RIEG1, RGS		9539779, 7581385	Standard	NM_000325		Approved	IGDS, RS, Brx1, Otlx2, ARP1	uc021xqr.1	Q99697	OTTHUMG00000132837	ENST00000354925.2:c.185-992G>T	chr4.hg19:g.111543517C>A		518.0	0.0		442.0	92.0	NM_000325	A8K6C6|B2RA02|B3KXS0|O60578|O60579|O60580|Q3KQX9|Q9BY17	Missense_Mutation	SNP	ENST00000354925.2	hg19	CCDS3692.1	.	.	.	.	.	.	.	.	.	.	C	14.88	2.666144	0.47677	.	.	ENSG00000164093	ENST00000306732	D	0.90504	-2.68	5.17	3.33	0.38152	.	0.895466	0.09905	N	0.740565	D	0.82277	0.5002	.	.	.	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.65841	-0.6070	9	0.07030	T	0.85	.	14.5773	0.68258	0.0:0.7208:0.2792:0.0	.	34	Q99697-2	.	S	34	ENSP00000304169:A34S	ENSP00000304169:A34S	A	-	1	0	PITX2	111762966	1.000000	0.71417	0.894000	0.35097	0.899000	0.52679	2.630000	0.46494	0.486000	0.27676	0.655000	0.94253	GCC	.	.		0.642	PITX2-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256308.2			A	111543517	C	A	111543517	1	1	328	0	1	0	0	0	0	0	0	0	11964	797	28	3		3	PITX2	4	111543517	Intron	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10	4904583	111543517	79610759	27	45957										
SYNPO2	171024	hgsc.bcm.edu	37	chr4	119951690	119951690	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	gaggatggtccccatgaataGaacggccaaacccttcccag	10	13	0	2			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr4:119951690G>T	ENST00000429713.2	+	4	1942	c.1760G>T	c.(1759-1761)aGa>aTa	p.R587I	SYNPO2_ENST00000434046.2_Missense_Mutation_p.R587I|SYNPO2_ENST00000448416.2_Intron|SYNPO2_ENST00000307142.4_Missense_Mutation_p.R587I	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	587						actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|Z disc (GO:0030018)	14-3-3 protein binding (GO:0071889)|muscle alpha-actinin binding (GO:0051371)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						CCCATGAATAGAACGGCCAAA	0.537																																					p.R587I		Atlas-SNP	.											.	SYNPO2	353	.	0			c.G1760T						.						102	95	97					4																	119951690		2203	4300	6503	SO:0001583	missense	171024	exon4			TGAATAGAACGGC	AJ010482	CCDS34054.1, CCDS47128.1, CCDS47129.1, CCDS75185.1, CCDS75186.1	4q26	2008-08-29			ENSG00000172403	ENSG00000172403			17732	protein-coding gene	gene with protein product						11673475, 17828378	Standard	NM_133477		Approved	MYOPODIN	uc010inb.3	Q9UMS6	OTTHUMG00000161165	ENST00000429713.2:c.1760G>T	chr4.hg19:g.119951690G>T	ENSP00000395143:p.Arg587Ile	135.0	0.0		138.0	25.0	NM_001128934	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Missense_Mutation	SNP	ENST00000429713.2	hg19	CCDS47129.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.93|12.93	2.084096|2.084096	0.36758|0.36758	.|.	.|.	ENSG00000172403|ENSG00000172403	ENST00000307142;ENST00000429713;ENST00000434046|ENST00000504178	T;T;T|.	0.43294|.	0.95;0.95;0.95|.	5.42|5.42	5.42|5.42	0.78866|0.78866	.|.	0.000000|.	0.64402|.	D|.	0.000001|.	T|.	0.71929|.	0.3398|.	M|M	0.71581|0.71581	2.175|2.175	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.76494|.	0.999;0.998;0.999;0.999|.	D;D;D;D|.	0.85130|.	0.997;0.914;0.997;0.994|.	T|.	0.71869|.	-0.4462|.	9|.	.|.	.|.	.|.	-17.4592|-17.4592	12.7569|12.7569	0.57341|0.57341	0.0783:0.0:0.9217:0.0|0.0783:0.0:0.9217:0.0	.|.	587;587;587;587|.	B9EG60;Q9UMS6-2;E9PEM2;Q9UMS6|.	.;.;.;SYNP2_HUMAN|.	I|Y	587|538	ENSP00000306015:R587I;ENSP00000395143:R587I;ENSP00000390965:R587I|.	.|.	R|X	+|+	2|3	0|2	SYNPO2|SYNPO2	120171138|120171138	1.000000|1.000000	0.71417|0.71417	0.950000|0.950000	0.38849|0.38849	0.015000|0.015000	0.08874|0.08874	4.749000|4.749000	0.62155|0.62155	2.530000|2.530000	0.85305|0.85305	0.655000|0.655000	0.94253|0.94253	AGA|TAG	.	.		0.537	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1			T	119951690	G	T	119951690	3	4	328	1	0	0	0	0	1	0	0	0	15472	942	33	3	1774	3	SYNPO2	4	119951690	Missense_Mutation	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10	8408173	119951690	71202586	28	45958										
MAB21L2	10586	hgsc.bcm.edu	37	chr4	151505054	151505054	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	cacccacgagaaacggactgGgacgagtcgtgcctgggcga	15	12	0	1			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr4:151505054G>A	ENST00000317605.4	+	1	1978	c.873G>A	c.(871-873)tgG>tgA	p.W291*	LRBA_ENST00000507224.1_Intron|LRBA_ENST00000535741.1_Intron|LRBA_ENST00000357115.3_Intron|RP11-1336O20.2_ENST00000507934.1_RNA|LRBA_ENST00000510413.1_Intron|LRBA_ENST00000503716.1_5'Flank	NM_006439.4	NP_006430.1	Q9Y586	MB212_HUMAN	mab-21-like 2 (C. elegans)	291					camera-type eye development (GO:0043010)|embryonic body morphogenesis (GO:0010172)|eye development (GO:0001654)|nervous system development (GO:0007399)|positive regulation of cell proliferation (GO:0008284)	nucleus (GO:0005634)				breast(2)|endometrium(6)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|skin(2)	21	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.159)		AAACGGACTGGGACGAGTCGT	0.637																																					p.W291X		Atlas-SNP	.											.	MAB21L2	53	.	0			c.G873A						.						97	86	90					4																	151505054		2203	4300	6503	SO:0001587	stop_gained	10586	exon1			GGACTGGGACGAG	AF155219	CCDS3774.1	4q31.3	2013-10-22	2001-11-28		ENSG00000181541	ENSG00000181541			6758	protein-coding gene	gene with protein product		604357	"mab-21 (C. elegans)-like 2"				Standard	NM_006439		Approved		uc003ilw.3	Q9Y586	OTTHUMG00000161442	ENST00000317605.4:c.873G>A	chr4.hg19:g.151505054G>A	ENSP00000324701:p.Trp291*	154.0	0.0		145.0	55.0	NM_006439	B3KP37|Q9HBA7	Nonsense_Mutation	SNP	ENST00000317605.4	hg19	CCDS3774.1	.	.	.	.	.	.	.	.	.	.	G	45	12.033157	0.99629	.	.	ENSG00000181541	ENST00000317605	.	.	.	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.9011	18.9656	0.92695	0.0:0.0:1.0:0.0	.	.	.	.	X	291	.	ENSP00000324701:W291X	W	+	3	0	MAB21L2	151724504	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.813000	0.99286	2.550000	0.86006	0.462000	0.41574	TGG	.	.		0.637	MAB21L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364937.1	NM_006439		A	151505054	G	A	151505054	4	1	328	1	0	0	0	0	0	1	0	0	9151	1241	43	3	875	3	MAB21L2	4	151505054	Nonsense_Mutation	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10	31553364	151505054	39649222	29	45959										
SEMA5A	9037	hgsc.bcm.edu	37	chr5	9227034	9227034	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	ggtcccacaggtgaataaccGgtcgccacccaccagaagca	10	15	0	2	rs139668453		TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr5:9227034G>A	ENST00000382496.5	-	7	1044	c.379C>T	c.(379-381)Cgg>Tgg	p.R127W		NM_003966.2	NP_003957.2	Q13591	SEM5A_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	127	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|diencephalon development (GO:0021536)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|nervous system development (GO:0007399)|patterning of blood vessels (GO:0001569)|positive chemotaxis (GO:0050918)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of angiogenesis (GO:0045766)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein kinase B signaling (GO:0051897)|signal clustering (GO:1990256)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|chondroitin sulfate proteoglycan binding (GO:0035373)|heparan sulfate proteoglycan binding (GO:0043395)|semaphorin receptor binding (GO:0030215)|syndecan binding (GO:0045545)			biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(13)|lung(40)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	81						GTGAATAACCGGTCGCCACCC	0.403																																					p.R127W		Atlas-SNP	.											.	SEMA5A	236	.	0			c.C379T						.	G	TRP/ARG	0,4406		0,0,2203	65	68	67		379	1	0	5	dbSNP_134	67	2,8598	2.2+/-6.3	0,2,4298	yes	missense	SEMA5A	NM_003966.2	101	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign	127/1075	9227034	2,13004	2203	4300	6503	SO:0001583	missense	9037	exon7			ATAACCGGTCGCC	U52840	CCDS3875.1	5p15.2	2008-05-15			ENSG00000112902	ENSG00000112902		"Semaphorins"	10736	protein-coding gene	gene with protein product		609297		SEMAF		8817451, 9464278	Standard	NM_003966		Approved	semF	uc003jek.2	Q13591	OTTHUMG00000090501	ENST00000382496.5:c.379C>T	chr5.hg19:g.9227034G>A	ENSP00000371936:p.Arg127Trp	803.0	1.0		555.0	250.0	NM_003966	D3DTC6|O60408|Q1RLL9	Missense_Mutation	SNP	ENST00000382496.5	hg19	CCDS3875.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.86|13.86	2.363229|2.363229	0.41902|0.41902	0.0|0.0	2.33E-4|2.33E-4	ENSG00000112902|ENSG00000112902	ENST00000514923|ENST00000382496;ENST00000513968	.|T;T	.|0.12039	.|2.72;2.72	4.93|4.93	1.05|1.05	0.20165|0.20165	.|WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	.|0.179987	.|0.47852	.|N	.|0.000216	T|T	0.16041|0.16041	0.0386|0.0386	M|M	0.84082|0.84082	2.675|2.675	0.48511|0.48511	D|D	0.999665|0.999665	.|B	.|0.11235	.|0.004	.|B	.|0.08055	.|0.003	T|T	0.03898|0.03898	-1.0994|-1.0994	5|10	.|0.56958	.|D	.|0.05	.|.	4.3178|4.3178	0.11002|0.11002	0.1732:0.0:0.5138:0.3131|0.1732:0.0:0.5138:0.3131	.|.	.|127	.|Q13591	.|SEM5A_HUMAN	L|W	74|127	.|ENSP00000371936:R127W;ENSP00000421961:R127W	.|ENSP00000371936:R127W	P|R	-|-	2|1	0|2	SEMA5A|SEMA5A	9280034|9280034	1.000000|1.000000	0.71417|0.71417	0.039000|0.039000	0.18376|0.18376	0.989000|0.989000	0.77384|0.77384	0.819000|0.819000	0.27308|0.27308	-0.025000|-0.025000	0.13918|0.13918	0.655000|0.655000	0.94253|0.94253	CCG|CGG	.	G|1.000;A|0.000		0.403	SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206989.2			A	9227034	G	A	9227034	3	1	328	1	0	0	0	0	1	0	0	0	14052	1115	39	1	2913	1	SEMA5A	5	9227034	Missense_Mutation	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10		9227034	171688226	30	45960										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13894846	13894846	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	gccaggttggagagcttcatCcactttggccaagtgaggga	14	9	1	2			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr5:13894846C>T	ENST00000265104.4	-	16	2448	c.2344G>A	c.(2344-2346)Gat>Aat	p.D782N	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	782	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					AGAGCTTCATCCACTTTGGCC	0.438									Kartagener syndrome																												p.D782N		Atlas-SNP	.											.	DNAH5	868	.	0			c.G2344A						.						177	164	169					5																	13894846		2203	4300	6503	SO:0001583	missense	1767	exon16	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CTTCATCCACTTT	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.2344G>A	chr5.hg19:g.13894846C>T	ENSP00000265104:p.Asp782Asn	108.0	0.0		60.0	13.0	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	hg19	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	C	15.39	2.819972	0.50633	.	.	ENSG00000039139	ENST00000265104	T	0.57273	0.41	5.44	3.63	0.41609	Dynein heavy chain, domain-1 (1);	0.095346	0.64402	D	0.000001	T	0.58509	0.2127	M	0.82630	2.6	0.50813	D	0.999893	B	0.26845	0.161	B	0.35899	0.213	T	0.55604	-0.8115	10	0.37606	T	0.19	.	10.895	0.47017	0.0:0.7982:0.1309:0.0709	.	782	Q8TE73	DYH5_HUMAN	N	782	ENSP00000265104:D782N	ENSP00000265104:D782N	D	-	1	0	DNAH5	13947846	1.000000	0.71417	0.993000	0.49108	0.596000	0.36781	4.314000	0.59166	0.648000	0.30732	-0.479000	0.04858	GAT	.	.		0.438	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		T	13894846	C	T	13894846	3	4	328	1	0	0	0	0	1	0	0	0	4606	855	30	3	11786	3	DNAH5	5	13894846	Missense_Mutation	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10	4667812	13894846	167020414	31	45961										
MTMR12	54545	hgsc.bcm.edu	37	chr5	32230150	32230150	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	ttccaagagtttgctcagagTggccacttggccaccaccta	9	13	1	2			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr5:32230150T>C	ENST00000382142.3	-	16	2148	c.1978A>G	c.(1978-1980)Act>Gct	p.T660A	MTMR12_ENST00000264934.5_Missense_Mutation_p.T550A|MTMR12_ENST00000280285.5_Missense_Mutation_p.T606A|MTMR12_ENST00000510216.1_5'Flank	NM_001040446.1	NP_001035536.1	Q9C0I1	MTMRC_HUMAN	myotubularin related protein 12	660						cytoplasm (GO:0005737)	phosphatase activity (GO:0016791)			breast(3)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						TTGCTCAGAGTGGCCACTTGG	0.562																																					p.T660A		Atlas-SNP	.											.	MTMR12	76	.	0			c.A1978G						.						104	113	110					5																	32230150		2203	4300	6503	SO:0001583	missense	54545	exon16			TCAGAGTGGCCAC	AB051469	CCDS34138.1, CCDS75230.1	5p15.33	2011-06-09	2005-04-07	2005-04-07	ENSG00000150712	ENSG00000150712		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	18191	protein-coding gene	gene with protein product		606501	"phosphatidylinositol-3-phosphate associated protein"	PIP3AP		11504939, 12495846	Standard	XM_005248313		Approved	3-PAP, FLJ20476, KIAA1682, 3PAP	uc003jhq.3	Q9C0I1	OTTHUMG00000161978	ENST00000382142.3:c.1978A>G	chr5.hg19:g.32230150T>C	ENSP00000371577:p.Thr660Ala	111.0	0.0		107.0	44.0	NM_001040446	Q69YJ4|Q6PFW3|Q96QU2|Q9NX27	Missense_Mutation	SNP	ENST00000382142.3	hg19	CCDS34138.1	.	.	.	.	.	.	.	.	.	.	T	3.410	-0.120354	0.06838	.	.	ENSG00000150712	ENST00000280285;ENST00000382142;ENST00000264934	T;T;T	0.39229	1.09;1.09;1.09	5.78	1.99	0.26369	.	0.344395	0.27139	N	0.020755	T	0.28632	0.0709	L	0.39633	1.23	0.20563	N	0.999883	B;B;P	0.34837	0.003;0.287;0.472	B;B;B	0.35182	0.004;0.124;0.197	T	0.14309	-1.0477	10	0.19590	T	0.45	.	6.7996	0.23744	0.0:0.1339:0.128:0.7381	.	550;606;660	Q9C0I1-3;Q9C0I1-2;Q9C0I1	.;.;MTMRC_HUMAN	A	606;660;550	ENSP00000280285:T606A;ENSP00000371577:T660A;ENSP00000264934:T550A	ENSP00000264934:T550A	T	-	1	0	MTMR12	32265907	1.000000	0.71417	0.211000	0.23655	0.917000	0.54804	2.762000	0.47597	0.107000	0.17824	0.459000	0.35465	ACT	.	.		0.562	MTMR12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366579.1	NM_019061		C	32230150	T	C	32230150	3	2	328	1	0	0	0	0	1	0	0	0	9950	1696	59	2	269	2	MTMR12	5	32230150	Missense_Mutation	SNP	T	TCGA-NI-A8LF-01A-11D-A35Z-10	18335304	32230150	148685110	32	45962										
NPR3	4883	hgsc.bcm.edu	37	chr5	32711930	32711930	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	tccccgtgcgtactactcggCtgggcgttgctggccggcgg	16	14	0	0			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr5:32711930C>T	ENST00000265074.8	+	1	391	c.48C>T	c.(46-48)ggC>ggT	p.G16G	NPR3_ENST00000434067.2_Intron|NPR3_ENST00000415685.2_Intron|NPR3_ENST00000415167.2_Silent_p.G16G	NM_000908.3|NM_001204375.1	NP_000899.1|NP_001191304.1	P17342	ANPRC_HUMAN	natriuretic peptide receptor 3	16					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of smooth muscle cell proliferation (GO:0048662)|osteoclast proliferation (GO:0002158)|pancreatic juice secretion (GO:0030157)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of urine volume (GO:0035810)|regulation of blood pressure (GO:0008217)|regulation of osteoblast proliferation (GO:0033688)|skeletal system development (GO:0001501)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	G-protein coupled peptide receptor activity (GO:0008528)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	24					Nesiritide(DB04899)	TACTACTCGGCTGGGCGTTGC	0.736																																					p.G16G		Atlas-SNP	.											.	NPR3	65	.	0			c.C48T						.						3	4	4					5																	32711930		1436	2889	4325	SO:0001819	synonymous_variant	4883	exon1			ACTCGGCTGGGCG		CCDS47196.1, CCDS56356.1, CCDS56357.1	5p13.3	2014-03-03	2014-03-03		ENSG00000113389	ENSG00000113389			7945	protein-coding gene	gene with protein product	"guanylate cyclase C"	108962	"chromosome 5 open reading frame 23", "atrionatriuretic peptide receptor C", "natriuretic peptide receptor C/guanylate cyclase C (atrionatriuretic peptide receptor C)", "natriuretic peptide receptor C"	NPRC, ANPRC, C5orf23		2162522, 1979052	Standard	NM_000908		Approved	GUCY2B, FLJ14054	uc003jhv.3	P17342	OTTHUMG00000150316	ENST00000265074.8:c.48C>T	chr5.hg19:g.32711930C>T		157.0	0.0		135.0	44.0	NM_000908	A2RRD1|B4DT84|E7EPG9	Silent	SNP	ENST00000265074.8	hg19	CCDS56357.1																																																																																			.	.		0.736	NPR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317550.3	NM_000908		T	32711930	C	T	32711930	2	4	328	1	0	0	0	0	0	0	0	1	10605	784	28	3		3	NPR3	5	32711930	Silent	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10	481780	32711930	148203330	33	45963										
DAB2	1601	hgsc.bcm.edu	37	chr5	39392502	39392502	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	aattatttttatcccagaaaGggaaatgttgacccagatcc	7	8	0	3			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr5:39392502G>T	ENST00000320816.6	-	4	762	c.295C>A	c.(295-297)Ctt>Att	p.L99I	DAB2_ENST00000339788.6_Missense_Mutation_p.L99I|DAB2_ENST00000545653.1_Missense_Mutation_p.L99I|DAB2_ENST00000509337.1_Missense_Mutation_p.L99I|DAB2_ENST00000512525.1_5'UTR	NM_001343.3	NP_001334.2	P98082	DAB2_HUMAN	Dab, mitogen-responsive phosphoprotein, homolog 2 (Drosophila)	99	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cell morphogenesis involved in differentiation (GO:0000904)|cell proliferation (GO:0008283)|cellular response to transforming growth factor beta stimulus (GO:0071560)|clathrin coat assembly (GO:0048268)|endoderm development (GO:0007492)|excretion (GO:0007588)|in utero embryonic development (GO:0001701)|leading edge cell differentiation (GO:0035026)|membrane organization (GO:0061024)|myeloid cell differentiation (GO:0030099)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of protein binding (GO:0032091)|negative regulation of protein localization to plasma membrane (GO:1903077)|negative regulation of transcription, DNA-templated (GO:0045892)|pinocytosis (GO:0006907)|positive regulation of cell migration (GO:0030335)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of endocytosis (GO:0045807)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of receptor recycling (GO:0001921)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|clathrin coat of coated pit (GO:0030132)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	cargo receptor activity (GO:0038024)|clathrin adaptor activity (GO:0035615)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein C-terminus binding (GO:0008022)|SMAD binding (GO:0046332)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(9)|lung(19)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	47	all_lung(31;0.000197)		Epithelial(62;0.137)			ATCCCAGAAAGGGAAATGTTG	0.428																																					p.L99I		Atlas-SNP	.											.	DAB2	124	.	0			c.C295A						.						94	99	98					5																	39392502		2203	4300	6503	SO:0001583	missense	1601	exon4			CAGAAAGGGAAAT	U53446	CCDS34149.1, CCDS58946.1	5p13.1	2013-10-03	2013-03-08		ENSG00000153071	ENSG00000153071			2662	protein-coding gene	gene with protein product		601236	"disabled (Drosophila) homolog 2 (mitogen-responsive phosphoprotein)", "disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)"			8660969, 9620555	Standard	NM_001343		Approved	DOC-2	uc003jlx.3	P98082	OTTHUMG00000162043	ENST00000320816.6:c.295C>A	chr5.hg19:g.39392502G>T	ENSP00000313391:p.Leu99Ile	60.0	0.0		67.0	11.0	NM_001343	A6NES5|Q13598|Q9BTY0|Q9UK04	Missense_Mutation	SNP	ENST00000320816.6	hg19	CCDS34149.1	.	.	.	.	.	.	.	.	.	.	G	14.98	2.696212	0.48202	.	.	ENSG00000153071	ENST00000320816;ENST00000339788;ENST00000545653;ENST00000509337	T;T;T;T	0.19394	2.15;2.15;2.15;2.15	5.71	3.92	0.45320	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.052775	0.85682	D	0.000000	T	0.28699	0.0711	N	0.25426	0.745	0.44595	D	0.997561	B;B	0.34214	0.442;0.282	P;B	0.53549	0.729;0.301	T	0.07385	-1.0775	10	0.25106	T	0.35	-13.0302	12.6941	0.56992	0.1348:0.0:0.8652:0.0	.	99;99	P98082;P98082-3	DAB2_HUMAN;.	I	99	ENSP00000313391:L99I;ENSP00000345508:L99I;ENSP00000439919:L99I;ENSP00000426245:L99I	ENSP00000313391:L99I	L	-	1	0	DAB2	39428259	1.000000	0.71417	0.772000	0.31596	0.991000	0.79684	3.380000	0.52448	0.761000	0.33130	-0.136000	0.14681	CTT	.	.		0.428	DAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367014.1	NM_001343		T	39392502	G	T	39392502	3	4	328	1	0	0	0	0	1	0	0	0	4220	1000	35	3	2061	3	DAB2	5	39392502	Missense_Mutation	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10	6680572	39392502	141522758	34	45964										
MAP1B	4131	hgsc.bcm.edu	37	chr5	71496132	71496132	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	tgcacgtggggaagagaaagAcaaggagaccaagaatgctg	15	6	0	4			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr5:71496132A>T	ENST00000296755.7	+	5	7248	c.6950A>T	c.(6949-6951)gAc>gTc	p.D2317V		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	2317	Mediates interaction with TMEM185A.				axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		GAAGAGAAAGACAAGGAGACC	0.522																																					p.D2317V	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.A6950T						.						119	121	120					5																	71496132		2203	4300	6503	SO:0001583	missense	4131	exon5			AGAAAGACAAGGA	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.6950A>T	chr5.hg19:g.71496132A>T	ENSP00000296755:p.Asp2317Val	194.0	0.0		179.0	72.0	NM_005909	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	hg19	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	A	18.38	3.612111	0.66672	.	.	ENSG00000131711	ENST00000296755	T	0.03663	3.85	5.84	5.84	0.93424	.	0.000000	0.64402	D	0.000001	T	0.13200	0.0320	L	0.43152	1.355	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.74348	0.983;0.942	T	0.00461	-1.1725	10	0.87932	D	0	-27.9704	16.2302	0.82332	1.0:0.0:0.0:0.0	.	2191;2317	A2BDK6;P46821	.;MAP1B_HUMAN	V	2317	ENSP00000296755:D2317V	ENSP00000296755:D2317V	D	+	2	0	MAP1B	71531888	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.715000	0.74697	2.228000	0.72767	0.533000	0.62120	GAC	.	.		0.522	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		T	71496132	A	T	71496132	3	4	328	1	0	0	0	0	1	0	0	0	9237	275	10	4	6968	4	MAP1B	5	71496132	Missense_Mutation	SNP	A	TCGA-NI-A8LF-01A-11D-A35Z-10	32103630	71496132	109419128	35	45965										
LYSMD3	116068	hgsc.bcm.edu	37	chr5	89815032	89815032	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	aggttctctctcttattgtcTgtacactttactatttgttc	5	9	3	0			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr5:89815032T>A	ENST00000315948.6	-	3	669	c.525A>T	c.(523-525)acA>acT	p.T175T	LYSMD3_ENST00000500869.2_Intron|LYSMD3_ENST00000509384.1_3'UTR	NM_198273.1	NP_938014.1	Q7Z3D4	LYSM3_HUMAN	LysM, putative peptidoglycan-binding, domain containing 3	175						integral component of membrane (GO:0016021)				breast(2)|large_intestine(1)|lung(2)|prostate(1)|urinary_tract(1)	7		all_cancers(142;5.03e-09)|all_epithelial(76;1.23e-11)|Lung NSC(167;2.46e-05)|all_lung(232;3.25e-05)|Ovarian(174;0.00832)|Colorectal(57;0.122)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(54;1.94e-31)|Epithelial(54;5.22e-26)|all cancers(79;2.42e-22)		TCTTATTGTCTGTACACTTTA	0.388																																					p.T175T		Atlas-SNP	.											.	LYSMD3	25	.	0			c.A525T						.						201	193	195					5																	89815032		1859	4107	5966	SO:0001819	synonymous_variant	116068	exon3			ATTGTCTGTACAC	BX537972	CCDS43338.1, CCDS68911.1	5q14.3	2010-12-09			ENSG00000176018	ENSG00000176018			26969	protein-coding gene	gene with protein product							Standard	NM_001286812		Approved	FLJ13542	uc003kjr.3	Q7Z3D4	OTTHUMG00000162667	ENST00000315948.6:c.525A>T	chr5.hg19:g.89815032T>A		104.0	0.0		110.0	20.0	NM_198273	Q5H9U0|Q6PEK0|Q9NTE9	Silent	SNP	ENST00000315948.6	hg19	CCDS43338.1																																																																																			.	.		0.388	LYSMD3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369987.2	XM_371760		A	89815032	T	A	89815032	2	1	328	1	0	0	0	0	0	0	0	1	9135	1567	55	4		4	LYSMD3	5	89815032	Silent	SNP	T	TCGA-NI-A8LF-01A-11D-A35Z-10	18318900	89815032	91100228	36	45966										
TCOF1	6949	hgsc.bcm.edu	37	chr5	149772339	149772339	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	agtccagcgaggatgatgtgGtggcgccatcccaggtaact	14	10	0	1			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr5:149772339G>T	ENST00000504761.2	+	22	3586	c.3586G>T	c.(3586-3588)Gtg>Ttg	p.V1196L	TCOF1_ENST00000377797.3_Missense_Mutation_p.V1197L|TCOF1_ENST00000445265.2_Missense_Mutation_p.V1120L|TCOF1_ENST00000513346.1_Missense_Mutation_p.V1196L|TCOF1_ENST00000439160.2_Missense_Mutation_p.V1159L|TCOF1_ENST00000451292.1_Missense_Mutation_p.V1233L|TCOF1_ENST00000323668.7_Missense_Mutation_p.V1119L			Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	1196					skeletal system development (GO:0001501)|transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:0042790)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transporter activity (GO:0005215)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	35		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGATGATGTGGTGGCGCCATC	0.622																																					p.V1196L		Atlas-SNP	.											.	TCOF1	154	.	0			c.G3586T						.						53	50	51					5																	149772339		2203	4300	6503	SO:0001583	missense	6949	exon22			GATGTGGTGGCGC		CCDS4306.1, CCDS47305.1, CCDS47306.1, CCDS47307.1, CCDS54936.1	5q32	2014-06-18			ENSG00000070814	ENSG00000070814			11654	protein-coding gene	gene with protein product		606847				1765376	Standard	NM_001008657		Approved	treacle, TCS	uc003lry.3	Q13428	OTTHUMG00000130081	ENST00000504761.2:c.3586G>T	chr5.hg19:g.149772339G>T	ENSP00000421655:p.Val1196Leu	94.0	0.0		79.0	8.0	NM_001135243	A0JLU0|B4E111|Q6SC72|Q7Z5W9|Q96A52|Q99408|Q99860	Missense_Mutation	SNP	ENST00000504761.2	hg19	CCDS54936.1	.	.	.	.	.	.	.	.	.	.	G	19.24	3.790003	0.70337	.	.	ENSG00000070814	ENST00000451292;ENST00000377797;ENST00000445265;ENST00000323668;ENST00000439160;ENST00000427724;ENST00000504761;ENST00000513346	T;T;T;T;T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15	5.55	3.37	0.38596	.	0.000000	0.35936	N	0.002893	T	0.59376	0.2189	L	0.36672	1.1	0.20196	N	0.999927	D;D;D;D;D	0.60160	0.974;0.987;0.974;0.978;0.987	P;P;P;P;P	0.54100	0.742;0.742;0.742;0.557;0.742	T	0.51988	-0.8635	10	0.72032	D	0.01	-10.0827	7.514	0.27590	0.1013:0.1735:0.7252:0.0	.	1159;1119;1158;1196;1120	Q13428-7;Q13428-2;Q13428-6;Q13428;Q13428-8	.;.;.;TCOF_HUMAN;.	L	1233;1197;1120;1119;1159;1158;1196;1196	ENSP00000400939:V1233L;ENSP00000367028:V1197L;ENSP00000409944:V1120L;ENSP00000325223:V1119L;ENSP00000406888:V1159L;ENSP00000390717:V1158L;ENSP00000421655:V1196L;ENSP00000427484:V1196L	ENSP00000325223:V1119L	V	+	1	0	TCOF1	149752532	1.000000	0.71417	0.967000	0.41034	0.977000	0.68977	2.246000	0.43142	1.293000	0.44690	0.561000	0.74099	GTG	.	.		0.622	TCOF1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380552.1	NM_001008656		T	149772339	G	T	149772339	3	4	328	1	0	0	0	0	1	0	0	0	15723	1261	44	3	3697	3	TCOF1	5	149772339	Missense_Mutation	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10	59957307	149772339	31142921	37	45967										
ATP10B	23120	hgsc.bcm.edu	37	chr5	160071238	160071238	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	gccaaagccagtcctggtctGgtcaggatgctccctgggga	14	12	2	0			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr5:160071238G>T	ENST00000327245.5	-	9	1621	c.775C>A	c.(775-777)Cag>Aag	p.Q259K		NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	259					phospholipid translocation (GO:0045332)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1)	75	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GTCCTGGTCTGGTCAGGATGC	0.522																																					p.Q259K		Atlas-SNP	.											.	ATP10B	201	.	0			c.C775A						.						95	95	95					5																	160071238		1988	4156	6144	SO:0001583	missense	23120	exon9			TGGTCTGGTCAGG	AB018258	CCDS43394.1	5q34	2010-04-20	2007-09-19		ENSG00000118322	ENSG00000118322		"ATPases / P-type"	13543	protein-coding gene	gene with protein product			"ATPase, Class V, type 10B"			9872452, 11015572	Standard	NM_025153		Approved	ATPVB, KIAA0715, FLJ21477	uc003lym.1	O94823	OTTHUMG00000163551	ENST00000327245.5:c.775C>A	chr5.hg19:g.160071238G>T	ENSP00000313600:p.Gln259Lys	110.0	0.0		94.0	31.0	NM_025153	Q9H725	Missense_Mutation	SNP	ENST00000327245.5	hg19	CCDS43394.1	.	.	.	.	.	.	.	.	.	.	G	2.002	-0.429275	0.04701	.	.	ENSG00000118322	ENST00000327245	T	0.73258	-0.73	4.8	-2.03	0.07365	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.441709	0.24452	N	0.038409	T	0.36220	0.0959	N	0.02158	-0.66	0.24060	N	0.996015	B;B;B;B	0.10296	0.003;0.0;0.001;0.0	B;B;B;B	0.09377	0.004;0.001;0.002;0.002	T	0.28522	-1.0041	9	.	.	.	.	9.8556	0.41084	0.0:0.3255:0.2316:0.443	.	303;259;231;259	B4DHG1;O94823-2;O94823-3;O94823	.;.;.;AT10B_HUMAN	K	259	ENSP00000313600:Q259K	.	Q	-	1	0	ATP10B	160003816	0.372000	0.25064	0.640000	0.29408	0.990000	0.78478	-0.020000	0.12525	-0.937000	0.03719	-0.261000	0.10672	CAG	.	.		0.522	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374127.1	NM_025153		T	160071238	G	T	160071238	3	4	328	1	0	0	0	0	1	0	0	0	1117	1357	47	3	3682	3	ATP10B	5	160071238	Missense_Mutation	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10	10298899	160071238	20844022	38	45968										
CRISP1	167	hgsc.bcm.edu	37	chr6	49806179	49806179	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	tgtcttcacagttacttgggCaggcttcacatgggacgcct	11	11	3	0			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr6:49806179C>T	ENST00000335847.4	-	7	694	c.593G>A	c.(592-594)tGc>tAc	p.C198Y	CRISP1_ENST00000505118.1_Missense_Mutation_p.C198Y|CRISP1_ENST00000536021.1_Intron|CRISP1_ENST00000355791.2_Missense_Mutation_p.C198Y|CRISP1_ENST00000507853.1_Intron|CRISP1_ENST00000329411.5_Intron	NM_001131.2	NP_001122.2	P54107	CRIS1_HUMAN	cysteine-rich secretory protein 1	198					binding of sperm to zona pellucida (GO:0007339)|fusion of sperm to egg plasma membrane (GO:0007342)|regulation of acrosome reaction (GO:0060046)	extracellular space (GO:0005615)|nucleus (GO:0005634)	calcium channel regulator activity (GO:0005246)			endometrium(1)|kidney(2)|large_intestine(6)|lung(15)|skin(2)|upper_aerodigestive_tract(1)	27	Lung NSC(77;0.0358)					GTTACTTGGGCAGGCTTCACA	0.358																																					p.C198Y		Atlas-SNP	.											.	CRISP1	45	.	0			c.G593A						.						167	161	163					6																	49806179		2203	4300	6503	SO:0001583	missense	167	exon7			CTTGGGCAGGCTT	D38451	CCDS4931.1, CCDS4932.1	6p21.2-p21.1	2008-02-05	2003-09-03	2003-09-05	ENSG00000124812	ENSG00000124812			304	protein-coding gene	gene with protein product		601193	"acidic epididymal glycoprotein-like 1"	AEGL1		8838800	Standard	NM_001131		Approved	CRISP-1, ARP, HUMARP, HSCRISP1D, HSCRISP1G	uc003ozw.2	P54107	OTTHUMG00000014827	ENST00000335847.4:c.593G>A	chr6.hg19:g.49806179C>T	ENSP00000338276:p.Cys198Tyr	99.0	0.0		136.0	20.0	NM_001205220	B5BU98|O00698|Q13248|Q14082|Q96SF6	Missense_Mutation	SNP	ENST00000335847.4	hg19	CCDS4931.1	.	.	.	.	.	.	.	.	.	.	C	14.91	2.676642	0.47886	.	.	ENSG00000124812	ENST00000335847;ENST00000355791;ENST00000505118	T;T;T	0.25579	1.79;1.79;1.79	4.85	3.97	0.46021	Cysteine-rich secretory protein (1);	0.000000	0.85682	D	0.000000	T	0.49064	0.1535	M	0.92649	3.33	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.62039	-0.6938	9	.	.	.	.	11.4627	0.50219	0.0:0.818:0.182:0.0	.	198	P54107	CRIS1_HUMAN	Y	198	ENSP00000338276:C198Y;ENSP00000348044:C198Y;ENSP00000427589:C198Y	.	C	-	2	0	CRISP1	49914138	0.999000	0.42202	0.235000	0.24058	0.007000	0.05969	2.277000	0.43417	1.150000	0.42419	0.650000	0.86243	TGC	.	.		0.358	CRISP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040875.2	NM_001131		T	49806179	C	T	49806179	3	4	328	1	0	0	0	0	1	0	0	0	3881	710	25	3	164	3	CRISP1	6	49806179	Missense_Mutation	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10		49806179	121308888	39	45969										
GCM1	8521	hgsc.bcm.edu	37	chr6	52999070	52999070	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	tgtcctccgagctgtagatgTgtttggcataggaatctggc	13	8	1	1			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr6:52999070T>A	ENST00000259803.7	-	3	339	c.128A>T	c.(127-129)cAc>cTc	p.H43L		NM_003643.3	NP_003634.2	Q9NP62	GCM1_HUMAN	glial cells missing homolog 1 (Drosophila)	43					anatomical structure morphogenesis (GO:0009653)|astrocyte fate commitment (GO:0060018)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|cell differentiation involved in embryonic placenta development (GO:0060706)|positive regulation of syncytium formation by plasma membrane fusion (GO:0060143)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(15)|ovary(1)|skin(1)	24	Lung NSC(77;0.0755)					GCTGTAGATGTGTTTGGCATA	0.488																																					p.H43L		Atlas-SNP	.											.	GCM1	47	.	0			c.A128T						.						119	110	113					6																	52999070		2203	4300	6503	SO:0001583	missense	8521	exon3			TAGATGTGTTTGG	D88613	CCDS4950.1	6p21-p12	2008-08-29	2001-11-28	2002-09-27	ENSG00000137270	ENSG00000137270			4197	protein-coding gene	gene with protein product		603715	"glial cells missing (Drosophila) homolog a"	GCMA		8962155	Standard	NM_003643		Approved	hGCMa	uc003pbp.3	Q9NP62	OTTHUMG00000014871	ENST00000259803.7:c.128A>T	chr6.hg19:g.52999070T>A	ENSP00000259803:p.His43Leu	137.0	0.0		149.0	17.0	NM_003643	Q4VAQ7|Q5T0X0|Q99468|Q9P1X3	Missense_Mutation	SNP	ENST00000259803.7	hg19	CCDS4950.1	.	.	.	.	.	.	.	.	.	.	T	8.363	0.833474	0.16820	.	.	ENSG00000137270	ENST00000259803	T	0.72942	-0.7	4.84	3.66	0.41972	.	0.090351	0.47093	D	0.000250	T	0.30885	0.0779	N	0.05078	-0.115	0.39922	D	0.974165	P	0.46142	0.873	P	0.46825	0.528	T	0.13469	-1.0508	10	0.15066	T	0.55	-2.2513	5.4822	0.16729	0.1428:0.1234:0.0:0.7338	.	43	Q9NP62	GCM1_HUMAN	L	43	ENSP00000259803:H43L	ENSP00000259803:H43L	H	-	2	0	GCM1	53107029	1.000000	0.71417	0.988000	0.46212	0.236000	0.25371	0.988000	0.29616	0.833000	0.34828	0.533000	0.62120	CAC	.	.		0.488	GCM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040953.1			A	52999070	T	A	52999070	3	1	328	1	0	0	0	0	1	0	0	0	6305	1696	59	4	1198	4	GCM1	6	52999070	Missense_Mutation	SNP	T	TCGA-NI-A8LF-01A-11D-A35Z-10	3192891	52999070	118115997	40	45970										
POU3F2	5454	hgsc.bcm.edu	37	chr6	99283620	99283620	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	tgggatttacccaagcggacGtggggctggctctgggcacc	16	11	1	0			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr6:99283620G>A	ENST00000328345.5	+	1	1041	c.871G>A	c.(871-873)Gtg>Atg	p.V291M		NM_005604.3	NP_005595.2	P20265	PO3F2_HUMAN	POU class 3 homeobox 2	291	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.				astrocyte development (GO:0014002)|cellular response to organic substance (GO:0071310)|cerebral cortex radially oriented cell migration (GO:0021799)|epidermis development (GO:0008544)|forebrain ventricular zone progenitor cell division (GO:0021869)|hypothalamus cell differentiation (GO:0021979)|myelination in peripheral nervous system (GO:0022011)|neurohypophysis development (GO:0021985)|neuron differentiation (GO:0030182)|positive regulation of cell proliferation (GO:0008284)|positive regulation of multicellular organism growth (GO:0040018)|regulation of axonogenesis (GO:0050770)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	identical protein binding (GO:0042802)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|large_intestine(3)|lung(5)	10		all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197)		BRCA - Breast invasive adenocarcinoma(108;0.0355)		CCAAGCGGACGTGGGGCTGGC	0.607																																					p.V291M		Atlas-SNP	.											.	POU3F2	33	.	0			c.G871A						.						184	193	190					6																	99283620		2203	4300	6503	SO:0001583	missense	5454	exon1			GCGGACGTGGGGC	Z11933	CCDS5040.1	6q16.2	2011-06-20	2007-07-13		ENSG00000184486	ENSG00000184486		"Homeoboxes / POU class"	9215	protein-coding gene	gene with protein product		600494	"POU domain class 3, transcription factor 2"	OTF7		8441633	Standard	NM_005604		Approved	POUF3, BRN2, OCT7	uc003ppe.3	P20265	OTTHUMG00000015258	ENST00000328345.5:c.871G>A	chr6.hg19:g.99283620G>A	ENSP00000329170:p.Val291Met	168.0	0.0		135.0	27.0	NM_005604	Q14960|Q86V54|Q9UJL0	Missense_Mutation	SNP	ENST00000328345.5	hg19	CCDS5040.1	.	.	.	.	.	.	.	.	.	.	G	19.21	3.783505	0.70222	.	.	ENSG00000184486	ENST00000328345;ENST00000425116	D	0.89875	-2.58	4.47	4.47	0.54385	POU-specific (4);Lambda repressor-like, DNA-binding (2);POU (1);	0.000000	0.64402	U	0.000019	D	0.94135	0.8119	M	0.84683	2.71	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95003	0.8145	10	0.87932	D	0	.	16.042	0.80691	0.0:0.0:1.0:0.0	.	291	P20265	PO3F2_HUMAN	M	291;224	ENSP00000329170:V291M	ENSP00000329170:V291M	V	+	1	0	POU3F2	99390341	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	9.530000	0.98051	2.306000	0.77630	0.305000	0.20034	GTG	.	.		0.607	POU3F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041586.2			A	99283620	G	A	99283620	3	1	328	1	0	0	0	0	1	0	0	0	12284	1145	40	1	873	1	POU3F2	6	99283620	Missense_Mutation	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10	46284550	99283620	71831447	41	45971										
STXBP5	134957	hgsc.bcm.edu	37	chr6	147704135	147704135	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	tttctaaacatgctcatgagGtacgactctcaaacagatat	6	9	3	2			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr6:147704135G>A	ENST00000321680.6	+	27	3414		c.e27+1		STXBP5_ENST00000367480.3_Splice_Site|STXBP5_ENST00000367481.3_Splice_Site|STXBP5_ENST00000179882.6_Splice_Site	NM_001127715.2	NP_001121187.1	Q5T5C0	STXB5_HUMAN	syntaxin binding protein 5 (tomosyn)						exocytosis (GO:0006887)|negative regulation of exocytosis (GO:0045920)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|synapse (GO:0045202)	syntaxin-1 binding (GO:0017075)			breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(21)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	42		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.77e-09)|GBM - Glioblastoma multiforme(68;0.0694)		TGCTCATGAGGTACGACTCTC	0.383																																					.		Atlas-SNP	.											.	STXBP5	163	.	0			c.3306+1G>A						.						59	61	61					6																	147704135		2203	4300	6503	SO:0001630	splice_region_variant	134957	exon25			CATGAGGTACGAC	AK055484	CCDS5211.1, CCDS47499.1	6q24.3	2013-01-10			ENSG00000164506	ENSG00000164506		"WD repeat domain containing"	19665	protein-coding gene	gene with protein product		604586				9620695, 14767561	Standard	NM_139244		Approved	tomosyn, LLGL3	uc010khz.2	Q5T5C0	OTTHUMG00000015766	ENST00000321680.6:c.3414+1G>A	chr6.hg19:g.147704135G>A		116.0	0.0		65.0	48.0	NM_139244	Q14DF3|Q5T5C1|Q5T5C2|Q8NBG8|Q96NG9	Splice_Site	SNP	ENST00000321680.6	hg19	CCDS47499.1	.	.	.	.	.	.	.	.	.	.	G	19.08	3.757575	0.69648	.	.	ENSG00000164506	ENST00000367481;ENST00000321680;ENST00000367480;ENST00000179882	.	.	.	5.31	5.31	0.75309	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.3423	0.94349	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	STXBP5	147745828	1.000000	0.71417	1.000000	0.80357	0.533000	0.34776	9.794000	0.99096	2.652000	0.90054	0.460000	0.39030	.	.	.		0.383	STXBP5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042606.1		Intron	A	147704135	G	A	147704135	5	1	328	1	0	0	0	0	0	0	1	0	15371	1275	44	3	3521	3	STXBP5	6	147704135	Splice_Site	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10	48420515	147704135	23410932	42	45972										
HOXA4	3201	hgsc.bcm.edu	37	chr7	27170333	27170333	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	cgatgtagttggagtttatcAaaaacgagctcatggtcatt	10	6	3	0			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr7:27170333A>G	ENST00000360046.5	-	1	85	c.20T>C	c.(19-21)tTg>tCg	p.L7S	HOXA-AS2_ENST00000521687.1_RNA|HOXA-AS2_ENST00000517550.1_RNA|HOXA3_ENST00000521401.1_Intron|RP1-170O19.22_ENST00000467897.2_RNA|HOXA4_ENST00000428284.2_Missense_Mutation_p.L7S|HOXA-AS2_ENST00000521159.1_RNA|HOXA-AS3_ENST00000518848.1_RNA	NM_002141.4	NP_002132.3	Q00056	HXA4_HUMAN	homeobox A4	7					anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(6)	12						GGAGTTTATCAAAAACGAGCT	0.582																																					p.L7S		Atlas-SNP	.											.	HOXA4	21	.	0			c.T20C						.						16	16	16					7																	27170333		2201	4291	6492	SO:0001583	missense	3201	exon1			TTTATCAAAAACG		CCDS5405.1	7p15.2	2011-06-20	2005-12-22		ENSG00000197576	ENSG00000197576		"Homeoboxes / ANTP class : HOXL subclass"	5105	protein-coding gene	gene with protein product		142953	"homeo box A4"	HOX1D, HOX1		1973146, 1358459	Standard	NM_002141		Approved		uc003sym.4	Q00056	OTTHUMG00000023213	ENST00000360046.5:c.20T>C	chr7.hg19:g.27170333A>G	ENSP00000353151:p.Leu7Ser	310.0	0.0		255.0	43.0	NM_002141	A4D180|O43366	Missense_Mutation	SNP	ENST00000360046.5	hg19	CCDS5405.1	.	.	.	.	.	.	.	.	.	.	A	13.72	2.321792	0.41096	.	.	ENSG00000197576	ENST00000360046;ENST00000428284;ENST00000552601;ENST00000548581	D;D	0.83419	-1.72;-1.72	3.63	3.63	0.41609	.	0.000000	0.28877	N	0.013857	D	0.90051	0.6893	M	0.78637	2.42	0.58432	D	0.999998	D	0.89917	1.0	D	0.83275	0.996	D	0.91178	0.4974	10	0.87932	D	0	.	12.6889	0.56964	1.0:0.0:0.0:0.0	.	7	Q00056	HXA4_HUMAN	S	7	ENSP00000353151:L7S;ENSP00000408845:L7S	ENSP00000353151:L7S	L	-	2	0	HOXA4	27136858	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.663000	0.83820	1.644000	0.50603	0.491000	0.48974	TTG	.	.		0.582	HOXA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059534.4			G	27170333	A	G	27170333	3	3	328	1	0	0	0	0	1	0	0	0	7303	131	5	2	950	2	HOXA4	7	27170333	Missense_Mutation	SNP	A	TCGA-NI-A8LF-01A-11D-A35Z-10		27170333	131968330	43	45973										
URGCP	55665	hgsc.bcm.edu	37	chr7	43921551	43921551	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	tccttccatttctctccattCcaaatctagaagaaaaaaga	3	11	2	3			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr7:43921551C>A	ENST00000453200.1	-	4	611	c.118G>T	c.(118-120)Gaa>Taa	p.E40*	URGCP_ENST00000446958.1_Nonsense_Mutation_p.E31*|URGCP_ENST00000443736.1_5'UTR|URGCP-MRPS24_ENST00000603700.1_Nonsense_Mutation_p.E31*|URGCP_ENST00000497914.1_5'UTR|URGCP_ENST00000447717.3_5'UTR|URGCP_ENST00000336086.6_5'UTR|URGCP_ENST00000223341.7_5'UTR|URGCP_ENST00000402306.3_Nonsense_Mutation_p.E31*			Q8TCY9	URGCP_HUMAN	upregulator of cell proliferation	40					cell cycle (GO:0007049)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|liver(1)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						tcTCTCCATTCCAAATCTAGA	0.418																																					p.E40X		Atlas-SNP	.											.	URGCP	170	.	0			c.G118T						.						137	135	136					7																	43921551		1847	4084	5931	SO:0001587	stop_gained	55665	exon4			TCCATTCCAAATC		CCDS43572.1, CCDS47577.1, CCDS47578.1	7p13	2010-02-17			ENSG00000106608	ENSG00000106608			30890	protein-coding gene	gene with protein product	"up-regulated gene 4"	610337				10819331, 12082552	Standard	NM_017920		Approved	URG4, KIAA1507, FLJ20654, DKFZp666G166, DKFZp686O0457	uc003tiw.3	Q8TCY9	OTTHUMG00000155245	ENST00000453200.1:c.118G>T	chr7.hg19:g.43921551C>A	ENSP00000396918:p.Glu40*	89.0	0.0		91.0	10.0	NM_001077663	E9PFF6|Q658M4|Q68DH6|Q6MZZ5|Q8WV98|Q9NWR7|Q9P221	Nonsense_Mutation	SNP	ENST00000453200.1	hg19	CCDS47578.1	.	.	.	.	.	.	.	.	.	.	C	41	8.824523	0.98968	.	.	ENSG00000106608	ENST00000402306;ENST00000453200;ENST00000446958	.	.	.	4.68	4.68	0.58851	.	0.000000	0.49305	D	0.000154	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-26.3343	13.4128	0.60952	0.0:1.0:0.0:0.0	.	.	.	.	X	31;40;31	.	ENSP00000384955:E31X	E	-	1	0	URGCP	43888076	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.650000	0.46665	2.884000	0.98904	0.655000	0.94253	GAA	.	.		0.418	URGCP-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338995.1	NM_001077664		A	43921551	C	A	43921551	4	1	328	1	0	0	0	0	0	1	0	0	17041	864	30	3	2689	3	URGCP	7	43921551	Nonsense_Mutation	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10	16751218	43921551	115217112	44	45974										
ZNF479	90827	hgsc.bcm.edu	37	chr7	57188071	57188071	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	ttcttcacaggcatagggttTctctctagtatgaattctct	7	9	5	1			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr7:57188071T>C	ENST00000331162.4	-	5	1321	c.1051A>G	c.(1051-1053)Aaa>Gaa	p.K351E		NM_033273.1	NP_150376.1	Q96JC4	ZN479_HUMAN	zinc finger protein 479	351					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(53)|ovary(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	84			GBM - Glioblastoma multiforme(1;9.18e-12)			GCATAGGGTTTCTCTCTAGTA	0.433																																					p.K351E		Atlas-SNP	.											.	ZNF479	193	.	0			c.A1051G						.						25	27	26					7																	57188071		2088	4253	6341	SO:0001583	missense	90827	exon5			AGGGTTTCTCTCT	AF277624	CCDS43590.1	7p11.2	2013-01-08			ENSG00000185177	ENSG00000185177		"Zinc fingers, C2H2-type", "-"	23258	protein-coding gene	gene with protein product						11410164	Standard	NM_033273		Approved	KR19	uc010kzo.3	Q96JC4	OTTHUMG00000156682	ENST00000331162.4:c.1051A>G	chr7.hg19:g.57188071T>C	ENSP00000333776:p.Lys351Glu	350.0	0.0		272.0	117.0	NM_033273		Missense_Mutation	SNP	ENST00000331162.4	hg19	CCDS43590.1	.	.	.	.	.	.	.	.	.	.	t	11.06	1.526538	0.27299	.	.	ENSG00000185177	ENST00000331162	T	0.27104	1.69	0.946	0.946	0.19549	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.36991	0.0987	M	0.76328	2.33	0.29448	N	0.858676	D	0.67145	0.996	P	0.53954	0.738	T	0.31138	-0.9954	9	0.87932	D	0	.	5.7317	0.18042	0.0:0.0:0.0:1.0	.	351	Q96JC4	ZN479_HUMAN	E	351	ENSP00000333776:K351E	ENSP00000333776:K351E	K	-	1	0	ZNF479	57192013	0.407000	0.25352	0.037000	0.18230	0.035000	0.12851	2.842000	0.48230	0.339000	0.23719	0.329000	0.21502	AAA	.	.		0.433	ZNF479-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345302.1	XM_291202		C	57188071	T	C	57188071	3	2	328	1	0	0	0	0	1	0	0	0	17948	1792	62	2	527	2	ZNF479	7	57188071	Missense_Mutation	SNP	T	TCGA-NI-A8LF-01A-11D-A35Z-10	13266520	57188071	101950592	45	45975										
SEMA3E	9723	hgsc.bcm.edu	37	chr7	83119477	83119477	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	caagctgagggaatatacaaGgtccctgcctcccacgaaga	10	12	0	2			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr7:83119477G>A	ENST00000307792.3	-	2	696	c.229C>T	c.(229-231)Ctt>Ttt	p.L77F	SEMA3E_ENST00000427262.1_Missense_Mutation_p.L17F	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	77	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell-matrix adhesion (GO:0001953)|patterning of blood vessels (GO:0001569)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell shape (GO:0008360)|semaphorin-plexin signaling pathway (GO:0071526)|sprouting angiogenesis (GO:0002040)|synapse organization (GO:0050808)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(19)|ovary(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	51		Medulloblastoma(109;0.109)				GAATATACAAGGTCCCTGCCT	0.413																																					p.L77F		Atlas-SNP	.											.	SEMA3E	125	.	0			c.C229T						.						89	82	85					7																	83119477		2203	4300	6503	SO:0001583	missense	9723	exon2			ATACAAGGTCCCT	AB002329	CCDS34674.1, CCDS55121.1	7q21.11	2013-01-11			ENSG00000170381	ENSG00000170381		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10727	protein-coding gene	gene with protein product	"M-sema H"	608166		SEMAH		9205841, 9515811	Standard	NM_012431		Approved	M-SemaK, KIAA0331, coll-5	uc003uhy.2	O15041	OTTHUMG00000154693	ENST00000307792.3:c.229C>T	chr7.hg19:g.83119477G>A	ENSP00000303212:p.Leu77Phe	99.0	0.0		77.0	22.0	NM_012431	B4E1P1|Q75M94|Q75M97	Missense_Mutation	SNP	ENST00000307792.3	hg19	CCDS34674.1	.	.	.	.	.	.	.	.	.	.	G	19.38	3.815992	0.70912	.	.	ENSG00000170381	ENST00000307792;ENST00000427262;ENST00000541514;ENST00000442159	T;T;T	0.11063	2.81;2.81;2.81	5.92	4.99	0.66335	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.276307	0.36778	N	0.002409	T	0.19087	0.0458	L	0.34521	1.04	0.40511	D	0.980733	D	0.54964	0.969	P	0.61800	0.894	T	0.02326	-1.1176	10	0.20519	T	0.43	.	15.9138	0.79496	0.0:0.0:0.8642:0.1358	.	77	O15041	SEM3E_HUMAN	F	77;17;77;17	ENSP00000303212:L77F;ENSP00000405052:L17F;ENSP00000412867:L17F	ENSP00000303212:L77F	L	-	1	0	SEMA3E	82957413	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.177000	0.50871	2.814000	0.96858	0.585000	0.79938	CTT	.	.		0.413	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431		A	83119477	G	A	83119477	3	1	328	1	0	0	0	0	1	0	0	0	14043	1000	35	3	2162	3	SEMA3E	7	83119477	Missense_Mutation	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10	25931406	83119477	76019186	46	45976										
CROT	54677	hgsc.bcm.edu	37	chr7	86978406	86978406	+	Frame_Shift_Del	DEL	T	T	-													0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	tggaaaatcaattggctaaaTcaactgaagaacgaacattt							TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr7:86978406delT	ENST00000331536.3	+	3	207	c.22delT	c.(22-24)tcafs	p.S8fs	CROT_ENST00000412227.2_Frame_Shift_Del_p.S8fs|CROT_ENST00000419147.2_Frame_Shift_Del_p.S8fs|CROT_ENST00000442291.1_Frame_Shift_Del_p.S8fs	NM_021151.3	NP_066974.2	Q9UKG9	OCTC_HUMAN	carnitine O-octanoyltransferase	8					carnitine metabolic process (GO:0009437)|cellular lipid metabolic process (GO:0044255)|coenzyme A metabolic process (GO:0015936)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|fatty acid metabolic process (GO:0006631)|fatty acid transport (GO:0015908)|generation of precursor metabolites and energy (GO:0006091)|medium-chain fatty acid metabolic process (GO:0051791)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carnitine O-octanoyltransferase activity (GO:0008458)|receptor binding (GO:0005102)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				L-Carnitine(DB00583)	ATTGGCTAAATCAACTGAAGA	0.358																																					p.K7fs		Atlas-INDEL	.											.	CROT	81	.	0			c.21delA						.						81	82	82					7																	86978406		2203	4300	6503	SO:0001589	frameshift_variant	54677	exon3			.		CCDS5604.1, CCDS47634.1, CCDS59062.1	7q21.1	2010-02-26			ENSG00000005469	ENSG00000005469			2366	protein-coding gene	gene with protein product		606090				10486279	Standard	NM_021151		Approved	COT	uc003uit.3	Q9UKG9	OTTHUMG00000023653	ENST00000331536.3:c.22delT	chr7.hg19:g.86978406delT	ENSP00000331981:p.Ser8fs	528.0	0.0		376.0	143.0	NM_001243745	A4D1D6|E7EQF2|Q86V17|Q8IUW9|Q9Y6I2	Frame_Shift_Del	DEL	ENST00000331536.3	hg19	CCDS5604.1																																																																																			.	.		0.358	CROT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253485.1	NM_021151		-	86978406	T	-	86978406	7	5	328	1	0	1	0	1	0	0	0	0	3896	1435	50	0	24	0	CROT	7	86978406	Frame_Shift_Del	DEL	T	TCGA-NI-A8LF-01A-11D-A35Z-10	3858929	86978406	72160257	47	45977										
ZNF804B	219578	hgsc.bcm.edu	37	chr7	88963831	88963831	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	cttggaattgaagactaaaaGagagagccaagtctcaggtt	11	6	1	4			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr7:88963831G>T	ENST00000333190.4	+	4	2144	c.1535G>T	c.(1534-1536)aGa>aTa	p.R512I		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	512							metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			AAGACTAAAAGAGAGAGCCAA	0.373										HNSCC(36;0.09)																											p.R512I		Atlas-SNP	.											.	ZNF804B	322	.	0			c.G1535T						.						39	41	41					7																	88963831		2202	4299	6501	SO:0001583	missense	219578	exon4			CTAAAAGAGAGAG	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"zinc finger 804B"				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.1535G>T	chr7.hg19:g.88963831G>T	ENSP00000329638:p.Arg512Ile	338.0	0.0		298.0	67.0	NM_181646	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	hg19	CCDS5613.1	.	.	.	.	.	.	.	.	.	.	G	7.034	0.561250	0.13498	.	.	ENSG00000182348	ENST00000333190	T	0.04862	3.54	5.3	-9.86	0.00473	.	1.851780	0.02014	N	0.047226	T	0.01421	0.0046	N	0.00538	-1.39	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.47824	-0.9087	10	0.36615	T	0.2	3.2589	2.1295	0.03747	0.313:0.1584:0.3848:0.1438	.	512	A4D1E1	Z804B_HUMAN	I	512	ENSP00000329638:R512I	ENSP00000329638:R512I	R	+	2	0	ZNF804B	88801767	0.000000	0.05858	0.000000	0.03702	0.300000	0.27592	-0.224000	0.09164	-1.337000	0.02236	-0.262000	0.10625	AGA	.	.		0.373	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646		T	88963831	G	T	88963831	3	4	328	1	0	0	0	0	1	0	0	0	18186	942	33	3	1549	3	ZNF804B	7	88963831	Missense_Mutation	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10	1985425	88963831	70174832	48	45978										
PEX1	5189	hgsc.bcm.edu	37	chr7	92118609	92118609	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	acagaatctgttacttacagCtcagcaaaattcttccagtc	5	11	3	1			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr7:92118609C>G	ENST00000248633.4	-	23	3860	c.3765G>C	c.(3763-3765)gaG>gaC	p.E1255D	PEX1_ENST00000438045.1_Missense_Mutation_p.E933D|AC007566.10_ENST00000441539.1_RNA|AC007566.10_ENST00000427458.1_RNA|PEX1_ENST00000428214.1_Missense_Mutation_p.E1198D	NM_000466.2	NP_000457.1	O43933	PEX1_HUMAN	peroxisomal biogenesis factor 1	1255					ATP catabolic process (GO:0006200)|microtubule-based peroxisome localization (GO:0060152)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein targeting to peroxisome (GO:0006625)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			TTACTTACAGCTCAGCAAAAT	0.338																																					p.E1255D		Atlas-SNP	.											.	PEX1	102	.	0			c.G3765C						.						109	92	98					7																	92118609		2203	4300	6503	SO:0001583	missense	5189	exon23			TTACAGCTCAGCA	AF026086	CCDS5627.1, CCDS64710.1	7q21.2	2010-04-21	2008-08-26		ENSG00000127980	ENSG00000127980		"ATPases / AAA-type"	8850	protein-coding gene	gene with protein product		602136	"peroxisome biogenesis factor 1", "Zellweger syndrome 1", "Zellweger syndrome"	ZWS1, ZWS		9398848	Standard	NM_001282677		Approved		uc003uly.3	O43933	OTTHUMG00000023926	ENST00000248633.4:c.3765G>C	chr7.hg19:g.92118609C>G	ENSP00000248633:p.Glu1255Asp	97.0	0.0		115.0	15.0	NM_000466	A4D1G3|A8KA90|B4DIM7|E9PE75|Q96S71|Q96S72|Q96S73|Q99994	Missense_Mutation	SNP	ENST00000248633.4	hg19	CCDS5627.1	.	.	.	.	.	.	.	.	.	.	C	10.97	1.500221	0.26861	.	.	ENSG00000127980	ENST00000438045;ENST00000248633;ENST00000428214	D;D;D	0.94576	-3.41;-3.42;-3.46	5.32	0.00308	0.14053	.	0.312771	0.39146	N	0.001451	D	0.86981	0.6064	L	0.35723	1.085	0.80722	D	1	B;B;B	0.09022	0.002;0.002;0.002	B;B;B	0.09377	0.004;0.004;0.004	T	0.75519	-0.3289	10	0.46703	T	0.11	-3.5957	1.3274	0.02128	0.1533:0.2427:0.1502:0.4538	.	933;1047;1255	E9PE75;B4DER6;O43933	.;.;PEX1_HUMAN	D	933;1255;1198	ENSP00000410438:E933D;ENSP00000248633:E1255D;ENSP00000394413:E1198D	ENSP00000248633:E1255D	E	-	3	2	PEX1	91956545	0.954000	0.32549	0.998000	0.56505	0.657000	0.38888	-0.012000	0.12699	0.290000	0.22444	-0.140000	0.14226	GAG	.	.		0.338	PEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254066.3	NM_000466		G	92118609	C	G	92118609	3	3	328	1	0	0	0	0	1	0	0	0	11744	796	28	4	94	4	PEX1	7	92118609	Missense_Mutation	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10	3154778	92118609	67020054	49	45979										
CALCR	799	hgsc.bcm.edu	37	chr7	93055707	93055707	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	tctatgatattcaaagggatGatctcagcactctcctcgcc	7	12	4	2	rs138214388		TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr7:93055707G>A	ENST00000394441.1	-	13	1701	c.1386C>T	c.(1384-1386)atC>atT	p.I462I	CALCR_ENST00000421592.1_Silent_p.I478I|CALCR_ENST00000360249.4_Silent_p.I478I|CALCR_ENST00000359558.2_Silent_p.I496I|CALCR_ENST00000426151.1_Silent_p.I462I	NM_001164738.1	NP_001158210.1	P30988	CALCR_HUMAN	calcitonin receptor	496	Poly-Ala.				adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|response to glucocorticoid (GO:0051384)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcitonin binding (GO:0032841)|calcitonin receptor activity (GO:0004948)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)	p.I462I(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(3)	45	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Pramlintide(DB01278)|Salmon Calcitonin(DB00017)	TCAAAGGGATGATCTCAGCAC	0.507																																					p.I496I		Atlas-SNP	.											CALCR,arm,malignant_melanoma,0,1	CALCR	200	.	1	Substitution - coding silent(1)	skin(1)	c.C1488T						.						198	171	180					7																	93055707		2203	4300	6503	SO:0001819	synonymous_variant	799	exon16			AGGGATGATCTCA	L00587	CCDS5631.1, CCDS55125.1	7q21.3	2012-08-10			ENSG00000004948	ENSG00000004948		"GPCR / Class B : Calcitonin receptors"	1440	protein-coding gene	gene with protein product		114131				1331173	Standard	NM_001742		Approved	CTR	uc003umw.2	P30988	OTTHUMG00000023599	ENST00000394441.1:c.1386C>T	chr7.hg19:g.93055707G>A		97.0	0.0		81.0	26.0	NM_001164737	A4D1G6|F5H605|O14585|Q13941|Q5ZGL8|Q659U6|Q6DJU8|Q6T712	Silent	SNP	ENST00000394441.1	hg19	CCDS5631.1																																																																																			.	.		0.507	CALCR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254661.2	NM_001742		A	93055707	G	A	93055707	2	1	328	1	0	0	0	0	0	0	0	1	2581	1280	45	3		3	CALCR	7	93055707	Silent	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10	937098	93055707	66082956	50	45980										
PODXL	5420	hgsc.bcm.edu	37	chr7	131241049	131241049	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	gggcgacggcgacggcgacgGcgacgacggcagcagcggcg	21	13	0	0	rs201847316		TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr7:131241049G>A	ENST00000378555.3	-	1	317	c.70C>T	c.(70-72)Ccg>Tcg	p.P24S	PODXL_ENST00000465001.1_Intron|PODXL_ENST00000537928.1_Missense_Mutation_p.P24S|PODXL_ENST00000322985.9_Missense_Mutation_p.P24S|PODXL_ENST00000541194.1_Missense_Mutation_p.P24S			O00592	PODXL_HUMAN	podocalyxin-like	24					cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					gacggcgacggcgacgacggc	0.736																																					p.P24S		Atlas-SNP	.											.	PODXL	53	.	0			c.C70T						.						4	7	6					7																	131241049		1890	3825	5715	SO:0001583	missense	5420	exon1			GCGACGGCGACGA		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.70C>T	chr7.hg19:g.131241049G>A	ENSP00000367817:p.Pro24Ser	170.0	0.0		125.0	7.0	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Missense_Mutation	SNP	ENST00000378555.3	hg19	CCDS34755.1	.	.	.	.	.	.	.	.	.	.	G	10.47	1.359685	0.24598	.	.	ENSG00000128567	ENST00000541194;ENST00000537928;ENST00000378555;ENST00000322985	T;T;T;T	0.11604	2.96;2.76;2.97;2.95	.	.	.	.	7739.210000	0.00166	N	0.000002	T	0.11495	0.0280	N	0.08118	0	0.09310	N	0.999992	P;P	0.51449	0.945;0.909	P;P	0.56648	0.803;0.641	T	0.21008	-1.0258	8	0.34782	T	0.22	.	.	.	.	.	24;24	O00592-2;O00592	.;PODXL_HUMAN	S	24	ENSP00000440518:P24S;ENSP00000442655:P24S;ENSP00000367817:P24S;ENSP00000319782:P24S	ENSP00000319782:P24S	P	-	1	0	PODXL	130891589	0.006000	0.16342	0.042000	0.18584	0.043000	0.13939	1.910000	0.39927	0.088000	0.17205	0.089000	0.15464	CCG	.	.		0.736	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111		A	131241049	G	A	131241049	3	1	328	1	0	0	0	0	1	0	0	0	12189	1203	42	3	1642	3	PODXL	7	131241049	Missense_Mutation	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10	38185342	131241049	27897614	51	45981										
SSPO	23145	hgsc.bcm.edu	37	chr7	149480011	149480011	+	RNA	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	ctcagtgtgcgccgagcttcCtctgcctttctgctgctgcg	11	15	3	0			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr7:149480011C>G	ENST00000378016.2	+	0	1977							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GCCGAGCTTCCTCTGCCTTTC	0.657																																					p.S659S		Atlas-SNP	.											.	.	.	.	0			c.C1977G						.						42	52	49					7																	149480011		2150	4253	6403			23145	exon15			AGCTTCCTCTGCC	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		chr7.hg19:g.149480011C>G		91.0	0.0		72.0	9.0	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	hg19																																																																																				.	.		0.657	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				G	149480011	C	G	149480011	1	3	328	0	1	0	0	0	0	0	0	0	15204	668	24	4		4	SSPO	7	149480011	RNA	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10	18238962	149480011	9658652	52	45982										
SSPO	23145	hgsc.bcm.edu	37	chr7	149480083	149480083	+	RNA	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	tctgaccctgtagcctacatCaccctggacccccgccatgc	7	19	2	1			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr7:149480083C>T	ENST00000378016.2	+	0	2049							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			TAGCCTACATCACCCTGGACC	0.657																																					p.I683I		Atlas-SNP	.											.	.	.	.	0			c.C2049T						.						31	37	35					7																	149480083		2090	4203	6293			23145	exon15			CTACATCACCCTG	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		chr7.hg19:g.149480083C>T		110.0	0.0		95.0	11.0	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	hg19																																																																																				.	.		0.657	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				T	149480083	C	T	149480083	1	4	328	0	1	0	0	0	0	0	0	0	15204	816	29	3		3	SSPO	7	149480083	RNA	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10	72	149480083	9658580	53	45983										
GIMAP8	155038	hgsc.bcm.edu	37	chr7	150171329	150171329	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	gtttcgatcattgatgctccGgacatctcatctttaaagaa	7	9	3	2			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr7:150171329G>A	ENST00000307271.3	+	4	1486	c.912G>A	c.(910-912)ccG>ccA	p.P304P		NM_175571.2	NP_783161.1	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	304	AIG1-type G 2.					cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(26)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)		TTGATGCTCCGGACATCTCAT	0.458																																					p.P304P		Atlas-SNP	.											GIMAP8,NS,carcinoma,0,2	GIMAP8	136	.	0			c.G912A						.						78	85	83					7																	150171329		2203	4300	6503	SO:0001819	synonymous_variant	155038	exon4			TGCTCCGGACATC	AL834361	CCDS34777.1	7q36.1	2014-04-04			ENSG00000171115	ENSG00000171115		"GTPases, IMAP"	21792	protein-coding gene	gene with protein product	"immune-associated nucleotide-binding protein 9"					15474311	Standard	XM_005249951		Approved	DKFZp667I133, hIAN6, IAN9	uc003whj.3	Q8ND71	OTTHUMG00000158327	ENST00000307271.3:c.912G>A	chr7.hg19:g.150171329G>A		184.0	0.0		90.0	6.0	NM_175571		Silent	SNP	ENST00000307271.3	hg19	CCDS34777.1																																																																																			.	.		0.458	GIMAP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350701.1	NM_175571		A	150171329	G	A	150171329	2	1	328	1	0	0	0	0	0	0	0	1	6393	1103	39	1		1	GIMAP8	7	150171329	Silent	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10	691246	150171329	8967334	54	45984										
GIMAP4	55303	hgsc.bcm.edu	37	chr7	150269493	150269493	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	ctgcattcttctgacctcccCagggcctcatgctctgcttc	7	17	4	1			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr7:150269493C>T	ENST00000255945.2	+	3	510	c.335C>T	c.(334-336)cCa>cTa	p.P112L	GIMAP4_ENST00000461940.1_Missense_Mutation_p.P126L|GIMAP4_ENST00000494750.1_3'UTR	NM_018326.2	NP_060796.1	Q9NUV9	GIMA4_HUMAN	GTPase, IMAP family member 4	112	AIG1-type G.					cytosol (GO:0005829)	GTP binding (GO:0005525)			breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(82;0.0179)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CTGACCTCCCCAGGGCCTCAT	0.512																																					p.P112L		Atlas-SNP	.											.	GIMAP4	61	.	0			c.C335T						.						101	92	95					7																	150269493		2203	4300	6503	SO:0001583	missense	55303	exon3			CCTCCCCAGGGCC	AK001972	CCDS5904.1	7q36.1	2014-04-04			ENSG00000133574	ENSG00000133574		"GTPases, IMAP"	21872	protein-coding gene	gene with protein product	"immune-associated nucleotide-binding protein 1"	608087				15474311, 18701445	Standard	NM_018326		Approved	HIMAP4, FLJ11110, IMAP4, IAN1	uc003whl.3	Q9NUV9	OTTHUMG00000157475	ENST00000255945.2:c.335C>T	chr7.hg19:g.150269493C>T	ENSP00000255945:p.Pro112Leu	176.0	0.0		203.0	33.0	NM_018326		Missense_Mutation	SNP	ENST00000255945.2	hg19	CCDS5904.1	.	.	.	.	.	.	.	.	.	.	C	17.24	3.340210	0.60963	.	.	ENSG00000133574	ENST00000255945;ENST00000461940;ENST00000479232	T;T;T	0.06068	3.35;3.35;3.35	4.72	4.72	0.59763	AIG1 (1);	0.059524	0.64402	D	0.000002	T	0.33177	0.0854	M	0.93638	3.44	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.87578	0.98;0.998	T	0.37197	-0.9716	10	0.87932	D	0	.	13.0417	0.58904	0.0:1.0:0.0:0.0	.	126;112	G5E9W9;Q9NUV9	.;GIMA4_HUMAN	L	112;126;126	ENSP00000255945:P112L;ENSP00000419545:P126L;ENSP00000418615:P126L	ENSP00000255945:P112L	P	+	2	0	GIMAP4	149900426	0.969000	0.33509	0.661000	0.29709	0.125000	0.20455	4.031000	0.57267	2.473000	0.83533	0.655000	0.94253	CCA	.	.		0.512	GIMAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348927.1	NM_018326		T	150269493	C	T	150269493	3	4	328	1	0	0	0	0	1	0	0	0	6389	594	21	3	341	3	GIMAP4	7	150269493	Missense_Mutation	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10	98164	150269493	8869170	55	45985										
KCNH2	3757	hgsc.bcm.edu	37	chr7	150649763	150649763	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	tagcaggcgggccttcttccGtctccttcagcaggaaggca	12	13	3	0	rs199472901		TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr7:150649763G>A	ENST00000262186.5	-	6	1708	c.1307C>T	c.(1306-1308)aCg>aTg	p.T436M	KCNH2_ENST00000330883.4_Missense_Mutation_p.T96M|KCNH2_ENST00000392968.2_Missense_Mutation_p.T340M|KCNH2_ENST00000430723.3_Missense_Mutation_p.T436M	NM_000238.3	NP_000229.1	Q12809	KCNH2_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 2	436			T -> M (in LQT2).		cardiac muscle contraction (GO:0060048)|cellular response to drug (GO:0035690)|membrane depolarization during action potential (GO:0086010)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of potassium ion export (GO:1902303)|negative regulation of potassium ion transmembrane transport (GO:1901380)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|identical protein binding (GO:0042802)|inward rectifier potassium channel activity (GO:0005242)|phosphorelay sensor kinase activity (GO:0000155)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			NS(1)|cervix(1)|endometrium(10)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	42	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Alfuzosin(DB00346)|Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Cisapride(DB00604)|Dofetilide(DB00204)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Halofantrine(DB01218)|Ibutilide(DB00308)|Imipramine(DB00458)|Miconazole(DB01110)|Pimozide(DB01100)|Prazosin(DB00457)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terazosin(DB01162)|Thioridazine(DB00679)|Verapamil(DB00661)	GCCTTCTTCCGTCTCCTTCAG	0.597																																					p.T436M	GBM(137;110 1844 13671 20123 45161)	Atlas-SNP	.											.	KCNH2	157	.	0			c.C1307T	GRCh37	CM993712	KCNH2	M		.						139	125	129					7																	150649763		2203	4300	6503	SO:0001583	missense	3757	exon6			TCTTCCGTCTCCT	U04270	CCDS5910.1, CCDS5911.1	7q36.1	2014-09-17			ENSG00000055118	ENSG00000055118		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6251	protein-coding gene	gene with protein product		152427		LQT2		18616963, 7842012, 8159766, 16382104	Standard	NM_000238		Approved	Kv11.1, HERG, erg1	uc003wic.3	Q12809	OTTHUMG00000158341	ENST00000262186.5:c.1307C>T	chr7.hg19:g.150649763G>A	ENSP00000262186:p.Thr436Met	129.0	0.0		59.0	21.0	NM_000238	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Missense_Mutation	SNP	ENST00000262186.5	hg19	CCDS5910.1	.	.	.	.	.	.	.	.	.	.	G	8.326	0.825346	0.16749	.	.	ENSG00000055118	ENST00000330883;ENST00000392968;ENST00000262186;ENST00000350328;ENST00000430723	D;D;D;D	0.94457	-3.43;-3.43;-3.43;-3.43	4.59	2.68	0.31781	.	0.377546	0.27896	N	0.017420	T	0.82047	0.4952	N	0.03608	-0.345	0.09310	N	1	P;B;B;B;B	0.46327	0.876;0.137;0.302;0.021;0.008	B;B;B;B;B	0.31442	0.13;0.027;0.042;0.018;0.005	T	0.76399	-0.2973	10	0.40728	T	0.16	.	12.5371	0.56147	0.0:0.3865:0.6135:0.0	.	340;436;96;436;96	C4PFH9;G5E9I0;Q708S9;Q12809;Q12809-2	.;.;.;KCNH2_HUMAN;.	M	96;340;436;96;436	ENSP00000328531:T96M;ENSP00000376695:T340M;ENSP00000262186:T436M;ENSP00000387657:T436M	ENSP00000262186:T436M	T	-	2	0	KCNH2	150280696	0.002000	0.14202	0.696000	0.30242	0.687000	0.40016	1.205000	0.32308	0.916000	0.36871	0.549000	0.68633	ACG	.	.		0.597	KCNH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350741.2	NM_000238		A	150649763	G	A	150649763	3	1	328	1	0	0	0	0	1	0	0	0	8041	1145	40	1	2481	1	KCNH2	7	150649763	Missense_Mutation	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10	380270	150649763	8488900	56	45986										
EPHX2	2053	hgsc.bcm.edu	37	chr8	27369359	27369359	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	tttcctgcttacagcttctcAataccccggcccctctgccg	6	18	2	0			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr8:27369359A>T	ENST00000521400.1	+	6	1097	c.667A>T	c.(667-669)Aat>Tat	p.N223Y	EPHX2_ENST00000380476.3_Missense_Mutation_p.N170Y|EPHX2_ENST00000521780.1_Missense_Mutation_p.N157Y|EPHX2_ENST00000517536.1_Intron|EPHX2_ENST00000518379.1_Missense_Mutation_p.N223Y	NM_001979.5	NP_001970.2	P34913	HYES_HUMAN	epoxide hydrolase 2, cytoplasmic	223	Phosphatase.				arachidonic acid metabolic process (GO:0019369)|cellular calcium ion homeostasis (GO:0006874)|cholesterol homeostasis (GO:0042632)|dephosphorylation (GO:0016311)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|inflammatory response (GO:0006954)|phospholipid dephosphorylation (GO:0046839)|positive regulation of gene expression (GO:0010628)|positive regulation of vasodilation (GO:0045909)|reactive oxygen species metabolic process (GO:0072593)|regulation of blood pressure (GO:0008217)|regulation of cholesterol metabolic process (GO:0090181)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|stilbene catabolic process (GO:0046272)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)	10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity (GO:0033885)|epoxide hydrolase activity (GO:0004301)|lipid phosphatase activity (GO:0042577)|magnesium ion binding (GO:0000287)|phosphatase activity (GO:0016791)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxic substance binding (GO:0015643)			cervix(1)|endometrium(8)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|skin(5)|stomach(1)|urinary_tract(1)	27		Ovarian(32;2.61e-05)|all_epithelial(46;0.207)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0226)|Epithelial(17;1.12e-09)|Colorectal(74;0.157)		ACAGCTTCTCAATACCCCGGC	0.532																																					p.N223Y		Atlas-SNP	.											.	EPHX2	57	.	0			c.A667T						.						188	163	171					8																	27369359		2203	4300	6503	SO:0001583	missense	2053	exon6			CTTCTCAATACCC	L05779	CCDS6060.1, CCDS59097.1, CCDS59098.1	8p21	2010-04-23			ENSG00000120915	ENSG00000120915	3.3.2.10		3402	protein-coding gene	gene with protein product		132811					Standard	NM_001979		Approved		uc003xfu.4	P34913	OTTHUMG00000102115	ENST00000521400.1:c.667A>T	chr8.hg19:g.27369359A>T	ENSP00000430269:p.Asn223Tyr	122.0	0.0		61.0	35.0	NM_001979	B2Z3B1|B3KTU8|B3KUA0|G3V134|J3KPH7|Q16764|Q9HBJ1|Q9HBJ2	Missense_Mutation	SNP	ENST00000521400.1	hg19	CCDS6060.1	.	.	.	.	.	.	.	.	.	.	A	11.90	1.776149	0.31411	.	.	ENSG00000120915	ENST00000521400;ENST00000521780;ENST00000380476;ENST00000415449;ENST00000518379	T;T;T;T	0.36520	1.63;1.25;1.39;3.51	4.76	-9.52	0.00578	HAD-like domain (1);	1.266460	0.05101	N	0.487138	T	0.17023	0.0409	N	0.08118	0	0.09310	N	1	B;B;B	0.28801	0.014;0.223;0.038	B;B;B	0.23852	0.019;0.049;0.044	T	0.36163	-0.9759	10	0.62326	D	0.03	-11.9592	11.8602	0.52461	0.1262:0.5323:0.3415:0.0	.	223;223;223	E5RFU2;E7ETW9;P34913	.;.;HYES_HUMAN	Y	223;157;170;227;223	ENSP00000430269:N223Y;ENSP00000430302:N157Y;ENSP00000369843:N170Y;ENSP00000427956:N223Y	ENSP00000369843:N170Y	N	+	1	0	EPHX2	27425276	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-1.003000	0.03682	-1.961000	0.01016	0.459000	0.35465	AAT	.	.		0.532	EPHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219954.4			T	27369359	A	T	27369359	3	4	328	1	0	0	0	0	1	0	0	0	5182	130	5	4	689	4	EPHX2	8	27369359	Missense_Mutation	SNP	A	TCGA-NI-A8LF-01A-11D-A35Z-10		27369359	118994663	57	45987										
PREX2	80243	hgsc.bcm.edu	37	chr8	68950408	68950408	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	acttaggggtccaacatcacTgacacctgcactgaaatgct	8	12	1	2			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr8:68950408T>C	ENST00000288368.4	+	7	997	c.720T>C	c.(718-720)acT>acC	p.T240T	PREX2_ENST00000529398.1_3'UTR	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	240					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						CCAACATCACTGACACCTGCA	0.353																																					p.T240T		Atlas-SNP	.											.	PREX2	614	.	0			c.T720C						.						124	118	120					8																	68950408		2203	4300	6503	SO:0001819	synonymous_variant	80243	exon7			CATCACTGACACC	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.720T>C	chr8.hg19:g.68950408T>C		105.0	0.0		115.0	11.0	NM_025170	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Silent	SNP	ENST00000288368.4	hg19	CCDS6201.1																																																																																			.	.		0.353	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		C	68950408	T	C	68950408	2	2	328	1	0	0	0	0	0	0	0	1	12489	1567	55	2		2	PREX2	8	68950408	Silent	SNP	T	TCGA-NI-A8LF-01A-11D-A35Z-10	41581049	68950408	77413614	58	45988										
RUNX1T1	862	hgsc.bcm.edu	37	chr8	93003931	93003931	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	cgataggagtccctgtagtgGtgggcaatggccatatcatc	13	9	1	0			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr8:93003931G>C	ENST00000523629.1	-	7	1381	c.927C>G	c.(925-927)caC>caG	p.H309Q	RUNX1T1_ENST00000396218.1_Missense_Mutation_p.H282Q|RUNX1T1_ENST00000520724.1_Missense_Mutation_p.H272Q|RUNX1T1_ENST00000265814.3_Missense_Mutation_p.H309Q|RUNX1T1_ENST00000360348.2_Missense_Mutation_p.H272Q|RUNX1T1_ENST00000436581.2_Missense_Mutation_p.H320Q|RUNX1T1_ENST00000518844.1_Missense_Mutation_p.H282Q|RUNX1T1_ENST00000422361.2_Missense_Mutation_p.H272Q	NM_001198626.1|NM_001198630.1|NM_001198633.1|NM_175634.2	NP_001185555.1|NP_001185559.1|NP_001185562.1|NP_783552.1	Q06455	MTG8_HUMAN	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	309					fat cell differentiation (GO:0045444)|generation of precursor metabolites and energy (GO:0006091)|regulation of DNA binding (GO:0051101)|transcription, DNA-templated (GO:0006351)	nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(54)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	86			BRCA - Breast invasive adenocarcinoma(11;0.0141)			CCCTGTAGTGGTGGGCAATGG	0.537																																					p.H368Q		Atlas-SNP	.											.	RUNX1T1	516	.	0			c.C1104G						.						221	182	195					8																	93003931		2203	4300	6503	SO:0001583	missense	862	exon7			GTAGTGGTGGGCA	D43638	CCDS6256.1, CCDS6257.1, CCDS47891.1, CCDS56544.1, CCDS75766.1, CCDS75767.1	8q22	2007-01-29	2005-01-20	2005-01-22	ENSG00000079102	ENSG00000079102		"Zinc fingers, MYND-type"	1535	protein-coding gene	gene with protein product		133435	"core-binding factor, runt domain, alpha subunit 2; translocated to, 1; cyclin D-related"	AML1T1, CBFA2T1		1391946, 9790752	Standard	NM_004349		Approved	CDR, ETO, MTG8, ZMYND2	uc011lgi.2	Q06455	OTTHUMG00000164066	ENST00000523629.1:c.927C>G	chr8.hg19:g.93003931G>C	ENSP00000428543:p.His309Gln	182.0	0.0		166.0	32.0	NM_001198679	B7Z4P4|E7EPN4|O14784|Q06456|Q14873|Q16239|Q16346|Q16347|Q6IBL1|Q6NXH1|Q7Z4J5|Q92479|Q9BRZ0	Missense_Mutation	SNP	ENST00000523629.1	hg19	CCDS6256.1	.	.	.	.	.	.	.	.	.	.	G	18.69	3.678132	0.68042	.	.	ENSG00000079102	ENST00000523629;ENST00000396218;ENST00000265814;ENST00000360348;ENST00000422361;ENST00000520724;ENST00000436581;ENST00000518844	T;T;T;T;T;T;T;T	0.34667	1.37;1.35;1.37;1.35;1.35;1.35;1.36;1.35	6.17	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.51007	0.1649	L	0.55103	1.725	0.58432	D	0.999997	B;B;D	0.69078	0.415;0.129;0.997	B;B;D	0.71656	0.083;0.041;0.974	T	0.45293	-0.9271	10	0.29301	T	0.29	-21.2245	11.3316	0.49479	0.139:0.0:0.861:0.0	.	320;309;282	E7EPN4;Q06455;Q06455-2	.;MTG8_HUMAN;.	Q	309;282;309;272;272;272;320;282	ENSP00000428543:H309Q;ENSP00000379520:H282Q;ENSP00000265814:H309Q;ENSP00000353504:H272Q;ENSP00000390137:H272Q;ENSP00000428742:H272Q;ENSP00000402257:H320Q;ENSP00000430728:H282Q	ENSP00000265814:H309Q	H	-	3	2	RUNX1T1	93073107	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.167000	0.64972	1.634000	0.50500	0.655000	0.94253	CAC	.	.		0.537	RUNX1T1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377045.3	NM_004349, NM_175635		C	93003931	G	C	93003931	3	2	328	1	0	0	0	0	1	0	0	0	13762	1252	44	4	911	4	RUNX1T1	8	93003931	Missense_Mutation	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10	24053523	93003931	53360091	59	45989										
TTF1	7270	hgsc.bcm.edu	37	chr9	135277372	135277373	+	Frame_Shift_Ins	INS	-	-	T													0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	ggtgattggactttttcttcINSttttttttcttagacttttt					rs531537365		TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr9:135277372_135277373insT	ENST00000334270.2	-	2	875_876	c.836_837insA	c.(835-837)aagfs	p.K279fs		NM_001205296.1|NM_007344.3	NP_001192225.1|NP_031370.2	Q15361	TTF1_HUMAN	transcription termination factor, RNA polymerase I	279	Poly-Lys.				chromatin remodeling (GO:0006338)|DNA-templated transcription, termination (GO:0006353)|gene expression (GO:0010467)|negative regulation of DNA replication (GO:0008156)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(2)|pancreas(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;4.25e-06)|Epithelial(140;9.09e-05)		ACTTTTTCTTCTTTTTTTTCTT	0.48																																					p.K279fs		Atlas-INDEL	.											.	TTF1	82	.	0			c.837_838insA						.																																			SO:0001589	frameshift_variant	7270	exon2			.	BC050734	CCDS6948.1, CCDS75925.1	9q34.3	2008-02-05			ENSG00000125482	ENSG00000125482			12397	protein-coding gene	gene with protein product		600777				7597036	Standard	NM_007344		Approved		uc004cbl.3	Q15361	OTTHUMG00000020836	ENST00000334270.2:c.837dupA	chr9.hg19:g.135277380_135277380dupT	ENSP00000333920:p.Lys279fs	78.0	0.0		68.0	16.0	NM_007344	A1L160|Q4VXF3|Q58EY2|Q6P5T5	Frame_Shift_Ins	INS	ENST00000334270.2	hg19	CCDS6948.1																																																																																			.	.		0.48	TTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054784.2	NM_007344		T	135277373	-	T	135277372	7	5	328	1	0	1	1	0	0	0	0	0	16733	912	32	0	1920	0	TTF1	9	135277372	Frame_Shift_Ins	INS	-	TCGA-NI-A8LF-01A-11D-A35Z-10		135277372	5936059	60	45990										
SEC16A	9919	hgsc.bcm.edu	37	chr9	139355726	139355726	+	Splice_Site	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	cattgcagactccaaagcatCctgcaaaaggcatttcaggg	9	11	1	1			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr9:139355726C>A	ENST00000371706.3	-	11	4393	c.4360G>T	c.(4360-4362)Gat>Tat	p.D1454Y	SEC16A_ENST00000431893.2_Splice_Site_p.D1454Y|SEC16A_ENST00000290037.6_Splice_Site_p.D1454Y|SEC16A_ENST00000313050.7_Splice_Site_p.D1632Y			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	1454					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|protein transport (GO:0015031)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)				breast(1)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(15)|lung(14)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)		TCCAAAGCATCCTGCAAAAGG	0.547																																					p.D1632Y		Atlas-SNP	.											.	SEC16A	249	.	0			c.G4894T						.						47	49	49					9																	139355726		2078	4211	6289	SO:0001630	splice_region_variant	9919	exon13			AAGCATCCTGCAA	AK074565	CCDS55351.1, CCDS75936.1	9q34.3	2007-06-20	2007-06-20	2007-06-20	ENSG00000148396	ENSG00000148396			29006	protein-coding gene	gene with protein product		612854	"KIAA0310"	KIAA0310		9205841	Standard	NM_014866		Approved	p250	uc004chx.3	O15027	OTTHUMG00000020932	ENST00000371706.3:c.4360-1G>T	chr9.hg19:g.139355726C>A		91.0	0.0		66.0	26.0	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Missense_Mutation	SNP	ENST00000371706.3	hg19		.	.	.	.	.	.	.	.	.	.	C	21.0	4.076652	0.76415	.	.	ENSG00000148396	ENST00000313050;ENST00000277537;ENST00000453963;ENST00000371706;ENST00000290037;ENST00000431893;ENST00000404925	T;T;T;T;T;T	0.50813	1.73;0.73;1.35;1.74;1.74;1.73	5.23	5.23	0.72850	.	0.098725	0.64402	D	0.000002	T	0.70868	0.3273	M	0.77103	2.36	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.997;1.0;0.999;1.0	T	0.74601	-0.3611	10	0.87932	D	0	-24.6315	18.1559	0.89690	0.0:1.0:0.0:0.0	.	1632;1454;1454;1022	F1T0I1;O15027-5;O15027-4;A4QN19	.;.;.;.	Y	1632;26;354;1454;1454;1454;1022	ENSP00000325827:D1632Y;ENSP00000277537:D26Y;ENSP00000403525:D354Y;ENSP00000360771:D1454Y;ENSP00000290037:D1454Y;ENSP00000387583:D1454Y	ENSP00000277537:D26Y	D	-	1	0	SEC16A	138475547	1.000000	0.71417	0.999000	0.59377	0.559000	0.35586	7.432000	0.80349	2.612000	0.88384	0.561000	0.74099	GAT	.	.		0.547	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459	Missense_Mutation	A	139355726	C	A	139355726	5	1	328	1	0	0	0	0	0	0	1	0	14001	869	30	3	2259	3	SEC16A	9	139355726	Splice_Site	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10	4078354	139355726	1857705	61	45991										
ANK3	288	hgsc.bcm.edu	37	chr10	61832737	61832737	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	gccagcagttctgtcagtagCactttctcagggctgctact	10	12	3	0			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr10:61832737C>T	ENST00000280772.2	-	37	8093	c.7902G>A	c.(7900-7902)gtG>gtA	p.V2634V	ANK3_ENST00000355288.2_Intron|ANK3_ENST00000503366.1_Intron|ANK3_ENST00000373827.2_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	2634					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						CTGTCAGTAGCACTTTCTCAG	0.507																																					p.V2634V		Atlas-SNP	.											.	ANK3	703	.	0			c.G7902A						.						105	82	90					10																	61832737		2203	4300	6503	SO:0001819	synonymous_variant	288	exon37			CAGTAGCACTTTC	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.7902G>A	chr10.hg19:g.61832737C>T		105.0	0.0		92.0	31.0	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Silent	SNP	ENST00000280772.2	hg19	CCDS7258.1																																																																																			.	.		0.507	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		T	61832737	C	T	61832737	2	4	328	1	0	0	0	0	0	0	0	1	622	697	25	3		3	ANK3	10	61832737	Silent	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10		61832737	73702010	62	45992										
JMJD1C	221037	hgsc.bcm.edu	37	chr10	64950795	64950795	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	gacacaagaggtgatgttctGccatttggagattcagagtt	12	6	2	4			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr10:64950795G>C	ENST00000399262.2	-	17	6368	c.6150C>G	c.(6148-6150)ggC>ggG	p.G2050G	JMJD1C_ENST00000399251.1_3'UTR|JMJD1C_ENST00000402544.1_Silent_p.G1813G|JMJD1C_ENST00000542921.1_Silent_p.G1868G	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	2050					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					GTGATGTTCTGCCATTTGGAG	0.393																																					p.G2050G		Atlas-SNP	.											.	JMJD1C	347	.	0			c.C6150G						.						300	289	292					10																	64950795		1896	4109	6005	SO:0001819	synonymous_variant	221037	exon17			TGTTCTGCCATTT	L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"thyroid hormone receptor interactor 8"	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.6150C>G	chr10.hg19:g.64950795G>C		156.0	0.0		124.0	5.0	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Silent	SNP	ENST00000399262.2	hg19	CCDS41532.1	.	.	.	.	.	.	.	.	.	.	G	8.451	0.852998	0.17106	.	.	ENSG00000171988	ENST00000327520	.	.	.	5.35	3.51	0.40186	.	.	.	.	.	T	0.62221	0.2410	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58629	-0.7603	4	.	.	.	-0.2904	11.6312	0.51175	0.1463:0.0:0.8537:0.0	.	.	.	.	G	597	.	.	A	-	2	0	JMJD1C	64620801	0.997000	0.39634	0.999000	0.59377	0.992000	0.81027	0.451000	0.21779	0.766000	0.33244	0.650000	0.86243	GCA	.	.		0.393	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241		C	64950795	G	C	64950795	2	2	328	1	0	0	0	0	0	0	0	1	7959	1306	46	4		4	JMJD1C	10	64950795	Silent	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10	3118058	64950795	70583952	63	45993										
MGEA5	10724	hgsc.bcm.edu	37	chr10	103560098	103560098	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	tacatcagtttcaatatcttCatcactgccttcattttcta	2	11	7	0			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr10:103560098C>T	ENST00000361464.3	-	8	1491	c.1096G>A	c.(1096-1098)Gaa>Aaa	p.E366K	MGEA5_ENST00000370094.3_Missense_Mutation_p.E366K|MGEA5_ENST00000357797.5_Intron|MGEA5_ENST00000482611.1_5'Flank|MGEA5_ENST00000439817.1_Intron	NM_012215.3	NP_036347.1	O60502	OGA_HUMAN	meningioma expressed antigen 5 (hyaluronidase)	366					aging (GO:0007568)|dATP metabolic process (GO:0046060)|glycoprotein catabolic process (GO:0006516)|N-acetylglucosamine metabolic process (GO:0006044)|necrotic cell death (GO:0070265)|negative regulation of cardiac muscle adaptation (GO:0010616)|negative regulation of protein glycosylation (GO:0060051)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cell killing (GO:0031343)|positive regulation of DNA metabolic process (GO:0051054)|positive regulation of glucose import (GO:0046326)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of insulin secretion (GO:0032024)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of protein complex disassembly (GO:0043243)|positive regulation of proteolysis (GO:0045862)|protein targeting to membrane (GO:0006612)|response to steroid hormone (GO:0048545)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|hyalurononglucosaminidase activity (GO:0004415)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	23		Colorectal(252;0.207)		Epithelial(162;4.67e-09)|all cancers(201;2.54e-07)		TCAATATCTTCATCACTGCCT	0.353																																					p.E366K		Atlas-SNP	.											.	MGEA5	53	.	0			c.G1096A						.						163	138	147					10																	103560098		2203	4300	6503	SO:0001583	missense	10724	exon8			TATCTTCATCACT	AF036144	CCDS7520.1, CCDS44471.1	10q24.1-q24.3	2008-08-01			ENSG00000198408	ENSG00000198408			7056	protein-coding gene	gene with protein product	"nuclear cytoplasmic O-GlcNAcase and acetyltransferase"	604039				9811929, 16356930	Standard	NM_012215		Approved	MEA5, NCOAT, OGA	uc001ktv.2	O60502	OTTHUMG00000018939	ENST00000361464.3:c.1096G>A	chr10.hg19:g.103560098C>T	ENSP00000354850:p.Glu366Lys	63.0	0.0		59.0	24.0	NM_012215	B7WPB9|D3DR79|E9PGF9|O75166|Q86WV0|Q8IV98|Q9BVA5|Q9HAR0	Missense_Mutation	SNP	ENST00000361464.3	hg19	CCDS7520.1	.	.	.	.	.	.	.	.	.	.	C	33	5.277177	0.95459	.	.	ENSG00000198408	ENST00000361464;ENST00000370094	T;T	0.33865	1.41;1.39	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.42017	0.1184	L	0.29908	0.895	0.80722	D	1	D;P	0.53885	0.963;0.938	P;P	0.53313	0.723;0.554	T	0.03684	-1.1013	10	0.26408	T	0.33	-21.983	20.0572	0.97657	0.0:1.0:0.0:0.0	.	366;366	O60502-3;O60502	.;NCOAT_HUMAN	K	366	ENSP00000354850:E366K;ENSP00000359112:E366K	ENSP00000354850:E366K	E	-	1	0	MGEA5	103550088	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.445000	0.80570	2.826000	0.97356	0.655000	0.94253	GAA	.	.		0.353	MGEA5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049987.1	NM_012215		T	103560098	C	T	103560098	3	4	328	1	0	0	0	0	1	0	0	0	9564	835	29	3	1690	3	MGEA5	10	103560098	Missense_Mutation	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10	38609303	103560098	31974649	64	45994										
C10orf79	80217	hgsc.bcm.edu	37	chr10	105944833	105944833	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	ttcaccagaatgttttgtccAtccattgaaattctcattga	5	9	2	3			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr10:105944833A>C	ENST00000278064.2	-	16	2200	c.1875T>G	c.(1873-1875)gaT>gaG	p.D625E	WDR96_ENST00000428666.1_Missense_Mutation_p.D695E|WDR96_ENST00000357060.3_Missense_Mutation_p.D694E																NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(14)|lung(21)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						TGTTTTGTCCATCCATTGAAA	0.403																																					p.D694E		Atlas-SNP	.											.	WDR96	183	.	0			c.T2082G						.						195	171	179					10																	105944833		2203	4300	6503	SO:0001583	missense	80217	exon16			TTGTCCATCCATT																												ENST00000278064.2:c.1875T>G	chr10.hg19:g.105944833A>C	ENSP00000278064:p.Asp625Glu	82.0	0.0		87.0	17.0	NM_025145		Missense_Mutation	SNP	ENST00000278064.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.53|17.53	3.413482|3.413482	0.62511|0.62511	.|.	.|.	ENSG00000197748|ENSG00000197748	ENST00000357060;ENST00000428666;ENST00000278064|ENST00000434629	T;T;T|.	0.38240|.	1.15;1.15;1.15|.	5.18|5.18	4.05|4.05	0.47172|0.47172	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);|.	0.136364|.	0.47093|.	D|.	0.000260|.	T|T	0.52805|0.52805	0.1757|0.1757	L|L	0.41415|0.41415	1.275|1.275	0.38840|0.38840	D|D	0.956045|0.956045	D;D;D|.	0.89917|.	0.998;1.0;1.0|.	D;D;D|.	0.83275|.	0.972;0.988;0.996|.	T|T	0.49560|0.49560	-0.8927|-0.8927	10|5	0.49607|.	T|.	0.09|.	.|.	8.4011|8.4011	0.32586|0.32586	0.9037:0.0:0.0963:0.0|0.9037:0.0:0.0963:0.0	.|.	695;695;694|.	G5E9L1;B4DHB6;Q8NDM7|.	.;.;WDR96_HUMAN|.	E|R	694;695;625|55	ENSP00000349568:D694E;ENSP00000400289:D695E;ENSP00000278064:D625E|.	ENSP00000278064:D625E|.	D|M	-|-	3|2	2|0	WDR96|WDR96	105934823|105934823	1.000000|1.000000	0.71417|0.71417	0.974000|0.974000	0.42286|0.42286	0.519000|0.519000	0.34347|0.34347	2.679000|2.679000	0.46909|0.46909	0.819000|0.819000	0.34492|0.34492	0.533000|0.533000	0.62120|0.62120	GAT|ATG	.	.		0.403	WDR96-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050200.1			C	105944833	A	C	105944833	3	2	328	1	0	0	0	0	1	0	0	0	1620	214	8	5	3007	5	C10orf79	10	105944833	Missense_Mutation	SNP	A	TCGA-NI-A8LF-01A-11D-A35Z-10	2384735	105944833	29589914	65	45995										
TACC2	10579	hgsc.bcm.edu	37	chr10	123844186	123844186	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	atcagagaaatcagattttcCaccaactcctgttgcagagg	8	10	2	3			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr10:123844186C>T	ENST00000369005.1	+	4	2511	c.2171C>T	c.(2170-2172)cCa>cTa	p.P724L	TACC2_ENST00000358010.1_Intron|TACC2_ENST00000515603.1_Missense_Mutation_p.P724L|TACC2_ENST00000453444.2_Missense_Mutation_p.P724L|TACC2_ENST00000515273.1_Missense_Mutation_p.P724L|TACC2_ENST00000334433.3_Missense_Mutation_p.P724L|TACC2_ENST00000513429.1_Intron	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	724					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				TCAGATTTTCCACCAACTCCT	0.502																																					p.P724L		Atlas-SNP	.											.	TACC2	271	.	0			c.C2171T						.						60	67	65					10																	123844186		2203	4300	6503	SO:0001583	missense	10579	exon4			ATTTTCCACCAAC	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.2171C>T	chr10.hg19:g.123844186C>T	ENSP00000358001:p.Pro724Leu	195.0	0.0		175.0	67.0	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	hg19	CCDS7626.1	.	.	.	.	.	.	.	.	.	.	C	0.109	-1.140435	0.01728	.	.	ENSG00000138162	ENST00000369005;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000453444;ENST00000340076	T;T;T;T;T	0.02258	4.37;4.39;4.4;4.37;4.39	5.47	-3.6	0.04570	.	0.844828	0.09380	N	0.810141	T	0.00695	0.0023	N	0.01048	-1.04	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.46569	-0.9182	10	0.02654	T	1	-0.0103	6.9713	0.24650	0.0:0.2605:0.4041:0.3354	.	724;724;724	E9PBC6;E7EMZ9;O95359	.;.;TACC2_HUMAN	L	724;724;724;724;724;714	ENSP00000358001:P724L;ENSP00000424467:P724L;ENSP00000427618:P724L;ENSP00000334280:P724L;ENSP00000395048:P724L	ENSP00000334280:P724L	P	+	2	0	TACC2	123834176	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.294000	0.08309	-0.524000	0.06400	-0.415000	0.06103	CCA	.	.		0.502	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1			T	123844186	C	T	123844186	3	4	328	1	0	0	0	0	1	0	0	0	15517	594	21	3	2181	3	TACC2	10	123844186	Missense_Mutation	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10	17899353	123844186	11690561	66	45996										
SPTBN2	6712	hgsc.bcm.edu	37	chr11	66468343	66468343	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	ggcctagccaggcctggaagTcatccaagctgcgcaagaag	13	12	1	1			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr11:66468343T>A	ENST00000533211.1	-	17	3558	c.3227A>T	c.(3226-3228)gAc>gTc	p.D1076V	SPTBN2_ENST00000529997.1_Missense_Mutation_p.D1076V|SPTBN2_ENST00000309996.2_Missense_Mutation_p.D1076V			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	1076					actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						GGCCTGGAAGTCATCCAAGCT	0.682																																					p.D1076V		Atlas-SNP	.											.	SPTBN2	188	.	0			c.A3227T						.						19	21	21					11																	66468343		2194	4283	6477	SO:0001583	missense	6712	exon16			TGGAAGTCATCCA	AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"Pleckstrin homology (PH) domain containing"	11276	protein-coding gene	gene with protein product		604985	"spinocerebellar ataxia 5"	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.3227A>T	chr11.hg19:g.66468343T>A	ENSP00000432568:p.Asp1076Val	75.0	0.0		39.0	8.0	NM_006946	O14872|O14873	Missense_Mutation	SNP	ENST00000533211.1	hg19	CCDS8150.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.283163	0.80803	.	.	ENSG00000173898	ENST00000533211;ENST00000309996;ENST00000529997	T;T;T	0.55588	0.51;0.51;0.51	4.7	4.7	0.59300	.	0.000000	0.85682	D	0.000000	T	0.70046	0.3179	M	0.75777	2.31	0.80722	D	1	D	0.67145	0.996	D	0.68621	0.959	T	0.74414	-0.3673	10	0.72032	D	0.01	.	13.264	0.60122	0.0:0.0:0.0:1.0	.	1076	O15020	SPTN2_HUMAN	V	1076	ENSP00000432568:D1076V;ENSP00000311489:D1076V;ENSP00000433593:D1076V	ENSP00000311489:D1076V	D	-	2	0	SPTBN2	66224919	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.074000	0.57577	1.979000	0.57680	0.402000	0.26972	GAC	.	.		0.682	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946		A	66468343	T	A	66468343	3	1	328	1	0	0	0	0	1	0	0	0	15135	1667	58	4	4033	4	SPTBN2	11	66468343	Missense_Mutation	SNP	T	TCGA-NI-A8LF-01A-11D-A35Z-10		66468343	68538173	67	45997										
FAT3	120114	hgsc.bcm.edu	37	chr11	92624158	92624158	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	cacctcatcctcggatgtgtCtgccaactgcggctttgacg	10	14	2	1			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr11:92624158C>A	ENST00000298047.6	+	27	13666	c.13649C>A	c.(13648-13650)tCt>tAt	p.S4550Y	FAT3_ENST00000525166.1_Missense_Mutation_p.S4400Y|FAT3_ENST00000409404.2_Missense_Mutation_p.S4518Y|FAT3_ENST00000533797.1_Missense_Mutation_p.S853Y			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	4550					homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				TCGGATGTGTCTGCCAACTGC	0.567										TCGA Ovarian(4;0.039)																											p.S4518Y		Atlas-SNP	.											.	FAT3	1822	.	0			c.C13553A						.						39	41	41					11																	92624158		2076	4212	6288	SO:0001583	missense	120114	exon25			ATGTGTCTGCCAA	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.13649C>A	chr11.hg19:g.92624158C>A	ENSP00000298047:p.Ser4550Tyr	97.0	0.0		71.0	9.0	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	hg19		.	.	.	.	.	.	.	.	.	.	C	20.3	3.963441	0.74016	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166;ENST00000533797	D;T;D;D	0.89681	-1.94;-1.46;-1.97;-2.55	5.55	5.55	0.83447	.	.	.	.	.	D	0.91928	0.7444	M	0.76574	2.34	0.80722	D	1	P;B	0.49358	0.923;0.091	P;B	0.49276	0.605;0.141	D	0.92769	0.6230	9	0.87932	D	0	.	19.4974	0.95079	0.0:1.0:0.0:0.0	.	4518;4550	Q8TDW7-3;Q8TDW7	.;FAT3_HUMAN	Y	4550;4518;4400;853	ENSP00000298047:S4550Y;ENSP00000387040:S4518Y;ENSP00000432586:S4400Y;ENSP00000436399:S853Y	ENSP00000298047:S4550Y	S	+	2	0	FAT3	92263806	1.000000	0.71417	0.634000	0.29324	0.654000	0.38779	6.009000	0.70745	2.606000	0.88127	0.655000	0.94253	TCT	.	.		0.567	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		A	92624158	C	A	92624158	3	1	328	1	0	0	0	0	1	0	0	0	5699	913	32	3	13651	3	FAT3	11	92624158	Missense_Mutation	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10	26155815	92624158	42382358	68	45998										
ARHGAP32	9743	hgsc.bcm.edu	37	chr11	128840898	128840898	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	gtgcagcagcgggacccgggCaccgtcccgcactttctcag	13	16	1	0			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr11:128840898C>T	ENST00000310343.9	-	22	4167	c.4168G>A	c.(4168-4170)Gcc>Acc	p.A1390T	ARHGAP32_ENST00000527272.1_Missense_Mutation_p.A1041T|ARHGAP32_ENST00000524655.1_3'UTR|ARHGAP32_ENST00000392657.3_Missense_Mutation_p.A1041T	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	1390					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)|phosphatidylinositol binding (GO:0035091)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(28)|ovary(3)|prostate(6)|urinary_tract(3)	60						GGGACCCGGGCACCGTCCCGC	0.642																																					p.A1390T		Atlas-SNP	.											.	ARHGAP32	307	.	0			c.G4168A						.						47	48	48					11																	128840898		2201	4297	6498	SO:0001583	missense	9743	exon22			CCCGGGCACCGTC	AB018255	CCDS31718.1, CCDS44769.1	11q24.3	2011-06-29			ENSG00000134909	ENSG00000134909		"Rho GTPase activating proteins"	17399	protein-coding gene	gene with protein product		608541				12446789, 12819203, 17663722	Standard	NM_014715		Approved	GRIT, KIAA0712, MGC1892, RICS, GC-GAP	uc009zcp.3	A7KAX9	OTTHUMG00000165774	ENST00000310343.9:c.4168G>A	chr11.hg19:g.128840898C>T	ENSP00000310561:p.Ala1390Thr	66.0	0.0		35.0	7.0	NM_001142685	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Missense_Mutation	SNP	ENST00000310343.9	hg19	CCDS44769.1	.	.	.	.	.	.	.	.	.	.	C	2.420	-0.333262	0.05278	.	.	ENSG00000134909	ENST00000310343;ENST00000392657;ENST00000527272	T;T;T	0.07688	3.18;3.17;3.17	5.71	-4.52	0.03472	.	0.938103	0.09066	N	0.853533	T	0.05318	0.0141	L	0.38175	1.15	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.41124	-0.9526	10	0.37606	T	0.19	.	2.6734	0.05074	0.1929:0.2074:0.0959:0.5037	.	1390	A7KAX9	RHG32_HUMAN	T	1390;1041;1041	ENSP00000310561:A1390T;ENSP00000376425:A1041T;ENSP00000432862:A1041T	ENSP00000310561:A1390T	A	-	1	0	ARHGAP32	128346108	0.000000	0.05858	0.000000	0.03702	0.251000	0.25915	-0.983000	0.03759	-0.938000	0.03714	0.655000	0.94253	GCC	.	.		0.642	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715		T	128840898	C	T	128840898	3	4	328	1	0	0	0	0	1	0	0	0	881	710	25	3	2099	3	ARHGAP32	11	128840898	Missense_Mutation	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10	36216740	128840898	6165618	69	45999										
CLEC1A	51267	hgsc.bcm.edu	37	chr12	10233967	10233967	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	ctaatctttcttccatttgaGaaatggtgtcttgaccagta	7	8	3	2			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr12:10233967G>C	ENST00000315330.4	-	3	322	c.260C>G	c.(259-261)tCt>tGt	p.S87C	CLEC1A_ENST00000457018.2_Missense_Mutation_p.S54C|CLEC1A_ENST00000420265.2_Intron|RN7SKP161_ENST00000411110.1_RNA	NM_016511.2	NP_057595.2	Q8NC01	CLC1A_HUMAN	C-type lectin domain family 1, member A	87					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	23						TTCCATTTGAGAAATGGTGTC	0.393																																					p.S87C		Atlas-SNP	.											.	CLEC1A	48	.	0			c.C260G						.						119	117	118					12																	10233967		2203	4300	6503	SO:0001583	missense	51267	exon3			ATTTGAGAAATGG	AY358587	CCDS8612.1, CCDS73443.1	12p13.31	2005-02-09				ENSG00000150048		"C-type lectin domain containing"	24355	protein-coding gene	gene with protein product		606782				10671229, 11745369	Standard	XM_005253383		Approved	CLEC1, MGC34328	uc001qxb.3	Q8NC01		ENST00000315330.4:c.260C>G	chr12.hg19:g.10233967G>C	ENSP00000326407:p.Ser87Cys	191.0	0.0		145.0	54.0	NM_016511	Q8IUW7|Q9NZH3	Missense_Mutation	SNP	ENST00000315330.4	hg19	CCDS8612.1	.	.	.	.	.	.	.	.	.	.	G	8.337	0.827802	0.16749	.	.	ENSG00000150048	ENST00000315330;ENST00000457018	T;T	0.01505	4.82;4.89	4.71	2.86	0.33363	.	1.095560	0.07058	N	0.833228	T	0.03783	0.0107	L	0.46157	1.445	0.09310	N	0.999999	D;B	0.58620	0.983;0.028	P;B	0.50231	0.635;0.016	T	0.47195	-0.9136	10	0.59425	D	0.04	.	5.6287	0.17497	0.1:0.0:0.7062:0.1937	.	54;87	E9PFB4;Q8NC01	.;CLC1A_HUMAN	C	87;54	ENSP00000326407:S87C;ENSP00000415048:S54C	ENSP00000326407:S87C	S	-	2	0	CLEC1A	10125234	0.000000	0.05858	0.044000	0.18714	0.005000	0.04900	0.554000	0.23407	0.570000	0.29347	0.563000	0.77884	TCT	.	.		0.393	CLEC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399924.1	NM_016511		C	10233967	G	C	10233967	3	2	328	1	0	0	0	0	1	0	0	0	3507	942	33	4	598	4	CLEC1A	12	10233967	Missense_Mutation	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10		10233967	123617928	70	46000										
COPZ1	22818	hgsc.bcm.edu	37	chr12	54743441	54743441	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	tacggagcagaccgtgtctcAggtatgactctcccttcttc	9	13	3	2			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr12:54743441A>G	ENST00000262061.2	+	8	522	c.485A>G	c.(484-486)cAg>cGg	p.Q162R	COPZ1_ENST00000455864.2_Splice_Site_p.Q139R|COPZ1_ENST00000549043.1_Splice_Site_p.Q170R|COPZ1_ENST00000551779.1_Missense_Mutation_p.Q162R|COPZ1_ENST00000552362.1_Intron|COPZ1_ENST00000416254.2_Splice_Site_p.Q111R|COPZ1_ENST00000552218.1_Splice_Site_p.Q183R|COPZ1_ENST00000553231.1_Splice_Site_p.Q139R|COPZ1_ENST00000548281.1_3'UTR|COPZ1_ENST00000548753.1_Splice_Site_p.Q74R|COPZ1_ENST00000549116.1_Splice_Site_p.Q104R	NM_001271734.1|NM_001271736.1|NM_016057.1	NP_001258663.1|NP_001258665.1|NP_057141.1	P61923	COPZ1_HUMAN	coatomer protein complex, subunit zeta 1	162					COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)				kidney(1)|lung(4)	5						ACCGTGTCTCAGGTATGACTC	0.488																																					p.Q170R		Atlas-SNP	.											.	COPZ1	10	.	0			c.A509G						.						277	249	258					12																	54743441		2203	4300	6503	SO:0001630	splice_region_variant	22818	exon8			TGTCTCAGGTATG	AF151878	CCDS8877.1, CCDS61137.1, CCDS61138.1, CCDS61139.1	12q13.2-q13.3	2008-02-05		2003-07-23					2243	protein-coding gene	gene with protein product		615472	"coatomer protein complex, subunit zeta"	COPZ			Standard	NM_001271734		Approved	CGI-120	uc009znm.2	P61923		ENST00000262061.2:c.486+1A>G	chr12.hg19:g.54743441A>G		150.0	0.0		113.0	41.0	NM_001271736	B4DDX8|B4DHZ0|F8VS17|F8VWL5|Q549N6|Q9Y3C3	Missense_Mutation	SNP	ENST00000262061.2	hg19	CCDS8877.1	.	.	.	.	.	.	.	.	.	.	A	19.02	3.745670	0.69418	.	.	ENSG00000111481	ENST00000262061;ENST00000549043;ENST00000552218;ENST00000553231;ENST00000455864;ENST00000416254;ENST00000549116;ENST00000551779;ENST00000548753	.	.	.	4.52	4.52	0.55395	.	0.000000	0.85682	D	0.000000	D	0.84433	0.5471	M	0.93854	3.465	0.80722	D	1	P;D;D;P	0.76494	0.872;0.995;0.999;0.676	P;D;D;P	0.68621	0.512;0.92;0.959;0.512	D	0.88126	0.2835	9	0.87932	D	0	0.3815	12.1292	0.53934	1.0:0.0:0.0:0.0	.	139;170;111;162	B4DDX8;F8VWL5;B4DHZ0;P61923	.;.;.;COPZ1_HUMAN	R	162;170;183;139;139;111;104;162;74	.	ENSP00000262061:Q162R	Q	+	2	0	COPZ1	53029708	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	6.841000	0.75374	2.032000	0.59987	0.454000	0.30748	CAG	.	.		0.488	COPZ1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405753.1	NM_016057	Missense_Mutation	G	54743441	A	G	54743441	5	3	328	1	0	0	0	0	0	0	1	0	3743	202	7	2	515	2	COPZ1	12	54743441	Splice_Site	SNP	A	TCGA-NI-A8LF-01A-11D-A35Z-10	44509474	54743441	79108454	71	46001										
OR6C4	341418	hgsc.bcm.edu	37	chr12	55945104	55945104	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	tattcatctttctgttcctcAcctacatgctaagtatccta	3	12	4	0			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr12:55945104A>C	ENST00000394256.2	+	1	122	c.94A>C	c.(94-96)Acc>Ccc	p.T32P	RP11-110A12.2_ENST00000555138.1_RNA|RP11-110A12.2_ENST00000556750.1_RNA	NM_001005494.1	NP_001005494.1	Q8NGE1	OR6C4_HUMAN	olfactory receptor, family 6, subfamily C, member 4	32						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|skin(1)	11						TCTGTTCCTCACCTACATGCT	0.423																																					p.T32P		Atlas-SNP	.											.	OR6C4	34	.	0			c.A94C						.						161	159	160					12																	55945104		2203	4300	6503	SO:0001583	missense	341418	exon1			TTCCTCACCTACA	BK004261	CCDS31827.1	12q14.2	2012-08-09				ENSG00000179626		"GPCR / Class A : Olfactory receptors"	19632	protein-coding gene	gene with protein product							Standard	NM_001005494		Approved		uc010spp.2	Q8NGE1	OTTHUMG00000169959	ENST00000394256.2:c.94A>C	chr12.hg19:g.55945104A>C	ENSP00000377799:p.Thr32Pro	178.0	0.0		178.0	64.0	NM_001005494	A8MZG7|B2RNN2|Q6IFK1	Missense_Mutation	SNP	ENST00000394256.2	hg19	CCDS31827.1	.	.	.	.	.	.	.	.	.	.	A	14.65	2.600178	0.46423	.	.	ENSG00000179626	ENST00000394256	T	0.00514	6.88	4.81	-1.84	0.07809	.	0.129427	0.34853	N	0.003638	T	0.01029	0.0034	M	0.78285	2.405	0.09310	N	1	P	0.48089	0.905	P	0.53988	0.739	T	0.19582	-1.0301	10	0.87932	D	0	.	11.7152	0.51647	0.4861:0.0:0.5139:0.0	.	32	Q8NGE1	OR6C4_HUMAN	P	32	ENSP00000377799:T32P	ENSP00000377799:T32P	T	+	1	0	OR6C4	54231371	0.000000	0.05858	0.010000	0.14722	0.768000	0.43524	-1.044000	0.03532	-0.400000	0.07656	0.528000	0.53228	ACC	.	.		0.423	OR6C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406678.1			C	55945104	A	C	55945104	3	2	328	1	0	0	0	0	1	0	0	0	11202	159	6	5	96	5	OR6C4	12	55945104	Missense_Mutation	SNP	A	TCGA-NI-A8LF-01A-11D-A35Z-10	1201663	55945104	77906791	72	46002										
METTL1	25895	hgsc.bcm.edu	37	chr12	58163586	58163586	+	5'Flank	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	agaagaagttaggaaggtgcTtcatggcattgctacggaga	14	5	1	3			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr12:58163586T>C	ENST00000300209.8	+	0	0				METTL21B_ENST00000551420.1_5'Flank|METTL1_ENST00000257848.7_Intron|CYP27B1_ENST00000228606.4_5'Flank|METTL1_ENST00000324871.7_Missense_Mutation_p.K143R|METTL1_ENST00000548681.1_5'Flank|METTL21B_ENST00000333012.5_5'Flank|METTL21B_ENST00000548256.1_5'Flank	NM_015433.2	NP_056248.2	Q96AZ1	MT21B_HUMAN	methyltransferase like 21B							cytoplasm (GO:0005737)|intracellular (GO:0005622)	methyltransferase activity (GO:0008168)			endometrium(1)|lung(1)	2						AGGAAGGTGCTTCATGGCATT	0.602																																					p.K143R		Atlas-SNP	.											.	METTL1	14	.	0			c.A428G						.						70	63	66					12																	58163586		2203	4300	6503	SO:0001631	upstream_gene_variant	4234	exon3			AGGTGCTTCATGG	AL050100, AF455816	CCDS8957.1, CCDS31848.1	12q14.1	2011-03-03	2011-03-03	2011-03-03	ENSG00000123427	ENSG00000123427			24936	protein-coding gene	gene with protein product		615258	"family with sequence similarity 119, member B"	FAM119B		12477932	Standard	NM_015433		Approved	DKFZP586D0919	uc001sqg.3	Q96AZ1	OTTHUMG00000170459		chr12.hg19:g.58163586T>C	Exception_encountered	135.0	0.0		109.0	36.0	NM_005371	Q9H749|Q9Y3W2	Missense_Mutation	SNP	ENST00000300209.8	hg19	CCDS8957.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.577573	0.86645	.	.	ENSG00000037897	ENST00000324871	T	0.44881	0.91	5.08	5.08	0.68730	.	0.162430	0.52532	N	0.000068	T	0.59972	0.2233	M	0.85777	2.775	0.80722	D	1	P	0.40834	0.73	P	0.49953	0.627	T	0.65442	-0.6167	10	0.54805	T	0.06	-15.3727	13.8131	0.63274	0.0:0.0:0.0:1.0	.	143	Q9UBP6	TRMB_HUMAN	R	143	ENSP00000314441:K143R	ENSP00000314441:K143R	K	-	2	0	METTL1	56449853	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.020000	0.76419	1.905000	0.55150	0.533000	0.62120	AAG	.	.		0.602	METTL21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409268.1	NM_015433		C	58163586	T	C	58163586	1	2	328	0	1	0	0	0	0	0	0	0	9502	1609	56	2		2	METTL1	12	58163586	5'Flank	SNP	T	TCGA-NI-A8LF-01A-11D-A35Z-10	2218482	58163586	75688309	73	46003										
TNFRSF19	55504	hgsc.bcm.edu	37	chr13	24242840	24242840	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	cgtgtgtgcagaaacgcaggCccagccggggagatggtgcc	17	11	0	2			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr13:24242840C>T	ENST00000382258.4	+	9	1053	c.849C>T	c.(847-849)ggC>ggT	p.G283G	TNFRSF19_ENST00000403372.2_Silent_p.G151G|TNFRSF19_ENST00000248484.4_Silent_p.G283G|TNFRSF19_ENST00000382263.3_Silent_p.G283G	NM_018647.3	NP_061117.2	Q9NS68	TNR19_HUMAN	tumor necrosis factor receptor superfamily, member 19	283					apoptotic process (GO:0006915)|hair follicle development (GO:0001942)|JNK cascade (GO:0007254)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	integral component of membrane (GO:0016021)	tumor necrosis factor-activated receptor activity (GO:0005031)			breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	22		all_cancers(29;3.4e-22)|all_epithelial(30;8.75e-19)|all_lung(29;5.09e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00193)|Epithelial(112;0.0137)|OV - Ovarian serous cystadenocarcinoma(117;0.0465)|GBM - Glioblastoma multiforme(144;0.184)|Lung(94;0.19)		GAAACGCAGGCCCAGCCGGGG	0.493																																					p.G283G		Atlas-SNP	.											.	TNFRSF19	52	.	0			c.C849T						.						79	80	80					13																	24242840		2203	4300	6503	SO:0001819	synonymous_variant	55504	exon9			CGCAGGCCCAGCC	AB040434	CCDS9301.1, CCDS9302.1, CCDS55893.1	13q12.11-q12.3	2008-07-18			ENSG00000127863	ENSG00000127863		"Tumor necrosis factor receptor superfamily"	11915	protein-coding gene	gene with protein product	"toxicity and JNK inducer"	606122				10764796, 10809768	Standard	NM_018647		Approved	TAJ-alpha, TROY, TAJ, TRADE	uc001uov.2	Q9NS68	OTTHUMG00000016568	ENST00000382258.4:c.849C>T	chr13.hg19:g.24242840C>T		73.0	0.0		83.0	26.0	NM_018647	A8KA09|A8KA26|B1AM40|B1AM41|B4E2I6|Q9BXZ9|Q9BY00|Q9NZV2	Silent	SNP	ENST00000382258.4	hg19	CCDS9302.1																																																																																			.	.		0.493	TNFRSF19-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044156.2	NM_018647		T	24242840	C	T	24242840	2	4	328	1	0	0	0	0	0	0	0	1	16307	726	26	3		3	TNFRSF19	13	24242840	Silent	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10		24242840	90927038	74	46004										
COG6	57511	hgsc.bcm.edu	37	chr13	40256393	40256393	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	gccctgcaggacagacctgtCttatataagttggtgacttt	10	9	1	2			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr13:40256393C>A	ENST00000455146.3	+	8	830	c.780C>A	c.(778-780)gtC>gtA	p.V260V	COG6_ENST00000416691.1_Silent_p.V260V|COG6_ENST00000465775.1_3'UTR	NM_020751.2	NP_065802.1	Q9Y2V7	COG6_HUMAN	component of oligomeric golgi complex 6	260					glycosylation (GO:0070085)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				NS(1)|kidney(2)|large_intestine(5)|lung(4)|skin(1)	13		Lung NSC(96;0.000124)|Breast(139;0.0199)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.03e-09)|Epithelial(112;7e-07)|OV - Ovarian serous cystadenocarcinoma(117;0.00015)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.0168)		ACAGACCTGTCTTATATAAGT	0.318																																					p.V260V		Atlas-SNP	.											.	COG6	49	.	0			c.C780A						.						67	69	69					13																	40256393		2203	4300	6503	SO:0001819	synonymous_variant	57511	exon8			ACCTGTCTTATAT	AK026638	CCDS9370.1, CCDS45042.1	13q13.2	2011-08-01			ENSG00000133103	ENSG00000133103		"Components of oligomeric golgi complex"	18621	protein-coding gene	gene with protein product		606977				11980916	Standard	NM_020751		Approved	COD2, KIAA1134	uc001uxh.2	Q9Y2V7	OTTHUMG00000016768	ENST00000455146.3:c.780C>A	chr13.hg19:g.40256393C>A		436.0	0.0		200.0	68.0	NM_001145079	Q5T0U1|Q6AI19|Q86V49|Q9ULT5	Silent	SNP	ENST00000455146.3	hg19	CCDS9370.1																																																																																			.	.		0.318	COG6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044622.3			A	40256393	C	A	40256393	2	1	328	1	0	0	0	0	0	0	0	1	3664	900	32	3		3	COG6	13	40256393	Silent	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10	16013553	40256393	74913485	75	46005										
LIG4	3981	hgsc.bcm.edu	37	chr13	108863529	108863529	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	gattttttctgcacgtccttTacttttctgtattcgttcta	5	9	3	0			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr13:108863529T>C	ENST00000356922.4	-	2	360	c.88A>G	c.(88-90)Aaa>Gaa	p.K30E	LIG4_ENST00000405925.1_Missense_Mutation_p.K30E|LIG4_ENST00000442234.1_Missense_Mutation_p.K30E	NM_002312.3|NM_206937.1	NP_002303.2|NP_996820.1	P49917	DNLI4_HUMAN	ligase IV, DNA, ATP-dependent	30					cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|chromosome organization (GO:0051276)|DNA biosynthetic process (GO:0071897)|DNA ligation (GO:0006266)|DNA ligation involved in DNA recombination (GO:0051102)|DNA ligation involved in DNA repair (GO:0051103)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|in utero embryonic development (GO:0001701)|isotype switching (GO:0045190)|lagging strand elongation (GO:0006273)|negative regulation of neuron apoptotic process (GO:0043524)|neuron apoptotic process (GO:0051402)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of neurogenesis (GO:0050769)|pro-B cell differentiation (GO:0002328)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|single strand break repair (GO:0000012)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA ligase IV complex (GO:0032807)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|focal adhesion (GO:0005925)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	42	all_lung(23;0.000238)|all_neural(89;0.00256)|Lung NSC(43;0.0056)|Medulloblastoma(90;0.00596)|Lung SC(71;0.104)					GCACGTCCTTTACTTTTCTGT	0.388								Non-homologous end-joining																													p.K30E		Atlas-SNP	.											.	LIG4	91	.	0			c.A88G						.						43	44	43					13																	108863529		2203	4297	6500	SO:0001583	missense	3981	exon3			GTCCTTTACTTTT	X83441	CCDS9508.1	13q33-q34	2014-09-17			ENSG00000174405	ENSG00000174405	6.5.1.1		6601	protein-coding gene	gene with protein product	"polydeoxyribonucleotide synthase [ATP] 4", "polynucleotide ligase", "sealase", "DNA repair enzyme", "DNA joinase"	601837				7760816	Standard	NM_001098268		Approved		uc001vqo.3	P49917	OTTHUMG00000017328	ENST00000356922.4:c.88A>G	chr13.hg19:g.108863529T>C	ENSP00000349393:p.Lys30Glu	99.0	0.0		104.0	17.0	NM_206937	Q8IY66|Q8TEU5	Missense_Mutation	SNP	ENST00000356922.4	hg19	CCDS9508.1	.	.	.	.	.	.	.	.	.	.	T	14.26	2.482176	0.44147	.	.	ENSG00000174405	ENST00000405925;ENST00000442234;ENST00000356922	T;T;T	0.17691	2.26;2.26;2.26	6.15	6.15	0.99193	DNA ligase, ATP-dependent, N-terminal (3);	0.089927	0.85682	D	0.000000	T	0.29588	0.0738	L	0.52126	1.63	0.58432	D	0.999999	B	0.34349	0.45	P	0.47705	0.555	T	0.01966	-1.1238	10	0.31617	T	0.26	.	15.9697	0.80004	0.0:0.0:0.0:1.0	.	30	P49917	DNLI4_HUMAN	E	30	ENSP00000385955:K30E;ENSP00000402030:K30E;ENSP00000349393:K30E	ENSP00000349393:K30E	K	-	1	0	LIG4	107661530	1.000000	0.71417	0.991000	0.47740	0.911000	0.54048	7.590000	0.82653	2.363000	0.80096	0.523000	0.50628	AAA	.	.		0.388	LIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045738.4	NM_002312		C	108863529	T	C	108863529	3	2	328	1	0	0	0	0	1	0	0	0	8792	1763	61	2	2651	2	LIG4	13	108863529	Missense_Mutation	SNP	T	TCGA-NI-A8LF-01A-11D-A35Z-10	68607136	108863529	6306349	76	46006										
OR4K2	390431	hgsc.bcm.edu	37	chr14	20345061	20345061	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	aattgcgttgtcctgttttaTtgttttatttaattcatatg	6	4	1	0			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr14:20345061T>G	ENST00000298642.2	+	1	671	c.635T>G	c.(634-636)aTt>aGt	p.I212S		NM_001005501.1	NP_001005501.1	Q8NGD2	OR4K2_HUMAN	olfactory receptor, family 4, subfamily K, member 2	212						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(16)|ovary(2)|skin(9)|upper_aerodigestive_tract(2)	43	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TCCTGTTTTATTGTTTTATTT	0.393																																					p.I212S		Atlas-SNP	.											.	OR4K2	97	.	0			c.T635G						.						273	278	276					14																	20345061		2203	4299	6502	SO:0001583	missense	390431	exon1			GTTTTATTGTTTT		CCDS32023.1	14q11.2	2013-09-23			ENSG00000165762	ENSG00000165762		"GPCR / Class A : Olfactory receptors"	14728	protein-coding gene	gene with protein product							Standard	NM_001005501		Approved		uc001vwh.1	Q8NGD2	OTTHUMG00000170624	ENST00000298642.2:c.635T>G	chr14.hg19:g.20345061T>G	ENSP00000298642:p.Ile212Ser	91.0	0.0		78.0	10.0	NM_001005501	B2RNK8|Q6IFA5	Missense_Mutation	SNP	ENST00000298642.2	hg19	CCDS32023.1	.	.	.	.	.	.	.	.	.	.	.	7.595	0.671511	0.14776	.	.	ENSG00000165762	ENST00000298642	T	0.38887	1.11	5.0	5.0	0.66597	GPCR, rhodopsin-like superfamily (1);	0.135127	0.33650	N	0.004700	T	0.28167	0.0695	N	0.17278	0.47	0.41615	D	0.98893	B	0.16166	0.016	B	0.22880	0.042	T	0.09250	-1.0683	10	0.45353	T	0.12	.	11.0079	0.47646	0.0:0.0:0.0:1.0	.	212	Q8NGD2	OR4K2_HUMAN	S	212	ENSP00000298642:I212S	ENSP00000298642:I212S	I	+	2	0	OR4K2	19414901	0.248000	0.23930	1.000000	0.80357	0.110000	0.19582	2.910000	0.48766	2.097000	0.63578	0.383000	0.25322	ATT	.	.		0.393	OR4K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409864.1			G	20345061	T	G	20345061	3	3	328	1	0	0	0	0	1	0	0	0	11081	1493	52	5	637	5	OR4K2	14	20345061	Missense_Mutation	SNP	T	TCGA-NI-A8LF-01A-11D-A35Z-10		20345061	87004479	77	46007										
C14orf39	317761	hgsc.bcm.edu	37	chr14	60928094	60928094	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	ttatcccctttttccgaccaCtgattggaatttgattgttt	6	9	0	2			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr14:60928094C>T	ENST00000321731.3	-	13	1254	c.1095G>A	c.(1093-1095)caG>caA	p.Q365Q		NM_174978.2	NP_777638	Q8N1H7	S6OS1_HUMAN	chromosome 14 open reading frame 39	365					multicellular organismal development (GO:0007275)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)					breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(108;0.0448)		TTTCCGACCACTGATTGGAAT	0.279																																					p.Q365Q		Atlas-SNP	.											.	C14orf39	79	.	0			c.G1095A						.						67	62	64					14																	60928094		2202	4299	6501	SO:0001819	synonymous_variant	317761	exon13			CGACCACTGATTG	AK098187	CCDS9746.1	14q23.1	2012-11-05	2012-11-05	2012-11-05	ENSG00000179008	ENSG00000179008			19849	protein-coding gene	gene with protein product							Standard	NM_174978		Approved	SIX6OS1	uc001xez.4	Q8N1H7	OTTHUMG00000140332	ENST00000321731.3:c.1095G>A	chr14.hg19:g.60928094C>T		174.0	0.0		96.0	34.0	NM_174978	Q08AQ4	Silent	SNP	ENST00000321731.3	hg19	CCDS9746.1																																																																																			.	.		0.279	C14orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276948.1	NM_174978		T	60928094	C	T	60928094	2	4	328	1	0	0	0	0	0	0	0	1	1774	564	20	3		3	C14orf39	14	60928094	Silent	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10	40583033	60928094	46421446	78	46008										
TMEM30B	161291	hgsc.bcm.edu	37	chr14	61747677	61747677	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	tcgcctgtatagtcgtactcCagctccttgatgccgttgga	10	12	0	1			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr14:61747677C>T	ENST00000555868.1	-	1	881	c.189G>A	c.(187-189)ctG>ctA	p.L63L	TMEM30B_ENST00000355702.2_Silent_p.L63L|TMEM30B_ENST00000557163.1_Intron	NM_001017970.2	NP_001017970.1	Q3MIR4	CC50B_HUMAN	transmembrane protein 30B	63					lipid transport (GO:0006869)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|large_intestine(1)|lung(1)|prostate(1)|stomach(1)	6				OV - Ovarian serous cystadenocarcinoma(108;0.107)|BRCA - Breast invasive adenocarcinoma(234;0.181)		AGTCGTACTCCAGCTCCTTGA	0.701																																					p.L63L		Atlas-SNP	.											.	TMEM30B	13	.	0			c.G189A						.						7	6	6					14																	61747677		1969	3870	5839	SO:0001819	synonymous_variant	161291	exon1			GTACTCCAGCTCC	AK091169	CCDS32093.1	14q23.1	2006-09-20				ENSG00000182107			27254	protein-coding gene	gene with protein product		611029				15375526	Standard	NM_001017970		Approved	CDC50B	uc001xfl.3	Q3MIR4		ENST00000555868.1:c.189G>A	chr14.hg19:g.61747677C>T		38.0	0.0		34.0	12.0	NM_001017970	B3KR84|Q14D00	Silent	SNP	ENST00000555868.1	hg19	CCDS32093.1																																																																																			.	.		0.701	TMEM30B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413358.1	XM_090844		T	61747677	C	T	61747677	2	4	328	1	0	0	0	0	0	0	0	1	16169	581	21	3		3	TMEM30B	14	61747677	Silent	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10	819583	61747677	45601863	79	46009										
SHC4	399694	hgsc.bcm.edu	37	chr15	49255156	49255156	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	tgcagcatcccggggtgcccGaagagtcctacatacagcac	11	14	0	1			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr15:49255156G>A	ENST00000332408.4	-	1	485	c.57C>T	c.(55-57)ttC>ttT	p.F19F		NM_203349.3	NP_976224.3	Q6S5L8	SHC4_HUMAN	SHC (Src homology 2 domain containing) family, member 4	19	CH2.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of cell proliferation (GO:0008284)|regulation of gene expression (GO:0010468)|stem cell differentiation (GO:0048863)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				breast(1)|endometrium(2)|large_intestine(8)|lung(11)|ovary(3)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	29		all_lung(180;0.00466)		all cancers(107;9.4e-08)|GBM - Glioblastoma multiforme(94;5.94e-07)		CGGGGTGCCCGAAGAGTCCTA	0.592																																					p.F19F		Atlas-SNP	.											SHC4,bladder,carcinoma,0,1	SHC4	70	.	0			c.C57T						.						75	81	79					15																	49255156		2194	4285	6479	SO:0001819	synonymous_variant	399694	exon1			GTGCCCGAAGAGT	AY358250	CCDS10130.1	15q21.1-q21.2	2013-02-14			ENSG00000185634	ENSG00000185634		"SH2 domain containing"	16743	protein-coding gene	gene with protein product	"rai-like protein"						Standard	NM_203349		Approved	RaLP	uc001zxb.1	Q6S5L8	OTTHUMG00000131513	ENST00000332408.4:c.57C>T	chr15.hg19:g.49255156G>A		107.0	0.0		56.0	10.0	NM_203349	Q6UXQ3|Q8IYW3	Silent	SNP	ENST00000332408.4	hg19	CCDS10130.1																																																																																			.	.		0.592	SHC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254371.1	NM_203349		A	49255156	G	A	49255156	2	1	328	1	0	0	0	0	0	0	0	1	14288	1049	37	1		1	SHC4	15	49255156	Silent	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10		49255156	53276236	80	46010										
MAN2C1	4123	hgsc.bcm.edu	37	chr15	75651670	75651671	+	Splice_Site	DNP	TC	TC	GA													0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	cagggcatgcaggactcaccTcttgcactacgaacacaggc							TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr15:75651670_75651671TC>GA	ENST00000267978.5	-	17	2090_2091	c.2044_2045GA>TC	c.(2044-2046)GAg>TCg	p.E682S	MAN2C1_ENST00000563622.1_Splice_Site_p.E583S|MAN2C1_ENST00000569482.1_Splice_Site_p.E682S|MAN2C1_ENST00000565683.1_Splice_Site_p.R686I	NM_006715.3	NP_006706.2	Q9NTJ4	MA2C1_HUMAN	mannosidase, alpha, class 2C, member 1	682					mannose metabolic process (GO:0006013)		alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(4)|kidney(6)|large_intestine(6)|lung(20)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	44						AGGACTCACCTCTTGCACTACG	0.629																																					p.R686S|p.E682X		Atlas-SNP	.											.	MAN2C1	76	.	0			c.A2058C|c.G2044T						.																																			SO:0001630	splice_region_variant	4123	exon17			CTCACCTCTTGCA|TCACCTCTTGCAC	AF044414	CCDS32298.1, CCDS58389.1, CCDS58390.1, CCDS58391.1	15q24.2	2013-09-19			ENSG00000140400	ENSG00000140400	3.2.1.24		6827	protein-coding gene	gene with protein product		154580		MANA1, MANA		1757461, 752528	Standard	NM_006715		Approved		uc002bah.4	Q9NTJ4	OTTHUMG00000172698	ENST00000267978.5:c.2044_2045delinsGA	chr15.hg19:g.75651670_75651671delinsGA		122.0|123.0	0.0		75.0|76.0	19.0	NM_001256494|NM_006715	H3BMX2|H3BQY8|H3BUT6|Q13358|Q68EM8|Q9UL64	Missense_Mutation|Nonsense_Mutation	SNP	ENST00000267978.5	hg19	CCDS32298.1																																																																																			.	.		0.629	MAN2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419965.1		Missense_Mutation	GA	75651671	TC	GA	75651670	5	3	328	1	0	0	0	0	0	0	1	0	9227	1565	54	5	1117	5	MAN2C1	15	75651670	Splice_Site	DNP	TC	TCGA-NI-A8LF-01A-11D-A35Z-10	26396514	75651670	26879722	81	46011										
STARD5	80765	hgsc.bcm.edu	37	chr15	81616431	81616432	+	Frame_Shift_Ins	INS	-	-	CGGGTCCATTGCGT													0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	ctcatctgggctgccagcgcINScgggtccattgcgtcgggag					rs567953882		TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr15:81616431_81616432insCGGGTCCATTGCGT	ENST00000302824.6	-	1	34_35	c.9_10insACGCAATGGACCCG	c.(7-12)ccggcgfs	p.A4fs	RP11-761I4.3_ENST00000560973.1_RNA|RP11-761I4.3_ENST00000559781.1_RNA|STARD5_ENST00000559913.1_De_novo_Start_OutOfFrame	NM_181900.2	NP_871629.1	Q9NSY2	STAR5_HUMAN	StAR-related lipid transfer (START) domain containing 5	4	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				C21-steroid hormone biosynthetic process (GO:0006700)|lipid transport (GO:0006869)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	cytosol (GO:0005829)	lipid binding (GO:0008289)			large_intestine(3)|ovary(1)|skin(1)|stomach(1)	6						GCTGCCAGCGCCGGGTCCATTG	0.673																																					p.A4fs		Atlas-INDEL	.											.	STARD5	20	.	0			c.10_11insACGCAATGGACCCG						.																																			SO:0001589	frameshift_variant	80765	exon1			.	AF480304	CCDS10318.1	15q26	2011-09-12	2007-08-16		ENSG00000172345	ENSG00000172345		"StAR-related lipid transfer (START) domain containing"	18065	protein-coding gene	gene with protein product		607050	"START domain containing 5"			12011452	Standard	NM_181900		Approved	MGC10327	uc002bgm.3	Q9NSY2	OTTHUMG00000147342	ENST00000302824.6:c.-4_9dupACGCAATGGACCCG	chr15.hg19:g.81616431_81616432insCGGGTCCATTGCGT	ENSP00000304032:p.Ala4fs	143.0	0.0		83.0	14.0	NM_181900	P59094	Frame_Shift_Ins	INS	ENST00000302824.6	hg19	CCDS10318.1																																																																																			.	.		0.673	STARD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303950.2			CGGGTCCATTGCGT	81616432	-	CGGGTCCATTGCGT	81616431	7	5	328	1	0	1	1	0	0	0	0	0	15275	739	26	0	655	0	STARD5	15	81616431	Frame_Shift_Ins	INS	-	TCGA-NI-A8LF-01A-11D-A35Z-10	5964761	81616431	20914961	82	46012										
ITGAM	3684	hgsc.bcm.edu	37	chr16	31336283	31336283	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	atttattttttaaaagtttcCctttgagaagaattgtggca	7	4	0	2			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr16:31336283C>T	ENST00000287497.8	+	19	2369	c.2294C>T	c.(2293-2295)cCc>cTc	p.P765L	ITGAM_ENST00000544665.3_Missense_Mutation_p.P766L			P11215	ITAM_HUMAN	integrin, alpha M (complement component 3 receptor 3 subunit)	765					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular extravasation (GO:0045123)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|microglia development (GO:0014005)|neutrophil chemotaxis (GO:0030593)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)			endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(1)|prostate(4)|skin(1)	56						TAAAAGTTTCCCTTTGAGAAG	0.343																																					p.P766L		Atlas-SNP	.											.	ITGAM	137	.	0			c.C2297T						.						57	52	54					16																	31336283		1842	4087	5929	SO:0001583	missense	3684	exon19			AGTTTCCCTTTGA	J03925	CCDS45470.1, CCDS54004.1	16p11.2	2010-03-23	2006-02-10			ENSG00000169896		"CD molecules", "Complement system", "Integrins"	6149	protein-coding gene	gene with protein product		120980	"integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide)"	CR3A, CD11B			Standard	NM_001145808		Approved	MAC-1, CD11b	uc002ebr.3	P11215		ENST00000287497.8:c.2294C>T	chr16.hg19:g.31336283C>T	ENSP00000287497:p.Pro765Leu	48.0	0.0		57.0	10.0	NM_001145808	Q4VAK0|Q4VAK1|Q4VAK2	Missense_Mutation	SNP	ENST00000287497.8	hg19	CCDS45470.1	.	.	.	.	.	.	.	.	.	.	C	18.89	3.720534	0.68959	.	.	ENSG00000169896	ENST00000544665;ENST00000287497	T;T	0.51325	0.71;0.71	4.94	4.94	0.65067	Integrin alpha-2 (1);	.	.	.	.	T	0.70718	0.3256	M	0.81682	2.555	0.58432	D	0.99999	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.79784	0.993;0.979;0.979	T	0.75391	-0.3334	9	0.87932	D	0	.	17.0841	0.86606	0.0:1.0:0.0:0.0	.	171;765;765	B3KXM6;Q4VAK1;P11215	.;.;ITAM_HUMAN	L	766;765	ENSP00000441691:P766L;ENSP00000287497:P765L	ENSP00000287497:P765L	P	+	2	0	ITGAM	31243784	0.998000	0.40836	1.000000	0.80357	0.742000	0.42306	2.916000	0.48813	2.571000	0.86741	0.655000	0.94253	CCC	.	.		0.343	ITGAM-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432816.1	NM_000632		T	31336283	C	T	31336283	3	4	328	1	0	0	0	0	1	0	0	0	7896	623	22	3	2371	3	ITGAM	16	31336283	Missense_Mutation	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10		31336283	59018470	83	46013										
TP53	7157	hgsc.bcm.edu	37	chr17	7577112	7577113	+	Frame_Shift_Ins	INS	-	-	ACAA													0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	cggtctctcccaggacaggcINSacaaacacgcacctcaaagc							TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr17:7577112_7577113insACAA	ENST00000269305.4	-	8	1014_1015	c.825_826insTTGT	c.(823-828)tgtgccfs	p.A276fs	TP53_ENST00000455263.2_Frame_Shift_Ins_p.A276fs|TP53_ENST00000413465.2_Intron|TP53_ENST00000420246.2_Frame_Shift_Ins_p.A276fs|TP53_ENST00000445888.2_Frame_Shift_Ins_p.A276fs|TP53_ENST00000359597.4_Frame_Shift_Ins_p.A276fs|TP53_ENST00000574684.1_5'Flank	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	276	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		A -> D (in sporadic cancers; somatic mutation).|A -> G (in sporadic cancers; somatic mutation).|A -> P (in sporadic cancers; somatic mutation).|A -> S (in sporadic cancers; somatic mutation).|A -> T (in sporadic cancers; somatic mutation).|A -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.A276P(15)|p.A276S(9)|p.0?(8)|p.C275W(7)|p.A276T(7)|p.C275C(4)|p.?(2)|p.A276_R283delACPGRDRR(1)|p.A276fs*64(1)|p.A276fs*68(1)|p.R273_C275delRVC(1)|p.C275_A276ins10(1)|p.V274_P278del(1)|p.C275*(1)|p.F270_D281del12(1)|p.A276fs*31(1)|p.C275_R283delCACPGRDRR(1)|p.A276fs*70(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.A276_C277delAC(1)|p.C275fs*67(1)|p.V272_K292del21(1)|p.C275fs*20(1)|p.A276fs*29(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CCAGGACAGGCACAAACACGCA	0.55		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.A276fs	Pancreas(47;798 1329 9957 10801)	Atlas-INDEL	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,NS,NS,+1,2	TP53	33396	.	70	Substitution - Missense(38)|Deletion - In frame(8)|Whole gene deletion(8)|Deletion - Frameshift(6)|Substitution - coding silent(4)|Insertion - Frameshift(2)|Unknown(2)|Substitution - Nonsense(1)|Insertion - In frame(1)	haematopoietic_and_lymphoid_tissue(13)|upper_aerodigestive_tract(6)|stomach(6)|large_intestine(6)|breast(6)|bone(6)|biliary_tract(4)|central_nervous_system(4)|thymus(3)|urinary_tract(3)|oesophagus(3)|skin(3)|ovary(2)|soft_tissue(1)|kidney(1)|endometrium(1)|lung(1)|prostate(1)	c.826_827insTTGT						.																																			SO:0001589	frameshift_variant	7157	exon8	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	.	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.822_825dupTTGT	chr17.hg19:g.7577113_7577116dupACAA	ENSP00000269305:p.Ala276fs	138.0	0.0		58.0	36.0	NM_001126112	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Ins	INS	ENST00000269305.4	hg19	CCDS11118.1																																																																																			.	.		0.55	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		ACAA	7577113	-	ACAA	7577112	7	5	328	1	0	1	1	0	0	0	0	0	16396	710	25	0	460	0	TP53	17	7577112	Frame_Shift_Ins	INS	-	TCGA-NI-A8LF-01A-11D-A35Z-10		7577112	73618098	84	46014										
SUPT6H	6830	hgsc.bcm.edu	37	chr17	27024667	27024667	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	gatttggatgagattgttgcTcgctatgtccagcccatggc	12	9	0	1			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr17:27024667T>G	ENST00000314616.6	+	31	4522	c.4239T>G	c.(4237-4239)gcT>gcG	p.A1413A	SUPT6H_ENST00000347486.4_Silent_p.A1413A	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	1413	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					AGATTGTTGCTCGCTATGTCC	0.512																																					p.A1413A		Atlas-SNP	.											.	SUPT6H	165	.	0			c.T4239G						.						89	81	84					17																	27024667		2203	4300	6503	SO:0001819	synonymous_variant	6830	exon31			TGTTGCTCGCTAT	U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"SH2 domain containing"	11470	protein-coding gene	gene with protein product		601333	"suppressor of Ty (S.cerevisiae) 6 homolog"			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85		ENST00000314616.6:c.4239T>G	chr17.hg19:g.27024667T>G		115.0	0.0		77.0	23.0	NM_003170	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Silent	SNP	ENST00000314616.6	hg19	CCDS32596.1																																																																																			.	.		0.512	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170		G	27024667	T	G	27024667	2	3	328	1	0	0	0	0	0	0	0	1	15415	1538	54	5		5	SUPT6H	17	27024667	Silent	SNP	T	TCGA-NI-A8LF-01A-11D-A35Z-10	19447555	27024667	54170543	85	46015										
ACACA	31	hgsc.bcm.edu	37	chr17	35615246	35615246	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	caccccagggagataccccaTacatcatacggatatccttg	7	14	1	1			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr17:35615246T>A	ENST00000394406.2	-	13	1629	c.1439A>T	c.(1438-1440)tAt>tTt	p.Y480F	ACACA_ENST00000360679.3_Missense_Mutation_p.Y422F|ACACA_ENST00000353139.5_Missense_Mutation_p.Y517F|ACACA_ENST00000335166.5_Missense_Mutation_p.Y402F	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	480	Biotin carboxylation.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	AGATACCCCATACATCATACG	0.408																																					p.Y517F	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)	Atlas-SNP	.											.	ACACA	395	.	0			c.A1550T						.						87	84	85					17																	35615246		2203	4300	6503	SO:0001583	missense	31	exon13			ACCCCATACATCA	U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 1"	200350	"acetyl-Coenzyme A carboxylase alpha"	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.1439A>T	chr17.hg19:g.35615246T>A	ENSP00000377928:p.Tyr480Phe	232.0	0.0		216.0	38.0	NM_198834	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Missense_Mutation	SNP	ENST00000394406.2	hg19	CCDS11317.1	.	.	.	.	.	.	.	.	.	.	T	28.6	4.937431	0.92458	.	.	ENSG00000132142	ENST00000353139;ENST00000360679;ENST00000394406;ENST00000452074;ENST00000335166	D;D;D;D	0.97811	-4.55;-4.55;-4.55;-4.55	5.93	5.93	0.95920	ATP-grasp fold, subdomain 2 (1);Biotin carboxylation domain (1);	0.000000	0.85682	D	0.000000	D	0.98093	0.9371	M	0.83692	2.655	0.80722	D	1	B;P;P	0.49447	0.174;0.587;0.924	B;B;P	0.51866	0.159;0.354;0.682	D	0.98336	1.0536	10	0.52906	T	0.07	-12.7689	15.5755	0.76380	0.0:0.0:0.0:1.0	.	517;480;422	Q13085-4;Q13085;Q13085-2	.;ACACA_HUMAN;.	F	517;422;480;504;402	ENSP00000344789:Y517F;ENSP00000353898:Y422F;ENSP00000377928:Y480F;ENSP00000335323:Y402F	ENSP00000335323:Y402F	Y	-	2	0	ACACA	32689359	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	8.040000	0.89188	2.281000	0.76405	0.533000	0.62120	TAT	.	.		0.408	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836		A	35615246	T	A	35615246	3	1	328	1	0	0	0	0	1	0	0	0	106	1406	49	4	5777	4	ACACA	17	35615246	Missense_Mutation	SNP	T	TCGA-NI-A8LF-01A-11D-A35Z-10	8590579	35615246	45579964	86	46016										
MPP2	4355	hgsc.bcm.edu	37	chr17	41975687	41975687	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	cctcgaaggaagatcaggtcCagctctgcagcccccgtggc	12	15	2	1			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr17:41975687C>A	ENST00000461854.1	-	3	178	c.93G>T	c.(91-93)ctG>ctT	p.L31L	MPP2_ENST00000520305.1_Intron|MPP2_ENST00000377184.3_Silent_p.L48L|MPP2_ENST00000536246.1_Silent_p.L20L|MPP2_ENST00000523501.1_Silent_p.L20L|MPP2_ENST00000473246.1_5'UTR|MPP2_ENST00000518766.1_Silent_p.L76L|MPP2_ENST00000269095.4_Silent_p.L31L			Q14168	MPP2_HUMAN	membrane protein, palmitoylated 2 (MAGUK p55 subfamily member 2)	31	L27 1. {ECO:0000255|PROSITE- ProRule:PRU00365}.				nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|liver(1)|lung(4)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)	29		Breast(137;0.00314)		BRCA - Breast invasive adenocarcinoma(366;0.12)		AGATCAGGTCCAGCTCTGCAG	0.587																																					p.L31L		Atlas-SNP	.											.	MPP2	67	.	0			c.G93T						.						123	106	112					17																	41975687		2203	4300	6503	SO:0001819	synonymous_variant	4355	exon3			CAGGTCCAGCTCT		CCDS11471.1, CCDS62206.1, CCDS62207.1, CCDS62208.1, CCDS62209.1, CCDS62210.1	17q12-q21	2008-07-18			ENSG00000108852	ENSG00000108852			7220	protein-coding gene	gene with protein product	"MAGUK p55 subfamily member 2", "discs large, homolog 2"	600723		DLG2		7590743	Standard	NM_001278370		Approved	DKFZp761D0712	uc002ieo.1	Q14168	OTTHUMG00000133840	ENST00000461854.1:c.93G>T	chr17.hg19:g.41975687C>A		130.0	0.0		97.0	16.0	NM_005374	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Silent	SNP	ENST00000461854.1	hg19																																																																																				.	.		0.587	MPP2-003	KNOWN	non_canonical_polymorphism|basic	protein_coding	protein_coding	OTTHUMT00000258388.2	NM_005374		A	41975687	C	A	41975687	2	1	328	1	0	0	0	0	0	0	0	1	9743	581	21	3		3	MPP2	17	41975687	Silent	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10	6360441	41975687	39219523	87	46017										
AXIN2	8313	hgsc.bcm.edu	37	chr17	63545701	63545701	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	cactggatatctcactgtcgTtggcgctggtggctggtgca	14	10	1	0	rs139274803		TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr17:63545701T>C	ENST00000375702.5	-	2	1001	c.893A>G	c.(892-894)aAc>aGc	p.N298S	AXIN2_ENST00000307078.5_Missense_Mutation_p.N298S|CTD-2535L24.2_ENST00000577662.1_3'UTR			Q9Y2T1	AXIN2_HUMAN	axin 2	298					bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to organic cyclic compound (GO:0071407)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|dorsal/ventral axis specification (GO:0009950)|intramembranous ossification (GO:0001957)|maintenance of DNA repeat elements (GO:0043570)|mRNA stabilization (GO:0048255)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell proliferation (GO:0008285)|negative regulation of osteoblast differentiation (GO:0045668)|odontogenesis (GO:0042476)|positive regulation of cell death (GO:0010942)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein phosphorylation (GO:0001934)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of chondrocyte development (GO:0061181)|regulation of mismatch repair (GO:0032423)|secondary heart field specification (GO:0003139)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)			NS(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	34						CTCACTGTCGTTGGCGCTGGT	0.522									Oligodontia, Ectodermal Dysplasia and Colorectal Polyp syndrome																												p.N298S		Atlas-SNP	.											.	AXIN2	92	.	0			c.A893G						.	T	SER/ASN	1,4405	2.1+/-5.4	0,1,2202	180	118	139		893	5.9	1	17	dbSNP_134	139	0,8600		0,0,4300	no	missense	AXIN2	NM_004655.3	46	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	probably-damaging	298/844	63545701	1,13005	2203	4300	6503	SO:0001583	missense	8313	exon3	Familial Cancer Database	Oligodontia-Colorectal Cancer syndrome, Tooth Agenesis-Colorectal Cancer Syndrome	CTGTCGTTGGCGC	AF078165	CCDS11662.1	17q24.1	2014-09-17	2008-08-01		ENSG00000168646				904	protein-coding gene	gene with protein product	"conductin", "axil"	604025				10049590	Standard	NM_004655		Approved	MGC126582, DKFZp781B0869	uc002jfi.3	Q9Y2T1	OTTHUMG00000179353	ENST00000375702.5:c.893A>G	chr17.hg19:g.63545701T>C	ENSP00000364854:p.Asn298Ser	128.0	0.0		100.0	30.0	NM_004655	Q3MJ88|Q9H3M6|Q9UH84	Missense_Mutation	SNP	ENST00000375702.5	hg19		.	.	.	.	.	.	.	.	.	.	T	27.1	4.797842	0.90538	2.27E-4	0.0	ENSG00000168646	ENST00000307078;ENST00000375702	D;D	0.81908	-1.55;-1.55	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	D	0.91734	0.7386	M	0.82323	2.585	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.83275	0.996;0.992;0.996	D	0.92799	0.6255	10	0.87932	D	0	-36.2622	16.3483	0.83171	0.0:0.0:0.0:1.0	.	298;298;298	B7ZKL5;Q9Y2T1;E7ES00	.;AXIN2_HUMAN;.	S	298	ENSP00000302625:N298S;ENSP00000364854:N298S	ENSP00000302625:N298S	N	-	2	0	AXIN2	60976163	1.000000	0.71417	0.993000	0.49108	0.865000	0.49528	7.990000	0.88215	2.254000	0.74563	0.533000	0.62120	AAC	.	T|1.000;C|0.000		0.522	AXIN2-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000445901.1	NM_004655		C	63545701	T	C	63545701	3	2	328	1	0	0	0	0	1	0	0	0	1237	1725	60	2	1674	2	AXIN2	17	63545701	Missense_Mutation	SNP	T	TCGA-NI-A8LF-01A-11D-A35Z-10	21570014	63545701	17649509	88	46018										
H3F3B	3021	hgsc.bcm.edu	37	chr17	73775166	73775166	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	ttcaccccgccggtagagggAgcgcttttcctggcggcttt	13	13	1	1			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr17:73775166A>C	ENST00000254810.4	-	2	222	c.90T>G	c.(88-90)gcT>gcG	p.A30A	H3F3B_ENST00000593254.1_Intron|H3F3B_ENST00000592643.1_Silent_p.A30A|H3F3B_ENST00000587560.1_Silent_p.A30A|H3F3B_ENST00000591890.1_Silent_p.A30A|H3F3B_ENST00000589599.1_Silent_p.A30A|H3F3B_ENST00000586607.1_Silent_p.A30A	NM_005324.3	NP_005315.1	P84243	H33_HUMAN	H3 histone, family 3B (H3.3B)	30					blood coagulation (GO:0007596)|brain development (GO:0007420)|DNA replication-independent nucleosome assembly (GO:0006336)|positive regulation of cell growth (GO:0030307)|response to hormone (GO:0009725)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nuclear nucleosome (GO:0000788)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	nucleosomal DNA binding (GO:0031492)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)			large_intestine(1)|lung(4)|ovary(2)|skin(1)	8	all_cancers(13;1.5e-07)		all cancers(21;2.61e-06)|Epithelial(20;7.39e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|LUSC - Lung squamous cell carcinoma(166;0.154)			CGGTAGAGGGAGCGCTTTTCC	0.642											OREG0024740	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A30A		Atlas-SNP	.											.	H3F3B	12	.	0			c.T90G						.						26	28	28					17																	73775166		2202	4300	6502	SO:0001819	synonymous_variant	3021	exon2			AGAGGGAGCGCTT	Z48950	CCDS11729.1	17q25.1	2011-06-01			ENSG00000132475	ENSG00000132475		"Histones / Replication-independent"	4765	protein-coding gene	gene with protein product		601058				8586426	Standard	NM_005324		Approved	H3.3B	uc002jpl.3	P84243		ENST00000254810.4:c.90T>G	chr17.hg19:g.73775166A>C		143.0	0.0	1147	112.0	37.0	NM_005324	P06351|P33155|Q5VV55|Q5VV56|Q66I33|Q9V3W4	Silent	SNP	ENST00000254810.4	hg19	CCDS11729.1																																																																																			.	.		0.642	H3F3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448499.1	NM_005324		C	73775166	A	C	73775166	2	2	328	1	0	0	0	0	0	0	0	1	6943	291	11	5		5	H3F3B	17	73775166	Silent	SNP	A	TCGA-NI-A8LF-01A-11D-A35Z-10	10229465	73775166	7420044	89	46019										
CEP192	55125	hgsc.bcm.edu	37	chr18	13100343	13100343	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	ttcgagaagatttaactcaaGtggaacttttaactcgtttg	8	6	1	2			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr18:13100343G>T	ENST00000325971.8	+	36	6508	c.4915G>T	c.(4915-4917)Gtg>Ttg	p.V1639L	CEP192_ENST00000430049.2_Missense_Mutation_p.V1760L|CEP192_ENST00000506447.1_Missense_Mutation_p.V2235L|CEP192_ENST00000540847.2_3'UTR			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	1639					centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						TTTAACTCAAGTGGAACTTTT	0.363																																					p.V2235L		Atlas-SNP	.											.	CEP192	340	.	0			c.G6703T						.						66	64	65					18																	13100343		2203	4300	6503	SO:0001583	missense	55125	exon38			ACTCAAGTGGAAC	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	25515	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 62"					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.4915G>T	chr18.hg19:g.13100343G>T	ENSP00000317156:p.Val1639Leu	189.0	0.0		161.0	47.0	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	hg19		.	.	.	.	.	.	.	.	.	.	G	5.392	0.257472	0.10239	.	.	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049;ENST00000540847	T;T;T	0.05513	3.43;3.43;3.43	5.15	0.0428	0.14219	.	0.817735	0.11458	N	0.562074	T	0.02571	0.0078	N	0.08118	0	0.09310	N	1	B;B;B;B	0.25667	0.131;0.003;0.001;0.008	B;B;B;B	0.21151	0.033;0.009;0.0;0.006	T	0.44742	-0.9308	10	0.30854	T	0.27	-2.4109	1.6192	0.02710	0.3154:0.1289:0.4234:0.1323	.	1760;2235;239;837	C9JT09;E9PF99;F5GZ47;Q9HCK3	.;.;.;.	L	2235;1639;1639;1760;239	ENSP00000427550:V2235L;ENSP00000317156:V1639L;ENSP00000389190:V1760L	ENSP00000317156:V1639L	V	+	1	0	CEP192	13090343	0.011000	0.17503	0.001000	0.08648	0.123000	0.20343	0.136000	0.15974	-0.225000	0.09913	0.655000	0.94253	GTG	.	.		0.363	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142		T	13100343	G	T	13100343	3	4	328	1	0	0	0	0	1	0	0	0	3253	1029	36	3	6849	3	CEP192	18	13100343	Missense_Mutation	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10		13100343	64976905	90	46020										
FAM59A	64762	hgsc.bcm.edu	37	chr18	29890207	29890207	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	tacacgcgttcaggaaatgcCttagccacctcctccacact	6	16	1	0			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr18:29890207C>G	ENST00000269209.6	-	3	345	c.342G>C	c.(340-342)aaG>aaC	p.K114N	GAREM_ENST00000399218.4_Missense_Mutation_p.K114N|GAREM_ENST00000578619.1_5'UTR			Q9H706	GAREM_HUMAN	GRB2 associated, regulator of MAPK1	114	CABIT.				cellular response to epidermal growth factor stimulus (GO:0071364)|epidermal growth factor receptor signaling pathway (GO:0007173)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)										CAGGAAATGCCTTAGCCACCT	0.413																																					p.K114N		Atlas-SNP	.											.	.	.	.	0			c.G342C						.						256	218	231					18																	29890207		2203	4300	6503	SO:0001583	missense	64762	exon3			AAATGCCTTAGCC	AK025263	CCDS11905.1, CCDS56057.1	18q12.1	2012-11-30	2012-11-30	2012-11-30	ENSG00000141441	ENSG00000141441			26136	protein-coding gene	gene with protein product	"Grb2-associated and regulator of Erk/MAPK"		"chromosome 18 open reading frame 11", "family with sequence similarity 59, member A"	C18orf11, FAM59A		19509291	Standard	NM_001242409		Approved	FLJ21610	uc002kxl.3	Q9H706	OTTHUMG00000132273	ENST00000269209.6:c.342G>C	chr18.hg19:g.29890207C>G	ENSP00000269209:p.Lys114Asn	201.0	0.0		109.0	20.0	NM_022751	Q0VAG3|Q0VAG4|Q8ND03|Q9BSF5	Missense_Mutation	SNP	ENST00000269209.6	hg19	CCDS56057.1	.	.	.	.	.	.	.	.	.	.	C	16.03	3.006715	0.54361	.	.	ENSG00000141441	ENST00000399218;ENST00000269209	T;T	0.14516	2.5;2.5	5.76	2.12	0.27331	.	0.000000	0.85682	D	0.000000	T	0.25717	0.0626	L	0.47716	1.5	0.58432	D	0.999996	D;P	0.89917	1.0;0.741	D;P	0.87578	0.998;0.636	T	0.00295	-1.1839	10	0.33940	T	0.23	-23.8486	10.1079	0.42544	0.0:0.1584:0.0:0.8416	.	114;114	Q9H706;Q9H706-3	FA59A_HUMAN;.	N	114	ENSP00000382165:K114N;ENSP00000269209:K114N	ENSP00000269209:K114N	K	-	3	2	FAM59A	28144205	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.598000	0.36740	0.125000	0.18397	-0.140000	0.14226	AAG	.	.		0.413	GAREM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255365.1	NM_022751		G	29890207	C	G	29890207	3	3	328	1	0	0	0	0	1	0	0	0	5600	680	24	4	2301	4	FAM59A	18	29890207	Missense_Mutation	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10	16789864	29890207	48187041	91	46021										
MYO5B	4645	hgsc.bcm.edu	37	chr18	47364067	47364067	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	ggcggatgatagcttccaggCagtatgagttatccccatct	11	10	1	2			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr18:47364067C>T	ENST00000285039.7	-	37	5257	c.4958G>A	c.(4957-4959)tGc>tAc	p.C1653Y	SCARNA17_ENST00000589499.1_RNA|RP11-886H22.1_ENST00000590532.2_5'Flank|MYO5B_ENST00000324581.6_Missense_Mutation_p.C768Y|MYO5B_ENST00000592688.1_Missense_Mutation_p.C223Y	NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	1653	Dilute. {ECO:0000255|PROSITE- ProRule:PRU00503}.				endosome localization (GO:0032439)|metabolic process (GO:0008152)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)|vesicle-mediated transport (GO:0016192)|water transport (GO:0006833)	apical cortex (GO:0045179)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|protein complex (GO:0043234)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|Rab GTPase binding (GO:0017137)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(4)	87				READ - Rectum adenocarcinoma(32;0.103)		AGCTTCCAGGCAGTATGAGTT	0.522																																					p.C1653Y		Atlas-SNP	.											.	MYO5B	178	.	0			c.G4958A						.						75	70	72					18																	47364067		1950	4153	6103	SO:0001583	missense	4645	exon37			TCCAGGCAGTATG	AB032945	CCDS42436.1	18q	2011-09-27			ENSG00000167306	ENSG00000167306		"Myosins / Myosin superfamily : Class V"	7603	protein-coding gene	gene with protein product		606540				8884266, 17462998	Standard	NM_001080467		Approved	KIAA1119	uc002leb.2	Q9ULV0		ENST00000285039.7:c.4958G>A	chr18.hg19:g.47364067C>T	ENSP00000285039:p.Cys1653Tyr	159.0	0.0		94.0	8.0	NM_001080467	B0I1R3|Q0P656|Q9H6Y6	Missense_Mutation	SNP	ENST00000285039.7	hg19	CCDS42436.1	.	.	.	.	.	.	.	.	.	.	C	11.38	1.622644	0.28889	.	.	ENSG00000167306	ENST00000285039;ENST00000324581	D;T	0.85861	-2.04;2.59	4.87	3.99	0.46301	Dilute (1);	0.125660	0.52532	D	0.000064	T	0.72087	0.3417	N	0.08118	0	0.38104	D	0.937366	B;P	0.39131	0.08;0.661	B;B	0.37387	0.105;0.248	T	0.77536	-0.2551	10	0.49607	T	0.09	.	14.543	0.68008	0.0:0.7219:0.2781:0.0	.	1653;768	Q9ULV0;Q9H6Y6	MYO5B_HUMAN;.	Y	1653;768	ENSP00000285039:C1653Y;ENSP00000315531:C768Y	ENSP00000285039:C1653Y	C	-	2	0	MYO5B	45618065	1.000000	0.71417	1.000000	0.80357	0.483000	0.33249	2.257000	0.43240	1.389000	0.46526	0.655000	0.94253	TGC	.	.		0.522	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2			T	47364067	C	T	47364067	3	4	328	1	0	0	0	0	1	0	0	0	10088	710	25	3	604	3	MYO5B	18	47364067	Missense_Mutation	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10	17473860	47364067	30713181	92	46022										
ZNF443	10224	hgsc.bcm.edu	37	chr19	12542634	12542634	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	aactctgatgtaacaattaaGggatgaatgacccatgactt	8	7	1	4			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr19:12542634G>C	ENST00000301547.5	-	4	549	c.352C>G	c.(352-354)Ctt>Gtt	p.L118V	CTD-3105H18.16_ENST00000595562.1_Intron	NM_005815.4	NP_005806	Q9Y2A4	ZN443_HUMAN	zinc finger protein 443	118					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|pancreas(1)|prostate(1)	28						TAACAATTAAGGGATGAATGA	0.438																																					p.L118V		Atlas-SNP	.											.	ZNF443	63	.	0			c.C352G						.						137	118	125					19																	12542634		2203	4300	6503	SO:0001583	missense	10224	exon4			AATTAAGGGATGA	AB011414	CCDS32918.1	19p13.13	2013-01-08			ENSG00000180855	ENSG00000180855		"Zinc fingers, C2H2-type", "-"	20878	protein-coding gene	gene with protein product		606697				9731181	Standard	NM_005815		Approved	ZK1	uc002mtu.3	Q9Y2A4	OTTHUMG00000156404	ENST00000301547.5:c.352C>G	chr19.hg19:g.12542634G>C	ENSP00000301547:p.Leu118Val	207.0	0.0		133.0	56.0	NM_005815		Missense_Mutation	SNP	ENST00000301547.5	hg19	CCDS32918.1	.	.	.	.	.	.	.	.	.	.	G	10.39	1.336580	0.24253	.	.	ENSG00000180855	ENST00000301547;ENST00000411622	T	0.08370	3.1	1.37	-2.74	0.05932	.	.	.	.	.	T	0.22551	0.0544	M	0.84846	2.72	0.09310	N	1	D	0.65815	0.995	D	0.65443	0.935	T	0.06935	-1.0799	9	0.66056	D	0.02	.	3.5813	0.07954	0.3219:0.2117:0.4664:0.0	.	118	Q9Y2A4	ZN443_HUMAN	V	118	ENSP00000301547:L118V	ENSP00000301547:L118V	L	-	1	0	ZNF443	12403634	0.001000	0.12720	0.000000	0.03702	0.073000	0.16967	0.351000	0.20096	-0.771000	0.04608	0.461000	0.40582	CTT	.	.		0.438	ZNF443-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344084.1	NM_005815		C	12542634	G	C	12542634	3	2	328	1	0	0	0	0	1	0	0	0	17931	1000	35	4	1667	4	ZNF443	19	12542634	Missense_Mutation	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10		12542634	46586349	93	46023										
CACNA1A	773	hgsc.bcm.edu	37	chr19	13387894	13387894	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	tgcactcaccttgatcaccaTctcaaaggtaaagacgcctg	7	13	3	2			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr19:13387894T>C	ENST00000360228.5	-	23	3870	c.3871A>G	c.(3871-3873)Atg>Gtg	p.M1291V	CACNA1A_ENST00000573710.2_Missense_Mutation_p.M1292V	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	1292					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	TTGATCACCATCTCAAAGGTA	0.453											OREG0025295	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.M1292V		Atlas-SNP	.											.	CACNA1A	715	.	0			c.A3874G						.						106	95	99					19																	13387894		1908	4123	6031	SO:0001583	missense	773	exon23			TCACCATCTCAAA	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.3871A>G	chr19.hg19:g.13387894T>C	ENSP00000353362:p.Met1291Val	135.0	0.0	687	108.0	20.0	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	hg19	CCDS45998.1	.	.	.	.	.	.	.	.	.	.	T	12.94	2.089448	0.36855	.	.	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084	D	0.97529	-4.42	4.54	4.54	0.55810	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.97876	0.9302	M	0.80332	2.49	0.54753	D	0.999987	P;D;B	0.53885	0.938;0.963;0.136	P;P;B	0.59825	0.864;0.729;0.177	D	0.98383	1.0559	10	0.72032	D	0.01	.	12.8714	0.57966	0.0:0.0:0.0:1.0	.	1292;1295;1291	O00555;E9PD31;Q9NS88	CAC1A_HUMAN;.;.	V	1291;1295;1292;1292	ENSP00000353362:M1291V	ENSP00000317661:M1292V	M	-	1	0	CACNA1A	13248894	1.000000	0.71417	1.000000	0.80357	0.818000	0.46254	5.693000	0.68264	1.690000	0.51089	0.482000	0.46254	ATG	.	.		0.453	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		C	13387894	T	C	13387894	3	2	328	1	0	0	0	0	1	0	0	0	2540	1435	50	2	3851	2	CACNA1A	19	13387894	Missense_Mutation	SNP	T	TCGA-NI-A8LF-01A-11D-A35Z-10	845260	13387894	45741089	94	46024										
COMP	1311	hgsc.bcm.edu	37	chr19	18895754	18895754	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	gcacggaaggggttcgcctgCcaatacgtttgctccatctg	12	12	1	0			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr19:18895754C>T	ENST00000222271.2	-	16	1910	c.1866G>A	c.(1864-1866)tgG>tgA	p.W622*	COMP_ENST00000425807.1_Nonsense_Mutation_p.W569*|COMP_ENST00000542601.2_Nonsense_Mutation_p.W589*	NM_000095.2	NP_000086.2	P49747	COMP_HUMAN	cartilage oligomeric matrix protein	622	Mediates cell survival and induction of the IAP family of survival proteins.|TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|limb development (GO:0060173)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|protease binding (GO:0002020)			breast(6)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						GGTTCGCCTGCCAATACGTTT	0.602																																					p.W622X		Atlas-SNP	.											.	COMP	62	.	0			c.G1866A						.						151	113	126					19																	18895754		2203	4300	6503	SO:0001587	stop_gained	1311	exon16			CGCCTGCCAATAC	L32137	CCDS12385.1	19p13.1	2008-02-05				ENSG00000105664			2227	protein-coding gene	gene with protein product	"thrombospondin-5"	600310	"cartilage oligomeric matrix protein (pseudoachondroplasia, epiphyseal dysplasia 1, multiple)"	PSACH, EDM1, EPD1		7713493, 8307576	Standard	NM_000095		Approved	MED, THBS5	uc002nke.3	P49747	OTTHUMG00000169318	ENST00000222271.2:c.1866G>A	chr19.hg19:g.18895754C>T	ENSP00000222271:p.Trp622*	110.0	0.0		97.0	20.0	NM_000095	B4DKJ3|O14592|Q16388|Q16389|Q2NL86|Q8N4T2	Nonsense_Mutation	SNP	ENST00000222271.2	hg19	CCDS12385.1	.	.	.	.	.	.	.	.	.	.	C	41	9.065774	0.99053	.	.	ENSG00000105664	ENST00000542601;ENST00000222271;ENST00000425807;ENST00000454701	.	.	.	3.99	3.99	0.46301	.	0.000000	0.64402	U	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-23.2722	14.7691	0.69662	0.0:1.0:0.0:0.0	.	.	.	.	X	589;622;569;609	.	ENSP00000222271:W622X	W	-	3	0	COMP	18756754	1.000000	0.71417	1.000000	0.80357	0.655000	0.38815	7.507000	0.81676	2.056000	0.61249	0.471000	0.43371	TGG	.	.		0.602	COMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403457.1	NM_000095		T	18895754	C	T	18895754	4	4	328	1	0	0	0	0	0	1	0	0	3726	740	26	3	423	3	COMP	19	18895754	Nonsense_Mutation	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10	5507860	18895754	40233229	95	46025										
LIPE	3991	hgsc.bcm.edu	37	chr19	42914801	42914801	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	gggtccaggtcaaagaggtgCgccacacccagcaggcggcc	15	14	1	1			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr19:42914801C>A	ENST00000244289.4	-	2	1353	c.1077G>T	c.(1075-1077)gcG>gcT	p.A359A	LIPE_ENST00000602000.1_Intron|LIPE-AS1_ENST00000597203.1_RNA|LIPE-AS1_ENST00000599276.1_RNA|LIPE-AS1_ENST00000594624.2_RNA|LIPE-AS1_ENST00000593491.2_RNA	NM_005357.2	NP_005348.2	Q05469	LIPS_HUMAN	lipase, hormone-sensitive	359					cholesterol metabolic process (GO:0008203)|diacylglycerol catabolic process (GO:0046340)|lipid catabolic process (GO:0016042)|long-chain fatty acid catabolic process (GO:0042758)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)	hormone-sensitive lipase activity (GO:0033878)|triglyceride lipase activity (GO:0004806)			breast(2)|endometrium(4)|kidney(7)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		Prostate(69;0.00682)				CAAAGAGGTGCGCCACACCCA	0.692																																					p.A359A		Atlas-SNP	.											.	LIPE	83	.	0			c.G1077T						.						24	24	24					19																	42914801		2202	4296	6498	SO:0001819	synonymous_variant	3991	exon2			GAGGTGCGCCACA	L11706	CCDS12607.1	19q13.1-q13.2	2014-03-14			ENSG00000079435	ENSG00000079435	3.1.1.3		6621	protein-coding gene	gene with protein product		151750				8506334	Standard	NM_005357		Approved	HSL	uc002otr.3	Q05469	OTTHUMG00000182814	ENST00000244289.4:c.1077G>T	chr19.hg19:g.42914801C>A		141.0	0.0		113.0	45.0	NM_005357	Q3LRT2|Q6NSL7	Silent	SNP	ENST00000244289.4	hg19	CCDS12607.1																																																																																			.	.		0.692	LIPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463861.1	NM_005357		A	42914801	C	A	42914801	2	1	328	1	0	0	0	0	0	0	0	1	8830	755	27	1		1	LIPE	19	42914801	Silent	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10	24019047	42914801	16214182	96	46026										
ARHGAP35	2909	hgsc.bcm.edu	37	chr19	47422764	47422764	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	ctacagcaaaagacaagtatGagtggctggtgagtcgcatt	12	7	0	3			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr19:47422764G>T	ENST00000404338.3	+	1	832	c.832G>T	c.(832-834)Gag>Tag	p.E278*		NM_004491.4	NP_004482.4	Q9NRY4	RHG35_HUMAN	Rho GTPase activating protein 35	278	FF 1.				axon guidance (GO:0007411)|camera-type eye development (GO:0043010)|forebrain development (GO:0030900)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular permeability (GO:0043116)|neural tube closure (GO:0001843)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|GTP binding (GO:0005525)|Rho GTPase activator activity (GO:0005100)|transcription corepressor activity (GO:0003714)										AGACAAGTATGAGTGGCTGGT	0.448																																					p.E278X		Atlas-SNP	.											.	.	.	.	0			c.G832T						.						54	55	55					19																	47422764		2019	4213	6232	SO:0001587	stop_gained	2909	exon1			AAGTATGAGTGGC	M73077	CCDS46127.1	19q13.32	2011-06-29	2011-06-07	2011-06-07	ENSG00000160007	ENSG00000160007		"Rho GTPase activating proteins"	4591	protein-coding gene	gene with protein product		605277	"glucocorticoid receptor DNA binding factor 1"	GRLF1		1894621, 20675588	Standard	NM_004491		Approved	GRF-1, p190ARhoGAP, P190A, KIAA1722, p190RhoGAP	uc010ekv.3	Q9NRY4		ENST00000404338.3:c.832G>T	chr19.hg19:g.47422764G>T	ENSP00000385720:p.Glu278*	124.0	0.0		83.0	4.0	NM_004491	A7E2A4|Q14452|Q9C0E1	Nonsense_Mutation	SNP	ENST00000404338.3	hg19	CCDS46127.1	.	.	.	.	.	.	.	.	.	.	G	36	5.791456	0.96945	.	.	ENSG00000160007	ENST00000317082;ENST00000501576;ENST00000404338	.	.	.	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	-39.3794	19.2296	0.93833	0.0:0.0:1.0:0.0	.	.	.	.	X	278	.	ENSP00000324820:E278X	E	+	1	0	ARHGAP35	52114604	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.062000	0.89475	2.835000	0.97688	0.650000	0.86243	GAG	.	.		0.448	ARHGAP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466652.1	NM_004491		T	47422764	G	T	47422764	4	4	328	1	0	0	0	0	0	1	0	0	6804	1291	45	3	834	3	ARHGAP35	19	47422764	Nonsense_Mutation	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10	4507963	47422764	11706219	97	46027										
CACNG6	59285	hgsc.bcm.edu	37	chr19	54515342	54515342	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	tgggctgcggcgtgggggccGgcctgatcctgctgttgggg	21	10	0	1			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr19:54515342G>A	ENST00000252729.2	+	4	1272	c.682G>A	c.(682-684)Ggc>Agc	p.G228S	CACNG6_ENST00000352529.1_Missense_Mutation_p.G157S|CACNG6_ENST00000346968.2_Missense_Mutation_p.G182S	NM_145814.1	NP_665813.1	Q9BXT2	CCG6_HUMAN	calcium channel, voltage-dependent, gamma subunit 6	228					calcium ion transport (GO:0006816)	voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	15	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.168)		CGTGGGGGCCGGCCTGATCCT	0.711																																					p.G228S		Atlas-SNP	.											.	CACNG6	42	.	0			c.G682A						.						23	28	26					19																	54515342		2183	4263	6446	SO:0001583	missense	59285	exon4			GGGGCCGGCCTGA	AF288386	CCDS12870.1, CCDS12871.1	19q13.4	2008-05-02			ENSG00000130433	ENSG00000130433		"Calcium channel subunits"	13625	protein-coding gene	gene with protein product		606898				11170751	Standard	NM_145814		Approved		uc002qct.3	Q9BXT2	OTTHUMG00000064907	ENST00000252729.2:c.682G>A	chr19.hg19:g.54515342G>A	ENSP00000252729:p.Gly228Ser	46.0	0.0		57.0	11.0	NM_145814		Missense_Mutation	SNP	ENST00000252729.2	hg19	CCDS12870.1	.	.	.	.	.	.	.	.	.	.	G	9.064	0.995102	0.19043	.	.	ENSG00000130433	ENST00000252729;ENST00000352529;ENST00000346968	T;T;T	0.67865	-0.29;1.44;1.43	3.76	-0.149	0.13420	.	0.302241	0.29508	N	0.011955	T	0.52677	0.1749	L	0.57536	1.79	0.09310	N	1	P;B;B	0.45428	0.858;0.131;0.028	B;B;B	0.40009	0.316;0.03;0.035	T	0.48625	-0.9019	10	0.17832	T	0.49	-3.3502	6.2253	0.20703	0.3787:0.0:0.6213:0.0	.	157;182;228	A6NP74;A6NFR2;Q9BXT2	.;.;CCG6_HUMAN	S	228;157;182	ENSP00000252729:G228S;ENSP00000319135:G157S;ENSP00000319097:G182S	ENSP00000252729:G228S	G	+	1	0	CACNG6	59207154	0.183000	0.23186	0.168000	0.22838	0.945000	0.59286	0.438000	0.21559	0.064000	0.16427	-0.261000	0.10672	GGC	.	.		0.711	CACNG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139359.1			A	54515342	G	A	54515342	3	1	328	1	0	0	0	0	1	0	0	0	2563	1116	39	1	696	1	CACNG6	19	54515342	Missense_Mutation	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10	7092578	54515342	4613641	98	46028										
ZNF135	7694	hgsc.bcm.edu	37	chr19	58579098	58579098	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	cctatgagtgtggtgagtgtGggaaagccttcagtcagagc	15	7	2	3			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr19:58579098G>A	ENST00000313434.5	+	5	1347	c.1246G>A	c.(1246-1248)Ggg>Agg	p.G416R	ZNF135_ENST00000401053.4_Missense_Mutation_p.G440R|ZNF135_ENST00000511556.1_Missense_Mutation_p.G428R|ZNF135_ENST00000506786.1_Missense_Mutation_p.G374R|ZNF135_ENST00000439855.2_Missense_Mutation_p.G416R|ZNF135_ENST00000359978.6_Intron|RN7SL526P_ENST00000469492.2_RNA	NM_003436.3	NP_003427.3	P52742	ZN135_HUMAN	zinc finger protein 135	416					cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(26)|ovary(1)|skin(1)|urinary_tract(1)	41		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0161)		TGGTGAGTGTGGGAAAGCCTT	0.537																																					p.G440R		Atlas-SNP	.											.	ZNF135	159	.	0			c.G1318A						.						72	75	74					19																	58579098		2203	4300	6503	SO:0001583	missense	7694	exon4			GAGTGTGGGAAAG	U09413	CCDS12970.1, CCDS12970.2, CCDS54329.1, CCDS54330.1, CCDS74471.1, CCDS74472.1	19q13.4	2013-01-08	2006-05-12			ENSG00000176293		"Zinc fingers, C2H2-type", "-"	12919	protein-coding gene	gene with protein product		604077	"zinc finger protein 61", "zinc finger protein 135 (clone pHZ-17)"	ZNF61, ZNF78L1		7557990, 1505991	Standard	NM_003436		Approved	pHZ-17	uc002qrg.3	P52742		ENST00000313434.5:c.1246G>A	chr19.hg19:g.58579098G>A	ENSP00000321406:p.Gly416Arg	135.0	0.0		133.0	67.0	NM_007134	B4DHH9|E9PEV2|F5GYY9|I3L0B3|Q5U5L3|Q8N1I7	Missense_Mutation	SNP	ENST00000313434.5	hg19		.	.	.	.	.	.	.	.	.	.	G	12.17	1.858541	0.32791	.	.	ENSG00000176293	ENST00000401053;ENST00000439855;ENST00000313434;ENST00000511556;ENST00000506786	T;T;T;T;T	0.01484	4.84;4.84;4.84;4.84;4.84	3.1	3.1	0.35709	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09069	0.0224	M	0.71920	2.185	0.32425	N	0.548872	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.963	T	0.02588	-1.1137	9	0.87932	D	0	.	13.4044	0.60903	0.0:0.0:1.0:0.0	.	428;416	E9PEV2;P52742	.;ZN135_HUMAN	R	440;416;416;428;374	ENSP00000441410:G440R;ENSP00000444828:G416R;ENSP00000321406:G416R;ENSP00000422074:G428R;ENSP00000427691:G374R	ENSP00000321406:G416R	G	+	1	0	ZNF135	63270910	1.000000	0.71417	0.530000	0.27963	0.010000	0.07245	6.676000	0.74498	1.736000	0.51660	0.557000	0.71058	GGG	.	.		0.537	ZNF135-003	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000361899.2	NM_003436		A	58579098	G	A	58579098	3	1	328	1	0	0	0	0	1	0	0	0	17740	1348	47	3	1449	3	ZNF135	19	58579098	Missense_Mutation	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10	4063756	58579098	549885	99	46029										
POFUT1	23509	hgsc.bcm.edu	37	chr20	30803178	30803178	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	gctggcacccacccactggcCccctgagaagcgggtggcat	13	16	0	1			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr20:30803178C>A	ENST00000375749.3	+	3	415	c.353C>A	c.(352-354)cCc>cAc	p.P118H	POFUT1_ENST00000539210.1_Intron|POFUT1_ENST00000486717.1_3'UTR|POFUT1_ENST00000375730.3_Missense_Mutation_p.P118H	NM_015352.1	NP_056167.1	Q9H488	OFUT1_HUMAN	protein O-fucosyltransferase 1	118					angiogenesis (GO:0001525)|embryo development (GO:0009790)|fucose metabolic process (GO:0006004)|heart development (GO:0007507)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|O-glycan processing (GO:0016266)|protein O-linked fucosylation (GO:0036066)|protein O-linked glycosylation (GO:0006493)|regulation of transcription, DNA-templated (GO:0006355)|somitogenesis (GO:0001756)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	fucosyltransferase activity (GO:0008417)|peptide-O-fucosyltransferase activity (GO:0046922)			breast(1)|endometrium(1)|large_intestine(1)|lung(2)|urinary_tract(1)	6			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			ACCCACTGGCCCCCTGAGAAG	0.602																																					p.P118H		Atlas-SNP	.											.	POFUT1	52	.	0			c.C353A						.						79	84	82					20																	30803178		2203	4300	6503	SO:0001583	missense	23509	exon3			ACTGGCCCCCTGA	AF375884	CCDS13198.1, CCDS13199.1	20q11	2013-03-06			ENSG00000101346	ENSG00000101346	2.4.1.221	"Fucosyltransferases"	14988	protein-coding gene	gene with protein product	"peptide-O-fucosyltransferase", "GDP-fucose protein O-fucosyltransferase 1"	607491				9023546, 9525914	Standard	NM_015352		Approved	O-FUT, O-Fuc-T, KIAA0180, FUT12	uc002wxp.3	Q9H488	OTTHUMG00000133268	ENST00000375749.3:c.353C>A	chr20.hg19:g.30803178C>A	ENSP00000364902:p.Pro118His	143.0	0.0		174.0	22.0	NM_172236	A8K4R8|E1P5M4|Q14685|Q5W185|Q9BW76	Missense_Mutation	SNP	ENST00000375749.3	hg19	CCDS13198.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.036603	0.93630	.	.	ENSG00000101346	ENST00000375749;ENST00000375730	T;T	0.32023	1.47;1.47	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.66703	0.2816	M	0.90977	3.165	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.987	T	0.74182	-0.3748	10	0.87932	D	0	-13.4122	19.7154	0.96115	0.0:1.0:0.0:0.0	.	118;118	Q9H488;Q9H488-2	OFUT1_HUMAN;.	H	118	ENSP00000364902:P118H;ENSP00000364882:P118H	ENSP00000364882:P118H	P	+	2	0	POFUT1	30266839	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.539000	0.67199	2.664000	0.90586	0.655000	0.94253	CCC	.	.		0.602	POFUT1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078613.1	NM_015352		A	30803178	C	A	30803178	3	1	328	1	0	0	0	0	1	0	0	0	12192	623	22	3	363	3	POFUT1	20	30803178	Missense_Mutation	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10		30803178	32222342	100	46030										
MTP18	51537	hgsc.bcm.edu	37	chr22	30823227	30823227	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	tggacacctttgtatggcagGctctagcctctgtggccatt	11	11	2	0			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr22:30823227G>T	ENST00000266263.5	+	3	615	c.265G>T	c.(265-267)Gct>Tct	p.A89S	RP4-539M6.19_ENST00000439838.1_Missense_Mutation_p.A261S|MTFP1_ENST00000355143.4_Intron|MTFP1_ENST00000407550.3_Splice_Site_p.A66S	NM_016498.4	NP_057582.2	Q9UDX5	MTFP1_HUMAN	mitochondrial fission process 1	89					apoptotic process (GO:0006915)|mitochondrial fission (GO:0000266)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				endometrium(1)|large_intestine(1)|lung(2)	4						TGTATGGCAGGCTCTAGCCTC	0.642																																					p.A89S		Atlas-SNP	.											.	MTFP1	7	.	0			c.G265T						.						124	110	115					22																	30823227		2203	4300	6503	SO:0001583	missense	51537	exon3			TGGCAGGCTCTAG	AF151076	CCDS33634.1, CCDS33635.1	22q	2010-09-02			ENSG00000242114	ENSG00000242114			26945	protein-coding gene	gene with protein product		610235				15155745, 15985469	Standard	NM_016498		Approved	MTP18, HSPC242		Q9UDX5	OTTHUMG00000151057	ENST00000266263.5:c.265G>T	chr22.hg19:g.30823227G>T	ENSP00000266263:p.Ala89Ser	72.0	0.0		41.0	6.0	NM_016498	A6NFQ5|Q9H3K1|Q9P0N6	Missense_Mutation	SNP	ENST00000266263.5	hg19	CCDS33635.1	.	.	.	.	.	.	.	.	.	.	G	13.56	2.274720	0.40194	.	.	ENSG00000249590;ENSG00000242114;ENSG00000242114	ENST00000439838;ENST00000266263;ENST00000407550	T	0.65549	-0.16	4.87	3.83	0.44106	.	0.164767	0.52532	N	0.000066	T	0.34395	0.0896	N	0.05330	-0.07	0.80722	D	1	B	0.06786	0.001	B	0.11329	0.006	T	0.16158	-1.0412	10	0.06365	T	0.9	-20.1429	8.7535	0.34633	0.0815:0.0:0.7609:0.1576	.	89	Q9UDX5	MTFP1_HUMAN	S	261;89;66	ENSP00000415178:A261S	ENSP00000266263:A89S	A	+	1	0	MTFP1;RP4-539M6.19	29153227	1.000000	0.71417	1.000000	0.80357	0.623000	0.37688	5.245000	0.65405	1.211000	0.43351	0.655000	0.94253	GCT	.	.		0.642	MTFP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321126.3	NM_016498		T	30823227	G	T	30823227	3	4	328	1	0	0	0	0	1	0	0	0	9964	1203	42	3	275	3	MTP18	22	30823227	Missense_Mutation	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10		30823227	20481339	101	46031										
TCF20	6942	hgsc.bcm.edu	37	chr22	42607116	42607116	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	ctatgtcagcatcctgaacaGcaacactcccaccttcagga	6	15	2	1			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chr22:42607116G>T	ENST00000359486.3	-	1	4332	c.4196C>A	c.(4195-4197)gCt>gAt	p.A1399D	TCF20_ENST00000335626.4_Missense_Mutation_p.A1399D|TCF20_ENST00000404876.1_5'Flank	NM_005650.1	NP_005641.1	Q9UGU0	TCF20_HUMAN	transcription factor 20 (AR1)	1399					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(13)|lung(22)|ovary(5)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(5)	66						ATCCTGAACAGCAACACTCCC	0.522																																					p.A1399D		Atlas-SNP	.											.	TCF20	164	.	0			c.C4196A						.						120	116	117					22																	42607116		2203	4300	6503	SO:0001583	missense	6942	exon1			TGAACAGCAACAC	U19345	CCDS14032.1, CCDS14033.1	22q13.3	2011-02-08			ENSG00000100207	ENSG00000100207			11631	protein-coding gene	gene with protein product	"stromelysin-1 platelet-derived growth factor-responsive element binding protein"	603107				9730594, 10995766	Standard	NM_005650		Approved	AR1, SPBP	uc003bcj.1	Q9UGU0	OTTHUMG00000150920	ENST00000359486.3:c.4196C>A	chr22.hg19:g.42607116G>T	ENSP00000352463:p.Ala1399Asp	133.0	0.0		86.0	27.0	NM_181492	A9JX12|O14528|Q13078|Q4V353|Q9H4M0	Missense_Mutation	SNP	ENST00000359486.3	hg19	CCDS14033.1	.	.	.	.	.	.	.	.	.	.	G	14.52	2.560700	0.45590	.	.	ENSG00000100207	ENST00000359486;ENST00000335626	T;T	0.62941	-0.01;-0.01	5.8	5.8	0.92144	.	0.172580	0.39834	N	0.001251	T	0.56934	0.2019	N	0.24115	0.695	0.80722	D	1	P;P	0.46142	0.873;0.799	B;B	0.43916	0.436;0.252	T	0.62483	-0.6845	10	0.87932	D	0	-5.3152	20.0609	0.97674	0.0:0.0:1.0:0.0	.	1399;1399	Q9UGU0-2;Q9UGU0	.;TCF20_HUMAN	D	1399	ENSP00000352463:A1399D;ENSP00000335561:A1399D	ENSP00000335561:A1399D	A	-	2	0	TCF20	40937060	0.101000	0.21875	0.063000	0.19743	0.900000	0.52787	2.733000	0.47360	2.755000	0.94549	0.655000	0.94253	GCT	.	.		0.522	TCF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320531.1	NM_181492		T	42607116	G	T	42607116	3	4	328	1	0	0	0	0	1	0	0	0	15705	971	34	3	1724	3	TCF20	22	42607116	Missense_Mutation	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10	11783889	42607116	8697450	102	46032										
FAM120C	54954	hgsc.bcm.edu	37	chrX	54209040	54209040	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	cttgttgcccacgtgtcccaCgatcagttgcgctgtctgcc	10	15	2	0			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chrX:54209040C>T	ENST00000375180.2	-	1	648	c.592G>A	c.(592-594)Gtg>Atg	p.V198M	FAM120C_ENST00000328235.4_Missense_Mutation_p.V198M|FAM120C_ENST00000477084.1_Missense_Mutation_p.V198M|FAM120C_ENST00000497680.1_5'UTR	NM_017848.4	NP_060318.3	Q9NX05	F120C_HUMAN	family with sequence similarity 120C	198							poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28						ACGTGTCCCACGATCAGTTGC	0.706																																					p.V198M		Atlas-SNP	.											.	FAM120C	89	.	0			c.G592A						.						31	23	25					X																	54209040		2190	4290	6480	SO:0001583	missense	54954	exon1			GTCCCACGATCAG	AY150025	CCDS14356.1, CCDS55421.1, CCDS75987.1	Xp11.22	2011-04-13	2006-07-04	2006-07-04	ENSG00000184083	ENSG00000184083			16949	protein-coding gene	gene with protein product		300741	"chromosome X open reading frame 17"	CXorf17		14585507	Standard	XM_006724589		Approved	ORF34, FLJ20506	uc004dsz.4	Q9NX05	OTTHUMG00000021625	ENST00000375180.2:c.592G>A	chrX.hg19:g.54209040C>T	ENSP00000364324:p.Val198Met	80.0	0.0		88.0	45.0	NM_017848	B2RMT7	Missense_Mutation	SNP	ENST00000375180.2	hg19	CCDS14356.1	.	.	.	.	.	.	.	.	.	.	c	15.32	2.799408	0.50208	.	.	ENSG00000184083	ENST00000375180;ENST00000328235;ENST00000477084	T;T;T	0.60672	0.17;0.17;0.17	3.38	3.38	0.38709	.	0.079920	0.49305	U	0.000160	T	0.59473	0.2196	N	0.24115	0.695	0.42452	D	0.99275	P;D;P	0.89917	0.854;1.0;0.759	B;D;B	0.76071	0.157;0.987;0.161	T	0.61397	-0.7071	10	0.51188	T	0.08	-0.5376	10.0371	0.42135	0.0:0.7963:0.2037:0.0	.	198;198;198	F8W881;Q9NX05-2;Q9NX05	.;.;F120C_HUMAN	M	198	ENSP00000364324:V198M;ENSP00000329896:V198M;ENSP00000420718:V198M	ENSP00000329896:V198M	V	-	1	0	FAM120C	54225765	1.000000	0.71417	0.999000	0.59377	0.974000	0.67602	4.248000	0.58760	1.694000	0.51137	0.513000	0.50165	GTG	.	.		0.706	FAM120C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056795.2	NM_017848		T	54209040	C	T	54209040	3	4	328	1	0	0	0	0	1	0	0	0	5423	536	19	1	2784	1	FAM120C	23	54209040	Missense_Mutation	SNP	C	TCGA-NI-A8LF-01A-11D-A35Z-10		54209040	101061520	103	46033										
POF1B	79983	hgsc.bcm.edu	37	chrX	84600900	84600900	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	ggcttgatccactatggcacAgttcatttccaatatgtgta	8	9	1	1			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chrX:84600900A>T	ENST00000262753.4	-	6	834	c.689T>A	c.(688-690)cTg>cAg	p.L230Q	POF1B_ENST00000373145.3_Missense_Mutation_p.L230Q	NM_024921.3	NP_079197.3	Q8WVV4	POF1B_HUMAN	premature ovarian failure, 1B	230						tight junction (GO:0005923)				central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|liver(2)|lung(17)|ovary(1)|prostate(1)	35						ACTATGGCACAGTTCATTTCC	0.408																																					p.L230Q		Atlas-SNP	.											.	POF1B	77	.	0			c.T689A						.						228	193	205					X																	84600900		2203	4300	6503	SO:0001583	missense	79983	exon6			TGGCACAGTTCAT	BC017500	CCDS14452.1	Xq21.2	2008-02-05			ENSG00000124429	ENSG00000124429			13711	protein-coding gene	gene with protein product		300603				11299520	Standard	NM_024921		Approved	POF, FLJ22792	uc004eer.2	Q8WVV4	OTTHUMG00000021934	ENST00000262753.4:c.689T>A	chrX.hg19:g.84600900A>T	ENSP00000262753:p.Leu230Gln	74.0	0.0		83.0	34.0	NM_024921	A8K2U5|Q5H9E9|Q5H9F0|Q8NG12|Q9H5Y2|Q9H738|Q9H744	Missense_Mutation	SNP	ENST00000262753.4	hg19	CCDS14452.1	.	.	.	.	.	.	.	.	.	.	A	8.074	0.770971	0.15983	.	.	ENSG00000124429	ENST00000262753;ENST00000373145;ENST00000276124	T;T	0.13196	2.61;2.61	4.32	1.87	0.25490	.	0.518620	0.16008	N	0.233929	T	0.15565	0.0375	L	0.47716	1.5	0.09310	N	1	P;P	0.44195	0.828;0.571	P;B	0.48400	0.576;0.236	T	0.12142	-1.0559	10	0.66056	D	0.02	.	3.799	0.08751	0.6638:0.2179:0.1183:0.0	.	230;230	Q8WVV4-1;Q8WVV4	.;POF1B_HUMAN	Q	230	ENSP00000262753:L230Q;ENSP00000362238:L230Q	ENSP00000262753:L230Q	L	-	2	0	POF1B	84487556	0.009000	0.17119	0.000000	0.03702	0.110000	0.19582	1.580000	0.36547	0.153000	0.19213	0.481000	0.45027	CTG	.	.		0.408	POF1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057391.2	NM_024921		T	84600900	A	T	84600900	3	4	328	1	0	0	0	0	1	0	0	0	12191	188	7	4	1128	4	POF1B	23	84600900	Missense_Mutation	SNP	A	TCGA-NI-A8LF-01A-11D-A35Z-10	30391860	84600900	70669660	104	46034										
GPC4	2239	hgsc.bcm.edu	37	chrX	132548888	132548888	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	gaagcctttggacacgtaaaGacgtcgcacttccgagcaac	10	12	0	1			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chrX:132548888G>C	ENST00000370828.3	-	1	630	c.106C>G	c.(106-108)Ctt>Gtt	p.L36V	GPC4_ENST00000535467.1_5'Flank	NM_001448.2	NP_001439.2	O75487	GPC4_HUMAN	glypican 4	36					anatomical structure morphogenesis (GO:0009653)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(16)|skin(1)|upper_aerodigestive_tract(1)	28	Acute lymphoblastic leukemia(192;0.000127)					GACACGTAAAGACGTCGCACT	0.627																																					p.L36V		Atlas-SNP	.											.	GPC4	58	.	0			c.C106G						.						90	81	84					X																	132548888		2203	4300	6503	SO:0001583	missense	2239	exon1			CGTAAAGACGTCG	AF030186	CCDS14637.1	Xq26.1	2008-02-05			ENSG00000076716	ENSG00000076716		"Proteoglycans / Cell Surface : Glypicans"	4452	protein-coding gene	gene with protein product	"glypican proteoglycan 4"	300168				9787072	Standard	NM_001448		Approved	K-glypican	uc004exc.1	O75487	OTTHUMG00000022434	ENST00000370828.3:c.106C>G	chrX.hg19:g.132548888G>C	ENSP00000359864:p.Leu36Val	162.0	0.0		138.0	43.0	NM_001448	B2R6J7|B4E2C0|Q6ZMA6|Q96L43|Q9NU08|Q9UJN1|Q9UPD9	Missense_Mutation	SNP	ENST00000370828.3	hg19	CCDS14637.1	.	.	.	.	.	.	.	.	.	.	G	2.549	-0.304433	0.05495	.	.	ENSG00000076716	ENST00000370828;ENST00000536418	T	0.49139	0.79	4.42	3.49	0.39957	.	0.300521	0.31747	N	0.007130	T	0.22244	0.0536	N	0.04297	-0.235	0.80722	D	1	B	0.09022	0.002	B	0.09377	0.004	T	0.08743	-1.0707	10	0.08179	T	0.78	-5.201	12.5219	0.56065	0.0:0.1856:0.8144:0.0	.	36	O75487	GPC4_HUMAN	V	36	ENSP00000359864:L36V	ENSP00000359864:L36V	L	-	1	0	GPC4	132376554	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	2.999000	0.49473	1.782000	0.52362	0.529000	0.55759	CTT	.	.		0.627	GPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058338.1	NM_001448		C	132548888	G	C	132548888	3	2	328	1	0	0	0	0	1	0	0	0	6608	942	33	4	1600	4	GPC4	23	132548888	Missense_Mutation	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10	47947988	132548888	22721672	105	46035										
PNMA3	29944	hgsc.bcm.edu	37	chrX	152225496	152225496	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	ctcatcctggggatccccgaGgactgtggcgaggatgagtt	15	10	1	1			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chrX:152225496G>C	ENST00000370264.4	+	1	110	c.84G>C	c.(82-84)gaG>gaC	p.E28D	PNMA3_ENST00000370265.4_Missense_Mutation_p.E28D|PNMA3_ENST00000447306.1_Missense_Mutation_p.E28D			Q9UL41	PNMA3_HUMAN	paraneoplastic Ma antigen 3	28					positive regulation of apoptotic process (GO:0043065)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)	16	Acute lymphoblastic leukemia(192;6.56e-05)					ggatccccgaggactgtggcg	0.587																																					p.E28D		Atlas-SNP	.											.	PNMA3	81	.	0			c.G84C						.						102	86	91					X																	152225496		2203	4300	6503	SO:0001583	missense	29944	exon2			CCCCGAGGACTGT	AF083116	CCDS35435.2, CCDS65344.1	Xq28	2012-02-09	2012-02-09		ENSG00000183837	ENSG00000183837		"Paraneoplastic Ma antigens"	18742	protein-coding gene	gene with protein product	"paraneoplastic cancer-testis-brain antigen"	300675	"paraneoplastic antigen MA3"			11558790	Standard	NM_013364		Approved	MA5, MA3, MGC132756, MGC132758	uc004fhc.2	Q9UL41	OTTHUMG00000024195	ENST00000370264.4:c.84G>C	chrX.hg19:g.152225496G>C	ENSP00000359286:p.Glu28Asp	140.0	0.0		121.0	47.0	NM_013364	D3DWT7|Q9H0A4	Missense_Mutation	SNP	ENST00000370264.4	hg19	CCDS35435.2	.	.	.	.	.	.	.	.	.	.	g	11.47	1.649080	0.29336	.	.	ENSG00000183837	ENST00000370265;ENST00000447306;ENST00000370264	T;T;T	0.10288	2.89;2.89;2.89	2.23	1.31	0.21738	.	.	.	.	.	T	0.08891	0.0220	L	0.28274	0.84	0.09310	N	1	P	0.45348	0.856	P	0.48598	0.583	T	0.25502	-1.0130	9	0.14656	T	0.56	.	4.7598	0.13102	0.1979:0.0:0.8021:0.0	.	28	Q9UL41	PNMA3_HUMAN	D	28	ENSP00000359288:E28D;ENSP00000407642:E28D;ENSP00000359286:E28D	ENSP00000359286:E28D	E	+	3	2	PNMA3	151976152	0.829000	0.29322	0.016000	0.15963	0.404000	0.30871	0.733000	0.26087	0.349000	0.23975	0.411000	0.27672	GAG	.	.		0.587	PNMA3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060946.2	NM_013364		C	152225496	G	C	152225496	3	2	328	1	0	0	0	0	1	0	0	0	12164	991	35	4	86	4	PNMA3	23	152225496	Missense_Mutation	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10	19676608	152225496	3045064	106	46036										
ARHGAP4	393	hgsc.bcm.edu	37	chrX	153174961	153174961	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0654205607476635	7	1	1.03473581213307	1.31693648816936	0.953046142754146	0.378260869565217	1	0	agactcccctgcagtctgcaGccctgcgcccaccacctgct	8	20	1	1			TCGA-NI-A8LF-01A-11D-A35Z-10	TCGA-NI-A8LF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	591e019d-1317-490a-b687-1d8f75118e1f	9145d9de-76f8-4fbf-863f-d7f80611dcd9	g.chrX:153174961G>A	ENST00000350060.5	-	20	2484	c.2443C>T	c.(2443-2445)Ctg>Ttg	p.L815L	ARHGAP4_ENST00000370016.1_Silent_p.L794L|ARHGAP4_ENST00000467421.1_Intron|ARHGAP4_ENST00000537206.1_Silent_p.L792L|ARHGAP4_ENST00000370028.3_Silent_p.L855L|ARHGAP4_ENST00000393721.1_Silent_p.L637L	NM_001666.4	NP_001657.3	P98171	RHG04_HUMAN	Rho GTPase activating protein 4	815					apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|negative regulation of axon extension (GO:0030517)|negative regulation of fibroblast migration (GO:0010764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of signal transduction (GO:0009967)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)	Rho GTPase activator activity (GO:0005100)|SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	14	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GCAGTCTGCAGCCCTGCGCCC	0.697																																					p.L855L		Atlas-SNP	.											.	ARHGAP4	103	.	0			c.C2563T						.						32	30	30					X																	153174961		2202	4300	6502	SO:0001819	synonymous_variant	393	exon21			TCTGCAGCCCTGC	X78817	CCDS14736.1, CCDS55540.1	Xq28	2010-02-09			ENSG00000089820	ENSG00000089820		"Rho GTPase activating proteins"	674	protein-coding gene	gene with protein product	"Rho-GAP hematopoietic protein C1"	300023				8570618	Standard	NM_001666		Approved	KIAA0131, C1, p115, RhoGAP4, SrGAP4	uc004fjk.2	P98171	OTTHUMG00000024226	ENST00000350060.5:c.2443C>T	chrX.hg19:g.153174961G>A		142.0	0.0		114.0	87.0	NM_001164741	Q14144|Q86UY3	Silent	SNP	ENST00000350060.5	hg19	CCDS14736.1																																																																																			.	.		0.697	ARHGAP4-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061119.1	NM_001666		A	153174961	G	A	153174961	2	1	328	1	0	0	0	0	0	0	0	1	885	962	34	3		3	ARHGAP4	23	153174961	Silent	SNP	G	TCGA-NI-A8LF-01A-11D-A35Z-10	949465	153174961	2095599	107	46037										
TMEM51	55092	hgsc.bcm.edu	37	chr1	15541674	15541674	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	ttggggtgatcatggccatgTggaacctggtacccggcttc	14	10	1	1			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr1:15541674T>A	ENST00000428417.1	+	2	537	c.91T>A	c.(91-93)Tgg>Agg	p.W31R	TMEM51_ENST00000376008.2_Missense_Mutation_p.W31R|TMEM51_ENST00000434578.2_Missense_Mutation_p.W31R|TMEM51_ENST00000376014.3_Missense_Mutation_p.W31R|TMEM51_ENST00000400796.3_Missense_Mutation_p.W31R	NM_001136217.1	NP_001129689.1	Q9NW97	TMM51_HUMAN	transmembrane protein 51	31						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(3)|large_intestine(2)|lung(5)|prostate(2)	14		Renal(390;0.00145)|Breast(348;0.00186)|Colorectal(325;0.00215)|all_lung(284;0.00459)|Lung NSC(340;0.0104)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;2.07e-06)|COAD - Colon adenocarcinoma(227;7.14e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000175)|KIRC - Kidney renal clear cell carcinoma(229;0.00141)|STAD - Stomach adenocarcinoma(313;0.00644)|READ - Rectum adenocarcinoma(331;0.0751)		CATGGCCATGTGGAACCTGGT	0.622																																					p.W31R		Atlas-SNP	.											.	TMEM51	28	.	0			c.T91A						.						124	128	127					1																	15541674		2203	4300	6503	SO:0001583	missense	55092	exon2			GCCATGTGGAACC	AK098467	CCDS154.1	1p36.21	2008-02-05	2005-05-22	2005-05-22	ENSG00000171729	ENSG00000171729			25488	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 72"	C1orf72		12477932	Standard	NM_018022		Approved	FLJ10199	uc001avx.3	Q9NW97	OTTHUMG00000002046	ENST00000428417.1:c.91T>A	chr1.hg19:g.15541674T>A	ENSP00000394899:p.Trp31Arg	39.0	0.0		36.0	16.0	NM_018022	A8K819	Missense_Mutation	SNP	ENST00000428417.1	hg19	CCDS154.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.686444	0.88639	.	.	ENSG00000171729	ENST00000428417;ENST00000376014;ENST00000451326;ENST00000434578;ENST00000400796;ENST00000376008;ENST00000303840	T;T;T;T;T;T	0.64803	-0.12;-0.12;-0.12;-0.12;-0.12;-0.12	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.78000	0.4215	M	0.70275	2.135	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.80786	-0.1227	10	0.87932	D	0	-0.5077	14.6591	0.68855	0.0:0.0:0.0:1.0	.	31;31	Q9BSA0;Q9NW97	.;TMM51_HUMAN	R	31	ENSP00000394899:W31R;ENSP00000365182:W31R;ENSP00000412298:W31R;ENSP00000409665:W31R;ENSP00000383600:W31R;ENSP00000365176:W31R	ENSP00000303666:W31R	W	+	1	0	TMEM51	15414261	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.117000	0.77129	2.073000	0.62155	0.533000	0.62120	TGG	.	.		0.622	TMEM51-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005699.3	NM_018022		A	15541674	T	A	15541674	3	1	329	1	0	0	0	0	1	0	0	0	16192	1696	59	4	93	4	TMEM51	1	15541674	Missense_Mutation	SNP	T	TCGA-O8-A75V-01A-11D-A32G-10		15541674	233708947	1	46038										
TCHH	7062	hgsc.bcm.edu	37	chr1	152084224	152084224	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	gcctctcctcctcctcgagcTtcagccaacgttcgcgcctc	7	20	2	0			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr1:152084224T>C	ENST00000368804.1	-	2	1468	c.1469A>G	c.(1468-1470)aAg>aGg	p.K490R		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	490	9 X 28 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTCCTCGAGCTTCAGCCAACG	0.672																																					p.K490R		Atlas-SNP	.											.	TCHH	275	.	0			c.A1469G						.						65	71	69					1																	152084224		2109	4224	6333	SO:0001583	missense	7062	exon3			TCGAGCTTCAGCC	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"EF-hand domain containing"	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.1469A>G	chr1.hg19:g.152084224T>C	ENSP00000357794:p.Lys490Arg	69.0	0.0		120.0	11.0	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	hg19	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	t	8.419	0.845945	0.16963	.	.	ENSG00000159450	ENST00000368804	T	0.04654	3.58	2.98	-5.97	0.02227	.	.	.	.	.	T	0.00524	0.0017	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48547	-0.9026	9	0.09590	T	0.72	.	5.0277	0.14393	0.1398:0.4054:0.0:0.4548	.	490	Q07283	TRHY_HUMAN	R	490	ENSP00000357794:K490R	ENSP00000357794:K490R	K	-	2	0	TCHH	150350848	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.247000	0.00266	-1.053000	0.03218	-1.396000	0.01147	AAG	.	.		0.672	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		C	152084224	T	C	152084224	3	2	329	1	0	0	0	0	1	0	0	0	15715	1609	56	2	4366	2	TCHH	1	152084224	Missense_Mutation	SNP	T	TCGA-O8-A75V-01A-11D-A32G-10	136542550	152084224	97166397	2	46039										
FLG	2312	hgsc.bcm.edu	37	chr1	152277443	152277443	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	ggagctgtctgctgactgctGgtggcgggatccgtgtctct	16	10	2	1			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr1:152277443G>T	ENST00000368799.1	-	3	9954	c.9919C>A	c.(9919-9921)Cag>Aag	p.Q3307K	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3307	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCTGACTGCTGGTGGCGGGAT	0.572									Ichthyosis																												p.Q3307K		Atlas-SNP	.											.	FLG	900	.	0			c.C9919A						.						391	384	386					1																	152277443		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	ACTGCTGGTGGCG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.9919C>A	chr1.hg19:g.152277443G>T	ENSP00000357789:p.Gln3307Lys	130.0	0.0		166.0	101.0	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	hg19	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	G	9.636	1.137653	0.21123	.	.	ENSG00000143631	ENST00000368799;ENST00000368796	T	0.00724	5.78	3.18	-4.02	0.04034	.	.	.	.	.	T	0.00998	0.0033	L	0.57536	1.79	0.09310	N	1	P	0.50617	0.937	P	0.62089	0.898	T	0.09292	-1.0681	9	0.37606	T	0.19	.	14.928	0.70893	0.0:0.7461:0.2539:0.0	.	3307	P20930	FILA_HUMAN	K	3307;245	ENSP00000357789:Q3307K	ENSP00000357786:Q245K	Q	-	1	0	FLG	150544067	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-1.090000	0.03372	-0.701000	0.05063	-0.876000	0.02978	CAG	.	.		0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		T	152277443	G	T	152277443	3	4	329	1	0	0	0	0	1	0	0	0	5930	1357	47	3	2270	3	FLG	1	152277443	Missense_Mutation	SNP	G	TCGA-O8-A75V-01A-11D-A32G-10	193219	152277443	96973178	3	46040										
FLG	2312	hgsc.bcm.edu	37	chr1	152287879	152287879	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	gtgtttttatctttttttgaAtattgcttgaaaagattaat	6	2	1	3			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr1:152287879A>T	ENST00000368799.1	-	2	89	c.54T>A	c.(52-54)taT>taA	p.Y18*	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	18	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTTTTTTTGAATATTGCTTGA	0.338									Ichthyosis																												p.Y18X		Atlas-SNP	.											.	FLG	900	.	0			c.T54A						.						118	117	118					1																	152287879		2202	4300	6502	SO:0001587	stop_gained	2312	exon2	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TTTTGAATATTGC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.54T>A	chr1.hg19:g.152287879A>T	ENSP00000357789:p.Tyr18*	327.0	0.0		437.0	87.0	NM_002016	Q01720|Q5T583|Q9UC71	Nonsense_Mutation	SNP	ENST00000368799.1	hg19	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	A	17.62	3.435657	0.62955	.	.	ENSG00000143631	ENST00000368799	.	.	.	5.2	1.68	0.24146	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-21.5857	6.4054	0.21662	0.7042:0.0:0.2958:0.0	.	.	.	.	X	18	.	ENSP00000357789:Y18X	Y	-	3	2	FLG	150554503	0.556000	0.26538	0.501000	0.27601	0.032000	0.12392	0.173000	0.16724	0.131000	0.18576	0.456000	0.33151	TAT	.	.		0.338	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		T	152287879	A	T	152287879	4	4	329	1	0	0	0	0	0	1	0	0	5930	108	4	4	12139	4	FLG	1	152287879	Nonsense_Mutation	SNP	A	TCGA-O8-A75V-01A-11D-A32G-10	10436	152287879	96962742	4	46041										
PYGO2	90780	hgsc.bcm.edu	37	chr1	154931467	154931467	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	ggcatcctggtcatcgttcaCctcactccgacaggcaccac	8	17	3	0			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr1:154931467C>A	ENST00000368457.2	-	3	1180	c.1009G>T	c.(1009-1011)Gtg>Ttg	p.V337L	RP11-307C12.12_ENST00000605085.1_RNA|PBXIP1_ENST00000539880.1_5'Flank|PBXIP1_ENST00000368465.1_5'Flank|PYGO2_ENST00000368456.1_Missense_Mutation_p.V300L|PBXIP1_ENST00000368463.3_5'Flank|PBXIP1_ENST00000368460.3_5'Flank|PBXIP1_ENST00000542459.1_5'Flank|PYGO2_ENST00000483463.1_5'Flank	NM_138300.3	NP_612157.1	Q9BRQ0	PYGO2_HUMAN	pygopus family PHD finger 2	337					brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|developmental growth (GO:0048589)|in utero embryonic development (GO:0001701)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|mammary gland development (GO:0030879)|palate development (GO:0060021)|positive regulation of chromatin binding (GO:0035563)|post-embryonic development (GO:0009791)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|spermatid nucleus differentiation (GO:0007289)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone acetyltransferase regulator activity (GO:0035034)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(3)|skin(2)|urinary_tract(1)	10	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			TCATCGTTCACCTCACTCCGA	0.627																																					p.V337L	NSCLC(87;357 1460 1955 21029 23522)	Atlas-SNP	.											.	PYGO2	32	.	0			c.G1009T						.						74	58	63					1																	154931467		2203	4300	6503	SO:0001583	missense	90780	exon3			CGTTCACCTCACT	BC006132	CCDS1075.1	1q22	2013-10-09	2013-10-09		ENSG00000163348	ENSG00000163348		"Zinc fingers, PHD-type"	30257	protein-coding gene	gene with protein product		606903	"pygopus homolog 2 (Drosophila)"			11988739	Standard	NM_138300		Approved		uc001fft.3	Q9BRQ0	OTTHUMG00000037370	ENST00000368457.2:c.1009G>T	chr1.hg19:g.154931467C>A	ENSP00000357442:p.Val337Leu	59.0	0.0		100.0	24.0	NM_138300	Q8WYZ4|Q96CY2	Missense_Mutation	SNP	ENST00000368457.2	hg19	CCDS1075.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.056857	0.76074	.	.	ENSG00000163348	ENST00000368457;ENST00000368456	T;T	0.62788	0.0;0.0	4.85	4.85	0.62838	Zinc finger, PHD-finger (2);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.64402	D	0.000004	T	0.67571	0.2907	L	0.47190	1.495	0.58432	D	0.999993	D	0.61080	0.989	D	0.66497	0.944	T	0.71334	-0.4624	10	0.87932	D	0	-9.8878	16.926	0.86176	0.0:1.0:0.0:0.0	.	337	Q9BRQ0	PYGO2_HUMAN	L	337;300	ENSP00000357442:V337L;ENSP00000357441:V300L	ENSP00000357441:V300L	V	-	1	0	PYGO2	153198091	1.000000	0.71417	1.000000	0.80357	0.822000	0.46500	7.619000	0.83057	2.524000	0.85096	0.561000	0.74099	GTG	.	.		0.627	PYGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090949.1	NM_138300		A	154931467	C	A	154931467	3	1	329	1	0	0	0	0	1	0	0	0	12879	507	18	3	215	3	PYGO2	1	154931467	Missense_Mutation	SNP	C	TCGA-O8-A75V-01A-11D-A32G-10	2643588	154931467	94319154	5	46042										
INSRR	3645	hgsc.bcm.edu	37	chr1	156815580	156815580	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	ttcgccgtcgaagcgcggatCgttgttgctggtgggcagcc	16	11	0	0			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr1:156815580C>T	ENST00000368195.3	-	10	2401	c.2005G>A	c.(2005-2007)Gat>Aat	p.D669N	NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	669	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton reorganization (GO:0031532)|cellular response to alkaline pH (GO:0071469)|male sex determination (GO:0030238)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(7)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	42	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					AAGCGCGGATCGTTGTTGCTG	0.682																																					p.D669N		Atlas-SNP	.											.	INSRR	309	.	0			c.G2005A						.						26	23	24					1																	156815580		2203	4298	6501	SO:0001583	missense	3645	exon10			GCGGATCGTTGTT	J05046	CCDS1160.1	1q21-q23	2013-02-11			ENSG00000027644	ENSG00000027644		"Fibronectin type III domain containing"	6093	protein-coding gene	gene with protein product		147671				2768234, 2249481	Standard	NM_014215		Approved	IRR	uc010pht.2	P14616	OTTHUMG00000041291	ENST00000368195.3:c.2005G>A	chr1.hg19:g.156815580C>T	ENSP00000357178:p.Asp669Asn	108.0	0.0		180.0	70.0	NM_014215	O60724|Q5VZS3	Missense_Mutation	SNP	ENST00000368195.3	hg19	CCDS1160.1	.	.	.	.	.	.	.	.	.	.	C	13.55	2.270751	0.40194	.	.	ENSG00000027644	ENST00000368195	T	0.71817	-0.6	4.69	4.69	0.59074	Fibronectin, type III (3);	0.000000	0.51477	D	0.000099	T	0.41858	0.1177	.	.	.	0.35068	D	0.762207	B	0.20052	0.041	B	0.08055	0.003	T	0.27088	-1.0084	9	0.21014	T	0.42	.	15.4999	0.75691	0.0:1.0:0.0:0.0	.	669	P14616	INSRR_HUMAN	N	669	ENSP00000357178:D669N	ENSP00000357178:D669N	D	-	1	0	INSRR	155082204	0.988000	0.35896	1.000000	0.80357	0.839000	0.47603	2.734000	0.47368	2.606000	0.88127	0.561000	0.74099	GAT	.	.		0.682	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215		T	156815580	C	T	156815580	3	4	329	1	0	0	0	0	1	0	0	0	7783	884	31	1	1939	1	INSRR	1	156815580	Missense_Mutation	SNP	C	TCGA-O8-A75V-01A-11D-A32G-10	1884113	156815580	92435041	6	46043										
TRAF3IP3	80342	hgsc.bcm.edu	37	chr1	209953855	209953855	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	agtccaaagtccttccctaaCgaagtggagcctgagggtac	11	11	0	1	rs147808288		TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr1:209953855C>G	ENST00000367024.1	+	15	1869	c.1353C>G	c.(1351-1353)aaC>aaG	p.N451K	TRAF3IP3_ENST00000367025.3_Missense_Mutation_p.N451K|TRAF3IP3_ENST00000010338.4_Missense_Mutation_p.N431K|TRAF3IP3_ENST00000477431.1_Intron|TRAF3IP3_ENST00000367026.3_Missense_Mutation_p.N431K			Q9Y228	T3JAM_HUMAN	TRAF3 interacting protein 3	451						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32				OV - Ovarian serous cystadenocarcinoma(81;0.045)		CCTTCCCTAACGAAGTGGAGC	0.537																																					p.N451K		Atlas-SNP	.											.	TRAF3IP3	68	.	0			c.C1353G						.	C	LYS/ASN	0,4406		0,0,2203	119	116	117		1353	-10.5	0	1	dbSNP_134	117	1,8599	1.2+/-3.3	0,1,4299	no	missense	TRAF3IP3	NM_025228.2	94	0,1,6502	GG,GC,CC		0.0116,0.0,0.0077	possibly-damaging	451/552	209953855	1,13005	2203	4300	6503	SO:0001583	missense	80342	exon15			CCCTAACGAAGTG		CCDS1490.1, CCDS1490.2, CCDS73023.1	1q32.3-q41	2008-02-05			ENSG00000009790	ENSG00000009790			30766	protein-coding gene	gene with protein product	"TRAF3 interacting Jun N terminal kinase (JNK) activating modulator"	608255				14572659	Standard	XR_247044		Approved	T3JAM	uc001hho.3	Q9Y228	OTTHUMG00000036480	ENST00000367024.1:c.1353C>G	chr1.hg19:g.209953855C>G	ENSP00000355991:p.Asn451Lys	98.0	0.0		121.0	26.0	NM_025228	A1L464|A6NIU9|Q2YDB5|Q4VY06|Q7Z706	Missense_Mutation	SNP	ENST00000367024.1	hg19	CCDS1490.2	.	.	.	.	.	.	.	.	.	.	C	0.014	-1.591468	0.00864	0.0	1.16E-4	ENSG00000009790	ENST00000367025;ENST00000367026;ENST00000367024;ENST00000010338	T;T;T;T	0.74632	-0.86;-0.86;-0.86;-0.86	5.24	-10.5	0.00291	.	1.377270	0.04492	N	0.379749	T	0.57359	0.2048	L	0.51422	1.61	0.38779	D	0.95471	B;B	0.09022	0.002;0.002	B;B	0.13407	0.009;0.009	T	0.25187	-1.0139	10	0.32370	T	0.25	0.0096	0.141	0.00083	0.2846:0.2051:0.1741:0.3362	.	451;431	Q9Y228;Q9Y228-2	T3JAM_HUMAN;.	K	451;431;451;431	ENSP00000355992:N451K;ENSP00000355993:N431K;ENSP00000355991:N451K;ENSP00000010338:N431K	ENSP00000010338:N431K	N	+	3	2	TRAF3IP3	208020478	0.000000	0.05858	0.000000	0.03702	0.077000	0.17291	-2.464000	0.00996	-3.257000	0.00203	-2.051000	0.00406	AAC	.	C|1.000;G|0.000		0.537	TRAF3IP3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088734.2			G	209953855	C	G	209953855	3	3	329	1	0	0	0	0	1	0	0	0	16457	535	19	4	1403	4	TRAF3IP3	1	209953855	Missense_Mutation	SNP	C	TCGA-O8-A75V-01A-11D-A32G-10	53138275	209953855	39296766	7	46044										
KIAA1383	54627	hgsc.bcm.edu	37	chr1	232943321	232943321	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	tgatttgtctagcccttgctAttctgaagatttctgtacca	7	9	3	3			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr1:232943321A>G	ENST00000418460.1	+	1	2679	c.2552A>G	c.(2551-2553)tAt>tGt	p.Y851C		NM_019090.2	NP_061963.2	Q9P2G4	MAP10_HUMAN	microtubule-associated protein 10	709	Ser-rich.				cytoplasmic microtubule organization (GO:0031122)|positive regulation of cytokinesis (GO:0032467)|regulation of microtubule-based process (GO:0032886)|spindle midzone assembly involved in mitosis (GO:0051256)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|mitotic spindle pole (GO:0097431)	microtubule binding (GO:0008017)										AGCCCTTGCTATTCTGAAGAT	0.368																																					p.Y851C		Atlas-SNP	.											.	.	.	.	0			c.A2552G						.						39	37	37					1																	232943321		1859	4097	5956	SO:0001583	missense	54627	exon1			CTTGCTATTCTGA	AB037804	CCDS44334.1	1q42.2	2013-02-12	2013-02-12	2013-02-12	ENSG00000212916	ENSG00000212916			29265	protein-coding gene	gene with protein product	"microtubule regulator 120 KDa"		"KIAA1383"	KIAA1383		23264731	Standard	NM_019090		Approved	MTR120	uc001hvh.2	Q9P2G4	OTTHUMG00000037819	ENST00000418460.1:c.2552A>G	chr1.hg19:g.232943321A>G	ENSP00000403208:p.Tyr851Cys	105.0	0.0		113.0	17.0	NM_019090	A8K2F1|Q32MI1|Q58EZ9|Q5VV83	Missense_Mutation	SNP	ENST00000418460.1	hg19	CCDS44334.1	.	.	.	.	.	.	.	.	.	.	A	9.895	1.205211	0.22205	.	.	ENSG00000212916	ENST00000418460	.	.	.	6.08	-0.784	0.10954	.	0.725019	0.11209	U	0.587917	T	0.18087	0.0434	L	0.28115	0.83	0.28640	N	0.907237	B	0.34200	0.441	B	0.28139	0.086	T	0.15378	-1.0439	9	0.40728	T	0.16	-1.4459	2.4469	0.04508	0.5292:0.2301:0.1301:0.1106	.	709	Q9P2G4	K1383_HUMAN	C	851	.	ENSP00000403208:Y851C	Y	+	2	0	KIAA1383	231009944	0.991000	0.36638	0.951000	0.38953	0.443000	0.32047	0.360000	0.20250	-0.073000	0.12842	-0.326000	0.08463	TAT	.	.		0.368	MAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092317.3	NM_019090		G	232943321	A	G	232943321	3	3	329	1	0	0	0	0	1	0	0	0	8237	449	16	2	2554	2	KIAA1383	1	232943321	Missense_Mutation	SNP	A	TCGA-O8-A75V-01A-11D-A32G-10	22989466	232943321	16307300	8	46045										
C2orf71	388939	hgsc.bcm.edu	37	chr2	29294547	29294547	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	cggccctggctcctgggtttCcttgggggagttctctgtgg	16	11	1	0			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr2:29294547C>A	ENST00000331664.5	-	1	2580	c.2581G>T	c.(2581-2583)Gaa>Taa	p.E861*		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	861					response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						TCCTGGGTTTCCTTGGGGGAG	0.612																																					p.E861X		Atlas-SNP	.											.	C2orf71	146	.	0			c.G2581T						.						54	56	55					2																	29294547		1853	4105	5958	SO:0001587	stop_gained	388939	exon1			GGGTTTCCTTGGG		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.2581G>T	chr2.hg19:g.29294547C>A	ENSP00000332809:p.Glu861*	119.0	0.0		109.0	35.0	NM_001029883		Nonsense_Mutation	SNP	ENST00000331664.5	hg19	CCDS42669.1	.	.	.	.	.	.	.	.	.	.	C	37	6.401860	0.97537	.	.	ENSG00000179270	ENST00000331664	.	.	.	5.54	2.61	0.31194	.	1.065440	0.07224	N	0.861344	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	-4.5644	7.1416	0.25558	0.0:0.6003:0.2553:0.1443	.	.	.	.	X	861	.	ENSP00000332809:E861X	E	-	1	0	C2orf71	29148051	0.001000	0.12720	0.002000	0.10522	0.004000	0.04260	1.638000	0.37165	0.698000	0.31739	0.585000	0.79938	GAA	.	.		0.612	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883		A	29294547	C	A	29294547	4	1	329	1	0	0	0	0	0	1	0	0	2193	864	30	3	1293	3	C2orf71	2	29294547	Nonsense_Mutation	SNP	C	TCGA-O8-A75V-01A-11D-A32G-10		29294547	213904826	9	46046										
DNAH6	1768	hgsc.bcm.edu	37	chr2	84784866	84784866	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	ttctctttaacaggatggtaTtttgggtgcagttaatcact	9	6	2	0			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr2:84784866T>G	ENST00000237449.6	+	10	1618	c.1610T>G	c.(1609-1611)aTt>aGt	p.I537S	DNAH6_ENST00000389394.3_Missense_Mutation_p.I537S|DNAH6_ENST00000398278.2_Missense_Mutation_p.I537S			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	537	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						CAGGATGGTATTTTGGGTGCA	0.313																																					p.I537S		Atlas-SNP	.											.	DNAH6	194	.	0			c.T1610G						.						134	127	129					2																	84784866		2203	4300	6503	SO:0001583	missense	1768	exon11			ATGGTATTTTGGG	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.1610T>G	chr2.hg19:g.84784866T>G	ENSP00000237449:p.Ile537Ser	159.0	0.0		165.0	37.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	hg19	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	T	10.39	1.337324	0.24253	.	.	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.28069	1.63;1.75;1.63	5.22	5.22	0.72569	.	0.123056	0.36034	N	0.002826	T	0.37732	0.1014	L	0.57536	1.79	0.39225	D	0.963578	B;P	0.41265	0.415;0.744	B;B	0.44044	0.239;0.439	T	0.41980	-0.9478	10	0.87932	D	0	.	14.0916	0.64995	0.0:0.0:0.0:1.0	.	537;116	Q9C0G6;Q9C0G6-3	DYH6_HUMAN;.	S	537	ENSP00000374045:I537S;ENSP00000381326:I537S;ENSP00000237449:I537S	ENSP00000237449:I537S	I	+	2	0	DNAH6	84638377	1.000000	0.71417	0.996000	0.52242	0.041000	0.13682	3.504000	0.53347	1.969000	0.57287	0.533000	0.62120	ATT	.	.		0.313	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		G	84784866	T	G	84784866	3	3	329	1	0	0	0	0	1	0	0	0	4607	1493	52	5	1648	5	DNAH6	2	84784866	Missense_Mutation	SNP	T	TCGA-O8-A75V-01A-11D-A32G-10	55490319	84784866	158414507	10	46047										
LYPD6B	130576	hgsc.bcm.edu	37	chr2	150061778	150061778	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	tcaccatagatataagagttCggaccgcccagcacacaagg	9	12	1	2			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr2:150061778C>T	ENST00000409029.1	+	4	219	c.17C>T	c.(16-18)tCg>tTg	p.S6L	LYPD6B_ENST00000498249.1_3'UTR|LYPD6B_ENST00000409642.3_Missense_Mutation_p.S30L|LYPD6B_ENST00000280115.7_Missense_Mutation_p.S30L|LYPD6B_ENST00000409876.1_Missense_Mutation_p.S6L			Q8NI32	LPD6B_HUMAN	LY6/PLAUR domain containing 6B	6						anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.S30L(1)		endometrium(3)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	11						TATAAGAGTTCGGACCGCCCA	0.453																																					p.S30L		Atlas-SNP	.											LYPD6B,NS,carcinoma,0,2	LYPD6B	25	.	1	Substitution - Missense(1)	large_intestine(1)	c.C89T						.						90	92	92					2																	150061778		2065	4201	6266	SO:0001583	missense	130576	exon4			AGAGTTCGGACCG		CCDS46423.1	2q23.2	2012-07-20			ENSG00000150556	ENSG00000150556			27018	protein-coding gene	gene with protein product	"cancer/testis antigen 116"					18360792	Standard	NM_177964		Approved	CT116, LYPD7	uc002twv.1	Q8NI32	OTTHUMG00000153743	ENST00000409029.1:c.17C>T	chr2.hg19:g.150061778C>T	ENSP00000386650:p.Ser6Leu	84.0	0.0		96.0	4.0	NM_177964	D3DP90|Q53TK0|Q7Z747|Q8IXK7	Missense_Mutation	SNP	ENST00000409029.1	hg19		.	.	.	.	.	.	.	.	.	.	C	13.19	2.162272	0.38217	.	.	ENSG00000150556	ENST00000409642;ENST00000409876;ENST00000409029;ENST00000280115	T;T;T;T	0.11385	2.78;2.78;2.78;2.78	5.72	-0.241	0.13043	.	1.238790	0.05654	N	0.585732	T	0.04318	0.0119	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42632	-0.9440	9	.	.	.	-4.2651	4.6818	0.12738	0.0:0.3053:0.2051:0.4896	.	30	Q8NI32-2	.	L	30;6;6;30	ENSP00000387077:S30L;ENSP00000386479:S6L;ENSP00000386650:S6L;ENSP00000280115:S30L	.	S	+	2	0	LYPD6B	149770024	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.393000	0.07305	0.126000	0.18424	-0.294000	0.09567	TCG	.	.		0.453	LYPD6B-003	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000332299.2	NM_177964		T	150061778	C	T	150061778	3	4	329	1	0	0	0	0	1	0	0	0	9124	893	31	1	99	1	LYPD6B	2	150061778	Missense_Mutation	SNP	C	TCGA-O8-A75V-01A-11D-A32G-10	65276912	150061778	93137595	11	46048										
TTN	7273	hgsc.bcm.edu	37	chr2	179593438	179593438	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	ggtgttccagccacaacacaTtccaaggtcatgggatcttt	9	11	2	0			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr2:179593438T>C	ENST00000591111.1	-	64	18488	c.18264A>G	c.(18262-18264)gaA>gaG	p.E6088E	TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Silent_p.E6405E|TTN_ENST00000342992.6_Silent_p.E5161E|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|RP11-171I2.1_ENST00000590024.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12875	Ig-like 42.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCACAACACATTCCAAGGTCA	0.378																																					p.E6405E		Atlas-SNP	.											.	TTN	18412	.	0			c.A19215G						.						92	86	88					2																	179593438		1876	4109	5985	SO:0001819	synonymous_variant	7273	exon66			AACACATTCCAAG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.18264A>G	chr2.hg19:g.179593438T>C		197.0	0.0		180.0	54.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.378	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179593438	T	C	179593438	2	2	329	1	0	0	0	0	0	0	0	1	16750	1490	52	2		2	TTN	2	179593438	Silent	SNP	T	TCGA-O8-A75V-01A-11D-A32G-10	29531660	179593438	63605935	12	46049										
TRAK2	66008	hgsc.bcm.edu	37	chr2	202250957	202250957	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	tcacctgtaactggtccaccTgctgaagtaatgggtggcag	12	10	1	1			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr2:202250957T>C	ENST00000332624.3	-	14	2375	c.1947A>G	c.(1945-1947)gcA>gcG	p.A649A		NM_015049.2	NP_055864.2	O60296	TRAK2_HUMAN	trafficking protein, kinesin binding 2	649					protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|endosome (GO:0005768)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GABA receptor binding (GO:0050811)|receptor binding (GO:0005102)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	23						CTGGTCCACCTGCTGAAGTAA	0.443																																					p.A649A		Atlas-SNP	.											.	TRAK2	62	.	0			c.A1947G						.						107	95	99					2																	202250957		2203	4300	6503	SO:0001819	synonymous_variant	66008	exon14			TCCACCTGCTGAA	AB038951	CCDS2347.1	2q33.1	2012-03-05	2005-12-13	2005-12-13	ENSG00000115993	ENSG00000115993			13206	protein-coding gene	gene with protein product	"gamma-aminobutyric acid(A) receptor-interacting factor", "milton homolog 2 (Drosophila)", "O-linked N-acetylglucosamine transferase interacting protein 98"	607334	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 3"	ALS2CR3		11161814, 16380713, 20230862	Standard	NM_015049		Approved	CALS-C, KIAA0549, GRIF-1, OIP98, MILT2	uc002uyb.4	O60296	OTTHUMG00000132822	ENST00000332624.3:c.1947A>G	chr2.hg19:g.202250957T>C		152.0	0.0		122.0	36.0	NM_015049	E7EV21|Q8WVH7|Q96NS2|Q9C0K5|Q9C0K6	Silent	SNP	ENST00000332624.3	hg19	CCDS2347.1																																																																																			.	.		0.443	TRAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256284.3	NM_015049		C	202250957	T	C	202250957	2	2	329	1	0	0	0	0	0	0	0	1	16465	1567	55	2		2	TRAK2	2	202250957	Silent	SNP	T	TCGA-O8-A75V-01A-11D-A32G-10	22657519	202250957	40948416	13	46050										
TRIP12	9320	hgsc.bcm.edu	37	chr2	230661327	230661327	+	Frame_Shift_Del	DEL	G	G	-													0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	tggagaagaaaaaaatacatGaagaaatcgctttaatctga							TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr2:230661327delG	ENST00000283943.5	-	24	3749	c.3571delC	c.(3571-3573)catfs	p.H1191fs	TRIP12_ENST00000389045.3_Frame_Shift_Del_p.H921fs|TRIP12_ENST00000389044.4_Frame_Shift_Del_p.H1239fs	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	1191					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		AAAAATACATGAAGAAATCGC	0.323																																					p.H1191fs		Atlas-Indel,Pindel	.											.	TRIP12	207	.	0			c.3572delA						.						102	105	104					2																	230661327		2203	4300	6503	SO:0001589	frameshift_variant	9320	exon24			.	L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.3571delC	chr2.hg19:g.230661327delG	ENSP00000283943:p.His1191fs	142.0	0.0		183.0	46.0	NM_004238	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Frame_Shift_Del	DEL	ENST00000283943.5	hg19	CCDS33391.1																																																																																			.	.		0.323	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238		-	230661327	G	-	230661327	7	5	329	1	0	1	0	1	0	0	0	0	16571	1290	45	0	2479	0	TRIP12	2	230661327	Frame_Shift_Del	DEL	G	TCGA-O8-A75V-01A-11D-A32G-10	28410370	230661327	12538046	14	46051										
COL6A3	1293	hgsc.bcm.edu	37	chr2	238253847	238253847	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	gatggagtcgcccctgttgcCcttgggaccctgtaaaacca	11	13	0	0			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr2:238253847C>A	ENST00000295550.4	-	33	7554	c.7102G>T	c.(7102-7104)Ggc>Tgc	p.G2368C	COL6A3_ENST00000472056.1_Missense_Mutation_p.G1761C|COL6A3_ENST00000347401.3_Missense_Mutation_p.G2167C|COL6A3_ENST00000409809.1_Missense_Mutation_p.G2162C|COL6A3_ENST00000353578.4_Missense_Mutation_p.G2162C|COL6A3_ENST00000346358.4_Missense_Mutation_p.G2168C	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2368	Collagen-like 5.|Triple-helical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		CCCCTGTTGCCCTTGGGACCC	0.453																																					p.G2368C		Atlas-SNP	.											.	COL6A3	608	.	0			c.G7102T						.						67	71	70					2																	238253847		2203	4300	6503	SO:0001583	missense	1293	exon33			TGTTGCCCTTGGG	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.7102G>T	chr2.hg19:g.238253847C>A	ENSP00000295550:p.Gly2368Cys	113.0	0.0		86.0	13.0	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	hg19	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	11.26	1.585032	0.28268	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	D;D;D;D;D;D	0.99637	-6.29;-6.29;-6.29;-6.29;-6.29;-6.29	5.03	5.03	0.67393	.	0.000000	0.51477	D	0.000100	D	0.99792	0.9912	H	0.96861	3.895	0.80722	D	1	D;D;D;D	0.89917	0.993;0.993;0.991;1.0	D;P;P;D	0.97110	0.93;0.889;0.823;1.0	D	0.96833	0.9612	10	0.87932	D	0	.	18.381	0.90451	0.0:1.0:0.0:0.0	.	1761;1761;2162;2368	E9PFQ6;B7ZMJ7;P12111-2;P12111	.;.;.;CO6A3_HUMAN	C	2368;2167;2162;1761;2162;2168	ENSP00000295550:G2368C;ENSP00000315609:G2167C;ENSP00000315873:G2162C;ENSP00000418285:G1761C;ENSP00000386844:G2162C;ENSP00000295546:G2168C	ENSP00000295550:G2368C	G	-	1	0	COL6A3	237918586	1.000000	0.71417	0.991000	0.47740	0.392000	0.30506	4.266000	0.58871	2.315000	0.78130	0.655000	0.94253	GGC	.	.		0.453	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		A	238253847	C	A	238253847	3	1	329	1	0	0	0	0	1	0	0	0	3703	623	22	3	2479	3	COL6A3	2	238253847	Missense_Mutation	SNP	C	TCGA-O8-A75V-01A-11D-A32G-10	7592520	238253847	4945526	15	46052										
FANCD2	2177	hgsc.bcm.edu	37	chr3	10076196	10076196	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	aagaagctctttcagaccctGaggagacacccttcctatcc	7	14	2	4			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr3:10076196G>C	ENST00000419585.1	+	4	410	c.249G>C	c.(247-249)ctG>ctC	p.L83L	FANCD2_ENST00000383807.1_Silent_p.L83L|FANCD2_ENST00000383806.1_Silent_p.L83L|FANCD2_ENST00000287647.3_Silent_p.L83L|FANCD2_ENST00000431693.1_Silent_p.L83L			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2	83	Interaction with FANCE.				DNA repair (GO:0006281)|gamete generation (GO:0007276)|response to gamma radiation (GO:0010332)|synapsis (GO:0007129)	condensed chromosome (GO:0000793)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA polymerase binding (GO:0070182)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	51				OV - Ovarian serous cystadenocarcinoma(96;0.148)		TTCAGACCCTGAGGAGACACC	0.403			"D, Mis, N, F"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.L83L		Atlas-SNP	.	yes	Rec		Fanconi anaemia D2	3	3p26	2177	"Fanconi anemia, complementation group D2"		L	.	FANCD2	253	.	0			c.G249C						.						151	157	155					3																	10076196		2203	4300	6503	SO:0001819	synonymous_variant	2177	exon4	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GACCCTGAGGAGA	AF340183	CCDS2595.1, CCDS33696.1	3p25.3	2014-09-17		2001-10-05	ENSG00000144554	ENSG00000144554		"Fanconi anemia, complementation groups"	3585	protein-coding gene	gene with protein product		613984		FACD, FANCD		7581463, 11239453, 18475298	Standard	XM_005264946		Approved	FAD, FA-D2	uc003buw.3	Q9BXW9	OTTHUMG00000128670	ENST00000419585.1:c.249G>C	chr3.hg19:g.10076196G>C		163.0	0.0		133.0	27.0	NM_001018115	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	Silent	SNP	ENST00000419585.1	hg19	CCDS33696.1																																																																																			.	.		0.403	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339873.1			C	10076196	G	C	10076196	2	2	329	1	0	0	0	0	0	0	0	1	5673	1277	45	4		4	FANCD2	3	10076196	Silent	SNP	G	TCGA-O8-A75V-01A-11D-A32G-10		10076196	187946234	16	46053										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266136	41266136	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	gtgccactaccacagctcctTctctgagtggtaaaggcaat	9	12	1	1	rs121913407		TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr3:41266136T>C	ENST00000349496.5	+	3	413	c.133T>C	c.(133-135)Tct>Cct	p.S45P	CTNNB1_ENST00000396183.3_Missense_Mutation_p.S45P|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S45P|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S45P|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S38P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	45			Missing (in colorectal cancer). {ECO:0000269|PubMed:9065402}.|S -> F (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> P (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S45P(168)|p.A5_A80del(53)|p.S45del(50)|p.S45A(11)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.S45_G48del(1)|p.Q28_Q61del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.S45_L46del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.P44_N51del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.T40_L46del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.S45E(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.S45T(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.T42_K49>Q(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CACAGCTCCTTCTCTGAGTGG	0.502		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S45P	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,carcinoma,0,1	CTNNB1	4904	.	355	Substitution - Missense(181)|Deletion - In frame(149)|Complex - deletion inframe(18)|Unknown(7)	liver(151)|kidney(53)|soft_tissue(47)|large_intestine(37)|adrenal_gland(28)|endometrium(9)|stomach(7)|skin(6)|pituitary(3)|prostate(3)|thyroid(2)|small_intestine(2)|bone(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)	c.T133C						.						84	74	78					3																	41266136		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	GCTCCTTCTCTGA	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.133T>C	chr3.hg19:g.41266136T>C	ENSP00000344456:p.Ser45Pro	169.0	0.0		157.0	48.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.440246	0.83993	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.65903	0.2736	M	0.65677	2.01	0.80722	D	1	D	0.60575	0.988	P	0.62649	0.905	T	0.69083	-0.5239	10	0.87932	D	0	-13.6823	16.3453	0.83126	0.0:0.0:0.0:1.0	.	45	P35222	CTNB1_HUMAN	P	38;45;45;45;45;38;45;45;45	ENSP00000400508:S38P;ENSP00000385604:S45P;ENSP00000412219:S45P;ENSP00000379486:S45P;ENSP00000344456:S45P;ENSP00000411226:S38P;ENSP00000379488:S45P;ENSP00000409302:S45P;ENSP00000401599:S45P	ENSP00000344456:S45P	S	+	1	0	CTNNB1	41241140	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.261000	0.74972	0.533000	0.62120	TCT	.	.		0.502	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266136	T	C	41266136	3	2	329	1	0	0	0	0	1	0	0	0	4018	1783	62	2	139	2	CTNNB1	3	41266136	Missense_Mutation	SNP	T	TCGA-O8-A75V-01A-11D-A32G-10	31189940	41266136	156756294	17	46054										
RAD54L2	23132	hgsc.bcm.edu	37	chr3	51690041	51690041	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	gccagtgttcgtcctgtgcaGtccacccccatccccatgat	8	17	0	1			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr3:51690041G>A	ENST00000409535.2	+	19	3206	c.3081G>A	c.(3079-3081)caG>caA	p.Q1027Q	RAD54L2_ENST00000296477.3_Silent_p.Q721Q	NM_015106.2	NP_055921.2	Q9Y4B4	ARIP4_HUMAN	RAD54-like 2 (S. cerevisiae)	1027						nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|transcription cofactor activity (GO:0003712)			NS(2)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|liver(2)|lung(9)|ovary(4)|skin(2)	31				BRCA - Breast invasive adenocarcinoma(193;0.000102)|Kidney(197;0.000758)|KIRC - Kidney renal clear cell carcinoma(197;0.000896)		GTCCTGTGCAGTCCACCCCCA	0.507																																					p.Q1027Q		Atlas-SNP	.											.	RAD54L2	94	.	0			c.G3081A						.						158	144	148					3																	51690041		2203	4300	6503	SO:0001819	synonymous_variant	23132	exon19			TGTGCAGTCCACC	AB018352	CCDS33765.2	3p21.2	2006-01-17			ENSG00000164080	ENSG00000164080			29123	protein-coding gene	gene with protein product						9872452	Standard	NM_015106		Approved	KIAA0809, SRISNF2L	uc011bdt.2	Q9Y4B4	OTTHUMG00000152936	ENST00000409535.2:c.3081G>A	chr3.hg19:g.51690041G>A		109.0	0.0		72.0	20.0	NM_015106	Q8TB57|Q9BV54	Silent	SNP	ENST00000409535.2	hg19	CCDS33765.2	.	.	.	.	.	.	.	.	.	.	G	9.162	1.019044	0.19355	.	.	ENSG00000164080	ENST00000432863	.	.	.	6.04	4.26	0.50523	.	.	.	.	.	T	0.62036	0.2395	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58651	-0.7599	4	.	.	.	-14.8414	10.7866	0.46409	0.2092:0.0:0.7908:0.0	.	.	.	.	I	856	.	.	V	+	1	0	RAD54L2	51665081	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.253000	0.51469	0.889000	0.36185	0.563000	0.77884	GTC	.	.		0.507	RAD54L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328700.2	NM_015106		A	51690041	G	A	51690041	2	1	329	1	0	0	0	0	0	0	0	1	13009	1020	36	3		3	RAD54L2	3	51690041	Silent	SNP	G	TCGA-O8-A75V-01A-11D-A32G-10	10423905	51690041	146332389	18	46055										
KLF15	28999	hgsc.bcm.edu	37	chr3	126071030	126071030	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	caggagctgggcaaccttgaCattctctggggcttgcccag	13	12	1	1			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr3:126071030C>A	ENST00000296233.3	-	2	966	c.736G>T	c.(736-738)Gtc>Ttc	p.V246F	KLF15_ENST00000509675.1_5'Flank	NM_014079.3	NP_054798.1	Q9UIH9	KLF15_HUMAN	Kruppel-like factor 15	246					cardiac muscle hypertrophy in response to stress (GO:0014898)|cellular response to peptide (GO:1901653)|glial cell differentiation (GO:0010001)|glomerular visceral epithelial cell differentiation (GO:0072112)|glucose transport (GO:0015758)|negative regulation of peptidyl-lysine acetylation (GO:2000757)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|lung(7)|ovary(2)|skin(2)	12				GBM - Glioblastoma multiforme(114;0.147)		GCAACCTTGACATTCTCTGGG	0.622																																					p.V246F		Atlas-SNP	.											.	KLF15	40	.	0			c.G736T						.						36	27	30					3																	126071030		2202	4299	6501	SO:0001583	missense	28999	exon2			CCTTGACATTCTC	AB029254	CCDS3036.1	3q21.3	2013-01-08			ENSG00000163884	ENSG00000163884		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	14536	protein-coding gene	gene with protein product	"kidney-enriched Kruppel-like factor"	606465				10982849	Standard	NM_014079		Approved	KKLF	uc011bkk.1	Q9UIH9	OTTHUMG00000162689	ENST00000296233.3:c.736G>T	chr3.hg19:g.126071030C>A	ENSP00000296233:p.Val246Phe	137.0	0.0		141.0	38.0	NM_014079		Missense_Mutation	SNP	ENST00000296233.3	hg19	CCDS3036.1	.	.	.	.	.	.	.	.	.	.	C	15.42	2.827128	0.50739	.	.	ENSG00000163884	ENST00000296233	T	0.08546	3.08	4.44	2.62	0.31277	.	0.152058	0.56097	D	0.000024	T	0.09468	0.0233	L	0.50333	1.59	0.40588	D	0.981462	P	0.50272	0.933	P	0.46479	0.518	T	0.15122	-1.0448	10	0.38643	T	0.18	.	5.2394	0.15464	0.0:0.6723:0.0:0.3277	.	246	Q9UIH9	KLF15_HUMAN	F	246	ENSP00000296233:V246F	ENSP00000296233:V246F	V	-	1	0	KLF15	127553720	0.999000	0.42202	0.845000	0.33349	0.937000	0.57800	1.717000	0.37991	1.177000	0.42855	0.491000	0.48974	GTC	.	.		0.622	KLF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370096.1	NM_014079		A	126071030	C	A	126071030	3	1	329	1	0	0	0	0	1	0	0	0	8352	478	17	3	522	3	KLF15	3	126071030	Missense_Mutation	SNP	C	TCGA-O8-A75V-01A-11D-A32G-10	74380989	126071030	71951400	19	46056										
TF	7018	hgsc.bcm.edu	37	chr3	133494329	133494330	+	Frame_Shift_Del	DEL	GC	GC	-													0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	aatgaaaaagactatgagttGctgtgccttgatggtaccag							TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr3:133494329_133494330delGC	ENST00000402696.3	+	15	2225_2226	c.1740_1741delGC	c.(1738-1743)ttgctgfs	p.LL580fs	TF_ENST00000264998.3_Frame_Shift_Del_p.LL453fs	NM_001063.3	NP_001054	P02787	TRFE_HUMAN	transferrin	580	Transferrin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00741}.				blood coagulation (GO:0007596)|cellular iron ion homeostasis (GO:0006879)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|retina homeostasis (GO:0001895)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basal part of cell (GO:0045178)|basal plasma membrane (GO:0009925)|blood microparticle (GO:0072562)|cell surface (GO:0009986)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|secretory granule lumen (GO:0034774)|vesicle (GO:0031982)	ferric iron binding (GO:0008199)			NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(7)|large_intestine(13)|liver(2)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49					Aluminium(DB01370)|Bismuth Subsalicylate(DB01294)|Gallium nitrate(DB05260)|Iron Dextran(DB00893)	ACTATGAGTTGCTGTGCCTTGA	0.51																																					p.580_580del		Pindel	.											.	TF	116	.	0			c.1739_1740del						.																																			SO:0001589	frameshift_variant	7018	exon15			.		CCDS3080.1	3q21	2012-10-02			ENSG00000091513	ENSG00000091513			11740	protein-coding gene	gene with protein product		190000				6585826	Standard	NM_001063		Approved	PRO1557, PRO2086	uc003epv.2	P02787	OTTHUMG00000150356	ENST00000402696.3:c.1740_1741delGC	chr3.hg19:g.133494329_133494330delGC	ENSP00000385834:p.Leu580fs	63.0	0.0		59.0	10.0	NM_001063	O43890|Q1HBA5|Q9NQB8|Q9UHV0	Frame_Shift_Del	DEL	ENST00000402696.3	hg19	CCDS3080.1																																																																																			.	.		0.51	TF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317775.1	NM_001063		-	133494330	GC	-	133494329	7	5	329	1	0	1	0	1	0	0	0	0	15800	1310	46	0	1798	0	TF	3	133494329	Frame_Shift_Del	DEL	GC	TCGA-O8-A75V-01A-11D-A32G-10	7423299	133494329	64528101	20	46057										
CCDC96	257236	hgsc.bcm.edu	37	chr4	7043534	7043534	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	ctgcttcagctgaatgttctCcagccgcacggcgctcatct	9	15	4	1			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr4:7043534C>T	ENST00000310085.4	-	1	1194	c.1132G>A	c.(1132-1134)Gag>Aag	p.E378K	TADA2B_ENST00000512388.1_5'Flank|TADA2B_ENST00000310074.7_5'Flank|RP11-367J11.2_ENST00000500031.1_RNA	NM_153376.2	NP_699207.1	Q2M329	CCD96_HUMAN	coiled-coil domain containing 96	378										endometrium(3)|kidney(1)|large_intestine(3)|lung(2)|skin(1)|urinary_tract(1)	11						TGAATGTTCTCCAGCCGCACG	0.572																																					p.E378K		Atlas-SNP	.											.	CCDC96	34	.	0			c.G1132A						.						76	82	80					4																	7043534		2203	4300	6503	SO:0001583	missense	257236	exon1			TGTTCTCCAGCCG	AK075056	CCDS3395.1	4p16.1	2008-02-05			ENSG00000173013	ENSG00000173013			26900	protein-coding gene	gene with protein product							Standard	NM_153376		Approved	FLJ90575	uc003gjv.2	Q2M329	OTTHUMG00000125511	ENST00000310085.4:c.1132G>A	chr4.hg19:g.7043534C>T	ENSP00000309285:p.Glu378Lys	93.0	0.0		81.0	18.0	NM_153376	Q8N2I7	Missense_Mutation	SNP	ENST00000310085.4	hg19	CCDS3395.1	.	.	.	.	.	.	.	.	.	.	C	15.81	2.942752	0.53079	.	.	ENSG00000173013	ENST00000310085	T	0.41758	0.99	3.98	3.98	0.46160	.	0.182364	0.35096	N	0.003448	T	0.48943	0.1528	L	0.28344	0.845	0.32848	D	0.506269	D	0.76494	0.999	D	0.74674	0.984	T	0.55023	-0.8205	10	0.23891	T	0.37	-23.9438	15.8476	0.78903	0.0:1.0:0.0:0.0	.	378	Q2M329	CCD96_HUMAN	K	378	ENSP00000309285:E378K	ENSP00000309285:E378K	E	-	1	0	CCDC96	7094435	0.999000	0.42202	0.999000	0.59377	0.634000	0.38068	4.307000	0.59123	2.068000	0.61886	0.462000	0.41574	GAG	.	.		0.572	CCDC96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246838.1	NM_153376		T	7043534	C	T	7043534	3	4	329	1	0	0	0	0	1	0	0	0	2876	864	30	3	539	3	CCDC96	4	7043534	Missense_Mutation	SNP	C	TCGA-O8-A75V-01A-11D-A32G-10		7043534	184110742	21	46058										
SORCS2	57537	hgsc.bcm.edu	37	chr4	7725465	7725465	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	taccaggtagaccttggggaCggcttcaaggccatgtacgt	13	10	1	1	rs373781482		TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr4:7725465C>T	ENST00000507866.2	+	19	2575	c.2466C>T	c.(2464-2466)gaC>gaT	p.D822D	SORCS2_ENST00000329016.9_Silent_p.D650D	NM_020777.2	NP_065828.2	Q96PQ0	SORC2_HUMAN	sortilin-related VPS10 domain containing receptor 2	822	PKD. {ECO:0000255|PROSITE- ProRule:PRU00151}.				neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(8)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	42						ACCTTGGGGACGGCTTCAAGG	0.607																																					p.D822D		Atlas-SNP	.											.	SORCS2	98	.	0			c.C2466T						.						157	158	158					4																	7725465		2094	4216	6310	SO:0001819	synonymous_variant	57537	exon19			TGGGGACGGCTTC	AB037750	CCDS47008.1	4p16.1	2008-02-05			ENSG00000184985	ENSG00000184985			16698	protein-coding gene	gene with protein product		606284				11499680	Standard	NM_020777		Approved	KIAA1329	uc003gkb.4	Q96PQ0	OTTHUMG00000159981	ENST00000507866.2:c.2466C>T	chr4.hg19:g.7725465C>T		68.0	0.0		50.0	17.0	NM_020777	Q9P2L7	Silent	SNP	ENST00000507866.2	hg19	CCDS47008.1																																																																																			.	.		0.607	SORCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358685.4	NM_020777		T	7725465	C	T	7725465	2	4	329	1	0	0	0	0	0	0	0	1	14946	535	19	1		1	SORCS2	4	7725465	Silent	SNP	C	TCGA-O8-A75V-01A-11D-A32G-10	681931	7725465	183428811	22	46059										
CXCL2	2920	hgsc.bcm.edu	37	chr4	74964377	74964377	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	gatgcggggttgagacaagcTttctgcccattcttgagtgt	13	8	2	2			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr4:74964377T>C	ENST00000508487.2	-	3	421	c.249A>G	c.(247-249)aaA>aaG	p.K83K	CXCL2_ENST00000296031.4_5'UTR	NM_002089.3	NP_002080.1	P19875	CXCL2_HUMAN	chemokine (C-X-C motif) ligand 2	83					cell chemotaxis (GO:0060326)|chemotaxis (GO:0006935)|immune response (GO:0006955)|inflammatory response (GO:0006954)|response to molecule of bacterial origin (GO:0002237)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)			lung(1)	1	Breast(15;0.00612)		all cancers(17;0.00317)|Lung(101;0.196)			TGAGACAAGCTTTCTGCCCAT	0.512																																					p.K83K		Atlas-SNP	.											.	CXCL2	6	.	0			c.A249G						.						129	125	127					4																	74964377		2203	4300	6503	SO:0001819	synonymous_variant	2920	exon3			ACAAGCTTTCTGC	M36820	CCDS34008.1	4q13.3	2013-02-25	2002-08-22	2002-08-23		ENSG00000081041		"Endogenous ligands"	4603	protein-coding gene	gene with protein product		139110	"GRO2 oncogene"	GRO2		2217207	Standard	NM_002089		Approved	SCYB2, GROb, MIP-2a, MGSA-b, CINC-2a	uc003hhm.4	P19875		ENST00000508487.2:c.249A>G	chr4.hg19:g.74964377T>C		153.0	0.0		113.0	44.0	NM_002089	Q6FGD6|Q9UPB8	Silent	SNP	ENST00000508487.2	hg19	CCDS34008.1																																																																																			.	.		0.512	CXCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362731.2	NM_002089		C	74964377	T	C	74964377	2	2	329	1	0	0	0	0	0	0	0	1	4087	1606	56	2		2	CXCL2	4	74964377	Silent	SNP	T	TCGA-O8-A75V-01A-11D-A32G-10	67238912	74964377	116189899	23	46060										
MTHFD2L	441024	hgsc.bcm.edu	37	chr4	75040279	75040279	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	caagcatatccagaaagaaaTacagcgaggtgtggaatcat	10	7	1	2			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr4:75040279T>C	ENST00000395759.2	+	2	227	c.200T>C	c.(199-201)aTa>aCa	p.I67T	MTHFD2L_ENST00000325278.6_Missense_Mutation_p.I9T|MTHFD2L_ENST00000433372.1_5'UTR|MTHFD2L_ENST00000331145.6_Missense_Mutation_p.I9T	NM_001144978.1	NP_001138450.1	Q9H903	MTD2L_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2-like	67					folic acid-containing compound biosynthetic process (GO:0009396)|histidine biosynthetic process (GO:0000105)|methionine biosynthetic process (GO:0009086)|one-carbon metabolic process (GO:0006730)|purine nucleotide biosynthetic process (GO:0006164)|tetrahydrofolate interconversion (GO:0035999)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	methenyltetrahydrofolate cyclohydrolase activity (GO:0004477)|methylenetetrahydrofolate dehydrogenase (NAD+) activity (GO:0004487)|methylenetetrahydrofolate dehydrogenase (NADP+) activity (GO:0004488)			central_nervous_system(1)|endometrium(1)|lung(4)|ovary(2)	8			all cancers(17;0.0101)|Lung(101;0.196)			CAGAAAGAAATACAGCGAGGT	0.388																																					p.I67T		Atlas-SNP	.											.	MTHFD2L	41	.	0			c.T200C						.						67	68	68					4																	75040279		2203	4300	6503	SO:0001583	missense	441024	exon2			AAGAAATACAGCG	BC065771	CCDS47075.1	4q13.3	2011-08-03			ENSG00000163738	ENSG00000163738			31865	protein-coding gene	gene with protein product		614047				21163947	Standard	NM_001144978		Approved	MGC72244	uc011cbk.2	Q9H903	OTTHUMG00000157135	ENST00000395759.2:c.200T>C	chr4.hg19:g.75040279T>C	ENSP00000379108:p.Ile67Thr	108.0	0.0		78.0	32.0	NM_001144978	Q6P079|Q8N560	Missense_Mutation	SNP	ENST00000395759.2	hg19	CCDS47075.1	.	.	.	.	.	.	.	.	.	.	T	15.86	2.959234	0.53400	.	.	ENSG00000163738	ENST00000395759;ENST00000331145;ENST00000359107;ENST00000325278	T;T;T;T	0.37235	1.63;1.25;1.21;1.63	5.36	4.14	0.48551	Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain (1);	0.214037	0.51477	D	0.000085	T	0.42539	0.1207	M	0.64170	1.965	0.80722	D	1	P;P	0.38863	0.65;0.609	P;B	0.45913	0.497;0.197	T	0.44390	-0.9331	10	0.87932	D	0	-12.5868	9.7124	0.40254	0.0:0.0841:0.0:0.9159	.	67;9	Q9H903;Q9H903-3	MTD2L_HUMAN;.	T	67;9;9;9	ENSP00000379108:I67T;ENSP00000330982:I9T;ENSP00000352012:I9T;ENSP00000321984:I9T	ENSP00000321984:I9T	I	+	2	0	MTHFD2L	75259143	1.000000	0.71417	0.861000	0.33841	0.611000	0.37282	4.404000	0.59735	2.248000	0.74166	0.523000	0.50628	ATA	.	.		0.388	MTHFD2L-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004346		C	75040279	T	C	75040279	3	2	329	1	0	0	0	0	1	0	0	0	9939	1406	49	2	206	2	MTHFD2L	4	75040279	Missense_Mutation	SNP	T	TCGA-O8-A75V-01A-11D-A32G-10	75902	75040279	116113997	24	46061										
FAT1	2195	hgsc.bcm.edu	37	chr4	187539094	187539094	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	gcaaccactttaatctggtaAttgtctctcttttcatggtc	6	10	4	0			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr4:187539094A>G	ENST00000441802.2	-	10	8855	c.8646T>C	c.(8644-8646)aaT>aaC	p.N2882N		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2882	Cadherin 26. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						TAATCTGGTAATTGTCTCTCT	0.418										HNSCC(5;0.00058)																											p.N2882N	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.T8646C						.						184	165	171					4																	187539094		1964	4158	6122	SO:0001819	synonymous_variant	2195	exon10			CTGGTAATTGTCT	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.8646T>C	chr4.hg19:g.187539094A>G		107.0	0.0		95.0	28.0	NM_005245		Silent	SNP	ENST00000441802.2	hg19	CCDS47177.1																																																																																			.	.		0.418	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		G	187539094	A	G	187539094	2	3	329	1	0	0	0	0	0	0	0	1	5697	98	4	2		2	FAT1	4	187539094	Silent	SNP	A	TCGA-O8-A75V-01A-11D-A32G-10	112498815	187539094	3615182	25	46062										
TAS2R1	50834	hgsc.bcm.edu	37	chr5	9630121	9630121	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	atcactgcaagaagaaaataGataatgaggtgagactctag	10	5	2	5			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr5:9630121G>A	ENST00000382492.2	-	1	342	c.24C>T	c.(22-24)atC>atT	p.I8I	CTD-2001E22.1_ENST00000504182.2_RNA	NM_019599.2	NP_062545.1	Q9NYW7	TA2R1_HUMAN	taste receptor, type 2, member 1	8					chemosensory behavior (GO:0007635)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(19)|ovary(3)|prostate(1)|skin(1)|stomach(1)	39						GAAGAAAATAGATAATGAGGT	0.333																																					p.I8I		Atlas-SNP	.											.	TAS2R1	84	.	0			c.C24T						.						41	43	43					5																	9630121		2136	4281	6417	SO:0001819	synonymous_variant	50834	exon1			AAAATAGATAATG	AF227129	CCDS3876.1	5p15	2012-08-22			ENSG00000169777	ENSG00000169777		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14909	protein-coding gene	gene with protein product		604796				10761934, 10766242	Standard	NM_019599		Approved	T2R1, TRB7	uc003jem.1	Q9NYW7	OTTHUMG00000090500	ENST00000382492.2:c.24C>T	chr5.hg19:g.9630121G>A		234.0	1.0		261.0	119.0	NM_019599	Q646G8	Silent	SNP	ENST00000382492.2	hg19	CCDS3876.1																																																																																			.	.		0.333	TAS2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206988.2			A	9630121	G	A	9630121	2	1	329	1	0	0	0	0	0	0	0	1	15580	932	33	3		3	TAS2R1	5	9630121	Silent	SNP	G	TCGA-O8-A75V-01A-11D-A32G-10		9630121	171285139	26	46063										
C5orf33	133686	hgsc.bcm.edu	37	chr5	36219713	36219713	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	cctacctgaactcaccacgaTagaacttctgtaaggcttct	6	13	3	2	rs376035643		TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr5:36219713T>C	ENST00000381937.4	-	5	628	c.629A>G	c.(628-630)tAt>tGt	p.Y210C	NADK2_ENST00000397338.1_Missense_Mutation_p.Y47C|NADK2_ENST00000282512.3_Missense_Mutation_p.Y47C|NADK2-AS1_ENST00000501794.2_RNA|NADK2_ENST00000506945.1_Missense_Mutation_p.Y47C|NADK2_ENST00000514504.1_Missense_Mutation_p.Y210C	NM_001085411.1	NP_001078880.1	Q4G0N4	NAKD2_HUMAN	NAD kinase 2, mitochondrial	210					NAD metabolic process (GO:0019674)|NADP biosynthetic process (GO:0006741)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|NAD+ kinase activity (GO:0003951)|protein homodimerization activity (GO:0042803)										CTCACCACGATAGAACTTCTG	0.348																																					p.Y210C		Atlas-SNP	.											.	NADKD1	47	.	0			c.A629G						.	T	CYS/TYR,CYS/TYR	2,4404	4.2+/-10.8	0,2,2201	114	109	111		629,140	-5	0.9	5		111	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	NADKD1	NM_001085411.1,NM_153013.3	194,194	0,3,6500	CC,CT,TT		0.0116,0.0454,0.0231	probably-damaging,probably-damaging	210/443,47/280	36219713	3,13003	2203	4300	6503	SO:0001583	missense	133686	exon5			CCACGATAGAACT	BC062567	CCDS3917.1, CCDS47197.1, CCDS75235.1	5p13.2	2013-04-30	2013-04-30	2013-04-30	ENSG00000152620	ENSG00000152620			26404	protein-coding gene	gene with protein product	"mitochondrial NAD kinase"	615787	"chromosome 5 open reading frame 33", "NAD kinase domain containing 1"	C5orf33, NADKD1		23616928	Standard	NM_001085411		Approved	FLJ30596, MNADK	uc003jkf.4	Q4G0N4	OTTHUMG00000131105	ENST00000381937.4:c.629A>G	chr5.hg19:g.36219713T>C	ENSP00000371362:p.Tyr210Cys	45.0	0.0		49.0	9.0	NM_001085411	B5MC93|Q6UTX5|Q96NM0	Missense_Mutation	SNP	ENST00000381937.4	hg19	CCDS47197.1	.	.	.	.	.	.	.	.	.	.	T	12.30	1.895917	0.33442	4.54E-4	1.16E-4	ENSG00000152620	ENST00000397338;ENST00000282512;ENST00000381937;ENST00000506945;ENST00000514504;ENST00000511088	T;T;T;T;T;T	0.42900	0.96;0.96;0.98;0.96;0.98;0.96	5.77	-5.04	0.02964	ATP-NAD kinase, PpnK-type, alpha/beta (1);ATP-NAD kinase, PpnK-type (1);	0.703006	0.15269	N	0.271376	T	0.26376	0.0644	L	0.40543	1.245	0.25338	N	0.988972	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.08055	0.002;0.001;0.003	T	0.13522	-1.0506	10	0.41790	T	0.15	-1.0699	7.6134	0.28144	0.0:0.1977:0.4572:0.345	.	47;210;210	B7Z8V7;Q4G0N4-2;Q4G0N4	.;.;NAKD1_HUMAN	C	47;47;210;47;210;47	ENSP00000380499:Y47C;ENSP00000282512:Y47C;ENSP00000371362:Y210C;ENSP00000422250:Y47C;ENSP00000421029:Y210C;ENSP00000426084:Y47C	ENSP00000282512:Y47C	Y	-	2	0	NADKD1	36255470	0.997000	0.39634	0.877000	0.34402	0.929000	0.56500	0.482000	0.22276	-0.748000	0.04753	-0.321000	0.08615	TAT	.	.		0.348	NADK2-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367541.1	NM_153013		C	36219713	T	C	36219713	3	2	329	1	0	0	0	0	1	0	0	0	2294	1406	49	2	731	2	C5orf33	5	36219713	Missense_Mutation	SNP	T	TCGA-O8-A75V-01A-11D-A32G-10	26589592	36219713	144695547	27	46064										
ZNF366	167465	hgsc.bcm.edu	37	chr5	71756953	71756953	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	ggtcgatcatctgagagtcaTacttggggcgcgggggctgc	17	9	3	1			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr5:71756953T>C	ENST00000318442.5	-	2	861	c.371A>G	c.(370-372)tAt>tGt	p.Y124C		NM_152625.1	NP_689838.1	Q8N895	ZN366_HUMAN	zinc finger protein 366	124					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|estrogen receptor binding (GO:0030331)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	35		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)		CTGAGAGTCATACTTGGGGCG	0.587																																					p.Y124C		Atlas-SNP	.											.	ZNF366	108	.	0			c.A371G						.						147	166	160					5																	71756953		2203	4300	6503	SO:0001583	missense	167465	exon2			GAGTCATACTTGG	AK097115	CCDS4015.1	5q13.1	2013-01-08			ENSG00000178175	ENSG00000178175		"Zinc fingers, C2H2-type"	18316	protein-coding gene	gene with protein product		610159					Standard	NM_152625		Approved	FLJ39796	uc003kce.1	Q8N895	OTTHUMG00000100965	ENST00000318442.5:c.371A>G	chr5.hg19:g.71756953T>C	ENSP00000313158:p.Tyr124Cys	163.0	0.0		218.0	56.0	NM_152625	Q5HYI9|Q7RTV4	Missense_Mutation	SNP	ENST00000318442.5	hg19	CCDS4015.1	.	.	.	.	.	.	.	.	.	.	T	8.834	0.940543	0.18281	.	.	ENSG00000178175	ENST00000318442	T	0.36699	1.24	5.92	-1.93	0.07594	.	0.874296	0.10129	N	0.712320	T	0.15782	0.0380	N	0.11560	0.145	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.17684	-1.0361	10	0.37606	T	0.19	-5.042	3.5965	0.08008	0.3581:0.2433:0.0:0.3986	.	124	Q8N895	ZN366_HUMAN	C	124	ENSP00000313158:Y124C	ENSP00000313158:Y124C	Y	-	2	0	ZNF366	71792709	0.036000	0.19791	0.009000	0.14445	0.974000	0.67602	0.253000	0.18296	-0.539000	0.06273	0.459000	0.35465	TAT	.	.		0.587	ZNF366-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218574.3			C	71756953	T	C	71756953	3	2	329	1	0	0	0	0	1	0	0	0	17885	1406	49	2	1879	2	ZNF366	5	71756953	Missense_Mutation	SNP	T	TCGA-O8-A75V-01A-11D-A32G-10	35537240	71756953	109158307	28	46065										
THBS4	7060	hgsc.bcm.edu	37	chr5	79351761	79351761	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	gctctacctggactgcatccAggtggattccgttcacaatc	9	13	2	0			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr5:79351761A>G	ENST00000350881.2	+	3	636	c.446A>G	c.(445-447)cAg>cGg	p.Q149R	THBS4_ENST00000511733.1_Missense_Mutation_p.Q58R|CTD-2201I18.1_ENST00000503007.1_RNA	NM_003248.4	NP_003239.2	P35443	TSP4_HUMAN	thrombospondin 4	149	Laminin G-like.				behavioral response to pain (GO:0048266)|endothelial cell-cell adhesion (GO:0071603)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|positive regulation of cell division (GO:0051781)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of tissue remodeling (GO:0034103)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)|tissue remodeling (GO:0048771)	basement membrane (GO:0005604)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)|integrin binding (GO:0005178)			breast(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|stomach(3)	34		Lung NSC(167;0.00328)|all_lung(232;0.00355)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;6.3e-45)|Epithelial(54;1.77e-39)|all cancers(79;3.2e-34)		GACTGCATCCAGGTGGATTCC	0.587																																					p.Q149R		Atlas-SNP	.											.	THBS4	82	.	0			c.A446G						.						57	62	60					5																	79351761		2203	4300	6503	SO:0001583	missense	7060	exon3			GCATCCAGGTGGA		CCDS4049.1	5q13	2008-05-15			ENSG00000113296	ENSG00000113296			11788	protein-coding gene	gene with protein product		600715				7852353	Standard	NM_003248		Approved		uc021yaw.1	P35443	OTTHUMG00000108173	ENST00000350881.2:c.446A>G	chr5.hg19:g.79351761A>G	ENSP00000339730:p.Gln149Arg	85.0	0.0		135.0	23.0	NM_003248	B2R909|Q86TG2	Missense_Mutation	SNP	ENST00000350881.2	hg19	CCDS4049.1	.	.	.	.	.	.	.	.	.	.	A	10.40	1.338829	0.24253	.	.	ENSG00000113296	ENST00000350881;ENST00000511733	T;T	0.02067	4.47;4.47	5.93	3.59	0.41128	Concanavalin A-like lectin/glucanase (1);Laminin G, thrombospondin-type, N-terminal (1);	0.196433	0.46758	N	0.000274	T	0.02342	0.0072	L	0.45581	1.43	0.34312	D	0.685576	B	0.02656	0.0	B	0.04013	0.001	T	0.31641	-0.9936	9	.	.	.	-5.7053	5.8409	0.18633	0.7146:0.1413:0.1441:0.0	.	149	P35443	TSP4_HUMAN	R	149;58	ENSP00000339730:Q149R;ENSP00000422298:Q58R	.	Q	+	2	0	THBS4	79387517	1.000000	0.71417	0.884000	0.34674	0.974000	0.67602	3.026000	0.49689	1.069000	0.40788	0.533000	0.62120	CAG	.	.		0.587	THBS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226977.1			G	79351761	A	G	79351761	3	3	329	1	0	0	0	0	1	0	0	0	15871	188	7	2	456	2	THBS4	5	79351761	Missense_Mutation	SNP	A	TCGA-O8-A75V-01A-11D-A32G-10	7594808	79351761	101563499	29	46066										
PCDHB16	57717	hgsc.bcm.edu	37	chr5	140564287	140564287	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	gcggctgtgcaggaggagcaGggcggcctcggtgggccgct	21	11	0	0			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr5:140564287G>T	ENST00000361016.2	+	1	3308	c.2153G>T	c.(2152-2154)aGg>aTg	p.R718M		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	718					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AGGAGGAGCAGGGCGGCCTCG	0.662																																					p.R718M		Atlas-SNP	.											.	PCDHB16	159	.	0			c.G2153T						.						64	75	71					5																	140564287		2200	4296	6496	SO:0001583	missense	57717	exon1			GGAGCAGGGCGGC	AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"Cadherins / Protocadherins : Clustered"	14546	other	protocadherin	"cadherin ME1", "protocadherin-3x", "PCDHbeta 16"	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325	ENST00000361016.2:c.2153G>T	chr5.hg19:g.140564287G>T	ENSP00000354293:p.Arg718Met	88.0	0.0		80.0	45.0	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	hg19	CCDS4251.1	.	.	.	.	.	.	.	.	.	.	g	11.88	1.771170	0.31320	.	.	ENSG00000196963	ENST00000361016	T	0.14022	2.54	3.91	3.04	0.35103	.	0.981373	0.08278	N	0.970377	T	0.29652	0.0740	H	0.96015	3.755	0.09310	N	1	B	0.27416	0.178	B	0.28784	0.094	T	0.40831	-0.9542	10	0.62326	D	0.03	.	5.2203	0.15366	0.1875:0.0:0.6478:0.1647	.	718	Q9NRJ7	PCDBG_HUMAN	M	718	ENSP00000354293:R718M	ENSP00000354293:R718M	R	+	2	0	PCDHB16	140544471	0.184000	0.23200	0.002000	0.10522	0.054000	0.15201	1.391000	0.34475	0.640000	0.30582	-0.346000	0.07831	AGG	.	.		0.662	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957		T	140564287	G	T	140564287	3	4	329	1	0	0	0	0	1	0	0	0	11550	1000	35	3	2155	3	PCDHB16	5	140564287	Missense_Mutation	SNP	G	TCGA-O8-A75V-01A-11D-A32G-10	61212526	140564287	40350973	30	46067										
PCDHB13	56123	hgsc.bcm.edu	37	chr5	140595793	140595793	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	cgttggcctcggtgtcttcgCtcttcctcttttcggtgctc	10	14	3	0			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr5:140595793C>A	ENST00000341948.4	+	1	2285	c.2098C>A	c.(2098-2100)Ctc>Atc	p.L700I		NM_018933.2	NP_061756.1	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13	700					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(4)|lung(24)|ovary(5)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	66			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGTGTCTTCGCTCTTCCTCTT	0.697																																					p.L700I		Atlas-SNP	.											.	PCDHB13	142	.	0			c.C2098A						.						89	94	92					5																	140595793		2201	4293	6494	SO:0001583	missense	56123	exon1			TCTTCGCTCTTCC	AF152492	CCDS4255.1	5q31	2010-01-26			ENSG00000187372	ENSG00000187372		"Cadherins / Protocadherins : Clustered"	8684	other	protocadherin		606339				10380929	Standard	NM_018933		Approved	PCDH-BETA13	uc003lja.1	Q9Y5F0	OTTHUMG00000129615	ENST00000341948.4:c.2098C>A	chr5.hg19:g.140595793C>A	ENSP00000345491:p.Leu700Ile	65.0	0.0		60.0	28.0	NM_018933	A8K9V6	Missense_Mutation	SNP	ENST00000341948.4	hg19	CCDS4255.1	.	.	.	.	.	.	.	.	.	.	-	19.49	3.837698	0.71373	.	.	ENSG00000187372	ENST00000341948;ENST00000430318;ENST00000419217	T	0.28454	1.61	3.5	3.5	0.40072	.	.	.	.	.	T	0.57740	0.2074	M	0.92026	3.265	0.27852	N	0.94069	D	0.89917	1.0	D	0.74674	0.984	T	0.52064	-0.8625	9	0.51188	T	0.08	.	6.2763	0.20983	0.0:0.7031:0.1903:0.1066	.	700	Q9Y5F0	PCDBD_HUMAN	I	700;700;646	ENSP00000345491:L700I	ENSP00000345491:L700I	L	+	1	0	PCDHB13	140575977	0.003000	0.15002	0.996000	0.52242	0.548000	0.35241	0.290000	0.18975	1.688000	0.51068	0.298000	0.19748	CTC	.	.		0.697	PCDHB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251810.1	NM_018933		A	140595793	C	A	140595793	3	1	329	1	0	0	0	0	1	0	0	0	11547	797	28	3	2100	3	PCDHB13	5	140595793	Missense_Mutation	SNP	C	TCGA-O8-A75V-01A-11D-A32G-10	31506	140595793	40319467	31	46068										
GABRG2	2566	hgsc.bcm.edu	37	chr5	161569259	161569259	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	atatcccctgcacactcattGtcgtcctatcctgggtgtct	7	14	2	0			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr5:161569259G>A	ENST00000361925.4	+	7	1079	c.859G>A	c.(859-861)Gtc>Atc	p.V287I	GABRG2_ENST00000414552.2_Missense_Mutation_p.V327I|GABRG2_ENST00000356592.3_Missense_Mutation_p.V287I|GABRG2_ENST00000393933.4_Missense_Mutation_p.V192I			P18507	GBRG2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 2	287					adult behavior (GO:0030534)|cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|post-embryonic development (GO:0009791)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|GABA-A receptor complex (GO:1902711)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(15)|lung(24)|ovary(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	62	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CACACTCATTGTCGTCCTATC	0.438																																					p.V327I		Atlas-SNP	.											.	GABRG2	142	.	0			c.G979A						.						273	230	245					5																	161569259		2203	4300	6503	SO:0001583	missense	2566	exon8			CTCATTGTCGTCC		CCDS4358.1, CCDS4359.1, CCDS47333.1	5q34	2012-06-22			ENSG00000113327	ENSG00000113327		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4087	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma 2"	137164					Standard	NM_198904		Approved		uc010jjc.3	P18507	OTTHUMG00000130350	ENST00000361925.4:c.859G>A	chr5.hg19:g.161569259G>A	ENSP00000354651:p.Val287Ile	168.0	0.0		178.0	39.0	NM_198903	F5HB82|Q6GRL6|Q6PCC3|Q9UDB3|Q9UN15	Missense_Mutation	SNP	ENST00000361925.4	hg19	CCDS4358.1	.	.	.	.	.	.	.	.	.	.	G	35	5.492648	0.96339	.	.	ENSG00000113327	ENST00000356592;ENST00000414552;ENST00000361925;ENST00000393933;ENST00000522053	D;D;D;D;D	0.87887	-2.31;-2.31;-2.31;-2.31;-2.31	5.75	5.75	0.90469	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.92724	0.7687	M	0.69185	2.1	0.80722	D	1	D;P;P	0.60160	0.987;0.944;0.931	D;P;P	0.64410	0.925;0.877;0.805	D	0.92858	0.6303	10	0.87932	D	0	.	19.9447	0.97177	0.0:0.0:1.0:0.0	.	327;287;287	F5HB82;P18507;P18507-2	.;GBRG2_HUMAN;.	I	287;327;287;192;192	ENSP00000349000:V287I;ENSP00000410732:V327I;ENSP00000354651:V287I;ENSP00000377510:V192I;ENSP00000430182:V192I	ENSP00000349000:V287I	V	+	1	0	GABRG2	161501837	1.000000	0.71417	0.156000	0.22583	0.992000	0.81027	9.751000	0.98889	2.719000	0.93026	0.655000	0.94253	GTC	.	.		0.438	GABRG2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252706.1			A	161569259	G	A	161569259	3	1	329	1	0	0	0	0	1	0	0	0	6180	1377	48	3	1009	3	GABRG2	5	161569259	Missense_Mutation	SNP	G	TCGA-O8-A75V-01A-11D-A32G-10	20973466	161569259	19346001	32	46069										
CLTB	1212	hgsc.bcm.edu	37	chr5	175819809	175819809	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	gcgtctgcttcagggacatgAgcaccgagcgcaggcgggac	16	12	2	1			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr5:175819809A>G	ENST00000310418.4	-	6	861	c.656T>C	c.(655-657)cTc>cCc	p.L219P	CLTB_ENST00000345807.2_Missense_Mutation_p.L201P	NM_007097.3	NP_009028.1	P09497	CLCB_HUMAN	clathrin, light chain B	219					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	ciliary membrane (GO:0060170)|clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|trans-Golgi network (GO:0005802)	peptide binding (GO:0042277)|structural molecule activity (GO:0005198)			lung(1)	1	all_cancers(89;0.00522)|Renal(175;0.000269)|Lung NSC(126;0.0105)|all_lung(126;0.0168)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	Kidney(146;0.098)		CAGGGACATGAGCACCGAGCG	0.622																																					p.L219P		Atlas-SNP	.											.	CLTB	17	.	0			c.T656C						.						205	174	184					5																	175819809		2203	4300	6503	SO:0001583	missense	1212	exon6			GACATGAGCACCG	M20470	CCDS4402.1, CCDS4403.1	5q35.2	2010-05-11	2010-05-11		ENSG00000175416	ENSG00000175416			2091	protein-coding gene	gene with protein product		118970	"clathrin, light polypeptide (Lcb)"			7713494	Standard	NM_007097		Approved	Lcb	uc003meh.4	P09497	OTTHUMG00000130662	ENST00000310418.4:c.656T>C	chr5.hg19:g.175819809A>G	ENSP00000309415:p.Leu219Pro	93.0	0.0		133.0	27.0	NM_007097	Q53Y37|Q6FHW1	Missense_Mutation	SNP	ENST00000310418.4	hg19	CCDS4403.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.482485	0.84747	.	.	ENSG00000175416	ENST00000310418;ENST00000345807;ENST00000502877	.	.	.	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	D	0.85146	0.5630	M	0.91249	3.19	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.88794	0.3280	9	0.87932	D	0	.	15.0249	0.71663	1.0:0.0:0.0:0.0	.	201;219	P09497-2;P09497	.;CLCB_HUMAN	P	219;201;121	.	ENSP00000309415:L219P	L	-	2	0	CLTB	175752415	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.307000	0.96226	1.949000	0.56562	0.454000	0.30748	CTC	.	.		0.622	CLTB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253153.1			G	175819809	A	G	175819809	3	3	329	1	0	0	0	0	1	0	0	0	3567	304	11	2	37	2	CLTB	5	175819809	Missense_Mutation	SNP	A	TCGA-O8-A75V-01A-11D-A32G-10	14250550	175819809	5095451	33	46070										
HIVEP1	3096	hgsc.bcm.edu	37	chr6	12122422	12122422	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	ttccagtttgatttaaaaccAgtgggacggagaacaagttc	10	7	0	2			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr6:12122422A>T	ENST00000379388.2	+	4	2726	c.2394A>T	c.(2392-2394)ccA>ccT	p.P798P		NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	798					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				ATTTAAAACCAGTGGGACGGA	0.418																																					p.P798P		Atlas-SNP	.											.	HIVEP1	242	.	0			c.A2394T						.						112	105	107					6																	12122422		1884	4103	5987	SO:0001819	synonymous_variant	3096	exon4			AAAACCAGTGGGA	J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"Zinc fingers, C2H2-type"	4920	protein-coding gene	gene with protein product		194540	"human immunodeficiency virus type I enhancer-binding protein 1", "zinc finger protein 40"	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.2394A>T	chr6.hg19:g.12122422A>T		130.0	0.0		211.0	75.0	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Silent	SNP	ENST00000379388.2	hg19	CCDS43426.1																																																																																			.	.		0.418	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114		T	12122422	A	T	12122422	2	4	329	1	0	0	0	0	0	0	0	1	7195	175	7	4		4	HIVEP1	6	12122422	Silent	SNP	A	TCGA-O8-A75V-01A-11D-A32G-10		12122422	158992645	34	46071										
DEK	7913	hgsc.bcm.edu	37	chr6	18258580	18258580	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	ctgtaaggaagagacttgcaTtgtcaacctctctacttttt	7	9	2	1	rs147997771		TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr6:18258580T>C	ENST00000397239.3	-	3	649	c.202A>G	c.(202-204)Atg>Gtg	p.M68V	DEK_ENST00000244776.7_Intron	NM_003472.3	NP_003463.1	P35659	DEK_HUMAN	DEK proto-oncogene	68					chromatin modification (GO:0016568)|regulation of double-strand break repair (GO:2000779)|regulation of double-strand break repair via nonhomologous end joining (GO:2001032)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	7	Ovarian(93;0.00769)|Breast(50;0.0495)	all_hematologic(90;0.053)	OV - Ovarian serous cystadenocarcinoma(7;0.00291)|all cancers(50;0.031)|Epithelial(50;0.0332)			GAGACTTGCATTGTCAACCTC	0.338			T	NUP214	AML																																p.M68V		Atlas-SNP	.		Dom	yes		6	6p23	7913	DEK oncogene (DNA binding)		L	.	DEK	31	.	0			c.A202G						.	T	,VAL/MET	0,4406		0,0,2203	160	152	155		,202	5.8	1	6	dbSNP_134	155	1,8599	1.2+/-3.3	0,1,4299	no	intron,missense	DEK	NM_001134709.1,NM_003472.3	,21	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	,benign	,68/376	18258580	1,13005	2203	4300	6503	SO:0001583	missense	7913	exon3			CTTGCATTGTCAA	X64229	CCDS34344.1, CCDS47382.1	6p23	2014-06-25	2014-06-25		ENSG00000124795	ENSG00000124795			2768	protein-coding gene	gene with protein product		125264	"DEK oncogene (DNA binding)", "DEK oncogene"			1549122	Standard	NM_003472		Approved	D6S231E	uc003ncr.1	P35659	OTTHUMG00000014319	ENST00000397239.3:c.202A>G	chr6.hg19:g.18258580T>C	ENSP00000380414:p.Met68Val	218.0	0.0		281.0	89.0	NM_003472	B2R6K6|B4DN37|Q5TGV4|Q5TGV5	Missense_Mutation	SNP	ENST00000397239.3	hg19	CCDS34344.1	.	.	.	.	.	.	.	.	.	.	T	15.60	2.880527	0.51801	0.0	1.16E-4	ENSG00000124795	ENST00000397239;ENST00000503715;ENST00000515742	T;T;T	0.43688	1.14;0.94;1.07	5.84	5.84	0.93424	.	0.173402	0.64402	D	0.000009	T	0.31451	0.0797	N	0.16790	0.44	0.80722	D	1	P	0.40332	0.713	P	0.54815	0.761	T	0.21930	-1.0231	10	0.30854	T	0.27	-13.125	14.7839	0.69787	0.0:0.0:0.0:1.0	.	68	P35659	DEK_HUMAN	V	68;1;73	ENSP00000380414:M68V;ENSP00000425399:M1V;ENSP00000423553:M73V	ENSP00000380414:M68V	M	-	1	0	DEK	18366559	1.000000	0.71417	0.992000	0.48379	0.971000	0.66376	4.834000	0.62774	2.220000	0.72140	0.482000	0.46254	ATG	.	T|1.000;C|0.000		0.338	DEK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039962.4			C	18258580	T	C	18258580	3	2	329	1	0	0	0	0	1	0	0	0	4426	1493	52	2	961	2	DEK	6	18258580	Missense_Mutation	SNP	T	TCGA-O8-A75V-01A-11D-A32G-10	6136158	18258580	152856487	35	46072										
TNXB	7148	hgsc.bcm.edu	37	chr6	32064613	32064613	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	cagtcccaggggcagctccgCgtaccacagtcctcgccagt	11	17	0	0			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr6:32064613C>T	ENST00000479795.1	-	3	1157	c.1017G>A	c.(1015-1017)acG>acA	p.T339T	TNXB_ENST00000375247.2_Silent_p.T339T|TNXB_ENST00000375244.3_Silent_p.T339T			P22105	TENX_HUMAN	tenascin XB	339	EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00076}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						GGCAGCTCCGCGTACCACAGT	0.726																																					p.T339T		Atlas-SNP	.											.	TNXB	553	.	0			c.G1017A						.						14	17	16					6																	32064613		2140	4225	6365	SO:0001819	synonymous_variant	7148	exon3			GCTCCGCGTACCA	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000479795.1:c.1017G>A	chr6.hg19:g.32064613C>T		97.0	0.0		104.0	23.0	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Silent	SNP	ENST00000479795.1	hg19																																																																																				.	.		0.726	TNXB-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000357059.1	NM_019105		T	32064613	C	T	32064613	2	4	329	1	0	0	0	0	0	0	0	1	16361	755	27	1		1	TNXB	6	32064613	Silent	SNP	C	TCGA-O8-A75V-01A-11D-A32G-10	13806033	32064613	139050454	36	46073										
DSE	29940	hgsc.bcm.edu	37	chr6	116720771	116720771	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	gtgtgctgtatcctgagaacAttgaagcccgagacatggcc	12	10	0	3			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr6:116720771A>T	ENST00000331677.3	+	3	802	c.358A>T	c.(358-360)Att>Ttt	p.I120F	DSE_ENST00000537543.1_Missense_Mutation_p.I139F|DSE_ENST00000359564.2_Missense_Mutation_p.I120F|DSE_ENST00000540275.1_3'UTR|DSE_ENST00000452085.3_Missense_Mutation_p.I120F			Q9UL01	DSE_HUMAN	dermatan sulfate epimerase	120					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin-glucuronate 5-epimerase activity (GO:0047757)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35		all_cancers(87;0.00019)|all_epithelial(87;0.000416)|Ovarian(999;0.133)|Colorectal(196;0.234)		Epithelial(106;0.00915)|OV - Ovarian serous cystadenocarcinoma(136;0.0149)|GBM - Glioblastoma multiforme(226;0.0189)|all cancers(137;0.0262)		TCCTGAGAACATTGAAGCCCG	0.488																																					p.I120F		Atlas-SNP	.											.	DSE	98	.	0			c.A358T						.						78	79	79					6																	116720771		2203	4300	6503	SO:0001583	missense	29940	exon2			GAGAACATTGAAG	AF098066	CCDS5107.1	6q22	2008-02-05	2007-01-29	2007-01-29	ENSG00000111817	ENSG00000111817	5.1.3.19		21144	protein-coding gene	gene with protein product		605942	"squamous cell carcinoma antigen recognized by T cells 2"	SART2		11920522, 16505484	Standard	NM_001080976		Approved	DSEPI	uc003pws.3	Q9UL01	OTTHUMG00000015434	ENST00000331677.3:c.358A>T	chr6.hg19:g.116720771A>T	ENSP00000332151:p.Ile120Phe	88.0	0.0		78.0	25.0	NM_001080976	Q5R3K6	Missense_Mutation	SNP	ENST00000331677.3	hg19	CCDS5107.1	.	.	.	.	.	.	.	.	.	.	A	14.16	2.453416	0.43531	.	.	ENSG00000111817	ENST00000430252;ENST00000452085;ENST00000537543;ENST00000331677;ENST00000359564	T;T;T;T;T	0.42900	1.83;0.96;0.96;0.96;0.96	5.45	1.6	0.23607	.	0.532258	0.21368	N	0.075689	T	0.11495	0.0280	N	0.22421	0.69	0.28156	N	0.929203	B;B	0.14012	0.009;0.009	B;B	0.20767	0.031;0.009	T	0.23119	-1.0197	10	0.56958	D	0.05	-3.7785	7.777	0.29043	0.6693:0.2628:0.0679:0.0	.	139;120	B7Z765;Q9UL01	.;DSE_HUMAN	F	120;120;139;120;120	ENSP00000397597:I120F;ENSP00000404049:I120F;ENSP00000441152:I139F;ENSP00000332151:I120F;ENSP00000352567:I120F	ENSP00000332151:I120F	I	+	1	0	DSE	116827464	0.997000	0.39634	0.933000	0.37362	0.992000	0.81027	1.663000	0.37429	0.125000	0.18397	0.528000	0.53228	ATT	.	.		0.488	DSE-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041940.2	NM_013352		T	116720771	A	T	116720771	3	4	329	1	0	0	0	0	1	0	0	0	4776	217	8	4	360	4	DSE	6	116720771	Missense_Mutation	SNP	A	TCGA-O8-A75V-01A-11D-A32G-10	84656158	116720771	54394296	37	46074										
IGF2R	3482	hgsc.bcm.edu	37	chr6	160494446	160494446	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	catgctcatctccctggacaAgcagacatgcactctcttct	6	15	4	1			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr6:160494446A>G	ENST00000356956.1	+	34	5040	c.4892A>G	c.(4891-4893)aAg>aGg	p.K1631R		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	1631					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	TCCCTGGACAAGCAGACATGC	0.577																																					p.K1631R		Atlas-SNP	.											.	IGF2R	251	.	0			c.A4892G						.						135	111	119					6																	160494446		2203	4300	6503	SO:0001583	missense	3482	exon34			TGGACAAGCAGAC	J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"CD molecules"	5467	protein-coding gene	gene with protein product	"cation-independent mannose-6 phosphate receptor"	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.4892A>G	chr6.hg19:g.160494446A>G	ENSP00000349437:p.Lys1631Arg	100.0	0.0		88.0	25.0	NM_000876	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	hg19	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	A	16.37	3.105052	0.56291	.	.	ENSG00000197081	ENST00000356956	T	0.02121	4.44	5.3	5.3	0.74995	Mannose-6-phosphate receptor, binding (1);	0.384799	0.29260	N	0.012676	T	0.01558	0.0050	L	0.43152	1.355	0.31838	N	0.623782	B	0.34226	0.443	B	0.42555	0.391	T	0.50110	-0.8866	10	0.36615	T	0.2	-5.7255	9.9754	0.41779	0.9238:0.0:0.0762:0.0	.	1631	P11717	MPRI_HUMAN	R	1631	ENSP00000349437:K1631R	ENSP00000349437:K1631R	K	+	2	0	IGF2R	160414436	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	5.448000	0.66612	2.132000	0.65825	0.459000	0.35465	AAG	.	.		0.577	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876		G	160494446	A	G	160494446	3	3	329	1	0	0	0	0	1	0	0	0	7585	72	3	2	5026	2	IGF2R	6	160494446	Missense_Mutation	SNP	A	TCGA-O8-A75V-01A-11D-A32G-10	43773675	160494446	10620621	38	46075										
IGF2R	3482	hgsc.bcm.edu	37	chr6	160523558	160523558	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	gacgtccttgcagggtgggcTttgacagcgagaatcccggg	16	10	0	2			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr6:160523558T>G	ENST00000356956.1	+	46	6998	c.6850T>G	c.(6850-6852)Ttt>Gtt	p.F2284V	IGF2R_ENST00000475584.1_3'UTR	NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	2284					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	CAGGGTGGGCTTTGACAGCGA	0.642																																					p.F2284V		Atlas-SNP	.											.	IGF2R	251	.	0			c.T6850G						.						60	53	56					6																	160523558		2202	4300	6502	SO:0001583	missense	3482	exon46			GTGGGCTTTGACA	J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"CD molecules"	5467	protein-coding gene	gene with protein product	"cation-independent mannose-6 phosphate receptor"	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.6850T>G	chr6.hg19:g.160523558T>G	ENSP00000349437:p.Phe2284Val	192.0	0.0		158.0	31.0	NM_000876	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	hg19	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	T	8.583	0.882728	0.17467	.	.	ENSG00000197081	ENST00000356956	T	0.08102	3.13	5.34	-0.16	0.13375	.	0.727958	0.13098	N	0.414034	T	0.02193	0.0068	M	0.63428	1.95	0.09310	N	1	B	0.10296	0.003	B	0.14023	0.01	T	0.45483	-0.9258	10	0.15952	T	0.53	-7.7614	4.0838	0.09939	0.1878:0.4092:0.0:0.403	.	2284	P11717	MPRI_HUMAN	V	2284	ENSP00000349437:F2284V	ENSP00000349437:F2284V	F	+	1	0	IGF2R	160443548	0.001000	0.12720	0.010000	0.14722	0.023000	0.10783	0.087000	0.14958	0.342000	0.23796	0.482000	0.46254	TTT	.	.		0.642	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876		G	160523558	T	G	160523558	3	3	329	1	0	0	0	0	1	0	0	0	7585	1609	56	5	7032	5	IGF2R	6	160523558	Missense_Mutation	SNP	T	TCGA-O8-A75V-01A-11D-A32G-10	29112	160523558	10591509	39	46076										
NUDCD3	23386	hgsc.bcm.edu	37	chr7	44425666	44425666	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	ggcagggtcgaatcgctggcCtcggaagggagaaccttcag	16	10	1	1			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr7:44425666C>A	ENST00000355451.7	-	6	1309	c.1030G>T	c.(1030-1032)Ggc>Tgc	p.G344C	NUDCD3_ENST00000460110.1_5'UTR	NM_015332.3	NP_056147.2	Q8IVD9	NUDC3_HUMAN	NudC domain containing 3	344										endometrium(2)|large_intestine(1)|lung(3)|skin(1)	7						AATCGCTGGCCTCGGAAGGGA	0.532																																					p.G344C		Atlas-SNP	.											.	NUDCD3	20	.	0			c.G1030T						.						90	82	85					7																	44425666		2203	4300	6503	SO:0001583	missense	23386	exon6			GCTGGCCTCGGAA	BC003691	CCDS5490.2	7p13-p12	2005-03-18			ENSG00000015676	ENSG00000015676			22208	protein-coding gene	gene with protein product		610296					Standard	NM_015332		Approved	KIAA1068	uc003tkz.3	Q8IVD9	OTTHUMG00000129174	ENST00000355451.7:c.1030G>T	chr7.hg19:g.44425666C>A	ENSP00000347626:p.Gly344Cys	75.0	0.0		66.0	19.0	NM_015332	Q9BTI3|Q9H7W9|Q9UPT4	Missense_Mutation	SNP	ENST00000355451.7	hg19	CCDS5490.2	.	.	.	.	.	.	.	.	.	.	C	32	5.146243	0.94603	.	.	ENSG00000015676	ENST00000355451;ENST00000338427	T	0.66280	-0.2	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	T	0.82157	0.4976	M	0.82823	2.61	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.83601	0.0128	10	0.87932	D	0	-18.37	19.8237	0.96607	0.0:1.0:0.0:0.0	.	344	Q8IVD9	NUDC3_HUMAN	C	344;100	ENSP00000347626:G344C	ENSP00000345922:G100C	G	-	1	0	NUDCD3	44392191	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.507000	0.81676	2.786000	0.95864	0.655000	0.94253	GGC	.	.		0.532	NUDCD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251248.3	NM_015332		A	44425666	C	A	44425666	3	1	329	1	0	0	0	0	1	0	0	0	10733	681	24	3	59	3	NUDCD3	7	44425666	Missense_Mutation	SNP	C	TCGA-O8-A75V-01A-11D-A32G-10		44425666	114712997	40	46077										
ABCB1	5243	hgsc.bcm.edu	37	chr7	87168617	87168617	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	gatcggaaaaccatgtatcgGagccgcttggtgaggatctc	13	9	1	1			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr7:87168617G>T	ENST00000265724.3	-	20	2781	c.2364C>A	c.(2362-2364)ctC>ctA	p.L788L	ABCB1_ENST00000543898.1_Silent_p.L724L	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	788	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				drug transmembrane transport (GO:0006855)|G2/M transition of mitotic cell cycle (GO:0000086)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|stem cell proliferation (GO:0072089)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(14)|kidney(9)|large_intestine(14)|lung(48)|ovary(4)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	111	Esophageal squamous(14;0.00164)				Acebutolol(DB01193)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Adenosine triphosphate(DB00171)|ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Albendazole(DB00518)|Alfentanil(DB00802)|Alitretinoin(DB00523)|Amantadine(DB00915)|Aminohippurate(DB00345)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Amsacrine(DB00276)|Apixaban(DB06605)|Arsenic trioxide(DB01169)|Astemizole(DB00637)|Atazanavir(DB01072)|Atenolol(DB00335)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzocaine(DB01086)|Bepridil(DB01244)|Betamethasone(DB00443)|Biperiden(DB00810)|Boceprevir(DB08873)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Bromocriptine(DB01200)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Canagliflozin(DB08907)|Candesartan(DB00796)|Captopril(DB01197)|Carbamazepine(DB00564)|Carfilzomib(DB08889)|Carvedilol(DB01136)|Caspofungin(DB00520)|Chloroquine(DB00608)|Chlorpromazine(DB00477)|Chlorpropamide(DB00672)|Chlorprothixene(DB01239)|Cilazapril(DB01340)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisplatin(DB00515)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Clofazimine(DB00845)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabigatran etexilate(DB06695)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dipyridamole(DB00975)|Docetaxel(DB01248)|Domperidone(DB01184)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Dronedarone(DB04855)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Etravirine(DB06414)|Ezetimibe(DB00973)|Felodipine(DB01023)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fidaxomicin(DB08874)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluticasone furoate(DB08906)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gemcitabine(DB00441)|Glyburide(DB01016)|Gramicidin D(DB00027)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Imatinib(DB00619)|Imipramine(DB00458)|Indacaterol(DB05039)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketoconazole(DB01026)|Lamivudine(DB00709)|Lamotrigine(DB00555)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lenalidomide(DB00480)|Levetiracetam(DB01202)|Levofloxacin(DB01137)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Liothyronine(DB00279)|Liotrix(DB01583)|Lisinopril(DB00722)|Lomitapide(DB08827)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Mannitol(DB00742)|Maprotiline(DB00934)|Mebendazole(DB00643)|Mefloquine(DB00358)|Megestrol acetate(DB00351)|Meprobamate(DB00371)|Methadone(DB00333)|Methotrexate(DB00563)|Methylprednisolone(DB00959)|Metoprolol(DB00264)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mitomycin(DB00305)|Mitoxantrone(DB01204)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nadolol(DB01203)|Naloxone(DB01183)|Naltrexone(DB00704)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Neostigmine(DB01400)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nizatidine(DB00585)|Norethindrone(DB00717)|Olanzapine(DB00334)|Omeprazole(DB00338)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paroxetine(DB00715)|Pazopanib(DB06589)|Perindopril(DB00790)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Pitavastatin(DB08860)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pravastatin(DB00175)|Prazosin(DB00457)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Progesterone(DB00396)|Promethazine(DB01069)|Propafenone(DB01182)|Propranolol(DB00571)|Protriptyline(DB00344)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reboxetine(DB00234)|Regorafenib(DB08896)|Reserpine(DB00206)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Roxithromycin(DB00778)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Scopolamine(DB00747)|Selegiline(DB01037)|Sertraline(DB01104)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|SOFOSBUVIR(DB08934)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Streptozocin(DB00428)|Sulfinpyrazone(DB01138)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telaprevir(DB05521)|Telmisartan(DB00966)|Temsirolimus(DB06287)|Terazosin(DB01162)|Testosterone(DB00624)|Ticagrelor(DB08816)|Timolol(DB00373)|Tolvaptan(DB06212)|Topotecan(DB01030)|Toremifene(DB00539)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Vecuronium(DB01339)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voacamine(DB04877)|Zidovudine(DB00495)	CCATGTATCGGAGCCGCTTGG	0.527																																					p.L788L		Atlas-SNP	.											.	ABCB1	263	.	0			c.C2364A						.						129	107	114					7																	87168617		2203	4300	6503	SO:0001819	synonymous_variant	5243	exon20			GTATCGGAGCCGC	M14758	CCDS5608.1	7q21.12	2012-03-14	2004-05-12		ENSG00000085563	ENSG00000085563		"CD molecules", "ATP binding cassette transporters / subfamily B"	40	protein-coding gene	gene with protein product	"multidrug resistance protein 1"	171050	"colchicin sensitivity"	PGY1, MDR1, CLCS		3027054	Standard	NM_000927		Approved	P-gp, CD243, GP170, ABC20	uc003uiz.2	P08183	OTTHUMG00000023393	ENST00000265724.3:c.2364C>A	chr7.hg19:g.87168617G>T		29.0	0.0		46.0	10.0	NM_000927	A8K294|B5AK60|Q12755|Q14812	Silent	SNP	ENST00000265724.3	hg19	CCDS5608.1																																																																																			.	.		0.527	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2	NM_000927		T	87168617	G	T	87168617	2	4	329	1	0	0	0	0	0	0	0	1	40	1161	41	3		3	ABCB1	7	87168617	Silent	SNP	G	TCGA-O8-A75V-01A-11D-A32G-10	42742951	87168617	71970046	41	46078										
PEG10	23089	hgsc.bcm.edu	37	chr7	94293280	94293280	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	gttgggcctcagcaaagctgGagcgctcccactacctgatg	12	13	1	1			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr7:94293280G>A	ENST00000482108.1	+	2	891	c.412G>A	c.(412-414)Gag>Aag	p.E138K	PEG10_ENST00000488574.1_Missense_Mutation_p.E138K	NM_001040152.1|NM_001172438.1|NM_001184962.1	NP_001035242.1|NP_001165909.1|NP_001171891.1	Q86TG7	PEG10_HUMAN	paternally expressed 10	138	Necessary for interaction with ALK1.				apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|placenta development (GO:0001890)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(9)|prostate(3)|skin(1)	21	all_cancers(62;8.26e-10)|all_epithelial(64;5.59e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			AGCAAAGCTGGAGCGCTCCCA	0.537																																					p.E214K		Atlas-SNP	.											.	PEG10	36	.	0			c.G640A						.						93	99	97					7																	94293280		2049	4198	6247	SO:0001583	missense	23089	exon2			AAGCTGGAGCGCT	AB049834	CCDS55126.1, CCDS75636.1, CCDS75637.1	7q21	2007-12-07			ENSG00000242265	ENSG00000242265			14005	protein-coding gene	gene with protein product		609810				11318613, 15716091, 16093683	Standard	NM_001172437		Approved	KIAA1051, HB-1, MEF3L, RGAG3, Mar2, Mart2	uc011kie.2	Q86TG7	OTTHUMG00000155578	ENST00000482108.1:c.412G>A	chr7.hg19:g.94293280G>A	ENSP00000417587:p.Glu138Lys	79.0	0.0		62.0	23.0	NM_001172438	Q96A68|Q9UPV1	Missense_Mutation	SNP	ENST00000482108.1	hg19	CCDS55126.1	.	.	.	.	.	.	.	.	.	.	G	11.64	1.698943	0.30142	.	.	ENSG00000242265	ENST00000482108;ENST00000488574	T;T	0.13657	2.57;2.57	4.23	2.16	0.27623	Retrotransposon gag protein (1);	.	.	.	.	T	0.07503	0.0189	N	0.12961	0.28	0.09310	N	0.999994	P;P	0.38300	0.626;0.626	B;B	0.34489	0.184;0.184	T	0.30090	-0.9990	9	0.31617	T	0.26	.	9.8918	0.41294	0.0:0.4088:0.5912:0.0	.	214;138	B4DSP0;Q86TG7	.;PEG10_HUMAN	K	138	ENSP00000417587:E138K;ENSP00000418944:E138K	ENSP00000417587:E138K	E	+	1	0	PEG10	94131216	1.000000	0.71417	0.997000	0.53966	0.982000	0.71751	2.221000	0.42917	1.092000	0.41356	0.555000	0.69702	GAG	.	.		0.537	PEG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340751.1	NM_015068		A	94293280	G	A	94293280	3	1	329	1	0	0	0	0	1	0	0	0	11728	1175	41	3	646	3	PEG10	7	94293280	Missense_Mutation	SNP	G	TCGA-O8-A75V-01A-11D-A32G-10	7124663	94293280	64845383	42	46079										
ATP6V0A4	50617	hgsc.bcm.edu	37	chr7	138394373	138394373	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	ggacaaccatccttaccagtGcagtcgcagggcgtgcagga	13	12	0	0			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr7:138394373G>C	ENST00000310018.2	-	21	2707	c.2425C>G	c.(2425-2427)Cac>Gac	p.H809D	ATP6V0A4_ENST00000393054.1_Missense_Mutation_p.H809D|ATP6V0A4_ENST00000353492.4_Missense_Mutation_p.H809D	NM_020632.2|NM_130840.2	NP_065683.2|NP_570855.2	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a4	809					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|excretion (GO:0007588)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|regulation of pH (GO:0006885)|sensory perception of sound (GO:0007605)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	ATPase binding (GO:0051117)|hydrogen ion transmembrane transporter activity (GO:0015078)			NS(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36						CCTTACCAGTGCAGTCGCAGG	0.547																																					p.H809D		Atlas-SNP	.											.	ATP6V0A4	93	.	0			c.C2425G						.						167	166	166					7																	138394373		2203	4300	6503	SO:0001583	missense	50617	exon20			ACCAGTGCAGTCG	AF245517	CCDS5849.1	7q34	2011-06-09	2006-01-20	2002-05-10	ENSG00000105929	ENSG00000105929		"ATPases / V-type"	866	protein-coding gene	gene with protein product		605239	"ATPase, H+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1B", "ATPase, H+ transporting, lysosomal V0 subunit a isoform 4", "ATPase, H+ transporting, lysosomal V0 subunit A4"	ATP6N1B, ATP6N2, RTA1C		10577919, 10973252	Standard	XM_005250393		Approved	RDRTA2, VPP2, RTADR, a4, Vph1, Stv1	uc003vuf.3	Q9HBG4	OTTHUMG00000157122	ENST00000310018.2:c.2425C>G	chr7.hg19:g.138394373G>C	ENSP00000308122:p.His809Asp	85.0	0.0		67.0	13.0	NM_130841	A4D1R4|A8KA80|Q32M47	Missense_Mutation	SNP	ENST00000310018.2	hg19	CCDS5849.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.857080	0.91433	.	.	ENSG00000105929	ENST00000310018;ENST00000393054;ENST00000353492	D;D;D	0.89270	-2.49;-2.49;-2.49	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	D	0.96784	0.8950	H	0.97131	3.945	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97559	1.0097	10	0.72032	D	0.01	.	19.8636	0.96797	0.0:0.0:1.0:0.0	.	809	Q9HBG4	VPP4_HUMAN	D	809	ENSP00000308122:H809D;ENSP00000376774:H809D;ENSP00000253856:H809D	ENSP00000308122:H809D	H	-	1	0	ATP6V0A4	138044913	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	9.869000	0.99810	2.694000	0.91930	0.655000	0.94253	CAC	.	.		0.547	ATP6V0A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347514.1	NM_020632		C	138394373	G	C	138394373	3	2	329	1	0	0	0	0	1	0	0	0	1170	1319	46	4	105	4	ATP6V0A4	7	138394373	Missense_Mutation	SNP	G	TCGA-O8-A75V-01A-11D-A32G-10	44101093	138394373	20744290	43	46080										
ZNF467	168544	hgsc.bcm.edu	37	chr7	149462853	149462853	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	aagcgcttgccgcactccgcGcacgggtagggccgctcgcc	14	17	0	0			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr7:149462853G>A	ENST00000302017.3	-	5	1151	c.738C>T	c.(736-738)tgC>tgT	p.C246C	ZNF467_ENST00000484747.1_Intron	NM_207336.1	NP_997219.1	Q7Z7K2	ZN467_HUMAN	zinc finger protein 467	246					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|kidney(1)|large_intestine(2)|liver(1)|lung(7)|urinary_tract(1)	13	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CGCACTCCGCGCACGGGTAGG	0.677																																					p.C246C		Atlas-SNP	.											ZNF467,right_lower_lobe,carcinoma,0,1	ZNF467	50	.	0			c.C738T						.						26	21	22					7																	149462853		2203	4300	6503	SO:0001819	synonymous_variant	168544	exon5			CTCCGCGCACGGG	BC029296	CCDS5899.1	7q36.1	2013-01-08			ENSG00000181444	ENSG00000181444		"Zinc fingers, C2H2-type"	23154	protein-coding gene	gene with protein product		614040				12426389	Standard	NM_207336		Approved	EZI, Zfp467	uc003wgd.2	Q7Z7K2	OTTHUMG00000157883	ENST00000302017.3:c.738C>T	chr7.hg19:g.149462853G>A		113.0	1.0		116.0	30.0	NM_207336		Silent	SNP	ENST00000302017.3	hg19	CCDS5899.1																																																																																			.	.		0.677	ZNF467-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349833.1	NM_207336		A	149462853	G	A	149462853	2	1	329	1	0	0	0	0	0	0	0	1	17942	1079	38	1		1	ZNF467	7	149462853	Silent	SNP	G	TCGA-O8-A75V-01A-11D-A32G-10	11068480	149462853	9675810	44	46081										
CYP7B1	9420	hgsc.bcm.edu	37	chr8	65537039	65537039	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	aaggggtcttttcgtaagttCaggaccactccaagataagg	11	8	2	1			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr8:65537039C>A	ENST00000310193.3	-	2	353	c.180G>T	c.(178-180)ctG>ctT	p.L60L		NM_004820.3	NP_004811.1	O75881	CP7B1_HUMAN	cytochrome P450, family 7, subfamily B, polypeptide 1	60					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cell death (GO:0008219)|cholesterol metabolic process (GO:0008203)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|positive regulation of epithelial cell proliferation (GO:0050679)|prostate gland epithelium morphogenesis (GO:0060740)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	25-hydroxycholesterol 7alpha-hydroxylase activity (GO:0033783)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxysterol 7-alpha-hydroxylase activity (GO:0008396)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(11)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28		all_cancers(86;0.217)|Lung NSC(129;0.0521)|all_lung(136;0.0906)|all_epithelial(80;0.215)				TTCGTAAGTTCAGGACCACTC	0.378																																					p.L60L		Atlas-SNP	.											.	CYP7B1	94	.	0			c.G180T						.						137	135	136					8																	65537039		2203	4300	6503	SO:0001819	synonymous_variant	9420	exon2			TAAGTTCAGGACC	AF029403	CCDS6180.1	8q21.3	2008-07-04	2003-01-14		ENSG00000172817	ENSG00000172817		"Cytochrome P450s"	2652	protein-coding gene	gene with protein product		603711	"cytochrome P450, subfamily VIIB (oxysterol 7 alpha-hydroxylase), polypeptide 1", "spastic paraplegia 5A (autosomal recessive)"	SPG5A		9802883, 18252231	Standard	NM_004820		Approved		uc003xvj.2	O75881	OTTHUMG00000164387	ENST00000310193.3:c.180G>T	chr8.hg19:g.65537039C>A		105.0	0.0		212.0	157.0	NM_004820	B2RN07|Q9UNF5	Silent	SNP	ENST00000310193.3	hg19	CCDS6180.1																																																																																			.	.		0.378	CYP7B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378550.1			A	65537039	C	A	65537039	2	1	329	1	0	0	0	0	0	0	0	1	4199	813	29	3		3	CYP7B1	8	65537039	Silent	SNP	C	TCGA-O8-A75V-01A-11D-A32G-10		65537039	80826983	45	46082										
FAM83H	286077	hgsc.bcm.edu	37	chr8	144810754	144810754	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	cagggcataggcgtccatgcGggccagggccgcggccgagg	19	13	0	0			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr8:144810754G>A	ENST00000388913.3	-	5	1002	c.877C>T	c.(877-879)Cgc>Tgc	p.R293C		NM_198488.3	NP_940890	Q6ZRV2	FA83H_HUMAN	family with sequence similarity 83, member H	293					biomineral tissue development (GO:0031214)					central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(12)|pancreas(1)|prostate(3)|urinary_tract(1)	21	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			GCGTCCATGCGGGCCAGGGCC	0.697																																					p.R293C		Atlas-SNP	.											.	FAM83H	68	.	0			c.C877T						.						10	12	11					8																	144810754		1934	4099	6033	SO:0001583	missense	286077	exon5			CCATGCGGGCCAG	AK127960	CCDS6410.2	8q24.3	2014-03-13			ENSG00000180921	ENSG00000180921			24797	protein-coding gene	gene with protein product		611927				18252228	Standard	NM_198488		Approved	FLJ46072	uc003yzk.3	Q6ZRV2	OTTHUMG00000133559	ENST00000388913.3:c.877C>T	chr8.hg19:g.144810754G>A	ENSP00000373565:p.Arg293Cys	55.0	0.0		105.0	34.0	NM_198488	A0JLS2|Q8N4W0	Missense_Mutation	SNP	ENST00000388913.3	hg19	CCDS6410.2	.	.	.	.	.	.	.	.	.	.	g	15.62	2.887816	0.52014	.	.	ENSG00000180921	ENST00000388913	T	0.15603	2.41	4.75	3.8	0.43715	.	0.840786	0.09676	U	0.770482	T	0.21387	0.0515	N	0.24115	0.695	0.37036	D	0.896905	D	0.76494	0.999	P	0.54706	0.759	T	0.10064	-1.0646	10	0.62326	D	0.03	.	10.466	0.44607	0.0:0.0:0.6459:0.3541	.	293	Q6ZRV2	FA83H_HUMAN	C	293	ENSP00000373565:R293C	ENSP00000373565:R293C	R	-	1	0	FAM83H	144882742	1.000000	0.71417	1.000000	0.80357	0.608000	0.37181	2.684000	0.46951	2.326000	0.78906	0.561000	0.74099	CGC	.	.		0.697	FAM83H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257632.2	NM_198488		A	144810754	G	A	144810754	3	1	329	1	0	0	0	0	1	0	0	0	5648	1116	39	1	2666	1	FAM83H	8	144810754	Missense_Mutation	SNP	G	TCGA-O8-A75V-01A-11D-A32G-10	79273715	144810754	1553268	46	46083										
SCRIB	23513	hgsc.bcm.edu	37	chr8	144885835	144885835	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	accttggagatgaagatgccCtcgtctgtggggtcgcgggg	17	9	1	3			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr8:144885835C>T	ENST00000320476.3	-	23	3402	c.3396G>A	c.(3394-3396)gaG>gaA	p.E1132E	SCRIB_ENST00000356994.2_Silent_p.E1132E|SCRIB_ENST00000377533.3_Silent_p.E1051E	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	1132	Interaction with ARHGEF7.|PDZ 4. {ECO:0000255|PROSITE- ProRule:PRU00143}.				activation of Rac GTPase activity (GO:0032863)|apoptotic process involved in morphogenesis (GO:0060561)|astrocyte cell migration (GO:0043615)|asymmetric protein localization (GO:0008105)|auditory receptor cell stereocilium organization (GO:0060088)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cochlear nucleus development (GO:0021747)|establishment of apical/basal cell polarity (GO:0035089)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of mitotic cell cycle (GO:0045930)|neural tube closure (GO:0001843)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of receptor recycling (GO:0001921)|protein localization to adherens junction (GO:0071896)|single organismal cell-cell adhesion (GO:0016337)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle targeting (GO:0016080)|viral process (GO:0016032)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)|Scrib-APC-beta-catenin complex (GO:0034750)				NS(1)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(20)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	42	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			TGAAGATGCCCTCGTCTGTGG	0.697																																					p.E1132E	Pancreas(51;966 1133 10533 14576 29674)	Atlas-SNP	.											.	SCRIB	192	.	0			c.G3396A						.						3	5	4					8																	144885835		1879	3830	5709	SO:0001819	synonymous_variant	23513	exon23			GATGCCCTCGTCT	AY062238	CCDS6411.1, CCDS6412.1	8q24.3	2013-03-05	2013-03-05		ENSG00000180900	ENSG00000180900			30377	protein-coding gene	gene with protein product		607733	"scribbled homolog (Drosophila)"			11027293, 14681682	Standard	NM_182706		Approved	KIAA0147, SCRB1, Vartul	uc003yzo.1	Q14160	OTTHUMG00000165154	ENST00000320476.3:c.3396G>A	chr8.hg19:g.144885835C>T		45.0	0.0		62.0	14.0	NM_015356	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Silent	SNP	ENST00000320476.3	hg19	CCDS6411.1	.	.	.	.	.	.	.	.	.	.	c	0.834	-0.744378	0.03065	.	.	ENSG00000180900	ENST00000526832	.	.	.	4.52	1.12	0.20585	.	.	.	.	.	T	0.51312	0.1667	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39722	-0.9600	4	.	.	.	.	5.1092	0.14800	0.0:0.4824:0.0:0.5176	.	.	.	.	R	128	.	.	G	-	1	0	SCRIB	144957823	0.959000	0.32827	0.993000	0.49108	0.199000	0.23934	0.099000	0.15210	0.460000	0.27045	-0.400000	0.06385	GGG	.	.		0.697	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356		T	144885835	C	T	144885835	2	4	329	1	0	0	0	0	0	0	0	1	13952	680	24	3		3	SCRIB	8	144885835	Silent	SNP	C	TCGA-O8-A75V-01A-11D-A32G-10	75081	144885835	1478187	47	46084										
MFSD3	113655	hgsc.bcm.edu	37	chr8	145735205	145735205	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	ctgctgcccaccttctcgtgGccgcaactctttctgctcct	7	18	3	0			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr8:145735205G>T	ENST00000301327.4	+	1	749	c.489G>T	c.(487-489)tgG>tgT	p.W163C	CTD-2517M22.17_ENST00000580385.1_RNA|RECQL4_ENST00000532237.1_5'Flank	NM_138431.1	NP_612440.1	Q96ES6	MFSD3_HUMAN	major facilitator superfamily domain containing 3	163	Leu-rich.				transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(1)|kidney(1)|lung(4)	8	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			CCTTCTCGTGGCCGCAACTCT	0.726											OREG0019059	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.W163C		Atlas-SNP	.											.	MFSD3	17	.	0			c.G489T						.						7	7	7					8																	145735205		2084	4077	6161	SO:0001583	missense	113655	exon1			CTCGTGGCCGCAA		CCDS6431.1	8q24.3	2005-11-17			ENSG00000167700	ENSG00000167700			25157	protein-coding gene	gene with protein product							Standard	NM_138431		Approved		uc003zdi.1	Q96ES6	OTTHUMG00000165177	ENST00000301327.4:c.489G>T	chr8.hg19:g.145735205G>T	ENSP00000301327:p.Trp163Cys	53.0	0.0	1696	121.0	56.0	NM_138431		Missense_Mutation	SNP	ENST00000301327.4	hg19	CCDS6431.1	.	.	.	.	.	.	.	.	.	.	G	16.71	3.198655	0.58126	.	.	ENSG00000167700	ENST00000301327	T	0.71934	-0.61	5.02	5.02	0.67125	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	D	0.86410	0.5926	M	0.88105	2.93	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89046	0.3452	10	0.87932	D	0	-13.5672	16.1659	0.81754	0.0:0.0:1.0:0.0	.	163	Q96ES6	MFSD3_HUMAN	C	163	ENSP00000301327:W163C	ENSP00000301327:W163C	W	+	3	0	MFSD3	145706013	1.000000	0.71417	0.980000	0.43619	0.032000	0.12392	4.076000	0.57591	2.484000	0.83849	0.561000	0.74099	TGG	.	.		0.726	MFSD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382478.2	NM_138431		T	145735205	G	T	145735205	3	4	329	1	0	0	0	0	1	0	0	0	9541	1212	42	3	491	3	MFSD3	8	145735205	Missense_Mutation	SNP	G	TCGA-O8-A75V-01A-11D-A32G-10	849370	145735205	628817	48	46085										
ZNF16	7564	hgsc.bcm.edu	37	chr8	146157910	146157910	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	tttctgatatttctgcctgtGattccaaatcttcatgaatg	6	8	4	3			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr8:146157910G>T	ENST00000276816.4	-	4	449	c.263C>A	c.(262-264)tCa>tAa	p.S88*	ZNF16_ENST00000394909.2_Nonsense_Mutation_p.S88*	NM_001029976.2	NP_001025147.2	P17020	ZNF16_HUMAN	zinc finger protein 16	88	Necessary for transcription activation.				cell cycle (GO:0007049)|cell division (GO:0051301)|cellular response to sodium dodecyl sulfate (GO:0072707)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell cycle phase transition (GO:1901989)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of kinase activity (GO:0033674)|positive regulation of megakaryocyte differentiation (GO:0045654)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|kidney(4)|large_intestine(5)|lung(9)|ovary(5)|prostate(1)|skin(1)|urinary_tract(1)	29	all_cancers(97;8.72e-12)|all_epithelial(106;1.07e-10)|Lung NSC(106;7.18e-05)|all_lung(105;0.00021)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;0.136)	Epithelial(56;3.45e-38)|all cancers(56;3.04e-33)|BRCA - Breast invasive adenocarcinoma(115;0.0424)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.02)|KIRC - Kidney renal clear cell carcinoma(644;0.0486)		TTCTGCCTGTGATTCCAAATC	0.428																																					p.S88X		Atlas-SNP	.											.	ZNF16	80	.	0			c.C263A						.						108	102	104					8																	146157910		2203	4300	6503	SO:0001587	stop_gained	7564	exon3			GCCTGTGATTCCA	X52340	CCDS6437.1	8q24	2013-01-08	2006-05-10		ENSG00000170631	ENSG00000170631		"Zinc fingers, C2H2-type"	12947	protein-coding gene	gene with protein product		601262	"zinc finger protein 16 (KOX 9)"				Standard	NM_006958		Approved	KOX9	uc003zeu.3	P17020	OTTHUMG00000165253	ENST00000276816.4:c.263C>A	chr8.hg19:g.146157910G>T	ENSP00000276816:p.Ser88*	239.0	0.0		500.0	48.0	NM_006958	B3KXM4|D3DWP2|Q45SH7|Q96FG0|Q9NRA4	Nonsense_Mutation	SNP	ENST00000276816.4	hg19	CCDS6437.1	.	.	.	.	.	.	.	.	.	.	G	13.16	2.153540	0.38021	.	.	ENSG00000170631	ENST00000276816;ENST00000394909;ENST00000532351;ENST00000527811	.	.	.	4.24	2.45	0.29901	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	.	8.0479	0.30559	0.2009:0.0:0.7991:0.0	.	.	.	.	X	88	.	ENSP00000276816:S88X	S	-	2	0	ZNF16	146128714	0.537000	0.26386	0.243000	0.24186	0.525000	0.34531	0.711000	0.25764	0.439000	0.26476	0.563000	0.77884	TCA	.	.		0.428	ZNF16-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000382978.1	NM_006958		T	146157910	G	T	146157910	4	4	329	1	0	0	0	0	0	1	0	0	17753	1294	45	3	1789	3	ZNF16	8	146157910	Nonsense_Mutation	SNP	G	TCGA-O8-A75V-01A-11D-A32G-10	422705	146157910	206112	49	46086										
GAPVD1	26130	hgsc.bcm.edu	37	chr9	128094293	128094293	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	tctgatgatacggatgtcagGgaggtcagttcccgccccag	13	11	3	2			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr9:128094293G>T	ENST00000495955.1	+	14	2552	c.2262G>T	c.(2260-2262)agG>agT	p.R754S	GAPVD1_ENST00000470056.1_Missense_Mutation_p.R754S|GAPVD1_ENST00000265956.4_Missense_Mutation_p.R754S|GAPVD1_ENST00000394105.2_Missense_Mutation_p.R754S|GAPVD1_ENST00000312123.9_Missense_Mutation_p.R733S|GAPVD1_ENST00000394104.2_Missense_Mutation_p.R754S|GAPVD1_ENST00000394083.2_Missense_Mutation_p.R733S|GAPVD1_ENST00000297933.6_Missense_Mutation_p.R754S			Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1	754					endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|regulation of protein transport (GO:0051223)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	GTPase activating protein binding (GO:0032794)|GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						CGGATGTCAGGGAGGTCAGTT	0.532																																					p.R754S		Atlas-SNP	.											.	GAPVD1	124	.	0			c.G2262T						.						113	90	98					9																	128094293		2203	4300	6503	SO:0001583	missense	26130	exon12			TGTCAGGGAGGTC		CCDS65130.1, CCDS65131.1, CCDS65132.1	9q34.11	2008-02-05			ENSG00000165219	ENSG00000165219			23375	protein-coding gene	gene with protein product		611714					Standard	XM_005251901		Approved	DKFZP434C212, KIAA1521	uc004bpr.3	Q14C86	OTTHUMG00000020678	ENST00000495955.1:c.2262G>T	chr9.hg19:g.128094293G>T	ENSP00000419063:p.Arg754Ser	82.0	0.0		72.0	22.0	NM_015635	A8MYK3|B0QZ62|B0QZ63|B0QZ64|Q14C76|Q2Q1W1|Q8ND92|Q8WU86|Q96CZ4|Q9NXQ1|Q9P207|Q9Y4N0	Missense_Mutation	SNP	ENST00000495955.1	hg19		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	22.4|22.4|22.4	4.280191|4.280191|4.280191	0.80692|0.80692|0.80692	.|.|.	.|.|.	ENSG00000165219|ENSG00000165219|ENSG00000165219	ENST00000431329|ENST00000436712|ENST00000470056;ENST00000394105;ENST00000394104;ENST00000265956;ENST00000394083;ENST00000495955;ENST00000467750;ENST00000297933;ENST00000312123	.|.|T;T;T;T;T;T;T;T;T	.|.|0.13657	.|.|2.57;2.57;2.57;2.57;2.57;2.57;2.57;2.57;2.57	6.01|6.01|6.01	6.01|6.01|6.01	0.97437|0.97437|0.97437	.|.|.	.|.|0.000000	.|.|0.85682	.|.|D	.|.|0.000000	T|.|T	0.17831|.|0.17831	0.0428|.|0.0428	N|N|N	0.14661|0.14661|0.14661	0.345|0.345|0.345	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|.|D;D;D;D;D;D	.|.|0.63046	.|.|0.981;0.967;0.981;0.981;0.981;0.992	.|.|D;D;D;D;D;D	.|.|0.71656	.|.|0.962;0.916;0.962;0.962;0.962;0.974	T|.|T	0.13791|.|0.13791	-1.0496|.|-1.0496	5|.|10	.|.|0.12430	.|.|T	.|.|0.62	.|.|.	12.7684|12.7684|12.7684	0.57405|0.57405|0.57405	0.0742:0.0:0.9258:0.0|0.0742:0.0:0.9258:0.0|0.0742:0.0:0.9258:0.0	.|.|.	.|.|754;754;754;733;754;754	.|.|Q14C86-5;Q14C86;Q14C86-3;Q14C86-4;Q14C86-2;Q14C86-6	.|.|.;GAPD1_HUMAN;.;.;.;.	V|X|S	617|591|754;754;754;754;733;754;754;754;733	.|.|ENSP00000419767:R754S;ENSP00000377665:R754S;ENSP00000377664:R754S;ENSP00000265956:R754S;ENSP00000377645:R733S;ENSP00000419063:R754S;ENSP00000418747:R754S;ENSP00000297933:R754S;ENSP00000309582:R733S	.|.|ENSP00000265956:R754S	G|G|R	+|+|+	2|1|3	0|0|2	GAPVD1|GAPVD1|GAPVD1	127134114|127134114|127134114	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.998000|0.998000|0.998000	0.95712|0.95712|0.95712	6.419000|6.419000|6.419000	0.73345|0.73345|0.73345	2.850000|2.850000|2.850000	0.98022|0.98022|0.98022	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	GGG|GGA|AGG	.	.		0.532	GAPVD1-014	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000355644.1			T	128094293	G	T	128094293	3	4	329	1	0	0	0	0	1	0	0	0	6247	1223	43	3	2304	3	GAPVD1	9	128094293	Missense_Mutation	SNP	G	TCGA-O8-A75V-01A-11D-A32G-10		128094293	13119138	50	46087										
TMEM26	219623	hgsc.bcm.edu	37	chr10	63195964	63195964	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	aattcaagaagccataatgaTggaacgatgctaatcagata	8	6	2	3			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr10:63195964T>C	ENST00000399298.3	-	2	602	c.234A>G	c.(232-234)ccA>ccG	p.P78P	TMEM26_ENST00000399293.1_Silent_p.P78P	NM_178505.6	NP_848600.2	Q6ZUK4	TMM26_HUMAN	transmembrane protein 26	78						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	18	Prostate(12;0.0112)					GCCATAATGATGGAACGATGC	0.338																																					p.P78P		Atlas-SNP	.											.	TMEM26	47	.	0			c.A234G						.						69	68	68					10																	63195964		1823	4075	5898	SO:0001819	synonymous_variant	219623	exon2			TAATGATGGAACG	BC042872	CCDS41530.1	10q21.3	2008-10-20			ENSG00000196932	ENSG00000196932			28550	protein-coding gene	gene with protein product						12477932	Standard	NM_178505		Approved	MGC35010, Em:AC068892.1	uc001jlo.2	Q6ZUK4	OTTHUMG00000018293	ENST00000399298.3:c.234A>G	chr10.hg19:g.63195964T>C		56.0	0.0		40.0	12.0	NM_178505	Q6ZVM0|Q8IVN9	Silent	SNP	ENST00000399298.3	hg19	CCDS41530.1																																																																																			.	.		0.338	TMEM26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359121.1	NM_178505		C	63195964	T	C	63195964	2	2	329	1	0	0	0	0	0	0	0	1	16166	1451	51	2		2	TMEM26	10	63195964	Silent	SNP	T	TCGA-O8-A75V-01A-11D-A32G-10		63195964	72338783	51	46088										
C10orf27	219793	hgsc.bcm.edu	37	chr10	72541762	72541764	+	In_Frame_Del	DEL	CTT	CTT	-													0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	ctccttggcttgcgccctgaCttcttctccagtttcagctc							TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr10:72541762_72541764delCTT	ENST00000299290.1	-	4	459_461	c.70_72delAAG	c.(70-72)aagdel	p.K24del	TBATA_ENST00000456372.2_In_Frame_Del_p.K24del|TBATA_ENST00000545575.1_In_Frame_Del_p.K14del	NM_152710.2	NP_689923	Q96M53	TBATA_HUMAN	thymus, brain and testes associated	24					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|nucleus (GO:0005634)											TGCGCCCTGACTTCTTCTCCAGT	0.586																																					p.24_25del		Atlas-INDEL	.											.	.	.	.	0			c.71_73del						.																																			SO:0001651	inframe_deletion	219793	exon4			.	AK057382	CCDS7308.1	10q22.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000166220	ENSG00000166220			23511	protein-coding gene	gene with protein product		612640	"chromosome 10 open reading frame 27"	C10orf27		20937703	Standard	NM_152710		Approved	FLJ32820, spatial	uc001jrj.1	Q96M53	OTTHUMG00000018413	ENST00000299290.1:c.70_72delAAG	chr10.hg19:g.72541765_72541767delCTT	ENSP00000299290:p.Lys24del	70.0	0.0		72.0	10.0	NM_152710	A4QPA8|B2RPQ2|Q5T4G2	In_Frame_Del	DEL	ENST00000299290.1	hg19	CCDS7308.1																																																																																			.	.		0.586	TBATA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048519.1	NM_152710		-	72541764	CTT	-	72541762	7	5	329	1	0	1	0	1	0	0	0	0	1602	564	20	0	1015	0	C10orf27	10	72541762	In_Frame_Del	DEL	CTT	TCGA-O8-A75V-01A-11D-A32G-10	9345798	72541762	62992985	52	46089										
KNDC1	85442	hgsc.bcm.edu	37	chr10	135015133	135015133	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	ggtttcggcctcagaggtccGtaaaagccgagagagcgcag	15	10	1	2	rs368551158		TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr10:135015133G>T	ENST00000304613.3	+	17	3139	c.3118G>T	c.(3118-3120)Gta>Tta	p.V1040L	KNDC1_ENST00000368571.2_Missense_Mutation_p.V975L|KNDC1_ENST00000368572.2_Missense_Mutation_p.V1042L			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	1040					cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		TCAGAGGTCCGTAAAAGCCGA	0.667																																					p.V1040L		Atlas-SNP	.											.	KNDC1	155	.	0			c.G3118T						.						45	53	50					10																	135015133		2203	4300	6503	SO:0001583	missense	85442	exon17			AGGTCCGTAAAAG	AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"RasGEF domain family, member 2"	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.3118G>T	chr10.hg19:g.135015133G>T	ENSP00000304437:p.Val1040Leu	101.0	0.0		112.0	35.0	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	hg19	CCDS7674.1	.	.	.	.	.	.	.	.	.	.	G	13.78	2.337933	0.41398	.	.	ENSG00000171798	ENST00000304613;ENST00000368572;ENST00000368571	T;T;T	0.11495	2.77;2.77;2.77	5.06	-4.93	0.03066	.	0.964186	0.08524	N	0.932960	T	0.08268	0.0206	L	0.51422	1.61	0.09310	N	1	P;B;P	0.35844	0.484;0.023;0.524	B;B;B	0.31390	0.097;0.016;0.129	T	0.21177	-1.0253	10	0.48119	T	0.1	-6.0095	6.3875	0.21569	0.6225:0.2391:0.1383:0.0	.	1040;975;1040	Q76NI1-4;Q76NI1-2;Q76NI1	.;.;VKIND_HUMAN	L	1040;1042;975	ENSP00000304437:V1040L;ENSP00000357561:V1042L;ENSP00000357560:V975L	ENSP00000304437:V1040L	V	+	1	0	KNDC1	134865123	0.000000	0.05858	0.000000	0.03702	0.576000	0.36127	-0.517000	0.06275	-0.891000	0.03940	-0.657000	0.03884	GTA	.	.		0.667	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643		T	135015133	G	T	135015133	3	4	329	1	0	0	0	0	1	0	0	0	8435	1145	40	1	3184	1	KNDC1	10	135015133	Missense_Mutation	SNP	G	TCGA-O8-A75V-01A-11D-A32G-10	62473371	135015133	519614	53	46090										
NAT10	55226	hgsc.bcm.edu	37	chr11	34152419	34152419	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	tcagcagctccgtcaacagaGcgcccagagccaggtcagca	11	15	3	2			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr11:34152419G>A	ENST00000257829.3	+	13	1510	c.1304G>A	c.(1303-1305)aGc>aAc	p.S435N	NAT10_ENST00000527971.1_Intron|NAT10_ENST00000531159.2_Missense_Mutation_p.S363N	NM_024662.2	NP_078938	Q9H0A0	NAT10_HUMAN	N-acetyltransferase 10 (GCN5-related)	435						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|N-acetyltransferase activity (GO:0008080)|poly(A) RNA binding (GO:0044822)			endometrium(4)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	23		Acute lymphoblastic leukemia(5;0.0119)|all_hematologic(20;0.0231)				CGTCAACAGAGCGCCCAGAGC	0.567																																					p.S435N		Atlas-SNP	.											.	NAT10	78	.	0			c.G1304A						.						108	98	102					11																	34152419		2202	4298	6500	SO:0001583	missense	55226	exon13			AACAGAGCGCCCA	AF489535	CCDS7889.1, CCDS44568.1	11p13	2011-11-16	2008-09-24		ENSG00000135372	ENSG00000135372	2.3.1.-		29830	protein-coding gene	gene with protein product		609221	"N-acetyltransferase 10"			14592445, 21177859	Standard	NM_024662		Approved	hALP, FLJ10774, FLJ12179, NET43, KIAA1709	uc001mvk.3	Q9H0A0	OTTHUMG00000166249	ENST00000257829.3:c.1304G>A	chr11.hg19:g.34152419G>A	ENSP00000257829:p.Ser435Asn	58.0	0.0		60.0	16.0	NM_024662	B4DFD5|E7ESU4|E9PMN9|Q86WK5|Q9C0F4|Q9HA61|Q9NVF2	Missense_Mutation	SNP	ENST00000257829.3	hg19	CCDS7889.1	.	.	.	.	.	.	.	.	.	.	G	19.17	3.776677	0.70107	.	.	ENSG00000135372	ENST00000257829;ENST00000531159	T;T	0.34275	1.37;1.37	5.53	5.53	0.82687	Domain of unknown function DUF699, exodeoxyribonuclease V alpha chain (1);	0.000000	0.85682	D	0.000000	T	0.38081	0.1027	L	0.52573	1.65	0.80722	D	1	B	0.20368	0.044	B	0.26614	0.071	T	0.12142	-1.0559	10	0.21540	T	0.41	-17.198	19.8251	0.96614	0.0:0.0:1.0:0.0	.	435	Q9H0A0	NAT10_HUMAN	N	435;363	ENSP00000257829:S435N;ENSP00000433011:S363N	ENSP00000257829:S435N	S	+	2	0	NAT10	34108995	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.689000	0.84165	2.763000	0.94921	0.561000	0.74099	AGC	.	.		0.567	NAT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388693.1	NM_024662		A	34152419	G	A	34152419	3	1	329	1	0	0	0	0	1	0	0	0	10183	971	34	3	1350	3	NAT10	11	34152419	Missense_Mutation	SNP	G	TCGA-O8-A75V-01A-11D-A32G-10		34152419	100854097	54	46091										
BRMS1	25855	hgsc.bcm.edu	37	chr11	66109566	66109566	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	tctgtgtgtgtaggggctcaCcggagctctcctcttctgac	12	12	5	1			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr11:66109566C>A	ENST00000359957.3	-	2	300		c.e2+1		RP11-867G23.12_ENST00000526655.1_RNA|BRMS1_ENST00000425825.2_Splice_Site	NM_015399.3	NP_056214.1	Q9HCU9	BRMS1_HUMAN	breast cancer metastasis suppressor 1						apoptotic process (GO:0006915)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of anoikis (GO:2000210)|positive regulation of protein deacetylation (GO:0090312)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	NF-kappaB binding (GO:0051059)			large_intestine(1)|liver(1)|lung(1)|prostate(1)|skin(1)	5						tAGGGGCTCACCGGAGCTCTC	0.572																																					.	GBM(7;55 307 2662 20856 28942)	Atlas-SNP	.											.	BRMS1	42	.	0			c.139+1G>T						.						116	85	95					11																	66109566		2200	4295	6495	SO:0001630	splice_region_variant	25855	exon3			GGCTCACCGGAGC	AF147350	CCDS8135.1, CCDS44654.1	11q13-q13.2	2008-02-05				ENSG00000174744			17262	protein-coding gene	gene with protein product		606259				10850410	Standard	XM_005273883		Approved	DKFZP564A063	uc001oho.1	Q9HCU9		ENST00000359957.3:c.139+1G>T	chr11.hg19:g.66109566C>A		80.0	0.0		54.0	12.0	NM_015399	Q6IAI2	Splice_Site	SNP	ENST00000359957.3	hg19	CCDS8135.1	.	.	.	.	.	.	.	.	.	.	C	12.79	2.044642	0.36085	.	.	ENSG00000174744	ENST00000425825;ENST00000524699;ENST00000359957;ENST00000530756	.	.	.	4.49	4.49	0.54785	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0486	0.71846	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	BRMS1	65866142	1.000000	0.71417	1.000000	0.80357	0.511000	0.34104	2.406000	0.44557	2.234000	0.73211	0.591000	0.81541	.	.	.		0.572	BRMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392958.2	NM_015399	Intron	A	66109566	C	A	66109566	5	1	329	1	0	0	0	0	0	0	1	0	1518	521	18	3	780	3	BRMS1	11	66109566	Splice_Site	SNP	C	TCGA-O8-A75V-01A-11D-A32G-10	31957147	66109566	68896950	55	46092										
NCAM1	4684	hgsc.bcm.edu	37	chr11	113103884	113103884	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	cacagacaccccctcttcacCatccatcgaccaggtggagc	7	18	2	1			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr11:113103884C>T	ENST00000533760.1	+	12	1753	c.1154C>T	c.(1153-1155)cCa>cTa	p.P385L	NCAM1_ENST00000397957.4_3'UTR|NCAM1_ENST00000316851.7_Missense_Mutation_p.P503L|NCAM1_ENST00000401611.2_Missense_Mutation_p.P512L	NM_001242608.1	NP_001229537.1	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1	513	Ig-like C2-type 4.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		CCCTCTTCACCATCCATCGAC	0.547																																					p.P539L		Atlas-SNP	.											.	NCAM1	372	.	0			c.C1616T						.						67	68	68					11																	113103884		2023	4180	6203	SO:0001583	missense	4684	exon15			CTTCACCATCCAT		CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000533760.1:c.1154C>T	chr11.hg19:g.113103884C>T	ENSP00000473281:p.Pro385Leu	80.0	0.0		78.0	22.0	NM_001242607	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Missense_Mutation	SNP	ENST00000533760.1	hg19		.	.	.	.	.	.	.	.	.	.	C	34	5.293049	0.95546	.	.	ENSG00000149294	ENST00000531044;ENST00000401611;ENST00000316851	T;T	0.79749	-0.58;-1.3	6.06	6.06	0.98353	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	U	0.000000	D	0.90899	0.7140	.	.	.	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.90796	0.4690	9	0.87932	D	0	-15.3726	20.6208	0.99490	0.0:1.0:0.0:0.0	.	513;503;513;503	P13591-5;P13591-1;P13591;P13591-3	.;.;NCAM1_HUMAN;.	L	385;512;503	ENSP00000384055:P512L;ENSP00000318472:P503L	ENSP00000318472:P503L	P	+	2	0	NCAM1	112609094	1.000000	0.71417	0.969000	0.41365	0.995000	0.86356	7.818000	0.86416	2.882000	0.98803	0.655000	0.94253	CCA	.	.		0.547	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394068.2	NM_000615		T	113103884	C	T	113103884	3	4	329	1	0	0	0	0	1	0	0	0	10211	594	21	3	1589	3	NCAM1	11	113103884	Missense_Mutation	SNP	C	TCGA-O8-A75V-01A-11D-A32G-10	46994318	113103884	21902632	56	46093										
NLRX1	79671	hgsc.bcm.edu	37	chr11	119054109	119054109	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	ctgcgagtggagggcgaggtCagggccctcctggagcagct	18	11	1	0			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr11:119054109C>A	ENST00000409109.1	+	10	3476	c.2889C>A	c.(2887-2889)gtC>gtA	p.V963V	PDZD3_ENST00000322712.4_5'Flank|NLRX1_ENST00000409991.1_Silent_p.V963V|NLRX1_ENST00000292199.2_Silent_p.V963V|NLRX1_ENST00000409265.4_Intron|PDZD3_ENST00000525131.1_5'Flank|PDZD3_ENST00000355547.5_5'Flank|PDZD3_ENST00000531114.1_5'Flank|NLRX1_ENST00000525863.1_Intron|PDZD3_ENST00000392817.2_5'Flank	NM_001282144.1	NP_001269073.1	Q86UT6	NLRX1_HUMAN	NLR family member X1	963	LRRCT.|Required for the repression of MAVS- induced interferon signaling.				innate immune response (GO:0045087)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of RIG-I signaling pathway (GO:0039536)|negative regulation of type I interferon production (GO:0032480)|viral process (GO:0016032)	mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)			cervix(1)|endometrium(2)|kidney(2)|lung(10)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	22	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		AGGGCGAGGTCAGGGCCCTCC	0.622																																					p.V963V		Atlas-SNP	.											.	NLRX1	128	.	0			c.C2889A						.						27	29	28					11																	119054109		2200	4295	6495	SO:0001819	synonymous_variant	79671	exon10			CGAGGTCAGGGCC	AB094095	CCDS8416.1	11q23.3	2007-02-07			ENSG00000160703	ENSG00000160703		"Nucleotide-binding domain and leucine rich repeat containing"	29890	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat containing X1", "NOD-like receptor X1", "NLR family, X1"	611947				12766759	Standard	XM_005271669		Approved	NOD9, CLR11.3	uc001pvw.3	Q86UT6	OTTHUMG00000154476	ENST00000409109.1:c.2889C>A	chr11.hg19:g.119054109C>A		31.0	0.0		30.0	6.0	NM_024618	A8K6Q1|B3KPK2|B3KTA2|Q7RTR3|Q96D51|Q9H724	Silent	SNP	ENST00000409109.1	hg19	CCDS8416.1																																																																																			.	.		0.622	NLRX1-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335403.1	NM_170722		A	119054109	C	A	119054109	2	1	329	1	0	0	0	0	0	0	0	1	10494	813	29	3		3	NLRX1	11	119054109	Silent	SNP	C	TCGA-O8-A75V-01A-11D-A32G-10	5950225	119054109	15952407	57	46094										
ST14	6768	hgsc.bcm.edu	37	chr11	130058517	130058517	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	acgagaactccaactccactGagtttgtaagcctggccagc	9	13	0	2			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr11:130058517G>A	ENST00000278742.5	+	3	752	c.334G>A	c.(334-336)Gag>Aag	p.E112K		NM_021978.3	NP_068813.1	Q9Y5Y6	ST14_HUMAN	suppression of tumorigenicity 14 (colon carcinoma)	112	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.				keratinocyte differentiation (GO:0030216)|proteolysis (GO:0006508)	basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|ovary(3)|pancreas(2)|prostate(1)|skin(3)	32	all_hematologic(175;0.0429)	Lung NSC(97;0.000602)|Breast(109;0.000962)|all_lung(97;0.00126)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0183)|Lung(977;0.228)	Urokinase(DB00013)	CAACTCCACTGAGTTTGTAAG	0.567																																					p.E112K		Atlas-SNP	.											.	ST14	82	.	0			c.G334A						.						105	95	98					11																	130058517		2201	4297	6498	SO:0001583	missense	6768	exon3			TCCACTGAGTTTG	AF118224	CCDS8487.1	11q24-q25	2011-08-31	2005-11-19		ENSG00000149418	ENSG00000149418		"Serine peptidases / Transmembrane"	11344	protein-coding gene	gene with protein product	"epithin", "matriptase"	606797		PRSS14		9925927, 10373424	Standard	NM_021978		Approved	SNC19, HAI, MT-SP1, TMPRSS14	uc001qfw.3	Q9Y5Y6	OTTHUMG00000165768	ENST00000278742.5:c.334G>A	chr11.hg19:g.130058517G>A	ENSP00000278742:p.Glu112Lys	60.0	0.0		52.0	10.0	NM_021978	Q9BS01|Q9H3S0|Q9HB36|Q9HCA3	Missense_Mutation	SNP	ENST00000278742.5	hg19	CCDS8487.1	.	.	.	.	.	.	.	.	.	.	G	33	5.243791	0.95272	.	.	ENSG00000149418	ENST00000278742	T	0.48201	0.82	5.54	5.54	0.83059	SEA (1);	0.000000	0.35320	N	0.003292	T	0.70343	0.3213	M	0.80183	2.485	0.80722	D	1	D	0.71674	0.998	D	0.69654	0.965	T	0.73898	-0.3837	10	0.66056	D	0.02	.	17.2464	0.87029	0.0:0.0:1.0:0.0	.	112	Q9Y5Y6	ST14_HUMAN	K	112	ENSP00000278742:E112K	ENSP00000278742:E112K	E	+	1	0	ST14	129563727	1.000000	0.71417	0.926000	0.36857	0.916000	0.54674	5.317000	0.65822	2.594000	0.87642	0.655000	0.94253	GAG	.	.		0.567	ST14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386119.1			A	130058517	G	A	130058517	3	1	329	1	0	0	0	0	1	0	0	0	15226	1291	45	3	344	3	ST14	11	130058517	Missense_Mutation	SNP	G	TCGA-O8-A75V-01A-11D-A32G-10	11004408	130058517	4947999	58	46095										
IGSF9B	22997	hgsc.bcm.edu	37	chr11	133790932	133790932	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	gtgggcaccagtgggtcctcGttctcctcgtccgactggcg	14	14	1	0			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr11:133790932G>A	ENST00000321016.8	-	18	2918	c.2688C>T	c.(2686-2688)aaC>aaT	p.N896N	IGSF9B_ENST00000533871.2_Silent_p.N896N			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	896					homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		GTGGGTCCTCGTTCTCCTCGT	0.647																																					p.N896N		Atlas-SNP	.											.	IGSF9B	290	.	0			c.C2688T						.						75	91	86					11																	133790932		2123	4205	6328	SO:0001819	synonymous_variant	22997	exon18			GTCCTCGTTCTCC	AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.2688C>T	chr11.hg19:g.133790932G>A		46.0	0.0		34.0	10.0	NM_014987	G5EA26	Silent	SNP	ENST00000321016.8	hg19																																																																																				.	.		0.647	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502		A	133790932	G	A	133790932	2	1	329	1	0	0	0	0	0	0	0	1	7615	1136	40	1		1	IGSF9B	11	133790932	Silent	SNP	G	TCGA-O8-A75V-01A-11D-A32G-10	3732415	133790932	1215584	59	46096										
AKAP3	10566	hgsc.bcm.edu	37	chr12	4737115	4737115	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	gcttgagcagaaccttcttcAgtaggatggtggcaatggtt	13	7	2	2			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr12:4737115A>T	ENST00000545990.2	-	5	1477	c.953T>A	c.(952-954)cTg>cAg	p.L318Q	AKAP3_ENST00000228850.1_Missense_Mutation_p.L318Q|RP11-500M8.7_ENST00000536588.1_Intron	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	318					acrosome reaction (GO:0007340)|cellular component movement (GO:0006928)|protein localization (GO:0008104)|single fertilization (GO:0007338)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	acrosomal vesicle (GO:0001669)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	protein kinase A binding (GO:0051018)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						AACCTTCTTCAGTAGGATGGT	0.473																																					p.L318Q		Atlas-SNP	.											.	AKAP3	212	.	0			c.T953A						.						153	134	140					12																	4737115		2203	4300	6503	SO:0001583	missense	10566	exon4			TTCTTCAGTAGGA	U85715	CCDS8531.1	12p13.3	2009-03-12				ENSG00000111254		"A-kinase anchor proteins"	373	protein-coding gene	gene with protein product	"Fibrous Sheath Protein of 95 kDa", "cancer/testis antigen 82"	604689				10334916, 10319321	Standard	NM_001278309		Approved	FSP95, SOB1, AKAP110, CT82	uc001qnb.4	O75969		ENST00000545990.2:c.953T>A	chr12.hg19:g.4737115A>T	ENSP00000440994:p.Leu318Gln	108.0	0.0		120.0	35.0	NM_006422	O75945|Q86X01|Q9UM61	Missense_Mutation	SNP	ENST00000545990.2	hg19	CCDS8531.1	.	.	.	.	.	.	.	.	.	.	A	16.85	3.235330	0.58886	.	.	ENSG00000111254	ENST00000228850;ENST00000545990	T;T	0.15834	2.39;2.39	5.67	5.67	0.87782	A-kinase anchor 110kDa, C-terminal (1);	0.000000	0.49305	D	0.000144	T	0.43478	0.1249	M	0.78801	2.425	0.36697	D	0.879915	D	0.89917	1.0	D	0.91635	0.999	T	0.55256	-0.8169	10	0.87932	D	0	-12.8942	13.7212	0.62728	1.0:0.0:0.0:0.0	.	318	O75969	AKAP3_HUMAN	Q	318	ENSP00000228850:L318Q;ENSP00000440994:L318Q	ENSP00000228850:L318Q	L	-	2	0	AKAP3	4607376	0.770000	0.28543	0.982000	0.44146	0.683000	0.39861	3.704000	0.54815	2.281000	0.76405	0.533000	0.62120	CTG	.	.		0.473	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	NM_006422		T	4737115	A	T	4737115	3	4	329	1	0	0	0	0	1	0	0	0	452	188	7	4	1616	4	AKAP3	12	4737115	Missense_Mutation	SNP	A	TCGA-O8-A75V-01A-11D-A32G-10		4737115	129114780	60	46097										
SLCO1B3	28234	hgsc.bcm.edu	37	chr12	21008043	21008043	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	aaatttccatcactcaaataGaaaggagatttgacatatcc	5	8	2	3			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr12:21008043G>A	ENST00000381545.3	+	4	385	c.166G>A	c.(166-168)Gaa>Aaa	p.E56K	SLCO1B7_ENST00000554957.1_Missense_Mutation_p.E56K|LST3_ENST00000540229.1_Missense_Mutation_p.E56K|SLCO1B3_ENST00000545880.1_3'UTR|SLCO1B3_ENST00000553473.1_Missense_Mutation_p.E56K|LST3_ENST00000381541.3_Missense_Mutation_p.E56K|SLCO1B3_ENST00000261196.2_Missense_Mutation_p.E56K	NM_019844.3	NP_062818.1	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family, member 1B3	56					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	organic anion transmembrane transporter activity (GO:0008514)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(23)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(2)	63	Esophageal squamous(101;0.149)				Atorvastatin(DB01076)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Dabrafenib(DB08912)|Digoxin(DB00390)|Docetaxel(DB01248)|Estradiol(DB00783)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Olmesartan(DB00275)|Ouabain(DB01092)|Paclitaxel(DB01229)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Rosuvastatin(DB01098)|Valsartan(DB00177)	CACTCAAATAGAAAGGAGATT	0.323																																					p.E56K		Atlas-SNP	.											.	SLCO1B3	151	.	0			c.G166A						.						85	80	82					12																	21008043		2203	4297	6500	SO:0001583	missense	28234	exon4			CAAATAGAAAGGA		CCDS8684.1	12p12	2013-05-22	2003-11-25	2003-11-26		ENSG00000111700		"Solute carriers"	10961	protein-coding gene	gene with protein product		605495	"solute carrier family 21 (organic anion transporter), member 8"	SLC21A8			Standard	NM_019844		Approved	OATP8, OATP1B3	uc001rel.4	Q9NPD5	OTTHUMG00000169011	ENST00000381545.3:c.166G>A	chr12.hg19:g.21008043G>A	ENSP00000370956:p.Glu56Lys	143.0	0.0		139.0	33.0	NM_019844	E7EMT8|Q5JAR4	Missense_Mutation	SNP	ENST00000381545.3	hg19	CCDS8684.1	.	.	.	.	.	.	.	.	.	.	G	17.80	3.477973	0.63849	.	.	ENSG00000111700;ENSG00000111700;ENSG00000111700;ENSG00000111700;ENSG00000257046;ENSG00000257046;ENSG00000205754	ENST00000540853;ENST00000261196;ENST00000381545;ENST00000553473;ENST00000381541;ENST00000540229;ENST00000554957	T;T;T;T;T;T;T	0.71222	-0.55;-0.55;-0.55;-0.55;-0.55;-0.55;-0.55	3.76	3.76	0.43208	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.88385	0.6422	H	0.95645	3.7	0.53688	D	0.99997	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.92397	0.5926	10	0.87932	D	0	.	15.7766	0.78224	0.0:0.0:1.0:0.0	.	56;56;56	F5H094;Q5JAR4;Q9NPD5	.;.;SO1B3_HUMAN	K	56	ENSP00000442000:E56K;ENSP00000261196:E56K;ENSP00000370956:E56K;ENSP00000451758:E56K;ENSP00000370952:E56K;ENSP00000441269:E56K;ENSP00000452013:E56K	ENSP00000370952:E56K	E	+	1	0	SLCO1B3;SLCO1B7;RP11-545J16.1	20899310	1.000000	0.71417	0.996000	0.52242	0.219000	0.24729	8.799000	0.91895	1.926000	0.55796	0.460000	0.39030	GAA	.	.		0.323	SLCO1B3-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401936.1	NM_019844		A	21008043	G	A	21008043	3	1	329	1	0	0	0	0	1	0	0	0	14739	943	33	3	172	3	SLCO1B3	12	21008043	Missense_Mutation	SNP	G	TCGA-O8-A75V-01A-11D-A32G-10	16270928	21008043	112843852	61	46098										
TROAP	10024	hgsc.bcm.edu	37	chr12	49723688	49723688	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	aggagagttgtataaggtcaCtggagggttctgggaaacca	15	5	2	1			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr12:49723688C>T	ENST00000257909.3	+	12	1289	c.1213C>T	c.(1213-1215)Ctg>Ttg	p.L405L	TROAP_ENST00000551245.1_Silent_p.L405L|TROAP_ENST00000547923.1_Silent_p.L113L	NM_005480.3	NP_005471.3	Q12815	TROAP_HUMAN	trophinin associated protein	405					cell adhesion (GO:0007155)	cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	32						TATAAGGTCACTGGAGGGTTC	0.567																																					p.L405L		Atlas-SNP	.											.	TROAP	80	.	0			c.C1213T						.						118	118	118					12																	49723688		2203	4300	6503	SO:0001819	synonymous_variant	10024	exon12			AGGTCACTGGAGG	U04810	CCDS8784.1, CCDS41779.1, CCDS61117.1	12q13.12	2012-10-17	2012-10-17		ENSG00000135451	ENSG00000135451			12327	protein-coding gene	gene with protein product	"tastin"	603872				7758945	Standard	NM_005480		Approved	TASTIN	uc001rtx.4	Q12815	OTTHUMG00000169486	ENST00000257909.3:c.1213C>T	chr12.hg19:g.49723688C>T		121.0	0.0		127.0	8.0	NM_005480	F8VSF9|Q6PJU7|Q8N5B2	Silent	SNP	ENST00000257909.3	hg19	CCDS8784.1																																																																																			.	.		0.567	TROAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404300.1	NM_005480		T	49723688	C	T	49723688	2	4	329	1	0	0	0	0	0	0	0	1	16590	564	20	3		3	TROAP	12	49723688	Silent	SNP	C	TCGA-O8-A75V-01A-11D-A32G-10	28715645	49723688	84128207	62	46099										
KRT79	338785	hgsc.bcm.edu	37	chr12	53223841	53223841	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	gctgcaggaagtcaatctccTgggtcaaggtgcccactttg	12	11	3	0			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr12:53223841T>G	ENST00000330553.5	-	4	855	c.821A>C	c.(820-822)cAg>cCg	p.Q274P		NM_175834.2	NP_787028.1	Q5XKE5	K2C79_HUMAN	keratin 79	274	Coil 1B.|Rod.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	enzyme binding (GO:0019899)|structural molecule activity (GO:0005198)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GTCAATCTCCTGGGTCAAGGT	0.542																																					p.Q274P		Atlas-SNP	.											.	KRT79	78	.	0			c.A821C						.						139	113	122					12																	53223841		2203	4300	6503	SO:0001583	missense	338785	exon4			ATCTCCTGGGTCA	AJ564105	CCDS8839.1	12q13.13	2014-02-12	2007-07-03		ENSG00000185640	ENSG00000185640		"-", "Intermediate filaments type II, keratins (basic)"	28930	protein-coding gene	gene with protein product	"keratin 6-like"	611160				11683385	Standard	NM_175834		Approved	K6L, KRT6L	uc001sbb.3	Q5XKE5	OTTHUMG00000169878	ENST00000330553.5:c.821A>C	chr12.hg19:g.53223841T>G	ENSP00000328358:p.Gln274Pro	114.0	0.0		107.0	26.0	NM_175834	Q6P465|Q7Z793	Missense_Mutation	SNP	ENST00000330553.5	hg19	CCDS8839.1	.	.	.	.	.	.	.	.	.	.	T	18.55	3.647889	0.67358	.	.	ENSG00000185640	ENST00000330553	D	0.88975	-2.45	4.54	3.39	0.38822	Filament (1);	0.653695	0.13294	N	0.398792	D	0.87172	0.6111	M	0.64404	1.975	0.32998	D	0.525895	B	0.30542	0.284	B	0.34346	0.18	D	0.88158	0.2855	10	0.87932	D	0	.	8.717	0.34416	0.0:0.0914:0.0:0.9086	.	274	Q5XKE5	K2C79_HUMAN	P	274	ENSP00000328358:Q274P	ENSP00000328358:Q274P	Q	-	2	0	KRT79	51510108	1.000000	0.71417	0.388000	0.26195	0.981000	0.71138	5.601000	0.67606	1.063000	0.40649	0.533000	0.62120	CAG	.	.		0.542	KRT79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406376.1	NM_175834		G	53223841	T	G	53223841	3	3	329	1	0	0	0	0	1	0	0	0	8501	1580	55	5	810	5	KRT79	12	53223841	Missense_Mutation	SNP	T	TCGA-O8-A75V-01A-11D-A32G-10	3500153	53223841	80628054	63	46100										
AVIL	10677	hgsc.bcm.edu	37	chr12	58207158	58207158	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	atcctgggaggagtccttccCgatccagaagtggatgtcct	12	11	0	1			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr12:58207158C>G	ENST00000257861.3	-	3	620	c.190G>C	c.(190-192)Ggg>Cgg	p.G64R	RP11-571M6.18_ENST00000602327.1_lincRNA|AVIL_ENST00000537081.1_Missense_Mutation_p.G57R	NM_006576.3	NP_006567.3	O75366	AVIL_HUMAN	advillin	64	Core. {ECO:0000250}.				actin filament capping (GO:0051693)|cilium morphogenesis (GO:0060271)|cytoskeleton organization (GO:0007010)|nervous system development (GO:0007399)|positive regulation of neuron projection development (GO:0010976)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)	actin binding (GO:0003779)	p.G64W(2)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(9)|ovary(1)|prostate(6)	32	Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)					GAGTCCTTCCCGATCCAGAAG	0.597																																					p.G64R		Atlas-SNP	.											.	AVIL	60	.	2	Substitution - Missense(2)	lung(2)	c.G190C						.						100	90	94					12																	58207158		2203	4300	6503	SO:0001583	missense	10677	exon3			CCTTCCCGATCCA	AF041449	CCDS8959.1	12q13.11	2006-03-30				ENSG00000135407			14188	protein-coding gene	gene with protein product		613397				9664034, 12034507	Standard	NM_006576		Approved	p92, FLJ12386, ADVIL, DOC6	uc001sqj.2	O75366	OTTHUMG00000170461	ENST00000257861.3:c.190G>C	chr12.hg19:g.58207158C>G	ENSP00000257861:p.Gly64Arg	106.0	0.0		65.0	10.0	NM_006576	B2RAU7|Q2NKM9	Missense_Mutation	SNP	ENST00000257861.3	hg19	CCDS8959.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.818955	0.90873	.	.	ENSG00000135407	ENST00000537081;ENST00000257861;ENST00000549994	D;D;D	0.83335	-1.71;-1.71;-1.71	4.73	4.73	0.59995	Gelsolin domain (1);	0.000000	0.85682	D	0.000000	D	0.94991	0.8379	H	0.98738	4.315	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;1.0;1.0	D	0.96959	0.9700	10	0.87932	D	0	-25.3166	16.9725	0.86304	0.0:1.0:0.0:0.0	.	57;64;64	O75366-2;F8VVU1;O75366	.;.;AVIL_HUMAN	R	57;64;64	ENSP00000443207:G57R;ENSP00000257861:G64R;ENSP00000449239:G64R	ENSP00000257861:G64R	G	-	1	0	AVIL	56493425	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	7.504000	0.81646	2.610000	0.88304	0.655000	0.94253	GGG	.	.		0.597	AVIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409276.1	NM_006576		G	58207158	C	G	58207158	3	3	329	1	0	0	0	0	1	0	0	0	1227	652	23	4	2337	4	AVIL	12	58207158	Missense_Mutation	SNP	C	TCGA-O8-A75V-01A-11D-A32G-10	4983317	58207158	75644737	64	46101										
FAM19A2	338811	hgsc.bcm.edu	37	chr12	62148740	62148740	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	tgtttgtgaccgttcttctaTcttgttcttattacagcatc	6	9	4	1			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr12:62148740T>C	ENST00000416284.3	-	3	1756	c.172A>G	c.(172-174)Ata>Gta	p.I58V	FAM19A2_ENST00000551449.1_Intron|FAM19A2_ENST00000551619.1_Missense_Mutation_p.I58V|FAM19A2_ENST00000550003.1_5'UTR	NM_178539.4	NP_848634.1	Q8N3H0	F19A2_HUMAN	family with sequence similarity 19 (chemokine (C-C motif)-like), member A2	58						cytoplasm (GO:0005737)				endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)	15			GBM - Glioblastoma multiforme(1;0.00484)	GBM - Glioblastoma multiforme(3;0.02)		CGTTCTTCTATCTTGTTCTTA	0.483																																					p.I58V		Atlas-SNP	.											.	FAM19A2	38	.	0			c.A172G						.						206	143	164					12																	62148740		2203	4300	6503	SO:0001583	missense	338811	exon3			CTTCTATCTTGTT	AY325115	CCDS8962.1	12q14.1	2012-10-03			ENSG00000198673	ENSG00000198673			21589	protein-coding gene	gene with protein product						15028294	Standard	NM_178539		Approved	TAFA-2	uc001sqw.3	Q8N3H0	OTTHUMG00000170207	ENST00000416284.3:c.172A>G	chr12.hg19:g.62148740T>C	ENSP00000393987:p.Ile58Val	145.0	0.0		130.0	37.0	NM_178539	B3KVV4|Q4G0R9|Q68DK0|Q6GTX6	Missense_Mutation	SNP	ENST00000416284.3	hg19	CCDS8962.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.360113	0.82353	.	.	ENSG00000198673	ENST00000416284;ENST00000551619;ENST00000552075;ENST00000549958;ENST00000548780	.	.	.	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.77665	0.4164	M	0.70903	2.155	0.80722	D	1	D	0.69078	0.997	D	0.80764	0.994	T	0.78324	-0.2248	8	.	.	.	.	15.511	0.75782	0.0:0.0:0.0:1.0	.	58	Q8N3H0	F19A2_HUMAN	V	58;58;59;65;59	.	.	I	-	1	0	FAM19A2	60435007	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.969000	0.87988	2.067000	0.61834	0.456000	0.33151	ATA	.	.		0.483	FAM19A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407967.2	NM_178539		C	62148740	T	C	62148740	3	2	329	1	0	0	0	0	1	0	0	0	5537	1435	50	2	235	2	FAM19A2	12	62148740	Missense_Mutation	SNP	T	TCGA-O8-A75V-01A-11D-A32G-10	3941582	62148740	71703155	65	46102										
FGD6	55785	hgsc.bcm.edu	37	chr12	95603889	95603889	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	taagtcctgtgcatcactgtTggattccatattcaattcac	6	10	3	0			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr12:95603889T>G	ENST00000343958.4	-	2	1394	c.1171A>C	c.(1171-1173)Aac>Cac	p.N391H	FGD6_ENST00000550368.1_5'Flank|FGD6_ENST00000546711.1_Missense_Mutation_p.N391H|FGD6_ENST00000549499.1_Missense_Mutation_p.N391H	NM_018351.3	NP_060821.3	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	391					actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(14)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56						GCATCACTGTTGGATTCCATA	0.338																																					p.N391H		Atlas-SNP	.											.	FGD6	127	.	0			c.A1171C						.						155	154	154					12																	95603889		2203	4300	6503	SO:0001583	missense	55785	exon2			CACTGTTGGATTC	AB037783	CCDS31878.1	12q23.1	2013-01-10				ENSG00000180263		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	21740	protein-coding gene	gene with protein product		613520					Standard	NM_018351		Approved	ZFYVE24, FLJ11183	uc001tdp.4	Q6ZV73	OTTHUMG00000170133	ENST00000343958.4:c.1171A>C	chr12.hg19:g.95603889T>G	ENSP00000344446:p.Asn391His	109.0	0.0		85.0	22.0	NM_018351	Q6ZR53|Q7Z2Z7|Q96D44|Q9NUR8|Q9P2I5	Missense_Mutation	SNP	ENST00000343958.4	hg19	CCDS31878.1	.	.	.	.	.	.	.	.	.	.	T	2.479	-0.320147	0.05386	.	.	ENSG00000180263	ENST00000343958;ENST00000546711;ENST00000549499	T;T;T	0.68025	-0.19;-0.3;-0.21	5.71	1.97	0.26223	.	0.821389	0.10634	N	0.651848	T	0.50735	0.1633	L	0.44542	1.39	0.09310	N	1	P	0.35600	0.511	B	0.31751	0.135	T	0.47142	-0.9140	10	0.49607	T	0.09	-1.4466	1.5446	0.02562	0.1644:0.1649:0.1156:0.5551	.	391	Q6ZV73	FGD6_HUMAN	H	391	ENSP00000344446:N391H;ENSP00000450342:N391H;ENSP00000449005:N391H	ENSP00000344446:N391H	N	-	1	0	FGD6	94128020	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	-0.067000	0.11579	0.412000	0.25729	0.459000	0.35465	AAC	.	.		0.338	FGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407600.1	NM_018351		G	95603889	T	G	95603889	3	3	329	1	0	0	0	0	1	0	0	0	5845	1812	63	5	3201	5	FGD6	12	95603889	Missense_Mutation	SNP	T	TCGA-O8-A75V-01A-11D-A32G-10	33455149	95603889	38248006	66	46103										
DNAH10	196385	hgsc.bcm.edu	37	chr12	124419244	124419244	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	tgtcttatcaagagcaaaccCaaggtgctggttgtggacct	11	9	2	1			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr12:124419244C>T	ENST00000409039.3	+	77	13225	c.13200C>T	c.(13198-13200)ccC>ccT	p.P4400P	RP11-380L11.3_ENST00000602292.1_RNA|CCDC92_ENST00000544798.1_Intron|DNAH10OS_ENST00000514254.2_5'UTR	NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	4400					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		AGAGCAAACCCAAGGTGCTGG	0.537																																					p.P4400P		Atlas-SNP	.											.	DNAH10	888	.	0			c.C13200T						.						65	71	69					12																	124419244		2019	4187	6206	SO:0001819	synonymous_variant	196385	exon77			CAAACCCAAGGTG	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.13200C>T	chr12.hg19:g.124419244C>T		112.0	0.0		105.0	30.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	hg19	CCDS9255.2																																																																																			.	.		0.537	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			T	124419244	C	T	124419244	2	4	329	1	0	0	0	0	0	0	0	1	4600	581	21	3		3	DNAH10	12	124419244	Silent	SNP	C	TCGA-O8-A75V-01A-11D-A32G-10	28815355	124419244	9432651	67	46104										
AKAP11	11215	hgsc.bcm.edu	37	chr13	42876851	42876851	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	ccgtttattctttcattaccAccaagttcttgtatgtcagg	6	10	4	0			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr13:42876851A>T	ENST00000025301.2	+	8	4144	c.3969A>T	c.(3967-3969)ccA>ccT	p.P1323P		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	1323					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2)	56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		TTTCATTACCACCAAGTTCTT	0.398																																					p.P1323P		Atlas-SNP	.											.	AKAP11	146	.	0			c.A3969T						.						102	99	100					13																	42876851		2203	4300	6503	SO:0001819	synonymous_variant	11215	exon8			ATTACCACCAAGT	AB014529	CCDS9383.1	13q	2012-04-17			ENSG00000023516	ENSG00000023516		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	369	protein-coding gene	gene with protein product	"AKAP 220", "A-kinase anchoring protein, 220kDa", "protein kinase A anchoring protein 11", "protein phosphatase 1, regulatory subunit 44"	604696				9734811, 8621616	Standard	NM_016248		Approved	KIAA0629, AKAP220, PRKA11, FLJ11304, DKFZp781I12161, PPP1R44	uc001uys.2	Q9UKA4	OTTHUMG00000016805	ENST00000025301.2:c.3969A>T	chr13.hg19:g.42876851A>T		193.0	0.0		132.0	24.0	NM_016248	O75124|Q9NUK7	Silent	SNP	ENST00000025301.2	hg19	CCDS9383.1																																																																																			.	.		0.398	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248		T	42876851	A	T	42876851	2	4	329	1	0	0	0	0	0	0	0	1	447	146	6	4		4	AKAP11	13	42876851	Silent	SNP	A	TCGA-O8-A75V-01A-11D-A32G-10		42876851	72293027	68	46105										
POU4F1	5457	hgsc.bcm.edu	37	chr13	79175699	79175699	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	ctgcacggcgaagtaggcctCgagggagcgcttctcgggcg	17	12	1	0			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr13:79175699C>T	ENST00000377208.5	-	2	1322	c.1111G>A	c.(1111-1113)Gag>Aag	p.E371K	RNF219-AS1_ENST00000560209.2_RNA|RNF219-AS1_ENST00000430549.2_RNA|RNF219-AS1_ENST00000607205.1_RNA|RNF219-AS1_ENST00000607220.1_RNA|RNF219-AS1_ENST00000607860.1_RNA|RNF219-AS1_ENST00000606376.1_RNA|RP11-52L5.6_ENST00000607269.1_RNA|RNF219-AS1_ENST00000444769.3_RNA|RNF219-AS1_ENST00000560584.2_RNA|RNF219-AS1_ENST00000606429.1_RNA|RNF219-AS1_ENST00000606124.1_RNA	NM_006237.3	NP_006228.3	Q01851	PO4F1_HUMAN	POU class 4 homeobox 1	371					axonogenesis (GO:0007409)|cell migration in hindbrain (GO:0021535)|central nervous system neuron differentiation (GO:0021953)|habenula development (GO:0021986)|innervation (GO:0060384)|mesoderm development (GO:0007498)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron fate specification (GO:0048665)|peripheral nervous system neuron development (GO:0048935)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proprioception involved in equilibrioception (GO:0051355)|regulation of neurogenesis (GO:0050767)|sensory system development (GO:0048880)|suckling behavior (GO:0001967)|synapse assembly (GO:0007416)|transcription from RNA polymerase II promoter (GO:0006366)|trigeminal nerve development (GO:0021559)|ventricular compact myocardium morphogenesis (GO:0003223)	neuron projection (GO:0043005)|nuclear chromatin (GO:0000790)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)			central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(5)|ovary(1)	16		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.129)		AAGTAGGCCTCGAGGGAGCGC	0.637																																					p.E371K	Melanoma(109;347 2166 14574 42843)|Ovarian(81;1394 1854 22417 48351)	Atlas-SNP	.											POU4F1,NS,carcinoma,0,1	POU4F1	43	.	0			c.G1111A						.						49	54	53					13																	79175699		2203	4300	6503	SO:0001583	missense	5457	exon2			AGGCCTCGAGGGA	X64624	CCDS31996.1	13q31.1	2011-06-20	2007-07-13		ENSG00000152192	ENSG00000152192		"Homeoboxes / POU class"	9218	protein-coding gene	gene with protein product		601632	"POU domain class 4, transcription factor 1"	BRN3A		1357630	Standard	NM_006237		Approved	RDC-1	uc001vkv.3	Q01851	OTTHUMG00000017119	ENST00000377208.5:c.1111G>A	chr13.hg19:g.79175699C>T	ENSP00000366413:p.Glu371Lys	51.0	0.0		42.0	8.0	NM_006237	Q14986|Q15318|Q5T227	Missense_Mutation	SNP	ENST00000377208.5	hg19	CCDS31996.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.270368	0.80469	.	.	ENSG00000152192	ENST00000377208	D	0.97575	-4.44	4.35	4.35	0.52113	Homeodomain-related (1);Homeobox (3);POU (1);Homeodomain-like (1);	0.000000	0.85682	U	0.000000	D	0.98018	0.9347	M	0.67625	2.065	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	D	0.99257	1.0889	10	0.87932	D	0	.	16.8947	0.86097	0.0:1.0:0.0:0.0	.	371	Q01851	PO4F1_HUMAN	K	371	ENSP00000366413:E371K	ENSP00000366413:E371K	E	-	1	0	POU4F1	78073700	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	7.622000	0.83099	2.159000	0.67721	0.499000	0.49734	GAG	.	.		0.637	POU4F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045360.3			T	79175699	C	T	79175699	3	4	329	1	0	0	0	0	1	0	0	0	12287	893	31	1	152	1	POU4F1	13	79175699	Missense_Mutation	SNP	C	TCGA-O8-A75V-01A-11D-A32G-10	36298848	79175699	35994179	69	46106										
FANCM	57697	hgsc.bcm.edu	37	chr14	45650881	45650882	+	Frame_Shift_Ins	INS	-	-	A													0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	attctccacttcatgctgtcINSaaaaagcgcagatttcctat							TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr14:45650881_45650882insA	ENST00000267430.5	+	16	4444_4445	c.4359_4360insA	c.(4360-4362)aaafs	p.K1454fs	FANCM_ENST00000555013.1_3'UTR|FANCM_ENST00000542564.2_Frame_Shift_Ins_p.K1428fs	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1454					DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						TTCATGCTGTCAAAAAGCGCAG	0.317								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.V1453fs		Atlas-Indel,Pindel	.											.	FANCM	225	.	0			c.4359_4360insA						.																																			SO:0001589	frameshift_variant	57697	exon16	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	.	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"Fanconi anemia, complementation groups"	23168	protein-coding gene	gene with protein product		609644	"KIAA1596"	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.4364dupA	chr14.hg19:g.45650886_45650886dupA	ENSP00000267430:p.Lys1454fs	148.0	0.0		120.0	32.0	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Frame_Shift_Ins	INS	ENST00000267430.5	hg19	CCDS32070.1																																																																																			.	.		0.317	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		A	45650882	-	A	45650881	7	5	329	1	0	1	1	0	0	0	0	0	5679	813	29	0	4421	0	FANCM	14	45650881	Frame_Shift_Ins	INS	-	TCGA-O8-A75V-01A-11D-A32G-10		45650881	61698659	70	46107										
SLC8A3	6547	hgsc.bcm.edu	37	chr14	70634966	70634966	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	gggtaccagattggcaggatGacaccctccttgcagtccga	12	12	0	2			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr14:70634966G>A	ENST00000381269.2	-	2	927	c.174C>T	c.(172-174)gtC>gtT	p.V58V	SLC8A3_ENST00000528359.1_Silent_p.V58V|SLC8A3_ENST00000356921.2_Silent_p.V58V|SLC8A3_ENST00000534137.1_Silent_p.V58V|SLC8A3_ENST00000357887.3_Silent_p.V58V	NM_058240.2|NM_183002.1	NP_489479.1|NP_892114.1	P57103	NAC3_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 3	58					blood coagulation (GO:0007596)|calcium ion export from cell (GO:1990034)|calcium ion import into cell (GO:1990035)|calcium ion transport into cytosol (GO:0060402)|cell communication (GO:0007154)|cellular response to cAMP (GO:0071320)|hematopoietic progenitor cell differentiation (GO:0002244)|ion transport (GO:0006811)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	calcium:sodium antiporter activity (GO:0005432)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(18)|ovary(2)|pancreas(2)|prostate(3)|skin(6)	54				BRCA - Breast invasive adenocarcinoma(234;0.0079)|all cancers(60;0.0102)|OV - Ovarian serous cystadenocarcinoma(108;0.0555)		TTGGCAGGATGACACCCTCCT	0.547																																					p.V58V		Atlas-SNP	.											.	SLC8A3	234	.	0			c.C174T						.						72	61	65					14																	70634966		2203	4300	6503	SO:0001819	synonymous_variant	6547	exon2			CAGGATGACACCC	AJ304852	CCDS9799.1, CCDS9800.1, CCDS35498.1, CCDS41967.1, CCDS45131.1, CCDS53904.1	14q24.1	2013-05-22	2008-09-02		ENSG00000100678	ENSG00000100678		"Solute carriers"	11070	protein-coding gene	gene with protein product		607991				8798769	Standard	XM_005268017		Approved	NCX3	uc001xly.3	P57103	OTTHUMG00000152342	ENST00000381269.2:c.174C>T	chr14.hg19:g.70634966G>A		94.0	0.0		76.0	5.0	NM_183002	Q5K3P6|Q5K3P7|Q8IUE9|Q8IUF0|Q8NFI7|Q96QG1|Q96QG2	Silent	SNP	ENST00000381269.2	hg19	CCDS35498.1																																																																																			.	.		0.547	SLC8A3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390736.1			A	70634966	G	A	70634966	2	1	329	1	0	0	0	0	0	0	0	1	14723	1277	45	3		3	SLC8A3	14	70634966	Silent	SNP	G	TCGA-O8-A75V-01A-11D-A32G-10	24984085	70634966	36714574	71	46108										
TRMT61A	115708	hgsc.bcm.edu	37	chr14	103996384	103996384	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	atcctgtcactgggccatggTgcaatggtggcggtgcgtgt	16	9	1	0			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr14:103996384T>A	ENST00000389749.4	+	2	176	c.69T>A	c.(67-69)ggT>ggA	p.G23G	RP11-600F24.7_ENST00000568177.1_RNA	NM_152307.2	NP_689520.2	Q96FX7	TRM61_HUMAN	tRNA methyltransferase 61 homolog A (S. cerevisiae)	23						nucleus (GO:0005634)|tRNA (m1A) methyltransferase complex (GO:0031515)	tRNA (adenine-N1-)-methyltransferase activity (GO:0016429)			skin(1)	1						TGGGCCATGGTGCAATGGTGG	0.627																																					p.G23G		Atlas-SNP	.											.	TRMT61A	15	.	0			c.T69A						.						47	51	49					14																	103996384		2199	4298	6497	SO:0001819	synonymous_variant	115708	exon2			CCATGGTGCAATG	AK097771	CCDS41994.1	14q32	2009-01-09	2009-01-09	2009-01-09		ENSG00000166166			23790	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 172"	C14orf172		16043508	Standard	NM_152307		Approved	FLJ40452, GCD14, Gcd14p, hTRM61	uc010aws.3	Q96FX7		ENST00000389749.4:c.69T>A	chr14.hg19:g.103996384T>A		64.0	0.0		42.0	11.0	NM_152307	A6NN78|Q8N7Q9	Silent	SNP	ENST00000389749.4	hg19	CCDS41994.1																																																																																			.	.		0.627	TRMT61A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414988.1	NM_152307		A	103996384	T	A	103996384	2	1	329	1	0	0	0	0	0	0	0	1	16584	1683	59	4		4	TRMT61A	14	103996384	Silent	SNP	T	TCGA-O8-A75V-01A-11D-A32G-10	33361418	103996384	3353156	72	46109										
TRPM1	4308	hgsc.bcm.edu	37	chr15	31325061	31325061	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	caatcatgaatgtggaaatgGccacgagatctgtgatgttc	11	7	2	3			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr15:31325061G>A	ENST00000256552.6	-	22	2930	c.2783C>T	c.(2782-2784)gCc>gTc	p.A928V	TRPM1_ENST00000397795.2_Missense_Mutation_p.A906V|TRPM1_ENST00000542188.1_Missense_Mutation_p.A945V|RP11-348B17.1_ENST00000561299.1_RNA|RP11-348B17.1_ENST00000558755.1_RNA	NM_001252024.1	NP_001238953.1			transient receptor potential cation channel, subfamily M, member 1											NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		TGTGGAAATGGCCACGAGATC	0.468																																					p.A945V		Atlas-SNP	.											.	TRPM1	183	.	0			c.C2834T						.						171	163	165					15																	31325061		1957	4144	6101	SO:0001583	missense	4308	exon21			GAAATGGCCACGA	AF071787	CCDS10024.2, CCDS58345.1, CCDS58346.1, CCDS58347.1	15q13.3	2014-01-28		2002-01-18	ENSG00000134160	ENSG00000134160		"Voltage-gated ion channels / Transient receptor potential cation channels"	7146	protein-coding gene	gene with protein product		603576	"melastatin 1"	MLSN1		9806836, 9537257, 16382100	Standard	NM_001252020		Approved	LTRPC1, CSNB1C	uc021sia.1	Q7Z4N2	OTTHUMG00000129267	ENST00000256552.6:c.2783C>T	chr15.hg19:g.31325061G>A	ENSP00000256552:p.Ala928Val	170.0	0.0		126.0	29.0	NM_001252020		Missense_Mutation	SNP	ENST00000256552.6	hg19	CCDS58346.1	.	.	.	.	.	.	.	.	.	.	G	33	5.277508	0.95459	.	.	ENSG00000134160	ENST00000397795;ENST00000542188;ENST00000256552;ENST00000397793	D;D;D	0.98150	-4.75;-4.75;-4.75	5.59	5.59	0.84812	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98513	0.9504	M	0.69358	2.11	0.80722	D	1	D;D	0.89917	0.998;1.0	P;D	0.79108	0.891;0.992	D	0.99797	1.1034	10	0.87932	D	0	-27.6228	19.5857	0.95489	0.0:0.0:1.0:0.0	.	900;906	Q7Z4N2-3;Q7Z4N2	.;TRPM1_HUMAN	V	906;945;928;906	ENSP00000380897:A906V;ENSP00000437849:A945V;ENSP00000256552:A928V	ENSP00000256552:A928V	A	-	2	0	TRPM1	29112353	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.823000	0.86660	2.616000	0.88540	0.643000	0.83706	GCC	.	.		0.468	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420		A	31325061	G	A	31325061	3	1	329	1	0	0	0	0	1	0	0	0	16600	1203	42	3	2122	3	TRPM1	15	31325061	Missense_Mutation	SNP	G	TCGA-O8-A75V-01A-11D-A32G-10		31325061	71206331	73	46110										
TGM5	9333	hgsc.bcm.edu	37	chr15	43552276	43552276	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	accagggattgaaaagcaggAtgaactcccctagctggtag	12	9	0	2			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr15:43552276A>T	ENST00000220420.5	-	3	417	c.410T>A	c.(409-411)aTc>aAc	p.I137N	TGM5_ENST00000349114.4_Intron	NM_201631.3	NP_963925.2	O43548	TGM5_HUMAN	transglutaminase 5	137					cellular protein modification process (GO:0006464)|epidermis development (GO:0008544)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(11)|lung(15)|skin(6)|urinary_tract(1)	44		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;4e-07)	L-Glutamine(DB00130)	GAAAAGCAGGATGAACTCCCC	0.597																																					p.I137N		Atlas-SNP	.											.	TGM5	88	.	0			c.T410A						.						60	68	65					15																	43552276		2202	4299	6501	SO:0001583	missense	9333	exon3			AGCAGGATGAACT	AF035960	CCDS32211.1, CCDS32212.1	15q15	2004-07-07				ENSG00000104055		"Transglutaminases"	11781	protein-coding gene	gene with protein product		603805				9452468, 11390390	Standard	NM_201631		Approved	TGX	uc001zrd.2	O43548		ENST00000220420.5:c.410T>A	chr15.hg19:g.43552276A>T	ENSP00000220420:p.Ile137Asn	42.0	0.0		55.0	7.0	NM_201631	O43549|Q0VF40|Q9UEZ4	Missense_Mutation	SNP	ENST00000220420.5	hg19	CCDS32212.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.011226	0.75046	.	.	ENSG00000104055	ENST00000220420;ENST00000396996	D	0.88975	-2.45	5.24	5.24	0.73138	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.134038	0.51477	D	0.000097	D	0.92280	0.7551	M	0.69358	2.11	0.80722	D	1	D	0.63046	0.992	P	0.60068	0.868	D	0.92796	0.6252	10	0.62326	D	0.03	-25.2619	13.3764	0.60741	1.0:0.0:0.0:0.0	.	137	O43548	TGM5_HUMAN	N	137;136	ENSP00000220420:I137N	ENSP00000220420:I137N	I	-	2	0	TGM5	41339568	0.992000	0.36948	1.000000	0.80357	0.998000	0.95712	2.411000	0.44600	2.103000	0.63969	0.533000	0.62120	ATC	.	.		0.597	TGM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432257.1	NM_004245		T	43552276	A	T	43552276	3	4	329	1	0	0	0	0	1	0	0	0	15848	333	12	4	1796	4	TGM5	15	43552276	Missense_Mutation	SNP	A	TCGA-O8-A75V-01A-11D-A32G-10	12227215	43552276	58979116	74	46111										
CRAMP1L	57585	hgsc.bcm.edu	37	chr16	1676129	1676129	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	ggcagtgggagtcgtggagcAcagaggacaagaacaccttc	15	9	0	2			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr16:1676129A>T	ENST00000397412.3	+	3	601	c.502A>T	c.(502-504)Aca>Tca	p.T168S	LA16c-395F10.1_ENST00000415176.1_RNA|CRAMP1L_ENST00000436138.3_Missense_Mutation_p.T165S|CRAMP1L_ENST00000293925.5_Missense_Mutation_p.T168S			Q96RY5	CRML_HUMAN	Crm, cramped-like (Drosophila)	168	SANT. {ECO:0000255|PROSITE- ProRule:PRU00624}.					nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(6)|pancreas(1)	22						GTCGTGGAGCACAGAGGACAA	0.647																																					p.T168S		Atlas-SNP	.											.	CRAMP1L	60	.	0			c.A502T						.						67	72	70					16																	1676129		692	1591	2283	SO:0001583	missense	57585	exon2			TGGAGCACAGAGG	AB037847	CCDS10440.2	16p13.3	2008-07-30	2001-11-28		ENSG00000007545	ENSG00000007545			14122	protein-coding gene	gene with protein product			"Crm (Cramped Drosophila)-like"				Standard	NM_020825		Approved	KIAA1426	uc010uvh.2	Q96RY5	OTTHUMG00000074087	ENST00000397412.3:c.502A>T	chr16.hg19:g.1676129A>T	ENSP00000380559:p.Thr168Ser	90.0	0.0		95.0	16.0	NM_020825	A8MZL1|B1AJY1|Q8NDN1|Q9P2C1	Missense_Mutation	SNP	ENST00000397412.3	hg19	CCDS10440.2	.	.	.	.	.	.	.	.	.	.	A	24.5	4.533192	0.85812	.	.	ENSG00000007545	ENST00000397412;ENST00000293925;ENST00000436138	T;T	0.28666	1.6;1.6	5.81	5.81	0.92471	SANT domain, DNA binding (1);SANT, eukarya (1);	0.121235	0.56097	D	0.000040	T	0.23370	0.0565	N	0.01352	-0.895	0.80722	D	1	D	0.65815	0.995	P	0.57152	0.814	T	0.51116	-0.8746	10	0.39692	T	0.17	-15.3045	16.1612	0.81712	1.0:0.0:0.0:0.0	.	168	Q96RY5	CRML_HUMAN	S	168;168;165	ENSP00000380559:T168S;ENSP00000293925:T168S	ENSP00000293925:T168S	T	+	1	0	CRAMP1L	1616130	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	3.782000	0.55401	2.216000	0.71823	0.533000	0.62120	ACA	.	.		0.647	CRAMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157297.4			T	1676129	A	T	1676129	3	4	329	1	0	0	0	0	1	0	0	0	3848	159	6	4	508	4	CRAMP1L	16	1676129	Missense_Mutation	SNP	A	TCGA-O8-A75V-01A-11D-A32G-10		1676129	88678624	75	46112										
SMG1	23049	hgsc.bcm.edu	37	chr16	18852978	18852978	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	ctacccactggattagtcctGatcttgttcctagtggtgtt	9	10	1	1			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr16:18852978G>T	ENST00000446231.2	-	41	7017	c.6605C>A	c.(6604-6606)tCa>tAa	p.S2202*	SMG1_ENST00000389467.3_Nonsense_Mutation_p.S2202*			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	2202	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						GATTAGTCCTGATCTTGTTCC	0.433																																					p.S2202X		Atlas-SNP	.											.	SMG1	401	.	0			c.C6605A						.						236	223	227					16																	18852978		1953	4142	6095	SO:0001587	stop_gained	23049	exon41			AGTCCTGATCTTG	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase-related kinase"	607032	"smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.6605C>A	chr16.hg19:g.18852978G>T	ENSP00000402515:p.Ser2202*	181.0	0.0		184.0	85.0	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Nonsense_Mutation	SNP	ENST00000446231.2	hg19	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	G	50	16.663238	0.99869	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	.	.	.	5.48	5.48	0.80851	.	0.000000	0.56097	D	0.000036	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.7139	0.96107	0.0:0.0:1.0:0.0	.	.	.	.	X	2202	.	ENSP00000374118:S2202X	S	-	2	0	SMG1	18760479	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	9.733000	0.98818	2.722000	0.93159	0.655000	0.94253	TCA	.	.		0.433	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		T	18852978	G	T	18852978	4	4	329	1	0	0	0	0	0	1	0	0	14810	1294	45	3	4472	3	SMG1	16	18852978	Nonsense_Mutation	SNP	G	TCGA-O8-A75V-01A-11D-A32G-10	17176849	18852978	71501775	76	46113										
SLC12A4	6560	hgsc.bcm.edu	37	chr16	67995581	67995581	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	cgagctttcccagaagagacGatacctttgggcggatgtcc	12	11	0	2			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr16:67995581G>C	ENST00000316341.3	-	3	379	c.239C>G	c.(238-240)tCg>tGg	p.S80W	SLC12A4_ENST00000572010.1_5'UTR|SLC12A4_ENST00000572037.1_Missense_Mutation_p.S32W|SLC12A4_ENST00000338335.3_Missense_Mutation_p.S80W|SLC12A4_ENST00000422611.2_Missense_Mutation_p.S82W|SLC12A4_ENST00000576616.1_Missense_Mutation_p.S80W|SLC12A4_ENST00000541864.2_Missense_Mutation_p.S49W|SLC12A4_ENST00000537830.2_Missense_Mutation_p.S74W	NM_001145961.1|NM_005072.4	NP_001139433.1|NP_005063.1	Q9UP95	S12A4_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 4	80					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(2)|ovary(2)|prostate(4)|skin(2)|urinary_tract(3)	29		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)	Bumetanide(DB00887)|Potassium Chloride(DB00761)	CAGAAGAGACGATACCTTTGG	0.637																																					p.S82W		Atlas-SNP	.											SLC12A4,colon,carcinoma,+1,1	SLC12A4	81	.	0			c.C245G						.						112	100	104					16																	67995581		2198	4300	6498	SO:0001583	missense	6560	exon2			AGAGACGATACCT		CCDS10855.1, CCDS54030.1, CCDS54031.1, CCDS54032.1	16q22.1	2013-07-18	2013-07-18		ENSG00000124067	ENSG00000124067		"Solute carriers"	10913	protein-coding gene	gene with protein product		604119				8663127	Standard	NM_005072		Approved	KCC1	uc010ceu.2	Q9UP95	OTTHUMG00000137535	ENST00000316341.3:c.239C>G	chr16.hg19:g.67995581G>C	ENSP00000318557:p.Ser80Trp	84.0	0.0		51.0	18.0	NM_001145962	B4DF69|B4DR04|B4DZ82|B7ZAV0|F5H066|F5H0S9|F5H3C0|O60632|O75893|Q13953|Q96LD5	Missense_Mutation	SNP	ENST00000316341.3	hg19	CCDS10855.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.878438	0.91740	.	.	ENSG00000124067	ENST00000422611;ENST00000541864;ENST00000537830;ENST00000338335;ENST00000316341	D;D;D;D;D	0.89681	-2.16;-2.02;-2.03;-2.55;-2.02	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	D	0.95010	0.8385	M	0.80982	2.52	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.91635	0.987;0.995;0.999;0.998;0.987;0.996	D	0.94933	0.8084	10	0.87932	D	0	.	20.0787	0.97763	0.0:0.0:1.0:0.0	.	82;80;49;74;80;80	F5H3C0;B4DF30;F5H066;F5H0S9;Q9UP95-2;Q9UP95	.;.;.;.;.;S12A4_HUMAN	W	82;49;74;80;80	ENSP00000395983:S82W;ENSP00000438334:S49W;ENSP00000445962:S74W;ENSP00000343374:S80W;ENSP00000318557:S80W	ENSP00000318557:S80W	S	-	2	0	SLC12A4	66553082	1.000000	0.71417	1.000000	0.80357	0.879000	0.50718	9.420000	0.97426	2.757000	0.94681	0.462000	0.41574	TCG	.	.		0.637	SLC12A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268864.4	NM_005072		C	67995581	G	C	67995581	3	2	329	1	0	0	0	0	1	0	0	0	14400	1059	37	4	3106	4	SLC12A4	16	67995581	Missense_Mutation	SNP	G	TCGA-O8-A75V-01A-11D-A32G-10	49142603	67995581	22359172	77	46114										
SRCIN1	80725	hgsc.bcm.edu	37	chr17	36719591	36719591	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	agctcgtagaagacgttgcgAgcctcgtctttgatgaggat	13	8	1	4			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr17:36719591A>C	ENST00000264659.7	-	5	932	c.708T>G	c.(706-708)gcT>gcG	p.A236A	SRCIN1_ENST00000578925.1_Silent_p.A270A|SRCIN1_ENST00000398579.4_5'UTR	NM_025248.2	NP_079524.2	Q9C0H9	SRCN1_HUMAN	SRC kinase signaling inhibitor 1	108					exocytosis (GO:0006887)|negative regulation of protein tyrosine kinase activity (GO:0061099)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell migration (GO:0030334)|regulation of dendritic spine morphogenesis (GO:0061001)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	protein kinase binding (GO:0019901)			endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)	19						AGACGTTGCGAGCCTCGTCTT	0.632																																					p.A236A		Atlas-SNP	.											.	SRCIN1	66	.	0			c.T708G						.						46	50	49					17																	36719591		2153	4233	6386	SO:0001819	synonymous_variant	80725	exon5			GTTGCGAGCCTCG		CCDS45660.1	17q12	2009-12-14			ENSG00000017373	ENSG00000277363			29506	protein-coding gene	gene with protein product	"p130Cas-associated protein", "SNAP-25-interacting protein"	610786				11214970	Standard	NM_025248		Approved	SNIP, p140Cap, KIAA1684	uc002hqd.3	Q9C0H9		ENST00000264659.7:c.708T>G	chr17.hg19:g.36719591A>C		63.0	0.0		79.0	15.0	NM_025248	Q75T46|Q8N4W8	Silent	SNP	ENST00000264659.7	hg19	CCDS45660.1																																																																																			.	.		0.632	SRCIN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441878.4	NM_025248		C	36719591	A	C	36719591	2	2	329	1	0	0	0	0	0	0	0	1	15151	291	11	5		5	SRCIN1	17	36719591	Silent	SNP	A	TCGA-O8-A75V-01A-11D-A32G-10		36719591	44475619	78	46115										
KRTAP4-5	85289	hgsc.bcm.edu	37	chr17	39305911	39305911	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	gggcttgcagcagctggggcGgcagcaggtggtcctgcagc	19	11	0	0	rs557154279|rs141058010	byFrequency	TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr17:39305911G>T	ENST00000343246.4	-	1	143	c.109C>A	c.(109-111)Cgc>Agc	p.R37S		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	37	26 X 5 AA repeats of C-C-[GRQVCHIEK]- [SPTR]-[VSTQYC].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(4)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			CAGCTGGGGCGGCAGCAGGTG	0.657																																					p.R37S		Atlas-SNP	.											KRTAP4-5,NS,carcinoma,0,1	KRTAP4-5	34	.	0			c.C109A						.						25	29	27					17																	39305911		2176	4272	6448	SO:0001583	missense	85289	exon1			TGGGGCGGCAGCA	AJ406937	CCDS32650.1	17q21.2	2013-06-25			ENSG00000198271	ENSG00000198271		"Keratin associated proteins"	18899	protein-coding gene	gene with protein product						11279113	Standard	NM_033188		Approved	KAP4.5	uc002hwb.3	Q9BYR2	OTTHUMG00000133638	ENST00000343246.4:c.109C>A	chr17.hg19:g.39305911G>T	ENSP00000340546:p.Arg37Ser	66.0	0.0		74.0	8.0	NM_033188		Missense_Mutation	SNP	ENST00000343246.4	hg19	CCDS32650.1	.	.	.	.	.	.	.	.	.	.	.	11.33	1.605928	0.28623	.	.	ENSG00000198271	ENST00000343246	T	0.01369	4.97	3.22	-1.8	0.07907	.	2.080600	0.03668	U	0.243553	T	0.01870	0.0059	L	0.57536	1.79	0.09310	N	1	B	0.18461	0.028	B	0.17722	0.019	T	0.51741	-0.8667	10	0.10636	T	0.68	.	5.7249	0.18008	0.1011:0.0:0.4232:0.4757	.	37	Q9BYR2	KRA45_HUMAN	S	37	ENSP00000340546:R37S	ENSP00000340546:R37S	R	-	1	0	KRTAP4-5	36559437	0.000000	0.05858	0.674000	0.29902	0.928000	0.56348	-0.202000	0.09451	-0.272000	0.09259	0.556000	0.70494	CGC	.	.		0.657	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1			T	39305911	G	T	39305911	3	4	329	1	0	0	0	0	1	0	0	0	8563	1116	39	1	440	1	KRTAP4-5	17	39305911	Missense_Mutation	SNP	G	TCGA-O8-A75V-01A-11D-A32G-10	2586320	39305911	41889299	79	46116			1	57		2	2	30	N	TG_G	8.524439e-05
KRTAP4-5	85289	hgsc.bcm.edu	37	chr17	39305940	39305941	+	Missense_Mutation	DNP	TG	TG	CT													0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	tggtcctgcagcaggtggtcTggcagcagctggggcggcag							TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	T|G	T|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr17:39305940_39305941TG>CT	ENST00000343246.4	-	1	113_114	c.79_80CA>AG	c.(79-81)CAg>AGg	p.Q27R		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	27	26 X 5 AA repeats of C-C-[GRQVCHIEK]- [SPTR]-[VSTQYC].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(4)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			GCAGGTGGTCTGGCAGCAGCTG	0.649																																					p.Q27R|p.Q27K		Atlas-SNP	.											.	KRTAP4-5	34	.	0			c.A80G|c.C79A						.																																			SO:0001583	missense	85289	exon1			GTGGTCTGGCAGC|TGGTCTGGCAGCA	AJ406937	CCDS32650.1	17q21.2	2013-06-25			ENSG00000198271	ENSG00000198271		"Keratin associated proteins"	18899	protein-coding gene	gene with protein product						11279113	Standard	NM_033188		Approved	KAP4.5	uc002hwb.3	Q9BYR2	OTTHUMG00000133638	ENST00000343246.4:c.79_80delinsCT	chr17.hg19:g.39305940_39305941delinsCT	ENSP00000340546:p.Gln27Arg	80.0	0.0		93.0|94.0	9.0	NM_033188		Missense_Mutation	SNP	ENST00000343246.4	hg19	CCDS32650.1																																																																																			.	.		0.649	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1			CT	39305941	TG	CT	39305940	3	2	329	1	0	0	0	0	1	0	0	0	8563	1580	55	2	469	2	KRTAP4-5	17	39305940	Missense_Mutation	DNP	TG	TCGA-O8-A75V-01A-11D-A32G-10	29	39305940	41889270	80	46117			1	57		2	2	30	N	TG_G	8.524439e-05
DHX8	1659	hgsc.bcm.edu	37	chr17	41590858	41590858	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	attgaccagctcgtggtgacGcctatttctcaggtatgacg	11	10	1	3			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr17:41590858G>T	ENST00000262415.3	+	17	2703	c.2631G>T	c.(2629-2631)acG>acT	p.T877T	DHX8_ENST00000540306.1_Silent_p.T877T	NM_004941.1	NP_004932.1	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8	877	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.08)		TCGTGGTGACGCCTATTTCTC	0.403																																					p.T877T	NSCLC(56;1548 1661 49258 49987)	Atlas-SNP	.											.	DHX8	98	.	0			c.G2631T						.						154	124	134					17																	41590858		2203	4300	6503	SO:0001819	synonymous_variant	1659	exon17			GGTGACGCCTATT	D50487	CCDS11464.1	17q21.31	2005-08-19	2003-06-13	2003-06-20		ENSG00000067596		"DEAH-boxes"	2749	protein-coding gene	gene with protein product		600396	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 8 (RNA helicase)"	DDX8		7935475	Standard	NM_004941		Approved	HRH1, PRP22, PRPF22	uc002idu.1	Q14562		ENST00000262415.3:c.2631G>T	chr17.hg19:g.41590858G>T		151.0	0.0		77.0	26.0	NM_004941		Silent	SNP	ENST00000262415.3	hg19	CCDS11464.1																																																																																			.	.		0.403	DHX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453485.1			T	41590858	G	T	41590858	2	4	329	1	0	0	0	0	0	0	0	1	4517	1074	38	1		1	DHX8	17	41590858	Silent	SNP	G	TCGA-O8-A75V-01A-11D-A32G-10	2284918	41590858	39604352	81	46118										
GPATCH8	23131	hgsc.bcm.edu	37	chr17	42552196	42552196	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	attaagcactgattatcttaCcgattctataggcttgtcaa	6	8	3	1			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr17:42552196C>A	ENST00000591680.1	-	2	151		c.e2+1		GPATCH8_ENST00000592154.1_Splice_Site|GPATCH8_ENST00000434000.1_Splice_Site|GPATCH8_ENST00000588554.1_Missense_Mutation_p.V41L	NM_001002909.2	NP_001002909.1	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8								metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(7)|kidney(6)|large_intestine(4)|liver(2)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.206)		GATTATCTTACCGATTCTATA	0.358																																					.		Atlas-SNP	.											.	GPATCH8	114	.	0			c.120+1G>T						.						108	85	93					17																	42552196		2202	4299	6501	SO:0001630	splice_region_variant	23131	exon3			ATCTTACCGATTC	AB011125	CCDS32666.1	17q21.31	2013-01-28	2006-08-22	2006-12-13	ENSG00000186566	ENSG00000186566		"G patch domain containing"	29066	protein-coding gene	gene with protein product		614396	"KIAA0553"	KIAA0553, GPATC8		9628581	Standard	NM_001002909		Approved		uc002igw.2	Q9UKJ3	OTTHUMG00000181818	ENST00000591680.1:c.120+1G>T	chr17.hg19:g.42552196C>A		112.0	0.0		106.0	27.0	NM_001002909	B9EGP9|O60300|Q8TB99	Splice_Site	SNP	ENST00000591680.1	hg19	CCDS32666.1	.	.	.	.	.	.	.	.	.	.	C	31	5.088341	0.94100	.	.	ENSG00000186566	ENST00000335500;ENST00000541307	.	.	.	5.78	5.78	0.91487	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.9771	0.97313	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	GPATCH8	39907722	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.980000	0.70516	2.894000	0.99253	0.655000	0.94253	.	.	.		0.358	GPATCH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457797.1	NM_001002909	Intron	A	42552196	C	A	42552196	5	1	329	1	0	0	0	0	0	0	1	0	6602	521	18	3	4415	3	GPATCH8	17	42552196	Splice_Site	SNP	C	TCGA-O8-A75V-01A-11D-A32G-10	961338	42552196	38643014	82	46119										
NPB	256933	hgsc.bcm.edu	37	chr17	79860624	79860624	+	Nonstop_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	gccgactgcctcgccgcctgAgcccggacctctcctggcac	11	20	1	1			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr17:79860624A>G	ENST00000333383.7	+	2	547	c.378A>G	c.(376-378)tgA>tgG	p.*126W	NPB_ENST00000573081.1_Nonstop_Mutation_p.*157W|PCYT2_ENST00000538936.2_3'UTR	NM_148896.3	NP_683694.1	Q8NG41	NPB_HUMAN	neuropeptide B	0					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)						all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)			TCGCCGCCTGAGCCCGGACCT	0.761																																					p.X126W		Atlas-SNP	.											.	.	.	.	0			c.A378G						.						17	23	21					17																	79860624		2179	4284	6463	SO:0001578	stop_lost	256933	exon2			CGCCTGAGCCCGG		CCDS11790.1	17q25.3	2013-02-26			ENSG00000183979	ENSG00000183979		"Endogenous ligands"	30099	protein-coding gene	gene with protein product	"prepro-NPB"	607996				12118011, 12401809	Standard	NM_148896		Approved	PPL7, PPNPB	uc002kcd.3	Q8NG41	OTTHUMG00000177983	ENST00000333383.7:c.378A>G	chr17.hg19:g.79860624A>G	ENSP00000332766:p.*126Trpext*41	159.0	0.0		177.0	53.0	NM_148896	A0AUX9|A6NJD6|B9EJC3	Missense_Mutation	SNP	ENST00000333383.7	hg19	CCDS11790.1	.	.	.	.	.	.	.	.	.	.	a	11.88	1.769416	0.31320	.	.	ENSG00000183979	ENST00000333383	.	.	.	3.61	3.61	0.41365	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.9285	0.47205	1.0:0.0:0.0:0.0	.	.	.	.	W	126	.	.	X	+	3	0	NPB	77453916	1.000000	0.71417	0.264000	0.24511	0.126000	0.20510	3.761000	0.55242	1.494000	0.48533	0.454000	0.30748	TGA	.	.		0.761	NPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440109.2	NM_148896		G	79860624	A	G	79860624	4	3	329	1	0	0	0	0	0	0	0	0	10576	317	11	2	384	2	NPB	17	79860624	Nonstop_Mutation	SNP	A	TCGA-O8-A75V-01A-11D-A32G-10	37308428	79860624	1334586	83	46120										
LINGO3	645191	hgsc.bcm.edu	37	chr19	2290105	2290105	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	gagaagttgtttttgtgctgCccgcggccgcggctccacac	13	13	0	1			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr19:2290105C>G	ENST00000585527.1	-	1	1918	c.1671G>C	c.(1669-1671)ggG>ggC	p.G557G	LINGO3_ENST00000404279.1_Silent_p.G557G			P0C6S8	LIGO3_HUMAN	leucine rich repeat and Ig domain containing 3	557						integral component of membrane (GO:0016021)				lung(1)|urinary_tract(1)	2						TTTTGTGCTGCCCGCGGCCGC	0.647																																					p.G557G		Atlas-SNP	.											.	LINGO3	19	.	0			c.G1671C						.						16	20	19					19																	2290105		1952	4155	6107	SO:0001819	synonymous_variant	645191	exon2			GTGCTGCCCGCGG	AK091795	CCDS45905.1	19p13.3	2013-01-11	2007-02-01	2007-02-01		ENSG00000220008		"Immunoglobulin superfamily / I-set domain containing"	21206	protein-coding gene	gene with protein product		609792	"leucine rich repeat neuronal 6B"	LRRN6B		14686891	Standard	NM_001101391		Approved	LERN2	uc010dsx.1	P0C6S8		ENST00000585527.1:c.1671G>C	chr19.hg19:g.2290105C>G		166.0	0.0		120.0	29.0	NM_001101391		Silent	SNP	ENST00000585527.1	hg19	CCDS45905.1																																																																																			.	.		0.647	LINGO3-001	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451291.2	NM_001101391		G	2290105	C	G	2290105	2	3	329	1	0	0	0	0	0	0	0	1	8825	726	26	4		4	LINGO3	19	2290105	Silent	SNP	C	TCGA-O8-A75V-01A-11D-A32G-10		2290105	56838878	84	46121										
ARHGEF18	23370	hgsc.bcm.edu	37	chr19	7528840	7528840	+	Splice_Site	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	tgcacaaacagccccaccaaGagtaagagcggggccgtctc	11	14	1	2			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr19:7528840G>A	ENST00000359920.6	+	12	2461	c.2208G>A	c.(2206-2208)aaG>aaA	p.K736K	ARHGEF18_ENST00000319670.9_Splice_Site_p.K578K|CTD-2207O23.3_ENST00000593531.1_Splice_Site_p.R694K	NM_001130955.1	NP_001124427.1	Q6ZSZ5	ARHGI_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 18	736					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transforming growth factor beta receptor signaling pathway (GO:0007179)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	23		Renal(5;0.0902)				GCCCCACCAAGAGTAAGAGCG	0.612																																					p.K736K		Atlas-SNP	.											.	ARHGEF18	129	.	0			c.G2208A						.						20	22	21					19																	7528840		2190	4290	6480	SO:0001630	splice_region_variant	23370	exon12			CACCAAGAGTAAG	AK074372	CCDS12177.1, CCDS45946.1	19p13.3	2013-01-10	2009-06-12			ENSG00000104880		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	17090	protein-coding gene	gene with protein product	"Rho-specific guanine nucleotide exchange factor p114"		"rho/rac guanine nucleotide exchange factor (GEF) 18"			9628581, 11318610	Standard	NM_015318		Approved	P114-RhoGEF, KIAA0521, MGC15913	uc002mgi.3	Q6ZSZ5		ENST00000359920.6:c.2209+1G>A	chr19.hg19:g.7528840G>A		104.0	0.0		80.0	22.0	NM_001130955	A8MV62|B5ME81|O60274|Q6DD92	Silent	SNP	ENST00000359920.6	hg19	CCDS45946.1																																																																																			.	.		0.612	ARHGEF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436340.1	NM_015318	Silent	A	7528840	G	A	7528840	5	1	329	1	0	0	0	0	0	0	1	0	901	956	33	3	2254	3	ARHGEF18	19	7528840	Splice_Site	SNP	G	TCGA-O8-A75V-01A-11D-A32G-10	5238735	7528840	51600143	85	46122										
MUC16	94025	hgsc.bcm.edu	37	chr19	9088914	9088914	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	aatctgggactagtctctggCcaagttgtgctttggggtgc	14	8	2	0			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr19:9088914C>T	ENST00000397910.4	-	1	3104	c.2901G>A	c.(2899-2901)tgG>tgA	p.W967*		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	967	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TAGTCTCTGGCCAAGTTGTGC	0.468																																					p.W967X		Atlas-SNP	.											.	MUC16	4315	.	0			c.G2901A						.						237	230	232					19																	9088914		2010	4178	6188	SO:0001587	stop_gained	94025	exon1			CTCTGGCCAAGTT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.2901G>A	chr19.hg19:g.9088914C>T	ENSP00000381008:p.Trp967*	163.0	0.0		131.0	35.0	NM_024690	Q6ZQW5|Q96RK2	Nonsense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	41	8.930720	0.99006	.	.	ENSG00000181143	ENST00000397910	.	.	.	1.27	1.27	0.21489	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	5.9117	0.19031	0.0:1.0:0.0:0.0	.	.	.	.	X	967	.	ENSP00000381008:W967X	W	-	3	0	MUC16	8949914	0.000000	0.05858	0.002000	0.10522	0.481000	0.33189	-0.172000	0.09868	0.995000	0.38917	0.205000	0.17691	TGG	.	.		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9088914	C	T	9088914	4	4	329	1	0	0	0	0	0	1	0	0	9982	740	26	3	40958	3	MUC16	19	9088914	Nonsense_Mutation	SNP	C	TCGA-O8-A75V-01A-11D-A32G-10	1560074	9088914	50040069	86	46123										
AP1M1	8907	hgsc.bcm.edu	37	chr19	16319967	16319967	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	aatgaggtgttcttggacgtCatcgagtctgtcaacctctt	10	9	5	1			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr19:16319967C>A	ENST00000291439.3	+	5	974	c.525C>A	c.(523-525)gtC>gtA	p.V175V	AP1M1_ENST00000541844.1_Silent_p.V103V|AP1M1_ENST00000444449.2_Silent_p.V175V|AP1M1_ENST00000429941.2_Silent_p.V175V|AP1M1_ENST00000590756.1_Silent_p.V103V	NM_032493.3	NP_115882.1	Q9BXS5	AP1M1_HUMAN	adaptor-related protein complex 1, mu 1 subunit	175	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|endosome to melanosome transport (GO:0035646)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|trans-Golgi network membrane (GO:0032588)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|ovary(3)|prostate(2)	21						TCTTGGACGTCATCGAGTCTG	0.512																																					p.V175V		Atlas-SNP	.											.	AP1M1	48	.	0			c.C525A						.						216	194	201					19																	16319967		2203	4300	6503	SO:0001819	synonymous_variant	8907	exon5			GGACGTCATCGAG		CCDS12342.1, CCDS46008.1	19p13.12	2008-05-23							13667	protein-coding gene	gene with protein product		603535				9653655, 17988225	Standard	NM_032493		Approved	AP47, CLAPM2	uc002ndv.2	Q9BXS5		ENST00000291439.3:c.525C>A	chr19.hg19:g.16319967C>A		144.0	0.0		122.0	25.0	NM_001130524	Q4TTY5	Silent	SNP	ENST00000291439.3	hg19	CCDS12342.1																																																																																			.	.		0.512	AP1M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460492.1	NM_032493		A	16319967	C	A	16319967	2	1	329	1	0	0	0	0	0	0	0	1	734	813	29	3		3	AP1M1	19	16319967	Silent	SNP	C	TCGA-O8-A75V-01A-11D-A32G-10	7231053	16319967	42809016	87	46124										
ANKLE1	126549	hgsc.bcm.edu	37	chr19	17397348	17397348	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	gcttcatccccaggacatccAggcccggggctgagtgctgg	14	14	1	1			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr19:17397348A>T	ENST00000394458.3	+	9	2111	c.1835A>T	c.(1834-1836)cAg>cTg	p.Q612L	ANKLE1_ENST00000598347.1_Missense_Mutation_p.R540W|ANKLE1_ENST00000404085.1_Missense_Mutation_p.Q608L|ANKLE1_ENST00000594072.1_Missense_Mutation_p.Q575L	NM_152363.4	NP_689576	Q8NAG6	ANKL1_HUMAN	ankyrin repeat and LEM domain containing 1	612										large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	7						CAGGACATCCAGGCCCGGGGC	0.637																																					p.Q612L		Atlas-SNP	.											.	ANKLE1	27	.	0			c.A1835T						.						17	15	16					19																	17397348		2203	4293	6496	SO:0001583	missense	126549	exon9			ACATCCAGGCCCG	AK096688	CCDS12354.2, CCDS12354.3	19p13.11	2013-01-10	2008-03-25	2008-03-25	ENSG00000160117	ENSG00000160117		"Ankyrin repeat domain containing"	26812	protein-coding gene	gene with protein product	"LEM domain containing 6"		"ankyrin repeat domain 41"	ANKRD41			Standard	NM_152363		Approved	FLJ39369, LEMD6	uc002nga.2	Q8NAG6	OTTHUMG00000150839	ENST00000394458.3:c.1835A>T	chr19.hg19:g.17397348A>T	ENSP00000377971:p.Gln612Leu	82.0	0.0		91.0	25.0	NM_152363	A8VU82|Q8N8J8	Missense_Mutation	SNP	ENST00000394458.3	hg19	CCDS12354.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.40|18.40	3.616075|3.616075	0.66672|0.66672	.|.	.|.	ENSG00000160117|ENSG00000160117	ENST00000404261;ENST00000404085;ENST00000394458|ENST00000438921	T|.	0.72942|.	-0.7|.	5.48|5.48	3.29|3.29	0.37713|0.37713	.|.	0.153243|.	0.40385|.	N|.	0.001104|.	T|T	0.54095|0.54095	0.1837|0.1837	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	D|D	1|1	D;P;P|D	0.57571|0.71674	0.98;0.948;0.948|0.998	P;P;P|D	0.53102|0.72625	0.718;0.666;0.666|0.978	T|T	0.55711|0.55711	-0.8098|-0.8098	10|8	0.66056|0.62326	D|D	0.02|0.03	-0.2046|-0.2046	5.0826|5.0826	0.14664|0.14664	0.7205:0.1851:0.0944:0.0|0.7205:0.1851:0.0944:0.0	.|.	572;612;575|540	Q8NAG6-1;Q8NAG6;A0JLW0|E7ETZ9	.;ANKL1_HUMAN;.|.	L|W	612;608;575|540	ENSP00000384008:Q608L|.	ENSP00000377971:Q575L|ENSP00000415429:R540W	Q|R	+|+	2|1	0|2	ANKLE1|ANKLE1	17258348|17258348	0.999000|0.999000	0.42202|0.42202	0.999000|0.999000	0.59377|0.59377	0.476000|0.476000	0.33039|0.33039	0.881000|0.881000	0.28173|0.28173	2.081000|2.081000	0.62600|0.62600	0.402000|0.402000	0.26972|0.26972	CAG|AGG	.	.		0.637	ANKLE1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325392.2	NM_152363		T	17397348	A	T	17397348	3	4	329	1	0	0	0	0	1	0	0	0	632	188	7	4	1869	4	ANKLE1	19	17397348	Missense_Mutation	SNP	A	TCGA-O8-A75V-01A-11D-A32G-10	1077381	17397348	41731635	88	46125										
CCDC123	84902	hgsc.bcm.edu	37	chr19	33370231	33370231	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	ggagaagttctcggattcttCggttttccctgaaggtagat	12	7	2	3			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr19:33370231C>A	ENST00000305768.5	-	19	2277	c.2189G>T	c.(2188-2190)cGa>cTa	p.R730L	CTD-2085J24.4_ENST00000586628.2_lincRNA	NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	730					cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	35						TCGGATTCTTCGGTTTTCCCT	0.458																																					p.R730L		Atlas-SNP	.											.	CEP89	82	.	0			c.G2189T						.						158	157	157					19																	33370231		2203	4300	6503	SO:0001583	missense	84902	exon19			ATTCTTCGGTTTT	AL832158	CCDS32987.1	19q13.11	2014-02-20	2011-05-06	2011-05-06		ENSG00000121289			25907	protein-coding gene	gene with protein product		615470	"coiled-coil domain containing 123"	CCDC123		16395595	Standard	NM_032816		Approved	FLJ14640	uc002nty.3	Q96ST8		ENST00000305768.5:c.2189G>T	chr19.hg19:g.33370231C>A	ENSP00000306105:p.Arg730Leu	72.0	0.0		65.0	15.0	NM_032816	B9EGA6|Q8N5J8	Missense_Mutation	SNP	ENST00000305768.5	hg19	CCDS32987.1	.	.	.	.	.	.	.	.	.	.	C	18.34	3.603169	0.66445	.	.	ENSG00000121289	ENST00000305768	T	0.34072	1.38	5.12	-6.09	0.02145	.	0.727465	0.12015	N	0.507501	T	0.38852	0.1056	L	0.59436	1.845	0.09310	N	0.999999	P	0.51537	0.946	P	0.49683	0.619	T	0.45041	-0.9288	10	0.44086	T	0.13	-7.0E-4	14.2988	0.66331	0.0:0.3211:0.0:0.6789	.	730	Q96ST8	CEP89_HUMAN	L	730	ENSP00000306105:R730L	ENSP00000306105:R730L	R	-	2	0	CEP89	38062071	0.271000	0.24162	0.001000	0.08648	0.231000	0.25187	-0.222000	0.09190	-0.994000	0.03463	-0.258000	0.10820	CGA	.	.		0.458	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816		A	33370231	C	A	33370231	3	1	329	1	0	0	0	0	1	0	0	0	2761	884	31	1	166	1	CCDC123	19	33370231	Missense_Mutation	SNP	C	TCGA-O8-A75V-01A-11D-A32G-10	15972883	33370231	25758752	89	46126										
HLCS	3141	hgsc.bcm.edu	37	chr21	38128887	38128887	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	aggggaaggacgctgttgggCcctttgtcctgaaactcttt	13	9	1	1			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chr21:38128887C>A	ENST00000399120.1	-	11	3195	c.1965G>T	c.(1963-1965)ggG>ggT	p.G655G	HLCS_ENST00000336648.4_Silent_p.G655G	NM_001242784.1	NP_001229713.1	P50747	BPL1_HUMAN	holocarboxylase synthetase (biotin-(proprionyl-CoA-carboxylase (ATP-hydrolysing)) ligase)	655					biotin metabolic process (GO:0006768)|cell proliferation (GO:0008283)|histone biotinylation (GO:0071110)|histone modification (GO:0016570)|protein biotinylation (GO:0009305)|response to biotin (GO:0070781)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nuclear lamina (GO:0005652)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin-[acetyl-CoA-carboxylase] ligase activity (GO:0004077)|biotin-[methylcrotonoyl-CoA-carboxylase] ligase activity (GO:0004078)|biotin-[methylmalonyl-CoA-carboxytransferase] ligase activity (GO:0004079)|biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activity (GO:0004080)|biotin-protein ligase activity (GO:0018271)|enzyme binding (GO:0019899)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(46;0.0422)			Biotin(DB00121)	CGCTGTTGGGCCCTTTGTCCT	0.458																																					p.G655G		Atlas-SNP	.											.	HLCS	64	.	0			c.G1965T						.						193	157	169					21																	38128887		2203	4300	6503	SO:0001819	synonymous_variant	3141	exon11			GTTGGGCCCTTTG		CCDS13647.1	21q22.1	2012-07-13	2010-04-30		ENSG00000159267	ENSG00000159267	6.3.4.9, 6.3.4.10, 6.3.4.11, 6.3.4.15		4976	protein-coding gene	gene with protein product		609018	"holocarboxylase synthetase (biotin-[proprionyl-Coenzyme A-carboxylase (ATP-hydrolysing)] ligase)", "holocarboxylase synthetase (biotin-(proprionyl-Coenzyme A-carboxylase (ATP-hydrolysing)) ligase)"			7842009	Standard	NM_000411		Approved	HCS	uc021wjb.1	P50747	OTTHUMG00000086636	ENST00000399120.1:c.1965G>T	chr21.hg19:g.38128887C>A		155.0	0.0		159.0	44.0	NM_000411	B2RAH1|D3DSG6|Q99451	Silent	SNP	ENST00000399120.1	hg19	CCDS13647.1																																																																																			.	.		0.458	HLCS-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194687.2			A	38128887	C	A	38128887	2	1	329	1	0	0	0	0	0	0	0	1	7222	726	26	3		3	HLCS	21	38128887	Silent	SNP	C	TCGA-O8-A75V-01A-11D-A32G-10		38128887	10001008	90	46127										
ENOX2	10495	hgsc.bcm.edu	37	chrX	129813673	129813673	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0659340659340659	6	1	1.59668049792531	1.33056708160443	1.66320885200553	0.148606811145511	0.7490586561794	0	tcaggcagaccacccacaaaTactgttttgcatcctggtgg	9	12	1	1			TCGA-O8-A75V-01A-11D-A32G-10	TCGA-O8-A75V-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a1fc125-b2f3-4a19-aeb1-faf45a3ee8ed	296a0e3f-6a54-44cf-bb8d-480cda70d695	g.chrX:129813673T>C	ENST00000370927.1	-	4	411	c.390A>G	c.(388-390)gtA>gtG	p.V130V	ENOX2_ENST00000370935.1_Silent_p.V101V|ENOX2_ENST00000492263.1_5'UTR|ENOX2_ENST00000394363.1_Silent_p.V101V|ENOX2_ENST00000338144.3_Silent_p.V130V			Q16206	ENOX2_HUMAN	ecto-NOX disulfide-thiol exchanger 2	130	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cell growth (GO:0016049)|oxidation-reduction process (GO:0055114)|regulation of growth (GO:0040008)|ultradian rhythm (GO:0007624)	cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)	nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|protein disulfide oxidoreductase activity (GO:0015035)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(3)	33						CACCCACAAATACTGTTTTGC	0.443																																					p.V130V	Ovarian(101;828 1506 2951 9500 35258)	Atlas-SNP	.											.	ENOX2	70	.	0			c.A390G						.						120	103	109					X																	129813673		2203	4300	6503	SO:0001819	synonymous_variant	10495	exon7			CACAAATACTGTT	AF207881	CCDS14626.1, CCDS14627.1	Xq25	2013-02-12	2007-03-23	2007-03-23	ENSG00000165675	ENSG00000165675		"RNA binding motif (RRM) containing"	2259	protein-coding gene	gene with protein product		300282	"cytosolic ovarian carcinoma antigen 1"	COVA1		8150545, 11888291	Standard	NM_006375		Approved	APK1, tNOX	uc004evw.3	Q16206	OTTHUMG00000022401	ENST00000370927.1:c.390A>G	chrX.hg19:g.129813673T>C		148.0	0.0		121.0	65.0	NM_182314	A8K197|A8K1C2|Q5VTJ1|Q5VTJ2|Q8WUX0|Q9NTP6|Q9UH82	Silent	SNP	ENST00000370927.1	hg19	CCDS14626.1																																																																																			.	.		0.443	ENOX2-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058277.1	NM_182314		C	129813673	T	C	129813673	2	2	329	1	0	0	0	0	0	0	0	1	5129	1393	49	2		2	ENOX2	23	129813673	Silent	SNP	T	TCGA-O8-A75V-01A-11D-A32G-10		129813673	25456887	91	46128										
VPS13D	55187	hgsc.bcm.edu	37	chr1	12422877	12422877	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	aatcatctcacaagcttgcaTttgcacagagggaatttgcc	8	10	2	1			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr1:12422877T>C	ENST00000358136.3	+	51	10373	c.10243T>C	c.(10243-10245)Ttt>Ctt	p.F3415L	VPS13D_ENST00000356315.4_Missense_Mutation_p.F3390L	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		CAAGCTTGCATTTGCACAGAG	0.428																																					p.F3415L		Atlas-SNP	.											.	VPS13D	316	.	0			c.T10243C						.						179	174	176					1																	12422877		2203	4300	6503	SO:0001583	missense	55187	exon51			CTTGCATTTGCAC	AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"vacuolar protein sorting 13D (yeast)"				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.10243T>C	chr1.hg19:g.12422877T>C	ENSP00000350854:p.Phe3415Leu	110.0	0.0		199.0	103.0	NM_015378		Missense_Mutation	SNP	ENST00000358136.3	hg19	CCDS30588.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.136323	0.77662	.	.	ENSG00000048707	ENST00000356315;ENST00000358136	T;T	0.29655	1.56;1.56	5.7	5.7	0.88788	Vacuolar protein sorting-associated protein (1);	0.000000	0.85682	D	0.000000	T	0.37404	0.1002	L	0.47716	1.5	0.80722	D	1	B;P	0.41498	0.323;0.752	B;P	0.47891	0.348;0.56	T	0.04579	-1.0941	10	0.23302	T	0.38	.	15.9745	0.80049	0.0:0.0:0.0:1.0	.	3390;3414	Q5THJ4-2;Q5THJ4	.;VP13D_HUMAN	L	3390;3415	ENSP00000348666:F3390L;ENSP00000350854:F3415L	ENSP00000348666:F3390L	F	+	1	0	VPS13D	12345464	1.000000	0.71417	0.998000	0.56505	0.932000	0.56968	7.393000	0.79851	2.168000	0.68352	0.533000	0.62120	TTT	.	.		0.428	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		C	12422877	T	C	12422877	3	2	330	1	0	0	0	0	1	0	0	0	17207	1493	52	2	10441	2	VPS13D	1	12422877	Missense_Mutation	SNP	T	TCGA-PD-A5DF-01A-11D-A27I-10		12422877	236827744	1	46129										
HSPG2	3339	hgsc.bcm.edu	37	chr1	22182073	22182073	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	agcgctgctgtgggctcggcAcaagtactgggcctgatccg	15	12	0	1			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr1:22182073A>G	ENST00000374695.3	-	46	5876	c.5797T>C	c.(5797-5799)Tgc>Cgc	p.C1933R	HSPG2_ENST00000430507.1_5'Flank	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	1933	Ig-like C2-type 4.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	TGGGCTCGGCACAAGTACTGG	0.711																																					p.C1933R		Atlas-SNP	.											.	HSPG2	311	.	0			c.T5797C						.						13	14	14					1																	22182073		2194	4291	6485	SO:0001583	missense	3339	exon46			CTCGGCACAAGTA	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"Proteoglycans / Extracellular Matrix : Other", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5273	protein-coding gene	gene with protein product	"perlecan proteoglycan"	142461	"Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.5797T>C	chr1.hg19:g.22182073A>G	ENSP00000363827:p.Cys1933Arg	8.0	0.0		16.0	4.0	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	hg19	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.030646	0.75504	.	.	ENSG00000142798	ENST00000374695	T	0.61627	0.09	5.12	5.12	0.69794	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.43579	D	0.000547	D	0.84547	0.5496	H	0.98466	4.24	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.89903	0.4046	10	0.87932	D	0	.	12.8664	0.57941	1.0:0.0:0.0:0.0	.	1933	P98160	PGBM_HUMAN	R	1933	ENSP00000363827:C1933R	ENSP00000363827:C1933R	C	-	1	0	HSPG2	22054660	1.000000	0.71417	0.996000	0.52242	0.880000	0.50808	7.787000	0.85759	1.943000	0.56356	0.379000	0.24179	TGC	.	.		0.711	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		G	22182073	A	G	22182073	3	3	330	1	0	0	0	0	1	0	0	0	7439	159	6	2	7586	2	HSPG2	1	22182073	Missense_Mutation	SNP	A	TCGA-PD-A5DF-01A-11D-A27I-10	9759196	22182073	227068548	2	46130										
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144879542	144879542	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	ccatcaggaccatttccttgAggctgttgtgctcctcacac	8	14	2	1			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr1:144879542A>C	ENST00000369354.3	-	27	4097	c.3908T>G	c.(3907-3909)cTc>cGc	p.L1303R	PDE4DIP_ENST00000369359.4_Missense_Mutation_p.L1439R|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.L1439R|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.L1303R|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.L1259R|AL138796.1_ENST00000582173.1_RNA|PDE4DIP_ENST00000524974.1_5'UTR|RP4-791M13.5_ENST00000531288.1_RNA			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1303					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)	p.L1303P(2)		NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		CATTTCCTTGAGGCTGTTGTG	0.522			T	PDGFRB	MPD																																p.L1303R		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	PDE4DIP,NS,carcinoma,0,2	PDE4DIP	817	.	2	Substitution - Missense(2)	NS(1)|prostate(1)	c.T3908G						.						64	68	67					1																	144879542		2203	4295	6498	SO:0001583	missense	9659	exon27			TCCTTGAGGCTGT	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"myomegalin"	608117	"cardiomyopathy associated 2"	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.3908T>G	chr1.hg19:g.144879542A>C	ENSP00000358360:p.Leu1303Arg	27.0	1.0		45.0	7.0	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	hg19	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	A	13.49	2.253522	0.39797	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	T;T;T;T;T	0.01918	4.56;4.69;4.69;4.69;4.69	5.69	2.15	0.27550	.	.	.	.	.	T	0.02156	0.0067	L	0.54323	1.7	0.09310	N	0.999996	D;P	0.53151	0.958;0.916	P;P	0.54312	0.748;0.627	T	0.43163	-0.9408	9	0.87932	D	0	.	8.1849	0.31333	0.7638:0.0:0.2362:0.0	.	1259;1303	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	R	1259;1303;1303;1439;1439	ENSP00000327209:L1259R;ENSP00000358360:L1303R;ENSP00000358363:L1303R;ENSP00000435654:L1439R;ENSP00000358366:L1439R	ENSP00000327209:L1259R	L	-	2	0	PDE4DIP	143590899	0.977000	0.34250	0.017000	0.16124	0.163000	0.22366	2.118000	0.41949	0.114000	0.18032	-0.250000	0.11733	CTC	.	.		0.522	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		C	144879542	A	C	144879542	3	2	330	1	0	0	0	0	1	0	0	0	11652	304	11	5	3204	5	PDE4DIP	1	144879542	Missense_Mutation	SNP	A	TCGA-PD-A5DF-01A-11D-A27I-10	122697469	144879542	104371079	3	46131			1	58		2	2	20	A		3.130125e-05
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144879561	144879561	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	gaggctgttgtgctcctcacActctgaaaaaagacaaagat	9	9	2	3			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr1:144879561A>G	ENST00000369354.3	-	27	4078	c.3889T>C	c.(3889-3891)Tgt>Cgt	p.C1297R	PDE4DIP_ENST00000369359.4_Missense_Mutation_p.C1433R|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.C1433R|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.C1297R|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.C1253R|AL138796.1_ENST00000582173.1_RNA|PDE4DIP_ENST00000524974.1_5'UTR|RP4-791M13.5_ENST00000531288.1_RNA			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1297					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)	p.C1297R(2)		NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TGCTCCTCACACTCTGAAAAA	0.502			T	PDGFRB	MPD																																p.C1297R		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	PDE4DIP_ENST00000369356,NS,carcinoma,0,7	PDE4DIP	817	.	2	Substitution - Missense(2)	lung(2)	c.T3889C						.						46	49	48					1																	144879561		2203	4290	6493	SO:0001583	missense	9659	exon27			CCTCACACTCTGA	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"myomegalin"	608117	"cardiomyopathy associated 2"	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.3889T>C	chr1.hg19:g.144879561A>G	ENSP00000358360:p.Cys1297Arg	22.0	0.0		35.0	8.0	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	hg19	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	A	16.19	3.052829	0.55218	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	T;T;T;T;T	0.01665	4.7;4.79;4.79;4.8;4.8	5.79	5.79	0.91817	.	.	.	.	.	T	0.04048	0.0113	L	0.57536	1.79	0.80722	D	1	D;D	0.71674	0.998;0.96	D;B	0.67548	0.952;0.421	T	0.51568	-0.8689	9	0.44086	T	0.13	.	14.0875	0.64968	1.0:0.0:0.0:0.0	.	1253;1297	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	R	1253;1297;1297;1433;1433	ENSP00000327209:C1253R;ENSP00000358360:C1297R;ENSP00000358363:C1297R;ENSP00000435654:C1433R;ENSP00000358366:C1433R	ENSP00000327209:C1253R	C	-	1	0	PDE4DIP	143590918	1.000000	0.71417	1.000000	0.80357	0.718000	0.41266	5.716000	0.68437	2.207000	0.71202	0.533000	0.62120	TGT	.	.		0.502	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		G	144879561	A	G	144879561	3	3	330	1	0	0	0	0	1	0	0	0	11652	159	6	2	3223	2	PDE4DIP	1	144879561	Missense_Mutation	SNP	A	TCGA-PD-A5DF-01A-11D-A27I-10	19	144879561	104371060	4	46132			1	58		2	2	20	A		3.130125e-05
NOTCH2NL	388677	hgsc.bcm.edu	37	chr1	145281614	145281614	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	caggccagtactgtgacagcCtgtatgtgccctgtgcaccc	11	14	0	1			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr1:145281614C>T	ENST00000369340.3	+	5	988	c.544C>T	c.(544-546)Ctg>Ttg	p.L182L	NOTCH2NL_ENST00000362074.6_Silent_p.L182L|NOTCH2NL_ENST00000344859.3_Silent_p.L182L|RP11-458D21.5_ENST00000468030.1_Silent_p.L182L			Q7Z3S9	NT2NL_HUMAN	notch 2 N-terminal like	182	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|Notch signaling pathway (GO:0007219)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	27						CTGTGACAGCCTGTATGTGCC	0.577																																					p.L182L		Atlas-SNP	.											.	NOTCH2NL	100	.	0			c.C544T						.						176	177	176					1																	145281614		2203	4300	6503	SO:0001819	synonymous_variant	388677	exon4			GACAGCCTGTATG		CCDS72880.1	1q21.2	2010-06-24	2010-06-24		ENSG00000213240	ENSG00000213240			31862	protein-coding gene	gene with protein product			"Notch homolog 2 (Drosophila) N-terminal like"			14673143	Standard	NM_203458		Approved	N2N	uc001emn.4	Q7Z3S9	OTTHUMG00000013754	ENST00000369340.3:c.544C>T	chr1.hg19:g.145281614C>T		1284.0	1.0		2183.0	249.0	NM_203458	Q5BKT8|Q5VTG9|Q5XG84|Q6P192|Q8NC23|Q8WUQ9|Q96FY1	Silent	SNP	ENST00000369340.3	hg19	CCDS909.1																																																																																			.	.		0.577	NOTCH2NL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000038546.1	NM_203458		T	145281614	C	T	145281614	2	4	330	1	0	0	0	0	0	0	0	1	10558	680	24	3		3	NOTCH2NL	1	145281614	Silent	SNP	C	TCGA-PD-A5DF-01A-11D-A27I-10	402053	145281614	103969007	5	46133										
TPO	7173	hgsc.bcm.edu	37	chr2	1520727	1520727	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	gctgatcggaggcttcgcagGtctcacctcgacggtgattt	13	11	1	2			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr2:1520727G>T	ENST00000345913.4	+	15	2682	c.2591G>T	c.(2590-2592)gGt>gTt	p.G864V	TPO_ENST00000349624.3_Missense_Mutation_p.G691V|TPO_ENST00000329066.4_Missense_Mutation_p.G864V|TPO_ENST00000382201.3_Missense_Mutation_p.G807V|TPO_ENST00000497517.2_3'UTR|TPO_ENST00000382198.1_Missense_Mutation_p.G691V|TPO_ENST00000346956.3_Missense_Mutation_p.G820V|TPO_ENST00000337415.3_Missense_Mutation_p.G864V	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	864					cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	GGCTTCGCAGGTCTCACCTCG	0.537																																					p.G864V		Atlas-SNP	.											.	TPO	224	.	0			c.G2591T						.						79	71	74					2																	1520727		2203	4300	6503	SO:0001583	missense	7173	exon15			TCGCAGGTCTCAC		CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.2591G>T	chr2.hg19:g.1520727G>T	ENSP00000318820:p.Gly864Val	70.0	0.0		116.0	36.0	NM_001206744	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	hg19	CCDS1643.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	4.395|4.395	0.072996|0.072996	0.08485|0.08485	.|.	.|.	ENSG00000115705|ENSG00000115705	ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000329066;ENST00000382201;ENST00000382198;ENST00000422464;ENST00000469607;ENST00000425083|ENST00000446278	T;T;T;T;T;T;T;T;T;T|.	0.70399|.	-0.31;-0.24;-0.36;0.04;-0.24;-0.2;0.04;-0.4;0.41;-0.48|.	5.52|5.52	-4.48|-4.48	0.03515|0.03515	.|.	703.491000|.	0.00397|.	N|.	0.000056|.	T|T	0.17238|0.17238	0.0414|0.0414	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B;P;B;B|.	0.35011|.	0.021;0.48;0.084;0.012|.	B;B;B;B|.	0.30782|.	0.022;0.12;0.022;0.01|.	T|T	0.32771|0.32771	-0.9894|-0.9894	10|5	0.37606|.	T|.	0.19|.	-2.5756|-2.5756	11.3787|11.3787	0.49743|0.49743	0.0:0.6074:0.1582:0.2344|0.0:0.6074:0.1582:0.2344	.|.	820;691;807;864|.	P07202-4;P07202-5;P07202-2;P07202|.	.;.;.;PERT_HUMAN|.	V|F	864;864;820;691;864;807;691;749;294;85|339	ENSP00000337263:G864V;ENSP00000318820:G864V;ENSP00000263886:G820V;ENSP00000332044:G691V;ENSP00000329869:G864V;ENSP00000371636:G807V;ENSP00000371633:G691V;ENSP00000405788:G749V;ENSP00000419461:G294V;ENSP00000389659:G85V|.	ENSP00000329869:G864V|.	G|V	+|+	2|1	0|0	TPO|TPO	1499734|1499734	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.005000|0.005000	0.04900|0.04900	0.104000|0.104000	0.15313|0.15313	-0.660000|-0.660000	0.05352|0.05352	-0.181000|-0.181000	0.13052|0.13052	GGT|GTC	.	.		0.537	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547		T	1520727	G	T	1520727	3	4	330	1	0	0	0	0	1	0	0	0	16425	1261	44	3	2645	3	TPO	2	1520727	Missense_Mutation	SNP	G	TCGA-PD-A5DF-01A-11D-A27I-10		1520727	241678646	6	46134										
CLIP4	79745	hgsc.bcm.edu	37	chr2	29386810	29386810	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	gaatatttgctcccccatccAgggtgcaaaggtgagagaat	11	9	0	2			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr2:29386810A>G	ENST00000320081.5	+	13	1903	c.1648A>G	c.(1648-1650)Agg>Ggg	p.R550G	CLIP4_ENST00000404424.1_Missense_Mutation_p.R550G|CLIP4_ENST00000401605.1_Missense_Mutation_p.R550G|CLIP4_ENST00000401617.2_Missense_Mutation_p.R443G	NM_024692.4	NP_078968.3	Q8N3C7	CLIP4_HUMAN	CAP-GLY domain containing linker protein family, member 4	550										endometrium(4)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|prostate(1)|skin(1)	26	Acute lymphoblastic leukemia(172;0.155)					TCCCCCATCCAGGGTGCAAAG	0.358																																					p.R550G		Atlas-SNP	.											.	CLIP4	69	.	0			c.A1648G						.						93	87	89					2																	29386810		2203	4300	6503	SO:0001583	missense	79745	exon13			CCATCCAGGGTGC	AK024722	CCDS1770.1, CCDS74502.1	2p23	2013-01-10	2007-01-04	2007-01-04	ENSG00000115295	ENSG00000115295		"Ankyrin repeat domain containing"	26108	protein-coding gene	gene with protein product			"restin-like 2"	RSNL2			Standard	XM_005264562		Approved	FLJ21069	uc002rmv.3	Q8N3C7	OTTHUMG00000097837	ENST00000320081.5:c.1648A>G	chr2.hg19:g.29386810A>G	ENSP00000327009:p.Arg550Gly	67.0	0.0		83.0	4.0	NM_024692	A0AV10|B2RMQ3|B7Z7N8|Q7Z4U3|Q96BR7|Q96MA5|Q9H7C0	Missense_Mutation	SNP	ENST00000320081.5	hg19	CCDS1770.1	.	.	.	.	.	.	.	.	.	.	A	18.73	3.686991	0.68157	.	.	ENSG00000115295	ENST00000401605;ENST00000401617;ENST00000404424;ENST00000402240;ENST00000320081;ENST00000379543;ENST00000530644	T;T;T;T	0.76060	-0.99;-0.99;-0.99;-0.99	6.06	6.06	0.98353	Cytoskeleton-associated protein, Gly-rich domain (3);	0.099960	0.64402	D	0.000004	D	0.89181	0.6642	H	0.94542	3.55	0.53005	D	0.999969	D	0.89917	1.0	D	0.87578	0.998	D	0.91199	0.4990	10	0.62326	D	0.03	.	11.5833	0.50904	0.851:0.149:0.0:0.0	.	550	Q8N3C7	CLIP4_HUMAN	G	550;443;550;552;550;568;510	ENSP00000384242:R550G;ENSP00000385148:R443G;ENSP00000385594:R550G;ENSP00000327009:R550G	ENSP00000327009:R550G	R	+	1	2	CLIP4	29240314	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.466000	0.53071	2.323000	0.78572	0.528000	0.53228	AGG	.	.		0.358	CLIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215123.2	NM_024692		G	29386810	A	G	29386810	3	3	330	1	0	0	0	0	1	0	0	0	3537	179	7	2	1694	2	CLIP4	2	29386810	Missense_Mutation	SNP	A	TCGA-PD-A5DF-01A-11D-A27I-10	27866083	29386810	213812563	7	46135										
CEBPZ	10153	hgsc.bcm.edu	37	chr2	37454714	37454714	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	atgctgtgtaatatcgatccGatattgtctgctgagaattc	9	7	1	1			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr2:37454714G>A	ENST00000234170.5	-	2	1767	c.1622C>T	c.(1621-1623)tCg>tTg	p.S541L		NM_005760.2	NP_005751.2	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein (C/EBP), zeta	541					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|endometrium(2)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28		all_hematologic(82;0.21)				ATATCGATCCGATATTGTCTG	0.363																																					p.S541L		Atlas-SNP	.											CEBPZ,NS,carcinoma,0,3	CEBPZ	68	.	0			c.C1622T						.						116	117	117					2																	37454714		2203	4300	6503	SO:0001583	missense	10153	exon2			CGATCCGATATTG	M37197	CCDS1787.1	2p22.3	2008-09-03	2008-09-03		ENSG00000115816	ENSG00000115816			24218	protein-coding gene	gene with protein product		612828				2247079, 12534345	Standard	NM_005760		Approved	CBF2, CTF2	uc002rpz.3	Q03701	OTTHUMG00000100960	ENST00000234170.5:c.1622C>T	chr2.hg19:g.37454714G>A	ENSP00000234170:p.Ser541Leu	44.0	0.0		69.0	3.0	NM_005760	Q8NE75	Missense_Mutation	SNP	ENST00000234170.5	hg19	CCDS1787.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.483652	0.84854	.	.	ENSG00000115816	ENST00000234170;ENST00000545744	T	0.20200	2.09	5.71	5.71	0.89125	Armadillo-type fold (1);CCAAT-binding factor (1);	0.000000	0.85682	D	0.000000	T	0.48660	0.1512	M	0.71581	2.175	0.80722	D	1	D	0.76494	0.999	D	0.71414	0.973	T	0.45775	-0.9238	10	0.87932	D	0	.	19.8557	0.96758	0.0:0.0:1.0:0.0	.	541	Q03701	CEBPZ_HUMAN	L	541	ENSP00000234170:S541L	ENSP00000234170:S541L	S	-	2	0	CEBPZ	37308218	1.000000	0.71417	0.964000	0.40570	0.958000	0.62258	9.357000	0.97099	2.694000	0.91930	0.585000	0.79938	TCG	.	.		0.363	CEBPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218569.2	NM_005760		A	37454714	G	A	37454714	3	1	330	1	0	0	0	0	1	0	0	0	3206	1059	37	1	1602	1	CEBPZ	2	37454714	Missense_Mutation	SNP	G	TCGA-PD-A5DF-01A-11D-A27I-10	8067904	37454714	205744659	8	46136										
FSIP2	401024	hgsc.bcm.edu	37	chr2	186673528	186673528	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	cccaagaacatgcttttaatGtgattcctgaattagagcaa	7	8	0	4			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr2:186673528G>A	ENST00000424728.1	+	17	19495	c.19495G>A	c.(19495-19497)Gtg>Atg	p.V6499M	FSIP2_ENST00000343098.5_Missense_Mutation_p.V6588M			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	6499										NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						TGCTTTTAATGTGATTCCTGA	0.323																																					p.V6588M		Atlas-SNP	.											.	FSIP2	251	.	0			c.G19762A						.						58	57	57					2																	186673528		1816	4064	5880	SO:0001583	missense	401024	exon17			TTTAATGTGATTC	AK092099	CCDS54426.1	2q32.1	2010-06-18			ENSG00000188738	ENSG00000188738			21675	protein-coding gene	gene with protein product		615796				14702039	Standard	NM_173651		Approved	FLJ34780	uc002upl.3	Q5CZC0	OTTHUMG00000153874	ENST00000424728.1:c.19495G>A	chr2.hg19:g.186673528G>A	ENSP00000401306:p.Val6499Met	90.0	0.0		67.0	20.0	NM_173651	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Missense_Mutation	SNP	ENST00000424728.1	hg19		.	.	.	.	.	.	.	.	.	.	G	0.082	-1.181143	0.01633	.	.	ENSG00000188738	ENST00000343098;ENST00000424728	T;T	0.39787	1.06;1.06	5.46	0.147	0.14838	.	1.007950	0.07960	N	0.982250	T	0.15478	0.0373	N	0.01874	-0.695	0.09310	N	1	.	.	.	.	.	.	T	0.21415	-1.0246	8	0.20519	T	0.43	.	7.6903	0.28565	0.65:0.0:0.35:0.0	.	.	.	.	M	6588;6499	ENSP00000344403:V6588M;ENSP00000401306:V6499M	ENSP00000344403:V6588M	V	+	1	0	FSIP2	186381773	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.879000	0.28146	-0.063000	0.13065	-0.423000	0.05987	GTG	.	.		0.323	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651		A	186673528	G	A	186673528	3	1	330	1	0	0	0	0	1	0	0	0	6083	1377	48	3	19828	3	FSIP2	2	186673528	Missense_Mutation	SNP	G	TCGA-PD-A5DF-01A-11D-A27I-10	149218814	186673528	56525845	9	46137										
BARD1	580	hgsc.bcm.edu	37	chr2	215617259	215617259	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	catcatctgtataatcgacaGgccgcagaccaaatatatta	6	10	2	1			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr2:215617259G>A	ENST00000260947.4	-	7	1723	c.1589C>T	c.(1588-1590)cCt>cTt	p.P530L	BARD1_ENST00000449967.2_Missense_Mutation_p.P386L	NM_000465.2|NM_001282543.1|NM_001282545.1|NM_001282548.1	NP_000456.2|NP_001269472.1|NP_001269474.1|NP_001269477.1	Q99728	BARD1_HUMAN	BRCA1 associated RING domain 1	530					cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mRNA 3'-end processing (GO:0031441)|negative regulation of protein export from nucleus (GO:0046826)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein catabolic process (GO:0045732)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of phosphorylation (GO:0042325)|tissue homeostasis (GO:0001894)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	kinase binding (GO:0019900)|ligase activity (GO:0016874)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(14)|prostate(4)|upper_aerodigestive_tract(1)	35		Renal(323;0.0243)		Epithelial(149;3.2e-06)|all cancers(144;0.000461)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		ATAATCGACAGGCCGCAGACC	0.368									Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																												p.P530L		Atlas-SNP	.											.	BARD1	138	.	0			c.C1589T						.						97	94	95					2																	215617259		2203	4300	6503	SO:0001583	missense	580	exon7	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	TCGACAGGCCGCA		CCDS2397.1, CCDS74645.1, CCDS74646.1, CCDS74647.1, CCDS74648.1	2q34-q35	2013-01-10			ENSG00000138376	ENSG00000138376		"Ankyrin repeat domain containing"	952	protein-coding gene	gene with protein product		601593				8944023, 9425226, 15159397	Standard	NM_001282548		Approved		uc002veu.2	Q99728	OTTHUMG00000133016	ENST00000260947.4:c.1589C>T	chr2.hg19:g.215617259G>A	ENSP00000260947:p.Pro530Leu	51.0	0.0		80.0	36.0	NM_000465	F6MDH7|F6MDH8|F6MDH9|O43574|Q53SS5	Missense_Mutation	SNP	ENST00000260947.4	hg19	CCDS2397.1	.	.	.	.	.	.	.	.	.	.	G	16.36	3.100709	0.56183	.	.	ENSG00000138376	ENST00000260947;ENST00000449967;ENST00000421162	T;T;D	0.88818	-0.41;-0.41;-2.43	4.64	4.64	0.57946	Ankyrin repeat-containing domain (2);	0.000000	0.85682	D	0.000000	D	0.93949	0.8063	M	0.70275	2.135	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.94683	0.7867	10	0.87932	D	0	-18.4088	17.7245	0.88361	0.0:0.0:1.0:0.0	.	386;530	E7EUI3;Q99728	.;BARD1_HUMAN	L	530;386;79	ENSP00000260947:P530L;ENSP00000406752:P386L;ENSP00000392245:P79L	ENSP00000260947:P530L	P	-	2	0	BARD1	215325504	1.000000	0.71417	1.000000	0.80357	0.291000	0.27294	6.257000	0.72480	2.411000	0.81874	0.460000	0.39030	CCT	.	.		0.368	BARD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256602.1	NM_000465		A	215617259	G	A	215617259	3	1	330	1	0	0	0	0	1	0	0	0	1312	1000	35	3	764	3	BARD1	2	215617259	Missense_Mutation	SNP	G	TCGA-PD-A5DF-01A-11D-A27I-10	28943731	215617259	27582114	10	46138										
FGD5	152273	hgsc.bcm.edu	37	chr3	14861791	14861791	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	gctccctacagggtggagcgGccgagggtcccgcagcccct	15	16	0	0			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr3:14861791G>T	ENST00000285046.5	+	1	1323	c.1213G>T	c.(1213-1215)Gcc>Tcc	p.A405S	FGD5_ENST00000543601.1_Missense_Mutation_p.A164S	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	405					actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			NS(2)|breast(2)|endometrium(3)|kidney(5)|large_intestine(10)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(1)	54						GGGTGGAGCGGCCGAGGGTCC	0.647																																					p.A405S		Atlas-SNP	.											.	FGD5	248	.	0			c.G1213T						.						24	29	27					3																	14861791		2032	4157	6189	SO:0001583	missense	152273	exon1			GGAGCGGCCGAGG	AK097276	CCDS46767.1	3p25.1	2013-01-10			ENSG00000154783	ENSG00000154783		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	19117	protein-coding gene	gene with protein product		614788					Standard	NM_152536		Approved	ZFYVE23, FLJ39957, FLJ00274	uc003bzc.3	Q6ZNL6	OTTHUMG00000155556	ENST00000285046.5:c.1213G>T	chr3.hg19:g.14861791G>T	ENSP00000285046:p.Ala405Ser	74.0	0.0		84.0	37.0	NM_152536	B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	Missense_Mutation	SNP	ENST00000285046.5	hg19	CCDS46767.1	.	.	.	.	.	.	.	.	.	.	G	7.241	0.601229	0.13939	.	.	ENSG00000154783	ENST00000285046;ENST00000543601	T;T	0.75050	-0.9;-0.75	4.54	2.4	0.29515	.	1.862650	0.02991	N	0.146895	T	0.57110	0.2031	N	0.14661	0.345	0.09310	N	1	B;B	0.18741	0.009;0.03	B;B	0.14578	0.007;0.011	T	0.44907	-0.9297	10	0.14656	T	0.56	-0.9812	6.0863	0.19968	0.1159:0.0:0.6372:0.2469	.	164;405	B7ZM68;Q6ZNL6	.;FGD5_HUMAN	S	405;164	ENSP00000285046:A405S;ENSP00000445949:A164S	ENSP00000285046:A405S	A	+	1	0	FGD5	14836795	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	0.084000	0.14891	0.831000	0.34780	0.491000	0.48974	GCC	.	.		0.647	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340628.1	NM_152536		T	14861791	G	T	14861791	3	4	330	1	0	0	0	0	1	0	0	0	5844	1203	42	3	1215	3	FGD5	3	14861791	Missense_Mutation	SNP	G	TCGA-PD-A5DF-01A-11D-A27I-10		14861791	183160639	11	46139										
KAT2B	8850	hgsc.bcm.edu	37	chr3	20113881	20113881	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	cctaacccctcacccactccCcccagagccgacctgcagca	5	23	1	1			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr3:20113881C>G	ENST00000263754.4	+	2	815	c.360C>G	c.(358-360)ccC>ccG	p.P120P	KAT2B_ENST00000426228.1_3'UTR	NM_003884.4	NP_003875.3	Q92831	KAT2B_HUMAN	K(lysine) acetyltransferase 2B	120					cell cycle arrest (GO:0007050)|cellular response to insulin stimulus (GO:0032869)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|histone H3-K9 acetylation (GO:0043970)|internal peptidyl-lysine acetylation (GO:0018393)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|Notch signaling pathway (GO:0007219)|peptidyl-lysine acetylation (GO:0018394)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein acetylation (GO:0006473)|regulation of protein ADP-ribosylation (GO:0010835)|rhythmic process (GO:0048511)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	A band (GO:0031672)|actomyosin (GO:0042641)|Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|I band (GO:0031674)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)	acetyltransferase activity (GO:0016407)|cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|histone acetyltransferase activity (GO:0004402)|histone deacetylase binding (GO:0042826)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	40						CACCCACTCCCCCCAGAGCCG	0.438																																					p.P120P		Atlas-SNP	.											.	KAT2B	73	.	0			c.C360G						.						107	117	113					3																	20113881		2203	4300	6503	SO:0001819	synonymous_variant	8850	exon2			CACTCCCCCCAGA	U57316	CCDS2634.1	3p24	2011-07-01	2008-07-04	2008-07-04	ENSG00000114166	ENSG00000114166		"Chromatin-modifying enzymes / K-acetyltransferases"	8638	protein-coding gene	gene with protein product		602303	"p300/CBP-associated factor"	PCAF		8684459, 9722949	Standard	NM_003884		Approved	P/CAF, GCN5, GCN5L	uc003cbq.3	Q92831	OTTHUMG00000130481	ENST00000263754.4:c.360C>G	chr3.hg19:g.20113881C>G		71.0	0.0		87.0	31.0	NM_003884	Q6NSK1	Silent	SNP	ENST00000263754.4	hg19	CCDS2634.1																																																																																			.	.		0.438	KAT2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252880.1	NM_003884		G	20113881	C	G	20113881	2	3	330	1	0	0	0	0	0	0	0	1	7991	610	22	4		4	KAT2B	3	20113881	Silent	SNP	C	TCGA-PD-A5DF-01A-11D-A27I-10	5252090	20113881	177908549	12	46140										
CACNA2D3	55799	hgsc.bcm.edu	37	chr3	54905638	54905638	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	ctgaggtggagtgggaagacCgagatgacgtggtaagtgat	18	4	0	5			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr3:54905638C>A	ENST00000474759.1	+	18	1747	c.1699C>A	c.(1699-1701)Cga>Aga	p.R567R	CACNA2D3_ENST00000415676.2_Silent_p.R567R|CACNA2D3-AS1_ENST00000471265.1_RNA|CACNA2D3_ENST00000288197.5_Silent_p.R567R|CACNA2D3_ENST00000490478.1_Silent_p.R473R	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3	567						integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(3)	59				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)	Amlodipine(DB00381)|Nilvadipine(DB06712)|Spironolactone(DB00421)	GTGGGAAGACCGAGATGACGT	0.493																																					p.R567R		Atlas-SNP	.											.	CACNA2D3	159	.	0			c.C1699A						.						178	176	177					3																	54905638		1968	4148	6116	SO:0001819	synonymous_variant	55799	exon18			GAAGACCGAGATG	AJ272268	CCDS54598.1	3p21.1	2010-10-05	2008-02-26		ENSG00000157445	ENSG00000157445		"Calcium channel subunits"	15460	protein-coding gene	gene with protein product		606399				11245980	Standard	XM_005265318		Approved	HSA272268	uc003dhf.3	Q8IZS8	OTTHUMG00000158580	ENST00000474759.1:c.1699C>A	chr3.hg19:g.54905638C>A		141.0	0.0		198.0	69.0	NM_018398	B2RPL6|Q9NY16|Q9NY18	Silent	SNP	ENST00000474759.1	hg19	CCDS54598.1																																																																																			.	.		0.493	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351402.1			A	54905638	C	A	54905638	2	1	330	1	0	0	0	0	0	0	0	1	2552	644	23	1		1	CACNA2D3	3	54905638	Silent	SNP	C	TCGA-PD-A5DF-01A-11D-A27I-10	34791757	54905638	143116792	13	46141										
PRICKLE2	166336	hgsc.bcm.edu	37	chr3	64148733	64148742	+	Frame_Shift_Del	DEL	TTCGCAGTTT	TTCGCAGTTT	-													0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	ctggtgtagtagctgcttgaTtcgcagtttctctccaggac							TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	TTCGCAGTTT	TTCGCAGTTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr3:64148733_64148742delTTCGCAGTTT	ENST00000295902.6	-	3	793_802	c.208_217delAAACTGCGAA	c.(208-219)aaactgcgaatcfs	p.KLRI70fs	PRICKLE2_ENST00000564377.1_Frame_Shift_Del_p.KLRI126fs	NM_198859.3	NP_942559.1	Q7Z3G6	PRIC2_HUMAN	prickle homolog 2 (Drosophila)	70	PET. {ECO:0000255|PROSITE- ProRule:PRU00636}.				establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|neuron projection development (GO:0031175)	apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.R72*(1)		breast(2)|endometrium(1)|large_intestine(9)|liver(1)|lung(10)|ovary(4)|prostate(2)|skin(2)|stomach(1)	32		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000971)|KIRC - Kidney renal clear cell carcinoma(15;0.00443)|Kidney(15;0.00497)		AGCTGCTTGATTCGCAGTTTCTCTCCAGGA	0.462																																					p.70_73del		Atlas-Indel,Pindel	.											.	PRICKLE2	88	.	1	Substitution - Nonsense(1)	stomach(1)	c.209_218del						.																																			SO:0001589	frameshift_variant	166336	exon3			.	AK127839	CCDS2902.1	3p14.3	2006-09-12	2006-09-12		ENSG00000163637	ENSG00000163637			20340	protein-coding gene	gene with protein product		608501	"prickle-like 2 (Drosophila)"			12525887	Standard	NM_198859		Approved	DKFZp686D143	uc003dmf.3	Q7Z3G6	OTTHUMG00000158789	ENST00000295902.6:c.208_217delAAACTGCGAA	chr3.hg19:g.64148733_64148742delTTCGCAGTTT	ENSP00000295902:p.Lys70fs	121.0	0.0		155.0	34.0	NM_198859	Q0VF44	Frame_Shift_Del	DEL	ENST00000295902.6	hg19	CCDS2902.1																																																																																			.	.		0.462	PRICKLE2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352219.1	NM_198859		-	64148742	TTCGCAGTTT	-	64148733	7	5	330	1	0	1	0	1	0	0	0	0	12499	1493	52	0	2341	0	PRICKLE2	3	64148733	Frame_Shift_Del	DEL	TTCGCAGTTT	TCGA-PD-A5DF-01A-11D-A27I-10	9243095	64148733	133873697	14	46142										
CASR	846	hgsc.bcm.edu	37	chr3	121994752	121994752	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	acctggtggggaactattccAtcatcaactggcacctctcc	8	14	3	0			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr3:121994752A>G	ENST00000490131.1	+	5	1843	c.1471A>G	c.(1471-1473)Atc>Gtc	p.I491V	CASR_ENST00000498619.1_Missense_Mutation_p.I491V|CASR_ENST00000296154.5_Missense_Mutation_p.I491V	NM_000388.3	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor	491					anatomical structure morphogenesis (GO:0009653)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|chemosensory behavior (GO:0007635)|detection of calcium ion (GO:0005513)|G-protein coupled receptor signaling pathway (GO:0007186)|metabolic process (GO:0008152)|ossification (GO:0001503)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|phosphatidylinositol phospholipase C activity (GO:0004435)			NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(45)|ovary(4)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	84				GBM - Glioblastoma multiforme(114;0.226)	Cinacalcet(DB01012)	GAACTATTCCATCATCAACTG	0.478																																					p.I491V		Atlas-SNP	.											.	CASR	190	.	0			c.A1471G						.						166	148	154					3																	121994752		2203	4300	6503	SO:0001583	missense	846	exon5			TATTCCATCATCA	U20760	CCDS3010.1, CCDS54632.1	3q21.1	2012-08-29	2008-08-01		ENSG00000036828	ENSG00000036828		"GPCR / Class C : Calcium-sensing receptors"	1514	protein-coding gene	gene with protein product	"severe neonatal hyperparathyroidism"	601199	"hypocalciuric hypercalcemia 1"	HHC, HHC1		7677761	Standard	NM_000388		Approved	FHH, NSHPT, GPRC2A	uc003eew.4	P41180	OTTHUMG00000159491	ENST00000490131.1:c.1471A>G	chr3.hg19:g.121994752A>G	ENSP00000418685:p.Ile491Val	168.0	0.0		241.0	96.0	NM_001178065	Q13912|Q16108|Q16109|Q16110|Q16379|Q2M1T0|Q4PJ19	Missense_Mutation	SNP	ENST00000490131.1	hg19	CCDS3010.1	.	.	.	.	.	.	.	.	.	.	A	15.62	2.886349	0.51908	.	.	ENSG00000036828	ENST00000490131;ENST00000498619;ENST00000296154	D;D;D	0.87103	-2.21;-2.21;-2.21	5.69	5.69	0.88448	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.91260	0.7245	L	0.55103	1.725	0.80722	D	1	P;D	0.63880	0.689;0.993	B;D	0.76071	0.265;0.987	D	0.89659	0.3875	10	0.30078	T	0.28	.	15.4289	0.75077	1.0:0.0:0.0:0.0	.	491;491	E7ENE0;P41180	.;CASR_HUMAN	V	491	ENSP00000418685:I491V;ENSP00000420194:I491V;ENSP00000296154:I491V	ENSP00000296154:I491V	I	+	1	0	CASR	123477442	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.013000	0.70776	2.291000	0.77112	0.533000	0.62120	ATC	.	.		0.478	CASR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355761.1	NM_000388		G	121994752	A	G	121994752	3	3	330	1	0	0	0	0	1	0	0	0	2684	217	8	2	1485	2	CASR	3	121994752	Missense_Mutation	SNP	A	TCGA-PD-A5DF-01A-11D-A27I-10	57846019	121994752	76027678	15	46143										
SORCS2	57537	hgsc.bcm.edu	37	chr4	7714544	7714544	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	ttctccaggcagtgcggcgaGgaggactacagctcctggga	15	11	1	0			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr4:7714544G>A	ENST00000507866.2	+	15	2062	c.1953G>A	c.(1951-1953)gaG>gaA	p.E651E	SORCS2_ENST00000329016.9_Silent_p.E479E	NM_020777.2	NP_065828.2	Q96PQ0	SORC2_HUMAN	sortilin-related VPS10 domain containing receptor 2	651					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(8)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	42						AGTGCGGCGAGGAGGACTACA	0.637																																					p.E651E		Atlas-SNP	.											.	SORCS2	98	.	0			c.G1953A						.						44	49	48					4																	7714544		2014	4192	6206	SO:0001819	synonymous_variant	57537	exon15			CGGCGAGGAGGAC	AB037750	CCDS47008.1	4p16.1	2008-02-05			ENSG00000184985	ENSG00000184985			16698	protein-coding gene	gene with protein product		606284				11499680	Standard	NM_020777		Approved	KIAA1329	uc003gkb.4	Q96PQ0	OTTHUMG00000159981	ENST00000507866.2:c.1953G>A	chr4.hg19:g.7714544G>A		87.0	0.0		170.0	70.0	NM_020777	Q9P2L7	Silent	SNP	ENST00000507866.2	hg19	CCDS47008.1																																																																																			.	.		0.637	SORCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358685.4	NM_020777		A	7714544	G	A	7714544	2	1	330	1	0	0	0	0	0	0	0	1	14946	991	35	3		3	SORCS2	4	7714544	Silent	SNP	G	TCGA-PD-A5DF-01A-11D-A27I-10		7714544	183439732	16	46144										
PIK3R1	5295	hgsc.bcm.edu	37	chr5	67591127	67591129	+	In_Frame_Del	DEL	AGA	AGA	-													0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	aaccagaccttatccagctgAgaaagacgagagaccaatac							TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr5:67591127_67591129delAGA	ENST00000521381.1	+	13	2336_2338	c.1720_1722delAGA	c.(1720-1722)agadel	p.R574del	PIK3R1_ENST00000274335.5_In_Frame_Del_p.R574del|PIK3R1_ENST00000396611.1_In_Frame_Del_p.R574del|PIK3R1_ENST00000521657.1_In_Frame_Del_p.R574del|PIK3R1_ENST00000336483.5_In_Frame_Del_p.R304del|PIK3R1_ENST00000320694.8_In_Frame_Del_p.R274del|PIK3R1_ENST00000523872.1_In_Frame_Del_p.R211del	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	574					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.R574_T576del(2)|p.R574T(2)|p.R574I(1)|p.R574fs*27(1)|p.0?(1)|p.?(1)|p.L570_D578del(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	TATCCAGCTGAGAAAGACGAGAG	0.379			"Mis, F, O"		"gliobastoma, ovarian, colorectal"					TCGA GBM(4;<1E-08)																											p.573_574del		Atlas-Indel,Pindel	.		Rec	yes		5	5q13.1	5295	"phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"		"E, O"	PIK3R1_ENST00000336483,NS,carcinoma,+1,5	PIK3R1	869	.	9	Substitution - Missense(3)|Deletion - In frame(3)|Whole gene deletion(1)|Deletion - Frameshift(1)|Unknown(1)	large_intestine(2)|endometrium(2)|central_nervous_system(1)|urinary_tract(1)|lung(1)|breast(1)|ovary(1)	c.1719_1721del						.																																			SO:0001651	inframe_deletion	5295	exon13			.	M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"SH2 domain containing"	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.1720_1722delAGA	chr5.hg19:g.67591127_67591129delAGA	ENSP00000428056:p.Arg574del	99.0	0.0		108.0	65.0	NM_181523	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	In_Frame_Del	DEL	ENST00000521381.1	hg19	CCDS3993.1																																																																																			.	.		0.379	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504		-	67591129	AGA	-	67591127	7	5	330	1	0	1	0	1	0	0	0	0	11927	296	11	0	1896	0	PIK3R1	5	67591127	In_Frame_Del	DEL	AGA	TCGA-PD-A5DF-01A-11D-A27I-10		67591127	113324133	17	46145										
NME5	8382	hgsc.bcm.edu	37	chr5	137465065	137465065	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	gcgacaagtggtccagaactCatgtaagctgttaagttggg	13	7	1	1			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr5:137465065C>T	ENST00000265191.2	-	3	271	c.222G>A	c.(220-222)atG>atA	p.M74I	NME5_ENST00000508252.1_5'UTR	NM_003551.2	NP_003542.1	P56597	NDK5_HUMAN	NME/NM23 family member 5	74					cilium assembly (GO:0042384)|CTP biosynthetic process (GO:0006241)|epithelial cilium movement (GO:0003351)|GTP biosynthetic process (GO:0006183)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|nucleoside metabolic process (GO:0009116)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|UTP biosynthetic process (GO:0006228)|ventricular system development (GO:0021591)	sperm flagellum (GO:0036126)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)			kidney(1)|large_intestine(1)|lung(2)|skin(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			GTCCAGAACTCATGTAAGCTG	0.378																																					p.M74I		Atlas-SNP	.											.	NME5	15	.	0			c.G222A						.						136	128	131					5																	137465065		2203	4300	6503	SO:0001583	missense	8382	exon3			AGAACTCATGTAA	Y14992	CCDS4197.1	5q31.2	2012-05-18	2012-05-18		ENSG00000112981	ENSG00000112981			7853	protein-coding gene	gene with protein product	"radial spoke 23 homolog (Chlamydomonas)"	603575	"non-metastatic cells 5, protein expressed in (nucleoside-diphosphate kinase)"			9742940, 19852809	Standard	NM_003551		Approved	nm23-H5, RSPH23	uc003lce.3	P56597	OTTHUMG00000129207	ENST00000265191.2:c.222G>A	chr5.hg19:g.137465065C>T	ENSP00000265191:p.Met74Ile	144.0	0.0		135.0	41.0	NM_003551	B2R5G7	Missense_Mutation	SNP	ENST00000265191.2	hg19	CCDS4197.1	.	.	.	.	.	.	.	.	.	.	C	31	5.074894	0.94000	.	.	ENSG00000112981	ENST00000265191	T	0.54071	0.59	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.61035	0.2315	L	0.42686	1.345	0.58432	D	0.999999	P	0.43578	0.811	P	0.52646	0.705	T	0.56733	-0.7930	10	0.39692	T	0.17	.	19.5106	0.95140	0.0:1.0:0.0:0.0	.	74	P56597	NDK5_HUMAN	I	74	ENSP00000265191:M74I	ENSP00000265191:M74I	M	-	3	0	NME5	137492964	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.743000	0.85020	2.600000	0.87896	0.655000	0.94253	ATG	.	.		0.378	NME5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251286.1	NM_003551		T	137465065	C	T	137465065	3	4	330	1	0	0	0	0	1	0	0	0	10503	826	29	3	432	3	NME5	5	137465065	Missense_Mutation	SNP	C	TCGA-PD-A5DF-01A-11D-A27I-10	69873938	137465065	43450195	18	46146										
KLHL32	114792	hgsc.bcm.edu	37	chr6	97561726	97561726	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	cgagctcctgcaatacatccGctttggcctaatggatgtgg	11	11	0	0			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr6:97561726G>A	ENST00000369261.4	+	7	1058	c.695G>A	c.(694-696)cGc>cAc	p.R232H	KLHL32_ENST00000539200.1_Missense_Mutation_p.R163H|KLHL32_ENST00000536676.1_Missense_Mutation_p.R196H|KLHL32_ENST00000544166.1_Intron	NM_052904.3	NP_443136.2	Q96NJ5	KLH32_HUMAN	kelch-like family member 32	232										breast(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(13)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		all_cancers(76;1.19e-06)|Acute lymphoblastic leukemia(125;5.83e-10)|all_hematologic(75;3.67e-07)|all_epithelial(107;0.00778)|Colorectal(196;0.122)		BRCA - Breast invasive adenocarcinoma(108;0.0558)		CAATACATCCGCTTTGGCCTA	0.532																																					p.R232H		Atlas-SNP	.											.	KLHL32	85	.	0			c.G695A						.						190	161	171					6																	97561726		2203	4300	6503	SO:0001583	missense	114792	exon7			ACATCCGCTTTGG	AB067487	CCDS5038.1, CCDS69154.1, CCDS69155.1, CCDS75495.1	6q16.3	2013-02-22	2013-02-22	2007-01-09	ENSG00000186231	ENSG00000186231		"Kelch-like", "BTB/POZ domain containing"	21221	protein-coding gene	gene with protein product			"BTB and kelch domain containing 5", "KIAA1900", "kelch-like 32 (Drosophila)"	BKLHD5, KIAA1900			Standard	NM_052904		Approved		uc010kcm.1	Q96NJ5	OTTHUMG00000015247	ENST00000369261.4:c.695G>A	chr6.hg19:g.97561726G>A	ENSP00000358265:p.Arg232His	183.0	0.0		180.0	95.0	NM_052904	B7Z346|B7Z4E2|E1P528|Q5THT0|Q96PY7	Missense_Mutation	SNP	ENST00000369261.4	hg19	CCDS5038.1	.	.	.	.	.	.	.	.	.	.	G	16.47	3.132779	0.56828	.	.	ENSG00000186231	ENST00000369261;ENST00000536676;ENST00000539200	T;T;T	0.80738	-1.41;-1.41;-1.41	5.09	5.09	0.68999	BTB/Kelch-associated (2);	0.000000	0.85682	D	0.000000	D	0.89487	0.6729	M	0.85630	2.765	0.80722	D	1	D;D;P;D	0.89917	0.997;0.999;0.947;1.0	D;P;P;D	0.69307	0.916;0.903;0.606;0.963	D	0.90725	0.4638	10	0.87932	D	0	.	18.6745	0.91524	0.0:0.0:1.0:0.0	.	163;196;232;232	B7Z4E2;B7Z346;Q96NJ5;Q6IQ08	.;.;KLH32_HUMAN;.	H	232;196;163	ENSP00000358265:R232H;ENSP00000440382:R196H;ENSP00000441527:R163H	ENSP00000358265:R232H	R	+	2	0	KLHL32	97668447	1.000000	0.71417	1.000000	0.80357	0.721000	0.41392	9.229000	0.95273	2.632000	0.89209	0.655000	0.94253	CGC	.	.		0.532	KLHL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041570.1	NM_052904		A	97561726	G	A	97561726	3	1	330	1	0	0	0	0	1	0	0	0	8395	1087	38	1	717	1	KLHL32	6	97561726	Missense_Mutation	SNP	G	TCGA-PD-A5DF-01A-11D-A27I-10		97561726	73553341	19	46147										
RFX6	222546	hgsc.bcm.edu	37	chr6	117237178	117237178	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	ttccttgaaataggttgataCgctcataatgatgtacaaaa	7	6	1	3			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr6:117237178C>T	ENST00000332958.2	+	8	804	c.788C>T	c.(787-789)aCg>aTg	p.T263M	RFX6_ENST00000471966.1_3'UTR	NM_173560.3	NP_775831.2	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	263					endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|pancreatic A cell differentiation (GO:0003310)|pancreatic D cell differentiation (GO:0003311)|pancreatic epsilon cell differentiation (GO:0090104)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of insulin secretion (GO:0050796)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell differentiation (GO:0003309)	nucleus (GO:0005634)	transcription regulatory region DNA binding (GO:0044212)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(29)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	59						TAGGTTGATACGCTCATAATG	0.333																																					p.T263M		Atlas-SNP	.											.	RFX6	141	.	0			c.C788T						.						136	135	135					6																	117237178		2203	4300	6503	SO:0001583	missense	222546	exon8			TTGATACGCTCAT	BC039248	CCDS5113.1	6q22.31	2008-08-04	2008-08-04	2008-08-04	ENSG00000185002	ENSG00000185002			21478	protein-coding gene	gene with protein product		612659	"regulatory factor X domain containing 1"	RFXDC1			Standard	NM_173560		Approved	MGC33442, dJ955L16.1	uc003pxm.3	Q8HWS3	OTTHUMG00000015449	ENST00000332958.2:c.788C>T	chr6.hg19:g.117237178C>T	ENSP00000332208:p.Thr263Met	104.0	0.0		143.0	53.0	NM_173560	Q5T6B3	Missense_Mutation	SNP	ENST00000332958.2	hg19	CCDS5113.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.823219	0.90873	.	.	ENSG00000185002	ENST00000332958	T	0.59772	0.24	5.97	5.97	0.96955	.	0.050665	0.85682	D	0.000000	T	0.75428	0.3848	M	0.78049	2.395	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.76556	-0.2916	10	0.87932	D	0	-21.3208	20.4324	0.99085	0.0:1.0:0.0:0.0	.	263	Q8HWS3	RFX6_HUMAN	M	263	ENSP00000332208:T263M	ENSP00000332208:T263M	T	+	2	0	RFX6	117343871	1.000000	0.71417	0.998000	0.56505	0.981000	0.71138	7.487000	0.81328	2.833000	0.97629	0.585000	0.79938	ACG	.	.		0.333	RFX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041970.2	NM_173560		T	117237178	C	T	117237178	3	4	330	1	0	0	0	0	1	0	0	0	13282	536	19	1	818	1	RFX6	6	117237178	Missense_Mutation	SNP	C	TCGA-PD-A5DF-01A-11D-A27I-10	19675452	117237178	53877889	20	46148										
ZBTB2	57621	hgsc.bcm.edu	37	chr6	151694605	151694605	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	aaccactttagttacctggtCtgatggacaaacaacatctt	6	10	2	1			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr6:151694605C>G	ENST00000325144.4	-	2	308	c.168G>C	c.(166-168)caG>caC	p.Q56H		NM_020861.1	NP_065912.1	Q8N680	ZBTB2_HUMAN	zinc finger and BTB domain containing 2	56	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|large_intestine(2)|lung(6)|skin(1)	12			BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.63e-11)		GTTACCTGGTCTGATGGACAA	0.443																																					p.Q56H		Atlas-SNP	.											.	ZBTB2	30	.	0			c.G168C						.						143	124	130					6																	151694605		2203	4300	6503	SO:0001583	missense	57621	exon2			CCTGGTCTGATGG	BC020172	CCDS5231.1	6q25.1	2013-01-09			ENSG00000181472	ENSG00000181472		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	20868	protein-coding gene	gene with protein product						10819331	Standard	NM_020861		Approved	KIAA1483, ZNF437, bA351K16.2	uc003qoh.3	Q8N680	OTTHUMG00000015834	ENST00000325144.4:c.168G>C	chr6.hg19:g.151694605C>G	ENSP00000323183:p.Gln56His	154.0	0.0		256.0	86.0	NM_020861	A8K7C7|Q5SZ81|Q9P245	Missense_Mutation	SNP	ENST00000325144.4	hg19	CCDS5231.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.402003	0.83120	.	.	ENSG00000181472	ENST00000325144	T	0.22336	1.96	5.4	5.4	0.78164	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	T	0.23572	0.0570	L	0.49571	1.57	0.80722	D	1	P	0.48503	0.911	P	0.57548	0.823	T	0.00920	-1.1514	10	0.59425	D	0.04	-33.2641	10.3457	0.43906	0.0:0.8789:0.0:0.1211	.	56	Q8N680	ZBTB2_HUMAN	H	56	ENSP00000323183:Q56H	ENSP00000323183:Q56H	Q	-	3	2	ZBTB2	151736298	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.738000	0.47401	2.515000	0.84797	0.462000	0.41574	CAG	.	.		0.443	ZBTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042715.1	NM_020861		G	151694605	C	G	151694605	3	3	330	1	0	0	0	0	1	0	0	0	17543	912	32	4	1384	4	ZBTB2	6	151694605	Missense_Mutation	SNP	C	TCGA-PD-A5DF-01A-11D-A27I-10	34457427	151694605	19420462	21	46149										
MTERF	7978	hgsc.bcm.edu	37	chr7	91503047	91503053	+	Frame_Shift_Del	DEL	GAATCCA	GAATCCA	-													0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	tttttaaagtacttatgcttGaatccagaacccgaggattt					rs138162673		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	GAATCCA	GAATCCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr7:91503047_91503053delGAATCCA	ENST00000351870.3	-	3	1148_1154	c.1055_1061delTGGATTC	c.(1054-1062)ctggattcafs	p.LDS352fs	MTERF_ENST00000406735.2_Frame_Shift_Del_p.LDS332fs|MTERF_ENST00000419292.1_Frame_Shift_Del_p.LDS332fs	NM_006980.3	NP_008911.1	Q99551	MTEF1_HUMAN		352					DNA geometric change (GO:0032392)|DNA-templated transcription, termination (GO:0006353)|gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of mitochondrial transcription (GO:0006393)|transcription from mitochondrial promoter (GO:0006390)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|liver(1)|lung(2)|skin(1)	14	all_cancers(62;2.28e-09)|all_epithelial(64;1.07e-07)|Breast(17;0.00371)|all_hematologic(106;0.091)|all_lung(186;0.178)|Lung NSC(181;0.235)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.0993)|Kidney(17;0.118)|Epithelial(20;0.136)|LUSC - Lung squamous cell carcinoma(200;0.176)			ACTTATGCTTGAATCCAGAACCCGAGG	0.333																																					p.352_354del		Atlas-INDEL	.											.	MTERF	32	.	0			c.1056_1062del						.																																			SO:0001589	frameshift_variant	7978	exon3			.																												ENST00000351870.3:c.1055_1061delTGGATTC	chr7.hg19:g.91503047_91503053delGAATCCA	ENSP00000248643:p.Leu352fs	73.0	0.0		71.0	11.0	NM_006980	A4D1E3|Q32NF8|Q53H51|Q9BVR7	Frame_Shift_Del	DEL	ENST00000351870.3	hg19	CCDS5621.1																																																																																			.	.		0.333	MTERF-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000342896.1			-	91503053	GAATCCA	-	91503047	7	5	330	1	0	1	0	1	0	0	0	0	9927	1294	45	0	142	0	MTERF	7	91503047	Frame_Shift_Del	DEL	GAATCCA	TCGA-PD-A5DF-01A-11D-A27I-10		91503047	67635616	22	46150										
ZNF3	7589	hgsc.bcm.edu	37	chr7	99662525	99662525	+	3'UTR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	ttttgcgtagttaaacagacGtgtatccagtctagttaagg	10	6	1	1			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr7:99662525G>A	ENST00000292450.4	+	0	1871				ZSCAN21_ENST00000543588.1_3'UTR|ZSCAN21_ENST00000456748.2_3'UTR|ZNF3_ENST00000413658.2_Silent_p.H94H	NM_145914.2	NP_666019.1	Q9Y5A6	ZSC21_HUMAN	zinc finger and SCAN domain containing 21						positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|skin(1)	21	Lung NSC(181;0.0211)|all_lung(186;0.0323)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)			TTAAACAGACGTGTATCCAGT	0.393																																					p.H94H		Atlas-SNP	.											.	ZNF3	54	.	0			c.C282T						.						130	129	129					7																	99662525		1990	4158	6148	SO:0001624	3_prime_UTR_variant	7551	exon6			ACAGACGTGTATC	AL136865	CCDS5681.1	7q11.1	2013-01-08	2006-10-06	2006-10-06	ENSG00000166529	ENSG00000166529		"-", "Zinc fingers, C2H2-type"	13104	protein-coding gene	gene with protein product		601261	"zinc finger protein 38 (KOX 25)", "zinc finger protein 38"	ZNF38		2288909, 2014798	Standard	NM_145914		Approved	DKFZp434L134, NY-REN-21, Zipro1	uc003uso.3	Q9Y5A6	OTTHUMG00000154583	ENST00000292450.4:c.*285G>A	chr7.hg19:g.99662525G>A		100.0	0.0		214.0	64.0	NM_017715	A4D2A6|D6W5T9|Q9H0B5	Silent	SNP	ENST00000292450.4	hg19	CCDS5681.1																																																																																			.	.		0.393	ZSCAN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336166.1	NM_145914		A	99662525	G	A	99662525	1	1	330	0	1	0	0	0	0	0	0	0	17844	1136	40	1		1	ZNF3	7	99662525	3'UTR	SNP	G	TCGA-PD-A5DF-01A-11D-A27I-10	8159478	99662525	59476138	23	46151										
SSPO	23145	hgsc.bcm.edu	37	chr7	149523815	149523815	+	RNA	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	cccactgcctgcccctgcacCcagcattctctgccctgggg	9	20	1	0			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr7:149523815C>G	ENST00000378016.2	+	0	14628							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GCCCCTGCACCCAGCATTCTC	0.672																																					p.T4875T		Atlas-SNP	.											.	.	.	.	0			c.C14625G						.						21	27	25					7																	149523815		2154	4256	6410			23145	exon103			CTGCACCCAGCAT	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		chr7.hg19:g.149523815C>G		24.0	0.0		37.0	11.0	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	hg19																																																																																				.	.		0.672	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				G	149523815	C	G	149523815	1	3	330	0	1	0	0	0	0	0	0	0	15204	610	22	4		4	SSPO	7	149523815	RNA	SNP	C	TCGA-PD-A5DF-01A-11D-A27I-10	49861290	149523815	9614848	24	46152										
EN2	2020	hgsc.bcm.edu	37	chr7	155251239	155251239	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	gctgcccgcggtcctgcaggCgcccggcaaccaccagcacc	12	20	0	0			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr7:155251239C>A	ENST00000297375.4	+	1	416	c.167C>A	c.(166-168)gCg>gAg	p.A56E	AC008060.8_ENST00000419225.1_lincRNA	NM_001427.3	NP_001418.2	P19622	HME2_HUMAN	engrailed homeobox 2	56					hindbrain development (GO:0030902)|midbrain development (GO:0030901)|multicellular organismal development (GO:0007275)|neuron development (GO:0048666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|large_intestine(1)|lung(2)	4	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GTCCTGCAGGCGCCCGGCAAC	0.741																																					p.A56E		Atlas-SNP	.											.	EN2	14	.	0			c.C167A						.						7	6	7					7																	155251239		1949	3820	5769	SO:0001583	missense	2020	exon1			TGCAGGCGCCCGG		CCDS5940.1	7q36.2	2011-06-20	2007-02-15		ENSG00000164778	ENSG00000164778		"Homeoboxes / ANTP class : NKL subclass"	3343	protein-coding gene	gene with protein product		131310					Standard	NM_001427		Approved		uc003wmb.3	P19622	OTTHUMG00000151354	ENST00000297375.4:c.167C>A	chr7.hg19:g.155251239C>A	ENSP00000297375:p.Ala56Glu	13.0	0.0		12.0	6.0	NM_001427	A4D252|Q549U3|Q9UD58	Missense_Mutation	SNP	ENST00000297375.4	hg19	CCDS5940.1	.	.	.	.	.	.	.	.	.	.	C	10.46	1.355211	0.24512	.	.	ENSG00000164778	ENST00000297375	D	0.91464	-2.85	3.6	1.7	0.24286	.	0.426630	0.22570	U	0.058359	D	0.83275	0.5219	N	0.19112	0.55	0.42593	D	0.993253	D	0.54397	0.966	P	0.45946	0.498	T	0.80248	-0.1461	10	0.66056	D	0.02	-2.4522	7.9384	0.29944	0.0:0.7436:0.1622:0.0942	.	56	P19622	HME2_HUMAN	E	56	ENSP00000297375:A56E	ENSP00000297375:A56E	A	+	2	0	EN2	154944000	1.000000	0.71417	0.012000	0.15200	0.127000	0.20565	3.570000	0.53834	0.209000	0.20645	-0.510000	0.04470	GCG	.	.		0.741	EN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322337.1	NM_001427		A	155251239	C	A	155251239	3	1	330	1	0	0	0	0	1	0	0	0	5112	768	27	1	169	1	EN2	7	155251239	Missense_Mutation	SNP	C	TCGA-PD-A5DF-01A-11D-A27I-10	5727424	155251239	3887424	25	46153										
TTPA	7274	hgsc.bcm.edu	37	chr8	63973814	63973814	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	tcacatgacataacttctcaTtgaatgctctcagaaatgct	5	10	3	3			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr8:63973814T>C	ENST00000260116.4	-	5	865	c.834A>G	c.(832-834)caA>caG	p.Q278Q	TTPA_ENST00000521138.1_Intron	NM_000370.3	NP_000361.1	P49638	TTPA_HUMAN	tocopherol (alpha) transfer protein	278					embryonic placenta development (GO:0001892)|intermembrane transport (GO:0046909)|intracellular pH reduction (GO:0051452)|lipid metabolic process (GO:0006629)|negative regulation of cell death (GO:0060548)|negative regulation of establishment of blood-brain barrier (GO:0090212)|response to nutrient (GO:0007584)|response to pH (GO:0009268)|response to toxic substance (GO:0009636)|transport (GO:0006810)|vitamin E metabolic process (GO:0042360)|vitamin transport (GO:0051180)	cytosol (GO:0005829)|late endosome (GO:0005770)	phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|transporter activity (GO:0005215)|vitamin E binding (GO:0008431)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)	15	Breast(64;0.0716)	all_cancers(86;0.145)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.123)			Vitamin E(DB00163)	TAACTTCTCATTGAATGCTCT	0.348																																					p.Q278Q		Atlas-SNP	.											.	TTPA	29	.	0			c.A834G						.						62	60	61					8																	63973814		2203	4300	6503	SO:0001819	synonymous_variant	7274	exon5			TTCTCATTGAATG	BC058000	CCDS6178.1	8q12.3	2007-07-18	2007-07-16			ENSG00000137561			12404	protein-coding gene	gene with protein product		600415	"ataxia (Friedreich-like) with vitamin E deficiency"	AVED		7719340, 7887897	Standard	NM_000370		Approved		uc003xux.2	P49638		ENST00000260116.4:c.834A>G	chr8.hg19:g.63973814T>C		31.0	0.0		45.0	17.0	NM_000370	Q71V64	Silent	SNP	ENST00000260116.4	hg19	CCDS6178.1																																																																																			.	.		0.348	TTPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378460.1	NM_000370		C	63973814	T	C	63973814	2	2	330	1	0	0	0	0	0	0	0	1	16751	1490	52	2		2	TTPA	8	63973814	Silent	SNP	T	TCGA-PD-A5DF-01A-11D-A27I-10		63973814	82390208	26	46154										
FAM82B	51115	hgsc.bcm.edu	37	chr8	87520767	87520767	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	cgcaatgcccgcggctgcccGaagtccccgcagggagacga	14	16	0	1			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr8:87520767G>T	ENST00000406452.3	-	1	242	c.83C>A	c.(82-84)tCg>tAg	p.S28*	RMDN1_ENST00000430676.2_Nonsense_Mutation_p.S28*|RMDN1_ENST00000518772.1_5'UTR|RMDN1_ENST00000519966.1_Nonsense_Mutation_p.S28*|CPNE3_ENST00000198765.4_Intron|RMDN1_ENST00000523911.1_Intron	NM_016033.2	NP_057117.2	Q96DB5	RMD1_HUMAN	regulator of microtubule dynamics 1	28						microtubule (GO:0005874)|mitochondrion (GO:0005739)											GCGGCTGCCCGAAGTCCCCGC	0.697																																					p.S28X		Atlas-SNP	.											.	.	.	.	0			c.C83A						.						10	13	12					8																	87520767		2175	4257	6432	SO:0001587	stop_gained	51115	exon1			CTGCCCGAAGTCC	AK000672	CCDS34918.1, CCDS69509.1, CCDS69510.1	8q21.3	2013-01-11	2013-01-11	2013-01-11	ENSG00000176623	ENSG00000176623			24285	protein-coding gene	gene with protein product		611871	"family with sequence similarity 82, member B"	FAM82B		10810093	Standard	NM_016033		Approved	CGI-90, FLJ20665, RMD1	uc003ydu.3	Q96DB5	OTTHUMG00000163692	ENST00000406452.3:c.83C>A	chr8.hg19:g.87520767G>T	ENSP00000385927:p.Ser28*	20.0	0.0		9.0	5.0	NM_016033	A9UMZ8|B4DNF5|B4DZW6|B5MC61|C9JSC6|E7EVI2|Q9Y398	Nonsense_Mutation	SNP	ENST00000406452.3	hg19	CCDS34918.1	.	.	.	.	.	.	.	.	.	.	g	18.51	3.640460	0.67244	.	.	ENSG00000176623	ENST00000406452;ENST00000519966;ENST00000430676	.	.	.	3.87	0.886	0.19194	.	2.004110	0.02652	N	0.106541	.	.	.	.	.	.	0.09310	N	0.999993	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	3.7802	6.7219	0.23334	0.1135:0.2801:0.6065:0.0	.	.	.	.	X	28	.	ENSP00000385927:S28X	S	-	2	0	FAM82B	87589883	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.828000	0.27435	0.043000	0.15746	-0.119000	0.15052	TCG	.	.		0.697	RMDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374770.2	NM_016033		T	87520767	G	T	87520767	4	4	330	1	0	0	0	0	0	1	0	0	5640	1059	37	1	901	1	FAM82B	8	87520767	Nonsense_Mutation	SNP	G	TCGA-PD-A5DF-01A-11D-A27I-10	23546953	87520767	58843255	27	46155										
COL14A1	7373	hgsc.bcm.edu	37	chr8	121381587	121381587	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	aggaccttcaggggagagtcGgcctggcagccctgggcccc	16	14	1	1			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr8:121381587G>A	ENST00000297848.3	+	47	5444	c.5174G>A	c.(5173-5175)cGg>cAg	p.R1725Q	COL14A1_ENST00000247781.3_Missense_Mutation_p.R1630Q|COL14A1_ENST00000309791.4_Missense_Mutation_p.R1725Q	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1									p.R1725Q(1)		NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			GGGGAGAGTCGGCCTGGCAGC	0.562																																					p.R1725Q		Atlas-SNP	.											COL14A1,colon,carcinoma,0,1	COL14A1	292	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5174A						.						49	53	52					8																	121381587		2203	4300	6503	SO:0001583	missense	7373	exon47			AGAGTCGGCCTGG		CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"Collagens", "Fibronectin type III domain containing"	2191	protein-coding gene	gene with protein product		120324	"undulin"	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.5174G>A	chr8.hg19:g.121381587G>A	ENSP00000297848:p.Arg1725Gln	22.0	0.0		40.0	13.0	NM_021110		Missense_Mutation	SNP	ENST00000297848.3	hg19	CCDS34938.1	.	.	.	.	.	.	.	.	.	.	G	32	5.115046	0.94339	.	.	ENSG00000187955	ENST00000309791;ENST00000297848;ENST00000247781;ENST00000440844	D;D;D;D	0.94184	-2.16;-2.2;-3.14;-3.37	4.84	4.84	0.62591	.	0.058095	0.64402	D	0.000003	D	0.89371	0.6696	L	0.28740	0.885	0.80722	D	1	D	0.59357	0.985	P	0.44447	0.45	D	0.87133	0.2198	10	0.13470	T	0.59	.	18.4389	0.90658	0.0:0.0:1.0:0.0	.	1725	Q05707	COEA1_HUMAN	Q	1725;1725;1630;72	ENSP00000311809:R1725Q;ENSP00000297848:R1725Q;ENSP00000247781:R1630Q;ENSP00000403640:R72Q	ENSP00000247781:R1630Q	R	+	2	0	COL14A1	121450768	1.000000	0.71417	0.999000	0.59377	0.980000	0.70556	7.673000	0.83973	2.618000	0.88619	0.561000	0.74099	CGG	.	.		0.562	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		A	121381587	G	A	121381587	3	1	330	1	0	0	0	0	1	0	0	0	3673	1116	39	1	5356	1	COL14A1	8	121381587	Missense_Mutation	SNP	G	TCGA-PD-A5DF-01A-11D-A27I-10	33860820	121381587	24982435	28	46156										
MLLT10	8028	hgsc.bcm.edu	37	chr10	21901356	21901356	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	gacatgtaataaacatggatGtcgacaggctttccatgtaa	9	7	0	0			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr10:21901356G>T	ENST00000307729.7	+	6	663	c.485G>T	c.(484-486)tGt>tTt	p.C162F	MLLT10_ENST00000495130.1_3'UTR|MLLT10_ENST00000377059.3_Missense_Mutation_p.C162F|MLLT10_ENST00000377072.3_Missense_Mutation_p.C162F|MLLT10_ENST00000446906.2_Missense_Mutation_p.C162F			P55197	AF10_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10	162	Interaction with FSTL3.|Self-association.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6						AAACATGGATGTCGACAGGCT	0.373			T	"MLL, PICALM, CDK6"	AL																																p.C162F		Atlas-SNP	.		Dom	yes		10	10p12	8028	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10 (AF10)"		L	.	MLLT10	183	.	0			c.G485T						.						116	103	107					10																	21901356		2203	4300	6503	SO:0001583	missense	8028	exon5			ATGGATGTCGACA	U13948	CCDS7135.1, CCDS55706.1, CCDS55707.1, CCDS55708.1	10p12	2013-01-28	2001-11-28		ENSG00000078403	ENSG00000078403		"Zinc fingers, PHD-type"	16063	protein-coding gene	gene with protein product		602409	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 10"			7888665	Standard	NM_004641		Approved	AF10	uc021pny.1	P55197	OTTHUMG00000017799	ENST00000307729.7:c.485G>T	chr10.hg19:g.21901356G>T	ENSP00000307411:p.Cys162Phe	50.0	0.0		48.0	20.0	NM_001195626	B1ANA8|Q5JT37|Q5VX90|Q66K63	Missense_Mutation	SNP	ENST00000307729.7	hg19	CCDS55708.1	.	.	.	.	.	.	.	.	.	.	G	32	5.162787	0.94727	.	.	ENSG00000078403	ENST00000377072;ENST00000446906;ENST00000307729;ENST00000396529;ENST00000377059	T;T;T;T	0.53206	0.63;0.63;0.63;0.63	5.98	5.98	0.97165	Zinc finger, PHD-finger (1);Zinc finger, PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.83640	0.5298	H	0.99249	4.485	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.87578	0.998;0.998;0.998	D	0.89840	0.4002	10	0.87932	D	0	.	20.4434	0.99119	0.0:0.0:1.0:0.0	.	162;162;162	E9PBP4;Q5VX90;P55197	.;.;AF10_HUMAN	F	162;162;162;8;162	ENSP00000366272:C162F;ENSP00000401406:C162F;ENSP00000307411:C162F;ENSP00000366258:C162F	ENSP00000307411:C162F	C	+	2	0	MLLT10	21941362	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.838000	0.97847	0.655000	0.94253	TGT	.	.		0.373	MLLT10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047136.1			T	21901356	G	T	21901356	3	4	330	1	0	0	0	0	1	0	0	0	9635	1377	48	3	503	3	MLLT10	10	21901356	Missense_Mutation	SNP	G	TCGA-PD-A5DF-01A-11D-A27I-10		21901356	113633391	29	46157										
OR51B6	390058	hgsc.bcm.edu	37	chr11	5372775	5372775	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	tgcttccaccttccagcttaCtggcttcccaggcatggaga	9	14	0	1			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr11:5372775C>T	ENST00000380219.1	+	1	38	c.38C>T	c.(37-39)aCt>aTt	p.T13I	HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	13					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|skin(2)|urinary_tract(1)	21		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TTCCAGCTTACTGGCTTCCCA	0.443																																					p.T13I		Atlas-SNP	.											.	OR51B6	53	.	0			c.C38T						.						91	77	82					11																	5372775		2201	4297	6498	SO:0001583	missense	390058	exon1			AGCTTACTGGCTT		CCDS31379.1	11p15.4	2012-08-09			ENSG00000176239	ENSG00000176239		"GPCR / Class A : Olfactory receptors"	19600	protein-coding gene	gene with protein product							Standard	NM_001004750		Approved		uc010qzb.2	Q9H340	OTTHUMG00000066669	ENST00000380219.1:c.38C>T	chr11.hg19:g.5372775C>T	ENSP00000369568:p.Thr13Ile	148.0	0.0		229.0	87.0	NM_001004750		Missense_Mutation	SNP	ENST00000380219.1	hg19	CCDS31379.1	.	.	.	.	.	.	.	.	.	.	C	15.10	2.733416	0.48939	.	.	ENSG00000176239	ENST00000537299;ENST00000380219	T	0.00289	8.28	4.93	4.93	0.64822	.	0.420400	0.20173	N	0.097698	T	0.00412	0.0013	L	0.58510	1.815	0.27040	N	0.964047	D	0.59357	0.985	P	0.61070	0.883	T	0.55134	-0.8188	10	0.46703	T	0.11	.	6.9526	0.24554	0.0:0.7309:0.1775:0.0916	.	13	Q9H340	O51B6_HUMAN	I	12;13	ENSP00000369568:T13I	ENSP00000369568:T13I	T	+	2	0	OR51B6	5329351	0.018000	0.18449	0.991000	0.47740	0.823000	0.46562	0.948000	0.29096	2.554000	0.86153	0.557000	0.71058	ACT	.	.		0.443	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750		T	5372775	C	T	5372775	3	4	330	1	0	0	0	0	1	0	0	0	11101	565	20	3	40	3	OR51B6	11	5372775	Missense_Mutation	SNP	C	TCGA-PD-A5DF-01A-11D-A27I-10		5372775	129633741	30	46158										
EED	8726	hgsc.bcm.edu	37	chr11	85975252	85975260	+	In_Frame_Del	DEL	CTGGTGGCA	CTGGTGGCA	-													0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	ggaatatccagacggacactCtggtggcaatatttggaggc							TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	CTGGTGGCA	CTGGTGGCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr11:85975252_85975260delCTGGTGGCA	ENST00000263360.6	+	7	1359_1367	c.673_681delCTGGTGGCA	c.(673-681)ctggtggcadel	p.LVA225del	EED_ENST00000351625.6_In_Frame_Del_p.LVA225del|EED_ENST00000528180.1_In_Frame_Del_p.LVA225del|EED_ENST00000327320.4_In_Frame_Del_p.LVA225del	NM_003797.3	NP_003788.2	O75530	EED_HUMAN	embryonic ectoderm development	225	Interaction with EZH2. {ECO:0000250}.|Required for interaction with the matrix protein MA of HIV-1.				negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K27 methylation (GO:0061087)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|histone methyltransferase activity (GO:0042054)|identical protein binding (GO:0042802)			haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	21		Acute lymphoblastic leukemia(157;7.24e-07)|all_hematologic(158;0.00092)				GACGGACACTCTGGTGGCAATATTTGGAG	0.388																																					p.224_227del		Atlas-Indel,Pindel	.											.	EED	50	.	0			c.672_680del						.																																			SO:0001651	inframe_deletion	8726	exon7			.	AF078933	CCDS8273.1, CCDS8274.1	11q14.2-q22.3	2013-01-10			ENSG00000074266	ENSG00000074266		"WD repeat domain containing"	3188	protein-coding gene	gene with protein product	"WD protein associating with integrin cytoplasmic tails 1"	605984				9765275, 9806832	Standard	NM_003797		Approved	WAIT-1, HEED	uc001pbp.3	O75530	OTTHUMG00000167209	ENST00000263360.6:c.673_681delCTGGTGGCA	chr11.hg19:g.85975252_85975260delCTGGTGGCA	ENSP00000263360:p.Leu225_Ala227del	113.0	0.0		110.0	15.0	NM_152991	A8K7V5|O00149|Q6NTH2|Q7LDA5|Q7LDG8|Q86VV2|Q9UNY7	In_Frame_Del	DEL	ENST00000263360.6	hg19	CCDS8273.1																																																																																			.	.		0.388	EED-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393733.1	NM_003797		-	85975260	CTGGTGGCA	-	85975252	7	5	330	1	0	1	0	1	0	0	0	0	4924	912	32	0	699	0	EED	11	85975252	In_Frame_Del	DEL	CTGGTGGCA	TCGA-PD-A5DF-01A-11D-A27I-10	80602477	85975252	49031264	31	46159										
IL10RA	3587	hgsc.bcm.edu	37	chr11	117860190	117860190	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	tcctggaactccatctccaaCtgtagccagaccctgtccta	6	16	1	1			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr11:117860190C>A	ENST00000227752.3	+	3	342	c.222C>A	c.(220-222)aaC>aaA	p.N74K	IL10RA_ENST00000545409.1_Intron|IL10RA_ENST00000541785.1_Missense_Mutation_p.N54K|IL10RA_ENST00000533700.1_3'UTR	NM_001558.3	NP_001549.2	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha	74					cytokine-mediated signaling pathway (GO:0019221)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-10 receptor activity (GO:0004920)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(2)|prostate(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.07e-05)|Epithelial(105;0.00108)		CCATCTCCAACTGTAGCCAGA	0.562																																					p.N74K		Atlas-SNP	.											.	IL10RA	46	.	0			c.C222A						.						160	131	141					11																	117860190		2200	4296	6496	SO:0001583	missense	3587	exon3			CTCCAACTGTAGC	U00672	CCDS8388.1	11q23	2014-09-17			ENSG00000110324	ENSG00000110324		"Interleukins and interleukin receptors", "CD molecules"	5964	protein-coding gene	gene with protein product		146933		IL10R		8120391	Standard	NR_026691		Approved	HIL-10R, CDW210A, CD210a, CD210	uc001prv.3	Q13651	OTTHUMG00000166523	ENST00000227752.3:c.222C>A	chr11.hg19:g.117860190C>A	ENSP00000227752:p.Asn74Lys	231.0	0.0		308.0	100.0	NM_001558	A8K6I0|B0YJ27	Missense_Mutation	SNP	ENST00000227752.3	hg19	CCDS8388.1	.	.	.	.	.	.	.	.	.	.	C	9.135	1.012470	0.19277	.	.	ENSG00000110324	ENST00000227752;ENST00000541785;ENST00000536858	T;T	0.72725	-0.68;-0.68	5.14	3.26	0.37387	Fibronectin, type III (1);Immunoglobulin-like fold (1);	1.049110	0.07325	N	0.878265	T	0.55784	0.1942	L	0.27053	0.805	0.80722	D	1	B;B	0.21381	0.045;0.055	B;B	0.28139	0.032;0.086	T	0.36237	-0.9756	10	0.05620	T	0.96	-0.0674	8.5193	0.33266	0.0:0.7638:0.1531:0.0831	.	54;74	F5GYV8;Q13651	.;I10R1_HUMAN	K	74;54;54	ENSP00000227752:N74K;ENSP00000441397:N54K	ENSP00000227752:N74K	N	+	3	2	IL10RA	117365400	0.693000	0.27728	0.158000	0.22627	0.014000	0.08584	0.960000	0.29253	0.675000	0.31264	-0.244000	0.11960	AAC	.	.		0.562	IL10RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390167.1			A	117860190	C	A	117860190	3	1	330	1	0	0	0	0	1	0	0	0	7629	564	20	3	232	3	IL10RA	11	117860190	Missense_Mutation	SNP	C	TCGA-PD-A5DF-01A-11D-A27I-10	31884938	117860190	17146326	32	46160										
OVCH1	341350	hgsc.bcm.edu	37	chr12	29626033	29626033	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	ttggttcaaatttgtttaaaGactctgtagaagaaaaaaaa	7	3	2	3			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr12:29626033G>A	ENST00000318184.5	-	15	1603	c.1604C>T	c.(1603-1605)tCt>tTt	p.S535F	OVCH1-AS1_ENST00000551108.1_Intron|OVCH1-AS1_ENST00000549411.1_Intron	NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	535						extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					TTTGTTTAAAGACTCTGTAGA	0.348																																					p.S535F		Atlas-SNP	.											.	OVCH1	195	.	0			c.C1604T						.						86	81	82					12																	29626033		1818	4077	5895	SO:0001583	missense	341350	exon15			TTTAAAGACTCTG	BN000128		12p11.23	2012-11-08			ENSG00000187950	ENSG00000187950			23080	protein-coding gene	gene with protein product						12838346	Standard	NM_183378		Approved	OVCH	uc001rix.1	Q7RTY7	OTTHUMG00000167741	ENST00000318184.5:c.1604C>T	chr12.hg19:g.29626033G>A	ENSP00000326708:p.Ser535Phe	63.0	0.0		51.0	17.0	NM_183378		Missense_Mutation	SNP	ENST00000318184.5	hg19		.	.	.	.	.	.	.	.	.	.	G	9.533	1.111348	0.20714	.	.	ENSG00000187950	ENST00000318184	D	0.87103	-2.21	2.46	-1.93	0.07594	.	.	.	.	.	T	0.69450	0.3112	N	0.08118	0	0.09310	N	1	B	0.15930	0.015	B	0.14578	0.011	T	0.55211	-0.8176	9	0.45353	T	0.12	.	3.8777	0.09064	0.2632:0.3973:0.3395:0.0	.	535	Q7RTY7	OVCH1_HUMAN	F	535	ENSP00000326708:S535F	ENSP00000326708:S535F	S	-	2	0	OVCH1	29517300	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.268000	0.08607	-0.516000	0.06470	-0.176000	0.13171	TCT	.	.		0.348	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378		A	29626033	G	A	29626033	3	1	330	1	0	0	0	0	1	0	0	0	11332	942	33	3	1856	3	OVCH1	12	29626033	Missense_Mutation	SNP	G	TCGA-PD-A5DF-01A-11D-A27I-10		29626033	104225862	33	46161										
EP400	57634	hgsc.bcm.edu	37	chr12	132512744	132512744	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	gggaaggaggccgggccagcGcacagttacacttcatcctc	13	13	1	0	rs34531099	byFrequency	TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr12:132512744G>T	ENST00000333577.4	+	28	5509	c.5400G>T	c.(5398-5400)gcG>gcT	p.A1800A	EP400_ENST00000389561.2_Silent_p.A1764A|EP400_ENST00000389562.2_Silent_p.A1763A|EP400_ENST00000332482.4_Silent_p.A1727A|EP400_ENST00000330386.6_Silent_p.A1683A			Q96L91	EP400_HUMAN	E1A binding protein p400	1800					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		CCGGGCCAGCGCACAGTTACA	0.557																																					p.A1764A		Atlas-SNP	.											.	EP400	370	.	0			c.G5292T						.						155	138	144					12																	132512744		2203	4300	6503	SO:0001819	synonymous_variant	57634	exon27			GCCAGCGCACAGT	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"trinucleotide repeat containing 12"	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.5400G>T	chr12.hg19:g.132512744G>T		135.0	0.0		329.0	141.0	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	hg19																																																																																				.	G|0.997;A|0.003		0.557	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		T	132512744	G	T	132512744	2	4	330	1	0	0	0	0	0	0	0	1	5151	1074	38	1		1	EP400	12	132512744	Silent	SNP	G	TCGA-PD-A5DF-01A-11D-A27I-10	102886711	132512744	1339151	34	46162										
C14orf49	161176	hgsc.bcm.edu	37	chr14	95909555	95909555	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	tccattttgtgctggtggttGgggttctcctggaccagagg	15	8	1	1			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr14:95909555G>A	ENST00000334258.5	-	10	1862	c.1848C>T	c.(1846-1848)ccC>ccT	p.P616P	SYNE3_ENST00000554873.1_Silent_p.P373P|SYNE3_ENST00000557275.1_Silent_p.P616P	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	616					cytoskeletal anchoring at nuclear membrane (GO:0090286)|cytoskeleton organization (GO:0007010)|establishment of protein localization to membrane (GO:0090150)|regulation of cell shape (GO:0008360)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear outer membrane (GO:0005640)|SUN-KASH complex (GO:0034993)	actin filament binding (GO:0051015)			breast(1)|endometrium(2)|lung(25)	28						GCTGGTGGTTGGGGTTCTCCT	0.602																																					p.P616P		Atlas-SNP	.											.	SYNE3	130	.	0			c.C1848T						.						116	121	119					14																	95909555		2203	4300	6503	SO:0001819	synonymous_variant	161176	exon10			GTGGTTGGGGTTC	AK098471	CCDS9935.1	14q32.13	2012-05-31	2012-05-31	2012-05-31	ENSG00000176438	ENSG00000176438			19861	protein-coding gene	gene with protein product		610861	"chromosome 14 open reading frame 49"	C14orf49			Standard	NM_152592		Approved	FLJ25605, NET53, Nesprin-3, Nesp3	uc001yei.4	Q6ZMZ3	OTTHUMG00000171632	ENST00000334258.5:c.1848C>T	chr14.hg19:g.95909555G>A		103.0	0.0		170.0	58.0	NM_152592	A6H8H3|Q86SX5|Q8N7G8	Silent	SNP	ENST00000334258.5	hg19	CCDS9935.1																																																																																			.	.		0.602	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592		A	95909555	G	A	95909555	2	1	330	1	0	0	0	0	0	0	0	1	1778	1335	47	3		3	C14orf49	14	95909555	Silent	SNP	G	TCGA-PD-A5DF-01A-11D-A27I-10		95909555	11439985	35	46163										
AP4E1	23431	hgsc.bcm.edu	37	chr15	51223097	51223097	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	ccagtagaattcaattaccaCagtgtgccagcaccatggtt	8	11	1	1			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr15:51223097C>T	ENST00000261842.5	+	7	904	c.798C>T	c.(796-798)caC>caT	p.H266H	AP4E1_ENST00000560508.1_Silent_p.H191H	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	266					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	coated pit (GO:0005905)|Golgi apparatus (GO:0005794)|membrane coat (GO:0030117)				breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(5)|skin(2)	27				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		TCAATTACCACAGTGTGCCAG	0.378																																					p.H266H		Atlas-SNP	.											.	AP4E1	78	.	0			c.C798T						.						110	111	110					15																	51223097		2196	4294	6490	SO:0001819	synonymous_variant	23431	exon7			TTACCACAGTGTG	AB030653	CCDS32240.1, CCDS58362.1	15q21.2	2014-09-17			ENSG00000081014	ENSG00000081014			573	protein-coding gene	gene with protein product		607244				10436028, 21620353	Standard	NM_007347		Approved	AP-4-EPSILON, SPG51	uc001zyx.2	Q9UPM8	OTTHUMG00000172458	ENST00000261842.5:c.798C>T	chr15.hg19:g.51223097C>T		70.0	0.0		107.0	40.0	NM_007347	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	Silent	SNP	ENST00000261842.5	hg19	CCDS32240.1																																																																																			.	.		0.378	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418656.1			T	51223097	C	T	51223097	2	4	330	1	0	0	0	0	0	0	0	1	752	477	17	3		3	AP4E1	15	51223097	Silent	SNP	C	TCGA-PD-A5DF-01A-11D-A27I-10		51223097	51308295	36	46164										
CORO2B	10391	hgsc.bcm.edu	37	chr15	69011111	69011111	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	acaagctggtgactctcaagGgcctgatcgagcccatctcc	10	14	2	2			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr15:69011111G>T	ENST00000566799.1	+	9	1071	c.1042G>T	c.(1042-1044)Ggc>Tgc	p.G348C	CORO2B_ENST00000540068.1_Missense_Mutation_p.G343C|CORO2B_ENST00000261861.5_Missense_Mutation_p.G343C|CORO2B_ENST00000543950.1_Missense_Mutation_p.G343C			Q9UQ03	COR2B_HUMAN	coronin, actin binding protein, 2B	348					actin cytoskeleton organization (GO:0030036)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|membrane (GO:0016020)	actin binding (GO:0003779)|actin filament binding (GO:0051015)			kidney(3)|large_intestine(13)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36						GACTCTCAAGGGCCTGATCGA	0.627																																					p.G348C		Atlas-SNP	.											.	CORO2B	68	.	0			c.G1042T						.						84	63	71					15																	69011111		2200	4298	6498	SO:0001583	missense	10391	exon9			CTCAAGGGCCTGA	AB010098	CCDS53952.1, CCDS10229.2	15q22.31	2013-01-10	2001-11-28		ENSG00000103647	ENSG00000103647		"Coronins", "WD repeat domain containing"	2256	protein-coding gene	gene with protein product	"clipin C", "coronin, actin-binding, 2B"	605002	"coronin, actin-binding protein, 2B"			10224093, 10231032	Standard	NM_001190456		Approved	ClipinC, KIAA0925	uc021spj.1	Q9UQ03	OTTHUMG00000133288	ENST00000566799.1:c.1042G>T	chr15.hg19:g.69011111G>T	ENSP00000454783:p.Gly348Cys	78.0	0.0		175.0	64.0	NM_006091	A8K0W3|O94767|Q8TAN1	Missense_Mutation	SNP	ENST00000566799.1	hg19	CCDS10229.2	.	.	.	.	.	.	.	.	.	.	G	22.2	4.260590	0.80246	.	.	ENSG00000103647	ENST00000261861;ENST00000540068;ENST00000543950	T;T	0.60040	0.22;0.22	5.48	5.48	0.80851	Domain of unknown function DUF1900 (1);	0.096141	0.64402	D	0.000001	T	0.76421	0.3985	M	0.85777	2.775	0.58432	D	0.999995	D	0.71674	0.998	D	0.73708	0.981	T	0.79841	-0.1633	10	0.87932	D	0	-28.3831	11.3953	0.49838	0.0835:0.0:0.9165:0.0	.	348	Q9UQ03	COR2B_HUMAN	C	348;343;343	ENSP00000446250:G343C;ENSP00000443819:G343C	ENSP00000261861:G348C	G	+	1	0	CORO2B	66798165	1.000000	0.71417	1.000000	0.80357	0.832000	0.47134	6.298000	0.72763	2.575000	0.86900	0.467000	0.42956	GGC	.	.		0.627	CORO2B-203	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_006091		T	69011111	G	T	69011111	3	4	330	1	0	0	0	0	1	0	0	0	3759	1232	43	3	1076	3	CORO2B	15	69011111	Missense_Mutation	SNP	G	TCGA-PD-A5DF-01A-11D-A27I-10	17788014	69011111	33520281	37	46165										
SLC47A1	55244	hgsc.bcm.edu	37	chr17	19452981	19452981	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	tatgtcacgatcttcattccAgctcttcctgtaagtgctca	6	12	5	0			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr17:19452981A>T	ENST00000270570.4	+	5	575	c.489A>T	c.(487-489)ccA>ccT	p.P163P	SLC47A1_ENST00000542886.1_Silent_p.P163P|SLC47A1_ENST00000584348.1_3'UTR|SLC47A1_ENST00000575023.1_Silent_p.P163P|SLC47A1_ENST00000457293.1_Silent_p.P163P|SLC47A1_ENST00000395585.1_Silent_p.P163P|SLC47A1_ENST00000436810.2_Silent_p.P140P|SLC47A1_ENST00000571335.1_Missense_Mutation_p.Q15L	NM_018242.2	NP_060712.2	Q96FL8	S47A1_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 1	163					organic cation transport (GO:0015695)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane-bounded vesicle (GO:0031988)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|monovalent cation:proton antiporter activity (GO:0005451)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(4)|lung(5)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	23	all_cancers(12;2.49e-05)|all_epithelial(12;0.00263)|Hepatocellular(7;0.00345)				Aciclovir(DB00787)|Bromodiphenhydramine(DB01237)|Cephalexin(DB00567)|Cimetidine(DB00501)|Metformin(DB00331)|Sirolimus(DB00877)	TCTTCATTCCAGCTCTTCCTG	0.463																																					p.P163P		Atlas-SNP	.											.	SLC47A1	55	.	0			c.A489T						.						205	179	188					17																	19452981		2203	4300	6503	SO:0001819	synonymous_variant	55244	exon5			CATTCCAGCTCTT		CCDS11209.1	17p11.2	2013-07-17	2013-07-17		ENSG00000142494	ENSG00000142494		"Solute carriers"	25588	protein-coding gene	gene with protein product	"multidrug and toxin extrusion 1"	609832				16330770, 16996621, 16928787	Standard	NM_018242		Approved	FLJ10847, MATE1	uc002gvy.1	Q96FL8	OTTHUMG00000059466	ENST00000270570.4:c.489A>T	chr17.hg19:g.19452981A>T		94.0	0.0		102.0	65.0	NM_018242	Q53HF5|Q6PD77|Q86VL4|Q9NVA3	Silent	SNP	ENST00000270570.4	hg19	CCDS11209.1																																																																																			.	.		0.463	SLC47A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132250.1	NM_018242		T	19452981	A	T	19452981	2	4	330	1	0	0	0	0	0	0	0	1	14662	175	7	4		4	SLC47A1	17	19452981	Silent	SNP	A	TCGA-PD-A5DF-01A-11D-A27I-10		19452981	61742229	38	46166										
PPP1R1B	84152	hgsc.bcm.edu	37	chr17	37792089	37792089	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	agcctggggaggaacctcagCgcccttccccctctgagcct	11	17	2	1			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr17:37792089C>T	ENST00000254079.4	+	7	1055	c.586C>T	c.(586-588)Cgc>Tgc	p.R196C	PPP1R1B_ENST00000580825.1_Missense_Mutation_p.R196C|STARD3_ENST00000336308.5_5'Flank|STARD3_ENST00000394250.4_5'Flank|PPP1R1B_ENST00000579000.1_Missense_Mutation_p.R163C|PPP1R1B_ENST00000394267.2_Missense_Mutation_p.R160C|STARD3_ENST00000580611.1_5'Flank|STARD3_ENST00000544210.2_5'Flank|PPP1R1B_ENST00000394265.1_Missense_Mutation_p.R160C	NM_032192.3	NP_115568.2	Q9UD71	PPR1B_HUMAN	protein phosphatase 1, regulatory (inhibitor) subunit 1B	196					intracellular signal transduction (GO:0035556)|negative regulation of catalytic activity (GO:0043086)|negative regulation of female receptivity (GO:0007621)|negative regulation of protein kinase activity (GO:0006469)|regulation of catalytic activity (GO:0050790)|response to amphetamine (GO:0001975)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	protein kinase inhibitor activity (GO:0004860)|protein phosphatase inhibitor activity (GO:0004864)|protein phosphatase type 1 regulator activity (GO:0008599)			kidney(1)|large_intestine(1)|liver(1)|lung(2)	5	Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;1.04e-44)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			GGAACCTCAGCGCCCTTCCCC	0.632																																					p.R196C		Atlas-SNP	.											.	PPP1R1B	9	.	0			c.C586T						.						47	45	46					17																	37792089		2203	4300	6503	SO:0001583	missense	84152	exon7			CCTCAGCGCCCTT	AI124650	CCDS11339.1, CCDS11340.1	17q12	2012-04-17	2008-07-31		ENSG00000131771	ENSG00000131771	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9287	protein-coding gene	gene with protein product	"dopamine and cAMP regulated phosphoprotein"	604399				8120638	Standard	NM_032192		Approved	DARPP-32, FLJ20940	uc002hrz.3	Q9UD71	OTTHUMG00000133210	ENST00000254079.4:c.586C>T	chr17.hg19:g.37792089C>T	ENSP00000254079:p.Arg196Cys	29.0	0.0		75.0	27.0	NM_032192	Q547V9|Q547W0|Q9H7G1	Missense_Mutation	SNP	ENST00000254079.4	hg19	CCDS11339.1	.	.	.	.	.	.	.	.	.	.	C	14.77	2.634286	0.47049	.	.	ENSG00000131771	ENST00000254079;ENST00000357165;ENST00000394271;ENST00000394267;ENST00000394265	T	0.48836	0.8	4.79	2.77	0.32553	.	0.877205	0.09779	N	0.756886	T	0.30572	0.0769	N	0.14661	0.345	0.31765	N	0.632832	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.31888	-0.9927	10	0.72032	D	0.01	-11.8428	7.3081	0.26459	0.0:0.7177:0.1885:0.0938	.	196;207;196	B3KVQ9;E7ENN5;Q9UD71	.;.;PPR1B_HUMAN	C	196;196;207;160;160	ENSP00000254079:R196C	ENSP00000254079:R196C	R	+	1	0	PPP1R1B	35045615	0.066000	0.20996	0.554000	0.28268	0.629000	0.37895	1.413000	0.34725	0.609000	0.30018	0.555000	0.69702	CGC	.	.		0.632	PPP1R1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256925.2	NM_032192		T	37792089	C	T	37792089	3	4	330	1	0	0	0	0	1	0	0	0	12380	768	27	1	612	1	PPP1R1B	17	37792089	Missense_Mutation	SNP	C	TCGA-PD-A5DF-01A-11D-A27I-10	18339108	37792089	43403121	39	46167										
QRICH2	84074	hgsc.bcm.edu	37	chr17	74289942	74289954	+	Frame_Shift_Del	DEL	CCAGATCCTGATG	CCAGATCCTGATG	-													0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	cagaggggtgtgctgtgccaCcagatcctgatgcagtccga							TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	CCAGATCCTGATG	CCAGATCCTGATG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr17:74289942_74289954delCCAGATCCTGATG	ENST00000262765.5	-	4	535_547	c.356_368delCATCAGGATCTGG	c.(355-369)gcatcaggatctggtfs	p.ASGSG119fs		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	119										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4)	62						TGCTGTGCCACCAGATCCTGATGCAGTCCGATC	0.563																																					p.119_123del		Atlas-Indel,Pindel	.											.	QRICH2	143	.	0			c.357_369del						.																																			SO:0001589	frameshift_variant	84074	exon4			.	AK058102	CCDS32741.1	17q25.1	2009-03-19			ENSG00000129646	ENSG00000129646			25326	protein-coding gene	gene with protein product							Standard	NM_032134		Approved	DKFZP434P0316	uc002jrd.1	Q9H0J4	OTTHUMG00000167578	ENST00000262765.5:c.356_368delCATCAGGATCTGG	chr17.hg19:g.74289942_74289954delCCAGATCCTGATG	ENSP00000262765:p.Ala119fs	74.0	0.0		115.0	22.0	NM_032134	A2RRE1|Q96LM3	Frame_Shift_Del	DEL	ENST00000262765.5	hg19	CCDS32741.1																																																																																			.	.		0.563	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134		-	74289954	CCAGATCCTGATG	-	74289942	7	5	330	1	0	1	0	1	0	0	0	0	12895	507	18	0	4687	0	QRICH2	17	74289942	Frame_Shift_Del	DEL	CCAGATCCTGATG	TCGA-PD-A5DF-01A-11D-A27I-10	36497853	74289942	6905268	40	46168										
DCC	1630	hgsc.bcm.edu	37	chr18	51025826	51025826	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	ctaatcctttgctacctccaCcaatgagtgcaatagaaccg	6	13	0	2			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr18:51025826C>G	ENST00000442544.2	+	27	4673	c.4057C>G	c.(4057-4059)Cca>Gca	p.P1353A	RP11-671P2.1_ENST00000582064.1_RNA|DCC_ENST00000581580.1_Missense_Mutation_p.P986A	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	1353					anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		GCTACCTCCACCAATGAGTGC	0.468																																					p.P1353A		Atlas-SNP	.											.	DCC	360	.	0			c.C4057G						.						192	157	169					18																	51025826		2203	4300	6503	SO:0001583	missense	1630	exon27			CCTCCACCAATGA	X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2701	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 1"	120470	"deleted in colorectal carcinoma"			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.4057C>G	chr18.hg19:g.51025826C>G	ENSP00000389140:p.Pro1353Ala	204.0	0.0		290.0	90.0	NM_005215		Missense_Mutation	SNP	ENST00000442544.2	hg19	CCDS11952.1	.	.	.	.	.	.	.	.	.	.	C	13.99	2.402506	0.42613	.	.	ENSG00000187323	ENST00000442544	T	0.40476	1.03	6.17	6.17	0.99709	Neogenin, C-terminal (1);	0.233791	0.35407	N	0.003236	T	0.36963	0.0986	L	0.34521	1.04	0.58432	D	0.999999	B	0.24186	0.099	B	0.28305	0.088	T	0.11084	-1.0602	10	0.15499	T	0.54	-7.2902	19.6509	0.95805	0.0:1.0:0.0:0.0	.	1353	P43146	DCC_HUMAN	A	1353	ENSP00000389140:P1353A	ENSP00000389140:P1353A	P	+	1	0	DCC	49279824	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.259000	0.72494	2.941000	0.99782	0.655000	0.94253	CCA	.	.		0.468	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215		G	51025826	C	G	51025826	3	3	330	1	0	0	0	0	1	0	0	0	4284	507	18	4	4163	4	DCC	18	51025826	Missense_Mutation	SNP	C	TCGA-PD-A5DF-01A-11D-A27I-10		51025826	27051422	41	46169										
HNRNPM	4670	hgsc.bcm.edu	37	chr19	8520429	8520429	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	accttttgatgtgaaatggcAgtcacttaaagacctggtta	9	7	1	3			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr19:8520429A>G	ENST00000325495.4	+	2	295	c.254A>G	c.(253-255)cAg>cGg	p.Q85R	HNRNPM_ENST00000348943.3_Missense_Mutation_p.Q85R	NM_005968.4	NP_005959.2	P52272	HNRPM_HUMAN	heterogeneous nuclear ribonucleoprotein M	85	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|RNA binding (GO:0003723)			endometrium(5)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)	25						GTGAAATGGCAGTCACTTAAA	0.388																																					p.Q85R		Atlas-SNP	.											.	HNRNPM	61	.	0			c.A254G						.						97	92	94					19																	8520429		2203	4300	6503	SO:0001583	missense	4670	exon2			AATGGCAGTCACT	L03532	CCDS12203.1, CCDS12204.1	19p13.2	2013-06-12		2008-04-18	ENSG00000099783	ENSG00000099783		"RNA binding motif (RRM) containing"	5046	protein-coding gene	gene with protein product	"CEA receptor"	160994		NAGR1, HNRPM		8441656, 7558047	Standard	NM_005968		Approved	HTGR1, HNRNPM4, HNRPM4, CEAR	uc010dwe.3	P52272	OTTHUMG00000182383	ENST00000325495.4:c.254A>G	chr19.hg19:g.8520429A>G	ENSP00000325376:p.Gln85Arg	70.0	0.0		117.0	39.0	NM_031203	Q15584|Q8WZ44|Q96H56|Q9BWL9|Q9Y492	Missense_Mutation	SNP	ENST00000325495.4	hg19	CCDS12203.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.2|20.2	3.954341|3.954341	0.73902|0.73902	.|.	.|.	ENSG00000099783|ENSG00000099783	ENST00000325495;ENST00000348943|ENST00000544159	T;T|.	0.17054|.	2.3;2.3|.	6.04|6.04	6.04|6.04	0.98038|0.98038	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.65471|0.65471	0.2694|0.2694	L|L	0.47716|0.47716	1.5|1.5	0.80722|0.80722	D|D	1|1	D;D;B|.	0.76494|.	0.99;0.999;0.387|.	D;D;B|.	0.79108|.	0.985;0.992;0.246|.	T|T	0.67772|0.67772	-0.5584|-0.5584	10|6	0.72032|0.87932	D|D	0.01|0	.|.	15.4125|15.4125	0.74937|0.74937	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	85;85;85|.	P52272;P52272-2;B4DEG4|.	HNRPM_HUMAN;.;.|.	R|G	85|3	ENSP00000325376:Q85R;ENSP00000325732:Q85R|.	ENSP00000325376:Q85R|ENSP00000442876:S3G	Q|S	+|+	2|1	0|0	HNRNPM|HNRNPM	8426429|8426429	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	8.962000|8.962000	0.93254|0.93254	2.317000|2.317000	0.78254|0.78254	0.460000|0.460000	0.39030|0.39030	CAG|AGT	.	.		0.388	HNRNPM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460894.1			G	8520429	A	G	8520429	3	3	330	1	0	0	0	0	1	0	0	0	7280	188	7	2	260	2	HNRNPM	19	8520429	Missense_Mutation	SNP	A	TCGA-PD-A5DF-01A-11D-A27I-10		8520429	50608554	42	46170										
CC2D1A	54862	hgsc.bcm.edu	37	chr19	14020723	14020723	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	aactggaggctgagttcttgGctttggtcgggggccagccc	16	10	1	1	rs368933699		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr19:14020723G>C	ENST00000318003.7	+	2	389	c.148G>C	c.(148-150)Gct>Cct	p.A50P	CC2D1A_ENST00000589606.1_Missense_Mutation_p.A50P	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	50					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	27			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)			TGAGTTCTTGGCTTTGGTCGG	0.567																																					p.A50P		Atlas-SNP	.											.	CC2D1A	67	.	0			c.G148C						.						78	79	79					19																	14020723		1947	4142	6089	SO:0001583	missense	54862	exon2			TTCTTGGCTTTGG	AF536205	CCDS42512.1	19p13.12	2007-01-08				ENSG00000132024			30237	protein-coding gene	gene with protein product	"mental retardation, nonsyndromic, autosomal recessive, 3"	610055				12761501, 16033914	Standard	NM_017721		Approved	FLJ20241, MRT3	uc002mxo.2	Q6P1N0		ENST00000318003.7:c.148G>C	chr19.hg19:g.14020723G>C	ENSP00000313601:p.Ala50Pro	136.0	0.0		223.0	22.0	NM_017721	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Missense_Mutation	SNP	ENST00000318003.7	hg19	CCDS42512.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.512190	0.85389	.	.	ENSG00000132024	ENST00000318003;ENST00000389233	T	0.23348	1.91	5.43	5.43	0.79202	.	0.258182	0.38492	N	0.001670	T	0.40862	0.1134	M	0.83118	2.625	0.50171	D	0.999857	P;P	0.50710	0.83;0.938	B;P	0.45971	0.401;0.499	T	0.47548	-0.9109	10	0.56958	D	0.05	-16.1937	16.153	0.81636	0.0:0.0:1.0:0.0	.	50;50	Q6P1N0-2;Q6P1N0	.;C2D1A_HUMAN	P	50;25	ENSP00000313601:A50P	ENSP00000313601:A50P	A	+	1	0	CC2D1A	13881723	1.000000	0.71417	0.997000	0.53966	0.969000	0.65631	4.466000	0.60148	2.547000	0.85894	0.655000	0.94253	GCT	.	.		0.567	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721		C	14020723	G	C	14020723	3	2	330	1	0	0	0	0	1	0	0	0	2728	1203	42	4	154	4	CC2D1A	19	14020723	Missense_Mutation	SNP	G	TCGA-PD-A5DF-01A-11D-A27I-10	5500294	14020723	45108260	43	46171										
PLEKHA4	57664	hgsc.bcm.edu	37	chr19	49364729	49364729	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	attgtagctggggagcaggaCgctgcctaggacactctcct	13	11	1	0	rs369244059		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr19:49364729C>T	ENST00000263265.6	-	5	850	c.295G>A	c.(295-297)Gtc>Atc	p.V99I	PLEKHA4_ENST00000596713.1_5'Flank|PLEKHA4_ENST00000355496.5_Missense_Mutation_p.V99I	NM_020904.2	NP_065955.2	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4	99	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.					cytoplasm (GO:0005737)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	30		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;0.000108)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.00027)|all cancers(93;0.00084)|GBM - Glioblastoma multiforme(486;0.0244)|Epithelial(262;0.0364)		GGGAGCAGGACGCTGCCTAGG	0.602																																					p.V99I		Atlas-SNP	.											.	PLEKHA4	70	.	0			c.G295A						.		ILE/VAL,ILE/VAL	0,4406		0,0,2203	45	55	51		295,295	4.6	1	19		51	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	PLEKHA4	NM_001161354.1,NM_020904.2	29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	99/584,99/780	49364729	1,13005	2203	4300	6503	SO:0001583	missense	57664	exon5			GCAGGACGCTGCC	AY007233	CCDS12737.1, CCDS54291.1	19q13.33	2013-01-10	2002-01-14			ENSG00000105559		"Pleckstrin homology (PH) domain containing"	14339	protein-coding gene	gene with protein product		607769	"pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 4"			11001876	Standard	NM_020904		Approved	PEPP1	uc002pkx.3	Q9H4M7		ENST00000263265.6:c.295G>A	chr19.hg19:g.49364729C>T	ENSP00000263265:p.Val99Ile	22.0	0.0		36.0	10.0	NM_001161354	Q8N4M8|Q8N658	Missense_Mutation	SNP	ENST00000263265.6	hg19	CCDS12737.1	.	.	.	.	.	.	.	.	.	.	c	10.34	1.321866	0.23994	0.0	1.16E-4	ENSG00000105559	ENST00000263265;ENST00000355496	T;T	0.64438	-0.1;-0.1	4.56	4.56	0.56223	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.075469	0.49916	D	0.000128	T	0.31295	0.0792	N	0.00224	-1.81	0.34981	D	0.754097	P;P	0.44627	0.839;0.476	P;P	0.51777	0.484;0.679	T	0.46020	-0.9221	10	0.15499	T	0.54	.	8.7517	0.34620	0.0:0.8987:0.0:0.1013	.	99;99	Q9H4M7-2;Q9H4M7	.;PKHA4_HUMAN	I	99	ENSP00000263265:V99I;ENSP00000347683:V99I	ENSP00000263265:V99I	V	-	1	0	PLEKHA4	54056541	1.000000	0.71417	0.998000	0.56505	0.945000	0.59286	3.633000	0.54295	2.548000	0.85928	0.457000	0.33378	GTC	.	.		0.602	PLEKHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466216.1			T	49364729	C	T	49364729	3	4	330	1	0	0	0	0	1	0	0	0	12067	536	19	1	2108	1	PLEKHA4	19	49364729	Missense_Mutation	SNP	C	TCGA-PD-A5DF-01A-11D-A27I-10	35344006	49364729	9764254	44	46172										
ACPT	93650	hgsc.bcm.edu	37	chr19	51298384	51298384	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	cctgctggcctggagaccagGgtgcctgcgggccttggggg	19	12	0	1			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr19:51298384G>A	ENST00000270593.1	+	11	1250	c.1250G>A	c.(1249-1251)gGg>gAg	p.G417E	CTD-2568A17.8_ENST00000594114.1_RNA|ACPT_ENST00000270594.3_Missense_Mutation_p.G324E	NM_033068.2	NP_149059.1	Q9BZG2	PPAT_HUMAN	acid phosphatase, testicular	417						integral component of membrane (GO:0016021)	acid phosphatase activity (GO:0003993)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|skin(3)	11		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00641)|GBM - Glioblastoma multiforme(134;0.028)		TGGAGACCAGGGTGCCTGCGG	0.662																																					p.G417E		Atlas-SNP	.											.	ACPT	43	.	0			c.G1250A						.						12	14	13					19																	51298384		2152	4243	6395	SO:0001583	missense	93650	exon11			GACCAGGGTGCCT	AF321918	CCDS12802.1	19q13.33	2012-10-02			ENSG00000142513	ENSG00000142513			14376	protein-coding gene	gene with protein product		606362				11414767	Standard	NM_033068		Approved		uc002pta.1	Q9BZG2		ENST00000270593.1:c.1250G>A	chr19.hg19:g.51298384G>A	ENSP00000270593:p.Gly417Glu	8.0	0.0		14.0	10.0	NM_033068	C0H3P7|Q9BZG3|Q9BZG4	Missense_Mutation	SNP	ENST00000270593.1	hg19	CCDS12802.1	.	.	.	.	.	.	.	.	.	.	g	13.25	2.180031	0.38511	.	.	ENSG00000142513	ENST00000270593;ENST00000270594	T;T	0.12465	2.9;2.68	4.14	3.1	0.35709	.	3.229290	0.01729	N	0.028745	T	0.12433	0.0302	L	0.27053	0.805	0.09310	N	1	B	0.27823	0.19	B	0.21360	0.034	T	0.25328	-1.0135	10	0.62326	D	0.03	-26.4165	8.0273	0.30444	0.1161:0.0:0.8839:0.0	.	417	Q9BZG2	PPAT_HUMAN	E	417;324	ENSP00000270593:G417E;ENSP00000270594:G324E	ENSP00000270593:G417E	G	+	2	0	ACPT	55990196	0.030000	0.19436	0.145000	0.22337	0.787000	0.44495	0.824000	0.27379	0.877000	0.35895	0.561000	0.74099	GGG	.	.		0.662	ACPT-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464434.1	NM_033068		A	51298384	G	A	51298384	3	1	330	1	0	0	0	0	1	0	0	0	168	1232	43	3	1292	3	ACPT	19	51298384	Missense_Mutation	SNP	G	TCGA-PD-A5DF-01A-11D-A27I-10	1933655	51298384	7830599	45	46173										
ZSCAN1	284312	hgsc.bcm.edu	37	chr19	58565260	58565260	+	Frame_Shift_Del	DEL	C	C	-													0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	aaagccccccggagcaagggCccccgggagtccgtcccacc							TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr19:58565260delC	ENST00000282326.1	+	6	1315	c.1068delC	c.(1066-1068)ggcfs	p.G356fs		NM_182572.3	NP_872378.3	Q8NBB4	ZSCA1_HUMAN	zinc finger and SCAN domain containing 1	356					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)		GGAGCAAGGGCCCCCGGGAGT	0.662																																					p.G356fs		Atlas-Indel,Pindel	.											.	ZSCAN1	102	.	0			c.1067delG						.						33	34	34					19																	58565260		2203	4300	6503	SO:0001589	frameshift_variant	284312	exon6			.	AK091098	CCDS12969.1	19q13.43	2013-06-13	2004-04-21		ENSG00000152467	ENSG00000152467		"-", "Zinc fingers, C2H2-type"	23712	protein-coding gene	gene with protein product			"zinc finger with SCAN domain 1"			12477932	Standard	NM_182572		Approved	FLJ33779, ZNF915	uc002qrc.1	Q8NBB4	OTTHUMG00000183381	ENST00000282326.1:c.1068delC	chr19.hg19:g.58565260delC	ENSP00000282326:p.Gly356fs	99.0	0.0		153.0	54.0	NM_182572	Q3B798|Q6WLH8|Q86WS8	Frame_Shift_Del	DEL	ENST00000282326.1	hg19	CCDS12969.1																																																																																			.	.		0.662	ZSCAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466427.1	NM_182572		-	58565260	C	-	58565260	7	5	330	1	0	1	0	1	0	0	0	0	18241	726	26	0	1082	0	ZSCAN1	19	58565260	Frame_Shift_Del	DEL	C	TCGA-PD-A5DF-01A-11D-A27I-10	7266876	58565260	563723	46	46174										
COL20A1	57642	hgsc.bcm.edu	37	chr20	61937235	61937235	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	ctttgtgtctccctgcagttGaggatctgaagagtagctcc	11	10	2	3			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr20:61937235G>T	ENST00000358894.6	+	5	440	c.340G>T	c.(340-342)Gag>Tag	p.E114*	COL20A1_ENST00000326996.6_Nonsense_Mutation_p.E114*|COL20A1_ENST00000435874.1_Nonsense_Mutation_p.E114*|COL20A1_ENST00000422202.1_Nonsense_Mutation_p.E114*	NM_020882.2	NP_065933.2	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1	114	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)				NS(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(21)|ovary(1)|prostate(3)|urinary_tract(2)	36	all_cancers(38;1.39e-10)					CCCTGCAGTTGAGGATCTGAA	0.657																																					p.E114X		Atlas-SNP	.											.	COL20A1	137	.	0			c.G340T						.						41	43	42					20																	61937235		1986	4164	6150	SO:0001587	stop_gained	57642	exon5			GCAGTTGAGGATC	BC043183	CCDS46628.1	20q13.33	2014-02-12			ENSG00000101203	ENSG00000101203		"Collagens", "Fibronectin type III domain containing"	14670	protein-coding gene	gene with protein product						10819331	Standard	NM_020882		Approved	KIAA1510	uc011aau.2	Q9P218	OTTHUMG00000032964	ENST00000358894.6:c.340G>T	chr20.hg19:g.61937235G>T	ENSP00000351767:p.Glu114*	41.0	0.0		125.0	19.0	NM_020882	Q4VXQ4|Q6PI59|Q8WUT2|Q96CY9|Q9BQU6|Q9BQU7	Nonsense_Mutation	SNP	ENST00000358894.6	hg19	CCDS46628.1	.	.	.	.	.	.	.	.	.	.	G	17.00	3.278003	0.59758	.	.	ENSG00000101203	ENST00000358894;ENST00000326996;ENST00000435874;ENST00000422202	.	.	.	3.95	1.93	0.25924	.	0.065070	0.64402	U	0.000011	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07030	T	0.85	.	8.0499	0.30572	0.2036:0.0:0.7964:0.0	.	.	.	.	X	114	.	ENSP00000323077:E114X	E	+	1	0	COL20A1	61407680	0.005000	0.15991	0.057000	0.19452	0.113000	0.19764	0.145000	0.16157	0.265000	0.21872	0.467000	0.42956	GAG	.	.		0.657	COL20A1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000144595.2	NM_020882		T	61937235	G	T	61937235	4	4	330	1	0	0	0	0	0	1	0	0	3681	1291	45	3	354	3	COL20A1	20	61937235	Nonsense_Mutation	SNP	G	TCGA-PD-A5DF-01A-11D-A27I-10		61937235	1088285	47	46175										
POTEH	23784	hgsc.bcm.edu	37	chr22	16287641	16287641	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	aatcgtcgtggtctccagaaGtgcccacgttgctcttgccg	11	13	2	1			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr22:16287641G>A	ENST00000343518.6	-	1	296	c.245C>T	c.(244-246)aCt>aTt	p.T82I		NM_001136213.1	NP_001129685.1	Q6S545	POTEH_HUMAN	POTE ankyrin domain family, member H	82										NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(20)|ovary(1)|skin(7)|urinary_tract(2)	37						GTCTCCAGAAGTGCCCACGTT	0.597																																					p.T82I		Atlas-SNP	.											.	POTEH	114	.	0			c.C245T						.																																			SO:0001583	missense	23784	exon1			CCAGAAGTGCCCA	AY462874	CCDS74808.1	22q11.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000198062	ENSG00000198062		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	133	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 7"	608913	"actin, beta-like 1", "ANKRD26-like family C, member 3"	ACTBL1, A26C3		10591208, 15276201, 21439273	Standard	NM_001136213		Approved	POTE22, CT104.7	uc010gqp.2	Q6S545	OTTHUMG00000140314	ENST00000343518.6:c.245C>T	chr22.hg19:g.16287641G>A	ENSP00000340610:p.Thr82Ile	370.0	0.0		551.0	154.0	NM_001136213	A2CEK4|A6NCI1|A9Z1W0	Missense_Mutation	SNP	ENST00000343518.6	hg19	CCDS46658.1	.	.	.	.	.	.	.	.	.	.	.	8.790	0.930427	0.18131	.	.	ENSG00000198062	ENST00000343518;ENST00000355872	T	0.32753	1.44	.	.	.	.	.	.	.	.	T	0.22399	0.0540	L	0.43152	1.355	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.22695	-1.0209	7	0.37606	T	0.19	.	.	.	.	.	82	Q6S545	POTEH_HUMAN	I	82	ENSP00000340610:T82I	ENSP00000340610:T82I	T	-	2	0	POTEH	14667641	0.002000	0.14202	0.024000	0.17045	0.024000	0.10985	0.327000	0.19663	0.149000	0.19098	0.152000	0.16155	ACT	.	.		0.597	POTEH-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276918.4	NM_001136213		A	16287641	G	A	16287641	3	1	330	1	0	0	0	0	1	0	0	0	12276	1029	36	3	1432	3	POTEH	22	16287641	Missense_Mutation	SNP	G	TCGA-PD-A5DF-01A-11D-A27I-10		16287641	35016925	48	46176										
YPEL1	29799	hgsc.bcm.edu	37	chr22	22064931	22064931	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	acttgccttggagatgagctCgtcatgattggccaggtgtg	14	8	1	3			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chr22:22064931C>T	ENST00000339468.3	-	2	486	c.103G>A	c.(103-105)Gag>Aag	p.E35K	YPEL1_ENST00000403503.1_Missense_Mutation_p.E35K	NM_013313.3	NP_037445.1	O60688	YPEL1_HUMAN	yippee-like 1 (Drosophila)	35						nucleus (GO:0005634)				breast(1)|large_intestine(1)|lung(1)	3	Colorectal(54;0.105)					GAGATGAGCTCGTCATGATTG	0.443																																					p.E35K		Atlas-SNP	.											.	YPEL1	6	.	0			c.G103A						.						314	267	283					22																	22064931		2203	4300	6503	SO:0001583	missense	29799	exon2			TGAGCTCGTCATG	AF060862	CCDS13794.1	22q11.2	2008-02-04	2001-11-28		ENSG00000100027	ENSG00000100027			12845	protein-coding gene	gene with protein product		608082	"yippee (Drosophila) homolog-like 1"			11473580	Standard	NM_013313		Approved		uc002zvl.3	O60688	OTTHUMG00000150830	ENST00000339468.3:c.103G>A	chr22.hg19:g.22064931C>T	ENSP00000342832:p.Glu35Lys	231.0	0.0		398.0	43.0	NM_013313	Q65ZA1|Q6GLI6	Missense_Mutation	SNP	ENST00000339468.3	hg19	CCDS13794.1	.	.	.	.	.	.	.	.	.	.	C	35	5.557313	0.96514	.	.	ENSG00000100027	ENST00000339468;ENST00000403503	.	.	.	4.86	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.67287	0.2877	M	0.88704	2.975	0.80722	D	1	P	0.43477	0.808	B	0.34452	0.183	T	0.78265	-0.2271	9	0.72032	D	0.01	.	18.5625	0.91105	0.0:1.0:0.0:0.0	.	35	O60688	YPEL1_HUMAN	K	35	.	ENSP00000342832:E35K	E	-	1	0	YPEL1	20394931	1.000000	0.71417	0.975000	0.42487	0.832000	0.47134	7.564000	0.82326	2.704000	0.92352	0.561000	0.74099	GAG	.	.		0.443	YPEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320245.1	NM_013313		T	22064931	C	T	22064931	3	4	330	1	0	0	0	0	1	0	0	0	17504	893	31	1	272	1	YPEL1	22	22064931	Missense_Mutation	SNP	C	TCGA-PD-A5DF-01A-11D-A27I-10	5777290	22064931	29239635	49	46177										
CCNB3	85417	hgsc.bcm.edu	37	chrX	50090667	50090667	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	cactgaccttgtcccgctacAtctgcgagatgaccctgcag	9	15	1	3			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chrX:50090667A>G	ENST00000376042.1	+	11	4151	c.3853A>G	c.(3853-3855)Atc>Gtc	p.I1285V	CCNB3_ENST00000276014.7_Missense_Mutation_p.I1285V|CCNB3_ENST00000376038.1_Missense_Mutation_p.I181V|CCNB3_ENST00000348603.2_Missense_Mutation_p.I181V			Q8WWL7	CCNB3_HUMAN	cyclin B3	1285					meiotic nuclear division (GO:0007126)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)	nucleus (GO:0005634)				breast(3)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Ovarian(276;0.236)					GTCCCGCTACATCTGCGAGAT	0.498																																					p.I1285V		Atlas-SNP	.											.	CCNB3	367	.	0			c.A3853G						.						124	91	102					X																	50090667		2203	4300	6503	SO:0001583	missense	85417	exon10			CGCTACATCTGCG	AJ314764	CCDS14331.1, CCDS14332.1	Xp11	2008-07-03			ENSG00000147082	ENSG00000147082			18709	protein-coding gene	gene with protein product		300456				11846420, 12185076	Standard	XM_006724610		Approved		uc004doy.3	Q8WWL7	OTTHUMG00000021519	ENST00000376042.1:c.3853A>G	chrX.hg19:g.50090667A>G	ENSP00000365210:p.Ile1285Val	131.0	0.0		183.0	22.0	NM_033031	B1AQI5|B1AQI6|Q96SB5|Q96SB6|Q96SB7|Q9NT38	Missense_Mutation	SNP	ENST00000376042.1	hg19	CCDS14331.1	.	.	.	.	.	.	.	.	.	.	A	10.94	1.493431	0.26774	.	.	ENSG00000147082	ENST00000376042;ENST00000376038;ENST00000348603;ENST00000276014	T;T;T;T	0.23348	1.91;1.91;1.91;1.91	4.79	3.62	0.41486	Cyclin, C-terminal (1);Cyclin-like (3);	0.335186	0.29692	N	0.011459	T	0.28234	0.0697	L	0.42487	1.325	0.36374	D	0.861493	P;P;P	0.45428	0.722;0.858;0.549	P;B;P	0.51777	0.679;0.386;0.604	T	0.20273	-1.0280	9	.	.	.	.	5.6864	0.17805	0.7373:0.1679:0.0948:0.0	.	1285;181;1285	A8K8T9;Q8WWL7-2;Q8WWL7	.;.;CCNB3_HUMAN	V	1285;181;181;1285	ENSP00000365210:I1285V;ENSP00000365206:I181V;ENSP00000338682:I181V;ENSP00000276014:I1285V	.	I	+	1	0	CCNB3	50107407	1.000000	0.71417	1.000000	0.80357	0.671000	0.39405	1.981000	0.40628	0.611000	0.30052	0.413000	0.27773	ATC	.	.		0.498	CCNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056558.1			G	50090667	A	G	50090667	3	3	330	1	0	0	0	0	1	0	0	0	2916	217	8	2	3887	2	CCNB3	23	50090667	Missense_Mutation	SNP	A	TCGA-PD-A5DF-01A-11D-A27I-10		50090667	105179893	50	46178										
ZNF280C	55609	hgsc.bcm.edu	37	chrX	129349844	129349844	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0588235294117647	3	1	1.11261261261261	1.78018018018018	0.936936936936937	1	1	0	gtaagagggttttgctttggActtagctatacgtccccttg	11	8	0	1			TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	g.chrX:129349844A>T	ENST00000370978.4	-	14	1912	c.1759T>A	c.(1759-1761)Tcc>Acc	p.S587T		NM_017666.4	NP_060136.1	Q8ND82	Z280C_HUMAN	zinc finger protein 280C	587					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(4)|large_intestine(9)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	26						TTTGCTTTGGACTTAGCTATA	0.368																																					p.S587T		Atlas-SNP	.											.	ZNF280C	63	.	0			c.T1759A						.						319	283	295					X																	129349844		2203	4300	6503	SO:0001583	missense	55609	exon14			CTTTGGACTTAGC	AL834333	CCDS14622.1	Xq25	2008-05-02	2007-09-20	2007-09-20	ENSG00000056277	ENSG00000056277			25955	protein-coding gene	gene with protein product			"suppressor of hairy wing homolog 3 (Drosophila)"	SUHW3		12477932	Standard	NM_017666		Approved	FLJ20095, ZNF633	uc004evm.3	Q8ND82	OTTHUMG00000022393	ENST00000370978.4:c.1759T>A	chrX.hg19:g.129349844A>T	ENSP00000360017:p.Ser587Thr	155.0	0.0		222.0	89.0	NM_017666	A8K2V8|Q9NXR3	Missense_Mutation	SNP	ENST00000370978.4	hg19	CCDS14622.1	.	.	.	.	.	.	.	.	.	.	A	5.828	0.336966	0.11013	.	.	ENSG00000056277	ENST00000066465;ENST00000370978;ENST00000447817	T;T	0.04809	4.31;3.55	3.85	-0.259	0.12971	.	.	.	.	.	T	0.03348	0.0097	L	0.32530	0.975	0.09310	N	1	B;B	0.19200	0.005;0.034	B;B	0.22386	0.004;0.039	T	0.47749	-0.9093	9	0.22706	T	0.39	.	1.4371	0.02345	0.5415:0.1778:0.1058:0.175	.	538;587	Q9UJJ2;Q8ND82	.;Z280C_HUMAN	T	538;587;538	ENSP00000360017:S587T;ENSP00000408521:S538T	ENSP00000066465:S538T	S	-	1	0	ZNF280C	129177525	0.001000	0.12720	0.000000	0.03702	0.009000	0.06853	-0.356000	0.07661	-0.239000	0.09710	0.350000	0.21858	TCC	.	.		0.368	ZNF280C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058251.1	NM_017666		T	129349844	A	T	129349844	3	4	330	1	0	0	0	0	1	0	0	0	17831	275	10	4	478	4	ZNF280C	23	129349844	Missense_Mutation	SNP	A	TCGA-PD-A5DF-01A-11D-A27I-10	79259177	129349844	25920716	51	46179										
MMEL1	79258	hgsc.bcm.edu	37	chr1	2524344	2524344	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	cactctgactgctcccggaaGtgctgggtggagaagttact	13	10	1	2			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr1:2524344G>A	ENST00000378412.3	-	20	2090	c.1929C>T	c.(1927-1929)caC>caT	p.H643H	MMEL1_ENST00000502556.1_Silent_p.H486H|MMEL1_ENST00000288709.6_Silent_p.H634H			Q495T6	MMEL1_HUMAN	membrane metallo-endopeptidase-like 1	643						endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|urinary_tract(1)	27	all_cancers(77;0.000233)|all_epithelial(69;8.55e-05)|all_lung(157;0.0228)|Lung NSC(156;0.0402)|Ovarian(185;0.0634)	all_epithelial(116;1.03e-20)|all_lung(118;5.15e-09)|Lung NSC(185;9.02e-07)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;8.52e-23)|GBM - Glioblastoma multiforme(42;1.49e-08)|Colorectal(212;4.79e-05)|COAD - Colon adenocarcinoma(227;0.000213)|Kidney(185;0.000371)|BRCA - Breast invasive adenocarcinoma(365;0.00219)|KIRC - Kidney renal clear cell carcinoma(229;0.00571)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.131)		GCTCCCGGAAGTGCTGGGTGG	0.602																																					p.H643H		Atlas-SNP	.											.	MMEL1	64	.	0			c.C1929T						.						132	108	116					1																	2524344		2203	4300	6503	SO:0001819	synonymous_variant	79258	exon20			CCGGAAGTGCTGG	AF336981	CCDS30569.1, CCDS30569.2	1p36	2008-02-05			ENSG00000142606	ENSG00000142606			14668	protein-coding gene	gene with protein product			"membrane metallo-endopeptidase-like 2"	MMEL2			Standard	NM_033467		Approved	SEP, NL1, NL2, NEPII	uc001ajy.2	Q495T6	OTTHUMG00000000846	ENST00000378412.3:c.1929C>T	chr1.hg19:g.2524344G>A		65.0	0.0		76.0	36.0	NM_033467	B9DI79|Q495T7|Q495T8|Q5SZS6|Q96PH9	Silent	SNP	ENST00000378412.3	hg19	CCDS30569.2																																																																																			.	.		0.602	MMEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002395.2	NM_033467		A	2524344	G	A	2524344	2	1	331	1	0	0	0	0	0	0	0	1	9655	1020	36	3		3	MMEL1	1	2524344	Silent	SNP	G	TCGA-QA-A7B7-01A-11D-A32G-10		2524344	246726277	1	46180										
AIM1L	55057	hgsc.bcm.edu	37	chr1	26655355	26655355	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	atacaggaaaatggaaggctCtgaaaagtgctggggcccag	14	7	1	1			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr1:26655355C>T	ENST00000308182.5	-	15	1618	c.1189G>A	c.(1189-1191)Gag>Aag	p.E397K	AIM1L_ENST00000527815.1_Missense_Mutation_p.E568K			Q8N1P7	AIM1L_HUMAN	absent in melanoma 1-like	397							carbohydrate binding (GO:0030246)			endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|pancreas(1)|skin(2)	12		all_cancers(24;4.67e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.51e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000792)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.00858)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.165)|LUSC - Lung squamous cell carcinoma(448;0.239)		ATGGAAGGCTCTGAAAAGTGC	0.592																																					p.E1442K		Atlas-SNP	.											.	AIM1L	98	.	0			c.G4324A						.						72	69	70					1																	26655355		2203	4300	6503	SO:0001583	missense	55057	exon16			AAGGCTCTGAAAA			1p35	2010-07-14			ENSG00000176092	ENSG00000176092			17295	protein-coding gene	gene with protein product	"beta-gamma crystallin domain containing 2"						Standard	NM_001039775		Approved	CRYBG2, FLJ38020	uc001bmd.4	Q8N1P7	OTTHUMG00000003490	ENST00000308182.5:c.1189G>A	chr1.hg19:g.26655355C>T	ENSP00000310435:p.Glu397Lys	57.0	0.0		59.0	28.0	NM_001039775	B2RNG3|Q5T137|Q5T150	Missense_Mutation	SNP	ENST00000308182.5	hg19		.	.	.	.	.	.	.	.	.	.	C	17.36	3.370985	0.61624	.	.	ENSG00000176092	ENST00000527815;ENST00000308182	T;T	0.75367	-0.93;-0.93	5.03	5.03	0.67393	Beta/gamma crystallin (1);Gamma-crystallin-related (1);	0.125962	0.52532	D	0.000073	T	0.78704	0.4325	M	0.75085	2.285	0.80722	D	1	D	0.57257	0.979	P	0.51777	0.679	T	0.77395	-0.2604	10	0.33141	T	0.24	.	11.6205	0.51115	0.0:0.9182:0.0:0.0818	.	397	Q8N1P7	AIM1L_HUMAN	K	568;397	ENSP00000433931:E568K;ENSP00000310435:E397K	ENSP00000310435:E397K	E	-	1	0	AIM1L	26527942	0.997000	0.39634	0.998000	0.56505	0.135000	0.20990	3.929000	0.56514	2.607000	0.88179	0.561000	0.74099	GAG	.	.		0.592	AIM1L-201	KNOWN	basic	protein_coding	protein_coding		NM_001039775.2		T	26655355	C	T	26655355	3	4	331	1	0	0	0	0	1	0	0	0	431	922	32	3	681	3	AIM1L	1	26655355	Missense_Mutation	SNP	C	TCGA-QA-A7B7-01A-11D-A32G-10	24131011	26655355	222595266	2	46181										
PCSK9	255738	hgsc.bcm.edu	37	chr1	55527146	55527146	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	agtgcgtgggccacagggagGccagcatccacgcttcctgc	14	14	0	0			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr1:55527146G>A	ENST00000302118.5	+	11	2070	c.1780G>A	c.(1780-1782)Gcc>Acc	p.A594T	PCSK9_ENST00000543384.1_3'UTR|PCSK9_ENST00000490692.1_3'UTR	NM_174936.3	NP_777596.2	Q8NBP7	PCSK9_HUMAN	proprotein convertase subtilisin/kexin type 9	594	C-terminal domain.				apoptotic process (GO:0006915)|cellular response to insulin stimulus (GO:0032869)|cellular response to starvation (GO:0009267)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|kidney development (GO:0001822)|lipoprotein metabolic process (GO:0042157)|liver development (GO:0001889)|low-density lipoprotein particle receptor catabolic process (GO:0032802)|lysosomal transport (GO:0007041)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|negative regulation of receptor recycling (GO:0001920)|neurogenesis (GO:0022008)|neuron differentiation (GO:0030182)|phospholipid metabolic process (GO:0006644)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of receptor internalization (GO:0002092)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)|regulation of neuron apoptotic process (GO:0043523)|regulation of receptor activity (GO:0010469)|triglyceride metabolic process (GO:0006641)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	apolipoprotein binding (GO:0034185)|apolipoprotein receptor binding (GO:0034190)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein particle receptor binding (GO:0050750)|poly(A) RNA binding (GO:0044822)|protein self-association (GO:0043621)|serine-type endopeptidase activity (GO:0004252)|sodium channel inhibitor activity (GO:0019871)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(1)|liver(2)|lung(4)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	32						CCACAGGGAGGCCAGCATCCA	0.652																																					p.A594T	Pancreas(137;1454 1827 5886 22361 42375)	Atlas-SNP	.											.	PCSK9	76	.	0			c.G1780A						.						30	27	28					1																	55527146		2201	4299	6500	SO:0001583	missense	255738	exon11			AGGGAGGCCAGCA	AX207686	CCDS603.1	1p34.1-p32	2014-09-17	2003-05-13		ENSG00000169174	ENSG00000169174			20001	protein-coding gene	gene with protein product		607786	"hypercholesterolemia, autosomal dominant 3"	HCHOLA3		12552133, 12730697	Standard	NM_174936		Approved	NARC-1, FH3	uc001cyf.2	Q8NBP7	OTTHUMG00000008136	ENST00000302118.5:c.1780G>A	chr1.hg19:g.55527146G>A	ENSP00000303208:p.Ala594Thr	135.0	0.0		176.0	76.0	NM_174936	A8T640|C0JYY9|Q5PSM5|Q5SZQ2	Missense_Mutation	SNP	ENST00000302118.5	hg19	CCDS603.1	.	.	.	.	.	.	.	.	.	.	G	13.73	2.325484	0.41197	.	.	ENSG00000169174	ENST00000302118	T	0.71341	-0.56	3.82	2.87	0.33458	.	0.619911	0.12806	U	0.437547	T	0.59266	0.2181	L	0.36672	1.1	0.27995	N	0.93551	B	0.28713	0.22	B	0.21708	0.036	T	0.56523	-0.7965	10	0.49607	T	0.09	-13.7968	11.8331	0.52307	0.0951:0.0:0.9049:0.0	.	594	Q8NBP7	PCSK9_HUMAN	T	594	ENSP00000303208:A594T	ENSP00000303208:A594T	A	+	1	0	PCSK9	55299734	0.555000	0.26530	0.867000	0.34043	0.043000	0.13939	1.485000	0.35519	1.830000	0.53286	0.456000	0.33151	GCC	.	.		0.652	PCSK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022280.1	NM_174936		A	55527146	G	A	55527146	3	1	331	1	0	0	0	0	1	0	0	0	11615	1203	42	3	1822	3	PCSK9	1	55527146	Missense_Mutation	SNP	G	TCGA-QA-A7B7-01A-11D-A32G-10	28871791	55527146	193723475	3	46182										
EFCAB7	84455	hgsc.bcm.edu	37	chr1	63998376	63998376	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	actcgagaagaagtaaatgcCataataaatttggctgatgt	9	5	0	3			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr1:63998376C>T	ENST00000371088.4	+	4	681	c.435C>T	c.(433-435)gcC>gcT	p.A145A	RN7SL488P_ENST00000585186.1_RNA	NM_032437.2	NP_115813.2	A8K855	EFCB7_HUMAN	EF-hand calcium binding domain 7	145	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	19						AAGTAAATGCCATAATAAATT	0.328																																					p.A145A		Atlas-SNP	.											.	EFCAB7	45	.	0			c.C435T						.						117	118	118					1																	63998376		2203	4298	6501	SO:0001819	synonymous_variant	84455	exon4			AAATGCCATAATA	BC015814	CCDS30737.1	1p31.3	2013-01-10			ENSG00000203965	ENSG00000203965		"EF-hand domain containing"	29379	protein-coding gene	gene with protein product						11347906	Standard	NM_032437		Approved	KIAA1799, RP4-534K7.1	uc001dbf.3	A8K855	OTTHUMG00000008983	ENST00000371088.4:c.435C>T	chr1.hg19:g.63998376C>T		274.0	1.0		316.0	123.0	NM_032437	Q658P0|Q96B95|Q96JM6	Silent	SNP	ENST00000371088.4	hg19	CCDS30737.1																																																																																			.	.		0.328	EFCAB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024910.1	NM_032437		T	63998376	C	T	63998376	2	4	331	1	0	0	0	0	0	0	0	1	4942	581	21	3		3	EFCAB7	1	63998376	Silent	SNP	C	TCGA-QA-A7B7-01A-11D-A32G-10	8471230	63998376	185252245	4	46183										
AGL	178	hgsc.bcm.edu	37	chr1	100350158	100350158	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	ccacatgcacaagtcgctgtTggaattcttcgaaatcatct	7	11	3	0			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr1:100350158T>C	ENST00000294724.4	+	20	3058	c.2580T>C	c.(2578-2580)gtT>gtC	p.V860V	AGL_ENST00000361522.4_Silent_p.V843V|AGL_ENST00000370165.3_Silent_p.V860V|AGL_ENST00000370163.3_Silent_p.V860V|AGL_ENST00000361302.3_Silent_p.V844V|AGL_ENST00000370161.2_Silent_p.V844V|AGL_ENST00000361915.3_Silent_p.V860V	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	860					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|inclusion body (GO:0016234)|isoamylase complex (GO:0043033)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)	4-alpha-glucanotransferase activity (GO:0004134)|amylo-alpha-1,6-glucosidase activity (GO:0004135)|glycogen debranching enzyme activity (GO:0004133)|polysaccharide binding (GO:0030247)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(9)|lung(35)|ovary(1)|prostate(4)|skin(3)|urinary_tract(1)	69		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		AAGTCGCTGTTGGAATTCTTC	0.333																																					p.V860V		Atlas-SNP	.											.	AGL	137	.	0			c.T2580C						.						76	74	74					1																	100350158		2203	4300	6503	SO:0001819	synonymous_variant	178	exon20			CGCTGTTGGAATT	BC078663	CCDS759.1, CCDS760.1, CCDS761.1	1p21	2010-04-27	2010-04-27		ENSG00000162688	ENSG00000162688	2.4.1.25, 3.2.1.33		321	protein-coding gene	gene with protein product	"glycogen debranching enzyme", "glycogen storage disease type III"	610860	"amylo-1, 6-glucosidase, 4-alpha-glucanotransferase"			1505983	Standard	NM_000028		Approved		uc001dsi.1	P35573	OTTHUMG00000010803	ENST00000294724.4:c.2580T>C	chr1.hg19:g.100350158T>C		173.0	0.0		188.0	69.0	NM_000644	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Silent	SNP	ENST00000294724.4	hg19	CCDS759.1																																																																																			.	.		0.333	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028		C	100350158	T	C	100350158	2	2	331	1	0	0	0	0	0	0	0	1	384	1799	63	2		2	AGL	1	100350158	Silent	SNP	T	TCGA-QA-A7B7-01A-11D-A32G-10	36351782	100350158	148900463	5	46184										
MAN1A2	10905	hgsc.bcm.edu	37	chr1	118065534	118065534	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	gctcaccctctgcctgtgttAcatttagccaacaccacact	5	16	2	0			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr1:118065534A>G	ENST00000356554.3	+	13	2616	c.1881A>G	c.(1879-1881)ttA>ttG	p.L627L		NM_006699.3	NP_006690.1	O60476	MA1A2_HUMAN	mannosidase, alpha, class 1A, member 2	627					cellular protein metabolic process (GO:0044267)|lung alveolus development (GO:0048286)|N-glycan processing (GO:0006491)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleolus (GO:0005730)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|urinary_tract(1)	27	Lung SC(450;0.225)	all_cancers(81;7.9e-06)|all_epithelial(167;7.39e-07)|all_lung(203;2.84e-06)|Lung NSC(69;1.99e-05)		Lung(183;0.0688)|Kidney(133;0.114)|LUSC - Lung squamous cell carcinoma(189;0.223)|KIRC - Kidney renal clear cell carcinoma(1967;0.237)|Colorectal(144;0.243)		TGCCTGTGTTACATTTAGCCA	0.423																																					p.L627L	Ovarian(33;199 881 8228 13687 31538)	Atlas-SNP	.											.	MAN1A2	50	.	0			c.A1881G						.						146	139	142					1																	118065534		2203	4299	6502	SO:0001819	synonymous_variant	10905	exon13			TGTGTTACATTTA	AF027156	CCDS895.1	1p13	2008-02-05			ENSG00000198162	ENSG00000198162			6822	protein-coding gene	gene with protein product		604345				9592125	Standard	NM_006699		Approved	MAN1B	uc001ehd.1	O60476	OTTHUMG00000012149	ENST00000356554.3:c.1881A>G	chr1.hg19:g.118065534A>G		76.0	0.0		78.0	43.0	NM_006699	Q9H510	Silent	SNP	ENST00000356554.3	hg19	CCDS895.1	.	.	.	.	.	.	.	.	.	.	A	7.714	0.695836	0.15106	.	.	ENSG00000198162	ENST00000421535	.	.	.	5.93	1.71	0.24356	.	.	.	.	.	T	0.35008	0.0917	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.16778	-1.0391	4	.	.	.	-12.3858	4.8577	0.13568	0.5027:0.1579:0.3394:0.0	.	.	.	.	A	194	.	.	T	+	1	0	MAN1A2	117867057	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	1.808000	0.38912	0.033000	0.15463	0.454000	0.30748	ACA	.	.		0.423	MAN1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033593.1	NM_006699		G	118065534	A	G	118065534	2	3	331	1	0	0	0	0	0	0	0	1	9220	388	14	2		2	MAN1A2	1	118065534	Silent	SNP	A	TCGA-QA-A7B7-01A-11D-A32G-10	17715376	118065534	131185087	6	46185										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186017888	186017888	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	ttttcagattgaagatgctcAggttcaagacactggtcgtt	10	7	3	4			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr1:186017888A>G	ENST00000271588.4	+	42	6723	c.6494A>G	c.(6493-6495)cAg>cGg	p.Q2165R	HMCN1_ENST00000367492.2_Missense_Mutation_p.Q2165R	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2165	Ig-like C2-type 19.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						GAAGATGCTCAGGTTCAAGAC	0.328																																					p.Q2165R		Atlas-SNP	.											.	HMCN1	797	.	0			c.A6494G						.						98	100	99					1																	186017888		2203	4300	6503	SO:0001583	missense	83872	exon42			ATGCTCAGGTTCA	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.6494A>G	chr1.hg19:g.186017888A>G	ENSP00000271588:p.Gln2165Arg	86.0	0.0		129.0	27.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.625992	0.87560	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.67865	-0.29;-0.29	5.08	5.08	0.68730	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.62146	0.2404	L	0.31157	0.91	0.58432	D	0.999999	P	0.49961	0.93	P	0.50192	0.634	T	0.58002	-0.7713	10	0.18276	T	0.48	.	15.1496	0.72687	1.0:0.0:0.0:0.0	.	2165	Q96RW7	HMCN1_HUMAN	R	2165	ENSP00000271588:Q2165R;ENSP00000356462:Q2165R	ENSP00000271588:Q2165R	Q	+	2	0	HMCN1	184284511	1.000000	0.71417	0.975000	0.42487	0.991000	0.79684	8.910000	0.92685	2.026000	0.59711	0.455000	0.32223	CAG	.	.		0.328	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		G	186017888	A	G	186017888	3	3	331	1	0	0	0	0	1	0	0	0	7229	188	7	2	6660	2	HMCN1	1	186017888	Missense_Mutation	SNP	A	TCGA-QA-A7B7-01A-11D-A32G-10	67952354	186017888	63232733	7	46186										
SPATA17	128153	hgsc.bcm.edu	37	chr1	217915436	217915436	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	gcattacctcctcagcacaaAgcaggttggtttacctgtcc	8	13	1	0			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr1:217915436A>T	ENST00000366933.4	+	6	570	c.515A>T	c.(514-516)aAg>aTg	p.K172M		NM_138796.2	NP_620151.1	Q96L03	SPT17_HUMAN	spermatogenesis associated 17	172						cytoplasm (GO:0005737)				endometrium(1)|kidney(1)|large_intestine(9)|lung(6)|pancreas(2)|prostate(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(81;0.0516)|all cancers(67;0.0891)|GBM - Glioblastoma multiforme(131;0.117)		CTCAGCACAAAGCAGGTTGGT	0.468																																					p.K172M		Atlas-SNP	.											.	SPATA17	59	.	0			c.A515T						.						167	159	162					1																	217915436		2203	4300	6503	SO:0001583	missense	128153	exon6			GCACAAAGCAGGT	AK098591	CCDS1519.1	1q41	2008-02-05			ENSG00000162814	ENSG00000162814			25184	protein-coding gene	gene with protein product	"IQ motif containing H"	611032				16395525	Standard	NM_138796		Approved	IQCH	uc001hlh.1	Q96L03	OTTHUMG00000037875	ENST00000366933.4:c.515A>T	chr1.hg19:g.217915436A>T	ENSP00000355900:p.Lys172Met	50.0	0.0		69.0	42.0	NM_138796	A5D6N2	Missense_Mutation	SNP	ENST00000366933.4	hg19	CCDS1519.1	.	.	.	.	.	.	.	.	.	.	A	19.10	3.762650	0.69763	.	.	ENSG00000162814	ENST00000366933	T	0.51574	0.7	5.83	4.69	0.59074	.	0.560746	0.20316	N	0.094740	T	0.55305	0.1912	M	0.69823	2.125	0.37495	D	0.916542	D	0.53885	0.963	P	0.49502	0.613	T	0.60110	-0.7327	10	0.34782	T	0.22	-6.15	13.2872	0.60249	0.868:0.132:0.0:0.0	.	172	Q96L03	SPT17_HUMAN	M	172	ENSP00000355900:K172M	ENSP00000355900:K172M	K	+	2	0	SPATA17	215982059	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.983000	0.56916	0.990000	0.38787	0.528000	0.53228	AAG	.	.		0.468	SPATA17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092433.2	NM_138796		T	217915436	A	T	217915436	3	4	331	1	0	0	0	0	1	0	0	0	15017	72	3	4	537	4	SPATA17	1	217915436	Missense_Mutation	SNP	A	TCGA-QA-A7B7-01A-11D-A32G-10	31897548	217915436	31335185	8	46187										
TARBP1	6894	hgsc.bcm.edu	37	chr1	234614188	234614188	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	cctctacgcggccggaccccAgggacgccccaggcgcggcc	14	20	1	0	rs12082990		TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr1:234614188A>G	ENST00000040877.1	-	1	661	c.662T>C	c.(661-663)cTg>cCg	p.L221P		NM_005646.3	NP_005637.3	Q13395	TARB1_HUMAN	TAR (HIV-1) RNA binding protein 1	221			L -> P (in dbSNP:rs12082990).		regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA processing (GO:0006396)	nucleus (GO:0005634)	RNA binding (GO:0003723)|RNA methyltransferase activity (GO:0008173)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(7)|large_intestine(6)|lung(22)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	55	Ovarian(103;0.0339)	all_cancers(173;0.00995)|Prostate(94;0.0115)|all_epithelial(177;0.172)	OV - Ovarian serous cystadenocarcinoma(106;0.000263)			GCCGGACCCCAGGGACGCCCC	0.791																																					p.L221P		Atlas-SNP	.											.	TARBP1	111	.	0			c.T662C						.	G	PRO/LEU	19,1975		0,19,978	1	1	1		662	-0.3	0	1	dbSNP_120	1	0,4340		0,0,2170	no	missense	TARBP1	NM_005646.3	98	0,19,3148	GG,GA,AA		0.0,0.9529,0.3	benign	221/1622	234614188	19,6315	997	2170	3167	SO:0001583	missense	6894	exon1			GACCCCAGGGACG		CCDS1601.1	1q42.2	2012-06-12	2007-06-26		ENSG00000059588	ENSG00000059588			11568	protein-coding gene	gene with protein product	"tRNA methyltransferase 3 homolog (S. cerevisiae)"	605052	"Tar (HIV-1) RNA binding protein 1"			1936997	Standard	NM_005646		Approved	TRP-185, TRM3	uc001hwd.3	Q13395	OTTHUMG00000037947	ENST00000040877.1:c.662T>C	chr1.hg19:g.234614188A>G	ENSP00000040877:p.Leu221Pro	0.0	0.0		4.0	4.0	NM_005646	Q9H581	Missense_Mutation	SNP	ENST00000040877.1	hg19	CCDS1601.1	.	.	.	.	.	.	.	.	.	.	G	2.049	-0.418136	0.04766	0.009529	0.0	ENSG00000059588	ENST00000040877	T	0.06142	3.34	4.08	-0.306	0.12780	.	1.497540	0.04333	N	0.352680	T	0.02012	0.0063	N	0.04508	-0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42649	-0.9439	10	0.24483	T	0.36	-15.5763	3.6255	0.08112	0.3353:0.0:0.3872:0.2774	rs12082990	221	Q13395	TARB1_HUMAN	P	221	ENSP00000040877:L221P	ENSP00000040877:L221P	L	-	2	0	TARBP1	232680811	0.000000	0.05858	0.004000	0.12327	0.050000	0.14768	-0.190000	0.09615	0.047000	0.15862	-0.684000	0.03749	CTG	.	.		0.791	TARBP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092616.1	NM_005646		G	234614188	A	G	234614188	3	3	331	1	0	0	0	0	1	0	0	0	15570	188	7	2	4323	2	TARBP1	1	234614188	Missense_Mutation	SNP	A	TCGA-QA-A7B7-01A-11D-A32G-10	16698752	234614188	14636433	9	46188										
HEATR1	55127	hgsc.bcm.edu	37	chr1	236720605	236720605	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	gacctcgctggagaccagctCgctggtgttcttcattgttg	12	11	2	1			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr1:236720605C>T	ENST00000366582.3	-	37	5359	c.5245G>A	c.(5245-5247)Gag>Aag	p.E1749K	HEATR1_ENST00000366581.2_Missense_Mutation_p.E1668K	NM_018072.5	NP_060542.4	Q9H583	HEAT1_HUMAN	HEAT repeat containing 1	1749					rRNA processing (GO:0006364)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(18)|lung(28)|ovary(3)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	87	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			GAGACCAGCTCGCTGGTGTTC	0.512																																					p.E1749K		Atlas-SNP	.											.	HEATR1	197	.	0			c.G5245A						.						71	71	71					1																	236720605		2203	4300	6503	SO:0001583	missense	55127	exon37			CCAGCTCGCTGGT	BC065205	CCDS31066.1	1q43	2011-08-12			ENSG00000119285	ENSG00000119285			25517	protein-coding gene	gene with protein product	"UTP10, small subunit (SSU) processome component, homolog (yeast)"					17699751	Standard	NM_018072		Approved	FLJ10359, BAP28, UTP10	uc001hyd.2	Q9H583	OTTHUMG00000040061	ENST00000366582.3:c.5245G>A	chr1.hg19:g.236720605C>T	ENSP00000355541:p.Glu1749Lys	129.0	0.0		203.0	64.0	NM_018072	Q5T3Q8|Q6P197|Q9NW23	Missense_Mutation	SNP	ENST00000366582.3	hg19	CCDS31066.1	.	.	.	.	.	.	.	.	.	.	C	15.74	2.923011	0.52653	.	.	ENSG00000119285	ENST00000366582;ENST00000366581	T;T	0.64260	-0.09;-0.09	5.36	4.45	0.53987	Armadillo-like helical (1);Armadillo-type fold (1);	0.161191	0.53938	D	0.000044	T	0.63803	0.2542	M	0.70595	2.14	0.80722	D	1	B;D	0.64830	0.006;0.994	B;P	0.45538	0.002;0.484	T	0.65759	-0.6090	10	0.33141	T	0.24	.	14.0273	0.64592	0.0:0.9279:0.0:0.0721	.	1668;1749	Q5T3Q7;Q9H583	.;HEAT1_HUMAN	K	1749;1668	ENSP00000355541:E1749K;ENSP00000355540:E1668K	ENSP00000355540:E1668K	E	-	1	0	HEATR1	234787228	1.000000	0.71417	0.039000	0.18376	0.841000	0.47740	7.254000	0.78329	1.497000	0.48584	0.655000	0.94253	GAG	.	.		0.512	HEATR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096635.1	XM_375853		T	236720605	C	T	236720605	3	4	331	1	0	0	0	0	1	0	0	0	7036	893	31	1	1225	1	HEATR1	1	236720605	Missense_Mutation	SNP	C	TCGA-QA-A7B7-01A-11D-A32G-10	2106417	236720605	12530016	10	46189										
FMN2	56776	hgsc.bcm.edu	37	chr1	240370856	240370856	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	gccaccccctccccctcctcTtcccggagcgggcatacctc	7	23	1	0			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr1:240370856T>C	ENST00000319653.9	+	5	2974	c.2744T>C	c.(2743-2745)cTt>cCt	p.L915P		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	915	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CCCCCTCCTCTTCCCGGAGCG	0.652																																					p.L915P		Atlas-SNP	.											.	FMN2	451	.	0			c.T2744C						.						41	46	44					1																	240370856		2202	4299	6501	SO:0001583	missense	56776	exon5			CTCCTCTTCCCGG	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2744T>C	chr1.hg19:g.240370856T>C	ENSP00000318884:p.Leu915Pro	52.0	0.0		132.0	7.0	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	hg19	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	T	8.160	0.789405	0.16258	.	.	ENSG00000155816	ENST00000319653	T	0.65549	-0.16	3.89	-0.223	0.13118	Actin-binding FH2/DRF autoregulatory (1);Formin Homology 1 (1);	0.382297	0.16991	N	0.191281	T	0.58308	0.2113	M	0.87547	2.89	0.09310	N	1	B	0.10296	0.003	B	0.12156	0.007	T	0.52711	-0.8539	9	.	.	.	.	3.2044	0.06661	0.1367:0.0819:0.1414:0.6401	.	915	Q9NZ56	FMN2_HUMAN	P	915	ENSP00000318884:L915P	.	L	+	2	0	FMN2	238437479	0.998000	0.40836	0.000000	0.03702	0.227000	0.25037	0.291000	0.18994	0.167000	0.19631	0.254000	0.18369	CTT	.	.		0.652	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		C	240370856	T	C	240370856	3	2	331	1	0	0	0	0	1	0	0	0	5958	1609	56	2	2762	2	FMN2	1	240370856	Missense_Mutation	SNP	T	TCGA-QA-A7B7-01A-11D-A32G-10	3650251	240370856	8879765	11	46190										
AHCTF1	25909	hgsc.bcm.edu	37	chr1	247031037	247031037	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	attttagataacacattgttGatgaaaacagatcttgtcaa	6	5	2	4			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr1:247031037G>T	ENST00000391829.2	-	25	3288	c.3165C>A	c.(3163-3165)atC>atA	p.I1055I	AHCTF1_ENST00000366508.1_Silent_p.I1090I|AHCTF1_ENST00000326225.3_Silent_p.I1064I|AHCTF1_ENST00000470300.1_5'UTR			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	1055	Disordered. {ECO:0000250}.				cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(6)|cervix(3)|endometrium(8)|kidney(6)|large_intestine(12)|liver(2)|lung(21)|ovary(5)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	74	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			ACACATTGTTGATGAAAACAG	0.363																																					p.I1064I	Colon(145;197 1800 4745 15099 26333)	Atlas-SNP	.											.	AHCTF1	187	.	0			c.C3192A						.						127	122	124					1																	247031037		2202	4291	6493	SO:0001819	synonymous_variant	25909	exon25			ATTGTTGATGAAA		CCDS1629.1, CCDS1629.2	1q44	2008-09-09			ENSG00000153207	ENSG00000153207			24618	protein-coding gene	gene with protein product	"ELYS transcription factor like protein TMBS62"	610853				11952839	Standard	NM_015446		Approved	ELYS	uc001ibv.2	Q8WYP5	OTTHUMG00000040706	ENST00000391829.2:c.3165C>A	chr1.hg19:g.247031037G>T		242.0	1.0		381.0	213.0	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Silent	SNP	ENST00000391829.2	hg19																																																																																				.	.		0.363	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446		T	247031037	G	T	247031037	2	4	331	1	0	0	0	0	0	0	0	1	408	1280	45	3		3	AHCTF1	1	247031037	Silent	SNP	G	TCGA-QA-A7B7-01A-11D-A32G-10	6660181	247031037	2219584	12	46191										
CAPN13	92291	hgsc.bcm.edu	37	chr2	31010123	31010123	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	ctcaggcagtgatcccgcaaGgtggtaaagtcctggtcttt	12	10	2	1			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr2:31010123G>T	ENST00000295055.8	-	2	245	c.69C>A	c.(67-69)acC>acA	p.T23T	CAPN13_ENST00000534090.2_Silent_p.T23T|CAPN13_ENST00000465960.2_5'UTR	NM_144575.2	NP_653176.2	Q6MZZ7	CAN13_HUMAN	calpain 13	23					proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	30	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					GATCCCGCAAGGTGGTAAAGT	0.522																																					p.T23T		Atlas-SNP	.											.	CAPN13	70	.	0			c.C69A						.						46	47	47					2																	31010123		1985	4165	6150	SO:0001819	synonymous_variant	92291	exon2			CCGCAAGGTGGTA		CCDS46252.1	2p22-p21	2008-02-05			ENSG00000162949	ENSG00000162949			16663	protein-coding gene	gene with protein product		610228				11675017	Standard	NM_144575		Approved	FLJ23523	uc021vfm.1	Q6MZZ7	OTTHUMG00000152053	ENST00000295055.8:c.69C>A	chr2.hg19:g.31010123G>T		137.0	0.0		154.0	63.0	NM_144575	Q17RF0|Q580X1|Q8TE80	Silent	SNP	ENST00000295055.8	hg19	CCDS46252.1																																																																																			.	.		0.522	CAPN13-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325101.2	NM_144575		T	31010123	G	T	31010123	2	4	331	1	0	0	0	0	0	0	0	1	2628	987	35	3		3	CAPN13	2	31010123	Silent	SNP	G	TCGA-QA-A7B7-01A-11D-A32G-10		31010123	212189250	13	46192										
SPTBN1	6711	hgsc.bcm.edu	37	chr2	54859797	54859797	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	cttcatgaccaccatggacgCcaatgaggagaagatcaatg	10	10	2	4			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr2:54859797C>T	ENST00000356805.4	+	17	3940	c.3659C>T	c.(3658-3660)gCc>gTc	p.A1220V	SPTBN1_ENST00000333896.5_Missense_Mutation_p.A1207V	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	1220					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			ACCATGGACGCCAATGAGGAG	0.498																																					p.A1220V		Atlas-SNP	.											.	SPTBN1	378	.	0			c.C3659T						.						119	106	111					2																	54859797		2203	4300	6503	SO:0001583	missense	6711	exon17			TGGACGCCAATGA		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"Pleckstrin homology (PH) domain containing"	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.3659C>T	chr2.hg19:g.54859797C>T	ENSP00000349259:p.Ala1220Val	85.0	0.0		128.0	50.0	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Missense_Mutation	SNP	ENST00000356805.4	hg19	CCDS33198.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.020635	0.93462	.	.	ENSG00000115306	ENST00000356805;ENST00000333896	T;T	0.55234	0.53;0.53	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.67887	0.2941	M	0.79614	2.46	0.80722	D	1	P;P	0.38745	0.593;0.645	B;P	0.48952	0.381;0.596	T	0.66866	-0.5815	10	0.40728	T	0.16	.	19.3216	0.94243	0.0:1.0:0.0:0.0	.	1207;1220	Q01082-3;Q01082	.;SPTB2_HUMAN	V	1220;1207	ENSP00000349259:A1220V;ENSP00000334156:A1207V	ENSP00000334156:A1207V	A	+	2	0	SPTBN1	54713301	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.770000	0.85390	2.573000	0.86826	0.655000	0.94253	GCC	.	.		0.498	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			T	54859797	C	T	54859797	3	4	331	1	0	0	0	0	1	0	0	0	15134	739	26	3	3834	3	SPTBN1	2	54859797	Missense_Mutation	SNP	C	TCGA-QA-A7B7-01A-11D-A32G-10	23849674	54859797	188339576	14	46193										
ZNF638	27332	hgsc.bcm.edu	37	chr2	71654499	71654499	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	tgggtccagtaaatgagaatGttatggaagaagatctaaaa	11	3	1	3			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr2:71654499G>A	ENST00000409544.1	+	24	6130	c.5500G>A	c.(5500-5502)Gtt>Att	p.V1834I	ZNF638_ENST00000264447.4_Missense_Mutation_p.V1834I|ZNF638_ENST00000409407.1_Missense_Mutation_p.V774I|ZNF638_ENST00000355812.3_3'UTR	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	1834					regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						AAATGAGAATGTTATGGAAGA	0.368																																					p.V1834I		Atlas-SNP	.											.	ZNF638	179	.	0			c.G5500A						.						57	58	57					2																	71654499		2203	4299	6502	SO:0001583	missense	27332	exon24			GAGAATGTTATGG	D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"RNA binding motif (RRM) containing"	17894	protein-coding gene	gene with protein product		614349	"zinc finger, matrin-like"	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.5500G>A	chr2.hg19:g.71654499G>A	ENSP00000386433:p.Val1834Ile	21.0	0.0		26.0	8.0	NM_014497	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Missense_Mutation	SNP	ENST00000409544.1	hg19	CCDS1917.1	.	.	.	.	.	.	.	.	.	.	G	4.580	0.107791	0.08780	.	.	ENSG00000075292	ENST00000264447;ENST00000409544;ENST00000409407	T;T;T	0.31247	1.5;1.5;1.89	5.18	0.219	0.15274	.	0.208610	0.29868	N	0.010981	T	0.16685	0.0401	N	0.19112	0.55	0.51482	D	0.999927	B;B	0.11235	0.004;0.003	B;B	0.14578	0.011;0.007	T	0.06110	-1.0845	10	0.36615	T	0.2	-3.0624	7.9563	0.30045	0.4404:0.0:0.5596:0.0	.	1834;1834	Q14966-3;Q14966	.;ZN638_HUMAN	I	1834;1834;774	ENSP00000264447:V1834I;ENSP00000386433:V1834I;ENSP00000386813:V774I	ENSP00000264447:V1834I	V	+	1	0	ZNF638	71508007	0.908000	0.30866	0.730000	0.30809	0.430000	0.31655	-0.019000	0.12546	0.073000	0.16731	0.655000	0.94253	GTT	.	.		0.368	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497		A	71654499	G	A	71654499	3	1	331	1	0	0	0	0	1	0	0	0	18070	1377	48	3	5590	3	ZNF638	2	71654499	Missense_Mutation	SNP	G	TCGA-QA-A7B7-01A-11D-A32G-10	16794702	71654499	171544874	15	46194										
SH3RF3	344558	hgsc.bcm.edu	37	chr2	110015366	110015366	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	gccgcggccaggattggagaCcttgctcatctgtcgtgcgc	14	13	2	1			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr2:110015366C>G	ENST00000309415.6	+	4	1266	c.1266C>G	c.(1264-1266)gaC>gaG	p.D422E		NM_001099289.1	NP_001092759.1	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3	422							zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(5)|ovary(2)	18						GGATTGGAGACCTTGCTCATC	0.612																																					p.D422E		Atlas-SNP	.											.	SH3RF3	62	.	0			c.C1266G						.						39	44	42					2																	110015366		2099	4234	6333	SO:0001583	missense	344558	exon4			TGGAGACCTTGCT	AK074131	CCDS74557.1	2q13	2013-01-11	2008-05-14	2008-05-14	ENSG00000172985	ENSG00000172985		"RING-type (C3HC4) zinc fingers"	24699	protein-coding gene	gene with protein product			"SH3 multiple domains 4"	SH3MD4		16374509	Standard	XM_006712493		Approved	FLJ00204, POSH2	uc010ywt.1	Q8TEJ3	OTTHUMG00000153439	ENST00000309415.6:c.1266C>G	chr2.hg19:g.110015366C>G	ENSP00000309186:p.Asp422Glu	40.0	0.0		60.0	28.0	NM_001099289	A0SDZ7|A8MPR1|Q8NDU1	Missense_Mutation	SNP	ENST00000309415.6	hg19		.	.	.	.	.	.	.	.	.	.	C	0.247	-1.009595	0.02095	.	.	ENSG00000172985	ENST00000418513;ENST00000309415	T;T	0.54279	0.58;2.34	5.0	2.17	0.27698	.	0.461885	0.20658	N	0.088061	T	0.23649	0.0572	.	.	.	0.27209	N	0.959977	B	0.06786	0.001	B	0.08055	0.003	T	0.28364	-1.0046	9	0.02654	T	1	-26.7133	7.2751	0.26279	0.0908:0.3276:0.4999:0.0817	.	422	Q8TEJ3	SH3R3_HUMAN	E	422	ENSP00000414997:D422E;ENSP00000309186:D422E	ENSP00000309186:D422E	D	+	3	2	SH3RF3	109381798	0.171000	0.23029	0.429000	0.26710	0.732000	0.41865	-0.011000	0.12721	0.287000	0.22375	0.561000	0.74099	GAC	.	.		0.612	SH3RF3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001099289		G	110015366	C	G	110015366	3	3	331	1	0	0	0	0	1	0	0	0	14275	506	18	4	1280	4	SH3RF3	2	110015366	Missense_Mutation	SNP	C	TCGA-QA-A7B7-01A-11D-A32G-10	38360867	110015366	133184007	16	46195										
LCT	3938	hgsc.bcm.edu	37	chr2	136567036	136567036	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	tcggagcatattcagatcggCatccagctggtgatagctgt	12	9	1	2			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr2:136567036C>T	ENST00000264162.2	-	8	2891	c.2881G>A	c.(2881-2883)Gcc>Acc	p.A961T	Y_RNA_ENST00000363794.1_RNA	NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	961	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	TTCAGATCGGCATCCAGCTGG	0.517																																					p.A961T		Atlas-SNP	.											.	LCT	309	.	0			c.G2881A						.						95	94	95					2																	136567036		2203	4300	6503	SO:0001583	missense	3938	exon8			GATCGGCATCCAG	X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.2881G>A	chr2.hg19:g.136567036C>T	ENSP00000264162:p.Ala961Thr	57.0	0.0		84.0	30.0	NM_002299	Q4ZG58	Missense_Mutation	SNP	ENST00000264162.2	hg19	CCDS2178.1	.	.	.	.	.	.	.	.	.	.	C	33	5.215871	0.95104	.	.	ENSG00000115850	ENST00000264162;ENST00000455227	T	0.51071	0.72	5.78	5.78	0.91487	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.258408	0.44483	D	0.000449	T	0.54415	0.1857	N	0.26042	0.785	0.53688	D	0.999979	P	0.46578	0.88	P	0.59221	0.854	T	0.40001	-0.9586	10	0.22706	T	0.39	-23.6568	20.0139	0.97470	0.0:1.0:0.0:0.0	.	961	P09848	LPH_HUMAN	T	961;393	ENSP00000264162:A961T	ENSP00000264162:A961T	A	-	1	0	LCT	136283506	1.000000	0.71417	0.984000	0.44739	0.989000	0.77384	7.818000	0.86416	2.724000	0.93272	0.563000	0.77884	GCC	.	.		0.517	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299		T	136567036	C	T	136567036	3	4	331	1	0	0	0	0	1	0	0	0	8702	710	25	3	2942	3	LCT	2	136567036	Missense_Mutation	SNP	C	TCGA-QA-A7B7-01A-11D-A32G-10	26551670	136567036	106632337	17	46196										
NEB	4703	hgsc.bcm.edu	37	chr2	152497166	152497166	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	ccgagctgcttacgatagccTtctttgtacttgaactaaaa	7	10	1	1			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr2:152497166T>G	ENST00000172853.10	-	61	8535	c.8388A>C	c.(8386-8388)gaA>gaC	p.E2796D	NEB_ENST00000603639.1_Missense_Mutation_p.E2796D|NEB_ENST00000409198.1_Missense_Mutation_p.E2796D|NEB_ENST00000397345.3_Missense_Mutation_p.E2796D|NEB_ENST00000604864.1_Missense_Mutation_p.E2796D|NEB_ENST00000427231.2_Missense_Mutation_p.E2796D			P20929	NEBU_HUMAN	nebulin	2796					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TACGATAGCCTTCTTTGTACT	0.413																																					p.E2796D		Atlas-SNP	.											.	NEB	1697	.	0			c.A8388C						.						102	92	95					2																	152497166		1836	4090	5926	SO:0001583	missense	4703	exon61			ATAGCCTTCTTTG	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.8388A>C	chr2.hg19:g.152497166T>G	ENSP00000172853:p.Glu2796Asp	109.0	0.0		119.0	47.0	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	hg19		.	.	.	.	.	.	.	.	.	.	T	11.44	1.640068	0.29157	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.57907	0.37;3.34;3.34;0.37	6.17	3.7	0.42460	.	0.247003	0.41097	N	0.000957	T	0.40956	0.1138	L	0.39898	1.24	0.80722	D	1	B	0.12013	0.005	B	0.17979	0.02	T	0.29027	-1.0025	10	0.44086	T	0.13	.	7.9747	0.30149	0.1222:0.0656:0.0:0.8122	.	2796	P20929	NEBU_HUMAN	D	2796	ENSP00000386259:E2796D;ENSP00000380505:E2796D;ENSP00000416578:E2796D;ENSP00000172853:E2796D	ENSP00000172853:E2796D	E	-	3	2	NEB	152205412	0.953000	0.32496	1.000000	0.80357	0.932000	0.56968	1.155000	0.31700	1.161000	0.42604	-0.250000	0.11733	GAA	.	.		0.413	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		G	152497166	T	G	152497166	3	3	331	1	0	0	0	0	1	0	0	0	10311	1606	56	5	17786	5	NEB	2	152497166	Missense_Mutation	SNP	T	TCGA-QA-A7B7-01A-11D-A32G-10	15930130	152497166	90702207	18	46197										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196620969	196620969	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	ttttgacattcaaaatgctgCtaaccacttcttcaagatct	4	10	4	2			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr2:196620969C>T	ENST00000312428.6	-	62	11574	c.11474G>A	c.(11473-11475)aGc>aAc	p.S3825N	DNAH7_ENST00000409063.1_Missense_Mutation_p.S308N	NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	3825					cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						CAAAATGCTGCTAACCACTTC	0.373																																					p.S3825N		Atlas-SNP	.											.	DNAH7	512	.	0			c.G11474A						.						116	108	111					2																	196620969		1841	4099	5940	SO:0001583	missense	56171	exon62			ATGCTGCTAACCA	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.11474G>A	chr2.hg19:g.196620969C>T	ENSP00000311273:p.Ser3825Asn	273.0	0.0		327.0	130.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	hg19	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	C	4.034	0.003777	0.07866	.	.	ENSG00000118997	ENST00000312428;ENST00000409063	T;T	0.08282	3.11;3.11	5.23	3.28	0.37604	Dynein heavy chain (1);	0.659459	0.16266	N	0.222030	T	0.02848	0.0085	N	0.03209	-0.39	0.80722	D	1	B	0.02656	0.0	B	0.12837	0.008	T	0.30679	-0.9970	10	0.02654	T	1	.	7.1366	0.25531	0.0:0.7192:0.0:0.2808	.	3825	Q8WXX0	DYH7_HUMAN	N	3825;308	ENSP00000311273:S3825N;ENSP00000386912:S308N	ENSP00000311273:S3825N	S	-	2	0	DNAH7	196329214	0.974000	0.33945	0.999000	0.59377	0.988000	0.76386	0.812000	0.27211	1.427000	0.47276	0.650000	0.86243	AGC	.	.		0.373	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		T	196620969	C	T	196620969	3	4	331	1	0	0	0	0	1	0	0	0	4608	797	28	3	616	3	DNAH7	2	196620969	Missense_Mutation	SNP	C	TCGA-QA-A7B7-01A-11D-A32G-10	44123803	196620969	46578404	19	46198										
WNT6	7475	hgsc.bcm.edu	37	chr2	219735837	219735837	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	ggcaggccgagttgtgccagGctgagccggaagtggtggca	19	9	0	1			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr2:219735837G>T	ENST00000233948.3	+	2	386	c.169G>T	c.(169-171)Gct>Tct	p.A57S	WNT6_ENST00000486233.1_Intron	NM_006522.3	NP_006513.1	Q9Y6F9	WNT6_HUMAN	wingless-type MMTV integration site family, member 6	57					axis specification (GO:0009798)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell fate commitment (GO:0045165)|cellular response to retinoic acid (GO:0071300)|cornea development in camera-type eye (GO:0061303)|epithelial-mesenchymal cell signaling (GO:0060684)|nephron tubule formation (GO:0072079)|neuron differentiation (GO:0030182)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of gene expression (GO:0010628)|positive regulation of tooth mineralization (GO:0070172)|positive regulation of transcription, DNA-templated (GO:0045893)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			large_intestine(1)|ovary(2)|skin(1)	4		Renal(207;0.0474)		Epithelial(149;4.53e-07)|all cancers(144;9.3e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GTTGTGCCAGGCTGAGCCGGA	0.677																																					p.A57S		Atlas-SNP	.											.	WNT6	21	.	0			c.G169T						.						50	60	57					2																	219735837		2203	4298	6501	SO:0001583	missense	7475	exon2			TGCCAGGCTGAGC	AF079522	CCDS2425.1	2q35	2008-05-23			ENSG00000115596	ENSG00000115596		"Wingless-type MMTV integration sites"	12785	protein-coding gene	gene with protein product		604663				10343101, 11350055	Standard	NM_006522		Approved		uc002vjc.1	Q9Y6F9	OTTHUMG00000133082	ENST00000233948.3:c.169G>T	chr2.hg19:g.219735837G>T	ENSP00000233948:p.Ala57Ser	87.0	0.0		107.0	47.0	NM_006522	Q9H1J6|Q9H238	Missense_Mutation	SNP	ENST00000233948.3	hg19	CCDS2425.1	.	.	.	.	.	.	.	.	.	.	g	10.25	1.298856	0.23650	.	.	ENSG00000115596	ENST00000233948	T	0.75367	-0.93	5.17	4.29	0.51040	.	0.318671	0.34110	N	0.004243	T	0.49966	0.1588	N	0.08118	0	0.25083	N	0.990915	B	0.16396	0.017	B	0.25614	0.062	T	0.33137	-0.9880	10	0.15952	T	0.53	.	5.9699	0.19346	0.172:0.1704:0.6577:0.0	.	57	Q9Y6F9	WNT6_HUMAN	S	57	ENSP00000233948:A57S	ENSP00000233948:A57S	A	+	1	0	WNT6	219444081	1.000000	0.71417	0.903000	0.35520	0.986000	0.74619	3.299000	0.51826	1.172000	0.42781	0.586000	0.80456	GCT	.	.		0.677	WNT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256727.2	NM_006522		T	219735837	G	T	219735837	3	4	331	1	0	0	0	0	1	0	0	0	17408	1203	42	3	175	3	WNT6	2	219735837	Missense_Mutation	SNP	G	TCGA-QA-A7B7-01A-11D-A32G-10	23114868	219735837	23463536	20	46199										
CADM2	253559	hgsc.bcm.edu	37	chr3	85935378	85935378	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	agattagtggattctcatcaCcagttatggagggtgacttg	12	6	2	2			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr3:85935378C>A	ENST00000407528.2	+	4	465	c.403C>A	c.(403-405)Cca>Aca	p.P135T	CADM2_ENST00000405615.2_Missense_Mutation_p.P137T|CADM2_ENST00000383699.3_Missense_Mutation_p.P144T	NM_001167674.1	NP_001161146.1	Q8N3J6	CADM2_HUMAN	cell adhesion molecule 2	135	Ig-like C2-type 1.				adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|synapse (GO:0045202)				endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(1)|prostate(1)|skin(4)	38		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		ATTCTCATCACCAGTTATGGA	0.388																																					p.P144T		Atlas-SNP	.											.	CADM2	195	.	0			c.C430A						.						101	93	96					3																	85935378		2203	4300	6503	SO:0001583	missense	253559	exon5			TCATCACCAGTTA	AF538973	CCDS33792.1, CCDS54613.1, CCDS54614.1	3p12.2	2013-01-11	2007-02-07	2007-02-07	ENSG00000175161	ENSG00000175161		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing"	29849	protein-coding gene	gene with protein product	"nectin-like 3"	609938	"immunoglobulin superfamily, member 4D"	IGSF4D			Standard	NM_153184		Approved	NECL3, Necl-3, SynCAM2	uc003dqj.3	Q8N3J6	OTTHUMG00000158990	ENST00000407528.2:c.403C>A	chr3.hg19:g.85935378C>A	ENSP00000384575:p.Pro135Thr	244.0	0.0		249.0	88.0	NM_001167675	G3XHN7|G3XHN8|Q3KQY9|Q658Q7|Q8IZP8	Missense_Mutation	SNP	ENST00000407528.2	hg19	CCDS54614.1	.	.	.	.	.	.	.	.	.	.	C	12.18	1.859446	0.32884	.	.	ENSG00000175161	ENST00000383699;ENST00000407528;ENST00000405615	T;T;T	0.65549	-0.06;-0.16;-0.14	5.57	5.57	0.84162	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.69682	0.3138	L	0.39397	1.21	0.80722	D	1	D;D;D	0.89917	0.997;1.0;1.0	D;D;D	0.91635	0.947;0.999;0.999	T	0.61282	-0.7094	10	0.02654	T	1	.	19.5761	0.95444	0.0:1.0:0.0:0.0	.	137;144;135	Q8N3J6-3;G3XHN4;Q8N3J6	.;.;CADM2_HUMAN	T	144;135;137	ENSP00000373200:P144T;ENSP00000384575:P135T;ENSP00000384193:P137T	ENSP00000373200:P144T	P	+	1	0	CADM2	86018068	1.000000	0.71417	0.999000	0.59377	0.971000	0.66376	7.442000	0.80503	2.619000	0.88677	0.650000	0.86243	CCA	.	.		0.388	CADM2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352822.1	NM_153184		A	85935378	C	A	85935378	3	1	331	1	0	0	0	0	1	0	0	0	2569	507	18	3	488	3	CADM2	3	85935378	Missense_Mutation	SNP	C	TCGA-QA-A7B7-01A-11D-A32G-10		85935378	112087052	21	46200										
EPHA3	2042	hgsc.bcm.edu	37	chr3	89391190	89391190	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	taatggggtgtcagagctgaGctccccaccaagacagtttg	12	10	1	3			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr3:89391190G>T	ENST00000336596.2	+	5	1481	c.1256G>T	c.(1255-1257)aGc>aTc	p.S419I	EPHA3_ENST00000452448.2_Missense_Mutation_p.S419I|EPHA3_ENST00000494014.1_Missense_Mutation_p.S419I	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	419	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)	p.S419T(2)		NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		TCAGAGCTGAGCTCCCCACCA	0.473										TSP Lung(6;0.00050)																											p.S419I		Atlas-SNP	.											EPHA3_ENST00000452448,NS,carcinoma,0,2	EPHA3	501	.	2	Substitution - Missense(2)	endometrium(2)	c.G1256T						.						77	63	68					3																	89391190		2203	4300	6503	SO:0001583	missense	2042	exon5			AGCTGAGCTCCCC	M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3387	protein-coding gene	gene with protein product		179611	"EphA3"	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.1256G>T	chr3.hg19:g.89391190G>T	ENSP00000337451:p.Ser419Ile	62.0	0.0		81.0	39.0	NM_005233	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	hg19	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	G	17.07	3.293997	0.60086	.	.	ENSG00000044524	ENST00000336596;ENST00000452448;ENST00000494014	T;T;T	0.53640	0.61;0.61;0.61	5.53	4.6	0.57074	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.180477	0.64402	D	0.000008	T	0.57946	0.2088	M	0.72479	2.2	0.46874	D	0.999238	P;P	0.39665	0.627;0.682	B;P	0.48030	0.17;0.564	T	0.57159	-0.7859	9	.	.	.	.	16.1804	0.81895	0.0:0.1331:0.8669:0.0	.	419;419	P29320;P29320-2	EPHA3_HUMAN;.	I	419	ENSP00000337451:S419I;ENSP00000399926:S419I;ENSP00000419190:S419I	.	S	+	2	0	EPHA3	89473880	1.000000	0.71417	1.000000	0.80357	0.894000	0.52154	5.705000	0.68355	2.763000	0.94921	0.563000	0.77884	AGC	.	.		0.473	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		T	89391190	G	T	89391190	3	4	331	1	0	0	0	0	1	0	0	0	5170	971	34	3	1274	3	EPHA3	3	89391190	Missense_Mutation	SNP	G	TCGA-QA-A7B7-01A-11D-A32G-10	3455812	89391190	108631240	22	46201										
HEG1	57493	hgsc.bcm.edu	37	chr3	124732434	124732434	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	gaagaagaggaggaggaggaAgaggaggaggaggagtcact	21	2	1	3	rs374949821		TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr3:124732434A>G	ENST00000311127.4	-	6	2056	c.1989T>C	c.(1987-1989)tcT>tcC	p.S663S	HEG1_ENST00000477536.1_5'UTR	NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	663	Ser-rich.				cardiac atrium morphogenesis (GO:0003209)|cell-cell junction assembly (GO:0007043)|endothelial cell morphogenesis (GO:0001886)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|lymph circulation (GO:0003017)|lymph vessel development (GO:0001945)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|post-embryonic development (GO:0009791)|regulation of body fluid levels (GO:0050878)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|ventricular septum development (GO:0003281)	cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(24)|ovary(2)|urinary_tract(4)	47						aggaggaggaagaggaggagg	0.488																																					p.S663S		Atlas-SNP	.											.	HEG1	109	.	0			c.T1989C						.						60	66	64					3																	124732434		2169	4257	6426	SO:0001819	synonymous_variant	57493	exon6			GGAGGAAGAGGAG	AK074987	CCDS46898.1	3q21.2	2013-03-08	2013-03-08		ENSG00000173706	ENSG00000173706			29227	protein-coding gene	gene with protein product	"heart of glass"	614182	"HEG homolog 1 (zebrafish)"			10574462, 19151727, 23007647	Standard	NM_020733		Approved	KIAA1237, HEG	uc003ehs.4	Q9ULI3	OTTHUMG00000159486	ENST00000311127.4:c.1989T>C	chr3.hg19:g.124732434A>G		71.0	0.0		100.0	5.0	NM_020733	Q6NX66|Q8NC40|Q9BSV0	Silent	SNP	ENST00000311127.4	hg19	CCDS46898.1																																																																																			.	.		0.488	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386		G	124732434	A	G	124732434	2	3	331	1	0	0	0	0	0	0	0	1	7053	59	3	2		2	HEG1	3	124732434	Silent	SNP	A	TCGA-QA-A7B7-01A-11D-A32G-10	35341244	124732434	73289996	23	46202										
ATP13A4	84239	hgsc.bcm.edu	37	chr3	193175188	193175188	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	ctggctggctgttctgcaggGcttaactaccatggcatgtg	13	10	1	0			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr3:193175188G>A	ENST00000342695.4	-	15	2063	c.1741C>T	c.(1741-1743)Ccc>Tcc	p.P581S	ATP13A4_ENST00000392443.3_Missense_Mutation_p.P562S	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	581						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(27)|ovary(2)|prostate(3)|skin(11)|upper_aerodigestive_tract(2)	71	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		GTTCTGCAGGGCTTAACTACC	0.483																																					p.P581S		Atlas-SNP	.											.	ATP13A4	154	.	0			c.C1741T						.						184	185	185					3																	193175188		2203	4300	6503	SO:0001583	missense	84239	exon15			TGCAGGGCTTAAC	AK095277	CCDS3304.2	3q29	2010-04-20			ENSG00000127249	ENSG00000127249		"ATPases / P-type"	25422	protein-coding gene	gene with protein product		609556				14702039, 12975309	Standard	XM_005247829		Approved	DKFZp761I1011, FLJ37958	uc003ftd.3	Q4VNC1	OTTHUMG00000074067	ENST00000342695.4:c.1741C>T	chr3.hg19:g.193175188G>A	ENSP00000339182:p.Pro581Ser	169.0	0.0		197.0	81.0	NM_032279	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	Missense_Mutation	SNP	ENST00000342695.4	hg19	CCDS3304.2	.	.	.	.	.	.	.	.	.	.	G	16.30	3.083257	0.55861	.	.	ENSG00000127249	ENST00000392443;ENST00000342695	D;D	0.86627	-1.87;-2.15	4.95	4.95	0.65309	ATPase, cation-transporting, domain N (1);ATPase, P-type, cytoplasmic domain N (1);	0.183867	0.38720	N	0.001594	D	0.92450	0.7603	M	0.67517	2.055	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	D	0.92927	0.6360	10	0.62326	D	0.03	-21.5642	16.0609	0.80838	0.0:0.0:1.0:0.0	.	562;581;581	B7WPN9;Q4VNC1-2;Q4VNC1	.;.;AT134_HUMAN	S	562;581	ENSP00000376238:P562S;ENSP00000339182:P581S	ENSP00000339182:P581S	P	-	1	0	ATP13A4	194657882	1.000000	0.71417	1.000000	0.80357	0.333000	0.28666	5.343000	0.65976	2.457000	0.83068	0.655000	0.94253	CCC	.	.		0.483	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157244.4	NM_032279		A	193175188	G	A	193175188	3	1	331	1	0	0	0	0	1	0	0	0	1126	1203	42	3	1913	3	ATP13A4	3	193175188	Missense_Mutation	SNP	G	TCGA-QA-A7B7-01A-11D-A32G-10	68442754	193175188	4847242	24	46203										
CHIC2	26511	hgsc.bcm.edu	37	chr4	54915246	54915246	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	taagacaactgttaactctgTtgatgctggctttaaattct	7	7	2	2	rs374480856		TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr4:54915246T>C	ENST00000263921.3	-	3	595	c.206A>G	c.(205-207)aAc>aGc	p.N69S	FIP1L1_ENST00000507166.1_Intron|CHIC2_ENST00000512964.1_Missense_Mutation_p.N69S	NM_012110.3	NP_036242.1	Q9UKJ5	CHIC2_HUMAN	cysteine-rich hydrophobic domain 2	69						Golgi-associated vesicle (GO:0005798)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|large_intestine(1)|lung(1)	4	all_cancers(7;0.0193)|all_neural(26;0.0209)|Lung NSC(11;0.0281)|Glioma(25;0.08)		LUSC - Lung squamous cell carcinoma(32;0.00216)			GTTAACTCTGTTGATGCTGGC	0.363			T	ETV6	AML																																p.N69S		Atlas-SNP	.		Dom	yes		4	4q11-q12	26511	cysteine-rich hydrophobic domain 2		L	.	CHIC2	20	.	0			c.A206G						.	T	SER/ASN	0,4406		0,0,2203	42	37	39		206	3.3	1	4		39	1,8595	1.2+/-3.3	0,1,4297	no	missense	CHIC2	NM_012110.3	46	0,1,6500	CC,CT,TT		0.0116,0.0,0.0077	benign	69/166	54915246	1,13001	2203	4298	6501	SO:0001583	missense	26511	exon3			ACTCTGTTGATGC	AF159423	CCDS3493.1	4q12	2013-09-04			ENSG00000109220	ENSG00000109220			1935	protein-coding gene	gene with protein product		604332				10477709	Standard	NM_012110		Approved	BTL	uc003haj.2	Q9UKJ5	OTTHUMG00000102101	ENST00000263921.3:c.206A>G	chr4.hg19:g.54915246T>C	ENSP00000263921:p.Asn69Ser	183.0	0.0		208.0	90.0	NM_012110	B2R639	Missense_Mutation	SNP	ENST00000263921.3	hg19	CCDS3493.1	.	.	.	.	.	.	.	.	.	.	T	2.259	-0.369651	0.05069	0.0	1.16E-4	ENSG00000109220	ENST00000263921;ENST00000512964	.	.	.	5.81	3.35	0.38373	Golgin subfamily A member 7/ERF4 (1);	0.089901	0.85682	D	0.000000	T	0.21674	0.0522	N	0.04203	-0.255	0.46631	D	0.999139	B	0.02656	0.0	B	0.10450	0.005	T	0.18023	-1.0350	9	0.02654	T	1	-24.0801	5.2613	0.15576	0.0:0.188:0.15:0.662	.	69	Q9UKJ5	CHIC2_HUMAN	S	69	.	ENSP00000263921:N69S	N	-	2	0	CHIC2	54610003	1.000000	0.71417	1.000000	0.80357	0.862000	0.49288	4.607000	0.61133	0.460000	0.27045	-0.361000	0.07541	AAC	.	.		0.363	CHIC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219937.2			C	54915246	T	C	54915246	3	2	331	1	0	0	0	0	1	0	0	0	3346	1725	60	2	307	2	CHIC2	4	54915246	Missense_Mutation	SNP	T	TCGA-QA-A7B7-01A-11D-A32G-10		54915246	136239030	25	46204										
C4orf31	79625	hgsc.bcm.edu	37	chr4	121958596	121958596	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	catctactcttgggtcatagGgtaactcagggtatggctga	12	8	4	1			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr4:121958596G>T	ENST00000379692.4	-	4	1056	c.530C>A	c.(529-531)cCc>cAc	p.P177H	NDNF_ENST00000506900.1_5'UTR	NM_024574.3	NP_078850.3	Q8TB73	NDNF_HUMAN	neuron-derived neurotrophic factor	177					cell growth (GO:0016049)|extracellular matrix organization (GO:0030198)|negative regulation of neuron apoptotic process (GO:0043524)|neuron migration (GO:0001764)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of neuron projection development (GO:0010976)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(3)|skin(1)|urinary_tract(1)	29						TGGGTCATAGGGTAACTCAGG	0.478																																					p.P177H		Atlas-SNP	.											.	NDNF	72	.	0			c.C530A						.						204	205	204					4																	121958596		2066	4214	6280	SO:0001583	missense	79625	exon4			TCATAGGGTAACT	BC019351	CCDS3717.2	4q27	2011-07-05	2011-07-05	2011-07-05	ENSG00000173376	ENSG00000173376			26256	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 31"	C4orf31		12975309, 20969804	Standard	NM_024574		Approved	FLJ23191	uc003idq.1	Q8TB73	OTTHUMG00000132973	ENST00000379692.4:c.530C>A	chr4.hg19:g.121958596G>T	ENSP00000369014:p.Pro177His	206.0	0.0		196.0	90.0	NM_024574	A8K0Q0|Q6UWE5|Q9H5P7	Missense_Mutation	SNP	ENST00000379692.4	hg19	CCDS3717.2	.	.	.	.	.	.	.	.	.	.	G	19.56	3.850892	0.71719	.	.	ENSG00000173376	ENST00000379692	T	0.79940	-1.32	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	D	0.89674	0.6783	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89316	0.3636	10	0.87932	D	0	-22.2687	20.6208	0.99490	0.0:0.0:1.0:0.0	.	177	Q8TB73	NDNF_HUMAN	H	177	ENSP00000369014:P177H	ENSP00000369014:P177H	P	-	2	0	NDNF	122178046	1.000000	0.71417	0.584000	0.28653	0.776000	0.43924	9.833000	0.99426	2.882000	0.98803	0.655000	0.94253	CCC	.	.		0.478	NDNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256532.2	NM_024574		T	121958596	G	T	121958596	3	4	331	1	0	0	0	0	1	0	0	0	2263	1232	43	3	1180	3	C4orf31	4	121958596	Missense_Mutation	SNP	G	TCGA-QA-A7B7-01A-11D-A32G-10	67043350	121958596	69195680	26	46205										
PAPD7	11044	hgsc.bcm.edu	37	chr5	6737736	6737736	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	tgtggtgaaagacctttggcCgacggctgatgtgagtatgt	15	6	0	4			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr5:6737736C>G	ENST00000230859.6	+	2	209	c.80C>G	c.(79-81)cCg>cGg	p.P27R		NM_001171805.1|NM_001171806.1|NM_006999.4	NP_001165276.1|NP_001165277.1|NP_008930.1	Q5XG87	PAPD7_HUMAN	PAP associated domain containing 7	257	Ala-rich.				double-strand break repair (GO:0006302)|mitotic chromosome condensation (GO:0007076)|response to drug (GO:0042493)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|SMC family protein binding (GO:0043221)			cervix(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						GACCTTTGGCCGACGGCTGAT	0.453																																					p.P27R	NSCLC(7;212 333 5667 23379 46547)	Atlas-SNP	.											.	PAPD7	69	.	0			c.C80G						.						251	199	217					5																	6737736		2203	4300	6503	SO:0001583	missense	11044	exon2			TTTGGCCGACGGC	AF089896	CCDS3871.1	5p15	2010-11-18	2010-01-19	2010-01-19	ENSG00000112941	ENSG00000112941			16705	protein-coding gene	gene with protein product	"topoisomerase-related function protein 4-1", "polymerase (DNA-directed) sigma", "DNA polymerase kappa", "TUTase5"	605198	"polymerase (DNA directed) sigma"	POLS		10066793, 10926539	Standard	NM_006999		Approved	POLK, TRF4, LAK-1, TRF4-1	uc003jdx.1	Q5XG87	OTTHUMG00000090457	ENST00000230859.6:c.80C>G	chr5.hg19:g.6737736C>G	ENSP00000230859:p.Pro27Arg	266.0	0.0		282.0	110.0	NM_001171805	A8K1E2|M1JCE6|O43289|Q17RZ1|Q9Y6C1	Missense_Mutation	SNP	ENST00000230859.6	hg19	CCDS3871.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.732789	0.89482	.	.	ENSG00000112941	ENST00000230859;ENST00000515721	T	0.56611	0.45	5.05	5.05	0.67936	Nucleotidyl transferase domain (1);	0.000000	0.85682	D	0.000000	T	0.75361	0.3839	M	0.84156	2.68	0.80722	D	1	D;D	0.71674	0.998;0.995	D;D	0.74674	0.982;0.984	T	0.79621	-0.1727	10	0.66056	D	0.02	-15.5341	18.4239	0.90602	0.0:1.0:0.0:0.0	.	27;27	B7ZLL4;Q5XG87	.;PAPD7_HUMAN	R	27	ENSP00000230859:P27R	ENSP00000230859:P27R	P	+	2	0	PAPD7	6790736	1.000000	0.71417	0.876000	0.34364	0.978000	0.69477	6.990000	0.76225	2.346000	0.79739	0.484000	0.47621	CCG	.	.		0.453	PAPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206904.1	NM_006999		G	6737736	C	G	6737736	3	3	331	1	0	0	0	0	1	0	0	0	11435	652	23	4	82	4	PAPD7	5	6737736	Missense_Mutation	SNP	C	TCGA-QA-A7B7-01A-11D-A32G-10		6737736	174177524	27	46206										
ADAMTS12	81792	hgsc.bcm.edu	37	chr5	33881413	33881415	+	In_Frame_Del	DEL	CTT	CTT	-													0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	gtcaagttaaaaaacaggtcCttctcctcgtgagaaattct					rs141295692	byFrequency	TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr5:33881413_33881415delCTT	ENST00000504830.1	-	2	633_635	c.298_300delAAG	c.(298-300)aagdel	p.K100del	ADAMTS12_ENST00000352040.3_In_Frame_Del_p.K100del|ADAMTS12_ENST00000515401.1_In_Frame_Del_p.K100del	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	100					cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						AAAACAGGTCCTTCTCCTCGTGA	0.443										HNSCC(64;0.19)																											p.100_101del		Pindel	.											ADAMTS12_ENST00000515401,caecum,carcinoma,0,2	ADAMTS12	464	.	0			c.299_301del						.																																			SO:0001651	inframe_deletion	81792	exon2			.	AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"ADAM metallopeptidases with thrombospondin type 1 motif"	14605	protein-coding gene	gene with protein product		606184	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.298_300delAAG	chr5.hg19:g.33881413_33881415delCTT	ENSP00000422554:p.Lys100del	100.0	0.0		112.0	32.0	NM_030955	A2RRN9|A5D6V6|Q6UWL3	In_Frame_Del	DEL	ENST00000504830.1	hg19	CCDS34140.1																																																																																			.	.		0.443	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		-	33881415	CTT	-	33881413	7	5	331	1	0	1	0	1	0	0	0	0	257	680	24	0	4576	0	ADAMTS12	5	33881413	In_Frame_Del	DEL	CTT	TCGA-QA-A7B7-01A-11D-A32G-10	27143677	33881413	147033847	28	46207										
LOX	4015	hgsc.bcm.edu	37	chr5	121411127	121411127	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	actgtgccattcccaggaatAtcttggtcggctgggtaaga	12	9	1	1			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr5:121411127A>T	ENST00000231004.4	-	3	1149	c.850T>A	c.(850-852)Tat>Aat	p.Y284N	SRFBP1_ENST00000504881.1_3'UTR|LOX_ENST00000513319.1_5'UTR	NM_001178102.1|NM_002317.5	NP_001171573.1|NP_002308.2	P28300	LYOX_HUMAN	lysyl oxidase	284	Lysyl-oxidase like.				blood vessel development (GO:0001568)|cellular protein modification process (GO:0006464)|collagen fibril organization (GO:0030199)|elastic fiber assembly (GO:0048251)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|wound healing (GO:0042060)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)			endometrium(1)|lung(6)|prostate(1)	8		all_cancers(142;0.0124)|Prostate(80;0.0322)|Ovarian(225;0.0814)|Breast(839;0.143)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	Epithelial(69;2.14e-11)|OV - Ovarian serous cystadenocarcinoma(64;7.87e-10)|all cancers(49;2.49e-09)|COAD - Colon adenocarcinoma(49;0.02)		TCCCAGGAATATCTTGGTCGG	0.443																																					p.Y284N		Atlas-SNP	.											.	LOX	29	.	0			c.T850A						.						133	127	129					5																	121411127		2203	4300	6503	SO:0001583	missense	4015	exon3			AGGAATATCTTGG		CCDS4129.1	5q23.3-q31.2	2008-02-05			ENSG00000113083	ENSG00000113083	1.4.3.13		6664	protein-coding gene	gene with protein product		153455				1685472	Standard	NM_002317		Approved		uc003ksu.3	P28300	OTTHUMG00000128914	ENST00000231004.4:c.850T>A	chr5.hg19:g.121411127A>T	ENSP00000231004:p.Tyr284Asn	202.0	0.0		220.0	90.0	NM_002317	B2R5Q3|Q5FWF0	Missense_Mutation	SNP	ENST00000231004.4	hg19	CCDS4129.1	.	.	.	.	.	.	.	.	.	.	A	17.87	3.494200	0.64186	.	.	ENSG00000113083	ENST00000231004;ENST00000543620	T	0.29142	1.58	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.41396	0.1157	L	0.54323	1.7	0.58432	D	0.999997	B	0.29188	0.236	B	0.42062	0.374	T	0.39231	-0.9624	10	0.72032	D	0.01	.	15.3085	0.74011	1.0:0.0:0.0:0.0	.	284	P28300	LYOX_HUMAN	N	284;244	ENSP00000231004:Y284N	ENSP00000231004:Y284N	Y	-	1	0	LOX	121439026	1.000000	0.71417	0.896000	0.35187	0.997000	0.91878	5.970000	0.70431	2.080000	0.62538	0.533000	0.62120	TAT	.	.		0.443	LOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250887.2			T	121411127	A	T	121411127	3	4	331	1	0	0	0	0	1	0	0	0	8907	449	16	4	423	4	LOX	5	121411127	Missense_Mutation	SNP	A	TCGA-QA-A7B7-01A-11D-A32G-10	87529714	121411127	59504133	29	46208										
PCDHGA12	26025	hgsc.bcm.edu	37	chr5	140811445	140811445	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	gcccttttaaatgtaaatgaCcaagattctgaggaaaacgg	9	7	1	3			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr5:140811445C>A	ENST00000252085.3	+	1	1261	c.1119C>A	c.(1117-1119)gaC>gaA	p.D373E	PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA5_ENST00000518069.1_Intron	NM_003735.2|NM_032094.1	NP_003726.1|NP_115265.1	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12	373	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(23)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	58			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATGTAAATGACCAAGATTCTG	0.428																																					p.D373E		Atlas-SNP	.											.	PCDHGA12	271	.	0			c.C1119A						.						52	58	56					5																	140811445		2203	4300	6503	SO:0001583	missense	26025	exon1			AAATGACCAAGAT	AF152506	CCDS4260.1, CCDS75346.1	5q31	2010-01-26	2002-05-23		ENSG00000253159	ENSG00000253159		"Cadherins / Protocadherins : Clustered"	8699	other	protocadherin	"fibroblast cadherin FIB3"	603059	"cadherin 21"	CDH21		10380929	Standard	NM_003735		Approved	KIAA0588, FIB3, PCDH-GAMMA-A12		O60330	OTTHUMG00000129611	ENST00000252085.3:c.1119C>A	chr5.hg19:g.140811445C>A	ENSP00000252085:p.Asp373Glu	64.0	0.0		74.0	37.0	NM_032094	O15100|Q6UW70|Q9Y5D7	Missense_Mutation	SNP	ENST00000252085.3	hg19	CCDS4260.1	.	.	.	.	.	.	.	.	.	.	c	16.45	3.125421	0.56721	.	.	ENSG00000253159	ENST00000252085	T	0.73152	-0.72	4.69	-4.35	0.03656	Cadherin (4);Cadherin-like (1);	.	.	.	.	D	0.89469	0.6724	H	0.99444	4.57	0.21445	N	0.999686	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.82430	-0.0461	9	0.87932	D	0	.	12.7084	0.57076	0.0:0.4743:0.0:0.5257	.	373;373	O60330-2;O60330	.;PCDGC_HUMAN	E	373	ENSP00000252085:D373E	ENSP00000252085:D373E	D	+	3	2	PCDHGA12	140791629	0.000000	0.05858	0.962000	0.40283	0.885000	0.51271	-0.781000	0.04648	-0.830000	0.04262	0.655000	0.94253	GAC	.	.		0.428	PCDHGA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251806.2	NM_003735		A	140811445	C	A	140811445	3	1	331	1	0	0	0	0	1	0	0	0	11562	506	18	3	1121	3	PCDHGA12	5	140811445	Missense_Mutation	SNP	C	TCGA-QA-A7B7-01A-11D-A32G-10	19400318	140811445	40103815	30	46209										
HIST1H3B	8358	hgsc.bcm.edu	37	chr6	26032226	26032226	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	ttgcgagcagccttggtagcCagctgcttgcgtggcgcttt	14	11	0	0			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr6:26032226C>A	ENST00000244661.2	-	1	62	c.63G>T	c.(61-63)ctG>ctT	p.L21L		NM_003537.3	NP_003528.1	P68431	H31_HUMAN	histone cluster 1, H3b	21					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(10)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|skin(1)	25						CCTTGGTAGCCAGCTGCTTGC	0.622																																					p.L21L		Atlas-SNP	.											.	HIST1H3B	59	.	0			c.G63T						.						69	84	79					6																	26032226		2165	4219	6384	SO:0001819	synonymous_variant	8358	exon1			GGTAGCCAGCTGC	X00090	CCDS4573.1	6p22.1	2011-01-27	2006-10-11	2003-03-14	ENSG00000124693	ENSG00000274267		"Histones / Replication-dependent"	4776	protein-coding gene	gene with protein product		602819	"H3 histone family, member L", "histone 1, H3b"	H3FL		6647026, 9119399, 12408966	Standard	NM_003537		Approved	H3/l	uc003nfs.1	P68431	OTTHUMG00000014415	ENST00000244661.2:c.63G>T	chr6.hg19:g.26032226C>A		35.0	0.0		52.0	19.0	NM_003537	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Silent	SNP	ENST00000244661.2	hg19	CCDS4573.1																																																																																			.	.		0.622	HIST1H3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040077.1	NM_003537		A	26032226	C	A	26032226	2	1	331	1	0	0	0	0	0	0	0	1	7165	581	21	3		3	HIST1H3B	6	26032226	Silent	SNP	C	TCGA-QA-A7B7-01A-11D-A32G-10		26032226	145082841	31	46210										
CNR1	1268	hgsc.bcm.edu	37	chr6	88854612	88854612	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	gttctccaggaccgtgaaggTgcccagcgtgagggacagga	16	10	1	2			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr6:88854612T>A	ENST00000537554.1	-	2	3944	c.382A>T	c.(382-384)Acc>Tcc	p.T128S	CNR1_ENST00000549890.1_Missense_Mutation_p.T128S|CNR1_ENST00000468898.1_Missense_Mutation_p.T95S|CNR1_ENST00000362094.5_3'UTR|CNR1_ENST00000549716.1_Missense_Mutation_p.T67S|CNR1_ENST00000428600.2_Missense_Mutation_p.T128S|CNR1_ENST00000369499.2_Missense_Mutation_p.T128S|CNR1_ENST00000369501.2_Missense_Mutation_p.T128S|CNR1_ENST00000535130.1_Missense_Mutation_p.T128S	NM_001160226.1|NM_001160258.1	NP_001153698.1|NP_001153730.1	P21554	CNR1_HUMAN	cannabinoid receptor 1 (brain)	128					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|aging (GO:0007568)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose homeostasis (GO:0042593)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|negative regulation of action potential (GO:0045759)|negative regulation of blood pressure (GO:0045776)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of mast cell activation (GO:0033004)|negative regulation of nitric-oxide synthase activity (GO:0051001)|positive regulation of acute inflammatory response to antigenic stimulus (GO:0002866)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood pressure (GO:0045777)|positive regulation of fever generation (GO:0031622)|positive regulation of neuron projection development (GO:0010976)|regulation of feeding behavior (GO:0060259)|regulation of insulin secretion (GO:0050796)|regulation of penile erection (GO:0060405)|regulation of synaptic transmission, GABAergic (GO:0032228)|regulation of synaptic transmission, glutamatergic (GO:0051966)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to morphine (GO:0043278)|response to nicotine (GO:0035094)|response to nutrient (GO:0007584)|sensory perception of pain (GO:0019233)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)|drug binding (GO:0008144)			breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|prostate(1)|skin(10)|urinary_tract(1)	37		all_cancers(76;8.24e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;4.11e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.00011)		BRCA - Breast invasive adenocarcinoma(108;0.15)	Dronabinol(DB00470)|Nabilone(DB00486)|Rimonabant(DB06155)	ACCGTGAAGGTGCCCAGCGTG	0.607																																					p.T128S		Atlas-SNP	.											CNR1,NS,carcinoma,0,1	CNR1	91	.	0			c.A382T						.						59	52	54					6																	88854612		2203	4300	6503	SO:0001583	missense	1268	exon4			TGAAGGTGCCCAG	AF107262	CCDS5015.1, CCDS5016.1, CCDS5016.2	6q14-q15	2012-08-08			ENSG00000118432	ENSG00000118432		"GPCR / Class A : Cannabinoid receptors"	2159	protein-coding gene	gene with protein product		114610		CNR			Standard	NM_016083		Approved	CB1K5, CB-R, CB1, CANN6, CB1A	uc003pmq.4	P21554	OTTHUMG00000015184	ENST00000537554.1:c.382A>T	chr6.hg19:g.88854612T>A	ENSP00000441046:p.Thr128Ser	56.0	0.0		70.0	26.0	NM_001160258	B2R9T4|E1P512|Q13949|Q495Z0|Q4PLI4|Q4VBM6|Q5JVL5|Q5UB37|Q9UNN0	Missense_Mutation	SNP	ENST00000537554.1	hg19	CCDS5015.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.073890	0.76415	.	.	ENSG00000118432	ENST00000369501;ENST00000535130;ENST00000537554;ENST00000369499;ENST00000549890;ENST00000468898;ENST00000428600;ENST00000549716	T;T;T;T;T;T;T;T	0.37235	1.21;1.21;1.21;1.21;1.21;1.21;1.21;1.21	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.47967	0.1474	L	0.58101	1.795	0.80722	D	1	D;P	0.67145	0.996;0.944	D;P	0.73380	0.98;0.554	T	0.46624	-0.9178	10	0.49607	T	0.09	.	16.1022	0.81184	0.0:0.0:0.0:1.0	.	95;128	P21554-3;P21554	.;CNR1_HUMAN	S	128;128;128;128;128;95;128;67	ENSP00000358513:T128S;ENSP00000442689:T128S;ENSP00000441046:T128S;ENSP00000358511:T128S;ENSP00000446819:T128S;ENSP00000420188:T95S;ENSP00000412192:T128S;ENSP00000449549:T67S	ENSP00000358511:T128S	T	-	1	0	CNR1	88911331	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.040000	0.89188	2.205000	0.71048	0.460000	0.39030	ACC	.	.		0.607	CNR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354204.2			A	88854612	T	A	88854612	3	1	331	1	0	0	0	0	1	0	0	0	3633	1696	59	4	1040	4	CNR1	6	88854612	Missense_Mutation	SNP	T	TCGA-QA-A7B7-01A-11D-A32G-10	62822386	88854612	82260455	32	46211										
NCOA7	135112	hgsc.bcm.edu	37	chr6	126202239	126202239	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	ttctctcccattctcaggtcCtttttgtgccagatgccaac	6	14	2	1			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr6:126202239C>A	ENST00000368357.3	+	7	815	c.463C>A	c.(463-465)Ctt>Att	p.L155I	NCOA7_ENST00000229634.9_Missense_Mutation_p.L51I|NCOA7_ENST00000392477.2_Missense_Mutation_p.L155I	NM_001199619.1|NM_001199620.1	NP_001186548.1|NP_001186549.1	Q8NI08	NCOA7_HUMAN	nuclear receptor coactivator 7	155					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(2)	39				UCEC - Uterine corpus endometrioid carcinoma (4;0.0803)|GBM - Glioblastoma multiforme(226;0.0193)|all cancers(137;0.237)		TTCTCAGGTCCTTTTTGTGCC	0.458																																					p.L155I		Atlas-SNP	.											.	NCOA7	92	.	0			c.C463A						.						152	110	124					6																	126202239		2203	4300	6503	SO:0001583	missense	135112	exon7			CAGGTCCTTTTTG	AJ420542	CCDS5132.1, CCDS56448.1	6q22.33	2013-03-14			ENSG00000111912	ENSG00000111912			21081	protein-coding gene	gene with protein product	"TBC/LysM-associated domain containing 4"	609752				11971969	Standard	NM_001199619		Approved	ERAP140, dJ187J11.3, TLDC4	uc003qai.3	Q8NI08	OTTHUMG00000015513	ENST00000368357.3:c.463C>A	chr6.hg19:g.126202239C>A	ENSP00000357341:p.Leu155Ile	198.0	0.0		230.0	95.0	NM_001199619	B2RNS2|B7Z2C4|B9EH71|G8JL91|Q3LID6|Q4G0V1|Q5TF95|Q6IPQ4|Q6NE83|Q86T89|Q8N1W4	Missense_Mutation	SNP	ENST00000368357.3	hg19	CCDS5132.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.404412	0.83230	.	.	ENSG00000111912	ENST00000368357;ENST00000392477;ENST00000417494;ENST00000229634	T;T;T;T	0.56103	0.48;0.48;0.48;0.48	5.72	5.72	0.89469	Peptidoglycan-binding Lysin subgroup (1);Peptidoglycan-binding lysin domain (1);	0.066231	0.64402	N	0.000014	T	0.54951	0.1890	L	0.39514	1.22	0.41132	D	0.985894	D;D;B;D	0.89917	1.0;0.998;0.197;1.0	D;D;B;D	0.91635	0.998;0.996;0.062;0.999	T	0.54702	-0.8254	10	0.44086	T	0.13	-8.8356	13.184	0.59670	0.0:0.9275:0.0:0.0725	.	155;155;155;155	B3KXK4;Q8NI08-2;Q8NI08-4;Q8NI08	.;.;.;NCOA7_HUMAN	I	155;155;155;51	ENSP00000357341:L155I;ENSP00000376269:L155I;ENSP00000406363:L155I;ENSP00000229634:L51I	ENSP00000229634:L51I	L	+	1	0	NCOA7	126243932	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.550000	0.45811	2.714000	0.92807	0.644000	0.83932	CTT	.	.		0.458	NCOA7-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042083.4	XM_059748		A	126202239	C	A	126202239	3	1	331	1	0	0	0	0	1	0	0	0	10243	681	24	3	481	3	NCOA7	6	126202239	Missense_Mutation	SNP	C	TCGA-QA-A7B7-01A-11D-A32G-10	37347627	126202239	44912828	33	46212										
GRM1	2911	hgsc.bcm.edu	37	chr6	146708066	146708066	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	gagctgctgctggatttgcaCggcctgcaaagagaatgaat	13	8	0	2	rs201399008		TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr6:146708066C>A	ENST00000282753.1	+	6	1878	c.1643C>A	c.(1642-1644)aCg>aAg	p.T548K	GRM1_ENST00000392299.2_Missense_Mutation_p.T548K|GRM1_ENST00000361719.2_Missense_Mutation_p.T548K|GRM1_ENST00000355289.4_Missense_Mutation_p.T548K|GRM1_ENST00000492807.2_Missense_Mutation_p.T548K|GRM1_ENST00000507907.1_Missense_Mutation_p.T548K			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	548					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		TGGATTTGCACGGCCTGCAAA	0.418																																					p.T548K		Atlas-SNP	.											GRM1_ENST00000392299,colon,carcinoma,0,6	GRM1	419	.	0			c.C1643A						.						132	125	128					6																	146708066		2203	4300	6503	SO:0001583	missense	2911	exon7			TTTGCACGGCCTG	U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4593	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 85"	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	ENST00000282753.1:c.1643C>A	chr6.hg19:g.146708066C>A	ENSP00000282753:p.Thr548Lys	84.0	0.0		120.0	49.0	NM_000838	B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Missense_Mutation	SNP	ENST00000282753.1	hg19	CCDS5209.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.545701	0.86022	.	.	ENSG00000152822	ENST00000361719;ENST00000392299;ENST00000492807;ENST00000282753;ENST00000355289;ENST00000507907	D;D;D;D;D;D	0.89810	-2.57;-2.57;-2.57;-2.57;-2.57;-2.57	5.45	5.45	0.79879	GPCR, family 3, conserved site (1);GPCR, family 3, nine cysteines domain (1);	0.043920	0.85682	D	0.000000	D	0.92110	0.7499	L	0.52126	1.63	0.80722	D	1	D;D;D	0.89917	0.998;1.0;0.998	D;D;D	0.91635	0.977;0.999;0.971	D	0.92435	0.5957	10	0.62326	D	0.03	.	18.8729	0.92324	0.0:1.0:0.0:0.0	.	548;548;548	F8W805;Q13255;Q13255-2	.;GRM1_HUMAN;.	K	548	ENSP00000354896:T548K;ENSP00000376119:T548K;ENSP00000424095:T548K;ENSP00000282753:T548K;ENSP00000347437:T548K;ENSP00000425599:T548K	ENSP00000282753:T548K	T	+	2	0	GRM1	146749759	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.223000	0.78033	2.533000	0.85409	0.585000	0.79938	ACG	.	.		0.418	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838		A	146708066	C	A	146708066	3	1	331	1	0	0	0	0	1	0	0	0	6805	536	19	1	1665	1	GRM1	6	146708066	Missense_Mutation	SNP	C	TCGA-QA-A7B7-01A-11D-A32G-10	20505827	146708066	24407001	34	46213										
THBS2	7058	hgsc.bcm.edu	37	chr6	169639701	169639701	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	tggcgatactcacagtggagGcaggaagggcagcattcgcc	15	10	1	0			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr6:169639701G>T	ENST00000366787.3	-	8	1371	c.1122C>A	c.(1120-1122)tgC>tgA	p.C374*	XXyac-YX65C7_A.2_ENST00000444188.1_RNA	NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	374	VWFC. {ECO:0000255|PROSITE- ProRule:PRU00220}.				cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		CACAGTGGAGGCAGGAAGGGC	0.478																																					p.C374X	Esophageal Squamous(91;219 1934 18562 44706)	Atlas-SNP	.											.	THBS2	230	.	0			c.C1122A						.						60	43	49					6																	169639701		2201	4295	6496	SO:0001587	stop_gained	7058	exon8			GTGGAGGCAGGAA		CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.1122C>A	chr6.hg19:g.169639701G>T	ENSP00000355751:p.Cys374*	46.0	0.0		31.0	14.0	NM_003247	A6H8N1|A7E232|Q5RI52	Nonsense_Mutation	SNP	ENST00000366787.3	hg19	CCDS34574.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.056218	0.76074	.	.	ENSG00000186340	ENST00000366787	.	.	.	5.34	1.49	0.22878	.	0.000000	0.44902	U	0.000408	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-48.3649	8.5014	0.33161	0.311:0.0:0.689:0.0	.	.	.	.	X	374	.	ENSP00000355751:C374X	C	-	3	2	THBS2	169381626	0.998000	0.40836	0.957000	0.39632	0.021000	0.10359	1.496000	0.35638	0.611000	0.30052	0.655000	0.94253	TGC	.	.		0.478	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247		T	169639701	G	T	169639701	4	4	331	1	0	0	0	0	0	1	0	0	15869	1195	42	3	2460	3	THBS2	6	169639701	Nonsense_Mutation	SNP	G	TCGA-QA-A7B7-01A-11D-A32G-10	22931635	169639701	1475366	35	46214										
IQCE	23288	hgsc.bcm.edu	37	chr7	2649728	2649728	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	cacctctacctggggatgacGtcaactccgatgattccgac	9	14	2	2			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr7:2649728G>A	ENST00000402050.2	+	22	2204	c.2020G>A	c.(2020-2022)Gtc>Atc	p.V674I	IQCE_ENST00000325979.7_Missense_Mutation_p.V609I|IQCE_ENST00000404984.1_Missense_Mutation_p.V623I|IQCE_ENST00000438376.2_Missense_Mutation_p.V658I	NM_001100390.1|NM_152558.3	NP_001093860.1|NP_689771.3	Q6IPM2	IQCE_HUMAN	IQ motif containing E	674						mitochondrion (GO:0005739)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;1.23e-13)		TGGGGATGACGTCAACTCCGA	0.587																																					p.V674I		Atlas-SNP	.											.	IQCE	66	.	0			c.G2020A						.						96	99	98					7																	2649728		2104	4225	6329	SO:0001583	missense	23288	exon22			GATGACGTCAACT	AL136792	CCDS43542.1, CCDS47527.1, CCDS47527.2, CCDS75559.1, CCDS75560.1	7p22.3	2006-04-12			ENSG00000106012	ENSG00000106012			29171	protein-coding gene	gene with protein product						10470851	Standard	XR_242067		Approved	KIAA1023	uc003smo.4	Q6IPM2	OTTHUMG00000152047	ENST00000402050.2:c.2020G>A	chr7.hg19:g.2649728G>A	ENSP00000385597:p.Val674Ile	65.0	0.0		94.0	37.0	NM_152558	Q4G0P7|Q6P7T4|Q9H0H7|Q9UPX7	Missense_Mutation	SNP	ENST00000402050.2	hg19	CCDS43542.1	.	.	.	.	.	.	.	.	.	.	G	12.57	1.976895	0.34848	.	.	ENSG00000106012	ENST00000402050;ENST00000404984;ENST00000438376;ENST00000325979	T;T;T;T	0.13657	2.58;2.57;2.58;2.59	4.9	-1.0	0.10196	.	0.760191	0.11028	N	0.607556	T	0.08223	0.0205	N	0.24115	0.695	0.09310	N	1	B;B	0.17465	0.013;0.022	B;B	0.08055	0.001;0.003	T	0.37407	-0.9707	10	0.27785	T	0.31	.	8.324	0.32145	0.5666:0.0:0.4334:0.0	.	674;658	Q6IPM2;Q6IPM2-4	IQCE_HUMAN;.	I	674;623;658;609	ENSP00000385597:V674I;ENSP00000385945:V623I;ENSP00000396178:V658I;ENSP00000313772:V609I	ENSP00000313772:V609I	V	+	1	0	IQCE	2616254	0.000000	0.05858	0.000000	0.03702	0.224000	0.24922	-0.724000	0.04947	-0.604000	0.05760	0.561000	0.74099	GTC	.	.		0.587	IQCE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325063.2	NM_152558		A	2649728	G	A	2649728	3	1	331	1	0	0	0	0	1	0	0	0	7815	1145	40	1	2106	1	IQCE	7	2649728	Missense_Mutation	SNP	G	TCGA-QA-A7B7-01A-11D-A32G-10		2649728	156488935	36	46215										
CCDC136	64753	hgsc.bcm.edu	37	chr7	128449530	128449530	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	acactgctgtccagactgacAgaattgcaggaaaagtacaa	9	9	0	3			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr7:128449530A>G	ENST00000297788.4	+	11	1999	c.1632A>G	c.(1630-1632)acA>acG	p.T544T	CCDC136_ENST00000464832.1_Intron|CCDC136_ENST00000487361.1_Intron|CCDC136_ENST00000378685.4_Intron	NM_022742.4	NP_073579	Q96JN2	CC136_HUMAN	coiled-coil domain containing 136	544						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(3)	24						CCAGACTGACAGAATTGCAGG	0.567																																					p.T544T		Atlas-SNP	.											.	CCDC136	170	.	0			c.A1632G						.						21	23	22					7																	128449530		1983	4055	6038	SO:0001819	synonymous_variant	64753	exon11			ACTGACAGAATTG		CCDS47704.1, CCDS56510.1	7q33	2007-08-01			ENSG00000128596	ENSG00000128596			22225	protein-coding gene	gene with protein product		611902				15112360	Standard	NM_022742		Approved	KIAA1793, NAG6, DKFZP434G156	uc003vnv.2	Q96JN2	OTTHUMG00000158310	ENST00000297788.4:c.1632A>G	chr7.hg19:g.128449530A>G		158.0	1.0		120.0	99.0	NM_022742	A4D1K1|A7MCY7|A8MYA7|Q6ZVK7|Q9H8M3|Q9UFE1	Silent	SNP	ENST00000297788.4	hg19	CCDS47704.1	.	.	.	.	.	.	.	.	.	.	A	10.39	1.336417	0.24253	.	.	ENSG00000128596	ENST00000494552	.	.	.	6.07	3.75	0.43078	.	.	.	.	.	T	0.55862	0.1947	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51826	-0.8656	4	.	.	.	-4.6257	6.8338	0.23925	0.826:0.0:0.174:0.0	.	.	.	.	R	421	.	.	Q	+	2	0	CCDC136	128236766	0.998000	0.40836	1.000000	0.80357	0.987000	0.75469	0.410000	0.21098	1.128000	0.42052	0.533000	0.62120	CAG	.	.		0.567	CCDC136-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350641.1	NM_022742		G	128449530	A	G	128449530	2	3	331	1	0	0	0	0	0	0	0	1	2772	175	7	2		2	CCDC136	7	128449530	Silent	SNP	A	TCGA-QA-A7B7-01A-11D-A32G-10	125799802	128449530	30689133	37	46216										
ESYT2	57488	hgsc.bcm.edu	37	chr7	158540904	158540904	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	cctcaacttcaaggtcctggCgcttgggattgtgaatgaag	12	9	2	2			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr7:158540904C>T	ENST00000251527.5	-	15	1771	c.1706G>A	c.(1705-1707)cGc>cAc	p.R569H		NM_020728.2	NP_065779.1	A0FGR8	ESYT2_HUMAN	extended synaptotagmin-like protein 2	597	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				endocytosis (GO:0006897)|lipid transport (GO:0006869)	extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|membrane (GO:0016020)|organelle membrane contact site (GO:0044232)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|identical protein binding (GO:0042802)|phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(16)|prostate(2)	32						AAGGTCCTGGCGCTTGGGATT	0.338																																					p.R569H		Atlas-SNP	.											.	ESYT2	70	.	0			c.G1706A						.						120	124	123					7																	158540904		2203	4300	6503	SO:0001583	missense	57488	exon15			TCCTGGCGCTTGG	AB033054	CCDS34791.1	7q36.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000117868	ENSG00000117868		"Synaptotagmins"	22211	protein-coding gene	gene with protein product			"family with sequence similarity 62 (C2 domain containing), member B"	FAM62B		17672888	Standard	NM_020728		Approved	KIAA1228, CHR2SYT	uc003wob.1	A0FGR8	OTTHUMG00000151436	ENST00000251527.5:c.1706G>A	chr7.hg19:g.158540904C>T	ENSP00000251527:p.Arg569His	103.0	0.0		62.0	50.0	NM_020728	A4D229|Q69YJ2|Q6UKI4|Q6ZTU0|Q6ZVU1|Q9BQS0|Q9NW47|Q9ULJ2	Missense_Mutation	SNP	ENST00000251527.5	hg19	CCDS34791.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.949205	0.73787	.	.	ENSG00000117868	ENST00000251527;ENST00000421679;ENST00000275418;ENST00000429474	T;T	0.69040	-0.37;-0.37	4.98	4.98	0.66077	.	0.117564	0.52532	D	0.000062	T	0.75975	0.3923	L	0.44542	1.39	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.70016	0.967;0.939	T	0.76647	-0.2882	10	0.48119	T	0.1	-21.6892	17.2579	0.87062	0.0:1.0:0.0:0.0	.	618;569	A0FGR8-6;A0FGR8-2	.;.	H	569;618;560;393	ENSP00000251527:R569H;ENSP00000275418:R560H	ENSP00000251527:R569H	R	-	2	0	ESYT2	158233665	0.859000	0.29813	1.000000	0.80357	0.998000	0.95712	1.507000	0.35758	2.308000	0.77769	0.563000	0.77884	CGC	.	.		0.338	ESYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322647.1	NM_020728		T	158540904	C	T	158540904	3	4	331	1	0	0	0	0	1	0	0	0	5267	768	27	1	1007	1	ESYT2	7	158540904	Missense_Mutation	SNP	C	TCGA-QA-A7B7-01A-11D-A32G-10	30091374	158540904	597759	38	46217										
HR	55806	hgsc.bcm.edu	37	chr8	21986325	21986325	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	tatgctcaggcatcagggggCcacagcgaggtgggcacgct	16	11	2	0			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr8:21986325C>G	ENST00000381418.4	-	2	1839	c.359G>C	c.(358-360)gGc>gCc	p.G120A	HR_ENST00000518377.1_5'Flank|HR_ENST00000312841.8_Missense_Mutation_p.G120A	NM_005144.4	NP_005135.2	O43593	HAIR_HUMAN	hair growth associated	120					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	27		Breast(100;0.000162)|Acute lymphoblastic leukemia(644;0.0775)|Prostate(55;0.116)		KIRC - Kidney renal clear cell carcinoma(542;1.19e-05)|BRCA - Breast invasive adenocarcinoma(99;3.56e-05)|Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)		CATCAGGGGGCCACAGCGAGG	0.627																																					p.G120A		Atlas-SNP	.											.	HR	71	.	0			c.G359C						.						35	32	33					8																	21986325		2203	4299	6502	SO:0001583	missense	55806	exon2			AGGGGGCCACAGC	AF039196	CCDS6022.1, CCDS6023.1	8p12	2012-12-07	2012-12-07		ENSG00000168453	ENSG00000168453			5172	protein-coding gene	gene with protein product		602302	"hairless (mouse) homolog", "hairless homolog (mouse)"	ALUNC		10051399, 9463324	Standard	NM_018411		Approved	AU	uc003xas.3	O43593	OTTHUMG00000097089	ENST00000381418.4:c.359G>C	chr8.hg19:g.21986325C>G	ENSP00000370826:p.Gly120Ala	60.0	0.0		52.0	41.0	NM_018411	Q6GS30|Q96H33|Q9NPE1	Missense_Mutation	SNP	ENST00000381418.4	hg19	CCDS6022.1	.	.	.	.	.	.	.	.	.	.	C	13.48	2.248812	0.39797	.	.	ENSG00000168453	ENST00000381418;ENST00000312841	T;T	0.71698	-0.58;-0.59	4.82	2.87	0.33458	.	0.819977	0.10525	N	0.664520	T	0.55226	0.1907	L	0.27053	0.805	0.09310	N	1	P;P;P	0.51351	0.944;0.901;0.841	B;B;B	0.41271	0.352;0.269;0.138	T	0.49418	-0.8942	10	0.72032	D	0.01	-4.6596	5.959	0.19289	0.0:0.7656:0.0:0.2344	.	120;120;120	A6NCE3;O43593-2;O43593	.;.;HAIR_HUMAN	A	120	ENSP00000370826:G120A;ENSP00000326765:G120A	ENSP00000326765:G120A	G	-	2	0	HR	22042270	0.599000	0.26891	0.722000	0.30670	0.693000	0.40251	1.265000	0.33027	1.267000	0.44247	0.561000	0.74099	GGC	.	.		0.627	HR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214213.1			G	21986325	C	G	21986325	3	3	331	1	0	0	0	0	1	0	0	0	7356	739	26	4	3282	4	HR	8	21986325	Missense_Mutation	SNP	C	TCGA-QA-A7B7-01A-11D-A32G-10		21986325	124377697	39	46218										
PNMA2	10687	hgsc.bcm.edu	37	chr8	26365742	26365742	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	agacctcaaaggactcttccTctggggctgggacagcactc	11	13	3	1			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr8:26365742T>A	ENST00000522362.2	-	3	1424	c.530A>T	c.(529-531)gAg>gTg	p.E177V	PNMA2_ENST00000522764.1_5'Flank	NM_007257.5	NP_009188.1	Q9UL42	PNMA2_HUMAN	paraneoplastic Ma antigen 2	177					positive regulation of apoptotic process (GO:0043065)	nucleus (GO:0005634)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)	11		all_cancers(63;0.109)|Ovarian(32;2.61e-05)|all_epithelial(46;0.105)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0196)|Epithelial(17;3.13e-11)|Colorectal(74;0.123)		ggactcttcctctggggctgg	0.552																																					p.E177V		Atlas-SNP	.											.	PNMA2	33	.	0			c.A530T						.						66	66	66					8																	26365742		2203	4300	6503	SO:0001583	missense	10687	exon3			TCTTCCTCTGGGG		CCDS34868.1	8p21.1	2012-02-09	2012-02-09		ENSG00000240694	ENSG00000240694		"Paraneoplastic Ma antigens"	9159	protein-coding gene	gene with protein product		603970	"paraneoplastic antigen MA2"			10362822	Standard	NM_007257		Approved	MA2, RGAG2	uc003xez.2	Q9UL42	OTTHUMG00000163816	ENST00000522362.2:c.530A>T	chr8.hg19:g.26365742T>A	ENSP00000429344:p.Glu177Val	69.0	0.0		43.0	36.0	NM_007257	B3KNY9|O94959|O95145|Q49A18|Q9UL43	Missense_Mutation	SNP	ENST00000522362.2	hg19	CCDS34868.1	.	.	.	.	.	.	.	.	.	.	T	15.34	2.804993	0.50315	.	.	ENSG00000240694	ENST00000522362	T	0.12774	2.65	4.22	3.06	0.35304	.	.	.	.	.	T	0.14013	0.0339	L	0.43152	1.355	0.32544	N	0.53326	P	0.52316	0.952	P	0.45998	0.5	T	0.17501	-1.0367	9	0.62326	D	0.03	-11.9143	6.4336	0.21811	0.0:0.1095:0.0:0.8905	.	177	Q9UL42	PNMA2_HUMAN	V	177	ENSP00000429344:E177V	ENSP00000429344:E177V	E	-	2	0	PNMA2	26421659	0.994000	0.37717	0.988000	0.46212	0.556000	0.35491	1.677000	0.37576	0.954000	0.37851	0.533000	0.62120	GAG	.	.		0.552	PNMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375709.2	NM_007257		A	26365742	T	A	26365742	3	1	331	1	0	0	0	0	1	0	0	0	12163	1551	54	4	568	4	PNMA2	8	26365742	Missense_Mutation	SNP	T	TCGA-QA-A7B7-01A-11D-A32G-10	4379417	26365742	119998280	40	46219										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113569077	113569140	+	Frame_Shift_Del	DEL	TGGATTGCATCCATAAATGATGGTGCTACCAGCAAAGTGGCCTTGGTCACTGATCTTGTATCCA	TGGATTGCATCCATAAATGATGGTGCTACCAGCAAAGTGGCCTTGGTCACTGATCTTGTATCCA	-													0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	cttccgtggagagtgtagccTggattgcatccataaatgat					rs145750770|rs201327971|rs202053990|rs143731892	byFrequency	TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	TGGATTGCATCCATAAATGATGGTGCTACCAGCAAAGTGGCCTTGGTCACTGATCTTGTATCCA	TGGATTGCATCCATAAATGATGGTGCTACCAGCAAAGTGGCCTTGGTCACTGATCTTGTATCCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr8:113569077_113569140delTGGATTGCATCCATAAATGATGGTGCTACCAGCAAAGTGGCCTTGGTCACTGATCTTGTATCCA	ENST00000297405.5	-	25	4330_4393	c.4086_4149delTGGATACAAGATCAGTGACCAAGGCCACTTTGCTGGTAGCACCATCATTTATGGATGCAATCCA	c.(4084-4149)tttggatacaagatcagtgaccaaggccactttgctggtagcaccatcatttatggatgcaatccafs	p.FGYKISDQGHFAGSTIIYGCNP1362fs	CSMD3_ENST00000352409.3_Frame_Shift_Del_p.FGYKISDQGHFAGSTIIYGCNP1362fs|CSMD3_ENST00000343508.3_Frame_Shift_Del_p.FGYKISDQGHFAGSTIIYGCNP1322fs|CSMD3_ENST00000455883.2_Frame_Shift_Del_p.FGYKISDQGHFAGSTIIYGCNP1258fs	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1362	Sushi 7. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.Q1369H(2)|p.Q1329H(2)|p.G1380*(1)|p.G1323*(1)|p.G1363*(1)|p.C1341F(1)|p.S1367C(1)|p.C1381F(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						GAGTGTAGCCTGGATTGCATCCATAAATGATGGTGCTACCAGCAAAGTGGCCTTGGTCACTGATCTTGTATCCAAATTGTGGAA	0.436										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.1363_1384del		Pindel	.											.	CSMD3	2325	.	10	Substitution - Missense(7)|Substitution - Nonsense(3)	lung(8)|upper_aerodigestive_tract(1)|ovary(1)	c.4087_4150del						.																																			SO:0001589	frameshift_variant	114788	exon25			.	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.4086_4149delTGGATACAAGATCAGTGACCAAGGCCACTTTGCTGGTAGCACCATCATTTATGGATGCAATCCA	chr8.hg19:g.113569077_113569140delTGGATTGCATCCATAAATGATGGTGCTACCAGCAAAGTGGCCTTGGTCACTGATCTTGTATCCA	ENSP00000297405:p.Phe1362fs	68.0	0.0		18.0	15.0	NM_198123	Q96PZ3	Frame_Shift_Del	DEL	ENST00000297405.5	hg19	CCDS6315.1																																																																																			.	.		0.436	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		-	113569140	TGGATTGCATCCATAAATGATGGTGCTACCAGCAAAGTGGCCTTGGTCACTGATCTTGTATCCA	-	113569077	7	5	331	1	0	1	0	1	0	0	0	0	3948	1567	55	0	7162	0	CSMD3	8	113569077	Frame_Shift_Del	DEL	TGGATTGCATCCATAAATGATGGTGCTACCAGCAAAGTGGCCTTGGTCACTGATCTTGTATCCA	TCGA-QA-A7B7-01A-11D-A32G-10	87203335	113569077	32794945	41	46220										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113569137	113569137	+	Silent	SNP	T	T	G													0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	ccttggtcactgatcttgtaTccaaattgtggaatgccagg							TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr8:113569137T>G	ENST00000297405.5	-	25	4333	c.4089A>C	c.(4087-4089)ggA>ggC	p.G1363G	CSMD3_ENST00000352409.3_Silent_p.G1363G|CSMD3_ENST00000343508.3_Silent_p.G1323G|CSMD3_ENST00000455883.2_Silent_p.G1259G	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1363	Sushi 7. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TGATCTTGTATCCAAATTGTG	0.413										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.G1363G		Atlas-SNP	.											.	CSMD3	2325	.	0			c.A4089C						.						94	85	88					8																	113569137		2203	4299	6502	SO:0001819	synonymous_variant	114788	exon25			CTTGTATCCAAAT	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.4089A>C	chr8.hg19:g.113569137T>G		66.0	0.0		20.0	10.0	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	hg19	CCDS6315.1																																																																																			.	.		0.413	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		G	113569137	T	G	113569137	2	3	331	1	0	0	0	0	0	0	0	1	3948	1422	50	5		5	CSMD3	8	113569137	Silent	SNP	T	TCGA-QA-A7B7-01A-11D-A32G-10	60	113569137	32794885	42	46221	245	2								
CSMD3	114788	hgsc.bcm.edu	37	chr8	113569140	113569140	+	Frame_Shift_Del	DEL	A	A	-													0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	tggtcactgatcttgtatccAaattgtggaatgccaggatc							TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr8:113569140delA	ENST00000297405.5	-	25	4330	c.4086delT	c.(4084-4086)tttfs	p.F1362fs	CSMD3_ENST00000352409.3_Frame_Shift_Del_p.F1362fs|CSMD3_ENST00000343508.3_Frame_Shift_Del_p.F1322fs|CSMD3_ENST00000455883.2_Frame_Shift_Del_p.F1258fs	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1362	Sushi 7. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TCTTGTATCCAAATTGTGGAA	0.413										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.G1363fs		Atlas-INDEL	.											CSMD3_ENST00000343508,NS,carcinoma,0,2	CSMD3	2325	.	0			c.4087delG						.						90	83	85					8																	113569140		2203	4299	6502	SO:0001589	frameshift_variant	114788	exon25			.	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.4086delT	chr8.hg19:g.113569140delA	ENSP00000297405:p.Phe1362fs	65.0	0.0		20.0	11.0	NM_198123	Q96PZ3	Frame_Shift_Del	DEL	ENST00000297405.5	hg19	CCDS6315.1																																																																																			.	.		0.413	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		-	113569140	A	-	113569140	7	5	331	1	0	1	0	1	0	0	0	0	3948	127	5	0	7225	0	CSMD3	8	113569140	Frame_Shift_Del	DEL	A	TCGA-QA-A7B7-01A-11D-A32G-10	3	113569140	32794882	43	46222	245	2								
SETX	23064	hgsc.bcm.edu	37	chr9	135176017	135176017	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	atgcctcattatttacttacTgactgacgtgcggcgaaatt	8	9	1	2			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr9:135176017T>C	ENST00000224140.5	-	12	5730	c.5548A>G	c.(5548-5550)Atg>Gtg	p.M1850V	SETX_ENST00000393220.1_Splice_Site_p.M1850V|SETX_ENST00000372169.2_Splice_Site_p.M1850V	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	1850					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		ATTTACTTACTGACTGACGTG	0.333																																					p.M1850V		Atlas-SNP	.											.	SETX	234	.	0			c.A5548G						.						197	184	188					9																	135176017		2203	4300	6503	SO:0001630	splice_region_variant	23064	exon12			ACTTACTGACTGA	AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"amyotrophic lateral sclerosis 4", "spinocerebellar ataxia, recessive, non-Friedreich type 1"	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.5548+1A>G	chr9.hg19:g.135176017T>C		159.0	0.0		176.0	66.0	NM_015046	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Missense_Mutation	SNP	ENST00000224140.5	hg19	CCDS6947.1	.	.	.	.	.	.	.	.	.	.	T	12.69	2.014925	0.35511	.	.	ENSG00000107290	ENST00000224140;ENST00000436441;ENST00000372169;ENST00000393220	D;D;D;D	0.89617	-1.98;-2.54;-2.06;-1.67	5.02	3.88	0.44766	.	0.847483	0.10530	N	0.663948	T	0.82181	0.4981	L	0.29908	0.895	0.34310	D	0.685386	B;B;B	0.22003	0.02;0.037;0.063	B;B;B	0.21917	0.023;0.017;0.037	T	0.76228	-0.3036	9	.	.	.	.	9.8167	0.40858	0.0:0.0823:0.0:0.9177	.	1850;1850;1850	Q7Z333-3;Q7Z333;Q7Z333-4	.;SETX_HUMAN;.	V	1850;92;1850;1850	ENSP00000224140:M1850V;ENSP00000409143:M92V;ENSP00000361242:M1850V;ENSP00000376913:M1850V	.	M	-	1	0	SETX	134165838	0.999000	0.42202	0.997000	0.53966	0.940000	0.58332	2.807000	0.47955	0.875000	0.35847	0.533000	0.62120	ATG	.	.		0.333	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046	Missense_Mutation	C	135176017	T	C	135176017	5	2	331	1	0	0	0	0	0	0	1	0	14156	1594	55	2	2545	2	SETX	9	135176017	Splice_Site	SNP	T	TCGA-QA-A7B7-01A-11D-A32G-10		135176017	6037414	44	46223										
COL5A1	1289	hgsc.bcm.edu	37	chr9	137715262	137715262	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	attcttttctttctccccagGgtccaactggcccgaagggt	9	13	3	0			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr9:137715262G>A	ENST00000371817.3	+	61	5059	c.4645G>A	c.(4645-4647)Ggt>Agt	p.G1549S		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	1549	Triple-helical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		TTCTCCCCAGGGTCCAACTGG	0.602																																					p.G1549S		Atlas-SNP	.											.	COL5A1	323	.	0			c.G4645A						.						113	131	125					9																	137715262		2203	4300	6503	SO:0001630	splice_region_variant	1289	exon61			CCCCAGGGTCCAA	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"Collagens"	2209	protein-coding gene	gene with protein product	"alpha 1 type V collagen"	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.4645-1G>A	chr9.hg19:g.137715262G>A		114.0	0.0		140.0	50.0	NM_000093	Q15094|Q5SUX4	Missense_Mutation	SNP	ENST00000371817.3	hg19	CCDS6982.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.499060	0.85069	.	.	ENSG00000130635	ENST00000371817;ENST00000355306	D	0.99329	-5.75	5.14	5.14	0.70334	.	0.070767	0.56097	N	0.000030	D	0.99658	0.9873	H	0.97103	3.94	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97473	1.0042	9	.	.	.	.	18.5897	0.91206	0.0:0.0:1.0:0.0	.	1549	P20908	CO5A1_HUMAN	S	1549;86	ENSP00000360882:G1549S	.	G	+	1	0	COL5A1	136855083	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	9.770000	0.98971	2.389000	0.81357	0.643000	0.83706	GGT	.	.		0.602	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	Missense_Mutation	A	137715262	G	A	137715262	5	1	331	1	0	0	0	0	0	0	1	0	3698	1246	43	3	4887	3	COL5A1	9	137715262	Splice_Site	SNP	G	TCGA-QA-A7B7-01A-11D-A32G-10	2539245	137715262	3498169	45	46224										
CACNA1B	774	hgsc.bcm.edu	37	chr9	140865851	140865851	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	tcaggatcccccttcgcccgCgccagcctcaagagcgggaa	11	17	2	1	rs201843778		TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr9:140865851C>T	ENST00000371372.1	+	11	1495	c.1350C>T	c.(1348-1350)cgC>cgT	p.R450R	CACNA1B_ENST00000277549.5_5'UTR|CACNA1B_ENST00000277551.2_Silent_p.R450R|CACNA1B_ENST00000371363.1_Silent_p.R450R|CACNA1B_ENST00000371355.4_Silent_p.R451R|CACNA1B_ENST00000371357.1_Silent_p.R451R	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	450					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	CCTTCGCCCGCGCCAGCCTCA	0.607																																					p.R450R		Atlas-SNP	.											.	CACNA1B	266	.	0			c.C1350T						.	C		2,3922		0,2,1960	36	41	39		1350	-10.5	0	9		39	0,8266		0,0,4133	no	coding-synonymous	CACNA1B	NM_000718.3		0,2,6093	TT,TC,CC		0.0,0.051,0.0164		450/2340	140865851	2,12188	1962	4133	6095	SO:0001819	synonymous_variant	774	exon11			CGCCCGCGCCAGC	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.1350C>T	chr9.hg19:g.140865851C>T		66.0	0.0		87.0	37.0	NM_001243812	B1AQK5	Silent	SNP	ENST00000371372.1	hg19	CCDS59522.1																																																																																			.	.		0.607	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718		T	140865851	C	T	140865851	2	4	331	1	0	0	0	0	0	0	0	1	2541	755	27	1		1	CACNA1B	9	140865851	Silent	SNP	C	TCGA-QA-A7B7-01A-11D-A32G-10	3150589	140865851	347580	46	46225										
CUL2	8453	hgsc.bcm.edu	37	chr10	35333758	35333758	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	caaaggagttaataaccccaTggattactttctggtttggg	10	7	1	0			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr10:35333758T>C	ENST00000374748.1	-	8	858	c.545A>G	c.(544-546)cAt>cGt	p.H182R	CUL2_ENST00000537177.1_Missense_Mutation_p.H201R|CUL2_ENST00000374751.3_Missense_Mutation_p.H182R|CUL2_ENST00000374749.3_Missense_Mutation_p.H182R|CUL2_ENST00000602371.1_Missense_Mutation_p.H125R|CUL2_ENST00000374742.1_Missense_Mutation_p.H182R|CUL2_ENST00000374746.1_Missense_Mutation_p.H182R			Q13617	CUL2_HUMAN	cullin 2	182					cell cycle arrest (GO:0007050)|cellular response to hypoxia (GO:0071456)|G1/S transition of mitotic cell cycle (GO:0000082)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	Cul2-RING ubiquitin ligase complex (GO:0031462)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|VCB complex (GO:0030891)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|prostate(2)|skin(1)|urinary_tract(2)	31						AATAACCCCATGGATTACTTT	0.323																																					p.H201R		Atlas-SNP	.											.	CUL2	63	.	0			c.A602G						.						84	84	84					10																	35333758		2203	4297	6500	SO:0001583	missense	8453	exon7			ACCCCATGGATTA	U83410	CCDS7179.1, CCDS73086.1	10p11.2	2011-05-24			ENSG00000108094	ENSG00000108094			2552	protein-coding gene	gene with protein product		603135				8681378	Standard	NM_003591		Approved		uc021ppa.1	Q13617	OTTHUMG00000017950	ENST00000374748.1:c.545A>G	chr10.hg19:g.35333758T>C	ENSP00000363880:p.His182Arg	109.0	0.0		199.0	134.0	NM_001198778	B3KT95|B7Z6K8|D3DRY6|G3V1S2|O00200|Q5T2B6|Q9UNF9	Missense_Mutation	SNP	ENST00000374748.1	hg19	CCDS7179.1	.	.	.	.	.	.	.	.	.	.	T	7.395	0.631579	0.14322	.	.	ENSG00000108094	ENST00000374751;ENST00000374748;ENST00000374746;ENST00000374749;ENST00000374754;ENST00000374742;ENST00000537177;ENST00000421317	T;T;T;T;T;T;T	0.26067	1.76;1.76;1.76;1.76;1.76;1.76;1.76	5.89	5.89	0.94794	Cullin, N-terminal (1);Cullin repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.13798	0.0334	N	0.08118	0	0.80722	D	1	B;B;B	0.21071	0.051;0.023;0.028	B;B;B	0.18871	0.023;0.014;0.023	T	0.11891	-1.0569	10	0.08381	T	0.77	-24.9147	16.3123	0.82883	0.0:0.0:0.0:1.0	.	182;201;182	Q5T2B5;G3V1S2;Q13617	.;.;CUL2_HUMAN	R	182;182;182;182;125;182;201;182	ENSP00000363883:H182R;ENSP00000363880:H182R;ENSP00000363878:H182R;ENSP00000363881:H182R;ENSP00000363874:H182R;ENSP00000444856:H201R;ENSP00000414095:H182R	ENSP00000363874:H182R	H	-	2	0	CUL2	35373764	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	8.015000	0.88690	2.254000	0.74563	0.459000	0.35465	CAT	.	.		0.323	CUL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047538.1	NM_003591		C	35333758	T	C	35333758	3	2	331	1	0	0	0	0	1	0	0	0	4057	1464	51	2	1752	2	CUL2	10	35333758	Missense_Mutation	SNP	T	TCGA-QA-A7B7-01A-11D-A32G-10		35333758	100200989	47	46226										
PTEN	5728	hgsc.bcm.edu	37	chr10	89720726	89720726	+	Frame_Shift_Del	DEL	G	G	-													0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	cctcagaaaaagtagaaaatGgaagtctatgtgatcaagaa							TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr10:89720726delG	ENST00000371953.3	+	8	2234	c.877delG	c.(877-879)ggafs	p.G293fs	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	293	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.W274_F341del(1)|p.G293*(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		AGTAGAAAATGGAAGTCTATG	0.313		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																											p.N292fs		Atlas-Indel,Pindel	.	yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	.	PTEN	3652	.	51	Whole gene deletion(37)|Deletion - Frameshift(9)|Deletion - In frame(2)|Unknown(2)|Substitution - Nonsense(1)	prostate(16)|central_nervous_system(12)|skin(6)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|ovary(3)|urinary_tract(2)|soft_tissue(1)|endometrium(1)	c.876delT						.						72	74	73					10																	89720726		2203	4298	6501	SO:0001589	frameshift_variant	5728	exon8	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.877delG	chr10.hg19:g.89720726delG	ENSP00000361021:p.Gly293fs	132.0	0.0		94.0	72.0	NM_000314	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Frame_Shift_Del	DEL	ENST00000371953.3	hg19	CCDS31238.1																																																																																			.	.		0.313	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		-	89720726	G	-	89720726	7	5	331	1	0	1	0	1	0	0	0	0	12750	1349	47	0	907	0	PTEN	10	89720726	Frame_Shift_Del	DEL	G	TCGA-QA-A7B7-01A-11D-A32G-10	54386968	89720726	45814021	48	46227										
BTAF1	9044	hgsc.bcm.edu	37	chr10	93742473	93742473	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	tccaagtctgctttacagagGattagtgtagctttggtaat	10	6	1	1			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr10:93742473G>T	ENST00000265990.6	+	18	2486	c.2178G>T	c.(2176-2178)agG>agT	p.R726S	BTAF1_ENST00000471217.1_3'UTR	NM_003972.2	NP_003963.1	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170kDa	726					negative regulation of chromatin binding (GO:0035562)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(2)|urinary_tract(6)	59		Colorectal(252;0.0846)				CTTTACAGAGGATTAGTGTAG	0.378																																					p.R726S		Atlas-SNP	.											.	BTAF1	148	.	0			c.G2178T						.						123	117	119					10																	93742473		2203	4300	6503	SO:0001583	missense	9044	exon18			ACAGAGGATTAGT	AJ001017	CCDS7419.1	10q22-q23	2013-05-01	2013-05-01		ENSG00000095564	ENSG00000095564			17307	protein-coding gene	gene with protein product	"Mot1 homolog (S. cerevisiae)"	605191	"BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170 kD (Mot1 homolog, S. cerevisiae)"			9342322, 9488487	Standard	NM_003972		Approved	TAFII170, TAF172, MOT1, TAF-172, TAF(II)170	uc001khr.3	O14981	OTTHUMG00000018752	ENST00000265990.6:c.2178G>T	chr10.hg19:g.93742473G>T	ENSP00000265990:p.Arg726Ser	85.0	0.0		67.0	48.0	NM_003972	B4E0W6|O43578	Missense_Mutation	SNP	ENST00000265990.6	hg19	CCDS7419.1	.	.	.	.	.	.	.	.	.	.	G	16.45	3.127279	0.56721	.	.	ENSG00000095564	ENST00000265990	T	0.74106	-0.81	5.81	-1.07	0.09968	Domain of unknown function DUF3535 (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.83147	0.5191	M	0.81802	2.56	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.79784	0.993;0.993	T	0.82147	-0.0601	10	0.87932	D	0	-10.4349	10.4584	0.44563	0.6396:0.0:0.3604:0.0	.	726;726	Q2M1V9;O14981	.;BTAF1_HUMAN	S	726	ENSP00000265990:R726S	ENSP00000265990:R726S	R	+	3	2	BTAF1	93732453	0.995000	0.38212	0.994000	0.49952	0.940000	0.58332	0.365000	0.20348	-0.208000	0.10171	0.462000	0.41574	AGG	.	.		0.378	BTAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049380.4	NM_003972		T	93742473	G	T	93742473	3	4	331	1	0	0	0	0	1	0	0	0	1538	1165	41	3	2248	3	BTAF1	10	93742473	Missense_Mutation	SNP	G	TCGA-QA-A7B7-01A-11D-A32G-10	4021747	93742473	41792274	49	46228										
PNLIP	5406	hgsc.bcm.edu	37	chr10	118314762	118314762	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	ggaccccagcgatgccaaatTtgtggatgtaattcacacgg	11	10	1	0			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr10:118314762T>C	ENST00000369221.2	+	7	672	c.644T>C	c.(643-645)tTt>tCt	p.F215S		NM_000936.2	NP_000927.1	P16233	LIPP_HUMAN	pancreatic lipase	215					intestinal cholesterol absorption (GO:0030299)|lipid catabolic process (GO:0016042)|lipid digestion (GO:0044241)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|triglyceride lipase activity (GO:0004806)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|liver(2)|lung(22)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	43				all cancers(201;0.0131)	Glycerol Phenylbutyrate(DB08909)|Orlistat(DB01083)	GATGCCAAATTTGTGGATGTA	0.473																																					p.F215S		Atlas-SNP	.											.	PNLIP	166	.	0			c.T644C						.						82	74	77					10																	118314762		2203	4300	6503	SO:0001583	missense	5406	exon7			CCAAATTTGTGGA	BC014309	CCDS7594.1	10q25.3	2012-07-31			ENSG00000175535	ENSG00000175535	3.1.1.3		9155	protein-coding gene	gene with protein product		246600				1783385	Standard	NM_000936		Approved	PL	uc001lcm.3	P16233	OTTHUMG00000019103	ENST00000369221.2:c.644T>C	chr10.hg19:g.118314762T>C	ENSP00000358223:p.Phe215Ser	120.0	0.0		69.0	48.0	NM_000936	Q5VSQ2	Missense_Mutation	SNP	ENST00000369221.2	hg19	CCDS7594.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.254911	0.80135	.	.	ENSG00000175535	ENST00000369221	D	0.97016	-4.21	6.07	6.07	0.98685	Lipase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98915	0.9632	H	0.97983	4.12	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99466	1.0944	10	0.87932	D	0	.	15.6176	0.76780	0.0:0.0:0.0:1.0	.	215	P16233	LIPP_HUMAN	S	215	ENSP00000358223:F215S	ENSP00000358223:F215S	F	+	2	0	PNLIP	118304752	1.000000	0.71417	0.996000	0.52242	0.607000	0.37147	6.590000	0.74085	2.330000	0.79161	0.477000	0.44152	TTT	.	.		0.473	PNLIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050524.1	NM_000936		C	118314762	T	C	118314762	3	2	331	1	0	0	0	0	1	0	0	0	12158	1841	64	2	666	2	PNLIP	10	118314762	Missense_Mutation	SNP	T	TCGA-QA-A7B7-01A-11D-A32G-10	24572289	118314762	17219985	50	46229										
DNHD1	144132	hgsc.bcm.edu	37	chr11	6565467	6565467	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	tggagtgggtggccatcatgCatggcctgggtaagtgcagg	18	7	1	0			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr11:6565467C>A	ENST00000527990.2	+	17	3745	c.3745C>A	c.(3745-3747)Cat>Aat	p.H1249N	DNHD1_ENST00000254579.6_Missense_Mutation_p.H1249N			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	1249					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		GGCCATCATGCATGGCCTGGG	0.542																																					p.H1249N		Atlas-SNP	.											.	DNHD1	198	.	0			c.C3745A						.						68	61	63					11																	6565467		692	1591	2283	SO:0001583	missense	144132	exon19			ATCATGCATGGCC	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 47", "dynein heavy chain domain 1-like", "coiled-coil domain containing 35"	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.3745C>A	chr11.hg19:g.6565467C>A	ENSP00000436180:p.His1249Asn	64.0	0.0		62.0	23.0	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	hg19	CCDS44532.1	.	.	.	.	.	.	.	.	.	.	C	9.931	1.214938	0.22373	.	.	ENSG00000179532	ENST00000254579;ENST00000527990	T;T	0.58797	0.31;0.31	5.09	3.17	0.36434	Dynein heavy chain, domain-2 (1);	.	.	.	.	T	0.34454	0.0898	N	0.14661	0.345	0.22292	N	0.999229	B	0.18166	0.026	B	0.18871	0.023	T	0.22208	-1.0223	9	0.13470	T	0.59	.	6.2383	0.20776	0.1845:0.7168:0.0:0.0987	.	1249	Q96M86	DNHD1_HUMAN	N	1249	ENSP00000254579:H1249N;ENSP00000436180:H1249N	ENSP00000254579:H1249N	H	+	1	0	DNHD1	6522043	0.880000	0.30214	0.916000	0.36221	0.319000	0.28217	0.780000	0.26760	0.767000	0.33267	0.561000	0.74099	CAT	.	.		0.542	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666		A	6565467	C	A	6565467	3	1	331	1	0	0	0	0	1	0	0	0	4670	710	25	3	3820	3	DNHD1	11	6565467	Missense_Mutation	SNP	C	TCGA-QA-A7B7-01A-11D-A32G-10		6565467	128441049	51	46230										
INTS5	80789	hgsc.bcm.edu	37	chr11	62415200	62415200	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	cctggggcactgcagcagtgAaccaggaggctgaggaggct	17	10	0	2			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr11:62415200A>T	ENST00000330574.2	-	2	2404	c.2352T>A	c.(2350-2352)gtT>gtA	p.V784V	GANAB_ENST00000534779.1_5'Flank|GANAB_ENST00000356638.3_5'Flank|GANAB_ENST00000540933.1_5'Flank|GANAB_ENST00000346178.4_5'Flank	NM_030628.1	NP_085131.1	Q6P9B9	INT5_HUMAN	integrator complex subunit 5	784					snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				breast(1)|endometrium(4)|large_intestine(6)|lung(20)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	36						TGCAGCAGTGAACCAGGAGGC	0.582																																					p.V784V		Atlas-SNP	.											.	INTS5	81	.	0			c.T2352A						.						54	61	59					11																	62415200		2202	4299	6501	SO:0001819	synonymous_variant	80789	exon2			GCAGTGAACCAGG	AK123587	CCDS8027.1	11q12.3	2006-04-26	2006-03-15	2006-03-15	ENSG00000185085	ENSG00000185085			29352	protein-coding gene	gene with protein product		611349	"KIAA1698"	KIAA1698		16239144	Standard	NM_030628		Approved	INT5	uc001nud.3	Q6P9B9	OTTHUMG00000167605	ENST00000330574.2:c.2352T>A	chr11.hg19:g.62415200A>T		91.0	0.0		135.0	59.0	NM_030628	Q8N6W5|Q9C0G5	Silent	SNP	ENST00000330574.2	hg19	CCDS8027.1																																																																																			.	.		0.582	INTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395327.1	NM_030628		T	62415200	A	T	62415200	2	4	331	1	0	0	0	0	0	0	0	1	7790	233	9	4		4	INTS5	11	62415200	Silent	SNP	A	TCGA-QA-A7B7-01A-11D-A32G-10	55849733	62415200	72591316	52	46231										
PELI3	246330	hgsc.bcm.edu	37	chr11	66243202	66243202	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	ggaggcccagcggcaggaggCaaatgcagcgcggccccagt	17	13	0	0			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr11:66243202C>A	ENST00000320740.7	+	8	1134	c.974C>A	c.(973-975)gCa>gAa	p.A325E	CTD-3074O7.5_ENST00000525142.1_RNA|CTD-3074O7.5_ENST00000602951.1_RNA|PELI3_ENST00000531856.1_Intron|CTD-3074O7.5_ENST00000527274.2_RNA|PELI3_ENST00000349459.6_Missense_Mutation_p.A301E|CTD-3074O7.5_ENST00000527092.1_RNA|CTD-3074O7.5_ENST00000533502.1_RNA	NM_001243136.1|NM_145065.2	NP_001230065.1|NP_659502.2	Q8N2H9	PELI3_HUMAN	pellino E3 ubiquitin protein ligase family member 3	325					defense response to Gram-negative bacterium (GO:0050829)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of Toll signaling pathway (GO:0045751)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|negative regulation of type I interferon production (GO:0032480)|positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070434)|protein K63-linked ubiquitination (GO:0070534)|regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070428)|Toll signaling pathway (GO:0008063)	cytosol (GO:0005829)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|skin(1)	15						CGGCAGGAGGCAAATGCAGCG	0.706																																					p.A325E		Atlas-SNP	.											.	PELI3	36	.	0			c.C974A						.						16	18	17					11																	66243202		2175	4257	6432	SO:0001583	missense	246330	exon8			AGGAGGCAAATGC	AL834395	CCDS31615.1, CCDS41675.1, CCDS73328.1	11q13.2	2012-02-23	2012-02-23		ENSG00000174516	ENSG00000174516		"Pellino homologs"	30010	protein-coding gene	gene with protein product		609827	"pellino homolog 3 (Drosophila)"			12874243, 15917247	Standard	NM_145065		Approved	MGC35521	uc001oic.4	Q8N2H9	OTTHUMG00000167109	ENST00000320740.7:c.974C>A	chr11.hg19:g.66243202C>A	ENSP00000322532:p.Ala325Glu	65.0	0.0		104.0	41.0	NM_145065	Q8N3E1|Q8N9Q6|Q8TAW7|Q8TED5	Missense_Mutation	SNP	ENST00000320740.7	hg19	CCDS31615.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.067753	0.76301	.	.	ENSG00000174516	ENST00000349459;ENST00000320740;ENST00000526296	T;T;T	0.44482	0.92;0.92;0.92	5.14	4.21	0.49690	.	0.173579	0.39687	N	0.001298	T	0.28830	0.0715	N	0.08118	0	0.80722	D	1	P;P	0.51653	0.892;0.947	P;P	0.49887	0.491;0.625	T	0.14615	-1.0466	10	0.87932	D	0	-21.4884	6.8759	0.24147	0.0:0.7295:0.179:0.0915	.	301;325	Q8N2H9-2;Q8N2H9	.;PELI3_HUMAN	E	301;325;218	ENSP00000309848:A301E;ENSP00000322532:A325E;ENSP00000436722:A218E	ENSP00000322532:A325E	A	+	2	0	PELI3	65999778	1.000000	0.71417	0.972000	0.41901	0.988000	0.76386	4.808000	0.62583	1.358000	0.45922	0.561000	0.74099	GCA	.	.		0.706	PELI3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393226.1	NM_145065		A	66243202	C	A	66243202	3	1	331	1	0	0	0	0	1	0	0	0	11732	710	25	3	1000	3	PELI3	11	66243202	Missense_Mutation	SNP	C	TCGA-QA-A7B7-01A-11D-A32G-10	3828002	66243202	68763314	53	46232										
CLCF1	23529	hgsc.bcm.edu	37	chr11	67135026	67135026	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	aggccctgggtcccctgtgcGattgagagctggcactgcag	15	12	0	1	rs76168219	byFrequency	TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr11:67135026G>T	ENST00000312438.7	-	2	285	c.88C>A	c.(88-90)Cgc>Agc	p.R30S	AP003419.11_ENST00000543494.1_RNA|CLCF1_ENST00000533438.1_Missense_Mutation_p.R20S|CLCF1_ENST00000528474.1_Missense_Mutation_p.R20S	NM_013246.2	NP_037378.1	Q9UBD9	CLCF1_HUMAN	cardiotrophin-like cytokine factor 1	30					B cell differentiation (GO:0030183)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|JAK-STAT cascade (GO:0007259)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell proliferation (GO:0008284)|positive regulation of immunoglobulin production (GO:0002639)|positive regulation of isotype switching to IgE isotypes (GO:0048295)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)	CNTFR-CLCF1 complex (GO:0097059)|CRLF-CLCF1 complex (GO:0097058)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	ciliary neurotrophic factor receptor binding (GO:0005127)|cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|protein heterodimerization activity (GO:0046982)|receptor binding (GO:0005102)			endometrium(1)|urinary_tract(1)	2			BRCA - Breast invasive adenocarcinoma(15;2.39e-06)			TCCCCTGTGCGATTGAGAGCT	0.627																																					p.R30S		Atlas-SNP	.											.	CLCF1	15	.	0			c.C88A						.						106	87	94					11																	67135026		2200	4295	6495	SO:0001583	missense	23529	exon2			CTGTGCGATTGAG	BC012939	CCDS31617.1, CCDS53666.1	11q13.3	2014-01-28	2006-07-03		ENSG00000175505	ENSG00000175505			17412	protein-coding gene	gene with protein product	"B-cell stimulating factor 3", "cold-induced sweating syndrome 2", "novel neurotrophin-1"	607672	"CRLF1 associated cytokine-like factor 1"			10500198, 10448081, 16782820	Standard	NM_001166212		Approved	NNT1, BSF3, CLC, NR6, CISS2, BSF-3, NNT-1	uc010rpp.2	Q9UBD9	OTTHUMG00000167669	ENST00000312438.7:c.88C>A	chr11.hg19:g.67135026G>T	ENSP00000309338:p.Arg30Ser	79.0	0.0		78.0	30.0	NM_013246	B4DNT4|Q6NZA4	Missense_Mutation	SNP	ENST00000312438.7	hg19	CCDS31617.1	.	.	.	.	.	.	.	.	.	.	G	8.627	0.892775	0.17613	.	.	ENSG00000175505	ENST00000312438;ENST00000533438;ENST00000528474	T;T;T	0.76316	-1.01;-1.01;-1.01	5.43	4.52	0.55395	.	0.311666	0.26556	N	0.023705	T	0.54481	0.1861	N	0.08118	0	0.25048	N	0.991152	B	0.12013	0.005	B	0.10450	0.005	T	0.46665	-0.9175	10	0.87932	D	0	-0.5423	2.9791	0.05947	0.1557:0.1416:0.5562:0.1465	.	30	Q9UBD9	CLCF1_HUMAN	S	30;20;20	ENSP00000309338:R30S;ENSP00000434122:R20S;ENSP00000432553:R20S	ENSP00000309338:R30S	R	-	1	0	CLCF1	66891602	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	2.473000	0.45145	1.433000	0.47394	0.591000	0.81541	CGC	.	G|0.997;A|0.003		0.627	CLCF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395478.1	NM_013246		T	67135026	G	T	67135026	3	4	331	1	0	0	0	0	1	0	0	0	3463	1058	37	1	597	1	CLCF1	11	67135026	Missense_Mutation	SNP	G	TCGA-QA-A7B7-01A-11D-A32G-10	891824	67135026	67871490	54	46233										
GPR152	390212	hgsc.bcm.edu	37	chr11	67219232	67219232	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	agtgggcgtgaagctgcccgGccgctcctcgcagagagctg	16	13	0	2			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr11:67219232G>C	ENST00000312457.2	-	1	968	c.964C>G	c.(964-966)Ccg>Gcg	p.P322A	CABP4_ENST00000438189.2_5'Flank	NM_206997.1	NP_996880.1	Q8TDT2	GP152_HUMAN	G protein-coupled receptor 152	322						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	16			BRCA - Breast invasive adenocarcinoma(15;8.18e-06)			AAGCTGCCCGGCCGCTCCTCG	0.657																																					p.P322A	Pancreas(102;800 1581 2723 7382 33622)	Atlas-SNP	.											.	GPR152	41	.	0			c.C964G						.						42	43	43					11																	67219232		2200	4295	6495	SO:0001583	missense	390212	exon1			TGCCCGGCCGCTC	AY255600	CCDS8165.1	11q13.2	2013-09-20			ENSG00000175514	ENSG00000175514		"GPCR / Class A : Orphans"	23622	protein-coding gene	gene with protein product						12679517	Standard	NM_206997		Approved	PGR5	uc001olm.3	Q8TDT2	OTTHUMG00000168032	ENST00000312457.2:c.964C>G	chr11.hg19:g.67219232G>C	ENSP00000310255:p.Pro322Ala	55.0	0.0		61.0	25.0	NM_206997	Q0VD88|Q86SM0	Missense_Mutation	SNP	ENST00000312457.2	hg19	CCDS8165.1	.	.	.	.	.	.	.	.	.	.	G	7.618	0.676230	0.14841	.	.	ENSG00000175514	ENST00000312457	T	0.36520	1.25	4.3	3.3	0.37823	.	0.376128	0.19551	N	0.111577	T	0.24661	0.0598	L	0.36672	1.1	0.09310	N	1	P	0.42735	0.788	B	0.38985	0.287	T	0.07385	-1.0775	10	0.21014	T	0.42	.	8.9472	0.35767	0.1216:0.0:0.8784:0.0	.	322	Q8TDT2	GP152_HUMAN	A	322	ENSP00000310255:P322A	ENSP00000310255:P322A	P	-	1	0	GPR152	66975808	0.886000	0.30341	0.243000	0.24186	0.055000	0.15305	2.228000	0.42981	2.216000	0.71823	0.462000	0.41574	CCG	.	.		0.657	GPR152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397623.1			C	67219232	G	C	67219232	3	2	331	1	0	0	0	0	1	0	0	0	6666	1203	42	4	452	4	GPR152	11	67219232	Missense_Mutation	SNP	G	TCGA-QA-A7B7-01A-11D-A32G-10	84206	67219232	67787284	55	46234										
IGHMBP2	3508	hgsc.bcm.edu	37	chr11	68701272	68701272	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	ctgtgtgccagggacctcccAggtgtggctgccacagaaga	14	12	0	2			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr11:68701272A>T	ENST00000255078.3	+	10	1539	c.1428A>T	c.(1426-1428)ccA>ccT	p.P476P	IGHMBP2_ENST00000541229.1_3'UTR	NM_002180.2	NP_002171.2	P38935	SMBP2_HUMAN	immunoglobulin mu binding protein 2	476					ATP catabolic process (GO:0006200)|cell death (GO:0008219)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|protein homooligomerization (GO:0051260)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)	axon (GO:0030424)|cytoplasm (GO:0005737)|growth cone (GO:0030426)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|ATP-dependent 5'-3' RNA helicase activity (GO:0032575)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|ribosome binding (GO:0043022)|RNA binding (GO:0003723)|RNA-dependent ATPase activity (GO:0008186)|single-stranded DNA binding (GO:0003697)|transcription factor binding (GO:0008134)|tRNA binding (GO:0000049)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|liver(1)|lung(15)|ovary(2)|prostate(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			GGGACCTCCCAGGTGTGGCTG	0.642																																					p.P476P		Atlas-SNP	.											.	IGHMBP2	83	.	0			c.A1428T						.						33	34	34					11																	68701272		2199	4294	6493	SO:0001819	synonymous_variant	3508	exon10			CCTCCCAGGTGTG	L14754	CCDS8187.1	11q13.3	2014-09-17			ENSG00000132740	ENSG00000132740		"Zinc fingers, AN1-type domain containing"	5542	protein-coding gene	gene with protein product	"cardiac transcription factor 1", "zinc finger, AN1-type domain 7"	600502				8349627	Standard	NM_002180		Approved	ZFAND7, SMUBP2, CATF1, SMARD1, HCSA, HMN6	uc001ook.1	P38935	OTTHUMG00000167894	ENST00000255078.3:c.1428A>T	chr11.hg19:g.68701272A>T		72.0	0.0		63.0	36.0	NM_002180	A0PJD2|Q00443|Q14177	Silent	SNP	ENST00000255078.3	hg19	CCDS8187.1																																																																																			.	.		0.642	IGHMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396862.1	NM_002180		T	68701272	A	T	68701272	2	4	331	1	0	0	0	0	0	0	0	1	7600	175	7	4		4	IGHMBP2	11	68701272	Silent	SNP	A	TCGA-QA-A7B7-01A-11D-A32G-10	1482040	68701272	66305244	56	46235										
MAML2	84441	hgsc.bcm.edu	37	chr11	95825257	95825257	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	tgttgctgctgctgctgctgTtgttgctgctgctgctgctg	14	10	0	0	rs575986134	byFrequency	TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr11:95825257T>C	ENST00000524717.1	-	2	3222	c.1938A>G	c.(1936-1938)caA>caG	p.Q646Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	646					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				gctgctgctgttgttgctgct	0.517			T	"MECT1, CRTC3"	salivary gland mucoepidermoid								T|||	5	0.000998403	0	0	5008	,	,		17451	0.005		0	False		,,,				2504	0				p.Q646Q		Atlas-SNP	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	MAML2,colon,carcinoma,0,1	MAML2	94	.	0			c.A1938G						.						37	42	40					11																	95825257		2095	4114	6209	SO:0001819	synonymous_variant	84441	exon2			CTGCTGTTGTTGC	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"mastermind (Drosophila)-like 2"			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1938A>G	chr11.hg19:g.95825257T>C		156.0	1.0		184.0	9.0	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	hg19	CCDS44714.1																																																																																			.	.		0.517	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			C	95825257	T	C	95825257	2	2	331	1	0	0	0	0	0	0	0	1	9215	1722	60	2		2	MAML2	11	95825257	Silent	SNP	T	TCGA-QA-A7B7-01A-11D-A32G-10	27123985	95825257	39181259	57	46236										
CACNA2D4	93589	hgsc.bcm.edu	37	chr12	1902886	1902886	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	caggagtaggggcggcgaggCtgaggtgtccgaggcgccgc	21	10	0	1			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr12:1902886C>G	ENST00000382722.5	-	38	3711	c.3349G>C	c.(3349-3351)Gcc>Ccc	p.A1117P	CACNA2D4_ENST00000588077.1_Missense_Mutation_p.A1053P|CACNA2D4_ENST00000587995.1_Missense_Mutation_p.A1092P|CACNA2D4_ENST00000538027.2_Missense_Mutation_p.A262P|CACNA2D4_ENST00000538450.1_Missense_Mutation_p.A247P	NM_172364.4	NP_758952.4	Q7Z3S7	CA2D4_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 4	1117					calcium ion transmembrane transport (GO:0070588)|detection of light stimulus involved in visual perception (GO:0050908)	voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			endometrium(3)|kidney(2)|large_intestine(1)|liver(1)|lung(27)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	39	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		GGCGGCGAGGCTGAGGTGTCC	0.657																																					p.A1117P	Colon(2;101 179 21030 23310 28141)	Atlas-SNP	.											.	CACNA2D4	220	.	0			c.G3349C						.						30	38	35					12																	1902886		2062	4200	6262	SO:0001583	missense	93589	exon38			GCGAGGCTGAGGT	AF516695	CCDS44785.1	12p13.33	2003-03-05			ENSG00000151062	ENSG00000151062		"Calcium channel subunits"	20202	protein-coding gene	gene with protein product		608171				12181424	Standard	NM_172364		Approved		uc021qsx.1	Q7Z3S7	OTTHUMG00000168111	ENST00000382722.5:c.3349G>C	chr12.hg19:g.1902886C>G	ENSP00000372169:p.Ala1117Pro	104.0	0.0		138.0	55.0	NM_172364	Q7Z3S8|Q86XZ5|Q8IZS9	Missense_Mutation	SNP	ENST00000382722.5	hg19	CCDS44785.1	.	.	.	.	.	.	.	.	.	.	C	11.13	1.547709	0.27652	.	.	ENSG00000151062	ENST00000456077;ENST00000537784;ENST00000545595;ENST00000382722;ENST00000538027;ENST00000538450	T;T	0.61510	0.1;0.1	4.8	3.87	0.44632	.	0.405160	0.23908	N	0.043375	T	0.40322	0.1112	L	0.31578	0.945	0.80722	D	1	B	0.09022	0.002	B	0.08055	0.003	T	0.23655	-1.0182	10	0.05620	T	0.96	.	12.9306	0.58284	0.0:0.7761:0.2239:0.0	.	1117	Q7Z3S7	CA2D4_HUMAN	P	1053;184;184;1117;184;247	ENSP00000372169:A1117P;ENSP00000446341:A247P	ENSP00000372169:A1117P	A	-	1	0	CACNA2D4	1773147	0.882000	0.30256	0.169000	0.22859	0.491000	0.33493	1.587000	0.36622	1.117000	0.41842	0.561000	0.74099	GCC	.	.		0.657	CACNA2D4-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398230.2			G	1902886	C	G	1902886	3	3	331	1	0	0	0	0	1	0	0	0	2553	797	28	4	68	4	CACNA2D4	12	1902886	Missense_Mutation	SNP	C	TCGA-QA-A7B7-01A-11D-A32G-10		1902886	131949009	58	46237										
C1RL	51279	hgsc.bcm.edu	37	chr12	7249108	7249108	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	tgcccgtggccacccagtgaTgggcatgattgtcccatacc	11	14	0	2			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr12:7249108T>C	ENST00000266542.4	-	6	1435	c.1343A>G	c.(1342-1344)cAt>cGt	p.H448R	C1RL_ENST00000504702.2_Intron|C1RL_ENST00000544702.1_3'UTR|C1RL_ENST00000545280.1_Intron	NM_016546.2	NP_057630.2	Q9NZP8	C1RL_HUMAN	complement component 1, r subcomponent-like	448	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						CACCCAGTGATGGGCATGATT	0.542																																					p.H448R		Atlas-SNP	.											.	C1RL	39	.	0			c.A1343G						.						133	114	120					12																	7249108		2203	4300	6503	SO:0001583	missense	51279	exon6			CAGTGATGGGCAT	AF178985	CCDS8573.1, CCDS73431.1	12p13.31	2008-02-05				ENSG00000139178			21265	protein-coding gene	gene with protein product		608974				12838346	Standard	XM_005253385		Approved	C1r-LP, C1RL1	uc001qsn.3	Q9NZP8		ENST00000266542.4:c.1343A>G	chr12.hg19:g.7249108T>C	ENSP00000266542:p.His448Arg	85.0	0.0		91.0	31.0	NM_016546	Q53GX9	Missense_Mutation	SNP	ENST00000266542.4	hg19	CCDS8573.1	.	.	.	.	.	.	.	.	.	.	T	7.051	0.564428	0.13498	.	.	ENSG00000139178	ENST00000266542	T	0.40225	1.04	4.98	-3.9	0.04181	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.848408	0.10475	N	0.670333	T	0.15825	0.0381	N	0.03224	-0.385	0.20307	N	0.999911	B	0.06786	0.001	B	0.15052	0.012	T	0.28808	-1.0032	10	0.18710	T	0.47	.	7.67	0.28453	0.1236:0.4755:0.0:0.4009	.	448	Q9NZP8	C1RL_HUMAN	R	448	ENSP00000266542:H448R	ENSP00000266542:H448R	H	-	2	0	C1RL	7140250	0.000000	0.05858	0.145000	0.22337	0.603000	0.37013	0.019000	0.13444	-0.912000	0.03837	-0.558000	0.04189	CAT	.	.		0.542	C1RL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398367.1	NM_016546		C	7249108	T	C	7249108	3	2	331	1	0	0	0	0	1	0	0	0	1975	1464	51	2	124	2	C1RL	12	7249108	Missense_Mutation	SNP	T	TCGA-QA-A7B7-01A-11D-A32G-10	5346222	7249108	126602787	59	46238										
AICDA	57379	hgsc.bcm.edu	37	chr12	8759531	8759531	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	gcctcttcactacgtagcacAggtaggtctcacgccgaccc	9	16	3	0			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr12:8759531A>C	ENST00000229335.6	-	2	189	c.86T>G	c.(85-87)cTg>cGg	p.L29R	AICDA_ENST00000537228.1_Missense_Mutation_p.L29R	NM_020661.2	NP_065712.1	Q9GZX7	AICDA_HUMAN	activation-induced cytidine deaminase	29	Nuclear localization signal.				B cell differentiation (GO:0030183)|cellular response to lipopolysaccharide (GO:0071222)|DNA demethylation (GO:0080111)|isotype switching (GO:0045190)|mRNA processing (GO:0006397)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|somatic diversification of immunoglobulins (GO:0016445)|somatic hypermutation of immunoglobulin genes (GO:0016446)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cytidine deaminase activity (GO:0004126)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(4)|ovary(2)|pancreas(1)	16	Lung SC(5;0.184)					TACGTAGCACAGGTAGGTCTC	0.483																																					p.L29R	GBM(62;896 1067 5527 26594 30137)	Atlas-SNP	.											.	AICDA	37	.	0			c.T86G						.						81	77	78					12																	8759531		1957	4141	6098	SO:0001583	missense	57379	exon2			TAGCACAGGTAGG	AB040430	CCDS41747.1	12p13	2014-09-17			ENSG00000111732	ENSG00000111732		"Apolipoprotein B mRNA editing enzymes"	13203	protein-coding gene	gene with protein product		605257					Standard	NM_020661		Approved	HIGM2, CDA2, ARP2, AID	uc001qur.2	Q9GZX7	OTTHUMG00000168676	ENST00000229335.6:c.86T>G	chr12.hg19:g.8759531A>C	ENSP00000229335:p.Leu29Arg	47.0	0.0		77.0	29.0	NM_020661	Q6QJ81|Q8NFC1	Missense_Mutation	SNP	ENST00000229335.6	hg19	CCDS41747.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.479854|4.479854	0.84747|0.84747	.|.	.|.	ENSG00000111732|ENSG00000111732	ENST00000543081;ENST00000544516;ENST00000545512|ENST00000229335;ENST00000537228	.|D;D	.|0.83591	.|-1.74;-1.74	5.36|5.36	5.36|5.36	0.76844|0.76844	.|APOBEC-like, N-terminal (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.92760|0.92760	0.7698|0.7698	M|M	0.92122|0.92122	3.275|3.275	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.79784	.|0.993;0.993;0.993	D|D	0.94335|0.94335	0.7565|0.7565	5|10	.|0.87932	.|D	.|0	-15.8062|-15.8062	14.17|14.17	0.65503|0.65503	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|29;29;29	.|Q9GZX7;Q6QJ80;Q6QJ81	.|AICDA_HUMAN;.;.	G|R	28|29	.|ENSP00000229335:L29R;ENSP00000445691:L29R	.|ENSP00000229335:L29R	C|L	-|-	1|2	0|0	AICDA|AICDA	8650798|8650798	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.984000|0.984000	0.73092|0.73092	8.669000|8.669000	0.91163|0.91163	2.026000|2.026000	0.59711|0.59711	0.383000|0.383000	0.25322|0.25322	TGT|CTG	.	.		0.483	AICDA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400575.1	NM_020661		C	8759531	A	C	8759531	3	2	331	1	0	0	0	0	1	0	0	0	422	188	7	5	526	5	AICDA	12	8759531	Missense_Mutation	SNP	A	TCGA-QA-A7B7-01A-11D-A32G-10	1510423	8759531	125092364	60	46239										
ADAMTS20	80070	hgsc.bcm.edu	37	chr12	43828114	43828114	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	gtggcaagtggtcacattctTtatcagacacaacactatga	8	9	3	2			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr12:43828114T>G	ENST00000389420.3	-	19	2653	c.2654A>C	c.(2653-2655)aAa>aCa	p.K885T	ADAMTS20_ENST00000553158.1_Missense_Mutation_p.K885T|ADAMTS20_ENST00000395541.2_Missense_Mutation_p.K39T	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	885	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		GTCACATTCTTTATCAGACAC	0.323																																					p.K885T		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.A2654C						.						88	74	79					12																	43828114		2203	4300	6503	SO:0001583	missense	80070	exon19			CATTCTTTATCAG	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.2654A>C	chr12.hg19:g.43828114T>G	ENSP00000374071:p.Lys885Thr	147.0	0.0		147.0	71.0	NM_025003	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	hg19	CCDS31778.2	.	.	.	.	.	.	.	.	.	.	T	14.31	2.498144	0.44455	.	.	ENSG00000173157	ENST00000389420;ENST00000549670;ENST00000395541;ENST00000553158;ENST00000389417	T;T;T;T	0.60797	0.16;0.16;0.16;0.16	4.91	3.72	0.42706	.	0.291163	0.24400	N	0.038860	T	0.32133	0.0819	N	0.03608	-0.345	0.24389	N	0.994751	B;B	0.25235	0.002;0.121	B;B	0.21546	0.004;0.035	T	0.18085	-1.0348	10	0.33141	T	0.24	.	11.2484	0.49010	0.0:0.0744:0.0:0.9256	.	885;39	P59510;E9PBD5	ATS20_HUMAN;.	T	885;51;39;885;885	ENSP00000374071:K885T;ENSP00000447427:K51T;ENSP00000378911:K39T;ENSP00000448341:K885T	ENSP00000374068:K885T	K	-	2	0	ADAMTS20	42114381	1.000000	0.71417	0.964000	0.40570	0.851000	0.48451	4.532000	0.60608	0.918000	0.36919	0.533000	0.62120	AAA	.	.		0.323	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		G	43828114	T	G	43828114	3	3	331	1	0	0	0	0	1	0	0	0	266	1841	64	5	3161	5	ADAMTS20	12	43828114	Missense_Mutation	SNP	T	TCGA-QA-A7B7-01A-11D-A32G-10	35068583	43828114	90023781	61	46240										
ADAMTS20	80070	hgsc.bcm.edu	37	chr12	43828156	43828156	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	cactcttatgtatgcaagttAtgtttcttcgctgaagacct	7	9	2	2			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr12:43828156A>G	ENST00000389420.3	-	19	2611	c.2612T>C	c.(2611-2613)aTa>aCa	p.I871T	ADAMTS20_ENST00000553158.1_Missense_Mutation_p.I871T|ADAMTS20_ENST00000395541.2_Missense_Mutation_p.I25T	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	871	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		TATGCAAGTTATGTTTCTTCG	0.333																																					p.I871T		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.T2612C						.						73	59	64					12																	43828156		2203	4298	6501	SO:0001583	missense	80070	exon19			CAAGTTATGTTTC	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.2612T>C	chr12.hg19:g.43828156A>G	ENSP00000374071:p.Ile871Thr	121.0	0.0		120.0	53.0	NM_025003	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	hg19	CCDS31778.2	.	.	.	.	.	.	.	.	.	.	A	14.70	2.612922	0.46631	.	.	ENSG00000173157	ENST00000389420;ENST00000549670;ENST00000395541;ENST00000553158;ENST00000389417	T;T;T;T	0.61040	0.14;0.14;0.14;0.14	4.91	4.91	0.64330	.	0.256439	0.27060	N	0.021133	T	0.57873	0.2083	M	0.76002	2.32	0.25405	N	0.988402	P;D	0.54207	0.791;0.965	B;B	0.41860	0.368;0.366	T	0.58387	-0.7645	10	0.26408	T	0.33	.	15.2455	0.73504	1.0:0.0:0.0:0.0	.	871;25	P59510;E9PBD5	ATS20_HUMAN;.	T	871;37;25;871;871	ENSP00000374071:I871T;ENSP00000447427:I37T;ENSP00000378911:I25T;ENSP00000448341:I871T	ENSP00000374068:I871T	I	-	2	0	ADAMTS20	42114423	0.688000	0.27680	0.475000	0.27278	0.855000	0.48748	2.689000	0.46993	2.127000	0.65507	0.533000	0.62120	ATA	.	.		0.333	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		G	43828156	A	G	43828156	3	3	331	1	0	0	0	0	1	0	0	0	266	449	16	2	3203	2	ADAMTS20	12	43828156	Missense_Mutation	SNP	A	TCGA-QA-A7B7-01A-11D-A32G-10	42	43828156	90023739	62	46241										
GRIP1	23426	hgsc.bcm.edu	37	chr12	66838427	66838427	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	tgaagagtctcggaggagctGactggcttcttcgaaggtgc	15	8	2	3			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr12:66838427G>A	ENST00000398016.3	-	12	1536	c.1468C>T	c.(1468-1470)Cag>Tag	p.Q490*	GRIP1_ENST00000286445.7_Nonsense_Mutation_p.Q542*|GRIP1_ENST00000359742.4_Nonsense_Mutation_p.Q542*	NM_021150.3	NP_066973.2	Q96DT0	LEG12_HUMAN	glutamate receptor interacting protein 1	0					intrinsic apoptotic signaling pathway (GO:0097193)	nucleus (GO:0005634)	lactose binding (GO:0030395)			NS(3)|breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(19)|ovary(2)|prostate(2)|skin(1)	50			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		CGGAGGAGCTGACTGGCTTCT	0.463																																					p.Q490X		Atlas-SNP	.											.	GRIP1	106	.	0			c.C1468T						.						122	123	122					12																	66838427		1961	4146	6107	SO:0001587	stop_gained	23426	exon12			GGAGCTGACTGGC	AJ133439	CCDS41807.1	12q13.13	2008-05-02			ENSG00000155974	ENSG00000155974			18708	protein-coding gene	gene with protein product		604597				10197531	Standard	NM_021150		Approved		uc001stk.3	Q9Y3R0	OTTHUMG00000169019	ENST00000398016.3:c.1468C>T	chr12.hg19:g.66838427G>A	ENSP00000381098:p.Gln490*	187.0	0.0		171.0	58.0	NM_001178074	B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Nonsense_Mutation	SNP	ENST00000398016.3	hg19	CCDS41807.1	.	.	.	.	.	.	.	.	.	.	G	39	7.661230	0.98419	.	.	ENSG00000155974	ENST00000398016;ENST00000359742;ENST00000286445;ENST00000538211;ENST00000540433;ENST00000536215	.	.	.	5.61	5.61	0.85477	.	0.114988	0.64402	D	0.000012	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-7.2371	19.6387	0.95748	0.0:0.0:1.0:0.0	.	.	.	.	X	490;542;542;490;434;382	.	.	Q	-	1	0	GRIP1	65124694	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.476000	0.97823	2.641000	0.89580	0.544000	0.68410	CAG	.	.		0.463	GRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401975.2			A	66838427	G	A	66838427	4	1	331	1	0	0	0	0	0	1	0	0	6796	1299	45	3	1814	3	GRIP1	12	66838427	Nonsense_Mutation	SNP	G	TCGA-QA-A7B7-01A-11D-A32G-10	23010271	66838427	67013468	63	46242										
CCDC63	160762	hgsc.bcm.edu	37	chr12	111336787	111336787	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	gatatgtatgagagcaagtaCggggaggtcagcaagacctt	14	6	1	2	rs141258896		TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr12:111336787C>T	ENST00000308208.5	+	10	1442	c.1200C>T	c.(1198-1200)taC>taT	p.Y400Y	CCDC63_ENST00000545036.1_Silent_p.Y360Y|CCDC63_ENST00000552694.1_Silent_p.Y321Y	NM_152591.1	NP_689804.1	Q8NA47	CCD63_HUMAN	coiled-coil domain containing 63	400										NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(1)	39						AGAGCAAGTACGGGGAGGTCA	0.512													C|||	1	0.000199681	8e-04	0	5008	,	,		17309	0		0	False		,,,				2504	0				p.Y400Y		Atlas-SNP	.											.	CCDC63	89	.	0			c.C1200T						.	C		2,4404	4.2+/-10.8	0,2,2201	111	104	106		1200	4.5	0	12	dbSNP_134	106	0,8600		0,0,4300	no	coding-synonymous	CCDC63	NM_152591.1		0,2,6501	TT,TC,CC		0.0,0.0454,0.0154		400/564	111336787	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	160762	exon10			CAAGTACGGGGAG	AK093162	CCDS9151.1, CCDS66470.1, CCDS73528.1	12q24.11	2013-02-19				ENSG00000173093			26669	protein-coding gene	gene with protein product	"outer row dynein assembly 5 homolog (Chlamydomonas)"						Standard	NM_001286243		Approved	ODA5, FLJ35843	uc001trv.1	Q8NA47	OTTHUMG00000169534	ENST00000308208.5:c.1200C>T	chr12.hg19:g.111336787C>T		65.0	0.0		76.0	39.0	NM_152591	B4DY03|Q0P603|Q6P2E1	Silent	SNP	ENST00000308208.5	hg19	CCDS9151.1																																																																																			.	C|1.000;T|0.000		0.512	CCDC63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404673.2	NM_152591		T	111336787	C	T	111336787	2	4	331	1	0	0	0	0	0	0	0	1	2836	547	19	1		1	CCDC63	12	111336787	Silent	SNP	C	TCGA-QA-A7B7-01A-11D-A32G-10	44498360	111336787	22515108	64	46243										
UGGT2	55757	hgsc.bcm.edu	37	chr13	96579585	96579585	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	gcattcgtgcgatcatttaaTgtgccctaaaaaaacaaaaa	6	8	1	0			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr13:96579585T>C	ENST00000376747.3	-	18	2053	c.1983A>G	c.(1981-1983)acA>acG	p.T661T		NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	661					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-glucosylation (GO:0097359)	endoplasmic reticulum lumen (GO:0005788)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(17)|lung(20)|ovary(3)|pancreas(1)|prostate(4)|urinary_tract(2)	60						GATCATTTAATGTGCCCTAAA	0.299																																					p.T661T		Atlas-SNP	.											.	UGGT2	127	.	0			c.A1983G						.						58	57	58					13																	96579585		2203	4295	6498	SO:0001819	synonymous_variant	55757	exon18			ATTTAATGTGCCC	AF227906	CCDS9480.1	13q32.1	2009-07-23	2009-07-23	2009-07-23	ENSG00000102595	ENSG00000102595			15664	protein-coding gene	gene with protein product	"UDP-glucose:glycoprotein glucosyltransferase 2"	605898	"UDP-glucose ceramide glucosyltransferase-like 2"	UGCGL2		10694380	Standard	NM_020121		Approved	FLJ11485, HUGT2, FLJ10873, MGC150689, MGC87276, MGC117360	uc001vmt.3	Q9NYU1	OTTHUMG00000017230	ENST00000376747.3:c.1983A>G	chr13.hg19:g.96579585T>C		136.0	0.0		198.0	88.0	NM_020121	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Silent	SNP	ENST00000376747.3	hg19	CCDS9480.1																																																																																			.	.		0.299	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121		C	96579585	T	C	96579585	2	2	331	1	0	0	0	0	0	0	0	1	16957	1451	51	2		2	UGGT2	13	96579585	Silent	SNP	T	TCGA-QA-A7B7-01A-11D-A32G-10		96579585	18590293	65	46244										
RABGGTA	5875	hgsc.bcm.edu	37	chr14	24734864	24734864	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	aaggcagcagttcagccagtTgctccaagatgcccaccgct	10	14	1	1			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr14:24734864T>A	ENST00000399409.3	-	16	2144	c.1661A>T	c.(1660-1662)cAa>cTa	p.Q554L	RABGGTA_ENST00000216840.6_Missense_Mutation_p.Q554L|RABGGTA_ENST00000560777.1_Missense_Mutation_p.Q163L|TGM1_ENST00000544573.1_5'Flank|TGM1_ENST00000206765.6_5'Flank	NM_004581.5	NP_004572.3	Q92696	PGTA_HUMAN	Rab geranylgeranyltransferase, alpha subunit	554					cellular protein modification process (GO:0006464)|protein geranylgeranylation (GO:0018344)|visual perception (GO:0007601)	Rab-protein geranylgeranyltransferase complex (GO:0005968)	Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)	12				GBM - Glioblastoma multiforme(265;0.0184)		TTCAGCCAGTTGCTCCAAGAT	0.587																																					p.Q554L		Atlas-SNP	.											.	RABGGTA	43	.	0			c.A1661T						.						40	44	43					14																	24734864		2025	4191	6216	SO:0001583	missense	5875	exon16			GCCAGTTGCTCCA		CCDS45088.1	14q11.2	2011-06-27				ENSG00000100949		"Prenyltransferase alpha subunit repeat containing"	9795	protein-coding gene	gene with protein product	"protein prenyltransferase alpha subunit repeat containing 3"	601905				8954794	Standard	NM_182836		Approved	PTAR3	uc001wog.4	Q92696		ENST00000399409.3:c.1661A>T	chr14.hg19:g.24734864T>A	ENSP00000382341:p.Gln554Leu	45.0	0.0		46.0	20.0	NM_004581	A8K5N2|D3DS69	Missense_Mutation	SNP	ENST00000399409.3	hg19	CCDS45088.1	.	.	.	.	.	.	.	.	.	.	T	10.87	1.471824	0.26423	.	.	ENSG00000100949	ENST00000216840;ENST00000399409	T;T	0.49720	0.77;0.77	5.67	3.33	0.38152	.	1.031460	0.07628	N	0.928062	T	0.33177	0.0854	N	0.22421	0.69	0.21950	N	0.999459	B	0.02656	0.0	B	0.01281	0.0	T	0.26744	-1.0094	10	0.25106	T	0.35	-0.2127	7.4138	0.27032	0.0:0.1775:0.0:0.8225	.	554	Q92696	PGTA_HUMAN	L	554	ENSP00000216840:Q554L;ENSP00000382341:Q554L	ENSP00000216840:Q554L	Q	-	2	0	RABGGTA	23804704	0.997000	0.39634	0.123000	0.21794	0.582000	0.36321	2.630000	0.46494	0.445000	0.26639	0.379000	0.24179	CAA	.	.		0.587	RABGGTA-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415308.5	NM_182836		A	24734864	T	A	24734864	3	1	331	1	0	0	0	0	1	0	0	0	12982	1812	63	4	46	4	RABGGTA	14	24734864	Missense_Mutation	SNP	T	TCGA-QA-A7B7-01A-11D-A32G-10		24734864	82614676	66	46245										
DCAF5	8816	hgsc.bcm.edu	37	chr14	69520835	69520835	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	cctggggaagagtaggccacCacctccagctcccccaagtt	10	16	0	1			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr14:69520835C>T	ENST00000341516.5	-	9	2715	c.2568G>A	c.(2566-2568)gtG>gtA	p.V856V	DCAF5_ENST00000553293.1_5'Flank|DCAF5_ENST00000554215.1_Silent_p.V774V|DCAF5_ENST00000557386.1_Silent_p.V855V|DCAF5_ENST00000556847.1_Silent_p.V774V	NM_001284206.1|NM_001284207.1|NM_003861.2	NP_001271135.1|NP_001271136.1|NP_003852.1	Q96JK2	DCAF5_HUMAN	DDB1 and CUL4 associated factor 5	856					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|mitochondrion (GO:0005739)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|upper_aerodigestive_tract(2)	29						AGTAGGCCACCACCTCCAGCT	0.562																																					p.V856V		Atlas-SNP	.											.	DCAF5	67	.	0			c.G2568A						.						128	112	118					14																	69520835		2203	4300	6503	SO:0001819	synonymous_variant	8816	exon9			GGCCACCACCTCC	AB058727	CCDS32106.1, CCDS61480.1, CCDS61481.1, CCDS73646.1	14q23-q24.1	2013-01-09	2009-07-17	2009-07-17				"WD repeat domain containing", "DDB1 and CUL4 associated factors"	20224	protein-coding gene	gene with protein product		603812	"WD repeat domain 22"	WDR22		9740667, 9521877	Standard	NM_003861		Approved	BCRP2, D14S1461E, BCRG2, KIAA1824	uc001xkp.3	Q96JK2		ENST00000341516.5:c.2568G>A	chr14.hg19:g.69520835C>T		73.0	0.0		93.0	28.0	NM_003861	B2RN31|G3V4J7|O60559|Q8N3V3|Q8N3V5	Silent	SNP	ENST00000341516.5	hg19	CCDS32106.1																																																																																			.	.		0.562	DCAF5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000414806.2	NM_003861		T	69520835	C	T	69520835	2	4	331	1	0	0	0	0	0	0	0	1	4275	581	21	3		3	DCAF5	14	69520835	Silent	SNP	C	TCGA-QA-A7B7-01A-11D-A32G-10	44785971	69520835	37828705	67	46246										
CHGA	1113	hgsc.bcm.edu	37	chr14	93397788	93397788	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	gaggaggaggccaccaacacCcaccctccagccagcctccc	9	20	0	0			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr14:93397788C>G	ENST00000216492.5	+	6	829	c.549C>G	c.(547-549)acC>acG	p.T183T	CHGA_ENST00000553866.1_3'UTR|CHGA_ENST00000334654.4_Intron	NM_001275.3	NP_001266.1	P10645	CMGA_HUMAN	chromogranin A (parathyroid secretory protein 1)	183	O-glycosylated at one site only in cerebrospinal fluid.				regulation of blood pressure (GO:0008217)	extracellular region (GO:0005576)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|secretory granule (GO:0030141)				cervix(1)|large_intestine(1)|lung(3)|skin(3)	8		all_cancers(154;0.0843)		Epithelial(152;0.102)|COAD - Colon adenocarcinoma(157;0.208)|all cancers(159;0.224)		CCACCAACACCCACCCTCCAG	0.677																																					p.T183T	Colon(31;154 822 45066 49155)|NSCLC(28;804 1157 13734 25204)	Atlas-SNP	.											.	CHGA	32	.	0			c.C549G						.						25	28	27					14																	93397788		2200	4299	6499	SO:0001819	synonymous_variant	1113	exon6			CAACACCCACCCT		CCDS9906.1	14q32	2012-10-02			ENSG00000100604	ENSG00000100604			1929	protein-coding gene	gene with protein product	"vasostatin", "pancreastatin", "parastatin"	118910				3403545	Standard	NM_001275		Approved		uc001ybc.4	P10645		ENST00000216492.5:c.549C>G	chr14.hg19:g.93397788C>G		34.0	0.0		14.0	12.0	NM_001275	B2R9E9|Q53FA8|Q6NR84|Q96E84|Q96GL7|Q9BQB5	Silent	SNP	ENST00000216492.5	hg19	CCDS9906.1																																																																																			.	.		0.677	CHGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412411.1	NM_001275		G	93397788	C	G	93397788	2	3	331	1	0	0	0	0	0	0	0	1	3340	610	22	4		4	CHGA	14	93397788	Silent	SNP	C	TCGA-QA-A7B7-01A-11D-A32G-10	23876953	93397788	13951752	68	46247										
MYO1E	4643	hgsc.bcm.edu	37	chr15	59500993	59500993	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	ctgatctgccccctcacccaCcgcatgcatcgtggcgcaca	8	19	2	1			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr15:59500993C>A	ENST00000288235.4	-	14	1816	c.1417G>T	c.(1417-1419)Gtg>Ttg	p.V473L		NM_004998.3	NP_004989.2	Q12965	MYO1E_HUMAN	myosin IE	473	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(6)|lung(10)|pancreas(2)|prostate(1)|urinary_tract(1)	33				all cancers(107;0.207)		CCCTCACCCACCGCATGCATC	0.537																																					p.V473L		Atlas-SNP	.											.	MYO1E	99	.	0			c.G1417T						.						148	124	132					15																	59500993		2191	4290	6481	SO:0001583	missense	4643	exon14			CACCCACCGCATG	U14391	CCDS32254.1	15q21-q22	2011-09-27				ENSG00000157483		"Myosins / Myosin superfamily : Class I"	7599	protein-coding gene	gene with protein product	"myosin-IC"	601479				8884266	Standard	NM_004998		Approved	MYO1C, HuncM-IC, MGC104638	uc002aga.4	Q12965		ENST00000288235.4:c.1417G>T	chr15.hg19:g.59500993C>A	ENSP00000288235:p.Val473Leu	76.0	0.0		95.0	37.0	NM_004998	Q14778	Missense_Mutation	SNP	ENST00000288235.4	hg19	CCDS32254.1	.	.	.	.	.	.	.	.	.	.	C	15.43	2.832662	0.50845	.	.	ENSG00000157483	ENST00000288235	D	0.86097	-2.07	5.37	5.37	0.77165	Myosin head, motor domain (2);	0.119081	0.64402	D	0.000020	D	0.85626	0.5740	L	0.60455	1.87	0.50171	D	0.999851	B	0.34061	0.436	B	0.39935	0.314	T	0.82563	-0.0395	10	0.27082	T	0.32	.	19.4857	0.95027	0.0:1.0:0.0:0.0	.	473	Q12965	MYO1E_HUMAN	L	473	ENSP00000288235:V473L	ENSP00000288235:V473L	V	-	1	0	MYO1E	57288285	1.000000	0.71417	0.988000	0.46212	0.952000	0.60782	4.443000	0.59994	2.677000	0.91161	0.561000	0.74099	GTG	.	.		0.537	MYO1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416024.1	NM_004998		A	59500993	C	A	59500993	3	1	331	1	0	0	0	0	1	0	0	0	10081	507	18	3	1969	3	MYO1E	15	59500993	Missense_Mutation	SNP	C	TCGA-QA-A7B7-01A-11D-A32G-10		59500993	43030399	69	46248										
HERC1	8925	hgsc.bcm.edu	37	chr15	63978599	63978599	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	agttactcctgtagatgccaAtccatatcctttccctccac	4	15	0	1			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr15:63978599A>G	ENST00000443617.2	-	34	6271	c.6184T>C	c.(6184-6186)Ttg>Ctg	p.L2062L	RP11-317G6.1_ENST00000559303.2_RNA	NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	2062	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						GTAGATGCCAATCCATATCCT	0.418																																					p.L2062L		Atlas-SNP	.											.	HERC1	624	.	0			c.T6184C						.						189	190	190					15																	63978599		1933	4145	6078	SO:0001819	synonymous_variant	8925	exon34			ATGCCAATCCATA	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.6184T>C	chr15.hg19:g.63978599A>G		137.0	0.0		124.0	67.0	NM_003922	Q8IW65	Silent	SNP	ENST00000443617.2	hg19	CCDS45277.1																																																																																			.	.		0.418	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		G	63978599	A	G	63978599	2	3	331	1	0	0	0	0	0	0	0	1	7066	98	4	2		2	HERC1	15	63978599	Silent	SNP	A	TCGA-QA-A7B7-01A-11D-A32G-10	4477606	63978599	38552793	70	46249										
SNX33	257364	hgsc.bcm.edu	37	chr15	75942327	75942327	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	cctgcctgagaagcaggccaCtggccgcttcgaggaggact	14	13	0	1			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr15:75942327C>T	ENST00000308527.5	+	1	2081	c.884C>T	c.(883-885)aCt>aTt	p.T295I	IMP3_ENST00000565349.1_5'Flank|IMP3_ENST00000314852.2_5'Flank	NM_153271.1	NP_695003.1	Q8WV41	SNX33_HUMAN	sorting nexin 33	295	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				cleavage furrow formation (GO:0036089)|endocytosis (GO:0006897)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|intracellular protein transport (GO:0006886)|macropinocytosis (GO:0044351)|membrane tubulation (GO:0097320)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|negative regulation of endocytosis (GO:0045806)|negative regulation of protein localization to cell surface (GO:2000009)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein localization to cell surface (GO:2000010)|protein import (GO:0017038)	cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of membrane (GO:0019898)|membrane (GO:0016020)	identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)|soft_tissue(1)|urinary_tract(2)	19						AAGCAGGCCACTGGCCGCTTC	0.582																																					p.T295I		Atlas-SNP	.											.	SNX33	43	.	0			c.C884T						.						93	99	97					15																	75942327		2197	4294	6491	SO:0001583	missense	257364	exon1			AGGCCACTGGCCG	AK091291	CCDS10283.1	15q23	2008-04-18	2008-03-25	2008-03-25	ENSG00000173548	ENSG00000173548			28468	protein-coding gene	gene with protein product			"SH3 and PX domain containing 3"	SH3PX3		16374509, 16782399, 18353773	Standard	NM_153271		Approved	MGC32065, SH3PXD3C, SNX30	uc002bau.3	Q8WV41	OTTHUMG00000142835	ENST00000308527.5:c.884C>T	chr15.hg19:g.75942327C>T	ENSP00000311427:p.Thr295Ile	68.0	0.0		81.0	31.0	NM_153271	B1NM17	Missense_Mutation	SNP	ENST00000308527.5	hg19	CCDS10283.1	.	.	.	.	.	.	.	.	.	.	C	12.63	1.995793	0.35226	.	.	ENSG00000173548	ENST00000308527	T	0.37411	1.2	5.68	5.68	0.88126	Phox homologous domain (5);	0.097518	0.64402	D	0.000002	T	0.50803	0.1637	L	0.37466	1.105	0.80722	D	1	D	0.69078	0.997	D	0.72982	0.979	T	0.50398	-0.8833	10	0.87932	D	0	-2.935	15.928	0.79635	0.0:0.865:0.135:0.0	.	295	Q8WV41	SNX33_HUMAN	I	295	ENSP00000311427:T295I	ENSP00000311427:T295I	T	+	2	0	SNX33	73729382	1.000000	0.71417	0.986000	0.45419	0.993000	0.82548	7.817000	0.86213	2.692000	0.91855	0.561000	0.74099	ACT	.	.		0.582	SNX33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286471.1	NM_153271		T	75942327	C	T	75942327	3	4	331	1	0	0	0	0	1	0	0	0	14918	565	20	3	886	3	SNX33	15	75942327	Missense_Mutation	SNP	C	TCGA-QA-A7B7-01A-11D-A32G-10	11963728	75942327	26589065	71	46250										
ITFG3	83986	hgsc.bcm.edu	37	chr16	312457	312457	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	ggctgctctgtgaagggtctCtacgagaaggtgaccgggag	17	8	2	3			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr16:312457C>T	ENST00000399932.3	+	8	1327	c.876C>T	c.(874-876)ctC>ctT	p.L292L	ITFG3_ENST00000450082.2_Silent_p.L292L|ITFG3_ENST00000600536.1_Silent_p.L292L|ITFG3_ENST00000442458.2_Silent_p.L292L|ITFG3_ENST00000301679.2_Silent_p.L292L|ITFG3_ENST00000301678.3_Silent_p.L292L	NM_001284497.1	NP_001271426.1	Q9H0X4	ITFG3_HUMAN	integrin alpha FG-GAP repeat containing 3	292						cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(3)|endometrium(2)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	16		all_cancers(16;0.000129)|all_epithelial(16;0.000206)|Hepatocellular(16;0.00264)|Lung NSC(18;0.0626)|all_lung(18;0.13)				TGAAGGGTCTCTACGAGAAGG	0.632																																					p.L292L		Atlas-SNP	.											.	ITFG3	42	.	0			c.C876T						.						48	53	51					16																	312457		1939	4129	6068	SO:0001819	synonymous_variant	83986	exon8			GGGTCTCTACGAG	AL136542	CCDS10402.1	16p13.3	2006-03-31	2006-03-31	2006-03-31	ENSG00000167930	ENSG00000167930			14163	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 9"	C16orf9			Standard	XM_005255622		Approved	DKFZP761D0211, FLJ32603	uc002cgf.3	Q9H0X4	OTTHUMG00000060728	ENST00000399932.3:c.876C>T	chr16.hg19:g.312457C>T		34.0	0.0		72.0	24.0	NM_032039	D3DU45|Q7L416|Q96FR1|Q96MC7|Q96S30	Silent	SNP	ENST00000399932.3	hg19	CCDS10402.1																																																																																			.	.		0.632	ITFG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134227.2	NM_032039		T	312457	C	T	312457	2	4	331	1	0	0	0	0	0	0	0	1	7880	900	32	3		3	ITFG3	16	312457	Silent	SNP	C	TCGA-QA-A7B7-01A-11D-A32G-10		312457	90042296	72	46251										
ZG16B	124220	hgsc.bcm.edu	37	chr16	2880717	2880717	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	atgtatggccctggaggaggCaagtatttcagcaccactga	12	9	1	1			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr16:2880717C>T	ENST00000382280.3	+	3	262	c.183C>T	c.(181-183)ggC>ggT	p.G61G	ZG16B_ENST00000572863.1_Silent_p.G31G	NM_145252.2	NP_660295.2	Q96DA0	ZG16B_HUMAN	zymogen granule protein 16B	61					retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|lung(2)|ovary(1)|prostate(1)	5						CTGGAGGAGGCAAGTATTTCA	0.522																																					p.G61G		Atlas-SNP	.											.	ZG16B	16	.	0			c.C183T						.						202	206	205					16																	2880717		1936	4140	6076	SO:0001819	synonymous_variant	124220	exon3			AGGAGGCAAGTAT	BC009722	CCDS10479.2	16p13.3	2014-02-12	2012-12-07		ENSG00000162078	ENSG00000162078			30456	protein-coding gene	gene with protein product	"jacalin-like lectin domain containing 2"		"zymogen granule protein 16 homolog B (rat)"			12477932	Standard	NM_145252		Approved	HRPE773, PRO1567, JCLN2	uc002cru.3	Q96DA0	OTTHUMG00000128933	ENST00000382280.3:c.183C>T	chr16.hg19:g.2880717C>T		87.0	0.0		119.0	22.0	NM_145252	A6NIY1|B2R4F6|Q6UW28	Silent	SNP	ENST00000382280.3	hg19	CCDS10479.2																																																																																			.	.		0.522	ZG16B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250912.1	NM_145252		T	2880717	C	T	2880717	2	4	331	1	0	0	0	0	0	0	0	1	17687	697	25	3		3	ZG16B	16	2880717	Silent	SNP	C	TCGA-QA-A7B7-01A-11D-A32G-10	2568260	2880717	87474036	73	46252										
MTSS1L	92154	hgsc.bcm.edu	37	chr16	70698047	70698047	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	aggcaccgtgggcgtcttcaCagggacgatgggcggccgga	18	11	2	0			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr16:70698047C>T	ENST00000338779.6	-	15	2051	c.1777G>A	c.(1777-1779)Gtg>Atg	p.V593M	FLJ00418_ENST00000597002.1_5'UTR	NM_138383.2	NP_612392.1	Q765P7	MTSSL_HUMAN	metastasis suppressor 1-like	593					filopodium assembly (GO:0046847)|signal transduction (GO:0007165)					breast(1)|central_nervous_system(2)|endometrium(1)|liver(1)|lung(1)|skin(1)	7						GGCGTCTTCACAGGGACGATG	0.716																																					p.V593M		Atlas-SNP	.											.	MTSS1L	22	.	0			c.G1777A						.						23	20	21					16																	70698047		2185	4262	6447	SO:0001583	missense	92154	exon15			TCTTCACAGGGAC		CCDS32476.1	16q22.1	2008-12-16				ENSG00000132613			25094	protein-coding gene	gene with protein product	"actin-bundling protein with BAIAP2 homology"					12477932	Standard	XM_006721335		Approved	ABBA-1, LOC92154	uc002ezj.3	Q765P7		ENST00000338779.6:c.1777G>A	chr16.hg19:g.70698047C>T	ENSP00000341171:p.Val593Met	36.0	0.0		27.0	19.0	NM_138383	A6NJI7|Q9BUA8	Missense_Mutation	SNP	ENST00000338779.6	hg19	CCDS32476.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.615168	0.87359	.	.	ENSG00000132613	ENST00000338779	T	0.39229	1.09	4.38	4.38	0.52667	.	0.000000	0.85682	D	0.000000	T	0.63224	0.2493	M	0.72894	2.215	0.50467	D	0.999879	D	0.89917	1.0	D	0.79784	0.993	T	0.65150	-0.6238	10	0.41790	T	0.15	-20.8792	16.5688	0.84606	0.0:1.0:0.0:0.0	.	593	Q765P7	MTSSL_HUMAN	M	593	ENSP00000341171:V593M	ENSP00000341171:V593M	V	-	1	0	MTSS1L	69255548	1.000000	0.71417	0.983000	0.44433	0.959000	0.62525	5.912000	0.69948	1.964000	0.57103	0.462000	0.41574	GTG	.	.		0.716	MTSS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434927.3	NM_138383		T	70698047	C	T	70698047	3	4	331	1	0	0	0	0	1	0	0	0	9972	478	17	3	470	3	MTSS1L	16	70698047	Missense_Mutation	SNP	C	TCGA-QA-A7B7-01A-11D-A32G-10	67817330	70698047	19656706	74	46253										
TP53	7157	hgsc.bcm.edu	37	chr17	7577534	7577534	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	gtgatgatggtgaggatgggCctccggttcatgccgcccat	15	10	1	3	rs28934571		TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr17:7577534C>A	ENST00000269305.4	-	7	936	c.747G>T	c.(745-747)agG>agT	p.R249S	TP53_ENST00000359597.4_Missense_Mutation_p.R249S|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Missense_Mutation_p.R249S|TP53_ENST00000455263.2_Missense_Mutation_p.R249S|TP53_ENST00000445888.2_Missense_Mutation_p.R249S|TP53_ENST00000420246.2_Missense_Mutation_p.R249S	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	249	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> G (in sporadic cancers; somatic mutation).|R -> I (in a sporadic cancer; somatic mutation).|R -> K (in sporadic cancers; somatic mutation).|R -> M (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:17224074}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> S (in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; dbSNP:rs28934571). {ECO:0000269|PubMed:1694291, ECO:0000269|PubMed:16959974}.|R -> T (in sporadic cancers; somatic mutation).|R -> W (in sporadic cancers; somatic mutation).|RP -> SA (in a sporadic cancer; somatic mutation).|RP -> SS (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R249S(348)|p.0?(8)|p.R249R(5)|p.?(5)|p.M246_P250delMNRRP(2)|p.R248_P250delRRP(1)|p.R249_P250delRP(1)|p.R249_P250insR(1)|p.R249_P250>SS(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*14(1)|p.R249_T256delRPILTIIT(1)|p.P250fs*14(1)|p.R249_I251delRPI(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TGAGGATGGGCCTCCGGTTCA	0.572		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.R249S	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,right_lower_lobe,carcinoma,-2,1	TP53	33396	.	378	Substitution - Missense(348)|Deletion - In frame(8)|Whole gene deletion(8)|Unknown(5)|Substitution - coding silent(5)|Insertion - Frameshift(1)|Insertion - In frame(1)|Deletion - Frameshift(1)|Complex - compound substitution(1)	liver(240)|lung(44)|upper_aerodigestive_tract(12)|breast(12)|central_nervous_system(10)|stomach(7)|ovary(6)|prostate(6)|cervix(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(5)|biliary_tract(5)|urinary_tract(5)|bone(4)|endometrium(3)|oesophagus(3)|skin(2)|peritoneum(1)|kidney(1)|salivary_gland(1)|pancreas(1)	c.G747T						.						155	113	127					17																	7577534		2203	4300	6503	SO:0001583	missense	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GATGGGCCTCCGG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.747G>T	chr17.hg19:g.7577534C>A	ENSP00000269305:p.Arg249Ser	74.0	0.0		51.0	39.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.344264	0.61073	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D;D	0.99865	-7.29;-7.29;-7.29;-7.29;-7.29;-7.29;-7.29	4.62	-0.0929	0.13654	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99792	0.9912	M	0.92367	3.3	0.50039	D	0.999848	D;D;D;D;D	0.89917	0.996;0.996;0.997;0.99;1.0	D;D;D;D;D	0.79108	0.968;0.966;0.981;0.955;0.992	D	0.98720	1.0708	10	0.72032	D	0.01	-3.0658	3.2479	0.06803	0.1392:0.5551:0.1362:0.1695	rs28934571	249;249;249;249;249	P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;P53_HUMAN;.;.	S	249;249;249;249;249;249;238;117	ENSP00000410739:R249S;ENSP00000352610:R249S;ENSP00000269305:R249S;ENSP00000398846:R249S;ENSP00000391127:R249S;ENSP00000391478:R249S;ENSP00000425104:R117S	ENSP00000269305:R249S	R	-	3	2	TP53	7518259	0.011000	0.17503	0.998000	0.56505	0.783000	0.44284	-1.379000	0.02554	0.253000	0.21552	0.462000	0.41574	AGG	.	.		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577534	C	A	7577534	3	1	331	1	0	0	0	0	1	0	0	0	16396	738	26	3	543	3	TP53	17	7577534	Missense_Mutation	SNP	C	TCGA-QA-A7B7-01A-11D-A32G-10		7577534	73617676	75	46254										
SLC35B1	10237	hgsc.bcm.edu	37	chr17	47784394	47784394	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	gttaaggcaaaggtgaacgtCtcctgcttggctccttcccc	10	13	1	1			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr17:47784394C>T	ENST00000240333.6	-	2	262	c.141G>A	c.(139-141)gaG>gaA	p.E47E	SLC35B1_ENST00000415270.2_Silent_p.E84E|RP11-613C6.2_ENST00000512720.1_RNA			P78383	S35B1_HUMAN	solute carrier family 35, member B1	47					transport (GO:0006810)|UDP-galactose transmembrane transport (GO:0072334)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	UDP-galactose transmembrane transporter activity (GO:0005459)			endometrium(1)|large_intestine(2)|lung(3)|urinary_tract(1)	7						AGGTGAACGTCTCCTGCTTGG	0.408																																					p.E47E		Atlas-SNP	.											.	SLC35B1	21	.	0			c.G141A						.						239	189	206					17																	47784394		2203	4300	6503	SO:0001819	synonymous_variant	10237	exon2			GAACGTCTCCTGC	D16978	CCDS11552.1, CCDS11552.2	17q21.32	2013-05-22			ENSG00000121073	ENSG00000121073		"Solute carriers"	20798	protein-coding gene	gene with protein product		610790				9010752	Standard	NM_005827		Approved	UGTREL1	uc002iph.1	P78383	OTTHUMG00000161638	ENST00000240333.6:c.141G>A	chr17.hg19:g.47784394C>T		51.0	0.0		68.0	31.0	NM_005827	B4DEC4|J3KQV4|Q96EW7	Silent	SNP	ENST00000240333.6	hg19	CCDS11552.1																																																																																			.	.		0.408	SLC35B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365564.2	NM_005827		T	47784394	C	T	47784394	2	4	331	1	0	0	0	0	0	0	0	1	14590	912	32	3		3	SLC35B1	17	47784394	Silent	SNP	C	TCGA-QA-A7B7-01A-11D-A32G-10	40206860	47784394	33410816	76	46255										
KLHL14	57565	hgsc.bcm.edu	37	chr18	30257147	30257147	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	gacacataccatactccagcTgtagcctcccacaaggtaaa	6	14	0	0			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr18:30257147T>C	ENST00000359358.4	-	8	2173	c.1735A>G	c.(1735-1737)Agc>Ggc	p.S579G		NM_020805.1	NP_065856.1	Q9P2G3	KLH14_HUMAN	kelch-like family member 14	579						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(20)|ovary(2)	31						ATACTCCAGCTGTAGCCTCCC	0.463																																					p.S579G		Atlas-SNP	.											.	KLHL14	92	.	0			c.A1735G						.						215	179	191					18																	30257147		2203	4300	6503	SO:0001583	missense	57565	exon8			TCCAGCTGTAGCC	AB037805	CCDS32813.1	18q12.1	2013-10-15	2013-01-30		ENSG00000197705	ENSG00000197705		"Kelch-like", "BTB/POZ domain containing"	29266	protein-coding gene	gene with protein product	"printor"	613772	"kelch-like 14 (Drosophila)"			10718198, 19535332	Standard	NM_020805		Approved	KIAA1384	uc002kxm.1	Q9P2G3	OTTHUMG00000179819	ENST00000359358.4:c.1735A>G	chr18.hg19:g.30257147T>C	ENSP00000352314:p.Ser579Gly	103.0	0.0		142.0	61.0	NM_020805	A6NNW1|B4DHA0|Q8WU41	Missense_Mutation	SNP	ENST00000359358.4	hg19	CCDS32813.1	.	.	.	.	.	.	.	.	.	.	T	27.1	4.798844	0.90538	.	.	ENSG00000197705	ENST00000359358	T	0.78707	-1.2	5.73	5.73	0.89815	Galactose oxidase, beta-propeller (1);	0.000000	0.85682	D	0.000000	D	0.82277	0.5002	L	0.28608	0.87	0.80722	D	1	D	0.53885	0.963	D	0.69824	0.966	D	0.84332	0.0522	10	0.72032	D	0.01	.	16.3197	0.82945	0.0:0.0:0.0:1.0	.	579	Q9P2G3	KLH14_HUMAN	G	579	ENSP00000352314:S579G	ENSP00000352314:S579G	S	-	1	0	KLHL14	28511145	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.648000	0.83479	2.302000	0.77476	0.533000	0.62120	AGC	.	.		0.463	KLHL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448376.1			C	30257147	T	C	30257147	3	2	331	1	0	0	0	0	1	0	0	0	8379	1580	55	2	159	2	KLHL14	18	30257147	Missense_Mutation	SNP	T	TCGA-QA-A7B7-01A-11D-A32G-10		30257147	47820101	77	46256										
KCNG2	26251	hgsc.bcm.edu	37	chr18	77623988	77623988	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	ttccgcgacgagctggcctaCtggggcatcgacgaggcgcg	16	13	0	0			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr18:77623988C>A	ENST00000316249.3	+	1	321	c.321C>A	c.(319-321)taC>taA	p.Y107*		NM_012283.1	NP_036415.1	Q9UJ96	KCNG2_HUMAN	potassium voltage-gated channel, subfamily G, member 2	107					energy reserve metabolic process (GO:0006112)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of heart contraction (GO:0008016)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			breast(2)|endometrium(4)|lung(7)|skin(1)|upper_aerodigestive_tract(4)	18		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;6.92e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0244)		AGCTGGCCTACTGGGGCATCG	0.786																																					p.Y107X		Atlas-SNP	.											.	KCNG2	48	.	0			c.C321A						.						5	5	5					18																	77623988		1971	3882	5853	SO:0001587	stop_gained	26251	exon1			GGCCTACTGGGGC	AJ011021	CCDS12019.1	18q23	2011-07-05			ENSG00000178342	ENSG00000178342		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6249	protein-coding gene	gene with protein product		605696				10551266, 16382104	Standard	NM_012283		Approved	Kv6.2, KCNF2	uc010xfl.2	Q9UJ96	OTTHUMG00000044541	ENST00000316249.3:c.321C>A	chr18.hg19:g.77623988C>A	ENSP00000315654:p.Tyr107*	13.0	0.0		16.0	14.0	NM_012283		Nonsense_Mutation	SNP	ENST00000316249.3	hg19	CCDS12019.1	.	.	.	.	.	.	.	.	.	.	C	37	6.037401	0.97226	.	.	ENSG00000178342	ENST00000316249	.	.	.	3.77	1.89	0.25635	.	0.000000	0.64402	U	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.3085	0.32058	0.0:0.728:0.0:0.272	.	.	.	.	X	107	.	ENSP00000315654:Y107X	Y	+	3	2	KCNG2	75724976	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.797000	0.38804	0.585000	0.29608	0.478000	0.44815	TAC	.	.		0.786	KCNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103906.1	NM_012283		A	77623988	C	A	77623988	4	1	331	1	0	0	0	0	0	1	0	0	8037	576	20	3	323	3	KCNG2	18	77623988	Nonsense_Mutation	SNP	C	TCGA-QA-A7B7-01A-11D-A32G-10	47366841	77623988	453260	78	46257										
DPP9	91039	hgsc.bcm.edu	37	chr19	4695540	4695540	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	acgagctggagccactgctgGggccggtccaggaacatggc	16	12	0	0			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr19:4695540G>T	ENST00000598800.1	-	13	1621	c.1116C>A	c.(1114-1116)ccC>ccA	p.P372P	DPP9_ENST00000262960.9_Silent_p.P401P|DPP9_ENST00000594671.1_Silent_p.P372P|DPP9_ENST00000597849.1_Silent_p.P401P			Q86TI2	DPP9_HUMAN	dipeptidyl-peptidase 9	372						cytoplasm (GO:0005737)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|identical protein binding (GO:0042802)|serine-type peptidase activity (GO:0008236)			cervix(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00884)		GCCACTGCTGGGGCCGGTCCA	0.657																																					p.P401P		Atlas-SNP	.											.	DPP9	59	.	0			c.C1203A						.						8	10	9					19																	4695540		1989	4151	6140	SO:0001819	synonymous_variant	91039	exon12			CTGCTGGGGCCGG	AF452102	CCDS45928.1	19p13.3	2014-06-11	2006-01-12		ENSG00000142002	ENSG00000142002			18648	protein-coding gene	gene with protein product		608258	"dipeptidylpeptidase 9"				Standard	NM_139159		Approved		uc002mba.3	Q86TI2	OTTHUMG00000182040	ENST00000598800.1:c.1116C>A	chr19.hg19:g.4695540G>T		42.0	0.0		76.0	5.0	NM_139159	O75273|O75868|Q1ZZB8|Q6AI37|Q6UAL0|Q6ZMT2|Q6ZNJ5|Q8N2J7|Q8N3F5|Q8WXD8|Q96NT8|Q9BVR3	Silent	SNP	ENST00000598800.1	hg19																																																																																				.	.		0.657	DPP9-026	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000459343.2			T	4695540	G	T	4695540	2	4	331	1	0	0	0	0	0	0	0	1	4735	1219	43	3		3	DPP9	19	4695540	Silent	SNP	G	TCGA-QA-A7B7-01A-11D-A32G-10		4695540	54433443	79	46258										
C3	718	hgsc.bcm.edu	37	chr19	6714044	6714046	+	In_Frame_Del	DEL	GTA	GTA	-													0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	aggcccttctcgttatagatGtagtagaatttctctgtagg							TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	GTA	GTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr19:6714044_6714046delGTA	ENST00000245907.6	-	7	822_824	c.730_732delTAC	c.(730-732)tacdel	p.Y244del		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	244					complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	CGTTATAGATGTAGTAGAATTTC	0.616																																					p.244_245del		Atlas-Indel,Pindel	.											.	C3	192	.	0			c.731_733del						.																																			SO:0001651	inframe_deletion	718	exon7			.	J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"Complement system", "Endogenous ligands"	1318	protein-coding gene	gene with protein product	"C3a anaphylatoxin", "complement component C3a", "complement component C3b", "prepro-C3"	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.730_732delTAC	chr19.hg19:g.6714047_6714049delGTA	ENSP00000245907:p.Tyr244del	33.0	0.0		41.0	16.0	NM_000064	A7E236	In_Frame_Del	DEL	ENST00000245907.6	hg19	CCDS32883.1																																																																																			.	.		0.616	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064		-	6714046	GTA	-	6714044	7	5	331	1	0	1	0	1	0	0	0	0	2206	1372	48	0	4399	0	C3	19	6714044	In_Frame_Del	DEL	GTA	TCGA-QA-A7B7-01A-11D-A32G-10	2018504	6714044	52414939	80	46259										
ZNF708	7562	hgsc.bcm.edu	37	chr19	21476555	21476555	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	cttatgataagtaagagttgAggacttggtaaaggctttac	11	4	0	3			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr19:21476555A>C	ENST00000356929.3	-	4	1410	c.1213T>G	c.(1213-1215)Tca>Gca	p.S405A		NM_021269.2	NP_067092.2	P17019	ZN708_HUMAN	zinc finger protein 708	341					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|skin(2)|stomach(1)	32						GTAAGAGTTGAGGACTTGGTA	0.358																																					p.S405A		Atlas-SNP	.											.	ZNF708	66	.	0			c.T1213G						.						62	66	65					19																	21476555		2199	4297	6496	SO:0001583	missense	7562	exon4			GAGTTGAGGACTT	X52339	CCDS32980.1	19p12	2014-02-14	2006-08-22	2005-08-16	ENSG00000182141	ENSG00000182141		"Zinc fingers, C2H2-type", "-"	12945	protein-coding gene	gene with protein product			"zinc finger protein 15-like 1 (KOX 8)", "zinc finger protein 708", "zinc finger protein 708 (KOX8)"	ZNF15, ZNF15L1		2014798	Standard	NM_021269		Approved	KOX8	uc002npq.1	P17019	OTTHUMG00000182841	ENST00000356929.3:c.1213T>G	chr19.hg19:g.21476555A>C	ENSP00000349401:p.Ser405Ala	68.0	0.0		62.0	18.0	NM_021269	Q6ZMR0	Missense_Mutation	SNP	ENST00000356929.3	hg19	CCDS32980.1	.	.	.	.	.	.	.	.	.	.	.	6.100	0.386725	0.11524	.	.	ENSG00000182141	ENST00000356929	T	0.35605	1.3	1.05	-0.848	0.10727	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.33118	0.0852	L	0.55213	1.73	0.09310	N	1	P	0.45474	0.859	P	0.45610	0.487	T	0.24297	-1.0164	9	0.54805	T	0.06	.	4.4652	0.11685	0.548:0.0:0.0:0.4519	.	405	P17019	ZN708_HUMAN	A	405	ENSP00000349401:S405A	ENSP00000349401:S405A	S	-	1	0	ZNF708	21268395	0.001000	0.12720	0.013000	0.15412	0.013000	0.08279	0.357000	0.20199	0.408000	0.25621	0.397000	0.26171	TCA	.	.		0.358	ZNF708-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463953.1	NM_021269		C	21476555	A	C	21476555	3	2	331	1	0	0	0	0	1	0	0	0	18127	304	11	5	482	5	ZNF708	19	21476555	Missense_Mutation	SNP	A	TCGA-QA-A7B7-01A-11D-A32G-10	14762511	21476555	37652428	81	46260										
LRP3	4037	hgsc.bcm.edu	37	chr19	33696163	33696163	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	accccacagggaagctgggcCaggcatcctgccaggcagat	13	14	0	1			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr19:33696163C>T	ENST00000253193.7	+	5	689	c.487C>T	c.(487-489)Cag>Tag	p.Q163*	CTD-2540B15.13_ENST00000609744.1_RNA	NM_002333.3	NP_002324.2	O75074	LRP3_HUMAN	low density lipoprotein receptor-related protein 3	163					receptor-mediated endocytosis (GO:0006898)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|pancreas(2)	15	Esophageal squamous(110;0.137)					GAAGCTGGGCCAGGCATCCTG	0.662																																					p.Q163X		Atlas-SNP	.											.	LRP3	46	.	0			c.C487T						.						15	14	14					19																	33696163		2202	4298	6500	SO:0001587	stop_gained	4037	exon5			CTGGGCCAGGCAT	AB009462	CCDS12430.1	19q13.11	2013-05-30			ENSG00000130881	ENSG00000130881		"Low density lipoprotein receptors"	6695	protein-coding gene	gene with protein product		603159				9693042, 7959795	Standard	NM_002333		Approved	LRP-3, hLRp105	uc010edh.3	O75074	OTTHUMG00000180343	ENST00000253193.7:c.487C>T	chr19.hg19:g.33696163C>T	ENSP00000253193:p.Gln163*	27.0	0.0		38.0	20.0	NM_002333	B3KQD6|B4DKF2	Nonsense_Mutation	SNP	ENST00000253193.7	hg19	CCDS12430.1	.	.	.	.	.	.	.	.	.	.	C	33	5.242988	0.95272	.	.	ENSG00000130881	ENST00000431491;ENST00000253193	.	.	.	4.02	4.02	0.46733	.	0.075315	0.56097	D	0.000032	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.17832	T	0.49	-16.0617	15.328	0.74182	0.0:1.0:0.0:0.0	.	.	.	.	X	37;163	.	ENSP00000253193:Q163X	Q	+	1	0	LRP3	38388003	1.000000	0.71417	0.994000	0.49952	0.806000	0.45545	3.541000	0.53618	2.100000	0.63781	0.462000	0.41574	CAG	.	.		0.662	LRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450842.4			T	33696163	C	T	33696163	4	4	331	1	0	0	0	0	0	1	0	0	8967	595	21	3	505	3	LRP3	19	33696163	Nonsense_Mutation	SNP	C	TCGA-QA-A7B7-01A-11D-A32G-10	12219608	33696163	25432820	82	46261										
KIAA0355	9710	hgsc.bcm.edu	37	chr19	34839933	34839933	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	gctttcagggatggcctgcaCggtggctggtcgggtgctca	17	10	2	0	rs150651317		TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr19:34839933C>T	ENST00000299505.6	+	12	3573	c.2700C>T	c.(2698-2700)caC>caT	p.H900H	AC010504.2_ENST00000591311.1_RNA	NM_014686.3	NP_055501.2	O15063	K0355_HUMAN	KIAA0355	900										breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	41	Esophageal squamous(110;0.162)					ATGGCCTGCACGGTGGCTGGT	0.632																																					p.H900H		Atlas-SNP	.											.	KIAA0355	105	.	0			c.C2700T						.	C		1,4405	2.1+/-5.4	0,1,2202	78	70	73		2700	-0.5	0	19	dbSNP_134	73	0,8600		0,0,4300	no	coding-synonymous	KIAA0355	NM_014686.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		900/1071	34839933	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9710	exon12			CCTGCACGGTGGC		CCDS12436.1	19q13.12	2012-11-29			ENSG00000166398	ENSG00000166398			29016	protein-coding gene	gene with protein product						9205841	Standard	NM_014686		Approved		uc002nvd.4	O15063	OTTHUMG00000180505	ENST00000299505.6:c.2700C>T	chr19.hg19:g.34839933C>T		61.0	0.0		75.0	35.0	NM_014686	Q2M3W4	Silent	SNP	ENST00000299505.6	hg19	CCDS12436.1																																																																																			.	C|1.000;T|0.000		0.632	KIAA0355-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451678.4	NM_014686		T	34839933	C	T	34839933	2	4	331	1	0	0	0	0	0	0	0	1	8179	535	19	1		1	KIAA0355	19	34839933	Silent	SNP	C	TCGA-QA-A7B7-01A-11D-A32G-10	1143770	34839933	24289050	83	46262										
LRRC4B	94030	hgsc.bcm.edu	37	chr19	51021678	51021678	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	ccatgcacgtgtactggcccGtgtcctgcacggtgacgttg	13	13	0	1			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr19:51021678G>A	ENST00000599957.1	-	3	1489	c.1292C>T	c.(1291-1293)aCg>aTg	p.T431M	LRRC4B_ENST00000389201.3_Missense_Mutation_p.T431M			Q9NT99	LRC4B_HUMAN	leucine rich repeat containing 4B	431	Ig-like C2-type.				positive regulation of synapse assembly (GO:0051965)	cell junction (GO:0030054)|cerebellar mossy fiber (GO:0044300)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|liver(1)|lung(11)|prostate(4)|skin(1)|urinary_tract(1)	30		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00284)|GBM - Glioblastoma multiforme(134;0.0188)		GTACTGGCCCGTGTCCTGCAC	0.677																																					p.T431M		Atlas-SNP	.											LRRC4B,NS,carcinoma,0,1	LRRC4B	89	.	0			c.C1292T						.						61	69	66					19																	51021678		2191	4271	6462	SO:0001583	missense	94030	exon3			TGGCCCGTGTCCT	BC032460	CCDS42595.1	19q13.33	2014-01-30	2004-06-14	2004-06-16	ENSG00000131409	ENSG00000131409		"Immunoglobulin superfamily / I-set domain containing", "Endogenous ligands"	25042	protein-coding gene	gene with protein product	"netrin-G3 ligand"		"leucine-rich repeats and immunoglobulin-like domains 4"	LRIG4		11441184	Standard	NM_001080457		Approved	DKFZp761A179, HSM	uc002pss.3	Q9NT99		ENST00000599957.1:c.1292C>T	chr19.hg19:g.51021678G>A	ENSP00000471502:p.Thr431Met	47.0	0.0		49.0	23.0	NM_001080457	Q3ZCQ4|Q58F20	Missense_Mutation	SNP	ENST00000599957.1	hg19	CCDS42595.1	.	.	.	.	.	.	.	.	.	.	G	18.97	3.735436	0.69189	.	.	ENSG00000131409	ENST00000389201	T	0.28895	1.59	3.45	3.45	0.39498	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	U	0.000001	T	0.31857	0.0810	N	0.04686	-0.185	0.54753	D	0.999985	D	0.89917	1.0	D	0.72075	0.976	T	0.42378	-0.9455	10	0.72032	D	0.01	.	12.7732	0.57434	0.0:0.0:1.0:0.0	.	431	Q9NT99	LRC4B_HUMAN	M	431	ENSP00000373853:T431M	ENSP00000373853:T431M	T	-	2	0	LRRC4B	55713490	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.577000	0.98196	1.934000	0.56057	0.462000	0.41574	ACG	.	.		0.677	LRRC4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464907.1	NM_001080457		A	51021678	G	A	51021678	3	1	331	1	0	0	0	0	1	0	0	0	9016	1145	40	1	853	1	LRRC4B	19	51021678	Missense_Mutation	SNP	G	TCGA-QA-A7B7-01A-11D-A32G-10	16181745	51021678	8107305	84	46263										
SHANK1	50944	hgsc.bcm.edu	37	chr19	51169904	51169904	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	tctcggagtcccccgctgggGccaggccgcaggcctccgct	14	18	1	0			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr19:51169904G>T	ENST00000293441.1	-	22	5331	c.5313C>A	c.(5311-5313)ggC>ggA	p.G1771G	SHANK1_ENST00000359082.3_Silent_p.G1762G|SHANK1_ENST00000391814.1_Silent_p.G1779G|SYT3_ENST00000544769.1_Intron|SHANK1_ENST00000391813.1_Silent_p.G1158G	NM_016148.2	NP_057232.2	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	1771					adult behavior (GO:0030534)|associative learning (GO:0008306)|cytoskeletal anchoring at plasma membrane (GO:0007016)|dendritic spine morphogenesis (GO:0060997)|determination of affect (GO:0050894)|habituation (GO:0046959)|long-term memory (GO:0007616)|negative regulation of actin filament bundle assembly (GO:0032232)|neuromuscular process controlling balance (GO:0050885)|olfactory behavior (GO:0042048)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|protein complex assembly (GO:0006461)|protein localization to synapse (GO:0035418)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|righting reflex (GO:0060013)|social behavior (GO:0035176)|synapse maturation (GO:0060074)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|excitatory synapse (GO:0060076)|intracellular (GO:0005622)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ankyrin repeat binding (GO:0071532)|GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|somatostatin receptor binding (GO:0031877)			breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	64		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)		CCCCGCTGGGGCCAGGCCGCA	0.706																																					p.G1771G		Atlas-SNP	.											.	SHANK1	210	.	0			c.C5313A						.						4	6	5					19																	51169904		1834	3755	5589	SO:0001819	synonymous_variant	50944	exon22			GCTGGGGCCAGGC	AF163302	CCDS12799.1	19q13.3	2013-01-10			ENSG00000161681	ENSG00000161681		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	15474	protein-coding gene	gene with protein product	"somatostatin receptor-interacting protein"	604999				10551867	Standard	NM_016148		Approved	SSTRIP, SPANK-1, synamon	uc002psx.1	Q9Y566	OTTHUMG00000137380	ENST00000293441.1:c.5313C>A	chr19.hg19:g.51169904G>T		41.0	0.0		27.0	12.0	NM_016148	A8MXP5|B7WNY6|Q9NYW9	Silent	SNP	ENST00000293441.1	hg19	CCDS12799.1																																																																																			.	.		0.706	SHANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268071.1	NM_016148		T	51169904	G	T	51169904	2	4	331	1	0	0	0	0	0	0	0	1	14279	1190	42	3		3	SHANK1	19	51169904	Silent	SNP	G	TCGA-QA-A7B7-01A-11D-A32G-10	148226	51169904	7959079	85	46264										
PLCB1	23236	hgsc.bcm.edu	37	chr20	8113326	8113326	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	gggctcaacccggagtgcacGccttgcaactcaagcccgtg	12	15	2	0	rs150241349		TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr20:8113326G>T	ENST00000338037.6	+	1	55	c.28G>T	c.(28-30)Gcc>Tcc	p.A10S	PLCB1_ENST00000378641.3_Missense_Mutation_p.A10S|PLCB1_ENST00000378637.2_Missense_Mutation_p.A10S	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	10				MAGAQPGVHALQLKPVCVSDSLKKGTKFVKWDDD -> MGS LQGIATKILIRILSDALIRKETDLKS (in Ref. 2; AAF86613). {ECO:0000305}.	activation of meiosis involved in egg activation (GO:0060466)|cerebral cortex development (GO:0021987)|fat cell differentiation (GO:0045444)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G2/M transition of mitotic cell cycle (GO:0000086)|glutamate receptor signaling pathway (GO:0007215)|inositol phosphate metabolic process (GO:0043647)|insulin-like growth factor receptor signaling pathway (GO:0048009)|interleukin-1-mediated signaling pathway (GO:0070498)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-15-mediated signaling pathway (GO:0035723)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|memory (GO:0007613)|negative regulation of monocyte extravasation (GO:2000438)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of CD24 biosynthetic process (GO:2000560)|positive regulation of developmental growth (GO:0048639)|positive regulation of embryonic development (GO:0040019)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of GTPase activity (GO:0043547)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fertilization (GO:0080154)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						CGGAGTGCACGCCTTGCAACT	0.697																																					p.A10S		Atlas-SNP	.											.	PLCB1	394	.	0			c.G28T						.		SER/ALA,SER/ALA	0,4406		0,0,2203	40	33	35		28,28	4.8	1	20	dbSNP_134	35	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	PLCB1	NM_015192.2,NM_182734.1	99,99	0,3,6500	TT,TG,GG		0.0349,0.0,0.0231	benign,benign	10/1217,10/1174	8113326	3,13003	2203	4300	6503	SO:0001583	missense	23236	exon1			GTGCACGCCTTGC	AB011153	CCDS13102.1, CCDS13103.1	20p12	2008-03-18			ENSG00000182621	ENSG00000182621	3.1.4.11		15917	protein-coding gene	gene with protein product		607120				10760467, 11118617	Standard	NM_015192		Approved	KIAA0581, PLC-I, PLC154	uc002wnb.4	Q9NQ66	OTTHUMG00000031849	ENST00000338037.6:c.28G>T	chr20.hg19:g.8113326G>T	ENSP00000338185:p.Ala10Ser	131.0	0.0		111.0	55.0	NM_015192	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Missense_Mutation	SNP	ENST00000338037.6	hg19	CCDS13102.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.085057	0.76642	0.0	3.49E-4	ENSG00000182621	ENST00000378641;ENST00000338037;ENST00000378637;ENST00000404098	T;T;T;T	0.46063	2.2;2.19;2.2;0.88	4.82	4.82	0.62117	.	0.188937	0.34555	N	0.003873	T	0.57184	0.2036	L	0.43923	1.385	0.49483	D	0.999799	P;D;D	0.89917	0.823;1.0;0.998	B;D;D	0.87578	0.219;0.998;0.995	T	0.53287	-0.8460	10	0.33940	T	0.23	.	17.8576	0.88771	0.0:0.0:1.0:0.0	.	10;10;9	Q9NQ66;Q9NQ66-2;B1AK73	PLCB1_HUMAN;.;.	S	10;10;10;9	ENSP00000367908:A10S;ENSP00000338185:A10S;ENSP00000367904:A10S;ENSP00000384001:A9S	ENSP00000338185:A10S	A	+	1	0	PLCB1	8061326	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.182000	0.89698	2.378000	0.81104	0.558000	0.71614	GCC	.	G|1.000;T|0.000		0.697	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3			T	8113326	G	T	8113326	3	4	331	1	0	0	0	0	1	0	0	0	12036	1087	38	1	30	1	PLCB1	20	8113326	Missense_Mutation	SNP	G	TCGA-QA-A7B7-01A-11D-A32G-10		8113326	54912194	86	46265										
C21orf63	59271	hgsc.bcm.edu	37	chr21	33887198	33887198	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	ccctcacactgtgcgccctgGtcatcagagagtcctgtgcc	10	16	3	1			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr21:33887198G>T	ENST00000300255.2	+	8	1497	c.1024G>T	c.(1024-1026)Gtc>Ttc	p.V342F	EVA1C_ENST00000382699.3_Missense_Mutation_p.V339F|EVA1C_ENST00000401402.3_Missense_Mutation_p.V294F|EVA1C_ENST00000485488.1_3'UTR	NM_058187.3	NP_478067.2	P58658	EVA1C_HUMAN	eva-1 homolog C (C. elegans)	342						integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)										GTGCGCCCTGGTCATCAGAGA	0.622																																					p.V342F		Atlas-SNP	.											.	.	.	.	0			c.G1024T						.						56	54	55					21																	33887198		2203	4300	6503	SO:0001583	missense	59271	exon8			GCCCTGGTCATCA	AF358258	CCDS13614.1, CCDS68186.1	21q22.11	2012-11-05	2012-11-05	2012-11-05	ENSG00000166979	ENSG00000166979			13239	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 64", "chromosome 21 open reading frame 63", "family with sequence similarity 176, member C"	C21orf64, C21orf63, FAM176C		11707072, 19470522	Standard	NM_058187		Approved	B18, PRED34, B19	uc002ypr.1	P58658	OTTHUMG00000064922	ENST00000300255.2:c.1024G>T	chr21.hg19:g.33887198G>T	ENSP00000300255:p.Val342Phe	44.0	0.0		54.0	33.0	NM_058187	A6ND58|Q8IXZ0	Missense_Mutation	SNP	ENST00000300255.2	hg19	CCDS13614.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.973029	0.74246	.	.	ENSG00000166979	ENST00000300255;ENST00000401402;ENST00000382699	T;T;T	0.59772	0.24;0.24;0.24	5.75	5.75	0.90469	.	0.124635	0.56097	D	0.000031	T	0.80864	0.4705	M	0.87456	2.885	0.50813	D	0.999896	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.983	T	0.82948	-0.0204	10	0.66056	D	0.02	-9.0884	19.9428	0.97171	0.0:0.0:1.0:0.0	.	339;342	A6ND58;P58658	.;CU063_HUMAN	F	342;294;339	ENSP00000300255:V342F;ENSP00000384594:V294F;ENSP00000372146:V339F	ENSP00000300255:V342F	V	+	1	0	C21orf63	32809069	1.000000	0.71417	0.988000	0.46212	0.616000	0.37450	6.902000	0.75699	2.704000	0.92352	0.655000	0.94253	GTC	.	.		0.622	EVA1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139403.1	NM_058187		T	33887198	G	T	33887198	3	4	331	1	0	0	0	0	1	0	0	0	2133	1261	44	3	1054	3	C21orf63	21	33887198	Missense_Mutation	SNP	G	TCGA-QA-A7B7-01A-11D-A32G-10		33887198	14242697	87	46266										
PDE9A	5152	hgsc.bcm.edu	37	chr21	44117597	44117597	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	aaggagtcatgggcgtcccaCcaggtgaatacttgcatgtt	12	9	1	1			TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr21:44117597C>T	ENST00000291539.6	+	4	278				PDE9A_ENST00000398232.3_Intron|PDE9A_ENST00000398225.3_Intron|PDE9A_ENST00000398224.3_Intron|PDE9A_ENST00000398227.3_Intron|PDE9A_ENST00000380328.2_Silent_p.H97H|PDE9A_ENST00000539837.1_Intron|PDE9A_ENST00000335512.4_Intron|PDE9A_ENST00000328862.6_Intron|PDE9A_ENST00000349112.3_Intron|PDE9A_ENST00000335440.6_Intron|PDE9A_ENST00000398234.3_Intron|PDE9A_ENST00000398236.3_Intron|PDE9A_ENST00000470987.1_3'UTR|PDE9A_ENST00000398229.3_Intron	NM_002606.2	NP_002597.1	O76083	PDE9A_HUMAN	phosphodiesterase 9A						blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|metabolic process (GO:0008152)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|large_intestine(6)|lung(8)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Caffeine(DB00201)	GGGCGTCCCACCAGGTGAATA	0.418																																					p.H97H		Atlas-SNP	.											.	PDE9A	69	.	0			c.C291T						.						283	245	258					21																	44117597		2203	4300	6503	SO:0001627	intron_variant	5152	exon4			GTCCCACCAGGTG	AF048837	CCDS13690.1, CCDS33567.1, CCDS33568.1, CCDS33569.1, CCDS33570.1, CCDS33571.1, CCDS42941.1, CCDS42942.1, CCDS42943.1, CCDS42944.1, CCDS42945.1, CCDS42946.1, CCDS42947.1	21q22.3	2005-11-29			ENSG00000160191	ENSG00000160191	3.1.4.17	"Phosphodiesterases"	8795	protein-coding gene	gene with protein product		602973				9624146	Standard	NM_001001584		Approved		uc002zbm.3	O76083	OTTHUMG00000086825	ENST00000291539.6:c.219-1481C>T	chr21.hg19:g.44117597C>T		199.0	0.0		249.0	68.0	NM_001001570	B2RBI5|B4DFI5|D3DSJ8|D3DSJ9|O75490|O75491|O95225|Q53Y40|Q5QD39|Q86SF7|Q86SI6|Q86SJ3|Q86WN3|Q86WN4|Q86WN5|Q86WN6|Q86WN7|Q86WN8|Q86WN9|Q86WP0	Silent	SNP	ENST00000291539.6	hg19	CCDS13690.1																																																																																			.	.		0.418	PDE9A-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195466.1			T	44117597	C	T	44117597	1	4	331	0	1	0	0	0	0	0	0	0	11664	506	18	3		3	PDE9A	21	44117597	Intron	SNP	C	TCGA-QA-A7B7-01A-11D-A32G-10	10230399	44117597	4012298	88	46267										
KRTAP10-7	386675	hgsc.bcm.edu	37	chr21	46021011	46021012	+	In_Frame_Ins	INS	-	-	TCTGCTGCGTGCCCA													0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	gcaggcctgctgtgtgcccaINStctgctgcaagcctgtctgc					rs7283052		TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chr21:46021011_46021012insTCTGCTGCGTGCCCA	ENST00000380102.2	+	1	515_516	c.490_491insTCTGCTGCGTGCCCA	c.(490-492)atc>aTCTGCTGCGTGCCCAtc	p.164_164I>ICCVPI	TSPEAR_ENST00000323084.4_Intron	NM_198689.2	NP_941962.1	P60409	KR107_HUMAN	keratin associated protein 10-7	164	30 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)		p.I164V(1)		breast(1)|large_intestine(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8						CTGTGTGCCCATCTGCTGCAAG	0.614																																					p.I159delinsICCVPI		Pindel	.											KRTAP10-7,trunk,malignant_melanoma,0,1	KRTAP10-7	41	.	1	Substitution - Missense(1)	skin(1)	c.475_476insTCTGCTGCGTGCCCA						.																																			SO:0001652	inframe_insertion	386675	exon2			.	AJ566385	CCDS74803.1	21q22.3	2014-04-10			ENSG00000205441	ENSG00000272804		"Keratin associated proteins"	22970	protein-coding gene	gene with protein product				KRTAP18-7			Standard	NM_198689		Approved	KAP10.7, KAP18.7	uc002zfn.4	P60409	OTTHUMG00000188307	Exception_encountered	chr21.hg19:g.46021011_46021012insTCTGCTGCGTGCCCA	ENSP00000369445:p.CysCysValProIle164dup	84.0	0.0		107.0	13.0	NM_198689	Q0VDJ8|Q70LJ2	In_Frame_Ins	INS	ENST00000380102.2	hg19																																																																																				.	.		0.614	KRTAP10-7-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000128038.1	NM_198689		TCTGCTGCGTGCCCA	46021012	-	TCTGCTGCGTGCCCA	46021011	7	5	331	1	0	1	1	0	0	0	0	0	8523	217	8	0	481	0	KRTAP10-7	21	46021011	In_Frame_Ins	INS	-	TCGA-QA-A7B7-01A-11D-A32G-10	1903414	46021011	2108884	89	46268										
AR	367	hgsc.bcm.edu	37	chrX	66765176	66765176	+	Missense_Mutation	SNP	A	A	T													0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	gctgcagcagcagcagcagcAgcagcagcagcagcagcagc					rs62636527		TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chrX:66765176A>T	ENST00000374690.3	+	1	712	c.188A>T	c.(187-189)cAg>cTg	p.Q63L	AR_ENST00000396044.3_Missense_Mutation_p.Q63L|AR_ENST00000504326.1_Missense_Mutation_p.Q63L|AR_ENST00000513847.1_3'UTR	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	63	Gln-rich.|Modulating.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	cagcagcagcagcagcagcag	0.672									Androgen Insensitivity Syndrome																												p.Q63L		Atlas-SNP	.											.	AR	249	.	0			c.A188T						.						5	8	7					X																	66765176		1640	3236	4876	SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	AGCAGCAGCAGCA	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.188A>T	chrX.hg19:g.66765176A>T	ENSP00000363822:p.Gln63Leu	19.0	0.0		39.0	8.0	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	hg19	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	a	11.08	1.532203	0.27387	.	.	ENSG00000169083	ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	T;T;T	0.78246	-1.16;-1.16;-1.16	.	.	.	.	0.479323	0.15343	U	0.267412	T	0.62624	0.2443	N	0.19112	0.55	0.09310	N	0.999992	P;D;.	0.58268	0.755;0.982;.	B;P;.	0.48627	0.089;0.584;.	T	0.56408	-0.7984	8	0.17832	T	0.49	.	.	.	.	rs62636527	63;63;61	E7EVX6;D3YPQ2;P10275	.;.;ANDR_HUMAN	L	63	ENSP00000363822:Q63L;ENSP00000421155:Q63L;ENSP00000379359:Q63L	ENSP00000363822:Q63L	Q	+	2	0	AR	66681901	0.810000	0.29049	0.871000	0.34182	0.555000	0.35460	1.078000	0.30754	0.000000	0.14550	0.000000	0.15137	CAG	.	A|0.982;T|0.018		0.672	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		T	66765176	A	T	66765176	3	4	331	1	0	0	0	0	1	0	0	0	836	188	7	4	190	4	AR	23	66765176	Missense_Mutation	SNP	A	TCGA-QA-A7B7-01A-11D-A32G-10		66765176	88505384	90	46269	246	2								
AR	367	hgsc.bcm.edu	37	chrX	66765179	66765179	+	Missense_Mutation	SNP	A	A	T													0.0449438202247191	4	1	1.15408415841584	0	1.42041127189642	0.0476190476190476	0.422902494331066	0	gcagcagcagcagcagcagcAgcagcagcagcagcagcagc							TCGA-QA-A7B7-01A-11D-A32G-10	TCGA-QA-A7B7-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5e551b27-70d1-46fd-9a37-83d2cecac02d	6f59797f-d0a5-43b4-ae29-7f21022909d2	g.chrX:66765179A>T	ENST00000374690.3	+	1	715	c.191A>T	c.(190-192)cAg>cTg	p.Q64L	AR_ENST00000396044.3_Missense_Mutation_p.Q64L|AR_ENST00000504326.1_Missense_Mutation_p.Q64L|AR_ENST00000513847.1_3'UTR	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	64	Gln-rich.|Modulating.|Poly-Gln.		Q -> R (in prostate cancer).		androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	cagcagcagcagcagcagcag	0.677									Androgen Insensitivity Syndrome																												p.Q64L		Atlas-SNP	.											.	AR	249	.	0			c.A191T						.						4	8	7					X																	66765179		1590	3143	4733	SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	AGCAGCAGCAGCA	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.191A>T	chrX.hg19:g.66765179A>T	ENSP00000363822:p.Gln64Leu	19.0	0.0		37.0	10.0	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	hg19	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	a	11.28	1.591655	0.28357	.	.	ENSG00000169083	ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	T;T;T	0.67865	-0.29;-0.29;-0.29	.	.	.	.	1.847110	0.03494	N	0.217131	T	0.56124	0.1964	N	0.19112	0.55	0.09310	N	0.999991	P;D;.	0.58268	0.755;0.982;.	B;P;.	0.48627	0.089;0.584;.	T	0.50381	-0.8835	8	0.38643	T	0.18	.	.	.	.	.	64;64;62	E7EVX6;D3YPQ2;P10275	.;.;ANDR_HUMAN	L	64	ENSP00000363822:Q64L;ENSP00000421155:Q64L;ENSP00000379359:Q64L	ENSP00000363822:Q64L	Q	+	2	0	AR	66681904	0.024000	0.19004	0.883000	0.34634	0.574000	0.36063	-0.145000	0.10265	0.000000	0.14550	0.000000	0.15137	CAG	.	.		0.677	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		T	66765179	A	T	66765179	3	4	331	1	0	0	0	0	1	0	0	0	836	188	7	4	193	4	AR	23	66765179	Missense_Mutation	SNP	A	TCGA-QA-A7B7-01A-11D-A32G-10	3	66765179	88505381	91	46270	246	2								
PER3	8863	hgsc.bcm.edu	37	chr1	7887481	7887481	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	ccccggaactgcaccggaagGcctgcatgggctgcccttgt	13	15	0	0			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr1:7887481G>A	ENST00000361923.2	+	17	2643	c.2468G>A	c.(2467-2469)gGc>gAc	p.G823D	RP3-467L1.4_ENST00000451646.1_RNA|PER3_ENST00000377532.3_Missense_Mutation_p.G831D	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	823	Pro-rich.				circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		GCACCGGAAGGCCTGCATGGG	0.607																																					p.G823D		Atlas-SNP	.											.	PER3	95	.	0			c.G2468A						.						89	90	89					1																	7887481		2203	4300	6503	SO:0001583	missense	8863	exon17			CGGAAGGCCTGCA	BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"period (Drosophila) homolog 3", "period homolog 3 (Drosophila)"			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.2468G>A	chr1.hg19:g.7887481G>A	ENSP00000355031:p.Gly823Asp	101.0	0.0		100.0	38.0	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	hg19	CCDS89.1	.	.	.	.	.	.	.	.	.	.	G	10.41	1.343053	0.24339	.	.	ENSG00000049246	ENST00000377532;ENST00000361923;ENST00000539773	T;T	0.09817	2.95;2.94	4.04	-1.84	0.07809	.	2.607050	0.00945	N	0.002889	T	0.04003	0.0112	N	0.08118	0	0.09310	N	1	B;B;B;B	0.31730	0.112;0.337;0.082;0.112	B;B;B;B	0.25759	0.039;0.063;0.037;0.039	T	0.19353	-1.0308	10	0.12103	T	0.63	.	0.4408	0.00486	0.2089:0.2182:0.3026:0.2703	.	823;831;831;823	A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;PER3_HUMAN	D	831;823;34	ENSP00000366755:G831D;ENSP00000355031:G823D	ENSP00000355031:G823D	G	+	2	0	PER3	7810068	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.443000	0.21644	-0.197000	0.10350	-1.157000	0.01802	GGC	.	.		0.607	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831		A	7887481	G	A	7887481	3	1	332	1	0	0	0	0	1	0	0	0	11740	1203	42	3	2534	3	PER3	1	7887481	Missense_Mutation	SNP	G	TCGA-RC-A6M3-01A-11D-A32G-10		7887481	241363140	1	46271										
EIF4G3	8672	hgsc.bcm.edu	37	chr1	21276594	21276594	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	ggctgtgctcggggacctggCtgggcagctgctgggatttg	19	9	0	0			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr1:21276594C>T	ENST00000264211.8	-	7	751	c.557G>A	c.(556-558)aGc>aAc	p.S186N	EIF4G3_ENST00000374937.3_Missense_Mutation_p.S192N|EIF4G3_ENST00000374935.3_Missense_Mutation_p.S186N|EIF4G3_ENST00000602326.1_Missense_Mutation_p.S192N|EIF4G3_ENST00000356916.3_Missense_Mutation_p.S197N|EIF4G3_ENST00000536266.1_Intron|EIF4G3_ENST00000400422.1_Missense_Mutation_p.S186N|EIF4G3_ENST00000374927.4_Missense_Mutation_p.S186N	NM_003760.4	NP_003751.2	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4 gamma, 3	186					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of meiosis I (GO:0060903)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|regulation of translational initiation (GO:0006446)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(18)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(1)|urinary_tract(3)	70		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		GGGGACCTGGCTGGGCAGCTG	0.532																																					p.S197N		Atlas-SNP	.											.	EIF4G3	300	.	0			c.G590A						.						46	47	47					1																	21276594		2203	4300	6503	SO:0001583	missense	8672	exon13			ACCTGGCTGGGCA	AF012072	CCDS214.1, CCDS55580.1, CCDS59192.1, CCDS72723.1	1p36.12	2008-02-05			ENSG00000075151	ENSG00000075151			3298	protein-coding gene	gene with protein product		603929				9418880	Standard	NM_001198801		Approved	eIF4GII	uc001bef.3	O43432	OTTHUMG00000002624	ENST00000264211.8:c.557G>A	chr1.hg19:g.21276594C>T	ENSP00000264211:p.Ser186Asn	27.0	0.0		57.0	14.0	NM_001198803	B9EGQ7|Q15597|Q504Z1|Q5SWC3|Q8NEN1	Missense_Mutation	SNP	ENST00000264211.8	hg19	CCDS214.1	.	.	.	.	.	.	.	.	.	.	C	16.90	3.249850	0.59212	.	.	ENSG00000075151	ENST00000264211;ENST00000400415;ENST00000400422;ENST00000374935;ENST00000374937;ENST00000356916;ENST00000374927;ENST00000537059;ENST00000438975	T;T;T;T;T;T	0.23348	1.91;1.91;1.91;1.91;1.91;1.91	5.85	5.85	0.93711	.	0.402206	0.31922	N	0.006859	T	0.32102	0.0818	N	0.08118	0	0.80722	D	1	D;D;D;D;D;D	0.69078	0.997;0.995;0.993;0.996;0.993;0.997	D;D;D;D;D;D	0.78314	0.991;0.966;0.968;0.986;0.953;0.986	T	0.25745	-1.0123	10	0.19147	T	0.46	-9.7486	20.1663	0.98152	0.0:1.0:0.0:0.0	.	186;381;186;312;192;186	B4DXR2;Q59GJ0;Q504Z1;B1AN89;B9EGQ7;O43432	.;.;.;.;.;IF4G3_HUMAN	N	186;382;186;186;192;312;186;197;186	ENSP00000264211:S186N;ENSP00000383274:S186N;ENSP00000364071:S186N;ENSP00000364073:S192N;ENSP00000364062:S186N;ENSP00000395381:S186N	ENSP00000264211:S186N	S	-	2	0	EIF4G3	21149181	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.069000	0.57541	2.773000	0.95371	0.585000	0.79938	AGC	.	.		0.532	EIF4G3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000007467.3	NM_003760		T	21276594	C	T	21276594	3	4	332	1	0	0	0	0	1	0	0	0	5040	797	28	3	4300	3	EIF4G3	1	21276594	Missense_Mutation	SNP	C	TCGA-RC-A6M3-01A-11D-A32G-10	13389113	21276594	227974027	2	46272										
MPL	4352	hgsc.bcm.edu	37	chr1	43805039	43805039	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	ccagctccagaaatcagtgaTttcctgaggtacgaactccg	9	12	1	3			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr1:43805039T>C	ENST00000372470.3	+	4	531	c.489T>C	c.(487-489)gaT>gaC	p.D163D	MPL_ENST00000413998.2_Silent_p.D163D	NM_005373.2	NP_005364.1	P40238	TPOR_HUMAN	MPL proto-oncogene, thrombopoietin receptor	163					blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|homeostasis of number of cells (GO:0048872)|platelet activation (GO:0030168)|regulation of chemokine production (GO:0032642)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(551)|large_intestine(3)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	567	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			Eltrombopag(DB06210)|Romiplostim(DB05332)	AAATCAGTGATTTCCTGAGGT	0.592			Mis		MPD	MPD	congenital amegakaryocytic thrombocytopenia																														p.D163D	NSCLC(52;534 1204 10016 41452 44427)	Atlas-SNP	.	yes	Dom	yes	Familial essential thrombocythemia	1	p34	4352	"myeloproliferative leukemia virus oncogene, thrombopoietin receptor"	yes	L	.	MPL	651	.	0			c.T489C						.						71	65	67					1																	43805039		2203	4300	6503	SO:0001819	synonymous_variant	4352	exon4			CAGTGATTTCCTG	M90102	CCDS483.1	1p34	2014-09-17	2014-06-26		ENSG00000117400	ENSG00000117400		"CD molecules", "Fibronectin type III domain containing"	7217	protein-coding gene	gene with protein product		159530	"myeloproliferative leukemia virus oncogene"			1608974	Standard	NM_005373		Approved	CD110, TPOR	uc001ciw.3	P40238	OTTHUMG00000007429	ENST00000372470.3:c.489T>C	chr1.hg19:g.43805039T>C		105.0	0.0		145.0	41.0	NM_005373	Q5JUZ0	Silent	SNP	ENST00000372470.3	hg19	CCDS483.1																																																																																			.	.		0.592	MPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019522.1	NM_005373		C	43805039	T	C	43805039	2	2	332	1	0	0	0	0	0	0	0	1	9739	1490	52	2		2	MPL	1	43805039	Silent	SNP	T	TCGA-RC-A6M3-01A-11D-A32G-10	22528445	43805039	205445582	3	46273										
NRD1	4898	hgsc.bcm.edu	37	chr1	52269532	52269532	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	ctcgaataattaaaccatgtTctccagctaccagtttatac	4	11	1	0			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr1:52269532T>C	ENST00000354831.7	-	22	2660	c.2471A>G	c.(2470-2472)gAa>gGa	p.E824G	NRD1_ENST00000485608.1_5'UTR|NRD1_ENST00000544028.1_Missense_Mutation_p.E624G|RP4-657D16.6_ENST00000607338.1_RNA|NRD1_ENST00000352171.7_Missense_Mutation_p.E756G|NRD1_ENST00000539524.1_Missense_Mutation_p.E692G	NM_002525.2	NP_002516.2	O43847	NRDC_HUMAN	nardilysin (N-arginine dibasic convertase)	755					cell migration (GO:0016477)|cell proliferation (GO:0008283)|neuromuscular junction development (GO:0007528)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)	cell surface (GO:0009986)|cytosol (GO:0005829)	epidermal growth factor binding (GO:0048408)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)	27						TAAACCATGTTCTCCAGCTAC	0.373																																					p.E824G		Atlas-SNP	.											.	NRD1	89	.	0			c.A2471G						.						97	94	95					1																	52269532		2203	4300	6503	SO:0001583	missense	4898	exon22			CCATGTTCTCCAG	X93207	CCDS559.1, CCDS41335.1, CCDS55599.1	1p32.2-p32.1	2008-07-18			ENSG00000078618	ENSG00000078618			7995	protein-coding gene	gene with protein product		602651				9581555, 9479496	Standard	NM_002525		Approved	hNRD1, hNRD2	uc001ctc.4	O43847	OTTHUMG00000008278	ENST00000354831.7:c.2471A>G	chr1.hg19:g.52269532T>C	ENSP00000346890:p.Glu824Gly	100.0	0.0		81.0	28.0	NM_002525	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	Missense_Mutation	SNP	ENST00000354831.7	hg19	CCDS559.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.681688	0.88542	.	.	ENSG00000078618	ENST00000352171;ENST00000354831;ENST00000539524;ENST00000371665;ENST00000546169;ENST00000544028	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	4.82	4.82	0.62117	Peptidase M16, core (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.000000	0.85682	D	0.000000	T	0.63390	0.2507	M	0.85197	2.74	0.80722	D	1	D;D;D	0.67145	0.996;0.992;0.992	P;P;P	0.59424	0.857;0.821;0.821	T	0.68100	-0.5498	10	0.42905	T	0.14	-13.6702	14.5576	0.68113	0.0:0.0:0.0:1.0	.	756;755;824	F5H6R2;O43847;B1AKJ5	.;NRDC_HUMAN;.	G	756;824;692;186;756;624	ENSP00000262679:E756G;ENSP00000346890:E824G;ENSP00000444416:E692G;ENSP00000442262:E624G	ENSP00000262679:E756G	E	-	2	0	NRD1	52042120	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.525000	0.81892	2.031000	0.59945	0.482000	0.46254	GAA	.	.		0.373	NRD1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023045.1	NM_002525		C	52269532	T	C	52269532	3	2	332	1	0	0	0	0	1	0	0	0	10654	1783	62	2	1236	2	NRD1	1	52269532	Missense_Mutation	SNP	T	TCGA-RC-A6M3-01A-11D-A32G-10	8464493	52269532	196981089	4	46274										
ZFYVE9	9372	hgsc.bcm.edu	37	chr1	52732378	52732378	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	aagccagagccctaaccctaAcaatcctgctgaatactgtt	6	13	0	2			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr1:52732378A>C	ENST00000371591.1	+	5	2461	c.2330A>C	c.(2329-2331)aAc>aCc	p.N777T	ZFYVE9_ENST00000287727.3_Missense_Mutation_p.N777T|ZFYVE9_ENST00000357206.2_Intron	NM_004799.2|NM_007324.2	NP_004790.2|NP_015563.2	O95405	ZFYV9_HUMAN	zinc finger, FYVE domain containing 9	777	SBD.				endocytosis (GO:0006897)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|SMAD protein complex assembly (GO:0007183)|SMAD protein import into nucleus (GO:0007184)|transforming growth factor beta receptor signaling pathway (GO:0007179)	early endosome (GO:0005769)|early endosome membrane (GO:0031901)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|serine-type peptidase activity (GO:0008236)			breast(1)|central_nervous_system(4)|endometrium(3)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	53						CCTAACCCTAACAATCCTGCT	0.493																																					p.N777T		Atlas-SNP	.											.	ZFYVE9	131	.	0			c.A2330C						.						173	154	161					1																	52732378		2203	4300	6503	SO:0001583	missense	9372	exon6			ACCCTAACAATCC	AF104304	CCDS563.1, CCDS564.1	1p32.3	2014-06-13	2004-05-21	2004-05-26	ENSG00000157077	ENSG00000157077		"Zinc fingers, FYVE domain containing"	6775	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 173"	603755	"MAD, mothers against decapentaplegic homolog (Drosophila) interacting protein, receptor activation anchor"	MADHIP		9865696	Standard	NM_007324		Approved	SMADIP, SARA, PPP1R173	uc001cto.4	O95405	OTTHUMG00000008061	ENST00000371591.1:c.2330A>C	chr1.hg19:g.52732378A>C	ENSP00000360647:p.Asn777Thr	45.0	0.0		62.0	9.0	NM_004799	Q5T0F6|Q5T0F7|Q9UNE1|Q9Y5R7	Missense_Mutation	SNP	ENST00000371591.1	hg19	CCDS563.1	.	.	.	.	.	.	.	.	.	.	A	18.88	3.718036	0.68844	.	.	ENSG00000157077	ENST00000287727;ENST00000371591	T;T	0.43688	0.94;0.94	5.25	5.25	0.73442	Smad anchor for receptor activation, Smad-binding domain (2);	0.000000	0.85682	D	0.000000	T	0.51312	0.1667	L	0.55990	1.75	0.80722	D	1	P	0.38677	0.642	P	0.48304	0.573	T	0.54536	-0.8279	10	0.66056	D	0.02	.	15.1582	0.72761	1.0:0.0:0.0:0.0	.	777	O95405	ZFYV9_HUMAN	T	777	ENSP00000287727:N777T;ENSP00000360647:N777T	ENSP00000287727:N777T	N	+	2	0	ZFYVE9	52504966	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.203000	0.95033	1.975000	0.57531	0.533000	0.62120	AAC	.	.		0.493	ZFYVE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022083.1	NM_007324		C	52732378	A	C	52732378	3	2	332	1	0	0	0	0	1	0	0	0	17686	43	2	5	2355	5	ZFYVE9	1	52732378	Missense_Mutation	SNP	A	TCGA-RC-A6M3-01A-11D-A32G-10	462846	52732378	196518243	5	46275										
ARHGEF11	9826	hgsc.bcm.edu	37	chr1	156917232	156917232	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	cgcaggtgggaagcttcagtCacaaacagctctgagcggtg	14	10	3	1			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr1:156917232C>T	ENST00000361409.2	-	25	2974	c.2232G>A	c.(2230-2232)gtG>gtA	p.V744V	ARHGEF11_ENST00000487682.1_5'Flank|ARHGEF11_ENST00000315174.8_Silent_p.V160V|ARHGEF11_ENST00000368194.3_Silent_p.V784V	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	744	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cytokinesis (GO:0000910)|establishment of cell polarity (GO:0030010)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)|striated muscle contraction (GO:0006941)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(27)|ovary(4)|pancreas(2)|pleura(1)|prostate(4)|skin(7)|stomach(1)|urinary_tract(2)	81	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					AAGCTTCAGTCACAAACAGCT	0.577																																					p.V784V		Atlas-SNP	.											.	ARHGEF11	168	.	0			c.G2352A						.						29	31	30					1																	156917232		2203	4300	6503	SO:0001819	synonymous_variant	9826	exon26			TTCAGTCACAAAC	AB002378	CCDS1162.1, CCDS1163.1	1q21	2011-11-16			ENSG00000132694	ENSG00000132694		"Rho guanine nucleotide exchange factors"	14580	protein-coding gene	gene with protein product		605708				10526156, 9205841	Standard	NM_014784		Approved	KIAA0380, GTRAP48, PDZ-RHOGEF	uc001fqn.3	O15085	OTTHUMG00000041292	ENST00000361409.2:c.2232G>A	chr1.hg19:g.156917232C>T		36.0	0.0		47.0	22.0	NM_198236	D3DVD0|Q5VY40|Q6PFW2	Silent	SNP	ENST00000361409.2	hg19	CCDS1162.1																																																																																			.	.		0.577	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236		T	156917232	C	T	156917232	2	4	332	1	0	0	0	0	0	0	0	1	896	813	29	3		3	ARHGEF11	1	156917232	Silent	SNP	C	TCGA-RC-A6M3-01A-11D-A32G-10	104184854	156917232	92333389	6	46276										
PYHIN1	149628	hgsc.bcm.edu	37	chr1	158913594	158913594	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	ttgcagaaaattgtaaatagGaagacgacaatctatgaaat	8	4	1	3			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr1:158913594G>T	ENST00000368140.1	+	6	1262	c.1017G>T	c.(1015-1017)agG>agT	p.R339S	PYHIN1_ENST00000392252.3_Missense_Mutation_p.R330S|PYHIN1_ENST00000392254.2_Missense_Mutation_p.R339S|PYHIN1_ENST00000485134.1_3'UTR|PYHIN1_ENST00000368138.3_Missense_Mutation_p.R330S	NM_152501.4|NM_198928.4|NM_198929.4	NP_689714.2|NP_945146.1|NP_945147.1	Q6K0P9	IFIX_HUMAN	pyrin and HIN domain family, member 1	339	HIN-200. {ECO:0000255|PROSITE- ProRule:PRU00106}.				cell cycle (GO:0007049)	nucleus (GO:0005634)				breast(2)|endometrium(3)|large_intestine(10)|lung(32)|ovary(3)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_hematologic(112;0.0378)					TTGTAAATAGGAAGACGACAA	0.343																																					p.R339S		Atlas-SNP	.											.	PYHIN1	208	.	0			c.G1017T						.						63	65	64					1																	158913594		2203	4300	6503	SO:0001583	missense	149628	exon6			AAATAGGAAGACG	AY185344	CCDS1178.1, CCDS1179.1, CCDS30907.1, CCDS30908.1	1q23.1	2008-02-05			ENSG00000163564	ENSG00000163564			28894	protein-coding gene	gene with protein product		612677				15122330	Standard	NM_152501		Approved	IFIX, MGC23885	uc001ftb.3	Q6K0P9	OTTHUMG00000037109	ENST00000368140.1:c.1017G>T	chr1.hg19:g.158913594G>T	ENSP00000357122:p.Arg339Ser	177.0	0.0		183.0	29.0	NM_152501	Q5T3W6|Q6K0P6|Q6K0P7|Q6K0P8|Q8WW65	Missense_Mutation	SNP	ENST00000368140.1	hg19	CCDS1178.1	.	.	.	.	.	.	.	.	.	.	G	0.826	-0.746839	0.03065	.	.	ENSG00000163564	ENST00000368140;ENST00000368138;ENST00000392254;ENST00000392252	T;T;T;T	0.13420	2.59;2.59;2.59;2.59	3.13	-6.26	0.02033	HIN-200/IF120x (2);Nucleic acid-binding, OB-fold (1);	.	.	.	.	T	0.01905	0.0060	L	0.36672	1.1	0.09310	N	1	B;B;B;B	0.22541	0.058;0.032;0.058;0.071	B;B;B;B	0.25884	0.023;0.064;0.023;0.038	T	0.44528	-0.9322	9	0.18710	T	0.47	.	1.7041	0.02878	0.402:0.3137:0.1595:0.1248	.	330;339;330;339	Q6K0P9-4;Q6K0P9-3;Q6K0P9-2;Q6K0P9	.;.;.;IFIX_HUMAN	S	339;330;339;330	ENSP00000357122:R339S;ENSP00000357120:R330S;ENSP00000376083:R339S;ENSP00000376082:R330S	ENSP00000357120:R330S	R	+	3	2	PYHIN1	157180218	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-4.421000	0.00236	-1.716000	0.01387	-0.150000	0.13652	AGG	.	.		0.343	PYHIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090110.1	NM_152501		T	158913594	G	T	158913594	3	4	332	1	0	0	0	0	1	0	0	0	12880	1165	41	3	1035	3	PYHIN1	1	158913594	Missense_Mutation	SNP	G	TCGA-RC-A6M3-01A-11D-A32G-10	1996362	158913594	90337027	7	46277										
RYR2	6262	hgsc.bcm.edu	37	chr1	237693789	237693789	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	acatgctgaagacaaggtgaAaaaaatgaagctacccaaga	9	7	0	5			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr1:237693789A>G	ENST00000366574.2	+	25	3202	c.2885A>G	c.(2884-2886)aAa>aGa	p.K962R	RYR2_ENST00000360064.6_Missense_Mutation_p.K960R|RYR2_ENST00000542537.1_Missense_Mutation_p.K946R	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	962	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GACAAGGTGAAAAAAATGAAG	0.358																																					p.K962R		Atlas-SNP	.											.	RYR2	1273	.	0			c.A2885G						.						101	94	96					1																	237693789		1860	4097	5957	SO:0001583	missense	6262	exon25			AGGTGAAAAAAAT	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.2885A>G	chr1.hg19:g.237693789A>G	ENSP00000355533:p.Lys962Arg	59.0	0.0		68.0	15.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	A	11.79	1.742337	0.30865	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.96774	-4.12;-4.1;-4.11	5.21	5.21	0.72293	.	0.000000	0.64402	D	0.000004	D	0.90724	0.7089	N	0.20610	0.595	0.80722	D	1	P	0.48230	0.907	B	0.41036	0.346	D	0.89441	0.3723	10	0.09843	T	0.71	.	12.6068	0.56527	1.0:0.0:0.0:0.0	.	962	Q92736	RYR2_HUMAN	R	962;960;946	ENSP00000355533:K962R;ENSP00000353174:K960R;ENSP00000443798:K946R	ENSP00000353174:K960R	K	+	2	0	RYR2	235760412	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	6.453000	0.73488	1.952000	0.56665	0.455000	0.32223	AAA	.	.		0.358	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		G	237693789	A	G	237693789	3	3	332	1	0	0	0	0	1	0	0	0	13784	14	1	2	2983	2	RYR2	1	237693789	Missense_Mutation	SNP	A	TCGA-RC-A6M3-01A-11D-A32G-10	78780195	237693789	11556832	8	46278										
ZAP70	7535	hgsc.bcm.edu	37	chr2	98340508	98340508	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	ggcccaggggcgatgccagaCcccgcggcgcacctgccctt	14	18	0	1			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr2:98340508C>A	ENST00000264972.5	+	3	224	c.9C>A	c.(7-9)gaC>gaA	p.D3E	ZAP70_ENST00000442208.1_5'Flank	NM_001079.3	NP_001070.2	P43403	ZAP70_HUMAN	zeta-chain (TCR) associated protein kinase 70kDa	3					adaptive immune response (GO:0002250)|B cell activation (GO:0042113)|beta selection (GO:0043366)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative thymic T cell selection (GO:0045060)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of T cell differentiation (GO:0045582)|positive thymic T cell selection (GO:0045059)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell activation (GO:0042110)|T cell aggregation (GO:0070489)|T cell differentiation (GO:0030217)|T cell migration (GO:0072678)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	29						CGATGCCAGACCCCGCGGCGC	0.692																																					p.D3E		Atlas-SNP	.											.	ZAP70	77	.	0			c.C9A						.						7	9	8					2																	98340508		2158	4230	6388	SO:0001583	missense	7535	exon3			GCCAGACCCCGCG	L05148	CCDS33254.1, CCDS33255.1	2q11-q13	2014-09-17	2002-08-29		ENSG00000115085	ENSG00000115085		"SH2 domain containing"	12858	protein-coding gene	gene with protein product		176947	"zeta-chain (TCR) associated protein kinase (70 kD)"	SRK		1423621	Standard	NM_001079		Approved	ZAP-70, STD	uc002syd.1	P43403	OTTHUMG00000153060	ENST00000264972.5:c.9C>A	chr2.hg19:g.98340508C>A	ENSP00000264972:p.Asp3Glu	23.0	0.0		20.0	14.0	NM_001079	A6NFP4|Q6PIA4|Q8IXD6|Q9UBS6	Missense_Mutation	SNP	ENST00000264972.5	hg19	CCDS33254.1	.	.	.	.	.	.	.	.	.	.	C	15.48	2.845964	0.51164	.	.	ENSG00000115085	ENST00000264972	T	0.73575	-0.76	4.99	1.58	0.23477	.	0.000000	0.51477	D	0.000098	T	0.63710	0.2534	L	0.56769	1.78	0.80722	D	1	B;B	0.14012	0.009;0.001	B;B	0.14578	0.011;0.003	T	0.58555	-0.7616	10	0.51188	T	0.08	.	3.4075	0.07347	0.0:0.479:0.2006:0.3204	.	3;3	B4E0E2;P43403	.;ZAP70_HUMAN	E	3	ENSP00000264972:D3E	ENSP00000264972:D3E	D	+	3	2	ZAP70	97706940	0.990000	0.36364	1.000000	0.80357	0.965000	0.64279	0.544000	0.23253	0.607000	0.29982	0.585000	0.79938	GAC	.	.		0.692	ZAP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329278.1			A	98340508	C	A	98340508	3	1	332	1	0	0	0	0	1	0	0	0	17529	506	18	3	11	3	ZAP70	2	98340508	Missense_Mutation	SNP	C	TCGA-RC-A6M3-01A-11D-A32G-10		98340508	144858865	9	46279										
FN1	2335	hgsc.bcm.edu	37	chr2	216261911	216261911	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	gagcactccagtgtcagggtTtgcctccagatgcaagtttg	12	10	1	1			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr2:216261911T>C	ENST00000359671.1	-	23	3818	c.3553A>G	c.(3553-3555)Aac>Gac	p.N1185D	FN1_ENST00000354785.4_Missense_Mutation_p.N1185D|FN1_ENST00000357009.2_Missense_Mutation_p.N1185D|FN1_ENST00000323926.6_Missense_Mutation_p.N1185D|FN1_ENST00000421182.1_Missense_Mutation_p.N1185D|FN1_ENST00000336916.4_Missense_Mutation_p.N1185D|FN1_ENST00000346544.3_Missense_Mutation_p.N1185D|FN1_ENST00000432072.2_Missense_Mutation_p.N1185D|FN1_ENST00000345488.5_Missense_Mutation_p.N1185D|FN1_ENST00000357867.4_Missense_Mutation_p.N1185D|FN1_ENST00000443816.1_Missense_Mutation_p.N1185D|FN1_ENST00000446046.1_Missense_Mutation_p.N1185D|FN1_ENST00000356005.4_Missense_Mutation_p.N1185D			P02751	FINC_HUMAN	fibronectin 1	1185	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316, ECO:0000255|PROSITE-ProRule:PRU00478, ECO:0000255|PROSITE-ProRule:PRU00479}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	GTGTCAGGGTTTGCCTCCAGA	0.478																																					p.N1185D		Atlas-SNP	.											.	FN1	521	.	0			c.A3553G						.						191	189	189					2																	216261911		2203	4300	6503	SO:0001583	missense	2335	exon23			CAGGGTTTGCCTC		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"Fibronectin type III domain containing", "Endogenous ligands"	3778	protein-coding gene	gene with protein product	"migration-stimulating factor", "cold-insoluble globulin"	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.3553A>G	chr2.hg19:g.216261911T>C	ENSP00000352696:p.Asn1185Asp	61.0	0.0		49.0	8.0	NM_212476	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Missense_Mutation	SNP	ENST00000359671.1	hg19		.	.	.	.	.	.	.	.	.	.	T	13.23	2.176311	0.38413	.	.	ENSG00000115414	ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000265313;ENST00000359671;ENST00000346544;ENST00000345488;ENST00000357009;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005	T;T;T;T;T;T;T;T;T;T;T;T;T	0.56941	0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43	5.62	4.44	0.53790	.	0.069763	0.64402	D	0.000016	T	0.56455	0.1986	N	0.24115	0.695	0.52501	D	0.999954	D;P;P;P;P;P;D;P;P;D	0.61080	0.961;0.84;0.868;0.945;0.791;0.615;0.989;0.897;0.942;0.962	P;P;P;P;P;P;D;D;D;P	0.67103	0.839;0.713;0.687;0.508;0.641;0.46;0.918;0.949;0.949;0.878	T	0.56396	-0.7986	10	0.42905	T	0.14	.	12.9834	0.58577	0.0:0.0:0.135:0.8649	.	1185;1185;1185;1185;1185;1185;1185;1185;1185;1185	P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;E7ERA1;P02751-9;P02751-14;P02751-15	.;.;.;.;.;.;.;.;.;.	D	1185	ENSP00000394423:N1185D;ENSP00000323534:N1185D;ENSP00000338200:N1185D;ENSP00000350534:N1185D;ENSP00000346839:N1185D;ENSP00000352696:N1185D;ENSP00000265312:N1185D;ENSP00000273049:N1185D;ENSP00000349509:N1185D;ENSP00000410422:N1185D;ENSP00000415018:N1185D;ENSP00000399538:N1185D;ENSP00000348285:N1185D	ENSP00000265313:N1185D	N	-	1	0	FN1	215970156	1.000000	0.71417	0.789000	0.31954	0.215000	0.24574	7.434000	0.80377	1.032000	0.39892	0.477000	0.44152	AAC	.	.		0.478	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		C	216261911	T	C	216261911	3	2	332	1	0	0	0	0	1	0	0	0	5970	1841	64	2	3976	2	FN1	2	216261911	Missense_Mutation	SNP	T	TCGA-RC-A6M3-01A-11D-A32G-10	117921403	216261911	26937462	10	46280										
STK25	10494	hgsc.bcm.edu	37	chr2	242439594	242439594	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	acccccagcaggacctttgaTgtctcggtggatcttgcgtt	11	12	2	1			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr2:242439594T>C	ENST00000316586.4	-	5	770	c.421A>G	c.(421-423)Atc>Gtc	p.I141V	STK25_ENST00000478403.1_5'Flank|STK25_ENST00000401869.1_Missense_Mutation_p.I141V|STK25_ENST00000405883.3_Missense_Mutation_p.I64V|STK25_ENST00000403346.3_Missense_Mutation_p.I141V|STK25_ENST00000405585.1_Missense_Mutation_p.I64V|STK25_ENST00000535007.1_Missense_Mutation_p.I47V|STK25_ENST00000543554.1_Missense_Mutation_p.I47V	NM_001271977.1|NM_001271978.1|NM_001282308.1	NP_001258906.1|NP_001258907.1|NP_001269237.1	O00506	STK25_HUMAN	serine/threonine kinase 25	141	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				establishment or maintenance of cell polarity (GO:0007163)|Golgi localization (GO:0051645)|positive regulation of axonogenesis (GO:0050772)|response to oxidative stress (GO:0006979)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|kidney(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	10		all_cancers(19;2.09e-34)|all_epithelial(40;2.09e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Ovarian(221;0.069)|Lung NSC(271;0.0886)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.2)		Epithelial(32;8.24e-34)|all cancers(36;3.46e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.6e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.1e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0839)		GGACCTTTGATGTCTCGGTGG	0.582																																					p.I141V	NSCLC(99;1100 1566 7679 28647 48345)	Atlas-SNP	.											.	STK25	32	.	0			c.A421G						.						113	103	106					2																	242439594		2203	4300	6503	SO:0001583	missense	10494	exon5			CTTTGATGTCTCG	D63780	CCDS2549.1, CCDS63199.1, CCDS63200.1	2q37.3	2010-06-25	2010-06-25		ENSG00000115694	ENSG00000115694			11404	protein-coding gene	gene with protein product		602255	"serine/threonine kinase 25 (Ste20, yeast homolog)"			8887545, 9160885, 15037601	Standard	NM_001271977		Approved	SOK1, YSK1	uc002wbp.4	O00506	OTTHUMG00000133408	ENST00000316586.4:c.421A>G	chr2.hg19:g.242439594T>C	ENSP00000325748:p.Ile141Val	85.0	0.0		64.0	20.0	NM_006374	A8K6Z3|A8K7D2|B7Z9K1|Q15522|Q5BJF1	Missense_Mutation	SNP	ENST00000316586.4	hg19	CCDS2549.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.387266	0.82902	.	.	ENSG00000115694	ENST00000316586;ENST00000403346;ENST00000401869;ENST00000405883;ENST00000545437;ENST00000405585;ENST00000543554;ENST00000535007;ENST00000450497;ENST00000424537;ENST00000442307;ENST00000413760;ENST00000429279;ENST00000436402;ENST00000440109;ENST00000435225	T;T;T;T;T;T;T;T;T;T;T;D;T;D;D	0.85339	1.54;1.54;1.54;1.54;1.54;1.54;1.54;2.28;2.28;2.28;2.28;-1.97;0.76;-1.97;-1.97	5.07	5.07	0.68467	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.87160	0.6108	L	0.48260	1.515	0.80722	D	1	P;P;P;P	0.42973	0.796;0.791;0.576;0.576	P;P;P;B	0.53035	0.716;0.667;0.501;0.304	D	0.86704	0.1931	10	0.41790	T	0.15	.	15.1502	0.72692	0.0:0.0:0.0:1.0	.	141;67;64;141	B4DZ52;B4DVS7;A8K6Z3;O00506	.;.;.;STK25_HUMAN	V	141;141;141;64;47;64;47;47;47;45;47;47;47;141;47;47	ENSP00000325748:I141V;ENSP00000384162:I141V;ENSP00000385687:I141V;ENSP00000384444:I64V;ENSP00000385541:I64V;ENSP00000444886:I47V;ENSP00000446008:I47V;ENSP00000399212:I47V;ENSP00000417020:I45V;ENSP00000403607:I47V;ENSP00000395104:I47V;ENSP00000404960:I47V;ENSP00000412617:I141V;ENSP00000403866:I47V;ENSP00000401114:I47V	ENSP00000325748:I141V	I	-	1	0	STK25	242088267	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.834000	0.86773	2.035000	0.60131	0.533000	0.62120	ATC	.	.		0.582	STK25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257265.4	NM_006374		C	242439594	T	C	242439594	3	2	332	1	0	0	0	0	1	0	0	0	15309	1464	51	2	891	2	STK25	2	242439594	Missense_Mutation	SNP	T	TCGA-RC-A6M3-01A-11D-A32G-10	26177683	242439594	759779	11	46281										
UBA7	7318	hgsc.bcm.edu	37	chr3	49848783	49848783	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	acctgcactgcttagggcgaCtgtccgcactagggcctcat	11	14	1	0			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr3:49848783C>G	ENST00000333486.3	-	9	1203	c.1045G>C	c.(1045-1047)Gtc>Ctc	p.V349L	UBA7_ENST00000494212.1_5'Flank	NM_003335.2	NP_003326.2	P41226	UBA7_HUMAN	ubiquitin-like modifier activating enzyme 7	349	2 approximate repeats.				cellular protein modification process (GO:0006464)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|modification-dependent protein catabolic process (GO:0019941)|negative regulation of type I interferon production (GO:0032480)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ISG15 activating enzyme activity (GO:0019782)|ubiquitin activating enzyme activity (GO:0004839)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(15)|large_intestine(4)|lung(7)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;3.58e-06)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		CTTAGGGCGACTGTCCGCACT	0.622																																					p.V349L		Atlas-SNP	.											.	UBA7	64	.	0			c.G1045C						.						145	114	125					3																	49848783		2203	4300	6503	SO:0001583	missense	7318	exon9			GGGCGACTGTCCG	BC006378	CCDS2805.1	3p21	2007-11-30	2007-11-30	2007-11-30	ENSG00000182179	ENSG00000182179		"Ubiquitin-like modifier activating enzymes"	12471	protein-coding gene	gene with protein product	"UBA1, ubiquitin-activating enzyme E1 homolog B (yeast)", "UBA7, ubiquitin-activating enzyme E1"	191325	"ubiquitin-activating enzyme E1-like"	UBE1L		8327486	Standard	NM_003335		Approved	D8, UBE2, UBA1B	uc003cxr.3	P41226	OTTHUMG00000158267	ENST00000333486.3:c.1045G>C	chr3.hg19:g.49848783C>G	ENSP00000333266:p.Val349Leu	80.0	0.0		81.0	38.0	NM_003335	Q9BRB2	Missense_Mutation	SNP	ENST00000333486.3	hg19	CCDS2805.1	.	.	.	.	.	.	.	.	.	.	C	0.266	-0.996159	0.02145	.	.	ENSG00000182179	ENST00000333486	T	0.28666	1.6	5.76	0.164	0.14990	Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.472532	0.24222	N	0.040426	T	0.08582	0.0213	N	0.05078	-0.115	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.25467	-1.0131	10	0.02654	T	1	-6.9929	1.0506	0.01579	0.192:0.3541:0.1076:0.3464	.	349	P41226	UBA7_HUMAN	L	349	ENSP00000333266:V349L	ENSP00000333266:V349L	V	-	1	0	UBA7	49823787	0.000000	0.05858	0.000000	0.03702	0.497000	0.33675	0.025000	0.13577	0.073000	0.16731	-0.379000	0.06801	GTC	.	.		0.622	UBA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350503.1	NM_003335		G	49848783	C	G	49848783	3	3	332	1	0	0	0	0	1	0	0	0	16848	565	20	4	2057	4	UBA7	3	49848783	Missense_Mutation	SNP	C	TCGA-RC-A6M3-01A-11D-A32G-10		49848783	148173647	12	46282										
POLQ	10721	hgsc.bcm.edu	37	chr3	121215700	121215700	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	caaagattgaatctgcccacGattgcatccatatttctgat	6	10	2	3	rs373455498		TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr3:121215700G>T	ENST00000264233.5	-	14	2361	c.2233C>A	c.(2233-2235)Cgt>Agt	p.R745S		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	745					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		ATCTGCCCACGATTGCATCCA	0.363								DNA polymerases (catalytic subunits)																													p.R745S	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.C2233A						.						102	101	101					3																	121215700		2203	4300	6503	SO:0001583	missense	10721	exon14			GCCCACGATTGCA	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.2233C>A	chr3.hg19:g.121215700G>T	ENSP00000264233:p.Arg745Ser	63.0	0.0		59.0	24.0	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	hg19	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	G	18.06	3.538819	0.65085	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.59083	0.29	5.63	5.63	0.86233	.	0.110946	0.64402	D	0.000006	T	0.78142	0.4237	M	0.88775	2.98	0.80722	D	1	D	0.55800	0.973	P	0.56751	0.805	T	0.82269	-0.0541	10	0.87932	D	0	.	19.753	0.96275	0.0:0.0:1.0:0.0	.	745	O75417	DPOLQ_HUMAN	S	368;745;881	ENSP00000264233:R745S	ENSP00000264233:R745S	R	-	1	0	POLQ	122698390	1.000000	0.71417	1.000000	0.80357	0.048000	0.14542	8.799000	0.91895	2.669000	0.90835	0.461000	0.40582	CGT	.	.		0.363	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		T	121215700	G	T	121215700	3	4	332	1	0	0	0	0	1	0	0	0	12217	1058	37	1	5607	1	POLQ	3	121215700	Missense_Mutation	SNP	G	TCGA-RC-A6M3-01A-11D-A32G-10	71366917	121215700	76806730	13	46283										
STAG1	10274	hgsc.bcm.edu	37	chr3	136057110	136057110	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	cagacttcagaacataggcaTtccaaatccctagaaaaatg	6	10	1	3			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr3:136057110T>G	ENST00000383202.2	-	34	4019	c.3763A>C	c.(3763-3765)Atg>Ctg	p.M1255L	STAG1_ENST00000236698.5_Missense_Mutation_p.M1218L|STAG1_ENST00000434713.2_Missense_Mutation_p.M995L|STAG1_ENST00000536929.1_Missense_Mutation_p.M839L	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	1255					chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						AACATAGGCATTCCAAATCCC	0.318																																					p.M1255L		Atlas-SNP	.											.	STAG1	135	.	0			c.A3763C						.						59	62	61					3																	136057110		2203	4300	6503	SO:0001583	missense	10274	exon34			TAGGCATTCCAAA	Z75330	CCDS3090.1	3q22.2-q22.3	2011-08-12			ENSG00000118007	ENSG00000118007			11354	protein-coding gene	gene with protein product		604358				9305759	Standard	XM_006713471		Approved	SA-1, SCC3A	uc003era.1	Q8WVM7	OTTHUMG00000159798	ENST00000383202.2:c.3763A>C	chr3.hg19:g.136057110T>G	ENSP00000372689:p.Met1255Leu	128.0	0.0		144.0	29.0	NM_005862	O00539|Q6P275	Missense_Mutation	SNP	ENST00000383202.2	hg19	CCDS3090.1	.	.	.	.	.	.	.	.	.	.	T	12.04	1.819704	0.32145	.	.	ENSG00000118007	ENST00000383202;ENST00000236698;ENST00000434713;ENST00000536929	T;T;T;T	0.27104	2.1;2.02;2.05;1.69	5.76	5.76	0.90799	.	0.042059	0.85682	D	0.000000	T	0.28599	0.0708	L	0.54323	1.7	0.58432	D	0.999999	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.02498	-1.1150	10	0.48119	T	0.1	.	16.0645	0.80861	0.0:0.0:0.0:1.0	.	1218;1255	Q6P275;Q8WVM7	.;STAG1_HUMAN	L	1255;1218;995;839	ENSP00000372689:M1255L;ENSP00000236698:M1218L;ENSP00000404396:M995L;ENSP00000445787:M839L	ENSP00000236698:M1218L	M	-	1	0	STAG1	137539800	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.344000	0.79328	2.200000	0.70718	0.482000	0.46254	ATG	.	.		0.318	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357366.1	NM_005862		G	136057110	T	G	136057110	3	3	332	1	0	0	0	0	1	0	0	0	15257	1493	52	5	17	5	STAG1	3	136057110	Missense_Mutation	SNP	T	TCGA-RC-A6M3-01A-11D-A32G-10	14841410	136057110	61965320	14	46284										
IL12A	3592	hgsc.bcm.edu	37	chr3	159711492	159711492	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	ttgtcatgtcacccaggcccTgtgccttagtagtatttatg	9	10	2	0			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr3:159711492T>A	ENST00000305579.2	+	6	774	c.467T>A	c.(466-468)cTg>cAg	p.L156Q	IL12A_ENST00000466512.1_Missense_Mutation_p.L142Q|IL12A_ENST00000480787.1_Missense_Mutation_p.L118Q|IL12A-AS1_ENST00000497452.1_RNA	NM_000882.3	NP_000873.2	P29459	IL12A_HUMAN	interleukin 12A	122					cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|defense response to Gram-positive bacterium (GO:0050830)|defense response to protozoan (GO:0042832)|extrinsic apoptotic signaling pathway (GO:0097191)|immune response (GO:0006955)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cell adhesion (GO:0045785)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of mononuclear cell proliferation (GO:0032946)|positive regulation of natural killer cell activation (GO:0032816)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|positive regulation of NK T cell activation (GO:0051135)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat4 protein (GO:0042520)|response to lipopolysaccharide (GO:0032496)|response to UV-B (GO:0010224)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|interleukin-12 complex (GO:0043514)	interleukin-12 beta subunit binding (GO:0042163)|interleukin-12 receptor binding (GO:0005143)|interleukin-27 binding (GO:0045513)|protein heterodimerization activity (GO:0046982)			endometrium(3)|kidney(1)|large_intestine(1)|lung(4)	9			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			ACCCAGGCCCTGTGCCTTAGT	0.438																																					p.L156Q		Atlas-SNP	.											.	IL12A	23	.	0			c.T467A						.						137	131	133					3																	159711492		2203	4300	6503	SO:0001583	missense	3592	exon6			AGGCCCTGTGCCT	M65271	CCDS3187.1	3q25.33	2014-04-04	2014-04-04		ENSG00000168811	ENSG00000168811		"Interleukins and interleukin receptors"	5969	protein-coding gene	gene with protein product	"natural killer cell stimulatory factor 1, 35 kD subunit", "cytotoxic lymphocyte maturation factor 1, p35", "interleukin 12, p35", "IL-12, subunit p35", "NF cell stimulatory factor chain 1", "interleukin-12 alpha chain", "IL35 subunit"	161560	"interleukin 12A (natural killer cell stimulatory factor 1, cytotoxic lymphocyte maturation factor 1, p35)"	NKSF1		1673147	Standard	NM_000882		Approved	CLMF, IL-12A, p35, NFSK	uc003fcx.3	P29459	OTTHUMG00000158942	ENST00000305579.2:c.467T>A	chr3.hg19:g.159711492T>A	ENSP00000303231:p.Leu156Gln	118.0	0.0		125.0	5.0	NM_000882	Q96QZ1	Missense_Mutation	SNP	ENST00000305579.2	hg19	CCDS3187.1	.	.	.	.	.	.	.	.	.	.	T	12.66	2.005378	0.35415	.	.	ENSG00000168811	ENST00000305579;ENST00000480787;ENST00000466512	.	.	.	5.44	1.34	0.21922	.	1.184600	0.05890	N	0.628057	T	0.69151	0.3079	M	0.78049	2.395	0.32999	D	0.52594	D	0.89917	1.0	D	0.91635	0.999	T	0.63189	-0.6693	9	0.25751	T	0.34	-6.2614	6.1194	0.20144	0.1452:0.0:0.2527:0.6021	.	156	O60595	.	Q	156;118;142	.	ENSP00000303231:L156Q	L	+	2	0	IL12A	161194186	0.658000	0.27402	0.997000	0.53966	0.419000	0.31324	0.355000	0.20163	0.882000	0.36016	-0.327000	0.08410	CTG	.	.		0.438	IL12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352602.2	NM_000882		A	159711492	T	A	159711492	3	1	332	1	0	0	0	0	1	0	0	0	7633	1580	55	4	489	4	IL12A	3	159711492	Missense_Mutation	SNP	T	TCGA-RC-A6M3-01A-11D-A32G-10	23654382	159711492	38310938	15	46285										
PHC3	80012	hgsc.bcm.edu	37	chr3	169867033	169867033	+	Splice_Site	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	ggagaagtggagaggttgatCtaaggaagaaaacatattag	14	2	1	4			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr3:169867033C>G	ENST00000494943.1	-	5	447		c.e5-1		PHC3_ENST00000474275.1_Splice_Site|PHC3_ENST00000495893.2_Splice_Site|RNU6-315P_ENST00000362666.1_RNA|PHC3_ENST00000467570.1_Intron			Q8NDX5	PHC3_HUMAN	polyhomeotic homolog 3 (Drosophila)						multicellular organismal development (GO:0007275)	actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(1)|upper_aerodigestive_tract(2)	26	all_cancers(22;2.67e-22)|all_epithelial(15;4.73e-27)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)			AGAGGTTGATCTAAGGAAGAA	0.433																																					.		Atlas-SNP	.											.	PHC3	113	.	0			c.415-1G>C						.						78	73	75					3																	169867033		1884	4119	6003	SO:0001630	splice_region_variant	80012	exon6			GTTGATCTAAGGA		CCDS46952.1	3q26.32	2014-01-28	2006-09-12		ENSG00000173889	ENSG00000173889		"Sterile alpha motif (SAM) domain containing"	15682	protein-coding gene	gene with protein product	"early development regulator 3", "polyhomeotic like 3"		"polyhomeotic like 3 (Drosophila)"			12167701, 12384788	Standard	NM_024947		Approved	EDR3, FLJ12967, FLJ12729, HPH3	uc003fgl.2	Q8NDX5	OTTHUMG00000158777	ENST00000494943.1:c.379-1G>C	chr3.hg19:g.169867033C>G		39.0	0.0		25.0	9.0	NM_024947	A2RRP9|Q5HYF0|Q6NSG2|Q8NFT7|Q8NFZ1|Q8TBM2|Q9H971|Q9H9I4	Splice_Site	SNP	ENST00000494943.1	hg19		.	.	.	.	.	.	.	.	.	.	C	22.8	4.331147	0.81690	.	.	ENSG00000173889	ENST00000494943;ENST00000495893;ENST00000475729;ENST00000474275	.	.	.	5.81	5.81	0.92471	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.0784	0.97758	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PHC3	171349727	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.266000	0.78452	2.736000	0.93811	0.655000	0.94253	.	.	.		0.433	PHC3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000352182.3	NM_024947	Intron	G	169867033	C	G	169867033	5	3	332	1	0	0	0	0	0	0	1	0	11827	927	32	4	2617	4	PHC3	3	169867033	Splice_Site	SNP	C	TCGA-RC-A6M3-01A-11D-A32G-10	10155541	169867033	28155397	16	46286										
LRRC15	131578	hgsc.bcm.edu	37	chr3	194080170	194080170	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	aatggccagcccgctctgggCctgggtcatgccccaaacgc	12	16	2	0			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr3:194080170C>T	ENST00000347624.3	-	2	1688	c.1603G>A	c.(1603-1605)Gcc>Acc	p.A535T	LRRC15_ENST00000439944.2_Missense_Mutation_p.A541T|LRRC15_ENST00000428839.1_Missense_Mutation_p.A541T	NM_130830.4	NP_570843.2	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15	535					negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|positive regulation of cell migration (GO:0030335)|receptor-mediated virion attachment to host cell (GO:0046813)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	collagen binding (GO:0005518)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)			biliary_tract(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(20)|ovary(4)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.94e-05)		CCGCTCTGGGCCTGGGTCATG	0.592																																					p.A541T		Atlas-SNP	.											.	LRRC15	137	.	0			c.G1621A						.						81	81	81					3																	194080170		2203	4300	6503	SO:0001583	missense	131578	exon3			TCTGGGCCTGGGT	AB071037	CCDS3306.1, CCDS46984.1	3q29	2008-02-05			ENSG00000172061	ENSG00000172061			20818	protein-coding gene	gene with protein product						12923058	Standard	NM_001135057		Approved	LIB	uc003ftu.3	Q8TF66	OTTHUMG00000156048	ENST00000347624.3:c.1603G>A	chr3.hg19:g.194080170C>T	ENSP00000306276:p.Ala535Thr	81.0	0.0		76.0	32.0	NM_001135057	Q495Q6|Q7RTN7	Missense_Mutation	SNP	ENST00000347624.3	hg19	CCDS3306.1	.	.	.	.	.	.	.	.	.	.	C	5.869	0.344505	0.11126	.	.	ENSG00000172061	ENST00000347624;ENST00000439944;ENST00000428839	T;T;T	0.58797	0.31;0.36;0.36	5.25	3.45	0.39498	.	0.750699	0.12463	N	0.466711	T	0.35537	0.0935	N	0.14661	0.345	0.27643	N	0.947656	B;B	0.02656	0.0;0.0	B;B	0.08055	0.001;0.003	T	0.22521	-1.0214	10	0.19590	T	0.45	.	6.4735	0.22022	0.0:0.5481:0.2658:0.1861	.	535;541	Q8TF66;Q8TF66-2	LRC15_HUMAN;.	T	535;541;541	ENSP00000306276:A535T;ENSP00000389128:A541T;ENSP00000413707:A541T	ENSP00000306276:A535T	A	-	1	0	LRRC15	195561465	0.174000	0.23070	0.877000	0.34402	0.621000	0.37620	0.328000	0.19681	0.722000	0.32252	0.563000	0.77884	GCC	.	.		0.592	LRRC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342858.2			T	194080170	C	T	194080170	3	4	332	1	0	0	0	0	1	0	0	0	8979	739	26	3	146	3	LRRC15	3	194080170	Missense_Mutation	SNP	C	TCGA-RC-A6M3-01A-11D-A32G-10	24213137	194080170	3942260	17	46287										
SHROOM3	57619	hgsc.bcm.edu	37	chr4	77660340	77660340	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	ggtagggaggcccgagcctcAgcaaatggtcagggctatga	16	9	2	1			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr4:77660340A>C	ENST00000296043.6	+	5	1967	c.1014A>C	c.(1012-1014)tcA>tcC	p.S338S		NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	338					actin cytoskeleton organization (GO:0030036)|apical protein localization (GO:0045176)|cell morphogenesis (GO:0000902)|cellular pigment accumulation (GO:0043482)|columnar/cuboidal epithelial cell development (GO:0002066)|neural tube closure (GO:0001843)|pattern specification process (GO:0007389)|regulation of cell shape (GO:0008360)	adherens junction (GO:0005912)|apical junction complex (GO:0043296)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)				NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(29)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	60			Lung(101;0.0903)			CCCGAGCCTCAGCAAATGGTC	0.562																																					p.S338S		Atlas-SNP	.											.	SHROOM3	134	.	0			c.A1014C						.						56	61	59					4																	77660340		2203	4300	6503	SO:0001819	synonymous_variant	57619	exon5			AGCCTCAGCAAAT	AB055660	CCDS3579.2	4q21.1	2009-11-25			ENSG00000138771	ENSG00000138771			30422	protein-coding gene	gene with protein product		604570				10589677, 16615870	Standard	NM_020859		Approved	ShrmL, SHRM, KIAA1481, APXL3	uc011cbx.2	Q8TF72	OTTHUMG00000157075	ENST00000296043.6:c.1014A>C	chr4.hg19:g.77660340A>C		67.0	0.0		43.0	10.0	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Silent	SNP	ENST00000296043.6	hg19	CCDS3579.2																																																																																			.	.		0.562	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859		C	77660340	A	C	77660340	2	2	332	1	0	0	0	0	0	0	0	1	14310	175	7	5		5	SHROOM3	4	77660340	Silent	SNP	A	TCGA-RC-A6M3-01A-11D-A32G-10		77660340	113493936	18	46288										
COPS4	51138	hgsc.bcm.edu	37	chr4	83970469	83970469	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	agtcatttcatttgaggagcAggtaaaaatctagagaagtg	11	4	3	2			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr4:83970469A>T	ENST00000264389.2	+	3	440	c.305A>T	c.(304-306)cAg>cTg	p.Q102L	COPS4_ENST00000509093.1_Splice_Site_p.Q102L|COPS4_ENST00000511653.1_Splice_Site_p.Q102L|COPS4_ENST00000503682.1_Splice_Site_p.Q102L	NM_016129.2	NP_057213.2	Q9BT78	CSN4_HUMAN	COP9 signalosome subunit 4	102					cullin deneddylation (GO:0010388)|protein deneddylation (GO:0000338)	cell junction (GO:0030054)|COP9 signalosome (GO:0008180)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)				endometrium(2)|kidney(2)|large_intestine(3)|lung(4)|urinary_tract(2)	13		Hepatocellular(203;0.114)				TTTGAGGAGCAGGTAAAAATC	0.353																																					p.Q102L		Atlas-SNP	.											.	COPS4	31	.	0			c.A305T						.						75	74	74					4																	83970469		2203	4300	6503	SO:0001630	splice_region_variant	51138	exon3			AGGAGCAGGTAAA	AF100757	CCDS3600.1, CCDS58909.1	4q21.22	2013-03-14	2013-03-14		ENSG00000138663	ENSG00000138663			16702	protein-coding gene	gene with protein product			"COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 4", "COP9 constitutive photomorphogenic homolog subunit 4 (Arabidopsis)"			9707402	Standard	NM_016129		Approved	CSN4	uc003hoa.3	Q9BT78	OTTHUMG00000130298	ENST00000264389.2:c.306+1A>T	chr4.hg19:g.83970469A>T		59.0	0.0		49.0	12.0	NM_016129	B3KN88|B3KST5|Q561W7|Q9NW31|Q9Y677	Missense_Mutation	SNP	ENST00000264389.2	hg19	CCDS3600.1	.	.	.	.	.	.	.	.	.	.	A	27.5	4.838993	0.91117	.	.	ENSG00000138663	ENST00000509093;ENST00000264389;ENST00000503682;ENST00000511653	T;T;T;T	0.54479	0.61;0.64;0.57;0.61	4.78	4.78	0.61160	.	0.057874	0.64402	D	0.000001	T	0.78194	0.4245	M	0.92219	3.285	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;0.999;0.999	D;D;D;D	0.80764	0.94;0.987;0.994;0.962	D	0.84350	0.0532	10	0.87932	D	0	-8.9026	14.6034	0.68460	1.0:0.0:0.0:0.0	.	102;102;102;102	B3KST5;D6RFN0;D6RAX7;Q9BT78	.;.;.;CSN4_HUMAN	L	102	ENSP00000425976:Q102L;ENSP00000264389:Q102L;ENSP00000424791:Q102L;ENSP00000424655:Q102L	ENSP00000264389:Q102L	Q	+	2	0	COPS4	84189493	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	9.071000	0.93980	1.920000	0.55613	0.482000	0.46254	CAG	.	.		0.353	COPS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252643.1		Missense_Mutation	T	83970469	A	T	83970469	5	4	332	1	0	0	0	0	0	0	1	0	3737	202	7	4	315	4	COPS4	4	83970469	Splice_Site	SNP	A	TCGA-RC-A6M3-01A-11D-A32G-10	6310129	83970469	107183807	19	46289										
PPP3CA	5530	hgsc.bcm.edu	37	chr4	102117189	102117189	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	ttccctccttcataagatgcGcctttaagatatccacacga	5	13	1	2			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr4:102117189G>A	ENST00000394854.3	-	2	826	c.143C>T	c.(142-144)gCg>gTg	p.A48V	PPP3CA_ENST00000523694.2_Intron|PPP3CA_ENST00000394853.4_Missense_Mutation_p.A48V|PPP3CA_ENST00000323055.6_Missense_Mutation_p.A48V|PPP3CA_ENST00000512215.1_Missense_Mutation_p.A48V|PPP3CA_ENST00000507176.1_Intron	NM_000944.4	NP_000935.1	Q08209	PP2BA_HUMAN	protein phosphatase 3, catalytic subunit, alpha isozyme	48	Catalytic.				calcineurin-NFAT signaling cascade (GO:0033173)|calcium ion transport (GO:0006816)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|dephosphorylation (GO:0016311)|Fc-epsilon receptor signaling pathway (GO:0038095)|G1/S transition of mitotic cell cycle (GO:0000082)|innate immune response (GO:0045087)|multicellular organismal response to stress (GO:0033555)|negative regulation of insulin secretion (GO:0046676)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein dephosphorylation (GO:0006470)|protein import into nucleus (GO:0006606)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic transmission (GO:0050804)|response to amphetamine (GO:0001975)|response to calcium ion (GO:0051592)|skeletal muscle fiber development (GO:0048741)|T cell activation (GO:0042110)|transition between fast and slow fiber (GO:0014883)	calcineurin complex (GO:0005955)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|calmodulin-dependent protein phosphatase activity (GO:0033192)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|protein dimerization activity (GO:0046983)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	20				OV - Ovarian serous cystadenocarcinoma(123;6.79e-08)		CATAAGATGCGCCTTTAAGAT	0.408																																					p.A48V		Atlas-SNP	.											.	PPP3CA	51	.	0			c.C143T						.						129	130	130					4																	102117189		2203	4300	6503	SO:0001583	missense	5530	exon2			AGATGCGCCTTTA		CCDS34037.1, CCDS47113.1, CCDS47114.1	4q24	2010-03-17	2010-03-05		ENSG00000138814	ENSG00000138814	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9314	protein-coding gene	gene with protein product	"calcineurin A alpha", "protein phosphatase 2B, catalytic subunit, alpha isoform"	114105	"protein phosphatase 3 (formerly 2B), catalytic subunit, alpha isoform (calcineurin A alpha)", "protein phosphatase 3 (formerly 2B), catalytic subunit, alpha isoform"	CALN, CALNA		2848250, 1659808	Standard	NM_000944		Approved	CNA1, PPP2B	uc011cen.1	Q08209	OTTHUMG00000133839	ENST00000394854.3:c.143C>T	chr4.hg19:g.102117189G>A	ENSP00000378323:p.Ala48Val	101.0	0.0		96.0	25.0	NM_000944	A1A441|A8K3B7|A8W6Z7|A8W6Z8|B5BUA2|Q8TAW9	Missense_Mutation	SNP	ENST00000394854.3	hg19	CCDS34037.1	.	.	.	.	.	.	.	.	.	.	G	18.04	3.535778	0.64972	.	.	ENSG00000138814	ENST00000512215;ENST00000394854;ENST00000323055;ENST00000394853	T;T;T;T	0.62941	3.4;-0.01;-0.01;-0.01	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.64159	0.2573	L	0.55481	1.735	0.80722	D	1	P;D;B;B	0.54772	0.577;0.968;0.259;0.155	B;P;B;B	0.44772	0.016;0.46;0.016;0.009	T	0.67833	-0.5568	10	0.59425	D	0.04	-12.4637	19.0843	0.93196	0.0:0.0:1.0:0.0	.	48;48;48;48	Q08209;A8W6Z8;A8W6Z7;Q08209-2	PP2BA_HUMAN;.;.;.	V	48	ENSP00000422781:A48V;ENSP00000378323:A48V;ENSP00000320580:A48V;ENSP00000378322:A48V	ENSP00000320580:A48V	A	-	2	0	PPP3CA	102336212	1.000000	0.71417	1.000000	0.80357	0.863000	0.49368	6.157000	0.71846	2.824000	0.97209	0.655000	0.94253	GCG	.	.		0.408	PPP3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258379.2	NM_000944		A	102117189	G	A	102117189	3	1	332	1	0	0	0	0	1	0	0	0	12409	1087	38	1	1474	1	PPP3CA	4	102117189	Missense_Mutation	SNP	G	TCGA-RC-A6M3-01A-11D-A32G-10	18146720	102117189	89037087	20	46290										
NDST3	9348	hgsc.bcm.edu	37	chr4	119154228	119154228	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	atccttagtaactcccccagCccaaaaacctttgaggaggt	7	13	0	1			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr4:119154228C>G	ENST00000296499.5	+	9	2284	c.1881C>G	c.(1879-1881)agC>agG	p.S627R	NDST3_ENST00000433996.2_Missense_Mutation_p.S546R	NM_004784.2	NP_004775.1	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	627	Heparan sulfate N-sulfotransferase 3.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			NS(1)|breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	54						ACTCCCCCAGCCCAAAAACCT	0.358																																					p.S627R		Atlas-SNP	.											.	NDST3	107	.	0			c.C1881G						.						147	146	147					4																	119154228		2203	4300	6503	SO:0001583	missense	9348	exon9			CCCCAGCCCAAAA	AF074924	CCDS3708.1	4q26	2008-08-04			ENSG00000164100	ENSG00000164100		"Sulfotransferases, membrane-bound"	7682	protein-coding gene	gene with protein product		603950				9915799	Standard	NM_004784		Approved	HSST3	uc003ibx.3	O95803	OTTHUMG00000132959	ENST00000296499.5:c.1881C>G	chr4.hg19:g.119154228C>G	ENSP00000296499:p.Ser627Arg	119.0	0.0		80.0	27.0	NM_004784	B4DI67|Q4W5C1|Q4W5D0|Q6UWC5|Q9UP21	Missense_Mutation	SNP	ENST00000296499.5	hg19	CCDS3708.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.188441	0.78789	.	.	ENSG00000164100	ENST00000296499;ENST00000433996	T;T	0.56611	0.45;0.45	5.64	5.64	0.86602	Sulfotransferase domain (1);	0.042915	0.85682	D	0.000000	T	0.75421	0.3847	M	0.80982	2.52	0.41180	D	0.986227	D;D	0.76494	0.996;0.999	D;D	0.74674	0.913;0.984	T	0.77726	-0.2480	10	0.62326	D	0.03	.	19.7051	0.96069	0.0:1.0:0.0:0.0	.	546;627	B4DI67;O95803	.;NDST3_HUMAN	R	627;546	ENSP00000296499:S627R;ENSP00000396625:S546R	ENSP00000296499:S627R	S	+	3	2	NDST3	119373676	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.498000	0.45363	2.645000	0.89757	0.637000	0.83480	AGC	.	.		0.358	NDST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256517.4	NM_004784		G	119154228	C	G	119154228	3	3	332	1	0	0	0	0	1	0	0	0	10266	738	26	4	1911	4	NDST3	4	119154228	Missense_Mutation	SNP	C	TCGA-RC-A6M3-01A-11D-A32G-10	17037039	119154228	72000048	21	46291										
ARHGAP10	79658	hgsc.bcm.edu	37	chr4	148984418	148984418	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	gtcccctttccccttttctcCtcctgctactgtagcggaca	6	17	1	0			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr4:148984418C>T	ENST00000336498.3	+	21	2386	c.2147C>T	c.(2146-2148)cCt>cTt	p.P716L	ARHGAP10_ENST00000414545.2_Intron	NM_024605.3	NP_078881.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 10	0					establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			autonomic_ganglia(2)|endometrium(5)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		CCCTTTTCTCCTCCTGCTACT	0.542																																					p.P716L		Atlas-SNP	.											.	ARHGAP10	92	.	0			c.C2147T						.						133	93	106					4																	148984418		2203	4300	6503	SO:0001583	missense	79658	exon21			TTTCTCCTCCTGC	BC047914	CCDS34075.1	4q31.23	2013-09-20			ENSG00000071205	ENSG00000071205		"Rho GTPase activating proteins"	26099	protein-coding gene	gene with protein product		609746				8288572	Standard	NM_024605		Approved	FLJ20896, FLJ41791, GRAF2	uc003ilf.3	A1A4S6	OTTHUMG00000161460	ENST00000336498.3:c.2147C>T	chr4.hg19:g.148984418C>T	ENSP00000336923:p.Pro716Leu	77.0	0.0		65.0	16.0	NM_024605	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000336498.3	hg19	CCDS34075.1	.	.	.	.	.	.	.	.	.	.	C	7.301	0.612987	0.14066	.	.	ENSG00000071205	ENST00000336498	T	0.10960	2.82	5.32	-0.0926	0.13656	Src homology-3 domain (1);	1.180830	0.05937	N	0.636303	T	0.04952	0.0133	N	0.04203	-0.255	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.42481	-0.9449	10	0.30854	T	0.27	.	5.0433	0.14471	0.155:0.5414:0.0:0.3036	.	149;297;716	Q9H7G7;Q86T21;A1A4S6	.;.;RHG10_HUMAN	L	716	ENSP00000336923:P716L	ENSP00000336923:P716L	P	+	2	0	ARHGAP10	149203868	0.000000	0.05858	0.001000	0.08648	0.048000	0.14542	-0.760000	0.04756	-0.394000	0.07727	0.455000	0.32223	CCT	.	.		0.542	ARHGAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365005.1	NM_024605		T	148984418	C	T	148984418	3	4	332	1	0	0	0	0	1	0	0	0	862	681	24	3	2229	3	ARHGAP10	4	148984418	Missense_Mutation	SNP	C	TCGA-RC-A6M3-01A-11D-A32G-10	29830190	148984418	42169858	22	46292										
PDGFC	56034	hgsc.bcm.edu	37	chr4	157892010	157892019	+	Frame_Shift_Del	DEL	GGCCGGCCAG	GGCCGGCCAG	-													0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	cgcctgagtcccctgtctctGgccggccagggcagatgtca					rs200141022		TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	GGCCGGCCAG	GGCCGGCCAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr4:157892010_157892019delGGCCGGCCAG	ENST00000502773.1	-	1	527_536	c.37_46delCTGGCCGGCC	c.(37-48)ctggccggccagfs	p.LAGQ13fs	PDGFC_ENST00000541126.1_5'UTR|PDGFC_ENST00000422544.2_Frame_Shift_Del_p.LAGQ13fs	NM_016205.2	NP_057289.1	Q9NRA1	PDGFC_HUMAN	platelet derived growth factor C	13					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cellular response to amino acid stimulus (GO:0071230)|central nervous system development (GO:0007417)|organ morphogenesis (GO:0009887)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell division (GO:0051781)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.08)|Kidney(143;0.0977)|COAD - Colon adenocarcinoma(41;0.212)		CCCTGTCTCTGGCCGGCCAGGGCAGATGTC	0.581											OREG0016375	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.13_16del		Atlas-Indel,Pindel	.											.	PDGFC	46	.	0			c.38_47del						.																																			SO:0001589	frameshift_variant	56034	exon1			.	AF091434	CCDS3795.1	4q32	2008-02-05			ENSG00000145431	ENSG00000145431			8801	protein-coding gene	gene with protein product		608452				10858496, 10858548	Standard	NM_016205		Approved	SCDGF, fallotein	uc003iph.2	Q9NRA1	OTTHUMG00000161803	ENST00000502773.1:c.37_46delCTGGCCGGCC	chr4.hg19:g.157892010_157892019delGGCCGGCCAG	ENSP00000422464:p.Leu13fs	71.0	0.0	1789	43.0	11.0	NM_016205	B4DU34|B9EGR8|Q4W5M9|Q9UL22	Frame_Shift_Del	DEL	ENST00000502773.1	hg19	CCDS3795.1																																																																																			.	.		0.581	PDGFC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366123.1			-	157892019	GGCCGGCCAG	-	157892010	7	5	332	1	0	1	0	1	0	0	0	0	11668	1357	47	0	1015	0	PDGFC	4	157892010	Frame_Shift_Del	DEL	GGCCGGCCAG	TCGA-RC-A6M3-01A-11D-A32G-10	8907592	157892010	33262266	23	46293										
ADAMTS16	170690	hgsc.bcm.edu	37	chr5	5200316	5200316	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	caacatcatgtcccctacatTggcaggacgcaatggagtct	9	12	2	0			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr5:5200316T>C	ENST00000274181.7	+	9	1523	c.1385T>C	c.(1384-1386)tTg>tCg	p.L462S	ADAMTS16_ENST00000511368.1_Missense_Mutation_p.L462S	NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16	462	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				branching involved in ureteric bud morphogenesis (GO:0001658)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(72)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	107						TCCCCTACATTGGCAGGACGC	0.473																																					p.L462S		Atlas-SNP	.											.	ADAMTS16	543	.	0			c.T1385C						.						88	91	90					5																	5200316		1972	4176	6148	SO:0001583	missense	170690	exon9			CTACATTGGCAGG	AJ315734	CCDS43299.1	5p15	2008-07-18	2005-08-19		ENSG00000145536	ENSG00000145536		"ADAM metallopeptidases with thrombospondin type 1 motif"	17108	protein-coding gene	gene with protein product		607510	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 16"			11867212	Standard	NM_139056		Approved	ADAMTS16s	uc003jdl.3	Q8TE57	OTTHUMG00000161663	ENST00000274181.7:c.1385T>C	chr5.hg19:g.5200316T>C	ENSP00000274181:p.Leu462Ser	71.0	0.0		92.0	24.0	NM_139056	C6G490|Q8IVE2	Missense_Mutation	SNP	ENST00000274181.7	hg19	CCDS43299.1	.	.	.	.	.	.	.	.	.	.	T	17.97	3.518284	0.64634	.	.	ENSG00000145536	ENST00000274181;ENST00000511368;ENST00000536857	D;D	0.87029	-2.2;-2.2	4.76	4.76	0.60689	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.64402	D	0.000017	D	0.92622	0.7656	M	0.75777	2.31	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.93472	0.6820	10	0.87932	D	0	.	13.5732	0.61858	0.0:0.0:0.0:1.0	.	462;462;462	Q8TE57;Q8TE57-2;Q2XQZ0	ATS16_HUMAN;.;.	S	462	ENSP00000274181:L462S;ENSP00000421631:L462S	ENSP00000274181:L462S	L	+	2	0	ADAMTS16	5253316	1.000000	0.71417	0.826000	0.32828	0.535000	0.34838	7.425000	0.80255	1.903000	0.55091	0.533000	0.62120	TTG	.	.		0.473	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365657.1	NM_139056		C	5200316	T	C	5200316	3	2	332	1	0	0	0	0	1	0	0	0	261	1821	63	2	1419	2	ADAMTS16	5	5200316	Missense_Mutation	SNP	T	TCGA-RC-A6M3-01A-11D-A32G-10		5200316	175714944	24	46294										
SEMA6A	57556	hgsc.bcm.edu	37	chr5	115782757	115782757	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	ccagggaggcctcccgctgtGgaactttggggggcaggctg	18	11	0	0			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr5:115782757G>A	ENST00000343348.6	-	19	3432	c.2645C>T	c.(2644-2646)cCa>cTa	p.P882L	CTB-118N6.3_ENST00000508640.1_RNA|CTB-118N6.3_ENST00000510682.1_RNA|SEMA6A_ENST00000282394.6_Missense_Mutation_p.P359L|SEMA6A_ENST00000257414.8_Missense_Mutation_p.P899L|CTB-118N6.3_ENST00000508424.1_RNA|CTB-118N6.3_ENST00000512128.1_RNA|SEMA6A_ENST00000510263.1_Missense_Mutation_p.P882L|SEMA6A_ENST00000503865.1_Missense_Mutation_p.P261L|SEMA6A_ENST00000513137.1_Missense_Mutation_p.P309L|CTB-118N6.3_ENST00000514214.1_RNA	NM_020796.3	NP_065847	Q9H2E6	SEM6A_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	882					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|centrosome localization (GO:0051642)|cytoskeleton organization (GO:0007010)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|positive regulation of neuron migration (GO:2001224)|semaphorin-plexin signaling pathway (GO:0071526)	axon (GO:0030424)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31		all_cancers(142;0.00316)|all_epithelial(76;5.71e-05)|Prostate(80;0.00845)|Ovarian(225;0.0796)|Lung NSC(810;0.171)|all_lung(232;0.203)		OV - Ovarian serous cystadenocarcinoma(64;1.59e-08)|Epithelial(69;2e-08)|all cancers(49;5.7e-08)|COAD - Colon adenocarcinoma(49;0.151)		CTCCCGCTGTGGAACTTTGGG	0.592																																					p.P882L		Atlas-SNP	.											.	SEMA6A	93	.	0			c.C2645T						.						108	114	112					5																	115782757		1948	4111	6059	SO:0001583	missense	57556	exon19			CGCTGTGGAACTT	AB037789	CCDS47256.1, CCDS75288.1	5q23.1	2014-07-29			ENSG00000092421			"Semaphorins"	10738	protein-coding gene	gene with protein product	"sema VIa"	605885		SEMAQ		9204478, 10993894	Standard	XM_006714663		Approved	KIAA1368, SEMA6A1, SEMA, HT018	uc010jck.3	Q9H2E6	OTTHUMG00000162987	ENST00000343348.6:c.2645C>T	chr5.hg19:g.115782757G>A	ENSP00000345512:p.Pro882Leu	129.0	0.0		110.0	36.0	NM_020796	Q9P2H9	Missense_Mutation	SNP	ENST00000343348.6	hg19	CCDS47256.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.34|19.34	3.809732|3.809732	0.70797|0.70797	.|.	.|.	ENSG00000092421|ENSG00000092421	ENST00000515129|ENST00000343348;ENST00000257414;ENST00000513137;ENST00000282394;ENST00000503865;ENST00000510263	.|T;T;T;T;T;T	.|0.79247	.|0.34;0.34;-1.25;0.76;-1.08;0.34	5.22|5.22	5.22|5.22	0.72569|0.72569	.|.	.|0.508000	.|0.20614	.|N	.|0.088904	D|D	0.87148|0.87148	0.6105|0.6105	L|L	0.61218|0.61218	1.895|1.895	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D;D	.|0.91635	.|0.998;0.998;0.999;0.999;0.999;0.999	D|D	0.88163|0.88163	0.2859|0.2859	5|10	.|0.87932	.|D	.|0	.|.	18.3651|18.3651	0.90388|0.90388	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|261;882;426;899;359;309	.|E9PDV9;Q9H2E6;Q96SM8;Q9H2E6-2;E7ERF3;B3KU01	.|.;SEM6A_HUMAN;.;.;.;.	Y|L	397|882;899;309;359;261;882	.|ENSP00000345512:P882L;ENSP00000257414:P899L;ENSP00000422997:P309L;ENSP00000282394:P359L;ENSP00000425364:P261L;ENSP00000424388:P882L	.|ENSP00000257414:P899L	H|P	-|-	1|2	0|0	SEMA6A|SEMA6A	115810656|115810656	1.000000|1.000000	0.71417|0.71417	0.902000|0.902000	0.35471|0.35471	0.914000|0.914000	0.54420|0.54420	9.417000|9.417000	0.97391|0.97391	2.436000|2.436000	0.82500|0.82500	0.563000|0.563000	0.77884|0.77884	CAC|CCA	.	.		0.592	SEMA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371270.1	NM_020796		A	115782757	G	A	115782757	3	1	332	1	0	0	0	0	1	0	0	0	14054	1348	47	3	451	3	SEMA6A	5	115782757	Missense_Mutation	SNP	G	TCGA-RC-A6M3-01A-11D-A32G-10	110582441	115782757	65132503	25	46295										
ZNF454	285676	hgsc.bcm.edu	37	chr5	178391941	178391941	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	acctagcaaaaatgcctttgAgtgtagtgagtgtggaaaag	12	5	0	2			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr5:178391941A>G	ENST00000320129.3	+	5	839	c.536A>G	c.(535-537)gAg>gGg	p.E179G	ZNF454_ENST00000519564.1_Missense_Mutation_p.E179G	NM_001178090.1|NM_182594.2	NP_001171561.1|NP_872400.2	Q8N9F8	ZN454_HUMAN	zinc finger protein 454	179					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(11)|lung(18)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	46	all_cancers(89;0.000904)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.225)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.234)		AATGCCTTTGAGTGTAGTGAG	0.363																																					p.E179G		Atlas-SNP	.											.	ZNF454	99	.	0			c.A536G						.						59	60	60					5																	178391941		2203	4300	6503	SO:0001583	missense	285676	exon5			CCTTTGAGTGTAG	AK094763	CCDS4441.1	5q35.3	2013-01-08			ENSG00000178187	ENSG00000178187		"Zinc fingers, C2H2-type", "-"	21200	protein-coding gene	gene with protein product							Standard	NM_182594		Approved	FLJ37444	uc021yjc.1	Q8N9F8	OTTHUMG00000130891	ENST00000320129.3:c.536A>G	chr5.hg19:g.178391941A>G	ENSP00000326249:p.Glu179Gly	78.0	0.0		87.0	10.0	NM_001178089	Q2M1P2|Q2M323	Missense_Mutation	SNP	ENST00000320129.3	hg19	CCDS4441.1	.	.	.	.	.	.	.	.	.	.	A	6.641	0.486839	0.12641	.	.	ENSG00000178187	ENST00000320129;ENST00000519564	T;T	0.53206	0.63;0.63	4.75	4.75	0.60458	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.182769	0.26390	N	0.024657	T	0.39358	0.1075	L	0.41356	1.27	0.20307	N	0.999916	B	0.27316	0.175	B	0.31390	0.129	T	0.38394	-0.9663	10	0.59425	D	0.04	-15.3568	8.7512	0.34616	0.8087:0.1913:0.0:0.0	.	179	Q8N9F8	ZN454_HUMAN	G	179	ENSP00000326249:E179G;ENSP00000430354:E179G	ENSP00000326249:E179G	E	+	2	0	ZNF454	178324547	0.003000	0.15002	0.979000	0.43373	0.243000	0.25628	2.021000	0.41020	2.117000	0.64856	0.528000	0.53228	GAG	.	.		0.363	ZNF454-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253476.2	XM_209718		G	178391941	A	G	178391941	3	3	332	1	0	0	0	0	1	0	0	0	17938	304	11	2	550	2	ZNF454	5	178391941	Missense_Mutation	SNP	A	TCGA-RC-A6M3-01A-11D-A32G-10	62609184	178391941	2523319	26	46296										
LGSN	51557	hgsc.bcm.edu	37	chr6	63990999	63990999	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	caaaactctaaaggttgataActctggcattaggactatgt	8	7	2	1			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr6:63990999A>C	ENST00000370657.4	-	4	490	c.457T>G	c.(457-459)Tta>Gta	p.L153V	LGSN_ENST00000370658.5_Missense_Mutation_p.L153V			Q5TDP6	LGSN_HUMAN	lengsin, lens protein with glutamine synthetase domain	153					glutamine biosynthetic process (GO:0006542)	plasma membrane (GO:0005886)	glutamate-ammonia ligase activity (GO:0004356)			NS(1)|endometrium(2)|large_intestine(5)|lung(16)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						AAGGTTGATAACTCTGGCATT	0.423																																					p.L153V		Atlas-SNP	.											.	LGSN	82	.	0			c.T457G						.						141	132	135					6																	63990999		2203	4300	6503	SO:0001583	missense	51557	exon4			TTGATAACTCTGG	AF242388	CCDS4964.1, CCDS55027.1	6q12	2013-09-19	2008-09-19	2008-09-19	ENSG00000146166	ENSG00000146166			21016	protein-coding gene	gene with protein product		611470	"glutamate-ammonia ligase (glutamine synthetase) domain containing 1"	GLULD1		12107412	Standard	NM_016571		Approved	LGS	uc003peh.3	Q5TDP6	OTTHUMG00000014946	ENST00000370657.4:c.457T>G	chr6.hg19:g.63990999A>C	ENSP00000359691:p.Leu153Val	124.0	0.0		135.0	19.0	NM_016571	A1L421|Q0PVN9|Q0PVP0|Q9NYJ0	Missense_Mutation	SNP	ENST00000370657.4	hg19	CCDS4964.1	.	.	.	.	.	.	.	.	.	.	A	3.089	-0.187352	0.06299	.	.	ENSG00000146166	ENST00000370658;ENST00000370657	T;T	0.47869	0.83;0.83	5.7	-11.4	0.00090	Glutamine synthetase, beta-Grasp (3);	0.061115	0.64402	D	0.000004	T	0.27489	0.0675	M	0.82193	2.58	0.20307	N	0.999912	B;B	0.22800	0.075;0.019	B;B	0.37731	0.107;0.257	T	0.51212	-0.8734	10	0.52906	T	0.07	-7.0035	10.5622	0.45152	0.6646:0.0643:0.2064:0.0647	.	153;153	Q5TDP6-2;Q5TDP6	.;LGSN_HUMAN	V	153	ENSP00000359692:L153V;ENSP00000359691:L153V	ENSP00000359691:L153V	L	-	1	2	LGSN	64048958	0.998000	0.40836	0.000000	0.03702	0.003000	0.03518	0.589000	0.23939	-3.794000	0.00106	-3.611000	0.00028	TTA	.	.		0.423	LGSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041076.2	NM_016571		C	63990999	A	C	63990999	3	2	332	1	0	0	0	0	1	0	0	0	8768	40	2	5	1076	5	LGSN	6	63990999	Missense_Mutation	SNP	A	TCGA-RC-A6M3-01A-11D-A32G-10		63990999	107124068	27	46297										
COL12A1	1303	hgsc.bcm.edu	37	chr6	75861697	75861697	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	ttttcgagctcgaggtctcaTgccagcttgggtcctgaagt	12	10	1	1			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr6:75861697T>C	ENST00000322507.8	-	20	4195	c.3886A>G	c.(3886-3888)Atg>Gtg	p.M1296V	COL12A1_ENST00000483888.2_Missense_Mutation_p.M1296V|COL12A1_ENST00000416123.2_Missense_Mutation_p.M1296V|COL12A1_ENST00000345356.6_Missense_Mutation_p.M132V	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	1296	VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						CGAGGTCTCATGCCAGCTTGG	0.438																																					p.M1296V		Atlas-SNP	.											.	COL12A1	385	.	0			c.A3886G						.						173	166	168					6																	75861697		1948	4160	6108	SO:0001583	missense	1303	exon20			GTCTCATGCCAGC	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.3886A>G	chr6.hg19:g.75861697T>C	ENSP00000325146:p.Met1296Val	116.0	0.0		112.0	37.0	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	hg19	CCDS43482.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.55|14.55	2.567415|2.567415	0.45694|0.45694	.|.	.|.	ENSG00000111799|ENSG00000111799	ENST00000419671|ENST00000322507;ENST00000432784;ENST00000345356;ENST00000416123;ENST00000483888	.|D;D;D;D	.|0.82893	.|-1.66;-1.66;-1.66;-1.66	5.68|5.68	4.49|4.49	0.54785|0.54785	.|von Willebrand factor, type A (3);	.|0.115748	.|0.64402	.|D	.|0.000017	T|T	0.61776|0.61776	0.2374|0.2374	L|L	0.41961|0.41961	1.31|1.31	0.37323|0.37323	D|D	0.909637|0.909637	.|B;B	.|0.22211	.|0.007;0.066	.|B;B	.|0.25759	.|0.039;0.063	T|T	0.56805|0.56805	-0.7918|-0.7918	5|10	.|0.26408	.|T	.|0.33	.|.	8.4367|8.4367	0.32791|0.32791	0.1369:0.0:0.1271:0.7361|0.1369:0.0:0.1271:0.7361	.|.	.|132;1296	.|Q99715-2;Q99715	.|.;COCA1_HUMAN	R|V	37|1296;1296;132;1296;1296	.|ENSP00000325146:M1296V;ENSP00000305147:M132V;ENSP00000412864:M1296V;ENSP00000421216:M1296V	.|ENSP00000325146:M1296V	H|M	-|-	2|1	0|0	COL12A1|COL12A1	75918417|75918417	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	3.124000|3.124000	0.50461|0.50461	0.945000|0.945000	0.37605|0.37605	0.528000|0.528000	0.53228|0.53228	CAT|ATG	.	.		0.438	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		C	75861697	T	C	75861697	3	2	332	1	0	0	0	0	1	0	0	0	3671	1464	51	2	5493	2	COL12A1	6	75861697	Missense_Mutation	SNP	T	TCGA-RC-A6M3-01A-11D-A32G-10	11870698	75861697	95253370	28	46298										
SNAP91	9892	hgsc.bcm.edu	37	chr6	84270639	84270639	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	ggccccggcaacaggaggaaCtgaactggttggaggtacag	16	9	0	1			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr6:84270639C>G	ENST00000439399.2	-	27	2786	c.2470G>C	c.(2470-2472)Gtt>Ctt	p.V824L	SNAP91_ENST00000428679.2_Missense_Mutation_p.V824L|SNAP91_ENST00000195649.6_Missense_Mutation_p.V819L|SNAP91_ENST00000520302.1_Missense_Mutation_p.V794L|SNAP91_ENST00000521743.1_Missense_Mutation_p.V824L|SNAP91_ENST00000437520.1_Missense_Mutation_p.V517L|SNAP91_ENST00000521485.1_Missense_Mutation_p.V819L|SNAP91_ENST00000520213.1_Missense_Mutation_p.V517L|SNAP91_ENST00000369694.2_Missense_Mutation_p.V824L	NM_014841.2	NP_055656.1	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa	824	Pro-rich.				clathrin coat assembly (GO:0048268)|protein transport (GO:0015031)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|protein kinase binding (GO:0019901)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(22)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		ACAGGAGGAACTGAACTGGTT	0.428																																					p.V824L		Atlas-SNP	.											.	SNAP91	199	.	0			c.G2470C						.						46	46	46					6																	84270639		1947	4158	6105	SO:0001583	missense	9892	exon26			GAGGAACTGAACT	AB014556	CCDS47455.1, CCDS56437.1, CCDS56438.1	6q15	2012-12-07	2012-12-07		ENSG00000065609	ENSG00000065609			14986	protein-coding gene	gene with protein product		607923	"synaptosomal-associated protein, 91 kDa (mouse) homolog", "synaptosomal-associated protein, 91kDa homolog (mouse)"			9734811, 12493563, 10436022	Standard	NM_014841		Approved	KIAA0656, AP180, CALM	uc003pka.3	O60641	OTTHUMG00000015114	ENST00000439399.2:c.2470G>C	chr6.hg19:g.84270639C>G	ENSP00000400459:p.Val824Leu	120.0	0.0		124.0	40.0	NM_001242792	A8K0L7|E5RI02|Q5JX13|Q68DL9|Q6P9D3|Q9NTY7	Missense_Mutation	SNP	ENST00000439399.2	hg19	CCDS47455.1	.	.	.	.	.	.	.	.	.	.	C	16.29	3.082577	0.55861	.	.	ENSG00000065609	ENST00000521485;ENST00000369694;ENST00000439399;ENST00000195649;ENST00000428679;ENST00000437520;ENST00000520302;ENST00000521743;ENST00000520213;ENST00000523448	T;T;T;T;T;T;T;T;T;T	0.23348	2.48;2.49;2.49;2.48;2.49;2.51;2.48;2.49;2.51;1.91	5.46	5.46	0.80206	.	0.669551	0.14796	N	0.297925	T	0.39306	0.1073	M	0.66939	2.045	0.28030	N	0.934172	B;P;P;P;P	0.47910	0.034;0.902;0.841;0.841;0.841	B;P;P;P;P	0.61722	0.023;0.893;0.846;0.846;0.846	T	0.16335	-1.0406	10	0.49607	T	0.09	-7.8988	18.8976	0.92430	0.0:1.0:0.0:0.0	.	700;517;794;824;822	B7Z2N2;O60641-3;E5RI02;O60641;E1P549	.;.;.;AP180_HUMAN;.	L	819;824;824;819;824;517;794;824;517;165	ENSP00000429776:V819L;ENSP00000358708:V824L;ENSP00000400459:V824L;ENSP00000195649:V819L;ENSP00000412492:V824L;ENSP00000413277:V517L;ENSP00000428511:V794L;ENSP00000428215:V824L;ENSP00000428026:V517L;ENSP00000430255:V165L	ENSP00000195649:V819L	V	-	1	0	SNAP91	84327358	0.999000	0.42202	0.995000	0.50966	0.763000	0.43281	3.668000	0.54554	2.542000	0.85734	0.555000	0.69702	GTT	.	.		0.428	SNAP91-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375296.1			G	84270639	C	G	84270639	3	3	332	1	0	0	0	0	1	0	0	0	14848	565	20	4	265	4	SNAP91	6	84270639	Missense_Mutation	SNP	C	TCGA-RC-A6M3-01A-11D-A32G-10	8408942	84270639	86844428	29	46299										
SOBP	55084	hgsc.bcm.edu	37	chr6	107956286	107956286	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	ccgcctcccgagcagccgccGccgccgccgccgcccgcgcc	12	26	0	0	rs541688197	byFrequency	TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr6:107956286G>A	ENST00000317357.5	+	6	2897	c.2238G>A	c.(2236-2238)ccG>ccA	p.P746P	SOBP_ENST00000494935.1_3'UTR	NM_018013.3	NP_060483.3			sine oculis binding protein homolog (Drosophila)											endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	26		all_cancers(87;5.26e-06)|Acute lymphoblastic leukemia(125;2.87e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.00193)|Colorectal(196;0.156)		BRCA - Breast invasive adenocarcinoma(108;0.026)|all cancers(137;0.087)|Epithelial(106;0.104)|OV - Ovarian serous cystadenocarcinoma(136;0.154)		AGCAgccgccgccgccgccgc	0.731																																					p.P746P		Atlas-SNP	.											.	SOBP	53	.	0			c.G2238A						.						5	7	6					6																	107956286		1616	3651	5267	SO:0001819	synonymous_variant	55084	exon6			GCCGCCGCCGCCG	AK001021	CCDS43488.1	6q21	2007-03-15			ENSG00000112320	ENSG00000112320			29256	protein-coding gene	gene with protein product		613667					Standard	NM_018013		Approved	FLJ10159	uc003prx.3	A7XYQ1	OTTHUMG00000015312	ENST00000317357.5:c.2238G>A	chr6.hg19:g.107956286G>A		39.0	0.0		38.0	12.0	NM_018013		Silent	SNP	ENST00000317357.5	hg19	CCDS43488.1																																																																																			.	.		0.731	SOBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041693.2	NM_018013		A	107956286	G	A	107956286	2	1	332	1	0	0	0	0	0	0	0	1	14927	1074	38	1		1	SOBP	6	107956286	Silent	SNP	G	TCGA-RC-A6M3-01A-11D-A32G-10	23685647	107956286	63158781	30	46300										
FAM184A	79632	hgsc.bcm.edu	37	chr6	119338099	119338099	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	cttgctgagttctctttgctTcatttactttctaaaattaa	4	8	3	1			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr6:119338099T>C	ENST00000338891.7	-	5	1786	c.1343A>G	c.(1342-1344)gAa>gGa	p.E448G	FAM184A_ENST00000368475.4_Missense_Mutation_p.E328G|FAM184A_ENST00000522284.1_Missense_Mutation_p.E328G|FAM184A_ENST00000521531.1_Missense_Mutation_p.E448G|FAM184A_ENST00000352896.5_Missense_Mutation_p.E328G|RP11-351A11.1_ENST00000518570.1_RNA	NM_024581.4	NP_078857.5	Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A	448						extracellular space (GO:0005615)				breast(2)|central_nervous_system(2)|endometrium(2)|kidney(5)|large_intestine(19)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(5)	52						TCTCTTTGCTTCATTTACTTT	0.333																																					p.E448G		Atlas-SNP	.											.	FAM184A	109	.	0			c.A1343G						.						77	73	74					6																	119338099		1802	4065	5867	SO:0001583	missense	79632	exon5			TTTGCTTCATTTA	BC009055	CCDS43499.1, CCDS43500.1, CCDS75508.1	6q22.31	2008-08-14	2008-08-14	2008-08-14	ENSG00000111879	ENSG00000111879			20991	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 60"	C6orf60		11230166	Standard	NM_024581		Approved	FLJ13942	uc003pyj.3	Q8NB25	OTTHUMG00000015471	ENST00000338891.7:c.1343A>G	chr6.hg19:g.119338099T>C	ENSP00000342604:p.Glu448Gly	310.0	0.0		292.0	103.0	NM_024581	B9DI75|F8W8D6|Q5TBS9|Q7Z323|Q96GY8|Q9H0J8|Q9H851	Missense_Mutation	SNP	ENST00000338891.7	hg19	CCDS43499.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.2|20.2	3.946402|3.946402	0.73672|0.73672	.|.	.|.	ENSG00000111879|ENSG00000111879	ENST00000338891;ENST00000352896;ENST00000368475;ENST00000521531;ENST00000522284|ENST00000448815	T;T;T;T;T|.	0.42513|.	0.97;0.97;0.97;0.97;0.97|.	4.94|4.94	4.94|4.94	0.65067|0.65067	.|.	0.052144|.	0.64402|.	D|.	0.000001|.	T|T	0.63558|0.63558	0.2521|0.2521	M|M	0.66939|0.66939	2.045|2.045	0.80722|0.80722	D|D	1|1	P;B;P|.	0.44044|.	0.787;0.449;0.825|.	B;B;B|.	0.44044|.	0.439;0.154;0.398|.	T|T	0.65001|0.65001	-0.6274|-0.6274	10|5	0.42905|.	T|.	0.14|.	-7.9209|-7.9209	14.5917|14.5917	0.68371|0.68371	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	448;328;448|.	Q8NB25-2;F8W8D6;Q8NB25|.	.;.;F184A_HUMAN|.	G|E	448;328;328;448;328|34	ENSP00000342604:E448G;ENSP00000326608:E328G;ENSP00000357460:E328G;ENSP00000430442:E448G;ENSP00000429826:E328G|.	ENSP00000342604:E448G|.	E|K	-|-	2|1	0|0	FAM184A|FAM184A	119379798|119379798	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.899000|0.899000	0.52679|0.52679	6.519000|6.519000	0.73768|0.73768	1.876000|1.876000	0.54355|0.54355	0.402000|0.402000	0.26972|0.26972	GAA|AAG	.	.		0.333	FAM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042009.3	NM_024581		C	119338099	T	C	119338099	3	2	332	1	0	0	0	0	1	0	0	0	5516	1783	62	2	2135	2	FAM184A	6	119338099	Missense_Mutation	SNP	T	TCGA-RC-A6M3-01A-11D-A32G-10	11381813	119338099	51776968	31	46301										
OPRM1	4988	hgsc.bcm.edu	37	chr6	154414480	154414480	+	Intron	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	tgtaccctggaccactgcaaGgacctcttgtcagatatgac	9	12	2	2	rs200463796		TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr6:154414480G>C	ENST00000330432.7	+	3	1401				OPRM1_ENST00000337049.4_Intron|OPRM1_ENST00000518759.1_Intron|OPRM1_ENST00000419506.2_Intron|OPRM1_ENST00000522236.1_Intron|OPRM1_ENST00000452687.2_Intron|OPRM1_ENST00000520708.1_Intron|OPRM1_ENST00000414028.2_Intron|OPRM1_ENST00000522555.1_Intron|OPRM1_ENST00000435918.2_Intron|OPRM1_ENST00000360422.4_Intron|OPRM1_ENST00000434900.2_Intron|OPRM1_ENST00000524163.1_Intron|OPRM1_ENST00000229768.5_Missense_Mutation_p.G414R	NM_000914.3	NP_000905.3	P35372	OPRM_HUMAN	opioid receptor, mu 1						adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavioral response to ethanol (GO:0048149)|calcium ion transmembrane transport (GO:0070588)|cellular response to stress (GO:0033554)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|locomotory behavior (GO:0007626)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of Wnt protein secretion (GO:0061358)|neuropeptide signaling pathway (GO:0007218)|opioid receptor signaling pathway (GO:0038003)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neurogenesis (GO:0050769)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-endorphin receptor activity (GO:0004979)|G-protein alpha-subunit binding (GO:0001965)|G-protein coupled receptor activity (GO:0004930)|morphine receptor activity (GO:0038047)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(15)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	33		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;9.26e-11)|BRCA - Breast invasive adenocarcinoma(81;0.0154)	Alfentanil(DB00802)|Alvimopan(DB06274)|Amitriptyline(DB00321)|Anileridine(DB00913)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dezocine(DB01209)|Diphenoxylate(DB01081)|Ethylmorphine(DB01466)|Fentanyl(DB00813)|Heroin(DB01452)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levallorphan(DB00504)|Levomethadyl Acetate(DB01227)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Methadyl Acetate(DB01433)|Methylnaltrexone(DB06800)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Ondansetron(DB00904)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Pentazocine(DB00652)|Pethidine(DB00454)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	ACCACTGCAAGGACCTCTTGT	0.517																																					p.G414R		Atlas-SNP	.											OPRM1,NS,carcinoma,0,1	OPRM1	241	.	0			c.G1240C						.						241	231	234					6																	154414480		1984	4167	6151	SO:0001627	intron_variant	4988	exon4			CTGCAAGGACCTC	L29301	CCDS43517.1, CCDS43518.1, CCDS47503.1, CCDS47504.1, CCDS47505.1, CCDS47506.1, CCDS47507.1, CCDS47508.1, CCDS55071.1, CCDS55068.1, CCDS55069.1, CCDS55070.1	6q24-q25	2012-08-08			ENSG00000112038	ENSG00000112038		"GPCR / Class A : Opioid receptors"	8156	protein-coding gene	gene with protein product		600018					Standard	NM_001145285		Approved	MOR1	uc003qpo.1	P35372	OTTHUMG00000015870	ENST00000330432.7:c.1164+1873G>C	chr6.hg19:g.154414480G>C		109.0	0.0		84.0	31.0	NM_001008505	B0FXJ1|B2R9S7|B8Q1L7|B8Q1L8|B8Q1L9|E7EWZ3|G8XRH6|G8XRH8|Q12930|Q4VWM1|Q4VWM2|Q4VWM3|Q4VWM4|Q4VWM6|Q4VWX6|Q5TDA1|Q6UPP1|Q6UQ80|Q7Z2D8|Q86V80|Q8IWW3|Q8IWW4|Q9UCZ4|Q9UN57	Missense_Mutation	SNP	ENST00000330432.7	hg19	CCDS55070.1	.	.	.	.	.	.	.	.	.	.	G	12.41	1.929945	0.34096	.	.	ENSG00000112038	ENST00000229768	T	0.71341	-0.56	5.56	0.708	0.18144	.	.	.	.	.	T	0.35068	0.0919	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.32981	-0.9886	8	0.66056	D	0.02	.	3.9214	0.09245	0.3373:0.0:0.506:0.1567	.	414	P35372-3	.	R	414	ENSP00000229768:G414R	ENSP00000229768:G414R	G	+	1	0	OPRM1	154456173	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.194000	0.17135	0.044000	0.15775	-0.140000	0.14226	GGA	.	.		0.517	OPRM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042786.2	NM_000914		C	154414480	G	C	154414480	1	2	332	0	1	0	0	0	0	0	0	0	10896	1001	35	4		4	OPRM1	6	154414480	Intron	SNP	G	TCGA-RC-A6M3-01A-11D-A32G-10	35076381	154414480	16700587	32	46302										
RNF216	54476	hgsc.bcm.edu	37	chr7	5754691	5754691	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	acacagttcttacctttccaGatccaaagactgcctcttgg	6	13	2	2			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr7:5754691G>C	ENST00000425013.2	-	11	1879	c.1655C>G	c.(1654-1656)tCt>tGt	p.S552C	RNF216_ENST00000389902.3_Missense_Mutation_p.S609C	NM_207111.3|NM_207116.2	NP_996994.1|NP_996999.1	Q9NWF9	RN216_HUMAN	ring finger protein 216	552					apoptotic process (GO:0006915)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|regulation of defense response to virus by host (GO:0050691)|regulation of interferon-beta production (GO:0032648)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)		FBXL18/RNF216(2)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)|skin(1)|urinary_tract(4)	33		Ovarian(82;0.07)		UCEC - Uterine corpus endometrioid carcinoma (126;0.135)|OV - Ovarian serous cystadenocarcinoma(56;2.69e-13)		TACCTTTCCAGATCCAAAGAC	0.448																																					p.S609C		Atlas-SNP	.											.	RNF216	71	.	0			c.C1826G						.						136	125	128					7																	5754691		2203	4300	6503	SO:0001583	missense	54476	exon11			TTTCCAGATCCAA	AY062174	CCDS34594.1, CCDS34595.1	7p22.1	2014-02-12	2007-08-20		ENSG00000011275	ENSG00000011275		"RING-type (C3HC4) zinc fingers"	21698	protein-coding gene	gene with protein product		609948					Standard	NM_207111		Approved	TRIAD3, UBCE7IP1, ZIN	uc003sox.2	Q9NWF9	OTTHUMG00000155500	ENST00000425013.2:c.1655C>G	chr7.hg19:g.5754691G>C	ENSP00000404602:p.Ser552Cys	54.0	0.0		62.0	20.0	NM_207111	Q6Y691|Q75ML7|Q7Z2H7|Q7Z7C1|Q8NHW7|Q9NYT1	Missense_Mutation	SNP	ENST00000425013.2	hg19	CCDS34595.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.127690	0.77549	.	.	ENSG00000011275	ENST00000425013;ENST00000389902;ENST00000458425	T;T	0.32515	1.45;1.45	5.88	5.88	0.94601	.	0.166604	0.49916	D	0.000130	T	0.56046	0.1959	M	0.61703	1.905	0.51012	D	0.9999	D;D	0.89917	0.998;1.0	D;D	0.87578	0.956;0.998	T	0.54050	-0.8351	10	0.66056	D	0.02	-17.5102	19.2161	0.93778	0.0:0.0:1.0:0.0	.	552;609	Q9NWF9;Q9NWF9-1	RN216_HUMAN;.	C	552;609;364	ENSP00000404602:S552C;ENSP00000374552:S609C	ENSP00000374552:S609C	S	-	2	0	RNF216	5721217	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.044000	0.71012	2.778000	0.95560	0.655000	0.94253	TCT	.	.		0.448	RNF216-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000340374.1	NM_207111		C	5754691	G	C	5754691	3	2	332	1	0	0	0	0	1	0	0	0	13495	942	33	4	973	4	RNF216	7	5754691	Missense_Mutation	SNP	G	TCGA-RC-A6M3-01A-11D-A32G-10		5754691	153383972	33	46303										
ZPBP	11055	hgsc.bcm.edu	37	chr7	49977181	49977181	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	ttgcattgaaggcaatgaatTccatcacgggggttatatga	11	6	1	3			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr7:49977181T>A	ENST00000046087.2	-	8	1068	c.999A>T	c.(997-999)ggA>ggT	p.G333G	ZPBP_ENST00000491129.1_Intron|ZPBP_ENST00000419417.1_Silent_p.G332G	NM_001159878.1|NM_007009.2	NP_001153350.1|NP_008940.2	Q9BS86	ZPBP1_HUMAN	zona pellucida binding protein	333					acrosome assembly (GO:0001675)|binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|extracellular region (GO:0005576)|nucleus (GO:0005634)|zona pellucida receptor complex (GO:0002199)				NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(3)	29	Glioma(55;0.08)|all_neural(89;0.245)					GGCAATGAATTCCATCACGGG	0.348																																					p.G333G		Atlas-SNP	.											.	ZPBP	65	.	0			c.A999T						.						101	102	101					7																	49977181		2203	4300	6503	SO:0001819	synonymous_variant	11055	exon8			ATGAATTCCATCA	D17570	CCDS5509.1, CCDS55110.1	7p14.3	2013-01-11			ENSG00000042813	ENSG00000042813		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15662	protein-coding gene	gene with protein product		608498				9378618	Standard	NM_007009		Approved	SP38, ZPBP1	uc003tou.3	Q9BS86	OTTHUMG00000023528	ENST00000046087.2:c.999A>T	chr7.hg19:g.49977181T>A		64.0	0.0		69.0	14.0	NM_007009	A4D253|C9JPU1|Q15941|Q75KX9|Q75MI3	Silent	SNP	ENST00000046087.2	hg19	CCDS5509.1																																																																																			.	.		0.348	ZPBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251374.1	NM_007009		A	49977181	T	A	49977181	2	1	332	1	0	0	0	0	0	0	0	1	18234	1770	62	4		4	ZPBP	7	49977181	Silent	SNP	T	TCGA-RC-A6M3-01A-11D-A32G-10	44222490	49977181	109161482	34	46304										
CCDC146	57639	hgsc.bcm.edu	37	chr7	76908085	76908085	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	tcagcaaaaatacaccaacaTtgttaaagaaatgaaagcaa	5	7	1	2			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr7:76908085T>C	ENST00000285871.4	+	12	1584	c.1457T>C	c.(1456-1458)aTt>aCt	p.I486T	CCDC146_ENST00000415740.2_3'UTR|CCDC146_ENST00000431197.1_Missense_Mutation_p.I200T	NM_020879.2	NP_065930.2	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	486										breast(3)|central_nervous_system(3)|endometrium(1)|kidney(4)|large_intestine(7)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	34		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)				TACACCAACATTGTTAAAGAA	0.299																																					p.I486T		Atlas-SNP	.											.	CCDC146	87	.	0			c.T1457C						.						68	64	66					7																	76908085		2202	4298	6500	SO:0001583	missense	57639	exon12			CCAACATTGTTAA	BC029458	CCDS34671.1	7q11.23	2011-09-07			ENSG00000135205	ENSG00000135205			29296	protein-coding gene	gene with protein product						10819331	Standard	NM_020879		Approved	KIAA1505	uc003uga.3	Q8IYE0	OTTHUMG00000162595	ENST00000285871.4:c.1457T>C	chr7.hg19:g.76908085T>C	ENSP00000285871:p.Ile486Thr	119.0	0.0		149.0	55.0	NM_020879	A8K8X6|Q9P223	Missense_Mutation	SNP	ENST00000285871.4	hg19	CCDS34671.1	.	.	.	.	.	.	.	.	.	.	T	6.083	0.383528	0.11524	.	.	ENSG00000135205	ENST00000285871;ENST00000431197	T;T	0.28069	1.63;1.63	5.17	2.69	0.31865	.	0.627918	0.17149	N	0.185140	T	0.20047	0.0482	L	0.34521	1.04	0.09310	N	1	B;B	0.27416	0.178;0.098	B;B	0.29942	0.053;0.109	T	0.29731	-1.0002	10	0.12103	T	0.63	-1.4516	7.7051	0.28646	0.0:0.0746:0.1401:0.7854	.	200;486	Q8IYE0-2;Q8IYE0	.;CC146_HUMAN	T	486;200	ENSP00000285871:I486T;ENSP00000413885:I200T	ENSP00000285871:I486T	I	+	2	0	AC007000.1	76746021	0.001000	0.12720	0.002000	0.10522	0.410000	0.31052	1.056000	0.30480	0.256000	0.21614	0.533000	0.62120	ATT	.	.		0.299	CCDC146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341449.1	NM_020879		C	76908085	T	C	76908085	3	2	332	1	0	0	0	0	1	0	0	0	2782	1493	52	2	1499	2	CCDC146	7	76908085	Missense_Mutation	SNP	T	TCGA-RC-A6M3-01A-11D-A32G-10	26930904	76908085	82230578	35	46305										
RP1L1	94137	hgsc.bcm.edu	37	chr8	10466938	10466938	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	cgtcctgctgcagctcggccGccatctggtccagcagatca	11	16	2	1			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr8:10466938G>T	ENST00000382483.3	-	4	4893	c.4670C>A	c.(4669-4671)gCg>gAg	p.A1557E		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1637					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		CAGCTCGGCCGCCATCTGGTC	0.657																																					p.A1557E		Atlas-SNP	.											.	RP1L1	453	.	0			c.C4670A						.						15	18	17					8																	10466938		2103	4222	6325	SO:0001583	missense	94137	exon4			TCGGCCGCCATCT	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.4670C>A	chr8.hg19:g.10466938G>T	ENSP00000371923:p.Ala1557Glu	49.0	0.0		57.0	4.0	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	hg19	CCDS43708.1	.	.	.	.	.	.	.	.	.	.	G	9.337	1.062151	0.19987	.	.	ENSG00000183638	ENST00000382483	T	0.04234	3.67	5.32	-0.25	0.13007	.	0.286195	0.18802	U	0.130778	T	0.03136	0.0092	N	0.14661	0.345	0.19575	N	0.999965	B	0.31730	0.337	B	0.30029	0.11	T	0.40079	-0.9582	10	0.44086	T	0.13	-11.317	11.6311	0.51175	0.8314:0.0:0.1686:0.0	.	1557	A6NKC6	.	E	1557	ENSP00000371923:A1557E	ENSP00000371923:A1557E	A	-	2	0	RP1L1	10504348	0.976000	0.34144	0.182000	0.23118	0.054000	0.15201	2.591000	0.46163	-0.285000	0.09089	-1.469000	0.01011	GCG	.	.		0.657	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			T	10466938	G	T	10466938	3	4	332	1	0	0	0	0	1	0	0	0	13548	1087	38	1	2536	1	RP1L1	8	10466938	Missense_Mutation	SNP	G	TCGA-RC-A6M3-01A-11D-A32G-10		10466938	135897084	36	46306										
SGCZ	137868	hgsc.bcm.edu	37	chr8	14181674	14181674	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	ctcagatataccttcaagtcGgattcccttcttggtgactc	7	12	3	2			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr8:14181674G>A	ENST00000382080.1	-	3	989	c.274C>T	c.(274-276)Cga>Tga	p.R92*	SGCZ_ENST00000421524.2_Intron	NM_139167.2	NP_631906.2	Q96LD1	SGCZ_HUMAN	sarcoglycan, zeta	79					membrane organization (GO:0061024)|muscle cell cellular homeostasis (GO:0046716)|muscle cell development (GO:0055001)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|sarcoglycan complex (GO:0016012)		p.R92*(1)		NS(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(14)|lung(15)|ovary(2)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	47				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)		CCTTCAAGTCGGATTCCCTTC	0.358																																					p.R92X		Atlas-SNP	.											SGCZ,colon,carcinoma,0,1	SGCZ	96	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C274T						.						118	112	114					8																	14181674		2203	4300	6503	SO:0001587	stop_gained	137868	exon3			CAAGTCGGATTCC	AY028700	CCDS5992.2	8p22	2014-09-17	2010-04-21		ENSG00000185053	ENSG00000185053			14075	protein-coding gene	gene with protein product		608113				12189167	Standard	XM_006716287		Approved	ZSG1	uc003wwq.3	Q96LD1	OTTHUMG00000090827	ENST00000382080.1:c.274C>T	chr8.hg19:g.14181674G>A	ENSP00000371512:p.Arg92*	61.0	0.0		48.0	9.0	NM_139167	Q6REU0	Nonsense_Mutation	SNP	ENST00000382080.1	hg19	CCDS5992.2	.	.	.	.	.	.	.	.	.	.	G	43	10.493145	0.99415	.	.	ENSG00000185053	ENST00000382080	.	.	.	5.27	5.27	0.74061	.	0.079076	0.52532	D	0.000064	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	17.8551	0.88760	0.0:0.0:1.0:0.0	.	.	.	.	X	92	.	ENSP00000371512:R92X	R	-	1	2	SGCZ	14226045	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.014000	0.64029	2.642000	0.89623	0.563000	0.77884	CGA	.	.		0.358	SGCZ-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207636.2	NM_139167		A	14181674	G	A	14181674	4	1	332	1	0	0	0	0	0	1	0	0	14219	1124	39	1	688	1	SGCZ	8	14181674	Nonsense_Mutation	SNP	G	TCGA-RC-A6M3-01A-11D-A32G-10	3714736	14181674	132182348	37	46307										
IDO2	169355	hgsc.bcm.edu	37	chr8	39836668	39836668	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	cctgagcttcctcaccatggGttatgtctggcaggaaggag	13	10	2	1			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr8:39836668G>C	ENST00000389060.4	+	3	278	c.278G>C	c.(277-279)gGt>gCt	p.G93A	IDO2_ENST00000502986.2_Missense_Mutation_p.G106A|IDO2_ENST00000343295.4_3'UTR|RP11-44K6.3_ENST00000517623.1_RNA			Q6ZQW0	I23O2_HUMAN	indoleamine 2,3-dioxygenase 2	93					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)|tryptophan catabolic process to kynurenine (GO:0019441)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	heme binding (GO:0020037)|indoleamine 2,3-dioxygenase activity (GO:0033754)|metal ion binding (GO:0046872)|tryptophan 2,3-dioxygenase activity (GO:0004833)	p.G93A(1)|p.G106A(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)	18						CTCACCATGGGTTATGTCTGG	0.612																																					p.G106A		Atlas-SNP	.											IDO2_ENST00000502986,NS,carcinoma,0,2	IDO2	78	.	2	Substitution - Missense(2)	kidney(2)	c.G317C						.						32	35	34					8																	39836668		2023	4183	6206	SO:0001583	missense	169355	exon4			CCATGGGTTATGT	AK128691		8p11.21	2012-04-19	2009-01-07	2009-01-07	ENSG00000188676	ENSG00000188676			27269	protein-coding gene	gene with protein product		612129	"indoleamine-pyrrole 2,3 dioxygenase-like 1"	INDOL1			Standard	NM_194294		Approved		uc010lwy.1	Q6ZQW0	OTTHUMG00000141271	ENST00000389060.4:c.278G>C	chr8.hg19:g.39836668G>C	ENSP00000426447:p.Gly93Ala	42.0	0.0		29.0	5.0	NM_194294	A4UD41	Missense_Mutation	SNP	ENST00000389060.4	hg19		.	.	.	.	.	.	.	.	.	.	G	12.76	2.034699	0.35893	.	.	ENSG00000188676	ENST00000502986;ENST00000389060	T;T	0.35789	1.29;1.29	5.36	5.36	0.76844	.	0.103335	0.64402	D	0.000003	T	0.37972	0.1023	N	0.21617	0.685	0.42214	D	0.991825	P	0.47677	0.899	P	0.54060	0.741	T	0.07404	-1.0774	9	.	.	.	.	14.5911	0.68365	0.0:0.0:1.0:0.0	.	106	F5H5G0	.	A	106;93	ENSP00000443432:G106A;ENSP00000426447:G93A	.	G	+	2	0	IDO2	39955825	1.000000	0.71417	0.882000	0.34594	0.438000	0.31896	7.396000	0.79891	2.533000	0.85409	0.467000	0.42956	GGT	.	.		0.612	IDO2-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372742.1	NM_194294		C	39836668	G	C	39836668	3	2	332	1	0	0	0	0	1	0	0	0	7511	1261	44	4	331	4	IDO2	8	39836668	Missense_Mutation	SNP	G	TCGA-RC-A6M3-01A-11D-A32G-10	25654994	39836668	106527354	38	46308										
RP1	6101	hgsc.bcm.edu	37	chr8	55539235	55539235	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	ccatatccaactttaaagccTataaaatcagctccagtatg	4	11	1	0			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr8:55539235T>C	ENST00000220676.1	+	4	2941	c.2793T>C	c.(2791-2793)ccT>ccC	p.P931P		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	931					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			CTTTAAAGCCTATAAAATCAG	0.323																																					p.P931P	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.T2793C						.						36	38	37					8																	55539235		2202	4300	6502	SO:0001819	synonymous_variant	6101	exon4			AAAGCCTATAAAA	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.2793T>C	chr8.hg19:g.55539235T>C		107.0	0.0		109.0	15.0	NM_006269		Silent	SNP	ENST00000220676.1	hg19	CCDS6160.1																																																																																			.	.		0.323	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		C	55539235	T	C	55539235	2	2	332	1	0	0	0	0	0	0	0	1	13547	1509	53	2		2	RP1	8	55539235	Silent	SNP	T	TCGA-RC-A6M3-01A-11D-A32G-10	15702567	55539235	90824787	39	46309										
TRPA1	8989	hgsc.bcm.edu	37	chr8	72958753	72958753	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	aaacattgaacttacgttgaGggctgtaagcggttcatata	10	6	1	2			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr8:72958753G>T	ENST00000262209.4	-	17	2263	c.2056C>A	c.(2056-2058)Ctc>Atc	p.L686I	RP11-383H13.1_ENST00000537896.1_Intron|RP11-383H13.1_ENST00000457356.4_Intron|RP11-383H13.1_ENST00000524152.1_Intron	NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	686					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	CTTACGTTGAGGGCTGTAAGC	0.294																																					p.L686I		Atlas-SNP	.											.	TRPA1	256	.	0			c.C2056A						.						169	181	177					8																	72958753		2203	4299	6502	SO:0001583	missense	8989	exon17			CGTTGAGGGCTGT	Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	497	protein-coding gene	gene with protein product		604775	"ankyrin-like with transmembrane domains 1"	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.2056C>A	chr8.hg19:g.72958753G>T	ENSP00000262209:p.Leu686Ile	63.0	0.0		121.0	15.0	NM_007332	A6NIN6	Missense_Mutation	SNP	ENST00000262209.4	hg19	CCDS34908.1	.	.	.	.	.	.	.	.	.	.	G	7.043	0.562975	0.13498	.	.	ENSG00000104321	ENST00000523582;ENST00000262209	T;T	0.79033	-1.23;-1.23	4.65	3.75	0.43078	.	0.241300	0.32314	N	0.006273	T	0.75206	0.3818	M	0.79805	2.47	0.50632	D	0.999887	B	0.23650	0.089	B	0.25140	0.058	T	0.73322	-0.4019	10	0.66056	D	0.02	-7.6287	5.4294	0.16444	0.1688:0.0:0.6603:0.1708	.	686	O75762	TRPA1_HUMAN	I	538;686	ENSP00000428151:L538I;ENSP00000262209:L686I	ENSP00000262209:L686I	L	-	1	0	TRPA1	73121307	0.996000	0.38824	0.768000	0.31515	0.064000	0.16182	2.454000	0.44979	1.033000	0.39918	0.555000	0.69702	CTC	.	.		0.294	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332		T	72958753	G	T	72958753	3	4	332	1	0	0	0	0	1	0	0	0	16592	1000	35	3	1347	3	TRPA1	8	72958753	Missense_Mutation	SNP	G	TCGA-RC-A6M3-01A-11D-A32G-10	17419518	72958753	73405269	40	46310										
RIPK2	8767	hgsc.bcm.edu	37	chr8	90796369	90796370	+	Splice_Site	INS	-	-	AAAA													0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	aatcatggtccacaagaggtINSaaaaaaaaaaaaaaaaaaaa					rs200269713|rs200988597|rs377038313|rs398008705|rs374266923|rs560035192|rs71268283	byFrequency	TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr8:90796369_90796370insAAAA	ENST00000220751.4	+	8	1343		c.e8+2		RIPK2_ENST00000540020.1_Splice_Site	NM_003821.5	NP_003812.1	O43353	RIPK2_HUMAN	receptor-interacting serine-threonine kinase 2						activation of MAPK activity (GO:0000187)|adaptive immune response (GO:0002250)|apoptotic process (GO:0006915)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to peptidoglycan (GO:0071224)|defense response to Gram-positive bacterium (GO:0050830)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070427)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of immature T cell proliferation (GO:0033091)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|response to exogenous dsRNA (GO:0043330)|response to interleukin-1 (GO:0070555)|response to interleukin-12 (GO:0070671)|response to interleukin-18 (GO:0070673)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|T cell proliferation (GO:0042098)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|protein complex (GO:0043234)|vesicle (GO:0031982)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|LIM domain binding (GO:0030274)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(2)	10			BRCA - Breast invasive adenocarcinoma(11;0.0474)			CCACAAGAGGTaaaaaaaaaaa	0.297																																					.		Atlas-INDEL	.											.	RIPK2	37	.	0			c.1029+2->AAAA						.																																			SO:0001630	splice_region_variant	8767	exon8			.	AC004003	CCDS6247.1	8q21	2008-05-02			ENSG00000104312	ENSG00000104312			10020	protein-coding gene	gene with protein product		603455				9575181, 9705938	Standard	XM_005251092		Approved	RICK, RIP2, CARDIAK, CARD3	uc003yee.3	O43353	OTTHUMG00000163809	ENST00000220751.4:c.1029+2->AAAA	chr8.hg19:g.90796374_90796377dupAAAA		75.0	0.0		136.0	13.0	NM_003821	B7Z748|Q6UWF0	Splice_Site	INS	ENST00000220751.4	hg19	CCDS6247.1																																																																																			.	.		0.297	RIPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375686.1		Intron	AAAA	90796370	-	AAAA	90796369	8	5	332	1	0	1	1	0	0	0	1	0	13396	1652	57	0	1061	0	RIPK2	8	90796369	Splice_Site	INS	-	TCGA-RC-A6M3-01A-11D-A32G-10	17837616	90796369	55567653	41	46311										
TMEM2	23670	hgsc.bcm.edu	37	chr9	74355007	74355007	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	cattcactataagctgtcacAgagaacttctggccatccac	6	13	3	1			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr9:74355007A>G	ENST00000377044.4	-	5	1715	c.1176T>C	c.(1174-1176)tcT>tcC	p.S392S	TMEM2_ENST00000377066.5_Silent_p.S392S	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	392					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		AAGCTGTCACAGAGAACTTCT	0.373																																					p.S392S		Atlas-SNP	.											.	TMEM2	112	.	0			c.T1176C						.						115	111	112					9																	74355007		2203	4300	6503	SO:0001819	synonymous_variant	23670	exon5			TGTCACAGAGAAC		CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.1176T>C	chr9.hg19:g.74355007A>G		51.0	0.0		53.0	9.0	NM_001135820	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Silent	SNP	ENST00000377044.4	hg19	CCDS6638.1																																																																																			.	.		0.373	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390		G	74355007	A	G	74355007	2	3	332	1	0	0	0	0	0	0	0	1	16136	175	7	2		2	TMEM2	9	74355007	Silent	SNP	A	TCGA-RC-A6M3-01A-11D-A32G-10		74355007	66858424	42	46312										
BAT2L1	84726	hgsc.bcm.edu	37	chr9	134357801	134357801	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	agatagtggcgttgacttgaGtgccgagtctcgggagtcgt	16	7	1	3			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr9:134357801G>T	ENST00000357304.4	+	20	5082	c.5027G>T	c.(5026-5028)aGt>aTt	p.S1676I	PRRC2B_ENST00000458550.1_Missense_Mutation_p.S982I|PRRC2B_ENST00000405995.1_Missense_Mutation_p.S982I|PRRC2B_ENST00000372249.1_5'UTR	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	1676							poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						GTTGACTTGAGTGCCGAGTCT	0.582																																					p.S1676I		Atlas-SNP	.											.	PRRC2B	266	.	0			c.G5027T						.						154	161	159					9																	134357801		2006	4177	6183	SO:0001583	missense	84726	exon20			ACTTGAGTGCCGA	AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"KIAA0515", "HLA-B associated transcript 2-like", "HLA-B associated transcript 2-like 1"	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.5027G>T	chr9.hg19:g.134357801G>T	ENSP00000349856:p.Ser1676Ile	124.0	0.0		134.0	37.0	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Missense_Mutation	SNP	ENST00000357304.4	hg19	CCDS48044.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.7|20.7	4.033066|4.033066	0.75504|0.75504	.|.	.|.	ENSG00000130723|ENSG00000130723	ENST00000451855|ENST00000405995;ENST00000357304;ENST00000458550	.|T;T;T	.|0.03982	.|3.74;4.18;3.74	4.92|4.92	4.92|4.92	0.64577|0.64577	.|.	.|0.000000	.|0.48767	.|U	.|0.000163	T|T	0.19725|0.19725	0.0474|0.0474	M|M	0.65498|0.65498	2.005|2.005	0.80722|0.80722	D|D	1|1	.|D;D	.|0.76494	.|0.999;0.998	.|D;D	.|0.71656	.|0.974;0.957	T|T	0.00316|0.00316	-1.1823|-1.1823	5|10	.|0.56958	.|D	.|0.05	-15.1703|-15.1703	17.105|17.105	0.86660|0.86660	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|408;1676	.|Q5JSZ8;Q5JSZ5	.|.;PRC2B_HUMAN	D|I	408|982;1676;982	.|ENSP00000384606:S982I;ENSP00000349856:S1676I;ENSP00000398853:S982I	.|ENSP00000349856:S1676I	E|S	+|+	3|2	2|0	PRRC2B|PRRC2B	133347622|133347622	1.000000|1.000000	0.71417|0.71417	0.989000|0.989000	0.46669|0.46669	0.840000|0.840000	0.47671|0.47671	7.507000|7.507000	0.81676|0.81676	2.275000|2.275000	0.75901|0.75901	0.561000|0.561000	0.74099|0.74099	GAG|AGT	.	.		0.582	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	134357801	G	T	134357801	3	4	332	1	0	0	0	0	1	0	0	0	1320	1029	36	3	5105	3	BAT2L1	9	134357801	Missense_Mutation	SNP	G	TCGA-RC-A6M3-01A-11D-A32G-10	60002794	134357801	6855630	43	46313										
SARDH	1757	hgsc.bcm.edu	37	chr9	136597702	136597702	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	gctccacctccacgtcactgGgccgcagctgccacagcagg	11	18	1	0			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr9:136597702G>A	ENST00000371872.4	-	3	610	c.353C>T	c.(352-354)cCc>cTc	p.P118L	SARDH_ENST00000422262.2_5'UTR|SARDH_ENST00000298628.5_Missense_Mutation_p.P118L|SARDH_ENST00000439388.1_Missense_Mutation_p.P118L|SARDH_ENST00000371867.1_Missense_Mutation_p.P29L	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	118					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|sarcosine dehydrogenase activity (GO:0008480)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(13)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	44				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		CACGTCACTGGGCCGCAGCTG	0.667																																					p.P118L		Atlas-SNP	.											.	SARDH	112	.	0			c.C353T						.						46	48	47					9																	136597702		2203	4300	6503	SO:0001583	missense	1757	exon3			TCACTGGGCCGCA		CCDS6978.1	9q33-q34	2008-02-05			ENSG00000123453	ENSG00000123453	1.5.99.2		10536	protein-coding gene	gene with protein product		604455		DMGDHL1		10444331	Standard	NM_007101		Approved	SDH	uc004cep.4	Q9UL12	OTTHUMG00000020879	ENST00000371872.4:c.353C>T	chr9.hg19:g.136597702G>A	ENSP00000360938:p.Pro118Leu	34.0	0.0		46.0	23.0	NM_007101	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Missense_Mutation	SNP	ENST00000371872.4	hg19	CCDS6978.1	.	.	.	.	.	.	.	.	.	.	G	31	5.080959	0.94050	.	.	ENSG00000123453	ENST00000371872;ENST00000439388;ENST00000427237;ENST00000539227;ENST00000535281;ENST00000371867;ENST00000393050;ENST00000298628	D;D;D;D	0.82344	-1.6;-1.6;-1.6;-1.6	4.32	4.32	0.51571	FAD dependent oxidoreductase (1);	0.000000	0.85682	D	0.000000	D	0.91415	0.7291	M	0.83603	2.65	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	D	0.93142	0.6542	10	0.87932	D	0	-29.0247	16.7821	0.85565	0.0:0.0:1.0:0.0	.	118	Q9UL12	SARDH_HUMAN	L	118;118;118;118;118;29;96;118	ENSP00000360938:P118L;ENSP00000403084:P118L;ENSP00000360933:P29L;ENSP00000298628:P118L	ENSP00000298628:P118L	P	-	2	0	SARDH	135587523	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.229000	0.95273	1.942000	0.56320	0.462000	0.41574	CCC	.	.		0.667	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054931.1			A	136597702	G	A	136597702	3	1	332	1	0	0	0	0	1	0	0	0	13856	1232	43	3	2479	3	SARDH	9	136597702	Missense_Mutation	SNP	G	TCGA-RC-A6M3-01A-11D-A32G-10	2239901	136597702	4615729	44	46314										
GSTO1	9446	hgsc.bcm.edu	37	chr10	106025865	106025865	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	ctgactaataagaagacgacCttctttggtggcaattctat	8	8	2	3			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr10:106025865C>T	ENST00000369713.5	+	5	683	c.489C>T	c.(487-489)acC>acT	p.T163T	GSTO1_ENST00000493946.1_3'UTR|MIR4482-1_ENST00000583050.1_RNA|GSTO1_ENST00000369710.4_Silent_p.T130T|GSTO2_ENST00000450629.2_5'Flank|GSTO1_ENST00000539281.1_Silent_p.T135T	NM_004832.2	NP_004823.1	P78417	GSTO1_HUMAN	glutathione S-transferase omega 1	163	GST C-terminal.				cellular response to arsenic-containing substance (GO:0071243)|glutathione derivative biosynthetic process (GO:1901687)|L-ascorbic acid metabolic process (GO:0019852)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|positive regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014810)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|small molecule metabolic process (GO:0044281)|xenobiotic catabolic process (GO:0042178)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glutathione dehydrogenase (ascorbate) activity (GO:0045174)|glutathione transferase activity (GO:0004364)|methylarsonate reductase activity (GO:0050610)|oxidoreductase activity (GO:0016491)			large_intestine(1)|lung(1)|stomach(1)	3		Colorectal(252;0.102)|Breast(234;0.122)		Epithelial(162;8.07e-10)|all cancers(201;2.72e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0147)	Glutathione(DB00143)|Vitamin E(DB00163)	AGAAGACGACCTTCTTTGGTG	0.358																																					p.T163T		Atlas-SNP	.											.	GSTO1	14	.	0			c.C489T						.						209	202	204					10																	106025865		2203	4300	6503	SO:0001819	synonymous_variant	9446	exon5			GACGACCTTCTTT	AF212303	CCDS7555.1, CCDS53572.1, CCDS53573.1	10q25.1	2012-06-21			ENSG00000148834	ENSG00000148834	2.5.1.18, 1.8.5.1, 1.20.4.2	"Glutathione S-transferases / Soluble"	13312	protein-coding gene	gene with protein product		605482				10783391, 12618591	Standard	NM_004832		Approved	GSTTLp28, P28	uc001kya.3	P78417	OTTHUMG00000019001	ENST00000369713.5:c.489C>T	chr10.hg19:g.106025865C>T		131.0	0.0		99.0	28.0	NM_004832	D3DRA3|F5H7H0|Q5TA03|Q7Z3T2	Silent	SNP	ENST00000369713.5	hg19	CCDS7555.1																																																																																			.	.		0.358	GSTO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050193.1	NM_004832		T	106025865	C	T	106025865	2	4	332	1	0	0	0	0	0	0	0	1	6851	668	24	3		3	GSTO1	10	106025865	Silent	SNP	C	TCGA-RC-A6M3-01A-11D-A32G-10		106025865	29508882	45	46315										
ARAP1	116985	hgsc.bcm.edu	37	chr11	72406835	72406836	+	Frame_Shift_Ins	INS	-	-	TGGGA													0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	tgtagtcctgcccatctgtcINStggaagagcgtgggcccaaa							TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr11:72406835_72406836insTGGGA	ENST00000393609.3	-	24	3549_3550	c.3347_3348insTCCCA	c.(3346-3348)cagfs	p.Q1116fs	ARAP1-AS1_ENST00000542022.1_RNA|ARAP1_ENST00000495878.1_5'UTR|ARAP1_ENST00000455638.2_Frame_Shift_Ins_p.Q1116fs|ARAP1_ENST00000393605.3_Frame_Shift_Ins_p.Q876fs|ARAP1_ENST00000359373.5_Frame_Shift_Ins_p.Q1116fs|ARAP1_ENST00000426523.1_Frame_Shift_Ins_p.Q871fs|ARAP1_ENST00000334211.8_Frame_Shift_Ins_p.Q871fs|ARAP1_ENST00000429686.1_Frame_Shift_Ins_p.Q810fs	NM_001040118.2	NP_001035207.1	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	1116	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				actin filament reorganization involved in cell cycle (GO:0030037)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of receptor recycling (GO:0001921)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of cellular component movement (GO:0051270)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|large_intestine(10)|lung(8)|ovary(1)|skin(3)|urinary_tract(1)	27						GCCCATCTGTCTGGAAGAGCGT	0.564																																					p.Q1116fs	Ovarian(102;1198 1520 13195 17913 37529)	Atlas-Indel,Pindel	.											.	ARAP1	168	.	0			c.3348_3349insTCCCA						.																																			SO:0001589	frameshift_variant	116985	exon24			.	AF411983	CCDS8217.2, CCDS41687.1, CCDS44671.1	11q13.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000186635	ENSG00000186635		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16925	protein-coding gene	gene with protein product		606646	"centaurin, delta 2"	CENTD2			Standard	NM_001040118		Approved		uc001osu.3	Q96P48	OTTHUMG00000157102	ENST00000393609.3:c.3347_3348insTCCCA	chr11.hg19:g.72406835_72406836insTGGGA	ENSP00000377233:p.Gln1116fs	62.0	0.0		43.0	20.0	NM_001040118	A3KLL7|B2RTS2|O94879|Q4LDD5|Q59FI7|Q6PHS3|Q8WU51|Q96HP6|Q96L71	Frame_Shift_Ins	INS	ENST00000393609.3	hg19	CCDS41687.1																																																																																			.	.		0.564	ARAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347428.1	NM_001040118		TGGGA	72406836	-	TGGGA	72406835	7	5	332	1	0	1	1	0	0	0	0	0	838	912	32	0	1052	0	ARAP1	11	72406835	Frame_Shift_Ins	INS	-	TCGA-RC-A6M3-01A-11D-A32G-10		72406835	62599681	46	46316										
ARHGEF17	9828	hgsc.bcm.edu	37	chr11	73020542	73020542	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	accgagacggtgagggcggcCaccgctggggagggaggccc	20	12	0	2			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr11:73020542C>T	ENST00000263674.3	+	1	1209	c.859C>T	c.(859-861)Cac>Tac	p.H287Y	RP11-800A3.7_ENST00000546324.1_RNA	NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	287					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(2)	32						TGAGGGCGGCCACCGCTGGGG	0.667																																					p.H287Y		Atlas-SNP	.											.	ARHGEF17	117	.	0			c.C859T						.						20	26	24					11																	73020542		2162	4262	6424	SO:0001583	missense	9828	exon1			GGCGGCCACCGCT	AF378754	CCDS8221.1	11q13.3	2011-11-16			ENSG00000110237	ENSG00000110237		"Rho guanine nucleotide exchange factors"	21726	protein-coding gene	gene with protein product	"Rho-specific guanine-nucleotide exchange factor 164 kDa", "tumor endothelial marker 4"					11559528, 12071859	Standard	NM_014786		Approved	TEM4, KIAA0337, p164-RhoGEF	uc001otu.3	Q96PE2	OTTHUMG00000167971	ENST00000263674.3:c.859C>T	chr11.hg19:g.73020542C>T	ENSP00000263674:p.His287Tyr	31.0	0.0		26.0	15.0	NM_014786	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Missense_Mutation	SNP	ENST00000263674.3	hg19	CCDS8221.1	.	.	.	.	.	.	.	.	.	.	C	7.148	0.583216	0.13749	.	.	ENSG00000110237	ENST00000263674	T	0.57907	0.37	3.84	2.91	0.33838	.	0.382913	0.19293	N	0.117841	T	0.32556	0.0833	N	0.19112	0.55	0.09310	N	1	B	0.24483	0.104	B	0.15052	0.012	T	0.20338	-1.0278	10	0.72032	D	0.01	-2.6484	6.3799	0.21529	0.0:0.8675:0.0:0.1325	.	287	Q96PE2	ARHGH_HUMAN	Y	287	ENSP00000263674:H287Y	ENSP00000263674:H287Y	H	+	1	0	ARHGEF17	72698190	0.008000	0.16893	0.101000	0.21167	0.459000	0.32528	1.540000	0.36115	2.101000	0.63845	0.313000	0.20887	CAC	.	.		0.667	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786		T	73020542	C	T	73020542	3	4	332	1	0	0	0	0	1	0	0	0	900	594	21	3	861	3	ARHGEF17	11	73020542	Missense_Mutation	SNP	C	TCGA-RC-A6M3-01A-11D-A32G-10	613707	73020542	61985974	47	46317										
GRAMD1B	57476	hgsc.bcm.edu	37	chr11	123448102	123448102	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	agtaactccaaccgcagcacGccggcctgctcgcccatcct	8	19	0	0			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr11:123448102G>T	ENST00000529750.1	+	2	378	c.51G>T	c.(49-51)acG>acT	p.T17T	GRAMD1B_ENST00000322282.7_Silent_p.T17T|GRAMD1B_ENST00000456860.2_Silent_p.T17T	NM_020716.1	NP_065767.1	Q3KR37	GRM1B_HUMAN	GRAM domain containing 1B	17						integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394)		ACCGCAGCACGCCGGCCTGCT	0.637											OREG0021454	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T17T		Atlas-SNP	.											GRAMD1B_ENST00000529750,NS,carcinoma,0,2	GRAMD1B	122	.	0			c.G51T						.						15	19	18					11																	123448102		2111	4218	6329	SO:0001819	synonymous_variant	57476	exon2			CAGCACGCCGGCC	AB033027	CCDS53720.1, CCDS66253.1, CCDS66254.1	11q24.1	2005-11-02				ENSG00000023171			29214	protein-coding gene	gene with protein product						10574462	Standard	NM_001286564		Approved	KIAA1201	uc001pyx.2	Q3KR37		ENST00000529750.1:c.51G>T	chr11.hg19:g.123448102G>T		85.0	0.0	1526	47.0	2.0	NM_020716	Q6UW85|Q9ULL9	Silent	SNP	ENST00000529750.1	hg19	CCDS53720.1																																																																																			.	.		0.637	GRAMD1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387404.2	XM_370660		T	123448102	G	T	123448102	2	4	332	1	0	0	0	0	0	0	0	1	6757	1074	38	1		1	GRAMD1B	11	123448102	Silent	SNP	G	TCGA-RC-A6M3-01A-11D-A32G-10	50427560	123448102	11558414	48	46318										
KRT85	3891	hgsc.bcm.edu	37	chr12	52754698	52754698	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	tggaggaacgaggctggcagGgggcacaggagtcaggggcc	21	8	1	0			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr12:52754698G>A	ENST00000257901.3	-	9	1538	c.1463C>T	c.(1462-1464)cCc>cTc	p.P488L	KRT85_ENST00000544265.1_Missense_Mutation_p.P276L	NM_002283.3	NP_002274.1	P78386	KRT85_HUMAN	keratin 85	488	Tail.				epidermis development (GO:0008544)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(6)|kidney(1)|large_intestine(7)|liver(1)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	36	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		AGGCTGGCAGGGGGCACAGGA	0.667																																					p.P488L		Atlas-SNP	.											.	KRT85	78	.	0			c.C1463T						.						37	45	42					12																	52754698		2202	4300	6502	SO:0001583	missense	3891	exon9			TGGCAGGGGGCAC	X99140	CCDS8824.1, CCDS73472.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000135443	ENSG00000135443		"-", "Intermediate filaments type II, keratins (basic)"	6462	protein-coding gene	gene with protein product	"hard keratin type II"	602767	"keratin, hair, basic, 5"	KRTHB5		9084137, 16831889	Standard	NM_002283		Approved	Hb-5	uc001sag.3	P78386	OTTHUMG00000169633	ENST00000257901.3:c.1463C>T	chr12.hg19:g.52754698G>A	ENSP00000257901:p.Pro488Leu	40.0	0.0		42.0	18.0	NM_002283	Q9NSB1	Missense_Mutation	SNP	ENST00000257901.3	hg19	CCDS8824.1	.	.	.	.	.	.	.	.	.	.	G	18.73	3.687351	0.68157	.	.	ENSG00000135443	ENST00000257901;ENST00000544265	D;T	0.82081	-1.57;-1.48	5.22	5.22	0.72569	.	0.000000	0.64402	D	0.000013	D	0.88078	0.6340	M	0.71036	2.16	0.43545	D	0.995843	D	0.69078	0.997	P	0.58210	0.835	D	0.88348	0.2979	10	0.54805	T	0.06	.	14.1477	0.65360	0.0:0.0:1.0:0.0	.	488	P78386	KRT85_HUMAN	L	488;276	ENSP00000257901:P488L;ENSP00000440240:P276L	ENSP00000257901:P488L	P	-	2	0	KRT85	51040965	1.000000	0.71417	0.991000	0.47740	0.582000	0.36321	2.419000	0.44671	2.711000	0.92665	0.609000	0.83330	CCC	.	.		0.667	KRT85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405184.1	NM_002283		A	52754698	G	A	52754698	3	1	332	1	0	0	0	0	1	0	0	0	8508	1232	43	3	64	3	KRT85	12	52754698	Missense_Mutation	SNP	G	TCGA-RC-A6M3-01A-11D-A32G-10		52754698	81097197	49	46319										
OR9K2	441639	hgsc.bcm.edu	37	chr12	55524501	55524501	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	ctttgatttactctctgaggAacaaagatgtccaagaggct	9	8	1	4			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr12:55524501A>G	ENST00000305377.5	+	1	1037	c.949A>G	c.(949-951)Aac>Gac	p.N317D		NM_001005243.1	NP_001005243.1	Q8NGE7	OR9K2_HUMAN	olfactory receptor, family 9, subfamily K, member 2	317						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(3)|central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(2)	31						CTCTCTGAGGAACAAAGATGT	0.343																																					p.N317D		Atlas-SNP	.											.	OR9K2	63	.	0			c.A949G						.						84	84	84					12																	55524501		2203	4300	6503	SO:0001583	missense	441639	exon1			CTGAGGAACAAAG	BK004326	CCDS31814.1	12q13.2	2012-08-09						"GPCR / Class A : Olfactory receptors"	15339	protein-coding gene	gene with protein product							Standard	NM_001005243		Approved		uc010spe.2	Q8NGE7	OTTHUMG00000169827	ENST00000305377.5:c.949A>G	chr12.hg19:g.55524501A>G	ENSP00000307598:p.Asn317Asp	131.0	0.0		135.0	54.0	NM_001005243	B9EH19|Q6IFD6	Missense_Mutation	SNP	ENST00000305377.5	hg19	CCDS31814.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.040964	0.75732	.	.	ENSG00000170605	ENST00000305377	T	0.48836	0.8	4.86	4.86	0.63082	.	0.000000	0.56097	D	0.000023	T	0.78291	0.4260	H	0.97940	4.11	0.33353	D	0.57132	D	0.62365	0.991	D	0.63033	0.91	D	0.89802	0.3976	10	0.87932	D	0	-23.6752	14.5967	0.68413	1.0:0.0:0.0:0.0	.	317	Q8NGE7	OR9K2_HUMAN	D	317	ENSP00000307598:N317D	ENSP00000307598:N317D	N	+	1	0	OR9K2	53810768	0.985000	0.35326	1.000000	0.80357	0.982000	0.71751	5.778000	0.68940	2.176000	0.68965	0.528000	0.53228	AAC	.	.		0.343	OR9K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406105.1			G	55524501	A	G	55524501	3	3	332	1	0	0	0	0	1	0	0	0	11263	246	9	2	951	2	OR9K2	12	55524501	Missense_Mutation	SNP	A	TCGA-RC-A6M3-01A-11D-A32G-10	2769803	55524501	78327394	50	46320										
GRIP1	23426	hgsc.bcm.edu	37	chr12	66856725	66856725	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	atggtcgggcccctttagggCcagccgggtctgatgatggg	17	10	1	2			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr12:66856725C>G	ENST00000398016.3	-	9	1089	c.1021G>C	c.(1021-1023)Gcc>Ccc	p.A341P	GRIP1_ENST00000286445.7_Missense_Mutation_p.A341P|GRIP1_ENST00000359742.4_Missense_Mutation_p.A341P	NM_021150.3	NP_066973.2	Q96DT0	LEG12_HUMAN	glutamate receptor interacting protein 1	0					intrinsic apoptotic signaling pathway (GO:0097193)	nucleus (GO:0005634)	lactose binding (GO:0030395)			NS(3)|breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(19)|ovary(2)|prostate(2)|skin(1)	50			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		CCCTTTAGGGCCAGCCGGGTC	0.552																																					p.A341P		Atlas-SNP	.											.	GRIP1	106	.	0			c.G1021C						.						90	86	87					12																	66856725		1922	4138	6060	SO:0001583	missense	23426	exon9			TTAGGGCCAGCCG	AJ133439	CCDS41807.1	12q13.13	2008-05-02			ENSG00000155974	ENSG00000155974			18708	protein-coding gene	gene with protein product		604597				10197531	Standard	NM_021150		Approved		uc001stk.3	Q9Y3R0	OTTHUMG00000169019	ENST00000398016.3:c.1021G>C	chr12.hg19:g.66856725C>G	ENSP00000381098:p.Ala341Pro	97.0	0.0		105.0	40.0	NM_001178074	B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Missense_Mutation	SNP	ENST00000398016.3	hg19	CCDS41807.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	8.233|8.233|8.233	0.805203|0.805203|0.805203	0.16467|0.16467|0.16467	.|.|.	.|.|.	ENSG00000155974|ENSG00000155974|ENSG00000155974	ENST00000398016;ENST00000359742;ENST00000286445;ENST00000538211;ENST00000540433;ENST00000536215|ENST00000543172|ENST00000538164	T;T;T;T;T;T|.|.	0.41400|.|.	2.05;1.0;1.0;2.06;2.12;1.0|.|.	5.21|5.21|5.21	5.21|5.21|5.21	0.72293|0.72293|0.72293	PDZ/DHR/GLGF (1);|.|.	0.000000|.|.	0.85682|.|.	D|.|.	0.000000|.|.	T|T|T	0.56046|0.56046|0.56046	0.1959|0.1959|0.1959	N|N|N	0.21142|0.21142|0.21142	0.635|0.635|0.635	0.58432|0.58432|0.58432	D|D|D	0.999997|0.999997|0.999997	B;B;B;B|.|.	0.28584|.|.	0.019;0.216;0.009;0.019|.|.	B;B;B;B|.|.	0.25759|.|.	0.02;0.063;0.014;0.034|.|.	T|T|T	0.48758|0.48758|0.48758	-0.9007|-0.9007|-0.9007	9|5|5	.|.|.	.|.|.	.|.|.	-17.9385|-17.9385|-17.9385	19.6542|19.6542|19.6542	0.95830|0.95830|0.95830	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	341;341;341;341|.|.	F5H4N6;Q9Y3R0;Q9Y3R0-3;Q9Y3R0-2|.|.	.;GRIP1_HUMAN;.;.|.|.	P|A|C	341;341;341;341;285;285|161|155	ENSP00000381098:A341P;ENSP00000352780:A341P;ENSP00000286445:A341P;ENSP00000446047:A341P;ENSP00000446024:A285P;ENSP00000446011:A285P|.|.	.|.|.	A|G|W	-|-|-	1|2|3	0|0|0	GRIP1|GRIP1|GRIP1	65142992|65142992|65142992	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.432000|0.432000|0.432000	0.31715|0.31715|0.31715	3.136000|3.136000|3.136000	0.50554|0.50554|0.50554	2.816000|2.816000|2.816000	0.96949|0.96949|0.96949	0.561000|0.561000|0.561000	0.74099|0.74099|0.74099	GCC|GGC|TGG	.	.		0.552	GRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401975.2			G	66856725	C	G	66856725	3	3	332	1	0	0	0	0	1	0	0	0	6796	739	26	4	2273	4	GRIP1	12	66856725	Missense_Mutation	SNP	C	TCGA-RC-A6M3-01A-11D-A32G-10	11332224	66856725	66995170	51	46321										
SOX21	11166	hgsc.bcm.edu	37	chr13	95363707	95363707	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	tggaaggcgcccgcgcccgcGgtcgggtagcccagcgacga	17	15	0	0			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr13:95363707G>A	ENST00000376945.2	-	1	682	c.597C>T	c.(595-597)acC>acT	p.T199T	SOX21-AS1_ENST00000438290.2_lincRNA	NM_007084.2	NP_009015.1	Q9Y651	SOX21_HUMAN	SRY (sex determining region Y)-box 21	199					hair follicle development (GO:0001942)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(3)|lung(1)|prostate(1)|skin(1)	6	all_neural(89;0.0646)|Medulloblastoma(90;0.163)					CCGCGCCCGCGGTCGGGTAGC	0.776																																					p.T199T		Atlas-SNP	.											.	SOX21	21	.	0			c.C597T						.						2	3	3					13																	95363707		1157	2292	3449	SO:0001819	synonymous_variant	11166	exon1			GCCCGCGGTCGGG	AF107044	CCDS9473.1	13q31-q32	2008-07-18			ENSG00000125285	ENSG00000125285		"SRY (sex determining region Y)-boxes"	11197	protein-coding gene	gene with protein product	"SRY-box 21"	604974				10441749	Standard	NM_007084		Approved	SOX25	uc001vma.3	Q9Y651	OTTHUMG00000017209	ENST00000376945.2:c.597C>T	chr13.hg19:g.95363707G>A		26.0	0.0		18.0	9.0	NM_007084	P35715|Q15504|Q5TBS1	Silent	SNP	ENST00000376945.2	hg19	CCDS9473.1																																																																																			.	.		0.776	SOX21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045467.4	NM_007084		A	95363707	G	A	95363707	2	1	332	1	0	0	0	0	0	0	0	1	14965	1103	39	1		1	SOX21	13	95363707	Silent	SNP	G	TCGA-RC-A6M3-01A-11D-A32G-10		95363707	19806171	52	46322										
RNASE1	6035	hgsc.bcm.edu	37	chr14	21269973	21269973	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	gtgaccttttcctggaaacaGacattctggacatctaccag	8	11	2	2			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr14:21269973G>A	ENST00000397967.4	-	2	761	c.255C>T	c.(253-255)gtC>gtT	p.V85V	RNASE1_ENST00000555698.1_Silent_p.V45V|RNASE1_ENST00000412779.2_Silent_p.V85V|RNASE1_ENST00000340900.3_Silent_p.V85V|RNASE1_ENST00000397970.4_Silent_p.V85V	NM_002933.4	NP_002924.1	P07998	RNAS1_HUMAN	ribonuclease, RNase A family, 1 (pancreatic)	85					RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	extracellular vesicular exosome (GO:0070062)	nucleic acid binding (GO:0003676)|pancreatic ribonuclease activity (GO:0004522)			central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	5	all_cancers(95;0.00671)	all_lung(585;0.235)	Epithelial(56;9.21e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0126)	Guanidine(DB00536)|L-Aspartic Acid(DB00128)	CCTGGAAACAGACATTCTGGA	0.542																																					p.V85V		Atlas-SNP	.											.	RNASE1	14	.	0			c.C255T						.						158	141	147					14																	21269973		2203	4300	6503	SO:0001819	synonymous_variant	6035	exon3			GAAACAGACATTC	BC005324	CCDS9559.1	14q11.2	2014-03-13			ENSG00000129538	ENSG00000129538	3.1.27.5	"Ribonucleases, RNase A"	10044	protein-coding gene	gene with protein product		180440		RNS1		8588814	Standard	NM_002933		Approved		uc001vyi.3	P07998	OTTHUMG00000029603	ENST00000397967.4:c.255C>T	chr14.hg19:g.21269973G>A		130.0	0.0		135.0	65.0	NM_198235	B2R589|D3DS06|Q16830|Q16869|Q1KHR2|Q6ICS5|Q9UCB4|Q9UCB5	Silent	SNP	ENST00000397967.4	hg19	CCDS9559.1																																																																																			.	.		0.542	RNASE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073791.3			A	21269973	G	A	21269973	2	1	332	1	0	0	0	0	0	0	0	1	13414	929	33	3		3	RNASE1	14	21269973	Silent	SNP	G	TCGA-RC-A6M3-01A-11D-A32G-10		21269973	86079567	53	46323										
C15orf60	283677	hgsc.bcm.edu	37	chr15	73766189	73766189	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	caaggtttttgattccaatgAagaatctggatatcttgttc	8	6	2	3			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr15:73766189A>C	ENST00000331090.6	+	2	204	c.176A>C	c.(175-177)gAa>gCa	p.E59A	C15orf60_ENST00000560581.1_Missense_Mutation_p.E59A	NM_001042367.1	NP_001035826.1	Q7Z4M0	RE114_HUMAN		59					DNA recombination (GO:0006310)|meiotic nuclear division (GO:0007126)					endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|pancreas(1)|prostate(2)	17						GATTCCAATGAAGAATCTGGA	0.313																																					p.E59A		Atlas-SNP	.											.	C15orf60	26	.	0			c.A176C						.						94	83	86					15																	73766189		1812	4063	5875	SO:0001583	missense	283677	exon2			CCAATGAAGAATC																												ENST00000331090.6:c.176A>C	chr15.hg19:g.73766189A>C	ENSP00000328423:p.Glu59Ala	68.0	0.0		86.0	16.0	NM_001042367		Missense_Mutation	SNP	ENST00000331090.6	hg19	CCDS45296.1	.	.	.	.	.	.	.	.	.	.	A	15.77	2.930580	0.52866	.	.	ENSG00000183324	ENST00000331090	T	0.54071	0.59	5.69	4.58	0.56647	.	0.119294	0.56097	D	0.000038	T	0.55673	0.1935	M	0.64997	1.995	0.40368	D	0.97931	D	0.56035	0.974	P	0.50659	0.647	T	0.61763	-0.6996	10	0.72032	D	0.01	-1.874	7.6117	0.28135	0.9072:0.0:0.0928:0.0	.	59	Q7Z4M0	CO060_HUMAN	A	59	ENSP00000328423:E59A	ENSP00000328423:E59A	E	+	2	0	C15orf60	71553242	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	3.805000	0.55575	2.170000	0.68504	0.528000	0.53228	GAA	.	.		0.313	C15orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419069.1			C	73766189	A	C	73766189	3	2	332	1	0	0	0	0	1	0	0	0	1810	246	9	5	182	5	C15orf60	15	73766189	Missense_Mutation	SNP	A	TCGA-RC-A6M3-01A-11D-A32G-10		73766189	28765203	54	46324										
IFT140	9742	hgsc.bcm.edu	37	chr16	1630796	1630796	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	tgaactcggtttgactccacCgtgtaaacgttttcttcatg	8	10	2	2			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr16:1630796C>T	ENST00000426508.2	-	13	1851	c.1488G>A	c.(1486-1488)acG>acA	p.T496T	IFT140_ENST00000439987.2_5'UTR|LA16c-395F10.2_ENST00000563162.1_RNA|LA16c-425C2.1_ENST00000568149.1_RNA	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	496					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)|protein localization to cilium (GO:0061512)|regulation of cilium assembly (GO:1902017)|renal system development (GO:0072001)|retina development in camera-type eye (GO:0060041)|skeletal system morphogenesis (GO:0048705)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)|photoreceptor connecting cilium (GO:0032391)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(12)|lung(10)|ovary(5)|pancreas(1)|prostate(4)|skin(4)|stomach(2)|urinary_tract(1)	53		Hepatocellular(780;0.219)				TTGACTCCACCGTGTAAACGT	0.488																																					p.T496T		Atlas-SNP	.											.	IFT140	128	.	0			c.G1488A						.						121	96	104					16																	1630796		2199	4300	6499	SO:0001819	synonymous_variant	9742	exon13			CTCCACCGTGTAA	AB011162	CCDS10439.1	16p13.3	2014-07-03	2014-07-03	2005-11-02	ENSG00000187535	ENSG00000187535		"Intraflagellar transport homologs", "WD repeat domain containing"	29077	protein-coding gene	gene with protein product		614620	"WD and tetratricopeptide repeats 2", "intraflagellar transport 140 homolog (Chlamydomonas)"	WDTC2		9628581	Standard	NM_014714		Approved	gs114, KIAA0590	uc002cmb.3	Q96RY7	OTTHUMG00000128585	ENST00000426508.2:c.1488G>A	chr16.hg19:g.1630796C>T		83.0	0.0		63.0	26.0	NM_014714	A2A2A8|D3DU75|O60332|Q9UG52	Silent	SNP	ENST00000426508.2	hg19	CCDS10439.1																																																																																			.	.		0.488	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714		T	1630796	C	T	1630796	2	4	332	1	0	0	0	0	0	0	0	1	7565	639	23	1		1	IFT140	16	1630796	Silent	SNP	C	TCGA-RC-A6M3-01A-11D-A32G-10		1630796	88723957	55	46325										
TRIM72	493829	hgsc.bcm.edu	37	chr16	31235616	31235616	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	gccgccggccggggaggaccCgcgccagttcgacaaggcgg	18	15	0	0			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr16:31235616C>T	ENST00000322122.3	+	7	1258	c.974C>T	c.(973-975)cCg>cTg	p.P325L	RP11-388M20.9_ENST00000576745.1_lincRNA	NM_001008274.3	NP_001008275.2			tripartite motif containing 72, E3 ubiquitin protein ligase											breast(1)|endometrium(2)|large_intestine(2)|lung(9)|skin(1)	15						GGGGAGGACCCGCGCCAGTTC	0.711																																					p.P325L		Atlas-SNP	.											TRIM72,NS,lymphoid_neoplasm,0,2	TRIM72	32	.	0			c.C974T						.						14	15	14					16																	31235616		2190	4279	6469	SO:0001583	missense	493829	exon7			AGGACCCGCGCCA	AK090695	CCDS32437.1	16p11.2	2014-02-10	2014-02-10					"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	32671	protein-coding gene	gene with protein product	"mitsugumin 53"	613288	"tripartite motif-containing 72", "tripartite motif containing 72"			20399744, 23354051	Standard	NM_001008274		Approved	MG53	uc002ebn.2	Q6ZMU5		ENST00000322122.3:c.974C>T	chr16.hg19:g.31235616C>T	ENSP00000312675:p.Pro325Leu	44.0	0.0		39.0	18.0	NM_001008274		Missense_Mutation	SNP	ENST00000322122.3	hg19	CCDS32437.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.246196	0.80024	.	.	ENSG00000177238	ENST00000322122	T	0.24151	1.87	5.44	3.46	0.39613	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);B30.2/SPRY domain (1);	0.086125	0.49305	D	0.000159	T	0.43077	0.1231	M	0.86864	2.845	0.58432	D	0.999996	P	0.46784	0.884	P	0.50659	0.647	T	0.41142	-0.9525	10	0.56958	D	0.05	.	9.3522	0.38145	0.1445:0.7787:0.0:0.0768	.	325	Q6ZMU5	TRI72_HUMAN	L	325	ENSP00000312675:P325L	ENSP00000312675:P325L	P	+	2	0	TRIM72	31143117	0.950000	0.32346	0.830000	0.32933	0.860000	0.49131	3.447000	0.52936	0.661000	0.30985	0.491000	0.48974	CCG	.	.		0.711	TRIM72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433567.1	NM_001008274		T	31235616	C	T	31235616	3	4	332	1	0	0	0	0	1	0	0	0	16560	652	23	1	996	1	TRIM72	16	31235616	Missense_Mutation	SNP	C	TCGA-RC-A6M3-01A-11D-A32G-10	29604820	31235616	59119137	56	46326										
ITGAD	3681	hgsc.bcm.edu	37	chr16	31419205	31419205	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	agcccttggcagcatccagaAgcagctgcaggagaagatct	12	11	1	3			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr16:31419205A>G	ENST00000389202.2	+	9	1026	c.977A>G	c.(976-978)aAg>aGg	p.K326R		NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	326	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				activated T cell proliferation (GO:0050798)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)	cell surface (GO:0009986)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(43)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						AGCATCCAGAAGCAGCTGCAG	0.582																																					p.K326R		Atlas-SNP	.											.	ITGAD	154	.	0			c.A977G						.						59	58	59					16																	31419205		2197	4300	6497	SO:0001583	missense	3681	exon9			TCCAGAAGCAGCT	U40274	CCDS32438.1	16p13.1-p11	2010-03-23				ENSG00000156886		"CD molecules", "Integrins"	6146	protein-coding gene	gene with protein product		602453				8666289, 9598326	Standard	NM_005353		Approved	CD11d, ADB2	uc002ebv.1	Q13349		ENST00000389202.2:c.977A>G	chr16.hg19:g.31419205A>G	ENSP00000373854:p.Lys326Arg	55.0	0.0		67.0	12.0	NM_005353	Q15575|Q15576	Missense_Mutation	SNP	ENST00000389202.2	hg19	CCDS32438.1	.	.	.	.	.	.	.	.	.	.	a	13.09	2.133649	0.37630	.	.	ENSG00000156886	ENST00000444228;ENST00000389202	D	0.83914	-1.78	5.01	3.33	0.38152	von Willebrand factor, type A (3);	.	.	.	.	T	0.73210	0.3558	L	0.37850	1.14	0.21553	N	0.999644	B;B	0.14012	0.009;0.005	B;B	0.15484	0.013;0.013	T	0.58463	-0.7632	9	0.31617	T	0.26	.	7.2029	0.25891	0.8363:0.0:0.1637:0.0	.	342;326	Q59H14;Q13349	.;ITAD_HUMAN	R	342;326	ENSP00000373854:K326R	ENSP00000373854:K326R	K	+	2	0	ITGAD	31326706	0.912000	0.30974	0.931000	0.37212	0.962000	0.63368	2.009000	0.40903	0.432000	0.26286	0.477000	0.44152	AAG	.	.		0.582	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353		G	31419205	A	G	31419205	3	3	332	1	0	0	0	0	1	0	0	0	7893	72	3	2	1011	2	ITGAD	16	31419205	Missense_Mutation	SNP	A	TCGA-RC-A6M3-01A-11D-A32G-10	183589	31419205	58935548	57	46327										
HSDL1	83693	hgsc.bcm.edu	37	chr16	84163813	84163813	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	aacacacccacgttatttacCaagatgccaacgtctttgtc	5	13	1	1			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr16:84163813C>T	ENST00000219439.4	-	4	620	c.444G>A	c.(442-444)ttG>ttA	p.L148L	HSDL1_ENST00000434463.3_Intron	NM_001146051.1|NM_031463.4	NP_001139523.1|NP_113651.4	Q3SXM5	HSDL1_HUMAN	hydroxysteroid dehydrogenase like 1	148						mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7						CGTTATTTACCAAGATGCCAA	0.473																																					p.L148L		Atlas-SNP	.											.	HSDL1	23	.	0			c.G444A						.						147	130	135					16																	84163813		2200	4300	6500	SO:0001819	synonymous_variant	83693	exon4			ATTTACCAAGATG	AF237684	CCDS10942.1, CCDS54046.1	16q24	2011-09-20			ENSG00000103160	ENSG00000103160		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	16475	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 12C, member 3"					12153137, 19027726	Standard	NM_031463		Approved	SDR12C3	uc002fhk.2	Q3SXM5	OTTHUMG00000137635	ENST00000219439.4:c.444G>A	chr16.hg19:g.84163813C>T		97.0	0.0		93.0	20.0	NM_031463	B4DSL2|D3DUL4|Q3SXM4|Q8NC98|Q9BY22	Silent	SNP	ENST00000219439.4	hg19	CCDS10942.1																																																																																			.	.		0.473	HSDL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269076.3	NM_031463		T	84163813	C	T	84163813	2	4	332	1	0	0	0	0	0	0	0	1	7402	593	21	3		3	HSDL1	16	84163813	Silent	SNP	C	TCGA-RC-A6M3-01A-11D-A32G-10	52744608	84163813	6190940	58	46328										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11784551	11784551	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	ttaaaattggagacaaagaaTgtgaatacaatcccaagttc	7	6	0	3			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr17:11784551T>C	ENST00000262442.4	+	55	10695	c.10627T>C	c.(10627-10629)Tgt>Cgt	p.C3543R	DNAH9_ENST00000608377.1_5'Flank|DNAH9_ENST00000454412.2_Missense_Mutation_p.C3543R	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	3543	AAA 5. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		AGACAAAGAATGTGAATACAA	0.458																																					p.C3543R		Atlas-SNP	.											.	DNAH9	695	.	0			c.T10627C						.						99	93	95					17																	11784551		2203	4300	6503	SO:0001583	missense	1770	exon55			AAAGAATGTGAAT	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.10627T>C	chr17.hg19:g.11784551T>C	ENSP00000262442:p.Cys3543Arg	82.0	0.0		69.0	42.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	hg19	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.141712	0.77775	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.22945	1.93;1.93	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	T	0.49881	0.1583	M	0.81682	2.555	0.80722	D	1	P	0.52842	0.956	P	0.60345	0.873	T	0.56571	-0.7957	10	0.72032	D	0.01	.	14.8948	0.70636	0.0:0.0:0.0:1.0	.	3543	Q9NYC9	DYH9_HUMAN	R	3543;3543;2125	ENSP00000262442:C3543R;ENSP00000414874:C3543R	ENSP00000262442:C3543R	C	+	1	0	DNAH9	11725276	1.000000	0.71417	0.996000	0.52242	0.955000	0.61496	3.995000	0.57001	2.159000	0.67721	0.533000	0.62120	TGT	.	.		0.458	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		C	11784551	T	C	11784551	3	2	332	1	0	0	0	0	1	0	0	0	4610	1464	51	2	10845	2	DNAH9	17	11784551	Missense_Mutation	SNP	T	TCGA-RC-A6M3-01A-11D-A32G-10		11784551	69410659	59	46329										
ZNF624	57547	hgsc.bcm.edu	37	chr17	16527675	16527675	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	tgattattttgtaatctcaaTatcctatcattccatttcca	2	9	2	1			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr17:16527675T>C	ENST00000311331.7	-	6	616	c.525A>G	c.(523-525)atA>atG	p.I175M		NM_020787.3	NP_065838.2	Q9P2J8	ZN624_HUMAN	zinc finger protein 624	175					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(4)|endometrium(1)|kidney(1)|large_intestine(8)|lung(9)|ovary(1)|prostate(1)|skin(1)	26				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		GTAATCTCAATATCCTATCAT	0.363																																					p.I175M	NSCLC(186;1023 2134 13330 38202 39800)	Atlas-SNP	.											.	ZNF624	91	.	0			c.A525G						.						101	100	100					17																	16527675		2203	4300	6503	SO:0001583	missense	57547	exon6			TCTCAATATCCTA	AB037770	CCDS11180.1	17p11.2	2013-01-08			ENSG00000197566	ENSG00000197566		"Zinc fingers, C2H2-type", "-"	29254	protein-coding gene	gene with protein product						10718198	Standard	NM_020787		Approved	KIAA1349	uc010cpi.2	Q9P2J8	OTTHUMG00000058996	ENST00000311331.7:c.525A>G	chr17.hg19:g.16527675T>C	ENSP00000310472:p.Ile175Met	160.0	0.0		90.0	54.0	NM_020787	Q3SY62|Q3SY63|Q6ZN27	Missense_Mutation	SNP	ENST00000311331.7	hg19	CCDS11180.1	.	.	.	.	.	.	.	.	.	.	T	6.844	0.524884	0.13066	.	.	ENSG00000197566	ENST00000311331	T	0.05139	3.49	2.95	0.508	0.16972	.	.	.	.	.	T	0.03053	0.0090	N	0.08118	0	0.23298	N	0.997958	B	0.19583	0.037	B	0.15870	0.014	T	0.45220	-0.9276	9	0.33940	T	0.23	.	5.534	0.17001	0.4969:0.0:0.0:0.5031	.	175	Q9P2J8	ZN624_HUMAN	M	175	ENSP00000310472:I175M	ENSP00000310472:I175M	I	-	3	3	ZNF624	16468400	0.093000	0.21703	0.087000	0.20705	0.117000	0.20001	0.665000	0.25083	0.048000	0.15891	0.533000	0.62120	ATA	.	.		0.363	ZNF624-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130512.3	XM_047617		C	16527675	T	C	16527675	3	2	332	1	0	0	0	0	1	0	0	0	18063	1396	49	2	2076	2	ZNF624	17	16527675	Missense_Mutation	SNP	T	TCGA-RC-A6M3-01A-11D-A32G-10	4743124	16527675	64667535	60	46330										
CHMP6	79643	hgsc.bcm.edu	37	chr17	78972941	78972941	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	cccaggcaggcggagctggtGgcagcttcgtaacgtggcct	16	12	0	0			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr17:78972941G>A	ENST00000325167.5	+	8	672	c.594G>A	c.(592-594)gtG>gtA	p.V198V	CTD-2561B21.7_ENST00000576215.1_RNA|CTD-2561B21.7_ENST00000577061.2_RNA	NM_024591.4	NP_078867.2	Q96FZ7	CHMP6_HUMAN	charged multivesicular body protein 6	198					endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	protein N-terminus binding (GO:0047485)			lung(2)|ovary(1)	3	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0175)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			CGGAGCTGGTGGCAGCTTCGT	0.617																																					p.V198V		Atlas-SNP	.											.	CHMP6	16	.	0			c.G594A						.						120	100	107					17																	78972941		2203	4300	6503	SO:0001819	synonymous_variant	79643	exon8			GCTGGTGGCAGCT	BC010108	CCDS11774.1	17q25.3	2014-08-13	2011-09-21		ENSG00000176108	ENSG00000176108		"Charged multivesicular body proteins"	25675	protein-coding gene	gene with protein product		610901	"chromatin modifying protein 6"			11559748, 15511219	Standard	NM_024591		Approved	FLJ11749, VPS20	uc002jyw.4	Q96FZ7	OTTHUMG00000177645	ENST00000325167.5:c.594G>A	chr17.hg19:g.78972941G>A		50.0	0.0		37.0	13.0	NM_024591	A8K7U0|Q53FU4|Q9HAE8	Silent	SNP	ENST00000325167.5	hg19	CCDS11774.1																																																																																			.	.		0.617	CHMP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438215.1	NM_024591		A	78972941	G	A	78972941	2	1	332	1	0	0	0	0	0	0	0	1	3362	1335	47	3		3	CHMP6	17	78972941	Silent	SNP	G	TCGA-RC-A6M3-01A-11D-A32G-10	62445266	78972941	2222269	61	46331										
NETO1	81832	hgsc.bcm.edu	37	chr18	70423359	70423359	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	acacatgttactatggcagaAgaatgtgttgccttcacaag	9	8	1	2			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr18:70423359A>C	ENST00000327305.6	-	8	1549	c.892T>G	c.(892-894)Ttc>Gtc	p.F298V	NETO1_ENST00000583169.1_Missense_Mutation_p.F298V|NETO1_ENST00000299430.2_Missense_Mutation_p.F297V	NM_138966.3	NP_620416	Q8TDF5	NETO1_HUMAN	neuropilin (NRP) and tolloid (TLL)-like 1	298	LDL-receptor class A. {ECO:0000255|PROSITE-ProRule:PRU00124}.				memory (GO:0007613)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|receptor localization to synapse (GO:0097120)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|visual learning (GO:0008542)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|kainate selective glutamate receptor complex (GO:0032983)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				NS(3)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(36)|ovary(2)|prostate(3)|skin(3)|stomach(1)	63		Esophageal squamous(42;0.129)		READ - Rectum adenocarcinoma(1;0.0487)		CTATGGCAGAAGAATGTGTTG	0.353																																					p.F298V		Atlas-SNP	.											NETO1,NS,carcinoma,0,2	NETO1	178	.	0			c.T892G						.						100	96	97					18																	70423359		2203	4300	6503	SO:0001583	missense	81832	exon8			GGCAGAAGAATGT	AF448838	CCDS12000.1, CCDS42444.1	18q22.2	2008-08-01			ENSG00000166342	ENSG00000166342			13823	protein-coding gene	gene with protein product		607973				11943477, 12810072	Standard	NM_138999		Approved	BTCL1, BCTL1	uc002lkw.3	Q8TDF5	OTTHUMG00000132834	ENST00000327305.6:c.892T>G	chr18.hg19:g.70423359A>C	ENSP00000313088:p.Phe298Val	152.0	0.0		158.0	26.0	NM_001201465	Q86W85|Q8ND78|Q8TDF4	Missense_Mutation	SNP	ENST00000327305.6	hg19	CCDS12000.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.349816	0.82132	.	.	ENSG00000166342	ENST00000327305;ENST00000299430	D;D	0.95238	-3.65;-3.65	5.41	5.41	0.78517	.	0.000000	0.56097	D	0.000035	D	0.96494	0.8856	M	0.61703	1.905	0.80722	D	1	D;D	0.89917	0.996;1.0	D;D	0.80764	0.986;0.994	D	0.96705	0.9521	10	0.56958	D	0.05	-14.5672	15.7499	0.77976	1.0:0.0:0.0:0.0	.	297;298	Q8TDF5-2;Q8TDF5	.;NETO1_HUMAN	V	298;297	ENSP00000313088:F298V;ENSP00000299430:F297V	ENSP00000299430:F297V	F	-	1	0	NETO1	68574339	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.287000	0.95975	2.188000	0.69820	0.533000	0.62120	TTC	.	.		0.353	NETO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256301.2	NM_138999		C	70423359	A	C	70423359	3	2	332	1	0	0	0	0	1	0	0	0	10348	72	3	5	721	5	NETO1	18	70423359	Missense_Mutation	SNP	A	TCGA-RC-A6M3-01A-11D-A32G-10		70423359	7653889	62	46332										
FBN3	84467	hgsc.bcm.edu	37	chr19	8161856	8161856	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	atgcagtcagcattctgctgGcagggactctccctgctgcc	11	14	3	0			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr19:8161856G>A	ENST00000600128.1	-	43	5736	c.5322C>T	c.(5320-5322)tgC>tgT	p.C1774C	FBN3_ENST00000601739.1_Silent_p.C1774C|FBN3_ENST00000270509.2_Silent_p.C1774C			Q75N90	FBN3_HUMAN	fibrillin 3	1774	EGF-like 27; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						CATTCTGCTGGCAGGGACTCT	0.567																																					p.C1774C		Atlas-SNP	.											.	FBN3	300	.	0			c.C5322T						.						66	60	62					19																	8161856		2203	4300	6503	SO:0001819	synonymous_variant	84467	exon42			CTGCTGGCAGGGA		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.5322C>T	chr19.hg19:g.8161856G>A		37.0	0.0		30.0	11.0	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	hg19	CCDS12196.1																																																																																			.	.		0.567	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447		A	8161856	G	A	8161856	2	1	332	1	0	0	0	0	0	0	0	1	5712	1195	42	3		3	FBN3	19	8161856	Silent	SNP	G	TCGA-RC-A6M3-01A-11D-A32G-10		8161856	50967127	63	46333										
OR7D2	162998	hgsc.bcm.edu	37	chr19	9297230	9297230	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	ttatgggacaggcattggggTccacttcacttctgcggtga	13	9	2	1			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr19:9297230T>C	ENST00000344248.2	+	1	952	c.773T>C	c.(772-774)gTc>gCc	p.V258A		NM_175883.2	NP_787079.1	Q96RA2	OR7D2_HUMAN	olfactory receptor, family 7, subfamily D, member 2	258					regulation of transcription, DNA-templated (GO:0006355)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|upper_aerodigestive_tract(2)	20						GGCATTGGGGTCCACTTCACT	0.502																																					p.V258A		Atlas-SNP	.											.	OR7D2	55	.	0			c.T773C						.						91	80	83					19																	9297230		2203	4300	6503	SO:0001583	missense	162998	exon1			TTGGGGTCCACTT	AK095468	CCDS32900.1	19p13.2	2012-08-09						"GPCR / Class A : Olfactory receptors"	8378	protein-coding gene	gene with protein product							Standard	NM_175883		Approved	OR19-4, HTPCRH03, FLJ38149	uc002mkz.1	Q96RA2		ENST00000344248.2:c.773T>C	chr19.hg19:g.9297230T>C	ENSP00000345563:p.Val258Ala	69.0	0.0		60.0	21.0	NM_175883	Q6IFJ7|Q8N133	Missense_Mutation	SNP	ENST00000344248.2	hg19	CCDS32900.1	.	.	.	.	.	.	.	.	.	.	T	13.05	2.120735	0.37436	.	.	ENSG00000188000	ENST00000344248	T	0.00036	8.86	2.21	2.21	0.28008	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35970	U	0.002869	T	0.00300	0.0009	L	0.61218	1.895	0.09310	N	1	D	0.69078	0.997	D	0.72075	0.976	T	0.46219	-0.9207	10	0.72032	D	0.01	.	3.6433	0.08176	0.0:0.3113:0.0:0.6887	.	258	Q96RA2	OR7D2_HUMAN	A	258	ENSP00000345563:V258A	ENSP00000345563:V258A	V	+	2	0	OR7D2	9158230	0.000000	0.05858	0.003000	0.11579	0.019000	0.09904	-0.008000	0.12788	1.296000	0.44742	0.418000	0.28097	GTC	.	.		0.502	OR7D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449002.1			C	9297230	T	C	9297230	3	2	332	1	0	0	0	0	1	0	0	0	11228	1667	58	2	775	2	OR7D2	19	9297230	Missense_Mutation	SNP	T	TCGA-RC-A6M3-01A-11D-A32G-10	1135374	9297230	49831753	64	46334										
IL27RA	9466	hgsc.bcm.edu	37	chr19	14150478	14150478	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	cgtgaacctagaaacccaaaGtaacgtggcaggagggtggg	15	8	0	2			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr19:14150478G>A	ENST00000263379.2	+	3	501		c.e3+1			NM_004843.3	NP_004834.1	Q6UWB1	I27RA_HUMAN	interleukin 27 receptor, alpha						cell surface receptor signaling pathway (GO:0007166)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T-helper 1 type immune response (GO:0002827)|regulation of isotype switching to IgG isotypes (GO:0048302)	integral component of plasma membrane (GO:0005887)	interleukin-27 receptor activity (GO:0045509)|transmembrane signaling receptor activity (GO:0004888)			breast(3)|endometrium(3)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	26						GAAACCCAAAGTAACGTGGCA	0.607																																					.	Colon(164;1849 1896 4443 37792 47834)	Atlas-SNP	.											.	IL27RA	56	.	0			c.376+1G>A						.						60	62	62					19																	14150478		2203	4300	6503	SO:0001630	splice_region_variant	9466	exon3			CCCAAAGTAACGT	AF053004	CCDS12303.1	19p13.11	2013-02-11				ENSG00000104998		"Interleukins and interleukin receptors", "Fibronectin type III domain containing"	17290	protein-coding gene	gene with protein product	"T-cell cytokine receptor type 1"	605350				9600072, 11057672	Standard	NM_004843		Approved	WSX-1, TCCR, CRL1, WSX1, zcytor1, IL-27R	uc002mxx.4	Q6UWB1		ENST00000263379.2:c.376+1G>A	chr19.hg19:g.14150478G>A		53.0	0.0		65.0	22.0	NM_004843	A0N0L1|O60624	Splice_Site	SNP	ENST00000263379.2	hg19	CCDS12303.1	.	.	.	.	.	.	.	.	.	.	G	10.60	1.396688	0.25205	.	.	ENSG00000104998	ENST00000263379	.	.	.	4.86	4.86	0.63082	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.6941	0.62567	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	IL27RA	14011478	1.000000	0.71417	0.934000	0.37439	0.084000	0.17831	4.443000	0.59994	2.704000	0.92352	0.555000	0.69702	.	.	.		0.607	IL27RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458539.1	NM_004843	Intron	A	14150478	G	A	14150478	5	1	332	1	0	0	0	0	0	0	1	0	7690	1043	36	3	387	3	IL27RA	19	14150478	Splice_Site	SNP	G	TCGA-RC-A6M3-01A-11D-A32G-10	4853248	14150478	44978505	65	46335										
ZNF429	353088	hgsc.bcm.edu	37	chr19	21720356	21720356	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	caaaccttaacagtcataaaAaaattcatagtggagagaaa	6	6	2	1			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr19:21720356A>G	ENST00000358491.4	+	4	1709	c.1501A>G	c.(1501-1503)Aaa>Gaa	p.K501E	ZNF429_ENST00000597078.1_Intron	NM_001001415.2	NP_001001415.2	Q86V71	ZN429_HUMAN	zinc finger protein 429	501					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(13)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	34						CAGTCATAAAAAAATTCATAG	0.378																																					p.K501E		Atlas-SNP	.											.	ZNF429	338	.	0			c.A1501G						.						39	43	42					19																	21720356		2103	4255	6358	SO:0001583	missense	353088	exon4			CATAAAAAAATTC	AY269786	CCDS42537.1	19p12	2014-02-14			ENSG00000197013	ENSG00000197013		"Zinc fingers, C2H2-type", "-"	20817	protein-coding gene	gene with protein product							Standard	NM_001001415		Approved		uc002nqd.1	Q86V71	OTTHUMG00000182848	ENST00000358491.4:c.1501A>G	chr19.hg19:g.21720356A>G	ENSP00000351280:p.Lys501Glu	33.0	0.0		29.0	10.0	NM_001001415	A6NLV7|Q9BZE6	Missense_Mutation	SNP	ENST00000358491.4	hg19	CCDS42537.1	.	.	.	.	.	.	.	.	.	.	.	5.812	0.334056	0.11013	.	.	ENSG00000197013	ENST00000358491	T	0.01068	5.38	0.81	0.81	0.18732	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01489	0.0048	L	0.50333	1.59	0.21147	N	0.999771	P	0.45827	0.867	B	0.41271	0.352	T	0.50083	-0.8869	9	0.52906	T	0.07	.	6.5745	0.22557	1.0:0.0:0.0:0.0	.	501	Q86V71	ZN429_HUMAN	E	501	ENSP00000351280:K501E	ENSP00000351280:K501E	K	+	1	0	ZNF429	21512196	0.000000	0.05858	0.644000	0.29465	0.643000	0.38383	-0.256000	0.08757	0.156000	0.19299	0.155000	0.16302	AAA	.	.		0.378	ZNF429-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463981.1	NM_001001415		G	21720356	A	G	21720356	3	3	332	1	0	0	0	0	1	0	0	0	17917	15	1	2	1515	2	ZNF429	19	21720356	Missense_Mutation	SNP	A	TCGA-RC-A6M3-01A-11D-A32G-10	7569878	21720356	37408627	66	46336										
AP2A1	160	hgsc.bcm.edu	37	chr19	50306439	50306439	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	gtcaagtcagagttccgacaGaacctgggtgtgtcccgggg	15	10	2	2			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr19:50306439G>A	ENST00000359032.5	+	18	2313	c.2313G>A	c.(2311-2313)caG>caA	p.Q771Q	AP2A1_ENST00000354293.5_Silent_p.Q749Q	NM_014203.2	NP_055018.2	O95782	AP2A1_HUMAN	adaptor-related protein complex 2, alpha 1 subunit	771					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Golgi to endosome transport (GO:0006895)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	AP-2 adaptor complex (GO:0030122)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)	19		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.0023)|GBM - Glioblastoma multiforme(134;0.0157)		AGTTCCGACAGAACCTGGGTG	0.607																																					p.Q771Q		Atlas-SNP	.											.	AP2A1	108	.	0			c.G2313A						.						70	76	74					19																	50306439		1973	4156	6129	SO:0001819	synonymous_variant	160	exon18			CCGACAGAACCTG	AA993745	CCDS46148.1, CCDS46149.1	19q13.3	2008-05-23				ENSG00000196961			561	protein-coding gene	gene with protein product		601026		CLAPA1, ADTAA		2564002	Standard	NM_014203		Approved		uc002ppn.3	O95782		ENST00000359032.5:c.2313G>A	chr19.hg19:g.50306439G>A		34.0	0.0		35.0	14.0	NM_014203	Q96CI7|Q96PP6|Q96PP7|Q9H070	Silent	SNP	ENST00000359032.5	hg19	CCDS46148.1																																																																																			.	.		0.607	AP2A1-008	NOVEL	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465809.1			A	50306439	G	A	50306439	2	1	332	1	0	0	0	0	0	0	0	1	739	933	33	3		3	AP2A1	19	50306439	Silent	SNP	G	TCGA-RC-A6M3-01A-11D-A32G-10	28586083	50306439	8822544	67	46337										
ZNF470	388566	hgsc.bcm.edu	37	chr19	57088623	57088623	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	cccaccttgctcaacatcagAgaatacacacaggagaaaaa	6	12	2	2			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr19:57088623A>G	ENST00000330619.8	+	6	1512	c.826A>G	c.(826-828)Aga>Gga	p.R276G	ZNF470_ENST00000391709.3_Missense_Mutation_p.R276G|ZNF470_ENST00000601902.1_Intron	NM_001001668.3	NP_001001668.3	Q6ECI4	ZN470_HUMAN	zinc finger protein 470	276					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(7)|large_intestine(12)|lung(11)|ovary(1)|pancreas(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	41		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0294)		TCAACATCAGAGAATACACAC	0.428																																					p.R276G		Atlas-SNP	.											.	ZNF470	103	.	0			c.A826G						.						78	83	81					19																	57088623		2201	4300	6501	SO:0001583	missense	388566	exon6			CATCAGAGAATAC	AK129686	CCDS33122.1	19q13.43	2013-01-08				ENSG00000197016		"Zinc fingers, C2H2-type", "-"	22220	protein-coding gene	gene with protein product						15302581	Standard	NM_001001668		Approved	CZF-1, FLJ26175	uc002qnl.4	Q6ECI4		ENST00000330619.8:c.826A>G	chr19.hg19:g.57088623A>G	ENSP00000333223:p.Arg276Gly	93.0	0.0		132.0	26.0	NM_001001668	A8MTW0|B9EGU1|Q6ZPA1|Q9Y2N9	Missense_Mutation	SNP	ENST00000330619.8	hg19	CCDS33122.1	.	.	.	.	.	.	.	.	.	.	A	19.16	3.772897	0.69992	.	.	ENSG00000197016	ENST00000391709;ENST00000330619	T;T	0.02421	4.3;4.3	3.89	3.89	0.44902	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10637	0.0260	L	0.52126	1.63	0.21652	N	0.999602	D	0.89917	1.0	D	0.80764	0.994	T	0.06481	-1.0824	9	0.72032	D	0.01	.	11.8193	0.52228	1.0:0.0:0.0:0.0	.	276	Q6ECI4	ZN470_HUMAN	G	276	ENSP00000375590:R276G;ENSP00000333223:R276G	ENSP00000333223:R276G	R	+	1	2	ZNF470	61780435	0.000000	0.05858	1.000000	0.80357	0.996000	0.88848	0.088000	0.14979	1.640000	0.50565	0.377000	0.23210	AGA	.	.		0.428	ZNF470-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459707.2	NM_001001668		G	57088623	A	G	57088623	3	3	332	1	0	0	0	0	1	0	0	0	17944	296	11	2	840	2	ZNF470	19	57088623	Missense_Mutation	SNP	A	TCGA-RC-A6M3-01A-11D-A32G-10	6782184	57088623	2040360	68	46338										
ZNF17	7565	hgsc.bcm.edu	37	chr19	57931549	57931549	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	tggcaaattgtttaggtacaActccgaccttattaaacatc	6	9	0	0			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr19:57931549A>G	ENST00000601808.1	+	3	902	c.689A>G	c.(688-690)aAc>aGc	p.N230S	AC004076.7_ENST00000597410.1_Intron|ZNF17_ENST00000307658.7_Missense_Mutation_p.N232S	NM_006959.2	NP_008890.2	P17021	ZNF17_HUMAN	zinc finger protein 17	230					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0234)|GBM - Glioblastoma multiforme(193;0.000426)|Lung(386;0.176)		TTTAGGTACAACTCCGACCTT	0.403																																					p.N230S	Melanoma(149;1637 1853 29914 42869 44988)	Atlas-SNP	.											.	ZNF17	49	.	0			c.A689G						.						89	92	91					19																	57931549		2199	4299	6498	SO:0001583	missense	7565	exon3			GGTACAACTCCGA	X52341	CCDS42636.1	19q13.43	2013-01-08	2006-05-10			ENSG00000186272		"Zinc fingers, C2H2-type", "-"	12958	protein-coding gene	gene with protein product			"zinc finger protein 17 (HPF3, KOX 10)"			2115127, 2014798	Standard	NM_006959		Approved	HPF3, KOX10, KIAA1947, FLJ40864, FLJ46058, FLJ46615	uc002qoo.1	P17021		ENST00000601808.1:c.689A>G	chr19.hg19:g.57931549A>G	ENSP00000471905:p.Asn230Ser	59.0	0.0		84.0	34.0	NM_006959	B3KXU2|B3KY20|Q8N7M1|Q8N893|Q8TF54	Missense_Mutation	SNP	ENST00000601808.1	hg19	CCDS42636.1	.	.	.	.	.	.	.	.	.	.	A	0.005	-2.195553	0.00299	.	.	ENSG00000186272	ENST00000307658	.	.	.	2.0	0.954	0.19595	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07638	0.0192	N	0.00926	-1.1	0.09310	N	1	B;B	0.24768	0.111;0.015	B;B	0.19391	0.025;0.002	T	0.35895	-0.9770	8	0.07030	T	0.85	.	4.9605	0.14063	0.5197:0.0:0.4803:0.0	.	232;230	P17021-2;P17021	.;ZNF17_HUMAN	S	230	.	ENSP00000302455:N230S	N	+	2	0	ZNF17	62623361	0.000000	0.05858	0.009000	0.14445	0.533000	0.34776	-1.843000	0.01680	0.219000	0.20840	0.528000	0.53228	AAC	.	.		0.403	ZNF17-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466384.1	NM_006959		G	57931549	A	G	57931549	3	3	332	1	0	0	0	0	1	0	0	0	17758	43	2	2	699	2	ZNF17	19	57931549	Missense_Mutation	SNP	A	TCGA-RC-A6M3-01A-11D-A32G-10	842926	57931549	1197434	69	46339										
CHD6	84181	hgsc.bcm.edu	37	chr20	40085989	40085989	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	tggccttgtcaaacatctcgCgctcgtaggaatttcgagtg	11	10	2	0			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chr20:40085989C>T	ENST00000373233.3	-	18	2921	c.2744G>A	c.(2743-2745)cGc>cAc	p.R915H	CHD6_ENST00000309279.7_Intron	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	915	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				AAACATCTCGCGCTCGTAGGA	0.552																																					p.R915H		Atlas-SNP	.											.	CHD6	312	.	0			c.G2744A						.						137	106	117					20																	40085989		2203	4300	6503	SO:0001583	missense	84181	exon18			ATCTCGCGCTCGT	AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.2744G>A	chr20.hg19:g.40085989C>T	ENSP00000362330:p.Arg915His	70.0	0.0		67.0	34.0	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	ENST00000373233.3	hg19	CCDS13317.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.933703	0.92458	.	.	ENSG00000124177	ENST00000373233	T	0.75821	-0.97	5.42	5.42	0.78866	Helicase, C-terminal (1);	0.000000	0.51477	D	0.000088	T	0.80031	0.4549	N	0.21142	0.635	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.82534	-0.0409	10	0.87932	D	0	-18.213	19.5951	0.95533	0.0:1.0:0.0:0.0	.	915	Q8TD26	CHD6_HUMAN	H	915	ENSP00000362330:R915H	ENSP00000362330:R915H	R	-	2	0	CHD6	39519403	1.000000	0.71417	0.998000	0.56505	0.453000	0.32348	7.729000	0.84864	2.705000	0.92388	0.591000	0.81541	CGC	.	.		0.552	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			T	40085989	C	T	40085989	3	4	332	1	0	0	0	0	1	0	0	0	3331	768	27	1	5483	1	CHD6	20	40085989	Missense_Mutation	SNP	C	TCGA-RC-A6M3-01A-11D-A32G-10		40085989	22939531	70	46340										
MED14	9282	hgsc.bcm.edu	37	chrX	40562816	40562816	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	agctgggagtgcagtctctaTggaagctgaacaatcaagaa	12	7	2	2			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chrX:40562816T>C	ENST00000324817.1	-	11	1409	c.1291A>G	c.(1291-1293)Ata>Gta	p.I431V		NM_004229.3	NP_004220.2	O60244	MED14_HUMAN	mediator complex subunit 14	431	Interaction with STAT2.				androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(2)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GCAGTCTCTATGGAAGCTGAA	0.338																																					p.I431V		Atlas-SNP	.											.	MED14	108	.	0			c.A1291G						.						45	40	42					X																	40562816		2203	4300	6503	SO:0001583	missense	9282	exon11			TCTCTATGGAAGC	AB006651	CCDS14254.1	Xp11.4	2008-05-14	2007-07-30	2007-07-30	ENSG00000180182	ENSG00000180182			2370	protein-coding gene	gene with protein product		300182	"cofactor required for Sp1 transcriptional activation, subunit 2, 150kDa"	CXorf4, CRSP2		9989412, 9598311	Standard	NM_004229		Approved	EXLM1, CRSP150, TRAP170, RGR1, CSRP	uc004dex.4	O60244	OTTHUMG00000024107	ENST00000324817.1:c.1291A>G	chrX.hg19:g.40562816T>C	ENSP00000323720:p.Ile431Val	214.0	0.0		153.0	88.0	NM_004229	Q4KMR7|Q9UNB3	Missense_Mutation	SNP	ENST00000324817.1	hg19	CCDS14254.1	.	.	.	.	.	.	.	.	.	.	T	9.951	1.220037	0.22373	.	.	ENSG00000180182	ENST00000324817	T	0.39406	1.08	5.57	5.57	0.84162	.	0.040402	0.85682	D	0.000000	T	0.26011	0.0634	N	0.17082	0.46	0.58432	D	0.99999	B	0.02656	0.0	B	0.06405	0.002	T	0.08391	-1.0724	10	0.31617	T	0.26	.	9.3415	0.38082	0.0:0.0809:0.0:0.9191	.	431	O60244	MED14_HUMAN	V	431	ENSP00000323720:I431V	ENSP00000323720:I431V	I	-	1	0	MED14	40447760	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.971000	0.70440	1.866000	0.54105	0.437000	0.28790	ATA	.	.		0.338	MED14-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060692.1	NM_004229		C	40562816	T	C	40562816	3	2	332	1	0	0	0	0	1	0	0	0	9441	1464	51	2	3157	2	MED14	23	40562816	Missense_Mutation	SNP	T	TCGA-RC-A6M3-01A-11D-A32G-10		40562816	114707744	71	46341										
KLHL13	90293	hgsc.bcm.edu	37	chrX	117053617	117053617	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0694444444444444	5	1	1.22877038043478	1.96603260869565	0.983016304347826	1	1	0	aaatgaaatcaataattttcCttagaccgactttgctcaca	4	9	2	2			TCGA-RC-A6M3-01A-11D-A32G-10	TCGA-RC-A6M3-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	00fb960e-81b6-45ea-bf27-b39c7dcdce6a	58134b29-9c26-4b08-8b60-e053d9564b76	g.chrX:117053617C>T	ENST00000262820.3	-	4	1346	c.437G>A	c.(436-438)aGg>aAg	p.R146K	KLHL13_ENST00000371878.1_Missense_Mutation_p.R95K|KLHL13_ENST00000540167.1_Missense_Mutation_p.R130K|KLHL13_ENST00000539496.1_Missense_Mutation_p.R149K|KLHL13_ENST00000371882.1_Missense_Mutation_p.R95K|KLHL13_ENST00000469946.1_Missense_Mutation_p.R95K|KLHL13_ENST00000371876.1_Missense_Mutation_p.R95K|KLHL13_ENST00000545703.1_Missense_Mutation_p.R104K|KLHL13_ENST00000541812.1_Missense_Mutation_p.R130K	NM_033495.3	NP_277030.2	Q9P2N7	KLH13_HUMAN	kelch-like family member 13	146	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)				NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(9)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	34						AATAATTTTCCTTAGACCGAC	0.353																																					p.R149K		Atlas-SNP	.											.	KLHL13	87	.	0			c.G446A						.						68	69	69					X																	117053617		2203	4300	6503	SO:0001583	missense	90293	exon5			ATTTTCCTTAGAC	AB037730	CCDS14571.1, CCDS55479.1, CCDS55480.1, CCDS55481.1	Xq23-q24	2013-01-30	2013-01-30	2004-02-18	ENSG00000003096	ENSG00000003096		"Kelch-like", "BTB/POZ domain containing"	22931	protein-coding gene	gene with protein product		300655	"BTB and kelch domain containing 2, KIAA1309", "kelch-like 13 (Drosophila)"	BKLHD2, KIAA1309		10718198	Standard	NM_033495		Approved	FLJ10262	uc011mtp.2	Q9P2N7	OTTHUMG00000022252	ENST00000262820.3:c.437G>A	chrX.hg19:g.117053617C>T	ENSP00000262820:p.Arg146Lys	168.0	0.0		113.0	66.0	NM_001168299	B3KV78|B3KWM7|B7Z3S9|B7Z5P2|B7Z802|D3DWH6|Q6P2E3|Q96QI7|Q9UDN9	Missense_Mutation	SNP	ENST00000262820.3	hg19	CCDS14571.1	.	.	.	.	.	.	.	.	.	.	C	0.135	-1.109328	0.01813	.	.	ENSG00000003096	ENST00000371882;ENST00000371876;ENST00000371878;ENST00000447671;ENST00000541812;ENST00000540167;ENST00000539496;ENST00000262820;ENST00000545703;ENST00000469946	T;T;T;T;T;T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18	5.21	4.27	0.50696	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.098404	0.64402	N	0.000002	T	0.26011	0.0634	N	0.01640	-0.785	0.29187	N	0.876121	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.001;0.002;0.001;0.001	T	0.16247	-1.0409	10	0.10636	T	0.68	.	3.568	0.07907	0.0:0.3964:0.0:0.6036	.	130;149;140;146	Q9P2N7-3;Q9P2N7-5;Q9P2N7-4;Q9P2N7	.;.;.;KLH13_HUMAN	K	95;95;95;95;130;130;149;146;104;95	ENSP00000360949:R95K;ENSP00000360943:R95K;ENSP00000360945:R95K;ENSP00000412640:R95K;ENSP00000444450:R130K;ENSP00000441029:R130K;ENSP00000443191:R149K;ENSP00000262820:R146K;ENSP00000440707:R104K;ENSP00000419803:R95K	ENSP00000262820:R146K	R	-	2	0	KLHL13	116937645	1.000000	0.71417	0.987000	0.45799	0.003000	0.03518	4.943000	0.63554	1.042000	0.40150	0.506000	0.49869	AGG	.	.		0.353	KLHL13-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_033495		T	117053617	C	T	117053617	3	4	332	1	0	0	0	0	1	0	0	0	8378	681	24	3	1546	3	KLHL13	23	117053617	Missense_Mutation	SNP	C	TCGA-RC-A6M3-01A-11D-A32G-10	76490801	117053617	38216943	72	46342										
FBXO44	93611	hgsc.bcm.edu	37	chr1	11718615	11718615	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gcctcaagtcccaggtggtgGacctcaaggccgaagggtat	14	11	2	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr1:11718615G>A	ENST00000251547.5	+	4	500	c.418G>A	c.(418-420)Gac>Aac	p.D140N	FBXO44_ENST00000376770.1_Missense_Mutation_p.D140N|FBXO44_ENST00000376768.1_Missense_Mutation_p.G130E|FBXO44_ENST00000251546.4_Intron|FBXO44_ENST00000376762.4_Intron|FBXO44_ENST00000376760.1_Intron	NM_033182.5	NP_149438.2	Q9H4M3	FBX44_HUMAN	F-box protein 44	140	FBA. {ECO:0000255|PROSITE- ProRule:PRU00482}.					SCF ubiquitin ligase complex (GO:0019005)				kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	8	Ovarian(185;0.249)	Lung NSC(185;4.15e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.41e-06)|COAD - Colon adenocarcinoma(227;0.000255)|BRCA - Breast invasive adenocarcinoma(304;0.0003)|Kidney(185;0.000758)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0649)		CCAGGTGGTGGACCTCAAGGC	0.662																																					p.D140N		Atlas-SNP	.											.	FBXO44	20	.	0			c.G418A						.						36	39	38					1																	11718615		2203	4300	6503	SO:0001583	missense	93611	exon4			GTGGTGGACCTCA	AY040878	CCDS131.1, CCDS132.1	1p36.21	2008-03-26			ENSG00000132879	ENSG00000132879		"F-boxes /  "other""	24847	protein-coding gene	gene with protein product		609111				12383498	Standard	XM_005263535		Approved	FBX30, FBG3, MGC14140, Fbxo6a, Fbx44	uc001asm.3	Q9H4M3	OTTHUMG00000002071	ENST00000251547.5:c.418G>A	chr1.hg19:g.11718615G>A	ENSP00000251547:p.Asp140Asn	47.0	0.0		39.0	18.0	NM_033182	B3KNZ2|B7Z743|Q5TGX2|Q5TGX4|Q5TGX5|Q68DJ9|Q8WWY2	Missense_Mutation	SNP	ENST00000251547.5	hg19	CCDS132.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.88|18.88	3.718457|3.718457	0.68844|0.68844	.|.	.|.	ENSG00000132879|ENSG00000132879	ENST00000376770;ENST00000251547|ENST00000376768	T;T|T	0.53423|0.47528	0.62;0.62|0.84	5.37|5.37	5.37|5.37	0.77165|0.77165	Galactose-binding domain-like (1);F-box associated (FBA) domain (2);|.	.|0.155509	.|0.56097	.|D	.|0.000023	T|T	0.61702|0.61702	0.2368|0.2368	M|M	0.69358|0.69358	2.11|2.11	0.32830|0.32830	D|D	0.503958|0.503958	B|D	0.19445|0.69078	0.036|0.997	B|P	0.20184|0.60789	0.028|0.879	T|T	0.72843|0.72843	-0.4170|-0.4170	9|10	0.54805|0.66056	T|D	0.06|0.02	.|.	11.7153|11.7153	0.51650|0.51650	0.0844:0.0:0.9156:0.0|0.0844:0.0:0.9156:0.0	.|.	140|130	Q9H4M3|B7Z1P2	FBX44_HUMAN|.	N|E	140|130	ENSP00000365961:D140N;ENSP00000251547:D140N|ENSP00000365959:G130E	ENSP00000251547:D140N|ENSP00000365959:G130E	D|G	+|+	1|2	0|0	FBXO44|FBXO44	11641202|11641202	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	2.221000|2.221000	0.42917|0.42917	2.520000|2.520000	0.84964|0.84964	0.549000|0.549000	0.68633|0.68633	GAC|GGA	.	.		0.662	FBXO44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005761.1	NM_183412		A	11718615	G	A	11718615	3	1	333	1	0	0	0	0	1	0	0	0	5761	1174	41	3	428	3	FBXO44	1	11718615	Missense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10		11718615	237532006	1	46343										
CROCC	9696	hgsc.bcm.edu	37	chr1	17280833	17280833	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gcagaaacgagatgcccagaGccggcaggagcaggaccggg	17	11	0	3			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr1:17280833G>T	ENST00000375541.5	+	22	3371	c.3302G>T	c.(3301-3303)aGc>aTc	p.S1101I	CROCC_ENST00000467938.1_3'UTR	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		GATGCCCAGAGCCGGCAGGAG	0.647																																					p.S1101I		Atlas-SNP	.											.	CROCC	185	.	0			c.G3302T						.						38	42	41					1																	17280833		2203	4299	6502	SO:0001583	missense	9696	exon22			CCCAGAGCCGGCA	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"rootletin, ciliary rootlet protein"	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.3302G>T	chr1.hg19:g.17280833G>T	ENSP00000364691:p.Ser1101Ile	58.0	0.0		71.0	31.0	NM_014675		Missense_Mutation	SNP	ENST00000375541.5	hg19	CCDS30616.1	.	.	.	.	.	.	.	.	.	.	G	12.03	1.814195	0.32053	.	.	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.52057	0.68	4.5	2.61	0.31194	.	.	.	.	.	T	0.28896	0.0717	N	0.20401	0.57	0.28496	N	0.914225	B;B;B	0.19706	0.038;0.005;0.009	B;B;B	0.18561	0.022;0.015;0.015	T	0.18681	-1.0329	9	0.40728	T	0.16	.	4.5226	0.11966	0.1945:0.0:0.6292:0.1763	.	964;404;1101	A1L0S8;Q5TZA2-2;Q5TZA2	.;.;CROCC_HUMAN	I	1101;982	ENSP00000364691:S1101I	ENSP00000364691:S1101I	S	+	2	0	CROCC	17153420	0.923000	0.31300	1.000000	0.80357	0.939000	0.58152	0.937000	0.28951	0.597000	0.29811	0.561000	0.74099	AGC	.	.		0.647	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675		T	17280833	G	T	17280833	3	4	333	1	0	0	0	0	1	0	0	0	3895	971	34	3	3388	3	CROCC	1	17280833	Missense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	5562218	17280833	231969788	2	46344										
NR0B2	8431	hgsc.bcm.edu	37	chr1	27240140	27240140	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	agcatcttgggccaacccaaGcaggaagagggggccccagc	14	13	1	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr1:27240140G>T	ENST00000254227.3	-	1	317	c.292C>A	c.(292-294)Ctt>Att	p.L98I		NM_021969.2	NP_068804.1	Q15466	NR0B2_HUMAN	nuclear receptor subfamily 0, group B, member 2	98	Ligand-binding. {ECO:0000250}.				cholesterol metabolic process (GO:0008203)|gene expression (GO:0010467)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ regeneration (GO:0031100)|positive regulation of insulin secretion (GO:0032024)|response to glucose (GO:0009749)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription corepressor activity (GO:0003714)			NS(1)|large_intestine(1)|lung(3)	5		all_cancers(24;1.23e-26)|all_epithelial(13;1.19e-23)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Breast(348;0.00017)|Renal(390;0.0007)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.01e-51)|OV - Ovarian serous cystadenocarcinoma(117;8.22e-30)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419)		GCCAACCCAAGCAGGAAGAGG	0.637																																					p.L98I		Atlas-SNP	.											NR0B2,NS,carcinoma,0,1	NR0B2	14	.	0			c.C292A						.						16	20	19					1																	27240140		2192	4292	6484	SO:0001583	missense	8431	exon1			ACCCAAGCAGGAA	AF044316	CCDS291.1	1p36.1	2013-01-16			ENSG00000131910	ENSG00000131910		"Nuclear hormone receptors"	7961	protein-coding gene	gene with protein product		604630				9603951	Standard	NM_021969		Approved	SHP	uc001bnf.3	Q15466	OTTHUMG00000004231	ENST00000254227.3:c.292C>A	chr1.hg19:g.27240140G>T	ENSP00000254227:p.Leu98Ile	55.0	1.0		59.0	38.0	NM_021969	F1D8P5|Q5QP36	Missense_Mutation	SNP	ENST00000254227.3	hg19	CCDS291.1	.	.	.	.	.	.	.	.	.	.	G	15.29	2.789745	0.50102	.	.	ENSG00000131910	ENST00000254227	D	0.97850	-4.57	5.48	3.54	0.40534	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.067623	0.64402	N	0.000011	D	0.97250	0.9101	M	0.80746	2.51	0.53005	D	0.999962	P	0.35628	0.513	B	0.39706	0.307	D	0.95823	0.8851	10	0.62326	D	0.03	-28.6225	14.4706	0.67514	0.0:0.0:0.7091:0.2909	.	98	Q15466	NR0B2_HUMAN	I	98	ENSP00000254227:L98I	ENSP00000254227:L98I	L	-	1	0	NR0B2	27112727	1.000000	0.71417	0.934000	0.37439	0.995000	0.86356	3.731000	0.55013	0.603000	0.29913	0.561000	0.74099	CTT	.	.		0.637	NR0B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012185.1			T	27240140	G	T	27240140	3	4	333	1	0	0	0	0	1	0	0	0	10623	971	34	3	489	3	NR0B2	1	27240140	Missense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	9959307	27240140	222010481	3	46345										
KIAA1522	57648	hgsc.bcm.edu	37	chr1	33235646	33235646	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ggaggctggcgctgagacagAggccatgctgcagcgccaca	16	12	0	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr1:33235646A>T	ENST00000373480.1	+	6	792	c.689A>T	c.(688-690)gAg>gTg	p.E230V	KIAA1522_ENST00000294521.3_Intron|KIAA1522_ENST00000401073.2_Missense_Mutation_p.E289V|KIAA1522_ENST00000373481.3_Missense_Mutation_p.E241V	NM_001198972.1	NP_001185901.1	Q9P206	K1522_HUMAN	KIAA1522	230										breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(2)|lung(5)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				GCTGAGACAGAGGCCATGCTG	0.701																																					p.E289V		Atlas-SNP	.											.	KIAA1522	68	.	0			c.A866T						.						22	28	26					1																	33235646		2067	4203	6270	SO:0001583	missense	57648	exon6			AGACAGAGGCCAT	AL713671	CCDS41298.1, CCDS55588.1, CCDS55589.1	1p35.1	2009-02-18			ENSG00000162522	ENSG00000162522			29301	protein-coding gene	gene with protein product						10819331	Standard	NM_020888		Approved		uc001bvu.1	Q9P206	OTTHUMG00000008088	ENST00000373480.1:c.689A>T	chr1.hg19:g.33235646A>T	ENSP00000362579:p.Glu230Val	50.0	0.0		64.0	24.0	NM_020888	B4DQU8|B5MDY0|C9JH84|Q8TCQ0	Missense_Mutation	SNP	ENST00000373480.1	hg19	CCDS55588.1	.	.	.	.	.	.	.	.	.	.	A	14.48	2.548340	0.45383	.	.	ENSG00000162522	ENST00000401073;ENST00000373481;ENST00000373480	T;T;T	0.31769	1.48;1.48;1.48	4.47	4.47	0.54385	.	0.091308	0.46145	D	0.000313	T	0.48021	0.1477	L	0.50333	1.59	0.37837	D	0.928911	D;D;D	0.71674	0.998;0.978;0.991	D;P;P	0.68943	0.961;0.725;0.852	T	0.56318	-0.7999	10	0.72032	D	0.01	-18.902	14.062	0.64806	1.0:0.0:0.0:0.0	.	241;230;289	Q9P206-3;Q9P206;Q9P206-2	.;K1522_HUMAN;.	V	289;241;230	ENSP00000383851:E289V;ENSP00000362580:E241V;ENSP00000362579:E230V	ENSP00000362579:E230V	E	+	2	0	KIAA1522	33008233	0.998000	0.40836	0.994000	0.49952	0.898000	0.52572	2.466000	0.45084	1.776000	0.52262	0.402000	0.26972	GAG	.	.		0.701	KIAA1522-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022130.1			T	33235646	A	T	33235646	3	4	333	1	0	0	0	0	1	0	0	0	8247	304	11	4	888	4	KIAA1522	1	33235646	Missense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	5995506	33235646	216014975	4	46346										
MACF1	23499	hgsc.bcm.edu	37	chr1	39929343	39929343	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tttcaggtggagcagatcggAgagaataaataccgggtaag	14	5	1	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr1:39929343A>C	ENST00000372915.3	+	93	21522	c.21435A>C	c.(21433-21435)ggA>ggC	p.G7145G	MACF1_ENST00000539005.1_Silent_p.G5057G|MACF1_ENST00000317713.7_Silent_p.G5187G|MACF1_ENST00000545844.1_Silent_p.G5187G|MACF1_ENST00000361689.2_Silent_p.G5187G|MACF1_ENST00000567887.1_Silent_p.G7283G|MACF1_ENST00000289893.4_Silent_p.G5689G|MACF1_ENST00000564288.1_Silent_p.G7246G			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	7145	C-terminal tail. {ECO:0000250}.|GAR. {ECO:0000255|PROSITE- ProRule:PRU00792}.				ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			AGCAGATCGGAGAGAATAAAT	0.453																																					p.G5187G		Atlas-SNP	.											.	MACF1	909	.	0			c.A15561C						.						121	113	116					1																	39929343		2203	4300	6503	SO:0001819	synonymous_variant	23499	exon91			GATCGGAGAGAAT	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.21435A>C	chr1.hg19:g.39929343A>C		92.0	0.0		135.0	66.0	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Silent	SNP	ENST00000372915.3	hg19		.	.	.	.	.	.	.	.	.	.	A	10.12	1.262924	0.23051	.	.	ENSG00000127603	ENST00000360115;ENST00000442046	.	.	.	5.71	1.95	0.26073	.	.	.	.	.	T	0.56863	0.2014	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52888	-0.8515	4	.	.	.	.	9.1486	0.36948	0.6087:0.3215:0.0697:0.0	.	.	.	.	A	294;88	.	.	E	+	2	0	MACF1	39701930	0.991000	0.36638	1.000000	0.80357	0.990000	0.78478	0.446000	0.21694	1.066000	0.40716	0.528000	0.53228	GAG	.	.		0.453	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		C	39929343	A	C	39929343	2	2	333	1	0	0	0	0	0	0	0	1	9153	291	11	5		5	MACF1	1	39929343	Silent	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	6693697	39929343	209321278	5	46347										
ATPAF1	64756	hgsc.bcm.edu	37	chr1	47110923	47110923	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tcccttcttggcagagcacaTagaaactgtgaaaaacagat	8	9	1	4			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr1:47110923T>C	ENST00000371937.4	-	7	698	c.594A>G	c.(592-594)ctA>ctG	p.L198L	ATPAF1_ENST00000532925.1_Silent_p.L110L|ATPAF1_ENST00000574428.1_Intron|ATPAF1_ENST00000542495.1_Silent_p.L47L|ATPAF1_ENST00000329231.4_Intron|ATPAF1_ENST00000576409.1_Silent_p.L221L	NM_022745.4	NP_073582.3	Q5TC12	ATPF1_HUMAN	ATP synthase mitochondrial F1 complex assembly factor 1	198					protein complex assembly (GO:0006461)	mitochondrion (GO:0005739)				endometrium(1)|kidney(1)|large_intestine(2)|lung(4)	8	Acute lymphoblastic leukemia(166;0.155)					GCAGAGCACATAGAAACTGTG	0.373																																					p.L221L	Melanoma(138;107 1777 21672 30337 52312)	Atlas-SNP	.											.	ATPAF1	19	.	0			c.A663G						.						124	118	120					1																	47110923		2203	4300	6503	SO:0001819	synonymous_variant	64756	exon7			AGCACATAGAAAC	AK026004	CCDS541.1, CCDS41327.1, CCDS541.2, CCDS41327.2, CCDS57997.1, CCDS57998.1	1p33-p32.3	2012-10-12			ENSG00000123472	ENSG00000123472		"Mitochondrial respiratory chain complex assembly factors"	18803	protein-coding gene	gene with protein product		608917				11410595	Standard	NM_022745		Approved	FLJ22351, Atp11p, ATP11	uc001cqh.4	Q5TC12	OTTHUMG00000007988	ENST00000371937.4:c.594A>G	chr1.hg19:g.47110923T>C		34.0	0.0		42.0	27.0	NM_022745	B1AQW7|B7Z7D6|B7Z7I6|Q9H6E3	Silent	SNP	ENST00000371937.4	hg19		.	.	.	.	.	.	.	.	.	.	T	7.749	0.702937	0.15172	.	.	ENSG00000123472	ENST00000534216	.	.	.	5.81	-8.29	0.01009	.	.	.	.	.	T	0.32010	0.0815	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43212	-0.9405	4	.	.	.	-8.3799	0.3819	0.00396	0.2212:0.2637:0.2117:0.3034	.	.	.	.	C	53	.	.	Y	-	2	0	ATPAF1	46883510	0.000000	0.05858	0.796000	0.32109	0.834000	0.47266	-2.665000	0.00848	-1.173000	0.02758	-0.137000	0.14449	TAT	.	.		0.373	ATPAF1-201	KNOWN	basic	protein_coding	protein_coding		NM_022745		C	47110923	T	C	47110923	2	2	333	1	0	0	0	0	0	0	0	1	1200	1393	49	2		2	ATPAF1	1	47110923	Silent	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	7181580	47110923	202139698	6	46348										
INADL	10207	hgsc.bcm.edu	37	chr1	62516654	62516654	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ataggatcagagcggcaccgAacctattagtagtgaggaag	13	7	1	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr1:62516654A>T	ENST00000371158.2	+	31	4163	c.4049A>T	c.(4048-4050)gAa>gTa	p.E1350V	INADL_ENST00000543708.1_Missense_Mutation_p.E134V|INADL_ENST00000316485.6_Missense_Mutation_p.E1350V|INADL_ENST00000545929.1_Missense_Mutation_p.E23V	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1350					cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						AGCGGCACCGAACCTATTAGT	0.393																																					p.E1350V		Atlas-SNP	.											.	INADL	179	.	0			c.A4049T						.						129	125	126					1																	62516654		2203	4300	6503	SO:0001583	missense	10207	exon31			GCACCGAACCTAT	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.4049A>T	chr1.hg19:g.62516654A>T	ENSP00000360200:p.Glu1350Val	48.0	0.0		42.0	20.0	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	hg19	CCDS617.2	.	.	.	.	.	.	.	.	.	.	A	8.289	0.817214	0.16607	.	.	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000307297;ENST00000543708;ENST00000545929	T;T;T;T;T	0.50001	2.58;2.44;3.16;2.16;0.76	5.08	5.08	0.68730	.	0.370903	0.26688	N	0.023006	T	0.52853	0.1760	L	0.54323	1.7	0.20196	N	0.999921	D;B;P;B;B;B	0.57257	0.979;0.224;0.943;0.079;0.167;0.035	P;B;P;B;B;B	0.52957	0.714;0.035;0.489;0.033;0.15;0.046	T	0.49707	-0.8911	10	0.44086	T	0.13	.	11.4185	0.49967	1.0:0.0:0.0:0.0	.	23;134;809;1350;1350;1350	F5GY89;B4DE90;Q8NI35-5;F8W8T2;Q8NI35;Q8NI35-4	.;.;.;.;INADL_HUMAN;.	V	1350;1350;1350;1350;134;134;23	ENSP00000360200:E1350V;ENSP00000326199:E1350V;ENSP00000307496:E134V;ENSP00000445790:E134V;ENSP00000440094:E23V	ENSP00000307496:E134V	E	+	2	0	INADL	62289242	0.646000	0.27295	0.095000	0.20976	0.139000	0.21198	2.682000	0.46934	2.260000	0.74910	0.533000	0.62120	GAA	.	.		0.393	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		T	62516654	A	T	62516654	3	4	333	1	0	0	0	0	1	0	0	0	7740	246	9	4	4167	4	INADL	1	62516654	Missense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	15405731	62516654	186733967	7	46349										
ABCA4	24	hgsc.bcm.edu	37	chr1	94510167	94510167	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tctcagttcctgtgtcgcttActggtggaacaggatgttgt	12	8	1	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr1:94510167A>C	ENST00000370225.3	-	20	3137		c.e20+1			NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4						phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			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)		TGTGTCGCTTACTGGTGGAAC	0.612																																					.		Atlas-SNP	.											.	ABCA4	275	.	0			c.3050+2T>G						.						140	120	126					1																	94510167		2203	4300	6503	SO:0001630	splice_region_variant	24	exon21			TCGCTTACTGGTG	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.3050+1T>G	chr1.hg19:g.94510167A>C		79.0	0.0		86.0	31.0	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Splice_Site	SNP	ENST00000370225.3	hg19	CCDS747.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.491407	0.84962	.	.	ENSG00000198691	ENST00000370225	.	.	.	5.99	5.99	0.97316	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.4943	0.84223	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ABCA4	94282755	1.000000	0.71417	1.000000	0.80357	0.837000	0.47467	9.339000	0.96797	2.291000	0.77112	0.533000	0.62120	.	.	.		0.612	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350	Intron	C	94510167	A	C	94510167	5	2	333	1	0	0	0	0	0	0	1	0	34	405	14	5	3893	5	ABCA4	1	94510167	Splice_Site	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	31993513	94510167	154740454	8	46350										
SPAG17	200162	hgsc.bcm.edu	37	chr1	118623785	118623785	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tgctctaacagctgtctattAtcagggactgagagtttgag	11	7	3	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr1:118623785A>G	ENST00000336338.5	-	15	2213	c.2148T>C	c.(2146-2148)gaT>gaC	p.D716D		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	716						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		GCTGTCTATTATCAGGGACTG	0.433																																					p.D716D		Atlas-SNP	.											SPAG17,NS,carcinoma,0,1	SPAG17	263	.	0			c.T2148C						.						184	169	174					1																	118623785		2203	4300	6503	SO:0001819	synonymous_variant	200162	exon15			TCTATTATCAGGG		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.2148T>C	chr1.hg19:g.118623785A>G		152.0	0.0		150.0	66.0	NM_206996	Q8NAZ1|Q9NT21	Silent	SNP	ENST00000336338.5	hg19	CCDS899.1																																																																																			.	.		0.433	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		G	118623785	A	G	118623785	2	3	333	1	0	0	0	0	0	0	0	1	14994	446	16	2		2	SPAG17	1	118623785	Silent	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	24113618	118623785	130626836	9	46351										
ITGA10	8515	hgsc.bcm.edu	37	chr1	145532113	145532113	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	cctcactcctttctcttctcAgcacagaagggttcagtcag	7	14	5	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr1:145532113A>T	ENST00000369304.3	+	8	933		c.e8-1		ITGA10_ENST00000538811.1_Splice_Site|ITGA10_ENST00000539363.1_Splice_Site|ITGA10_ENST00000481236.1_Splice_Site	NM_003637.3	NP_003628.2	O75578	ITA10_HUMAN	integrin, alpha 10						axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	integrin alpha10-beta1 complex (GO:0034680)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					TTCTCTTCTCAGCACAGAAGG	0.537																																					.		Atlas-SNP	.											.	ITGA10	131	.	0			c.759-2A>T						.						92	89	90					1																	145532113		2203	4300	6503	SO:0001630	splice_region_variant	8515	exon8			CTTCTCAGCACAG	AF074015	CCDS72869.1	1q21.1	2010-03-23			ENSG00000143127	ENSG00000143127		"Integrins"	6135	protein-coding gene	gene with protein product		604042				9685391, 10702680	Standard	NM_003637		Approved		uc001eoa.3	O75578	OTTHUMG00000013751	ENST00000369304.3:c.759-1A>T	chr1.hg19:g.145532113A>T		26.0	0.0		24.0	11.0	NM_003637	B2RAM4|B2RTV5|Q6UXJ6|Q9UHZ8	Splice_Site	SNP	ENST00000369304.3	hg19	CCDS918.1	.	.	.	.	.	.	.	.	.	.	A	19.50	3.839483	0.71488	.	.	ENSG00000143127	ENST00000369304;ENST00000543043;ENST00000539363;ENST00000538811	.	.	.	5.2	5.2	0.72013	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.3258	0.60459	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ITGA10	144243470	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.001000	0.88508	2.116000	0.64780	0.418000	0.28097	.	.	.		0.537	ITGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038537.2	NM_003637	Intron	T	145532113	A	T	145532113	5	4	333	1	0	0	0	0	0	0	1	0	7882	202	7	4	787	4	ITGA10	1	145532113	Splice_Site	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	26908328	145532113	103718508	10	46352										
VPS72	6944	hgsc.bcm.edu	37	chr1	151156881	151156881	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	cgctcacagtggggccccttTcgccgtcttgactggccctg	12	16	2	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr1:151156881T>A	ENST00000354473.4	-	4	510	c.474A>T	c.(472-474)cgA>cgT	p.R158R	VPS72_ENST00000496809.1_5'UTR			Q15906	VPS72_HUMAN	vacuolar protein sorting 72 homolog (S. cerevisiae)	158					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(6)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	14	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			GGGGCCCCTTTCGCCGTCTTG	0.562																																					p.R158R	Pancreas(109;1131 2287 3209 24201)	Atlas-SNP	.											.	VPS72	31	.	0			c.A474T						.						96	100	99					1																	151156881		2203	4300	6503	SO:0001819	synonymous_variant	6944	exon4			CCCCTTTCGCCGT	D43642	CCDS989.1, CCDS59201.1	1q21	2008-02-05	2006-12-19	2005-09-08	ENSG00000163159	ENSG00000163159			11644	protein-coding gene	gene with protein product		600607	"transcription factor-like 1", "vacuolar protein sorting 72 (yeast)"	TCFL1		7702631	Standard	NM_001271087		Approved	YL-1, YL1, Swc2	uc001exe.2	Q15906	OTTHUMG00000012345	ENST00000354473.4:c.474A>T	chr1.hg19:g.151156881T>A		55.0	0.0		77.0	36.0	NM_001271087	A6NLK9|A6PW55|Q53GJ2|Q5U0R4	Silent	SNP	ENST00000354473.4	hg19	CCDS59201.1																																																																																			.	.		0.562	VPS72-002	NOVEL	mRNA_start_NF|basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000034394.3	NM_005997		A	151156881	T	A	151156881	2	1	333	1	0	0	0	0	0	0	0	1	17232	1770	62	4		4	VPS72	1	151156881	Silent	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	5624768	151156881	98093740	11	46353										
FLAD1	80308	hgsc.bcm.edu	37	chr1	154961247	154961247	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	cctacctgactgcccgtttgCcccagggatcgctggtcccc	10	18	0	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr1:154961247C>A	ENST00000292180.3	+	2	1361	c.1039C>A	c.(1039-1041)Ccc>Acc	p.P347T	FLAD1_ENST00000295530.2_Missense_Mutation_p.P80T|FLAD1_ENST00000405236.2_Missense_Mutation_p.P248T|FLAD1_ENST00000368431.3_Missense_Mutation_p.P248T|FLAD1_ENST00000368433.1_Missense_Mutation_p.P347T|FLAD1_ENST00000315144.10_Missense_Mutation_p.P250T|FLAD1_ENST00000368428.1_5'UTR|FLAD1_ENST00000368432.1_Missense_Mutation_p.P250T	NM_025207.4	NP_079483.3	Q8NFF5	FAD1_HUMAN	flavin adenine dinucleotide synthetase 1	347					FAD biosynthetic process (GO:0006747)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|riboflavin metabolic process (GO:0006771)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|FMN adenylyltransferase activity (GO:0003919)			endometrium(3)|kidney(4)|large_intestine(2)|lung(7)|ovary(3)|skin(3)	22	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			TGCCCGTTTGCCCCAGGGATC	0.577																																					p.P347T		Atlas-SNP	.											.	FLAD1	52	.	0			c.C1039A						.						65	63	64					1																	154961247		2203	4300	6503	SO:0001583	missense	80308	exon2			CGTTTGCCCCAGG		CCDS1078.1, CCDS1079.1, CCDS53371.1, CCDS53372.1	1q22	2013-03-05	2013-03-05		ENSG00000160688	ENSG00000160688	2.7.7.2		24671	protein-coding gene	gene with protein product		610595	"Fad1, flavin adenine dinucleotide synthetase, homolog (yeast)", "FAD1 flavin adenine dinucleotide synthetase homolog (S. cerevisiae)", "flavin adenine dinucleotide synthetase"				Standard	NM_001184891		Approved	PP591, FAD1	uc001fgf.2	Q8NFF5	OTTHUMG00000037416	ENST00000292180.3:c.1039C>A	chr1.hg19:g.154961247C>A	ENSP00000292180:p.Pro347Thr	41.0	0.0		71.0	25.0	NM_025207	Q8N5J1|Q8N686|Q8WU93|Q8WUJ4|Q96CR8|Q99764|Q9HBN6	Missense_Mutation	SNP	ENST00000292180.3	hg19	CCDS1078.1	.	.	.	.	.	.	.	.	.	.	C	18.71	3.682819	0.68157	.	.	ENSG00000160688	ENST00000368433;ENST00000315144;ENST00000368432;ENST00000368431;ENST00000292180;ENST00000405236;ENST00000295530	.	.	.	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.75466	0.3853	M	0.65498	2.005	0.80722	D	1	D;D;D	0.89917	1.0;0.992;1.0	D;D;D	0.97110	1.0;0.914;0.999	T	0.74297	-0.3711	9	0.56958	D	0.05	-26.9382	19.5221	0.95189	0.0:1.0:0.0:0.0	.	80;347;248	Q5T191;Q8NFF5;Q8NFF5-4	.;FAD1_HUMAN;.	T	347;250;250;248;347;248;80	.	ENSP00000292180:P347T	P	+	1	0	FLAD1	153227871	1.000000	0.71417	0.997000	0.53966	0.396000	0.30629	6.729000	0.74775	2.941000	0.99782	0.655000	0.94253	CCC	.	.		0.577	FLAD1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000091089.1	NM_025207		A	154961247	C	A	154961247	3	1	333	1	0	0	0	0	1	0	0	0	5928	739	26	3	1120	3	FLAD1	1	154961247	Missense_Mutation	SNP	C	TCGA-RC-A6M4-01A-11D-A32G-10	3804366	154961247	94289374	12	46354										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158589013	158589013	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gggatgtagcatagcacaccTggtttccaggatccattgaa	11	9	0	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr1:158589013T>G	ENST00000368147.4	-	45	6709	c.6529A>C	c.(6529-6531)Agg>Cgg	p.R2177R		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2177					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					ATAGCACACCTGGTTTCCAGG	0.483																																					p.R2177R		Atlas-SNP	.											.	SPTA1	720	.	0			c.A6529C						.						223	216	218					1																	158589013		1997	4165	6162	SO:0001630	splice_region_variant	6708	exon45			CACACCTGGTTTC	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.6530+1A>C	chr1.hg19:g.158589013T>G		108.0	0.0		107.0	39.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Silent	SNP	ENST00000368147.4	hg19	CCDS41423.1																																																																																			.	.		0.483	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	Silent	G	158589013	T	G	158589013	5	3	333	1	0	0	0	0	0	0	1	0	15131	1594	55	5	762	5	SPTA1	1	158589013	Splice_Site	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	3627766	158589013	90661608	13	46355										
TNN	63923	hgsc.bcm.edu	37	chr1	175046732	175046732	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ctgccttggttcaggttgacGctgaccctcagcccctcagt	10	15	3	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr1:175046732G>A	ENST00000239462.4	+	2	291	c.178G>A	c.(178-180)Gct>Act	p.A60T		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	60					axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		TCAGGTTGACGCTGACCCTCA	0.592																																					p.A60T		Atlas-SNP	.											.	TNN	297	.	0			c.G178A						.						82	56	65					1																	175046732		2203	4300	6503	SO:0001583	missense	63923	exon2			GTTGACGCTGACC	AK127044	CCDS30943.1	1q23-q24	2013-02-11			ENSG00000120332	ENSG00000120332		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	22942	protein-coding gene	gene with protein product							Standard	NM_022093		Approved		uc001gkl.1	Q9UQP3	OTTHUMG00000034882	ENST00000239462.4:c.178G>A	chr1.hg19:g.175046732G>A	ENSP00000239462:p.Ala60Thr	77.0	0.0		96.0	49.0	NM_022093	B9EGP3|Q5R360	Missense_Mutation	SNP	ENST00000239462.4	hg19	CCDS30943.1	.	.	.	.	.	.	.	.	.	.	G	11.13	1.547875	0.27652	.	.	ENSG00000120332	ENST00000239462;ENST00000539081	T	0.26810	1.71	5.51	0.199	0.15175	.	0.578666	0.18353	N	0.143817	T	0.11793	0.0287	N	0.24115	0.695	0.09310	N	1	B;B	0.20550	0.005;0.046	B;B	0.14578	0.003;0.011	T	0.18085	-1.0348	10	0.30078	T	0.28	.	1.382	0.02232	0.2969:0.2373:0.3445:0.1213	.	60;60	B3KXB6;Q9UQP3	.;TENN_HUMAN	T	60	ENSP00000239462:A60T	ENSP00000239462:A60T	A	+	1	0	TNN	173313355	0.001000	0.12720	0.150000	0.22450	0.782000	0.44232	0.213000	0.17521	-0.216000	0.10048	-0.175000	0.13238	GCT	.	.		0.592	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527		A	175046732	G	A	175046732	3	1	333	1	0	0	0	0	1	0	0	0	16338	1087	38	1	180	1	TNN	1	175046732	Missense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	16457719	175046732	74203889	14	46356										
KIAA1614	57710	hgsc.bcm.edu	37	chr1	180904469	180904469	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gcagcagcgccagcgccaggTgctgagcaccgtgttgcagg	16	13	0	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr1:180904469T>A	ENST00000367588.4	+	5	1479	c.1424T>A	c.(1423-1425)gTg>gAg	p.V475E	KIAA1614_ENST00000367587.1_Missense_Mutation_p.V96E	NM_020950.1	NP_066001.1	Q5VZ46	K1614_HUMAN	KIAA1614	475										NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	33						CAGCGCCAGGTGCTGAGCACC	0.736																																					p.V475E		Atlas-SNP	.											.	KIAA1614	75	.	0			c.T1424A						.						5	8	7					1																	180904469		1895	4022	5917	SO:0001583	missense	57710	exon5			GCCAGGTGCTGAG	AB046834	CCDS41442.1	1q25.3	2008-02-05			ENSG00000135835	ENSG00000135835			29327	protein-coding gene	gene with protein product							Standard	NM_020950		Approved		uc001gok.2	Q5VZ46	OTTHUMG00000035183	ENST00000367588.4:c.1424T>A	chr1.hg19:g.180904469T>A	ENSP00000356560:p.Val475Glu	31.0	0.0		47.0	22.0	NM_020950	Q5VZ45|Q9HCF8	Missense_Mutation	SNP	ENST00000367588.4	hg19	CCDS41442.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.021172	0.75275	.	.	ENSG00000135835	ENST00000367588;ENST00000367587	T;T	0.27890	2.18;1.64	4.68	-2.64	0.06114	.	0.826580	0.10512	N	0.666045	T	0.34221	0.0890	L	0.53249	1.67	0.26129	N	0.980448	D	0.54047	0.964	P	0.53006	0.715	T	0.44205	-0.9343	9	0.52906	T	0.07	-1.4174	6.1299	0.20199	0.0:0.1558:0.3911:0.4531	.	475	Q5VZ46	K1614_HUMAN	E	475;96	ENSP00000356560:V475E;ENSP00000356559:V96E	ENSP00000356559:V96E	V	+	2	0	KIAA1614	179171092	0.000000	0.05858	0.002000	0.10522	0.359000	0.29487	-0.593000	0.05740	-0.379000	0.07906	-0.473000	0.04963	GTG	.	.		0.736	KIAA1614-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085151.1	XM_046531		A	180904469	T	A	180904469	3	1	333	1	0	0	0	0	1	0	0	0	8257	1696	59	4	1442	4	KIAA1614	1	180904469	Missense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	5857737	180904469	68346152	15	46357										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186056637	186056637	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tagttaatgtaagagagggaActtctgtgtctttggagtgt	13	3	2	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr1:186056637A>T	ENST00000271588.4	+	60	9452	c.9223A>T	c.(9223-9225)Act>Tct	p.T3075S	HMCN1_ENST00000367492.2_Missense_Mutation_p.T3075S	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	3075	Ig-like C2-type 29.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						AAGAGAGGGAACTTCTGTGTC	0.428																																					p.T3075S		Atlas-SNP	.											.	HMCN1	797	.	0			c.A9223T						.						102	101	102					1																	186056637		2203	4299	6502	SO:0001583	missense	83872	exon60			GAGGGAACTTCTG	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.9223A>T	chr1.hg19:g.186056637A>T	ENSP00000271588:p.Thr3075Ser	85.0	0.0		113.0	44.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	A	4.011	-0.000682	0.07819	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.70869	-0.52;-0.52	5.59	0.0385	0.14200	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.360497	0.34507	N	0.003904	T	0.37544	0.1007	N	0.02658	-0.545	0.09310	N	1	P	0.44309	0.832	B	0.43508	0.422	T	0.48980	-0.8986	10	0.10377	T	0.69	.	4.8784	0.13667	0.4643:0.0:0.1411:0.3947	.	3075	Q96RW7	HMCN1_HUMAN	S	3075	ENSP00000271588:T3075S;ENSP00000356462:T3075S	ENSP00000271588:T3075S	T	+	1	0	HMCN1	184323260	0.000000	0.05858	0.022000	0.16811	0.334000	0.28698	0.912000	0.28597	0.050000	0.15949	0.533000	0.62120	ACT	.	.		0.428	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		T	186056637	A	T	186056637	3	4	333	1	0	0	0	0	1	0	0	0	7229	43	2	4	9461	4	HMCN1	1	186056637	Missense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	5152168	186056637	63193984	16	46358										
C1orf27	54953	hgsc.bcm.edu	37	chr1	186348970	186348970	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tggccagtatctttcaaacaTaaatctccaaggaaaggctt	7	9	3	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr1:186348970T>A	ENST00000287859.6	+	2	178	c.53T>A	c.(52-54)aTa>aAa	p.I18K	C1orf27_ENST00000432021.3_Missense_Mutation_p.I18K|C1orf27_ENST00000367470.3_Missense_Mutation_p.I18K|C1orf27_ENST00000419367.3_Missense_Mutation_p.I18K	NM_017847.5	NP_060317.3	Q5SWX8	ODR4_HUMAN	chromosome 1 open reading frame 27	18						integral component of membrane (GO:0016021)	oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)	9						CTTTCAAACATAAATCTCCAA	0.323																																					p.I18K		Atlas-SNP	.											.	C1orf27	41	.	0			c.T53A						.						137	137	137					1																	186348970		1814	4075	5889	SO:0001583	missense	54953	exon2			CAAACATAAATCT	BC003397	CCDS53448.1, CCDS53449.1, CCDS53450.1	1q25	2012-06-25			ENSG00000157181	ENSG00000157181			24299	protein-coding gene	gene with protein product	"transactivated by recombinant transforming growth factor beta"	609335				12868032	Standard	NM_017847		Approved	FLJ20505, odr-4, TTG1	uc021pgj.1	Q5SWX8	OTTHUMG00000035579	ENST00000287859.6:c.53T>A	chr1.hg19:g.186348970T>A	ENSP00000287859:p.Ile18Lys	120.0	0.0		203.0	82.0	NM_001164245	B4DNY0|E9PFR7|Q19CC6|Q8WYB6|Q9BTS2|Q9H6A6|Q9NX06	Missense_Mutation	SNP	ENST00000287859.6	hg19	CCDS53448.1	.	.	.	.	.	.	.	.	.	.	T	16.07	3.017445	0.54576	.	.	ENSG00000157181	ENST00000367470;ENST00000419367;ENST00000432021;ENST00000287859	T;T	0.48836	0.8;0.82	5.33	5.33	0.75918	.	0.467872	0.20767	N	0.086055	T	0.45276	0.1334	L	0.50333	1.59	0.30318	N	0.787863	P;B;B	0.35208	0.49;0.21;0.21	B;B;B	0.37422	0.249;0.148;0.148	T	0.53236	-0.8467	10	0.46703	T	0.11	-26.9905	12.8427	0.57813	0.0:0.0:0.0:1.0	.	18;18;18	E9PFR7;Q5SWX8-2;Q5SWX8	.;.;ODR4_HUMAN	K	18	ENSP00000395084:I18K;ENSP00000287859:I18K	ENSP00000287859:I18K	I	+	2	0	C1orf27	184615593	0.906000	0.30813	0.435000	0.26784	0.981000	0.71138	5.728000	0.68531	2.011000	0.59026	0.528000	0.53228	ATA	.	.		0.323	C1orf27-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086352.2	NM_017847		A	186348970	T	A	186348970	3	1	333	1	0	0	0	0	1	0	0	0	2038	1406	49	4	55	4	C1orf27	1	186348970	Missense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	292333	186348970	62901651	17	46359										
FAIM3	9214	hgsc.bcm.edu	37	chr1	207087190	207087190	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	catagactccgctgtcacttTctgtcagctgtgttacctcc	7	14	3	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr1:207087190T>C	ENST00000367091.3	-	2	430	c.287A>G	c.(286-288)gAa>gGa	p.E96G	FAIM3_ENST00000528654.1_Intron|FAIM3_ENST00000442471.2_Intron|FAIM3_ENST00000420007.2_Missense_Mutation_p.E96G	NM_005449.4	NP_005440.1	O60667	FAIM3_HUMAN	Fas apoptotic inhibitory molecule 3	96	Ig-like.				cellular defense response (GO:0006968)|immune system process (GO:0002376)|negative regulation of apoptotic process (GO:0043066)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	15	Breast(84;0.201)					GCTGTCACTTTCTGTCAGCTG	0.532																																					p.E96G		Atlas-SNP	.											.	FAIM3	36	.	0			c.A287G						.						124	117	119					1																	207087190		2203	4300	6503	SO:0001583	missense	9214	exon2			TCACTTTCTGTCA	AF057557	CCDS1473.1, CCDS44304.1	1q32.1	2013-01-11			ENSG00000162894	ENSG00000162894		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14315	protein-coding gene	gene with protein product		606015				9586636, 1563211	Standard	NM_005449		Approved	TOSO	uc001hey.3	O60667	OTTHUMG00000036457	ENST00000367091.3:c.287A>G	chr1.hg19:g.207087190T>C	ENSP00000356058:p.Glu96Gly	133.0	0.0		190.0	52.0	NM_005449	A8K7J2|B7Z6Z0|D9MWM3	Missense_Mutation	SNP	ENST00000367091.3	hg19	CCDS1473.1	.	.	.	.	.	.	.	.	.	.	T	14.68	2.607150	0.46527	.	.	ENSG00000162894	ENST00000367091;ENST00000420007;ENST00000525793;ENST00000529560;ENST00000530505	T;T;T;T;T	0.22134	1.97;1.97;1.97;1.97;1.97	5.28	5.28	0.74379	Immunoglobulin subtype (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.557125	0.16209	N	0.224579	T	0.33585	0.0868	M	0.79011	2.435	0.09310	N	1	P	0.43231	0.801	P	0.46419	0.516	T	0.22521	-1.0214	10	0.37606	T	0.19	-2.0442	11.6259	0.51145	0.0:0.0:0.0:1.0	.	96	O60667	FAIM3_HUMAN	G	96;96;96;96;127	ENSP00000356058:E96G;ENSP00000403356:E96G;ENSP00000432936:E96G;ENSP00000437331:E96G;ENSP00000436316:E127G	ENSP00000356058:E96G	E	-	2	0	FAIM3	205153813	0.001000	0.12720	0.005000	0.12908	0.248000	0.25809	0.917000	0.28665	1.998000	0.58463	0.533000	0.62120	GAA	.	.		0.532	FAIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088677.1	NM_005449		C	207087190	T	C	207087190	3	2	333	1	0	0	0	0	1	0	0	0	5382	1783	62	2	913	2	FAIM3	1	207087190	Missense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	20738220	207087190	42163431	18	46360										
KCNH1	3756	hgsc.bcm.edu	37	chr1	211093249	211093249	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gatctcatagtccccaatgcTgtaccagatgcaggccatcc	8	14	1	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr1:211093249T>A	ENST00000271751.4	-	7	1222	c.1195A>T	c.(1195-1197)Agc>Tgc	p.S399C	KCNH1_ENST00000367007.4_Missense_Mutation_p.S372C			O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 1	399					myoblast fusion (GO:0007520)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|phosphorelay sensor kinase activity (GO:0000155)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|lung(35)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)		TCCCCAATGCTGTACCAGATG	0.532																																					p.S399C		Atlas-SNP	.											.	KCNH1	199	.	0			c.A1195T						.						175	158	164					1																	211093249		2203	4300	6503	SO:0001583	missense	3756	exon7			CAATGCTGTACCA	AJ001366	CCDS1496.1, CCDS31015.1	1q32.2	2012-07-05			ENSG00000143473	ENSG00000143473		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6250	protein-coding gene	gene with protein product		603305				9738473, 16382104	Standard	NM_172362		Approved	Kv10.1, eag, h-eag, eag1	uc001hib.2	O95259	OTTHUMG00000036309	ENST00000271751.4:c.1195A>T	chr1.hg19:g.211093249T>A	ENSP00000271751:p.Ser399Cys	138.0	0.0		227.0	70.0	NM_172362	B1AQ26|O76035|Q14CL3	Missense_Mutation	SNP	ENST00000271751.4	hg19	CCDS1496.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.095697	0.76870	.	.	ENSG00000143473	ENST00000271751;ENST00000367007	D;D	0.98602	-5.02;-5.02	5.8	4.66	0.58398	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98096	0.9372	L	0.55834	1.745	0.80722	D	1	P;P	0.52577	0.954;0.954	P;P	0.61533	0.89;0.89	D	0.97804	1.0246	10	0.52906	T	0.07	.	12.4351	0.55595	0.0:0.0:0.1404:0.8596	.	372;399	Q14CL3;O95259	.;KCNH1_HUMAN	C	399;372	ENSP00000271751:S399C;ENSP00000355974:S372C	ENSP00000271751:S399C	S	-	1	0	KCNH1	209159872	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.751000	0.85126	1.011000	0.39340	0.533000	0.62120	AGC	.	.		0.532	KCNH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088332.1	NM_002238		A	211093249	T	A	211093249	3	1	333	1	0	0	0	0	1	0	0	0	8040	1580	55	4	1794	4	KCNH1	1	211093249	Missense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	4006059	211093249	38157372	19	46361										
CDC42BPA	8476	hgsc.bcm.edu	37	chr1	227216680	227216680	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tctttaaattttctgtgacgGgtcttgctctgaaatagttc	8	7	4	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr1:227216680G>T	ENST00000366769.3	-	29	5296	c.4005C>A	c.(4003-4005)acC>acA	p.T1335T	CDC42BPA_ENST00000535525.1_Silent_p.T1315T|CDC42BPA_ENST00000366767.3_Silent_p.T1254T|CDC42BPA_ENST00000366765.3_Silent_p.T1348T|CDC42BPA_ENST00000366764.2_Silent_p.T1307T|CDC42BPA_ENST00000366766.2_Silent_p.T1370T|CDC42BPA_ENST00000334218.5_Silent_p.T1335T	NM_003607.3	NP_003598.2			CDC42 binding protein kinase alpha (DMPK-like)											NS(1)|breast(4)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(12)|lung(32)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|urinary_tract(2)	77		all_cancers(173;0.156)|Prostate(94;0.0792)				TTCTGTGACGGGTCTTGCTCT	0.438																																					p.T1335T		Atlas-SNP	.											.	CDC42BPA	528	.	0			c.C4005A						.						73	67	69					1																	227216680		2203	4300	6503	SO:0001819	synonymous_variant	8476	exon29			GTGACGGGTCTTG	U59305	CCDS1558.1, CCDS1559.1	1q42.11	2011-11-23	2001-11-28		ENSG00000143776	ENSG00000143776			1737	protein-coding gene	gene with protein product	"myotonic dystrophy kinase-related Cdc42-binding kinase"	603412	"CDC42-binding protein kinase alpha (DMPK-like)"				Standard	NM_003607		Approved	MRCKA, PK428, FLJ23347, KIAA0451, MRCK	uc001hqr.3	Q5VT25	OTTHUMG00000037618	ENST00000366769.3:c.4005C>A	chr1.hg19:g.227216680G>T		26.0	0.0		56.0	14.0	NM_003607		Silent	SNP	ENST00000366769.3	hg19	CCDS1558.1	.	.	.	.	.	.	.	.	.	.	G	5.784	0.328964	0.10956	.	.	ENSG00000143776	ENST00000448940;ENST00000442054;ENST00000429440;ENST00000441725	.	.	.	5.32	1.29	0.21616	.	.	.	.	.	T	0.44746	0.1308	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.20773	-1.0265	4	.	.	.	.	2.8943	0.05686	0.1889:0.2564:0.4215:0.1331	.	.	.	.	T	538;664;233;560	.	.	P	-	1	0	CDC42BPA	225283303	0.127000	0.22367	0.995000	0.50966	0.964000	0.63967	-0.620000	0.05565	-0.128000	0.11641	-1.128000	0.01989	CCG	.	.		0.438	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	NM_014826		T	227216680	G	T	227216680	2	4	333	1	0	0	0	0	0	0	0	1	3074	1219	43	3		3	CDC42BPA	1	227216680	Silent	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	16123431	227216680	22033941	20	46362										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228528927	228528927	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gactcccgcaccgataccgtCagctacgtgttccggaacat	9	15	1	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr1:228528927C>A	ENST00000422127.1	+	73	17873	c.17829C>A	c.(17827-17829)gtC>gtA	p.V5943V	OBSCN_ENST00000570156.2_Silent_p.V6900V|OBSCN_ENST00000366707.4_Silent_p.V3577V|OBSCN_ENST00000366709.4_Silent_p.V3062V|OBSCN_ENST00000284548.11_Silent_p.V5943V	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5943	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CCGATACCGTCAGCTACGTGT	0.657																																					p.V6900V		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C20700A						.						32	35	34					1																	228528927		2062	4202	6264	SO:0001819	synonymous_variant	84033	exon84			TACCGTCAGCTAC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.17829C>A	chr1.hg19:g.228528927C>A		38.0	0.0		72.0	17.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	C	10.63	1.404978	0.25378	.	.	ENSG00000154358	ENST00000441106	.	.	.	5.71	4.79	0.61399	.	.	.	.	.	T	0.60235	0.2253	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58463	-0.7632	4	.	.	.	.	9.4968	0.38993	0.1439:0.7853:0.0:0.0708	.	.	.	.	K	560	.	.	Q	+	1	0	OBSCN	226595550	0.999000	0.42202	1.000000	0.80357	0.058000	0.15608	0.655000	0.24933	1.405000	0.46838	-0.182000	0.12963	CAG	.	.		0.657	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228528927	C	A	228528927	2	1	333	1	0	0	0	0	0	0	0	1	10821	813	29	3		3	OBSCN	1	228528927	Silent	SNP	C	TCGA-RC-A6M4-01A-11D-A32G-10	1312247	228528927	20721694	21	46363										
CHML	1122	hgsc.bcm.edu	37	chr1	241799048	241799048	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	attataaccacatcaaactcTgtgggaagattgtccgccat	7	10	2	1	rs369552093		TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr1:241799048T>G	ENST00000366553.1	-	1	184	c.21A>C	c.(19-21)acA>acC	p.T7T	OPN3_ENST00000469376.1_Intron|OPN3_ENST00000366554.2_Intron|OPN3_ENST00000331838.5_Intron	NM_001821.3	NP_001812.2	P26374	RAE2_HUMAN	choroideremia-like (Rab escort protein 2)	7					intracellular protein transport (GO:0006886)|protein geranylgeranylation (GO:0018344)	Rab-protein geranylgeranyltransferase complex (GO:0005968)	GTPase activator activity (GO:0005096)|Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(7)|ovary(4)|skin(3)|stomach(1)	26	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)			CATCAAACTCTGTGGGAAGAT	0.428																																					p.T7T		Atlas-SNP	.											.	CHML	82	.	0			c.A21C						.	T	,	0,4406		0,0,2203	60	62	62		21,	2.8	1	1		62	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,intron	CHML,OPN3	NM_001821.3,NM_014322.2	,	0,1,6502	GG,GT,TT		0.0116,0.0,0.0077	,	7/657,	241799048	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	1122	exon1			AAACTCTGTGGGA	X64728	CCDS31073.1	1q43	2013-09-19			ENSG00000203668	ENSG00000203668			1941	protein-coding gene	gene with protein product		118825				7981670	Standard	NM_001821		Approved	REP-2	uc001hzd.3	P26374	OTTHUMG00000039690	ENST00000366553.1:c.21A>C	chr1.hg19:g.241799048T>G		130.0	0.0		197.0	51.0	NM_001821	B2RAB9|Q17RE0|Q9H1Y4	Silent	SNP	ENST00000366553.1	hg19	CCDS31073.1																																																																																			.	.		0.428	CHML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095712.1	NM_001821		G	241799048	T	G	241799048	2	3	333	1	0	0	0	0	0	0	0	1	3353	1567	55	5		5	CHML	1	241799048	Silent	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	13270121	241799048	7451573	22	46364										
MYT1L	23040	hgsc.bcm.edu	37	chr2	1843065	1843065	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tctgcctcttggccgccaagGggcacccggaggcgctgcga	15	15	2	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr2:1843065G>C	ENST00000399161.2	-	21	3683	c.2936C>G	c.(2935-2937)cCc>cGc	p.P979R	MYT1L_ENST00000407844.1_5'UTR|MYT1L_ENST00000471668.1_5'UTR|MYT1L_ENST00000428368.2_Missense_Mutation_p.P977R	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	979					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		GGCCGCCAAGGGGCACCCGGA	0.657																																					p.P977R		Atlas-SNP	.											.	MYT1L	241	.	0			c.C2930G						.						46	54	52					2																	1843065		2012	4141	6153	SO:0001583	missense	23040	exon21			GCCAAGGGGCACC	AF036943	CCDS46222.1	2p25.3	2013-01-10			ENSG00000186487	ENSG00000186487		"Zinc fingers, C2HC-type containing"	7623	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 1"	613084				9373037	Standard	XM_006711862		Approved	KIAA1106, NZF1, ZC2HC4B	uc002qxd.3	Q9UL68	OTTHUMG00000151407	ENST00000399161.2:c.2936C>G	chr2.hg19:g.1843065G>C	ENSP00000382114:p.Pro979Arg	63.0	0.0		52.0	31.0	NM_015025	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Missense_Mutation	SNP	ENST00000399161.2	hg19		.	.	.	.	.	.	.	.	.	.	G	29.1	4.978293	0.92982	.	.	ENSG00000186487	ENST00000399161;ENST00000295067;ENST00000399157;ENST00000428368	T;T	0.66460	-0.19;-0.21	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	D	0.86573	0.5965	M	0.91717	3.235	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.88727	0.3234	10	0.87932	D	0	-28.8261	19.9772	0.97314	0.0:0.0:1.0:0.0	.	979;977	Q9UL68;Q9UL68-4	MYT1L_HUMAN;.	R	979;925;33;977	ENSP00000382114:P979R;ENSP00000396103:P977R	ENSP00000295067:P925R	P	-	2	0	MYT1L	1822072	1.000000	0.71417	0.942000	0.38095	0.844000	0.47949	9.787000	0.99055	2.724000	0.93272	0.563000	0.77884	CCC	.	.		0.657	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025		C	1843065	G	C	1843065	3	2	333	1	0	0	0	0	1	0	0	0	10116	1232	43	4	644	4	MYT1L	2	1843065	Missense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10		1843065	241356308	23	46365										
DDX1	1653	hgsc.bcm.edu	37	chr2	15736869	15736869	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ctcattcaggctgcagaaacAggaagtggcaaaactggtgt	12	8	2	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr2:15736869A>T	ENST00000381341.2	+	5	533	c.144A>T	c.(142-144)acA>acT	p.T48T	DDX1_ENST00000233084.3_Silent_p.T48T			Q92499	DDX1_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 1	48	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.|Necessary for interaction with HNRNPK.|Necessary for interaction with RELA.				ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|multicellular organismal development (GO:0007275)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translational initiation (GO:0006446)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|spliceosomal complex assembly (GO:0000245)|transcription, DNA-templated (GO:0006351)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	cleavage body (GO:0071920)|cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|tRNA-splicing ligase complex (GO:0072669)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA/RNA helicase activity (GO:0033677)|double-stranded RNA binding (GO:0003725)|exonuclease activity (GO:0004527)|nuclease activity (GO:0004518)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|transcription cofactor activity (GO:0003712)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(13)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)	all_epithelial(98;2.96e-07)|Acute lymphoblastic leukemia(84;4.24e-05)|Ovarian(717;0.0694)	GBM - Glioblastoma multiforme(3;0.00969)	Epithelial(75;4.35e-05)|OV - Ovarian serous cystadenocarcinoma(76;0.133)		CTGCAGAAACAGGAAGTGGCA	0.274																																					p.T48T		Atlas-SNP	.											.	DDX1	70	.	0			c.A144T						.						75	80	78					2																	15736869		2203	4300	6503	SO:0001819	synonymous_variant	1653	exon4			AGAAACAGGAAGT	X70649	CCDS1686.1	2p24	2012-02-23	2012-02-23		ENSG00000079785	ENSG00000079785		"DEAD-boxes"	2734	protein-coding gene	gene with protein product		601257	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 1", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 1"			1552844, 19058135	Standard	NM_004939		Approved	DBP-RB	uc002rce.4	Q92499	OTTHUMG00000090593	ENST00000381341.2:c.144A>T	chr2.hg19:g.15736869A>T		474.0	1.0		528.0	236.0	NM_004939	B4DME8|B4DPN6	Silent	SNP	ENST00000381341.2	hg19	CCDS1686.1																																																																																			.	.		0.274	DDX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207141.2	NM_004939		T	15736869	A	T	15736869	2	4	333	1	0	0	0	0	0	0	0	1	4343	175	7	4		4	DDX1	2	15736869	Silent	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	13893804	15736869	227462504	24	46366										
APOB	338	hgsc.bcm.edu	37	chr2	21236253	21236253	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tagggacttggaactctcgaGatggcagatggaatcccaca	12	9	1	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr2:21236253G>C	ENST00000233242.1	-	25	4122	c.3995C>G	c.(3994-3996)tCt>tGt	p.S1332C		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	1332					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GAACTCTCGAGATGGCAGATG	0.483																																					p.S1332C		Atlas-SNP	.											.	APOB	761	.	0			c.C3995G						.						137	134	135					2																	21236253		2203	4300	6503	SO:0001583	missense	338	exon25			TCTCGAGATGGCA	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.3995C>G	chr2.hg19:g.21236253G>C	ENSP00000233242:p.Ser1332Cys	59.0	0.0		56.0	20.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	G	15.52	2.857566	0.51376	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.00940	5.52	5.53	5.53	0.82687	.	0.415780	0.23165	N	0.051196	T	0.04588	0.0125	M	0.64997	1.995	0.80722	D	1	D	0.71674	0.998	P	0.60789	0.879	T	0.33007	-0.9885	10	0.87932	D	0	.	19.8609	0.96783	0.0:0.0:1.0:0.0	.	1332	P04114	APOB_HUMAN	C	1332	ENSP00000233242:S1332C	ENSP00000233242:S1332C	S	-	2	0	APOB	21089758	0.981000	0.34729	0.368000	0.25939	0.152000	0.21847	6.188000	0.72045	2.771000	0.95319	0.563000	0.77884	TCT	.	.		0.483	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			C	21236253	G	C	21236253	3	2	333	1	0	0	0	0	1	0	0	0	785	942	33	4	9716	4	APOB	2	21236253	Missense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	5499384	21236253	221963120	25	46367										
APOB	338	hgsc.bcm.edu	37	chr2	21255274	21255274	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	aggtggctcggctgcgctgaTccctcgccatgttgaagatc	13	12	0	3			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr2:21255274T>C	ENST00000233242.1	-	10	1431	c.1304A>G	c.(1303-1305)gAt>gGt	p.D435G	APOB_ENST00000399256.4_Missense_Mutation_p.D435G	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	435	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.				artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCTGCGCTGATCCCTCGCCAT	0.572																																					p.D435G		Atlas-SNP	.											.	APOB	761	.	0			c.A1304G						.						82	77	79					2																	21255274		2203	4300	6503	SO:0001583	missense	338	exon10			CGCTGATCCCTCG	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.1304A>G	chr2.hg19:g.21255274T>C	ENSP00000233242:p.Asp435Gly	42.0	0.0		18.0	6.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	T	12.54	1.969959	0.34754	.	.	ENSG00000084674	ENST00000233242;ENST00000535079;ENST00000399256	T;T	0.42513	0.97;0.97	5.26	4.09	0.47781	Lipid transport protein, N-terminal (3);Vitellinogen, superhelical (2);	0.320212	0.26328	N	0.025009	T	0.28764	0.0713	N	0.22421	0.69	0.22710	N	0.99883	B	0.17465	0.022	B	0.21360	0.034	T	0.15435	-1.0437	10	0.26408	T	0.33	.	11.7308	0.51735	0.1324:0.0:0.0:0.8676	.	435	P04114	APOB_HUMAN	G	435	ENSP00000233242:D435G;ENSP00000382200:D435G	ENSP00000233242:D435G	D	-	2	0	APOB	21108779	1.000000	0.71417	0.992000	0.48379	0.968000	0.65278	2.969000	0.49232	0.924000	0.37069	0.528000	0.53228	GAT	.	.		0.572	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			C	21255274	T	C	21255274	3	2	333	1	0	0	0	0	1	0	0	0	785	1435	50	2	12467	2	APOB	2	21255274	Missense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	19021	21255274	221944099	26	46368										
NCOA1	8648	hgsc.bcm.edu	37	chr2	24881562	24881562	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tcaacatgagtggcctcgggGacagttcatccgaccctgct	11	13	2	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr2:24881562G>T	ENST00000406961.1	+	5	668	c.16G>T	c.(16-18)Gac>Tac	p.D6Y	NCOA1_ENST00000407230.1_5'UTR|NCOA1_ENST00000395856.3_Missense_Mutation_p.D6Y|NCOA1_ENST00000538539.1_Missense_Mutation_p.D6Y|NCOA1_ENST00000405141.1_Missense_Mutation_p.D6Y|NCOA1_ENST00000348332.3_Missense_Mutation_p.D6Y|NCOA1_ENST00000288599.5_Missense_Mutation_p.D6Y			Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1	6					androgen receptor signaling pathway (GO:0030521)|cellular lipid metabolic process (GO:0044255)|cellular response to hormone stimulus (GO:0032870)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|estrous cycle phase (GO:0060206)|hippocampus development (GO:0021766)|histone H4 acetylation (GO:0043967)|hypothalamus development (GO:0021854)|labyrinthine layer morphogenesis (GO:0060713)|lactation (GO:0007595)|male gonad development (GO:0008584)|male mating behavior (GO:0060179)|ovulation cycle (GO:0042698)|positive regulation of apoptotic process (GO:0043065)|positive regulation of female receptivity (GO:0045925)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by galactose (GO:0000435)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular response to drug (GO:2001038)|response to estradiol (GO:0032355)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region DNA binding (GO:0001012)|RNA polymerase II transcription coactivator activity (GO:0001105)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)		PAX3/NCOA1(8)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(26)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	53	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGGCCTCGGGGACAGTTCATC	0.453			T	PAX3	alveolar rhadomyosarcoma																																p.D6Y		Atlas-SNP	.		Dom	yes		2	2p23	8648	nuclear receptor coactivator 1		M	.	NCOA1	210	.	0			c.G16T						.						87	74	78					2																	24881562		2203	4300	6503	SO:0001583	missense	8648	exon3			CTCGGGGACAGTT	U40396	CCDS1712.1, CCDS1713.1, CCDS42660.1	2p23	2011-07-01			ENSG00000084676	ENSG00000084676		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7668	protein-coding gene	gene with protein product		602691				7481822, 9575154	Standard	XM_005264625		Approved	SRC1, F-SRC-1, NCoA-1, KAT13A, RIP160, bHLHe74	uc002rfk.3	Q15788	OTTHUMG00000125523	ENST00000406961.1:c.16G>T	chr2.hg19:g.24881562G>T	ENSP00000385216:p.Asp6Tyr	87.0	0.0		75.0	34.0	NM_147223	O00150|O43792|O43793|Q13071|Q13420|Q2T9G5|Q53SX3|Q6GVI5|Q7KYV3	Missense_Mutation	SNP	ENST00000406961.1	hg19	CCDS1712.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.589977	0.86851	.	.	ENSG00000084676	ENST00000406961;ENST00000405141;ENST00000538539;ENST00000348332;ENST00000288599;ENST00000395856	T;T;T;T;T;T	0.02236	4.39;4.38;4.38;4.39;4.38;4.39	5.41	5.41	0.78517	.	0.048436	0.85682	D	0.000000	T	0.06781	0.0173	L	0.40543	1.245	0.58432	D	0.999997	D;D;D	0.63880	0.986;0.969;0.993	P;P;P	0.61592	0.814;0.781;0.891	T	0.09314	-1.0680	10	0.72032	D	0.01	-17.6952	13.2849	0.60237	0.0759:0.0:0.9241:0.0	.	6;6;6	Q15788-3;Q15788;Q15788-2	.;NCOA1_HUMAN;.	Y	6	ENSP00000385216:D6Y;ENSP00000385097:D6Y;ENSP00000444039:D6Y;ENSP00000320940:D6Y;ENSP00000288599:D6Y;ENSP00000379197:D6Y	ENSP00000288599:D6Y	D	+	1	0	NCOA1	24735066	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.895000	0.75660	2.826000	0.97356	0.655000	0.94253	GAC	.	.		0.453	NCOA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246852.3	NM_147223		T	24881562	G	T	24881562	3	4	333	1	0	0	0	0	1	0	0	0	10237	1174	41	3	18	3	NCOA1	2	24881562	Missense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	3626288	24881562	218317811	27	46369										
PLB1	151056	hgsc.bcm.edu	37	chr2	28824137	28824137	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	agagagtaaatttccatgaaGactggaaggtcatcacagtg	11	6	2	3			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr2:28824137G>A	ENST00000327757.5	+	37	2589	c.2545G>A	c.(2545-2547)Gac>Aac	p.D849N	PLB1_ENST00000541605.1_5'Flank|PLB1_ENST00000422425.2_Missense_Mutation_p.D838N	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	849	4 X 308-326 AA approximate repeats.				glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(31)|ovary(6)|prostate(1)|skin(7)|stomach(2)	69	Acute lymphoblastic leukemia(172;0.155)					TTTCCATGAAGACTGGAAGGT	0.448																																					p.D849N		Atlas-SNP	.											.	PLB1	255	.	0			c.G2545A						.						121	117	119					2																	28824137		2203	4300	6503	SO:0001583	missense	151056	exon37			CATGAAGACTGGA		CCDS33168.1, CCDS54340.1	2p23.3	2014-03-14			ENSG00000163803	ENSG00000163803	3.1.1.4, 3.1.1.5		30041	protein-coding gene	gene with protein product		610179				12150957	Standard	NM_153021		Approved	PLB, FLJ30866	uc002rmb.2	Q6P1J6	OTTHUMG00000152014	ENST00000327757.5:c.2545G>A	chr2.hg19:g.28824137G>A	ENSP00000330442:p.Asp849Asn	79.0	0.0		78.0	37.0	NM_153021	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Missense_Mutation	SNP	ENST00000327757.5	hg19	CCDS33168.1	.	.	.	.	.	.	.	.	.	.	G	15.95	2.983258	0.53827	.	.	ENSG00000163803	ENST00000327757;ENST00000422425	T;T	0.14144	2.53;2.53	5.85	3.98	0.46160	Esterase, SGNH hydrolase-type (1);Esterase, SGNH hydrolase-type, subgroup (1);Lipase, GDSL (1);	0.171126	0.41294	D	0.000913	T	0.44180	0.1281	M	0.88775	2.98	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.54200	-0.8329	10	0.66056	D	0.02	-21.6499	15.2965	0.73913	0.0:0.2661:0.7339:0.0	.	838;849	Q6P1J6-3;Q6P1J6	.;PLB1_HUMAN	N	849;838	ENSP00000330442:D849N;ENSP00000416440:D838N	ENSP00000330442:D849N	D	+	1	0	PLB1	28677641	1.000000	0.71417	0.714000	0.30535	0.391000	0.30476	3.259000	0.51515	0.749000	0.32854	0.561000	0.74099	GAC	.	.		0.448	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2			A	28824137	G	A	28824137	3	1	333	1	0	0	0	0	1	0	0	0	12033	942	33	3	2724	3	PLB1	2	28824137	Missense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	3942575	28824137	214375236	28	46370										
BIRC6	57448	hgsc.bcm.edu	37	chr2	32706429	32706429	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tggaaaaagataaagaaattGaccttgagttacttcaggat	9	4	1	4			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr2:32706429G>C	ENST00000421745.2	+	38	7584	c.7450G>C	c.(7450-7452)Gac>Cac	p.D2484H		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	2484					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					TAAAGAAATTGACCTTGAGTT	0.348																																					p.D2484H	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.G7450C						.						98	106	103					2																	32706429		2203	4300	6503	SO:0001583	missense	57448	exon38			GAAATTGACCTTG	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.7450G>C	chr2.hg19:g.32706429G>C	ENSP00000393596:p.Asp2484His	210.0	0.0		215.0	110.0	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	hg19	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	G	27.4	4.823696	0.90873	.	.	ENSG00000115760	ENST00000421745	T	0.77098	-1.07	5.22	5.22	0.72569	.	0.126770	0.50627	D	0.000111	T	0.81927	0.4926	N	0.24115	0.695	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.84845	0.0810	10	0.87932	D	0	.	18.7825	0.91939	0.0:0.0:1.0:0.0	.	2484	Q9NR09	BIRC6_HUMAN	H	2484	ENSP00000393596:D2484H	ENSP00000393596:D2484H	D	+	1	0	BIRC6	32559933	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.447000	0.97595	2.446000	0.82766	0.460000	0.39030	GAC	.	.		0.348	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		C	32706429	G	C	32706429	3	2	333	1	0	0	0	0	1	0	0	0	1438	1290	45	4	7600	4	BIRC6	2	32706429	Missense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	3882292	32706429	210492944	29	46371										
TSPYL6	388951	hgsc.bcm.edu	37	chr2	54482488	54482488	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	aacatctcggcatcttggccTctaatcatggcagacagctg	9	12	4	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr2:54482488T>A	ENST00000317802.7	-	1	921	c.801A>T	c.(799-801)agA>agT	p.R267S	ACYP2_ENST00000607452.1_Intron|ACYP2_ENST00000394666.3_Intron|ACYP2_ENST00000303536.4_Intron|ACYP2_ENST00000606865.1_Intron	NM_001003937.2	NP_001003937.2	Q8N831	TSYL6_HUMAN	TSPY-like 6	267					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(1)|ovary(1)|skin(1)|stomach(2)	20						CATCTTGGCCTCTAATCATGG	0.478																																					p.R267S		Atlas-SNP	.											.	TSPYL6	54	.	0			c.A801T						.						86	85	86					2																	54482488		2139	4283	6422	SO:0001583	missense	388951	exon1			TTGGCCTCTAATC	AK097417	CCDS42682.1	2p16.3	2007-10-22			ENSG00000178021	ENSG00000178021			14521	protein-coding gene	gene with protein product							Standard	NM_001003937		Approved		uc002rxr.2	Q8N831	OTTHUMG00000151823	ENST00000317802.7:c.801A>T	chr2.hg19:g.54482488T>A	ENSP00000417919:p.Arg267Ser	74.0	0.0		95.0	49.0	NM_001003937	Q6NUJ3	Missense_Mutation	SNP	ENST00000317802.7	hg19	CCDS42682.1	.	.	.	.	.	.	.	.	.	.	T	1.266	-0.614551	0.03663	.	.	ENSG00000178021	ENST00000317802	T	0.24538	1.85	1.34	0.106	0.14540	.	.	.	.	.	T	0.09024	0.0223	N	0.01431	-0.87	0.09310	N	1	B	0.25719	0.132	B	0.40009	0.316	T	0.45160	-0.9280	9	0.02654	T	1	.	3.231	0.06749	0.0:0.2559:0.0:0.7441	.	267	Q8N831	TSYL6_HUMAN	S	267	ENSP00000417919:R267S	ENSP00000417919:R267S	R	-	3	2	TSPYL6	54335992	0.674000	0.27549	0.003000	0.11579	0.055000	0.15305	-0.791000	0.04599	0.022000	0.15160	0.383000	0.25322	AGA	.	.		0.478	TSPYL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324069.3	XM_371494		A	54482488	T	A	54482488	3	1	333	1	0	0	0	0	1	0	0	0	16678	1548	54	4	435	4	TSPYL6	2	54482488	Missense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	21776059	54482488	188716885	30	46372										
MXD1	4084	hgsc.bcm.edu	37	chr2	70165400	70165400	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gctgcaggacagtcacaaggCgtgtcttggtctctaagaga	13	9	3	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr2:70165400C>T	ENST00000264444.2	+	6	910	c.650C>T	c.(649-651)gCg>gTg	p.A217V	MXD1_ENST00000540449.1_Missense_Mutation_p.A207V|MXD1_ENST00000465446.1_3'UTR	NM_001202513.1|NM_001202514.1|NM_002357.3	NP_001189442.1|NP_001189443.1|NP_002348.1	Q05195	MAD1_HUMAN	MAX dimerization protein 1	217					cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(1)|large_intestine(3)|lung(1)|upper_aerodigestive_tract(1)	7						AGTCACAAGGCGTGTCTTGGT	0.552																																					p.A217V		Atlas-SNP	.											.	MXD1	23	.	0			c.C650T						.						91	90	90					2																	70165400		2203	4300	6503	SO:0001583	missense	4084	exon6			ACAAGGCGTGTCT		CCDS1896.1, CCDS56123.1	2p13-p12	2010-07-07		2005-02-11	ENSG00000059728	ENSG00000059728		"MAX dimerization proteins", "Basic helix-loop-helix proteins"	6761	protein-coding gene	gene with protein product		600021		MAD		7829091	Standard	NM_002357		Approved	MAD1, bHLHc58	uc002sfy.3	Q05195	OTTHUMG00000129646	ENST00000264444.2:c.650C>T	chr2.hg19:g.70165400C>T	ENSP00000264444:p.Ala217Val	71.0	0.0		79.0	33.0	NM_002357	B2R6V8|B7ZLI6|D6W5G2|Q6FI41	Missense_Mutation	SNP	ENST00000264444.2	hg19	CCDS1896.1	.	.	.	.	.	.	.	.	.	.	C	8.024	0.760190	0.15846	.	.	ENSG00000059728	ENST00000264444;ENST00000540449	T;T	0.45668	0.89;0.9	5.75	4.84	0.62591	.	1.595380	0.02791	N	0.122042	T	0.27697	0.0681	N	0.08118	0	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.21759	-1.0236	10	0.18276	T	0.48	.	9.9272	0.41501	0.0:0.8259:0.0:0.1741	.	207;216;217	B7ZLI6;B7ZLI7;Q05195	.;.;MAD1_HUMAN	V	217;207	ENSP00000264444:A217V;ENSP00000443935:A207V	ENSP00000264444:A217V	A	+	2	0	MXD1	70018904	0.004000	0.15560	0.002000	0.10522	0.119000	0.20118	1.215000	0.32431	1.478000	0.48253	0.650000	0.86243	GCG	.	.		0.552	MXD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251845.3	NM_002357		T	70165400	C	T	70165400	3	4	333	1	0	0	0	0	1	0	0	0	10008	768	27	1	672	1	MXD1	2	70165400	Missense_Mutation	SNP	C	TCGA-RC-A6M4-01A-11D-A32G-10	15682912	70165400	173033973	31	46373										
GPR45	11250	hgsc.bcm.edu	37	chr2	105858703	105858703	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ccatcctgctcatcatcagcGtggaccgcttcctcatcatc	6	17	5	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr2:105858703G>A	ENST00000258456.1	+	1	504	c.388G>A	c.(388-390)Gtg>Atg	p.V130M		NM_007227.3	NP_009158.3	Q9Y5Y3	GPR45_HUMAN	G protein-coupled receptor 45	130						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	28						CATCATCAGCGTGGACCGCTT	0.622																																					p.V130M		Atlas-SNP	.											.	GPR45	73	.	0			c.G388A						.						66	62	63					2																	105858703		2203	4300	6503	SO:0001583	missense	11250	exon1			ATCAGCGTGGACC	AF118266	CCDS2066.1	2q11.1-q12	2012-08-21			ENSG00000135973	ENSG00000135973		"GPCR / Class A : Orphans"	4503	protein-coding gene	gene with protein product		604838				10036181	Standard	NM_007227		Approved	PSP24, PSP24A	uc002tco.1	Q9Y5Y3	OTTHUMG00000130805	ENST00000258456.1:c.388G>A	chr2.hg19:g.105858703G>A	ENSP00000258456:p.Val130Met	114.0	0.0		117.0	64.0	NM_007227	Q6NWS4|Q6NXU6	Missense_Mutation	SNP	ENST00000258456.1	hg19	CCDS2066.1	.	.	.	.	.	.	.	.	.	.	G	19.34	3.809463	0.70797	.	.	ENSG00000135973	ENST00000258456	T	0.44083	0.93	5.04	5.04	0.67666	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000001	T	0.61540	0.2355	M	0.65975	2.015	0.58432	D	0.99999	D	0.89917	1.0	D	0.85130	0.997	T	0.64918	-0.6294	10	0.87932	D	0	-20.3605	12.7943	0.57551	0.0821:0.0:0.9179:0.0	.	130	Q9Y5Y3	GPR45_HUMAN	M	130	ENSP00000258456:V130M	ENSP00000258456:V130M	V	+	1	0	GPR45	105225135	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.440000	0.52886	2.337000	0.79520	0.462000	0.41574	GTG	.	.		0.622	GPR45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253348.1	NM_007227		A	105858703	G	A	105858703	3	1	333	1	0	0	0	0	1	0	0	0	6704	1145	40	1	390	1	GPR45	2	105858703	Missense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	35693303	105858703	137340670	32	46374										
UGGT1	56886	hgsc.bcm.edu	37	chr2	128870806	128870806	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	aaagcaatgcaggcaaaatcAattatgtattcagacattat	6	6	2	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr2:128870806A>T	ENST00000259253.6	+	6	717	c.670A>T	c.(670-672)Aat>Tat	p.N224Y	UGGT1_ENST00000375990.3_Missense_Mutation_p.N200Y	NM_020120.3	NP_064505.1	Q9NYU2	UGGG1_HUMAN	UDP-glucose glycoprotein glucosyltransferase 1	224					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)|unfolded protein binding (GO:0051082)			NS(1)|breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(14)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						AGGCAAAATCAATTATGTATT	0.333																																					p.N224Y		Atlas-SNP	.											.	UGGT1	126	.	0			c.A670T						.						58	61	60					2																	128870806		2203	4300	6503	SO:0001583	missense	56886	exon6			AAAATCAATTATG	AF227905	CCDS2154.1	2q14.3	2009-07-23	2009-07-23	2009-07-23	ENSG00000136731	ENSG00000136731			15663	protein-coding gene	gene with protein product		605897	"UDP-glucose ceramide glucosyltransferase-like 1"	UGCGL1		10694380	Standard	NM_020120		Approved	HUGT1	uc002tps.3	Q9NYU2	OTTHUMG00000131570	ENST00000259253.6:c.670A>T	chr2.hg19:g.128870806A>T	ENSP00000259253:p.Asn224Tyr	275.0	0.0		247.0	93.0	NM_020120	Q53QP2|Q53SL3|Q8IW30|Q9H8I4	Missense_Mutation	SNP	ENST00000259253.6	hg19	CCDS2154.1	.	.	.	.	.	.	.	.	.	.	A	15.38	2.815604	0.50527	.	.	ENSG00000136731	ENST00000375990;ENST00000259253	T;T	0.08546	3.08;3.08	5.58	4.4	0.53042	.	0.150932	0.64402	D	0.000015	T	0.14787	0.0357	M	0.63843	1.955	0.33916	D	0.640318	P;B	0.42296	0.775;0.001	P;B	0.45474	0.482;0.001	T	0.12993	-1.0526	10	0.59425	D	0.04	.	12.6435	0.56721	0.8616:0.1384:0.0:0.0	.	200;224	Q9NYU2-2;Q9NYU2	.;UGGG1_HUMAN	Y	200;224	ENSP00000365158:N200Y;ENSP00000259253:N224Y	ENSP00000259253:N224Y	N	+	1	0	UGGT1	128587276	1.000000	0.71417	0.999000	0.59377	0.887000	0.51463	5.040000	0.64191	0.909000	0.36697	0.477000	0.44152	AAT	.	.		0.333	UGGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254435.2	NM_020120		T	128870806	A	T	128870806	3	4	333	1	0	0	0	0	1	0	0	0	16956	130	5	4	692	4	UGGT1	2	128870806	Missense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	23012103	128870806	114328567	33	46375										
TMEM163	81615	hgsc.bcm.edu	37	chr2	135260482	135260482	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	aggaccttaccacttctgggAgcagcctagttgagaggtca	12	10	2	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr2:135260482A>G	ENST00000281924.6	-	5	609	c.545T>C	c.(544-546)cTc>cCc	p.L182P		NM_030923.4	NP_112185.1	Q8TC26	TM163_HUMAN	transmembrane protein 163	182						cell junction (GO:0030054)|early endosome membrane (GO:0031901)|integral component of synaptic vesicle membrane (GO:0030285)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(5)|lung(8)|stomach(1)|urinary_tract(1)	16				BRCA - Breast invasive adenocarcinoma(221;0.154)		CACTTCTGGGAGCAGCCTAGT	0.527																																					p.L182P		Atlas-SNP	.											.	TMEM163	34	.	0			c.T545C						.						131	106	115					2																	135260482		2203	4300	6503	SO:0001583	missense	81615	exon5			TCTGGGAGCAGCC		CCDS2172.1	2q21.3	2008-02-05			ENSG00000152128	ENSG00000152128			25380	protein-coding gene	gene with protein product						17623043	Standard	NM_030923		Approved	DKFZP566N034, SV31	uc002ttx.3	Q8TC26	OTTHUMG00000131713	ENST00000281924.6:c.545T>C	chr2.hg19:g.135260482A>G	ENSP00000281924:p.Leu182Pro	96.0	0.0		94.0	39.0	NM_030923	Q53QM3|Q53SV7|Q69YH3|Q9UFG3	Missense_Mutation	SNP	ENST00000281924.6	hg19	CCDS2172.1	.	.	.	.	.	.	.	.	.	.	A	12.93	2.085387	0.36758	.	.	ENSG00000152128	ENST00000281924	T	0.61980	0.06	6.06	6.06	0.98353	.	0.068202	0.64402	D	0.000013	T	0.53384	0.1793	L	0.36672	1.1	0.80722	D	1	B	0.24186	0.099	B	0.22753	0.041	T	0.48103	-0.9064	10	0.28530	T	0.3	.	15.5919	0.76537	1.0:0.0:0.0:0.0	.	182	Q8TC26	TM163_HUMAN	P	182	ENSP00000281924:L182P	ENSP00000281924:L182P	L	-	2	0	TMEM163	134976952	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.137000	0.71710	2.324000	0.78689	0.533000	0.62120	CTC	.	.		0.527	TMEM163-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254631.2	NM_030923		G	135260482	A	G	135260482	3	3	333	1	0	0	0	0	1	0	0	0	16093	304	11	2	340	2	TMEM163	2	135260482	Missense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	6389676	135260482	107938891	34	46376										
NR4A2	4929	hgsc.bcm.edu	37	chr2	157186238	157186238	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gcgtagtggccacgtagttcTggtggaagttgtggagagat	17	5	1	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr2:157186238T>A	ENST00000339562.4	-	3	823	c.461A>T	c.(460-462)cAg>cTg	p.Q154L	NR4A2_ENST00000409572.1_Missense_Mutation_p.Q154L|NR4A2_ENST00000539077.1_Missense_Mutation_p.Q165L|NR4A2_ENST00000409108.2_Missense_Mutation_p.Q154L|NR4A2_ENST00000429376.1_Missense_Mutation_p.Q91L|NR4A2_ENST00000426264.1_Missense_Mutation_p.Q91L	NM_006186.3	NP_006177.1	P43354	NR4A2_HUMAN	nuclear receptor subfamily 4, group A, member 2	154	Pro-rich.				adult locomotory behavior (GO:0008344)|cellular response to extracellular stimulus (GO:0031668)|cellular response to oxidative stress (GO:0034599)|central nervous system projection neuron axonogenesis (GO:0021952)|death (GO:0016265)|dopamine biosynthetic process (GO:0042416)|dopaminergic neuron differentiation (GO:0071542)|gene expression (GO:0010467)|general adaptation syndrome (GO:0051866)|habenula development (GO:0021986)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of neuron apoptotic process (GO:0043524)|neuron maturation (GO:0042551)|neuron migration (GO:0001764)|positive regulation of catalytic activity (GO:0043085)|post-embryonic development (GO:0009791)|regulation of dopamine metabolic process (GO:0042053)|regulation of respiratory gaseous exchange (GO:0043576)|response to amphetamine (GO:0001975)|response to hypoxia (GO:0001666)|response to inorganic substance (GO:0010035)|response to insecticide (GO:0017085)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(1)	40						CACGTAGTTCTGGTGGAAGTT	0.632																																					p.Q154L		Atlas-SNP	.											.	NR4A2	82	.	0			c.A461T						.						94	108	103					2																	157186238		2203	4300	6503	SO:0001583	missense	4929	exon3			TAGTTCTGGTGGA	X75918	CCDS2201.1	2q22-q23	2013-01-16			ENSG00000153234	ENSG00000153234		"Nuclear hormone receptors"	7981	protein-coding gene	gene with protein product		601828		NURR1		7706727	Standard	NM_006186		Approved	TINUR, NOT, RNR1, HZF-3	uc002tyz.4	P43354	OTTHUMG00000131950	ENST00000339562.4:c.461A>T	chr2.hg19:g.157186238T>A	ENSP00000344479:p.Gln154Leu	75.0	0.0		88.0	39.0	NM_006186	Q16311|Q53RZ2|Q6NXU0	Missense_Mutation	SNP	ENST00000339562.4	hg19	CCDS2201.1	.	.	.	.	.	.	.	.	.	.	T	14.68	2.609046	0.46527	.	.	ENSG00000153234	ENST00000339562;ENST00000426264;ENST00000409572;ENST00000539077;ENST00000409108;ENST00000429376;ENST00000424077;ENST00000421709	D;D;D;D;D;D;T;D	0.92397	-2.81;-2.86;-2.81;-2.82;-3.03;-2.96;-1.25;-2.45	5.87	5.87	0.94306	.	1.981290	0.01704	N	0.027368	D	0.92067	0.7486	L	0.55481	1.735	0.58432	D	0.999993	B	0.17268	0.021	B	0.20955	0.032	T	0.70890	-0.4749	10	0.62326	D	0.03	.	12.496	0.55929	0.0:0.0:0.1774:0.8226	.	154	P43354	NR4A2_HUMAN	L	154;91;154;165;154;91;154;91	ENSP00000344479:Q154L;ENSP00000389986:Q91L;ENSP00000386747:Q154L;ENSP00000444925:Q165L;ENSP00000386993:Q154L;ENSP00000410952:Q91L;ENSP00000406808:Q154L;ENSP00000388120:Q91L	ENSP00000344479:Q154L	Q	-	2	0	NR4A2	156894484	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.097000	0.71452	2.242000	0.73789	0.533000	0.62120	CAG	.	.		0.632	NR4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254909.2			A	157186238	T	A	157186238	3	1	333	1	0	0	0	0	1	0	0	0	10642	1580	55	4	1359	4	NR4A2	2	157186238	Missense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	21925756	157186238	86013135	35	46377										
CWC22	57703	hgsc.bcm.edu	37	chr2	180851443	180851443	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gtgactccatgctactatcaTaagaacgtcctcttcttgaa	6	11	3	3			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr2:180851443T>C	ENST00000410053.3	-	4	484	c.185A>G	c.(184-186)tAt>tGt	p.Y62C	CWC22_ENST00000295749.6_Missense_Mutation_p.Y62C	NM_020943.2	NP_065994.1	Q9HCG8	CWC22_HUMAN	CWC22 spliceosome-associated protein	62	Arg-rich.				mRNA splicing, via spliceosome (GO:0000398)|regulation of mRNA splicing, via spliceosome (GO:0048024)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(8)|stomach(1)	30						GCTACTATCATAAGAACGTCC	0.343																																					p.Y62C		Atlas-SNP	.											.	CWC22	62	.	0			c.A185G						.						82	76	78					2																	180851443		1854	4090	5944	SO:0001583	missense	57703	exon4			CTATCATAAGAAC		CCDS46465.1	2q31.3	2014-07-03	2014-07-03		ENSG00000163510	ENSG00000163510			29322	protein-coding gene	gene with protein product	"functional spliceosome-associated protein b"	615186	"CWC22 spliceosome-associated protein homolog (S. cerevisiae)"			9136012, 23236153	Standard	NM_020943		Approved	KIAA1604, EIF4GL, fSAPb, NCM	uc010frh.1	Q9HCG8	OTTHUMG00000154244	ENST00000410053.3:c.185A>G	chr2.hg19:g.180851443T>C	ENSP00000387006:p.Tyr62Cys	46.0	0.0		60.0	23.0	NM_020943	Q05DC2|Q4G135|Q52LF0|Q6PEX2|Q7Z6I0|Q9H5L3|Q9H6Q6	Missense_Mutation	SNP	ENST00000410053.3	hg19	CCDS46465.1	.	.	.	.	.	.	.	.	.	.	T	18.02	3.529659	0.64860	.	.	ENSG00000163510	ENST00000410053;ENST00000295749;ENST00000404136	T;T;T	0.29397	2.02;2.02;1.57	5.95	5.95	0.96441	.	0.557628	0.19602	N	0.110375	T	0.34279	0.0892	L	0.47716	1.5	0.32634	N	0.521591	D	0.59357	0.985	P	0.46796	0.527	T	0.45760	-0.9239	10	0.36615	T	0.2	-15.8069	14.1434	0.65334	0.0:0.0:0.0:1.0	.	62	Q9HCG8	CWC22_HUMAN	C	62	ENSP00000387006:Y62C;ENSP00000295749:Y62C;ENSP00000384159:Y62C	ENSP00000295749:Y62C	Y	-	2	0	CWC22	180559688	1.000000	0.71417	0.996000	0.52242	0.843000	0.47879	3.014000	0.49590	2.268000	0.75426	0.533000	0.62120	TAT	.	.		0.343	CWC22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334537.1	NM_020943		C	180851443	T	C	180851443	3	2	333	1	0	0	0	0	1	0	0	0	4070	1406	49	2	2609	2	CWC22	2	180851443	Missense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	23665205	180851443	62347930	36	46378										
FSIP2	401024	hgsc.bcm.edu	37	chr2	186670102	186670102	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	aaatatccaattttgtatatGaacagttcatagaaaaatgc	5	5	1	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr2:186670102G>T	ENST00000424728.1	+	17	16069	c.16069G>T	c.(16069-16071)Gaa>Taa	p.E5357*	FSIP2_ENST00000343098.5_Nonsense_Mutation_p.E5446*			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	5357				E -> D (in Ref. 2; BX648733). {ECO:0000305}.						NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						TTTTGTATATGAACAGTTCAT	0.303																																					p.E5446X		Atlas-SNP	.											.	FSIP2	251	.	0			c.G16336T						.						62	59	60					2																	186670102		1839	4080	5919	SO:0001587	stop_gained	401024	exon17			GTATATGAACAGT	AK092099	CCDS54426.1	2q32.1	2010-06-18			ENSG00000188738	ENSG00000188738			21675	protein-coding gene	gene with protein product		615796				14702039	Standard	NM_173651		Approved	FLJ34780	uc002upl.3	Q5CZC0	OTTHUMG00000153874	ENST00000424728.1:c.16069G>T	chr2.hg19:g.186670102G>T	ENSP00000401306:p.Glu5357*	217.0	0.0		168.0	85.0	NM_173651	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Nonsense_Mutation	SNP	ENST00000424728.1	hg19		.	.	.	.	.	.	.	.	.	.	G	56	25.340874	0.99964	.	.	ENSG00000188738	ENST00000343098;ENST00000424728	.	.	.	5.28	4.41	0.53225	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.45353	T	0.12	.	9.5051	0.39042	0.0943:0.0:0.9057:0.0	.	.	.	.	X	5446;5357	.	ENSP00000344403:E5446X	E	+	1	0	FSIP2	186378347	1.000000	0.71417	1.000000	0.80357	0.476000	0.33039	3.088000	0.50175	1.466000	0.48025	0.460000	0.39030	GAA	.	.		0.303	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651		T	186670102	G	T	186670102	4	4	333	1	0	0	0	0	0	1	0	0	6083	1291	45	3	16402	3	FSIP2	2	186670102	Nonsense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	5818659	186670102	56529271	37	46379										
DOCK10	55619	hgsc.bcm.edu	37	chr2	225652011	225652011	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ctttgaagtctcgttgtttcTcaaagacagcaatgatgggc	10	8	2	3			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr2:225652011T>A	ENST00000258390.7	-	49	5589	c.5522A>T	c.(5521-5523)gAg>gTg	p.E1841V	DOCK10_ENST00000409592.3_Missense_Mutation_p.E1835V	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	1841	DHR-2.				regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		TCGTTGTTTCTCAAAGACAGC	0.368																																					p.E1841V		Atlas-SNP	.											.	DOCK10	308	.	0			c.A5522T						.						150	143	145					2																	225652011		1923	4142	6065	SO:0001583	missense	55619	exon49			TGTTTCTCAAAGA	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"Pleckstrin homology (PH) domain containing"	23479	protein-coding gene	gene with protein product	"zizimin3"	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.5522A>T	chr2.hg19:g.225652011T>A	ENSP00000258390:p.Glu1841Val	73.0	0.0		61.0	24.0	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Missense_Mutation	SNP	ENST00000258390.7	hg19	CCDS46528.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.127142	0.77549	.	.	ENSG00000135905	ENST00000409592;ENST00000258390;ENST00000373702	T;T	0.29917	1.55;1.56	5.83	4.67	0.58626	.	0.000000	0.85682	D	0.000000	T	0.63283	0.2498	M	0.93763	3.455	0.52501	D	0.999955	D;D;D;D	0.89917	0.986;0.999;1.0;1.0	P;D;D;D	0.81914	0.844;0.983;0.995;0.992	T	0.70916	-0.4742	10	0.87932	D	0	.	10.9579	0.47368	0.0:0.0728:0.0:0.9272	.	1841;662;1835;503	Q96BY6;B4DF07;B3FL70;B4DEY4	DOC10_HUMAN;.;.;.	V	1835;1841;346	ENSP00000386694:E1835V;ENSP00000258390:E1841V	ENSP00000258390:E1841V	E	-	2	0	DOCK10	225360255	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.698000	0.84413	1.030000	0.39839	0.528000	0.53228	GAG	.	.		0.368	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1			A	225652011	T	A	225652011	3	1	333	1	0	0	0	0	1	0	0	0	4687	1551	54	4	1070	4	DOCK10	2	225652011	Missense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	38981909	225652011	17547362	38	46380										
THAP4	51078	hgsc.bcm.edu	37	chr2	242542471	242542471	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ctctgtgcatcggcttgcgcGtgtccgggtggaaggagttg	17	9	1	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr2:242542471G>A	ENST00000407315.1	-	4	1855	c.1424C>T	c.(1423-1425)aCg>aTg	p.T475M	THAP4_ENST00000497486.1_5'Flank|THAP4_ENST00000402136.1_Missense_Mutation_p.T63M|THAP4_ENST00000402545.1_Missense_Mutation_p.T63M	NM_015963.5	NP_057047.4	Q8WY91	THAP4_HUMAN	THAP domain containing 4	475							DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)	9		all_cancers(19;2.09e-34)|all_epithelial(40;2.09e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Ovarian(221;0.069)|Lung NSC(271;0.0886)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.2)		Epithelial(32;2.3e-33)|all cancers(36;8.99e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.68e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0844)		CGGCTTGCGCGTGTCCGGGTG	0.602																																					p.T475M		Atlas-SNP	.											.	THAP4	27	.	0			c.C1424T						.						114	93	100					2																	242542471		2203	4296	6499	SO:0001583	missense	51078	exon4			TTGCGCGTGTCCG	AF258556	CCDS2551.1, CCDS54440.1	2q37.3	2013-01-25			ENSG00000176946	ENSG00000176946		"THAP (C2CH-type zinc finger) domain containing"	23187	protein-coding gene	gene with protein product		612533				12575992, 10810093	Standard	NM_015963		Approved	CGI-36	uc002wbt.3	Q8WY91	OTTHUMG00000133410	ENST00000407315.1:c.1424C>T	chr2.hg19:g.242542471G>A	ENSP00000385006:p.Thr475Met	31.0	0.0		23.0	13.0	NM_015963	Q53NU7|Q6GRN0|Q6IPJ3|Q9NW26|Q9Y325	Missense_Mutation	SNP	ENST00000407315.1	hg19	CCDS2551.1	.	.	.	.	.	.	.	.	.	.	g	19.51	3.840828	0.71488	.	.	ENSG00000176946	ENST00000402136;ENST00000407315;ENST00000402545;ENST00000512346	D	0.96300	-3.97	5.51	5.51	0.81932	Domain of unknown function DUF1794 (1);Calycin-like (1);	0.251457	0.27397	N	0.019555	D	0.97838	0.9290	M	0.68593	2.085	0.53005	D	0.999963	D;D	0.89917	1.0;1.0	D;P	0.76575	0.988;0.741	D	0.98481	1.0605	10	0.72032	D	0.01	-27.3523	19.4119	0.94677	0.0:0.0:1.0:0.0	.	475;63	Q8WY91;Q8WY91-2	THAP4_HUMAN;.	M	63;475;63;150	ENSP00000385006:T475M	ENSP00000385931:T63M	T	-	2	0	THAP4	242191144	1.000000	0.71417	0.879000	0.34478	0.835000	0.47333	5.173000	0.65010	2.592000	0.87571	0.591000	0.81541	ACG	.	.		0.602	THAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257267.3	NM_015963		A	242542471	G	A	242542471	3	1	333	1	0	0	0	0	1	0	0	0	15861	1145	40	1	321	1	THAP4	2	242542471	Missense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	16890460	242542471	656902	39	46381										
GLB1	2720	hgsc.bcm.edu	37	chr3	33110391	33110391	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	catgagccagccgaagaaaaTattccacatcatggtcctca	7	12	2	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr3:33110391T>A	ENST00000399402.3	-	3	358	c.227A>T	c.(226-228)tAt>tTt	p.Y76F	GLB1_ENST00000445488.2_Missense_Mutation_p.Y154F|GLB1_ENST00000307363.5_Missense_Mutation_p.Y106F|GLB1_ENST00000307377.8_Intron	NM_001079811.1	NP_001073279	P16278	BGAL_HUMAN	galactosidase, beta 1	106					carbohydrate metabolic process (GO:0005975)|galactose catabolic process (GO:0019388)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|glycosphingolipid metabolic process (GO:0006687)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)	beta-galactosidase activity (GO:0004565)|galactoside binding (GO:0016936)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	21		Melanoma(143;0.104)				CCGAAGAAAATATTCCACATC	0.557																																					p.Y106F		Atlas-SNP	.											.	GLB1	51	.	0			c.A317T						.						117	118	118					3																	33110391		1959	4162	6121	SO:0001583	missense	2720	exon3			AGAAAATATTCCA	M22590	CCDS43061.1, CCDS43062.1, CCDS46785.1	3p22.3	2012-10-02			ENSG00000170266	ENSG00000170266	3.2.1.23		4298	protein-coding gene	gene with protein product		611458	"elastin receptor 1, 67kDa", "elastin receptor 1 (67kD)"	ELNR1		110522, 3143362	Standard	NM_000404		Approved	EBP	uc003cfi.1	P16278	OTTHUMG00000155781	ENST00000399402.3:c.227A>T	chr3.hg19:g.33110391T>A	ENSP00000382333:p.Tyr76Phe	75.0	0.0		78.0	35.0	NM_000404	B2R7H8|B7Z6B0|P16279	Missense_Mutation	SNP	ENST00000399402.3	hg19	CCDS43062.1	.	.	.	.	.	.	.	.	.	.	T	9.618	1.133071	0.21041	.	.	ENSG00000170266	ENST00000399402;ENST00000307363;ENST00000445488;ENST00000450835	D;D;D;D	0.97976	-4.64;-4.64;-4.64;-4.64	4.1	2.94	0.34122	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.828672	0.11361	N	0.571919	D	0.94899	0.8351	L	0.33485	1.01	0.22127	N	0.99934	B;B;B	0.32604	0.377;0.377;0.377	B;B;B	0.38985	0.173;0.173;0.287	D	0.89970	0.4093	10	0.48119	T	0.1	-0.9445	5.5218	0.16938	0.0:0.0913:0.1736:0.7351	.	106;106;154	Q53G40;P16278;B7Z6Q5	.;BGAL_HUMAN;.	F	76;106;154;76	ENSP00000382333:Y76F;ENSP00000306920:Y106F;ENSP00000393377:Y154F;ENSP00000403264:Y76F	ENSP00000306920:Y106F	Y	-	2	0	GLB1	33085395	1.000000	0.71417	0.018000	0.16275	0.259000	0.26198	5.788000	0.69020	0.636000	0.30508	-0.250000	0.11733	TAT	.	.		0.557	GLB1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000341570.2	NM_000404		A	33110391	T	A	33110391	3	1	333	1	0	0	0	0	1	0	0	0	6435	1406	49	4	1772	4	GLB1	3	33110391	Missense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10		33110391	164912039	40	46382										
STAC	6769	hgsc.bcm.edu	37	chr3	36485045	36485045	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ccacacccgccagggctggtCtgcatccaggtggcaaggct	13	15	1	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr3:36485045C>G	ENST00000273183.3	+	2	601	c.301C>G	c.(301-303)Ctg>Gtg	p.L101V	STAC_ENST00000476388.1_3'UTR|STAC_ENST00000457375.2_Missense_Mutation_p.L101V	NM_003149.1	NP_003140.1	Q99469	STAC_HUMAN	SH3 and cysteine rich domain	101					cellular response to heat (GO:0034605)|intracellular signal transduction (GO:0035556)|signal transduction (GO:0007165)	cytosol (GO:0005829)	metal ion binding (GO:0046872)			endometrium(5)|large_intestine(9)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(5)	32						CAGGGCTGGTCTGCATCCAGG	0.562																																					p.L101V		Atlas-SNP	.											.	STAC	78	.	0			c.C301G						.						117	108	111					3																	36485045		2203	4300	6503	SO:0001583	missense	6769	exon2			GCTGGTCTGCATC	D86640	CCDS2662.1	3p22.3	2007-06-08			ENSG00000144681	ENSG00000144681			11353	protein-coding gene	gene with protein product		602317	"src homology three (SH3) and cysteine rich domain"			8954993, 10393425	Standard	XM_006713308		Approved	STAC1	uc003cgh.1	Q99469	OTTHUMG00000130798	ENST00000273183.3:c.301C>G	chr3.hg19:g.36485045C>G	ENSP00000273183:p.Leu101Val	36.0	0.0		41.0	23.0	NM_003149	B2R8S8	Missense_Mutation	SNP	ENST00000273183.3	hg19	CCDS2662.1	.	.	.	.	.	.	.	.	.	.	C	5.778	0.327917	0.10956	.	.	ENSG00000144681	ENST00000273183;ENST00000457375;ENST00000544687;ENST00000434649	T;T;T	0.75589	-0.95;0.88;0.74	4.63	3.67	0.42095	.	0.210227	0.32918	N	0.005500	T	0.57489	0.2057	N	0.25647	0.755	0.25769	N	0.984857	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.28490	-1.0042	10	0.07990	T	0.79	.	13.4428	0.61123	0.0:0.7236:0.2764:0.0	.	101;101	E9PEA7;Q99469	.;STAC_HUMAN	V	101;101;33;90	ENSP00000273183:L101V;ENSP00000393713:L101V;ENSP00000398403:L90V	ENSP00000273183:L101V	L	+	1	2	STAC	36460049	0.868000	0.29978	0.999000	0.59377	0.509000	0.34042	2.765000	0.47621	2.505000	0.84491	0.557000	0.71058	CTG	.	.		0.562	STAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253338.2	NM_003149		G	36485045	C	G	36485045	3	3	333	1	0	0	0	0	1	0	0	0	15254	912	32	4	307	4	STAC	3	36485045	Missense_Mutation	SNP	C	TCGA-RC-A6M4-01A-11D-A32G-10	3374654	36485045	161537385	41	46383										
ITGA9	3680	hgsc.bcm.edu	37	chr3	37574811	37574811	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ctcttgccctgcagagcaagGcctgtcattacggtggatgt	12	11	2	1	rs530318185		TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr3:37574811G>T	ENST00000264741.5	+	14	1636	c.1380G>T	c.(1378-1380)agG>agT	p.R460S	ITGA9_ENST00000422441.1_Missense_Mutation_p.R460S	NM_002207.2	NP_002198.2	Q13797	ITA9_HUMAN	integrin, alpha 9	460					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|neutrophil chemotaxis (GO:0030593)|wound healing (GO:0042060)	basal plasma membrane (GO:0009925)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(17)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|urinary_tract(1)	44				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		GCAGAGCAAGGCCTGTCATTA	0.537																																					p.R460S		Atlas-SNP	.											.	ITGA9	98	.	0			c.G1380T						.						110	87	95					3																	37574811		2203	4300	6503	SO:0001583	missense	3680	exon14			AGCAAGGCCTGTC	L24158	CCDS2669.1	3p21.3	2010-03-23			ENSG00000144668	ENSG00000144668		"Integrins"	6145	protein-coding gene	gene with protein product	"integrin, alpha 4-like"	603963				8245132, 8290272	Standard	NM_002207		Approved	RLC, ITGA4L, ALPHA-RLC	uc003chd.3	Q13797	OTTHUMG00000130815	ENST00000264741.5:c.1380G>T	chr3.hg19:g.37574811G>T	ENSP00000264741:p.Arg460Ser	45.0	0.0		43.0	22.0	NM_002207	Q14638	Missense_Mutation	SNP	ENST00000264741.5	hg19	CCDS2669.1	.	.	.	.	.	.	.	.	.	.	G	16.26	3.072238	0.55646	.	.	ENSG00000144668	ENST00000422441;ENST00000264741	T;T	0.69685	-0.42;-0.42	6.07	-4.8	0.03190	Integrin alpha-2 (1);	0.000000	0.85682	D	0.000000	T	0.78755	0.4333	M	0.76574	2.34	0.53688	D	0.999977	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.81428	-0.0937	10	0.87932	D	0	.	18.7658	0.91871	0.2972:0.0:0.7028:0.0	.	460;460	Q13797;E9PDS3	ITA9_HUMAN;.	S	460	ENSP00000397258:R460S;ENSP00000264741:R460S	ENSP00000264741:R460S	R	+	3	2	ITGA9	37549815	0.989000	0.36119	0.805000	0.32314	0.243000	0.25628	0.364000	0.20325	-0.618000	0.05656	-0.345000	0.07892	AGG	.	.		0.537	ITGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253361.1	NM_002207		T	37574811	G	T	37574811	3	4	333	1	0	0	0	0	1	0	0	0	7892	1194	42	3	1434	3	ITGA9	3	37574811	Missense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	1089766	37574811	160447619	42	46384										
MYD88	4615	hgsc.bcm.edu	37	chr3	38181897	38181897	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	agggcatatgcctgagcgttTcgatgccttcatctgctatt	10	10	2	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr3:38181897T>A	ENST00000396334.3	+	3	705	c.521T>A	c.(520-522)tTc>tAc	p.F174Y	MYD88_ENST00000443433.2_Intron|MYD88_ENST00000424893.1_Missense_Mutation_p.F129Y|MYD88_ENST00000481122.1_3'UTR|MYD88_ENST00000417037.2_Missense_Mutation_p.F174Y|MYD88_ENST00000495303.1_Intron	NM_002468.4	NP_002459.2	Q99836	MYD88_HUMAN	myeloid differentiation primary response 88	161	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|cell surface receptor signaling pathway (GO:0007166)|cellular response to mechanical stimulus (GO:0071260)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-positive bacterium (GO:0050830)|establishment of endothelial intestinal barrier (GO:0090557)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of apoptotic process (GO:0043066)|negative regulation of growth of symbiont in host (GO:0044130)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-23 production (GO:0032747)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon production (GO:0032481)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)|response to molecule of fungal origin (GO:0002238)|response to peptidoglycan (GO:0032494)|response to virus (GO:0009615)|signal transduction (GO:0007165)|Toll signaling pathway (GO:0008063)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|type I interferon biosynthetic process (GO:0045351)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)	death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|TIR domain binding (GO:0070976)			breast(1)|haematopoietic_and_lymphoid_tissue(226)|large_intestine(3)|lung(6)|upper_aerodigestive_tract(1)	237				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		CCTGAGCGTTTCGATGCCTTC	0.557			Mis		ABC-DLBCL																																p.F174Y		Atlas-SNP	.		Dom	yes		3	3p22	4615	myeloid differentiation primary response gene (88)		L	.	MYD88	900	.	0			c.T521A						.						97	75	82					3																	38181897		2203	4300	6503	SO:0001583	missense	4615	exon3			AGCGTTTCGATGC	U84408	CCDS2674.2, CCDS54565.1, CCDS54566.1, CCDS54567.1, CCDS54568.1	3p22	2014-09-17	2012-11-15		ENSG00000172936	ENSG00000172936			7562	protein-coding gene	gene with protein product		602170	"myeloid differentiation primary response gene (88)"			9013863	Standard	NM_002468		Approved		uc003chx.3	Q99836	OTTHUMG00000131083	ENST00000396334.3:c.521T>A	chr3.hg19:g.38181897T>A	ENSP00000379625:p.Phe174Tyr	58.0	0.0		84.0	38.0	NM_002468	B4DKH8|B4DKU4|B4DQ60|B4DQ72|J3KPU4|J3KQ87|J3KQJ6|P78397|Q53XS7	Missense_Mutation	SNP	ENST00000396334.3	hg19	CCDS2674.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	28.5|28.5	4.923047|4.923047	0.92319|0.92319	.|.	.|.	ENSG00000172936|ENSG00000172936	ENST00000417037;ENST00000396334;ENST00000424893;ENST00000421516;ENST00000415158|ENST00000421571	T;T;T;T|.	0.12255|.	2.7;2.7;2.7;2.7|.	5.61|5.61	5.61|5.61	0.85477|0.85477	Toll/interleukin-1 receptor homology (TIR) domain (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.42765|0.42765	0.1217|0.1217	N|N	0.04787|0.04787	-0.16|-0.16	0.80722|0.80722	D|D	1|1	P;P;P|.	0.43909|.	0.821;0.592;0.592|.	P;P;B|.	0.51229|.	0.643;0.663;0.328|.	T|T	0.54390|0.54390	-0.8301|-0.8301	10|6	0.07990|0.87932	T|D	0.79|0	.|.	15.3005|15.3005	0.73945|0.73945	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	116;161;150|.	Q99836-2;Q99836;B4E3D6|.	.;MYD88_HUMAN;.|.	Y|T	174;174;129;173;150|153	ENSP00000401399:F174Y;ENSP00000379625:F174Y;ENSP00000389979:F129Y;ENSP00000391753:F173Y|.	ENSP00000379625:F174Y|ENSP00000409901:S153T	F|S	+|+	2|1	0|0	MYD88|MYD88	38156901|38156901	1.000000|1.000000	0.71417|0.71417	0.229000|0.229000	0.23960|0.23960	0.989000|0.989000	0.77384|0.77384	7.415000|7.415000	0.80131|0.80131	2.281000|2.281000	0.76405|0.76405	0.533000|0.533000	0.62120|0.62120	TTC|TCG	.	.		0.557	MYD88-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253743.4	NM_002468		A	38181897	T	A	38181897	3	1	333	1	0	0	0	0	1	0	0	0	10032	1783	62	4	531	4	MYD88	3	38181897	Missense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	607086	38181897	159840533	43	46385										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266098	41266098	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gcagcaacagtcttacctggActctggaatccattctggtg	10	11	3	0	rs121913396|rs121913416		TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr3:41266098A>T	ENST00000349496.5	+	3	375	c.95A>T	c.(94-96)gAc>gTc	p.D32V	CTNNB1_ENST00000396185.3_Missense_Mutation_p.D32V|CTNNB1_ENST00000396183.3_Missense_Mutation_p.D32V|CTNNB1_ENST00000405570.1_Missense_Mutation_p.D32V|CTNNB1_ENST00000453024.1_Missense_Mutation_p.D25V	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	32			D -> A (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|D -> G (in PTR and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629}.|D -> Y (in PTR, hepatoblastoma and hepatocellular carcinoma; dbSNP:rs28931588). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:11703283, ECO:0000269|PubMed:9927029}.|Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.D32G(65)|p.A5_A80del(53)|p.D32V(33)|p.D32A(16)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.WQQQSYLD25?(5)|p.W25_D32del(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.S29_H36del(1)|p.D32del(1)|p.M14_S45del(1)|p.Q28_D32>H(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.D32fs*9(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TCTTACCTGGACTCTGGAATC	0.483	D32V(HEC265_ENDOMETRIUM)|D32V(HEC6_ENDOMETRIUM)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.D32V	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,+1,128	CTNNB1	4904	.	260	Deletion - In frame(120)|Substitution - Missense(114)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(154)|large_intestine(24)|pancreas(19)|central_nervous_system(16)|stomach(14)|endometrium(7)|skin(7)|ovary(4)|prostate(3)|pituitary(3)|small_intestine(2)|NS(2)|adrenal_gland(1)|soft_tissue(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)	c.A95T						.						92	77	82					3																	41266098		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	ACCTGGACTCTGG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.95A>T	chr3.hg19:g.41266098A>T	ENSP00000344456:p.Asp32Val	122.0	0.0		150.0	73.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.184569	0.78677	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.50001	0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.70037	0.3178	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.74325	-0.3702	10	0.87932	D	0	0.3843	16.0676	0.80897	1.0:0.0:0.0:0.0	.	32	P35222	CTNB1_HUMAN	V	25;32;32;32;32;25;32;32;32	ENSP00000400508:D25V;ENSP00000385604:D32V;ENSP00000412219:D32V;ENSP00000379486:D32V;ENSP00000344456:D32V;ENSP00000411226:D25V;ENSP00000379488:D32V;ENSP00000409302:D32V;ENSP00000401599:D32V	ENSP00000344456:D32V	D	+	2	0	CTNNB1	41241102	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.201000	0.70794	0.533000	0.62120	GAC	.	.		0.483	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41266098	A	T	41266098	3	4	333	1	0	0	0	0	1	0	0	0	4018	275	10	4	101	4	CTNNB1	3	41266098	Missense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	3084201	41266098	156756332	44	46386										
ZNF167	55888	hgsc.bcm.edu	37	chr3	44612664	44612665	+	Frame_Shift_Ins	INS	-	-	A													0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tcagagaacccatactggggINSaaaaaccctataaatgcaat							TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr3:44612664_44612665insA	ENST00000273320.3	+	6	2491_2492	c.2062_2063insA	c.(2062-2064)gaafs	p.E688fs	ZKSCAN7_ENST00000431636.1_Intron|ZKSCAN7_ENST00000341840.3_Intron|RP11-944L7.4_ENST00000457331.1_RNA|RP11-944L7.5_ENST00000419137.1_Intron|ZKSCAN7_ENST00000426540.1_Frame_Shift_Ins_p.E688fs	NM_018651.2	NP_061121.2	Q9P0L1	ZKSC7_HUMAN	zinc finger with KRAB and SCAN domains 7	688					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E688G(1)									CCATACTGGGGAAAAACCCTAT	0.426																																					p.E688fs		Atlas-Indel,Pindel	.											.	.	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.2062_2063insA						.																																			SO:0001589	frameshift_variant	55888	exon6			.	L32164, AY280798	CCDS2714.1, CCDS2715.1, CCDS74924.1	3p21.32	2013-01-09	2013-01-09	2013-01-09	ENSG00000196345	ENSG00000196345		"Zinc fingers, C2H2-type", "-", "-", "-"	12955	protein-coding gene	gene with protein product			"zinc finger protein 64", "zinc finger protein 448", "zinc finger protein 167"	ZNF64, ZNF448, ZNF167		7814019, 1505991	Standard	XM_005265323		Approved	FLJ12738, ZSCAN39	uc003cnj.3	Q9P0L1	OTTHUMG00000133094	ENST00000273320.3:c.2067dupA	chr3.hg19:g.44612669_44612669dupA	ENSP00000273320:p.Glu688fs	65.0	0.0		56.0	21.0	NM_018651	A0PJV3|A8K5H0|Q6WL09|Q96FQ2	Frame_Shift_Ins	INS	ENST00000273320.3	hg19	CCDS2715.1																																																																																			.	.		0.426	ZKSCAN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256752.4	NM_018651		A	44612665	-	A	44612664	7	5	333	1	0	1	1	0	0	0	0	0	17756	1175	41	0	2080	0	ZNF167	3	44612664	Frame_Shift_Ins	INS	-	TCGA-RC-A6M4-01A-11D-A32G-10	3346566	44612664	153409766	45	46387										
STAB1	23166	hgsc.bcm.edu	37	chr3	52558211	52558211	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	cctgtctttggcagcgacacCttttgtgaacccttcgatgt	9	12	1	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr3:52558211C>T	ENST00000321725.6	+	68	7714	c.7638C>T	c.(7636-7638)acC>acT	p.T2546T		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	2546					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)			breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		GCAGCGACACCTTTTGTGAAC	0.577																																					p.T2546T		Atlas-SNP	.											.	STAB1	178	.	0			c.C7638T						.						211	192	198					3																	52558211		2203	4300	6503	SO:0001819	synonymous_variant	23166	exon68			CGACACCTTTTGT	AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"MS-1 antigen", "fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1", "common lymphatic endothelial and vascular endothelial receptor-1"	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.7638C>T	chr3.hg19:g.52558211C>T		62.0	0.0		86.0	48.0	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Silent	SNP	ENST00000321725.6	hg19	CCDS33768.1	.	.	.	.	.	.	.	.	.	.	C	1.405	-0.577116	0.03854	.	.	ENSG00000010327	ENST00000469989	.	.	.	5.67	1.09	0.20402	.	.	.	.	.	T	0.26122	0.0637	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.24548	-1.0157	4	.	.	.	.	5.3108	0.15829	0.1333:0.5589:0.0:0.3078	.	.	.	.	F	153	.	.	L	+	1	0	STAB1	52533251	0.006000	0.16342	0.002000	0.10522	0.314000	0.28054	0.226000	0.17776	-0.016000	0.14127	0.561000	0.74099	CTT	.	.		0.577	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136		T	52558211	C	T	52558211	2	4	333	1	0	0	0	0	0	0	0	1	15252	668	24	3		3	STAB1	3	52558211	Silent	SNP	C	TCGA-RC-A6M4-01A-11D-A32G-10	7945547	52558211	145464219	46	46388										
FRMD4B	23150	hgsc.bcm.edu	37	chr3	69221075	69221075	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ctctgctcactactctccagGttgtcttccagctggtttcc	7	15	4	0	rs373666395		TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr3:69221075G>A	ENST00000398540.3	-	23	3125	c.3042C>T	c.(3040-3042)aaC>aaT	p.N1014N	FRMD4B_ENST00000542259.1_Silent_p.N960N|FRMD4B_ENST00000478263.1_Silent_p.N666N	NM_015123.1	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B	1014					establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|ruffle (GO:0001726)				NS(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(2)	19		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)		TACTCTCCAGGTTGTCTTCCA	0.433																																					p.N1014N		Atlas-SNP	.											.	FRMD4B	90	.	0			c.C3042T						.						253	233	239					3																	69221075		1904	4125	6029	SO:0001819	synonymous_variant	23150	exon23			CTCCAGGTTGTCT	AL832231	CCDS46863.1	3p14.2	2006-04-12			ENSG00000114541	ENSG00000114541			24886	protein-coding gene	gene with protein product						10231032, 11445584	Standard	XM_005264720		Approved	KIAA1013, GRSP1	uc003dnv.2	Q9Y2L6	OTTHUMG00000158772	ENST00000398540.3:c.3042C>T	chr3.hg19:g.69221075G>A		171.0	0.0		143.0	53.0	NM_015123	Q8TAI3	Silent	SNP	ENST00000398540.3	hg19	CCDS46863.1																																																																																			.	.		0.433	FRMD4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352111.1			A	69221075	G	A	69221075	2	1	333	1	0	0	0	0	0	0	0	1	6060	1252	44	3		3	FRMD4B	3	69221075	Silent	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	16662864	69221075	128801355	47	46389										
ROBO1	6091	hgsc.bcm.edu	37	chr3	78737868	78737868	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	cttcacactgaaaagttacaGtccgtcccaaagcaacaacc	5	14	1	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr3:78737868G>T	ENST00000464233.1	-	9	1213	c.1100C>A	c.(1099-1101)aCt>aAt	p.T367N	ROBO1_ENST00000436010.2_Missense_Mutation_p.T328N|ROBO1_ENST00000495273.1_Missense_Mutation_p.T331N|ROBO1_ENST00000467549.1_Missense_Mutation_p.T331N	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	367	Ig-like C2-type 4.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		AAAAGTTACAGTCCGTCCCAA	0.418																																					p.T367N		Atlas-SNP	.											.	ROBO1	833	.	0			c.C1100A						.						64	60	62					3																	78737868		1870	4104	5974	SO:0001583	missense	6091	exon9			GTTACAGTCCGTC	AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.1100C>A	chr3.hg19:g.78737868G>T	ENSP00000420321:p.Thr367Asn	57.0	0.0		51.0	16.0	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Missense_Mutation	SNP	ENST00000464233.1	hg19	CCDS54611.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.175468	0.78564	.	.	ENSG00000169855	ENST00000436010;ENST00000398412;ENST00000464233;ENST00000495273;ENST00000467549;ENST00000398414	T;T;T;T	0.75260	-0.92;-0.92;1.58;1.58	5.38	5.38	0.77491	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin V-set, subgroup (1);Immunoglobulin-like fold (1);	0.095949	0.64402	D	0.000001	T	0.79534	0.4462	N	0.25332	0.735	0.80722	D	1	D;D;D;D;D	0.89917	0.988;1.0;1.0;1.0;0.985	D;D;D;D;D	0.83275	0.911;0.996;0.995;0.996;0.964	T	0.77582	-0.2534	9	.	.	.	.	19.115	0.93334	0.0:0.0:1.0:0.0	.	331;367;331;331;328	Q1RMC7;Q9Y6N7;B2RXI1;E9PD49;Q9Y6N7-4	.;ROBO1_HUMAN;.;.;.	N	328;331;367;331;331;367	ENSP00000406043:T328N;ENSP00000420321:T367N;ENSP00000420637:T331N;ENSP00000417992:T331N	.	T	-	2	0	ROBO1	78820558	1.000000	0.71417	1.000000	0.80357	0.608000	0.37181	7.465000	0.80898	2.522000	0.85027	0.585000	0.79938	ACT	.	.		0.418	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		T	78737868	G	T	78737868	3	4	333	1	0	0	0	0	1	0	0	0	13528	1029	36	3	3947	3	ROBO1	3	78737868	Missense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	9516793	78737868	119284562	48	46390										
POLQ	10721	hgsc.bcm.edu	37	chr3	121264699	121264699	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ctgattctgaacgccgccgtTtcccactccgacgcagaaga	9	15	1	4			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr3:121264699T>A	ENST00000264233.5	-	1	154	c.26A>T	c.(25-27)aAa>aTa	p.K9I		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	9					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		ACGCCGCCGTTTCCCACTCCG	0.642								DNA polymerases (catalytic subunits)																													p.K9I	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.A26T						.						31	31	31					3																	121264699		2203	4300	6503	SO:0001583	missense	10721	exon1			CGCCGTTTCCCAC	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.26A>T	chr3.hg19:g.121264699T>A	ENSP00000264233:p.Lys9Ile	37.0	0.0		40.0	15.0	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	hg19	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	T	19.54	3.847607	0.71603	.	.	ENSG00000051341	ENST00000264233;ENST00000393672	T	0.54071	0.59	5.16	5.16	0.70880	.	0.180887	0.38217	N	0.001769	T	0.51719	0.1691	L	0.27053	0.805	0.30114	N	0.806267	D	0.63880	0.993	P	0.57371	0.819	T	0.55392	-0.8148	10	0.72032	D	0.01	.	8.9585	0.35832	0.0:0.0837:0.0:0.9163	.	9	O75417	DPOLQ_HUMAN	I	9;144	ENSP00000264233:K9I	ENSP00000264233:K9I	K	-	2	0	POLQ	122747389	0.998000	0.40836	0.999000	0.59377	0.992000	0.81027	2.542000	0.45744	2.291000	0.77112	0.533000	0.62120	AAA	.	.		0.642	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		A	121264699	T	A	121264699	3	1	333	1	0	0	0	0	1	0	0	0	12217	1841	64	4	7866	4	POLQ	3	121264699	Missense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	42526831	121264699	76757731	49	46391										
ILDR1	286676	hgsc.bcm.edu	37	chr3	121712723	121712723	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	aggttgaggttccgcagttcTttctccaaatactccaggac	9	11	2	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr3:121712723T>A	ENST00000344209.5	-	7	999	c.873A>T	c.(871-873)aaA>aaT	p.K291N	ILDR1_ENST00000462014.1_Missense_Mutation_p.K259N|ILDR1_ENST00000460554.1_5'UTR|ILDR1_ENST00000273691.3_Missense_Mutation_p.K247N|ILDR1_ENST00000393631.1_Missense_Mutation_p.K202N	NM_001199799.1	NP_001186728.1	Q86SU0	ILDR1_HUMAN	immunoglobulin-like domain containing receptor 1	291					positive regulation of peptide hormone secretion (GO:0090277)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-density lipoprotein particle receptor activity (GO:0070506)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				GBM - Glioblastoma multiforme(114;0.156)		TCCGCAGTTCTTTCTCCAAAT	0.587																																					p.K291N		Atlas-SNP	.											.	ILDR1	120	.	0			c.A873T						.						77	73	74					3																	121712723		2203	4300	6503	SO:0001583	missense	286676	exon7			CAGTTCTTTCTCC	BC044240	CCDS3008.1, CCDS56270.1, CCDS56271.1	3q21.1	2013-10-11			ENSG00000145103	ENSG00000145103			28741	protein-coding gene	gene with protein product		609739	"deafness, autosomal recessive 42"	DFNB42		15641023, 21255762	Standard	NM_175924		Approved	MGC50831	uc003ees.3	Q86SU0	OTTHUMG00000159481	ENST00000344209.5:c.873A>T	chr3.hg19:g.121712723T>A	ENSP00000345667:p.Lys291Asn	25.0	0.0		30.0	17.0	NM_001199799	Q6ZP61|Q7Z578	Missense_Mutation	SNP	ENST00000344209.5	hg19	CCDS56271.1	.	.	.	.	.	.	.	.	.	.	T	13.74	2.327743	0.41197	.	.	ENSG00000145103	ENST00000273691;ENST00000344209;ENST00000383663;ENST00000393631;ENST00000462014	T;T;T;T	0.77750	-0.61;-0.6;-1.12;-0.2	5.14	-3.39	0.04868	.	0.343618	0.35838	N	0.002948	T	0.57681	0.2070	L	0.31120	0.905	0.36771	D	0.883805	B;B;B;B	0.18461	0.028;0.0;0.002;0.004	B;B;B;B	0.17098	0.017;0.001;0.005;0.005	T	0.24512	-1.0158	10	0.25751	T	0.34	-16.5813	6.981	0.24704	0.1409:0.5283:0.0:0.3308	.	202;291;247;259	Q86SU0-5;Q86SU0;Q86SU0-2;Q86SU0-6	.;ILDR1_HUMAN;.;.	N	247;291;174;202;259	ENSP00000273691:K247N;ENSP00000345667:K291N;ENSP00000377251:K202N;ENSP00000419414:K259N	ENSP00000273691:K247N	K	-	3	2	ILDR1	123195413	0.987000	0.35691	0.988000	0.46212	0.992000	0.81027	0.037000	0.13840	-0.538000	0.06281	-0.301000	0.09380	AAA	.	.		0.587	ILDR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355666.1	NM_175924		A	121712723	T	A	121712723	3	1	333	1	0	0	0	0	1	0	0	0	7718	1606	56	4	775	4	ILDR1	3	121712723	Missense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	448024	121712723	76309707	50	46392										
SLC12A8	84561	hgsc.bcm.edu	37	chr3	124826958	124826958	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gatggcagccacgggtgtttTgtttggccccttctgcagga	14	10	1	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr3:124826958T>C	ENST00000393469.4	-	9	1121	c.1072A>G	c.(1072-1074)Aaa>Gaa	p.K358E	SLC12A8_ENST00000430155.2_Missense_Mutation_p.K159E|SLC12A8_ENST00000423114.2_Missense_Mutation_p.K387E|SLC12A8_ENST00000314584.7_Missense_Mutation_p.K111E|SLC12A8_ENST00000465475.1_5'UTR|SLC12A8_ENST00000469902.1_Missense_Mutation_p.K358E	NM_001195483.1	NP_001182412	A0AV02	S12A8_HUMAN	solute carrier family 12, member 8	358					potassium ion transport (GO:0006813)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			endometrium(2)|kidney(2)|lung(12)	16						ACGGGTGTTTTGTTTGGCCCC	0.468																																					p.K358E		Atlas-SNP	.											.	SLC12A8	81	.	0			c.A1072G						.						38	39	39					3																	124826958		1941	4141	6082	SO:0001583	missense	84561	exon10			GTGTTTTGTTTGG		CCDS43143.1	3q21.2	2013-07-18	2013-07-18		ENSG00000221955	ENSG00000221955		"Solute carriers"	15595	protein-coding gene	gene with protein product	"solute carrier family 12 (sodium/potassium/chloride transporters), member 8", "cation-chloride cotransporter 9"	611316				11863360	Standard	NM_024628		Approved	CCC9	uc003ehv.4	A0AV02	OTTHUMG00000159483	ENST00000393469.4:c.1072A>G	chr3.hg19:g.124826958T>C	ENSP00000377112:p.Lys358Glu	48.0	0.0		49.0	14.0	NM_024628	C9JJJ2|Q68D04|Q6I9Z2|Q6P4C0|Q7Z3A6|Q86WK0|Q8NFX9|Q8WUI3|Q96RF9|Q9H5P9	Missense_Mutation	SNP	ENST00000393469.4	hg19	CCDS43143.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.271132	0.80469	.	.	ENSG00000221955	ENST00000430155;ENST00000393469;ENST00000423114;ENST00000469902;ENST00000314584	D;D;D;D;D	0.98792	-5.14;-5.14;-5.14;-5.14;-5.14	4.9	4.9	0.64082	Amino acid permease domain (1);	.	.	.	.	D	0.98321	0.9443	L	0.43923	1.385	0.48452	D	0.999653	D;D;D;D	0.76494	0.999;0.97;0.975;0.997	D;P;P;D	0.74348	0.983;0.73;0.875;0.94	D	0.98498	1.0613	9	0.59425	D	0.04	.	11.6463	0.51263	0.0:0.0:0.1482:0.8518	.	111;387;358;159	A0AV02-4;A0AV02-2;A0AV02;A0AV02-3	.;.;S12A8_HUMAN;.	E	159;358;387;358;111	ENSP00000415713:K159E;ENSP00000377112:K358E;ENSP00000404243:K387E;ENSP00000418783:K358E;ENSP00000323632:K111E	ENSP00000323632:K111E	K	-	1	0	SLC12A8	126309648	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	3.927000	0.56499	2.172000	0.68678	0.533000	0.62120	AAA	.	.		0.468	SLC12A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355711.4	NM_024628		C	124826958	T	C	124826958	3	2	333	1	0	0	0	0	1	0	0	0	14404	1821	63	2	1092	2	SLC12A8	3	124826958	Missense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	3114235	124826958	73195472	51	46393										
SLC41A3	54946	hgsc.bcm.edu	37	chr3	125769824	125769824	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tgccagtgtcatctccaggtTccccttcaggcccaccaggg	10	16	3	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr3:125769824T>A	ENST00000315891.6	-	3	581	c.343A>T	c.(343-345)Aac>Tac	p.N115Y	SLC41A3_ENST00000514023.1_Intron|SLC41A3_ENST00000346785.5_Intron|SLC41A3_ENST00000360370.4_Missense_Mutation_p.N115Y|SLC41A3_ENST00000508835.1_5'UTR|SLC41A3_ENST00000383598.2_Missense_Mutation_p.N89Y	NM_001008485.1|NM_017836.3	NP_001008485|NP_060306.3	Q96GZ6	S41A3_HUMAN	solute carrier family 41, member 3	115						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation transmembrane transporter activity (GO:0008324)			breast(1)|endometrium(4)|large_intestine(6)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18				GBM - Glioblastoma multiforme(114;0.167)		ATCTCCAGGTTCCCCTTCAGG	0.572																																					p.N115Y		Atlas-SNP	.											.	SLC41A3	80	.	0			c.A343T						.						98	72	81					3																	125769824		2203	4300	6503	SO:0001583	missense	54946	exon3			CCAGGTTCCCCTT		CCDS33842.1, CCDS33843.1, CCDS33844.1, CCDS43144.1, CCDS54635.1	3q21.2	2013-09-02			ENSG00000114544	ENSG00000114544		"Solute carriers"	31046	protein-coding gene	gene with protein product		610803					Standard	NM_001164475		Approved	FLJ20473	uc003eij.3	Q96GZ6	OTTHUMG00000162678	ENST00000315891.6:c.343A>T	chr3.hg19:g.125769824T>A	ENSP00000326070:p.Asn115Tyr	30.0	0.0		25.0	15.0	NM_017836	A6ND60|B3KSD9|B7Z4Y2|C9JE96|E7ENY4|Q8N342|Q8NB27|Q9H9I6|Q9HAB1|Q9NX30	Missense_Mutation	SNP	ENST00000315891.6	hg19	CCDS33843.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.575764	0.86645	.	.	ENSG00000114544	ENST00000360370;ENST00000383598;ENST00000458524;ENST00000315891;ENST00000514677;ENST00000513723;ENST00000512470;ENST00000510651;ENST00000507280;ENST00000514891;ENST00000504035;ENST00000509064	T;T;T;T;T;T;T;T;T;T;T	0.50277	0.75;0.75;0.75;0.75;0.75;0.75;0.75;0.75;0.75;0.75;0.75	5.18	5.18	0.71444	MgtE magnesium transporter, integral membrane (1);	0.000000	0.85682	D	0.000000	T	0.71660	0.3366	M	0.86805	2.84	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;1.0;1.0	T	0.77424	-0.2593	10	0.87932	D	0	-16.3959	12.9765	0.58540	0.0:0.0:0.0:1.0	.	115;115;115;89	A8MQ22;E7ENY4;Q96GZ6;Q96GZ6-7	.;.;S41A3_HUMAN;.	Y	115;89;106;115;115;167;115;115;115;115;115;115	ENSP00000353533:N115Y;ENSP00000373092:N89Y;ENSP00000326070:N115Y;ENSP00000422828:N115Y;ENSP00000425373:N167Y;ENSP00000421008:N115Y;ENSP00000423524:N115Y;ENSP00000422531:N115Y;ENSP00000423154:N115Y;ENSP00000421940:N115Y;ENSP00000424882:N115Y	ENSP00000326070:N115Y	N	-	1	0	SLC41A3	127252514	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	7.627000	0.83176	1.949000	0.56562	0.383000	0.25322	AAC	.	.		0.572	SLC41A3-024	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000370886.1	NM_017836		A	125769824	T	A	125769824	3	1	333	1	0	0	0	0	1	0	0	0	14646	1783	62	4	1318	4	SLC41A3	3	125769824	Missense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	942866	125769824	72252606	52	46394										
CLDN18	51208	hgsc.bcm.edu	37	chr3	137748665	137748665	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	atttggtgcggctctgttcgTgggctgggtcgctggaggcc	18	9	1	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr3:137748665T>C	ENST00000183605.5	+	4	756	c.530T>C	c.(529-531)gTg>gCg	p.V177A	CLDN18_ENST00000343735.4_Missense_Mutation_p.V177A	NM_016369.3	NP_057453.1	P56856	CLD18_HUMAN	claudin 18	177					calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(2)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	6						GCTCTGTTCGTGGGCTGGGTC	0.587																																					p.V177A		Atlas-SNP	.											.	CLDN18	33	.	0			c.T530C						.						59	50	53					3																	137748665		2203	4299	6502	SO:0001583	missense	51208	exon4			TGTTCGTGGGCTG	AF221069, AY102073	CCDS3095.1, CCDS33862.1	3q	2008-08-27			ENSG00000066405	ENSG00000066405		"Claudins"	2039	protein-coding gene	gene with protein product		609210	"surfactant associated protein J"	SFTPJ			Standard	NM_001002026		Approved		uc003ero.1	P56856	OTTHUMG00000159762	ENST00000183605.5:c.530T>C	chr3.hg19:g.137748665T>C	ENSP00000183605:p.Val177Ala	106.0	0.0		62.0	33.0	NM_016369	A5PL21|Q96PH4	Missense_Mutation	SNP	ENST00000183605.5	hg19	CCDS3095.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.646182	0.87958	.	.	ENSG00000066405	ENST00000343735;ENST00000183605;ENST00000536138	D;D	0.89123	-2.47;-2.47	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	D	0.93667	0.7977	M	0.69823	2.125	0.58432	D	0.999999	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.76575	0.988;0.988;0.982	D	0.94417	0.7637	10	0.87932	D	0	.	15.2795	0.73770	0.0:0.0:0.0:1.0	.	166;177;177	B4DNX6;P56856;P56856-2	.;CLD18_HUMAN;.	A	177;177;166	ENSP00000340939:V177A;ENSP00000183605:V177A	ENSP00000183605:V177A	V	+	2	0	CLDN18	139231355	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.687000	0.74552	2.070000	0.61991	0.533000	0.62120	GTG	.	.		0.587	CLDN18-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000357199.2	NM_001002026		C	137748665	T	C	137748665	3	2	333	1	0	0	0	0	1	0	0	0	3481	1696	59	2	768	2	CLDN18	3	137748665	Missense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	11978841	137748665	60273765	53	46395										
DZIP1L	199221	hgsc.bcm.edu	37	chr3	137787109	137787109	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ctgccatggctctgacgagtTggtgggggtggctctgccgg	18	10	2	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr3:137787109T>G	ENST00000327532.2	-	13	2078	c.1716A>C	c.(1714-1716)ccA>ccC	p.P572P	DZIP1L_ENST00000488595.1_5'Flank	NM_173543.2	NP_775814.2	Q8IYY4	DZI1L_HUMAN	DAZ interacting zinc finger protein 1-like	572					cilium assembly (GO:0042384)	ciliary basal body (GO:0036064)	metal ion binding (GO:0046872)			breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(2)|prostate(1)|skin(1)	35						TCTGACGAGTTGGTGGGGGTG	0.662																																					p.P572P		Atlas-SNP	.											.	DZIP1L	88	.	0			c.A1716C						.						55	64	61					3																	137787109		2203	4300	6503	SO:0001819	synonymous_variant	199221	exon13			ACGAGTTGGTGGG	AK057406	CCDS3096.1, CCDS54645.1	3q22.3	2013-05-22	2013-05-22		ENSG00000158163	ENSG00000158163			26551	protein-coding gene	gene with protein product			"DAZ interacting protein 1-like"			12477932	Standard	NM_173543		Approved	FLJ32844, DZIP2	uc003erq.3	Q8IYY4	OTTHUMG00000159819	ENST00000327532.2:c.1716A>C	chr3.hg19:g.137787109T>G		86.0	0.0		78.0	17.0	NM_173543	C9JUG5|Q96M38	Silent	SNP	ENST00000327532.2	hg19	CCDS3096.1																																																																																			.	.		0.662	DZIP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357548.1	NM_173543		G	137787109	T	G	137787109	2	3	333	1	0	0	0	0	0	0	0	1	4866	1799	63	5		5	DZIP1L	3	137787109	Silent	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	38444	137787109	60235321	54	46396										
HTR3D	200909	hgsc.bcm.edu	37	chr3	183756700	183756700	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gcgatggacgccctgctcttCcgcctctacctgctcttcat	8	17	4	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr3:183756700C>A	ENST00000382489.3	+	8	1302	c.1302C>A	c.(1300-1302)ttC>ttA	p.F434L	HTR3D_ENST00000334128.2_Missense_Mutation_p.F259L|HTR3D_ENST00000453435.1_Missense_Mutation_p.F213L|HTR3D_ENST00000428798.2_Missense_Mutation_p.F384L	NM_001163646.1	NP_001157118.1	Q70Z44	5HT3D_HUMAN	5-hydroxytryptamine (serotonin) receptor 3D, ionotropic	434					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)			large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(2)	10	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;6.23e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Ergoloid mesylate(DB01049)	CCCTGCTCTTCCGCCTCTACC	0.592																																					p.F434L		Atlas-SNP	.											.	HTR3D	65	.	0			c.C1302A						.						175	159	165					3																	183756700		2203	4300	6503	SO:0001583	missense	200909	exon8			GCTCTTCCGCCTC	AY159812	CCDS3249.1, CCDS46966.1, CCDS54685.1	3q27	2012-05-22	2012-02-03		ENSG00000186090	ENSG00000186090		"5-HT (serotonin) receptors", "Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"	24004	protein-coding gene	gene with protein product		610122	"5-hydroxytryptamine (serotonin) receptor 3 family member D"			12801637	Standard	NM_001145143		Approved		uc011bqv.2	Q70Z44	OTTHUMG00000156858	ENST00000382489.3:c.1302C>A	chr3.hg19:g.183756700C>A	ENSP00000371929:p.Phe434Leu	95.0	0.0		85.0	23.0	NM_001163646	C9J2I6|J3QT78|Q495N5|Q495N6|Q7Z6B3	Missense_Mutation	SNP	ENST00000382489.3	hg19	CCDS54685.1	.	.	.	.	.	.	.	.	.	.	.	19.70	3.876841	0.72180	.	.	ENSG00000186090	ENST00000334128;ENST00000428798;ENST00000382489;ENST00000453435	T;T;T;T	0.79033	-1.23;-1.23;-1.23;-1.23	4.11	4.11	0.48088	Neurotransmitter-gated ion-channel transmembrane domain (1);	0.000000	0.64402	D	0.000004	D	0.84795	0.5551	M	0.69358	2.11	0.24484	N	0.994339	D;D;D;D	0.71674	0.998;0.984;0.968;0.984	D;P;P;D	0.68765	0.96;0.892;0.758;0.916	T	0.76772	-0.2836	10	0.72032	D	0.01	-30.7823	12.0322	0.53403	0.0:1.0:0.0:0.0	.	434;259;213;259	Q70Z44;Q70Z44-2;Q70Z44-3;F6WC43	5HT3D_HUMAN;.;.;.	L	259;384;434;213	ENSP00000334315:F259L;ENSP00000405409:F384L;ENSP00000371929:F434L;ENSP00000389268:F213L	ENSP00000334315:F259L	F	+	3	2	HTR3D	185239394	0.961000	0.32948	0.997000	0.53966	0.934000	0.57294	2.211000	0.42825	2.271000	0.75665	0.563000	0.77884	TTC	.	.		0.592	HTR3D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346289.1	NM_182537		A	183756700	C	A	183756700	3	1	333	1	0	0	0	0	1	0	0	0	7456	854	30	3	1502	3	HTR3D	3	183756700	Missense_Mutation	SNP	C	TCGA-RC-A6M4-01A-11D-A32G-10	45969591	183756700	14265730	55	46397										
OTOP1	133060	hgsc.bcm.edu	37	chr4	4228502	4228502	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ctcggggccgaggacgagggAggcgagcaggccgctggccc	20	13	0	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr4:4228502A>T	ENST00000296358.4	-	1	114	c.90T>A	c.(88-90)ccT>ccA	p.P30P		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	30					biomineral tissue development (GO:0031214)|detection of gravity (GO:0009590)|inner ear morphogenesis (GO:0042472)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		AGGACGAGGGAGGCGAGCAGG	0.756																																					p.P30P		Atlas-SNP	.											.	OTOP1	118	.	0			c.T90A						.						2	2	2					4																	4228502		1485	3042	4527	SO:0001819	synonymous_variant	133060	exon1			CGAGGGAGGCGAG	BK000653	CCDS3372.1	4p16.2	2008-02-05			ENSG00000163982	ENSG00000163982			19656	protein-coding gene	gene with protein product		607806				12651873	Standard	NM_177998		Approved		uc003ghp.1	Q7RTM1	OTTHUMG00000090301	ENST00000296358.4:c.90T>A	chr4.hg19:g.4228502A>T		8.0	0.0		15.0	11.0	NM_177998	A1L476	Silent	SNP	ENST00000296358.4	hg19	CCDS3372.1																																																																																			.	.		0.756	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206661.2	NM_177998		T	4228502	A	T	4228502	2	4	333	1	0	0	0	0	0	0	0	1	11314	291	11	4		4	OTOP1	4	4228502	Silent	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10		4228502	186925774	56	46398										
BOD1L	259282	hgsc.bcm.edu	37	chr4	13601419	13601419	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	catggggaccttgtgcttgcTcacttctgtggctgacaggt	13	10	2	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr4:13601419T>A	ENST00000040738.5	-	10	7240	c.7105A>T	c.(7105-7107)Agc>Tgc	p.S2369C		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	2369						nucleus (GO:0005634)	DNA binding (GO:0003677)										TTGTGCTTGCTCACTTCTGTG	0.542																																					p.S2369C		Atlas-SNP	.											.	.	.	.	0			c.A7105T						.						132	112	119					4																	13601419		2203	4300	6503	SO:0001583	missense	259282	exon10			GCTTGCTCACTTC	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.7105A>T	chr4.hg19:g.13601419T>A	ENSP00000040738:p.Ser2369Cys	144.0	0.0		135.0	50.0	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	hg19	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	T	16.16	3.043323	0.55003	.	.	ENSG00000038219	ENST00000040738	T	0.08807	3.05	5.22	1.43	0.22495	.	0.611515	0.15479	N	0.260187	T	0.12475	0.0303	L	0.54323	1.7	0.09310	N	1	D	0.63046	0.992	P	0.52710	0.707	T	0.14254	-1.0479	10	0.87932	D	0	-3.7656	3.5239	0.07752	0.0:0.2654:0.1966:0.538	.	2369	Q8NFC6	BOD1L_HUMAN	C	2369	ENSP00000040738:S2369C	ENSP00000040738:S2369C	S	-	1	0	BOD1L	13210517	0.002000	0.14202	0.001000	0.08648	0.018000	0.09664	1.219000	0.32479	0.305000	0.22832	0.528000	0.53228	AGC	.	.		0.542	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		A	13601419	T	A	13601419	3	1	333	1	0	0	0	0	1	0	0	0	1483	1551	54	4	2118	4	BOD1L	4	13601419	Missense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	9372917	13601419	177552857	57	46399										
SLC10A4	201780	hgsc.bcm.edu	37	chr4	48490859	48490859	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tgaagatacagatatttcttAtaaaaaactaaaagaagagg	7	3	1	5			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr4:48490859A>T	ENST00000273861.4	+	3	1436	c.1217A>T	c.(1216-1218)tAt>tTt	p.Y406F	ZAR1_ENST00000327939.4_5'Flank	NM_152679.3	NP_689892.1	Q96EP9	NTCP4_HUMAN	solute carrier family 10, member 4	406						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bile acid:sodium symporter activity (GO:0008508)			central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|urinary_tract(1)	6						GATATTTCTTATAAAAAACTA	0.353																																					p.Y406F		Atlas-SNP	.											.	SLC10A4	23	.	0			c.A1217T						.						44	48	47					4																	48490859		2199	4298	6497	SO:0001583	missense	201780	exon3			TTTCTTATAAAAA	BC012048	CCDS3482.1	4p12	2013-07-18	2013-07-18		ENSG00000145248	ENSG00000145248		"Solute carriers"	22980	protein-coding gene	gene with protein product							Standard	NM_152679		Approved	MGC29802	uc003gyc.2	Q96EP9	OTTHUMG00000102092	ENST00000273861.4:c.1217A>T	chr4.hg19:g.48490859A>T	ENSP00000273861:p.Tyr406Phe	60.0	0.0		76.0	34.0	NM_152679	Q8WUZ2	Missense_Mutation	SNP	ENST00000273861.4	hg19	CCDS3482.1	.	.	.	.	.	.	.	.	.	.	A	12.54	1.968072	0.34754	.	.	ENSG00000145248	ENST00000273861	T	0.09911	2.93	6.17	6.17	0.99709	.	0.970544	0.08587	N	0.923648	T	0.12135	0.0295	L	0.43701	1.375	0.45172	D	0.998184	B	0.30664	0.289	B	0.23716	0.048	T	0.10567	-1.0624	10	0.42905	T	0.14	-14.744	11.8437	0.52371	0.8695:0.0:0.0:0.1305	.	406	Q96EP9	NTCP4_HUMAN	F	406	ENSP00000273861:Y406F	ENSP00000273861:Y406F	Y	+	2	0	SLC10A4	48185616	1.000000	0.71417	0.986000	0.45419	0.221000	0.24807	6.982000	0.76173	2.371000	0.80710	0.533000	0.62120	TAT	.	.		0.353	SLC10A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219926.3	NM_152679		T	48490859	A	T	48490859	3	4	333	1	0	0	0	0	1	0	0	0	14391	449	16	4	1227	4	SLC10A4	4	48490859	Missense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	34889440	48490859	142663417	58	46400										
UGT2B4	7363	hgsc.bcm.edu	37	chr4	70346460	70346460	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	caggccagcaggaacccagtCacatccaaagagtggtactg	11	12	1	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr4:70346460C>G	ENST00000305107.6	-	6	1525	c.1479G>C	c.(1477-1479)gtG>gtC	p.V493V	UGT2B4_ENST00000381096.3_Silent_p.V357V|AC108078.1_ENST00000583573.1_RNA|UGT2B4_ENST00000506580.1_5'UTR|UGT2B4_ENST00000512583.1_3'UTR	NM_021139.2	NP_066962.2	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B4	493					cellular glucuronidation (GO:0052695)|estrogen catabolic process (GO:0006711)|metabolic process (GO:0008152)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(29)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	47					Canagliflozin(DB08907)|Codeine(DB00318)|Dapagliflozin(DB06292)|Flurbiprofen(DB00712)|Ibuprofen(DB01050)|Morphine(DB00295)	GGAACCCAGTCACATCCAAAG	0.478																																					p.V493V		Atlas-SNP	.											.	UGT2B4	105	.	0			c.G1479C						.						148	142	144					4																	70346460		2203	4300	6503	SO:0001819	synonymous_variant	7363	exon6			CCCAGTCACATCC	BC026264	CCDS43234.1, CCDS75137.1	4q13	2008-02-05	2005-07-20			ENSG00000156096		"UDP glucuronosyltransferases"	12553	protein-coding gene	gene with protein product		600067	"UDP glycosyltransferase 2 family, polypeptide B4"			3109396, 7835904	Standard	NM_021139		Approved	UGT2B11	uc003hek.4	P06133		ENST00000305107.6:c.1479G>C	chr4.hg19:g.70346460C>G		117.0	0.0		107.0	55.0	NM_021139	A6NCP7|B4DT75|G5E9X8|O60731|O60867|O75614|P36538|Q1HBF9|Q6QQX7	Silent	SNP	ENST00000305107.6	hg19	CCDS43234.1																																																																																			.	.		0.478	UGT2B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365526.1	NM_021139		G	70346460	C	G	70346460	2	3	333	1	0	0	0	0	0	0	0	1	16976	813	29	4		4	UGT2B4	4	70346460	Silent	SNP	C	TCGA-RC-A6M4-01A-11D-A32G-10	21855601	70346460	120807816	59	46401										
RUFY3	22902	hgsc.bcm.edu	37	chr4	71659507	71659507	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gtggctcacatccagattgcGccaggctgagcgaagccgcc	13	14	1	2	rs372273317		TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr4:71659507G>A	ENST00000226328.4	+	0	4233				RUFY3_ENST00000381006.3_Missense_Mutation_p.R448H|RUFY3_ENST00000502653.1_Missense_Mutation_p.R395H	NM_014961.3	NP_055776.1	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3						negative regulation of axonogenesis (GO:0050771)	filopodium (GO:0030175)|growth cone (GO:0030426)				endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	16		all_hematologic(202;0.248)	Lung(101;0.235)			TCCAGATTGCGCCAGGCTGAG	0.478																																					p.R448H		Atlas-SNP	.											.	RUFY3	61	.	0			c.G1343A						.	G	HIS/ARG	0,4406		0,0,2203	46	46	46		1343	5	1	4		46	1,8599	1.2+/-3.3	0,1,4299	no	missense	RUFY3	NM_001037442.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	448/621	71659507	1,13005	2203	4300	6503	SO:0001628	intergenic_variant	22902	exon13			GATTGCGCCAGGC	AF112221	CCDS3547.1, CCDS34001.1, CCDS47068.1, CCDS75138.1	4q13.3	2009-05-29			ENSG00000018189	ENSG00000018189		"Zinc fingers, FYVE domain containing"	30285	protein-coding gene	gene with protein product	"single axon-related 1"	611194				17439943	Standard	NM_001130709		Approved	RIPx, KIAA0871, Singar1	uc003hfr.3	Q7L099	OTTHUMG00000129910		chr4.hg19:g.71659507G>A		155.0	0.0		195.0	41.0	NM_001037442	B3KM25|B4DYW7|D9N163|O94948|Q9UI00	Missense_Mutation	SNP	ENST00000226328.4	hg19	CCDS3547.1	.	.	.	.	.	.	.	.	.	.	G	11.26	1.587493	0.28268	0.0	1.16E-4	ENSG00000018189	ENST00000381006;ENST00000502653	T;T	0.08720	3.07;3.06	5.88	5.01	0.66863	.	0.350601	0.29653	N	0.011551	T	0.08670	0.0215	.	.	.	0.80722	D	1	B	0.16396	0.017	B	0.08055	0.003	T	0.08330	-1.0727	9	0.54805	T	0.06	1.3898	11.3509	0.49587	0.1501:0.0:0.8499:0.0	.	448	Q7L099-3	.	H	448;395	ENSP00000370394:R448H;ENSP00000425400:R395H	ENSP00000370394:R448H	R	+	2	0	RUFY3	71878371	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.211000	0.58507	1.422000	0.47177	0.655000	0.94253	CGC	.	.		0.478	RUFY3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252161.2	NM_014961		A	71659507	G	A	71659507	1	1	333	0	1	0	0	0	0	0	0	0	13755	1087	38	1		1	RUFY3	4	71659507	IGR	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	1313047	71659507	119494769	60	46402										
DCHS2	54798	hgsc.bcm.edu	37	chr4	155256019	155256019	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gcataagaaataagtacttaCtcaagggctctcttgctttc	7	9	2	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr4:155256019C>G	ENST00000357232.4	-	8	1216		c.e8+1		DCHS2_ENST00000507542.1_Splice_Site|DCHS2_ENST00000339452.1_Splice_Site	NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2						homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		TAAGTACTTACTCAAGGGCTC	0.373																																					.		Atlas-SNP	.											.	DCHS2	594	.	0			c.1216+1G>C						.						103	102	102					4																	155256019		2203	4300	6503	SO:0001630	splice_region_variant	54798	exon9			TACTTACTCAAGG	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.1216+1G>C	chr4.hg19:g.155256019C>G		47.0	0.0		26.0	9.0	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Splice_Site	SNP	ENST00000357232.4	hg19	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.029069	0.75504	.	.	ENSG00000197410	ENST00000357232;ENST00000339452;ENST00000544161	.	.	.	6.17	6.17	0.99709	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DCHS2	155475469	1.000000	0.71417	1.000000	0.80357	0.726000	0.41606	5.137000	0.64789	2.941000	0.99782	0.655000	0.94253	.	.	.		0.373	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	Intron	G	155256019	C	G	155256019	5	3	333	1	0	0	0	0	0	0	1	0	4290	579	20	4	7701	4	DCHS2	4	155256019	Splice_Site	SNP	C	TCGA-RC-A6M4-01A-11D-A32G-10	83596512	155256019	35898257	61	46403										
ENPP6	133121	hgsc.bcm.edu	37	chr4	185074757	185074757	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tggccttggtcagagtgaccCacagaggttctgatccattc	11	11	2	4			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr4:185074757C>T	ENST00000296741.2	-	2	512	c.371G>A	c.(370-372)tGg>tAg	p.W124*		NM_153343.3	NP_699174.1	Q6UWR7	ENPP6_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 6	124					choline metabolic process (GO:0019695)|lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	glycerophosphocholine cholinephosphodiesterase activity (GO:0047390)|glycerophosphodiester phosphodiesterase activity (GO:0008889)|phosphoric diester hydrolase activity (GO:0008081)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|skin(2)	15		all_lung(41;7.99e-12)|Lung NSC(41;1.46e-11)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;4.98e-27)|Epithelial(43;3.15e-24)|OV - Ovarian serous cystadenocarcinoma(60;4.09e-12)|Colorectal(24;3.78e-05)|STAD - Stomach adenocarcinoma(60;4.5e-05)|COAD - Colon adenocarcinoma(29;0.000154)|GBM - Glioblastoma multiforme(59;0.000167)|BRCA - Breast invasive adenocarcinoma(30;0.000378)|LUSC - Lung squamous cell carcinoma(40;0.0151)		CAGAGTGACCCACAGAGGTTC	0.488																																					p.W124X		Atlas-SNP	.											.	ENPP6	61	.	0			c.G371A						.						136	115	122					4																	185074757		2203	4300	6503	SO:0001587	stop_gained	133121	exon2			GTGACCCACAGAG	AK057370	CCDS3834.1	4q35.1	2008-02-05			ENSG00000164303	ENSG00000164303			23409	protein-coding gene	gene with protein product							Standard	NM_153343		Approved	MGC33971	uc003iwc.3	Q6UWR7	OTTHUMG00000160617	ENST00000296741.2:c.371G>A	chr4.hg19:g.185074757C>T	ENSP00000296741:p.Trp124*	130.0	0.0		113.0	55.0	NM_153343	Q4W5Q1|Q96M57	Nonsense_Mutation	SNP	ENST00000296741.2	hg19	CCDS3834.1	.	.	.	.	.	.	.	.	.	.	C	39	7.334371	0.98217	.	.	ENSG00000164303	ENST00000296741;ENST00000512353	.	.	.	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.1584	19.2788	0.94042	0.0:1.0:0.0:0.0	.	.	.	.	X	124;36	.	ENSP00000296741:W124X	W	-	2	0	ENPP6	185311751	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.487000	0.81328	2.567000	0.86603	0.655000	0.94253	TGG	.	.		0.488	ENPP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361428.1	NM_153343		T	185074757	C	T	185074757	4	4	333	1	0	0	0	0	0	1	0	0	5136	595	21	3	979	3	ENPP6	4	185074757	Nonsense_Mutation	SNP	C	TCGA-RC-A6M4-01A-11D-A32G-10	29818738	185074757	6079519	62	46404										
ADAMTS12	81792	hgsc.bcm.edu	37	chr5	33649699	33649699	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ctcctcgctgcacttggaccAtgtcagcggagtgggatcgt	13	12	1	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr5:33649699A>G	ENST00000504830.1	-	8	1629	c.1294T>C	c.(1294-1296)Tgg>Cgg	p.W432R	ADAMTS12_ENST00000504582.1_5'UTR|ADAMTS12_ENST00000352040.3_Missense_Mutation_p.W432R	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	432	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						CACTTGGACCATGTCAGCGGA	0.537										HNSCC(64;0.19)																											p.W432R		Atlas-SNP	.											.	ADAMTS12	464	.	0			c.T1294C						.						161	135	144					5																	33649699		2203	4300	6503	SO:0001583	missense	81792	exon8			TGGACCATGTCAG	AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"ADAM metallopeptidases with thrombospondin type 1 motif"	14605	protein-coding gene	gene with protein product		606184	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.1294T>C	chr5.hg19:g.33649699A>G	ENSP00000422554:p.Trp432Arg	30.0	0.0		46.0	14.0	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	hg19	CCDS34140.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.028153	0.75390	.	.	ENSG00000151388	ENST00000504830;ENST00000352040	T;T	0.10477	2.87;2.87	5.73	5.73	0.89815	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.85682	D	0.000000	T	0.49932	0.1586	H	0.97491	4.015	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.69049	-0.5248	10	0.87932	D	0	.	16.024	0.80528	1.0:0.0:0.0:0.0	.	432;432	P58397-3;P58397	.;ATS12_HUMAN	R	432	ENSP00000422554:W432R;ENSP00000344847:W432R	ENSP00000344847:W432R	W	-	1	0	ADAMTS12	33685456	1.000000	0.71417	0.972000	0.41901	0.509000	0.34042	9.197000	0.94985	2.190000	0.69967	0.448000	0.29417	TGG	.	.		0.537	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		G	33649699	A	G	33649699	3	3	333	1	0	0	0	0	1	0	0	0	257	217	8	2	3558	2	ADAMTS12	5	33649699	Missense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10		33649699	147265561	63	46405										
OXCT1	5019	hgsc.bcm.edu	37	chr5	41739504	41739504	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	atacttactgcaaaatcacaCccagtactcttctgtacgtc	4	13	3	0	rs560172270	byFrequency	TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr5:41739504C>G	ENST00000196371.5	-	16	1669	c.1509G>C	c.(1507-1509)ggG>ggC	p.G503G	OXCT1_ENST00000509987.1_Silent_p.G317G|OXCT1_ENST00000510634.1_Silent_p.G106G|OXCT1_ENST00000512084.1_Silent_p.G106G	NM_000436.3	NP_000427.1	P55809	SCOT1_HUMAN	3-oxoacid CoA transferase 1	503					adipose tissue development (GO:0060612)|brain development (GO:0007420)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|cellular response to acid chemical (GO:0071229)|cellular response to glucose stimulus (GO:0071333)|heart development (GO:0007507)|ketone body catabolic process (GO:0046952)|ketone catabolic process (GO:0042182)|positive regulation of insulin secretion (GO:0032024)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to hormone (GO:0009725)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	3-oxoacid CoA-transferase activity (GO:0008260)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(2)	28					Succinic acid(DB00139)	CAAAATCACACCCAGTACTCT	0.423																																					p.G503G		Atlas-SNP	.											OXCT1,NS,carcinoma,0,1	OXCT1	54	.	0			c.G1509C						.						143	129	134					5																	41739504		2203	4300	6503	SO:0001819	synonymous_variant	5019	exon16			ATCACACCCAGTA	U62961	CCDS3937.1	5p13	2008-02-05		2004-05-12	ENSG00000083720	ENSG00000083720			8527	protein-coding gene	gene with protein product		601424	"3-oxoacid CoA transferase"	OXCT		8751852	Standard	NM_000436		Approved	SCOT	uc003jmn.3	P55809	OTTHUMG00000094783	ENST00000196371.5:c.1509G>C	chr5.hg19:g.41739504C>G		123.0	0.0		128.0	52.0	NM_000436	B2R5V2|B7Z528	Silent	SNP	ENST00000196371.5	hg19	CCDS3937.1																																																																																			.	.		0.423	OXCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211594.2	NM_000436		G	41739504	C	G	41739504	2	3	333	1	0	0	0	0	0	0	0	1	11338	494	18	4		4	OXCT1	5	41739504	Silent	SNP	C	TCGA-RC-A6M4-01A-11D-A32G-10	8089805	41739504	139175756	64	46406										
IL31RA	133396	hgsc.bcm.edu	37	chr5	55178923	55178923	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gaaaccagttttgggcatcaAacgaatgattcaaattgaat	8	6	2	2	rs541486912		TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr5:55178923A>T	ENST00000447346.2	+	5	571	c.506A>T	c.(505-507)aAa>aTa	p.K169I	IL31RA_ENST00000297015.3_Missense_Mutation_p.K27I|IL31RA_ENST00000490985.1_Missense_Mutation_p.K27I|IL31RA_ENST00000396836.2_Missense_Mutation_p.K169I|IL31RA_ENST00000359040.5_Missense_Mutation_p.K169I|IL31RA_ENST00000396834.1_Missense_Mutation_p.K150I|IL31RA_ENST00000354961.4_Missense_Mutation_p.K150I	NM_001242636.1|NM_139017.5	NP_001229565.1|NP_620586.3	Q8NI17	IL31R_HUMAN	interleukin 31 receptor A	137	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|homeostatic process (GO:0042592)|JAK-STAT cascade (GO:0007259)|macrophage differentiation (GO:0030225)|MAPK cascade (GO:0000165)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of macrophage activation (GO:0043031)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cytokine binding (GO:0019955)|cytokine receptor activity (GO:0004896)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)	21		Lung NSC(810;6.93e-05)|Prostate(74;0.00741)|Breast(144;0.0544)|Ovarian(174;0.223)				TTGGGCATCAAACGAATGATT	0.373																																					p.K169I		Atlas-SNP	.											.	IL31RA	84	.	0			c.A506T						.						103	100	101					5																	55178923		2203	4300	6503	SO:0001583	missense	133396	exon5			GCATCAAACGAAT	AY499339	CCDS3970.2, CCDS56365.1, CCDS56366.1, CCDS56367.1, CCDS75244.1, CCDS75245.1	5q11.2	2013-02-11			ENSG00000164509	ENSG00000164509		"Interleukins and interleukin receptors", "Fibronectin type III domain containing"	18969	protein-coding gene	gene with protein product		609510				15184896, 11877449	Standard	NM_139017		Approved	CRL3, GLM-R, CRL, Glmr, IL-31RA	uc003jql.3	Q8NI17	OTTHUMG00000097045	ENST00000447346.2:c.506A>T	chr5.hg19:g.55178923A>T	ENSP00000415900:p.Lys169Ile	122.0	0.0		114.0	54.0	NM_001242637	A6NIF8|Q2TBA1|Q6EBC3|Q6EBC4|Q6EBC5|Q6EBC6|Q6UWL8|Q8WYJ0	Missense_Mutation	SNP	ENST00000447346.2	hg19	CCDS3970.2	.	.	.	.	.	.	.	.	.	.	A	17.45	3.392720	0.62066	.	.	ENSG00000164509	ENST00000396836;ENST00000396834;ENST00000447346;ENST00000359040;ENST00000297015;ENST00000490985;ENST00000354961	T;T;T;T;T;T;T	0.57907	0.37;0.37;0.37;0.37;0.37;0.37;0.37	5.63	3.17	0.36434	Fibronectin, type III (4);Immunoglobulin-like fold (1);	2.131810	0.02452	N	0.085668	T	0.69251	0.3090	M	0.62723	1.935	0.09310	N	1	D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0	D;D;D;D;D	0.76575	0.987;0.983;0.964;0.977;0.988	T	0.24977	-1.0145	10	0.40728	T	0.16	-18.0797	5.6216	0.17459	0.7389:0.1726:0.0885:0.0	.	137;169;150;169;169	Q8NI17;Q8NI17-5;Q8NI17-3;Q8NI17-2;Q8NI17-8	IL31R_HUMAN;.;.;.;.	I	169;150;169;169;27;27;150	ENSP00000380048:K169I;ENSP00000380046:K150I;ENSP00000415900:K169I;ENSP00000351935:K169I;ENSP00000297015:K27I;ENSP00000427533:K27I;ENSP00000347047:K150I	ENSP00000297015:K27I	K	+	2	0	IL31RA	55214680	0.006000	0.16342	0.024000	0.17045	0.202000	0.24057	1.426000	0.34870	0.387000	0.25024	0.528000	0.53228	AAA	.	.		0.373	IL31RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214148.1	NM_139017		T	55178923	A	T	55178923	3	4	333	1	0	0	0	0	1	0	0	0	7700	14	1	4	524	4	IL31RA	5	55178923	Missense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	13439419	55178923	125736337	65	46407										
VCAN	1462	hgsc.bcm.edu	37	chr5	82816442	82816442	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tggaggaagactttacagcaActccaggtactacaaaatat	8	8	0	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr5:82816442A>T	ENST00000265077.3	+	7	2882	c.2317A>T	c.(2317-2319)Act>Tct	p.T773S	VCAN_ENST00000343200.5_Intron|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000342785.4_Missense_Mutation_p.T773S|VCAN_ENST00000512590.2_Missense_Mutation_p.T725S	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	773	GAG-alpha (glucosaminoglycan attachment domain).				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	CTTTACAGCAACTCCAGGTAC	0.383																																					p.T773S		Atlas-SNP	.											.	VCAN	498	.	0			c.A2317T						.						67	65	66					5																	82816442		2203	4300	6503	SO:0001583	missense	1462	exon7			ACAGCAACTCCAG	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.2317A>T	chr5.hg19:g.82816442A>T	ENSP00000265077:p.Thr773Ser	45.0	0.0		53.0	27.0	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	hg19	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	A	9.190	1.025765	0.19512	.	.	ENSG00000038427	ENST00000265077;ENST00000342785;ENST00000512590	T;T;T	0.20598	2.06;2.06;2.06	5.0	-2.59	0.06209	.	0.935039	0.08961	N	0.868753	T	0.10078	0.0247	N	0.19112	0.55	0.09310	N	1	B;B	0.27498	0.081;0.18	B;B	0.23419	0.046;0.03	T	0.38457	-0.9660	10	0.17832	T	0.49	.	5.7186	0.17974	0.2775:0.4503:0.2722:0.0	.	773;773	P13611-3;P13611	.;CSPG2_HUMAN	S	773;773;725	ENSP00000265077:T773S;ENSP00000342768:T773S;ENSP00000425959:T725S	ENSP00000265077:T773S	T	+	1	0	VCAN	82852198	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-0.179000	0.09768	-0.320000	0.08640	-0.456000	0.05471	ACT	.	.		0.383	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		T	82816442	A	T	82816442	3	4	333	1	0	0	0	0	1	0	0	0	17153	43	2	4	2339	4	VCAN	5	82816442	Missense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	27637519	82816442	98098818	66	46408										
PCDHA6	56142	hgsc.bcm.edu	37	chr5	140209357	140209357	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tcgtgctggacgagaacgacAacgcgccggcgctgctggcg	16	13	0	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr5:140209357A>T	ENST00000529310.1	+	1	1795	c.1681A>T	c.(1681-1683)Aac>Tac	p.N561Y	PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000527624.1_Intron	NM_018909.2|NM_031848.2|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6	561	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(42)|prostate(8)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	89			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGAGAACGACAACGCGCCGGC	0.687																																					p.N561Y		Atlas-SNP	.											.	PCDHA6	442	.	0			c.A1681T						.						70	76	74					5																	140209357		2202	4298	6500	SO:0001583	missense	56142	exon1			AACGACAACGCGC	AF152484	CCDS47281.1, CCDS47282.1	5q31	2010-11-26			ENSG00000081842	ENSG00000081842		"Cadherins / Protocadherins : Clustered"	8672	other	complex locus constituent	"KIAA0345-like 8"	606312		CNRS2		10380929, 10662547	Standard	NM_018909		Approved	CNR2, CRNR2, PCDH-ALPHA6		Q9UN73	OTTHUMG00000163353	ENST00000529310.1:c.1681A>T	chr5.hg19:g.140209357A>T	ENSP00000433378:p.Asn561Tyr	51.0	0.0		56.0	26.0	NM_018909	O75283|Q9NRT8	Missense_Mutation	SNP	ENST00000529310.1	hg19	CCDS47281.1	.	.	.	.	.	.	.	.	.	.	A	12.75	2.031176	0.35797	.	.	ENSG00000081842	ENST00000529310	T	0.53423	0.62	3.83	2.61	0.31194	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	0.000000	0.39687	U	0.001288	T	0.75376	0.3841	H	0.95950	3.745	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.99;0.996	T	0.79531	-0.1765	10	0.87932	D	0	.	10.3547	0.43956	0.8344:0.1656:0.0:0.0	.	561;561	Q9UN73-3;Q9UN73	.;PCDA6_HUMAN	Y	561	ENSP00000433378:N561Y	ENSP00000433378:N561Y	N	+	1	0	PCDHA6	140189541	1.000000	0.71417	1.000000	0.80357	0.133000	0.20885	2.455000	0.44988	0.605000	0.29947	0.254000	0.18369	AAC	.	.		0.687	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372829.3	NM_018909		T	140209357	A	T	140209357	3	4	333	1	0	0	0	0	1	0	0	0	11537	130	5	4	1683	4	PCDHA6	5	140209357	Missense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	57392915	140209357	40705903	67	46409										
PCDHB6	56130	hgsc.bcm.edu	37	chr5	140531345	140531345	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tgcccctctcttccctggtcTccatcaacgcggacaacggc	8	18	3	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr5:140531345T>A	ENST00000231136.1	+	1	1507	c.1507T>A	c.(1507-1509)Tcc>Acc	p.S503T	PCDHB6_ENST00000543635.1_Missense_Mutation_p.S367T	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	503	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TTCCCTGGTCTCCATCAACGC	0.662																																					p.S503T		Atlas-SNP	.											.	PCDHB6	161	.	0			c.T1507A						.						78	84	82					5																	140531345		2202	4297	6499	SO:0001583	missense	56130	exon1			CTGGTCTCCATCA	AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"Cadherins / Protocadherins : Clustered"	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.1507T>A	chr5.hg19:g.140531345T>A	ENSP00000231136:p.Ser503Thr	36.0	0.0		42.0	14.0	NM_018939	B2R8R9	Missense_Mutation	SNP	ENST00000231136.1	hg19	CCDS4248.1	.	.	.	.	.	.	.	.	.	.	T	16.53	3.149925	0.57151	.	.	ENSG00000113211	ENST00000543635;ENST00000231136;ENST00000542861	T;T	0.50001	0.76;0.76	4.07	4.07	0.47477	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.64494	0.2603	L	0.58810	1.83	0.31071	N	0.713014	D	0.89917	1.0	D	0.91635	0.999	T	0.67703	-0.5602	9	0.87932	D	0	.	13.4001	0.60879	0.0:0.0:0.0:1.0	.	503	Q9Y5E3	PCDB6_HUMAN	T	367;503;288	ENSP00000438466:S367T;ENSP00000231136:S503T	ENSP00000231136:S503T	S	+	1	0	PCDHB6	140511529	0.000000	0.05858	0.971000	0.41717	0.527000	0.34593	0.418000	0.21230	1.617000	0.50277	0.454000	0.30748	TCC	.	.		0.662	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939		A	140531345	T	A	140531345	3	1	333	1	0	0	0	0	1	0	0	0	11555	1551	54	4	1509	4	PCDHB6	5	140531345	Missense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	321988	140531345	40383915	68	46410										
AFAP1L1	134265	hgsc.bcm.edu	37	chr5	148687115	148687115	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gatatgtgccttcctgctgcGgaaaaagcgtttcgggcagt	13	9	0	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr5:148687115G>C	ENST00000296721.4	+	7	784	c.686G>C	c.(685-687)cGg>cCg	p.R229P	AFAP1L1_ENST00000522492.1_3'UTR|AFAP1L1_ENST00000515000.1_Missense_Mutation_p.R229P	NM_001146337.1|NM_152406.2	NP_001139809.1|NP_689619.1	Q8TED9	AF1L1_HUMAN	actin filament associated protein 1-like 1	229	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.					cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(10)|ovary(1)|pancreas(1)|skin(2)	26			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCCTGCTGCGGAAAAAGCGT	0.627																																					p.R229P		Atlas-SNP	.											.	AFAP1L1	86	.	0			c.G686C						.						72	59	64					5																	148687115		2203	4300	6503	SO:0001583	missense	134265	exon7			TGCTGCGGAAAAA	AK094067	CCDS34274.1, CCDS54932.1	5q33.1	2013-01-10			ENSG00000157510	ENSG00000157510		"Pleckstrin homology (PH) domain containing"	26714	protein-coding gene	gene with protein product		614410					Standard	NM_152406		Approved	FLJ36748	uc003lqh.3	Q8TED9	OTTHUMG00000163441	ENST00000296721.4:c.686G>C	chr5.hg19:g.148687115G>C	ENSP00000296721:p.Arg229Pro	45.0	0.0		56.0	23.0	NM_001146337	Q08AN4|Q08AN5|Q8IW82|Q8N8Z5|Q8N9Q4	Missense_Mutation	SNP	ENST00000296721.4	hg19	CCDS34274.1	.	.	.	.	.	.	.	.	.	.	G	31	5.067216	0.93898	.	.	ENSG00000157510	ENST00000296721;ENST00000515000	T;T	0.13538	2.58;2.58	4.89	4.89	0.63831	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.053504	0.64402	D	0.000001	T	0.44159	0.1280	M	0.85197	2.74	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.997	D;D;P	0.83275	0.996;0.992;0.899	T	0.51020	-0.8758	10	0.87932	D	0	-28.754	18.243	0.89974	0.0:0.0:1.0:0.0	.	229;229;229	Q8TED9-2;Q8TED9;Q8TED9-3	.;AF1L1_HUMAN;.	P	229	ENSP00000296721:R229P;ENSP00000424427:R229P	ENSP00000296721:R229P	R	+	2	0	AFAP1L1	148667308	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.657000	0.98554	2.543000	0.85770	0.561000	0.74099	CGG	.	.		0.627	AFAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373443.1	NM_152406		C	148687115	G	C	148687115	3	2	333	1	0	0	0	0	1	0	0	0	354	1116	39	4	712	4	AFAP1L1	5	148687115	Missense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	8155770	148687115	32228145	69	46411										
PDE6A	5145	hgsc.bcm.edu	37	chr5	149314265	149314265	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ctgtgaggatgtccacaaagTcacagaaatgctcatcctaa	8	10	2	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr5:149314265T>C	ENST00000255266.5	-	2	610	c.491A>G	c.(490-492)gAc>gGc	p.D164G		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	164	GAF 1.				cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	44			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Caffeine(DB00201)	GTCCACAAAGTCACAGAAATG	0.473																																					p.D164G		Atlas-SNP	.											.	PDE6A	98	.	0			c.A491G						.						112	97	102					5																	149314265		2203	4300	6503	SO:0001583	missense	5145	exon2			ACAAAGTCACAGA		CCDS4299.1	5q31.2-q34	2013-02-14			ENSG00000132915	ENSG00000132915	3.1.4.17	"Phosphodiesterases"	8785	protein-coding gene	gene with protein product		180071		PDEA		2155175	Standard	NM_000440		Approved	RP43	uc003lrg.4	P16499	OTTHUMG00000130047	ENST00000255266.5:c.491A>G	chr5.hg19:g.149314265T>C	ENSP00000255266:p.Asp164Gly	66.0	0.0		68.0	30.0	NM_000440	Q0P638	Missense_Mutation	SNP	ENST00000255266.5	hg19	CCDS4299.1	.	.	.	.	.	.	.	.	.	.	T	13.54	2.268470	0.40095	.	.	ENSG00000132915	ENST00000255266	T	0.67171	-0.25	5.99	5.99	0.97316	GAF (2);	0.109283	0.64402	D	0.000012	T	0.60431	0.2268	L	0.43757	1.38	0.38794	D	0.955057	B	0.14012	0.009	B	0.23852	0.049	T	0.57458	-0.7808	10	0.27785	T	0.31	.	14.4463	0.67352	0.0:0.0:0.0:1.0	.	164	P16499	PDE6A_HUMAN	G	164	ENSP00000255266:D164G	ENSP00000255266:D164G	D	-	2	0	PDE6A	149294458	0.946000	0.32159	1.000000	0.80357	0.970000	0.65996	0.982000	0.29539	2.291000	0.77112	0.533000	0.62120	GAC	.	.		0.473	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2			C	149314265	T	C	149314265	3	2	333	1	0	0	0	0	1	0	0	0	11654	1667	58	2	2175	2	PDE6A	5	149314265	Missense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	627150	149314265	31600995	70	46412										
SLC36A2	153201	hgsc.bcm.edu	37	chr5	150701730	150701730	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gtagaactgcagggcataggTgcacaggatgccggcaatgt	15	8	0	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr5:150701730T>A	ENST00000335244.4	-	9	1186	c.1057A>T	c.(1057-1059)Acc>Tcc	p.T353S	SLC36A2_ENST00000450886.1_Missense_Mutation_p.T77S|SLC36A2_ENST00000521967.1_Missense_Mutation_p.T353S	NM_181776.2	NP_861441.2	Q495M3	S36A2_HUMAN	solute carrier family 36 (proton/amino acid symporter), member 2	353					amino acid transport (GO:0006865)|ion transport (GO:0006811)|proline transmembrane transport (GO:0035524)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine transmembrane transporter activity (GO:0015187)|hydrogen:amino acid symporter activity (GO:0005280)|L-alanine transmembrane transporter activity (GO:0015180)|L-proline transmembrane transporter activity (GO:0015193)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(14)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Cycloserine(DB00260)	AGGGCATAGGTGCACAGGATG	0.562																																					p.T353S		Atlas-SNP	.											.	SLC36A2	71	.	0			c.A1057T						.						139	124	129					5																	150701730		2203	4300	6503	SO:0001583	missense	153201	exon9			CATAGGTGCACAG	AY162214	CCDS4315.1	5q33.1	2013-05-22			ENSG00000186335	ENSG00000186335		"Solute carriers"	18762	protein-coding gene	gene with protein product		608331				11959859	Standard	NM_181776		Approved	PAT2, tramdorin, TRAMD1	uc003lty.3	Q495M3	OTTHUMG00000130129	ENST00000335244.4:c.1057A>T	chr5.hg19:g.150701730T>A	ENSP00000334223:p.Thr353Ser	49.0	0.0		63.0	26.0	NM_181776	Q495M4|Q495M6|Q6ZWK5|Q7Z6B5	Missense_Mutation	SNP	ENST00000335244.4	hg19	CCDS4315.1	.	.	.	.	.	.	.	.	.	.	T	14.94	2.685269	0.47991	.	.	ENSG00000186335	ENST00000335244;ENST00000450886;ENST00000521967	T;T;T	0.02067	4.47;4.47;4.47	4.76	2.2	0.27929	.	0.265519	0.42172	N	0.000756	T	0.02230	0.0069	L	0.31294	0.92	0.42132	D	0.991476	B;B	0.27823	0.09;0.19	B;B	0.34590	0.186;0.186	T	0.55598	-0.8116	10	0.14656	T	0.56	-36.0228	9.9267	0.41496	0.2718:0.0:0.0:0.7282	.	353;353	E5RJJ5;Q495M3	.;S36A2_HUMAN	S	353;77;353	ENSP00000334223:T353S;ENSP00000399479:T77S;ENSP00000430535:T353S	ENSP00000334223:T353S	T	-	1	0	SLC36A2	150681923	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.757000	0.55212	0.343000	0.23821	0.460000	0.39030	ACC	.	.		0.562	SLC36A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252437.1			A	150701730	T	A	150701730	3	1	333	1	0	0	0	0	1	0	0	0	14609	1696	59	4	402	4	SLC36A2	5	150701730	Missense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	1387465	150701730	30213530	71	46413										
ZNF391	346157	hgsc.bcm.edu	37	chr6	27368962	27368962	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	actgaacatcagagaacacaCactggggagaacccctatga	9	11	1	4			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr6:27368962C>G	ENST00000244576.4	+	3	1358	c.813C>G	c.(811-813)caC>caG	p.H271Q	RP1-153G14.4_ENST00000607727.1_lincRNA	NM_001076781.1	NP_001070249.1	Q9UJN7	ZN391_HUMAN	zinc finger protein 391	271					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|large_intestine(6)|lung(7)|pancreas(2)|skin(3)|upper_aerodigestive_tract(1)	21						AGAGAACACACACTGGGGAGA	0.453																																					p.H271Q		Atlas-SNP	.											.	ZNF391	90	.	0			c.C813G						.						64	72	69					6																	27368962		2194	4296	6490	SO:0001583	missense	346157	exon3			AACACACACTGGG	BC132797	CCDS43429.1	6p21	2013-01-08			ENSG00000124613	ENSG00000124613		"Zinc fingers, C2H2-type"	18779	protein-coding gene	gene with protein product							Standard	NM_001076781		Approved	dJ153G14.3	uc003njf.1	Q9UJN7	OTTHUMG00000014477	ENST00000244576.4:c.813C>G	chr6.hg19:g.27368962C>G	ENSP00000244576:p.His271Gln	86.0	0.0		118.0	38.0	NM_001076781	B4DH77	Missense_Mutation	SNP	ENST00000244576.4	hg19	CCDS43429.1	.	.	.	.	.	.	.	.	.	.	C	17.06	3.292190	0.59976	.	.	ENSG00000124613	ENST00000244576	T	0.66995	-0.24	4.0	0.541	0.17168	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.73528	0.3598	M	0.87038	2.855	0.30623	N	0.758269	D	0.89917	1.0	D	0.91635	0.999	T	0.66110	-0.6005	9	0.87932	D	0	.	8.3667	0.32391	0.0:0.6513:0.0:0.3487	.	271	Q9UJN7	ZN391_HUMAN	Q	271	ENSP00000244576:H271Q	ENSP00000244576:H271Q	H	+	3	2	ZNF391	27476941	1.000000	0.71417	0.006000	0.13384	0.976000	0.68499	2.237000	0.43061	0.177000	0.19895	0.557000	0.71058	CAC	.	.		0.453	ZNF391-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040145.2	NM_001076781		G	27368962	C	G	27368962	3	3	333	1	0	0	0	0	1	0	0	0	17894	477	17	4	815	4	ZNF391	6	27368962	Missense_Mutation	SNP	C	TCGA-RC-A6M4-01A-11D-A32G-10		27368962	143746105	72	46414										
TRIM31	11074	hgsc.bcm.edu	37	chr6	30080321	30080321	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tgtagcctctttccttttggActgcacctcagaggcttgta	9	11	2	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr6:30080321A>G	ENST00000376734.3	-	2	387	c.262T>C	c.(262-264)Tcc>Ccc	p.S88P	TRIM31_ENST00000485864.1_5'Flank|TRIM31-AS1_ENST00000440874.1_RNA|TRIM31_ENST00000540829.1_Missense_Mutation_p.S88P	NM_007028.3	NP_008959.3	Q9BZY9	TRI31_HUMAN	tripartite motif containing 31	88					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral release from host cell (GO:1902186)	mitochondrion (GO:0005739)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(2)	15						TTCCTTTTGGACTGCACCTCA	0.493																																					p.S88P		Atlas-SNP	.											.	TRIM31	40	.	0			c.T262C						.						136	129	132					6																	30080321		1511	2708	4219	SO:0001583	missense	11074	exon2			TTTTGGACTGCAC	AF230386	CCDS34374.1	6p21.3	2013-01-09	2011-01-25		ENSG00000204616	ENSG00000204616		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16289	protein-coding gene	gene with protein product		609316	"tripartite motif-containing 31"			11331580	Standard	XM_006714977		Approved	RNF, HCGI, C6orf13, HCG1	uc003npg.1	Q9BZY9	OTTHUMG00000031064	ENST00000376734.3:c.262T>C	chr6.hg19:g.30080321A>G	ENSP00000365924:p.Ser88Pro	85.0	0.0		126.0	35.0	NM_007028	A6NLX6|A9R9Q4|Q53H52|Q5RI37|Q5SRJ7|Q5SRJ8|Q5SS28|Q96AK4|Q96AP8|Q99579|Q9BZY8	Missense_Mutation	SNP	ENST00000376734.3	hg19	CCDS34374.1	.	.	.	.	.	.	.	.	.	.	A	4.948	0.176188	0.09443	.	.	ENSG00000204616	ENST00000376734;ENST00000376728;ENST00000540829	T;T	0.57595	0.39;0.39	3.55	-1.12	0.09808	Zinc finger, RING/FYVE/PHD-type (1);	0.797101	0.10257	N	0.696386	T	0.10294	0.0252	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.35798	-0.9774	10	0.20046	T	0.44	.	7.8249	0.29309	0.1057:0.4531:0.4412:0.0	.	88	Q9BZY9	TRI31_HUMAN	P	88	ENSP00000365924:S88P;ENSP00000444311:S88P	ENSP00000365918:S88P	S	-	1	0	TRIM31	30188300	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.313000	0.08103	-0.049000	0.13379	-0.384000	0.06662	TCC	.	.		0.493	TRIM31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076081.2			G	30080321	A	G	30080321	3	3	333	1	0	0	0	0	1	0	0	0	16520	275	10	2	1047	2	TRIM31	6	30080321	Missense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	2711359	30080321	141034746	73	46415										
NOTCH4	4855	hgsc.bcm.edu	37	chr6	32170085	32170085	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tctgccctcacaccccttggCtccgggtttctgacaccggg	10	17	3	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr6:32170085C>A	ENST00000375023.3	-	21	3661	c.3523G>T	c.(3523-3525)Gcc>Tcc	p.A1175S		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	1175					cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						CACCCCTTGGCTCCGGGTTTC	0.652																																					p.A1175S		Atlas-SNP	.											NOTCH4,NS,carcinoma,0,1	NOTCH4	201	.	0			c.G3523T						.						22	24	23					6																	32170085		1509	2707	4216	SO:0001583	missense	4855	exon21			CCTTGGCTCCGGG		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"Ankyrin repeat domain containing"	7884	protein-coding gene	gene with protein product		164951	"Notch (Drosophila) homolog 4", "Notch homolog 4 (Drosophila)"	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.3523G>T	chr6.hg19:g.32170085C>A	ENSP00000364163:p.Ala1175Ser	42.0	0.0		60.0	21.0	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Missense_Mutation	SNP	ENST00000375023.3	hg19	CCDS34420.1	.	.	.	.	.	.	.	.	.	.	C	7.254	0.603913	0.14002	.	.	ENSG00000204301	ENST00000375023	D	0.91843	-2.92	4.77	3.9	0.45041	Notch domain (3);	0.153666	0.30383	N	0.009745	T	0.76307	0.3969	N	0.17082	0.46	0.09310	N	1	B	0.29955	0.263	P	0.45099	0.469	T	0.69131	-0.5226	10	0.06757	T	0.87	.	7.1342	0.25519	0.0:0.8014:0.0:0.1986	.	1175	Q99466	NOTC4_HUMAN	S	1175	ENSP00000364163:A1175S	ENSP00000364163:A1175S	A	-	1	0	NOTCH4	32278063	0.001000	0.12720	0.013000	0.15412	0.143000	0.21401	0.379000	0.20585	1.229000	0.43630	0.561000	0.74099	GCC	.	.		0.652	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2			A	32170085	C	A	32170085	3	1	333	1	0	0	0	0	1	0	0	0	10560	797	28	3	2528	3	NOTCH4	6	32170085	Missense_Mutation	SNP	C	TCGA-RC-A6M4-01A-11D-A32G-10	2089764	32170085	138944982	74	46416										
DNAH8	1769	hgsc.bcm.edu	37	chr6	38802359	38802359	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	atattcttccttacaggaagGacctatggttccaaatatac	6	9	1	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr6:38802359G>A	ENST00000359357.3	+	30	3910	c.3656G>A	c.(3655-3657)gGa>gAa	p.G1219E	DNAH8_ENST00000441566.1_Missense_Mutation_p.G1219E|DNAH8_ENST00000449981.2_Missense_Mutation_p.G1436E			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	1219					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						TTACAGGAAGGACCTATGGTT	0.323																																					p.G1436E		Atlas-SNP	.											.	DNAH8	1239	.	0			c.G4307A						.						115	117	117					6																	38802359		2203	4299	6502	SO:0001583	missense	1769	exon32			AGGAAGGACCTAT	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.3656G>A	chr6.hg19:g.38802359G>A	ENSP00000352312:p.Gly1219Glu	177.0	0.0		256.0	70.0	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	hg19		.	.	.	.	.	.	.	.	.	.	G	24.8	4.572165	0.86542	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.26660	1.78;1.78;1.72	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	T	0.55178	0.1904	M	0.90425	3.115	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.62891	-0.6758	10	0.59425	D	0.04	.	19.8002	0.96504	0.0:0.0:1.0:0.0	.	1219	Q96JB1	DYH8_HUMAN	E	1424;1424;1219;1219	ENSP00000333363:G1424E;ENSP00000352312:G1219E;ENSP00000402294:G1219E	ENSP00000333363:G1424E	G	+	2	0	DNAH8	38910337	1.000000	0.71417	1.000000	0.80357	0.757000	0.42996	9.213000	0.95133	2.674000	0.91012	0.655000	0.94253	GGA	.	.		0.323	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		A	38802359	G	A	38802359	3	1	333	1	0	0	0	0	1	0	0	0	4609	1174	41	3	3766	3	DNAH8	6	38802359	Missense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	6632274	38802359	132312708	75	46417										
ABCC10	89845	hgsc.bcm.edu	37	chr6	43402429	43402429	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ggagcaggcactgggagcccGagtagaggcctgccgggctc	18	12	0	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr6:43402429G>T	ENST00000372530.4	+	4	1666	c.1451G>T	c.(1450-1452)cGa>cTa	p.R484L	ABCC10_ENST00000443426.2_3'UTR|ABCC10_ENST00000244533.3_Missense_Mutation_p.R441L	NM_001198934.1	NP_001185863.1	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	484	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(8)|lung(21)|ovary(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)		Cyclosporine(DB00091)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Estradiol(DB00783)|Etoposide(DB00773)|Gemcitabine(DB00441)|Methotrexate(DB00563)|Paclitaxel(DB01229)|Sildenafil(DB00203)|Tenofovir(DB00300)|Verapamil(DB00661)|Vincristine(DB00541)	CTGGGAGCCCGAGTAGAGGCC	0.612																																					p.R484L		Atlas-SNP	.											.	ABCC10	118	.	0			c.G1451T						.						91	100	97					6																	43402429		2203	4300	6503	SO:0001583	missense	89845	exon4			GAGCCCGAGTAGA	U66684	CCDS4896.1, CCDS56430.1	6p12.3	2012-03-14			ENSG00000124574	ENSG00000124574		"ATP binding cassette transporters / subfamily C"	52	protein-coding gene	gene with protein product		612509				8894702	Standard	NM_033450		Approved	EST182763, MRP7, SIMRP7	uc003ouy.1	Q5T3U5	OTTHUMG00000014733	ENST00000372530.4:c.1451G>T	chr6.hg19:g.43402429G>T	ENSP00000361608:p.Arg484Leu	53.0	0.0		103.0	29.0	NM_001198934	Q8NHX7|Q9H7N2|Q9NXY3|Q9UF48	Missense_Mutation	SNP	ENST00000372530.4	hg19	CCDS56430.1	.	.	.	.	.	.	.	.	.	.	G	18.39	3.613558	0.66672	.	.	ENSG00000124574	ENST00000372515;ENST00000372530;ENST00000244533	D;D;D	0.90955	-2.76;-2.76;-2.76	5.93	5.07	0.68467	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.063358	0.64402	D	0.000009	D	0.85750	0.5769	L	0.55103	1.725	0.39852	D	0.973255	B;P	0.48503	0.257;0.911	B;P	0.48840	0.313;0.592	D	0.83983	0.0333	10	0.22706	T	0.39	-29.659	11.9694	0.53055	0.1379:0.0:0.8621:0.0	.	441;484	Q5T3U5-2;Q5T3U5	.;MRP7_HUMAN	L	40;484;441	ENSP00000361593:R40L;ENSP00000361608:R484L;ENSP00000244533:R441L	ENSP00000244533:R441L	R	+	2	0	ABCC10	43510407	1.000000	0.71417	0.901000	0.35422	0.959000	0.62525	5.277000	0.65586	1.529000	0.49120	0.655000	0.94253	CGA	.	.		0.612	ABCC10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040603.2	NM_033450		T	43402429	G	T	43402429	3	4	333	1	0	0	0	0	1	0	0	0	50	1058	37	1	1328	1	ABCC10	6	43402429	Missense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	4600070	43402429	127712638	76	46418										
TMEM63B	55362	hgsc.bcm.edu	37	chr6	44116103	44116103	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tggcctttgtcaccttccacAatgagactatcaccgccatg	7	14	2	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr6:44116103A>G	ENST00000259746.9	+	13	1285	c.1102A>G	c.(1102-1104)Aat>Gat	p.N368D	TMEM63B_ENST00000323267.6_Missense_Mutation_p.N368D			Q5T3F8	CSCL2_HUMAN	transmembrane protein 63B	368					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	nucleotide binding (GO:0000166)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(2)|prostate(2)|stomach(4)	35	all_cancers(18;1.66e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00309)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0215)			CACCTTCCACAATGAGACTAT	0.577																																					p.N368D		Atlas-SNP	.											.	TMEM63B	77	.	0			c.A1102G						.						119	104	109					6																	44116103		2203	4300	6503	SO:0001583	missense	55362	exon13			TTCCACAATGAGA	BC022095	CCDS34461.1	6p21.1	2008-02-05	2005-07-25	2005-07-25	ENSG00000137216	ENSG00000137216			17735	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 110"	C6orf110			Standard	XM_005249211		Approved	DKFZp434P0531, dJ421H19.2	uc003owr.3	Q5T3F8	OTTHUMG00000014757	ENST00000259746.9:c.1102A>G	chr6.hg19:g.44116103A>G	ENSP00000259746:p.Asn368Asp	25.0	0.0		63.0	12.0	NM_018426	B9EGU3|Q5T3F9|Q6AHX4|Q6P5A0|Q8N219|Q8NDE1|Q9NSG5	Missense_Mutation	SNP	ENST00000259746.9	hg19	CCDS34461.1	.	.	.	.	.	.	.	.	.	.	A	6.188	0.402775	0.11696	.	.	ENSG00000137216	ENST00000259746;ENST00000323267	T;T	0.39406	1.08;1.08	4.61	4.61	0.57282	Domain of unknown function DUF221 (1);Nucleotide-binding, alpha-beta plait (1);	0.000000	0.85682	D	0.000000	T	0.08582	0.0213	N	0.05510	-0.035	0.45284	D	0.998281	B;B	0.19583	0.008;0.037	B;B	0.20384	0.029;0.024	T	0.13737	-1.0498	10	0.02654	T	1	.	13.644	0.62270	1.0:0.0:0.0:0.0	.	368;368	Q5T3F8;Q5T3F8-2	TM63B_HUMAN;.	D	368	ENSP00000259746:N368D;ENSP00000327154:N368D	ENSP00000259746:N368D	N	+	1	0	TMEM63B	44224081	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.429000	0.59901	2.072000	0.62099	0.460000	0.39030	AAT	.	.		0.577	TMEM63B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040712.2	XM_166410		G	44116103	A	G	44116103	3	3	333	1	0	0	0	0	1	0	0	0	16206	130	5	2	1148	2	TMEM63B	6	44116103	Missense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	713674	44116103	126998964	77	46419										
RIMS1	22999	hgsc.bcm.edu	37	chr6	73102430	73102430	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	cctggagtgcgactgggagcTgacagtcaattcagtgattt	13	8	2	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr6:73102430T>A	ENST00000521978.1	+	31	4536	c.4536T>A	c.(4534-4536)gcT>gcA	p.A1512A	RIMS1_ENST00000517960.1_Silent_p.A1295A|RIMS1_ENST00000522291.1_Silent_p.A1111A|RIMS1_ENST00000518273.1_Silent_p.A1191A|RIMS1_ENST00000517827.1_Silent_p.A646A|RIMS1_ENST00000538414.1_Silent_p.A318A|RIMS1_ENST00000523963.1_Silent_p.A637A|RIMS1_ENST00000348717.5_Silent_p.A1295A|RIMS1_ENST00000431478.2_3'UTR|RIMS1_ENST00000401910.3_Silent_p.A832A|RIMS1_ENST00000425662.2_Silent_p.A580A|RIMS1_ENST00000520567.1_Silent_p.A1162A|RIMS1_ENST00000264839.7_Silent_p.A1361A|RIMS1_ENST00000491071.2_Silent_p.A1335A|RIMS1_ENST00000414192.2_Silent_p.A39A	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	1512					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				GACTGGGAGCTGACAGTCAAT	0.413																																					p.A1512A		Atlas-SNP	.											.	RIMS1	278	.	0			c.T4536A						.						97	91	93					6																	73102430		1854	4104	5958	SO:0001819	synonymous_variant	22999	exon31			GGGAGCTGACAGT	AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"Rab3-interacting molecule"	606629	"RAB3 interacting protein 2"	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.4536T>A	chr6.hg19:g.73102430T>A		126.0	0.0		72.0	64.0	NM_014989	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Silent	SNP	ENST00000521978.1	hg19	CCDS47449.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.08|12.08	1.832091|1.832091	0.32421|0.32421	.|.	.|.	ENSG00000079841|ENSG00000079841	ENST00000522211|ENST00000517433	.|.	.|.	.|.	5.5|5.5	-11.0|-11.0	0.00169|0.00169	.|.	.|.	.|.	.|.	.|.	T|.	0.16896|.	0.0406|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.41466|.	-0.9507|.	4|.	.|.	.|.	.|.	-9.6235|-9.6235	3.0007|3.0007	0.06012|0.06012	0.1311:0.1159:0.4052:0.3478|0.1311:0.1159:0.4052:0.3478	.|.	.|.	.|.	.|.	Q|R	430|858	.|.	.|.	L|X	+|+	2|1	0|0	RIMS1|RIMS1	73159151|73159151	0.734000|0.734000	0.28142|0.28142	0.660000|0.660000	0.29694|0.29694	0.990000|0.990000	0.78478|0.78478	-0.127000|-0.127000	0.10547|0.10547	-2.107000|-2.107000	0.00840|0.00840	-0.353000|-0.353000	0.07706|0.07706	CTG|TGA	.	.		0.413	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1			A	73102430	T	A	73102430	2	1	333	1	0	0	0	0	0	0	0	1	13382	1567	55	4		4	RIMS1	6	73102430	Silent	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	28986327	73102430	98012637	78	46420										
TBX18	9096	hgsc.bcm.edu	37	chr6	85446945	85446945	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	caaagatgtgctgtatcggtTgagggtgaggcctgagcggg	18	6	0	4			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr6:85446945T>A	ENST00000369663.5	-	8	1619	c.1282A>T	c.(1282-1284)Aac>Tac	p.N428Y	TBX18_ENST00000606784.1_Intron	NM_001080508.1	NP_001073977.1	O95935	TBX18_HUMAN	T-box 18	428					anterior/posterior axis specification (GO:0009948)|cochlea morphogenesis (GO:0090103)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060829)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation involved in ureter development (GO:2000729)|sensory perception of sound (GO:0007605)|sinoatrial node development (GO:0003163)|smooth muscle cell differentiation (GO:0051145)|somitogenesis (GO:0001756)|ureter development (GO:0072189)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(9)|liver(1)|lung(31)|ovary(2)|pancreas(3)|prostate(6)|skin(3)	61		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)		CTGTATCGGTTGAGGGTGAGG	0.607																																					p.N428Y		Atlas-SNP	.											.	TBX18	131	.	0			c.A1282T						.						111	100	104					6																	85446945		2203	4300	6503	SO:0001583	missense	9096	exon8			ATCGGTTGAGGGT	AJ010278	CCDS34495.1	6q14.1-q15	2012-12-19			ENSG00000112837	ENSG00000112837		"T-boxes"	11595	protein-coding gene	gene with protein product		604613				9888994, 16688725, 23242162	Standard	NM_001080508		Approved		uc003pkl.2	O95935	OTTHUMG00000015129	ENST00000369663.5:c.1282A>T	chr6.hg19:g.85446945T>A	ENSP00000358677:p.Asn428Tyr	100.0	0.0		72.0	66.0	NM_001080508	A2RU13|Q7Z6U4|Q9UJI6	Missense_Mutation	SNP	ENST00000369663.5	hg19	CCDS34495.1	.	.	.	.	.	.	.	.	.	.	T	13.12	2.142488	0.37825	.	.	ENSG00000112837	ENST00000369663	D	0.87029	-2.2	5.18	5.18	0.71444	.	.	.	.	.	T	0.71221	0.3314	N	0.24115	0.695	0.50039	D	0.999848	P	0.46656	0.882	P	0.47891	0.56	T	0.76066	-0.3095	9	0.02654	T	1	.	15.0095	0.71539	0.0:0.0:0.0:1.0	.	428	O95935	TBX18_HUMAN	Y	428	ENSP00000358677:N428Y	ENSP00000358677:N428Y	N	-	1	0	TBX18	85503664	1.000000	0.71417	1.000000	0.80357	0.413000	0.31143	5.433000	0.66520	1.950000	0.56595	0.477000	0.44152	AAC	.	.		0.607	TBX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041378.2	NM_001080508		A	85446945	T	A	85446945	3	1	333	1	0	0	0	0	1	0	0	0	15668	1812	63	4	545	4	TBX18	6	85446945	Missense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	12344515	85446945	85668122	79	46421										
THEMIS	387357	hgsc.bcm.edu	37	chr6	128134158	128134158	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ctgagctttcatatctccgcAtcatgtaatattgctcttca	5	11	5	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr6:128134158A>G	ENST00000368248.2	-	4	1776	c.1628T>C	c.(1627-1629)aTg>aCg	p.M543T	THEMIS_ENST00000543064.1_Missense_Mutation_p.M543T|THEMIS_ENST00000368250.1_Missense_Mutation_p.M464T|THEMIS_ENST00000537166.1_Missense_Mutation_p.M508T	NM_001010923.2	NP_001010923.1	Q8N1K5	THMS1_HUMAN	thymocyte selection associated	543					negative T cell selection (GO:0043383)|positive T cell selection (GO:0043368)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(3)	60						ATATCTCCGCATCATGTAATA	0.443																																					p.M543T		Atlas-SNP	.											.	THEMIS	168	.	0			c.T1628C						.						102	102	102					6																	128134158		2203	4300	6503	SO:0001583	missense	387357	exon4			CTCCGCATCATGT	AK094863	CCDS34534.1, CCDS55055.1	6q22.33	2012-02-08	2009-06-25	2009-06-25	ENSG00000172673	ENSG00000172673			21569	protein-coding gene	gene with protein product	"thymocyte expressed molecule involved in selection"	613607	"chromosome 6 open reading frame 207", "chromosome 6 open reading frame 190", "thymocyte selection pathway associated"	C6orf207, C6orf190, TSEPA		19597499, 19597498, 19597497	Standard	NM_001010923		Approved	bA325O24.4, FLJ40584, bA325O24.3	uc011ebt.2	Q8N1K5	OTTHUMG00000015534	ENST00000368248.2:c.1628T>C	chr6.hg19:g.128134158A>G	ENSP00000357231:p.Met543Thr	77.0	0.0		35.0	31.0	NM_001010923	A1L4F0|A8K7N1|B3KT31|B3KW32|B3KY07|F5H1J9|Q5T3C4|Q5T3C5|Q6MZT7	Missense_Mutation	SNP	ENST00000368248.2	hg19	CCDS34534.1	.	.	.	.	.	.	.	.	.	.	A	13.28	2.189073	0.38707	.	.	ENSG00000172673	ENST00000368250;ENST00000543064;ENST00000368248;ENST00000537166	T;T;T;T	0.18174	2.23;2.26;2.24;2.24	5.9	5.9	0.94986	.	0.385434	0.30538	N	0.009419	T	0.09555	0.0235	L	0.47716	1.5	0.39745	D	0.971807	B;B	0.32467	0.372;0.094	B;B	0.26864	0.074;0.026	T	0.02868	-1.1100	10	0.72032	D	0.01	-7.6567	16.3245	0.82970	1.0:0.0:0.0:0.0	.	543;543	F5H1J9;Q8N1K5	.;THMS1_HUMAN	T	464;543;543;508	ENSP00000357233:M464T;ENSP00000439594:M543T;ENSP00000357231:M543T;ENSP00000439863:M508T	ENSP00000357231:M543T	M	-	2	0	THEMIS	128175851	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.425000	0.80255	2.254000	0.74563	0.460000	0.39030	ATG	.	.		0.443	THEMIS-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_001010923		G	128134158	A	G	128134158	3	3	333	1	0	0	0	0	1	0	0	0	15875	217	8	2	430	2	THEMIS	6	128134158	Missense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	42687213	128134158	42980909	80	46422										
VTA1	51534	hgsc.bcm.edu	37	chr6	142468439	142468439	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gtagagatggccgcgcttgcAccgctgcccccgctccccgc	12	19	0	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr6:142468439A>G	ENST00000367630.4	+	1	73	c.15A>G	c.(13-15)gcA>gcG	p.A5A	VTA1_ENST00000452973.2_5'UTR|VTA1_ENST00000367621.1_5'UTR	NM_016485.3	NP_057569.2	Q9NP79	VTA1_HUMAN	vesicle (multivesicular body) trafficking 1	5	Interaction with CHMP5.|Interaction with IST1.				endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				endometrium(2)|large_intestine(1)|lung(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	Breast(32;0.155)			OV - Ovarian serous cystadenocarcinoma(155;1.34e-05)|GBM - Glioblastoma multiforme(68;0.00182)		CCGCGCTTGCACCGCTGCCCC	0.617											OREG0017699	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A5A		Atlas-SNP	.											.	VTA1	29	.	0			c.A15G						.						78	71	74					6																	142468439		2203	4300	6503	SO:0001819	synonymous_variant	51534	exon1			GCTTGCACCGCTG	AF060225	CCDS5197.1, CCDS69214.1, CCDS75531.1	6q24.1	2013-08-05	2013-08-05	2007-04-03	ENSG00000009844	ENSG00000009844			20954	protein-coding gene	gene with protein product		610902	"chromosome 6 open reading frame 55", "Vps20-associated 1 homolog (S. cerevisiae)"	C6orf55		11489251, 15644320	Standard	NM_001286372		Approved	HSPC228, My012	uc003qiw.3	Q9NP79	OTTHUMG00000015707	ENST00000367630.4:c.15A>G	chr6.hg19:g.142468439A>G		35.0	0.0	1671	22.0	18.0	NM_016485	B4DW55|E1P594|E7ETQ7|Q5TGM1|Q6IAE8|Q9H0R2|Q9H3K9|Q9P0Q0	Silent	SNP	ENST00000367630.4	hg19	CCDS5197.1																																																																																			.	.		0.617	VTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042483.2	NM_016485		G	142468439	A	G	142468439	2	3	333	1	0	0	0	0	0	0	0	1	17248	146	6	2		2	VTA1	6	142468439	Silent	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	14334281	142468439	28646628	81	46423										
LATS1	9113	hgsc.bcm.edu	37	chr6	150005471	150005471	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tggagggggagtctggcctcTtggaggtggtggaggagtaa	21	4	2	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr6:150005471T>A	ENST00000543571.1	-	4	1301	c.754A>T	c.(754-756)Aga>Tga	p.R252*	LATS1_ENST00000253339.5_Nonsense_Mutation_p.R252*|LATS1_ENST00000542747.1_5'UTR|LATS1_ENST00000392273.3_Nonsense_Mutation_p.R252*	NM_004690.3	NP_004681.1			large tumor suppressor kinase 1											central_nervous_system(1)|lung(5)	6		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116)		GTCTGGCCTCTTGGAGGTGGT	0.507																																					p.R252X		Atlas-SNP	.											LATS1_ENST00000543571,colon,carcinoma,+2,4	LATS1	241	.	0			c.A754T						.						161	151	155					6																	150005471		2203	4300	6503	SO:0001587	stop_gained	9113	exon4			GGCCTCTTGGAGG	AF104413	CCDS34551.1, CCDS59040.1	6q25.1	2013-04-25	2013-04-25		ENSG00000131023	ENSG00000131023			6514	protein-coding gene	gene with protein product		603473	"LATS (large tumor suppressor, Drosophila) homolog 1", "LATS, large tumor suppressor, homolog 1 (Drosophila)"			9988268, 15122335	Standard	NM_004690		Approved	WARTS	uc003qmu.2	O95835	OTTHUMG00000016437	ENST00000543571.1:c.754A>T	chr6.hg19:g.150005471T>A	ENSP00000437550:p.Arg252*	88.0	0.0		52.0	46.0	NM_001270519		Nonsense_Mutation	SNP	ENST00000543571.1	hg19	CCDS34551.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.388042	0.82902	.	.	ENSG00000131023	ENST00000543571;ENST00000253339;ENST00000392273;ENST00000458696	.	.	.	4.8	4.8	0.61643	.	0.000000	0.52532	D	0.000065	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.2988	0.49294	0.0:0.0:0.1638:0.8362	.	.	.	.	X	252;252;252;198	.	.	R	-	1	2	LATS1	150047164	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.687000	0.46976	1.780000	0.52325	0.533000	0.62120	AGA	.	.		0.507	LATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043923.4	NM_004690		A	150005471	T	A	150005471	4	1	333	1	0	0	0	0	0	1	0	0	8655	1617	56	4	2658	4	LATS1	6	150005471	Nonsense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	7537032	150005471	21109596	82	46424										
NOX3	50508	hgsc.bcm.edu	37	chr6	155774563	155774563	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ttaacagctatcccataggcGaccagtttgtgaaatctgag	9	9	1	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr6:155774563G>A	ENST00000159060.2	-	4	417	c.315C>T	c.(313-315)gtC>gtT	p.V105V		NM_015718.2	NP_056533.1	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	105	Ferric oxidoreductase.				detection of gravity (GO:0009590)|otolith development (GO:0048840)|superoxide anion generation (GO:0042554)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NADPH oxidase complex (GO:0043020)	superoxide-generating NADPH oxidase activity (GO:0016175)			cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	45		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)		TCCCATAGGCGACCAGTTTGT	0.368																																					p.V105V		Atlas-SNP	.											.	NOX3	93	.	0			c.C315T						.						261	270	267					6																	155774563		2203	4300	6503	SO:0001819	synonymous_variant	50508	exon4			ATAGGCGACCAGT	AF190122	CCDS5250.1	6q25.3	2008-05-15			ENSG00000074771	ENSG00000074771			7890	protein-coding gene	gene with protein product		607105				11376945	Standard	NM_015718		Approved	GP91-3	uc003qqm.3	Q9HBY0	OTTHUMG00000015883	ENST00000159060.2:c.315C>T	chr6.hg19:g.155774563G>A		174.0	0.0		63.0	57.0	NM_015718	Q9HBJ9	Silent	SNP	ENST00000159060.2	hg19	CCDS5250.1																																																																																			.	.		0.368	NOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042819.1			A	155774563	G	A	155774563	2	1	333	1	0	0	0	0	0	0	0	1	10566	1045	37	1		1	NOX3	6	155774563	Silent	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	5769092	155774563	15340504	83	46425										
CARD11	84433	hgsc.bcm.edu	37	chr7	2987241	2987241	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tcttggatggcagcatagggGcattaagcacttcatcttca	10	9	4	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr7:2987241G>A	ENST00000396946.4	-	3	591	c.188C>T	c.(187-189)gCc>gTc	p.A63V	AC004906.3_ENST00000423194.1_RNA	NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	63	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		CAGCATAGGGGCATTAAGCAC	0.542			Mis		DLBCL																																p.A63V		Atlas-SNP	.		Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	.	CARD11	339	.	0			c.C188T						.						263	194	218					7																	2987241		2203	4300	6503	SO:0001583	missense	84433	exon3			ATAGGGGCATTAA	AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"card-maguk protein 1", "bcl10-interacting maguk protein 3"	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.188C>T	chr7.hg19:g.2987241G>A	ENSP00000380150:p.Ala63Val	118.0	0.0		121.0	61.0	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	hg19	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	G	17.95	3.513505	0.64522	.	.	ENSG00000198286	ENST00000396946;ENST00000356408	T;T	0.25749	1.78;2.04	5.15	5.15	0.70609	DEATH-like (2);Caspase Recruitment (2);	0.050244	0.85682	D	0.000000	T	0.20981	0.0505	N	0.22421	0.69	0.42369	D	0.992445	P	0.37731	0.607	B	0.39465	0.3	T	0.04041	-1.0982	10	0.59425	D	0.04	-21.0585	13.9603	0.64175	0.0:0.0:0.8482:0.1518	.	63	Q9BXL7	CAR11_HUMAN	V	63	ENSP00000380150:A63V;ENSP00000348779:A63V	ENSP00000348779:A63V	A	-	2	0	CARD11	2953767	1.000000	0.71417	0.109000	0.21407	0.843000	0.47879	7.169000	0.77578	2.585000	0.87301	0.650000	0.86243	GCC	.	.		0.542	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		A	2987241	G	A	2987241	3	1	333	1	0	0	0	0	1	0	0	0	2647	1203	42	3	3368	3	CARD11	7	2987241	Missense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10		2987241	156151422	84	46426										
AHR	196	hgsc.bcm.edu	37	chr7	17375399	17375399	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gattatatcattgtaactcaGagaccactaacgtaagcaca	6	9	2	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr7:17375399G>T	ENST00000242057.4	+	9	1792	c.1149G>T	c.(1147-1149)caG>caT	p.Q383H	AHR_ENST00000492120.1_3'UTR	NM_001621.4	NP_001612.1	P35869	AHR_HUMAN	aryl hydrocarbon receptor	383	PAC.				apoptotic process (GO:0006915)|blood vessel development (GO:0001568)|cell cycle (GO:0007049)|circadian regulation of gene expression (GO:0032922)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|regulation of B cell proliferation (GO:0030888)|regulation of gene expression (GO:0010468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to toxic substance (GO:0009636)|response to xenobiotic stimulus (GO:0009410)|transcription from RNA polymerase II promoter (GO:0006366)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosolic aryl hydrocarbon receptor complex (GO:0034752)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|Hsp90 protein binding (GO:0051879)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.Q383H(2)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(11)|ovary(1)|pancreas(1)|urinary_tract(3)	33	Lung NSC(10;0.0392)|all_lung(11;0.0754)				Atorvastatin(DB01076)|Flutamide(DB00499)|Ginseng(DB01404)|Leflunomide(DB01097)|Mexiletine(DB00379)|Nimodipine(DB00393)	TTGTAACTCAGAGACCACTAA	0.348																																					p.Q383H		Atlas-SNP	.											AHR,NS,carcinoma,0,1	AHR	89	.	2	Substitution - Missense(2)	lung(2)	c.G1149T						.						71	63	66					7																	17375399		2202	4300	6502	SO:0001583	missense	196	exon9			AACTCAGAGACCA	L19872	CCDS5366.1	7p15	2013-05-21			ENSG00000106546	ENSG00000106546		"Basic helix-loop-helix proteins"	348	protein-coding gene	gene with protein product		600253				8125016	Standard	NM_001621		Approved	bHLHe76	uc011jxz.1	P35869	OTTHUMG00000149967	ENST00000242057.4:c.1149G>T	chr7.hg19:g.17375399G>T	ENSP00000242057:p.Gln383His	71.0	0.0		76.0	26.0	NM_001621	A4D130|Q13728|Q13803|Q13804	Missense_Mutation	SNP	ENST00000242057.4	hg19	CCDS5366.1	.	.	.	.	.	.	.	.	.	.	G	15.97	2.990438	0.54041	.	.	ENSG00000106546	ENST00000242057	T	0.05447	3.44	5.98	-1.41	0.08941	.	0.000000	0.85682	D	0.000000	T	0.06917	0.0176	L	0.43152	1.355	0.44798	D	0.997802	B	0.28128	0.201	B	0.31390	0.129	T	0.22277	-1.0221	10	0.62326	D	0.03	.	12.8346	0.57765	0.6126:0.0:0.3874:0.0	.	383	P35869	AHR_HUMAN	H	383	ENSP00000242057:Q383H	ENSP00000242057:Q383H	Q	+	3	2	AHR	17341924	0.995000	0.38212	0.977000	0.42913	0.859000	0.49053	0.361000	0.20267	-0.292000	0.08999	0.591000	0.81541	CAG	.	.		0.348	AHR-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314620.2	NM_001621		T	17375399	G	T	17375399	3	4	333	1	0	0	0	0	1	0	0	0	416	933	33	3	1183	3	AHR	7	17375399	Missense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	14388158	17375399	141763264	85	46427										
RAPGEF5	9771	hgsc.bcm.edu	37	chr7	22259519	22259519	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	cctgttcttttttgtccgtcTgcaaaaactgatagttttct	6	9	3	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr7:22259519T>A	ENST00000405243.1	-	9	1045	c.962A>T	c.(961-963)cAg>cTg	p.Q321L	RAPGEF5_ENST00000475788.1_5'UTR|RAPGEF5_ENST00000344041.6_Missense_Mutation_p.Q168L			Q92565	RPGF5_HUMAN	Rap guanine nucleotide exchange factor (GEF) 5	0					nervous system development (GO:0007399)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|small GTPase mediated signal transduction (GO:0007264)	nucleus (GO:0005634)	GTP-dependent protein binding (GO:0030742)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(2)|ovary(1)	6						TTTGTCCGTCTGCAAAAACTG	0.448																																					p.Q168L		Atlas-SNP	.											.	RAPGEF5	96	.	0			c.A503T						.						131	123	125					7																	22259519		1840	4094	5934	SO:0001583	missense	9771	exon9			TCCGTCTGCAAAA	D87467	CCDS55093.1	7p15.3	2004-03-01			ENSG00000136237	ENSG00000136237			16862	protein-coding gene	gene with protein product	"M-Ras-regulated GEF"	609527				9039502, 10486569	Standard	NM_012294		Approved	KIAA0277, GFR, MR-GEF	uc003svg.3	Q92565	OTTHUMG00000152525	ENST00000405243.1:c.962A>T	chr7.hg19:g.22259519T>A	ENSP00000384870:p.Gln321Leu	161.0	0.0		153.0	76.0	NM_012294	A4D140|Q8IXU5	Missense_Mutation	SNP	ENST00000405243.1	hg19		.	.	.	.	.	.	.	.	.	.	T	15.18	2.756724	0.49362	.	.	ENSG00000136237	ENST00000344041;ENST00000420196;ENST00000405243	D;D;D	0.86030	-2.06;-2.06;-2.06	5.69	5.69	0.88448	.	1.329770	0.04923	N	0.455320	T	0.81969	0.4935	L	0.44542	1.39	0.44000	D	0.996702	B	0.31680	0.335	B	0.25140	0.058	T	0.65434	-0.6169	10	0.42905	T	0.14	.	11.8726	0.52529	0.0:0.0:0.1457:0.8543	.	168	A8MQ07	.	L	168;49;321	ENSP00000343656:Q168L;ENSP00000395729:Q49L;ENSP00000384870:Q321L	ENSP00000343656:Q168L	Q	-	2	0	RAPGEF5	22226044	1.000000	0.71417	0.997000	0.53966	0.958000	0.62258	3.068000	0.50018	2.173000	0.68751	0.459000	0.35465	CAG	.	.		0.448	RAPGEF5-002	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000326591.1	NM_012294		A	22259519	T	A	22259519	3	1	333	1	0	0	0	0	1	0	0	0	13062	1580	55	4	1761	4	RAPGEF5	7	22259519	Missense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	4884120	22259519	136879144	86	46428										
VPS37D	155382	hgsc.bcm.edu	37	chr7	73085576	73085576	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ggccgcccgggggccaccagCagtgccccggagcctgcccc	15	20	0	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr7:73085576C>T	ENST00000324941.4	+	4	760	c.626C>T	c.(625-627)gCa>gTa	p.A209V	VPS37D_ENST00000451519.1_Missense_Mutation_p.A124V	NM_001077621.1	NP_001071089.1			vacuolar protein sorting 37 homolog D (S. cerevisiae)											central_nervous_system(1)|ovary(1)	2		Lung NSC(55;0.0908)|all_lung(88;0.198)				GGGCCACCAGCAGTGCCCCGG	0.766																																					p.A209V		Atlas-SNP	.											.	VPS37D	10	.	0			c.C626T						.						3	4	4					7																	73085576		1334	3199	4533	SO:0001583	missense	155382	exon4			CACCAGCAGTGCC	AY081952	CCDS43596.1	7q11.23	2007-07-27	2006-04-04	2005-08-18	ENSG00000176428	ENSG00000176428			18287	protein-coding gene	gene with protein product		610039	"Williams Beuren syndrome chromosome region 24", "vacuolar protein sorting 37D (yeast)"	WBSCR24		15218037	Standard	NM_001077621		Approved	MGC35352	uc003tyr.3	Q86XT2	OTTHUMG00000157227	ENST00000324941.4:c.626C>T	chr7.hg19:g.73085576C>T	ENSP00000320416:p.Ala209Val	36.0	0.0		40.0	17.0	NM_001077621		Missense_Mutation	SNP	ENST00000324941.4	hg19	CCDS43596.1	.	.	.	.	.	.	.	.	.	.	C	17.81	3.479765	0.63849	.	.	ENSG00000176428	ENST00000324941;ENST00000451519	T;T	0.58506	0.33;1.34	4.07	4.07	0.47477	.	0.463838	0.18854	N	0.129318	T	0.43433	0.1247	N	0.08118	0	0.34193	D	0.672291	D	0.58268	0.982	P	0.51657	0.676	T	0.46624	-0.9178	10	0.15499	T	0.54	.	11.6008	0.51001	0.0:1.0:0.0:0.0	.	209	Q86XT2	VP37D_HUMAN	V	209;124	ENSP00000320416:A209V;ENSP00000413337:A124V	ENSP00000320416:A209V	A	+	2	0	VPS37D	72723512	0.815000	0.29118	0.999000	0.59377	0.977000	0.68977	2.187000	0.42602	2.086000	0.62901	0.561000	0.74099	GCA	.	.		0.766	VPS37D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348064.1	NM_152560		T	73085576	C	T	73085576	3	4	333	1	0	0	0	0	1	0	0	0	17223	710	25	3	640	3	VPS37D	7	73085576	Missense_Mutation	SNP	C	TCGA-RC-A6M4-01A-11D-A32G-10	50826057	73085576	86053087	87	46429										
CLIP2	7461	hgsc.bcm.edu	37	chr7	73752825	73752825	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gaccctcctcctccccggccGcagctgctgcccccgagaag	10	21	0	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr7:73752825G>A	ENST00000395060.1	+	2	169	c.169G>A	c.(169-171)Gca>Aca	p.A57T	CLIP2_ENST00000223398.6_Missense_Mutation_p.A57T|CLIP2_ENST00000361545.5_Missense_Mutation_p.A57T			Q9UDT6	CLIP2_HUMAN	CAP-GLY domain containing linker protein 2	57						cytoplasmic microtubule (GO:0005881)|microtubule associated complex (GO:0005875)|microtubule plus-end (GO:0035371)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(13)|pancreas(1)|prostate(2)|skin(3)	30						CTCCCCGGCCGCAGCTGCTGC	0.667																																					p.A57T		Atlas-SNP	.											.	CLIP2	134	.	0			c.G169A						.						17	16	17					7																	73752825		2200	4297	6497	SO:0001583	missense	7461	exon3			CCGGCCGCAGCTG	AB006629	CCDS5569.1, CCDS5570.1	7q11.23	2008-06-12	2007-01-04	2007-01-04	ENSG00000106665	ENSG00000106665			2586	protein-coding gene	gene with protein product		603432	"cytoplasmic linker 2", "Williams-Beuren syndrome chromosome region 3"	WBSCR4, CYLN2, WBSCR3		8812460, 9799601	Standard	NM_003388		Approved	CLIP-115, KIAA0291, WSCR4, CLIP, WSCR3	uc003uam.3	Q9UDT6	OTTHUMG00000022980	ENST00000395060.1:c.169G>A	chr7.hg19:g.73752825G>A	ENSP00000378500:p.Ala57Thr	72.0	0.0		79.0	34.0	NM_032421	O14527|O43611	Missense_Mutation	SNP	ENST00000395060.1	hg19	CCDS5569.1	.	.	.	.	.	.	.	.	.	.	G	7.788	0.710979	0.15239	.	.	ENSG00000106665	ENST00000539676;ENST00000223398;ENST00000361545;ENST00000395060	T;T;T	0.59502	0.26;0.27;0.26	4.75	-0.955	0.10356	Cytoskeleton-associated protein, Gly-rich domain (1);	0.685507	0.13103	N	0.413608	T	0.28797	0.0714	N	0.12182	0.205	0.09310	N	1	B;B	0.10296	0.003;0.0	B;B	0.04013	0.001;0.0	T	0.13495	-1.0507	10	0.16420	T	0.52	-5.5102	2.8167	0.05458	0.3051:0.0:0.3593:0.3356	.	57;57	Q9UDT6-2;Q9UDT6	.;CLIP2_HUMAN	T	57	ENSP00000223398:A57T;ENSP00000355151:A57T;ENSP00000378500:A57T	ENSP00000223398:A57T	A	+	1	0	CLIP2	73390761	0.000000	0.05858	0.000000	0.03702	0.552000	0.35366	-0.839000	0.04368	-0.054000	0.13266	0.462000	0.41574	GCA	.	.		0.667	CLIP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252556.1	NM_003388		A	73752825	G	A	73752825	3	1	333	1	0	0	0	0	1	0	0	0	3535	1087	38	1	175	1	CLIP2	7	73752825	Missense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	667249	73752825	85385838	88	46430										
PION	54103	hgsc.bcm.edu	37	chr7	76982269	76982269	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gtgttaacttactgtattccAagtgagcactgaggaatgtg	11	6	0	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr7:76982269A>C	ENST00000257626.7	-	18	1561	c.1483T>G	c.(1483-1485)Tgg>Ggg	p.W495G		NM_017439.3	NP_059135.2	A4D1B5	GSAP_HUMAN	gamma-secretase activating protein	495					positive regulation of beta-amyloid formation (GO:1902004)|regulation of proteolysis (GO:0030162)	trans-Golgi network (GO:0005802)	beta-amyloid binding (GO:0001540)										ACTGTATTCCAAGTGAGCACT	0.393																																					p.W495G		Atlas-SNP	.											.	PION	74	.	0			c.T1483G						.						217	184	195					7																	76982269		2203	4300	6503	SO:0001583	missense	54103	exon18			TATTCCAAGTGAG		CCDS34672.2	7q11.23	2013-04-05	2013-04-05	2013-04-05	ENSG00000186088	ENSG00000186088			28042	protein-coding gene	gene with protein product		613552	"pigeon homolog (Drosophila)"	PION		20811458	Standard	NM_017439		Approved	LOC54103	uc003ugf.3	A4D1B5	OTTHUMG00000150504	ENST00000257626.7:c.1483T>G	chr7.hg19:g.76982269A>C	ENSP00000257626:p.Trp495Gly	113.0	0.0		92.0	41.0	NM_017439	A4D1B6|Q3MJC0|Q8ND73|Q9UMH3|Q9Y4L9	Missense_Mutation	SNP	ENST00000257626.7	hg19	CCDS34672.2	.	.	.	.	.	.	.	.	.	.	A	18.39	3.614033	0.66672	.	.	ENSG00000186088	ENST00000257626	T	0.18338	2.22	6.06	6.06	0.98353	.	0.187170	0.36234	U	0.002708	T	0.40322	0.1112	M	0.67953	2.075	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.983;0.998	T	0.10613	-1.0622	10	0.46703	T	0.11	.	14.1235	0.65205	1.0:0.0:0.0:0.0	.	495;495	A4D1B5-3;A4D1B5	.;GSAP_HUMAN	G	495	ENSP00000257626:W495G	ENSP00000257626:W495G	W	-	1	0	PION	76820205	0.998000	0.40836	0.946000	0.38457	0.997000	0.91878	5.176000	0.65026	2.319000	0.78375	0.533000	0.62120	TGG	.	.		0.393	GSAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318672.2	NM_017439		C	76982269	A	C	76982269	3	2	333	1	0	0	0	0	1	0	0	0	11943	130	5	5	1137	5	PION	7	76982269	Missense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	3229444	76982269	82156394	89	46431										
MTERF	7978	hgsc.bcm.edu	37	chr7	91503797	91503797	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ggaacatcttcaggtcctgcTcattggtaatcatcctatga	8	10	4	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr7:91503797T>A	ENST00000351870.3	-	3	404	c.311A>T	c.(310-312)gAg>gTg	p.E104V	MTERF_ENST00000481516.1_5'Flank|MTERF_ENST00000419292.1_Missense_Mutation_p.E84V|MTERF_ENST00000406735.2_Missense_Mutation_p.E84V	NM_006980.3	NP_008911.1	Q99551	MTEF1_HUMAN		104					DNA geometric change (GO:0032392)|DNA-templated transcription, termination (GO:0006353)|gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of mitochondrial transcription (GO:0006393)|transcription from mitochondrial promoter (GO:0006390)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|liver(1)|lung(2)|skin(1)	14	all_cancers(62;2.28e-09)|all_epithelial(64;1.07e-07)|Breast(17;0.00371)|all_hematologic(106;0.091)|all_lung(186;0.178)|Lung NSC(181;0.235)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.0993)|Kidney(17;0.118)|Epithelial(20;0.136)|LUSC - Lung squamous cell carcinoma(200;0.176)			CAGGTCCTGCTCATTGGTAAT	0.418																																					p.E104V		Atlas-SNP	.											.	MTERF	32	.	0			c.A311T						.						153	138	143					7																	91503797		2203	4300	6503	SO:0001583	missense	7978	exon3			TCCTGCTCATTGG																												ENST00000351870.3:c.311A>T	chr7.hg19:g.91503797T>A	ENSP00000248643:p.Glu104Val	92.0	0.0		91.0	35.0	NM_006980	A4D1E3|Q32NF8|Q53H51|Q9BVR7	Missense_Mutation	SNP	ENST00000351870.3	hg19	CCDS5621.1	.	.	.	.	.	.	.	.	.	.	T	9.736	1.163574	0.21538	.	.	ENSG00000127989	ENST00000419292;ENST00000351870;ENST00000406735;ENST00000456229;ENST00000442961	T;T;T;T;T	0.11169	2.8;2.8;2.8;2.8;2.8	4.51	4.51	0.55191	.	0.058358	0.64402	D	0.000003	T	0.24236	0.0587	L	0.54323	1.7	0.42130	D	0.991466	D	0.89917	1.0	D	0.91635	0.999	T	0.05517	-1.0880	10	0.12103	T	0.63	-9.0643	13.4852	0.61361	0.0:0.0:0.0:1.0	.	104	Q99551	MTERF_HUMAN	V	84;104;84;84;104	ENSP00000414116:E84V;ENSP00000248643:E104V;ENSP00000384986:E84V;ENSP00000402175:E84V;ENSP00000395097:E104V	ENSP00000248643:E104V	E	-	2	0	MTERF	91341733	1.000000	0.71417	1.000000	0.80357	0.096000	0.18686	5.062000	0.64326	1.969000	0.57287	0.482000	0.46254	GAG	.	.		0.418	MTERF-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000342896.1			A	91503797	T	A	91503797	3	1	333	1	0	0	0	0	1	0	0	0	9927	1551	54	4	892	4	MTERF	7	91503797	Missense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	14521528	91503797	67634866	90	46432										
CFTR	1080	hgsc.bcm.edu	37	chr7	117307000	117307000	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gtgcggcagtacgattccatCcagaaactgctgaacgagag	12	10	0	3			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr7:117307000C>T	ENST00000003084.6	+	27	4413	c.4281C>T	c.(4279-4281)atC>atT	p.I1427I	CFTR_ENST00000454343.1_Silent_p.I1366I	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	1427	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular response to cAMP (GO:0071320)|cellular response to hormone stimulus (GO:0032870)|chloride transmembrane transport (GO:1902476)|cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intracellular pH elevation (GO:0051454)|iodide transport (GO:0015705)|lung development (GO:0030324)|membrane hyperpolarization (GO:0060081)|positive regulation of vasodilation (GO:0045909)|positive regulation of voltage-gated chloride channel activity (GO:1902943)|respiratory gaseous exchange (GO:0007585)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to peptide hormone (GO:0043434)|sperm capacitation (GO:0048240)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vasodilation (GO:0042311)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|chloride channel complex (GO:0034707)|cytoplasmic vesicle membrane (GO:0030659)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-binding and phosphorylation-dependent chloride channel activity (GO:0005224)|bicarbonate transmembrane transporter activity (GO:0015106)|channel-conductance-controlling ATPase activity (GO:0005260)|chloride channel activity (GO:0005254)|chloride channel inhibitor activity (GO:0019869)|chloride transmembrane transporter activity (GO:0015108)|enzyme binding (GO:0019899)|PDZ domain binding (GO:0030165)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(15)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(9)	69	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Crofelemer(DB04941)|Glyburide(DB01016)|Ibuprofen(DB01050)|Ivacaftor(DB08820)	ACGATTCCATCCAGAAACTGC	0.542									Cystic Fibrosis																												p.I1427I		Atlas-SNP	.											.	CFTR	171	.	0			c.C4281T						.						58	50	53					7																	117307000		2203	4300	6503	SO:0001819	synonymous_variant	1080	exon27	Familial Cancer Database	CF	TTCCATCCAGAAA	M28668	CCDS5773.1	7q31-q32	2014-09-17	2006-09-18		ENSG00000001626	ENSG00000001626		"Ion channels / Chloride channels : Cystic fibrosis transmembrane conductance regulators", "ATP binding cassette transporters / subfamily C"	1884	protein-coding gene	gene with protein product	"ATP-binding cassette sub-family C, member 7"	602421	"cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)"	CF, ABCC7		2772657	Standard	XM_006715842		Approved	MRP7, ABC35, TNR-CFTR, dJ760C5.1, CFTR/MRP	uc003vjd.3	P13569	OTTHUMG00000023076	ENST00000003084.6:c.4281C>T	chr7.hg19:g.117307000C>T		89.0	0.0		105.0	47.0	NM_000492	Q20BG8|Q20BH2|Q2I0A1|Q2I102	Silent	SNP	ENST00000003084.6	hg19	CCDS5773.1																																																																																			.	.		0.542	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492		T	117307000	C	T	117307000	2	4	333	1	0	0	0	0	0	0	0	1	3296	845	30	3		3	CFTR	7	117307000	Silent	SNP	C	TCGA-RC-A6M4-01A-11D-A32G-10	25803203	117307000	41831663	91	46433										
CPA5	93979	hgsc.bcm.edu	37	chr7	130002351	130002351	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	actcccgggagtggatcaccCatgccaccggcatctggact	11	15	2	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr7:130002351C>A	ENST00000485477.1	+	7	1736	c.607C>A	c.(607-609)Cat>Aat	p.H203N	CPA5_ENST00000393213.3_Missense_Mutation_p.H203N|CPA5_ENST00000461828.1_Missense_Mutation_p.H203N|CPA5_ENST00000431780.2_Missense_Mutation_p.H203N|CPA5_ENST00000355388.3_Missense_Mutation_p.H203N|CPA5_ENST00000466363.2_Missense_Mutation_p.H203N|CPA5_ENST00000474905.1_Missense_Mutation_p.H203N			Q8WXQ8	CBPA5_HUMAN	carboxypeptidase A5	203						extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(2)|large_intestine(7)|lung(4)|ovary(3)|pancreas(1)|skin(2)	23	Melanoma(18;0.0435)					GTGGATCACCCATGCCACCGG	0.562																																					p.H203N		Atlas-SNP	.											.	CPA5	61	.	0			c.C607A						.						48	44	45					7																	130002351		2203	4300	6503	SO:0001583	missense	93979	exon8			ATCACCCATGCCA	AF384667	CCDS5819.1, CCDS47713.1	7q32	2008-07-18			ENSG00000158525	ENSG00000158525			15722	protein-coding gene	gene with protein product		609561				11836249	Standard	NM_080385		Approved		uc003vps.2	Q8WXQ8	OTTHUMG00000157824	ENST00000485477.1:c.607C>A	chr7.hg19:g.130002351C>A	ENSP00000420237:p.His203Asn	34.0	0.0		35.0	22.0	NM_080385	G3V0G8|Q6ZNI6|Q86SE2|Q86XM3|Q8NA08	Missense_Mutation	SNP	ENST00000485477.1	hg19	CCDS5819.1	.	.	.	.	.	.	.	.	.	.	C	18.48	3.632346	0.67015	.	.	ENSG00000158525	ENST00000355388;ENST00000461828;ENST00000466363;ENST00000485477;ENST00000431780;ENST00000474905;ENST00000393213	T;T;T;T;T;T;T	0.10288	2.89;2.89;2.89;2.89;2.89;2.89;2.89	5.61	5.61	0.85477	Peptidase M14, carboxypeptidase A (3);	0.090096	0.49305	D	0.000160	T	0.15825	0.0381	L	0.53729	1.69	0.44194	D	0.997015	P;B	0.35944	0.529;0.271	B;B	0.38156	0.236;0.266	T	0.02037	-1.1225	9	.	.	.	.	18.6123	0.91290	0.0:1.0:0.0:0.0	.	203;203	G3V0G8;Q8WXQ8	.;CBPA5_HUMAN	N	203	ENSP00000347549:H203N;ENSP00000418183:H203N;ENSP00000419025:H203N;ENSP00000420237:H203N;ENSP00000393045:H203N;ENSP00000417314:H203N;ENSP00000376907:H203N	.	H	+	1	0	CPA5	129789587	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	7.389000	0.79806	2.627000	0.88993	0.591000	0.81541	CAT	.	.		0.562	CPA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349712.1	NM_001127441		A	130002351	C	A	130002351	3	1	333	1	0	0	0	0	1	0	0	0	3795	594	21	3	629	3	CPA5	7	130002351	Missense_Mutation	SNP	C	TCGA-RC-A6M4-01A-11D-A32G-10	12695351	130002351	29136312	92	46434										
CHRM2	1129	hgsc.bcm.edu	37	chr7	136700608	136700608	+	Frame_Shift_Del	DEL	A	A	-													0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	agaattggcaccaagaccccAaaaagtgactcatgtacccc							TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr7:136700608delA	ENST00000445907.2	+	3	1524	c.996delA	c.(994-996)ccafs	p.P332fs	hsa-mir-490_ENST00000439694.1_RNA|hsa-mir-490_ENST00000597642.1_RNA|hsa-mir-490_ENST00000593789.1_RNA|hsa-mir-490_ENST00000425981.2_RNA|hsa-mir-490_ENST00000592183.1_RNA|CHRM2_ENST00000401861.1_Frame_Shift_Del_p.P332fs|hsa-mir-490_ENST00000598184.1_RNA|CHRM2_ENST00000453373.1_Frame_Shift_Del_p.P332fs|CHRM2_ENST00000397608.3_Frame_Shift_Del_p.P332fs|CHRM2_ENST00000402486.3_Frame_Shift_Del_p.P332fs|CHRM2_ENST00000320658.5_Frame_Shift_Del_p.P332fs|hsa-mir-490_ENST00000586239.1_RNA	NM_001006627.1|NM_001006629.1	NP_001006628.1|NP_001006630.1	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	332					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|nervous system development (GO:0007399)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|regulation of heart contraction (GO:0008016)|response to virus (GO:0009615)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(13)|liver(1)|lung(29)|ovary(4)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	68					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Bethanechol(DB01019)|Brompheniramine(DB00835)|Carbachol(DB00411)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Dimetindene(DB08801)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxacurium chloride(DB01135)|Doxepin(DB01142)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Rocuronium(DB00728)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	CCAAGACCCCAAAAAGTGACT	0.453																																					p.P332fs		Atlas-Indel,Pindel	.											.	CHRM2	167	.	0			c.995delC						.						103	103	103					7																	136700608		2203	4300	6503	SO:0001589	frameshift_variant	1129	exon4			.		CCDS5843.1	7q35-q36	2014-09-17			ENSG00000181072	ENSG00000181072		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1951	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 2"	118493					Standard	NM_000739		Approved		uc003vtl.1	P08172	OTTHUMG00000155658	ENST00000445907.2:c.996delA	chr7.hg19:g.136700608delA	ENSP00000399745:p.Pro332fs	73.0	0.0		75.0	40.0	NM_001006630	Q4VBK6|Q9P1X9	Frame_Shift_Del	DEL	ENST00000445907.2	hg19	CCDS5843.1																																																																																			.	.		0.453	CHRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341010.1			-	136700608	A	-	136700608	7	5	333	1	0	1	0	1	0	0	0	0	3379	117	5	0	998	0	CHRM2	7	136700608	Frame_Shift_Del	DEL	A	TCGA-RC-A6M4-01A-11D-A32G-10	6698257	136700608	22438055	93	46435										
PTK2B	2185	hgsc.bcm.edu	37	chr8	27315905	27315905	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	cgccgtgacctccctaagtgAggagtgcaagaggcagatgc	14	11	0	4			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr8:27315905A>T	ENST00000397501.1	+	36	3717	c.2909A>T	c.(2908-2910)gAg>gTg	p.E970V	PTK2B_ENST00000420218.2_Missense_Mutation_p.E928V|PTK2B_ENST00000517339.1_Missense_Mutation_p.E928V|PTK2B_ENST00000338238.4_Missense_Mutation_p.E928V|PTK2B_ENST00000346049.5_Missense_Mutation_p.E970V|PTK2B_ENST00000544172.1_Missense_Mutation_p.E970V	NM_173174.2	NP_775266.1	Q14289	FAK2_HUMAN	protein tyrosine kinase 2 beta	970	Focal adhesion targeting (FAT).|Interaction with TGFB1I1. {ECO:0000250}.		E -> K (in dbSNP:rs56263944). {ECO:0000269|PubMed:17344846}.		activation of Janus kinase activity (GO:0042976)|activation of Rac GTPase activity (GO:0032863)|apoptotic process (GO:0006915)|blood vessel endothelial cell migration (GO:0043534)|bone resorption (GO:0045453)|cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|cellular response to retinoic acid (GO:0071300)|chemokine-mediated signaling pathway (GO:0070098)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|glial cell proliferation (GO:0014009)|integrin-mediated signaling pathway (GO:0007229)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term synaptic potentiation (GO:0060291)|MAPK cascade (GO:0000165)|marginal zone B cell differentiation (GO:0002315)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cell proliferation (GO:0008285)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of potassium ion transport (GO:0043267)|neuron projection development (GO:0031175)|oocyte maturation (GO:0001556)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell chemotaxis (GO:2000538)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell adhesion (GO:0030155)|regulation of cell shape (GO:0008360)|regulation of establishment of cell polarity (GO:2000114)|regulation of inositol trisphosphate biosynthetic process (GO:0032960)|regulation of macrophage chemotaxis (GO:0010758)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000058)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to hormone (GO:0009725)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to lithium ion (GO:0010226)|response to mechanical stimulus (GO:0009612)|response to osmotic stress (GO:0006970)|response to stress (GO:0006950)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|stress fiber assembly (GO:0043149)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	apical dendrite (GO:0097440)|axon (GO:0030424)|cell body (GO:0044297)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(17)|ovary(4)|skin(12)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Ovarian(32;2.72e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|Epithelial(17;6.61e-10)|BRCA - Breast invasive adenocarcinoma(99;0.226)|Colorectal(74;0.229)	Leflunomide(DB01097)	TCCCTAAGTGAGGAGTGCAAG	0.582																																					p.E970V		Atlas-SNP	.											.	PTK2B	304	.	0			c.A2909T						.						85	57	67					8																	27315905		2203	4300	6503	SO:0001583	missense	2185	exon36			TAAGTGAGGAGTG	U33284	CCDS6057.1, CCDS6058.1	8p21.1	2013-02-18	2013-02-18		ENSG00000120899	ENSG00000120899			9612	protein-coding gene	gene with protein product		601212	"protein tyrosine kinase 2 beta", "PTK2B protein tyrosine kinase 2 beta"	FAK2		7544443, 7499242	Standard	NM_173174		Approved	CAKB, PYK2, RAFTK, PTK, CADTK	uc003xfp.2	Q14289	OTTHUMG00000102082	ENST00000397501.1:c.2909A>T	chr8.hg19:g.27315905A>T	ENSP00000380638:p.Glu970Val	43.0	0.0		16.0	15.0	NM_173174	D3DST0|Q13475|Q14290|Q16709|Q6PID4	Missense_Mutation	SNP	ENST00000397501.1	hg19	CCDS6057.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.398527	0.83120	.	.	ENSG00000120899	ENST00000397501;ENST00000338238;ENST00000544172;ENST00000346049;ENST00000420218;ENST00000517339	T;T;T;T;T;T	0.33865	1.39;1.39;1.39;1.39;1.39;1.39	4.91	4.91	0.64330	Focal adhesion kinase, targeting (FAT) domain (3);	0.050900	0.85682	D	0.000000	T	0.52092	0.1713	L	0.60455	1.87	0.80722	D	1	D;D	0.65815	0.995;0.988	P;D	0.63113	0.843;0.911	T	0.53989	-0.8360	10	0.59425	D	0.04	.	12.5376	0.56150	1.0:0.0:0.0:0.0	.	928;970	Q14289-2;Q14289	.;FAK2_HUMAN	V	970;928;970;970;928;928	ENSP00000380638:E970V;ENSP00000342242:E928V;ENSP00000440926:E970V;ENSP00000332816:E970V;ENSP00000391995:E928V;ENSP00000427931:E928V	ENSP00000342242:E928V	E	+	2	0	PTK2B	27371822	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	4.242000	0.58714	2.048000	0.60808	0.460000	0.39030	GAG	.	.		0.582	PTK2B-009	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219916.1	NM_004103		T	27315905	A	T	27315905	3	4	333	1	0	0	0	0	1	0	0	0	12776	304	11	4	3027	4	PTK2B	8	27315905	Missense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10		27315905	119048117	94	46436										
SULF1	23213	hgsc.bcm.edu	37	chr8	70541750	70541750	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ttggaacagggaggctgctcAggaagtagatagcaaactgc	14	7	1	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr8:70541750A>T	ENST00000260128.4	+	19	2837	c.2120A>T	c.(2119-2121)cAg>cTg	p.Q707L	SULF1_ENST00000521946.1_3'UTR|SULF1_ENST00000402687.4_Missense_Mutation_p.Q707L|SULF1_ENST00000419716.3_Missense_Mutation_p.Q707L|SULF1_ENST00000458141.2_Missense_Mutation_p.Q707L	NM_015170.2	NP_055985.2	Q8IWU6	SULF1_HUMAN	sulfatase 1	707					apoptotic process (GO:0006915)|bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of prostatic bud formation (GO:0060686)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|central_nervous_system(3)|endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)			GAGGCTGCTCAGGAAGTAGAT	0.463																																					p.Q707L		Atlas-SNP	.											.	SULF1	153	.	0			c.A2120T						.						68	64	65					8																	70541750		2203	4300	6503	SO:0001583	missense	23213	exon19			CTGCTCAGGAAGT	AB029000	CCDS6204.1	8q13.2	2014-09-11			ENSG00000137573	ENSG00000137573			20391	protein-coding gene	gene with protein product		610012				12368295	Standard	NM_015170		Approved	KIAA1077, SULF-1	uc003xyd.2	Q8IWU6	OTTHUMG00000164466	ENST00000260128.4:c.2120A>T	chr8.hg19:g.70541750A>T	ENSP00000260128:p.Gln707Leu	117.0	0.0		224.0	54.0	NM_001128205	Q86YV8|Q8NCA2|Q9UPS5	Missense_Mutation	SNP	ENST00000260128.4	hg19	CCDS6204.1	.	.	.	.	.	.	.	.	.	.	A	11.37	1.619752	0.28801	.	.	ENSG00000137573	ENST00000458141;ENST00000260128;ENST00000402687;ENST00000419716	T;T;T;T	0.21932	1.98;1.98;1.98;1.98	4.75	4.75	0.60458	Alkaline-phosphatase-like, core domain (1);	0.399171	0.28647	N	0.014618	T	0.21509	0.0518	L	0.46157	1.445	0.80722	D	1	B	0.09022	0.002	B	0.04013	0.001	T	0.02860	-1.1101	10	0.54805	T	0.06	.	14.4268	0.67220	1.0:0.0:0.0:0.0	.	707	Q8IWU6	SULF1_HUMAN	L	707	ENSP00000403040:Q707L;ENSP00000260128:Q707L;ENSP00000385704:Q707L;ENSP00000390315:Q707L	ENSP00000260128:Q707L	Q	+	2	0	SULF1	70704304	1.000000	0.71417	0.617000	0.29091	0.028000	0.11728	6.815000	0.75242	1.977000	0.57605	0.533000	0.62120	CAG	.	.		0.463	SULF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378885.2	NM_015170		T	70541750	A	T	70541750	3	4	333	1	0	0	0	0	1	0	0	0	15385	188	7	4	2178	4	SULF1	8	70541750	Missense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	43225845	70541750	75822272	95	46437										
TERF1	7013	hgsc.bcm.edu	37	chr8	73939235	73939235	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	taacttctcaagataaacctAgtggtaatgatgttgaaatg	8	5	1	3			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr8:73939235A>T	ENST00000276603.5	+	6	858	c.835A>T	c.(835-837)Agt>Tgt	p.S279C	TERF1_ENST00000276602.6_Missense_Mutation_p.S279C	NM_017489.2	NP_059523.2	P54274	TERF1_HUMAN	telomeric repeat binding factor (NIMA-interacting) 1	279	Interaction with RLIM.				age-dependent telomere shortening (GO:0001309)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of DNA replication (GO:0008156)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via semi-conservative replication (GO:0032214)|negative regulation of telomere maintenance via telomerase (GO:0032211)|positive regulation of apoptotic process (GO:0043065)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of mitosis (GO:0045840)|positive regulation of mitotic cell cycle (GO:0045931)|protein homooligomerization (GO:0051260)|response to drug (GO:0042493)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)|telomere maintenance via telomere shortening (GO:0010834)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nuclear telomere cap complex (GO:0000783)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|double-stranded telomeric DNA binding (GO:0003691)|microtubule binding (GO:0008017)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|telomeric DNA binding (GO:0042162)			central_nervous_system(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	9	Breast(64;0.218)		Epithelial(68;0.0984)			AGATAAACCTAGTGGTAATGA	0.323																																					p.S279C		Atlas-SNP	.											.	TERF1	48	.	0			c.A835T						.						79	77	78					8																	73939235		2203	4300	6503	SO:0001583	missense	7013	exon6			AAACCTAGTGGTA	U74382	CCDS6210.1, CCDS6211.1	8q21.11	2011-05-24			ENSG00000147601	ENSG00000147601			11728	protein-coding gene	gene with protein product		600951		TRBF1		9391075	Standard	NM_003218		Approved	PIN2, TRF1, TRF	uc003xzd.2	P54274	OTTHUMG00000164522	ENST00000276603.5:c.835A>T	chr8.hg19:g.73939235A>T	ENSP00000276603:p.Ser279Cys	24.0	0.0		42.0	10.0	NM_017489	A7XP29|Q15553|Q8NHT6|Q93029	Missense_Mutation	SNP	ENST00000276603.5	hg19	CCDS6211.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.969069	0.74131	.	.	ENSG00000147601	ENST00000276603;ENST00000276602;ENST00000517390	.	.	.	4.25	1.81	0.25067	.	1.157320	0.06254	N	0.692565	T	0.19565	0.0470	N	0.08118	0	0.09310	N	1	P;P	0.47106	0.733;0.89	P;B	0.45276	0.475;0.145	T	0.16630	-1.0396	9	0.59425	D	0.04	.	5.4624	0.16624	0.7697:0.0:0.2303:0.0	.	279;279	P54274-2;P54274	.;TERF1_HUMAN	C	279;279;175	.	ENSP00000276602:S279C	S	+	1	0	TERF1	74101789	0.000000	0.05858	0.025000	0.17156	0.981000	0.71138	-0.038000	0.12144	0.692000	0.31613	0.528000	0.53228	AGT	.	.		0.323	TERF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379093.1	NM_017489		T	73939235	A	T	73939235	3	4	333	1	0	0	0	0	1	0	0	0	15776	420	15	4	857	4	TERF1	8	73939235	Missense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	3397485	73939235	72424787	96	46438										
FAM164A	51101	hgsc.bcm.edu	37	chr8	79590890	79590890	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gctgaaggaactgatattccAacagtaaaacctctcaaacc	6	11	1	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr8:79590890A>G	ENST00000263849.4	+	3	288	c.186A>G	c.(184-186)ccA>ccG	p.P62P	ZC2HC1A_ENST00000521176.1_3'UTR	NM_016010.2	NP_057094.2	Q96GY0	ZC21A_HUMAN	zinc finger, C2HC-type containing 1A	62							metal ion binding (GO:0046872)										CTGATATTCCAACAGTAAAAC	0.348																																					p.P62P		Atlas-SNP	.											.	.	.	.	0			c.A186G						.						113	118	116					8																	79590890		2203	4300	6503	SO:0001819	synonymous_variant	51101	exon3			TATTCCAACAGTA		CCDS6223.1	8q21.11	2013-01-10	2012-02-03	2012-02-03	ENSG00000104427	ENSG00000104427		"Zinc fingers, C2HC-type containing"	24277	protein-coding gene	gene with protein product			"chromosome 8 open reading frame 70", "family with sequence similarity 164, member A"	C8orf70, FAM164A		10810093	Standard	NM_016010		Approved	CGI-62	uc003ybd.3	Q96GY0	OTTHUMG00000164619	ENST00000263849.4:c.186A>G	chr8.hg19:g.79590890A>G		99.0	0.0		146.0	61.0	NM_016010	Q9Y372	Silent	SNP	ENST00000263849.4	hg19	CCDS6223.1																																																																																			.	.		0.348	ZC2HC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379423.2	NM_016010		G	79590890	A	G	79590890	2	3	333	1	0	0	0	0	0	0	0	1	5483	117	5	2		2	FAM164A	8	79590890	Silent	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	5651655	79590890	66773132	97	46439										
CNBD1	168975	hgsc.bcm.edu	37	chr8	88249211	88249211	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	cgacctcaaacaaacgtgtaTaaaaatctgattgaaggaag	8	7	2	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr8:88249211T>C	ENST00000518476.1	+	6	693	c.642T>C	c.(640-642)taT>taC	p.Y214Y	CNBD1_ENST00000522427.1_3'UTR	NM_173538.2	NP_775809.1	Q8NA66	CNBD1_HUMAN	cyclic nucleotide binding domain containing 1	214										breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(4)|urinary_tract(1)	32						CAAACGTGTATAAAAATCTGA	0.363																																					p.Y214Y		Atlas-SNP	.											.	CNBD1	206	.	0			c.T642C						.						143	128	133					8																	88249211		1841	4087	5928	SO:0001819	synonymous_variant	168975	exon6			CGTGTATAAAAAT	AK093121	CCDS55259.1	8q21.3	2005-08-09				ENSG00000176571			26663	protein-coding gene	gene with protein product							Standard	NM_173538		Approved	FLJ35802	uc003ydy.2	Q8NA66		ENST00000518476.1:c.642T>C	chr8.hg19:g.88249211T>C		87.0	0.0		153.0	53.0	NM_173538		Silent	SNP	ENST00000518476.1	hg19	CCDS55259.1																																																																																			.	.		0.363	CNBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375113.2	NM_173538		C	88249211	T	C	88249211	2	2	333	1	0	0	0	0	0	0	0	1	3593	1413	49	2		2	CNBD1	8	88249211	Silent	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	8658321	88249211	58114811	98	46440										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113529405	113529405	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tctcttccatccccatttcgAgtcccattcatggggacccc	6	17	2	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr8:113529405A>T	ENST00000297405.5	-	28	4858	c.4614T>A	c.(4612-4614)acT>acA	p.T1538T	CSMD3_ENST00000455883.2_Silent_p.T1434T|CSMD3_ENST00000352409.3_Silent_p.T1538T|CSMD3_ENST00000343508.3_Silent_p.T1498T	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1538	Sushi 8. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						CCCCATTTCGAGTCCCATTCA	0.438										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.T1538T		Atlas-SNP	.											.	CSMD3	2325	.	0			c.T4614A						.						76	68	71					8																	113529405		2203	4300	6503	SO:0001819	synonymous_variant	114788	exon28			ATTTCGAGTCCCA	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.4614T>A	chr8.hg19:g.113529405A>T		72.0	0.0		125.0	14.0	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	hg19	CCDS6315.1																																																																																			.	.		0.438	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	113529405	A	T	113529405	2	4	333	1	0	0	0	0	0	0	0	1	3948	291	11	4		4	CSMD3	8	113529405	Silent	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	25280194	113529405	32834617	99	46441										
KCNQ3	3786	hgsc.bcm.edu	37	chr8	133192469	133192469	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	acctctccggtccatccgcaGcatgcgcaggatctgcagga	11	15	2	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr8:133192469G>T	ENST00000388996.4	-	4	1132	c.712C>A	c.(712-714)Ctg>Atg	p.L238M	KCNQ3_ENST00000519445.1_Missense_Mutation_p.L238M|KCNQ3_ENST00000521134.1_Missense_Mutation_p.L118M	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	238					axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	70	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	TCCATCCGCAGCATGCGCAGG	0.592																																					p.L238M		Atlas-SNP	.											.	KCNQ3	164	.	0			c.C712A						.						97	87	91					8																	133192469		2203	4300	6503	SO:0001583	missense	3786	exon4			TCCGCAGCATGCG	AB208890	CCDS34943.1, CCDS56554.1	8q24	2012-07-05			ENSG00000184156	ENSG00000184156		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6297	protein-coding gene	gene with protein product		602232		EBN2		9425900, 16382104	Standard	NM_004519		Approved	Kv7.3	uc003ytj.3	O43525	OTTHUMG00000137472	ENST00000388996.4:c.712C>A	chr8.hg19:g.133192469G>T	ENSP00000373648:p.Leu238Met	35.0	0.0		57.0	9.0	NM_004519	A2VCT8|B4DJY4|E7EQ89	Missense_Mutation	SNP	ENST00000388996.4	hg19	CCDS34943.1	.	.	.	.	.	.	.	.	.	.	G	19.39	3.819329	0.71028	.	.	ENSG00000184156	ENST00000388996;ENST00000521134;ENST00000519445;ENST00000542679;ENST00000423790	D;D;D	0.99158	-5.5;-5.5;-5.5	5.66	5.66	0.87406	Ion transport (1);	0.159984	0.43110	D	0.000615	D	0.98767	0.9585	L	0.54323	1.7	0.51482	D	0.999921	D;D	0.62365	0.991;0.991	P;P	0.62740	0.906;0.906	D	0.98928	1.0786	10	0.87932	D	0	-14.317	13.6735	0.62440	0.0:0.0:0.8457:0.1543	.	238;238	E7ET42;O43525	.;KCNQ3_HUMAN	M	238;118;238;227;117	ENSP00000373648:L238M;ENSP00000429799:L118M;ENSP00000428790:L238M	ENSP00000373648:L238M	L	-	1	2	KCNQ3	133261651	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.810000	0.55613	2.680000	0.91292	0.561000	0.74099	CTG	.	.		0.592	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519		T	133192469	G	T	133192469	3	4	333	1	0	0	0	0	1	0	0	0	8093	962	34	3	1954	3	KCNQ3	8	133192469	Missense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	19663064	133192469	13171553	100	46442										
DENND3	22898	hgsc.bcm.edu	37	chr8	142190927	142190927	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gggggaggcgttcccacaagCggtggacgtgctgctctaca	16	11	1	0	rs201075864	byFrequency	TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr8:142190927C>T	ENST00000262585.2	+	17	2956	c.2678C>T	c.(2677-2679)gCg>gTg	p.A893V	DENND3_ENST00000518806.1_3'UTR|DENND3_ENST00000424248.1_Missense_Mutation_p.A841V|DENND3_ENST00000519811.1_Missense_Mutation_p.A973V	NM_014957.2	NP_055772.2	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	893					cellular protein catabolic process (GO:0044257)|endosome to lysosome transport (GO:0008333)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.A893V(1)		breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(4)|stomach(2)|urinary_tract(1)	55	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)			TTCCCACAAGCGGTGGACGTG	0.577													C|||	2	0.000399361	0	0	5008	,	,		17918	0		0	False		,,,				2504	0.002				p.A893V		Atlas-SNP	.											DENND3,colon,carcinoma,0,1	DENND3	127	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2678T						.						62	58	59					8																	142190927		2203	4300	6503	SO:0001583	missense	22898	exon17			CACAAGCGGTGGA	AB020677	CCDS34947.1	8q24.3	2013-01-10				ENSG00000105339		"DENN/MADD domain containing", "WD repeat domain containing"	29134	protein-coding gene	gene with protein product						10048485	Standard	NM_014957		Approved	KIAA0870	uc003yvy.3	A2RUS2		ENST00000262585.2:c.2678C>T	chr8.hg19:g.142190927C>T	ENSP00000262585:p.Ala893Val	25.0	0.0		66.0	16.0	NM_014957	B7ZM28|O94947|Q2TAM7|Q6ZMS6|Q96DK3	Missense_Mutation	SNP	ENST00000262585.2	hg19	CCDS34947.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.390099	0.82902	.	.	ENSG00000105339	ENST00000262585;ENST00000424248;ENST00000519811;ENST00000517985	T;T;T	0.15834	2.84;2.39;2.82	4.61	3.74	0.42951	WD40 repeat-like-containing domain (1);	0.207546	0.45361	D	0.000370	T	0.27594	0.0678	M	0.64997	1.995	0.37300	D	0.908673	D;D	0.69078	0.997;0.997	P;P	0.51055	0.657;0.657	T	0.26849	-1.0091	10	0.72032	D	0.01	-25.6476	12.675	0.56889	0.0:0.9196:0.0:0.0804	.	973;893	E9PF32;A2RUS2	.;DEND3_HUMAN	V	893;841;973;53	ENSP00000262585:A893V;ENSP00000410594:A841V;ENSP00000428714:A973V	ENSP00000262585:A893V	A	+	2	0	DENND3	142260109	0.993000	0.37304	0.010000	0.14722	0.001000	0.01503	3.643000	0.54374	0.936000	0.37367	0.563000	0.77884	GCG	.	C|0.999;T|0.001		0.577	DENND3-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_014957		T	142190927	C	T	142190927	3	4	333	1	0	0	0	0	1	0	0	0	4434	768	27	1	2740	1	DENND3	8	142190927	Missense_Mutation	SNP	C	TCGA-RC-A6M4-01A-11D-A32G-10	8998458	142190927	4173095	101	46443										
TOP1MT	116447	hgsc.bcm.edu	37	chr8	144408432	144408432	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ggactttccgggctgcggccTtgtccacaaagtatctgtgg	13	11	1	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr8:144408432T>C	ENST00000329245.4	-	4	477	c.443A>G	c.(442-444)aAg>aGg	p.K148R	TOP1MT_ENST00000519148.1_Missense_Mutation_p.K50R|TOP1MT_ENST00000523676.1_Missense_Mutation_p.K50R|TOP1MT_ENST00000521193.1_Missense_Mutation_p.K50R	NM_052963.2	NP_443195.1	Q969P6	TOP1M_HUMAN	topoisomerase (DNA) I, mitochondrial	148					DNA replication (GO:0006260)|DNA topological change (GO:0006265)	chromosome (GO:0005694)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)			endometrium(5)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	23	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)		Irinotecan(DB00762)|Topotecan(DB01030)	GGCTGCGGCCTTGTCCACAAA	0.577																																					p.K148R		Atlas-SNP	.											.	TOP1MT	63	.	0			c.A443G						.						148	127	134					8																	144408432		2203	4300	6503	SO:0001583	missense	116447	exon4			GCGGCCTTGTCCA	AF349018	CCDS6400.1, CCDS59115.1	8q24.3	2006-04-12				ENSG00000184428			29787	protein-coding gene	gene with protein product		606387				11526219	Standard	NM_052963		Approved		uc003yxz.4	Q969P6		ENST00000329245.4:c.443A>G	chr8.hg19:g.144408432T>C	ENSP00000328835:p.Lys148Arg	68.0	0.0		163.0	9.0	NM_052963	B7ZAR5|E7ES89|Q86ST4|Q86V82	Missense_Mutation	SNP	ENST00000329245.4	hg19	CCDS6400.1	.	.	.	.	.	.	.	.	.	.	T	12.21	1.870449	0.33069	.	.	ENSG00000184428	ENST00000329245;ENST00000521193;ENST00000519148;ENST00000523676;ENST00000522041;ENST00000519591;ENST00000518007	T;T;T;T;T;T;T	0.31510	1.49;1.49;1.49;1.49;1.49;1.49;1.49	3.36	-0.293	0.12835	DNA topoisomerase I, domain 1 (1);DNA topoisomerase I, DNA binding, eukaryotic-type (2);	0.138563	0.31697	N	0.007213	T	0.19565	0.0470	L	0.34521	1.04	0.30357	N	0.784224	B	0.20459	0.045	B	0.26693	0.072	T	0.12451	-1.0547	10	0.33141	T	0.24	-7.9517	6.7769	0.23624	0.0:0.2847:0.0:0.7153	.	148	Q969P6	TOP1M_HUMAN	R	148;50;50;50;50;50;117	ENSP00000328835:K148R;ENSP00000428369:K50R;ENSP00000429169:K50R;ENSP00000429181:K50R;ENSP00000427998:K50R;ENSP00000429177:K50R;ENSP00000430209:K117R	ENSP00000328835:K148R	K	-	2	0	TOP1MT	144479807	0.001000	0.12720	0.020000	0.16555	0.808000	0.45660	0.470000	0.22084	-0.275000	0.09219	0.334000	0.21626	AAG	.	.		0.577	TOP1MT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381247.3	NM_052963		C	144408432	T	C	144408432	3	2	333	1	0	0	0	0	1	0	0	0	16379	1609	56	2	1406	2	TOP1MT	8	144408432	Missense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	2217505	144408432	1955590	102	46444										
RRAGA	10670	hgsc.bcm.edu	37	chr9	19050112	19050112	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ggaagacctgaggcgtctgtCtcgcccgctggagtgtgctt	15	11	2	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr9:19050112C>T	ENST00000380527.1	+	1	741	c.455C>T	c.(454-456)tCt>tTt	p.S152F		NM_006570.4	NP_006561.1			Ras-related GTP binding A											endometrium(1)|large_intestine(1)|lung(1)	3						AGGCGTCTGTCTCGCCCGCTG	0.527																																					p.S152F		Atlas-SNP	.											.	RRAGA	17	.	0			c.C455T						.						64	62	63					9																	19050112		2203	4300	6503	SO:0001583	missense	10670	exon1			GTCTGTCTCGCCC	BC006433	CCDS6488.1	9p21.3	2008-02-05			ENSG00000155876	ENSG00000155876			16963	protein-coding gene	gene with protein product		612194				7499430, 8995684	Standard	NM_006570		Approved	RAGA, FIP-1	uc003znj.3	Q7L523	OTTHUMG00000019621	ENST00000380527.1:c.455C>T	chr9.hg19:g.19050112C>T	ENSP00000369899:p.Ser152Phe	62.0	0.0		52.0	18.0	NM_006570		Missense_Mutation	SNP	ENST00000380527.1	hg19	CCDS6488.1	.	.	.	.	.	.	.	.	.	.	C	17.50	3.405538	0.62288	.	.	ENSG00000155876	ENST00000380527	T	0.66995	-0.24	4.98	4.98	0.66077	.	0.000000	0.85682	D	0.000000	T	0.71609	0.3360	M	0.82132	2.575	0.80722	D	1	P	0.34815	0.47	B	0.41036	0.346	T	0.68006	-0.5523	10	0.18710	T	0.47	-4.4958	16.1608	0.81704	0.0:1.0:0.0:0.0	.	152	Q7L523	RRAGA_HUMAN	F	152	ENSP00000369899:S152F	ENSP00000369899:S152F	S	+	2	0	RRAGA	19040112	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.212000	0.77941	2.770000	0.95276	0.655000	0.94253	TCT	.	.		0.527	RRAGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051824.1	NM_006570		T	19050112	C	T	19050112	3	4	333	1	0	0	0	0	1	0	0	0	13687	913	32	3	457	3	RRAGA	9	19050112	Missense_Mutation	SNP	C	TCGA-RC-A6M4-01A-11D-A32G-10		19050112	122163319	103	46445										
IFNA6	3443	hgsc.bcm.edu	37	chr9	21350829	21350829	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	cagatcacagtccagagagcAgcttgacttgcagctgagca	11	11	1	4			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr9:21350829A>T	ENST00000380210.1	-	1	548	c.58T>A	c.(58-60)Tgc>Agc	p.C20S		NM_021002.2	NP_066282.1	P05013	IFNA6_HUMAN	interferon, alpha 6	20					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			large_intestine(3)|lung(7)|skin(1)	11				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.116)		TCCAGAGAGCAGCTTGACTTG	0.517																																					p.C20S		Atlas-SNP	.											.	IFNA6	27	.	0			c.T58A						.						104	102	103					9																	21350829		2203	4300	6503	SO:0001583	missense	3443	exon1			GAGAGCAGCTTGA		CCDS6504.1	9p22	2010-12-10			ENSG00000120235	ENSG00000120235		"Interferons"	5427	protein-coding gene	gene with protein product		147566				1385305	Standard	NM_021002		Approved	IFN-alphaK	uc011lni.2	P05013	OTTHUMG00000019676	ENST00000380210.1:c.58T>A	chr9.hg19:g.21350829A>T	ENSP00000369558:p.Cys20Ser	87.0	0.0		69.0	23.0	NM_021002	Q5VYQ1	Missense_Mutation	SNP	ENST00000380210.1	hg19	CCDS6504.1	.	.	.	.	.	.	.	.	.	.	A	11.60	1.688300	0.29962	.	.	ENSG00000120235	ENST00000380210	T	0.03035	4.07	3.78	-0.727	0.11166	Four-helical cytokine-like, core (1);	0.536026	0.18939	N	0.126999	T	0.04998	0.0134	M	0.73598	2.24	0.09310	N	1	B	0.31009	0.303	B	0.31337	0.128	T	0.24835	-1.0149	10	0.49607	T	0.09	.	4.873	0.13642	0.5283:0.3635:0.1081:0.0	.	20	P05013	IFNA6_HUMAN	S	20	ENSP00000369558:C20S	ENSP00000369558:C20S	C	-	1	0	IFNA6	21340829	0.000000	0.05858	0.000000	0.03702	0.136000	0.21042	-1.122000	0.03267	0.006000	0.14734	0.482000	0.46254	TGC	.	.		0.517	IFNA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051905.1	NM_021002		T	21350829	A	T	21350829	3	4	333	1	0	0	0	0	1	0	0	0	7550	188	7	4	513	4	IFNA6	9	21350829	Missense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	2300717	21350829	119862602	104	46446										
TRPM6	140803	hgsc.bcm.edu	37	chr9	77435310	77435310	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	aaagtgttctgaatcatgcaGatgatctcctctttcacctg	7	10	5	3			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr9:77435310G>T	ENST00000360774.1	-	9	1281	c.1044C>A	c.(1042-1044)atC>atA	p.I348I	TRPM6_ENST00000376872.3_Silent_p.I348I|TRPM6_ENST00000376864.4_Silent_p.I348I|TRPM6_ENST00000361255.3_Silent_p.I343I|TRPM6_ENST00000449912.2_Silent_p.I343I|TRPM6_ENST00000451710.3_Silent_p.I348I|TRPM6_ENST00000376871.3_Silent_p.I348I|TRPM6_ENST00000483186.1_5'UTR	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	348					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						GAATCATGCAGATGATCTCCT	0.438																																					p.I348I		Atlas-SNP	.											.	TRPM6	377	.	0			c.C1044A						.						131	121	125					9																	77435310		2203	4300	6503	SO:0001819	synonymous_variant	140803	exon9			CATGCAGATGATC	AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"Voltage-gated ion channels / Transient receptor potential cation channels"	17995	protein-coding gene	gene with protein product		607009	"hypomagnesemia, secondary hypocalcemia"	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.1044C>A	chr9.hg19:g.77435310G>T		32.0	0.0		52.0	18.0	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Silent	SNP	ENST00000360774.1	hg19	CCDS6647.1																																																																																			.	.		0.438	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662		T	77435310	G	T	77435310	2	4	333	1	0	0	0	0	0	0	0	1	16605	932	33	3		3	TRPM6	9	77435310	Silent	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	56084481	77435310	63778121	105	46447										
ERP44	23071	hgsc.bcm.edu	37	chr9	102784454	102784454	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tcttcatcatcatcccattaCgaaacaatttgagggttggg	8	9	4	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr9:102784454C>T	ENST00000262455.6	-	5	540	c.341G>A	c.(340-342)cGt>cAt	p.R114H		NM_015051.1	NP_055866.1	Q9BS26	ERP44_HUMAN	endoplasmic reticulum protein 44	114	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|glycoprotein metabolic process (GO:0009100)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)	protein disulfide isomerase activity (GO:0003756)			NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|prostate(2)	19						CATCCCATTACGAAACAATTT	0.393																																					p.R114H		Atlas-SNP	.											.	ERP44	38	.	0			c.G341A						.						150	140	144					9																	102784454		2203	4300	6503	SO:0001583	missense	23071	exon5			CCATTACGAAACA	AB011145	CCDS35082.1	9q22.33	2011-10-19	2009-02-23	2009-02-23	ENSG00000023318	ENSG00000023318		"Protein disulfide isomerases"	18311	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 10"	609170	"thioredoxin domain containing 4 (endoplasmic reticulum)"	TXNDC4		11847130	Standard	NM_015051		Approved	KIAA0573, PDIA10	uc004bam.3	Q9BS26	OTTHUMG00000020363	ENST00000262455.6:c.341G>A	chr9.hg19:g.102784454C>T	ENSP00000262455:p.Arg114His	220.0	0.0		243.0	52.0	NM_015051	O60319|Q4VXC1|Q5VWZ7|Q6UW14|Q8WX67	Missense_Mutation	SNP	ENST00000262455.6	hg19	CCDS35082.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.131960	0.77662	.	.	ENSG00000023318	ENST00000262455	T	0.42131	0.98	5.81	4.91	0.64330	Thioredoxin domain (1);Thioredoxin-like fold (3);	0.000000	0.85682	D	0.000000	T	0.41743	0.1172	L	0.49513	1.565	0.80722	D	1	B	0.34181	0.44	B	0.36418	0.224	T	0.44081	-0.9351	10	0.72032	D	0.01	-2.8096	15.3023	0.73962	0.0:0.9319:0.0:0.0681	.	114	Q9BS26	ERP44_HUMAN	H	114	ENSP00000262455:R114H	ENSP00000262455:R114H	R	-	2	0	ERP44	101824275	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.406000	0.80017	2.752000	0.94435	0.557000	0.71058	CGT	.	.		0.393	ERP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053402.1	XM_088476		T	102784454	C	T	102784454	3	4	333	1	0	0	0	0	1	0	0	0	5245	536	19	1	911	1	ERP44	9	102784454	Missense_Mutation	SNP	C	TCGA-RC-A6M4-01A-11D-A32G-10	25349144	102784454	38428977	106	46448										
DBC1	1620	hgsc.bcm.edu	37	chr9	121930107	121930107	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gccaccgagggtcaaagaagGtgtcgaggcggatctcgttg	16	9	2	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr9:121930107G>T	ENST00000265922.3	-	8	2002	c.1541C>A	c.(1540-1542)aCc>aAc	p.T514N	BRINP1_ENST00000482797.1_Intron	NM_014618.2	NP_055433.2	O60477	BRNP1_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 1	514					cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell cycle (GO:0045786)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	cytoplasm (GO:0005737)											GTCAAAGAAGGTGTCGAGGCG	0.567																																					p.T514N		Atlas-SNP	.											.	DBC1	194	.	0			c.C1541A						.						225	161	183					9																	121930107		2203	4300	6503	SO:0001583	missense	1620	exon8			AAGAAGGTGTCGA	AF027734	CCDS6822.1	9q32-q33	2013-08-06	2013-08-06	2013-07-31	ENSG00000078725	ENSG00000078725			2687	protein-coding gene	gene with protein product		602865	"deleted in bladder cancer chromosome region candidate 1", "deleted in bladder cancer 1"	DBCCR1, DBC1		9175739, 10444335, 15193422	Standard	NM_014618		Approved	FAM5A	uc004bkc.2	O60477	OTTHUMG00000021020	ENST00000265922.3:c.1541C>A	chr9.hg19:g.121930107G>T	ENSP00000265922:p.Thr514Asn	57.0	0.0		68.0	25.0	NM_014618	Q6IPV6|Q6P1A0|Q8WU22	Missense_Mutation	SNP	ENST00000265922.3	hg19	CCDS6822.1	.	.	.	.	.	.	.	.	.	.	G	18.93	3.727914	0.69074	.	.	ENSG00000078725	ENST00000373969;ENST00000265922	T	0.14640	2.49	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.24044	0.0582	N	0.16368	0.405	0.80722	D	1	D	0.57899	0.981	D	0.67231	0.95	T	0.03453	-1.1035	10	0.42905	T	0.14	-25.0014	19.91	0.97023	0.0:0.0:1.0:0.0	.	514	O60477	DBC1_HUMAN	N	514	ENSP00000265922:T514N	ENSP00000265922:T514N	T	-	2	0	DBC1	120969928	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.911000	0.87458	2.702000	0.92279	0.655000	0.94253	ACC	.	.		0.567	BRINP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055440.2	NM_014618		T	121930107	G	T	121930107	3	4	333	1	0	0	0	0	1	0	0	0	4249	1261	44	3	748	3	DBC1	9	121930107	Missense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	19145653	121930107	19283324	107	46449										
CIZ1	25792	hgsc.bcm.edu	37	chr9	130929424	130929424	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	agcccttccactcctctctgGatatatctctggacctcacc	5	17	3	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr9:130929424G>T	ENST00000393608.1	-	15	2517	c.2315C>A	c.(2314-2316)tCc>tAc	p.S772Y	CIZ1_ENST00000325721.8_Missense_Mutation_p.S743Y|CIZ1_ENST00000476727.2_5'UTR|CIZ1_ENST00000538431.1_Missense_Mutation_p.S798Y|CIZ1_ENST00000372948.3_Missense_Mutation_p.S716Y|CIZ1_ENST00000372938.5_Missense_Mutation_p.S772Y|CIZ1_ENST00000541172.1_Missense_Mutation_p.S671Y|CIZ1_ENST00000357558.5_Missense_Mutation_p.S744Y|CIZ1_ENST00000277465.4_Missense_Mutation_p.S744Y|CIZ1_ENST00000372954.1_Missense_Mutation_p.S692Y	NM_012127.2	NP_036259.2	Q9ULV3	CIZ1_HUMAN	CDKN1A interacting zinc finger protein 1	772					maintenance of protein location in nucleus (GO:0051457)|positive regulation of DNA-dependent DNA replication initiation (GO:0032298)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|liver(1)|lung(9)|ovary(3)|prostate(2)|urinary_tract(2)	35						CTCCTCTCTGGATATATCTCT	0.597																																					p.S828Y		Atlas-SNP	.											.	CIZ1	75	.	0			c.C2483A						.						91	69	76					9																	130929424		2203	4300	6503	SO:0001583	missense	25792	exon16			TCTCTGGATATAT	AB030835	CCDS6894.1, CCDS48033.1, CCDS48034.1, CCDS75910.1	9q34.1	2012-10-05			ENSG00000148337	ENSG00000148337			16744	protein-coding gene	gene with protein product		611420				10529385	Standard	NM_001131015		Approved	LSFR1, ZNF356	uc011mas.2	Q9ULV3	OTTHUMG00000020735	ENST00000393608.1:c.2315C>A	chr9.hg19:g.130929424G>T	ENSP00000377232:p.Ser772Tyr	53.0	0.0		60.0	29.0	NM_001257975	A8K9J8|B4E131|B7ZAS8|Q5SYW3|Q5SYW5|Q8WU72|Q9H868|Q9NYM8|Q9UHK4|Q9Y3F9|Q9Y3G0	Missense_Mutation	SNP	ENST00000393608.1	hg19	CCDS6894.1	.	.	.	.	.	.	.	.	.	.	G	18.89	3.719921	0.68844	.	.	ENSG00000148337	ENST00000372954;ENST00000393608;ENST00000538431;ENST00000357558;ENST00000325721;ENST00000537314;ENST00000541172;ENST00000277465;ENST00000372948;ENST00000372938;ENST00000415526	T;T;T;T;T;T;T;T;T;T	0.37915	1.17;1.34;1.35;1.49;1.34;1.76;1.49;1.17;1.34;1.92	5.15	3.25	0.37280	.	0.671596	0.13180	N	0.407638	T	0.48169	0.1485	L	0.48642	1.525	0.09310	N	1	D;D;D;D;D;D;D	0.76494	0.999;0.996;0.998;0.997;0.998;0.998;0.984	D;P;D;D;D;D;P	0.68039	0.949;0.851;0.929;0.955;0.931;0.953;0.804	T	0.26258	-1.0108	10	0.72032	D	0.01	-6.3263	7.7015	0.28625	0.0835:0.0:0.7545:0.1621	.	798;711;716;692;772;743;744	B7Z3U7;B4E0A3;Q9ULV3-4;Q9ULV3-3;Q9ULV3;Q9ULV3-2;Q5SYW2	.;.;.;.;CIZ1_HUMAN;.;.	Y	692;772;798;744;743;711;671;744;716;772;694	ENSP00000362045:S692Y;ENSP00000377232:S772Y;ENSP00000439244:S798Y;ENSP00000350169:S744Y;ENSP00000320374:S743Y;ENSP00000445057:S671Y;ENSP00000277465:S744Y;ENSP00000362039:S716Y;ENSP00000362029:S772Y;ENSP00000398011:S694Y	ENSP00000277465:S744Y	S	-	2	0	CIZ1	129969245	0.150000	0.22732	0.000000	0.03702	0.691000	0.40173	3.056000	0.49923	0.642000	0.30620	0.655000	0.94253	TCC	.	.		0.597	CIZ1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054399.1	NM_012127		T	130929424	G	T	130929424	3	4	333	1	0	0	0	0	1	0	0	0	3443	1174	41	3	393	3	CIZ1	9	130929424	Missense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	8999317	130929424	10284007	108	46450										
IDI1	22884	hgsc.bcm.edu	37	chr10	1094803	1094803	+	5'Flank	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tccgccgcccgtccacagtaCctgatcagcctccggccaca	8	20	1	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr10:1094803C>T	ENST00000358220.1	+	0	0				IDI1_ENST00000491735.1_Splice_Site|IDI1_ENST00000381344.3_Splice_Site			Q9Y2I8	WDR37_HUMAN	WD repeat domain 37											breast(2)|endometrium(2)|kidney(1)|lung(9)|prostate(2)|skin(1)	17		all_epithelial(10;0.0449)|Colorectal(49;0.142)		Epithelial(11;0.134)		GTCCACAGTACCTGATCAGCC	0.756																																					.		Atlas-SNP	.											.	IDI1	22	.	0			c.140+1G>A						.						12	12	12					10																	1094803		2186	4268	6454	SO:0001631	upstream_gene_variant	3422	exon2			ACAGTACCTGATC	AB023199	CCDS7057.1	10p15.3	2013-01-09			ENSG00000047056	ENSG00000047056		"WD repeat domain containing"	31406	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_014023		Approved	KIAA0982	uc001igf.1	Q9Y2I8	OTTHUMG00000017540		chr10.hg19:g.1094803C>T	Exception_encountered	56.0	0.0		52.0	22.0	NM_004508	A8K976|D3DRQ7|Q5SW03|Q8WVG2|Q9NTJ6	Splice_Site	SNP	ENST00000358220.1	hg19	CCDS7057.1	.	.	.	.	.	.	.	.	.	.	C	7.409	0.634434	0.14322	.	.	ENSG00000067064	ENST00000381344	.	.	.	0.91	0.91	0.19337	.	.	.	.	.	.	.	.	.	.	.	0.27152	N	0.961373	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.117	0.14840	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	IDI1	1084803	0.001000	0.12720	0.004000	0.12327	0.061000	0.15899	1.312000	0.33574	0.780000	0.33566	0.430000	0.28490	.	.	.		0.756	WDR37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046418.1	NM_014023		T	1094803	C	T	1094803	1	4	333	0	1	0	0	0	0	0	0	0	7508	521	18	3		3	IDI1	10	1094803	5'Flank	SNP	C	TCGA-RC-A6M4-01A-11D-A32G-10		1094803	134439944	109	46451										
PIP4K2A	5305	hgsc.bcm.edu	37	chr10	22829005	22829005	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	acctccttcctaggcgagtcTgcagagacaggagagcaatg	12	11	1	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr10:22829005T>A	ENST00000376573.4	-	9	1265		c.e9-2		PIP4K2A_ENST00000545335.1_Splice_Site|PIP4K2A_ENST00000323883.7_Splice_Site	NM_005028.4	NP_005019.2	P48426	PI42A_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, alpha						megakaryocyte development (GO:0035855)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|1-phosphatidylinositol-5-phosphate 4-kinase activity (GO:0016309)|ATP binding (GO:0005524)			endometrium(4)|kidney(13)|large_intestine(4)|lung(6)|ovary(1)|skin(1)	29						TAGGCGAGTCTGCAGAGACAG	0.502																																					.		Atlas-SNP	.											.	PIP4K2A	59	.	0			c.1037-2A>T						.						112	103	106					10																	22829005		2203	4300	6503	SO:0001630	splice_region_variant	5305	exon10			CGAGTCTGCAGAG	S78798	CCDS7141.1	10p12.2	2007-08-21	2007-08-14	2007-08-14	ENSG00000150867	ENSG00000150867			8997	protein-coding gene	gene with protein product		603140	"phosphatidylinositol-4-phosphate 5-kinase, type II, alpha"	PIP5K2A		7852364, 9367159	Standard	NM_005028		Approved	PIP5KIIA, PIP5KIIalpha	uc001irl.4	P48426	OTTHUMG00000017810	ENST00000376573.4:c.1037-2A>T	chr10.hg19:g.22829005T>A		36.0	0.0		46.0	22.0	NM_005028	B0YJ66|B4DGX2|D3DRV1|P53807|Q5VUX3	Splice_Site	SNP	ENST00000376573.4	hg19	CCDS7141.1	.	.	.	.	.	.	.	.	.	.	T	12.74	2.027360	0.35797	.	.	ENSG00000150867	ENST00000376573;ENST00000323883;ENST00000545335	.	.	.	5.91	5.91	0.95273	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3351	0.83056	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	PIP4K2A	22869011	1.000000	0.71417	0.995000	0.50966	0.118000	0.20060	7.443000	0.80521	2.262000	0.75019	0.528000	0.53228	.	.	.		0.502	PIP4K2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047193.1	NM_005028	Intron	A	22829005	T	A	22829005	5	1	333	1	0	0	0	0	0	0	1	0	11945	1594	55	4	193	4	PIP4K2A	10	22829005	Splice_Site	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	21734202	22829005	112705742	110	46452										
RAB18	22931	hgsc.bcm.edu	37	chr10	27793366	27793366	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gagtggggtgggcaagtccaGgtgaggcggaggtgcgggtc	23	6	0	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr10:27793366G>C	ENST00000356940.6	+	1	170	c.68G>C	c.(67-69)aGc>aCc	p.S23T	RAB18_ENST00000465772.1_3'UTR|RAB18_ENST00000375802.3_Splice_Site_p.S23T|RAB18_ENST00000535776.1_Splice_Site_p.S23T	NM_001256410.1|NM_001256415.1|NM_021252.4	NP_001243339.1|NP_001243344.1|NP_067075.1	Q9NP72	RAB18_HUMAN	RAB18, member RAS oncogene family	23					brain development (GO:0007420)|endoplasmic reticulum tubular network organization (GO:0071786)|eye development (GO:0001654)|GTP catabolic process (GO:0006184)|lipid particle organization (GO:0034389)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	endoplasmic reticulum tubular network (GO:0071782)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			kidney(1)|large_intestine(1)|lung(1)	3						GGCAAGTCCAGGTGAGGCGGA	0.667																																					p.S23T		Atlas-SNP	.											.	RAB18	18	.	0			c.G68C						.						78	74	75					10																	27793366		2184	4274	6458	SO:0001630	splice_region_variant	22931	exon1			AGTCCAGGTGAGG	AJ277145	CCDS7155.1, CCDS58073.1, CCDS73080.1, CCDS73081.1	10p12	2011-03-07			ENSG00000099246	ENSG00000099246		"RAB, member RAS oncogene"	14244	protein-coding gene	gene with protein product		602207				10648831	Standard	NM_021252		Approved		uc001itw.4	Q9NP72	OTTHUMG00000017861	ENST00000356940.6:c.68+1G>C	chr10.hg19:g.27793366G>C		44.0	0.0		55.0	31.0	NM_001256415	B3KMC7|B7Z333|D3DRW1|Q53FX8|Q56UN9|Q6FIH1	Missense_Mutation	SNP	ENST00000356940.6	hg19	CCDS7155.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.847570	0.91277	.	.	ENSG00000099246	ENST00000356940;ENST00000535776;ENST00000540268;ENST00000375802	T;T;T	0.79247	-0.06;-1.25;-0.06	5.54	4.63	0.57726	RNA polymerase sigma factor 54, interaction (1);Small GTP-binding protein domain (1);	.	.	.	.	D	0.88362	0.6416	M	0.83012	2.62	0.43283	D	0.995251	D;D;D;D	0.76494	0.987;0.998;0.998;0.999	P;D;D;D	0.78314	0.9;0.944;0.991;0.965	D	0.89814	0.3984	9	0.62326	D	0.03	.	15.1112	0.72359	0.0:0.1423:0.8577:0.0	.	23;23;23;23	B7Z333;B7Z4P9;Q56UN9;Q9NP72	.;.;.;RAB18_HUMAN	T	23	ENSP00000349415:S23T;ENSP00000439321:S23T;ENSP00000364960:S23T	ENSP00000349415:S23T	S	+	2	0	RAB18	27833372	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	6.959000	0.76031	1.328000	0.45358	0.561000	0.74099	AGC	.	.		0.667	RAB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047326.2	NM_021252	Missense_Mutation	C	27793366	G	C	27793366	5	2	333	1	0	0	0	0	0	0	1	0	12918	1014	35	4	70	4	RAB18	10	27793366	Splice_Site	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	4964361	27793366	107741381	111	46453										
OPN4	94233	hgsc.bcm.edu	37	chr10	88415951	88415951	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ctgcctgggtccccctccccAcggttgatgttccagaccat	9	17	0	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr10:88415951A>G	ENST00000241891.5	+	2	351	c.184A>G	c.(184-186)Acg>Gcg	p.T62A	OPN4_ENST00000372071.2_Missense_Mutation_p.T62A	NM_033282.3	NP_150598.1	Q9UHM6	OPN4_HUMAN	opsin 4	62					phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|rhodopsin mediated signaling pathway (GO:0016056)|rhythmic process (GO:0048511)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	11-cis retinal binding (GO:0005502)|G-protein coupled photoreceptor activity (GO:0008020)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(5)|ovary(3)	18						CCCCCTCCCCACGGTTGATGT	0.567																																					p.T62A		Atlas-SNP	.											.	OPN4	61	.	0			c.A184G						.						119	109	112					10																	88415951		2203	4300	6503	SO:0001583	missense	94233	exon2			CTCCCCACGGTTG	AF147788	CCDS7376.1, CCDS31237.1	10q22	2012-08-08	2008-04-16		ENSG00000122375	ENSG00000122375		"GPCR / Class A : Opsin receptors"	14449	protein-coding gene	gene with protein product	"melanopsin"	606665	"opsin 4 (melanopsin)"			10632589	Standard	NM_001030015		Approved	MOP, melanopsin	uc001kdp.3	Q9UHM6	OTTHUMG00000018654	ENST00000241891.5:c.184A>G	chr10.hg19:g.88415951A>G	ENSP00000241891:p.Thr62Ala	105.0	0.0		104.0	43.0	NM_033282	B7ZLB3|Q14D01|Q2PP22|Q8NGQ9	Missense_Mutation	SNP	ENST00000241891.5	hg19	CCDS7376.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.470896	0.84533	.	.	ENSG00000122375	ENST00000372071;ENST00000241891;ENST00000443292	T;T;T	0.36699	1.24;1.24;1.24	5.46	5.46	0.80206	.	.	.	.	.	T	0.60919	0.2306	M	0.81497	2.545	0.51482	D	0.999928	D;D;D	0.89917	0.997;0.997;1.0	D;D;D	0.87578	0.917;0.917;0.998	T	0.60777	-0.7196	9	0.28530	T	0.3	.	14.7117	0.69238	1.0:0.0:0.0:0.0	.	62;62;62	C9JWU6;Q9UHM6;Q9UHM6-2	.;OPN4_HUMAN;.	A	62	ENSP00000361141:T62A;ENSP00000241891:T62A;ENSP00000393132:T62A	ENSP00000241891:T62A	T	+	1	0	OPN4	88405931	1.000000	0.71417	0.965000	0.40720	0.924000	0.55760	8.994000	0.93529	2.083000	0.62718	0.459000	0.35465	ACG	.	.		0.567	OPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049158.2	NM_033282		G	88415951	A	G	88415951	3	3	333	1	0	0	0	0	1	0	0	0	10891	159	6	2	190	2	OPN4	10	88415951	Missense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	60622585	88415951	47118796	112	46454										
HPSE2	60495	hgsc.bcm.edu	37	chr10	100995494	100995494	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	aagtagagagcccccggggcTaggcacgcgggggggcggga	21	10	0	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr10:100995494T>A	ENST00000370552.3	-	1	125	c.66A>T	c.(64-66)ctA>ctT	p.L22L	HPSE2_ENST00000404542.1_Silent_p.L22L|HPSE2_ENST00000370549.1_Silent_p.L22L|HPSE2_ENST00000370546.1_Silent_p.L22L	NM_021828.4	NP_068600.4	Q8WWQ2	HPSE2_HUMAN	heparanase 2 (inactive)	22					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	intracellular (GO:0005622)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	heparan sulfate proteoglycan binding (GO:0043395)|heparanase activity (GO:0030305)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	40				Epithelial(162;1.8e-09)|all cancers(201;4.72e-07)		CCCCCGGGGCTAGGCACGCGG	0.587																																					p.L22L		Atlas-SNP	.											.	HPSE2	203	.	0			c.A66T						.						44	52	49					10																	100995494		2203	4300	6503	SO:0001819	synonymous_variant	60495	exon1			CGGGGCTAGGCAC	AF282885	CCDS7477.1, CCDS53567.1, CCDS53568.1	10q23-q24	2014-05-09	2014-05-09		ENSG00000172987	ENSG00000172987			18374	protein-coding gene	gene with protein product		613469	"urofacial syndrome", "heparanase 2"	UFS		11027606, 20605132, 9199567, 20576607	Standard	NM_021828		Approved	HPA2, HPR2	uc001kpn.2	Q8WWQ2	OTTHUMG00000018880	ENST00000370552.3:c.66A>T	chr10.hg19:g.100995494T>A		103.0	0.0		103.0	49.0	NM_001166246	Q5VUH4|Q5VUH5|Q5VUH6|Q8WWQ1|Q9HB37|Q9HB38|Q9HB39	Silent	SNP	ENST00000370552.3	hg19	CCDS7477.1																																																																																			.	.		0.587	HPSE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049789.1	NM_021828		A	100995494	T	A	100995494	2	1	333	1	0	0	0	0	0	0	0	1	7354	1509	53	4		4	HPSE2	10	100995494	Silent	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	12579543	100995494	34539253	113	46455										
SEC31B	25956	hgsc.bcm.edu	37	chr10	102269083	102269083	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	aatgtagtacctggaaaggaTtcaagtcgagggctctgaca	12	7	2	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr10:102269083T>C	ENST00000370345.3	-	4	486	c.389A>G	c.(388-390)aAt>aGt	p.N130S	SEC31B_ENST00000451524.1_Missense_Mutation_p.N130S|NDUFB8_ENST00000557395.1_Intron|SEC31B_ENST00000535773.1_Intron|SEC31B_ENST00000370329.5_Missense_Mutation_p.N130S|NDUFB8_ENST00000531258.1_Intron	NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	130					protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|vesicle coat (GO:0030120)				NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(3)|lung(17)|ovary(1)|urinary_tract(1)	36		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)		CTGGAAAGGATTCAAGTCGAG	0.493											OREG0020441	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N130S		Atlas-SNP	.											.	SEC31B	84	.	0			c.A389G						.						162	170	168					10																	102269083		2203	4300	6503	SO:0001583	missense	25956	exon4			AAAGGATTCAAGT	AF274863	CCDS7495.1	10q24.32	2013-01-10	2006-10-05	2006-09-07	ENSG00000075826	ENSG00000075826		"WD repeat domain containing"	23197	protein-coding gene	gene with protein product		610258	"SEC31-like 2 (S. cerevisiae)"	SEC31L2		16495487	Standard	NM_015490		Approved	SEC31B-1, DKFZP434M183	uc001krc.1	Q9NQW1	OTTHUMG00000019342	ENST00000370345.3:c.389A>G	chr10.hg19:g.102269083T>C	ENSP00000359370:p.Asn130Ser	70.0	0.0	1365	70.0	22.0	NM_015490	B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Missense_Mutation	SNP	ENST00000370345.3	hg19	CCDS7495.1	.	.	.	.	.	.	.	.	.	.	T	27.1	4.798740	0.90538	.	.	ENSG00000075826	ENST00000370345;ENST00000451524;ENST00000370329	T;T;T	0.54279	0.58;0.58;0.58	5.9	5.9	0.94986	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.59932	0.2230	N	0.20530	0.585	0.80722	D	1	D;D;D;D	0.89917	0.998;1.0;0.99;1.0	D;D;D;D	0.85130	0.946;0.994;0.946;0.997	T	0.65529	-0.6146	10	0.87932	D	0	-17.0889	15.5056	0.75739	0.0:0.0:0.0:1.0	.	130;130;130;130	B4DGE3;Q9NQW1-5;E9PKR7;Q9NQW1	.;.;.;SC31B_HUMAN	S	130	ENSP00000359370:N130S;ENSP00000391178:N130S;ENSP00000359354:N130S	ENSP00000359354:N130S	N	-	2	0	SEC31B	102259073	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	6.197000	0.72100	2.254000	0.74563	0.460000	0.39030	AAT	.	.		0.493	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	NM_015490		C	102269083	T	C	102269083	3	2	333	1	0	0	0	0	1	0	0	0	14014	1493	52	2	3242	2	SEC31B	10	102269083	Missense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	1273589	102269083	33265664	114	46456										
CTBP2	1488	hgsc.bcm.edu	37	chr10	126715391	126715391	+	Intron	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	cggccggggagtcaaagcccTgctgcagtagggctcccagc	15	14	1	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr10:126715391T>A	ENST00000337195.5	-	3	458				CTBP2_ENST00000494626.2_Intron|CTBP2_ENST00000411419.2_Intron|CTBP2_ENST00000309035.6_Missense_Mutation_p.Q313L|CTBP2_ENST00000531469.1_Intron	NM_001329.2	NP_001320.1	P56545	CTBP2_HUMAN	C-terminal binding protein 2						negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)|white fat cell differentiation (GO:0050872)	cell junction (GO:0030054)|nucleus (GO:0005634)|synapse (GO:0045202)|transcriptional repressor complex (GO:0017053)	NAD binding (GO:0051287)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)		GTCAAAGCCCTGCTGCAGTAG	0.677																																					p.Q313L		Atlas-SNP	.											.	CTBP2	100	.	0			c.A938T						.						33	35	34					10																	126715391		2203	4300	6503	SO:0001627	intron_variant	1488	exon1			AAGCCCTGCTGCA	AF016507	CCDS7643.1, CCDS7644.1	10q26.13	2008-08-01			ENSG00000175029	ENSG00000175029			2495	protein-coding gene	gene with protein product		602619				9479502, 11864595	Standard	NM_022802		Approved	ribeye	uc001lie.4	P56545	OTTHUMG00000019224	ENST00000337195.5:c.58+12174A>T	chr10.hg19:g.126715391T>A		74.0	0.0		30.0	27.0	NM_022802	A8K2X5|D3DRF5|O43449|Q5SQP7|Q69YI3|Q86SV0|Q9H2T8	Missense_Mutation	SNP	ENST00000337195.5	hg19	CCDS7643.1	.	.	.	.	.	.	.	.	.	.	T	15.97	2.989875	0.54041	.	.	ENSG00000175029	ENST00000309035	D	0.84442	-1.85	4.88	3.66	0.41972	.	0.336302	0.27406	N	0.019501	T	0.79569	0.4468	.	.	.	0.80722	D	1	B	0.20052	0.041	B	0.23716	0.048	T	0.77851	-0.2434	9	0.54805	T	0.06	.	10.7314	0.46098	0.1424:0.0:0.0:0.8576	.	313	P56545-2	.	L	313	ENSP00000311825:Q313L	ENSP00000311825:Q313L	Q	-	2	0	CTBP2	126705381	1.000000	0.71417	0.987000	0.45799	0.252000	0.25951	4.911000	0.63328	1.962000	0.57031	0.533000	0.62120	CAG	.	.		0.677	CTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050900.3	NM_001083914		A	126715391	T	A	126715391	1	1	333	0	1	0	0	0	0	0	0	0	4000	1580	55	4		4	CTBP2	10	126715391	Intron	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	24446308	126715391	8819356	115	46457										
OR52R1	119695	hgsc.bcm.edu	37	chr11	4824853	4824853	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	aaagggctgggatataaagaGccaagatgacacagatatgg	13	5	0	4			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr11:4824853G>T	ENST00000356069.2	-	1	757	c.758C>A	c.(757-759)gCt>gAt	p.A253D	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron|OR52R1_ENST00000380382.1_Missense_Mutation_p.A332D	NM_001005177.3	NP_001005177.3	Q8NGF1	O52R1_HUMAN	olfactory receptor, family 52, subfamily R, member 1	253						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|prostate(1)|skin(3)	29		Medulloblastoma(188;0.0025)|Breast(177;0.0184)|all_neural(188;0.0227)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		GATATAAAGAGCCAAGATGAC	0.468																																					p.A253D		Atlas-SNP	.											.	OR52R1	81	.	0			c.C758A						.						101	102	102					11																	4824853		2201	4298	6499	SO:0001583	missense	119695	exon1			TAAAGAGCCAAGA	BK004282	CCDS31360.1, CCDS31360.2	11p15.4	2012-08-09			ENSG00000176937	ENSG00000176937		"GPCR / Class A : Olfactory receptors"	15235	protein-coding gene	gene with protein product							Standard	NM_001005177		Approved		uc021qcs.1	Q8NGF1	OTTHUMG00000066510	ENST00000356069.2:c.758C>A	chr11.hg19:g.4824853G>T	ENSP00000348368:p.Ala253Asp	50.0	0.0		58.0	13.0	NM_001005177	Q6IFI0	Missense_Mutation	SNP	ENST00000356069.2	hg19	CCDS31360.2	.	.	.	.	.	.	.	.	.	.	G	14.79	2.642014	0.47153	.	.	ENSG00000176937	ENST00000356069;ENST00000380382	T;T	0.00174	8.62;8.62	5.57	3.68	0.42216	GPCR, rhodopsin-like superfamily (1);	0.133360	0.33610	N	0.004722	T	0.00384	0.0012	M	0.79805	2.47	0.09310	N	1	P	0.50369	0.934	P	0.53760	0.734	T	0.37314	-0.9711	10	0.56958	D	0.05	.	8.8168	0.35000	0.2327:0.0:0.7673:0.0	.	253	Q8NGF1	O52R1_HUMAN	D	253;332	ENSP00000348368:A253D;ENSP00000369742:A332D	ENSP00000348368:A253D	A	-	2	0	OR52R1	4781429	0.000000	0.05858	0.200000	0.23457	0.819000	0.46315	0.040000	0.13905	1.593000	0.50029	0.650000	0.86243	GCT	.	.		0.468	OR52R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142183.1	NM_001005177		T	4824853	G	T	4824853	3	4	333	1	0	0	0	0	1	0	0	0	11140	971	34	3	192	3	OR52R1	11	4824853	Missense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10		4824853	130181663	116	46458										
SYT9	143425	hgsc.bcm.edu	37	chr11	7437386	7437386	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	aaggcaatggacataacaggAgcatcaggtggggcattttc	13	7	1	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr11:7437386A>G	ENST00000318881.6	+	4	1395	c.1158A>G	c.(1156-1158)ggA>ggG	p.G386G		NM_175733.3	NP_783860.1	Q86SS6	SYT9_HUMAN	synaptotagmin IX	386	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of insulin secretion (GO:0050796)	cell junction (GO:0030054)|dense core granule (GO:0031045)|integral component of membrane (GO:0016021)|secretory granule membrane (GO:0030667)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)			NS(1)|endometrium(2)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	38				Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)		ACATAACAGGAGCATCAGGTG	0.408																																					p.G386G		Atlas-SNP	.											.	SYT9	91	.	0			c.A1158G						.						109	101	104					11																	7437386		2201	4296	6497	SO:0001819	synonymous_variant	143425	exon4			AACAGGAGCATCA	AK055003	CCDS7778.1	11p15.4	2013-01-21			ENSG00000170743	ENSG00000170743		"Synaptotagmins"	19265	protein-coding gene	gene with protein product		613528				11543631	Standard	NM_175733		Approved		uc001mfe.3	Q86SS6	OTTHUMG00000165499	ENST00000318881.6:c.1158A>G	chr11.hg19:g.7437386A>G		67.0	0.0		52.0	14.0	NM_175733		Silent	SNP	ENST00000318881.6	hg19	CCDS7778.1																																																																																			.	.		0.408	SYT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384483.1	NM_175733		G	7437386	A	G	7437386	2	3	333	1	0	0	0	0	0	0	0	1	15496	291	11	2		2	SYT9	11	7437386	Silent	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	2612533	7437386	127569130	117	46459										
TRIM49	57093	hgsc.bcm.edu	37	chr11	89531677	89531677	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gaacaccccatgcaagaaaaCttctaggtgttgcagtgaaa	9	9	1	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr11:89531677C>T	ENST00000329758.1	-	8	1308	c.980G>A	c.(979-981)aGt>aAt	p.S327N	TRIM49_ENST00000532501.2_Missense_Mutation_p.S250N	NM_020358.2	NP_065091.1	P0CI25	TRI49_HUMAN	tripartite motif containing 49	327	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(1)|lung(14)|prostate(1)|skin(2)|stomach(1)	27		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				TGCAAGAAAACTTCTAGGTGT	0.423																																					p.S327N		Atlas-SNP	.											.	TRIM49	45	.	0			c.G980A						.						13	17	15					11																	89531677		2019	4182	6201	SO:0001583	missense	57093	exon8			AGAAAACTTCTAG	AB037682	CCDS8287.1	11p11.12-q12	2012-05-21	2011-01-25	2004-11-17	ENSG00000168930	ENSG00000168930		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	13431	protein-coding gene	gene with protein product		606124	"ring finger protein 18", "tripartite motif-containing 49"	RNF18		11018261	Standard	NM_020358		Approved	TRIM49A	uc001pdb.3	P0CI25		ENST00000329758.1:c.980G>A	chr11.hg19:g.89531677C>T	ENSP00000327604:p.Ser327Asn	96.0	0.0		74.0	17.0	NM_020358	A0AVR7|A0AVR9|Q6DJV1|Q9NS80	Missense_Mutation	SNP	ENST00000329758.1	hg19	CCDS8287.1	.	.	.	.	.	.	.	.	.	.	C	1.463	-0.561816	0.03939	.	.	ENSG00000168930	ENST00000329758;ENST00000532501	T	0.08008	3.14	0.539	-0.656	0.11436	Concanavalin A-like lectin/glucanase (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	.	.	.	.	T	0.05410	0.0143	L	0.28504	0.86	0.09310	N	1	B	0.14438	0.01	B	0.17098	0.017	T	0.44574	-0.9319	7	.	.	.	.	.	.	.	.	327	P0CI25	TRI49_HUMAN	N	327;250	ENSP00000327604:S327N	.	S	-	2	0	TRIM49	89171325	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.022000	0.03611	-0.288000	0.09051	0.194000	0.17425	AGT	.	.		0.423	TRIM49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395435.1	NM_020358		T	89531677	C	T	89531677	3	4	333	1	0	0	0	0	1	0	0	0	16539	565	20	3	382	3	TRIM49	11	89531677	Missense_Mutation	SNP	C	TCGA-RC-A6M4-01A-11D-A32G-10	82094291	89531677	45474839	118	46460										
ASAM	79827	hgsc.bcm.edu	37	chr11	122954395	122954395	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gaagatgacttaccaatcctAgatttgggaggcagacgttc	11	8	0	4			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr11:122954395A>T	ENST00000448775.2	-	4	889	c.549T>A	c.(547-549)tcT>tcA	p.S183S	CLMP_ENST00000530371.1_5'UTR	NM_024769.2	NP_079045.1	Q9H6B4	CLMP_HUMAN	CXADR-like membrane protein	183	Ig-like C2-type 2.				digestive tract development (GO:0048565)	cell surface (GO:0009986)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				endometrium(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	14						TACCAATCCTAGATTTGGGAG	0.468																																					p.S183S		Atlas-SNP	.											.	CLMP	39	.	0			c.T549A						.						148	118	128					11																	122954395		2202	4299	6501	SO:0001819	synonymous_variant	79827	exon4			AATCCTAGATTTG	BC009371	CCDS8441.1	11q24	2013-01-29			ENSG00000166250	ENSG00000166250		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	24039	protein-coding gene	gene with protein product	"adipocyte-specific adhesion molecule", "coxsackie- and adenovirus receptor-like membrane protein", "adipocyte adhesion molecule"	611693				12851705, 14573622	Standard	NM_024769		Approved	ASAM, FLJ22415, ACAM	uc001pyt.3	Q9H6B4		ENST00000448775.2:c.549T>A	chr11.hg19:g.122954395A>T		61.0	0.0		44.0	10.0	NM_024769		Silent	SNP	ENST00000448775.2	hg19	CCDS8441.1																																																																																			.	.		0.468	CLMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387542.1	NM_024769		T	122954395	A	T	122954395	2	4	333	1	0	0	0	0	0	0	0	1	1009	407	15	4		4	ASAM	11	122954395	Silent	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	33422718	122954395	12052121	119	46461										
GLB1L3	112937	hgsc.bcm.edu	37	chr11	134188589	134188589	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gcgatattggaatattgggcCtcagaaaacactgtaccttc	9	9	1	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr11:134188589C>A	ENST00000431683.2	+	19	1844	c.1844C>A	c.(1843-1845)cCt>cAt	p.P615H		NM_001080407.2	NP_001073876.2	Q8NCI6	GLBL3_HUMAN	galactosidase, beta 1-like 3	615					carbohydrate metabolic process (GO:0005975)		beta-galactosidase activity (GO:0004565)			endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|pancreas(1)	13	all_hematologic(175;0.127)	all_cancers(12;5.52e-23)|all_epithelial(12;2.15e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|all_neural(223;0.0182)|Medulloblastoma(222;0.0208)|Esophageal squamous(93;0.0559)		Epithelial(10;1.3e-11)|all cancers(11;2.07e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000873)|Lung(977;0.222)		AATATTGGGCCTCAGAAAACA	0.423																																					p.P615H		Atlas-SNP	.											.	GLB1L3	102	.	0			c.C1844A						.						142	130	133					11																	134188589		1924	4118	6042	SO:0001583	missense	112937	exon19			TTGGGCCTCAGAA		CCDS44780.1	11q25	2008-11-06	2008-01-29		ENSG00000166105	ENSG00000166105			25147	protein-coding gene	gene with protein product						12477932	Standard	NM_001080407		Approved	FLJ90231	uc009zdf.3	Q8NCI6	OTTHUMG00000133524	ENST00000431683.2:c.1844C>A	chr11.hg19:g.134188589C>A	ENSP00000396615:p.Pro615His	120.0	0.0		84.0	37.0	NM_001080407	A6NEM0|A6NN15|Q6P3S3|Q96FF8	Missense_Mutation	SNP	ENST00000431683.2	hg19	CCDS44780.1	.	.	.	.	.	.	.	.	.	.	C	14.14	2.446167	0.43429	.	.	ENSG00000166105	ENST00000431683	D	0.99667	-6.34	5.01	5.01	0.66863	Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	D	0.99708	0.9888	M	0.94021	3.485	0.58432	D	0.999997	D	0.89917	1.0	D	0.97110	1.0	D	0.97461	1.0034	10	0.87932	D	0	.	15.75	0.77976	0.0:1.0:0.0:0.0	.	615	Q8NCI6	GLBL3_HUMAN	H	615	ENSP00000396615:P615H	ENSP00000396615:P615H	P	+	2	0	GLB1L3	133693799	1.000000	0.71417	0.384000	0.26145	0.006000	0.05464	5.493000	0.66899	2.776000	0.95493	0.558000	0.71614	CCT	.	.		0.423	GLB1L3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393625.1	NM_138416		A	134188589	C	A	134188589	3	1	333	1	0	0	0	0	1	0	0	0	6438	681	24	3	1918	3	GLB1L3	11	134188589	Missense_Mutation	SNP	C	TCGA-RC-A6M4-01A-11D-A32G-10	11234194	134188589	817927	120	46462										
DENND5B	160518	hgsc.bcm.edu	37	chr12	31576572	31576572	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	cttgtttctcttctctgtccTgaaattgaattaaatgtgac	6	8	2	3			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr12:31576572T>A	ENST00000389082.5	-	11	2693	c.2429A>T	c.(2428-2430)cAg>cTg	p.Q810L	DENND5B_ENST00000536562.1_Missense_Mutation_p.Q845L|DENND5B_ENST00000306833.6_Missense_Mutation_p.Q845L	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	810	RUN 1. {ECO:0000255|PROSITE- ProRule:PRU00178}.				positive regulation of Rab GTPase activity (GO:0032851)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						TTCTCTGTCCTGAAATTGAAT	0.358																																					p.Q810L		Atlas-SNP	.											.	DENND5B	114	.	0			c.A2429T						.						239	226	230					12																	31576572		1896	4121	6017	SO:0001583	missense	160518	exon11			CTGTCCTGAAATT	AF086301	CCDS44857.1	12p11.21	2012-10-03			ENSG00000170456	ENSG00000170456		"DENN/MADD domain containing"	28338	protein-coding gene	gene with protein product						12477932	Standard	NM_144973		Approved	MGC24039	uc001rki.1	Q6ZUT9	OTTHUMG00000169034	ENST00000389082.5:c.2429A>T	chr12.hg19:g.31576572T>A	ENSP00000373734:p.Gln810Leu	134.0	0.0		134.0	85.0	NM_144973	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	Missense_Mutation	SNP	ENST00000389082.5	hg19	CCDS44857.1	.	.	.	.	.	.	.	.	.	.	T	16.20	3.057133	0.55325	.	.	ENSG00000170456	ENST00000389082;ENST00000306833;ENST00000536562	T;T;T	0.04406	3.63;3.74;3.74	4.99	4.99	0.66335	RUN (2);	0.066096	0.64402	D	0.000009	T	0.07324	0.0185	L	0.58669	1.825	0.80722	D	1	B;B	0.17038	0.02;0.016	B;B	0.21708	0.029;0.036	T	0.22208	-1.0223	10	0.21540	T	0.41	-21.5486	13.9354	0.64021	0.0:0.0:0.0:1.0	.	810;845	Q6ZUT9;G3V1S3	DEN5B_HUMAN;.	L	810;845;845	ENSP00000373734:Q810L;ENSP00000306482:Q845L;ENSP00000444889:Q845L	ENSP00000306482:Q845L	Q	-	2	0	DENND5B	31467839	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.251000	0.78297	2.213000	0.71641	0.533000	0.62120	CAG	.	.		0.358	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1	NM_144973		A	31576572	T	A	31576572	3	1	333	1	0	0	0	0	1	0	0	0	4439	1580	55	4	1439	4	DENND5B	12	31576572	Missense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10		31576572	102275323	121	46463										
ZCRB1	85437	hgsc.bcm.edu	37	chr12	42711634	42711634	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	cagttttgtgcagagtctttAtccaaaaataaaataaatgc	6	6	1	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr12:42711634A>G	ENST00000266529.3	-	4	363	c.180T>C	c.(178-180)gaT>gaC	p.D60D	PPHLN1_ENST00000549190.1_Intron|ZCRB1_ENST00000552673.1_Silent_p.D19D	NM_033114.3	NP_149105.3	Q8TBF4	ZCRB1_HUMAN	zinc finger CCHC-type and RNA binding motif 1	60	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	U12-type spliceosomal complex (GO:0005689)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(2)|lung(1)|skin(2)	8	all_cancers(12;0.000348)|Breast(8;0.221)	Lung NSC(34;0.123)		GBM - Glioblastoma multiforme(48;0.0689)		CAGAGTCTTTATCCAAAAATA	0.363																																					p.D60D		Atlas-SNP	.											.	ZCRB1	20	.	0			c.T180C						.						117	120	119					12																	42711634		2203	4299	6502	SO:0001819	synonymous_variant	85437	exon4			GTCTTTATCCAAA	BC022543	CCDS8740.1	12q12	2013-02-12				ENSG00000139168		"Zinc fingers, CCHC domain containing", "RNA binding motif (RRM) containing"	29620	protein-coding gene	gene with protein product	"U11/U12 snRNP 31K"	610750				15146077, 16959469	Standard	NM_033114		Approved	MADP-1, MADP1, RBM36, ZCCHC19, SNRNP31	uc001rmz.3	Q8TBF4	OTTHUMG00000169382	ENST00000266529.3:c.180T>C	chr12.hg19:g.42711634A>G		133.0	0.0		98.0	62.0	NM_033114	Q6PJX0|Q96TA6	Silent	SNP	ENST00000266529.3	hg19	CCDS8740.1																																																																																			.	.		0.363	ZCRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403813.1	NM_033114		G	42711634	A	G	42711634	2	3	333	1	0	0	0	0	0	0	0	1	17611	446	16	2		2	ZCRB1	12	42711634	Silent	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	11135062	42711634	91140261	122	46464										
COL2A1	1280	hgsc.bcm.edu	37	chr12	48370680	48370680	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gctctccagcctctcctttgTcacctctggggccttgagga	10	15	4	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr12:48370680T>A	ENST00000380518.3	-	48	3514	c.3350A>T	c.(3349-3351)gAc>gTc	p.D1117V	COL2A1_ENST00000337299.6_Missense_Mutation_p.D1048V|COL2A1_ENST00000493991.1_5'UTR	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	1117	Triple-helical region.				axon guidance (GO:0007411)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to BMP stimulus (GO:0071773)|central nervous system development (GO:0007417)|chondrocyte differentiation (GO:0002062)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal joint morphogenesis (GO:0060272)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|limb bud formation (GO:0060174)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|notochord development (GO:0030903)|otic vesicle development (GO:0071599)|palate development (GO:0060021)|proteoglycan metabolic process (GO:0006029)|regulation of gene expression (GO:0010468)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|tissue homeostasis (GO:0001894)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen type II trimer (GO:0005585)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(3)	64		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	CTCTCCTTTGTCACCTCTGGG	0.637																																					p.D1117V		Atlas-SNP	.											.	COL2A1	368	.	0			c.A3350T						.						36	30	32					12																	48370680		2203	4300	6503	SO:0001583	missense	1280	exon48			CCTTTGTCACCTC	X16468	CCDS8759.1, CCDS41778.1	12q12-q13.2	2013-11-14	2008-02-04		ENSG00000139219	ENSG00000139219		"Collagens"	2200	protein-coding gene	gene with protein product		120140	"collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital)", "arthroophthalmopathy, progressive (Stickler syndrome)"	SEDC, AOM		1677770	Standard	NM_033150		Approved	STL1	uc001rqu.3	P02458	OTTHUMG00000149896	ENST00000380518.3:c.3350A>T	chr12.hg19:g.48370680T>A	ENSP00000369889:p.Asp1117Val	55.0	0.0		41.0	17.0	NM_001844	A6NGA0|Q12985|Q14009|Q14044|Q14045|Q14046|Q14047|Q14056|Q14058|Q16672|Q1JQ82|Q2V4X7|Q6LBY1|Q6LBY2|Q6LBY3|Q96IT5|Q99227|Q9UE38|Q9UE39|Q9UE40|Q9UE41|Q9UE42|Q9UE43	Missense_Mutation	SNP	ENST00000380518.3	hg19	CCDS41778.1	.	.	.	.	.	.	.	.	.	.	T	19.22	3.786203	0.70337	.	.	ENSG00000139219	ENST00000380518;ENST00000395281;ENST00000337299	D;D	0.92858	-3.12;-3.12	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	D	0.93064	0.7792	L	0.27053	0.805	0.80722	D	1	D;D	0.69078	0.997;0.995	D;D	0.87578	0.998;0.995	D	0.94252	0.7494	10	0.87932	D	0	.	15.1548	0.72733	0.0:0.0:0.0:1.0	.	1048;1117	P02458-1;P02458	.;CO2A1_HUMAN	V	1117;1048;1048	ENSP00000369889:D1117V;ENSP00000338213:D1048V	ENSP00000338213:D1048V	D	-	2	0	COL2A1	46656947	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.991000	0.88244	2.064000	0.61679	0.460000	0.39030	GAC	.	.		0.637	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844		A	48370680	T	A	48370680	3	1	333	1	0	0	0	0	1	0	0	0	3689	1667	58	4	1141	4	COL2A1	12	48370680	Missense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	5659046	48370680	85481215	123	46465										
MLL2	8085	hgsc.bcm.edu	37	chr12	49433836	49433836	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gtttgtgctttgaggcttgcCcaaggtggggccgggcccaa	16	10	0	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr12:49433836C>T	ENST00000301067.7	-	31	7716	c.7717G>A	c.(7717-7719)Ggc>Agc	p.G2573S	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	2573	Pro-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										TGAGGCTTGCCCAAGGTGGGG	0.642																																					p.G2573S		Atlas-SNP	.											.	MLL2	1173	.	0			c.G7717A						.						44	48	47					12																	49433836		1912	4120	6032	SO:0001583	missense	8085	exon31			GCTTGCCCAAGGT	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.7717G>A	chr12.hg19:g.49433836C>T	ENSP00000301067:p.Gly2573Ser	60.0	0.0		53.0	8.0	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	hg19	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	C	13.62	2.292079	0.40594	.	.	ENSG00000167548	ENST00000301067	T	0.78924	-1.22	5.3	5.3	0.74995	.	0.000000	0.38164	N	0.001782	T	0.76730	0.4028	N	0.19112	0.55	0.40785	D	0.983209	D	0.69078	0.997	P	0.56042	0.79	T	0.81037	-0.1114	10	0.87932	D	0	.	16.2715	0.82624	0.0:1.0:0.0:0.0	.	2573	O14686	MLL2_HUMAN	S	2573	ENSP00000301067:G2573S	ENSP00000301067:G2573S	G	-	1	0	MLL2	47720103	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.716000	0.37981	2.644000	0.89710	0.591000	0.81541	GGC	.	.		0.642	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			T	49433836	C	T	49433836	3	4	333	1	0	0	0	0	1	0	0	0	9630	623	22	3	8992	3	MLL2	12	49433836	Missense_Mutation	SNP	C	TCGA-RC-A6M4-01A-11D-A32G-10	1063156	49433836	84418059	124	46466										
CSAD	51380	hgsc.bcm.edu	37	chr12	53553988	53553988	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tgagccacagcttcagacagTccacacggcggccacactgc	10	16	1	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr12:53553988T>G	ENST00000444623.1	-	14	1349	c.1082A>C	c.(1081-1083)gAc>gCc	p.D361A	RP11-1136G11.8_ENST00000550908.1_lincRNA|CSAD_ENST00000267085.4_Missense_Mutation_p.D388A|CSAD_ENST00000379843.3_Missense_Mutation_p.D214A|CSAD_ENST00000379846.1_Missense_Mutation_p.D214A|CSAD_ENST00000453446.2_Missense_Mutation_p.D361A	NM_001244705.1	NP_001231634.1	Q9Y600	CSAD_HUMAN	cysteine sulfinic acid decarboxylase	361					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)|taurine biosynthetic process (GO:0042412)		pyridoxal phosphate binding (GO:0030170)|sulfinoalanine decarboxylase activity (GO:0004782)			kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(4)	14					L-Cysteine(DB00151)	CTTCAGACAGTCCACACGGCG	0.622																																					p.D388A	Ovarian(109;252 1546 16882 28524 44645)	Atlas-SNP	.											.	CSAD	66	.	0			c.A1163C						.						114	101	105					12																	53553988		2203	4300	6503	SO:0001583	missense	51380	exon14			AGACAGTCCACAC	AB044561	CCDS8848.2, CCDS58235.1	12q13.11-q14.3	2008-08-04			ENSG00000139631	ENSG00000139631			18966	protein-coding gene	gene with protein product	"P-selectin cytoplasmic tail-associated protein"					15489334	Standard	NM_015989		Approved	PCAP, CSD	uc001sbz.3	Q9Y600	OTTHUMG00000048076	ENST00000444623.1:c.1082A>C	chr12.hg19:g.53553988T>G	ENSP00000415485:p.Asp361Ala	29.0	0.0		33.0	5.0	NM_015989	A8K0U4|Q4QQH9|Q9UNJ5|Q9Y601	Missense_Mutation	SNP	ENST00000444623.1	hg19	CCDS58235.1	.	.	.	.	.	.	.	.	.	.	T	27.9	4.870587	0.91587	.	.	ENSG00000139631	ENST00000308926;ENST00000379843;ENST00000267085;ENST00000379846;ENST00000444623;ENST00000398047;ENST00000453446	T;T;T;T;T	0.37915	1.17;1.17;1.17;1.17;1.17	4.67	4.67	0.58626	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.095813	0.64402	D	0.000001	T	0.69223	0.3087	H	0.94964	3.605	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.78843	-0.2044	10	0.87932	D	0	-21.8356	13.5402	0.61671	0.0:0.0:0.0:1.0	.	388;361;214	Q9Y600-3;Q9Y600;Q9Y600-2	.;CSAD_HUMAN;.	A	450;214;388;214;361;322;361	ENSP00000369172:D214A;ENSP00000267085:D388A;ENSP00000369175:D214A;ENSP00000415485:D361A;ENSP00000410648:D361A	ENSP00000267085:D388A	D	-	2	0	CSAD	51840255	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.430000	0.80321	2.100000	0.63781	0.533000	0.62120	GAC	.	.		0.622	CSAD-017	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343697.1	NM_015989		G	53553988	T	G	53553988	3	3	333	1	0	0	0	0	1	0	0	0	3927	1667	58	5	415	5	CSAD	12	53553988	Missense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	4120152	53553988	80297907	125	46467										
OR6C2	341416	hgsc.bcm.edu	37	chr12	55846722	55846722	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	cttttctacctgttcatcccAcatgattgtggtttccattg	6	11	2	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr12:55846722A>T	ENST00000322678.1	+	1	725	c.725A>T	c.(724-726)cAc>cTc	p.H242L	RP11-110A12.2_ENST00000556750.1_RNA|RP11-110A12.2_ENST00000554049.1_RNA|RP11-110A12.2_ENST00000555146.1_RNA|RP11-110A12.2_ENST00000555138.1_RNA	NM_054105.1	NP_473446.1	Q9NZP2	OR6C2_HUMAN	olfactory receptor, family 6, subfamily C, member 2	242					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(2)|large_intestine(5)|lung(8)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	23						TGTTCATCCCACATGATTGTG	0.408																																					p.H242L		Atlas-SNP	.											.	OR6C2	39	.	0			c.A725T						.						135	129	131					12																	55846722		2203	4300	6503	SO:0001583	missense	341416	exon1			CATCCCACATGAT	AF179766	CCDS31824.1	12q13.2	2012-08-09				ENSG00000179695		"GPCR / Class A : Olfactory receptors"	15436	protein-coding gene	gene with protein product							Standard	NM_054105		Approved	OR6C67	uc001sgz.1	Q9NZP2	OTTHUMG00000169957	ENST00000322678.1:c.725A>T	chr12.hg19:g.55846722A>T	ENSP00000323606:p.His242Leu	175.0	0.0		134.0	47.0	NM_054105		Missense_Mutation	SNP	ENST00000322678.1	hg19	CCDS31824.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.150028	0.78001	.	.	ENSG00000179695	ENST00000322678	T	0.00307	8.17	5.42	4.26	0.50523	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000006	T	0.01421	0.0046	H	0.99464	4.58	0.40357	D	0.979195	D	0.76494	0.999	D	0.85130	0.997	T	0.03587	-1.1022	10	0.87932	D	0	.	11.6003	0.50999	0.8506:0.1494:0.0:0.0	.	242	Q9NZP2	OR6C2_HUMAN	L	242	ENSP00000323606:H242L	ENSP00000323606:H242L	H	+	2	0	OR6C2	54132989	1.000000	0.71417	0.997000	0.53966	0.838000	0.47535	6.487000	0.73633	1.048000	0.40298	0.496000	0.49642	CAC	.	.		0.408	OR6C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406676.1	NM_054105		T	55846722	A	T	55846722	3	4	333	1	0	0	0	0	1	0	0	0	11200	159	6	4	727	4	OR6C2	12	55846722	Missense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	2292734	55846722	78005173	126	46468										
MDM2	4193	hgsc.bcm.edu	37	chr12	69233083	69233083	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	aaatgcacttcatgcaatgaAatgaatcccccccttccatc	4	14	1	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr12:69233083A>C	ENST00000350057.5	+	9	855	c.855A>C	c.(853-855)gaA>gaC	p.E285D	MDM2_ENST00000517852.1_Intron|MDM2_ENST00000356290.4_Missense_Mutation_p.E140D|MDM2_ENST00000393410.1_Missense_Mutation_p.E62D|MDM2_ENST00000360430.2_Missense_Mutation_p.E115D|MDM2_ENST00000545204.1_Intron|MDM2_ENST00000258149.5_Missense_Mutation_p.E255D|MDM2_ENST00000393413.3_Missense_Mutation_p.E37D|MDM2_ENST00000299252.4_Missense_Mutation_p.E140D|MDM2_ENST00000428863.2_Missense_Mutation_p.E89D|MDM2_ENST00000393412.3_Missense_Mutation_p.E37D|MDM2_ENST00000540827.1_Missense_Mutation_p.E115D|MDM2_ENST00000258148.7_Missense_Mutation_p.E261D|MDM2_ENST00000544561.1_Intron|MDM2_ENST00000478070.1_Missense_Mutation_p.K49T|MDM2_ENST00000348801.2_Missense_Mutation_p.E84D|RP11-611O2.5_ENST00000553141.1_RNA|MDM2_ENST00000462284.1_Missense_Mutation_p.E316D			Q00987	MDM2_HUMAN	MDM2 proto-oncogene, E3 ubiquitin protein ligase	310	ARF-binding.|Asp/Glu-rich (acidic).|Interaction with MTBP. {ECO:0000250}.|Necessary for interaction with USP2.|Region II.				cellular response to acid chemical (GO:0071229)|cellular response to alkaloid (GO:0071312)|cellular response to antibiotic (GO:0071236)|cellular response to estrogen stimulus (GO:0071391)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to UV-C (GO:0071494)|cellular response to vitamin B1 (GO:0071301)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment of protein localization (GO:0045184)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of protein processing (GO:0010955)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-lysine modification (GO:0018205)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein export from nucleus (GO:0046827)|protein complex assembly (GO:0006461)|protein destabilization (GO:0031648)|protein localization to nucleus (GO:0034504)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of protein catabolic process (GO:0042176)|response to antibiotic (GO:0046677)|response to carbohydrate (GO:0009743)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ether (GO:0045472)|response to iron ion (GO:0010039)|response to magnesium ion (GO:0032026)|response to morphine (GO:0043278)|synaptic transmission (GO:0007268)|traversing start control point of mitotic cell cycle (GO:0007089)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|p53 binding (GO:0002039)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(8)|prostate(1)|urinary_tract(1)	19	all_cancers(1;8.46e-121)|all_epithelial(5;3.21e-36)|Lung NSC(4;2.16e-33)|all_lung(4;3.03e-31)|Glioma(1;1.9e-09)|Breast(13;1.59e-06)|all_neural(1;1.03e-05)|Melanoma(1;0.0171)|Renal(347;0.0684)		all cancers(2;8.67e-65)|GBM - Glioblastoma multiforme(2;8.89e-62)|BRCA - Breast invasive adenocarcinoma(5;2.43e-08)|Lung(24;1.5e-05)|LUAD - Lung adenocarcinoma(15;8.5e-05)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143)			CATGCAATGAAATGAATCCCC	0.428			A		"sarcoma, glioma, colorectal, other"																																p.E316D		Atlas-SNP	.		Dom	yes		12	12q15	4193	Mdm2 p53 binding protein homolog		"M, O, E, L"	.	MDM2	92	.	0			c.A948C						.						110	96	101					12																	69233083		1876	4121	5997	SO:0001583	missense	4193	exon11			CAATGAAATGAAT		CCDS8986.2, CCDS61189.1	12q13-q14	2014-06-26	2014-06-26		ENSG00000135679	ENSG00000135679			6973	protein-coding gene	gene with protein product		164785	"mouse double minute 2, human homolog of; p53-binding protein", "Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse)", "Mdm2 p53 binding protein homolog (mouse)"			1614537, 16905769	Standard	NM_002392		Approved	HDM2, MGC5370	uc001sui.4	Q00987	OTTHUMG00000142827	ENST00000350057.5:c.855A>C	chr12.hg19:g.69233083A>C	ENSP00000266624:p.Glu285Asp	45.0	0.0		33.0	16.0	NM_002392	A6NL51|A8K2S6|Q13226|Q13297|Q13298|Q13299|Q13300|Q13301|Q53XW0|Q71TW9|Q8WYJ1|Q8WYJ2|Q9UGI3|Q9UMT8	Missense_Mutation	SNP	ENST00000350057.5	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.54|14.54	2.564877|2.564877	0.45694|0.45694	.|.	.|.	ENSG00000135679|ENSG00000135679	ENST00000462284;ENST00000544648;ENST00000258149;ENST00000356290;ENST00000540827;ENST00000428863;ENST00000393412;ENST00000311420;ENST00000258148;ENST00000543323;ENST00000523991;ENST00000393413;ENST00000350057;ENST00000393410;ENST00000299252;ENST00000360430;ENST00000348801|ENST00000478070	T;T;T;T;T;T;T;T;T;T;T;T;T|.	0.55234|.	0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53|.	5.5|5.5	0.481|0.481	0.16809|0.16809	Zinc finger, RanBP2-type (3);|.	0.138749|.	0.64402|.	D|.	0.000005|.	T|T	0.59689|0.59689	0.2212|0.2212	L|L	0.59436|0.59436	1.845|1.845	0.50813|0.50813	D|D	0.999892|0.999892	D;D;P;D;D;B;B;P;P|.	0.63880|.	0.981;0.981;0.915;0.993;0.968;0.299;0.346;0.633;0.95|.	P;P;P;D;P;B;B;B;P|.	0.63283|.	0.848;0.848;0.648;0.913;0.802;0.145;0.253;0.221;0.574|.	T|T	0.53940|0.53940	-0.8367|-0.8367	9|5	.|.	.|.	.|.	-21.3321|-21.3321	10.2776|10.2776	0.43519|0.43519	0.5744:0.0:0.4256:0.0|0.5744:0.0:0.4256:0.0	.|.	265;89;37;62;140;310;261;115;316|.	Q00987-9;Q00987-3;Q00987-4;Q9H4C5;Q00987-5;Q00987;G3XA89;Q00987-2;Q00987-11|.	.;.;.;.;.;MDM2_HUMAN;.;.;.|.	D|T	316;265;255;140;115;89;37;271;261;114;140;37;285;62;140;115;84|49	ENSP00000417281:E316D;ENSP00000258149:E255D;ENSP00000348637:E140D;ENSP00000440932:E115D;ENSP00000410694:E89D;ENSP00000377064:E37D;ENSP00000258148:E261D;ENSP00000377065:E37D;ENSP00000266624:E285D;ENSP00000377062:E62D;ENSP00000299252:E140D;ENSP00000353611:E115D;ENSP00000335096:E84D|.	.|.	E|K	+|+	3|2	2|0	MDM2|MDM2	67519350|67519350	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.719000|0.719000	0.41307|0.41307	1.193000|1.193000	0.32162|0.32162	-0.078000|-0.078000	0.12730|0.12730	0.528000|0.528000	0.53228|0.53228	GAA|AAA	.	.		0.428	MDM2-033	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000402665.1	NM_006880		C	69233083	A	C	69233083	3	2	333	1	0	0	0	0	1	0	0	0	9422	11	1	5	990	5	MDM2	12	69233083	Missense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	13386361	69233083	64618812	127	46469										
MPHOSPH9	10198	hgsc.bcm.edu	37	chr12	123702951	123702951	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ttggtgtcttcttactttgcTcatttccttgtttagatctt	6	8	4	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr12:123702951T>A	ENST00000606320.1	-	6	1174	c.968A>T	c.(967-969)gAg>gTg	p.E323V	MPHOSPH9_ENST00000541076.2_Missense_Mutation_p.E293V|MPHOSPH9_ENST00000302349.5_Missense_Mutation_p.E171V|MPHOSPH9_ENST00000392425.3_Missense_Mutation_p.E171V			Q99550	MPP9_HUMAN	M-phase phosphoprotein 9	323						centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(18)|prostate(2)|skin(1)	33	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000182)|Epithelial(86;0.00046)|BRCA - Breast invasive adenocarcinoma(302;0.169)		CTTACTTTGCTCATTTCCTTG	0.413																																					p.E171V		Atlas-SNP	.											.	MPHOSPH9	75	.	0			c.A512T						.						283	240	255					12																	123702951		2203	4300	6503	SO:0001583	missense	10198	exon2			CTTTGCTCATTTC	X98258	CCDS9243.1, CCDS9243.2	12q24	2008-03-03			ENSG00000051825	ENSG00000051825			7215	protein-coding gene	gene with protein product		605501				8885239	Standard	NM_022782		Approved	MPP9	uc001uel.3	Q99550	OTTHUMG00000168849	ENST00000606320.1:c.968A>T	chr12.hg19:g.123702951T>A	ENSP00000475489:p.Glu323Val	349.0	0.0		312.0	76.0	NM_022782	A1L486|A6NEE2|B3KR87|Q9H976|U3KQ28	Missense_Mutation	SNP	ENST00000606320.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.65|14.65	2.598952|2.598952	0.46318|0.46318	.|.	.|.	ENSG00000051825|ENSG00000257076	ENST00000302349;ENST00000541076|ENST00000539336	T;T|.	0.42513|.	0.97;1.0|.	4.93|4.93	3.78|3.78	0.43462|0.43462	.|.	0.370404|.	0.25352|.	N|.	0.031291|.	T|.	0.54319|.	0.1851|.	M|M	0.64997|0.64997	1.995|1.995	0.09310|0.09310	N|N	0.999999|0.999999	D|.	0.89917|.	1.0|.	D|.	0.87578|.	0.998|.	T|.	0.42849|.	-0.9427|.	10|.	0.42905|.	T|.	0.14|.	-13.7252|-13.7252	12.6994|12.6994	0.57022|0.57022	0.0:0.0:0.1381:0.8619|0.0:0.0:0.1381:0.8619	.|.	171|.	Q99550|.	MPP9_HUMAN|.	V|C	171|180	ENSP00000303597:E171V;ENSP00000445859:E171V|.	ENSP00000303597:E171V|.	E|X	-|-	2|3	0|0	MPHOSPH9|RP11-546D6.2	122268904|122268904	0.944000|0.944000	0.32072|0.32072	0.005000|0.005000	0.12908|0.12908	0.043000|0.043000	0.13939|0.13939	2.949000|2.949000	0.49074|0.49074	0.309000|0.309000	0.22966|0.22966	-1.874000|-1.874000	0.00550|0.00550	GAG|TGA	.	.		0.413	MPHOSPH9-030	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000471390.2			A	123702951	T	A	123702951	3	1	333	1	0	0	0	0	1	0	0	0	9737	1551	54	4	2659	4	MPHOSPH9	12	123702951	Missense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	54469868	123702951	10148944	128	46470										
KTN1	3895	hgsc.bcm.edu	37	chr14	56122805	56122805	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	aagaggttagaagccatgctAaaagagagggagagtgatct	14	4	1	5	rs143735954		TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr14:56122805A>G	ENST00000395314.3	+	29	2915	c.2847A>G	c.(2845-2847)ctA>ctG	p.L949L	KTN1_ENST00000395311.1_Silent_p.L926L|KTN1_ENST00000438792.2_Silent_p.L949L|KTN1_ENST00000554507.1_Silent_p.L244L|KTN1_ENST00000416613.1_Silent_p.L949L|KTN1_ENST00000395309.3_Silent_p.L949L|KTN1_ENST00000413890.2_Silent_p.L926L|KTN1_ENST00000395308.1_Silent_p.L926L	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	949					microtubule-based movement (GO:0007018)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|large_intestine(8)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	19						AAGCCATGCTAAAAGAGAGGG	0.308			T	RET	papillary thryoid																																p.L949L		Atlas-SNP	.		Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	.	KTN1	147	.	0			c.A2847G						.	A	,,,	0,4406		0,0,2203	66	69	68		2847,2778,2847,2847	1.9	0.2	14	dbSNP_134	68	3,8595	3.0+/-9.4	0,3,4296	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KTN1	NM_001079521.1,NM_001079522.1,NM_004986.2,NM_182926.2	,,,	0,3,6499	GG,GA,AA		0.0349,0.0,0.0231	,,,	949/1358,926/1307,949/1301,949/1358	56122805	3,13001	2203	4299	6502	SO:0001819	synonymous_variant	3895	exon29			CATGCTAAAAGAG		CCDS41957.1, CCDS41958.1, CCDS41959.1	14q22.1	2008-05-02			ENSG00000126777	ENSG00000126777			6467	protein-coding gene	gene with protein product		600381				9605849	Standard	NM_001079521		Approved	KIAA0004, CG1	uc001xcc.3	Q86UP2	OTTHUMG00000140312	ENST00000395314.3:c.2847A>G	chr14.hg19:g.56122805A>G		249.0	1.0		278.0	127.0	NM_004986	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Silent	SNP	ENST00000395314.3	hg19	CCDS41957.1																																																																																			.	A|1.000;G|0.000		0.308	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2			G	56122805	A	G	56122805	2	3	333	1	0	0	0	0	0	0	0	1	8594	349	13	2		2	KTN1	14	56122805	Silent	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10		56122805	51226735	129	46471										
C14orf4	64207	hgsc.bcm.edu	37	chr14	77493776	77493777	+	In_Frame_Ins	INS	-	-	TGCTGCTGCTGT													0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gttgttgctgctgctgctgcINStgctgctgctgctgctgttg							TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr14:77493776_77493777insTGCTGCTGCTGT	ENST00000238647.3	-	1	1257_1258	c.359_360insACAGCAGCAGCA	c.(358-360)cag>caACAGCAGCAGCAg	p.120_120Q>QQQQQ		NM_024496.3	NP_078772.1	Q9H1B7	I2BPL_HUMAN	interferon regulatory factor 2 binding protein-like	120	Poly-Gln.				development of secondary female sexual characteristics (GO:0046543)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	extracellular space (GO:0005615)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	11						gctgctgctgctgctgctgctg	0.698																																					p.Q120delinsQQQQQ		Atlas-INDEL	.											.	IRF2BPL	40	.	0			c.360_361insACAGCAGCAGCA						.																																			SO:0001652	inframe_insertion	64207	exon1			.	AJ277365	CCDS9854.1	14q24.3	2011-02-23	2011-02-23	2011-02-23	ENSG00000119669	ENSG00000119669			14282	protein-coding gene	gene with protein product	"enhanced at puberty 1"	611720	"chromosome 14 open reading frame 4"	C14orf4		11095982, 17627301	Standard	NM_024496		Approved	EAP1, KIAA1865	uc001xsy.4	Q9H1B7		ENST00000238647.3:c.359_360insACAGCAGCAGCA	chr14.hg19:g.77493776_77493777insTGCTGCTGCTGT	ENSP00000238647:p.GlnGlnGlnGln124dup	30.0	0.0		29.0	17.0	NM_024496	Q8NDQ2|Q96JG2|Q9H3I7	In_Frame_Ins	INS	ENST00000238647.3	hg19	CCDS9854.1																																																																																			.	CTG|1.000;|0.000		0.698	IRF2BPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414298.1	NM_024496		TGCTGCTGCTGT	77493777	-	TGCTGCTGCTGT	77493776	7	5	333	1	0	1	1	0	0	0	0	0	1775	796	28	0	2034	0	C14orf4	14	77493776	In_Frame_Ins	INS	-	TCGA-RC-A6M4-01A-11D-A32G-10	21370971	77493776	29855764	130	46472										
KCNK10	54207	hgsc.bcm.edu	37	chr14	88652001	88652001	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	cgtcagcatggctgtgctggAgttgtctgagttacacatct	12	9	3	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr14:88652001A>T	ENST00000340700.5	-	7	1946	c.1495T>A	c.(1495-1497)Tcc>Acc	p.S499T	KCNK10_ENST00000319231.5_Missense_Mutation_p.S504T|KCNK10_ENST00000312350.5_Missense_Mutation_p.S504T	NM_021161.4	NP_066984.1	P57789	KCNKA_HUMAN	potassium channel, subfamily K, member 10	499					signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	47						GCTGTGCTGGAGTTGTCTGAG	0.532																																					p.S504T		Atlas-SNP	.											.	KCNK10	273	.	0			c.T1510A						.						167	159	162					14																	88652001		2203	4300	6503	SO:0001583	missense	54207	exon7			TGCTGGAGTTGTC	AF279890	CCDS9880.1, CCDS9881.1, CCDS9882.1	14q31	2014-06-12						"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6273	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 97"	605873				10880510, 16382106	Standard	NM_021161		Approved	K2p10.1, TREK-2, TREK2, PPP1R97	uc001xwn.3	P57789		ENST00000340700.5:c.1495T>A	chr14.hg19:g.88652001A>T	ENSP00000343104:p.Ser499Thr	219.0	1.0		254.0	122.0	NM_138318	B2R8T4|B2RCT3|B5TJL4|Q6B014|Q8TDK7|Q8TDK8|Q9HB59	Missense_Mutation	SNP	ENST00000340700.5	hg19	CCDS9880.1	.	.	.	.	.	.	.	.	.	.	A	17.65	3.442146	0.63067	.	.	ENSG00000100433	ENST00000340700;ENST00000312350;ENST00000319231	D;D;D	0.91295	-2.81;-2.82;-2.79	5.5	5.5	0.81552	.	1.070570	0.07007	N	0.824408	D	0.85080	0.5615	N	0.22421	0.69	0.35439	D	0.794706	B;B;B	0.11235	0.004;0.004;0.004	B;B;B	0.08055	0.003;0.002;0.003	T	0.71540	-0.4562	10	0.15499	T	0.54	.	13.3629	0.60667	1.0:0.0:0.0:0.0	.	499;504;504	P57789;B2R8T4;Q6B014	KCNKA_HUMAN;.;.	T	499;504;504	ENSP00000343104:S499T;ENSP00000310568:S504T;ENSP00000312811:S504T	ENSP00000310568:S504T	S	-	1	0	KCNK10	87721754	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.067000	0.71193	2.102000	0.63906	0.533000	0.62120	TCC	.	.		0.532	KCNK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410167.1	NM_021161		T	88652001	A	T	88652001	3	4	333	1	0	0	0	0	1	0	0	0	8068	304	11	4	125	4	KCNK10	14	88652001	Missense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	11158225	88652001	18697539	131	46473										
BCL11B	64919	hgsc.bcm.edu	37	chr14	99641711	99641711	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ggccgagagcccgtcgtcggAgcggccggccagcgagccgg	19	15	0	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr14:99641711A>T	ENST00000357195.3	-	4	1471	c.1462T>A	c.(1462-1464)Tcc>Acc	p.S488T	BCL11B_ENST00000443726.2_Missense_Mutation_p.S294T|BCL11B_ENST00000345514.2_Missense_Mutation_p.S417T	NM_001282237.1|NM_138576.2	NP_001269166.1|NP_612808.1	Q9C0K0	BC11B_HUMAN	B-cell CLL/lymphoma 11B (zinc finger protein)	488					alpha-beta T cell differentiation (GO:0046632)|epithelial cell morphogenesis (GO:0003382)|keratinocyte development (GO:0003334)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|odontogenesis of dentin-containing tooth (GO:0042475)|olfactory bulb axon guidance (GO:0071678)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive T cell selection (GO:0043368)|post-embryonic camera-type eye development (GO:0031077)|regulation of keratinocyte proliferation (GO:0010837)|regulation of lipid metabolic process (GO:0019216)|regulation of neuron differentiation (GO:0045664)|striatal medium spiny neuron differentiation (GO:0021773)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|thymus development (GO:0048538)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(3)|breast(1)|central_nervous_system(9)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(9)|prostate(2)|skin(2)	34		Melanoma(154;0.0866)|all_epithelial(191;0.241)		COAD - Colon adenocarcinoma(157;0.103)		CCGTCGTCGGAGCGGCCGGCC	0.716			T	TLX3	T-ALL																																p.S488T		Atlas-SNP	.		Dom	yes		14	14q32.1	64919	B-cell CLL/lymphoma 11B  (CTIP2)		L	.	BCL11B	108	.	0			c.T1462A						.						7	8	7					14																	99641711		2147	4190	6337	SO:0001583	missense	64919	exon4			CGTCGGAGCGGCC	AJ404614	CCDS9949.1, CCDS9950.1	14q32	2013-01-08			ENSG00000127152	ENSG00000127152		"Zinc fingers, C2H2-type"	13222	protein-coding gene	gene with protein product		606558		ZNF856B		11719382, 16950772	Standard	NM_138576		Approved	CTIP-2, CTIP2, hRIT1-alpha	uc001yga.3	Q9C0K0	OTTHUMG00000028967	ENST00000357195.3:c.1462T>A	chr14.hg19:g.99641711A>T	ENSP00000349723:p.Ser488Thr	28.0	0.0		27.0	13.0	NM_138576	Q9H162	Missense_Mutation	SNP	ENST00000357195.3	hg19	CCDS9950.1	.	.	.	.	.	.	.	.	.	.	A	17.90	3.502345	0.64298	.	.	ENSG00000127152	ENST00000357195;ENST00000345514;ENST00000443726	T;T;T	0.13307	2.61;2.63;2.6	3.62	3.62	0.41486	.	0.000000	0.64402	D	0.000010	T	0.26557	0.0649	L	0.52905	1.665	0.51012	D	0.999907	D;D	0.63046	0.992;0.991	D;P	0.65140	0.932;0.771	T	0.02617	-1.1133	10	0.20046	T	0.44	-11.4963	12.5401	0.56165	1.0:0.0:0.0:0.0	.	417;488	Q9C0K0-2;Q9C0K0	.;BC11B_HUMAN	T	488;417;294	ENSP00000349723:S488T;ENSP00000280435:S417T;ENSP00000387419:S294T	ENSP00000280435:S417T	S	-	1	0	BCL11B	98711464	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.101000	0.76997	1.426000	0.47256	0.379000	0.24179	TCC	.	.		0.716	BCL11B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000072332.2	NM_138576		T	99641711	A	T	99641711	3	4	333	1	0	0	0	0	1	0	0	0	1364	304	11	4	1226	4	BCL11B	14	99641711	Missense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	10989710	99641711	7707829	132	46474										
RTL1	388015	hgsc.bcm.edu	37	chr14	101350239	101350239	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	cagtggcagagcggccgcccTgcctgatggtgaacatggcc	15	13	0	3			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr14:101350239T>A	ENST00000534062.1	-	1	945	c.887A>T	c.(886-888)cAg>cTg	p.Q296L	MIR433_ENST00000384837.1_RNA|MIR432_ENST00000606207.1_RNA|MIR136_ENST00000385207.1_RNA|MIR127_ENST00000384876.1_RNA|MIR431_ENST00000385266.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	296					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)				breast(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(5)|pancreas(1)|prostate(2)|skin(2)	21						GCGGCCGCCCTGCCTGATGGT	0.607																																					p.Q296L		Atlas-SNP	.											.	RTL1	120	.	0			c.A887T						.						53	53	53					14																	101350239		692	1591	2283	SO:0001583	missense	388015	exon1			CCGCCCTGCCTGA		CCDS53910.1	14q32.2	2012-04-18			ENSG00000254656	ENSG00000254656			14665	protein-coding gene	gene with protein product		611896				16155747, 15854907, 12796779	Standard	NM_001134888		Approved	PEG11, MART1, Mar1	uc010txj.1	A6NKG5	OTTHUMG00000167573	ENST00000534062.1:c.887A>T	chr14.hg19:g.101350239T>A	ENSP00000435342:p.Gln296Leu	34.0	0.0		33.0	16.0	NM_001134888	E9PKS8	Missense_Mutation	SNP	ENST00000534062.1	hg19	CCDS53910.1	.	.	.	.	.	.	.	.	.	.	T	16.23	3.063277	0.55432	.	.	ENSG00000254656	ENST00000534062	T	0.38722	1.12	3.57	3.57	0.40892	.	.	.	.	.	T	0.60586	0.2280	M	0.70595	2.14	0.38640	D	0.951584	D	0.76494	0.999	D	0.91635	0.999	T	0.67007	-0.5779	9	0.87932	D	0	.	10.7447	0.46172	0.0:0.0:0.0:1.0	.	296	E9PKS8	.	L	296	ENSP00000435342:Q296L	ENSP00000435342:Q296L	Q	-	2	0	RTL1	100419992	1.000000	0.71417	0.925000	0.36789	0.276000	0.26787	4.532000	0.60608	1.853000	0.53794	0.459000	0.35465	CAG	.	.		0.607	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888		A	101350239	T	A	101350239	3	1	333	1	0	0	0	0	1	0	0	0	13739	1580	55	4	3193	4	RTL1	14	101350239	Missense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	1708528	101350239	5999301	133	46475										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105414443	105414443	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ggcctcgacatccacctccaCgctgggctgagacacctcca	9	18	0	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr14:105414443C>A	ENST00000333244.5	-	7	7464	c.7345G>T	c.(7345-7347)Gtg>Ttg	p.V2449L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2449						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				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)			TCCACCTCCACGCTGGGCTGA	0.637																																					p.V2449L		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G7345T						.						119	139	132					14																	105414443		2022	4165	6187	SO:0001583	missense	113146	exon7			CCTCCACGCTGGG	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.7345G>T	chr14.hg19:g.105414443C>A	ENSP00000353114:p.Val2449Leu	60.0	0.0		57.0	20.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	hg19	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	-	7.724	0.697765	0.15106	.	.	ENSG00000185567	ENST00000333244	T	0.00675	5.88	3.74	-0.409	0.12378	.	.	.	.	.	T	0.01870	0.0059	L	0.56396	1.775	0.09310	N	1	D	0.76494	0.999	D	0.79784	0.993	T	0.48151	-0.9060	9	0.22706	T	0.39	.	1.0989	0.01680	0.1388:0.268:0.3048:0.2885	.	2449	Q8IVF2	AHNK2_HUMAN	L	2449	ENSP00000353114:V2449L	ENSP00000353114:V2449L	V	-	1	0	AHNAK2	104485488	0.839000	0.29477	0.003000	0.11579	0.029000	0.11900	1.122000	0.31295	-0.169000	0.10834	-1.440000	0.01072	GTG	.	.		0.637	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105414443	C	A	105414443	3	1	333	1	0	0	0	0	1	0	0	0	415	536	19	1	10046	1	AHNAK2	14	105414443	Missense_Mutation	SNP	C	TCGA-RC-A6M4-01A-11D-A32G-10	4064204	105414443	1935097	134	46476										
TUBGCP5	114791	hgsc.bcm.edu	37	chr15	22848918	22848918	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	acaaatagcagcatatggccAggttgtgtttcgactccagg	11	9	0	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr15:22848918A>T	ENST00000283645.4	+	10	1095	c.965A>T	c.(964-966)cAg>cTg	p.Q322L	TUBGCP5_ENST00000453949.2_Missense_Mutation_p.Q322L|TUBGCP5_ENST00000559846.1_3'UTR	NM_052903.4	NP_443135.3	Q96RT8	GCP5_HUMAN	tubulin, gamma complex associated protein 5	322					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gamma-tubulin ring complex (GO:0008274)|microtubule (GO:0005874)|nucleus (GO:0005634)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(5)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(23)|prostate(1)|skin(2)|urinary_tract(1)	46		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.86e-06)|Epithelial(43;2.63e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000949)		GCATATGGCCAGGTTGTGTTT	0.433																																					p.Q322L		Atlas-SNP	.											.	TUBGCP5	82	.	0			c.A965T						.						160	144	149					15																	22848918		2203	4300	6503	SO:0001583	missense	114791	exon10			ATGGCCAGGTTGT	AB067486	CCDS73697.1, CCDS73698.1	15q11.1	2014-04-17			ENSG00000153575	ENSG00000275835			18600	protein-coding gene	gene with protein product	"gamma-tubulin complex component GCP5"	608147				11694571	Standard	NM_052903		Approved	GCP5, KIAA1899	uc001yur.4	Q96RT8	OTTHUMG00000188371	ENST00000283645.4:c.965A>T	chr15.hg19:g.22848918A>T	ENSP00000283645:p.Gln322Leu	62.0	0.0		52.0	27.0	NM_052903	E9PB12|Q6IQ52|Q96PY8	Missense_Mutation	SNP	ENST00000283645.4	hg19	CCDS10008.1	.	.	.	.	.	.	.	.	.	.	.	28.1	4.886321	0.91814	.	.	ENSG00000153575	ENST00000283645;ENST00000453949	T;T	0.06933	3.24;3.24	5.55	5.55	0.83447	.	0.111333	0.64402	D	0.000007	T	0.21267	0.0512	L	0.51422	1.61	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.71414	0.973;0.973	T	0.04229	-1.0967	10	0.16420	T	0.52	-16.3728	15.9885	0.80179	1.0:0.0:0.0:0.0	.	322;322	Q96RT8;E9PB12	GCP5_HUMAN;.	L	322	ENSP00000283645:Q322L;ENSP00000409217:Q322L	ENSP00000283645:Q322L	Q	+	2	0	TUBGCP5	20400359	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.749000	0.91619	2.234000	0.73211	0.533000	0.62120	CAG	.	.		0.433	TUBGCP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250998.2	NM_052903		T	22848918	A	T	22848918	3	4	333	1	0	0	0	0	1	0	0	0	16784	188	7	4	1003	4	TUBGCP5	15	22848918	Missense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10		22848918	79682474	135	46477										
MGA	23269	hgsc.bcm.edu	37	chr15	42052625	42052625	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	cggacacacactgccaatgaGcggcggcggcgtggtgaaat	15	11	0	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr15:42052625G>T	ENST00000570161.1	+	19	7296	c.7296G>T	c.(7294-7296)gaG>gaT	p.E2432D	MGA_ENST00000545763.1_Missense_Mutation_p.E2223D|MGA_ENST00000219905.7_Missense_Mutation_p.E2432D|MGA_ENST00000566586.1_Missense_Mutation_p.E2223D|MGA_ENST00000389936.4_Missense_Mutation_p.E2393D			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	CTGCCAATGAGCGGCGGCGGC	0.438																																					p.E2432D		Atlas-SNP	.											.	MGA	264	.	0			c.G7296T						.						111	113	112					15																	42052625		1898	4110	6008	SO:0001583	missense	23269	exon20			CAATGAGCGGCGG	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.7296G>T	chr15.hg19:g.42052625G>T	ENSP00000457035:p.Glu2432Asp	98.0	0.0		77.0	4.0	NM_001164273	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	hg19	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.275049	0.80580	.	.	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	D;D;D	0.99716	-6.51;-6.51;-6.51	5.53	4.41	0.53225	.	0.000000	0.52532	D	0.000063	D	0.99548	0.9838	M	0.83223	2.63	0.24841	N	0.99246	D;D;D	0.89917	1.0;1.0;0.994	D;D;D	0.87578	0.998;0.996;0.97	D	0.97578	1.0109	10	0.87932	D	0	.	6.4033	0.21650	0.2634:0.0:0.7366:0.0	.	1048;2223;2432	B4DVS1;F5H7K2;E7ENI0	.;.;.	D	2432;2393;2223	ENSP00000219905:E2432D;ENSP00000374586:E2393D;ENSP00000442467:E2223D	ENSP00000219905:E2432D	E	+	3	2	MGA	39839917	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.637000	0.24659	2.583000	0.87209	0.655000	0.94253	GAG	.	.		0.438	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		T	42052625	G	T	42052625	3	4	333	1	0	0	0	0	1	0	0	0	9549	962	34	3	7370	3	MGA	15	42052625	Missense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	19203707	42052625	60478767	136	46478										
TGM7	116179	hgsc.bcm.edu	37	chr15	43574767	43574767	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	acctgccacccgttgtatccTggtgggagatctttccggat	11	12	1	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr15:43574767T>A	ENST00000452443.2	-	8	1060	c.1056A>T	c.(1054-1056)ccA>ccT	p.P352P		NM_052955.2	NP_443187.1	Q96PF1	TGM7_HUMAN	transglutaminase 7	352					peptide cross-linking (GO:0018149)		metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(2)|prostate(4)|skin(1)	39		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.14e-07)	L-Glutamine(DB00130)	CGTTGTATCCTGGTGGGAGAT	0.557																																					p.P352P		Atlas-SNP	.											.	TGM7	86	.	0			c.A1056T						.						85	72	76					15																	43574767		2202	4299	6501	SO:0001819	synonymous_variant	116179	exon8			GTATCCTGGTGGG	AF363393	CCDS32213.1	15q15.2	2004-07-01				ENSG00000159495		"Transglutaminases"	30790	protein-coding gene	gene with protein product	"transglutaminase Z"	606776				11390390	Standard	NM_052955		Approved	TGMZ	uc001zrf.1	Q96PF1		ENST00000452443.2:c.1056A>T	chr15.hg19:g.43574767T>A		41.0	0.0		41.0	23.0	NM_052955		Silent	SNP	ENST00000452443.2	hg19	CCDS32213.1																																																																																			.	.		0.557	TGM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432489.1	NM_052955		A	43574767	T	A	43574767	2	1	333	1	0	0	0	0	0	0	0	1	15850	1567	55	4		4	TGM7	15	43574767	Silent	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	1522142	43574767	58956625	137	46479										
SMAD3	4088	hgsc.bcm.edu	37	chr15	67477190	67477190	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ggcacccggccaccgtctgcAagatcccaccaggtaaacga	10	16	1	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr15:67477190A>G	ENST00000327367.4	+	7	1307	c.997A>G	c.(997-999)Aag>Gag	p.K333E	SMAD3_ENST00000439724.3_Missense_Mutation_p.K289E|SMAD3_ENST00000540846.2_Missense_Mutation_p.K228E|SMAD3_ENST00000537194.2_Missense_Mutation_p.K138E	NM_005902.3	NP_005893.1	P84022	SMAD3_HUMAN	SMAD family member 3	333	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell-cell junction organization (GO:0045216)|developmental growth (GO:0048589)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic foregut morphogenesis (GO:0048617)|embryonic pattern specification (GO:0009880)|endoderm development (GO:0007492)|evasion or tolerance of host defenses by virus (GO:0019049)|extrinsic apoptotic signaling pathway (GO:0097191)|gene expression (GO:0010467)|heart looping (GO:0001947)|immune response (GO:0006955)|immune system development (GO:0002520)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|lens fiber cell differentiation (GO:0070306)|liver development (GO:0001889)|mesoderm formation (GO:0001707)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)|nodal signaling pathway (GO:0038092)|osteoblast development (GO:0002076)|paraxial mesoderm morphogenesis (GO:0048340)|pericardium development (GO:0060039)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone mineralization (GO:0030501)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta3 production (GO:0032916)|primary miRNA processing (GO:0031053)|protein stabilization (GO:0050821)|regulation of binding (GO:0051098)|regulation of epithelial cell proliferation (GO:0050678)|regulation of immune response (GO:0050776)|regulation of striated muscle tissue development (GO:0016202)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein complex assembly (GO:0007183)|somitogenesis (GO:0001756)|T cell activation (GO:0042110)|thyroid gland development (GO:0030878)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transdifferentiation (GO:0060290)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transport (GO:0006810)|ureteric bud development (GO:0001657)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nuclear inner membrane (GO:0005637)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|SMAD protein complex (GO:0071141)|SMAD2-SMAD3 protein complex (GO:0071144)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|bHLH transcription factor binding (GO:0043425)|chromatin DNA binding (GO:0031490)|co-SMAD binding (GO:0070410)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(11)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(7;0.125)		CACCGTCTGCAAGATCCCACC	0.597																																					p.K333E		Atlas-SNP	.											.	SMAD3	119	.	0			c.A997G						.						70	63	65					15																	67477190		2201	4299	6500	SO:0001583	missense	4088	exon7			GTCTGCAAGATCC	BC050743	CCDS10222.1, CCDS45288.1, CCDS53950.1, CCDS53951.1	15q21-q22	2006-11-06	2006-11-06	2004-05-26	ENSG00000166949	ENSG00000166949		"SMADs"	6769	protein-coding gene	gene with protein product		603109	"MAD, mothers against decapentaplegic homolog 3 (Drosophila)", "SMAD, mothers against DPP homolog 3 (Drosophila)"	MADH3		8774881, 8673135	Standard	NM_001145102		Approved	JV15-2, HsT17436	uc002aqj.3	P84022	OTTHUMG00000133230	ENST00000327367.4:c.997A>G	chr15.hg19:g.67477190A>G	ENSP00000332973:p.Lys333Glu	57.0	0.0		43.0	24.0	NM_005902	A8K4B6|B7Z4Z5|B7Z6M9|B7Z9Q2|F5H383|O09064|O09144|O14510|O35273|Q92940|Q93002|Q9GKR4	Missense_Mutation	SNP	ENST00000327367.4	hg19	CCDS10222.1	.	.	.	.	.	.	.	.	.	.	A	33	5.253541	0.95336	.	.	ENSG00000166949	ENST00000327367;ENST00000535241;ENST00000540846;ENST00000439724;ENST00000537194	D;D;D;D	0.99311	-5.73;-5.73;-5.73;-5.73	5.19	5.19	0.71726	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.99591	0.9852	H	0.96833	3.89	0.80722	D	1	D;D	0.69078	0.994;0.997	D;D	0.65874	0.917;0.939	D	0.97747	1.0212	10	0.87932	D	0	.	15.0667	0.72002	1.0:0.0:0.0:0.0	.	289;333	B7Z4Z5;P84022	.;SMAD3_HUMAN	E	333;333;228;289;138	ENSP00000332973:K333E;ENSP00000437757:K228E;ENSP00000401133:K289E;ENSP00000445348:K138E	ENSP00000332973:K333E	K	+	1	0	SMAD3	65264244	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.118000	0.94355	1.954000	0.56735	0.528000	0.53228	AAG	.	.		0.597	SMAD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256967.2	NM_005902		G	67477190	A	G	67477190	3	3	333	1	0	0	0	0	1	0	0	0	14774	131	5	2	1101	2	SMAD3	15	67477190	Missense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	23902423	67477190	35054202	138	46480										
HCN4	10021	hgsc.bcm.edu	37	chr15	73615218	73615218	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	aggcggccgggggtgagcggGggtgtgccccggcgctgggg	25	10	0	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr15:73615218G>A	ENST00000261917.3	-	8	4209	c.3216C>T	c.(3214-3216)ccC>ccT	p.P1072P		NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	1072	Pro-rich.				blood circulation (GO:0008015)|cation transport (GO:0006812)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)	cAMP binding (GO:0030552)|cation channel activity (GO:0005261)|identical protein binding (GO:0042802)|intracellular cAMP activated cation channel activity (GO:0005222)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(13)|liver(1)|lung(18)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				COAD - Colon adenocarcinoma(1;0.142)		GGGTGAGCGGGGGTGTGCCCC	0.741																																					p.P1072P		Atlas-SNP	.											.	HCN4	150	.	0			c.C3216T						.						4	7	6					15																	73615218		1952	3920	5872	SO:0001819	synonymous_variant	10021	exon8			GAGCGGGGGTGTG	AJ132429	CCDS10248.1	15q24.1	2011-07-05			ENSG00000138622	ENSG00000138622		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	16882	protein-coding gene	gene with protein product		605206				10228147, 10430953, 16382102	Standard	NM_005477		Approved		uc002avp.3	Q9Y3Q4	OTTHUMG00000137563	ENST00000261917.3:c.3216C>T	chr15.hg19:g.73615218G>A		29.0	0.0		21.0	14.0	NM_005477	Q9UMQ7	Silent	SNP	ENST00000261917.3	hg19	CCDS10248.1																																																																																			.	.		0.741	HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268900.2	NM_005477		A	73615218	G	A	73615218	2	1	333	1	0	0	0	0	0	0	0	1	7008	1219	43	3		3	HCN4	15	73615218	Silent	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	6138028	73615218	28916174	139	46481										
TRAP1	10131	hgsc.bcm.edu	37	chr16	3716009	3716009	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tggcggtcacaatgccctccCgcatgaacaggccgtaatct	10	14	2	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr16:3716009C>T	ENST00000246957.5	-	12	1434	c.1346G>A	c.(1345-1347)cGg>cAg	p.R449Q	TRAP1_ENST00000538171.1_Missense_Mutation_p.R396Q|TRAP1_ENST00000573872.1_5'Flank|TRAP1_ENST00000575671.1_Missense_Mutation_p.R240Q	NM_016292.2	NP_057376.2	Q12931	TRAP1_HUMAN	TNF receptor-associated protein 1	449					chaperone-mediated protein folding (GO:0061077)|negative regulation of cellular respiration (GO:1901856)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to stress (GO:0006950)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|tumor necrosis factor receptor binding (GO:0005164)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		Ovarian(90;0.0261)				AATGCCCTCCCGCATGAACAG	0.502																																					p.R449Q		Atlas-SNP	.											.	TRAP1	53	.	0			c.G1346A						.						103	98	100					16																	3716009		2197	4300	6497	SO:0001583	missense	10131	exon12			CCCTCCCGCATGA	AF154108	CCDS10508.1, CCDS61824.1	16p13.3	2011-09-02			ENSG00000126602	ENSG00000126602		"Heat shock proteins / HSPC"	16264	protein-coding gene	gene with protein product		606219				10652318, 7876093	Standard	NM_016292		Approved	HSP75, HSP90L	uc002cvt.4	Q12931	OTTHUMG00000129427	ENST00000246957.5:c.1346G>A	chr16.hg19:g.3716009C>T	ENSP00000246957:p.Arg449Gln	88.0	0.0		95.0	41.0	NM_016292	B4DR68|D3DUC8|F5H897|O43642|O75235|Q9UHL5	Missense_Mutation	SNP	ENST00000246957.5	hg19	CCDS10508.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.968459	0.92855	.	.	ENSG00000126602	ENST00000246957;ENST00000538171	T;T	0.09817	2.94;2.94	5.78	5.78	0.91487	Ribosomal protein S5 domain 2-type fold (1);	0.103312	0.64402	D	0.000006	T	0.33673	0.0871	M	0.69823	2.125	0.80722	D	1	D;D	0.69078	0.996;0.997	P;D	0.66084	0.902;0.941	T	0.01298	-1.1392	10	0.87932	D	0	-41.7894	18.9999	0.92829	0.0:1.0:0.0:0.0	.	396;449	F5H897;Q12931	.;TRAP1_HUMAN	Q	449;396	ENSP00000246957:R449Q;ENSP00000442070:R396Q	ENSP00000246957:R449Q	R	-	2	0	TRAP1	3656010	1.000000	0.71417	1.000000	0.80357	0.460000	0.32559	7.261000	0.78400	2.744000	0.94065	0.563000	0.77884	CGG	.	.		0.502	TRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251586.2	NM_016292		T	3716009	C	T	3716009	3	4	333	1	0	0	0	0	1	0	0	0	16470	652	23	1	796	1	TRAP1	16	3716009	Missense_Mutation	SNP	C	TCGA-RC-A6M4-01A-11D-A32G-10		3716009	86638744	140	46482										
KIAA0556	23247	hgsc.bcm.edu	37	chr16	27751968	27751968	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gtcccgagaagcccctggccTggaagggcaggctcccatca	13	15	1	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr16:27751968T>A	ENST00000261588.4	+	15	2369	c.2350T>A	c.(2350-2352)Tgg>Agg	p.W784R		NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	784						extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						GCCCCTGGCCTGGAAGGGCAG	0.622																																					p.W784R		Atlas-SNP	.											.	KIAA0556	348	.	0			c.T2350A						.						65	68	67					16																	27751968		2196	4300	6496	SO:0001583	missense	23247	exon15			CTGGCCTGGAAGG	AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.2350T>A	chr16.hg19:g.27751968T>A	ENSP00000261588:p.Trp784Arg	26.0	0.0		26.0	12.0	NM_015202	A7E2C2	Missense_Mutation	SNP	ENST00000261588.4	hg19	CCDS32415.1	.	.	.	.	.	.	.	.	.	.	T	4.837	0.155672	0.09236	.	.	ENSG00000047578	ENST00000261588	T	0.09073	3.02	4.31	-4.77	0.03219	.	1.007080	0.07969	N	0.983612	T	0.06142	0.0159	L	0.44542	1.39	0.09310	N	1	B	0.33583	0.418	B	0.33339	0.162	T	0.39881	-0.9592	10	0.13853	T	0.58	-20.8096	7.0308	0.24967	0.0:0.4391:0.2613:0.2997	.	784	O60303	K0556_HUMAN	R	784	ENSP00000261588:W784R	ENSP00000261588:W784R	W	+	1	0	KIAA0556	27659469	0.004000	0.15560	0.000000	0.03702	0.147000	0.21601	-0.128000	0.10531	-1.101000	0.03027	-0.366000	0.07423	TGG	.	.		0.622	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202		A	27751968	T	A	27751968	3	1	333	1	0	0	0	0	1	0	0	0	8192	1580	55	4	2408	4	KIAA0556	16	27751968	Missense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	24035959	27751968	62602785	141	46483										
RNF40	9810	hgsc.bcm.edu	37	chr16	30779293	30779293	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gctaaaaggggacgcccagcGatacaagcggaagcttcgag	14	10	0	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr16:30779293G>A	ENST00000324685.6	+	12	1943	c.1508G>A	c.(1507-1509)cGa>cAa	p.R503Q	RNF40_ENST00000563683.1_Missense_Mutation_p.R463Q|RNF40_ENST00000402121.3_Missense_Mutation_p.R195Q|RNF40_ENST00000357890.5_Missense_Mutation_p.R403Q	NM_001207033.1|NM_014771.3	NP_001193962.1|NP_055586	O75150	BRE1B_HUMAN	ring finger protein 40, E3 ubiquitin protein ligase	503					histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|ubiquitin-dependent protein catabolic process (GO:0006511)	HULC complex (GO:0033503)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(10)|prostate(2)	30			Colorectal(24;0.198)			GACGCCCAGCGATACAAGCGG	0.527																																					p.R503Q		Atlas-SNP	.											.	RNF40	83	.	0			c.G1508A						.						105	104	104					16																	30779293		2197	4300	6497	SO:0001583	missense	9810	exon12			CCCAGCGATACAA	AB014561	CCDS10691.1, CCDS55994.1	16p11.2-p11.1	2012-02-23	2012-02-23		ENSG00000103549	ENSG00000103549		"RING-type (C3HC4) zinc fingers"	16867	protein-coding gene	gene with protein product	"BRE1 E3 ubiquitin ligase homolog B (S. cerevisiae)"	607700	"ring finger protein 40"			9734811, 10944455, 12121982	Standard	NM_014771		Approved	KIAA0661, RBP95, BRE1B, STARING	uc002dzq.3	O75150	OTTHUMG00000132394	ENST00000324685.6:c.1508G>A	chr16.hg19:g.30779293G>A	ENSP00000325677:p.Arg503Gln	51.0	0.0		49.0	17.0	NM_014771	Q6AHZ6|Q6N005|Q7L3T6|Q8N615|Q96T18|Q9BSV9|Q9HC82	Missense_Mutation	SNP	ENST00000324685.6	hg19	CCDS10691.1	.	.	.	.	.	.	.	.	.	.	G	33	5.242085	0.95272	.	.	ENSG00000103549	ENST00000324685;ENST00000357890;ENST00000402121	T;T;T	0.38077	1.16;1.16;1.16	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.65059	0.2655	M	0.84326	2.69	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;0.999	D;D;D;D	0.72338	0.977;0.975;0.963;0.951	T	0.67503	-0.5654	10	0.59425	D	0.04	-10.2864	18.742	0.91777	0.0:0.0:1.0:0.0	.	195;403;503;503	F8W8Z4;O75150-4;A8K6K1;O75150	.;.;.;BRE1B_HUMAN	Q	503;403;195	ENSP00000325677:R503Q;ENSP00000350563:R403Q;ENSP00000384942:R195Q	ENSP00000325677:R503Q	R	+	2	0	RNF40	30686794	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.444000	0.97578	2.728000	0.93425	0.655000	0.94253	CGA	.	.		0.527	RNF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255524.2	NM_014771		A	30779293	G	A	30779293	3	1	333	1	0	0	0	0	1	0	0	0	13508	1058	37	1	1550	1	RNF40	16	30779293	Missense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	3027325	30779293	59575460	142	46484										
SALL1	6299	hgsc.bcm.edu	37	chr16	51174758	51174758	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ctgcaaggcactgtcactccCaaagaccttcgcgcagaacc	8	16	1	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr16:51174758C>T	ENST00000251020.4	-	2	1408	c.1375G>A	c.(1375-1377)Ggg>Agg	p.G459R	SALL1_ENST00000566102.1_Intron|SALL1_ENST00000562674.1_5'Flank|SALL1_ENST00000440970.1_Missense_Mutation_p.G362R|SALL1_ENST00000541611.1_Intron	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	459					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G459W(1)		NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			CTGTCACTCCCAAAGACCTTC	0.502																																					p.G459R	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											.	SALL1	301	.	1	Substitution - Missense(1)	lung(1)	c.G1375A						.						104	96	99					16																	51174758		2198	4300	6498	SO:0001583	missense	6299	exon2			CACTCCCAAAGAC	X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"Zinc fingers, C2H2-type"	10524	protein-coding gene	gene with protein product		602218	"sal (Drosophila)-like 1", "sal-like 1 (Drosophila)"	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.1375G>A	chr16.hg19:g.51174758C>T	ENSP00000251020:p.Gly459Arg	57.0	0.0		52.0	26.0	NM_002968	Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	hg19	CCDS10747.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.018854	0.75275	.	.	ENSG00000103449	ENST00000251020;ENST00000440970;ENST00000457559	T;T	0.06933	3.24;3.24	5.18	5.18	0.71444	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.33147	0.0853	M	0.83774	2.66	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.06250	-1.0837	10	0.33940	T	0.23	.	18.685	0.91560	0.0:1.0:0.0:0.0	.	459	Q9NSC2	SALL1_HUMAN	R	459;362;423	ENSP00000251020:G459R;ENSP00000407914:G362R	ENSP00000251020:G459R	G	-	1	0	SALL1	49732259	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	7.814000	0.86154	2.386000	0.81285	0.563000	0.77884	GGG	.	.		0.502	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968		T	51174758	C	T	51174758	3	4	333	1	0	0	0	0	1	0	0	0	13825	594	21	3	2607	3	SALL1	16	51174758	Missense_Mutation	SNP	C	TCGA-RC-A6M4-01A-11D-A32G-10	20395465	51174758	39179995	143	46485										
CES1	1066	hgsc.bcm.edu	37	chr16	55850865	55850865	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gtctccctgtaagtccagagAtaagaatttctgtgaagaca	9	8	2	4			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr16:55850865A>G	ENST00000361503.4	-	8	1043	c.913T>C	c.(913-915)Tct>Cct	p.S305P	CES1_ENST00000360526.3_Missense_Mutation_p.S306P|CES1_ENST00000422046.2_Missense_Mutation_p.S305P			P23141	EST1_HUMAN	carboxylesterase 1	305				S -> M (in Ref. 14; AA sequence). {ECO:0000305}.	epithelial cell differentiation (GO:0030855)|metabolic process (GO:0008152)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)	carboxylic ester hydrolase activity (GO:0052689)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)								all cancers(182;0.13)|Epithelial(162;0.137)	Benzocaine(DB01086)|Capecitabine(DB01101)|Ciclesonide(DB01410)|Clopidogrel(DB00758)|Cyclandelate(DB04838)|Dabigatran etexilate(DB06695)|Indomethacin(DB00328)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Mycophenolate mofetil(DB00688)|Oseltamivir(DB00198)|Probucol(DB01599)|Rufinamide(DB06201)|Tamoxifen(DB00675)|Trandolapril(DB00519)	AAGTCCAGAGATAAGAATTTC	0.483																																					p.S306P	NSCLC(162;1801 2756 42904 52896)	Atlas-SNP	.											.	CES1	78	.	0			c.T916C						.						126	140	135					16																	55850865		2198	4300	6498	SO:0001583	missense	1066	exon8			CCAGAGATAAGAA	BC012418	CCDS32450.1, CCDS45488.1, CCDS45489.1	16q22.2	2010-10-12	2010-10-12		ENSG00000198848	ENSG00000198848	3.1.1.1	"Carboxylesterases"	1863	protein-coding gene	gene with protein product	"human monocyte/macrophage serine esterase 1"	114835	"carboxylesterase 1 (monocyte/macrophage serine esterase 1)"			2070086, 20931200	Standard	XM_005255774		Approved	HMSE, CES2, HMSE1, SES1, CEH, CES1A1, CES1A2	uc002eil.3	P23141		ENST00000361503.4:c.913T>C	chr16.hg19:g.55850865A>G	ENSP00000355193:p.Ser305Pro	53.0	0.0		60.0	9.0	NM_001025195	A6NIM1|A8K3K8|A8K844|E9PAU8|P82127|Q00015|Q13657|Q14062|Q16737|Q16788|Q549X7|Q549X8|Q86UK2|Q96EE8|Q9UC52|Q9UDG8|Q9UK77|Q9ULY2	Missense_Mutation	SNP	ENST00000361503.4	hg19	CCDS45488.1	.	.	.	.	.	.	.	.	.	.	.	12.17	1.856645	0.32791	.	.	ENSG00000198848	ENST00000360526;ENST00000361503;ENST00000422046;ENST00000426667	T;T;T	0.68765	-0.35;-0.35;-0.35	4.4	-7.66	0.01277	Carboxylesterase, type B (1);	3.847600	0.00868	N	0.001992	T	0.37019	0.0988	N	0.04203	-0.255	0.09310	N	1	B;B;B	0.25390	0.125;0.125;0.103	B;B;B	0.27380	0.079;0.079;0.047	T	0.23368	-1.0190	10	0.29301	T	0.29	.	2.1327	0.03754	0.1177:0.3691:0.2497:0.2634	.	305;305;306	E9PAU8;P23141;P23141-2	.;EST1_HUMAN;.	P	306;305;305;170	ENSP00000353720:S306P;ENSP00000355193:S305P;ENSP00000390492:S305P	ENSP00000353720:S306P	S	-	1	0	CES1	54408366	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.357000	0.00499	-1.568000	0.01670	-0.475000	0.04921	TCT	.	.		0.483	CES1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000433285.1	NM_001266		G	55850865	A	G	55850865	3	3	333	1	0	0	0	0	1	0	0	0	3271	333	12	2	818	2	CES1	16	55850865	Missense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	4676107	55850865	34503888	144	46486										
PLEKHG4	25894	hgsc.bcm.edu	37	chr16	67320230	67320230	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	aagaataagcctcgctccgaTgccctgatgtcaagctatgg	10	11	1	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr16:67320230T>C	ENST00000360461.5	+	14	5031	c.2496T>C	c.(2494-2496)gaT>gaC	p.D832D	PLEKHG4_ENST00000379344.3_Silent_p.D832D|PLEKHG4_ENST00000427155.2_Silent_p.D832D|PLEKHG4_ENST00000450733.1_Silent_p.D751D	NM_001129727.1|NM_015432.3	NP_001123199.1|NP_056247.1	Q58EX7	PKHG4_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4	832	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)|Kidney(780;0.119)		CTCGCTCCGATGCCCTGATGT	0.567																																					p.D832D		Atlas-SNP	.											.	PLEKHG4	94	.	0			c.T2496C						.						158	120	133					16																	67320230		2198	4300	6498	SO:0001819	synonymous_variant	25894	exon15			CTCCGATGCCCTG	AK024475	CCDS32466.1, CCDS45512.1	16q22.1	2013-01-11						"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	24501	protein-coding gene	gene with protein product	"puratrophin-1"	609526	"spinocerebellar ataxia 4"	SCA4		16491300, 16001362	Standard	NM_015432		Approved	DKFZP434I216, ARHGEF44	uc010cef.3	Q58EX7		ENST00000360461.5:c.2496T>C	chr16.hg19:g.67320230T>C		45.0	0.0		63.0	27.0	NM_001129728	Q4G0J8|Q4H485|Q56A69|Q9H7K4|Q9UFW0	Silent	SNP	ENST00000360461.5	hg19	CCDS32466.1																																																																																			.	.		0.567	PLEKHG4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421395.2	NM_015432		C	67320230	T	C	67320230	2	2	333	1	0	0	0	0	0	0	0	1	12080	1461	51	2		2	PLEKHG4	16	67320230	Silent	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	11469365	67320230	23034523	145	46487										
MTSS1L	92154	hgsc.bcm.edu	37	chr16	70698128	70698128	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gggcttggtggagggtgtgcGgcggatggtggccacgccgg	23	8	0	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr16:70698128G>A	ENST00000338779.6	-	15	1970	c.1696C>T	c.(1696-1698)Cgc>Tgc	p.R566C	FLJ00418_ENST00000597002.1_5'UTR	NM_138383.2	NP_612392.1	Q765P7	MTSSL_HUMAN	metastasis suppressor 1-like	566					filopodium assembly (GO:0046847)|signal transduction (GO:0007165)					breast(1)|central_nervous_system(2)|endometrium(1)|liver(1)|lung(1)|skin(1)	7						GAGGGTGTGCGGCGGATGGTG	0.766																																					p.R566C		Atlas-SNP	.											.	MTSS1L	22	.	0			c.C1696T						.						13	16	15					16																	70698128		2167	4195	6362	SO:0001583	missense	92154	exon15			GTGTGCGGCGGAT		CCDS32476.1	16q22.1	2008-12-16				ENSG00000132613			25094	protein-coding gene	gene with protein product	"actin-bundling protein with BAIAP2 homology"					12477932	Standard	XM_006721335		Approved	ABBA-1, LOC92154	uc002ezj.3	Q765P7		ENST00000338779.6:c.1696C>T	chr16.hg19:g.70698128G>A	ENSP00000341171:p.Arg566Cys	30.0	0.0		41.0	21.0	NM_138383	A6NJI7|Q9BUA8	Missense_Mutation	SNP	ENST00000338779.6	hg19	CCDS32476.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.385410	0.82792	.	.	ENSG00000132613	ENST00000338779	T	0.53857	0.6	4.38	4.38	0.52667	.	0.000000	0.85682	D	0.000000	T	0.73210	0.3558	M	0.77820	2.39	0.58432	D	0.999995	D	0.89917	1.0	D	0.97110	1.0	T	0.78414	-0.2213	10	0.72032	D	0.01	-21.8297	16.5688	0.84606	0.0:0.0:1.0:0.0	.	566	Q765P7	MTSSL_HUMAN	C	566	ENSP00000341171:R566C	ENSP00000341171:R566C	R	-	1	0	MTSS1L	69255629	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.338000	0.72963	1.964000	0.57103	0.462000	0.41574	CGC	.	.		0.766	MTSS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434927.3	NM_138383		A	70698128	G	A	70698128	3	1	333	1	0	0	0	0	1	0	0	0	9972	1116	39	1	551	1	MTSS1L	16	70698128	Missense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	3377898	70698128	19656625	146	46488										
ATMIN	23300	hgsc.bcm.edu	37	chr16	81076059	81076059	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	cagtctcacatctaccgaacTgggcacgagatacctgcaga	9	13	2	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr16:81076059T>C	ENST00000299575.4	+	3	660	c.636T>C	c.(634-636)acT>acC	p.T212T	ATMIN_ENST00000564241.1_Silent_p.T56T|ATMIN_ENST00000539819.1_Intron|ATMIN_ENST00000566488.1_Silent_p.T56T	NM_015251.2	NP_056066.2	O43313	ATMIN_HUMAN	ATM interactor	212					cellular response to DNA damage stimulus (GO:0006974)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dynein binding (GO:0045502)|metal ion binding (GO:0046872)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	20						TCTACCGAACTGGGCACGAGA	0.517																																					p.T212T		Atlas-SNP	.											.	ATMIN	50	.	0			c.T636C						.						85	62	70					16																	81076059		2202	4300	6502	SO:0001819	synonymous_variant	23300	exon3			CCGAACTGGGCAC	BC002701	CCDS32494.1, CCDS73917.1	16q23.2	2013-01-07			ENSG00000166454	ENSG00000166454		"Zinc fingers, C2H2-type"	29034	protein-coding gene	gene with protein product	"ATM/ATR-Substrate Chk2-Interacting Zn++-finger protein", "ATM INteracting protein"	614693				15933716, 17525732, 19001856	Standard	XM_005255866		Approved	ASCIZ, KIAA0431, ZNF822	uc002ffz.1	O43313	OTTHUMG00000176469	ENST00000299575.4:c.636T>C	chr16.hg19:g.81076059T>C		32.0	0.0		31.0	14.0	NM_015251	A8K4H8|Q68DC9	Silent	SNP	ENST00000299575.4	hg19	CCDS32494.1																																																																																			.	.		0.517	ATMIN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432140.1	NM_015251		C	81076059	T	C	81076059	2	2	333	1	0	0	0	0	0	0	0	1	1110	1567	55	2		2	ATMIN	16	81076059	Silent	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	10377931	81076059	9278694	147	46489										
PMP22	5376	hgsc.bcm.edu	37	chr17	15162456	15162456	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gtggacatttcctgaggaagAggtgctacagttctgccaga	13	8	1	3			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr17:15162456A>G	ENST00000395938.2	-	3	327	c.133T>C	c.(133-135)Tct>Cct	p.S45P	PMP22_ENST00000312280.3_Missense_Mutation_p.S45P|PMP22_ENST00000395936.1_Missense_Mutation_p.S45P|PMP22_ENST00000426385.3_Missense_Mutation_p.S45P|PMP22_ENST00000494511.1_Intron|RP11-849N15.1_ENST00000579159.1_RNA	NM_001281455.1|NM_153321.1	NP_001268384.1|NP_696996.1	Q01453	PMP22_HUMAN	peripheral myelin protein 22	45					cell death (GO:0008219)|peripheral nervous system development (GO:0007422)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|kidney(1)|large_intestine(2)|lung(3)	8				UCEC - Uterine corpus endometrioid carcinoma (92;0.0884)|BRCA - Breast invasive adenocarcinoma(8;4.92e-06)		CCTGAGGAAGAGGTGCTACAG	0.507																																					p.S45P		Atlas-SNP	.											.	PMP22	18	.	0			c.T133C						.						223	169	187					17																	15162456		2203	4300	6503	SO:0001583	missense	5376	exon2			AGGAAGAGGTGCT	D11428	CCDS11168.1	17p12	2014-09-17			ENSG00000109099	ENSG00000109099			9118	protein-coding gene	gene with protein product		601097				8482547, 1497668	Standard	NM_001281456		Approved	HNPP, GAS-3, Sp110	uc002goj.3	Q01453	OTTHUMG00000058960	ENST00000395938.2:c.133T>C	chr17.hg19:g.15162456A>G	ENSP00000379269:p.Ser45Pro	74.0	0.0		51.0	46.0	NM_153322	Q8WV01	Missense_Mutation	SNP	ENST00000395938.2	hg19	CCDS11168.1	.	.	.	.	.	.	.	.	.	.	A	11.69	1.714517	0.30413	.	.	ENSG00000109099	ENST00000395938;ENST00000312280;ENST00000426385;ENST00000395936	D;D;D;D	0.89415	-2.51;-2.51;-2.51;-2.51	4.75	1.34	0.21922	.	1.156650	0.06258	N	0.693442	D	0.82545	0.5060	L	0.39898	1.24	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.67868	-0.5559	10	0.54805	T	0.06	-6.3579	2.8351	0.05512	0.6142:0.0:0.1993:0.1865	.	45	Q01453	PMP22_HUMAN	P	45	ENSP00000379269:S45P;ENSP00000308937:S45P;ENSP00000409824:S45P;ENSP00000379268:S45P	ENSP00000308937:S45P	S	-	1	0	PMP22	15103181	0.001000	0.12720	0.002000	0.10522	0.550000	0.35303	0.756000	0.26419	0.391000	0.25143	0.460000	0.39030	TCT	.	.		0.507	PMP22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130378.1	NM_000304		G	15162456	A	G	15162456	3	3	333	1	0	0	0	0	1	0	0	0	12148	304	11	2	361	2	PMP22	17	15162456	Missense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10		15162456	66032754	148	46490										
ULK2	9706	hgsc.bcm.edu	37	chr17	19698995	19698995	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gccctgatgtcgacatatagGagtctttccttgttgatctg	10	9	2	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr17:19698995G>T	ENST00000395544.4	-	20	2540	c.2041C>A	c.(2041-2043)Cct>Act	p.P681T	ULK2_ENST00000361658.2_Missense_Mutation_p.P681T|ULK2_ENST00000580130.1_5'Flank	NM_014683.3	NP_055498.3	Q8IYT8	ULK2_HUMAN	unc-51 like autophagy activating kinase 2	681					autophagic vacuole assembly (GO:0000045)|axon extension (GO:0048675)|negative regulation of collateral sprouting (GO:0048671)|protein autophosphorylation (GO:0046777)|regulation of autophagy (GO:0010506)|response to starvation (GO:0042594)|signal transduction (GO:0007165)	ATG1/UKL1 signaling complex (GO:0034273)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|pre-autophagosomal structure membrane (GO:0034045)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			large_intestine(1)|skin(4)|stomach(1)	6	all_cancers(12;4.97e-05)|all_epithelial(12;0.00362)|Breast(13;0.186)					CGACATATAGGAGTCTTTCCT	0.338																																					p.P681T		Atlas-SNP	.											.	ULK2	142	.	0			c.C2041A						.						220	220	220					17																	19698995		2203	4300	6503	SO:0001583	missense	9706	exon20			ATATAGGAGTCTT	AB014523	CCDS11213.1	17p11.2	2014-02-12	2013-07-02		ENSG00000083290	ENSG00000083290	2.7.11.1		13480	protein-coding gene	gene with protein product		608650	"unc-51 (C. elegans)-like kinase 2", "unc-51-like kinase 2 (C. elegans)"			10557072	Standard	NM_014683		Approved	KIAA0623, Unc51.2, ATG1B	uc002gwn.3	Q8IYT8	OTTHUMG00000059511	ENST00000395544.4:c.2041C>A	chr17.hg19:g.19698995G>T	ENSP00000378914:p.Pro681Thr	204.0	0.0		116.0	109.0	NM_001142610	A8MY69|O75119	Missense_Mutation	SNP	ENST00000395544.4	hg19	CCDS11213.1	.	.	.	.	.	.	.	.	.	.	G	4.929	0.172615	0.09391	.	.	ENSG00000083290	ENST00000361658;ENST00000395544	T;T	0.39997	1.05;1.05	5.57	3.5	0.40072	.	0.339495	0.34555	N	0.003862	T	0.23649	0.0572	N	0.17674	0.51	0.29435	N	0.859549	B	0.02656	0.0	B	0.04013	0.001	T	0.15378	-1.0439	10	0.21014	T	0.42	-2.7807	7.0504	0.25069	0.0843:0.0:0.5004:0.4153	.	681	Q8IYT8	ULK2_HUMAN	T	681	ENSP00000354877:P681T;ENSP00000378914:P681T	ENSP00000354877:P681T	P	-	1	0	ULK2	19639587	0.885000	0.30320	0.447000	0.26932	0.021000	0.10359	0.596000	0.24044	0.642000	0.30620	0.655000	0.94253	CCT	.	.		0.338	ULK2-001	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132375.2	NM_014683		T	19698995	G	T	19698995	3	4	333	1	0	0	0	0	1	0	0	0	16991	1174	41	3	1101	3	ULK2	17	19698995	Missense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	4536539	19698995	61496215	149	46491										
RHBDL3	162494	hgsc.bcm.edu	37	chr17	30621329	30621329	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ccaggttgcctttttcctctAcaatggggtgtcactaggtc	10	11	2	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr17:30621329A>G	ENST00000269051.4	+	5	550	c.536A>G	c.(535-537)tAc>tGc	p.Y179C	RHBDL3_ENST00000536287.1_Missense_Mutation_p.Y81C|RHBDL3_ENST00000538145.1_Missense_Mutation_p.Y171C	NM_138328.2	NP_612201.1	P58872	RHBL3_HUMAN	rhomboid, veinlet-like 3 (Drosophila)	179						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)|skin(1)	16		Breast(31;0.116)|Ovarian(249;0.182)				TTTTTCCTCTACAATGGGGTG	0.502																																					p.Y179C		Atlas-SNP	.											.	RHBDL3	49	.	0			c.A536G						.						226	185	199					17																	30621329		2203	4300	6503	SO:0001583	missense	162494	exon5			TCCTCTACAATGG	AJ313480	CCDS32613.1	17q11.2	2013-01-10				ENSG00000141314		"EF-hand domain containing"	16502	protein-coding gene	gene with protein product			"rhomboid, veinlet-like 4 (Drosophila)"	RHBDL4		11900977	Standard	XM_006721733		Approved	VRHO	uc002hhe.1	P58872		ENST00000269051.4:c.536A>G	chr17.hg19:g.30621329A>G	ENSP00000269051:p.Tyr179Cys	112.0	0.0		118.0	55.0	NM_138328	A6NMH1|Q495Y4|Q495Y5|Q495Y6	Missense_Mutation	SNP	ENST00000269051.4	hg19	CCDS32613.1	.	.	.	.	.	.	.	.	.	.	A	14.56	2.571743	0.45798	.	.	ENSG00000141314	ENST00000431505;ENST00000269051;ENST00000538145;ENST00000536287	T;T;T;T	0.11712	2.75;2.75;2.75;2.75	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.26846	0.0657	L	0.44542	1.39	0.80722	D	1	D;B;B	0.89917	1.0;0.022;0.022	D;B;B	0.87578	0.998;0.008;0.008	T	0.00382	-1.1775	10	0.37606	T	0.19	-18.623	16.8222	0.85835	1.0:0.0:0.0:0.0	.	179;171;179	E9PD28;Q495Y5;P58872	.;.;RHBL3_HUMAN	C	179;179;171;81	ENSP00000394849:Y179C;ENSP00000269051:Y179C;ENSP00000442092:Y171C;ENSP00000466508:Y81C	ENSP00000269051:Y179C	Y	+	2	0	RHBDL3	27645442	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.161000	0.77505	2.371000	0.80710	0.533000	0.62120	TAC	.	.		0.502	RHBDL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447120.1	NM_138328		G	30621329	A	G	30621329	3	3	333	1	0	0	0	0	1	0	0	0	13338	391	14	2	554	2	RHBDL3	17	30621329	Missense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	10922334	30621329	50573881	150	46492										
UNC45B	146862	hgsc.bcm.edu	37	chr17	33504605	33504605	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tctcctaggcctcaccaaccTgtctgggcggagtgacaaac	10	14	3	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr17:33504605T>A	ENST00000268876.5	+	17	2334	c.2237T>A	c.(2236-2238)cTg>cAg	p.L746Q	UNC45B_ENST00000433649.1_Missense_Mutation_p.L744Q|UNC45B_ENST00000591048.1_Missense_Mutation_p.L665Q|UNC45B_ENST00000378449.1_Missense_Mutation_p.L665Q|UNC45B_ENST00000394570.2_Missense_Mutation_p.L744Q	NM_173167.2	NP_775259.1	Q8IWX7	UN45B_HUMAN	unc-45 homolog B (C. elegans)	746					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(10)|lung(24)|ovary(3)|prostate(2)|skin(1)|stomach(1)|urinary_tract(3)	59		Ovarian(249;0.17)				CTCACCAACCTGTCTGGGCGG	0.532																																					p.L746Q		Atlas-SNP	.											.	UNC45B	133	.	0			c.T2237A						.						37	28	31					17																	33504605		2197	4284	6481	SO:0001583	missense	146862	exon17			CCAACCTGTCTGG	AW755253	CCDS11292.1, CCDS45648.1	17q12	2008-02-05	2005-11-17	2005-11-17	ENSG00000141161	ENSG00000141161			14304	protein-coding gene	gene with protein product		611220	"cardiomyopathy associated 4"	CMYA4		12356907	Standard	NM_001267052		Approved	UNC45	uc002hja.3	Q8IWX7	OTTHUMG00000132931	ENST00000268876.5:c.2237T>A	chr17.hg19:g.33504605T>A	ENSP00000268876:p.Leu746Gln	31.0	0.0		47.0	24.0	NM_173167	Q495Q8|Q495Q9	Missense_Mutation	SNP	ENST00000268876.5	hg19	CCDS11292.1	.	.	.	.	.	.	.	.	.	.	T	26.9	4.782779	0.90282	.	.	ENSG00000141161	ENST00000394570;ENST00000268876;ENST00000433649;ENST00000378449	T;T;T	0.62498	0.02;1.0;0.02	5.3	5.3	0.74995	Armadillo-like helical (1);Armadillo-type fold (1);	0.160460	0.42548	D	0.000684	D	0.82930	0.5144	M	0.93106	3.38	0.53005	D	0.999969	D;D;D	0.89917	0.982;1.0;1.0	P;D;D	0.71656	0.875;0.973;0.974	D	0.87285	0.2295	10	0.87932	D	0	-13.9521	14.5819	0.68298	0.0:0.0:0.0:1.0	.	665;744;746	Q8IWX7-2;Q8IWX7-3;Q8IWX7	.;.;UN45B_HUMAN	Q	746;746;744;665	ENSP00000268876:L746Q;ENSP00000412840:L744Q;ENSP00000367710:L665Q	ENSP00000268876:L746Q	L	+	2	0	UNC45B	30528718	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.756000	0.85195	2.225000	0.72522	0.460000	0.39030	CTG	.	.		0.532	UNC45B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256458.2	NM_173167		A	33504605	T	A	33504605	3	1	333	1	0	0	0	0	1	0	0	0	17004	1580	55	4	2299	4	UNC45B	17	33504605	Missense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	2883276	33504605	47690605	151	46493										
KRT31	3881	hgsc.bcm.edu	37	chr17	39550414	39550414	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ggtcgtggcacagggattgcTgggcagactggagacaaaag	17	7	0	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr17:39550414T>A	ENST00000251645.2	-	7	1157	c.1105A>T	c.(1105-1107)Agc>Tgc	p.S369C		NM_002277.2	NP_002268.2	Q15323	K1H1_HUMAN	keratin 31	369	Tail.				epidermis development (GO:0008544)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	31		Breast(137;0.000496)				CAGGGATTGCTGGGCAGACTG	0.527																																					p.S369C		Atlas-SNP	.											.	KRT31	158	.	0			c.A1105T						.						105	88	94					17																	39550414		2203	4300	6503	SO:0001583	missense	3881	exon7			GATTGCTGGGCAG	X86570	CCDS11391.1	17q21.2	2014-05-20	2006-07-17	2006-07-17	ENSG00000094796	ENSG00000094796		"-", "Intermediate filaments type I, keratins (acidic)"	6448	protein-coding gene	gene with protein product	"hard keratin type I 1"	601077	"keratin, hair, acidic, 1"	KRTHA1		7578244, 16831889	Standard	NM_002277		Approved	Ha-1	uc002hwn.3	Q15323	OTTHUMG00000133423	ENST00000251645.2:c.1105A>T	chr17.hg19:g.39550414T>A	ENSP00000251645:p.Ser369Cys	44.0	0.0		53.0	27.0	NM_002277	Q9UE12	Missense_Mutation	SNP	ENST00000251645.2	hg19	CCDS11391.1	.	.	.	.	.	.	.	.	.	.	t	2.700	-0.271220	0.05716	.	.	ENSG00000094796	ENST00000251645	D	0.81908	-1.55	5.76	0.608	0.17569	.	0.509560	0.19860	N	0.104444	T	0.41213	0.1149	N	0.00408	-1.53	0.23492	N	0.997568	B	0.02656	0.0	B	0.01281	0.0	T	0.50065	-0.8871	10	0.02654	T	1	.	1.4325	0.02336	0.423:0.1442:0.085:0.3478	.	369	Q15323	K1H1_HUMAN	C	369	ENSP00000251645:S369C	ENSP00000251645:S369C	S	-	1	0	KRT31	36803940	1.000000	0.71417	0.959000	0.39883	0.881000	0.50899	0.680000	0.25306	0.074000	0.16767	-0.438000	0.05819	AGC	.	.		0.527	KRT31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257286.1	NM_002277		A	39550414	T	A	39550414	3	1	333	1	0	0	0	0	1	0	0	0	8476	1580	55	4	149	4	KRT31	17	39550414	Missense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	6045809	39550414	41644796	152	46494										
ADAM11	4185	hgsc.bcm.edu	37	chr17	42854925	42854925	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ggggacctggtgggagacatCagtagtgtcaccttctacca	13	10	3	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr17:42854925C>T	ENST00000200557.6	+	22	2026	c.1857C>T	c.(1855-1857)atC>atT	p.I619I	ADAM11_ENST00000535346.1_Silent_p.I419I	NM_002390.4	NP_002381.2	O75078	ADA11_HUMAN	ADAM metallopeptidase domain 11	619	Cys-rich.				integrin-mediated signaling pathway (GO:0007229)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(15)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33		Prostate(33;0.0959)				TGGGAGACATCAGTAGTGTCA	0.592																																					p.I619I		Atlas-SNP	.											.	ADAM11	118	.	0			c.C1857T						.						104	100	101					17																	42854925		2203	4300	6503	SO:0001819	synonymous_variant	4185	exon22			AGACATCAGTAGT	D17390	CCDS11486.1	17q21.3	2014-08-12	2005-08-18		ENSG00000073670			"ADAM metallopeptidase domain containing"	189	protein-coding gene	gene with protein product	"metalloproteinase-like, disintegrin-like, cysteine-rich protein"	155120	"a disintegrin and metalloproteinase domain 11"	MDC		8252040	Standard	XM_005257373		Approved		uc002ihh.3	O75078	OTTHUMG00000179038	ENST00000200557.6:c.1857C>T	chr17.hg19:g.42854925C>T		63.0	0.0		64.0	28.0	NM_002390	Q14808|Q14809|Q14810	Silent	SNP	ENST00000200557.6	hg19	CCDS11486.1	.	.	.	.	.	.	.	.	.	.	C	8.381	0.837598	0.16891	.	.	ENSG00000073670	ENST00000355638	.	.	.	4.8	4.8	0.61643	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	17.011	0.86406	0.0:1.0:0.0:0.0	.	.	.	.	X	523	.	ENSP00000347856:Q523X	Q	+	1	0	ADAM11	40210451	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	0.776000	0.26704	2.374000	0.81015	0.561000	0.74099	CAG	.	.		0.592	ADAM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444531.1	NM_002390		T	42854925	C	T	42854925	2	4	333	1	0	0	0	0	0	0	0	1	235	816	29	3		3	ADAM11	17	42854925	Silent	SNP	C	TCGA-RC-A6M4-01A-11D-A32G-10	3304511	42854925	38340285	153	46495										
KIF18B	146909	hgsc.bcm.edu	37	chr17	43010040	43010040	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ggaatgggcagtggaactcaCtgttctggtggtggtcccga	16	8	2	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr17:43010040C>A	ENST00000593135.1	-	9	1336		c.e9+1		KIF18B_ENST00000587309.1_Splice_Site|KIF18B_ENST00000590129.1_Splice_Site|KIF18B_ENST00000438933.2_Splice_Site|KIF18B_ENST00000339151.4_Splice_Site	NM_001265577.1	NP_001252506.1	Q86Y91	KI18B_HUMAN	kinesin family member 18B						ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|regulation of cell division (GO:0051302)	astral microtubule (GO:0000235)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule plus-end (GO:0035371)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	21		Prostate(33;0.155)				GTGGAACTCACTGTTCTGGTG	0.622																																					.		Atlas-SNP	.											.	KIF18B	63	.	0			c.1238+1G>T						.						90	102	98					17																	43010040		1963	4131	6094	SO:0001630	splice_region_variant	146909	exon10			AACTCACTGTTCT		CCDS45709.1, CCDS58555.1, CCDS45709.2	17q21.31	2014-09-04			ENSG00000186185			"Kinesins"	27102	protein-coding gene	gene with protein product		614570				16084724	Standard	NM_001264573		Approved		uc010wjh.3	Q86Y91	OTTHUMG00000179867	ENST00000593135.1:c.1238+1G>T	chr17.hg19:g.43010040C>A		22.0	0.0		27.0	11.0	NM_001264573	A6NJI2|B7ZM49|B9EGM8|D5L6I1	Splice_Site	SNP	ENST00000593135.1	hg19	CCDS45709.2	.	.	.	.	.	.	.	.	.	.	C	18.60	3.659434	0.67586	.	.	ENSG00000186185	ENST00000438933;ENST00000339151;ENST00000376982	.	.	.	5.51	4.52	0.55395	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.4848	0.55866	0.0:0.8317:0.1683:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	KIF18B	40365566	0.224000	0.23674	0.979000	0.43373	0.429000	0.31625	1.243000	0.32767	1.425000	0.47237	0.650000	0.86243	.	.	.		0.622	KIF18B-001	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000448724.1	NM_001080443	Intron	A	43010040	C	A	43010040	5	1	333	1	0	0	0	0	0	0	1	0	8290	579	20	3	1359	3	KIF18B	17	43010040	Splice_Site	SNP	C	TCGA-RC-A6M4-01A-11D-A32G-10	155115	43010040	38185170	154	46496										
OSBPL7	114881	hgsc.bcm.edu	37	chr17	45890656	45890656	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tcactgatgaagcggaagccTcggtcaggccgctcacactc	11	14	3	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr17:45890656T>C	ENST00000007414.3	-	16	1904	c.1713A>G	c.(1711-1713)cgA>cgG	p.R571R	OSBPL7_ENST00000392507.3_Silent_p.R571R	NM_145798.2	NP_665741.1	Q9BZF2	OSBL7_HUMAN	oxysterol binding protein-like 7	571					cellular response to cholesterol (GO:0071397)|lipid transport (GO:0006869)|positive regulation of proteasomal protein catabolic process (GO:1901800)	autophagic vacuole (GO:0005776)|cytosol (GO:0005829)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			autonomic_ganglia(1)|endometrium(6)|kidney(2)|large_intestine(5)|liver(2)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32						AGCGGAAGCCTCGGTCAGGCC	0.627																																					p.R571R		Atlas-SNP	.											.	OSBPL7	65	.	0			c.A1713G						.						67	63	65					17																	45890656		2203	4300	6503	SO:0001819	synonymous_variant	114881	exon16			GAAGCCTCGGTCA	AF392446	CCDS11515.1	17q21	2013-01-10				ENSG00000006025		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16387	protein-coding gene	gene with protein product		606735				14593528, 11735225	Standard	NM_145798		Approved	ORP7, MGC71150	uc002ilx.1	Q9BZF2		ENST00000007414.3:c.1713A>G	chr17.hg19:g.45890656T>C		26.0	0.0		30.0	13.0	NM_145798	D3DTT6|Q6PIV6	Silent	SNP	ENST00000007414.3	hg19	CCDS11515.1																																																																																			.	.		0.627	OSBPL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441367.1	NM_017731		C	45890656	T	C	45890656	2	2	333	1	0	0	0	0	0	0	0	1	11291	1538	54	2		2	OSBPL7	17	45890656	Silent	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	2880616	45890656	35304554	155	46497										
CD300LB	124599	hgsc.bcm.edu	37	chr17	72519756	72519756	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	aacactgccatattgctgttGgtaggtgagcttgctgttgt	12	7	0	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr17:72519756G>A	ENST00000392621.1	-	3	520	c.516C>T	c.(514-516)acC>acT	p.T172T	CD300LB_ENST00000314401.3_Silent_p.T172T	NM_174892.2	NP_777552	A8K4G0	CLM7_HUMAN	CD300 molecule-like family member b	135					cellular response to lipopolysaccharide (GO:0071222)|innate immune response (GO:0045087)|neutrophil mediated immunity (GO:0002446)|positive regulation of mast cell activation (GO:0033005)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|skin(1)	21						TATTGCTGTTGGTAGGTGAGC	0.547																																					p.T172T		Atlas-SNP	.											.	CD300LB	38	.	0			c.C516T						.						198	141	160					17																	72519756		2203	4300	6503	SO:0001819	synonymous_variant	124599	exon3			GCTGTTGGTAGGT	AF427618	CCDS11700.1, CCDS11700.2	17q25.1	2013-01-11	2006-03-29		ENSG00000178789	ENSG00000178789		"Immunoglobulin superfamily / V-set domain containing"	30811	protein-coding gene	gene with protein product	"triggering receptor expressed on myeloid cells 5"	610705	"CD300 antigen like family member B"			12975309	Standard	NM_174892		Approved	TREM5, CLM7	uc002jkx.2	A8K4G0	OTTHUMG00000067606	ENST00000392621.1:c.516C>T	chr17.hg19:g.72519756G>A		77.0	0.0		87.0	34.0	NM_174892	Q1EG73|Q8IX40|Q8N6D1	Silent	SNP	ENST00000392621.1	hg19	CCDS11700.1																																																																																			.	.		0.547	CD300LB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145082.2	NM_174892		A	72519756	G	A	72519756	2	1	333	1	0	0	0	0	0	0	0	1	3001	1335	47	3		3	CD300LB	17	72519756	Silent	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	26629100	72519756	8675454	156	46498										
UNK	85451	hgsc.bcm.edu	37	chr17	73805856	73805856	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tgcaggtacctgaaagaattCcgcacagagcagtgcccact	10	12	0	3			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr17:73805856C>A	ENST00000589666.1	+	2	230	c.120C>A	c.(118-120)ttC>ttA	p.F40L	UNK_ENST00000293218.3_Missense_Mutation_p.F116L	NM_001080419.2	NP_001073888.2	Q9C0B0	UNK_HUMAN	unkempt family zinc finger	40							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			cervix(3)|endometrium(8)|kidney(2)|large_intestine(5)|lung(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	25			all cancers(21;2.61e-06)|Epithelial(20;7.39e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|LUSC - Lung squamous cell carcinoma(166;0.154)			TGAAAGAATTCCGCACAGAGC	0.602																																					p.F40L		Atlas-SNP	.											.	UNK	87	.	0			c.C120A						.						17	20	19					17																	73805856		2120	4255	6375	SO:0001583	missense	85451	exon2			AGAATTCCGCACA	AB051540	CCDS45778.1, CCDS45778.2	17q25.3	2013-10-17	2013-10-17	2007-02-06		ENSG00000132478		"Zinc fingers, CCCH-type domain containing"	29369	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 5", "zinc finger CCCH-type containing 5", "unkempt homolog (Drosophila)"	ZC3HDC5, ZC3H5		11214970	Standard	NM_001080419		Approved	KIAA1753	uc021udd.2	Q9C0B0		ENST00000589666.1:c.120C>A	chr17.hg19:g.73805856C>A	ENSP00000464893:p.Phe40Leu	45.0	0.0		54.0	21.0	NM_001080419		Missense_Mutation	SNP	ENST00000589666.1	hg19	CCDS45778.2	.	.	.	.	.	.	.	.	.	.	C	22.4	4.280902	0.80692	.	.	ENSG00000132478	ENST00000293218	.	.	.	5.12	3.93	0.45458	.	0.000000	0.85682	D	0.000000	T	0.78786	0.4338	M	0.85630	2.765	0.58432	D	0.999999	D	0.63880	0.993	D	0.68192	0.956	T	0.82291	-0.0530	9	0.87932	D	0	-9.9919	12.3658	0.55228	0.0:0.8562:0.0:0.1438	.	40	Q9C0B0	UNK_HUMAN	L	116	.	ENSP00000293218:F116L	F	+	3	2	UNK	71317451	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.003000	0.29809	2.377000	0.81083	0.561000	0.74099	TTC	.	.		0.602	UNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448835.1	NM_001080419		A	73805856	C	A	73805856	3	1	333	1	0	0	0	0	1	0	0	0	17015	854	30	3	358	3	UNK	17	73805856	Missense_Mutation	SNP	C	TCGA-RC-A6M4-01A-11D-A32G-10	1286100	73805856	7389354	157	46499										
NETO1	81832	hgsc.bcm.edu	37	chr18	70417483	70417483	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gcatctctgtcaagatagaaGcatctcttgtgctgaggtta	10	8	3	3			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr18:70417483G>T	ENST00000327305.6	-	9	2012	c.1355C>A	c.(1354-1356)gCt>gAt	p.A452D	NETO1_ENST00000583169.1_Missense_Mutation_p.A452D|NETO1_ENST00000299430.2_Missense_Mutation_p.A451D|RNA5SP460_ENST00000516789.1_RNA	NM_138966.3	NP_620416	Q8TDF5	NETO1_HUMAN	neuropilin (NRP) and tolloid (TLL)-like 1	452					memory (GO:0007613)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|receptor localization to synapse (GO:0097120)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|visual learning (GO:0008542)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|kainate selective glutamate receptor complex (GO:0032983)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				NS(3)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(36)|ovary(2)|prostate(3)|skin(3)|stomach(1)	63		Esophageal squamous(42;0.129)		READ - Rectum adenocarcinoma(1;0.0487)		CAAGATAGAAGCATCTCTTGT	0.483																																					p.A452D		Atlas-SNP	.											.	NETO1	178	.	0			c.C1355A						.						184	165	171					18																	70417483		2203	4300	6503	SO:0001583	missense	81832	exon9			ATAGAAGCATCTC	AF448838	CCDS12000.1, CCDS42444.1	18q22.2	2008-08-01			ENSG00000166342	ENSG00000166342			13823	protein-coding gene	gene with protein product		607973				11943477, 12810072	Standard	NM_138999		Approved	BTCL1, BCTL1	uc002lkw.3	Q8TDF5	OTTHUMG00000132834	ENST00000327305.6:c.1355C>A	chr18.hg19:g.70417483G>T	ENSP00000313088:p.Ala452Asp	170.0	0.0		202.0	117.0	NM_001201465	Q86W85|Q8ND78|Q8TDF4	Missense_Mutation	SNP	ENST00000327305.6	hg19	CCDS12000.1	.	.	.	.	.	.	.	.	.	.	G	16.46	3.129102	0.56721	.	.	ENSG00000166342	ENST00000327305;ENST00000299430	T;T	0.26373	1.74;1.74	5.76	4.86	0.63082	.	0.000000	0.64402	D	0.000014	T	0.29288	0.0729	L	0.56769	1.78	0.80722	D	1	B;B	0.12630	0.006;0.003	B;B	0.14578	0.011;0.003	T	0.07009	-1.0795	10	0.59425	D	0.04	-21.7302	16.2419	0.82418	0.0:0.0:0.8668:0.1332	.	451;452	Q8TDF5-2;Q8TDF5	.;NETO1_HUMAN	D	452;451	ENSP00000313088:A452D;ENSP00000299430:A451D	ENSP00000299430:A451D	A	-	2	0	NETO1	68568463	1.000000	0.71417	0.992000	0.48379	0.983000	0.72400	6.093000	0.71422	2.725000	0.93324	0.460000	0.39030	GCT	.	.		0.483	NETO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256301.2	NM_138999		T	70417483	G	T	70417483	3	4	333	1	0	0	0	0	1	0	0	0	10348	971	34	3	254	3	NETO1	18	70417483	Missense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10		70417483	7659765	158	46500										
FUT5	2527	hgsc.bcm.edu	37	chr19	5866696	5866696	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	caggccttgcagaaagccagTgcccagctgaaggagcgagg	15	11	0	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr19:5866696T>A	ENST00000588525.1	-	2	1128	c.1041A>T	c.(1039-1041)gcA>gcT	p.A347A	FUT5_ENST00000252675.5_Silent_p.A347A	NM_002034.2	NP_002025.2	Q11128	FUT5_HUMAN	fucosyltransferase 5 (alpha (1,3) fucosyltransferase)	347					carbohydrate metabolic process (GO:0005975)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12						AGAAAGCCAGTGCCCAGCTGA	0.642																																					p.A347A		Atlas-SNP	.											.	FUT5	29	.	0			c.A1041T						.						43	48	46					19																	5866696		2203	4300	6503	SO:0001819	synonymous_variant	2527	exon2			AGCCAGTGCCCAG		CCDS12154.1	19p13.3	2013-02-26				ENSG00000130383	2.4.1.65	"Fucosyltransferases"	4016	protein-coding gene	gene with protein product		136835				1740457	Standard	NM_002034		Approved	FUC-TV	uc002mdo.4	Q11128	OTTHUMG00000180616	ENST00000588525.1:c.1041A>T	chr19.hg19:g.5866696T>A		115.0	0.0		115.0	41.0	NM_002034	A8K4X2	Silent	SNP	ENST00000588525.1	hg19	CCDS12154.1																																																																																			.	.		0.642	FUT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452213.1	NM_002034		A	5866696	T	A	5866696	2	1	333	1	0	0	0	0	0	0	0	1	6115	1683	59	4		4	FUT5	19	5866696	Silent	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10		5866696	53262287	159	46501										
VAV1	7409	hgsc.bcm.edu	37	chr19	6773000	6773000	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	catcaacctgcgtgaggtcaAcctgcgcccccagatgtccc	9	17	2	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr19:6773000A>T	ENST00000602142.1	+	1	264	c.182A>T	c.(181-183)aAc>aTc	p.N61I	VAV1_ENST00000596764.1_Missense_Mutation_p.N61I|VAV1_ENST00000539284.1_5'UTR|VAV1_ENST00000304076.2_Missense_Mutation_p.N61I	NM_005428.3	NP_005419.2	P15498	VAV_HUMAN	vav 1 guanine nucleotide exchange factor	61	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.|Leu-rich.				apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|reactive oxygen species metabolic process (GO:0072593)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(16)|lung(18)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	62						CGTGAGGTCAACCTGCGCCCC	0.652																																					p.N61I		Atlas-SNP	.											.	VAV1	140	.	0			c.A182T						.						127	96	107					19																	6773000		2203	4300	6503	SO:0001583	missense	7409	exon1			AGGTCAACCTGCG		CCDS12174.1, CCDS59341.1, CCDS59342.1	19p13.2	2013-02-14	2007-07-25			ENSG00000141968		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "SH2 domain containing"	12657	protein-coding gene	gene with protein product		164875	"vav 1 oncogene"	VAV		9438848	Standard	NM_005428		Approved		uc010xjh.2	P15498		ENST00000602142.1:c.182A>T	chr19.hg19:g.6773000A>T	ENSP00000472929:p.Asn61Ile	78.0	0.0		67.0	29.0	NM_005428	B4DVK9|M0QXX6|Q15860	Missense_Mutation	SNP	ENST00000602142.1	hg19	CCDS12174.1	.	.	.	.	.	.	.	.	.	.	a	25.2	4.610302	0.87258	.	.	ENSG00000141968	ENST00000304076	T	0.62105	0.05	4.32	4.32	0.51571	Calponin homology domain (5);	0.000000	0.64402	U	0.000003	T	0.78317	0.4264	M	0.84219	2.685	0.80722	D	1	D;D	0.65815	0.995;0.992	D;D	0.74023	0.963;0.982	T	0.80434	-0.1384	10	0.54805	T	0.06	.	11.4548	0.50176	1.0:0.0:0.0:0.0	.	61;61	B2R8B5;P15498	.;VAV_HUMAN	I	61	ENSP00000302269:N61I	ENSP00000302269:N61I	N	+	2	0	VAV1	6724000	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	6.542000	0.73869	1.590000	0.49995	0.255000	0.18592	AAC	.	.		0.652	VAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458475.1			T	6773000	A	T	6773000	3	4	333	1	0	0	0	0	1	0	0	0	17146	43	2	4	184	4	VAV1	19	6773000	Missense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	906304	6773000	52355983	160	46502										
LYL1	4066	hgsc.bcm.edu	37	chr19	13211833	13211833	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ggtggcagcctggggggcgaGgagcctcctcggtggcccac	19	13	0	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr19:13211833G>A	ENST00000264824.4	-	2	513	c.153C>T	c.(151-153)tcC>tcT	p.S51S		NM_005583.4	NP_005574.2	P12980	LYL1_HUMAN	lymphoblastic leukemia associated hematopoiesis regulator 1	51					B cell differentiation (GO:0030183)|blood vessel maturation (GO:0001955)|definitive hemopoiesis (GO:0060216)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(2)|kidney(1)|lung(2)|prostate(1)	7			OV - Ovarian serous cystadenocarcinoma(19;6.08e-22)			TGGGGGGCGAGGAGCCTCCTC	0.721			T	TRB@	T-ALL																																p.S51S		Atlas-SNP	.		Dom	yes		19	19p13.2-p13.1	4066	lymphoblastic leukemia derived sequence 1		L	.	LYL1	17	.	0			c.C153T						.						5	7	6					19																	13211833		2051	4079	6130	SO:0001819	synonymous_variant	4066	exon2			GGGCGAGGAGCCT		CCDS12292.1	19p13.2	2014-01-20	2014-01-20			ENSG00000104903		"Basic helix-loop-helix proteins"	6734	protein-coding gene	gene with protein product		151440	"lymphoblastic leukemia derived sequence 1"			2752424	Standard	NM_005583		Approved	bHLHa18	uc002mwi.3	P12980		ENST00000264824.4:c.153C>T	chr19.hg19:g.13211833G>A		45.0	0.0		32.0	8.0	NM_005583	O76102	Silent	SNP	ENST00000264824.4	hg19	CCDS12292.1																																																																																			.	.		0.721	LYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452827.1	NM_005583		A	13211833	G	A	13211833	2	1	333	1	0	0	0	0	0	0	0	1	9115	987	35	3		3	LYL1	19	13211833	Silent	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	6438833	13211833	45917150	161	46503										
UNC13A	23025	hgsc.bcm.edu	37	chr19	17716933	17716933	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tgagcttcacgaactccttgGccacctcgtcgttgctgcgc	10	15	1	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr19:17716933G>T	ENST00000519716.2	-	44	5041	c.5042C>A	c.(5041-5043)gCc>gAc	p.A1681D	UNC13A_ENST00000550896.1_Missense_Mutation_p.A1654D|UNC13A_ENST00000551649.1_Missense_Mutation_p.A1700D|UNC13A_ENST00000252773.7_Missense_Mutation_p.A1681D|UNC13A_ENST00000552293.1_Missense_Mutation_p.A1675D|UNC13A_ENST00000428389.2_Missense_Mutation_p.A1769D	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	1681					beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						GAACTCCTTGGCCACCTCGTC	0.726																																					p.A1681D		Atlas-SNP	.											.	UNC13A	299	.	0			c.C5042A						.						10	10	10					19																	17716933		1933	4095	6028	SO:0001583	missense	23025	exon42			TCCTTGGCCACCT	AB028955	CCDS46013.1, CCDS46013.2	19p13.12	2008-02-05				ENSG00000130477			23150	protein-coding gene	gene with protein product		609894					Standard	NM_001080421		Approved	KIAA1032, Munc13-1	uc031rjv.1	Q9UPW8		ENST00000519716.2:c.5042C>A	chr19.hg19:g.17716933G>T	ENSP00000429562:p.Ala1681Asp	76.0	0.0		53.0	16.0	NM_001080421	E5RHY9	Missense_Mutation	SNP	ENST00000519716.2	hg19	CCDS46013.2	.	.	.	.	.	.	.	.	.	.	G	22.6	4.317132	0.81469	.	.	ENSG00000130477	ENST00000519716;ENST00000428389;ENST00000252773;ENST00000551649;ENST00000552293;ENST00000550896	D;D;D;D;D;D	0.95001	-3.5;-3.58;-3.49;-3.16;-3.03;-3.42	2.98	1.9	0.25705	.	0.067783	0.64402	U	0.000020	D	0.96565	0.8879	M	0.84683	2.71	0.51767	D	0.999938	D	0.71674	0.998	D	0.69307	0.963	D	0.95718	0.8764	10	0.87932	D	0	-3.6154	9.7149	0.40268	0.0:0.215:0.785:0.0	.	1681	Q9UPW8	UN13A_HUMAN	D	1681;1769;1681;1700;1675;1654	ENSP00000429562:A1681D;ENSP00000400409:A1769D;ENSP00000252773:A1681D;ENSP00000447236:A1700D;ENSP00000447572:A1675D;ENSP00000446831:A1654D	ENSP00000252773:A1681D	A	-	2	0	UNC13A	17577933	1.000000	0.71417	0.998000	0.56505	0.761000	0.43186	7.394000	0.79862	0.580000	0.29522	0.306000	0.20318	GCC	.	.		0.726	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604		T	17716933	G	T	17716933	3	4	333	1	0	0	0	0	1	0	0	0	16999	1203	42	3	73	3	UNC13A	19	17716933	Missense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	4505100	17716933	41412050	162	46504										
CRLF1	9244	hgsc.bcm.edu	37	chr19	18710417	18710417	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	agccaggatgctgccgtcacGggcgtggcacacgaggttgt	16	11	1	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr19:18710417G>T	ENST00000392386.3	-	2	548	c.355C>A	c.(355-357)Cgt>Agt	p.R119S		NM_004750.4	NP_004741.1	O75462	CRLF1_HUMAN	cytokine receptor-like factor 1	119	Ig-like C2-type.				negative regulation of motor neuron apoptotic process (GO:2000672)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of cell proliferation (GO:0008284)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|ureteric bud development (GO:0001657)	CRLF-CLCF1 complex (GO:0097058)|extracellular space (GO:0005615)	cytokine binding (GO:0019955)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)	9						CTGCCGTCACGGGCGTGGCAC	0.652																																					p.R119S		Atlas-SNP	.											CRLF1,colon,carcinoma,0,1	CRLF1	32	.	0			c.C355A						.																																			SO:0001583	missense	9244	exon2			CGTCACGGGCGTG	AF059293	CCDS32962.1	19p12	2013-02-11				ENSG00000006016		"Fibronectin type III domain containing"	2364	protein-coding gene	gene with protein product	"cold-induced sweating syndrome"	604237				9686600	Standard	NM_004750		Approved	CLF-1, CLF, CISS, CISS1	uc010ebt.2	O75462		ENST00000392386.3:c.355C>A	chr19.hg19:g.18710417G>T	ENSP00000376188:p.Arg119Ser	39.0	0.0		45.0	18.0	NM_004750	Q9UHH5	Missense_Mutation	SNP	ENST00000392386.3	hg19	CCDS32962.1	.	.	.	.	.	.	.	.	.	.	G	9.078	0.998652	0.19121	.	.	ENSG00000006016	ENST00000392386	D	0.85773	-2.03	5.23	5.23	0.72850	Immunoglobulin-like fold (1);	0.681186	0.15402	N	0.264279	T	0.65523	0.2699	N	0.02539	-0.55	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.48019	-0.9071	10	0.12103	T	0.63	-5.7136	12.4733	0.55799	0.0:0.0:0.8324:0.1676	.	119	O75462	CRLF1_HUMAN	S	119	ENSP00000376188:R119S	ENSP00000376188:R119S	R	-	1	0	CRLF1	18571417	0.670000	0.27512	0.485000	0.27403	0.546000	0.35178	1.277000	0.33167	2.449000	0.82847	0.511000	0.50034	CGT	.	.		0.652	CRLF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465129.1			T	18710417	G	T	18710417	3	4	333	1	0	0	0	0	1	0	0	0	3888	1116	39	1	945	1	CRLF1	19	18710417	Missense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	993484	18710417	40418566	163	46505										
SFRS14	10147	hgsc.bcm.edu	37	chr19	19136956	19136956	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tctctagagtgagctacagaTccactgagggagtatctgcc	11	10	2	4	rs144099788		TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr19:19136956T>A	ENST00000601879.1	-	3	498	c.201A>T	c.(199-201)ggA>ggT	p.G67G	SUGP2_ENST00000456085.2_5'UTR|SUGP2_ENST00000598202.1_5'UTR|SUGP2_ENST00000600377.1_Silent_p.G81G|SUGP2_ENST00000452918.2_Silent_p.G67G|SUGP2_ENST00000337018.6_Silent_p.G67G			Q8IX01	SUGP2_HUMAN	SURP and G patch domain containing 2	67					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						GAGCTACAGATCCACTGAGGG	0.483																																					p.G67G		Atlas-SNP	.											.	SUGP2	107	.	0			c.A201T						.						54	45	48					19																	19136956		2203	4300	6503	SO:0001819	synonymous_variant	10147	exon3			TACAGATCCACTG	AB002363	CCDS12392.1	19p13	2013-01-28	2010-08-10	2010-08-10	ENSG00000064607	ENSG00000064607		"G patch domain containing"	18641	protein-coding gene	gene with protein product		607993	"splicing factor, arginine/serine-rich 14"	SFRS14		12594045	Standard	NM_014884		Approved	KIAA0365	uc002nkx.2	Q8IX01		ENST00000601879.1:c.201A>T	chr19.hg19:g.19136956T>A		27.0	0.0		23.0	8.0	NM_014884	C9JI71|O15071|O60369|Q5JPH7|Q8WUF7	Silent	SNP	ENST00000601879.1	hg19	CCDS12392.1																																																																																			.	T|1.000;C|0.000		0.483	SUGP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464627.1	NM_001017392		A	19136956	T	A	19136956	2	1	333	1	0	0	0	0	0	0	0	1	14185	1422	50	4		4	SFRS14	19	19136956	Silent	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	426539	19136956	39992027	164	46506										
PAK4	10298	hgsc.bcm.edu	37	chr19	39664257	39664257	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	cctaacgggccatcagcgggGggcctggccatcccccagtc	13	17	1	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr19:39664257G>T	ENST00000593690.1	+	6	1132	c.705G>T	c.(703-705)ggG>ggT	p.G235G	PAK4_ENST00000599386.1_Silent_p.G82G|PAK4_ENST00000358301.3_Silent_p.G235G|PAK4_ENST00000599470.1_Silent_p.G82G|PAK4_ENST00000435673.2_Silent_p.G235G|PAK4_ENST00000360442.3_Silent_p.G235G|PAK4_ENST00000321944.4_Silent_p.G145G	NM_001014831.2	NP_001014831.1	O96013	PAK4_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 4	235	Linker.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|cytoskeleton organization (GO:0007010)|signal transduction (GO:0007165)	focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	13	all_cancers(60;1.03e-07)|all_epithelial(25;9.66e-08)|all_lung(34;1.58e-07)|Lung NSC(34;1.88e-07)|Ovarian(47;0.0454)		Epithelial(26;4.82e-25)|all cancers(26;2.94e-22)|Lung(45;0.000797)|LUSC - Lung squamous cell carcinoma(53;0.00113)			CATCAGCGGGGGGCCTGGCCA	0.687																																					p.G235G		Atlas-SNP	.											.	PAK4	40	.	0			c.G705T						.						11	14	13					19																	39664257		2125	4190	6315	SO:0001819	synonymous_variant	10298	exon4			AGCGGGGGGCCTG	AJ011855	CCDS12528.1, CCDS33019.1	19p11-q11	2008-06-17	2008-06-17						16059	protein-coding gene	gene with protein product		605451	"p21(CDKN1A)-activated kinase 4"			9822598, 10461188	Standard	NM_001014831		Approved		uc002okn.1	O96013		ENST00000593690.1:c.705G>T	chr19.hg19:g.39664257G>T		24.0	0.0		28.0	17.0	NM_001014832	B4DGG6|Q8N4E1|Q8NCH5|Q8NDE3|Q9BU33|Q9ULS8	Silent	SNP	ENST00000593690.1	hg19	CCDS12528.1	.	.	.	.	.	.	.	.	.	.	G	0.020	-1.444567	0.01089	.	.	ENSG00000130669	ENST00000542377	.	.	.	4.27	-0.766	0.11020	.	0.988715	0.08243	N	0.975814	T	0.42653	0.1212	.	.	.	0.33285	D	0.56281	.	.	.	.	.	.	T	0.56189	-0.8020	6	0.66056	D	0.02	.	2.581	0.04818	0.25:0.0:0.3491:0.4009	.	.	.	.	V	11	.	ENSP00000443258:G11V	G	+	2	0	PAK4	44356097	0.000000	0.05858	0.062000	0.19696	0.007000	0.05969	-0.008000	0.12788	0.066000	0.16515	-0.268000	0.10319	GGG	.	.		0.687	PAK4-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463823.1			T	39664257	G	T	39664257	2	4	333	1	0	0	0	0	0	0	0	1	11412	1219	43	3		3	PAK4	19	39664257	Silent	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	20527301	39664257	19464726	165	46507										
CARD8	22900	hgsc.bcm.edu	37	chr19	48734142	48734142	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ccactgttcatggtgctgcaGgtccagggccaggtgctgac	14	12	1	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr19:48734142G>C	ENST00000359009.4	-	5	661	c.349C>G	c.(349-351)Ctg>Gtg	p.L117V	CARD8_ENST00000521613.1_Missense_Mutation_p.L172V|CARD8_ENST00000357778.5_5'UTR|CARD8_ENST00000520753.1_Missense_Mutation_p.L222V|CARD8_ENST00000391898.3_Missense_Mutation_p.L222V|CARD8_ENST00000520153.1_Missense_Mutation_p.L172V|CARD8_ENST00000519940.1_Missense_Mutation_p.L222V|ZNF114_ENST00000597695.1_Intron|CARD8_ENST00000447740.2_Missense_Mutation_p.L172V|CARD8_ENST00000520015.1_Missense_Mutation_p.L222V			Q9Y2G2	CARD8_HUMAN	caspase recruitment domain family, member 8	117					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)|NLRP3 inflammasome complex (GO:0072559)|nucleus (GO:0005634)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|NACHT domain binding (GO:0032089)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(4)|lung(8)|prostate(1)|skin(1)	15		all_lung(116;0.000112)|Lung NSC(112;0.000192)|all_epithelial(76;0.000349)|all_neural(266;0.0228)|Ovarian(192;0.113)|Prostate(7;0.184)		OV - Ovarian serous cystadenocarcinoma(262;0.000112)|all cancers(93;0.000293)|Epithelial(262;0.0129)|GBM - Glioblastoma multiforme(486;0.0336)		TGGTGCTGCAGGTCCAGGGCC	0.597																																					p.L222V		Atlas-SNP	.											.	CARD8	53	.	0			c.C664G						.						52	45	47					19																	48734142		2203	4300	6503	SO:0001583	missense	22900	exon6			GCTGCAGGTCCAG	AB023172	CCDS12712.1, CCDS12712.2, CCDS54287.1, CCDS54288.1, CCDS54289.1	19q13.33	2011-05-24			ENSG00000105483	ENSG00000105483			17057	protein-coding gene	gene with protein product		609051				10231032, 11408476	Standard	NM_001184900		Approved	TUCAN, KIAA0955, CARDINAL, NDPP, Dakar	uc010xzj.2	Q9Y2G2	OTTHUMG00000165047	ENST00000359009.4:c.349C>G	chr19.hg19:g.48734142G>C	ENSP00000351901:p.Leu117Val	27.0	0.0		28.0	8.0	NM_001184900	B5KVR6|B7Z496|B7Z4A2|E9PEM7|G3XAM9|Q6PGP8|Q96P82	Missense_Mutation	SNP	ENST00000359009.4	hg19		.	.	.	.	.	.	.	.	.	.	G	9.334	1.061243	0.19987	.	.	ENSG00000105483	ENST00000447740;ENST00000391898;ENST00000359009;ENST00000520753;ENST00000520153;ENST00000520015;ENST00000521613;ENST00000519940	T;T;T;T;T;T;T;T	0.16597	2.33;2.33;2.33;2.33;2.33;2.33;2.33;2.33	1.7	0.644	0.17776	.	.	.	.	.	T	0.20700	0.0498	L	0.31664	0.95	0.09310	N	1	D;D;D;D;D;D;D;D	0.69078	0.997;0.997;0.997;0.997;0.974;0.996;0.996;0.997	D;D;D;D;D;D;D;D	0.79108	0.992;0.987;0.987;0.987;0.953;0.978;0.986;0.992	T	0.21518	-1.0243	9	0.16896	T	0.51	.	3.9882	0.09525	0.2263:0.0:0.7737:0.0	.	141;222;222;155;222;172;117;117	B5KVR7;E9PEM7;B5KVR6;Q6MZI8;Q9Y2G2-3;G3XAM9;Q9Y2G2-2;Q9Y2G2	.;.;.;.;.;.;.;CARD8_HUMAN	V	172;222;117;222;172;222;172;222	ENSP00000391248:L172V;ENSP00000375767:L222V;ENSP00000351901:L117V;ENSP00000429839:L222V;ENSP00000428736:L172V;ENSP00000430747:L222V;ENSP00000427858:L172V;ENSP00000428883:L222V	ENSP00000351901:L117V	L	-	1	2	CARD8	53425954	0.012000	0.17670	0.011000	0.14972	0.108000	0.19459	0.573000	0.23699	0.266000	0.21894	0.655000	0.94253	CTG	.	.		0.597	CARD8-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014959		C	48734142	G	C	48734142	3	2	333	1	0	0	0	0	1	0	0	0	2653	991	35	4	973	4	CARD8	19	48734142	Missense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	9069885	48734142	10394841	166	46508										
GRIN2D	2906	hgsc.bcm.edu	37	chr19	48925128	48925128	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	aagaacatccgcagcaactaTcccgacatgcacagctacat	6	14	0	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr19:48925128T>A	ENST00000263269.3	+	10	2266	c.2178T>A	c.(2176-2178)taT>taA	p.Y726*		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	726					adult locomotory behavior (GO:0008344)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|regulation of sensory perception of pain (GO:0051930)|signal transduction (GO:0007165)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)			autonomic_ganglia(1)|breast(6)|endometrium(2)|large_intestine(9)|lung(12)|ovary(5)|pancreas(1)|prostate(1)	37		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GCAGCAACTATCCCGACATGC	0.637																																					p.Y726X		Atlas-SNP	.											.	GRIN2D	76	.	0			c.T2178A						.						100	92	95					19																	48925128		2203	4300	6503	SO:0001587	stop_gained	2906	exon10			CAACTATCCCGAC	U77783	CCDS12719.1	19q13.33	2012-08-29			ENSG00000105464	ENSG00000105464		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4588	protein-coding gene	gene with protein product	"N-methyl-d-aspartate receptor subunit 2D"	602717		NMDAR2D		9480759, 9418891	Standard	NM_000836		Approved	GluN2D, EB11, NR2D	uc002pjc.4	O15399		ENST00000263269.3:c.2178T>A	chr19.hg19:g.48925128T>A	ENSP00000263269:p.Tyr726*	93.0	0.0		87.0	28.0	NM_000836		Nonsense_Mutation	SNP	ENST00000263269.3	hg19	CCDS12719.1	.	.	.	.	.	.	.	.	.	.	T	40	8.002541	0.98605	.	.	ENSG00000105464	ENST00000263269	.	.	.	4.43	2.31	0.28768	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.4031	0.21650	0.0:0.6572:0.0:0.3428	.	.	.	.	X	726	.	ENSP00000263269:Y726X	Y	+	3	2	GRIN2D	53616940	0.996000	0.38824	1.000000	0.80357	0.998000	0.95712	0.591000	0.23969	1.144000	0.42321	0.533000	0.62120	TAT	.	.		0.637	GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466121.1			A	48925128	T	A	48925128	4	1	333	1	0	0	0	0	0	1	0	0	6791	1442	50	4	2212	4	GRIN2D	19	48925128	Nonsense_Mutation	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	190986	48925128	10203855	167	46509										
SHANK1	50944	hgsc.bcm.edu	37	chr19	51169670	51169670	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gccaagggcccgggcagaggTggtggcggtgggcccgggcc	22	12	0	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr19:51169670T>C	ENST00000293441.1	-	22	5565	c.5547A>G	c.(5545-5547)ccA>ccG	p.P1849P	SHANK1_ENST00000391814.1_Silent_p.P1857P|SHANK1_ENST00000391813.1_Silent_p.P1236P|SYT3_ENST00000544769.1_Intron|SHANK1_ENST00000359082.3_Silent_p.P1840P	NM_016148.2	NP_057232.2	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	1849	Poly-Pro.				adult behavior (GO:0030534)|associative learning (GO:0008306)|cytoskeletal anchoring at plasma membrane (GO:0007016)|dendritic spine morphogenesis (GO:0060997)|determination of affect (GO:0050894)|habituation (GO:0046959)|long-term memory (GO:0007616)|negative regulation of actin filament bundle assembly (GO:0032232)|neuromuscular process controlling balance (GO:0050885)|olfactory behavior (GO:0042048)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|protein complex assembly (GO:0006461)|protein localization to synapse (GO:0035418)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|righting reflex (GO:0060013)|social behavior (GO:0035176)|synapse maturation (GO:0060074)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|excitatory synapse (GO:0060076)|intracellular (GO:0005622)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ankyrin repeat binding (GO:0071532)|GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|somatostatin receptor binding (GO:0031877)			breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	64		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)		CGGGCAGAGGTGGTGGCGGTG	0.667																																					p.P1849P		Atlas-SNP	.											.	SHANK1	210	.	0			c.A5547G						.						15	17	16					19																	51169670		2201	4297	6498	SO:0001819	synonymous_variant	50944	exon22			CAGAGGTGGTGGC	AF163302	CCDS12799.1	19q13.3	2013-01-10			ENSG00000161681	ENSG00000161681		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	15474	protein-coding gene	gene with protein product	"somatostatin receptor-interacting protein"	604999				10551867	Standard	NM_016148		Approved	SSTRIP, SPANK-1, synamon	uc002psx.1	Q9Y566	OTTHUMG00000137380	ENST00000293441.1:c.5547A>G	chr19.hg19:g.51169670T>C		56.0	0.0		53.0	27.0	NM_016148	A8MXP5|B7WNY6|Q9NYW9	Silent	SNP	ENST00000293441.1	hg19	CCDS12799.1																																																																																			.	.		0.667	SHANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268071.1	NM_016148		C	51169670	T	C	51169670	2	2	333	1	0	0	0	0	0	0	0	1	14279	1683	59	2		2	SHANK1	19	51169670	Silent	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	2244542	51169670	7959313	168	46510										
ZNF665	79788	hgsc.bcm.edu	37	chr19	53668959	53668959	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gccacactcattacacttgtAaggtttctctccagtatgaa	6	11	2	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr19:53668959A>T	ENST00000600412.1	-	2	704	c.589T>A	c.(589-591)Tac>Aac	p.Y197N	ZNF665_ENST00000396424.3_Missense_Mutation_p.Y262N|CTD-2245F17.2_ENST00000600257.1_RNA			Q9H7R5	ZN665_HUMAN	zinc finger protein 665	197					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	35				GBM - Glioblastoma multiforme(134;0.0196)		TTACACTTGTAAGGTTTCTCT	0.383																																					p.Y262N		Atlas-SNP	.											.	ZNF665	136	.	0			c.T784A						.						110	120	116					19																	53668959		2203	4300	6503	SO:0001583	missense	79788	exon4			ACTTGTAAGGTTT		CCDS46169.1	19q13.42	2013-01-08				ENSG00000197497		"Zinc fingers, C2H2-type", "-"	25885	protein-coding gene	gene with protein product							Standard	NM_024733		Approved	FLJ14345	uc010eqm.1	Q9H7R5		ENST00000600412.1:c.589T>A	chr19.hg19:g.53668959A>T	ENSP00000469154:p.Tyr197Asn	67.0	0.0		85.0	27.0	NM_024733	A8K5T8	Missense_Mutation	SNP	ENST00000600412.1	hg19		.	.	.	.	.	.	.	.	.	.	A	13.78	2.338054	0.41398	.	.	ENSG00000197497	ENST00000396424	T	0.25749	1.78	2.31	1.24	0.21308	.	.	.	.	.	T	0.45816	0.1361	M	0.76433	2.335	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.20706	-1.0267	9	0.87932	D	0	.	6.4488	0.21892	0.8656:0.0:0.1344:0.0	.	262	Q9H7R5-2	.	N	262	ENSP00000379702:Y262N	ENSP00000379702:Y262N	Y	-	1	0	ZNF665	58360771	0.000000	0.05858	0.117000	0.21633	0.731000	0.41821	0.715000	0.25822	0.136000	0.18733	0.358000	0.22013	TAC	.	.		0.383	ZNF665-002	PUTATIVE	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000464179.1	NM_024733		T	53668959	A	T	53668959	3	4	333	1	0	0	0	0	1	0	0	0	18088	362	13	4	1256	4	ZNF665	19	53668959	Missense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	2499289	53668959	5460024	169	46511										
TGM6	343641	hgsc.bcm.edu	37	chr20	2384055	2384055	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tgtggcaggaatttccatgtCtggaatgagagctggtttgc	14	6	1	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr20:2384055C>G	ENST00000202625.2	+	8	1063	c.1002C>G	c.(1000-1002)gtC>gtG	p.V334V	TGM6_ENST00000381423.1_Silent_p.V334V	NM_198994.2	NP_945345.2	O95932	TGM3L_HUMAN	transglutaminase 6	334					cell death (GO:0008219)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(1)|endometrium(6)|kidney(2)|large_intestine(2)|lung(32)|ovary(4)|prostate(1)|skin(4)	52					L-Glutamine(DB00130)	ATTTCCATGTCTGGAATGAGA	0.582																																					p.V334V		Atlas-SNP	.											.	TGM6	126	.	0			c.C1002G						.						44	39	41					20																	2384055		2203	4300	6503	SO:0001819	synonymous_variant	343641	exon8			CCATGTCTGGAAT	AF540970	CCDS13025.1, CCDS58761.1	20p13	2010-12-19	2004-07-05	2004-07-07	ENSG00000166948	ENSG00000166948		"Transglutaminases"	16255	protein-coding gene	gene with protein product	"spinocerebellar ataxia 35"	613900	"transglutaminase 3-like"	TGM3L		11390390, 21106500	Standard	NM_198994		Approved	dJ734P14.3, TGY, SCA35	uc002wfy.1	O95932	OTTHUMG00000031692	ENST00000202625.2:c.1002C>G	chr20.hg19:g.2384055C>G		60.0	0.0		72.0	35.0	NM_198994	Q5JXU4|Q5JXU5|Q719M2|Q719M3|Q9Y4U8	Silent	SNP	ENST00000202625.2	hg19	CCDS13025.1																																																																																			.	.		0.582	TGM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077581.2	NM_198994		G	2384055	C	G	2384055	2	3	333	1	0	0	0	0	0	0	0	1	15849	900	32	4		4	TGM6	20	2384055	Silent	SNP	C	TCGA-RC-A6M4-01A-11D-A32G-10		2384055	60641465	170	46512										
PHF20	51230	hgsc.bcm.edu	37	chr20	34451299	34451299	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	acccaaaagaaaacgaggcaGacccccttccatagctccta	6	15	0	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr20:34451299G>A	ENST00000374012.3	+	6	914	c.785G>A	c.(784-786)aGa>aAa	p.R262K	PHF20_ENST00000481202.1_3'UTR|PHF20_ENST00000439301.1_Silent_p.Q240Q			Q9BVI0	PHF20_HUMAN	PHD finger protein 20	262					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(5)|endometrium(1)|kidney(7)|large_intestine(6)|lung(11)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(12;0.00631)|all_lung(11;0.0145)					AAACGAGGCAGACCCCCTTCC	0.448																																					p.R262K		Atlas-SNP	.											.	PHF20	94	.	0			c.G785A						.						102	112	108					20																	34451299		2201	4299	6500	SO:0001583	missense	51230	exon6			GAGGCAGACCCCC	AL109965	CCDS13268.1	20q11.22-q11.23	2013-01-28	2004-12-01	2004-12-01	ENSG00000025293	ENSG00000025293		"Tudor domain containing", "Zinc fingers, PHD-type"	16098	protein-coding gene	gene with protein product	"tudor domain containing 20A"	610335	"chromosome 20 open reading frame 104"	C20orf104			Standard	NM_016436		Approved	dJ1121G12.1, TDRD20A	uc002xek.1	Q9BVI0	OTTHUMG00000032367	ENST00000374012.3:c.785G>A	chr20.hg19:g.34451299G>A	ENSP00000363124:p.Arg262Lys	76.0	0.0		78.0	31.0	NM_016436	A7E235|B2RB56|E1P5S3|Q566Q2|Q5JWY9|Q66K49|Q9BWV4|Q9BXA3|Q9BZW3|Q9H421|Q9H4J6|Q9NZ22	Missense_Mutation	SNP	ENST00000374012.3	hg19	CCDS13268.1	.	.	.	.	.	.	.	.	.	.	G	32	5.179483	0.94846	.	.	ENSG00000025293	ENST00000374012;ENST00000339089;ENST00000374000	T;T;T	0.63744	0.88;-0.06;-0.05	5.83	5.83	0.93111	AT hook, DNA-binding motif (1);	0.312796	0.34853	N	0.003622	T	0.70168	0.3193	L	0.29908	0.895	0.80722	D	1	D;D;D	0.89917	0.999;0.997;1.0	D;D;D	0.87578	0.994;0.992;0.998	T	0.62807	-0.6776	10	0.18276	T	0.48	.	20.1218	0.97964	0.0:0.0:1.0:0.0	.	262;262;262	Q566Q2;Q9BVI0;Q66K49	.;PHF20_HUMAN;.	K	262	ENSP00000363124:R262K;ENSP00000341900:R262K;ENSP00000363112:R262K	ENSP00000341900:R262K	R	+	2	0	PHF20	33914713	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.778000	0.75043	2.763000	0.94921	0.561000	0.74099	AGA	.	.		0.448	PHF20-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078949.2	NM_016436		A	34451299	G	A	34451299	3	1	333	1	0	0	0	0	1	0	0	0	11840	942	33	3	803	3	PHF20	20	34451299	Missense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	32067244	34451299	28574221	171	46513										
PI3	5266	hgsc.bcm.edu	37	chr20	43804641	43804641	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ggtccagtctccactaagccTggctcctgccccattatctt	7	16	2	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr20:43804641T>G	ENST00000243924.3	+	2	266	c.219T>G	c.(217-219)ccT>ccG	p.P73P		NM_002638.3	NP_002629.1	P19957	ELAF_HUMAN	peptidase inhibitor 3, skin-derived	73	WAP. {ECO:0000255|PROSITE- ProRule:PRU00722}.				copulation (GO:0007620)|negative regulation of endopeptidase activity (GO:0010951)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			large_intestine(1)|lung(5)|skin(1)	7		Myeloproliferative disorder(115;0.0122)				CCACTAAGCCTGGCTCCTGCC	0.483																																					p.P73P		Atlas-SNP	.											.	PI3	21	.	0			c.T219G						.						133	115	121					20																	43804641		2203	4300	6503	SO:0001819	synonymous_variant	5266	exon2			TAAGCCTGGCTCC	D13156	CCDS13344.1	20q13.12	2013-01-21	2008-10-03		ENSG00000124102	ENSG00000124102		"WAP four-disulfide core domain containing"	8947	protein-coding gene	gene with protein product	"skin-derived antileukoproteinase", "trappin-2"	182257	"protease inhibitor 3, skin-derived (SKALP)"			8287685, 12206714	Standard	NM_002638		Approved	ESI, SKALP, ELAFIN, WAP3, WFDC14, cementoin	uc002xng.3	P19957	OTTHUMG00000032567	ENST00000243924.3:c.219T>G	chr20.hg19:g.43804641T>G		69.0	0.0		89.0	48.0	NM_002638	E1P618|Q6FG74	Silent	SNP	ENST00000243924.3	hg19	CCDS13344.1																																																																																			.	.		0.483	PI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079418.3	NM_002638		G	43804641	T	G	43804641	2	3	333	1	0	0	0	0	0	0	0	1	11879	1567	55	5		5	PI3	20	43804641	Silent	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	9353342	43804641	19220879	172	46514										
DOPEY2	9980	hgsc.bcm.edu	37	chr21	37618611	37618611	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	agattgagctgctgaagctgCtgcaggtgctgattgtcttg	14	7	1	4			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr21:37618611C>T	ENST00000399151.3	+	19	4418	c.4333C>T	c.(4333-4335)Ctg>Ttg	p.L1445L		NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	1445					cognition (GO:0050890)|endoplasmic reticulum organization (GO:0007029)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(6)|lung(25)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						GCTGAAGCTGCTGCAGGTGCT	0.597																																					p.L1445L		Atlas-SNP	.											.	DOPEY2	184	.	0			c.C4333T						.						35	37	36					21																	37618611		2203	4300	6503	SO:0001819	synonymous_variant	9980	exon19			AAGCTGCTGCAGG	AJ237839	CCDS13643.1	21q22.2	2013-03-05	2006-02-02	2006-02-02	ENSG00000142197	ENSG00000142197			1291	protein-coding gene	gene with protein product		604803	"chromosome 21 open reading frame 5"	C21orf5		16301316, 16303751, 10931277	Standard	NM_005128		Approved	KIAA0933	uc002yvg.3	Q9Y3R5	OTTHUMG00000086619	ENST00000399151.3:c.4333C>T	chr21.hg19:g.37618611C>T		30.0	0.0		49.0	14.0	NM_005128	D3DSG5|Q6PJQ7|Q9UEZ3	Silent	SNP	ENST00000399151.3	hg19	CCDS13643.1																																																																																			.	.		0.597	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	NM_005128		T	37618611	C	T	37618611	2	4	333	1	0	0	0	0	0	0	0	1	4710	796	28	3		3	DOPEY2	21	37618611	Silent	SNP	C	TCGA-RC-A6M4-01A-11D-A32G-10		37618611	10511284	173	46515										
COL18A1	80781	hgsc.bcm.edu	37	chr21	46911137	46911137	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gacgcgtggcctcctcttccAgggagatccagggaaggacg	15	12	1	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr21:46911137A>T	ENST00000359759.4	+	21	3333		c.e21-1		COL18A1_ENST00000400337.2_Splice_Site|COL18A1_ENST00000355480.5_Splice_Site			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1						angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		CTCCTCTTCCAGGGAGATCCA	0.701																																					.		Atlas-SNP	.											.	COL18A1	129	.	0			c.2068-2A>T						.						26	32	30					21																	46911137		1933	4117	6050	SO:0001630	splice_region_variant	80781	exon22			TCTTCCAGGGAGA		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"Collagens"	2195	protein-coding gene	gene with protein product	"endostatin"	120328	"Knobloch syndrome, type 1"	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.3313-1A>T	chr21.hg19:g.46911137A>T		146.0	0.0		165.0	69.0	NM_130445	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Splice_Site	SNP	ENST00000359759.4	hg19		.	.	.	.	.	.	.	.	.	.	A	9.978	1.227280	0.22542	.	.	ENSG00000182871	ENST00000400337;ENST00000400347;ENST00000355480;ENST00000359759;ENST00000539645;ENST00000342220	.	.	.	3.85	3.85	0.44370	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.4665	0.27324	0.7793:0.2206:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	COL18A1	45735565	0.992000	0.36948	1.000000	0.80357	0.162000	0.22319	1.727000	0.38095	1.753000	0.51906	0.459000	0.35465	.	.	.		0.701	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		Intron	T	46911137	A	T	46911137	5	4	333	1	0	0	0	0	0	0	1	0	3677	202	7	4	3507	4	COL18A1	21	46911137	Splice_Site	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	9292526	46911137	1218758	174	46516										
P2RX6	9127	hgsc.bcm.edu	37	chr22	21369505	21369505	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	gctggcagcatgggctccccAggggctacgacaggctgggg	18	12	0	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chr22:21369505A>T	ENST00000413302.2	+	1	190	c.42A>T	c.(40-42)ccA>ccT	p.P14P	P2RX6_ENST00000336296.2_Silent_p.P4P|P2RX6_ENST00000401443.1_Silent_p.P14P|P2RX6_ENST00000402329.3_Silent_p.P4P|P2RX6_ENST00000443995.3_De_novo_Start_OutOfFrame|TUBA3FP_ENST00000422086.1_RNA|P2RX6_ENST00000591411.1_Intron			O15547	P2RX6_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 6	14					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|muscle contraction (GO:0006936)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|channel activity (GO:0015267)|extracellular ATP-gated cation channel activity (GO:0004931)|identical protein binding (GO:0042802)|purinergic nucleotide receptor activity (GO:0001614)|transmembrane signaling receptor activity (GO:0004888)										TGGGCTCCCCAGGGGCTACGA	0.632																																					p.P14P		Atlas-SNP	.											.	.	.	.	0			c.A42T						.						46	56	53					22																	21369505		2203	4300	6503	SO:0001819	synonymous_variant	9127	exon1			CTCCCCAGGGGCT		CCDS13788.2, CCDS54504.1	22q11.21	2012-01-17	2008-03-28	2008-03-28	ENSG00000099957	ENSG00000099957		"Purinergic receptors", "Ligand-gated ion channels / Purinergic receptors, ionotropic"	8538	protein-coding gene	gene with protein product		608077	"purinergic receptor P2X-like 1, orphan receptor"	P2RXL1		9242461, 10591208, 8786426	Standard	NM_005446		Approved	P2XM, MGC129625, P2X6	uc010gsu.1	O15547	OTTHUMG00000150689	ENST00000413302.2:c.42A>T	chr22.hg19:g.21369505A>T		35.0	0.0		40.0	18.0	NM_001159554	F6V3D7|Q32MB6|Q58F04|Q6IC33|Q9UL50	Silent	SNP	ENST00000413302.2	hg19	CCDS13788.2																																																																																			.	.		0.632	P2RX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319625.2	NM_005446		T	21369505	A	T	21369505	2	4	333	1	0	0	0	0	0	0	0	1	11353	175	7	4		4	P2RX6	22	21369505	Silent	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10		21369505	29935061	175	46517										
NHS	4810	hgsc.bcm.edu	37	chrX	17745541	17745541	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	aacaaaccattccaccaccgTcatccactgcatgtttttac	3	15	1	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chrX:17745541T>C	ENST00000380060.3	+	6	3590	c.3252T>C	c.(3250-3252)cgT>cgC	p.R1084R	NHS_ENST00000398097.3_Silent_p.R928R	NM_198270.2	NP_938011.1	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome (congenital cataracts and dental anomalies)	1105					cell differentiation (GO:0030154)|lens development in camera-type eye (GO:0002088)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(5)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(26)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	71	Hepatocellular(33;0.183)					TCCACCACCGTCATCCACTGC	0.423																																					p.R1084R		Atlas-SNP	.											.	NHS	302	.	0			c.T3252C						.						178	166	170					X																	17745541		2203	4300	6503	SO:0001819	synonymous_variant	4810	exon6			CCACCGTCATCCA		CCDS14181.1, CCDS48087.1	Xp22.3-p21.1	2014-06-18			ENSG00000188158	ENSG00000188158			7820	protein-coding gene	gene with protein product		300457					Standard	NM_001136024		Approved		uc004cxx.3	Q6T4R5	OTTHUMG00000022799	ENST00000380060.3:c.3252T>C	chrX.hg19:g.17745541T>C		143.0	0.0		143.0	75.0	NM_198270	B7ZVX8|E2DH69|Q5J7Q0|Q5J7Q1|Q68DR5	Silent	SNP	ENST00000380060.3	hg19	CCDS14181.1																																																																																			.	.		0.423	NHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059120.1	NM_198270		C	17745541	T	C	17745541	2	2	333	1	0	0	0	0	0	0	0	1	10420	1654	58	2		2	NHS	23	17745541	Silent	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10		17745541	137525019	176	46518										
EFHC2	80258	hgsc.bcm.edu	37	chrX	44109644	44109644	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tactggaggaactgtttcagGgtgtcgagggattcgtaggg	17	5	1	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chrX:44109644G>T	ENST00000420999.1	-	5	737	c.654C>A	c.(652-654)acC>acA	p.T218T		NM_025184.3	NP_079460.2	Q5JST6	EFHC2_HUMAN	EF-hand domain (C-terminal) containing 2	218							calcium ion binding (GO:0005509)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	29						ACTGTTTCAGGGTGTCGAGGG	0.453																																					p.T218T		Atlas-SNP	.											.	EFHC2	81	.	0			c.C654A						.						75	70	72					X																	44109644		1936	4124	6060	SO:0001819	synonymous_variant	80258	exon5			TTTCAGGGTGTCG	AK026254	CCDS55405.1	Xp11	2014-01-31			ENSG00000183690	ENSG00000183690		"EF-hand domain containing"	26233	protein-coding gene	gene with protein product		300817	"mental retardation, X-linked 74"	MRX74		17221867	Standard	NM_025184		Approved	FLJ22843	uc004dgb.4	Q5JST6	OTTHUMG00000021393	ENST00000420999.1:c.654C>A	chrX.hg19:g.44109644G>T		91.0	0.0		85.0	33.0	NM_025184	Q5JST8|Q68DK4|Q8NEI0|Q9H653	Silent	SNP	ENST00000420999.1	hg19	CCDS55405.1	.	.	.	.	.	.	.	.	.	.	G	0.067	-1.211491	0.01555	.	.	ENSG00000183690	ENST00000441230	.	.	.	5.8	-3.49	0.04724	.	.	.	.	.	T	0.41511	0.1162	.	.	.	0.43857	D	0.996452	.	.	.	.	.	.	T	0.30736	-0.9968	4	.	.	.	-7.8933	3.9001	0.09157	0.5455:0.0883:0.1923:0.1739	.	.	.	.	T	199	.	.	P	-	1	0	EFHC2	43994588	0.961000	0.32948	0.007000	0.13788	0.005000	0.04900	0.015000	0.13355	-1.037000	0.03283	-0.853000	0.03031	CCT	.	.		0.453	EFHC2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056312.2	NM_025184		T	44109644	G	T	44109644	2	4	333	1	0	0	0	0	0	0	0	1	4949	1219	43	3		3	EFHC2	23	44109644	Silent	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	26364103	44109644	111160916	177	46519										
ITIH5L	347365	hgsc.bcm.edu	37	chrX	54783459	54783459	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ttcaaggactccacgaacttGgattccaccattgattcaga	7	11	2	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chrX:54783459G>A	ENST00000218436.6	-	8	3077	c.3048C>T	c.(3046-3048)tcC>tcT	p.S1016S		NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	1016					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)										CCACGAACTTGGATTCCACCA	0.532																																					p.S1016S		Atlas-SNP	.											.	.	.	.	0			c.C3048T						.						83	67	73					X																	54783459		2203	4300	6503	SO:0001819	synonymous_variant	347365	exon8			GAACTTGGATTCC	AY358170	CCDS14361.1	Xp11.22-p11.21	2011-10-26	2011-10-26	2011-10-26	ENSG00000102313	ENSG00000102313			28907	protein-coding gene	gene with protein product			"inter-alpha (globulin) inhibitor H5-like"	ITIH5L		12975309	Standard	NM_198510		Approved	UNQ6369	uc004dtj.2	Q6UXX5	OTTHUMG00000021634	ENST00000218436.6:c.3048C>T	chrX.hg19:g.54783459G>A		37.0	0.0		47.0	22.0	NM_198510	A6NN03	Silent	SNP	ENST00000218436.6	hg19	CCDS14361.1																																																																																			.	.		0.532	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056814.2	NM_198510		A	54783459	G	A	54783459	2	1	333	1	0	0	0	0	0	0	0	1	7917	1335	47	3		3	ITIH5L	23	54783459	Silent	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	10673815	54783459	100487101	178	46520										
HMGN5	79366	hgsc.bcm.edu	37	chrX	80370663	80370663	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tgcttctttcttttctcctcCcttttctgtggcatcttcaa	4	13	6	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chrX:80370663C>A	ENST00000358130.2	-	7	662	c.334G>T	c.(334-336)Gga>Tga	p.G112*	HMGN5_ENST00000491275.1_5'UTR	NM_030763.2	NP_110390.1	P82970	HMGN5_HUMAN	high mobility group nucleosome binding domain 5	112					chromatin modification (GO:0016568)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)	10						ttttctcctcccttttctGTG	0.368																																					p.G112X		Atlas-SNP	.											.	HMGN5	29	.	0			c.G334T						.						56	39	45					X																	80370663		2196	4289	6485	SO:0001587	stop_gained	79366	exon7			CTCCTCCCTTTTC	AF250329	CCDS14448.1	Xq13.3	2011-07-01	2011-04-05	2009-09-15	ENSG00000198157	ENSG00000198157		"High-mobility group / Canonical"	8013	protein-coding gene	gene with protein product		300385	"nucleosomal binding protein 1", "high-mobility group nucleosome binding domain 5"	NSBP1		11161810, 19748358	Standard	NM_030763		Approved		uc004eee.1	P82970	OTTHUMG00000021911	ENST00000358130.2:c.334G>T	chrX.hg19:g.80370663C>A	ENSP00000350848:p.Gly112*	547.0	0.0		532.0	257.0	NM_030763	Q5JSL1	Nonsense_Mutation	SNP	ENST00000358130.2	hg19	CCDS14448.1	.	.	.	.	.	.	.	.	.	.	C	15.93	2.978415	0.53720	.	.	ENSG00000198157	ENST00000358130;ENST00000447319;ENST00000373250;ENST00000430960	.	.	.	3.79	2.92	0.33932	.	0.264959	0.19931	U	0.102873	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	.	6.5942	0.22664	0.0:0.8663:0.0:0.1337	.	.	.	.	X	112;92;102;112	.	ENSP00000350848:G112X	G	-	1	0	HMGN5	80257319	0.000000	0.05858	0.016000	0.15963	0.270000	0.26580	0.036000	0.13819	0.966000	0.38159	0.544000	0.68410	GGA	.	.		0.368	HMGN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057354.1	NM_030763		A	80370663	C	A	80370663	4	1	333	1	0	0	0	0	0	1	0	0	7247	632	22	3	518	3	HMGN5	23	80370663	Nonsense_Mutation	SNP	C	TCGA-RC-A6M4-01A-11D-A32G-10	25587204	80370663	74899897	179	46521										
POU3F4	5456	hgsc.bcm.edu	37	chrX	82764109	82764109	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	aacaagtggctggaggaggcGgattcgtccacagggagccc	16	10	0	0			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chrX:82764109G>T	ENST00000373200.2	+	1	841	c.777G>T	c.(775-777)gcG>gcT	p.A259A	RP3-326L13.3_ENST00000607789.1_lincRNA|RP3-326L13.2_ENST00000607095.1_RNA	NM_000307.3	NP_000298	P49335	PO3F4_HUMAN	POU class 3 homeobox 4	259	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.				cochlea morphogenesis (GO:0090103)|forebrain neuron differentiation (GO:0021879)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|sensory perception of sound (GO:0007605)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	AT DNA binding (GO:0003680)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	37						TGGAGGAGGCGGATTCGTCCA	0.577																																					p.A259A		Atlas-SNP	.											.	POU3F4	136	.	0			c.G777T						.						42	37	39					X																	82764109		2203	4300	6503	SO:0001819	synonymous_variant	5456	exon1			GGAGGCGGATTCG	X82324	CCDS14450.1	Xq21.1	2011-06-20	2007-07-13		ENSG00000196767	ENSG00000196767		"Homeoboxes / POU class"	9217	protein-coding gene	gene with protein product	"brain-4"	300039	"POU domain class 3, transcription factor 4"	DFN3		7911044, 7581392	Standard	NM_000307		Approved	BRN4, OTF9, DFNX2	uc004eeg.2	P49335	OTTHUMG00000021919	ENST00000373200.2:c.777G>T	chrX.hg19:g.82764109G>T		114.0	0.0		127.0	54.0	NM_000307	B2RC71|Q5H9G9|Q99410	Silent	SNP	ENST00000373200.2	hg19	CCDS14450.1																																																																																			.	.		0.577	POU3F4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057368.2	NM_000307		T	82764109	G	T	82764109	2	4	333	1	0	0	0	0	0	0	0	1	12286	1103	39	1		1	POU3F4	23	82764109	Silent	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	2393446	82764109	72506451	180	46522										
APOOL	139322	hgsc.bcm.edu	37	chrX	84301522	84301522	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tgtacatgcagccaaacaagAggaatccaaaaagcagctag	9	9	0	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chrX:84301522A>G	ENST00000373173.2	+	2	173	c.86A>G	c.(85-87)gAg>gGg	p.E29G		NM_198450.5	NP_940852.3	Q6UXV4	MIC27_HUMAN	apolipoprotein O-like	29						integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	8						GCCAAACAAGAGGAATCCAAA	0.348																																					p.E29G		Atlas-SNP	.											.	APOOL	20	.	0			c.A86G						.						82	74	77					X																	84301522		1857	4089	5946	SO:0001583	missense	139322	exon2			AACAAGAGGAATC	AK130506	CCDS48138.1	Xq21.1	2007-01-17	2007-01-17	2007-01-17	ENSG00000155008	ENSG00000155008			24009	protein-coding gene	gene with protein product			"chromosome X open reading frame 33", "family with sequence similarity 121A"	CXorf33, FAM121A		12975309	Standard	NM_198450		Approved	UNQ8193, AAIR8193	uc004eem.3	Q6UXV4	OTTHUMG00000021930	ENST00000373173.2:c.86A>G	chrX.hg19:g.84301522A>G	ENSP00000362268:p.Glu29Gly	560.0	0.0		505.0	250.0	NM_198450	Q3KNU7|Q5H9D1	Missense_Mutation	SNP	ENST00000373173.2	hg19	CCDS48138.1	.	.	.	.	.	.	.	.	.	.	A	15.38	2.817798	0.50633	.	.	ENSG00000155008	ENST00000373173;ENST00000373169	.	.	.	4.53	4.53	0.55603	.	0.386776	0.28566	N	0.014881	T	0.38825	0.1055	L	0.57536	1.79	0.30455	N	0.774838	P	0.40578	0.722	B	0.41374	0.355	T	0.49072	-0.8977	9	0.48119	T	0.1	-15.6633	7.151	0.25610	0.8951:0.0:0.1049:0.0	.	29	Q6UXV4	APOOL_HUMAN	G	29	.	ENSP00000362264:E29G	E	+	2	0	APOOL	84188178	1.000000	0.71417	0.491000	0.27477	0.811000	0.45836	3.436000	0.52856	1.776000	0.52262	0.481000	0.45027	GAG	.	.		0.348	APOOL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057385.2	NM_198450		G	84301522	A	G	84301522	3	3	333	1	0	0	0	0	1	0	0	0	814	304	11	2	92	2	APOOL	23	84301522	Missense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	1537413	84301522	70969038	181	46523										
NOX1	27035	hgsc.bcm.edu	37	chrX	100104832	100104832	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tttcaagatagaagcaaaggGggtgaccccaattcctgctc	10	10	1	3			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chrX:100104832G>C	ENST00000372966.3	-	10	1430	c.1225C>G	c.(1225-1227)Ccc>Gcc	p.P409A	NOX1_ENST00000372964.1_Intron|NOX1_ENST00000217885.5_Missense_Mutation_p.P409A|NOX1_ENST00000372960.4_Missense_Mutation_p.P372A	NM_007052.4|NM_013955.2	NP_008983.2|NP_039249.1	Q9Y5S8	NOX1_HUMAN	NADPH oxidase 1	409	Interaction with NOXO1.				angiogenesis (GO:0001525)|cell migration (GO:0016477)|cellular response to hyperoxia (GO:0071455)|cellular stress response to acidic pH (GO:1990451)|extracellular matrix organization (GO:0030198)|hydrogen peroxide metabolic process (GO:0042743)|inflammatory response (GO:0006954)|intracellular pH elevation (GO:0051454)|NADP metabolic process (GO:0006739)|oxidation-reduction process (GO:0055114)|oxygen metabolic process (GO:0072592)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of JNK cascade (GO:0046330)|positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902177)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation vascular endothelial growth factor production (GO:0010575)|proton transport (GO:0015992)|regulation of blood pressure (GO:0008217)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|respiratory burst (GO:0045730)|signal transduction (GO:0007165)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|early endosome (GO:0005769)|integral component of membrane (GO:0016021)|invadopodium membrane (GO:0071438)|NADPH oxidase complex (GO:0043020)	metal ion binding (GO:0046872)|NADP binding (GO:0050661)|Rac GTPase binding (GO:0048365)|superoxide-generating NADPH oxidase activity (GO:0016175)|voltage-gated proton channel activity (GO:0030171)			cervix(1)|lung(3)|ovary(1)|skin(2)	7						GAAGCAAAGGGGGTGACCCCA	0.458																																					p.P409A		Atlas-SNP	.											.	NOX1	79	.	0			c.C1225G						.						93	80	85					X																	100104832		2203	4300	6503	SO:0001583	missense	27035	exon10			CAAAGGGGGTGAC	AF127763	CCDS14474.1, CCDS14475.1, CCDS65298.1	Xq22	2008-08-01			ENSG00000007952	ENSG00000007952			7889	protein-coding gene	gene with protein product	"mitogenic oxidase (pyridine nucleotide-dependent superoxide-generating)", "NADPH oxidase homolog-1", "NADPH oxidase 1 variant NOH-1L"	300225				10485709, 10615049	Standard	NM_007052		Approved	NOH1, NOH-1, MOX1, GP91-2	uc004egj.3	Q9Y5S8	OTTHUMG00000022007	ENST00000372966.3:c.1225C>G	chrX.hg19:g.100104832G>C	ENSP00000362057:p.Pro409Ala	241.0	0.0		293.0	163.0	NM_013955	A8K836|O95691|Q2PP02	Missense_Mutation	SNP	ENST00000372966.3	hg19	CCDS14474.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.16|18.16	3.563168|3.563168	0.65538|0.65538	.|.	.|.	ENSG00000007952|ENSG00000007952	ENST00000372966;ENST00000217885;ENST00000372960;ENST00000372957|ENST00000427768	D;D;D|.	0.99527|.	-6.09;-2.35;-6.09|.	3.73|3.73	3.73|3.73	0.42828|0.42828	Ferric reductase, NAD binding (1);|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	D|D	0.87026|0.87026	0.6075|0.6075	H|H	0.96889|0.96889	3.9|3.9	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	0.998;1.0;1.0|.	D|D	0.91391|0.91391	0.5135|0.5135	10|6	0.87932|.	D|.	0|.	.|.	14.0605|14.0605	0.64797|0.64797	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	372;409;409|.	A6NGA6;Q9Y5S8-3;Q9Y5S8|.	.;.;NOX1_HUMAN|.	A|R	409;409;372;98|93	ENSP00000362057:P409A;ENSP00000217885:P409A;ENSP00000362051:P372A|.	ENSP00000217885:P409A|.	P|P	-|-	1|2	0|0	NOX1|NOX1	99991488|99991488	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.971000|0.971000	0.66376|0.66376	6.744000|6.744000	0.74854|0.74854	1.822000|1.822000	0.53115|0.53115	0.600000|0.600000	0.82982|0.82982	CCC|CCC	.	.		0.458	NOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057495.1	NM_007052		C	100104832	G	C	100104832	3	2	333	1	0	0	0	0	1	0	0	0	10565	1232	43	4	485	4	NOX1	23	100104832	Missense_Mutation	SNP	G	TCGA-RC-A6M4-01A-11D-A32G-10	15803310	100104832	55165728	182	46524										
IL1RAPL2	26280	hgsc.bcm.edu	37	chrX	105011034	105011034	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	taactccagactatattctcAgacggggatggagtattttc	9	8	1	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chrX:105011034A>T	ENST00000372582.1	+	11	2197	c.1441A>T	c.(1441-1443)Aga>Tga	p.R481*	IL1RAPL2_ENST00000344799.4_Nonsense_Mutation_p.R481*	NM_017416.1	NP_059112.1	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2	481	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				central nervous system development (GO:0007417)|cytokine-mediated signaling pathway (GO:0019221)	integral component of membrane (GO:0016021)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)			breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(23)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						CTATATTCTCAGACGGGGATG	0.378																																					p.R481X		Atlas-SNP	.											.	IL1RAPL2	105	.	0			c.A1441T						.						91	83	86					X																	105011034		2203	4300	6503	SO:0001587	stop_gained	26280	exon11			ATTCTCAGACGGG	AF181285	CCDS14517.1	Xq22	2013-01-11			ENSG00000189108	ENSG00000189108		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5997	protein-coding gene	gene with protein product		300277				10757639	Standard	NM_017416		Approved	IL-1R9, TIGIRR-1, IL1RAPL-2, IL1R9	uc004elz.1	Q9NP60	OTTHUMG00000022141	ENST00000372582.1:c.1441A>T	chrX.hg19:g.105011034A>T	ENSP00000361663:p.Arg481*	227.0	0.0		236.0	112.0	NM_017416	Q2M3U3|Q9NZN0	Nonsense_Mutation	SNP	ENST00000372582.1	hg19	CCDS14517.1	.	.	.	.	.	.	.	.	.	.	A	36	5.709833	0.96821	.	.	ENSG00000189108	ENST00000372582;ENST00000344799;ENST00000538500	.	.	.	5.39	5.39	0.77823	.	0.082759	0.52532	D	0.000076	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.5324	0.61629	1.0:0.0:0.0:0.0	.	.	.	.	X	481;481;86	.	ENSP00000344976:R481X	R	+	1	2	IL1RAPL2	104897690	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.394000	0.66285	1.790000	0.52503	0.486000	0.48141	AGA	.	.		0.378	IL1RAPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057785.1	NM_017416		T	105011034	A	T	105011034	4	4	333	1	0	0	0	0	0	1	0	0	7671	180	7	4	1479	4	IL1RAPL2	23	105011034	Nonsense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	4906202	105011034	50259526	183	46525										
COL4A6	1288	hgsc.bcm.edu	37	chrX	107423750	107423750	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	cactccttttcttacctggtAattcaggaagatgaaccaat	6	10	2	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chrX:107423750A>T	ENST00000372216.4	-	25	2229	c.2129T>A	c.(2128-2130)tTa>tAa	p.L710*	COL4A6_ENST00000394872.2_Nonsense_Mutation_p.L710*|COL4A6_ENST00000334504.7_Nonsense_Mutation_p.L709*|COL4A6_ENST00000538570.1_Nonsense_Mutation_p.L709*|COL4A6_ENST00000545689.1_Nonsense_Mutation_p.L709*	NM_001847.2	NP_001838.2	Q14031	CO4A6_HUMAN	collagen, type IV, alpha 6	710	Triple-helical region.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(41)|ovary(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	92						CTTACCTGGTAATTCAGGAAG	0.527									Alport syndrome with Diffuse Leiomyomatosis																												p.L710X	Melanoma(87;1895 1945 2589 7165)	Atlas-SNP	.											.	COL4A6	270	.	0			c.T2129A						.						67	51	56					X																	107423750		2203	4299	6502	SO:0001587	stop_gained	1288	exon25	Familial Cancer Database		CCTGGTAATTCAG	U04845	CCDS14541.1, CCDS14542.1, CCDS76008.1, CCDS76009.1, CCDS76010.1	Xq22	2014-09-17			ENSG00000197565	ENSG00000197565		"Collagens"	2208	protein-coding gene	gene with protein product		303631				8356449	Standard	NM_033641		Approved		uc004env.4	Q14031	OTTHUMG00000022179	ENST00000372216.4:c.2129T>A	chrX.hg19:g.107423750A>T	ENSP00000361290:p.Leu710*	114.0	0.0		120.0	53.0	NM_001847	Q12823|Q14053|Q5JYH6|Q5JYH8|Q9NQM5|Q9NTX3|Q9UJ76|Q9UMG6|Q9Y4L4	Nonsense_Mutation	SNP	ENST00000372216.4	hg19	CCDS14541.1	.	.	.	.	.	.	.	.	.	.	A	37	6.271289	0.97431	.	.	ENSG00000197565	ENST00000372216;ENST00000334504;ENST00000394872;ENST00000541389;ENST00000545689;ENST00000538570	.	.	.	5.07	5.07	0.68467	.	0.238854	0.21755	N	0.069617	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05721	T	0.95	.	9.1344	0.36866	0.8238:0.0:0.0:0.1762	.	.	.	.	X	710;709;710;709;709;709	.	ENSP00000334733:L709X	L	-	2	0	COL4A6	107310406	0.058000	0.20735	0.893000	0.35052	0.194000	0.23727	1.471000	0.35365	1.940000	0.56252	0.417000	0.27973	TTA	.	.		0.527	COL4A6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057875.2			T	107423750	A	T	107423750	4	4	333	1	0	0	0	0	0	1	0	0	3697	372	13	4	3030	4	COL4A6	23	107423750	Nonsense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	2412716	107423750	47846810	184	46526										
RGAG1	57529	hgsc.bcm.edu	37	chrX	109693862	109693862	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	agatatgtcaatacccttacAttcactgcgattcaacaata	4	10	3	1			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chrX:109693862A>G	ENST00000465301.2	+	3	263	c.17A>G	c.(16-18)cAt>cGt	p.H6R	RGAG1_ENST00000540313.1_Missense_Mutation_p.H6R	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	6										NS(1)|autonomic_ganglia(1)|breast(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	73						ATACCCTTACATTCACTGCGA	0.453											OREG0019909	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.H6R		Atlas-SNP	.											.	RGAG1	168	.	0			c.A17G						.						155	146	149					X																	109693862		2203	4300	6503	SO:0001583	missense	57529	exon3			CCTTACATTCACT	AY121804	CCDS14552.1	Xq23	2008-02-05			ENSG00000243978	ENSG00000243978			29245	protein-coding gene	gene with protein product						10718198, 15716091, 16093683	Standard	NM_020769		Approved	KIAA1318, Mart9, Mar9	uc004eor.2	Q8NET4	OTTHUMG00000022196	ENST00000465301.2:c.17A>G	chrX.hg19:g.109693862A>G	ENSP00000419786:p.His6Arg	61.0	0.0	1421	65.0	29.0	NM_020769	Q9P2M8	Missense_Mutation	SNP	ENST00000465301.2	hg19	CCDS14552.1	.	.	.	.	.	.	.	.	.	.	A	0.390	-0.923925	0.02377	.	.	ENSG00000243978	ENST00000520821;ENST00000465301;ENST00000540313;ENST00000540483	T;T	0.60424	0.19;0.19	4.16	1.77	0.24775	.	0.899723	0.09155	N	0.841030	T	0.38746	0.1052	N	0.24115	0.695	0.09310	N	1	B	0.14012	0.009	B	0.14578	0.011	T	0.24621	-1.0155	9	.	.	.	0.8516	5.1088	0.14798	0.7527:0.0:0.2473:0.0	.	6	Q8NET4	RGAG1_HUMAN	R	6	ENSP00000419786:H6R;ENSP00000441452:H6R	.	H	+	2	0	RGAG1	109580518	0.028000	0.19301	0.074000	0.20217	0.023000	0.10783	0.069000	0.14552	0.245000	0.21373	-0.314000	0.08810	CAT	.	.		0.453	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	NM_020769		G	109693862	A	G	109693862	3	3	333	1	0	0	0	0	1	0	0	0	13289	217	8	2	19	2	RGAG1	23	109693862	Missense_Mutation	SNP	A	TCGA-RC-A6M4-01A-11D-A32G-10	2270112	109693862	45576698	185	46527										
MAGEA8	4107	hgsc.bcm.edu	37	chrX	149013280	149013280	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	ctgactgtcaccgacagcacTctgtggagccaatccgatga	10	13	2	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chrX:149013280T>A	ENST00000542674.1	+	3	755	c.234T>A	c.(232-234)acT>acA	p.T78T	MAGEA8_ENST00000286482.1_Silent_p.T78T|MAGEA8_ENST00000535454.1_Silent_p.T78T|MAGEA8_ENST00000493910.1_3'UTR	NM_001166401.1	NP_001159873.1	P43361	MAGA8_HUMAN	melanoma antigen family A, 8	78										NS(1)|breast(2)|endometrium(2)|large_intestine(2)|lung(12)|upper_aerodigestive_tract(1)	20	Acute lymphoblastic leukemia(192;6.56e-05)					CCGACAGCACTCTGTGGAGCC	0.602																																					p.T78T		Atlas-SNP	.											.	MAGEA8	40	.	0			c.T234A						.						67	61	63					X																	149013280		2203	4298	6501	SO:0001819	synonymous_variant	4107	exon3			CAGCACTCTGTGG		CCDS14692.1	Xq28	2009-03-13			ENSG00000156009	ENSG00000156009			6806	protein-coding gene	gene with protein product	"MAGE-8 antigen", "cancer/testis antigen family 1, member 8"	300341		MAGE8		8575766	Standard	NM_005364		Approved	MGC2182, CT1.8	uc004fdw.2	P43361	OTTHUMG00000022635	ENST00000542674.1:c.234T>A	chrX.hg19:g.149013280T>A		56.0	0.0		62.0	27.0	NM_005364	Q9BUN9	Silent	SNP	ENST00000542674.1	hg19	CCDS14692.1																																																																																			.	.		0.602	MAGEA8-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058728.1	NM_005364		A	149013280	T	A	149013280	2	1	333	1	0	0	0	0	0	0	0	1	9180	1538	54	4		4	MAGEA8	23	149013280	Silent	SNP	T	TCGA-RC-A6M4-01A-11D-A32G-10	39319418	149013280	6257280	186	46528										
ZNF185	7739	hgsc.bcm.edu	37	chrX	152110314	152110314	+	Intron	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0481283422459893	9	1	1.52385093167702	2.9956043956044	0.944069264069264	1	1	0	tgaggccatgcccgtgccggCcgccagaggtcgcccgagga	16	15	0	2			TCGA-RC-A6M4-01A-11D-A32G-10	TCGA-RC-A6M4-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	559b7362-9b75-4be3-b8bc-5f3e28b71cd8	eb1e50b4-ccfb-4b5d-8180-a19d2e42b2a2	g.chrX:152110314C>A	ENST00000370268.4	+	16	1245				ZNF185_ENST00000539731.1_Intron|ZNF185_ENST00000318529.8_Intron|ZNF185_ENST00000318504.7_Intron|ZNF185_ENST00000449285.2_Intron|ZNF185_ENST00000324823.6_Intron|ZNF185_ENST00000535861.1_Intron|ZNF185_ENST00000370270.2_Intron|ZNF185_ENST00000454925.1_Missense_Mutation_p.A21D			O15231	ZN185_HUMAN	zinc finger protein 185 (LIM domain)							actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(3)	12	Acute lymphoblastic leukemia(192;6.56e-05)					CCCGTGCCGGCCGCCAGAGGT	0.687																																					p.A21D		Atlas-SNP	.											.	ZNF185	92	.	0			c.C62A						.																																			SO:0001627	intron_variant	7739	exon1			TGCCGGCCGCCAG	AK056517	CCDS48184.1, CCDS55528.1, CCDS55529.1, CCDS55530.1, CCDS55531.1, CCDS55532.1, CCDS69832.1	Xq28	2012-08-08			ENSG00000147394	ENSG00000147394		"Zinc fingers, C2H2-type"	12976	protein-coding gene	gene with protein product		300381				9268636	Standard	NM_001178106		Approved		uc011myg.2	O15231	OTTHUMG00000024187	ENST00000370268.4:c.1209-3497C>A	chrX.hg19:g.152110314C>A		91.0	0.0		108.0	46.0	NM_001178115	A4FTV3|A6NME5|B4DLE9|B7Z771|B8K2L9|B8K2M0|B8K2M1|B8K2M2|E9PFR6|F5GXF7|F5GZL4|F8W8V7|H0Y4M8|O00345|Q8N1R8|Q9NSD2	Missense_Mutation	SNP	ENST00000370268.4	hg19	CCDS48184.1	.	.	.	.	.	.	.	.	.	.	C	14.58	2.578695	0.46006	.	.	ENSG00000147394	ENST00000454925	.	.	.	3.38	1.54	0.23209	.	.	.	.	.	T	0.15262	0.0368	N	0.08118	0	0.21147	N	0.999771	.	.	.	.	.	.	T	0.24297	-1.0164	5	.	.	.	.	3.9207	0.09242	0.0:0.6085:0.2463:0.1453	.	.	.	.	T	24	.	.	P	+	1	0	ZNF185	151860970	0.056000	0.20664	0.024000	0.17045	0.031000	0.12232	0.752000	0.26362	0.276000	0.22118	0.523000	0.50628	CCG	.	.		0.687	ZNF185-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000377480.1	NM_007150		A	152110314	C	A	152110314	1	1	333	0	1	0	0	0	0	0	0	0	17767	739	26	3		3	ZNF185	23	152110314	Intron	SNP	C	TCGA-RC-A6M4-01A-11D-A32G-10	3097034	152110314	3160246	187	46529										
NRD1	4898	hgsc.bcm.edu	37	chr1	52306079	52306079	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	catcatcttcttcttcttccTccacctcctcttcttcttca	0	18	9	0	rs62648104		TCGA-RC-A6M5-01A-11D-A32G-10	TCGA-RC-A6M5-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bc57f84-c45f-45a1-9a62-0e2972598fa7	76a1244e-bd30-4dbb-95ee-857b135bb56e	g.chr1:52306079T>A	ENST00000354831.7	-	2	638	c.449A>T	c.(448-450)gAg>gTg	p.E150V	NRD1_ENST00000544028.1_Missense_Mutation_p.E18V|NRD1_ENST00000352171.7_Missense_Mutation_p.E150V|NRD1_ENST00000539524.1_Missense_Mutation_p.E18V|NRD1_ENST00000485608.1_5'UTR	NM_002525.2	NP_002516.2	O43847	NRDC_HUMAN	nardilysin (N-arginine dibasic convertase)	0	Asp/Glu-rich (highly acidic).|Poly-Glu.				cell migration (GO:0016477)|cell proliferation (GO:0008283)|neuromuscular junction development (GO:0007528)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)	cell surface (GO:0009986)|cytosol (GO:0005829)	epidermal growth factor binding (GO:0048408)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)	27						ttcttcttcctccacctcctc	0.378																																					p.E150V		Atlas-SNP	.											.	NRD1	89	.	0			c.A449T						.						163	138	146					1																	52306079		2203	4300	6503	SO:0001583	missense	4898	exon2			TCTTCCTCCACCT	X93207	CCDS559.1, CCDS41335.1, CCDS55599.1	1p32.2-p32.1	2008-07-18			ENSG00000078618	ENSG00000078618			7995	protein-coding gene	gene with protein product		602651				9581555, 9479496	Standard	NM_002525		Approved	hNRD1, hNRD2	uc001ctc.4	O43847	OTTHUMG00000008278	ENST00000354831.7:c.449A>T	chr1.hg19:g.52306079T>A	ENSP00000346890:p.Glu150Val	303.0	0.0		268.0	18.0	NM_002525	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	Missense_Mutation	SNP	ENST00000354831.7	hg19	CCDS559.1	.	.	.	.	.	.	.	.	.	.	T	3.056	-0.194350	0.06259	.	.	ENSG00000078618	ENST00000352171;ENST00000354831;ENST00000539524;ENST00000546169;ENST00000544028	T;T;T;T	0.38240	1.31;3.15;1.15;1.22	5.25	2.92	0.33932	Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.525899	0.19688	N	0.108344	T	0.18341	0.0440	N	0.14661	0.345	0.09310	N	1	B;B;B	0.23650	0.062;0.089;0.01	B;B;B	0.17098	0.017;0.007;0.007	T	0.14755	-1.0461	10	0.38643	T	0.18	-0.0317	5.1939	0.15225	0.0:0.1704:0.2022:0.6274	rs62648104	150;150;150	F5H6R2;O43847;B1AKJ5	.;NRDC_HUMAN;.	V	150;150;18;150;18	ENSP00000262679:E150V;ENSP00000346890:E150V;ENSP00000444416:E18V;ENSP00000442262:E18V	ENSP00000262679:E150V	E	-	2	0	NRD1	52078667	0.129000	0.22400	0.012000	0.15200	0.145000	0.21501	0.870000	0.28010	0.317000	0.23160	0.454000	0.30748	GAG	.	T|0.024;A|0.976		0.378	NRD1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023045.1	NM_002525		A	52306079	T	A	52306079	3	1	334	1	0	0	0	0	1	0	0	0	10654	1551	54	4	3338	4	NRD1	1	52306079	Missense_Mutation	SNP	T	TCGA-RC-A6M5-01A-11D-A32G-10		52306079	196944542	1	46530										
BIRC6	57448	hgsc.bcm.edu	37	chr2	32768519	32768519	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tggattatttcttcgtcttcCgggctatgcggaagtgctac	11	9	2	0			TCGA-RC-A6M5-01A-11D-A32G-10	TCGA-RC-A6M5-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bc57f84-c45f-45a1-9a62-0e2972598fa7	76a1244e-bd30-4dbb-95ee-857b135bb56e	g.chr2:32768519C>T	ENST00000421745.2	+	62	12637	c.12503C>T	c.(12502-12504)cCg>cTg	p.P4168L		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	4168					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					CTTCGTCTTCCGGGCTATGCG	0.473																																					p.P4168L	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.C12503T						.						222	192	202					2																	32768519		2203	4300	6503	SO:0001583	missense	57448	exon62			GTCTTCCGGGCTA	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.12503C>T	chr2.hg19:g.32768519C>T	ENSP00000393596:p.Pro4168Leu	90.0	0.0		90.0	12.0	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	hg19	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	C	33	5.203441	0.95033	.	.	ENSG00000115760	ENST00000421745	T	0.78595	-1.19	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	D	0.87378	0.6162	M	0.62723	1.935	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.88034	0.2777	10	0.87932	D	0	.	19.4789	0.95000	0.0:1.0:0.0:0.0	.	4168	Q9NR09	BIRC6_HUMAN	L	4168	ENSP00000393596:P4168L	ENSP00000393596:P4168L	P	+	2	0	BIRC6	32622023	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.975000	0.70475	2.598000	0.87819	0.650000	0.86243	CCG	.	.		0.473	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		T	32768519	C	T	32768519	3	4	334	1	0	0	0	0	1	0	0	0	1438	652	23	1	12749	1	BIRC6	2	32768519	Missense_Mutation	SNP	C	TCGA-RC-A6M5-01A-11D-A32G-10		32768519	210430854	2	46531										
USP34	9736	hgsc.bcm.edu	37	chr2	61607465	61607465	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gttacgagctgcactctgtcGtaactcctgatccgagagct	10	12	1	2			TCGA-RC-A6M5-01A-11D-A32G-10	TCGA-RC-A6M5-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bc57f84-c45f-45a1-9a62-0e2972598fa7	76a1244e-bd30-4dbb-95ee-857b135bb56e	g.chr2:61607465G>A	ENST00000398571.2	-	7	929	c.853C>T	c.(853-855)Cga>Tga	p.R285*		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	285					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.R285*(1)		autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			GCACTCTGTCGTAACTCCTGA	0.368																																					p.R285X		Atlas-SNP	.											USP34,bladder,carcinoma,0,2	USP34	334	.	1	Substitution - Nonsense(1)	urinary_tract(1)	c.C853T						.						106	92	96					2																	61607465		1891	4119	6010	SO:0001587	stop_gained	9736	exon7			TCTGTCGTAACTC	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"Ubiquitin-specific peptidases"	20066	protein-coding gene	gene with protein product		615295	"ubiquitin specific protease 34"			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.853C>T	chr2.hg19:g.61607465G>A	ENSP00000381577:p.Arg285*	132.0	0.0		84.0	12.0	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Nonsense_Mutation	SNP	ENST00000398571.2	hg19	CCDS42686.1	.	.	.	.	.	.	.	.	.	.	G	29.4	4.999830	0.93227	.	.	ENSG00000115464	ENST00000263989;ENST00000398569;ENST00000398571	.	.	.	5.2	-0.0234	0.13943	.	0.117422	0.64402	D	0.000019	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.0792	0.42379	0.0763:0.0:0.3927:0.5309	.	.	.	.	X	133;133;285	.	ENSP00000263989:R133X	R	-	1	2	USP34	61460969	1.000000	0.71417	0.999000	0.59377	0.908000	0.53690	1.038000	0.30254	0.171000	0.19730	0.557000	0.71058	CGA	.	.		0.368	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			A	61607465	G	A	61607465	4	1	334	1	0	0	0	0	0	1	0	0	17080	1153	40	1	10083	1	USP34	2	61607465	Nonsense_Mutation	SNP	G	TCGA-RC-A6M5-01A-11D-A32G-10	28838946	61607465	181591908	3	46532										
GADL1	339896	hgsc.bcm.edu	37	chr3	30903143	30903143	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ccattattagcctacaggccTcttcaacaaatttttctcca	3	13	3	0			TCGA-RC-A6M5-01A-11D-A32G-10	TCGA-RC-A6M5-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bc57f84-c45f-45a1-9a62-0e2972598fa7	76a1244e-bd30-4dbb-95ee-857b135bb56e	g.chr3:30903143T>A	ENST00000282538.5	-	2	302	c.152A>T	c.(151-153)gAg>gTg	p.E51V	GADL1_ENST00000454381.3_Missense_Mutation_p.E51V	NM_207359.2	NP_997242.2	Q6ZQY3	GADL1_HUMAN	glutamate decarboxylase-like 1	51					carboxylic acid metabolic process (GO:0019752)		aspartate 1-decarboxylase activity (GO:0004068)|pyridoxal phosphate binding (GO:0030170)|sulfinoalanine decarboxylase activity (GO:0004782)			breast(2)|endometrium(3)|kidney(2)|lung(17)|upper_aerodigestive_tract(1)	25						CCTACAGGCCTCTTCAACAAA	0.388																																					p.E51V		Atlas-SNP	.											.	GADL1	91	.	0			c.A152T						.						167	138	147					3																	30903143		692	1591	2283	SO:0001583	missense	339896	exon2			CAGGCCTCTTCAA	AK128643	CCDS2649.2	3p23-p22	2009-01-14			ENSG00000144644	ENSG00000144644			27949	protein-coding gene	gene with protein product		615601					Standard	NM_207359		Approved		uc003cep.2	Q6ZQY3	OTTHUMG00000130621	ENST00000282538.5:c.152A>T	chr3.hg19:g.30903143T>A	ENSP00000282538:p.Glu51Val	265.0	0.0		244.0	18.0	NM_207359		Missense_Mutation	SNP	ENST00000282538.5	hg19	CCDS2649.2	.	.	.	.	.	.	.	.	.	.	T	17.27	3.347265	0.61183	.	.	ENSG00000144644	ENST00000282538;ENST00000454381	T;T	0.39229	2.79;1.09	5.42	5.42	0.78866	Pyridoxal phosphate-dependent transferase, major domain (1);	.	.	.	.	T	0.32912	0.0845	N	0.24115	0.695	0.42295	D	0.992157	B	0.26635	0.155	B	0.26517	0.07	T	0.18053	-1.0349	9	0.66056	D	0.02	.	15.1216	0.72447	0.0:0.0:0.0:1.0	.	51	Q6ZQY3	GADL1_HUMAN	V	51	ENSP00000282538:E51V;ENSP00000427059:E51V	ENSP00000282538:E51V	E	-	2	0	GADL1	30878147	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.498000	0.73679	2.048000	0.60808	0.454000	0.30748	GAG	.	.		0.388	GADL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253106.2	NM_207359		A	30903143	T	A	30903143	3	1	334	1	0	0	0	0	1	0	0	0	6193	1551	54	4	1469	4	GADL1	3	30903143	Missense_Mutation	SNP	T	TCGA-RC-A6M5-01A-11D-A32G-10		30903143	167119287	4	46533										
ADH4	127	hgsc.bcm.edu	37	chr4	100052694	100052694	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gcacagtcaagggcaaaatcCacacctcccttggtcaattc	7	14	2	0			TCGA-RC-A6M5-01A-11D-A32G-10	TCGA-RC-A6M5-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bc57f84-c45f-45a1-9a62-0e2972598fa7	76a1244e-bd30-4dbb-95ee-857b135bb56e	g.chr4:100052694C>G	ENST00000265512.7	-	6	878	c.804G>C	c.(802-804)gtG>gtC	p.V268V	RP11-696N14.1_ENST00000500358.2_RNA|ADH4_ENST00000508393.1_Silent_p.V287V|ADH4_ENST00000423445.1_Silent_p.V287V|ADH4_ENST00000505590.1_Silent_p.V287V	NM_000670.3	NP_000661.2	P08319	ADH4_HUMAN	alcohol dehydrogenase 4 (class II), pi polypeptide	268					alcohol catabolic process (GO:0046164)|alcohol metabolic process (GO:0006066)|cellular aldehyde metabolic process (GO:0006081)|ethanol oxidation (GO:0006069)|quinone metabolic process (GO:1901661)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|all-trans retinal binding (GO:0005503)|benzaldehyde dehydrogenase activity (GO:0019115)|ethanol binding (GO:0035276)|NAD binding (GO:0051287)|NADPH:quinone reductase activity (GO:0003960)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)|retinol binding (GO:0019841)|retinol dehydrogenase activity (GO:0004745)|zinc ion binding (GO:0008270)			NS(1)|cervix(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)|skin(2)	18				OV - Ovarian serous cystadenocarcinoma(123;4.48e-08)		GGGCAAAATCCACACCTCCCT	0.418																																					p.V268V		Atlas-SNP	.											.	ADH4	35	.	0			c.G804C						.						123	121	122					4																	100052694		2203	4300	6503	SO:0001819	synonymous_variant	127	exon6			AAAATCCACACCT	M15943	CCDS34032.1	4q22	2008-02-05				ENSG00000198099	1.1.1.1	"Alcohol dehydrogenases"	252	protein-coding gene	gene with protein product		103740					Standard	NM_000670		Approved	ADH-2	uc003hun.3	P08319		ENST00000265512.7:c.804G>C	chr4.hg19:g.100052694C>G		86.0	0.0		98.0	10.0	NM_000670	A8K470|B4DIE7|C9J4A9|Q8TCD7	Silent	SNP	ENST00000265512.7	hg19	CCDS34032.1																																																																																			.	.		0.418	ADH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364220.2	NM_000670		G	100052694	C	G	100052694	2	3	334	1	0	0	0	0	0	0	0	1	310	581	21	4		4	ADH4	4	100052694	Silent	SNP	C	TCGA-RC-A6M5-01A-11D-A32G-10		100052694	91101582	5	46534										
TCERG1	10915	hgsc.bcm.edu	37	chr5	145838623	145838624	+	In_Frame_Ins	INS	-	-	CAGGCT													0	0	1	0	0	0	1	1	0	cccaggcacaagctcaggccINScaggctcaggctcaggccca							TCGA-RC-A6M5-01A-11D-A32G-10	TCGA-RC-A6M5-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bc57f84-c45f-45a1-9a62-0e2972598fa7	76a1244e-bd30-4dbb-95ee-857b135bb56e	g.chr5:145838623_145838624insCAGGCT	ENST00000296702.5	+	4	653_654	c.615_616insCAGGCT	c.(616-618)cag>CAGGCTcag	p.206_206Q>QAQ	TCERG1_ENST00000394421.2_In_Frame_Ins_p.206_206Q>QAQ	NM_006706.3	NP_006697.2	O14776	TCRG1_HUMAN	transcription elongation regulator 1	206	Ala/Gln-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(18)|lung(9)|ovary(2)|prostate(3)|skin(1)	46		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			aagctcaggcccaggctcaggc	0.708																																					p.A205delinsAQA		Atlas-INDEL	.											.	TCERG1	148	.	0			c.615_616insCAGGCT						.																																			SO:0001652	inframe_insertion	10915	exon4			.	AF017789	CCDS4282.1, CCDS43379.1	5q31	2010-01-25	2002-01-24	2002-01-25	ENSG00000113649	ENSG00000113649			15630	protein-coding gene	gene with protein product	"transcription factor CA150", "co-activator of 150 kDa", "TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD", "TATA box-binding protein-associated factor 2S"	605409	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"	TAF2S		9315662, 11003711	Standard	XM_005268365		Approved	CA150, Urn1	uc003lob.3	O14776	OTTHUMG00000129683	ENST00000296702.5:c.622_627dupCAGGCT	chr5.hg19:g.145838624_145838629dupCAGGCT	ENSP00000296702:p.AlaGln242dup	93.0	0.0		103.0	35.0	NM_006706	Q2NKN2|Q59EA1	In_Frame_Ins	INS	ENST00000296702.5	hg19	CCDS4282.1																																																																																			.	.		0.708	TCERG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251886.1	NM_001040006		CAGGCT	145838624	-	CAGGCT	145838623	7	5	334	1	0	1	1	0	0	0	0	0	15700	610	22	0	629	0	TCERG1	5	145838623	In_Frame_Ins	INS	-	TCGA-RC-A6M5-01A-11D-A32G-10		145838623	35076637	6	46535										
FNDC1	84624	hgsc.bcm.edu	37	chr6	159646689	159646689	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgtgtatgaatttgcagtccGtatttcacagggtgaaagag	12	5	1	3			TCGA-RC-A6M5-01A-11D-A32G-10	TCGA-RC-A6M5-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bc57f84-c45f-45a1-9a62-0e2972598fa7	76a1244e-bd30-4dbb-95ee-857b135bb56e	g.chr6:159646689G>A	ENST00000297267.9	+	8	1207	c.1007G>A	c.(1006-1008)cGt>cAt	p.R336H	FNDC1_ENST00000340366.6_Missense_Mutation_p.R336H|FNDC1_ENST00000480856.1_3'UTR	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	336	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		TTTGCAGTCCGTATTTCACAG	0.438																																					p.R336H		Atlas-SNP	.											.	FNDC1	250	.	0			c.G1007A						.						159	161	160					6																	159646689		1926	4130	6056	SO:0001583	missense	84624	exon8			CAGTCCGTATTTC	AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"Fibronectin type III domain containing"	21184	protein-coding gene	gene with protein product		609991	"fibronectin type III domain containing 2"	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.1007G>A	chr6.hg19:g.159646689G>A	ENSP00000297267:p.Arg336His	80.0	0.0		78.0	18.0	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	hg19	CCDS47512.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.015182	0.75161	.	.	ENSG00000164694	ENST00000297267;ENST00000340366	T;T	0.58358	0.34;0.34	5.75	5.75	0.90469	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.108020	0.64402	D	0.000011	T	0.63141	0.2486	M	0.74881	2.28	0.34265	D	0.680406	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.989	T	0.69610	-0.5099	10	0.62326	D	0.03	-17.9844	10.9433	0.47285	0.1131:0.0:0.8869:0.0	.	336;336	Q4ZHG4-2;Q4ZHG4	.;FNDC1_HUMAN	H	336	ENSP00000297267:R336H;ENSP00000342460:R336H	ENSP00000297267:R336H	R	+	2	0	FNDC1	159566677	1.000000	0.71417	0.239000	0.24122	0.981000	0.71138	5.286000	0.65639	2.718000	0.92993	0.591000	0.81541	CGT	.	.		0.438	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532		A	159646689	G	A	159646689	3	1	334	1	0	0	0	0	1	0	0	0	5976	1145	40	1	1037	1	FNDC1	6	159646689	Missense_Mutation	SNP	G	TCGA-RC-A6M5-01A-11D-A32G-10		159646689	11468378	7	46536										
CBLL1	79872	hgsc.bcm.edu	37	chr7	107399297	107399297	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tgacctctgctccaccaccaAtaacccctccccctggacat	4	20	1	1			TCGA-RC-A6M5-01A-11D-A32G-10	TCGA-RC-A6M5-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bc57f84-c45f-45a1-9a62-0e2972598fa7	76a1244e-bd30-4dbb-95ee-857b135bb56e	g.chr7:107399297A>G	ENST00000440859.3	+	6	1617	c.1150A>G	c.(1150-1152)Ata>Gta	p.I384V	CBLL1_ENST00000222597.2_Missense_Mutation_p.I383V	NM_001284291.1|NM_024814.2	NP_001271220.1|NP_079090.2	Q75N03	HAKAI_HUMAN	Cbl proto-oncogene-like 1, E3 ubiquitin protein ligase	384	Pro-rich.				negative regulation of cell adhesion (GO:0007162)|positive regulation of cell migration (GO:0030335)|positive regulation of endocytosis (GO:0045807)|protein ubiquitination (GO:0016567)|single organismal cell-cell adhesion (GO:0016337)	ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(3)|skin(3)	21						TCCACCACCAATAACCCCTCC	0.532																																					p.I384V		Atlas-SNP	.											.	CBLL1	54	.	0			c.A1150G						.						208	209	209					7																	107399297		2203	4300	6503	SO:0001583	missense	79872	exon6			CCACCAATAACCC	AK026762	CCDS5747.1, CCDS64754.1	7q22.3	2013-07-09	2013-07-09		ENSG00000105879	ENSG00000105879		"RING-type (C3HC4) zinc fingers"	21225	protein-coding gene	gene with protein product	"Casitas B-lineage lymphoma-like"	606872	"Cas-Br-M (murine) ecotropic retroviral transforming sequence-like 1"			11836526, 11944035	Standard	NM_001284291		Approved	HAKAI, FLJ23109, RNF188	uc003veq.3	Q75N03	OTTHUMG00000154809	ENST00000440859.3:c.1150A>G	chr7.hg19:g.107399297A>G	ENSP00000401277:p.Ile384Val	92.0	0.0		89.0	21.0	NM_024814	B7ZM03|Q8TAJ4|Q9H5S6	Missense_Mutation	SNP	ENST00000440859.3	hg19	CCDS5747.1	.	.	.	.	.	.	.	.	.	.	A	11.37	1.617284	0.28801	.	.	ENSG00000105879	ENST00000440859;ENST00000535365;ENST00000222597	T;T	0.30981	1.51;1.51	4.96	3.81	0.43845	.	0.000000	0.85682	D	0.000000	T	0.23210	0.0561	L	0.38531	1.155	0.80722	D	1	B;B	0.23128	0.08;0.08	B;B	0.26614	0.071;0.071	T	0.04053	-1.0981	10	0.18710	T	0.47	-2.8001	10.6908	0.45870	0.924:0.0:0.076:0.0	.	383;384	B7ZM03;Q75N03	.;HAKAI_HUMAN	V	384;263;383	ENSP00000401277:I384V;ENSP00000222597:I383V	ENSP00000222597:I383V	I	+	1	0	CBLL1	107186533	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.822000	0.75277	0.853000	0.35312	0.402000	0.26972	ATA	.	.		0.532	CBLL1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337156.2	NM_024814		G	107399297	A	G	107399297	3	3	334	1	0	0	0	0	1	0	0	0	2705	101	4	2	1172	2	CBLL1	7	107399297	Missense_Mutation	SNP	A	TCGA-RC-A6M5-01A-11D-A32G-10		107399297	51739366	8	46537										
MYOM2	9172	hgsc.bcm.edu	37	chr8	2017578	2017578	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tcttgcagggttccggggagAcgaggaaccattccgttcgg	15	10	1	1			TCGA-RC-A6M5-01A-11D-A32G-10	TCGA-RC-A6M5-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bc57f84-c45f-45a1-9a62-0e2972598fa7	76a1244e-bd30-4dbb-95ee-857b135bb56e	g.chr8:2017578A>T	ENST00000262113.4	+	8	896	c.755A>T	c.(754-756)gAc>gTc	p.D252V	MYOM2_ENST00000523438.1_Intron	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	252					muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		TTCCGGGGAGACGAGGAACCA	0.517																																					p.D252V		Atlas-SNP	.											.	MYOM2	251	.	0			c.A755T						.						177	173	174					8																	2017578		2203	4300	6503	SO:0001583	missense	9172	exon8			GGGGAGACGAGGA		CCDS5957.1	8p23.3	2014-06-06	2012-10-17		ENSG00000036448	ENSG00000036448		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7614	protein-coding gene	gene with protein product		603509	"myomesin (M-protein) 2 (165kD)", "myomesin (M-protein) 2, 165kDa"				Standard	XM_006716237		Approved		uc003wpx.4	P54296	OTTHUMG00000129175	ENST00000262113.4:c.755A>T	chr8.hg19:g.2017578A>T	ENSP00000262113:p.Asp252Val	272.0	0.0		271.0	33.0	NM_003970	Q7Z3Y2	Missense_Mutation	SNP	ENST00000262113.4	hg19	CCDS5957.1	.	.	.	.	.	.	.	.	.	.	A	3.952	-0.012131	0.07727	.	.	ENSG00000036448	ENST00000262113	T	0.53423	0.62	5.4	5.4	0.78164	.	1.010530	0.07916	N	0.975015	T	0.44993	0.1320	L	0.44542	1.39	0.41865	D	0.990245	B	0.14805	0.011	B	0.10450	0.005	T	0.27571	-1.0070	10	0.72032	D	0.01	.	11.4081	0.49911	0.927:0.0:0.073:0.0	.	252	P54296	MYOM2_HUMAN	V	252	ENSP00000262113:D252V	ENSP00000262113:D252V	D	+	2	0	MYOM2	2004985	0.939000	0.31865	0.052000	0.19188	0.084000	0.17831	2.313000	0.43735	2.043000	0.60533	0.533000	0.62120	GAC	.	.		0.517	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970		T	2017578	A	T	2017578	3	4	334	1	0	0	0	0	1	0	0	0	10101	275	10	4	781	4	MYOM2	8	2017578	Missense_Mutation	SNP	A	TCGA-RC-A6M5-01A-11D-A32G-10		2017578	144346444	9	46538										
LONRF1	91694	hgsc.bcm.edu	37	chr8	12600698	12600698	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gccaatctggaagttgaaaaAgaactgcatttaaatcttct	7	7	3	2			TCGA-RC-A6M5-01A-11D-A32G-10	TCGA-RC-A6M5-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bc57f84-c45f-45a1-9a62-0e2972598fa7	76a1244e-bd30-4dbb-95ee-857b135bb56e	g.chr8:12600698A>C	ENST00000398246.3	-	2	884	c.815T>G	c.(814-816)cTt>cGt	p.L272R	LONRF1_ENST00000533751.1_5'UTR|LONRF1_ENST00000530693.1_5'UTR	NM_152271.3	NP_689484.3	Q17RB8	LONF1_HUMAN	LON peptidase N-terminal domain and ring finger 1	272							ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)|upper_aerodigestive_tract(2)	19				READ - Rectum adenocarcinoma(644;0.236)		AAGTTGAAAAAGAACTGCATT	0.338																																					p.L272R		Atlas-SNP	.											.	LONRF1	45	.	0			c.T815G						.						62	60	61					8																	12600698		1799	4056	5855	SO:0001583	missense	91694	exon2			TGAAAAAGAACTG	AK074329	CCDS5987.2	8p23.1	2013-01-09			ENSG00000154359	ENSG00000154359		"RING-type (C3HC4) zinc fingers"	26302	protein-coding gene	gene with protein product						18253036	Standard	XM_005273685		Approved	FLJ23749, RNF191	uc003wwd.1	Q17RB8	OTTHUMG00000165475	ENST00000398246.3:c.815T>G	chr8.hg19:g.12600698A>C	ENSP00000381298:p.Leu272Arg	216.0	0.0		222.0	20.0	NM_152271	B4DM29|B4DU84|Q8TEA0|Q9BSV1	Missense_Mutation	SNP	ENST00000398246.3	hg19	CCDS5987.2	.	.	.	.	.	.	.	.	.	.	A	17.36	3.368794	0.61624	.	.	ENSG00000154359	ENST00000398246	T	0.38887	1.11	5.04	5.04	0.67666	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.663946	0.12572	U	0.457252	T	0.39064	0.1064	L	0.34521	1.04	0.80722	D	1	D	0.54047	0.964	P	0.47044	0.535	T	0.12319	-1.0552	10	0.48119	T	0.1	-7.0354	10.7218	0.46044	0.9241:0.0:0.0759:0.0	.	272	Q17RB8	LONF1_HUMAN	R	272	ENSP00000381298:L272R	ENSP00000381298:L272R	L	-	2	0	LONRF1	12645069	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	2.737000	0.47393	2.202000	0.70862	0.533000	0.62120	CTT	.	.		0.338	LONRF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251693.2	NM_152271		C	12600698	A	C	12600698	3	2	334	1	0	0	0	0	1	0	0	0	8903	72	3	5	1550	5	LONRF1	8	12600698	Missense_Mutation	SNP	A	TCGA-RC-A6M5-01A-11D-A32G-10	10583120	12600698	133763324	10	46539										
SGCZ	137868	hgsc.bcm.edu	37	chr8	13948007	13948007	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aagtggaacctactcctgctGgagaaaggtaaagtttgcca	11	8	0	1			TCGA-RC-A6M5-01A-11D-A32G-10	TCGA-RC-A6M5-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bc57f84-c45f-45a1-9a62-0e2972598fa7	76a1244e-bd30-4dbb-95ee-857b135bb56e	g.chr8:13948007G>T	ENST00000382080.1	-	8	1599	c.884C>A	c.(883-885)cCa>cAa	p.P295Q	SGCZ_ENST00000421524.2_Missense_Mutation_p.P248Q	NM_139167.2	NP_631906.2	Q96LD1	SGCZ_HUMAN	sarcoglycan, zeta	282					membrane organization (GO:0061024)|muscle cell cellular homeostasis (GO:0046716)|muscle cell development (GO:0055001)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|sarcoglycan complex (GO:0016012)				NS(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(14)|lung(15)|ovary(2)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	47				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)		TACTCCTGCTGGAGAAAGGTA	0.498																																					p.P295Q		Atlas-SNP	.											.	SGCZ	96	.	0			c.C884A						.						175	159	164					8																	13948007		2203	4300	6503	SO:0001583	missense	137868	exon8			CCTGCTGGAGAAA	AY028700	CCDS5992.2	8p22	2014-09-17	2010-04-21		ENSG00000185053	ENSG00000185053			14075	protein-coding gene	gene with protein product		608113				12189167	Standard	XM_006716287		Approved	ZSG1	uc003wwq.3	Q96LD1	OTTHUMG00000090827	ENST00000382080.1:c.884C>A	chr8.hg19:g.13948007G>T	ENSP00000371512:p.Pro295Gln	66.0	0.0		66.0	5.0	NM_139167	Q6REU0	Missense_Mutation	SNP	ENST00000382080.1	hg19	CCDS5992.2	.	.	.	.	.	.	.	.	.	.	G	15.35	2.808692	0.50421	.	.	ENSG00000185053	ENST00000382080;ENST00000421524	D;D	0.93953	-3.32;-3.32	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	D	0.93936	0.8059	L	0.35414	1.06	0.50467	D	0.999871	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.89947	0.4077	10	0.08381	T	0.77	.	18.7556	0.91832	0.0:0.0:1.0:0.0	.	248;295	Q08AT0;Q96LD1-2	.;.	Q	295;248	ENSP00000371512:P295Q;ENSP00000405224:P248Q	ENSP00000371512:P295Q	P	-	2	0	SGCZ	13992378	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	6.179000	0.71974	2.760000	0.94817	0.655000	0.94253	CCA	.	.		0.498	SGCZ-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207636.2	NM_139167		T	13948007	G	T	13948007	3	4	334	1	0	0	0	0	1	0	0	0	14219	1348	47	3	58	3	SGCZ	8	13948007	Missense_Mutation	SNP	G	TCGA-RC-A6M5-01A-11D-A32G-10	1347309	13948007	132416015	11	46540										
MRC1	4360	hgsc.bcm.edu	37	chr10	18122743	18122743	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	aaaagctgccaacaacagaaCgctgagctcctgagcatcac	8	13	1	3			TCGA-RC-A6M5-01A-11D-A32G-10	TCGA-RC-A6M5-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bc57f84-c45f-45a1-9a62-0e2972598fa7	76a1244e-bd30-4dbb-95ee-857b135bb56e	g.chr10:18122743C>T	ENST00000239761.3	+	4	856	c.753C>T	c.(751-753)aaC>aaT	p.N251N		NM_002438.2	NP_002429.1	P22897	MRC1_HUMAN	mannose receptor, C type 1	251	C-type lectin 1. {ECO:0000255|PROSITE- ProRule:PRU00040}.				receptor-mediated endocytosis (GO:0006898)	cell surface (GO:0009986)|endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	mannose binding (GO:0005537)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|kidney(1)|lung(2)|prostate(1)|urinary_tract(1)	6						AACAACAGAACGCTGAGCTCC	0.438																																					p.N251N	GBM(115;1153 1594 28187 28781 35884)	Atlas-SNP	.											.	MRC1	13	.	0			c.C753T						.						80	77	78					10																	18122743		1600	3556	5156	SO:0001819	synonymous_variant	4360	exon4			ACAGAACGCTGAG	J05550	CCDS7123.1, CCDS7123.2	10p13	2014-04-10			ENSG00000120586	ENSG00000260314		"CD molecules", "C-type lectin domain containing"	7228	protein-coding gene	gene with protein product		153618	"mannose receptor, C type 1-like 1"	MRC1L1		1294118	Standard	NM_002438		Approved	CLEC13D, CD206, bA541I19.1, CLEC13DL	uc031ptj.1	P22897	OTTHUMG00000174646	ENST00000239761.3:c.753C>T	chr10.hg19:g.18122743C>T		181.0	0.0		189.0	18.0	NM_002438	A5PKW3|Q5VSJ2|Q5VSK2	Silent	SNP	ENST00000239761.3	hg19	CCDS7123.1																																																																																			.	.		0.438	MRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047057.1	NM_002438		T	18122743	C	T	18122743	2	4	334	1	0	0	0	0	0	0	0	1	9765	535	19	1		1	MRC1	10	18122743	Silent	SNP	C	TCGA-RC-A6M5-01A-11D-A32G-10		18122743	117412004	12	46541										
MKI67	4288	hgsc.bcm.edu	37	chr10	129903267	129903267	+	Frame_Shift_Del	DEL	C	C	-													0	0	1	0	0	0	1	1	0	ggagttcccataaatgctttCatgtctttctcatcacctcc							TCGA-RC-A6M5-01A-11D-A32G-10	TCGA-RC-A6M5-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bc57f84-c45f-45a1-9a62-0e2972598fa7	76a1244e-bd30-4dbb-95ee-857b135bb56e	g.chr10:129903267delC	ENST00000368654.3	-	13	7212	c.6837delG	c.(6835-6837)atgfs	p.M2279fs	MKI67_ENST00000368653.3_Frame_Shift_Del_p.M1919fs	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2279	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TAAATGCTTTCATGTCTTTCT	0.483																																					p.K2280fs		Atlas-Indel,Pindel	.											.	MKI67	363	.	0			c.6838delA						.						257	236	243					10																	129903267		2203	4300	6503	SO:0001589	frameshift_variant	4288	exon13			.	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 105"	176741	"antigen identified by monoclonal antibody Ki-67"			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.6837delG	chr10.hg19:g.129903267delC	ENSP00000357643:p.Met2279fs	198.0	0.0		202.0	23.0	NM_002417	Q5VWH2	Frame_Shift_Del	DEL	ENST00000368654.3	hg19	CCDS7659.1																																																																																			.	.		0.483	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		-	129903267	C	-	129903267	7	5	334	1	0	1	0	1	0	0	0	0	9607	826	29	0	2945	0	MKI67	10	129903267	Frame_Shift_Del	DEL	C	TCGA-RC-A6M5-01A-11D-A32G-10	111780524	129903267	5631480	13	46542										
FAM155A	728215	hgsc.bcm.edu	37	chr13	108518523	108518523	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctcggttgcccttgccgccgCcgccgccgccgtctcccggg	13	21	1	0			TCGA-RC-A6M5-01A-11D-A32G-10	TCGA-RC-A6M5-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bc57f84-c45f-45a1-9a62-0e2972598fa7	76a1244e-bd30-4dbb-95ee-857b135bb56e	g.chr13:108518523C>G	ENST00000375915.2	-	1	560	c.422G>C	c.(421-423)gGc>gCc	p.G141A		NM_001080396.2	NP_001073865.1	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A	141	Poly-Gly.					integral component of membrane (GO:0016021)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33						CTTGCCGCCGCCGCCGCCGCC	0.701																																					p.G141A		Atlas-SNP	.											.	FAM155A	82	.	0			c.G422C						.						6	10	9					13																	108518523		1737	3638	5375	SO:0001583	missense	728215	exon1			CCGCCGCCGCCGC	L10374	CCDS32006.1	13q33.3	2008-04-15			ENSG00000204442	ENSG00000204442			33877	protein-coding gene	gene with protein product							Standard	NM_001080396		Approved		uc001vql.3	B1AL88	OTTHUMG00000017326	ENST00000375915.2:c.422G>C	chr13.hg19:g.108518523C>G	ENSP00000365080:p.Gly141Ala	50.0	0.0		65.0	15.0	NM_001080396	B2RUV1|B7Z334	Missense_Mutation	SNP	ENST00000375915.2	hg19	CCDS32006.1	.	.	.	.	.	.	.	.	.	.	C	4.495	0.091725	0.08632	.	.	ENSG00000204442	ENST00000375915	.	.	.	3.47	2.59	0.31030	.	0.358947	0.20540	N	0.090335	T	0.26846	0.0657	L	0.41492	1.28	0.24195	N	0.995532	B	0.26483	0.15	B	0.17722	0.019	T	0.25745	-1.0123	9	0.05620	T	0.96	.	10.3731	0.44066	0.0:0.6119:0.3881:0.0	.	141	B1AL88	F155A_HUMAN	A	141	.	ENSP00000365080:G141A	G	-	2	0	FAM155A	107316524	1.000000	0.71417	0.997000	0.53966	0.083000	0.17756	1.425000	0.34859	0.385000	0.24970	0.655000	0.94253	GGC	.	.		0.701	FAM155A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045736.2	NM_001080396		G	108518523	C	G	108518523	3	3	334	1	0	0	0	0	1	0	0	0	5470	739	26	4	966	4	FAM155A	13	108518523	Missense_Mutation	SNP	C	TCGA-RC-A6M5-01A-11D-A32G-10		108518523	6651355	14	46543										
CDAN1	146059	hgsc.bcm.edu	37	chr15	43021296	43021296	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggcgcaaggagggcggctggTtgtggaaaaaggcctgggcg	21	7	0	0			TCGA-RC-A6M5-01A-11D-A32G-10	TCGA-RC-A6M5-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bc57f84-c45f-45a1-9a62-0e2972598fa7	76a1244e-bd30-4dbb-95ee-857b135bb56e	g.chr15:43021296T>C	ENST00000356231.3	-	19	2593	c.2570A>G	c.(2569-2571)aAc>aGc	p.N857S		NM_138477.2	NP_612486.2	Q8IWY9	CDAN1_HUMAN	codanin 1	857					chromatin assembly (GO:0031497)|chromatin organization (GO:0006325)|negative regulation of DNA replication (GO:0008156)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	24		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;2.49e-07)		GGGCGGCTGGTTGTGGAAAAA	0.587																																					p.N857S		Atlas-SNP	.											.	CDAN1	70	.	0			c.A2570G						.						74	77	76					15																	43021296		2203	4299	6502	SO:0001583	missense	146059	exon19			GGCTGGTTGTGGA	AF525398	CCDS32209.1	15q15.2	2012-04-25	2012-04-25			ENSG00000140326			1713	protein-coding gene	gene with protein product		607465	"congenital dyserythropoietic anemia, type I"			8634422, 12434312	Standard	XM_005254177		Approved	CDA-I, CDAI	uc001zql.3	Q8IWY9		ENST00000356231.3:c.2570A>G	chr15.hg19:g.43021296T>C	ENSP00000348564:p.Asn857Ser	55.0	0.0		69.0	6.0	NM_138477	Q6NYD0|Q7Z7L5|Q969N3	Missense_Mutation	SNP	ENST00000356231.3	hg19	CCDS32209.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.628326	0.87560	.	.	ENSG00000140326	ENST00000356231;ENST00000267892	T	0.76060	-0.99	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.79246	0.4413	L	0.42686	1.345	0.58432	D	0.999997	D;D	0.69078	0.997;0.974	P;P	0.60789	0.879;0.736	T	0.79107	-0.1939	10	0.41790	T	0.15	-17.1404	15.0056	0.71510	0.0:0.0:0.0:1.0	.	857;855	Q8IWY9;C9K0H8	CDAN1_HUMAN;.	S	857;855	ENSP00000348564:N857S	ENSP00000267892:N855S	N	-	2	0	CDAN1	40808588	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	7.646000	0.83445	1.947000	0.56498	0.379000	0.24179	AAC	.	.		0.587	CDAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431103.1	XM_085300		C	43021296	T	C	43021296	3	2	334	1	0	0	0	0	1	0	0	0	3056	1725	60	2	1153	2	CDAN1	15	43021296	Missense_Mutation	SNP	T	TCGA-RC-A6M5-01A-11D-A32G-10		43021296	59510096	15	46544										
LRRK1	79705	hgsc.bcm.edu	37	chr15	101608980	101608980	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctggaggggctggggcgccaGggagttcgacattttctacc	16	10	1	0			TCGA-RC-A6M5-01A-11D-A32G-10	TCGA-RC-A6M5-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bc57f84-c45f-45a1-9a62-0e2972598fa7	76a1244e-bd30-4dbb-95ee-857b135bb56e	g.chr15:101608980G>A	ENST00000388948.3	+	34	6334	c.5975G>A	c.(5974-5976)aGg>aAg	p.R1992K	LRRK1_ENST00000532145.1_3'UTR|LRRK1_ENST00000284395.5_Missense_Mutation_p.R1989K|RP11-505E24.2_ENST00000559857.1_RNA	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1											breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			TGGGGCGCCAGGGAGTTCGAC	0.562																																					p.R1992K		Atlas-SNP	.											.	LRRK1	310	.	0			c.G5975A						.						74	88	83					15																	101608980		2034	4171	6205	SO:0001583	missense	79705	exon34			GCGCCAGGGAGTT	AB058693	CCDS42086.1	15q26.3	2007-01-29			ENSG00000154237	ENSG00000154237			18608	protein-coding gene	gene with protein product		610986				11347906, 14654223	Standard	XM_005254979		Approved	FLJ23119, KIAA1790, Roco1, RIPK6	uc002bwr.3	Q38SD2	OTTHUMG00000165514	ENST00000388948.3:c.5975G>A	chr15.hg19:g.101608980G>A	ENSP00000373600:p.Arg1992Lys	96.0	0.0		112.0	8.0	NM_024652		Missense_Mutation	SNP	ENST00000388948.3	hg19	CCDS42086.1	.	.	.	.	.	.	.	.	.	.	G	16.52	3.146675	0.57151	.	.	ENSG00000154237	ENST00000388948;ENST00000284395	T;T	0.72615	-0.64;-0.67	5.83	3.97	0.46021	.	0.250821	0.38720	N	0.001581	T	0.62563	0.2438	L	0.54323	1.7	0.23101	N	0.9983	B	0.06786	0.001	B	0.06405	0.002	T	0.53634	-0.8411	10	0.39692	T	0.17	.	8.6962	0.34298	0.2843:0.0:0.7157:0.0	.	1992	Q38SD2	LRRK1_HUMAN	K	1992;1989	ENSP00000373600:R1992K;ENSP00000284395:R1989K	ENSP00000284395:R1989K	R	+	2	0	LRRK1	99426503	0.738000	0.28186	0.988000	0.46212	0.994000	0.84299	0.574000	0.23714	0.818000	0.34468	0.655000	0.94253	AGG	.	.		0.562	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652		A	101608980	G	A	101608980	3	1	334	1	0	0	0	0	1	0	0	0	9041	1000	35	3	6105	3	LRRK1	15	101608980	Missense_Mutation	SNP	G	TCGA-RC-A6M5-01A-11D-A32G-10	58587684	101608980	922412	16	46545										
MYH11	4629	hgsc.bcm.edu	37	chr16	15815347	15815347	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tttgagcattttgttggtccGctcgagttcctctttggctt	10	9	1	1	rs144823441		TCGA-RC-A6M5-01A-11D-A32G-10	TCGA-RC-A6M5-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bc57f84-c45f-45a1-9a62-0e2972598fa7	76a1244e-bd30-4dbb-95ee-857b135bb56e	g.chr16:15815347G>T	ENST00000300036.5	-	32	4619	c.4510C>A	c.(4510-4512)Cgg>Agg	p.R1504R	NDE1_ENST00000396354.1_Intron|NDE1_ENST00000342673.5_Intron|MYH11_ENST00000452625.2_Silent_p.R1511R|MYH11_ENST00000576790.2_Silent_p.R1504R|NDE1_ENST00000396355.1_Intron|MYH11_ENST00000396324.3_Silent_p.R1511R	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	1504					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						TTGTTGGTCCGCTCGAGTTCC	0.562			T	CBFB	AML																																p.R1511R		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"myosin, heavy polypeptide 11, smooth muscle"		L	MYH11_ENST00000396324,colon,carcinoma,0,2	MYH11	520	.	0			c.C4531A						.						115	102	106					16																	15815347		2197	4300	6497	SO:0001819	synonymous_variant	4629	exon33			TGGTCCGCTCGAG	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"Myosins / Myosin superfamily : Class II"	7569	protein-coding gene	gene with protein product		160745	"myosin, heavy polypeptide 11, smooth muscle"			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.4510C>A	chr16.hg19:g.15815347G>T		175.0	0.0		182.0	31.0	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Silent	SNP	ENST00000300036.5	hg19	CCDS10565.1																																																																																			.	G|1.000;A|0.000		0.562	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113		T	15815347	G	T	15815347	2	4	334	1	0	0	0	0	0	0	0	1	10040	1086	38	1		1	MYH11	16	15815347	Silent	SNP	G	TCGA-RC-A6M5-01A-11D-A32G-10		15815347	74539406	17	46546										
PCSK4	54760	hgsc.bcm.edu	37	chr19	1487019	1487019	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gttgtcgtagtgcaggccgcCgttgcccgaggcccagatga	15	12	0	2			TCGA-RC-A6M5-01A-11D-A32G-10	TCGA-RC-A6M5-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bc57f84-c45f-45a1-9a62-0e2972598fa7	76a1244e-bd30-4dbb-95ee-857b135bb56e	g.chr19:1487019C>T	ENST00000300954.5	-	8	962	c.901G>A	c.(901-903)Ggc>Agc	p.G301S	CTB-25B13.6_ENST00000585643.1_RNA|PCSK4_ENST00000587784.1_5'Flank	NM_017573.3	NP_060043.2			proprotein convertase subtilisin/kexin type 4											cervix(2)|endometrium(2)|kidney(1)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	15		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGCAGGCCGCCGTTGCCCGAG	0.711																																					p.G301S		Atlas-SNP	.											.	PCSK4	44	.	0			c.G901A						.						66	56	60					19																	1487019		2203	4299	6502	SO:0001583	missense	54760	exon8			GGCCGCCGTTGCC	AK057235	CCDS12069.2	19p13.3	2008-02-05			ENSG00000115257	ENSG00000115257			8746	protein-coding gene	gene with protein product		600487				7782070	Standard	XM_005259586		Approved	PC4, SPC5, DKFZp434B217, MGC34749	uc002ltb.1	Q6UW60	OTTHUMG00000128541	ENST00000300954.5:c.901G>A	chr19.hg19:g.1487019C>T	ENSP00000300954:p.Gly301Ser	50.0	0.0		69.0	4.0	NM_017573		Missense_Mutation	SNP	ENST00000300954.5	hg19	CCDS12069.2	.	.	.	.	.	.	.	.	.	.	C	21.5	4.152669	0.78001	.	.	ENSG00000115257	ENST00000300954;ENST00000441747	T	0.80909	-1.43	3.08	3.08	0.35506	Peptidase S8/S53, subtilisin/kexin/sedolisin (3);	0.000000	0.50627	U	0.000114	D	0.87378	0.6162	M	0.68728	2.09	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.88684	0.3204	10	0.87932	D	0	.	13.0304	0.58839	0.0:1.0:0.0:0.0	.	301;113	Q6UW60;B3KQ28	PCSK4_HUMAN;.	S	301;113	ENSP00000300954:G301S	ENSP00000300954:G301S	G	-	1	0	PCSK4	1438019	1.000000	0.71417	0.999000	0.59377	0.462000	0.32619	5.804000	0.69135	1.434000	0.47414	0.491000	0.48974	GGC	.	.		0.711	PCSK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449703.1	NM_017573		T	1487019	C	T	1487019	3	4	334	1	0	0	0	0	1	0	0	0	11611	652	23	1	1398	1	PCSK4	19	1487019	Missense_Mutation	SNP	C	TCGA-RC-A6M5-01A-11D-A32G-10		1487019	57641964	18	46547										
ZFR2	23217	hgsc.bcm.edu	37	chr19	3806099	3806099	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	caggaccttgtgggtctgccGgaaggccagcattcgcaggg	16	11	1	0			TCGA-RC-A6M5-01A-11D-A32G-10	TCGA-RC-A6M5-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bc57f84-c45f-45a1-9a62-0e2972598fa7	76a1244e-bd30-4dbb-95ee-857b135bb56e	g.chr19:3806099G>A	ENST00000262961.4	-	19	2678	c.2668C>T	c.(2668-2670)Cgg>Tgg	p.R890W		NM_015174.1	NP_055989.1	Q9UPR6	ZFR2_HUMAN	zinc finger RNA binding protein 2	890	DZF. {ECO:0000255|PROSITE- ProRule:PRU01040}.						nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(5)|pancreas(1)|prostate(1)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00514)|STAD - Stomach adenocarcinoma(1328;0.19)		TGGGTCTGCCGGAAGGCCAGC	0.706																																					p.R890W		Atlas-SNP	.											.	ZFR2	63	.	0			c.C2668T						.						8	11	10					19																	3806099		1968	4122	6090	SO:0001583	missense	23217	exon19			TCTGCCGGAAGGC	AB029009	CCDS45921.1, CCDS45922.1	19p13.3	2012-10-05	2008-03-25	2008-03-25	ENSG00000105278	ENSG00000105278			29189	protein-coding gene	gene with protein product			"KIAA1086"	KIAA1086		10470851	Standard	NM_015174		Approved		uc002lyw.2	Q9UPR6	OTTHUMG00000180918	ENST00000262961.4:c.2668C>T	chr19.hg19:g.3806099G>A	ENSP00000262961:p.Arg890Trp	69.0	0.0		88.0	10.0	NM_015174		Missense_Mutation	SNP	ENST00000262961.4	hg19	CCDS45921.1	.	.	.	.	.	.	.	.	.	.	G	13.70	2.315727	0.40996	.	.	ENSG00000105278	ENST00000262961	T	0.42131	0.98	3.42	0.39	0.16275	DZF (2);	0.000000	0.64402	U	0.000010	T	0.62768	0.2455	M	0.87180	2.865	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.63655	-0.6588	10	0.87932	D	0	-27.2308	8.1182	0.30955	0.0:0.0:0.4064:0.5936	.	890	Q9UPR6	ZFR2_HUMAN	W	890	ENSP00000262961:R890W	ENSP00000262961:R890W	R	-	1	2	ZFR2	3757099	1.000000	0.71417	0.998000	0.56505	0.136000	0.21042	0.971000	0.29396	0.229000	0.21039	0.643000	0.83706	CGG	.	.		0.706	ZFR2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453648.2	NM_015174		A	3806099	G	A	3806099	3	1	334	1	0	0	0	0	1	0	0	0	17675	1115	39	1	155	1	ZFR2	19	3806099	Missense_Mutation	SNP	G	TCGA-RC-A6M5-01A-11D-A32G-10	2319080	3806099	55322884	19	46548										
ZNF700	90592	hgsc.bcm.edu	37	chr19	12059950	12059950	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gtaagatatgtgggaaaggcTtttattctgccaagtcattt	10	5	2	1			TCGA-RC-A6M5-01A-11D-A32G-10	TCGA-RC-A6M5-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bc57f84-c45f-45a1-9a62-0e2972598fa7	76a1244e-bd30-4dbb-95ee-857b135bb56e	g.chr19:12059950T>C	ENST00000254321.5	+	4	1254	c.1111T>C	c.(1111-1113)Ttt>Ctt	p.F371L	ZNF763_ENST00000538752.1_Intron|ZNF700_ENST00000482090.1_Missense_Mutation_p.F353L|ZNF763_ENST00000590798.1_Intron|CTD-2006C1.12_ENST00000586394.1_RNA|ZNF763_ENST00000591944.1_Intron	NM_001271848.1|NM_144566.1	NP_001258777.1|NP_653167.1	Q9H0M5	ZN700_HUMAN	zinc finger protein 700	371					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)		ZNF700/MAST1_ENST00000251472(2)	breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(13)|pancreas(1)|prostate(1)|urinary_tract(1)	33						TGGGAAAGGCTTTTATTCTGC	0.363																																					p.F374L		Atlas-SNP	.											.	ZNF700	81	.	0			c.T1120C						.						58	62	61					19																	12059950		2203	4299	6502	SO:0001583	missense	90592	exon4			AAAGGCTTTTATT	AL136732	CCDS32915.1, CCDS74289.1	19p13.2	2013-01-08			ENSG00000196757	ENSG00000196757		"Zinc fingers, C2H2-type", "-"	25292	protein-coding gene	gene with protein product							Standard	NM_144566		Approved	DKFZp434I1610	uc031rjk.1	Q9H0M5	OTTHUMG00000156421	ENST00000254321.5:c.1111T>C	chr19.hg19:g.12059950T>C	ENSP00000254321:p.Phe371Leu	69.0	0.0		68.0	9.0	NM_001271848	B9EGU4	Missense_Mutation	SNP	ENST00000254321.5	hg19	CCDS32915.1	.	.	.	.	.	.	.	.	.	.	t	15.68	2.904734	0.52333	.	.	ENSG00000196757	ENST00000254321	T	0.46063	0.88	0.672	0.672	0.17935	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.64427	0.2597	M	0.89601	3.045	0.09310	N	1	D	0.89917	1.0	D	0.80764	0.994	T	0.50021	-0.8876	9	0.66056	D	0.02	.	5.5733	0.17208	0.0:0.0:0.0:1.0	.	371	Q9H0M5	ZN700_HUMAN	L	371	ENSP00000254321:F371L	ENSP00000254321:F371L	F	+	1	0	ZNF700	11920950	0.560000	0.26570	0.003000	0.11579	0.526000	0.34562	1.795000	0.38784	0.524000	0.28502	0.254000	0.18369	TTT	.	.		0.363	ZNF700-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344126.2	NM_144566		C	12059950	T	C	12059950	3	2	334	1	0	0	0	0	1	0	0	0	18119	1609	56	2	1125	2	ZNF700	19	12059950	Missense_Mutation	SNP	T	TCGA-RC-A6M5-01A-11D-A32G-10	8253851	12059950	47069033	20	46549										
LGALS2	3957	hgsc.bcm.edu	37	chr22	37966624	37966626	+	In_Frame_Del	DEL	GTT	GTT	-													0	0	1	0	0	0	1	1	0	gaagcacaggtgatcttcccGttgttcttgcccccagttgc					rs144405269	byFrequency	TCGA-RC-A6M5-01A-11D-A32G-10	TCGA-RC-A6M5-10A-01D-A32G-10	GTT	GTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bc57f84-c45f-45a1-9a62-0e2972598fa7	76a1244e-bd30-4dbb-95ee-857b135bb56e	g.chr22:37966624_37966626delGTT	ENST00000215886.4	-	3	380_382	c.206_208delAAC	c.(205-210)caacgg>cgg	p.Q69del		NM_006498.2	NP_006489.1	P05162	LEG2_HUMAN	lectin, galactoside-binding, soluble, 2	69	Beta-galactoside binding. {ECO:0000255}.|Galectin. {ECO:0000255|PROSITE- ProRule:PRU00639}.						carbohydrate binding (GO:0030246)|galactoside binding (GO:0016936)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|stomach(1)	11	Melanoma(58;0.0574)					TGATCTTCCCGTTGTTCTTGCCC	0.576																																					p.69_70del	GBM(193;1840 2185 13711 20676 24505)	Atlas-INDEL	.											.	LGALS2	16	.	0			c.207_209del						.																																			SO:0001651	inframe_deletion	3957	exon3			.		CCDS13950.1	22q13.1	2011-08-04	2007-02-01		ENSG00000100079	ENSG00000100079		"Lectins, galactoside-binding"	6562	protein-coding gene	gene with protein product	"galectin 2"	150571				1988031, 15356130	Standard	NM_006498		Approved	HL14	uc003ata.3	P05162	OTTHUMG00000150590	ENST00000215886.4:c.206_208delAAC	chr22.hg19:g.37966627_37966629delGTT	ENSP00000215886:p.Gln69del	122.0	0.0		135.0	11.0	NM_006498	Q6FGY4	In_Frame_Del	DEL	ENST00000215886.4	hg19	CCDS13950.1																																																																																			.	.		0.576	LGALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318991.1	NM_006498		-	37966626	GTT	-	37966624	7	5	334	1	0	1	0	1	0	0	0	0	8751	1144	40	0	198	0	LGALS2	22	37966624	In_Frame_Del	DEL	GTT	TCGA-RC-A6M5-01A-11D-A32G-10		37966624	13337942	21	46550										
NUP50	10762	hgsc.bcm.edu	37	chr22	45580526	45580526	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	caaaattttactggagaaaaAggatgcctgaacacgcaaag	9	7	0	2			TCGA-RC-A6M5-01A-11D-A32G-10	TCGA-RC-A6M5-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bc57f84-c45f-45a1-9a62-0e2972598fa7	76a1244e-bd30-4dbb-95ee-857b135bb56e	g.chr22:45580526A>G	ENST00000347635.4	+	8	1863	c.1397A>G	c.(1396-1398)aAg>aGg	p.K466R	NUP50_ENST00000396096.2_Missense_Mutation_p.K438R|NUP50_ENST00000425733.2_Missense_Mutation_p.K216R|NUP50_ENST00000407019.2_Missense_Mutation_p.K438R	NM_007172.3	NP_009103.2	Q9UKX7	NUP50_HUMAN	nucleoporin 50kDa	466	RanBD1. {ECO:0000255|PROSITE- ProRule:PRU00164}.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|intracellular transport (GO:0046907)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	9		Ovarian(80;0.00965)|all_neural(38;0.0244)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		CTGGAGAAAAAGGATGCCTGA	0.458																																					p.K466R		Atlas-SNP	.											.	NUP50	24	.	0			c.A1397G						.						41	41	41					22																	45580526		2203	4300	6503	SO:0001583	missense	10762	exon8			AGAAAAAGGATGC	AF107840	CCDS14062.1, CCDS14063.1	22q13.3	2007-01-22	2002-08-29		ENSG00000093000	ENSG00000093000			8065	protein-coding gene	gene with protein product		604646	"nucleoporin 50kD"	NPAP60L		10449902	Standard	XM_005261312		Approved		uc003bfr.3	Q9UKX7	OTTHUMG00000151265	ENST00000347635.4:c.1397A>G	chr22.hg19:g.45580526A>G	ENSP00000345895:p.Lys466Arg	155.0	0.0		118.0	7.0	NM_007172	B1AHA4|B2RB15|O75644|Q8N6V5|Q9NPM9|Q9NPR6|Q9P1K5	Missense_Mutation	SNP	ENST00000347635.4	hg19	CCDS14062.1	.	.	.	.	.	.	.	.	.	.	A	13.01	2.110274	0.37242	.	.	ENSG00000093000	ENST00000347635;ENST00000407019;ENST00000425733;ENST00000396096	.	.	.	5.22	1.93	0.25924	Pleckstrin homology-type (1);Ran binding protein 1 (1);	0.093789	0.64402	N	0.000001	T	0.53899	0.1825	L	0.53780	1.695	0.47819	D	0.999523	B	0.06786	0.001	B	0.22880	0.042	T	0.43556	-0.9384	9	0.37606	T	0.19	-17.884	9.2235	0.37390	0.7909:0.0:0.2091:0.0	.	466	Q9UKX7	NUP50_HUMAN	R	466;438;216;438	.	ENSP00000345895:K466R	K	+	2	0	NUP50	43959190	1.000000	0.71417	0.227000	0.23927	0.733000	0.41908	5.978000	0.70501	0.073000	0.16731	-0.274000	0.10170	AAG	.	.		0.458	NUP50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321993.2			G	45580526	A	G	45580526	3	3	334	1	0	0	0	0	1	0	0	0	10775	72	3	2	1423	2	NUP50	22	45580526	Missense_Mutation	SNP	A	TCGA-RC-A6M5-01A-11D-A32G-10	7613902	45580526	5724040	22	46551										
ZBTB48	3104	hgsc.bcm.edu	37	chr1	6642352	6642352	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gcaaatattatctaaaagtcCacaacaggtaaacgttctgt	6	8	2	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:6642352C>T	ENST00000377674.4	+	3	1083	c.925C>T	c.(925-927)Cac>Tac	p.H309Y		NM_001278647.1|NM_001278648.1|NM_005341.2	NP_001265576.1|NP_001265577.1|NP_005332.1	P10074	ZBT48_HUMAN	zinc finger and BTB domain containing 48	309					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	11	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;7.39e-28)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;1.35e-07)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(304;0.00109)|STAD - Stomach adenocarcinoma(132;0.017)|READ - Rectum adenocarcinoma(331;0.0642)		TCTAAAAGTCCACAACAGGTA	0.493																																					p.H309Y	Esophageal Squamous(125;1449 1657 4031 29866 49542)	Atlas-SNP	.											.	ZBTB48	33	.	0			c.C925T						.						80	87	84					1																	6642352		2203	4300	6503	SO:0001583	missense	3104	exon3			AAAGTCCACAACA	BC013573	CCDS84.1	1p36.3	2013-01-08	2006-09-20	2006-09-20	ENSG00000204859	ENSG00000204859		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	4930	protein-coding gene	gene with protein product		165270	"GLI-Kruppel family member HKR3"	HKR3		2850480, 8661141	Standard	NM_001278647		Approved	ZNF855	uc001anx.3	P10074	OTTHUMG00000001438	ENST00000377674.4:c.925C>T	chr1.hg19:g.6642352C>T	ENSP00000366902:p.His309Tyr	84.0	0.0		63.0	27.0	NM_005341	Q5SY19	Missense_Mutation	SNP	ENST00000377674.4	hg19	CCDS84.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.368859	0.82463	.	.	ENSG00000204859	ENST00000319084;ENST00000377674	T;D	0.86769	0.44;-2.17	5.52	5.52	0.82312	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.90270	0.6957	M	0.83384	2.64	0.80722	D	1	B	0.32968	0.392	B	0.38842	0.283	D	0.90571	0.4522	10	0.87932	D	0	-27.4086	18.4319	0.90628	0.0:1.0:0.0:0.0	.	309	P10074	ZBT48_HUMAN	Y	309	ENSP00000313416:H309Y;ENSP00000366902:H309Y	ENSP00000313416:H309Y	H	+	1	0	ZBTB48	6564939	1.000000	0.71417	0.997000	0.53966	0.988000	0.76386	5.336000	0.65935	2.600000	0.87896	0.561000	0.74099	CAC	.	.		0.493	ZBTB48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004193.1	NM_005341		T	6642352	C	T	6642352	3	4	335	1	0	0	0	0	1	0	0	0	17564	594	21	3	931	3	ZBTB48	1	6642352	Missense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10		6642352	242608269	1	46552										
KIF1B	23095	hgsc.bcm.edu	37	chr1	10408742	10408742	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	atcacagtgaccattatccaTgagaaggggagcgagctcca	11	10	1	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:10408742T>A	ENST00000377086.1	+	37	4102	c.3900T>A	c.(3898-3900)caT>caA	p.H1300Q	KIF1B_ENST00000263934.6_Missense_Mutation_p.H1254Q|KIF1B_ENST00000465635.1_3'UTR|KIF1B_ENST00000377081.1_Missense_Mutation_p.H1300Q			O60333	KIF1B_HUMAN	kinesin family member 1B	1300					anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		CCATTATCCATGAGAAGGGGA	0.453																																					p.H1254Q		Atlas-SNP	.											.	KIF1B	242	.	0			c.T3762A						.						138	106	116					1																	10408742		2203	4300	6503	SO:0001583	missense	23095	exon35			TATCCATGAGAAG	AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"Kinesins", "Pleckstrin homology (PH) domain containing"	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.3900T>A	chr1.hg19:g.10408742T>A	ENSP00000366290:p.His1300Gln	78.0	0.0		79.0	25.0	NM_015074	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Missense_Mutation	SNP	ENST00000377086.1	hg19		.	.	.	.	.	.	.	.	.	.	T	22.7	4.319781	0.81469	.	.	ENSG00000054523	ENST00000355249;ENST00000263934;ENST00000377086;ENST00000377081	T;T;T	0.75367	-0.85;-0.93;-0.93	5.52	-3.19	0.05171	.	0.000000	0.85682	D	0.000000	D	0.84911	0.5577	M	0.88640	2.97	0.58432	D	0.999994	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;1.0;0.96	D;D;D;D;D;D	0.97110	1.0;0.999;0.999;0.999;0.999;0.962	D	0.84182	0.0440	10	0.44086	T	0.13	.	13.1574	0.59524	0.0:0.4586:0.0:0.5414	.	1286;1260;1300;1274;1300;1254	Q4R9M9;Q4R9M7;Q4VXC4;Q4R9M8;O60333;O60333-2	.;.;.;.;KIF1B_HUMAN;.	Q	1300;1254;1300;1300	ENSP00000263934:H1254Q;ENSP00000366290:H1300Q;ENSP00000366284:H1300Q	ENSP00000263934:H1254Q	H	+	3	2	KIF1B	10331329	0.014000	0.17966	0.989000	0.46669	0.996000	0.88848	-0.903000	0.04084	-0.526000	0.06383	-0.256000	0.11100	CAT	.	.		0.453	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1			A	10408742	T	A	10408742	3	1	335	1	0	0	0	0	1	0	0	0	8293	1461	51	4	5385	4	KIF1B	1	10408742	Missense_Mutation	SNP	T	TCGA-RC-A6M6-01A-11D-A32G-10	3766390	10408742	238841879	2	46553										
CELA2A	63036	hgsc.bcm.edu	37	chr1	15788106	15788106	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tggtaccacacctgcggaggGtccctgatagccaacagctg	12	13	0	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:15788106G>T	ENST00000359621.4	+	3	205	c.180G>T	c.(178-180)ggG>ggT	p.G60G		NM_033440.2	NP_254275.1	P08217	CEL2A_HUMAN	chymotrypsin-like elastase family, member 2A	60	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)|keratohyalin granule (GO:0036457)	serine hydrolase activity (GO:0017171)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)|ovary(2)|prostate(1)	16						CCTGCGGAGGGTCCCTGATAG	0.592																																					p.G60G		Atlas-SNP	.											.	CELA2A	32	.	0			c.G180T						.						121	106	111					1																	15788106		2203	4300	6503	SO:0001819	synonymous_variant	63036	exon3			CGGAGGGTCCCTG		CCDS157.1	1p36.21	2009-07-09			ENSG00000142615	ENSG00000142615	3.4.21.71		24609	protein-coding gene	gene with protein product	"elastase 2A"	609443				3646943, 2834346	Standard	NM_033440		Approved	ELA2A	uc001awk.3	P08217	OTTHUMG00000002258	ENST00000359621.4:c.180G>T	chr1.hg19:g.15788106G>T		142.0	0.0		122.0	39.0	NM_033440	B2R5I4|Q14243	Silent	SNP	ENST00000359621.4	hg19	CCDS157.1																																																																																			.	.		0.592	CELA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006445.1	NM_033440		T	15788106	G	T	15788106	2	4	335	1	0	0	0	0	0	0	0	1	3213	1248	44	3		3	CELA2A	1	15788106	Silent	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	5379364	15788106	233462515	3	46554										
EIF2C4	192670	hgsc.bcm.edu	37	chr1	36292423	36292423	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gtaatgtgactagacggccaGccagtcatcaaacgtatgtt	10	9	2	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:36292423G>T	ENST00000373210.3	+	7	1080	c.835G>T	c.(835-837)Gcc>Tcc	p.A279S		NM_017629.3	NP_060099.2	Q9HCK5	AGO4_HUMAN	argonaute RISC catalytic component 4	279	PAZ. {ECO:0000255|HAMAP-Rule:MF_03033}.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA catabolic process (GO:0006402)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|RISC complex (GO:0016442)	miRNA binding (GO:0035198)										TAGACGGCCAGCCAGTCATCA	0.358																																					p.A279S		Atlas-SNP	.											.	.	.	.	0			c.G835T						.						81	69	73					1																	36292423		2203	4300	6503	SO:0001583	missense	192670	exon7			CGGCCAGCCAGTC	AB046787	CCDS397.1	1p34	2013-02-15	2013-02-15	2013-02-15	ENSG00000134698	ENSG00000134698		"Argonaute/PIWI family"	18424	protein-coding gene	gene with protein product	"argonaute 4"	607356	"eukaryotic translation initiation factor 2C, 4"	EIF2C4		12906857	Standard	NM_017629		Approved	hAGO4, KIAA1567, FLJ20033	uc001bzj.2	Q9HCK5	OTTHUMG00000004243	ENST00000373210.3:c.835G>T	chr1.hg19:g.36292423G>T	ENSP00000362306:p.Ala279Ser	59.0	0.0		47.0	25.0	NM_017629	A7MD27	Missense_Mutation	SNP	ENST00000373210.3	hg19	CCDS397.1	.	.	.	.	.	.	.	.	.	.	G	33	5.259789	0.95368	.	.	ENSG00000134698	ENST00000373210	T	0.08720	3.06	5.66	5.66	0.87406	Argonaute/Dicer protein, PAZ (4);	0.217896	0.47093	N	0.000245	T	0.34687	0.0906	M	0.82193	2.58	0.80722	D	1	B	0.20671	0.047	P	0.50617	0.646	T	0.17684	-1.0361	10	0.56958	D	0.05	-1.4061	18.4995	0.90876	0.0:0.0:1.0:0.0	.	279	Q9HCK5	AGO4_HUMAN	S	279	ENSP00000362306:A279S	ENSP00000362306:A279S	A	+	1	0	EIF2C4	36065010	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.679000	0.98649	2.673000	0.90976	0.585000	0.79938	GCC	.	.		0.358	AGO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012213.3	NM_017629		T	36292423	G	T	36292423	3	4	335	1	0	0	0	0	1	0	0	0	5010	971	34	3	861	3	EIF2C4	1	36292423	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	20504317	36292423	212958198	4	46555										
HPDL	84842	hgsc.bcm.edu	37	chr1	45793225	45793225	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	agcctgaccttgctggagcgCgctggctaccgcggaccctt	13	15	0	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:45793225C>T	ENST00000334815.3	+	1	681	c.405C>T	c.(403-405)cgC>cgT	p.R135R		NM_032756.2	NP_116145.1	Q96IR7	HPDL_HUMAN	4-hydroxyphenylpyruvate dioxygenase-like	135					aromatic amino acid family metabolic process (GO:0009072)		4-hydroxyphenylpyruvate dioxygenase activity (GO:0003868)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4	Acute lymphoblastic leukemia(166;0.155)					TGCTGGAGCGCGCTGGCTACC	0.716																																					p.R135R		Atlas-SNP	.											.	HPDL	14	.	0			c.C405T						.						15	14	14					1																	45793225		2182	4260	6442	SO:0001819	synonymous_variant	84842	exon1			GGAGCGCGCTGGC	BC007293	CCDS519.1	1p34.1	2008-02-05	2007-03-14	2007-03-14	ENSG00000186603	ENSG00000186603			28242	protein-coding gene	gene with protein product			"glyoxalase domain containing 1"	GLOXD1		12477932	Standard	NM_032756		Approved	MGC15668, 4-HPPD-L	uc001cne.3	Q96IR7	OTTHUMG00000007681	ENST00000334815.3:c.405C>T	chr1.hg19:g.45793225C>T		80.0	0.0		104.0	40.0	NM_032756	B2R9B0	Silent	SNP	ENST00000334815.3	hg19	CCDS519.1																																																																																			.	.		0.716	HPDL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020527.1	NM_032756		T	45793225	C	T	45793225	2	4	335	1	0	0	0	0	0	0	0	1	7342	755	27	1		1	HPDL	1	45793225	Silent	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	9500802	45793225	203457396	5	46556										
NPR1	4881	hgsc.bcm.edu	37	chr1	153653014	153653014	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tcccctgatgccttcagaacCctcatgctcctggccctgga	8	17	2	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:153653014C>T	ENST00000368680.3	+	2	1231	c.759C>T	c.(757-759)acC>acT	p.T253T		NM_000906.3	NP_000897.3	P16066	ANPRA_HUMAN	natriuretic peptide receptor 1	253					body fluid secretion (GO:0007589)|cell surface receptor signaling pathway (GO:0007166)|cGMP biosynthetic process (GO:0006182)|dopamine metabolic process (GO:0042417)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cGMP biosynthetic process (GO:0030828)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|regulation of blood vessel size (GO:0050880)|regulation of vascular permeability (GO:0043114)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|G-protein coupled peptide receptor activity (GO:0008528)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(17)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)		Amyl Nitrite(DB01612)|Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Nesiritide(DB04899)|Nitroglycerin(DB00727)|Nitroprusside(DB00325)	CCTTCAGAACCCTCATGCTCC	0.552																																					p.T253T	Pancreas(141;1349 1870 15144 15830 40702)	Atlas-SNP	.											.	NPR1	104	.	0			c.C759T						.						121	108	112					1																	153653014		2203	4300	6503	SO:0001819	synonymous_variant	4881	exon2			CAGAACCCTCATG	BC063304	CCDS1051.1	1q21-q22	2014-03-03	2014-03-03		ENSG00000169418	ENSG00000169418			7943	protein-coding gene	gene with protein product	"guanylate cyclase A"	108960	"atrionatriuretic peptide receptor A", "natriuretic peptide receptor A"	ANPRA, NPRA		1979052	Standard	NM_000906		Approved	GUCY2A, ANPa	uc001fcs.4	P16066	OTTHUMG00000037085	ENST00000368680.3:c.759C>T	chr1.hg19:g.153653014C>T		88.0	0.0		97.0	82.0	NM_000906	B0ZBF0|Q5SR08|Q6P4Q3	Silent	SNP	ENST00000368680.3	hg19	CCDS1051.1																																																																																			.	.		0.552	NPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090034.1	NM_000906		T	153653014	C	T	153653014	2	4	335	1	0	0	0	0	0	0	0	1	10603	610	22	3		3	NPR1	1	153653014	Silent	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	107859789	153653014	95597607	6	46557										
OR6K2	81448	hgsc.bcm.edu	37	chr1	158669510	158669510	+	Silent	SNP	T	T	A													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	cctggtcttacggaaaaaaaTatcttagcttgacctatgtg							TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:158669510T>A	ENST00000359610.2	-	1	976	c.933A>T	c.(931-933)atA>atT	p.I311I		NM_001005279.1	NP_001005279.1	Q8NGY2	OR6K2_HUMAN	olfactory receptor, family 6, subfamily K, member 2	311						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	46	all_hematologic(112;0.0378)					CGGAAAAAAATATCTTAGCTT	0.378																																					p.I311I		Atlas-SNP	.											.	OR6K2	104	.	0			c.A933T						.						72	71	71					1																	158669510		2203	4300	6503	SO:0001819	synonymous_variant	81448	exon1			AAAAAATATCTTA	BK004196	CCDS30902.1	1q23.1	2012-08-09			ENSG00000196171	ENSG00000196171		"GPCR / Class A : Olfactory receptors"	15029	protein-coding gene	gene with protein product							Standard	NM_001005279		Approved		uc001fsu.1	Q8NGY2	OTTHUMG00000022768	ENST00000359610.2:c.933A>T	chr1.hg19:g.158669510T>A		130.0	0.0		117.0	43.0	NM_001005279	B9EH33|Q6IFR6	Silent	SNP	ENST00000359610.2	hg19	CCDS30902.1																																																																																			.	.		0.378	OR6K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059061.1	NM_001005279		A	158669510	T	A	158669510	2	1	335	1	0	0	0	0	0	0	0	1	11211	1396	49	4		4	OR6K2	1	158669510	Silent	SNP	T	TCGA-RC-A6M6-01A-11D-A32G-10	5016496	158669510	90581111	7	46558	247	2								
OR6K2	81448	hgsc.bcm.edu	37	chr1	158669512	158669512	+	Missense_Mutation	SNP	T	T	A													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tggtcttacggaaaaaaataTcttagcttgacctatgtgct							TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:158669512T>A	ENST00000359610.2	-	1	974	c.931A>T	c.(931-933)Ata>Tta	p.I311L		NM_001005279.1	NP_001005279.1	Q8NGY2	OR6K2_HUMAN	olfactory receptor, family 6, subfamily K, member 2	311						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	46	all_hematologic(112;0.0378)					GAAAAAAATATCTTAGCTTGA	0.388																																					p.I311L		Atlas-SNP	.											.	OR6K2	104	.	0			c.A931T						.						72	71	71					1																	158669512		2203	4300	6503	SO:0001583	missense	81448	exon1			AAAATATCTTAGC	BK004196	CCDS30902.1	1q23.1	2012-08-09			ENSG00000196171	ENSG00000196171		"GPCR / Class A : Olfactory receptors"	15029	protein-coding gene	gene with protein product							Standard	NM_001005279		Approved		uc001fsu.1	Q8NGY2	OTTHUMG00000022768	ENST00000359610.2:c.931A>T	chr1.hg19:g.158669512T>A	ENSP00000352626:p.Ile311Leu	130.0	0.0		115.0	41.0	NM_001005279	B9EH33|Q6IFR6	Missense_Mutation	SNP	ENST00000359610.2	hg19	CCDS30902.1	.	.	.	.	.	.	.	.	.	.	T	0.316	-0.964707	0.02249	.	.	ENSG00000196171	ENST00000359610	T	0.36340	1.26	0.235	-0.47	0.12131	.	0.634765	0.12827	N	0.435973	T	0.03915	0.0110	N	0.04880	-0.145	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38628	-0.9652	10	0.34782	T	0.22	-0.1467	2.1533	0.03806	0.2522:0.2471:0.0:0.5007	.	311	Q8NGY2	OR6K2_HUMAN	L	311	ENSP00000352626:I311L	ENSP00000352626:I311L	I	-	1	0	OR6K2	156936136	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.498000	0.22530	-1.858000	0.01158	-1.843000	0.00578	ATA	.	.		0.388	OR6K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059061.1	NM_001005279		A	158669512	T	A	158669512	3	1	335	1	0	0	0	0	1	0	0	0	11211	1435	50	4	47	4	OR6K2	1	158669512	Missense_Mutation	SNP	T	TCGA-RC-A6M6-01A-11D-A32G-10	2	158669512	90581109	8	46559	247	2								
MNDA	4332	hgsc.bcm.edu	37	chr1	158817562	158817562	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	atttatgaaatacaggataaTacaggatccatggatgtagt	9	4	0	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:158817562T>C	ENST00000368141.4	+	6	1293	c.1032T>C	c.(1030-1032)aaT>aaC	p.N344N		NM_002432.1	NP_002423.1	P41218	MNDA_HUMAN	myeloid cell nuclear differentiation antigen	344	HIN-200. {ECO:0000255|PROSITE- ProRule:PRU00106}.				B cell receptor signaling pathway (GO:0050853)|cellular defense response (GO:0006968)|cellular response to DNA damage stimulus (GO:0006974)|negative regulation of B cell proliferation (GO:0030889)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(2)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(26)|ovary(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	all_hematologic(112;0.0378)					TACAGGATAATACAGGATCCA	0.378																																					p.N344N		Atlas-SNP	.											.	MNDA	147	.	0			c.T1032C						.						130	126	128					1																	158817562		2203	4300	6503	SO:0001819	synonymous_variant	4332	exon6			GGATAATACAGGA	BC032319	CCDS1177.1	1q22	2008-02-05			ENSG00000163563	ENSG00000163563			7183	protein-coding gene	gene with protein product		159553				1644857, 7512843	Standard	NM_002432		Approved	PYHIN3	uc001fsz.1	P41218	OTTHUMG00000022776	ENST00000368141.4:c.1032T>C	chr1.hg19:g.158817562T>C		58.0	0.0		42.0	36.0	NM_002432		Silent	SNP	ENST00000368141.4	hg19	CCDS1177.1	.	.	.	.	.	.	.	.	.	.	T	4.680	0.126526	0.08931	.	.	ENSG00000163563	ENST00000438394	.	.	.	3.81	-3.59	0.04583	.	.	.	.	.	T	0.07007	0.0178	.	.	.	0.23577	N	0.997378	.	.	.	.	.	.	T	0.34229	-0.9837	4	.	.	.	-4.0499	2.8998	0.05701	0.3359:0.316:0.0:0.3481	.	.	.	.	H	50	.	.	Y	+	1	0	MNDA	157084186	0.000000	0.05858	0.044000	0.18714	0.114000	0.19823	-2.487000	0.00977	-0.895000	0.03920	0.460000	0.39030	TAC	.	.		0.378	MNDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059069.1	NM_002432		C	158817562	T	C	158817562	2	2	335	1	0	0	0	0	0	0	0	1	9685	1403	49	2		2	MNDA	1	158817562	Silent	SNP	T	TCGA-RC-A6M6-01A-11D-A32G-10	148050	158817562	90433059	9	46560										
DUSP27	92235	hgsc.bcm.edu	37	chr1	167096118	167096118	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gggagaagaacccctccgacGtcagcctgacagcctaccag	11	15	1	3	rs369939829		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:167096118G>A	ENST00000361200.2	+	6	1916	c.1750G>A	c.(1750-1752)Gtc>Atc	p.V584I	DUSP27_ENST00000271385.5_Missense_Mutation_p.V584I|DUSP27_ENST00000443333.1_Missense_Mutation_p.V584I|DUSP27_ENST00000485151.1_Intron			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	584					protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.V584I(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						CCCCTCCGACGTCAGCCTGAC	0.582																																					p.V584I		Atlas-SNP	.											DUSP27,NS,carcinoma,0,2	DUSP27	235	.	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G1750A						.						46	47	46					1																	167096118		2203	4300	6503	SO:0001583	missense	92235	exon5			TCCGACGTCAGCC	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.1750G>A	chr1.hg19:g.167096118G>A	ENSP00000354483:p.Val584Ile	37.0	0.0		46.0	31.0	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	hg19	CCDS30932.1	.	.	.	.	.	.	.	.	.	.	g	2.890	-0.229957	0.06022	.	.	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.05081	3.5;3.5;3.5	5.32	2.43	0.29744	.	0.324845	0.23454	N	0.048008	T	0.03220	0.0094	M	0.66939	2.045	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.35574	-0.9783	10	0.46703	T	0.11	-10.7021	13.2231	0.59899	0.2361:0.0:0.7639:0.0	.	584	Q5VZP5	DUS27_HUMAN	I	584	ENSP00000354483:V584I;ENSP00000271385:V584I;ENSP00000404874:V584I	ENSP00000271385:V584I	V	+	1	0	DUSP27	165362742	0.998000	0.40836	0.000000	0.03702	0.000000	0.00434	2.635000	0.46537	0.008000	0.14787	-1.985000	0.00452	GTC	.	.		0.582	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426		A	167096118	G	A	167096118	3	1	335	1	0	0	0	0	1	0	0	0	4826	1145	40	1	1768	1	DUSP27	1	167096118	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	8278556	167096118	82154503	10	46561										
RCSD1	92241	hgsc.bcm.edu	37	chr1	167666934	167666934	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tccccctggaggagtgaaggGcggagatgtccccaagcagg	16	11	0	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:167666934G>T	ENST00000367854.3	+	6	1404	c.1073G>T	c.(1072-1074)gGc>gTc	p.G358V	RCSD1_ENST00000537350.1_Missense_Mutation_p.G328V	NM_052862.3	NP_443094.3	Q6JBY9	CPZIP_HUMAN	RCSD domain containing 1	358					cellular hyperosmotic response (GO:0071474)|skeletal muscle contraction (GO:0003009)	actin filament (GO:0005884)	actin filament binding (GO:0051015)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(2)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	24	all_hematologic(923;0.215)					GGAGTGAAGGGCGGAGATGTC	0.612																																					p.G358V		Atlas-SNP	.											.	RCSD1	64	.	0			c.G1073T						.						33	32	32					1																	167666934		2200	4296	6496	SO:0001583	missense	92241	exon6			TGAAGGGCGGAGA	BC072399	CCDS1263.1	1q24.2	2008-02-05			ENSG00000198771	ENSG00000198771			28310	protein-coding gene	gene with protein product		610579				12477932	Standard	NM_052862		Approved	MK2S4, MGC21854	uc001gem.3	Q6JBY9	OTTHUMG00000035318	ENST00000367854.3:c.1073G>T	chr1.hg19:g.167666934G>T	ENSP00000356828:p.Gly358Val	37.0	0.0		29.0	27.0	NM_052862	B1AK48|Q4G0E7|Q6IN93|Q8IZM2|Q96DX0|Q9NST4	Missense_Mutation	SNP	ENST00000367854.3	hg19	CCDS1263.1	.	.	.	.	.	.	.	.	.	.	G	14.49	2.550229	0.45383	.	.	ENSG00000198771	ENST00000367854;ENST00000537350	T;T	0.71461	-0.33;-0.57	4.64	2.65	0.31530	.	0.848487	0.10531	N	0.663853	T	0.58018	0.2093	L	0.34521	1.04	0.30576	N	0.762964	P;D	0.67145	0.906;0.996	P;P	0.61940	0.521;0.896	T	0.48115	-0.9063	9	0.36615	T	0.2	-5.3467	6.5071	0.22202	0.3321:0.0:0.6679:0.0	.	328;358	B7ZKW8;Q6JBY9	.;CPZIP_HUMAN	V	358;328	ENSP00000356828:G358V;ENSP00000439409:G328V	ENSP00000356828:G358V	G	+	2	0	RCSD1	165933558	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-0.018000	0.12568	0.403000	0.25479	0.585000	0.79938	GGC	.	.		0.612	RCSD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085451.1	NM_052862		T	167666934	G	T	167666934	3	4	335	1	0	0	0	0	1	0	0	0	13200	1203	42	3	1095	3	RCSD1	1	167666934	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	570816	167666934	81583687	11	46562										
ASTN1	460	hgsc.bcm.edu	37	chr1	177030375	177030375	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ctgcctccagcgcaccaaagGgatatcctctgtgttccctg	9	15	1	0	rs138326291		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:177030375G>T	ENST00000367654.3	-	2	521	c.310C>A	c.(310-312)Cct>Act	p.P104T	ASTN1_ENST00000281881.3_5'UTR|ASTN1_ENST00000424564.2_Missense_Mutation_p.P104T|ASTN1_ENST00000361833.2_Missense_Mutation_p.P104T|ASTN1_ENST00000367657.3_Missense_Mutation_p.P104T	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	104					locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						CGCACCAAAGGGATATCCTCT	0.502																																					p.P104T		Atlas-SNP	.											.	ASTN1	314	.	0			c.C310A						.						147	141	143					1																	177030375		2203	4300	6503	SO:0001583	missense	460	exon2			CCAAAGGGATATC	AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"astrotactin"	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.310C>A	chr1.hg19:g.177030375G>T	ENSP00000356626:p.Pro104Thr	79.0	0.0		63.0	50.0	NM_004319	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Missense_Mutation	SNP	ENST00000367654.3	hg19		.	.	.	.	.	.	.	.	.	.	G	27.0	4.793774	0.90453	.	.	ENSG00000152092	ENST00000367657;ENST00000361833;ENST00000367654;ENST00000424564;ENST00000541808	T;T;T;T	0.14266	2.52;2.94;2.94;2.52	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.32164	0.0820	L	0.47716	1.5	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.998	T	0.00498	-1.1704	10	0.19147	T	0.46	-20.2983	20.2159	0.98296	0.0:0.0:1.0:0.0	.	104;104;104	O14525;O14525-2;B1AJS1	ASTN1_HUMAN;.;.	T	104	ENSP00000356629:P104T;ENSP00000354536:P104T;ENSP00000356626:P104T;ENSP00000395041:P104T	ENSP00000354536:P104T	P	-	1	0	ASTN1	175296998	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.689000	0.98673	2.882000	0.98803	0.655000	0.94253	CCT	.	G|1.000;C|0.000		0.502	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319		T	177030375	G	T	177030375	3	4	335	1	0	0	0	0	1	0	0	0	1064	1232	43	3	3666	3	ASTN1	1	177030375	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	9363441	177030375	72220246	12	46563										
SLC45A3	85414	hgsc.bcm.edu	37	chr1	205628667	205628667	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	cgcgggtggaggtgggagcaGgccactgcctccagcaccca	16	14	0	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:205628667G>T	ENST00000367145.3	-	5	1652	c.1357C>A	c.(1357-1359)Ctg>Atg	p.L453M	SLC45A3_ENST00000460934.1_5'UTR	NM_033102.2	NP_149093.1	Q96JT2	S45A3_HUMAN	solute carrier family 45, member 3	453					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)			SLC45A3/BRAF(2)|SLC45A3/ELK4(18)|SLC45A3/ETV1(3)|SLC45A3/ETV5_ENST00000306376(2)|SLC45A3/ERG(50)	cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(7)|ovary(3)|prostate(5)	21	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0194)			GGTGGGAGCAGGCCACTGCCT	0.667			T	"ETV1, ETV5, ELK4, ERG"	prostate						OREG0014161	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L453M		Atlas-SNP	.		Dom	yes		1	1q32	85414	"solute carrier family 45, member 3"		E	.	SLC45A3	54	.	0			c.C1357A						.						45	43	44					1																	205628667		2202	4300	6502	SO:0001583	missense	85414	exon5			GGAGCAGGCCACT	AF109301	CCDS1458.1	1q32.1	2013-05-22	2005-10-04	2005-10-04	ENSG00000158715	ENSG00000158715		"Solute carriers"	8642	protein-coding gene	gene with protein product		605097	"prostate cancer associated protein 6", "prostate cancer associated protein 2", "prostate cancer associated protein 8"	PCANAP6, PCANAP2, PCANAP8		10613842, 11245466	Standard	XM_005245556		Approved	IPCA-6, prostein, IPCA-2, IPCA-8	uc001hda.1	Q96JT2	OTTHUMG00000037223	ENST00000367145.3:c.1357C>A	chr1.hg19:g.205628667G>T	ENSP00000356113:p.Leu453Met	73.0	0.0	2153	76.0	60.0	NM_033102	A8K2U9	Missense_Mutation	SNP	ENST00000367145.3	hg19	CCDS1458.1	.	.	.	.	.	.	.	.	.	.	G	10.27	1.303763	0.23736	.	.	ENSG00000158715	ENST00000367145	T	0.45276	0.9	5.38	4.44	0.53790	.	0.803881	0.10968	N	0.614223	T	0.30696	0.0773	N	0.22421	0.69	0.24516	N	0.994189	B	0.29805	0.257	B	0.26310	0.068	T	0.14671	-1.0464	10	0.30854	T	0.27	-4.4745	13.0093	0.58722	0.0:0.0:0.8327:0.1673	.	453	Q96JT2	S45A3_HUMAN	M	453	ENSP00000356113:L453M	ENSP00000356113:L453M	L	-	1	2	SLC45A3	203895290	0.994000	0.37717	0.812000	0.32479	0.234000	0.25298	2.062000	0.41413	1.201000	0.43203	0.491000	0.48974	CTG	.	.		0.667	SLC45A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090619.1	NM_033102		T	205628667	G	T	205628667	3	4	335	1	0	0	0	0	1	0	0	0	14657	991	35	3	308	3	SLC45A3	1	205628667	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	28598292	205628667	43621954	13	46564										
KIF26B	55083	hgsc.bcm.edu	37	chr1	245530263	245530263	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gaaccagttgaagcaggaggCcatccagatggtgctgacgt	14	9	0	3			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:245530263C>A	ENST00000407071.2	+	3	1033	c.593C>A	c.(592-594)gCc>gAc	p.A198D	KIF26B_ENST00000479506.1_3'UTR	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	198					establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			AAGCAGGAGGCCATCCAGATG	0.627																																					p.A198D		Atlas-SNP	.											.	KIF26B	343	.	0			c.C593A						.						42	46	45					1																	245530263		2183	4267	6450	SO:0001583	missense	55083	exon3			AGGAGGCCATCCA	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"Kinesins"	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.593C>A	chr1.hg19:g.245530263C>A	ENSP00000385545:p.Ala198Asp	69.0	0.0		67.0	29.0	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Missense_Mutation	SNP	ENST00000407071.2	hg19	CCDS44342.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.303731	0.81136	.	.	ENSG00000162849	ENST00000407071	D	0.87966	-2.32	5.44	5.44	0.79542	.	.	.	.	.	D	0.93559	0.7944	M	0.74881	2.28	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93799	0.7099	9	0.87932	D	0	.	19.6436	0.95767	0.0:1.0:0.0:0.0	.	198	Q2KJY2	KI26B_HUMAN	D	198	ENSP00000385545:A198D	ENSP00000385545:A198D	A	+	2	0	KIF26B	243596886	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.445000	0.80570	2.712000	0.92718	0.650000	0.86243	GCC	.	.		0.627	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354		A	245530263	C	A	245530263	3	1	335	1	0	0	0	0	1	0	0	0	8304	739	26	3	603	3	KIF26B	1	245530263	Missense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	39901596	245530263	3720358	14	46565										
NLRP3	114548	hgsc.bcm.edu	37	chr1	247588229	247588229	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	cctcaggaatcatggactgcAgaaggcggatgtgtctgctt	13	9	3	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:247588229A>G	ENST00000336119.3	+	3	2230	c.1484A>G	c.(1483-1485)cAg>cGg	p.Q495R	NLRP3_ENST00000391828.3_Missense_Mutation_p.Q495R|NLRP3_ENST00000366496.2_Missense_Mutation_p.Q495R|NLRP3_ENST00000366497.2_Missense_Mutation_p.Q495R|NLRP3_ENST00000348069.2_Missense_Mutation_p.Q495R|NLRP3_ENST00000474792.1_3'UTR|NLRP3_ENST00000391827.2_Missense_Mutation_p.Q495R	NM_001127462.2|NM_001243133.1|NM_004895.4	NP_001120934.1|NP_001230062.1|NP_004886.3	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3	495	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|defense response (GO:0006952)|defense response to virus (GO:0051607)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|interleukin-1 secretion (GO:0050701)|interleukin-18 production (GO:0032621)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|NLRP3 inflammasome complex assembly (GO:0044546)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|NLRP3 inflammasome complex (GO:0072559)	ATP binding (GO:0005524)|peptidoglycan binding (GO:0042834)			NS(1)|breast(3)|endometrium(6)|kidney(1)|large_intestine(19)|lung(85)|ovary(9)|pancreas(2)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	142	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			CATGGACTGCAGAAGGCGGAT	0.522																																					p.Q495R		Atlas-SNP	.											.	NLRP3	286	.	0			c.A1484G						.						52	51	52					1																	247588229		2203	4300	6503	SO:0001583	missense	114548	exon3			GACTGCAGAAGGC	AF054176	CCDS1632.1, CCDS1633.1, CCDS44346.1, CCDS44347.1	1q44	2014-09-17	2006-12-08	2006-12-08	ENSG00000162711	ENSG00000162711		"Nucleotide-binding domain and leucine rich repeat containing"	16400	protein-coding gene	gene with protein product	"Cryopyrin", "nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 3"	606416	"cold autoinflammatory syndrome 1"	C1orf7, CIAS1		10741953	Standard	NM_183395		Approved	AGTAVPRL, AII, AVP, FCAS, FCU, NALP3, PYPAF1, MWS, CLR1.1	uc001icr.3	Q96P20	OTTHUMG00000040647	ENST00000336119.3:c.1484A>G	chr1.hg19:g.247588229A>G	ENSP00000337383:p.Gln495Arg	21.0	0.0		40.0	28.0	NM_183395	B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Missense_Mutation	SNP	ENST00000336119.3	hg19	CCDS1632.1	.	.	.	.	.	.	.	.	.	.	A	4.169	0.029902	0.08101	.	.	ENSG00000162711	ENST00000391828;ENST00000366497;ENST00000336119;ENST00000348069;ENST00000366496;ENST00000391827	D;D;D;D;D;D	0.83992	-1.79;-1.79;-1.79;-1.79;-1.79;-1.79	4.17	1.86	0.25419	NACHT nucleoside triphosphatase (1);	0.133374	0.35013	N	0.003504	T	0.68842	0.3045	N	0.17723	0.515	0.26785	N	0.969515	B;B;B;B;B	0.25048	0.086;0.117;0.094;0.02;0.016	B;B;B;B;B	0.31442	0.061;0.13;0.07;0.07;0.032	T	0.58741	-0.7583	10	0.42905	T	0.14	.	5.6856	0.17801	0.7826:0.0:0.2174:0.0	.	495;495;495;495;495	B7ZKS9;Q96P20-4;Q96P20-2;Q96P20-5;Q96P20	.;.;.;.;NALP3_HUMAN	R	495	ENSP00000375704:Q495R;ENSP00000355453:Q495R;ENSP00000337383:Q495R;ENSP00000294752:Q495R;ENSP00000355452:Q495R;ENSP00000375703:Q495R	ENSP00000337383:Q495R	Q	+	2	0	NLRP3	245654852	0.901000	0.30685	0.939000	0.37840	0.020000	0.10135	1.959000	0.40412	0.404000	0.25506	-0.250000	0.11733	CAG	.	.		0.522	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	NM_004895		G	247588229	A	G	247588229	3	3	335	1	0	0	0	0	1	0	0	0	10487	188	7	2	1494	2	NLRP3	1	247588229	Missense_Mutation	SNP	A	TCGA-RC-A6M6-01A-11D-A32G-10	2057966	247588229	1662392	15	46566										
OR14A16	284532	hgsc.bcm.edu	37	chr1	247978654	247978654	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	atgacatcatagtgcagaggGtgacatatagcagtatagcg	12	6	1	3			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:247978654G>T	ENST00000357627.1	-	1	377	c.378C>A	c.(376-378)caC>caA	p.H126Q		NM_001001966.1	NP_001001966.1	Q8NHC5	O14AG_HUMAN	olfactory receptor, family 14, subfamily A, member 16	126						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(32)|skin(2)|stomach(1)	45						AGTGCAGAGGGTGACATATAG	0.507																																					p.H126Q	Ovarian(112;180 1586 15073 21914 33526)	Atlas-SNP	.											.	OR14A16	90	.	0			c.C378A						.						121	113	116					1																	247978654		2203	4300	6503	SO:0001583	missense	284532	exon1			CAGAGGGTGACAT	BK004366	CCDS31097.1	1q44	2012-08-09	2008-04-02	2008-04-02	ENSG00000196772	ENSG00000196772		"GPCR / Class A : Olfactory receptors"	15022	protein-coding gene	gene with protein product			"olfactory receptor, family 5, subfamily AT, member 1"	OR5AT1			Standard	NM_001001966		Approved		uc001idm.1	Q8NHC5	OTTHUMG00000040199	ENST00000357627.1:c.378C>A	chr1.hg19:g.247978654G>T	ENSP00000350248:p.His126Gln	88.0	0.0		60.0	46.0	NM_001001966	Q6IF96	Missense_Mutation	SNP	ENST00000357627.1	hg19	CCDS31097.1	.	.	.	.	.	.	.	.	.	.	G	0.049	-1.256553	0.01457	.	.	ENSG00000196772	ENST00000357627	T	0.01068	5.38	3.65	-2.42	0.06542	GPCR, rhodopsin-like superfamily (1);	1.138130	0.06749	U	0.779703	T	0.01222	0.0040	L	0.37466	1.105	0.21802	N	0.999534	B	0.26081	0.141	B	0.23419	0.046	T	0.46247	-0.9205	10	0.35671	T	0.21	.	7.2542	0.26166	0.3799:0.1364:0.4836:0.0	.	126	Q8NHC5	O14AG_HUMAN	Q	126	ENSP00000350248:H126Q	ENSP00000350248:H126Q	H	-	3	2	OR14A16	246045277	0.000000	0.05858	0.697000	0.30258	0.157000	0.22087	-6.769000	0.00054	-0.517000	0.06461	-0.225000	0.12378	CAC	.	.		0.507	OR14A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096856.1	NM_001001966		T	247978654	G	T	247978654	3	4	335	1	0	0	0	0	1	0	0	0	10954	1252	44	3	555	3	OR14A16	1	247978654	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	390425	247978654	1271967	16	46567										
OR2T8	343172	hgsc.bcm.edu	37	chr1	248085221	248085221	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ggtgaagggagccctgacaaGgtgtatgggtcggtgtgtgg	20	5	0	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:248085221G>T	ENST00000319968.4	+	1	902	c.902G>T	c.(901-903)aGg>aTg	p.R301M		NM_001005522.1	NP_001005522.1	A6NH00	OR2T8_HUMAN	olfactory receptor, family 2, subfamily T, member 8	301						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R301K(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(20)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0211)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			GCCCTGACAAGGTGTATGGGT	0.443																																					p.R301M		Atlas-SNP	.											OR2T8,NS,carcinoma,0,1	OR2T8	67	.	1	Substitution - Missense(1)	lung(1)	c.G902T						.						156	152	154					1																	248085221		2203	4300	6503	SO:0001583	missense	343172	exon1			TGACAAGGTGTAT		CCDS31100.1	1q44	2012-08-09		2004-03-10	ENSG00000177462	ENSG00000177462		"GPCR / Class A : Olfactory receptors"	15020	protein-coding gene	gene with protein product				OR2T8P			Standard	XM_005273117		Approved		uc010pzc.2	A6NH00	OTTHUMG00000040205	ENST00000319968.4:c.902G>T	chr1.hg19:g.248085221G>T	ENSP00000326225:p.Arg301Met	86.0	0.0		70.0	52.0	NM_001005522		Missense_Mutation	SNP	ENST00000319968.4	hg19	CCDS31100.1	.	.	.	.	.	.	.	.	.	.	G	9.211	1.030912	0.19590	.	.	ENSG00000177462	ENST00000319968	T	0.41065	1.01	3.54	0.688	0.18027	.	0.928799	0.08661	N	0.912382	T	0.39172	0.1068	L	0.58969	1.84	0.09310	N	1	B	0.18968	0.032	B	0.22601	0.04	T	0.43278	-0.9401	10	0.72032	D	0.01	.	7.4323	0.27134	0.763:0.0:0.237:0.0	.	301	A6NH00	OR2T8_HUMAN	M	301	ENSP00000326225:R301M	ENSP00000326225:R301M	R	+	2	0	OR2T8	246151844	0.000000	0.05858	0.001000	0.08648	0.056000	0.15407	-0.126000	0.10563	0.266000	0.21894	-0.310000	0.09108	AGG	.	.		0.443	OR2T8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096862.1	NM_001005522		T	248085221	G	T	248085221	3	4	335	1	0	0	0	0	1	0	0	0	11039	1000	35	3	904	3	OR2T8	1	248085221	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	106567	248085221	1165400	17	46568										
MATN3	4148	hgsc.bcm.edu	37	chr2	20202976	20202976	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tccttggctacactcacagtGgtgcttgccttccccatcac	7	16	2	0	rs376404727		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:20202976G>A	ENST00000407540.3	-	3	924	c.862C>T	c.(862-864)Cac>Tac	p.H288Y	AC079145.4_ENST00000416575.1_RNA|MATN3_ENST00000421259.2_Intron	NM_002381.4	NP_002372.1	O15232	MATN3_HUMAN	matrilin 3	288	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(6)|skin(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CACTCACAGTGGTGCTTGCCT	0.532																																					p.H288Y		Atlas-SNP	.											.	MATN3	28	.	0			c.C862T						.	G	TYR/HIS	0,4076		0,0,2038	118	113	115		862	5.5	1	2		115	1,8381		0,1,4190	no	missense	MATN3	NM_002381.4	83	0,1,6228	AA,AG,GG		0.0119,0.0,0.0080	benign	288/487	20202976	1,12457	2038	4191	6229	SO:0001583	missense	4148	exon3			CACAGTGGTGCTT	AJ001047	CCDS46226.1	2p24-p23	2008-06-03			ENSG00000132031	ENSG00000132031			6909	protein-coding gene	gene with protein product		602109				9287130, 9350998	Standard	NM_002381		Approved	EDM5, HOA	uc002rdl.3	O15232	OTTHUMG00000151788	ENST00000407540.3:c.862C>T	chr2.hg19:g.20202976G>A	ENSP00000383894:p.His288Tyr	68.0	0.0		89.0	39.0	NM_002381	B2CPU0|Q4ZG02	Missense_Mutation	SNP	ENST00000407540.3	hg19	CCDS46226.1	.	.	.	.	.	.	.	.	.	.	G	3.172	-0.169756	0.06461	0.0	1.19E-4	ENSG00000132031	ENST00000407540	D	0.87029	-2.2	5.5	5.5	0.81552	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.252898	0.40302	N	0.001125	T	0.74989	0.3789	N	0.11106	0.095	0.80722	D	1	B	0.17852	0.024	B	0.11329	0.006	T	0.70099	-0.4965	10	0.11182	T	0.66	-33.7623	16.1448	0.81559	0.0:0.0:1.0:0.0	.	288	O15232	MATN3_HUMAN	Y	288	ENSP00000383894:H288Y	ENSP00000383894:H288Y	H	-	1	0	MATN3	20066457	0.950000	0.32346	1.000000	0.80357	0.783000	0.44284	0.555000	0.23422	2.596000	0.87737	0.650000	0.86243	CAC	.	.		0.532	MATN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323925.1	NM_002381		A	20202976	G	A	20202976	3	1	335	1	0	0	0	0	1	0	0	0	9344	1348	47	3	622	3	MATN3	2	20202976	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10		20202976	222996397	18	46569										
C2orf71	388939	hgsc.bcm.edu	37	chr2	29297116	29297116	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	acaaggtcactgtgtgaaggTgtacaccccatgatttcagc	10	10	2	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:29297116T>C	ENST00000331664.5	-	1	11	c.12A>G	c.(10-12)acA>acG	p.T4T		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	4					response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						TGTGTGAAGGTGTACACCCCA	0.433																																					p.T4T		Atlas-SNP	.											.	C2orf71	146	.	0			c.A12G						.						80	73	75					2																	29297116		1965	4156	6121	SO:0001819	synonymous_variant	388939	exon1			TGAAGGTGTACAC		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.12A>G	chr2.hg19:g.29297116T>C		52.0	0.0		47.0	17.0	NM_001029883		Silent	SNP	ENST00000331664.5	hg19	CCDS42669.1																																																																																			.	.		0.433	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883		C	29297116	T	C	29297116	2	2	335	1	0	0	0	0	0	0	0	1	2193	1683	59	2		2	C2orf71	2	29297116	Silent	SNP	T	TCGA-RC-A6M6-01A-11D-A32G-10	9094140	29297116	213902257	19	46570										
LRPPRC	10128	hgsc.bcm.edu	37	chr2	44162019	44162019	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	agcagtagataggtcgccccTtagaaacaaaaaaattagca	8	8	0	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:44162019T>A	ENST00000260665.7	-	24	2562		c.e24-2			NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing						mitochondrion transport along microtubule (GO:0047497)|mRNA transport (GO:0051028)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of mitochondrial translation (GO:0070129)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(3)|endometrium(3)|kidney(5)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|skin(2)	41		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				AGGTCGCCCCTTAGAAACAAA	0.333																																					.		Atlas-SNP	.											.	LRPPRC	105	.	0			c.2505-2A>T						.						49	50	50					2																	44162019		2202	4299	6501	SO:0001630	splice_region_variant	10128	exon25			CGCCCCTTAGAAA	M92439	CCDS33189.1	2p21	2012-02-24	2012-02-24		ENSG00000138095	ENSG00000138095			15714	protein-coding gene	gene with protein product		607544	"Leigh syndrome, French-Canadian type (cytochrome oxidase deficiency)"	LSFC		8012652, 8619474, 22045337	Standard	NM_133259		Approved	GP130, LRP130	uc002rtr.2	P42704	OTTHUMG00000152782	ENST00000260665.7:c.2505-2A>T	chr2.hg19:g.44162019T>A		144.0	0.0		108.0	44.0	NM_133259	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Splice_Site	SNP	ENST00000260665.7	hg19	CCDS33189.1	.	.	.	.	.	.	.	.	.	.	T	12.63	1.995152	0.35226	.	.	ENSG00000138095	ENST00000465633;ENST00000260665	.	.	.	5.84	5.84	0.93424	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9036	0.79403	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	LRPPRC	44015523	1.000000	0.71417	0.989000	0.46669	0.058000	0.15608	7.246000	0.78247	2.228000	0.72767	0.533000	0.62120	.	.	.		0.333	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259	Intron	A	44162019	T	A	44162019	5	1	335	1	0	0	0	0	0	0	1	0	8974	1623	56	4	1741	4	LRPPRC	2	44162019	Splice_Site	SNP	T	TCGA-RC-A6M6-01A-11D-A32G-10	14864903	44162019	199037354	20	46571										
PRKCE	5581	hgsc.bcm.edu	37	chr2	45879477	45879477	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tgtgcaacggacgcaagatcGagctggctgtctttcacgat	12	10	2	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:45879477G>T	ENST00000306156.3	+	1	565	c.238G>T	c.(238-240)Gag>Tag	p.E80*		NM_005400.2	NP_005391.1	Q02156	KPCE_HUMAN	protein kinase C, epsilon	80	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|cellular response to ethanol (GO:0071361)|cellular response to hypoxia (GO:0071456)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|locomotory exploration behavior (GO:0035641)|macrophage activation involved in immune response (GO:0002281)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cellular glucuronidation (GO:2001031)|positive regulation of cytokinesis (GO:0032467)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of insulin secretion (GO:0032024)|positive regulation of lipid catabolic process (GO:0050996)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mucus secretion (GO:0070257)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|release of sequestered calcium ion into cytosol (GO:0051209)|response to morphine (GO:0043278)|signal transduction (GO:0007165)|TRAM-dependent toll-like receptor 4 signaling pathway (GO:0035669)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|ethanol binding (GO:0035276)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|receptor activator activity (GO:0030546)|signal transducer activity (GO:0004871)		MBOAT2/PRKCE(2)	breast(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(13)|ovary(3)|upper_aerodigestive_tract(2)	34		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)		Tamoxifen(DB00675)	ACGCAAGATCGAGCTGGCTGT	0.612																																					p.E80X		Atlas-SNP	.											.	PRKCE	58	.	0			c.G238T						.						81	68	73					2																	45879477		2203	4300	6503	SO:0001587	stop_gained	5581	exon1			AAGATCGAGCTGG		CCDS1824.1	2p21	2009-07-10			ENSG00000171132	ENSG00000171132	2.7.11.1		9401	protein-coding gene	gene with protein product		176975				1382605, 7877991	Standard	NM_005400		Approved		uc002rut.3	Q02156	OTTHUMG00000128817	ENST00000306156.3:c.238G>T	chr2.hg19:g.45879477G>T	ENSP00000306124:p.Glu80*	27.0	0.0		30.0	15.0	NM_005400	B0LPH7|Q32MQ3|Q53SL4|Q53SM5|Q9UE81	Nonsense_Mutation	SNP	ENST00000306156.3	hg19	CCDS1824.1	.	.	.	.	.	.	.	.	.	.	G	43	10.189166	0.99355	.	.	ENSG00000171132	ENST00000421201;ENST00000306156	.	.	.	4.71	4.71	0.59529	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	17.673	0.88224	0.0:0.0:1.0:0.0	.	.	.	.	X	80	.	ENSP00000306124:E80X	E	+	1	0	PRKCE	45732981	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.802000	0.99131	2.152000	0.67230	0.561000	0.74099	GAG	.	.		0.612	PRKCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250751.2			T	45879477	G	T	45879477	4	4	335	1	0	0	0	0	0	1	0	0	12523	1059	37	1	240	1	PRKCE	2	45879477	Nonsense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	1717458	45879477	197319896	21	46572										
C2orf55	343990	hgsc.bcm.edu	37	chr2	99439712	99439712	+	Frame_Shift_Del	DEL	C	C	-													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gggggccgactcgggctcggCgagctccggggtggccgggc							TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:99439712delC	ENST00000397899.2	-	7	1355	c.1024delG	c.(1024-1026)gccfs	p.A342fs		NM_207362.2	NP_997245.2	Q6NV74	K121L_HUMAN	KIAA1211-like	342	Pro-rich.																TCGGGCTCGGCGAGCTCCGGG	0.786																																					p.A342fs		Atlas-INDEL	.											.	.	.	.	0			c.1025delC						.																																			SO:0001589	frameshift_variant	343990	exon7			.	BC068277	CCDS42720.1	2q11.2	2012-08-03	2012-08-03	2012-08-03	ENSG00000196872	ENSG00000196872			33454	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 55"	C2orf55			Standard	NM_207362		Approved	MGC42367	uc002szf.1	Q6NV74	OTTHUMG00000153171	ENST00000397899.2:c.1024delG	chr2.hg19:g.99439712delC	ENSP00000380996:p.Ala342fs	11.0	0.0		19.0	11.0	NM_207362		Frame_Shift_Del	DEL	ENST00000397899.2	hg19	CCDS42720.1																																																																																			.	.		0.786	KIAA1211L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329933.1	NM_207362		-	99439712	C	-	99439712	7	5	335	1	0	1	0	1	0	0	0	0	2178	768	27	0	1880	0	C2orf55	2	99439712	Frame_Shift_Del	DEL	C	TCGA-RC-A6M6-01A-11D-A32G-10	53560235	99439712	143759661	22	46573										
SLC9A4	389015	hgsc.bcm.edu	37	chr2	103121886	103121912	+	In_Frame_Del	DEL	TCATCTGCTTCACCCTGGCCTTCTGCC	TCATCTGCTTCACCCTGGCCTTCTGCC	-													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tcacgagtggaactgggcctTcatctgcttcaccctggcct					rs377204289		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	TCATCTGCTTCACCCTGGCCTTCTGCC	TCATCTGCTTCACCCTGGCCTTCTGCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:103121886_103121912delTCATCTGCTTCACCCTGGCCTTCTGCC	ENST00000295269.4	+	4	1611_1637	c.1154_1180delTCATCTGCTTCACCCTGGCCTTCTGCC	c.(1153-1182)ttcatctgcttcaccctggccttctgccaa>taa	p.385_394FICFTLAFCQ>*		NM_001011552.3	NP_001011552.2	Q6AI14	SL9A4_HUMAN	solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4	385					epithelial cell development (GO:0002064)|gastric acid secretion (GO:0001696)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						AACTGGGCCTTCATCTGCTTCACCCTGGCCTTCTGCCAAATCTGGAG	0.511																																					p.385_393del		Atlas-INDEL	.											.	SLC9A4	115	.	0			c.1153_1179del						.																																			SO:0001651	inframe_deletion	389015	exon4			.		CCDS33264.1	2q12.1	2013-05-22	2012-03-22		ENSG00000180251	ENSG00000180251		"Solute carriers"	11077	protein-coding gene	gene with protein product		600531	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 4", "solute carrier family 9 (sodium/hydrogen exchanger), member 4"			8199403	Standard	NM_001011552		Approved	NHE4	uc002tbz.4	Q6AI14	OTTHUMG00000153093	ENST00000295269.4:c.1154_1180delTCATCTGCTTCACCCTGGCCTTCTGCC	chr2.hg19:g.103121886_103121912delTCATCTGCTTCACCCTGGCCTTCTGCC	ENSP00000295269:p.Phe385_Gln394delins*	47.0	0.0		38.0	10.0	NM_001011552	Q69YK0	In_Frame_Del	DEL	ENST00000295269.4	hg19	CCDS33264.1																																																																																			.	.		0.511	SLC9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329498.1	NM_001011552.3		-	103121912	TCATCTGCTTCACCCTGGCCTTCTGCC	-	103121886	7	5	335	1	0	1	0	1	0	0	0	0	14731	1783	62	0	1168	0	SLC9A4	2	103121886	In_Frame_Del	DEL	TCATCTGCTTCACCCTGGCCTTCTGCC	TCGA-RC-A6M6-01A-11D-A32G-10	3682174	103121886	140077487	23	46574										
ERCC3	2071	hgsc.bcm.edu	37	chr2	128038082	128038082	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	cagctccatccagttggcttCgtagagcttaggcccaatca	9	13	1	1	rs367552856		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:128038082C>A	ENST00000285398.2	-	9	1562	c.1468G>T	c.(1468-1470)Gaa>Taa	p.E490*	ERCC3_ENST00000493187.2_Nonsense_Mutation_p.E426*	NM_000122.1	NP_000113.1	P19447	ERCC3_HUMAN	excision repair cross-complementation group 3	490					7-methylguanosine mRNA capping (GO:0006370)|apoptotic process (GO:0006915)|DNA repair (GO:0006281)|DNA topological change (GO:0006265)|gene expression (GO:0010467)|hair cell differentiation (GO:0035315)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA duplex unwinding (GO:0000717)|nucleotide-excision repair, DNA incision (GO:0033683)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein localization (GO:0008104)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|response to UV (GO:0009411)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)|viral process (GO:0016032)	holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' DNA helicase activity (GO:0043138)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|damaged DNA binding (GO:0003684)|dATP binding (GO:0032564)|DNA binding (GO:0003677)|GTP binding (GO:0005525)|peptide binding (GO:0042277)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	31	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.073)		CAGTTGGCTTCGTAGAGCTTA	0.547			"Mis, S"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.E490X		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (B)	2	2q21	2071	"excision repair cross-complementing rodent repair deficiency, complementation group 3 (xeroderma pigmentosum group B complementing)"		E	.	ERCC3	73	.	0			c.G1468T						.						58	52	54					2																	128038082		2203	4300	6503	SO:0001587	stop_gained	2071	exon9	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	TGGCTTCGTAGAG	M31899	CCDS2144.1	2q21	2014-09-17	2014-03-07		ENSG00000163161	ENSG00000163161		"General transcription factors", "General transcription factor IIH complex subunits"	3435	protein-coding gene	gene with protein product	"xeroderma pigmentosum group B complementing"	133510	"excision repair cross-complementing rodent repair deficiency, complementation group 3"			8202161	Standard	NM_000122		Approved	XPB, BTF2, RAD25, TFIIH, GTF2H	uc002toh.1	P19447	OTTHUMG00000131530	ENST00000285398.2:c.1468G>T	chr2.hg19:g.128038082C>A	ENSP00000285398:p.Glu490*	107.0	0.0		114.0	40.0	NM_000122	Q53QM0	Nonsense_Mutation	SNP	ENST00000285398.2	hg19	CCDS2144.1	.	.	.	.	.	.	.	.	.	.	c	43	10.103434	0.99337	.	.	ENSG00000163161	ENST00000285398;ENST00000493187	.	.	.	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-25.294	19.6423	0.95763	0.0:1.0:0.0:0.0	.	.	.	.	X	490;426	.	ENSP00000285398:E490X	E	-	1	0	ERCC3	127754552	1.000000	0.71417	0.998000	0.56505	0.978000	0.69477	7.808000	0.86044	2.636000	0.89361	0.645000	0.84053	GAA	.	.		0.547	ERCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331028.1	NM_000122		A	128038082	C	A	128038082	4	1	335	1	0	0	0	0	0	1	0	0	5216	893	31	1	908	1	ERCC3	2	128038082	Nonsense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	24916196	128038082	115161291	24	46575										
ACVR2A	92	hgsc.bcm.edu	37	chr2	148674983	148674983	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gatctttggctgatcacagcAtttcatgaaaaggtaaaact	8	7	3	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:148674983A>G	ENST00000241416.7	+	6	1440	c.804A>G	c.(802-804)gcA>gcG	p.A268A	ACVR2A_ENST00000404590.1_Silent_p.A268A|ACVR2A_ENST00000535787.1_Silent_p.A160A	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	268	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		TGATCACAGCATTTCATGAAA	0.398																																					p.A268A		Atlas-SNP	.											.	ACVR2A	125	.	0			c.A804G						.						101	86	91					2																	148674983		2203	4299	6502	SO:0001819	synonymous_variant	92	exon6			CACAGCATTTCAT		CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"activin A receptor, type II"	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.804A>G	chr2.hg19:g.148674983A>G		127.0	0.0		110.0	29.0	NM_001616	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	Silent	SNP	ENST00000241416.7	hg19	CCDS33301.1																																																																																			.	.		0.398	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616		G	148674983	A	G	148674983	2	3	335	1	0	0	0	0	0	0	0	1	223	204	8	2		2	ACVR2A	2	148674983	Silent	SNP	A	TCGA-RC-A6M6-01A-11D-A32G-10	20636901	148674983	94524390	25	46576										
CYTIP	9595	hgsc.bcm.edu	37	chr2	158283867	158283867	+	Frame_Shift_Del	DEL	A	A	-													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	cattaaattaaattacctttAaaacctgcagctttgcttca							TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:158283867delA	ENST00000264192.3	-	6	663	c.542delT	c.(541-543)ttafs	p.L181fs	CYTIP_ENST00000540637.1_Frame_Shift_Del_p.L75fs	NM_004288.4	NP_004279.3	O60759	CYTIP_HUMAN	cytohesin 1 interacting protein	181	Interaction with CYTH1.				regulation of cell adhesion (GO:0030155)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|endosome (GO:0005768)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	15						AATTACCTTTAAAACCTGCAG	0.353																																					p.L181fs		Atlas-Indel,Pindel	.											.	CYTIP	45	.	0			c.543delA						.						59	58	58					2																	158283867		2201	4297	6498	SO:0001589	frameshift_variant	9595	exon6			.	L06633	CCDS2204.1	2q11.2	2011-09-08	2008-08-14	2008-08-19	ENSG00000115165	ENSG00000115165			9506	protein-coding gene	gene with protein product	"cytohesin binding protein HE", "cytohesin binder and regulator"	604448	"pleckstrin homology, Sec7 and coiled-coil domains, binding protein"	PSCDBP		18926288, 10343115, 11867758, 20530790, 21562043	Standard	NM_004288		Approved	B3-1, HE, CYBR, CASP, CYTHIP	uc002tzj.1	O60759	OTTHUMG00000154551	ENST00000264192.3:c.542delT	chr2.hg19:g.158283867delA	ENSP00000264192:p.Leu181fs	91.0	0.0		96.0	38.0	NM_004288	B4DWH9|Q15630|Q8NE32	Frame_Shift_Del	DEL	ENST00000264192.3	hg19	CCDS2204.1																																																																																			.	.		0.353	CYTIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254926.1	NM_004288		-	158283867	A	-	158283867	7	5	335	1	0	1	0	1	0	0	0	0	4209	372	13	0	549	0	CYTIP	2	158283867	Frame_Shift_Del	DEL	A	TCGA-RC-A6M6-01A-11D-A32G-10	9608884	158283867	84915506	26	46577										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168102891	168102891	+	Frame_Shift_Del	DEL	A	A	-													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ggtgatgtacaacaagcaatAaaaaacctgttctctgagga							TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:168102891delA	ENST00000409195.1	+	9	5078	c.4989delA	c.(4987-4989)atafs	p.I1663fs	XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409273.1_Frame_Shift_Del_p.I1441fs|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000295237.9_Frame_Shift_Del_p.I1663fs|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1488					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AACAAGCAATAAAAAACCTGT	0.313																																					p.I1663fs		Atlas-Indel,Pindel	.											.	XIRP2	914	.	0			c.4988delT						.						67	63	64					2																	168102891		1856	4084	5940	SO:0001589	frameshift_variant	129446	exon9			.	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.4989delA	chr2.hg19:g.168102891delA	ENSP00000386840:p.Ile1663fs	207.0	0.0		211.0	95.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Frame_Shift_Del	DEL	ENST00000409195.1	hg19	CCDS42769.1																																																																																			.	.		0.313	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		-	168102891	A	-	168102891	7	5	335	1	0	1	0	1	0	0	0	0	17445	352	13	0	5019	0	XIRP2	2	168102891	Frame_Shift_Del	DEL	A	TCGA-RC-A6M6-01A-11D-A32G-10	9819024	168102891	75096482	27	46578										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168105997	168105997	+	Frame_Shift_Del	DEL	C	C	-													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	atttggagcagttgcacttgCcccaaagcaaaccaatttcc							TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:168105997delC	ENST00000409195.1	+	9	8184	c.8095delC	c.(8095-8097)cccfs	p.P2699fs	XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409273.1_Frame_Shift_Del_p.P2477fs|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000295237.9_Frame_Shift_Del_p.P2699fs|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2524					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						GTTGCACTTGCCCCAAAGCAA	0.368																																					p.L2698fs		Atlas-Indel,Pindel	.											.	XIRP2	914	.	0			c.8094delG						.						93	91	92					2																	168105997		1853	4088	5941	SO:0001589	frameshift_variant	129446	exon9			.	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.8095delC	chr2.hg19:g.168105997delC	ENSP00000386840:p.Pro2699fs	135.0	0.0		127.0	43.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Frame_Shift_Del	DEL	ENST00000409195.1	hg19	CCDS42769.1																																																																																			.	.		0.368	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		-	168105997	C	-	168105997	7	5	335	1	0	1	0	1	0	0	0	0	17445	739	26	0	8125	0	XIRP2	2	168105997	Frame_Shift_Del	DEL	C	TCGA-RC-A6M6-01A-11D-A32G-10	3106	168105997	75093376	28	46579										
TTN	7273	hgsc.bcm.edu	37	chr2	179472259	179472259	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tggttccaacgttgtctattAcaacacggtctttatccagc	7	11	2	0	rs564121832		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:179472259A>T	ENST00000591111.1	-	227	48457	c.48233T>A	c.(48232-48234)gTa>gAa	p.V16078E	TTN_ENST00000589042.1_Missense_Mutation_p.V17719E|TTN_ENST00000342175.6_Missense_Mutation_p.V8846E|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.V8779E|TTN_ENST00000460472.2_Missense_Mutation_p.V8654E|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V15151E|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA			Q8WZ42	TITIN_HUMAN	titin	16078	Ig-like 99.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTTGTCTATTACAACACGGTC	0.448																																					p.V17719E		Atlas-SNP	.											.	TTN	18412	.	0			c.T53156A						.						434	410	418					2																	179472259		1899	4124	6023	SO:0001583	missense	7273	exon277			TCTATTACAACAC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.48233T>A	chr2.hg19:g.179472259A>T	ENSP00000465570:p.Val16078Glu	152.0	0.0		165.0	57.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	10.42	1.344158	0.24339	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17	5.99	4.81	0.61882	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.43077	0.1231	N	0.05534	-0.03	0.40995	D	0.984883	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.08055	0.003;0.003;0.003;0.001	T	0.35301	-0.9794	9	0.87932	D	0	.	12.5224	0.56067	0.8689:0.0:0.0:0.1311	.	8654;8779;8846;16078	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	E	15151;8654;8846;8779;8654	ENSP00000343764:V15151E;ENSP00000434586:V8654E;ENSP00000340554:V8846E;ENSP00000352154:V8779E	ENSP00000340554:V8846E	V	-	2	0	TTN	179180504	0.931000	0.31567	0.997000	0.53966	0.922000	0.55478	1.555000	0.36277	1.041000	0.40125	0.533000	0.62120	GTA	.	.		0.448	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179472259	A	T	179472259	3	4	335	1	0	0	0	0	1	0	0	0	16750	391	14	4	54881	4	TTN	2	179472259	Missense_Mutation	SNP	A	TCGA-RC-A6M6-01A-11D-A32G-10	11366262	179472259	63727114	29	46580										
TTN	7273	hgsc.bcm.edu	37	chr2	179501228	179501228	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tgaacatcaatgatgtgcagCtttctgtctttaccatctgc	7	10	4	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:179501228C>A	ENST00000591111.1	-	175	36527	c.36303G>T	c.(36301-36303)aaG>aaT	p.K12101N	TTN_ENST00000589042.1_Missense_Mutation_p.K13742N|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.K4869N|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000418062.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.K4802N|TTN_ENST00000460472.2_Missense_Mutation_p.K4677N|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.K11174N|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12101	Ig-like 80.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGATGTGCAGCTTTCTGTCTT	0.443																																					p.K13742N		Atlas-SNP	.											.	TTN	18412	.	0			c.G41226T						.						110	103	106					2																	179501228		1863	4114	5977	SO:0001583	missense	7273	exon225			GTGCAGCTTTCTG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.36303G>T	chr2.hg19:g.179501228C>A	ENSP00000465570:p.Lys12101Asn	146.0	0.0		148.0	54.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	9.284	1.048873	0.19827	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29	5.68	4.8	0.61643	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.73202	0.3557	L	0.39245	1.2	0.46078	D	0.998852	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.998;0.998;0.998	T	0.75158	-0.3416	9	0.87932	D	0	.	10.1437	0.42751	0.0:0.791:0.0:0.209	.	4677;4802;4869;12101	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	N	11174;4677;4869;4802;4677	ENSP00000343764:K11174N;ENSP00000434586:K4677N;ENSP00000340554:K4869N;ENSP00000352154:K4802N	ENSP00000340554:K4869N	K	-	3	2	TTN	179209473	0.994000	0.37717	1.000000	0.80357	0.584000	0.36387	0.475000	0.22164	1.415000	0.47037	-0.162000	0.13425	AAG	.	.		0.443	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179501228	C	A	179501228	3	1	335	1	0	0	0	0	1	0	0	0	16750	796	28	3	67019	3	TTN	2	179501228	Missense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	28969	179501228	63698145	30	46581										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196771386	196771387	+	Frame_Shift_Ins	INS	-	-	A													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ataactccttccataccttcINSaggttatctggcagttctga							TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:196771386_196771387insA	ENST00000312428.6	-	27	4431_4432	c.4331_4332insT	c.(4330-4332)ctgfs	p.L1444fs		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	1444	AAA 1. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						TCCATACCTTCAGGTTATCTGG	0.391																																					p.L1444fs		Atlas-Indel,Pindel	.											.	DNAH7	512	.	0			c.4332_4333insT						.																																			SO:0001589	frameshift_variant	56171	exon27			.	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.4332dupT	chr2.hg19:g.196771387_196771387dupA	ENSP00000311273:p.Leu1444fs	326.0	0.0		303.0	107.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Frame_Shift_Ins	INS	ENST00000312428.6	hg19	CCDS42794.1																																																																																			.	.		0.391	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		A	196771387	-	A	196771386	7	5	335	1	0	1	1	0	0	0	0	0	4608	813	29	0	7898	0	DNAH7	2	196771386	Frame_Shift_Ins	INS	-	TCGA-RC-A6M6-01A-11D-A32G-10	17270158	196771386	46427987	31	46582										
SPEG	10290	hgsc.bcm.edu	37	chr2	220326629	220326631	+	In_Frame_Del	DEL	CCC	CCC	-													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tctacatcccctttcagcagCcccatcacctccgacgagga							TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	CCC	CCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:220326629_220326631delCCC	ENST00000312358.7	+	7	2598_2600	c.2466_2468delCCC	c.(2464-2469)agcccc>agc	p.P823del	SPEG_ENST00000396686.1_5'UTR|SPEG_ENST00000396698.1_In_Frame_Del_p.P719del|SPEG_ENST00000485813.1_3'UTR|SPEG_ENST00000396689.2_5'UTR|SPEG_ENST00000396688.1_5'UTR|SPEG_ENST00000396695.2_In_Frame_Del_p.P31del	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	823					cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		CTTTCAGCAGCCCCATCACCTCC	0.635																																					p.822_823del		Atlas-Indel,Pindel	.											.	SPEG	272	.	0			c.2465_2467del						.																																			SO:0001651	inframe_deletion	10290	exon7			.	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"Immunoglobulin superfamily / I-set domain containing"	16901	protein-coding gene	gene with protein product		615950	"aortic preferentially expressed gene 1"	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.2466_2468delCCC	chr2.hg19:g.220326629_220326631delCCC	ENSP00000311684:p.Pro823del	60.0	0.0		65.0	24.0	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	In_Frame_Del	DEL	ENST00000312358.7	hg19	CCDS42824.1																																																																																			.	.		0.635	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		-	220326631	CCC	-	220326629	7	5	335	1	0	1	0	1	0	0	0	0	15051	738	26	0	2492	0	SPEG	2	220326629	In_Frame_Del	DEL	CCC	TCGA-RC-A6M6-01A-11D-A32G-10	23555243	220326629	22872744	32	46583										
SPEG	10290	hgsc.bcm.edu	37	chr2	220348586	220348586	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gagcagcagcttctcccaggGtgaggcggagccccggggcc	17	14	1	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:220348586G>T	ENST00000312358.7	+	30	6533	c.6401G>T	c.(6400-6402)gGt>gTt	p.G2134V	AC053503.11_ENST00000429882.1_RNA|SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	2134					cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		TTCTCCCAGGGTGAGGCGGAg	0.731																																					p.G2134V		Atlas-SNP	.											.	SPEG	272	.	0			c.G6401T						.						7	9	8					2																	220348586		1801	3972	5773	SO:0001583	missense	10290	exon30			CCCAGGGTGAGGC	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"Immunoglobulin superfamily / I-set domain containing"	16901	protein-coding gene	gene with protein product		615950	"aortic preferentially expressed gene 1"	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.6401G>T	chr2.hg19:g.220348586G>T	ENSP00000311684:p.Gly2134Val	13.0	0.0		11.0	5.0	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	hg19	CCDS42824.1	.	.	.	.	.	.	.	.	.	.	G	11.78	1.741843	0.30865	.	.	ENSG00000072195	ENST00000312358;ENST00000265327	T	0.65916	-0.18	4.16	2.31	0.28768	.	0.000000	0.35870	U	0.002936	T	0.49474	0.1559	L	0.29908	0.895	0.80722	D	1	B	0.20052	0.041	B	0.18263	0.021	T	0.46925	-0.9156	10	0.66056	D	0.02	.	13.0329	0.58854	0.0:0.3093:0.6907:0.0	.	2134	Q15772	SPEG_HUMAN	V	2134	ENSP00000311684:G2134V	ENSP00000265327:G2134V	G	+	2	0	SPEG	220056830	1.000000	0.71417	0.159000	0.22649	0.951000	0.60555	4.955000	0.63638	0.387000	0.25024	0.455000	0.32223	GGT	.	.		0.731	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		T	220348586	G	T	220348586	3	4	335	1	0	0	0	0	1	0	0	0	15051	1261	44	3	6531	3	SPEG	2	220348586	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	21957	220348586	22850787	33	46584										
SLC4A3	6508	hgsc.bcm.edu	37	chr2	220500505	220500505	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	atgtgaggcgccggtacccgCactaccccagtgacctgcga	12	15	0	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:220500505C>T	ENST00000358055.3	+	14	2595	c.2083C>T	c.(2083-2085)Cac>Tac	p.H695Y	SLC4A3_ENST00000317151.3_Missense_Mutation_p.H695Y|SLC4A3_ENST00000373762.3_Missense_Mutation_p.H722Y|SLC4A3_ENST00000373760.2_Missense_Mutation_p.H695Y|SLC4A3_ENST00000273063.6_Missense_Mutation_p.H722Y			P48751	B3A3_HUMAN	solute carrier family 4 (anion exchanger), member 3	695					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	51		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCGGTACCCGCACTACCCCAG	0.647																																					p.H722Y		Atlas-SNP	.											SLC4A3,NS,carcinoma,0,1	SLC4A3	144	.	0			c.C2164T						.						35	35	35					2																	220500505		2203	4300	6503	SO:0001583	missense	6508	exon14			TACCCGCACTACC		CCDS2445.1, CCDS2446.1	2q35	2013-07-19	2013-07-19		ENSG00000114923	ENSG00000114923		"Solute carriers"	11029	protein-coding gene	gene with protein product	"Anion exchanger 3, neuronal"	106195	"solute carrier family 4, anion exchanger, member 3"			8001971	Standard	NM_005070		Approved	AE3, SLC2C	uc002vmo.4	P48751	OTTHUMG00000059238	ENST00000358055.3:c.2083C>T	chr2.hg19:g.220500505C>T	ENSP00000350756:p.His695Tyr	63.0	0.0		66.0	31.0	NM_201574	A6H8L2|A8K1Q9|B7ZVX6|B9EGD1|Q6YIQ9	Missense_Mutation	SNP	ENST00000358055.3	hg19	CCDS2445.1	.	.	.	.	.	.	.	.	.	.	C	12.72	2.022579	0.35701	.	.	ENSG00000114923	ENST00000358055;ENST00000373760;ENST00000273063;ENST00000373762;ENST00000317151	T;T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2;-1.2	4.09	3.21	0.36854	Bicarbonate transporter, C-terminal (1);	0.889253	0.09963	N	0.733115	T	0.63307	0.2500	L	0.33624	1.015	0.24725	N	0.993126	B;B;B	0.13145	0.001;0.007;0.005	B;B;B	0.19391	0.002;0.019;0.025	T	0.49283	-0.8956	10	0.09843	T	0.71	.	5.7029	0.17893	0.3353:0.5635:0.0:0.1012	.	399;695;722	P48751-2;P48751;P48751-3	.;B3A3_HUMAN;.	Y	695;695;722;722;695	ENSP00000350756:H695Y;ENSP00000362865:H695Y;ENSP00000273063:H722Y;ENSP00000362867:H722Y;ENSP00000314006:H695Y	ENSP00000273063:H722Y	H	+	1	0	SLC4A3	220208749	0.806000	0.28996	0.861000	0.33841	0.991000	0.79684	1.638000	0.37165	1.059000	0.40554	0.643000	0.83706	CAC	.	.		0.647	SLC4A3-009	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316472.1	NM_005070		T	220500505	C	T	220500505	3	4	335	1	0	0	0	0	1	0	0	0	14670	710	25	3	2214	3	SLC4A3	2	220500505	Missense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	151919	220500505	22698868	34	46585										
AGAP1	116987	hgsc.bcm.edu	37	chr2	237032735	237032735	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gagaaacaataaccggaacaAcagcagtgggagggtgccca	13	9	0	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:237032735A>G	ENST00000304032.8	+	18	3123	c.2543A>G	c.(2542-2544)aAc>aGc	p.N848S	AGAP1_ENST00000428334.2_Missense_Mutation_p.N687S|AGAP1_ENST00000409538.1_Missense_Mutation_p.N1060S|AGAP1_ENST00000336665.5_Missense_Mutation_p.N795S	NM_001037131.2	NP_001032208.1	Q9UPQ3	AGAP1_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	848					protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|phospholipid binding (GO:0005543)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						AACCGGAACAACAGCAGTGGG	0.637																																					p.N848S		Atlas-SNP	.											.	AGAP1	95	.	0			c.A2543G						.						58	63	61					2																	237032735		2203	4300	6503	SO:0001583	missense	116987	exon18			GGAACAACAGCAG	AF413078	CCDS2514.1, CCDS33408.1, CCDS58756.1	2q37	2013-01-10	2008-09-22	2008-09-22	ENSG00000157985	ENSG00000157985		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16922	protein-coding gene	gene with protein product		608651	"centaurin, gamma 2"	CENTG2			Standard	NM_001037131		Approved	KIAA1099, GGAP1	uc002vvs.3	Q9UPQ3	OTTHUMG00000133293	ENST00000304032.8:c.2543A>G	chr2.hg19:g.237032735A>G	ENSP00000307634:p.Asn848Ser	80.0	0.0		124.0	26.0	NM_001037131	B2RTX7|Q541S5|Q6P9D7|Q9NV93	Missense_Mutation	SNP	ENST00000304032.8	hg19	CCDS33408.1	.	.	.	.	.	.	.	.	.	.	A	14.34	2.507666	0.44558	.	.	ENSG00000157985	ENST00000304032;ENST00000336665;ENST00000409538;ENST00000428334	T;T;T;T	0.70516	-0.49;-0.44;-0.44;0.59	4.5	3.27	0.37495	.	0.476338	0.22398	N	0.060589	T	0.70971	0.3285	L	0.38175	1.15	0.45108	D	0.998124	B;P	0.52842	0.002;0.956	B;D	0.65010	0.002;0.931	T	0.63449	-0.6635	10	0.15066	T	0.55	.	8.9317	0.35675	0.9001:0.0:0.0999:0.0	.	795;848	Q9UPQ3-2;Q9UPQ3	.;AGAP1_HUMAN	S	848;795;1060;687	ENSP00000307634:N848S;ENSP00000338378:N795S;ENSP00000386897:N1060S;ENSP00000411824:N687S	ENSP00000307634:N848S	N	+	2	0	AGAP1	236697474	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.418000	0.52721	0.530000	0.28619	0.460000	0.39030	AAC	.	.		0.637	AGAP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257076.2	NM_014914		G	237032735	A	G	237032735	3	3	335	1	0	0	0	0	1	0	0	0	366	43	2	2	2613	2	AGAP1	2	237032735	Missense_Mutation	SNP	A	TCGA-RC-A6M6-01A-11D-A32G-10	16532230	237032735	6166638	35	46586										
HDAC4	9759	hgsc.bcm.edu	37	chr2	240056268	240056268	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	cccagcgtgatgttgggcaaGgatggcgatgtgtagagggg	19	6	0	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:240056268G>A	ENST00000345617.3	-	10	1841	c.1050C>T	c.(1048-1050)tcC>tcT	p.S350S	HDAC4_ENST00000553145.1_5'UTR|HDAC4_ENST00000543185.1_5'UTR|HDAC4_ENST00000541256.1_Silent_p.S319S	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	350					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		TGTTGGGCAAGGATGGCGATG	0.637																																					p.S350S		Atlas-SNP	.											.	HDAC4	127	.	0			c.C1050T						.						117	118	117					2																	240056268		2203	4300	6503	SO:0001819	synonymous_variant	9759	exon10			GGGCAAGGATGGC	AB006626	CCDS2529.1	2q37.3	2014-02-12			ENSG00000068024	ENSG00000068024			14063	protein-coding gene	gene with protein product		605314	"brachydactyly-mental retardation syndrome"	BDMR		10206986, 10220385, 20691407	Standard	NM_006037		Approved	KIAA0288, HDAC-A, HDACA, HD4, HA6116, HDAC-4	uc002vyk.4	P56524	OTTHUMG00000133344	ENST00000345617.3:c.1050C>T	chr2.hg19:g.240056268G>A		52.0	0.0		71.0	16.0	NM_006037	Q9UND6	Silent	SNP	ENST00000345617.3	hg19	CCDS2529.1	.	.	.	.	.	.	.	.	.	.	G	1.601	-0.526577	0.04141	.	.	ENSG00000068024	ENST00000445704	.	.	.	4.32	3.44	0.39384	.	.	.	.	.	T	0.54431	0.1858	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50145	-0.8862	4	.	.	.	.	5.5916	0.17303	0.2438:0.1494:0.6068:0.0	.	.	.	.	L	94	.	.	P	-	2	0	HDAC4	239721205	0.429000	0.25530	0.584000	0.28653	0.117000	0.20001	0.304000	0.19228	1.126000	0.42016	0.561000	0.74099	CCT	.	.		0.637	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037		A	240056268	G	A	240056268	2	1	335	1	0	0	0	0	0	0	0	1	7018	987	35	3		3	HDAC4	2	240056268	Silent	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	3023533	240056268	3143105	36	46587										
PDCD1	5133	hgsc.bcm.edu	37	chr2	242793440	242793440	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gaacacaggcacggctgaggGgtcctccttctttgaggaga	14	10	1	3			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:242793440G>A	ENST00000334409.5	-	5	706	c.637C>T	c.(637-639)Ccc>Tcc	p.P213S		NM_005018.2	NP_005009.2	Q15116	PDCD1_HUMAN	programmed cell death 1	213					apoptotic process (GO:0006915)|humoral immune response (GO:0006959)|multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			endometrium(1)|lung(2)|ovary(1)|prostate(3)|skin(1)	8		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;3.84e-33)|all cancers(36;8.08e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.41e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0219)		ACGGCTGAGGGGTCCTCCTTC	0.662																																					p.P213S		Atlas-SNP	.											.	PDCD1	31	.	0			c.C637T						.						34	39	37					2																	242793440		2203	4300	6503	SO:0001583	missense	5133	exon5			CTGAGGGGTCCTC	AY206416	CCDS33428.1	2q37.3	2014-01-29			ENSG00000188389	ENSG00000188389		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	8760	protein-coding gene	gene with protein product		600244	"systemic lupus erythematosus susceptibility 2"	SLEB2		7851902, 12402038	Standard	NM_005018		Approved	CD279, PD1, hSLE1	uc002wcq.4	Q15116	OTTHUMG00000151342	ENST00000334409.5:c.637C>T	chr2.hg19:g.242793440G>A	ENSP00000335062:p.Pro213Ser	46.0	0.0		44.0	20.0	NM_005018	O00517|Q8IX89	Missense_Mutation	SNP	ENST00000334409.5	hg19	CCDS33428.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.63|13.63	2.294624|2.294624	0.40594|0.40594	.|.	.|.	ENSG00000188389|ENSG00000188389	ENST00000343705|ENST00000334409;ENST00000539073	.|T	.|0.68025	.|-0.3	3.79|3.79	1.78|1.78	0.24846|0.24846	.|.	0.503154|0.503154	0.16273|0.16273	N|N	0.221708|0.221708	T|T	0.51907|0.51907	0.1702|0.1702	L|L	0.43152|0.43152	1.355|1.355	0.09310|0.09310	N|N	0.999999|0.999999	.|B;B	.|0.25235	.|0.121;0.121	.|B;B	.|0.20577	.|0.03;0.03	T|T	0.40739|0.40739	-0.9547|-0.9547	6|10	.|0.41790	.|T	.|0.15	-4.7864|-4.7864	5.037|5.037	0.14440|0.14440	0.133:0.214:0.653:0.0|0.133:0.214:0.653:0.0	.|.	.|213;213	.|Q8IX89;Q15116	.|.;PDCD1_HUMAN	L|S	104|213;161	.|ENSP00000335062:P213S	.|ENSP00000335062:P213S	P|P	-|-	2|1	0|0	PDCD1|PDCD1	242442113|242442113	0.001000|0.001000	0.12720|0.12720	0.003000|0.003000	0.11579|0.11579	0.741000|0.741000	0.42261|0.42261	0.304000|0.304000	0.19228|0.19228	0.283000|0.283000	0.22279|0.22279	0.555000|0.555000	0.69702|0.69702	CCC|CCC	.	.		0.662	PDCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322313.1	NM_005018		A	242793440	G	A	242793440	3	1	335	1	0	0	0	0	1	0	0	0	11624	1232	43	3	233	3	PDCD1	2	242793440	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	2737172	242793440	405933	37	46588										
XIRP1	165904	hgsc.bcm.edu	37	chr3	39228092	39228092	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	cactggactcgggtcagccgGgggctcccaccgcagactgt	14	15	1	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr3:39228092G>A	ENST00000340369.3	-	2	3073	c.2845C>T	c.(2845-2847)Ccg>Tcg	p.P949S	XIRP1_ENST00000396251.1_Missense_Mutation_p.P949S|XIRP1_ENST00000421646.1_Intron	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	949					cardiac muscle cell development (GO:0055013)|negative regulation of cell proliferation (GO:0008285)|regulation of membrane potential (GO:0042391)|sarcomere organization (GO:0045214)	fascia adherens (GO:0005916)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(14)|lung(22)|ovary(4)|pancreas(1)|prostate(2)|skin(6)	71				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		GGGTCAGCCGGGGGCTCCCAC	0.632																																					p.P949S		Atlas-SNP	.											.	XIRP1	173	.	0			c.C2845T						.						32	35	34					3																	39228092		2203	4300	6503	SO:0001583	missense	165904	exon2			CAGCCGGGGGCTC	AW755250	CCDS2683.1, CCDS56245.1	3p21.33	2008-02-05	2007-06-27	2007-06-27	ENSG00000168334	ENSG00000168334			14301	protein-coding gene	gene with protein product		609777	"cardiomyopathy associated 1"	CMYA1		12203715, 15454575	Standard	NM_001198621		Approved	DKFZp451D042, Xin	uc003cjk.2	Q702N8	OTTHUMG00000131297	ENST00000340369.3:c.2845C>T	chr3.hg19:g.39228092G>A	ENSP00000343140:p.Pro949Ser	63.0	0.0		53.0	38.0	NM_001198621	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Missense_Mutation	SNP	ENST00000340369.3	hg19	CCDS2683.1	.	.	.	.	.	.	.	.	.	.	G	7.739	0.700886	0.15172	.	.	ENSG00000168334	ENST00000396251;ENST00000340369	T;T	0.05580	3.42;3.72	5.03	4.16	0.48862	.	0.999489	0.08095	N	0.998728	T	0.15435	0.0372	L	0.57536	1.79	0.80722	D	1	P;P	0.43094	0.799;0.748	P;P	0.50537	0.643;0.541	T	0.00880	-1.1529	10	0.56958	D	0.05	.	10.0178	0.42024	0.0943:0.0:0.9057:0.0	.	949;949	Q702N8;Q702N8-2	XIRP1_HUMAN;.	S	949	ENSP00000379550:P949S;ENSP00000343140:P949S	ENSP00000343140:P949S	P	-	1	0	XIRP1	39203096	0.900000	0.30661	0.231000	0.23993	0.119000	0.20118	2.049000	0.41288	1.289000	0.44618	-0.126000	0.14955	CCG	.	.		0.632	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522		A	39228092	G	A	39228092	3	1	335	1	0	0	0	0	1	0	0	0	17444	1232	43	3	2690	3	XIRP1	3	39228092	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10		39228092	158794338	38	46589										
BSN	8927	hgsc.bcm.edu	37	chr3	49690047	49690048	+	In_Frame_Ins	INS	-	-	AGCAGC													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gcagcgtctagaagaagcaaINSagcagcagcgcaaggcccgg							TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr3:49690047_49690048insAGCAGC	ENST00000296452.4	+	5	3172_3173	c.3058_3059insAGCAGC	c.(3058-3060)aag>aAGCAGCag	p.1022_1023insQQ		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	1022					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		AGAAGAAGCAAAGCAGCAGCGC	0.653																																					p.K1020delinsKQQ		Atlas-Indel,Pindel	.											.	BSN	272	.	0			c.3058_3059insAGCAGC						.																																			SO:0001652	inframe_insertion	8927	exon5			.	AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"zinc finger protein 231", "neuronal double zinc finger protein"	604020	"bassoon (presynaptic cytomatrix protein)"	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.3059_3064dupAGCAGC	chr3.hg19:g.49690048_49690053dupAGCAGC	ENSP00000296452:p.Gln1021_Gln1022dup	44.0	0.0		49.0	17.0	NM_003458	O43161|Q7LGH3	In_Frame_Ins	INS	ENST00000296452.4	hg19	CCDS2800.1																																																																																			.	.		0.653	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458		AGCAGC	49690048	-	AGCAGC	49690047	7	5	335	1	0	1	1	0	0	0	0	0	1532	15	1	0	3076	0	BSN	3	49690047	In_Frame_Ins	INS	-	TCGA-RC-A6M6-01A-11D-A32G-10	10461955	49690047	148332383	39	46590										
STAB1	23166	hgsc.bcm.edu	37	chr3	52553354	52553354	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gtgaacggcatcctgcacttCattgaccgtgtcctgctgcc	10	14	1	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr3:52553354C>A	ENST00000321725.6	+	49	5185	c.5109C>A	c.(5107-5109)ttC>ttA	p.F1703L		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	1703	FAS1 5. {ECO:0000255|PROSITE- ProRule:PRU00082, ECO:0000305}.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)			breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		TCCTGCACTTCATTGACCGTG	0.642																																					p.F1703L		Atlas-SNP	.											.	STAB1	178	.	0			c.C5109A						.						122	122	122					3																	52553354		2203	4299	6502	SO:0001583	missense	23166	exon49			GCACTTCATTGAC	AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"MS-1 antigen", "fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1", "common lymphatic endothelial and vascular endothelial receptor-1"	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.5109C>A	chr3.hg19:g.52553354C>A	ENSP00000312946:p.Phe1703Leu	99.0	0.0		74.0	50.0	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Missense_Mutation	SNP	ENST00000321725.6	hg19	CCDS33768.1	.	.	.	.	.	.	.	.	.	.	C	15.62	2.886623	0.51908	.	.	ENSG00000010327	ENST00000321725	D	0.90004	-2.6	5.5	5.5	0.81552	FAS1 domain (5);	0.121338	0.64402	D	0.000018	D	0.88969	0.6582	N	0.16790	0.44	0.44531	D	0.997487	D	0.67145	0.996	D	0.64776	0.929	D	0.88017	0.2766	10	0.30078	T	0.28	.	17.5833	0.87973	0.0:1.0:0.0:0.0	.	1703	Q9NY15	STAB1_HUMAN	L	1703	ENSP00000312946:F1703L	ENSP00000312946:F1703L	F	+	3	2	STAB1	52528394	1.000000	0.71417	1.000000	0.80357	0.040000	0.13550	1.229000	0.32600	2.574000	0.86865	0.655000	0.94253	TTC	.	.		0.642	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136		A	52553354	C	A	52553354	3	1	335	1	0	0	0	0	1	0	0	0	15252	825	29	3	5303	3	STAB1	3	52553354	Missense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	2863307	52553354	145469076	40	46591										
GPR15	2838	hgsc.bcm.edu	37	chr3	98251158	98251158	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tctctgggtggataaagaagCatctctaggactgtggagga	14	6	2	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr3:98251158C>A	ENST00000284311.3	+	1	416	c.281C>A	c.(280-282)gCa>gAa	p.A94E		NM_005290.1	NP_005281.1	P49685	GPR15_HUMAN	G protein-coupled receptor 15	94					G-protein coupled receptor signaling pathway (GO:0007186)|T cell migration (GO:0072678)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			endometrium(1)|kidney(3)|large_intestine(1)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Lung NSC(201;7.93e-06)|all_neural(597;0.00172)|Hepatocellular(537;0.00825)|Myeloproliferative disorder(1037;0.0255)		Lung(72;0.246)		GATAAAGAAGCATCTCTAGGA	0.502																																					p.A94E		Atlas-SNP	.											GPR15,NS,carcinoma,+1,1	GPR15	55	.	0			c.C281A						.						79	80	79					3																	98251158		2203	4300	6503	SO:0001583	missense	2838	exon1			AAGAAGCATCTCT		CCDS2931.1	3q11.2-q13.1	2014-01-30			ENSG00000154165	ENSG00000154165		"GPCR / Class A : Orphans"	4469	protein-coding gene	gene with protein product		601166				8838812	Standard	NM_005290		Approved		uc011bgy.3	P49685	OTTHUMG00000160017	ENST00000284311.3:c.281C>A	chr3.hg19:g.98251158C>A	ENSP00000284311:p.Ala94Glu	115.0	0.0		85.0	32.0	NM_005290	Q3MIL4|Q6ISN6	Missense_Mutation	SNP	ENST00000284311.3	hg19	CCDS2931.1	.	.	.	.	.	.	.	.	.	.	C	15.90	2.968982	0.53614	.	.	ENSG00000154165	ENST00000284311	T	0.38401	1.14	4.8	4.8	0.61643	GPCR, rhodopsin-like superfamily (1);	0.000000	0.50627	D	0.000101	T	0.49712	0.1573	M	0.80422	2.495	0.22500	N	0.999046	P	0.47841	0.901	P	0.47299	0.543	T	0.53690	-0.8403	10	0.72032	D	0.01	-2.4607	15.7547	0.78015	0.0:1.0:0.0:0.0	.	94	P49685	GPR15_HUMAN	E	94	ENSP00000284311:A94E	ENSP00000284311:A94E	A	+	2	0	GPR15	99733848	0.000000	0.05858	0.986000	0.45419	0.970000	0.65996	-0.160000	0.10041	2.656000	0.90262	0.591000	0.81541	GCA	.	.		0.502	GPR15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358907.1			A	98251158	C	A	98251158	3	1	335	1	0	0	0	0	1	0	0	0	6663	710	25	3	283	3	GPR15	3	98251158	Missense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	45697804	98251158	99771272	41	46592										
PODXL2	50512	hgsc.bcm.edu	37	chr3	127379537	127379537	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ggggccaccaaaagcaggcaTgaagactccggggaccaggc	15	12	0	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr3:127379537T>A	ENST00000342480.6	+	3	705	c.666T>A	c.(664-666)caT>caA	p.H222Q		NM_015720.2	NP_056535.1	Q9NZ53	PDXL2_HUMAN	podocalyxin-like 2	222					leukocyte tethering or rolling (GO:0050901)	integral component of plasma membrane (GO:0005887)	glycosaminoglycan binding (GO:0005539)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	26						AAAGCAGGCATGAAGACTCCG	0.602																																					p.H222Q		Atlas-SNP	.											.	PODXL2	53	.	0			c.T666A						.						80	90	87					3																	127379537		2203	4300	6503	SO:0001583	missense	50512	exon3			CAGGCATGAAGAC	AF219137	CCDS3044.1	3q21.3	2005-02-18			ENSG00000114631	ENSG00000114631			17936	protein-coding gene	gene with protein product	"endoglycan"					10722749	Standard	NM_015720		Approved	PODLX2, endoglycan	uc003ejq.3	Q9NZ53	OTTHUMG00000159642	ENST00000342480.6:c.666T>A	chr3.hg19:g.127379537T>A	ENSP00000345359:p.His222Gln	67.0	0.0		85.0	26.0	NM_015720	Q6UVY4|Q8WUV6	Missense_Mutation	SNP	ENST00000342480.6	hg19	CCDS3044.1	.	.	.	.	.	.	.	.	.	.	T	0.015	-1.564193	0.00903	.	.	ENSG00000114631	ENST00000342480;ENST00000302192	T	0.21031	2.03	4.67	-9.34	0.00636	.	1.210160	0.06044	N	0.655417	T	0.06462	0.0166	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.21109	-1.0255	10	0.12766	T	0.61	0.7936	1.9438	0.03352	0.2678:0.2701:0.3304:0.1318	.	222	Q9NZ53	PDXL2_HUMAN	Q	222	ENSP00000345359:H222Q	ENSP00000304498:H222Q	H	+	3	2	PODXL2	128862227	0.001000	0.12720	0.000000	0.03702	0.004000	0.04260	-2.370000	0.01075	-3.428000	0.00165	-0.415000	0.06103	CAT	.	.		0.602	PODXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356638.1	NM_015720		A	127379537	T	A	127379537	3	1	335	1	0	0	0	0	1	0	0	0	12190	1461	51	4	676	4	PODXL2	3	127379537	Missense_Mutation	SNP	T	TCGA-RC-A6M6-01A-11D-A32G-10	29128379	127379537	70642893	42	46593										
MFSD1	64747	hgsc.bcm.edu	37	chr3	158519925	158519925	+	5'UTR	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tgtcaccactttcccctctcCgtctcctgcgggcgcaatgg	9	17	3	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr3:158519925C>G	ENST00000264266.8	+	0	46				MFSD1_ENST00000392813.4_Missense_Mutation_p.P44R|MFSD1_ENST00000415822.2_Missense_Mutation_p.P44R|RP11-379F4.9_ENST00000607044.1_RNA			Q9H3U5	MFSD1_HUMAN	major facilitator superfamily domain containing 1						transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	26			Lung(72;0.00372)|LUSC - Lung squamous cell carcinoma(72;0.00523)			TTCCCCTCTCCGTCTCCTGCG	0.677																																					p.P44R	Pancreas(62;1186 1654 36636 37908)	Atlas-SNP	.											.	MFSD1	88	.	0			c.C131G						.						18	21	20					3																	158519925		2198	4287	6485	SO:0001623	5_prime_UTR_variant	64747	exon1			CCTCTCCGTCTCC	BC017661	CCDS3185.1, CCDS3185.2, CCDS54666.1	3q25.32	2005-11-17			ENSG00000118855	ENSG00000118855			25874	protein-coding gene	gene with protein product							Standard	NM_022736		Approved	FLJ14153, UG0581B09	uc003fcl.2	Q9H3U5	OTTHUMG00000158835	ENST00000264266.8:c.-17C>G	chr3.hg19:g.158519925C>G		59.0	0.0		74.0	25.0	NM_022736	B4DGJ8|B4DMR8|B4DU49|B4DWU1|C9JS94|J3KQL7|Q05C07|Q5XKJ1|Q8IVS1|Q8IXG4|Q9H7X1	Missense_Mutation	SNP	ENST00000264266.8	hg19		.	.	.	.	.	.	.	.	.	.	C	0.004	-2.300542	0.00243	.	.	ENSG00000118855	ENST00000415822;ENST00000392813	T;T	0.21734	1.99;1.99	2.8	-5.61	0.02489	.	.	.	.	.	T	0.05547	0.0146	N	0.03608	-0.345	0.20196	N	0.999926	.	.	.	.	.	.	T	0.19844	-1.0293	7	0.12766	T	0.61	.	0.6164	0.00770	0.2113:0.2615:0.1845:0.3427	.	.	.	.	R	44	ENSP00000403117:P44R;ENSP00000376560:P44R	ENSP00000376560:P44R	P	+	2	0	MFSD1	160002619	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.031000	0.00637	-3.388000	0.00173	-2.100000	0.00362	CCG	.	.		0.677	MFSD1-018	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470730.1	NM_022736		G	158519925	C	G	158519925	1	3	335	0	1	0	0	0	0	0	0	0	9536	652	23	4		4	MFSD1	3	158519925	5'UTR	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	31140388	158519925	39502505	43	46594										
SLITRK3	22865	hgsc.bcm.edu	37	chr3	164908256	164908256	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tttaaaatcttaagaccattGaaagctccagtctgaatgtc	6	8	2	3			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr3:164908256G>A	ENST00000475390.1	-	2	806	c.363C>T	c.(361-363)ttC>ttT	p.F121F	SLITRK3_ENST00000241274.3_Silent_p.F121F			O94933	SLIK3_HUMAN	SLIT and NTRK-like family, member 3	121					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(66)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(5)	119						TAAGACCATTGAAAGCTCCAG	0.348										HNSCC(40;0.11)																											p.F121F		Atlas-SNP	.											.	SLITRK3	263	.	0			c.C363T						.						45	45	45					3																	164908256		2202	4299	6501	SO:0001819	synonymous_variant	22865	exon2			ACCATTGAAAGCT	AB020655	CCDS3197.1	3q26.1	2004-07-28			ENSG00000121871	ENSG00000121871			23501	protein-coding gene	gene with protein product		609679				10048485, 14557068	Standard	NM_014926		Approved	KIAA0848	uc003fek.3	O94933	OTTHUMG00000158072	ENST00000475390.1:c.363C>T	chr3.hg19:g.164908256G>A		80.0	0.0		80.0	34.0	NM_014926	Q1RMY6	Silent	SNP	ENST00000475390.1	hg19	CCDS3197.1																																																																																			.	.		0.348	SLITRK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350126.1	NM_014926		A	164908256	G	A	164908256	2	1	335	1	0	0	0	0	0	0	0	1	14759	1281	45	3		3	SLITRK3	3	164908256	Silent	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	6388331	164908256	33114174	44	46595										
SENP2	59343	hgsc.bcm.edu	37	chr3	185318578	185318578	+	Frame_Shift_Del	DEL	T	T	-													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	aaatctcctaatggaataagTgactatccaaagatcagagt							TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr3:185318578delT	ENST00000296257.5	+	5	624	c.384delT	c.(382-384)agtfs	p.S128fs	SENP2_ENST00000545472.1_Frame_Shift_Del_p.S118fs|SENP2_ENST00000465201.1_3'UTR|SENP2_ENST00000427465.2_5'UTR	NM_021627.2	NP_067640.2	Q9HC62	SENP2_HUMAN	SUMO1/sentrin/SMT3 specific peptidase 2	128					cellular protein metabolic process (GO:0044267)|dorsal/ventral axis specification (GO:0009950)|heart development (GO:0007507)|labyrinthine layer development (GO:0060711)|mRNA transport (GO:0051028)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of protein binding (GO:0032091)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-translational protein modification (GO:0043687)|protein desumoylation (GO:0016926)|protein sumoylation (GO:0016925)|protein transport (GO:0015031)|regulation of DNA endoreduplication (GO:0032875)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of Wnt signaling pathway (GO:0030111)|spongiotrophoblast layer development (GO:0060712)|trophoblast giant cell differentiation (GO:0060707)|Wnt signaling pathway (GO:0016055)	cytoplasmic vesicle (GO:0031410)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	SUMO-specific protease activity (GO:0016929)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|skin(3)	12	all_cancers(143;1.28e-10)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;1.31e-21)			ATGGAATAAGTGACTATCCAA	0.338																																					p.S128fs		Atlas-Indel,Pindel	.											.	SENP2	88	.	0			c.383delG						.						150	160	156					3																	185318578		2203	4300	6503	SO:0001589	frameshift_variant	59343	exon5			.	AF151697	CCDS33902.1	3q28	2005-08-17	2005-08-17		ENSG00000163904	ENSG00000163904			23116	protein-coding gene	gene with protein product		608261	"SUMO1/sentrin/SMT3 specific protease 2"			11896061, 11489887	Standard	XM_005247690		Approved	SMT3IP2, KIAA1331, DKFZp762A2316, AXAM2	uc003fpn.3	Q9HC62	OTTHUMG00000156658	ENST00000296257.5:c.384delT	chr3.hg19:g.185318578delT	ENSP00000296257:p.Ser128fs	136.0	0.0		153.0	56.0	NM_021627	B4DQ42|Q8IW97|Q96SR2|Q9P2L5	Frame_Shift_Del	DEL	ENST00000296257.5	hg19	CCDS33902.1																																																																																			.	.		0.338	SENP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345159.1	NM_021627		-	185318578	T	-	185318578	7	5	335	1	0	1	0	1	0	0	0	0	14062	1693	59	0	402	0	SENP2	3	185318578	Frame_Shift_Del	DEL	T	TCGA-RC-A6M6-01A-11D-A32G-10	20410322	185318578	12703852	45	46596										
TNK2	10188	hgsc.bcm.edu	37	chr3	195610026	195610026	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ccctcccgcccgcagtactcAccatcttcatgggcggcgtg	10	18	3	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr3:195610026A>T	ENST00000333602.6	-	5	1227		c.e5+1		TNK2_ENST00000381916.2_Splice_Site|TNK2_ENST00000468819.1_Splice_Site|TNK2_ENST00000392400.1_Splice_Site|TNK2_ENST00000316664.3_Splice_Site|TNK2_ENST00000428187.1_Splice_Site	NM_005781.4	NP_005772.3	Q07912	ACK1_HUMAN	tyrosine kinase, non-receptor, 2						cell surface receptor signaling pathway (GO:0007166)|endocytosis (GO:0006897)|negative regulation of catalytic activity (GO:0043086)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of clathrin-mediated endocytosis (GO:2000369)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|endosome (GO:0005768)|Grb2-EGFR complex (GO:0070436)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|WW domain binding (GO:0050699)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(11)|ovary(3)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	29	all_cancers(143;6.48e-09)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;1.46e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.3e-19)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;0.000757)	Adenosine triphosphate(DB00171)	CGCAGTACTCACCATCTTCAT	0.627																																					.		Atlas-SNP	.											.	TNK2	246	.	0			c.609+2T>A						.						55	48	51					3																	195610026		2203	4300	6503	SO:0001630	splice_region_variant	10188	exon6			GTACTCACCATCT	L13738	CCDS33927.1, CCDS33928.1	3q29	2013-09-02			ENSG00000061938	ENSG00000061938			19297	protein-coding gene	gene with protein product	"activated Cdc42-associated kinase 1"	606994				8497321, 14506255	Standard	XM_006713460		Approved	p21cdc42Hs, ACK, ACK1	uc003fvt.1	Q07912	OTTHUMG00000155737	ENST00000333602.6:c.609+1T>A	chr3.hg19:g.195610026A>T		23.0	0.0		12.0	6.0	NM_005781	Q6ZMQ0|Q8N6U7|Q96H59	Splice_Site	SNP	ENST00000333602.6	hg19	CCDS33928.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.271323	0.80469	.	.	ENSG00000061938	ENST00000333602;ENST00000381916;ENST00000428187;ENST00000392400;ENST00000316664;ENST00000438207	.	.	.	5.44	5.44	0.79542	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3226	0.66496	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TNK2	197094423	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.192000	0.77771	2.068000	0.61886	0.533000	0.62120	.	.	.		0.627	TNK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341437.3	NM_005781	Intron	T	195610026	A	T	195610026	5	4	335	1	0	0	0	0	0	0	1	0	16333	173	6	4	2598	4	TNK2	3	195610026	Splice_Site	SNP	A	TCGA-RC-A6M6-01A-11D-A32G-10	10291448	195610026	2412404	46	46597										
APBB2	323	hgsc.bcm.edu	37	chr4	40892391	40892391	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	agggactcaccggccattgtCgcggcccacgccccacacgc	11	19	1	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr4:40892391C>T	ENST00000295974.8	-	12	2145	c.1516G>A	c.(1516-1518)Gac>Aac	p.D506N	APBB2_ENST00000506352.1_Missense_Mutation_p.D485N|APBB2_ENST00000508593.1_Missense_Mutation_p.D507N|APBB2_ENST00000513140.1_Missense_Mutation_p.D485N	NM_001166050.1|NM_004307.1	NP_001159522.1|NP_004298.1	Q92870	APBB2_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 2	506	PID 1. {ECO:0000255|PROSITE- ProRule:PRU00148}.				axon guidance (GO:0007411)|cell cycle arrest (GO:0007050)|extracellular matrix organization (GO:0030198)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|transcription factor binding (GO:0008134)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|skin(2)|urinary_tract(1)	34						CGGCCATTGTCGCGGCCCACG	0.642																																					p.D507N	Ovarian(3;20 75 16686 49997)	Atlas-SNP	.											.	APBB2	61	.	0			c.G1519A						.						40	44	43					4																	40892391		2140	4262	6402	SO:0001583	missense	323	exon12			CATTGTCGCGGCC	U62325	CCDS43224.1, CCDS54760.1, CCDS54761.1, CCDS54762.1	4p13	2011-10-10	2008-07-31		ENSG00000163697	ENSG00000163697			582	protein-coding gene	gene with protein product	"Fe65-like"	602710				8955346, 9585438	Standard	NM_173075		Approved	FE65L, FE65L1, MGC35575	uc003gvn.3	Q92870	OTTHUMG00000160416	ENST00000295974.8:c.1516G>A	chr4.hg19:g.40892391C>T	ENSP00000295974:p.Asp506Asn	64.0	0.0		57.0	24.0	NM_004307	B4DSL4|E9PG87|Q8IUI6	Missense_Mutation	SNP	ENST00000295974.8	hg19	CCDS54761.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	27.4|27.4	4.828290|4.828290	0.90955|0.90955	.|.	.|.	ENSG00000163697|ENSG00000163697	ENST00000295974;ENST00000316212;ENST00000513140;ENST00000508593;ENST00000506352;ENST00000512510|ENST00000513611	T;T;T;T;T|T	0.26373|0.14391	2.39;2.39;2.39;2.39;1.74|2.51	5.98|5.98	5.98|5.98	0.97165|0.97165	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.23451|0.23451	0.0567|0.0567	L|L	0.43757|0.43757	1.38|1.38	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.69078|.	0.997;0.988;0.985;0.988|.	P;P;P;P|.	0.57324|.	0.818;0.647;0.515;0.647|.	T|T	0.00067|0.00067	-1.2142|-1.2142	10|7	0.49607|0.87932	T|D	0.09|0	-30.3771|-30.3771	13.6272|13.6272	0.62173|0.62173	0.0:0.9295:0.0:0.0705|0.0:0.9295:0.0:0.0705	.|.	468;507;485;506|.	B4DJ88;E9PG87;Q92870-2;Q92870|.	.;.;.;APBB2_HUMAN|.	N|Q	506;505;485;507;485;18|475	ENSP00000295974:D506N;ENSP00000426018:D485N;ENSP00000427211:D507N;ENSP00000421539:D485N;ENSP00000426429:D18N|ENSP00000427307:R475Q	ENSP00000295974:D506N|ENSP00000427307:R475Q	D|R	-|-	1|2	0|0	APBB2|APBB2	40587148|40587148	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.968000|0.968000	0.65278|0.65278	7.406000|7.406000	0.80017|0.80017	2.838000|2.838000	0.97847|0.97847	0.591000|0.591000	0.81541|0.81541	GAC|CGA	.	.		0.642	APBB2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360523.3	NM_173075		T	40892391	C	T	40892391	3	4	335	1	0	0	0	0	1	0	0	0	761	884	31	1	788	1	APBB2	4	40892391	Missense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10		40892391	150261885	47	46598										
SHISA3	152573	hgsc.bcm.edu	37	chr4	42400220	42400220	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	cagtgcccagaggacttcgaCacgctggacgctaccatctg	11	14	1	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr4:42400220C>T	ENST00000319234.4	+	1	365	c.147C>T	c.(145-147)gaC>gaT	p.D49D		NM_001080505.1	NP_001073974.1	A0PJX4	SHSA3_HUMAN	shisa family member 3	49					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	12						AGGACTTCGACACGCTGGACG	0.716																																					p.D49D		Atlas-SNP	.											.	SHISA3	27	.	0			c.C147T						.						23	22	22					4																	42400220		2199	4298	6497	SO:0001819	synonymous_variant	152573	exon1			CTTCGACACGCTG	BC012029	CCDS33979.1	4p13	2013-07-31	2013-07-31		ENSG00000178343	ENSG00000178343		"Shisa homologs"	25159	protein-coding gene	gene with protein product			"shisa homolog 3 (Xenopus laevis)"				Standard	NM_001080505		Approved	hShisa3	uc003gwp.3	A0PJX4	OTTHUMG00000161043	ENST00000319234.4:c.147C>T	chr4.hg19:g.42400220C>T		53.0	0.0		75.0	21.0	NM_001080505	A0PJX3|Q96EQ5	Silent	SNP	ENST00000319234.4	hg19	CCDS33979.1																																																																																			.	.		0.716	SHISA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363539.1	NM_001080505		T	42400220	C	T	42400220	2	4	335	1	0	0	0	0	0	0	0	1	14296	477	17	3		3	SHISA3	4	42400220	Silent	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	1507829	42400220	148754056	48	46599										
ADAD1	132612	hgsc.bcm.edu	37	chr4	123302161	123302161	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ttttaggtaattttccagagCcgttgctttccaagaatctt	7	8	1	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr4:123302161C>A	ENST00000296513.2	+	4	372	c.187C>A	c.(187-189)Ccg>Acg	p.P63T	ADAD1_ENST00000388725.2_Missense_Mutation_p.P45T|ADAD1_ENST00000388724.2_Missense_Mutation_p.P63T|ADAD1_ENST00000492454.1_3'UTR	NM_139243.3	NP_640336.1	Q96M93	ADAD1_HUMAN	adenosine deaminase domain containing 1 (testis-specific)	63					multicellular organismal development (GO:0007275)|RNA processing (GO:0006396)|spermatid development (GO:0007286)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	35						TTTTCCAGAGCCGTTGCTTTC	0.313																																					p.P63T		Atlas-SNP	.											.	ADAD1	94	.	0			c.C187A						.						64	66	66					4																	123302161		2203	4300	6503	SO:0001583	missense	132612	exon4			CCAGAGCCGTTGC	AK057303	CCDS34058.1, CCDS54800.1, CCDS54801.1	4q27	2007-05-31			ENSG00000164113	ENSG00000164113			30713	protein-coding gene	gene with protein product		614130				7543294, 9541871	Standard	NM_139243		Approved	Tenr	uc003iep.3	Q96M93	OTTHUMG00000150128	ENST00000296513.2:c.187C>A	chr4.hg19:g.123302161C>A	ENSP00000296513:p.Pro63Thr	289.0	0.0		357.0	96.0	NM_139243	A6NKN4|B7WPB0|D3DNX2|Q8IWG6|Q8NA06	Missense_Mutation	SNP	ENST00000296513.2	hg19	CCDS34058.1	.	.	.	.	.	.	.	.	.	.	C	11.77	1.736709	0.30774	.	.	ENSG00000164113	ENST00000446706;ENST00000296513;ENST00000439307;ENST00000388724;ENST00000388725	T;T;T	0.34667	1.35;1.35;1.37	5.23	4.37	0.52481	.	0.000000	0.64402	D	0.000005	T	0.41994	0.1183	L	0.32530	0.975	0.41237	D	0.986619	D;D	0.63880	0.993;0.993	P;P	0.59221	0.854;0.827	T	0.12915	-1.0529	10	0.32370	T	0.25	-15.9499	13.1832	0.59666	0.0:0.9193:0.0:0.0807	.	63;63	Q96M93-2;Q96M93	.;ADAD1_HUMAN	T	63;63;63;63;45	ENSP00000296513:P63T;ENSP00000373376:P63T;ENSP00000373377:P45T	ENSP00000296513:P63T	P	+	1	0	ADAD1	123521611	0.000000	0.05858	0.993000	0.49108	0.018000	0.09664	0.346000	0.19997	2.423000	0.82170	0.563000	0.77884	CCG	.	.		0.313	ADAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316452.1	NM_139243		A	123302161	C	A	123302161	3	1	335	1	0	0	0	0	1	0	0	0	231	739	26	3	193	3	ADAD1	4	123302161	Missense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	80901941	123302161	67852115	49	46600										
FAT4	79633	hgsc.bcm.edu	37	chr4	126367528	126367528	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	caccagcgcattgttagataGggaaacaaaagataattata	8	6	0	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr4:126367528G>A	ENST00000394329.3	+	8	7287	c.7274G>A	c.(7273-7275)aGg>aAg	p.R2425K	FAT4_ENST00000335110.5_Missense_Mutation_p.R723K	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	2425	Cadherin 23. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						TTGTTAGATAGGGAAACAAAA	0.448																																					p.R2425K		Atlas-SNP	.											.	FAT4	1752	.	0			c.G7274A						.						134	132	133					4																	126367528		2203	4300	6503	SO:0001583	missense	79633	exon8			TAGATAGGGAAAC	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.7274G>A	chr4.hg19:g.126367528G>A	ENSP00000377862:p.Arg2425Lys	92.0	0.0		69.0	30.0	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	hg19	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	26.3	4.722245	0.89298	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.59224	0.28;0.28	5.69	5.69	0.88448	Cadherin (4);Cadherin-like (1);	0.000000	0.34906	U	0.003596	T	0.82047	0.4952	M	0.92026	3.265	0.58432	D	0.99999	D;D	0.69078	0.984;0.997	D;D	0.80764	0.946;0.994	D	0.84515	0.0624	10	0.54805	T	0.06	.	19.8199	0.96589	0.0:0.0:1.0:0.0	.	723;2425	Q6V0I7-2;Q6V0I7	.;FAT4_HUMAN	K	2425;723	ENSP00000377862:R2425K;ENSP00000335169:R723K	ENSP00000335169:R723K	R	+	2	0	FAT4	126586978	1.000000	0.71417	0.996000	0.52242	0.266000	0.26442	9.666000	0.98612	2.677000	0.91161	0.655000	0.94253	AGG	.	.		0.448	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		A	126367528	G	A	126367528	3	1	335	1	0	0	0	0	1	0	0	0	5700	1000	35	3	7304	3	FAT4	4	126367528	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	3065367	126367528	64786748	50	46601										
ABCE1	6059	hgsc.bcm.edu	37	chr4	146032129	146032129	+	Frame_Shift_Del	DEL	A	A	-													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gttctttgtagatttaacccAcctaaaagaacgaaatgttg							TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr4:146032129delA	ENST00000296577.4	+	8	1138	c.623delA	c.(622-624)cacfs	p.H208fs	ABCE1_ENST00000502803.1_Intron|OTUD4_ENST00000455611.2_5'UTR	NM_001040876.1|NM_002940.2	NP_001035809.1|NP_002931.2	P61221	ABCE1_HUMAN	ATP-binding cassette, sub-family E (OABP), member 1	208	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				negative regulation of catalytic activity (GO:0043086)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|iron-sulfur cluster binding (GO:0051536)|ribonuclease inhibitor activity (GO:0008428)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|lung(5)|prostate(2)|skin(3)	18	all_hematologic(180;0.151)					GATTTAACCCACCTAAAAGAA	0.373																																					p.H208fs		Atlas-Indel,Pindel	.											.	ABCE1	47	.	0			c.622delC						.						113	105	108					4																	146032129		2203	4300	6503	SO:0001589	frameshift_variant	6059	exon8			.	X74987	CCDS34071.1	4q31	2012-03-14			ENSG00000164163	ENSG00000164163		"ATP binding cassette transporters / subfamily E"	69	protein-coding gene	gene with protein product		601213		RNASEL1, RNASELI, RNS4I		7539425	Standard	NM_002940		Approved	RLI, OABP	uc003ijy.3	P61221	OTTHUMG00000161478	ENST00000296577.4:c.623delA	chr4.hg19:g.146032129delA	ENSP00000296577:p.His208fs	114.0	0.0		122.0	47.0	NM_002940	O88793|Q13181|Q13864|Q6NR76|Q96AL0|Q96B10|Q99K66	Frame_Shift_Del	DEL	ENST00000296577.4	hg19	CCDS34071.1																																																																																			.	.		0.373	ABCE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365104.1	NM_002940		-	146032129	A	-	146032129	7	5	335	1	0	1	0	1	0	0	0	0	64	159	6	0	649	0	ABCE1	4	146032129	Frame_Shift_Del	DEL	A	TCGA-RC-A6M6-01A-11D-A32G-10	19664601	146032129	45122147	51	46602										
TKTL2	84076	hgsc.bcm.edu	37	chr4	164394657	164394657	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	agaggataggagcagcatgtCccctggagaggatgaaccgg	16	8	0	3			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr4:164394657C>T	ENST00000280605.3	-	1	390	c.230G>A	c.(229-231)gGa>gAa	p.G77E		NM_032136.4	NP_115512.3	Q9H0I9	TKTL2_HUMAN	transketolase-like 2	77						cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|transketolase activity (GO:0004802)			breast(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(42)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	70	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				AGCAGCATGTCCCCTGGAGAG	0.532																																					p.G77E		Atlas-SNP	.											.	TKTL2	130	.	0			c.G230A						.						174	117	136					4																	164394657		2203	4300	6503	SO:0001583	missense	84076	exon1			GCATGTCCCCTGG	BC028707	CCDS3805.1	4q32.2	2009-10-06			ENSG00000151005	ENSG00000151005			25313	protein-coding gene	gene with protein product	"similar to transketolase"					11230166	Standard	NM_032136		Approved	FLJ32975, DKFZP434L1717	uc003iqp.4	Q9H0I9	OTTHUMG00000161527	ENST00000280605.3:c.230G>A	chr4.hg19:g.164394657C>T	ENSP00000280605:p.Gly77Glu	148.0	0.0		129.0	47.0	NM_032136	A4FVB4|Q8NCT0|Q96M82	Missense_Mutation	SNP	ENST00000280605.3	hg19	CCDS3805.1	.	.	.	.	.	.	.	.	.	.	C	12.92	2.082657	0.36758	.	.	ENSG00000151005	ENST00000280605	T	0.71579	-0.58	3.8	2.95	0.34219	Transketolase, N-terminal (1);	0.000000	0.64402	U	0.000001	D	0.89546	0.6746	H	0.99507	4.6	0.58432	D	0.999999	D	0.76494	0.999	D	0.76575	0.988	D	0.90589	0.4535	10	0.87932	D	0	-14.6618	9.4321	0.38617	0.0:0.8921:0.0:0.1079	.	77	Q9H0I9	TKTL2_HUMAN	E	77	ENSP00000280605:G77E	ENSP00000280605:G77E	G	-	2	0	TKTL2	164614107	1.000000	0.71417	0.998000	0.56505	0.012000	0.07955	2.369000	0.44231	1.171000	0.42768	0.491000	0.48974	GGA	.	.		0.532	TKTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365207.1	NM_032136		T	164394657	C	T	164394657	3	4	335	1	0	0	0	0	1	0	0	0	15951	855	30	3	1654	3	TKTL2	4	164394657	Missense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	18362528	164394657	26759619	52	46603										
PALLD	23022	hgsc.bcm.edu	37	chr4	169825044	169825044	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tgggaattatacaattatggCtgcaaaccctcaggtaaaga	9	7	1	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr4:169825044C>A	ENST00000505667.1	+	15	2782	c.2609C>A	c.(2608-2610)gCt>gAt	p.A870D	CBR4_ENST00000509108.1_Intron|PALLD_ENST00000512127.1_Missense_Mutation_p.A471D|PALLD_ENST00000261509.6_Missense_Mutation_p.A853D|PALLD_ENST00000507735.1_Missense_Mutation_p.A366D|PALLD_ENST00000335742.7_Missense_Mutation_p.A695D			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	1077	Interaction with ACTN.				cytoskeleton organization (GO:0007010)	actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	muscle alpha-actinin binding (GO:0051371)			breast(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(18)|ovary(3)|prostate(3)|skin(4)	48		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)		ACAATTATGGCTGCAAACCCT	0.443									Pancreatic Cancer, Familial Clustering of																												p.A870D	Esophageal Squamous(109;1482 1532 18347 40239 51172)	Atlas-SNP	.											.	PALLD	179	.	0			c.C2609A						.						104	107	106					4																	169825044		2203	4300	6503	SO:0001583	missense	23022	exon15	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	TTATGGCTGCAAA	AB023209	CCDS34098.1, CCDS54818.1, CCDS54819.1, CCDS54820.1	4q32.3	2013-01-11			ENSG00000129116	ENSG00000129116		"Immunoglobulin superfamily / I-set domain containing"	17068	protein-coding gene	gene with protein product		608092				10231032, 10931874	Standard	NM_001166108		Approved	KIAA0992, SIH002, CGI-151	uc011cjx.2	Q8WX93	OTTHUMG00000161097	ENST00000505667.1:c.2609C>A	chr4.hg19:g.169825044C>A	ENSP00000425556:p.Ala870Asp	88.0	0.0		81.0	38.0	NM_001166108	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Missense_Mutation	SNP	ENST00000505667.1	hg19	CCDS54818.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.604519	0.87157	.	.	ENSG00000129116	ENST00000261509;ENST00000335742;ENST00000505667;ENST00000512127;ENST00000393726;ENST00000507735	T;T;T;T;T;T	0.76968	-1.06;-1.06;-1.06;-1.06;-1.06;-1.06	5.36	5.36	0.76844	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.31897	U	0.006890	D	0.93061	0.7791	H	0.97874	4.095	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;0.999;1.0	D	0.95170	0.8289	10	0.87932	D	0	.	19.277	0.94036	0.0:1.0:0.0:0.0	.	870;1077;471;853	B7ZMM5;Q8WX93;B3KTG2;B2RTX2	.;PALLD_HUMAN;.;.	D	853;695;870;471;146;366	ENSP00000261509:A853D;ENSP00000336735:A695D;ENSP00000425556:A870D;ENSP00000426947:A471D;ENSP00000377327:A146D;ENSP00000424016:A366D	ENSP00000261509:A853D	A	+	2	0	PALLD	170061619	1.000000	0.71417	1.000000	0.80357	0.636000	0.38137	7.644000	0.83416	2.782000	0.95742	0.655000	0.94253	GCT	.	.		0.443	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081		A	169825044	C	A	169825044	3	1	335	1	0	0	0	0	1	0	0	0	11416	797	28	3	3170	3	PALLD	4	169825044	Missense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	5430387	169825044	21329232	53	46604										
AADAT	51166	hgsc.bcm.edu	37	chr4	170991792	170991792	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tctattatgaggaaatcataTtttcttgcaagctaaaaaag	6	5	3	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr4:170991792T>C	ENST00000337664.4	-	6	942	c.666A>G	c.(664-666)aaA>aaG	p.K222K	AADAT_ENST00000353187.2_Silent_p.K222K|AADAT_ENST00000515480.1_Silent_p.K222K|AADAT_ENST00000509167.1_Silent_p.K226K	NM_016228.3	NP_057312.1	Q8N5Z0	AADAT_HUMAN	aminoadipate aminotransferase	222					2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|kynurenine metabolic process (GO:0070189)|L-kynurenine metabolic process (GO:0097052)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)|tryptophan catabolic process to kynurenine (GO:0019441)	mitochondrial matrix (GO:0005759)	2-aminoadipate transaminase activity (GO:0047536)|kynurenine-oxoglutarate transaminase activity (GO:0016212)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|pancreas(1)|stomach(1)	11		Prostate(90;0.00601)|Renal(120;0.0183)|all_neural(102;0.122)|Melanoma(52;0.17)		GBM - Glioblastoma multiforme(119;0.0355)|LUSC - Lung squamous cell carcinoma(193;0.118)		GGAAATCATATTTTCTTGCAA	0.239																																					p.K222K		Atlas-SNP	.											.	AADAT	28	.	0			c.A666G						.						62	66	65					4																	170991792		2197	4289	6486	SO:0001819	synonymous_variant	51166	exon7			ATCATATTTTCTT	AF097994	CCDS3814.1, CCDS75209.1	4q33	2010-12-09			ENSG00000109576	ENSG00000109576	2.6.1.39		17929	protein-coding gene	gene with protein product	"kynurenine aminotransferase II", "L kynurenine/alpha aminoadipate aminotransferase"	611754				12126930, 10441733	Standard	NM_182662		Approved	KATII, KAT2	uc003isr.3	Q8N5Z0	OTTHUMG00000160912	ENST00000337664.4:c.666A>G	chr4.hg19:g.170991792T>C		173.0	0.0		157.0	69.0	NM_182662	B3KP84|Q9UL02	Silent	SNP	ENST00000337664.4	hg19	CCDS3814.1																																																																																			.	.		0.239	AADAT-004	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000362952.1	NM_016228		C	170991792	T	C	170991792	2	2	335	1	0	0	0	0	0	0	0	1	14	1490	52	2		2	AADAT	4	170991792	Silent	SNP	T	TCGA-RC-A6M6-01A-11D-A32G-10	1166748	170991792	20162484	54	46605										
SLC6A3	6531	hgsc.bcm.edu	37	chr5	1422086	1422086	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ctgccaccgcggaggccccaGgtcgtcgatgccatggctct	13	16	1	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr5:1422086G>T	ENST00000270349.9	-	5	824	c.697C>A	c.(697-699)Ctg>Atg	p.L233M	SLC6A3_ENST00000453492.2_Missense_Mutation_p.L233M	NM_001044.4	NP_001035.1	Q01959	SC6A3_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 3	233					adenohypophysis development (GO:0021984)|aging (GO:0007568)|cation transmembrane transport (GO:0098655)|cell death (GO:0008219)|dopamine biosynthetic process (GO:0042416)|dopamine catabolic process (GO:0042420)|dopamine transport (GO:0015872)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|neurotransmitter biosynthetic process (GO:0042136)|positive regulation of multicellular organism growth (GO:0040018)|prepulse inhibition (GO:0060134)|regulation of dopamine metabolic process (GO:0042053)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to iron ion (GO:0010039)|response to nicotine (GO:0035094)|sensory perception of smell (GO:0007608)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	axon (GO:0030424)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine transmembrane transporter activity (GO:0005329)|dopamine:sodium symporter activity (GO:0005330)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)			breast(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(19)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38			OV - Ovarian serous cystadenocarcinoma(19;0.00928)|all cancers(22;0.0262)		Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Benzatropine(DB00245)|Benzphetamine(DB00865)|Bupropion(DB01156)|Chloroprocaine(DB01161)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Cocaine(DB00907)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Diethylpropion(DB00937)|Diphenylpyraline(DB01146)|Dopamine(DB00988)|Duloxetine(DB00476)|Ephedra(DB01363)|Escitalopram(DB01175)|Fencamfamine(DB01463)|Imipramine(DB00458)|Ioflupane I 123(DB08824)|Lisdexamfetamine(DB01255)|Loxapine(DB00408)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Mirtazapine(DB00370)|Modafinil(DB00745)|Nefazodone(DB01149)|Pethidine(DB00454)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Procaine(DB00721)|Pseudoephedrine(DB00852)|Sertraline(DB01104)|Sibutramine(DB01105)|Trimipramine(DB00726)|Venlafaxine(DB00285)	GGAGGCCCCAGGTCGTCGATG	0.647																																					p.L233M		Atlas-SNP	.											SLC6A3,right_upper_lobe,carcinoma,0,1	SLC6A3	102	.	0			c.C697A						.						73	70	71					5																	1422086		2203	4300	6503	SO:0001583	missense	6531	exon5			GCCCCAGGTCGTC		CCDS3863.1	5p15.3	2013-07-19	2013-07-19		ENSG00000142319	ENSG00000142319		"Solute carriers"	11049	protein-coding gene	gene with protein product	"dopamine transporter"	126455	"solute carrier family 6 (neurotransmitter transporter, dopamine), member 3", "dopamine transporter 1"	DAT1		1406597	Standard	NM_001044		Approved	DAT	uc003jck.3	Q01959	OTTHUMG00000131016	ENST00000270349.9:c.697C>A	chr5.hg19:g.1422086G>T	ENSP00000270349:p.Leu233Met	38.0	0.0		40.0	15.0	NM_001044	A2RUN4|Q14996	Missense_Mutation	SNP	ENST00000270349.9	hg19	CCDS3863.1	.	.	.	.	.	.	.	.	.	.	G	15.90	2.969409	0.53614	.	.	ENSG00000142319	ENST00000270349;ENST00000453492;ENST00000513308	T;T;T	0.75367	-0.93;-0.93;-0.93	4.4	0.848	0.18966	.	0.176408	0.38217	N	0.001772	T	0.67915	0.2944	L	0.42632	1.34	0.46478	D	0.99906	P	0.44429	0.835	P	0.49477	0.612	T	0.60939	-0.7163	10	0.34782	T	0.22	.	5.7503	0.18142	0.5699:0.0:0.4301:0.0	.	233	Q01959	SC6A3_HUMAN	M	233;233;159	ENSP00000270349:L233M;ENSP00000399806:L233M;ENSP00000429101:L159M	ENSP00000270349:L233M	L	-	1	2	SLC6A3	1475086	0.999000	0.42202	0.997000	0.53966	0.965000	0.64279	0.474000	0.22148	0.360000	0.24265	0.462000	0.41574	CTG	.	.		0.647	SLC6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253650.3	NM_001044		T	1422086	G	T	1422086	3	4	335	1	0	0	0	0	1	0	0	0	14700	991	35	3	1209	3	SLC6A3	5	1422086	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10		1422086	179493174	55	46606										
IRX1	79192	hgsc.bcm.edu	37	chr5	3596419	3596419	+	Frame_Shift_Del	DEL	C	C	-													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gctgggcatgtacgcggcggCggggccgtacgcgggcgcgc							TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr5:3596419delC	ENST00000302006.3	+	1	252	c.200delC	c.(199-201)gcgfs	p.A67fs	CTD-2012M11.3_ENST00000559410.1_RNA	NM_024337.3	NP_077313.3	P78414	IRX1_HUMAN	iroquois homeobox 1	67					proximal/distal pattern formation involved in metanephric nephron development (GO:0072272)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			biliary_tract(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(18)|ovary(2)|pancreas(1)|prostate(5)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						TACGCGGCGGCGGGGCCGTAC	0.776																																					p.A67fs		Atlas-INDEL	.											.	IRX1	106	.	0			c.199delG						.						6	7	7					5																	3596419		1838	3768	5606	SO:0001589	frameshift_variant	79192	exon1			.	U90307	CCDS34132.1	5p15.33	2011-12-16	2007-07-13		ENSG00000170549	ENSG00000170549		"Homeoboxes / TALE class"	14358	protein-coding gene	gene with protein product		606197					Standard	NM_024337		Approved	IRX-5	uc003jde.3	P78414	OTTHUMG00000161632	ENST00000302006.3:c.200delC	chr5.hg19:g.3596419delC	ENSP00000305244:p.Ala67fs	28.0	0.0		37.0	13.0	NM_024337	Q7Z2F8|Q8N312	Frame_Shift_Del	DEL	ENST00000302006.3	hg19	CCDS34132.1																																																																																			.	.		0.776	IRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365546.1	NM_024337		-	3596419	C	-	3596419	7	5	335	1	0	1	0	1	0	0	0	0	7852	768	27	0	202	0	IRX1	5	3596419	Frame_Shift_Del	DEL	C	TCGA-RC-A6M6-01A-11D-A32G-10	2174333	3596419	177318841	56	46607										
CAST	831	hgsc.bcm.edu	37	chr5	96083056	96083056	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	atttcatttacaggataaagAtggaaaaccactattgccag	7	7	1	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr5:96083056A>G	ENST00000341926.3	+	16	1205	c.1043A>G	c.(1042-1044)gAt>gGt	p.D348G	CAST_ENST00000511782.1_Missense_Mutation_p.D334G|CAST_ENST00000508830.1_Missense_Mutation_p.D431G|CAST_ENST00000359176.4_Missense_Mutation_p.D412G|CAST_ENST00000509903.1_Missense_Mutation_p.D313G|CAST_ENST00000508579.1_Missense_Mutation_p.D63G|CAST_ENST00000348386.3_3'UTR|CAST_ENST00000338252.3_Missense_Mutation_p.D335G|CAST_ENST00000508608.1_Missense_Mutation_p.D394G|CAST_ENST00000515663.1_Missense_Mutation_p.D71G|CAST_ENST00000325674.7_Missense_Mutation_p.D396G|CAST_ENST00000395812.2_Missense_Mutation_p.D390G|CAST_ENST00000395813.1_Missense_Mutation_p.D431G|CAST_ENST00000511049.1_Missense_Mutation_p.D334G|CAST_ENST00000309190.5_Missense_Mutation_p.D326G|CAST_ENST00000504465.1_Missense_Mutation_p.D276G|CAST_ENST00000510756.1_Missense_Mutation_p.D409G			P20810	ICAL_HUMAN	calpastatin	348					negative regulation of endopeptidase activity (GO:0010951)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|endopeptidase inhibitor activity (GO:0004866)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(5)|ovary(1)|skin(2)	22		all_cancers(142;5.27e-07)|all_epithelial(76;8.21e-10)|all_lung(232;0.000396)|Lung NSC(167;0.000539)|Ovarian(225;0.024)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;6.85e-15)		CAGGATAAAGATGGAAAACCA	0.303																																					p.D390G		Atlas-SNP	.											.	CAST	58	.	0			c.A1169G						.						41	44	43					5																	96083056		2201	4300	6501	SO:0001583	missense	831	exon16			ATAAAGATGGAAA	AF327443	CCDS4082.1, CCDS54882.1, CCDS54883.1, CCDS75279.1	5q15	2012-09-20			ENSG00000153113	ENSG00000153113			1515	protein-coding gene	gene with protein product		114090				8340353, 14685690, 15820218	Standard	NM_173060		Approved		uc003klx.3	P20810	OTTHUMG00000128413	ENST00000341926.3:c.1043A>G	chr5.hg19:g.96083056A>G	ENSP00000339914:p.Asp348Gly	319.0	0.0		279.0	77.0	NM_001042440	B7Z468|G5E946|G5E9D3|O95360|Q05DE8|Q7Z4K0|Q96D08|Q9H1Z5	Missense_Mutation	SNP	ENST00000341926.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.02|17.02	3.281934|3.281934	0.59867|0.59867	.|.	.|.	ENSG00000153113|ENSG00000153113	ENST00000338252;ENST00000508830;ENST00000395813;ENST00000359176;ENST00000325674;ENST00000395812;ENST00000510756;ENST00000508608;ENST00000341926;ENST00000511049;ENST00000309190;ENST00000510156;ENST00000504465;ENST00000509903;ENST00000511782;ENST00000508579;ENST00000509259;ENST00000503828;ENST00000515663|ENST00000437034	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T|.	0.55930|.	2.04;2.04;2.04;2.04;2.04;2.04;2.04;2.04;2.04;2.04;2.04;2.04;2.04;2.04;2.04;2.04;0.49;2.04;2.04|.	5.73|5.73	5.73|5.73	0.89815|0.89815	.|.	0.412813|.	0.27549|.	N|.	0.018863|.	T|T	0.79953|0.79953	0.4535|0.4535	M|M	0.88775|0.88775	2.98|2.98	0.51233|0.51233	D|D	0.999917|0.999917	P;P;P;B;D;P;D;P;B;P;P;P;P;B;B;P;P|.	0.89917|.	0.614;0.942;0.725;0.1;1.0;0.472;0.968;0.942;0.41;0.56;0.942;0.822;0.658;0.281;0.368;0.783;0.716|.	P;P;B;B;D;B;P;P;P;P;P;P;P;B;B;P;P|.	0.97110|.	0.671;0.813;0.335;0.101;1.0;0.438;0.908;0.813;0.542;0.542;0.813;0.542;0.565;0.424;0.226;0.565;0.61|.	T|T	0.83322|0.83322	-0.0017|-0.0017	10|5	0.66056|.	D|.	0.02|.	-19.7012|-19.7012	13.5561|13.5561	0.61759|0.61759	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	276;196;394;71;99;71;334;313;326;307;348;396;390;412;409;431;335|.	E9PDE4;B7Z8S8;B7Z468;E7EQA0;Q86YM9;E7EPY6;E7EVY3;E9PCH5;G5E946;P20810-4;P20810;P20810-5;G5E9D3;P20810-7;E7ESM9;P20810-6;P20810-2|.	.;.;.;.;.;.;.;.;.;.;ICAL_HUMAN;.;.;.;.;.;.|.	G|V	335;431;431;412;396;390;409;394;348;334;326;348;276;313;334;63;35;63;71|100	ENSP00000343421:D335G;ENSP00000425721:D431G;ENSP00000379158:D431G;ENSP00000352098:D412G;ENSP00000320319:D396G;ENSP00000379157:D390G;ENSP00000422176:D409G;ENSP00000422677:D394G;ENSP00000339914:D348G;ENSP00000421130:D334G;ENSP00000312523:D326G;ENSP00000422325:D348G;ENSP00000425670:D276G;ENSP00000426946:D313G;ENSP00000423638:D334G;ENSP00000425787:D63G;ENSP00000423846:D35G;ENSP00000422807:D63G;ENSP00000422929:D71G|.	ENSP00000312523:D326G|.	D|M	+|+	2|1	0|0	CAST|CAST	96108812|96108812	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.978000|0.978000	0.69477|0.69477	5.319000|5.319000	0.65835|0.65835	2.197000|2.197000	0.70478|0.70478	0.533000|0.533000	0.62120|0.62120	GAT|ATG	.	.		0.303	CAST-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000250199.2	NM_173062		G	96083056	A	G	96083056	3	3	335	1	0	0	0	0	1	0	0	0	2686	333	12	2	1486	2	CAST	5	96083056	Missense_Mutation	SNP	A	TCGA-RC-A6M6-01A-11D-A32G-10	92486637	96083056	84832204	57	46608										
RGMB	285704	hgsc.bcm.edu	37	chr5	98109681	98109682	+	5'UTR	INS	-	-	C													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	agaagaggaagcgaagcgcgINSccccccggcccatgccgcag							TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr5:98109681_98109682insC	ENST00000513185.1	+	0	343_344				RGMB-AS1_ENST00000501938.2_RNA|RGMB_ENST00000308234.7_Frame_Shift_Ins_p.P11fs|RGMB-AS1_ENST00000505677.1_RNA|RGMB_ENST00000504776.1_3'UTR|RGMB-AS1_ENST00000498871.2_RNA|RGMB-AS1_ENST00000515003.1_RNA|RGMB-AS1_ENST00000505362.1_RNA			Q6NW40	RGMB_HUMAN	repulsive guidance molecule family member b						axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|cell adhesion (GO:0007155)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	anchored component of plasma membrane (GO:0046658)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)	identical protein binding (GO:0042802)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	10		all_cancers(142;2.76e-08)|all_epithelial(76;2.98e-11)|all_lung(232;0.000485)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0587)		AGCGAAGCGCGCCCCCCGGCCC	0.752																																					p.A10fs		Atlas-Indel,Pindel	.											.	RGMB	29	.	0			c.30_31insC						.																																			SO:0001623	5_prime_UTR_variant	285704	exon3			.	AK074887	CCDS47251.1	5q21.1	2013-11-06	2013-11-06		ENSG00000174136	ENSG00000174136			26896	protein-coding gene	gene with protein product		612687	"RGM domain family, member B"			19324014	Standard	NM_001012761		Approved	FLJ90406, DRAGON	uc003knc.3	Q6NW40	OTTHUMG00000162745	ENST00000513185.1:c.-93->C	chr5.hg19:g.98109687_98109687dupC		9.0	0.0		29.0	15.0	NM_001012761	D6R9A0|Q8NC92	Frame_Shift_Ins	INS	ENST00000513185.1	hg19																																																																																				.	.		0.752	RGMB-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000370308.1	NM_173670		C	98109682	-	C	98109681	6	5	335	0	1	1	1	0	0	0	0	0	13296	1074	38	0		0	RGMB	5	98109681	5'UTR	INS	-	TCGA-RC-A6M6-01A-11D-A32G-10	2026625	98109681	82805579	58	46609										
FTMT	94033	hgsc.bcm.edu	37	chr5	121188325	121188325	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tgaagatgggggccccggatGctggcctggcggagtacctt	17	10	0	2	rs149286328	byFrequency	TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr5:121188325G>A	ENST00000321339.1	+	1	676	c.667G>A	c.(667-669)Gct>Act	p.A223T		NM_177478.1	NP_803431.1	Q8N4E7	FTMT_HUMAN	ferritin mitochondrial	223					cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)|positive regulation of cell proliferation (GO:0008284)|positive regulation of lyase activity (GO:0051349)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of transferase activity (GO:0051347)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ferric iron binding (GO:0008199)|ferroxidase activity (GO:0004322)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	33		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	Epithelial(69;0.000171)|OV - Ovarian serous cystadenocarcinoma(64;0.000188)|all cancers(49;0.0027)		GGCCCCGGATGCTGGCCTGGC	0.507																																					p.A223T		Atlas-SNP	.											.	FTMT	71	.	0			c.G667A						.						104	117	112					5																	121188325		2203	4300	6503	SO:0001583	missense	94033	exon1			CCGGATGCTGGCC	BC034419	CCDS4128.1	5q23.1	2008-02-05			ENSG00000181867	ENSG00000181867			17345	protein-coding gene	gene with protein product		608847				11323407	Standard	NM_177478		Approved	MtF	uc003kss.3	Q8N4E7	OTTHUMG00000128912	ENST00000321339.1:c.667G>A	chr5.hg19:g.121188325G>A	ENSP00000313691:p.Ala223Thr	57.0	0.0		76.0	24.0	NM_177478		Missense_Mutation	SNP	ENST00000321339.1	hg19	CCDS4128.1	.	.	.	.	.	.	.	.	.	.	G	2.379	-0.342536	0.05243	.	.	ENSG00000181867	ENST00000321339	T	0.69040	-0.37	3.68	-1.23	0.09465	Ferritin/ribonucleotide reductase-like (1);Ferritin-related (1);	0.297217	0.29594	N	0.011703	T	0.48205	0.1487	L	0.34521	1.04	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.34601	-0.9822	10	0.48119	T	0.1	.	7.1617	0.25667	0.1098:0.0:0.2013:0.6889	.	223	Q8N4E7	FTMT_HUMAN	T	223	ENSP00000313691:A223T	ENSP00000313691:A223T	A	+	1	0	FTMT	121216224	0.974000	0.33945	0.000000	0.03702	0.040000	0.13550	1.944000	0.40263	-0.244000	0.09639	-1.296000	0.01341	GCT	.	G|0.999;T|0.001		0.507	FTMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250884.1	NM_177478		A	121188325	G	A	121188325	3	1	335	1	0	0	0	0	1	0	0	0	6093	1319	46	3	669	3	FTMT	5	121188325	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	23078644	121188325	59726935	59	46610										
FNIP1	96459	hgsc.bcm.edu	37	chr5	131007517	131007517	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ctgcttgttattttttgtacAcaatatttttgaaaactcta	4	6	1	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr5:131007517A>T	ENST00000510461.1	-	14	2715	c.2620T>A	c.(2620-2622)Tgt>Agt	p.C874S	FNIP1_ENST00000307954.8_Missense_Mutation_p.C829S|CTC-432M15.3_ENST00000514667.1_Intron|FNIP1_ENST00000307968.7_Missense_Mutation_p.C846S	NM_133372.2	NP_588613	Q8TF40	FNIP1_HUMAN	folliculin interacting protein 1	874					cellular response to starvation (GO:0009267)|immature B cell differentiation (GO:0002327)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell apoptotic process (GO:0002904)|positive regulation of GTPase activity (GO:0043547)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein phosphorylation (GO:0001934)|regulation of pro-B cell differentiation (GO:2000973)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34		all_cancers(142;0.00347)|Lung NSC(810;0.106)|all_lung(232;0.123)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0665)		TTTTTTGTACACAATATTTTT	0.328																																					p.C874S		Atlas-SNP	.											.	FNIP1	104	.	0			c.T2620A						.						61	63	63					5																	131007517		2203	4300	6503	SO:0001583	missense	96459	exon14			TTGTACACAATAT	DQ145719	CCDS34226.1, CCDS34227.1	5q23.3	2014-01-28				ENSG00000217128			29418	protein-coding gene	gene with protein product		610594				11853319, 17028174	Standard	NM_001008738		Approved	KIAA1961		Q8TF40		ENST00000510461.1:c.2620T>A	chr5.hg19:g.131007517A>T	ENSP00000421985:p.Cys874Ser	110.0	0.0		135.0	58.0	NM_133372	D6RJH5|Q86T47|Q9BUT0	Missense_Mutation	SNP	ENST00000510461.1	hg19	CCDS34227.1	.	.	.	.	.	.	.	.	.	.	A	7.006	0.555848	0.13436	.	.	ENSG00000217128	ENST00000307968;ENST00000307954;ENST00000544351;ENST00000510461	T;T;T	0.12255	2.72;2.7;2.71	5.16	5.16	0.70880	.	.	.	.	.	T	0.15565	0.0375	L	0.54323	1.7	0.80722	D	1	B;B;B	0.16603	0.005;0.018;0.002	B;B;B	0.17722	0.007;0.019;0.001	T	0.04360	-1.0957	9	0.21540	T	0.41	0.0848	14.9998	0.71462	1.0:0.0:0.0:0.0	.	874;846;874	A8K8V8;Q8TF40-3;Q8TF40	.;.;FNIP1_HUMAN	S	846;829;626;874	ENSP00000309266:C846S;ENSP00000310453:C829S;ENSP00000421985:C874S	ENSP00000310453:C829S	C	-	1	0	FNIP1	131035416	0.996000	0.38824	0.986000	0.45419	0.495000	0.33615	4.050000	0.57404	1.950000	0.56595	0.260000	0.18958	TGT	.	.		0.328	FNIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370077.1	NM_133372		T	131007517	A	T	131007517	3	4	335	1	0	0	0	0	1	0	0	0	5983	159	6	4	900	4	FNIP1	5	131007517	Missense_Mutation	SNP	A	TCGA-RC-A6M6-01A-11D-A32G-10	9819192	131007517	49907743	60	46611										
PCDHA8	56140	hgsc.bcm.edu	37	chr5	140222105	140222105	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ccccttcaagctggtgtccaCcttcaagaattactactcgt	6	14	2	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr5:140222105C>T	ENST00000531613.1	+	1	1199	c.1199C>T	c.(1198-1200)aCc>aTc	p.T400I	PCDHA8_ENST00000378123.3_Missense_Mutation_p.T400I|PCDHA5_ENST00000529859.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	400	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(31)|ovary(2)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(6)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGGTGTCCACCTTCAAGAAT	0.602																																					p.T400I		Atlas-SNP	.											.	PCDHA8	366	.	0			c.C1199T						.						150	136	140					5																	140222105		2203	4300	6503	SO:0001583	missense	56140	exon1			TGTCCACCTTCAA	AF152486	CCDS54919.1	5q31	2010-11-26				ENSG00000204962		"Cadherins / Protocadherins : Clustered"	8674	other	complex locus constituent	"KIAA0345-like 6"	606314				10380929	Standard	NM_018911		Approved			Q9Y5H6		ENST00000531613.1:c.1199C>T	chr5.hg19:g.140222105C>T	ENSP00000434655:p.Thr400Ile	192.0	0.0		184.0	68.0	NM_031856	B9EGT7|O75281	Missense_Mutation	SNP	ENST00000531613.1	hg19	CCDS54919.1	.	.	.	.	.	.	.	.	.	.	C	17.75	3.466874	0.63625	.	.	ENSG00000204962	ENST00000531613;ENST00000378123	T;T	0.29142	1.58;1.58	3.57	3.57	0.40892	Cadherin (4);Cadherin-like (1);	0.000000	0.37761	U	0.001960	T	0.46249	0.1383	L	0.39633	1.23	0.30253	N	0.793912	D;D	0.76494	0.999;0.998	D;D	0.77004	0.989;0.989	T	0.50955	-0.8766	10	0.87932	D	0	.	15.5787	0.76414	0.0:1.0:0.0:0.0	.	400;400	Q9Y5H6;Q9Y5H6-2	PCDA8_HUMAN;.	I	400	ENSP00000434655:T400I;ENSP00000367363:T400I	ENSP00000367363:T400I	T	+	2	0	PCDHA8	140202289	0.011000	0.17503	1.000000	0.80357	0.781000	0.44180	2.166000	0.42406	1.709000	0.51313	0.306000	0.20318	ACC	.	.		0.602	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911		T	140222105	C	T	140222105	3	4	335	1	0	0	0	0	1	0	0	0	11539	507	18	3	1201	3	PCDHA8	5	140222105	Missense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	9214588	140222105	40693155	61	46612										
PCDHB8	56128	hgsc.bcm.edu	37	chr5	140558291	140558291	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gctctccgcccagatctggcActgctcaggtctacattgaa	9	14	4	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr5:140558291A>T	ENST00000239444.2	+	1	921	c.676A>T	c.(676-678)Act>Tct	p.T226S	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	226	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(14)|liver(1)|lung(38)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CAGATCTGGCACTGCTCAGGT	0.522																																					p.T226S		Atlas-SNP	.											.	PCDHB8	199	.	0			c.A676T						.						133	169	157					5																	140558291		2203	4296	6499	SO:0001583	missense	56128	exon1			TCTGGCACTGCTC	AF152501	CCDS4250.1	5q31	2010-01-26			ENSG00000120322	ENSG00000120322		"Cadherins / Protocadherins : Clustered"	8693	other	protocadherin		606334				10380929	Standard	NM_019120		Approved	PCDH-BETA8, PCDH3I	uc011dai.2	Q9UN66	OTTHUMG00000129621	ENST00000239444.2:c.676A>T	chr5.hg19:g.140558291A>T	ENSP00000239444:p.Thr226Ser	340.0	0.0		301.0	77.0	NM_019120	B9EGV1	Missense_Mutation	SNP	ENST00000239444.2	hg19	CCDS4250.1	.	.	.	.	.	.	.	.	.	.	a	12.14	1.847870	0.32606	.	.	ENSG00000120322	ENST00000239444	T	0.55760	0.5	4.25	1.69	0.24217	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.49915	0.1585	M	0.65975	2.015	0.19775	N	0.999955	B	0.27656	0.184	B	0.33196	0.159	T	0.51012	-0.8759	9	0.66056	D	0.02	.	5.814	0.18481	0.7677:0.0:0.0855:0.1468	.	226	Q9UN66	PCDB8_HUMAN	S	226	ENSP00000239444:T226S	ENSP00000239444:T226S	T	+	1	0	PCDHB8	140538475	0.000000	0.05858	0.104000	0.21259	0.263000	0.26337	1.528000	0.35985	0.470000	0.27294	0.477000	0.44152	ACT	.	.		0.522	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120		T	140558291	A	T	140558291	3	4	335	1	0	0	0	0	1	0	0	0	11557	159	6	4	678	4	PCDHB8	5	140558291	Missense_Mutation	SNP	A	TCGA-RC-A6M6-01A-11D-A32G-10	336186	140558291	40356969	62	46613										
DOCK2	1794	hgsc.bcm.edu	37	chr5	169111319	169111319	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gaagatgctgagctcttcatGtctctctacgaccccaacaa	7	13	4	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr5:169111319G>C	ENST00000256935.8	+	8	806	c.726G>C	c.(724-726)atG>atC	p.M242I		NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	242					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			AGCTCTTCATGTCTCTCTACG	0.488																																					p.M242I		Atlas-SNP	.											.	DOCK2	389	.	0			c.G726C						.						188	168	175					5																	169111319		2203	4300	6503	SO:0001583	missense	1794	exon8			CTTCATGTCTCTC	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.726G>C	chr5.hg19:g.169111319G>C	ENSP00000256935:p.Met242Ile	96.0	0.0		147.0	44.0	NM_004946	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	hg19	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	G	19.33	3.807494	0.70797	.	.	ENSG00000134516	ENST00000256935	T	0.49720	0.77	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.62356	0.2421	L	0.53249	1.67	0.80722	D	1	D	0.54964	0.969	D	0.63381	0.914	T	0.54450	-0.8292	10	0.21540	T	0.41	.	19.2567	0.93948	0.0:0.0:1.0:0.0	.	242	Q92608	DOCK2_HUMAN	I	242	ENSP00000256935:M242I	ENSP00000256935:M242I	M	+	3	0	DOCK2	169043897	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.476000	0.97823	2.544000	0.85801	0.655000	0.94253	ATG	.	.		0.488	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		C	169111319	G	C	169111319	3	2	335	1	0	0	0	0	1	0	0	0	4689	1377	48	4	756	4	DOCK2	5	169111319	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	28553028	169111319	11803941	63	46614										
EIF4E1B	253314	hgsc.bcm.edu	37	chr5	176070686	176070686	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	accgcagccgggcctggcagGacaacctgcacctggtcacc	12	17	1	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr5:176070686G>T	ENST00000318682.6	+	5	831	c.247G>T	c.(247-249)Gac>Tac	p.D83Y	EIF4E1B_ENST00000504597.1_Missense_Mutation_p.D83Y	NM_001099408.1	NP_001092878.1	A6NMX2	I4E1B_HUMAN	eukaryotic translation initiation factor 4E family member 1B	83					regulation of translation (GO:0006417)	cytoplasm (GO:0005737)|mRNA cap binding complex (GO:0005845)	translation initiation factor activity (GO:0003743)			breast(1)|large_intestine(1)|lung(2)|pancreas(1)	5	all_cancers(89;0.00185)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.00498)|all_neural(177;0.0212)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GGCCTGGCAGGACAACCTGCA	0.637																																					p.D83Y		Atlas-SNP	.											.	EIF4E1B	24	.	0			c.G247T						.						30	33	32					5																	176070686		2051	4179	6230	SO:0001583	missense	253314	exon5			TGGCAGGACAACC		CCDS47345.1	5q35.2	2008-06-12			ENSG00000175766	ENSG00000175766			33179	protein-coding gene	gene with protein product						16191198	Standard	NM_001099408		Approved	FLJ36951	uc010jkf.1	A6NMX2	OTTHUMG00000163227	ENST00000318682.6:c.247G>T	chr5.hg19:g.176070686G>T	ENSP00000323714:p.Asp83Tyr	75.0	0.0		90.0	25.0	NM_001099408		Missense_Mutation	SNP	ENST00000318682.6	hg19	CCDS47345.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.58|19.58	3.855048|3.855048	0.71719|0.71719	.|.	.|.	ENSG00000175766|ENSG00000175766	ENST00000318682;ENST00000510660;ENST00000504597|ENST00000505497	T;T;T|.	0.46819|.	0.86;0.86;0.86|.	5.33|5.33	4.46|4.46	0.54185|0.54185	Translation Initiation factor eIF- 4e-like  domain (2);|.	0.350201|.	0.28853|.	N|.	0.013925|.	T|T	0.79417|0.79417	0.4442|0.4442	M|M	0.93062|0.93062	3.375|3.375	0.50313|0.50313	D|D	0.999863|0.999863	D|.	0.59357|.	0.985|.	D|.	0.65323|.	0.934|.	T|T	0.82143|0.82143	-0.0603|-0.0603	10|5	0.87932|.	D|.	0|.	.|.	8.7057|8.7057	0.34354|0.34354	0.0772:0.0:0.7731:0.1497|0.0772:0.0:0.7731:0.1497	.|.	83|.	A6NMX2|.	I4E1B_HUMAN|.	Y|S	83|23	ENSP00000323714:D83Y;ENSP00000421009:D83Y;ENSP00000427633:D83Y|.	ENSP00000323714:D83Y|.	D|R	+|+	1|3	0|2	EIF4E1B|EIF4E1B	176003292|176003292	1.000000|1.000000	0.71417|0.71417	0.800000|0.800000	0.32199|0.32199	0.905000|0.905000	0.53344|0.53344	6.445000|6.445000	0.73456|0.73456	1.263000|1.263000	0.44181|0.44181	0.491000|0.491000	0.48974|0.48974	GAC|AGG	.	.		0.637	EIF4E1B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372187.1	NM_001099408		T	176070686	G	T	176070686	3	4	335	1	0	0	0	0	1	0	0	0	5031	1174	41	3	257	3	EIF4E1B	5	176070686	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	6959367	176070686	4844574	64	46615										
DBN1	1627	hgsc.bcm.edu	37	chr5	176893949	176893949	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ctgctcccgctcccggtagcGccgctcgcgctcctcttgct	10	20	1	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr5:176893949G>A	ENST00000309007.5	-	7	889	c.670C>T	c.(670-672)Cgc>Tgc	p.R224C	DBN1_ENST00000393565.1_Missense_Mutation_p.R224C|DBN1_ENST00000292385.5_Missense_Mutation_p.R226C	NM_004395.3	NP_004386	Q16643	DREB_HUMAN	drebrin 1	224					actin filament organization (GO:0007015)|cell communication by chemical coupling (GO:0010643)|cell communication by electrical coupling (GO:0010644)|maintenance of protein location in cell (GO:0032507)|neural precursor cell proliferation (GO:0061351)|regulation of dendrite development (GO:0050773)|regulation of neuronal synaptic plasticity (GO:0048168)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|gap junction (GO:0005921)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|profilin binding (GO:0005522)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(12)|ovary(1)|skin(2)	25	all_cancers(89;2.17e-05)|Renal(175;0.000269)|Lung NSC(126;0.0014)|all_lung(126;0.0025)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TCCCGGTAGCGCCGCTCGCGC	0.716																																					p.R226C		Atlas-SNP	.											.	DBN1	122	.	0			c.C676T						.						51	52	52					5																	176893949		2203	4300	6503	SO:0001583	missense	1627	exon8			GGTAGCGCCGCTC		CCDS4420.1, CCDS4421.1	5q35.3	2008-02-05			ENSG00000113758	ENSG00000113758			2695	protein-coding gene	gene with protein product		126660		D0S117E		8216329	Standard	NM_004395		Approved		uc003mgy.2	Q16643	OTTHUMG00000130856	ENST00000309007.5:c.670C>T	chr5.hg19:g.176893949G>A	ENSP00000308532:p.Arg224Cys	39.0	0.0		31.0	14.0	NM_080881	A8MV58|B2RBG0|Q9UFZ5	Missense_Mutation	SNP	ENST00000309007.5	hg19	CCDS4420.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.805042	0.90623	.	.	ENSG00000113758	ENST00000309007;ENST00000292385;ENST00000393565;ENST00000477391	T;T;T	0.45668	0.89;0.89;1.5	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	T	0.66228	0.2768	M	0.75777	2.31	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.995;0.996;0.998	T	0.70182	-0.4942	10	0.87932	D	0	-17.5793	18.0729	0.89417	0.0:0.0:1.0:0.0	.	174;224;224;226	B3KSQ7;A8MV58;Q16643;Q16643-2	.;.;DREB_HUMAN;.	C	224;226;224;223	ENSP00000308532:R224C;ENSP00000292385:R226C;ENSP00000377195:R224C	ENSP00000292385:R226C	R	-	1	0	DBN1	176826555	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.286000	0.51724	2.586000	0.87340	0.655000	0.94253	CGC	.	.		0.716	DBN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253429.2	NM_080881		A	176893949	G	A	176893949	3	1	335	1	0	0	0	0	1	0	0	0	4254	1087	38	1	1311	1	DBN1	5	176893949	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	823263	176893949	4021311	65	46616										
OR5V1	81696	hgsc.bcm.edu	37	chr6	29323327	29323327	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gattatgcaaatgtaggaaaGtacgatacaaaggaaaggag	12	3	0	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr6:29323327G>C	ENST00000377154.1	-	4	945	c.646C>G	c.(646-648)Ctt>Gtt	p.L216V	OR5V1_ENST00000543825.1_Missense_Mutation_p.L216V			Q9UGF6	OR5V1_HUMAN	olfactory receptor, family 5, subfamily V, member 1	216						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(3)|large_intestine(3)|liver(1)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						ATGTAGGAAAGTACGATACAA	0.473																																					p.L216V	Ovarian(32;43 883 21137 32120 42650)	Atlas-SNP	.											OR5V1,NS,carcinoma,0,1	OR5V1	63	.	0			c.C646G						.						100	90	93					6																	29323327		2203	4300	6503	SO:0001583	missense	81696	exon1			AGGAAAGTACGAT		CCDS4657.1	6p22.1	2013-09-23				ENSG00000243729		"GPCR / Class A : Olfactory receptors"	13972	protein-coding gene	gene with protein product							Standard	NM_030876		Approved	hs6M1-21	uc011dlo.2	Q9UGF6		ENST00000377154.1:c.646C>G	chr6.hg19:g.29323327G>C	ENSP00000366359:p.Leu216Val	38.0	0.0		34.0	10.0	NM_030876	A2BDZ0|B0S860|Q5SQI9|Q6NTB5|Q8IVL3	Missense_Mutation	SNP	ENST00000377154.1	hg19	CCDS4657.1	.	.	.	.	.	.	.	.	.	.	G	0.001	-3.139742	0.00030	.	.	ENSG00000243729	ENST00000377154;ENST00000377151;ENST00000543825	T;T	0.35421	1.31;1.31	4.43	0.346	0.16017	GPCR, rhodopsin-like superfamily (1);	0.000000	0.30068	N	0.010488	T	0.01870	0.0059	N	0.00811	-1.165	0.09310	N	1	B	0.11235	0.004	B	0.12156	0.007	T	0.41893	-0.9483	10	0.02654	T	1	-13.8363	4.4796	0.11760	0.1502:0.4738:0.2548:0.1211	.	216	Q9UGF6	OR5V1_HUMAN	V	216	ENSP00000366359:L216V;ENSP00000443309:L216V	ENSP00000366356:L216V	L	-	1	0	OR5V1	29431306	0.000000	0.05858	0.036000	0.18154	0.019000	0.09904	-1.970000	0.01504	-0.055000	0.13244	0.543000	0.68304	CTT	.	.		0.473	OR5V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076398.3			C	29323327	G	C	29323327	3	2	335	1	0	0	0	0	1	0	0	0	11193	1029	36	4	322	4	OR5V1	6	29323327	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10		29323327	141791740	66	46617										
UBD	10537	hgsc.bcm.edu	37	chr6	29524084	29524084	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tcacgctgtcatatgggttgGcatcaaaggtcattaaatcc	9	9	4	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr6:29524084G>C	ENST00000377050.4	-	2	294	c.71C>G	c.(70-72)gCc>gGc	p.A24G	GABBR1_ENST00000355973.3_3'UTR	NM_006398.3	NP_006389.2	O15205	UBD_HUMAN	ubiquitin D	24	Ubiquitin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00214}.				aggresome assembly (GO:0070842)|myeloid dendritic cell differentiation (GO:0043011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein modification by small protein conjugation (GO:0032446)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|response to interferon-gamma (GO:0034341)|response to organonitrogen compound (GO:0010243)|response to tumor necrosis factor (GO:0034612)|ubiquitin-dependent protein catabolic process (GO:0006511)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	proteasome binding (GO:0070628)			kidney(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						ATATGGGTTGGCATCAAAGGT	0.473																																					p.A24G		Atlas-SNP	.											.	UBD	13	.	0			c.C71G						.						97	77	84					6																	29524084		1511	2709	4220	SO:0001583	missense	10537	exon2			GGGTTGGCATCAA	Y12653	CCDS4662.1	6p21.3	2008-04-11			ENSG00000213886	ENSG00000213886			18795	protein-coding gene	gene with protein product		606050				9368598, 8662070	Standard	NM_006398		Approved	FAT10	uc003nmo.3	O15205	OTTHUMG00000031289	ENST00000377050.4:c.71C>G	chr6.hg19:g.29524084G>C	ENSP00000366249:p.Ala24Gly	86.0	0.0		69.0	23.0	NM_006398	B0UZT6|Q5STL2|Q5SUK2|Q96EC7	Missense_Mutation	SNP	ENST00000377050.4	hg19	CCDS4662.1	.	.	.	.	.	.	.	.	.	.	G	16.96	3.265470	0.59431	.	.	ENSG00000213886	ENST00000377050	T	0.12361	2.69	5.38	3.58	0.41010	Ubiquitin supergroup (1);Ubiquitin (2);	0.232106	0.21375	U	0.075571	T	0.08358	0.0208	M	0.64567	1.98	0.21020	N	0.999801	B	0.33266	0.404	B	0.39590	0.304	T	0.11348	-1.0591	10	0.87932	D	0	-22.1327	8.7048	0.34347	0.1819:0.0:0.8181:0.0	.	24	O15205	UBD_HUMAN	G	24	ENSP00000366249:A24G	ENSP00000366249:A24G	A	-	2	0	UBD	29632063	0.015000	0.18098	0.038000	0.18304	0.169000	0.22640	1.133000	0.31430	1.260000	0.44134	-0.192000	0.12808	GCC	.	.		0.473	UBD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076628.3			C	29524084	G	C	29524084	3	2	335	1	0	0	0	0	1	0	0	0	16858	1203	42	4	430	4	UBD	6	29524084	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	200757	29524084	141590983	67	46618										
TRIM39	56658	hgsc.bcm.edu	37	chr6	30298592	30298593	+	Frame_Shift_Del	DEL	AG	AG	-													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gtgtctggagcccctggaacAgaagctgcaggagatcactc							TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr6:30298592_30298593delAG	ENST00000396547.1	+	3	648_649	c.488_489delAG	c.(487-489)cagfs	p.Q163fs	TRIM39_ENST00000376659.5_Frame_Shift_Del_p.Q163fs|TRIM39-RPP21_ENST00000513556.1_Frame_Shift_Del_p.Q75fs|TRIM39_ENST00000376656.4_Frame_Shift_Del_p.Q163fs|TRIM39_ENST00000396551.3_Frame_Shift_Del_p.Q163fs|TRIM39_ENST00000396548.1_Frame_Shift_Del_p.Q163fs|TRIM39_ENST00000540416.1_Frame_Shift_Del_p.Q163fs			Q9HCM9	TRI39_HUMAN	tripartite motif containing 39	163					apoptotic process (GO:0006915)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|positive regulation of apoptotic signaling pathway (GO:2001235)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			ovary(3)	3						CCCCTGGAACAGAAGCTGCAGG	0.535																																					p.163_163del		Atlas-Indel,Pindel	.											.	TRIM39	56	.	0			c.487_488del						.																																			SO:0001589	frameshift_variant	56658	exon4			.	BC034985	CCDS34377.1, CCDS34378.1	6p22.1	2013-01-09	2011-01-25	2002-06-07	ENSG00000204599	ENSG00000204599		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	10065	protein-coding gene	gene with protein product		605700	"ring finger protein 23", "tripartite motif-containing 39"	RNF23		11006080	Standard	NM_021253		Approved			Q9HCM9	OTTHUMG00000031066	ENST00000396547.1:c.488_489delAG	chr6.hg19:g.30298592_30298593delAG	ENSP00000379796:p.Gln163fs	72.0	0.0		68.0	21.0	NM_172016	Q5STG3|Q5STG4|Q76BL3|Q8IYT9|Q96IB6	Frame_Shift_Del	DEL	ENST00000396547.1	hg19	CCDS34377.1																																																																																			.	.		0.535	TRIM39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076086.2	NM_172016		-	30298593	AG	-	30298592	7	5	335	1	0	1	0	1	0	0	0	0	16528	188	7	0	494	0	TRIM39	6	30298592	Frame_Shift_Del	DEL	AG	TCGA-RC-A6M6-01A-11D-A32G-10	774508	30298592	140816475	68	46619										
HLA-DMA	3108	hgsc.bcm.edu	37	chr6	32918508	32918508	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	cagagagtcccacactgggaCtcccatcctggcagtacact	9	15	0	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr6:32918508C>T	ENST00000374843.4	-	2	246	c.161G>A	c.(160-162)aGt>aAt	p.S54N	HLA-DMA_ENST00000395303.3_Missense_Mutation_p.S54N|HLA-DMA_ENST00000395305.3_Intron|XXbac-BPG181M17.5_ENST00000429234.1_Intron|HLA-DMA_ENST00000464392.1_Intron	NM_006120.3	NP_006111.2	P28067	DMA_HUMAN	major histocompatibility complex, class II, DM alpha	54	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|chaperone mediated protein folding requiring cofactor (GO:0051085)|immunoglobulin mediated immune response (GO:0016064)|inner ear development (GO:0048839)|peptide antigen assembly with MHC class II protein complex (GO:0002503)|positive regulation of immune response (GO:0050778)|positive regulation of T cell differentiation (GO:0045582)|positive thymic T cell selection (GO:0045059)|protein transport (GO:0015031)	cell surface (GO:0009986)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|multivesicular body (GO:0005771)	MHC class II protein complex binding (GO:0023026)			kidney(1)|large_intestine(2)|lung(8)	11						CACACTGGGACTCCCATCCTG	0.557																																					p.S54N		Atlas-SNP	.											.	HLA-DMA	20	.	0			c.G161A						.						116	119	118					6																	32918508		1508	2708	4216	SO:0001583	missense	3108	exon2			CTGGGACTCCCAT		CCDS4761.1	6p21.3	2013-01-11			ENSG00000204257	ENSG00000204257		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4934	protein-coding gene	gene with protein product		142855				1922385	Standard	NM_006120		Approved	D6S222E, RING6	uc003ocm.2	P28067	OTTHUMG00000031173	ENST00000374843.4:c.161G>A	chr6.hg19:g.32918508C>T	ENSP00000363976:p.Ser54Asn	45.0	0.0		46.0	13.0	NM_006120	Q29639|Q29640	Missense_Mutation	SNP	ENST00000374843.4	hg19	CCDS4761.1	.	.	.	.	.	.	.	.	.	.	C	8.301	0.819933	0.16678	.	.	ENSG00000204257	ENST00000395303;ENST00000374843;ENST00000456800;ENST00000422832;ENST00000341486	T;T;T;T	0.00669	5.9;5.9;5.9;5.9	5.53	-2.42	0.06542	MHC class II, alpha/beta chain, N-terminal (1);MHC classes I/II-like antigen recognition protein (1);MHC class II, alpha chain, N-terminal (2);	0.498364	0.24559	N	0.037487	T	0.00178	0.0005	N	0.22421	0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46803	-0.9165	10	0.39692	T	0.17	.	1.1982	0.01879	0.128:0.2924:0.2629:0.3167	.	54;54	P28067;Q31604	DMA_HUMAN;.	N	54;54;84;21;46	ENSP00000378714:S54N;ENSP00000363976:S54N;ENSP00000409668:S84N;ENSP00000403122:S21N	ENSP00000345804:S46N	S	-	2	0	HLA-DMA	33026486	0.000000	0.05858	0.002000	0.10522	0.432000	0.31715	-5.566000	0.00113	-0.104000	0.12154	0.643000	0.83706	AGT	.	.		0.557	HLA-DMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076325.2	NM_006120		T	32918508	C	T	32918508	3	4	335	1	0	0	0	0	1	0	0	0	7207	565	20	3	640	3	HLA-DMA	6	32918508	Missense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	2619916	32918508	138196559	69	46620										
DEF6	50619	hgsc.bcm.edu	37	chr6	35285774	35285774	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ccagcgccaggagtggacagCtggtgagtgctcgctaggtg	17	10	0	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr6:35285774C>T	ENST00000316637.5	+	6	919	c.914C>T	c.(913-915)gCt>gTt	p.A305V	DEF6_ENST00000468102.1_3'UTR|DEF6_ENST00000542066.1_Missense_Mutation_p.A50V	NM_022047.3	NP_071330.3	Q9H4E7	DEFI6_HUMAN	differentially expressed in FDCP 6 homolog (mouse)	305	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.					cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				cervix(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)	15						GAGTGGACAGCTGGTGAGTGC	0.592																																					p.A305V		Atlas-SNP	.											.	DEF6	36	.	0			c.C914T						.						37	34	35					6																	35285774		2203	4300	6503	SO:0001583	missense	50619	exon6			GGACAGCTGGTGA	AJ276095	CCDS4802.1	6p21.33-p21.1	2013-01-10	2001-11-28		ENSG00000023892	ENSG00000023892		"Pleckstrin homology (PH) domain containing"	2760	protein-coding gene	gene with protein product	"SWAP-70-like adaptor protein of T cells"	610094	"differentially expressed in FDCP (mouse homolog) 6"			19251698	Standard	NM_022047		Approved	IBP, SLAT, SWAP70L	uc003okk.3	Q9H4E7	OTTHUMG00000014563	ENST00000316637.5:c.914C>T	chr6.hg19:g.35285774C>T	ENSP00000319831:p.Ala305Val	72.0	0.0		56.0	20.0	NM_022047	Q86VF4	Missense_Mutation	SNP	ENST00000316637.5	hg19	CCDS4802.1	.	.	.	.	.	.	.	.	.	.	C	14.20	2.465389	0.43839	.	.	ENSG00000023892	ENST00000542066;ENST00000316637	T;T	0.32023	1.47;2.64	5.35	5.35	0.76521	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.384871	0.29034	N	0.013356	T	0.11196	0.0273	L	0.52823	1.66	0.18873	N	0.999981	B;P;B	0.35656	0.144;0.514;0.292	B;B;B	0.34931	0.107;0.192;0.138	T	0.14783	-1.0460	10	0.12430	T	0.62	-7.3359	8.2534	0.31739	0.0:0.8643:0.0:0.1357	.	50;305;305	F5H853;B2RBP7;Q9H4E7	.;.;DEFI6_HUMAN	V	50;305	ENSP00000442166:A50V;ENSP00000319831:A305V	ENSP00000319831:A305V	A	+	2	0	DEF6	35393752	0.846000	0.29590	0.793000	0.32043	0.950000	0.60333	4.687000	0.61708	2.516000	0.84829	0.460000	0.39030	GCT	.	.		0.592	DEF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040276.1	NM_022047		T	35285774	C	T	35285774	3	4	335	1	0	0	0	0	1	0	0	0	4388	797	28	3	936	3	DEF6	6	35285774	Missense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	2367266	35285774	135829293	70	46621										
LRFN2	57497	hgsc.bcm.edu	37	chr6	40360374	40360374	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gctgggggcctcgtggttgcAgaccttgtagcgcaccatga	15	11	0	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr6:40360374A>T	ENST00000338305.6	-	3	2220	c.1678T>A	c.(1678-1680)Tgc>Agc	p.C560S		NM_020737.1	NP_065788.1	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III domain containing 2	560						cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	58	Ovarian(28;0.0418)|Colorectal(47;0.196)					TCGTGGTTGCAGACCTTGTAG	0.642																																					p.C560S		Atlas-SNP	.											.	LRFN2	133	.	0			c.T1678A						.						62	51	54					6																	40360374		2203	4300	6503	SO:0001583	missense	57497	exon3			GGTTGCAGACCTT	AB033072	CCDS34443.1	6p21.2-p21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000156564	ENSG00000156564		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	21226	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 2"	612808	"KIAA1246"	KIAA1246, SALM1		16495444, 16828986	Standard	NM_020737		Approved	FIGLER2	uc003oph.1	Q9ULH4	OTTHUMG00000014662	ENST00000338305.6:c.1678T>A	chr6.hg19:g.40360374A>T	ENSP00000345985:p.Cys560Ser	52.0	0.0		51.0	21.0	NM_020737	A5PKU3|Q5SYP9	Missense_Mutation	SNP	ENST00000338305.6	hg19	CCDS34443.1	.	.	.	.	.	.	.	.	.	.	a	11.20	1.567480	0.28003	.	.	ENSG00000156564	ENST00000338305	T	0.56611	0.45	5.41	4.25	0.50352	.	0.244211	0.48767	D	0.000169	T	0.31451	0.0797	M	0.64404	1.975	0.36600	D	0.874602	B	0.22541	0.071	B	0.25987	0.065	T	0.12243	-1.0555	10	0.30078	T	0.28	.	9.9406	0.41578	0.919:0.0:0.081:0.0	.	560	Q9ULH4	LRFN2_HUMAN	S	560	ENSP00000345985:C560S	ENSP00000345985:C560S	C	-	1	0	LRFN2	40468352	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.779000	0.62375	0.891000	0.36235	0.529000	0.55759	TGC	.	.		0.642	LRFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040488.1	XM_166372		T	40360374	A	T	40360374	3	4	335	1	0	0	0	0	1	0	0	0	8947	188	7	4	695	4	LRFN2	6	40360374	Missense_Mutation	SNP	A	TCGA-RC-A6M6-01A-11D-A32G-10	5074600	40360374	130754693	71	46622										
TFEB	7942	hgsc.bcm.edu	37	chr6	41658400	41658400	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	actggccagctcctcactcaCctccctctcagggttggagc	9	17	3	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr6:41658400C>T	ENST00000230323.4	-	4	770		c.e4+1		TFEB_ENST00000394283.1_Splice_Site|TFEB_ENST00000403298.4_Splice_Site|TFEB_ENST00000373033.1_Splice_Site|TFEB_ENST00000358871.2_Splice_Site|TFEB_ENST00000420312.1_Intron	NM_001271945.1|NM_007162.2	NP_001258874.1|NP_009093.1	P19484	TFEB_HUMAN	transcription factor EB						autophagy (GO:0006914)|embryonic placenta development (GO:0001892)|humoral immune response (GO:0006959)|lysosome organization (GO:0007040)|positive regulation of autophagy (GO:0010508)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	11	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;7.61e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)			TCCTCACTCACCTCCCTCTCA	0.622			T	ALPHA	renal (childhood epithelioid)																																.		Atlas-SNP	.		Dom	yes		6	6p21	7942	transcription factor EB		"E,M"	.	TFEB	37	.	0			c.468+1G>A						.						23	23	23					6																	41658400		2203	4300	6503	SO:0001630	splice_region_variant	7942	exon5			CACTCACCTCCCT	M33782	CCDS4858.1, CCDS64424.1, CCDS64425.1	6p21	2013-05-21			ENSG00000112561	ENSG00000112561		"Basic helix-loop-helix proteins"	11753	protein-coding gene	gene with protein product		600744				2115126	Standard	NM_007162		Approved	TCFEB, bHLHe35	uc003oqu.2	P19484	OTTHUMG00000014684	ENST00000230323.4:c.468+1G>A	chr6.hg19:g.41658400C>T		27.0	0.0		19.0	8.0	NM_007162	Q709B3|Q7Z6P9|Q9BRJ5|Q9UJD8	Splice_Site	SNP	ENST00000230323.4	hg19	CCDS4858.1	.	.	.	.	.	.	.	.	.	.	C	12.12	1.842283	0.32513	.	.	ENSG00000112561	ENST00000343317;ENST00000230323;ENST00000358871;ENST00000403298;ENST00000373033;ENST00000394283;ENST00000419396;ENST00000416140;ENST00000419574	.	.	.	5.06	5.06	0.68205	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.0186	0.89249	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TFEB	41766378	1.000000	0.71417	0.999000	0.59377	0.311000	0.27955	5.978000	0.70501	2.351000	0.79841	0.462000	0.41574	.	.	.		0.622	TFEB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040522.3		Intron	T	41658400	C	T	41658400	5	4	335	1	0	0	0	0	0	0	1	0	15816	521	18	3	989	3	TFEB	6	41658400	Splice_Site	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	1298026	41658400	129456667	72	46623										
TCTE1	202500	hgsc.bcm.edu	37	chr6	44254246	44254246	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	cttctgctggtgttccgggaGcatctgcttcaggatagggt	14	9	3	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr6:44254246G>C	ENST00000371505.4	-	3	423	c.301C>G	c.(301-303)Ctc>Gtc	p.L101V	TMEM151B_ENST00000438774.2_Intron|RP11-444E17.6_ENST00000505802.1_Intron|TCTE1_ENST00000371504.1_5'Flank|TCTE1_ENST00000371503.3_5'UTR	NM_182539.3	NP_872345.2	Q5JU00	TCTE1_HUMAN	t-complex-associated-testis-expressed 1	101										breast(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			TGTTCCGGGAGCATCTGCTTC	0.582																																					p.L101V		Atlas-SNP	.											.	TCTE1	77	.	0			c.C301G						.						122	112	116					6																	44254246		2203	4300	6503	SO:0001583	missense	202500	exon3			CCGGGAGCATCTG	BC035022	CCDS4910.1	6q21.1	2014-07-18			ENSG00000146221	ENSG00000146221			11693	protein-coding gene	gene with protein product		186975				2568335, 8646886	Standard	NM_182539		Approved	D6S46, MGC33600, FAP155	uc003oxi.2	Q5JU00	OTTHUMG00000014763	ENST00000371505.4:c.301C>G	chr6.hg19:g.44254246G>C	ENSP00000360560:p.Leu101Val	87.0	0.0		73.0	17.0	NM_182539	B4DX59|Q8IYS6	Missense_Mutation	SNP	ENST00000371505.4	hg19	CCDS4910.1	.	.	.	.	.	.	.	.	.	.	G	13.34	2.209162	0.39003	.	.	ENSG00000146221	ENST00000371505	T	0.22743	1.94	4.95	3.03	0.35002	.	0.607447	0.17402	N	0.175484	T	0.10294	0.0252	M	0.71581	2.175	0.80722	D	1	B	0.29378	0.243	B	0.21360	0.034	T	0.05599	-1.0875	10	0.17369	T	0.5	-7.2632	13.5372	0.61653	0.0:0.0:0.7172:0.2828	.	101	Q5JU00	TCTE1_HUMAN	V	101	ENSP00000360560:L101V	ENSP00000360560:L101V	L	-	1	0	TCTE1	44362224	0.997000	0.39634	0.985000	0.45067	0.983000	0.72400	2.473000	0.45145	1.027000	0.39758	0.563000	0.77884	CTC	.	.		0.582	TCTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040736.1	NM_182539		C	44254246	G	C	44254246	3	2	335	1	0	0	0	0	1	0	0	0	15732	971	34	4	1216	4	TCTE1	6	44254246	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	2595846	44254246	126860821	73	46624										
DEFB114	245928	hgsc.bcm.edu	37	chr6	49928115	49928115	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	acagtctcttttacaacgacCgtaacgtttggtgcaacgat	8	10	1	0	rs533824519		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr6:49928115C>G	ENST00000322066.3	-	2	99	c.100G>C	c.(100-102)Ggt>Cgt	p.G34R		NM_001037499.1	NP_001032588.1	Q30KQ6	DB114_HUMAN	defensin, beta 114	34					defense response to bacterium (GO:0042742)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)	extracellular region (GO:0005576)	lipopolysaccharide binding (GO:0001530)			kidney(1)|large_intestine(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	8	Lung NSC(77;0.042)					TTACAACGACCGTAACGTTTG	0.353																																					p.G34R		Atlas-SNP	.											.	DEFB114	12	.	0			c.G100C						.						110	99	103					6																	49928115		2203	4299	6502	SO:0001583	missense	245928	exon2			AACGACCGTAACG	DQ012018	CCDS34474.1	6p12.3	2010-03-30			ENSG00000177684	ENSG00000177684		"Defensins, beta"	18095	protein-coding gene	gene with protein product		615243				11854508, 16033865	Standard	NM_001037499		Approved	DEFB-14	uc011dwp.2	Q30KQ6	OTTHUMG00000160209	ENST00000322066.3:c.100G>C	chr6.hg19:g.49928115C>G	ENSP00000312702:p.Gly34Arg	126.0	0.0		121.0	54.0	NM_001037499	Q8NES9	Missense_Mutation	SNP	ENST00000322066.3	hg19	CCDS34474.1	.	.	.	.	.	.	.	.	.	.	C	11.73	1.727238	0.30593	.	.	ENSG00000177684	ENST00000322066	T	0.62639	0.01	3.55	3.55	0.40652	.	0.000000	0.39407	N	0.001367	T	0.66268	0.2772	.	.	.	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.54997	-0.8209	8	.	.	.	-20.8631	10.939	0.47262	0.0:1.0:0.0:0.0	.	34	Q30KQ6	DB114_HUMAN	R	34	ENSP00000312702:G34R	.	G	-	1	0	DEFB114	50036074	0.121000	0.22262	0.140000	0.22221	0.008000	0.06430	3.207000	0.51106	2.288000	0.76882	0.650000	0.86243	GGT	.	.		0.353	DEFB114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359665.1	NM_001037499		G	49928115	C	G	49928115	3	3	335	1	0	0	0	0	1	0	0	0	4405	652	23	4	112	4	DEFB114	6	49928115	Missense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	5673869	49928115	121186952	74	46625										
LATS1	9113	hgsc.bcm.edu	37	chr6	150004716	150004717	+	De_novo_Start_OutOfFrame	INS	-	-	ACACGCATACTTTTCACAGGCTGTTGAATAGG													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tctgtagctctggttttaatINSacacgcatacttttcacagg							TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr6:150004716_150004717insACACGCATACTTTTCACAGGCTGTTGAATAGG	ENST00000542747.1	-	0	1344_1345				LATS1_ENST00000543571.1_Frame_Shift_Ins_p.V503fs|LATS1_ENST00000253339.5_Frame_Shift_Ins_p.V503fs|LATS1_ENST00000392273.3_Frame_Shift_Ins_p.V503fs					large tumor suppressor kinase 1											central_nervous_system(1)|lung(5)	6		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116)		CTGGTTTTAATACACGCATACT	0.455																																					p.V503_L504delinsVLFNSLX		Pindel	.											.	LATS1	241	.	0			c.1509_1510insCCTATTCAACAGCCTGTGAAAAGTATGCGTGT						.																																					9113	exon4			.	AF104413	CCDS34551.1, CCDS59040.1	6q25.1	2013-04-25	2013-04-25		ENSG00000131023	ENSG00000131023			6514	protein-coding gene	gene with protein product		603473	"LATS (large tumor suppressor, Drosophila) homolog 1", "LATS, large tumor suppressor, homolog 1 (Drosophila)"			9988268, 15122335	Standard	NM_004690		Approved	WARTS	uc003qmu.2	O95835	OTTHUMG00000016437	ENST00000542747.1:c.-1940->CCTATTCAACAGCCTGTGAAAAGTATGCGTGT	chr6.hg19:g.150004716_150004717insACACGCATACTTTTCACAGGCTGTTGAATAGG		127.0	0.0		64.0	14.0	NM_004690		Frame_Shift_Ins	INS	ENST00000542747.1	hg19																																																																																				.	.		0.455	LATS1-006	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000396940.1	NM_004690		ACACGCATACTTTTCACAGGCTGTTGAATAGG	150004717	-	ACACGCATACTTTTCACAGGCTGTTGAATAGG	150004716	6	5	335	1	0	1	1	0	0	0	0	0	8655	1393	49	0		0	LATS1	6	150004716	De_novo_Start_OutOfFrame	INS	-	TCGA-RC-A6M6-01A-11D-A32G-10	100076601	150004716	21110351	75	46626										
C7orf28A	51622	hgsc.bcm.edu	37	chr7	5944735	5944735	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tttcccacagtatttgcaaaCgctacatttgcagtcatgtg	7	10	1	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr7:5944735C>T	ENST00000325974.6	+	7	599	c.533C>T	c.(532-534)aCg>aTg	p.T178M	CCZ1_ENST00000537980.1_Missense_Mutation_p.T35M	NM_015622.5	NP_056437.4	P86791	CCZ1_HUMAN	CCZ1 vacuolar protein trafficking and biogenesis associated homolog (S. cerevisiae)	178						lysosome (GO:0005764)|membrane (GO:0016020)				large_intestine(3)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	6						TATTTGCAAACGCTACATTTG	0.323																																					p.T178M		Atlas-SNP	.											.	CCZ1	21	.	0			c.C533T						.						79	80	79					7																	5944735		2179	4298	6477	SO:0001583	missense	51622	exon7			TGCAAACGCTACA	AF151801	CCDS34597.1	7p22.1	2014-02-13	2010-06-29	2010-06-29	ENSG00000122674	ENSG00000122674			21691	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 28A"	C7orf28A		10810093, 20305638	Standard	NM_015622		Approved	CGI-43, CCZ1A	uc003spf.3	P86791	OTTHUMG00000155502	ENST00000325974.6:c.533C>T	chr7.hg19:g.5944735C>T	ENSP00000325681:p.Thr178Met	737.0	0.0		638.0	208.0	NM_015622	A2RU45|O95766|Q9UG65|Q9Y359	Missense_Mutation	SNP	ENST00000325974.6	hg19	CCDS34597.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.262753	0.80358	.	.	ENSG00000122674	ENST00000325974;ENST00000537980	.	.	.	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.59905	0.2228	L	0.46157	1.445	0.80722	D	1	P	0.52061	0.95	P	0.47206	0.541	T	0.57130	-0.7864	9	0.37606	T	0.19	-18.35	19.1488	0.93479	0.0:1.0:0.0:0.0	.	178	P86790	CCZ1L_HUMAN	M	178;35	.	ENSP00000325681:T178M	T	+	2	0	CCZ1	5911261	1.000000	0.71417	0.956000	0.39512	0.907000	0.53573	7.722000	0.84778	2.772000	0.95346	0.650000	0.86243	ACG	.	.		0.323	CCZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340391.1	NM_015622		T	5944735	C	T	5944735	3	4	335	1	0	0	0	0	1	0	0	0	2385	536	19	1	559	1	C7orf28A	7	5944735	Missense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10		5944735	153193928	76	46627										
DAGLB	221955	hgsc.bcm.edu	37	chr7	6474591	6474591	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gaggaatatggagccattttCcccccaagagggtcaaagac	11	10	1	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr7:6474591C>T	ENST00000297056.6	-	4	649	c.480G>A	c.(478-480)ggG>ggA	p.G160G	DAGLB_ENST00000479922.2_5'Flank|DAGLB_ENST00000421761.2_Intron|DAGLB_ENST00000425398.2_Intron|DAGLB_ENST00000436575.1_Silent_p.G119G|DAGLB_ENST00000428902.2_Silent_p.G33G	NM_139179.3	NP_631918.3	Q8NCG7	DGLB_HUMAN	diacylglycerol lipase, beta	160					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|lipid catabolic process (GO:0016042)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|urinary_tract(2)	26		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.102)		GAGCCATTTTCCCCCCAAGAG	0.527																																					p.G160G		Atlas-SNP	.											.	DAGLB	74	.	0			c.G480A						.						86	87	87					7																	6474591		2203	4300	6503	SO:0001819	synonymous_variant	221955	exon4			CATTTTCCCCCCA	AF450090	CCDS5350.1, CCDS47536.1	7p22.1	2008-03-18			ENSG00000164535	ENSG00000164535	3.1.1.-		28923	protein-coding gene	gene with protein product		614016					Standard	NM_139179		Approved	KCCR13L, DAGLBETA	uc003sqa.3	Q8NCG7	OTTHUMG00000125513	ENST00000297056.6:c.480G>A	chr7.hg19:g.6474591C>T		61.0	0.0		72.0	28.0	NM_139179	A4D2P3|B3KV90|B4DQU0|Q6PIX3|Q8N2N2|Q8N9S1|Q8TED3|Q8WXE6	Silent	SNP	ENST00000297056.6	hg19	CCDS5350.1																																																																																			.	.		0.527	DAGLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246840.2	NM_139179		T	6474591	C	T	6474591	2	4	335	1	0	0	0	0	0	0	0	1	4229	842	30	3		3	DAGLB	7	6474591	Silent	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	529856	6474591	152664072	77	46628										
ZNF107	51427	hgsc.bcm.edu	37	chr7	64166839	64166839	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	aaggctgtaaacatgtggatGagtgtacggggcacaaagga	15	5	0	1	rs201422104		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr7:64166839G>T	ENST00000395391.1	+	4	1532	c.157G>T	c.(157-159)Gag>Tag	p.E53*	ZNF107_ENST00000344930.3_Nonsense_Mutation_p.E53*|ZNF107_ENST00000423627.1_Nonsense_Mutation_p.E53*			Q9UII5	ZN107_HUMAN	zinc finger protein 107	53					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(18)|ovary(1)|stomach(1)	37		Lung NSC(55;0.00948)|all_lung(88;0.0249)				ACATGTGGATGAGTGTACGGG	0.363																																					p.E53X		Atlas-SNP	.											.	ZNF107	107	.	0			c.G157T						.						80	72	74					7																	64166839		2203	4300	6503	SO:0001587	stop_gained	51427	exon7			GTGGATGAGTGTA	AB027251	CCDS5527.1, CCDS75605.1, CCDS75606.1	7q11.2	2013-01-08	2007-06-26			ENSG00000196247		"Zinc fingers, C2H2-type"	12887	protein-coding gene	gene with protein product		603989	"zinc finger protein 588", "zinc finger protein 107 (Y8)"	ZNF588		8467795	Standard	NM_016220		Approved	ZFD25, smap-7	uc003tte.3	Q9UII5		ENST00000395391.1:c.157G>T	chr7.hg19:g.64166839G>T	ENSP00000378789:p.Glu53*	176.0	0.0		208.0	67.0	NM_016220		Nonsense_Mutation	SNP	ENST00000395391.1	hg19	CCDS5527.1	.	.	.	.	.	.	.	.	.	.	.	17.87	3.495890	0.64186	.	.	ENSG00000196247	ENST00000541526;ENST00000360117;ENST00000344930;ENST00000423627;ENST00000395391	.	.	.	0.828	-0.215	0.13157	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.23302	T	0.38	.	3.0584	0.06191	0.3639:0.0:0.6361:0.0	.	.	.	.	X	53	.	ENSP00000343443:E53X	E	+	1	0	ZNF107	63804274	0.129000	0.22400	0.002000	0.10522	0.048000	0.14542	0.703000	0.25646	-0.092000	0.12417	0.305000	0.20034	GAG	.	.		0.363	ZNF107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251593.1	NM_016220		T	64166839	G	T	64166839	4	4	335	1	0	0	0	0	0	1	0	0	17730	1291	45	3	163	3	ZNF107	7	64166839	Nonsense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	57692248	64166839	94971824	78	46629										
CCDC146	57639	hgsc.bcm.edu	37	chr7	76889445	76889445	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gaaggaaaatgtaataaaggAagttgaaggcaaacgagcct	12	4	0	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr7:76889445A>T	ENST00000285871.4	+	8	1005	c.878A>T	c.(877-879)gAa>gTa	p.E293V	CCDC146_ENST00000415740.2_3'UTR|AC073635.5_ENST00000476561.2_RNA|CCDC146_ENST00000431197.1_Missense_Mutation_p.E39V	NM_020879.2	NP_065930.2	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	293										breast(3)|central_nervous_system(3)|endometrium(1)|kidney(4)|large_intestine(7)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	34		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)				GTAATAAAGGAAGTTGAAGGC	0.363																																					p.E293V		Atlas-SNP	.											.	CCDC146	87	.	0			c.A878T						.						111	109	110					7																	76889445		2203	4300	6503	SO:0001583	missense	57639	exon8			TAAAGGAAGTTGA	BC029458	CCDS34671.1	7q11.23	2011-09-07			ENSG00000135205	ENSG00000135205			29296	protein-coding gene	gene with protein product						10819331	Standard	NM_020879		Approved	KIAA1505	uc003uga.3	Q8IYE0	OTTHUMG00000162595	ENST00000285871.4:c.878A>T	chr7.hg19:g.76889445A>T	ENSP00000285871:p.Glu293Val	146.0	0.0		178.0	31.0	NM_020879	A8K8X6|Q9P223	Missense_Mutation	SNP	ENST00000285871.4	hg19	CCDS34671.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.577866	0.86645	.	.	ENSG00000135205	ENST00000285871;ENST00000431197	T;T	0.28255	1.62;1.95	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.41328	0.1154	L	0.34521	1.04	0.80722	D	1	D;D	0.62365	0.976;0.991	P;P	0.59643	0.629;0.861	T	0.18681	-1.0329	10	0.51188	T	0.08	-23.4368	15.3627	0.74492	1.0:0.0:0.0:0.0	.	39;293	Q8IYE0-2;Q8IYE0	.;CC146_HUMAN	V	293;39	ENSP00000285871:E293V;ENSP00000413885:E39V	ENSP00000285871:E293V	E	+	2	0	AC007000.1	76727381	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.286000	0.72665	2.330000	0.79161	0.528000	0.53228	GAA	.	.		0.363	CCDC146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341449.1	NM_020879		T	76889445	A	T	76889445	3	4	335	1	0	0	0	0	1	0	0	0	2782	246	9	4	904	4	CCDC146	7	76889445	Missense_Mutation	SNP	A	TCGA-RC-A6M6-01A-11D-A32G-10	12722606	76889445	82249218	79	46630										
SEMA3E	9723	hgsc.bcm.edu	37	chr7	83014738	83014738	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	cagatgttcttcagtcttatCcaaagcatcccctacaacag	5	13	3	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr7:83014738C>A	ENST00000307792.3	-	16	2214	c.1747G>T	c.(1747-1749)Gat>Tat	p.D583Y	SEMA3E_ENST00000427262.1_Missense_Mutation_p.D523Y	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	583	Ig-like C2-type.				axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell-matrix adhesion (GO:0001953)|patterning of blood vessels (GO:0001569)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell shape (GO:0008360)|semaphorin-plexin signaling pathway (GO:0071526)|sprouting angiogenesis (GO:0002040)|synapse organization (GO:0050808)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(19)|ovary(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	51		Medulloblastoma(109;0.109)				TCAGTCTTATCCAAAGCATCC	0.363																																					p.D583Y		Atlas-SNP	.											.	SEMA3E	125	.	0			c.G1747T						.						178	157	164					7																	83014738		2203	4300	6503	SO:0001583	missense	9723	exon16			TCTTATCCAAAGC	AB002329	CCDS34674.1, CCDS55121.1	7q21.11	2013-01-11			ENSG00000170381	ENSG00000170381		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10727	protein-coding gene	gene with protein product	"M-sema H"	608166		SEMAH		9205841, 9515811	Standard	NM_012431		Approved	M-SemaK, KIAA0331, coll-5	uc003uhy.2	O15041	OTTHUMG00000154693	ENST00000307792.3:c.1747G>T	chr7.hg19:g.83014738C>A	ENSP00000303212:p.Asp583Tyr	213.0	0.0		255.0	63.0	NM_012431	B4E1P1|Q75M94|Q75M97	Missense_Mutation	SNP	ENST00000307792.3	hg19	CCDS34674.1	.	.	.	.	.	.	.	.	.	.	C	17.61	3.432817	0.62844	.	.	ENSG00000170381	ENST00000307792;ENST00000427262;ENST00000541514	T;T	0.32023	1.52;1.47	5.54	5.54	0.83059	.	1.159070	0.06007	N	0.648826	T	0.32255	0.0823	N	0.19112	0.55	0.38789	D	0.954931	P	0.36909	0.573	B	0.38500	0.275	T	0.36744	-0.9735	10	0.62326	D	0.03	.	19.4854	0.95027	0.0:1.0:0.0:0.0	.	583	O15041	SEM3E_HUMAN	Y	583;523;583	ENSP00000303212:D583Y;ENSP00000405052:D523Y	ENSP00000303212:D583Y	D	-	1	0	SEMA3E	82852674	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.615000	0.67702	2.597000	0.87782	0.650000	0.86243	GAT	.	.		0.363	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431		A	83014738	C	A	83014738	3	1	335	1	0	0	0	0	1	0	0	0	14043	855	30	3	588	3	SEMA3E	7	83014738	Missense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	6125293	83014738	76123925	80	46631										
ANKIB1	54467	hgsc.bcm.edu	37	chr7	92015870	92015870	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	cttgaagagtggaaaaaacaTagttcgtccactggaggtta	11	6	0	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr7:92015870T>G	ENST00000265742.3	+	12	2041	c.1665T>G	c.(1663-1665)caT>caG	p.H555Q		NM_019004.1	NP_061877.1	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1	555							zinc ion binding (GO:0008270)			cervix(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(19)|skin(1)	41	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			GGAAAAAACATAGTTCGTCCA	0.388																																					p.H555Q		Atlas-SNP	.											.	ANKIB1	92	.	0			c.T1665G						.						130	115	120					7																	92015870		1877	4122	5999	SO:0001583	missense	54467	exon12			AAAACATAGTTCG	AB037807	CCDS47639.1	7q21.3	2013-01-10			ENSG00000001629	ENSG00000001629		"Ankyrin repeat domain containing"	22215	protein-coding gene	gene with protein product							Standard	NM_019004		Approved	DKFZP434A0225, KIAA1386	uc003ulw.2	Q9P2G1	OTTHUMG00000155859	ENST00000265742.3:c.1665T>G	chr7.hg19:g.92015870T>G	ENSP00000265742:p.His555Gln	196.0	0.0		278.0	51.0	NM_019004	Q6GMS4|Q6P3S9|Q9NTD7|Q9NW49	Missense_Mutation	SNP	ENST00000265742.3	hg19	CCDS47639.1	.	.	.	.	.	.	.	.	.	.	T	12.70	2.015192	0.35511	.	.	ENSG00000001629	ENST00000265742	T	0.80304	-1.36	5.37	4.33	0.51752	Zinc finger, C6HC-type (2);Zinc finger, RING-type (1);	0.095503	0.64402	D	0.000001	D	0.90109	0.6910	M	0.93763	3.455	0.47621	D	0.99947	D	0.89917	1.0	D	0.97110	1.0	D	0.88865	0.3329	10	0.87932	D	0	.	4.5802	0.12255	0.0:0.4313:0.0:0.5687	.	555	Q9P2G1	AKIB1_HUMAN	Q	555	ENSP00000265742:H555Q	ENSP00000265742:H555Q	H	+	3	2	ANKIB1	91853806	0.996000	0.38824	1.000000	0.80357	0.995000	0.86356	0.499000	0.22546	1.028000	0.39785	0.533000	0.62120	CAT	.	.		0.388	ANKIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342018.1			G	92015870	T	G	92015870	3	3	335	1	0	0	0	0	1	0	0	0	630	1403	49	5	1707	5	ANKIB1	7	92015870	Missense_Mutation	SNP	T	TCGA-RC-A6M6-01A-11D-A32G-10	9001132	92015870	67122793	81	46632										
CYP3A43	64816	hgsc.bcm.edu	37	chr7	99434099	99434099	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tgggacccattcacataaacTttttaagaagctgggaattc	8	8	1	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr7:99434099T>G	ENST00000354829.2	+	2	198	c.95T>G	c.(94-96)cTt>cGt	p.L32R	CYP3A43_ENST00000312017.5_Missense_Mutation_p.L32R|CYP3A43_ENST00000342499.4_Intron|CYP3A43_ENST00000222382.5_Missense_Mutation_p.L32R|CYP3A43_ENST00000415413.1_Missense_Mutation_p.L32R|CYP3A43_ENST00000444905.1_Intron|CYP3A43_ENST00000421837.2_Missense_Mutation_p.L32R|CYP3A43_ENST00000477658.1_Intron|CYP3A43_ENST00000417625.1_Missense_Mutation_p.L32R	NM_022820.3|NM_057095.1	NP_073731.1|NP_476436.1	Q9HB55	CP343_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 43	32			YGTHSHKLFKKLGIPGPTPLPFLGTILFYLRGLWNFDRECN EKYGEMWGLYEGQQPMLVIMDPD -> LGPIHINFLRSWEF LGQPLCLFWELFCSTLGVFGILTENVMKNTEKCGGCMRGNS PCWSSWIPT (in allele CYP3A43*2).		small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(1)	19	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)				Dexamethasone(DB01234)|Dolutegravir(DB08930)|Ethosuximide(DB00593)|Oxazepam(DB00842)|Phenelzine(DB00780)|Praziquantel(DB01058)|Rifampicin(DB01045)|Rifapentine(DB01201)|Testosterone(DB00624)|Troleandomycin(DB01361)|Zalcitabine(DB00943)	TCACATAAACTTTTTAAGAAG	0.403																																					p.L32R		Atlas-SNP	.											.	CYP3A43	52	.	0			c.T95G						.						87	86	86					7																	99434099		2203	4300	6503	SO:0001583	missense	64816	exon2			ATAAACTTTTTAA	AF319634	CCDS5675.1, CCDS5676.1, CCDS5677.1, CCDS64723.1	7q21.1	2007-12-14	2003-01-14		ENSG00000021461	ENSG00000021461		"Cytochrome P450s"	17450	protein-coding gene	gene with protein product		606534	"cytochrome P450, subfamily IIIA, polypeptide 43"			11160876, 11266076	Standard	NM_022820		Approved		uc003ury.1	Q9HB55	OTTHUMG00000156498	ENST00000354829.2:c.95T>G	chr7.hg19:g.99434099T>G	ENSP00000346887:p.Leu32Arg	150.0	0.0		262.0	124.0	NM_057096	Q495Y1|Q75MK2|Q75MK3|Q9HB52|Q9HB53|Q9HB54|Q9HB57	Missense_Mutation	SNP	ENST00000354829.2	hg19	CCDS5676.1	.	.	.	.	.	.	.	.	.	.	T	14.83	2.653775	0.47362	.	.	ENSG00000021461	ENST00000354829;ENST00000421837;ENST00000417625;ENST00000415413;ENST00000312017;ENST00000222382;ENST00000379654	T;T;T;T;T;T	0.11277	2.79;2.79;2.79;2.79;2.79;2.79	2.44	-0.424	0.12321	.	0.747128	0.11878	N	0.520777	T	0.17280	0.0415	L	0.54323	1.7	0.09310	N	1	D;P;P;P	0.57257	0.979;0.697;0.886;0.69	P;P;B;B	0.56612	0.802;0.52;0.407;0.105	T	0.12167	-1.0558	10	0.66056	D	0.02	.	4.8642	0.13600	0.5131:0.0:0.0:0.4869	.	32;32;32;32	Q495Y1;Q9HB55-3;Q75MK2;Q9HB55	.;.;.;CP343_HUMAN	R	32	ENSP00000346887:L32R;ENSP00000397332:L32R;ENSP00000416581:L32R;ENSP00000401521:L32R;ENSP00000312110:L32R;ENSP00000222382:L32R	ENSP00000222382:L32R	L	+	2	0	CYP3A43	99272035	0.000000	0.05858	0.004000	0.12327	0.687000	0.40016	-0.630000	0.05502	-0.088000	0.12506	0.172000	0.16884	CTT	.	.		0.403	CYP3A43-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000344379.1			G	99434099	T	G	99434099	3	3	335	1	0	0	0	0	1	0	0	0	4181	1609	56	5	101	5	CYP3A43	7	99434099	Missense_Mutation	SNP	T	TCGA-RC-A6M6-01A-11D-A32G-10	7418229	99434099	59704564	82	46633										
CYP3A43	64816	hgsc.bcm.edu	37	chr7	99447235	99447235	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ggagtgaacttggattctctCaacaatccacaagatccctt	7	11	2	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr7:99447235C>T	ENST00000354829.2	+	7	691	c.588C>T	c.(586-588)ctC>ctT	p.L196L	CYP3A43_ENST00000312017.5_Silent_p.L196L|CYP3A43_ENST00000342499.4_Nonsense_Mutation_p.Q59*|CYP3A43_ENST00000222382.5_Silent_p.L196L|CYP3A43_ENST00000415413.1_Intron|CYP3A43_ENST00000444905.1_Intron|CYP3A43_ENST00000477658.1_Intron|CYP3A43_ENST00000417625.1_Intron	NM_022820.3|NM_057095.1	NP_073731.1|NP_476436.1	Q9HB55	CP343_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 43	196			Missing (in allele CYP3A43*2).		small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(1)	19	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)				Dexamethasone(DB01234)|Dolutegravir(DB08930)|Ethosuximide(DB00593)|Oxazepam(DB00842)|Phenelzine(DB00780)|Praziquantel(DB01058)|Rifampicin(DB01045)|Rifapentine(DB01201)|Testosterone(DB00624)|Troleandomycin(DB01361)|Zalcitabine(DB00943)	TGGATTCTCTCAACAATCCAC	0.343																																					p.L196L		Atlas-SNP	.											.	CYP3A43	52	.	0			c.C588T						.						150	139	143					7																	99447235		2203	4300	6503	SO:0001819	synonymous_variant	64816	exon7			TTCTCTCAACAAT	AF319634	CCDS5675.1, CCDS5676.1, CCDS5677.1, CCDS64723.1	7q21.1	2007-12-14	2003-01-14		ENSG00000021461	ENSG00000021461		"Cytochrome P450s"	17450	protein-coding gene	gene with protein product		606534	"cytochrome P450, subfamily IIIA, polypeptide 43"			11160876, 11266076	Standard	NM_022820		Approved		uc003ury.1	Q9HB55	OTTHUMG00000156498	ENST00000354829.2:c.588C>T	chr7.hg19:g.99447235C>T		173.0	0.0		246.0	145.0	NM_057096	Q495Y1|Q75MK2|Q75MK3|Q9HB52|Q9HB53|Q9HB54|Q9HB57	Silent	SNP	ENST00000354829.2	hg19	CCDS5676.1	.	.	.	.	.	.	.	.	.	.	C	17.50	3.405889	0.62288	.	.	ENSG00000021461	ENST00000342499;ENST00000379654	.	.	.	3.14	-0.235	0.13071	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	3.2478	0.06803	0.0:0.3795:0.2144:0.4061	.	.	.	.	X	59;90	.	ENSP00000345351:Q59X	Q	+	1	0	CYP3A43	99285171	0.999000	0.42202	0.757000	0.31301	0.224000	0.24922	0.467000	0.22035	0.142000	0.18901	0.195000	0.17529	CAA	.	.		0.343	CYP3A43-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000344379.1			T	99447235	C	T	99447235	2	4	335	1	0	0	0	0	0	0	0	1	4181	813	29	3		3	CYP3A43	7	99447235	Silent	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	13136	99447235	59691428	83	46634										
ZCWPW1	55063	hgsc.bcm.edu	37	chr7	99999574	99999574	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ccattctgggtgcaggaggaGctgtggatttcctgcctaga	14	9	1	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr7:99999574G>C	ENST00000398027.2	-	17	1809	c.1562C>G	c.(1561-1563)gCt>gGt	p.A521G	ZCWPW1_ENST00000324725.6_Intron|ZCWPW1_ENST00000360951.4_Intron|ZCWPW1_ENST00000490721.1_Intron	NM_017984.4	NP_060454.3	Q9H0M4	ZCPW1_HUMAN	zinc finger, CW type with PWWP domain 1	521							zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)	16	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TGCAGGAGGAGCTGTGGATTT	0.542																																					p.A521G		Atlas-SNP	.											.	ZCWPW1	41	.	0			c.C1562G						.						151	147	149					7																	99999574		1966	4159	6125	SO:0001583	missense	55063	exon17			GGAGGAGCTGTGG	AK000919	CCDS43623.1, CCDS59067.1	7q22.1	2012-02-10	2004-11-03		ENSG00000078487	ENSG00000078487			23486	protein-coding gene	gene with protein product			"zinc finger, CW-type with PWWP domain 1"			11230166, 14607086, 20826339	Standard	NM_017984		Approved	FLJ10057, DKFZp434N0510, ZCW1	uc003uut.4	Q9H0M4	OTTHUMG00000159537	ENST00000398027.2:c.1562C>G	chr7.hg19:g.99999574G>C	ENSP00000381109:p.Ala521Gly	142.0	0.0		268.0	17.0	NM_017984	A8MVF5|B4DUQ2|Q8NA98|Q9BUD0|Q9NWF7	Missense_Mutation	SNP	ENST00000398027.2	hg19	CCDS43623.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.51|14.51	2.556654|2.556654	0.45487|0.45487	.|.	.|.	ENSG00000078487|ENSG00000233389	ENST00000398027|ENST00000449355	T|.	0.54866|.	0.55|.	5.0|5.0	3.0|3.0	0.34707|0.34707	.|.	.|.	.|.	.|.	.|.	T|T	0.22551|0.22551	0.0544|0.0544	N|N	0.24115|0.24115	0.695|0.695	0.20975|0.20975	N|N	0.999812|0.999812	P;P|.	0.45044|.	0.849;0.849|.	B;B|.	0.42798|.	0.398;0.398|.	T|T	0.19844|0.19844	-1.0293|-1.0293	8|5	.|.	.|.	.|.	-0.0893|-0.0893	3.9574|3.9574	0.09396|0.09396	0.1367:0.0:0.6343:0.2291|0.1367:0.0:0.6343:0.2291	.|.	482;521|.	B4DXS7;Q9H0M4|.	.;ZCPW1_HUMAN|.	G|P	521|98	ENSP00000381109:A521G|.	.|.	A|A	-|+	2|1	0|0	ZCWPW1|AC005071.3	99837510|99837510	0.216000|0.216000	0.23585|0.23585	0.050000|0.050000	0.19076|0.19076	0.276000|0.276000	0.26787|0.26787	0.285000|0.285000	0.18883|0.18883	0.626000|0.626000	0.30322|0.30322	0.655000|0.655000	0.94253|0.94253	GCT|GCT	.	.		0.542	ZCWPW1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356083.1	NM_017984		C	99999574	G	C	99999574	3	2	335	1	0	0	0	0	1	0	0	0	17612	971	34	4	392	4	ZCWPW1	7	99999574	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	552339	99999574	59139089	84	46635										
MUC17	140453	hgsc.bcm.edu	37	chr7	100682876	100682876	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gcacacctgtcaccacttctGctgaagccagttcttctcct	6	16	4	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr7:100682876G>A	ENST00000306151.4	+	3	8243	c.8179G>A	c.(8179-8181)Gct>Act	p.A2727T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2727	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					CACCACTTCTGCTGAAGCCAG	0.463																																					p.A2727T		Atlas-SNP	.											.	MUC17	804	.	0			c.G8179A						.						250	253	252					7																	100682876		2203	4300	6503	SO:0001583	missense	140453	exon3			ACTTCTGCTGAAG	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.8179G>A	chr7.hg19:g.100682876G>A	ENSP00000302716:p.Ala2727Thr	55.0	0.0		78.0	9.0	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	G	4.278	0.050786	0.08243	.	.	ENSG00000169876	ENST00000306151	T	0.01998	4.51	1.21	-2.42	0.06542	.	.	.	.	.	T	0.00845	0.0028	N	0.04203	-0.255	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.44267	-0.9339	9	0.02654	T	1	.	2.5247	0.04689	0.2649:0.0:0.329:0.4061	.	2727	Q685J3	MUC17_HUMAN	T	2727	ENSP00000302716:A2727T	ENSP00000302716:A2727T	A	+	1	0	MUC17	100469596	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.971000	0.03806	-1.404000	0.02050	-1.616000	0.00795	GCT	.	.		0.463	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		A	100682876	G	A	100682876	3	1	335	1	0	0	0	0	1	0	0	0	9983	1319	46	3	8189	3	MUC17	7	100682876	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	683302	100682876	58455787	85	46636			1	59		2	2	15	N	T_G	8.547063e-05
MUC17	140453	hgsc.bcm.edu	37	chr7	100682890	100682890	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	acttctgctgaagccagttcTtctcctacaactgctgaagg	8	12	3	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr7:100682890T>C	ENST00000306151.4	+	3	8257	c.8193T>C	c.(8191-8193)tcT>tcC	p.S2731S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2731	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					AAGCCAGTTCTTCTCCTACAA	0.502																																					p.S2731S		Atlas-SNP	.											.	MUC17	804	.	0			c.T8193C						.						255	256	256					7																	100682890		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			CAGTTCTTCTCCT	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.8193T>C	chr7.hg19:g.100682890T>C		58.0	0.0		75.0	5.0	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	hg19	CCDS34711.1																																																																																			.	.		0.502	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		C	100682890	T	C	100682890	2	2	335	1	0	0	0	0	0	0	0	1	9983	1596	56	2		2	MUC17	7	100682890	Silent	SNP	T	TCGA-RC-A6M6-01A-11D-A32G-10	14	100682890	58455773	86	46637			1	59		2	2	15	N	T_G	8.547063e-05
RAB19	401409	hgsc.bcm.edu	37	chr7	140111745	140111745	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	agctactaccgcagtgcccaCgcagccatcatcgcctatga	8	16	1	1	rs375880877		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr7:140111745C>G	ENST00000356407.3	+	2	341	c.273C>G	c.(271-273)caC>caG	p.H91Q	RAB19_ENST00000537763.1_Missense_Mutation_p.H91Q|RAB19_ENST00000275874.5_Missense_Mutation_p.H138Q			A4D1S5	RAB19_HUMAN	RAB19, member RAS oncogene family	91					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			breast(3)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	9	Melanoma(164;0.0142)					GCAGTGCCCACGCAGCCATCA	0.562																																					p.H91Q		Atlas-SNP	.											.	RAB19	21	.	0			c.C273G						.						145	118	127					7																	140111745		2203	4300	6503	SO:0001583	missense	401409	exon3			TGCCCACGCAGCC		CCDS34762.1, CCDS34762.2	7q34	2014-05-09			ENSG00000146955	ENSG00000146955		"RAB, member RAS oncogene"	19982	protein-coding gene	gene with protein product							Standard	NM_001008749		Approved	RAB19B	uc010lni.2	A4D1S5	OTTHUMG00000157410	ENST00000356407.3:c.273C>G	chr7.hg19:g.140111745C>G	ENSP00000348778:p.His91Gln	39.0	0.0		46.0	21.0	NM_001008749	A4D1S6|B2RTS6|B5MDR2|Q9UL27	Missense_Mutation	SNP	ENST00000356407.3	hg19	CCDS34762.2	.	.	.	.	.	.	.	.	.	.	C	13.77	2.336151	0.41398	.	.	ENSG00000146955	ENST00000495590;ENST00000275874;ENST00000537763;ENST00000356407	T;T;T;T	0.80214	-1.35;-1.35;-1.35;-1.35	5.59	0.691	0.18045	Small GTP-binding protein domain (1);	0.087311	0.85682	N	0.000000	T	0.79353	0.4431	L	0.38838	1.175	0.80722	D	1	D	0.53312	0.959	P	0.61533	0.89	T	0.75741	-0.3211	10	0.87932	D	0	.	5.8763	0.18830	0.1208:0.5255:0.0:0.3536	.	91	A4D1S5	RAB19_HUMAN	Q	91;138;91;91	ENSP00000420782:H91Q;ENSP00000275874:H138Q;ENSP00000440167:H91Q;ENSP00000348778:H91Q	ENSP00000275874:H138Q	H	+	3	2	RAB19	139758214	0.055000	0.20627	0.969000	0.41365	0.304000	0.27724	-0.541000	0.06099	0.066000	0.16515	-1.177000	0.01723	CAC	.	.		0.562	RAB19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348740.1			G	140111745	C	G	140111745	3	3	335	1	0	0	0	0	1	0	0	0	12919	535	19	4	279	4	RAB19	7	140111745	Missense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	39428855	140111745	19026918	87	46638										
GIMAP4	55303	hgsc.bcm.edu	37	chr7	150269571	150269571	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	caaagccacagagaagatccTgaaaatgtttggagagaggg	13	6	0	4			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr7:150269571T>A	ENST00000255945.2	+	3	588	c.413T>A	c.(412-414)cTg>cAg	p.L138Q	GIMAP4_ENST00000494750.1_3'UTR|GIMAP4_ENST00000461940.1_Missense_Mutation_p.L152Q	NM_018326.2	NP_060796.1	Q9NUV9	GIMA4_HUMAN	GTPase, IMAP family member 4	138	AIG1-type G.					cytosol (GO:0005829)	GTP binding (GO:0005525)			breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(82;0.0179)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GAGAAGATCCTGAAAATGTTT	0.488																																					p.L138Q		Atlas-SNP	.											.	GIMAP4	61	.	0			c.T413A						.						79	76	77					7																	150269571		2203	4300	6503	SO:0001583	missense	55303	exon3			AGATCCTGAAAAT	AK001972	CCDS5904.1	7q36.1	2014-04-04			ENSG00000133574	ENSG00000133574		"GTPases, IMAP"	21872	protein-coding gene	gene with protein product	"immune-associated nucleotide-binding protein 1"	608087				15474311, 18701445	Standard	NM_018326		Approved	HIMAP4, FLJ11110, IMAP4, IAN1	uc003whl.3	Q9NUV9	OTTHUMG00000157475	ENST00000255945.2:c.413T>A	chr7.hg19:g.150269571T>A	ENSP00000255945:p.Leu138Gln	91.0	0.0		66.0	18.0	NM_018326		Missense_Mutation	SNP	ENST00000255945.2	hg19	CCDS5904.1	.	.	.	.	.	.	.	.	.	.	T	10.74	1.436104	0.25813	.	.	ENSG00000133574	ENST00000255945;ENST00000461940;ENST00000466938	T;T	0.04454	3.62;3.62	4.72	3.55	0.40652	AIG1 (1);	0.340109	0.28338	N	0.015706	T	0.07683	0.0193	N	0.25647	0.755	0.20873	N	0.999833	D;P	0.89917	1.0;0.898	D;P	0.91635	0.999;0.84	T	0.10543	-1.0625	10	0.05525	T	0.97	.	7.5774	0.27944	0.1894:0.0:0.0:0.8106	.	152;138	G5E9W9;Q9NUV9	.;GIMA4_HUMAN	Q	138;152;70	ENSP00000255945:L138Q;ENSP00000419545:L152Q	ENSP00000255945:L138Q	L	+	2	0	GIMAP4	149900504	0.000000	0.05858	0.026000	0.17262	0.001000	0.01503	0.622000	0.24433	0.831000	0.34780	-0.327000	0.08410	CTG	.	.		0.488	GIMAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348927.1	NM_018326		A	150269571	T	A	150269571	3	1	335	1	0	0	0	0	1	0	0	0	6389	1580	55	4	419	4	GIMAP4	7	150269571	Missense_Mutation	SNP	T	TCGA-RC-A6M6-01A-11D-A32G-10	10157826	150269571	8869092	88	46639										
MLL3	58508	hgsc.bcm.edu	37	chr7	151927092	151927092	+	Frame_Shift_Del	DEL	G	G	-													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tctgctccttggccaaaactGccacaaactacacacatatc							TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr7:151927092delG	ENST00000262189.6	-	18	3110	c.2892delC	c.(2890-2892)ggcfs	p.G964fs	KMT2C_ENST00000355193.2_Frame_Shift_Del_p.G964fs	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	964					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										GGCCAAAACTGCCACAAACTA	0.348																																					p.S965fs		Atlas-INDEL	.											.	MLL3	1564	.	0			c.2893delA						.						62	51	55					7																	151927092		2200	4278	6478	SO:0001589	frameshift_variant	58508	exon18			.	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.2892delC	chr7.hg19:g.151927092delG	ENSP00000262189:p.Gly964fs	730.0	0.0		565.0	44.0	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Frame_Shift_Del	DEL	ENST00000262189.6	hg19	CCDS5931.1																																																																																			.	.		0.348	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			-	151927092	G	-	151927092	7	5	335	1	0	1	0	1	0	0	0	0	9631	1306	46	0	12011	0	MLL3	7	151927092	Frame_Shift_Del	DEL	G	TCGA-RC-A6M6-01A-11D-A32G-10	1657521	151927092	7211571	89	46640										
LMBR1	64327	hgsc.bcm.edu	37	chr7	156619307	156619308	+	Frame_Shift_Ins	INS	-	-	G													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tatatactaaccatgaatcaINSgggagccatttagccactga							TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr7:156619307_156619308insG	ENST00000353442.5	-	4	546_547	c.310_311insC	c.(310-312)ctgfs	p.L104fs	LMBR1_ENST00000540390.1_Frame_Shift_Ins_p.L83fs|LMBR1_ENST00000354505.4_Frame_Shift_Ins_p.L104fs	NM_022458.3	NP_071903.2	Q8WVP7	LMBR1_HUMAN	limb development membrane protein 1	104					embryonic digit morphogenesis (GO:0042733)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	18	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.208)		ACCATGAATCAGGGAGCCATTT	0.322																																					p.L104fs		Atlas-Indel,Pindel	.											.	LMBR1	35	.	0			c.311_312insC						.																																			SO:0001589	frameshift_variant	64327	exon4			.	AF107454	CCDS5945.1	7q36.3	2013-08-05	2013-08-05	2005-07-25	ENSG00000105983	ENSG00000105983			13243	protein-coding gene	gene with protein product		605522	"chromosome 7 open reading frame 2", "limb region 1 homolog (mouse)"	C7orf2		10329000, 11090342	Standard	NM_022458		Approved	ACHP, FLJ11665, ZRS	uc003wmw.4	Q8WVP7	OTTHUMG00000151510	ENST00000353442.5:c.311dupC	chr7.hg19:g.156619310_156619310dupG	ENSP00000326604:p.Leu104fs	60.0	0.0		42.0	30.0	NM_022458	A4D242|Q8N3E3|Q96QZ5|Q9H5N0|Q9HAG9|Q9UDN5|Q9Y6U2	Frame_Shift_Ins	INS	ENST00000353442.5	hg19	CCDS5945.1																																																																																			.	.		0.322	LMBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347939.3	NM_022458		G	156619308	-	G	156619307	7	5	335	1	0	1	1	0	0	0	0	0	8849	188	7	0	1217	0	LMBR1	7	156619307	Frame_Shift_Ins	INS	-	TCGA-RC-A6M6-01A-11D-A32G-10	4692215	156619307	2519356	90	46641										
ANK1	286	hgsc.bcm.edu	37	chr8	41574509	41574514	+	In_Frame_Del	DEL	AATATT	AATATT	-													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tttggctttgttctggagtaAatatttggccacttccgtgt							TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	AATATT	AATATT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr8:41574509_41574514delAATATT	ENST00000347528.4	-	13	1444_1449	c.1361_1366delAATATT	c.(1360-1368)aaatattta>ata	p.454_456KYL>I	ANK1_ENST00000396942.1_In_Frame_Del_p.454_456KYL>I|ANK1_ENST00000352337.4_In_Frame_Del_p.454_456KYL>I|ANK1_ENST00000396945.1_In_Frame_Del_p.454_456KYL>I|ANK1_ENST00000289734.7_In_Frame_Del_p.454_456KYL>I|ANK1_ENST00000379758.2_In_Frame_Del_p.454_456KYL>I|ANK1_ENST00000265709.8_In_Frame_Del_p.487_489KYL>I	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	454	89 kDa domain.				axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			TTCTGGAGTAAATATTTGGCCACTTC	0.481																																					p.487_489del		Atlas-Indel,Pindel	.											.	ANK1	497	.	0			c.1461_1466del						.																																			SO:0001651	inframe_deletion	286	exon13			.	M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"Ankyrin repeat domain containing"	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.1361_1366delAATATT	chr8.hg19:g.41574509_41574514delAATATT	ENSP00000339620:p.Lys454_Leu456delinsIle	237.0	0.0		217.0	49.0	NM_001142446	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	In_Frame_Del	DEL	ENST00000347528.4	hg19	CCDS6119.1																																																																																			.	.		0.481	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475		-	41574514	AATATT	-	41574509	7	5	335	1	0	1	0	1	0	0	0	0	620	11	1	0	4753	0	ANK1	8	41574509	In_Frame_Del	DEL	AATATT	TCGA-RC-A6M6-01A-11D-A32G-10		41574509	104789513	91	46642										
XKR4	114786	hgsc.bcm.edu	37	chr8	56436755	56436757	+	In_Frame_Del	DEL	AGG	AGG	-													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	caaagatgatgcccttattcAggagcggttggagtacgaaa							TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr8:56436755_56436757delAGG	ENST00000327381.6	+	3	2022_2024	c.1922_1924delAGG	c.(1921-1926)caggag>cag	p.E642del		NM_052898.1	NP_443130.1	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related family, member 4	642						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(3)|large_intestine(4)|liver(2)|lung(12)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	34			Epithelial(17;0.000117)|all cancers(17;0.000836)			GCCCTTATTCAGGAGCGGTTGGA	0.483																																					p.641_641del		Atlas-Indel,Pindel	.											.	XKR4	104	.	0			c.1921_1923del						.																																			SO:0001651	inframe_deletion	114786	exon3			.	AY534241	CCDS34893.1	8q12.1	2006-01-12	2006-01-12		ENSG00000206579	ENSG00000206579			29394	protein-coding gene	gene with protein product			"X Kell blood group precursor-related family, member 4"				Standard	NM_052898		Approved	KIAA1889	uc003xsf.3	Q5GH76	OTTHUMG00000164288	ENST00000327381.6:c.1922_1924delAGG	chr8.hg19:g.56436755_56436757delAGG	ENSP00000328326:p.Glu642del	33.0	0.0		41.0	11.0	NM_052898	Q96PZ8	In_Frame_Del	DEL	ENST00000327381.6	hg19	CCDS34893.1																																																																																			.	.		0.483	XKR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378129.2	NM_052898		-	56436757	AGG	-	56436755	7	5	335	1	0	1	0	1	0	0	0	0	17448	188	7	0	1932	0	XKR4	8	56436755	In_Frame_Del	DEL	AGG	TCGA-RC-A6M6-01A-11D-A32G-10	14862246	56436755	89927267	92	46643										
BHLHE22	27319	hgsc.bcm.edu	37	chr8	65494023	65494023	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gcggtagcggcagcggcggcAgcagcagcagcagcagcagc	18	13	0	0	rs62519837		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr8:65494023A>G	ENST00000321870.1	+	1	1210	c.676A>G	c.(676-678)Agc>Ggc	p.S226G	RP11-21C4.1_ENST00000517909.1_RNA	NM_152414.4	NP_689627.1	Q8NFJ8	BHE22_HUMAN	basic helix-loop-helix family, member e22	226	Ser-rich.				anterior commissure morphogenesis (GO:0021960)|cerebral cortex regionalization (GO:0021796)|corpus callosum morphogenesis (GO:0021540)|corticospinal tract morphogenesis (GO:0021957)|negative regulation of transcription, DNA-templated (GO:0045892)|retinal bipolar neuron differentiation (GO:0060040)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.S234delS(1)|p.S226G(1)		NS(1)|central_nervous_system(1)|lung(1)|prostate(1)|skin(1)	5						cagcggcggcagcagcagcag	0.706																																					p.S226G	Colon(113;104 1586 2865 9855 18065)	Atlas-SNP	.											BHLHE22,extremity,malignant_melanoma,0,1	BHLHE22	21	.	2	Substitution - Missense(1)|Deletion - In frame(1)	central_nervous_system(1)|skin(1)	c.A676G						.						3	4	4					8																	65494023		1652	3428	5080	SO:0001583	missense	27319	exon1			GGCGGCAGCAGCA	U80755	CCDS6179.1	8q12.1	2009-01-12	2009-01-12	2009-01-12		ENSG00000180828		"Basic helix-loop-helix proteins"	11963	protein-coding gene	gene with protein product		613483	"trinucleotide repeat containing 20", "basic helix-loop-helix domain containing, class B, 5"	TNRC20, BHLHB5		9225980, 12213201, 18557763	Standard	NM_152414		Approved	CAGL85, Beta3, bHLHe22	uc003xvi.3	Q8NFJ8		ENST00000321870.1:c.676A>G	chr8.hg19:g.65494023A>G	ENSP00000318799:p.Ser226Gly	2.0	1.0		9.0	3.0	NM_152414		Missense_Mutation	SNP	ENST00000321870.1	hg19	CCDS6179.1	.	.	.	.	.	.	.	.	.	.	A	0.001	-3.714868	0.00005	.	.	ENSG00000180828	ENST00000321870	T	0.80033	-1.33	0.79	-1.26	0.09376	.	.	.	.	.	T	0.48642	0.1511	N	0.00926	-1.1	0.09310	N	1	B	0.26041	0.14	B	0.32805	0.153	T	0.47368	-0.9123	9	0.15499	T	0.54	.	3.5404	0.07809	0.3747:0.0:0.6253:0.0	rs62519837	226	Q8NFJ8	BHE22_HUMAN	G	226	ENSP00000318799:S226G	ENSP00000318799:S226G	S	+	1	0	BHLHE22	65656577	0.273000	0.24181	0.215000	0.23724	0.107000	0.19398	-0.535000	0.06142	-0.333000	0.08476	0.136000	0.15936	AGC	.	G|1.000;|0.000		0.706	BHLHE22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378549.1	NM_152414		G	65494023	A	G	65494023	3	3	335	1	0	0	0	0	1	0	0	0	1421	188	7	2	678	2	BHLHE22	8	65494023	Missense_Mutation	SNP	A	TCGA-RC-A6M6-01A-11D-A32G-10	9057268	65494023	80869999	93	46644										
EXT1	2131	hgsc.bcm.edu	37	chr8	118817113	118817113	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gctggctggcaggtaatgggAgtataggtagtgataatatc	15	4	0	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr8:118817113A>C	ENST00000378204.2	-	10	2709	c.1903T>G	c.(1903-1905)Tcc>Gcc	p.S635A		NM_000127.2	NP_000118.2	Q16394	EXT1_HUMAN	exostosin glycosyltransferase 1	635					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cellular polysaccharide biosynthetic process (GO:0033692)|embryonic skeletal joint development (GO:0072498)|endoderm development (GO:0007492)|gastrulation (GO:0007369)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0015014)|mesoderm development (GO:0007498)|olfactory bulb development (GO:0021772)|ossification (GO:0001503)|protein glycosylation (GO:0006486)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)|glucuronosyltransferase activity (GO:0015020)|heparan sulfate N-acetylglucosaminyltransferase activity (GO:0042328)|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity (GO:0050509)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|endometrium(7)|kidney(1)|large_intestine(12)|lung(10)|ovary(3)|prostate(1)|stomach(1)|urinary_tract(2)	38	all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.012)			AGGTAATGGGAGTATAGGTAG	0.443			"Mis, N, F, S"			"exostoses, osteosarcoma"			Langer-Giedion syndrome;Hereditary Multiple Exostoses																												p.S635A		Atlas-SNP	.	yes	Rec		Multiple Exostoses Type 1	8	8q24.11-q24.13	2131	multiple exostoses type 1 gene		M	.	EXT1	98	.	0			c.T1903G						.						138	131	133					8																	118817113		2203	4300	6503	SO:0001583	missense	2131	exon10	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II;HME, Hereditary Exostoses, Multiple Osteochondromatosis, Multiple Cartilaginous Exostoses	AATGGGAGTATAG	S79639	CCDS6324.1	8q24.11	2014-09-17	2013-03-01		ENSG00000182197	ENSG00000182197	2.4.1.224, 2.4.1.225	"Exostosin glycosyltransferase family"	3512	protein-coding gene	gene with protein product	"Glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase", "N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase"	608177	"Langer-Giedion syndrome chromosome region", "exostoses (multiple) 1", "exostosin 1"	LGCR, LGS			Standard	NM_000127		Approved	ttv	uc003yok.1	Q16394	OTTHUMG00000059718	ENST00000378204.2:c.1903T>G	chr8.hg19:g.118817113A>C	ENSP00000367446:p.Ser635Ala	101.0	0.0		177.0	74.0	NM_000127	B2R7V2|Q9BVI9	Missense_Mutation	SNP	ENST00000378204.2	hg19	CCDS6324.1	.	.	.	.	.	.	.	.	.	.	a	15.26	2.779734	0.49891	.	.	ENSG00000182197	ENST00000378204	T	0.78126	-1.15	5.68	1.79	0.24919	EXTL2, alpha-1,4-N-acetylhexosaminyltransferase (1);	0.142966	0.64402	D	0.000007	T	0.74275	0.3695	M	0.67517	2.055	0.30894	N	0.730014	B	0.12013	0.005	B	0.19946	0.027	T	0.71052	-0.4704	10	0.66056	D	0.02	-5.5207	11.7874	0.52049	0.2458:0.0:0.0:0.7542	.	635	Q16394	EXT1_HUMAN	A	635	ENSP00000367446:S635A	ENSP00000367446:S635A	S	-	1	0	EXT1	118886294	1.000000	0.71417	0.993000	0.49108	0.995000	0.86356	2.388000	0.44398	0.062000	0.16340	0.477000	0.44152	TCC	.	.		0.443	EXT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132768.3	NM_000127		C	118817113	A	C	118817113	3	2	335	1	0	0	0	0	1	0	0	0	5325	304	11	5	345	5	EXT1	8	118817113	Missense_Mutation	SNP	A	TCGA-RC-A6M6-01A-11D-A32G-10	53323090	118817113	27546909	94	46645										
TNFRSF11B	4982	hgsc.bcm.edu	37	chr8	119936632	119936632	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gttataagcagcttatttttActgattggacctggttacct	8	7	0	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr8:119936632A>C	ENST00000297350.4	-	5	1565	c.1187T>G	c.(1186-1188)gTa>gGa	p.V396G		NM_002546.3	NP_002537.3	O00300	TR11B_HUMAN	tumor necrosis factor receptor superfamily, member 11b	396					apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|negative regulation of bone resorption (GO:0045779)|negative regulation of odontogenesis of dentin-containing tooth (GO:0042489)|response to arsenic-containing substance (GO:0046685)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to magnesium ion (GO:0032026)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|receptor activity (GO:0004872)			breast(1)|central_nervous_system(3)|endometrium(4)|large_intestine(6)|lung(7)|prostate(3)|skin(1)	25	all_cancers(13;3.71e-26)|Lung NSC(37;1.69e-07)|Ovarian(258;0.018)|all_neural(195;0.0592)|Hepatocellular(40;0.234)		STAD - Stomach adenocarcinoma(47;0.00193)			GCTTATTTTTACTGATTGGAC	0.398																																					p.V396G		Atlas-SNP	.											.	TNFRSF11B	87	.	0			c.T1187G						.						154	153	153					8																	119936632		2203	4300	6503	SO:0001583	missense	4982	exon5			ATTTTTACTGATT	U94332	CCDS6326.1	8q24	2008-07-31	2008-07-31		ENSG00000164761	ENSG00000164761		"Tumor necrosis factor receptor superfamily"	11909	protein-coding gene	gene with protein product		602643	"osteoprotegerin"	OPG		9108485	Standard	NM_002546		Approved	OCIF, TR1	uc003yon.4	O00300	OTTHUMG00000164969	ENST00000297350.4:c.1187T>G	chr8.hg19:g.119936632A>C	ENSP00000297350:p.Val396Gly	111.0	0.0		151.0	55.0	NM_002546	B2R9A8|O60236|Q53FX6|Q9UHP4	Missense_Mutation	SNP	ENST00000297350.4	hg19	CCDS6326.1	.	.	.	.	.	.	.	.	.	.	A	7.844	0.722642	0.15439	.	.	ENSG00000164761	ENST00000297350	T	0.74737	-0.87	5.69	3.12	0.35913	.	0.774326	0.11707	N	0.537358	T	0.53658	0.1810	N	0.12182	0.205	0.23751	N	0.996945	B	0.02656	0.0	B	0.04013	0.001	T	0.36359	-0.9751	9	.	.	.	-4.0333	8.4443	0.32833	0.6648:0.2656:0.0696:0.0	.	396	O00300	TR11B_HUMAN	G	396	ENSP00000297350:V396G	.	V	-	2	0	TNFRSF11B	120005813	0.099000	0.21834	0.997000	0.53966	0.997000	0.91878	1.762000	0.38451	0.970000	0.38263	0.533000	0.62120	GTA	.	.		0.398	TNFRSF11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381220.1			C	119936632	A	C	119936632	3	2	335	1	0	0	0	0	1	0	0	0	16300	391	14	5	22	5	TNFRSF11B	8	119936632	Missense_Mutation	SNP	A	TCGA-RC-A6M6-01A-11D-A32G-10	1119519	119936632	26427390	95	46646										
TG	7038	hgsc.bcm.edu	37	chr8	133935646	133935646	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ccagaatggccagtatcgagCcagccagaaggacaggggca	14	11	0	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr8:133935646C>G	ENST00000220616.4	+	22	4632	c.4592C>G	c.(4591-4593)gCc>gGc	p.A1531G	TG_ENST00000542445.1_5'UTR|TG_ENST00000377869.1_Intron	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1531	Thyroglobulin type-1 11. {ECO:0000255|PROSITE-ProRule:PRU00500}.				hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		CAGTATCGAGCCAGCCAGAAG	0.572																																					p.A1531G		Atlas-SNP	.											.	TG	416	.	0			c.C4592G						.						90	83	86					8																	133935646		2203	4300	6503	SO:0001583	missense	7038	exon22			ATCGAGCCAGCCA	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.4592C>G	chr8.hg19:g.133935646C>G	ENSP00000220616:p.Ala1531Gly	65.0	0.0		101.0	51.0	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	hg19	CCDS34944.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.433|9.433	1.086002|1.086002	0.20390|0.20390	.|.	.|.	ENSG00000042832|ENSG00000042832	ENST00000543313;ENST00000220616|ENST00000519178	D|.	0.82984|.	-1.67|.	4.84|4.84	3.95|3.95	0.45737|0.45737	Thyroglobulin type-1 (5);|.	0.116516|.	0.38164|.	N|.	0.001788|.	T|T	0.64472|0.64472	0.2601|0.2601	M|M	0.68317|0.68317	2.08|2.08	0.58432|0.58432	D|D	0.999999|0.999999	B|.	0.30741|.	0.293|.	B|.	0.24269|.	0.052|.	T|T	0.62690|0.62690	-0.6801|-0.6801	10|5	0.52906|.	T|.	0.07|.	.|.	10.4246|10.4246	0.44369|0.44369	0.1954:0.8046:0.0:0.0|0.1954:0.8046:0.0:0.0	.|.	1531|.	P01266|.	THYG_HUMAN|.	G|R	337;1531|50	ENSP00000220616:A1531G|.	ENSP00000220616:A1531G|.	A|S	+|+	2|3	0|2	TG|TG	134004828|134004828	0.932000|0.932000	0.31603|0.31603	0.999000|0.999000	0.59377|0.59377	0.023000|0.023000	0.10783|0.10783	2.916000|2.916000	0.48813|0.48813	1.020000|1.020000	0.39573|0.39573	-0.324000|-0.324000	0.08512|0.08512	GCC|AGC	.	.		0.572	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		G	133935646	C	G	133935646	3	3	335	1	0	0	0	0	1	0	0	0	15828	739	26	4	4678	4	TG	8	133935646	Missense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	13999014	133935646	12428376	96	46647										
COL22A1	169044	hgsc.bcm.edu	37	chr8	139620230	139620230	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gatcccggtgatccattcttGccctggtggaagaaacagag	12	10	1	3			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr8:139620230G>T	ENST00000303045.6	-	57	4427	c.3981C>A	c.(3979-3981)ggC>ggA	p.G1327G	COL22A1_ENST00000435777.1_Silent_p.G1307G|COL22A1_ENST00000341807.4_5'UTR	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	1327	Collagen-like 13.|Gly-rich.|Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			ATCCATTCTTGCCCTGGTGGA	0.517										HNSCC(7;0.00092)																											p.G1327G		Atlas-SNP	.											COL22A1,NS,carcinoma,0,1	COL22A1	390	.	0			c.C3981A						.						85	86	85					8																	139620230		2203	4300	6503	SO:0001819	synonymous_variant	169044	exon57			ATTCTTGCCCTGG	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"Collagens"	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.3981C>A	chr8.hg19:g.139620230G>T		54.0	1.0		68.0	29.0	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Silent	SNP	ENST00000303045.6	hg19	CCDS6376.1																																																																																			.	.		0.517	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257		T	139620230	G	T	139620230	2	4	335	1	0	0	0	0	0	0	0	1	3683	1306	46	3		3	COL22A1	8	139620230	Silent	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	5684584	139620230	6743792	97	46648										
LINGO2	158038	hgsc.bcm.edu	37	chr9	27949554	27949554	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tgctggccaccaaactgcagGgtgggctgtcgctgcaagat	14	11	0	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr9:27949554G>T	ENST00000379992.2	-	6	1565	c.1116C>A	c.(1114-1116)acC>acA	p.T372T	LINGO2_ENST00000308675.3_Silent_p.T372T	NM_152570.2	NP_689783.1	Q7L985	LIGO2_HUMAN	leucine rich repeat and Ig domain containing 2	372	LRRCT.					integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(1)|lung(13)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	44	Melanoma(11;0.242)	all_neural(11;2.78e-09)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0818)|GBM - Glioblastoma multiforme(2;1.31e-34)|all cancers(2;2.37e-25)|Lung(2;7.48e-08)|LUSC - Lung squamous cell carcinoma(38;5.09e-07)|KIRC - Kidney renal clear cell carcinoma(2;0.0465)|Kidney(2;0.0604)		CAAACTGCAGGGTGGGCTGTC	0.532																																					p.T372T		Atlas-SNP	.											.	LINGO2	244	.	0			c.C1116A						.						41	39	40					9																	27949554		2203	4300	6503	SO:0001819	synonymous_variant	158038	exon7			CTGCAGGGTGGGC	AL353746	CCDS6524.1	9p21.2	2013-01-11	2007-02-01	2007-02-01	ENSG00000174482	ENSG00000174482		"Immunoglobulin superfamily / I-set domain containing"	21207	protein-coding gene	gene with protein product		609793	"leucine rich repeat neuronal 6C"	LRRN6C		14686891	Standard	NM_152570		Approved	LERN3	uc003zqu.2	Q7L985	OTTHUMG00000019721	ENST00000379992.2:c.1116C>A	chr9.hg19:g.27949554G>T		51.0	0.0		33.0	22.0	NM_001258282	A8K4K7|B2RPM5|Q6ZMD0	Silent	SNP	ENST00000379992.2	hg19	CCDS6524.1																																																																																			.	.		0.532	LINGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051978.2	NM_152570		T	27949554	G	T	27949554	2	4	335	1	0	0	0	0	0	0	0	1	8824	1219	43	3		3	LINGO2	9	27949554	Silent	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10		27949554	113263877	98	46649										
PIGO	84720	hgsc.bcm.edu	37	chr9	35094331	35094331	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	aaaaggtctttccaggtatcAtctcccatgaagactacacg	7	11	3	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr9:35094331A>C	ENST00000378617.3	-	3	931	c.537T>G	c.(535-537)gaT>gaG	p.D179E	PIGO_ENST00000341666.3_Missense_Mutation_p.D179E|PIGO_ENST00000361778.2_Missense_Mutation_p.D179E|PIGO_ENST00000492770.1_5'Flank|PIGO_ENST00000298004.5_Missense_Mutation_p.D179E|RP11-182N22.8_ENST00000431804.1_RNA	NM_032634.3	NP_116023.2	Q8TEQ8	PIGO_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class O	179				DDT -> ARG (in Ref. 7; AAH13987). {ECO:0000305}.	C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)			endometrium(3)|kidney(2)|large_intestine(8)|lung(13)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)	38			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			TCCAGGTATCATCTCCCATGA	0.488																																					p.D179E		Atlas-SNP	.											.	PIGO	86	.	0			c.T537G						.						110	95	100					9																	35094331		2203	4300	6503	SO:0001583	missense	84720	exon4			GGTATCATCTCCC	AB083625	CCDS6575.1, CCDS6576.1	9p13.2	2013-02-26	2006-06-28		ENSG00000165282	ENSG00000165282		"Phosphatidylinositol glycan anchor biosynthesis"	23215	protein-coding gene	gene with protein product		614730	"phosphatidylinositol glycan, class O"			10781593	Standard	NM_032634		Approved	DKFZp434M222, FLJ00135	uc003zwd.3	Q8TEQ8	OTTHUMG00000019854	ENST00000378617.3:c.537T>G	chr9.hg19:g.35094331A>C	ENSP00000367880:p.Asp179Glu	42.0	0.0		43.0	23.0	NM_001201484	B1AML3|Q6P154|Q6UX80|Q8TDS8|Q96CS9|Q9BVN9|Q9Y4B0	Missense_Mutation	SNP	ENST00000378617.3	hg19	CCDS6575.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.112297	0.77210	.	.	ENSG00000165282	ENST00000298004;ENST00000378617;ENST00000341666;ENST00000361778	T;T;T;T	0.32753	1.44;1.44;1.44;1.44	5.84	1.09	0.20402	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	T	0.59569	0.2203	M	0.93016	3.37	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.996;0.999	T	0.65685	-0.6108	10	0.87932	D	0	-19.2345	9.9491	0.41628	0.6816:0.0:0.3184:0.0	.	179;179	Q8TEQ8-2;Q8TEQ8	.;PIGO_HUMAN	E	179	ENSP00000298004:D179E;ENSP00000367880:D179E;ENSP00000339382:D179E;ENSP00000354678:D179E	ENSP00000298004:D179E	D	-	3	2	PIGO	35084331	0.980000	0.34600	1.000000	0.80357	0.996000	0.88848	0.373000	0.20484	0.496000	0.27904	-0.250000	0.11733	GAT	.	.		0.488	PIGO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052284.1	NM_032634		C	35094331	A	C	35094331	3	2	335	1	0	0	0	0	1	0	0	0	11903	214	8	5	2768	5	PIGO	9	35094331	Missense_Mutation	SNP	A	TCGA-RC-A6M6-01A-11D-A32G-10	7144777	35094331	106119100	99	46650										
ANKS6	203286	hgsc.bcm.edu	37	chr9	101498813	101498813	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	aaggaggatcacgcacagggGctgttgccaggggccctggt	17	10	1	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr9:101498813G>C	ENST00000353234.4	-	15	2651	c.2604C>G	c.(2602-2604)agC>agG	p.S868R	ANKS6_ENST00000375019.2_Missense_Mutation_p.S567R|ANKS6_ENST00000540940.1_Missense_Mutation_p.S673R|ANKS6_ENST00000375018.1_Missense_Mutation_p.S869R			Q68DC2	ANKS6_HUMAN	ankyrin repeat and sterile alpha motif domain containing 6	868						cilium (GO:0005929)|cytoplasm (GO:0005737)				endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	21		Acute lymphoblastic leukemia(62;0.0527)				ACGCACAGGGGCTGTTGCCAG	0.602																																					p.S868R		Atlas-SNP	.											.	ANKS6	59	.	0			c.C2604G						.						52	58	56					9																	101498813		1994	4163	6157	SO:0001583	missense	203286	exon15			ACAGGGGCTGTTG	AK094247	CCDS43856.1	9q31.1	2013-09-10	2006-02-17	2006-02-17	ENSG00000165138	ENSG00000165138		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	26724	protein-coding gene	gene with protein product		615370	"sterile alpha motif domain containing 6", "ankyrin repeat domain 14"	SAMD6, ANKRD14		23793029	Standard	XM_005251793		Approved	FLJ36928, NPHP16	uc004ayu.3	Q68DC2	OTTHUMG00000020347	ENST00000353234.4:c.2604C>G	chr9.hg19:g.101498813G>C	ENSP00000297837:p.Ser868Arg	38.0	0.0		38.0	13.0	NM_173551	A0SE62|Q5VSL0|Q5VSL2|Q5VSL3|Q5VSL4|Q68DB8|Q6P2R2|Q8N9L6|Q96D62	Missense_Mutation	SNP	ENST00000353234.4	hg19	CCDS43856.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.18|12.18	1.860643|1.860643	0.32884|0.32884	.|.	.|.	ENSG00000165138|ENSG00000165138	ENST00000444472|ENST00000375019;ENST00000375018;ENST00000353234;ENST00000540940	.|T;T;T;T	.|0.69040	.|1.84;-0.37;-0.37;2.07	5.31|5.31	-1.61|-1.61	0.08399|0.08399	.|.	.|0.975523	.|0.08507	.|N	.|0.935498	T|T	0.42359|0.42359	0.1199|0.1199	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	0.999998|0.999998	.|B;B	.|0.20459	.|0.045;0.026	.|B;B	.|0.21151	.|0.033;0.018	T|T	0.29181|0.29181	-1.0020|-1.0020	5|10	.|0.59425	.|D	.|0.04	0.0805|0.0805	5.4632|5.4632	0.16627|0.16627	0.5934:0.1399:0.2668:0.0|0.5934:0.1399:0.2668:0.0	.|.	.|869;868	.|Q68DC2-4;Q68DC2	.|.;ANKS6_HUMAN	A|R	338|567;869;868;673	.|ENSP00000364159:S567R;ENSP00000364158:S869R;ENSP00000297837:S868R;ENSP00000442189:S673R	.|ENSP00000297837:S868R	P|S	-|-	1|3	0|2	ANKS6|ANKS6	100538634|100538634	0.009000|0.009000	0.17119|0.17119	0.136000|0.136000	0.22124|0.22124	0.905000|0.905000	0.53344|0.53344	-0.389000|-0.389000	0.07342|0.07342	-0.470000|-0.470000	0.06901|0.06901	0.655000|0.655000	0.94253|0.94253	CCC|AGC	.	.		0.602	ANKS6-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277053.1	NM_173551		C	101498813	G	C	101498813	3	2	335	1	0	0	0	0	1	0	0	0	692	1194	42	4	15	4	ANKS6	9	101498813	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	66404482	101498813	39714618	100	46651										
SPTAN1	6709	hgsc.bcm.edu	37	chr9	131369944	131369944	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	cctcagatgagctagccaagGatgtcaccggagctgaggca	13	11	2	3			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr9:131369944G>T	ENST00000372731.4	+	32	4218	c.4108G>T	c.(4108-4110)Gat>Tat	p.D1370Y	SPTAN1_ENST00000358161.5_Missense_Mutation_p.D1370Y|SPTAN1_ENST00000372739.3_Missense_Mutation_p.D1370Y	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1370					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						GCTAGCCAAGGATGTCACCGG	0.552																																					p.D1370Y	NSCLC(120;833 1744 2558 35612 37579)	Atlas-SNP	.											.	SPTAN1	266	.	0			c.G4108T						.						166	161	163					9																	131369944		2203	4300	6503	SO:0001583	missense	6709	exon32			GCCAAGGATGTCA	M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"EF-hand domain containing"	11273	protein-coding gene	gene with protein product	"alpha-fodrin"	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.4108G>T	chr9.hg19:g.131369944G>T	ENSP00000361816:p.Asp1370Tyr	98.0	0.0		56.0	15.0	NM_003127	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Missense_Mutation	SNP	ENST00000372731.4	hg19	CCDS6905.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.984460	0.93044	.	.	ENSG00000197694	ENST00000358161;ENST00000372731;ENST00000372739;ENST00000372719	T;T;T	0.50277	0.75;0.75;0.75	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.79191	0.4404	H	0.94847	3.59	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.997;0.998	D	0.84317	0.0514	10	0.87932	D	0	.	20.0442	0.97604	0.0:0.0:1.0:0.0	.	1350;1370;1370	Q13813-3;Q13813-2;Q13813	.;.;SPTA2_HUMAN	Y	1370;1370;1370;1350	ENSP00000350882:D1370Y;ENSP00000361816:D1370Y;ENSP00000361824:D1370Y	ENSP00000350882:D1370Y	D	+	1	0	SPTAN1	130409765	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.420000	0.97426	2.814000	0.96858	0.655000	0.94253	GAT	.	.		0.552	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127		T	131369944	G	T	131369944	3	4	335	1	0	0	0	0	1	0	0	0	15132	1174	41	3	4230	3	SPTAN1	9	131369944	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	29871131	131369944	9843487	101	46652										
C9orf86	55684	hgsc.bcm.edu	37	chr9	139722950	139722951	+	Frame_Shift_Ins	INS	-	-	AG													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ttgtttttaaataaggaaaaINStgcaaaaagcgaggcgacgg							TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr9:139722950_139722951insAG	ENST00000311502.7	+	4	554_555	c.318_319insAG	c.(319-321)tgcfs	p.C107fs	RABL6_ENST00000371663.4_Frame_Shift_Ins_p.C107fs|RP11-216L13.18_ENST00000471502.1_RNA|RABL6_ENST00000371675.3_5'UTR|RABL6_ENST00000466096.1_3'UTR|RABL6_ENST00000371671.4_Frame_Shift_Ins_p.C107fs|RABL6_ENST00000357466.2_Frame_Shift_Ins_p.C107fs|RABL6_ENST00000432842.2_Frame_Shift_Ins_p.C69fs|MIR4292_ENST00000585012.1_RNA			Q3YEC7	RABL6_HUMAN	RAB, member RAS oncogene family-like 6	107	Small GTPase-like.				small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)										AATAAGGAAAATGCAAAAAGCG	0.574																																					p.K106fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.318_319insAG						.																																			SO:0001589	frameshift_variant	55684	exon4			.	AK094382	CCDS48058.1, CCDS55352.1, CCDS55353.1	9q34.3	2012-06-28	2012-06-28	2012-06-28	ENSG00000196642	ENSG00000196642			24703	protein-coding gene	gene with protein product	"Rab-like protein 1", "partner of ARF"	610615	"chromosome 9 open reading frame 86"	C9orf86		14702039, 16582619, 17962191, 19433581	Standard	NM_024718		Approved	FLJ10101, FLJ13045, pp8875, bA216L13.9, Parf, RBEL1	uc004cjj.1	Q3YEC7	OTTHUMG00000020947	Exception_encountered	chr9.hg19:g.139722950_139722951insAG	ENSP00000311134:p.Cys107fs	27.0	0.0		69.0	46.0	NM_001173989	A8QVZ7|A8QVZ8|C6K8I4|C6K8I5|Q4F968|Q5T5R7|Q8IWK1|Q8TCL4|Q8WU94|Q96SR8|Q9BU21|Q9H935	Frame_Shift_Ins	INS	ENST00000311502.7	hg19	CCDS48058.1																																																																																			.	.		0.574	RABL6-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055141.4	NM_024718		AG	139722951	-	AG	139722950	7	5	335	1	0	1	1	0	0	0	0	0	2504	98	4	0	332	0	C9orf86	9	139722950	Frame_Shift_Ins	INS	-	TCGA-RC-A6M6-01A-11D-A32G-10	8353006	139722950	1490481	102	46653										
ITIH2	3698	hgsc.bcm.edu	37	chr10	7786905	7786905	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	cccctacaaacaagttctcaCctaaagcccacggactaata	4	15	1	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr10:7786905C>T	ENST00000358415.4	+	19	2726	c.2560C>T	c.(2560-2562)Cct>Tct	p.P854S	ITIH2_ENST00000379587.4_Missense_Mutation_p.P843S	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	854					hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(2)|breast(1)|endometrium(8)|kidney(1)|large_intestine(17)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64						CAAGTTCTCACCTAAAGCCCA	0.438																																					p.P854S		Atlas-SNP	.											.	ITIH2	144	.	0			c.C2560T						.						136	123	128					10																	7786905		2203	4300	6503	SO:0001583	missense	3698	exon19			TTCTCACCTAAAG	X07173	CCDS31141.1	10p14	2011-10-26	2011-10-26		ENSG00000151655	ENSG00000151655			6167	protein-coding gene	gene with protein product		146640	"inter-alpha (globulin) inhibitor, H2 polypeptide"			1385302, 10100603	Standard	NM_002216		Approved	H2P	uc001ijs.3	P19823	OTTHUMG00000017633	ENST00000358415.4:c.2560C>T	chr10.hg19:g.7786905C>T	ENSP00000351190:p.Pro854Ser	98.0	0.0		146.0	13.0	NM_002216	Q14659|Q15484|Q5T986	Missense_Mutation	SNP	ENST00000358415.4	hg19	CCDS31141.1	.	.	.	.	.	.	.	.	.	.	C	8.329	0.826124	0.16749	.	.	ENSG00000151655	ENST00000358415;ENST00000379587	T;T	0.09817	2.94;2.94	5.88	4.98	0.66077	Inter-alpha-trypsin inhibitor heavy chain, C-terminal (1);	0.309508	0.35555	N	0.003131	T	0.07683	0.0193	L	0.39514	1.22	0.09310	N	1	B	0.26577	0.153	B	0.27262	0.078	T	0.39921	-0.9590	10	0.06625	T	0.88	-7.1882	7.4463	0.27213	0.0:0.7191:0.1447:0.1363	.	854	P19823	ITIH2_HUMAN	S	854;843	ENSP00000351190:P854S;ENSP00000368906:P843S	ENSP00000351190:P854S	P	+	1	0	ITIH2	7826911	0.060000	0.20803	0.207000	0.23584	0.005000	0.04900	1.714000	0.37961	2.785000	0.95823	0.655000	0.94253	CCT	.	.		0.438	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	NM_002216		T	7786905	C	T	7786905	3	4	335	1	0	0	0	0	1	0	0	0	7913	507	18	3	2634	3	ITIH2	10	7786905	Missense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10		7786905	127747842	103	46654										
ITGA8	8516	hgsc.bcm.edu	37	chr10	15688879	15688879	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tggttcaggtctcctaagtgTgccatagcactaccgaatct	9	11	3	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr10:15688879T>G	ENST00000378076.3	-	12	1526	c.1173A>C	c.(1171-1173)gcA>gcC	p.A391A		NM_003638.1	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8	391					brain development (GO:0007420)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|metanephros development (GO:0001656)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|substrate adhesion-dependent cell spreading (GO:0034446)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|dendritic spine membrane (GO:0032591)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integrin alpha8-beta1 complex (GO:0034678)|integrin complex (GO:0008305)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	metal ion binding (GO:0046872)			NS(2)|breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(57)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	96						CTCCTAAGTGTGCCATAGCAC	0.478																																					p.A391A		Atlas-SNP	.											.	ITGA8	230	.	0			c.A1173C						.						114	103	107					10																	15688879		2203	4300	6503	SO:0001819	synonymous_variant	8516	exon12			TAAGTGTGCCATA	L36531	CCDS31155.1	10p13	2010-03-23			ENSG00000077943	ENSG00000077943		"Integrins"	6144	protein-coding gene	gene with protein product		604063				7768999	Standard	XM_005252633		Approved		uc001ioc.1	P53708	OTTHUMG00000017733	ENST00000378076.3:c.1173A>C	chr10.hg19:g.15688879T>G		80.0	0.0		79.0	26.0	NM_003638	B0YJ31|Q5VX94	Silent	SNP	ENST00000378076.3	hg19	CCDS31155.1																																																																																			.	.		0.478	ITGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046987.1	NM_003638		G	15688879	T	G	15688879	2	3	335	1	0	0	0	0	0	0	0	1	7891	1683	59	5		5	ITGA8	10	15688879	Silent	SNP	T	TCGA-RC-A6M6-01A-11D-A32G-10	7901974	15688879	119845868	104	46655										
C10orf79	80217	hgsc.bcm.edu	37	chr10	105944803	105944803	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	aggtagacaagggtgccatcAtctctcccattcaccagaat	8	12	3	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr10:105944803A>T	ENST00000278064.2	-	16	2230	c.1905T>A	c.(1903-1905)gaT>gaA	p.D635E	WDR96_ENST00000357060.3_Missense_Mutation_p.D704E|WDR96_ENST00000428666.1_Missense_Mutation_p.D705E																NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(14)|lung(21)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						GGGTGCCATCATCTCTCCCAT	0.378																																					p.D704E		Atlas-SNP	.											.	WDR96	183	.	0			c.T2112A						.						208	181	190					10																	105944803		2203	4300	6503	SO:0001583	missense	80217	exon16			GCCATCATCTCTC																												ENST00000278064.2:c.1905T>A	chr10.hg19:g.105944803A>T	ENSP00000278064:p.Asp635Glu	83.0	0.0		65.0	12.0	NM_025145		Missense_Mutation	SNP	ENST00000278064.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	5.124|5.124	0.208527|0.208527	0.09757|0.09757	.|.	.|.	ENSG00000197748|ENSG00000197748	ENST00000357060;ENST00000428666;ENST00000278064|ENST00000434629	T;T;T|.	0.12879|.	2.66;2.65;2.64|.	5.18|5.18	-3.37|-3.37	0.04898|0.04898	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);|.	0.434585|.	0.22991|.	N|.	0.053199|.	T|T	0.25644|0.25644	0.0624|0.0624	L|L	0.42245|0.42245	1.32|1.32	0.20821|0.20821	N|N	0.999842|0.999842	B;B;B|.	0.16603|.	0.016;0.018;0.012|.	B;B;B|.	0.17722|.	0.01;0.019;0.01|.	T|T	0.33266|0.33266	-0.9875|-0.9875	10|5	0.18276|.	T|.	0.48|.	.|.	2.0703|2.0703	0.03612|0.03612	0.5127:0.218:0.1503:0.1189|0.5127:0.218:0.1503:0.1189	.|.	705;705;704|.	G5E9L1;B4DHB6;Q8NDM7|.	.;.;WDR96_HUMAN|.	E|K	704;705;635|65	ENSP00000349568:D704E;ENSP00000400289:D705E;ENSP00000278064:D635E|.	ENSP00000278064:D635E|.	D|M	-|-	3|2	2|0	WDR96|WDR96	105934793|105934793	0.118000|0.118000	0.22208|0.22208	0.906000|0.906000	0.35671|0.35671	0.997000|0.997000	0.91878|0.91878	-0.034000|-0.034000	0.12225|0.12225	-0.313000|-0.313000	0.08728|0.08728	0.533000|0.533000	0.62120|0.62120	GAT|ATG	.	.		0.378	WDR96-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050200.1			T	105944803	A	T	105944803	3	4	335	1	0	0	0	0	1	0	0	0	1620	214	8	4	2977	4	C10orf79	10	105944803	Missense_Mutation	SNP	A	TCGA-RC-A6M6-01A-11D-A32G-10	90255924	105944803	29589944	105	46656										
PNLIPRP1	5407	hgsc.bcm.edu	37	chr10	118360697	118360697	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ttcttcttgaacacaggagaGgctagcaatttcgctcgtaa	9	9	2	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr10:118360697G>T	ENST00000528052.1	+	10	1118	c.1047G>T	c.(1045-1047)gaG>gaT	p.E349D	PNLIPRP1_ENST00000358834.4_Missense_Mutation_p.E349D|PNLIPRP1_ENST00000534537.1_Missense_Mutation_p.E349D			P54315	LIPR1_HUMAN	pancreatic lipase-related protein 1	349					lipid metabolic process (GO:0006629)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|triglyceride lipase activity (GO:0004806)			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)		ACACAGGAGAGGCTAGCAATT	0.438																																					p.E349D		Atlas-SNP	.											.	PNLIPRP1	82	.	0			c.G1047T						.						132	108	116					10																	118360697		2203	4300	6503	SO:0001583	missense	5407	exon10			AGGAGAGGCTAGC	BC025784	CCDS7595.1	10q26.12	2006-07-04			ENSG00000187021	ENSG00000187021			9156	protein-coding gene	gene with protein product		604422				1379598	Standard	NM_006229		Approved	PLRP1	uc001lco.1	P54315	OTTHUMG00000019109	ENST00000528052.1:c.1047G>T	chr10.hg19:g.118360697G>T	ENSP00000433933:p.Glu349Asp	55.0	0.0		57.0	22.0	NM_006229	Q68D83|Q68DR6|Q8TAU2|Q9BS82	Missense_Mutation	SNP	ENST00000528052.1	hg19	CCDS7595.1	.	.	.	.	.	.	.	.	.	.	G	0	-2.689179	0.00100	.	.	ENSG00000187021	ENST00000358834;ENST00000528052;ENST00000534537	D;D;D	0.90069	-2.61;-2.61;-2.61	5.25	-10.5	0.00291	Lipase, N-terminal (1);	0.537821	0.19744	N	0.107057	T	0.49064	0.1535	N	0.00633	-1.31	0.34251	D	0.678819	B	0.02656	0.0	B	0.01281	0.0	T	0.66787	-0.5835	10	0.02654	T	1	-4.0281	1.1013	0.01684	0.2985:0.1768:0.3364:0.1883	.	349	P54315	LIPR1_HUMAN	D	349	ENSP00000351695:E349D;ENSP00000433933:E349D;ENSP00000434159:E349D	ENSP00000351695:E349D	E	+	3	2	PNLIPRP1	118350687	0.000000	0.05858	0.088000	0.20740	0.436000	0.31835	-3.641000	0.00406	-3.289000	0.00195	-1.564000	0.00881	GAG	.	.		0.438	PNLIPRP1-011	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384633.1	NM_006229		T	118360697	G	T	118360697	3	4	335	1	0	0	0	0	1	0	0	0	12159	991	35	3	1081	3	PNLIPRP1	10	118360697	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	12415894	118360697	17174050	106	46657										
FGFR2	2263	hgsc.bcm.edu	37	chr10	123274695	123274695	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	cagccggctggctgctgaagTctggcttcttggtcgtgttc	14	11	2	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr10:123274695T>C	ENST00000358487.5	-	9	1495	c.1223A>G	c.(1222-1224)gAc>gGc	p.D408G	FGFR2_ENST00000360144.3_Missense_Mutation_p.D320G|FGFR2_ENST00000369059.1_Missense_Mutation_p.D294G|FGFR2_ENST00000356226.4_Missense_Mutation_p.D293G|FGFR2_ENST00000357555.5_Missense_Mutation_p.D319G|FGFR2_ENST00000369056.1_Missense_Mutation_p.D409G|FGFR2_ENST00000346997.2_Missense_Mutation_p.D408G|FGFR2_ENST00000369061.4_Missense_Mutation_p.D296G|FGFR2_ENST00000351936.6_Missense_Mutation_p.D408G|FGFR2_ENST00000369060.4_Intron|FGFR2_ENST00000478859.1_Missense_Mutation_p.D180G|FGFR2_ENST00000457416.2_Missense_Mutation_p.D409G|FGFR2_ENST00000490349.1_5'Flank	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2	408					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)			breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	GCTGCTGAAGTCTGGCTTCTT	0.478		5	Mis		"gastric. NSCLC, endometrial"		"Crouzon, Pfeiffer, and Apert syndromes"		Saethre-Chotzen syndrome;Apert syndrome																												p.D409G		Atlas-SNP	.		Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	.	FGFR2	758	.	0			c.A1226G						.						109	115	113					10																	123274695		2203	4300	6503	SO:0001583	missense	2263	exon9	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	CTGAAGTCTGGCT	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3689	protein-coding gene	gene with protein product	"Crouzon syndrome", "Pfeiffer syndrome"	176943	"bacteria-expressed kinase", "keratinocyte growth factor receptor", "craniofacial dysostosis 1", "Jackson-Weiss syndrome"	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.1223A>G	chr10.hg19:g.123274695T>C	ENSP00000351276:p.Asp408Gly	172.0	0.0		158.0	31.0	NM_022970	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	Missense_Mutation	SNP	ENST00000358487.5	hg19	CCDS31298.1	.	.	.	.	.	.	.	.	.	.	T	19.28	3.797616	0.70567	.	.	ENSG00000066468	ENST00000357555;ENST00000369062;ENST00000369061;ENST00000358487;ENST00000356226;ENST00000369059;ENST00000346997;ENST00000457416;ENST00000351936;ENST00000360144;ENST00000369056;ENST00000369058;ENST00000336553	T;T;T;T;T;T;T;T;T;T;T;T	0.79454	-1.21;-1.27;-1.21;-1.19;-1.17;-1.22;-1.2;-1.21;-1.19;-1.19;-1.19;-1.2	6.03	6.03	0.97812	.	0.086489	0.85682	D	0.000000	D	0.83876	0.5349	M	0.79926	2.475	0.58432	D	0.999999	B;P;P;D;B;B;B;P	0.55385	0.004;0.734;0.717;0.971;0.086;0.05;0.225;0.917	B;P;B;P;B;B;B;P	0.50109	0.002;0.562;0.373;0.631;0.066;0.022;0.233;0.524	D	0.84937	0.0863	10	0.45353	T	0.12	.	16.5655	0.84588	0.0:0.0:0.0:1.0	.	427;409;319;293;408;320;409;313	D3DRD5;P21802-18;P21802-21;P21802-20;P21802;P21802-22;P21802-17;D3DRD3	.;.;.;.;FGFR2_HUMAN;.;.;.	G	319;411;296;408;293;294;408;409;408;320;409;409;319	ENSP00000350166:D319G;ENSP00000358057:D296G;ENSP00000351276:D408G;ENSP00000348559:D293G;ENSP00000358055:D294G;ENSP00000263451:D408G;ENSP00000410294:D409G;ENSP00000309878:D408G;ENSP00000353262:D320G;ENSP00000358052:D409G;ENSP00000358054:D409G;ENSP00000337665:D319G	ENSP00000337665:D319G	D	-	2	0	FGFR2	123264685	1.000000	0.71417	0.999000	0.59377	0.949000	0.60115	6.113000	0.71553	2.302000	0.77476	0.533000	0.62120	GAC	.	.		0.478	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141		C	123274695	T	C	123274695	3	2	335	1	0	0	0	0	1	0	0	0	5874	1667	58	2	1386	2	FGFR2	10	123274695	Missense_Mutation	SNP	T	TCGA-RC-A6M6-01A-11D-A32G-10	4913998	123274695	12260052	107	46658										
OR51M1	390059	hgsc.bcm.edu	37	chr11	5410935	5410935	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tcttctggtttaactcccatAgtatctactttggagcgtgt	8	9	3	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr11:5410935A>T	ENST00000328611.3	+	1	329	c.307A>T	c.(307-309)Agt>Tgt	p.S103C	HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron	NM_001004756.2	NP_001004756.2	Q9H341	O51M1_HUMAN	olfactory receptor, family 51, subfamily M, member 1	103					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(16)|upper_aerodigestive_tract(1)	30		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;1.98e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TAACTCCCATAGTATCTACTT	0.498																																					p.S103C		Atlas-SNP	.											.	OR51M1	60	.	0			c.A307T						.						187	176	179					11																	5410935		1996	4185	6181	SO:0001583	missense	390059	exon1			TCCCATAGTATCT	BK004382	CCDS53596.1	11p15.4	2012-08-09			ENSG00000184698	ENSG00000184698		"GPCR / Class A : Olfactory receptors"	14847	protein-coding gene	gene with protein product							Standard	NM_001004756		Approved		uc010qzc.2	Q9H341	OTTHUMG00000066680	ENST00000328611.3:c.307A>T	chr11.hg19:g.5410935A>T	ENSP00000333196:p.Ser103Cys	104.0	0.0		66.0	30.0	NM_001004756	Q6IF80	Missense_Mutation	SNP	ENST00000328611.3	hg19	CCDS53596.1	.	.	.	.	.	.	.	.	.	.	A	6.444	0.450050	0.12223	.	.	ENSG00000184698	ENST00000328611	T	0.00605	6.27	5.15	-1.98	0.07480	GPCR, rhodopsin-like superfamily (1);	1.434210	0.04961	U	0.462006	T	0.01189	0.0039	M	0.74546	2.27	0.09310	N	1	P	0.40250	0.709	P	0.44359	0.447	T	0.33675	-0.9859	10	0.87932	D	0	.	5.8339	0.18597	0.3836:0.2404:0.376:0.0	.	92	Q9H341	O51M1_HUMAN	C	103	ENSP00000333196:S103C	ENSP00000333196:S103C	S	+	1	0	OR51M1	5367511	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.581000	0.05820	-0.973000	0.03555	-1.334000	0.01262	AGT	.	.		0.498	OR51M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142981.1	NM_001004756		T	5410935	A	T	5410935	3	4	335	1	0	0	0	0	1	0	0	0	11112	420	15	4	309	4	OR51M1	11	5410935	Missense_Mutation	SNP	A	TCGA-RC-A6M6-01A-11D-A32G-10		5410935	129595581	108	46659										
CNGA4	1262	hgsc.bcm.edu	37	chr11	6261787	6261787	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tgggcgacttcctgctggccGtcatgggtttcgccaccatc	12	14	1	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr11:6261787G>A	ENST00000379936.2	+	4	878	c.763G>A	c.(763-765)Gtc>Atc	p.V255I	CNGA4_ENST00000533426.1_Intron	NM_001037329.3	NP_001032406.1	Q8IV77	CNGA4_HUMAN	cyclic nucleotide gated channel alpha 4	255					phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sensory perception of smell (GO:0007608)	integral component of plasma membrane (GO:0005887)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			endometrium(2)|kidney(1)|large_intestine(9)|lung(24)|prostate(3)|skin(1)	40		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.04e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CCTGCTGGCCGTCATGGGTTT	0.532																																					p.V255I		Atlas-SNP	.											.	CNGA4	96	.	0			c.G763A						.						85	78	81					11																	6261787		2201	4296	6497	SO:0001583	missense	1262	exon4			CTGGCCGTCATGG	AK122736	CCDS31408.1	11p15.4	2011-07-05		2002-01-18		ENSG00000132259		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2152	protein-coding gene	gene with protein product		609472	"cyclic nucleotide gated channel beta 2"	CNCA2, CNGB2		11764791, 16382102	Standard	NM_001037329		Approved	OCNC2, OCNCb, CNG5	uc001mco.3	Q8IV77		ENST00000379936.2:c.763G>A	chr11.hg19:g.6261787G>A	ENSP00000369268:p.Val255Ile	60.0	0.0		76.0	24.0	NM_001037329		Missense_Mutation	SNP	ENST00000379936.2	hg19	CCDS31408.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.861084	0.91433	.	.	ENSG00000132259	ENST00000379936	D	0.98400	-4.91	5.3	5.3	0.74995	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98074	0.9365	M	0.84846	2.72	0.58432	D	0.999999	P;P	0.51147	0.942;0.893	P;B	0.45167	0.472;0.436	D	0.98939	1.0790	10	0.56958	D	0.05	.	17.8807	0.88840	0.0:0.0:1.0:0.0	.	255;215	Q8IV77;Q8IV77-2	CNGA4_HUMAN;.	I	255	ENSP00000369268:V255I	ENSP00000369268:V255I	V	+	1	0	CNGA4	6218363	1.000000	0.71417	0.970000	0.41538	0.980000	0.70556	9.420000	0.97426	2.640000	0.89533	0.561000	0.74099	GTC	.	.		0.532	CNGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383765.2	NM_001037329		A	6261787	G	A	6261787	3	1	335	1	0	0	0	0	1	0	0	0	3601	1145	40	1	777	1	CNGA4	11	6261787	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	850852	6261787	128744729	109	46660										
USH1C	10083	hgsc.bcm.edu	37	chr11	17544442	17544442	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gctgccgcgcctctgccagcCgctcccggtctgtcatgaac	11	18	3	1	rs397517884		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr11:17544442C>A	ENST00000318024.4	-	12	1016	c.908G>T	c.(907-909)cGg>cTg	p.R303L	USH1C_ENST00000005226.7_Missense_Mutation_p.R303L|USH1C_ENST00000527720.1_Missense_Mutation_p.R272L|USH1C_ENST00000527020.1_Missense_Mutation_p.R284L	NM_005709.3	NP_005700.2	Q9Y6N9	USH1C_HUMAN	Usher syndrome 1C (autosomal recessive, severe)	303					auditory receptor cell differentiation (GO:0042491)|equilibrioception (GO:0050957)|G2/M transition of mitotic cell cycle (GO:0000086)|inner ear morphogenesis (GO:0042472)|parallel actin filament bundle assembly (GO:0030046)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	spectrin binding (GO:0030507)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	48						CTCTGCCAGCCGCTCCCGGTC	0.662																																					p.R303L		Atlas-SNP	.											.	USH1C	157	.	0			c.G908T						.						10	13	12					11																	17544442		2044	4076	6120	SO:0001583	missense	10083	exon12			GCCAGCCGCTCCC	AB006955	CCDS7825.1, CCDS31438.1, CCDS73265.1	11p14.3	2013-06-19	2004-05-19		ENSG00000006611	ENSG00000006611			12597	protein-coding gene	gene with protein product	"harmonin"	605242	"deafness, autosomal recessive 18"	DFNB18		10973247, 12107438	Standard	NM_005709		Approved	PDZ73, harmonin, NY-CO-37, NY-CO-38, PDZ-73, AIE-75, PDZD7C	uc001mne.3	Q9Y6N9	OTTHUMG00000166323	ENST00000318024.4:c.908G>T	chr11.hg19:g.17544442C>A	ENSP00000317018:p.Arg303Leu	61.0	0.0		69.0	28.0	NM_005709	A8K423|Q7RTU8|Q96B29|Q9UM04|Q9UM17|Q9UPC3	Missense_Mutation	SNP	ENST00000318024.4	hg19	CCDS31438.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.690131	0.88735	.	.	ENSG00000006611	ENST00000318024;ENST00000527720;ENST00000527020;ENST00000005226;ENST00000526181	T;T;T;T;T	0.65364	1.72;1.7;1.94;-0.15;2.01	5.33	5.33	0.75918	PDZ/DHR/GLGF (1);	0.193191	0.44902	D	0.000404	T	0.65678	0.2714	L	0.29908	0.895	0.54753	D	0.999982	D;P;D	0.60575	0.969;0.91;0.988	P;P;P	0.57468	0.753;0.47;0.821	T	0.69007	-0.5259	10	0.66056	D	0.02	.	15.9446	0.79784	0.0:1.0:0.0:0.0	.	284;303;303	Q9Y6N9-4;Q9Y6N9;Q7RTU8	.;USH1C_HUMAN;.	L	303;272;284;303;314	ENSP00000317018:R303L;ENSP00000432944:R272L;ENSP00000436934:R284L;ENSP00000005226:R303L;ENSP00000437128:R314L	ENSP00000005226:R303L	R	-	2	0	USH1C	17501018	1.000000	0.71417	1.000000	0.80357	0.621000	0.37620	3.077000	0.50089	2.509000	0.84616	0.455000	0.32223	CGG	.	.		0.662	USH1C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389146.1	NM_005709		A	17544442	C	A	17544442	3	1	335	1	0	0	0	0	1	0	0	0	17049	652	23	1	1933	1	USH1C	11	17544442	Missense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	11282655	17544442	117462074	110	46661										
WT1	7490	hgsc.bcm.edu	37	chr11	32414292	32414292	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ccttgaagtcacactggtatGgtttctcaccttggggaaga	11	9	2	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr11:32414292G>C	ENST00000379079.2	-	8	896	c.623C>G	c.(622-624)cCa>cGa	p.P208R	WT1_ENST00000448076.3_Missense_Mutation_p.P420R|WT1_ENST00000530998.1_Missense_Mutation_p.P191R|WT1_ENST00000332351.3_Missense_Mutation_p.P420R	NM_001198551.1	NP_001185480.1	P19544	WT1_HUMAN	Wilms tumor 1	352					adrenal cortex formation (GO:0035802)|adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye development (GO:0043010)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|diaphragm development (GO:0060539)|epithelial cell differentiation (GO:0030855)|germ cell development (GO:0007281)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|gonad development (GO:0008406)|heart development (GO:0007507)|kidney development (GO:0001822)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|mesenchymal to epithelial transition (GO:0060231)|metanephric epithelium development (GO:0072207)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of female gonad development (GO:2000195)|negative regulation of metanephric glomerular mesangial cell proliferation (GO:0072302)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of heart growth (GO:0060421)|positive regulation of male gonad development (GO:2000020)|positive regulation of metanephric ureteric bud development (GO:2001076)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior mesonephric tubule development (GO:0072166)|regulation of organ formation (GO:0003156)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|sex determination (GO:0007530)|thorax and anterior abdomen determination (GO:0007356)|tissue development (GO:0009888)|ureteric bud development (GO:0001657)|vasculogenesis (GO:0001570)|visceral serous pericardium development (GO:0061032)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.?(1)	EWSR1/WT1(234)	NS(1)|haematopoietic_and_lymphoid_tissue(348)|kidney(149)|large_intestine(9)|lung(20)|peritoneum(1)|pleura(2)|skin(2)|upper_aerodigestive_tract(1)	533	Breast(20;0.247)		OV - Ovarian serous cystadenocarcinoma(30;0.128)			ACACTGGTATGGTTTCTCACC	0.433			"D, Mis, N, F, S"	EWSR1	"Wilms, desmoplastic small round cell tumor"	Wilms			Wilms' tumor-Aniridia-ambiguous Genitals-mental Retardation;Frasier syndrome;Familial Wilms' tumor;Denys-Drash syndrome																												p.P420R		Atlas-SNP	.	yes	Rec	yes	"Denys-Drash syndrome, Frasier syndrome, Familial Wilms tumor"	11	11p13	7490	Wilms tumour 1 gene		O	.	WT1	744	.	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	c.C1259G						.						143	125	131					11																	32414292		2202	4299	6501	SO:0001583	missense	7490	exon8	Familial Cancer Database	WAGR syndrome; ; ;incl.: Early Onset Nephrotic Syndrome-WT1 associated	TGGTATGGTTTCT		CCDS7878.2, CCDS44561.1, CCDS44562.1, CCDS55750.1, CCDS55751.1	11p13	2014-09-17			ENSG00000184937	ENSG00000184937		"Zinc fingers, C2H2-type"	12796	protein-coding gene	gene with protein product		607102		GUD		14681303	Standard	NM_024424		Approved	WAGR, WIT-2, AWT1	uc001mtn.2	P19544	OTTHUMG00000039556	ENST00000379079.2:c.623C>G	chr11.hg19:g.32414292G>C	ENSP00000368370:p.Pro208Arg	90.0	0.0		81.0	28.0	NM_024424	A8K6S1|B3KSA5|Q15881|Q16256|Q16575|Q4VXV4|Q4VXV5|Q4VXV6|Q8IYZ5	Missense_Mutation	SNP	ENST00000379079.2	hg19	CCDS55751.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.939603	0.92526	.	.	ENSG00000184937	ENST00000379079;ENST00000332351;ENST00000530998;ENST00000452863;ENST00000448076	T;T;T;T;T	0.27890	1.64;1.64;1.64;1.64;1.64	5.73	5.73	0.89815	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	U	0.000002	T	0.62527	0.2435	M	0.84082	2.675	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	T	0.65302	-0.6201	10	0.87932	D	0	.	20.263	0.98456	0.0:0.0:1.0:0.0	.	408;352;425;191;208	P19544-8;P19544;P19544-7;B3KSA5;P19544-6	.;WT1_HUMAN;.;.;.	R	208;420;191;403;420	ENSP00000368370:P208R;ENSP00000331327:P420R;ENSP00000435307:P191R;ENSP00000415516:P403R;ENSP00000413452:P420R	ENSP00000331327:P420R	P	-	2	0	WT1	32370868	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.782000	0.99034	2.868000	0.98415	0.555000	0.69702	CCA	.	.		0.433	WT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000095434.1	NM_000378		C	32414292	G	C	32414292	3	2	335	1	0	0	0	0	1	0	0	0	17423	1348	47	4	306	4	WT1	11	32414292	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	14869850	32414292	102592224	111	46662										
OR5T2	219464	hgsc.bcm.edu	37	chr11	56000068	56000068	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	aggctaaatgtagccactgtAtgtatagtagcatgtaaaat	9	5	0	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr11:56000068A>G	ENST00000313264.4	-	1	669	c.594T>C	c.(592-594)caT>caC	p.H198H		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	198						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(3)	41	Esophageal squamous(21;0.00448)					TAGCCACTGTATGTATAGTAG	0.433																																					p.H198H		Atlas-SNP	.											.	OR5T2	107	.	0			c.T594C						.						186	164	172					11																	56000068		2201	4296	6497	SO:0001819	synonymous_variant	219464	exon1			CACTGTATGTATA	AB065838	CCDS31523.1	11q11	2012-08-09			ENSG00000181718	ENSG00000181718		"GPCR / Class A : Olfactory receptors"	15296	protein-coding gene	gene with protein product							Standard	NM_001004746		Approved		uc010rjc.2	Q8NGG2	OTTHUMG00000166851	ENST00000313264.4:c.594T>C	chr11.hg19:g.56000068A>G		139.0	0.0		133.0	58.0	NM_001004746	B9EGX5|Q6IFC8	Silent	SNP	ENST00000313264.4	hg19	CCDS31523.1																																																																																			.	.		0.433	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746		G	56000068	A	G	56000068	2	3	335	1	0	0	0	0	0	0	0	1	11191	446	16	2		2	OR5T2	11	56000068	Silent	SNP	A	TCGA-RC-A6M6-01A-11D-A32G-10	23585776	56000068	79006448	112	46663										
MS4A2	2206	hgsc.bcm.edu	37	chr11	59861471	59861472	+	Missense_Mutation	DNP	TG	TG	AT													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gatgctgtttctcaccattcTgggacttggtagtgctgtgt							TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T|G	T|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr11:59861471_59861472TG>AT	ENST00000278888.3	+	6	674_675	c.572_573TG>AT	c.(571-573)cTG>cAT	p.L191H		NM_000139.4	NP_000130.1	Q01362	FCERB_HUMAN	membrane-spanning 4-domains, subfamily A, member 2	191					activation of phospholipase C activity (GO:0007202)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of mast cell degranulation (GO:0043306)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|Fc-epsilon receptor I complex (GO:0032998)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(4)|lung(9)|ovary(1)|upper_aerodigestive_tract(2)	17		all_epithelial(135;0.245)			Omalizumab(DB00043)	CTCACCATTCTGGGACTTGGTA	0.406																																					p.L191Q|p.L191L		Atlas-SNP	.											.	MS4A2	41	.	0			c.T572A|c.G573T						.																																			SO:0001583	missense	2206	exon6			CCATTCTGGGACT|CATTCTGGGACTT	M89796	CCDS7980.1, CCDS73292.1	11q12-q13	2012-02-28	2012-02-28		ENSG00000149534	ENSG00000149534			7316	protein-coding gene	gene with protein product	"Fc fragment of IgE, high affinity I, receptor for; beta polypeptide"	147138	"IgE responsiveness (atopic)", "membrane-spanning 4-domains, subfamily A, member 2 (Fc fragment of IgE, high affinity I, receptor for; beta polypeptide)"	FCER1B, IGER, APY		1386024	Standard	NM_000139		Approved	MS4A1	uc001nop.3	Q01362	OTTHUMG00000167239	Exception_encountered	chr11.hg19:g.59861471_59861472delinsAT	ENSP00000278888:p.Leu191His	112.0|113.0	0.0		91.0|90.0	39.0	NM_000139	Q54A81	Missense_Mutation|Silent	SNP	ENST00000278888.3	hg19	CCDS7980.1																																																																																			.	.		0.406	MS4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393844.1			AT	59861472	TG	AT	59861471	3	1	335	1	0	0	0	0	1	0	0	0	9869	1580	55	4	645	4	MS4A2	11	59861471	Missense_Mutation	DNP	TG	TCGA-RC-A6M6-01A-11D-A32G-10	3861403	59861471	75145045	113	46664	248	2								
MS4A2	2206	hgsc.bcm.edu	37	chr11	59861474	59861474	+	Missense_Mutation	SNP	G	G	T													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gctgtttctcaccattctggGacttggtagtgctgtgtcac							TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr11:59861474G>T	ENST00000278888.3	+	6	677	c.575G>T	c.(574-576)gGa>gTa	p.G192V		NM_000139.4	NP_000130.1	Q01362	FCERB_HUMAN	membrane-spanning 4-domains, subfamily A, member 2	192					activation of phospholipase C activity (GO:0007202)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of mast cell degranulation (GO:0043306)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|Fc-epsilon receptor I complex (GO:0032998)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(4)|lung(9)|ovary(1)|upper_aerodigestive_tract(2)	17		all_epithelial(135;0.245)			Omalizumab(DB00043)	ACCATTCTGGGACTTGGTAGT	0.403																																					p.G192V		Atlas-SNP	.											.	MS4A2	41	.	0			c.G575T						.						123	110	115					11																	59861474		2201	4295	6496	SO:0001583	missense	2206	exon6			TTCTGGGACTTGG	M89796	CCDS7980.1, CCDS73292.1	11q12-q13	2012-02-28	2012-02-28		ENSG00000149534	ENSG00000149534			7316	protein-coding gene	gene with protein product	"Fc fragment of IgE, high affinity I, receptor for; beta polypeptide"	147138	"IgE responsiveness (atopic)", "membrane-spanning 4-domains, subfamily A, member 2 (Fc fragment of IgE, high affinity I, receptor for; beta polypeptide)"	FCER1B, IGER, APY		1386024	Standard	NM_000139		Approved	MS4A1	uc001nop.3	Q01362	OTTHUMG00000167239	ENST00000278888.3:c.575G>T	chr11.hg19:g.59861474G>T	ENSP00000278888:p.Gly192Val	113.0	0.0		89.0	38.0	NM_000139	Q54A81	Missense_Mutation	SNP	ENST00000278888.3	hg19	CCDS7980.1	.	.	.	.	.	.	.	.	.	.	G	13.01	2.109866	0.37242	.	.	ENSG00000149534	ENST00000278888	T	0.02301	4.35	4.23	1.26	0.21427	.	0.581365	0.17388	N	0.176033	T	0.06917	0.0176	M	0.63428	1.95	0.45415	D	0.998393	D	0.76494	0.999	D	0.68353	0.957	T	0.32929	-0.9888	10	0.56958	D	0.05	-6.5188	4.0346	0.09724	0.222:0.2093:0.5686:0.0	.	192	Q01362	FCERB_HUMAN	V	192	ENSP00000278888:G192V	ENSP00000278888:G192V	G	+	2	0	MS4A2	59618050	0.994000	0.37717	0.925000	0.36789	0.446000	0.32137	0.265000	0.18515	0.295000	0.22570	0.573000	0.79308	GGA	.	.		0.403	MS4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393844.1			T	59861474	G	T	59861474	3	4	335	1	0	0	0	0	1	0	0	0	9869	1174	41	3	648	3	MS4A2	11	59861474	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	3	59861474	75145042	114	46665	248	2								
MYO7A	4647	hgsc.bcm.edu	37	chr11	76925722	76925722	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	agccatgagcaaacagcgggGctccaggagcggcaagtgaa	15	10	0	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr11:76925722G>T	ENST00000409709.3	+	49	6901	c.6629G>T	c.(6628-6630)gGc>gTc	p.G2210V	MYO7A_ENST00000605744.1_3'UTR|MYO7A_ENST00000409619.2_Missense_Mutation_p.G2161V|MYO7A_ENST00000458637.2_Missense_Mutation_p.G2170V	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	2210					actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						AAACAGCGGGGCTCCAGGAGC	0.592																																					p.G2210V		Atlas-SNP	.											.	MYO7A	164	.	0			c.G6629T						.						28	31	30					11																	76925722		2031	4167	6198	SO:0001583	missense	4647	exon49			AGCGGGGCTCCAG	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"A-kinase anchor proteins", "Myosins / Myosin superfamily : Class VII"	7606	protein-coding gene	gene with protein product		276903	"myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.6629G>T	chr11.hg19:g.76925722G>T	ENSP00000386331:p.Gly2210Val	66.0	0.0		60.0	26.0	NM_000260	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Missense_Mutation	SNP	ENST00000409709.3	hg19	CCDS53683.1	.	.	.	.	.	.	.	.	.	.	G	14.62	2.589804	0.46214	.	.	ENSG00000137474	ENST00000409709;ENST00000458637;ENST00000409619;ENST00000545136;ENST00000358342;ENST00000343356;ENST00000341717;ENST00000458169	D;D;D;D	0.87412	-2.24;-2.23;-2.25;-2.04	5.47	4.54	0.55810	.	0.422930	0.28921	N	0.013718	D	0.82430	0.5035	N	0.22421	0.69	0.58432	D	0.999992	B;B	0.29136	0.234;0.164	B;B	0.37650	0.255;0.075	T	0.81219	-0.1032	10	0.62326	D	0.03	.	13.3396	0.60537	0.0769:0.0:0.9231:0.0	.	2170;2210	F8VUN5;Q13402	.;MYO7A_HUMAN	V	2210;2170;2161;1383;2209;2179;2086;1352	ENSP00000386331:G2210V;ENSP00000392185:G2170V;ENSP00000386635:G2161V;ENSP00000417017:G1352V	ENSP00000345075:G2086V	G	+	2	0	MYO7A	76603370	0.995000	0.38212	1.000000	0.80357	0.558000	0.35554	2.761000	0.47589	1.272000	0.44329	0.467000	0.42956	GGC	.	.		0.592	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260		T	76925722	G	T	76925722	3	4	335	1	0	0	0	0	1	0	0	0	10091	1203	42	3	6853	3	MYO7A	11	76925722	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	17064248	76925722	58080794	115	46666										
PCF11	51585	hgsc.bcm.edu	37	chr11	82895887	82895887	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ttgtacagaggaaagcatagCaacaccctctgaaattaaaa	7	8	1	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr11:82895887C>T	ENST00000298281.4	+	16	5071	c.4619C>T	c.(4618-4620)gCa>gTa	p.A1540V	RP11-727A23.11_ENST00000602322.1_lincRNA|RP11-727A23.4_ENST00000528133.1_RNA	NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	1540					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						GAAAGCATAGCAACACCCTCT	0.368																																					p.A1540V		Atlas-SNP	.											.	PCF11	220	.	0			c.C4619T						.						83	77	79					11																	82895887		1860	4101	5961	SO:0001583	missense	51585	exon16			GCATAGCAACACC	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)", "PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.4619C>T	chr11.hg19:g.82895887C>T	ENSP00000298281:p.Ala1540Val	65.0	0.0		70.0	24.0	NM_015885	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	hg19	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	C	12.62	1.993321	0.35131	.	.	ENSG00000165494	ENST00000298281	T	0.22743	1.94	5.4	3.51	0.40186	.	0.369985	0.23060	N	0.052388	T	0.10895	0.0266	N	0.12182	0.205	0.24550	N	0.994026	B	0.02656	0.0	B	0.06405	0.002	T	0.26292	-1.0107	9	.	.	.	-4.0911	10.5959	0.45338	0.0:0.7941:0.1342:0.0718	.	1540	O94913	PCF11_HUMAN	V	1540	ENSP00000298281:A1540V	.	A	+	2	0	PCF11	82573535	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	1.091000	0.30915	1.278000	0.44430	0.585000	0.79938	GCA	.	.		0.368	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		T	82895887	C	T	82895887	3	4	335	1	0	0	0	0	1	0	0	0	11582	710	25	3	4681	3	PCF11	11	82895887	Missense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	5970165	82895887	52110629	116	46667										
B3GAT1	27087	hgsc.bcm.edu	37	chr11	134252717	134252717	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	cagcttgaagtaggcctggcTtcgctgcagaatgagccgca	13	11	0	3			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr11:134252717T>G	ENST00000524765.1	-	4	5349	c.805A>C	c.(805-807)Agc>Cgc	p.S269R	B3GAT1_ENST00000312527.4_Missense_Mutation_p.S269R|B3GAT1_ENST00000392580.1_Missense_Mutation_p.S269R|B3GAT1_ENST00000531510.1_5'Flank|B3GAT1_ENST00000537389.1_Missense_Mutation_p.S282R			Q9P2W7	B3GA1_HUMAN	beta-1,3-glucuronyltransferase 1	269					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity (GO:0015018)|metal ion binding (GO:0046872)|UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity (GO:0008499)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_hematologic(175;0.127)	all_cancers(12;1.39e-23)|all_epithelial(12;7.17e-17)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|Medulloblastoma(222;0.0125)|all_neural(223;0.0137)|Esophageal squamous(93;0.0559)		Epithelial(10;2.58e-11)|all cancers(11;5.75e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.000879)|Lung(977;0.0864)		TAGGCCTGGCTTCGCTGCAGA	0.587																																					p.S269R		Atlas-SNP	.											.	B3GAT1	49	.	0			c.A805C						.						123	95	104					11																	134252717		2201	4297	6498	SO:0001583	missense	27087	exon4			CCTGGCTTCGCTG	AB029396	CCDS8500.1	11q25	2014-07-08	2014-07-08		ENSG00000109956	ENSG00000109956	2.4.1.135	"CD molecules", "Beta-1,3-glucuronyltransferases"	921	protein-coding gene	gene with protein product	"galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1", "glucuronosyltransferase P"	151290	"CD57 antigen"	CD57, LEU7			Standard	XM_005271506		Approved	GlcAT-P, HNK-1, NK-1	uc001qhq.3	Q9P2W7	OTTHUMG00000167180	ENST00000524765.1:c.805A>C	chr11.hg19:g.134252717T>G	ENSP00000433847:p.Ser269Arg	76.0	0.0		76.0	34.0	NM_054025	Q96FS7	Missense_Mutation	SNP	ENST00000524765.1	hg19	CCDS8500.1	.	.	.	.	.	.	.	.	.	.	T	18.42	3.620610	0.66787	.	.	ENSG00000109956	ENST00000392580;ENST00000312527;ENST00000524765;ENST00000537389	T;T;T;T	0.64803	-0.12;-0.12;-0.12;-0.12	5.22	5.22	0.72569	.	0.230399	0.52532	D	0.000078	T	0.45875	0.1364	N	0.21373	0.66	0.42993	D	0.994499	B;B	0.19935	0.032;0.04	B;B	0.24394	0.053;0.019	T	0.48536	-0.9027	10	0.72032	D	0.01	-49.614	6.2368	0.20768	0.1528:0.0:0.2643:0.5829	.	282;269	F5H0S0;Q9P2W7	.;B3GA1_HUMAN	R	269;269;269;282	ENSP00000376359:S269R;ENSP00000307875:S269R;ENSP00000433847:S269R;ENSP00000445983:S282R	ENSP00000307875:S269R	S	-	1	0	B3GAT1	133757927	0.979000	0.34478	0.954000	0.39281	0.990000	0.78478	1.915000	0.39976	2.197000	0.70478	0.402000	0.26972	AGC	.	.		0.587	B3GAT1-002	KNOWN	alternative_3_UTR|alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393639.1	NM_018644		G	134252717	T	G	134252717	3	3	335	1	0	0	0	0	1	0	0	0	1253	1609	56	5	207	5	B3GAT1	11	134252717	Missense_Mutation	SNP	T	TCGA-RC-A6M6-01A-11D-A32G-10	51356830	134252717	753799	117	46668										
SLC6A13	6540	hgsc.bcm.edu	37	chr12	335639	335639	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	agatggcaaagccggccacaAagctggtgccgctgttgagg	15	10	0	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr12:335639A>C	ENST00000343164.4	-	9	1029	c.977T>G	c.(976-978)tTt>tGt	p.F326C	SLC6A13_ENST00000445055.2_Missense_Mutation_p.F234C|SLC6A13_ENST00000539668.1_5'Flank	NM_016615.4	NP_057699.2	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 13	326					neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(1)	28	all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239)			GCCGGCCACAAAGCTGGTGCC	0.617																																					p.F326C		Atlas-SNP	.											.	SLC6A13	62	.	0			c.T977G						.						64	56	59					12																	335639		2203	4300	6503	SO:0001583	missense	6540	exon9			GCCACAAAGCTGG	U76343	CCDS8502.1, CCDS53729.1, CCDS58198.1	12p13.33	2013-07-19	2013-07-19		ENSG00000010379	ENSG00000010379		"Solute carriers"	11046	protein-coding gene	gene with protein product	"GABA transporter 2"	615097	"solute carrier family 6 (neurotransmitter transporter, GABA), member 13"				Standard	NM_001243392		Approved	GAT2	uc001qic.2	Q9NSD5	OTTHUMG00000168053	ENST00000343164.4:c.977T>G	chr12.hg19:g.335639A>C	ENSP00000339260:p.Phe326Cys	47.0	0.0		31.0	11.0	NM_016615	B4DJL1|Q8TCC2|Q8WW56	Missense_Mutation	SNP	ENST00000343164.4	hg19	CCDS8502.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.531110	0.85706	.	.	ENSG00000010379	ENST00000445055;ENST00000313154;ENST00000343164	T;T	0.76316	-1.01;-1.01	5.34	5.34	0.76211	.	0.046786	0.85682	D	0.000000	D	0.92701	0.7680	H	0.98314	4.2	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.79108	0.992;0.99;0.984	D	0.95445	0.8529	10	0.87932	D	0	.	15.3028	0.73966	1.0:0.0:0.0:0.0	.	234;305;326	B4DJL1;B4DJS3;Q9NSD5	.;.;S6A13_HUMAN	C	234;305;326	ENSP00000407104:F234C;ENSP00000339260:F326C	ENSP00000318097:F305C	F	-	2	0	SLC6A13	205900	1.000000	0.71417	0.993000	0.49108	0.984000	0.73092	9.260000	0.95568	2.010000	0.58986	0.402000	0.26972	TTT	.	.		0.617	SLC6A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397801.1	NM_016615		C	335639	A	C	335639	3	2	335	1	0	0	0	0	1	0	0	0	14691	14	1	5	859	5	SLC6A13	12	335639	Missense_Mutation	SNP	A	TCGA-RC-A6M6-01A-11D-A32G-10		335639	133516256	118	46669										
PRB2	653247	hgsc.bcm.edu	37	chr12	11545952	11546074	+	In_Frame_Del	DEL	TGCCTCCTTGTGGGGGTGGTCCTTGTGGCTTTCCTGGAGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGGGGGTGGTCCTTGTGGCTTTCCTGGAGGAGGTGGGGGACCTTGAGGCTGGT	TGCCTCCTTGTGGGGGTGGTCCTTGTGGCTTTCCTGGAGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGGGGGTGGTCCTTGTGGCTTTCCTGGAGGAGGTGGGGGACCTTGAGGCTGGT	-													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tcgggcacttcgggacttgcTgcctccttgtgggggtggtc					rs372626172|rs77906063|rs375050877|rs370021759|rs201391404|rs568468055|rs377197500|rs374100662|rs202244094|rs75059624|rs368880039|rs560061246|rs200026492|rs540027572|rs200510401|rs201001689|rs547882513|rs185711312|rs376831456|rs527497030|rs201848322|rs545655808|rs538733280	byFrequency	TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	TGCCTCCTTGTGGGGGTGGTCCTTGTGGCTTTCCTGGAGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGGGGGTGGTCCTTGTGGCTTTCCTGGAGGAGGTGGGGGACCTTGAGGCTGGT	TGCCTCCTTGTGGGGGTGGTCCTTGTGGCTTTCCTGGAGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGGGGGTGGTCCTTGTGGCTTTCCTGGAGGAGGTGGGGGACCTTGAGGCTGGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr12:11545952_11546074delTGCCTCCTTGTGGGGGTGGTCCTTGTGGCTTTCCTGGAGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGGGGGTGGTCCTTGTGGCTTTCCTGGAGGAGGTGGGGGACCTTGAGGCTGGT	ENST00000389362.4	-	3	973_1095	c.938_1060delACCAGCCTCAAGGTCCCCCACCTCCTCCAGGAAAGCCACAAGGACCACCCCCACAAGGAGGCAACAAACCTCAAGGTCCCCCACCTCCAGGAAAGCCACAAGGACCACCCCCACAAGGAGGCA	c.(937-1062)aaccagcctcaaggtcccccacctcctccaggaaagccacaaggaccacccccacaaggaggcaacaaacctcaaggtcccccacctccaggaaagccacaaggaccacccccacaaggaggcagc>agc	p.NQPQGPPPPPGKPQGPPPQGGNKPQGPPPPGKPQGPPPQGG313del	PRB1_ENST00000546254.1_Intron|PRB2_ENST00000545829.1_5'Flank	NM_006248.3	NP_006239.3	P02812	PRB2_HUMAN	proline-rich protein BstNI subfamily 2	313	15 X 20 AA approximate tandem repeats of P-P-G-K-P-Q-G-P-P-P-Q-G-[GD]-[NKS]-[KSQ]- [PRS]-[QRS] [GPS]-[PSAR]-[PSR].					extracellular region (GO:0005576)		p.P315P(3)|p.P294P(3)		NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(5)|skin(4)|stomach(2)|urinary_tract(1)	37		all_cancers(2;0.00558)|Acute lymphoblastic leukemia(2;3.94e-11)|all_hematologic(2;3.6e-09)	OV - Ovarian serous cystadenocarcinoma(49;0.185)			CGGGACTTGCTGCCTCCTTGTGGGGGTGGTCCTTGTGGCTTTCCTGGAGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGGGGGTGGTCCTTGTGGCTTTCCTGGAGGAGGTGGGGGACCTTGAGGCTGGTTGCCTCCTTG	0.604																																					p.313_354del		Pindel	.											.	PRB2	168	.	6	Substitution - coding silent(6)	large_intestine(4)|prostate(2)	c.939_1061del						.																																			SO:0001651	inframe_deletion	653247	exon3			.	K03208	CCDS41757.2	12p13.2	2012-10-02			ENSG00000121335	ENSG00000121335			9338	protein-coding gene	gene with protein product		168810				8554050	Standard	NM_006248		Approved	PRPPRB1, Ps, cP7	uc010shk.1	P02812	OTTHUMG00000156975	ENST00000389362.4:c.938_1060delACCAGCCTCAAGGTCCCCCACCTCCTCCAGGAAAGCCACAAGGACCACCCCCACAAGGAGGCAACAAACCTCAAGGTCCCCCACCTCCAGGAAAGCCACAAGGACCACCCCCACAAGGAGGCA	chr12.hg19:g.11545952_11546074delTGCCTCCTTGTGGGGGTGGTCCTTGTGGCTTTCCTGGAGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGGGGGTGGTCCTTGTGGCTTTCCTGGAGGAGGTGGGGGACCTTGAGGCTGGT	ENSP00000374013:p.Asn313_Gly353del	322.0	0.0		321.0	13.0	NM_006248	O00599|P02811|P04281	In_Frame_Del	DEL	ENST00000389362.4	hg19	CCDS41757.2																																																																																			.	.		0.604	PRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346925.2	NM_006248		-	11546074	TGCCTCCTTGTGGGGGTGGTCCTTGTGGCTTTCCTGGAGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGGGGGTGGTCCTTGTGGCTTTCCTGGAGGAGGTGGGGGACCTTGAGGCTGGT	-	11545952	7	5	335	1	0	1	0	1	0	0	0	0	12455	1580	55	0	194	0	PRB2	12	11545952	In_Frame_Del	DEL	TGCCTCCTTGTGGGGGTGGTCCTTGTGGCTTTCCTGGAGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGGGGGTGGTCCTTGTGGCTTTCCTGGAGGAGGTGGGGGACCTTGAGGCTGGT	TCGA-RC-A6M6-01A-11D-A32G-10	11210313	11545952	122305943	119	46670										
EMP1	2012	hgsc.bcm.edu	37	chr12	13366481	13366481	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	aactgtaccaacattagctgCagtgacagcctgtcatatgc	8	11	1	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr12:13366481C>A	ENST00000256951.5	+	3	346	c.147C>A	c.(145-147)tgC>tgA	p.C49*	EMP1_ENST00000431267.2_Intron|EMP1_ENST00000544053.1_5'UTR|EMP1_ENST00000396301.3_Nonsense_Mutation_p.C49*|EMP1_ENST00000537612.1_Nonsense_Mutation_p.C49*|EMP1_ENST00000542289.1_Intron	NM_001423.2	NP_001414.1	P54849	EMP1_HUMAN	epithelial membrane protein 1	49					cell growth (GO:0016049)|cell proliferation (GO:0008283)|epidermis development (GO:0008544)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)							Prostate(47;0.194)		BRCA - Breast invasive adenocarcinoma(232;0.153)		ACATTAGCTGCAGTGACAGCC	0.433																																					p.C49X		Atlas-SNP	.											.	EMP1	14	.	0			c.C147A						.						169	156	160					12																	13366481		2203	4300	6503	SO:0001587	stop_gained	2012	exon3			TAGCTGCAGTGAC	U43916	CCDS8660.1	12p12.3	2008-08-04				ENSG00000134531			3333	protein-coding gene	gene with protein product		602333				8996089, 9126480	Standard	NM_001423		Approved	TMP, CL-20	uc001rbr.3	P54849		ENST00000256951.5:c.147C>A	chr12.hg19:g.13366481C>A	ENSP00000256951:p.Cys49*	294.0	0.0		254.0	69.0	NM_001423	B2R5N1|B4DRR1|O00681|Q13481|Q13834	Nonsense_Mutation	SNP	ENST00000256951.5	hg19	CCDS8660.1	.	.	.	.	.	.	.	.	.	.	C	16.98	3.271341	0.59649	.	.	ENSG00000134531	ENST00000256951;ENST00000538364;ENST00000396301;ENST00000537612	.	.	.	5.78	-3.22	0.05125	.	0.341114	0.39759	N	0.001275	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-17.357	13.8116	0.63266	0.0:0.4345:0.0:0.5655	.	.	.	.	X	49	.	ENSP00000256951:C49X	C	+	3	2	EMP1	13257748	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-1.457000	0.02374	-0.577000	0.05967	-0.150000	0.13652	TGC	.	.		0.433	EMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401019.1	NM_001423		A	13366481	C	A	13366481	4	1	335	1	0	0	0	0	0	1	0	0	5103	718	25	3	153	3	EMP1	12	13366481	Nonsense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	1820529	13366481	120485414	120	46671										
IRAK4	51135	hgsc.bcm.edu	37	chr12	44165082	44165083	+	Missense_Mutation	DNP	GG	GG	TT													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ttctgaattactgtttgactGgggcaccacaaattgcacag							TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr12:44165082_44165083GG>TT	ENST00000448290.2	+	3	292_293	c.221_222GG>TT	c.(220-222)tGG>tTT	p.W74F	IRAK4_ENST00000551736.1_Missense_Mutation_p.W74F|IRAK4_ENST00000431837.1_Intron|IRAK4_ENST00000440781.2_Intron	NM_016123.3	NP_057207.2	Q9NWZ3	IRAK4_HUMAN	interleukin-1 receptor-associated kinase 4	74	Death.				cytokine production (GO:0001816)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)					all_cancers(12;0.00149)	Lung NSC(34;0.0804)|all_lung(34;0.181)		GBM - Glioblastoma multiforme(48;0.04)		CTGTTTGACTGGGGCACCACAA	0.371																																					p.W74L|p.W74C		Atlas-SNP	.											.	IRAK4	77	.	0			c.G221T|c.G222T						.																																			SO:0001583	missense	51135	exon3			TTGACTGGGGCAC|TGACTGGGGCACC	AF155118	CCDS8744.1, CCDS44862.1	12q12	2014-09-17				ENSG00000198001			17967	protein-coding gene	gene with protein product		606883				3772297, 10508479	Standard	NM_001114182		Approved	NY-REN-64	uc001rnt.3	Q9NWZ3		Exception_encountered	chr12.hg19:g.44165082_44165083delinsTT	ENSP00000390651:p.Trp74Phe	143.0|142.0	0.0		114.0|115.0	47.0	NM_016123	Q69FE1|Q8TDF7|Q9Y589	Missense_Mutation	SNP	ENST00000448290.2	hg19	CCDS8744.1																																																																																			.	.		0.371	IRAK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403947.1			TT	44165083	GG	TT	44165082	3	4	335	1	0	0	0	0	1	0	0	0	7834	1357	47	3	227	3	IRAK4	12	44165082	Missense_Mutation	DNP	GG	TCGA-RC-A6M6-01A-11D-A32G-10	30798601	44165082	89686813	121	46672										
RAPGEF3	10411	hgsc.bcm.edu	37	chr12	48134734	48134734	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	aagaggctccagtcgtggtcCgtcagctggcctgccaggtc	14	13	1	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr12:48134734C>A	ENST00000449771.2	-	20	2101	c.2013G>T	c.(2011-2013)acG>acT	p.T671T	RAPGEF3_ENST00000171000.4_Silent_p.T629T|RAPGEF3_ENST00000389212.3_Silent_p.T671T|RAPGEF3_ENST00000548919.1_Silent_p.T580T|RAPGEF3_ENST00000549151.1_Silent_p.T629T|RAPGEF3_ENST00000405493.2_Silent_p.T629T|RP1-197B17.3_ENST00000547799.1_lincRNA			O95398	RPGF3_HUMAN	Rap guanine nucleotide exchange factor (GEF) 3	671	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP-mediated signaling (GO:0019933)|cell proliferation (GO:0008283)|cellular response to cAMP (GO:0071320)|energy reserve metabolic process (GO:0006112)|establishment of endothelial barrier (GO:0061028)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cAMP catabolic process (GO:0030822)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of stress fiber assembly (GO:0051496)|Rap protein signal transduction (GO:0032486)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cAMP-dependent protein kinase complex (GO:0005952)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase regulator activity (GO:0008603)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)			endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|skin(7)	25	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.0375)		AGTCGTGGTCCGTCAGCTGGC	0.687																																					p.T671T		Atlas-SNP	.											.	RAPGEF3	98	.	0			c.G2013T						.						35	32	33					12																	48134734		2203	4300	6503	SO:0001819	synonymous_variant	10411	exon20			GTGGTCCGTCAGC	AK092448	CCDS31784.1, CCDS41775.1	12q13.1	2006-04-12	2004-03-26		ENSG00000079337	ENSG00000079337			16629	protein-coding gene	gene with protein product	"exchange protein directly activated by cAMP 1"	606057	"RAP guanine-nucleotide-exchange factor (GEF) 3"			10777494, 9856955	Standard	NM_001098531		Approved	cAMP-GEFI, EPAC, bcm910	uc001rpz.4	O95398	OTTHUMG00000133667	ENST00000449771.2:c.2013G>T	chr12.hg19:g.48134734C>A		79.0	0.0		84.0	4.0	NM_001098531	A8K2G5|E7EQC8|O95634|Q8WVN0	Silent	SNP	ENST00000449771.2	hg19	CCDS41775.1																																																																																			.	.		0.687	RAPGEF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257848.1	NM_006105		A	48134734	C	A	48134734	2	1	335	1	0	0	0	0	0	0	0	1	13060	639	23	1		1	RAPGEF3	12	48134734	Silent	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	3969652	48134734	85717161	122	46673										
STAC3	246329	hgsc.bcm.edu	37	chr12	57640644	57640644	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tttgccatgatcaccccagtGcgcagggtttcaaacacagg	10	12	2	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr12:57640644G>A	ENST00000332782.2	-	6	747	c.546C>T	c.(544-546)cgC>cgT	p.R182R	STAC3_ENST00000546246.2_5'UTR|STAC3_ENST00000554578.1_Silent_p.R143R	NM_145064.1	NP_659501.1	Q96MF2	STAC3_HUMAN	SH3 and cysteine rich domain 3	182					intracellular signal transduction (GO:0035556)|neuromuscular synaptic transmission (GO:0007274)|skeletal muscle contraction (GO:0003009)|skeletal muscle fiber development (GO:0048741)		identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(10)|ovary(2)|skin(1)	18						TCACCCCAGTGCGCAGGGTTT	0.507																																					p.R182R		Atlas-SNP	.											.	STAC3	32	.	0			c.C546T						.						263	211	228					12																	57640644		2203	4300	6503	SO:0001819	synonymous_variant	246329	exon6			CCCAGTGCGCAGG	AK057013	CCDS8936.1, CCDS66405.1, CCDS66406.1	12q13.3	2014-08-12			ENSG00000185482	ENSG00000185482			28423	protein-coding gene	gene with protein product		615521				12477932	Standard	NM_001286257		Approved	MGC2793	uc009zpl.2	Q96MF2	OTTHUMG00000171271	ENST00000332782.2:c.546C>T	chr12.hg19:g.57640644G>A		122.0	0.0		125.0	40.0	NM_145064	B4DUK9|Q96HU5	Silent	SNP	ENST00000332782.2	hg19	CCDS8936.1																																																																																			.	.		0.507	STAC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412724.2	NM_145064		A	57640644	G	A	57640644	2	1	335	1	0	0	0	0	0	0	0	1	15256	1306	46	3		3	STAC3	12	57640644	Silent	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	9505910	57640644	76211251	123	46674										
FAM119B	25895	hgsc.bcm.edu	37	chr12	58166537	58166537	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	cccggcccagatcccgaatcTgagtcggaatcggtgttccc	11	15	1	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr12:58166537T>A	ENST00000300209.8	+	1	155	c.30T>A	c.(28-30)tcT>tcA	p.S10S	RP11-571M6.15_ENST00000471530.1_5'Flank|METTL1_ENST00000324871.7_5'UTR|METTL21B_ENST00000333012.5_Silent_p.S10S|METTL1_ENST00000548681.1_5'Flank|METTL21B_ENST00000548256.1_Intron|AC025165.1_ENST00000582738.1_RNA|METTL21B_ENST00000551420.1_Intron|METTL1_ENST00000257848.7_5'Flank|METTL21B_ENST00000552307.1_3'UTR	NM_015433.2	NP_056248.2	Q96AZ1	MT21B_HUMAN	methyltransferase like 21B	10						cytoplasm (GO:0005737)|intracellular (GO:0005622)	methyltransferase activity (GO:0008168)			endometrium(1)|lung(1)	2						ATCCCGAATCTGAGTCGGAAT	0.662																																					p.S10S		Atlas-SNP	.											.	METTL21B	16	.	0			c.T30A						.						26	26	26					12																	58166537		2201	4299	6500	SO:0001819	synonymous_variant	25895	exon1			CGAATCTGAGTCG	AL050100, AF455816	CCDS8957.1, CCDS31848.1	12q14.1	2011-03-03	2011-03-03	2011-03-03	ENSG00000123427	ENSG00000123427			24936	protein-coding gene	gene with protein product		615258	"family with sequence similarity 119, member B"	FAM119B		12477932	Standard	NM_015433		Approved	DKFZP586D0919	uc001sqg.3	Q96AZ1	OTTHUMG00000170459	ENST00000300209.8:c.30T>A	chr12.hg19:g.58166537T>A		52.0	0.0		73.0	26.0	NM_015433	Q9H749|Q9Y3W2	Silent	SNP	ENST00000300209.8	hg19	CCDS8957.1																																																																																			.	.		0.662	METTL21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409268.1	NM_015433		A	58166537	T	A	58166537	2	1	335	1	0	0	0	0	0	0	0	1	5419	1567	55	4		4	FAM119B	12	58166537	Silent	SNP	T	TCGA-RC-A6M6-01A-11D-A32G-10	525893	58166537	75685358	124	46675										
PTPRR	5801	hgsc.bcm.edu	37	chr12	71054875	71054875	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	acatgttgggtgtggcttccTtgctgaaaatagcaacagcc	11	9	0	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr12:71054875T>G	ENST00000283228.2	-	12	2063	c.1611A>C	c.(1609-1611)caA>caC	p.Q537H	PTPRR_ENST00000440835.2_Missense_Mutation_p.Q292H|PTPRR_ENST00000342084.4_Missense_Mutation_p.Q425H|PTPRR_ENST00000549308.1_Missense_Mutation_p.Q292H|PTPRR_ENST00000537619.2_5'UTR|PTPRR_ENST00000378778.1_Missense_Mutation_p.Q331H	NM_002849.3	NP_002840.2	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R	537	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				ERBB2 signaling pathway (GO:0038128)|in utero embryonic development (GO:0001701)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(2;5.67e-07)|Lung(24;0.00283)|OV - Ovarian serous cystadenocarcinoma(12;0.00578)|LUSC - Lung squamous cell carcinoma(43;0.132)	COAD - Colon adenocarcinoma(1;0.136)		TGTGGCTTCCTTGCTGAAAAT	0.478																																					p.Q537H		Atlas-SNP	.											.	PTPRR	109	.	0			c.A1611C						.						120	79	93					12																	71054875		2203	4300	6503	SO:0001583	missense	5801	exon12			GCTTCCTTGCTGA	D64053	CCDS8998.1, CCDS44945.1, CCDS55847.1, CCDS55848.1	12q15	2011-10-07			ENSG00000153233	ENSG00000153233		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9680	protein-coding gene	gene with protein product		602853		PTPRQ		7557444, 10393441	Standard	NM_002849		Approved	PTPBR7, PTP-SL, EC-PTP, PCPTP1	uc001swi.2	Q15256	OTTHUMG00000169502	ENST00000283228.2:c.1611A>C	chr12.hg19:g.71054875T>G	ENSP00000283228:p.Gln537His	84.0	0.0		62.0	20.0	NM_002849	B2R5Z7|B7Z3J1|F5GXR7|O00342|Q92682|Q9UE65	Missense_Mutation	SNP	ENST00000283228.2	hg19	CCDS8998.1	.	.	.	.	.	.	.	.	.	.	T	13.17	2.158540	0.38119	.	.	ENSG00000153233	ENST00000440835;ENST00000283228;ENST00000378778;ENST00000342084;ENST00000549308	D;D;D;D;D	0.83075	-1.68;-1.68;-1.68;-1.68;-1.68	5.02	3.83	0.44106	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.257379	0.27473	N	0.019209	T	0.72070	0.3415	N	0.11818	0.18	0.47094	D	0.999312	P;P;P	0.38395	0.576;0.576;0.629	B;B;B	0.43990	0.311;0.106;0.438	T	0.66217	-0.5979	10	0.23302	T	0.38	-3.3389	11.1591	0.48505	0.1382:0.0:0.0:0.8618	.	425;331;537	F5GXR7;Q15256-4;Q15256	.;.;PTPRR_HUMAN	H	292;537;331;425;292	ENSP00000391750:Q292H;ENSP00000283228:Q537H;ENSP00000368054:Q331H;ENSP00000339605:Q425H;ENSP00000446943:Q292H	ENSP00000283228:Q537H	Q	-	3	2	PTPRR	69341142	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.014000	0.40951	0.814000	0.34374	0.528000	0.53228	CAA	.	.		0.478	PTPRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404485.1	NM_002849		G	71054875	T	G	71054875	3	3	335	1	0	0	0	0	1	0	0	0	12825	1606	56	5	374	5	PTPRR	12	71054875	Missense_Mutation	SNP	T	TCGA-RC-A6M6-01A-11D-A32G-10	12888338	71054875	62797020	125	46676										
ANKS1B	56899	hgsc.bcm.edu	37	chr12	99640465	99640465	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gagactgcttgaaaggcaaaGgactgtttgccaaactgact	11	8	0	3			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr12:99640465G>C	ENST00000547776.2	-	13	1933	c.1934C>G	c.(1933-1935)cCt>cGt	p.P645R	ANKS1B_ENST00000547010.1_Missense_Mutation_p.P225R|ANKS1B_ENST00000550833.1_5'UTR|ANKS1B_ENST00000329257.7_Missense_Mutation_p.P645R	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	645						cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(15)|lung(38)|pancreas(1)|prostate(2)|skin(1)	70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		GAAAGGCAAAGGACTGTTTGC	0.383																																					p.P645R		Atlas-SNP	.											.	ANKS1B	180	.	0			c.C1934G						.						93	85	87					12																	99640465		1838	4088	5926	SO:0001583	missense	56899	exon13			GGCAAAGGACTGT	AF145204	CCDS55864.1, CCDS55865.1, CCDS55866.1, CCDS55867.1, CCDS55868.1, CCDS55869.1, CCDS55870.1, CCDS55871.1, CCDS55872.1	12q23.1	2013-01-10						"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	24600	protein-coding gene	gene with protein product		607815				10490826, 12415113	Standard	NM_020140		Approved	EB-1, AIDA-1, cajalin-2, ANKS2	uc001tge.2	Q7Z6G8		ENST00000547776.2:c.1934C>G	chr12.hg19:g.99640465G>C	ENSP00000449629:p.Pro645Arg	206.0	0.0		180.0	73.0	NM_152788	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Missense_Mutation	SNP	ENST00000547776.2	hg19	CCDS55872.1	.	.	.	.	.	.	.	.	.	.	G	12.75	2.032079	0.35893	.	.	ENSG00000185046	ENST00000547776;ENST00000547010;ENST00000329257;ENST00000538702	T;T;T	0.61040	0.95;0.14;0.95	5.25	5.25	0.73442	.	0.140861	0.48286	D	0.000197	T	0.36608	0.0973	N	0.12182	0.205	0.80722	D	1	B;B	0.23650	0.012;0.089	B;B	0.21151	0.022;0.033	T	0.21449	-1.0245	9	.	.	.	-8.2951	11.8254	0.52265	0.0814:0.0:0.9186:0.0	.	225;645	Q7Z6G8-6;Q7Z6G8	.;ANS1B_HUMAN	R	645;225;645;224	ENSP00000449629:P645R;ENSP00000448512:P225R;ENSP00000331381:P645R	.	P	-	2	0	ANKS1B	98164596	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.777000	0.62361	2.619000	0.88677	0.462000	0.41574	CCT	.	.		0.383	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140		C	99640465	G	C	99640465	3	2	335	1	0	0	0	0	1	0	0	0	689	1000	35	4	2156	4	ANKS1B	12	99640465	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	28585590	99640465	34211430	126	46677										
NUAK1	9891	hgsc.bcm.edu	37	chr12	106532400	106532400	+	Missense_Mutation	SNP	T	T	G													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ccagccccaagtcggggcggTcccccgccacaggcgcggcg					rs201298691		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr12:106532400T>G	ENST00000261402.2	-	1	1411	c.32A>C	c.(31-33)gAc>gCc	p.D11A		NM_014840.2	NP_055655.1	O60285	NUAK1_HUMAN	NUAK family, SNF1-like kinase, 1	11					cell adhesion (GO:0007155)|cellular response to DNA damage stimulus (GO:0006974)|regulation of cell adhesion (GO:0030155)|regulation of cell proliferation (GO:0042127)|regulation of cellular senescence (GO:2000772)|regulation of myosin-light-chain-phosphatase activity (GO:0035507)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37						GTCGGGGCGGTCCCCCGCCAC	0.771																																					p.D11A		Atlas-SNP	.											.	NUAK1	196	.	0			c.A32C						.						4	5	5					12																	106532400		2004	3866	5870	SO:0001583	missense	9891	exon1			GGGCGGTCCCCCG	AB011109	CCDS31892.1	12q23.3	2005-08-09				ENSG00000074590			14311	protein-coding gene	gene with protein product	"AMP-activated protein kinase family member 5"	608130				12409306, 13679856	Standard	NM_014840		Approved	ARK5, KIAA0537, NuaK1	uc001tlj.1	O60285	OTTHUMG00000169763	ENST00000261402.2:c.32A>C	chr12.hg19:g.106532400T>G	ENSP00000261402:p.Asp11Ala	26.0	0.0		24.0	15.0	NM_014840	A7MD39|Q96KA8	Missense_Mutation	SNP	ENST00000261402.2	hg19	CCDS31892.1	.	.	.	.	.	.	.	.	.	.	T	1.939	-0.444155	0.04604	.	.	ENSG00000074590	ENST00000261402;ENST00000359413	T	0.72394	-0.65	2.76	1.52	0.23074	.	0.497641	0.16531	U	0.210347	T	0.43366	0.1244	N	0.08118	0	0.09310	N	1	B	0.15930	0.015	B	0.06405	0.002	T	0.18808	-1.0325	10	0.30854	T	0.27	.	4.6048	0.12372	0.0:0.1699:0.0:0.8301	.	11	O60285	NUAK1_HUMAN	A	11	ENSP00000261402:D11A	ENSP00000261402:D11A	D	-	2	0	NUAK1	105056530	0.000000	0.05858	0.774000	0.31636	0.236000	0.25371	-0.289000	0.08365	1.154000	0.42482	0.260000	0.18958	GAC	.	.		0.771	NUAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405767.2	NM_014840		G	106532400	T	G	106532400	3	3	335	1	0	0	0	0	1	0	0	0	10721	1667	58	5	1981	5	NUAK1	12	106532400	Missense_Mutation	SNP	T	TCGA-RC-A6M6-01A-11D-A32G-10	6891935	106532400	27319495	127	46678	249	2								
NUAK1	9891	hgsc.bcm.edu	37	chr12	106532406	106532406	+	Missense_Mutation	SNP	G	G	T													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ccaagtcggggcggtcccccGccacaggcgcggcggcccct							TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr12:106532406G>T	ENST00000261402.2	-	1	1405	c.26C>A	c.(25-27)gCg>gAg	p.A9E		NM_014840.2	NP_055655.1	O60285	NUAK1_HUMAN	NUAK family, SNF1-like kinase, 1	9					cell adhesion (GO:0007155)|cellular response to DNA damage stimulus (GO:0006974)|regulation of cell adhesion (GO:0030155)|regulation of cell proliferation (GO:0042127)|regulation of cellular senescence (GO:2000772)|regulation of myosin-light-chain-phosphatase activity (GO:0035507)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37						GCGGTCCCCCGCCACAGGCGC	0.771																																					p.A9E		Atlas-SNP	.											NUAK1_ENST00000261402,NS,carcinoma,0,2	NUAK1	196	.	0			c.C26A						.						3	5	4					12																	106532406		1637	3215	4852	SO:0001583	missense	9891	exon1			TCCCCCGCCACAG	AB011109	CCDS31892.1	12q23.3	2005-08-09				ENSG00000074590			14311	protein-coding gene	gene with protein product	"AMP-activated protein kinase family member 5"	608130				12409306, 13679856	Standard	NM_014840		Approved	ARK5, KIAA0537, NuaK1	uc001tlj.1	O60285	OTTHUMG00000169763	ENST00000261402.2:c.26C>A	chr12.hg19:g.106532406G>T	ENSP00000261402:p.Ala9Glu	23.0	0.0		25.0	17.0	NM_014840	A7MD39|Q96KA8	Missense_Mutation	SNP	ENST00000261402.2	hg19	CCDS31892.1	.	.	.	.	.	.	.	.	.	.	G	12.76	2.035473	0.35893	.	.	ENSG00000074590	ENST00000261402;ENST00000359413	T	0.72725	-0.68	3.75	2.76	0.32466	.	0.298784	0.23608	N	0.046363	T	0.49813	0.1579	N	0.08118	0	0.34977	D	0.753727	P	0.43431	0.807	B	0.42163	0.378	T	0.62186	-0.6907	10	0.40728	T	0.16	.	10.2065	0.43116	0.0:0.2049:0.7951:0.0	.	9	O60285	NUAK1_HUMAN	E	9	ENSP00000261402:A9E	ENSP00000261402:A9E	A	-	2	0	NUAK1	105056536	0.063000	0.20901	0.719000	0.30619	0.503000	0.33858	1.713000	0.37951	1.663000	0.50791	0.313000	0.20887	GCG	.	.		0.771	NUAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405767.2	NM_014840		T	106532406	G	T	106532406	3	4	335	1	0	0	0	0	1	0	0	0	10721	1087	38	1	1987	1	NUAK1	12	106532406	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	6	106532406	27319489	128	46679	249	2								
RIMBP2	23504	hgsc.bcm.edu	37	chr12	130929724	130929724	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ccttcatagaacccatcctcAtccatgtctccatagacgta	4	15	3	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr12:130929724A>T	ENST00000261655.4	-	7	784	c.621T>A	c.(619-621)gaT>gaA	p.D207E	RIMBP2_ENST00000536002.1_Missense_Mutation_p.D115E|RIMBP2_ENST00000535703.1_Missense_Mutation_p.D115E	NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	207	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.				negative regulation of phosphatase activity (GO:0010923)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|synapse (GO:0045202)				NS(2)|breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(33)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	96	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		ACCCATCCTCATCCATGTCTC	0.572																																					p.D207E		Atlas-SNP	.											.	RIMBP2	220	.	0			c.T621A						.						165	147	153					12																	130929724		2203	4300	6503	SO:0001583	missense	23504	exon7			ATCCTCATCCATG	AB002316	CCDS31925.1	12q24.33	2014-06-13				ENSG00000060709			30339	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 133"	611602				10748113	Standard	NM_015347		Approved	KIAA0318, RBP2, MGC15831, RIM-BP2, PPP1R133	uc001uil.2	O15034		ENST00000261655.4:c.621T>A	chr12.hg19:g.130929724A>T	ENSP00000261655:p.Asp207Glu	63.0	0.0		33.0	25.0	NM_015347	Q96ID2	Missense_Mutation	SNP	ENST00000261655.4	hg19	CCDS31925.1	.	.	.	.	.	.	.	.	.	.	A	19.80	3.893886	0.72639	.	.	ENSG00000060709	ENST00000261655;ENST00000392375;ENST00000535703;ENST00000536002	T;T;T	0.34667	1.35;1.35;1.35	3.38	-5.1	0.02911	Src homology-3 domain (3);Variant SH3 (1);	0.000000	0.85682	D	0.000000	T	0.48484	0.1502	L	0.60067	1.865	0.42729	D	0.993702	D;D	0.89917	1.0;0.998	D;D	0.85130	0.997;0.997	T	0.51092	-0.8749	10	0.52906	T	0.07	-26.3678	13.1646	0.59562	0.7814:0.0:0.2186:0.0	.	115;207	O15034-2;O15034	.;RIMB2_HUMAN	E	207;115;115;115	ENSP00000261655:D207E;ENSP00000440347:D115E;ENSP00000439159:D115E	ENSP00000261655:D207E	D	-	3	2	RIMBP2	129495677	0.986000	0.35501	0.931000	0.37212	0.918000	0.54935	0.411000	0.21115	-1.128000	0.02922	-0.366000	0.07423	GAT	.	.		0.572	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399520.1	NM_015347		T	130929724	A	T	130929724	3	4	335	1	0	0	0	0	1	0	0	0	13378	214	8	4	2589	4	RIMBP2	12	130929724	Missense_Mutation	SNP	A	TCGA-RC-A6M6-01A-11D-A32G-10	24397318	130929724	2922171	129	46680										
ZMYM2	7750	hgsc.bcm.edu	37	chr13	20657109	20657109	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	attggaaaaaaaatcctttaAcgatggaaaacaaagcgtgt	8	5	0	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr13:20657109A>G	ENST00000382874.2	+	24	3947	c.3757A>G	c.(3757-3759)Acg>Gcg	p.T1253A	ZMYM2_ENST00000382869.3_Missense_Mutation_p.T1253A|ZMYM2_ENST00000382871.2_Missense_Mutation_p.T1253A|ZMYM2_ENST00000494061.2_3'UTR	NM_001190964.1	NP_001177893.1	Q9UBW7	ZMYM2_HUMAN	zinc finger, MYM-type 2	1253					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|PML body (GO:0016605)	ubiquitin conjugating enzyme binding (GO:0031624)|zinc ion binding (GO:0008270)			large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	10		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)		AAATCCTTTAACGATGGAAAA	0.338																																					p.T1253A		Atlas-SNP	.											.	ZMYM2	191	.	0			c.A3757G						.						85	80	81					13																	20657109		1860	4097	5957	SO:0001583	missense	7750	exon24			CCTTTAACGATGG	AF012126	CCDS45016.1	13q11-q12	2013-01-08	2006-07-13	2006-07-13	ENSG00000121741	ENSG00000121741		"Zinc fingers, MYM type"	12989	protein-coding gene	gene with protein product		602221	"zinc finger protein 198"	ZNF198		9499416, 9425908	Standard	XM_005266517		Approved	RAMP, FIM, MYM	uc001ums.3	Q9UBW7	OTTHUMG00000016507	ENST00000382874.2:c.3757A>G	chr13.hg19:g.20657109A>G	ENSP00000372327:p.Thr1253Ala	249.0	0.0		229.0	100.0	NM_001190964	A6NDG0|A6NI02|O43212|O43434|O60898|Q5W0Q4|Q5W0T3|Q63HP0|Q8NE39|Q9H0V5|Q9H538|Q9UEU2	Missense_Mutation	SNP	ENST00000382874.2	hg19	CCDS45016.1	.	.	.	.	.	.	.	.	.	.	A	15.04	2.714502	0.48622	.	.	ENSG00000121741	ENST00000382869;ENST00000456228;ENST00000382874;ENST00000382871;ENST00000382870	T	0.17691	2.26	5.0	5.0	0.66597	.	0.143070	0.64402	D	0.000007	T	0.12646	0.0307	L	0.29908	0.895	0.80722	D	1	P	0.36909	0.573	B	0.36666	0.23	T	0.05289	-1.0894	10	0.07990	T	0.79	-14.803	14.9966	0.71436	1.0:0.0:0.0:0.0	.	1253	Q9UBW7	ZMYM2_HUMAN	A	1253;1253;1251;1251;631	ENSP00000372322:T1253A	ENSP00000372322:T1253A	T	+	1	0	ZMYM2	19555109	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.150000	0.64869	2.001000	0.58596	0.397000	0.26171	ACG	.	.		0.338	ZMYM2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044051.2	NM_003453		G	20657109	A	G	20657109	3	3	335	1	0	0	0	0	1	0	0	0	17715	43	2	2	3839	2	ZMYM2	13	20657109	Missense_Mutation	SNP	A	TCGA-RC-A6M6-01A-11D-A32G-10		20657109	94512769	130	46681										
CSNK1A1L	122011	hgsc.bcm.edu	37	chr13	37679220	37679220	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gtgtagagtttgctctcataCagcaactgggggtgcttgac	13	8	1	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr13:37679220C>G	ENST00000379800.3	-	1	583	c.174G>C	c.(172-174)ctG>ctC	p.L58L		NM_145203.5	NP_660204.2	Q8N752	KC1AL_HUMAN	casein kinase 1, alpha 1-like	58	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell morphogenesis (GO:0000902)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	37		Lung NSC(96;7.97e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.109)		all cancers(112;3.58e-07)|Epithelial(112;1.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00695)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0407)		TGCTCTCATACAGCAACTGGG	0.522																																					p.L58L		Atlas-SNP	.											.	CSNK1A1L	69	.	0			c.G174C						.						160	135	143					13																	37679220		2203	4300	6503	SO:0001819	synonymous_variant	122011	exon1			CTCATACAGCAAC	BC028723	CCDS9363.1	13q13.2	2008-02-05			ENSG00000180138	ENSG00000180138			20289	protein-coding gene	gene with protein product							Standard	NM_145203		Approved	MGC33182	uc001uwm.1	Q8N752	OTTHUMG00000016748	ENST00000379800.3:c.174G>C	chr13.hg19:g.37679220C>G		54.0	0.0		48.0	18.0	NM_145203	Q5T2N2	Silent	SNP	ENST00000379800.3	hg19	CCDS9363.1																																																																																			.	.		0.522	CSNK1A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044563.1	NM_145203		G	37679220	C	G	37679220	2	3	335	1	0	0	0	0	0	0	0	1	3953	465	17	4		4	CSNK1A1L	13	37679220	Silent	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	17022111	37679220	77490658	131	46682										
EDNRB	1910	hgsc.bcm.edu	37	chr13	78477336	78477336	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ggatgaagcaagcagattcgCagataacttcctttgtagtc	10	8	0	3			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr13:78477336C>G	ENST00000334286.5	-	3	992	c.756G>C	c.(754-756)ctG>ctC	p.L252L	EDNRB_ENST00000446573.1_Silent_p.L252L|EDNRB_ENST00000377211.4_Silent_p.L342L	NM_000115.3|NM_001122659.2	NP_000106.1|NP_001116131.1	P24530	EDNRB_HUMAN	endothelin receptor type B	252					aging (GO:0007568)|cell surface receptor signaling pathway (GO:0007166)|cellular response to lipopolysaccharide (GO:0071222)|cGMP-mediated signaling (GO:0019934)|endothelin receptor signaling pathway (GO:0086100)|enteric nervous system development (GO:0048484)|enteric smooth muscle cell differentiation (GO:0035645)|epithelial fluid transport (GO:0042045)|macrophage chemotaxis (GO:0048246)|melanocyte differentiation (GO:0030318)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of neuron maturation (GO:0014043)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|peripheral nervous system development (GO:0007422)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of penile erection (GO:0060406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|posterior midgut development (GO:0007497)|regulation of blood pressure (GO:0008217)|regulation of epithelial cell proliferation (GO:0050678)|regulation of fever generation (GO:0031620)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|response to organic cyclic compound (GO:0014070)|response to pain (GO:0048265)|sensory perception of pain (GO:0019233)|vasoconstriction (GO:0042310)|vasodilation (GO:0042311)|vein smooth muscle contraction (GO:0014826)	integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)	endothelin receptor activity (GO:0004962)|peptide hormone binding (GO:0017046)			breast(2)|endometrium(2)|kidney(1)|large_intestine(18)|lung(16)|skin(3)	42		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0933)	Bosentan(DB00559)|MACITENTAN(DB08932)|Sitaxentan(DB06268)	AGCAGATTCGCAGATAACTTC	0.383																																					p.L342L		Atlas-SNP	.											.	EDNRB	172	.	0			c.G1026C						.						150	151	151					13																	78477336		2203	4300	6503	SO:0001819	synonymous_variant	1910	exon4			GATTCGCAGATAA	L06623	CCDS9461.1, CCDS55902.1	13q22	2012-08-08			ENSG00000136160	ENSG00000136160		"GPCR / Class A : Endothelin receptors"	3180	protein-coding gene	gene with protein product		131244		HSCR2, HSCR		1659806, 9556633	Standard	NM_000115		Approved	ETB	uc001vkp.1	P24530	OTTHUMG00000017111	ENST00000334286.5:c.756G>C	chr13.hg19:g.78477336C>G		130.0	0.0		87.0	26.0	NM_001201397	A2A2Z8|A8K3T4|O15343|Q59GB1|Q5W0G9|Q8NHM6|Q8NHM7|Q8NHM8|Q8NHM9|Q9UD23|Q9UQK3	Silent	SNP	ENST00000334286.5	hg19	CCDS9461.1																																																																																			.	.		0.383	EDNRB-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276505.1			G	78477336	C	G	78477336	2	3	335	1	0	0	0	0	0	0	0	1	4922	697	25	4		4	EDNRB	13	78477336	Silent	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	40798116	78477336	36692542	132	46683										
OR4Q3	441669	hgsc.bcm.edu	37	chr14	20215690	20215690	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	cttactatttttgtttttttAcattgctattgtcctgggaa	6	6	0	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr14:20215690A>C	ENST00000331723.1	+	1	104	c.104A>C	c.(103-105)tAc>tCc	p.Y35S		NM_172194.1	NP_751944.1	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q, member 3	35						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(4)|endometrium(3)|kidney(2)|large_intestine(1)|lung(28)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	47	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TTGTTTTTTTACATTGCTATT	0.378																																					p.Y35S		Atlas-SNP	.											OR4Q3,NS,carcinoma,0,1	OR4Q3	117	.	0			c.A104C						.						169	173	172					14																	20215690		2203	4300	6503	SO:0001583	missense	441669	exon1			TTTTTTACATTGC	AF179768	CCDS32020.1	14p13	2012-08-09				ENSG00000182652		"GPCR / Class A : Olfactory receptors"	15426	protein-coding gene	gene with protein product				OR4Q4			Standard	NM_172194		Approved	C14orf13	uc010tkt.2	Q8NH05		ENST00000331723.1:c.104A>C	chr14.hg19:g.20215690A>C	ENSP00000330049:p.Tyr35Ser	348.0	0.0		311.0	63.0	NM_172194	Q6IEX4	Missense_Mutation	SNP	ENST00000331723.1	hg19	CCDS32020.1	.	.	.	.	.	.	.	.	.	.	.	15.54	2.862966	0.51482	.	.	ENSG00000182652	ENST00000331723	T	0.04654	3.58	4.32	3.09	0.35607	.	0.000000	0.36591	U	0.002508	T	0.29355	0.0731	H	0.97265	3.97	0.32490	N	0.540313	D	0.89917	1.0	D	0.74674	0.984	T	0.53294	-0.8459	10	0.87932	D	0	.	8.4189	0.32687	0.8259:0.0:0.0:0.1741	.	35	Q8NH05	OR4Q3_HUMAN	S	35	ENSP00000330049:Y35S	ENSP00000330049:Y35S	Y	+	2	0	OR4Q3	19285530	0.740000	0.28207	0.136000	0.22124	0.867000	0.49689	1.606000	0.36826	1.814000	0.52955	0.416000	0.27883	TAC	.	.		0.378	OR4Q3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409818.2			C	20215690	A	C	20215690	3	2	335	1	0	0	0	0	1	0	0	0	11090	391	14	5	106	5	OR4Q3	14	20215690	Missense_Mutation	SNP	A	TCGA-RC-A6M6-01A-11D-A32G-10		20215690	87133850	133	46684										
OR4Q3	441669	hgsc.bcm.edu	37	chr14	20216358	20216358	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tcttcgtgccatgcgtattcAtctatttgaggcctttctgc	8	11	4	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr14:20216358A>T	ENST00000331723.1	+	1	772	c.772A>T	c.(772-774)Atc>Ttc	p.I258F		NM_172194.1	NP_751944.1	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q, member 3	258						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(4)|endometrium(3)|kidney(2)|large_intestine(1)|lung(28)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	47	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		ATGCGTATTCATCTATTTGAG	0.478																																					p.I258F		Atlas-SNP	.											.	OR4Q3	117	.	0			c.A772T						.						174	175	174					14																	20216358		2203	4300	6503	SO:0001583	missense	441669	exon1			GTATTCATCTATT	AF179768	CCDS32020.1	14p13	2012-08-09				ENSG00000182652		"GPCR / Class A : Olfactory receptors"	15426	protein-coding gene	gene with protein product				OR4Q4			Standard	NM_172194		Approved	C14orf13	uc010tkt.2	Q8NH05		ENST00000331723.1:c.772A>T	chr14.hg19:g.20216358A>T	ENSP00000330049:p.Ile258Phe	189.0	0.0		164.0	19.0	NM_172194	Q6IEX4	Missense_Mutation	SNP	ENST00000331723.1	hg19	CCDS32020.1	.	.	.	.	.	.	.	.	.	.	.	13.40	2.225277	0.39300	.	.	ENSG00000182652	ENST00000331723	T	0.00158	8.65	4.37	1.83	0.25207	GPCR, rhodopsin-like superfamily (1);	0.368833	0.19196	U	0.120319	T	0.00328	0.0010	M	0.84683	2.71	0.31834	N	0.624428	P	0.41420	0.749	P	0.51550	0.673	T	0.18053	-1.0349	10	0.66056	D	0.02	.	5.6496	0.17608	0.7335:0.1704:0.0961:0.0	.	258	Q8NH05	OR4Q3_HUMAN	F	258	ENSP00000330049:I258F	ENSP00000330049:I258F	I	+	1	0	OR4Q3	19286198	0.000000	0.05858	1.000000	0.80357	0.476000	0.33039	0.382000	0.20635	0.718000	0.32166	0.416000	0.27883	ATC	.	.		0.478	OR4Q3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409818.2			T	20216358	A	T	20216358	3	4	335	1	0	0	0	0	1	0	0	0	11090	217	8	4	774	4	OR4Q3	14	20216358	Missense_Mutation	SNP	A	TCGA-RC-A6M6-01A-11D-A32G-10	668	20216358	87133182	134	46685										
APEX1	328	hgsc.bcm.edu	37	chr14	20925548	20925548	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ctcgatccaagaatgttggtTggcgccttgattactttttg	10	8	0	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr14:20925548T>A	ENST00000216714.3	+	5	1106	c.838T>A	c.(838-840)Tgg>Agg	p.W280R	OSGEP_ENST00000556252.1_5'Flank|APEX1_ENST00000557054.1_3'UTR|OSGEP_ENST00000206542.4_5'Flank|APEX1_ENST00000398030.4_Missense_Mutation_p.W280R|APEX1_ENST00000555414.1_Missense_Mutation_p.W280R	NM_001244249.1|NM_001641.3	NP_001231178.1|NP_001632.2	P27695	APEX1_HUMAN	APEX nuclease (multifunctional DNA repair enzyme) 1	280					aging (GO:0007568)|base-excision repair (GO:0006284)|cell redox homeostasis (GO:0045454)|cellular response to cAMP (GO:0071320)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to peptide hormone stimulus (GO:0071375)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA demethylation (GO:0080111)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|negative regulation of smooth muscle cell migration (GO:0014912)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|oxidation-reduction process (GO:0055114)|positive regulation of DNA repair (GO:0045739)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribosome (GO:0005840)|transcription factor complex (GO:0005667)	3'-5' exonuclease activity (GO:0008408)|chromatin DNA binding (GO:0031490)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008311)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|phosphodiesterase I activity (GO:0004528)|phosphoric diester hydrolase activity (GO:0008081)|poly(A) RNA binding (GO:0044822)|RNA-DNA hybrid ribonuclease activity (GO:0004523)|site-specific endodeoxyribonuclease activity, specific for altered base (GO:0016890)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|uracil DNA N-glycosylase activity (GO:0004844)			breast(2)|endometrium(1)|large_intestine(4)|ovary(2)	9	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;1.09e-07)|all cancers(55;1.19e-06)	GBM - Glioblastoma multiforme(265;0.0224)|READ - Rectum adenocarcinoma(17;0.193)	Lucanthone(DB04967)	GAATGTTGGTTGGCGCCTTGA	0.493								Other BER factors																													p.W280R		Atlas-SNP	.											.	APEX1	23	.	0			c.T838A						.						251	216	228					14																	20925548		2203	4300	6503	SO:0001583	missense	328	exon5			GTTGGTTGGCGCC	X59764	CCDS9550.1	14q11.2	2008-02-05	2002-09-11	2002-09-13	ENSG00000100823	ENSG00000100823	4.2.99.18		587	protein-coding gene	gene with protein product		107748	"APEX nuclease (multifunctional DNA repair enzyme)"	APEX			Standard	NM_001641		Approved	APE, REF1, HAP1, APX, APEN, REF-1, APE-1	uc021rnr.1	P27695	OTTHUMG00000029544	ENST00000216714.3:c.838T>A	chr14.hg19:g.20925548T>A	ENSP00000216714:p.Trp280Arg	175.0	0.0		156.0	52.0	NM_080648	Q969L5|Q99775	Missense_Mutation	SNP	ENST00000216714.3	hg19	CCDS9550.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.036268	0.75617	.	.	ENSG00000100823	ENST00000555414;ENST00000216714;ENST00000398030;ENST00000557054	T;T;T	0.64438	-0.1;-0.1;-0.1	6.06	6.06	0.98353	Endonuclease/exonuclease/phosphatase (2);AP endonuclease, family 1, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.82495	0.5049	M	0.88640	2.97	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85810	0.1379	10	0.87932	D	0	.	15.5919	0.76537	0.0:0.0:0.0:1.0	.	280	P27695	APEX1_HUMAN	R	280;280;280;11	ENSP00000451979:W280R;ENSP00000216714:W280R;ENSP00000381111:W280R	ENSP00000216714:W280R	W	+	1	0	APEX1	19995388	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.610000	0.82949	2.324000	0.78689	0.533000	0.62120	TGG	.	.		0.493	APEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073641.3	NM_001641		A	20925548	T	A	20925548	3	1	335	1	0	0	0	0	1	0	0	0	769	1812	63	4	852	4	APEX1	14	20925548	Missense_Mutation	SNP	T	TCGA-RC-A6M6-01A-11D-A32G-10	709190	20925548	86423992	135	46686										
RIPK3	11035	hgsc.bcm.edu	37	chr14	24807239	24807239	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tcgtacacgagtgatggttcGgttggcactggagtagggga	17	6	0	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr14:24807239G>T	ENST00000216274.5	-	6	890	c.672C>A	c.(670-672)acC>acA	p.T224T	RIPK3_ENST00000554338.1_5'Flank|RP11-934B9.3_ENST00000555591.1_5'Flank|ADCY4_ENST00000558563.1_5'Flank|ADCY4_ENST00000310677.4_5'Flank|ADCY4_ENST00000554068.2_5'Flank	NM_006871.3	NP_006862.2	Q9Y572	RIPK3_HUMAN	receptor-interacting serine-threonine kinase 3	224	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|amyloid fibril formation (GO:1990000)|apoptotic signaling pathway (GO:0097190)|cellular protein modification process (GO:0006464)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|lymph node development (GO:0048535)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of ligase activity (GO:0051351)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phosphatase activity (GO:0010922)|positive regulation of protein deacetylation (GO:0090312)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of type I interferon production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of activated T cell proliferation (GO:0046006)|regulation of activation-induced cell death of T cells (GO:0070235)|regulation of adaptive immune response (GO:0002819)|regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation (GO:2000452)|regulation of interferon-gamma production (GO:0032649)|regulation of T cell mediated cytotoxicity (GO:0001914)|signal transduction (GO:0007165)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|NF-kappaB-inducing kinase activity (GO:0004704)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				GBM - Glioblastoma multiforme(265;0.0181)		GTGATGGTTCGGTTGGCACTG	0.552																																					p.T224T	Pancreas(58;918 1191 4668 13304 15331)	Atlas-SNP	.											.	RIPK3	43	.	0			c.C672A						.						75	70	72					14																	24807239		2203	4300	6503	SO:0001819	synonymous_variant	11035	exon6			TGGTTCGGTTGGC	AF156884	CCDS9628.1	14q12	2006-05-15			ENSG00000129465	ENSG00000129465			10021	protein-coding gene	gene with protein product		605817				10339433, 10358032	Standard	NM_006871		Approved	RIP3	uc001wpb.3	Q9Y572	OTTHUMG00000029349	ENST00000216274.5:c.672C>A	chr14.hg19:g.24807239G>T		77.0	0.0		80.0	36.0	NM_006871	B4DJL9|C4AM87|Q5J795|Q5J796|Q6P5Y1	Silent	SNP	ENST00000216274.5	hg19	CCDS9628.1																																																																																			.	.		0.552	RIPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073203.4	NM_006871		T	24807239	G	T	24807239	2	4	335	1	0	0	0	0	0	0	0	1	13397	1103	39	1		1	RIPK3	14	24807239	Silent	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	3881691	24807239	82542301	136	46687										
JKAMP	51528	hgsc.bcm.edu	37	chr14	59961929	59961929	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	cagtacactgtactcatgaaGccgtctacccactgtaagtg	8	12	2	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr14:59961929G>T	ENST00000261247.9	+	4	592	c.445G>T	c.(445-447)Gcc>Tcc	p.A149S	JKAMP_ENST00000556985.1_Missense_Mutation_p.A149S|JKAMP_ENST00000554271.1_Missense_Mutation_p.A163S|JKAMP_ENST00000356057.5_Missense_Mutation_p.A157S|RP11-701B16.2_ENST00000554253.1_RNA|JKAMP_ENST00000425728.2_Missense_Mutation_p.A143S	NM_001098625.1|NM_001284203.1|NM_016475.3	NP_001092095.1|NP_001271132.1|NP_057559.2	Q9P055	JKAMP_HUMAN	JNK1/MAPK8-associated membrane protein	164				N -> S (in Ref. 2; AAF36133). {ECO:0000305}.	ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(1)|kidney(1)|lung(3)	6						TACTCATGAAGCCGTCTACCC	0.363																																					p.A149S		Atlas-SNP	.											.	JKAMP	49	.	0			c.G445T						.						158	139	145					14																	59961929		1891	4118	6009	SO:0001583	missense	51528	exon4			CATGAAGCCGTCT	AF212245	CCDS45116.1, CCDS45117.1, CCDS61462.1, CCDS61463.1	14q22.3	2014-02-14	2009-08-13	2009-08-13	ENSG00000050130	ENSG00000050130			20184	protein-coding gene	gene with protein product	"Jun N-terminal kinase 1-associated membrane protein"	611176	"chromosome 14 open reading frame 100"	C14orf100		16166642, 19269966	Standard	NM_001284202		Approved	HSPC213, JAMP, HSPC327, CDA06	uc001xef.4	Q9P055	OTTHUMG00000171054	ENST00000261247.9:c.445G>T	chr14.hg19:g.59961929G>T	ENSP00000261247:p.Ala149Ser	211.0	0.0		190.0	69.0	NM_016475	B4DP67|Q6FIB6|Q6IAJ2|Q7Z5D4|Q86SY6|Q9H0Q6|Q9H2W0|Q9HAH5|Q9P0R3	Missense_Mutation	SNP	ENST00000261247.9	hg19	CCDS45116.1	.	.	.	.	.	.	.	.	.	.	G	32	5.106693	0.94292	.	.	ENSG00000050130	ENST00000261247;ENST00000425728;ENST00000556985;ENST00000554271;ENST00000554795;ENST00000356057	.	.	.	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	D	0.83658	0.5302	M	0.81112	2.525	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.999;0.999;0.999;0.999	D;D;D;D;D	0.85130	0.997;0.994;0.994;0.994;0.994	D	0.85237	0.1036	9	0.87932	D	0	-45.1741	19.6948	0.96021	0.0:0.0:1.0:0.0	.	164;163;143;157;149	Q9P055;G3V2M4;Q9P055-3;Q9P055-5;Q9P055-4	JKAMP_HUMAN;.;.;.;.	S	149;143;149;163;157;157	.	ENSP00000261247:A149S	A	+	1	0	JKAMP	59031682	1.000000	0.71417	1.000000	0.80357	0.832000	0.47134	9.710000	0.98732	2.723000	0.93209	0.655000	0.94253	GCC	.	.		0.363	JKAMP-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411430.1	NM_001098625		T	59961929	G	T	59961929	3	4	335	1	0	0	0	0	1	0	0	0	7958	971	34	3	459	3	JKAMP	14	59961929	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	35154690	59961929	47387611	137	46688										
BCL11B	64919	hgsc.bcm.edu	37	chr14	99640967	99640967	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ctcggacgacgtggcgaaggGcgactgtcgtgcgtccgtga	17	11	0	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr14:99640967G>T	ENST00000357195.3	-	4	2215	c.2206C>A	c.(2206-2208)Ccc>Acc	p.P736T	BCL11B_ENST00000345514.2_Missense_Mutation_p.P665T|BCL11B_ENST00000443726.2_Missense_Mutation_p.P542T	NM_001282237.1|NM_138576.2	NP_001269166.1|NP_612808.1	Q9C0K0	BC11B_HUMAN	B-cell CLL/lymphoma 11B (zinc finger protein)	736					alpha-beta T cell differentiation (GO:0046632)|epithelial cell morphogenesis (GO:0003382)|keratinocyte development (GO:0003334)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|odontogenesis of dentin-containing tooth (GO:0042475)|olfactory bulb axon guidance (GO:0071678)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive T cell selection (GO:0043368)|post-embryonic camera-type eye development (GO:0031077)|regulation of keratinocyte proliferation (GO:0010837)|regulation of lipid metabolic process (GO:0019216)|regulation of neuron differentiation (GO:0045664)|striatal medium spiny neuron differentiation (GO:0021773)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|thymus development (GO:0048538)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(3)|breast(1)|central_nervous_system(9)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(9)|prostate(2)|skin(2)	34		Melanoma(154;0.0866)|all_epithelial(191;0.241)		COAD - Colon adenocarcinoma(157;0.103)		GTGGCGAAGGGCGACTGTCGT	0.706			T	TLX3	T-ALL																																p.P736T		Atlas-SNP	.		Dom	yes		14	14q32.1	64919	B-cell CLL/lymphoma 11B  (CTIP2)		L	.	BCL11B	108	.	0			c.C2206A						.						17	15	16					14																	99640967		2189	4287	6476	SO:0001583	missense	64919	exon4			CGAAGGGCGACTG	AJ404614	CCDS9949.1, CCDS9950.1	14q32	2013-01-08			ENSG00000127152	ENSG00000127152		"Zinc fingers, C2H2-type"	13222	protein-coding gene	gene with protein product		606558		ZNF856B		11719382, 16950772	Standard	NM_138576		Approved	CTIP-2, CTIP2, hRIT1-alpha	uc001yga.3	Q9C0K0	OTTHUMG00000028967	ENST00000357195.3:c.2206C>A	chr14.hg19:g.99640967G>T	ENSP00000349723:p.Pro736Thr	14.0	0.0		33.0	14.0	NM_138576	Q9H162	Missense_Mutation	SNP	ENST00000357195.3	hg19	CCDS9950.1	.	.	.	.	.	.	.	.	.	.	G	20.0	3.930812	0.73327	.	.	ENSG00000127152	ENST00000357195;ENST00000345514;ENST00000443726	T;T;T	0.14766	2.48;2.56;2.5	4.07	4.07	0.47477	.	0.000000	0.56097	D	0.000024	T	0.35998	0.0951	M	0.68952	2.095	0.80722	D	1	D;B	0.89917	1.0;0.022	D;B	0.97110	1.0;0.002	T	0.18524	-1.0334	10	0.51188	T	0.08	-11.0253	16.6199	0.84927	0.0:0.0:1.0:0.0	.	665;736	Q9C0K0-2;Q9C0K0	.;BC11B_HUMAN	T	736;665;542	ENSP00000349723:P736T;ENSP00000280435:P665T;ENSP00000387419:P542T	ENSP00000280435:P665T	P	-	1	0	BCL11B	98710720	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.498000	0.90492	1.975000	0.57531	0.561000	0.74099	CCC	.	.		0.706	BCL11B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000072332.2	NM_138576		T	99640967	G	T	99640967	3	4	335	1	0	0	0	0	1	0	0	0	1364	1203	42	3	482	3	BCL11B	14	99640967	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	39679038	99640967	7708573	138	46689										
CYFIP1	23191	hgsc.bcm.edu	37	chr15	22947043	22947043	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tgaagagtacgagcgtgccaCgcgctacaactacaccagcg	11	13	0	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr15:22947043C>T	ENST00000313077.7	+	13	1441	c.1316C>T	c.(1315-1317)aCg>aTg	p.T439M	CYFIP1_ENST00000560848.1_Missense_Mutation_p.T439M	NM_014608.2	NP_055423.1			cytoplasmic FMR1 interacting protein 1											endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(1)|lung(14)|ovary(4)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	40		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.22e-06)|Epithelial(43;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00101)		GAGCGTGCCACGCGCTACAAC	0.577																																					p.T439M		Atlas-SNP	.											CYFIP1,NS,carcinoma,0,1	CYFIP1	159	.	0			c.C1316T						.						147	123	131					15																	22947043		2203	4300	6503	SO:0001583	missense	23191	exon13			GTGCCACGCGCTA	D38549	CCDS73695.1, CCDS73696.1	15q11	2008-07-18			ENSG00000068793	ENSG00000273749			13759	protein-coding gene	gene with protein product	"selective hybridizing clone", "cytoplasmic FMRP interacting protein 1"	606322				11438699	Standard	XM_005272543		Approved	KIAA0068, P140SRA-1, SHYC	uc001yus.3	Q7L576	OTTHUMG00000129100	ENST00000313077.7:c.1316C>T	chr15.hg19:g.22947043C>T	ENSP00000324549:p.Thr439Met	63.0	0.0		58.0	3.0	NM_014608		Missense_Mutation	SNP	ENST00000313077.7	hg19	CCDS10009.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.522217	0.85600	.	.	ENSG00000068793	ENST00000313077;ENST00000412127	T	0.22743	1.94	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.53318	0.1789	M	0.85710	2.77	0.80722	D	1	D;D	0.89917	1.0;0.97	D;P	0.87578	0.998;0.768	T	0.59337	-0.7473	10	0.72032	D	0.01	-28.2339	18.3595	0.90370	0.0:1.0:0.0:0.0	.	467;439	E7EQ04;Q7L576	.;CYFP1_HUMAN	M	439;467	ENSP00000324549:T439M	ENSP00000324549:T439M	T	+	2	0	CYFIP1	20498484	1.000000	0.71417	0.960000	0.40013	0.484000	0.33280	7.610000	0.82949	2.575000	0.86900	0.655000	0.94253	ACG	.	.		0.577	CYFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251136.2	NM_014608		T	22947043	C	T	22947043	3	4	335	1	0	0	0	0	1	0	0	0	4139	536	19	1	1362	1	CYFIP1	15	22947043	Missense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10		22947043	79584349	139	46690										
CCDC33	80125	hgsc.bcm.edu	37	chr15	74560789	74560789	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ctacatcggctgcaaccacaTggctctggaggtaccagggc	12	13	1	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr15:74560789T>C	ENST00000398814.3	+	5	967	c.536T>C	c.(535-537)aTg>aCg	p.M179T	CCDC33_ENST00000321288.5_Missense_Mutation_p.M382T	NM_025055.3	NP_079331.3	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33	382										breast(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						TGCAACCACATGGCTCTGGAG	0.622																																					p.M179T		Atlas-SNP	.											.	CCDC33	160	.	0			c.T536C						.						38	44	42					15																	74560789		1920	4139	6059	SO:0001583	missense	80125	exon5			ACCACATGGCTCT	BC025689	CCDS42058.1, CCDS42059.1, CCDS73753.1	15q24.1	2009-08-06				ENSG00000140481			26552	protein-coding gene	gene with protein product	"cancer/testis antigen 61"					12477932	Standard	NM_025055		Approved	FLJ32855, CT61	uc002axo.4	Q8N5R6		ENST00000398814.3:c.536T>C	chr15.hg19:g.74560789T>C	ENSP00000381795:p.Met179Thr	32.0	0.0		25.0	6.0	NM_025055	A8K3U4|A8MPQ6|A8MV61|A8MVU9|B3KQ49|Q8TAX6|Q9H5Q6	Missense_Mutation	SNP	ENST00000398814.3	hg19	CCDS42058.1	.	.	.	.	.	.	.	.	.	.	T	0.005	-2.192316	0.00302	.	.	ENSG00000140481	ENST00000321288;ENST00000398814	T;T	0.20332	2.08;2.43	4.69	2.75	0.32379	.	0.596788	0.14684	N	0.304556	T	0.04048	0.0113	N	0.00138	-2.015	0.20196	N	0.999923	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39418	-0.9615	10	0.21014	T	0.42	.	6.4392	0.21841	0.0:0.7136:0.1844:0.1021	.	382;179	C9JFX2;Q8N5R6-6	.;.	T	382;179	ENSP00000325012:M382T;ENSP00000381795:M179T	ENSP00000325012:M382T	M	+	2	0	CCDC33	72347842	0.908000	0.30866	0.790000	0.31976	0.116000	0.19942	1.639000	0.37176	0.396000	0.25283	-0.300000	0.09419	ATG	.	.		0.622	CCDC33-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419491.2	NM_182791		C	74560789	T	C	74560789	3	2	335	1	0	0	0	0	1	0	0	0	2808	1464	51	2	554	2	CCDC33	15	74560789	Missense_Mutation	SNP	T	TCGA-RC-A6M6-01A-11D-A32G-10	51613746	74560789	27970603	140	46691										
SIN3A	25942	hgsc.bcm.edu	37	chr15	75705361	75705361	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tttgaatagctgggacacacGactaatcactcctggggtgt	11	9	1	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr15:75705361G>A	ENST00000394947.3	-	5	813	c.499C>T	c.(499-501)Cgt>Tgt	p.R167C	SIN3A_ENST00000394949.4_Missense_Mutation_p.R167C|SIN3A_ENST00000360439.4_Missense_Mutation_p.R167C	NM_001145358.1	NP_001138830.1			SIN3 transcription regulator family member A											breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	63						TGGGACACACGACTAATCACT	0.408																																					p.R167C		Atlas-SNP	.											.	SIN3A	152	.	0			c.C499T						.						97	92	94					15																	75705361		2197	4294	6491	SO:0001583	missense	25942	exon5			ACACACGACTAAT	AK027559	CCDS10279.1	15q22.33	2013-08-21	2013-08-21		ENSG00000169375	ENSG00000169375			19353	protein-coding gene	gene with protein product		607776	"SIN3 homolog A, transcription regulator (yeast)", "SIN3 transcription regulator homolog A (yeast)"			10773092, 7601471	Standard	NM_001145357		Approved	KIAA0700, DKFZP434K2235	uc002bai.3	Q96ST3	OTTHUMG00000142834	ENST00000394947.3:c.499C>T	chr15.hg19:g.75705361G>A	ENSP00000378402:p.Arg167Cys	108.0	0.0		123.0	41.0	NM_001145358		Missense_Mutation	SNP	ENST00000394947.3	hg19	CCDS10279.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.813041	0.90707	.	.	ENSG00000169375	ENST00000394947;ENST00000394949;ENST00000360439	T;T;T	0.62941	-0.01;-0.01;-0.01	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	D	0.87569	0.6210	H	0.97491	4.015	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90993	0.4836	10	0.87932	D	0	-15.5025	19.5674	0.95401	0.0:0.0:1.0:0.0	.	167	Q96ST3	SIN3A_HUMAN	C	167	ENSP00000378402:R167C;ENSP00000378403:R167C;ENSP00000353622:R167C	ENSP00000353622:R167C	R	-	1	0	SIN3A	73492414	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.809000	0.62591	2.873000	0.98535	0.561000	0.74099	CGT	.	.		0.408	SIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286469.1	NM_015477		A	75705361	G	A	75705361	3	1	335	1	0	0	0	0	1	0	0	0	14340	1058	37	1	3390	1	SIN3A	15	75705361	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	1144572	75705361	26826031	141	46692										
PIGQ	9091	hgsc.bcm.edu	37	chr16	625870	625870	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tctggcccctgtccttcctcGggagcaaactctccacgtgc	9	17	2	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr16:625870G>A	ENST00000026218.5	+	3	809	c.721G>A	c.(721-723)Ggg>Agg	p.G241R	PIGQ_ENST00000470411.2_Missense_Mutation_p.G241R|PIGQ_ENST00000409527.2_Missense_Mutation_p.G241R|PIGQ_ENST00000321878.5_Missense_Mutation_p.G241R	NM_148920.2	NP_683721.1	Q9BRB3	PIGQ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Q	241	Leu-rich.				C-terminal protein lipidation (GO:0006501)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)	phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13		Hepatocellular(780;0.00335)				GTCCTTCCTCGGGAGCAAACT	0.617																																					p.G241R		Atlas-SNP	.											.	PIGQ	43	.	0			c.G721A						.						85	73	77					16																	625870		2186	4290	6476	SO:0001583	missense	9091	exon3			TTCCTCGGGAGCA	AB003723	CCDS10411.1, CCDS10412.1	16p13.3	2013-03-28	2006-06-28		ENSG00000007541	ENSG00000007541		"Phosphatidylinositol glycan anchor biosynthesis"	14135	protein-coding gene	gene with protein product		605754	"phosphatidylinositol glycan, class Q"			9463366, 9729469	Standard	NM_004204		Approved	hGPI1, GPI1	uc002cho.3	Q9BRB3	OTTHUMG00000168047	ENST00000026218.5:c.721G>A	chr16.hg19:g.625870G>A	ENSP00000026218:p.Gly241Arg	33.0	0.0		18.0	14.0	NM_148920	A2IDE1|D3DU52|O14927|Q96G00|Q96S22|Q9UJH4	Missense_Mutation	SNP	ENST00000026218.5	hg19	CCDS10411.1	.	.	.	.	.	.	.	.	.	.	G	4.288	0.052620	0.08291	.	.	ENSG00000007541	ENST00000409527;ENST00000409439;ENST00000422307;ENST00000321878;ENST00000026218;ENST00000470411	T;T;T;T;T;T	0.41065	1.01;1.03;1.03;1.01;2.28;1.02	4.88	0.087	0.14448	.	0.637390	0.17677	N	0.165753	T	0.13030	0.0316	N	0.01352	-0.895	0.09310	N	1	B;B;B;B	0.21309	0.018;0.03;0.004;0.054	B;B;B;B	0.14578	0.004;0.005;0.004;0.011	T	0.19943	-1.0290	10	0.34782	T	0.22	0.2096	5.6045	0.17371	0.2336:0.0:0.3524:0.414	.	255;241;241;241	E7ERP4;Q9BRB3;Q9BRB3-2;Q9BRB3-3	.;PIGQ_HUMAN;.;.	R	241	ENSP00000386760:G241R;ENSP00000386554:G241R;ENSP00000413753:G241R;ENSP00000326674:G241R;ENSP00000026218:G241R;ENSP00000439650:G241R	ENSP00000026218:G241R	G	+	1	0	PIGQ	565871	0.997000	0.39634	0.000000	0.03702	0.434000	0.31775	2.798000	0.47884	-0.165000	0.10908	0.591000	0.81541	GGG	.	.		0.617	PIGQ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000239270.2	NM_004204		A	625870	G	A	625870	3	1	335	1	0	0	0	0	1	0	0	0	11905	1116	39	1	727	1	PIGQ	16	625870	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10		625870	89728883	142	46693										
PTX4	390667	hgsc.bcm.edu	37	chr16	1537527	1537527	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ggtcgggcccagctcctcagGctgggttggggttgggacca	18	11	1	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr16:1537527G>T	ENST00000447419.2	-	2	611	c.586C>A	c.(586-588)Cct>Act	p.P196T	PTX4_ENST00000293922.1_Missense_Mutation_p.P191T|PTX4_ENST00000440447.2_Intron			Q96A99	PTX4_HUMAN	pentraxin 4, long	196						extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						AGCTCCTCAGGCTGGGTTGGG	0.736																																					p.P191T		Atlas-SNP	.											.	PTX4	46	.	0			c.C571A						.						10	12	11					16																	1537527		2177	4253	6430	SO:0001583	missense	390667	exon2			CCTCAGGCTGGGT		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"chromosome 16 open reading frame 38"	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.586C>A	chr16.hg19:g.1537527G>T	ENSP00000445277:p.Pro196Thr	71.0	0.0		55.0	34.0	NM_001013658		Missense_Mutation	SNP	ENST00000447419.2	hg19		.	.	.	.	.	.	.	.	.	.	G	11.15	1.552971	0.27739	.	.	ENSG00000251692	ENST00000447419;ENST00000293922	T;T	0.05319	3.62;3.46	4.92	1.9	0.25705	.	1.497440	0.04395	N	0.363053	T	0.14743	0.0356	L	0.48642	1.525	0.09310	N	1	D	0.63880	0.993	P	0.59424	0.857	T	0.27571	-1.0070	10	0.23891	T	0.37	.	7.2869	0.26344	0.2795:0.0:0.7205:0.0	.	191	Q96A99-2	.	T	196;191	ENSP00000445277:P196T;ENSP00000293922:P191T	ENSP00000293922:P191T	P	-	1	0	PTX4	1477528	0.003000	0.15002	0.001000	0.08648	0.001000	0.01503	0.450000	0.21762	0.237000	0.21200	-0.768000	0.03414	CCT	.	.		0.736	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658		T	1537527	G	T	1537527	3	4	335	1	0	0	0	0	1	0	0	0	12838	1203	42	3	857	3	PTX4	16	1537527	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	911657	1537527	88817226	143	46694										
CLEC16A	23274	hgsc.bcm.edu	37	chr16	11056338	11056338	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	cctggagaagaatatgtttgTtttcttcttgaacatcttgc	8	7	3	3			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr16:11056338T>G	ENST00000409790.1	+	3	466	c.236T>G	c.(235-237)gTt>gGt	p.V79G	CLEC16A_ENST00000409552.3_Missense_Mutation_p.V79G	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A											breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						AATATGTTTGTTTTCTTCTTG	0.453																																					p.V79G		Atlas-SNP	.											.	CLEC16A	101	.	0			c.T236G						.						195	183	187					16																	11056338		1970	4162	6132	SO:0001583	missense	23274	exon3			TGTTTGTTTTCTT	AB002348	CCDS45409.1, CCDS58423.1	16p13.13	2010-04-27	2007-07-17	2007-07-17	ENSG00000038532	ENSG00000038532		"C-type lectin domain containing"	29013	protein-coding gene	gene with protein product		611303	"KIAA0350"	KIAA0350		9205841, 17632545	Standard	NM_015226		Approved	Gop-1	uc002dao.3	Q2KHT3	OTTHUMG00000152915	ENST00000409790.1:c.236T>G	chr16.hg19:g.11056338T>G	ENSP00000387122:p.Val79Gly	99.0	0.0		94.0	38.0	NM_015226		Missense_Mutation	SNP	ENST00000409790.1	hg19	CCDS45409.1	.	.	.	.	.	.	.	.	.	.	T	12.71	2.018863	0.35606	.	.	ENSG00000038532	ENST00000409790;ENST00000542102;ENST00000409552	T	0.41065	1.01	4.78	4.78	0.61160	.	0.054657	0.64402	D	0.000001	T	0.17109	0.0411	N	0.00413	-1.525	0.80722	D	1	P;B	0.35684	0.515;0.4	B;B	0.41412	0.356;0.173	T	0.35276	-0.9795	10	0.21540	T	0.41	-14.0854	13.8146	0.63283	0.0:0.0:0.0:1.0	.	79;79	Q2KHT3;Q2KHT3-2	CL16A_HUMAN;.	G	79	ENSP00000387122:V79G	ENSP00000386495:V79G	V	+	2	0	CLEC16A	10963839	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.923000	0.56469	1.926000	0.55796	0.460000	0.39030	GTT	.	.		0.453	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226		G	11056338	T	G	11056338	3	3	335	1	0	0	0	0	1	0	0	0	3502	1725	60	5	246	5	CLEC16A	16	11056338	Missense_Mutation	SNP	T	TCGA-RC-A6M6-01A-11D-A32G-10	9518811	11056338	79298415	144	46695										
SYT17	51760	hgsc.bcm.edu	37	chr16	19234475	19234475	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	aacttcttcagacagatgtgAgccaaggttcaggtaccgtg	11	9	3	3			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr16:19234475A>T	ENST00000355377.2	+	6	1458	c.1060A>T	c.(1060-1062)Agc>Tgc	p.S354C	SYT17_ENST00000568115.1_Missense_Mutation_p.S293C|SYT17_ENST00000568433.1_Missense_Mutation_p.S48C|SYT17_ENST00000562034.1_Missense_Mutation_p.S293C|SYT17_ENST00000562711.2_Missense_Mutation_p.S350C	NM_016524.2	NP_057608.2	Q9BSW7	SYT17_HUMAN	synaptotagmin XVII	354	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)	membrane (GO:0016020)|synaptic vesicle (GO:0008021)|trans-Golgi network (GO:0005802)	transporter activity (GO:0005215)			NS(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)	17						GACAGATGTGAGCCAAGGTTC	0.483																																					p.S354C		Atlas-SNP	.											.	SYT17	51	.	0			c.A1060T						.						110	87	95					16																	19234475		2197	4300	6497	SO:0001583	missense	51760	exon6			GATGTGAGCCAAG		CCDS10575.1	16p12.3	2013-01-21			ENSG00000103528	ENSG00000103528		"Synaptotagmins"	24119	protein-coding gene	gene with protein product	"B/K protein"					10493829	Standard	NM_016524		Approved		uc002dfw.3	Q9BSW7	OTTHUMG00000131461	ENST00000355377.2:c.1060A>T	chr16.hg19:g.19234475A>T	ENSP00000347538:p.Ser354Cys	91.0	0.0		89.0	33.0	NM_016524	O43330|Q9NZ18	Missense_Mutation	SNP	ENST00000355377.2	hg19	CCDS10575.1	.	.	.	.	.	.	.	.	.	.	A	14.83	2.652025	0.47362	.	.	ENSG00000103528	ENST00000355377	T	0.70869	-0.52	4.83	4.83	0.62350	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.315023	0.29178	N	0.012906	T	0.60843	0.2300	L	0.31752	0.955	0.48632	D	0.999682	B;B	0.10296	0.002;0.003	B;B	0.20577	0.021;0.03	T	0.57429	-0.7813	10	0.38643	T	0.18	.	15.1215	0.72447	1.0:0.0:0.0:0.0	.	354;293	Q9BSW7;B4DJB2	SYT17_HUMAN;.	C	354	ENSP00000347538:S354C	ENSP00000347538:S354C	S	+	1	0	SYT17	19141976	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.210000	0.65214	2.099000	0.63709	0.533000	0.62120	AGC	.	.		0.483	SYT17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254286.2	NM_016524		T	19234475	A	T	19234475	3	4	335	1	0	0	0	0	1	0	0	0	15488	304	11	4	1082	4	SYT17	16	19234475	Missense_Mutation	SNP	A	TCGA-RC-A6M6-01A-11D-A32G-10	8178137	19234475	71120278	145	46696										
ERN2	5347	hgsc.bcm.edu	37	chr16	23703609	23703609	+	IGR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ggctgccaccagaaagcacgTagtagaacacgcagcctgca	11	13	0	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr16:23703609T>C	ENST00000300093.4	+	0	2227				ERN2_ENST00000256797.4_Missense_Mutation_p.Y763C|ERN2_ENST00000457008.2_Missense_Mutation_p.Y663C	NM_005030.3	NP_005021.2	P53350	PLK1_HUMAN	polo-like kinase 1						activation of mitotic anaphase-promoting complex activity (GO:0007092)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|centrosome organization (GO:0051297)|cytokinesis (GO:0000910)|establishment of protein localization (GO:0045184)|G2 DNA damage checkpoint (GO:0031572)|G2/M transition of mitotic cell cycle (GO:0000086)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-serine phosphorylation (GO:0018105)|polar body extrusion after meiotic divisions (GO:0040038)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of proteolysis (GO:0045862)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein destabilization (GO:0031648)|protein localization to chromatin (GO:0071168)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|regulation of mitotic cell cycle (GO:0007346)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of protein binding (GO:0043393)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to antibiotic (GO:0046677)	centrosome (GO:0005813)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	anaphase-promoting complex binding (GO:0010997)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|microtubule binding (GO:0008017)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23				GBM - Glioblastoma multiforme(48;0.0156)		AGAAAGCACGTAGTAGAACAC	0.567																																					p.Y763C	Colon(12;240 564 27038 33155)	Atlas-SNP	.											.	ERN2	131	.	0			c.A2288G						.						75	74	74					16																	23703609		2197	4300	6497	SO:0001628	intergenic_variant	10595	exon18			AGCACGTAGTAGA		CCDS10616.1	16p	2013-01-17	2010-06-24	2004-01-28	ENSG00000166851	ENSG00000166851			9077	protein-coding gene	gene with protein product		602098	"polo-like kinase (Drosophila)"	PLK		8127874	Standard	NM_005030		Approved		uc002dlz.1	P53350	OTTHUMG00000096984		chr16.hg19:g.23703609T>C		21.0	0.0		21.0	8.0	NM_033266	Q15153|Q99746	Missense_Mutation	SNP	ENST00000300093.4	hg19	CCDS10616.1	.	.	.	.	.	.	.	.	.	.	T	19.62	3.861209	0.71949	.	.	ENSG00000134398	ENST00000256797;ENST00000457008	T;T	0.50277	0.75;0.75	5.65	5.65	0.86999	.	0.137817	0.50627	D	0.000113	T	0.63105	0.2483	L	0.52206	1.635	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.65882	-0.6060	10	0.87932	D	0	.	13.8429	0.63451	0.0:0.0:0.0:1.0	.	663;715	E7ETG2;A5YM65	.;.	C	763;663	ENSP00000256797:Y763C;ENSP00000413812:Y663C	ENSP00000256797:Y763C	Y	-	2	0	ERN2	23611110	1.000000	0.71417	0.982000	0.44146	0.974000	0.67602	5.877000	0.69675	2.146000	0.66826	0.533000	0.62120	TAC	.	.		0.567	PLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214057.2	NM_005030		C	23703609	T	C	23703609	1	2	335	0	1	0	0	0	0	0	0	0	5240	1638	57	2		2	ERN2	16	23703609	IGR	SNP	T	TCGA-RC-A6M6-01A-11D-A32G-10	4469134	23703609	66651144	146	46697										
GPR114	221188	hgsc.bcm.edu	37	chr16	57604440	57604440	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	atggcacaggcttccagaacAtgtccatgtgagtgccctca	10	12	1	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr16:57604440A>T	ENST00000340339.4	+	10	1724	c.1201A>T	c.(1201-1203)Atg>Ttg	p.M401L	GPR114_ENST00000349457.3_Missense_Mutation_p.M401L|GPR114_ENST00000394361.4_Intron	NM_153837.1	NP_722579.1	Q8IZF4	GP114_HUMAN	G protein-coupled receptor 114	401					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(5)|ovary(2)|stomach(1)|urinary_tract(1)	23						CTTCCAGAACATGTCCATGTG	0.592																																					p.M401L		Atlas-SNP	.											.	GPR114	52	.	0			c.A1201T						.						58	50	53					16																	57604440		2198	4300	6498	SO:0001583	missense	221188	exon10			CAGAACATGTCCA	AY140956	CCDS10785.1	16q13	2014-08-08			ENSG00000159618	ENSG00000159618		"-", "GPCR / Class B : Orphans"	19010	protein-coding gene	gene with protein product						12435584	Standard	NM_153837		Approved	PGR27	uc002ely.3	Q8IZF4	OTTHUMG00000133461	ENST00000340339.4:c.1201A>T	chr16.hg19:g.57604440A>T	ENSP00000342981:p.Met401Leu	18.0	0.0		20.0	8.0	NM_153837	B3KXZ5|Q6ZMH7|Q6ZML4|Q86SL8|Q8IZ14	Missense_Mutation	SNP	ENST00000340339.4	hg19	CCDS10785.1	.	.	.	.	.	.	.	.	.	.	A	10.80	1.452929	0.26161	.	.	ENSG00000159618	ENST00000340339;ENST00000349457	T;T	0.27557	1.66;1.66	4.58	-5.32	0.02722	GPCR, family 2-like (1);	2.158560	0.01693	N	0.026755	T	0.19366	0.0465	N	0.19112	0.55	0.09310	N	1	B	0.12013	0.005	B	0.11329	0.006	T	0.22661	-1.0210	10	0.29301	T	0.29	.	9.4502	0.38721	0.1622:0.0:0.6956:0.1423	.	401	Q8IZF4	GP114_HUMAN	L	401	ENSP00000342981:M401L;ENSP00000290823:M401L	ENSP00000342981:M401L	M	+	1	0	GPR114	56161941	0.000000	0.05858	0.001000	0.08648	0.056000	0.15407	-1.029000	0.03585	-0.507000	0.06549	-0.421000	0.06004	ATG	.	.		0.592	GPR114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257336.3	NM_153837		T	57604440	A	T	57604440	3	4	335	1	0	0	0	0	1	0	0	0	6639	217	8	4	1235	4	GPR114	16	57604440	Missense_Mutation	SNP	A	TCGA-RC-A6M6-01A-11D-A32G-10	33900831	57604440	32750313	147	46698										
VAC14	55697	hgsc.bcm.edu	37	chr16	70778459	70778459	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gaggaagcgatttctgccagCacctccaggtccttcaggat	11	12	2	0	rs145571853		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr16:70778459C>A	ENST00000261776.5	-	13	1655	c.1395G>T	c.(1393-1395)gtG>gtT	p.V465V	RP11-394B2.6_ENST00000567186.1_RNA	NM_018052.3	NP_060522.3	Q08AM6	VAC14_HUMAN	Vac14 homolog (S. cerevisiae)	465					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of lipid kinase activity (GO:0043550)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|PAS complex (GO:0070772)	receptor activity (GO:0004872)			breast(2)|endometrium(2)|kidney(10)|large_intestine(1)|lung(10)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	33		Ovarian(137;0.0699)				TTTCTGCCAGCACCTCCAGGT	0.662																																					p.V465V		Atlas-SNP	.											.	VAC14	65	.	0			c.G1395T						.						38	41	40					16																	70778459		2198	4300	6498	SO:0001819	synonymous_variant	55697	exon13			TGCCAGCACCTCC	AK056433	CCDS10896.1	16q22.1	2010-03-23	2005-02-09		ENSG00000103043	ENSG00000103043			25507	protein-coding gene	gene with protein product		604632	"Tax1 (human T-cell leukemia virus type I) binding protein 2"	TAX1BP2		15542851, 12719380	Standard	NM_018052		Approved	FLJ10305, ArPIKfyve	uc002ezm.3	Q08AM6	OTTHUMG00000137583	ENST00000261776.5:c.1395G>T	chr16.hg19:g.70778459C>A		54.0	0.0		64.0	16.0	NM_018052	B3KPJ5|B3KSM8|Q13174|Q6IA12|Q7L4Y1|Q9BW96|Q9H6V6	Silent	SNP	ENST00000261776.5	hg19	CCDS10896.1																																																																																			.	C|1.000;T|0.000		0.662	VAC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268973.3	NM_018052		A	70778459	C	A	70778459	2	1	335	1	0	0	0	0	0	0	0	1	17126	697	25	3		3	VAC14	16	70778459	Silent	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	13174019	70778459	19576294	148	46699										
HPR	3250	hgsc.bcm.edu	37	chr16	72108240	72108240	+	Frame_Shift_Del	DEL	G	G	-													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ctatgtggagcacttgtttcGctaccagtgtaagaactact							TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr16:72108240delG	ENST00000540303.2	+	3	181	c.149delG	c.(148-150)cgcfs	p.R50fs	HPR_ENST00000228226.8_Frame_Shift_Del_p.R87fs|HPR_ENST00000561690.1_Frame_Shift_Del_p.R50fs|HPR_ENST00000356967.5_Frame_Shift_Del_p.R50fs	NM_020995.3	NP_066275.3	P00739	HPTR_HUMAN	haptoglobin-related protein	50	Sushi.					blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|spherical high-density lipoprotein particle (GO:0034366)	hemoglobin binding (GO:0030492)|serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|stomach(1)|urinary_tract(2)	20		Ovarian(137;0.125)				CACTTGTTTCGCTACCAGTGT	0.483																																					p.R50fs		Atlas-Indel,Pindel	.											HPR,NS,carcinoma,0,1	HPR	43	.	0			c.148delC						.						216	133	160					16																	72108240		1966	4141	6107	SO:0001589	frameshift_variant	3250	exon3			.	BC160066	CCDS42193.1	16q22.2	2012-10-03			ENSG00000261701	ENSG00000261701			5156	protein-coding gene	gene with protein product		140210				2987228, 16778136	Standard	NM_020995		Approved		uc002fby.3	P00739	OTTHUMG00000173010	ENST00000540303.2:c.149delG	chr16.hg19:g.72108240delG	ENSP00000441828:p.Arg50fs	346.0	0.0		345.0	106.0	NM_020995	Q7LE20|Q92658|Q92659|Q9ULB0	Frame_Shift_Del	DEL	ENST00000540303.2	hg19	CCDS42193.1																																																																																			.	.		0.483	HPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421696.1	NM_020995		-	72108240	G	-	72108240	7	5	335	1	0	1	0	1	0	0	0	0	7346	1087	38	0	159	0	HPR	16	72108240	Frame_Shift_Del	DEL	G	TCGA-RC-A6M6-01A-11D-A32G-10	1329781	72108240	18246513	149	46700										
KIAA1609	57707	hgsc.bcm.edu	37	chr16	84514214	84514214	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tctcctgagccgacagctgcGggctgttgtacgtggtgcac	14	12	1	1	rs149378530		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr16:84514214G>A	ENST00000343629.6	-	7	1360	c.1178C>T	c.(1177-1179)cCg>cTg	p.P393L	TLDC1_ENST00000535580.1_Missense_Mutation_p.P366L	NM_020947.3	NP_065998.3	Q6P9B6	TLDC1_HUMAN	TBC/LysM-associated domain containing 1	393	TLD.					lysosomal membrane (GO:0005765)											CGACAGCTGCGGGCTGTTGTA	0.567																																					p.P393L		Atlas-SNP	.											.	KIAA1609	39	.	0			c.C1178T						.	G	LEU/PRO	0,4400		0,0,2200	113	91	98		1178	5.2	1	16	dbSNP_134	98	1,8599	1.2+/-3.3	0,1,4299	no	missense	KIAA1609	NM_020947.3	98	0,1,6499	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	393/457	84514214	1,12999	2200	4300	6500	SO:0001583	missense	57707	exon7			AGCTGCGGGCTGT	AB046829	CCDS32498.1	16q24.1	2013-03-14	2013-03-14	2013-03-14	ENSG00000140950	ENSG00000140950			29325	protein-coding gene	gene with protein product	"TLD domain containing 1"		"KIAA1609"	KIAA1609		10997877	Standard	NM_020947		Approved		uc002fib.3	Q6P9B6	OTTHUMG00000176739	ENST00000343629.6:c.1178C>T	chr16.hg19:g.84514214G>A	ENSP00000343635:p.Pro393Leu	88.0	0.0		91.0	43.0	NM_020947	Q8IZ64|Q9HCG3|Q9NTE8	Missense_Mutation	SNP	ENST00000343629.6	hg19	CCDS32498.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.850028	0.91277	0.0	1.16E-4	ENSG00000140950	ENST00000343629;ENST00000545792;ENST00000535580	T;T	0.46819	0.86;0.86	5.18	5.18	0.71444	TLDc (2);	0.000000	0.85682	D	0.000000	T	0.72961	0.3526	M	0.85542	2.76	0.80722	D	1	D;D	0.89917	1.0;0.996	D;P	0.97110	1.0;0.88	T	0.78006	-0.2373	10	0.72032	D	0.01	-31.88	17.6786	0.88236	0.0:0.0:1.0:0.0	.	366;393	F5GWS3;Q6P9B6	.;K1609_HUMAN	L	393;61;366	ENSP00000343635:P393L;ENSP00000441997:P366L	ENSP00000343635:P393L	P	-	2	0	KIAA1609	83071715	1.000000	0.71417	1.000000	0.80357	0.770000	0.43624	9.267000	0.95665	2.415000	0.81967	0.563000	0.77884	CCG	.	G|1.000;T|0.000		0.567	TLDC1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433421.1	NM_020947		A	84514214	G	A	84514214	3	1	335	1	0	0	0	0	1	0	0	0	8256	1116	39	1	200	1	KIAA1609	16	84514214	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	12405974	84514214	5840539	150	46701										
KIAA0182	23199	hgsc.bcm.edu	37	chr16	85696964	85696964	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	atctagaagctagagtttttGcaactttttggcttgaccac	8	8	1	3			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr16:85696964G>A	ENST00000253458.7	+	11	2564	c.2388G>A	c.(2386-2388)ttG>ttA	p.L796L	GSE1_ENST00000393243.1_Silent_p.L723L|GSE1_ENST00000405402.2_Silent_p.L692L	NM_014615.2	NP_055430.1	Q14687	GSE1_HUMAN	Gse1 coiled-coil protein	796																	TAGAGTTTTTGCAACTTTTTG	0.562																																					p.L796L		Atlas-SNP	.											.	.	.	.	0			c.G2388A						.						104	123	116					16																	85696964		2198	4300	6498	SO:0001819	synonymous_variant	23199	exon11			GTTTTTGCAACTT	D80004	CCDS10952.1, CCDS45539.1, CCDS62007.1	16q24.1	2012-12-07	2012-12-07	2012-10-02	ENSG00000131149	ENSG00000131149			28979	protein-coding gene	gene with protein product	"genetic suppressor element 1"		"KIAA0182", "Gse1 coiled-coil protein homolog (mouse)"	KIAA0182		8724849, 8786132	Standard	NM_014615		Approved		uc002fix.4	Q14687	OTTHUMG00000137650	ENST00000253458.7:c.2388G>A	chr16.hg19:g.85696964G>A		20.0	0.0		20.0	9.0	NM_014615	D3DUM4|Q8IY61|Q96GA4|Q9BW09	Silent	SNP	ENST00000253458.7	hg19	CCDS10952.1	.	.	.	.	.	.	.	.	.	.	G	8.887	0.953023	0.18431	.	.	ENSG00000131149	ENST00000412692	.	.	.	5.21	4.25	0.50352	.	.	.	.	.	T	0.54287	0.1849	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52177	-0.8610	4	.	.	.	-12.8675	5.6565	0.17644	0.1538:0.0:0.6779:0.1683	.	.	.	.	Y	603	.	.	C	+	2	0	KIAA0182	84254465	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.943000	0.49026	2.438000	0.82558	0.561000	0.74099	TGC	.	.		0.562	GSE1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325527.1	NM_014615		A	85696964	G	A	85696964	2	1	335	1	0	0	0	0	0	0	0	1	8168	1310	46	3		3	KIAA0182	16	85696964	Silent	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	1182750	85696964	4657789	151	46702										
ACAP1	9744	hgsc.bcm.edu	37	chr17	7254302	7254302	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	aagatgagggaggctgaagcGgcccaggggcaggcaggtaa	19	7	0	3			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr17:7254302G>A	ENST00000158762.3	+	21	2312	c.2106G>A	c.(2104-2106)gcG>gcA	p.A702A	KCTD11_ENST00000333751.3_5'Flank|ACAP1_ENST00000574499.1_Silent_p.A27A|ACAP1_ENST00000570504.1_Silent_p.A6A|ACAP1_ENST00000571471.1_Silent_p.A6A|ACAP1_ENST00000575415.1_Silent_p.A6A|RP11-542C16.1_ENST00000572417.1_RNA	NM_014716.3	NP_055531.1	Q15027	ACAP1_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 1	702	Required for interaction with GULP1.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)	endosome (GO:0005768)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(3)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|prostate(3)|skin(1)|urinary_tract(1)	33						AGGCTGAAGCGGCCCAGGGGC	0.597																																					p.A702A		Atlas-SNP	.											.	ACAP1	66	.	0			c.G2106A						.						81	80	80					17																	7254302		2203	4300	6503	SO:0001819	synonymous_variant	9744	exon21			TGAAGCGGCCCAG	D30758	CCDS11101.1	17p13.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000072818	ENSG00000072818		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16467	protein-coding gene	gene with protein product		607763	"centaurin, beta 1"	CENTB1		11050434, 11062263	Standard	NM_014716		Approved	KIAA0050	uc002ggd.2	Q15027	OTTHUMG00000102199	ENST00000158762.3:c.2106G>A	chr17.hg19:g.7254302G>A		53.0	0.0		30.0	20.0	NM_014716	Q53XN9	Silent	SNP	ENST00000158762.3	hg19	CCDS11101.1																																																																																			.	.		0.597	ACAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220049.4	NM_014716		A	7254302	G	A	7254302	2	1	335	1	0	0	0	0	0	0	0	1	118	1103	39	1		1	ACAP1	17	7254302	Silent	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10		7254302	73940908	152	46703										
TP53	7157	hgsc.bcm.edu	37	chr17	7577064	7577064	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ctcgtggtgaggctccccttTcttgcggagattctcttcct	10	13	2	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr17:7577064T>A	ENST00000269305.4	-	8	1063	c.874A>T	c.(874-876)Aaa>Taa	p.K292*	TP53_ENST00000420246.2_Nonsense_Mutation_p.K292*|TP53_ENST00000445888.2_Nonsense_Mutation_p.K292*|TP53_ENST00000455263.2_Nonsense_Mutation_p.K292*|TP53_ENST00000413465.2_Intron|TP53_ENST00000359597.4_Nonsense_Mutation_p.K292*|TP53_ENST00000574684.1_5'Flank	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	292	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		K -> E (in sporadic cancers; somatic mutation).|K -> G (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|K -> I (in LFS; germline mutation and in a sporadic cancer; somatic mutation). {ECO:0000269|PubMed:10484981}.|K -> N (in sporadic cancers; somatic mutation).|K -> Q (in a sporadic cancer; somatic mutation).|K -> R (in sporadic cancers; somatic mutation).|K -> T (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.K291fs*48(8)|p.0?(8)|p.?(2)|p.E294fs*51(2)|p.K292E(2)|p.K292*(2)|p.K292fs*13(1)|p.T284_G293del10(1)|p.L265_K305del41(1)|p.R290fs*12(1)|p.R290fs*50(1)|p.K291fs*12(1)|p.R290_P295>X(1)|p.E285fs*13(1)|p.V272_K292del21(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGCTCCCCTTTCTTGCGGAGA	0.577		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.K292X	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000269305,NS,carcinoma,0,1	TP53	33396	.	33	Deletion - Frameshift(15)|Whole gene deletion(8)|Deletion - In frame(3)|Substitution - Nonsense(2)|Unknown(2)|Substitution - Missense(2)|Complex - deletion inframe(1)	upper_aerodigestive_tract(12)|urinary_tract(4)|bone(4)|haematopoietic_and_lymphoid_tissue(3)|stomach(2)|central_nervous_system(2)|breast(2)|salivary_gland(1)|large_intestine(1)|endometrium(1)|oesophagus(1)	c.A874T						.						104	89	94					17																	7577064		2203	4300	6503	SO:0001587	stop_gained	7157	exon8	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	CCCCTTTCTTGCG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.874A>T	chr17.hg19:g.7577064T>A	ENSP00000269305:p.Lys292*	60.0	0.0		35.0	17.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.521424	0.85600	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	.	.	.	5.12	4.03	0.46877	.	0.183996	0.46145	D	0.000309	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-23.716	5.2408	0.15471	0.0:0.0898:0.182:0.7282	.	.	.	.	X	292;292;292;292;292;281;160	.	ENSP00000269305:K292X	K	-	1	0	TP53	7517789	0.998000	0.40836	0.909000	0.35828	0.257000	0.26127	1.203000	0.32284	0.944000	0.37579	0.459000	0.35465	AAA	.	.		0.577	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577064	T	A	7577064	4	1	335	1	0	0	0	0	0	1	0	0	16396	1792	62	4	412	4	TP53	17	7577064	Nonsense_Mutation	SNP	T	TCGA-RC-A6M6-01A-11D-A32G-10	322762	7577064	73618146	153	46704										
GAS7	8522	hgsc.bcm.edu	37	chr17	9846500	9846500	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	cccttcagctgtttctggagCagtagttcaaacccagccac	8	14	3	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr17:9846500C>A	ENST00000432992.2	-	7	829	c.669G>T	c.(667-669)ctG>ctT	p.L223L	GAS7_ENST00000585266.1_Silent_p.L163L|GAS7_ENST00000580865.1_Silent_p.L83L|GAS7_ENST00000323816.4_Silent_p.L163L|GAS7_ENST00000396115.2_Intron|GAS7_ENST00000540214.1_Intron|GAS7_ENST00000583882.1_Intron|GAS7_ENST00000579158.1_Silent_p.L159L|GAS7_ENST00000578655.1_5'Flank|GAS7_ENST00000542249.1_Silent_p.L159L|GAS7_ENST00000437099.2_Silent_p.L159L	NM_201433.1	NP_958839.1	O60861	GAS7_HUMAN	growth arrest-specific 7	223	FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.				actin filament bundle assembly (GO:0051017)|actin filament polymerization (GO:0030041)|cell cycle arrest (GO:0007050)|neuron projection morphogenesis (GO:0048812)|regulation of cell shape (GO:0008360)|regulation of transcription, DNA-templated (GO:0006355)	actin filament (GO:0005884)|cytoplasm (GO:0005737)|ruffle (GO:0001726)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(7)|lung(18)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	39						GTTTCTGGAGCAGTAGTTCAA	0.552			T	MLL	AML*																																p.L223L		Atlas-SNP	.		Dom	yes		17	17p	8522	growth arrest-specific 7		L	.	GAS7	113	.	0			c.G669T						.						181	163	169					17																	9846500		2203	4300	6503	SO:0001819	synonymous_variant	8522	exon7			CTGGAGCAGTAGT	AB007854	CCDS11152.1, CCDS42263.1, CCDS45611.1, CCDS58518.1	17p13.1	2004-02-18							4169	protein-coding gene	gene with protein product		603127				9736752	Standard	NM_001130831		Approved	KIAA0394, MGC1348	uc002gmg.1	O60861		ENST00000432992.2:c.669G>T	chr17.hg19:g.9846500C>A		84.0	0.0		36.0	24.0	NM_201433	A8KAC2|B2RCK9|O43144|Q53Y77|Q7Z571	Silent	SNP	ENST00000432992.2	hg19	CCDS11152.1																																																																																			.	.		0.552	GAS7-017	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439883.1	NM_003644, NM_201432, NM_201433		A	9846500	C	A	9846500	2	1	335	1	0	0	0	0	0	0	0	1	6258	697	25	3		3	GAS7	17	9846500	Silent	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	2269436	9846500	71348710	154	46705										
MYH8	4626	hgsc.bcm.edu	37	chr17	10307807	10307807	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tctcggtctctgcactcttgAggaggggcttaatcttgaaa	11	9	4	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr17:10307807A>T	ENST00000403437.2	-	22	2622	c.2528T>A	c.(2527-2529)cTc>cAc	p.L843H	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	843					ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)			NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						TGCACTCTTGAGGAGGGGCTT	0.478									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling																												p.L843H		Atlas-SNP	.											.	MYH8	346	.	0			c.T2528A						.						129	123	125					17																	10307807		2203	4300	6503	SO:0001583	missense	4626	exon22	Familial Cancer Database	Carney Complex Variant	CTCTTGAGGAGGG		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020		"Myosins / Myosin superfamily : Class II"	7578	protein-coding gene	gene with protein product		160741	"myosin, heavy polypeptide 8, skeletal muscle, perinatal"			2373371	Standard	NM_002472		Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.2528T>A	chr17.hg19:g.10307807A>T	ENSP00000384330:p.Leu843His	411.0	1.0		257.0	169.0	NM_002472	Q14910	Missense_Mutation	SNP	ENST00000403437.2	hg19	CCDS11153.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.582791	0.86748	.	.	ENSG00000133020	ENST00000252173;ENST00000403437	D	0.87491	-2.26	5.31	5.31	0.75309	.	0.000000	0.36444	U	0.002587	D	0.96358	0.8812	H	0.98965	4.385	0.54753	D	0.999988	D	0.89917	1.0	D	0.91635	0.999	D	0.98081	1.0404	10	0.87932	D	0	.	15.4343	0.75133	1.0:0.0:0.0:0.0	.	843	P13535	MYH8_HUMAN	H	843	ENSP00000384330:L843H	ENSP00000252173:L843H	L	-	2	0	MYH8	10248532	1.000000	0.71417	0.997000	0.53966	0.904000	0.53231	9.058000	0.93896	2.231000	0.72958	0.533000	0.62120	CTC	.	.		0.478	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472		T	10307807	A	T	10307807	3	4	335	1	0	0	0	0	1	0	0	0	10050	304	11	4	3361	4	MYH8	17	10307807	Missense_Mutation	SNP	A	TCGA-RC-A6M6-01A-11D-A32G-10	461307	10307807	70887403	155	46706										
MYH1	4619	hgsc.bcm.edu	37	chr17	10411951	10411951	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gtgtctgtcgccttggggaaCatgcactcctcttccaggat	11	12	2	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr17:10411951C>T	ENST00000226207.5	-	16	1720	c.1626G>A	c.(1624-1626)atG>atA	p.M542I	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	542	Myosin motor.				muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						CCTTGGGGAACATGCACTCCT	0.433																																					p.M542I		Atlas-SNP	.											.	MYH1	403	.	0			c.G1626A						.						111	116	114					17																	10411951		2203	4300	6503	SO:0001583	missense	4619	exon16			GGGGAACATGCAC		CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"Myosins / Myosin superfamily : Class II"	7567	protein-coding gene	gene with protein product	"myosin heavy chain IIx/d"	160730	"myosin, heavy polypeptide 1, skeletal muscle, adult"			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.1626G>A	chr17.hg19:g.10411951C>T	ENSP00000226207:p.Met542Ile	81.0	0.0		46.0	33.0	NM_005963	Q14CA4|Q9Y622	Missense_Mutation	SNP	ENST00000226207.5	hg19	CCDS11155.1	.	.	.	.	.	.	.	.	.	.	C	31	5.087659	0.94100	.	.	ENSG00000109061	ENST00000226207	T	0.71341	-0.56	4.8	4.8	0.61643	Myosin head, motor domain (2);	0.000000	0.52532	U	0.000072	T	0.71239	0.3316	L	0.49571	1.57	0.58432	D	0.999999	B	0.17038	0.02	B	0.33295	0.161	T	0.69026	-0.5254	10	0.51188	T	0.08	.	18.405	0.90532	0.0:1.0:0.0:0.0	.	542	P12882	MYH1_HUMAN	I	542	ENSP00000226207:M542I	ENSP00000226207:M542I	M	-	3	0	MYH1	10352676	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.414000	0.80117	2.665000	0.90641	0.650000	0.86243	ATG	.	.		0.433	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963		T	10411951	C	T	10411951	3	4	335	1	0	0	0	0	1	0	0	0	10038	478	17	3	4293	3	MYH1	17	10411951	Missense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	104144	10411951	70783259	156	46707										
LHX1	3975	hgsc.bcm.edu	37	chr17	35298050	35298050	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	agaacctgggcgccaagcggCggggaccgcgcaccaccatc	14	16	0	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr17:35298050C>T	ENST00000254457.5	+	3	1952	c.541C>T	c.(541-543)Cgg>Tgg	p.R181W	RP11-445F12.2_ENST00000607336.1_RNA	NM_005568.3	NP_005559.2	P48742	LHX1_HUMAN	LIM homeobox 1	181					anatomical structure formation involved in morphogenesis (GO:0048646)|anatomical structure morphogenesis (GO:0009653)|anterior/posterior axis specification (GO:0009948)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell-cell signaling (GO:0007267)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation (GO:0021937)|cerebellum development (GO:0021549)|cervix development (GO:0060067)|comma-shaped body morphogenesis (GO:0072049)|dorsal/ventral pattern formation (GO:0009953)|ectoderm formation (GO:0001705)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|embryonic viscerocranium morphogenesis (GO:0048703)|endoderm formation (GO:0001706)|epithelium development (GO:0060429)|forebrain regionalization (GO:0021871)|gastrulation with mouth forming second (GO:0001702)|head development (GO:0060322)|horizontal cell localization (GO:0035852)|kidney development (GO:0001822)|lateral motor column neuron migration (GO:0097477)|mesonephric duct development (GO:0072177)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric glomerulus development (GO:0072224)|metanephric part of ureteric bud development (GO:0035502)|metanephric renal vesicle morphogenesis (GO:0072283)|metanephric S-shaped body morphogenesis (GO:0072284)|motor neuron axon guidance (GO:0008045)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct elongation (GO:0035849)|nephric duct morphogenesis (GO:0072178)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|oviduct development (GO:0060066)|oviduct epithelium development (GO:0035846)|paramesonephric duct development (GO:0061205)|pattern specification process (GO:0007389)|positive regulation of anterior head development (GO:2000744)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of embryonic development (GO:0040019)|positive regulation of gastrulation (GO:2000543)|positive regulation of nephron tubule epithelial cell differentiation (GO:2000768)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|primitive streak formation (GO:0090009)|pronephros development (GO:0048793)|regulation of gene expression (GO:0010468)|renal vesicle morphogenesis (GO:0072077)|retina layer formation (GO:0010842)|S-shaped body morphogenesis (GO:0072050)|somite rostral/caudal axis specification (GO:0032525)|spinal cord association neuron differentiation (GO:0021527)|telencephalon development (GO:0021537)|transcription from RNA polymerase II promoter (GO:0006366)|ureteric bud development (GO:0001657)|urogenital system development (GO:0001655)|uterine epithelium development (GO:0035847)|uterus development (GO:0060065)|vagina development (GO:0060068)|ventral spinal cord development (GO:0021517)	nucleus (GO:0005634)|protein complex (GO:0043234)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	16		Breast(25;0.00607)				CGCCAAGCGGCGGGGACCGCG	0.667																																					p.R181W		Atlas-SNP	.											.	LHX1	48	.	0			c.C541T						.						41	47	45					17																	35298050		2203	4300	6503	SO:0001583	missense	3975	exon3			AAGCGGCGGGGAC	U14755	CCDS11316.1	17q12	2014-04-11			ENSG00000132130	ENSG00000273706		"Homeoboxes / LIM class"	6593	protein-coding gene	gene with protein product		601999				9212161	Standard	NM_005568		Approved	LIM-1, LIM1	uc002hnh.2	P48742	OTTHUMG00000188456	ENST00000254457.5:c.541C>T	chr17.hg19:g.35298050C>T	ENSP00000254457:p.Arg181Trp	28.0	0.0		39.0	14.0	NM_005568	Q3MIW0	Missense_Mutation	SNP	ENST00000254457.5	hg19	CCDS11316.1	.	.	.	.	.	.	.	.	.	.	C	19.75	3.884970	0.72410	.	.	ENSG00000132130	ENST00000254457	D	0.97352	-4.35	4.26	-0.887	0.10587	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.64402	D	0.000001	D	0.98394	0.9466	M	0.88377	2.95	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98556	1.0639	10	0.87932	D	0	.	16.8083	0.85711	0.75:0.25:0.0:0.0	.	167;181	B4DPA6;P48742	.;LHX1_HUMAN	W	181	ENSP00000254457:R181W	ENSP00000254457:R181W	R	+	1	2	LHX1	32372163	0.049000	0.20398	0.812000	0.32479	0.986000	0.74619	0.110000	0.15437	-0.086000	0.12550	-0.268000	0.10319	CGG	.	.		0.667	LHX1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256704.3	NM_005568		T	35298050	C	T	35298050	3	4	335	1	0	0	0	0	1	0	0	0	8779	759	27	1	551	1	LHX1	17	35298050	Missense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	24886099	35298050	45897160	157	46708										
KRT9	3857	hgsc.bcm.edu	37	chr17	39723992	39723992	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	aaggccaatttttccagctcCggaggattcactaagaaaga	9	9	1	2	rs201817471		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr17:39723992C>A	ENST00000246662.4	-	7	1470	c.1405G>T	c.(1405-1407)Gga>Tga	p.G469*	KRT9_ENST00000588431.1_Nonsense_Mutation_p.G236*	NM_000226.3	NP_000217.2	P35527	K1C9_HUMAN	keratin 9	469	Tail.				epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		Breast(137;0.000307)				TTTCCAGCTCCGGAGGATTCA	0.502																																					p.G469X		Atlas-SNP	.											.	KRT9	78	.	0			c.G1405T						.						72	70	71					17																	39723992		2203	4300	6503	SO:0001587	stop_gained	3857	exon7			CAGCTCCGGAGGA		CCDS32654.1	17q21.2	2013-06-20	2008-08-01		ENSG00000171403	ENSG00000171403		"-", "Intermediate filaments type I, keratins (acidic)"	6447	protein-coding gene	gene with protein product	"cytokeratin 9", "type I cytoskeletal 9", "epidermolytic palmoplantar keratoderma"	607606				7512862, 16831889	Standard	NM_000226		Approved	EPPK, K9, CK-9	uc002hxe.4	P35527	OTTHUMG00000133599	ENST00000246662.4:c.1405G>T	chr17.hg19:g.39723992C>A	ENSP00000246662:p.Gly469*	32.0	0.0		29.0	17.0	NM_000226	O00109|Q0IJ47|Q14665	Nonsense_Mutation	SNP	ENST00000246662.4	hg19	CCDS32654.1	.	.	.	.	.	.	.	.	.	.	C	37	6.064804	0.97251	.	.	ENSG00000171403	ENST00000246662	.	.	.	3.64	3.64	0.41730	.	0.873431	0.09295	N	0.821854	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	.	10.7325	0.46104	0.0:1.0:0.0:0.0	.	.	.	.	X	469	.	ENSP00000246662:G469X	G	-	1	0	KRT9	36977518	0.236000	0.23804	0.781000	0.31783	0.600000	0.36913	1.783000	0.38664	1.886000	0.54624	0.465000	0.42564	GGA	.	C|1.000;G|0.000		0.502	KRT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257707.1	NM_000226		A	39723992	C	A	39723992	4	1	335	1	0	0	0	0	0	1	0	0	8510	661	23	1	470	1	KRT9	17	39723992	Nonsense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	4425942	39723992	41471218	158	46709										
EVPL	2125	hgsc.bcm.edu	37	chr17	74014610	74014611	+	Frame_Shift_Ins	INS	-	-	CCCT													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gcttggtctccccgccagggINSccctgcacgacccaggcgtg							TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr17:74014610_74014611insCCCT	ENST00000301607.3	-	12	1608_1609	c.1355_1356insAGGG	c.(1354-1356)ggcfs	p.G452fs	EVPL_ENST00000586740.1_Frame_Shift_Ins_p.G452fs	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	452	Globular 1.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						CCCCGCCAGGGCCCTGCACGAC	0.653																																					p.G452fs		Atlas-Indel,Pindel	.											.	EVPL	155	.	0			c.1356_1357insAGGG						.																																			SO:0001589	frameshift_variant	2125	exon12			.	U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.1352_1355dupAGGG	chr17.hg19:g.74014611_74014614dupCCCT	ENSP00000301607:p.Gly452fs	77.0	0.0		125.0	26.0	NM_001988	A0AUV5	Frame_Shift_Ins	INS	ENST00000301607.3	hg19	CCDS11737.1																																																																																			.	.		0.653	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988		CCCT	74014611	-	CCCT	74014610	7	5	335	1	0	1	1	0	0	0	0	0	5294	1190	42	0	4789	0	EVPL	17	74014610	Frame_Shift_Ins	INS	-	TCGA-RC-A6M6-01A-11D-A32G-10	34290618	74014610	7180600	159	46710										
TMC6	11322	hgsc.bcm.edu	37	chr17	76120809	76120809	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	cgcttcagggcgtagcgccaCggcatcagggcctgcagggc	16	14	2	0	rs369185930		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr17:76120809C>T	ENST00000590602.1	-	8	846	c.687G>A	c.(685-687)ccG>ccA	p.P229P	TMC6_ENST00000589553.1_Silent_p.P2P|TMC6_ENST00000322933.4_De_novo_Start_OutOfFrame|TMC6_ENST00000306591.7_Silent_p.P229P|TMC6_ENST00000591436.1_5'Flank|TMC6_ENST00000392467.3_Silent_p.P229P|TMC6_ENST00000592076.1_5'Flank|TMC6_ENST00000322914.3_Silent_p.P229P			Q7Z403	TMC6_HUMAN	transmembrane channel-like 6	229					ion transport (GO:0006811)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	14			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			CGTAGCGCCACGGCATCAGGG	0.677																																					p.P229P		Atlas-SNP	.											.	TMC6	42	.	0			c.G687A						.	C	,	0,4322		0,0,2161	12	11	11		687,687	-6.3	0	17		11	4,8442		0,4,4219	no	coding-synonymous,coding-synonymous	TMC6	NM_001127198.1,NM_007267.6	,	0,4,6380	TT,TC,CC		0.0474,0.0,0.0313	,	229/806,229/806	76120809	4,12764	2161	4223	6384	SO:0001819	synonymous_variant	11322	exon8			GCGCCACGGCATC	AY057379	CCDS32748.1	17q25.3	2014-09-17	2005-11-10	2005-11-10	ENSG00000141524	ENSG00000141524			18021	protein-coding gene	gene with protein product		605828	"epidermodysplasia verruciformis 1"	EVER1		12426567	Standard	NM_007267		Approved	LAK-4P, EVIN1	uc002juk.2	Q7Z403	OTTHUMG00000177466	ENST00000590602.1:c.687G>A	chr17.hg19:g.76120809C>T		50.0	0.0		89.0	26.0	NM_001127198	O43284|Q45VJ2|Q8IU98|Q8IUI7|Q8IWU8|Q8TEQ7|Q9HAG5	Silent	SNP	ENST00000590602.1	hg19	CCDS32748.1																																																																																			.	.		0.677	TMC6-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437146.1			T	76120809	C	T	76120809	2	4	335	1	0	0	0	0	0	0	0	1	16004	523	19	1		1	TMC6	17	76120809	Silent	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	2106199	76120809	5074401	160	46711										
DNAH17	8632	hgsc.bcm.edu	37	chr17	76490821	76490821	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	catgagcacctggtcctctgCccggctggggtcgcccctct	12	17	2	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr17:76490821C>G	ENST00000585328.1	-	40	6233	c.6109G>C	c.(6109-6111)Gca>Cca	p.A2037P	DNAH17_ENST00000389840.5_Missense_Mutation_p.A2028P|RP11-559N14.5_ENST00000591373.1_RNA|RP11-559N14.5_ENST00000585969.1_RNA	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	2028					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			TGGTCCTCTGCCCGGCTGGGG	0.622																																					p.A2042P		Atlas-SNP	.											.	DNAH17	347	.	0			c.G6124C						.						31	37	35					17																	76490821		2130	4252	6382	SO:0001583	missense	8632	exon40			CCTCTGCCCGGCT	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"Axonemal dyneins"	2946	protein-coding gene	gene with protein product		610063	"dynein, axonemal, heavy polypeptide 17", "dynein, axonemal, heavy chain like 1", "dynein, axonemal, heavy like 1"	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.6109G>C	chr17.hg19:g.76490821C>G	ENSP00000465516:p.Ala2037Pro	32.0	0.0		33.0	15.0	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Missense_Mutation	SNP	ENST00000585328.1	hg19		.	.	.	.	.	.	.	.	.	.	C	1.406	-0.576862	0.03854	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.24151	1.87	4.12	4.12	0.48240	.	.	.	.	.	T	0.05318	0.0141	N	0.00186	-1.895	0.35981	D	0.835992	.	.	.	.	.	.	T	0.28332	-1.0047	7	0.02654	T	1	.	12.4486	0.55666	0.0:0.8309:0.1691:0.0	.	.	.	.	P	2037;2028	ENSP00000374490:A2028P	ENSP00000300671:A2037P	A	-	1	0	DNAH17	74002416	0.888000	0.30383	0.920000	0.36463	0.611000	0.37282	1.414000	0.34736	2.105000	0.64084	0.511000	0.50034	GCA	.	.		0.622	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		G	76490821	C	G	76490821	3	3	335	1	0	0	0	0	1	0	0	0	4603	739	26	4	7432	4	DNAH17	17	76490821	Missense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	370012	76490821	4704389	161	46712										
DLGAP1	9229	hgsc.bcm.edu	37	chr18	3879551	3879551	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tgccatagcgcgccgcctgcGcctcgtcagggctggccttg	14	16	1	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr18:3879551G>A	ENST00000315677.3	-	4	1113	c.518C>T	c.(517-519)gCg>gTg	p.A173V	DLGAP1_ENST00000515196.2_Missense_Mutation_p.A173V|DLGAP1_ENST00000584874.1_Missense_Mutation_p.A173V|DLGAP1_ENST00000581527.1_Missense_Mutation_p.A173V|DLGAP1-AS3_ENST00000577649.1_RNA	NM_004746.3	NP_004737.2	O14490	DLGP1_HUMAN	discs, large (Drosophila) homolog-associated protein 1	173					synaptic transmission (GO:0007268)	cell junction (GO:0030054)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)				breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	56		Colorectal(8;0.0257)				CGCCGCCTGCGCCTCGTCAGG	0.706																																					p.A173V		Atlas-SNP	.											.	DLGAP1	201	.	0			c.C518T						.						51	60	57					18																	3879551		2201	4299	6500	SO:0001583	missense	9229	exon4			GCCTGCGCCTCGT	AB000277	CCDS11836.1, CCDS42406.1, CCDS56049.1, CCDS56050.1, CCDS56051.1, CCDS56052.1, CCDS56053.1, CCDS74191.1	18p11.3	2008-07-28	2001-11-28		ENSG00000170579	ENSG00000170579			2905	protein-coding gene	gene with protein product		605445	"discs, large (Drosophila) homolog-associated protein 1"			9024696, 9286858	Standard	NM_004746		Approved	GKAP, SAPAP1, DAP-1	uc002kmf.3	O14490	OTTHUMG00000131537	ENST00000315677.3:c.518C>T	chr18.hg19:g.3879551G>A	ENSP00000316377:p.Ala173Val	26.0	0.0		31.0	11.0	NM_001242761	A8MWN8|B2RMU8|B7WPA1|B7Z2H2|B7Z2I2|B7Z9Y4|O14489|P78335	Missense_Mutation	SNP	ENST00000315677.3	hg19	CCDS11836.1	.	.	.	.	.	.	.	.	.	.	G	13.41	2.228993	0.39399	.	.	ENSG00000170579	ENST00000315677;ENST00000515196	T;T	0.17054	2.3;2.3	5.75	4.88	0.63580	.	0.864654	0.10464	N	0.671579	T	0.12050	0.0293	N	0.14661	0.345	0.21719	N	0.999575	B;B;B	0.12013	0.0;0.003;0.005	B;B;B	0.04013	0.0;0.001;0.001	T	0.21484	-1.0244	10	0.52906	T	0.07	-1.1329	10.8725	0.46891	0.1435:0.0:0.8565:0.0	.	173;173;173	B7Z9Y4;Q6IS01;O14490	.;.;DLGP1_HUMAN	V	173	ENSP00000316377:A173V;ENSP00000445973:A173V	ENSP00000316377:A173V	A	-	2	0	DLGAP1	3869551	0.999000	0.42202	0.960000	0.40013	0.863000	0.49368	5.382000	0.66213	1.442000	0.47568	0.655000	0.94253	GCG	.	.		0.706	DLGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254394.4			A	3879551	G	A	3879551	3	1	335	1	0	0	0	0	1	0	0	0	4561	1087	38	1	2510	1	DLGAP1	18	3879551	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10		3879551	74197697	162	46713										
SPIRE1	56907	hgsc.bcm.edu	37	chr18	12454401	12454401	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ctgttggtatttttccagctCtgccttcaccaggacctggc	9	13	2	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr18:12454401C>T	ENST00000409402.4	-	13	1987	c.1720G>A	c.(1720-1722)Gag>Aag	p.E574K	SPIRE1_ENST00000309836.5_Missense_Mutation_p.E363K|SPIRE1_ENST00000383356.2_Missense_Mutation_p.E401K|SPIRE1_ENST00000410092.3_Missense_Mutation_p.E560K|SPIRE1_ENST00000453447.2_Missense_Mutation_p.E440K|SPIRE1_ENST00000464481.1_5'UTR	NM_001128626.1	NP_001122098.1			spire-type actin nucleation factor 1											breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)	28						TTTTCCAGCTCTGCCTTCACC	0.433																																					p.E574K		Atlas-SNP	.											.	SPIRE1	120	.	0			c.G1720A						.						223	201	208					18																	12454401		2203	4300	6503	SO:0001583	missense	56907	exon13			CCAGCTCTGCCTT	AL833817	CCDS32790.2, CCDS45829.1, CCDS45830.1	18p11.21	2013-08-27	2013-08-27		ENSG00000134278	ENSG00000134278			30622	protein-coding gene	gene with protein product		609216	"spire homolog 1 (Drosophila)", "spire family actin nucleation factor 1"			10574461, 11747823	Standard	NM_001128626		Approved	spir-1, KIAA1135	uc002kre.3	Q08AE8	OTTHUMG00000153940	ENST00000409402.4:c.1720G>A	chr18.hg19:g.12454401C>T	ENSP00000387266:p.Glu574Lys	183.0	0.0		174.0	63.0	NM_001128626		Missense_Mutation	SNP	ENST00000409402.4	hg19	CCDS45829.1	.	.	.	.	.	.	.	.	.	.	C	36	5.867872	0.97043	.	.	ENSG00000134278	ENST00000453447;ENST00000409402;ENST00000410092;ENST00000309836;ENST00000383356	T;T;T;T;T	0.77489	-1.1;-1.1;-1.1;-1.1;-1.1	5.96	5.96	0.96718	Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.89784	0.6815	M	0.84082	2.675	0.80722	D	1	D;D;D	0.89917	0.998;1.0;0.999	D;D;D	0.91635	0.991;0.999;0.997	D	0.90074	0.4165	10	0.87932	D	0	-13.7881	20.3928	0.98949	0.0:1.0:0.0:0.0	.	560;363;574	Q08AE8-2;B4DWX0;Q08AE8	.;.;SPIR1_HUMAN	K	440;574;560;363;401	ENSP00000407050:E440K;ENSP00000387266:E574K;ENSP00000387226:E560K;ENSP00000309661:E363K;ENSP00000372847:E401K	ENSP00000309661:E363K	E	-	1	0	SPIRE1	12444401	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.294000	0.78760	2.813000	0.96785	0.655000	0.94253	GAG	.	.		0.433	SPIRE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333109.2	XM_290818		T	12454401	C	T	12454401	3	4	335	1	0	0	0	0	1	0	0	0	15086	922	32	3	570	3	SPIRE1	18	12454401	Missense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	8574850	12454401	65622847	163	46714										
LAMA3	3909	hgsc.bcm.edu	37	chr18	21523852	21523852	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ctctttatctttcaaaaggaCgtctggtctttgcactgggg	10	9	5	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr18:21523852C>A	ENST00000313654.9	+	69	9368	c.9127C>A	c.(9127-9129)Cgt>Agt	p.R3043S	LAMA3_ENST00000587184.1_Missense_Mutation_p.R1378S|LAMA3_ENST00000399516.3_Missense_Mutation_p.R2987S|LAMA3_ENST00000269217.6_Missense_Mutation_p.R1434S|LAMA3_ENST00000588770.1_3'UTR	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	3043	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					TTCAAAAGGACGTCTGGTCTT	0.473																																					p.R3043S		Atlas-SNP	.											.	LAMA3	397	.	0			c.C9127A						.						125	113	117					18																	21523852		2203	4300	6503	SO:0001583	missense	3909	exon69			AAAGGACGTCTGG	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"Laminins"	6483	protein-coding gene	gene with protein product		600805	"laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.9127C>A	chr18.hg19:g.21523852C>A	ENSP00000324532:p.Arg3043Ser	85.0	0.0		74.0	31.0	NM_198129	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	hg19	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	C	17.61	3.432036	0.62844	.	.	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000269217	T;T;T	0.78481	-1.18;-1.18;-1.18	5.23	4.36	0.52297	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.	.	.	.	D	0.83110	0.5183	M	0.69185	2.1	0.19945	N	0.999942	B;B;D;D	0.56968	0.251;0.299;0.978;0.962	B;B;P;P	0.54924	0.142;0.187;0.764;0.684	T	0.75031	-0.3461	9	0.52906	T	0.07	.	13.7668	0.62999	0.0:0.9266:0.0:0.0734	.	1378;1434;2987;3043	Q6VU69;B0YJ33;Q6VU67;Q16787	.;.;.;LAMA3_HUMAN	S	3043;2987;1434	ENSP00000324532:R3043S;ENSP00000382432:R2987S;ENSP00000269217:R1434S	ENSP00000269217:R1434S	R	+	1	0	LAMA3	19777850	0.290000	0.24343	0.006000	0.13384	0.927000	0.56198	1.326000	0.33735	1.442000	0.47568	0.655000	0.94253	CGT	.	.		0.473	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		A	21523852	C	A	21523852	3	1	335	1	0	0	0	0	1	0	0	0	8616	536	19	1	9576	1	LAMA3	18	21523852	Missense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	9069451	21523852	56553396	164	46715										
RTTN	25914	hgsc.bcm.edu	37	chr18	67802444	67802444	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tatccattctcgatacttcaTcaaataatagaagacaaaat	3	8	3	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr18:67802444T>C	ENST00000255674.6	-	22	3147	c.2861A>G	c.(2860-2862)gAt>gGt	p.D954G	RTTN_ENST00000437017.1_Missense_Mutation_p.D954G|RTTN_ENST00000454359.1_3'UTR	NM_173630.3	NP_775901.3	Q86VV8	RTTN_HUMAN	rotatin	954					determination of left/right symmetry (GO:0007368)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(35)|ovary(4)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Esophageal squamous(42;0.129)				CGATACTTCATCAAATAATAG	0.303																																					p.D954G		Atlas-SNP	.											.	RTTN	184	.	0			c.A2861G						.						85	75	78					18																	67802444		1799	4069	5868	SO:0001583	missense	25914	exon22			ACTTCATCAAATA	AL117635	CCDS42443.1	18q22.1	2008-08-01				ENSG00000176225			18654	protein-coding gene	gene with protein product		610436				11900971	Standard	NM_173630		Approved	DKFZP434G145	uc002lkp.2	Q86VV8		ENST00000255674.6:c.2861A>G	chr18.hg19:g.67802444T>C	ENSP00000255674:p.Asp954Gly	171.0	0.0		193.0	42.0	NM_173630	Q68CS9|Q6ZRL8|Q6ZTK3|Q86TG4|Q8N8N8|Q8TBQ4|Q96IN9|Q9UFJ4	Missense_Mutation	SNP	ENST00000255674.6	hg19	CCDS42443.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.295111	0.81025	.	.	ENSG00000176225	ENST00000255674;ENST00000437017	T;T	0.69435	0.31;-0.4	5.22	5.22	0.72569	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.80783	0.4689	M	0.70275	2.135	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.83150	-0.0104	10	0.72032	D	0.01	.	15.0872	0.72165	0.0:0.0:0.0:1.0	.	954	Q86VV8	RTTN_HUMAN	G	954	ENSP00000255674:D954G;ENSP00000399520:D954G	ENSP00000255674:D954G	D	-	2	0	RTTN	65953424	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.134000	0.71689	1.969000	0.57287	0.454000	0.30748	GAT	.	.		0.303	RTTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442988.1	NM_173630		C	67802444	T	C	67802444	3	2	335	1	0	0	0	0	1	0	0	0	13752	1435	50	2	3931	2	RTTN	18	67802444	Missense_Mutation	SNP	T	TCGA-RC-A6M6-01A-11D-A32G-10	46278592	67802444	10274804	165	46716										
ABCA7	10347	hgsc.bcm.edu	37	chr19	1051046	1051046	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	cctcagtacaacgtgctgttTgacatgtgcgtctcggcagg	12	11	2	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr19:1051046T>A	ENST00000263094.6	+	19	2910	c.2679T>A	c.(2677-2679)ttT>ttA	p.F893L	ABCA7_ENST00000433129.1_Missense_Mutation_p.F893L|ABCA7_ENST00000435683.2_Missense_Mutation_p.F755L	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	893	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACGTGCTGTTTGACATGTGCG	0.652																																					p.F893L		Atlas-SNP	.											.	ABCA7	174	.	0			c.T2679A						.						60	61	61					19																	1051046		2196	4292	6488	SO:0001583	missense	10347	exon19			GCTGTTTGACATG	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"ATP binding cassette transporters / subfamily A"	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.2679T>A	chr19.hg19:g.1051046T>A	ENSP00000263094:p.Phe893Leu	47.0	0.0		24.0	14.0	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	hg19	CCDS12055.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.327090	0.81690	.	.	ENSG00000064687	ENST00000263094;ENST00000433129	T;T	0.80480	-1.38;-1.38	4.07	0.231	0.15377	ATPase, AAA+ type, core (1);ABC transporter-like (2);	.	.	.	.	D	0.83138	0.5189	L	0.43701	1.375	0.30328	N	0.786934	D;D	0.89917	0.998;1.0	D;D	0.85130	0.984;0.997	T	0.76567	-0.2912	9	0.87932	D	0	.	7.5503	0.27793	0.0:0.3303:0.0:0.6697	.	755;893	Q8IZY2-2;Q8IZY2	.;ABCA7_HUMAN	L	893	ENSP00000263094:F893L;ENSP00000414062:F893L	ENSP00000263094:F893L	F	+	3	2	ABCA7	1002046	0.324000	0.24652	0.598000	0.28837	0.949000	0.60115	-0.399000	0.07250	-0.205000	0.10219	0.374000	0.22700	TTT	.	.		0.652	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112		A	1051046	T	A	1051046	3	1	335	1	0	0	0	0	1	0	0	0	37	1809	63	4	2749	4	ABCA7	19	1051046	Missense_Mutation	SNP	T	TCGA-RC-A6M6-01A-11D-A32G-10		1051046	58077937	166	46717										
APC2	10297	hgsc.bcm.edu	37	chr19	1468353	1468354	+	In_Frame_Ins	INS	-	-	AGT													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ctccgacctggatagcgtggINSagtggcgcgccatccaggag							TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr19:1468353_1468354insAGT	ENST00000535453.1	+	14	6766_6767	c.5053_5054insAGT	c.(5053-5055)gag>gAGTag	p.1685_1686ins*	APC2_ENST00000238483.4_In_Frame_Ins_p.1411_1412ins*|C19orf25_ENST00000588427.1_Intron|APC2_ENST00000233607.2_In_Frame_Ins_p.1685_1686ins*			P02655	APOC2_HUMAN	adenomatosis polyposis coli 2	0					cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|chylomicron remnant clearance (GO:0034382)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle clearance (GO:0034384)|lipid catabolic process (GO:0016042)|lipoprotein metabolic process (GO:0042157)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of lipid metabolic process (GO:0045833)|negative regulation of receptor-mediated endocytosis (GO:0048261)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipid catabolic process (GO:0060697)|positive regulation of triglyceride catabolic process (GO:0010898)|positive regulation of very-low-density lipoprotein particle remodeling (GO:0010902)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)|triglyceride-rich lipoprotein particle remodeling (GO:0034370)|very-low-density lipoprotein particle remodeling (GO:0034372)	chylomicron (GO:0042627)|early endosome (GO:0005769)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate-density lipoprotein particle (GO:0034363)|low-density lipoprotein particle (GO:0034362)|spherical high-density lipoprotein particle (GO:0034366)|very-low-density lipoprotein particle (GO:0034361)	lipase inhibitor activity (GO:0055102)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|kidney(4)|large_intestine(2)|lung(5)|pancreas(1)|skin(2)	18		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGATAGCGTGGAGTGGCGCGCC	0.718																																					p.E1685delinsEX		Atlas-Indel,Pindel	.											.	APC2	50	.	0			c.5053_5054insAGT						.																																			SO:0001652	inframe_insertion	10297	exon15			.		CCDS12068.1	19p13.3	2013-02-14			ENSG00000115266	ENSG00000115266		"Armadillo repeat containing"	24036	protein-coding gene	gene with protein product	"adenomatous polyposis coli like"	612034				9823329, 10021369	Standard	XM_005259475		Approved	APCL	uc002lsr.1	O95996		ENST00000535453.1:c.5054_5056dupAGT	chr19.hg19:g.1468354_1468356dupAGT	ENSP00000442954:p.Trp1686*	50.0	0.0		36.0	24.0	NM_005883	C0JYY4|Q9BS39|Q9UDE3|Q9UNK3	In_Frame_Ins	INS	ENST00000535453.1	hg19	CCDS12068.1																																																																																			.	.		0.718	APC2-004	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449539.2	NM_005883		AGT	1468354	-	AGT	1468353	7	5	335	1	0	1	1	0	0	0	0	0	764	1175	41	0	5107	0	APC2	19	1468353	In_Frame_Ins	INS	-	TCGA-RC-A6M6-01A-11D-A32G-10	417307	1468353	57660630	167	46718										
MATK	4145	hgsc.bcm.edu	37	chr19	3783884	3783884	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tggccgtcgcggtgcagcacGcggtagtggatgacgtcgcg	18	11	0	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr19:3783884G>A	ENST00000310132.6	-	6	908	c.510C>T	c.(508-510)cgC>cgT	p.R170R	MATK_ENST00000585778.1_Silent_p.R170R|MATK_ENST00000395040.2_Silent_p.R129R|MATK_ENST00000395045.2_Silent_p.R171R	NM_139355.2	NP_647612.1	P42679	MATK_HUMAN	megakaryocyte-associated tyrosine kinase	170	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cell proliferation (GO:0008283)|mesoderm development (GO:0007498)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)	cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|skin(2)|stomach(2)|urinary_tract(1)	26		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)		GGTGCAGCACGCGGTAGTGGA	0.667																																					p.R171R		Atlas-SNP	.											.	MATK	108	.	0			c.C513T						.						57	48	51					19																	3783884		2203	4300	6503	SO:0001819	synonymous_variant	4145	exon6			CAGCACGCGGTAG	L18974	CCDS12113.1, CCDS12114.1, CCDS42468.1	19p13.3	2013-02-14						"SH2 domain containing"	6906	protein-coding gene	gene with protein product	"Csk-homologous kinase", "tyrosine-protein kinase CTK", "protein kinase HYL", "hematopoietic consensus tyrosine-lacking kinase", "tyrosylprotein kinase", "hydroxyaryl-protein kinase", "Csk-type protein tyrosine kinase", "HYL tyrosine kinase", "tyrosine kinase MATK", "leukocyte carboxyl-terminal src kinase related"	600038				8288563, 7530249	Standard	NM_139355		Approved	HYLTK, CTK, HYL, Lsk, CHK, HHYLTK, DKFZp434N1212, MGC1708, MGC2101	uc002lyt.3	P42679		ENST00000310132.6:c.510C>T	chr19.hg19:g.3783884G>A		80.0	0.0		59.0	39.0	NM_002378	B3KNZ9|Q9NST8	Silent	SNP	ENST00000310132.6	hg19	CCDS12114.1																																																																																			.	.		0.667	MATK-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453639.1	NM_139355		A	3783884	G	A	3783884	2	1	335	1	0	0	0	0	0	0	0	1	9341	1074	38	1		1	MATK	19	3783884	Silent	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	2315531	3783884	55345099	168	46719										
C3	718	hgsc.bcm.edu	37	chr19	6678293	6678293	+	Frame_Shift_Del	DEL	C	C	-													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ctgtccaacctgcacctcatCcgagcctggagtggagggga							TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr19:6678293delC	ENST00000245907.6	-	40	4812	c.4720delG	c.(4720-4722)gatfs	p.D1574fs	C3_ENST00000599668.1_5'UTR	NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	1574	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	TGCACCTCATCCGAGCCTGGA	0.597																																					p.D1574fs		Atlas-Indel,Pindel	.											.	C3	192	.	0			c.4721delA						.						83	65	71					19																	6678293		2203	4300	6503	SO:0001589	frameshift_variant	718	exon40			.	J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"Complement system", "Endogenous ligands"	1318	protein-coding gene	gene with protein product	"C3a anaphylatoxin", "complement component C3a", "complement component C3b", "prepro-C3"	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.4720delG	chr19.hg19:g.6678293delC	ENSP00000245907:p.Asp1574fs	93.0	0.0		51.0	29.0	NM_000064	A7E236	Frame_Shift_Del	DEL	ENST00000245907.6	hg19	CCDS32883.1																																																																																			.	.		0.597	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064		-	6678293	C	-	6678293	7	5	335	1	0	1	0	1	0	0	0	0	2206	855	30	0	279	0	C3	19	6678293	Frame_Shift_Del	DEL	C	TCGA-RC-A6M6-01A-11D-A32G-10	2894409	6678293	52450690	169	46720										
KEAP1	9817	hgsc.bcm.edu	37	chr19	10610444	10610444	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gggccatgaactgggcggccGgtgcatcctggtacttgacc	15	12	0	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr19:10610444G>A	ENST00000171111.5	-	2	813	c.266C>T	c.(265-267)cCg>cTg	p.P89L	KEAP1_ENST00000588024.1_5'Flank|KEAP1_ENST00000393623.2_Missense_Mutation_p.P89L	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	89	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)				breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	CTGGGCGGCCGGTGCATCCTG	0.612																																					p.P89L		Atlas-SNP	.											.	KEAP1	182	.	0			c.C266T						.						95	72	80					19																	10610444		2203	4300	6503	SO:0001583	missense	9817	exon2			GCGGCCGGTGCAT	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"Kelch-like", "BTB/POZ domain containing"	23177	protein-coding gene	gene with protein product	"kelch-like family member 19"	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.266C>T	chr19.hg19:g.10610444G>A	ENSP00000171111:p.Pro89Leu	54.0	0.0		38.0	30.0	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Missense_Mutation	SNP	ENST00000171111.5	hg19	CCDS12239.1	.	.	.	.	.	.	.	.	.	.	G	12.58	1.981897	0.34942	.	.	ENSG00000079999	ENST00000171111;ENST00000393623	T;T	0.72282	-0.64;-0.64	4.68	4.68	0.58851	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.234176	0.44097	D	0.000491	T	0.53818	0.1820	L	0.33293	1	0.41368	D	0.987472	P	0.36378	0.55	B	0.28784	0.094	T	0.56238	-0.8012	10	0.33940	T	0.23	.	10.3791	0.44101	0.0:0.0:0.8042:0.1958	.	89	Q14145	KEAP1_HUMAN	L	89	ENSP00000171111:P89L;ENSP00000377245:P89L	ENSP00000171111:P89L	P	-	2	0	KEAP1	10471444	1.000000	0.71417	0.048000	0.18961	0.137000	0.21094	4.407000	0.59754	2.162000	0.67917	0.462000	0.41574	CCG	.	.		0.612	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289		A	10610444	G	A	10610444	3	1	335	1	0	0	0	0	1	0	0	0	8150	1116	39	1	1628	1	KEAP1	19	10610444	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	3932151	10610444	48518539	170	46721										
F2RL3	9002	hgsc.bcm.edu	37	chr19	17001135	17001135	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gcgctgaggctgaccgcagtGgtgctggcctccgccgtggc	17	14	0	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr19:17001135G>T	ENST00000248076.3	+	2	1191	c.861G>T	c.(859-861)gtG>gtT	p.V287V		NM_003950.2	NP_003941.2	Q96RI0	PAR4_HUMAN	coagulation factor II (thrombin) receptor-like 3	287					blood coagulation (GO:0007596)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|platelet activation (GO:0030168)|platelet dense granule organization (GO:0060155)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|response to wounding (GO:0009611)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	thrombin receptor activity (GO:0015057)			cervix(1)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	7						TGACCGCAGTGGTGCTGGCCT	0.706																																					p.V287V		Atlas-SNP	.											.	F2RL3	20	.	0			c.G861T						.						10	11	11					19																	17001135		2179	4277	6456	SO:0001819	synonymous_variant	9002	exon2			CGCAGTGGTGCTG	AF055917	CCDS12350.1	19p12	2012-08-08						"GPCR / Class A : Protease activated receptors"	3540	protein-coding gene	gene with protein product	"proteinase-activated receptor-4"	602779				9618465	Standard	XM_005260139		Approved	PAR4	uc002nfa.3	Q96RI0		ENST00000248076.3:c.861G>T	chr19.hg19:g.17001135G>T		18.0	0.0		36.0	19.0	NM_003950	O76067|Q6DK42	Silent	SNP	ENST00000248076.3	hg19	CCDS12350.1																																																																																			.	.		0.706	F2RL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462875.1			T	17001135	G	T	17001135	2	4	335	1	0	0	0	0	0	0	0	1	5348	1335	47	3		3	F2RL3	19	17001135	Silent	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	6390691	17001135	42127848	171	46722										
ZNF98	148198	hgsc.bcm.edu	37	chr19	22574550	22574550	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	aggactggttaaaagctttgCcacattcttcacatttgtag	8	8	2	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr19:22574550C>G	ENST00000357774.5	-	4	1608	c.1487G>C	c.(1486-1488)gGc>gCc	p.G496A		NM_001098626.1	NP_001092096.1	A6NK75	ZNF98_HUMAN	zinc finger protein 98	496					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)				AAAAGCTTTGCCACATTCTTC	0.393																																					p.G496A		Atlas-SNP	.											ZNF98_ENST00000357774,NS,carcinoma,+1,2	ZNF98	230	.	0			c.G1487C						.						77	69	71					19																	22574550		2186	4284	6470	SO:0001583	missense	148198	exon4			GCTTTGCCACATT		CCDS46031.1	19p12	2014-02-14	2010-04-20	2008-06-12	ENSG00000197360	ENSG00000197360		"Zinc fingers, C2H2-type", "-"	13174	protein-coding gene	gene with protein product	"zinc finger protein 739"	603980					Standard	NM_001098626		Approved	ZNF739, F7175	uc002nqt.2	A6NK75	OTTHUMG00000182940	ENST00000357774.5:c.1487G>C	chr19.hg19:g.22574550C>G	ENSP00000350418:p.Gly496Ala	257.0	0.0		330.0	85.0	NM_001098626		Missense_Mutation	SNP	ENST00000357774.5	hg19	CCDS46031.1	.	.	.	.	.	.	.	.	.	.	.	12.60	1.987010	0.35036	.	.	ENSG00000197360	ENST00000357774	T	0.57595	0.39	1.26	1.26	0.21427	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.69504	0.3118	M	0.79805	2.47	0.25332	N	0.989022	D	0.69078	0.997	D	0.69824	0.966	T	0.57533	-0.7795	9	0.87932	D	0	.	9.3872	0.38349	0.0:1.0:0.0:0.0	.	496	A6NK75	ZNF98_HUMAN	A	496	ENSP00000350418:G496A	ENSP00000350418:G496A	G	-	2	0	ZNF98	22366390	0.865000	0.29922	0.024000	0.17045	0.026000	0.11368	1.422000	0.34826	0.665000	0.31066	0.289000	0.19496	GGC	.	.		0.393	ZNF98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464398.1	NM_001098626		G	22574550	C	G	22574550	3	3	335	1	0	0	0	0	1	0	0	0	18218	739	26	4	235	4	ZNF98	19	22574550	Missense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	5573415	22574550	36554433	172	46723										
CEACAM3	1084	hgsc.bcm.edu	37	chr19	42301829	42301829	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gattctacaccctacaagtcAtaaagtcagatcttgtgaat	6	9	4	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr19:42301829A>T	ENST00000357396.3	+	2	614	c.373A>T	c.(373-375)Ata>Tta	p.I125L	CEACAM3_ENST00000344550.4_Missense_Mutation_p.I125L|CEACAM3_ENST00000595255.1_3'UTR|CEACAM3_ENST00000221999.4_Missense_Mutation_p.I125L	NM_001815.2	NP_001806.2	P40198	CEAM3_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 3	125	Ig-like V-type.					integral component of membrane (GO:0016021)				endometrium(2)|kidney(4)|large_intestine(1)|lung(4)|prostate(3)|skin(4)|stomach(1)	19						CCTACAAGTCATAAAGTCAGA	0.473																																					p.I125L		Atlas-SNP	.											.	CEACAM3	37	.	0			c.A373T						.						241	248	245					19																	42301829		2203	4300	6503	SO:0001583	missense	1084	exon2			CAAGTCATAAAGT	E03349	CCDS12586.2, CCDS62685.1	19q13.2	2013-01-11			ENSG00000170956	ENSG00000170956		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	1815	protein-coding gene	gene with protein product		609142		CGM1			Standard	NM_001815		Approved	CD66d	uc002orn.2	P40198	OTTHUMG00000150142	ENST00000357396.3:c.373A>T	chr19.hg19:g.42301829A>T	ENSP00000349971:p.Ile125Leu	99.0	0.0		63.0	38.0	NM_001815	G5E978|Q3KPH9	Missense_Mutation	SNP	ENST00000357396.3	hg19	CCDS12586.2	.	.	.	.	.	.	.	.	.	.	A	13.89	2.371809	0.42003	.	.	ENSG00000170956	ENST00000357396;ENST00000389667;ENST00000221999;ENST00000344550	T;T;T	0.66099	-0.19;-0.19;-0.19	2.91	-2.78	0.05859	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.65048	0.2654	L	0.56199	1.76	0.09310	N	1	P;P	0.50369	0.934;0.599	P;P	0.62560	0.904;0.728	T	0.57033	-0.7880	9	0.87932	D	0	.	2.4276	0.04463	0.408:0.0:0.252:0.34	.	125;125	G5E978;P40198	.;CEAM3_HUMAN	L	125	ENSP00000349971:I125L;ENSP00000221999:I125L;ENSP00000341725:I125L	ENSP00000221999:I125L	I	+	1	0	CEACAM3	46993669	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.368000	0.02580	-0.974000	0.03550	-0.476000	0.04901	ATA	.	.		0.473	CEACAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316509.2	NM_001815		T	42301829	A	T	42301829	3	4	335	1	0	0	0	0	1	0	0	0	3195	217	8	4	379	4	CEACAM3	19	42301829	Missense_Mutation	SNP	A	TCGA-RC-A6M6-01A-11D-A32G-10	19727279	42301829	16827154	173	46724										
LRRC4B	94030	hgsc.bcm.edu	37	chr19	51021453	51021453	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gttccttctccgtcccccgcGgctgcagggcctcctctccg	10	20	2	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr19:51021453G>A	ENST00000599957.1	-	3	1714	c.1517C>T	c.(1516-1518)cCg>cTg	p.P506L	LRRC4B_ENST00000389201.3_Missense_Mutation_p.P506L			Q9NT99	LRC4B_HUMAN	leucine rich repeat containing 4B	506	Gly-rich.				positive regulation of synapse assembly (GO:0051965)	cell junction (GO:0030054)|cerebellar mossy fiber (GO:0044300)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|liver(1)|lung(11)|prostate(4)|skin(1)|urinary_tract(1)	30		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00284)|GBM - Glioblastoma multiforme(134;0.0188)		CGTCCCCCGCGGCTGCAGGGC	0.716																																					p.P506L		Atlas-SNP	.											.	LRRC4B	89	.	0			c.C1517T						.						8	10	9					19																	51021453		1824	3931	5755	SO:0001583	missense	94030	exon3			CCCCGCGGCTGCA	BC032460	CCDS42595.1	19q13.33	2014-01-30	2004-06-14	2004-06-16	ENSG00000131409	ENSG00000131409		"Immunoglobulin superfamily / I-set domain containing", "Endogenous ligands"	25042	protein-coding gene	gene with protein product	"netrin-G3 ligand"		"leucine-rich repeats and immunoglobulin-like domains 4"	LRIG4		11441184	Standard	NM_001080457		Approved	DKFZp761A179, HSM	uc002pss.3	Q9NT99		ENST00000599957.1:c.1517C>T	chr19.hg19:g.51021453G>A	ENSP00000471502:p.Pro506Leu	15.0	0.0		15.0	14.0	NM_001080457	Q3ZCQ4|Q58F20	Missense_Mutation	SNP	ENST00000599957.1	hg19	CCDS42595.1	.	.	.	.	.	.	.	.	.	.	G	6.564	0.472324	0.12461	.	.	ENSG00000131409	ENST00000389201	T	0.58940	0.3	3.15	3.15	0.36227	.	1.571100	0.04028	U	0.300945	T	0.31263	0.0791	N	0.01048	-1.04	0.09310	N	0.999993	B	0.25206	0.12	B	0.16289	0.015	T	0.14420	-1.0473	10	0.30854	T	0.27	.	12.1443	0.54014	0.0:0.0:1.0:0.0	.	506	Q9NT99	LRC4B_HUMAN	L	506	ENSP00000373853:P506L	ENSP00000373853:P506L	P	-	2	0	LRRC4B	55713265	0.962000	0.33011	0.988000	0.46212	0.473000	0.32948	3.486000	0.53215	1.764000	0.52075	0.462000	0.41574	CCG	.	.		0.716	LRRC4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464907.1	NM_001080457		A	51021453	G	A	51021453	3	1	335	1	0	0	0	0	1	0	0	0	9016	1116	39	1	628	1	LRRC4B	19	51021453	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	8719624	51021453	8107530	174	46725										
ZNF577	84765	hgsc.bcm.edu	37	chr19	52376841	52376841	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gggctgctgggtttaacacaTctatggtatttaactccagt	10	8	1	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr19:52376841T>A	ENST00000301399.5	-	7	767	c.402A>T	c.(400-402)agA>agT	p.R134S	ZNF577_ENST00000451628.2_Intron|ZNF577_ENST00000420592.1_Intron|ZNF577_ENST00000485702.1_Intron|ZNF577_ENST00000412216.1_Intron	NM_032679.2	NP_116068.2	Q9BSK1	ZN577_HUMAN	zinc finger protein 577	134					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		GTTTAACACATCTATGGTATT	0.433																																					p.R134S		Atlas-SNP	.											.	ZNF577	63	.	0			c.A402T						.						118	115	116					19																	52376841		2203	4300	6503	SO:0001583	missense	84765	exon7			AACACATCTATGG	AL832871	CCDS12842.2, CCDS46160.1	19q13.41	2013-09-20			ENSG00000161551	ENSG00000161551		"Zinc fingers, C2H2-type", "-"	28673	protein-coding gene	gene with protein product						12477932	Standard	NM_032679		Approved	MGC4400	uc010yde.2	Q9BSK1	OTTHUMG00000157045	ENST00000301399.5:c.402A>T	chr19.hg19:g.52376841T>A	ENSP00000301399:p.Arg134Ser	135.0	0.0		60.0	37.0	NM_032679	A8K0B4|A8K6Z7|C9JFB9	Missense_Mutation	SNP	ENST00000301399.5	hg19	CCDS12842.2	.	.	.	.	.	.	.	.	.	.	.	7.067	0.567571	0.13560	.	.	ENSG00000161551	ENST00000301399;ENST00000458390	T;T	0.06294	3.33;3.32	2.4	0.197	0.15164	.	.	.	.	.	T	0.03608	0.0103	N	0.22421	0.69	0.80722	D	1	B	0.16603	0.018	B	0.08055	0.003	T	0.43940	-0.9360	9	0.72032	D	0.01	.	0.8947	0.01261	0.1838:0.1249:0.2087:0.4826	.	134	Q9BSK1	ZN577_HUMAN	S	134	ENSP00000301399:R134S;ENSP00000404509:R134S	ENSP00000301399:R134S	R	-	3	2	ZNF577	57068653	0.000000	0.05858	0.129000	0.21949	0.522000	0.34438	-2.710000	0.00818	-0.029000	0.13827	0.383000	0.25322	AGA	.	.		0.433	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679		A	52376841	T	A	52376841	3	1	335	1	0	0	0	0	1	0	0	0	18024	1432	50	4	1059	4	ZNF577	19	52376841	Missense_Mutation	SNP	T	TCGA-RC-A6M6-01A-11D-A32G-10	1355388	52376841	6752142	175	46726										
ZNF577	84765	hgsc.bcm.edu	37	chr19	52376925	52376925	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ccaccaaatgcatcagaatcTtttcctgcatatcttctact	3	13	4	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr19:52376925T>A	ENST00000301399.5	-	7	683	c.318A>T	c.(316-318)aaA>aaT	p.K106N	ZNF577_ENST00000451628.2_Intron|ZNF577_ENST00000420592.1_Intron|ZNF577_ENST00000485702.1_Intron|ZNF577_ENST00000412216.1_Intron	NM_032679.2	NP_116068.2	Q9BSK1	ZN577_HUMAN	zinc finger protein 577	106					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		CATCAGAATCTTTTCCTGCAT	0.363																																					p.K106N		Atlas-SNP	.											.	ZNF577	63	.	0			c.A318T						.						60	54	56					19																	52376925		2203	4300	6503	SO:0001583	missense	84765	exon7			AGAATCTTTTCCT	AL832871	CCDS12842.2, CCDS46160.1	19q13.41	2013-09-20			ENSG00000161551	ENSG00000161551		"Zinc fingers, C2H2-type", "-"	28673	protein-coding gene	gene with protein product						12477932	Standard	NM_032679		Approved	MGC4400	uc010yde.2	Q9BSK1	OTTHUMG00000157045	ENST00000301399.5:c.318A>T	chr19.hg19:g.52376925T>A	ENSP00000301399:p.Lys106Asn	93.0	0.0		49.0	33.0	NM_032679	A8K0B4|A8K6Z7|C9JFB9	Missense_Mutation	SNP	ENST00000301399.5	hg19	CCDS12842.2	.	.	.	.	.	.	.	.	.	.	.	9.540	1.113190	0.20795	.	.	ENSG00000161551	ENST00000301399;ENST00000458390	T;T	0.07444	3.2;3.19	2.68	-0.81	0.10860	.	.	.	.	.	T	0.08492	0.0211	M	0.66439	2.03	0.18873	N	0.999982	B	0.25312	0.123	B	0.17979	0.02	T	0.32188	-0.9916	9	0.44086	T	0.13	.	3.522	0.07745	0.1756:0.4689:0.0:0.3555	.	106	Q9BSK1	ZN577_HUMAN	N	106	ENSP00000301399:K106N;ENSP00000404509:K106N	ENSP00000301399:K106N	K	-	3	2	ZNF577	57068737	0.000000	0.05858	0.001000	0.08648	0.018000	0.09664	-1.363000	0.02592	-0.102000	0.12197	-0.456000	0.05471	AAA	.	.		0.363	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679		A	52376925	T	A	52376925	3	1	335	1	0	0	0	0	1	0	0	0	18024	1606	56	4	1143	4	ZNF577	19	52376925	Missense_Mutation	SNP	T	TCGA-RC-A6M6-01A-11D-A32G-10	84	52376925	6752058	176	46727										
PRPF31	26121	hgsc.bcm.edu	37	chr19	54626868	54626868	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ctggacaagtgcaagaacaaTgagaacctgcagcagatcct	10	10	0	3			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr19:54626868T>A	ENST00000321030.4	+	6	805	c.456T>A	c.(454-456)aaT>aaA	p.N152K	PRPF31_ENST00000498612.1_3'UTR|PRPF31_ENST00000419967.1_Missense_Mutation_p.N152K|AC012314.8_ENST00000452097.1_RNA|PRPF31_ENST00000391755.1_Missense_Mutation_p.N152K	NM_015629.3	NP_056444.3	Q8WWY3	PRP31_HUMAN	pre-mRNA processing factor 31	152					mRNA splicing, via spliceosome (GO:0000398)|spliceosomal tri-snRNP complex assembly (GO:0000244)	Cajal body (GO:0015030)|MLL1 complex (GO:0071339)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|U2-type spliceosomal complex (GO:0005684)|U4 snRNP (GO:0005687)|U4/U6 x U5 tri-snRNP complex (GO:0046540)|U4atac snRNP (GO:0005690)	poly(A) RNA binding (GO:0044822)|ribonucleoprotein complex binding (GO:0043021)|snRNP binding (GO:0070990)			breast(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(2)|urinary_tract(3)	12	all_cancers(19;0.00681)|all_epithelial(19;0.00362)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					GCAAGAACAATGAGAACCTGC	0.617																																					p.N152K		Atlas-SNP	.											.	PRPF31	48	.	0			c.T456A						.						171	149	157					19																	54626868		2203	4300	6503	SO:0001583	missense	26121	exon6			GAACAATGAGAAC	AL050369	CCDS12879.1	19q13.4	2013-07-16	2013-06-10		ENSG00000105618	ENSG00000105618			15446	protein-coding gene	gene with protein product		606419	"PRP31 pre-mRNA processing factor 31 homolog (yeast)", "PRP31 pre-mRNA processing factor 31 homolog (S. cerevisiae)"	RP11		11545739	Standard	NM_015629		Approved	NY-BR-99, PRP31, hPrp31, SNRNP61	uc002qdh.2	Q8WWY3	OTTHUMG00000066040	ENST00000321030.4:c.456T>A	chr19.hg19:g.54626868T>A	ENSP00000324122:p.Asn152Lys	74.0	0.0		81.0	44.0	NM_015629	Q17RB4|Q8N7F9|Q9H271|Q9Y439	Missense_Mutation	SNP	ENST00000321030.4	hg19	CCDS12879.1	.	.	.	.	.	.	.	.	.	.	T	14.43	2.532455	0.45073	.	.	ENSG00000105618	ENST00000321030;ENST00000445811;ENST00000263436;ENST00000419967;ENST00000445124;ENST00000447810;ENST00000391755	T;T;T;T;T;T	0.75821	-0.97;-0.97;-0.97;-0.97;-0.97;-0.97	4.82	-9.38	0.00623	.	0.000000	0.85682	D	0.000000	T	0.51941	0.1704	L	0.52011	1.625	0.48975	D	0.999733	P;P	0.45283	0.855;0.577	B;B	0.32724	0.151;0.065	T	0.64114	-0.6483	10	0.22109	T	0.4	-35.0544	11.5211	0.50551	0.0:0.209:0.0932:0.6978	.	152;152	E7ESA8;Q8WWY3	.;PRP31_HUMAN	K	152	ENSP00000324122:N152K;ENSP00000395894:N152K;ENSP00000405166:N152K;ENSP00000408980:N152K;ENSP00000395089:N152K;ENSP00000375635:N152K	ENSP00000263436:N152K	N	+	3	2	PRPF31	59318680	0.003000	0.15002	0.666000	0.29783	0.995000	0.86356	-1.374000	0.02566	-1.692000	0.01428	-0.290000	0.09829	AAT	.	.		0.617	PRPF31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141417.2			A	54626868	T	A	54626868	3	1	335	1	0	0	0	0	1	0	0	0	12578	1461	51	4	474	4	PRPF31	19	54626868	Missense_Mutation	SNP	T	TCGA-RC-A6M6-01A-11D-A32G-10	2249943	54626868	4502115	177	46728										
NFATC2	4773	hgsc.bcm.edu	37	chr20	50071174	50071174	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ggccgccatagaccaggcagCtgtctgtgtcttgtctttca	11	12	4	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr20:50071174C>T	ENST00000396009.3	-	6	1979	c.1760G>A	c.(1759-1761)aGc>aAc	p.S587N	NFATC2_ENST00000609507.1_Missense_Mutation_p.S368N|NFATC2_ENST00000414705.1_Missense_Mutation_p.S567N|MIR3194_ENST00000582236.1_RNA|NFATC2_ENST00000610033.1_Missense_Mutation_p.S368N|NFATC2_ENST00000609943.1_Missense_Mutation_p.S567N|NFATC2_ENST00000371564.3_Missense_Mutation_p.S587N	NM_001258297.1|NM_173091.3	NP_001245226.1|NP_775114.1	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	587					B cell receptor signaling pathway (GO:0050853)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear transcription factor complex (GO:0044798)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)		EWSR1/NFATC2(9)	breast(2)|endometrium(7)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	53	Hepatocellular(150;0.248)					GACCAGGCAGCTGTCTGTGTC	0.512																																					p.S587N		Atlas-SNP	.											.	NFATC2	112	.	0			c.G1760A						.						168	166	167					20																	50071174		2203	4300	6503	SO:0001583	missense	4773	exon6			AGGCAGCTGTCTG	U43342, U43341	CCDS13437.1, CCDS33488.1, CCDS46614.1, CCDS68156.1, CCDS68157.1	20q13.2	2009-11-24			ENSG00000101096	ENSG00000101096		"Nuclear factor of activated T-cells"	7776	protein-coding gene	gene with protein product		600490				8202141	Standard	NM_012340		Approved	NF-ATP, NFATp, NFAT1	uc002xwd.4	Q13469	OTTHUMG00000032747	ENST00000396009.3:c.1760G>A	chr20.hg19:g.50071174C>T	ENSP00000379330:p.Ser587Asn	74.0	0.0		120.0	71.0	NM_012340	B5B2N8|B5B2N9|B5B2P0|B5B2P2|B5B2P3|Q13468|Q5TFW7|Q5TFW8|Q9NPX6|Q9NQH3|Q9UJR2	Missense_Mutation	SNP	ENST00000396009.3	hg19	CCDS13437.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.622635	0.87460	.	.	ENSG00000101096	ENST00000371564;ENST00000396009;ENST00000414705	D;D;D	0.84070	-1.8;-1.8;-1.8	5.9	5.9	0.94986	Cell surface receptor IPT/TIG (1);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.081544	0.85682	D	0.000000	D	0.89729	0.6799	L	0.54323	1.7	0.45464	D	0.998436	P;D;P;P	0.52996	0.818;0.957;0.85;0.91	P;D;P;P	0.68483	0.565;0.958;0.565;0.565	D	0.89099	0.3488	10	0.59425	D	0.04	-27.6046	20.2789	0.98501	0.0:1.0:0.0:0.0	.	567;567;587;587	B5B2N9;B5B2P2;Q13469;B5B2N8	.;.;NFAC2_HUMAN;.	N	587;587;567	ENSP00000360619:S587N;ENSP00000379330:S587N;ENSP00000396471:S567N	ENSP00000360619:S587N	S	-	2	0	NFATC2	49504581	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	2.901000	0.48695	2.788000	0.95919	0.650000	0.86243	AGC	.	.		0.512	NFATC2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079730.2	NM_012340		T	50071174	C	T	50071174	3	4	335	1	0	0	0	0	1	0	0	0	10371	797	28	3	1085	3	NFATC2	20	50071174	Missense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10		50071174	12954346	178	46729										
ATP9A	10079	hgsc.bcm.edu	37	chr20	50292712	50292712	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	attcatgacactccggagttCtctgccagtgtaaagaacaa	8	10	2	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr20:50292712C>G	ENST00000338821.5	-	10	1099	c.835G>C	c.(835-837)Gaa>Caa	p.E279Q	ATP9A_ENST00000311637.5_Missense_Mutation_p.E143Q|ATP9A_ENST00000402822.1_Missense_Mutation_p.E158Q	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	279					phospholipid translocation (GO:0045332)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(10)|lung(18)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						CTCCGGAGTTCTCTGCCAGTG	0.438																																					p.E279Q		Atlas-SNP	.											.	ATP9A	135	.	0			c.G835C						.						95	84	88					20																	50292712		2203	4300	6503	SO:0001583	missense	10079	exon10			GGAGTTCTCTGCC	AB014511	CCDS33489.1	20q13.2	2010-04-20	2007-09-19		ENSG00000054793	ENSG00000054793		"ATPases / P-type"	13540	protein-coding gene	gene with protein product		609126	"ATPase, Class II, type 9A"			9734811, 11015572	Standard	NM_006045		Approved	KIAA0611, ATPIIA	uc002xwg.1	O75110	OTTHUMG00000032751	ENST00000338821.5:c.835G>C	chr20.hg19:g.50292712C>G	ENSP00000342481:p.Glu279Gln	105.0	0.0		132.0	7.0	NM_006045	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Missense_Mutation	SNP	ENST00000338821.5	hg19	CCDS33489.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.477373	0.84640	.	.	ENSG00000054793	ENST00000311637;ENST00000338821;ENST00000402822	T;D;T	0.88818	-1.32;-2.43;-1.32	5.61	5.61	0.85477	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.103305	0.64402	D	0.000004	D	0.93572	0.7948	M	0.61703	1.905	0.80722	D	1	B;D	0.89917	0.174;1.0	B;D	0.97110	0.071;1.0	D	0.91715	0.5384	10	0.31617	T	0.26	-23.1249	19.6283	0.95689	0.0:1.0:0.0:0.0	.	158;279	O75110-2;O75110	.;ATP9A_HUMAN	Q	143;279;158	ENSP00000309086:E143Q;ENSP00000342481:E279Q;ENSP00000385875:E158Q	ENSP00000309086:E143Q	E	-	1	0	ATP9A	49726119	1.000000	0.71417	0.999000	0.59377	0.981000	0.71138	7.429000	0.80309	2.627000	0.88993	0.655000	0.94253	GAA	.	.		0.438	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106494.1	NM_006045		G	50292712	C	G	50292712	3	3	335	1	0	0	0	0	1	0	0	0	1198	922	32	4	2384	4	ATP9A	20	50292712	Missense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	221538	50292712	12732808	179	46730										
PDXK	8566	hgsc.bcm.edu	37	chr21	45175644	45175644	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	aggaccatccagtgtgcaaaAggtacggcggccgggctgca	15	11	0	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr21:45175644A>T	ENST00000291565.4	+	10	1008	c.825A>T	c.(823-825)aaA>aaT	p.K275N	PDXK_ENST00000467908.1_Splice_Site_p.K235N|PDXK_ENST00000468090.1_Splice_Site_p.K247N	NM_003681.4	NP_003672.1	O00764	PDXK_HUMAN	pyridoxal (pyridoxine, vitamin B6) kinase	275					cell proliferation (GO:0008283)|pyridoxal 5'-phosphate salvage (GO:0009443)|pyridoxal phosphate biosynthetic process (GO:0042823)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|lithium ion binding (GO:0031403)|magnesium ion binding (GO:0000287)|potassium ion binding (GO:0030955)|protein homodimerization activity (GO:0042803)|pyridoxal kinase activity (GO:0008478)|pyridoxal phosphate binding (GO:0030170)|sodium ion binding (GO:0031402)|zinc ion binding (GO:0008270)			endometrium(1)|lung(2)|ovary(1)|urinary_tract(1)	5				Colorectal(79;0.109)|READ - Rectum adenocarcinoma(84;0.161)|STAD - Stomach adenocarcinoma(101;0.18)	Pyridoxal(DB00147)|Pyridoxine(DB00165)	AGTGTGCAAAAGGTACGGCGG	0.627																																					p.K275N		Atlas-SNP	.											.	PDXK	17	.	0			c.A825T						.						114	87	96					21																	45175644		2203	4300	6503	SO:0001630	splice_region_variant	8566	exon10			TGCAAAAGGTACG	U89606	CCDS13699.1	21q22.3	2007-05-10			ENSG00000160209	ENSG00000160209	2.7.1.35		8819	protein-coding gene	gene with protein product		179020	"chromosome 21 open reading frame 97", "chromosome 21 open reading frame 124"	C21orf97, C21orf124		9099727	Standard	NM_003681		Approved	PNK, PKH, FLJ21324, PRED79, FLJ31940, MGC15873	uc002zdm.4	O00764	OTTHUMG00000086870	ENST00000291565.4:c.826+1A>T	chr21.hg19:g.45175644A>T		24.0	0.0		14.0	8.0	NM_003681	Q7Z2Y0|Q9BS02	Missense_Mutation	SNP	ENST00000291565.4	hg19	CCDS13699.1	.	.	.	.	.	.	.	.	.	.	A	8.357	0.832196	0.16820	.	.	ENSG00000160209	ENST00000468090;ENST00000291565;ENST00000467908	T;T;T	0.75821	-0.97;-0.97;-0.97	5.14	2.66	0.31614	Carbohydrate/purine kinase (1);	0.334600	0.33792	N	0.004547	T	0.51381	0.1671	N	0.16098	0.37	0.58432	D	0.999999	B;B	0.09022	0.002;0.002	B;B	0.12156	0.005;0.007	T	0.36504	-0.9745	10	0.33940	T	0.23	-6.6336	4.3141	0.10984	0.6952:0.0:0.1583:0.1465	.	247;275	O00764-2;O00764	.;PDXK_HUMAN	N	247;275;235	ENSP00000418359:K247N;ENSP00000291565:K275N;ENSP00000420708:K235N	ENSP00000291565:K275N	K	+	3	2	PDXK	44000072	1.000000	0.71417	0.869000	0.34112	0.166000	0.22503	1.657000	0.37366	0.814000	0.34374	0.533000	0.62120	AAA	.	.		0.627	PDXK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195636.1	NM_003681	Missense_Mutation	T	45175644	A	T	45175644	5	4	335	1	0	0	0	0	0	0	1	0	11706	86	3	4	863	4	PDXK	21	45175644	Splice_Site	SNP	A	TCGA-RC-A6M6-01A-11D-A32G-10		45175644	2954251	180	46731										
PCNT	5116	hgsc.bcm.edu	37	chr21	47856895	47856895	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	cccatttatttttacaggacAgttaatgattggacgtcatc	7	8	1	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr21:47856895A>T	ENST00000359568.5	+	40	9107	c.9000A>T	c.(8998-9000)acA>acT	p.T3000T	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	3000	Interaction with NEK2.				brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					TTTACAGGACAGTTAATGATT	0.478																																					p.T3000T		Atlas-SNP	.											.	PCNT	283	.	0			c.A9000T						.						108	92	98					21																	47856895		2203	4300	6503	SO:0001819	synonymous_variant	5116	exon40			CAGGACAGTTAAT	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"kendrin", "Seckel syndrome 4"	605925	"pericentrin 2 (kendrin)"	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.9000A>T	chr21.hg19:g.47856895A>T		39.0	0.0		25.0	11.0	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	hg19	CCDS33592.1																																																																																			.	.		0.478	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031		T	47856895	A	T	47856895	2	4	335	1	0	0	0	0	0	0	0	1	11599	175	7	4		4	PCNT	21	47856895	Silent	SNP	A	TCGA-RC-A6M6-01A-11D-A32G-10	2681251	47856895	273000	181	46732										
RIMBP3	85376	hgsc.bcm.edu	37	chr22	20458090	20458090	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	aggtgacggtggaggacataGttccccaatacacctgcagc	12	11	0	1	rs563786718	byFrequency	TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr22:20458090G>T	ENST00000426804.1	-	1	3696	c.3212C>A	c.(3211-3213)aCt>aAt	p.T1071N	SCARNA17_ENST00000516762.1_RNA|SCARNA18_ENST00000516215.1_RNA|RN7SKP131_ENST00000363006.1_RNA	NM_015672.1	NP_056487.1	Q9UFD9	RIM3A_HUMAN	RIMS binding protein 3	1071	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.									breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	13	Colorectal(54;0.0993)|Melanoma(16;0.165)		LUSC - Lung squamous cell carcinoma(15;0.0405)|Lung(15;0.224)			GGAGGACATAGTTCCCCAATA	0.657													g|||	2	0.000399361	0.0015	0	5008	,	,		30441	0		0	False		,,,				2504	0				p.T1071N		Atlas-SNP	.											.	RIMBP3	42	.	0			c.C3212A						.						65	85	78					22																	20458090		2115	4238	6353	SO:0001583	missense	85376	exon1			GACATAGTTCCCC	AB051453	CCDS46665.1	22q11.21	2014-05-06			ENSG00000196622	ENSG00000275793			29344	protein-coding gene	gene with protein product		612699				11258795, 17855024	Standard	NM_015672		Approved	KIAA1666, RIMBP3.1, RIMBP3A	uc002zsd.4	Q9UFD9	OTTHUMG00000188355	ENST00000426804.1:c.3212C>A	chr22.hg19:g.20458090G>T	ENSP00000391564:p.Thr1071Asn	466.0	1.0		408.0	94.0	NM_015672	Q8IYP7|Q9BY94|Q9UFQ5	Missense_Mutation	SNP	ENST00000426804.1	hg19	CCDS46665.1	.	.	.	.	.	.	.	.	.	.	G	10.09	1.255813	0.22965	.	.	ENSG00000196622	ENST00000355186;ENST00000426804	T	0.53640	0.61	3.56	-1.62	0.08372	Fibronectin, type III (1);	0.628193	0.15951	N	0.236738	T	0.29976	0.0750	L	0.50919	1.6	0.09310	N	1	B	0.31769	0.339	B	0.27500	0.08	T	0.13980	-1.0489	10	0.18710	T	0.47	-5.0717	3.8307	0.08873	0.213:0.0:0.464:0.323	.	977	Q9UFD9	RIM3A_HUMAN	N	977;1071	ENSP00000391564:T1071N	ENSP00000347318:T977N	T	-	2	0	RIMBP3	18838090	0.000000	0.05858	0.038000	0.18304	0.506000	0.33950	-0.020000	0.12525	0.002000	0.14630	0.398000	0.26397	ACT	.	.		0.657	RIMBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318945.2	NM_015672		T	20458090	G	T	20458090	3	4	335	1	0	0	0	0	1	0	0	0	13379	1029	36	3	1711	3	RIMBP3	22	20458090	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10		20458090	30846476	182	46733										
PPIL2	23759	hgsc.bcm.edu	37	chr22	22025284	22025309	+	Splice_Site	DEL	TGTCCTTTTTCAGTCTCTCTCTGCAG	TGTCCTTTTTCAGTCTCTCTCTGCAG	-													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	aggaatgactgtcctttttcAgtctctctctgcagcccttt					rs370871572|rs202229100		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	TGTCCTTTTTCAGTCTCTCTCTGCAG	TGTCCTTTTTCAGTCTCTCTCTGCAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr22:22025284_22025309delTGTCCTTTTTCAGTCTCTCTCTGCAG	ENST00000335025.8	+	4	219_243	c.128_152delTGTCCTTTTTCAGTCTCTCTCTGCAG	c.(127-153)atgtcctttttcagtctctctctgcag>ag	p.MSFFSLSLQ43fs	PPIL2_ENST00000406385.1_Splice_Site_p.MSFFSLSLQ43fs|PPIL2_ENST00000398831.3_Splice_Site_p.MSFFSLSLQ43fs|PPIL2_ENST00000412327.1_Splice_Site_p.MSFFSLSLQ43fs|PPIL2_ENST00000456792.2_Intron|PPIL2_ENST00000492445.2_Splice_Site_p.MSFFSLSLQ43fs					peptidylprolyl isomerase (cyclophilin)-like 2											endometrium(4)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	17	Colorectal(54;0.105)					GTCCTTTTTCAGTCTCTCTCTGCAGCCCTTTGTCTACCCAGTCTGC	0.496																																					p.43_47del		Pindel	.											.	PPIL2	38	.	0			c.129_140del						.																																			SO:0001630	splice_region_variant	23759	exon4			.		CCDS13793.1	22q11.21	2013-01-29			ENSG00000100023	ENSG00000100023		"U-box domain containing"	9261	protein-coding gene	gene with protein product	"U-box domain containing 7"	607588				10591208	Standard	NM_014337		Approved	UBOX7, CYC4, Cyp-60	uc002zvh.4	Q13356	OTTHUMG00000030174	ENST00000335025.8:c.129-1TGTCCTTTTTCAGTCTCTCTCTGCAG>-	chr22.hg19:g.22025284_22025309delTGTCCTTTTTCAGTCTCTCTCTGCAG		213.0	0.0		160.0	21.0	NM_014337		In_Frame_Del	DEL	ENST00000335025.8	hg19	CCDS13793.1																																																																																			.	.		0.496	PPIL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075028.4		Frame_Shift_Del	-	22025309	TGTCCTTTTTCAGTCTCTCTCTGCAG	-	22025284	8	5	335	1	0	1	0	1	0	0	1	0	12339	202	7	0	141	0	PPIL2	22	22025284	Splice_Site	DEL	TGTCCTTTTTCAGTCTCTCTCTGCAG	TCGA-RC-A6M6-01A-11D-A32G-10	1567194	22025284	29279282	183	46734	250	2								
PPIL2	23759	hgsc.bcm.edu	37	chr22	22025285	22025298	+	Splice_Site	DEL	GTCTCTCTCTGCAG	GTCTCTCTCTGCAG	-													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ggaatgactgtcctttttcaGtctctctctgcagccctttg					rs370871572|rs202229100		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	GTCTCTCTCTGCAG	GTCTCTCTCTGCAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr22:22025285_22025298delGTCTCTCTCTGCAG	ENST00000335025.8	+	4	219_232	c.128_141delGTCTCTCTCTGCAG	c.(127-141)agtctctctctgcag>a	p.SLSLQ43fs	PPIL2_ENST00000406385.1_Splice_Site_p.SLSLQ43fs|PPIL2_ENST00000398831.3_Splice_Site_p.SLSLQ43fs|PPIL2_ENST00000412327.1_Splice_Site_p.SLSLQ43fs|PPIL2_ENST00000456792.2_Intron|PPIL2_ENST00000492445.2_Splice_Site_p.SLSLQ43fs					peptidylprolyl isomerase (cyclophilin)-like 2											endometrium(4)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	17	Colorectal(54;0.105)					TCCTTTTTCAGTCTCTCTCTGCAGCCCTTTGTCT	0.505																																					p.43_47del		Atlas-INDEL	.											.	PPIL2	38	.	0			c.129_140del						.																																			SO:0001630	splice_region_variant	23759	exon4			.		CCDS13793.1	22q11.21	2013-01-29			ENSG00000100023	ENSG00000100023		"U-box domain containing"	9261	protein-coding gene	gene with protein product	"U-box domain containing 7"	607588				10591208	Standard	NM_014337		Approved	UBOX7, CYC4, Cyp-60	uc002zvh.4	Q13356	OTTHUMG00000030174	ENST00000335025.8:c.129-1GTCTCTCTCTGCAG>-	chr22.hg19:g.22025285_22025298delGTCTCTCTCTGCAG		206.0	0.0		139.0	10.0	NM_014337		In_Frame_Del	DEL	ENST00000335025.8	hg19	CCDS13793.1																																																																																			.	.		0.505	PPIL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075028.4		Frame_Shift_Del	-	22025298	GTCTCTCTCTGCAG	-	22025285	8	5	335	1	0	1	0	1	0	0	1	0	12339	1043	36	0	142	0	PPIL2	22	22025285	Splice_Site	DEL	GTCTCTCTCTGCAG	TCGA-RC-A6M6-01A-11D-A32G-10	1	22025285	29279281	184	46735	250	2								
VPREB3	29802	hgsc.bcm.edu	37	chr22	24096504	24096504	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	ggcccaggaaagattcacctGacaggaaggtccccatcaga	11	12	2	3			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr22:24096504G>A	ENST00000248948.3	-	1	151	c.47C>T	c.(46-48)tCa>tTa	p.S16L	VPREB3_ENST00000398465.3_Missense_Mutation_p.S16L	NM_013378.2	NP_037510.1	Q9UKI3	VPRE3_HUMAN	pre-B lymphocyte 3	16						endoplasmic reticulum (GO:0005783)				large_intestine(1)|lung(1)|skin(1)	3		Medulloblastoma(6;7.87e-06)|all_neural(6;0.00334)				AGATTCACCTGACAGGAAGGT	0.597																																					p.S16L		Atlas-SNP	.											.	VPREB3	11	.	0			c.C47T						.						50	38	42					22																	24096504		2198	4299	6497	SO:0001583	missense	29802	exon1			TCACCTGACAGGA		CCDS13813.1	22q11.23	2013-01-11	2008-09-12		ENSG00000128218	ENSG00000128218		"Immunoglobulin superfamily / V-set domain containing"	12710	protein-coding gene	gene with protein product		605017				10702669, 14670953	Standard	NM_013378		Approved	8HS20	uc002zxt.3	Q9UKI3	OTTHUMG00000150738	ENST00000248948.3:c.47C>T	chr22.hg19:g.24096504G>A	ENSP00000248948:p.Ser16Leu	100.0	0.0		74.0	24.0	NM_013378	B2R587	Missense_Mutation	SNP	ENST00000248948.3	hg19	CCDS13813.1	.	.	.	.	.	.	.	.	.	.	G	8.457	0.854444	0.17106	.	.	ENSG00000128218	ENST00000398465;ENST00000248948	T;T	0.64803	-0.12;1.39	3.95	2.92	0.33932	.	1.312800	0.05641	N	0.583349	T	0.63908	0.2551	M	0.70842	2.15	0.26173	N	0.979831	B	0.19331	0.035	B	0.17433	0.018	T	0.56232	-0.8013	10	0.87932	D	0	.	9.7867	0.40681	0.0:0.2092:0.7908:0.0	.	16	Q9UKI3	VPRE3_HUMAN	L	16	ENSP00000381483:S16L;ENSP00000248948:S16L	ENSP00000248948:S16L	S	-	2	0	VPREB3	22426504	0.996000	0.38824	0.812000	0.32479	0.054000	0.15201	2.998000	0.49465	1.246000	0.43901	0.650000	0.86243	TCA	.	.		0.597	VPREB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319879.2	NM_013378		A	24096504	G	A	24096504	3	1	335	1	0	0	0	0	1	0	0	0	17202	1294	45	3	332	3	VPREB3	22	24096504	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	2071219	24096504	27208062	185	46736										
C22orf30	253143	hgsc.bcm.edu	37	chr22	32112941	32112941	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gtttacacaactcttccttcCcattgtccacattagaaatg	4	12	1	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr22:32112941C>T	ENST00000327423.6	-	4	1073	c.884G>A	c.(883-885)gGg>gAg	p.G295E	PRR14L_ENST00000434485.1_Missense_Mutation_p.G295E|PRR14L_ENST00000397493.2_Missense_Mutation_p.G295E|PRR14L_ENST00000461722.1_5'UTR	NM_173566.2	NP_775837.2	Q5THK1	PR14L_HUMAN	proline rich 14-like	295										endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(5)|skin(1)|urinary_tract(2)	14						CTCTTCCTTCCCATTGTCCAC	0.398																																					p.G295E		Atlas-SNP	.											.	PRR14L	198	.	0			c.G884A						.						324	254	275					22																	32112941		692	1591	2283	SO:0001583	missense	253143	exon4			TCCTTCCCATTGT	BC040859	CCDS13900.2	22q12.2	2011-01-25	2011-01-25	2011-01-25	ENSG00000183530	ENSG00000183530			28738	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 30"	C22orf30		12477932	Standard	NM_173566		Approved	MGC50372	uc003alp.4	Q5THK1	OTTHUMG00000030139	ENST00000327423.6:c.884G>A	chr22.hg19:g.32112941C>T	ENSP00000331845:p.Gly295Glu	201.0	0.0		181.0	39.0	NM_173566	Q5THK4|Q6ZNN1|Q6ZWH0|Q8IW74|Q9H5T4	Missense_Mutation	SNP	ENST00000327423.6	hg19	CCDS13900.2	.	.	.	.	.	.	.	.	.	.	C	11.65	1.702135	0.30232	.	.	ENSG00000183530	ENST00000397493;ENST00000327423;ENST00000434485	T;T;T	0.10288	2.89;2.91;2.89	4.56	3.54	0.40534	.	0.522514	0.17769	N	0.162655	T	0.12220	0.0297	L	0.53249	1.67	0.25093	N	0.990844	B;B;B	0.31680	0.221;0.221;0.335	B;B;B	0.34931	0.126;0.126;0.192	T	0.13495	-1.0507	10	0.52906	T	0.07	-3.8075	8.1195	0.30963	0.0:0.7544:0.1582:0.0875	.	295;295;295	Q5THK1-2;Q5THK1;Q5THK1-4	.;PR14L_HUMAN;.	E	295	ENSP00000380630:G295E;ENSP00000331845:G295E;ENSP00000388314:G295E	ENSP00000331845:G295E	G	-	2	0	PRR14L	30442941	0.000000	0.05858	0.749000	0.31150	0.774000	0.43823	-0.054000	0.11826	1.284000	0.44531	0.650000	0.86243	GGG	.	.		0.398	PRR14L-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074993.2	NM_173566		T	32112941	C	T	32112941	3	4	335	1	0	0	0	0	1	0	0	0	2144	623	22	3	5595	3	C22orf30	22	32112941	Missense_Mutation	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	8016437	32112941	19191625	186	46737										
CSF2RB	1439	hgsc.bcm.edu	37	chr22	37334154	37334154	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gggtttgagggctatgtggaGctccctccaattgagggccg	16	9	0	2	rs373820480		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr22:37334154G>T	ENST00000403662.3	+	14	2526	c.2304G>T	c.(2302-2304)gaG>gaT	p.E768D	CSF2RB_ENST00000406230.1_Missense_Mutation_p.E774D|CSF2RB_ENST00000262825.5_Missense_Mutation_p.E774D|CSF2RB_ENST00000536485.1_Missense_Mutation_p.E715D			P32927	IL3RB_HUMAN	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	768					cellular response to interleukin-3 (GO:0036016)|interleukin-3-mediated signaling pathway (GO:0038156)|interleukin-5-mediated signaling pathway (GO:0038043)|respiratory gaseous exchange (GO:0007585)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	granulocyte macrophage colony-stimulating factor receptor complex (GO:0030526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(18)|ovary(3)|pancreas(1)|skin(5)|upper_aerodigestive_tract(2)	42					Sargramostim(DB00020)	GCTATGTGGAGCTCCCTCCAA	0.652																																					p.E768D		Atlas-SNP	.											.	CSF2RB	104	.	0			c.G2304T						.						44	42	43					22																	37334154		2203	4300	6503	SO:0001583	missense	1439	exon14			TGTGGAGCTCCCT	M59941	CCDS13936.1	22q12.3	2014-09-09			ENSG00000100368	ENSG00000100368		"CD molecules", "Fibronectin type III domain containing"	2436	protein-coding gene	gene with protein product		138981		IL3RB		1833064, 1424804	Standard	NM_000395		Approved	IL5RB, CD131	uc003aqa.4	P32927	OTTHUMG00000150546	ENST00000403662.3:c.2304G>T	chr22.hg19:g.37334154G>T	ENSP00000384053:p.Glu768Asp	33.0	0.0		36.0	16.0	NM_000395	Q5JZI1|Q6ICE0	Missense_Mutation	SNP	ENST00000403662.3	hg19	CCDS13936.1	.	.	.	.	.	.	.	.	.	.	G	10.79	1.449283	0.26074	.	.	ENSG00000100368	ENST00000403662;ENST00000539104;ENST00000262825;ENST00000406230;ENST00000536485	D;D;D;D	0.93426	-2.7;-3.21;-3.21;-3.22	5.5	-0.294	0.12831	.	0.639614	0.13672	N	0.370808	D	0.83175	0.5197	N	0.21142	0.635	0.24286	N	0.995187	B;B	0.21606	0.058;0.034	B;B	0.16722	0.016;0.007	T	0.68762	-0.5323	10	0.25106	T	0.35	-7.4029	1.9057	0.03276	0.1563:0.1337:0.4347:0.2753	.	774;768	P32927-2;P32927	.;IL3RB_HUMAN	D	768;768;774;774;715	ENSP00000384053:E768D;ENSP00000262825:E774D;ENSP00000385271:E774D;ENSP00000440003:E715D	ENSP00000262825:E774D	E	+	3	2	CSF2RB	35664100	0.792000	0.28813	0.987000	0.45799	0.472000	0.32918	0.021000	0.13489	0.037000	0.15575	0.555000	0.69702	GAG	.	.		0.652	CSF2RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318854.1	NM_000395		T	37334154	G	T	37334154	3	4	335	1	0	0	0	0	1	0	0	0	3937	962	34	3	2354	3	CSF2RB	22	37334154	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	5221213	37334154	13970412	187	46738										
GTPBP1	9567	hgsc.bcm.edu	37	chr22	39125539	39125539	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	aaatgcagtcgacgaaaaagGgccccctgacgaaacgagac	11	11	0	2			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr22:39125539G>T	ENST00000216044.5	+	11	2022	c.1789G>T	c.(1789-1791)Ggc>Tgc	p.G597C		NM_004286.4	NP_004277.2	O00178	GTPB1_HUMAN	GTP binding protein 1	597					GTP catabolic process (GO:0006184)|immune response (GO:0006955)|positive regulation of mRNA catabolic process (GO:0061014)|signal transduction (GO:0007165)	cytoplasmic exosome (RNase complex) (GO:0000177)|cytosol (GO:0005829)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(9)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	18	Melanoma(58;0.04)					GACGAAAAAGGGCCCCCTGAC	0.612																																					p.G597C		Atlas-SNP	.											.	GTPBP1	51	.	0			c.G1789T						.						37	33	34					22																	39125539		2203	4300	6503	SO:0001583	missense	9567	exon11			AAAAAGGGCCCCC	U87964	CCDS13977.2	22q13.1	2008-07-01			ENSG00000100226	ENSG00000100226			4669	protein-coding gene	gene with protein product		602245				9070279	Standard	XM_005261857		Approved	GP-1, HSPC018	uc003awg.3	O00178	OTTHUMG00000151002	ENST00000216044.5:c.1789G>T	chr22.hg19:g.39125539G>T	ENSP00000216044:p.Gly597Cys	76.0	0.0		70.0	18.0	NM_004286	Q6IC67	Missense_Mutation	SNP	ENST00000216044.5	hg19	CCDS13977.2	.	.	.	.	.	.	.	.	.	.	G	20.5	3.997452	0.74818	.	.	ENSG00000100226	ENST00000216044;ENST00000458073	T	0.31769	1.48	5.26	5.26	0.73747	.	0.149182	0.46145	D	0.000315	T	0.28001	0.0690	L	0.44542	1.39	0.49299	D	0.999771	P	0.46020	0.871	B	0.40702	0.338	T	0.03898	-1.0994	10	0.66056	D	0.02	.	12.3971	0.55391	0.0761:0.0:0.9239:0.0	.	597	O00178	GTPB1_HUMAN	C	597;175	ENSP00000216044:G597C	ENSP00000216044:G597C	G	+	1	0	GTPBP1	37455485	1.000000	0.71417	0.998000	0.56505	0.931000	0.56810	5.428000	0.66489	2.731000	0.93534	0.650000	0.86243	GGC	.	.		0.612	GTPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075532.1	NM_004286		T	39125539	G	T	39125539	3	4	335	1	0	0	0	0	1	0	0	0	6887	1232	43	3	1831	3	GTPBP1	22	39125539	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	1791385	39125539	12179027	188	46739										
TUBGCP6	85378	hgsc.bcm.edu	37	chr22	50656529	50656539	+	Frame_Shift_Del	DEL	TTCTCCGTGAG	TTCTCCGTGAG	-													0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	cgttcatgacgggcgccgccTtctccgtgagcaggcccctg					rs35231253	byFrequency	TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	TTCTCCGTGAG	TTCTCCGTGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr22:50656529_50656539delTTCTCCGTGAG	ENST00000248846.5	-	24	5280_5290	c.5176_5186delCTCACGGAGAA	c.(5176-5187)ctcacggagaagfs	p.LTEK1726fs	TUBGCP6_ENST00000491449.1_5'UTR|TUBGCP6_ENST00000439308.2_3'UTR			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	1726					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(4)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(13)|ovary(3)|prostate(2)|skin(2)	45		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)		GGGCGCCGCCTTCTCCGTGAGCAGGCCCCTG	0.687																																					p.1726_1729del		Atlas-INDEL	.											.	TUBGCP6	132	.	0			c.5177_5187del						.																																			SO:0001589	frameshift_variant	85378	exon24			.	AB051456	CCDS14087.1	22q13.31-q13.33	2008-07-01			ENSG00000128159	ENSG00000128159			18127	protein-coding gene	gene with protein product	"gamma-tubulin complex component 6"	610053				11694571, 11258795	Standard	XR_244458		Approved	GCP6, KIAA1669, DJ402G11.6	uc003bkb.1	Q96RT7	OTTHUMG00000030150	ENST00000248846.5:c.5176_5186delCTCACGGAGAA	chr22.hg19:g.50656529_50656539delTTCTCCGTGAG	ENSP00000248846:p.Leu1726fs	37.0	0.0		34.0	12.0	NM_020461	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Frame_Shift_Del	DEL	ENST00000248846.5	hg19	CCDS14087.1																																																																																			.	.		0.687	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3	NM_020461		-	50656539	TTCTCCGTGAG	-	50656529	7	5	335	1	0	1	0	1	0	0	0	0	16785	1609	56	0	281	0	TUBGCP6	22	50656529	Frame_Shift_Del	DEL	TTCTCCGTGAG	TCGA-RC-A6M6-01A-11D-A32G-10	11530990	50656529	648037	189	46740										
FAM48B1	100130302	hgsc.bcm.edu	37	chrX	24383090	24383090	+	IGR	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	tttgagcacgcaagggcaggCcttccctgctcagcaacttc	10	14	1	1			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chrX:24383090C>A								AC004552.1 (16067 upstream) : PDK3 (100247 downstream)																							CAAGGGCAGGCCTTCCCTGCT	0.617																																					p.A738D		Atlas-SNP	.											.	.	.	.	0			c.C2213A						.						32	33	33					X																	24383090		1568	3582	5150	SO:0001628	intergenic_variant	100130302	exon1			GGCAGGCCTTCCC																													chrX.hg19:g.24383090C>A		113.0	0.0		124.0	96.0	NM_001136234		Missense_Mutation	SNP		hg19																																																																																				.	.	0	0.617									A	24383090	C	A	24383090	1	1	335	0	1	0	0	0	0	0	0	0	5581	739	26	3		3	FAM48B1	23	24383090	IGR	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10		24383090	130887470	190	46741										
FAM47A	158724	hgsc.bcm.edu	37	chrX	34149528	34149528	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	gtatttaccaggctctgtggGttcgtcagttgtcttctccc	10	11	4	0			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chrX:34149528G>C	ENST00000346193.3	-	1	919	c.868C>G	c.(868-870)Ccc>Gcc	p.P290A		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	290										NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	97						GGCTCTGTGGGTTCGTCAGTT	0.572																																					p.P290A		Atlas-SNP	.											.	FAM47A	249	.	0			c.C868G						.						25	26	26					X																	34149528		2202	4300	6502	SO:0001583	missense	158724	exon1			CTGTGGGTTCGTC	BC026171	CCDS43926.1	Xp21.1	2004-08-09			ENSG00000185448	ENSG00000185448			29962	protein-coding gene	gene with protein product	"similar to hypothetical protein FLJ35782"					12477932	Standard	NM_203408		Approved	MGC27003	uc004ddg.3	Q5JRC9	OTTHUMG00000021339	ENST00000346193.3:c.868C>G	chrX.hg19:g.34149528G>C	ENSP00000345029:p.Pro290Ala	70.0	0.0		71.0	56.0	NM_203408	A8K8I9|Q8TAA0	Missense_Mutation	SNP	ENST00000346193.3	hg19	CCDS43926.1	.	.	.	.	.	.	.	.	.	.	g	2.132	-0.398926	0.04865	.	.	ENSG00000185448	ENST00000346193	T	0.21734	1.99	0.13	0.13	0.14746	.	.	.	.	.	T	0.17066	0.0410	L	0.55990	1.75	0.09310	N	1	B	0.26445	0.149	B	0.14578	0.011	T	0.19910	-1.0291	8	0.46703	T	0.11	.	.	.	.	.	290	Q5JRC9	FA47A_HUMAN	A	290	ENSP00000345029:P290A	ENSP00000345029:P290A	P	-	1	0	FAM47A	34059449	0.250000	0.23951	0.019000	0.16419	0.019000	0.09904	0.136000	0.15974	0.171000	0.19730	0.173000	0.16961	CCC	.	.		0.572	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408		C	34149528	G	C	34149528	3	2	335	1	0	0	0	0	1	0	0	0	5577	1261	44	4	1511	4	FAM47A	23	34149528	Missense_Mutation	SNP	G	TCGA-RC-A6M6-01A-11D-A32G-10	9766438	34149528	121121032	191	46742										
POF1B	79983	hgsc.bcm.edu	37	chrX	84561303	84561303	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	agagagattgttttcttccaAtgcctggcattttgaacttg	9	7	1	3			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chrX:84561303A>G	ENST00000262753.4	-	12	1346	c.1201T>C	c.(1201-1203)Ttg>Ctg	p.L401L	POF1B_ENST00000373145.3_Silent_p.L401L	NM_024921.3	NP_079197.3	Q8WVV4	POF1B_HUMAN	premature ovarian failure, 1B	401						tight junction (GO:0005923)				central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|liver(2)|lung(17)|ovary(1)|prostate(1)	35						TTTTCTTCCAATGCCTGGCAT	0.358																																					p.L401L		Atlas-SNP	.											.	POF1B	77	.	0			c.T1201C						.						175	137	150					X																	84561303		2203	4300	6503	SO:0001819	synonymous_variant	79983	exon12			CTTCCAATGCCTG	BC017500	CCDS14452.1	Xq21.2	2008-02-05			ENSG00000124429	ENSG00000124429			13711	protein-coding gene	gene with protein product		300603				11299520	Standard	NM_024921		Approved	POF, FLJ22792	uc004eer.2	Q8WVV4	OTTHUMG00000021934	ENST00000262753.4:c.1201T>C	chrX.hg19:g.84561303A>G		113.0	0.0		87.0	67.0	NM_024921	A8K2U5|Q5H9E9|Q5H9F0|Q8NG12|Q9H5Y2|Q9H738|Q9H744	Silent	SNP	ENST00000262753.4	hg19	CCDS14452.1																																																																																			.	.		0.358	POF1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057391.2	NM_024921		G	84561303	A	G	84561303	2	3	335	1	0	0	0	0	0	0	0	1	12191	98	4	2		2	POF1B	23	84561303	Silent	SNP	A	TCGA-RC-A6M6-01A-11D-A32G-10	50411775	84561303	70709257	192	46743										
ODZ1	10178	hgsc.bcm.edu	37	chrX	123540198	123540198	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0264550264550265	5	1	0.645983213429257	0.459365840660805	0.719007402773433	0.265734265734266	0.917767417767419	0	atatatatggtactagttgcCgtcaagttggttgacatgag	11	5	1	2	rs148101479		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chrX:123540198C>T	ENST00000371130.3	-	25	5166	c.5103G>A	c.(5101-5103)acG>acA	p.T1701T	TENM1_ENST00000422452.2_Silent_p.T1708T|STAG2_ENST00000469481.1_Intron	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	1701					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										TACTAGTTGCCGTCAAGTTGG	0.438																																					p.T1708T		Atlas-SNP	.											.	.	.	.	0			c.G5124A						.	C	,,	2,3833		0,2,1630,571	201	181	188		5124,5121,5103	-1.6	1	X	dbSNP_134	188	0,6728		0,0,2428,1872	no	coding-synonymous,coding-synonymous,coding-synonymous	ODZ1	NM_001163278.1,NM_001163279.1,NM_014253.3	,,	0,2,4058,2443	TT,TC,CC,C		0.0,0.0522,0.0189	,,	1708/2733,1707/2732,1701/2726	123540198	2,10561	2203	4300	6503	SO:0001819	synonymous_variant	10178	exon26			AGTTGCCGTCAAG	AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.5103G>A	chrX.hg19:g.123540198C>T		83.0	0.0		76.0	59.0	NM_001163278	B2RTR5|Q5JZ17	Silent	SNP	ENST00000371130.3	hg19	CCDS14609.1																																																																																			.	C|1.000;T|0.000		0.438	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		T	123540198	C	T	123540198	2	4	335	1	0	0	0	0	0	0	0	1	10843	639	23	1		1	ODZ1	23	123540198	Silent	SNP	C	TCGA-RC-A6M6-01A-11D-A32G-10	38978895	123540198	31730362	193	46744										
FBXO42	54455	hgsc.bcm.edu	37	chr1	16577608	16577609	+	Frame_Shift_Ins	INS	-	-	C													0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	agtgctgcagaggccgagggINSgcctttggaggacatcgctt							TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr1:16577608_16577609insC	ENST00000375592.3	-	10	1926_1927	c.1710_1711insG	c.(1708-1713)ggccccfs	p.P571fs		NM_018994.1	NP_061867.1	Q6P3S6	FBX42_HUMAN	F-box protein 42	571										autonomic_ganglia(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	26		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00475)|all_lung(284;0.00671)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0193)|Colorectal(212;3.16e-07)|COAD - Colon adenocarcinoma(227;1.46e-05)|BRCA - Breast invasive adenocarcinoma(304;4.37e-05)|Kidney(64;0.000246)|KIRC - Kidney renal clear cell carcinoma(64;0.00336)|STAD - Stomach adenocarcinoma(313;0.0139)|READ - Rectum adenocarcinoma(331;0.0693)		GAGGCCGAGGGGCCTTTGGAGG	0.629																																					p.P571fs		Atlas-Indel,Pindel	.											.	FBXO42	53	.	0			c.1711_1712insG						.																																			SO:0001589	frameshift_variant	54455	exon10			.	BC063864	CCDS30613.1	1p36.23-p36.11	2008-02-05			ENSG00000037637	ENSG00000037637		"F-boxes /  "other""	29249	protein-coding gene	gene with protein product		609109				10718198	Standard	XM_006710698		Approved	KIAA1332, Fbx42	uc001ayg.3	Q6P3S6	OTTHUMG00000002218	ENST00000375592.3:c.1710_1711insG	chr1.hg19:g.16577608_16577609insC	ENSP00000364742:p.Pro571fs	91.0	0.0		31.0	23.0	NM_018994	B3KP30|Q5TEU8|Q86XI0|Q8N3N4|Q8N5F8|Q9BRM0|Q9P2L4	Frame_Shift_Ins	INS	ENST00000375592.3	hg19	CCDS30613.1																																																																																			.	.		0.629	FBXO42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006285.1			C	16577609	-	C	16577608	7	5	336	1	0	1	1	0	0	0	0	0	5759	1232	43	0	446	0	FBXO42	1	16577608	Frame_Shift_Ins	INS	-	TCGA-RC-A7S9-01A-11D-A33Q-10		16577608	232673013	1	46745										
GTF2B	2959	hgsc.bcm.edu	37	chr1	89318944	89318944	+	Frame_Shift_Del	DEL	A	A	-													0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	gtgtcaaatttgaagtctgtAggaaacagatctggggctcg							TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr1:89318944delA	ENST00000370500.5	-	7	1021	c.903delT	c.(901-903)cctfs	p.P301fs		NM_001514.5	NP_001505.1	Q00403	TF2B_HUMAN	general transcription factor IIB	301					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	nucleoplasm (GO:0005654)	core promoter binding (GO:0001047)|thyroid hormone receptor binding (GO:0046966)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	10		Lung NSC(277;0.123)		all cancers(265;0.0131)|Epithelial(280;0.0255)		TGAAGTCTGTAGGAAACAGAT	0.393																																					p.T302fs		Atlas-Indel,Pindel	.											.	GTF2B	32	.	0			c.904delA						.						170	172	171					1																	89318944		2203	4300	6503	SO:0001589	frameshift_variant	2959	exon7			.	M76766	CCDS715.1	1p22-p21	2010-03-23			ENSG00000137947	ENSG00000137947		"General transcription factors"	4648	protein-coding gene	gene with protein product		189963				1876184, 8162052	Standard	NM_001514		Approved	TFIIB	uc001dmo.4	Q00403	OTTHUMG00000010611	ENST00000370500.5:c.903delT	chr1.hg19:g.89318944delA	ENSP00000359531:p.Pro301fs	73.0	0.0		40.0	12.0	NM_001514	A8K1A7|Q5JS30	Frame_Shift_Del	DEL	ENST00000370500.5	hg19	CCDS715.1																																																																																			.	.		0.393	GTF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029279.1	NM_001514		-	89318944	A	-	89318944	7	5	336	1	0	1	0	1	0	0	0	0	6864	407	15	0	51	0	GTF2B	1	89318944	Frame_Shift_Del	DEL	A	TCGA-RC-A7S9-01A-11D-A33Q-10	72741336	89318944	159931677	2	46746										
C1orf111	284680	hgsc.bcm.edu	37	chr1	162343882	162343882	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	gccaatttgcctaaggtgttCagcaggactattgaaggcct	11	9	1	1			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr1:162343882C>T	ENST00000367935.5	-	3	821	c.742G>A	c.(742-744)Gaa>Aaa	p.E248K	RP11-565P22.6_ENST00000431696.1_Intron	NM_182581.3	NP_872387.2	Q5T0L3	CA111_HUMAN	chromosome 1 open reading frame 111	248										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)	11	all_hematologic(112;0.15)		BRCA - Breast invasive adenocarcinoma(70;0.0938)			CTAAGGTGTTCAGCAGGACTA	0.557																																					p.E248K		Atlas-SNP	.											.	C1orf111	26	.	0			c.G742A						.						165	174	171					1																	162343882		2203	4300	6503	SO:0001583	missense	284680	exon3			GGTGTTCAGCAGG	BC032957	CCDS1238.1	1q23.3	2008-02-05			ENSG00000171722	ENSG00000171722			27648	protein-coding gene	gene with protein product						12477932	Standard	NM_182581		Approved		uc001gbx.2	Q5T0L3	OTTHUMG00000031375	ENST00000367935.5:c.742G>A	chr1.hg19:g.162343882C>T	ENSP00000356912:p.Glu248Lys	108.0	0.0		117.0	28.0	NM_182581	Q6X961|Q8NEC3	Missense_Mutation	SNP	ENST00000367935.5	hg19	CCDS1238.1	.	.	.	.	.	.	.	.	.	.	C	12.61	1.989953	0.35131	.	.	ENSG00000171722	ENST00000367935	T	0.32988	1.43	4.71	-2.1	0.07210	.	1.795310	0.02923	N	0.138257	T	0.05227	0.0139	N	0.14661	0.345	0.23016	N	0.99843	B	0.17038	0.02	B	0.14023	0.01	T	0.26121	-1.0112	9	0.62326	D	0.03	-23.7402	1.1961	0.01875	0.1272:0.2943:0.2498:0.3288	.	248	Q5T0L3	CA111_HUMAN	K	248	ENSP00000356912:E248K	ENSP00000356912:E248K	E	-	1	0	C1orf111	160610506	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	0.126000	0.15769	-0.871000	0.04042	-0.302000	0.09304	GAA	.	.		0.557	C1orf111-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076791.2	NM_182581		T	162343882	C	T	162343882	3	4	336	1	0	0	0	0	1	0	0	0	1986	835	29	3	47	3	C1orf111	1	162343882	Missense_Mutation	SNP	C	TCGA-RC-A7S9-01A-11D-A33Q-10	73024938	162343882	86906739	3	46747										
LYST	1130	hgsc.bcm.edu	37	chr1	235955200	235955200	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	ggctatgtgccaagatgaaaGcagccgatggggaaaactct	13	8	1	2			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr1:235955200G>C	ENST00000389794.3	-	12	4516	c.4342C>G	c.(4342-4344)Ctt>Gtt	p.L1448V	LYST_ENST00000389793.2_Missense_Mutation_p.L1448V|LYST_ENST00000536965.1_Intron			Q99698	LYST_HUMAN	lysosomal trafficking regulator	1448					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			CAAGATGAAAGCAGCCGATGG	0.493																																					p.L1448V		Atlas-SNP	.											.	LYST	370	.	0			c.C4342G						.						108	107	107					1																	235955200		2203	4300	6503	SO:0001583	missense	1130	exon12			ATGAAAGCAGCCG	U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"WD repeat domain containing"	1968	protein-coding gene	gene with protein product		606897	"Chediak-Higashi syndrome 1"	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.4342C>G	chr1.hg19:g.235955200G>C	ENSP00000374444:p.Leu1448Val	137.0	0.0		164.0	30.0	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Missense_Mutation	SNP	ENST00000389794.3	hg19	CCDS31062.1	.	.	.	.	.	.	.	.	.	.	G	16.53	3.150410	0.57151	.	.	ENSG00000143669	ENST00000389794;ENST00000389793	T;T	0.62498	0.02;0.02	5.76	4.85	0.62838	.	0.431693	0.25523	N	0.030084	T	0.71533	0.3351	L	0.54323	1.7	0.80722	D	1	D;D	0.65815	0.995;0.969	P;B	0.61800	0.894;0.421	T	0.71922	-0.4446	10	0.45353	T	0.12	.	13.5336	0.61635	0.0723:0.0:0.9277:0.0	.	1448;1448	Q99698-3;Q99698	.;LYST_HUMAN	V	1448	ENSP00000374444:L1448V;ENSP00000374443:L1448V	ENSP00000374443:L1448V	L	-	1	0	LYST	234021823	1.000000	0.71417	0.992000	0.48379	0.840000	0.47671	3.130000	0.50508	1.572000	0.49736	0.650000	0.86243	CTT	.	.		0.493	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			C	235955200	G	C	235955200	3	2	336	1	0	0	0	0	1	0	0	0	9137	971	34	4	7231	4	LYST	1	235955200	Missense_Mutation	SNP	G	TCGA-RC-A7S9-01A-11D-A33Q-10	73611318	235955200	13295421	4	46748										
GPR137B	7107	hgsc.bcm.edu	37	chr1	236306038	236306038	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	gctgaccccggccgtgccccCctacgtgaagcttggcctca	11	18	1	2	rs199613305		TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr1:236306038C>A	ENST00000366592.3	+	1	207	c.116C>A	c.(115-117)cCc>cAc	p.P39H	GPR137B_ENST00000366591.4_Missense_Mutation_p.P39H	NM_003272.3	NP_003263.1	O60478	G137B_HUMAN	G protein-coupled receptor 137B	39						integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|membrane (GO:0016020)				endometrium(2)|large_intestine(1)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.197)|Prostate(94;0.219)|Acute lymphoblastic leukemia(190;0.226)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)			GCCGTGCCCCCCTACGTGAAG	0.711																																					p.P39H		Atlas-SNP	.											.	GPR137B	57	.	0			c.C116A						.						61	44	50					1																	236306038		2203	4300	6503	SO:0001583	missense	7107	exon1			TGCCCCCCTACGT	AF027826	CCDS1609.1	1q42-q43	2012-08-10	2006-01-26	2006-01-26	ENSG00000077585	ENSG00000077585			11862	protein-coding gene	gene with protein product		604658	"transmembrane 7 superfamily member 1 (upregulated in kidney)"	TM7SF1		9521871	Standard	NM_003272		Approved		uc001hxq.3	O60478	OTTHUMG00000037994	ENST00000366592.3:c.116C>A	chr1.hg19:g.236306038C>A	ENSP00000355551:p.Pro39His	67.0	0.0		104.0	31.0	NM_003272	Q53EK7|Q5TAE6|Q6FHI3	Missense_Mutation	SNP	ENST00000366592.3	hg19	CCDS1609.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.086274	0.76642	.	.	ENSG00000077585	ENST00000366592;ENST00000366591;ENST00000391852	T;T	0.14266	2.52;2.52	4.8	2.89	0.33648	.	0.053259	0.85682	D	0.000000	T	0.32071	0.0817	M	0.77103	2.36	0.53005	D	0.999969	D	0.69078	0.997	D	0.63192	0.912	T	0.02477	-1.1153	10	0.56958	D	0.05	-14.0193	10.022	0.42048	0.0:0.7855:0.1385:0.0761	.	39	O60478	G137B_HUMAN	H	39;39;38	ENSP00000355551:P39H;ENSP00000355550:P39H	ENSP00000355550:P39H	P	+	2	0	GPR137B	234372661	1.000000	0.71417	0.967000	0.41034	0.893000	0.52053	5.645000	0.67909	0.437000	0.26423	-0.510000	0.04470	CCC	.	C|0.999;T|0.001		0.711	GPR137B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092761.1	NM_003272		A	236306038	C	A	236306038	3	1	336	1	0	0	0	0	1	0	0	0	6654	623	22	3	118	3	GPR137B	1	236306038	Missense_Mutation	SNP	C	TCGA-RC-A7S9-01A-11D-A33Q-10	350838	236306038	12944583	5	46749										
RYR2	6262	hgsc.bcm.edu	37	chr1	237774131	237774131	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	ccgtgccgcagtgccccccgCgcctccacgtgcagttcctg	11	20	0	0	rs528206995		TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr1:237774131C>T	ENST00000366574.2	+	36	5070	c.4753C>T	c.(4753-4755)Cgc>Tgc	p.R1585C	RYR2_ENST00000360064.6_Missense_Mutation_p.R1583C|RYR2_ENST00000542537.1_Missense_Mutation_p.R1569C	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1585	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GTGCCCCCCGCGCCTCCACGT	0.537													C|||	1	0.000199681	8e-04	0	5008	,	,		16428	0		0	False		,,,				2504	0				p.R1585C		Atlas-SNP	.											.	RYR2	1273	.	0			c.C4753T						.						50	52	51					1																	237774131		1950	4124	6074	SO:0001583	missense	6262	exon36			CCCCCGCGCCTCC	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.4753C>T	chr1.hg19:g.237774131C>T	ENSP00000355533:p.Arg1585Cys	135.0	0.0		133.0	55.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.244925	0.79912	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.98345	-4.88;-4.86;-4.87	5.24	5.24	0.73138	.	0.192154	0.30501	N	0.009495	D	0.99029	0.9668	M	0.87682	2.9	0.80722	D	1	D	0.89917	1.0	D	0.68621	0.959	D	0.99709	1.1006	10	0.87932	D	0	.	19.0203	0.92912	0.0:1.0:0.0:0.0	.	1585	Q92736	RYR2_HUMAN	C	1585;1583;1569	ENSP00000355533:R1585C;ENSP00000353174:R1583C;ENSP00000443798:R1569C	ENSP00000353174:R1583C	R	+	1	0	RYR2	235840754	0.991000	0.36638	0.796000	0.32109	0.952000	0.60782	2.931000	0.48932	2.715000	0.92844	0.655000	0.94253	CGC	.	.		0.537	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		T	237774131	C	T	237774131	3	4	336	1	0	0	0	0	1	0	0	0	13784	768	27	1	4895	1	RYR2	1	237774131	Missense_Mutation	SNP	C	TCGA-RC-A7S9-01A-11D-A33Q-10	1468093	237774131	11476490	6	46750										
APOB	338	hgsc.bcm.edu	37	chr2	21229749	21229749	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	aatattgcccatggcaggaaTaaaaatatggcttatggtac	9	6	0	0			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr2:21229749T>C	ENST00000233242.1	-	26	10118	c.9991A>G	c.(9991-9993)Att>Gtt	p.I3331V		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	3331					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ATGGCAGGAATAAAAATATGG	0.383																																					p.I3331V		Atlas-SNP	.											.	APOB	761	.	0			c.A9991G						.						91	95	94					2																	21229749		2203	4300	6503	SO:0001583	missense	338	exon26			CAGGAATAAAAAT	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.9991A>G	chr2.hg19:g.21229749T>C	ENSP00000233242:p.Ile3331Val	229.0	0.0		147.0	55.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	T	12.69	2.013063	0.35511	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.39056	1.1	5.41	3.05	0.35203	.	0.186486	0.37857	N	0.001919	T	0.60011	0.2236	M	0.80746	2.51	0.80722	D	1	P	0.46020	0.871	P	0.61722	0.893	T	0.56890	-0.7904	10	0.45353	T	0.12	.	9.1651	0.37046	0.0:0.2142:0.0:0.7858	.	3331	P04114	APOB_HUMAN	V	3331	ENSP00000233242:I3331V	ENSP00000233242:I3331V	I	-	1	0	APOB	21083254	1.000000	0.71417	0.972000	0.41901	0.927000	0.56198	3.354000	0.52254	0.364000	0.24374	0.533000	0.62120	ATT	.	.		0.383	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			C	21229749	T	C	21229749	3	2	336	1	0	0	0	0	1	0	0	0	785	1406	49	2	3716	2	APOB	2	21229749	Missense_Mutation	SNP	T	TCGA-RC-A7S9-01A-11D-A33Q-10		21229749	221969624	7	46751										
AGBL5	60509	hgsc.bcm.edu	37	chr2	27282078	27282078	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	tgggttgcctgtctcctgctCcgaaaacaccttgagtcggg	12	12	1	1			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr2:27282078C>A	ENST00000360131.4	+	11	2054	c.1895C>A	c.(1894-1896)tCc>tAc	p.S632Y	AGBL5_ENST00000323064.8_Missense_Mutation_p.S632Y|AGBL5-IT1_ENST00000411862.1_RNA	NM_021831.5	NP_068603.4	Q8NDL9	CBPC5_HUMAN	ATP/GTP binding protein-like 5	632					protein branching point deglutamylation (GO:0035611)|protein deglutamylation (GO:0035608)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	28	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GTCTCCTGCTCCGAAAACACC	0.537																																					p.S632Y		Atlas-SNP	.											.	AGBL5	126	.	0			c.C1895A						.						90	97	94					2																	27282078		2203	4300	6503	SO:0001583	missense	60509	exon11			CCTGCTCCGAAAA	BC007415	CCDS1732.3, CCDS42665.1	2p23.3	2014-06-23			ENSG00000084693	ENSG00000084693			26147	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 5"	615900				24022482	Standard	NM_001035507		Approved	FLJ21839, CCP5	uc002rie.3	Q8NDL9	OTTHUMG00000128406	ENST00000360131.4:c.1895C>A	chr2.hg19:g.27282078C>A	ENSP00000353249:p.Ser632Tyr	235.0	0.0		152.0	68.0	NM_021831	A2VDI7|B7WPG9|B7Z7I7|D6W548|Q53SW0|Q53SZ0|Q96IK8|Q9H6V0|Q9H8P8	Missense_Mutation	SNP	ENST00000360131.4	hg19	CCDS1732.3	.	.	.	.	.	.	.	.	.	.	C	24.3	4.521300	0.85600	.	.	ENSG00000084693	ENST00000323064;ENST00000360131	T;T	0.20463	2.27;2.07	5.76	5.76	0.90799	.	0.115252	0.64402	D	0.000008	T	0.45498	0.1345	L	0.53249	1.67	0.54753	D	0.999982	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.28235	-1.0050	10	0.87932	D	0	-10.9051	19.571	0.95419	0.0:1.0:0.0:0.0	.	632;632	Q8NDL9;Q8NDL9-3	CBPC5_HUMAN;.	Y	632	ENSP00000323681:S632Y;ENSP00000353249:S632Y	ENSP00000323681:S632Y	S	+	2	0	AGBL5	27135582	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.350000	0.73017	2.713000	0.92767	0.655000	0.94253	TCC	.	.		0.537	AGBL5-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000309033.1	NM_021831		A	27282078	C	A	27282078	3	1	336	1	0	0	0	0	1	0	0	0	378	855	30	3	1933	3	AGBL5	2	27282078	Missense_Mutation	SNP	C	TCGA-RC-A7S9-01A-11D-A33Q-10	6052329	27282078	215917295	8	46752										
SULT1C3	442038	hgsc.bcm.edu	37	chr2	108872149	108872149	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	ttatgagaaattcatgtccgGaaaaggtgagttcaaactga	10	5	2	3			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr2:108872149G>C	ENST00000329106.2	+	4	521	c.521G>C	c.(520-522)gGa>gCa	p.G174A	SULT1C3_ENST00000376700.1_Missense_Mutation_p.G174A	NM_001008743.1	NP_001008743.1	Q6IMI6	ST1C3_HUMAN	sulfotransferase family, cytosolic, 1C, member 3	174					sulfur compound metabolic process (GO:0006790)	cytoplasm (GO:0005737)	alcohol sulfotransferase activity (GO:0004027)|aryl sulfotransferase activity (GO:0004062)			breast(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(1)|skin(4)	16						TTCATGTCCGGAAAAGGTGAG	0.433																																					p.G174A		Atlas-SNP	.											SULT1C3,NS,carcinoma,0,1	SULT1C3	53	.	0			c.G521C						.						60	58	59					2																	108872149		2203	4299	6502	SO:0001583	missense	442038	exon4			TGTCCGGAAAAGG	BC146362	CCDS33267.1	2q12.3	2007-07-26			ENSG00000196228	ENSG00000196228		"Sulfotransferases, cytosolic"	33543	protein-coding gene	gene with protein product						14676822, 17425406	Standard	NM_001008743		Approved		uc010ywo.2	Q6IMI6	OTTHUMG00000153227	ENST00000329106.2:c.521G>C	chr2.hg19:g.108872149G>C	ENSP00000333310:p.Gly174Ala	74.0	0.0		37.0	20.0	NM_001008743	Q6IMI5	Missense_Mutation	SNP	ENST00000329106.2	hg19	CCDS33267.1	.	.	.	.	.	.	.	.	.	.	G	15.98	2.992432	0.54041	.	.	ENSG00000196228	ENST00000329106;ENST00000376700	T;T	0.02421	4.3;4.3	3.58	2.7	0.31948	Sulfotransferase domain (1);	0.224260	0.31188	N	0.008099	T	0.21962	0.0529	H	0.96833	3.89	0.43874	D	0.996483	D	0.89917	1.0	D	0.91635	0.999	T	0.08827	-1.0703	10	0.87932	D	0	.	10.091	0.42447	0.1001:0.0:0.8999:0.0	.	174	Q6IMI6	ST1C3_HUMAN	A	174	ENSP00000333310:G174A;ENSP00000365890:G174A	ENSP00000333310:G174A	G	+	2	0	SULT1C3	108238581	1.000000	0.71417	0.001000	0.08648	0.026000	0.11368	5.235000	0.65348	0.834000	0.34852	0.650000	0.86243	GGA	.	.		0.433	SULT1C3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330255.1	NM_001008743		C	108872149	G	C	108872149	3	2	336	1	0	0	0	0	1	0	0	0	15393	1174	41	4	535	4	SULT1C3	2	108872149	Missense_Mutation	SNP	G	TCGA-RC-A7S9-01A-11D-A33Q-10	81590071	108872149	134327224	9	46753										
SCN9A	6335	hgsc.bcm.edu	37	chr2	167163101	167163101	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	tagtgcacatgatgagcatgCtgaataaggtagcttagaat	11	5	0	4			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr2:167163101C>A	ENST00000409435.1	-	3	385	c.386G>T	c.(385-387)aGc>aTc	p.S129I	SCN9A_ENST00000375387.4_Missense_Mutation_p.S130I|SCN9A_ENST00000303354.6_Missense_Mutation_p.S130I|SCN9A_ENST00000409672.1_Missense_Mutation_p.S129I			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	129					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GATGAGCATGCTGAATAAGGT	0.383																																					p.S129I		Atlas-SNP	.											.	SCN9A	296	.	0			c.G386T						.						70	70	70					2																	167163101		1938	4196	6134	SO:0001583	missense	6335	exon4			AGCATGCTGAATA	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10597	protein-coding gene	gene with protein product		603415	"sodium channel, voltage-gated, type IX, alpha polypeptide"			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.386G>T	chr2.hg19:g.167163101C>A	ENSP00000386330:p.Ser129Ile	65.0	0.0		59.0	24.0	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Missense_Mutation	SNP	ENST00000409435.1	hg19	CCDS46441.1	.	.	.	.	.	.	.	.	.	.	c	15.58	2.876801	0.51801	.	.	ENSG00000169432	ENST00000409672;ENST00000375387;ENST00000303354;ENST00000409435	D;D;D;D	0.97505	-4.41;-4.41;-4.41;-4.41	5.96	5.09	0.68999	.	0.232964	0.38492	N	0.001664	D	0.96775	0.8947	M	0.90650	3.135	0.44816	D	0.997822	B	0.09022	0.002	B	0.13407	0.009	D	0.95076	0.8209	10	0.87932	D	0	.	10.4649	0.44602	0.0:0.7977:0.0:0.2023	.	129	E7EUN6	.	I	129;130;130;129	ENSP00000386306:S129I;ENSP00000364536:S130I;ENSP00000304748:S130I;ENSP00000386330:S129I	ENSP00000304748:S130I	S	-	2	0	SCN9A	166871347	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.729000	0.47327	1.532000	0.49169	0.650000	0.86243	AGC	.	.		0.383	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977		A	167163101	C	A	167163101	3	1	336	1	0	0	0	0	1	0	0	0	13940	797	28	3	5643	3	SCN9A	2	167163101	Missense_Mutation	SNP	C	TCGA-RC-A7S9-01A-11D-A33Q-10	58290952	167163101	76036272	10	46754										
TTN	7273	hgsc.bcm.edu	37	chr2	179544684	179544699	+	Frame_Shift_Del	DEL	ACTCTTCTTCTTCTTC	ACTCTTCTTCTTCTTC	-													0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	ctcctcttcttcatgaatgtActcttcttcttcttctacaa					rs368327166	byFrequency	TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	ACTCTTCTTCTTCTTC	ACTCTTCTTCTTCTTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr2:179544684_179544699delACTCTTCTTCTTCTTC	ENST00000591111.1	-	138	32775_32790	c.32551_32566delGAAGAAGAAGAAGAGT	c.(32551-32568)gaagaagaagaagagtacfs	p.EEEEEY10851fs	TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Frame_Shift_Del_p.EEEEEY11168fs|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Frame_Shift_Del_p.EEEEEY9924fs|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron			Q8WZ42	TITIN_HUMAN	titin	0	Glu-rich.|Pro-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCATGAATGTACTCTTCTTCTTCTTCTACAAGATAT	0.417																																					p.11168_11173del		Atlas-INDEL	.											.	TTN	18412	.	0			c.33503_33518del						.																																			SO:0001589	frameshift_variant	7273	exon140			.	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.32551_32566delGAAGAAGAAGAAGAGT	chr2.hg19:g.179544684_179544699delACTCTTCTTCTTCTTC	ENSP00000465570:p.Glu10851fs	130.0	0.0		80.0	22.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Frame_Shift_Del	DEL	ENST00000591111.1	hg19																																																																																				.	.		0.417	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		-	179544699	ACTCTTCTTCTTCTTC	-	179544684	7	5	336	1	0	1	0	1	0	0	0	0	16750	391	14	0	70904	0	TTN	2	179544684	Frame_Shift_Del	DEL	ACTCTTCTTCTTCTTC	TCGA-RC-A7S9-01A-11D-A33Q-10	12381583	179544684	63654689	11	46755			1	60		2	2	19	N	C_ACTCTTCTTCTTCTTC	3.372391e-05
TTN	7273	hgsc.bcm.edu	37	chr2	179544702	179544702	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	gtactcttcttcttcttctaCaagatattcttctacatggg	5	10	7	1			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr2:179544702C>G	ENST00000591111.1	-	138	32772	c.32548G>C	c.(32548-32550)Gta>Cta	p.V10850L	TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.V11167L|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V9923L|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron			Q8WZ42	TITIN_HUMAN	titin	0	Glu-rich.|Pro-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCTTCTTCTACAAGATATTCT	0.398																																					p.V11167L		Atlas-SNP	.											.	TTN	18412	.	0			c.G33499C						.						140	127	131					2																	179544702		1893	4102	5995	SO:0001583	missense	7273	exon140			CTTCTACAAGATA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.32548G>C	chr2.hg19:g.179544702C>G	ENSP00000465570:p.Val10850Leu	150.0	0.0		85.0	24.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	5.618	0.298689	0.10622	.	.	ENSG00000155657	ENST00000342992	T	0.63255	-0.03	6.03	3.21	0.36854	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.50394	0.1613	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.47649	-0.9101	8	0.87932	D	0	.	7.9829	0.30194	0.0:0.5059:0.4034:0.0907	.	10850	Q8WZ42	TITIN_HUMAN	L	9923	ENSP00000343764:V9923L	ENSP00000343764:V9923L	V	-	1	0	TTN	179252947	0.102000	0.21896	0.058000	0.19502	0.210000	0.24377	0.359000	0.20233	0.873000	0.35799	0.655000	0.94253	GTA	.	.		0.398	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179544702	C	G	179544702	3	3	336	1	0	0	0	0	1	0	0	0	16750	478	17	4	70922	4	TTN	2	179544702	Missense_Mutation	SNP	C	TCGA-RC-A7S9-01A-11D-A33Q-10	18	179544702	63654671	12	46756			1	60		2	2	19	N	C_ACTCTTCTTCTTCTTC	3.372391e-05
AOX1	316	hgsc.bcm.edu	37	chr2	201527688	201527688	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	agactgcctgacgggggatcAtaaggtcagtaccggttgga	15	8	2	2			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr2:201527688A>G	ENST00000374700.2	+	31	3780	c.3539A>G	c.(3538-3540)cAt>cGt	p.H1180R	AOX1_ENST00000485106.1_3'UTR	NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	1180					inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)			breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	ACGGGGGATCATAAGGTCAGT	0.493																																					p.H1180R		Atlas-SNP	.											.	AOX1	152	.	0			c.A3539G						.						114	105	108					2																	201527688		2203	4300	6503	SO:0001583	missense	316	exon31			GGGATCATAAGGT	AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356			553	protein-coding gene	gene with protein product		602841				7570184	Standard	NM_001159		Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	ENST00000374700.2:c.3539A>G	chr2.hg19:g.201527688A>G	ENSP00000363832:p.His1180Arg	89.0	0.0		54.0	24.0	NM_001159	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	Missense_Mutation	SNP	ENST00000374700.2	hg19	CCDS33360.1	.	.	.	.	.	.	.	.	.	.	A	16.75	3.209964	0.58343	.	.	ENSG00000138356	ENST00000374700;ENST00000260930;ENST00000439380	T;T;T	0.38560	1.13;1.13;1.13	5.91	4.76	0.60689	Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding (3);	0.113642	0.64402	N	0.000006	T	0.52565	0.1742	M	0.82056	2.57	0.58432	D	0.999993	B	0.28378	0.209	B	0.38500	0.275	T	0.55354	-0.8154	10	0.72032	D	0.01	-43.5327	12.0302	0.53394	0.9326:0.0:0.0674:0.0	.	1180	Q06278	ADO_HUMAN	R	1180;66;20	ENSP00000363832:H1180R;ENSP00000260930:H66R;ENSP00000413326:H20R	ENSP00000260930:H66R	H	+	2	0	AOX1	201235933	1.000000	0.71417	0.989000	0.46669	0.860000	0.49131	5.937000	0.70162	1.061000	0.40601	0.454000	0.30748	CAT	.	.		0.493	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335844.1	NM_001159		G	201527688	A	G	201527688	3	3	336	1	0	0	0	0	1	0	0	0	729	217	8	2	3661	2	AOX1	2	201527688	Missense_Mutation	SNP	A	TCGA-RC-A7S9-01A-11D-A33Q-10	21982986	201527688	41671685	13	46757										
EPHA4	2043	hgsc.bcm.edu	37	chr2	222428734	222428734	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	tcctgaaaagccaggtaaaaCccctttttgcttaatggccc	7	12	0	1			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr2:222428734C>T	ENST00000281821.2	-	3	581	c.540G>A	c.(538-540)ggG>ggA	p.G180G	EPHA4_ENST00000392071.4_Silent_p.G129G|EPHA4_ENST00000409938.1_Silent_p.G180G|EPHA4_ENST00000409854.1_Silent_p.G180G	NM_004438.3	NP_004429.1	P54764	EPHA4_HUMAN	EPH receptor A4	180	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				adult walking behavior (GO:0007628)|cell adhesion (GO:0007155)|corticospinal tract morphogenesis (GO:0021957)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|glial cell migration (GO:0008347)|motor neuron axon guidance (GO:0008045)|negative regulation of axon regeneration (GO:0048681)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001108)|protein autophosphorylation (GO:0046777)|regulation of astrocyte differentiation (GO:0048710)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rap GTPase activity (GO:0032317)	axon (GO:0030424)|axon terminus (GO:0043679)|axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|DH domain binding (GO:0097161)|GPI-linked ephrin receptor activity (GO:0005004)|PH domain binding (GO:0042731)|protein kinase activity (GO:0004672)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		CCAGGTAAAACCCCTTTTTGC	0.512																																					p.G180G		Atlas-SNP	.											.	EPHA4	263	.	0			c.G540A						.						222	192	202					2																	222428734		2203	4300	6503	SO:0001819	synonymous_variant	2043	exon3			GTAAAACCCCTTT	L36645	CCDS2447.1	2q36.3	2013-02-11	2004-10-28		ENSG00000116106	ENSG00000116106	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3388	protein-coding gene	gene with protein product		602188	"EphA4"	TYRO1		9267020	Standard	NM_004438		Approved	Hek8	uc002vmq.3	P54764	OTTHUMG00000133142	ENST00000281821.2:c.540G>A	chr2.hg19:g.222428734C>T		92.0	0.0		49.0	23.0	NM_004438	A8K2P1|B2R601|B7Z6Q8|Q2M380	Silent	SNP	ENST00000281821.2	hg19	CCDS2447.1																																																																																			.	.		0.512	EPHA4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256836.3			T	222428734	C	T	222428734	2	4	336	1	0	0	0	0	0	0	0	1	5171	494	18	3		3	EPHA4	2	222428734	Silent	SNP	C	TCGA-RC-A7S9-01A-11D-A33Q-10	20901046	222428734	20770639	14	46758										
ATG16L1	55054	hgsc.bcm.edu	37	chr2	234198547	234198548	+	Frame_Shift_Ins	INS	-	-	C													0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	tgctgtctgctaagttcctgINSctggacaatgcgcggattgt							TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr2:234198547_234198548insC	ENST00000392017.4	+	13	1508_1509	c.1251_1252insC	c.(1252-1254)ctgfs	p.L418fs	SCARNA6_ENST00000515982.1_RNA|ATG16L1_ENST00000347464.5_Frame_Shift_Ins_p.L255fs|ATG16L1_ENST00000392020.4_Frame_Shift_Ins_p.L399fs|ATG16L1_ENST00000373525.5_Frame_Shift_Ins_p.L239fs|ATG16L1_ENST00000392018.1_Frame_Shift_Ins_p.L435fs	NM_001190266.1|NM_001190267.1|NM_030803.6	NP_001177195.1|NP_001177196.1|NP_110430.5	Q676U5	A16L1_HUMAN	autophagy related 16-like 1 (S. cerevisiae)	418					autophagic vacuole assembly (GO:0000045)|negative stranded viral RNA replication (GO:0039689)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)	autophagic vacuole (GO:0005776)|autophagic vacuole membrane (GO:0000421)|axoneme (GO:0005930)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(7)|prostate(3)|skin(1)	25		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0539)		Epithelial(121;1.53e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000379)|LUSC - Lung squamous cell carcinoma(224;0.00619)|Lung(119;0.00732)|GBM - Glioblastoma multiforme(43;0.11)		CTAAGTTCCTGCTGGACAATGC	0.554																																					p.L417fs		Pindel	.											.	ATG16L1	83	.	0			c.1251_1252insC						.																																			SO:0001589	frameshift_variant	55054	exon13			.	AK000897	CCDS2502.2, CCDS2503.2, CCDS54438.1	2q37.1	2014-02-12	2012-06-06	2005-09-13	ENSG00000085978	ENSG00000085978		"WD repeat domain containing"	21498	protein-coding gene	gene with protein product		610767	"APG16 autophagy 16-like (S. cerevisiae)", "ATG16 autophagy related 16-like (S. cerevisiae)", "ATG16 autophagy related 16-like 1 (S. cerevisiae)"	APG16L, ATG16L			Standard	NM_017974		Approved	WDR30, FLJ10035, ATG16A	uc002vty.3	Q676U5	OTTHUMG00000133619	ENST00000392017.4:c.1252dupC	chr2.hg19:g.234198548_234198548dupC	ENSP00000375872:p.Leu418fs	87.0	0.0		76.0	30.0	NM_030803	A3EXK9|A3EXL0|B6ZDH0|Q6IPN1|Q6UXW4|Q6ZVZ5|Q8NCY2|Q96JV5|Q9H619	Frame_Shift_Ins	INS	ENST00000392017.4	hg19	CCDS2503.2																																																																																			.	.		0.554	ATG16L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257069.2	NM_017974		C	234198548	-	C	234198547	7	5	336	1	0	1	1	0	0	0	0	0	1091	1306	46	0	1301	0	ATG16L1	2	234198547	Frame_Shift_Ins	INS	-	TCGA-RC-A7S9-01A-11D-A33Q-10	11769813	234198547	9000826	15	46759										
C3orf32	51066	hgsc.bcm.edu	37	chr3	8665330	8665330	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	gtctcgcagagggaagtccaCgatggggtacacctggggga	17	9	1	1			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr3:8665330C>T	ENST00000317371.4	-	18	2045	c.820G>A	c.(820-822)Gtg>Atg	p.V274M	SSUH2_ENST00000415132.1_Missense_Mutation_p.V274M|SSUH2_ENST00000544814.1_Missense_Mutation_p.V296M|SSUH2_ENST00000341795.3_Missense_Mutation_p.V274M			Q9Y2M2	SSUH2_HUMAN	ssu-2 homolog (C. elegans)	274						cytoplasm (GO:0005737)											GGGAAGTCCACGATGGGGTAC	0.632																																					p.V296M		Atlas-SNP	.											.	.	.	.	0			c.G886A						.						38	34	35					3																	8665330		2082	4021	6103	SO:0001583	missense	51066	exon11			AGTCCACGATGGG	AB024705	CCDS2568.1, CCDS58815.1	3p25.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000125046	ENSG00000125046			24809	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 32"	C3orf32		20205943	Standard	NM_001256748		Approved	fls485, ssu-2	uc011atg.3	Q9Y2M2	OTTHUMG00000122075	ENST00000317371.4:c.820G>A	chr3.hg19:g.8665330C>T	ENSP00000324551:p.Val274Met	64.0	0.0		35.0	9.0	NM_001256748	A6NFA9|B3KS84|B7Z6E3|F5H2S5|Q7Z7K4	Missense_Mutation	SNP	ENST00000317371.4	hg19	CCDS2568.1	.	.	.	.	.	.	.	.	.	.	C	15.57	2.872522	0.51695	.	.	ENSG00000125046	ENST00000341795;ENST00000317371;ENST00000415132;ENST00000544814	T;T;T;T	0.45276	0.92;0.92;0.9;0.92	5.2	3.39	0.38822	.	0.422550	0.25166	N	0.032631	T	0.45054	0.1323	L	0.49126	1.545	0.09310	N	0.999994	D;D	0.67145	0.985;0.996	P;P	0.54706	0.695;0.759	T	0.22730	-1.0208	10	0.40728	T	0.16	-15.4044	6.9013	0.24285	0.0:0.7964:0.0:0.2036	.	296;274	F5H2S5;Q9Y2M2	.;CC032_HUMAN	M	274;274;274;296	ENSP00000339150:V274M;ENSP00000324551:V274M;ENSP00000410757:V274M;ENSP00000439378:V296M	ENSP00000324551:V274M	V	-	1	0	C3orf32	8640330	0.000000	0.05858	0.761000	0.31378	0.733000	0.41908	-0.064000	0.11636	1.187000	0.43000	0.591000	0.81541	GTG	.	.		0.632	SSUH2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337900.1	NM_015931		T	8665330	C	T	8665330	3	4	336	1	0	0	0	0	1	0	0	0	2224	536	19	1	249	1	C3orf32	3	8665330	Missense_Mutation	SNP	C	TCGA-RC-A7S9-01A-11D-A33Q-10		8665330	189357100	16	46760										
LAMB2	3913	hgsc.bcm.edu	37	chr3	49162918	49162918	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	ctcgtggctgcactggcaggCtaggagcaaggcagagctga	16	10	0	2			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr3:49162918C>A	ENST00000418109.1	-	20	2653		c.e20-1		LAMB2_ENST00000464891.1_5'UTR|LAMB2_ENST00000305544.4_Splice_Site	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)						astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		CACTGGCAGGCTAGGAGCAAG	0.622																																					.		Atlas-SNP	.											.	LAMB2	156	.	0			c.2489-1G>T						.						19	18	18					3																	49162918		2196	4290	6486	SO:0001630	splice_region_variant	3913	exon20			GGCAGGCTAGGAG		CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"Laminins"	6487	protein-coding gene	gene with protein product	"laminin S"	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.2489-1G>T	chr3.hg19:g.49162918C>A		150.0	0.0		121.0	39.0	NM_002292	Q16321	Splice_Site	SNP	ENST00000418109.1	hg19	CCDS2789.1	.	.	.	.	.	.	.	.	.	.	C	19.69	3.874737	0.72180	.	.	ENSG00000172037	ENST00000418109;ENST00000305544	.	.	.	6.08	6.08	0.98989	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.6634	0.99662	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	LAMB2	49137922	1.000000	0.71417	1.000000	0.80357	0.843000	0.47879	5.837000	0.69381	2.894000	0.99253	0.655000	0.94253	.	.	.		0.622	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292	Intron	A	49162918	C	A	49162918	5	1	336	1	0	0	0	0	0	0	1	0	8620	811	28	3	2964	3	LAMB2	3	49162918	Splice_Site	SNP	C	TCGA-RC-A7S9-01A-11D-A33Q-10	40497588	49162918	148859512	17	46761										
DNAH1	25981	hgsc.bcm.edu	37	chr3	52361949	52361949	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	ctcccagagagtggatcaacAtgggcttggagccagggtct	14	10	2	1			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr3:52361949A>G	ENST00000420323.2	+	6	1051	c.790A>G	c.(790-792)Atg>Gtg	p.M264V		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	264	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		GTGGATCAACATGGGCTTGGA	0.562																																					p.M264V		Atlas-SNP	.											.	DNAH1	534	.	0			c.A790G						.						70	71	71					3																	52361949		1954	4143	6097	SO:0001583	missense	25981	exon6			ATCAACATGGGCT	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.790A>G	chr3.hg19:g.52361949A>G	ENSP00000401514:p.Met264Val	200.0	0.0		126.0	67.0	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	hg19	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	A	12.49	1.954543	0.34471	.	.	ENSG00000114841	ENST00000420323	T	0.21932	1.98	5.68	3.13	0.36017	.	0.473742	0.19154	N	0.121366	T	0.22627	0.0546	M	0.65975	2.015	0.30529	N	0.76759	B;B	0.22146	0.064;0.065	B;B	0.29524	0.031;0.103	T	0.12091	-1.0561	10	0.35671	T	0.21	.	7.2366	0.26074	0.4649:0.4059:0.0:0.1292	.	264;264	C9JXH6;Q9P2D7-3	.;.	V	264	ENSP00000401514:M264V	ENSP00000401514:M264V	M	+	1	0	DNAH1	52336989	0.202000	0.23423	1.000000	0.80357	0.953000	0.61014	0.749000	0.26320	0.968000	0.38212	0.533000	0.62120	ATG	.	.		0.562	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		G	52361949	A	G	52361949	3	3	336	1	0	0	0	0	1	0	0	0	4599	217	8	2	808	2	DNAH1	3	52361949	Missense_Mutation	SNP	A	TCGA-RC-A7S9-01A-11D-A33Q-10	3199031	52361949	145660481	18	46762										
ACOX2	8309	hgsc.bcm.edu	37	chr3	58520174	58520175	+	Missense_Mutation	DNP	GC	GC	TT													0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	ggaatgccctccgcatggcaGccttataacgctcattctgg							TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr3:58520174_58520175GC>TT	ENST00000302819.5	-	3	526_527	c.235_236GC>AA	c.(235-237)GCt>AAt	p.A79N	ACOX2_ENST00000459701.2_Missense_Mutation_p.A79N	NM_003500.3	NP_003491.1	Q99424	ACOX2_HUMAN	acyl-CoA oxidase 2, branched chain	79					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA 24-hydroxylase activity (GO:0033791)|acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)|flavin adenine dinucleotide binding (GO:0050660)|pristanoyl-CoA oxidase activity (GO:0016402)|receptor binding (GO:0005102)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(1)|skin(3)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(55;0.000194)|Kidney(10;0.00255)|KIRC - Kidney renal clear cell carcinoma(10;0.00268)|OV - Ovarian serous cystadenocarcinoma(275;0.156)		CCGCATGGCAGCCTTATAACGC	0.515																																					p.A79D|p.A79T		Atlas-SNP	.											.	ACOX2	53	.	0			c.C236A|c.G235A						.																																			SO:0001583	missense	8309	exon3			ATGGCAGCCTTAT|TGGCAGCCTTATA	X95190	CCDS33775.1	3p14.3	2012-07-13	2010-04-30		ENSG00000168306	ENSG00000168306	1.17.99.3		120	protein-coding gene	gene with protein product	"trihydroxycoprostanoyl-CoA oxidase", "3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholestanoyl-CoA 24-hydroxylase"	601641	"acyl-Coenzyme A oxidase 2, branched chain"			8943006, 9070889	Standard	NM_003500		Approved	BRCACOX, BRCOX, THCCox	uc003dkl.3	Q99424	OTTHUMG00000159154	ENST00000302819.5:c.235_236delinsTT	chr3.hg19:g.58520174_58520175delinsTT	ENSP00000307697:p.Ala79Asn	160.0|159.0	0.0		116.0|118.0	50.0	NM_003500	A6NF16|B2R8U5	Missense_Mutation	SNP	ENST00000302819.5	hg19	CCDS33775.1																																																																																			.	.		0.515	ACOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353541.1			TT	58520175	GC	TT	58520174	3	4	336	1	0	0	0	0	1	0	0	0	159	971	34	3	1861	3	ACOX2	3	58520174	Missense_Mutation	DNP	GC	TCGA-RC-A7S9-01A-11D-A33Q-10	6158225	58520174	139502256	19	46763										
CBLB	868	hgsc.bcm.edu	37	chr3	105459455	105459455	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	cccactgtcccaatcgagtgCaacttaaccggaaaatatag	7	12	0	0			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr3:105459455C>A	ENST00000264122.4	-	7	1187	c.866G>T	c.(865-867)tGc>tTc	p.C289F	CBLB_ENST00000405772.1_Missense_Mutation_p.C289F|CBLB_ENST00000545639.1_3'UTR|CBLB_ENST00000394027.3_Missense_Mutation_p.C311F|CBLB_ENST00000403724.1_Missense_Mutation_p.C289F	NM_170662.3	NP_733762.2	Q13191	CBLB_HUMAN	Cbl proto-oncogene B, E3 ubiquitin protein ligase	289	Cbl-PTB. {ECO:0000255|PROSITE- ProRule:PRU00839}.|SH2-like.				cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of alpha-beta T cell proliferation (GO:0046642)|negative regulation of T cell receptor signaling pathway (GO:0050860)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of T cell anergy (GO:0002669)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(2)|urinary_tract(2)	49						CAATCGAGTGCAACTTAACCG	0.368			Mis S		AML																																p.C289F	GBM(93;588 1337 9788 29341 43499)	Atlas-SNP	.		Rec	yes		3	3q13.11	868	Cas-Br-M (murine) ecotropic retroviral transforming sequence b		L	.	CBLB	118	.	0			c.G866T						.						107	90	96					3																	105459455		2203	4300	6503	SO:0001583	missense	868	exon7			CGAGTGCAACTTA	U26710	CCDS2948.1	3q	2013-07-09	2013-07-09		ENSG00000114423	ENSG00000114423		"RING-type (C3HC4) zinc fingers"	1542	protein-coding gene	gene with protein product		604491	"Cas-Br-M (murine) ectropic retroviral transforming sequence b", "Cas-Br-M (murine) ecotropic retroviral transforming sequence b"			7784085	Standard	XM_005247853		Approved	RNF56, Cbl-b	uc003dwc.3	Q13191	OTTHUMG00000150654	ENST00000264122.4:c.866G>T	chr3.hg19:g.105459455C>A	ENSP00000264122:p.Cys289Phe	93.0	0.0		54.0	21.0	NM_170662	A8K9S7|B7WNM4|Q13192|Q13193|Q3LIC0|Q63Z43|Q8IVC5	Missense_Mutation	SNP	ENST00000264122.4	hg19	CCDS2948.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.676253	0.88445	.	.	ENSG00000114423	ENST00000264122;ENST00000394027;ENST00000403724;ENST00000405772	D;D;D;D	0.86562	-2.14;-2.14;-2.14;-2.14	5.92	5.92	0.95590	Adaptor protein Cbl, PTB domain (1);SH2 motif (2);Adaptor protein Cbl, SH2-like (1);	0.000000	0.85682	D	0.000000	D	0.94374	0.8191	M	0.83012	2.62	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	D	0.94288	0.7526	10	0.87932	D	0	-10.3674	20.3172	0.98658	0.0:1.0:0.0:0.0	.	311;289;289	E7ENW2;Q13191-3;Q13191	.;.;CBLB_HUMAN	F	289;311;289;289	ENSP00000264122:C289F;ENSP00000377595:C311F;ENSP00000384816:C289F;ENSP00000384938:C289F	ENSP00000264122:C289F	C	-	2	0	CBLB	106942145	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.479000	0.81095	2.801000	0.96364	0.650000	0.86243	TGC	.	.		0.368	CBLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319417.2	NM_170662		A	105459455	C	A	105459455	3	1	336	1	0	0	0	0	1	0	0	0	2703	710	25	3	2134	3	CBLB	3	105459455	Missense_Mutation	SNP	C	TCGA-RC-A7S9-01A-11D-A33Q-10	46939281	105459455	92562975	20	46764										
PCDHA10	56139	hgsc.bcm.edu	37	chr5	140237151	140237151	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	gagcgctcgctgtcgagctaCgtgtcggtgcacgcggagag	17	11	0	1			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr5:140237151C>T	ENST00000307360.5	+	1	1518	c.1518C>T	c.(1516-1518)taC>taT	p.Y506Y	PCDHA9_ENST00000532602.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA10_ENST00000506939.2_Silent_p.Y506Y|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	506	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(11)|cervix(1)|endometrium(11)|kidney(5)|large_intestine(13)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	79			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGTCGAGCTACGTGTCGGTGC	0.682																																					p.Y506Y		Atlas-SNP	.											.	PCDHA10	358	.	0			c.C1518T						.						66	72	70					5																	140237151		2196	4273	6469	SO:0001819	synonymous_variant	56139	exon1			GAGCTACGTGTCG	AF152475	CCDS34255.1, CCDS54921.1, CCDS75325.1	5q31	2010-11-26			ENSG00000250120	ENSG00000250120		"Cadherins / Protocadherins : Clustered"	8664	other	complex locus constituent	"KIAA0345-like 4", "ortholog to mouse CNR8"	606316		CNRS8		10380929	Standard	NM_018901		Approved	CNR8, CRNR8, CNRN8, PCDH-ALPHA10		Q9Y5I2	OTTHUMG00000163372	ENST00000307360.5:c.1518C>T	chr5.hg19:g.140237151C>T		92.0	0.0		63.0	32.0	NM_031859	A1L493|O75280|Q9NRU2	Silent	SNP	ENST00000307360.5	hg19	CCDS54921.1																																																																																			.	.		0.682	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901		T	140237151	C	T	140237151	2	4	336	1	0	0	0	0	0	0	0	1	11529	547	19	1		1	PCDHA10	5	140237151	Silent	SNP	C	TCGA-RC-A7S9-01A-11D-A33Q-10		140237151	40678109	21	46765										
PCDHB8	56128	hgsc.bcm.edu	37	chr5	140558018	140558018	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	acgaccactctccagtatttCtggacaaacaaatgttggtg	8	10	2	0			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr5:140558018C>A	ENST00000239444.2	+	1	648	c.403C>A	c.(403-405)Ctg>Atg	p.L135M	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	135					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(14)|liver(1)|lung(38)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TCCAGTATTTCTGGACAAACA	0.438																																					p.L135M		Atlas-SNP	.											.	PCDHB8	199	.	0			c.C403A						.						33	52	45					5																	140558018		2196	4294	6490	SO:0001583	missense	56128	exon1			GTATTTCTGGACA	AF152501	CCDS4250.1	5q31	2010-01-26			ENSG00000120322	ENSG00000120322		"Cadherins / Protocadherins : Clustered"	8693	other	protocadherin		606334				10380929	Standard	NM_019120		Approved	PCDH-BETA8, PCDH3I	uc011dai.2	Q9UN66	OTTHUMG00000129621	ENST00000239444.2:c.403C>A	chr5.hg19:g.140558018C>A	ENSP00000239444:p.Leu135Met	1554.0	1.0		963.0	126.0	NM_019120	B9EGV1	Missense_Mutation	SNP	ENST00000239444.2	hg19	CCDS4250.1	.	.	.	.	.	.	.	.	.	.	c	6.300	0.423514	0.11928	.	.	ENSG00000120322	ENST00000239444	T	0.21543	2.0	4.25	-1.17	0.09648	Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.21022	0.0506	M	0.81112	2.525	0.09310	N	1	B	0.25441	0.126	B	0.23018	0.043	T	0.29088	-1.0023	9	0.33940	T	0.23	.	3.468	0.07557	0.1535:0.5299:0.1589:0.1578	.	135	Q9UN66	PCDB8_HUMAN	M	135	ENSP00000239444:L135M	ENSP00000239444:L135M	L	+	1	2	PCDHB8	140538202	0.000000	0.05858	0.115000	0.21578	0.793000	0.44817	-5.803000	0.00097	-0.307000	0.08804	0.585000	0.79938	CTG	.	.		0.438	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120		A	140558018	C	A	140558018	3	1	336	1	0	0	0	0	1	0	0	0	11557	912	32	3	405	3	PCDHB8	5	140558018	Missense_Mutation	SNP	C	TCGA-RC-A7S9-01A-11D-A33Q-10	320867	140558018	40357242	22	46766										
BTNL2	56244	hgsc.bcm.edu	37	chr6	32370894	32370894	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	ctccccggatgtcttcccaaTacacctggggctctgggaac	10	15	2	0			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr6:32370894T>C	ENST00000374993.1	-	3	526	c.527A>G	c.(526-528)tAt>tGt	p.Y176C	BTNL2_ENST00000454136.3_Missense_Mutation_p.Y176C|BTNL2_ENST00000414363.1_Intron|BTNL2_ENST00000429232.2_Intron|BTNL2_ENST00000544175.1_Intron|BTNL2_ENST00000374995.3_Intron|BTNL2_ENST00000540315.1_Intron	NM_019602.1	NP_062548.1	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2 (MHC class II associated)	176	Ig-like V-type 2.					integral component of membrane (GO:0016021)				central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)|urinary_tract(1)	19						GTCTTCCCAATACACCTGGGG	0.602																																					p.Y176C		Atlas-SNP	.											.	BTNL2	50	.	0			c.A527G						.						57	56	56					6																	32370894		1509	2709	4218	SO:0001583	missense	56244	exon3			TCCCAATACACCT	AF186588		6p21.3	2014-01-14			ENSG00000204290	ENSG00000204290		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Butyrophilins"	1142	protein-coding gene	gene with protein product		606000				10803852, 15735647	Standard	XM_006726138		Approved	HSBLMHC1, BTL-II, BTN7	uc003obg.1	Q9UIR0	OTTHUMG00000031102	ENST00000374993.1:c.527A>G	chr6.hg19:g.32370894T>C	ENSP00000364132:p.Tyr176Cys	151.0	0.0		170.0	100.0	NM_019602	A0PJV5|B0UYW9|B0V0N6|O98261|Q08E96|Q58R22|Q58R23|Q5JYF9|Q5MP42|Q5MP43|Q5RIF8|Q5SP08|Q5SP09|Q5SRW3|Q5SRW4|Q5SU36|Q95HK0	Missense_Mutation	SNP	ENST00000374993.1	hg19		.	.	.	.	.	.	.	.	.	.	T	15.04	2.714115	0.48622	.	.	ENSG00000204290	ENST00000468270;ENST00000374993	T	0.75589	-0.95	4.44	0.775	0.18527	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.368040	0.04773	N	0.428473	T	0.65249	0.2673	L	0.60455	1.87	0.09310	N	1	D	0.63880	0.993	P	0.57204	0.815	T	0.47947	-0.9077	10	0.40728	T	0.16	.	3.7103	0.08417	0.0:0.2191:0.2186:0.5623	.	176	Q9UIR0	BTNL2_HUMAN	C	176	ENSP00000364132:Y176C	ENSP00000364132:Y176C	Y	-	2	0	BTNL2	32478872	0.000000	0.05858	0.001000	0.08648	0.326000	0.28443	-0.269000	0.08596	0.059000	0.16252	0.509000	0.49947	TAT	.	.		0.602	BTNL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_019602		C	32370894	T	C	32370894	3	2	336	1	0	0	0	0	1	0	0	0	1567	1406	49	2	856	2	BTNL2	6	32370894	Missense_Mutation	SNP	T	TCGA-RC-A7S9-01A-11D-A33Q-10		32370894	138744173	23	46767										
CUL9	23113	hgsc.bcm.edu	37	chr6	43160821	43160821	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	tcgtgcaggccctgcgcctcCtttacctgctcatgaccaag	9	16	1	1			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr6:43160821C>T	ENST00000252050.4	+	9	2347	c.2263C>T	c.(2263-2265)Ctt>Ttt	p.L755F	CUL9_ENST00000354495.3_Missense_Mutation_p.L645F|CUL9_ENST00000372647.2_Missense_Mutation_p.L755F	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	755					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						CCTGCGCCTCCTTTACCTGCT	0.547																																					p.L755F		Atlas-SNP	.											.	CUL9	248	.	0			c.C2263T						.						183	155	164					6																	43160821		2203	4300	6503	SO:0001583	missense	23113	exon9			CGCCTCCTTTACC	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"parkin-like cytoplasmic p53 binding protein", "p53-associated parkin-like cytoplasmic protein"	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.2263C>T	chr6.hg19:g.43160821C>T	ENSP00000252050:p.Leu755Phe	75.0	0.0		87.0	54.0	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Missense_Mutation	SNP	ENST00000252050.4	hg19	CCDS4890.1	.	.	.	.	.	.	.	.	.	.	C	19.45	3.830562	0.71258	.	.	ENSG00000112659	ENST00000252050;ENST00000354495;ENST00000372647	T;T;T	0.56275	0.47;0.47;0.47	4.99	4.12	0.48240	Armadillo-like helical (1);Armadillo-type fold (1);	0.161948	0.42053	D	0.000779	T	0.35335	0.0928	N	0.24115	0.695	0.35424	D	0.793449	D;D	0.64830	0.994;0.994	P;P	0.59221	0.854;0.854	T	0.42666	-0.9438	10	0.51188	T	0.08	-14.8011	5.7408	0.18092	0.1409:0.6468:0.1364:0.0759	.	755;755	E9PEZ1;Q8IWT3	.;CUL9_HUMAN	F	755;645;755	ENSP00000252050:L755F;ENSP00000346490:L645F;ENSP00000361730:L755F	ENSP00000252050:L755F	L	+	1	0	CUL9	43268799	1.000000	0.71417	0.980000	0.43619	0.953000	0.61014	3.978000	0.56881	1.092000	0.41356	0.297000	0.19635	CTT	.	.		0.547	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		T	43160821	C	T	43160821	3	4	336	1	0	0	0	0	1	0	0	0	4063	681	24	3	2293	3	CUL9	6	43160821	Missense_Mutation	SNP	C	TCGA-RC-A7S9-01A-11D-A33Q-10	10789927	43160821	127954246	24	46768										
MEP1A	4224	hgsc.bcm.edu	37	chr6	46797206	46797206	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	agcagtgcctgcaatttttcTataaaatgacgggaagtcct	9	8	1	1			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr6:46797206T>C	ENST00000230588.4	+	10	1051	c.1042T>C	c.(1042-1044)Tat>Cat	p.Y348H		NM_005588.2	NP_005579.2	Q16819	MEP1A_HUMAN	meprin A, alpha (PABA peptide hydrolase)	348	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				digestion (GO:0007586)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|meprin A complex (GO:0017090)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42			Lung(136;0.192)			GCAATTTTTCTATAAAATGAC	0.522																																					p.Y348H		Atlas-SNP	.											.	MEP1A	93	.	0			c.T1042C						.						117	126	123					6																	46797206		2203	4300	6503	SO:0001583	missense	4224	exon10			TTTTTCTATAAAA		CCDS4918.1	6p12-p11	2010-10-18			ENSG00000112818	ENSG00000112818	3.4.24.18		7015	protein-coding gene	gene with protein product		600388				7774936	Standard	NM_005588		Approved	PPHA	uc010jzh.1	Q16819	OTTHUMG00000014790	ENST00000230588.4:c.1042T>C	chr6.hg19:g.46797206T>C	ENSP00000230588:p.Tyr348His	131.0	0.0		120.0	34.0	NM_005588	A2RRM4|B0AZP9|B2RCS2|Q8TDC9|Q9H1R1	Missense_Mutation	SNP	ENST00000230588.4	hg19	CCDS4918.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.707349	0.89018	.	.	ENSG00000112818	ENST00000230588	T	0.03272	3.99	5.67	5.67	0.87782	Concanavalin A-like lectin/glucanase (1);MAM domain (5);	0.000000	0.85682	D	0.000000	T	0.17238	0.0414	M	0.90870	3.155	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.02837	-1.1104	10	0.54805	T	0.06	-24.1644	15.9259	0.79615	0.0:0.0:0.0:1.0	.	376;348	B7ZL91;Q16819	.;MEP1A_HUMAN	H	348	ENSP00000230588:Y348H	ENSP00000230588:Y348H	Y	+	1	0	MEP1A	46905165	1.000000	0.71417	0.995000	0.50966	0.959000	0.62525	6.276000	0.72601	2.164000	0.68074	0.528000	0.53228	TAT	.	.		0.522	MEP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040803.1	NM_005588		C	46797206	T	C	46797206	3	2	336	1	0	0	0	0	1	0	0	0	9484	1522	53	2	1080	2	MEP1A	6	46797206	Missense_Mutation	SNP	T	TCGA-RC-A7S9-01A-11D-A33Q-10	3636385	46797206	124317861	25	46769										
REV3L	5980	hgsc.bcm.edu	37	chr6	111694495	111694495	+	Frame_Shift_Del	DEL	C	C	-													0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	catttttttctatagcttgtCctggaaaaagatcctgaaca							TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr6:111694495delC	ENST00000358835.3	-	14	5517	c.5063delG	c.(5062-5064)ggafs	p.G1688fs	REV3L_ENST00000435970.1_Frame_Shift_Del_p.G1610fs|REV3L_ENST00000368805.1_Frame_Shift_Del_p.G1688fs|REV3L_ENST00000368802.3_Frame_Shift_Del_p.G1688fs			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	1688					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		TATAGCTTGTCCTGGAAAAAG	0.393								DNA polymerases (catalytic subunits)																													p.G1688fs		Atlas-Indel,Pindel	.											.	REV3L	386	.	0			c.5064delA						.						60	60	60					6																	111694495		2203	4299	6502	SO:0001589	frameshift_variant	5980	exon13			.	AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"DNA polymerases"	9968	protein-coding gene	gene with protein product	"polymerase, DNA, zeta"	602776	"REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta", "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.5063delG	chr6.hg19:g.111694495delC	ENSP00000351697:p.Gly1688fs	114.0	0.0		61.0	22.0	NM_002912	O43214|Q5TC33	Frame_Shift_Del	DEL	ENST00000358835.3	hg19	CCDS5091.2																																																																																			.	.		0.393	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		-	111694495	C	-	111694495	7	5	336	1	0	1	0	1	0	0	0	0	13255	855	30	0	4409	0	REV3L	6	111694495	Frame_Shift_Del	DEL	C	TCGA-RC-A7S9-01A-11D-A33Q-10	64897289	111694495	59420572	26	46770										
C6orf58	352999	hgsc.bcm.edu	37	chr6	127899881	127899881	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	actgtggctatgaatctggaGatcatatgtgcatctctgtg	11	7	3	2			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr6:127899881G>C	ENST00000329722.7	+	2	364	c.352G>C	c.(352-354)Gat>Cat	p.D118H		NM_001010905.1	NP_001010905.1	Q6P5S2	CF058_HUMAN	chromosome 6 open reading frame 58	118						extracellular vesicular exosome (GO:0070062)				kidney(3)|large_intestine(3)|liver(1)|lung(7)|pancreas(1)	15				GBM - Glioblastoma multiforme(226;0.0405)|all cancers(137;0.156)		TGAATCTGGAGATCATATGTG	0.413																																					p.D118H		Atlas-SNP	.											.	C6orf58	35	.	0			c.G352C						.						228	212	218					6																	127899881		2203	4300	6503	SO:0001583	missense	352999	exon2			TCTGGAGATCATA	BC062712	CCDS34533.1	6q22.33	2011-12-13			ENSG00000184530	ENSG00000184530			20960	protein-coding gene	gene with protein product							Standard	NM_001010905		Approved		uc003qbh.4	Q6P5S2	OTTHUMG00000015530	ENST00000329722.7:c.352G>C	chr6.hg19:g.127899881G>C	ENSP00000328069:p.Asp118His	99.0	0.0		65.0	28.0	NM_001010905	B4E1I0|Q5VUP2	Missense_Mutation	SNP	ENST00000329722.7	hg19	CCDS34533.1	.	.	.	.	.	.	.	.	.	.	G	12.42	1.933092	0.34096	.	.	ENSG00000184530	ENST00000329722	T	0.55588	0.51	4.95	2.01	0.26516	.	0.290165	0.36628	N	0.002493	T	0.59418	0.2192	M	0.82923	2.615	0.35454	D	0.795954	D	0.89917	1.0	D	0.75020	0.985	T	0.62798	-0.6778	9	.	.	.	-12.8776	8.0287	0.30453	0.3607:0.0:0.6393:0.0	.	118	Q6P5S2	CF058_HUMAN	H	118	ENSP00000328069:D118H	.	D	+	1	0	C6orf58	127941574	0.057000	0.20700	0.101000	0.21167	0.183000	0.23260	0.140000	0.16056	0.427000	0.26145	0.591000	0.81541	GAT	.	.		0.413	C6orf58-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042152.1	NM_001010905		C	127899881	G	C	127899881	3	2	336	1	0	0	0	0	1	0	0	0	2369	942	33	4	358	4	C6orf58	6	127899881	Missense_Mutation	SNP	G	TCGA-RC-A7S9-01A-11D-A33Q-10	16205386	127899881	43215186	27	46771										
PCLO	27445	hgsc.bcm.edu	37	chr7	82390054	82390055	+	Frame_Shift_Ins	INS	-	-	T													0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	ttgtttttttcttgatcaccINStttttttgggtagaaatatt							TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr7:82390054_82390055insT	ENST00000333891.9	-	24	15525_15526	c.15188_15189insA	c.(15187-15189)aagfs	p.K5063fs		NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TCTTGATCACCTTTTTTTGGGT	0.317																																					p.K5063fs		Atlas-Indel,Pindel	.											.	PCLO	1506	.	0			c.15189_15190insA						.																																			SO:0001589	frameshift_variant	27445	exon24			.	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.15189dupA	chr7.hg19:g.82390061_82390061dupT	ENSP00000334319:p.Lys5063fs	325.0	0.0		196.0	73.0	NM_033026		Frame_Shift_Ins	INS	ENST00000333891.9	hg19	CCDS47630.1																																																																																			.	.		0.317	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		T	82390055	-	T	82390054	7	5	336	1	0	1	1	0	0	0	0	0	11592	680	24	0	247	0	PCLO	7	82390054	Frame_Shift_Ins	INS	-	TCGA-RC-A7S9-01A-11D-A33Q-10		82390054	76748609	28	46772										
GRM8	2918	hgsc.bcm.edu	37	chr7	126173751	126173751	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	agcctgtgcggttcatgttgGgtctctgatccagagggcaa	14	9	2	2			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr7:126173751G>C	ENST00000339582.2	-	9	2493	c.1685C>G	c.(1684-1686)cCc>cGc	p.P562R	GRM8_ENST00000444921.2_Missense_Mutation_p.P562R|GRM8_ENST00000358373.3_Missense_Mutation_p.P562R|GRM8_ENST00000480995.1_5'UTR			O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8	562					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of cAMP biosynthetic process (GO:0030818)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(16)|lung(62)|ovary(5)|pancreas(1)|prostate(1)|skin(14)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(4)	125		Prostate(267;0.186)				GTTCATGTTGGGTCTCTGATC	0.527										HNSCC(24;0.065)																											p.P562R		Atlas-SNP	.											.	GRM8	377	.	0			c.C1685G						.						147	131	136					7																	126173751		2203	4300	6503	SO:0001583	missense	2918	exon8			ATGTTGGGTCTCT		CCDS5794.1, CCDS47696.1	7q31.3-q32.1	2012-08-29			ENSG00000179603	ENSG00000179603		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4600	protein-coding gene	gene with protein product		601116				8824806	Standard	NM_000845		Approved	GLUR8, GPRC1H, mGlu8, MGLUR8	uc003vlr.2	O00222	OTTHUMG00000022888	ENST00000339582.2:c.1685C>G	chr7.hg19:g.126173751G>C	ENSP00000344173:p.Pro562Arg	186.0	0.0		110.0	62.0	NM_000845	A4D0Y3|B0FZ74|B0M0L0|O15493|O95945|O95946|Q3MIV9|Q52M02|Q6J165	Missense_Mutation	SNP	ENST00000339582.2	hg19	CCDS5794.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.107689	0.77096	.	.	ENSG00000179603	ENST00000339582;ENST00000444921;ENST00000358373	D;D;D	0.91521	-2.86;-2.86;-2.86	5.8	5.8	0.92144	GPCR, family 3, nine cysteines domain (1);	0.000000	0.85682	D	0.000000	D	0.97648	0.9229	H	0.98754	4.32	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.98837	1.0753	10	0.87932	D	0	.	19.0428	0.93008	0.0:0.0:1.0:0.0	.	562;562	O00222-2;O00222	.;GRM8_HUMAN	R	562	ENSP00000344173:P562R;ENSP00000409790:P562R;ENSP00000351142:P562R	ENSP00000344173:P562R	P	-	2	0	GRM8	125960987	1.000000	0.71417	0.997000	0.53966	0.994000	0.84299	9.859000	0.99545	2.758000	0.94735	0.643000	0.83706	CCC	.	.		0.527	GRM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059209.4			C	126173751	G	C	126173751	3	2	336	1	0	0	0	0	1	0	0	0	6812	1232	43	4	1103	4	GRM8	7	126173751	Missense_Mutation	SNP	G	TCGA-RC-A7S9-01A-11D-A33Q-10	43783697	126173751	32964912	29	46773										
CNTNAP2	26047	hgsc.bcm.edu	37	chr7	146825914	146825914	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	ttgccagaaggaagaaattaGagccctcaaatgtggtaagg	12	6	1	3			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr7:146825914G>T	ENST00000361727.3	+	7	1585	c.1069G>T	c.(1069-1071)Gag>Tag	p.E357*		NM_014141.5	NP_054860.1	Q9UHC6	CNTP2_HUMAN	contactin associated protein-like 2	357	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|cerebral cortex development (GO:0021987)|clustering of voltage-gated potassium channels (GO:0045163)|learning (GO:0007612)|limbic system development (GO:0021761)|neuron projection development (GO:0031175)|neuron recognition (GO:0008038)|protein localization to juxtaparanode region of axon (GO:0071205)|social behavior (GO:0035176)|striatum development (GO:0021756)|superior temporal gyrus development (GO:0071109)|thalamus development (GO:0021794)|transmission of nerve impulse (GO:0019226)|vocalization behavior (GO:0071625)	axolemma (GO:0030673)|axon (GO:0030424)|cell surface (GO:0009986)|dendrite (GO:0030425)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|voltage-gated potassium channel complex (GO:0008076)	enzyme binding (GO:0019899)			NS(3)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(105)|ovary(9)|pancreas(2)|prostate(5)|skin(7)|stomach(3)|upper_aerodigestive_tract(6)|urinary_tract(3)	188	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			GAAGAAATTAGAGCCCTCAAA	0.368										HNSCC(39;0.1)																											p.E357X		Atlas-SNP	.											.	CNTNAP2	392	.	0			c.G1069T						.						102	105	104					7																	146825914		2203	4300	6503	SO:0001587	stop_gained	26047	exon7			AAATTAGAGCCCT	AF193613	CCDS5889.1	7q35	2008-02-04			ENSG00000174469	ENSG00000174469			13830	protein-coding gene	gene with protein product		604569				10624965, 10048485	Standard	NM_014141		Approved	Caspr2, KIAA0868, NRXN4	uc003weu.2	Q9UHC6	OTTHUMG00000152743	ENST00000361727.3:c.1069G>T	chr7.hg19:g.146825914G>T	ENSP00000354778:p.Glu357*	179.0	0.0		115.0	32.0	NM_014141	D3DWG2|Q14DG2|Q52LV1|Q5H9Q7|Q9UQ12	Nonsense_Mutation	SNP	ENST00000361727.3	hg19	CCDS5889.1	.	.	.	.	.	.	.	.	.	.	G	44	11.125238	0.99519	.	.	ENSG00000174469	ENST00000361727	.	.	.	5.64	5.64	0.86602	.	0.080948	0.47852	D	0.000210	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.15952	T	0.53	.	18.2754	0.90081	0.0:0.0:1.0:0.0	.	.	.	.	X	357	.	ENSP00000354778:E357X	E	+	1	0	CNTNAP2	146456847	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.697000	0.98697	2.674000	0.91012	0.655000	0.94253	GAG	.	.		0.368	CNTNAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327668.1			T	146825914	G	T	146825914	4	4	336	1	0	0	0	0	0	1	0	0	3649	943	33	3	1095	3	CNTNAP2	7	146825914	Nonsense_Mutation	SNP	G	TCGA-RC-A7S9-01A-11D-A33Q-10	20652163	146825914	12312749	30	46774										
PSD3	23362	hgsc.bcm.edu	37	chr8	18730005	18730005	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	ggctgtaaactttgttccttGagatgactttgagagggggc	14	6	0	3			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr8:18730005G>A	ENST00000327040.8	-	3	471	c.369C>T	c.(367-369)ctC>ctT	p.L123L	PSD3_ENST00000523619.1_Silent_p.L58L|PSD3_ENST00000440756.2_Silent_p.L123L	NM_015310.3	NP_056125.3	Q9NYI0	PSD3_HUMAN	pleckstrin and Sec7 domain containing 3	123					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)		TTTGTTCCTTGAGATGACTTT	0.493																																					p.L123L		Atlas-SNP	.											.	PSD3	142	.	0			c.C369T						.						117	113	114					8																	18730005		1869	4102	5971	SO:0001819	synonymous_variant	23362	exon3			TTCCTTGAGATGA	AF243495	CCDS34854.1, CCDS43720.1	8p21.3	2013-01-10			ENSG00000156011	ENSG00000156011		"Pleckstrin homology (PH) domain containing"	19093	protein-coding gene	gene with protein product		614440					Standard	NM_206909		Approved	KIAA0942, HCA67, EFA6R, DKFZp761K1423	uc003wza.3	Q9NYI0	OTTHUMG00000163711	ENST00000327040.8:c.369C>T	chr8.hg19:g.18730005G>A		91.0	0.0		73.0	35.0	NM_015310	A6NFQ4|E9KL50|Q6B003|Q9Y2F1	Silent	SNP	ENST00000327040.8	hg19	CCDS43720.1																																																																																			.	.		0.493	PSD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000374867.1	NM_015310		A	18730005	G	A	18730005	2	1	336	1	0	0	0	0	0	0	0	1	12660	1277	45	3		3	PSD3	8	18730005	Silent	SNP	G	TCGA-RC-A7S9-01A-11D-A33Q-10		18730005	127634017	31	46775										
ATP6V1B2	526	hgsc.bcm.edu	37	chr8	20068787	20068787	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	cagtattgctagggggcagaAaattcctatcttctctgctg	10	9	2	1			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr8:20068787A>C	ENST00000276390.2	+	6	603	c.563A>C	c.(562-564)aAa>aCa	p.K188T		NM_001693.3	NP_001684.2	P21281	VATB2_HUMAN	ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B2	188					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|proton-transporting V-type ATPase, V1 domain (GO:0033180)|ruffle (GO:0001726)	ATP binding (GO:0005524)|hydrogen ion transmembrane transporter activity (GO:0015078)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			endometrium(1)|kidney(2)|lung(5)|prostate(1)	9				Colorectal(74;0.0535)|COAD - Colon adenocarcinoma(73;0.211)	Gallium nitrate(DB05260)	AGGGGGCAGAAAATTCCTATC	0.463																																					p.K188T	Pancreas(119;1230 1726 3901 4036 31644)	Atlas-SNP	.											.	ATP6V1B2	34	.	0			c.A563C						.						116	103	108					8																	20068787		2203	4300	6503	SO:0001583	missense	526	exon6			GGCAGAAAATTCC	L35249	CCDS6014.1	8p21.3	2010-04-21	2006-01-13	2002-05-10	ENSG00000147416	ENSG00000147416	3.6.3.14	"ATPases / V-type"	854	protein-coding gene	gene with protein product		606939	"ATPase, H+ transporting, lysosomal (vacuolar proton pump), beta polypeptide, 56/58kD, isoform 2", "ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B, isoform 2"	VPP3, ATP6B2		2145275, 14580332	Standard	NM_001693		Approved	VATB, Vma2, HO57	uc003wzp.3	P21281	OTTHUMG00000131073	ENST00000276390.2:c.563A>C	chr8.hg19:g.20068787A>C	ENSP00000276390:p.Lys188Thr	86.0	0.0		55.0	25.0	NM_001693	B2R5Z3|D3DSQ5|Q14544|Q15859|Q96IR0	Missense_Mutation	SNP	ENST00000276390.2	hg19	CCDS6014.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.38|19.38	3.817472|3.817472	0.70912|0.70912	.|.	.|.	ENSG00000147416|ENSG00000147416	ENST00000519667|ENST00000276390;ENST00000542368	.|T	.|0.78126	.|-1.15	5.65|5.65	5.65|5.65	0.86999|0.86999	.|ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.86347|0.86347	0.5911|0.5911	M|M	0.67625|0.67625	2.065|2.065	0.80722|0.80722	D|D	1|1	.|D	.|0.67145	.|0.996	.|D	.|0.70487	.|0.969	D|D	0.87744|0.87744	0.2587|0.2587	5|10	.|0.87932	.|D	.|0	-1.2234|-1.2234	14.9989|14.9989	0.71455|0.71455	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|188	.|P21281	.|VATB2_HUMAN	D|T	177|188;62	.|ENSP00000276390:K188T	.|ENSP00000276390:K188T	E|K	+|+	3|2	2|0	ATP6V1B2|ATP6V1B2	20113067|20113067	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	9.282000|9.282000	0.95840|0.95840	2.277000|2.277000	0.76020|0.76020	0.528000|0.528000	0.53228|0.53228	GAA|AAA	.	.		0.463	ATP6V1B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253732.1	NM_001693		C	20068787	A	C	20068787	3	2	336	1	0	0	0	0	1	0	0	0	1179	14	1	5	585	5	ATP6V1B2	8	20068787	Missense_Mutation	SNP	A	TCGA-RC-A7S9-01A-11D-A33Q-10	1338782	20068787	126295235	32	46776										
ZNF703	80139	hgsc.bcm.edu	37	chr8	37553564	37553564	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	gcggcagcggcagcggcggcGgcgggaagaggccggcggtg	24	11	0	1			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr8:37553564G>A	ENST00000331569.4	+	1	296	c.67G>A	c.(67-69)Ggc>Agc	p.G23S		NM_025069.1	NP_079345.1	Q9H7S9	ZN703_HUMAN	zinc finger protein 703	23	Poly-Gly.				adherens junction assembly (GO:0034333)|cellular response to estradiol stimulus (GO:0071392)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of homotypic cell-cell adhesion (GO:0034111)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of cell cycle (GO:0051726)|regulation of transcription, DNA-templated (GO:0006355)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|protein complex (GO:0043234)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)		FGFR1/ZNF703(2)	breast(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(1)|pancreas(1)	7			BRCA - Breast invasive adenocarcinoma(5;7.93e-25)|LUSC - Lung squamous cell carcinoma(8;1.05e-09)			cagcggcggcggcggGAAGAG	0.721																																					p.G23S		Atlas-SNP	.											.	ZNF703	16	.	0			c.G67A						.						3	4	4					8																	37553564		1484	3103	4587	SO:0001583	missense	80139	exon1			GGCGGCGGCGGGA	AK024361	CCDS6094.1	8p12	2008-05-02				ENSG00000183779			25883	protein-coding gene	gene with protein product						15897872	Standard	NM_025069		Approved	FLJ14299, ZNF503L	uc003xjy.1	Q9H7S9		ENST00000331569.4:c.67G>A	chr8.hg19:g.37553564G>A	ENSP00000332325:p.Gly23Ser	65.0	0.0		39.0	27.0	NM_025069	Q5XG76	Missense_Mutation	SNP	ENST00000331569.4	hg19	CCDS6094.1	.	.	.	.	.	.	.	.	.	.	g	13.99	2.400853	0.42613	.	.	ENSG00000183779	ENST00000331569;ENST00000397235	T	0.41758	0.99	3.58	2.65	0.31530	.	0.622662	0.15229	N	0.273541	T	0.23330	0.0564	L	0.34521	1.04	0.26094	N	0.980911	B	0.30211	0.273	B	0.20184	0.028	T	0.12889	-1.0530	10	0.15066	T	0.55	-10.3048	4.2354	0.10623	0.122:0.0:0.6475:0.2305	.	23	Q9H7S9	ZN703_HUMAN	S	23	ENSP00000332325:G23S	ENSP00000332325:G23S	G	+	1	0	ZNF703	37672722	0.995000	0.38212	1.000000	0.80357	0.753000	0.42808	3.802000	0.55553	0.780000	0.33566	0.461000	0.40582	GGC	.	.		0.721	ZNF703-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376683.2	NM_025069		A	37553564	G	A	37553564	3	1	336	1	0	0	0	0	1	0	0	0	18121	1116	39	1	69	1	ZNF703	8	37553564	Missense_Mutation	SNP	G	TCGA-RC-A7S9-01A-11D-A33Q-10	17484777	37553564	108810458	33	46777										
PREX2	80243	hgsc.bcm.edu	37	chr8	69030794	69030794	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	gttgttttcagtgactgcaaCagcaataggaattccatcgc	9	9	1	1			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr8:69030794C>A	ENST00000288368.4	+	27	3613	c.3336C>A	c.(3334-3336)aaC>aaA	p.N1112K		NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	1112					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						GTGACTGCAACAGCAATAGGA	0.443																																					p.N1112K		Atlas-SNP	.											.	PREX2	614	.	0			c.C3336A						.						140	123	129					8																	69030794		2203	4300	6503	SO:0001583	missense	80243	exon27			CTGCAACAGCAAT	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.3336C>A	chr8.hg19:g.69030794C>A	ENSP00000288368:p.Asn1112Lys	69.0	0.0		50.0	24.0	NM_024870	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	hg19	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.359913	0.82353	.	.	ENSG00000046889	ENST00000288368;ENST00000396539	T	0.39229	1.09	5.2	4.33	0.51752	.	0.000000	0.85682	D	0.000000	T	0.59487	0.2197	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.60063	-0.7336	10	0.48119	T	0.1	.	13.7303	0.62783	0.0:0.9254:0.0:0.0746	.	1112	Q70Z35	PREX2_HUMAN	K	1112;1117	ENSP00000288368:N1112K	ENSP00000288368:N1112K	N	+	3	2	PREX2	69193348	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.971000	0.49248	1.197000	0.43143	0.591000	0.81541	AAC	.	.		0.443	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		A	69030794	C	A	69030794	3	1	336	1	0	0	0	0	1	0	0	0	12489	477	17	3	3671	3	PREX2	8	69030794	Missense_Mutation	SNP	C	TCGA-RC-A7S9-01A-11D-A33Q-10	31477230	69030794	77333228	34	46778										
TRPA1	8989	hgsc.bcm.edu	37	chr8	72975718	72975718	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	caaaccttagtattatttccAtgcattctttggaacctgaa	5	9	1	1			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr8:72975718A>T	ENST00000262209.4	-	5	848	c.641T>A	c.(640-642)aTg>aAg	p.M214K		NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	214					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	TATTATTTCCATGCATTCTTT	0.318																																					p.M214K		Atlas-SNP	.											.	TRPA1	256	.	0			c.T641A						.						93	88	90					8																	72975718		2203	4300	6503	SO:0001583	missense	8989	exon5			ATTTCCATGCATT	Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	497	protein-coding gene	gene with protein product		604775	"ankyrin-like with transmembrane domains 1"	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.641T>A	chr8.hg19:g.72975718A>T	ENSP00000262209:p.Met214Lys	69.0	0.0		41.0	25.0	NM_007332	A6NIN6	Missense_Mutation	SNP	ENST00000262209.4	hg19	CCDS34908.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.468070	0.84533	.	.	ENSG00000104321	ENST00000523582;ENST00000262209	T;T	0.64618	-0.11;2.42	5.62	5.62	0.85841	Ankyrin repeat-containing domain (3);	0.153676	0.64402	D	0.000001	T	0.68458	0.3003	M	0.72894	2.215	0.80722	D	1	P	0.51351	0.944	P	0.47346	0.544	T	0.73845	-0.3854	10	0.72032	D	0.01	-21.1316	15.7734	0.78190	1.0:0.0:0.0:0.0	.	214	O75762	TRPA1_HUMAN	K	66;214	ENSP00000428151:M66K;ENSP00000262209:M214K	ENSP00000262209:M214K	M	-	2	0	TRPA1	73138272	1.000000	0.71417	1.000000	0.80357	0.858000	0.48976	7.594000	0.82698	2.260000	0.74910	0.528000	0.53228	ATG	.	.		0.318	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332		T	72975718	A	T	72975718	3	4	336	1	0	0	0	0	1	0	0	0	16592	217	8	4	2810	4	TRPA1	8	72975718	Missense_Mutation	SNP	A	TCGA-RC-A7S9-01A-11D-A33Q-10	3944924	72975718	73388304	35	46779										
RECQL4	9684	hgsc.bcm.edu	37	chr8	145742465	145742465	+	5'Flank	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	ctttcagattggccttgagcCgctgcccgtagtccggcacc	11	15	1	2			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr8:145742465C>A	ENST00000292524.1	+	0	0				RECQL4_ENST00000428558.2_Missense_Mutation_p.R108L|RECQL4_ENST00000532237.1_5'UTR|LRRC14_ENST00000529022.1_5'Flank	NM_001272036.1|NM_014665.2	NP_001258965.1|NP_055480.1	Q15048	LRC14_HUMAN	leucine rich repeat containing 14											endometrium(1)|lung(3)|prostate(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			GGCCTTGAGCCGCTGCCCGTA	0.677																																					p.R108L		Atlas-SNP	.											.	RECQL4	75	.	0			c.G323T						.						31	36	34					8																	145742465		2108	4222	6330	SO:0001631	upstream_gene_variant	9401	exon4			TTGAGCCGCTGCC	BC011377	CCDS6432.1	8q24.3	2012-08-20			ENSG00000160959	ENSG00000160959			20419	protein-coding gene	gene with protein product						7584026	Standard	NM_001272036		Approved	KIAA0014, LRRC14A	uc003zdk.3	Q15048	OTTHUMG00000165179		chr8.hg19:g.145742465C>A	Exception_encountered	86.0	0.0		57.0	4.0	NM_004260	A8K0A8|D3DWM8	Missense_Mutation	SNP	ENST00000292524.1	hg19	CCDS6432.1																																																																																			.	.		0.677	LRRC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382494.1	NM_014665		A	145742465	C	A	145742465	1	1	336	0	1	0	0	0	0	0	0	0	13217	652	23	1		1	RECQL4	8	145742465	5'Flank	SNP	C	TCGA-RC-A7S9-01A-11D-A33Q-10	72766747	145742465	621557	36	46780										
TUBAL3	79861	hgsc.bcm.edu	37	chr10	5437418	5437418	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	ggggtggaagagtgaacggtGctggcccgtccggatcccat	17	10	0	2			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr10:5437418G>T	ENST00000380419.3	-	3	305	c.268C>A	c.(268-270)Cac>Aac	p.H90N	TUBAL3_ENST00000479328.1_Missense_Mutation_p.H50N	NM_024803.2	NP_079079.1	A6NHL2	TBAL3_HUMAN	tubulin, alpha-like 3	90					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|liver(1)|lung(7)|prostate(2)|skin(3)	25						AGTGAACGGTGCTGGCCCGTC	0.597																																					p.H90N		Atlas-SNP	.											.	TUBAL3	54	.	0			c.C268A						.						136	135	135					10																	5437418		2203	4300	6503	SO:0001583	missense	79861	exon3			AACGGTGCTGGCC	AK025318	CCDS7066.2, CCDS53491.1	10p15.1	2007-03-15			ENSG00000178462	ENSG00000178462		"Tubulins"	23534	protein-coding gene	gene with protein product							Standard	NM_024803		Approved	FLJ21665	uc001ihy.3	A6NHL2	OTTHUMG00000017595	ENST00000380419.3:c.268C>A	chr10.hg19:g.5437418G>T	ENSP00000369784:p.His90Asn	123.0	0.0		98.0	38.0	NM_024803	B4DKL2|Q4QQJ5|Q9H6Z0	Missense_Mutation	SNP	ENST00000380419.3	hg19	CCDS7066.2	.	.	.	.	.	.	.	.	.	.	G	13.23	2.174832	0.38413	.	.	ENSG00000178462	ENST00000380419;ENST00000479328	T;T	0.66995	-0.24;-0.24	3.98	-2.09	0.07232	Tubulin/FtsZ, GTPase domain (4);	1.580760	0.03720	N	0.251702	T	0.55401	0.1918	L	0.31845	0.965	0.09310	N	0.999992	B;B	0.27679	0.185;0.048	B;B	0.23716	0.048;0.026	T	0.50874	-0.8776	10	0.87932	D	0	.	8.9977	0.36063	0.5836:0.0:0.4164:0.0	.	50;90	A6NHL2-2;A6NHL2	.;TBAL3_HUMAN	N	90;50	ENSP00000369784:H90N;ENSP00000418799:H50N	ENSP00000369784:H90N	H	-	1	0	TUBAL3	5427418	0.997000	0.39634	0.000000	0.03702	0.038000	0.13279	3.478000	0.53158	-0.494000	0.06669	-0.253000	0.11424	CAC	.	.		0.597	TUBAL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046548.2	NM_024803		T	5437418	G	T	5437418	3	4	336	1	0	0	0	0	1	0	0	0	16766	1319	46	3	1080	3	TUBAL3	10	5437418	Missense_Mutation	SNP	G	TCGA-RC-A7S9-01A-11D-A33Q-10		5437418	130097329	37	46781										
GLYAT	10249	hgsc.bcm.edu	37	chr11	58477472	58477472	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	tccagtctggtccattagatCccagcacacaggggtcccct	9	15	1	1			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr11:58477472C>T	ENST00000344743.3	-	6	799	c.658G>A	c.(658-660)Gat>Aat	p.D220N	GLYAT_ENST00000529732.1_Missense_Mutation_p.D220N	NM_201648.2	NP_964011.2	Q6IB77	GLYAT_HUMAN	glycine-N-acyltransferase	220					acyl-CoA metabolic process (GO:0006637)|glycine metabolic process (GO:0006544)|monocarboxylic acid metabolic process (GO:0032787)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)|glycine N-benzoyltransferase activity (GO:0047962)|transferase activity, transferring acyl groups (GO:0016746)			NS(1)|autonomic_ganglia(1)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	16		Breast(21;0.0044)|all_epithelial(135;0.0157)			Glycine(DB00145)	TCCATTAGATCCCAGCACACA	0.552																																					p.D220N		Atlas-SNP	.											.	GLYAT	53	.	0			c.G658A						.						68	70	69					11																	58477472		2201	4295	6496	SO:0001583	missense	10249	exon6			TTAGATCCCAGCA	AF023466	CCDS7970.1, CCDS7971.1	11q12.1	2008-03-11					2.3.1.13		13734	protein-coding gene	gene with protein product		607424					Standard	NM_201648		Approved	GAT, ACGNAT	uc001nnb.3	Q6IB77		ENST00000344743.3:c.658G>A	chr11.hg19:g.58477472C>T	ENSP00000340200:p.Asp220Asn	107.0	0.0		70.0	32.0	NM_201648	O14833|Q96QK7	Missense_Mutation	SNP	ENST00000344743.3	hg19	CCDS7970.1	.	.	.	.	.	.	.	.	.	.	C	6.786	0.513932	0.12944	.	.	ENSG00000149124	ENST00000344743;ENST00000529732	T;T	0.16743	2.32;2.32	6.06	-12.0	0.00017	Acyl-CoA N-acyltransferase (2);Glycine N-acyltransferase, C-terminal (1);	5.117170	0.00166	N	0.000006	T	0.07548	0.0190	N	0.14661	0.345	0.58432	D	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.21449	-1.0245	10	0.25106	T	0.35	1.504	6.8105	0.23802	0.5564:0.2867:0.0:0.1569	.	220	Q6IB77	GLYAT_HUMAN	N	220	ENSP00000340200:D220N;ENSP00000431688:D220N	ENSP00000340200:D220N	D	-	1	0	GLYAT	58234048	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-3.725000	0.00382	-2.379000	0.00595	-1.181000	0.01715	GAT	.	.		0.552	GLYAT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394593.1			T	58477472	C	T	58477472	3	4	336	1	0	0	0	0	1	0	0	0	6487	855	30	3	236	3	GLYAT	11	58477472	Missense_Mutation	SNP	C	TCGA-RC-A7S9-01A-11D-A33Q-10		58477472	76529044	38	46782										
ALG9	79796	hgsc.bcm.edu	37	chr11	111724383	111724383	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	aaaactcaccagaaatagtaTgagggccatcagcgaccaat	8	10	2	2			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr11:111724383T>C	ENST00000531154.1	-	7	737	c.265A>G	c.(265-267)Ata>Gta	p.I89V	ALG9_ENST00000527228.1_5'UTR|ALG9_ENST00000524880.1_3'UTR|ALG9_ENST00000398006.2_Missense_Mutation_p.I89V	NM_024740.2	NP_079016.2	Q9H6U8	ALG9_HUMAN	ALG9, alpha-1,2-mannosyltransferase	260					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	dol-P-Man:Man(6)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase activity (GO:0052926)|dol-P-Man:Man(8)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase activity (GO:0052918)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;6.81e-07)|BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|all cancers(92;1.3e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0587)		AGAAATAGTATGAGGGCCATC	0.378																																					p.I260V		Atlas-SNP	.											.	ALG9	77	.	0			c.A778G						.						109	103	105					11																	111724383		1836	4081	5917	SO:0001583	missense	79796	exon8			ATAGTATGAGGGC		CCDS41714.1, CCDS53709.1, CCDS73379.1, CCDS73380.1	11q23	2013-02-26	2013-02-26	2004-08-26	ENSG00000086848	ENSG00000086848	2.4.1.259, 2.4.1.261	"Dolichyl D-mannosyl phosphate dependent mannosyltransferases"	15672	protein-coding gene	gene with protein product	"dolichyl-P-Man:Man(6)GlcNAc(2)-PP-dolichol alpha-1,2-mannosyltransferase", "dolichyl-P-Man:Man(8)GlcNAc(2)-PP-dolichol alpha-1,2-mannosyltransferase", "dol-P-Man dependent alpha-1,2-mannosyltransferase"	606941	"disrupted in bipolar affective disorder 1", "asparagine-linked glycosylation 9 homolog (yeast, alpha 1,2 mannosyltransferase)", "asparagine-linked glycosylation 9, alpha- 1,2-mannosyltransferase homolog (S. cerevisiae, alpha- 1,2-mannosyltransferase)", "asparagine-linked glycosylation 9, alpha-1,2-mannosyltransferase homolog (S. cerevisiae)"	DIBD1		12030331, 15148656	Standard	NM_024740		Approved		uc021qql.1	Q9H6U8	OTTHUMG00000166819	ENST00000531154.1:c.265A>G	chr11.hg19:g.111724383T>C	ENSP00000435517:p.Ile89Val	292.0	0.0		170.0	37.0	NM_001077690	Q6ZMD5|Q7Z4R4|Q96GS7|Q96PB9|Q9H068	Missense_Mutation	SNP	ENST00000531154.1	hg19	CCDS41714.1	.	.	.	.	.	.	.	.	.	.	T	4.087	0.014093	0.07959	.	.	ENSG00000086848	ENST00000531154;ENST00000398006;ENST00000428306	T;T	0.61392	0.11;0.11	5.87	0.889	0.19212	.	0.423806	0.29722	N	0.011373	T	0.28732	0.0712	N	0.11201	0.11	0.09310	N	1	B;B;B;B	0.10296	0.0;0.0;0.003;0.0	B;B;B;B	0.12837	0.001;0.001;0.008;0.001	T	0.18272	-1.0342	10	0.09084	T	0.74	-0.4983	6.3005	0.21109	0.0:0.3361:0.1294:0.5345	.	89;260;493;260	B4DQI3;Q9H6U8-3;B4DYW0;Q9H6U8	.;.;.;ALG9_HUMAN	V	89;89;493	ENSP00000435517:I89V;ENSP00000381090:I89V	ENSP00000381090:I89V	I	-	1	0	ALG9	111229593	0.908000	0.30866	0.064000	0.19789	0.970000	0.65996	0.759000	0.26461	0.195000	0.20347	0.533000	0.62120	ATA	.	.		0.378	ALG9-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000391485.1	NM_024740		C	111724383	T	C	111724383	3	2	336	1	0	0	0	0	1	0	0	0	524	1464	51	2	1114	2	ALG9	11	111724383	Missense_Mutation	SNP	T	TCGA-RC-A7S9-01A-11D-A33Q-10	53246911	111724383	23282133	39	46783										
CHD4	1108	hgsc.bcm.edu	37	chr12	6701152	6701152	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	ccatcaccacattcagcagaGacacctggttgccaccacct	6	17	2	1			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr12:6701152G>A	ENST00000357008.2	-	20	3183	c.3020C>T	c.(3019-3021)tCt>tTt	p.S1007F	CHD4_ENST00000544040.1_Missense_Mutation_p.S1000F|CHD4_ENST00000544484.1_Missense_Mutation_p.S1004F|CHD4_ENST00000309577.6_Missense_Mutation_p.S1007F	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	1007					ATP-dependent chromatin remodeling (GO:0043044)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|RNA polymerase II repressing transcription factor binding (GO:0001103)|zinc ion binding (GO:0008270)			central_nervous_system(2)	2						ATTCAGCAGAGACACCTGGTT	0.483																																					p.S1007F	Colon(32;586 792 4568 16848 45314)	Atlas-SNP	.											.	CHD4	539	.	0			c.C3020T						.						164	150	155					12																	6701152		2203	4300	6503	SO:0001583	missense	1108	exon20			AGCAGAGACACCT	X86691	CCDS8552.1	12p13	2013-01-28				ENSG00000111642		"Zinc fingers, PHD-type"	1919	protein-coding gene	gene with protein product		603277				7575689, 8843877	Standard	XM_006718958		Approved	Mi-2b, Mi2-BETA	uc001qpo.3	Q14839		ENST00000357008.2:c.3020C>T	chr12.hg19:g.6701152G>A	ENSP00000349508:p.Ser1007Phe	133.0	0.0		83.0	41.0	NM_001273	Q8IXZ5	Missense_Mutation	SNP	ENST00000357008.2	hg19	CCDS8552.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.055626	0.75960	.	.	ENSG00000111642	ENST00000544484;ENST00000544040;ENST00000309577;ENST00000357008;ENST00000537464	D;D;D;D	0.94000	-3.33;-3.33;-3.33;-3.33	4.73	4.73	0.59995	SNF2-related (1);	0.000000	0.85682	D	0.000000	D	0.96473	0.8849	M	0.76727	2.345	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.997	D;D;D	0.83275	0.974;0.996;0.994	D	0.97038	0.9755	10	0.87932	D	0	.	17.8935	0.88879	0.0:0.0:1.0:0.0	.	1007;1007;1000	Q14839-2;Q14839;F5GWX5	.;CHD4_HUMAN;.	F	1004;1000;1007;1007;981	ENSP00000440392:S1004F;ENSP00000440542:S1000F;ENSP00000312419:S1007F;ENSP00000349508:S1007F	ENSP00000312419:S1007F	S	-	2	0	CHD4	6571413	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.591000	0.98241	2.450000	0.82876	0.563000	0.77884	TCT	.	.		0.483	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001273		A	6701152	G	A	6701152	3	1	336	1	0	0	0	0	1	0	0	0	3329	942	33	3	2802	3	CHD4	12	6701152	Missense_Mutation	SNP	G	TCGA-RC-A7S9-01A-11D-A33Q-10		6701152	127150743	40	46784										
STYK1	55359	hgsc.bcm.edu	37	chr12	10783658	10783658	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	ttttaccttttaaagccttgAgaataacactcttgggctta	6	8	1	1			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr12:10783658A>G	ENST00000075503.3	-	5	957	c.437T>C	c.(436-438)cTc>cCc	p.L146P		NM_018423.2	NP_060893.2	Q6J9G0	STYK1_HUMAN	serine/threonine/tyrosine kinase 1	146	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)			breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|liver(1)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	26						TAAAGCCTTGAGAATAACACT	0.433										HNSCC(73;0.22)																											p.L146P		Atlas-SNP	.											.	STYK1	55	.	0			c.T437C						.						76	73	74					12																	10783658		2203	4300	6503	SO:0001583	missense	55359	exon5			GCCTTGAGAATAA	AF251059	CCDS8629.1	12p13.2	2005-01-21							18889	protein-coding gene	gene with protein product		611433				12841579	Standard	NM_018423		Approved	SuRTK106, DKFZp761P1010, NOK	uc001qys.2	Q6J9G0		ENST00000075503.3:c.437T>C	chr12.hg19:g.10783658A>G	ENSP00000075503:p.Leu146Pro	151.0	0.0		87.0	13.0	NM_018423	B2R9T2|Q52LR3|Q9BXY2|Q9NSH1	Missense_Mutation	SNP	ENST00000075503.3	hg19	CCDS8629.1	.	.	.	.	.	.	.	.	.	.	A	16.88	3.244107	0.59103	.	.	ENSG00000060140	ENST00000075503	D	0.84070	-1.8	5.45	5.45	0.79879	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.200757	0.33670	N	0.004667	D	0.88032	0.6328	L	0.56199	1.76	0.80722	D	1	D	0.64830	0.994	D	0.65874	0.939	D	0.88990	0.3414	10	0.72032	D	0.01	-2.1767	13.7446	0.62868	1.0:0.0:0.0:0.0	.	146	Q6J9G0	STYK1_HUMAN	P	146	ENSP00000075503:L146P	ENSP00000075503:L146P	L	-	2	0	STYK1	10674925	1.000000	0.71417	1.000000	0.80357	0.521000	0.34408	5.604000	0.67626	2.193000	0.70182	0.529000	0.55759	CTC	.	.		0.433	STYK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399622.1	NM_018423		G	10783658	A	G	10783658	3	3	336	1	0	0	0	0	1	0	0	0	15374	304	11	2	859	2	STYK1	12	10783658	Missense_Mutation	SNP	A	TCGA-RC-A7S9-01A-11D-A33Q-10	4082506	10783658	123068237	41	46785										
RERGL	79785	hgsc.bcm.edu	37	chr12	18241889	18242060	+	Splice_Site	DEL	GGCTGCAAAGCAAACAATCTAGATTTAGGGCTGTTATATTTTAGGAAACAGCTAATTTGGTTATGTGCATAAGGCTTTAGTTCTTAAACCAAAAATATTCAAGAATTAATAAAGACTTTAAAATTAGACCAAATTCTGTTCTAAATAGTAGTTAACAATATTTCCATGGTAC	GGCTGCAAAGCAAACAATCTAGATTTAGGGCTGTTATATTTTAGGAAACAGCTAATTTGGTTATGTGCATAAGGCTTTAGTTCTTAAACCAAAAATATTCAAGAATTAATAAAGACTTTAAAATTAGACCAAATTCTGTTCTAAATAGTAGTTAACAATATTTCCATGGTAC	-													0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	gtaagaaacctcactgtaagGgctgcaaagcaaacaatcta					rs376792404|rs542021705|rs545855054|rs370962289|rs576765194|rs562457289|rs531466257	byFrequency	TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	GGCTGCAAAGCAAACAATCTAGATTTAGGGCTGTTATATTTTAGGAAACAGCTAATTTGGTTATGTGCATAAGGCTTTAGTTCTTAAACCAAAAATATTCAAGAATTAATAAAGACTTTAAAATTAGACCAAATTCTGTTCTAAATAGTAGTTAACAATATTTCCATGGTAC	GGCTGCAAAGCAAACAATCTAGATTTAGGGCTGTTATATTTTAGGAAACAGCTAATTTGGTTATGTGCATAAGGCTTTAGTTCTTAAACCAAAAATATTCAAGAATTAATAAAGACTTTAAAATTAGACCAAATTCTGTTCTAAATAGTAGTTAACAATATTTCCATGGTAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr12:18241889_18242060delGGCTGCAAAGCAAACAATCTAGATTTAGGGCTGTTATATTTTAGGAAACAGCTAATTTGGTTATGTGCATAAGGCTTTAGTTCTTAAACCAAAAATATTCAAGAATTAATAAAGACTTTAAAATTAGACCAAATTCTGTTCTAAATAGTAGTTAACAATATTTCCATGGTAC	ENST00000229002.2	-	3	262_263	c.56_57delGTACCATGGAAATATTGTTAACTACTATTTAGAACAGAATTTGGTCTAATTTTAAAGTCTTTATTAATTCTTGAATATTTTTGGTTTAAGAACTAAAGCCTTATGCACATAACCAAATTAGCTGTTTCCTAAAATATAACAGCCCTAAATCTAGATTGTTTGCTTTGCAGCC	c.(55-57)ggt>g	p.G19fs	RERGL_ENST00000536890.1_Splice_Site_p.G18fs|RERGL_ENST00000538724.1_Splice_Site_p.G18fs|RERGL_ENST00000541632.1_5'UTR	NM_024730.2	NP_079006.1	Q9H628	RERGL_HUMAN	RERG/RAS-like	19	Small GTPase-like.				GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)	GTP binding (GO:0005525)			endometrium(1)|large_intestine(5)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	17						TCACTGTAAGGGCTGCAAAGCAAACAATCTAGATTTAGGGCTGTTATATTTTAGGAAACAGCTAATTTGGTTATGTGCATAAGGCTTTAGTTCTTAAACCAAAAATATTCAAGAATTAATAAAGACTTTAAAATTAGACCAAATTCTGTTCTAAATAGTAGTTAACAATATTTCCATGGTACAAACAAATGA	0.304																																					p.19_20del		Pindel	.											.	RERGL	66	.	0			c.56_58del						.																																			SO:0001630	splice_region_variant	79785	exon3			.	AK026308	CCDS8679.1, CCDS66332.1	12p12.3	2014-08-12			ENSG00000111404	ENSG00000111404			26213	protein-coding gene	gene with protein product						24127187	Standard	NM_001286201		Approved	FLJ22655	uc001rdq.3	Q9H628	OTTHUMG00000168820	ENST00000229002.2:c.56-1GTACCATGGAAATATTGTTAACTACTATTTAGAACAGAATTTGGTCTAATTTTAAAGTCTTTATTAATTCTTGAATATTTTTGGTTTAAGAACTAAAGCCTTATGCACATAACCAAATTAGCTGTTTCCTAAAATATAACAGCCCTAAATCTAGATTGTTTGCTTTGCAGCC>-	chr12.hg19:g.18241889_18242060delGGCTGCAAAGCAAACAATCTAGATTTAGGGCTGTTATATTTTAGGAAACAGCTAATTTGGTTATGTGCATAAGGCTTTAGTTCTTAAACCAAAAATATTCAAGAATTAATAAAGACTTTAAAATTAGACCAAATTCTGTTCTAAATAGTAGTTAACAATATTTCCATGGTAC		95.0	0.0		57.0	12.0	NM_024730		In_Frame_Del	DEL	ENST00000229002.2	hg19	CCDS8679.1																																																																																			.	.		0.304	RERGL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000401198.1	NM_024730	Frame_Shift_Del	-	18242060	GGCTGCAAAGCAAACAATCTAGATTTAGGGCTGTTATATTTTAGGAAACAGCTAATTTGGTTATGTGCATAAGGCTTTAGTTCTTAAACCAAAAATATTCAAGAATTAATAAAGACTTTAAAATTAGACCAAATTCTGTTCTAAATAGTAGTTAACAATATTTCCATGGTAC	-	18241889	8	5	336	1	0	1	0	1	0	0	1	0	13248	1246	43	0	576	0	RERGL	12	18241889	Splice_Site	DEL	GGCTGCAAAGCAAACAATCTAGATTTAGGGCTGTTATATTTTAGGAAACAGCTAATTTGGTTATGTGCATAAGGCTTTAGTTCTTAAACCAAAAATATTCAAGAATTAATAAAGACTTTAAAATTAGACCAAATTCTGTTCTAAATAGTAGTTAACAATATTTCCATGGTAC	TCGA-RC-A7S9-01A-11D-A33Q-10	7458231	18241889	115610006	42	46786										
ACACB	32	hgsc.bcm.edu	37	chr12	109637211	109637211	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	tcctcctctctcccagttacCgaattaccatcggcaataag	5	15	1	0			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr12:109637211C>A	ENST00000338432.7	+	18	2751	c.2632C>A	c.(2632-2634)Cga>Aga	p.R878R	ACACB_ENST00000377848.3_Silent_p.R878R|ACACB_ENST00000377854.5_Silent_p.R878R			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	878					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	TCCCAGTTACCGAATTACCAT	0.522																																					p.R878R		Atlas-SNP	.											.	ACACB	330	.	0			c.C2632A						.						115	104	108					12																	109637211		2203	4300	6503	SO:0001819	synonymous_variant	32	exon17			AGTTACCGAATTA	U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 2"	601557	"acetyl-Coenzyme A carboxylase beta"			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.2632C>A	chr12.hg19:g.109637211C>A		115.0	0.0		80.0	42.0	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Silent	SNP	ENST00000338432.7	hg19	CCDS31898.1																																																																																			.	.		0.522	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093		A	109637211	C	A	109637211	2	1	336	1	0	0	0	0	0	0	0	1	107	644	23	1		1	ACACB	12	109637211	Silent	SNP	C	TCGA-RC-A7S9-01A-11D-A33Q-10	91395322	109637211	24214684	43	46787										
RB1	5925	hgsc.bcm.edu	37	chr13	48953788	48953788	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	ggaatccatgcttaaatcagTaagttaaaaacaatataaaa	5	5	1	0			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr13:48953788T>C	ENST00000267163.4	+	14	1527		c.e14+2			NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1						androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(8)		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(DB00071)|Insulin Regular(DB00030)"	CTTAAATCAGTAAGTTAAAAA	0.433		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)																											.		Atlas-SNP	.	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	.	RB1	1068	.	23	Whole gene deletion(15)|Unknown(8)	bone(11)|breast(5)|central_nervous_system(2)|adrenal_gland(1)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	c.1389+2T>C	GRCh37	CS023834	RB1	S		.						19	20	20					13																	48953788		2200	4300	6500	SO:0001630	splice_region_variant	5925	exon14	Familial Cancer Database		AATCAGTAAGTTA	M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1389+2T>C	chr13.hg19:g.48953788T>C		310.0	0.0		72.0	49.0	NM_000321	A8K5E3|P78499|Q5VW46|Q8IZL4	Splice_Site	SNP	ENST00000267163.4	hg19	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.096264	0.76870	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	.	.	.	4.75	4.75	0.60458	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.2452	0.65983	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	RB1	47851789	1.000000	0.71417	1.000000	0.80357	0.839000	0.47603	6.189000	0.72051	1.770000	0.52166	0.377000	0.23210	.	.	.		0.433	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1		Intron	C	48953788	T	C	48953788	5	2	336	1	0	0	0	0	0	0	1	0	13113	1652	57	2	1445	2	RB1	13	48953788	Splice_Site	SNP	T	TCGA-RC-A7S9-01A-11D-A33Q-10		48953788	66216090	44	46788										
VIPAR	63894	hgsc.bcm.edu	37	chr14	77895420	77895420	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	gtccacatcttccaccagatTgacatactcctgtaatatct	4	13	2	2			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr14:77895420T>G	ENST00000553888.1	-	18	1795	c.1285A>C	c.(1285-1287)Aat>Cat	p.N429H	VIPAS39_ENST00000557658.1_Missense_Mutation_p.N429H|VIPAS39_ENST00000448935.2_Missense_Mutation_p.N380H|VIPAS39_ENST00000556412.1_Missense_Mutation_p.N455H|VIPAS39_ENST00000327028.4_Missense_Mutation_p.N416H|VIPAS39_ENST00000343765.2_Missense_Mutation_p.N429H	NM_001193314.1|NM_001193317.1|NM_022067.3	NP_001180243.1|NP_001180246.1|NP_071350.2	Q9H9C1	SPE39_HUMAN	VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog	429					cell differentiation (GO:0030154)|endosome to lysosome transport (GO:0008333)|intracellular protein transport (GO:0006886)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|late endosome (GO:0005770)|recycling endosome (GO:0055037)											TCCACCAGATTGACATACTCC	0.443																																					p.N429H		Atlas-SNP	.											.	.	.	.	0			c.A1285C						.						131	102	112					14																	77895420		2203	4300	6503	SO:0001583	missense	63894	exon18			CCAGATTGACATA	AK022925	CCDS9862.1, CCDS53905.1	14q24.3-q31	2013-08-14	2012-07-24	2012-07-24	ENSG00000151445	ENSG00000151445			20347	protein-coding gene	gene with protein product	"VPS33B interacting protein, apical-basolateral polarity regulator"	613401	"chromosome 14 open reading frame 133"	C14orf133		20190753, 19109425, 22753090, 23002115, 23918659	Standard	NM_022067		Approved	VIPAR, VPS16B, SPE-39, SPE39, hSPE-39	uc001xtu.2	Q9H9C1		ENST00000553888.1:c.1285A>C	chr14.hg19:g.77895420T>G	ENSP00000452181:p.Asn429His	81.0	0.0		42.0	17.0	NM_001193314	B4DPI6|O95434|Q9H7E1|Q9H9I9	Missense_Mutation	SNP	ENST00000553888.1	hg19	CCDS9862.1	.	.	.	.	.	.	.	.	.	.	T	15.25	2.777664	0.49786	.	.	ENSG00000151445	ENST00000343765;ENST00000553888;ENST00000327028;ENST00000557658;ENST00000448935;ENST00000556412	T;T;T;T;T;T	0.51071	0.72;0.72;0.72;0.72;0.72;0.72	5.42	4.32	0.51571	.	0.306680	0.40469	N	0.001097	T	0.37758	0.1015	N	0.22421	0.69	0.35090	D	0.764222	P;P	0.40282	0.47;0.711	B;P	0.44359	0.273;0.447	T	0.52403	-0.8580	10	0.46703	T	0.11	-28.2457	9.9063	0.41377	0.0:0.0:0.3772:0.6228	.	380;429	B4DPI6;Q9H9C1	.;VIPAR_HUMAN	H	429;429;416;429;380;455	ENSP00000339122:N429H;ENSP00000452181:N429H;ENSP00000313098:N416H;ENSP00000452191:N429H;ENSP00000404815:N380H;ENSP00000451857:N455H	ENSP00000313098:N416H	N	-	1	0	VIPAR	76965173	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.521000	0.45563	2.047000	0.60756	0.533000	0.62120	AAT	.	.		0.443	VIPAS39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414008.1	NM_022067		G	77895420	T	G	77895420	3	3	336	1	0	0	0	0	1	0	0	0	17183	1812	63	5	208	5	VIPAR	14	77895420	Missense_Mutation	SNP	T	TCGA-RC-A7S9-01A-11D-A33Q-10		77895420	29454120	45	46789										
CDH1	999	hgsc.bcm.edu	37	chr16	68849486	68849486	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	acgaatgtggtaccttttgaGgtctctctcaccacctccac	7	14	2	1			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr16:68849486G>A	ENST00000261769.5	+	10	1580	c.1389G>A	c.(1387-1389)gaG>gaA	p.E463E	CDH1_ENST00000422392.2_Silent_p.E402E|CDH1_ENST00000562836.1_3'UTR|RP11-354M1.2_ENST00000563916.1_RNA	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	463	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.		E -> Q (in a gastric carcinoma sample).		adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)	p.G441_E463del(1)|p.?(1)		NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		TACCTTTTGAGGTCTCTCTCA	0.493			"Mis, N, F, S"		"lobular breast, gastric"	gastric			Hereditary Diffuse Gastric Cancer																												p.E463E		Atlas-SNP	.	yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"		E	.	CDH1	535	.	2	Unknown(1)|Deletion - In frame(1)	stomach(1)|breast(1)	c.G1389A						.						169	141	151					16																	68849486		2198	4300	6498	SO:0001819	synonymous_variant	999	exon10	Familial Cancer Database	HDGC	TTTTGAGGTCTCT	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"CD molecules", "Cadherins / Major cadherins"	1748	protein-coding gene	gene with protein product	"E-Cadherin"	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.1389G>A	chr16.hg19:g.68849486G>A		154.0	0.0		73.0	34.0	NM_004360	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Silent	SNP	ENST00000261769.5	hg19	CCDS10869.1																																																																																			.	.		0.493	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360		A	68849486	G	A	68849486	2	1	336	1	0	0	0	0	0	0	0	1	3097	991	35	3		3	CDH1	16	68849486	Silent	SNP	G	TCGA-RC-A7S9-01A-11D-A33Q-10		68849486	21505267	46	46790										
KIAA0100	9703	hgsc.bcm.edu	37	chr17	26970215	26970215	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	ttcaataaggatgggctgaaGgacagttccttttgatccac	10	8	1	2			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr17:26970215G>C	ENST00000528896.2	-	4	437	c.363C>G	c.(361-363)tcC>tcG	p.S121S	KIAA0100_ENST00000389003.3_5'UTR|KIAA0100_ENST00000544884.1_5'UTR	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	121						extracellular region (GO:0005576)				breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68	Lung NSC(42;0.00431)					ATGGGCTGAAGGACAGTTCCT	0.493																																					p.S121S		Atlas-SNP	.											.	KIAA0100	175	.	0			c.C363G						.						122	126	125					17																	26970215		2203	4300	6503	SO:0001819	synonymous_variant	9703	exon4			GCTGAAGGACAGT	D43947	CCDS32595.1	17q11.2	2012-11-29			ENSG00000007202	ENSG00000007202			28960	protein-coding gene	gene with protein product	"cancer/testis antigen 101", "breast cancer overexpressed gene 1"	610664				16289875	Standard	NM_014680		Approved	DKFZp686M0843, MGC111488, BCOX1, CT101, BCOX	uc002hbu.3	Q14667	OTTHUMG00000166587	ENST00000528896.2:c.363C>G	chr17.hg19:g.26970215G>C		81.0	0.0		51.0	21.0	NM_014680	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Silent	SNP	ENST00000528896.2	hg19	CCDS32595.1																																																																																			.	.		0.493	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680		C	26970215	G	C	26970215	2	2	336	1	0	0	0	0	0	0	0	1	8163	987	35	4		4	KIAA0100	17	26970215	Silent	SNP	G	TCGA-RC-A7S9-01A-11D-A33Q-10		26970215	54224995	47	46791										
NF1	4763	hgsc.bcm.edu	37	chr17	29592294	29592294	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	caaggctttgaaaacgttaaGtattttctaccaagctggga	9	7	1	1			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr17:29592294G>A	ENST00000358273.4	+	36	5155	c.4772G>A	c.(4771-4773)aGt>aAt	p.S1591N	NF1_ENST00000356175.3_Missense_Mutation_p.S1570N	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	1591	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.|Lipid binding.				actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		AAAACGTTAAGTATTTTCTAC	0.338			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																											p.S1591N		Atlas-SNP	.	yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	.	NF1	1586	.	12	Whole gene deletion(8)|Unknown(4)	soft_tissue(7)|autonomic_ganglia(2)|central_nervous_system(2)|lung(1)	c.G4772A						.						69	71	70					17																	29592294		2203	4297	6500	SO:0001583	missense	4763	exon36	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	CGTTAAGTATTTT		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.4772G>A	chr17.hg19:g.29592294G>A	ENSP00000351015:p.Ser1591Asn	148.0	0.0		90.0	34.0	NM_001042492	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	hg19	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	G	6.328	0.428635	0.11987	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735	T;T;T	0.59638	0.25;0.25;0.25	6.16	2.87	0.33458	Cellular retinaldehyde-binding/triple function, C-terminal (2);Armadillo-type fold (1);	0.204155	0.50627	N	0.000115	T	0.11965	0.0291	N	0.00066	-2.3	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.33394	-0.9870	10	0.02654	T	1	.	5.1909	0.15209	0.5174:0.0:0.4826:0.0	.	620;1570;1591	Q59FX3;P21359-2;P21359	.;.;NF1_HUMAN	N	1591;1570;1236	ENSP00000351015:S1591N;ENSP00000348498:S1570N;ENSP00000389907:S1236N	ENSP00000348498:S1570N	S	+	2	0	NF1	26616420	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.962000	0.63687	0.944000	0.37579	0.650000	0.86243	AGT	.	.		0.338	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		A	29592294	G	A	29592294	3	1	336	1	0	0	0	0	1	0	0	0	10365	1029	36	3	4975	3	NF1	17	29592294	Missense_Mutation	SNP	G	TCGA-RC-A7S9-01A-11D-A33Q-10	2622079	29592294	51602916	48	46792										
TAF15	8148	hgsc.bcm.edu	37	chr17	34149836	34149836	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	aactacagccaccacacacaAggtaagatttactgacctct	5	13	1	2			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr17:34149836A>C	ENST00000588240.1	+	6	598	c.483A>C	c.(481-483)caA>caC	p.Q161H	AC015849.13_ENST00000589356.1_RNA|TAF15_ENST00000311979.3_Splice_Site_p.Q158H|TAF15_ENST00000592237.1_Splice_Site_p.Q70H|AC015849.19_ENST00000588415.1_RNA	NM_003487.3|NM_139215.2	NP_003478.1|NP_631961.1	Q16514	TAF12_HUMAN	TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa	0					chromatin organization (GO:0006325)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of RNA biosynthetic process (GO:2001141)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)		TAF15/NR4A3(33)	lung(1)|ovary(1)|skin(2)|stomach(1)	5		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		ACCACACACAAGGTAAGATTT	0.363			T	"TEC, CHN1, ZNF384"	"extraskeletal myxoid chondrosarcomas, ALL"																																p.Q161H		Atlas-SNP	.		Dom	yes		17	17q11.1-q11.2	8148	"TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa"		"L, M"	.	TAF15	46	.	0			c.A483C						.						100	94	96					17																	34149836		2203	4300	6503	SO:0001630	splice_region_variant	8148	exon6			CACACAAGGTAAG	U51334	CCDS32623.1, CCDS59279.1	17q11.1-q11.2	2013-02-12	2002-08-29	2001-12-07		ENSG00000270647		"RNA binding motif (RRM) containing"	11547	protein-coding gene	gene with protein product		601574	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, N, 68kD (RNA-binding protein 56)"	TAF2N		8954779, 9795213	Standard	NM_003487		Approved	hTAFII68, RBP56, Npl3	uc002hkd.4	Q92804		ENST00000588240.1:c.484+1A>C	chr17.hg19:g.34149836A>C		264.0	0.0		144.0	55.0	NM_139215	D3DPM5|Q15775|Q5T077	Missense_Mutation	SNP	ENST00000588240.1	hg19	CCDS32623.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.067630	0.76301	.	.	ENSG00000172660	ENST00000311979	.	.	.	5.61	5.61	0.85477	.	.	.	.	.	T	0.77308	0.4111	M	0.76170	2.325	0.38470	D	0.947431	D;D	0.60575	0.98;0.988	D;D	0.74674	0.965;0.984	T	0.81046	-0.1110	8	0.59425	D	0.04	-4.2426	12.4866	0.55877	1.0:0.0:0.0:0.0	.	161;158	Q92804;Q92804-2	RBP56_HUMAN;.	H	161	.	ENSP00000309558:Q161H	Q	+	3	2	TAF15	31173949	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.420000	0.66441	2.252000	0.74401	0.533000	0.62120	CAA	.	.		0.363	TAF15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449134.1	NM_139215	Missense_Mutation	C	34149836	A	C	34149836	5	2	336	1	0	0	0	0	0	0	1	0	15533	86	3	5	505	5	TAF15	17	34149836	Splice_Site	SNP	A	TCGA-RC-A7S9-01A-11D-A33Q-10	4557542	34149836	47045374	49	46793										
POTEC	388468	hgsc.bcm.edu	37	chr18	14537872	14537872	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	aatttatcttcattgtggacAgcatagtgtagagtggtatt	10	4	2	1			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr18:14537872A>G	ENST00000358970.5	-	3	737	c.738T>C	c.(736-738)gcT>gcC	p.A246A	POTEC_ENST00000389891.4_5'UTR	NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	246										NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						CATTGTGGACAGCATAGTGTA	0.368																																					p.A246A		Atlas-SNP	.											.	POTEC	129	.	0			c.T738C						.						386	292	321					18																	14537872		692	1591	2283	SO:0001819	synonymous_variant	388468	exon3			GTGGACAGCATAG	BX649118	CCDS45835.1	18p11.21	2013-01-10	2008-11-26	2008-11-26	ENSG00000183206	ENSG00000183206		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	33894	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 6"		"ANKRD26-like family B, member 2"	A26B2			Standard	NM_001137671		Approved	POTE18, POTE-18, DKFZp686J0529, CT104.6	uc010dln.3	B2RU33	OTTHUMG00000162963	ENST00000358970.5:c.738T>C	chr18.hg19:g.14537872A>G		319.0	0.0		178.0	81.0	NM_001137671		Silent	SNP	ENST00000358970.5	hg19	CCDS45835.1																																																																																			.	.		0.368	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269		G	14537872	A	G	14537872	2	3	336	1	0	0	0	0	0	0	0	1	12271	175	7	2		2	POTEC	18	14537872	Silent	SNP	A	TCGA-RC-A7S9-01A-11D-A33Q-10		14537872	63539376	50	46794										
GATA6	2627	hgsc.bcm.edu	37	chr18	19756976	19756976	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	ctgcggctccatccagacgcCgctgtggcggcgggacggca	16	15	0	1			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr18:19756976C>T	ENST00000269216.3	+	3	1473	c.1196C>T	c.(1195-1197)cCg>cTg	p.P399L	GATA6_ENST00000581694.1_Missense_Mutation_p.P399L|RP11-627G18.2_ENST00000578504.1_RNA	NM_005257.4	NP_005248.2	Q92908	GATA6_HUMAN	GATA binding protein 6	399					blood coagulation (GO:0007596)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac vascular smooth muscle cell differentiation (GO:0060947)|cellular response to BMP stimulus (GO:0071773)|cellular response to gonadotropin stimulus (GO:0071371)|cellular response to hypoxia (GO:0071456)|Clara cell differentiation (GO:0060486)|endodermal cell fate determination (GO:0007493)|in utero embryonic development (GO:0001701)|intestinal epithelial cell differentiation (GO:0060575)|liver development (GO:0001889)|lung saccule development (GO:0060430)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta1 production (GO:0032911)|negative regulation of transforming growth factor beta2 production (GO:0032912)|organ formation (GO:0048645)|outflow tract septum morphogenesis (GO:0003148)|pancreatic A cell differentiation (GO:0003310)|phospholipid metabolic process (GO:0006644)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to growth factor (GO:0070848)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)|tube morphogenesis (GO:0035239)|type B pancreatic cell differentiation (GO:0003309)|Type II pneumocyte differentiation (GO:0060510)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	18	all_cancers(21;0.00271)|all_epithelial(16;7.31e-05)|Ovarian(2;0.116)|Lung NSC(20;0.123)|all_lung(20;0.246)		STAD - Stomach adenocarcinoma(5;0.106)			ATCCAGACGCCGCTGTGGCGG	0.701																																					p.P399L	Colon(8;48 282 46199 46856)|Melanoma(177;170 2725 12489 26999)	Atlas-SNP	.											.	GATA6	35	.	0			c.C1196T						.						6	7	6					18																	19756976		1990	3985	5975	SO:0001583	missense	2627	exon3			AGACGCCGCTGTG	U66075	CCDS11872.1	18q11-q12	2013-01-25	2001-11-28		ENSG00000141448	ENSG00000141448		"GATA zinc finger domain containing"	4174	protein-coding gene	gene with protein product		601656	"GATA-binding protein 6"			8975704	Standard	XM_005258248		Approved		uc002ktt.2	Q92908	OTTHUMG00000131767	ENST00000269216.3:c.1196C>T	chr18.hg19:g.19756976C>T	ENSP00000269216:p.Pro399Leu	36.0	0.0		35.0	14.0	NM_005257	B0YJ17|P78327	Missense_Mutation	SNP	ENST00000269216.3	hg19	CCDS11872.1	.	.	.	.	.	.	.	.	.	.	C	19.78	3.891845	0.72524	.	.	ENSG00000141448	ENST00000269216	D	0.99711	-6.49	4.99	4.11	0.48088	Zinc finger, NHR/GATA-type (1);Zinc finger, GATA-type (5);	0.128964	0.53938	N	0.000050	D	0.99495	0.9820	H	0.96333	3.805	0.80722	D	1	B	0.12630	0.006	B	0.13407	0.009	D	0.99612	1.0981	10	0.87932	D	0	-26.1673	15.5461	0.76101	0.0:0.8614:0.1386:0.0	.	399	Q92908	GATA6_HUMAN	L	399	ENSP00000269216:P399L	ENSP00000269216:P399L	P	+	2	0	GATA6	18010974	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.808000	0.69165	1.325000	0.45301	0.558000	0.71614	CCG	.	.		0.701	GATA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254696.1	NM_005257		T	19756976	C	T	19756976	3	4	336	1	0	0	0	0	1	0	0	0	6266	652	23	1	1202	1	GATA6	18	19756976	Missense_Mutation	SNP	C	TCGA-RC-A7S9-01A-11D-A33Q-10	5219104	19756976	58320272	51	46795										
CREB3L3	84699	hgsc.bcm.edu	37	chr19	4171379	4171379	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	ctctgccgctgtctccaccaGgtcctgttgctgtcctttgc	9	16	2	0	rs112561919		TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr19:4171379G>A	ENST00000078445.2	+	9	1122		c.e9-1		CREB3L3_ENST00000602147.1_Splice_Site|CREB3L3_ENST00000602257.1_Splice_Site|CREB3L3_ENST00000595923.1_Splice_Site|CREB3L3_ENST00000252587.3_Splice_Site	NM_001271995.1|NM_001271996.1|NM_032607.1	NP_001258924.1|NP_001258925.1|NP_115996.1	Q68CJ9	CR3L3_HUMAN	cAMP responsive element binding protein 3-like 3						positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|urinary_tract(3)	24				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0232)|STAD - Stomach adenocarcinoma(1328;0.18)		GTCTCCACCAGGTCCTGTTGC	0.607																																					.		Atlas-SNP	.											.	CREB3L3	53	.	0			c.973-1G>A						.						93	81	85					19																	4171379		2203	4300	6503	SO:0001630	splice_region_variant	84699	exon9			CCACCAGGTCCTG		CCDS12121.1, CCDS62498.1, CCDS62499.1, CCDS62500.1	19p13.3	2013-01-10				ENSG00000060566		"basic leucine zipper proteins"	18855	protein-coding gene	gene with protein product		611998				11353085	Standard	NM_032607		Approved	CREB-H	uc002lzl.4	Q68CJ9		ENST00000078445.2:c.976-1G>A	chr19.hg19:g.4171379G>A		96.0	0.0		115.0	27.0	NM_001271995	B2R7S6|B7ZL69|M0QYW7|Q6ZMC5|Q96TB9	Splice_Site	SNP	ENST00000078445.2	hg19	CCDS12121.1	.	.	.	.	.	.	.	.	.	.	G	14.32	2.499000	0.44455	.	.	ENSG00000060566	ENST00000078445;ENST00000381943;ENST00000252587	.	.	.	4.58	4.58	0.56647	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8629	0.70394	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CREB3L3	4122379	1.000000	0.71417	0.999000	0.59377	0.300000	0.27592	8.606000	0.90888	2.093000	0.63338	0.561000	0.74099	.	.	C|1.000		0.607	CREB3L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457922.1	NM_032607	Intron	A	4171379	G	A	4171379	5	1	336	1	0	0	0	0	0	0	1	0	3860	1014	35	3	1009	3	CREB3L3	19	4171379	Splice_Site	SNP	G	TCGA-RC-A7S9-01A-11D-A33Q-10		4171379	54957604	52	46796										
ANO8	57719	hgsc.bcm.edu	37	chr19	17442017	17442017	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	ttcacaccaaagtaatcacaGatgtcatctgccaggggaca	8	11	4	1			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr19:17442017G>T	ENST00000159087.4	-	7	869	c.711C>A	c.(709-711)atC>atA	p.I237I		NM_020959.2	NP_066010.1	Q9HCE9	ANO8_HUMAN	anoctamin 8	237					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			autonomic_ganglia(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(3)	27						AGTAATCACAGATGTCATCTG	0.572																																					p.I237I		Atlas-SNP	.											.	ANO8	67	.	0			c.C711A						.						78	83	81					19																	17442017		2203	4300	6503	SO:0001819	synonymous_variant	57719	exon7			ATCACAGATGTCA	AB046843	CCDS32949.1	19p13.12	2014-04-09	2008-08-28	2008-08-28		ENSG00000074855		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	29329	protein-coding gene	gene with protein product		610216	"KIAA1623", "transmembrane protein 16H"	KIAA1623, TMEM16H		10997877, 24692353	Standard	NM_020959		Approved		uc002ngf.2	Q9HCE9		ENST00000159087.4:c.711C>A	chr19.hg19:g.17442017G>T		59.0	0.0		43.0	22.0	NM_020959	A6NIJ0	Silent	SNP	ENST00000159087.4	hg19	CCDS32949.1																																																																																			.	.		0.572	ANO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462943.1	XM_050644		T	17442017	G	T	17442017	2	4	336	1	0	0	0	0	0	0	0	1	703	932	33	3		3	ANO8	19	17442017	Silent	SNP	G	TCGA-RC-A7S9-01A-11D-A33Q-10	13270638	17442017	41686966	53	46797										
ZNF257	113835	hgsc.bcm.edu	37	chr19	22271464	22271464	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	tcagctcttactacccttacTcaacataagagaattcatac	3	12	4	1			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr19:22271464T>C	ENST00000594947.1	+	4	1056	c.912T>C	c.(910-912)acT>acC	p.T304T		NM_033468.2	NP_258429.2	Q9Y2Q1	ZN257_HUMAN	zinc finger protein 257	304					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|lung(4)	6		all_lung(12;0.0961)|Lung NSC(12;0.103)				CTACCCTTACTCAACATAAGA	0.393																																					p.T304T		Atlas-SNP	.											.	ZNF257	156	.	0			c.T912C						.						47	51	50					19																	22271464		2122	4249	6371	SO:0001819	synonymous_variant	113835	exon4			CCTTACTCAACAT	AF070651	CCDS46030.1	19p12	2014-02-14			ENSG00000197134	ENSG00000197134		"Zinc fingers, C2H2-type", "-"	13498	protein-coding gene	gene with protein product		606957				10585455	Standard	NM_033468		Approved	BMZF-4	uc010ecx.3	Q9Y2Q1	OTTHUMG00000182927	ENST00000594947.1:c.912T>C	chr19.hg19:g.22271464T>C		114.0	0.0		95.0	52.0	NM_033468	B3KPS4|E9PG34|Q8NE34	Silent	SNP	ENST00000594947.1	hg19	CCDS46030.1																																																																																			.	.		0.393	ZNF257-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464382.1			C	22271464	T	C	22271464	2	2	336	1	0	0	0	0	0	0	0	1	17815	1538	54	2		2	ZNF257	19	22271464	Silent	SNP	T	TCGA-RC-A7S9-01A-11D-A33Q-10	4829447	22271464	36857519	54	46798										
ZNF350	59348	hgsc.bcm.edu	37	chr19	52468329	52468329	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	gaaggcacttgtgtagtcgcCccgttagcagagtttttctc	11	10	1	1			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr19:52468329C>T	ENST00000243644.4	-	5	1604	c.1377G>A	c.(1375-1377)ggG>ggA	p.G459G	HCCAT3_ENST00000595010.1_RNA|ZNF350_ENST00000600703.1_5'Flank|HCCAT3_ENST00000600253.1_RNA	NM_021632.3	NP_067645.3	Q9GZX5	ZN350_HUMAN	zinc finger protein 350	459					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(3)|kidney(3)|large_intestine(7)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		all_neural(266;0.0505)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0179)		GTGTAGTCGCCCCGTTAGCAG	0.532																																					p.G459G		Atlas-SNP	.											.	ZNF350	48	.	0			c.G1377A						.						90	77	82					19																	52468329		2203	4300	6503	SO:0001819	synonymous_variant	59348	exon5			AGTCGCCCCGTTA	AF295096	CCDS12845.1	19q13.41	2013-05-23			ENSG00000256683	ENSG00000256683		"Zinc fingers, C2H2-type", "-"	16656	protein-coding gene	gene with protein product		605422				11090615, 11161714	Standard	NM_021632		Approved	ZBRK1, ZFQR	uc002pyd.3	Q9GZX5	OTTHUMG00000182538	ENST00000243644.4:c.1377G>A	chr19.hg19:g.52468329C>T		100.0	0.0		76.0	10.0	NM_021632	Q96G73|Q9HAQ4	Silent	SNP	ENST00000243644.4	hg19	CCDS12845.1																																																																																			.	.		0.532	ZNF350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462278.1	NM_021632		T	52468329	C	T	52468329	2	4	336	1	0	0	0	0	0	0	0	1	17878	610	22	3		3	ZNF350	19	52468329	Silent	SNP	C	TCGA-RC-A7S9-01A-11D-A33Q-10	30196865	52468329	6660654	55	46799										
ITSN1	6453	hgsc.bcm.edu	37	chr21	35258604	35258604	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	cctccaggaaagagcaacccGtactgtgaggtgaccatggg	13	11	0	3			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr21:35258604G>A	ENST00000381318.3	+	39	5145	c.4857G>A	c.(4855-4857)ccG>ccA	p.P1619P	ITSN1_ENST00000399367.3_Silent_p.P1614P|ITSN1_ENST00000437442.2_Silent_p.P1558P|AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000381285.4_Silent_p.P1619P|ITSN1_ENST00000399326.3_3'UTR	NM_003024.2	NP_003015.2	Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)	1619	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				apoptotic signaling pathway (GO:0097190)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|kinase activator activity (GO:0019209)|proline-rich region binding (GO:0070064)|protein complex scaffold (GO:0032947)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(26)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	67						AGAGCAACCCGTACTGTGAGG	0.473																																					p.P1619P		Atlas-SNP	.											.	ITSN1	166	.	0			c.G4857A						.						98	85	89					21																	35258604		2203	4300	6503	SO:0001819	synonymous_variant	6453	exon39			CAACCCGTACTGT	AF064244	CCDS33545.1, CCDS33546.1	21q22.1-q22.2	2013-01-10			ENSG00000205726	ENSG00000205726		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "EF-hand domain containing"	6183	protein-coding gene	gene with protein product	"SH3 domain protein-1A", "human intersectin-SH3 domain-containing protein SH3P17", "Src homology 3 domain-containing protein", "intersectin 1 short form variant, 11", "intersectin 1 short form variant 3", "intersectin short variant 12"	602442		SH3D1A, ITSN		9799604, 9813051	Standard	NM_003024		Approved	SH3P17, MGC134948, MGC134949	uc002yta.1	Q15811	OTTHUMG00000065284	ENST00000381318.3:c.4857G>A	chr21.hg19:g.35258604G>A		166.0	0.0		113.0	51.0	NM_003024	A7Y322|A8CTX8|A8CTY3|A8CTY7|A8D7D0|A8DCP3|B4DTM2|E7ERJ1|E9PE44|E9PG01|E9PHV2|O95216|Q0PW94|Q0PW95|Q0PW97|Q14BD3|Q1ED40|Q20BK3|Q9UET5|Q9UK60|Q9UNK1|Q9UNK2|Q9UQ92	Silent	SNP	ENST00000381318.3	hg19	CCDS33545.1	.	.	.	.	.	.	.	.	.	.	G	6.083	0.383575	0.11524	.	.	ENSG00000205726	ENST00000381284	.	.	.	5.53	-11.1	0.00147	.	.	.	.	.	T	0.32255	0.0823	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42632	-0.9440	4	.	.	.	.	1.798	0.03065	0.2762:0.2896:0.2652:0.1691	.	.	.	.	I	299	.	.	V	+	1	0	ITSN1	34180474	0.000000	0.05858	0.283000	0.24790	0.864000	0.49448	-3.965000	0.00324	-3.109000	0.00242	-1.632000	0.00781	GTA	.	.		0.473	ITSN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000140070.4	NM_003024		A	35258604	G	A	35258604	2	1	336	1	0	0	0	0	0	0	0	1	7935	1132	40	1		1	ITSN1	21	35258604	Silent	SNP	G	TCGA-RC-A7S9-01A-11D-A33Q-10		35258604	12871291	56	46800										
PWP2	5822	hgsc.bcm.edu	37	chr21	45534063	45534063	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	cctctggcgtcctgcaggggGcgatgcgctgctggtcagcc	16	14	2	0			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chr21:45534063G>A	ENST00000291576.7	+	4	357	c.230G>A	c.(229-231)gGc>gAc	p.G77D		NM_005049.2	NP_005040.2	Q15269	PWP2_HUMAN	PWP2 periodic tryptophan protein homolog (yeast)	77					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(6)|large_intestine(6)|lung(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	21				STAD - Stomach adenocarcinoma(101;0.172)|Colorectal(79;0.2)		CCTGCAGGGGGCGATGCGCTG	0.612											OREG0026247	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G77D		Atlas-SNP	.											.	PWP2	64	.	0			c.G230A						.						97	87	90					21																	45534063		2203	4300	6503	SO:0001583	missense	5822	exon4			CAGGGGGCGATGC		CCDS33579.1	21q22.3	2013-01-10	2001-11-28	2006-11-24	ENSG00000241945	ENSG00000241945		"WD repeat domain containing"	9711	protein-coding gene	gene with protein product		601475	"PWP2 (periodic tryptophan protein, yeast) homolog"	PWP2H		8893822	Standard	NM_005049		Approved	EHOC-17, UTP1	uc002zeb.3	Q15269	OTTHUMG00000086893	ENST00000291576.7:c.230G>A	chr21.hg19:g.45534063G>A	ENSP00000291576:p.Gly77Asp	46.0	0.0	932	22.0	14.0	NM_005049	B2RAG8|Q96A77	Missense_Mutation	SNP	ENST00000291576.7	hg19	CCDS33579.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.939885	0.92526	.	.	ENSG00000241945	ENST00000291576	T	0.56611	0.45	4.64	4.64	0.57946	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);	0.000000	0.85682	D	0.000000	T	0.78616	0.4311	M	0.93016	3.37	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84472	0.0600	10	0.72032	D	0.01	-9.8646	15.6473	0.77065	0.0:0.0:1.0:0.0	.	77	Q15269	PWP2_HUMAN	D	77	ENSP00000291576:G77D	ENSP00000291576:G77D	G	+	2	0	PWP2	44358491	1.000000	0.71417	0.920000	0.36463	0.941000	0.58515	8.930000	0.92872	2.298000	0.77334	0.313000	0.20887	GGC	.	.		0.612	PWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195736.3	NM_005049		A	45534063	G	A	45534063	3	1	336	1	0	0	0	0	1	0	0	0	12859	1203	42	3	244	3	PWP2	21	45534063	Missense_Mutation	SNP	G	TCGA-RC-A7S9-01A-11D-A33Q-10	10275459	45534063	2595832	57	46801										
VSIG4	11326	hgsc.bcm.edu	37	chrX	65244890	65244890	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0689655172413793	4	1	1.39661466976435	1.33842239185751	1.4171531207903	0.559440559440559	1	0	gttgggatgtcttccgacagAgcatgatataggccatggta	13	7	1	2			TCGA-RC-A7S9-01A-11D-A33Q-10	TCGA-RC-A7S9-10A-02D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	51aa8270-daf2-45af-b4a7-b80b053bada3	0a31c7e6-f1af-4ff5-8011-67d8e91a85d6	g.chrX:65244890A>G	ENST00000374737.4	-	6	1025	c.917T>C	c.(916-918)cTc>cCc	p.L306P	VSIG4_ENST00000412866.2_Missense_Mutation_p.L212P|VSIG4_ENST00000455586.2_Missense_Mutation_p.L306P	NM_001257403.1|NM_007268.2	NP_001244332.1|NP_009199.1	Q9Y279	VSIG4_HUMAN	V-set and immunoglobulin domain containing 4	306					complement activation, alternative pathway (GO:0006957)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of T cell proliferation (GO:0042130)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CTTCCGACAGAGCATGATATA	0.428																																					p.L306P		Atlas-SNP	.											.	VSIG4	54	.	0			c.T917C						.						117	83	94					X																	65244890		2203	4300	6503	SO:0001583	missense	11326	exon6			CGACAGAGCATGA	AJ132502	CCDS14383.1, CCDS48132.1, CCDS55435.1	Xq12-q13.3	2013-01-29			ENSG00000155659	ENSG00000155659		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17032	protein-coding gene	gene with protein product		300353				10899594, 11004523, 17016555, 17016562	Standard	NM_007268		Approved	Z39IG	uc004dwh.2	Q9Y279	OTTHUMG00000021727	ENST00000374737.4:c.917T>C	chrX.hg19:g.65244890A>G	ENSP00000363869:p.Leu306Pro	456.0	0.0		269.0	58.0	NM_001257403	Q6UXI4	Missense_Mutation	SNP	ENST00000374737.4	hg19	CCDS14383.1	.	.	.	.	.	.	.	.	.	.	A	10.72	1.430334	0.25726	.	.	ENSG00000155659	ENST00000374737;ENST00000455586;ENST00000412866	T;T;T	0.38401	1.32;1.14;1.84	4.29	4.29	0.51040	.	0.911156	0.09226	N	0.831161	T	0.49695	0.1572	L	0.54323	1.7	0.21915	N	0.999479	P;D;D;D;D	0.58620	0.948;0.974;0.971;0.983;0.976	P;P;P;P;P	0.58331	0.548;0.748;0.641;0.837;0.656	T	0.31806	-0.9930	10	0.62326	D	0.03	-2.0675	8.7612	0.34676	1.0:0.0:0.0:0.0	.	212;306;296;212;306	C9J1L3;Q9Y279-2;C9JH67;Q9Y279-3;Q9Y279	.;.;.;.;VSIG4_HUMAN	P	306;306;212	ENSP00000363869:L306P;ENSP00000411581:L306P;ENSP00000394143:L212P	ENSP00000363869:L306P	L	-	2	0	VSIG4	65161615	0.011000	0.17503	0.053000	0.19242	0.078000	0.17371	1.941000	0.40233	1.583000	0.49898	0.486000	0.48141	CTC	.	.		0.428	VSIG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056986.1	NM_007268		G	65244890	A	G	65244890	3	3	336	1	0	0	0	0	1	0	0	0	17240	304	11	2	298	2	VSIG4	23	65244890	Missense_Mutation	SNP	A	TCGA-RC-A7S9-01A-11D-A33Q-10		65244890	90025670	58	46802										
AMY2A	279	hgsc.bcm.edu	37	chr1	104160634	104160634	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	tttcagaccttggtgggaaaGataccaaccagttagctata	9	8	1	2	rs371720173		TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr1:104160634G>T	ENST00000414303.2	+	2	291	c.227G>T	c.(226-228)aGa>aTa	p.R76I		NM_000699.2	NP_000690.1	P04746	AMYP_HUMAN	amylase, alpha 2A (pancreatic)	76					carbohydrate catabolic process (GO:0016052)|carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	alpha-amylase activity (GO:0004556)|calcium ion binding (GO:0005509)|chloride ion binding (GO:0031404)			endometrium(3)|kidney(1)|large_intestine(5)|liver(3)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0654)|all cancers(265;0.0808)|Epithelial(280;0.0921)|Lung(183;0.111)	Acarbose(DB00284)|Icodextrin(DB00702)|Miglitol(DB00491)	TGGTGGGAAAGATACCAACCA	0.353																																					p.R76I		Atlas-SNP	.											.	AMY2A	36	.	0			c.G227T						.						170	155	160					1																	104160634		2201	4279	6480	SO:0001583	missense	279	exon2			GGGAAAGATACCA	BC007060	CCDS783.1	1p21.1	2012-10-02	2007-05-03		ENSG00000243480	ENSG00000243480	3.2.1.1		477	protein-coding gene	gene with protein product		104650	"amylase, alpha 2A; pancreatic"	AMY2		3260028	Standard	NM_000699		Approved		uc001dut.3	P04746	OTTHUMG00000011023	ENST00000414303.2:c.227G>T	chr1.hg19:g.104160634G>T	ENSP00000397582:p.Arg76Ile	414.0	0.0		307.0	107.0	NM_000699	B9EJG1|Q9UBH3	Missense_Mutation	SNP	ENST00000414303.2	hg19	CCDS783.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	22.0|22.0	4.230811|4.230811	0.79688|0.79688	.|.	.|.	ENSG00000243480|ENSG00000243480	ENST00000423678|ENST00000414303;ENST00000393932	.|D	.|0.98437	.|-4.93	3.47|3.47	3.47|3.47	0.39725|0.39725	.|Glycoside hydrolase, subgroup, catalytic domain (1);Glycosyl hydrolase, family 13, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycosyl hydrolase, family 13, subfamily, catalytic domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.99080|0.99080	0.9684|0.9684	M|M	0.92738|0.92738	3.34|3.34	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|0.999;1.0	D|D	0.99285|0.99285	1.0897|1.0897	5|10	.|0.87932	.|D	.|0	.|.	15.0729|15.0729	0.72053|0.72053	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|76;76	.|B9EJG1;P04746	.|.;AMYP_HUMAN	N|I	74|76	.|ENSP00000397582:R76I	.|ENSP00000377509:R76I	K|R	+|+	3|2	2|0	AMY2A|AMY2A	103962157|103962157	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.951000|0.951000	0.60555|0.60555	9.276000|9.276000	0.95745|0.95745	1.927000|1.927000	0.55829|0.55829	0.455000|0.455000	0.32223|0.32223	AAG|AGA	.	.		0.353	AMY2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030315.1	NM_000699		T	104160634	G	T	104160634	3	4	337	1	0	0	0	0	1	0	0	0	594	942	33	3	233	3	AMY2A	1	104160634	Missense_Mutation	SNP	G	TCGA-RC-A7SB-01A-21D-A34Z-10		104160634	145089987	1	46803										
NEB	4703	hgsc.bcm.edu	37	chr2	152499357	152499357	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	atgtggacagtggttttatcTttatcccaagcttctgtata	8	7	2	0			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr2:152499357T>C	ENST00000172853.10	-	59	8334	c.8187A>G	c.(8185-8187)aaA>aaG	p.K2729K	NEB_ENST00000604864.1_Silent_p.K2729K|NEB_ENST00000397345.3_Silent_p.K2729K|NEB_ENST00000409198.1_Silent_p.K2729K|NEB_ENST00000603639.1_Silent_p.K2729K|NEB_ENST00000427231.2_Silent_p.K2729K			P20929	NEBU_HUMAN	nebulin	2729					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TGGTTTTATCTTTATCCCAAG	0.348																																					p.K2729K		Atlas-SNP	.											.	NEB	1697	.	0			c.A8187G						.						48	47	47					2																	152499357		1829	4080	5909	SO:0001819	synonymous_variant	4703	exon59			TTTATCTTTATCC	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.8187A>G	chr2.hg19:g.152499357T>C		88.0	0.0		73.0	22.0	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	hg19																																																																																				.	.		0.348	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		C	152499357	T	C	152499357	2	2	337	1	0	0	0	0	0	0	0	1	10311	1606	56	2		2	NEB	2	152499357	Silent	SNP	T	TCGA-RC-A7SB-01A-21D-A34Z-10		152499357	90700016	2	46804										
TBR1	10716	hgsc.bcm.edu	37	chr2	162273413	162273413	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	aacagcctcctgtccaactcCtcgccgcagggataccccac	7	19	0	0			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr2:162273413C>T	ENST00000389554.3	+	1	809	c.492C>T	c.(490-492)tcC>tcT	p.S164S	TBR1_ENST00000410035.1_5'Flank	NM_006593.2	NP_006584.1	Q16650	TBR1_HUMAN	T-box, brain, 1	164					axon guidance (GO:0007411)|brain development (GO:0007420)|hindbrain development (GO:0030902)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of neuron projection development (GO:0010975)|specification of organ identity (GO:0010092)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|prostate(1)|skin(3)	30						TGTCCAACTCCTCGCCGCAGG	0.662																																					p.S164S		Atlas-SNP	.											.	TBR1	59	.	0			c.C492T						.						71	74	73					2																	162273413		2203	4300	6503	SO:0001819	synonymous_variant	10716	exon1			CAACTCCTCGCCG	U49250	CCDS33310.1	2q24.2	2011-06-13			ENSG00000136535	ENSG00000136535		"T-boxes"	11590	protein-coding gene	gene with protein product		604616				7619531	Standard	NM_006593		Approved		uc002ubw.1	Q16650	OTTHUMG00000153888	ENST00000389554.3:c.492C>T	chr2.hg19:g.162273413C>T		80.0	0.0		50.0	19.0	NM_006593	B0AZS4|B2R6G5|Q14DC5|Q53TH0|Q56A81	Silent	SNP	ENST00000389554.3	hg19	CCDS33310.1																																																																																			.	.		0.662	TBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332845.1	NM_006593		T	162273413	C	T	162273413	2	4	337	1	0	0	0	0	0	0	0	1	15662	668	24	3		3	TBR1	2	162273413	Silent	SNP	C	TCGA-RC-A7SB-01A-21D-A34Z-10	9774056	162273413	80925960	3	46805										
HIBCH	26275	hgsc.bcm.edu	37	chr2	191110920	191110920	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	ttcctcaagtataaaagactTgtctcgatcaatcttagact	5	9	4	2			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr2:191110920T>A	ENST00000359678.5	-	10	1063	c.769A>T	c.(769-771)Aag>Tag	p.K257*	HIBCH_ENST00000392332.3_Nonsense_Mutation_p.K257*|HIBCH_ENST00000410045.1_Nonsense_Mutation_p.K34*	NM_014362.3|NM_198047.2	NP_055177.2|NP_932164.1	Q6NVY1	HIBCH_HUMAN	3-hydroxyisobutyryl-CoA hydrolase	257					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|valine catabolic process (GO:0006574)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	3-hydroxyisobutyryl-CoA hydrolase activity (GO:0003860)			NS(1)|breast(2)|endometrium(1)|large_intestine(1)|lung(5)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	13			OV - Ovarian serous cystadenocarcinoma(117;0.000586)|Epithelial(96;0.0286)|all cancers(119;0.0814)			ATAAAAGACTTGTCTCGATCA	0.249																																					p.K257X		Atlas-SNP	.											.	HIBCH	28	.	0			c.A769T						.						80	78	79					2																	191110920		2198	4294	6492	SO:0001587	stop_gained	26275	exon10			AAGACTTGTCTCG	U66669	CCDS2304.1, CCDS46475.1	2q32.3	2010-04-29	2010-04-29		ENSG00000198130	ENSG00000198130	3.1.2.4		4908	protein-coding gene	gene with protein product		610690	"3-hydroxyisobutyryl-Coenzyme A hydrolase"			8824301	Standard	NM_014362		Approved		uc002uru.3	Q6NVY1	OTTHUMG00000132673	ENST00000359678.5:c.769A>T	chr2.hg19:g.191110920T>A	ENSP00000352706:p.Lys257*	97.0	0.0		95.0	40.0	NM_014362	D3DPI4|Q53GA8|Q53GF2|Q53RF7|Q53TC6|Q92931|Q9BS94	Nonsense_Mutation	SNP	ENST00000359678.5	hg19	CCDS2304.1	.	.	.	.	.	.	.	.	.	.	T	39	7.798293	0.98495	.	.	ENSG00000198130	ENST00000392332;ENST00000359678;ENST00000410045;ENST00000416732;ENST00000409820	.	.	.	4.73	4.73	0.59995	.	0.418322	0.27715	N	0.018156	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-21.0883	12.3549	0.55169	0.0:0.0:0.0:1.0	.	.	.	.	X	257;257;34;8;37	.	ENSP00000352706:K257X	K	-	1	0	HIBCH	190819165	1.000000	0.71417	0.987000	0.45799	0.800000	0.45204	5.426000	0.66476	2.108000	0.64289	0.533000	0.62120	AAG	.	.		0.249	HIBCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255933.1			A	191110920	T	A	191110920	4	1	337	1	0	0	0	0	0	1	0	0	7109	1821	63	4	411	4	HIBCH	2	191110920	Nonsense_Mutation	SNP	T	TCGA-RC-A7SB-01A-21D-A34Z-10	28837507	191110920	52088453	4	46806										
SETD5	55209	hgsc.bcm.edu	37	chr3	9517712	9517712	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	caccgtgggagtgggggtgtGcaccagtaccgactccagcc	15	13	0	0			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr3:9517712G>A	ENST00000406341.1	+	22	4456	c.4266G>A	c.(4264-4266)gtG>gtA	p.V1422V	SETD5_ENST00000302463.6_Silent_p.V1324V|SETD5_ENST00000407969.1_Silent_p.V1441V|SETD5_ENST00000402198.1_Silent_p.V1422V|SETD5_ENST00000402466.1_Silent_p.V1324V			Q9C0A6	SETD5_HUMAN	SET domain containing 5	1422										NS(2)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(3)|prostate(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)		GTGGGGGTGTGCACCAGTACC	0.577																																					p.V1422V		Atlas-SNP	.											.	SETD5	210	.	0			c.G4266A						.						27	29	28					3																	9517712		1964	4153	6117	SO:0001819	synonymous_variant	55209	exon23			GGGTGTGCACCAG	BC020956	CCDS46741.1, CCDS74892.1	3p25.3	2011-12-13			ENSG00000168137	ENSG00000168137			25566	protein-coding gene	gene with protein product		615743				11214970	Standard	XM_005265299		Approved	FLJ10707	uc003brt.3	Q9C0A6	OTTHUMG00000150491	ENST00000406341.1:c.4266G>A	chr3.hg19:g.9517712G>A		49.0	0.0		46.0	19.0	NM_001080517	Q6AI17|Q8WUB6|Q9H3X4|Q9H6V7|Q9H7S3|Q9NVI9	Silent	SNP	ENST00000406341.1	hg19	CCDS46741.1																																																																																			.	.		0.577	SETD5-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318425.1	XM_371614		A	9517712	G	A	9517712	2	1	337	1	0	0	0	0	0	0	0	1	14149	1306	46	3		3	SETD5	3	9517712	Silent	SNP	G	TCGA-RC-A7SB-01A-21D-A34Z-10		9517712	188504718	5	46807										
GPD1L	23171	hgsc.bcm.edu	37	chr3	32181733	32181733	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	cttgtagggcatagacgaggGccccgaggggctgaagctca	16	10	1	2			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr3:32181733G>A	ENST00000282541.5	+	4	581	c.380G>A	c.(379-381)gGc>gAc	p.G127D		NM_015141.3	NP_055956.1	Q8N335	GPD1L_HUMAN	glycerol-3-phosphate dehydrogenase 1-like	127					carbohydrate metabolic process (GO:0005975)|cellular lipid metabolic process (GO:0044255)|glycerol-3-phosphate catabolic process (GO:0046168)|glycerophospholipid biosynthetic process (GO:0046474)|NAD metabolic process (GO:0019674)|NADH metabolic process (GO:0006734)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein kinase C signaling (GO:0090038)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of protein localization to cell surface (GO:2000010)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate (GO:0002027)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|ventricular cardiac muscle cell action potential (GO:0086005)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycerol-3-phosphate dehydrogenase complex (GO:0009331)|plasma membrane (GO:0005886)	glycerol-3-phosphate dehydrogenase [NAD+] activity (GO:0004367)|ion channel binding (GO:0044325)|NAD binding (GO:0051287)|sodium channel regulator activity (GO:0017080)			large_intestine(4)|lung(7)|ovary(1)	12						ATAGACGAGGGCCCCGAGGGG	0.507																																					p.G127D		Atlas-SNP	.											.	GPD1L	25	.	0			c.G380A						.						175	185	182					3																	32181733		2203	4300	6503	SO:0001583	missense	23171	exon4			ACGAGGGCCCCGA	D42047	CCDS33729.1	3p22.3	2014-09-17			ENSG00000152642	ENSG00000152642			28956	protein-coding gene	gene with protein product		611778				7788527	Standard	NM_015141		Approved	KIAA0089	uc003cew.3	Q8N335	OTTHUMG00000155846	ENST00000282541.5:c.380G>A	chr3.hg19:g.32181733G>A	ENSP00000282541:p.Gly127Asp	76.0	0.0		57.0	16.0	NM_015141	A8K9U3|Q14702|Q9BRM5	Missense_Mutation	SNP	ENST00000282541.5	hg19	CCDS33729.1	.	.	.	.	.	.	.	.	.	.	G	18.52	3.641917	0.67244	.	.	ENSG00000152642	ENST00000429432;ENST00000282541;ENST00000425459;ENST00000431009	T;T;T;T	0.56611	0.45;0.45;0.65;0.45	5.46	5.46	0.80206	Glycerol-3-phosphate dehydrogenase, NAD-dependent, N-terminal (1);NAD(P)-binding domain (1);	0.094278	0.64402	D	0.000001	T	0.53254	0.1785	L	0.60067	1.865	0.80722	D	1	P	0.44309	0.832	B	0.40940	0.344	T	0.51803	-0.8659	10	0.30854	T	0.27	-17.0625	19.6998	0.96048	0.0:0.0:1.0:0.0	.	127	Q8N335	GPD1L_HUMAN	D	88;127;80;88	ENSP00000393861:G88D;ENSP00000282541:G127D;ENSP00000408770:G80D;ENSP00000416518:G88D	ENSP00000282541:G127D	G	+	2	0	GPD1L	32156737	1.000000	0.71417	0.997000	0.53966	0.977000	0.68977	9.736000	0.98828	2.728000	0.93425	0.655000	0.94253	GGC	.	.		0.507	GPD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341975.2	NM_015141		A	32181733	G	A	32181733	3	1	337	1	0	0	0	0	1	0	0	0	6613	1203	42	3	394	3	GPD1L	3	32181733	Missense_Mutation	SNP	G	TCGA-RC-A7SB-01A-21D-A34Z-10	22664021	32181733	165840697	6	46808										
ADAMTS9	56999	hgsc.bcm.edu	37	chr3	64666990	64666990	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	cttcttgttcatccatagacTgtagtggttcaataaaataa	6	7	3	1			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr3:64666990T>A	ENST00000498707.1	-	3	908	c.566A>T	c.(565-567)cAg>cTg	p.Q189L	ADAMTS9_ENST00000459780.1_Missense_Mutation_p.Q189L|ADAMTS9_ENST00000295903.4_Missense_Mutation_p.Q189L	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	189					glycoprotein catabolic process (GO:0006516)|multicellular organismal development (GO:0007275)|positive regulation of melanocyte differentiation (GO:0045636)|protein transport (GO:0015031)|proteolysis (GO:0006508)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(17)|liver(4)|lung(43)|ovary(3)|prostate(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	100		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		ATCCATAGACTGTAGTGGTTC	0.468																																					p.Q189L		Atlas-SNP	.											.	ADAMTS9	206	.	0			c.A566T						.						181	168	172					3																	64666990		2203	4300	6503	SO:0001583	missense	56999	exon3			ATAGACTGTAGTG	AF261918	CCDS2903.1	3p14.1	2008-05-15	2005-08-19		ENSG00000163638	ENSG00000163638		"ADAM metallopeptidases with thrombospondin type 1 motif"	13202	protein-coding gene	gene with protein product		605421	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 9"			10936055	Standard	NM_182920		Approved	KIAA1312	uc003dmg.3	Q9P2N4	OTTHUMG00000158722	ENST00000498707.1:c.566A>T	chr3.hg19:g.64666990T>A	ENSP00000418735:p.Gln189Leu	176.0	0.0		156.0	74.0	NM_182920	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	Missense_Mutation	SNP	ENST00000498707.1	hg19	CCDS2903.1	.	.	.	.	.	.	.	.	.	.	T	3.539	-0.094104	0.07053	.	.	ENSG00000163638	ENST00000295903;ENST00000498707;ENST00000459780	T;T;T	0.61392	0.3;0.31;0.11	6.04	2.18	0.27775	Peptidase M12B, propeptide (1);	0.382752	0.24769	N	0.035749	T	0.27933	0.0688	N	0.01800	-0.715	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.17198	-1.0377	10	0.23891	T	0.37	.	11.2942	0.49269	0.6405:0.0:0.0:0.3595	.	189;189;189;189	B7ZVX9;Q9P2N4-2;Q9P2N4-1;Q9P2N4	.;.;.;ATS9_HUMAN	L	189	ENSP00000295903:Q189L;ENSP00000418735:Q189L;ENSP00000419217:Q189L	ENSP00000295903:Q189L	Q	-	2	0	ADAMTS9	64642030	0.911000	0.30947	0.007000	0.13788	0.335000	0.28730	2.693000	0.47027	0.122000	0.18314	-0.527000	0.04329	CAG	.	.		0.468	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351891.1			A	64666990	T	A	64666990	3	1	337	1	0	0	0	0	1	0	0	0	273	1580	55	4	5389	4	ADAMTS9	3	64666990	Missense_Mutation	SNP	T	TCGA-RC-A7SB-01A-21D-A34Z-10	32485257	64666990	133355440	7	46809										
BBX	56987	hgsc.bcm.edu	37	chr3	107491784	107491817	+	Frame_Shift_Del	DEL	TTTCCTGATTTTTCTTATTCTGCCAGTAGCAAGA	TTTCCTGATTTTTCTTATTCTGCCAGTAGCAAGA	-													0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	aagatcacaaatgtagtcatTttcctgatttttcttattct					rs113054196|rs566303124|rs557240456		TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	TTTCCTGATTTTTCTTATTCTGCCAGTAGCAAGA	TTTCCTGATTTTTCTTATTCTGCCAGTAGCAAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr3:107491784_107491817delTTTCCTGATTTTTCTTATTCTGCCAGTAGCAAGA	ENST00000325805.8	+	11	1503_1536	c.1216_1249delTTTCCTGATTTTTCTTATTCTGCCAGTAGCAAGA	c.(1216-1251)tttcctgatttttcttattctgccagtagcaagatafs	p.FPDFSYSASSKI406fs	BBX_ENST00000406780.1_Frame_Shift_Del_p.FPDFSYSASSKI406fs|BBX_ENST00000416476.2_Intron|BBX_ENST00000402543.1_Frame_Shift_Del_p.FPDFSYSASSKI406fs|BBX_ENST00000415149.2_Frame_Shift_Del_p.FPDFSYSASSKI406fs			Q8WY36	BBX_HUMAN	bobby sox homolog (Drosophila)	406					bone development (GO:0060348)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(18)|ovary(4)|pancreas(1)|skin(2)	49			OV - Ovarian serous cystadenocarcinoma(3;0.112)			ATGTAGTCATTTTCCTGATTTTTCTTATTCTGCCAGTAGCAAGATAATAATTAG	0.355																																					p.405_416del		Pindel	.											.	BBX	156	.	0			c.1215_1248del						.																																			SO:0001589	frameshift_variant	56987	exon11			.	AF168718	CCDS2950.1, CCDS46881.1, CCDS63712.1	3q13.1	2008-07-18			ENSG00000114439	ENSG00000114439			14422	protein-coding gene	gene with protein product	"x 001 protein"					11680820	Standard	NM_001142568		Approved	MDS001, HSPC339, HBP2	uc010hpr.4	Q8WY36	OTTHUMG00000150360	ENST00000325805.8:c.1216_1249delTTTCCTGATTTTTCTTATTCTGCCAGTAGCAAGA	chr3.hg19:g.107491784_107491817delTTTCCTGATTTTTCTTATTCTGCCAGTAGCAAGA	ENSP00000319974:p.Phe406fs	129.0	0.0		69.0	19.0	NM_001142568	A2RRM7|Q2TAJ1|Q7L3J8|Q7LBY8|Q8NDB0|Q8WY35|Q9H0J6	Frame_Shift_Del	DEL	ENST00000325805.8	hg19	CCDS46881.1																																																																																			.	.		0.355	BBX-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317820.1	NM_020235		-	107491817	TTTCCTGATTTTTCTTATTCTGCCAGTAGCAAGA	-	107491784	7	5	337	1	0	1	0	1	0	0	0	0	1343	1841	64	0	1246	0	BBX	3	107491784	Frame_Shift_Del	DEL	TTTCCTGATTTTTCTTATTCTGCCAGTAGCAAGA	TCGA-RC-A7SB-01A-21D-A34Z-10	42824794	107491784	90530646	8	46810										
ZBTB38	253461	hgsc.bcm.edu	37	chr3	141163098	141163098	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	gaatttccaagatactgtaaAcaccctgaccaacagtccag	6	12	0	2			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr3:141163098A>G	ENST00000514251.1	+	4	2147	c.1868A>G	c.(1867-1869)aAc>aGc	p.N623S	ZBTB38_ENST00000441582.2_Missense_Mutation_p.N623S|ZBTB38_ENST00000321464.5_Missense_Mutation_p.N624S					zinc finger and BTB domain containing 38											breast(3)|cervix(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	41						GATACTGTAAACACCCTGACC	0.453																																					p.N623S		Atlas-SNP	.											.	ZBTB38	92	.	0			c.A1868G						.						88	85	86					3																	141163098		1980	4180	6160	SO:0001583	missense	253461	exon8			CTGTAAACACCCT	BC015444	CCDS43157.1	3q23	2014-06-13			ENSG00000177311	ENSG00000177311		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	26636	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 171"	612218				12477932	Standard	NM_001080412		Approved	FLJ35036, CIBZ, ZNF921, PPP1R171	uc003etw.3	Q8NAP3	OTTHUMG00000160128	ENST00000514251.1:c.1868A>G	chr3.hg19:g.141163098A>G	ENSP00000426387:p.Asn623Ser	72.0	0.0		52.0	16.0	NM_001080412		Missense_Mutation	SNP	ENST00000514251.1	hg19	CCDS43157.1	.	.	.	.	.	.	.	.	.	.	A	5.842	0.339587	0.11069	.	.	ENSG00000177311	ENST00000509883;ENST00000514251;ENST00000441582;ENST00000321464	T;T;T;T	0.08370	3.58;3.1;3.1;3.1	5.55	-0.817	0.10836	.	0.630837	0.16193	N	0.225297	T	0.04318	0.0119	N	0.12182	0.205	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.43621	-0.9380	9	.	.	.	-4.4441	11.5098	0.50486	0.4476:0.0:0.5524:0.0	.	624;623	B4DYR8;Q8NAP3	.;ZBT38_HUMAN	S	623;623;623;624	ENSP00000424254:N623S;ENSP00000426387:N623S;ENSP00000406955:N623S;ENSP00000372635:N624S	.	N	+	2	0	ZBTB38	142645788	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.076000	0.11412	-0.138000	0.11434	0.528000	0.53228	AAC	.	.		0.453	ZBTB38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359329.2			G	141163098	A	G	141163098	3	3	337	1	0	0	0	0	1	0	0	0	17554	43	2	2	1870	2	ZBTB38	3	141163098	Missense_Mutation	SNP	A	TCGA-RC-A7SB-01A-21D-A34Z-10	33671314	141163098	56859332	9	46811										
HS3ST1	9957	hgsc.bcm.edu	37	chr4	11401189	11401189	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	agcacgcgctccgacgggtcTcgcaggatgagcagcagccg	15	14	1	1			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr4:11401189T>C	ENST00000002596.5	-	2	1615	c.441A>G	c.(439-441)cgA>cgG	p.R147R		NM_005114.2	NP_005105.1	O14792	HS3S1_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	147					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)|sulfotransferase activity (GO:0008146)	p.L146_D148delLRD(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(6)|skin(3)	15						CCGACGGGTCTCGCAGGATGA	0.592																																					p.R147R		Atlas-SNP	.											.	HS3ST1	41	.	1	Deletion - In frame(1)	liver(1)	c.A441G						.						63	59	61					4																	11401189		2203	4300	6503	SO:0001819	synonymous_variant	9957	exon2			CGGGTCTCGCAGG	AF019386	CCDS3408.1	4p16	2008-02-05			ENSG00000002587	ENSG00000002587	2.8.2.23	"Sulfotransferases, membrane-bound"	5194	protein-coding gene	gene with protein product		603244				9988767	Standard	NM_005114		Approved	3OST1	uc003gmq.3	O14792	OTTHUMG00000090547	ENST00000002596.5:c.441A>G	chr4.hg19:g.11401189T>C		59.0	0.0		46.0	20.0	NM_005114	B3KUA6|Q6PEY8	Silent	SNP	ENST00000002596.5	hg19	CCDS3408.1																																																																																			.	.		0.592	HS3ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207073.3	NM_005114		C	11401189	T	C	11401189	2	2	337	1	0	0	0	0	0	0	0	1	7372	1538	54	2		2	HS3ST1	4	11401189	Silent	SNP	T	TCGA-RC-A7SB-01A-21D-A34Z-10		11401189	179753087	10	46812										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13700904	13700904	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	tgggaggggcagaaatgtcgTccttcatccatttggtgact	13	8	1	2			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr5:13700904T>C	ENST00000265104.4	-	78	13672	c.13568A>G	c.(13567-13569)gAc>gGc	p.D4523G		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4523					cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					AGAAATGTCGTCCTTCATCCA	0.463									Kartagener syndrome																												p.D4523G		Atlas-SNP	.											.	DNAH5	868	.	0			c.A13568G						.						184	170	174					5																	13700904		2203	4300	6503	SO:0001583	missense	1767	exon78	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	ATGTCGTCCTTCA	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.13568A>G	chr5.hg19:g.13700904T>C	ENSP00000265104:p.Asp4523Gly	118.0	0.0		88.0	31.0	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	hg19	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.250156	0.80024	.	.	ENSG00000039139	ENST00000265104	T	0.09255	3.0	5.95	5.95	0.96441	Dynein heavy chain (1);	0.049262	0.85682	D	0.000000	T	0.19604	0.0471	L	0.55743	1.74	0.80722	D	1	B	0.28552	0.215	B	0.39465	0.3	T	0.01608	-1.1313	10	0.87932	D	0	.	16.4323	0.83853	0.0:0.0:0.0:1.0	.	4523	Q8TE73	DYH5_HUMAN	G	4523	ENSP00000265104:D4523G	ENSP00000265104:D4523G	D	-	2	0	DNAH5	13753904	1.000000	0.71417	0.985000	0.45067	0.989000	0.77384	7.992000	0.88273	2.281000	0.76405	0.528000	0.53228	GAC	.	.		0.463	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		C	13700904	T	C	13700904	3	2	337	1	0	0	0	0	1	0	0	0	4606	1667	58	2	314	2	DNAH5	5	13700904	Missense_Mutation	SNP	T	TCGA-RC-A7SB-01A-21D-A34Z-10		13700904	167214356	11	46813										
RAI14	26064	hgsc.bcm.edu	37	chr5	34823713	34823713	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	atattgctctgttattgagaAtatgaataaggagaaagcat	9	3	1	3			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr5:34823713A>G	ENST00000265109.3	+	15	2053	c.1766A>G	c.(1765-1767)aAt>aGt	p.N589S	RAI14_ENST00000512629.1_Missense_Mutation_p.N560S|RAI14_ENST00000428746.2_Missense_Mutation_p.N589S|RAI14_ENST00000503673.1_Missense_Mutation_p.N589S|RAI14_ENST00000397449.1_Missense_Mutation_p.N582S|RAI14_ENST00000515799.1_Missense_Mutation_p.N592S|RAI14_ENST00000506376.1_Missense_Mutation_p.N581S	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	589						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(19)|lung(22)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(31;0.000191)					GTTATTGAGAATATGAATAAG	0.358																																					p.N592S		Atlas-SNP	.											.	RAI14	100	.	0			c.A1775G						.						58	61	60					5																	34823713		2203	4300	6503	SO:0001583	missense	26064	exon17			TTGAGAATATGAA	AB037755	CCDS34142.1, CCDS54837.1, CCDS54838.1, CCDS54839.1	5p13.3-p13.2	2013-01-10			ENSG00000039560	ENSG00000039560		"Ankyrin repeat domain containing"	14873	protein-coding gene	gene with protein product	"novel retinal pigment epithelial"	606586				11042181	Standard	NM_015577		Approved	NORPEG, KIAA1334, RAI13, DKFZp564G013	uc011coj.2	Q9P0K7	OTTHUMG00000162019	ENST00000265109.3:c.1766A>G	chr5.hg19:g.34823713A>G	ENSP00000265109:p.Asn589Ser	96.0	0.0		73.0	26.0	NM_001145525	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Missense_Mutation	SNP	ENST00000265109.3	hg19	CCDS34142.1	.	.	.	.	.	.	.	.	.	.	A	17.05	3.289782	0.59976	.	.	ENSG00000039560	ENST00000265109;ENST00000512629;ENST00000428746;ENST00000503673;ENST00000515799;ENST00000506376;ENST00000397449	T;T;T;T;T;T;T	0.36878	1.26;1.23;1.26;1.26;1.26;1.3;1.3	5.42	5.42	0.78866	.	.	.	.	.	T	0.48537	0.1505	L	0.29908	0.895	0.45035	D	0.998058	D;D;D;D	0.71674	0.998;0.982;0.978;0.982	D;P;P;P	0.80764	0.994;0.473;0.741;0.473	T	0.48854	-0.8998	9	0.52906	T	0.07	-27.1897	15.4697	0.75432	1.0:0.0:0.0:0.0	.	581;560;592;589	Q9P0K7-3;E9PED3;Q9P0K7-2;Q9P0K7	.;.;.;RAI14_HUMAN	S	589;560;589;589;592;581;582	ENSP00000265109:N589S;ENSP00000422377:N560S;ENSP00000388725:N589S;ENSP00000422942:N589S;ENSP00000427123:N592S;ENSP00000423854:N581S;ENSP00000380591:N582S	ENSP00000265109:N589S	N	+	2	0	RAI14	34859470	1.000000	0.71417	0.989000	0.46669	0.917000	0.54804	6.348000	0.73009	2.067000	0.61834	0.454000	0.30748	AAT	.	.		0.358	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577		G	34823713	A	G	34823713	3	3	337	1	0	0	0	0	1	0	0	0	13023	101	4	2	1885	2	RAI14	5	34823713	Missense_Mutation	SNP	A	TCGA-RC-A7SB-01A-21D-A34Z-10	21122809	34823713	146091547	12	46814										
HAPLN1	1404	hgsc.bcm.edu	37	chr5	82940454	82940454	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	gaaaattgagattgtagcgcCccagtcgtggaaagtaaggg	14	6	0	1			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr5:82940454C>A	ENST00000274341.4	-	4	1353	c.503G>T	c.(502-504)gGg>gTg	p.G168V		NM_001884.3	NP_001875.1	P10915	HPLN1_HUMAN	hyaluronan and proteoglycan link protein 1	168	Link 1. {ECO:0000255|PROSITE- ProRule:PRU00323}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)			breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|liver(1)|lung(15)|ovary(1)|prostate(1)|skin(1)	34		Lung NSC(167;0.0484)|all_lung(232;0.0522)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;7.82e-42)|Epithelial(54;5.88e-35)|all cancers(79;1.14e-29)	Hyaluronan(DB08818)	ATTGTAGCGCCCCAGTCGTGG	0.552																																					p.G168V		Atlas-SNP	.											HAPLN1,right_upper_lobe,carcinoma,0,1	HAPLN1	79	.	0			c.G503T						.						34	32	33					5																	82940454		2203	4300	6503	SO:0001583	missense	1404	exon4			TAGCGCCCCAGTC		CCDS4061.1	5q14.3	2013-01-11	2004-03-16	2004-03-17	ENSG00000145681	ENSG00000145681		"Immunoglobulin superfamily / V-set domain containing"	2380	protein-coding gene	gene with protein product	"Cartilage link protein", "hyaluronan and proteoglycan link protein 1"	115435	"cartilage linking protein 1"	CRTL1		2286376, 2320422	Standard	NM_001884		Approved		uc003kin.3	P10915	OTTHUMG00000119045	ENST00000274341.4:c.503G>T	chr5.hg19:g.82940454C>A	ENSP00000274341:p.Gly168Val	68.0	0.0		44.0	20.0	NM_001884	B2R9A9	Missense_Mutation	SNP	ENST00000274341.4	hg19	CCDS4061.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.020264	0.93462	.	.	ENSG00000145681	ENST00000274341;ENST00000510978;ENST00000508307;ENST00000503117	T;T;T;T	0.13420	2.59;2.59;2.59;2.59	5.8	5.8	0.92144	C-type lectin fold (1);Link (3);C-type lectin-like (1);	0.000000	0.85682	D	0.000000	T	0.53706	0.1813	H	0.95294	3.65	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.67304	-0.5704	10	0.87932	D	0	.	20.0608	0.97674	0.0:1.0:0.0:0.0	.	168	P10915	HPLN1_HUMAN	V	168;168;168;167	ENSP00000274341:G168V;ENSP00000422592:G168V;ENSP00000421341:G168V;ENSP00000426610:G167V	ENSP00000274341:G168V	G	-	2	0	HAPLN1	82976210	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.466000	0.80914	2.733000	0.93635	0.650000	0.86243	GGG	.	.		0.552	HAPLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239256.2	NM_001884		A	82940454	C	A	82940454	3	1	337	1	0	0	0	0	1	0	0	0	6963	623	22	3	569	3	HAPLN1	5	82940454	Missense_Mutation	SNP	C	TCGA-RC-A7SB-01A-21D-A34Z-10	48116741	82940454	97974806	13	46815										
PCDHA7	56141	hgsc.bcm.edu	37	chr5	140216124	140216124	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	gcttaccctgctgctgtacaCggcgttgcggtgctcagcgc	13	14	1	0			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr5:140216124C>G	ENST00000525929.1	+	1	2156	c.2156C>G	c.(2155-2157)aCg>aGg	p.T719R	PCDHA1_ENST00000504120.2_Intron|PCDHA7_ENST00000378125.3_Missense_Mutation_p.T719R|PCDHA4_ENST00000530339.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA3_ENST00000522353.2_Intron	NM_018910.2	NP_061733.1	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7	719					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|biliary_tract(1)|breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGCTGTACACGGCGTTGCGG	0.607																																					p.T719R	NSCLC(160;258 2013 5070 22440 28951)	Atlas-SNP	.											.	PCDHA7	367	.	0			c.C2156G						.						106	88	94					5																	140216124		2203	4300	6503	SO:0001583	missense	56141	exon1			TGTACACGGCGTT	AF152485	CCDS54918.1	5q31	2010-11-26				ENSG00000204963		"Cadherins / Protocadherins : Clustered"	8673	other	complex locus constituent	"KIAA0345-like 7", "ortholog to mouse CNR4"	606313		CNRS4		10380929, 10662547	Standard	NM_018910		Approved	CNR4, CRNR4		Q9UN72		ENST00000525929.1:c.2156C>G	chr5.hg19:g.140216124C>G	ENSP00000436426:p.Thr719Arg	50.0	0.0		38.0	14.0	NM_031852	O75282	Missense_Mutation	SNP	ENST00000525929.1	hg19	CCDS54918.1	.	.	.	.	.	.	.	.	.	.	C	13.51	2.257257	0.39896	.	.	ENSG00000204963	ENST00000525929;ENST00000378125	T;T	0.15603	2.41;2.41	3.57	0.749	0.18381	.	0.739382	0.10174	U	0.706779	T	0.44540	0.1298	M	0.93720	3.45	0.09310	N	1	D;P	0.53462	0.96;0.934	P;P	0.58970	0.849;0.71	T	0.24261	-1.0165	10	0.62326	D	0.03	.	8.4633	0.32940	0.0:0.6311:0.0:0.3689	.	719;719	Q9UN72-2;Q9UN72	.;PCDA7_HUMAN	R	719	ENSP00000436426:T719R;ENSP00000367365:T719R	ENSP00000367365:T719R	T	+	2	0	PCDHA7	140196308	0.000000	0.05858	0.469000	0.27204	0.694000	0.40290	-1.159000	0.03150	0.304000	0.22809	0.462000	0.41574	ACG	.	.		0.607	PCDHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372887.2	NM_018910		G	140216124	C	G	140216124	3	3	337	1	0	0	0	0	1	0	0	0	11538	536	19	4	2158	4	PCDHA7	5	140216124	Missense_Mutation	SNP	C	TCGA-RC-A7SB-01A-21D-A34Z-10	57275670	140216124	40699136	14	46816										
PCDHGC3	5098	hgsc.bcm.edu	37	chr5	140856286	140856286	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	gagctggtgttggagcgcgcCctggaccgagaacgggagcc	18	11	0	1			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr5:140856286C>A	ENST00000308177.3	+	1	707	c.603C>A	c.(601-603)gcC>gcA	p.A201A	PCDHGB7_ENST00000398594.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron|RN7SL68P_ENST00000488078.2_RNA|PCDHGB6_ENST00000520790.1_Intron|PCDHGB4_ENST00000519479.1_Intron	NM_002588.2|NM_032402.1	NP_002579.2|NP_115778.1	Q9UN70	PCDGK_HUMAN	protocadherin gamma subfamily C, 3	201	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(2)|urinary_tract(1)	29			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGAGCGCGCCCTGGACCGAG	0.597																																					p.A201A		Atlas-SNP	.											.	PCDHGC3	173	.	0			c.C603A						.						39	33	35					5																	140856286		2203	4300	6503	SO:0001819	synonymous_variant	5098	exon1			GCGCGCCCTGGAC	AF152337	CCDS4261.1, CCDS75347.1, CCDS75348.1	5q31	2010-01-26			ENSG00000240184	ENSG00000240184		"Cadherins / Protocadherins : Clustered"	8716	other	protocadherin	"cadherin-like 2", "protocadherin 2", "protocadherin 43"	603627		PCDH2		9360932, 8508762	Standard	NM_032402		Approved	PC-43, PC43, PCDH-GAMMA-C3		Q9UN70	OTTHUMG00000129613	ENST00000308177.3:c.603C>A	chr5.hg19:g.140856286C>A		34.0	0.0		26.0	11.0	NM_032402	O60622|Q08192|Q9Y5C4	Silent	SNP	ENST00000308177.3	hg19	CCDS4261.1																																																																																			.	.		0.597	PCDHGC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251808.2	NM_002588		A	140856286	C	A	140856286	2	1	337	1	0	0	0	0	0	0	0	1	11578	610	22	3		3	PCDHGC3	5	140856286	Silent	SNP	C	TCGA-RC-A7SB-01A-21D-A34Z-10	640162	140856286	40058974	15	46817										
OPRM1	4988	hgsc.bcm.edu	37	chr6	154411035	154411035	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	agatgccttagccaccagtaCcctgcccttccagagtgtga	9	14	0	3			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr6:154411035C>G	ENST00000330432.7	+	2	602	c.365C>G	c.(364-366)aCc>aGc	p.T122S	OPRM1_ENST00000419506.2_Missense_Mutation_p.T122S|OPRM1_ENST00000229768.5_Missense_Mutation_p.T122S|OPRM1_ENST00000452687.2_Missense_Mutation_p.T122S|OPRM1_ENST00000522555.1_Missense_Mutation_p.T22S|OPRM1_ENST00000360422.4_Missense_Mutation_p.T122S|OPRM1_ENST00000414028.2_Missense_Mutation_p.T122S|OPRM1_ENST00000428397.2_Missense_Mutation_p.T122S|OPRM1_ENST00000524163.1_Missense_Mutation_p.T122S|OPRM1_ENST00000434900.2_Missense_Mutation_p.T215S|OPRM1_ENST00000520708.1_Missense_Mutation_p.T22S|OPRM1_ENST00000435918.2_Missense_Mutation_p.T122S|OPRM1_ENST00000522236.1_Missense_Mutation_p.T22S|OPRM1_ENST00000337049.4_Missense_Mutation_p.T122S|OPRM1_ENST00000518759.1_Missense_Mutation_p.T41S	NM_000914.3	NP_000905.3	P35372	OPRM_HUMAN	opioid receptor, mu 1	122					adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavioral response to ethanol (GO:0048149)|calcium ion transmembrane transport (GO:0070588)|cellular response to stress (GO:0033554)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|locomotory behavior (GO:0007626)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of Wnt protein secretion (GO:0061358)|neuropeptide signaling pathway (GO:0007218)|opioid receptor signaling pathway (GO:0038003)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neurogenesis (GO:0050769)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-endorphin receptor activity (GO:0004979)|G-protein alpha-subunit binding (GO:0001965)|G-protein coupled receptor activity (GO:0004930)|morphine receptor activity (GO:0038047)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(15)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	33		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;9.26e-11)|BRCA - Breast invasive adenocarcinoma(81;0.0154)	Alfentanil(DB00802)|Alvimopan(DB06274)|Amitriptyline(DB00321)|Anileridine(DB00913)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dezocine(DB01209)|Diphenoxylate(DB01081)|Ethylmorphine(DB01466)|Fentanyl(DB00813)|Heroin(DB01452)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levallorphan(DB00504)|Levomethadyl Acetate(DB01227)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Methadyl Acetate(DB01433)|Methylnaltrexone(DB06800)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Ondansetron(DB00904)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Pentazocine(DB00652)|Pethidine(DB00454)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	GCCACCAGTACCCTGCCCTTC	0.443																																					p.T215S		Atlas-SNP	.											.	OPRM1	241	.	0			c.C644G						.						141	135	137					6																	154411035		2065	4238	6303	SO:0001583	missense	4988	exon4			CCAGTACCCTGCC	L29301	CCDS43517.1, CCDS43518.1, CCDS47503.1, CCDS47504.1, CCDS47505.1, CCDS47506.1, CCDS47507.1, CCDS47508.1, CCDS55071.1, CCDS55068.1, CCDS55069.1, CCDS55070.1	6q24-q25	2012-08-08			ENSG00000112038	ENSG00000112038		"GPCR / Class A : Opioid receptors"	8156	protein-coding gene	gene with protein product		600018					Standard	NM_001145285		Approved	MOR1	uc003qpo.1	P35372	OTTHUMG00000015870	ENST00000330432.7:c.365C>G	chr6.hg19:g.154411035C>G	ENSP00000328264:p.Thr122Ser	64.0	0.0		63.0	30.0	NM_001145279	B0FXJ1|B2R9S7|B8Q1L7|B8Q1L8|B8Q1L9|E7EWZ3|G8XRH6|G8XRH8|Q12930|Q4VWM1|Q4VWM2|Q4VWM3|Q4VWM4|Q4VWM6|Q4VWX6|Q5TDA1|Q6UPP1|Q6UQ80|Q7Z2D8|Q86V80|Q8IWW3|Q8IWW4|Q9UCZ4|Q9UN57	Missense_Mutation	SNP	ENST00000330432.7	hg19	CCDS55070.1	.	.	.	.	.	.	.	.	.	.	C	17.57	3.422052	0.62622	.	.	ENSG00000112038	ENST00000434900;ENST00000520708;ENST00000518759;ENST00000330432;ENST00000360422;ENST00000428397;ENST00000452687;ENST00000229768;ENST00000419506;ENST00000524163;ENST00000414028;ENST00000435918;ENST00000337049;ENST00000522555;ENST00000522236	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.72942	-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7	5.7	5.7	0.88788	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.72542	0.3473	L	0.37850	1.14	0.58432	D	0.999999	D;D;D;D;D;D;D;D;D;D;P;D;D	0.89917	0.999;1.0;1.0;0.999;1.0;1.0;1.0;1.0;1.0;1.0;0.851;1.0;0.994	D;D;D;D;D;D;D;D;D;D;P;D;D	0.97110	0.997;1.0;1.0;0.997;1.0;1.0;1.0;1.0;1.0;1.0;0.673;1.0;0.966	T	0.65874	-0.6062	10	0.20046	T	0.44	.	19.8351	0.96655	0.0:1.0:0.0:0.0	.	122;122;122;122;215;41;122;22;122;122;122;122;122	P35372-4;P35372-8;P35372-11;P35372-9;P35372-10;B8Q1L9;P35372-6;Q6UPP1;P35372-5;P35372;P35372-7;P35372-3;P35372-2	.;.;.;.;.;.;.;.;.;OPRM_HUMAN;.;.;.	S	215;22;41;122;122;122;122;122;122;122;122;122;122;22;22	ENSP00000394624:T215S;ENSP00000430876:T22S;ENSP00000430260:T41S;ENSP00000328264:T122S;ENSP00000353598:T122S;ENSP00000411903:T122S;ENSP00000410497:T122S;ENSP00000229768:T122S;ENSP00000403549:T122S;ENSP00000430097:T122S;ENSP00000399359:T122S;ENSP00000413752:T122S;ENSP00000338381:T122S;ENSP00000429719:T22S;ENSP00000429373:T22S	ENSP00000229768:T122S	T	+	2	0	OPRM1	154452728	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	7.818000	0.86416	2.687000	0.91594	0.655000	0.94253	ACC	.	.		0.443	OPRM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042786.2	NM_000914		G	154411035	C	G	154411035	3	3	337	1	0	0	0	0	1	0	0	0	10896	507	18	4	705	4	OPRM1	6	154411035	Missense_Mutation	SNP	C	TCGA-RC-A7SB-01A-21D-A34Z-10		154411035	16704032	16	46818										
ARID1B	57492	hgsc.bcm.edu	37	chr6	157150470	157150470	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	gtacccaggaggttcctatgGccctccaggcccacagcggt	12	15	0	0			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr6:157150470G>A	ENST00000350026.5	+	2	1653	c.1652G>A	c.(1651-1653)gGc>gAc	p.G551D	ARID1B_ENST00000275248.4_Missense_Mutation_p.G493D|ARID1B_ENST00000346085.5_Missense_Mutation_p.G551D|ARID1B_ENST00000367148.1_Missense_Mutation_p.G551D	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	551					chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		GGTTCCTATGGCCCTCCAGGC	0.587																																					p.G551D		Atlas-SNP	.											.	ARID1B	320	.	0			c.G1652A						.						93	85	87					6																	157150470		2203	4300	6503	SO:0001583	missense	57492	exon2			CCTATGGCCCTCC	AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"-"	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.1652G>A	chr6.hg19:g.157150470G>A	ENSP00000055163:p.Gly551Asp	91.0	0.0		85.0	35.0	NM_017519	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Missense_Mutation	SNP	ENST00000350026.5	hg19	CCDS5251.2	.	.	.	.	.	.	.	.	.	.	G	15.88	2.964519	0.53507	.	.	ENSG00000049618	ENST00000346085;ENST00000350026;ENST00000367148;ENST00000275248;ENST00000414678	T;T;T;T;T	0.03553	4.05;3.89;3.96;3.99;4.07	5.09	5.09	0.68999	.	0.186876	0.33327	N	0.005028	T	0.07863	0.0197	L	0.43923	1.385	0.38507	D	0.948366	D;D;D	0.76494	0.997;0.999;0.999	P;D;D	0.65323	0.861;0.934;0.934	T	0.22906	-1.0203	10	0.56958	D	0.05	.	18.8734	0.92325	0.0:0.0:1.0:0.0	.	551;551;493	Q8NFD5;Q8NFD5-2;G3XAA0	ARI1B_HUMAN;.;.	D	551;551;551;493;50	ENSP00000344546:G551D;ENSP00000055163:G551D;ENSP00000356116:G551D;ENSP00000275248:G493D;ENSP00000412835:G50D	ENSP00000275248:G493D	G	+	2	0	ARID1B	157192162	1.000000	0.71417	0.960000	0.40013	0.982000	0.71751	6.257000	0.72480	2.515000	0.84797	0.650000	0.86243	GGC	.	.		0.587	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732		A	157150470	G	A	157150470	3	1	337	1	0	0	0	0	1	0	0	0	914	1203	42	3	1658	3	ARID1B	6	157150470	Missense_Mutation	SNP	G	TCGA-RC-A7SB-01A-21D-A34Z-10	2739435	157150470	13964597	17	46819										
FNDC1	84624	hgsc.bcm.edu	37	chr6	159655130	159655130	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	aaggcgggaaagaagaccttCtgtcttcctctgtgccaaag	11	10	3	2			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr6:159655130C>T	ENST00000297267.9	+	11	3786	c.3586C>T	c.(3586-3588)Ctg>Ttg	p.L1196L	FNDC1_ENST00000340366.6_Silent_p.L1133L	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1196					cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		AGAAGACCTTCTGTCTTCCTC	0.617																																					p.L1196L		Atlas-SNP	.											.	FNDC1	250	.	0			c.C3586T						.						22	25	24					6																	159655130		1886	4090	5976	SO:0001819	synonymous_variant	84624	exon11			GACCTTCTGTCTT	AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"Fibronectin type III domain containing"	21184	protein-coding gene	gene with protein product		609991	"fibronectin type III domain containing 2"	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.3586C>T	chr6.hg19:g.159655130C>T		64.0	0.0		38.0	19.0	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Silent	SNP	ENST00000297267.9	hg19	CCDS47512.1	.	.	.	.	.	.	.	.	.	.	C	5.706	0.314817	0.10789	.	.	ENSG00000164694	ENST00000329629	.	.	.	4.85	0.59	0.17458	.	.	.	.	.	T	0.08846	0.0219	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.32613	-0.9900	4	.	.	.	-7.7516	3.3856	0.07270	0.2295:0.4522:0.229:0.0893	.	.	.	.	F	1091	.	.	S	+	2	0	FNDC1	159575120	0.001000	0.12720	0.000000	0.03702	0.125000	0.20455	0.559000	0.23485	0.415000	0.25817	-0.244000	0.11960	TCT	.	.		0.617	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532		T	159655130	C	T	159655130	2	4	337	1	0	0	0	0	0	0	0	1	5976	912	32	3		3	FNDC1	6	159655130	Silent	SNP	C	TCGA-RC-A7SB-01A-21D-A34Z-10	2504660	159655130	11459937	18	46820										
PTPN12	5782	hgsc.bcm.edu	37	chr7	77240326	77240326	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	tgaaaaacagctacaactatAtgaaattcatggagctcaga	7	7	2	3			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr7:77240326A>T	ENST00000248594.6	+	11	1174	c.902A>T	c.(901-903)tAt>tTt	p.Y301F	PTPN12_ENST00000415482.2_Missense_Mutation_p.Y182F|PTPN12_ENST00000435495.2_Missense_Mutation_p.Y171F	NM_002835.3	NP_002826.3	Q05209	PTN12_HUMAN	protein tyrosine phosphatase, non-receptor type 12	301					protein dephosphorylation (GO:0006470)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|podosome (GO:0002102)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|SH3 domain binding (GO:0017124)			breast(2)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(12)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	39						CTACAACTATATGAAATTCAT	0.313																																					p.Y301F		Atlas-SNP	.											.	PTPN12	83	.	0			c.A902T						.						129	145	139					7																	77240326		2203	4298	6501	SO:0001583	missense	5782	exon11			AACTATATGAAAT		CCDS5592.1, CCDS47619.1, CCDS47620.1	7q11.23	2011-06-09			ENSG00000127947	ENSG00000127947		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9645	protein-coding gene	gene with protein product		600079				7509295	Standard	NM_002835		Approved	PTPG1, PTP-PEST	uc003ugh.2	Q05209	OTTHUMG00000023501	ENST00000248594.6:c.902A>T	chr7.hg19:g.77240326A>T	ENSP00000248594:p.Tyr301Phe	283.0	0.0		203.0	94.0	NM_002835	A4D1C5|B4DKY2|E9PBR5|E9PEH9|Q16130|Q59FD6|Q75MN8|Q86XU4	Missense_Mutation	SNP	ENST00000248594.6	hg19	CCDS5592.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.361736	0.82353	.	.	ENSG00000127947	ENST00000248594;ENST00000415482;ENST00000543073;ENST00000435495	T;T;T	0.07021	3.83;3.23;3.23	5.47	5.47	0.80525	.	0.208920	0.43579	D	0.000557	T	0.17280	0.0415	M	0.65975	2.015	0.48830	D	0.999714	P	0.50156	0.932	P	0.48304	0.573	T	0.00749	-1.1582	10	0.41790	T	0.15	.	15.8381	0.78814	1.0:0.0:0.0:0.0	.	301	Q05209	PTN12_HUMAN	F	301;182;182;171	ENSP00000248594:Y301F;ENSP00000392429:Y182F;ENSP00000397991:Y171F	ENSP00000248594:Y301F	Y	+	2	0	PTPN12	77078262	1.000000	0.71417	0.994000	0.49952	0.979000	0.70002	5.071000	0.64382	2.191000	0.70037	0.533000	0.62120	TAT	.	.		0.313	PTPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253183.3			T	77240326	A	T	77240326	3	4	337	1	0	0	0	0	1	0	0	0	12794	449	16	4	944	4	PTPN12	7	77240326	Missense_Mutation	SNP	A	TCGA-RC-A7SB-01A-21D-A34Z-10		77240326	81898337	19	46821										
RBM12B	389677	hgsc.bcm.edu	37	chr8	94748274	94748274	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	cttgattaattgaagagccaTatccagaattacttgcttct	6	8	1	4			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr8:94748274T>C	ENST00000399300.2	-	3	578	c.365A>G	c.(364-366)tAt>tGt	p.Y122C	RBM12B_ENST00000520961.1_Intron|RP11-10N23.4_ENST00000517998.1_RNA|RBM12B_ENST00000517700.1_Missense_Mutation_p.Y122C	NM_203390.2	NP_976324.2	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B	122							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	30	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			TGAAGAGCCATATCCAGAATT	0.438																																					p.Y122C		Atlas-SNP	.											.	RBM12B	78	.	0			c.A365G						.						143	137	139					8																	94748274		1856	4091	5947	SO:0001583	missense	389677	exon3			GAGCCATATCCAG		CCDS43755.1	8q22	2014-05-20			ENSG00000183808	ENSG00000183808		"RNA binding motif (RRM) containing"	32310	protein-coding gene	gene with protein product							Standard	NM_203390		Approved		uc003yfz.3	Q8IXT5	OTTHUMG00000164317	ENST00000399300.2:c.365A>G	chr8.hg19:g.94748274T>C	ENSP00000382239:p.Tyr122Cys	111.0	0.0		97.0	31.0	NM_203390	A8MYB5	Missense_Mutation	SNP	ENST00000399300.2	hg19	CCDS43755.1	.	.	.	.	.	.	.	.	.	.	T	13.48	2.250781	0.39797	.	.	ENSG00000183808	ENST00000399300;ENST00000517700;ENST00000519109;ENST00000518597;ENST00000520560	T;T;T;T;T	0.19394	2.72;2.76;2.29;2.32;2.15	5.08	5.08	0.68730	.	0.272209	0.26560	N	0.023700	T	0.31136	0.0787	N	0.24115	0.695	0.30625	N	0.758055	D	0.76494	0.999	D	0.66847	0.947	T	0.15178	-1.0446	10	0.54805	T	0.06	-28.0135	14.6864	0.69052	0.0:0.0:0.0:1.0	.	122	Q8IXT5	RB12B_HUMAN	C	122	ENSP00000382239:Y122C;ENSP00000427729:Y122C;ENSP00000430474:Y122C;ENSP00000428269:Y122C;ENSP00000429807:Y122C	ENSP00000382239:Y122C	Y	-	2	0	RBM12B	94817450	0.999000	0.42202	1.000000	0.80357	0.997000	0.91878	2.239000	0.43079	2.132000	0.65825	0.533000	0.62120	TAT	.	.		0.438	RBM12B-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383603.1	NM_203390		C	94748274	T	C	94748274	3	2	337	1	0	0	0	0	1	0	0	0	13129	1406	49	2	2644	2	RBM12B	8	94748274	Missense_Mutation	SNP	T	TCGA-RC-A7SB-01A-21D-A34Z-10		94748274	51615748	20	46822										
MTSS1	9788	hgsc.bcm.edu	37	chr8	125565827	125565828	+	In_Frame_Ins	INS	-	-	TAT													0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	tggcttggaacatccgtcggINStaggactggctgatgtcgct							TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr8:125565827_125565828insTAT	ENST00000518547.1	-	14	2146_2147	c.1673_1674insATA	c.(1672-1674)tac>taATAc	p.557_558ins*	MTSS1_ENST00000354184.4_In_Frame_Ins_p.275_276ins*|MTSS1_ENST00000524090.1_In_Frame_Ins_p.447_448ins*|NDUFB9_ENST00000522532.1_Intron|MTSS1_ENST00000395508.2_In_Frame_Ins_p.331_332ins*|MTSS1_ENST00000378017.3_In_Frame_Ins_p.532_533ins*|MTSS1_ENST00000523587.1_5'UTR|MTSS1_ENST00000431961.2_In_Frame_Ins_p.275_276ins*|MTSS1_ENST00000325064.5_In_Frame_Ins_p.561_562ins*	NM_001282971.1|NM_014751.4	NP_001269900.1|NP_055566.3	O43312	MTSS1_HUMAN	metastasis suppressor 1	557					actin cytoskeleton organization (GO:0030036)|actin filament polymerization (GO:0030041)|adherens junction maintenance (GO:0034334)|bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|cellular response to fluid shear stress (GO:0071498)|epithelial cell proliferation involved in renal tubule morphogenesis (GO:2001013)|filopodium assembly (GO:0046847)|glomerulus morphogenesis (GO:0072102)|in utero embryonic development (GO:0001701)|magnesium ion homeostasis (GO:0010960)|microspike assembly (GO:0030035)|negative regulation of epithelial cell proliferation (GO:0050680)|nephron tubule epithelial cell differentiation (GO:0072160)|positive regulation of actin filament bundle assembly (GO:0032233)|renal tubule morphogenesis (GO:0061333)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			ACATCCGTCGGTAGGACTGGCT	0.55																																					p.Y558delinsX	Esophageal Squamous(160;622 1893 3862 8546 12509)	Atlas-Indel,Pindel	.											.	MTSS1	79	.	0			c.1674_1675insATA						.																																			SO:0001652	inframe_insertion	9788	exon14			.	AF086645	CCDS6353.1, CCDS64968.1, CCDS64969.1	8p22	2008-02-05			ENSG00000170873	ENSG00000170873			20443	protein-coding gene	gene with protein product		608486				12482861, 12082544	Standard	XM_005251111		Approved	KIAA0429, MIMA, MIMB, MIM	uc003yrk.2	O43312	OTTHUMG00000048189	ENST00000518547.1:c.1673_1674insATA	chr8.hg19:g.125565827_125565828insTAT	ENSP00000429064:p.Tyr558*	121.0	0.0		96.0	33.0	NM_014751	J3KNK6|Q8TCA2|Q96RX2	In_Frame_Ins	INS	ENST00000518547.1	hg19	CCDS6353.1																																																																																			.	.		0.55	MTSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109625.3	NM_014751		TAT	125565828	-	TAT	125565827	7	5	337	1	0	1	1	0	0	0	0	0	9971	1256	44	0	597	0	MTSS1	8	125565827	In_Frame_Ins	INS	-	TCGA-RC-A7SB-01A-21D-A34Z-10	30817553	125565827	20798195	21	46823										
CCDC73	493860	hgsc.bcm.edu	37	chr11	32657339	32657339	+	Frame_Shift_Del	DEL	T	T	-													0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	ctttaagggatgataattcaTttttaatcttattaatttct							TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr11:32657339delT	ENST00000335185.5	-	14	1131	c.1088delA	c.(1087-1089)aatfs	p.N363fs	CCDC73_ENST00000534415.1_5'UTR	NM_001008391.2	NP_001008392.2	Q6ZRK6	CCD73_HUMAN	coiled-coil domain containing 73	363										NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	51	Breast(20;0.112)					TGATAATTCATTTTTAATCTT	0.244																																					p.X363X		Atlas-Indel,Pindel	.											.	CCDC73	136	.	0			c.1089delA						.						38	35	36					11																	32657339		1763	4012	5775	SO:0001589	frameshift_variant	493860	exon14			.	AK128159	CCDS41630.1	11p13	2006-02-11			ENSG00000186714	ENSG00000186714			23261	protein-coding gene	gene with protein product		612328					Standard	NM_001008391		Approved	NY-SAR-79	uc001mtv.4	Q6ZRK6	OTTHUMG00000166279	ENST00000335185.5:c.1088delA	chr11.hg19:g.32657339delT	ENSP00000335325:p.Asn363fs	118.0	0.0		67.0	38.0	NM_001008391	Q6P5Q7|Q6ZMW0|Q86WE7	In_Frame_Del	DEL	ENST00000335185.5	hg19	CCDS41630.1																																																																																			.	.		0.244	CCDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388874.2	NM_001008391		-	32657339	T	-	32657339	7	5	337	1	0	1	0	1	0	0	0	0	2848	1493	52	0	2171	0	CCDC73	11	32657339	Frame_Shift_Del	DEL	T	TCGA-RC-A7SB-01A-21D-A34Z-10		32657339	102349177	22	46824										
ACAD8	27034	hgsc.bcm.edu	37	chr11	134131730	134131730	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	ctgcaggaggagaggaaggaTgcagtggccttgtgctccat	16	8	0	1			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr11:134131730T>C	ENST00000281182.4	+	9	1144	c.1038T>C	c.(1036-1038)gaT>gaC	p.D346D	ACAD8_ENST00000543332.1_3'UTR|ACAD8_ENST00000524547.1_3'UTR|ACAD8_ENST00000374752.4_Silent_p.D219D|ACAD8_ENST00000537423.1_Silent_p.D269D	NM_014384.2	NP_055199.1	Q9UKU7	ACAD8_HUMAN	acyl-CoA dehydrogenase family, member 8	346					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|lipid metabolic process (GO:0006629)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|valine catabolic process (GO:0006574)	mitochondrial matrix (GO:0005759)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)			endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	14	all_hematologic(175;0.127)	all_cancers(12;8e-23)|all_epithelial(12;2.59e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|all_neural(223;0.0189)|Medulloblastoma(222;0.0245)|Esophageal squamous(93;0.0559)		Epithelial(10;1.92e-10)|all cancers(11;2.26e-09)|BRCA - Breast invasive adenocarcinoma(10;8.73e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00154)|Lung(977;0.21)	Flavin adenine dinucleotide(DB03147)	AGAGGAAGGATGCAGTGGCCT	0.562																																					p.D346D	GBM(65;238 1125 33403 41853 48889)	Atlas-SNP	.											.	ACAD8	33	.	0			c.T1038C						.						140	102	115					11																	134131730		2201	4297	6498	SO:0001819	synonymous_variant	27034	exon9			GAAGGATGCAGTG	AF126245	CCDS8498.1	11q25	2014-09-17	2010-04-30		ENSG00000151498	ENSG00000151498			87	protein-coding gene	gene with protein product		604773	"acyl-Coenzyme A dehydrogenase family, member 8"			10524212	Standard	NM_014384		Approved		uc001qhk.3	Q9UKU7	OTTHUMG00000167177	ENST00000281182.4:c.1038T>C	chr11.hg19:g.134131730T>C		61.0	0.0		25.0	13.0	NM_014384	B7Z5W4|Q6ZWP6|Q9BUS8	Silent	SNP	ENST00000281182.4	hg19	CCDS8498.1																																																																																			.	.		0.562	ACAD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393607.1	NM_014384		C	134131730	T	C	134131730	2	2	337	1	0	0	0	0	0	0	0	1	110	1461	51	2		2	ACAD8	11	134131730	Silent	SNP	T	TCGA-RC-A7SB-01A-21D-A34Z-10	101474391	134131730	874786	23	46825										
TAPBPL	55080	hgsc.bcm.edu	37	chr12	6570035	6570035	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	ctacagagcggagaacagccTtgggagtcatctttgccagc	12	11	2	2			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr12:6570035T>G	ENST00000266556.7	+	6	1387	c.1222T>G	c.(1222-1224)Ttg>Gtg	p.L408V	TAPBPL_ENST00000545700.1_3'UTR|VAMP1_ENST00000544432.1_5'Flank	NM_018009.4	NP_060479.3	Q9BX59	TPSNR_HUMAN	TAP binding protein-like	408					negative regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002590)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)			endometrium(2)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	6						GAGAACAGCCTTGGGAGTCAT	0.602																																					p.L408V		Atlas-SNP	.											.	TAPBPL	21	.	0			c.T1222G						.						219	165	183					12																	6570035		2203	4300	6503	SO:0001583	missense	55080	exon6			ACAGCCTTGGGAG	AK001005	CCDS8546.1	12p13.31	2013-01-11						"Immunoglobulin superfamily / C1-set domain containing"	30683	protein-coding gene	gene with protein product		607081				11920573	Standard	NM_018009		Approved	TAPBP-R, FLJ10143, TAPBPR	uc001qog.4	Q9BX59		ENST00000266556.7:c.1222T>G	chr12.hg19:g.6570035T>G	ENSP00000266556:p.Leu408Val	49.0	0.0		38.0	16.0	NM_018009	Q9NWB8	Missense_Mutation	SNP	ENST00000266556.7	hg19	CCDS8546.1	.	.	.	.	.	.	.	.	.	.	T	8.380	0.837234	0.16891	.	.	ENSG00000139192	ENST00000266556	T	0.08102	3.13	5.24	1.35	0.21983	Immunoglobulin-like fold (1);	0.776617	0.12688	N	0.447397	T	0.04998	0.0134	L	0.38175	1.15	0.09310	N	1	B	0.26318	0.146	B	0.21360	0.034	T	0.44528	-0.9322	10	0.07030	T	0.85	-0.11	4.3505	0.11153	0.2938:0.0866:0.0:0.6196	.	408	Q9BX59	TPSNR_HUMAN	V	408	ENSP00000266556:L408V	ENSP00000266556:L408V	L	+	1	2	TAPBPL	6440296	0.001000	0.12720	0.001000	0.08648	0.488000	0.33401	0.454000	0.21827	0.117000	0.18138	0.533000	0.62120	TTG	.	.		0.602	TAPBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399263.1	NM_018009		G	6570035	T	G	6570035	3	3	337	1	0	0	0	0	1	0	0	0	15568	1606	56	5	1244	5	TAPBPL	12	6570035	Missense_Mutation	SNP	T	TCGA-RC-A7SB-01A-21D-A34Z-10		6570035	127281860	24	46826										
MLL2	8085	hgsc.bcm.edu	37	chr12	49425062	49425062	+	Frame_Shift_Del	DEL	T	T	-													0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	cccctcggacccccgcccagTgctgagttgcacattctttg							TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr12:49425062delT	ENST00000301067.7	-	39	13425	c.13426delA	c.(13426-13428)actfs	p.T4476fs		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	4476					chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										CCCCGCCCAGTGCTGAGTTGC	0.607																																					p.T4476fs		Atlas-Indel,Pindel	.											.	MLL2	1173	.	0			c.13427delC						.						71	77	75					12																	49425062		2049	4201	6250	SO:0001589	frameshift_variant	8085	exon39			.	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.13426delA	chr12.hg19:g.49425062delT	ENSP00000301067:p.Thr4476fs	53.0	0.0		40.0	20.0	NM_003482	O14687	Frame_Shift_Del	DEL	ENST00000301067.7	hg19	CCDS44873.1																																																																																			.	.		0.607	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			-	49425062	T	-	49425062	7	5	337	1	0	1	0	1	0	0	0	0	9630	1696	59	0	3251	0	MLL2	12	49425062	Frame_Shift_Del	DEL	T	TCGA-RC-A7SB-01A-21D-A34Z-10	42855027	49425062	84426833	25	46827										
R3HDM2	22864	hgsc.bcm.edu	37	chr12	57663679	57663679	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	tgctgagggtgctgggagatAagtggggtctggaatagagc	19	4	1	3			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr12:57663679A>G	ENST00000347140.3	-	15	1791	c.1401T>C	c.(1399-1401)ctT>ctC	p.L467L	R3HDM2_ENST00000358907.2_Silent_p.L467L|R3HDM2_ENST00000546843.1_5'Flank|R3HDM2_ENST00000413953.2_Silent_p.L194L|R3HDM2_ENST00000402412.1_Silent_p.L481L|R3HDM2_ENST00000403821.2_Silent_p.L501L|RP11-123K3.4_ENST00000548184.1_3'UTR|R3HDM2_ENST00000441731.2_Silent_p.L162L			Q9Y2K5	R3HD2_HUMAN	R3H domain containing 2	467	Gln-rich.					nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	22						GCTGGGAGATAAGTGGGGTCT	0.547																																					p.L467L		Atlas-SNP	.											.	R3HDM2	125	.	0			c.T1401C						.						126	113	117					12																	57663679		2203	4300	6503	SO:0001819	synonymous_variant	22864	exon13			GGAGATAAGTGGG	AB023219	CCDS8937.2	12q13.3	2012-11-19			ENSG00000179912	ENSG00000179912			29167	protein-coding gene	gene with protein product							Standard	NM_014925		Approved	KIAA1002	uc009zpm.1	Q9Y2K5	OTTHUMG00000171568	ENST00000347140.3:c.1401T>C	chr12.hg19:g.57663679A>G		69.0	0.0		63.0	18.0	NM_014925	Q2M1T9|Q3ZCT5	Silent	SNP	ENST00000347140.3	hg19	CCDS8937.2	.	.	.	.	.	.	.	.	.	.	A	14.69	2.611037	0.46631	.	.	ENSG00000179912	ENST00000466401	.	.	.	5.15	2.73	0.32206	.	0.173114	0.42548	N	0.000681	T	0.57007	0.2024	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54886	-0.8226	6	0.56958	D	0.05	-10.9705	3.8692	0.09029	0.5704:0.1795:0.2501:0.0	.	.	.	.	S	65	.	ENSP00000449326:L65S	L	-	2	0	R3HDM2	55949946	0.942000	0.31987	1.000000	0.80357	0.917000	0.54804	0.452000	0.21795	0.500000	0.27991	0.528000	0.53228	TTA	.	.		0.547	R3HDM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326570.2	NM_014925		G	57663679	A	G	57663679	2	3	337	1	0	0	0	0	0	0	0	1	12903	349	13	2		2	R3HDM2	12	57663679	Silent	SNP	A	TCGA-RC-A7SB-01A-21D-A34Z-10	8238617	57663679	76188216	26	46828										
PAH	5053	hgsc.bcm.edu	37	chr12	103237549	103237549	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	agaagctttggcttctctgaTaagcagtactgtaggcccca	10	10	1	2	rs376480977		TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr12:103237549T>C	ENST00000553106.1	-	11	1546	c.1074A>G	c.(1072-1074)ttA>ttG	p.L358L	PAH_ENST00000307000.2_Silent_p.L353L	NM_000277.1	NP_000268.1	P00439	PH4H_HUMAN	phenylalanine hydroxylase	358					catecholamine biosynthetic process (GO:0042423)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|neurotransmitter biosynthetic process (GO:0042136)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|phenylalanine 4-monooxygenase activity (GO:0004505)			endometrium(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(5)|skin(2)|urinary_tract(1)	27					Droxidopa(DB06262)|Epinephrine(DB00668)|L-Phenylalanine(DB00120)|Norepinephrine(DB00368)|Tetrahydrobiopterin(DB00360)	GCTTCTCTGATAAGCAGTACT	0.483																																					p.L358L		Atlas-SNP	.											.	PAH	77	.	0			c.A1074G						.						85	84	84					12																	103237549		2203	4300	6503	SO:0001819	synonymous_variant	5053	exon11			CTCTGATAAGCAG	U49897	CCDS9092.1	12q22-q24.2	2010-04-27				ENSG00000171759	1.14.16.1		8582	protein-coding gene	gene with protein product	"phenylalanine 4-monooxygenase"	612349				2063869	Standard	NM_000277		Approved	PH	uc001tjq.1	P00439		ENST00000553106.1:c.1074A>G	chr12.hg19:g.103237549T>C		51.0	0.0		51.0	17.0	NM_000277	Q16717|Q8TC14	Silent	SNP	ENST00000553106.1	hg19	CCDS9092.1																																																																																			.	.		0.483	PAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406692.1			C	103237549	T	C	103237549	2	2	337	1	0	0	0	0	0	0	0	1	11403	1403	49	2		2	PAH	12	103237549	Silent	SNP	T	TCGA-RC-A7SB-01A-21D-A34Z-10	45573870	103237549	30614346	27	46829										
RPLP0	6175	hgsc.bcm.edu	37	chr12	120636498	120636498	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	atgttcagcagcgtggcttcGctggctcccactttgtctcc	10	14	2	0	rs138718343		TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr12:120636498G>A	ENST00000551150.1	-	5	825	c.510C>T	c.(508-510)agC>agT	p.S170S	PXN-AS1_ENST00000535200.1_RNA|PXN-AS1_ENST00000542265.1_RNA|RPLP0_ENST00000313104.5_Intron|PXN-AS1_ENST00000538804.1_RNA|RPLP0_ENST00000546989.1_Intron|RPLP0_ENST00000550296.1_5'Flank|RPLP0_ENST00000552292.1_5'Flank|PXN-AS1_ENST00000542314.1_RNA|PXN-AS1_ENST00000539446.1_RNA|RPLP0_ENST00000392514.4_Silent_p.S170S|RPLP0_ENST00000228306.4_Silent_p.S170S			P05388	RLA0_HUMAN	ribosomal protein, large, P0	170					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosome biogenesis (GO:0042254)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)	15	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GCGTGGCTTCGCTGGCTCCCA	0.527																																					p.S170S		Atlas-SNP	.											.	RPLP0	27	.	0			c.C510T						.	G	,	0,4406		0,0,2203	72	69	70		510,510	-0.5	1	12	dbSNP_134	70	3,8593	3.0+/-9.4	0,3,4295	no	coding-synonymous,coding-synonymous	RPLP0	NM_001002.3,NM_053275.3	,	0,3,6498	AA,AG,GG		0.0349,0.0,0.0231	,	170/318,170/318	120636498	3,12999	2203	4298	6501	SO:0001819	synonymous_variant	6175	exon6			GGCTTCGCTGGCT	AB007187	CCDS9193.1	12q24.2	2011-07-29			ENSG00000089157	ENSG00000089157		"L ribosomal proteins"	10371	protein-coding gene	gene with protein product	"acidic ribosomal phosphoprotein P0"	180510				9582194	Standard	NM_053275		Approved	PRLP0, P0, L10E, RPP0, LP0	uc001txq.3	P05388	OTTHUMG00000169317	ENST00000551150.1:c.510C>T	chr12.hg19:g.120636498G>A		68.0	0.0		52.0	16.0	NM_053275	Q3B7A4|Q9BVK4	Silent	SNP	ENST00000551150.1	hg19	CCDS9193.1																																																																																			.	G|1.000;A|0.000		0.527	RPLP0-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403448.3	NM_053275		A	120636498	G	A	120636498	2	1	337	1	0	0	0	0	0	0	0	1	13619	1078	38	1		1	RPLP0	12	120636498	Silent	SNP	G	TCGA-RC-A7SB-01A-21D-A34Z-10	17398949	120636498	13215397	28	46830										
ALG5	29880	hgsc.bcm.edu	37	chr13	37524129	37524129	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	ccaggcaccagtcaaatatcGaagtcgtataaaaagtaggt	9	8	1	0			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr13:37524129G>A	ENST00000239891.3	-	10	991	c.925C>T	c.(925-927)Cga>Tga	p.R309*	ALG5_ENST00000443765.1_Nonsense_Mutation_p.R279*	NM_013338.4	NP_037470.1	Q9Y673	ALG5_HUMAN	ALG5, dolichyl-phosphate beta-glucosyltransferase	309					cellular protein metabolic process (GO:0044267)|determination of left/right symmetry (GO:0007368)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	dolichyl-phosphate beta-glucosyltransferase activity (GO:0004581)|oligosaccharyl transferase activity (GO:0004576)	p.R309*(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	11		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)		all cancers(112;5.79e-07)|Epithelial(112;1.81e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00785)|BRCA - Breast invasive adenocarcinoma(63;0.0127)|GBM - Glioblastoma multiforme(144;0.0472)		GTCAAATATCGAAGTCGTATA	0.358																																					p.R309X		Atlas-SNP	.											ALG5,NS,carcinoma,0,3	ALG5	28	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C925T						.						85	83	84					13																	37524129		2203	4300	6503	SO:0001587	stop_gained	29880	exon10			AATATCGAAGTCG	AF088028	CCDS9361.1, CCDS45033.1	13q13.1	2013-02-22	2013-02-21		ENSG00000120697	ENSG00000120697	2.4.1.117	"Glycosyltransferase family 2 domain containing"	20266	protein-coding gene	gene with protein product		604565	"asparagine-linked glycosylation 5 homolog (yeast, dolichyl-phosphate beta-glucosyltransferase)", "asparagine-linked glycosylation 5, dolichyl-phosphate beta-glucosyltransferase homolog (S. cerevisiae)"			10359825	Standard	NM_013338		Approved	bA421P11.2	uc001uvy.3	Q9Y673	OTTHUMG00000016741	ENST00000239891.3:c.925C>T	chr13.hg19:g.37524129G>A	ENSP00000239891:p.Arg309*	52.0	0.0		31.0	16.0	NM_013338	B4DR37|Q5TBA6	Nonsense_Mutation	SNP	ENST00000239891.3	hg19	CCDS9361.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.245912	0.80024	.	.	ENSG00000120697	ENST00000443765;ENST00000239891	.	.	.	5.86	5.01	0.66863	.	0.054432	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.6453	0.62277	0.0:0.0:0.6013:0.3987	.	.	.	.	X	279;309	.	ENSP00000239891:R309X	R	-	1	2	ALG5	36422129	1.000000	0.71417	0.984000	0.44739	0.927000	0.56198	3.338000	0.52128	1.462000	0.47948	-0.182000	0.12963	CGA	.	.		0.358	ALG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044528.2	NM_013338		A	37524129	G	A	37524129	4	1	337	1	0	0	0	0	0	1	0	0	521	1066	37	1	53	1	ALG5	13	37524129	Nonsense_Mutation	SNP	G	TCGA-RC-A7SB-01A-21D-A34Z-10		37524129	77645749	29	46831										
PCDH17	27253	hgsc.bcm.edu	37	chr13	58299074	58299074	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	tcaagcagcccaaccaaggcGtgcatcgagccttgcacctc	9	16	1	0	rs534412507		TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr13:58299074G>C	ENST00000377918.3	+	4	3152	c.3126G>C	c.(3124-3126)gcG>gcC	p.A1042A		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	1042					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(30)|liver(2)|lung(54)|ovary(4)|pancreas(2)|prostate(5)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		CAACCAAGGCGTGCATCGAGC	0.532																																					p.A1042A	Melanoma(72;952 1291 1619 12849 33676)	Atlas-SNP	.											.	PCDH17	304	.	0			c.G3126C						.						85	84	84					13																	58299074		2203	4300	6503	SO:0001819	synonymous_variant	27253	exon4			CAAGGCGTGCATC	AF029343	CCDS31986.1	13q21.1	2010-01-26			ENSG00000118946	ENSG00000118946		"Cadherins / Protocadherins : Non-clustered"	14267	protein-coding gene	gene with protein product		611760				10835267	Standard	NM_001040429		Approved	PCDH68, PCH68	uc001vhq.1	O14917	OTTHUMG00000016992	ENST00000377918.3:c.3126G>C	chr13.hg19:g.58299074G>C		68.0	0.0		37.0	17.0	NM_001040429	A8K1R5|Q5VVW9|Q5VVX0	Silent	SNP	ENST00000377918.3	hg19	CCDS31986.1																																																																																			.	.		0.532	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429		C	58299074	G	C	58299074	2	2	337	1	0	0	0	0	0	0	0	1	11521	1132	40	4		4	PCDH17	13	58299074	Silent	SNP	G	TCGA-RC-A7SB-01A-21D-A34Z-10	20774945	58299074	56870804	30	46832										
TBC1D4	9882	hgsc.bcm.edu	37	chr13	75884197	75884197	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	cttcaatcttttctgggtcaTcctccccagacaggaataca	6	13	4	1	rs531614085	byFrequency	TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr13:75884197T>A	ENST00000377636.3	-	14	2820	c.2474A>T	c.(2473-2475)gAt>gTt	p.D825V	TBC1D4_ENST00000425511.1_Missense_Mutation_p.D42V|TBC1D4_ENST00000377625.2_Missense_Mutation_p.D762V|TBC1D4_ENST00000431480.2_Missense_Mutation_p.D817V	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	825					cellular response to insulin stimulus (GO:0032869)|membrane organization (GO:0061024)|negative regulation of vesicle fusion (GO:0031339)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		TTCTGGGTCATCCTCCCCAGA	0.463													T|||	2	0.000399361	0	0	5008	,	,		17576	0		0	False		,,,				2504	0.002				p.D825V		Atlas-SNP	.											.	TBC1D4	142	.	0			c.A2474T						.						107	95	99					13																	75884197		1858	4094	5952	SO:0001583	missense	9882	exon14			GGGTCATCCTCCC	AB011175	CCDS41901.1, CCDS66563.1, CCDS66564.1	13q22.2	2013-07-09			ENSG00000136111	ENSG00000136111			19165	protein-coding gene	gene with protein product	"Akt substrate of 160 kDa"	612465				11829485, 11994271, 15304337	Standard	XM_005266603		Approved	KIAA0603, AS160, DKFZp779C0666	uc001vjl.1	O60343	OTTHUMG00000017088	ENST00000377636.3:c.2474A>T	chr13.hg19:g.75884197T>A	ENSP00000366863:p.Asp825Val	94.0	0.0		60.0	30.0	NM_014832	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Missense_Mutation	SNP	ENST00000377636.3	hg19	CCDS41901.1	.	.	.	.	.	.	.	.	.	.	T	17.45	3.392953	0.62066	.	.	ENSG00000136111	ENST00000377636;ENST00000431480;ENST00000377625;ENST00000425511;ENST00000413735	T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;1.73	5.93	5.93	0.95920	.	0.244954	0.35436	N	0.003213	T	0.50854	0.1640	L	0.54323	1.7	0.52501	D	0.999954	B;B;B;P	0.40619	0.116;0.404;0.21;0.724	B;B;B;P	0.48063	0.046;0.281;0.124;0.565	T	0.48854	-0.8998	10	0.49607	T	0.09	-9.4382	16.3798	0.83452	0.0:0.0:0.0:1.0	.	42;762;817;825	O60343-4;O60343-2;O60343-3;O60343	.;.;.;TBCD4_HUMAN	V	825;817;762;42;274	ENSP00000366863:D825V;ENSP00000395986:D817V;ENSP00000366852:D762V;ENSP00000390654:D42V;ENSP00000396932:D274V	ENSP00000366852:D762V	D	-	2	0	TBC1D4	74782198	1.000000	0.71417	0.883000	0.34634	0.956000	0.61745	3.447000	0.52936	2.271000	0.75665	0.533000	0.62120	GAT	.	.		0.463	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832		A	75884197	T	A	75884197	3	1	337	1	0	0	0	0	1	0	0	0	15637	1435	50	4	1454	4	TBC1D4	13	75884197	Missense_Mutation	SNP	T	TCGA-RC-A7SB-01A-21D-A34Z-10	17585123	75884197	39285681	31	46833										
MAGEL2	54551	hgsc.bcm.edu	37	chr15	23889381	23889381	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	gctcagtgtaagggattcgcCtgtactctaggtacttctgc	11	10	3	0			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr15:23889381C>A	ENST00000532292.1	-	1	1794	c.1700G>T	c.(1699-1701)aGg>aTg	p.R567M		NM_019066.4	NP_061939.3	Q9UJ55	MAGL2_HUMAN	MAGE-like 2	450					Arp2/3 complex-mediated actin nucleation (GO:0034314)|protein K63-linked ubiquitination (GO:0070534)|retrograde transport, endosome to Golgi (GO:0042147)	endosome (GO:0005768)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;1.84e-06)|Epithelial(43;1.2e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)		AGGGATTCGCCTGTACTCTAG	0.502																																					p.R1170M		Atlas-SNP	.											.	MAGEL2	108	.	0			c.G3509T						.						49	49	49					15																	23889381		1910	4132	6042	SO:0001583	missense	54551	exon1			ATTCGCCTGTACT	AJ243531	CCDS73700.1	15q11-q12	2008-07-18				ENSG00000254585			6814	protein-coding gene	gene with protein product		605283		NDNL1		10556298	Standard	NM_019066		Approved	nM15	uc001ywj.4	Q9UJ55		ENST00000532292.1:c.1700G>T	chr15.hg19:g.23889381C>A	ENSP00000433433:p.Arg567Met	50.0	0.0		27.0	12.0	NM_019066		Missense_Mutation	SNP	ENST00000532292.1	hg19		.	.	.	.	.	.	.	.	.	.	C	15.88	2.963694	0.53507	.	.	ENSG00000254585	ENST00000532292	.	.	.	4.57	3.64	0.41730	.	.	.	.	.	T	0.66307	0.2776	M	0.91406	3.205	0.22737	N	0.998791	.	.	.	.	.	.	T	0.60480	-0.7255	5	.	.	.	.	7.8955	0.29704	0.0:0.8906:0.0:0.1094	.	.	.	.	C	599	.	.	G	-	1	0	MAGEL2	21440474	0.657000	0.27393	0.914000	0.36105	0.909000	0.53808	0.950000	0.29122	2.545000	0.85829	0.462000	0.41574	GGC	.	.		0.502	MAGEL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395182.2	NM_019066		A	23889381	C	A	23889381	3	1	337	1	0	0	0	0	1	0	0	0	9198	681	24	3	244	3	MAGEL2	15	23889381	Missense_Mutation	SNP	C	TCGA-RC-A7SB-01A-21D-A34Z-10		23889381	78642011	32	46834										
PLCB2	5330	hgsc.bcm.edu	37	chr15	40584571	40584571	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	ccaggtatgtagtccttcatCtccaggaagatgaagagcgc	11	10	2	3			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr15:40584571C>T	ENST00000260402.3	-	22	2649	c.2400G>A	c.(2398-2400)gaG>gaA	p.E800E	PLCB2_ENST00000456256.2_Silent_p.E800E|PLCB2_ENST00000557821.1_Silent_p.E796E	NM_001284297.1|NM_004573.2	NP_001271226.1|NP_004564.2	Q00722	PLCB2_HUMAN	phospholipase C, beta 2	800					activation of phospholipase C activity (GO:0007202)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|sensory perception of bitter taste (GO:0050913)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(3)	39		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0508)		AGTCCTTCATCTCCAGGAAGA	0.592																																					p.E800E		Atlas-SNP	.											.	PLCB2	177	.	0			c.G2400A						.						68	76	73					15																	40584571		2065	4204	6269	SO:0001819	synonymous_variant	5330	exon22			CTTCATCTCCAGG		CCDS42020.1, CCDS61591.1, CCDS61592.1, CCDS73704.1	15q15.1	2012-01-23			ENSG00000137841	ENSG00000137841	3.1.4.11		9055	protein-coding gene	gene with protein product		604114				1644792, 9925923	Standard	XM_005254448		Approved	FLJ38135	uc001zld.3	Q00722	OTTHUMG00000172412	ENST00000260402.3:c.2400G>A	chr15.hg19:g.40584571C>T		43.0	0.0		32.0	12.0	NM_004573	A8K6J2|B9EGH5	Silent	SNP	ENST00000260402.3	hg19	CCDS42020.1																																																																																			.	.		0.592	PLCB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418430.1			T	40584571	C	T	40584571	2	4	337	1	0	0	0	0	0	0	0	1	12037	912	32	3		3	PLCB2	15	40584571	Silent	SNP	C	TCGA-RC-A7SB-01A-21D-A34Z-10	16695190	40584571	61946821	33	46835										
CAPN3	825	hgsc.bcm.edu	37	chr15	42698136	42698151	+	Splice_Site	DEL	ACCAAGGTAGGTGTGT	ACCAAGGTAGGTGTGT	-													0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	ttatgcagaaaaagaaaaaaAccaaggtaggtgtgtgggta					rs373194123		TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	ACCAAGGTAGGTGTGT	ACCAAGGTAGGTGTGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr15:42698136_42698151delACCAAGGTAGGTGTGT	ENST00000397163.3	+	15	2014_2019	c.1795_1800delACCAAGGTAGGTGTGT	c.(1795-1800)accaagdel	p.TK599fs	CAPN3_ENST00000397200.4_Splice_Site_p.TK87fs|CAPN3_ENST00000349748.3_Intron|RP11-164J13.1_ENST00000495723.1_RNA|CAPN3_ENST00000569136.1_5'UTR|CAPN3_ENST00000561817.1_Intron|CAPN3_ENST00000357568.3_Intron|CAPN3_ENST00000397204.4_5'UTR|CAPN3_ENST00000337571.4_Intron|CAPN3_ENST00000318023.7_Intron|CAPN3_ENST00000356316.3_Intron	NM_000070.2	NP_000061.1	P20807	CAN3_HUMAN	calpain 3, (p94)	599	Linker.				apoptotic process (GO:0006915)|autolysis (GO:0001896)|cellular response to calcium ion (GO:0071277)|cellular response to salt stress (GO:0071472)|G1 to G0 transition involved in cell differentiation (GO:0070315)|muscle cell cellular homeostasis (GO:0046716)|muscle organ development (GO:0007517)|muscle structure development (GO:0061061)|myofibril assembly (GO:0030239)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of proteolysis (GO:0045862)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of satellite cell activation involved in skeletal muscle regeneration (GO:0014718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein localization to membrane (GO:0072657)|proteolysis (GO:0006508)|regulation of catalytic activity (GO:0050790)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of myoblast differentiation (GO:0045661)|response to calcium ion (GO:0051592)|response to muscle activity (GO:0014850)|sarcomere organization (GO:0045214)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|myofibril (GO:0030016)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)|ligase regulator activity (GO:0055103)|peptidase activity (GO:0008233)|protein complex scaffold (GO:0032947)|signal transducer activity (GO:0004871)|sodium ion binding (GO:0031402)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	47		all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;7.36e-07)		AAAGAAAAAAACCAAGGTAGGTGTGTGGGTAGAGAG	0.431																																					p.598_600del		Atlas-Indel,Pindel	.											.	CAPN3	172	.	0			c.1794_1800del	GRCh37	CI983047|CS052038	CAPN3	I|S	rs80338803	.																																			SO:0001630	splice_region_variant	825	exon15			.	X85030	CCDS10085.1, CCDS10086.1, CCDS32207.1, CCDS45245.1, CCDS45246.1	15q15.1	2014-09-17			ENSG00000092529	ENSG00000092529	3.4.22.52	"EF-hand domain containing"	1480	protein-coding gene	gene with protein product		114240		LGMD2, LGMD2A		2555341, 7720071	Standard	NM_024344		Approved	CANP3, p94, nCL-1	uc001zpn.1	P20807	OTTHUMG00000130619	ENST00000397163.3:c.1800+1ACCAAGGTAGGTGTGT>-	chr15.hg19:g.42698136_42698151delACCAAGGTAGGTGTGT		148.0	0.0		57.0	17.0	NM_000070	A6H8K6|Q7L4R0|Q9BQC8|Q9BTU4|Q9Y5S6|Q9Y5S7	Frame_Shift_Del	DEL	ENST00000397163.3	hg19	CCDS45245.1																																																																																			.	.		0.431	CAPN3-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421075.1		Frame_Shift_Del	-	42698151	ACCAAGGTAGGTGTGT	-	42698136	8	5	337	1	0	1	0	1	0	0	1	0	2630	43	2	0	1905	0	CAPN3	15	42698136	Splice_Site	DEL	ACCAAGGTAGGTGTGT	TCGA-RC-A7SB-01A-21D-A34Z-10	2113565	42698136	59833256	34	46836										
TP53	7157	hgsc.bcm.edu	37	chr17	7577509	7577509	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	ggctcctgacctggagtcttCcagtgtgatgatggtgagga	15	8	1	4	rs121912652		TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr17:7577509C>T	ENST00000269305.4	-	7	961	c.772G>A	c.(772-774)Gaa>Aaa	p.E258K	TP53_ENST00000413465.2_Missense_Mutation_p.E258K|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.E258K|TP53_ENST00000359597.4_Missense_Mutation_p.E258K|TP53_ENST00000445888.2_Missense_Mutation_p.E258K|TP53_ENST00000420246.2_Missense_Mutation_p.E258K	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	258	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		E -> A (in sporadic cancers; somatic mutation).|E -> D (in sporadic cancers; somatic mutation).|E -> G (in sporadic cancers; somatic mutation).|E -> K (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1978757}.|E -> L (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|E -> Q (in sporadic cancers; somatic mutation).|E -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.E258K(40)|p.E258*(15)|p.E258Q(9)|p.0?(8)|p.?(1)|p.E258fs*85(1)|p.E258>XX(1)|p.E258fs*71(1)|p.E258fs*2(1)|p.E258_S260delEDS(1)|p.E258del(1)|p.T256fs*87(1)|p.E258L(1)|p.E258fs*87(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CTGGAGTCTTCCAGTGTGATG	0.587		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.E258K	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,brain,glioma,0,1	TP53	33396	.	82	Substitution - Missense(50)|Substitution - Nonsense(15)|Whole gene deletion(8)|Deletion - Frameshift(5)|Deletion - In frame(2)|Unknown(1)|Complex - insertion inframe(1)	large_intestine(14)|urinary_tract(10)|upper_aerodigestive_tract(7)|haematopoietic_and_lymphoid_tissue(7)|skin(7)|lung(6)|oesophagus(5)|central_nervous_system(4)|breast(4)|ovary(4)|bone(4)|stomach(2)|liver(2)|thyroid(1)|soft_tissue(1)|peritoneum(1)|biliary_tract(1)|endometrium(1)|pancreas(1)	c.G772A	GRCh37	CM900213	TP53	M	rs121912652	.						137	97	111					17																	7577509		2203	4300	6503	SO:0001583	missense	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AGTCTTCCAGTGT	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.772G>A	chr17.hg19:g.7577509C>T	ENSP00000269305:p.Glu258Lys	67.0	1.0		24.0	18.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	19.81	3.896324	0.72639	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D;D	0.99856	-7.21;-7.21;-7.21;-7.21;-7.21;-7.21;-7.21	4.62	3.62	0.41486	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99871	0.9939	M	0.92367	3.3	0.80722	A	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.998;0.999;0.999;0.999;1.0	D	0.96542	0.9401	9	0.87932	D	0	-21.9865	12.6215	0.56605	0.0:0.8318:0.1682:0.0	.	258;258;258;258;258	P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;P53_HUMAN;.;.	K	258;258;258;258;258;258;247;126	ENSP00000410739:E258K;ENSP00000352610:E258K;ENSP00000269305:E258K;ENSP00000398846:E258K;ENSP00000391127:E258K;ENSP00000391478:E258K;ENSP00000425104:E126K	ENSP00000269305:E258K	E	-	1	0	TP53	7518234	1.000000	0.71417	1.000000	0.80357	0.402000	0.30811	7.609000	0.82925	1.266000	0.44231	0.462000	0.41574	GAA	.	.		0.587	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7577509	C	T	7577509	3	4	337	1	0	0	0	0	1	0	0	0	16396	864	30	3	518	3	TP53	17	7577509	Missense_Mutation	SNP	C	TCGA-RC-A7SB-01A-21D-A34Z-10		7577509	73617701	35	46837										
MRPL45	84311	hgsc.bcm.edu	37	chr17	36478418	36478418	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	atgatccctggccctcagctGaaaccagaagaagaatatga	9	10	1	6			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr17:36478418G>C	ENST00000312513.5	+	8	1022	c.861G>C	c.(859-861)ctG>ctC	p.L287L	GPR179_ENST00000584976.1_5'Flank	NM_032351.4	NP_115727.4	Q9BRJ2	RM45_HUMAN	mitochondrial ribosomal protein L45	287						mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	13	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				GCCCTCAGCTGAAACCAGAAG	0.542											OREG0024353	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L287L		Atlas-SNP	.											.	MRPL45	27	.	0			c.G861C						.						67	67	67					17																	36478418		2203	4300	6503	SO:0001819	synonymous_variant	84311	exon8			TCAGCTGAAACCA	BC006235	CCDS11326.1, CCDS74047.1	17q21.2	2014-05-06			ENSG00000174100	ENSG00000278845		"Mitochondrial ribosomal proteins / large subunits"	16651	protein-coding gene	gene with protein product		611850				11551941, 12706105	Standard	XM_006725366		Approved	MGC11321	uc002hpy.3	Q9BRJ2	OTTHUMG00000188489	ENST00000312513.5:c.861G>C	chr17.hg19:g.36478418G>C		51.0	0.0	863	41.0	20.0	NM_032351	A1L436|Q6ZMJ5	Silent	SNP	ENST00000312513.5	hg19	CCDS11326.1																																																																																			.	.		0.542	MRPL45-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256792.3	NM_032351		C	36478418	G	C	36478418	2	2	337	1	0	0	0	0	0	0	0	1	9818	1277	45	4		4	MRPL45	17	36478418	Silent	SNP	G	TCGA-RC-A7SB-01A-21D-A34Z-10	28900909	36478418	44716792	36	46838										
FAM104A	84923	hgsc.bcm.edu	37	chr17	71208818	71208818	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	cactcaattagaaacccaccGcgcagaacgctttgtttcct	6	14	1	2			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr17:71208818G>A	ENST00000403627.3	-	3	382				FAM104A_ENST00000405159.3_Splice_Site_p.A128V|FAM104A_ENST00000583178.1_Intron|FAM104A_ENST00000583024.1_Intron|FAM104A_ENST00000580032.1_Splice_Site_p.A17V|FAM104A_ENST00000581110.1_Intron	NM_032837.2	NP_116226.2	Q969W3	F104A_HUMAN	family with sequence similarity 104, member A											endometrium(1)|kidney(1)|large_intestine(1)|lung(3)	6			LUSC - Lung squamous cell carcinoma(166;0.197)			GAAACCCACCGCGCAGAACGC	0.393																																					p.A128V		Atlas-SNP	.											.	FAM104A	15	.	0			c.C383T						.						145	141	142					17																	71208818		1872	4095	5967	SO:0001627	intron_variant	84923	exon3			CCCACCGCGCAGA	AK027681	CCDS11693.2, CCDS45766.1, CCDS74143.1, CCDS74144.1	17q25.1	2005-12-16			ENSG00000133193	ENSG00000133193			25918	protein-coding gene	gene with protein product							Standard	NM_032837		Approved	FLJ14775	uc002jjj.4	Q969W3	OTTHUMG00000150564	ENST00000403627.3:c.322-2911C>T	chr17.hg19:g.71208818G>A		105.0	0.0		88.0	29.0	NM_001098832	B4E339	Missense_Mutation	SNP	ENST00000403627.3	hg19	CCDS11693.2	.	.	.	.	.	.	.	.	.	.	G	8.869	0.948798	0.18356	.	.	ENSG00000133193	ENST00000405159	T	0.46819	0.86	5.17	-2.07	0.07276	.	.	.	.	.	T	0.33118	0.0852	.	.	.	0.39723	D	0.971497	B	0.15719	0.014	B	0.09377	0.004	T	0.03175	-1.1064	8	0.48119	T	0.1	.	7.2665	0.26232	0.3617:0.1142:0.5241:0.0	.	128	Q969W3-2	.	V	128	ENSP00000384832:A128V	ENSP00000384832:A128V	A	-	2	0	FAM104A	68720413	0.302000	0.24454	0.016000	0.15963	0.653000	0.38743	0.098000	0.15189	-0.849000	0.04158	-1.731000	0.00696	GCG	.	.		0.393	FAM104A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318935.1	NM_032837		A	71208818	G	A	71208818	1	1	337	0	1	0	0	0	0	0	0	0	5390	1101	38	1		1	FAM104A	17	71208818	Intron	SNP	G	TCGA-RC-A7SB-01A-21D-A34Z-10	34730400	71208818	9986392	37	46839										
EXOC7	23265	hgsc.bcm.edu	37	chr17	74085293	74085293	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	aggtcttcttctggtggtgcTcggggatgatgtcggccagc	16	9	3	1			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr17:74085293T>A	ENST00000335146.7	-	9	1216	c.1163A>T	c.(1162-1164)gAg>gTg	p.E388V	EXOC7_ENST00000411744.2_Missense_Mutation_p.E329V|EXOC7_ENST00000405575.4_Missense_Mutation_p.E360V|EXOC7_ENST00000607838.1_Missense_Mutation_p.E360V|EXOC7_ENST00000467929.2_Missense_Mutation_p.E296V|EXOC7_ENST00000589210.1_Missense_Mutation_p.E337V|EXOC7_ENST00000332065.5_Missense_Mutation_p.E306V			Q9UPT5	EXOC7_HUMAN	exocyst complex component 7	388					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	centriolar satellite (GO:0034451)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)				NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	14			LUSC - Lung squamous cell carcinoma(166;0.187)			CTGGTGGTGCTCGGGGATGAT	0.627																																					p.E388V		Atlas-SNP	.											.	EXOC7	47	.	0			c.A1163T						.						105	105	105					17																	74085293		2203	4300	6503	SO:0001583	missense	23265	exon9			TGGTGCTCGGGGA	BC029432	CCDS11741.1, CCDS32738.1, CCDS45781.1, CCDS45782.1, CCDS45784.1, CCDS74164.1	17q25.3	2013-01-22			ENSG00000182473	ENSG00000182473			23214	protein-coding gene	gene with protein product		608163				12477932	Standard	NM_001013839		Approved	EXO70, KIAA1067, YJL085W, Exo70p	uc010wsw.2	Q9UPT5	OTTHUMG00000150720	ENST00000335146.7:c.1163A>T	chr17.hg19:g.74085293T>A	ENSP00000334100:p.Glu388Val	40.0	0.0		35.0	16.0	NM_001145297	B5MC69|B8XXP2|Q8ND93|Q8WV91|Q96FF0|Q9H8C3|Q9H9X3|Q9HA32	Missense_Mutation	SNP	ENST00000335146.7	hg19	CCDS45782.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.758980	0.89843	.	.	ENSG00000182473	ENST00000332065;ENST00000351709;ENST00000405575;ENST00000335146;ENST00000357231;ENST00000425372;ENST00000411744	.	.	.	4.98	4.98	0.66077	Cullin repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.72574	0.3477	M	0.70595	2.14	0.80722	D	1	P;B;D;P;B;P;B	0.57571	0.572;0.24;0.98;0.727;0.03;0.835;0.24	B;B;P;B;B;P;B	0.56088	0.349;0.092;0.791;0.266;0.045;0.65;0.062	T	0.73681	-0.3906	9	0.39692	T	0.17	-34.598	14.6773	0.68989	0.0:0.0:0.0:1.0	.	329;360;296;296;388;306;337	Q9UPT5-5;Q9UPT5-6;B4DJ07;F5H1P1;Q9UPT5;Q9UPT5-2;Q9UPT5-1	.;.;.;.;EXOC7_HUMAN;.;.	V	306;226;360;388;337;296;329	.	ENSP00000333806:E306V	E	-	2	0	EXOC7	71596888	1.000000	0.71417	0.992000	0.48379	0.935000	0.57460	7.571000	0.82399	1.864000	0.54056	0.455000	0.32223	GAG	.	.		0.627	EXOC7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000319768.2	NM_015219		A	74085293	T	A	74085293	3	1	337	1	0	0	0	0	1	0	0	0	5312	1551	54	4	1092	4	EXOC7	17	74085293	Missense_Mutation	SNP	T	TCGA-RC-A7SB-01A-21D-A34Z-10	2876475	74085293	7109917	38	46840										
MIB1	57534	hgsc.bcm.edu	37	chr18	19359600	19359600	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	caactggaactgtttgtggcAttgatgaagatcatgacatt	10	6	1	4			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr18:19359600A>T	ENST00000261537.6	+	6	1126	c.862A>T	c.(862-864)Att>Ttt	p.I288F	AC091038.1_ENST00000582102.1_RNA|MIB1_ENST00000578646.1_3'UTR	NM_020774.2	NP_065825.1	Q86YT6	MIB1_HUMAN	mindbomb E3 ubiquitin protein ligase 1	288					blood vessel development (GO:0001568)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|negative regulation of neuron differentiation (GO:0045665)|neural tube formation (GO:0001841)|Notch signaling pathway (GO:0007219)|positive regulation of endocytosis (GO:0045807)|somitogenesis (GO:0001756)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(13)|ovary(5)	27			STAD - Stomach adenocarcinoma(5;0.212)			TGTTTGTGGCATTGATGAAGA	0.378																																					p.I288F		Atlas-SNP	.											.	MIB1	87	.	0			c.A862T						.						303	266	279					18																	19359600		2203	4300	6503	SO:0001583	missense	57534	exon6			TGTGGCATTGATG	AB037744	CCDS11871.1	18q11.2	2014-09-17	2012-02-23		ENSG00000101752	ENSG00000101752		"Zinc fingers, ZZ-type", "Ankyrin repeat domain containing"	21086	protein-coding gene	gene with protein product		608677	"mindbomb homolog 1 (Drosophila)"				Standard	NM_020774		Approved	DIP-1, MIB, KIAA1323, ZZANK2, ZZZ6	uc002ktq.3	Q86YT6	OTTHUMG00000131753	ENST00000261537.6:c.862A>T	chr18.hg19:g.19359600A>T	ENSP00000261537:p.Ile288Phe	180.0	0.0		149.0	54.0	NM_020774	B0YJ38|Q2TB37|Q68D01|Q6YI51|Q8NBY0|Q8TCB5|Q8TCL7|Q9P2M3	Missense_Mutation	SNP	ENST00000261537.6	hg19	CCDS11871.1	.	.	.	.	.	.	.	.	.	.	A	19.31	3.802349	0.70682	.	.	ENSG00000101752	ENST00000261537	T	0.44482	0.92	4.65	4.65	0.58169	.	0.000000	0.85682	D	0.000000	T	0.58395	0.2119	M	0.84326	2.69	0.80722	D	1	P	0.40431	0.717	P	0.49047	0.599	T	0.65335	-0.6193	10	0.62326	D	0.03	-13.8232	14.365	0.66801	1.0:0.0:0.0:0.0	.	288	Q86YT6	MIB1_HUMAN	F	288	ENSP00000261537:I288F	ENSP00000261537:I288F	I	+	1	0	MIB1	17613598	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	9.279000	0.95777	1.869000	0.54173	0.240000	0.17902	ATT	.	.		0.378	MIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254675.1	NM_020774		T	19359600	A	T	19359600	3	4	337	1	0	0	0	0	1	0	0	0	9575	217	8	4	884	4	MIB1	18	19359600	Missense_Mutation	SNP	A	TCGA-RC-A7SB-01A-21D-A34Z-10		19359600	58717648	39	46841										
CDH7	1005	hgsc.bcm.edu	37	chr18	63526260	63526260	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	ggactatgagaccaccgtctGtgaaaatgcccagccggggc	13	12	1	2			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr18:63526260G>T	ENST00000397968.2	+	9	1898	c.1472G>T	c.(1471-1473)tGt>tTt	p.C491F	CDH7_ENST00000323011.3_Missense_Mutation_p.C491F|CDH7_ENST00000536984.2_Missense_Mutation_p.C491F	NM_004361.2	NP_004352.2	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2	491	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(43)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	80		Esophageal squamous(42;0.129)				ACCACCGTCTGTGAAAATGCC	0.438																																					p.C491F		Atlas-SNP	.											.	CDH7	362	.	0			c.G1472T						.						76	74	75					18																	63526260		2203	4300	6503	SO:0001583	missense	1005	exon9			CCGTCTGTGAAAA	AB035301	CCDS11993.1	18q22.1	2010-01-26			ENSG00000081138	ENSG00000081138		"Cadherins / Major cadherins"	1766	protein-coding gene	gene with protein product		605806				9615235	Standard	NM_033646		Approved		uc002ljz.3	Q9ULB5	OTTHUMG00000132800	ENST00000397968.2:c.1472G>T	chr18.hg19:g.63526260G>T	ENSP00000381058:p.Cys491Phe	164.0	0.0		127.0	49.0	NM_004361	Q9H157	Missense_Mutation	SNP	ENST00000397968.2	hg19	CCDS11993.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.575129	0.86542	.	.	ENSG00000081138	ENST00000323011;ENST00000536984;ENST00000397966;ENST00000397968	T;T;T	0.53423	0.62;0.62;0.62	5.32	5.32	0.75619	Cadherin (3);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.72293	0.3442	M	0.82056	2.57	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	T	0.75880	-0.3161	10	0.87932	D	0	.	19.347	0.94367	0.0:0.0:1.0:0.0	.	491;491	F5H5X9;Q9ULB5	.;CADH7_HUMAN	F	491	ENSP00000319166:C491F;ENSP00000443030:C491F;ENSP00000381058:C491F	ENSP00000319166:C491F	C	+	2	0	CDH7	61677240	1.000000	0.71417	0.961000	0.40146	0.978000	0.69477	9.666000	0.98612	2.648000	0.89879	0.467000	0.42956	TGT	.	.		0.438	CDH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256217.2	NM_033646		T	63526260	G	T	63526260	3	4	337	1	0	0	0	0	1	0	0	0	3117	1377	48	3	1502	3	CDH7	18	63526260	Missense_Mutation	SNP	G	TCGA-RC-A7SB-01A-21D-A34Z-10	44166660	63526260	14550988	40	46842										
SIRT2	22933	hgsc.bcm.edu	37	chr19	39374291	39374291	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	catccagcttagcgggtattCgtgccggcagctggcgctga	14	12	0	1	rs200953200		TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr19:39374291C>T	ENST00000249396.7	-	9	908	c.607G>A	c.(607-609)Gaa>Aaa	p.E203K	SIRT2_ENST00000392081.2_Missense_Mutation_p.E166K|SIRT2_ENST00000358931.5_Missense_Mutation_p.E203K	NM_012237.3	NP_036369.2	Q8IXJ6	SIR2_HUMAN	sirtuin 2	203	Deacetylase sirtuin-type. {ECO:0000255|PROSITE-ProRule:PRU00236}.				autophagy (GO:0006914)|cellular lipid catabolic process (GO:0044242)|cellular response to caloric restriction (GO:0061433)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cellular response to hypoxia (GO:0071456)|cellular response to molecule of bacterial origin (GO:0071219)|cellular response to oxidative stress (GO:0034599)|chromatin silencing (GO:0006342)|chromatin silencing at rDNA (GO:0000183)|chromatin silencing at telomere (GO:0006348)|gene silencing (GO:0016458)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|innate immune response (GO:0045087)|meiotic nuclear division (GO:0007126)|mitotic nuclear division (GO:0007067)|myelination in peripheral nervous system (GO:0022011)|negative regulation of autophagy (GO:0010507)|negative regulation of cell proliferation (GO:0008285)|negative regulation of defense response to bacterium (GO:1900425)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of oligodendrocyte progenitor proliferation (GO:0070446)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of attachment of spindle microtubules to kinetochore (GO:0051987)|positive regulation of cell division (GO:0051781)|positive regulation of DNA binding (GO:0043388)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of meiosis (GO:0045836)|positive regulation of oocyte maturation (GO:1900195)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process involved in cellular response to hypoxia (GO:2000777)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ADP-ribosylation (GO:0006471)|protein deacetylation (GO:0006476)|protein kinase B signaling (GO:0043491)|regulation of cell cycle (GO:0051726)|regulation of exit from mitosis (GO:0007096)|regulation of myelination (GO:0031641)|regulation of phosphorylation (GO:0042325)|response to redox state (GO:0051775)|ripoptosome assembly involved in necroptotic process (GO:1901026)|substantia nigra development (GO:0021762)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)	centriole (GO:0005814)|centrosome (GO:0005813)|chromatin silencing complex (GO:0005677)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|glial cell projection (GO:0097386)|juxtaparanode region of axon (GO:0044224)|lateral loop (GO:0043219)|meiotic spindle (GO:0072687)|microtubule (GO:0005874)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|myelin sheath (GO:0043209)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|spindle (GO:0005819)	chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (GO:0017136)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|NAD-dependent protein deacetylase activity (GO:0034979)|protein deacetylase activity (GO:0033558)|transcription factor binding (GO:0008134)|tubulin deacetylase activity (GO:0042903)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(5)|skin(1)	9	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00125)|LUSC - Lung squamous cell carcinoma(53;0.00191)			AGCGGGTATTCGTGCCGGCAG	0.617																																					p.E203K		Atlas-SNP	.											.	SIRT2	29	.	0			c.G607A						.						88	72	78					19																	39374291		2203	4300	6503	SO:0001583	missense	22933	exon9			GGTATTCGTGCCG	AF083107	CCDS12523.1, CCDS46069.1, CCDS74361.1	19q13	2010-06-25	2010-06-25		ENSG00000068903	ENSG00000068903			10886	protein-coding gene	gene with protein product		604480	"sirtuin (silent mating type information regulation 2, S.cerevisiae, homolog) 2", "sirtuin (silent mating type information regulation 2 homolog) 2 (S. cerevisiae)"	SIR2L		10393250, 10381378	Standard	NM_012237		Approved		uc002ojt.2	Q8IXJ6	OTTHUMG00000150480	ENST00000249396.7:c.607G>A	chr19.hg19:g.39374291C>T	ENSP00000249396:p.Glu203Lys	64.0	0.0		36.0	15.0	NM_012237	A8K3V1|B2RB45|O95889|Q924Y7|Q9P0G8|Q9UNT0|Q9Y6E9|U5TP13	Missense_Mutation	SNP	ENST00000249396.7	hg19	CCDS12523.1	.	.	.	.	.	.	.	.	.	.	C	13.20	2.165115	0.38217	.	.	ENSG00000068903	ENST00000249396;ENST00000392081;ENST00000358931;ENST00000456703;ENST00000414941;ENST00000407552	T;T;T;T;T	0.39406	1.08;1.08;1.08;1.08;2.29	4.31	4.31	0.51392	.	0.197758	0.40554	N	0.001067	T	0.23370	0.0565	N	0.16266	0.395	0.53005	D	0.999969	B;B;B;B	0.32409	0.196;0.125;0.37;0.24	B;B;B;B	0.27262	0.015;0.008;0.078;0.01	T	0.06625	-1.0816	10	0.25106	T	0.35	-9.9569	10.3892	0.44158	0.0:0.9032:0.0:0.0968	.	203;166;203;183	Q8IXJ6-4;Q8IXJ6-2;Q8IXJ6;Q8IXJ6-3	.;.;SIRT2_HUMAN;.	K	203;166;203;188;166;166	ENSP00000249396:E203K;ENSP00000375931:E166K;ENSP00000351809:E203K;ENSP00000404309:E166K;ENSP00000385146:E166K	ENSP00000249396:E203K	E	-	1	0	SIRT2	44066131	0.960000	0.32886	0.736000	0.30914	0.274000	0.26718	2.146000	0.42216	2.405000	0.81733	0.491000	0.48974	GAA	.	.		0.617	SIRT2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318278.1			T	39374291	C	T	39374291	3	4	337	1	0	0	0	0	1	0	0	0	14353	893	31	1	594	1	SIRT2	19	39374291	Missense_Mutation	SNP	C	TCGA-RC-A7SB-01A-21D-A34Z-10		39374291	19754692	41	46843										
PLD3	23646	hgsc.bcm.edu	37	chr19	40872766	40872766	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	ctgtttctatgggaatacggCgacttgcatctctttgggcc	11	10	2	0	rs375652785		TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr19:40872766C>T	ENST00000409587.1	+	5	586	c.189C>T	c.(187-189)ggC>ggT	p.G63G	PLD3_ENST00000356508.5_Silent_p.G63G|PLD3_ENST00000409419.1_Silent_p.G63G|PLD3_ENST00000409735.4_Silent_p.G63G|PLD3_ENST00000409281.1_Silent_p.G63G			Q8IV08	PLD3_HUMAN	phospholipase D family, member 3	63					cell death (GO:0008219)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phospholipase D activity (GO:0004630)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	20			Lung(22;0.000636)|LUSC - Lung squamous cell carcinoma(20;0.00248)			GGGAATACGGCGACTTGCATC	0.627																																					p.G63G		Atlas-SNP	.											.	PLD3	71	.	0			c.C189T						.	C	,	1,4405	2.1+/-5.4	0,1,2202	73	69	71		189,189	-5.5	0.9	19		71	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PLD3	NM_001031696.2,NM_012268.2	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	63/491,63/491	40872766	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	23646	exon5			ATACGGCGACTTG	BC000553	CCDS33027.1	19q13.2	2014-03-14	2005-05-20		ENSG00000105223	ENSG00000105223			17158	protein-coding gene	gene with protein product		615698	"phospholipase D3"			9140189, 15794758	Standard	XM_005258704		Approved	HU-K4	uc002onj.4	Q8IV08	OTTHUMG00000152736	ENST00000409587.1:c.189C>T	chr19.hg19:g.40872766C>T		49.0	0.0		33.0	16.0	NM_012268	Q92853|Q9BW87	Silent	SNP	ENST00000409587.1	hg19	CCDS33027.1																																																																																			.	.		0.627	PLD3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327721.1	NM_012268		T	40872766	C	T	40872766	2	4	337	1	0	0	0	0	0	0	0	1	12056	755	27	1		1	PLD3	19	40872766	Silent	SNP	C	TCGA-RC-A7SB-01A-21D-A34Z-10	1498475	40872766	18256217	42	46844										
CEACAM8	1088	hgsc.bcm.edu	37	chr19	43098033	43098033	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	tgagcagtggtgggcgggttCcagaaggtgaaaagtgaggc	19	5	0	4			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr19:43098033C>A	ENST00000244336.5	-	2	185	c.84G>T	c.(82-84)tgG>tgT	p.W28C	LIPE-AS1_ENST00000594688.1_RNA|CEACAM8_ENST00000599005.1_Intron|LIPE-AS1_ENST00000594624.2_RNA	NM_001816.3	NP_001807.2	P31997	CEAM8_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 8	28					immune response (GO:0006955)	anchored component of membrane (GO:0031225)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	16		Prostate(69;0.00899)				TGGGCGGGTTCCAGAAGGTGA	0.502																																					p.W28C		Atlas-SNP	.											.	CEACAM8	44	.	0			c.G84T						.						105	98	100					19																	43098033		2203	4300	6503	SO:0001583	missense	1088	exon2			CGGGTTCCAGAAG	D90064	CCDS12610.1	19q13.2	2013-01-29			ENSG00000124469	ENSG00000124469		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1820	protein-coding gene	gene with protein product		615747		CGM6		2208113, 2306228	Standard	NM_001816		Approved	CD66b	uc002oud.2	P31997	OTTHUMG00000151124	ENST00000244336.5:c.84G>T	chr19.hg19:g.43098033C>A	ENSP00000244336:p.Trp28Cys	42.0	0.0		44.0	19.0	NM_001816	O60399|Q16574	Missense_Mutation	SNP	ENST00000244336.5	hg19	CCDS12610.1	.	.	.	.	.	.	.	.	.	.	c	13.17	2.157915	0.38119	.	.	ENSG00000124469	ENST00000244336	T	0.22336	1.96	1.63	1.63	0.23807	.	.	.	.	.	T	0.35740	0.0942	M	0.66939	2.045	0.20638	N	0.999872	D	0.56035	0.974	P	0.60117	0.869	T	0.07462	-1.0771	9	0.87932	D	0	.	6.707	0.23257	0.0:1.0:0.0:0.0	.	28	P31997	CEAM8_HUMAN	C	28	ENSP00000244336:W28C	ENSP00000244336:W28C	W	-	3	0	CEACAM8	47789873	0.516000	0.26218	0.146000	0.22360	0.618000	0.37518	1.947000	0.40293	1.205000	0.43262	0.313000	0.20887	TGG	.	.		0.502	CEACAM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321430.1			A	43098033	C	A	43098033	3	1	337	1	0	0	0	0	1	0	0	0	3200	856	30	3	981	3	CEACAM8	19	43098033	Missense_Mutation	SNP	C	TCGA-RC-A7SB-01A-21D-A34Z-10	2225267	43098033	16030950	43	46845										
PSG9	5678	hgsc.bcm.edu	37	chr19	43762554	43762554	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	agcaggacaagtcgaggtttTctcctgaacggtaataggtg	13	7	1	1			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr19:43762554T>C	ENST00000270077.3	-	5	1139	c.1043A>G	c.(1042-1044)gAa>gGa	p.E348G	PSG9_ENST00000418820.2_Missense_Mutation_p.E255G|PSG9_ENST00000443718.3_Missense_Mutation_p.E255G|PSG9_ENST00000244293.7_Missense_Mutation_p.E255G|PSG9_ENST00000593948.1_Missense_Mutation_p.E255G|PSG9_ENST00000596730.1_Missense_Mutation_p.E162G|PSG9_ENST00000291752.5_Missense_Mutation_p.E162G	NM_002784.3	NP_002775.3	Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 9	348	Ig-like C2-type 3.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Prostate(69;0.00682)				GTCGAGGTTTTCTCCTGAACG	0.453																																					p.E348G		Atlas-SNP	.											.	PSG9	77	.	0			c.A1043G						.						134	163	153					19																	43762554		2137	4278	6415	SO:0001583	missense	5678	exon5			AGGTTTTCTCCTG	M34481	CCDS12618.1	19q13.2	2013-01-29			ENSG00000183668	ENSG00000183668		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9526	protein-coding gene	gene with protein product		176398		PSG11		7806221	Standard	XM_005259076		Approved	PSGII	uc002owd.4	Q00887	OTTHUMG00000182826	ENST00000270077.3:c.1043A>G	chr19.hg19:g.43762554T>C	ENSP00000270077:p.Glu348Gly	32.0	0.0		20.0	13.0	NM_002784	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Missense_Mutation	SNP	ENST00000270077.3	hg19	CCDS12618.1	.	.	.	.	.	.	.	.	.	.	N	10.10	1.257419	0.22965	.	.	ENSG00000183668	ENST00000270077;ENST00000291752;ENST00000443718;ENST00000435220;ENST00000244293	T;T;T;T	0.12879	2.64;2.64;2.64;2.64	1.58	-2.54	0.06307	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.19446	0.0467	L	0.43757	1.38	0.09310	N	1	P;D;P;P;B;P	0.53745	0.729;0.962;0.87;0.951;0.001;0.602	P;D;P;P;B;P	0.64410	0.791;0.925;0.654;0.823;0.053;0.73	T	0.13872	-1.0493	9	0.59425	D	0.04	.	2.2184	0.03966	0.2161:0.0:0.4831:0.3008	.	255;204;255;162;348;348	E7EW65;Q15225;Q15227;G3XAA7;Q6LEU7;Q00887	.;.;.;.;.;PSG9_HUMAN	G	348;162;255;309;255	ENSP00000270077:E348G;ENSP00000291752:E162G;ENSP00000396753:E255G;ENSP00000244293:E255G	ENSP00000244293:E255G	E	-	2	0	PSG9	48454394	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.759000	0.04761	-0.634000	0.05538	0.163000	0.16589	GAA	.	.		0.453	PSG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323065.1	NM_002784		C	43762554	T	C	43762554	3	2	337	1	0	0	0	0	1	0	0	0	12674	1783	62	2	245	2	PSG9	19	43762554	Missense_Mutation	SNP	T	TCGA-RC-A7SB-01A-21D-A34Z-10	664521	43762554	15366429	44	46846										
ZNF677	342926	hgsc.bcm.edu	37	chr19	53740390	53740390	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	tgtattttctggtgtctagtGaggtttgcaaattgggtaaa	12	3	2	1			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr19:53740390G>C	ENST00000598513.1	-	5	1740	c.1590C>G	c.(1588-1590)ctC>ctG	p.L530L	ZNF677_ENST00000333952.4_Silent_p.L530L	NM_182609.2	NP_872415.1	Q86XU0	ZN677_HUMAN	zinc finger protein 677	530					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(13)|lung(6)|ovary(1)|pancreas(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				GBM - Glioblastoma multiforme(134;0.00352)		GGTGTCTAGTGAGGTTTGCAA	0.333																																					p.L530L		Atlas-SNP	.											.	ZNF677	94	.	0			c.C1590G						.						134	127	130					19																	53740390		2203	4299	6502	SO:0001819	synonymous_variant	342926	exon5			TCTAGTGAGGTTT	BC050038	CCDS12861.1	19q13.42	2013-01-08				ENSG00000197928		"Zinc fingers, C2H2-type", "-"	28730	protein-coding gene	gene with protein product	"hypothetical protein MGC48625"					12477932	Standard	NM_182609		Approved	MGC48625	uc002qbg.1	Q86XU0		ENST00000598513.1:c.1590C>G	chr19.hg19:g.53740390G>C		229.0	0.0		157.0	68.0	NM_182609		Silent	SNP	ENST00000598513.1	hg19	CCDS12861.1																																																																																			.	.		0.333	ZNF677-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464189.1	NM_182609		C	53740390	G	C	53740390	2	2	337	1	0	0	0	0	0	0	0	1	18099	1277	45	4		4	ZNF677	19	53740390	Silent	SNP	G	TCGA-RC-A7SB-01A-21D-A34Z-10	9977836	53740390	5388593	45	46847										
NLRP12	91662	hgsc.bcm.edu	37	chr19	54307234	54307234	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	ccgtagtctgcagactgggtGcctcagtccctggcatagta	12	12	2	1			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr19:54307234G>T	ENST00000324134.6	-	6	2725	c.2557C>A	c.(2557-2559)Cac>Aac	p.H853N	NLRP12_ENST00000354278.3_Missense_Mutation_p.H853N|NLRP12_ENST00000535162.1_Missense_Mutation_p.H853N|NLRP12_ENST00000345770.5_Missense_Mutation_p.H854N|NLRP12_ENST00000391773.1_Missense_Mutation_p.H854N|NLRP12_ENST00000391772.1_Missense_Mutation_p.H854N|NLRP12_ENST00000351894.4_Missense_Mutation_p.H853N|NLRP12_ENST00000391775.3_Missense_Mutation_p.H853N	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	853					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to cytokine stimulus (GO:0071345)|dendritic cell migration (GO:0036336)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of signal transduction (GO:0009968)|negative regulation of Toll signaling pathway (GO:0045751)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of MHC class I biosynthetic process (GO:0045345)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of interleukin-18 biosynthetic process (GO:0045381)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)			NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(36)|ovary(5)|pancreas(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	80	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		CAGACTGGGTGCCTCAGTCCC	0.478																																					p.C853S		Atlas-SNP	.											.	NLRP12	236	.	0			c.T2557A						.						85	70	75					19																	54307234		2203	4300	6503	SO:0001583	missense	91662	exon6			CTGGGTGCCTCAG	AY095146	CCDS12864.1, CCDS62784.1, CCDS62785.1	19q13.42	2014-09-17	2006-12-08	2006-12-08	ENSG00000142405	ENSG00000142405		"Nucleotide-binding domain and leucine rich repeat containing"	22938	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 12"	609648	"NACHT, leucine rich repeat and PYD containing 12"	NALP12		12563287, 12019269	Standard	NM_001277129		Approved	RNO2, PYPAF7, Monarch1, PAN6, CLR19.3	uc002qcj.5	P59046	OTTHUMG00000060776	ENST00000324134.6:c.2557C>A	chr19.hg19:g.54307234G>T	ENSP00000319377:p.His853Asn	50.0	0.0		30.0	10.0	NM_144687	A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Missense_Mutation	SNP	ENST00000324134.6	hg19	CCDS12864.1	.	.	.	.	.	.	.	.	.	.	G	11.08	1.533586	0.27387	.	.	ENSG00000142405	ENST00000324134;ENST00000535162;ENST00000351894;ENST00000354278;ENST00000358661;ENST00000391775;ENST00000391773;ENST00000345770;ENST00000391772	T;T;T;T;T;T;T	0.49432	1.05;1.05;0.78;0.78;1.05;1.05;0.78	4.52	2.3	0.28687	.	0.458810	0.15793	N	0.244365	T	0.40909	0.1136	L	0.45698	1.435	0.09310	N	1	B;B;B;B;B	0.20368	0.009;0.044;0.005;0.009;0.006	B;B;B;B;B	0.24155	0.012;0.051;0.011;0.012;0.023	T	0.39057	-0.9632	10	0.56958	D	0.05	.	10.1919	0.43032	0.0:0.0:0.6431:0.3569	.	854;136;853;853;853	F2Z321;P59046-5;A8K407;A8MTQ2;P59046	.;.;.;.;NAL12_HUMAN	N	853;853;853;853;136;853;854;854;854	ENSP00000319377:H853N;ENSP00000438030:H853N;ENSP00000340473:H853N;ENSP00000346231:H853N;ENSP00000375655:H853N;ENSP00000375653:H854N;ENSP00000375652:H854N	ENSP00000319377:H853N	H	-	1	0	NLRP12	58999046	0.167000	0.22975	0.014000	0.15608	0.640000	0.38277	1.890000	0.39728	0.576000	0.29452	0.442000	0.29010	CAC	.	.		0.478	NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000134340.1	NM_144687		T	54307234	G	T	54307234	3	4	337	1	0	0	0	0	1	0	0	0	10483	1319	46	3	648	3	NLRP12	19	54307234	Missense_Mutation	SNP	G	TCGA-RC-A7SB-01A-21D-A34Z-10	566844	54307234	4821749	46	46848										
TCF15	6939	hgsc.bcm.edu	37	chr20	585251	585251	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	aggctcatctccgtggccctCgaaggggggccacccccctc	12	18	2	0			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr20:585251C>A	ENST00000246080.3	-	2	744	c.584G>T	c.(583-585)cGa>cTa	p.R195L		NM_004609.3	NP_004600.2	Q12870	TCF15_HUMAN	transcription factor 15 (basic helix-loop-helix)	195					death (GO:0016265)|ear development (GO:0043583)|eating behavior (GO:0042755)|establishment of epithelial cell apical/basal polarity (GO:0045198)|mesenchymal to epithelial transition (GO:0060231)|mesoderm development (GO:0007498)|muscle organ morphogenesis (GO:0048644)|neuromuscular process controlling posture (GO:0050884)|paraxial mesoderm development (GO:0048339)|post-anal tail morphogenesis (GO:0036342)|regulation of gene expression involved in extracellular matrix organization (GO:1901311)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|respiratory system process (GO:0003016)|skeletal system morphogenesis (GO:0048705)|skin development (GO:0043588)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|lung(2)|prostate(1)	4		Breast(17;0.231)				CCGTGGCCCTCGAAGGGGGGC	0.642																																					p.R195L		Atlas-SNP	.											.	TCF15	6	.	0			c.G584T						.						11	12	12					20																	585251		2121	4169	6290	SO:0001583	missense	6939	exon2			GGCCCTCGAAGGG		CCDS33432.1	20p13	2013-05-21			ENSG00000125878	ENSG00000125878		"Basic helix-loop-helix proteins"	11627	protein-coding gene	gene with protein product		601010				8825648, 8041747	Standard	NM_004609		Approved	EC2, PARAXIS, bHLHa40	uc002wdz.3	Q12870	OTTHUMG00000031640	ENST00000246080.3:c.584G>T	chr20.hg19:g.585251C>A	ENSP00000246080:p.Arg195Leu	82.0	0.0		80.0	36.0	NM_004609	Q9NQQ1	Missense_Mutation	SNP	ENST00000246080.3	hg19	CCDS33432.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.190772	0.78789	.	.	ENSG00000125878	ENST00000246080	D	0.96265	-3.96	5.08	4.13	0.48395	.	0.000000	0.64402	D	0.000003	D	0.96975	0.9012	L	0.55481	1.735	0.30769	N	0.743195	D	0.63880	0.993	D	0.67725	0.953	D	0.95442	0.8526	10	0.72032	D	0.01	-1.0614	13.52	0.61561	0.0:0.8441:0.1559:0.0	.	195	Q12870	TCF15_HUMAN	L	195	ENSP00000246080:R195L	ENSP00000246080:R195L	R	-	2	0	TCF15	533251	1.000000	0.71417	0.996000	0.52242	0.988000	0.76386	4.235000	0.58666	1.489000	0.48450	0.655000	0.94253	CGA	.	.		0.642	TCF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077475.2	NM_004609		A	585251	C	A	585251	3	1	337	1	0	0	0	0	1	0	0	0	15703	884	31	1	19	1	TCF15	20	585251	Missense_Mutation	SNP	C	TCGA-RC-A7SB-01A-21D-A34Z-10		585251	62440269	47	46849										
SLC4A11	83959	hgsc.bcm.edu	37	chr20	3209657	3209657	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	taggcagtgcccttcaccagCctgcagcagacgggcactcg	12	15	1	1			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr20:3209657C>A	ENST00000380056.3	-	16	2114	c.2067G>T	c.(2065-2067)agG>agT	p.R689S	SLC4A11_ENST00000488544.1_5'UTR|SLC4A11_ENST00000380059.3_Splice_Site_p.R716S|SLC4A11_ENST00000539553.2_Splice_Site_p.R673S	NM_032034.3	NP_114423.1	Q8NBS3	S4A11_HUMAN	solute carrier family 4, sodium borate transporter, member 11	689	Membrane (bicarbonate transporter).				bicarbonate transport (GO:0015701)|borate transmembrane transport (GO:0035445)|borate transport (GO:0046713)|cellular cation homeostasis (GO:0030003)|fluid transport (GO:0042044)|proton transport (GO:0015992)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	bicarbonate transmembrane transporter activity (GO:0015106)|borate transmembrane transporter activity (GO:0046715)|hydrogen ion channel activity (GO:0015252)|inorganic anion exchanger activity (GO:0005452)|protein dimerization activity (GO:0046983)|sodium channel activity (GO:0005272)|symporter activity (GO:0015293)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(4)|soft_tissue(1)|urinary_tract(1)	40						CCTTCACCAGCCTGCAGCAGA	0.657																																					p.R716S	NSCLC(190;922 2139 10266 10292 38692)	Atlas-SNP	.											.	SLC4A11	188	.	0			c.G2148T						.						85	71	76					20																	3209657		2202	4300	6502	SO:0001630	splice_region_variant	83959	exon17			CACCAGCCTGCAG	AF336127	CCDS13052.1, CCDS54445.1, CCDS54446.1	20p13	2014-02-14	2007-08-03		ENSG00000088836	ENSG00000088836		"Solute carriers"	16438	protein-coding gene	gene with protein product		610206	"corneal endothelial dystrophy 2 (autosomal recessive)", "solute carrier family 4, sodium bicarbonate transporter-like, member 11", "corneal dystrophy and perceptive deafness 1"	CHED2, CDPD1		10843999, 11302728, 16767101	Standard	NM_001174089		Approved	dJ794I6.2, BTR1, NaBC1, FECD4	uc010zqe.2	Q8NBS3	OTTHUMG00000031740	ENST00000380056.3:c.2067-1G>T	chr20.hg19:g.3209657C>A		18.0	0.0		21.0	10.0	NM_001174090	B4DKC8|B4DKX9|G3V1M3|Q2TB62|Q2TB63|Q9BXF4|Q9NTW9	Missense_Mutation	SNP	ENST00000380056.3	hg19	CCDS13052.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.085299	0.76642	.	.	ENSG00000088836	ENST00000380059;ENST00000380056;ENST00000539553	T;T;T	0.78924	-1.22;-1.22;-1.22	4.93	2.99	0.34606	Bicarbonate transporter, C-terminal (1);	0.096978	0.64402	D	0.000001	D	0.82600	0.5072	M	0.69185	2.1	0.80722	D	1	P;P;P	0.49635	0.909;0.926;0.844	P;P;P	0.56612	0.701;0.802;0.73	T	0.82961	-0.0197	10	0.87932	D	0	.	11.3086	0.49351	0.0:0.8502:0.0:0.1498	.	673;716;689	G3V1M3;B4DKC8;Q8NBS3	.;.;S4A11_HUMAN	S	716;689;673	ENSP00000369399:R716S;ENSP00000369396:R689S;ENSP00000441370:R673S	ENSP00000369396:R689S	R	-	3	2	SLC4A11	3157657	1.000000	0.71417	0.999000	0.59377	0.947000	0.59692	4.877000	0.63086	0.606000	0.29965	0.462000	0.41574	AGG	.	.		0.657	SLC4A11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077728.1		Missense_Mutation	A	3209657	C	A	3209657	5	1	337	1	0	0	0	0	0	0	1	0	14667	753	26	3	624	3	SLC4A11	20	3209657	Splice_Site	SNP	C	TCGA-RC-A7SB-01A-21D-A34Z-10	2624406	3209657	59815863	48	46850										
C20orf4	25980	hgsc.bcm.edu	37	chr20	34828481	34828481	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	agataaccaagcacagcatgGacctgagctatgccctggag	11	11	0	2			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr20:34828481G>A	ENST00000373932.3	+	2	1037	c.691G>A	c.(691-693)Gac>Aac	p.D231N	AAR2_ENST00000320849.4_Missense_Mutation_p.D231N|AAR2_ENST00000397286.3_Missense_Mutation_p.D231N	NM_015511.3	NP_056326.2	Q9Y312	AAR2_HUMAN	AAR2 splicing factor homolog (S. cerevisiae)	231																	GCACAGCATGGACCTGAGCTA	0.592																																					p.D231N		Atlas-SNP	.											.	.	.	.	0			c.G691A						.						36	36	36					20																	34828481		2203	4300	6503	SO:0001583	missense	25980	exon2			AGCATGGACCTGA		CCDS13273.1	20q11.23	2012-07-20	2012-07-20	2012-07-20	ENSG00000131043	ENSG00000131043			15886	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 4"	C20orf4			Standard	NM_015511		Approved	bA234K24.2	uc002xfc.3	Q9Y312	OTTHUMG00000032380	ENST00000373932.3:c.691G>A	chr20.hg19:g.34828481G>A	ENSP00000363043:p.Asp231Asn	55.0	0.0		40.0	13.0	NM_001271874	E1P5S7|Q9H4F9|Q9P1P3|Q9UFK9	Missense_Mutation	SNP	ENST00000373932.3	hg19	CCDS13273.1	.	.	.	.	.	.	.	.	.	.	G	32	5.184603	0.94885	.	.	ENSG00000131043	ENST00000397286;ENST00000320849;ENST00000373932	T;T;T	0.70045	-0.45;-0.45;-0.45	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	D	0.84862	0.5566	M	0.89353	3.025	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.87452	0.2402	10	0.87932	D	0	.	17.8963	0.88890	0.0:0.0:1.0:0.0	.	231;231	A2A2Q9;Q9Y312	.;CT004_HUMAN	N	231	ENSP00000380455:D231N;ENSP00000313674:D231N;ENSP00000363043:D231N	ENSP00000313674:D231N	D	+	1	0	C20orf4	34291895	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.959000	0.93110	2.775000	0.95449	0.655000	0.94253	GAC	.	.		0.592	AAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079001.2	NM_015511		A	34828481	G	A	34828481	3	1	337	1	0	0	0	0	1	0	0	0	2113	1174	41	3	693	3	C20orf4	20	34828481	Missense_Mutation	SNP	G	TCGA-RC-A7SB-01A-21D-A34Z-10	31618824	34828481	28197039	49	46851										
NLGN3	54413	hgsc.bcm.edu	37	chrX	70389592	70389592	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	ggccttcgctgccctctactAccgtaaggacaaacggcgcc	10	16	1	0			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chrX:70389592A>G	ENST00000358741.3	+	8	2495	c.2192A>G	c.(2191-2193)tAc>tGc	p.Y731C	NLGN3_ENST00000536169.1_Missense_Mutation_p.Y691C|NLGN3_ENST00000476589.1_3'UTR|NLGN3_ENST00000374051.3_Missense_Mutation_p.Y711C	NM_181303.1	NP_851820.1	Q9NZ94	NLGN3_HUMAN	neuroligin 3	731					adult behavior (GO:0030534)|axon extension (GO:0048675)|learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|oligodendrocyte differentiation (GO:0048709)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor-mediated endocytosis (GO:0006898)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term synaptic potentiation (GO:1900271)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of synaptic transmission (GO:0050804)|regulation of terminal button organization (GO:2000331)|rhythmic synaptic transmission (GO:0060024)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse organization (GO:0050808)|visual learning (GO:0008542)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|endocytic vesicle (GO:0030139)|excitatory synapse (GO:0060076)|integral component of plasma membrane (GO:0005887)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)			biliary_tract(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	37	Renal(35;0.156)					GCCCTCTACTACCGTAAGGAC	0.642																																					p.Y731C	Esophageal Squamous(103;760 1488 16849 22250 40351)	Atlas-SNP	.											.	NLGN3	159	.	0			c.A2192G						.						28	25	26					X																	70389592		2203	4300	6503	SO:0001583	missense	54413	exon8			TCTACTACCGTAA	AB040913	CCDS14407.1, CCDS55441.1, CCDS55442.1	Xq13.1	2008-08-01			ENSG00000196338	ENSG00000196338			14289	protein-coding gene	gene with protein product		300336				10767552, 10819331	Standard	NM_181303		Approved	HNL3, KIAA1480, ASPGX1, AUTSX1	uc004dzd.2	Q9NZ94	OTTHUMG00000021790	ENST00000358741.3:c.2192A>G	chrX.hg19:g.70389592A>G	ENSP00000351591:p.Tyr731Cys	36.0	0.0		23.0	20.0	NM_181303	B2RBK1|D2X2H6|D3DVV0|D3DVV1|Q86V51|Q8NCD0|Q9NZ95|Q9NZ96|Q9NZ97|Q9P248	Missense_Mutation	SNP	ENST00000358741.3	hg19	CCDS55441.1	.	.	.	.	.	.	.	.	.	.	A	17.38	3.373920	0.61735	.	.	ENSG00000196338	ENST00000536169;ENST00000374051;ENST00000358741	T;T;T	0.78481	-1.18;-1.18;-1.18	5.06	5.06	0.68205	.	0.000000	0.85682	D	0.000000	D	0.88698	0.6507	M	0.86268	2.805	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.997;0.999	D	0.90571	0.4522	10	0.87932	D	0	.	14.0645	0.64819	1.0:0.0:0.0:0.0	.	691;731;711	D3DVV1;Q9NZ94;Q9NZ94-2	.;NLGN3_HUMAN;.	C	691;711;731	ENSP00000445298:Y691C;ENSP00000363163:Y711C;ENSP00000351591:Y731C	ENSP00000351591:Y731C	Y	+	2	0	NLGN3	70306317	1.000000	0.71417	0.992000	0.48379	0.995000	0.86356	9.139000	0.94554	1.897000	0.54924	0.352000	0.21897	TAC	.	.		0.642	NLGN3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057121.1	NM_018977		G	70389592	A	G	70389592	3	3	337	1	0	0	0	0	1	0	0	0	10472	391	14	2	2218	2	NLGN3	23	70389592	Missense_Mutation	SNP	A	TCGA-RC-A7SB-01A-21D-A34Z-10		70389592	84880968	50	46852										
MAGEC3	139081	hgsc.bcm.edu	37	chrX	140953292	140953292	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	acagataaggactattctgcCtttcatcttgggcatctgag	9	9	4	2			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chrX:140953292C>T	ENST00000298296.1	+	2	159	c.159C>T	c.(157-159)gcC>gcT	p.A53A		NM_138702.1	NP_619647.1	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3	53								p.A53A(1)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|liver(1)|lung(32)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(2)	69	Acute lymphoblastic leukemia(192;6.56e-05)					ACTATTCTGCCTTTCATCTTG	0.512																																					p.A53A		Atlas-SNP	.											.	MAGEC3	228	.	1	Substitution - coding silent(1)	kidney(1)	c.C159T						.						190	150	164					X																	140953292		2203	4300	6503	SO:0001819	synonymous_variant	139081	exon2			TTCTGCCTTTCAT	AF490508	CCDS14676.1, CCDS14677.1	Xq27.2	2009-03-25			ENSG00000165509	ENSG00000165509			23798	protein-coding gene	gene with protein product	"cancer/testis antigen family 7, member 2"	300469				10861452	Standard	NM_138702		Approved	HCA2, MAGE-C3, CT7.2	uc011mwp.2	Q8TD91	OTTHUMG00000022570	ENST00000298296.1:c.159C>T	chrX.hg19:g.140953292C>T		59.0	0.0		30.0	23.0	NM_138702	Q3SYA7|Q5JZ43|Q9BZ80	Silent	SNP	ENST00000298296.1	hg19	CCDS14676.1																																																																																			.	.		0.512	MAGEC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058606.1	NM_138702		T	140953292	C	T	140953292	2	4	337	1	0	0	0	0	0	0	0	1	9191	668	24	3		3	MAGEC3	23	140953292	Silent	SNP	C	TCGA-RC-A7SB-01A-21D-A34Z-10	70563700	140953292	14317268	51	46853										
FMR1	2332	hgsc.bcm.edu	37	chrX	147014260	147014260	+	Frame_Shift_Del	DEL	A	A	-													0.0769230769230769	4	1	1.55852317360566	2.96119402985075	1.05756929637527	1	1	0	gaatttgctgaagatgtaatAcaagttccaaggaacttagt							TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chrX:147014260delA	ENST00000370475.4	+	9	986	c.858delA	c.(856-858)atafs	p.I286fs	FMR1_ENST00000439526.2_Frame_Shift_Del_p.I286fs|FMR1_ENST00000370470.1_Frame_Shift_Del_p.I286fs|FMR1_ENST00000370477.1_Frame_Shift_Del_p.I286fs|FMR1_ENST00000370471.3_Frame_Shift_Del_p.I286fs|FMR1_ENST00000334557.6_Frame_Shift_Del_p.I286fs|FMR1_ENST00000440235.2_5'UTR|FMR1_ENST00000218200.8_Frame_Shift_Del_p.I286fs	NM_002024.5	NP_002015.1	Q06787	FMR1_HUMAN	fragile X mental retardation 1	286	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.				central nervous system development (GO:0007417)|mRNA transport (GO:0051028)|negative regulation of translational initiation (GO:0045947)	cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|membrane (GO:0016020)|mRNA cap binding complex (GO:0005845)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|synapse (GO:0045202)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	35	Acute lymphoblastic leukemia(192;6.56e-05)					AAGATGTAATACAAGTTCCAA	0.338									Fragile X syndrome																												p.I286fs		Pindel	.											.	FMR1	93	.	0			c.857delT						.						66	63	64					X																	147014260		2202	4300	6502	SO:0001589	frameshift_variant	2332	exon9	Familial Cancer Database	Martin-Bell syndrome, FRAXA syndrome	.	X69962	CCDS14682.1, CCDS55518.1, CCDS55519.1, CCDS76039.1	Xq27.3	2014-09-17			ENSG00000102081	ENSG00000102081			3775	protein-coding gene	gene with protein product		309550	"premature ovarian failure 1"	POF1, POF		1572655	Standard	NM_002024		Approved	FMRP, FRAXA, MGC87458	uc010nst.3	Q06787	OTTHUMG00000022606	ENST00000370475.4:c.858delA	chrX.hg19:g.147014260delA	ENSP00000359506:p.Ile286fs	171.0	0.0		137.0	63.0	NM_002024	A6NNH4|D3DWT0|D3DWT1|D3DWT2|G8JL90|Q16578|Q5PQZ6|Q99054	Frame_Shift_Del	DEL	ENST00000370475.4	hg19	CCDS14682.1																																																																																			.	.		0.338	FMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058655.1	NM_002024		-	147014260	A	-	147014260	7	5	337	1	0	1	0	1	0	0	0	0	5968	381	14	0	892	0	FMR1	23	147014260	Frame_Shift_Del	DEL	A	TCGA-RC-A7SB-01A-21D-A34Z-10	6060968	147014260	8256300	52	46854										
KIAA1522	57648	hgsc.bcm.edu	37	chr1	33235673	33235673	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	gctgcagcgccacattgaccGtgtctaccgggatgacacct	11	14	1	2			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr1:33235673G>T	ENST00000373480.1	+	6	819	c.716G>T	c.(715-717)cGt>cTt	p.R239L	KIAA1522_ENST00000373481.3_Missense_Mutation_p.R250L|KIAA1522_ENST00000401073.2_Missense_Mutation_p.R298L|KIAA1522_ENST00000294521.3_Intron	NM_001198972.1	NP_001185901.1	Q9P206	K1522_HUMAN	KIAA1522	239										breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(2)|lung(5)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				CACATTGACCGTGTCTACCGG	0.682																																					p.R298L		Atlas-SNP	.											.	KIAA1522	68	.	0			c.G893T						.						31	37	35					1																	33235673		2060	4198	6258	SO:0001583	missense	57648	exon6			TTGACCGTGTCTA	AL713671	CCDS41298.1, CCDS55588.1, CCDS55589.1	1p35.1	2009-02-18			ENSG00000162522	ENSG00000162522			29301	protein-coding gene	gene with protein product						10819331	Standard	NM_020888		Approved		uc001bvu.1	Q9P206	OTTHUMG00000008088	ENST00000373480.1:c.716G>T	chr1.hg19:g.33235673G>T	ENSP00000362579:p.Arg239Leu	36.0	0.0		37.0	17.0	NM_020888	B4DQU8|B5MDY0|C9JH84|Q8TCQ0	Missense_Mutation	SNP	ENST00000373480.1	hg19	CCDS55588.1	.	.	.	.	.	.	.	.	.	.	G	14.16	2.452297	0.43531	.	.	ENSG00000162522	ENST00000401073;ENST00000373481;ENST00000373480	T;T;T	0.34667	1.35;1.35;1.35	4.47	3.52	0.40303	.	0.197037	0.33382	N	0.004971	T	0.51227	0.1662	L	0.50333	1.59	0.32657	N	0.518551	D;D;D	0.65815	0.975;0.988;0.995	P;P;D	0.64506	0.767;0.86;0.926	T	0.64592	-0.6371	10	0.62326	D	0.03	-1.2713	14.4256	0.67212	0.0:0.1489:0.8511:0.0	.	250;239;298	Q9P206-3;Q9P206;Q9P206-2	.;K1522_HUMAN;.	L	298;250;239	ENSP00000383851:R298L;ENSP00000362580:R250L;ENSP00000362579:R239L	ENSP00000362579:R239L	R	+	2	0	KIAA1522	33008260	0.008000	0.16893	0.479000	0.27329	0.888000	0.51559	0.356000	0.20181	0.953000	0.37825	0.491000	0.48974	CGT	.	.		0.682	KIAA1522-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022130.1			T	33235673	G	T	33235673	3	4	338	1	0	0	0	0	1	0	0	0	8247	1145	40	1	915	1	KIAA1522	1	33235673	Missense_Mutation	SNP	G	TCGA-RC-A7SF-01A-11D-A34Z-10		33235673	216014948	1	46855										
MACF1	23499	hgsc.bcm.edu	37	chr1	39748038	39748038	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	atgttcaatgcactcattcaCcgataccggtaagaacagtg	8	10	3	1			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr1:39748038C>A	ENST00000372915.3	+	6	789	c.702C>A	c.(700-702)caC>caA	p.H234Q	MACF1_ENST00000317713.7_Missense_Mutation_p.H234Q|MACF1_ENST00000564288.1_Missense_Mutation_p.H229Q|MACF1_ENST00000539005.1_Missense_Mutation_p.H234Q|MACF1_ENST00000545844.1_Missense_Mutation_p.H234Q|MACF1_ENST00000361689.2_Missense_Mutation_p.H234Q|MACF1_ENST00000536367.1_Missense_Mutation_p.H197Q|MACF1_ENST00000567887.1_Missense_Mutation_p.H266Q			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	234	Actin-binding.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			CACTCATTCACCGATACCGGT	0.438																																					p.H234Q		Atlas-SNP	.											.	MACF1	909	.	0			c.C702A						.						103	91	95					1																	39748038		2203	4300	6503	SO:0001583	missense	23499	exon8			CATTCACCGATAC	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.702C>A	chr1.hg19:g.39748038C>A	ENSP00000362006:p.His234Gln	62.0	0.0		50.0	16.0	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	hg19		.	.	.	.	.	.	.	.	.	.	C	19.21	3.783365	0.70222	.	.	ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000404645;ENST00000317713;ENST00000539005;ENST00000524432;ENST00000536367;ENST00000530262;ENST00000372900	D;D;D;D;D;D;D;D	0.95724	-3.79;-3.79;-3.79;-3.79;-3.79;-3.79;-3.79;-3.79	5.78	2.95	0.34219	.	.	.	.	.	D	0.98046	0.9356	H	0.94886	3.595	0.80722	D	1	D;B;D	0.89917	1.0;0.007;1.0	D;B;D	0.91635	0.999;0.001;0.968	D	0.97644	1.0150	9	0.87932	D	0	.	11.0288	0.47761	0.0:0.8001:0.0:0.1999	.	197;234;199	B4E2T3;F8W8Q1;Q9UPN3-3	.;.;.	Q	234;234;234;250;234;234;192;197;383;394	ENSP00000439537:H234Q;ENSP00000362006:H234Q;ENSP00000354573:H234Q;ENSP00000313438:H234Q;ENSP00000444364:H234Q;ENSP00000435070:H192Q;ENSP00000440369:H197Q;ENSP00000437059:H383Q	ENSP00000313438:H234Q	H	+	3	2	MACF1	39520625	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	3.372000	0.52387	0.383000	0.24910	-0.142000	0.14014	CAC	.	.		0.438	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		A	39748038	C	A	39748038	3	1	338	1	0	0	0	0	1	0	0	0	9153	506	18	3	724	3	MACF1	1	39748038	Missense_Mutation	SNP	C	TCGA-RC-A7SF-01A-11D-A34Z-10	6512365	39748038	209502583	2	46856										
ROR1	4919	hgsc.bcm.edu	37	chr1	64643503	64643503	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	ctggaccacggagattttctGcacattgcaattcagattgc	9	10	2	2			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr1:64643503G>T	ENST00000371079.1	+	9	2154	c.1779G>T	c.(1777-1779)ctG>ctT	p.L593L	ROR1_ENST00000545203.1_Silent_p.L44L	NM_005012.3	NP_005003.2	Q01973	ROR1_HUMAN	receptor tyrosine kinase-like orphan receptor 1	593	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				peptidyl-tyrosine phosphorylation (GO:0018108)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			breast(7)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(10)|ovary(6)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	51						GAGATTTTCTGCACATTGCAA	0.478																																					p.L593L		Atlas-SNP	.											.	ROR1	113	.	0			c.G1779T						.						71	74	73					1																	64643503		2203	4300	6503	SO:0001819	synonymous_variant	4919	exon9			TTTTCTGCACATT	M97675	CCDS626.1, CCDS41344.1	1p32-p31	2013-01-11			ENSG00000185483	ENSG00000185483		"Immunoglobulin superfamily / I-set domain containing"	10256	protein-coding gene	gene with protein product		602336		NTRKR1		1334494, 8875995	Standard	NM_001083592		Approved		uc001dbj.3	Q01973	OTTHUMG00000009022	ENST00000371079.1:c.1779G>T	chr1.hg19:g.64643503G>T		56.0	0.0		48.0	19.0	NM_005012	Q5VVX6|Q66K77|Q92776	Silent	SNP	ENST00000371079.1	hg19	CCDS626.1																																																																																			.	.		0.478	ROR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025002.1	NM_005012		T	64643503	G	T	64643503	2	4	338	1	0	0	0	0	0	0	0	1	13541	1306	46	3		3	ROR1	1	64643503	Silent	SNP	G	TCGA-RC-A7SF-01A-11D-A34Z-10	24895465	64643503	184607118	3	46857										
USF1	7391	hgsc.bcm.edu	37	chr1	161011514	161011514	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	acaacagcagctgtactcccCgatgtggtaccccctgcccc	8	18	0	0			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr1:161011514C>A	ENST00000368021.3	-	6	603	c.399G>T	c.(397-399)tcG>tcT	p.S133S	TSTD1_ENST00000318289.10_5'Flank|TSTD1_ENST00000466967.1_5'Flank|TSTD1_ENST00000368024.1_5'Flank|F11R_ENST00000289779.3_5'Flank|USF1_ENST00000368020.1_Silent_p.S133S|TSTD1_ENST00000368023.3_5'Flank|USF1_ENST00000435396.1_Silent_p.S74S|TSTD1_ENST00000423014.2_5'Flank|USF1_ENST00000368019.1_Intron	NM_007122.3	NP_009053.1	P22415	USF1_HUMAN	upstream transcription factor 1	133					carbon catabolite regulation of transcription (GO:0045990)|cellular response to insulin stimulus (GO:0032869)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|late viral transcription (GO:0019086)|lipid homeostasis (GO:0055088)|negative regulation of fibrinolysis (GO:0051918)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by glucose (GO:0000432)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter by glucose (GO:0000430)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|large_intestine(3)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9	all_cancers(52;6.73e-18)|Breast(13;0.012)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			CTGTACTCCCCGATGTGGTAC	0.597											OREG0013936	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S133S		Atlas-SNP	.											.	USF1	29	.	0			c.G399T						.						84	79	81					1																	161011514		2203	4300	6503	SO:0001819	synonymous_variant	7391	exon6			ACTCCCCGATGTG	BC035505	CCDS1214.1	1q22-q23	2013-05-21			ENSG00000158773	ENSG00000158773		"Basic helix-loop-helix proteins"	12593	protein-coding gene	gene with protein product		191523				8486371	Standard	NM_007122		Approved	UEF, MLTFI, bHLHb11	uc031pqv.1	P22415	OTTHUMG00000031472	ENST00000368021.3:c.399G>T	chr1.hg19:g.161011514C>A		53.0	0.0	1813	48.0	28.0	NM_001276373	B2RBZ4|Q5SY46|Q7Z5Y1	Silent	SNP	ENST00000368021.3	hg19	CCDS1214.1																																																																																			.	.		0.597	USF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077050.1	NM_007122		A	161011514	C	A	161011514	2	1	338	1	0	0	0	0	0	0	0	1	17047	639	23	1		1	USF1	1	161011514	Silent	SNP	C	TCGA-RC-A7SF-01A-11D-A34Z-10	96368011	161011514	88239107	4	46858										
RAB3GAP2	25782	hgsc.bcm.edu	37	chr1	220406191	220406191	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	tccccaaccatcatcttcccAgtctgttgatttacctgttt	4	14	3	1			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr1:220406191A>C	ENST00000358951.2	-	2	246	c.130T>G	c.(130-132)Tgg>Ggg	p.W44G		NM_012414.3	NP_036546.2	Q9H2M9	RBGPR_HUMAN	RAB3 GTPase activating protein subunit 2 (non-catalytic)	44					establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|intracellular protein transport (GO:0006886)|positive regulation of catalytic activity (GO:0043085)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of GTPase activity (GO:0043087)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	enzyme activator activity (GO:0008047)|enzyme regulator activity (GO:0030234)|GTPase activator activity (GO:0005096)|protein heterodimerization activity (GO:0046982)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(1)	39				GBM - Glioblastoma multiforme(131;0.0443)		TCATCTTCCCAGTCTGTTGAT	0.328																																					p.W44G		Atlas-SNP	.											.	RAB3GAP2	120	.	0			c.T130G						.						186	170	176					1																	220406191		2203	4300	6503	SO:0001583	missense	25782	exon2			CTTCCCAGTCTGT	AB020646	CCDS31028.1	1q41	2014-03-03			ENSG00000118873	ENSG00000118873			17168	protein-coding gene	gene with protein product		609275				15696165, 16532399, 24482476	Standard	NM_012414		Approved	RAB3-GAP150, KIAA0839, DKFZP434D245, SPG69	uc010puk.1	Q9H2M9	OTTHUMG00000037139	ENST00000358951.2:c.130T>G	chr1.hg19:g.220406191A>C	ENSP00000351832:p.Trp44Gly	219.0	0.0		174.0	76.0	NM_012414	A6H8V0|O75872|Q9HAB0|Q9UFJ7|Q9UQ15	Missense_Mutation	SNP	ENST00000358951.2	hg19	CCDS31028.1	.	.	.	.	.	.	.	.	.	.	A	19.83	3.899327	0.72754	.	.	ENSG00000118873	ENST00000358951	T	0.59224	0.28	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.62901	0.2466	N	0.22421	0.69	0.53005	D	0.999963	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.964	T	0.66988	-0.5784	10	0.72032	D	0.01	.	12.2973	0.54854	1.0:0.0:0.0:0.0	.	44;44	Q9H2M9-2;Q9H2M9	.;RBGPR_HUMAN	G	44	ENSP00000351832:W44G	ENSP00000351832:W44G	W	-	1	0	RAB3GAP2	218472814	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.023000	0.64084	2.224000	0.72417	0.533000	0.62120	TGG	.	.		0.328	RAB3GAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090205.2	NM_012414		C	220406191	A	C	220406191	3	2	338	1	0	0	0	0	1	0	0	0	12951	188	7	5	4187	5	RAB3GAP2	1	220406191	Missense_Mutation	SNP	A	TCGA-RC-A7SF-01A-11D-A34Z-10	59394677	220406191	28844430	5	46859										
SNTG2	54221	hgsc.bcm.edu	37	chr2	1204797	1204797	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	tcttctgtacaggccccatcGtcaccttcctcgcccatagc	6	18	3	0	rs141600263		TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr2:1204797G>T	ENST00000308624.5	+	9	729	c.600G>T	c.(598-600)tcG>tcT	p.S200S	SNTG2_ENST00000467759.1_3'UTR|SNTG2_ENST00000407292.1_Silent_p.S73S	NM_018968.3	NP_061841.2	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2	200			S -> L (in dbSNP:rs6751090).		central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|syntrophin complex (GO:0016013)	PDZ domain binding (GO:0030165)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		AGGCCCCATCGTCACCTTCCT	0.572																																					p.S200S		Atlas-SNP	.											.	SNTG2	125	.	0			c.G600T						.						69	76	74					2																	1204797		2091	4237	6328	SO:0001819	synonymous_variant	54221	exon9			CCCATCGTCACCT	AJ003029	CCDS46220.1	2p25	2008-05-23			ENSG00000172554	ENSG00000172554			13741	protein-coding gene	gene with protein product		608715				10747910	Standard	NM_018968		Approved	SYN5, G2SYN	uc002qwq.3	Q9NY99	OTTHUMG00000151370	ENST00000308624.5:c.600G>T	chr2.hg19:g.1204797G>T		58.0	0.0		24.0	12.0	NM_018968	Q05AH5	Silent	SNP	ENST00000308624.5	hg19	CCDS46220.1																																																																																			.	G|1.000;A|0.000		0.572	SNTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322454.1	NM_018968		T	1204797	G	T	1204797	2	4	338	1	0	0	0	0	0	0	0	1	14890	1132	40	1		1	SNTG2	2	1204797	Silent	SNP	G	TCGA-RC-A7SF-01A-11D-A34Z-10		1204797	241994576	6	46860										
CHRNA1	1134	hgsc.bcm.edu	37	chr2	175624301	175624301	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	ctggccgcaccacgctgctgTagtctttaaatagctttgcc	9	13	1	0			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr2:175624301T>G	ENST00000261007.5	-	2	170	c.104A>C	c.(103-105)tAc>tCc	p.Y35S	CHRNA1_ENST00000348749.5_Missense_Mutation_p.Y35S|CHRNA1_ENST00000409542.1_Missense_Mutation_p.Y35S|CHRNA1_ENST00000409323.1_Missense_Mutation_p.Y35S|CHRNA1_ENST00000409219.1_Missense_Mutation_p.Y35S|AC018890.6_ENST00000442996.1_RNA	NM_001039523.2	NP_001034612.1	P02708	ACHA_HUMAN	cholinergic receptor, nicotinic, alpha 1 (muscle)	35					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|muscle cell cellular homeostasis (GO:0046716)|musculoskeletal movement (GO:0050881)|neuromuscular junction development (GO:0007528)|neuromuscular process (GO:0050905)|neuromuscular synaptic transmission (GO:0007274)|neuron cellular homeostasis (GO:0070050)|neuronal action potential (GO:0019228)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue growth (GO:0048630)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cell surface (GO:0009986)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ion channel activity (GO:0005216)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(3)|prostate(3)|skin(4)	37					Galantamine(DB00674)	CACGCTGCTGTAGTCTTTAAA	0.567																																					p.Y35S		Atlas-SNP	.											.	CHRNA1	92	.	0			c.A104C						.						112	110	111					2																	175624301		2203	4300	6503	SO:0001583	missense	1134	exon2			CTGCTGTAGTCTT	Y00762	CCDS2261.1, CCDS33331.1	2q31.1	2012-02-11	2006-02-01		ENSG00000138435	ENSG00000138435		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1955	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 1 (muscle)"	100690	"cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle)"	CHRNA			Standard	NM_001039523		Approved		uc002uje.2	P02708	OTTHUMG00000132357	ENST00000261007.5:c.104A>C	chr2.hg19:g.175624301T>G	ENSP00000261007:p.Tyr35Ser	38.0	0.0		33.0	9.0	NM_001039523	B4DRV6|D3DPE8	Missense_Mutation	SNP	ENST00000261007.5	hg19	CCDS33331.1	.	.	.	.	.	.	.	.	.	.	T	29.3	4.997709	0.93227	.	.	ENSG00000138435	ENST00000348749;ENST00000261007;ENST00000409542;ENST00000409219;ENST00000409323	D;D;D;D;D	0.91464	-2.85;-2.85;-2.85;-2.85;-2.85	5.91	5.91	0.95273	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	D	0.96741	0.8936	H	0.94264	3.515	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.97766	1.0223	10	0.87932	D	0	.	16.3426	0.83092	0.0:0.0:0.0:1.0	.	35;35;35	G5E9G9;Q53SH4;P02708	.;.;ACHA_HUMAN	S	35	ENSP00000261008:Y35S;ENSP00000261007:Y35S;ENSP00000387026:Y35S;ENSP00000386611:Y35S;ENSP00000386684:Y35S	ENSP00000261007:Y35S	Y	-	2	0	CHRNA1	175332547	1.000000	0.71417	0.992000	0.48379	0.993000	0.82548	7.988000	0.88194	2.263000	0.75096	0.379000	0.24179	TAC	.	.		0.567	CHRNA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000334116.1			G	175624301	T	G	175624301	3	3	338	1	0	0	0	0	1	0	0	0	3383	1638	57	5	1380	5	CHRNA1	2	175624301	Missense_Mutation	SNP	T	TCGA-RC-A7SF-01A-11D-A34Z-10	174419504	175624301	67575072	7	46861										
NBEAL1	65065	hgsc.bcm.edu	37	chr2	204009591	204009591	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	tgaagattttcaagaatattGtaattcaaatgaatggcaag	8	3	2	4			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr2:204009591G>T	ENST00000449802.1	+	31	5363	c.5030G>T	c.(5029-5031)tGt>tTt	p.C1677F		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	1677										NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						CAAGAATATTGTAATTCAAAT	0.289																																					p.C1677F		Atlas-SNP	.											.	NBEAL1	266	.	0			c.G5030T						.						58	50	52					2																	204009591		1799	4067	5866	SO:0001583	missense	65065	exon31			AATATTGTAATTC	AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"WD repeat domain containing"	20681	protein-coding gene	gene with protein product		609816	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17", "amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.5030G>T	chr2.hg19:g.204009591G>T	ENSP00000399903:p.Cys1677Phe	103.0	0.0		81.0	29.0	NM_001114132	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Missense_Mutation	SNP	ENST00000449802.1	hg19	CCDS46495.1	.	.	.	.	.	.	.	.	.	.	G	18.29	3.591662	0.66219	.	.	ENSG00000144426	ENST00000449802;ENST00000340268	T	0.59638	0.25	5.8	5.8	0.92144	.	0.092035	0.85682	D	0.000000	T	0.69305	0.3096	M	0.76574	2.34	0.58432	D	0.999997	D;D	0.54397	0.966;0.966	P;P	0.49665	0.618;0.618	T	0.73452	-0.3978	10	0.87932	D	0	.	19.6495	0.95795	0.0:0.0:1.0:0.0	.	1677;1666	Q6ZS30;C9JGK5	NBEL1_HUMAN;.	F	1677	ENSP00000399903:C1677F	ENSP00000344985:C1677F	C	+	2	0	NBEAL1	203717836	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.502000	0.81614	2.748000	0.94277	0.655000	0.94253	TGT	.	.		0.289	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4			T	204009591	G	T	204009591	3	4	338	1	0	0	0	0	1	0	0	0	10197	1377	48	3	5148	3	NBEAL1	2	204009591	Missense_Mutation	SNP	G	TCGA-RC-A7SF-01A-11D-A34Z-10	28385290	204009591	39189782	8	46862										
TTLL4	9654	hgsc.bcm.edu	37	chr2	219614829	219614829	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	tcctgcccaatgcagaggatAtcatttccagccccagcagc	8	15	1	1			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr2:219614829A>G	ENST00000392102.1	+	15	3173	c.2833A>G	c.(2833-2835)Atc>Gtc	p.I945V	TTLL4_ENST00000258398.4_Missense_Mutation_p.I945V|TTLL4_ENST00000457313.1_Missense_Mutation_p.I780V|TTLL4_ENST00000442769.1_Missense_Mutation_p.I881V	NM_014640.4	NP_055455.3	Q14679	TTLL4_HUMAN	tubulin tyrosine ligase-like family, member 4	945	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				protein polyglutamylation (GO:0018095)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)|tubulin binding (GO:0015631)			endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	39		Renal(207;0.0915)		Epithelial(149;5.03e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0101)		TGCAGAGGATATCATTTCCAG	0.532																																					p.I945V	GBM(172;1818 2053 15407 20943 49753)	Atlas-SNP	.											.	TTLL4	96	.	0			c.A2833G						.						134	128	130					2																	219614829		2203	4300	6503	SO:0001583	missense	9654	exon15			GAGGATATCATTT		CCDS2422.1	2p24.3-p24.1	2013-02-14			ENSG00000135912	ENSG00000135912		"Tubulin tyrosine ligase-like family"	28976	protein-coding gene	gene with protein product						11054573	Standard	NM_014640		Approved	KIAA0173	uc002viy.3	Q14679	OTTHUMG00000133081	ENST00000392102.1:c.2833A>G	chr2.hg19:g.219614829A>G	ENSP00000375951:p.Ile945Val	61.0	0.0		42.0	14.0	NM_014640	A8K6V5|Q8WW29	Missense_Mutation	SNP	ENST00000392102.1	hg19	CCDS2422.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	0.691|0.691	-0.794509|-0.794509	0.02862|0.02862	.|.	.|.	ENSG00000135912|ENSG00000135912	ENST00000457313;ENST00000392102;ENST00000442769;ENST00000258398|ENST00000436668	T;T;T;T|.	0.03920|.	3.99;4.22;3.76;4.22|.	4.95|4.95	-4.9|-4.9	0.03094|0.03094	.|.	1.054690|.	0.07303|.	N|.	0.874420|.	T|T	0.27063|0.27063	0.0663|0.0663	N|N	0.16266|0.16266	0.395|0.395	0.09310|0.09310	N|N	1|1	B;B;B;B|.	0.25850|.	0.0;0.0;0.136;0.0|.	B;B;B;B|.	0.26094|.	0.002;0.004;0.066;0.001|.	T|T	0.29274|0.29274	-1.0017|-1.0017	10|5	0.02654|.	T|.	1|.	.|.	13.8909|13.8909	0.63738|0.63738	0.4219:0.0:0.5781:0.0|0.4219:0.0:0.5781:0.0	.|.	148;780;881;945|.	B4DJF5;E9PH58;E7EX20;Q14679|.	.;.;.;TTLL4_HUMAN|.	V|C	780;945;881;945|89	ENSP00000393332:I780V;ENSP00000375951:I945V;ENSP00000396555:I881V;ENSP00000258398:I945V|.	ENSP00000258398:I945V|.	I|Y	+|+	1|2	0|0	TTLL4|TTLL4	219323073|219323073	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.940000|0.940000	0.58332|0.58332	-0.306000|-0.306000	0.08178|0.08178	-0.826000|-0.826000	0.04284|0.04284	-0.137000|-0.137000	0.14449|0.14449	ATC|TAT	.	.		0.532	TTLL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256726.1	NM_014640		G	219614829	A	G	219614829	3	3	338	1	0	0	0	0	1	0	0	0	16744	449	16	2	2883	2	TTLL4	2	219614829	Missense_Mutation	SNP	A	TCGA-RC-A7SF-01A-11D-A34Z-10	15605238	219614829	23584544	9	46863										
KIAA1486	57624	hgsc.bcm.edu	37	chr2	226378129	226378129	+	Frame_Shift_Del	DEL	G	G	-													0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	ggccacgaaggaagttacgtGggcaaacatttccgcatggg							TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr2:226378129delG	ENST00000272907.6	+	3	677	c.264delG	c.(262-264)gtgfs	p.V88fs	NYAP2_ENST00000409269.2_Intron	NM_020864.1	NP_065915.1	Q9P242	NYAP2_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	88					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												GAAGTTACGTGGGCAAACATT	0.493																																					p.V88fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.263delT						.						77	81	80					2																	226378129		2046	4187	6233	SO:0001589	frameshift_variant	57624	exon3			.	AB040919	CCDS46529.1	2q36.3	2011-11-30	2011-11-30	2011-11-30	ENSG00000144460	ENSG00000144460			29291	protein-coding gene	gene with protein product		615478	"KIAA1486"	KIAA1486		10819331, 21946561	Standard	NM_020864		Approved		uc002voe.2	Q9P242	OTTHUMG00000153450	ENST00000272907.6:c.264delG	chr2.hg19:g.226378129delG	ENSP00000272907:p.Val88fs	100.0	0.0		55.0	26.0	NM_020864	A2RRN4|Q96NL2	Frame_Shift_Del	DEL	ENST00000272907.6	hg19	CCDS46529.1																																																																																			.	.		0.493	NYAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331258.1	NM_020864		-	226378129	G	-	226378129	7	5	338	1	0	1	0	1	0	0	0	0	8246	1335	47	0	270	0	KIAA1486	2	226378129	Frame_Shift_Del	DEL	G	TCGA-RC-A7SF-01A-11D-A34Z-10	6763300	226378129	16821244	10	46864										
FYCO1	79443	hgsc.bcm.edu	37	chr3	46000930	46000930	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	agctgaactcccgcttacagTcgaggcagtggtttgcctct	11	12	1	1			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr3:46000930T>C	ENST00000296137.2	-	12	3747	c.3542A>G	c.(3541-3543)gAc>gGc	p.D1181G	FYCO1_ENST00000438446.1_5'Flank|FYCO1_ENST00000535325.1_Missense_Mutation_p.D1181G	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	1181					plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)			NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		CCGCTTACAGTCGAGGCAGTG	0.607																																					p.D1181G		Atlas-SNP	.											.	FYCO1	115	.	0			c.A3542G						.						98	86	90					3																	46000930		2203	4300	6503	SO:0001583	missense	79443	exon12			TTACAGTCGAGGC	AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"Zinc fingers, FYVE domain containing"	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.3542A>G	chr3.hg19:g.46000930T>C	ENSP00000296137:p.Asp1181Gly	89.0	0.0		48.0	14.0	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Missense_Mutation	SNP	ENST00000296137.2	hg19	CCDS2734.1	.	.	.	.	.	.	.	.	.	.	T	13.94	2.386405	0.42308	.	.	ENSG00000163820	ENST00000296137;ENST00000535325	T;T	0.71698	-0.59;-0.59	4.94	4.94	0.65067	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, FYVE-type (2);Zinc finger, FYVE-related (1);Zinc finger, FYVE/PHD-type (1);	0.069340	0.64402	D	0.000007	T	0.70649	0.3248	N	0.12961	0.28	0.42524	D	0.99301	D;P	0.89917	1.0;0.681	D;B	0.91635	0.999;0.324	T	0.71148	-0.4677	10	0.31617	T	0.26	-30.1794	13.1792	0.59645	0.0:0.0:0.0:1.0	.	1181;1181	B7ZKT7;Q9BQS8	.;FYCO1_HUMAN	G	1181	ENSP00000296137:D1181G;ENSP00000441178:D1181G	ENSP00000296137:D1181G	D	-	2	0	FYCO1	45975934	1.000000	0.71417	0.992000	0.48379	0.741000	0.42261	2.001000	0.40825	1.863000	0.54032	0.533000	0.62120	GAC	.	.		0.607	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513		C	46000930	T	C	46000930	3	2	338	1	0	0	0	0	1	0	0	0	6133	1667	58	2	922	2	FYCO1	3	46000930	Missense_Mutation	SNP	T	TCGA-RC-A7SF-01A-11D-A34Z-10		46000930	152021500	11	46865										
CADPS	8618	hgsc.bcm.edu	37	chr3	62467525	62467525	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	attgggtaggttcacattggGtaggttactggttaaactcc	12	6	1	0			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr3:62467525G>T	ENST00000383710.4	-	22	3395	c.3046C>A	c.(3046-3048)Ccc>Acc	p.P1016T	CADPS_ENST00000283269.9_Intron|CADPS_ENST00000357948.3_Intron	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	1016	Interaction with DRD2.|MHD1. {ECO:0000255|PROSITE- ProRule:PRU00587}.				catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		TTCACATTGGGTAGGTTACTG	0.433																																					p.P1016T		Atlas-SNP	.											.	CADPS	387	.	0			c.C3046A						.						222	210	214					3																	62467525		1900	4135	6035	SO:0001583	missense	8618	exon22			CATTGGGTAGGTT	U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"Pleckstrin homology (PH) domain containing"	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.3046C>A	chr3.hg19:g.62467525G>T	ENSP00000373215:p.Pro1016Thr	164.0	0.0		110.0	34.0	NM_003716	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Missense_Mutation	SNP	ENST00000383710.4	hg19	CCDS46858.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.73|17.73	3.460924|3.460924	0.63513|0.63513	.|.	.|.	ENSG00000163618|ENSG00000163618	ENST00000383709;ENST00000383710|ENST00000473635	T|.	0.31769|.	1.48|.	5.28|5.28	5.28|5.28	0.74379|0.74379	Munc13 homology 1 (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.65811|.	0.2727|.	L|L	0.38838|0.38838	1.175|1.175	0.80722|0.80722	D|D	1|1	P|.	0.38395|.	0.629|.	B|.	0.39185|.	0.293|.	T|.	0.60707|.	-0.7210|.	10|.	0.72032|.	D|.	0.01|.	.|.	19.2786|19.2786	0.94042|0.94042	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1016|.	Q9ULU8|.	CAPS1_HUMAN|.	T|X	1016|2	ENSP00000373215:P1016T|.	ENSP00000373214:P1016T|.	P|Y	-|-	1|3	0|2	CADPS|CADPS	62442565|62442565	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.375000|9.375000	0.97178|0.97178	2.641000|2.641000	0.89580|0.89580	0.563000|0.563000	0.77884|0.77884	CCC|TAC	.	.		0.433	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394		T	62467525	G	T	62467525	3	4	338	1	0	0	0	0	1	0	0	0	2572	1261	44	3	1051	3	CADPS	3	62467525	Missense_Mutation	SNP	G	TCGA-RC-A7SF-01A-11D-A34Z-10	16466595	62467525	135554905	12	46866										
EGF	1950	hgsc.bcm.edu	37	chr4	110925746	110925746	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	gtcgcaggcctgctgacactGaggatgggatgtcctcttgc	14	11	1	2			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr4:110925746G>T	ENST00000265171.5	+	22	3704	c.3259G>T	c.(3259-3261)Gag>Tag	p.E1087*	EGF_ENST00000509793.1_Nonsense_Mutation_p.E1045*|EGF_ENST00000503392.1_Nonsense_Mutation_p.E1046*	NM_001178130.1|NM_001963.4	NP_001171601.1|NP_001954.2	P01133	EGF_HUMAN	epidermal growth factor	1087					activation of MAPKK activity (GO:0000186)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|branching morphogenesis of an epithelial tube (GO:0048754)|DNA replication (GO:0006260)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mammary gland alveolus development (GO:0060749)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of secretion (GO:0051048)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)|positive regulation of DNA binding (GO:0043388)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of calcium ion import (GO:0090279)|regulation of protein localization to cell surface (GO:2000008)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(1)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sucralfate(DB00364)	TGCTGACACTGAGGATGGGAT	0.453																																					p.E1087X		Atlas-SNP	.											.	EGF	113	.	0			c.G3259T						.						114	105	108					4																	110925746		2203	4300	6503	SO:0001587	stop_gained	1950	exon22			GACACTGAGGATG	X04571	CCDS3689.1, CCDS54794.1, CCDS54795.1	4q25	2012-10-02	2010-05-11		ENSG00000138798	ENSG00000138798			3229	protein-coding gene	gene with protein product		131530	"epidermal growth factor (beta-urogastrone)"				Standard	NM_001963		Approved		uc003hzy.4	P01133	OTTHUMG00000132044	ENST00000265171.5:c.3259G>T	chr4.hg19:g.110925746G>T	ENSP00000265171:p.Glu1087*	46.0	0.0		38.0	11.0	NM_001963	B4DRK7|E7EVD2|E9PBF0|Q52LZ6	Nonsense_Mutation	SNP	ENST00000265171.5	hg19	CCDS3689.1	.	.	.	.	.	.	.	.	.	.	G	39	7.909228	0.98557	.	.	ENSG00000138798	ENST00000509793;ENST00000265171;ENST00000503392	.	.	.	4.2	3.35	0.38373	.	0.679812	0.12713	N	0.445348	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	.	8.14	0.31078	0.1112:0.0:0.8888:0.0	.	.	.	.	X	1045;1087;1046	.	ENSP00000265171:E1087X	E	+	1	0	EGF	111145195	0.355000	0.24921	0.010000	0.14722	0.017000	0.09413	1.542000	0.36137	1.097000	0.41459	0.650000	0.86243	GAG	.	.		0.453	EGF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255065.1			T	110925746	G	T	110925746	4	4	338	1	0	0	0	0	0	1	0	0	4964	1291	45	3	3345	3	EGF	4	110925746	Nonsense_Mutation	SNP	G	TCGA-RC-A7SF-01A-11D-A34Z-10		110925746	80228530	13	46867										
TLL1	7092	hgsc.bcm.edu	37	chr4	166981307	166981307	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	acccagtacagaatttctgtGaagtttgagttttttgaatt	8	5	1	4			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr4:166981307G>A	ENST00000061240.2	+	15	2621	c.1974G>A	c.(1972-1974)gtG>gtA	p.V658V	TLL1_ENST00000507499.1_Silent_p.V681V	NM_012464.4	NP_036596.3	O43897	TLL1_HUMAN	tolloid-like 1	658	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(21)|lung(26)|ovary(2)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		GAATTTCTGTGAAGTTTGAGT	0.413																																					p.V658V		Atlas-SNP	.											.	TLL1	194	.	0			c.G1974A						.						95	97	97					4																	166981307		2203	4300	6503	SO:0001819	synonymous_variant	7092	exon15			TTCTGTGAAGTTT	AF282732	CCDS3811.1, CCDS56342.1	4q32-q33	2008-07-29			ENSG00000038295	ENSG00000038295			11843	protein-coding gene	gene with protein product		606742				10516436	Standard	NM_012464		Approved		uc003irh.2	O43897	OTTHUMG00000161112	ENST00000061240.2:c.1974G>A	chr4.hg19:g.166981307G>A		95.0	0.0		54.0	17.0	NM_012464	B2RMU2|Q96AN3|Q9NQS4	Silent	SNP	ENST00000061240.2	hg19	CCDS3811.1																																																																																			.	.		0.413	TLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363821.1			A	166981307	G	A	166981307	2	1	338	1	0	0	0	0	0	0	0	1	15960	1277	45	3		3	TLL1	4	166981307	Silent	SNP	G	TCGA-RC-A7SF-01A-11D-A34Z-10	56055561	166981307	24172969	14	46868										
SPCS3	60559	hgsc.bcm.edu	37	chr4	177241334	177241334	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	caccgccttcaaagacaggaGcgtcccggtgcggctgcacg	13	15	1	1			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr4:177241334G>A	ENST00000503362.1	+	1	220	c.107G>A	c.(106-108)aGc>aAc	p.S36N	RP11-87F15.2_ENST00000512634.1_RNA	NM_021928.3	NP_068747.1	P61009	SPCS3_HUMAN	signal peptidase complex subunit 3 homolog (S. cerevisiae)	36					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|regulation of insulin secretion (GO:0050796)|signal peptide processing (GO:0006465)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|signal peptidase complex (GO:0005787)	peptidase activity (GO:0008233)			ovary(2)	2		Breast(14;0.0011)|Prostate(90;0.0129)|Melanoma(52;0.0133)|Renal(120;0.0376)|all_hematologic(60;0.124)		all cancers(43;2.43e-19)|Epithelial(43;1.84e-16)|OV - Ovarian serous cystadenocarcinoma(60;4.51e-09)|GBM - Glioblastoma multiforme(59;0.000142)|STAD - Stomach adenocarcinoma(60;0.00279)|LUSC - Lung squamous cell carcinoma(193;0.0319)		AAAGACAGGAGCGTCCCGGTG	0.692																																					p.S36N		Atlas-SNP	.											.	SPCS3	15	.	0			c.G107A						.						39	46	44					4																	177241334		2014	4179	6193	SO:0001583	missense	60559	exon1			ACAGGAGCGTCCC	AK092634	CCDS54823.1	4q34.2	2008-02-05				ENSG00000129128			26212	protein-coding gene	gene with protein product						12477932	Standard	NM_021928		Approved	FLJ22649, SPC22/23, SPC3, YLR066W, PRO3567	uc003iur.4	P61009		ENST00000503362.1:c.107G>A	chr4.hg19:g.177241334G>A	ENSP00000427463:p.Ser36Asn	38.0	0.0		30.0	12.0	NM_021928	P12280|Q9H0S7	Missense_Mutation	SNP	ENST00000503362.1	hg19	CCDS54823.1	.	.	.	.	.	.	.	.	.	.	G	9.101	1.004234	0.19199	.	.	ENSG00000129128	ENST00000503362	.	.	.	3.11	3.11	0.35812	.	0.284907	0.39083	N	0.001467	T	0.42359	0.1199	L	0.38838	1.175	0.38828	D	0.955795	B	0.12630	0.006	B	0.23716	0.048	T	0.27872	-1.0061	9	0.18276	T	0.48	-4.2881	7.6483	0.28334	0.0:0.0:0.7472:0.2528	.	36	P61009	SPCS3_HUMAN	N	36	.	ENSP00000427463:S36N	S	+	2	0	SPCS3	177478328	1.000000	0.71417	1.000000	0.80357	0.076000	0.17211	4.516000	0.60496	1.702000	0.51228	0.455000	0.32223	AGC	.	.		0.692	SPCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362329.1	NM_021928		A	177241334	G	A	177241334	3	1	338	1	0	0	0	0	1	0	0	0	15040	971	34	3	109	3	SPCS3	4	177241334	Missense_Mutation	SNP	G	TCGA-RC-A7SF-01A-11D-A34Z-10	10260027	177241334	13912942	15	46869										
FAM135A	57579	hgsc.bcm.edu	37	chr6	71243558	71243558	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	ctaacagtctcaaaaataagGtatcttctttaatattatgc	4	7	3	0			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr6:71243558G>T	ENST00000418814.2	+	18	4579		c.e18+1		FAM135A_ENST00000370479.3_Splice_Site|FAM135A_ENST00000505769.1_Splice_Site|FAM135A_ENST00000361499.3_Splice_Site|FAM135A_ENST00000457062.2_Splice_Site|FAM135A_ENST00000505868.1_Splice_Site	NM_001105531.2|NM_001162529.1	NP_001099001.1|NP_001156001.1	Q9P2D6	F135A_HUMAN	family with sequence similarity 135, member A											breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38						CAAAAATAAGGTATCTTCTTT	0.264																																					.		Atlas-SNP	.											.	FAM135A	181	.	0			c.3377+1G>T						.						61	60	60					6																	71243558		2191	4268	6459	SO:0001630	splice_region_variant	57579	exon18			AATAAGGTATCTT	AK000183	CCDS34481.1, CCDS47448.1, CCDS55028.1	6q13	2008-10-30	2007-05-11	2007-05-11	ENSG00000082269	ENSG00000082269			21084	protein-coding gene	gene with protein product			"KIAA1411"	KIAA1411		10718198	Standard	NM_001105531		Approved	FLJ20176	uc003pfj.3	Q9P2D6	OTTHUMG00000014991	ENST00000418814.2:c.3965+1G>T	chr6.hg19:g.71243558G>T		65.0	0.0		63.0	16.0	NM_001105531	A2RRQ5|Q3C0H3|Q5JXK0|Q5JXK1|Q68DW0|Q6P081|Q9H0F2|Q9NU48|Q9NUQ5|Q9NXL5	Splice_Site	SNP	ENST00000418814.2	hg19	CCDS55028.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.209065	0.79240	.	.	ENSG00000082269	ENST00000418814;ENST00000370479;ENST00000505769;ENST00000457062;ENST00000361499;ENST00000505868	.	.	.	5.15	5.15	0.70609	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.9956	0.92812	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FAM135A	71300279	1.000000	0.71417	1.000000	0.80357	0.820000	0.46376	9.711000	0.98735	2.553000	0.86117	0.557000	0.71058	.	.	.		0.264	FAM135A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041137.2	NM_020819	Intron	T	71243558	G	T	71243558	5	4	338	1	0	0	0	0	0	0	1	0	5453	1275	44	3	4106	3	FAM135A	6	71243558	Splice_Site	SNP	G	TCGA-RC-A7SF-01A-11D-A34Z-10		71243558	99871509	16	46870										
TXNDC3	51314	hgsc.bcm.edu	37	chr7	37890296	37890296	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	aacctttattcagaaaattgAaaaatgaactgaacgaagac	6	6	1	5			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr7:37890296A>T	ENST00000199447.4	+	5	529	c.157A>T	c.(157-159)Aaa>Taa	p.K53*	EPDR1_ENST00000476620.1_Intron|NME8_ENST00000440017.1_Nonsense_Mutation_p.K53*	NM_016616.4	NP_057700.3	Q8N427	TXND3_HUMAN	NME/NM23 family member 8	53	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)|UTP biosynthetic process (GO:0006228)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)										CAGAAAATTGAAAAATGAACT	0.318																																					p.K53X		Atlas-SNP	.											.	.	.	.	0			c.A157T						.						109	120	116					7																	37890296		2203	4300	6503	SO:0001587	stop_gained	51314	exon5			AAATTGAAAAATG	AF202051	CCDS5452.1	7p15.2	2012-05-18	2012-05-18	2012-05-18	ENSG00000086288	ENSG00000086288			16473	protein-coding gene	gene with protein product	"sperm-specific thioredoxin 2"	607421	"thioredoxin domain containing 3 (spermatozoa)"	TXNDC3		11737268, 11768308, 19852809	Standard	NM_016616		Approved	CILD6, SPTRX2, NM23-H8	uc003tfn.3	Q8N427	OTTHUMG00000023716	ENST00000199447.4:c.157A>T	chr7.hg19:g.37890296A>T	ENSP00000199447:p.Lys53*	97.0	0.0		88.0	24.0	NM_016616	Q9NZH1	Nonsense_Mutation	SNP	ENST00000199447.4	hg19	CCDS5452.1	.	.	.	.	.	.	.	.	.	.	A	34	5.298407	0.95574	.	.	ENSG00000086288	ENST00000199447;ENST00000440017	.	.	.	5.01	5.01	0.66863	.	0.214969	0.33127	N	0.005252	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-31.9391	13.9841	0.64324	1.0:0.0:0.0:0.0	.	.	.	.	X	53	.	ENSP00000199447:K53X	K	+	1	0	TXNDC3	37856821	1.000000	0.71417	1.000000	0.80357	0.315000	0.28087	6.394000	0.73223	2.007000	0.58848	0.459000	0.35465	AAA	.	.		0.318	NME8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219946.1	NM_016616		T	37890296	A	T	37890296	4	4	338	1	0	0	0	0	0	1	0	0	16813	247	9	4	167	4	TXNDC3	7	37890296	Nonsense_Mutation	SNP	A	TCGA-RC-A7SF-01A-11D-A34Z-10		37890296	121248367	17	46871										
KIAA1967	57805	hgsc.bcm.edu	37	chr8	22471762	22471762	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	tccaggtctcttctgaaaagGaggcagctccagacgctggt	12	11	2	2			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr8:22471762G>C	ENST00000308511.4	+	9	1111	c.862G>C	c.(862-864)Gag>Cag	p.E288Q	RP11-582J16.5_ENST00000521025.1_RNA|CCAR2_ENST00000520861.1_5'UTR|CCAR2_ENST00000389279.3_Missense_Mutation_p.E288Q			Q8N163	CCAR2_HUMAN	cell cycle and apoptosis regulator 2	288					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mRNA processing (GO:0006397)|negative regulation of catalytic activity (GO:0043086)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage checkpoint (GO:2000003)|regulation of circadian rhythm (GO:0042752)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of protein stability (GO:0031647)|response to UV (GO:0009411)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|DBIRD complex (GO:0044609)|mitochondrial matrix (GO:0005759)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)										TTCTGAAAAGGAGGCAGCTCC	0.537																																					p.E288Q		Atlas-SNP	.											.	KIAA1967	72	.	0			c.G862C						.						54	49	51					8																	22471762		2203	4300	6503	SO:0001583	missense	57805	exon9			GAAAAGGAGGCAG	AL834351	CCDS34863.1	8p22	2013-08-22	2013-08-22	2013-08-22		ENSG00000158941			23360	protein-coding gene	gene with protein product	"deleted in breast cancer"	607359	"KIAA1967"	KIAA1967		12370419	Standard	NM_021174		Approved	DBC-1, DBC1, NET35	uc003xci.3	Q8N163		ENST00000308511.4:c.862G>C	chr8.hg19:g.22471762G>C	ENSP00000310670:p.Glu288Gln	70.0	0.0		23.0	15.0	NM_021174	A6NL03|B2RB79|D3DSR6|Q6P0Q9|Q8N3G7|Q8N8M1|Q8TF34|Q9H9Q9|Q9HD12|Q9NT55	Missense_Mutation	SNP	ENST00000308511.4	hg19	CCDS34863.1	.	.	.	.	.	.	.	.	.	.	G	18.97	3.736328	0.69189	.	.	ENSG00000158941	ENST00000308511;ENST00000389279;ENST00000522599	T;T;T	0.47869	1.38;1.38;0.83	5.47	5.47	0.80525	.	0.068742	0.56097	D	0.000035	T	0.36663	0.0975	N	0.22421	0.69	0.80722	D	1	B	0.31153	0.31	B	0.34138	0.176	T	0.11966	-1.0566	10	0.17832	T	0.49	-20.8075	16.6012	0.84816	0.0:0.0:1.0:0.0	.	288	Q8N163	K1967_HUMAN	Q	288;288;106	ENSP00000310670:E288Q;ENSP00000373930:E288Q;ENSP00000429739:E106Q	ENSP00000310670:E288Q	E	+	1	0	KIAA1967	22527707	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	8.109000	0.89561	2.723000	0.93209	0.655000	0.94253	GAG	.	.		0.537	CCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375865.1	NM_021174		C	22471762	G	C	22471762	3	2	338	1	0	0	0	0	1	0	0	0	8274	1175	41	4	892	4	KIAA1967	8	22471762	Missense_Mutation	SNP	G	TCGA-RC-A7SF-01A-11D-A34Z-10		22471762	123892260	18	46872										
ANK1	286	hgsc.bcm.edu	37	chr8	41552758	41552758	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	atagcggctcctgtgctcctTccacacggagccgttttcgc	10	15	0	0			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr8:41552758T>C	ENST00000347528.4	-	27	3135	c.3052A>G	c.(3052-3054)Aag>Gag	p.K1018E	ANK1_ENST00000352337.4_Missense_Mutation_p.K1018E|ANK1_ENST00000265709.8_Missense_Mutation_p.K1059E|ANK1_ENST00000396942.1_Missense_Mutation_p.K1018E|ANK1_ENST00000289734.7_Missense_Mutation_p.K1018E|ANK1_ENST00000379758.2_Missense_Mutation_p.K1018E|ANK1_ENST00000396945.1_Missense_Mutation_p.K1018E	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	1018	ZU5 1. {ECO:0000255|PROSITE- ProRule:PRU00485}.				axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			CTGTGCTCCTTCCACACGGAG	0.622																																					p.K1059E		Atlas-SNP	.											.	ANK1	497	.	0			c.A3175G						.						109	106	107					8																	41552758		2203	4300	6503	SO:0001583	missense	286	exon28			GCTCCTTCCACAC	M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"Ankyrin repeat domain containing"	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.3052A>G	chr8.hg19:g.41552758T>C	ENSP00000339620:p.Lys1018Glu	43.0	0.0		21.0	17.0	NM_001142446	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Missense_Mutation	SNP	ENST00000347528.4	hg19	CCDS6119.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	22.7|22.7	4.318432|4.318432	0.81469|0.81469	.|.	.|.	ENSG00000029534|ENSG00000029534	ENST00000520299|ENST00000347528;ENST00000289734;ENST00000379758;ENST00000396945;ENST00000396942;ENST00000352337;ENST00000265709;ENST00000358820	.|T;T;T;T;T;T;T	.|0.68479	.|-0.31;-0.32;-0.29;-0.27;-0.29;-0.28;-0.33	5.09|5.09	5.09|5.09	0.68999|0.68999	.|ZU5 (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.75236|0.75236	0.3822|0.3822	M|M	0.74467|0.74467	2.265|2.265	0.80722|0.80722	D|D	1|1	.|P;P;P;D;B;P	.|0.60160	.|0.462;0.838;0.899;0.987;0.325;0.66	.|B;B;B;P;B;P	.|0.52031	.|0.303;0.327;0.413;0.688;0.303;0.58	T|T	0.79921|0.79921	-0.1599|-0.1599	5|10	.|0.87932	.|D	.|0	.|.	14.87|14.87	0.70450|0.70450	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|1059;1018;1018;1018;1018;334	.|P16157-21;P16157-4;P16157;P16157-5;P16157-3;B3KX39	.|.;.;ANK1_HUMAN;.;.;.	G|E	339|1018;1018;1018;1018;1018;1018;1059;1018	.|ENSP00000339620:K1018E;ENSP00000289734:K1018E;ENSP00000369082:K1018E;ENSP00000380149:K1018E;ENSP00000380147:K1018E;ENSP00000309131:K1018E;ENSP00000265709:K1059E	.|ENSP00000265709:K1059E	E|K	-|-	2|1	0|0	ANK1|ANK1	41671915|41671915	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	6.186000|6.186000	0.72026|0.72026	1.904000|1.904000	0.55121|0.55121	0.460000|0.460000	0.39030|0.39030	GAA|AAG	.	.		0.622	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475		C	41552758	T	C	41552758	3	2	338	1	0	0	0	0	1	0	0	0	620	1792	62	2	2983	2	ANK1	8	41552758	Missense_Mutation	SNP	T	TCGA-RC-A7SF-01A-11D-A34Z-10	19080996	41552758	104811264	19	46873										
NOV	4856	hgsc.bcm.edu	37	chr8	120431544	120431544	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	aacagactcggctctgcatgGtgcggccctgtgaacaagag	13	11	1	3			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr8:120431544G>A	ENST00000259526.3	+	4	963	c.736G>A	c.(736-738)Gtg>Atg	p.V246M	RP11-775B15.2_ENST00000519786.1_RNA	NM_002514.3	NP_002505.1	Q9UIW2	PLXA1_HUMAN	nephroblastoma overexpressed	1566	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|skin(3)	21	all_cancers(13;3.84e-26)|Lung NSC(37;1.19e-08)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.000507)			GCTCTGCATGGTGCGGCCCTG	0.557																																					p.V246M		Atlas-SNP	.											.	NOV	51	.	0			c.G736A						.						114	108	110					8																	120431544		2203	4300	6503	SO:0001583	missense	4856	exon4			TGCATGGTGCGGC	X96584	CCDS6328.1	8q24.12	2012-02-27	2012-02-27		ENSG00000136999	ENSG00000136999			7885	protein-coding gene	gene with protein product		164958	"nephroblastoma overexpressed gene"			1334251	Standard	NM_002514		Approved	IGFBP9, CCN3	uc003yoq.2	P48745	OTTHUMG00000164984	ENST00000259526.3:c.736G>A	chr8.hg19:g.120431544G>A	ENSP00000259526:p.Val246Met	24.0	0.0		84.0	18.0	NM_002514		Missense_Mutation	SNP	ENST00000259526.3	hg19	CCDS6328.1	.	.	.	.	.	.	.	.	.	.	G	18.25	3.583257	0.65992	.	.	ENSG00000136999	ENST00000259526	T	0.50277	0.75	5.96	5.96	0.96718	.	0.127113	0.56097	D	0.000028	T	0.52725	0.1752	M	0.65498	2.005	0.36443	D	0.865631	P	0.47762	0.9	P	0.45794	0.493	T	0.64106	-0.6485	10	0.59425	D	0.04	-23.9678	14.0108	0.64495	0.0772:0.0:0.9228:0.0	.	246	P48745	NOV_HUMAN	M	246	ENSP00000259526:V246M	ENSP00000259526:V246M	V	+	1	0	NOV	120500725	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.311000	0.51919	2.832000	0.97577	0.655000	0.94253	GTG	.	.		0.557	NOV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381301.1	NM_002514		A	120431544	G	A	120431544	3	1	338	1	0	0	0	0	1	0	0	0	10562	1261	44	3	750	3	NOV	8	120431544	Missense_Mutation	SNP	G	TCGA-RC-A7SF-01A-11D-A34Z-10	78878786	120431544	25932478	20	46874										
TTC18	118491	hgsc.bcm.edu	37	chr10	75013758	75013758	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	aagatggatttccaaagccaActgtttcctgtagtgtgtgg	11	7	0	1			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr10:75013758A>G	ENST00000310715.3	-	28	3461	c.3341T>C	c.(3340-3342)gTt>gCt	p.V1114A	MRPS16_ENST00000416782.2_5'Flank|TTC18_ENST00000394865.1_Missense_Mutation_p.V1084A|RP11-152N13.5_ENST00000457758.1_RNA|TTC18_ENST00000493787.1_5'UTR|DNAJC9-AS1_ENST00000440197.2_RNA|RP11-152N13.5_ENST00000457147.1_RNA|TTC18_ENST00000401621.2_Missense_Mutation_p.V1114A|TTC18_ENST00000355577.3_Missense_Mutation_p.V583A|MRPS16_ENST00000372945.3_5'Flank|RP11-152N13.5_ENST00000394864.2_RNA|MRPS16_ENST00000479005.1_5'Flank|TTC18_ENST00000340329.3_Missense_Mutation_p.V354A|MRPS16_ENST00000372940.3_5'Flank	NM_145170.3	NP_660153.3	Q5T0N1	TTC18_HUMAN		1114						extracellular vesicular exosome (GO:0070062)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	Prostate(51;0.0119)					TCCAAAGCCAACTGTTTCCTG	0.428																																					p.V1114A		Atlas-SNP	.											.	TTC18	106	.	0			c.T3341C						.						166	149	155					10																	75013758		2203	4300	6503	SO:0001583	missense	118491	exon28			AAGCCAACTGTTT																												ENST00000310715.3:c.3341T>C	chr10.hg19:g.75013758A>G	ENSP00000310829:p.Val1114Ala	69.0	0.0		41.0	25.0	NM_145170	C9JIZ9|Q5T0M4|Q5T0M9|Q5T0N0|Q69YH9|Q8IYZ8|Q8N7D5|Q8NI30|Q8NI31	Missense_Mutation	SNP	ENST00000310715.3	hg19	CCDS7324.3	.	.	.	.	.	.	.	.	.	.	A	22.4	4.285467	0.80803	.	.	ENSG00000156042	ENST00000310715;ENST00000401621;ENST00000355577;ENST00000340329;ENST00000372928;ENST00000433268;ENST00000394865	T;T;T;T;T	0.52754	1.83;1.83;0.93;0.65;1.47	5.13	5.13	0.70059	.	0.078974	0.51477	D	0.000091	T	0.53498	0.1800	M	0.73962	2.25	0.39017	D	0.959676	P	0.50617	0.937	P	0.47827	0.558	T	0.59440	-0.7454	10	0.39692	T	0.17	-1.9903	11.2498	0.49020	1.0:0.0:0.0:0.0	.	1114	Q5T0N1	TTC18_HUMAN	A	1114;1114;1114;354;578;491;1084	ENSP00000310829:V1114A;ENSP00000384479:V1114A;ENSP00000343650:V354A;ENSP00000409527:V491A;ENSP00000378334:V1084A	ENSP00000310829:V1114A	V	-	2	0	TTC18	74683764	1.000000	0.71417	0.996000	0.52242	0.971000	0.66376	4.778000	0.62368	2.152000	0.67230	0.533000	0.62120	GTT	.	.		0.428	TTC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				G	75013758	A	G	75013758	3	3	338	1	0	0	0	0	1	0	0	0	16700	43	2	2	28	2	TTC18	10	75013758	Missense_Mutation	SNP	A	TCGA-RC-A7SF-01A-11D-A34Z-10		75013758	60520989	21	46875										
IDE	3416	hgsc.bcm.edu	37	chr10	94267913	94267913	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	acattaatgataaaaaacatAaaacctcgggctccttcctt	4	10	0	1			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr10:94267913A>G	ENST00000265986.6	-	8	1166	c.1110T>C	c.(1108-1110)ttT>ttC	p.F370F		NM_004969.3	NP_004960.2	P14735	IDE_HUMAN	insulin-degrading enzyme	370					beta-amyloid metabolic process (GO:0050435)|bradykinin catabolic process (GO:0010815)|determination of adult lifespan (GO:0008340)|hormone catabolic process (GO:0042447)|insulin catabolic process (GO:1901143)|insulin metabolic process (GO:1901142)|insulin receptor signaling pathway (GO:0008286)|negative regulation of proteolysis (GO:0045861)|positive regulation of protein oligomerization (GO:0032461)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein homotetramerization (GO:0051289)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|ubiquitin homeostasis (GO:0010992)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|beta-amyloid binding (GO:0001540)|beta-endorphin binding (GO:0031626)|glycoprotein binding (GO:0001948)|insulin binding (GO:0043559)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|urinary_tract(2)	33					"""Insulin(DB00071)|Bacitracin(DB00626)|Insulin Regular(DB00030)"	TAAAAAACATAAAACCTCGGG	0.358																																					p.F370F		Atlas-SNP	.											.	IDE	77	.	0			c.T1110C						.						151	161	158					10																	94267913		2203	4300	6503	SO:0001819	synonymous_variant	3416	exon8			AAACATAAAACCT	M21188	CCDS7421.1, CCDS53554.1	10q23-q25	2007-03-27			ENSG00000119912	ENSG00000119912			5381	protein-coding gene	gene with protein product	"insulysin"	146680				2293021	Standard	NM_004969		Approved		uc001kia.3	P14735	OTTHUMG00000018759	ENST00000265986.6:c.1110T>C	chr10.hg19:g.94267913A>G		170.0	0.0		111.0	41.0	NM_004969	B2R721|B7ZAU2|D3DR35|Q5T5N2	Silent	SNP	ENST00000265986.6	hg19	CCDS7421.1																																																																																			.	.		0.358	IDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049393.1	NM_004969		G	94267913	A	G	94267913	2	3	338	1	0	0	0	0	0	0	0	1	7502	359	13	2		2	IDE	10	94267913	Silent	SNP	A	TCGA-RC-A7SF-01A-11D-A34Z-10	19254155	94267913	41266834	22	46876										
PHRF1	57661	hgsc.bcm.edu	37	chr11	592654	592654	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	cgtgaggacaggcttttgctCtgcgacggctgcgatgcggg	17	10	1	1			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr11:592654C>G	ENST00000264555.5	+	6	728	c.600C>G	c.(598-600)ctC>ctG	p.L200L	PHRF1_ENST00000533464.1_Silent_p.L196L|PHRF1_ENST00000416188.2_Silent_p.L200L|PHRF1_ENST00000413872.2_Silent_p.L199L	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	200					mRNA processing (GO:0006397)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)	RNA polymerase binding (GO:0070063)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|urinary_tract(2)	28						GGCTTTTGCTCTGCGACGGCT	0.652																																					p.L200L		Atlas-SNP	.											.	PHRF1	188	.	0			c.C600G						.						116	134	128					11																	592654		2158	4246	6404	SO:0001819	synonymous_variant	57661	exon6			TTTGCTCTGCGAC	BC004950	CCDS44507.1, CCDS65987.1, CCDS65988.1, CCDS65989.1	11p15.5	2014-06-13			ENSG00000070047	ENSG00000070047		"RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	24351	protein-coding gene	gene with protein product	"CTD binding SR like protein rA9", "protein phosphatase 1, regulatory subunit 125"	611780		RNF221			Standard	XM_005253027		Approved	KIAA1542, PPP1R125	uc010qwc.2	Q9P1Y6	OTTHUMG00000165141	ENST00000264555.5:c.600C>G	chr11.hg19:g.592654C>G		40.0	0.0		26.0	8.0	NM_020901	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Silent	SNP	ENST00000264555.5	hg19																																																																																				.	.		0.652	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901		G	592654	C	G	592654	2	3	338	1	0	0	0	0	0	0	0	1	11870	900	32	4		4	PHRF1	11	592654	Silent	SNP	C	TCGA-RC-A7SF-01A-11D-A34Z-10		592654	134413862	23	46877										
PRKRIR	5612	hgsc.bcm.edu	37	chr11	76063483	76063483	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	ctctcacagatctctagcatCtgcctctgctgtgtttttga	7	12	4	2			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr11:76063483C>T	ENST00000260045.3	-	5	816	c.711G>A	c.(709-711)caG>caA	p.Q237Q	PRKRIR_ENST00000531878.1_5'Flank	NM_004705.2	NP_004696.2	O43422	P52K_HUMAN	protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor)	237					negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)|signal transduction (GO:0007165)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(3)|large_intestine(4)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	25						TCTCTAGCATCTGCCTCTGCT	0.438																																					p.Q237Q		Atlas-SNP	.											.	PRKRIR	65	.	0			c.G711A						.						28	27	27					11																	76063483		2152	4177	6329	SO:0001819	synonymous_variant	5612	exon5			TAGCATCTGCCTC	AF007393	CCDS8243.1	11q13.5	2013-01-25			ENSG00000137492	ENSG00000137492		"THAP (C2CH-type zinc finger) domain containing"	9440	protein-coding gene	gene with protein product	"THAP domain containing 12"	607374				9447982	Standard	NM_004705		Approved	P52rIPK, DAP4, THAP12	uc001oxh.1	O43422	OTTHUMG00000165280	ENST00000260045.3:c.711G>A	chr11.hg19:g.76063483C>T		176.0	0.0		313.0	200.0	NM_004705	A8K728|Q17RY9|Q8WTW1|Q9Y3Z4	Silent	SNP	ENST00000260045.3	hg19	CCDS8243.1																																																																																			.	.		0.438	PRKRIR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383188.1	NM_004705		T	76063483	C	T	76063483	2	4	338	1	0	0	0	0	0	0	0	1	12538	912	32	3		3	PRKRIR	11	76063483	Silent	SNP	C	TCGA-RC-A7SF-01A-11D-A34Z-10	75470829	76063483	58943033	24	46878										
SC5DL	6309	hgsc.bcm.edu	37	chr11	121177921	121177921	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	tatttaagtctgtacatcttGgttaatatctggacaatttc	6	6	3	0			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr11:121177921G>A	ENST00000392789.2	+	5	837	c.600G>A	c.(598-600)ttG>ttA	p.L200L	SC5D_ENST00000534230.1_Silent_p.L200L|SC5D_ENST00000528991.1_3'UTR|SC5D_ENST00000264027.4_Silent_p.L200L	NM_001024956.2	NP_001020127.1	O75845	SC5D_HUMAN	sterol-C5-desaturase	200					cholesterol biosynthetic process (GO:0006695)|cholesterol biosynthetic process via lathosterol (GO:0033490)|fatty acid biosynthetic process (GO:0006633)|lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	C-5 sterol desaturase activity (GO:0000248)|iron ion binding (GO:0005506)|lathosterol oxidase activity (GO:0050046)										TGTACATCTTGGTTAATATCT	0.378																																					p.L200L		Atlas-SNP	.											.	.	.	.	0			c.G600A						.						211	205	207					11																	121177921		2203	4299	6502	SO:0001819	synonymous_variant	6309	exon5			CATCTTGGTTAAT		CCDS8435.1	11q23.3	2013-03-04	2013-03-04	2013-03-04	ENSG00000109929	ENSG00000109929	1.14.21.6	"Fatty acid hydroxylase domain containing"	10547	protein-coding gene	gene with protein product	"lathosterol oxidase"	602286	"sterol-C5-desaturase (fungal ERG3, delta-5-desaturase)-like", "sterol-C5-desaturase (ERG3 delta-5-desaturase homolog, fungal)-like", "sterol-C5-desaturase (ERG3 delta-5-desaturase homolog, S. cerevisiae)-like"	SC5DL		8976377	Standard	NM_006918		Approved		uc001pxu.3	O75845	OTTHUMG00000166068	ENST00000392789.2:c.600G>A	chr11.hg19:g.121177921G>A		201.0	0.0		80.0	22.0	NM_001024956	O00119|Q6GTM5|Q9UK15	Silent	SNP	ENST00000392789.2	hg19	CCDS8435.1																																																																																			.	.		0.378	SC5D-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387702.1	NM_001024956		A	121177921	G	A	121177921	2	1	338	1	0	0	0	0	0	0	0	1	13881	1339	47	3		3	SC5DL	11	121177921	Silent	SNP	G	TCGA-RC-A7SF-01A-11D-A34Z-10	45114438	121177921	13828595	25	46879										
KRT6B	3854	hgsc.bcm.edu	37	chr12	52845422	52845422	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	gggtcaatttgcaggttgagGggagtcaggagactctggtt	17	5	3	2			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr12:52845422G>T	ENST00000252252.3	-	1	488	c.441C>A	c.(439-441)ccC>ccA	p.P147P		NM_005555.3	NP_005546.2	P04259	K2C6B_HUMAN	keratin 6B	147	Head.				ectoderm development (GO:0007398)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(19)|ovary(4)|prostate(2)	40				BRCA - Breast invasive adenocarcinoma(357;0.083)		GCAGGTTGAGGGGAGTCAGGA	0.617																																					p.P147P		Atlas-SNP	.											.	KRT6B	90	.	0			c.C441A						.						116	150	139					12																	52845422		2201	4300	6501	SO:0001819	synonymous_variant	3854	exon1			GTTGAGGGGAGTC	BC034535	CCDS8828.1	12q13.13	2013-01-16	2004-08-11		ENSG00000185479	ENSG00000185479		"-", "Intermediate filaments type II, keratins (basic)"	6444	protein-coding gene	gene with protein product		148042	"keratin-like 1 (a type II keratin sequence)"	KRTL1		1713141, 16831889	Standard	NM_005555		Approved		uc001sak.3	P04259	OTTHUMG00000169593	ENST00000252252.3:c.441C>A	chr12.hg19:g.52845422G>T		187.0	0.0		114.0	34.0	NM_005555	P48669	Silent	SNP	ENST00000252252.3	hg19	CCDS8828.1																																																																																			.	.		0.617	KRT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404969.1	NM_005555		T	52845422	G	T	52845422	2	4	338	1	0	0	0	0	0	0	0	1	8490	1219	43	3		3	KRT6B	12	52845422	Silent	SNP	G	TCGA-RC-A7SF-01A-11D-A34Z-10		52845422	81006473	26	46880										
E2F7	144455	hgsc.bcm.edu	37	chr12	77427753	77427753	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	gcttctgttttgcacagactTgaatctggccatatgtttct	8	9	3	2			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr12:77427753T>G	ENST00000322886.7	-	8	1428	c.1193A>C	c.(1192-1194)cAa>cCa	p.Q398P	E2F7_ENST00000416496.2_Missense_Mutation_p.Q398P	NM_203394.2	NP_976328.2	Q96AV8	E2F7_HUMAN	E2F transcription factor 7	398					chorionic trophoblast cell differentiation (GO:0060718)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|hepatocyte differentiation (GO:0070365)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokinesis (GO:0032466)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|identical protein binding (GO:0042802)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(15)|lung(14)|ovary(3)|upper_aerodigestive_tract(2)	42						TGCACAGACTTGAATCTGGCC	0.443																																					p.Q398P		Atlas-SNP	.											.	E2F7	201	.	0			c.A1193C						.						106	96	99					12																	77427753		2203	4300	6503	SO:0001583	missense	144455	exon8			CAGACTTGAATCT	BC016658	CCDS9016.1	12q21.1	2008-02-05				ENSG00000165891			23820	protein-coding gene	gene with protein product		612046				12893818	Standard	NM_203394		Approved		uc001sym.4	Q96AV8	OTTHUMG00000169969	ENST00000322886.7:c.1193A>C	chr12.hg19:g.77427753T>G	ENSP00000323246:p.Gln398Pro	113.0	0.0		67.0	36.0	NM_203394	A6NC74|B2RMR7|B3KTZ5|B3KUP8|B5MED9	Missense_Mutation	SNP	ENST00000322886.7	hg19	CCDS9016.1	.	.	.	.	.	.	.	.	.	.	T	11.62	1.692498	0.30052	.	.	ENSG00000165891	ENST00000322886;ENST00000416496;ENST00000550669	T;T;T	0.19532	2.4;2.14;2.15	6.17	1.03	0.20045	.	0.864831	0.10780	N	0.634984	T	0.17619	0.0423	M	0.62723	1.935	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.33803	-0.9854	10	0.27785	T	0.31	-1.8517	2.0996	0.03676	0.1237:0.1455:0.1459:0.5849	.	398	Q96AV8	E2F7_HUMAN	P	398	ENSP00000323246:Q398P;ENSP00000393639:Q398P;ENSP00000448245:Q398P	ENSP00000323246:Q398P	Q	-	2	0	E2F7	75951884	0.344000	0.24827	0.113000	0.21522	0.989000	0.77384	0.613000	0.24299	0.214000	0.20742	0.533000	0.62120	CAA	.	.		0.443	E2F7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406716.1	XM_084871		G	77427753	T	G	77427753	3	3	338	1	0	0	0	0	1	0	0	0	4874	1812	63	5	1566	5	E2F7	12	77427753	Missense_Mutation	SNP	T	TCGA-RC-A7SF-01A-11D-A34Z-10	24582331	77427753	56424142	27	46881										
SPRY2	10253	hgsc.bcm.edu	37	chr13	80911669	80911669	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	tcttgggacgacagtaggccCctctgtgtactcattggtgt	12	10	3	0			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr13:80911669C>A	ENST00000377102.1	-	2	1149	c.172G>T	c.(172-174)Ggg>Tgg	p.G58W	SPRY2_ENST00000377104.3_Missense_Mutation_p.G58W|SPRY2_ENST00000540649.1_Missense_Mutation_p.G58W			O43597	SPY2_HUMAN	sprouty homolog 2 (Drosophila)	58					bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment of mitotic spindle orientation (GO:0000132)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inner ear morphogenesis (GO:0042472)|lung growth (GO:0060437)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of Ras GTPase activity (GO:0034261)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|sensory perception of sound (GO:0007605)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase inhibitor activity (GO:0030291)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)	12	Medulloblastoma(90;0.18)	Acute lymphoblastic leukemia(28;0.218)|Breast(118;0.244)		GBM - Glioblastoma multiforme(99;0.0318)		ACAGTAGGCCCCTCTGTGTAC	0.617																																					p.G58W		Atlas-SNP	.											.	SPRY2	28	.	0			c.G172T						.						102	100	101					13																	80911669		2203	4300	6503	SO:0001583	missense	10253	exon2			TAGGCCCCTCTGT	AF039843	CCDS9463.1	13q31.1	2008-05-14	2001-11-28		ENSG00000136158	ENSG00000136158			11270	protein-coding gene	gene with protein product		602466	"sprouty (Drosophila) homolog 2"			9458049	Standard	NM_005842		Approved	hSPRY2	uc001vlj.3	O43597	OTTHUMG00000017140	ENST00000377102.1:c.172G>T	chr13.hg19:g.80911669C>A	ENSP00000366306:p.Gly58Trp	95.0	0.0		42.0	21.0	NM_005842	B2R9J9|Q5T6Z7	Missense_Mutation	SNP	ENST00000377102.1	hg19	CCDS9463.1	.	.	.	.	.	.	.	.	.	.	C	17.21	3.331054	0.60853	.	.	ENSG00000136158	ENST00000377104;ENST00000377102;ENST00000541655;ENST00000540649	T;T;T	0.57273	0.41;0.41;0.41	5.44	4.6	0.57074	.	0.052372	0.85682	D	0.000000	T	0.63141	0.2486	M	0.72894	2.215	0.58432	D	0.999998	D	0.54047	0.964	P	0.54706	0.759	T	0.66960	-0.5791	10	0.87932	D	0	.	10.4188	0.44338	0.0:0.7928:0.1348:0.0723	.	58	O43597	SPY2_HUMAN	W	58	ENSP00000366308:G58W;ENSP00000366306:G58W;ENSP00000439027:G58W	ENSP00000366306:G58W	G	-	1	0	SPRY2	79809670	1.000000	0.71417	0.976000	0.42696	0.998000	0.95712	4.577000	0.60922	1.313000	0.45069	0.650000	0.86243	GGG	.	.		0.617	SPRY2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045387.1			A	80911669	C	A	80911669	3	1	338	1	0	0	0	0	1	0	0	0	15121	623	22	3	779	3	SPRY2	13	80911669	Missense_Mutation	SNP	C	TCGA-RC-A7SF-01A-11D-A34Z-10		80911669	34258209	28	46882										
LIPC	3990	hgsc.bcm.edu	37	chr15	58830682	58830682	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	ggagtgcggcttcaactcctCcctgcctctggtgatgataa	11	12	2	2			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr15:58830682C>T	ENST00000356113.6	+	4	854	c.239C>T	c.(238-240)tCc>tTc	p.S80F	LIPC_ENST00000414170.3_Missense_Mutation_p.S80F|LIPC_ENST00000299022.5_Missense_Mutation_p.S80F|LIPC_ENST00000433326.2_Missense_Mutation_p.S80F			P11150	LIPC_HUMAN	lipase, hepatic	80					cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|chylomicron remnant clearance (GO:0034382)|fatty acid biosynthetic process (GO:0006633)|high-density lipoprotein particle remodeling (GO:0034375)|intermediate-density lipoprotein particle remodeling (GO:0034373)|low-density lipoprotein particle remodeling (GO:0034374)|phosphatidylcholine catabolic process (GO:0034638)|reverse cholesterol transport (GO:0043691)|triglyceride catabolic process (GO:0019433)|triglyceride homeostasis (GO:0070328)|very-low-density lipoprotein particle remodeling (GO:0034372)	extracellular space (GO:0005615)|high-density lipoprotein particle (GO:0034364)	apolipoprotein binding (GO:0034185)|heparin binding (GO:0008201)|low-density lipoprotein particle binding (GO:0030169)|phospholipase activity (GO:0004620)|triglyceride lipase activity (GO:0004806)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		Colorectal(260;0.215)		GBM - Glioblastoma multiforme(80;0.00213)|all cancers(107;0.00548)		TTCAACTCCTCCCTGCCTCTG	0.473																																					p.S80F		Atlas-SNP	.											.	LIPC	56	.	0			c.C239T						.						148	138	141					15																	58830682		2192	4292	6484	SO:0001583	missense	3990	exon2			ACTCCTCCCTGCC		CCDS10166.1	15q21-q23	2012-10-02			ENSG00000166035	ENSG00000166035	3.1.1.3		6619	protein-coding gene	gene with protein product		151670					Standard	NM_000236		Approved	HL, HTGL	uc002afa.2	P11150	OTTHUMG00000132632	ENST00000356113.6:c.239C>T	chr15.hg19:g.58830682C>T	ENSP00000348425:p.Ser80Phe	80.0	0.0		44.0	11.0	NM_000236	A2RUB4|A8K9B6|O43571|P78529|Q99465	Missense_Mutation	SNP	ENST00000356113.6	hg19	CCDS10166.1	.	.	.	.	.	.	.	.	.	.	C	17.89	3.500264	0.64298	.	.	ENSG00000166035	ENST00000356113;ENST00000414170;ENST00000299022;ENST00000433326	D;D;D;D	0.91631	-2.88;-2.88;-2.88;-2.88	5.08	5.08	0.68730	Lipase, N-terminal (1);	0.114849	0.64402	D	0.000011	D	0.96984	0.9015	M	0.90870	3.155	0.21220	N	0.999753	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.91873	0.5509	10	0.87932	D	0	.	18.6648	0.91485	0.0:1.0:0.0:0.0	.	80;80	E7EUK6;P11150	.;LIPC_HUMAN	F	80	ENSP00000348425:S80F;ENSP00000395569:S80F;ENSP00000299022:S80F;ENSP00000395002:S80F	ENSP00000299022:S80F	S	+	2	0	LIPC	56617974	0.965000	0.33210	0.388000	0.26195	0.851000	0.48451	3.191000	0.50981	2.632000	0.89209	0.514000	0.50259	TCC	.	.		0.473	LIPC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416209.1			T	58830682	C	T	58830682	3	4	338	1	0	0	0	0	1	0	0	0	8829	855	30	3	245	3	LIPC	15	58830682	Missense_Mutation	SNP	C	TCGA-RC-A7SF-01A-11D-A34Z-10		58830682	43700710	29	46883										
PDE8A	5151	hgsc.bcm.edu	37	chr15	85610299	85610299	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	gtaatggattctgcagggcaTgtgaaaaagcagggtttaag	14	4	1	1			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr15:85610299T>A	ENST00000310298.4	+	4	550	c.298T>A	c.(298-300)Tgt>Agt	p.C100S	PDE8A_ENST00000394553.1_Missense_Mutation_p.C100S|PDE8A_ENST00000339708.5_Missense_Mutation_p.C100S|PDE8A_ENST00000557819.2_3'UTR|PDE8A_ENST00000557957.1_Missense_Mutation_p.C28S			O60658	PDE8A_HUMAN	phosphodiesterase 8A	100					cAMP catabolic process (GO:0006198)|cyclic nucleotide metabolic process (GO:0009187)|phosphorelay signal transduction system (GO:0000160)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	25	Colorectal(223;0.227)		BRCA - Breast invasive adenocarcinoma(143;0.0608)		Caffeine(DB00201)|Ketotifen(DB00920)	CTGCAGGGCATGTGAAAAAGC	0.383																																					p.C100S		Atlas-SNP	.											.	PDE8A	50	.	0			c.T298A						.						153	135	141					15																	85610299		2203	4299	6502	SO:0001583	missense	5151	exon3			AGGGCATGTGAAA	AF056490	CCDS10336.1, CCDS10337.1, CCDS58397.1	15q25.3	2008-05-14			ENSG00000073417	ENSG00000073417	3.1.4.17	"Phosphodiesterases"	8793	protein-coding gene	gene with protein product		602972				9618252	Standard	NM_001243137		Approved	HsT19550	uc002blh.3	O60658	OTTHUMG00000148670	ENST00000310298.4:c.298T>A	chr15.hg19:g.85610299T>A	ENSP00000311453:p.Cys100Ser	61.0	0.0		41.0	17.0	NM_173454	B3KXE6|H0YMZ7|Q6P9H3|Q969I1|Q96PC9|Q96PD0|Q96PD1|Q96T71|Q9UMB7|Q9UMC3	Missense_Mutation	SNP	ENST00000310298.4	hg19	CCDS10336.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.166748	0.78339	.	.	ENSG00000073417	ENST00000310298;ENST00000394553;ENST00000339708	T;T;T	0.41758	0.99;0.99;0.99	4.79	4.79	0.61399	Signal transduction response regulator, receiver domain (1);	0.047145	0.85682	D	0.000000	T	0.56124	0.1964	L	0.50333	1.59	0.80722	D	1	P;D	0.89917	0.851;1.0	P;D	0.91635	0.493;0.999	T	0.52793	-0.8528	10	0.35671	T	0.21	.	12.6121	0.56556	0.0:0.0:0.0:1.0	.	100;100	O60658-2;O60658	.;PDE8A_HUMAN	S	100	ENSP00000311453:C100S;ENSP00000378056:C100S;ENSP00000340679:C100S	ENSP00000311453:C100S	C	+	1	0	PDE8A	83411303	1.000000	0.71417	0.984000	0.44739	0.996000	0.88848	7.180000	0.77674	2.136000	0.66102	0.533000	0.62120	TGT	.	.		0.383	PDE8A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000309018.1	NM_002605		A	85610299	T	A	85610299	3	1	338	1	0	0	0	0	1	0	0	0	11662	1464	51	4	308	4	PDE8A	15	85610299	Missense_Mutation	SNP	T	TCGA-RC-A7SF-01A-11D-A34Z-10	26779617	85610299	16921093	30	46884										
NFAT5	10725	hgsc.bcm.edu	37	chr16	69689669	69689669	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	aggcactactgttatagaagTcggccttgatcctagcaaca	9	10	0	2			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr16:69689669T>C	ENST00000354436.2	+	5	1427	c.1109T>C	c.(1108-1110)gTc>gCc	p.V370A	NFAT5_ENST00000566899.1_Missense_Mutation_p.V294A|NFAT5_ENST00000349945.1_Missense_Mutation_p.V294A|NFAT5_ENST00000567239.1_Missense_Mutation_p.V388A|NFAT5_ENST00000393742.2_Missense_Mutation_p.V294A|NFAT5_ENST00000432919.1_Missense_Mutation_p.V388A	NM_006599.3	NP_006590.1	O94916	NFAT5_HUMAN	nuclear factor of activated T-cells 5, tonicity-responsive	370	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				cytokine production (GO:0001816)|excretion (GO:0007588)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of calcineurin-NFAT signaling cascade (GO:0070884)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						GTTATAGAAGTCGGCCTTGAT	0.403																																					p.V388A		Atlas-SNP	.											.	NFAT5	184	.	0			c.T1163C						.						124	116	118					16																	69689669		2198	4300	6498	SO:0001583	missense	10725	exon6			TAGAAGTCGGCCT	AF134870	CCDS10881.1, CCDS10882.1, CCDS45519.1	16q22.1	2009-11-24			ENSG00000102908	ENSG00000102908		"Nuclear factor of activated T-cells"	7774	protein-coding gene	gene with protein product		604708				10377394	Standard	NM_173214		Approved	TONEBP, KIAA0827, NFATL1, OREBP, NFATZ, NF-AT5	uc002exl.2	O94916	OTTHUMG00000137572	ENST00000354436.2:c.1109T>C	chr16.hg19:g.69689669T>C	ENSP00000346420:p.Val370Ala	67.0	0.0		23.0	15.0	NM_001113178	A2RRB4|A6H8V5|E9PHR7|O95693|Q7LA65|Q969Q8|Q96QH3|Q9UN18	Missense_Mutation	SNP	ENST00000354436.2	hg19	CCDS10881.1	.	.	.	.	.	.	.	.	.	.	T	28.8	4.953608	0.92660	.	.	ENSG00000102908	ENST00000432919;ENST00000426654;ENST00000349945;ENST00000354436;ENST00000393742	T;T;T;T	0.50813	0.73;0.73;0.73;0.73	5.58	5.58	0.84498	Rel homology (3);p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.63248	0.2495	L	0.47190	1.495	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.85130	0.984;0.984;0.997;0.972	T	0.66110	-0.6005	10	0.87932	D	0	-2.5899	15.7498	0.77976	0.0:0.0:0.0:1.0	.	388;370;388;294	A2RRB4;O94916;E9PHR7;O94916-2	.;NFAT5_HUMAN;.;.	A	388;388;294;370;294	ENSP00000396538:V388A;ENSP00000338806:V294A;ENSP00000346420:V370A;ENSP00000377343:V294A	ENSP00000338806:V294A	V	+	2	0	NFAT5	68247170	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.988000	0.88194	2.131000	0.65755	0.383000	0.25322	GTC	.	.		0.403	NFAT5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268952.2	NM_138714		C	69689669	T	C	69689669	3	2	338	1	0	0	0	0	1	0	0	0	10369	1667	58	2	1185	2	NFAT5	16	69689669	Missense_Mutation	SNP	T	TCGA-RC-A7SF-01A-11D-A34Z-10		69689669	20665084	31	46885										
ABCC3	8714	hgsc.bcm.edu	37	chr17	48745041	48745041	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	aggtggagggcatcaggcagGgtgagctccagctgctgcgc	18	10	1	1			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr17:48745041G>A	ENST00000285238.8	+	12	1638	c.1558G>A	c.(1558-1560)Ggt>Agt	p.G520S	ABCC3_ENST00000427699.1_Missense_Mutation_p.G520S	NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	520	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33			BRCA - Breast invasive adenocarcinoma(22;3.05e-09)		Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Doxorubicin(DB00997)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indomethacin(DB00328)|Lamivudine(DB00709)|Leucovorin(DB00650)|Methotrexate(DB00563)|Metyrapone(DB01011)|Nifedipine(DB01115)|Omeprazole(DB00338)|Phenobarbital(DB01174)|Probenecid(DB01032)|Rifampicin(DB01045)|Sulfinpyrazone(DB01138)|Verapamil(DB00661)|Vincristine(DB00541)	CATCAGGCAGGGTGAGCTCCA	0.627																																					p.G520S		Atlas-SNP	.											.	ABCC3	138	.	0			c.G1558A						.						73	59	64					17																	48745041		2203	4300	6503	SO:0001583	missense	8714	exon12			AGGCAGGGTGAGC	Y17151	CCDS32681.1, CCDS45739.1	17q21	2012-03-14			ENSG00000108846	ENSG00000108846		"ATP binding cassette transporters / subfamily C"	54	protein-coding gene	gene with protein product	"canalicular multispecific organic anion transporter 2"	604323				8894702, 9827529	Standard	NM_003786		Approved	MRP3, cMOAT2, EST90757, MLP2, MOAT-D	uc002isl.3	O15438	OTTHUMG00000162245	ENST00000285238.8:c.1558G>A	chr17.hg19:g.48745041G>A	ENSP00000285238:p.Gly520Ser	38.0	0.0		29.0	11.0	NM_003786	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Missense_Mutation	SNP	ENST00000285238.8	hg19	CCDS32681.1	.	.	.	.	.	.	.	.	.	.	G	12.91	2.078803	0.36662	.	.	ENSG00000108846	ENST00000427699;ENST00000285238	D;D	0.91351	-2.83;-2.49	4.1	-3.37	0.04898	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.969547	0.08502	N	0.936248	T	0.77329	0.4114	N	0.04994	-0.135	0.09310	N	1	B;B	0.13594	0.008;0.001	B;B	0.17433	0.018;0.004	T	0.62623	-0.6815	10	0.44086	T	0.13	0.8153	7.6537	0.28363	0.701:0.0:0.1718:0.1272	.	520;520	O15438;O15438-5	MRP3_HUMAN;.	S	520	ENSP00000395160:G520S;ENSP00000285238:G520S	ENSP00000285238:G520S	G	+	1	0	ABCC3	46100040	0.008000	0.16893	0.005000	0.12908	0.978000	0.69477	0.102000	0.15272	-0.765000	0.04645	0.543000	0.68304	GGT	.	.		0.627	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038		A	48745041	G	A	48745041	3	1	338	1	0	0	0	0	1	0	0	0	54	1232	43	3	1604	3	ABCC3	17	48745041	Missense_Mutation	SNP	G	TCGA-RC-A7SF-01A-11D-A34Z-10		48745041	32450169	32	46886										
CD300C	10871	hgsc.bcm.edu	37	chr17	72540897	72540897	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	ggtttgcaggactgtccctgAtggacactcggccattcctt	11	12	0	1			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr17:72540897A>T	ENST00000330793.1	-	2	611	c.251T>A	c.(250-252)aTc>aAc	p.I84N		NM_006678.3	NP_006669.1	Q08708	CLM6_HUMAN	CD300c molecule	84	Ig-like V-type.				cellular defense response (GO:0006968)|immune system process (GO:0002376)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)			endometrium(2)|kidney(1)|large_intestine(4)|lung(11)|skin(2)|upper_aerodigestive_tract(1)	21						ACTGTCCCTGATGGACACTCG	0.547																																					p.I84N	Esophageal Squamous(66;421 1121 20537 25337 27468)	Atlas-SNP	.											.	CD300C	41	.	0			c.T251A						.						232	175	194					17																	72540897		2203	4300	6503	SO:0001583	missense	10871	exon2			TCCCTGATGGACA	BC022279	CCDS11701.1	17q25.2	2014-05-15	2006-03-28		ENSG00000167850	ENSG00000167850		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	19320	protein-coding gene	gene with protein product		606786	"CD300c antigen"			1349532, 10746781	Standard	NM_006678		Approved	CMRF35, LIR, CMRF-35A, CMRF35A, IGSF16	uc002jky.2	Q08708	OTTHUMG00000067608	ENST00000330793.1:c.251T>A	chr17.hg19:g.72540897A>T	ENSP00000329507:p.Ile84Asn	96.0	0.0		50.0	15.0	NM_006678		Missense_Mutation	SNP	ENST00000330793.1	hg19	CCDS11701.1	.	.	.	.	.	.	.	.	.	.	A	13.40	2.225356	0.39300	.	.	ENSG00000167850	ENST00000330793	T	0.68025	-0.3	4.33	4.33	0.51752	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.47455	D	0.000232	D	0.84915	0.5578	H	0.94886	3.595	0.26518	N	0.974482	D	0.89917	1.0	D	0.97110	1.0	T	0.79024	-0.1972	10	0.87932	D	0	.	10.5252	0.44943	1.0:0.0:0.0:0.0	.	84	Q08708	CLM6_HUMAN	N	84	ENSP00000329507:I84N	ENSP00000329507:I84N	I	-	2	0	CD300C	70052492	1.000000	0.71417	1.000000	0.80357	0.053000	0.15095	2.521000	0.45563	1.920000	0.55613	0.454000	0.30748	ATC	.	.		0.547	CD300C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145084.1	NM_006678		T	72540897	A	T	72540897	3	4	338	1	0	0	0	0	1	0	0	0	2999	333	12	4	435	4	CD300C	17	72540897	Missense_Mutation	SNP	A	TCGA-RC-A7SF-01A-11D-A34Z-10	23795856	72540897	8654313	33	46887										
ZFP161	7541	hgsc.bcm.edu	37	chr18	5291933	5291933	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	aatctttgctgtgtacatgtAgttcaggacctcttcaaata	7	8	4	0			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr18:5291933A>T	ENST00000357006.4	-	4	612	c.274T>A	c.(274-276)Tac>Aac	p.Y92N	ZBTB14_ENST00000400143.3_Missense_Mutation_p.Y92N	NM_001143823.2|NM_001243704.1	NP_001137295.1|NP_001230633.1	O43829	ZBT14_HUMAN	zinc finger and BTB domain containing 14	92	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)										GTGTACATGTAGTTCAGGACC	0.348																																					p.Y92N		Atlas-SNP	.											.	.	.	.	0			c.T274A						.						99	105	103					18																	5291933		2203	4300	6503	SO:0001583	missense	7541	exon4			ACATGTAGTTCAG	D89859	CCDS11837.1	18p11.31	2013-09-19	2013-01-08	2013-01-08	ENSG00000198081	ENSG00000198081		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	12860	protein-coding gene	gene with protein product		602126	"zinc finger protein 161 homolog (mouse)", "zinc finger protein 161", "ZFP161 zinc finger protein"	ZFP161		9244432	Standard	NM_001243702		Approved	ZNF478	uc010dkp.3	O43829	OTTHUMG00000131563	ENST00000357006.4:c.274T>A	chr18.hg19:g.5291933A>T	ENSP00000349503:p.Tyr92Asn	149.0	0.0		52.0	30.0	NM_001243702	O00403|Q2TB80	Missense_Mutation	SNP	ENST00000357006.4	hg19	CCDS11837.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.196790	0.79015	.	.	ENSG00000198081	ENST00000357006;ENST00000400143	T;T	0.71103	-0.54;-0.54	6.07	6.07	0.98685	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	D	0.87759	0.6258	H	0.95816	3.725	0.80722	D	1	D	0.69078	0.997	D	0.85130	0.997	D	0.87654	0.2530	10	0.11794	T	0.64	-34.2054	16.6288	0.85011	1.0:0.0:0.0:0.0	.	92	O43829	ZF161_HUMAN	N	92	ENSP00000349503:Y92N;ENSP00000383009:Y92N	ENSP00000349503:Y92N	Y	-	1	0	ZFP161	5281933	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.281000	0.95811	2.326000	0.78906	0.533000	0.62120	TAC	.	.		0.348	ZBTB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254425.1	NM_003409		T	5291933	A	T	5291933	3	4	338	1	0	0	0	0	1	0	0	0	17655	420	15	4	1079	4	ZFP161	18	5291933	Missense_Mutation	SNP	A	TCGA-RC-A7SF-01A-11D-A34Z-10		5291933	72785315	34	46888										
JUNB	3726	hgsc.bcm.edu	37	chr19	12902979	12902979	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	ggggcggcgtcaccgaggagCaggagggcttcgccgacggc	20	12	1	0			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr19:12902979C>A	ENST00000302754.4	+	1	670	c.394C>A	c.(394-396)Cag>Aag	p.Q132K		NM_002229.2	NP_002220.1	P17275	JUNB_HUMAN	jun B proto-oncogene	132					cellular response to calcium ion (GO:0071277)|cellular response to hormone stimulus (GO:0032870)|decidualization (GO:0046697)|embryonic process involved in female pregnancy (GO:0060136)|gene expression (GO:0010467)|labyrinthine layer blood vessel development (GO:0060716)|osteoblast differentiation (GO:0001649)|osteoblast proliferation (GO:0033687)|osteoclast differentiation (GO:0030316)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to corticosterone (GO:0051412)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to light stimulus (GO:0009416)|response to mechanical stimulus (GO:0009612)|response to peptide hormone (GO:0043434)|response to progesterone (GO:0032570)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|trophectodermal cell differentiation (GO:0001829)|vasculogenesis (GO:0001570)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|cervix(1)|kidney(1)|lung(3)	6						CACCGAGGAGCAGGAGGGCTT	0.687																																					p.Q132K		Atlas-SNP	.											.	JUNB	14	.	0			c.C394A						.						10	10	10					19																	12902979		2117	4203	6320	SO:0001583	missense	3726	exon1			GAGGAGCAGGAGG	M29039	CCDS12280.1	19p13.13	2013-01-10				ENSG00000171223		"basic leucine zipper proteins"	6205	protein-coding gene	gene with protein product		165161				2513129	Standard	NM_002229		Approved		uc002mvc.3	P17275		ENST00000302754.4:c.394C>A	chr19.hg19:g.12902979C>A	ENSP00000303315:p.Gln132Lys	35.0	0.0		33.0	16.0	NM_002229	Q96GH3	Missense_Mutation	SNP	ENST00000302754.4	hg19	CCDS12280.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.883833	0.91814	.	.	ENSG00000171223	ENST00000302754	T	0.35605	1.3	4.53	4.53	0.55603	Jun-like transcription factor (1);	0.000000	0.85682	U	0.000000	T	0.60843	0.2300	M	0.88241	2.94	0.80722	D	1	D	0.56287	0.975	P	0.56042	0.79	T	0.71909	-0.4450	10	0.87932	D	0	-8.7849	16.0705	0.80922	0.0:1.0:0.0:0.0	.	132	P17275	JUNB_HUMAN	K	132	ENSP00000303315:Q132K	ENSP00000303315:Q132K	Q	+	1	0	JUNB	12763979	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.884000	0.69729	2.058000	0.61347	0.549000	0.68633	CAG	.	.		0.687	JUNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451015.1	NM_002229		A	12902979	C	A	12902979	3	1	338	1	0	0	0	0	1	0	0	0	7979	711	25	3	396	3	JUNB	19	12902979	Missense_Mutation	SNP	C	TCGA-RC-A7SF-01A-11D-A34Z-10		12902979	46226004	35	46889										
LYL1	4066	hgsc.bcm.edu	37	chr19	13211948	13211948	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	tctctgccttctcagtcatgGtggggcccacctctgcctgt	10	15	4	0			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr19:13211948G>A	ENST00000264824.4	-	2	398	c.38C>T	c.(37-39)aCc>aTc	p.T13I		NM_005583.4	NP_005574.2	P12980	LYL1_HUMAN	lymphoblastic leukemia associated hematopoiesis regulator 1	13					B cell differentiation (GO:0030183)|blood vessel maturation (GO:0001955)|definitive hemopoiesis (GO:0060216)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(2)|kidney(1)|lung(2)|prostate(1)	7			OV - Ovarian serous cystadenocarcinoma(19;6.08e-22)			CTCAGTCATGGTGGGGCCCAC	0.692			T	TRB@	T-ALL																																p.T13I		Atlas-SNP	.		Dom	yes		19	19p13.2-p13.1	4066	lymphoblastic leukemia derived sequence 1		L	.	LYL1	17	.	0			c.C38T						.						5	6	6					19																	13211948		2084	4116	6200	SO:0001583	missense	4066	exon2			GTCATGGTGGGGC		CCDS12292.1	19p13.2	2014-01-20	2014-01-20			ENSG00000104903		"Basic helix-loop-helix proteins"	6734	protein-coding gene	gene with protein product		151440	"lymphoblastic leukemia derived sequence 1"			2752424	Standard	NM_005583		Approved	bHLHa18	uc002mwi.3	P12980		ENST00000264824.4:c.38C>T	chr19.hg19:g.13211948G>A	ENSP00000264824:p.Thr13Ile	35.0	0.0		37.0	10.0	NM_005583	O76102	Missense_Mutation	SNP	ENST00000264824.4	hg19	CCDS12292.1	.	.	.	.	.	.	.	.	.	.	G	15.59	2.878989	0.51801	.	.	ENSG00000104903	ENST00000264824	D	0.97688	-4.49	4.67	2.37	0.29283	.	0.492587	0.18312	N	0.145081	D	0.93946	0.8062	L	0.40543	1.245	0.23204	N	0.998127	B	0.15141	0.012	B	0.12156	0.007	D	0.88317	0.2960	10	0.59425	D	0.04	-19.1591	4.6531	0.12605	0.1875:0.0:0.6371:0.1754	.	13	P12980	LYL1_HUMAN	I	13	ENSP00000264824:T13I	ENSP00000264824:T13I	T	-	2	0	LYL1	13072948	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.123000	0.31308	0.953000	0.37825	0.555000	0.69702	ACC	.	.		0.692	LYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452827.1	NM_005583		A	13211948	G	A	13211948	3	1	338	1	0	0	0	0	1	0	0	0	9115	1261	44	3	816	3	LYL1	19	13211948	Missense_Mutation	SNP	G	TCGA-RC-A7SF-01A-11D-A34Z-10	308969	13211948	45917035	36	46890										
CYP2A13	1553	hgsc.bcm.edu	37	chr19	41594950	41594950	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	gaccaggctgaggagttcagCgggcgaggcgagcaggccac	18	11	1	1			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr19:41594950C>T	ENST00000330436.3	+	2	297	c.297C>T	c.(295-297)agC>agT	p.S99S		NM_000766.4	NP_000757.2	Q16696	CP2AD_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 13	99					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(6)|kidney(4)|large_intestine(8)|lung(13)|ovary(3)|prostate(3)|skin(2)	42					Methoxsalen(DB00553)|Nicotine(DB00184)|Testosterone(DB00624)	AGGAGTTCAGCGGGCGAGGCG	0.642																																					p.S99S		Atlas-SNP	.											.	CYP2A13	90	.	0			c.C297T						.						62	59	60					19																	41594950		2202	4277	6479	SO:0001819	synonymous_variant	1553	exon2			GTTCAGCGGGCGA	U22028	CCDS12571.1	19q13.2	2013-11-11	2003-01-14		ENSG00000197838	ENSG00000197838		"Cytochrome P450s"	2608	protein-coding gene	gene with protein product		608055	"cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 13"			7668294, 15128046	Standard	NM_000766		Approved	CPAD, CYP2A	uc002opt.4	Q16696	OTTHUMG00000182762	ENST00000330436.3:c.297C>T	chr19.hg19:g.41594950C>T		92.0	0.0		49.0	20.0	NM_000766	Q53YR8|Q6R569|Q6R570|Q9H2X2	Silent	SNP	ENST00000330436.3	hg19	CCDS12571.1																																																																																			.	.		0.642	CYP2A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463505.1	NM_000766		T	41594950	C	T	41594950	2	4	338	1	0	0	0	0	0	0	0	1	4163	767	27	1		1	CYP2A13	19	41594950	Silent	SNP	C	TCGA-RC-A7SF-01A-11D-A34Z-10	28383002	41594950	17534033	37	46891										
PTPRT	11122	hgsc.bcm.edu	37	chr20	40979316	40979316	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	gtttcagcatcactgtgatgGtcgtgtctgtctcattcaat	9	9	5	1			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr20:40979316G>T	ENST00000373187.1	-	11	1816	c.1817C>A	c.(1816-1818)aCc>aAc	p.T606N	PTPRT_ENST00000373184.1_Missense_Mutation_p.T606N|PTPRT_ENST00000373190.1_Missense_Mutation_p.T606N|PTPRT_ENST00000373198.4_Missense_Mutation_p.T606N|PTPRT_ENST00000356100.2_Missense_Mutation_p.T606N|PTPRT_ENST00000373201.1_Missense_Mutation_p.T606N|PTPRT_ENST00000373193.3_Missense_Mutation_p.T606N			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	606	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)			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)				CACTGTGATGGTCGTGTCTGT	0.527																																					p.T606N		Atlas-SNP	.											.	PTPRT	372	.	0			c.C1817A						.						185	192	190					20																	40979316		2082	4218	6300	SO:0001583	missense	11122	exon11			GTGATGGTCGTGT	AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.1817C>A	chr20.hg19:g.40979316G>T	ENSP00000362283:p.Thr606Asn	48.0	0.0		40.0	18.0	NM_007050	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Missense_Mutation	SNP	ENST00000373187.1	hg19	CCDS42874.1	.	.	.	.	.	.	.	.	.	.	G	33	5.269636	0.95429	.	.	ENSG00000196090	ENST00000373190;ENST00000373187;ENST00000373193;ENST00000356100;ENST00000373198;ENST00000373184;ENST00000373201	T;T;T;T;T;T;T	0.39787	1.07;1.06;1.06;1.08;1.08;1.09;1.09	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.69672	0.3137	M	0.84326	2.69	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.71184	0.972;0.937	T	0.70781	-0.4779	10	0.62326	D	0.03	.	20.6208	0.99490	0.0:0.0:1.0:0.0	.	606;606	O14522-1;O14522	.;PTPRT_HUMAN	N	606	ENSP00000362286:T606N;ENSP00000362283:T606N;ENSP00000362289:T606N;ENSP00000348408:T606N;ENSP00000362294:T606N;ENSP00000362280:T606N;ENSP00000362297:T606N	ENSP00000348408:T606N	T	-	2	0	PTPRT	40412730	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.569000	0.98170	2.882000	0.98803	0.655000	0.94253	ACC	.	.		0.527	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			T	40979316	G	T	40979316	3	4	338	1	0	0	0	0	1	0	0	0	12827	1261	44	3	2653	3	PTPRT	20	40979316	Missense_Mutation	SNP	G	TCGA-RC-A7SF-01A-11D-A34Z-10		40979316	22046204	38	46892										
CACNA1I	8911	hgsc.bcm.edu	37	chr22	40060133	40060133	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	cgtgtccaactacatcttcaCggccatcttcgtgggcgaga	10	13	3	1			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr22:40060133C>A	ENST00000402142.3	+	20	3635	c.3635C>A	c.(3634-3636)aCg>aAg	p.T1212K	CACNA1I_ENST00000336649.4_Missense_Mutation_p.T1218K|CACNA1I_ENST00000407673.1_Missense_Mutation_p.T1177K|CACNA1I_ENST00000401624.1_Missense_Mutation_p.T1212K|CACNA1I_ENST00000400164.3_Missense_Mutation_p.T1177K|CACNA1I_ENST00000404898.1_Missense_Mutation_p.T1177K	NM_021096.3	NP_066919.2	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type, alpha 1I subunit	1212					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|signal transduction (GO:0007165)|sleep (GO:0030431)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(2)|lung(27)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Melanoma(58;0.0749)				Cinnarizine(DB00568)|Flunarizine(DB04841)|Paramethadione(DB00617)|Spironolactone(DB00421)|Verapamil(DB00661)|Zonisamide(DB00909)	TACATCTTCACGGCCATCTTC	0.632																																					p.T1212K		Atlas-SNP	.											.	CACNA1I	264	.	0			c.C3635A						.						87	92	90					22																	40060133		1972	4152	6124	SO:0001583	missense	8911	exon20			TCTTCACGGCCAT	AF129133	CCDS46710.1, CCDS46711.1	22q13.1	2012-03-07	2007-02-16		ENSG00000100346	ENSG00000100346		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1396	protein-coding gene	gene with protein product		608230				10454147, 16382099	Standard	NM_021096		Approved	Cav3.3	uc003ayd.3	Q9P0X4	OTTHUMG00000151096	ENST00000402142.3:c.3635C>A	chr22.hg19:g.40060133C>A	ENSP00000385019:p.Thr1212Lys	53.0	0.0		46.0	16.0	NM_021096	B0QY12|B0QY13|B0QY14|O95504|Q5JZ88|Q7Z6S9|Q8NFX6|Q9NZC8|Q9UH15|Q9UH30|Q9ULU9|Q9UNE6	Missense_Mutation	SNP	ENST00000402142.3	hg19	CCDS46710.1	.	.	.	.	.	.	.	.	.	.	C	36	5.632153	0.96682	.	.	ENSG00000100346	ENST00000402142;ENST00000404898;ENST00000401624;ENST00000407673;ENST00000336649;ENST00000400164	D;D;D;D;D;D	0.98849	-5.18;-5.18;-5.18;-5.18;-5.18;-5.18	5.4	5.4	0.78164	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99551	0.9839	H	0.98664	4.295	0.80722	D	1	D;D;D;D	0.89917	0.999;0.996;1.0;0.998	D;D;D;D	0.76071	0.969;0.919;0.987;0.949	D	0.97805	1.0247	10	0.87932	D	0	.	19.1739	0.93594	0.0:1.0:0.0:0.0	.	1177;1212;1177;1212	Q9P0X4-3;Q9P0X4-2;Q9P0X4-4;Q9P0X4	.;.;.;CAC1I_HUMAN	K	1212;1177;1212;1177;1218;1177	ENSP00000385019:T1212K;ENSP00000384093:T1177K;ENSP00000383887:T1212K;ENSP00000385680:T1177K;ENSP00000337829:T1218K;ENSP00000383028:T1177K	ENSP00000337829:T1218K	T	+	2	0	CACNA1I	38390079	1.000000	0.71417	0.998000	0.56505	0.934000	0.57294	7.660000	0.83776	2.521000	0.84997	0.561000	0.74099	ACG	.	.		0.632	CACNA1I-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321290.1	NM_001003406		A	40060133	C	A	40060133	3	1	338	1	0	0	0	0	1	0	0	0	2548	536	19	1	3713	1	CACNA1I	22	40060133	Missense_Mutation	SNP	C	TCGA-RC-A7SF-01A-11D-A34Z-10		40060133	11244433	39	46893										
TTC38	55020	hgsc.bcm.edu	37	chr22	46677505	46677505	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	accctgcgtaggctttatctAttaacccgacagacgcatgg	9	12	1	1	rs370933560		TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chr22:46677505A>G	ENST00000381031.3	+	7	701	c.625A>G	c.(625-627)Att>Gtt	p.I209V	TTC38_ENST00000445282.2_Missense_Mutation_p.I151V	NM_017931.2	NP_060401	Q5R3I4	TTC38_HUMAN	tetratricopeptide repeat domain 38	209						extracellular vesicular exosome (GO:0070062)				endometrium(4)|large_intestine(3)|lung(4)|ovary(1)	12						GGCTTTATCTATTAACCCGAC	0.562																																					p.I209V		Atlas-SNP	.											.	TTC38	40	.	0			c.A625G						.	A	VAL/ILE	0,3988		0,0,1994	109	110	110		625	-8.9	0	22		110	1,8341		0,1,4170	no	missense	TTC38	NM_017931.2	29	0,1,6164	GG,GA,AA		0.012,0.0,0.0081	benign	209/470	46677505	1,12329	1994	4171	6165	SO:0001583	missense	55020	exon7			TTATCTATTAACC		CCDS43030.1	22q13	2013-01-11			ENSG00000075234	ENSG00000075234		"Tetratricopeptide (TTC) repeat domain containing"	26082	protein-coding gene	gene with protein product							Standard	NM_017931		Approved	FLJ20699	uc003bhi.3	Q5R3I4	OTTHUMG00000150494	ENST00000381031.3:c.625A>G	chr22.hg19:g.46677505A>G	ENSP00000370419:p.Ile209Val	64.0	0.0		43.0	14.0	NM_017931	Q8WV27|Q9NWP8	Missense_Mutation	SNP	ENST00000381031.3	hg19	CCDS43030.1	.	.	.	.	.	.	.	.	.	.	A	9.478	1.097324	0.20552	0.0	1.2E-4	ENSG00000075234	ENST00000381031;ENST00000445282	T;T	0.77620	1.41;-1.11	5.79	-8.87	0.00792	Tetratricopeptide-like helical (1);	0.640491	0.16711	N	0.202670	T	0.62307	0.2417	L	0.32530	0.975	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.10450	0.005;0.003	T	0.16837	-1.0389	10	0.44086	T	0.13	-15.3182	15.5879	0.76499	0.2753:0.0981:0.6266:0.0	.	151;209	E7ES35;Q5R3I4	.;TTC38_HUMAN	V	209;151	ENSP00000370419:I209V;ENSP00000393960:I151V	ENSP00000370419:I209V	I	+	1	0	TTC38	45056169	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.419000	0.07071	-2.126000	0.00820	-1.054000	0.02325	ATT	.	.		0.562	TTC38-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000318469.1	NM_017931		G	46677505	A	G	46677505	3	3	338	1	0	0	0	0	1	0	0	0	16721	449	16	2	651	2	TTC38	22	46677505	Missense_Mutation	SNP	A	TCGA-RC-A7SF-01A-11D-A34Z-10	6617372	46677505	4627061	40	46894										
TBL1X	6907	hgsc.bcm.edu	37	chrX	9677338	9677338	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	tctggaatgttgctggcatcCtgctcggatgacatgacatt	11	9	1	2			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chrX:9677338C>G	ENST00000217964.7	+	14	1927	c.1287C>G	c.(1285-1287)tcC>tcG	p.S429S	TBL1X_ENST00000407597.2_Silent_p.S429S|TBL1X_ENST00000424279.1_Silent_p.S378S|TBL1X_ENST00000380961.1_Silent_p.S378S|TBL1X_ENST00000536365.1_Silent_p.S378S	NM_005647.3	NP_005638.1	O60907	TBL1X_HUMAN	transducin (beta)-like 1X-linked	429					canonical Wnt signaling pathway (GO:0060070)|cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|histone binding (GO:0042393)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|cervix(1)|endometrium(5)|large_intestine(7)|lung(2)|ovary(1)|skin(2)	20		Hepatocellular(5;0.000888)				TGCTGGCATCCTGCTCGGATG	0.522											OREG0019658	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S429S		Atlas-SNP	.											.	TBL1X	103	.	0			c.C1287G						.						120	82	95					X																	9677338		2203	4300	6503	SO:0001819	synonymous_variant	6907	exon14			GGCATCCTGCTCG	Y12781	CCDS14133.1, CCDS48078.1	Xp22.3	2013-01-10	2002-05-22	2002-05-24	ENSG00000101849	ENSG00000101849		"WD repeat domain containing"	11585	protein-coding gene	gene with protein product		300196	"transducin (beta)-like 1"	TBL1		10330347	Standard	NM_005647		Approved	EBI	uc004csr.3	O60907	OTTHUMG00000021117	ENST00000217964.7:c.1287C>G	chrX.hg19:g.9677338C>G		93.0	0.0	658	52.0	33.0	NM_001139466	A8K044|A8K4J7|Q86UY2	Silent	SNP	ENST00000217964.7	hg19	CCDS14133.1																																																																																			.	.		0.522	TBL1X-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055709.1	NM_005647		G	9677338	C	G	9677338	2	3	338	1	0	0	0	0	0	0	0	1	15654	668	24	4		4	TBL1X	23	9677338	Silent	SNP	C	TCGA-RC-A7SF-01A-11D-A34Z-10		9677338	145593222	41	46895										
ENOX2	10495	hgsc.bcm.edu	37	chrX	129813524	129813524	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0714285714285714	3	1	1.74795081967213	2.33060109289617	1.55373406193078	1	1	0	ctaaacacctaccagacagaTacagggctttgtccaccatg	7	13	0	2			TCGA-RC-A7SF-01A-11D-A34Z-10	TCGA-RC-A7SF-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6704f86-2ea2-4f7c-8043-351f98123fc8	e9d14b6e-0f63-4c76-8189-1f7e8fad71db	g.chrX:129813524T>C	ENST00000370927.1	-	4	560	c.539A>G	c.(538-540)tAt>tGt	p.Y180C	ENOX2_ENST00000338144.3_Missense_Mutation_p.Y180C|ENOX2_ENST00000370935.1_Missense_Mutation_p.Y151C|ENOX2_ENST00000394363.1_Missense_Mutation_p.Y151C|ENOX2_ENST00000492263.1_5'Flank			Q16206	ENOX2_HUMAN	ecto-NOX disulfide-thiol exchanger 2	180	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cell growth (GO:0016049)|oxidation-reduction process (GO:0055114)|regulation of growth (GO:0040008)|ultradian rhythm (GO:0007624)	cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)	nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|protein disulfide oxidoreductase activity (GO:0015035)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(3)	33						ACCAGACAGATACAGGGCTTT	0.453																																					p.Y180C	Ovarian(101;828 1506 2951 9500 35258)	Atlas-SNP	.											.	ENOX2	70	.	0			c.A539G						.						217	189	198					X																	129813524		2203	4300	6503	SO:0001583	missense	10495	exon7			GACAGATACAGGG	AF207881	CCDS14626.1, CCDS14627.1	Xq25	2013-02-12	2007-03-23	2007-03-23	ENSG00000165675	ENSG00000165675		"RNA binding motif (RRM) containing"	2259	protein-coding gene	gene with protein product		300282	"cytosolic ovarian carcinoma antigen 1"	COVA1		8150545, 11888291	Standard	NM_006375		Approved	APK1, tNOX	uc004evw.3	Q16206	OTTHUMG00000022401	ENST00000370927.1:c.539A>G	chrX.hg19:g.129813524T>C	ENSP00000359965:p.Tyr180Cys	83.0	0.0		49.0	43.0	NM_182314	A8K197|A8K1C2|Q5VTJ1|Q5VTJ2|Q8WUX0|Q9NTP6|Q9UH82	Missense_Mutation	SNP	ENST00000370927.1	hg19	CCDS14626.1	.	.	.	.	.	.	.	.	.	.	t	19.34	3.809744	0.70797	.	.	ENSG00000165675	ENST00000538435;ENST00000370935;ENST00000338144;ENST00000394363;ENST00000350369;ENST00000370927;ENST00000432489	T;T;T;T;T	0.16073	2.37;2.37;2.37;2.37;2.37	5.36	5.36	0.76844	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.068024	0.64402	D	0.000008	T	0.25644	0.0624	L	0.35644	1.08	0.38372	D	0.944901	D;P	0.58970	0.984;0.944	P;P	0.58660	0.843;0.735	T	0.04427	-1.0952	9	.	.	.	-11.6689	12.0624	0.53570	0.0:0.0:0.0:1.0	.	180;208	Q16206;A4QPE1	ENOX2_HUMAN;.	C	151;151;180;151;208;180;151	ENSP00000359973:Y151C;ENSP00000337146:Y180C;ENSP00000377890:Y151C;ENSP00000359965:Y180C;ENSP00000400304:Y151C	.	Y	-	2	0	ENOX2	129641205	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.390000	0.59646	1.978000	0.57642	0.483000	0.47432	TAT	.	.		0.453	ENOX2-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058277.1	NM_182314		C	129813524	T	C	129813524	3	2	338	1	0	0	0	0	1	0	0	0	5129	1406	49	2	1333	2	ENOX2	23	129813524	Missense_Mutation	SNP	T	TCGA-RC-A7SF-01A-11D-A34Z-10	120136186	129813524	25457036	42	46896										
UBE4B	10277	hgsc.bcm.edu	37	chr1	10211424	10211424	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	atgagccctgtactcaggatAttgtgatgttccttgttgtg	11	7	1	2			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr1:10211424A>G	ENST00000253251.8	+	20	3183	c.2344A>G	c.(2344-2346)Att>Gtt	p.I782V	UBE4B_ENST00000343090.6_Missense_Mutation_p.I911V|UBE4B_ENST00000377157.3_Missense_Mutation_p.I666V					ubiquitination factor E4B											NS(3)|breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(14)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	48		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		TACTCAGGATATTGTGATGTT	0.463																																					p.I911V		Atlas-SNP	.											.	UBE4B	233	.	0			c.A2731G						.						144	138	140					1																	10211424		2203	4300	6503	SO:0001583	missense	10277	exon21			CAGGATATTGTGA	AF091093	CCDS110.1, CCDS41245.1	1p36.1	2013-01-28	2011-05-19		ENSG00000130939	ENSG00000130939		"U-box domain containing"	12500	protein-coding gene	gene with protein product		613565	"ubiquitination factor E4B (homologous to yeast UFD2)", "ubiquitination factor E4B (UFD2 homolog, yeast)"			9734811, 10089879	Standard	NM_006048		Approved	UBOX3, E4, UFD2, KIAA0684	uc001aqs.4	O95155	OTTHUMG00000001797	ENST00000253251.8:c.2344A>G	chr1.hg19:g.10211424A>G	ENSP00000253251:p.Ile782Val	146.0	0.0		96.0	84.0	NM_001105562		Missense_Mutation	SNP	ENST00000253251.8	hg19	CCDS110.1	.	.	.	.	.	.	.	.	.	.	A	13.18	2.159028	0.38119	.	.	ENSG00000130939	ENST00000253251;ENST00000377157;ENST00000343090	T;T;T	0.45668	0.89;0.89;0.89	5.33	1.76	0.24704	Ubiquitin conjugation factor E4, core (1);	0.049545	0.85682	D	0.000000	T	0.27454	0.0674	L	0.31926	0.97	0.44409	D	0.997324	B;B;B	0.18461	0.001;0.028;0.001	B;B;B	0.15870	0.004;0.014;0.003	T	0.06180	-1.0841	10	0.21540	T	0.41	-8.3086	8.8945	0.35455	0.6261:0.0:0.3739:0.0	.	782;911;782	A8K8S9;O95155;O95155-2	.;UBE4B_HUMAN;.	V	782;666;911	ENSP00000253251:I782V;ENSP00000366362:I666V;ENSP00000343001:I911V	ENSP00000253251:I782V	I	+	1	0	UBE4B	10134011	0.999000	0.42202	0.971000	0.41717	0.949000	0.60115	1.427000	0.34881	0.048000	0.15891	-0.467000	0.05162	ATT	.	.		0.463	UBE4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005017.1	NM_006048		G	10211424	A	G	10211424	3	3	339	1	0	0	0	0	1	0	0	0	16898	449	16	2	2813	2	UBE4B	1	10211424	Missense_Mutation	SNP	A	TCGA-RC-A7SH-01A-11D-A382-10		10211424	239039197	1	46897										
KIAA0494	9813	hgsc.bcm.edu	37	chr1	47150244	47150244	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	ctggagtttctctcttagctTggatacctgagaatttgaac	9	8	2	2			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr1:47150244T>C	ENST00000371933.3	-	9	2081	c.1105A>G	c.(1105-1107)Aag>Gag	p.K369E	EFCAB14_ENST00000484461.1_5'UTR|EFCAB14-AS1_ENST00000418985.1_RNA|EFCAB14-AS1_ENST00000442839.1_RNA|EFCAB14_ENST00000544071.1_Missense_Mutation_p.K305E	NM_014774.2	NP_055589.1	O75071	EFC14_HUMAN	EF-hand calcium binding domain 14	369							calcium ion binding (GO:0005509)										TCTCTTAGCTTGGATACCTGA	0.443																																					p.K369E		Atlas-SNP	.											.	.	.	.	0			c.A1105G						.						115	113	114					1																	47150244		2203	4300	6503	SO:0001583	missense	9813	exon9			TTAGCTTGGATAC	AB007963	CCDS30706.1	1p33	2013-01-10	2012-11-29	2012-11-29	ENSG00000159658	ENSG00000159658		"EF-hand domain containing"	29051	protein-coding gene	gene with protein product			"KIAA0494"	KIAA0494		9455484	Standard	NM_014774		Approved		uc001cqk.4	O75071	OTTHUMG00000007992	ENST00000371933.3:c.1105A>G	chr1.hg19:g.47150244T>C	ENSP00000361001:p.Lys369Glu	70.0	0.0		49.0	37.0	NM_014774	D3DQ23|Q5SXB8	Missense_Mutation	SNP	ENST00000371933.3	hg19	CCDS30706.1	.	.	.	.	.	.	.	.	.	.	T	13.43	2.236118	0.39498	.	.	ENSG00000159658	ENST00000544071;ENST00000371933	D;T	0.95518	-3.73;1.9	5.43	3.12	0.35913	.	0.448963	0.25783	N	0.028331	D	0.88392	0.6424	N	0.21448	0.665	0.23834	N	0.996718	B;B;B;B	0.14438	0.006;0.005;0.01;0.003	B;B;B;B	0.13407	0.009;0.006;0.006;0.004	T	0.74084	-0.3779	10	0.15066	T	0.55	-4.6064	6.6632	0.23027	0.0:0.0784:0.1545:0.7671	.	161;305;305;369	B7Z3D1;F5H7K3;B7Z444;O75071	.;.;.;K0494_HUMAN	E	305;369	ENSP00000442465:K305E;ENSP00000361001:K369E	ENSP00000361001:K369E	K	-	1	0	KIAA0494	46922831	1.000000	0.71417	0.992000	0.48379	0.998000	0.95712	1.814000	0.38972	0.511000	0.28236	0.528000	0.53228	AAG	.	.		0.443	EFCAB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021931.1	NM_014774		C	47150244	T	C	47150244	3	2	339	1	0	0	0	0	1	0	0	0	8188	1821	63	2	394	2	KIAA0494	1	47150244	Missense_Mutation	SNP	T	TCGA-RC-A7SH-01A-11D-A382-10	36938820	47150244	202100377	2	46898										
C1orf51	148523	hgsc.bcm.edu	37	chr1	150255908	150255908	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	tccggtaaccagcatacaccAtctcatccgaaacagcgggg	9	14	1	0			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr1:150255908A>G	ENST00000290363.5	+	1	680	c.231A>G	c.(229-231)ccA>ccG	p.P77P	C1orf51_ENST00000369094.1_5'UTR|C1orf51_ENST00000369095.1_Silent_p.P77P|C1orf51_ENST00000469255.1_3'UTR	NM_144697.2	NP_653298.1	Q8N365	CIART_HUMAN		77					circadian regulation of gene expression (GO:0032922)|locomotor rhythm (GO:0045475)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|E-box binding (GO:0070888)			endometrium(3)|large_intestine(2)|lung(3)|urinary_tract(2)	10	Lung NSC(24;7.29e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGCATACACCATCTCATCCGA	0.572																																					p.P77P		Atlas-SNP	.											.	C1orf51	35	.	0			c.A231G						.						142	139	140					1																	150255908		2203	4300	6503	SO:0001819	synonymous_variant	148523	exon1			TACACCATCTCAT																												ENST00000290363.5:c.231A>G	chr1.hg19:g.150255908A>G		155.0	0.0		304.0	141.0	NM_144697	B2RD43|D3DV01|Q8N795|Q96MG6	Silent	SNP	ENST00000290363.5	hg19	CCDS949.1																																																																																			.	.		0.572	C1orf51-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035058.1			G	150255908	A	G	150255908	2	3	339	1	0	0	0	0	0	0	0	1	2045	204	8	2		2	C1orf51	1	150255908	Silent	SNP	A	TCGA-RC-A7SH-01A-11D-A382-10	103105664	150255908	98994713	3	46899										
GON4L	54856	hgsc.bcm.edu	37	chr1	155735915	155735915	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	tcttctctttgagggtctccGtctcacatatggctttcgaa	8	11	4	1			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr1:155735915G>A	ENST00000368331.1	-	21	3397	c.3349C>T	c.(3349-3351)Cgg>Tgg	p.R1117W	GON4L_ENST00000361040.5_Missense_Mutation_p.R1117W|GON4L_ENST00000437809.1_Missense_Mutation_p.R1117W|GON4L_ENST00000271883.5_Missense_Mutation_p.R1117W|GON4L_ENST00000471341.1_5'UTR	NM_001282858.1|NM_001282860.1	NP_001269787.1|NP_001269789.1	Q3T8J9	GON4L_HUMAN	gon-4-like (C. elegans)	1117					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	45	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					GAGGGTCTCCGTCTCACATAT	0.532																																					p.R1117W		Atlas-SNP	.											.	GON4L	392	.	0			c.C3349T						.						128	122	124					1																	155735915		2203	4300	6503	SO:0001583	missense	54856	exon21			GTCTCCGTCTCAC	AB046826	CCDS1121.1, CCDS44242.1, CCDS60296.1	1q22	2013-10-31	2006-11-08	2006-02-16	ENSG00000116580	ENSG00000116580			25973	protein-coding gene	gene with protein product		610393	"gon-4 homolog (C.elegans)"	GON4		16545939, 21454521	Standard	XM_005245283		Approved	FLJ20203, GON-4	uc001fly.1	Q3T8J9	OTTHUMG00000014106	ENST00000368331.1:c.3349C>T	chr1.hg19:g.155735915G>A	ENSP00000357315:p.Arg1117Trp	141.0	0.0		294.0	16.0	NM_001037533	B7ZBL4|Q14C93|Q3T8J8|Q5VYZ5|Q5W0D5|Q6AWA6|Q6P1Q6|Q7Z3L3|Q8IY79|Q9BQI1|Q9HCG6	Missense_Mutation	SNP	ENST00000368331.1	hg19		.	.	.	.	.	.	.	.	.	.	G	9.775	1.173736	0.21704	.	.	ENSG00000116580	ENST00000437809;ENST00000368331;ENST00000271883;ENST00000361040	T;T;T;T	0.49720	0.77;0.77;0.77;0.77	5.28	3.32	0.38043	.	0.372495	0.23515	N	0.047351	T	0.12860	0.0312	N	0.19112	0.55	0.09310	N	1	B;B;B;B	0.28378	0.066;0.049;0.133;0.209	B;B;B;B	0.27500	0.011;0.007;0.037;0.08	T	0.05162	-1.0902	10	0.49607	T	0.09	.	4.9596	0.14059	0.1551:0.0:0.4804:0.3645	.	1117;313;1117;1117	Q3T8J9-2;Q1ED43;Q3T8J9;Q3T8J9-3	.;.;GON4L_HUMAN;.	W	1117	ENSP00000396117:R1117W;ENSP00000357315:R1117W;ENSP00000271883:R1117W;ENSP00000354322:R1117W	ENSP00000271883:R1117W	R	-	1	2	GON4L	154002539	0.035000	0.19736	0.958000	0.39756	0.362000	0.29581	0.963000	0.29293	1.415000	0.47037	0.655000	0.94253	CGG	.	.		0.532	GON4L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_032292		A	155735915	G	A	155735915	3	1	339	1	0	0	0	0	1	0	0	0	6580	1144	40	1	3538	1	GON4L	1	155735915	Missense_Mutation	SNP	G	TCGA-RC-A7SH-01A-11D-A382-10	5480007	155735915	93514706	4	46900										
ETV3	2117	hgsc.bcm.edu	37	chr1	157095415	157095415	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	aaggacacctccgcggccagGgattggagagacagcgaagg	16	10	0	1			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr1:157095415G>A	ENST00000368192.4	-	5	821	c.757C>T	c.(757-759)Cct>Tct	p.P253S		NM_001145312.1	NP_001138784.1	P41162	ETV3_HUMAN	ets variant 3	253					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)	9	Hepatocellular(266;0.158)	Prostate(1639;0.174)				CCGCGGCCAGGGATTGGAGAG	0.567																																					p.P253S		Atlas-SNP	.											.	ETV3	50	.	0			c.C757T						.						130	124	126					1																	157095415		692	1591	2283	SO:0001583	missense	2117	exon5			GGCCAGGGATTGG	BC022868	CCDS1164.1, CCDS44250.1	1q21-q23	2008-09-12	2008-09-12		ENSG00000117036	ENSG00000117036			3492	protein-coding gene	gene with protein product		164873	"ets variant gene 3, ETS family transcriptional repressor", "ets variant gene 3"			8020980	Standard	NM_005240		Approved	PE-1	uc001fqr.2	P41162	OTTHUMG00000034298	ENST00000368192.4:c.757C>T	chr1.hg19:g.157095415G>A	ENSP00000357175:p.Pro253Ser	197.0	0.0		355.0	74.0	NM_001145312	B4E3M7|Q8TAC8|Q9BX30	Missense_Mutation	SNP	ENST00000368192.4	hg19	CCDS44250.1	.	.	.	.	.	.	.	.	.	.	G	19.86	3.905351	0.72868	.	.	ENSG00000117036	ENST00000368192	T	0.32515	1.45	4.9	3.96	0.45880	.	0.090092	0.47852	D	0.000212	T	0.37598	0.1009	L	0.53249	1.67	0.80722	D	1	D	0.71674	0.998	D	0.66979	0.948	T	0.23619	-1.0183	10	0.49607	T	0.09	.	14.2903	0.66273	0.0:0.1503:0.8497:0.0	.	253	P41162	ETV3_HUMAN	S	253	ENSP00000357175:P253S	ENSP00000357175:P253S	P	-	1	0	ETV3	155362039	1.000000	0.71417	0.995000	0.50966	0.991000	0.79684	4.956000	0.63645	1.384000	0.46424	0.561000	0.74099	CCT	.	.		0.567	ETV3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082843.2	NM_005240		A	157095415	G	A	157095415	3	1	339	1	0	0	0	0	1	0	0	0	5281	1232	43	3	785	3	ETV3	1	157095415	Missense_Mutation	SNP	G	TCGA-RC-A7SH-01A-11D-A382-10	1359500	157095415	92155206	5	46901										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158607950	158607950	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	acgcttgttgacattatcttTtttcttcacaatctgatcaa	4	9	5	2			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr1:158607950T>G	ENST00000368147.4	-	36	5242	c.5062A>C	c.(5062-5064)Aaa>Caa	p.K1688Q		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1688					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					ACATTATCTTTTTTCTTCACA	0.443																																					p.K1688Q		Atlas-SNP	.											.	SPTA1	720	.	0			c.A5062C						.						96	89	91					1																	158607950		1882	4111	5993	SO:0001583	missense	6708	exon36			TATCTTTTTTCTT	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.5062A>C	chr1.hg19:g.158607950T>G	ENSP00000357129:p.Lys1688Gln	88.0	0.0		122.0	29.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	T	7.137	0.580974	0.13686	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.49139	0.79;0.79	5.36	2.93	0.34026	.	1.073180	0.07483	N	0.904274	T	0.09642	0.0237	N	0.04508	-0.205	0.23913	N	0.996486	B	0.11235	0.004	B	0.14023	0.01	T	0.28713	-1.0035	10	0.12103	T	0.63	.	11.4052	0.49894	0.0:0.0:0.3493:0.6507	.	1688	P02549	SPTA1_HUMAN	Q	1688	ENSP00000357130:K1688Q;ENSP00000357129:K1688Q	ENSP00000357129:K1688Q	K	-	1	0	SPTA1	156874574	0.886000	0.30341	0.135000	0.22099	0.002000	0.02628	3.527000	0.53517	1.010000	0.39314	0.482000	0.46254	AAA	.	.		0.443	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		G	158607950	T	G	158607950	3	3	339	1	0	0	0	0	1	0	0	0	15131	1850	64	5	2265	5	SPTA1	1	158607950	Missense_Mutation	SNP	T	TCGA-RC-A7SH-01A-11D-A382-10	1512535	158607950	90642671	6	46902										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181754899	181754899	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	ccttcatctctgcctcaggaGatcattgctaatgccaaagc	7	13	4	1			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr1:181754899G>A	ENST00000367573.2	+	43	5730	c.5730G>A	c.(5728-5730)gaG>gaA	p.E1910E	CACNA1E_ENST00000360108.3_Silent_p.E1891E|CACNA1E_ENST00000358338.5_Silent_p.E1842E|CACNA1E_ENST00000357570.5_Silent_p.E1861E|CACNA1E_ENST00000367567.4_Silent_p.E1517E|CACNA1E_ENST00000367570.1_Silent_p.E1910E|CACNA1E_ENST00000526775.1_Silent_p.E1891E	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1910					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)	p.E1910D(2)		NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						TGCCTCAGGAGATCATTGCTA	0.507																																					p.E1910E		Atlas-SNP	.											CACNA1E,NS,carcinoma,0,1	CACNA1E	778	.	2	Substitution - Missense(2)	endometrium(2)	c.G5730A						.						191	185	187					1																	181754899		1923	4144	6067	SO:0001819	synonymous_variant	777	exon43			TCAGGAGATCATT	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.5730G>A	chr1.hg19:g.181754899G>A		195.0	0.0		357.0	99.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Silent	SNP	ENST00000367573.2	hg19	CCDS55664.1																																																																																			.	.		0.507	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		A	181754899	G	A	181754899	2	1	339	1	0	0	0	0	0	0	0	1	2544	933	33	3		3	CACNA1E	1	181754899	Silent	SNP	G	TCGA-RC-A7SH-01A-11D-A382-10	23146949	181754899	67495722	7	46903										
NCOA1	8648	hgsc.bcm.edu	37	chr2	24930641	24930641	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	gatcaactccaaacctgagcCtggatgatgtaaaggtgaaa	10	8	1	3			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr2:24930641C>G	ENST00000406961.1	+	13	2954	c.2302C>G	c.(2302-2304)Ctg>Gtg	p.L768V	NCOA1_ENST00000407230.1_Missense_Mutation_p.L617V|NCOA1_ENST00000405141.1_Missense_Mutation_p.L768V|NCOA1_ENST00000348332.3_Missense_Mutation_p.L768V|NCOA1_ENST00000538539.1_Missense_Mutation_p.L768V|NCOA1_ENST00000288599.5_Missense_Mutation_p.L768V|NCOA1_ENST00000395856.3_Missense_Mutation_p.L768V			Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1	768					androgen receptor signaling pathway (GO:0030521)|cellular lipid metabolic process (GO:0044255)|cellular response to hormone stimulus (GO:0032870)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|estrous cycle phase (GO:0060206)|hippocampus development (GO:0021766)|histone H4 acetylation (GO:0043967)|hypothalamus development (GO:0021854)|labyrinthine layer morphogenesis (GO:0060713)|lactation (GO:0007595)|male gonad development (GO:0008584)|male mating behavior (GO:0060179)|ovulation cycle (GO:0042698)|positive regulation of apoptotic process (GO:0043065)|positive regulation of female receptivity (GO:0045925)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by galactose (GO:0000435)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular response to drug (GO:2001038)|response to estradiol (GO:0032355)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region DNA binding (GO:0001012)|RNA polymerase II transcription coactivator activity (GO:0001105)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)		PAX3/NCOA1(8)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(26)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	53	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AAACCTGAGCCTGGATGATGT	0.383			T	PAX3	alveolar rhadomyosarcoma																																p.L768V		Atlas-SNP	.		Dom	yes		2	2p23	8648	nuclear receptor coactivator 1		M	.	NCOA1	210	.	0			c.C2302G						.						66	63	64					2																	24930641		2203	4300	6503	SO:0001583	missense	8648	exon11			CTGAGCCTGGATG	U40396	CCDS1712.1, CCDS1713.1, CCDS42660.1	2p23	2011-07-01			ENSG00000084676	ENSG00000084676		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7668	protein-coding gene	gene with protein product		602691				7481822, 9575154	Standard	XM_005264625		Approved	SRC1, F-SRC-1, NCoA-1, KAT13A, RIP160, bHLHe74	uc002rfk.3	Q15788	OTTHUMG00000125523	ENST00000406961.1:c.2302C>G	chr2.hg19:g.24930641C>G	ENSP00000385216:p.Leu768Val	380.0	1.0		303.0	117.0	NM_147223	O00150|O43792|O43793|Q13071|Q13420|Q2T9G5|Q53SX3|Q6GVI5|Q7KYV3	Missense_Mutation	SNP	ENST00000406961.1	hg19	CCDS1712.1	.	.	.	.	.	.	.	.	.	.	C	15.41	2.826331	0.50739	.	.	ENSG00000084676	ENST00000406961;ENST00000405141;ENST00000407230;ENST00000538539;ENST00000348332;ENST00000288599;ENST00000395856	T;T;T;T;T;T;T	0.02525	4.36;4.35;4.26;4.35;4.36;4.35;4.36	6.04	2.22	0.28083	.	0.066860	0.64402	D	0.000008	T	0.07143	0.0181	L	0.34521	1.04	0.53688	D	0.999977	D;D;D;D	0.67145	0.996;0.993;0.958;0.993	D;D;P;D	0.76071	0.986;0.967;0.827;0.987	T	0.25467	-1.0131	10	0.40728	T	0.16	.	10.2693	0.43473	0.0:0.7304:0.0:0.2696	.	768;768;768;617	Q15788-3;Q15788;Q15788-2;B5MCN7	.;NCOA1_HUMAN;.;.	V	768;768;617;768;768;768;768	ENSP00000385216:L768V;ENSP00000385097:L768V;ENSP00000385195:L617V;ENSP00000444039:L768V;ENSP00000320940:L768V;ENSP00000288599:L768V;ENSP00000379197:L768V	ENSP00000288599:L768V	L	+	1	2	NCOA1	24784145	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	1.824000	0.39072	0.129000	0.18514	0.563000	0.77884	CTG	.	.		0.383	NCOA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246852.3	NM_147223		G	24930641	C	G	24930641	3	3	339	1	0	0	0	0	1	0	0	0	10237	680	24	4	2336	4	NCOA1	2	24930641	Missense_Mutation	SNP	C	TCGA-RC-A7SH-01A-11D-A382-10		24930641	218268732	8	46904										
TUBA3D	113457	hgsc.bcm.edu	37	chr2	132238155	132238155	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	agatcaccaatgcctgcttcGagccagccaatcaaatggtc	8	13	2	1			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr2:132238155G>A	ENST00000321253.6	+	4	996	c.889G>A	c.(889-891)Gag>Aag	p.E297K		NM_080386.3	NP_525125.2	Q13748	TBA3C_HUMAN	tubulin, alpha 3d	297					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	32				BRCA - Breast invasive adenocarcinoma(221;0.13)		TGCCTGCTTCGAGCCAGCCAA	0.597																																					p.E297K	Ovarian(137;2059 2432 35543 39401)	Atlas-SNP	.											.	TUBA3D	60	.	0			c.G889A						.						94	127	116					2																	132238155		2202	4300	6502	SO:0001583	missense	113457	exon4			TGCTTCGAGCCAG	K03460	CCDS33290.1	2q21.1	2007-03-16			ENSG00000075886	ENSG00000075886		"Tubulins"	24071	protein-coding gene	gene with protein product	"alpha-tubulin isotype H2-alpha"					3785200	Standard	NM_080386		Approved	H2-ALPHA	uc002tsu.4	Q13748	OTTHUMG00000153600	ENST00000321253.6:c.889G>A	chr2.hg19:g.132238155G>A	ENSP00000326042:p.Glu297Lys	136.0	0.0		99.0	27.0	NM_080386	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Missense_Mutation	SNP	ENST00000321253.6	hg19	CCDS33290.1	.	.	.	.	.	.	.	.	.	.	g	14.15	2.449913	0.43531	.	.	ENSG00000075886	ENST00000321253;ENST00000341158	D	0.84730	-1.89	2.24	2.24	0.28232	Tubulin/FtsZ, 2-layer sandwich domain (3);Tubulin/FtsZ, C-terminal (1);	0.000000	0.46442	U	0.000298	D	0.93403	0.7896	H	0.97707	4.06	0.47441	D	0.99942	D	0.58620	0.983	P	0.60886	0.88	D	0.93888	0.7177	10	0.87932	D	0	.	10.1507	0.42791	0.0:0.0:1.0:0.0	.	297	Q13748	TBA3C_HUMAN	K	297	ENSP00000326042:E297K	ENSP00000326042:E297K	E	+	1	0	TUBA3D	131954625	1.000000	0.71417	1.000000	0.80357	0.465000	0.32709	5.331000	0.65905	1.243000	0.43853	0.194000	0.17425	GAG	.	.		0.597	TUBA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331800.2	NM_080386		A	132238155	G	A	132238155	3	1	339	1	0	0	0	0	1	0	0	0	16762	1059	37	1	903	1	TUBA3D	2	132238155	Missense_Mutation	SNP	G	TCGA-RC-A7SH-01A-11D-A382-10	107307514	132238155	110961218	9	46905										
FIGN	55137	hgsc.bcm.edu	37	chr2	164466190	164466190	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	aacgggcctcaactggctggGcataatggctgaaaggtctg	14	9	2	1			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr2:164466190G>T	ENST00000333129.3	-	3	2466	c.2152C>A	c.(2152-2154)Ccc>Acc	p.P718T	FIGN_ENST00000409634.1_Intron|FIGN_ENST00000482917.1_5'Flank	NM_018086.2	NP_060556.2	Q5HY92	FIGN_HUMAN	fidgetin	718					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)			breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(1)|prostate(2)|skin(1)	47						AACTGGCTGGGCATAATGGCT	0.478																																					p.P718T		Atlas-SNP	.											.	FIGN	106	.	0			c.C2152A						.						57	60	59					2																	164466190		1965	4151	6116	SO:0001583	missense	55137	exon3			GGCTGGGCATAAT	AK001267	CCDS2221.2	2q24	2010-04-21			ENSG00000182263	ENSG00000182263		"ATPases / AAA-type"	13285	protein-coding gene	gene with protein product		605295				11017077	Standard	XM_005246661		Approved		uc002uck.1	Q5HY92	OTTHUMG00000074059	ENST00000333129.3:c.2152C>A	chr2.hg19:g.164466190G>T	ENSP00000333836:p.Pro718Thr	75.0	0.0		71.0	31.0	NM_018086	B3KWM0|Q9H6M5|Q9NVZ9	Missense_Mutation	SNP	ENST00000333129.3	hg19	CCDS2221.2	.	.	.	.	.	.	.	.	.	.	G	13.39	2.222143	0.39300	.	.	ENSG00000182263	ENST00000333129	D	0.98512	-4.97	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	D	0.95825	0.8641	L	0.31294	0.92	0.80722	D	1	B	0.30406	0.278	B	0.23018	0.043	D	0.93518	0.6859	10	0.45353	T	0.12	-22.3937	20.2527	0.98410	0.0:0.0:1.0:0.0	.	718	Q5HY92	FIGN_HUMAN	T	718	ENSP00000333836:P718T	ENSP00000333836:P718T	P	-	1	0	FIGN	164174436	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.004000	0.88535	2.788000	0.95919	0.557000	0.71058	CCC	.	.		0.478	FIGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157220.2	NM_018086		T	164466190	G	T	164466190	3	4	339	1	0	0	0	0	1	0	0	0	5899	1203	42	3	131	3	FIGN	2	164466190	Missense_Mutation	SNP	G	TCGA-RC-A7SH-01A-11D-A382-10	32228035	164466190	78733183	10	46906										
GORASP2	26003	hgsc.bcm.edu	37	chr2	171804921	171804921	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	tttctttgattttattgtttCtattaatggttcaagattag	6	3	3	2			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr2:171804921C>T	ENST00000234160.4	+	2	940	c.125C>T	c.(124-126)tCt>tTt	p.S42F	GORASP2_ENST00000452526.2_Missense_Mutation_p.S54F|GORASP2_ENST00000493692.1_3'UTR	NM_001201428.1|NM_015530.4	NP_001188357.1|NP_056345.3	Q9H8Y8	GORS2_HUMAN	golgi reassembly stacking protein 2, 55kDa	42	PDZ.				mitotic cell cycle (GO:0000278)|organelle organization (GO:0006996)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(3)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	14						TTTATTGTTTCTATTAATGGT	0.333																																					p.S42F		Atlas-SNP	.											.	GORASP2	40	.	0			c.C125T						.						105	110	109					2																	171804921		2203	4300	6503	SO:0001583	missense	26003	exon2			TTGTTTCTATTAA		CCDS33325.1	2q31.1	2012-09-20	2002-08-29		ENSG00000115806	ENSG00000115806			17500	protein-coding gene	gene with protein product		608693	"golgi reassembly stacking protein 2, 55 kDa"			10487747	Standard	NM_015530		Approved	GRASP55, GRS2, GOLPH6	uc002ugj.3	Q9H8Y8	OTTHUMG00000154072	ENST00000234160.4:c.125C>T	chr2.hg19:g.171804921C>T	ENSP00000234160:p.Ser42Phe	83.0	0.0		60.0	31.0	NM_015530	B4DKT0|Q53TE3|Q96I74|Q96K84|Q9H946|Q9UFW4	Missense_Mutation	SNP	ENST00000234160.4	hg19	CCDS33325.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.917866	0.92249	.	.	ENSG00000115806	ENST00000234160;ENST00000452526	T;T	0.34275	1.37;1.37	5.73	5.73	0.89815	PDZ/DHR/GLGF (2);	0.000000	0.85682	D	0.000000	T	0.68128	0.2967	M	0.87180	2.865	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.71777	-0.4490	10	0.72032	D	0.01	-14.6155	20.2786	0.98501	0.0:1.0:0.0:0.0	.	54;42	B4DKT0;Q9H8Y8	.;GORS2_HUMAN	F	42;54	ENSP00000234160:S42F;ENSP00000410208:S54F	ENSP00000234160:S42F	S	+	2	0	GORASP2	171513167	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.711000	0.84669	2.868000	0.98415	0.557000	0.71058	TCT	.	.		0.333	GORASP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333719.2			T	171804921	C	T	171804921	3	4	339	1	0	0	0	0	1	0	0	0	6584	913	32	3	131	3	GORASP2	2	171804921	Missense_Mutation	SNP	C	TCGA-RC-A7SH-01A-11D-A382-10	7338731	171804921	71394452	11	46907										
CCDC141	285025	hgsc.bcm.edu	37	chr2	179736264	179736264	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	aagtgcttcctgaagaagttTtaagttgtgagaagtctgaa	11	4	1	4			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr2:179736264T>A	ENST00000420890.2	-	14	2212	c.2095A>T	c.(2095-2097)Aaa>Taa	p.K699*	CCDC141_ENST00000295723.5_Nonsense_Mutation_p.K124*	NM_173648.3	NP_775919.3	Q6ZP82	CC141_HUMAN	coiled-coil domain containing 141	699										NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(37)|ovary(8)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)	78			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147)			TGAAGAAGTTTTAAGTTGTGA	0.408																																					p.K699X		Atlas-SNP	.											.	CCDC141	362	.	0			c.A2095T						.						118	121	120					2																	179736264		2203	4300	6503	SO:0001587	stop_gained	285025	exon14			GAAGTTTTAAGTT	AK096821		2q31.2	2013-01-14			ENSG00000163492	ENSG00000163492		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	26821	protein-coding gene	gene with protein product	"coiled-coil protein associated with myosin II and DISC1"					20956536	Standard	NM_173648		Approved	FLJ39502, CAMDI	uc002une.2	Q6ZP82	OTTHUMG00000132578	ENST00000420890.2:c.2095A>T	chr2.hg19:g.179736264T>A	ENSP00000395995:p.Lys699*	113.0	0.0		72.0	37.0	NM_173648	H7C0P1|J3KNW6|Q8N8H3	Nonsense_Mutation	SNP	ENST00000420890.2	hg19		.	.	.	.	.	.	.	.	.	.	T	39	7.432768	0.98282	.	.	ENSG00000163492	ENST00000420890;ENST00000343876;ENST00000295723;ENST00000443758	.	.	.	5.79	5.79	0.91817	.	0.101829	0.42821	D	0.000642	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-27.9236	13.6573	0.62346	0.0:0.0:0.0:1.0	.	.	.	.	X	699;143;124;699	.	ENSP00000295723:K124X	K	-	1	0	CCDC141	179444509	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	0.981000	0.29526	2.200000	0.70718	0.455000	0.32223	AAA	.	.		0.408	CCDC141-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173648		A	179736264	T	A	179736264	4	1	339	1	0	0	0	0	0	1	0	0	2777	1850	64	4	2297	4	CCDC141	2	179736264	Nonsense_Mutation	SNP	T	TCGA-RC-A7SH-01A-11D-A382-10	7931343	179736264	63463109	12	46908										
CWC22	57703	hgsc.bcm.edu	37	chr2	180810422	180810422	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	acttctggtcttcccatgtcCcttctttcttacatcattag	4	13	5	0			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr2:180810422C>G	ENST00000410053.3	-	20	2460	c.2161G>C	c.(2161-2163)Gga>Cga	p.G721R	CWC22_ENST00000295749.6_Missense_Mutation_p.G721R	NM_020943.2	NP_065994.1	Q9HCG8	CWC22_HUMAN	CWC22 spliceosome-associated protein	721					mRNA splicing, via spliceosome (GO:0000398)|regulation of mRNA splicing, via spliceosome (GO:0048024)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(8)|stomach(1)	30						TTCCCATGTCCCTTCTTTCTT	0.328																																					p.G721R		Atlas-SNP	.											.	CWC22	62	.	0			c.G2161C						.						53	49	51					2																	180810422		1842	4081	5923	SO:0001583	missense	57703	exon20			CATGTCCCTTCTT		CCDS46465.1	2q31.3	2014-07-03	2014-07-03		ENSG00000163510	ENSG00000163510			29322	protein-coding gene	gene with protein product	"functional spliceosome-associated protein b"	615186	"CWC22 spliceosome-associated protein homolog (S. cerevisiae)"			9136012, 23236153	Standard	NM_020943		Approved	KIAA1604, EIF4GL, fSAPb, NCM	uc010frh.1	Q9HCG8	OTTHUMG00000154244	ENST00000410053.3:c.2161G>C	chr2.hg19:g.180810422C>G	ENSP00000387006:p.Gly721Arg	22.0	0.0		16.0	7.0	NM_020943	Q05DC2|Q4G135|Q52LF0|Q6PEX2|Q7Z6I0|Q9H5L3|Q9H6Q6	Missense_Mutation	SNP	ENST00000410053.3	hg19	CCDS46465.1	.	.	.	.	.	.	.	.	.	.	C	0.005	-2.210574	0.00292	.	.	ENSG00000163510	ENST00000410053;ENST00000295749;ENST00000404136	T;T;T	0.21361	2.01;2.01;2.03	5.11	2.31	0.28768	.	1.095140	0.06803	N	0.789018	T	0.11153	0.0272	N	0.12182	0.205	0.22571	N	0.998974	B	0.02656	0.0	B	0.01281	0.0	T	0.38499	-0.9658	10	0.11794	T	0.64	-0.2803	6.8627	0.24076	0.0:0.5952:0.0:0.4048	.	721	Q9HCG8	CWC22_HUMAN	R	721	ENSP00000387006:G721R;ENSP00000295749:G721R;ENSP00000384159:G721R	ENSP00000295749:G721R	G	-	1	0	CWC22	180518667	0.009000	0.17119	0.989000	0.46669	0.199000	0.23934	0.185000	0.16958	0.261000	0.21753	-0.140000	0.14226	GGA	.	.		0.328	CWC22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334537.1	NM_020943		G	180810422	C	G	180810422	3	3	339	1	0	0	0	0	1	0	0	0	4070	632	22	4	569	4	CWC22	2	180810422	Missense_Mutation	SNP	C	TCGA-RC-A7SH-01A-11D-A382-10	1074158	180810422	62388951	13	46909										
KCNH8	131096	hgsc.bcm.edu	37	chr3	19556821	19556821	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	ttattttaagtaggattgttGatggaattgaagatggaaac	11	1	0	3	rs373726349		TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr3:19556821G>A	ENST00000328405.2	+	14	2709	c.2443G>A	c.(2443-2445)Gat>Aat	p.D815N		NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	815					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(3)|lung(37)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	77						TAGGATTGTTGATGGAATTGA	0.353																																					p.D815N	NSCLC(124;1625 1765 8018 24930 42026)	Atlas-SNP	.											.	KCNH8	189	.	0			c.G2443A						.	G	ASN/ASP	1,4405	2.1+/-5.4	0,1,2202	66	69	68		2443	5.6	1	3		68	0,8600		0,0,4300	no	missense	KCNH8	NM_144633.2	23	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	815/1108	19556821	1,13005	2203	4300	6503	SO:0001583	missense	131096	exon14			ATTGTTGATGGAA	AY053503	CCDS2632.1	3p24.3	2012-07-05			ENSG00000183960	ENSG00000183960		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18864	protein-coding gene	gene with protein product		608260				16382104	Standard	NM_144633		Approved	Kv12.1, elk3	uc003cbk.1	Q96L42	OTTHUMG00000129891	ENST00000328405.2:c.2443G>A	chr3.hg19:g.19556821G>A	ENSP00000328813:p.Asp815Asn	61.0	0.0		61.0	26.0	NM_144633	B7Z2I7|Q59GQ6	Missense_Mutation	SNP	ENST00000328405.2	hg19	CCDS2632.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.655270	0.88056	2.27E-4	0.0	ENSG00000183960	ENST00000328405	D	0.99829	-7.0	5.59	5.59	0.84812	.	0.000000	0.32372	U	0.006186	D	0.99746	0.9899	M	0.69358	2.11	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97739	1.0207	9	.	.	.	.	17.7599	0.88461	0.0:0.0:1.0:0.0	.	815	Q96L42	KCNH8_HUMAN	N	815	ENSP00000328813:D815N	.	D	+	1	0	KCNH8	19531825	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	6.328000	0.72915	2.630000	0.89119	0.650000	0.86243	GAT	.	.		0.353	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	NM_144633		A	19556821	G	A	19556821	3	1	339	1	0	0	0	0	1	0	0	0	8047	1290	45	3	2497	3	KCNH8	3	19556821	Missense_Mutation	SNP	G	TCGA-RC-A7SH-01A-11D-A382-10		19556821	178465609	14	46910										
HTR1F	3355	hgsc.bcm.edu	37	chr3	88040639	88040639	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	agtttccacatcctatgtacTagaaaagtctttatctgacc	5	10	2	2			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr3:88040639T>A	ENST00000319595.4	+	1	794	c.740T>A	c.(739-741)cTa>cAa	p.L247Q		NM_000866.3	NP_000857.1	P30939	5HT1F_HUMAN	5-hydroxytryptamine (serotonin) receptor 1F, G protein-coupled	247					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(12)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(8;0.147)	Lung NSC(201;0.0283)		LUSC - Lung squamous cell carcinoma(29;0.00353)|Lung(72;0.00664)	Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Ketamine(DB01221)|Methysergide(DB00247)|Mianserin(DB06148)|Naratriptan(DB00952)|Rizatriptan(DB00953)|Sumatriptan(DB00669)|Zolmitriptan(DB00315)	TCCTATGTACTAGAAAAGTCT	0.408																																					p.L247Q		Atlas-SNP	.											.	HTR1F	66	.	0			c.T740A						.						62	63	63					3																	88040639		2203	4300	6503	SO:0001583	missense	3355	exon2			ATGTACTAGAAAA	L05597	CCDS2920.1	3p12	2012-08-08	2012-02-03		ENSG00000179097	ENSG00000179097		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5292	protein-coding gene	gene with protein product		182134	"5-hydroxytryptamine (serotonin) receptor 1F"			8384716, 8380639	Standard	NM_000866		Approved	HTR1EL, 5-HT1F	uc003dqr.2	P30939	OTTHUMG00000159008	ENST00000319595.4:c.740T>A	chr3.hg19:g.88040639T>A	ENSP00000322924:p.Leu247Gln	114.0	0.0		54.0	48.0	NM_000866		Missense_Mutation	SNP	ENST00000319595.4	hg19	CCDS2920.1	.	.	.	.	.	.	.	.	.	.	T	0.003	-2.497188	0.00159	.	.	ENSG00000179097	ENST00000319595	T	0.71817	-0.6	5.14	-0.319	0.12725	GPCR, rhodopsin-like superfamily (1);	1.163830	0.06367	U	0.712788	T	0.52789	0.1756	L	0.29908	0.895	0.09310	N	1	B	0.12013	0.005	B	0.12156	0.007	T	0.27020	-1.0086	10	0.13108	T	0.6	.	4.8955	0.13748	0.146:0.3432:0.0:0.5108	.	247	P30939	5HT1F_HUMAN	Q	247	ENSP00000322924:L247Q	ENSP00000322924:L247Q	L	+	2	0	HTR1F	88123329	0.000000	0.05858	0.263000	0.24496	0.002000	0.02628	0.055000	0.14229	0.014000	0.14944	-1.481000	0.00988	CTA	.	.		0.408	HTR1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352890.1	NM_000866		A	88040639	T	A	88040639	3	1	339	1	0	0	0	0	1	0	0	0	7449	1522	53	4	742	4	HTR1F	3	88040639	Missense_Mutation	SNP	T	TCGA-RC-A7SH-01A-11D-A382-10	68483818	88040639	109981791	15	46911										
NCEH1	57552	hgsc.bcm.edu	37	chr3	172351356	172351356	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	agctagtgaaaatcatacatCcgtgaaagccatcctcaaag	7	10	2	2			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr3:172351356C>T	ENST00000475381.1	-	5	1369	c.1136G>A	c.(1135-1137)gGa>gAa	p.G379E	NCEH1_ENST00000273512.3_Missense_Mutation_p.G411E|NCEH1_ENST00000538775.1_Missense_Mutation_p.G419E|NCEH1_ENST00000543711.1_Missense_Mutation_p.G246E			Q6PIU2	NCEH1_HUMAN	neutral cholesterol ester hydrolase 1	379					lipid catabolic process (GO:0016042)|protein dephosphorylation (GO:0006470)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carboxylic ester hydrolase activity (GO:0052689)|phosphate ion binding (GO:0042301)|serine hydrolase activity (GO:0017171)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|prostate(1)|skin(1)	15						AATCATACATCCGTGAAAGCC	0.488																																					p.G419E		Atlas-SNP	.											.	NCEH1	63	.	0			c.G1256A						.						123	111	115					3																	172351356		2203	4300	6503	SO:0001583	missense	57552	exon5			ATACATCCGTGAA	AB037784	CCDS54681.1, CCDS54682.1	3q26.31	2009-07-23	2009-07-23	2009-07-23	ENSG00000144959	ENSG00000144959			29260	protein-coding gene	gene with protein product		613234	"arylacetamide deacetylase-like 1"	AADACL1		10718198	Standard	NM_001146276		Approved	KIAA1363, NCEH	uc011bpx.2	Q6PIU2	OTTHUMG00000156872	ENST00000475381.1:c.1136G>A	chr3.hg19:g.172351356C>T	ENSP00000418571:p.Gly379Glu	144.0	0.0		162.0	52.0	NM_001146276	B7Z2K4|B7Z3A1|B7Z5U2|B7Z906|B7ZAW6|F5H7K4|Q86WZ1|Q9P2I4	Missense_Mutation	SNP	ENST00000475381.1	hg19		.	.	.	.	.	.	.	.	.	.	C	16.27	3.076449	0.55753	.	.	ENSG00000144959	ENST00000475381;ENST00000538775;ENST00000273512;ENST00000543711	T;T;T;T	0.61980	0.06;0.06;0.06;0.06	5.7	4.82	0.62117	Alpha/beta hydrolase fold-3 (1);	0.000000	0.85682	D	0.000000	T	0.78426	0.4281	M	0.69523	2.12	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.81470	-0.0918	10	0.87932	D	0	-21.9418	16.0129	0.80417	0.1358:0.8642:0.0:0.0	.	419;379	F5H7K4;Q6PIU2	.;NCEH1_HUMAN	E	379;419;411;246	ENSP00000418571:G379E;ENSP00000442464:G419E;ENSP00000273512:G411E;ENSP00000443227:G246E	ENSP00000273512:G411E	G	-	2	0	NCEH1	173834050	1.000000	0.71417	0.157000	0.22605	0.189000	0.23516	7.484000	0.81180	1.382000	0.46385	-0.291000	0.09656	GGA	.	.		0.488	NCEH1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000346367.3	NM_020792		T	172351356	C	T	172351356	3	4	339	1	0	0	0	0	1	0	0	0	10224	855	30	3	94	3	NCEH1	3	172351356	Missense_Mutation	SNP	C	TCGA-RC-A7SH-01A-11D-A382-10	84310717	172351356	25671074	16	46912										
OPA1	4976	hgsc.bcm.edu	37	chr3	193380662	193380663	+	Missense_Mutation	DNP	GA	GA	TT													0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	agaagatgttgaaatgtaatGaggagcacccagcttatctt							TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr3:193380662_193380663GA>TT	ENST00000392438.3	+	24	2641_2642	c.2407_2408GA>TT	c.(2407-2409)GAg>TTg	p.E803L	OPA1_ENST00000361510.2_Missense_Mutation_p.E858L|OPA1_ENST00000361908.3_Missense_Mutation_p.E840L|OPA1_ENST00000361150.2_Missense_Mutation_p.E804L|OPA1_ENST00000361715.2_Missense_Mutation_p.E822L|OPA1_ENST00000361828.2_Missense_Mutation_p.E821L	NM_015560.2	NP_056375.2	O60313	OPA1_HUMAN	optic atrophy 1 (autosomal dominant)	803					apoptotic process (GO:0006915)|axon transport of mitochondrion (GO:0019896)|cellular senescence (GO:0090398)|GTP catabolic process (GO:0006184)|inner mitochondrial membrane organization (GO:0007007)|mitochondrial fission (GO:0000266)|mitochondrial fusion (GO:0008053)|mitochondrion organization (GO:0007005)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|neural tube closure (GO:0001843)|visual perception (GO:0007601)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial crista (GO:0030061)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)			breast(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(4)|lung(15)|upper_aerodigestive_tract(1)|urinary_tract(2)	31	all_cancers(143;9.56e-09)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;9.19e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000162)		GAAATGTAATGAGGAGCACCCA	0.366																																					p.E858X|p.E858V		Atlas-SNP	.											.	OPA1	79	.	0			c.G2572T|c.A2573T						.																																			SO:0001583	missense	4976	exon26			TGTAATGAGGAGC|GTAATGAGGAGCA	AB011139	CCDS33917.1, CCDS43186.1	3q29	2014-09-17			ENSG00000198836	ENSG00000198836			8140	protein-coding gene	gene with protein product	"mitochondrial dynamin-like GTPase", "dynamin-like guanosine triphosphatase", "Dynamin-like 120 kDa protein, mitochondrial"	605290				9490303	Standard	NM_015560		Approved	NTG, KIAA0567, FLJ12460, NPG, MGM1	uc003ftg.3	O60313	OTTHUMG00000149897	Exception_encountered	chr3.hg19:g.193380662_193380663delinsTT	ENSP00000376233:p.Glu803Leu	305.0|304.0	1.0|0.0		291.0|294.0	127.0|130.0	NM_130837	D3DNW4	Nonsense_Mutation|Missense_Mutation	SNP	ENST00000392438.3	hg19	CCDS43186.1																																																																																			.	.		0.366	OPA1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313812.2	NM_130837		TT	193380663	GA	TT	193380662	3	4	339	1	0	0	0	0	1	0	0	0	10880	1291	45	3	2674	3	OPA1	3	193380662	Missense_Mutation	DNP	GA	TCGA-RC-A7SH-01A-11D-A382-10	21029306	193380662	4641768	17	46913										
PACRGL	133015	hgsc.bcm.edu	37	chr4	20706145	20706145	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	tggaggtacacagttgaaaaAcagagcaacaggtacagagc	12	7	0	3			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr4:20706145A>T	ENST00000503585.1	+	2	432	c.41A>T	c.(40-42)aAc>aTc	p.N14I	PACRGL_ENST00000538990.1_Missense_Mutation_p.N14I|PACRGL_ENST00000513459.1_Missense_Mutation_p.N14I|PACRGL_ENST00000360916.5_Missense_Mutation_p.N14I|PACRGL_ENST00000507634.1_Missense_Mutation_p.N14I|PACRGL_ENST00000502938.1_Missense_Mutation_p.N14I|PACRGL_ENST00000444671.2_Missense_Mutation_p.N14I|PACRGL_ENST00000502374.1_Missense_Mutation_p.N14I|PACRGL_ENST00000295290.8_Missense_Mutation_p.N14I	NM_001258345.1	NP_001245274.1	Q8N7B6	PACRL_HUMAN	PARK2 co-regulated-like	14										endometrium(2)|lung(7)|prostate(1)	10						CAGTTGAAAAACAGAGCAACA	0.388																																					p.N14I		Atlas-SNP	.											.	PACRGL	30	.	0			c.A41T						.						75	78	77					4																	20706145		2203	4300	6503	SO:0001583	missense	133015	exon2			TGAAAAACAGAGC	AK098692	CCDS3427.1, CCDS47034.1, CCDS58895.1, CCDS58896.1	4p15.31	2008-10-02	2008-10-02	2008-10-02	ENSG00000163138	ENSG00000163138			28442	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 28"	C4orf28		12477932	Standard	NM_145048		Approved	MGC29898	uc010iek.3	Q8N7B6	OTTHUMG00000128550	ENST00000503585.1:c.41A>T	chr4.hg19:g.20706145A>T	ENSP00000423881:p.Asn14Ile	687.0	1.0		672.0	233.0	NM_001258345	B2RDB9|B4DFF8|B4DMN7|Q8TBA8	Missense_Mutation	SNP	ENST00000503585.1	hg19	CCDS58895.1	.	.	.	.	.	.	.	.	.	.	A	17.37	3.372967	0.61624	.	.	ENSG00000163138	ENST00000510051;ENST00000503585;ENST00000360916;ENST00000295290;ENST00000514485;ENST00000444671;ENST00000506745;ENST00000514663;ENST00000509469;ENST00000515339;ENST00000513861;ENST00000502374;ENST00000538990;ENST00000511160;ENST00000504630;ENST00000513590;ENST00000514292;ENST00000502938;ENST00000507634;ENST00000513459;ENST00000511089	.	.	.	5.87	-0.911	0.10507	.	0.454632	0.22985	N	0.053263	T	0.32615	0.0835	L	0.54323	1.7	0.30671	N	0.753412	D;B;P;P;P;P	0.53462	0.96;0.28;0.868;0.773;0.664;0.573	B;B;B;B;B;B	0.42422	0.387;0.117;0.312;0.246;0.08;0.232	T	0.39292	-0.9621	9	0.72032	D	0.01	-9.1787	5.7827	0.18316	0.5953:0.1289:0.2758:0.0	.	14;14;62;14;14;14	B4DFF8;Q8N7B6;D6R9N9;B4DMN7;D6RGK2;Q8N7B6-2	.;PACRL_HUMAN;.;.;.;.	I	62;14;14;14;14;14;14;14;14;14;14;14;14;14;14;14;14;14;14;14;14	.	ENSP00000295290:N14I	N	+	2	0	PACRGL	20315243	0.003000	0.15002	0.971000	0.41717	0.575000	0.36095	-0.825000	0.04433	-0.262000	0.09392	0.533000	0.62120	AAC	.	.		0.388	PACRGL-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360321.2	NM_145048		T	20706145	A	T	20706145	3	4	339	1	0	0	0	0	1	0	0	0	11380	43	2	4	43	4	PACRGL	4	20706145	Missense_Mutation	SNP	A	TCGA-RC-A7SH-01A-11D-A382-10		20706145	170448131	18	46914										
NHEDC2	133308	hgsc.bcm.edu	37	chr4	103987527	103987527	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	aaaccatgtggagggcaagcCagcatttgtctcagtctttg	11	9	2	0			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr4:103987527C>T	ENST00000394785.3	-	3	859	c.228G>A	c.(226-228)ctG>ctA	p.L76L	SLC9B2_ENST00000362026.3_Silent_p.L76L|SLC9B2_ENST00000503230.1_Silent_p.L76L|SLC9B2_ENST00000505838.1_5'UTR|SLC9B2_ENST00000339611.4_Silent_p.L76L|SLC9B2_ENST00000503103.1_Silent_p.L76L	NM_178833.4	NP_849155.2	Q86UD5	SL9B2_HUMAN	solute carrier family 9, subfamily B (NHA2, cation proton antiporter 2), member 2	76					ion transmembrane transport (GO:0034220)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	solute:proton antiporter activity (GO:0015299)										GAGGGCAAGCCAGCATTTGTC	0.383																																					p.L76L		Atlas-SNP	.											.	.	.	.	0			c.G228A						.						322	273	290					4																	103987527		2203	4300	6503	SO:0001819	synonymous_variant	133308	exon3			GCAAGCCAGCATT	AK172823	CCDS3662.1, CCDS75173.1, CCDS75174.1	4q24	2013-05-22	2012-03-22	2011-08-03	ENSG00000164038	ENSG00000164038		"Solute carriers"	25143	protein-coding gene	gene with protein product		611789	"Na+/H+ exchanger domain containing 2", "solute carrier family 9, subfamily B (cation proton antiporter 2), member 2"	NHEDC2		18600791	Standard	XM_005262758		Approved	FLJ23984, NHA2	uc003hwy.3	Q86UD5	OTTHUMG00000131125	ENST00000394785.3:c.228G>A	chr4.hg19:g.103987527C>T		112.0	0.0		67.0	55.0	NM_178833	B5ME52|Q6ZMD8|Q96D95	Silent	SNP	ENST00000394785.3	hg19	CCDS3662.1																																																																																			.	.		0.383	SLC9B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253805.1	NM_178833		T	103987527	C	T	103987527	2	4	339	1	0	0	0	0	0	0	0	1	10410	581	21	3		3	NHEDC2	4	103987527	Silent	SNP	C	TCGA-RC-A7SH-01A-11D-A382-10	83281382	103987527	87166749	19	46915										
CDH9	1007	hgsc.bcm.edu	37	chr5	26881658	26881658	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	gtaggtcacaatgttgtcccGgacatcgtcttttgaaatta	9	8	2	1			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr5:26881658G>A	ENST00000231021.4	-	12	2129	c.1957C>T	c.(1957-1959)Cgg>Tgg	p.R653W		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	653					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						ATGTTGTCCCGGACATCGTCT	0.413																																					p.R653W	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											.	CDH9	305	.	0			c.C1957T						.						120	124	122					5																	26881658		2203	4300	6503	SO:0001583	missense	1007	exon12			TGTCCCGGACATC	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"Cadherins / Major cadherins"	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.1957C>T	chr5.hg19:g.26881658G>A	ENSP00000231021:p.Arg653Trp	52.0	0.0		58.0	27.0	NM_016279	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	hg19	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	G	16.18	3.049021	0.55110	.	.	ENSG00000113100	ENST00000231021	D	0.84589	-1.87	4.96	4.06	0.47325	Cadherin, cytoplasmic domain (1);	0.000000	0.85682	D	0.000000	D	0.94604	0.8261	H	0.97265	3.97	0.49798	D	0.999828	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.95132	0.8256	9	.	.	.	.	11.3279	0.49458	0.0:0.0:0.6308:0.3692	.	246;653	B4DFP0;Q9ULB4	.;CADH9_HUMAN	W	653	ENSP00000231021:R653W	.	R	-	1	2	CDH9	26917415	1.000000	0.71417	0.987000	0.45799	0.788000	0.44548	2.029000	0.41098	1.145000	0.42336	0.557000	0.71058	CGG	.	.		0.413	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		A	26881658	G	A	26881658	3	1	339	1	0	0	0	0	1	0	0	0	3119	1115	39	1	416	1	CDH9	5	26881658	Missense_Mutation	SNP	G	TCGA-RC-A7SH-01A-11D-A382-10		26881658	154033602	20	46916										
LNPEP	4012	hgsc.bcm.edu	37	chr5	96315623	96315623	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	atagagtactcggcaaatatAtctagttcttattatgggtt	8	5	2	1			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr5:96315623A>G	ENST00000231368.5	+	2	1493	c.801A>G	c.(799-801)atA>atG	p.I267M	LNPEP_ENST00000395770.3_Missense_Mutation_p.I253M	NM_005575.2	NP_005566.2	Q9UIQ6	LCAP_HUMAN	leucyl/cystinyl aminopeptidase	267					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-cell signaling (GO:0007267)|female pregnancy (GO:0007565)|membrane organization (GO:0061024)|protein catabolic process (GO:0030163)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|early endosome lumen (GO:0031905)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	34		all_cancers(142;7e-07)|all_epithelial(76;9.52e-10)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0269)|Breast(839;0.244)		COAD - Colon adenocarcinoma(37;0.072)		CGGCAAATATATCTAGTTCTT	0.408																																					p.I267M		Atlas-SNP	.											.	LNPEP	80	.	0			c.A801G						.						60	57	58					5																	96315623		2203	4300	6503	SO:0001583	missense	4012	exon2			AAATATATCTAGT	D50810	CCDS4087.1, CCDS43346.1	5q15	2011-07-25			ENSG00000113441	ENSG00000113441	3.4.11.3		6656	protein-coding gene	gene with protein product	"cystinyl aminopeptidase", "placental leucine aminopeptidase"	151300				8550619	Standard	NM_175920		Approved	CAP, PLAP, P-LAP	uc003kmw.1	Q9UIQ6	OTTHUMG00000128719	ENST00000231368.5:c.801A>G	chr5.hg19:g.96315623A>G	ENSP00000231368:p.Ile267Met	140.0	0.0		147.0	80.0	NM_005575	O00769|Q15145|Q59H76|Q9TNQ2|Q9TNQ3|Q9UIQ7	Missense_Mutation	SNP	ENST00000231368.5	hg19	CCDS4087.1	.	.	.	.	.	.	.	.	.	.	A	7.268	0.606616	0.14002	.	.	ENSG00000113441	ENST00000231368;ENST00000395770	T;T	0.03212	4.01;4.01	5.83	-11.7	0.00046	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.174230	0.50627	D	0.000112	T	0.01592	0.0051	N	0.25992	0.78	0.24869	N	0.992291	B	0.12013	0.005	B	0.23018	0.043	T	0.33523	-0.9865	10	0.54805	T	0.06	.	0.919	0.01311	0.187:0.1719:0.2203:0.4208	.	267	Q9UIQ6	LCAP_HUMAN	M	267;253	ENSP00000231368:I267M;ENSP00000379117:I253M	ENSP00000231368:I267M	I	+	3	3	LNPEP	96341379	0.268000	0.24133	0.341000	0.25589	0.031000	0.12232	-0.200000	0.09478	-1.853000	0.01165	-1.070000	0.02257	ATA	.	.		0.408	LNPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250624.1	NM_005575		G	96315623	A	G	96315623	3	3	339	1	0	0	0	0	1	0	0	0	8873	439	16	2	807	2	LNPEP	5	96315623	Missense_Mutation	SNP	A	TCGA-RC-A7SH-01A-11D-A382-10	69433965	96315623	84599637	21	46917										
PCDHB7	56129	hgsc.bcm.edu	37	chr5	140554310	140554310	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	gtaccgccaggctgctgagcGagcgcgacgcagccaagcag	15	14	0	1	rs17844473	byFrequency	TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr5:140554310G>C	ENST00000231137.3	+	1	2068	c.1894G>C	c.(1894-1896)Gag>Cag	p.E632Q		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	632	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GCTGCTGAGCGAGCGCGACGC	0.692																																					p.E632Q		Atlas-SNP	.											.	PCDHB7	231	.	0			c.G1894C						.						40	64	56					5																	140554310		2180	4280	6460	SO:0001583	missense	56129	exon1			CTGAGCGAGCGCG	AF152500	CCDS4249.1	5q31	2010-01-26			ENSG00000113212	ENSG00000113212		"Cadherins / Protocadherins : Clustered"	8692	other	protocadherin		606333				10380929	Standard	NM_018940		Approved	PCDH-BETA7	uc003lit.3	Q9Y5E2	OTTHUMG00000129608	ENST00000231137.3:c.1894G>C	chr5.hg19:g.140554310G>C	ENSP00000231137:p.Glu632Gln	76.0	0.0		78.0	32.0	NM_018940	A1L3Y8	Missense_Mutation	SNP	ENST00000231137.3	hg19	CCDS4249.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.259888	0.80246	.	.	ENSG00000113212	ENST00000231137	T	0.51325	0.71	3.98	3.98	0.46160	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.70640	0.3247	M	0.83774	2.66	0.45284	D	0.998288	D	0.89917	1.0	D	0.81914	0.995	T	0.77797	-0.2453	9	0.87932	D	0	.	16.1064	0.81225	0.0:0.0:1.0:0.0	.	632	Q9Y5E2	PCDB7_HUMAN	Q	632	ENSP00000231137:E632Q	ENSP00000231137:E632Q	E	+	1	0	PCDHB7	140534494	0.999000	0.42202	1.000000	0.80357	0.923000	0.55619	4.242000	0.58714	1.922000	0.55676	0.449000	0.29647	GAG	.	G|0.995;T|0.005		0.692	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940		C	140554310	G	C	140554310	3	2	339	1	0	0	0	0	1	0	0	0	11556	1059	37	4	1896	4	PCDHB7	5	140554310	Missense_Mutation	SNP	G	TCGA-RC-A7SH-01A-11D-A382-10	44238687	140554310	40360950	22	46918										
GABRA6	2559	hgsc.bcm.edu	37	chr5	161116134	161116134	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	atgacaactcctaataaactCttcagaataatgcagaatgg	6	8	2	3			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr5:161116134C>T	ENST00000274545.5	+	4	838	c.405C>T	c.(403-405)ctC>ctT	p.L135L	GABRA6_ENST00000523217.1_Silent_p.L125L|RP11-348M17.2_ENST00000521984.1_RNA			Q16445	GBRA6_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 6	135					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|liver(2)|lung(22)|ovary(7)|skin(6)|urinary_tract(2)	57	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	CTAATAAACTCTTCAGAATAA	0.368										TCGA Ovarian(5;0.080)																											p.L135L		Atlas-SNP	.											.	GABRA6	139	.	0			c.C405T						.						64	65	64					5																	161116134		2203	4300	6503	SO:0001819	synonymous_variant	2559	exon4			TAAACTCTTCAGA		CCDS4356.1	5q34	2012-06-22			ENSG00000145863	ENSG00000145863		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4080	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 6"	137143				8020978	Standard	NM_000811		Approved		uc003lyu.2	Q16445	OTTHUMG00000130351	ENST00000274545.5:c.405C>T	chr5.hg19:g.161116134C>T		143.0	0.0		119.0	25.0	NM_000811	A8K096|Q4VAV2	Silent	SNP	ENST00000274545.5	hg19	CCDS4356.1	.	.	.	.	.	.	.	.	.	.	C	7.920	0.738319	0.15574	.	.	ENSG00000145863	ENST00000520000	.	.	.	5.65	0.687	0.18020	.	.	.	.	.	T	0.42675	0.1213	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.22521	-1.0214	4	.	.	.	.	1.9535	0.03371	0.1186:0.3951:0.232:0.2543	.	.	.	.	F	75	.	.	S	+	2	0	GABRA6	161048712	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	1.210000	0.32370	0.113000	0.18004	-0.181000	0.13052	TCT	.	.		0.368	GABRA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252707.2			T	161116134	C	T	161116134	2	4	339	1	0	0	0	0	0	0	0	1	6173	900	32	3		3	GABRA6	5	161116134	Silent	SNP	C	TCGA-RC-A7SH-01A-11D-A382-10	20561824	161116134	19799126	23	46919										
RARS	5917	hgsc.bcm.edu	37	chr5	167937603	167937603	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	taggaaaaagtttaaaacacGttcgggtgaaacagtgcgcc	11	7	0	1	rs199894860		TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr5:167937603G>A	ENST00000231572.3	+	12	1418	c.1364G>A	c.(1363-1365)cGt>cAt	p.R455H	RARS_ENST00000538719.1_Missense_Mutation_p.R249H	NM_002887.3	NP_002878.2	P54136	SYRC_HUMAN	arginyl-tRNA synthetase	455					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	arginine binding (GO:0034618)|arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|tRNA binding (GO:0000049)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|stomach(1)	22	Renal(175;0.000159)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0208)|all_neural(177;0.0227)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0693)|Epithelial(171;0.131)|OV - Ovarian serous cystadenocarcinoma(192;0.156)		TTTAAAACACGTTCGGGTGAA	0.373																																					p.R455H		Atlas-SNP	.											.	RARS	58	.	0			c.G1364A						.						54	55	55					5																	167937603		2203	4300	6503	SO:0001583	missense	5917	exon12			AAACACGTTCGGG	BC000528	CCDS4367.1	5q35.1	2011-07-01			ENSG00000113643	ENSG00000113643	6.1.1.19	"Aminoacyl tRNA synthetases / Class I"	9870	protein-coding gene	gene with protein product	"arginine tRNA ligase 1, cytoplasmic"	107820				7590355	Standard	NM_002887		Approved	DALRD1	uc003lzx.3	P54136	OTTHUMG00000130411	ENST00000231572.3:c.1364G>A	chr5.hg19:g.167937603G>A	ENSP00000231572:p.Arg455His	266.0	0.0		287.0	19.0	NM_002887	B2RBS9|Q53GY4|Q9BWA1	Missense_Mutation	SNP	ENST00000231572.3	hg19	CCDS4367.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.110347	0.77210	.	.	ENSG00000113643	ENST00000231572;ENST00000538719	D;D	0.82167	-1.58;-1.58	4.99	4.99	0.66335	Arginyl-tRNA synthetase, class Ia, core (1);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.097855	0.64402	D	0.000001	D	0.95730	0.8611	H	0.99740	4.74	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.98154	1.0443	10	0.87932	D	0	-9.6139	18.6482	0.91419	0.0:0.0:1.0:0.0	.	455	P54136	SYRC_HUMAN	H	455;249	ENSP00000231572:R455H;ENSP00000439108:R249H	ENSP00000231572:R455H	R	+	2	0	RARS	167870181	1.000000	0.71417	0.998000	0.56505	0.501000	0.33797	9.328000	0.96403	2.462000	0.83206	0.655000	0.94253	CGT	.	G|0.999;A|0.001		0.373	RARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252794.2	NM_002887		A	167937603	G	A	167937603	3	1	339	1	0	0	0	0	1	0	0	0	13073	1145	40	1	1410	1	RARS	5	167937603	Missense_Mutation	SNP	G	TCGA-RC-A7SH-01A-11D-A382-10	6821469	167937603	12977657	24	46920										
HDGFL1	154150	hgsc.bcm.edu	37	chr6	22570024	22570024	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	gcaagcccaacaagaggcgcGgcttcagcgcggggctgtgg	17	12	1	1			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr6:22570024G>A	ENST00000230012.3	+	1	347	c.220G>A	c.(220-222)Ggc>Agc	p.G74S	HDGFL1_ENST00000510882.2_Missense_Mutation_p.G74S	NM_138574.2	NP_612641.2	Q5TGJ6	HDGL1_HUMAN	hepatoma derived growth factor-like 1	74										kidney(1)|large_intestine(3)|lung(7)	11	Ovarian(93;0.163)					CAAGAGGCGCGGCTTCAGCGC	0.622																																					p.G74S		Atlas-SNP	.											.	HDGFL1	33	.	0			c.G220A						.						42	41	41					6																	22570024		2203	4300	6503	SO:0001583	missense	154150	exon1			AGGCGCGGCTTCA	AK056824	CCDS34347.1	6p22.2	2008-02-05	2005-04-07	2005-04-07	ENSG00000112273	ENSG00000112273			21095	protein-coding gene	gene with protein product			"PWWP domain containing 1"	PWWP1			Standard	NM_138574		Approved	dJ309H15.1	uc003nds.3	Q5TGJ6	OTTHUMG00000016206	ENST00000230012.3:c.220G>A	chr6.hg19:g.22570024G>A	ENSP00000230012:p.Gly74Ser	89.0	0.0		108.0	53.0	NM_138574	Q96MJ6	Missense_Mutation	SNP	ENST00000230012.3	hg19	CCDS34347.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.259295	0.80246	.	.	ENSG00000112273	ENST00000230012;ENST00000510882	T;T	0.69806	-0.43;-0.43	3.28	2.41	0.29592	.	0.060986	0.64402	N	0.000004	T	0.77082	0.4078	M	0.91510	3.215	0.42829	D	0.994013	D	0.76494	0.999	D	0.67725	0.953	T	0.80094	-0.1526	10	0.87932	D	0	-56.8526	8.6839	0.34225	0.118:0.0:0.882:0.0	.	74	Q5TGJ6	HDGL1_HUMAN	S	74	ENSP00000230012:G74S;ENSP00000442129:G74S	ENSP00000230012:G74S	G	+	1	0	HDGFL1	22678003	1.000000	0.71417	0.898000	0.35279	0.942000	0.58702	5.145000	0.64839	0.956000	0.37904	0.491000	0.48974	GGC	.	.		0.622	HDGFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043500.1	NM_138574		A	22570024	G	A	22570024	3	1	339	1	0	0	0	0	1	0	0	0	7028	1116	39	1	222	1	HDGFL1	6	22570024	Missense_Mutation	SNP	G	TCGA-RC-A7SH-01A-11D-A382-10		22570024	148545043	25	46921										
ELOVL4	6785	hgsc.bcm.edu	37	chr6	80629233	80629234	+	Missense_Mutation	DNP	GA	GA	TT													0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	tatgagtacataatcacatgGataaaggaattcaactgggc							TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr6:80629233_80629234GA>TT	ENST00000369816.4	-	5	872_873	c.572_573TC>AA	c.(571-573)aTC>aAA	p.I191K		NM_022726.3	NP_073563.1	Q9GZR5	ELOV4_HUMAN	ELOVL fatty acid elongase 4	191					cellular lipid metabolic process (GO:0044255)|detection of visible light (GO:0009584)|fatty acid biosynthetic process (GO:0006633)|fatty acid elongation, saturated fatty acid (GO:0019367)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|very long-chain fatty acid biosynthetic process (GO:0042761)	endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)	G-protein coupled photoreceptor activity (GO:0008020)|transferase activity (GO:0016740)			central_nervous_system(2)|cervix(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		all_cancers(76;1.83e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.011)		BRCA - Breast invasive adenocarcinoma(397;0.0168)	Alpha-Linolenic Acid(DB00132)	TAATCACATGGATAAAGGAATT	0.366																																					p.I191I|p.I191N		Atlas-SNP	.											.	ELOVL4	46	.	0			c.C573A|c.T572A						.																																			SO:0001583	missense	6785	exon5			CACATGGATAAAG|ACATGGATAAAGG	AF277094	CCDS4992.1	6q14	2013-01-08	2011-05-25		ENSG00000118402	ENSG00000118402			14415	protein-coding gene	gene with protein product	"cancer/testis antigen 118"	605512	"elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 4"	STGD2, STGD3		11138005	Standard	NM_022726		Approved	CT118	uc003pja.4	Q9GZR5	OTTHUMG00000015087	ENST00000369816.4:c.572_573delinsTT	chr6.hg19:g.80629233_80629234delinsTT	ENSP00000358831:p.Ile191Lys	130.0|131.0	0.0		139.0|138.0	53.0|51.0	NM_022726	B2R6B5|Q5TCS2|Q86YJ1|Q9H139	Silent|Missense_Mutation	SNP	ENST00000369816.4	hg19	CCDS4992.1																																																																																			.	.		0.366	ELOVL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041315.1			TT	80629234	GA	TT	80629233	3	4	339	1	0	0	0	0	1	0	0	0	5078	1164	41	3	379	3	ELOVL4	6	80629233	Missense_Mutation	DNP	GA	TCGA-RC-A7SH-01A-11D-A382-10	58059209	80629233	90485834	26	46922										
FAM26E	254228	hgsc.bcm.edu	37	chr6	116837131	116837131	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	gagacgacaatggtccttgtGggtactgcccacaatatgta	11	9	0	1			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr6:116837131G>T	ENST00000368599.3	+	2	960	c.909G>T	c.(907-909)gtG>gtT	p.V303V	TRAPPC3L_ENST00000368602.3_Intron	NM_153711.2	NP_714922.1	Q8N5C1	FA26E_HUMAN	family with sequence similarity 26, member E	303					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(1)	7		all_cancers(87;0.0608)|all_epithelial(87;0.05)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0242)|all cancers(137;0.0419)|OV - Ovarian serous cystadenocarcinoma(136;0.0671)|Epithelial(106;0.212)		TGGTCCTTGTGGGTACTGCCC	0.498																																					p.V303V		Atlas-SNP	.											.	FAM26E	26	.	0			c.G909T						.						118	103	108					6																	116837131		2203	4300	6503	SO:0001819	synonymous_variant	254228	exon2			CCTTGTGGGTACT	BC032556	CCDS5108.1	6q22.31	2008-02-05	2007-03-19	2007-03-19	ENSG00000178033	ENSG00000178033			21568	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 188"	C6orf188			Standard	NM_153711		Approved	dJ493F7.3, MGC45451	uc003pwy.3	Q8N5C1	OTTHUMG00000015442	ENST00000368599.3:c.909G>T	chr6.hg19:g.116837131G>T		40.0	0.0		59.0	8.0	NM_153711	B2RDJ9|B3KSR3	Silent	SNP	ENST00000368599.3	hg19	CCDS5108.1																																																																																			.	.		0.498	FAM26E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041956.1	NM_153711		T	116837131	G	T	116837131	2	4	339	1	0	0	0	0	0	0	0	1	5558	1335	47	3		3	FAM26E	6	116837131	Silent	SNP	G	TCGA-RC-A7SH-01A-11D-A382-10	36207898	116837131	54277936	27	46923										
HOXA7	3204	hgsc.bcm.edu	37	chr7	27196120	27196120	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	tggaacagagaagcccccgcCgtatatttgctaaaaagcgc	10	11	0	1	rs201461196		TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr7:27196120C>A	ENST00000242159.3	-	1	178	c.45G>T	c.(43-45)acG>acT	p.T15T	RP1-170O19.21_ENST00000602610.1_lincRNA|HOXA7_ENST00000523796.2_5'Flank|HOXA-AS3_ENST00000518947.2_RNA	NM_006896.3	NP_008827.2	P31268	HXA7_HUMAN	homeobox A7	15					angiogenesis (GO:0001525)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of monocyte differentiation (GO:0045656)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(3)|large_intestine(1)|lung(10)|prostate(1)|urinary_tract(1)	16						AAGCCCCCGCCGTATATTTGC	0.527																																					p.T15T		Atlas-SNP	.											.	HOXA7	34	.	0			c.G45T						.						65	81	76					7																	27196120		2197	4289	6486	SO:0001819	synonymous_variant	3204	exon1			CCCCGCCGTATAT		CCDS5408.1	7p15.2	2011-06-20	2005-12-22		ENSG00000122592	ENSG00000122592		"Homeoboxes / ANTP class : HOXL subclass"	5108	protein-coding gene	gene with protein product		142950	"homeo box A7"	HOX1A, HOX1		1973146, 1358459	Standard	NM_006896		Approved		uc003sys.3	P31268	OTTHUMG00000023217	ENST00000242159.3:c.45G>T	chr7.hg19:g.27196120C>A		203.0	0.0		216.0	88.0	NM_006896	A4D191|O43368|O43486|O95655|Q9NSC8|Q9UDM1	Silent	SNP	ENST00000242159.3	hg19	CCDS5408.1																																																																																			.	C|0.999;T|0.001		0.527	HOXA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358695.1			A	27196120	C	A	27196120	2	1	339	1	0	0	0	0	0	0	0	1	7306	639	23	1		1	HOXA7	7	27196120	Silent	SNP	C	TCGA-RC-A7SH-01A-11D-A382-10		27196120	131942543	28	46924										
CACNA2D1	781	hgsc.bcm.edu	37	chr7	81599250	81599250	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	cattatctaggctccttttaTagaagctgtcctcatatgtc	6	10	2	1			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr7:81599250T>A	ENST00000356253.5	-	28	2546	c.2291A>T	c.(2290-2292)tAt>tTt	p.Y764F	CACNA2D1_ENST00000535308.1_Intron|CACNA2D1_ENST00000356860.3_Missense_Mutation_p.Y752F			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	764					calcium ion transport (GO:0006816)|regulation of calcium ion transport (GO:0051924)	extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81					Amlodipine(DB00381)|Cyclandelate(DB04838)|Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)	GCTCCTTTTATAGAAGCTGTC	0.348																																					p.Y752F		Atlas-SNP	.											.	CACNA2D1	191	.	0			c.A2255T						.						151	147	149					7																	81599250		2203	4299	6502	SO:0001583	missense	781	exon28			CTTTTATAGAAGC	M76559	CCDS5598.1	7q21-q22	2014-09-17			ENSG00000153956	ENSG00000153956		"Calcium channel subunits"	1399	protein-coding gene	gene with protein product		114204	"long intergenic non-protein coding RNA 1112"	CACNL2A, CACNA2, MHS3, LINC01112		8188232	Standard	XM_005250570		Approved	lncRNA-N3	uc003uhr.1	P54289	OTTHUMG00000023622	ENST00000356253.5:c.2291A>T	chr7.hg19:g.81599250T>A	ENSP00000348589:p.Tyr764Phe	88.0	0.0		88.0	37.0	NM_000722	Q17R45|Q9UD80|Q9UD81|Q9UD82	Missense_Mutation	SNP	ENST00000356253.5	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	32|32	5.173693|5.173693	0.94807|0.94807	.|.	.|.	ENSG00000153956|ENSG00000153956	ENST00000443883|ENST00000356860;ENST00000284088;ENST00000356253	.|T;T	.|0.80393	.|-1.37;-1.37	5.81|5.81	5.81|5.81	0.92471|0.92471	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.87951|0.87951	0.6307|0.6307	L|L	0.59436|0.59436	1.845|1.845	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.78314	.|0.991	D|D	0.89011|0.89011	0.3428|0.3428	5|10	.|0.87932	.|D	.|0	-20.1323|-20.1323	16.1756|16.1756	0.81847|0.81847	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|752	.|P54289-2	.|.	L|F	263|752;771;764	.|ENSP00000349320:Y752F;ENSP00000348589:Y764F	.|ENSP00000284088:Y771F	I|Y	-|-	1|2	0|0	CACNA2D1|CACNA2D1	81437186|81437186	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.581000|7.581000	0.82535|0.82535	2.213000|2.213000	0.71641|0.71641	0.528000|0.528000	0.53228|0.53228	ATA|TAT	.	.		0.348	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding				A	81599250	T	A	81599250	3	1	339	1	0	0	0	0	1	0	0	0	2550	1406	49	4	1068	4	CACNA2D1	7	81599250	Missense_Mutation	SNP	T	TCGA-RC-A7SH-01A-11D-A382-10	54403130	81599250	77539413	29	46925			1	61		2	2	26	N	T_GGT	5.491384e-05
CACNA2D1	781	hgsc.bcm.edu	37	chr7	81599275	81599277	+	Missense_Mutation	TNP	GGT	GGT	AAC													0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	gctgtcctcatatgtctctgGgttttcttgccaattttctc							TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	G|G|T	G|G|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr7:81599275_81599277GGT>AAC	ENST00000356253.5	-	28	2519_2521	c.2264_2266ACC>GTT	c.(2263-2268)aACCca>aGTTca	p.755_756NP>SS	CACNA2D1_ENST00000535308.1_Intron|CACNA2D1_ENST00000356860.3_Missense_Mutation_p.743_744NP>SS			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	755					calcium ion transport (GO:0006816)|regulation of calcium ion transport (GO:0051924)	extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81					Amlodipine(DB00381)|Cyclandelate(DB04838)|Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)	TATGTCTCTGGGTTTTCTTGCCA	0.379																																					p.P744S|p.N743N|p.N743S		Atlas-SNP	.											.	CACNA2D1	191	.	0			c.C2230T|c.C2229T|c.A2228G						.																																			SO:0001583	missense	781	exon28			TCTCTGGGTTTTC|CTCTGGGTTTTCT|TCTGGGTTTTCTT	M76559	CCDS5598.1	7q21-q22	2014-09-17			ENSG00000153956	ENSG00000153956		"Calcium channel subunits"	1399	protein-coding gene	gene with protein product		114204	"long intergenic non-protein coding RNA 1112"	CACNL2A, CACNA2, MHS3, LINC01112		8188232	Standard	XM_005250570		Approved	lncRNA-N3	uc003uhr.1	P54289	OTTHUMG00000023622	ENST00000356253.5:c.2264_2266ACC>GTT	chr7.hg19:g.81599275GGT>AAC	ENSP00000348589:p.N755_P756delinsSS	90.0|89.0|89.0	0.0		83.0|82.0|81.0	33.0|32.0|32.0	NM_000722	Q17R45|Q9UD80|Q9UD81|Q9UD82	Missense_Mutation|Silent|Missense_Mutation	SNP	ENST00000356253.5	hg19																																																																																				.	.		0.379	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding				AAC	81599277	GGT	AAC	81599275	3	1	339	1	0	0	0	0	1	0	0	0	2550	1232	43	3	1093	3	CACNA2D1	7	81599275	Missense_Mutation	TNP	GGT	TCGA-RC-A7SH-01A-11D-A382-10	25	81599275	77539388	30	46926			1	61		2	2	26	N	T_GGT	5.491384e-05
PPP1R3A	5506	hgsc.bcm.edu	37	chr7	113519477	113519477	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	tagccaggtctctgttactaGctccaatccctgccacactt	6	15	1	0	rs536084008		TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr7:113519477G>A	ENST00000284601.3	-	4	1738	c.1670C>T	c.(1669-1671)gCt>gTt	p.A557V		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	557					glycogen metabolic process (GO:0005977)	integral component of membrane (GO:0016021)				NS(2)|breast(8)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|liver(1)|lung(43)|ovary(10)|pancreas(7)|prostate(3)|skin(15)|stomach(1)|upper_aerodigestive_tract(2)	121						TCTGTTACTAGCTCCAATCCC	0.423													G|||	1	0.000199681	0	0	5008	,	,		18250	0		0	False		,,,				2504	0.001				p.A557V		Atlas-SNP	.											.	PPP1R3A	317	.	0			c.C1670T						.						112	103	106					7																	113519477		2203	4300	6503	SO:0001583	missense	5506	exon4			TTACTAGCTCCAA	AF024578	CCDS5759.1	7q31.1	2012-04-17	2011-10-04	2001-07-02	ENSG00000154415	ENSG00000154415	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9291	protein-coding gene	gene with protein product	"glycogen-associated regulatory subunit of protein phosphatase-1", "protein phosphatase 1 regulatory subunit GM"	600917	"protein phosphatase 1, regulatory (inhibitor) subunit 3A (glycogen and sarcoplasmic reticulum binding subunit, skeletal muscle)", "protein phosphatase 1, regulatory (inhibitor) subunit 3A"	PPP1R3		7926294	Standard	NM_002711		Approved	GM	uc010ljy.1	Q16821	OTTHUMG00000156944	ENST00000284601.3:c.1670C>T	chr7.hg19:g.113519477G>A	ENSP00000284601:p.Ala557Val	97.0	0.0		131.0	66.0	NM_002711	A0AVQ2|A4D0T6|O43476|Q75LN8|Q7KYM8|Q86UI6	Missense_Mutation	SNP	ENST00000284601.3	hg19	CCDS5759.1	.	.	.	.	.	.	.	.	.	.	G	12.04	1.817134	0.32145	.	.	ENSG00000154415	ENST00000284601	T	0.23348	1.91	6.02	1.12	0.20585	.	0.506301	0.19399	N	0.115227	T	0.20292	0.0488	L	0.56769	1.78	0.09310	N	1	B	0.25719	0.132	B	0.20577	0.03	T	0.16808	-1.0390	10	0.46703	T	0.11	-0.608	4.3255	0.11038	0.2638:0.0:0.3737:0.3626	.	557	Q16821	PPR3A_HUMAN	V	557	ENSP00000284601:A557V	ENSP00000284601:A557V	A	-	2	0	PPP1R3A	113306713	0.000000	0.05858	0.002000	0.10522	0.007000	0.05969	0.138000	0.16016	0.146000	0.19002	-0.953000	0.02652	GCT	.	.		0.423	PPP1R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346724.1	NM_002711		A	113519477	G	A	113519477	3	1	339	1	0	0	0	0	1	0	0	0	12383	971	34	3	1702	3	PPP1R3A	7	113519477	Missense_Mutation	SNP	G	TCGA-RC-A7SH-01A-11D-A382-10	31920202	113519477	45619186	31	46927										
SLC4A2	6522	hgsc.bcm.edu	37	chr7	150767561	150767561	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	cagcgtgagctgccgcctccAgcaccaccagctggcatcac	10	18	1	1			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr7:150767561A>T	ENST00000485713.1	+	11	2507	c.1467A>T	c.(1465-1467)ccA>ccT	p.P489P	SLC4A2_ENST00000310317.5_Silent_p.P407P|SLC4A2_ENST00000392826.2_Silent_p.P480P|SLC4A2_ENST00000461735.1_Silent_p.P475P|SLC4A2_ENST00000413384.2_Silent_p.P489P	NM_001199692.1	NP_001186621.1	P04920	B3A2_HUMAN	solute carrier family 4 (anion exchanger), member 2	489					anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(14)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TGCCGCCTCCAGCACCACCAG	0.647																																					p.P489P		Atlas-SNP	.											.	SLC4A2	98	.	0			c.A1467T						.						29	27	27					7																	150767561		2203	4300	6503	SO:0001819	synonymous_variant	6522	exon11			GCCTCCAGCACCA		CCDS5917.1, CCDS56520.1, CCDS56521.1	7q36.1	2013-07-19	2013-07-19		ENSG00000164889	ENSG00000164889		"Solute carriers"	11028	protein-coding gene	gene with protein product	"anion exchanger 2 type a", "anion exchanger 2 type b1", "anion exchanger 2 type b2"	109280	"erythrocyte membrane protein band 3-like 1", "solute carrier family 4, anion exchanger, member 2 (erythrocyte membrane protein band 3-like 1)"	EPB3L1, AE2		8434259	Standard	NM_003040		Approved	HKB3, BND3L, NBND3	uc003wit.4	P04920	OTTHUMG00000158443	ENST00000485713.1:c.1467A>T	chr7.hg19:g.150767561A>T		89.0	0.0		96.0	57.0	NM_003040	B2R6T0|B4DIT0|D3DX05|F8W682|Q45EY5|Q969L3	Silent	SNP	ENST00000485713.1	hg19	CCDS5917.1																																																																																			.	.		0.647	SLC4A2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351039.1	NM_003040		T	150767561	A	T	150767561	2	4	339	1	0	0	0	0	0	0	0	1	14669	175	7	4		4	SLC4A2	7	150767561	Silent	SNP	A	TCGA-RC-A7SH-01A-11D-A382-10	37248084	150767561	8371102	32	46928										
MMP16	4325	hgsc.bcm.edu	37	chr8	89128908	89128908	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	agcggtgtgggggcactgtcGgtagaggtcttgtaggtgga	20	5	1	1			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr8:89128908G>A	ENST00000286614.6	-	6	1192	c.911C>T	c.(910-912)cCg>cTg	p.P304L	MMP16_ENST00000544227.1_5'UTR	NM_005941.4	NP_005932.2	P51512	MMP16_HUMAN	matrix metallopeptidase 16 (membrane-inserted)	304					chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)	Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.P304L(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(51)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	81					Marimastat(DB00786)	GGGCACTGTCGGTAGAGGTCT	0.517																																					p.P304L		Atlas-SNP	.											MMP16,rectum,carcinoma,+1,1	MMP16	176	.	1	Substitution - Missense(1)	lung(1)	c.C911T						.						198	205	203					8																	89128908		2203	4300	6503	SO:0001583	missense	4325	exon6			ACTGTCGGTAGAG	D85511	CCDS6246.1	8q21	2009-01-09	2005-08-08		ENSG00000156103	ENSG00000156103			7162	protein-coding gene	gene with protein product		602262	"matrix metalloproteinase 16 (membrane-inserted)", "chromosome 8 open reading frame 57"	C8orf57		7559440	Standard	NM_005941		Approved	MT3-MMP, DKFZp761D112	uc003yeb.4	P51512	OTTHUMG00000163769	ENST00000286614.6:c.911C>T	chr8.hg19:g.89128908G>A	ENSP00000286614:p.Pro304Leu	195.0	1.0		238.0	77.0	NM_005941	B2RAN7|Q14824|Q52H48	Missense_Mutation	SNP	ENST00000286614.6	hg19	CCDS6246.1	.	.	.	.	.	.	.	.	.	.	G	18.74	3.689527	0.68271	.	.	ENSG00000156103	ENST00000286614	T	0.18502	2.21	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.35098	0.0920	M	0.76574	2.34	0.80722	D	1	P;B	0.46912	0.886;0.055	P;B	0.49047	0.599;0.03	T	0.05954	-1.0854	10	0.66056	D	0.02	.	20.0498	0.97621	0.0:0.0:1.0:0.0	.	304;304	P51512-2;P51512	.;MMP16_HUMAN	L	304	ENSP00000286614:P304L	ENSP00000286614:P304L	P	-	2	0	MMP16	89198024	1.000000	0.71417	0.896000	0.35187	0.993000	0.82548	8.004000	0.88535	2.753000	0.94483	0.557000	0.71058	CCG	.	.		0.517	MMP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375304.2	NM_005941		A	89128908	G	A	89128908	3	1	339	1	0	0	0	0	1	0	0	0	9664	1116	39	1	1088	1	MMP16	8	89128908	Missense_Mutation	SNP	G	TCGA-RC-A7SH-01A-11D-A382-10		89128908	57235114	33	46929										
COL22A1	169044	hgsc.bcm.edu	37	chr8	139890313	139890313	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	cgtctcccgtgttggtgttgCccccgtggtaggcgagacgc	15	13	1	1	rs375895986		TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr8:139890313C>T	ENST00000303045.6	-	3	784	c.338G>A	c.(337-339)gGc>gAc	p.G113D	COL22A1_ENST00000435777.1_Missense_Mutation_p.G113D	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	113	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			GTTGGTGTTGCCCCCGTGGTA	0.711										HNSCC(7;0.00092)																											p.G113D		Atlas-SNP	.											.	COL22A1	390	.	0			c.G338A						.	C	ASP/GLY	0,4374		0,0,2187	18	21	20		338	5.1	1	8		20	1,8523		0,1,4261	no	missense	COL22A1	NM_152888.1	94	0,1,6448	TT,TC,CC		0.0117,0.0,0.0078	probably-damaging	113/1627	139890313	1,12897	2187	4262	6449	SO:0001583	missense	169044	exon3			GTGTTGCCCCCGT	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"Collagens"	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.338G>A	chr8.hg19:g.139890313C>T	ENSP00000303153:p.Gly113Asp	80.0	0.0		118.0	33.0	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Missense_Mutation	SNP	ENST00000303045.6	hg19	CCDS6376.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.425601	0.83667	0.0	1.17E-4	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	D;D	0.84370	-1.84;-1.84	5.11	5.11	0.69529	von Willebrand factor, type A (3);	0.000000	0.48767	U	0.000172	D	0.93530	0.7935	M	0.88704	2.975	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94382	0.7605	9	.	.	.	.	17.5098	0.87757	0.0:1.0:0.0:0.0	.	113	Q8NFW1	COMA1_HUMAN	D	113	ENSP00000303153:G113D;ENSP00000387655:G113D	.	G	-	2	0	COL22A1	139959495	1.000000	0.71417	1.000000	0.80357	0.340000	0.28889	7.366000	0.79548	2.341000	0.79615	0.591000	0.81541	GGC	.	.		0.711	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257		T	139890313	C	T	139890313	3	4	339	1	0	0	0	0	1	0	0	0	3683	739	26	3	4794	3	COL22A1	8	139890313	Missense_Mutation	SNP	C	TCGA-RC-A7SH-01A-11D-A382-10	50761405	139890313	6473709	34	46930										
C9orf150	286343	hgsc.bcm.edu	37	chr9	12821394	12821394	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	tttgtccataggttaacctcAgagccacagacgtcaggctc	9	12	2	2			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr9:12821394A>G	ENST00000319264.3	+	2	1017	c.322A>G	c.(322-324)Aga>Gga	p.R108G		NM_203403.1	NP_981948.1	Q8IV03	LUR1L_HUMAN	leucine rich adaptor protein 1-like	111																	GGTTAACCTCAGAGCCACAGA	0.468																																					p.R108G		Atlas-SNP	.											.	.	.	.	0			c.A322G						.						116	123	120					9																	12821394		2203	4300	6503	SO:0001583	missense	286343	exon2			AACCTCAGAGCCA	AK095824	CCDS6473.1	9p22.3	2012-02-01	2012-02-01	2012-02-01	ENSG00000153714	ENSG00000153714			31452	protein-coding gene	gene with protein product	"similar to DNA segment, Chr 4, Brigham & Womens Genetics 0951 expressed"		"chromosome 9 open reading frame 150"	C9orf150		12766061	Standard	NM_203403		Approved	MGC46502, FLJ38505, bA3L8.2	uc003zkw.3	Q8IV03	OTTHUMG00000019557	ENST00000319264.3:c.322A>G	chr9.hg19:g.12821394A>G	ENSP00000321026:p.Arg108Gly	48.0	0.0		47.0	23.0	NM_203403	Q5VZX7|Q8N923|Q8NCG2	Missense_Mutation	SNP	ENST00000319264.3	hg19	CCDS6473.1	.	.	.	.	.	.	.	.	.	.	A	17.86	3.493087	0.64186	.	.	ENSG00000153714	ENST00000319264	T	0.64085	-0.08	5.31	4.14	0.48551	.	0.000000	0.52532	D	0.000065	T	0.74230	0.3689	L	0.58810	1.83	0.51012	D	0.999907	D	0.89917	1.0	D	0.83275	0.996	T	0.75399	-0.3331	10	0.87932	D	0	.	11.9139	0.52755	0.5306:0.4694:0.0:0.0	.	111	Q8IV03	CI150_HUMAN	G	108	ENSP00000321026:R108G	ENSP00000321026:R108G	R	+	1	2	C9orf150	12811394	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	2.671000	0.46842	0.818000	0.34468	0.460000	0.39030	AGA	.	.		0.468	LURAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051730.1	NM_203403		G	12821394	A	G	12821394	3	3	339	1	0	0	0	0	1	0	0	0	2464	180	7	2	328	2	C9orf150	9	12821394	Missense_Mutation	SNP	A	TCGA-RC-A7SH-01A-11D-A382-10		12821394	128392037	35	46931										
BAT2L1	84726	hgsc.bcm.edu	37	chr9	134334701	134334701	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	gcgccagaccctcagccaccGcccaggaagcttcatggctg	11	17	2	1	rs565217318	byFrequency	TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr9:134334701G>A	ENST00000357304.4	+	10	1417	c.1362G>A	c.(1360-1362)ccG>ccA	p.P454P	PRRC2B_ENST00000372249.1_5'UTR|PRRC2B_ENST00000458550.1_Silent_p.P454P|PRRC2B_ENST00000405995.1_Silent_p.P454P	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	454							poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						CTCAGCCACCGCCCAGGAAGC	0.617													G|||	2	0.000399361	0	0	5008	,	,		15507	0		0	False		,,,				2504	0.002				p.P454P		Atlas-SNP	.											.	PRRC2B	266	.	0			c.G1362A						.						39	47	44					9																	134334701		2077	4213	6290	SO:0001819	synonymous_variant	84726	exon10			GCCACCGCCCAGG	AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"KIAA0515", "HLA-B associated transcript 2-like", "HLA-B associated transcript 2-like 1"	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.1362G>A	chr9.hg19:g.134334701G>A		100.0	0.0		76.0	13.0	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Silent	SNP	ENST00000357304.4	hg19	CCDS48044.1																																																																																			.	.		0.617	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	134334701	G	A	134334701	2	1	339	1	0	0	0	0	0	0	0	1	1320	1074	38	1		1	BAT2L1	9	134334701	Silent	SNP	G	TCGA-RC-A7SH-01A-11D-A382-10	121513307	134334701	6878730	36	46932										
BICC1	80114	hgsc.bcm.edu	37	chr10	60577443	60577443	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	cctgagctcttcagcaaactGggcctgggcaaatacacaga	10	12	2	2			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr10:60577443G>C	ENST00000373886.3	+	19	2659	c.2655G>C	c.(2653-2655)ctG>ctC	p.L885L		NM_001080512.1	NP_001073981.1	Q9H694	BICC1_HUMAN	BicC family RNA binding protein 1	885	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)	cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	44						TCAGCAAACTGGGCCTGGGCA	0.418																																					p.L885L		Atlas-SNP	.											.	BICC1	121	.	0			c.G2655C						.						85	81	82					10																	60577443		2203	4300	6503	SO:0001819	synonymous_variant	80114	exon19			CAAACTGGGCCTG	AK026129	CCDS31206.1	10q21.3	2014-09-17	2014-02-03		ENSG00000122870	ENSG00000122870		"Sterile alpha motif (SAM) domain containing"	19351	protein-coding gene	gene with protein product		614295	"bicaudal C homolog 1 (Drosophila)"				Standard	XM_005270166		Approved		uc001jki.1	Q9H694	OTTHUMG00000018271	ENST00000373886.3:c.2655G>C	chr10.hg19:g.60577443G>C		101.0	0.0		144.0	8.0	NM_001080512		Silent	SNP	ENST00000373886.3	hg19	CCDS31206.1																																																																																			.	.		0.418	BICC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048150.2	NM_025044		C	60577443	G	C	60577443	2	2	339	1	0	0	0	0	0	0	0	1	1427	1335	47	4		4	BICC1	10	60577443	Silent	SNP	G	TCGA-RC-A7SH-01A-11D-A382-10		60577443	74957304	37	46933										
HK1	3098	hgsc.bcm.edu	37	chr10	71119657	71119657	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	ttgtctccctaaacagaaaaGggagatttcattgccctgga	9	9	2	2			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr10:71119657G>T	ENST00000359426.6	+	3	335	c.231G>T	c.(229-231)aaG>aaT	p.K77N	HK1_ENST00000298649.3_Missense_Mutation_p.K76N|HK1_ENST00000448642.2_Missense_Mutation_p.K112N|HK1_ENST00000494253.1_3'UTR|HK1_ENST00000360289.2_Missense_Mutation_p.K65N|HK1_ENST00000404387.2_Missense_Mutation_p.K81N	NM_000188.2	NP_000179.2	P19367	HXK1_HUMAN	hexokinase 1	77	Hexokinase type-1 1.|Regulatory.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cell death (GO:0008219)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(1)|urinary_tract(2)	35						AAACAGAAAAGGGAGATTTCA	0.498																																					p.K81N		Atlas-SNP	.											.	HK1	170	.	0			c.G243T						.						143	125	131					10																	71119657		2203	4300	6503	SO:0001583	missense	3098	exon6			AGAAAAGGGAGAT	M75126	CCDS7289.1, CCDS7290.1, CCDS7291.1, CCDS7292.1	10q22	2014-09-17			ENSG00000156515	ENSG00000156515	2.7.1.1		4922	protein-coding gene	gene with protein product		142600					Standard	NM_033496		Approved		uc001jpi.4	P19367	OTTHUMG00000018380	ENST00000359426.6:c.231G>T	chr10.hg19:g.71119657G>T	ENSP00000352398:p.Lys77Asn	100.0	0.0		91.0	4.0	NM_033498	E9PCK0|O43443|O43444|O75574|Q5VTC3|Q96HC8|Q9NNZ4|Q9NNZ5	Missense_Mutation	SNP	ENST00000359426.6	hg19	CCDS7292.1	.	.	.	.	.	.	.	.	.	.	G	11.53	1.664767	0.29604	.	.	ENSG00000156515	ENST00000450646;ENST00000360289;ENST00000448642;ENST00000421088;ENST00000404387;ENST00000436817;ENST00000298649;ENST00000359426;ENST00000405407	T;T;T;T;T;T;T;T	0.57436	0.4;0.4;0.4;0.4;0.4;0.4;0.4;0.4	5.51	2.61	0.31194	Hexokinase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.42607	0.1210	L	0.51853	1.615	0.58432	D	0.999999	B;B;B;B;B	0.16603	0.001;0.0;0.001;0.0;0.018	B;B;B;B;B	0.12156	0.004;0.004;0.005;0.007;0.002	T	0.22941	-1.0202	10	0.26408	T	0.33	-1.7372	9.4688	0.38829	0.3362:0.0:0.6638:0.0	.	77;76;112;81;65	P19367;P19367-2;E7ENR4;P19367-3;P19367-4	HXK1_HUMAN;.;.;.;.	N	81;65;112;65;81;76;76;77;77	ENSP00000409761:K81N;ENSP00000353433:K65N;ENSP00000402103:K112N;ENSP00000398316:K65N;ENSP00000384774:K81N;ENSP00000415949:K76N;ENSP00000298649:K76N;ENSP00000352398:K77N	ENSP00000298649:K76N	K	+	3	2	HK1	70789663	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.377000	0.34317	0.691000	0.31592	0.561000	0.74099	AAG	.	.		0.498	HK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048429.2	NM_000188		T	71119657	G	T	71119657	3	4	339	1	0	0	0	0	1	0	0	0	7199	991	35	3	419	3	HK1	10	71119657	Missense_Mutation	SNP	G	TCGA-RC-A7SH-01A-11D-A382-10	10542214	71119657	64415090	38	46934										
C10orf28	27291	hgsc.bcm.edu	37	chr10	99994235	99994235	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	tgatattaaatgggtggatgAtacacatgccctaggagtat	11	5	0	2			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr10:99994235A>G	ENST00000298999.3	+	7	2297	c.1994A>G	c.(1993-1995)gAt>gGt	p.D665G	R3HCC1L_ENST00000370584.3_Missense_Mutation_p.D665G|R3HCC1L_ENST00000370586.2_Missense_Mutation_p.D71G|R3HCC1L_ENST00000314594.5_Missense_Mutation_p.D81G	NM_014472.4	NP_055287	Q7Z5L2	R3HCL_HUMAN	R3H domain and coiled-coil containing 1-like	679							nucleotide binding (GO:0000166)										TGGGTGGATGATACACATGCC	0.318																																					p.D679G		Atlas-SNP	.											.	R3HCC1L	3	.	0			c.A2036G						.						143	145	144					10																	99994235		2203	4300	6503	SO:0001583	missense	27291	exon8			TGGATGATACACA	AF525304	CCDS31267.1, CCDS58093.1, CCDS73178.1	10q24.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000166024	ENSG00000166024			23512	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 28"	C10orf28			Standard	NM_014472		Approved	GIDRP86, PSORT	uc001kox.4	Q7Z5L2	OTTHUMG00000018873	ENST00000298999.3:c.1994A>G	chr10.hg19:g.99994235A>G	ENSP00000298999:p.Asp665Gly	106.0	0.0		116.0	71.0	NM_001256619	O60598|Q5W0B4|Q5W0B5|Q86VT9|Q8N9H0	Missense_Mutation	SNP	ENST00000298999.3	hg19	CCDS31267.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.474899	0.84640	.	.	ENSG00000166024	ENST00000370584;ENST00000298999;ENST00000370586;ENST00000314594;ENST00000544834	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	5.93	5.93	0.95920	Nucleotide-binding, alpha-beta plait (1);	0.000000	0.85682	D	0.000000	T	0.67664	0.2917	M	0.83953	2.67	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;1.0;1.0	T	0.71104	-0.4689	9	.	.	.	-17.5791	15.3526	0.74402	1.0:0.0:0.0:0.0	.	71;679;665	Q7Z5L2-3;Q7Z5L2;Q7Z5L2-2	.;GIDRP_HUMAN;.	G	665;665;71;81;72	ENSP00000359616:D665G;ENSP00000298999:D665G;ENSP00000359618:D71G;ENSP00000314018:D81G	.	D	+	2	0	C10orf28	99984225	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.379000	0.79691	2.257000	0.74773	0.528000	0.53228	GAT	.	.		0.318	R3HCC1L-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049764.1	NM_014472		G	99994235	A	G	99994235	3	3	339	1	0	0	0	0	1	0	0	0	1603	333	12	2	2004	2	C10orf28	10	99994235	Missense_Mutation	SNP	A	TCGA-RC-A7SH-01A-11D-A382-10	28874578	99994235	35540512	39	46935										
INPP5F	79892	hgsc.bcm.edu	37	chr10	121587247	121587247	+	IGR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	caagtccagcaaaatgaactTaaaaagatgtttatacaatg	6	6	0	2			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr10:121587247T>C	ENST00000360003.3	-	0	4113				INPP5F_ENST00000369080.3_Silent_p.L508L|INPP5F_ENST00000361976.2_Silent_p.L1118L	NM_001256378.1|NM_001256379.1|NM_024834.3	NP_001243307.1|NP_001243308.1|NP_079110.1	Q9BTE3	MCMBP_HUMAN	minichromosome maintenance complex binding protein						DNA-dependent DNA replication (GO:0006261)|mitotic nuclear division (GO:0007067)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(2)|skin(2)	21						AAAATGAACTTAAAAAGATGT	0.348																																					p.L1118L		Atlas-SNP	.											.	INPP5F	112	.	0			c.T3354C						.						62	67	65					10																	121587247		2203	4300	6503	SO:0001628	intergenic_variant	22876	exon20			TGAACTTAAAAAG	BC007219	CCDS7617.1, CCDS58099.1	10q26.13	2013-10-11	2011-01-05	2011-01-05	ENSG00000197771	ENSG00000197771			25782	protein-coding gene	gene with protein product		610909	"chromosome 10 open reading frame 119"	C10orf119		17296731	Standard	NM_024834		Approved	FLJ13081, MCM-BP	uc001ler.3	Q9BTE3	OTTHUMG00000019159		chr10.hg19:g.121587247T>C		100.0	0.0		130.0	64.0	NM_014937	B3KSP7|Q6IA56|Q9BVT9|Q9H916	Silent	SNP	ENST00000360003.3	hg19	CCDS7617.1																																																																																			.	.		0.348	MCMBP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050684.1	NM_024834		C	121587247	T	C	121587247	1	2	339	0	1	0	0	0	0	0	0	0	7767	1741	61	2		2	INPP5F	10	121587247	IGR	SNP	T	TCGA-RC-A7SH-01A-11D-A382-10	21593012	121587247	13947500	40	46936										
GPR123	84435	hgsc.bcm.edu	37	chr10	134942342	134942342	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	acttgacgccaacggggccgCgctgggccgcgccgcctgcc	15	18	0	1	rs374092448	byFrequency	TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr10:134942342C>T	ENST00000392607.3	+	7	1446	c.1010C>T	c.(1009-1011)gCg>gTg	p.A337V	GPR123_ENST00000607359.1_Missense_Mutation_p.A1056V|GPR123_ENST00000392606.2_Missense_Mutation_p.A240V	NM_001083909.1	NP_001077378.1	Q86SQ6	GP123_HUMAN	G protein-coupled receptor 123	337					G-protein coupled receptor signaling pathway (GO:0007186)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(3)	14		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)		AACGGGGCCGCGCTGGGCCGC	0.741													C|||	2	0.000399361	0.0015	0	5008	,	,		10236	0		0	False		,,,				2504	0				p.A337V		Atlas-SNP	.											.	GPR123	118	.	0			c.C1010T						.	C	VAL/ALA	7,4021		0,7,2007	7	8	8		1010	-0.3	0	10		8	0,7888		0,0,3944	no	missense	GPR123	NM_001083909.1	64	0,7,5951	TT,TC,CC		0.0,0.1738,0.0587	probably-damaging	337/561	134942342	7,11909	2014	3944	5958	SO:0001583	missense	84435	exon7			GGGCCGCGCTGGG	AB058731	CCDS41580.1	10q26	2014-08-08			ENSG00000197177	ENSG00000197177		"-", "GPCR / Class B : Orphans"	13838	protein-coding gene	gene with protein product		612302				12565841	Standard	XM_005252695		Approved	KIAA1828	uc001llw.3	Q86SQ6	OTTHUMG00000019304	ENST00000392607.3:c.1010C>T	chr10.hg19:g.134942342C>T	ENSP00000376384:p.Ala337Val	63.0	0.0		110.0	35.0	NM_001083909	A5HL16|A6NG50|Q5T234|Q86SN7|Q96JJ9	Missense_Mutation	SNP	ENST00000392607.3	hg19	CCDS41580.1	.	.	.	.	.	.	.	.	.	.	.	9.521	1.108353	0.20714	0.001738	0.0	ENSG00000197177	ENST00000368577;ENST00000392607;ENST00000392606	T	0.04194	3.68	3.83	-0.313	0.12754	.	0.241123	0.28236	N	0.016092	T	0.08492	0.0211	M	0.71581	2.175	0.19945	N	0.999943	P;D	0.56035	0.609;0.974	B;P	0.48400	0.144;0.576	T	0.15178	-1.0446	10	0.44086	T	0.13	-2.8051	7.8744	0.29584	0.0:0.6171:0.0:0.3829	.	337;1056	Q86SQ6;Q86SQ6-1	GP123_HUMAN;.	V	1056;337;241	ENSP00000376384:A337V	ENSP00000357566:A1056V	A	+	2	0	GPR123	134792332	0.147000	0.22687	0.045000	0.18777	0.071000	0.16799	1.259000	0.32956	-0.136000	0.11475	0.561000	0.74099	GCG	.	.		0.741	GPR123-003	NOVEL	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051113.2			T	134942342	C	T	134942342	3	4	339	1	0	0	0	0	1	0	0	0	6645	768	27	1	1032	1	GPR123	10	134942342	Missense_Mutation	SNP	C	TCGA-RC-A7SH-01A-11D-A382-10	13355095	134942342	592405	41	46937										
OR52J3	119679	hgsc.bcm.edu	37	chr11	5068137	5068137	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	cttttgaccgttatgtggccGtctgtgctccactacattac	8	12	1	1	rs2500017	byFrequency	TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr11:5068137G>T	ENST00000380370.1	+	1	382	c.382G>T	c.(382-384)Gtc>Ttc	p.V128F		NM_001001916.2	NP_001001916.2	Q8NH60	O52J3_HUMAN	olfactory receptor, family 52, subfamily J, member 3	128			V -> I (in dbSNP:rs2500017). {ECO:0000269|PubMed:14983052, ECO:0000269|Ref.1, ECO:0000269|Ref.3}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|kidney(6)|large_intestine(6)|lung(19)|ovary(1)|skin(2)	36		Medulloblastoma(188;0.00131)|all_neural(188;0.0189)|Breast(177;0.0204)		Epithelial(150;9.29e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.19)		TTATGTGGCCGTCTGTGCTCC	0.483																																					p.V128F		Atlas-SNP	.											.	OR52J3	77	.	0			c.G382T						.						176	117	137					11																	5068137		2201	4298	6499	SO:0001583	missense	119679	exon1			GTGGCCGTCTGTG	AB065530	CCDS31370.1	11p15.4	2012-08-09			ENSG00000205495	ENSG00000205495		"GPCR / Class A : Olfactory receptors"	14799	protein-coding gene	gene with protein product							Standard	NM_001001916		Approved		uc010qyv.2	Q8NH60	OTTHUMG00000066600	ENST00000380370.1:c.382G>T	chr11.hg19:g.5068137G>T	ENSP00000369728:p.Val128Phe	72.0	0.0		94.0	36.0	NM_001001916	Q6IFE4	Missense_Mutation	SNP	ENST00000380370.1	hg19	CCDS31370.1	.	.	.	.	.	.	.	.	.	.	A	10.39	1.335962	0.24253	.	.	ENSG00000205495	ENST00000380370	T	0.49720	0.77	4.19	4.19	0.49359	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47852	D	0.000211	T	0.46870	0.1415	L	0.54908	1.71	0.51767	P	6.799999999995698E-5	B	0.31290	0.318	B	0.39217	0.294	T	0.59451	-0.7452	9	0.87932	D	0	.	8.6796	0.34201	0.9077:0.0:0.0923:0.0	.	128	Q8NH60	O52J3_HUMAN	F	128	ENSP00000369728:V128F	ENSP00000369728:V128F	V	+	1	0	OR52J3	5024713	0.985000	0.35326	0.891000	0.34965	0.100000	0.18952	2.872000	0.48467	0.651000	0.30788	-0.254000	0.11334	GTC	.	G|0.493;A|0.507		0.483	OR52J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142807.1	NM_001001916		T	5068137	G	T	5068137	3	4	339	1	0	0	0	0	1	0	0	0	11131	1145	40	1	384	1	OR52J3	11	5068137	Missense_Mutation	SNP	G	TCGA-RC-A7SH-01A-11D-A382-10		5068137	129938379	42	46938										
A2M	2	hgsc.bcm.edu	37	chr12	9248257	9248257	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	ctggtcattcaaaggcccagGgaagccagtgaggtcctttt	12	10	2	1			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr12:9248257G>T	ENST00000318602.7	-	16	2198	c.1891C>A	c.(1891-1893)Cct>Act	p.P631T		NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	631					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|stem cell differentiation (GO:0048863)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	calcium-dependent protein binding (GO:0048306)|enzyme binding (GO:0019899)|growth factor binding (GO:0019838)|interleukin-1 binding (GO:0019966)|interleukin-8 binding (GO:0019959)|protease binding (GO:0002020)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|tumor necrosis factor binding (GO:0043120)			breast(1)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(17)|lung(30)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	77					Bacitracin(DB00626)|Becaplermin(DB00102)|Ocriplasmin(DB08888)	AAAGGCCCAGGGAAGCCAGTG	0.348																																					p.P631T		Atlas-SNP	.											.	A2M	180	.	0			c.C1891A						.						93	90	91					12																	9248257		1850	4095	5945	SO:0001583	missense	2	exon16			GCCCAGGGAAGCC	BX647329, X68728, M11313	CCDS44827.1	12p13.31	2010-02-24			ENSG00000175899	ENSG00000175899			7	protein-coding gene	gene with protein product		103950					Standard	XM_006719056		Approved	FWP007, S863-7, CPAMD5	uc001qvk.1	P01023	OTTHUMG00000150267	ENST00000318602.7:c.1891C>A	chr12.hg19:g.9248257G>T	ENSP00000323929:p.Pro631Thr	99.0	0.0		83.0	36.0	NM_000014	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	Missense_Mutation	SNP	ENST00000318602.7	hg19	CCDS44827.1	.	.	.	.	.	.	.	.	.	.	G	7.387	0.630049	0.14257	.	.	ENSG00000175899	ENST00000318602;ENST00000540099	T	0.32023	1.47	5.65	5.65	0.86999	.	3.847120	0.00357	N	0.000035	T	0.46229	0.1382	M	0.85542	2.76	0.33882	D	0.636253	B	0.29955	0.263	B	0.29598	0.104	T	0.53443	-0.8438	10	0.23302	T	0.38	.	13.6006	0.62018	0.0:0.0:0.8447:0.1553	.	631	P01023	A2MG_HUMAN	T	631;646	ENSP00000323929:P631T	ENSP00000323929:P631T	P	-	1	0	A2M	9139524	1.000000	0.71417	0.995000	0.50966	0.247000	0.25773	4.205000	0.58466	2.821000	0.97095	0.650000	0.86243	CCT	.	.		0.348	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014		T	9248257	G	T	9248257	3	4	339	1	0	0	0	0	1	0	0	0	4	1232	43	3	2617	3	A2M	12	9248257	Missense_Mutation	SNP	G	TCGA-RC-A7SH-01A-11D-A382-10		9248257	124603638	43	46939										
BHLHE41	79365	hgsc.bcm.edu	37	chr12	26275005	26275005	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	cgggacgcaaggattcagggAgcttcctttcctggctgcga	14	11	1	0			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr12:26275005A>T	ENST00000242728.4	-	5	1790	c.1443T>A	c.(1441-1443)gcT>gcA	p.A481A		NM_030762.2	NP_110389.1	Q9C0J9	BHE41_HUMAN	basic helix-loop-helix family, member e41	481					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|circadian regulation of gene expression (GO:0032922)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)	nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|histone deacetylase binding (GO:0042826)|MRF binding (GO:0043426)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|transcription corepressor activity (GO:0003714)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(1)	5						GGATTCAGGGAGCTTCCTTTC	0.587																																					p.A481A		Atlas-SNP	.											.	BHLHE41	20	.	0			c.T1443A						.						3	2	2					12																	26275005		1667	3098	4765	SO:0001819	synonymous_variant	79365	exon5			TCAGGGAGCTTCC	AB044088	CCDS8706.1	12p12.1	2011-12-05	2009-01-12	2009-01-12	ENSG00000123095	ENSG00000123095		"Basic helix-loop-helix proteins"	16617	protein-coding gene	gene with protein product	"differentially expressed in chondrocytes 2", "Enhancer-of-split and hairy-related protein 1"	606200	"basic helix-loop-helix domain containing, class B, 3"	BHLHB3		11162494, 18557763	Standard	NM_030762		Approved	DEC2, SHARP-1, SHARP1, bHLHe41	uc001rhb.3	Q9C0J9	OTTHUMG00000169174	ENST00000242728.4:c.1443T>A	chr12.hg19:g.26275005A>T		135.0	0.0		135.0	54.0	NM_030762	A2I2N8	Silent	SNP	ENST00000242728.4	hg19	CCDS8706.1	.	.	.	.	.	.	.	.	.	.	A	1.076	-0.668390	0.03428	.	.	ENSG00000123095	ENST00000540731	.	.	.	3.95	-1.3	0.09259	.	.	.	.	.	T	0.50837	0.1639	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43556	-0.9384	5	0.39692	T	0.17	.	3.6405	0.08165	0.3994:0.0:0.4314:0.1692	.	.	.	.	H	350	.	ENSP00000437369:L350H	L	-	2	0	BHLHE41	26166272	0.088000	0.21588	0.219000	0.23793	0.080000	0.17528	0.616000	0.24344	-0.398000	0.07679	-3.390000	0.00040	CTC	.	.		0.587	BHLHE41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402714.1	NM_030762		T	26275005	A	T	26275005	2	4	339	1	0	0	0	0	0	0	0	1	1424	291	11	4		4	BHLHE41	12	26275005	Silent	SNP	A	TCGA-RC-A7SH-01A-11D-A382-10	17026748	26275005	107576890	44	46940										
TM7SF3	51768	hgsc.bcm.edu	37	chr12	27133508	27133508	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	ttttcacttaccatcatactTgataggtgtcagtcttgtaa	6	8	4	1			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr12:27133508T>C	ENST00000343028.4	-	8	1252	c.1027A>G	c.(1027-1029)Aag>Gag	p.K343E	TM7SF3_ENST00000542667.1_Intron|RP11-421F16.3_ENST00000500632.1_RNA	NM_016551.2	NP_057635.1	Q9NS93	TM7S3_HUMAN	transmembrane 7 superfamily member 3	343						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	18	Colorectal(261;0.0847)					CCATCATACTTGATAGGTGTC	0.353																																					p.K343E		Atlas-SNP	.											.	TM7SF3	41	.	0			c.A1027G						.						82	81	81					12																	27133508		2203	4299	6502	SO:0001583	missense	51768	exon8			CATACTTGATAGG	AB032470	CCDS8710.1	12q11-q12	2012-08-10			ENSG00000064115	ENSG00000064115			23049	protein-coding gene	gene with protein product		605181				10828615	Standard	NM_016551		Approved		uc010sjl.2	Q9NS93	OTTHUMG00000169243	ENST00000343028.4:c.1027A>G	chr12.hg19:g.27133508T>C	ENSP00000342322:p.Lys343Glu	78.0	0.0		62.0	14.0	NM_016551	B3KMZ3|Q9NUS4	Missense_Mutation	SNP	ENST00000343028.4	hg19	CCDS8710.1	.	.	.	.	.	.	.	.	.	.	T	8.721	0.914400	0.17907	.	.	ENSG00000064115	ENST00000343028;ENST00000545344;ENST00000537406;ENST00000543655;ENST00000535819	T;T;T	0.41400	1.57;1.0;1.0	5.09	-2.53	0.06326	.	0.589219	0.18894	N	0.128232	T	0.23133	0.0559	L	0.36672	1.1	0.09310	N	1	B	0.27013	0.166	B	0.28916	0.096	T	0.32824	-0.9892	10	0.07644	T	0.81	-1.8963	6.3213	0.21219	0.0:0.278:0.344:0.378	.	343	Q9NS93	TM7S3_HUMAN	E	343;57;12;134;134	ENSP00000342322:K343E;ENSP00000441924:K134E;ENSP00000445156:K134E	ENSP00000342322:K343E	K	-	1	0	TM7SF3	27024775	0.000000	0.05858	0.001000	0.08648	0.505000	0.33919	-0.072000	0.11486	-0.223000	0.09943	0.482000	0.46254	AAG	.	.		0.353	TM7SF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403033.1	NM_016551		C	27133508	T	C	27133508	3	2	339	1	0	0	0	0	1	0	0	0	15990	1821	63	2	705	2	TM7SF3	12	27133508	Missense_Mutation	SNP	T	TCGA-RC-A7SH-01A-11D-A382-10	858503	27133508	106718387	45	46941										
ARID2	196528	hgsc.bcm.edu	37	chr12	46244622	46244622	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	aacctctcccttctcagcaaGtttcatctacagtggtacag	6	13	4	0			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr12:46244622G>C	ENST00000334344.6	+	15	2888	c.2716G>C	c.(2716-2718)Gtt>Ctt	p.V906L	ARID2_ENST00000444670.1_Missense_Mutation_p.V516L|ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000422737.1_Missense_Mutation_p.V757L|ARID2_ENST00000457135.1_5'Flank	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	906	Gln-rich.			V -> F (in Ref. 3; CAD91164). {ECO:0000305}.	chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		TTCTCAGCAAGTTTCATCTAC	0.473			"N, S, F"		hepatocellular carcinoma																																p.V906L		Atlas-SNP	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	311	.	0			c.G2716C						.						136	120	125					12																	46244622		2203	4300	6503	SO:0001583	missense	196528	exon15			CAGCAAGTTTCAT		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.2716G>C	chr12.hg19:g.46244622G>C	ENSP00000335044:p.Val906Leu	153.0	0.0		175.0	13.0	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Missense_Mutation	SNP	ENST00000334344.6	hg19	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	G	15.23	2.773200	0.49680	.	.	ENSG00000189079	ENST00000334344;ENST00000422737;ENST00000444670	T	0.38077	1.16	5.54	4.65	0.58169	.	0.128362	0.52532	D	0.000067	T	0.25232	0.0613	N	0.24115	0.695	0.80722	D	1	B;P;B	0.37370	0.241;0.592;0.001	B;B;B	0.35971	0.157;0.215;0.001	T	0.03157	-1.1066	10	0.23302	T	0.38	-11.5509	14.5934	0.68386	0.0706:0.0:0.9294:0.0	.	906;516;906	Q68CP9-3;F8W108;Q68CP9	.;.;ARID2_HUMAN	L	906;757;516	ENSP00000335044:V906L	ENSP00000335044:V906L	V	+	1	0	ARID2	44530889	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.877000	0.63086	1.350000	0.45770	-0.254000	0.11334	GTT	.	.		0.473	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		C	46244622	G	C	46244622	3	2	339	1	0	0	0	0	1	0	0	0	915	1029	36	4	2774	4	ARID2	12	46244622	Missense_Mutation	SNP	G	TCGA-RC-A7SH-01A-11D-A382-10	19111114	46244622	87607273	46	46942										
HOXC4	3221	hgsc.bcm.edu	37	chr12	54448087	54448087	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	gcccccgaccatccctccagCgccgccagcaagcaacccat	7	22	0	0			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr12:54448087C>T	ENST00000430889.2	+	1	427	c.381C>T	c.(379-381)agC>agT	p.S127S	HOXC4_ENST00000609810.1_Silent_p.S127S|HOXC4_ENST00000303406.4_Silent_p.S127S	NM_153633.2	NP_705897.1	P09017	HXC4_HUMAN	homeobox C4	127					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	13						ATCCCTCCAGCGCCGCCAGCA	0.642																																					p.S127S		Atlas-SNP	.											.	HOXC4	29	.	0			c.C381T						.						22	22	22					12																	54448087		2198	4298	6496	SO:0001819	synonymous_variant	3221	exon3			CTCCAGCGCCGCC		CCDS8873.1	12q13.13	2011-06-20	2005-12-22		ENSG00000198353	ENSG00000198353		"Homeoboxes / ANTP class : HOXL subclass"	5126	protein-coding gene	gene with protein product		142974	"homeo box C4"	HOX3, HOX3E		1973146, 1358459	Standard	NM_014620		Approved		uc001sex.3	P09017	OTTHUMG00000160036	ENST00000430889.2:c.381C>T	chr12.hg19:g.54448087C>T		155.0	0.0		103.0	85.0	NM_014620		Silent	SNP	ENST00000430889.2	hg19	CCDS8873.1																																																																																			.	.		0.642	HOXC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358963.1			T	54448087	C	T	54448087	2	4	339	1	0	0	0	0	0	0	0	1	7322	767	27	1		1	HOXC4	12	54448087	Silent	SNP	C	TCGA-RC-A7SH-01A-11D-A382-10	8203465	54448087	79403808	47	46943										
APAF1	317	hgsc.bcm.edu	37	chr12	99071268	99071268	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	ccacacagatgctgtttaccAtgcctgcttttctgaggatg	9	11	1	2			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr12:99071268A>G	ENST00000551964.1	+	13	2595	c.1859A>G	c.(1858-1860)cAt>cGt	p.H620R	APAF1_ENST00000552268.1_Intron|APAF1_ENST00000357310.1_Missense_Mutation_p.H620R|APAF1_ENST00000549007.1_Missense_Mutation_p.H620R|APAF1_ENST00000333991.1_Intron|APAF1_ENST00000550527.1_Missense_Mutation_p.H609R|APAF1_ENST00000547045.1_Missense_Mutation_p.H620R|APAF1_ENST00000359972.2_Missense_Mutation_p.H609R|APAF1_ENST00000339433.3_Missense_Mutation_p.H620R	NM_181861.1	NP_863651.1	O14727	APAF_HUMAN	apoptotic peptidase activating factor 1	620				H -> R (in Ref. 2; CAB55587). {ECO:0000305}.	activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|forebrain development (GO:0030900)|intrinsic apoptotic signaling pathway (GO:0097193)|nervous system development (GO:0007399)|neural tube closure (GO:0001843)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|regulation of apoptotic DNA fragmentation (GO:1902510)|regulation of apoptotic process (GO:0042981)|response to G1 DNA damage checkpoint signaling (GO:0072432)	apoptosome (GO:0043293)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(1)	42					Adenosine triphosphate(DB00171)	GCTGTTTACCATGCCTGCTTT	0.388																																					p.H620R		Atlas-SNP	.											.	APAF1	111	.	0			c.A1859G						.						108	92	97					12																	99071268		2203	4300	6503	SO:0001583	missense	317	exon13			TTTACCATGCCTG	AF013263	CCDS9069.1, CCDS9070.1, CCDS9071.1, CCDS55862.1, CCDS55863.1	12q23	2013-01-10	2006-10-23			ENSG00000120868		"WD repeat domain containing"	576	protein-coding gene	gene with protein product		602233	"apoptotic protease activating factor", "apoptotic peptidase activating factor"			9267021, 10702682	Standard	NM_181861		Approved	CED4, APAF-1	uc001tfz.3	O14727	OTTHUMG00000170214	ENST00000551964.1:c.1859A>G	chr12.hg19:g.99071268A>G	ENSP00000448165:p.His620Arg	110.0	0.0		120.0	55.0	NM_181868	B2RMX8|O43297|Q7Z438|Q9BXZ6|Q9UBZ5|Q9UGN8|Q9UGN9|Q9UGP0|Q9UJ58|Q9UJ59|Q9UJ60|Q9UJ61|Q9UJ62|Q9UJ63|Q9UJ64|Q9UJ65|Q9UJ66|Q9UJ67|Q9UNC9	Missense_Mutation	SNP	ENST00000551964.1	hg19	CCDS9069.1	.	.	.	.	.	.	.	.	.	.	A	16.92	3.255707	0.59321	.	.	ENSG00000120868	ENST00000551964;ENST00000359972;ENST00000357310;ENST00000339433;ENST00000550527;ENST00000547045;ENST00000549007	T;T;T;T;T;T;T	0.59906	0.23;0.23;0.23;0.23;0.23;0.23;0.23	5.86	4.72	0.59763	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.205916	0.52532	D	0.000074	T	0.58921	0.2156	N	0.17838	0.53	0.80722	D	1	D;D;D;D;D	0.69078	0.971;0.995;0.964;0.995;0.997	P;D;P;D;D	0.74023	0.856;0.948;0.749;0.924;0.982	T	0.55029	-0.8204	10	0.25106	T	0.35	-15.9152	11.7691	0.51947	0.9314:0.0:0.0686:0.0	.	620;620;609;620;609	C9JLV4;O14727-4;O14727-3;O14727;O14727-2	.;.;.;APAF_HUMAN;.	R	620;609;620;620;609;620;620	ENSP00000448165:H620R;ENSP00000353059:H609R;ENSP00000349862:H620R;ENSP00000341830:H620R;ENSP00000448449:H609R;ENSP00000449791:H620R;ENSP00000448161:H620R	ENSP00000341830:H620R	H	+	2	0	APAF1	97595399	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.254000	0.65457	1.046000	0.40249	0.528000	0.53228	CAT	.	.		0.388	APAF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408006.1	NM_181861.1		G	99071268	A	G	99071268	3	3	339	1	0	0	0	0	1	0	0	0	755	217	8	2	1905	2	APAF1	12	99071268	Missense_Mutation	SNP	A	TCGA-RC-A7SH-01A-11D-A382-10	44623181	99071268	34780627	48	46944										
SPERT	220082	hgsc.bcm.edu	37	chr13	46288182	46288182	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	gtccgggccctccggggaggAggaggccaaggtgggcccgg	21	12	0	0			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr13:46288182A>G	ENST00000310521.1	+	3	1102	c.1022A>G	c.(1021-1023)gAg>gGg	p.E341G	SPERT_ENST00000378966.3_Missense_Mutation_p.E305G	NM_152719.1	NP_689932.1	Q8NA61	SPERT_HUMAN	spermatid associated	341						cytoplasmic membrane-bounded vesicle (GO:0016023)				NS(1)|central_nervous_system(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	15		Breast(56;0.000819)|Lung NSC(96;0.00227)|Prostate(109;0.00703)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;7.26e-05)		TCCGGGGAGGAGGAGGCCAAG	0.706																																					p.E341G		Atlas-SNP	.											.	SPERT	54	.	0			c.A1022G						.						5	5	5					13																	46288182		2110	4094	6204	SO:0001583	missense	220082	exon3			GGGAGGAGGAGGC	AK093129	CCDS9399.1, CCDS66540.1	13q14.13	2010-03-23			ENSG00000174015	ENSG00000174015			30720	protein-coding gene	gene with protein product	"spermatid flower-like structure protein", "testis specific leucine zipper protein nurit", "chibby homolog 2 (Drosophila)"					12204287, 20096028	Standard	NM_001286341		Approved	NURIT, CBY2	uc001van.1	Q8NA61	OTTHUMG00000016861	ENST00000310521.1:c.1022A>G	chr13.hg19:g.46288182A>G	ENSP00000309189:p.Glu341Gly	76.0	0.0		33.0	25.0	NM_152719	A8K8I5|Q8NHV2	Missense_Mutation	SNP	ENST00000310521.1	hg19	CCDS9399.1	.	.	.	.	.	.	.	.	.	.	A	17.34	3.364809	0.61513	.	.	ENSG00000174015	ENST00000310521;ENST00000378966	T;T	0.55588	0.55;0.51	4.83	4.83	0.62350	.	0.497398	0.18429	N	0.141494	T	0.61223	0.2330	L	0.32530	0.975	0.37858	D	0.929633	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.66172	-0.5990	10	0.62326	D	0.03	.	11.8769	0.52552	1.0:0.0:0.0:0.0	.	305;341	Q8NA61-2;Q8NA61	.;SPERT_HUMAN	G	341;305	ENSP00000309189:E341G;ENSP00000368249:E305G	ENSP00000309189:E341G	E	+	2	0	SPERT	45186183	0.994000	0.37717	0.525000	0.27900	0.573000	0.36030	2.934000	0.48956	2.032000	0.59987	0.496000	0.49642	GAG	.	.		0.706	SPERT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044786.2	NM_152719		G	46288182	A	G	46288182	3	3	339	1	0	0	0	0	1	0	0	0	15054	304	11	2	1032	2	SPERT	13	46288182	Missense_Mutation	SNP	A	TCGA-RC-A7SH-01A-11D-A382-10		46288182	68881696	49	46945										
TM9SF2	9375	hgsc.bcm.edu	37	chr13	100172304	100172304	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	tcccaggtttgatttttgccAagcatcagaaggaaagcgcc	10	10	1	2			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr13:100172304A>T	ENST00000376387.4	+	3	444	c.254A>T	c.(253-255)cAa>cTa	p.Q85L	TM9SF2_ENST00000463709.1_3'UTR	NM_004800.1	NP_004791.1	Q99805	TM9S2_HUMAN	transmembrane 9 superfamily member 2	85					transport (GO:0006810)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)	17	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.218)					GATTTTTGCCAAGCATCAGAA	0.363																																					p.Q85L		Atlas-SNP	.											.	TM9SF2	52	.	0			c.A254T						.						74	73	74					13																	100172304		2203	4300	6503	SO:0001583	missense	9375	exon3			TTTGCCAAGCATC	U81006	CCDS9493.1	13q32.2	2011-03-28			ENSG00000125304	ENSG00000125304			11865	protein-coding gene	gene with protein product		604678				9729438	Standard	NM_004800		Approved	P76	uc001voj.2	Q99805	OTTHUMG00000017272	ENST00000376387.4:c.254A>T	chr13.hg19:g.100172304A>T	ENSP00000365567:p.Gln85Leu	158.0	1.0		79.0	52.0	NM_004800	A8K399|Q2TAY5	Missense_Mutation	SNP	ENST00000376387.4	hg19	CCDS9493.1	.	.	.	.	.	.	.	.	.	.	A	12.57	1.978954	0.34942	.	.	ENSG00000125304	ENST00000376387	T	0.41758	0.99	5.75	4.53	0.55603	.	0.556104	0.21188	N	0.078691	T	0.33440	0.0863	L	0.36672	1.1	0.43025	D	0.994585	B;B	0.06786	0.001;0.001	B;B	0.12837	0.008;0.008	T	0.06643	-1.0815	10	0.25751	T	0.34	-13.4889	12.8755	0.57988	0.864:0.136:0.0:0.0	.	85;85	E9PHW5;Q99805	.;TM9S2_HUMAN	L	85	ENSP00000365567:Q85L	ENSP00000365567:Q85L	Q	+	2	0	TM9SF2	98970305	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	4.414000	0.59802	0.968000	0.38212	0.477000	0.44152	CAA	.	.		0.363	TM9SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045602.3			T	100172304	A	T	100172304	3	4	339	1	0	0	0	0	1	0	0	0	15993	130	5	4	264	4	TM9SF2	13	100172304	Missense_Mutation	SNP	A	TCGA-RC-A7SH-01A-11D-A382-10	53884122	100172304	14997574	50	46946										
ATP6V1D	51382	hgsc.bcm.edu	37	chr14	67805346	67805346	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	gaacaggaaagattattcaaAtagaagatcctcgtccttct	7	8	2	3			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr14:67805346A>G	ENST00000216442.7	-	9	1286	c.736T>C	c.(736-738)Ttt>Ctt	p.F246L	ATP6V1D_ENST00000555474.1_Missense_Mutation_p.F147L|Y_RNA_ENST00000362885.1_RNA|ATP6V1D_ENST00000555431.1_Missense_Mutation_p.F191L|ATP6V1D_ENST00000554236.1_3'UTR|ATP6V1D_ENST00000553974.1_5'Flank	NM_015994.3	NP_057078.1	Q9Y5K8	VATD_HUMAN	ATPase, H+ transporting, lysosomal 34kDa, V1 subunit D	246					cellular iron ion homeostasis (GO:0006879)|cilium assembly (GO:0042384)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|protein localization to cilium (GO:0061512)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			lung(3)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	7				all cancers(60;0.000739)|OV - Ovarian serous cystadenocarcinoma(108;0.00597)|BRCA - Breast invasive adenocarcinoma(234;0.00957)		GATTATTCAAATAGAAGATCC	0.403																																					p.F246L		Atlas-SNP	.											.	ATP6V1D	21	.	0			c.T736C						.						155	163	160					14																	67805346		2203	4300	6503	SO:0001583	missense	51382	exon9			ATTCAAATAGAAG	AF145316	CCDS9780.1	14q23-q24.2	2010-04-21	2002-08-29	2002-05-10	ENSG00000100554	ENSG00000100554		"ATPases / V-type"	13527	protein-coding gene	gene with protein product		609398	"ATPase, H+ transporting, lysosomal (vacuolar proton pump)"	ATP6M		9442887	Standard	NM_015994		Approved	VATD, VMA8	uc001xjf.3	Q9Y5K8		ENST00000216442.7:c.736T>C	chr14.hg19:g.67805346A>G	ENSP00000216442:p.Phe246Leu	98.0	0.0		52.0	43.0	NM_015994	B2RE33|Q9Y688	Missense_Mutation	SNP	ENST00000216442.7	hg19	CCDS9780.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.716225	0.89205	.	.	ENSG00000100554	ENST00000555474;ENST00000216442;ENST00000555431	.	.	.	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.61874	0.2382	N	0.24115	0.695	0.80722	D	1	D	0.67145	0.996	P	0.60682	0.878	T	0.67082	-0.5760	9	0.87932	D	0	-14.4258	16.0152	0.80434	1.0:0.0:0.0:0.0	.	246	Q9Y5K8	VATD_HUMAN	L	147;246;191	.	ENSP00000216442:F246L	F	-	1	0	ATP6V1D	66875099	1.000000	0.71417	0.997000	0.53966	0.539000	0.34962	8.395000	0.90188	2.180000	0.69256	0.533000	0.62120	TTT	.	.		0.403	ATP6V1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412511.1	NM_015994		G	67805346	A	G	67805346	3	3	339	1	0	0	0	0	1	0	0	0	1182	101	4	2	11	2	ATP6V1D	14	67805346	Missense_Mutation	SNP	A	TCGA-RC-A7SH-01A-11D-A382-10		67805346	39544194	51	46947										
C14orf68	283600	hgsc.bcm.edu	37	chr14	100795930	100795932	+	In_Frame_Del	DEL	TCT	TCT	-													0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	cttccctgtcaacatggtggTcttcgtcgcctatgaggcag							TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr14:100795930_100795932delTCT	ENST00000361529.3	+	6	953_955	c.875_877delTCT	c.(874-879)gtcttc>gtc	p.F293del	SLC25A47_ENST00000557052.1_In_Frame_Del_p.F147del	NM_207117.2	NP_997000.2	Q6Q0C1	S2547_HUMAN	solute carrier family 25, member 47	293					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|prostate(1)|skin(2)|urinary_tract(1)	13						AACATGGTGGTCTTCGTCGCCTA	0.64																																					p.292_292del	GBM(11;1289 1351)	Atlas-INDEL	.											.	SLC25A47	36	.	0			c.874_876del						.																																			SO:0001651	inframe_deletion	283600	exon6			.		CCDS9959.1	14q32.2	2013-05-22	2010-07-19	2010-07-19	ENSG00000140107	ENSG00000140107		"Solute carriers"	20115	protein-coding gene	gene with protein product		609911	"chromosome 14 open reading frame 68"	C14orf68			Standard	NM_207117		Approved		uc001yhc.3	Q6Q0C1	OTTHUMG00000171571	ENST00000361529.3:c.875_877delTCT	chr14.hg19:g.100795930_100795932delTCT	ENSP00000354886:p.Phe293del	48.0	0.0		33.0	23.0	NM_207117	B2RP39|Q68CL2|Q6PZD8|Q86U14	In_Frame_Del	DEL	ENST00000361529.3	hg19	CCDS9959.1																																																																																			.	.		0.64	SLC25A47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414231.1			-	100795932	TCT	-	100795930	7	5	339	1	0	1	0	1	0	0	0	0	1780	1667	58	0	897	0	C14orf68	14	100795930	In_Frame_Del	DEL	TCT	TCGA-RC-A7SH-01A-11D-A382-10	32990584	100795930	6553610	52	46948										
C15orf42	90381	hgsc.bcm.edu	37	chr15	90169017	90169017	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	acgaagaggtgtttgtttccGgtgagttcgtttttgaaacc	12	6	0	3			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr15:90169017G>T	ENST00000268138.7	+	20	5581	c.5476G>T	c.(5476-5478)Ggc>Tgc	p.G1826C	KIF7_ENST00000558928.1_Intron|TICRR_ENST00000560985.1_Splice_Site_p.G1825C			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	1826					cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|formation of translation preinitiation complex (GO:0001731)|mitotic DNA replication checkpoint (GO:0033314)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)	chromatin binding (GO:0003682)	p.G1826C(1)									GTTTGTTTCCGGTGAGTTCGT	0.502																																					p.G1826C		Atlas-SNP	.											C15orf42,NS,carcinoma,0,1	.	.	.	1	Substitution - Missense(1)	endometrium(1)	c.G5476T						.						80	90	87					15																	90169017		2195	4292	6487	SO:0001630	splice_region_variant	90381	exon20			GTTTCCGGTGAGT	AK123612	CCDS10352.2	15q26.1	2012-07-11	2012-07-11	2012-07-11	ENSG00000140534	ENSG00000140534			28704	protein-coding gene	gene with protein product	"TOPBP1-interacting replication-stimulating protein", "SLD3 homolog (S. cerevisiae)"	613298	"chromosome 15 open reading frame 42"	C15orf42		20116089, 20080954	Standard	NM_152259		Approved	MGC45866, FLJ41618, Treslin, SLD3	uc002boe.3	Q7Z2Z1	OTTHUMG00000149648	ENST00000268138.7:c.5476+1G>T	chr15.hg19:g.90169017G>T		81.0	0.0		86.0	4.0	NM_152259	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Missense_Mutation	SNP	ENST00000268138.7	hg19	CCDS10352.2	.	.	.	.	.	.	.	.	.	.	G	14.48	2.546689	0.45383	.	.	ENSG00000140534	ENST00000268138	T	0.13538	2.58	4.96	4.04	0.47022	.	0.397421	0.23021	N	0.052841	T	0.31544	0.0800	M	0.63843	1.955	0.80722	D	1	D	0.89917	1.0	D	0.69824	0.966	T	0.02603	-1.1135	10	0.72032	D	0.01	-14.9411	10.9939	0.47565	0.0906:0.0:0.9094:0.0	.	1826	Q7Z2Z1	TICRR_HUMAN	C	1826	ENSP00000268138:G1826C	ENSP00000268138:G1826C	G	+	1	0	C15orf42	87970021	1.000000	0.71417	0.912000	0.35992	0.194000	0.23727	3.463000	0.53050	1.210000	0.43336	0.557000	0.71058	GGC	.	.		0.502	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259	Missense_Mutation	T	90169017	G	T	90169017	5	4	339	1	0	0	0	0	0	0	1	0	1798	1130	39	1	5554	1	C15orf42	15	90169017	Splice_Site	SNP	G	TCGA-RC-A7SH-01A-11D-A382-10		90169017	12362375	53	46949										
ERCC4	2072	hgsc.bcm.edu	37	chr16	14041908	14041908	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	tgtttgaggagctgaaacaaAgcaagccacagcctgatgcg	12	9	0	3			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr16:14041908A>G	ENST00000311895.7	+	11	2464	c.2455A>G	c.(2455-2457)Agc>Ggc	p.S819G		NM_005236.2	NP_005227.1	Q92889	XPF_HUMAN	excision repair cross-complementation group 4	819					DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|negative regulation of telomere maintenance (GO:0032205)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair involved in interstrand cross-link repair (GO:1901255)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|nucleotide-excision repair, DNA incision, 5'-to lesion (GO:0006296)|resolution of meiotic recombination intermediates (GO:0000712)|response to UV (GO:0009411)|telomere maintenance (GO:0000723)|telomere maintenance via telomere shortening (GO:0010834)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	chromosome, telomeric region (GO:0000781)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleotide-excision repair factor 1 complex (GO:0000110)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	damaged DNA binding (GO:0003684)|endodeoxyribonuclease activity (GO:0004520)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(5)|lung(12)|ovary(4)|pancreas(1)|prostate(1)|skin(3)	38						GCTGAAACAAAGCAAGCCACA	0.512			"Mis, N, F"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.S819G		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (F)	16	16p13.3-p13.13	2072	"excision repair cross-complementing rodent repair deficiency, complementation group 4"		E	.	ERCC4	100	.	0			c.A2455G						.						48	46	47					16																	14041908		2197	4300	6497	SO:0001583	missense	2072	exon11	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	AAACAAAGCAAGC	L76568	CCDS32390.1	16p13.3	2014-09-17	2014-03-07		ENSG00000175595	ENSG00000175595			3436	protein-coding gene	gene with protein product	"xeroderma pigmentosum, complementation group F"	133520	"excision repair cross-complementing rodent repair deficiency, complementation group 4"	XPF		9579555, 8887684	Standard	NM_005236		Approved	RAD1, FANCQ	uc002dce.2	Q92889	OTTHUMG00000048194	ENST00000311895.7:c.2455A>G	chr16.hg19:g.14041908A>G	ENSP00000310520:p.Ser819Gly	99.0	0.0		107.0	42.0	NM_005236	A5PKV6|A8K111|O00140|Q8TD83	Missense_Mutation	SNP	ENST00000311895.7	hg19	CCDS32390.1	.	.	.	.	.	.	.	.	.	.	A	2.819	-0.245292	0.05906	.	.	ENSG00000175595	ENST00000311895;ENST00000389138	T	0.58358	0.34	6.16	2.66	0.31614	DNA repair nuclease, XPF-type/Helicase (1);Restriction endonuclease, type II-like (1);	0.138164	0.64402	D	0.000003	T	0.14527	0.0351	N	0.00332	-1.63	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.29912	-0.9996	10	0.11485	T	0.65	-19.1712	6.6597	0.23007	0.7356:0.1297:0.1346:0.0	.	819	Q92889	XPF_HUMAN	G	819;807	ENSP00000310520:S819G	ENSP00000310520:S819G	S	+	1	0	ERCC4	13949409	1.000000	0.71417	0.000000	0.03702	0.955000	0.61496	5.547000	0.67249	0.180000	0.19960	0.528000	0.53228	AGC	.	.		0.512	ERCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109634.2	NM_005236		G	14041908	A	G	14041908	3	3	339	1	0	0	0	0	1	0	0	0	5217	72	3	2	2497	2	ERCC4	16	14041908	Missense_Mutation	SNP	A	TCGA-RC-A7SH-01A-11D-A382-10		14041908	76312845	54	46950										
TCF25	22980	hgsc.bcm.edu	37	chr16	89967154	89967154	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	gtgagcagagctctgccaggCagaaggcctctctcctgata	12	12	2	4			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr16:89967154C>T	ENST00000263346.8	+	12	1389	c.1333C>T	c.(1333-1335)Cag>Tag	p.Q445*	TCF25_ENST00000263347.7_Nonsense_Mutation_p.Q210*	NM_014972.2	NP_055787.1	Q9BQ70	TCF25_HUMAN	transcription factor 25 (basic helix-loop-helix)	445					heart development (GO:0007507)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|large_intestine(1)|lung(8)|ovary(3)|skin(1)|urinary_tract(2)	18		all_cancers(9;4.71e-08)|Lung NSC(15;0.000192)|all_lung(18;0.000319)|all_neural(9;0.0122)|all_hematologic(23;0.027)		BRCA - Breast invasive adenocarcinoma(80;0.0288)		CTCTGCCAGGCAGAAGGCCTC	0.597																																					p.Q445X		Atlas-SNP	.											.	TCF25	61	.	0			c.C1333T						.						84	77	80					16																	89967154		2197	4300	6497	SO:0001587	stop_gained	22980	exon12			GCCAGGCAGAAGG	AF322111	CCDS10987.1	16q24.3	2008-02-05			ENSG00000141002	ENSG00000141002			29181	protein-coding gene	gene with protein product		612326				12107429, 16574069	Standard	NM_014972		Approved	Nulp1, KIAA1049	uc002fpb.2	Q9BQ70	OTTHUMG00000138986	ENST00000263346.8:c.1333C>T	chr16.hg19:g.89967154C>T	ENSP00000263346:p.Gln445*	60.0	0.0		42.0	35.0	NM_014972	Q2MK75|Q9UPV3	Nonsense_Mutation	SNP	ENST00000263346.8	hg19	CCDS10987.1	.	.	.	.	.	.	.	.	.	.	C	8.576	0.881236	0.17467	.	.	ENSG00000141002	ENST00000263346;ENST00000263347	.	.	.	5.52	3.54	0.40534	.	0.545274	0.21024	N	0.081450	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	.	16.0841	0.81025	0.0:0.3894:0.6106:0.0	.	.	.	.	X	445;210	.	ENSP00000263346:Q445X	Q	+	1	0	TCF25	88494655	1.000000	0.71417	0.286000	0.24833	0.016000	0.09150	3.582000	0.53921	0.685000	0.31468	-0.226000	0.12346	CAG	.	.		0.597	TCF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272875.2	NM_014972		T	89967154	C	T	89967154	4	4	339	1	0	0	0	0	0	1	0	0	15708	711	25	3	1379	3	TCF25	16	89967154	Nonsense_Mutation	SNP	C	TCGA-RC-A7SH-01A-11D-A382-10	75925246	89967154	387599	55	46951										
TP53	7157	hgsc.bcm.edu	37	chr17	7578260	7578260	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	cacacgcaaatttccttccaCtcggataagatgctgaggag	9	11	0	2			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr17:7578260C>A	ENST00000269305.4	-	6	778	c.589G>T	c.(589-591)Gtg>Ttg	p.V197L	TP53_ENST00000413465.2_Missense_Mutation_p.V197L|TP53_ENST00000574684.1_Intron|TP53_ENST00000445888.2_Missense_Mutation_p.V197L|TP53_ENST00000359597.4_Missense_Mutation_p.V197L|TP53_ENST00000420246.2_Missense_Mutation_p.V197L|TP53_ENST00000455263.2_Missense_Mutation_p.V197L	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	197	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		V -> E (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|V -> G (in sporadic cancers; somatic mutation).|V -> L (in sporadic cancers; somatic mutation).|V -> M (in LFS; germline mutation and in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.V197M(10)|p.0?(8)|p.V197L(6)|p.?(5)|p.A189_V197delAPPQHLIRV(4)|p.P191_E198>Q(3)|p.V104L(1)|p.V65L(1)|p.P191fs*6(1)|p.I195_G199delIRVEG(1)|p.P98_E105>Q(1)|p.P59_E66>Q(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TTTCCTTCCACTCGGATAAGA	0.552		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.V197L	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,carcinoma,+1,29	TP53	33396	.	42	Substitution - Missense(18)|Whole gene deletion(8)|Deletion - In frame(5)|Unknown(5)|Complex - deletion inframe(5)|Complex - frameshift(1)	breast(6)|biliary_tract(5)|large_intestine(5)|liver(5)|skin(4)|bone(4)|central_nervous_system(3)|lung(3)|haematopoietic_and_lymphoid_tissue(2)|urinary_tract(2)|stomach(1)|oesophagus(1)|ovary(1)	c.G589T	GRCh37	CM070297	TP53	M		.						108	96	100					17																	7578260		2203	4300	6503	SO:0001583	missense	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	CTTCCACTCGGAT	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.589G>T	chr17.hg19:g.7578260C>A	ENSP00000269305:p.Val197Leu	173.0	0.0		89.0	69.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	15.66	2.900571	0.52227	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99824	-6.96;-6.96;-6.96;-6.96;-6.96;-6.96;-6.96;-6.96	5.41	4.44	0.53790	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.059878	0.64402	D	0.000004	D	0.99739	0.9897	M	0.77820	2.39	0.51767	D	0.999939	D;P;P;D;B;D;D	0.89917	0.997;0.484;0.927;0.999;0.367;0.995;1.0	D;P;P;D;P;D;D	0.87578	0.972;0.735;0.856;0.975;0.72;0.985;0.998	D	0.97374	0.9978	10	0.54805	T	0.06	-16.054	12.3714	0.55256	0.0:0.9175:0.0:0.0824	.	158;197;197;104;197;197;197	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	L	197;197;197;197;197;197;186;104;65;104;65	ENSP00000410739:V197L;ENSP00000352610:V197L;ENSP00000269305:V197L;ENSP00000398846:V197L;ENSP00000391127:V197L;ENSP00000391478:V197L;ENSP00000425104:V65L;ENSP00000423862:V104L	ENSP00000269305:V197L	V	-	1	0	TP53	7518985	0.994000	0.37717	0.999000	0.59377	0.021000	0.10359	3.252000	0.51461	1.420000	0.47138	0.655000	0.94253	GTG	.	.		0.552	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7578260	C	A	7578260	3	1	339	1	0	0	0	0	1	0	0	0	16396	565	20	3	705	3	TP53	17	7578260	Missense_Mutation	SNP	C	TCGA-RC-A7SH-01A-11D-A382-10		7578260	73616950	56	46952										
CYTSB	92521	hgsc.bcm.edu	37	chr17	20013852	20013852	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	agccatctcggagctcacggAgagccgcctgaggagcggca	15	13	2	2			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr17:20013852A>G	ENST00000261503.5	+	3	311	c.260A>G	c.(259-261)gAg>gGg	p.E87G	SPECC1_ENST00000395527.4_Missense_Mutation_p.E87G|SPECC1_ENST00000395529.3_Missense_Mutation_p.E87G|SPECC1_ENST00000472876.1_Intron	NM_001033553.2	NP_001028725.1	Q5M775	CYTSB_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1	87					cell adhesion (GO:0007155)	nucleus (GO:0005634)				breast(1)|large_intestine(3)|ovary(4)	8				KIRC - Kidney renal clear cell carcinoma(2;0.166)|Kidney(2;0.196)		GAGCTCACGGAGAGCCGCCTG	0.652																																					p.E87G		Atlas-SNP	.											.	SPECC1	100	.	0			c.A260G						.						26	29	28					17																	20013852		2203	4299	6502	SO:0001583	missense	92521	exon3			TCACGGAGAGCCG	AY816329, AB041533	CCDS32590.1, CCDS42280.1, CCDS42281.1, CCDS45628.1, CCDS58531.1	17p11.2	2012-11-19	2010-09-17	2010-09-17	ENSG00000128487	ENSG00000128487			30615	protein-coding gene	gene with protein product	"sperm antigen HCMOGT 1", "cytokinesis and spindle organization B", "cytospin B"	608793				15602574, 18763323, 15087372	Standard	NM_001033553		Approved	HCMOGT-1, FLJ36955, NSP, CYTSB	uc002gwq.3	Q5M775	OTTHUMG00000179808	ENST00000261503.5:c.260A>G	chr17.hg19:g.20013852A>G	ENSP00000261503:p.Glu87Gly	146.0	0.0		175.0	78.0	NM_001033553	B4DHH0|B7WNS8|Q5IBP1|Q5IBP2|Q5IBP3|Q5IBP4|Q5M772|Q5M773|Q5M774|Q86XT8|Q8N4U4|Q8WU84|Q9HCQ3	Missense_Mutation	SNP	ENST00000261503.5	hg19	CCDS32590.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.166950	0.78339	.	.	ENSG00000128487	ENST00000395530;ENST00000261503;ENST00000395529	T;T	0.68903	-0.36;2.67	5.47	5.47	0.80525	.	0.128130	0.50627	D	0.000104	T	0.76414	0.3984	L	0.47716	1.5	0.80722	D	1	D;D	0.89917	1.0;0.996	D;P	0.85130	0.997;0.905	T	0.78051	-0.2355	10	0.62326	D	0.03	-26.4673	13.8105	0.63260	1.0:0.0:0.0:0.0	.	87;87	Q5M775-2;Q5M775	.;CYTSB_HUMAN	G	87	ENSP00000261503:E87G;ENSP00000378900:E87G	ENSP00000261503:E87G	E	+	2	0	SPECC1	19954444	1.000000	0.71417	0.997000	0.53966	0.293000	0.27360	4.079000	0.57613	2.219000	0.72066	0.533000	0.62120	GAG	.	.		0.652	SPECC1-018	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441206.1	NM_152904		G	20013852	A	G	20013852	3	3	339	1	0	0	0	0	1	0	0	0	4212	304	11	2	266	2	CYTSB	17	20013852	Missense_Mutation	SNP	A	TCGA-RC-A7SH-01A-11D-A382-10	12435592	20013852	61181358	57	46953										
FAM20A	54757	hgsc.bcm.edu	37	chr17	66538937	66538937	+	Frame_Shift_Del	DEL	G	G	-													0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	cactgttggcggcacccgtcGgaagtccagaatcctgcaag					rs387907215		TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr17:66538937delG	ENST00000592554.1	-	6	1548	c.826delC	c.(826-828)cgafs	p.R277fs	FAM20A_ENST00000226094.5_5'UTR|PRKAR1A_ENST00000588188.2_Intron|AC079210.1_ENST00000600820.1_5'Flank	NM_001243746.1|NM_017565.3	NP_001230675.1|NP_060035.2	Q96MK3	FA20A_HUMAN	family with sequence similarity 20, member A	277					calcium ion homeostasis (GO:0055074)|enamel mineralization (GO:0070166)|tooth eruption (GO:0044691)	cell (GO:0005623)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)				cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(1)	9	Breast(10;1.64e-13)					GGCACCCGTCGGAAGTCCAGA	0.522																																					p.R276fs		Atlas-INDEL	.											FAM20A,NS,carcinoma,0,1	FAM20A	35	.	0			c.827delG						.						98	95	96					17																	66538937		2203	4300	6503	SO:0001589	frameshift_variant	54757	exon6			.	AK056789	CCDS11679.1	17q24.2	2014-02-07			ENSG00000108950	ENSG00000108950			23015	protein-coding gene	gene with protein product		611062					Standard	NM_017565		Approved	DKFZp434F2322	uc002jho.3	Q96MK3	OTTHUMG00000180152	ENST00000592554.1:c.826delC	chr17.hg19:g.66538937delG	ENSP00000468308:p.Arg277fs	63.0	0.0		68.0	26.0	NM_017565	B2RN47|B2RN49|Q9UF95	Frame_Shift_Del	DEL	ENST00000592554.1	hg19	CCDS11679.1																																																																																			.	.		0.522	FAM20A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450029.2	NM_017565		-	66538937	G	-	66538937	7	5	339	1	0	1	0	1	0	0	0	0	5542	1124	39	0	823	0	FAM20A	17	66538937	Frame_Shift_Del	DEL	G	TCGA-RC-A7SH-01A-11D-A382-10	46525085	66538937	14656273	58	46954										
PSENEN	55851	hgsc.bcm.edu	37	chr19	36236844	36236844	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	gcgcagctatgaacctggagCgagtgtccaatgaggagaaa	14	8	0	3			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr19:36236844C>T	ENST00000587708.2	+	2	696	c.13C>T	c.(13-15)Cga>Tga	p.R5*	U2AF1L4_ENST00000378975.3_5'Flank|PSENEN_ENST00000591949.1_Nonsense_Mutation_p.R5*|U2AF1L4_ENST00000412391.2_5'Flank|PSENEN_ENST00000222266.2_Nonsense_Mutation_p.R5*|LIN37_ENST00000301159.9_5'Flank|U2AF1L4_ENST00000588100.1_5'Flank|AC002398.9_ENST00000591613.2_Nonsense_Mutation_p.R5*|U2AF1L4_ENST00000292879.5_5'Flank|AC002398.11_ENST00000585365.1_RNA|AD000671.6_ENST00000589807.1_5'Flank|AC002398.11_ENST00000591091.1_RNA			Q9NZ42	PEN2_HUMAN	presenilin enhancer gamma secretase subunit	5					amyloid precursor protein catabolic process (GO:0042987)|apoptotic signaling pathway (GO:0097190)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|protein processing (GO:0016485)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				central_nervous_system(1)|kidney(1)|liver(1)|lung(2)|ovary(2)|prostate(1)	8	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GAACCTGGAGCGAGTGTCCAA	0.567																																					p.R5X		Atlas-SNP	.											.	PSENEN	16	.	0			c.C13T						.						69	69	69					19																	36236844		2203	4300	6503	SO:0001587	stop_gained	55851	exon2			CTGGAGCGAGTGT	AF220053	CCDS12474.1	19q13.12	2014-09-17	2013-09-12			ENSG00000205155			30100	protein-coding gene	gene with protein product		607632	"presenilin enhancer 2 homolog (C. elegans)"			12110170, 12660785	Standard	NM_172341		Approved	PEN2	uc002obi.1	Q9NZ42		ENST00000587708.2:c.13C>T	chr19.hg19:g.36236844C>T	ENSP00000468411:p.Arg5*	70.0	0.0		87.0	5.0	NM_172341	B2R5L9	Nonsense_Mutation	SNP	ENST00000587708.2	hg19	CCDS12474.1	.	.	.	.	.	.	.	.	.	.	C	38	6.656232	0.97739	.	.	ENSG00000205155	ENST00000222266	.	.	.	5.4	4.37	0.52481	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10111	T	0.7	-0.9524	13.2086	0.59811	0.0:0.9228:0.0:0.0772	.	.	.	.	X	5	.	ENSP00000222266:R5X	R	+	1	2	PSENEN	40928684	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.305000	0.43664	1.536000	0.49237	0.650000	0.86243	CGA	.	.		0.567	PSENEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459101.2	NM_172341		T	36236844	C	T	36236844	4	4	339	1	0	0	0	0	0	1	0	0	12664	760	27	1	15	1	PSENEN	19	36236844	Nonsense_Mutation	SNP	C	TCGA-RC-A7SH-01A-11D-A382-10		36236844	22892139	59	46955										
ZFP30	22835	hgsc.bcm.edu	37	chr19	38126594	38126594	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	tctgatgtcgagtaaggtgtGcatactgcctaaaggccttc	11	9	1	1			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr19:38126594G>T	ENST00000351218.2	-	6	1405	c.848C>A	c.(847-849)gCa>gAa	p.A283E	ZFP30_ENST00000514101.2_Missense_Mutation_p.A283E|ZFP30_ENST00000392144.1_Missense_Mutation_p.A283E|ZFP30_ENST00000589018.1_Intron	NM_014898.2	NP_055713.1	Q9Y2G7	ZFP30_HUMAN	ZFP30 zinc finger protein	283					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	21			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AGTAAGGTGTGCATACTGCCT	0.448																																					p.A283E		Atlas-SNP	.											.	ZFP30	68	.	0			c.C848A						.						121	117	118					19																	38126594		2203	4300	6503	SO:0001583	missense	22835	exon6			AGGTGTGCATACT	AB023178	CCDS33005.1	19q13.13	2013-01-08	2012-11-27		ENSG00000120784	ENSG00000120784		"Zinc fingers, C2H2-type", "-"	29555	protein-coding gene	gene with protein product			"zinc finger protein 30 homolog (mouse)"			10231032	Standard	NM_014898		Approved	ZNF745, KIAA0961	uc002ogx.1	Q9Y2G7	OTTHUMG00000048177	ENST00000351218.2:c.848C>A	chr19.hg19:g.38126594G>T	ENSP00000343581:p.Ala283Glu	82.0	0.0		99.0	4.0	NM_014898	Q58EY8	Missense_Mutation	SNP	ENST00000351218.2	hg19	CCDS33005.1	.	.	.	.	.	.	.	.	.	.	G	17.29	3.352555	0.61293	.	.	ENSG00000120784	ENST00000351218;ENST00000514101;ENST00000392144	T;T;T	0.36699	1.24;1.24;1.24	3.99	3.99	0.46301	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.34802	N	0.003678	T	0.42743	0.1216	N	0.17474	0.49	0.30295	N	0.789964	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.43523	-0.9386	10	0.72032	D	0.01	.	13.4446	0.61134	0.0:0.0:1.0:0.0	.	283;283	D3Y2A0;Q9Y2G7	.;ZFP30_HUMAN	E	283	ENSP00000343581:A283E;ENSP00000422930:A283E;ENSP00000375988:A283E	ENSP00000343581:A283E	A	-	2	0	ZFP30	42818434	0.040000	0.19996	1.000000	0.80357	0.988000	0.76386	2.368000	0.44222	2.223000	0.72356	0.655000	0.94253	GCA	.	.		0.448	ZFP30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109601.2	NM_014898		T	38126594	G	T	38126594	3	4	339	1	0	0	0	0	1	0	0	0	17659	1319	46	3	715	3	ZFP30	19	38126594	Missense_Mutation	SNP	G	TCGA-RC-A7SH-01A-11D-A382-10	1889750	38126594	21002389	60	46956										
ZIM2	23619	hgsc.bcm.edu	37	chr19	57286077	57286077	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	caacagtgatcgcactcaacAgttttctcttgagaatggag	9	9	2	2			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr19:57286077A>G	ENST00000391708.3	-	12	2105	c.1563T>C	c.(1561-1563)acT>acC	p.T521T	AC006115.3_ENST00000595954.1_RNA|ZIM2_ENST00000593711.1_Silent_p.T521T|AC006115.3_ENST00000594400.1_RNA|ZIM2_ENST00000221722.5_Silent_p.T521T|AC006115.3_ENST00000597946.1_RNA|ZIM2_ENST00000601070.1_Silent_p.T521T|ZIM2_ENST00000599935.1_Silent_p.T521T	NM_001146326.1|NM_001146327.1	NP_001139798.1|NP_001139799.1	Q9NZV7	ZIM2_HUMAN	zinc finger, imprinted 2	521					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(20)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0314)		CGCACTCAACAGTTTTCTCTT	0.448																																					p.T521T		Atlas-SNP	.											.	ZIM2	511	.	0			c.T1563C						.						98	94	95					19																	57286077		2203	4300	6503	SO:0001819	synonymous_variant	23619	exon11			CTCAACAGTTTTC	AF166122	CCDS33123.1	19q13.4	2012-10-31				ENSG00000269699		"Zinc fingers, C2H2-type"	12875	protein-coding gene	gene with protein product							Standard	NM_015363		Approved	ZNF656		Q9NZV7		ENST00000391708.3:c.1563T>C	chr19.hg19:g.57286077A>G		98.0	0.0		125.0	55.0	NM_015363	Q2M3K1	Silent	SNP	ENST00000391708.3	hg19	CCDS33123.1																																																																																			.	.		0.448	ZIM2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416094.2			G	57286077	A	G	57286077	2	3	339	1	0	0	0	0	0	0	0	1	17699	175	7	2		2	ZIM2	19	57286077	Silent	SNP	A	TCGA-RC-A7SH-01A-11D-A382-10	19159483	57286077	1842906	61	46957										
HSPA13	6782	hgsc.bcm.edu	37	chr21	15750651	15750651	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	cctttaacttcaacaatagtCgagagccaacatattctggg	7	10	2	1			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chr21:15750651C>G	ENST00000285667.3	-	3	516	c.449G>C	c.(448-450)cGa>cCa	p.R150P	HSPA13_ENST00000544452.1_Intron|HSPA13_ENST00000478035.1_5'Flank	NM_006948.4	NP_008879.3	P48723	HSP13_HUMAN	heat shock protein 70kDa family, member 13	150						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	ATP binding (GO:0005524)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	13						CAACAATAGTCGAGAGCCAAC	0.393																																					p.R150P		Atlas-SNP	.											.	HSPA13	44	.	0			c.G449C						.						102	92	95					21																	15750651		2203	4300	6503	SO:0001583	missense	6782	exon3			AATAGTCGAGAGC		CCDS13567.1	21q11.1	2011-09-02	2008-06-17	2008-06-17	ENSG00000155304	ENSG00000155304		"Heat shock proteins / HSP70"	11375	protein-coding gene	gene with protein product		601100	"stress 70 protein chaperone, microsome-associated, 60kD", "stress 70 protein chaperone, microsome-associated, 60kDa"	STCH		8825657	Standard	NM_006948		Approved		uc002yjt.3	P48723	OTTHUMG00000074261	ENST00000285667.3:c.449G>C	chr21.hg19:g.15750651C>G	ENSP00000285667:p.Arg150Pro	89.0	0.0		150.0	50.0	NM_006948	B2R616|Q8NE40	Missense_Mutation	SNP	ENST00000285667.3	hg19	CCDS13567.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.026400	0.75390	.	.	ENSG00000155304	ENST00000285667	T	0.01025	5.43	5.88	4.98	0.66077	.	0.111621	0.64402	D	0.000012	T	0.03220	0.0094	M	0.72894	2.215	0.80722	D	1	D	0.59767	0.986	P	0.59761	0.863	T	0.35375	-0.9791	10	0.52906	T	0.07	-15.6822	7.9899	0.30235	0.0:0.7594:0.0:0.2406	.	150	P48723	HSP13_HUMAN	P	150	ENSP00000285667:R150P	ENSP00000285667:R150P	R	-	2	0	HSPA13	14672522	0.903000	0.30736	0.997000	0.53966	0.996000	0.88848	0.854000	0.27791	2.780000	0.95670	0.655000	0.94253	CGA	.	.		0.393	HSPA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157815.1			G	15750651	C	G	15750651	3	3	339	1	0	0	0	0	1	0	0	0	7415	884	31	4	978	4	HSPA13	21	15750651	Missense_Mutation	SNP	C	TCGA-RC-A7SH-01A-11D-A382-10		15750651	32379244	62	46958										
TBL1X	6907	hgsc.bcm.edu	37	chrX	9677726	9677726	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	gatcttcaggctcacaataaAgagatctacaccatcaagtg	7	10	5	1			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chrX:9677726A>G	ENST00000217964.7	+	15	2005	c.1365A>G	c.(1363-1365)aaA>aaG	p.K455K	TBL1X_ENST00000424279.1_Silent_p.K404K|TBL1X_ENST00000407597.2_Silent_p.K455K|TBL1X_ENST00000380961.1_Silent_p.K404K|TBL1X_ENST00000536365.1_Silent_p.K404K	NM_005647.3	NP_005638.1	O60907	TBL1X_HUMAN	transducin (beta)-like 1X-linked	455					canonical Wnt signaling pathway (GO:0060070)|cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|histone binding (GO:0042393)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|cervix(1)|endometrium(5)|large_intestine(7)|lung(2)|ovary(1)|skin(2)	20		Hepatocellular(5;0.000888)				CTCACAATAAAGAGATCTACA	0.517											OREG0019658	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K455K		Atlas-SNP	.											.	TBL1X	103	.	0			c.A1365G						.						58	40	46					X																	9677726		2203	4300	6503	SO:0001819	synonymous_variant	6907	exon15			CAATAAAGAGATC	Y12781	CCDS14133.1, CCDS48078.1	Xp22.3	2013-01-10	2002-05-22	2002-05-24	ENSG00000101849	ENSG00000101849		"WD repeat domain containing"	11585	protein-coding gene	gene with protein product		300196	"transducin (beta)-like 1"	TBL1		10330347	Standard	NM_005647		Approved	EBI	uc004csr.3	O60907	OTTHUMG00000021117	ENST00000217964.7:c.1365A>G	chrX.hg19:g.9677726A>G		147.0	0.0	658	178.0	165.0	NM_001139466	A8K044|A8K4J7|Q86UY2	Silent	SNP	ENST00000217964.7	hg19	CCDS14133.1																																																																																			.	.		0.517	TBL1X-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055709.1	NM_005647		G	9677726	A	G	9677726	2	3	339	1	0	0	0	0	0	0	0	1	15654	69	3	2		2	TBL1X	23	9677726	Silent	SNP	A	TCGA-RC-A7SH-01A-11D-A382-10		9677726	145592834	63	46959										
MAGEB18	286514	hgsc.bcm.edu	37	chrX	26157400	26157400	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	taggttcctcaagggaagctGagggctggaaagaagatcct	14	7	1	3			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chrX:26157400G>A	ENST00000325250.1	+	2	485	c.298G>A	c.(298-300)Gag>Aag	p.E100K		NM_173699.3	NP_775970	Q96M61	MAGBI_HUMAN	melanoma antigen family B, 18	100	Interaction with LNX1.					cytoplasm (GO:0005737)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(17)|skin(2)|stomach(1)|urinary_tract(2)	33						AAGGGAAGCTGAGGGCTGGAA	0.448																																					p.E100K		Atlas-SNP	.											.	MAGEB18	67	.	0			c.G298A						.						37	32	33					X																	26157400		2202	4300	6502	SO:0001583	missense	286514	exon2			GAAGCTGAGGGCT	AK057361	CCDS14216.1	Xp21.3	2008-02-05			ENSG00000176774	ENSG00000176774			28515	protein-coding gene	gene with protein product							Standard	NM_173699		Approved	MGC33889	uc004dbq.2	Q96M61	OTTHUMG00000021282	ENST00000325250.1:c.298G>A	chrX.hg19:g.26157400G>A	ENSP00000314543:p.Glu100Lys	55.0	0.0		50.0	46.0	NM_173699		Missense_Mutation	SNP	ENST00000325250.1	hg19	CCDS14216.1	.	.	.	.	.	.	.	.	.	.	G	12.34	1.909150	0.33721	.	.	ENSG00000176774	ENST00000325250	T	0.02197	4.4	4.79	2.11	0.27256	.	1.601550	0.03768	N	0.259320	T	0.03520	0.0101	L	0.52266	1.64	0.09310	N	1	B	0.24317	0.101	B	0.21708	0.036	T	0.46005	-0.9222	10	0.37606	T	0.19	.	6.1073	0.20081	0.3212:0.0:0.6788:0.0	.	100	Q96M61	MAGBI_HUMAN	K	100	ENSP00000314543:E100K	ENSP00000314543:E100K	E	+	1	0	MAGEB18	26067321	0.017000	0.18338	0.003000	0.11579	0.007000	0.05969	0.654000	0.24918	0.327000	0.23409	0.600000	0.82982	GAG	.	.		0.448	MAGEB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056120.1	NM_173699		A	26157400	G	A	26157400	3	1	339	1	0	0	0	0	1	0	0	0	9184	1291	45	3	300	3	MAGEB18	23	26157400	Missense_Mutation	SNP	G	TCGA-RC-A7SH-01A-11D-A382-10	16479674	26157400	129113160	64	46960										
MAGEB16	139604	hgsc.bcm.edu	37	chrX	35820424	35820424	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	tccaaggctctggagaagacCctcctctcctcctcccatcc	6	19	2	2			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chrX:35820424C>T	ENST00000399989.1	+	2	390	c.111C>T	c.(109-111)acC>acT	p.T37T	MAGEB16_ENST00000399988.1_Silent_p.T37T|MAGEB16_ENST00000399985.1_Silent_p.T37T|MAGEB16_ENST00000399987.1_Silent_p.T37T|MAGEB16_ENST00000399992.1_Silent_p.T69T	NM_001099921.1	NP_001093391.1	A2A368	MAGBG_HUMAN	melanoma antigen family B, 16	37										breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31						TGGAGAAGACCCTCCTCTCCT	0.552																																					p.T37T		Atlas-SNP	.											.	MAGEB16	64	.	0			c.C111T						.						42	42	42					X																	35820424		2025	4158	6183	SO:0001819	synonymous_variant	139604	exon2			GAAGACCCTCCTC		CCDS43927.1	Xp21.1	2010-05-26	2005-11-07		ENSG00000189023	ENSG00000189023			21188	protein-coding gene	gene with protein product		300762	"melanoma antigen family B, 16 (pseudogene)"			11454705	Standard	NM_001099921		Approved		uc010ngt.1	A2A368	OTTHUMG00000021348	ENST00000399989.1:c.111C>T	chrX.hg19:g.35820424C>T		66.0	0.0		81.0	19.0	NM_001099921	A8MU30	Silent	SNP	ENST00000399989.1	hg19	CCDS43927.1																																																																																			.	.		0.552	MAGEB16-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251034.1			T	35820424	C	T	35820424	2	4	339	1	0	0	0	0	0	0	0	1	9183	610	22	3		3	MAGEB16	23	35820424	Silent	SNP	C	TCGA-RC-A7SH-01A-11D-A382-10	9663024	35820424	119450136	65	46961										
ITIH5L	347365	hgsc.bcm.edu	37	chrX	54784679	54784679	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	ggcctgtttgggttgcaccaTgaccagtgaagtcagaggtg	15	8	1	3			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chrX:54784679T>C	ENST00000218436.6	-	8	1857	c.1828A>G	c.(1828-1830)Atg>Gtg	p.M610V		NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	610					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)										GGTTGCACCATGACCAGTGAA	0.567																																					p.M610V		Atlas-SNP	.											.	.	.	.	0			c.A1828G						.						52	40	44					X																	54784679		2203	4300	6503	SO:0001583	missense	347365	exon8			GCACCATGACCAG	AY358170	CCDS14361.1	Xp11.22-p11.21	2011-10-26	2011-10-26	2011-10-26	ENSG00000102313	ENSG00000102313			28907	protein-coding gene	gene with protein product			"inter-alpha (globulin) inhibitor H5-like"	ITIH5L		12975309	Standard	NM_198510		Approved	UNQ6369	uc004dtj.2	Q6UXX5	OTTHUMG00000021634	ENST00000218436.6:c.1828A>G	chrX.hg19:g.54784679T>C	ENSP00000218436:p.Met610Val	105.0	0.0		106.0	93.0	NM_198510	A6NN03	Missense_Mutation	SNP	ENST00000218436.6	hg19	CCDS14361.1	.	.	.	.	.	.	.	.	.	.	T	0	-2.634509	0.00114	.	.	ENSG00000102313	ENST00000218436	T	0.04275	3.66	3.88	1.44	0.22558	.	0.246831	0.32161	N	0.006485	T	0.02342	0.0072	N	0.19112	0.55	0.23550	N	0.997432	B	0.02656	0.0	B	0.01281	0.0	T	0.48186	-0.9057	10	0.02654	T	1	.	5.6045	0.17371	0.0:0.4751:0.0:0.5249	.	610	Q6UXX5	ITH5L_HUMAN	V	610	ENSP00000218436:M610V	ENSP00000218436:M610V	M	-	1	0	ITIH5L	54801404	1.000000	0.71417	0.906000	0.35671	0.110000	0.19582	1.595000	0.36708	0.272000	0.22027	0.483000	0.47432	ATG	.	.		0.567	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056814.2	NM_198510		C	54784679	T	C	54784679	3	2	339	1	0	0	0	0	1	0	0	0	7917	1464	51	2	2137	2	ITIH5L	23	54784679	Missense_Mutation	SNP	T	TCGA-RC-A7SH-01A-11D-A382-10	18964255	54784679	100485881	66	46962										
AR	367	hgsc.bcm.edu	37	chrX	66931524	66931524	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	gtggtcaagtgggccaaggcCttgcctggtaaggaaaaggg	17	7	1	0			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chrX:66931524C>A	ENST00000374690.3	+	4	2690	c.2166C>A	c.(2164-2166)gcC>gcA	p.A722A	AR_ENST00000396043.2_Silent_p.A190A|AR_ENST00000396044.3_Silent_p.A722A	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	721	Interaction with KAT7.|Interaction with LPXN.|Ligand-binding.		L -> F (in AIS).		androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	GGGCCAAGGCCTTGCCTGGTA	0.532									Androgen Insensitivity Syndrome																												p.A722A		Atlas-SNP	.											.	AR	249	.	0			c.C2166A	GRCh37	CD025334	AR	D		.						67	52	57					X																	66931524		2203	4300	6503	SO:0001819	synonymous_variant	367	exon4	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	CAAGGCCTTGCCT	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.2166C>A	chrX.hg19:g.66931524C>A		178.0	0.0		185.0	22.0	NM_000044	A2RUN2|B1AKD7|Q9UD95	Silent	SNP	ENST00000374690.3	hg19	CCDS14387.1																																																																																			.	.		0.532	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		A	66931524	C	A	66931524	2	1	339	1	0	0	0	0	0	0	0	1	836	668	24	3		3	AR	23	66931524	Silent	SNP	C	TCGA-RC-A7SH-01A-11D-A382-10	12146845	66931524	88339036	67	46963										
SLITRK2	84631	hgsc.bcm.edu	37	chrX	144904694	144904694	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0735294117647059	5	1	1.1566091954023	0	1.45833333333333	0.00793650793650794	0.227716727716728	0	agactccctttaggttgcatGggaaagacgtgacccagctg	12	10	0	3			TCGA-RC-A7SH-01A-11D-A382-10	TCGA-RC-A7SH-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd131049-2873-436b-8759-496f580bd84e	13d667d3-0fd0-4480-9de6-f626c9dc9128	g.chrX:144904694G>A	ENST00000370490.1	+	1	5006	c.751G>A	c.(751-753)Ggg>Agg	p.G251R	SLITRK2_ENST00000434188.2_Missense_Mutation_p.G251R|SLITRK2_ENST00000428560.2_Missense_Mutation_p.G251R|SLITRK2_ENST00000447897.2_Missense_Mutation_p.G251R|SLITRK2_ENST00000413937.2_Missense_Mutation_p.G251R			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	251	LRRCT 1.				axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					TAGGTTGCATGGGAAAGACGT	0.512																																					p.G251R		Atlas-SNP	.											.	SLITRK2	221	.	0			c.G751A						.						104	98	100					X																	144904694		2203	4300	6503	SO:0001583	missense	84631	exon5			TTGCATGGGAAAG	Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"slit-like 1 (Drosophila)"	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.751G>A	chrX.hg19:g.144904694G>A	ENSP00000359521:p.Gly251Arg	69.0	0.0		80.0	75.0	NM_001144005	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Missense_Mutation	SNP	ENST00000370490.1	hg19	CCDS14680.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.020340	0.75275	.	.	ENSG00000185985	ENST00000335565;ENST00000447897;ENST00000370490;ENST00000434188;ENST00000413937;ENST00000428560	T;T;T;T;T;T	0.60299	0.2;0.2;0.2;0.2;0.2;0.2	5.0	5.0	0.66597	Cysteine-rich flanking region, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.79947	0.4534	M	0.90483	3.12	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.84226	0.0464	10	0.62326	D	0.03	-7.7593	14.7267	0.69349	0.0:0.0:1.0:0.0	.	251	Q9H156	SLIK2_HUMAN	R	251	ENSP00000334374:G251R;ENSP00000411681:G251R;ENSP00000359521:G251R;ENSP00000397015:G251R;ENSP00000407347:G251R;ENSP00000412010:G251R	ENSP00000334374:G251R	G	+	1	0	SLITRK2	144712386	1.000000	0.71417	0.980000	0.43619	0.996000	0.88848	9.869000	0.99810	2.058000	0.61347	0.600000	0.82982	GGG	.	.		0.512	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539		A	144904694	G	A	144904694	3	1	339	1	0	0	0	0	1	0	0	0	14758	1348	47	3	753	3	SLITRK2	23	144904694	Missense_Mutation	SNP	G	TCGA-RC-A7SH-01A-11D-A382-10	77973170	144904694	10365866	68	46964										
VAMP3	9341	hgsc.bcm.edu	37	chr1	7837247	7837247	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	acataatgcgagttaacgtgGacaaggttctggaaagagac	12	6	1	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr1:7837247G>A	ENST00000054666.6	+	3	215	c.100G>A	c.(100-102)Gac>Aac	p.D34N	RP3-467L1.6_ENST00000602406.1_RNA|VAMP3_ENST00000470357.1_Missense_Mutation_p.D6N	NM_004781.3	NP_004772.1	Q15836	VAMP3_HUMAN	vesicle-associated membrane protein 3	34	v-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00290}.				calcium ion-dependent exocytosis (GO:0017156)|exocytosis (GO:0006887)|Golgi to plasma membrane protein transport (GO:0043001)|membrane fusion (GO:0061025)|positive regulation of receptor recycling (GO:0001921)|protein complex assembly (GO:0006461)|retrograde transport, endosome to Golgi (GO:0042147)|SNARE complex assembly (GO:0035493)|substrate adhesion-dependent cell spreading (GO:0034446)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cell junction (GO:0030054)|cell surface (GO:0009986)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|secretory granule (GO:0030141)|SNARE complex (GO:0031201)|synapse (GO:0045202)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)	6	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;6.33e-69)|GBM - Glioblastoma multiforme(8;2.07e-34)|Colorectal(212;1.36e-07)|COAD - Colon adenocarcinoma(227;1.38e-05)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000805)|KIRC - Kidney renal clear cell carcinoma(229;0.000917)|STAD - Stomach adenocarcinoma(132;0.000985)|READ - Rectum adenocarcinoma(331;0.0642)		AGTTAACGTGGACAAGGTTCT	0.527																																					p.D34N		Atlas-SNP	.											.	VAMP3	14	.	0			c.G100A						.						102	95	97					1																	7837247		2203	4300	6503	SO:0001583	missense	9341	exon3			AACGTGGACAAGG	BC003570	CCDS88.1	1p36.23	2013-02-13	2012-10-17		ENSG00000049245	ENSG00000049245		"Vesicle-associated membrane proteins"	12644	protein-coding gene	gene with protein product	"cellubrevin"	603657				9885218	Standard	NM_004781		Approved	CEB	uc001aol.3	Q15836	OTTHUMG00000001225	ENST00000054666.6:c.100G>A	chr1.hg19:g.7837247G>A	ENSP00000054666:p.Asp34Asn	112.0	0.0		41.0	9.0	NM_004781	Q9BRV4	Missense_Mutation	SNP	ENST00000054666.6	hg19	CCDS88.1	.	.	.	.	.	.	.	.	.	.	G	17.64	3.440217	0.63067	.	.	ENSG00000049245	ENST00000054666	T	0.33216	1.42	6.17	5.24	0.73138	Synaptobrevin (4);	0.000000	0.85682	D	0.000000	T	0.39358	0.1075	M	0.62723	1.935	0.80722	D	1	B	0.29766	0.256	B	0.36378	0.223	T	0.23940	-1.0174	10	0.49607	T	0.09	-0.399	17.4035	0.87467	0.0:0.1246:0.8754:0.0	.	34	Q15836	VAMP3_HUMAN	N	34	ENSP00000054666:D34N	ENSP00000054666:D34N	D	+	1	0	VAMP3	7759834	1.000000	0.71417	0.998000	0.56505	0.924000	0.55760	9.760000	0.98935	1.565000	0.49641	0.655000	0.94253	GAC	.	.		0.527	VAMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003625.1	NM_004781		A	7837247	G	A	7837247	3	1	340	1	0	0	0	0	1	0	0	0	17129	1174	41	3	110	3	VAMP3	1	7837247	Missense_Mutation	SNP	G	TCGA-RC-A7SK-01A-11D-A34Z-10		7837247	241413374	1	46965										
GMEB1	10691	hgsc.bcm.edu	37	chr1	29040743	29040743	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	ccaccactgtcttgagccctTctcctcctgtccagcagcct	6	19	2	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr1:29040743T>C	ENST00000294409.2	+	10	1270	c.1180T>C	c.(1180-1182)Tct>Cct	p.S394P	GMEB1_ENST00000361872.4_Missense_Mutation_p.S384P|GMEB1_ENST00000373816.1_Missense_Mutation_p.S384P|GMEB1_ENST00000480454.1_3'UTR	NM_006582.3	NP_006573.2	Q9Y692	GMEB1_HUMAN	glucocorticoid modulatory element binding protein 1	394					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(4)	11		Colorectal(325;3.46e-05)|Lung NSC(340;0.000451)|all_lung(284;0.00063)|Breast(348;0.00502)|Renal(390;0.00555)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0221)|KIRC - Kidney renal clear cell carcinoma(1967;0.0296)|READ - Rectum adenocarcinoma(331;0.0649)		CTTGAGCCCTTCTCCTCCTGT	0.557																																					p.S394P		Atlas-SNP	.											.	GMEB1	28	.	0			c.T1180C						.						104	99	101					1																	29040743		2203	4300	6503	SO:0001583	missense	10691	exon10			AGCCCTTCTCCTC	AF099013	CCDS327.1, CCDS328.1	1p35	2008-02-05			ENSG00000162419	ENSG00000162419			4370	protein-coding gene	gene with protein product		604409				10386584, 10523663	Standard	NM_006582		Approved	P96PIF, PIF96	uc001bra.3	Q9Y692	OTTHUMG00000003647	ENST00000294409.2:c.1180T>C	chr1.hg19:g.29040743T>C	ENSP00000294409:p.Ser394Pro	146.0	0.0		70.0	19.0	NM_006582	B1AT48|Q9NWH1|Q9UKD0	Missense_Mutation	SNP	ENST00000294409.2	hg19	CCDS327.1	.	.	.	.	.	.	.	.	.	.	T	16.95	3.264587	0.59431	.	.	ENSG00000162419	ENST00000373816;ENST00000456852;ENST00000361872;ENST00000294409	T;T;T	0.61980	0.06;0.06;0.06	5.47	5.47	0.80525	.	0.131431	0.52532	D	0.000066	T	0.54498	0.1862	L	0.52573	1.65	0.26378	N	0.976773	B;B	0.12630	0.006;0.006	B;B	0.09377	0.004;0.004	T	0.53599	-0.8416	10	0.72032	D	0.01	-15.6911	9.1279	0.36828	0.0:0.0828:0.0:0.9172	.	394;384	Q9Y692;B1AT47	GMEB1_HUMAN;.	P	384;360;384;394	ENSP00000362922:S384P;ENSP00000355186:S384P;ENSP00000294409:S394P	ENSP00000294409:S394P	S	+	1	0	GMEB1	28913330	0.973000	0.33851	1.000000	0.80357	0.998000	0.95712	1.856000	0.39389	2.076000	0.62316	0.533000	0.62120	TCT	.	.		0.557	GMEB1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000010333.1	NM_006582		C	29040743	T	C	29040743	3	2	340	1	0	0	0	0	1	0	0	0	6495	1783	62	2	1214	2	GMEB1	1	29040743	Missense_Mutation	SNP	T	TCGA-RC-A7SK-01A-11D-A34Z-10	21203496	29040743	220209878	2	46966										
EPHA10	284656	hgsc.bcm.edu	37	chr1	38185617	38185617	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	tcccagtaaggccgctccccAaaggccatcacctcccacat	6	19	1	0			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr1:38185617A>G	ENST00000373048.4	-	14	2525	c.2526T>C	c.(2524-2526)ttT>ttC	p.F842F	EPHA10_ENST00000427468.2_Silent_p.F842F|EPHA10_ENST00000446149.2_5'UTR|EPHA10_ENST00000540011.1_3'UTR|EPHA10_ENST00000330210.7_Silent_p.F337F	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	842	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				ephrin receptor signaling pathway (GO:0048013)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane-ephrin receptor activity (GO:0005005)			NS(2)|breast(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(13)|prostate(3)|skin(8)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GCCGCTCCCCAAAGGCCATCA	0.607																																					p.F842F		Atlas-SNP	.											.	EPHA10	120	.	0			c.T2526C						.						62	66	65					1																	38185617		2203	4300	6503	SO:0001819	synonymous_variant	284656	exon14			CTCCCCAAAGGCC	AK090974	CCDS425.1, CCDS41305.1	1p34.3	2013-02-11			ENSG00000183317	ENSG00000183317		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	19987	protein-coding gene	gene with protein product		611123				12477932	Standard	NM_001099439		Approved	FLJ16103, FLJ33655	uc009vvi.3	Q5JZY3	OTTHUMG00000004325	ENST00000373048.4:c.2526T>C	chr1.hg19:g.38185617A>G		96.0	0.0		49.0	28.0	NM_001099439	A4FU89|J3KPB5|Q6NW42	Silent	SNP	ENST00000373048.4	hg19	CCDS41305.1																																																																																			.	.		0.607	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000012497.2	NM_173641		G	38185617	A	G	38185617	2	3	340	1	0	0	0	0	0	0	0	1	5168	127	5	2		2	EPHA10	1	38185617	Silent	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	9144874	38185617	211065004	3	46967										
C1orf175	374977	hgsc.bcm.edu	37	chr1	55144944	55144944	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	cctttgtttcaggaatttggAgacttcctggggccccagca	11	11	1	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr1:55144944A>T	ENST00000421030.2	+	12	2343	c.2058A>T	c.(2056-2058)ggA>ggT	p.G686G	MROH7_ENST00000545244.1_Silent_p.G254G|MROH7_ENST00000339553.5_Silent_p.G686G|MROH7_ENST00000409996.1_Silent_p.G254G|MROH7_ENST00000454855.2_Silent_p.G204G|MROH7_ENST00000395690.2_Silent_p.G686G|MROH7-TTC4_ENST00000414150.2_Silent_p.G686G	NM_001039464.2	NP_001034553	Q68CQ1	MROH7_HUMAN	maestro heat-like repeat family member 7	686						extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											AGGAATTTGGAGACTTCCTGG	0.562																																					p.G686G		Atlas-SNP	.											.	.	.	.	0			c.A2058T						.						107	111	109					1																	55144944		1904	4121	6025	SO:0001819	synonymous_variant	374977	exon12			ATTTGGAGACTTC	AL832492	CCDS41342.2	1p32.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000184313	ENSG00000184313		"maestro heat-like repeat containing"	24802	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 175", "HEAT repeat containing 8"	C1orf175, HEATR8		12477932	Standard	NM_001039464		Approved	FLJ46354	uc010ooe.1	Q68CQ1	OTTHUMG00000009890	ENST00000421030.2:c.2058A>T	chr1.hg19:g.55144944A>T		209.0	0.0		71.0	19.0	NM_001039464	A0AUX8|Q5TA99|Q6ZP40|Q6ZRH6|Q8N311|Q8NA14	Silent	SNP	ENST00000421030.2	hg19	CCDS41342.2																																																																																			.	.		0.562	MROH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346978.1	NM_198547		T	55144944	A	T	55144944	2	4	340	1	0	0	0	0	0	0	0	1	2018	291	11	4		4	C1orf175	1	55144944	Silent	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	16959327	55144944	194105677	4	46968										
CRTC2	200186	hgsc.bcm.edu	37	chr1	153920974	153920974	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	cctgagccatggcgggaacaGtgggtcaagttctggtggtt	16	8	2	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr1:153920974G>A	ENST00000368633.1	-	13	1948	c.1821C>T	c.(1819-1821)caC>caT	p.H607H	CRTC2_ENST00000368630.3_Silent_p.H287H|DENND4B_ENST00000361217.4_5'Flank	NM_181715.2	NP_859066.1	Q53ET0	CRTC2_HUMAN	CREB regulated transcription coactivator 2	607					gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|histone H3-K9 acetylation (GO:0043970)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	cAMP response element binding protein binding (GO:0008140)			NS(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	27	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			GGCGGGAACAGTGGGTCAAGT	0.562																																					p.H607H		Atlas-SNP	.											.	CRTC2	58	.	0			c.C1821T						.						127	115	119					1																	153920974		2203	4300	6503	SO:0001819	synonymous_variant	200186	exon13			GGAACAGTGGGTC	AY360172	CCDS30875.1	1q21.3	2008-02-05			ENSG00000160741	ENSG00000160741			27301	protein-coding gene	gene with protein product		608972				14506290, 14536081	Standard	NM_181715		Approved	TORC2	uc021pab.1	Q53ET0	OTTHUMG00000037156	ENST00000368633.1:c.1821C>T	chr1.hg19:g.153920974G>A		150.0	0.0		87.0	16.0	NM_181715	Q6UUV8|Q7Z3X7|Q8N332	Silent	SNP	ENST00000368633.1	hg19	CCDS30875.1																																																																																			.	.		0.562	CRTC2-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090272.3	NM_181715		A	153920974	G	A	153920974	2	1	340	1	0	0	0	0	0	0	0	1	3902	1020	36	3		3	CRTC2	1	153920974	Silent	SNP	G	TCGA-RC-A7SK-01A-11D-A34Z-10	98776030	153920974	95329647	5	46969										
LMNA	4000	hgsc.bcm.edu	37	chr1	156100406	156100406	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	tactctcccctctcttctttAgcaataccaagaaggagggt	7	12	3	1	rs113610699		TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr1:156100406A>G	ENST00000368300.4	+	2	568		c.e2-1		LMNA_ENST00000368299.3_Splice_Site|LMNA_ENST00000448611.2_Splice_Site|LMNA_ENST00000392353.3_Splice_Site|LMNA_ENST00000368297.1_Splice_Site|LMNA_ENST00000368301.2_Splice_Site|LMNA_ENST00000473598.2_Splice_Site|LMNA_ENST00000347559.2_Splice_Site|LMNA_ENST00000361308.4_Splice_Site	NM_170707.3	NP_733821.1	P02545	LMNA_HUMAN	lamin A/C						activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to hypoxia (GO:0071456)|endoplasmic reticulum unfolded protein response (GO:0030968)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|muscle organ development (GO:0007517)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|positive regulation of cell aging (GO:0090343)|protein localization to nucleus (GO:0034504)|regulation of cell migration (GO:0030334)|regulation of protein localization to nucleus (GO:1900180)|sterol regulatory element binding protein import into nucleus (GO:0035105)|ventricular cardiac muscle cell development (GO:0055015)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|lamin filament (GO:0005638)|nuclear envelope (GO:0005635)|nuclear lamina (GO:0005652)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	structural molecule activity (GO:0005198)			NS(1)|endometrium(1)|kidney(1)|lung(3)|ovary(4)	10	Hepatocellular(266;0.158)					TCTCTTCTTTAGCAATACCAA	0.577									Werner syndrome;Hutchinson-Gilford Progeria Syndrome		OREG0013866	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.		Atlas-SNP	.											.	LMNA	31	.	0			c.357-2A>G						.						46	45	45					1																	156100406		2203	4300	6503	SO:0001630	splice_region_variant	4000	exon2	Familial Cancer Database	WS, Adult Progeria;HGPS, Progeria	TTCTTTAGCAATA	BC014507	CCDS1129.1, CCDS1131.1, CCDS58038.1, CCDS72941.1, CCDS72942.1	1q22	2014-09-17			ENSG00000160789	ENSG00000160789		"Intermediate filaments type V, lamins"	6636	protein-coding gene	gene with protein product		150330	"cardiomyopathy, dilated 1A (autosomal dominant)", "limb girdle muscular dystrophy 1B (autosomal dominant)", "progeria 1 (Hutchinson-Gilford type)", "lamin A/C-like 1"	LMN1, CMD1A, LGMD1B, PRO1, LMNL1		8511676, 8838815, 12702809	Standard	NM_005572		Approved	HGPS	uc001fni.3	P02545	OTTHUMG00000013961	ENST00000368300.4:c.357-1A>G	chr1.hg19:g.156100406A>G		89.0	0.0	1775	49.0	14.0	NM_170707	B4DI32|D3DVB0|D6RAQ3|E7EUI9|P02546|Q5I6Y4|Q5I6Y6|Q5TCJ2|Q5TCJ3|Q6UYC3|Q969I8|Q96JA2	Splice_Site	SNP	ENST00000368300.4	hg19	CCDS1129.1	.	.	.	.	.	.	.	.	.	.	A	16.19	3.054233	0.55218	.	.	ENSG00000160789	ENST00000368301;ENST00000347559;ENST00000361308;ENST00000368300;ENST00000368299;ENST00000292302;ENST00000392355;ENST00000448611;ENST00000368297;ENST00000504687;ENST00000473598;ENST00000392353	.	.	.	5.59	5.59	0.84812	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.7178	0.62708	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	LMNA	154367030	1.000000	0.71417	0.958000	0.39756	0.496000	0.33645	9.267000	0.95665	2.129000	0.65627	0.533000	0.62120	.	.	.		0.577	LMNA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039200.2	NM_170707	Intron	G	156100406	A	G	156100406	5	3	340	1	0	0	0	0	0	0	1	0	8857	434	15	2	361	2	LMNA	1	156100406	Splice_Site	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	2179432	156100406	93150215	6	46970										
BCAN	63827	hgsc.bcm.edu	37	chr1	156616630	156616630	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	gtgcgcatcgcgggcgacgcGccactgcagggcgtgctcgg	18	14	0	0			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr1:156616630G>A	ENST00000329117.5	+	3	465	c.129G>A	c.(127-129)gcG>gcA	p.A43A	BCAN_ENST00000361588.5_Silent_p.A43A|RP11-284F21.10_ENST00000605886.1_RNA|RP11-284F21.7_ENST00000448869.1_RNA	NM_021948.4	NP_068767.3	Q96GW7	PGCB_HUMAN	brevican	43	Ig-like V-type.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hippocampus development (GO:0021766)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	55	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CGGGCGACGCGCCACTGCAGG	0.721																																					p.A43A		Atlas-SNP	.											.	BCAN	174	.	0			c.G129A						.						15	17	17					1																	156616630		2177	4239	6416	SO:0001819	synonymous_variant	63827	exon3			CGACGCGCCACTG	BC027971	CCDS1149.1, CCDS1150.1	1q31	2013-05-07			ENSG00000132692	ENSG00000132692		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	23059	protein-coding gene	gene with protein product	"chondroitin sulfate proteoglycan 7", "brevican proteoglycan"	600347				11054543, 11873941	Standard	NM_021948		Approved	BEHAB, MGC13038, CSPG7	uc001fpp.3	Q96GW7	OTTHUMG00000033322	ENST00000329117.5:c.129G>A	chr1.hg19:g.156616630G>A		109.0	0.0		54.0	8.0	NM_198427	D3DVC2|Q5SZ10|Q5T3I5|Q8TBB9|Q9HBK1|Q9HBK4	Silent	SNP	ENST00000329117.5	hg19	CCDS1149.1																																																																																			.	.		0.721	BCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081844.2	NM_021948		A	156616630	G	A	156616630	2	1	340	1	0	0	0	0	0	0	0	1	1345	1074	38	1		1	BCAN	1	156616630	Silent	SNP	G	TCGA-RC-A7SK-01A-11D-A34Z-10	516224	156616630	92633991	7	46971										
HSPA6	3310	hgsc.bcm.edu	37	chr1	161494890	161494890	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	tgaagcacgcagtgatcaccGtgcccgcctatttcaatgac	9	13	2	3	rs373442940		TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr1:161494890G>C	ENST00000309758.4	+	1	855	c.442G>C	c.(442-444)Gtg>Ctg	p.V148L	RP11-25K21.6_ENST00000537821.2_RNA	NM_002155.3	NP_002146.2	P17066	HSP76_HUMAN	heat shock 70kDa protein 6 (HSP70B')	148					ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)	blood microparticle (GO:0072562)|centriole (GO:0005814)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|unfolded protein binding (GO:0051082)			endometrium(3)|large_intestine(5)|lung(9)|prostate(2)|skin(2)	21	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			AGTGATCACCGTGCCCGCCTA	0.637																																					p.V148L		Atlas-SNP	.											.	HSPA6	53	.	0			c.G442C						.						27	30	29					1																	161494890		2202	4300	6502	SO:0001583	missense	3310	exon1			ATCACCGTGCCCG		CCDS1231.1	1q23.3	2011-09-02	2002-08-29		ENSG00000173110	ENSG00000173110		"Heat shock proteins / HSP70"	5239	protein-coding gene	gene with protein product		140555	"heat shock 70kD protein 6 (HSP70B')"			1346391	Standard	NM_002155		Approved		uc001gaq.3	P17066	OTTHUMG00000034461	ENST00000309758.4:c.442G>C	chr1.hg19:g.161494890G>C	ENSP00000310219:p.Val148Leu	108.0	0.0		64.0	13.0	NM_002155	Q1HBA8|Q8IYK7|Q9BT95	Missense_Mutation	SNP	ENST00000309758.4	hg19	CCDS1231.1	.	.	.	.	.	.	.	.	.	.	.	17.50	3.405612	0.62288	.	.	ENSG00000173110	ENST00000309758;ENST00000545155	T	0.01745	4.66	3.43	3.43	0.39272	.	0.000000	0.38897	U	0.001534	T	0.17365	0.0417	H	0.99962	5.075	0.51482	D	0.999924	D	0.89917	1.0	D	0.91635	0.999	T	0.48019	-0.9071	10	0.87932	D	0	-27.8476	12.3829	0.55317	0.0:0.0:1.0:0.0	.	148	P17066	HSP76_HUMAN	L	148;124	ENSP00000310219:V148L	ENSP00000310219:V148L	V	+	1	0	HSPA6	159761514	1.000000	0.71417	0.318000	0.25279	0.472000	0.32918	8.329000	0.90017	1.725000	0.51514	0.586000	0.80456	GTG	.	.		0.637	HSPA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083308.1	NM_002155		C	161494890	G	C	161494890	3	2	340	1	0	0	0	0	1	0	0	0	7424	1145	40	4	444	4	HSPA6	1	161494890	Missense_Mutation	SNP	G	TCGA-RC-A7SK-01A-11D-A34Z-10	4878260	161494890	87755731	8	46972										
TNR	7143	hgsc.bcm.edu	37	chr1	175306706	175306707	+	Frame_Shift_Ins	INS	-	-	A													0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	tcatatcacagtacacttgtINSaatttctggctcagctcccc							TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr1:175306706_175306707insA	ENST00000367674.2	-	19	4199_4200	c.3491_3492insT	c.(3490-3492)ttafs	p.L1164fs	TNR_ENST00000263525.2_Frame_Shift_Ins_p.L1164fs|RP3-518E13.2_ENST00000569593.1_RNA			Q92752	TENR_HUMAN	tenascin R	1164	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					AGTACACTTGTAATTTCTGGCT	0.505																																					p.L1164fs		Atlas-Indel,Pindel	.											.	TNR	399	.	0			c.3492_3493insT						.																																			SO:0001589	frameshift_variant	7143	exon19			.	X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11953	protein-coding gene	gene with protein product	"restrictin", "janusin"	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.3492dupT	chr1.hg19:g.175306708_175306708dupA	ENSP00000356646:p.Leu1164fs	100.0	0.0		46.0	15.0	NM_003285	C9J563|Q15568|Q5R3G0	Frame_Shift_Ins	INS	ENST00000367674.2	hg19	CCDS1318.1																																																																																			.	.		0.505	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285		A	175306707	-	A	175306706	7	5	340	1	0	1	1	0	0	0	0	0	16353	1635	57	0	604	0	TNR	1	175306706	Frame_Shift_Ins	INS	-	TCGA-RC-A7SK-01A-11D-A34Z-10	13811816	175306706	73943915	9	46973										
PPP1R15B	84919	hgsc.bcm.edu	37	chr1	204380351	204380351	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	agctgggagagcagtttcgtCcagtaactgacccgagtctc	12	11	1	2			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr1:204380351C>A	ENST00000367188.4	-	1	568	c.189G>T	c.(187-189)tgG>tgT	p.W63C	RP11-739N20.2_ENST00000443515.1_RNA	NM_032833.3	NP_116222.3	Q5SWA1	PR15B_HUMAN	protein phosphatase 1, regulatory subunit 15B	63					ER overload response (GO:0006983)|regulation of translation (GO:0006417)|response to hydrogen peroxide (GO:0042542)	protein phosphatase type 1 complex (GO:0000164)	protein serine/threonine phosphatase activity (GO:0004722)			breast(3)|cervix(1)|kidney(4)|large_intestine(3)|lung(16)|ovary(1)|pancreas(2)|skin(1)|urinary_tract(3)	34	all_cancers(21;0.0032)|all_neural(3;0.0218)|Glioma(3;0.0382)|Breast(84;0.179)|all_epithelial(62;0.193)|Prostate(682;0.227)		all cancers(3;1.14e-29)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.139)			GCAGTTTCGTCCAGTAACTGA	0.577																																					p.W63C		Atlas-SNP	.											.	PPP1R15B	67	.	0			c.G189T						.						66	71	69					1																	204380351		2203	4300	6503	SO:0001583	missense	84919	exon1			TTTCGTCCAGTAA	AK027650	CCDS1445.1	1q32.1	2012-04-17	2011-10-04		ENSG00000158615	ENSG00000158615		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14951	protein-coding gene	gene with protein product		613257	"protein phosphatase 1, regulatory (inhibitor) subunit 15B"			11948623	Standard	XM_005245551		Approved	FLJ14744	uc001hav.4	Q5SWA1	OTTHUMG00000036105	ENST00000367188.4:c.189G>T	chr1.hg19:g.204380351C>A	ENSP00000356156:p.Trp63Cys	87.0	0.0		79.0	10.0	NM_032833	Q53GQ4|Q658M2|Q6P156|Q96SN1	Missense_Mutation	SNP	ENST00000367188.4	hg19	CCDS1445.1	.	.	.	.	.	.	.	.	.	.	C	15.64	2.893365	0.52121	.	.	ENSG00000158615	ENST00000367188	T	0.28666	1.6	5.22	5.22	0.72569	Protein phosphatase 1, regulatory subunit 15B, N-terminal (1);	0.095508	0.45867	D	0.000324	T	0.51890	0.1701	M	0.61703	1.905	0.58432	D	0.999995	D	0.76494	0.999	D	0.69824	0.966	T	0.53194	-0.8473	10	0.87932	D	0	-2.1296	14.6287	0.68640	0.0:1.0:0.0:0.0	.	63	Q5SWA1	PR15B_HUMAN	C	63	ENSP00000356156:W63C	ENSP00000356156:W63C	W	-	3	0	PPP1R15B	202646974	0.986000	0.35501	0.669000	0.29828	0.131000	0.20780	3.691000	0.54720	2.586000	0.87340	0.655000	0.94253	TGG	.	.		0.577	PPP1R15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087974.1	NM_032833		A	204380351	C	A	204380351	3	1	340	1	0	0	0	0	1	0	0	0	12376	856	30	3	1960	3	PPP1R15B	1	204380351	Missense_Mutation	SNP	C	TCGA-RC-A7SK-01A-11D-A34Z-10	29073645	204380351	44870270	10	46974										
PLXNA2	5362	hgsc.bcm.edu	37	chr1	208219347	208219347	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	ttagcaaggattggacattgTtaaagacaaatccaaactca	7	7	1	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr1:208219347T>G	ENST00000367033.3	-	18	4128	c.3371A>C	c.(3370-3372)aAc>aCc	p.N1124T		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	1124	IPT/TIG 3.				axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		TTGGACATTGTTAAAGACAAA	0.502																																					p.N1124T		Atlas-SNP	.											.	PLXNA2	178	.	0			c.A3371C						.						172	164	167					1																	208219347		2203	4300	6503	SO:0001583	missense	5362	exon18			ACATTGTTAAAGA	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"Plexins"	9100	protein-coding gene	gene with protein product	"plexin 2", "plexin-A2", "semaphorin receptor OCT", "transmembrane protein OCT"	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.3371A>C	chr1.hg19:g.208219347T>G	ENSP00000356000:p.Asn1124Thr	109.0	0.0		61.0	19.0	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	hg19	CCDS31013.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.411607	0.83340	.	.	ENSG00000076356	ENST00000367033	T	0.60171	0.21	4.51	4.51	0.55191	Cell surface receptor IPT/TIG (1);Immunoglobulin E-set (1);	0.000000	0.85682	D	0.000000	T	0.61874	0.2382	L	0.57536	1.79	0.80722	D	1	D	0.53151	0.958	P	0.49140	0.601	T	0.68138	-0.5488	10	0.87932	D	0	.	14.1385	0.65303	0.0:0.0:0.0:1.0	.	1124	O75051	PLXA2_HUMAN	T	1124	ENSP00000356000:N1124T	ENSP00000356000:N1124T	N	-	2	0	PLXNA2	206285970	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.708000	0.84633	1.804000	0.52760	0.460000	0.39030	AAC	.	.		0.502	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179		G	208219347	T	G	208219347	3	3	340	1	0	0	0	0	1	0	0	0	12129	1725	60	5	2373	5	PLXNA2	1	208219347	Missense_Mutation	SNP	T	TCGA-RC-A7SK-01A-11D-A34Z-10	3838996	208219347	41031274	11	46975										
RCOR3	55758	hgsc.bcm.edu	37	chr1	211451497	211451497	+	Nonsense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	gcaagccttgtaaaatattaCtattcttggaaaaaaactcg	6	7	1	0			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr1:211451497C>G	ENST00000367005.4	+	5	522	c.381C>G	c.(379-381)taC>taG	p.Y127*	RCOR3_ENST00000452621.2_Nonsense_Mutation_p.Y185*|RCOR3_ENST00000367006.4_Nonsense_Mutation_p.Y185*|RCOR3_ENST00000419091.2_Nonsense_Mutation_p.Y185*	NM_018254.3	NP_060724.1	Q9P2K3	RCOR3_HUMAN	REST corepressor 3	127	SANT 1. {ECO:0000255|PROSITE- ProRule:PRU00624}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(81;0.00961)|all cancers(67;0.0999)|Epithelial(68;0.171)		TAAAATATTACTATTCTTGGA	0.333																																					p.Y185X		Atlas-SNP	.											.	RCOR3	51	.	0			c.C555G						.						75	77	77					1																	211451497		2203	4300	6503	SO:0001587	stop_gained	55758	exon6			ATATTACTATTCT	AK001738	CCDS31016.1, CCDS44312.1, CCDS44313.1, CCDS44314.1	1q32.3	2008-02-05			ENSG00000117625	ENSG00000117625			25594	protein-coding gene	gene with protein product						10718198	Standard	NM_018254		Approved	FLJ10876	uc010psw.2	Q9P2K3	OTTHUMG00000036996	ENST00000367005.4:c.381C>G	chr1.hg19:g.211451497C>G	ENSP00000355972:p.Tyr127*	105.0	0.0		85.0	14.0	NM_001136223	B3KYA2|B4DYY7|Q5VT47|Q7L9I5|Q8N5U3|Q9NV83	Nonsense_Mutation	SNP	ENST00000367005.4	hg19	CCDS31016.1	.	.	.	.	.	.	.	.	.	.	C	34	5.381058	0.95945	.	.	ENSG00000117625	ENST00000533469;ENST00000367006;ENST00000452621;ENST00000419091;ENST00000367005	.	.	.	5.66	2.75	0.32379	.	0.055362	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.1984	11.2275	0.48892	0.0:0.7999:0.0:0.2001	.	.	.	.	X	127;185;185;185;127	.	ENSP00000355972:Y127X	Y	+	3	2	RCOR3	209518120	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.633000	0.46519	0.326000	0.23384	0.460000	0.39030	TAC	.	.		0.333	RCOR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089821.1	NM_018254		G	211451497	C	G	211451497	4	3	340	1	0	0	0	0	0	1	0	0	13199	576	20	4	577	4	RCOR3	1	211451497	Nonsense_Mutation	SNP	C	TCGA-RC-A7SK-01A-11D-A34Z-10	3232150	211451497	37799124	12	46976										
HEATR1	55127	hgsc.bcm.edu	37	chr1	236751283	236751283	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	agccgacaaaacaacatctaTattatcatcacctaatcggg	5	11	3	0			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr1:236751283T>C	ENST00000366582.3	-	13	1705	c.1591A>G	c.(1591-1593)Ata>Gta	p.I531V	HEATR1_ENST00000366581.2_Missense_Mutation_p.I531V	NM_018072.5	NP_060542.4	Q9H583	HEAT1_HUMAN	HEAT repeat containing 1	531					rRNA processing (GO:0006364)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(18)|lung(28)|ovary(3)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	87	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			ACAACATCTATATTATCATCA	0.343																																					p.I531V		Atlas-SNP	.											.	HEATR1	197	.	0			c.A1591G						.						123	116	119					1																	236751283		2203	4299	6502	SO:0001583	missense	55127	exon13			CATCTATATTATC	BC065205	CCDS31066.1	1q43	2011-08-12			ENSG00000119285	ENSG00000119285			25517	protein-coding gene	gene with protein product	"UTP10, small subunit (SSU) processome component, homolog (yeast)"					17699751	Standard	NM_018072		Approved	FLJ10359, BAP28, UTP10	uc001hyd.2	Q9H583	OTTHUMG00000040061	ENST00000366582.3:c.1591A>G	chr1.hg19:g.236751283T>C	ENSP00000355541:p.Ile531Val	239.0	0.0		122.0	20.0	NM_018072	Q5T3Q8|Q6P197|Q9NW23	Missense_Mutation	SNP	ENST00000366582.3	hg19	CCDS31066.1	.	.	.	.	.	.	.	.	.	.	T	0.046	-1.265675	0.01433	.	.	ENSG00000119285	ENST00000366582;ENST00000366581	T;T	0.66460	-0.11;-0.21	5.84	-7.28	0.01456	Armadillo-like helical (1);Armadillo-type fold (1);	0.475201	0.23973	N	0.042742	T	0.21267	0.0512	N	0.02011	-0.69	0.30579	N	0.762751	B	0.02656	0.0	B	0.04013	0.001	T	0.45687	-0.9244	10	0.02654	T	1	.	2.2291	0.03992	0.489:0.189:0.0855:0.2364	.	531	Q9H583	HEAT1_HUMAN	V	531	ENSP00000355541:I531V;ENSP00000355540:I531V	ENSP00000355540:I531V	I	-	1	0	HEATR1	234817906	0.000000	0.05858	0.032000	0.17829	0.370000	0.29829	-0.847000	0.04331	-0.736000	0.04831	0.533000	0.62120	ATA	.	.		0.343	HEATR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096635.1	XM_375853		C	236751283	T	C	236751283	3	2	340	1	0	0	0	0	1	0	0	0	7036	1406	49	2	4975	2	HEATR1	1	236751283	Missense_Mutation	SNP	T	TCGA-RC-A7SK-01A-11D-A34Z-10	25299786	236751283	12499338	13	46977										
AHCTF1	25909	hgsc.bcm.edu	37	chr1	247014692	247014692	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	ataactcattaaatgaaagaTtcctagcctcttctcctgaa	4	10	3	3			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr1:247014692T>C	ENST00000391829.2	-	33	4739	c.4616A>G	c.(4615-4617)aAt>aGt	p.N1539S	AHCTF1_ENST00000366508.1_Missense_Mutation_p.N1574S|AHCTF1_ENST00000326225.3_Missense_Mutation_p.N1548S|AHCTF1_ENST00000470300.1_5'UTR			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	1539	Disordered. {ECO:0000250}.|Mediates transcriptional activity. {ECO:0000250}.|Necessary for nuclear localization. {ECO:0000250}.				cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(6)|cervix(3)|endometrium(8)|kidney(6)|large_intestine(12)|liver(2)|lung(21)|ovary(5)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	74	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			AAATGAAAGATTCCTAGCCTC	0.328																																					p.N1548S	Colon(145;197 1800 4745 15099 26333)	Atlas-SNP	.											.	AHCTF1	187	.	0			c.A4643G						.						29	29	29					1																	247014692		2200	4297	6497	SO:0001583	missense	25909	exon33			GAAAGATTCCTAG		CCDS1629.1, CCDS1629.2	1q44	2008-09-09			ENSG00000153207	ENSG00000153207			24618	protein-coding gene	gene with protein product	"ELYS transcription factor like protein TMBS62"	610853				11952839	Standard	NM_015446		Approved	ELYS	uc001ibv.2	Q8WYP5	OTTHUMG00000040706	ENST00000391829.2:c.4616A>G	chr1.hg19:g.247014692T>C	ENSP00000375705:p.Asn1539Ser	235.0	0.0		127.0	43.0	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Missense_Mutation	SNP	ENST00000391829.2	hg19		.	.	.	.	.	.	.	.	.	.	T	0.335	-0.953685	0.02285	.	.	ENSG00000153207	ENST00000366508;ENST00000326225;ENST00000391829	T;T;T	0.28895	1.59;1.59;1.59	6.17	-4.03	0.04021	.	0.574707	0.18629	N	0.135631	T	0.08626	0.0214	N	0.08118	0	0.09310	N	1	B;B;B	0.20052	0.041;0.004;0.003	B;B;B	0.16722	0.016;0.007;0.003	T	0.31641	-0.9936	10	0.05525	T	0.97	-6.6212	3.355	0.07165	0.0954:0.3805:0.189:0.3351	.	400;1574;1539	B3KTD2;Q8WYP5-2;Q8WYP5	.;.;ELYS_HUMAN	S	1574;1548;1539	ENSP00000355464:N1574S;ENSP00000355465:N1548S;ENSP00000375705:N1539S	ENSP00000355465:N1548S	N	-	2	0	AHCTF1	245081315	0.026000	0.19158	0.016000	0.15963	0.653000	0.38743	-0.820000	0.04457	-0.589000	0.05874	0.533000	0.62120	AAT	.	.		0.328	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446		C	247014692	T	C	247014692	3	2	340	1	0	0	0	0	1	0	0	0	408	1493	52	2	2200	2	AHCTF1	1	247014692	Missense_Mutation	SNP	T	TCGA-RC-A7SK-01A-11D-A34Z-10	10263409	247014692	2235929	14	46978										
NBAS	51594	hgsc.bcm.edu	37	chr2	15523423	15523423	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	agcaacgttctccaatgagaCtcactgacaggaggctgcct	10	12	2	2			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr2:15523423C>T	ENST00000281513.5	-	29	3301	c.3276G>A	c.(3274-3276)gaG>gaA	p.E1092E	NBAS_ENST00000441750.1_Silent_p.E972E	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	1092					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				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						TCCAATGAGACTCACTGACAG	0.373																																					p.E1092E		Atlas-SNP	.											.	NBAS	246	.	0			c.G3276A						.						89	88	89					2																	15523423		2203	4300	6503	SO:0001819	synonymous_variant	51594	exon29			ATGAGACTCACTG	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.3276G>A	chr2.hg19:g.15523423C>T		218.0	0.0		142.0	25.0	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Silent	SNP	ENST00000281513.5	hg19	CCDS1685.1	.	.	.	.	.	.	.	.	.	.	C	8.232	0.804942	0.16467	.	.	ENSG00000151779	ENST00000442506	.	.	.	5.76	5.76	0.90799	.	.	.	.	.	T	0.76673	0.4020	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.74312	-0.3706	4	.	.	.	.	19.9559	0.97218	0.0:1.0:0.0:0.0	.	.	.	.	N	140	.	.	S	-	2	0	NBAS	15440874	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	3.274000	0.51631	2.728000	0.93425	0.462000	0.41574	AGT	.	.		0.373	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		T	15523423	C	T	15523423	2	4	340	1	0	0	0	0	0	0	0	1	10195	564	20	3		3	NBAS	2	15523423	Silent	SNP	C	TCGA-RC-A7SK-01A-11D-A34Z-10		15523423	227675950	15	46979										
TTC27	55622	hgsc.bcm.edu	37	chr2	32891709	32891709	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	attgttttttcaggtgctttGggaaaaagaacacggttcca	10	6	1	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr2:32891709G>T	ENST00000317907.4	+	7	1044	c.813G>T	c.(811-813)ttG>ttT	p.L271F		NM_001193509.1|NM_017735.4	NP_001180438.1|NP_060205.3	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27	271										breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38						CAGGTGCTTTGGGAAAAAGAA	0.368																																					p.L271F		Atlas-SNP	.											.	TTC27	71	.	0			c.G813T						.						104	110	108					2																	32891709		2203	4300	6503	SO:0001583	missense	55622	exon7			TGCTTTGGGAAAA	BC063791, AK000279	CCDS33176.1	2p22.3	2013-01-10			ENSG00000018699	ENSG00000018699		"Tetratricopeptide (TTC) repeat domain containing"	25986	protein-coding gene	gene with protein product							Standard	NM_001193509		Approved	FLJ20272	uc002rom.3	Q6P3X3	OTTHUMG00000152134	ENST00000317907.4:c.813G>T	chr2.hg19:g.32891709G>T	ENSP00000313953:p.Leu271Phe	91.0	0.0		37.0	8.0	NM_017735	A6NKJ0|Q96SS5|Q9BVF1|Q9NWR4|Q9NXG4	Missense_Mutation	SNP	ENST00000317907.4	hg19	CCDS33176.1	.	.	.	.	.	.	.	.	.	.	G	17.65	3.441403	0.63067	.	.	ENSG00000018699	ENST00000317907	T	0.71222	-0.55	5.74	0.907	0.19321	.	0.000000	0.64402	D	0.000001	D	0.83161	0.5194	M	0.88640	2.97	0.53688	D	0.999972	D	0.89917	1.0	D	0.73708	0.981	T	0.82452	-0.0450	10	0.72032	D	0.01	-0.8942	9.5603	0.39364	0.3601:0.0:0.6399:0.0	.	271	Q6P3X3	TTC27_HUMAN	F	271	ENSP00000313953:L271F	ENSP00000313953:L271F	L	+	3	2	TTC27	32745213	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	1.388000	0.34442	0.092000	0.17331	-0.218000	0.12543	TTG	.	.		0.368	TTC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325395.1	NM_017735		T	32891709	G	T	32891709	3	4	340	1	0	0	0	0	1	0	0	0	16710	1339	47	3	839	3	TTC27	2	32891709	Missense_Mutation	SNP	G	TCGA-RC-A7SK-01A-11D-A34Z-10	17368286	32891709	210307664	16	46980										
PLEKHH2	130271	hgsc.bcm.edu	37	chr2	43922295	43922295	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	ctcttagctggaattggagaAtcagaatcttcgtttgatca	9	7	4	3			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr2:43922295A>G	ENST00000282406.4	+	6	544	c.434A>G	c.(433-435)aAt>aGt	p.N145S		NM_172069.3	NP_742066.2	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	145					negative regulation of actin filament depolymerization (GO:0030835)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	actin binding (GO:0003779)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(24)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	56		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				GAATTGGAGAATCAGAATCTT	0.269																																					p.N145S		Atlas-SNP	.											.	PLEKHH2	156	.	0			c.A434G						.						49	47	48					2																	43922295		2199	4296	6495	SO:0001583	missense	130271	exon6			TGGAGAATCAGAA	AB095948	CCDS1812.1	2p22	2013-01-10			ENSG00000152527	ENSG00000152527		"Pleckstrin homology (PH) domain containing"	30506	protein-coding gene	gene with protein product		612723					Standard	NM_172069		Approved	KIAA2028, PLEKHH1L	uc010yny.2	Q8IVE3	OTTHUMG00000128657	ENST00000282406.4:c.434A>G	chr2.hg19:g.43922295A>G	ENSP00000282406:p.Asn145Ser	503.0	0.0		266.0	28.0	NM_172069	Q5JPJ6|Q6P4Q1|Q8N3Q3	Missense_Mutation	SNP	ENST00000282406.4	hg19	CCDS1812.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.353659	0.82243	.	.	ENSG00000152527	ENST00000282406	T	0.43688	0.94	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.61640	0.2363	L	0.58810	1.83	0.53688	D	0.999971	D;D	0.89917	0.996;1.0	P;D	0.91635	0.787;0.999	T	0.63550	-0.6612	10	0.59425	D	0.04	-30.3231	15.7573	0.78043	1.0:0.0:0.0:0.0	.	145;145	Q8IVE3;Q8IVE3-3	PKHH2_HUMAN;.	S	145	ENSP00000282406:N145S	ENSP00000282406:N145S	N	+	2	0	PLEKHH2	43775799	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.163000	0.77524	2.120000	0.65058	0.477000	0.44152	AAT	.	.		0.269	PLEKHH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250537.1	NM_172069		G	43922295	A	G	43922295	3	3	340	1	0	0	0	0	1	0	0	0	12086	101	4	2	452	2	PLEKHH2	2	43922295	Missense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	11030586	43922295	199277078	17	46981										
MSH6	2956	hgsc.bcm.edu	37	chr2	48027047	48027047	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	aactctccttgaggaagaatAttttagggaaaagctaagtg	10	5	1	2			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr2:48027047A>G	ENST00000234420.5	+	4	2077	c.1925A>G	c.(1924-1926)tAt>tGt	p.Y642C	MSH6_ENST00000540021.1_Missense_Mutation_p.Y512C|MSH6_ENST00000538136.1_Missense_Mutation_p.Y340C|FBXO11_ENST00000405808.1_Intron	NM_000179.2	NP_000170.1	P52701	MSH6_HUMAN	mutS homolog 6	642					ATP catabolic process (GO:0006200)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|response to UV (GO:0009411)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|MutSalpha complex (GO:0032301)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|guanine/thymine mispair binding (GO:0032137)|methylated histone binding (GO:0035064)|mismatched DNA binding (GO:0030983)	p.0?(2)		breast(8)|central_nervous_system(29)|cervix(1)|endometrium(32)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(75)|lung(25)|ovary(3)|prostate(3)|skin(10)|stomach(22)|thyroid(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	229		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GAGGAAGAATATTTTAGGGAA	0.453			"Mis, N, F, S"		colorectal	"colorectal, endometrial, ovarian"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.Y642C		Atlas-SNP	.	yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p16	2956	mutS homolog 6 (E. coli)		E	.	MSH6	341	.	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.A1925G						.						95	94	95					2																	48027047		2203	4300	6503	SO:0001583	missense	2956	exon4	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	AAGAATATTTTAG	U54777	CCDS1836.1, CCDS62906.1, CCDS62907.1	2p16	2014-09-17	2013-09-12		ENSG00000116062	ENSG00000116062			7329	protein-coding gene	gene with protein product		600678	"mutS (E. coli) homolog 6", "mutS homolog 6 (E. coli)"	GTBP		7604266	Standard	NM_000179		Approved		uc002rwd.4	P52701	OTTHUMG00000129129	ENST00000234420.5:c.1925A>G	chr2.hg19:g.48027047A>G	ENSP00000234420:p.Tyr642Cys	78.0	0.0		35.0	17.0	NM_000179	B4DF41|B4E3I4|F5H2F9|O43706|O43917|Q8TCX4|Q9BTB5	Missense_Mutation	SNP	ENST00000234420.5	hg19	CCDS1836.1	.	.	.	.	.	.	.	.	.	.	A	13.39	2.221981	0.39300	.	.	ENSG00000116062	ENST00000234420;ENST00000544857;ENST00000540021;ENST00000538136	D;D;D	0.87809	-2.3;-2.3;-2.3	5.49	5.49	0.81192	DNA mismatch repair protein MutS, connector (1);	0.118381	0.64402	D	0.000013	D	0.95149	0.8428	M	0.93197	3.39	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.97110	1.0;1.0;0.967	D	0.96333	0.9245	10	0.87932	D	0	-12.5268	15.5875	0.76495	1.0:0.0:0.0:0.0	.	512;642;642	B4DF41;P52701;P52701-2	.;MSH6_HUMAN;.	C	642;640;512;340	ENSP00000234420:Y642C;ENSP00000446475:Y512C;ENSP00000438580:Y340C	ENSP00000234420:Y642C	Y	+	2	0	MSH6	47880551	1.000000	0.71417	0.979000	0.43373	0.272000	0.26649	8.891000	0.92485	2.089000	0.63090	0.477000	0.44152	TAT	.	.		0.453	MSH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251180.4	NM_000179		G	48027047	A	G	48027047	3	3	340	1	0	0	0	0	1	0	0	0	9883	449	16	2	1939	2	MSH6	2	48027047	Missense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	4104752	48027047	195172326	18	46982										
DNAH6	1768	hgsc.bcm.edu	37	chr2	84844030	84844030	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	gacttctggaaacttttcaaAacaataatgcattacttgac	5	8	2	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr2:84844030A>T	ENST00000237449.6	+	22	3504	c.3496A>T	c.(3496-3498)Aac>Tac	p.N1166Y	DNAH6_ENST00000398278.2_Missense_Mutation_p.N1166Y|DNAH6_ENST00000389394.3_Missense_Mutation_p.N1166Y			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	1166	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						AACTTTTCAAAACAATAATGC	0.274																																					p.N1166Y		Atlas-SNP	.											.	DNAH6	194	.	0			c.A3496T						.						43	39	40					2																	84844030		692	1579	2271	SO:0001583	missense	1768	exon23			TTTCAAAACAATA	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.3496A>T	chr2.hg19:g.84844030A>T	ENSP00000237449:p.Asn1166Tyr	328.0	0.0		215.0	80.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	hg19	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	A	17.14	3.313751	0.60414	.	.	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.61510	0.1;0.1;0.1	5.14	5.14	0.70334	Dynein heavy chain, domain-2 (1);	.	.	.	.	T	0.71693	0.3370	M	0.64997	1.995	0.34886	D	0.745037	D	0.63046	0.992	D	0.67900	0.954	T	0.81022	-0.1121	9	0.66056	D	0.02	.	13.9504	0.64113	1.0:0.0:0.0:0.0	.	1166	Q9C0G6	DYH6_HUMAN	Y	1166	ENSP00000374045:N1166Y;ENSP00000381326:N1166Y;ENSP00000237449:N1166Y	ENSP00000237449:N1166Y	N	+	1	0	DNAH6	84697541	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.768000	0.62293	1.934000	0.56057	0.455000	0.32223	AAC	.	.		0.274	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		T	84844030	A	T	84844030	3	4	340	1	0	0	0	0	1	0	0	0	4607	14	1	4	3582	4	DNAH6	2	84844030	Missense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	36816983	84844030	158355343	19	46983										
CNTNAP5	129684	hgsc.bcm.edu	37	chr2	125192135	125192135	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	agaagttgatgagtactctcAaagatgtgatctccctgaag	10	7	2	6			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr2:125192135A>T	ENST00000431078.1	+	5	968	c.604A>T	c.(604-606)Aaa>Taa	p.K202*		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	202	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		GAGTACTCTCAAAGATGTGAT	0.483																																					p.K202X		Atlas-SNP	.											.	CNTNAP5	405	.	0			c.A604T						.						124	118	120					2																	125192135		2003	4197	6200	SO:0001587	stop_gained	129684	exon5			ACTCTCAAAGATG	AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.604A>T	chr2.hg19:g.125192135A>T	ENSP00000399013:p.Lys202*	161.0	0.0		65.0	28.0	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Nonsense_Mutation	SNP	ENST00000431078.1	hg19	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	A	42	9.240057	0.99111	.	.	ENSG00000155052	ENST00000431078	.	.	.	5.48	5.48	0.80851	.	0.000000	0.50627	D	0.000111	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.7735	0.69699	1.0:0.0:0.0:0.0	.	.	.	.	X	202	.	ENSP00000399013:K202X	K	+	1	0	CNTNAP5	124908605	1.000000	0.71417	0.995000	0.50966	0.973000	0.67179	9.169000	0.94788	2.084000	0.62774	0.533000	0.62120	AAA	.	.		0.483	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			T	125192135	A	T	125192135	4	4	340	1	0	0	0	0	0	1	0	0	3652	131	5	4	622	4	CNTNAP5	2	125192135	Nonsense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	40348105	125192135	118007238	20	46984										
POTEE	445582	hgsc.bcm.edu	37	chr2	132020969	132020969	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	gaaaaagacgtcttgcatgaAaatagtacgttgcgggaaga	12	5	1	3			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr2:132020969A>C	ENST00000356920.5	+	15	2035	c.1941A>C	c.(1939-1941)gaA>gaC	p.E647D	PLEKHB2_ENST00000303908.3_Intron|POTEE_ENST00000358087.5_3'UTR|PLEKHB2_ENST00000404460.1_Intron	NM_001083538.1	NP_001077007.1	Q6S8J3	POTEE_HUMAN	POTE ankyrin domain family, member E	647					retina homeostasis (GO:0001895)|substantia nigra development (GO:0021762)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.E647D(1)									TCTTGCATGAAAATAGTACGT	0.353																																					p.E647D		Atlas-SNP	.											ENSG00000188219,NS,carcinoma,0,1	.	.	.	1	Substitution - Missense(1)	lung(1)	c.A1941C						.						27	29	28					2																	132020969		1938	4163	6101	SO:0001583	missense	445582	exon15			GCATGAAAATAGT	AY462868	CCDS46414.1	2q21.1	2014-04-10	2008-11-26	2008-11-26	ENSG00000188219	ENSG00000188219		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	33895	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 2"	608914	"ANKRD26-like family C, member 1A"	A26C1A			Standard	NM_001083538		Approved	POTE2, POTE-2, A26C1, POTE2gamma, CT104.2	uc002tsn.2	Q6S8J3	OTTHUMG00000186974	ENST00000356920.5:c.1941A>C	chr2.hg19:g.132020969A>C	ENSP00000439189:p.Glu647Asp	491.0	0.0		229.0	106.0	NM_001083538	Q6S8J4|Q6S8J5|Q6S8J8	Missense_Mutation	SNP	ENST00000356920.5	hg19	CCDS46414.1	.	.	.	.	.	.	.	.	.	.	.	9.831	1.188323	0.21954	.	.	ENSG00000188219	ENST00000356920	T	0.79247	-1.25	0.993	-0.217	0.13149	.	.	.	.	.	T	0.67325	0.2881	M	0.76838	2.35	0.25569	N	0.986913	P	0.42584	0.784	B	0.28784	0.094	T	0.61667	-0.7016	9	0.87932	D	0	.	2.8547	0.05569	0.6759:0.0:0.3241:0.0	.	647	Q6S8J3	POTEE_HUMAN	D	647	ENSP00000439189:E647D	ENSP00000439189:E647D	E	+	3	2	AC131180.1	131737439	0.810000	0.29049	0.005000	0.12908	0.012000	0.07955	1.495000	0.35627	-0.075000	0.12798	0.155000	0.16302	GAA	.	.		0.353	POTEE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001083538		C	132020969	A	C	132020969	3	2	340	1	0	0	0	0	1	0	0	0	12273	11	1	5	1999	5	POTEE	2	132020969	Missense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	6828834	132020969	111178404	21	46985										
PLA2R1	22925	hgsc.bcm.edu	37	chr2	160808016	160808016	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	tttgcattaattattttgtaAgttctgtttccatattctaa	4	5	2	0			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr2:160808016A>T	ENST00000283243.7	-	24	3581	c.3375T>A	c.(3373-3375)acT>acA	p.T1125T	PLA2R1_ENST00000392771.1_Silent_p.T1125T	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	1125	C-type lectin 7. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)		PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						TTATTTTGTAAGTTCTGTTTC	0.378																																					p.T1125T		Atlas-SNP	.											.	PLA2R1	153	.	0			c.T3375A						.						198	182	187					2																	160808016		2203	4300	6503	SO:0001819	synonymous_variant	22925	exon24			TTTGTAAGTTCTG	U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"C-type lectin domain containing"	9042	protein-coding gene	gene with protein product		604939	"phospholipase A2 receptor 1, 180kD"			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.3375T>A	chr2.hg19:g.160808016A>T		301.0	0.0		175.0	73.0	NM_001195641	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Silent	SNP	ENST00000283243.7	hg19	CCDS33309.1																																																																																			.	.		0.378	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1			T	160808016	A	T	160808016	2	4	340	1	0	0	0	0	0	0	0	1	12019	59	3	4		4	PLA2R1	2	160808016	Silent	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	28787047	160808016	82391357	22	46986										
SCN7A	6332	hgsc.bcm.edu	37	chr2	167319005	167319005	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	agccttgatcaggatttatgCcagcttttacacacacatat	6	10	1	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr2:167319005C>G	ENST00000409855.1	-	9	1103	c.977G>C	c.(976-978)gGc>gCc	p.G326A		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	326					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	AGGATTTATGCCAGCTTTTAC	0.378																																					p.G326A		Atlas-SNP	.											.	SCN7A	410	.	0			c.G977C						.						75	67	69					2																	167319005		1847	4101	5948	SO:0001583	missense	6332	exon9			TTTATGCCAGCTT	M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10594	protein-coding gene	gene with protein product		182392	"sodium channel, voltage-gated, type VI, alpha", "sodium channel, voltage-gated, type VII, alpha"	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.977G>C	chr2.hg19:g.167319005C>G	ENSP00000386796:p.Gly326Ala	108.0	0.0		49.0	26.0	NM_002976		Missense_Mutation	SNP	ENST00000409855.1	hg19	CCDS46442.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.717331	0.89205	.	.	ENSG00000136546	ENST00000409855;ENST00000259060;ENST00000419992;ENST00000441411	D;D;D	0.98617	-5.03;-5.03;-5.03	4.43	4.43	0.53597	Ion transport (1);	0.000000	0.49916	D	0.000127	D	0.98754	0.9581	M	0.83692	2.655	0.48236	D	0.999613	D	0.53151	0.958	P	0.54431	0.752	D	0.99671	1.0996	10	0.87932	D	0	.	15.978	0.80086	0.0:1.0:0.0:0.0	.	326	Q01118	SCN7A_HUMAN	A	326	ENSP00000386796:G326A;ENSP00000413699:G326A;ENSP00000403846:G326A	ENSP00000259060:G326A	G	-	2	0	SCN7A	167027251	0.999000	0.42202	0.927000	0.36925	0.995000	0.86356	4.835000	0.62781	2.150000	0.67090	0.585000	0.79938	GGC	.	.		0.378	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1			G	167319005	C	G	167319005	3	3	340	1	0	0	0	0	1	0	0	0	13938	739	26	4	4139	4	SCN7A	2	167319005	Missense_Mutation	SNP	C	TCGA-RC-A7SK-01A-11D-A34Z-10	6510989	167319005	75880368	23	46987										
HOXD1	3231	hgsc.bcm.edu	37	chr2	177054752	177054752	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	acagaagaaaagggaacgagAagggcttctggccacggcca	14	9	1	3			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr2:177054752A>G	ENST00000331462.4	+	2	1092	c.869A>G	c.(868-870)gAa>gGa	p.E290G	HOXD-AS1_ENST00000425005.1_RNA|HOXD-AS1_ENST00000452365.1_RNA|HOXD-AS1_ENST00000436126.1_RNA|HOXD-AS1_ENST00000417086.1_RNA|HOXD-AS1_ENST00000413969.1_RNA	NM_024501.2	NP_078777.1	Q9GZZ0	HXD1_HUMAN	homeobox D1	290					embryonic skeletal system development (GO:0048706)|neuron differentiation (GO:0030182)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of pain (GO:0019233)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			kidney(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.00569)|Epithelial(96;0.0864)|all cancers(119;0.226)	Colorectal(32;0.0226)		AGGGAACGAGAAGGGCTTCTG	0.552																																					p.E290G		Atlas-SNP	.											.	HOXD1	33	.	0			c.A869G						.						117	126	123					2																	177054752		2203	4300	6503	SO:0001583	missense	3231	exon2			AACGAGAAGGGCT		CCDS2271.1	2q31.1	2011-06-20	2005-12-22		ENSG00000128645	ENSG00000128645		"Homeoboxes / ANTP class : HOXL subclass"	5132	protein-coding gene	gene with protein product		142987	"homeo box D1"	HOX4, HOX4G		1973146, 1358459	Standard	NM_024501		Approved		uc002ukv.5	Q9GZZ0	OTTHUMG00000132512	ENST00000331462.4:c.869A>G	chr2.hg19:g.177054752A>G	ENSP00000328598:p.Glu290Gly	137.0	0.0		109.0	8.0	NM_024501	B2RAB4	Missense_Mutation	SNP	ENST00000331462.4	hg19	CCDS2271.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.593027	0.86953	.	.	ENSG00000128645	ENST00000331462	D	0.91843	-2.92	5.66	5.66	0.87406	Homeobox (1);Homeodomain-like (1);	0.000000	0.48767	D	0.000163	D	0.93533	0.7936	L	0.34521	1.04	0.58432	D	0.999999	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.978	D	0.94038	0.7307	10	0.54805	T	0.06	.	15.5503	0.76145	1.0:0.0:0.0:0.0	.	290;290	Q96CA4;Q9GZZ0	.;HXD1_HUMAN	G	290	ENSP00000328598:E290G	ENSP00000328598:E290G	E	+	2	0	HOXD1	176762998	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.344000	0.79328	2.143000	0.66587	0.533000	0.62120	GAA	.	.		0.552	HOXD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255693.2			G	177054752	A	G	177054752	3	3	340	1	0	0	0	0	1	0	0	0	7327	246	9	2	875	2	HOXD1	2	177054752	Missense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	9735747	177054752	66144621	24	46988										
FKBP7	65977	hgsc.bcm.edu	37	chr2	179343059	179343059	+	5'Flank	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	tagccgtcataatgggcattTagtaggtctcccttcttgct	9	10	3	0			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr2:179343059T>C	ENST00000234453.5	+	0	0				FKBP7_ENST00000464248.1_5'UTR|FKBP7_ENST00000434643.2_Silent_p.L56L|FKBP7_ENST00000424785.2_Silent_p.L56L	NM_019091.3	NP_061964.3	Q9HB20	PKHA3_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 3							Golgi apparatus (GO:0005794)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phospholipid binding (GO:0005543)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.0266)|all cancers(119;0.0865)			AATGGGCATTTAGTAGGTCTC	0.468																																					p.L56L		Atlas-SNP	.											.	FKBP7	16	.	0			c.A168G						.						120	114	116					2																	179343059		2203	4300	6503	SO:0001631	upstream_gene_variant	51661	exon1			GGCATTTAGTAGG	AF286162	CCDS33336.1	2q31.2	2013-01-10	2002-01-14		ENSG00000116095	ENSG00000116095		"Pleckstrin homology (PH) domain containing"	14338	protein-coding gene	gene with protein product	"four-phosphate-adaptor protein 1"	607774	"pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3"			11001876, 15107860	Standard	NM_019091		Approved	FAPP1	uc002umn.3	Q9HB20	OTTHUMG00000154446		chr2.hg19:g.179343059T>C	Exception_encountered	147.0	0.0		123.0	9.0	NM_181342	Q4ZG69|Q86TQ1|Q9NXT3	Silent	SNP	ENST00000234453.5	hg19	CCDS33336.1																																																																																			.	.		0.468	PLEKHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335241.2	NM_019091		C	179343059	T	C	179343059	1	2	340	0	1	0	0	0	0	0	0	0	5921	1741	61	2		2	FKBP7	2	179343059	5'Flank	SNP	T	TCGA-RC-A7SK-01A-11D-A34Z-10	2288307	179343059	63856314	25	46989										
MSTN	2660	hgsc.bcm.edu	37	chr2	190924808	190924808	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	cagcccatcttctcctggtcCtgggaaggttacagcaagat	10	12	2	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr2:190924808C>T	ENST00000260950.4	-	2	859	c.727G>A	c.(727-729)Gga>Aga	p.G243R	C2orf88_ENST00000478197.1_Intron	NM_005259.2	NP_005250.1	O14793	GDF8_HUMAN	myostatin	243					cellular response to dexamethasone stimulus (GO:0071549)|muscle organ development (GO:0007517)|negative regulation of muscle hypertrophy (GO:0014741)|negative regulation of skeletal muscle tissue growth (GO:0048632)|ovulation cycle process (GO:0022602)|positive regulation of transcription, DNA-templated (GO:0045893)|response to electrical stimulus (GO:0051602)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to gravity (GO:0009629)|response to heat (GO:0009408)|response to muscle activity (GO:0014850)|response to testosterone (GO:0033574)|skeletal muscle atrophy (GO:0014732)|skeletal muscle tissue regeneration (GO:0043403)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)			endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|skin(1)	12			OV - Ovarian serous cystadenocarcinoma(117;0.000742)|Epithelial(96;0.0121)|all cancers(119;0.0395)			TCTCCTGGTCCTGGGAAGGTT	0.348																																					p.G243R		Atlas-SNP	.											MSTN,colon,carcinoma,0,1	MSTN	46	.	0			c.G727A						.						122	120	121					2																	190924808		2203	4300	6503	SO:0001583	missense	2660	exon2			CTGGTCCTGGGAA	AF019627	CCDS2303.1	2q32.1	2014-09-17	2007-06-21	2007-06-21	ENSG00000138379	ENSG00000138379			4223	protein-coding gene	gene with protein product		601788	"growth differentiation factor 8"	GDF8		9288100, 10610713, 17003236	Standard	NM_005259		Approved		uc002urp.3	O14793	OTTHUMG00000132663	ENST00000260950.4:c.727G>A	chr2.hg19:g.190924808C>T	ENSP00000260950:p.Gly243Arg	134.0	0.0		139.0	81.0	NM_005259	A1C2J7|A1C2K0|Q6B0H2	Missense_Mutation	SNP	ENST00000260950.4	hg19	CCDS2303.1	.	.	.	.	.	.	.	.	.	.	C	10.94	1.493228	0.26774	.	.	ENSG00000138379	ENST00000260950	T	0.66280	-0.2	5.25	4.38	0.52667	Transforming growth factor-beta, N-terminal (1);	0.218941	0.46442	N	0.000283	T	0.47967	0.1474	L	0.27053	0.805	0.43642	D	0.996043	B	0.02656	0.0	B	0.06405	0.002	T	0.37126	-0.9719	10	0.22706	T	0.39	-6.8459	14.0005	0.64431	0.0:0.9274:0.0:0.0726	.	243	O14793	GDF8_HUMAN	R	243	ENSP00000260950:G243R	ENSP00000260950:G243R	G	-	1	0	MSTN	190633053	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	3.183000	0.50918	1.453000	0.47775	0.585000	0.79938	GGA	.	.		0.348	MSTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255917.2	NM_005259		T	190924808	C	T	190924808	3	4	340	1	0	0	0	0	1	0	0	0	9902	690	24	3	408	3	MSTN	2	190924808	Missense_Mutation	SNP	C	TCGA-RC-A7SK-01A-11D-A34Z-10	11581749	190924808	52274565	26	46990										
SPEG	10290	hgsc.bcm.edu	37	chr2	220333678	220333678	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	ggcagcgaggacgaggggctCtatgcggtcagtgctgttaa	17	8	2	0			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr2:220333678C>T	ENST00000312358.7	+	12	3531	c.3399C>T	c.(3397-3399)ctC>ctT	p.L1133L	SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	1133	Ig-like 5.				cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		ACGAGGGGCTCTATGCGGTCA	0.647																																					p.L1133L		Atlas-SNP	.											.	SPEG	272	.	0			c.C3399T						.						43	53	49					2																	220333678		2088	4218	6306	SO:0001819	synonymous_variant	10290	exon12			GGGGCTCTATGCG	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"Immunoglobulin superfamily / I-set domain containing"	16901	protein-coding gene	gene with protein product		615950	"aortic preferentially expressed gene 1"	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.3399C>T	chr2.hg19:g.220333678C>T		68.0	0.0		30.0	14.0	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Silent	SNP	ENST00000312358.7	hg19	CCDS42824.1																																																																																			.	.		0.647	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		T	220333678	C	T	220333678	2	4	340	1	0	0	0	0	0	0	0	1	15051	900	32	3		3	SPEG	2	220333678	Silent	SNP	C	TCGA-RC-A7SK-01A-11D-A34Z-10	29408870	220333678	22865695	27	46991										
PSMD1	5707	hgsc.bcm.edu	37	chr2	231936937	231936937	+	Missense_Mutation	SNP	G	G	T													0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	agatgatcctcaggctgtgaGtgatatcttagagaaactgg							TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr2:231936937G>T	ENST00000308696.6	+	7	851	c.689G>T	c.(688-690)aGt>aTt	p.S230I	PSMD1_ENST00000409643.1_Missense_Mutation_p.S230I|PSMD1_ENST00000373635.4_Missense_Mutation_p.S230I	NM_002807.3	NP_002798.2	Q99460	PSMD1_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	230					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)	31		Ovarian(221;0.000626)|Medulloblastoma(418;0.0109)|Renal(207;0.0112)|Lung NSC(271;0.0538)|all_lung(227;0.0713)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;4e-26)|LUSC - Lung squamous cell carcinoma(224;0.0138)|Lung(119;0.0168)	Bortezomib(DB00188)	CAGGCTGTGAGTGATATCTTA	0.343																																					p.S230I		Atlas-SNP	.											.	PSMD1	77	.	0			c.G689T						.						173	167	169					2																	231936937		2203	4300	6503	SO:0001583	missense	5707	exon7			CTGTGAGTGATAT	D44466	CCDS2482.1, CCDS54436.1	2q37.1	2008-05-22			ENSG00000173692	ENSG00000173692		"Proteasome (prosome, macropain) subunits"	9554	protein-coding gene	gene with protein product						8816993	Standard	NM_002807		Approved	S1, P112, Rpn2	uc002vrn.2	Q99460	OTTHUMG00000133223	ENST00000308696.6:c.689G>T	chr2.hg19:g.231936937G>T	ENSP00000309474:p.Ser230Ile	189.0	0.0		80.0	11.0	NM_002807	B8ZZH9|Q24JU0|Q53TI2|Q6GMU5|Q6P2P4|Q6PJM7|Q6PKG9|Q86VU1|Q8IV79	Missense_Mutation	SNP	ENST00000308696.6	hg19	CCDS2482.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.065328	0.76187	.	.	ENSG00000173692	ENST00000308696;ENST00000373635;ENST00000409643	.	.	.	5.98	5.98	0.97165	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.65863	0.2732	L	0.46819	1.47	0.80722	D	1	B;P	0.35944	0.049;0.529	B;B	0.42386	0.01;0.386	T	0.64537	-0.6384	9	0.54805	T	0.06	-7.1736	20.4581	0.99154	0.0:0.0:1.0:0.0	.	230;230	Q99460;Q99460-2	PSMD1_HUMAN;.	I	230	.	ENSP00000309474:S230I	S	+	2	0	PSMD1	231645181	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.835000	0.97688	0.650000	0.86243	AGT	.	.		0.343	PSMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256958.2			T	231936937	G	T	231936937	3	4	340	1	0	0	0	0	1	0	0	0	12704	1029	36	3	715	3	PSMD1	2	231936937	Missense_Mutation	SNP	G	TCGA-RC-A7SK-01A-11D-A34Z-10	11603259	231936937	11262436	28	46992	251	2								
PSMD1	5707	hgsc.bcm.edu	37	chr2	231936939	231936939	+	Missense_Mutation	SNP	G	G	T													0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	atgatcctcaggctgtgagtGatatcttagagaaactggta							TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr2:231936939G>T	ENST00000308696.6	+	7	853	c.691G>T	c.(691-693)Gat>Tat	p.D231Y	PSMD1_ENST00000409643.1_Missense_Mutation_p.D231Y|PSMD1_ENST00000373635.4_Missense_Mutation_p.D231Y	NM_002807.3	NP_002798.2	Q99460	PSMD1_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	231					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)	31		Ovarian(221;0.000626)|Medulloblastoma(418;0.0109)|Renal(207;0.0112)|Lung NSC(271;0.0538)|all_lung(227;0.0713)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;4e-26)|LUSC - Lung squamous cell carcinoma(224;0.0138)|Lung(119;0.0168)	Bortezomib(DB00188)	GGCTGTGAGTGATATCTTAGA	0.343																																					p.D231Y		Atlas-SNP	.											.	PSMD1	77	.	0			c.G691T						.						177	170	172					2																	231936939		2203	4300	6503	SO:0001583	missense	5707	exon7			GTGAGTGATATCT	D44466	CCDS2482.1, CCDS54436.1	2q37.1	2008-05-22			ENSG00000173692	ENSG00000173692		"Proteasome (prosome, macropain) subunits"	9554	protein-coding gene	gene with protein product						8816993	Standard	NM_002807		Approved	S1, P112, Rpn2	uc002vrn.2	Q99460	OTTHUMG00000133223	ENST00000308696.6:c.691G>T	chr2.hg19:g.231936939G>T	ENSP00000309474:p.Asp231Tyr	190.0	0.0		80.0	12.0	NM_002807	B8ZZH9|Q24JU0|Q53TI2|Q6GMU5|Q6P2P4|Q6PJM7|Q6PKG9|Q86VU1|Q8IV79	Missense_Mutation	SNP	ENST00000308696.6	hg19	CCDS2482.1	.	.	.	.	.	.	.	.	.	.	G	19.93	3.918713	0.73098	.	.	ENSG00000173692	ENST00000308696;ENST00000373635;ENST00000409643	.	.	.	5.98	5.98	0.97165	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.78947	0.4364	M	0.69823	2.125	0.80722	D	1	B;D	0.67145	0.052;0.996	B;D	0.64877	0.04;0.93	T	0.78710	-0.2098	9	0.62326	D	0.03	-8.8292	20.4581	0.99154	0.0:0.0:1.0:0.0	.	231;231	Q99460;Q99460-2	PSMD1_HUMAN;.	Y	231	.	ENSP00000309474:D231Y	D	+	1	0	PSMD1	231645183	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.835000	0.97688	0.650000	0.86243	GAT	.	.		0.343	PSMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256958.2			T	231936939	G	T	231936939	3	4	340	1	0	0	0	0	1	0	0	0	12704	1290	45	3	717	3	PSMD1	2	231936939	Missense_Mutation	SNP	G	TCGA-RC-A7SK-01A-11D-A34Z-10	2	231936939	11262434	29	46993	251	2								
JAGN1	84522	hgsc.bcm.edu	37	chr3	9934999	9934999	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	aagtgcatgcctggcagttgTactacagcaagaagctccta	10	10	0	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr3:9934999T>C	ENST00000307768.4	+	2	659	c.490T>C	c.(490-492)Tac>Cac	p.Y164H		NM_032492.3	NP_115881.3			jagunal homolog 1 (Drosophila)											breast(1)|central_nervous_system(1)|endometrium(4)|lung(3)|ovary(1)	10	Medulloblastoma(99;0.227)					CTGGCAGTTGTACTACAGCAA	0.512																																					p.Y164H		Atlas-SNP	.											.	JAGN1	18	.	0			c.T490C						.						179	112	135					3																	9934999		2203	4300	6503	SO:0001583	missense	84522	exon2			CAGTTGTACTACA	AK074760	CCDS2588.1	3p25.2	2010-03-23			ENSG00000171135	ENSG00000171135			26926	protein-coding gene	gene with protein product						12477932	Standard	NM_032492		Approved	GL009, FLJ14602	uc003btt.4	Q8N5M9	OTTHUMG00000128523	ENST00000307768.4:c.490T>C	chr3.hg19:g.9934999T>C	ENSP00000306106:p.Tyr164His	241.0	0.0		154.0	54.0	NM_032492		Missense_Mutation	SNP	ENST00000307768.4	hg19	CCDS2588.1	.	.	.	.	.	.	.	.	.	.	T	17.93	3.508007	0.64410	.	.	ENSG00000171135	ENST00000307768;ENST00000543379	.	.	.	5.56	3.19	0.36642	.	0.059088	0.64402	N	0.000001	T	0.75443	0.3850	M	0.75264	2.295	0.58432	D	0.999999	D	0.89917	1.0	D	0.81914	0.995	T	0.74942	-0.3492	9	0.87932	D	0	-22.2684	9.5034	0.39031	0.0:0.145:0.0:0.855	.	164	Q8N5M9	JAGN1_HUMAN	H	164;162	.	ENSP00000306106:Y164H	Y	+	1	0	JAGN1	9909999	1.000000	0.71417	0.519000	0.27824	0.817000	0.46193	6.213000	0.72194	0.414000	0.25790	0.260000	0.18958	TAC	.	.		0.512	JAGN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250335.1	NM_032492		C	9934999	T	C	9934999	3	2	340	1	0	0	0	0	1	0	0	0	7945	1638	57	2	496	2	JAGN1	3	9934999	Missense_Mutation	SNP	T	TCGA-RC-A7SK-01A-11D-A34Z-10		9934999	188087431	30	46994										
TIMP4	7079	hgsc.bcm.edu	37	chr3	12195209	12195209	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	gggtactgtgtagcaggtggTgatctagagtcatggccaca	15	7	2	2			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr3:12195209T>C	ENST00000287814.4	-	5	991	c.481A>G	c.(481-483)Acc>Gcc	p.T161A	SYN2_ENST00000432424.2_RNA	NM_003256.3	NP_003247.1	Q99727	TIMP4_HUMAN	TIMP metallopeptidase inhibitor 4	161					central nervous system development (GO:0007417)|negative regulation of endopeptidase activity (GO:0010951)|ovulation cycle (GO:0042698)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to peptide hormone (GO:0043434)	extracellular space (GO:0005615)|sarcomere (GO:0030017)	metal ion binding (GO:0046872)|metalloendopeptidase inhibitor activity (GO:0008191)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	11						TAGCAGGTGGTGATCTAGAGT	0.502																																					p.T161A	Melanoma(199;1446 2144 30617 38794 51714)	Atlas-SNP	.											.	TIMP4	21	.	0			c.A481G						.						120	110	114					3																	12195209		2203	4300	6503	SO:0001583	missense	7079	exon5			AGGTGGTGATCTA	U76456	CCDS2608.1	3p25	2005-10-31	2005-08-08		ENSG00000157150	ENSG00000157150			11823	protein-coding gene	gene with protein product		601915	"tissue inhibitor of metalloproteinase 4"			8939999, 9693046	Standard	NM_003256		Approved		uc003bwo.3	Q99727	OTTHUMG00000129763	ENST00000287814.4:c.481A>G	chr3.hg19:g.12195209T>C	ENSP00000287814:p.Thr161Ala	56.0	0.0		44.0	12.0	NM_003256	B2R7K6	Missense_Mutation	SNP	ENST00000287814.4	hg19	CCDS2608.1	.	.	.	.	.	.	.	.	.	.	T	13.67	2.305396	0.40795	.	.	ENSG00000157150	ENST00000287814	D	0.93307	-3.2	4.88	4.88	0.63580	Tissue inhibitor of metalloproteinases-like, OB-fold (1);	0.118425	0.56097	D	0.000025	D	0.89989	0.6875	M	0.62723	1.935	0.42982	D	0.994464	B	0.28584	0.216	B	0.28553	0.091	D	0.85526	0.1206	10	0.12103	T	0.63	.	10.5746	0.45219	0.144:0.0:0.0:0.856	.	161	Q99727	TIMP4_HUMAN	A	161	ENSP00000287814:T161A	ENSP00000287814:T161A	T	-	1	0	TIMP4	12170209	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.220000	0.42908	2.052000	0.61016	0.402000	0.26972	ACC	.	.		0.502	TIMP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251978.1	NM_003256		C	12195209	T	C	12195209	3	2	340	1	0	0	0	0	1	0	0	0	15935	1696	59	2	197	2	TIMP4	3	12195209	Missense_Mutation	SNP	T	TCGA-RC-A7SK-01A-11D-A34Z-10	2260210	12195209	185827221	31	46995										
XIRP1	165904	hgsc.bcm.edu	37	chr3	39230338	39230338	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	ggcgggagcccaggcggtccAgcggccgcgtctcaaagagc	17	14	1	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr3:39230338A>G	ENST00000340369.3	-	2	827	c.599T>C	c.(598-600)cTg>cCg	p.L200P	XIRP1_ENST00000396251.1_Missense_Mutation_p.L200P|XIRP1_ENST00000421646.1_Intron	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	200					cardiac muscle cell development (GO:0055013)|negative regulation of cell proliferation (GO:0008285)|regulation of membrane potential (GO:0042391)|sarcomere organization (GO:0045214)	fascia adherens (GO:0005916)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(14)|lung(22)|ovary(4)|pancreas(1)|prostate(2)|skin(6)	71				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		CAGGCGGTCCAGCGGCCGCGT	0.627																																					p.L200P		Atlas-SNP	.											.	XIRP1	173	.	0			c.T599C						.						45	47	46					3																	39230338		2203	4300	6503	SO:0001583	missense	165904	exon2			CGGTCCAGCGGCC	AW755250	CCDS2683.1, CCDS56245.1	3p21.33	2008-02-05	2007-06-27	2007-06-27	ENSG00000168334	ENSG00000168334			14301	protein-coding gene	gene with protein product		609777	"cardiomyopathy associated 1"	CMYA1		12203715, 15454575	Standard	NM_001198621		Approved	DKFZp451D042, Xin	uc003cjk.2	Q702N8	OTTHUMG00000131297	ENST00000340369.3:c.599T>C	chr3.hg19:g.39230338A>G	ENSP00000343140:p.Leu200Pro	54.0	0.0		26.0	11.0	NM_001198621	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Missense_Mutation	SNP	ENST00000340369.3	hg19	CCDS2683.1	.	.	.	.	.	.	.	.	.	.	A	17.52	3.409130	0.62399	.	.	ENSG00000168334	ENST00000396251;ENST00000340369	T;T	0.58358	0.34;0.34	4.66	3.4	0.38934	.	0.000000	0.64402	D	0.000003	T	0.68339	0.2990	M	0.74881	2.28	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.71484	-0.4579	10	0.87932	D	0	.	9.3876	0.38352	0.8207:0.1793:0.0:0.0	.	200;200	Q702N8;Q702N8-2	XIRP1_HUMAN;.	P	200	ENSP00000379550:L200P;ENSP00000343140:L200P	ENSP00000343140:L200P	L	-	2	0	XIRP1	39205342	1.000000	0.71417	0.999000	0.59377	0.986000	0.74619	7.338000	0.79269	1.877000	0.54381	0.482000	0.46254	CTG	.	.		0.627	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522		G	39230338	A	G	39230338	3	3	340	1	0	0	0	0	1	0	0	0	17444	188	7	2	4936	2	XIRP1	3	39230338	Missense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	27035129	39230338	158792092	32	46996										
SETD2	29072	hgsc.bcm.edu	37	chr3	47098371	47098371	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	acaccatagactgttggacaTgtctgtccttgataatatat	7	8	1	2			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr3:47098371T>C	ENST00000409792.3	-	15	6945	c.6903A>G	c.(6901-6903)acA>acG	p.T2301T		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	2301	Gln-rich.|Low charge region.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		CTGTTGGACATGTCTGTCCTT	0.398			"N, F, S, Mis"		clear cell renal carcinoma																																p.T2301T		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.A6903G						.						119	114	116					3																	47098371		2203	4300	6503	SO:0001819	synonymous_variant	29072	exon15			TGGACATGTCTGT	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.6903A>G	chr3.hg19:g.47098371T>C		223.0	0.0		111.0	31.0	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Silent	SNP	ENST00000409792.3	hg19	CCDS2749.2																																																																																			.	.		0.398	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		C	47098371	T	C	47098371	2	2	340	1	0	0	0	0	0	0	0	1	14146	1451	51	2		2	SETD2	3	47098371	Silent	SNP	T	TCGA-RC-A7SK-01A-11D-A34Z-10	7868033	47098371	150924059	33	46997										
DZIP3	9666	hgsc.bcm.edu	37	chr3	108347953	108347953	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	tcataaaagcttacaagaaaTtggagacaaaaatgaccatt	6	6	1	3			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr3:108347953T>C	ENST00000361582.3	+	8	856	c.626T>C	c.(625-627)aTt>aCt	p.I209T	DZIP3_ENST00000463306.1_Missense_Mutation_p.I209T	NM_014648.3	NP_055463.1	Q86Y13	DZIP3_HUMAN	DAZ interacting zinc finger protein 3	209					protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|phosphatase binding (GO:0019902)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(21)|ovary(1)|pancreas(1)|prostate(5)|skin(1)	45						TTACAAGAAATTGGAGACAAA	0.308																																					p.I209T		Atlas-SNP	.											.	DZIP3	111	.	0			c.T626C						.						102	108	106					3																	108347953		2203	4300	6503	SO:0001583	missense	9666	exon8			AAGAAATTGGAGA	AF279370	CCDS2952.1	3q13.13	2013-05-22	2013-05-22		ENSG00000198919	ENSG00000198919		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	30938	protein-coding gene	gene with protein product	"human RNA-binding ubiquitin ligase of 138 kDa", "protein phosphatase 1, regulatory subunit 66"	608672	"DAZ interacting protein 3, zinc finger"			9734811, 12538761	Standard	NM_014648		Approved	hRUL138, PPP1R66	uc003dxd.3	Q86Y13	OTTHUMG00000159232	ENST00000361582.3:c.626T>C	chr3.hg19:g.108347953T>C	ENSP00000355028:p.Ile209Thr	141.0	0.0		81.0	15.0	NM_014648	B3KN01|O75162|Q6P3R9|Q6PH82|Q86Y14|Q86Y15|Q86Y16|Q8IWI0|Q96RS9	Missense_Mutation	SNP	ENST00000361582.3	hg19	CCDS2952.1	.	.	.	.	.	.	.	.	.	.	T	11.79	1.743053	0.30865	.	.	ENSG00000198919	ENST00000393969;ENST00000361582;ENST00000486815;ENST00000479138;ENST00000463306	T;T	0.30714	1.52;1.52	4.37	3.2	0.36748	.	0.000000	0.52532	D	0.000061	T	0.34571	0.0902	N	0.19112	0.55	0.31840	N	0.623543	D	0.76494	0.999	D	0.78314	0.991	T	0.38757	-0.9646	10	0.87932	D	0	-8.7949	6.6666	0.23044	0.0:0.109:0.0:0.891	.	209	Q86Y13	DZIP3_HUMAN	T	209;209;125;209;209	ENSP00000355028:I209T;ENSP00000419981:I209T	ENSP00000355028:I209T	I	+	2	0	DZIP3	109830643	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	2.064000	0.41432	0.701000	0.31803	0.482000	0.46254	ATT	.	.		0.308	DZIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353968.1	NM_014648		C	108347953	T	C	108347953	3	2	340	1	0	0	0	0	1	0	0	0	4867	1493	52	2	652	2	DZIP3	3	108347953	Missense_Mutation	SNP	T	TCGA-RC-A7SK-01A-11D-A34Z-10	61249582	108347953	89674477	34	46998										
SLC15A2	6565	hgsc.bcm.edu	37	chr3	121641941	121641941	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	gggtactattcctttatatcCcattgcccatgttctgggct	8	11	1	0			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr3:121641941C>A	ENST00000489711.1	+	10	1310	c.922C>A	c.(922-924)Cca>Aca	p.P308T	AC072031.1_ENST00000581491.1_RNA|SLC15A2_ENST00000295605.2_Missense_Mutation_p.P277T	NM_021082.3	NP_066568.3	Q16348	S15A2_HUMAN	solute carrier family 15 (oligopeptide transporter), member 2	308					drug transport (GO:0015893)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antibiotic transporter activity (GO:0042895)|dipeptide transporter activity (GO:0042936)|high-affinity oligopeptide transporter activity (GO:0015334)|peptide:proton symporter activity (GO:0015333)			NS(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(17)|skin(6)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(114;0.0967)	Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Fosinopril(DB00492)|Glyburide(DB01016)|Moexipril(DB00691)|Nateglinide(DB00731)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Tranexamic Acid(DB00302)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	CCTTTATATCCCATTGCCCAT	0.453																																					p.P308T		Atlas-SNP	.											.	SLC15A2	92	.	0			c.C922A						.						163	168	166					3																	121641941		2203	4300	6503	SO:0001583	missense	6565	exon10			TATATCCCATTGC	BC044572	CCDS3007.1, CCDS54631.1	3q21.1	2013-07-18	2013-07-18		ENSG00000163406	ENSG00000163406		"Solute carriers"	10921	protein-coding gene	gene with protein product		602339	"solute carrier family 15 (H+/peptide transporter), member 2"			7756356	Standard	NM_021082		Approved	PEPT2	uc003eep.2	Q16348	OTTHUMG00000159423	ENST00000489711.1:c.922C>A	chr3.hg19:g.121641941C>A	ENSP00000417085:p.Pro308Thr	192.0	0.0		95.0	19.0	NM_021082	A8K1A5|B4E2A7	Missense_Mutation	SNP	ENST00000489711.1	hg19	CCDS3007.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.828034	0.90955	.	.	ENSG00000163406	ENST00000489711;ENST00000542599;ENST00000295605	T;T	0.56941	0.43;0.43	5.86	5.86	0.93980	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	T	0.72898	0.3518	M	0.73372	2.23	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.74481	-0.3651	10	0.87932	D	0	-10.4065	17.6924	0.88272	0.0:1.0:0.0:0.0	.	277;308	B4E2A7;Q16348	.;S15A2_HUMAN	T	308;270;277	ENSP00000417085:P308T;ENSP00000295605:P277T	ENSP00000295605:P277T	P	+	1	0	SLC15A2	123124631	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.278000	0.78587	2.781000	0.95711	0.650000	0.86243	CCA	.	.		0.453	SLC15A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355239.1	NM_021082		A	121641941	C	A	121641941	3	1	340	1	0	0	0	0	1	0	0	0	14414	623	22	3	960	3	SLC15A2	3	121641941	Missense_Mutation	SNP	C	TCGA-RC-A7SK-01A-11D-A34Z-10	13293988	121641941	76380489	35	46999										
HEG1	57493	hgsc.bcm.edu	37	chr3	124732258	124732258	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	cagatgtagatgtcgttaagGatactggtaaaggtgatggt	14	3	0	3			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr3:124732258G>T	ENST00000311127.4	-	6	2232	c.2165C>A	c.(2164-2166)tCc>tAc	p.S722Y	HEG1_ENST00000477536.1_5'Flank	NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	722	Ser-rich.				cardiac atrium morphogenesis (GO:0003209)|cell-cell junction assembly (GO:0007043)|endothelial cell morphogenesis (GO:0001886)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|lymph circulation (GO:0003017)|lymph vessel development (GO:0001945)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|post-embryonic development (GO:0009791)|regulation of body fluid levels (GO:0050878)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|ventricular septum development (GO:0003281)	cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(24)|ovary(2)|urinary_tract(4)	47						TGTCGTTAAGGATACTGGTAA	0.493																																					p.S722Y		Atlas-SNP	.											.	HEG1	109	.	0			c.C2165A						.						200	201	201					3																	124732258		2061	4209	6270	SO:0001583	missense	57493	exon6			GTTAAGGATACTG	AK074987	CCDS46898.1	3q21.2	2013-03-08	2013-03-08		ENSG00000173706	ENSG00000173706			29227	protein-coding gene	gene with protein product	"heart of glass"	614182	"HEG homolog 1 (zebrafish)"			10574462, 19151727, 23007647	Standard	NM_020733		Approved	KIAA1237, HEG	uc003ehs.4	Q9ULI3	OTTHUMG00000159486	ENST00000311127.4:c.2165C>A	chr3.hg19:g.124732258G>T	ENSP00000311502:p.Ser722Tyr	112.0	0.0		57.0	19.0	NM_020733	Q6NX66|Q8NC40|Q9BSV0	Missense_Mutation	SNP	ENST00000311127.4	hg19	CCDS46898.1	.	.	.	.	.	.	.	.	.	.	G	13.27	2.186032	0.38609	.	.	ENSG00000173706	ENST00000311127	D	0.89415	-2.51	5.2	4.29	0.51040	.	0.000000	0.38492	U	0.001667	D	0.92743	0.7693	M	0.66939	2.045	0.09310	N	1	D;D	0.76494	0.999;0.999	D;D	0.74023	0.982;0.96	D	0.85642	0.1277	10	0.66056	D	0.02	.	12.7971	0.57565	0.0:0.0:0.8379:0.1621	.	722;722	Q9ULI3-2;Q9ULI3	.;HEG1_HUMAN	Y	722	ENSP00000311502:S722Y	ENSP00000311502:S722Y	S	-	2	0	HEG1	126214948	0.303000	0.24463	0.154000	0.22540	0.016000	0.09150	3.333000	0.52090	2.706000	0.92434	0.561000	0.74099	TCC	.	.		0.493	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386		T	124732258	G	T	124732258	3	4	340	1	0	0	0	0	1	0	0	0	7053	1174	41	3	2028	3	HEG1	3	124732258	Missense_Mutation	SNP	G	TCGA-RC-A7SK-01A-11D-A34Z-10	3090317	124732258	73290172	36	47000										
KBTBD12	166348	hgsc.bcm.edu	37	chr3	127702969	127702969	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	aggttatctccaaagaaataTtggaactggacccatgggaa	10	7	1	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr3:127702969T>C	ENST00000405109.1	+	6	2187	c.1720T>C	c.(1720-1722)Ttg>Ctg	p.L574L	KBTBD12_ENST00000405256.1_Silent_p.L574L|KBTBD12_ENST00000407609.3_Silent_p.L181L|KBTBD12_ENST00000343941.4_Silent_p.L149L|KBTBD12_ENST00000492025.1_3'UTR			Q3ZCT8	KBTBC_HUMAN	kelch repeat and BTB (POZ) domain containing 12	574										endometrium(1)|large_intestine(6)|lung(5)|ovary(1)	13						CAAAGAAATATTGGAACTGGA	0.453																																					p.L574L		Atlas-SNP	.											.	KBTBD12	41	.	0			c.T1720C						.						156	147	150					3																	127702969		2203	4300	6503	SO:0001819	synonymous_variant	166348	exon5			GAAATATTGGAAC		CCDS33848.2	3q21.3	2013-01-08	2009-10-01	2009-10-01	ENSG00000187715	ENSG00000187715		"BTB/POZ domain containing"	25731	protein-coding gene	gene with protein product			"kelch domain containing 6"	KLHDC6			Standard	NM_207335		Approved	FLJ46299	uc010hsr.3	Q3ZCT8	OTTHUMG00000150508	ENST00000405109.1:c.1720T>C	chr3.hg19:g.127702969T>C		177.0	0.0		94.0	18.0	NM_207335	B5MCC6|Q6ZRK1	Silent	SNP	ENST00000405109.1	hg19	CCDS33848.2																																																																																			.	.		0.453	KBTBD12-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318682.1	NM_207335		C	127702969	T	C	127702969	2	2	340	1	0	0	0	0	0	0	0	1	8000	1490	52	2		2	KBTBD12	3	127702969	Silent	SNP	T	TCGA-RC-A7SK-01A-11D-A34Z-10	2970711	127702969	70319461	37	47001										
DNAJC19	131118	hgsc.bcm.edu	37	chr3	180704791	180704791	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	tgggttcaaacccacctctaTaatagccaccactgaaggcc	7	14	2	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr3:180704791T>C	ENST00000382564.2	-	4	319	c.149A>G	c.(148-150)tAt>tGt	p.Y50C	DNAJC19_ENST00000491873.1_Missense_Mutation_p.Y25C|DNAJC19_ENST00000486355.1_Missense_Mutation_p.Y50C|DNAJC19_ENST00000479269.1_Missense_Mutation_p.Y25C	NM_145261.3	NP_660304.1	Q96DA6	TIM14_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 19	50					cellular protein metabolic process (GO:0044267)|genitalia development (GO:0048806)|protein folding (GO:0006457)|protein targeting to mitochondrion (GO:0006626)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)				large_intestine(2)|lung(1)	3	all_cancers(143;3.12e-14)|Ovarian(172;0.0212)		Epithelial(37;3.05e-36)|OV - Ovarian serous cystadenocarcinoma(80;1.55e-22)			CCCACCTCTATAATAGCCACC	0.328																																					p.Y50C		Atlas-SNP	.											.	DNAJC19	4	.	0			c.A149G						.						81	88	85					3																	180704791		2203	4300	6503	SO:0001583	missense	131118	exon4			CCTCTATAATAGC		CCDS33895.1, CCDS54684.1	3q26.33	2014-09-17			ENSG00000205981	ENSG00000205981		"Heat shock proteins / DNAJ (HSP40)"	30528	protein-coding gene	gene with protein product		608977				19564938	Standard	NM_145261		Approved	TIMM14, Tim14, Pam18	uc003fkt.3	Q96DA6	OTTHUMG00000158180	ENST00000382564.2:c.149A>G	chr3.hg19:g.180704791T>C	ENSP00000372005:p.Tyr50Cys	207.0	0.0		127.0	27.0	NM_145261	B2R4B1|C9JBV1	Missense_Mutation	SNP	ENST00000382564.2	hg19	CCDS33895.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.266136	0.80358	.	.	ENSG00000205981	ENST00000382564;ENST00000491873;ENST00000479269	.	.	.	5.77	5.77	0.91146	.	0.052954	0.85682	D	0.000000	T	0.79992	0.4542	M	0.93375	3.41	0.80722	D	1	D	0.59767	0.986	P	0.53722	0.733	D	0.85443	0.1156	9	0.66056	D	0.02	-1.6047	14.9515	0.71077	0.0:0.0:0.0:1.0	.	50	Q96DA6	TIM14_HUMAN	C	50;25;25	.	ENSP00000372005:Y50C	Y	-	2	0	DNAJC19	182187485	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.599000	0.74127	2.326000	0.78906	0.528000	0.53228	TAT	.	.		0.328	DNAJC19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350336.1	NM_145261		C	180704791	T	C	180704791	3	2	340	1	0	0	0	0	1	0	0	0	4640	1406	49	2	213	2	DNAJC19	3	180704791	Missense_Mutation	SNP	T	TCGA-RC-A7SK-01A-11D-A34Z-10	53001822	180704791	17317639	38	47002										
KIAA0232	9778	hgsc.bcm.edu	37	chr4	6862633	6862633	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	tactctgtttttcaggtactAtgaagcatttccaccacttt	5	10	2	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr4:6862633A>G	ENST00000307659.5	+	7	979	c.524A>G	c.(523-525)tAt>tGt	p.Y175C	KIAA0232_ENST00000425103.1_Missense_Mutation_p.Y175C	NM_014743.2	NP_055558.2	Q92628	K0232_HUMAN	KIAA0232	175							ATP binding (GO:0005524)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(12)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	41						TTCAGGTACTATGAAGCATTT	0.358																																					p.Y175C		Atlas-SNP	.											.	KIAA0232	102	.	0			c.A524G						.						129	124	125					4																	6862633		1902	4126	6028	SO:0001583	missense	9778	exon7			GGTACTATGAAGC	D86985	CCDS43209.1	4p16.1	2012-11-29			ENSG00000170871	ENSG00000170871			28992	protein-coding gene	gene with protein product						9039502	Standard	NM_014743		Approved		uc003gjq.4	Q92628	OTTHUMG00000160072	ENST00000307659.5:c.524A>G	chr4.hg19:g.6862633A>G	ENSP00000303928:p.Tyr175Cys	176.0	0.0		85.0	11.0	NM_014743	A7E2D2	Missense_Mutation	SNP	ENST00000307659.5	hg19	CCDS43209.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.222657	0.79464	.	.	ENSG00000170871	ENST00000425103;ENST00000307659	.	.	.	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.75657	0.3879	L	0.55481	1.735	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.78221	-0.2288	9	0.87932	D	0	-11.9197	15.6476	0.77068	1.0:0.0:0.0:0.0	.	175	Q92628	K0232_HUMAN	C	175	.	ENSP00000303928:Y175C	Y	+	2	0	KIAA0232	6913534	1.000000	0.71417	0.952000	0.39060	0.857000	0.48899	8.881000	0.92415	2.103000	0.63969	0.533000	0.62120	TAT	.	.		0.358	KIAA0232-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359102.2	NM_014743		G	6862633	A	G	6862633	3	3	340	1	0	0	0	0	1	0	0	0	8172	449	16	2	542	2	KIAA0232	4	6862633	Missense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10		6862633	184291643	39	47003										
KLB	152831	hgsc.bcm.edu	37	chr4	39448206	39448206	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	gcggtgaaccgacaggccctGaggtactacaggtgcgtggt	16	10	0	2			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr4:39448206G>T	ENST00000257408.4	+	4	1957	c.1860G>T	c.(1858-1860)ctG>ctT	p.L620L		NM_175737.3	NP_783864.1	Q86Z14	KLOTB_HUMAN	klotho beta	620	Glycosyl hydrolase-1 2.				carbohydrate metabolic process (GO:0005975)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fibroblast growth factor binding (GO:0017134)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|skin(6)	29						GACAGGCCCTGAGGTACTACA	0.602																																					p.L620L		Atlas-SNP	.											.	KLB	95	.	0			c.G1860T						.						91	88	89					4																	39448206		2203	4300	6503	SO:0001819	synonymous_variant	152831	exon4			GGCCCTGAGGTAC	AB079373	CCDS3451.1	4p14	2008-02-05			ENSG00000134962	ENSG00000134962			15527	protein-coding gene	gene with protein product		611135					Standard	NM_175737		Approved		uc003gua.3	Q86Z14	OTTHUMG00000128577	ENST00000257408.4:c.1860G>T	chr4.hg19:g.39448206G>T		35.0	0.0		22.0	16.0	NM_175737	Q2M3K8	Silent	SNP	ENST00000257408.4	hg19	CCDS3451.1																																																																																			.	.		0.602	KLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250429.1	NM_175737		T	39448206	G	T	39448206	2	4	340	1	0	0	0	0	0	0	0	1	8341	1277	45	3		3	KLB	4	39448206	Silent	SNP	G	TCGA-RC-A7SK-01A-11D-A34Z-10	32585573	39448206	151706070	40	47004										
ANKRD56	345079	hgsc.bcm.edu	37	chr4	77817982	77817982	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	aggctccgtggagccgggttCcaagggcagctggaggaagt	18	9	0	0			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr4:77817982C>G	ENST00000334306.2	-	1	1020	c.1021G>C	c.(1021-1023)Gaa>Caa	p.E341Q		NM_001029870.1	NP_001025041.1	A6NEL2	SWAHB_HUMAN	sosondowah ankyrin repeat domain family member B	341																	GAGCCGGGTTCCAAGGGCAGC	0.642																																					p.E341Q		Atlas-SNP	.											.	.	.	.	0			c.G1021C						.						42	52	48					4																	77817982		2203	4300	6503	SO:0001583	missense	345079	exon1			CGGGTTCCAAGGG		CCDS34017.1	4q21.1	2013-01-10	2012-01-12	2012-01-12	ENSG00000186212	ENSG00000186212		"Ankyrin repeat domain containing"	32958	protein-coding gene	gene with protein product			"ankyrin repeat domain 56"	ANKRD56		22234889	Standard	NM_001029870		Approved		uc003hki.3	A6NEL2	OTTHUMG00000160876	ENST00000334306.2:c.1021G>C	chr4.hg19:g.77817982C>G	ENSP00000334879:p.Glu341Gln	95.0	0.0		21.0	8.0	NM_001029870	B2RP29	Missense_Mutation	SNP	ENST00000334306.2	hg19	CCDS34017.1	.	.	.	.	.	.	.	.	.	.	C	15.76	2.929822	0.52759	.	.	ENSG00000186212	ENST00000334306	T	0.07216	3.21	3.83	2.87	0.33458	.	.	.	.	.	T	0.04907	0.0132	L	0.27053	0.805	0.09310	N	1	P	0.37466	0.596	B	0.29267	0.1	T	0.32745	-0.9895	9	0.30078	T	0.28	-3.6903	6.8808	0.24173	0.0:0.7959:0.0:0.2041	.	341	A6NEL2	ANR56_HUMAN	Q	341	ENSP00000334879:E341Q	ENSP00000334879:E341Q	E	-	1	0	ANKRD56	78037006	0.000000	0.05858	0.006000	0.13384	0.008000	0.06430	0.970000	0.29383	1.968000	0.57251	0.491000	0.48974	GAA	.	.		0.642	SOWAHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362762.1	NM_001029870		G	77817982	C	G	77817982	3	3	340	1	0	0	0	0	1	0	0	0	682	864	30	4	1364	4	ANKRD56	4	77817982	Missense_Mutation	SNP	C	TCGA-RC-A7SK-01A-11D-A34Z-10	38369776	77817982	113336294	41	47005										
NAA11	84779	hgsc.bcm.edu	37	chr4	80246710	80246710	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	actcttcctgacgtgcagagAcacgtatttggcgttaaagt	10	9	1	2			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr4:80246710A>G	ENST00000286794.4	-	1	494	c.322T>C	c.(322-324)Tct>Cct	p.S108P	NAA11_ENST00000513733.1_5'Flank	NM_032693.2	NP_116082.1	Q9BSU3	NAA11_HUMAN	N(alpha)-acetyltransferase 11, NatA catalytic subunit	108	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				N-terminal protein amino acid acetylation (GO:0006474)	NatA complex (GO:0031415)|nucleus (GO:0005634)	peptide alpha-N-acetyltransferase activity (GO:0004596)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|pancreas(1)|skin(2)	23						ACGTGCAGAGACACGTATTTG	0.532																																					p.S108P		Atlas-SNP	.											.	NAA11	43	.	0			c.T322C						.						58	62	61					4																	80246710		2109	4244	6353	SO:0001583	missense	84779	exon1			GCAGAGACACGTA		CCDS47084.1	4q21.23	2010-05-07	2010-01-14	2010-01-14		ENSG00000156269	2.3.1.88	"N(alpha)-acetyltransferase subunits"	28125	protein-coding gene	gene with protein product			"ARD1 homolog B (S. cerevisiae)"	ARD1B		16638120, 19660095	Standard	NM_032693		Approved	ARD2, hARD2	uc003hlt.4	Q9BSU3		ENST00000286794.4:c.322T>C	chr4.hg19:g.80246710A>G	ENSP00000286794:p.Ser108Pro	65.0	0.0		23.0	7.0	NM_032693	Q66K19|Q6P479	Missense_Mutation	SNP	ENST00000286794.4	hg19	CCDS47084.1	.	.	.	.	.	.	.	.	.	.	A	17.42	3.386248	0.61956	.	.	ENSG00000156269	ENST00000286794	T	0.35048	1.33	5.17	5.17	0.71159	GCN5-related N-acetyltransferase (GNAT) domain (2);Acyl-CoA N-acyltransferase (2);	0.000000	0.85682	U	0.000000	T	0.71281	0.3321	H	0.97103	3.94	0.80722	D	1	D	0.69078	0.997	D	0.72982	0.979	T	0.81243	-0.1021	9	.	.	.	-16.9732	13.3112	0.60380	1.0:0.0:0.0:0.0	.	108	Q9BSU3	NAA11_HUMAN	P	108	ENSP00000286794:S108P	.	S	-	1	0	NAA11	80465734	1.000000	0.71417	1.000000	0.80357	0.105000	0.19272	8.223000	0.89779	2.308000	0.77769	0.533000	0.62120	TCT	.	.		0.532	NAA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362922.1			G	80246710	A	G	80246710	3	3	340	1	0	0	0	0	1	0	0	0	10126	275	10	2	371	2	NAA11	4	80246710	Missense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	2428728	80246710	110907566	42	47006										
CCRN4L	25819	hgsc.bcm.edu	37	chr4	139965791	139965791	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	ctgactagctttttcttttcAgctcttggagaaggcaaaga	9	8	3	3			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr4:139965791A>T	ENST00000280614.2	+	3	653		c.e3-1		ELF2_ENST00000515489.1_Intron	NM_012118.2	NP_036250.2	Q9UK39	NOCT_HUMAN	CCR4 carbon catabolite repression 4-like (S. cerevisiae)						circadian regulation of gene expression (GO:0032922)|cytoplasmic mRNA processing body assembly (GO:0033962)|deadenylation-dependent decapping of nuclear-transcribed mRNA (GO:0000290)|mRNA processing (GO:0006397)|mRNA stabilization (GO:0048255)|negative regulation of gene expression (GO:0010629)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|regulation of circadian rhythm (GO:0042752)|regulation of embryonic development (GO:0045995)|regulation of transcription, DNA-templated (GO:0006355)|response to extracellular stimulus (GO:0009991)|response to lipopolysaccharide (GO:0032496)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	metal ion binding (GO:0046872)|mRNA binding (GO:0003729)|poly(A)-specific ribonuclease activity (GO:0004535)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(2)|large_intestine(3)|lung(3)|ovary(1)	9	all_hematologic(180;0.162)					TTTTCTTTTCAGCTCTTGGAG	0.458																																					.	Ovarian(144;566 1842 19130 21379 22209)	Atlas-SNP	.											.	CCRN4L	22	.	0			c.461-2A>T						.						44	45	45					4																	139965791		2203	4300	6503	SO:0001630	splice_region_variant	25819	exon3			CTTTTCAGCTCTT	AF183961	CCDS3743.1	4q31.1	2014-06-18	2001-11-28		ENSG00000151014	ENSG00000151014			14254	protein-coding gene	gene with protein product		608468	"CCR4-like (carbon catabolite repression 4, S.cerevisiae)"			10521507	Standard	NM_012118		Approved	CCR4L, Ccr4c	uc003ihl.3	Q9UK39	OTTHUMG00000161271	ENST00000280614.2:c.461-1A>T	chr4.hg19:g.139965791A>T		45.0	0.0		10.0	5.0	NM_012118	D3DNY5|Q14D51|Q9HD93|Q9HD94|Q9HD95	Splice_Site	SNP	ENST00000280614.2	hg19	CCDS3743.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.937617	0.73557	.	.	ENSG00000151014	ENST00000280614	.	.	.	5.14	5.14	0.70334	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.9463	0.71035	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CCRN4L	140185241	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.262000	0.95591	1.938000	0.56188	0.454000	0.30748	.	.	.		0.458	CCRN4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257231.3	NM_012118	Intron	T	139965791	A	T	139965791	5	4	340	1	0	0	0	0	0	0	1	0	2953	202	7	4	469	4	CCRN4L	4	139965791	Splice_Site	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	59719081	139965791	51188485	43	47007										
NAA15	80155	hgsc.bcm.edu	37	chr4	140299908	140299908	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	atcttactttctctttttatAgaaaagtttcttttgatgct	4	6	3	2			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr4:140299908A>G	ENST00000296543.5	+	17	2379		c.e17-1		NAA15_ENST00000398947.1_Splice_Site	NM_057175.3	NP_476516.1	Q9BXJ9	NAA15_HUMAN	N(alpha)-acetyltransferase 15, NatA auxiliary subunit						angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|N-terminal protein amino acid acetylation (GO:0006474)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|NatA complex (GO:0031415)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	N-acetyltransferase activity (GO:0008080)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)			NS(1)|endometrium(3)|large_intestine(7)|liver(2)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						CTCTTTTTATAGAAAAGTTTC	0.348																																					.		Atlas-SNP	.											.	NAA15	88	.	0			c.2057-2A>G						.						121	105	110					4																	140299908		1791	4067	5858	SO:0001630	splice_region_variant	80155	exon17			TTTTATAGAAAAG	AY039242	CCDS43270.1	4q31.1	2010-01-14	2010-01-14	2010-01-14	ENSG00000164134	ENSG00000164134		"N(alpha)-acetyltransferase subunits"	30782	protein-coding gene	gene with protein product		608000	"NMDA receptor regulated 1"	NARG1		12140756, 11478804, 19660095	Standard	XM_005263236		Approved	TBDN100, NATH, FLJ13340	uc003ihu.1	Q9BXJ9	OTTHUMG00000137363	ENST00000296543.5:c.2057-1A>G	chr4.hg19:g.140299908A>G		206.0	0.0		67.0	22.0	NM_057175	D3DNY6|Q52LG9|Q8IWH4|Q8NEV2|Q9H8P6	Splice_Site	SNP	ENST00000296543.5	hg19	CCDS43270.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.222284	0.79464	.	.	ENSG00000164134	ENST00000296543;ENST00000544077;ENST00000398947	.	.	.	5.83	5.83	0.93111	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.2127	0.82178	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NAA15	140519358	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	8.730000	0.91510	2.236000	0.73375	0.533000	0.62120	.	.	.		0.348	NAA15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000267839.2	NM_057175	Intron	G	140299908	A	G	140299908	5	3	340	1	0	0	0	0	0	0	1	0	10127	434	15	2	2121	2	NAA15	4	140299908	Splice_Site	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	334117	140299908	50854368	44	47008										
WDR17	116966	hgsc.bcm.edu	37	chr4	177071048	177071048	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	gtcattaacagccttagtcaCtcctgtacaaataaatattc	4	10	2	0			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr4:177071048C>A	ENST00000280190.4	+	15	2216	c.2060C>A	c.(2059-2061)aCt>aAt	p.T687N	WDR17_ENST00000507824.2_Missense_Mutation_p.T670N|WDR17_ENST00000393643.2_Missense_Mutation_p.T663N|WDR17_ENST00000508596.1_Missense_Mutation_p.T663N			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	687										breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(18)|lung(46)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	92		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)		GCCTTAGTCACTCCTGTACAA	0.408																																					p.T687N		Atlas-SNP	.											.	WDR17	198	.	0			c.C2060A						.						110	113	112					4																	177071048		2203	4300	6503	SO:0001583	missense	116966	exon15			TAGTCACTCCTGT	AF492460	CCDS3825.1, CCDS43284.1, CCDS43284.2	4q34	2013-01-09			ENSG00000150627	ENSG00000150627		"WD repeat domain containing"	16661	protein-coding gene	gene with protein product		609005				12401215	Standard	NM_170710		Approved		uc003iuj.3	Q8IZU2	OTTHUMG00000160791	ENST00000280190.4:c.2060C>A	chr4.hg19:g.177071048C>A	ENSP00000280190:p.Thr687Asn	379.0	0.0		126.0	45.0	NM_170710	E7EQX0|Q0QD35	Missense_Mutation	SNP	ENST00000280190.4	hg19	CCDS3825.1	.	.	.	.	.	.	.	.	.	.	C	11.53	1.667257	0.29604	.	.	ENSG00000150627	ENST00000508596;ENST00000393643;ENST00000280190;ENST00000507824	T;T;T	0.58506	0.36;0.38;0.33	5.38	5.38	0.77491	WD40/YVTN repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.364693	0.27319	N	0.019907	T	0.45915	0.1366	L	0.33485	1.01	0.33193	D	0.551143	B;B	0.12013	0.005;0.005	B;B	0.11329	0.006;0.006	T	0.51756	-0.8665	10	0.21014	T	0.42	-11.1321	13.9314	0.63998	0.1899:0.8101:0.0:0.0	.	663;687	E7EQX0;Q8IZU2	.;WDR17_HUMAN	N	663;663;687;670	ENSP00000422763:T663N;ENSP00000377258:T663N;ENSP00000280190:T687N	ENSP00000280190:T687N	T	+	2	0	WDR17	177308042	0.991000	0.36638	0.988000	0.46212	0.788000	0.44548	4.442000	0.59988	2.505000	0.84491	0.563000	0.77884	ACT	.	.		0.408	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2			A	177071048	C	A	177071048	3	1	340	1	0	0	0	0	1	0	0	0	17292	565	20	3	2114	3	WDR17	4	177071048	Missense_Mutation	SNP	C	TCGA-RC-A7SK-01A-11D-A34Z-10	36771140	177071048	14083228	45	47009										
KIAA0947	23379	hgsc.bcm.edu	37	chr5	5462475	5462475	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	ttccagccacagaagtgactGtgtcaggagggttttctgtt	12	8	2	2			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr5:5462475G>T	ENST00000296564.7	+	13	3250	c.3028G>T	c.(3028-3030)Gtg>Ttg	p.V1010L		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		1010					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						AGAAGTGACTGTGTCAGGAGG	0.547																																					p.V1010L		Atlas-SNP	.											.	KIAA0947	301	.	0			c.G3028T						.						70	73	72					5																	5462475		2012	4195	6207	SO:0001583	missense	23379	exon13			GTGACTGTGTCAG																												ENST00000296564.7:c.3028G>T	chr5.hg19:g.5462475G>T	ENSP00000296564:p.Val1010Leu	71.0	0.0		33.0	13.0	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Missense_Mutation	SNP	ENST00000296564.7	hg19	CCDS47187.1	.	.	.	.	.	.	.	.	.	.	a	1.978	-0.434756	0.04669	.	.	ENSG00000164151	ENST00000296564	T	0.08984	3.03	3.9	-5.33	0.02713	.	2.536700	0.01415	N	0.014178	T	0.02888	0.0086	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32929	-0.9888	10	0.02654	T	1	-0.0224	1.6646	0.02799	0.3694:0.2282:0.2877:0.1147	.	1010	Q9Y2F5	K0947_HUMAN	L	1010	ENSP00000296564:V1010L	ENSP00000296564:V1010L	V	+	1	0	KIAA0947	5515475	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	-0.373000	0.07494	-1.178000	0.02741	-0.871000	0.02989	GTG	.	.		0.547	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1			T	5462475	G	T	5462475	3	4	340	1	0	0	0	0	1	0	0	0	8211	1377	48	3	3078	3	KIAA0947	5	5462475	Missense_Mutation	SNP	G	TCGA-RC-A7SK-01A-11D-A34Z-10		5462475	175452785	46	47010										
ERAP1	51752	hgsc.bcm.edu	37	chr5	96116195	96116195	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	catgtgggctatggaagatgAgccaagttcaaacctagaga	12	7	1	3			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr5:96116195A>G	ENST00000443439.2	-	18	2668	c.2602T>C	c.(2602-2604)Tca>Cca	p.S868P	ERAP1_ENST00000514604.1_5'Flank|ERAP1_ENST00000296754.3_Missense_Mutation_p.S868P	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	868					angiogenesis (GO:0001525)|antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|fat cell differentiation (GO:0045444)|membrane protein ectodomain proteolysis (GO:0006509)|positive regulation of angiogenesis (GO:0045766)|regulation of blood pressure (GO:0008217)|regulation of innate immune response (GO:0045088)|response to bacterium (GO:0009617)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|interleukin-1, Type II receptor binding (GO:0005151)|interleukin-6 receptor binding (GO:0005138)|metalloexopeptidase activity (GO:0008235)|zinc ion binding (GO:0008270)			endometrium(7)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|stomach(2)	19		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)		ATGGAAGATGAGCCAAGTTCA	0.318																																					p.S868P		Atlas-SNP	.											.	ERAP1	59	.	0			c.T2602C						.						74	76	75					5																	96116195		2203	4300	6503	SO:0001583	missense	51752	exon18			AAGATGAGCCAAG	AB011097	CCDS4085.1, CCDS47250.1	5q15	2014-04-07			ENSG00000164307	ENSG00000164307			18173	protein-coding gene	gene with protein product	"aminopeptidase regulator of TNFR1 shedding", "adipocyte-derived leucine aminopeptidase", "puromycin-insensitive leucyl-specific aminopeptidase"	606832				10220586, 12189246, 16286653	Standard	NM_001198541		Approved	ARTS-1, A-LAP, PILS-AP, KIAA0525, ERAAP1	uc003kml.3	Q9NZ08	OTTHUMG00000128721	ENST00000443439.2:c.2602T>C	chr5.hg19:g.96116195A>G	ENSP00000406304:p.Ser868Pro	63.0	0.0		21.0	9.0	NM_001198541	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Missense_Mutation	SNP	ENST00000443439.2	hg19	CCDS47250.1	.	.	.	.	.	.	.	.	.	.	A	15.29	2.789163	0.49997	.	.	ENSG00000164307	ENST00000296754;ENST00000443439;ENST00000414384	T;T	0.07114	3.22;3.22	6.09	6.09	0.99107	.	0.063289	0.64402	D	0.000003	T	0.34454	0.0898	M	0.85197	2.74	0.54753	D	0.999983	B;D;D	0.89917	0.018;0.999;1.0	B;D;D	0.81914	0.315;0.995;0.995	T	0.14392	-1.0474	10	0.87932	D	0	.	16.331	0.83014	1.0:0.0:0.0:0.0	.	868;868;868	A8K6H1;Q9NZ08;Q9NZ08-2	.;ERAP1_HUMAN;.	P	868	ENSP00000296754:S868P;ENSP00000406304:S868P	ENSP00000296754:S868P	S	-	1	0	ERAP1	96141951	1.000000	0.71417	0.996000	0.52242	0.462000	0.32619	6.407000	0.73280	2.338000	0.79540	0.533000	0.62120	TCA	.	.		0.318	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442		G	96116195	A	G	96116195	3	3	340	1	0	0	0	0	1	0	0	0	5205	304	11	2	264	2	ERAP1	5	96116195	Missense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	90653720	96116195	84799065	47	47011										
SEC24A	10802	hgsc.bcm.edu	37	chr5	133997259	133997259	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	tggatatccttcacttcaaaAtagcttcataaagtcaggta	6	8	4	0			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr5:133997259A>G	ENST00000398844.2	+	2	836	c.548A>G	c.(547-549)aAt>aGt	p.N183S	SEC24A_ENST00000322887.4_Missense_Mutation_p.N183S	NM_021982.2	NP_068817.1	O95486	SC24A_HUMAN	SEC24 family member A	183	Pro-rich.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of protein secretion (GO:0050714)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045714)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	36			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TCACTTCAAAATAGCTTCATA	0.323																																					p.N183S		Atlas-SNP	.											.	SEC24A	77	.	0			c.A548G						.						62	57	58					5																	133997259		1848	4091	5939	SO:0001583	missense	10802	exon2			TTCAAAATAGCTT	AJ131244	CCDS43363.1, CCDS58967.1	5q31.1	2013-10-21	2013-10-21		ENSG00000113615	ENSG00000113615			10703	protein-coding gene	gene with protein product		607183	"SEC24 (S. cerevisiae) related gene family, member A", "SEC24 family, member A (S. cerevisiae)"			10075675, 10329445	Standard	NM_021982		Approved		uc003kzs.3	O95486	OTTHUMG00000163064	ENST00000398844.2:c.548A>G	chr5.hg19:g.133997259A>G	ENSP00000381823:p.Asn183Ser	71.0	0.0		52.0	13.0	NM_001252231	A8MVW3|Q8WUV2|Q96GP7	Missense_Mutation	SNP	ENST00000398844.2	hg19	CCDS43363.1	.	.	.	.	.	.	.	.	.	.	A	11.47	1.647317	0.29246	.	.	ENSG00000113615	ENST00000398844;ENST00000322887	D;D	0.96967	-4.19;-4.19	5.55	4.38	0.52667	.	1.361580	0.04318	N	0.350250	D	0.94768	0.8311	L	0.55481	1.735	0.25787	N	0.984663	B	0.26400	0.148	B	0.28385	0.089	T	0.81609	-0.0855	10	0.09338	T	0.73	-2.9968	12.4654	0.55755	0.8549:0.1451:0.0:0.0	.	183	O95486	SC24A_HUMAN	S	183	ENSP00000381823:N183S;ENSP00000321749:N183S	ENSP00000321749:N183S	N	+	2	0	SEC24A	134025158	1.000000	0.71417	1.000000	0.80357	0.482000	0.33219	3.240000	0.51368	0.914000	0.36822	0.533000	0.62120	AAT	.	.		0.323	SEC24A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371563.1			G	133997259	A	G	133997259	3	3	340	1	0	0	0	0	1	0	0	0	14009	101	4	2	554	2	SEC24A	5	133997259	Missense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	37881064	133997259	46918001	48	47012										
SEC24A	10802	hgsc.bcm.edu	37	chr5	134039534	134039535	+	Frame_Shift_Ins	INS	-	-	T													0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	acgtcaacccagacgctgggINStatgcagtacagatgtcagt							TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr5:134039534_134039535insT	ENST00000398844.2	+	16	2640_2641	c.2352_2353insT	c.(2353-2355)tatfs	p.Y785fs	RNU6-1164P_ENST00000364428.1_RNA	NM_021982.2	NP_068817.1	O95486	SC24A_HUMAN	SEC24 family member A	785					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of protein secretion (GO:0050714)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045714)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	36			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CAGACGCTGGGTATGCAGTACA	0.416																																					p.G784fs		Atlas-Indel,Pindel	.											.	SEC24A	77	.	0			c.2352_2353insT						.																																			SO:0001589	frameshift_variant	10802	exon16			.	AJ131244	CCDS43363.1, CCDS58967.1	5q31.1	2013-10-21	2013-10-21		ENSG00000113615	ENSG00000113615			10703	protein-coding gene	gene with protein product		607183	"SEC24 (S. cerevisiae) related gene family, member A", "SEC24 family, member A (S. cerevisiae)"			10075675, 10329445	Standard	NM_021982		Approved		uc003kzs.3	O95486	OTTHUMG00000163064	ENST00000398844.2:c.2353dupT	chr5.hg19:g.134039535_134039535dupT	ENSP00000381823:p.Tyr785fs	259.0	0.0		146.0	59.0	NM_021982	A8MVW3|Q8WUV2|Q96GP7	Frame_Shift_Ins	INS	ENST00000398844.2	hg19	CCDS43363.1																																																																																			.	.		0.416	SEC24A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371563.1			T	134039535	-	T	134039534	7	5	340	1	0	1	1	0	0	0	0	0	14009	1248	44	0	2414	0	SEC24A	5	134039534	Frame_Shift_Ins	INS	-	TCGA-RC-A7SK-01A-11D-A34Z-10	42275	134039534	46875726	49	47013										
PCDHA6	56142	hgsc.bcm.edu	37	chr5	140209555	140209555	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	tcccgtttcgcgtggggctgTacacgggcgagatcagcacc	14	13	1	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr5:140209555T>C	ENST00000529310.1	+	1	1993	c.1879T>C	c.(1879-1881)Tac>Cac	p.Y627H	PCDHA5_ENST00000529859.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018909.2|NM_031848.2|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6	627	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(42)|prostate(8)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	89			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGTGGGGCTGTACACGGGCGA	0.667																																					p.Y627H		Atlas-SNP	.											.	PCDHA6	442	.	0			c.T1879C						.						72	78	76					5																	140209555		2203	4300	6503	SO:0001583	missense	56142	exon1			GGGCTGTACACGG	AF152484	CCDS47281.1, CCDS47282.1	5q31	2010-11-26			ENSG00000081842	ENSG00000081842		"Cadherins / Protocadherins : Clustered"	8672	other	complex locus constituent	"KIAA0345-like 8"	606312		CNRS2		10380929, 10662547	Standard	NM_018909		Approved	CNR2, CRNR2, PCDH-ALPHA6		Q9UN73	OTTHUMG00000163353	ENST00000529310.1:c.1879T>C	chr5.hg19:g.140209555T>C	ENSP00000433378:p.Tyr627His	62.0	0.0		29.0	9.0	NM_018909	O75283|Q9NRT8	Missense_Mutation	SNP	ENST00000529310.1	hg19	CCDS47281.1	.	.	.	.	.	.	.	.	.	.	T	5.432	0.264827	0.10294	.	.	ENSG00000081842	ENST00000529310	T	0.51071	0.72	3.98	2.8	0.32819	Cadherin (4);Cadherin-like (1);	0.000000	0.33610	U	0.004721	T	0.29524	0.0736	L	0.31207	0.915	0.80722	D	1	B;B	0.29612	0.042;0.251	B;B	0.29353	0.036;0.101	T	0.03922	-1.0992	10	0.14656	T	0.56	.	7.1846	0.25793	0.0:0.1789:0.0:0.8211	.	627;627	Q9UN73-3;Q9UN73	.;PCDA6_HUMAN	H	627	ENSP00000433378:Y627H	ENSP00000433378:Y627H	Y	+	1	0	PCDHA6	140189739	0.240000	0.23847	1.000000	0.80357	0.187000	0.23431	0.196000	0.17176	0.692000	0.31613	0.254000	0.18369	TAC	.	.		0.667	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372829.3	NM_018909		C	140209555	T	C	140209555	3	2	340	1	0	0	0	0	1	0	0	0	11537	1638	57	2	1881	2	PCDHA6	5	140209555	Missense_Mutation	SNP	T	TCGA-RC-A7SK-01A-11D-A34Z-10	6170021	140209555	40705705	50	47014										
PCDHA8	56140	hgsc.bcm.edu	37	chr5	140222076	140222076	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	caggtgacctgctccctgatGccccatgtccccttcaagct	8	17	1	2			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr5:140222076G>A	ENST00000531613.1	+	1	1170	c.1170G>A	c.(1168-1170)atG>atA	p.M390I	PCDHA8_ENST00000378123.3_Missense_Mutation_p.M390I|PCDHA5_ENST00000529859.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	390	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(31)|ovary(2)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(6)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCTCCCTGATGCCCCATGTCC	0.562																																					p.M390I		Atlas-SNP	.											.	PCDHA8	366	.	0			c.G1170A						.						180	167	171					5																	140222076		2203	4300	6503	SO:0001583	missense	56140	exon1			CCTGATGCCCCAT	AF152486	CCDS54919.1	5q31	2010-11-26				ENSG00000204962		"Cadherins / Protocadherins : Clustered"	8674	other	complex locus constituent	"KIAA0345-like 6"	606314				10380929	Standard	NM_018911		Approved			Q9Y5H6		ENST00000531613.1:c.1170G>A	chr5.hg19:g.140222076G>A	ENSP00000434655:p.Met390Ile	218.0	0.0		85.0	39.0	NM_031856	B9EGT7|O75281	Missense_Mutation	SNP	ENST00000531613.1	hg19	CCDS54919.1	.	.	.	.	.	.	.	.	.	.	G	9.768	1.172031	0.21704	.	.	ENSG00000204962	ENST00000531613;ENST00000378123	T;T	0.01685	4.69;4.69	3.57	-5.89	0.02282	Cadherin (4);Cadherin-like (1);	1.579270	0.04935	U	0.457653	T	0.00875	0.0029	N	0.02129	-0.67	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.50668	-0.8801	10	0.46703	T	0.11	.	6.6828	0.23129	0.4666:0.0:0.4186:0.1148	.	390;390	Q9Y5H6;Q9Y5H6-2	PCDA8_HUMAN;.	I	390	ENSP00000434655:M390I;ENSP00000367363:M390I	ENSP00000367363:M390I	M	+	3	0	PCDHA8	140202260	0.000000	0.05858	0.000000	0.03702	0.088000	0.18126	-4.392000	0.00241	-1.411000	0.02032	0.306000	0.20318	ATG	.	.		0.562	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911		A	140222076	G	A	140222076	3	1	340	1	0	0	0	0	1	0	0	0	11539	1319	46	3	1172	3	PCDHA8	5	140222076	Missense_Mutation	SNP	G	TCGA-RC-A7SK-01A-11D-A34Z-10	12521	140222076	40693184	51	47015										
RNF145	153830	hgsc.bcm.edu	37	chr5	158588365	158588365	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	tcttattcacagcatccctgCggagaagaaagctcttccac	7	13	3	2			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr5:158588365C>T	ENST00000424310.2	-	10	1894	c.1535G>A	c.(1534-1536)cGc>cAc	p.R512H	RNF145_ENST00000518802.1_Missense_Mutation_p.R542H|RNF145_ENST00000520638.1_Missense_Mutation_p.R526H|RNF145_ENST00000519865.1_Missense_Mutation_p.R512H|RNF145_ENST00000274542.2_Missense_Mutation_p.R540H|RNF145_ENST00000521606.2_Missense_Mutation_p.R529H|RNF145_ENST00000518284.1_5'UTR	NM_001199383.1	NP_001186312.1	Q96MT1	RN145_HUMAN	ring finger protein 145	512						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			AGCATCCCTGCGGAGAAGAAA	0.448																																					p.R542H		Atlas-SNP	.											RNF145,caecum,carcinoma,-1,1	RNF145	110	.	0			c.G1625A						.						46	45	46					5																	158588365		2203	4300	6503	SO:0001583	missense	153830	exon10			TCCCTGCGGAGAA	BC042684	CCDS4344.1, CCDS56390.1, CCDS56391.1, CCDS56392.1, CCDS56393.1	5q33.3	2013-01-09			ENSG00000145860	ENSG00000145860		"RING-type (C3HC4) zinc fingers"	20853	protein-coding gene	gene with protein product							Standard	NM_001199380		Approved	FLJ31951	uc003lxo.2	Q96MT1	OTTHUMG00000130306	ENST00000424310.2:c.1535G>A	chr5.hg19:g.158588365C>T	ENSP00000409064:p.Arg512His	165.0	0.0		70.0	28.0	NM_001199380	B7Z903|B7Z949|E7EVI7|Q8IVP7	Missense_Mutation	SNP	ENST00000424310.2	hg19	CCDS56390.1	.	.	.	.	.	.	.	.	.	.	C	36	5.603213	0.96614	.	.	ENSG00000145860	ENST00000274542;ENST00000519865;ENST00000424310;ENST00000521606;ENST00000413445;ENST00000518802;ENST00000535312;ENST00000520638	D;D;D;D;D;D;D	0.82344	-1.6;-1.58;-1.58;-1.6;-1.6;-1.6;-1.6	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	D	0.91768	0.7396	M	0.79011	2.435	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.998;0.994;0.997;0.994;0.999	D	0.90729	0.4641	10	0.52906	T	0.07	-16.4831	20.6439	0.99570	0.0:1.0:0.0:0.0	.	529;526;542;512;540	B7Z949;B7Z903;E7EVI7;Q96MT1;Q96MT1-2	.;.;.;RN145_HUMAN;.	H	540;512;512;528;529;542;512;526	ENSP00000274542:R540H;ENSP00000430397:R512H;ENSP00000409064:R512H;ENSP00000430753:R528H;ENSP00000445115:R529H;ENSP00000430955:R542H;ENSP00000429071:R526H	ENSP00000274542:R540H	R	-	2	0	RNF145	158520943	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.711000	0.84669	2.890000	0.99128	0.650000	0.86243	CGC	.	.		0.448	RNF145-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374048.1	NM_144726		T	158588365	C	T	158588365	3	4	340	1	0	0	0	0	1	0	0	0	13462	768	27	1	464	1	RNF145	5	158588365	Missense_Mutation	SNP	C	TCGA-RC-A7SK-01A-11D-A34Z-10	18366289	158588365	22326895	52	47016										
ATP10B	23120	hgsc.bcm.edu	37	chr5	159992727	159992727	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	ctggcactgaagtcctgtccTgtgatagatgacactgggtg	13	9	0	4	rs528864040		TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr5:159992727T>C	ENST00000327245.5	-	26	4965	c.4119A>G	c.(4117-4119)acA>acG	p.T1373T		NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	1373					phospholipid translocation (GO:0045332)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1)	75	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			AGTCCTGTCCTGTGATAGATG	0.542													T|||	1	0.000199681	0	0	5008	,	,		15610	0		0	False		,,,				2504	0.001				p.T1373T		Atlas-SNP	.											.	ATP10B	201	.	0			c.A4119G						.						123	133	130					5																	159992727		1984	4168	6152	SO:0001819	synonymous_variant	23120	exon26			CTGTCCTGTGATA	AB018258	CCDS43394.1	5q34	2010-04-20	2007-09-19		ENSG00000118322	ENSG00000118322		"ATPases / P-type"	13543	protein-coding gene	gene with protein product			"ATPase, Class V, type 10B"			9872452, 11015572	Standard	NM_025153		Approved	ATPVB, KIAA0715, FLJ21477	uc003lym.1	O94823	OTTHUMG00000163551	ENST00000327245.5:c.4119A>G	chr5.hg19:g.159992727T>C		83.0	0.0		49.0	20.0	NM_025153	Q9H725	Silent	SNP	ENST00000327245.5	hg19	CCDS43394.1																																																																																			.	.		0.542	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374127.1	NM_025153		C	159992727	T	C	159992727	2	2	340	1	0	0	0	0	0	0	0	1	1117	1567	55	2		2	ATP10B	5	159992727	Silent	SNP	T	TCGA-RC-A7SK-01A-11D-A34Z-10	1404362	159992727	20922533	53	47017										
RGS14	10636	hgsc.bcm.edu	37	chr5	176793252	176793252	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	tcagcatccacagcctccccAgtggtcccagcagccccttc	7	20	1	0			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr5:176793252A>T	ENST00000408923.3	+	3	330	c.142A>T	c.(142-144)Agt>Tgt	p.S48C		NM_006480.4	NP_006471.2	O43566	RGS14_HUMAN	regulator of G-protein signaling 14	48					cell division (GO:0051301)|chromosome segregation (GO:0007059)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mitotic nuclear division (GO:0007067)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of synaptic plasticity (GO:0031914)|nucleocytoplasmic transport (GO:0006913)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of GTPase activity (GO:0043547)|positive regulation of neurogenesis (GO:0050769)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|response to oxidative stress (GO:0006979)|spindle organization (GO:0007051)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual learning (GO:0008542)|zygote asymmetric cell division (GO:0010070)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|microtubule (GO:0005874)|nuclear body (GO:0016604)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|spindle (GO:0005819)|spindle pole (GO:0000922)	GDP-dissociation inhibitor activity (GO:0005092)|GTPase activator activity (GO:0005096)|microtubule binding (GO:0008017)|receptor signaling complex scaffold activity (GO:0030159)|receptor signaling protein activity (GO:0005057)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|skin(3)|upper_aerodigestive_tract(1)	12	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CAGCCTCCCCAGTGGTCCCAG	0.692																																					p.S48C	NSCLC(47;353 1896 28036)	Atlas-SNP	.											.	RGS14	34	.	0			c.A142T						.						11	18	16					5																	176793252		1959	4141	6100	SO:0001583	missense	10636	exon3			CTCCCCAGTGGTC	AF037195	CCDS43405.1	5q35.3	2008-02-05	2007-08-14		ENSG00000169220	ENSG00000169220		"Regulators of G-protein signaling"	9996	protein-coding gene	gene with protein product		602513	"regulator of G-protein signalling 14"				Standard	NM_006480		Approved		uc003mgf.3	O43566	OTTHUMG00000163324	ENST00000408923.3:c.142A>T	chr5.hg19:g.176793252A>T	ENSP00000386229:p.Ser48Cys	67.0	0.0		41.0	10.0	NM_006480	O43565|Q506M1|Q6ZWA4|Q8TD62	Missense_Mutation	SNP	ENST00000408923.3	hg19	CCDS43405.1	.	.	.	.	.	.	.	.	.	.	A	18.34	3.601775	0.66445	.	.	ENSG00000169220	ENST00000408923;ENST00000336477	T	0.42900	0.96	4.44	3.18	0.36537	.	0.137147	0.50627	D	0.000103	T	0.39600	0.1084	L	0.57536	1.79	0.35940	D	0.833173	P	0.43885	0.82	B	0.44163	0.443	T	0.53892	-0.8374	10	0.72032	D	0.01	-7.7575	6.5417	0.22385	0.6343:0.2816:0.0841:0.0	.	48	O43566	RGS14_HUMAN	C	48	ENSP00000386229:S48C	ENSP00000336864:S48C	S	+	1	0	RGS14	176725858	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	2.821000	0.48065	1.645000	0.50612	0.363000	0.22086	AGT	.	.		0.692	RGS14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372676.1	NM_006480		T	176793252	A	T	176793252	3	4	340	1	0	0	0	0	1	0	0	0	13312	188	7	4	152	4	RGS14	5	176793252	Missense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	16800525	176793252	4122008	54	47018										
FLT4	2324	hgsc.bcm.edu	37	chr5	180048202	180048202	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	catctccagcgagtcgctcaCgttcaccaggaggtcggtca	11	14	4	0			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr5:180048202C>T	ENST00000261937.6	-	14	2149	c.2071G>A	c.(2071-2073)Gtg>Atg	p.V691M	FLT4_ENST00000393347.3_Missense_Mutation_p.V691M|FLT4_ENST00000502649.1_Missense_Mutation_p.V691M|FLT4_ENST00000424276.2_5'UTR	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	691	Ig-like C2-type 7.				blood vessel morphogenesis (GO:0048514)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|lymph vessel development (GO:0001945)|lymphangiogenesis (GO:0001946)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein autophosphorylation (GO:0046777)|regulation of blood vessel remodeling (GO:0060312)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(6)|large_intestine(5)|liver(2)|lung(37)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	GAGTCGCTCACGTTCACCAGG	0.627																																					p.V691M	Colon(97;1075 1466 27033 27547 35871)	Atlas-SNP	.											.	FLT4	356	.	0			c.G2071A						.						32	34	33					5																	180048202		2203	4298	6501	SO:0001583	missense	2324	exon14			CGCTCACGTTCAC	X68203	CCDS4457.1, CCDS43412.1	5q34-q35	2013-01-29			ENSG00000037280	ENSG00000037280	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3767	protein-coding gene	gene with protein product		136352				1319394	Standard	NM_002020		Approved	VEGFR3, PCL	uc003mlz.4	P35916	OTTHUMG00000130931	ENST00000261937.6:c.2071G>A	chr5.hg19:g.180048202C>T	ENSP00000261937:p.Val691Met	131.0	0.0		56.0	25.0	NM_182925	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Missense_Mutation	SNP	ENST00000261937.6	hg19	CCDS4457.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.397803	0.83120	.	.	ENSG00000037280	ENST00000261937;ENST00000393347;ENST00000502649;ENST00000376868	D;D;D	0.82803	-1.65;-1.65;-1.65	4.53	3.64	0.41730	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.89856	0.6836	M	0.79926	2.475	0.58432	D	0.999991	D;D;D;P	0.89917	1.0;0.984;0.972;0.946	D;P;P;P	0.75020	0.985;0.908;0.764;0.703	D	0.90474	0.4455	9	0.72032	D	0.01	.	11.2555	0.49052	0.0:0.8499:0.0:0.1501	.	691;501;691;691	P35916-3;E9PFB0;E9PD35;P35916	.;.;.;VGFR3_HUMAN	M	691;691;691;501	ENSP00000261937:V691M;ENSP00000377016:V691M;ENSP00000426057:V691M	ENSP00000261937:V691M	V	-	1	0	FLT4	179980808	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.941000	0.49011	2.249000	0.74217	0.561000	0.74099	GTG	.	.		0.627	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4			T	180048202	C	T	180048202	3	4	340	1	0	0	0	0	1	0	0	0	5952	536	19	1	2096	1	FLT4	5	180048202	Missense_Mutation	SNP	C	TCGA-RC-A7SK-01A-11D-A34Z-10	3254950	180048202	867058	55	47019										
DCDC2	51473	hgsc.bcm.edu	37	chr6	24205315	24205315	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	cagacctctctgctccagctTtgaaaatgccttcatctatt	5	13	3	2			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr6:24205315T>G	ENST00000378454.3	-	8	1239	c.938A>C	c.(937-939)aAa>aCa	p.K313T	DCDC2_ENST00000378450.3_Missense_Mutation_p.K66T	NM_001195610.1|NM_016356.3	NP_001182539.1|NP_057440.2	Q9UHG0	DCDC2_HUMAN	doublecortin domain containing 2	313					cellular defense response (GO:0006968)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|neuron migration (GO:0001764)|visual learning (GO:0008542)					breast(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32		Ovarian(999;0.101)				TGCTCCAGCTTTGAAAATGCC	0.433																																					p.K313T		Atlas-SNP	.											.	DCDC2	53	.	0			c.A938C						.						207	198	201					6																	24205315		2203	4299	6502	SO:0001583	missense	51473	exon9			CCAGCTTTGAAAA	AB032980	CCDS4550.1	6p22.1	2008-02-05			ENSG00000146038	ENSG00000146038			18141	protein-coding gene	gene with protein product		605755				10601354, 10574461	Standard	NM_001195610		Approved	RU2, KIAA1154, DCDC2A	uc003ndx.3	Q9UHG0	OTTHUMG00000016275	ENST00000378454.3:c.938A>C	chr6.hg19:g.24205315T>G	ENSP00000367715:p.Lys313Thr	207.0	0.0		131.0	16.0	NM_001195610	Q5VTR8|Q5VTR9|Q86W35|Q9UFD1|Q9UHG1|Q9ULR6	Missense_Mutation	SNP	ENST00000378454.3	hg19	CCDS4550.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.392928	0.83011	.	.	ENSG00000146038	ENST00000378454;ENST00000378450	T;T	0.59364	4.18;0.27	6.07	6.07	0.98685	.	0.170523	0.51477	D	0.000083	T	0.71151	0.3306	M	0.78049	2.395	0.42088	D	0.991287	P;D	0.71674	0.891;0.998	B;D	0.68039	0.439;0.955	T	0.76063	-0.3096	10	0.87932	D	0	-0.4623	16.3141	0.82909	0.0:0.0:0.0:1.0	.	313;66	Q9UHG0;Q9UHG0-2	DCDC2_HUMAN;.	T	313;66	ENSP00000367715:K313T;ENSP00000367711:K66T	ENSP00000367711:K66T	K	-	2	0	DCDC2	24313294	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.679000	0.54634	2.326000	0.78906	0.533000	0.62120	AAA	.	.		0.433	DCDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043604.1	NM_016356		G	24205315	T	G	24205315	3	3	340	1	0	0	0	0	1	0	0	0	4287	1841	64	5	504	5	DCDC2	6	24205315	Missense_Mutation	SNP	T	TCGA-RC-A7SK-01A-11D-A34Z-10		24205315	146909752	56	47020										
ZKSCAN4	387032	hgsc.bcm.edu	37	chr6	28217606	28217606	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	ttcttgcccctggtcaccaaCgggaacctagaagtcacgat	9	13	3	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr6:28217606C>G	ENST00000377294.2	-	2	673	c.430G>C	c.(430-432)Gtt>Ctt	p.V144L	ZKSCAN4_ENST00000423974.2_5'UTR	NM_019110.3	NP_061983.2	Q969J2	ZKSC4_HUMAN	zinc finger with KRAB and SCAN domains 4	144					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|large_intestine(2)|lung(10)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						TGGTCACCAACGGGAACCTAG	0.438																																					p.V144L		Atlas-SNP	.											.	ZKSCAN4	42	.	0			c.G430C						.						211	195	200					6																	28217606		2203	4300	6503	SO:0001583	missense	387032	exon2			CACCAACGGGAAC	AK056698	CCDS4647.1	6p21	2013-01-09	2007-02-20	2007-02-20	ENSG00000187626	ENSG00000187626		"Zinc fingers, C2H2-type", "-", "-", "-"	13854	protein-coding gene	gene with protein product		611643	"zinc finger protein 307", "zinc finger protein 427"	ZNF307, ZNF427		12477932	Standard	NM_019110		Approved	p373c6.1, P1P373C6, FLJ32136, ZSCAN36	uc003nks.1	Q969J2	OTTHUMG00000014511	ENST00000377294.2:c.430G>C	chr6.hg19:g.28217606C>G	ENSP00000366509:p.Val144Leu	81.0	0.0		44.0	9.0	NM_019110	B2RE32|Q5U7L4	Missense_Mutation	SNP	ENST00000377294.2	hg19	CCDS4647.1	.	.	.	.	.	.	.	.	.	.	C	0.719	-0.784323	0.02907	.	.	ENSG00000187626	ENST00000377294	T	0.05447	3.44	4.29	1.02	0.19986	Transcription regulator SCAN (1);	.	.	.	.	T	0.00875	0.0029	N	0.08118	0	0.09310	N	0.999998	B	0.19073	0.033	B	0.17722	0.019	T	0.47983	-0.9074	9	0.36615	T	0.2	.	3.063	0.06205	0.2038:0.5124:0.0:0.2837	.	144	Q969J2	ZKSC4_HUMAN	L	144	ENSP00000366509:V144L	ENSP00000366509:V144L	V	-	1	0	ZKSCAN4	28325585	0.027000	0.19231	0.002000	0.10522	0.029000	0.11900	0.216000	0.17585	0.042000	0.15717	-0.182000	0.12963	GTT	.	.		0.438	ZKSCAN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040179.1	NM_019110		G	28217606	C	G	28217606	3	3	340	1	0	0	0	0	1	0	0	0	17704	536	19	4	1223	4	ZKSCAN4	6	28217606	Missense_Mutation	SNP	C	TCGA-RC-A7SK-01A-11D-A34Z-10	4012291	28217606	142897461	57	47021										
OR5V1	81696	hgsc.bcm.edu	37	chr6	29323799	29323799	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	ttccctagaaaataatacatAggtgtatgcaggtgtggatc	10	6	0	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr6:29323799A>T	ENST00000377154.1	-	4	473	c.174T>A	c.(172-174)ccT>ccA	p.P58P	OR5V1_ENST00000543825.1_Silent_p.P58P			Q9UGF6	OR5V1_HUMAN	olfactory receptor, family 5, subfamily V, member 1	58						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(3)|large_intestine(3)|liver(1)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						AATAATACATAGGTGTATGCA	0.393																																					p.P58P	Ovarian(32;43 883 21137 32120 42650)	Atlas-SNP	.											.	OR5V1	63	.	0			c.T174A						.						153	150	151					6																	29323799		2203	4300	6503	SO:0001819	synonymous_variant	81696	exon1			ATACATAGGTGTA		CCDS4657.1	6p22.1	2013-09-23				ENSG00000243729		"GPCR / Class A : Olfactory receptors"	13972	protein-coding gene	gene with protein product							Standard	NM_030876		Approved	hs6M1-21	uc011dlo.2	Q9UGF6		ENST00000377154.1:c.174T>A	chr6.hg19:g.29323799A>T		116.0	0.0		58.0	18.0	NM_030876	A2BDZ0|B0S860|Q5SQI9|Q6NTB5|Q8IVL3	Silent	SNP	ENST00000377154.1	hg19	CCDS4657.1																																																																																			.	.		0.393	OR5V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076398.3			T	29323799	A	T	29323799	2	4	340	1	0	0	0	0	0	0	0	1	11193	407	15	4		4	OR5V1	6	29323799	Silent	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	1106193	29323799	141791268	58	47022										
OR2H1	26716	hgsc.bcm.edu	37	chr6	29430101	29430101	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	gtcccatctctgattcgactCtcctgtggagatacctccta	7	14	2	2			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr6:29430101C>A	ENST00000377136.1	+	4	1020	c.555C>A	c.(553-555)ctC>ctA	p.L185L	OR2H1_ENST00000473369.1_3'UTR|OR2H1_ENST00000442615.1_Silent_p.L185L|OR2H1_ENST00000396792.2_Silent_p.L185L|OR2H1_ENST00000377132.1_Silent_p.L185L|OR2H1_ENST00000377133.1_Silent_p.L185L			Q9GZK4	OR2H1_HUMAN	olfactory receptor, family 2, subfamily H, member 1	185						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(5)|lung(12)	17						TGATTCGACTCTCCTGTGGAG	0.502																																					p.L185L		Atlas-SNP	.											.	OR2H1	38	.	0			c.C555A						.						189	194	192					6																	29430101		1511	2709	4220	SO:0001819	synonymous_variant	26716	exon3			TCGACTCTCCTGT	AF044491	CCDS4660.1	6p22.1	2014-02-19	2002-02-28		ENSG00000204688	ENSG00000204688		"GPCR / Class A : Olfactory receptors"	8252	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily H, member 8"	OR2H6, OR2H8			Standard	NM_030883		Approved	OR6-2	uc003nmi.3	Q9GZK4	OTTHUMG00000031050	ENST00000377136.1:c.555C>A	chr6.hg19:g.29430101C>A		152.0	0.0		80.0	15.0	NM_030883	B0S7T4|O43629|O43661|O43662|Q5SUN6|Q9GZK9	Silent	SNP	ENST00000377136.1	hg19	CCDS4660.1																																																																																			.	.		0.502	OR2H1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194014.3			A	29430101	C	A	29430101	2	1	340	1	0	0	0	0	0	0	0	1	11010	900	32	3		3	OR2H1	6	29430101	Silent	SNP	C	TCGA-RC-A7SK-01A-11D-A34Z-10	106302	29430101	141684966	59	47023										
NRM	11270	hgsc.bcm.edu	37	chr6	30657906	30657906	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	atgtccatgccttcactcttTcagctgccatgaggctgtgc	9	13	3	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr6:30657906T>G	ENST00000259953.4	-	3	599	c.248A>C	c.(247-249)gAa>gCa	p.E83A	NRM_ENST00000376421.5_Missense_Mutation_p.E83A|PPP1R18_ENST00000274853.3_5'Flank|PPP1R18_ENST00000399199.3_5'Flank|NRM_ENST00000376420.5_Missense_Mutation_p.E83A|PPP1R18_ENST00000488324.1_5'Flank|NRM_ENST00000470733.1_5'UTR	NM_007243.2	NP_009174.1	Q8IXM6	NRM_HUMAN	nurim (nuclear envelope membrane protein)	83						integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)				large_intestine(1)|lung(2)	3						CTTCACTCTTTCAGCTGCCAT	0.607																																					p.E83A		Atlas-SNP	.											.	NRM	7	.	0			c.A248C						.						107	101	103					6																	30657906		1510	2708	4218	SO:0001583	missense	11270	exon2			ACTCTTTCAGCTG	AF143676	CCDS4686.1, CCDS59498.1	6p21.3	2010-02-17			ENSG00000137404	ENSG00000137404			8003	protein-coding gene	gene with protein product						10402458, 17517639	Standard	NM_007243		Approved	NRM29	uc031sng.1	Q8IXM6	OTTHUMG00000031223	ENST00000259953.4:c.248A>C	chr6.hg19:g.30657906T>G	ENSP00000259953:p.Glu83Ala	120.0	0.0		61.0	15.0	NM_001270709	B0S7R0|B0S7R1|I3XIE2|I3XIE3|Q5JP57|Q5JP58|Q5JP59|Q5JP60|Q8WU45|Q9BSX3|Q9UN92	Missense_Mutation	SNP	ENST00000259953.4	hg19	CCDS4686.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.06|14.06	2.422431|2.422431	0.43020|0.43020	.|.	.|.	ENSG00000137404|ENSG00000137404	ENST00000259953;ENST00000376420;ENST00000376421|ENST00000444096	T;T|.	0.30448|.	1.53;1.53|.	4.6|4.6	4.6|4.6	0.57074|0.57074	.|.	0.328653|.	0.29253|.	N|.	0.012684|.	T|.	0.07638|.	0.0192|.	N|N	0.05351|0.05351	-0.065|-0.065	0.09310|0.09310	N|N	1|1	B|.	0.21688|.	0.059|.	B|.	0.22386|.	0.039|.	T|.	0.20605|.	-1.0270|.	10|.	0.09590|.	T|.	0.72|.	-3.6807|-3.6807	8.3286|8.3286	0.32173|0.32173	0.0:0.0:0.2:0.8|0.0:0.0:0.2:0.8	.|.	83|.	Q8IXM6|.	NRM_HUMAN|.	A|C	83|82	ENSP00000259953:E83A;ENSP00000365603:E83A|.	ENSP00000259953:E83A|.	E|X	-|-	2|3	0|0	NRM|NRM	30765885|30765885	0.071000|0.071000	0.21146|0.21146	0.587000|0.587000	0.28692|0.28692	0.543000|0.543000	0.35085|0.35085	1.412000|1.412000	0.34714|0.34714	1.928000|1.928000	0.55862|0.55862	0.379000|0.379000	0.24179|0.24179	GAA|TGA	.	.		0.607	NRM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076466.2			G	30657906	T	G	30657906	3	3	340	1	0	0	0	0	1	0	0	0	10666	1783	62	5	552	5	NRM	6	30657906	Missense_Mutation	SNP	T	TCGA-RC-A7SK-01A-11D-A34Z-10	1227805	30657906	140457161	60	47024										
TNXB	7148	hgsc.bcm.edu	37	chr6	32012931	32012931	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	aaggcctggggctgcccgttCgtgtcctcatactggaccac	12	14	1	0	rs545042173		TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr6:32012931C>A	ENST00000375244.3	-	32	10980	c.10779G>T	c.(10777-10779)acG>acT	p.T3593T	TNXB_ENST00000375247.2_Silent_p.T3591T|TNXB_ENST00000451343.1_Silent_p.T22T			P22105	TENX_HUMAN	tenascin XB	3638					actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						GCTGCCCGTTCGTGTCCTCAT	0.637																																					p.T3591T		Atlas-SNP	.											TNXB_ENST00000375247,right_upper_lobe,carcinoma,0,3	TNXB	553	.	0			c.G10773T						.						62	54	57					6																	32012931		1507	2706	4213	SO:0001819	synonymous_variant	7148	exon32			CCCGTTCGTGTCC	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.10779G>T	chr6.hg19:g.32012931C>A		402.0	0.0		255.0	13.0	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Silent	SNP	ENST00000375244.3	hg19																																																																																				.	.		0.637	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		A	32012931	C	A	32012931	2	1	340	1	0	0	0	0	0	0	0	1	16361	871	31	1		1	TNXB	6	32012931	Silent	SNP	C	TCGA-RC-A7SK-01A-11D-A34Z-10	1355025	32012931	139102136	61	47025										
LMBRD1	55788	hgsc.bcm.edu	37	chr6	70408942	70408944	+	In_Frame_Del	DEL	AAG	AAG	-													0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	atatttcacttacctctattAagtaattttggcttccatac							TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr6:70408942_70408944delAAG	ENST00000370577.3	-	13	1558_1560	c.1329_1331delCTT	c.(1327-1332)tactta>taa	p.443_444YL>*	LMBRD1_ENST00000370570.1_In_Frame_Del_p.370_371YL>*	NM_018368.3	NP_060838.3	Q9NUN5	LMBD1_HUMAN	LMBR1 domain containing 1	443					cobalamin metabolic process (GO:0009235)|insulin receptor internalization (GO:0038016)|negative regulation of glucose import (GO:0046325)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein kinase B signaling (GO:0051898)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	clathrin-coated endocytic vesicle (GO:0045334)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cobalamin binding (GO:0031419)	p.Y443*(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)	31						TACCTCTATTAAGTAATTTTGGC	0.281																																					p.444_444del		Atlas-Indel,Pindel	.											.	LMBRD1	61	.	1	Substitution - Nonsense(1)	endometrium(1)	c.1330_1332del						.																																			SO:0001651	inframe_deletion	55788	exon13			.	AF113224	CCDS4969.1	6q13	2011-05-12	2005-07-25	2005-07-25	ENSG00000168216	ENSG00000168216			23038	protein-coding gene	gene with protein product		612625	"chromosome 6 open reading frame 209"	C6orf209		19136951	Standard	NM_018368		Approved	FLJ11240, bA810I22.1, cblF	uc003pfa.3	Q9NUN5	OTTHUMG00000014985	ENST00000370577.3:c.1329_1331delCTT	chr6.hg19:g.70408942_70408944delAAG	ENSP00000359609:p.Tyr443_Leu444delins*	46.0	0.0		45.0	14.0	NM_018368	A8K204|E1P531|Q5VUN6|Q86Y70|Q96FW4|Q9BY56|Q9NZD6	In_Frame_Del	DEL	ENST00000370577.3	hg19	CCDS4969.1																																																																																			.	.		0.281	LMBRD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041124.1	NM_018368		-	70408944	AAG	-	70408942	7	5	340	1	0	1	0	1	0	0	0	0	8851	372	13	0	307	0	LMBRD1	6	70408942	In_Frame_Del	DEL	AAG	TCGA-RC-A7SK-01A-11D-A34Z-10	38396011	70408942	100706125	62	47026										
OSTM1	28962	hgsc.bcm.edu	37	chr6	108372287	108372287	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	caggttcagccttattctcaAgttcattcattttttgcatt	5	9	4	0			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr6:108372287A>G	ENST00000193322.3	-	4	816	c.731T>C	c.(730-732)cTt>cCt	p.L244P		NM_014028.3	NP_054747.2	Q86WC4	OSTM1_HUMAN	osteopetrosis associated transmembrane protein 1	244					ion transmembrane transport (GO:0034220)|osteoclast differentiation (GO:0030316)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)				central_nervous_system(2)|endometrium(1)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	8		all_cancers(87;3.82e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000195)|Colorectal(196;0.0293)|all_lung(197;0.0938)		BRCA - Breast invasive adenocarcinoma(108;0.0131)|Epithelial(106;0.0438)|OV - Ovarian serous cystadenocarcinoma(136;0.0571)|all cancers(137;0.0581)		CTTATTCTCAAGTTCATTCAT	0.338																																					p.L244P	Melanoma(162;1427 1909 3096 17430 21396)	Atlas-SNP	.											.	OSTM1	22	.	0			c.T731C						.						212	186	195					6																	108372287		2203	4300	6503	SO:0001583	missense	28962	exon4			TTCTCAAGTTCAT	AF533891	CCDS5062.1	6q21	2014-06-17			ENSG00000081087	ENSG00000081087			21652	protein-coding gene	gene with protein product	"CLCN7 accessory beta subunit"	607649				12627228, 21527911	Standard	NM_014028		Approved	HSPC019, GL	uc003psd.3	Q86WC4	OTTHUMG00000015317	ENST00000193322.3:c.731T>C	chr6.hg19:g.108372287A>G	ENSP00000193322:p.Leu244Pro	264.0	0.0		103.0	14.0	NM_014028	E1P5E3|Q5R391|Q6PCA7|Q7RTW6|Q8NC29|Q8TC82|Q9Y2S9	Missense_Mutation	SNP	ENST00000193322.3	hg19	CCDS5062.1	.	.	.	.	.	.	.	.	.	.	a	16.32	3.090238	0.55968	.	.	ENSG00000081087	ENST00000193322;ENST00000440575	T	0.46063	0.88	5.79	-6.46	0.01908	.	0.795303	0.11237	N	0.585048	T	0.20047	0.0482	L	0.51422	1.61	0.20764	N	0.999856	P	0.52577	0.954	P	0.48952	0.596	T	0.19321	-1.0309	10	0.40728	T	0.16	-6.5411	6.8972	0.24262	0.2689:0.3795:0.0:0.3515	.	244	Q86WC4	OSTM1_HUMAN	P	244;97	ENSP00000193322:L244P	ENSP00000193322:L244P	L	-	2	0	OSTM1	108478980	0.001000	0.12720	0.152000	0.22495	0.998000	0.95712	-0.957000	0.03861	-0.462000	0.06984	0.533000	0.62120	CTT	.	.		0.338	OSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041709.3	NM_014028		G	108372287	A	G	108372287	3	3	340	1	0	0	0	0	1	0	0	0	11307	72	3	2	285	2	OSTM1	6	108372287	Missense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	37963345	108372287	62742780	63	47027										
TAAR5	9038	hgsc.bcm.edu	37	chr6	132910065	132910065	+	Frame_Shift_Del	DEL	A	A	-													0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	atatgcccacagcaatgcccAgggtcttggcagcttttctc					rs138145315		TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr6:132910065delA	ENST00000258034.2	-	1	812	c.761delT	c.(760-762)ctgfs	p.L254fs		NM_003967.2	NP_003958.2	O14804	TAAR5_HUMAN	trace amine associated receptor 5	254					G-protein coupled receptor signaling pathway (GO:0007186)|sensory perception of chemical stimulus (GO:0007606)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|trimethylamine receptor activity (GO:1990081)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	32	Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.00604)|GBM - Glioblastoma multiforme(226;0.015)		AGCAATGCCCAGGGTCTTGGC	0.527																																					p.L254fs		Atlas-INDEL	.											.	TAAR5	53	.	0			c.762delG						.						64	65	65					6																	132910065		2203	4300	6503	SO:0001589	frameshift_variant	9038	exon1			.	AF021818	CCDS5156.1	6q23.2	2012-08-08			ENSG00000135569	ENSG00000135569		"GPCR / Class A : Trace amine associated receptors"	30236	protein-coding gene	gene with protein product		607405				9464258, 15718104	Standard	NM_003967		Approved	PNR	uc003qdk.2	O14804	OTTHUMG00000015581	ENST00000258034.2:c.761delT	chr6.hg19:g.132910065delA	ENSP00000258034:p.Leu254fs	60.0	0.0		34.0	12.0	NM_003967	D8KZS1|Q2M1V1|Q4VBL1|Q5VUQ3|Q6NTA8	Frame_Shift_Del	DEL	ENST00000258034.2	hg19	CCDS5156.1																																																																																			.	.		0.527	TAAR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042257.1	NM_003967		-	132910065	A	-	132910065	7	5	340	1	0	1	0	1	0	0	0	0	15506	188	7	0	256	0	TAAR5	6	132910065	Frame_Shift_Del	DEL	A	TCGA-RC-A7SK-01A-11D-A34Z-10	24537778	132910065	38205002	64	47028										
KIF25	3834	hgsc.bcm.edu	37	chr6	168445527	168445527	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	gaggcgatgcgaagttactgGtgattctctgcatttctccc	11	10	2	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr6:168445527G>T	ENST00000443060.2	+	10	1397	c.1006G>T	c.(1006-1008)Gtg>Ttg	p.V336L	KIF25_ENST00000351261.3_Missense_Mutation_p.V284L|KIF25_ENST00000354419.2_Missense_Mutation_p.V336L			Q9UIL4	KIF25_HUMAN	kinesin family member 25	336	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of autophagy (GO:0010507)|organelle organization (GO:0006996)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	29		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)		GAAGTTACTGGTGATTCTCTG	0.562																																					p.V336L		Atlas-SNP	.											.	KIF25	75	.	0			c.G1006T						.						124	134	131					6																	168445527		2203	4300	6503	SO:0001583	missense	3834	exon9			TTACTGGTGATTC	AB012722	CCDS5305.1, CCDS43530.1	6q27	2008-02-05	2003-01-09	2003-01-10	ENSG00000125337	ENSG00000125337		"Kinesins"	6390	protein-coding gene	gene with protein product		603815	"kinesin-like 3"	KNSL3		9925910	Standard	NM_030615		Approved		uc003qwk.1	Q9UIL4	OTTHUMG00000016035	ENST00000443060.2:c.1006G>T	chr6.hg19:g.168445527G>T	ENSP00000388878:p.Val336Leu	69.0	0.0		27.0	13.0	NM_030615	O94775|Q5SZU9	Missense_Mutation	SNP	ENST00000443060.2	hg19	CCDS5305.1	.	.	.	.	.	.	.	.	.	.	G	7.299	0.612739	0.14066	.	.	ENSG00000125337	ENST00000443060;ENST00000354419;ENST00000351261	T;T;T	0.69175	-0.38;-0.38;1.14	4.12	3.24	0.37175	Kinesin, motor domain (3);	0.221217	0.31495	N	0.007550	T	0.25195	0.0612	N	0.12920	0.275	0.27757	N	0.943963	P;B	0.40638	0.725;0.043	B;B	0.36666	0.23;0.105	T	0.07751	-1.0756	10	0.72032	D	0.01	-18.3591	5.641	0.17565	0.1136:0.202:0.6844:0.0	.	284;336	Q9UIL4-2;Q9UIL4	.;KIF25_HUMAN	L	336;336;284	ENSP00000388878:V336L;ENSP00000346401:V336L;ENSP00000252688:V284L	ENSP00000252688:V284L	V	+	1	0	KIF25	168188376	1.000000	0.71417	0.128000	0.21923	0.087000	0.18053	2.977000	0.49297	0.692000	0.31613	0.609000	0.83330	GTG	.	.		0.562	KIF25-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362509.1			T	168445527	G	T	168445527	3	4	340	1	0	0	0	0	1	0	0	0	8302	1261	44	3	1036	3	KIF25	6	168445527	Missense_Mutation	SNP	G	TCGA-RC-A7SK-01A-11D-A34Z-10	35535462	168445527	2669540	65	47029										
AHR	196	hgsc.bcm.edu	37	chr7	17382597	17382597	+	Missense_Mutation	SNP	A	A	C													0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	agctgaattaaataacataaAtaacactcagactaccacac							TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr7:17382597A>C	ENST00000242057.4	+	11	3099	c.2456A>C	c.(2455-2457)aAt>aCt	p.N819T		NM_001621.4	NP_001612.1	P35869	AHR_HUMAN	aryl hydrocarbon receptor	819				LNETYPAELNNINNTQTTTHLQPLHHPSEARPFPDLTSSGF L -> FK (in Ref. 1; BAA03857). {ECO:0000305}.	apoptotic process (GO:0006915)|blood vessel development (GO:0001568)|cell cycle (GO:0007049)|circadian regulation of gene expression (GO:0032922)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|regulation of B cell proliferation (GO:0030888)|regulation of gene expression (GO:0010468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to toxic substance (GO:0009636)|response to xenobiotic stimulus (GO:0009410)|transcription from RNA polymerase II promoter (GO:0006366)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosolic aryl hydrocarbon receptor complex (GO:0034752)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|Hsp90 protein binding (GO:0051879)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(11)|ovary(1)|pancreas(1)|urinary_tract(3)	33	Lung NSC(10;0.0392)|all_lung(11;0.0754)				Atorvastatin(DB01076)|Flutamide(DB00499)|Ginseng(DB01404)|Leflunomide(DB01097)|Mexiletine(DB00379)|Nimodipine(DB00393)	AATAACATAAATAACACTCAG	0.373																																					p.N819T		Atlas-SNP	.											.	AHR	89	.	0			c.A2456C						.						176	168	171					7																	17382597		2203	4300	6503	SO:0001583	missense	196	exon11			ACATAAATAACAC	L19872	CCDS5366.1	7p15	2013-05-21			ENSG00000106546	ENSG00000106546		"Basic helix-loop-helix proteins"	348	protein-coding gene	gene with protein product		600253				8125016	Standard	NM_001621		Approved	bHLHe76	uc011jxz.1	P35869	OTTHUMG00000149967	ENST00000242057.4:c.2456A>C	chr7.hg19:g.17382597A>C	ENSP00000242057:p.Asn819Thr	168.0	0.0		91.0	25.0	NM_001621	A4D130|Q13728|Q13803|Q13804	Missense_Mutation	SNP	ENST00000242057.4	hg19	CCDS5366.1	.	.	.	.	.	.	.	.	.	.	A	8.702	0.909958	0.17833	.	.	ENSG00000106546	ENST00000242057	T	0.46451	0.87	5.35	-6.25	0.02039	.	0.673664	0.15455	N	0.261409	T	0.36413	0.0966	L	0.59436	1.845	0.09310	N	1	B	0.34181	0.44	B	0.30646	0.118	T	0.18999	-1.0319	10	0.59425	D	0.04	.	19.0415	0.93002	0.2359:0.0:0.7641:0.0	.	819	P35869	AHR_HUMAN	T	819	ENSP00000242057:N819T	ENSP00000242057:N819T	N	+	2	0	AHR	17349122	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-0.874000	0.04210	-1.090000	0.03069	0.533000	0.62120	AAT	.	.		0.373	AHR-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314620.2	NM_001621		C	17382597	A	C	17382597	3	2	340	1	0	0	0	0	1	0	0	0	416	101	4	5	2498	5	AHR	7	17382597	Missense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10		17382597	141756066	66	47030	252	3								
AHR	196	hgsc.bcm.edu	37	chr7	17382606	17382606	+	Missense_Mutation	SNP	A	A	C													0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	aaataacataaataacactcAgactaccacacatcttcagc							TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr7:17382606A>C	ENST00000242057.4	+	11	3108	c.2465A>C	c.(2464-2466)cAg>cCg	p.Q822P		NM_001621.4	NP_001612.1	P35869	AHR_HUMAN	aryl hydrocarbon receptor	822				LNETYPAELNNINNTQTTTHLQPLHHPSEARPFPDLTSSGF L -> FK (in Ref. 1; BAA03857). {ECO:0000305}.	apoptotic process (GO:0006915)|blood vessel development (GO:0001568)|cell cycle (GO:0007049)|circadian regulation of gene expression (GO:0032922)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|regulation of B cell proliferation (GO:0030888)|regulation of gene expression (GO:0010468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to toxic substance (GO:0009636)|response to xenobiotic stimulus (GO:0009410)|transcription from RNA polymerase II promoter (GO:0006366)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosolic aryl hydrocarbon receptor complex (GO:0034752)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|Hsp90 protein binding (GO:0051879)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(11)|ovary(1)|pancreas(1)|urinary_tract(3)	33	Lung NSC(10;0.0392)|all_lung(11;0.0754)				Atorvastatin(DB01076)|Flutamide(DB00499)|Ginseng(DB01404)|Leflunomide(DB01097)|Mexiletine(DB00379)|Nimodipine(DB00393)	AATAACACTCAGACTACCACA	0.363																																					p.Q822P		Atlas-SNP	.											.	AHR	89	.	0			c.A2465C						.						191	180	184					7																	17382606		2203	4300	6503	SO:0001583	missense	196	exon11			ACACTCAGACTAC	L19872	CCDS5366.1	7p15	2013-05-21			ENSG00000106546	ENSG00000106546		"Basic helix-loop-helix proteins"	348	protein-coding gene	gene with protein product		600253				8125016	Standard	NM_001621		Approved	bHLHe76	uc011jxz.1	P35869	OTTHUMG00000149967	ENST00000242057.4:c.2465A>C	chr7.hg19:g.17382606A>C	ENSP00000242057:p.Gln822Pro	179.0	0.0		96.0	26.0	NM_001621	A4D130|Q13728|Q13803|Q13804	Missense_Mutation	SNP	ENST00000242057.4	hg19	CCDS5366.1	.	.	.	.	.	.	.	.	.	.	A	5.009	0.187412	0.09547	.	.	ENSG00000106546	ENST00000242057	T	0.50277	0.75	4.92	3.74	0.42951	.	0.542144	0.19216	N	0.119809	T	0.36991	0.0987	L	0.47016	1.485	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.21245	-1.0251	10	0.30854	T	0.27	.	7.1893	0.25816	0.7009:0.1425:0.0:0.1566	.	822	P35869	AHR_HUMAN	P	822	ENSP00000242057:Q822P	ENSP00000242057:Q822P	Q	+	2	0	AHR	17349131	0.722000	0.28017	0.010000	0.14722	0.066000	0.16364	1.866000	0.39489	0.918000	0.36919	0.533000	0.62120	CAG	.	.		0.363	AHR-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314620.2	NM_001621		C	17382606	A	C	17382606	3	2	340	1	0	0	0	0	1	0	0	0	416	188	7	5	2507	5	AHR	7	17382606	Missense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	9	17382606	141756057	67	47031	252	3								
AHR	196	hgsc.bcm.edu	37	chr7	17382611	17382611	+	Missense_Mutation	SNP	A	A	G													0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	acataaataacactcagactAccacacatcttcagccactt							TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr7:17382611A>G	ENST00000242057.4	+	11	3113	c.2470A>G	c.(2470-2472)Acc>Gcc	p.T824A		NM_001621.4	NP_001612.1	P35869	AHR_HUMAN	aryl hydrocarbon receptor	824				LNETYPAELNNINNTQTTTHLQPLHHPSEARPFPDLTSSGF L -> FK (in Ref. 1; BAA03857). {ECO:0000305}.	apoptotic process (GO:0006915)|blood vessel development (GO:0001568)|cell cycle (GO:0007049)|circadian regulation of gene expression (GO:0032922)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|regulation of B cell proliferation (GO:0030888)|regulation of gene expression (GO:0010468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to toxic substance (GO:0009636)|response to xenobiotic stimulus (GO:0009410)|transcription from RNA polymerase II promoter (GO:0006366)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosolic aryl hydrocarbon receptor complex (GO:0034752)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|Hsp90 protein binding (GO:0051879)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(11)|ovary(1)|pancreas(1)|urinary_tract(3)	33	Lung NSC(10;0.0392)|all_lung(11;0.0754)				Atorvastatin(DB01076)|Flutamide(DB00499)|Ginseng(DB01404)|Leflunomide(DB01097)|Mexiletine(DB00379)|Nimodipine(DB00393)	CACTCAGACTACCACACATCT	0.378																																					p.T824A		Atlas-SNP	.											.	AHR	89	.	0			c.A2470G						.						200	188	192					7																	17382611		2203	4300	6503	SO:0001583	missense	196	exon11			CAGACTACCACAC	L19872	CCDS5366.1	7p15	2013-05-21			ENSG00000106546	ENSG00000106546		"Basic helix-loop-helix proteins"	348	protein-coding gene	gene with protein product		600253				8125016	Standard	NM_001621		Approved	bHLHe76	uc011jxz.1	P35869	OTTHUMG00000149967	ENST00000242057.4:c.2470A>G	chr7.hg19:g.17382611A>G	ENSP00000242057:p.Thr824Ala	184.0	0.0		100.0	26.0	NM_001621	A4D130|Q13728|Q13803|Q13804	Missense_Mutation	SNP	ENST00000242057.4	hg19	CCDS5366.1	.	.	.	.	.	.	.	.	.	.	A	0.004	-2.282525	0.00251	.	.	ENSG00000106546	ENST00000242057	T	0.41758	0.99	4.92	-9.85	0.00476	.	1.132360	0.06303	N	0.701195	T	0.14700	0.0355	N	0.02973	-0.45	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.37478	-0.9704	10	0.02654	T	1	.	14.1452	0.65347	0.164:0.084:0.673:0.079	.	824	P35869	AHR_HUMAN	A	824	ENSP00000242057:T824A	ENSP00000242057:T824A	T	+	1	0	AHR	17349136	0.000000	0.05858	0.000000	0.03702	0.085000	0.17905	-1.026000	0.03596	-3.335000	0.00184	-0.250000	0.11733	ACC	.	.		0.378	AHR-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314620.2	NM_001621		G	17382611	A	G	17382611	3	3	340	1	0	0	0	0	1	0	0	0	416	391	14	2	2512	2	AHR	7	17382611	Missense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	5	17382611	141756052	68	47032	252	3								
ABCB5	340273	hgsc.bcm.edu	37	chr7	20691108	20691109	+	Missense_Mutation	DNP	GG	GG	TT													0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	tatcgagaccatattggagtGgttagtcaagagcctgtttt					rs560906981		TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr7:20691108_20691109GG>TT	ENST00000404938.2	+	13	2050_2051	c.1398_1399GG>TT	c.(1396-1401)gtGGtt>gtTTtt	p.V467F	ABCB5_ENST00000258738.6_Missense_Mutation_p.V22F|ABCB5_ENST00000477094.1_3'UTR|ABCB5_ENST00000406935.1_Missense_Mutation_p.V22F|ABCB5_ENST00000443026.2_Missense_Mutation_p.V22F	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	467	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (GO:0002485)|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO:0002489)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|cell differentiation (GO:0030154)|compound eye corneal lens development (GO:0048058)|positive regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002591)|regulation of membrane potential (GO:0042391)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|efflux transmembrane transporter activity (GO:0015562)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(1)|pancreas(1)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)	77						ATATTGGAGTGGTTAGTCAAGA	0.446																																					p.V466V|p.V467F		Atlas-SNP	.											ABCB5,NS,carcinoma,0,1|.	ABCB5	357	.	0			c.G1398T|c.G1399T						.																																			SO:0001583	missense	340273	exon13			TGGAGTGGTTAGT|GGAGTGGTTAGTC	U66692	CCDS5371.1, CCDS55090.1, CCDS55091.1, CCDS55092.1	7p14	2012-03-14			ENSG00000004846	ENSG00000004846		"ATP binding cassette transporters / subfamily B"	46	protein-coding gene	gene with protein product	"P-glycoprotein ABCB5", "ATP-binding cassette protein"	611785				8894702, 12960149	Standard	NM_001163942		Approved	EST422562, ABCB5beta, ABCB5alpha	uc010kuh.3	Q2M3G0	OTTHUMG00000094789	Exception_encountered	chr7.hg19:g.20691108_20691109delinsTT	ENSP00000384881:p.Val467Phe	118.0|117.0	0.0		58.0|59.0	24.0	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Silent|Missense_Mutation	SNP	ENST00000404938.2	hg19	CCDS55090.1																																																																																			.	.		0.446	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559		TT	20691109	GG	TT	20691108	3	4	340	1	0	0	0	0	1	0	0	0	44	1335	47	3	1444	3	ABCB5	7	20691108	Missense_Mutation	DNP	GG	TCGA-RC-A7SK-01A-11D-A34Z-10	3308497	20691108	138447555	69	47033										
NPSR1	387129	hgsc.bcm.edu	37	chr7	34867130	34867130	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	cggtgaagtgcagtgctgggCcctgtggcctgacgactcct	15	12	0	2			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr7:34867130C>T	ENST00000360581.1	+	5	724	c.596C>T	c.(595-597)gCc>gTc	p.A199V	NPSR1_ENST00000381539.3_Missense_Mutation_p.A199V|NPSR1_ENST00000381542.1_Missense_Mutation_p.A133V|NPSR1_ENST00000531252.1_Missense_Mutation_p.A188V|NPSR1_ENST00000359791.1_Missense_Mutation_p.A199V	NM_207172.1	NP_997055.1	Q6W5P4	NPSR1_HUMAN	neuropeptide S receptor 1	199						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|vasopressin receptor activity (GO:0005000)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(7)	31					Halothane(DB01159)	CAGTGCTGGGCCCTGTGGCCT	0.537																																					p.A199V		Atlas-SNP	.											.	NPSR1	134	.	0			c.C596T						.						159	137	144					7																	34867130		2203	4300	6503	SO:0001583	missense	387129	exon5			GCTGGGCCCTGTG	AY255536	CCDS5443.1, CCDS5444.1, CCDS75579.1, CCDS75580.1, CCDS75581.1	7p14.3	2012-08-08	2006-05-10	2006-05-10	ENSG00000187258	ENSG00000187258		"GPCR / Class A : Neuropeptide receptors : S"	23631	protein-coding gene	gene with protein product		608595	"G protein-coupled receptor 154"	GPR154		12679517, 15073379	Standard	NM_207173		Approved	PGR14, GPRA	uc003tei.1	Q6W5P4	OTTHUMG00000099383	ENST00000360581.1:c.596C>T	chr7.hg19:g.34867130C>T	ENSP00000353788:p.Ala199Val	151.0	0.0		42.0	13.0	NM_207172	A2RTZ4|Q2XP58|Q56H76|Q56H77|Q56H78|Q6JSL4|Q6JSL5|Q6JSL6|Q6JSL7|Q6JSL8|Q6W5P3|Q6ZMB8	Missense_Mutation	SNP	ENST00000360581.1	hg19	CCDS5444.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.877943	0.91664	.	.	ENSG00000187258	ENST00000360581;ENST00000381542;ENST00000359791;ENST00000531252;ENST00000381539;ENST00000334481	T;T;T;T;T	0.35605	1.3;1.3;1.3;1.3;1.3	5.44	5.44	0.79542	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000003	T	0.57051	0.2027	L	0.55743	1.74	0.51012	D	0.999903	D;D;D;P;D;P	0.89917	0.999;0.992;1.0;0.767;0.99;0.898	D;P;D;P;P;P	0.85130	0.997;0.814;0.997;0.661;0.741;0.823	T	0.53865	-0.8378	10	0.45353	T	0.12	-26.2085	18.2637	0.90044	0.0:1.0:0.0:0.0	.	133;188;133;199;199;199	B7ZMA2;Q6W5P4-5;Q6W5P4-2;Q6W5P4-4;Q6W5P4-3;Q6W5P4	.;.;.;.;.;NPSR1_HUMAN	V	199;133;199;188;199;62	ENSP00000353788:A199V;ENSP00000370953:A133V;ENSP00000352839:A199V;ENSP00000433258:A188V;ENSP00000370950:A199V	ENSP00000334093:A62V	A	+	2	0	NPSR1	34833655	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.937000	0.56575	2.553000	0.86117	0.655000	0.94253	GCC	.	.		0.537	NPSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216837.1	NM_207173		T	34867130	C	T	34867130	3	4	340	1	0	0	0	0	1	0	0	0	10609	739	26	3	614	3	NPSR1	7	34867130	Missense_Mutation	SNP	C	TCGA-RC-A7SK-01A-11D-A34Z-10	14176022	34867130	124271533	70	47034										
NPC1L1	29881	hgsc.bcm.edu	37	chr7	44578553	44578553	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	ttgatgcagcagtcgtagagActggtattgtccggattgag	14	6	0	3			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr7:44578553A>G	ENST00000289547.4	-	2	1498	c.1443T>C	c.(1441-1443)agT>agC	p.S481S	NPC1L1_ENST00000423141.1_Silent_p.S481S|NPC1L1_ENST00000381160.3_Silent_p.S481S|NPC1L1_ENST00000546276.1_Silent_p.S481S	NM_013389.2	NP_037521.2	Q9UHC9	NPCL1_HUMAN	NPC1-like 1	481					cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intestinal cholesterol absorption (GO:0030299)|lipoprotein metabolic process (GO:0042157)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)	brush border membrane (GO:0031526)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|hedgehog receptor activity (GO:0008158)|myosin V binding (GO:0031489)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(7)|lung(27)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	57					Ezetimibe(DB00973)	AGTCGTAGAGACTGGTATTGT	0.597																																					p.S481S		Atlas-SNP	.											.	NPC1L1	141	.	0			c.T1443C						.						127	109	115					7																	44578553		2203	4300	6503	SO:0001819	synonymous_variant	29881	exon2			GTAGAGACTGGTA		CCDS5491.1, CCDS43575.1, CCDS75587.1	7p13	2012-11-15	2012-11-15		ENSG00000015520	ENSG00000015520			7898	protein-coding gene	gene with protein product		608010	"NPC1 (Niemann-Pick disease, type C1, gene)-like 1"			10783261	Standard	NM_013389		Approved		uc003tlb.3	Q9UHC9	OTTHUMG00000023691	ENST00000289547.4:c.1443T>C	chr7.hg19:g.44578553A>G		144.0	0.0		45.0	20.0	NM_001101648	A4D2J7|B7ZLE6|D3DVK9|Q17RV5|Q6R3Q4|Q9UHC8	Silent	SNP	ENST00000289547.4	hg19	CCDS5491.1																																																																																			.	.		0.597	NPC1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251256.1	NM_013389		G	44578553	A	G	44578553	2	3	340	1	0	0	0	0	0	0	0	1	10580	272	10	2		2	NPC1L1	7	44578553	Silent	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	9711423	44578553	114560110	71	47035										
GRM3	2913	hgsc.bcm.edu	37	chr7	86493597	86493597	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	ctgtcccactttgttttccaGcctctgcaagcacgtatgtg	8	13	1	0			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr7:86493597G>T	ENST00000361669.2	+	6	3665		c.e6-1		GRM3_ENST00000439827.1_Splice_Site|GRM3_ENST00000546348.1_Splice_Site|GRM3_ENST00000394720.2_Splice_Site|GRM3_ENST00000536043.1_Splice_Site	NM_000840.2	NP_000831.2	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3						adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of adenylate cyclase activity (GO:0007194)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|axon (GO:0030424)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group II metabotropic glutamate receptor activity (GO:0001641)			NS(2)|breast(6)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(43)|ovary(3)|pancreas(2)|prostate(4)|skin(25)|upper_aerodigestive_tract(5)	109	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)					TTGTTTTCCAGCCTCTGCAAG	0.498																																					.	GBM(52;969 1098 3139 52280)	Atlas-SNP	.											.	GRM3	237	.	0			c.2567-1G>T						.						219	185	197					7																	86493597		2203	4300	6503	SO:0001630	splice_region_variant	2913	exon6			TTTCCAGCCTCTG		CCDS5600.1	7q21.1-q21.2	2012-08-29			ENSG00000198822	ENSG00000198822		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4595	protein-coding gene	gene with protein product		601115				8824806	Standard	NM_000840		Approved	GPRC1C, mGlu3, MGLUR3	uc003uid.3	Q14832	OTTHUMG00000022884	ENST00000361669.2:c.2567-1G>T	chr7.hg19:g.86493597G>T		119.0	0.0		75.0	15.0	NM_000840	Q2PNZ6|Q75MV4|Q75N17|Q86YG6|Q8TBH9	Splice_Site	SNP	ENST00000361669.2	hg19	CCDS5600.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.472337	0.84533	.	.	ENSG00000198822	ENST00000361669;ENST00000546348;ENST00000536043;ENST00000439827;ENST00000394720	.	.	.	5.99	5.99	0.97316	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.4659	0.94939	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GRM3	86331533	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	8.502000	0.90505	2.840000	0.97914	0.655000	0.94253	.	.	.		0.498	GRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253362.2		Intron	T	86493597	G	T	86493597	5	4	340	1	0	0	0	0	0	0	1	0	6807	985	34	3	2584	3	GRM3	7	86493597	Splice_Site	SNP	G	TCGA-RC-A7SK-01A-11D-A34Z-10	41915044	86493597	72645066	72	47036										
PEX1	5189	hgsc.bcm.edu	37	chr7	92122372	92122372	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	gagtcagttactgatgctacAtgctgaaggtcaacatcatc	9	9	3	2			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr7:92122372A>C	ENST00000248633.4	-	20	3197	c.3102T>G	c.(3100-3102)caT>caG	p.H1034Q	AC007566.10_ENST00000441539.1_RNA|AC007566.10_ENST00000427458.1_RNA|PEX1_ENST00000438045.1_Missense_Mutation_p.H712Q|PEX1_ENST00000428214.1_Missense_Mutation_p.H977Q	NM_000466.2	NP_000457.1	O43933	PEX1_HUMAN	peroxisomal biogenesis factor 1	1034					ATP catabolic process (GO:0006200)|microtubule-based peroxisome localization (GO:0060152)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein targeting to peroxisome (GO:0006625)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			CTGATGCTACATGCTGAAGGT	0.413																																					p.H1034Q		Atlas-SNP	.											.	PEX1	102	.	0			c.T3102G						.						127	122	124					7																	92122372		2203	4300	6503	SO:0001583	missense	5189	exon20			TGCTACATGCTGA	AF026086	CCDS5627.1, CCDS64710.1	7q21.2	2010-04-21	2008-08-26		ENSG00000127980	ENSG00000127980		"ATPases / AAA-type"	8850	protein-coding gene	gene with protein product		602136	"peroxisome biogenesis factor 1", "Zellweger syndrome 1", "Zellweger syndrome"	ZWS1, ZWS		9398848	Standard	NM_001282677		Approved		uc003uly.3	O43933	OTTHUMG00000023926	ENST00000248633.4:c.3102T>G	chr7.hg19:g.92122372A>C	ENSP00000248633:p.His1034Gln	166.0	0.0		78.0	13.0	NM_000466	A4D1G3|A8KA90|B4DIM7|E9PE75|Q96S71|Q96S72|Q96S73|Q99994	Missense_Mutation	SNP	ENST00000248633.4	hg19	CCDS5627.1	.	.	.	.	.	.	.	.	.	.	A	6.505	0.461342	0.12342	.	.	ENSG00000127980	ENST00000438045;ENST00000248633;ENST00000428214	D;D;D	0.94723	-3.5;-3.5;-3.5	5.78	-5.7	0.02421	.	0.267324	0.43110	D	0.000616	T	0.81498	0.4835	N	0.05441	-0.05	0.42812	D	0.993966	B;P;B	0.42518	0.009;0.782;0.145	B;B;B	0.35813	0.017;0.211;0.031	T	0.74714	-0.3572	10	0.24483	T	0.36	-12.3631	11.2591	0.49071	0.3269:0.0:0.5678:0.1053	.	712;826;1034	E9PE75;B4DER6;O43933	.;.;PEX1_HUMAN	Q	712;1034;977	ENSP00000410438:H712Q;ENSP00000248633:H1034Q;ENSP00000394413:H977Q	ENSP00000248633:H1034Q	H	-	3	2	PEX1	91960308	0.818000	0.29161	0.906000	0.35671	0.188000	0.23474	0.050000	0.14120	-1.112000	0.02984	-0.481000	0.04817	CAT	.	.		0.413	PEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254066.3	NM_000466		C	92122372	A	C	92122372	3	2	340	1	0	0	0	0	1	0	0	0	11744	214	8	5	769	5	PEX1	7	92122372	Missense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	5628775	92122372	67016291	73	47037			1	62		2	2	16	A		6.347373e-05
PEX1	5189	hgsc.bcm.edu	37	chr7	92122387	92122387	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	gctacatgctgaaggtcaacAtcatctgccagaggtagaga	11	9	3	3			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr7:92122387A>G	ENST00000248633.4	-	20	3182	c.3087T>C	c.(3085-3087)gaT>gaC	p.D1029D	AC007566.10_ENST00000441539.1_RNA|AC007566.10_ENST00000427458.1_RNA|PEX1_ENST00000438045.1_Silent_p.D707D|PEX1_ENST00000428214.1_Silent_p.D972D	NM_000466.2	NP_000457.1	O43933	PEX1_HUMAN	peroxisomal biogenesis factor 1	1029					ATP catabolic process (GO:0006200)|microtubule-based peroxisome localization (GO:0060152)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein targeting to peroxisome (GO:0006625)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			GAAGGTCAACATCATCTGCCA	0.368																																					p.D1029D		Atlas-SNP	.											.	PEX1	102	.	0			c.T3087C						.						117	114	115					7																	92122387		2203	4300	6503	SO:0001819	synonymous_variant	5189	exon20			GTCAACATCATCT	AF026086	CCDS5627.1, CCDS64710.1	7q21.2	2010-04-21	2008-08-26		ENSG00000127980	ENSG00000127980		"ATPases / AAA-type"	8850	protein-coding gene	gene with protein product		602136	"peroxisome biogenesis factor 1", "Zellweger syndrome 1", "Zellweger syndrome"	ZWS1, ZWS		9398848	Standard	NM_001282677		Approved		uc003uly.3	O43933	OTTHUMG00000023926	ENST00000248633.4:c.3087T>C	chr7.hg19:g.92122387A>G		165.0	0.0		81.0	12.0	NM_000466	A4D1G3|A8KA90|B4DIM7|E9PE75|Q96S71|Q96S72|Q96S73|Q99994	Silent	SNP	ENST00000248633.4	hg19	CCDS5627.1																																																																																			.	.		0.368	PEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254066.3	NM_000466		G	92122387	A	G	92122387	2	3	340	1	0	0	0	0	0	0	0	1	11744	214	8	2		2	PEX1	7	92122387	Silent	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	15	92122387	67016276	74	47038			1	62		2	2	16	A		6.347373e-05
RUNX1T1	862	hgsc.bcm.edu	37	chr8	93023275	93023275	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	ctcagtgggaagttagtagcTtcttgcagtttggaatgaaa	12	5	2	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr8:93023275T>A	ENST00000523629.1	-	5	967	c.513A>T	c.(511-513)gaA>gaT	p.E171D	RUNX1T1_ENST00000520724.1_Missense_Mutation_p.E134D|RUNX1T1_ENST00000518844.1_Missense_Mutation_p.E144D|RUNX1T1_ENST00000521553.1_Missense_Mutation_p.E134D|RUNX1T1_ENST00000436581.2_Missense_Mutation_p.E182D|RUNX1T1_ENST00000422361.2_Missense_Mutation_p.E134D|RUNX1T1_ENST00000396218.1_Missense_Mutation_p.E144D|RUNX1T1_ENST00000360348.2_Missense_Mutation_p.E134D|RUNX1T1_ENST00000265814.3_Missense_Mutation_p.E171D	NM_001198626.1|NM_001198630.1|NM_001198633.1|NM_175634.2	NP_001185555.1|NP_001185559.1|NP_001185562.1|NP_783552.1	Q06455	MTG8_HUMAN	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	171	TAFH. {ECO:0000255|PROSITE- ProRule:PRU00440}.				fat cell differentiation (GO:0045444)|generation of precursor metabolites and energy (GO:0006091)|regulation of DNA binding (GO:0051101)|transcription, DNA-templated (GO:0006351)	nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(54)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	86			BRCA - Breast invasive adenocarcinoma(11;0.0141)			AGTTAGTAGCTTCTTGCAGTT	0.343																																					p.E230D		Atlas-SNP	.											.	RUNX1T1	516	.	0			c.A690T						.						137	134	135					8																	93023275		2203	4300	6503	SO:0001583	missense	862	exon5			AGTAGCTTCTTGC	D43638	CCDS6256.1, CCDS6257.1, CCDS47891.1, CCDS56544.1, CCDS75766.1, CCDS75767.1	8q22	2007-01-29	2005-01-20	2005-01-22	ENSG00000079102	ENSG00000079102		"Zinc fingers, MYND-type"	1535	protein-coding gene	gene with protein product		133435	"core-binding factor, runt domain, alpha subunit 2; translocated to, 1; cyclin D-related"	AML1T1, CBFA2T1		1391946, 9790752	Standard	NM_004349		Approved	CDR, ETO, MTG8, ZMYND2	uc011lgi.2	Q06455	OTTHUMG00000164066	ENST00000523629.1:c.513A>T	chr8.hg19:g.93023275T>A	ENSP00000428543:p.Glu171Asp	150.0	0.0		126.0	6.0	NM_001198679	B7Z4P4|E7EPN4|O14784|Q06456|Q14873|Q16239|Q16346|Q16347|Q6IBL1|Q6NXH1|Q7Z4J5|Q92479|Q9BRZ0	Missense_Mutation	SNP	ENST00000523629.1	hg19	CCDS6256.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.037425	0.75617	.	.	ENSG00000079102	ENST00000523629;ENST00000396218;ENST00000265814;ENST00000360348;ENST00000422361;ENST00000520724;ENST00000436581;ENST00000518844;ENST00000521553;ENST00000518992;ENST00000521054	T;T;T;T;T;T;T;T;T;T;T	0.47528	0.84;0.84;0.84;0.84;0.84;0.84;0.84;0.84;0.84;0.84;0.84	5.87	5.87	0.94306	TAFH/NHR1 (3);	0.000000	0.85682	D	0.000000	T	0.51907	0.1702	L	0.34521	1.04	0.80722	D	1	B;B;B;B;B	0.20261	0.011;0.043;0.025;0.043;0.02	B;B;B;B;B	0.42522	0.052;0.39;0.217;0.16;0.104	T	0.51957	-0.8639	10	0.46703	T	0.11	-14.2221	16.5764	0.84681	0.0:0.0:0.0:1.0	.	182;182;144;171;144	E7EPN4;B7Z4P4;B2R6I9;Q06455;Q06455-2	.;.;.;MTG8_HUMAN;.	D	171;144;171;134;134;134;182;144;134;171;134	ENSP00000428543:E171D;ENSP00000379520:E144D;ENSP00000265814:E171D;ENSP00000353504:E134D;ENSP00000390137:E134D;ENSP00000428742:E134D;ENSP00000402257:E182D;ENSP00000430728:E144D;ENSP00000429728:E134D;ENSP00000431094:E171D;ENSP00000427763:E134D	ENSP00000265814:E171D	E	-	3	2	RUNX1T1	93092451	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.914000	0.69964	2.371000	0.80710	0.533000	0.62120	GAA	.	.		0.343	RUNX1T1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377045.3	NM_004349, NM_175635		A	93023275	T	A	93023275	3	1	340	1	0	0	0	0	1	0	0	0	13762	1606	56	4	1333	4	RUNX1T1	8	93023275	Missense_Mutation	SNP	T	TCGA-RC-A7SK-01A-11D-A34Z-10		93023275	53340747	75	47039										
NUDCD1	84955	hgsc.bcm.edu	37	chr8	110283345	110283345	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	ttgcaaggtggtttttctttAtctggatttggattcttagt	10	4	3	0			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr8:110283345A>T	ENST00000239690.4	-	8	1562	c.1188T>A	c.(1186-1188)gaT>gaA	p.D396E	NUDCD1_ENST00000427660.2_Missense_Mutation_p.D367E	NM_032869.3	NP_116258.2			NudC domain containing 1											breast(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(1)|prostate(2)|skin(1)	25	all_neural(195;0.219)		OV - Ovarian serous cystadenocarcinoma(57;1.56e-12)			GTTTTTCTTTATCTGGATTTG	0.294																																					p.D396E		Atlas-SNP	.											.	NUDCD1	58	.	0			c.T1188A						.						108	114	112					8																	110283345		2202	4297	6499	SO:0001583	missense	84955	exon8			TTCTTTATCTGGA	AF283302	CCDS6312.1, CCDS47910.1	8q23	2005-02-07			ENSG00000120526	ENSG00000120526			24306	protein-coding gene	gene with protein product		606109				11416219	Standard	NM_032869		Approved	CML66, FLJ14991	uc003ynb.4	Q96RS6	OTTHUMG00000164931	ENST00000239690.4:c.1188T>A	chr8.hg19:g.110283345A>T	ENSP00000239690:p.Asp396Glu	158.0	0.0		243.0	24.0	NM_032869		Missense_Mutation	SNP	ENST00000239690.4	hg19	CCDS6312.1	.	.	.	.	.	.	.	.	.	.	A	8.817	0.936643	0.18206	.	.	ENSG00000120526	ENST00000239690;ENST00000427660	T;T	0.18338	2.22;2.22	5.7	1.99	0.26369	.	0.347524	0.34879	N	0.003613	T	0.05227	0.0139	N	0.04508	-0.205	0.25419	N	0.988283	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.06405	0.002;0.001;0.001	T	0.30736	-0.9968	10	0.17369	T	0.5	-5.9605	1.069	0.01617	0.4223:0.2724:0.1571:0.1482	.	309;396;367	Q96RS6-3;Q96RS6;Q96RS6-2	.;NUDC1_HUMAN;.	E	396;367	ENSP00000239690:D396E;ENSP00000410707:D367E	ENSP00000239690:D396E	D	-	3	2	NUDCD1	110352521	0.582000	0.26749	1.000000	0.80357	0.889000	0.51656	-0.341000	0.07811	0.499000	0.27970	0.529000	0.55759	GAT	.	.		0.294	NUDCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380996.1	NM_032869		T	110283345	A	T	110283345	3	4	340	1	0	0	0	0	1	0	0	0	10731	446	16	4	575	4	NUDCD1	8	110283345	Missense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	17260070	110283345	36080677	76	47040										
TNFRSF11B	4982	hgsc.bcm.edu	37	chr8	119936661	119936661	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	acctggttacctatcatttcTaaaaataacttctgatacaa	3	9	3	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr8:119936661T>G	ENST00000297350.4	-	5	1536	c.1158A>C	c.(1156-1158)ttA>ttC	p.L386F		NM_002546.3	NP_002537.3	O00300	TR11B_HUMAN	tumor necrosis factor receptor superfamily, member 11b	386					apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|negative regulation of bone resorption (GO:0045779)|negative regulation of odontogenesis of dentin-containing tooth (GO:0042489)|response to arsenic-containing substance (GO:0046685)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to magnesium ion (GO:0032026)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|receptor activity (GO:0004872)			breast(1)|central_nervous_system(3)|endometrium(4)|large_intestine(6)|lung(7)|prostate(3)|skin(1)	25	all_cancers(13;3.71e-26)|Lung NSC(37;1.69e-07)|Ovarian(258;0.018)|all_neural(195;0.0592)|Hepatocellular(40;0.234)		STAD - Stomach adenocarcinoma(47;0.00193)			CTATCATTTCTAAAAATAACT	0.398																																					p.L386F		Atlas-SNP	.											.	TNFRSF11B	87	.	0			c.A1158C						.						145	149	148					8																	119936661		2203	4300	6503	SO:0001583	missense	4982	exon5			CATTTCTAAAAAT	U94332	CCDS6326.1	8q24	2008-07-31	2008-07-31		ENSG00000164761	ENSG00000164761		"Tumor necrosis factor receptor superfamily"	11909	protein-coding gene	gene with protein product		602643	"osteoprotegerin"	OPG		9108485	Standard	NM_002546		Approved	OCIF, TR1	uc003yon.4	O00300	OTTHUMG00000164969	ENST00000297350.4:c.1158A>C	chr8.hg19:g.119936661T>G	ENSP00000297350:p.Leu386Phe	148.0	0.0		230.0	18.0	NM_002546	B2R9A8|O60236|Q53FX6|Q9UHP4	Missense_Mutation	SNP	ENST00000297350.4	hg19	CCDS6326.1	.	.	.	.	.	.	.	.	.	.	T	15.13	2.741784	0.49151	.	.	ENSG00000164761	ENST00000297350	T	0.78364	-1.17	5.69	2.15	0.27550	.	0.347193	0.24366	N	0.039155	T	0.78013	0.4217	L	0.29908	0.895	0.37574	D	0.919541	D	0.89917	1.0	D	0.85130	0.997	T	0.75377	-0.3339	9	.	.	.	-5.9162	8.6482	0.34018	0.0:0.2149:0.0:0.7851	.	386	O00300	TR11B_HUMAN	F	386	ENSP00000297350:L386F	.	L	-	3	2	TNFRSF11B	120005842	0.914000	0.31030	0.971000	0.41717	0.720000	0.41350	-0.145000	0.10265	0.468000	0.27243	0.533000	0.62120	TTA	.	.		0.398	TNFRSF11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381220.1			G	119936661	T	G	119936661	3	3	340	1	0	0	0	0	1	0	0	0	16300	1519	53	5	51	5	TNFRSF11B	8	119936661	Missense_Mutation	SNP	T	TCGA-RC-A7SK-01A-11D-A34Z-10	9653316	119936661	26427361	77	47041										
TNFRSF11B	4982	hgsc.bcm.edu	37	chr8	119936888	119936888	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	ctttattgttttttcaatgtCttctgctcccactttctttc	3	11	4	0			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr8:119936888C>G	ENST00000297350.4	-	5	1309	c.931G>C	c.(931-933)Gac>Cac	p.D311H		NM_002546.3	NP_002537.3	O00300	TR11B_HUMAN	tumor necrosis factor receptor superfamily, member 11b	311	Death 2.				apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|negative regulation of bone resorption (GO:0045779)|negative regulation of odontogenesis of dentin-containing tooth (GO:0042489)|response to arsenic-containing substance (GO:0046685)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to magnesium ion (GO:0032026)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|receptor activity (GO:0004872)			breast(1)|central_nervous_system(3)|endometrium(4)|large_intestine(6)|lung(7)|prostate(3)|skin(1)	25	all_cancers(13;3.71e-26)|Lung NSC(37;1.69e-07)|Ovarian(258;0.018)|all_neural(195;0.0592)|Hepatocellular(40;0.234)		STAD - Stomach adenocarcinoma(47;0.00193)			TTTTCAATGTCTTCTGCTCCC	0.478																																					p.D311H		Atlas-SNP	.											TNFRSF11B_ENST00000297350,NS,carcinoma,0,2	TNFRSF11B	87	.	0			c.G931C						.						193	151	165					8																	119936888		2203	4300	6503	SO:0001583	missense	4982	exon5			CAATGTCTTCTGC	U94332	CCDS6326.1	8q24	2008-07-31	2008-07-31		ENSG00000164761	ENSG00000164761		"Tumor necrosis factor receptor superfamily"	11909	protein-coding gene	gene with protein product		602643	"osteoprotegerin"	OPG		9108485	Standard	NM_002546		Approved	OCIF, TR1	uc003yon.4	O00300	OTTHUMG00000164969	ENST00000297350.4:c.931G>C	chr8.hg19:g.119936888C>G	ENSP00000297350:p.Asp311His	250.0	0.0		391.0	25.0	NM_002546	B2R9A8|O60236|Q53FX6|Q9UHP4	Missense_Mutation	SNP	ENST00000297350.4	hg19	CCDS6326.1	.	.	.	.	.	.	.	.	.	.	C	16.39	3.110816	0.56398	.	.	ENSG00000164761	ENST00000297350	D	0.94000	-3.33	5.65	5.65	0.86999	Death (1);	1.453660	0.03646	N	0.240271	D	0.96213	0.8765	L	0.54323	1.7	0.44843	D	0.997855	P	0.46512	0.879	P	0.56398	0.797	D	0.86941	0.2079	9	.	.	.	-14.9045	20.0822	0.97779	0.0:1.0:0.0:0.0	.	311	O00300	TR11B_HUMAN	H	311	ENSP00000297350:D311H	.	D	-	1	0	TNFRSF11B	120006069	1.000000	0.71417	0.988000	0.46212	0.231000	0.25187	5.574000	0.67424	2.826000	0.97356	0.563000	0.77884	GAC	.	.		0.478	TNFRSF11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381220.1			G	119936888	C	G	119936888	3	3	340	1	0	0	0	0	1	0	0	0	16300	913	32	4	278	4	TNFRSF11B	8	119936888	Missense_Mutation	SNP	C	TCGA-RC-A7SK-01A-11D-A34Z-10	227	119936888	26427134	78	47042										
MELK	9833	hgsc.bcm.edu	37	chr9	36677291	36677291	+	Frame_Shift_Del	DEL	A	A	-													0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	taagggcgatgcctgggtttAcaaaagattagtggaagaca							TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr9:36677291delA	ENST00000298048.2	+	18	2097	c.1913delA	c.(1912-1914)tacfs	p.Y638fs	MELK_ENST00000536987.1_Frame_Shift_Del_p.Y507fs|MELK_ENST00000543751.1_Frame_Shift_Del_p.Y606fs|MELK_ENST00000536860.1_Frame_Shift_Del_p.Y590fs|MELK_ENST00000545008.1_Frame_Shift_Del_p.Y567fs|MELK_ENST00000541717.1_Frame_Shift_Del_p.Y597fs|MELK_ENST00000538311.1_Frame_Shift_Del_p.Y444fs|MELK_ENST00000536329.1_Frame_Shift_Del_p.Y567fs	NM_014791.3	NP_055606.1	Q14680	MELK_HUMAN	maternal embryonic leucine zipper kinase	638	Autoinhibitory region.|KA1. {ECO:0000255|PROSITE- ProRule:PRU00565}.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|hemopoiesis (GO:0030097)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|neural precursor cell proliferation (GO:0061351)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)	cell cortex (GO:0005938)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)	29		Acute lymphoblastic leukemia(2;1.09e-08)|all_hematologic(2;8.15e-06)	STAD - Stomach adenocarcinoma(86;0.228)			GCCTGGGTTTACAAAAGATTA	0.463																																					p.Y638fs	Ovarian(82;980 1317 7225 14391 18624)	Atlas-INDEL	.											.	MELK	74	.	0			c.1912delT						.						90	86	87					9																	36677291		2203	4300	6503	SO:0001589	frameshift_variant	9833	exon18			.	D79997	CCDS6606.1, CCDS59123.1, CCDS59124.1, CCDS59125.1, CCDS59126.1, CCDS59127.1, CCDS59128.1	9p13.1	2008-02-05			ENSG00000165304	ENSG00000165304			16870	protein-coding gene	gene with protein product		607025				8724849, 9136115	Standard	NM_001256689		Approved	KIAA0175	uc003zzn.4	Q14680	OTTHUMG00000019906	ENST00000298048.2:c.1913delA	chr9.hg19:g.36677291delA	ENSP00000298048:p.Tyr638fs	70.0	0.0		22.0	16.0	NM_014791	A6P3A7|A6P3A8|B1AMQ6|B7Z1E6|B7Z5M5|B7Z6Q7|B7Z6R8|B7Z6Y0|B7Z7Q1|D3DRP8|F5H0Y0|F5H2R4|F5H689|Q7L3C3	Frame_Shift_Del	DEL	ENST00000298048.2	hg19	CCDS6606.1																																																																																			.	.		0.463	MELK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052428.3	NM_014791		-	36677291	A	-	36677291	7	5	340	1	0	1	0	1	0	0	0	0	9479	391	14	0	1979	0	MELK	9	36677291	Frame_Shift_Del	DEL	A	TCGA-RC-A7SK-01A-11D-A34Z-10		36677291	104536140	79	47043	253	3								
MELK	9833	hgsc.bcm.edu	37	chr9	36677293	36677293	+	Missense_Mutation	SNP	A	A	C													0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	agggcgatgcctgggtttacAaaagattagtggaagacatc							TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr9:36677293A>C	ENST00000298048.2	+	18	2099	c.1915A>C	c.(1915-1917)Aaa>Caa	p.K639Q	MELK_ENST00000536987.1_Missense_Mutation_p.K508Q|MELK_ENST00000543751.1_Missense_Mutation_p.K607Q|MELK_ENST00000536860.1_Missense_Mutation_p.K591Q|MELK_ENST00000545008.1_Missense_Mutation_p.K568Q|MELK_ENST00000541717.1_Missense_Mutation_p.K598Q|MELK_ENST00000538311.1_Missense_Mutation_p.K445Q|MELK_ENST00000536329.1_Missense_Mutation_p.K568Q	NM_014791.3	NP_055606.1	Q14680	MELK_HUMAN	maternal embryonic leucine zipper kinase	639	Autoinhibitory region.|KA1. {ECO:0000255|PROSITE- ProRule:PRU00565}.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|hemopoiesis (GO:0030097)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|neural precursor cell proliferation (GO:0061351)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)	cell cortex (GO:0005938)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)	29		Acute lymphoblastic leukemia(2;1.09e-08)|all_hematologic(2;8.15e-06)	STAD - Stomach adenocarcinoma(86;0.228)			CTGGGTTTACAAAAGATTAGT	0.458																																					p.K639Q	Ovarian(82;980 1317 7225 14391 18624)	Atlas-SNP	.											.	MELK	74	.	0			c.A1915C						.						87	83	84					9																	36677293		2203	4300	6503	SO:0001583	missense	9833	exon18			GTTTACAAAAGAT	D79997	CCDS6606.1, CCDS59123.1, CCDS59124.1, CCDS59125.1, CCDS59126.1, CCDS59127.1, CCDS59128.1	9p13.1	2008-02-05			ENSG00000165304	ENSG00000165304			16870	protein-coding gene	gene with protein product		607025				8724849, 9136115	Standard	NM_001256689		Approved	KIAA0175	uc003zzn.4	Q14680	OTTHUMG00000019906	ENST00000298048.2:c.1915A>C	chr9.hg19:g.36677293A>C	ENSP00000298048:p.Lys639Gln	70.0	0.0		22.0	17.0	NM_014791	A6P3A7|A6P3A8|B1AMQ6|B7Z1E6|B7Z5M5|B7Z6Q7|B7Z6R8|B7Z6Y0|B7Z7Q1|D3DRP8|F5H0Y0|F5H2R4|F5H689|Q7L3C3	Missense_Mutation	SNP	ENST00000298048.2	hg19	CCDS6606.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.341660	0.81911	.	.	ENSG00000165304	ENST00000298048;ENST00000538311;ENST00000536987;ENST00000545008;ENST00000536860;ENST00000536329;ENST00000541717;ENST00000543751	T;T;T;T;T;T;T;T	0.57436	0.4;0.4;0.4;0.4;0.4;0.4;0.4;0.4	5.75	5.75	0.90469	Kinase-associated KA1 (4);	0.092179	0.64402	D	0.000001	T	0.74512	0.3726	M	0.82056	2.57	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;0.999;1.0;1.0;1.0;1.0;1.0	T	0.78505	-0.2178	10	0.87932	D	0	-13.7741	16.0623	0.80847	1.0:0.0:0.0:0.0	.	559;568;591;598;568;607;639	B7Z1G6;F5H2R4;F5H0Y0;F5H689;A6P3A8;A6P3A7;Q14680	.;.;.;.;.;.;MELK_HUMAN	Q	639;445;508;568;591;568;598;607	ENSP00000298048:K639Q;ENSP00000438226:K445Q;ENSP00000439184:K508Q;ENSP00000445452:K568Q;ENSP00000439792:K591Q;ENSP00000443550:K568Q;ENSP00000437804:K598Q;ENSP00000441596:K607Q	ENSP00000298048:K639Q	K	+	1	0	MELK	36667293	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.683000	0.91236	2.195000	0.70347	0.533000	0.62120	AAA	.	.		0.458	MELK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052428.3	NM_014791		C	36677293	A	C	36677293	3	2	340	1	0	0	0	0	1	0	0	0	9479	131	5	5	1981	5	MELK	9	36677293	Missense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	2	36677293	104536138	80	47044	253	3								
MELK	9833	hgsc.bcm.edu	37	chr9	36677295	36677295	+	Frame_Shift_Del	DEL	A	A	-													0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	ggcgatgcctgggtttacaaAagattagtggaagacatcct							TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr9:36677295delA	ENST00000298048.2	+	18	2101	c.1917delA	c.(1915-1917)aaafs	p.K639fs	MELK_ENST00000536987.1_Frame_Shift_Del_p.K508fs|MELK_ENST00000543751.1_Frame_Shift_Del_p.K607fs|MELK_ENST00000536860.1_Frame_Shift_Del_p.K591fs|MELK_ENST00000545008.1_Frame_Shift_Del_p.K568fs|MELK_ENST00000541717.1_Frame_Shift_Del_p.K598fs|MELK_ENST00000538311.1_Frame_Shift_Del_p.K445fs|MELK_ENST00000536329.1_Frame_Shift_Del_p.K568fs	NM_014791.3	NP_055606.1	Q14680	MELK_HUMAN	maternal embryonic leucine zipper kinase	639	Autoinhibitory region.|KA1. {ECO:0000255|PROSITE- ProRule:PRU00565}.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|hemopoiesis (GO:0030097)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|neural precursor cell proliferation (GO:0061351)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)	cell cortex (GO:0005938)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)	29		Acute lymphoblastic leukemia(2;1.09e-08)|all_hematologic(2;8.15e-06)	STAD - Stomach adenocarcinoma(86;0.228)			GGGTTTACAAAAGATTAGTGG	0.458																																					p.K639fs	Ovarian(82;980 1317 7225 14391 18624)	Pindel	.											.	MELK	74	.	0			c.1916delA						.						87	83	84					9																	36677295		2203	4300	6503	SO:0001589	frameshift_variant	9833	exon18			.	D79997	CCDS6606.1, CCDS59123.1, CCDS59124.1, CCDS59125.1, CCDS59126.1, CCDS59127.1, CCDS59128.1	9p13.1	2008-02-05			ENSG00000165304	ENSG00000165304			16870	protein-coding gene	gene with protein product		607025				8724849, 9136115	Standard	NM_001256689		Approved	KIAA0175	uc003zzn.4	Q14680	OTTHUMG00000019906	ENST00000298048.2:c.1917delA	chr9.hg19:g.36677295delA	ENSP00000298048:p.Lys639fs	68.0	0.0		23.0	15.0	NM_014791	A6P3A7|A6P3A8|B1AMQ6|B7Z1E6|B7Z5M5|B7Z6Q7|B7Z6R8|B7Z6Y0|B7Z7Q1|D3DRP8|F5H0Y0|F5H2R4|F5H689|Q7L3C3	Frame_Shift_Del	DEL	ENST00000298048.2	hg19	CCDS6606.1																																																																																			.	.		0.458	MELK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052428.3	NM_014791		-	36677295	A	-	36677295	7	5	340	1	0	1	0	1	0	0	0	0	9479	11	1	0	1983	0	MELK	9	36677295	Frame_Shift_Del	DEL	A	TCGA-RC-A7SK-01A-11D-A34Z-10	2	36677295	104536136	81	47045	253	3								
TNC	3371	hgsc.bcm.edu	37	chr9	117808755	117808755	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	tattccatagagttcaatttCgtattcagtagcctctctga	6	9	3	2			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr9:117808755C>T	ENST00000350763.4	-	17	5470	c.5059G>A	c.(5059-5061)Gaa>Aaa	p.E1687K	TNC_ENST00000423613.2_Intron|TNC_ENST00000341037.4_Missense_Mutation_p.E1505K|TNC_ENST00000346706.3_Missense_Mutation_p.E1141K|TNC_ENST00000345230.3_Intron|TNC_ENST00000340094.3_Missense_Mutation_p.E1323K|TNC_ENST00000535648.1_Missense_Mutation_p.E1232K|TNC_ENST00000537320.1_Intron|TNC_ENST00000481475.1_5'Flank|TNC_ENST00000542877.1_Missense_Mutation_p.E1324K	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	1687	Fibronectin type-III 12. {ECO:0000255|PROSITE-ProRule:PRU00316}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)			NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						AGTTCAATTTCGTATTCAGTA	0.443																																					p.E1687K		Atlas-SNP	.											.	TNC	282	.	0			c.G5059A						.						223	209	214					9																	117808755		2203	4300	6503	SO:0001583	missense	3371	exon17			CAATTTCGTATTC		CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	5318	protein-coding gene	gene with protein product	"hexabrachion (tenascin)"	187380	"hexabrachion (tenascin C, cytotactin)", "deafness, autosomal dominant 56"	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.5059G>A	chr9.hg19:g.117808755C>T	ENSP00000265131:p.Glu1687Lys	334.0	0.0		97.0	76.0	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	ENST00000350763.4	hg19	CCDS6811.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.14|12.14	1.847912|1.847912	0.32699|0.32699	.|.	.|.	ENSG00000041982|ENSG00000041982	ENST00000340094;ENST00000535648;ENST00000346706;ENST00000350763;ENST00000341037;ENST00000542877|ENST00000544972	T;T;T;T;T;T|.	0.58210|.	0.35;0.35;0.35;0.35;0.35;0.35|.	5.81|5.81	4.91|4.91	0.64330|0.64330	Fibronectin, type III (4);Immunoglobulin-like fold (1);|.	0.240480|.	0.41294|.	D|.	0.000913|.	T|T	0.48768|0.48768	0.1518|0.1518	N|N	0.21194|0.21194	0.64|0.64	0.80722|0.80722	D|D	1|1	B|.	0.31519|.	0.327|.	B|.	0.27380|.	0.079|.	T|T	0.42258|0.42258	-0.9462|-0.9462	10|5	0.06099|.	T|.	0.92|.	.|.	11.8032|11.8032	0.52139|0.52139	0.0:0.8588:0.0:0.1412|0.0:0.8588:0.0:0.1412	.|.	1687|.	P24821|.	TENA_HUMAN|.	K|Q	1323;1232;1141;1687;1505;1324|249	ENSP00000344400:E1323K;ENSP00000438152:E1232K;ENSP00000344555:E1141K;ENSP00000265131:E1687K;ENSP00000339553:E1505K;ENSP00000442242:E1324K|.	ENSP00000344400:E1323K|.	E|R	-|-	1|2	0|0	TNC|TNC	116848576|116848576	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.993000|0.993000	0.82548|0.82548	3.744000|3.744000	0.55112|0.55112	1.438000|1.438000	0.47492|0.47492	0.563000|0.563000	0.77884|0.77884	GAA|CGA	.	.		0.443	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160		T	117808755	C	T	117808755	3	4	340	1	0	0	0	0	1	0	0	0	16285	893	31	1	1594	1	TNC	9	117808755	Missense_Mutation	SNP	C	TCGA-RC-A7SK-01A-11D-A34Z-10	81131460	117808755	23404676	82	47046										
TTF1	7270	hgsc.bcm.edu	37	chr9	135277159	135277159	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	tatgcactctcgaggctctcAggcatggccactgcctcaaa	9	14	3	0			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr9:135277159A>T	ENST00000334270.2	-	2	1089	c.1050T>A	c.(1048-1050)ccT>ccA	p.P350P		NM_001205296.1|NM_007344.3	NP_001192225.1|NP_031370.2	Q15361	TTF1_HUMAN	transcription termination factor, RNA polymerase I	350					chromatin remodeling (GO:0006338)|DNA-templated transcription, termination (GO:0006353)|gene expression (GO:0010467)|negative regulation of DNA replication (GO:0008156)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(2)|pancreas(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;4.25e-06)|Epithelial(140;9.09e-05)		CGAGGCTCTCAGGCATGGCCA	0.468																																					p.P350P		Atlas-SNP	.											.	TTF1	82	.	0			c.T1050A						.						129	124	125					9																	135277159		2203	4300	6503	SO:0001819	synonymous_variant	7270	exon2			GCTCTCAGGCATG	BC050734	CCDS6948.1, CCDS75925.1	9q34.3	2008-02-05			ENSG00000125482	ENSG00000125482			12397	protein-coding gene	gene with protein product		600777				7597036	Standard	NM_007344		Approved		uc004cbl.3	Q15361	OTTHUMG00000020836	ENST00000334270.2:c.1050T>A	chr9.hg19:g.135277159A>T		170.0	0.0		63.0	44.0	NM_007344	A1L160|Q4VXF3|Q58EY2|Q6P5T5	Silent	SNP	ENST00000334270.2	hg19	CCDS6948.1																																																																																			.	.		0.468	TTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054784.2	NM_007344		T	135277159	A	T	135277159	2	4	340	1	0	0	0	0	0	0	0	1	16733	175	7	4		4	TTF1	9	135277159	Silent	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	17468404	135277159	5936272	83	47047										
C10orf113	387638	hgsc.bcm.edu	37	chr10	21435299	21435299	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	gtctggaatgtacatttcagCcacacaagaaaaaaatgact	7	8	2	2			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr10:21435299C>G	ENST00000534331.1	-	1	189	c.139G>C	c.(139-141)Gct>Cct	p.A47P	NEBL_ENST00000417816.2_Intron|C10orf113_ENST00000377118.4_Missense_Mutation_p.A37P|C10orf113_ENST00000529198.1_Missense_Mutation_p.A47P	NM_001010896.2	NP_001010896.2	Q5VZT2	CJ113_HUMAN	chromosome 10 open reading frame 113	47										endometrium(1)|large_intestine(1)|lung(1)|ovary(3)|pancreas(1)	7						TACATTTCAGCCACACAAGAA	0.433																																					p.A47P		Atlas-SNP	.											.	C10orf113	32	.	0			c.G139C						.						153	136	142					10																	21435299		2203	4300	6503	SO:0001583	missense	387638	exon1			TTTCAGCCACACA		CCDS31162.1, CCDS31162.2, CCDS53496.1	10p12.31	2012-06-12			ENSG00000204683	ENSG00000204683			31447	protein-coding gene	gene with protein product							Standard	NM_001010896		Approved	bA165O3.1	uc001iqm.3	Q5VZT2	OTTHUMG00000017786	ENST00000534331.1:c.139G>C	chr10.hg19:g.21435299C>G	ENSP00000433646:p.Ala47Pro	94.0	0.0		45.0	27.0	NM_001177483	B9EIM9|E9PRX7	Missense_Mutation	SNP	ENST00000534331.1	hg19	CCDS31162.2	.	.	.	.	.	.	.	.	.	.	C	13.61	2.289650	0.40494	.	.	ENSG00000204683	ENST00000534331;ENST00000529198;ENST00000377118	T;T	0.39406	1.08;1.08	5.44	-7.19	0.01500	.	.	.	.	.	T	0.16428	0.0395	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.24368	-1.0162	9	0.87932	D	0	5.4267	2.2927	0.04143	0.321:0.1168:0.3841:0.178	.	47	Q5VZT2	CJ113_HUMAN	P	47;47;37	ENSP00000433646:A47P;ENSP00000366322:A37P	ENSP00000366322:A37P	A	-	1	0	C10orf113	21475305	0.000000	0.05858	0.000000	0.03702	0.117000	0.20001	-0.009000	0.12765	-0.789000	0.04498	-0.950000	0.02660	GCT	.	.		0.433	C10orf113-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047108.3	NM_001010896		G	21435299	C	G	21435299	3	3	340	1	0	0	0	0	1	0	0	0	1586	739	26	4	371	4	C10orf113	10	21435299	Missense_Mutation	SNP	C	TCGA-RC-A7SK-01A-11D-A34Z-10		21435299	114099448	84	47048										
WAC	51322	hgsc.bcm.edu	37	chr10	28884889	28884889	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	atcaccagccaaagaaatcaTttgatgctaatggagcatct	7	9	3	2			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr10:28884889T>C	ENST00000354911.4	+	7	999	c.838T>C	c.(838-840)Ttt>Ctt	p.F280L	WAC_ENST00000428935.1_Missense_Mutation_p.F235L|WAC_ENST00000375646.1_Intron|WAC_ENST00000347934.4_Intron|WAC_ENST00000375664.4_Missense_Mutation_p.F235L	NM_016628.4	NP_057712.2	Q9BTA9	WAC_HUMAN	WW domain containing adaptor with coiled-coil	280					cellular response to DNA damage stimulus (GO:0006974)|G1 DNA damage checkpoint (GO:0044783)|histone H2B conserved C-terminal lysine ubiquitination (GO:0071894)|histone monoubiquitination (GO:0010390)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	chromatin binding (GO:0003682)|RNA polymerase II core binding (GO:0000993)			NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|urinary_tract(1)	32						AAAGAAATCATTTGATGCTAA	0.433																																					p.F280L		Atlas-SNP	.											.	WAC	77	.	0			c.T838C						.						131	120	124					10																	28884889		2203	4300	6503	SO:0001583	missense	51322	exon7			AAATCATTTGATG	AK055852	CCDS7159.1, CCDS7160.1, CCDS7161.1	10p12.1	2007-05-17	2003-03-19		ENSG00000095787	ENSG00000095787			17327	protein-coding gene	gene with protein product		615049	"WW domain-containing adaptor with coiled coil"			11827461	Standard	NR_024557		Approved	Wwp4, FLJ31290, PRO1741, BM-016, MGC10753	uc001iuf.3	Q9BTA9	OTTHUMG00000017872	ENST00000354911.4:c.838T>C	chr10.hg19:g.28884889T>C	ENSP00000346986:p.Phe280Leu	70.0	0.0		42.0	9.0	NM_016628	A8K2A9|C9JBT9|D3DRW5|D3DRW6|D3DRW7|Q53EN9|Q5JU75|Q5JU77|Q5VXK0|Q5VXK2|Q8TCK1|Q96DP3|Q96FW6|Q96JI3	Missense_Mutation	SNP	ENST00000354911.4	hg19	CCDS7159.1	.	.	.	.	.	.	.	.	.	.	T	15.20	2.762548	0.49574	.	.	ENSG00000095787	ENST00000375664;ENST00000354911;ENST00000428935;ENST00000424454;ENST00000538000	T;T;T	0.30981	1.99;1.98;1.51	5.41	5.41	0.78517	.	0.307413	0.38897	N	0.001522	T	0.22627	0.0546	L	0.29908	0.895	0.38121	D	0.937842	B;B	0.25272	0.122;0.075	B;B	0.22601	0.04;0.018	T	0.09930	-1.0652	10	0.11794	T	0.64	-9.7218	15.4254	0.75045	0.0:0.0:0.0:1.0	.	235;280	Q9BTA9-2;Q9BTA9	.;WAC_HUMAN	L	235;280;235;235;235	ENSP00000364816:F235L;ENSP00000346986:F280L;ENSP00000399706:F235L	ENSP00000346986:F280L	F	+	1	0	WAC	28924895	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.331000	0.59273	2.047000	0.60756	0.454000	0.30748	TTT	.	.		0.433	WAC-017	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000047371.1	NM_100264		C	28884889	T	C	28884889	3	2	340	1	0	0	0	0	1	0	0	0	17262	1493	52	2	864	2	WAC	10	28884889	Missense_Mutation	SNP	T	TCGA-RC-A7SK-01A-11D-A34Z-10	7449590	28884889	106649858	85	47049										
PARG	8505	hgsc.bcm.edu	37	chr10	51027418	51027418	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	cctttgccctgaatggtcagCggtctctgcacaggactcga	11	13	2	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr10:51027418C>A	ENST00000402038.3	-	14	1443	c.1444G>T	c.(1444-1446)Gct>Tct	p.A482S		NM_003631.2	NP_003622.2	Q86W56	PARG_HUMAN	poly (ADP-ribose) glycohydrolase	967					carbohydrate metabolic process (GO:0005975)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	poly(ADP-ribose) glycohydrolase activity (GO:0004649)			endometrium(5)|kidney(2)|lung(1)|ovary(2)	10				Epithelial(53;0.213)		GAATGGTCAGCGGTCTCTGCA	0.517																																					p.A967S		Atlas-SNP	.											.	PARG	46	.	0			c.G2899T						.						161	142	148					10																	51027418		692	1591	2283	SO:0001583	missense	8505	exon18			GGTCAGCGGTCTC	AF005043	CCDS73130.1	10q11.23	2012-04-20			ENSG00000227345	ENSG00000227345	3.2.1.143		8605	protein-coding gene	gene with protein product		603501				9115250, 10449915	Standard	NM_003631		Approved		uc001jif.3	Q86W56	OTTHUMG00000018201	ENST00000402038.3:c.1444G>T	chr10.hg19:g.51027418C>A	ENSP00000384408:p.Ala482Ser	152.0	0.0		86.0	30.0	NM_003631	A5YBK3|B2RC24|B4DIU5|B4DYR4|I6RUV3|Q6E4P6|Q6E4P7|Q7Z742|Q9Y4W7	Missense_Mutation	SNP	ENST00000402038.3	hg19		.	.	.	.	.	.	.	.	.	.	C	1.001	-0.691062	0.03303	.	.	ENSG00000227345	ENST00000402038	.	.	.	5.59	-9.35	0.00633	.	.	.	.	.	T	0.04318	0.0119	N	0.00926	-1.1	.	.	.	B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B	0.04013	0.001;0.001;0.0;0.0;0.001;0.0;0.001	T	0.23511	-1.0186	7	0.07482	T	0.82	4.2817	0.626	0.00786	0.2909:0.2075:0.1096:0.392	.	885;967;518;235;482;507;967	Q86W56-2;Q86W56;A5YBK3;B4DHS4;Q5SQP4;B4DX76;Q0MQR4	.;PARG_HUMAN;.;.;.;.;.	S	482	.	ENSP00000384408:A482S	A	-	1	0	PARG	50697424	0.094000	0.21725	0.000000	0.03702	0.005000	0.04900	-0.006000	0.12833	-1.398000	0.02066	-0.982000	0.02568	GCT	.	.		0.517	PARG-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048011.2	NM_003631		A	51027418	C	A	51027418	3	1	340	1	0	0	0	0	1	0	0	0	11457	768	27	1	35	1	PARG	10	51027418	Missense_Mutation	SNP	C	TCGA-RC-A7SK-01A-11D-A34Z-10	22142529	51027418	84507329	86	47050										
ZNF365	22891	hgsc.bcm.edu	37	chr10	64148261	64148261	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	atctgttacagcgggtagaaCtggcggagaagcagcttgag	15	7	1	3			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr10:64148261C>G	ENST00000395254.3	+	3	1130	c.850C>G	c.(850-852)Ctg>Gtg	p.L284V	ZNF365_ENST00000466727.1_3'UTR|ZNF365_ENST00000395255.3_Missense_Mutation_p.L284V|ZNF365_ENST00000410046.3_Missense_Mutation_p.L284V	NM_014951.2	NP_055766.2	Q70YC4	TALAN_HUMAN	zinc finger protein 365	0										breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27	Prostate(12;0.0297)|all_hematologic(501;0.228)					GCGGGTAGAACTGGCGGAGAA	0.567																																					p.L284V		Atlas-SNP	.											.	ZNF365	174	.	0			c.C850G						.						55	57	56					10																	64148261		2203	4300	6503	SO:0001583	missense	22891	exon3			GTAGAACTGGCGG	AB020651	CCDS7264.1, CCDS7265.1, CCDS31209.1, CCDS41531.1	10q21.2	2008-10-28			ENSG00000138311	ENSG00000138311		"Zinc fingers, C2H2-type"	18194	protein-coding gene	gene with protein product	"Talanin"	607818				10048485, 12740763	Standard	NM_199450		Approved	KIAA0844, UAN	uc001jmc.2	Q70YC4	OTTHUMG00000018302	ENST00000395254.3:c.850C>G	chr10.hg19:g.64148261C>G	ENSP00000378674:p.Leu284Val	58.0	0.0		31.0	9.0	NM_014951		Missense_Mutation	SNP	ENST00000395254.3	hg19	CCDS31209.1	.	.	.	.	.	.	.	.	.	.	C	18.47	3.629947	0.67015	.	.	ENSG00000138311	ENST00000395254;ENST00000395255;ENST00000410046	T;T;T	0.35421	1.31;1.31;1.31	5.58	-1.35	0.09114	.	2.215180	0.02118	N	0.055432	T	0.54775	0.1879	M	0.69823	2.125	0.80722	D	1	D;D;P;D	0.69078	0.997;0.986;0.948;0.974	D;P;P;P	0.64042	0.921;0.78;0.706;0.706	T	0.51679	-0.8675	10	0.51188	T	0.08	-5.0613	6.445	0.21871	0.0:0.518:0.1143:0.3677	.	284;284;284;299	Q70YC5-3;Q70YC5-2;Q70YC5;Q70YC5-4	.;.;ZN365_HUMAN;.	V	284	ENSP00000378674:L284V;ENSP00000378675:L284V;ENSP00000387091:L284V	ENSP00000378674:L284V	L	+	1	2	ZNF365	63818267	0.002000	0.14202	0.984000	0.44739	0.985000	0.73830	-0.049000	0.11924	-0.201000	0.10284	0.655000	0.94253	CTG	.	.		0.567	ZNF365-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048238.2	NM_014951		G	64148261	C	G	64148261	3	3	340	1	0	0	0	0	1	0	0	0	17884	564	20	4	856	4	ZNF365	10	64148261	Missense_Mutation	SNP	C	TCGA-RC-A7SK-01A-11D-A34Z-10	13120843	64148261	71386486	87	47051										
AGAP11	119385	hgsc.bcm.edu	37	chr10	88768173	88768173	+	RNA	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	gagtttaaataactattcctCctccattccattgactccca	3	13	0	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr10:88768173C>T	ENST00000444431.1	+	0	2773				RP11-96C23.5_ENST00000433214.2_RNA|RP11-96C23.14_ENST00000444180.3_RNA|RP11-96C23.10_ENST00000451760.1_RNA			Q8TF27	AGA11_HUMAN	ankyrin repeat and GTPase domain Arf GTPase activating protein 11						regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)										AACTATTCCTCCTCCATTCCA	0.478																																					p.S55F		Atlas-SNP	.											.	.	.	.	0			c.C164T						.						109	113	111					10																	88768173		2135	4268	6403			119385	exon12			ATTCCTCCTCCAT			10q23.2	2013-01-11			ENSG00000151303	ENSG00000151303		"ADP-ribosylation factor GTPase activating proteins", "Ankyrin repeat domain containing"	29421	protein-coding gene	gene with protein product						11853319	Standard	NM_133447		Approved	KIAA1975	uc001kee.2	Q8TF27	OTTHUMG00000018667		chr10.hg19:g.88768173C>T		132.0	0.0		50.0	7.0	NM_133447	B9EIP7|D3DWE4	Missense_Mutation	SNP	ENST00000444431.1	hg19																																																																																				.	.		0.478	AGAP11-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000049193.1	NM_133447		T	88768173	C	T	88768173	1	4	340	0	1	0	0	0	0	0	0	0	367	855	30	3		3	AGAP11	10	88768173	RNA	SNP	C	TCGA-RC-A7SK-01A-11D-A34Z-10	24619912	88768173	46766574	88	47052										
PPAPDC1A	196051	hgsc.bcm.edu	37	chr10	122334705	122334705	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	gcaagctgcactgcttcaccGagagtgggcggggaaagagc	16	10	1	2			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr10:122334705G>A	ENST00000398250.1	+	6	860	c.508G>A	c.(508-510)Gag>Aag	p.E170K	PPAPDC1A_ENST00000541332.1_Missense_Mutation_p.E170K|PPAPDC1A_ENST00000496437.1_3'UTR|PPAPDC1A_ENST00000369073.3_Missense_Mutation_p.E160K|PPAPDC1A_ENST00000398248.1_Intron|PPAPDC1A_ENST00000439221.1_Missense_Mutation_p.E107K	NM_001030059.1	NP_001025230.1	Q5VZY2	PPC1A_HUMAN	phosphatidic acid phosphatase type 2 domain containing 1A	170					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|phospholipid dephosphorylation (GO:0046839)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	phosphatidate phosphatase activity (GO:0008195)	p.E170K(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|urinary_tract(1)	20		Lung NSC(174;0.1)|all_lung(145;0.132)		all cancers(201;0.0117)		CTGCTTCACCGAGAGTGGGCG	0.577																																					p.E170K		Atlas-SNP	.											PPAPDC1A,colon,carcinoma,0,1	PPAPDC1A	48	.	1	Substitution - Missense(1)	large_intestine(1)	c.G508A						.																																			SO:0001583	missense	196051	exon6			TTCACCGAGAGTG	AK098668	CCDS41573.1	10q26.13	2008-02-05		2005-07-15	ENSG00000203805	ENSG00000203805			23531	protein-coding gene	gene with protein product			"phosphatidic acid phosphatase type 2 domain containing 1"	PPAPDC1			Standard	XM_005269592		Approved		uc001lev.1	Q5VZY2	OTTHUMG00000019168	ENST00000398250.1:c.508G>A	chr10.hg19:g.122334705G>A	ENSP00000381302:p.Glu170Lys	159.0	0.0		57.0	6.0	NM_001030059	A2RU82|Q08EQ2|Q0IIP2|Q495B4|Q5VZY1	Missense_Mutation	SNP	ENST00000398250.1	hg19	CCDS41573.1	.	.	.	.	.	.	.	.	.	.	G	14.56	2.572924	0.45798	.	.	ENSG00000203805	ENST00000439221;ENST00000398250;ENST00000427079;ENST00000541332;ENST00000369073	T;T;T;T	0.40225	1.04;1.04;1.04;1.04	5.52	5.52	0.82312	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.092240	0.64402	D	0.000001	T	0.28732	0.0712	N	0.24115	0.695	0.80722	D	1	P;D;B	0.57899	0.676;0.981;0.023	B;B;B	0.39738	0.294;0.308;0.005	T	0.09840	-1.0656	10	0.08179	T	0.78	-6.7691	19.441	0.94821	0.0:0.0:1.0:0.0	.	170;107;170	B7Z3R3;Q5VZY2-2;Q5VZY2	.;.;PPC1A_HUMAN	K	107;170;170;170;160	ENSP00000381302:E170K;ENSP00000407979:E170K;ENSP00000440493:E170K;ENSP00000358069:E160K	ENSP00000358069:E160K	E	+	1	0	PPAPDC1A	122324695	1.000000	0.71417	0.967000	0.41034	0.997000	0.91878	9.785000	0.99042	2.603000	0.88011	0.655000	0.94253	GAG	.	.		0.577	PPAPDC1A-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_113641		A	122334705	G	A	122334705	3	1	340	1	0	0	0	0	1	0	0	0	12302	1059	37	1	530	1	PPAPDC1A	10	122334705	Missense_Mutation	SNP	G	TCGA-RC-A7SK-01A-11D-A34Z-10	33566532	122334705	13200042	89	47053										
ZNF195	7748	hgsc.bcm.edu	37	chr11	3381365	3381365	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	ttctctccagtgtcaatgttCtcaggttcagtaaagtgtga	9	8	4	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr11:3381365C>T	ENST00000399602.4	-	6	999	c.873G>A	c.(871-873)gaG>gaA	p.E291E	ZNF195_ENST00000354599.6_Silent_p.E219E|ZNF195_ENST00000005082.9_Silent_p.E268E|ZNF195_ENST00000343338.7_Silent_p.E223E|ZNF195_ENST00000526601.1_Silent_p.E272E|ZNF195_ENST00000528796.1_Intron|ZNF195_ENST00000438262.2_3'UTR|ZNF195_ENST00000429541.2_Silent_p.E223E	NM_001130520.2	NP_001123992.1	O14628	ZN195_HUMAN	zinc finger protein 195	291					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)	17		Medulloblastoma(188;0.00106)|Breast(177;0.00328)|all_neural(188;0.00681)|Ovarian(85;0.00965)		BRCA - Breast invasive adenocarcinoma(625;0.0361)|LUSC - Lung squamous cell carcinoma(625;0.2)		TGTCAATGTTCTCAGGTTCAG	0.378																																					p.E291E		Atlas-SNP	.											.	ZNF195	77	.	0			c.G873A						.						97	93	94					11																	3381365		1904	4155	6059	SO:0001819	synonymous_variant	7748	exon6			AATGTTCTCAGGT		CCDS41604.1, CCDS44521.1, CCDS44522.1, CCDS55736.1, CCDS55737.1, CCDS58111.1	11p15.5	2013-01-08			ENSG00000005801	ENSG00000005801		"Zinc fingers, C2H2-type", "-"	12986	protein-coding gene	gene with protein product		602187				9344677	Standard	NM_001130520		Approved		uc001lxt.3	O14628	OTTHUMG00000011694	ENST00000399602.4:c.873G>A	chr11.hg19:g.3381365C>T		142.0	0.0		81.0	16.0	NM_001130520	A8K234|B3KTK2|B4DEL0|C9JLY9|L7MNK2|Q0VAJ6|Q658N8|Q6ZNA9	Silent	SNP	ENST00000399602.4	hg19	CCDS44522.1																																																																																			.	.		0.378	ZNF195-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000032321.2			T	3381365	C	T	3381365	2	4	340	1	0	0	0	0	0	0	0	1	17773	912	32	3		3	ZNF195	11	3381365	Silent	SNP	C	TCGA-RC-A7SK-01A-11D-A34Z-10		3381365	131625151	90	47054										
MRVI1	10335	hgsc.bcm.edu	37	chr11	10613101	10613101	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	atcgacaaacttacttttccAaaagtgcaggcagtgctgaa	8	9	0	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr11:10613101A>G	ENST00000436272.1	-	17	2231	c.2153T>C	c.(2152-2154)tTg>tCg	p.L718S	MRVI1_ENST00000424001.1_Missense_Mutation_p.L430S|LYVE1_ENST00000531706.1_Intron|MRVI1_ENST00000423302.2_Missense_Mutation_p.L745S|MRVI1_ENST00000527509.2_Missense_Mutation_p.L654S|MRVI1_ENST00000531107.1_Missense_Mutation_p.L737S|MRVI1_ENST00000541483.1_Missense_Mutation_p.L539S|MRVI1_ENST00000547195.1_Missense_Mutation_p.L654S|MRVI1-AS1_ENST00000529979.1_RNA|MRVI1_ENST00000552103.1_Missense_Mutation_p.L654S|MRVI1_ENST00000534266.2_Missense_Mutation_p.L430S|MRVI1-AS1_ENST00000529829.1_RNA|MRVI1_ENST00000545852.1_Missense_Mutation_p.L430S|MRVI1_ENST00000421747.1_Missense_Mutation_p.L736S|MRVI1-AS1_ENST00000525578.1_RNA|MRVI1_ENST00000558540.1_Missense_Mutation_p.L430S			Q9Y6F6	MRVI1_HUMAN	murine retrovirus integration site 1 homolog	718					blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|relaxation of vascular smooth muscle (GO:0060087)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(2)	22				all cancers(16;2.68e-07)|Epithelial(150;3.04e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0723)		TTACTTTTCCAAAAGTGCAGG	0.443																																					p.L745S		Atlas-SNP	.											.	MRVI1	113	.	0			c.T2234C						.						51	49	50					11																	10613101		1915	4136	6051	SO:0001583	missense	10335	exon18			TTTTCCAAAAGTG	AF081249	CCDS44538.1, CCDS44539.1, CCDS44540.1, CCDS44538.2, CCDS55745.1, CCDS55746.1	11p15.4	2014-09-11			ENSG00000072952	ENSG00000072952			7237	protein-coding gene	gene with protein product	"inositol 1,4,5-triphosphate-associated cGMP kinase substrate", "IP3R-associated cGMP kinase substrate"	604673				10321731	Standard	NM_001098579		Approved	JAW1L, IRAG	uc010rcb.1	Q9Y6F6	OTTHUMG00000165773	ENST00000436272.1:c.2153T>C	chr11.hg19:g.10613101A>G	ENSP00000412229:p.Leu718Ser	87.0	0.0		35.0	12.0	NM_130385	B7Z3T4|B7Z6I2|B7Z9A3|E9PQY6|F5H6A1|J3KQZ7|Q17S00|Q9UNY1	Missense_Mutation	SNP	ENST00000436272.1	hg19		.	.	.	.	.	.	.	.	.	.	A	24.6	4.546730	0.86022	.	.	ENSG00000072952	ENST00000421747;ENST00000308763;ENST00000436272;ENST00000547195;ENST00000552103;ENST00000545852;ENST00000424001;ENST00000423302;ENST00000541483;ENST00000531107;ENST00000527509	T;T;T;T;T;T;T;T;T;T	0.15952	2.38;2.38;2.38;2.38;2.38;2.38;2.38;2.38;2.38;2.38	5.37	5.37	0.77165	.	0.187718	0.35124	N	0.003430	T	0.36193	0.0958	L	0.51422	1.61	0.42507	D	0.992953	P;D;D;D	0.76494	0.774;0.999;0.999;0.999	P;D;D;D	0.75484	0.465;0.986;0.986;0.976	T	0.04767	-1.0928	10	0.51188	T	0.08	-6.0099	15.204	0.73162	1.0:0.0:0.0:0.0	.	539;718;737;736	F5H6A1;Q9Y6F6;E9PQY6;Q9Y6F6-4	.;MRVI1_HUMAN;.;.	S	736;719;718;654;654;430;430;745;539;737;654	ENSP00000414598:L736S;ENSP00000412229:L718S;ENSP00000448278:L654S;ENSP00000446764:L654S;ENSP00000441971:L430S;ENSP00000401205:L430S;ENSP00000412130:L745S;ENSP00000437784:L539S;ENSP00000432436:L737S;ENSP00000432067:L654S	ENSP00000307885:L719S	L	-	2	0	MRVI1	10569677	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.682000	0.68182	2.254000	0.74563	0.533000	0.62120	TTG	.	.		0.443	MRVI1-203	KNOWN	basic	protein_coding	protein_coding		NM_001098579		G	10613101	A	G	10613101	3	3	340	1	0	0	0	0	1	0	0	0	9862	131	5	2	520	2	MRVI1	11	10613101	Missense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	7231736	10613101	124393415	91	47055										
CEP57	9702	hgsc.bcm.edu	37	chr11	95560987	95560987	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	tgccgtggtagccaatgttcAgcttgtcttgcatctaatga	10	9	3	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr11:95560987A>C	ENST00000325542.5	+	9	1161	c.923A>C	c.(922-924)cAg>cCg	p.Q308P	CEP57_ENST00000537677.1_Missense_Mutation_p.Q281P|CEP57_ENST00000541150.1_Missense_Mutation_p.Q299P|CEP57_ENST00000325486.5_Missense_Mutation_p.Q282P	NM_001243776.1|NM_014679.4	NP_001230705.1|NP_055494.2	Q86XR8	CEP57_HUMAN	centrosomal protein 57kDa	308	Mediates interaction with microtubules. {ECO:0000250}.				fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|mitotic cell cycle (GO:0000278)|protein homooligomerization (GO:0051260)|protein import into nucleus, translocation (GO:0000060)|spermatid development (GO:0007286)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	fibroblast growth factor binding (GO:0017134)|protein homodimerization activity (GO:0042803)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	13		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				GCCAATGTTCAGCTTGTCTTG	0.403									Mosaic Variegated Aneuploidy Syndrome																												p.Q308P		Atlas-SNP	.											.	CEP57	40	.	0			c.A923C						.						146	134	138					11																	95560987		2201	4298	6499	SO:0001583	missense	9702	exon9	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	ATGTTCAGCTTGT	D42054	CCDS8304.1, CCDS58166.1, CCDS58167.1	11q21	2014-09-17			ENSG00000166037	ENSG00000166037			30794	protein-coding gene	gene with protein product		607951				7788527	Standard	NM_014679		Approved	Translokin, TSP57, KIAA0092	uc001pfp.2	Q86XR8	OTTHUMG00000167740	ENST00000325542.5:c.923A>C	chr11.hg19:g.95560987A>C	ENSP00000317902:p.Gln308Pro	105.0	0.0		63.0	11.0	NM_014679	A0PJH1|A8K5D0|B4DDP5|F5H5F7|Q14704|Q5JB46|Q8IXP0|Q9BVF9	Missense_Mutation	SNP	ENST00000325542.5	hg19	CCDS8304.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.180260	0.78677	.	.	ENSG00000166037	ENST00000537677;ENST00000325542;ENST00000325486;ENST00000541150;ENST00000537093	T;T;T;T;T	0.60040	0.37;0.3;0.94;0.31;0.22	5.72	5.72	0.89469	.	0.000000	0.64402	D	0.000001	T	0.76997	0.4066	M	0.79258	2.445	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.998	D;D;D	0.97110	0.994;1.0;0.986	T	0.80221	-0.1472	10	0.87932	D	0	-3.107	15.9926	0.80217	1.0:0.0:0.0:0.0	.	299;282;308	F5H5F7;Q86XR8-2;Q86XR8	.;.;CEP57_HUMAN	P	281;308;282;299;67	ENSP00000441392:Q281P;ENSP00000317902:Q308P;ENSP00000317487:Q282P;ENSP00000443436:Q299P;ENSP00000444749:Q67P	ENSP00000317487:Q282P	Q	+	2	0	CEP57	95200635	1.000000	0.71417	1.000000	0.80357	0.792000	0.44763	7.705000	0.84606	2.185000	0.69588	0.260000	0.18958	CAG	.	.		0.403	CEP57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395983.1	NM_014679		C	95560987	A	C	95560987	3	2	340	1	0	0	0	0	1	0	0	0	3258	188	7	5	957	5	CEP57	11	95560987	Missense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	84947886	95560987	39445529	92	47056										
GRIA4	2893	hgsc.bcm.edu	37	chr11	105804564	105804564	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	gtccgcaaatccaagggcaaAtttgcctttctcctggagtc	9	12	1	0			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr11:105804564A>T	ENST00000530497.1	+	13	2163	c.2163A>T	c.(2161-2163)aaA>aaT	p.K721N	AP000673.1_ENST00000583628.1_RNA|GRIA4_ENST00000282499.5_Missense_Mutation_p.K721N|GRIA4_ENST00000393127.2_Missense_Mutation_p.K721N|GRIA4_ENST00000525187.1_Missense_Mutation_p.K721N			P48058	GRIA4_HUMAN	glutamate receptor, ionotropic, AMPA 4	721					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(24)|liver(2)|lung(25)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	82		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)		CCAAGGGCAAATTTGCCTTTC	0.468																																					p.K721N		Atlas-SNP	.											.	GRIA4	380	.	0			c.A2163T						.						90	79	83					11																	105804564		2202	4299	6501	SO:0001583	missense	2893	exon14			GGGCAAATTTGCC	U16129	CCDS8333.1, CCDS41706.1, CCDS41707.1	11q22	2012-08-29	2012-02-03		ENSG00000152578	ENSG00000152578		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4574	protein-coding gene	gene with protein product		138246	"glutamate receptor, ionotrophic, AMPA 4"	GLUR4			Standard	NM_001077244		Approved	GluA4, GLURD	uc001pix.2	P48058	OTTHUMG00000166236	ENST00000530497.1:c.2163A>T	chr11.hg19:g.105804564A>T	ENSP00000435775:p.Lys721Asn	154.0	0.0		74.0	12.0	NM_001077243	Q86XE8	Missense_Mutation	SNP	ENST00000530497.1	hg19	CCDS8333.1	.	.	.	.	.	.	.	.	.	.	A	17.44	3.388945	0.61956	.	.	ENSG00000152578	ENST00000282499;ENST00000393127;ENST00000530497;ENST00000525187;ENST00000539249	T;T;T;T	0.38401	1.14;1.14;1.14;1.14	5.51	3.19	0.36642	Ionotropic glutamate receptor (2);	0.000000	0.64402	D	0.000001	T	0.46737	0.1408	L	0.43554	1.36	0.58432	D	0.999995	D;D	0.89917	0.972;1.0	P;D	0.91635	0.896;0.999	T	0.20009	-1.0288	10	0.33940	T	0.23	.	8.8697	0.35309	0.6549:0.0:0.3451:0.0	.	721;721	P48058;G3V164	GRIA4_HUMAN;.	N	721;721;721;721;26	ENSP00000282499:K721N;ENSP00000376835:K721N;ENSP00000435775:K721N;ENSP00000432180:K721N	ENSP00000282499:K721N	K	+	3	2	GRIA4	105309774	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.552000	0.45828	0.390000	0.25115	0.482000	0.46254	AAA	.	.		0.468	GRIA4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388593.1			T	105804564	A	T	105804564	3	4	340	1	0	0	0	0	1	0	0	0	6779	98	4	4	2250	4	GRIA4	11	105804564	Missense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	10243577	105804564	29201952	93	47057										
TRAPPC4	51399	hgsc.bcm.edu	37	chr11	118889521	118889521	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	cagcgatggcgatttttagtGtgtatgtggtgaacaaagct	13	5	0	1	rs372565482		TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr11:118889521G>A	ENST00000533632.1	+	1	380	c.16G>A	c.(16-18)Gtg>Atg	p.V6M	MIR3656_ENST00000577421.1_RNA|RPS25_ENST00000528547.1_5'Flank|RPS25_ENST00000527673.1_5'Flank|TRAPPC4_ENST00000434101.2_Missense_Mutation_p.V6M|TRAPPC4_ENST00000525303.1_Missense_Mutation_p.V6M|TRAPPC4_ENST00000528230.1_Missense_Mutation_p.V6M|TRAPPC4_ENST00000359005.4_Missense_Mutation_p.V6M|TRAPPC4_ENST00000533058.1_Missense_Mutation_p.V6M	NM_016146.4	NP_057230.1	Q9Y296	TPPC4_HUMAN	trafficking protein particle complex 4	6					dendrite development (GO:0016358)|ER to Golgi vesicle-mediated transport (GO:0006888)|extracellular matrix organization (GO:0030198)	cis-Golgi network (GO:0005801)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi stack (GO:0005795)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)|TRAPP complex (GO:0030008)				NS(1)|endometrium(1)|large_intestine(2)|lung(1)	5	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_neural(223;0.224)|all_hematologic(192;0.243)		BRCA - Breast invasive adenocarcinoma(274;7.58e-05)		GATTTTTAGTGTGTATGTGGT	0.577																																					p.V6M		Atlas-SNP	.											.	TRAPPC4	8	.	0			c.G16A						.	G	MET/VAL	0,4400		0,0,2200	139	133	135		16	5.9	1	11		135	1,8589	1.2+/-3.3	0,1,4294	no	missense	TRAPPC4	NM_016146.4	21	0,1,6494	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	6/220	118889521	1,12989	2200	4295	6495	SO:0001583	missense	51399	exon1			TTTAGTGTGTATG	AF078862	CCDS8407.1	11q23.3	2011-10-10				ENSG00000196655		"Trafficking protein particle complex"	19943	protein-coding gene	gene with protein product		610971				10810093	Standard	NM_016146		Approved	TRS23, SBDN, PTD009	uc010ryo.2	Q9Y296		ENST00000533632.1:c.16G>A	chr11.hg19:g.118889521G>A	ENSP00000436005:p.Val6Met	91.0	0.0		61.0	12.0	NM_016146	A8K3A5|B4DME1	Missense_Mutation	SNP	ENST00000533632.1	hg19	CCDS8407.1	.	.	.	.	.	.	.	.	.	.	G	36	5.850332	0.97023	0.0	1.16E-4	ENSG00000196655	ENST00000533632;ENST00000528230;ENST00000525303;ENST00000434101;ENST00000359005;ENST00000533058	D;D;D;D;D;D	0.83837	-1.77;-1.77;-1.77;-1.77;-1.77;-1.77	5.86	5.86	0.93980	Longin-like (1);	0.052096	0.85682	D	0.000000	D	0.91462	0.7305	M	0.80982	2.52	0.80722	D	1	P;D;D;D	0.67145	0.946;0.996;0.985;0.994	P;D;P;P	0.64506	0.694;0.926;0.801;0.881	D	0.91756	0.5416	10	0.87932	D	0	-20.6589	20.1796	0.98194	0.0:0.0:1.0:0.0	.	6;6;6;6	B4DF86;B4DME1;Q9Y296;B4DF36	.;.;TPPC4_HUMAN;.	M	6	ENSP00000436005:V6M;ENSP00000436827:V6M;ENSP00000435339:V6M;ENSP00000405033:V6M;ENSP00000351896:V6M;ENSP00000432920:V6M	ENSP00000351896:V6M	V	+	1	0	TRAPPC4	118394731	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	9.408000	0.97327	2.784000	0.95788	0.655000	0.94253	GTG	.	.		0.577	TRAPPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389332.1	NM_016146		A	118889521	G	A	118889521	3	1	340	1	0	0	0	0	1	0	0	0	16476	1377	48	3	18	3	TRAPPC4	11	118889521	Missense_Mutation	SNP	G	TCGA-RC-A7SK-01A-11D-A34Z-10	13084957	118889521	16116995	94	47058										
KLRC2	3822	hgsc.bcm.edu	37	chr12	10584707	10584707	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	ccatacaaaagaacttacttAtgtttgaaagccaaaccatt	4	9	0	2			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr12:10584707A>G	ENST00000381902.2	-	5	588	c.582T>C	c.(580-582)caT>caC	p.H194H	NKG2-E_ENST00000539033.1_Intron|KLRC2_ENST00000536833.2_Silent_p.H135H|KLRC2_ENST00000381901.1_Silent_p.H194H	NM_002260.3	NP_002251.2	P26717	NKG2C_HUMAN	killer cell lectin-like receptor subfamily C, member 2	194	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cellular defense response (GO:0006968)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			kidney(2)|large_intestine(1)|lung(6)|ovary(1)|skin(1)	11						GAACTTACTTATGTTTGAAAG	0.318																																					p.H194H		Atlas-SNP	.											.	KLRC2	29	.	0			c.T582C						.						56	54	55					12																	10584707		2046	4138	6184	SO:0001819	synonymous_variant	3822	exon5			TTACTTATGTTTG	X54869	CCDS31745.1	12p13	2009-12-03				ENSG00000205809		"Killer cell lectin-like receptors", "CD molecules"	6375	protein-coding gene	gene with protein product		602891				9598306	Standard	NM_002260		Approved	NKG2-C, CD159c		P26717		ENST00000381902.2:c.582T>C	chr12.hg19:g.10584707A>G		377.0	0.0		157.0	24.0	NM_002260	O43802|Q52M74|Q9NR42	Silent	SNP	ENST00000381902.2	hg19	CCDS31745.1	.	.	.	.	.	.	.	.	.	.	a	0.022	-1.408978	0.01155	.	.	ENSG00000205809	ENST00000537017	.	.	.	1.72	-3.44	0.04796	.	.	.	.	.	T	0.37046	0.0989	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33548	-0.9864	4	.	.	.	.	0.5812	0.00712	0.231:0.1467:0.1671:0.4551	.	.	.	.	T	72	.	.	I	-	2	0	KLRC2	10475974	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.234000	0.02931	-2.238000	0.00712	-1.801000	0.00618	ATA	.	.		0.318	KLRC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400111.1	NM_002260		G	10584707	A	G	10584707	2	3	340	1	0	0	0	0	0	0	0	1	8425	446	16	2		2	KLRC2	12	10584707	Silent	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10		10584707	123267188	95	47059										
KIAA0528	9847	hgsc.bcm.edu	37	chr12	22610088	22610088	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	actggacttgctttttcaacTgtcatggctaaaattggaga	9	7	2	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr12:22610088T>A	ENST00000333957.4	-	23	2796	c.2541A>T	c.(2539-2541)acA>acT	p.T847T	C2CD5_ENST00000536386.1_Silent_p.T900T|C2CD5_ENST00000542676.1_Silent_p.T898T|C2CD5_ENST00000446597.1_Silent_p.T898T|C2CD5_ENST00000544930.1_Silent_p.T703T|C2CD5_ENST00000396028.2_Silent_p.T889T|C2CD5_ENST00000545552.1_Silent_p.T901T	NM_014802.1	NP_055617.1	Q86YS7	C2CD5_HUMAN	C2 calcium-dependent domain containing 5	847					cellular response to insulin stimulus (GO:0032869)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|intracellular protein transmembrane transport (GO:0065002)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)										CTTTTTCAACTGTCATGGCTA	0.413																																					p.T847T		Atlas-SNP	.											.	.	.	.	0			c.A2541T						.						86	79	81					12																	22610088		2203	4300	6503	SO:0001819	synonymous_variant	9847	exon23			TTCAACTGTCATG	AB011100	CCDS31758.1, CCDS66337.1, CCDS66338.1, CCDS66339.1, CCDS66340.1	12p12.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000111731	ENSG00000111731			29062	protein-coding gene	gene with protein product	"138 kDa C2 domain-containing phosphoprotein"		"KIAA0528"	KIAA0528		21907143	Standard	XM_005253538		Approved	CDP138	uc001rfq.3	Q86YS7	OTTHUMG00000169100	ENST00000333957.4:c.2541A>T	chr12.hg19:g.22610088T>A		183.0	0.0		90.0	16.0	NM_014802	B4DJ03|B4DRN7|B7ZLL0|F5H2A1|F5H5R1|O60280|Q17RY7|Q7Z619|Q86SU3	Silent	SNP	ENST00000333957.4	hg19	CCDS31758.1	.	.	.	.	.	.	.	.	.	.	T	5.333	0.246717	0.10130	.	.	ENSG00000111731	ENST00000539615	.	.	.	4.96	-0.673	0.11373	.	.	.	.	.	T	0.42223	0.1193	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.22382	-1.0218	4	.	.	.	-20.7239	2.6175	0.04907	0.238:0.0694:0.3488:0.3438	.	.	.	.	L	148	.	.	Q	-	2	0	KIAA0528	22501355	0.847000	0.29606	0.966000	0.40874	0.882000	0.50991	-0.013000	0.12678	-0.267000	0.09325	-0.316000	0.08728	CAG	.	.		0.413	C2CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402257.1	NM_014802		A	22610088	T	A	22610088	2	1	340	1	0	0	0	0	0	0	0	1	8191	1567	55	4		4	KIAA0528	12	22610088	Silent	SNP	T	TCGA-RC-A7SK-01A-11D-A34Z-10	12025381	22610088	111241807	96	47060										
ITPR2	3709	hgsc.bcm.edu	37	chr12	26647155	26647155	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	ccttctgaaaaaattctgtcAtttttggtgttcactataac	5	8	4	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr12:26647155A>G	ENST00000381340.3	-	39	5717	c.5301T>C	c.(5299-5301)aaT>aaC	p.N1767N		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1767					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	AAATTCTGTCATTTTTGGTGT	0.388																																					p.N1767N		Atlas-SNP	.											.	ITPR2	270	.	0			c.T5301C						.						109	96	100					12																	26647155		1866	4105	5971	SO:0001819	synonymous_variant	3709	exon39			TCTGTCATTTTTG	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"Ion channels / Inositol triphosphate receptors"	6181	protein-coding gene	gene with protein product	"cilia and flagella associated protein 48"	600144	"inositol 1,4,5-triphosphate receptor, type 2"			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.5301T>C	chr12.hg19:g.26647155A>G		91.0	0.0		22.0	10.0	NM_002223	O94773	Silent	SNP	ENST00000381340.3	hg19	CCDS41764.1																																																																																			.	.		0.388	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		G	26647155	A	G	26647155	2	3	340	1	0	0	0	0	0	0	0	1	7930	214	8	2		2	ITPR2	12	26647155	Silent	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	4037067	26647155	107204740	97	47061										
KRT18	3875	hgsc.bcm.edu	37	chr12	53345925	53345925	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	ggccagcttggagaacagccTgagggaggtggaggcccgct	18	10	0	2			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr12:53345925T>A	ENST00000388835.3	+	6	1181	c.971T>A	c.(970-972)cTg>cAg	p.L324Q	KRT8_ENST00000549198.1_5'Flank|AC107016.2_ENST00000581256.1_RNA|KRT18_ENST00000550600.1_Missense_Mutation_p.L324Q|KRT8_ENST00000552551.1_5'Flank|KRT18_ENST00000388837.2_Missense_Mutation_p.L324Q|KRT8_ENST00000546897.1_5'Flank	NM_000224.2	NP_000215.1	P05783	K1C18_HUMAN	keratin 18	324	Coil 2.|Interaction with DNAJB6.|Necessary for interaction with PNN.|Rod.				anatomical structure morphogenesis (GO:0009653)|cell cycle (GO:0007049)|extrinsic apoptotic signaling pathway (GO:0097191)|Golgi to plasma membrane CFTR protein transport (GO:0043000)|hepatocyte apoptotic process (GO:0097284)|intermediate filament cytoskeleton organization (GO:0045104)|negative regulation of apoptotic process (GO:0043066)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|viral process (GO:0016032)	cell periphery (GO:0071944)|centriolar satellite (GO:0034451)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|scaffold protein binding (GO:0097110)|structural molecule activity (GO:0005198)			central_nervous_system(1)|large_intestine(2)|lung(4)|prostate(3)|skin(1)	11						GAGAACAGCCTGAGGGAGGTG	0.612																																					p.L324Q		Atlas-SNP	.											.	KRT18	31	.	0			c.T971A						.						13	15	14					12																	53345925		2193	4282	6475	SO:0001583	missense	3875	exon6			ACAGCCTGAGGGA		CCDS31809.1	12q13	2013-01-16			ENSG00000111057	ENSG00000111057		"-", "Intermediate filaments type I, keratins (acidic)"	6430	protein-coding gene	gene with protein product		148070				1705144, 16831889	Standard	NM_000224		Approved		uc001sbg.3	P05783	OTTHUMG00000169882	ENST00000388835.3:c.971T>A	chr12.hg19:g.53345925T>A	ENSP00000373487:p.Leu324Gln	39.0	0.0		15.0	6.0	NM_000224	Q53G38|Q5U0N8|Q9BW26	Missense_Mutation	SNP	ENST00000388835.3	hg19	CCDS31809.1	.	.	.	.	.	.	.	.	.	.	t	21.0	4.084436	0.76642	.	.	ENSG00000111057	ENST00000388837;ENST00000550600;ENST00000388835	D;D;D	0.90788	-2.73;-2.73;-2.73	4.0	4.0	0.46444	Filament (1);	0.142260	0.29980	N	0.010713	D	0.96658	0.8909	H	0.98388	4.22	0.44825	D	0.997838	P;P	0.51057	0.941;0.92	P;P	0.61940	0.751;0.896	D	0.97270	0.9910	10	0.87932	D	0	.	11.5011	0.50437	0.0:0.0:0.0:1.0	.	324;324	F8VZY9;P05783	.;K1C18_HUMAN	Q	324	ENSP00000373489:L324Q;ENSP00000447278:L324Q;ENSP00000373487:L324Q	ENSP00000373487:L324Q	L	+	2	0	KRT18	51632192	0.991000	0.36638	1.000000	0.80357	0.955000	0.61496	7.682000	0.84083	2.049000	0.60858	0.459000	0.35465	CTG	.	.		0.612	KRT18-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406405.1	NM_199187		A	53345925	T	A	53345925	3	1	340	1	0	0	0	0	1	0	0	0	8464	1580	55	4	993	4	KRT18	12	53345925	Missense_Mutation	SNP	T	TCGA-RC-A7SK-01A-11D-A34Z-10	26698770	53345925	80505970	98	47062										
MARS	4141	hgsc.bcm.edu	37	chr12	57910051	57910051	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	aaaacgtccccgaagccagcAgttgtagagactgttacaac	9	11	0	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr12:57910051A>C	ENST00000262027.5	+	20	2621	c.2487A>C	c.(2485-2487)gcA>gcC	p.A829A	MIR616_ENST00000385293.1_RNA|MARS_ENST00000315473.5_3'UTR|RN7SL312P_ENST00000582079.1_RNA	NM_004990.3	NP_004981.2	P56192	SYMC_HUMAN	methionyl-tRNA synthetase	829					gene expression (GO:0010467)|methionyl-tRNA aminoacylation (GO:0006431)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|methionine-tRNA ligase activity (GO:0004825)|tRNA binding (GO:0000049)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	33			GBM - Glioblastoma multiforme(3;4.27e-41)		L-Methionine(DB00134)	CGAAGCCAGCAGTTGTAGAGA	0.463																																					p.A829A		Atlas-SNP	.											.	MARS	84	.	0			c.A2487C						.						67	63	64					12																	57910051		2203	4300	6503	SO:0001819	synonymous_variant	4141	exon20			GCCAGCAGTTGTA	X94754	CCDS8942.1	12q13.3	2014-05-06	2007-02-26		ENSG00000166986	ENSG00000166986	6.1.1.10	"Aminoacyl tRNA synthetases / Class I"	6898	protein-coding gene	gene with protein product	"methionine tRNA ligase 1, cytoplasmic"	156560				10448063, 24482476	Standard	NM_004990		Approved	MetRS, SPG70	uc001sog.3	P56192	OTTHUMG00000169996	ENST00000262027.5:c.2487A>C	chr12.hg19:g.57910051A>C		161.0	0.0		67.0	35.0	NM_004990	B3KVK7|Q14895|Q53H14|Q96A15|Q96BZ0|Q9NSE0	Silent	SNP	ENST00000262027.5	hg19	CCDS8942.1	.	.	.	.	.	.	.	.	.	.	A	8.087	0.773576	0.16051	.	.	ENSG00000166986	ENST00000547665	.	.	.	4.84	2.33	0.28932	.	.	.	.	.	T	0.57403	0.2051	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49844	-0.8896	4	.	.	.	-4.0E-4	8.4778	0.33023	0.6898:0.0:0.0:0.3101	.	.	.	.	R	95	.	.	S	+	1	0	MARS	56196318	0.009000	0.17119	0.759000	0.31340	0.015000	0.08874	0.255000	0.18333	0.371000	0.24564	0.459000	0.35465	AGT	.	.		0.463	MARS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407014.1	NM_004990		C	57910051	A	C	57910051	2	2	340	1	0	0	0	0	0	0	0	1	9325	175	7	5		5	MARS	12	57910051	Silent	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	4564126	57910051	75941844	99	47063										
CAND1	55832	hgsc.bcm.edu	37	chr12	67699601	67699602	+	Frame_Shift_Ins	INS	-	-	T													0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	gccatcagttttcttaccacINStttggcaaaagtatatccct							TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr12:67699601_67699602insT	ENST00000545606.1	+	10	2590_2591	c.2153_2154insT	c.(2152-2157)actttgfs	p.L719fs		NM_018448.3	NP_060918.2	Q86VP6	CAND1_HUMAN	cullin-associated and neddylation-dissociated 1	719					cell differentiation (GO:0030154)|negative regulation of catalytic activity (GO:0043086)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|protein ubiquitination (GO:0016567)|SCF complex assembly (GO:0010265)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				NS(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)	35			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)		TTTCTTACCACTTTGGCAAAAG	0.436																																					p.T718fs		Atlas-Indel,Pindel	.											.	CAND1	100	.	0			c.2153_2154insT						.																																			SO:0001589	frameshift_variant	55832	exon10			.		CCDS8977.1	12q14	2008-02-05			ENSG00000111530	ENSG00000111530			30688	protein-coding gene	gene with protein product	"TBP interacting protein"	607727				10048485, 8954946	Standard	NM_018448		Approved	TIP120A, DKFZp434M1414, KIAA0829, TIP120	uc001stn.2	Q86VP6	OTTHUMG00000169060	ENST00000545606.1:c.2156dupT	chr12.hg19:g.67699604_67699604dupT	ENSP00000442318:p.Leu719fs	108.0	0.0		54.0	32.0	NM_018448	B2RAU3|O94918|Q6PIY4|Q8NDJ4|Q96JZ9|Q96T19|Q9BTC4|Q9H0G2|Q9P0H7|Q9UF85	Frame_Shift_Ins	INS	ENST00000545606.1	hg19	CCDS8977.1																																																																																			.	.		0.436	CAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402105.1	NM_018448		T	67699602	-	T	67699601	7	5	340	1	0	1	1	0	0	0	0	0	2617	565	20	0	2191	0	CAND1	12	67699601	Frame_Shift_Ins	INS	-	TCGA-RC-A7SK-01A-11D-A34Z-10	9789550	67699601	66152294	100	47064										
PHLDA1	22822	hgsc.bcm.edu	37	chr12	76425490	76425490	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	gcgggggaaagcccagctccAagaggcgctcggcagccggc	17	14	0	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr12:76425490A>C	ENST00000266671.5	-	1	2222	c.32T>G	c.(31-33)tTg>tGg	p.L11W	PHLDA1_ENST00000602540.1_5'Flank|RP11-290L1.2_ENST00000547721.1_RNA|RP11-290L1.3_ENST00000552367.1_RNA			Q8WV24	PHLA1_HUMAN	pleckstrin homology-like domain, family A, member 1	11					apoptotic process (GO:0006915)|FasL biosynthetic process (GO:0045210)|forebrain neuron differentiation (GO:0021879)|positive regulation of apoptotic process (GO:0043065)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	14		Colorectal(145;0.09)				GCCCAGCTCCAAGAGGCGCTC	0.692																																					p.L11W		Atlas-SNP	.											.	PHLDA1	39	.	0			c.T32G						.						2	3	3					12																	76425490		1614	3601	5215	SO:0001583	missense	22822	exon1			AGCTCCAAGAGGC	Z50194	CCDS31861.1	12q15	2008-08-05				ENSG00000139289			8933	protein-coding gene	gene with protein product	"proline-histidine rich protein"	605335				12384558, 15037619	Standard	NM_007350		Approved	TDAG51, DT1P1B11, PHRIP	uc001sxu.3	Q8WV24		ENST00000266671.5:c.32T>G	chr12.hg19:g.76425490A>C	ENSP00000266671:p.Leu11Trp	70.0	0.0		36.0	18.0	NM_007350	A1A4G9|Q15184|Q2TAN2|Q9NZ17	Missense_Mutation	SNP	ENST00000266671.5	hg19	CCDS31861.1	.	.	.	.	.	.	.	.	.	.	A	11.57	1.678249	0.29783	.	.	ENSG00000139289	ENST00000266671	T	0.46451	0.87	4.71	2.87	0.33458	.	.	.	.	.	T	0.23766	0.0575	N	0.08118	0	0.09310	N	1	P	0.34757	0.467	B	0.35688	0.208	T	0.14952	-1.0454	9	0.87932	D	0	-2.3085	7.7246	0.28753	0.0897:0.1629:0.7474:0.0	.	11	Q8WV24	PHLA1_HUMAN	W	11	ENSP00000266671:L11W	ENSP00000266671:L11W	L	-	2	0	PHLDA1	74711757	0.000000	0.05858	0.352000	0.25734	0.299000	0.27559	0.161000	0.16481	0.583000	0.29574	-0.374000	0.07098	TTG	.	.		0.692	PHLDA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405846.2	NM_007350		C	76425490	A	C	76425490	3	2	340	1	0	0	0	0	1	0	0	0	11857	131	5	5	1177	5	PHLDA1	12	76425490	Missense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	8725889	76425490	57426405	101	47065										
ATP2B1	490	hgsc.bcm.edu	37	chr12	89992431	89992431	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	gtaggggtagaaatatttgtTacatcatgatgctggctggc	13	5	1	2			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr12:89992431T>C	ENST00000359142.3	-	20	3665	c.3441A>G	c.(3439-3441)gtA>gtG	p.V1147V	ATP2B1_ENST00000348959.3_Intron|ATP2B1_ENST00000393164.2_Intron|ATP2B1_ENST00000261173.2_Intron|ATP2B1_ENST00000428670.3_Intron	NM_001001323.1	NP_001001323.1	P20020	AT2B1_HUMAN	ATPase, Ca++ transporting, plasma membrane 1	1147					blood coagulation (GO:0007596)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	45						AAATATTTGTTACATCATGAT	0.453																																					p.V1147V		Atlas-SNP	.											.	ATP2B1	191	.	0			c.A3441G						.						198	197	198					12																	89992431		1980	4164	6144	SO:0001819	synonymous_variant	490	exon20			ATTTGTTACATCA	J04027	CCDS9035.1, CCDS41817.1	12q21.33	2010-04-20			ENSG00000070961	ENSG00000070961	3.6.3.8	"ATPases / P-type"	814	protein-coding gene	gene with protein product	"plasma membrane calcium-transporting ATPase 1"	108731				1674727	Standard	NM_001682		Approved	PMCA1	uc001tbh.3	P20020		ENST00000359142.3:c.3441A>G	chr12.hg19:g.89992431T>C		106.0	0.0		50.0	5.0	NM_001001323	Q12992|Q12993|Q13819|Q13820|Q13821|Q16504|Q93082	Silent	SNP	ENST00000359142.3	hg19	CCDS41817.1																																																																																			.	.		0.453	ATP2B1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000406652.1	NM_001682		C	89992431	T	C	89992431	2	2	340	1	0	0	0	0	0	0	0	1	1139	1741	61	2		2	ATP2B1	12	89992431	Silent	SNP	T	TCGA-RC-A7SK-01A-11D-A34Z-10	13566941	89992431	43859464	102	47066										
NR2C1	7181	hgsc.bcm.edu	37	chr12	95451647	95451647	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	tcaatgggttttctttcacaTtggacagctacaaaaatgtg	8	7	3	0			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr12:95451647T>C	ENST00000333003.5	-	6	882	c.552A>G	c.(550-552)caA>caG	p.Q184Q	NR2C1_ENST00000393101.3_Silent_p.Q184Q|NR2C1_ENST00000330677.7_Silent_p.Q184Q|NR2C1_ENST00000545833.1_5'UTR	NM_003297.3	NP_003288.2	P13056	NR2C1_HUMAN	nuclear receptor subfamily 2, group C, member 1	184					gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	DNA binding (GO:0003677)|receptor activity (GO:0004872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)	13						TTCTTTCACATTGGACAGCTA	0.348																																					p.Q184Q		Atlas-SNP	.											.	NR2C1	56	.	0			c.A552G						.						86	89	88					12																	95451647		2203	4300	6503	SO:0001819	synonymous_variant	7181	exon6			TTCACATTGGACA	M29960	CCDS9051.1, CCDS41821.1, CCDS44953.1	12q22	2013-01-16				ENSG00000120798		"Nuclear hormone receptors"	7971	protein-coding gene	gene with protein product		601529		TR2		2597158	Standard	NM_001032287		Approved	TR2-11	uc001tdm.5	P13056	OTTHUMG00000170131	ENST00000333003.5:c.552A>G	chr12.hg19:g.95451647T>C		135.0	0.0		75.0	20.0	NM_001032287	A8K5K4|Q15625|Q15626	Silent	SNP	ENST00000333003.5	hg19	CCDS9051.1																																																																																			.	.		0.348	NR2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407565.2	NM_003297		C	95451647	T	C	95451647	2	2	340	1	0	0	0	0	0	0	0	1	10631	1490	52	2		2	NR2C1	12	95451647	Silent	SNP	T	TCGA-RC-A7SK-01A-11D-A34Z-10	5459216	95451647	38400248	103	47067										
ANKS1B	56899	hgsc.bcm.edu	37	chr12	99638191	99638191	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	tggaactcattattttgtcaAtctgtaagaaacaaaaacca	5	7	3	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr12:99638191A>G	ENST00000547776.2	-	14	2347	c.2348T>C	c.(2347-2349)aTt>aCt	p.I783T	ANKS1B_ENST00000547010.1_Splice_Site_p.I363T|ANKS1B_ENST00000329257.7_Splice_Site_p.I783T|ANKS1B_ENST00000550833.1_5'Flank	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	783						cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(15)|lung(38)|pancreas(1)|prostate(2)|skin(1)	70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		TATTTTGTCAATCTGTAAGAA	0.299																																					p.I783T		Atlas-SNP	.											.	ANKS1B	180	.	0			c.T2348C						.						153	137	142					12																	99638191		1830	4069	5899	SO:0001630	splice_region_variant	56899	exon14			TTGTCAATCTGTA	AF145204	CCDS55864.1, CCDS55865.1, CCDS55866.1, CCDS55867.1, CCDS55868.1, CCDS55869.1, CCDS55870.1, CCDS55871.1, CCDS55872.1	12q23.1	2013-01-10						"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	24600	protein-coding gene	gene with protein product		607815				10490826, 12415113	Standard	NM_020140		Approved	EB-1, AIDA-1, cajalin-2, ANKS2	uc001tge.2	Q7Z6G8		ENST00000547776.2:c.2347-1T>C	chr12.hg19:g.99638191A>G		104.0	0.0		61.0	9.0	NM_152788	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Missense_Mutation	SNP	ENST00000547776.2	hg19	CCDS55872.1	.	.	.	.	.	.	.	.	.	.	A	19.59	3.857087	0.71834	.	.	ENSG00000185046	ENST00000547776;ENST00000547010;ENST00000329257;ENST00000538702	T;T;T	0.71817	-0.0;-0.6;0.0	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.80934	0.4719	L	0.57536	1.79	0.80722	D	1	D;D	0.89917	1.0;0.981	D;D	0.97110	1.0;0.966	T	0.80417	-0.1391	9	.	.	.	-8.7181	14.3914	0.66981	1.0:0.0:0.0:0.0	.	363;783	Q7Z6G8-6;Q7Z6G8	.;ANS1B_HUMAN	T	783;363;783;362	ENSP00000449629:I783T;ENSP00000448512:I363T;ENSP00000331381:I783T	.	I	-	2	0	ANKS1B	98162322	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.543000	0.82106	2.192000	0.70111	0.459000	0.35465	ATT	.	.		0.299	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140	Missense_Mutation	G	99638191	A	G	99638191	5	3	340	1	0	0	0	0	0	0	1	0	689	115	4	2	1738	2	ANKS1B	12	99638191	Splice_Site	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	4186544	99638191	34213704	104	47068										
ANKS1B	56899	hgsc.bcm.edu	37	chr12	99793570	99793570	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	gaaaatccagagaagacacaAtggatgttcgctgtttaggc	11	7	0	2			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr12:99793570A>G	ENST00000547776.2	-	12	1594	c.1595T>C	c.(1594-1596)aTt>aCt	p.I532T	ANKS1B_ENST00000547010.1_Missense_Mutation_p.I112T|ANKS1B_ENST00000329257.7_Missense_Mutation_p.I532T	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	532						cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(15)|lung(38)|pancreas(1)|prostate(2)|skin(1)	70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		AGAAGACACAATGGATGTTCG	0.388																																					p.I532T		Atlas-SNP	.											.	ANKS1B	180	.	0			c.T1595C						.						156	164	162					12																	99793570		1887	4113	6000	SO:0001583	missense	56899	exon12			GACACAATGGATG	AF145204	CCDS55864.1, CCDS55865.1, CCDS55866.1, CCDS55867.1, CCDS55868.1, CCDS55869.1, CCDS55870.1, CCDS55871.1, CCDS55872.1	12q23.1	2013-01-10						"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	24600	protein-coding gene	gene with protein product		607815				10490826, 12415113	Standard	NM_020140		Approved	EB-1, AIDA-1, cajalin-2, ANKS2	uc001tge.2	Q7Z6G8		ENST00000547776.2:c.1595T>C	chr12.hg19:g.99793570A>G	ENSP00000449629:p.Ile532Thr	125.0	0.0		75.0	14.0	NM_152788	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Missense_Mutation	SNP	ENST00000547776.2	hg19	CCDS55872.1	.	.	.	.	.	.	.	.	.	.	A	17.15	3.316865	0.60524	.	.	ENSG00000185046	ENST00000547776;ENST00000547010;ENST00000329257;ENST00000538702;ENST00000549866	T;T;T;T	0.61980	0.83;0.06;0.83;0.52	5.73	5.73	0.89815	.	0.266741	0.30879	N	0.008699	T	0.51432	0.1674	N	0.22421	0.69	0.80722	D	1	P;P;B	0.37330	0.59;0.59;0.18	B;B;B	0.41332	0.266;0.354;0.076	T	0.49960	-0.8883	9	.	.	.	-10.4795	13.5328	0.61631	1.0:0.0:0.0:0.0	.	498;112;532	F8VVQ4;Q7Z6G8-6;Q7Z6G8	.;.;ANS1B_HUMAN	T	532;112;532;111;498	ENSP00000449629:I532T;ENSP00000448512:I112T;ENSP00000331381:I532T;ENSP00000449894:I498T	.	I	-	2	0	ANKS1B	98317701	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	6.278000	0.72614	2.184000	0.69523	0.477000	0.44152	ATT	.	.		0.388	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140		G	99793570	A	G	99793570	3	3	340	1	0	0	0	0	1	0	0	0	689	101	4	2	2499	2	ANKS1B	12	99793570	Missense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	155379	99793570	34058325	105	47069										
ATP6V0A2	23545	hgsc.bcm.edu	37	chr12	124229432	124229432	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	tctgctttttgttacagtgaCagcgtcgttagacacaacag	9	9	1	2			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr12:124229432C>A	ENST00000330342.3	+	13	1766	c.1518C>A	c.(1516-1518)gaC>gaA	p.D506E		NM_012463.3	NP_036595.2	Q9Y487	VPP2_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a2	506					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|immune response (GO:0006955)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	hydrogen ion transmembrane transporter activity (GO:0015078)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.000625)|all cancers(50;0.00775)		GTTACAGTGACAGCGTCGTTA	0.522																																					p.D506E		Atlas-SNP	.											.	ATP6V0A2	68	.	0			c.C1518A						.						176	147	157					12																	124229432		2203	4300	6503	SO:0001583	missense	23545	exon13			CAGTGACAGCGTC	AF112972	CCDS9254.1	12q24.31	2010-04-21	2006-01-20		ENSG00000185344	ENSG00000185344		"ATPases / V-type"	18481	protein-coding gene	gene with protein product	"infantile malignant osteopetrosis"	611716	"infantile malignant osteopetrosis", "ATPase, H+ transporting, lysosomal V0 subunit a isoform 2", "ATPase, H+ transporting, lysosomal V0 subunit A2"			2247090, 18157129	Standard	NM_012463		Approved	TJ6, a2, TJ6s, TJ6M, ATP6a2, J6B7, ATP6N1D, Vph1, Stv1	uc001ufr.3	Q9Y487	OTTHUMG00000168723	ENST00000330342.3:c.1518C>A	chr12.hg19:g.124229432C>A	ENSP00000332247:p.Asp506Glu	106.0	0.0		40.0	17.0	NM_012463	A8K026|Q6NUM0	Missense_Mutation	SNP	ENST00000330342.3	hg19	CCDS9254.1	.	.	.	.	.	.	.	.	.	.	C	2.760	-0.258082	0.05791	.	.	ENSG00000185344	ENST00000330342	D	0.84146	-1.81	5.32	4.37	0.52481	.	0.625902	0.18375	N	0.143130	T	0.69806	0.3152	N	0.21240	0.645	0.37146	D	0.901955	B	0.06786	0.001	B	0.12837	0.008	T	0.61964	-0.6954	10	0.02654	T	1	-34.0027	7.9518	0.30019	0.1624:0.7527:0.0:0.0849	.	506	Q9Y487	VPP2_HUMAN	E	506	ENSP00000332247:D506E	ENSP00000332247:D506E	D	+	3	2	ATP6V0A2	122795385	0.031000	0.19500	0.937000	0.37676	0.018000	0.09664	0.737000	0.26144	2.503000	0.84419	0.555000	0.69702	GAC	.	.		0.522	ATP6V0A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400765.2	NM_012463		A	124229432	C	A	124229432	3	1	340	1	0	0	0	0	1	0	0	0	1169	477	17	3	1568	3	ATP6V0A2	12	124229432	Missense_Mutation	SNP	C	TCGA-RC-A7SK-01A-11D-A34Z-10	24435862	124229432	9622463	106	47070										
RALGAPA1	253959	hgsc.bcm.edu	37	chr14	36041819	36041819	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	gtgatttttcattggatataTtacaataaggacatcaccaa	6	6	2	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr14:36041819T>C	ENST00000389698.3	-	37	6187	c.5797A>G	c.(5797-5799)Ata>Gta	p.I1933V	RALGAPA1_ENST00000258840.6_Missense_Mutation_p.I1980V|RALGAPA1_ENST00000382366.3_Missense_Mutation_p.I1946V|RALGAPA1_ENST00000307138.6_Missense_Mutation_p.I1933V	NM_014990.1	NP_055805.1	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1 (catalytic)	1933	Minimal domain that binds to TCF3/E12. {ECO:0000250}.|Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				activation of Ral GTPase activity (GO:0032859)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(7)|large_intestine(14)|lung(21)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						ATTGGATATATTACAATAAGG	0.333																																					p.I1933V		Atlas-SNP	.											.	RALGAPA1	289	.	0			c.A5797G						.						97	99	98					14																	36041819		2203	4298	6501	SO:0001583	missense	253959	exon37			GATATATTACAAT	AK126975	CCDS32064.1, CCDS32065.1, CCDS61439.1	14q13.2	2012-01-26	2009-09-09	2009-09-09	ENSG00000174373	ENSG00000174373			17770	protein-coding gene	gene with protein product	"tuberin-like protein 1", "GAP-related interacting protein to E12"	608884	"GTPase activating RANGAP domain-like 1", "GTPase activating Rap/RanGAP domain-like 1"	GARNL1		19520869	Standard	NM_014990		Approved	GRIPE, DKFZp667F074, KIAA0884, Tulip1, RalGAPalpha1	uc001wtj.3	Q6GYQ0	OTTHUMG00000170619	ENST00000389698.3:c.5797A>G	chr14.hg19:g.36041819T>C	ENSP00000374348:p.Ile1933Val	82.0	0.0		31.0	11.0	NM_194301	A6NMA4|B9EK38|C5NU19|O94960|Q6GYP9|Q6ZT23|Q86YF3|Q86YF5|Q8ND69	Missense_Mutation	SNP	ENST00000389698.3	hg19	CCDS32065.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.257074	0.80246	.	.	ENSG00000174373	ENST00000389698;ENST00000307138;ENST00000335518;ENST00000258840;ENST00000554259;ENST00000382366;ENST00000553892	D;D;D;D;D;D	0.92545	-3.06;-3.06;-3.06;-3.06;-3.06;-3.06	5.15	5.15	0.70609	Rap/ran-GAP (2);	0.000000	0.85682	D	0.000000	D	0.94241	0.8151	L	0.49640	1.575	0.53005	D	0.999965	D;D;P;P	0.71674	0.958;0.998;0.926;0.846	D;D;P;P	0.91635	0.966;0.999;0.879;0.759	D	0.93300	0.6676	10	0.33141	T	0.24	-15.3646	14.9932	0.71406	0.0:0.0:0.0:1.0	.	1980;1946;1933;1933	Q6GYQ0-6;B9EK38;Q6GYQ0-2;Q6GYQ0	.;.;.;RGPA1_HUMAN	V	1933;1933;1933;1980;571;1946;1980	ENSP00000374348:I1933V;ENSP00000302647:I1933V;ENSP00000258840:I1980V;ENSP00000451133:I571V;ENSP00000371803:I1946V;ENSP00000451877:I1980V	ENSP00000258840:I1980V	I	-	1	0	RALGAPA1	35111570	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.040000	0.89188	1.947000	0.56498	0.377000	0.23210	ATA	.	.		0.333	RALGAPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409829.1	XM_210022		C	36041819	T	C	36041819	3	2	340	1	0	0	0	0	1	0	0	0	13028	1493	52	2	482	2	RALGAPA1	14	36041819	Missense_Mutation	SNP	T	TCGA-RC-A7SK-01A-11D-A34Z-10		36041819	71307721	107	47071										
KTN1	3895	hgsc.bcm.edu	37	chr14	56078888	56078888	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	tgatgaagttcttgcaaaacAgaaaagagaacaaaagctta	8	5	1	4			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr14:56078888A>G	ENST00000395314.3	+	2	190	c.122A>G	c.(121-123)cAg>cGg	p.Q41R	KTN1_ENST00000416613.1_Missense_Mutation_p.Q41R|KTN1_ENST00000395309.3_Missense_Mutation_p.Q41R|KTN1_ENST00000438792.2_Missense_Mutation_p.Q41R|KTN1_ENST00000395311.1_Missense_Mutation_p.Q41R|KTN1_ENST00000395308.1_Missense_Mutation_p.Q41R|KTN1_ENST00000413890.2_Missense_Mutation_p.Q41R	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	41					microtubule-based movement (GO:0007018)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|large_intestine(8)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	19						CTTGCAAAACAGAAAAGAGAA	0.284			T	RET	papillary thryoid																																p.Q41R		Atlas-SNP	.		Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	.	KTN1	147	.	0			c.A122G						.						35	37	37					14																	56078888		2202	4297	6499	SO:0001583	missense	3895	exon2			CAAAACAGAAAAG		CCDS41957.1, CCDS41958.1, CCDS41959.1	14q22.1	2008-05-02			ENSG00000126777	ENSG00000126777			6467	protein-coding gene	gene with protein product		600381				9605849	Standard	NM_001079521		Approved	KIAA0004, CG1	uc001xcc.3	Q86UP2	OTTHUMG00000140312	ENST00000395314.3:c.122A>G	chr14.hg19:g.56078888A>G	ENSP00000378725:p.Gln41Arg	212.0	0.0		98.0	33.0	NM_004986	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Missense_Mutation	SNP	ENST00000395314.3	hg19	CCDS41957.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.106183	0.77096	.	.	ENSG00000126777	ENST00000557267;ENST00000413890;ENST00000395309;ENST00000555498;ENST00000438792;ENST00000395314;ENST00000395308;ENST00000395311;ENST00000416613	D;D;D;D;D;D;D;D;D	0.98937	-5.25;-5.25;-5.25;-5.25;-5.25;-5.25;-5.25;-5.25;-5.25	5.49	5.49	0.81192	.	0.130124	0.34879	N	0.003603	D	0.97660	0.9233	L	0.59436	1.845	0.54753	D	0.999987	P;P;P;P	0.40834	0.64;0.73;0.64;0.561	B;B;B;B	0.42625	0.393;0.22;0.393;0.329	D	0.98010	1.0365	10	0.49607	T	0.09	-2.9399	15.5747	0.76368	1.0:0.0:0.0:0.0	.	41;41;41;41	B4DZ88;Q86UP2-2;Q17RZ5;Q86UP2	.;.;.;KTN1_HUMAN	R	41	ENSP00000451641:Q41R;ENSP00000394992:Q41R;ENSP00000378720:Q41R;ENSP00000451878:Q41R;ENSP00000391964:Q41R;ENSP00000378725:Q41R;ENSP00000378719:Q41R;ENSP00000378722:Q41R;ENSP00000388807:Q41R	ENSP00000378719:Q41R	Q	+	2	0	KTN1	55148641	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	8.596000	0.90844	2.074000	0.62210	0.482000	0.46254	CAG	.	.		0.284	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2			G	56078888	A	G	56078888	3	3	340	1	0	0	0	0	1	0	0	0	8594	188	7	2	124	2	KTN1	14	56078888	Missense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	20037069	56078888	51270652	108	47072										
SNW1	22938	hgsc.bcm.edu	37	chr14	78198864	78198864	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	tagagggcttctgccaatttGgcgaaattttcatttatgtg	10	6	2	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr14:78198864G>A	ENST00000261531.7	-	9	917	c.855C>T	c.(853-855)gcC>gcT	p.A285A	SNW1_ENST00000555761.1_Silent_p.A285A|SNW1_ENST00000554775.1_Silent_p.A123A|SLIRP_ENST00000557431.1_Intron	NM_012245.2	NP_036377.1	Q13573	SNW1_HUMAN	SNW domain containing 1	285	SNW.				cellular response to retinoic acid (GO:0071300)|gene expression (GO:0010467)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of vitamin D receptor signaling pathway (GO:0070564)|regulation of retinoic acid receptor signaling pathway (GO:0048385)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of vitamin D receptor signaling pathway (GO:0070562)|retinoic acid receptor signaling pathway (GO:0048384)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|chromatin (GO:0000785)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	Notch binding (GO:0005112)|nuclear hormone receptor binding (GO:0035257)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)|SMAD binding (GO:0046332)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|vitamin D receptor binding (GO:0042809)			NS(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0291)		CTGCCAATTTGGCGAAATTTT	0.383																																					p.A285A		Atlas-SNP	.											.	SNW1	44	.	0			c.C855T						.						118	111	113					14																	78198864		2203	4300	6503	SO:0001819	synonymous_variant	22938	exon9			CAATTTGGCGAAA	AF045184	CCDS9867.1	14q22.1-q22.3	2005-09-13	2005-09-13	2005-09-13		ENSG00000100603			16696	protein-coding gene	gene with protein product		603055	"SKI interacting protein"	SKIIP		8973337, 9632709	Standard	NM_012245		Approved	NCoA-62, SKIP, Prp45, PRPF45, Bx42	uc001xuf.3	Q13573		ENST00000261531.7:c.855C>T	chr14.hg19:g.78198864G>A		106.0	0.0		35.0	17.0	NM_012245	A8K8A9|Q13483|Q32N03|Q5D0D6	Silent	SNP	ENST00000261531.7	hg19	CCDS9867.1																																																																																			.	.		0.383	SNW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413912.1	NM_012245		A	78198864	G	A	78198864	2	1	340	1	0	0	0	0	0	0	0	1	14894	1335	47	3		3	SNW1	14	78198864	Silent	SNP	G	TCGA-RC-A7SK-01A-11D-A34Z-10	22119976	78198864	29150676	109	47073										
ZC3H14	79882	hgsc.bcm.edu	37	chr14	89034417	89034418	+	Missense_Mutation	DNP	GG	GG	TT													0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	gattacattatggtgatggtGgccaacaagaaaagtcagga							TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr14:89034417_89034418GG>TT	ENST00000251038.5	+	3	339_340	c.114_115GG>TT	c.(112-117)gtGGcc>gtTTcc	p.A39S	ZC3H14_ENST00000359301.3_Missense_Mutation_p.A5S|ZC3H14_ENST00000302216.8_Missense_Mutation_p.A39S|ZC3H14_ENST00000555755.1_Missense_Mutation_p.A39S|ZC3H14_ENST00000336693.4_Missense_Mutation_p.A5S|ZC3H14_ENST00000393514.5_Missense_Mutation_p.A39S|ZC3H14_ENST00000556945.1_Missense_Mutation_p.A39S|ZC3H14_ENST00000557607.1_Intron	NM_001160103.1|NM_001160104.1|NM_024824.4	NP_001153575.1|NP_001153576.1|NP_079100.2	Q6PJT7	ZC3HE_HUMAN	zinc finger CCCH-type containing 14	39						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(2)	21						TGGTGATGGTGGCCAACAAGAA	0.371																																					p.V38V|p.A39S		Atlas-SNP	.											.	ZC3H14	71	.	0			c.G114T|c.G115T						.																																			SO:0001583	missense	79882	exon3			GATGGTGGCCAAC|ATGGTGGCCAACA	AF155107	CCDS32133.1, CCDS32134.1, CCDS32135.1, CCDS32136.1, CCDS55938.1	14q31.3	2014-08-12			ENSG00000100722	ENSG00000100722		"Zinc fingers, CCCH-type domain containing"	20509	protein-coding gene	gene with protein product		613279				10508479	Standard	NM_024824		Approved	FLJ11806, UKp68, NY-REN-37	uc001xww.3	Q6PJT7	OTTHUMG00000170803	Exception_encountered	chr14.hg19:g.89034417_89034418delinsTT	ENSP00000251038:p.Ala39Ser	158.0|157.0	0.0		51.0	11.0	NM_001160104	A8MY46|B4DXU8|B4DZW7|B4E2H4|G3V5R4|Q6MZU4|Q6PJ32|Q6PUI6|Q6PUI8|Q86TQ5|Q86TW0|Q86TW1|Q8NCT6|Q8NCZ3|Q8TDE2|Q9HAC9|Q9Y5A0	Silent|Missense_Mutation	SNP	ENST00000251038.5	hg19	CCDS32133.1																																																																																			.	.		0.371	ZC3H14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410387.1	NM_024824		TT	89034418	GG	TT	89034417	3	4	340	1	0	0	0	0	1	0	0	0	17581	1335	47	3	124	3	ZC3H14	14	89034417	Missense_Mutation	DNP	GG	TCGA-RC-A7SK-01A-11D-A34Z-10	10835553	89034417	18315123	110	47074										
EIF2AK4	440275	hgsc.bcm.edu	37	chr15	40321621	40321621	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	ttttagagaagcttccgataAtcttgcagtgcaaaatctga	8	7	2	2			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr15:40321621A>G	ENST00000263791.5	+	34	4560	c.4517A>G	c.(4516-4518)aAt>aGt	p.N1506S	EIF2AK4_ENST00000382727.2_Missense_Mutation_p.N1478S	NM_001013703.2	NP_001013725.2	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha kinase 4	1506					cellular response to starvation (GO:0009267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of translation (GO:0017148)|protein phosphorylation (GO:0006468)|regulation of translational initiation (GO:0006446)|regulation of translational initiation in response to stress (GO:0043558)	cytosolic ribosome (GO:0022626)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)	40		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		GCTTCCGATAATCTTGCAGTG	0.323																																					p.N1506S		Atlas-SNP	.											.	EIF2AK4	107	.	0			c.A4517G						.						119	116	117					15																	40321621		1836	4074	5910	SO:0001583	missense	440275	exon34			CCGATAATCTTGC	AB037759	CCDS42016.1	15q13.3	2008-08-18				ENSG00000128829			19687	protein-coding gene	gene with protein product		609280				10504407	Standard	XM_005254392		Approved	GCN2, KIAA1338	uc001zkm.1	Q9P2K8		ENST00000263791.5:c.4517A>G	chr15.hg19:g.40321621A>G	ENSP00000263791:p.Asn1506Ser	135.0	0.0		65.0	19.0	NM_001013703	C9JEC4|Q69YL7|Q6DC97|Q96GN6|Q9H5K1|Q9NSQ3|Q9NSZ5|Q9UJ56	Missense_Mutation	SNP	ENST00000263791.5	hg19	CCDS42016.1	.	.	.	.	.	.	.	.	.	.	A	9.610	1.131109	0.21041	.	.	ENSG00000128829	ENST00000263791;ENST00000382727	T;T	0.40756	1.02;1.02	5.83	4.71	0.59529	Serine/threonine-protein kinase GCN2, anticodon binding domain (1);	0.092562	0.85682	D	0.000000	T	0.15825	0.0381	N	0.02916	-0.46	0.41036	D	0.985193	B;B	0.13145	0.006;0.007	B;B	0.15052	0.007;0.012	T	0.16247	-1.0409	10	0.05436	T	0.98	-28.7942	9.7267	0.40337	0.9215:0.0:0.0785:0.0	.	1478;1506	Q9P2K8-2;Q9P2K8	.;E2AK4_HUMAN	S	1506;1478	ENSP00000263791:N1506S;ENSP00000372174:N1478S	ENSP00000263791:N1506S	N	+	2	0	EIF2AK4	38108913	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.756000	0.38390	2.212000	0.71576	0.533000	0.62120	AAT	.	.		0.323	EIF2AK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418395.1			G	40321621	A	G	40321621	3	3	340	1	0	0	0	0	1	0	0	0	5001	101	4	2	4651	2	EIF2AK4	15	40321621	Missense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10		40321621	62209771	111	47075										
FBN1	2200	hgsc.bcm.edu	37	chr15	48808530	48808530	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	tggtctcccaggaattaccaTaggaacagagcacagcttgt	10	10	1	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr15:48808530T>C	ENST00000316623.5	-	11	1632	c.1177A>G	c.(1177-1179)Atg>Gtg	p.M393V		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	393					extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		GGAATTACCATAGGAACAGAG	0.483																																					p.M393V		Atlas-SNP	.											.	FBN1	310	.	0			c.A1177G						.						66	69	68					15																	48808530		2197	4296	6493	SO:0001583	missense	2200	exon11			TTACCATAGGAAC	X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.1177A>G	chr15.hg19:g.48808530T>C	ENSP00000325527:p.Met393Val	27.0	0.0		14.0	4.0	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	hg19	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	T	6.334	0.429725	0.11987	.	.	ENSG00000166147	ENST00000316623	T	0.80566	-1.39	5.54	-3.06	0.05379	Matrix fibril-associated (1);	0.827694	0.11605	N	0.547342	T	0.51635	0.1686	N	0.08118	0	0.21020	N	0.999809	B	0.02656	0.0	B	0.01281	0.0	T	0.38394	-0.9663	10	0.14656	T	0.56	.	2.0393	0.03546	0.1465:0.1959:0.4312:0.2265	.	393	P35555	FBN1_HUMAN	V	393	ENSP00000325527:M393V	ENSP00000325527:M393V	M	-	1	0	FBN1	46595822	0.789000	0.28775	0.957000	0.39632	0.797000	0.45037	0.226000	0.17776	-0.387000	0.07809	-0.316000	0.08728	ATG	.	.		0.483	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			C	48808530	T	C	48808530	3	2	340	1	0	0	0	0	1	0	0	0	5710	1406	49	2	7662	2	FBN1	15	48808530	Missense_Mutation	SNP	T	TCGA-RC-A7SK-01A-11D-A34Z-10	8486909	48808530	53722862	112	47076										
PGPEP1L	145814	hgsc.bcm.edu	37	chr15	99512764	99512764	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	tctgggctgccaggtaggcaCacgccgccctcgggccagaa	14	15	1	1	rs572947532	byFrequency	TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr15:99512764C>A	ENST00000378919.6	-	4	466	c.261G>T	c.(259-261)gtG>gtT	p.V87V	PGPEP1L_ENST00000535714.1_Silent_p.V33V|RP11-654A16.3_ENST00000559468.1_RNA	NM_001102612.2	NP_001096082.2	A6NFU8	PGPIL_HUMAN	pyroglutamyl-peptidase I-like	87							cysteine-type peptidase activity (GO:0008234)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(2)|skin(1)|stomach(1)	14						CAGGTAGGCACACGCCGCCCT	0.632																																					p.V87V		Atlas-SNP	.											.	PGPEP1L	26	.	0			c.G261T						.						105	112	110					15																	99512764		2194	4293	6487	SO:0001819	synonymous_variant	145814	exon4			TAGGCACACGCCG		CCDS53977.1, CCDS58400.1	15q26.3	2010-02-16			ENSG00000183571	ENSG00000183571			27080	protein-coding gene	gene with protein product							Standard	NM_001102612		Approved		uc002bum.3	A6NFU8		ENST00000378919.6:c.261G>T	chr15.hg19:g.99512764C>A		58.0	0.0		45.0	17.0	NM_001102612	H0YF86	Silent	SNP	ENST00000378919.6	hg19	CCDS53977.1																																																																																			.	.		0.632	PGPEP1L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415703.1	NM_001102612.2		A	99512764	C	A	99512764	2	1	340	1	0	0	0	0	0	0	0	1	11813	465	17	3		3	PGPEP1L	15	99512764	Silent	SNP	C	TCGA-RC-A7SK-01A-11D-A34Z-10	50704234	99512764	3018628	113	47077										
MYH11	4629	hgsc.bcm.edu	37	chr16	15931900	15931900	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	tggatgtcatctttcccaacCgtgaccttcttgccattctc	6	14	4	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr16:15931900C>A	ENST00000300036.5	-	2	319	c.210G>T	c.(208-210)acG>acT	p.T70T	MYH11_ENST00000452625.2_Silent_p.T70T|MYH11_ENST00000396324.3_Silent_p.T70T|MYH11_ENST00000576790.2_Silent_p.T70T	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	70					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						CTTTCCCAACCGTGACCTTCT	0.577			T	CBFB	AML																																p.T70T		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"myosin, heavy polypeptide 11, smooth muscle"		L	.	MYH11	520	.	0			c.G210T						.						310	261	277					16																	15931900		2197	4300	6497	SO:0001819	synonymous_variant	4629	exon2			CCCAACCGTGACC	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"Myosins / Myosin superfamily : Class II"	7569	protein-coding gene	gene with protein product		160745	"myosin, heavy polypeptide 11, smooth muscle"			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.210G>T	chr16.hg19:g.15931900C>A		103.0	0.0		53.0	12.0	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Silent	SNP	ENST00000300036.5	hg19	CCDS10565.1																																																																																			.	.		0.577	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113		A	15931900	C	A	15931900	2	1	340	1	0	0	0	0	0	0	0	1	10040	639	23	1		1	MYH11	16	15931900	Silent	SNP	C	TCGA-RC-A7SK-01A-11D-A34Z-10		15931900	74422853	114	47078										
FHOD1	29109	hgsc.bcm.edu	37	chr16	67267989	67267989	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	aagtccaggtccccaatagaGagcctgggtgcacgggtagg	15	10	0	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr16:67267989G>T	ENST00000258201.4	-	13	1864	c.1617C>A	c.(1615-1617)ctC>ctA	p.L539L		NM_013241.2	NP_037373.2	Q9Y613	FHOD1_HUMAN	formin homology 2 domain containing 1	539	FH1.				positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			breast(4)|endometrium(3)|kidney(3)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	34		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000691)|Epithelial(162;0.00462)|all cancers(182;0.0434)		CCCCAATAGAGAGCCTGGGTG	0.592																																					p.L539L		Atlas-SNP	.											.	FHOD1	86	.	0			c.C1617A						.						86	92	90					16																	67267989		2198	4300	6498	SO:0001819	synonymous_variant	29109	exon13			AATAGAGAGCCTG	AF113615	CCDS10834.1	16q22	2008-02-22			ENSG00000135723	ENSG00000135723			17905	protein-coding gene	gene with protein product		606881				10352228, 16112087	Standard	NM_013241		Approved	FHOS	uc002esl.3	Q9Y613	OTTHUMG00000137521	ENST00000258201.4:c.1617C>A	chr16.hg19:g.67267989G>T		65.0	0.0		30.0	10.0	NM_013241	Q59F76|Q6Y1F2|Q76MS8|Q8N521	Silent	SNP	ENST00000258201.4	hg19	CCDS10834.1																																																																																			.	.		0.592	FHOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268844.2			T	67267989	G	T	67267989	2	4	340	1	0	0	0	0	0	0	0	1	5890	929	33	3		3	FHOD1	16	67267989	Silent	SNP	G	TCGA-RC-A7SK-01A-11D-A34Z-10	51336089	67267989	23086764	115	47079										
AP1G1	164	hgsc.bcm.edu	37	chr16	71772938	71772938	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	actgttacactggggttggtAtttgaccgttcaaaggtgaa	12	6	1	2			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr16:71772938A>C	ENST00000299980.4	-	21	2616	c.2175T>G	c.(2173-2175)aaT>aaG	p.N725K	AP1G1_ENST00000393512.3_Missense_Mutation_p.N728K|AP1G1_ENST00000423132.2_Missense_Mutation_p.N728K|AP1G1_ENST00000433195.2_Missense_Mutation_p.N748K|AP1G1_ENST00000569748.1_Missense_Mutation_p.N725K|AP1G1_ENST00000564155.1_Missense_Mutation_p.N150K	NM_001128.5	NP_001119.3	O43747	AP1G1_HUMAN	adaptor-related protein complex 1, gamma 1 subunit	725	GAE. {ECO:0000255|PROSITE- ProRule:PRU00093}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|endosome to melanosome transport (GO:0035646)|Golgi to lysosome transport (GO:0090160)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network membrane (GO:0032588)	GTP-dependent protein binding (GO:0030742)|kinesin binding (GO:0019894)|protein transporter activity (GO:0008565)|Rab GTPase binding (GO:0017137)|transporter activity (GO:0005215)			breast(1)|endometrium(8)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|urinary_tract(1)	28		Ovarian(137;0.125)				TGGGGTTGGTATTTGACCGTT	0.433																																					p.N728K		Atlas-SNP	.											.	AP1G1	83	.	0			c.T2184G						.						251	221	231					16																	71772938		2198	4300	6498	SO:0001583	missense	164	exon22			GTTGGTATTTGAC	Y12226	CCDS32480.1, CCDS45522.1	16q23	2009-08-03				ENSG00000166747			555	protein-coding gene	gene with protein product	"gamma1-adaptin"	603533		CLAPG1, ADTG		9653655, 9733768	Standard	NM_001128		Approved		uc010cgg.3	O43747		ENST00000299980.4:c.2175T>G	chr16.hg19:g.71772938A>C	ENSP00000299980:p.Asn725Lys	325.0	0.0		159.0	61.0	NM_001030007	O75709|O75842|Q9UG09|Q9Y3U4	Missense_Mutation	SNP	ENST00000299980.4	hg19	CCDS32480.1	.	.	.	.	.	.	.	.	.	.	A	12.37	1.919106	0.33908	.	.	ENSG00000166747	ENST00000299980;ENST00000393512;ENST00000423132;ENST00000433195	T;T;T;T	0.39787	1.06;1.06;1.06;1.06	5.29	0.176	0.15049	Coatomer/clathrin adaptor appendage, Ig-like subdomain (1);Clathrin adaptor, gamma-adaptin, appendage (2);Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain (2);	0.040642	0.85682	D	0.000000	T	0.29061	0.0722	L	0.40543	1.245	0.50171	D	0.999855	B;B;B	0.18741	0.008;0.03;0.013	B;B;B	0.22386	0.039;0.039;0.023	T	0.07578	-1.0765	10	0.20519	T	0.43	-12.3069	9.006	0.36111	0.3551:0.0:0.6449:0.0	.	725;748;728	O43747;B3KXW5;O43747-2	AP1G1_HUMAN;.;.	K	725;728;728;748	ENSP00000299980:N725K;ENSP00000377148:N728K;ENSP00000409153:N728K;ENSP00000403259:N748K	ENSP00000299980:N725K	N	-	3	2	AP1G1	70330439	1.000000	0.71417	0.995000	0.50966	0.991000	0.79684	1.178000	0.31981	-0.224000	0.09928	0.528000	0.53228	AAT	.	.		0.433	AP1G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434147.1			C	71772938	A	C	71772938	3	2	340	1	0	0	0	0	1	0	0	0	732	446	16	5	305	5	AP1G1	16	71772938	Missense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	4504949	71772938	18581815	116	47080										
OSGIN1	29948	hgsc.bcm.edu	37	chr16	83994227	83994227	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	cgatcccaaagccccgtggcCctgctctttgatgcccttct	8	17	2	1	rs201580564		TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr16:83994227C>T	ENST00000343939.2	+	5	890	c.507C>T	c.(505-507)gcC>gcT	p.A169A	OSGIN1_ENST00000565123.1_Silent_p.A86A|OSGIN1_ENST00000393306.1_Silent_p.A86A|OSGIN1_ENST00000361711.3_Silent_p.A86A			Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1	169					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|negative regulation of cell growth (GO:0030308)|positive regulation of apoptotic process (GO:0043065)		growth factor activity (GO:0008083)			autonomic_ganglia(1)|large_intestine(1)|lung(7)|prostate(2)|upper_aerodigestive_tract(1)	12						GCCCCGTGGCCCTGCTCTTTG	0.642																																					p.A86A		Atlas-SNP	.											.	OSGIN1	33	.	0			c.C258T						.						63	59	60					16																	83994227		2200	4300	6500	SO:0001819	synonymous_variant	29948	exon4			CGTGGCCCTGCTC	AY258066	CCDS10939.1	16q23.3	2010-11-23			ENSG00000140961	ENSG00000140961			30093	protein-coding gene	gene with protein product	"bone marrow stromal cell-derived growth inhibitor", "pregnancy induced growth inhibitor"	607975				11459809, 14570898	Standard	NM_182981		Approved	BDGI, OKL38	uc002fhc.3	Q9UJX0	OTTHUMG00000137640	ENST00000343939.2:c.507C>T	chr16.hg19:g.83994227C>T		44.0	0.0		20.0	10.0	NM_182981	Q52M33|Q86UQ1|Q96S88|Q9BZ70	Silent	SNP	ENST00000343939.2	hg19																																																																																				.	C|0.999;G|0.001		0.642	OSGIN1-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000269081.1	NM_013370		T	83994227	C	T	83994227	2	4	340	1	0	0	0	0	0	0	0	1	11298	610	22	3		3	OSGIN1	16	83994227	Silent	SNP	C	TCGA-RC-A7SK-01A-11D-A34Z-10	12221289	83994227	6360526	117	47081										
ADAD2	161931	hgsc.bcm.edu	37	chr16	84230532	84230532	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	ctcctcctggaccagcagggCctgggggcttggccctcgaa	14	15	0	0			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr16:84230532C>T	ENST00000315906.5	+	10	1756	c.1704C>T	c.(1702-1704)ggC>ggT	p.G568G	RP11-486L19.2_ENST00000565643.1_RNA|RP11-486L19.2_ENST00000536986.1_RNA|RP11-486L19.2_ENST00000569834.1_RNA|RP11-486L19.2_ENST00000561900.1_RNA|ADAD2_ENST00000268624.3_Silent_p.G650G	NM_001145400.1	NP_001138872.1	Q8NCV1	ADAD2_HUMAN	adenosine deaminase domain containing 2	568	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				RNA processing (GO:0006396)		adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(1)	13						ACCAGCAGGGCCTGGGGGCTT	0.667																																					p.G650G		Atlas-SNP	.											.	ADAD2	46	.	0			c.C1950T						.						10	12	11					16																	84230532		2187	4289	6476	SO:0001819	synonymous_variant	161931	exon11			GCAGGGCCTGGGG	AF447586	CCDS10944.1, CCDS45536.1	16q24.1	2007-05-31			ENSG00000140955	ENSG00000140955			30714	protein-coding gene	gene with protein product							Standard	NM_139174		Approved	TENRL, FLJ00337	uc002fhr.2	Q8NCV1	OTTHUMG00000137637	ENST00000315906.5:c.1704C>T	chr16.hg19:g.84230532C>T		97.0	0.0		58.0	16.0	NM_139174	B2RCL6|Q8NA94	Silent	SNP	ENST00000315906.5	hg19	CCDS45536.1																																																																																			.	.		0.667	ADAD2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433385.1	NM_139174		T	84230532	C	T	84230532	2	4	340	1	0	0	0	0	0	0	0	1	232	726	26	3		3	ADAD2	16	84230532	Silent	SNP	C	TCGA-RC-A7SK-01A-11D-A34Z-10	236305	84230532	6124221	118	47082										
TP53	7157	hgsc.bcm.edu	37	chr17	7578410	7578410	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	ctcatggtgggggcagcgccTcacaacctccgtcatgtgct	12	14	3	0			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr17:7578410T>A	ENST00000269305.4	-	5	709	c.520A>T	c.(520-522)Agg>Tgg	p.R174W	TP53_ENST00000420246.2_Missense_Mutation_p.R174W|TP53_ENST00000455263.2_Missense_Mutation_p.R174W|TP53_ENST00000413465.2_Missense_Mutation_p.R174W|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000359597.4_Missense_Mutation_p.R174W|TP53_ENST00000445888.2_Missense_Mutation_p.R174W	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	174	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		R -> G (in LFS; germline mutation and in a sporadic cancer; somatic mutation).|R -> K (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:7682763}.|R -> M (in sporadic cancers; somatic mutation).|R -> S (in sporadic cancers; somatic mutation).|R -> T (in a sporadic cancer; somatic mutation).|R -> W (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R174W(12)|p.0?(8)|p.V173fs*59(2)|p.R174fs*1(2)|p.V157_C176del20(1)|p.V172_R174delVVR(1)|p.V173fs*69(1)|p.E171fs*61(1)|p.V173fs*23(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171fs*1(1)|p.R81W(1)|p.R174_C176delRRC(1)|p.H168fs*69(1)|p.R174fs*73(1)|p.R174fs*70(1)|p.R174G(1)|p.R42W(1)|p.E171_H179delEVVRRCPHH(1)|p.S149fs*72(1)|p.R174fs*3(1)|p.R174fs*7(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGGCAGCGCCTCACAACCTCC	0.657		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.R174W	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,carcinoma,+1,1	TP53	33396	.	43	Substitution - Missense(15)|Deletion - Frameshift(13)|Whole gene deletion(8)|Deletion - In frame(6)|Insertion - Frameshift(1)	liver(11)|breast(7)|lung(4)|oesophagus(4)|bone(4)|large_intestine(3)|stomach(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|upper_aerodigestive_tract(1)|urinary_tract(1)|ovary(1)|prostate(1)	c.A520T	GRCh37	CM942119	TP53	M		.						50	50	50					17																	7578410		2203	4300	6503	SO:0001583	missense	7157	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AGCGCCTCACAAC	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.520A>T	chr17.hg19:g.7578410T>A	ENSP00000269305:p.Arg174Trp	86.0	0.0		28.0	19.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	19.94	3.919495	0.73098	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99820	-6.93;-6.93;-6.93;-6.93;-6.93;-6.93;-6.93;-6.93	5.59	1.97	0.26223	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.297542	0.32190	N	0.006445	D	0.99764	0.9904	M	0.84585	2.705	0.39545	D	0.968872	D;D;D;D;D;D;D	0.89917	1.0;0.996;0.998;1.0;0.997;0.997;1.0	D;D;D;D;D;D;D	0.91635	0.998;0.978;0.977;0.999;0.997;0.987;0.998	D	0.98344	1.0540	10	0.87932	D	0	-14.7463	12.0783	0.53657	0.0:0.0:0.417:0.583	.	135;174;174;81;174;174;174	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	W	174;174;174;174;174;174;163;81;42;81;42	ENSP00000410739:R174W;ENSP00000352610:R174W;ENSP00000269305:R174W;ENSP00000398846:R174W;ENSP00000391127:R174W;ENSP00000391478:R174W;ENSP00000425104:R42W;ENSP00000423862:R81W	ENSP00000269305:R174W	R	-	1	2	TP53	7519135	0.002000	0.14202	0.176000	0.23000	0.618000	0.37518	1.330000	0.33781	0.094000	0.17404	0.533000	0.62120	AGG	.	.		0.657	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7578410	T	A	7578410	3	1	340	1	0	0	0	0	1	0	0	0	16396	1550	54	4	778	4	TP53	17	7578410	Missense_Mutation	SNP	T	TCGA-RC-A7SK-01A-11D-A34Z-10		7578410	73616800	119	47083										
KRT12	3859	hgsc.bcm.edu	37	chr17	39017949	39017949	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	atttcctgaacttgagatgaGaccacctcaccattcaccat	5	13	2	3			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr17:39017949G>C	ENST00000251643.4	-	8	1472	c.1449C>G	c.(1447-1449)gtC>gtG	p.V483V	RP5-1110E20.1_ENST00000579136.1_RNA	NM_000223.3	NP_000214.1	Q99456	K1C12_HUMAN	keratin 12	483	Tail.				visual perception (GO:0007601)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(2)	15		Breast(137;0.000301)			Griseofulvin(DB00400)	CTTGAGATGAGACCACCTCAC	0.378																																					p.V483V		Atlas-SNP	.											.	KRT12	53	.	0			c.C1449G						.						137	135	136					17																	39017949		2203	4300	6503	SO:0001819	synonymous_variant	3859	exon8			AGATGAGACCACC		CCDS11378.1	17q21.2	2013-06-20	2008-08-01		ENSG00000187242	ENSG00000187242		"-", "Intermediate filaments type I, keratins (acidic)"	6414	protein-coding gene	gene with protein product	"Meesmann corneal dystrophy"	601687				9171831, 16831889	Standard	NM_000223		Approved	K12	uc002hvk.2	Q99456	OTTHUMG00000133369	ENST00000251643.4:c.1449C>G	chr17.hg19:g.39017949G>C		204.0	0.0		91.0	21.0	NM_000223	B2R9E0	Silent	SNP	ENST00000251643.4	hg19	CCDS11378.1																																																																																			.	.		0.378	KRT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257214.2	NM_000223		C	39017949	G	C	39017949	2	2	340	1	0	0	0	0	0	0	0	1	8458	929	33	4		4	KRT12	17	39017949	Silent	SNP	G	TCGA-RC-A7SK-01A-11D-A34Z-10	31439539	39017949	42177261	120	47084										
GPATCH8	23131	hgsc.bcm.edu	37	chr17	42476641	42476641	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	actggctgcaactgaggctaTagtcatcatcagaagatgaa	10	8	3	4	rs542607889		TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr17:42476641T>C	ENST00000591680.1	-	8	2834	c.2804A>G	c.(2803-2805)tAt>tGt	p.Y935C	GPATCH8_ENST00000434000.1_Missense_Mutation_p.Y857C	NM_001002909.2	NP_001002909.1	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	935	Ser-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(7)|kidney(6)|large_intestine(4)|liver(2)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.206)		ACTGAGGCTATAGTCATCATC	0.542													T|||	1	0.000199681	8e-04	0	5008	,	,		17745	0		0	False		,,,				2504	0				p.Y935C		Atlas-SNP	.											.	GPATCH8	114	.	0			c.A2804G						.						95	94	94					17																	42476641		2203	4300	6503	SO:0001583	missense	23131	exon8			AGGCTATAGTCAT	AB011125	CCDS32666.1	17q21.31	2013-01-28	2006-08-22	2006-12-13	ENSG00000186566	ENSG00000186566		"G patch domain containing"	29066	protein-coding gene	gene with protein product		614396	"KIAA0553"	KIAA0553, GPATC8		9628581	Standard	NM_001002909		Approved		uc002igw.2	Q9UKJ3	OTTHUMG00000181818	ENST00000591680.1:c.2804A>G	chr17.hg19:g.42476641T>C	ENSP00000467556:p.Tyr935Cys	181.0	0.0		101.0	17.0	NM_001002909	B9EGP9|O60300|Q8TB99	Missense_Mutation	SNP	ENST00000591680.1	hg19	CCDS32666.1	.	.	.	.	.	.	.	.	.	.	T	11.17	1.559071	0.27827	.	.	ENSG00000186566	ENST00000335500;ENST00000434000	T	0.12465	2.68	5.2	5.2	0.72013	.	0.000000	0.64402	D	0.000003	T	0.21962	0.0529	N	0.19112	0.55	0.41506	D	0.988317	D	0.76494	0.999	D	0.80764	0.994	T	0.03887	-1.0995	10	0.39692	T	0.17	-14.2362	13.4516	0.61174	0.0:0.0:0.0:1.0	.	935	Q9UKJ3	GPTC8_HUMAN	C	935;857	ENSP00000395016:Y857C	ENSP00000335486:Y935C	Y	-	2	0	GPATCH8	39832167	1.000000	0.71417	0.998000	0.56505	0.747000	0.42532	3.731000	0.55013	2.190000	0.69967	0.454000	0.30748	TAT	.	.		0.542	GPATCH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457797.1	NM_001002909		C	42476641	T	C	42476641	3	2	340	1	0	0	0	0	1	0	0	0	6602	1406	49	2	1708	2	GPATCH8	17	42476641	Missense_Mutation	SNP	T	TCGA-RC-A7SK-01A-11D-A34Z-10	3458692	42476641	38718569	121	47085										
C17orf57	124989	hgsc.bcm.edu	37	chr17	45518054	45518054	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	attctaaggcaaatattgctAagcttaacccaaactcaaaa	4	9	2	0			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr17:45518054A>G	ENST00000331493.2	+	25	3307	c.2896A>G	c.(2896-2898)Aag>Gag	p.K966E		NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	966						cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)										AAATATTGCTAAGCTTAACCC	0.274																																					p.K966E		Atlas-SNP	.											.	.	.	.	0			c.A2896G						.						63	69	67					17																	45518054		2201	4287	6488	SO:0001583	missense	124989	exon25			ATTGCTAAGCTTA	BC036407	CCDS11512.1, CCDS56034.1	17q21.32	2013-01-11	2012-07-20	2012-07-20	ENSG00000178852	ENSG00000178852		"EF-hand domain containing"	26864	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 57"	C17orf57			Standard	NM_152347		Approved	FLJ40342	uc002iln.3	Q8IY85	OTTHUMG00000164767	ENST00000331493.2:c.2896A>G	chr17.hg19:g.45518054A>G	ENSP00000332111:p.Lys966Glu	263.0	0.0		159.0	61.0	NM_152347	G3V128|Q49AG9	Missense_Mutation	SNP	ENST00000331493.2	hg19	CCDS11512.1	.	.	.	.	.	.	.	.	.	.	.	11.74	1.729799	0.30684	.	.	ENSG00000178852	ENST00000331493	T	0.61510	0.1	1.77	1.77	0.24775	.	.	.	.	.	T	0.50274	0.1606	N	0.08118	0	0.09310	N	0.999995	D	0.60575	0.988	D	0.65010	0.931	T	0.33624	-0.9861	9	0.87932	D	0	.	5.6013	0.17355	1.0:0.0:0.0:0.0	.	966	Q8IY85	CQ057_HUMAN	E	966	ENSP00000332111:K966E	ENSP00000332111:K966E	K	+	1	0	C17orf57	42873053	0.006000	0.16342	0.005000	0.12908	0.279000	0.26890	0.557000	0.23454	1.066000	0.40716	0.255000	0.18592	AAG	.	.		0.274	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4	NM_152347		G	45518054	A	G	45518054	3	3	340	1	0	0	0	0	1	0	0	0	1867	363	13	2	2982	2	C17orf57	17	45518054	Missense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	3041413	45518054	35677156	122	47086										
SMARCD2	6603	hgsc.bcm.edu	37	chr17	61914891	61914891	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	tggtgggtggcatgccaggtCgaagcggagctgctgcacca	17	10	0	0			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr17:61914891C>T	ENST00000448276.2	-	2	576	c.311G>A	c.(310-312)cGa>cAa	p.R104Q	SMARCD2_ENST00000323347.10_Missense_Mutation_p.R56Q|RN7SL805P_ENST00000581353.1_RNA|SMARCD2_ENST00000225742.9_Missense_Mutation_p.R29Q	NM_001098426.1	NP_001091896.1	Q92925	SMRD2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2	104	Pro-rich.				ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|nucleosome disassembly (GO:0006337)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	transcription coactivator activity (GO:0003713)	p.R48L(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(1)	8						CATGCCAGGTCGAAGCGGAGC	0.657																																					p.R104Q		Atlas-SNP	.											SMARCD2,NS,carcinoma,0,2	SMARCD2	29	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.G311A						.						44	53	50					17																	61914891		1995	4159	6154	SO:0001583	missense	6603	exon2			CCAGGTCGAAGCG	U66618	CCDS45756.1	17q23.3	2014-07-16			ENSG00000108604	ENSG00000108604			11107	protein-coding gene	gene with protein product	"mammalian chromatin remodeling complex BRG1-associated factor 60B", "Swp73-like protein", "chromatin remodeling complex BAF60B subunit", "SWI/SNF complex 60 kDa subunit B"	601736				8804307, 9693044	Standard	NM_001098426		Approved	BAF60B, Rsc6p, CRACD2, PRO2451	uc010deb.1	Q92925	OTTHUMG00000179045	ENST00000448276.2:c.311G>A	chr17.hg19:g.61914891C>T	ENSP00000392617:p.Arg104Gln	70.0	0.0		39.0	17.0	NM_001098426	A5PLL5|A6NNQ7|B4DV56|B4E1R6|Q7L2I6|Q9UHZ1	Missense_Mutation	SNP	ENST00000448276.2	hg19	CCDS45756.1	.	.	.	.	.	.	.	.	.	.	.	18.48	3.632781	0.67015	.	.	ENSG00000108604	ENST00000448276;ENST00000450364;ENST00000323347	T;T	0.46451	0.87;0.91	5.17	5.17	0.71159	.	0.059356	0.64402	D	0.000002	T	0.57592	0.2064	L	0.46741	1.465	0.80722	D	1	D;D;D	0.71674	0.998;0.995;0.995	D;P;P	0.72982	0.979;0.623;0.743	T	0.55872	-0.8072	10	0.51188	T	0.08	0.9492	16.2004	0.82067	0.0:1.0:0.0:0.0	.	56;67;104	Q92925-3;B9EGA3;Q92925	.;.;SMRD2_HUMAN	Q	104;67;56	ENSP00000392617:R104Q;ENSP00000318451:R56Q	ENSP00000318451:R56Q	R	-	2	0	SMARCD2	59268623	0.990000	0.36364	1.000000	0.80357	0.938000	0.57974	6.846000	0.75399	2.702000	0.92279	0.491000	0.48974	CGA	.	.		0.657	SMARCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444544.1	NM_001098426		T	61914891	C	T	61914891	3	4	340	1	0	0	0	0	1	0	0	0	14793	884	31	1	1332	1	SMARCD2	17	61914891	Missense_Mutation	SNP	C	TCGA-RC-A7SK-01A-11D-A34Z-10	16396837	61914891	19280319	123	47087										
HGS	9146	hgsc.bcm.edu	37	chr17	79663472	79663473	+	Nonsense_Mutation	DNP	GA	GA	TT													0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	ctgcgcgaagagcaccgggaGaagcttcgccgggcagccga							TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr17:79663472_79663473GA>TT	ENST00000329138.4	+	16	1614_1615	c.1479_1480GA>TT	c.(1477-1482)gaGAag>gaTTag	p.493_494EK>D*		NM_004712.4	NP_004703.1	O14964	HGS_HUMAN	hepatocyte growth factor-regulated tyrosine kinase substrate	493	Interaction with NF2.|Interaction with SNAP25 and TRAK2. {ECO:0000250}.|Interaction with SNX1. {ECO:0000250}.|Interaction with STAM1. {ECO:0000250}.				endosomal transport (GO:0016197)|endosome to lysosome transport (GO:0008333)|epidermal growth factor receptor signaling pathway (GO:0007173)|membrane invagination (GO:0010324)|membrane organization (GO:0061024)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of JAK-STAT cascade (GO:0046426)|positive regulation of gene expression (GO:0010628)|protein localization to membrane (GO:0072657)|protein targeting to lysosome (GO:0006622)|regulation of protein catabolic process (GO:0042176)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|secretory granule (GO:0030141)	metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			endometrium(2)|kidney(3)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12	all_neural(118;0.0878)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)			AGCACCGGGAGAAGCTTCGCCG	0.658																																					p.E493D|p.K494X		Atlas-SNP	.											.	HGS	54	.	0			c.G1479T|c.A1480T						.																																			SO:0001587	stop_gained	9146	exon16			CCGGGAGAAGCTT|CGGGAGAAGCTTC	D84064	CCDS11784.1	17q25	2009-04-29				ENSG00000185359		"Zinc fingers, FYVE domain containing"	4897	protein-coding gene	gene with protein product		604375				9407053, 9630564	Standard	NM_004712		Approved	Hrs, ZFYVE8, Vps27	uc002kbg.3	O14964		Exception_encountered	chr17.hg19:g.79663472_79663473delinsTT	ENSP00000331201:p.E493_K494delinsD*	34.0|33.0	0.0		20.0	11.0|10.0	NM_004712	Q9NR36	Missense_Mutation|Nonsense_Mutation	SNP	ENST00000329138.4	hg19	CCDS11784.1																																																																																			.	.		0.658	HGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440541.1	NM_004712		TT	79663473	GA	TT	79663472	4	4	340	1	0	0	0	0	0	1	0	0	7096	933	33	3	1541	3	HGS	17	79663472	Nonsense_Mutation	DNP	GA	TCGA-RC-A7SK-01A-11D-A34Z-10	17748581	79663472	1531738	124	47088										
THEG	51298	hgsc.bcm.edu	37	chr19	367179	367179	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	ctttgacaactggaggatccGcgagctggggactgccattt	13	10	0	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr19:367179G>A	ENST00000342640.4	-	7	841	c.799C>T	c.(799-801)Cgg>Tgg	p.R267W	THEG_ENST00000346878.2_Missense_Mutation_p.R243W	NM_016585.4	NP_057669.1	Q9P2T0	THEG_HUMAN	theg spermatid protein	267			R -> Q (in dbSNP:rs2278287).		cell differentiation (GO:0030154)|chaperone-mediated protein complex assembly (GO:0051131)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)				NS(1)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(2)|soft_tissue(1)	29		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGGAGGATCCGCGAGCTGGGG	0.572																																					p.R267W		Atlas-SNP	.											.	THEG	58	.	0			c.C799T						.						81	85	84					19																	367179		2203	4300	6503	SO:0001583	missense	51298	exon7			GGATCCGCGAGCT	AF268610	CCDS12025.1, CCDS12026.1	19p13.3	2012-02-24	2012-02-24		ENSG00000105549	ENSG00000105549			13706	protein-coding gene	gene with protein product	"cancer/testis antigen 56"	609503	"Theg homolog (mouse)"			11173852	Standard	NM_016585		Approved	CT56, THEG1	uc002lol.3	Q9P2T0	OTTHUMG00000165491	ENST00000342640.4:c.799C>T	chr19.hg19:g.367179G>A	ENSP00000340088:p.Arg267Trp	127.0	0.0		40.0	11.0	NM_016585	A6NMJ8	Missense_Mutation	SNP	ENST00000342640.4	hg19	CCDS12025.1	.	.	.	.	.	.	.	.	.	.	G	10.34	1.323748	0.24080	.	.	ENSG00000105549	ENST00000342640;ENST00000346878	T;T	0.60548	0.18;0.18	3.32	2.28	0.28536	.	0.128748	0.34802	N	0.003662	T	0.71178	0.3309	M	0.79123	2.44	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.59478	-0.7447	10	0.87932	D	0	-10.9218	7.1811	0.25774	0.0:0.0:0.664:0.336	.	243;267	Q9P2T0-2;Q9P2T0	.;THEG_HUMAN	W	267;243	ENSP00000340088:R267W;ENSP00000264820:R243W	ENSP00000340088:R267W	R	-	1	2	THEG	318179	0.928000	0.31464	0.007000	0.13788	0.004000	0.04260	1.648000	0.37271	0.882000	0.36016	0.555000	0.69702	CGG	.	.		0.572	THEG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384431.2			A	367179	G	A	367179	3	1	340	1	0	0	0	0	1	0	0	0	15872	1086	38	1	348	1	THEG	19	367179	Missense_Mutation	SNP	G	TCGA-RC-A7SK-01A-11D-A34Z-10		367179	58761804	125	47089										
RAD23A	5886	hgsc.bcm.edu	37	chr19	13056794	13056794	+	Missense_Mutation	SNP	A	A	C													0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	catcacgctcaaaacgctgcAgcagcagaccttcaagatcc							TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr19:13056794A>C	ENST00000586534.1	+	1	93	c.32A>C	c.(31-33)cAg>cCg	p.Q11P	RAD23A_ENST00000541222.1_5'UTR|RAD23A_ENST00000592268.1_Missense_Mutation_p.Q11P|RAD23A_ENST00000316856.3_Missense_Mutation_p.Q11P|CTC-425F1.4_ENST00000589120.1_RNA			P54725	RD23A_HUMAN	RAD23 homolog A (S. cerevisiae)	11	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				nucleotide-excision repair (GO:0006289)|positive regulation of viral genome replication (GO:0045070)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	damaged DNA binding (GO:0003684)|polyubiquitin binding (GO:0031593)|single-stranded DNA binding (GO:0003697)|ubiquitin-specific protease binding (GO:1990381)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)|skin(1)	12						AAAACGCTGCAGCAGCAGACC	0.711								Nucleotide excision repair (NER)																													p.Q11P		Atlas-SNP	.											.	RAD23A	29	.	0			c.A32C						.						19	22	21					19																	13056794		2188	4282	6470	SO:0001583	missense	5886	exon1			CGCTGCAGCAGCA		CCDS12289.1, CCDS59357.1, CCDS59358.1	19p13.2	2008-07-17	2001-11-28			ENSG00000179262			9812	protein-coding gene	gene with protein product	"RAD23, yeast homolog, A"	600061	"RAD23 (S. cerevisiae) homolog A"			7851894	Standard	NM_005053		Approved	HHR23A, MGC111083	uc002mvw.2	P54725		ENST00000586534.1:c.32A>C	chr19.hg19:g.13056794A>C	ENSP00000467024:p.Gln11Pro	75.0	0.0		27.0	12.0	NM_005053	K7ESE3|Q59EU8|Q5M7Z1	Missense_Mutation	SNP	ENST00000586534.1	hg19	CCDS12289.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.574783	0.86542	.	.	ENSG00000179262	ENST00000316856	T	0.74421	-0.84	4.8	4.8	0.61643	Ubiquitin supergroup (1);Ubiquitin (2);	0.000000	0.85682	D	0.000000	D	0.85575	0.5728	M	0.87328	2.875	0.80722	D	1	B;D;B	0.56287	0.097;0.975;0.356	B;P;P	0.61940	0.204;0.896;0.478	D	0.87677	0.2545	10	0.66056	D	0.02	-15.5005	11.8748	0.52541	1.0:0.0:0.0:0.0	.	11;28;11	A8K1J3;Q59EU8;P54725	.;.;RD23A_HUMAN	P	11	ENSP00000321365:Q11P	ENSP00000321365:Q11P	Q	+	2	0	RAD23A	12917794	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.613000	0.67688	1.806000	0.52798	0.533000	0.62120	CAG	.	.		0.711	RAD23A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452752.1	NM_005053		C	13056794	A	C	13056794	3	2	340	1	0	0	0	0	1	0	0	0	12997	188	7	5	34	5	RAD23A	19	13056794	Missense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	12689615	13056794	46072189	126	47090	254	2								
RAD23A	5886	hgsc.bcm.edu	37	chr19	13056800	13056800	+	Missense_Mutation	SNP	A	A	C													0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	gctcaaaacgctgcagcagcAgaccttcaagatccgcatgg							TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr19:13056800A>C	ENST00000586534.1	+	1	99	c.38A>C	c.(37-39)cAg>cCg	p.Q13P	RAD23A_ENST00000541222.1_5'UTR|RAD23A_ENST00000592268.1_Missense_Mutation_p.Q13P|RAD23A_ENST00000316856.3_Missense_Mutation_p.Q13P|CTC-425F1.4_ENST00000589120.1_RNA			P54725	RD23A_HUMAN	RAD23 homolog A (S. cerevisiae)	13	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				nucleotide-excision repair (GO:0006289)|positive regulation of viral genome replication (GO:0045070)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	damaged DNA binding (GO:0003684)|polyubiquitin binding (GO:0031593)|single-stranded DNA binding (GO:0003697)|ubiquitin-specific protease binding (GO:1990381)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)|skin(1)	12						CTGCAGCAGCAGACCTTCAAG	0.726								Nucleotide excision repair (NER)																													p.Q13P		Atlas-SNP	.											.	RAD23A	29	.	0			c.A38C						.						19	21	21					19																	13056800		2187	4282	6469	SO:0001583	missense	5886	exon1			AGCAGCAGACCTT		CCDS12289.1, CCDS59357.1, CCDS59358.1	19p13.2	2008-07-17	2001-11-28			ENSG00000179262			9812	protein-coding gene	gene with protein product	"RAD23, yeast homolog, A"	600061	"RAD23 (S. cerevisiae) homolog A"			7851894	Standard	NM_005053		Approved	HHR23A, MGC111083	uc002mvw.2	P54725		ENST00000586534.1:c.38A>C	chr19.hg19:g.13056800A>C	ENSP00000467024:p.Gln13Pro	72.0	0.0		24.0	11.0	NM_005053	K7ESE3|Q59EU8|Q5M7Z1	Missense_Mutation	SNP	ENST00000586534.1	hg19	CCDS12289.1	.	.	.	.	.	.	.	.	.	.	a	19.23	3.788158	0.70337	.	.	ENSG00000179262	ENST00000316856	T	0.73789	-0.78	4.77	4.77	0.60923	Ubiquitin supergroup (1);Ubiquitin (2);	0.000000	0.64402	D	0.000001	D	0.88658	0.6496	M	0.93678	3.445	0.80722	D	1	B;D;B	0.53619	0.058;0.961;0.24	B;D;B	0.77557	0.156;0.99;0.305	D	0.90490	0.4466	10	0.59425	D	0.04	-12.34	11.8288	0.52282	1.0:0.0:0.0:0.0	.	13;30;13	A8K1J3;Q59EU8;P54725	.;.;RD23A_HUMAN	P	13	ENSP00000321365:Q13P	ENSP00000321365:Q13P	Q	+	2	0	RAD23A	12917800	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.602000	0.67612	1.795000	0.52594	0.520000	0.50463	CAG	.	.		0.726	RAD23A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452752.1	NM_005053		C	13056800	A	C	13056800	3	2	340	1	0	0	0	0	1	0	0	0	12997	188	7	5	40	5	RAD23A	19	13056800	Missense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10	6	13056800	46072183	127	47091	254	2								
GDF15	9518	hgsc.bcm.edu	37	chr19	18499150	18499150	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	tatctctcgggccgcccttcCcgaggggctccccgaggcct	12	18	1	0			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr19:18499150C>G	ENST00000252809.3	+	2	364	c.332C>G	c.(331-333)cCc>cGc	p.P111R	MIR3189_ENST00000578735.1_RNA	NM_004864.2	NP_004855.2	Q99988	GDF15_HUMAN	growth differentiation factor 15	111					cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)			kidney(2)|large_intestine(1)|liver(1)|lung(5)|prostate(2)|skin(1)	12						GCCGCCCTTCCCGAGGGGCTC	0.697											OREG0025363	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P111R		Atlas-SNP	.											.	GDF15	31	.	0			c.C332G						.						17	21	20					19																	18499150		2173	4281	6454	SO:0001583	missense	9518	exon2			CCCTTCCCGAGGG	BC008962	CCDS12376.1	19p13.11	2008-05-14				ENSG00000130513			30142	protein-coding gene	gene with protein product	"prostate differentiation factor"	605312				11895857, 9593718	Standard	NM_004864		Approved	PLAB, MIC-1, PDF, MIC1, NAG-1, PTGFB	uc002niv.2	Q99988		ENST00000252809.3:c.332C>G	chr19.hg19:g.18499150C>G	ENSP00000252809:p.Pro111Arg	118.0	0.0	726	57.0	11.0	NM_004864	O14629|P78360|Q9BWA0|Q9NRT0	Missense_Mutation	SNP	ENST00000252809.3	hg19	CCDS12376.1	.	.	.	.	.	.	.	.	.	.	C	13.55	2.269549	0.40095	.	.	ENSG00000130513	ENST00000252809	T	0.81415	-1.49	4.31	-1.01	0.10169	.	1.302550	0.05372	N	0.535644	T	0.65386	0.2686	N	0.19112	0.55	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.46911	-0.9157	10	0.21014	T	0.42	-1.9864	7.2446	0.26115	0.0:0.3754:0.5197:0.1049	.	111	Q99988	GDF15_HUMAN	R	111	ENSP00000252809:P111R	ENSP00000252809:P111R	P	+	2	0	GDF15	18360150	0.000000	0.05858	0.001000	0.08648	0.111000	0.19643	0.641000	0.24720	-0.005000	0.14395	0.305000	0.20034	CCC	.	.		0.697	GDF15-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466340.2	NM_004864		G	18499150	C	G	18499150	3	3	340	1	0	0	0	0	1	0	0	0	6321	623	22	4	338	4	GDF15	19	18499150	Missense_Mutation	SNP	C	TCGA-RC-A7SK-01A-11D-A34Z-10	5442350	18499150	40629833	128	47092										
VN1R2	317701	hgsc.bcm.edu	37	chr19	53762414	53762414	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	gaagtcacaaagtcagtataTgcagcattgacatccttcca	7	10	2	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr19:53762414T>A	ENST00000341702.3	+	1	870	c.786T>A	c.(784-786)taT>taA	p.Y262*		NM_173856.2	NP_776255.2	Q8NFZ6	VN1R2_HUMAN	vomeronasal 1 receptor 2	262					response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(134;0.00301)		AGTCAGTATATGCAGCATTGA	0.448																																					p.Y262X		Atlas-SNP	.											.	VN1R2	71	.	0			c.T786A						.						151	139	143					19																	53762414		2203	4300	6503	SO:0001587	stop_gained	317701	exon1			AGTATATGCAGCA	AF370359	CCDS12862.1	19q13.42	2012-08-22			ENSG00000196131	ENSG00000196131		"Vomeronasal receptors / Type 1", "GPCR / Unclassified : Vomeronasal receptors, type 1"	19872	protein-coding gene	gene with protein product						12123587	Standard	NM_173856		Approved	V1RL2	uc002qbi.2	Q8NFZ6		ENST00000341702.3:c.786T>A	chr19.hg19:g.53762414T>A	ENSP00000351244:p.Tyr262*	124.0	0.0		71.0	24.0	NM_173856	A1L411|Q8TDU4	Nonsense_Mutation	SNP	ENST00000341702.3	hg19	CCDS12862.1	.	.	.	.	.	.	.	.	.	.	T	16.39	3.111238	0.56398	.	.	ENSG00000196131	ENST00000341702	.	.	.	2.94	1.89	0.25635	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	3.3225	0.07056	0.0:0.1296:0.2441:0.6263	.	.	.	.	X	262	.	ENSP00000351244:Y262X	Y	+	3	2	VN1R2	58454226	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.271000	0.18626	0.529000	0.28599	0.486000	0.48141	TAT	.	.		0.448	VN1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464285.1	NM_173856		A	53762414	T	A	53762414	4	1	340	1	0	0	0	0	0	1	0	0	17194	1471	51	4	788	4	VN1R2	19	53762414	Nonsense_Mutation	SNP	T	TCGA-RC-A7SK-01A-11D-A34Z-10	35263264	53762414	5366569	129	47093										
VSTM1	284415	hgsc.bcm.edu	37	chr19	54554674	54554674	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	attatcttacctgttttcatTgagggagcttcaagttcatc	7	8	4	1	rs566804822		TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr19:54554674T>A	ENST00000338372.2	-	4	559	c.384A>T	c.(382-384)tcA>tcT	p.S128S	VSTM1_ENST00000425006.2_Silent_p.S128S|VSTM1_ENST00000366170.2_Silent_p.S40S|VSTM1_ENST00000376626.1_Silent_p.S128S	NM_198481.3	NP_940883.2	Q6UX27	VSTM1_HUMAN	V-set and transmembrane domain containing 1	128					immune system process (GO:0002376)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				breast(1)|large_intestine(3)|lung(11)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.165)		CTGTTTTCATTGAGGGAGCTT	0.383																																					p.S128S		Atlas-SNP	.											.	VSTM1	30	.	0			c.A384T						.						130	118	122					19																	54554674		2203	4300	6503	SO:0001819	synonymous_variant	284415	exon4			TTTCATTGAGGGA	AY358542	CCDS12872.1, CCDS74441.1, CCDS74442.1	19q13.42	2013-01-11			ENSG00000189068	ENSG00000189068		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29455	protein-coding gene	gene with protein product						12975309	Standard	NM_198481		Approved	UNQ3033	uc002qcw.4	Q6UX27	OTTHUMG00000064906	ENST00000338372.2:c.384A>T	chr19.hg19:g.54554674T>A		150.0	0.0		61.0	26.0	NM_198481	B6A8C6|D2DJS3|D2DJS4|Q496B6|Q496B7	Silent	SNP	ENST00000338372.2	hg19	CCDS12872.1																																																																																			.	.		0.383	VSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139358.3	NM_198481		A	54554674	T	A	54554674	2	1	340	1	0	0	0	0	0	0	0	1	17243	1799	63	4		4	VSTM1	19	54554674	Silent	SNP	T	TCGA-RC-A7SK-01A-11D-A34Z-10	792260	54554674	4574309	130	47094										
LILRB1	10859	hgsc.bcm.edu	37	chr19	55143685	55143685	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	atctcctggagctcctggtcCtaggtgagaaattcacagca	10	11	2	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr19:55143685C>A	ENST00000396331.1	+	6	1015	c.658C>A	c.(658-660)Cta>Ata	p.L220I	LILRB1_ENST00000396327.3_Missense_Mutation_p.L220I|LILRB1_ENST00000427581.2_Missense_Mutation_p.L256I|LILRB1_ENST00000396315.1_Missense_Mutation_p.L220I|LILRB1_ENST00000418536.2_Missense_Mutation_p.L220I|LILRB1_ENST00000324602.7_Missense_Mutation_p.L220I|LILRB1_ENST00000448689.1_Missense_Mutation_p.L220I|LILRB1_ENST00000396321.2_Missense_Mutation_p.L220I|LILRB1_ENST00000396332.4_Missense_Mutation_p.L220I|AC009892.1_ENST00000578908.1_RNA|LILRB1_ENST00000434867.2_Missense_Mutation_p.L220I|LILRB1_ENST00000396317.1_Missense_Mutation_p.L220I	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	220	Ig-like C2-type 2.				cellular response to lipopolysaccharide (GO:0071222)|defense response to virus (GO:0051607)|dendritic cell differentiation (GO:0097028)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma production (GO:0032609)|interferon-gamma secretion (GO:0072643)|negative regulation of alpha-beta T cell activation (GO:0046636)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of CD8-positive, alpha-beta T cell activation (GO:2001186)|negative regulation of cell cycle (GO:0045786)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of endocytosis (GO:0045806)|negative regulation of interferon-beta secretion (GO:0035548)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-12 secretion (GO:2001183)|negative regulation of mononuclear cell proliferation (GO:0032945)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of osteoclast development (GO:2001205)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transforming growth factor-beta secretion (GO:2001202)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of gamma-delta T cell activation involved in immune response (GO:2001193)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor internalization (GO:0031623)|regulation of immune response (GO:0050776)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation involved in immune response (GO:0002309)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	HLA-A specific inhibitory MHC class I receptor activity (GO:0030107)|HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)|MHC class I protein binding (GO:0042288)|MHC class I receptor activity (GO:0032393)|protein homodimerization activity (GO:0042803)|protein phosphatase 1 binding (GO:0008157)|SH2 domain binding (GO:0042169)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	74				GBM - Glioblastoma multiforme(193;0.0188)		GCTCCTGGTCCTAGGTGAGAA	0.582										HNSCC(37;0.09)																											p.L220I		Atlas-SNP	.											.	LILRB1	140	.	0			c.C658A						.						100	105	103					19																	55143685		2203	4300	6503	SO:0001583	missense	10859	exon5			CTGGTCCTAGGTG	AF009220	CCDS42614.1, CCDS42615.1, CCDS42616.1, CCDS42617.1, CCDS62803.1	19q13.4	2013-01-11						"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6605	protein-coding gene	gene with protein product		604811				9285411, 9382880	Standard	XM_006726246		Approved	LIR-1, ILT2, MIR-7, CD85, LIR1, CD85j	uc002qgm.3	Q8NHL6		ENST00000396331.1:c.658C>A	chr19.hg19:g.55143685C>A	ENSP00000379622:p.Leu220Ile	105.0	0.0		24.0	9.0	NM_001081637	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Missense_Mutation	SNP	ENST00000396331.1	hg19	CCDS42617.1	.	.	.	.	.	.	.	.	.	.	C	9.730	1.162140	0.21538	.	.	ENSG00000104972	ENST00000396321;ENST00000418536;ENST00000448689;ENST00000396331;ENST00000396327;ENST00000324602;ENST00000434867;ENST00000396332;ENST00000427581;ENST00000396317;ENST00000396315	T;T;T;T;T;T;T;T;T;T;T	0.22336	1.96;1.96;1.96;1.96;1.96;1.96;1.96;1.96;1.96;1.96;1.96	1.57	-2.74	0.05932	Immunoglobulin-like fold (1);	1.296060	0.05569	N	0.570701	T	0.11580	0.0282	N	0.11789	0.175	0.09310	N	1	B;B;B;B;B	0.12013	0.001;0.005;0.003;0.0;0.003	B;B;B;B;B	0.17433	0.008;0.018;0.008;0.001;0.008	T	0.36817	-0.9732	10	0.66056	D	0.02	.	5.8156	0.18490	0.0:0.3467:0.0:0.6533	.	220;220;220;220;220	A8MVE2;Q8NHL6-3;A2IXV4;Q8NHL6-2;Q8NHL6	.;.;.;.;LIRB1_HUMAN	I	220;220;220;220;220;220;220;220;256;220;220	ENSP00000379614:L220I;ENSP00000391514:L220I;ENSP00000409968:L220I;ENSP00000379622:L220I;ENSP00000379618:L220I;ENSP00000315997:L220I;ENSP00000405243:L220I;ENSP00000379623:L220I;ENSP00000395004:L256I;ENSP00000379610:L220I;ENSP00000379608:L220I	ENSP00000315997:L220I	L	+	1	2	LILRB1	59835497	0.000000	0.05858	0.011000	0.14972	0.344000	0.29017	-1.684000	0.01932	-0.860000	0.04099	0.184000	0.17185	CTA	.	.		0.582	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4			A	55143685	C	A	55143685	3	1	340	1	0	0	0	0	1	0	0	0	8799	680	24	3	672	3	LILRB1	19	55143685	Missense_Mutation	SNP	C	TCGA-RC-A7SK-01A-11D-A34Z-10	589011	55143685	3985298	131	47095										
ZNF211	10520	hgsc.bcm.edu	37	chr19	58152694	58152694	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	cagcaccagaaagtccacagTgaagaaaggccttatgaatg	10	9	0	4			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr19:58152694T>C	ENST00000347302.3	+	3	1019	c.840T>C	c.(838-840)agT>agC	p.S280S	ZNF211_ENST00000420680.1_Silent_p.S284S|ZNF211_ENST00000254182.7_Silent_p.S271S|ZNF211_ENST00000541801.1_Silent_p.S271S|ZNF211_ENST00000240731.4_Silent_p.S293S|ZNF211_ENST00000391703.3_Silent_p.S219S|ZNF211_ENST00000544273.1_Silent_p.S292S|ZNF211_ENST00000299871.5_Silent_p.S345S	NM_198855.2	NP_942152.1	Q13398	ZN211_HUMAN	zinc finger protein 211	280					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		AAGTCCACAGTGAAGAAAGGC	0.408																																					p.S345S		Atlas-SNP	.											.	ZNF211	78	.	0			c.T1035C						.						121	113	116					19																	58152694		2203	4300	6503	SO:0001819	synonymous_variant	10520	exon5			CCACAGTGAAGAA	U38904	CCDS12956.1, CCDS12957.1, CCDS58686.1, CCDS58687.1, CCDS58688.1, CCDS74468.1	19q13.4	2013-01-08			ENSG00000121417	ENSG00000121417		"Zinc fingers, C2H2-type", "-"	13003	protein-coding gene	gene with protein product		601856				7633419, 9096115	Standard	NM_006385		Approved	ZNF-25, CH2H2-25	uc031rng.1	Q13398	OTTHUMG00000168012	ENST00000347302.3:c.840T>C	chr19.hg19:g.58152694T>C		59.0	0.0		17.0	6.0	NM_001265597	B4DH10|B4DLC9|B4E3C9|B9ZVS7|B9ZVW1|F8WDV2|Q05BQ7|Q2TAL7|Q59EG4|Q59G36|Q5EBL6	Silent	SNP	ENST00000347302.3	hg19	CCDS12957.1	.	.	.	.	.	.	.	.	.	.	T	8.553	0.876040	0.17395	.	.	ENSG00000121417	ENST00000407202	.	.	.	3.27	3.27	0.37495	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.9252	0.24412	0.2057:0.0:0.0:0.7943	.	.	.	.	R	284	.	.	X	+	1	0	ZNF211	62844506	0.000000	0.05858	0.172000	0.22920	0.998000	0.95712	-0.704000	0.05058	1.486000	0.48398	0.472000	0.43445	TGA	.	.		0.408	ZNF211-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397502.1			C	58152694	T	C	58152694	2	2	340	1	0	0	0	0	0	0	0	1	17782	1693	59	2		2	ZNF211	19	58152694	Silent	SNP	T	TCGA-RC-A7SK-01A-11D-A34Z-10	3009009	58152694	976289	132	47096										
CSRP2BP	57325	hgsc.bcm.edu	37	chr20	18165423	18165423	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	gattgcaactttcatgatctAtcatctgattcaggtaagtt	7	7	5	2			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr20:18165423A>G	ENST00000435364.3	+	9	2503	c.2162A>G	c.(2161-2163)tAt>tGt	p.Y721C	CSRP2BP_ENST00000377681.3_Missense_Mutation_p.Y720C|CSRP2BP_ENST00000489634.2_Missense_Mutation_p.Y593C	NM_020536.4	NP_065397	Q9H8E8	CSR2B_HUMAN	CSRP2 binding protein	721	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				chromatin organization (GO:0006325)|G2/M transition of mitotic cell cycle (GO:0000086)|histone H3 acetylation (GO:0043966)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|LIM domain binding (GO:0030274)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(12)|ovary(2)|prostate(3)|skin(1)|stomach(1)	34						TTCATGATCTATCATCTGATT	0.443																																					p.Y721C		Atlas-SNP	.											.	CSRP2BP	80	.	0			c.A2162G						.						175	142	154					20																	18165423		2203	4300	6503	SO:0001583	missense	57325	exon9			TGATCTATCATCT	AF252257	CCDS13133.1	20p11.23	2012-06-06			ENSG00000149474	ENSG00000149474			15904	protein-coding gene	gene with protein product	"cysteine rich protein 2 binding protein", "ATAC component 2 homolog (Drosophila)"					9286703, 10924333, 19103755	Standard	NR_028402		Approved	CRP2BP, dJ717M23.1, PRO1194, ATAC2, KAT14	uc021wbb.1	Q9H8E8	OTTHUMG00000031962	ENST00000435364.3:c.2162A>G	chr20.hg19:g.18165423A>G	ENSP00000392318:p.Tyr721Cys	87.0	0.0		59.0	8.0	NM_020536	A2A2I5|Q96GW6|Q96IH3|Q9HBF0|Q9UIY5	Missense_Mutation	SNP	ENST00000435364.3	hg19	CCDS13133.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.421144	0.83559	.	.	ENSG00000149474	ENST00000278816;ENST00000377681;ENST00000435364;ENST00000489634	T;T;T;T	0.22134	1.97;1.97;1.97;1.97	5.99	5.99	0.97316	GCN5-related N-acetyltransferase (GNAT) domain (2);Acyl-CoA N-acyltransferase (2);	0.000000	0.85682	D	0.000000	T	0.30759	0.0775	N	0.12471	0.22	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	T	0.31052	-0.9957	10	0.87932	D	0	-15.7416	16.4943	0.84223	1.0:0.0:0.0:0.0	.	593;721	Q9H8E8-2;Q9H8E8	.;CSR2B_HUMAN	C	721;720;721;593	ENSP00000278816:Y721C;ENSP00000366909:Y720C;ENSP00000392318:Y721C;ENSP00000425909:Y593C	ENSP00000278816:Y721C	Y	+	2	0	CSRP2BP	18113423	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.228000	0.95250	2.291000	0.77112	0.533000	0.62120	TAT	.	.		0.443	CSRP2BP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078152.5	NM_020536		G	18165423	A	G	18165423	3	3	340	1	0	0	0	0	1	0	0	0	3970	449	16	2	2196	2	CSRP2BP	20	18165423	Missense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10		18165423	44860097	133	47097										
ITSN1	6453	hgsc.bcm.edu	37	chr21	35134244	35134244	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	taggtccccaagcaagaactAttcttatgcagtcaagttta	7	9	2	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr21:35134244A>G	ENST00000381318.3	+	9	1030	c.742A>G	c.(742-744)Att>Gtt	p.I248V	ITSN1_ENST00000399338.4_Missense_Mutation_p.I248V|ITSN1_ENST00000399349.1_Missense_Mutation_p.I248V|ITSN1_ENST00000488166.1_3'UTR|ITSN1_ENST00000399367.3_Missense_Mutation_p.I248V|ITSN1_ENST00000379960.5_Missense_Mutation_p.I248V|ITSN1_ENST00000381291.4_Missense_Mutation_p.I248V|AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000381285.4_Missense_Mutation_p.I248V|ITSN1_ENST00000399326.3_Missense_Mutation_p.I248V|ITSN1_ENST00000437442.2_Missense_Mutation_p.I248V|ITSN1_ENST00000399355.2_Missense_Mutation_p.I248V|ITSN1_ENST00000399352.1_Missense_Mutation_p.I248V|ITSN1_ENST00000399353.1_Missense_Mutation_p.I211V	NM_003024.2	NP_003015.2	Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)	248	EH 2. {ECO:0000255|PROSITE- ProRule:PRU00077}.				apoptotic signaling pathway (GO:0097190)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|kinase activator activity (GO:0019209)|proline-rich region binding (GO:0070064)|protein complex scaffold (GO:0032947)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(26)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	67						AGCAAGAACTATTCTTATGCA	0.433																																					p.I248V		Atlas-SNP	.											.	ITSN1	166	.	0			c.A742G						.						220	192	201					21																	35134244		2203	4300	6503	SO:0001583	missense	6453	exon9			AGAACTATTCTTA	AF064244	CCDS33545.1, CCDS33546.1	21q22.1-q22.2	2013-01-10			ENSG00000205726	ENSG00000205726		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "EF-hand domain containing"	6183	protein-coding gene	gene with protein product	"SH3 domain protein-1A", "human intersectin-SH3 domain-containing protein SH3P17", "Src homology 3 domain-containing protein", "intersectin 1 short form variant, 11", "intersectin 1 short form variant 3", "intersectin short variant 12"	602442		SH3D1A, ITSN		9799604, 9813051	Standard	NM_003024		Approved	SH3P17, MGC134948, MGC134949	uc002yta.1	Q15811	OTTHUMG00000065284	ENST00000381318.3:c.742A>G	chr21.hg19:g.35134244A>G	ENSP00000370719:p.Ile248Val	216.0	0.0		98.0	6.0	NM_001001132	A7Y322|A8CTX8|A8CTY3|A8CTY7|A8D7D0|A8DCP3|B4DTM2|E7ERJ1|E9PE44|E9PG01|E9PHV2|O95216|Q0PW94|Q0PW95|Q0PW97|Q14BD3|Q1ED40|Q20BK3|Q9UET5|Q9UK60|Q9UNK1|Q9UNK2|Q9UQ92	Missense_Mutation	SNP	ENST00000381318.3	hg19	CCDS33545.1	.	.	.	.	.	.	.	.	.	.	A	14.16	2.453537	0.43531	.	.	ENSG00000205726	ENST00000399353;ENST00000381318;ENST00000381291;ENST00000381285;ENST00000381288;ENST00000381289;ENST00000399367;ENST00000399352;ENST00000399355;ENST00000399349;ENST00000381283;ENST00000399338;ENST00000437442;ENST00000399326;ENST00000379960	T;T;T;T;T;T;T;T;T;T;T;T;T	0.25085	1.82;1.82;1.82;1.82;1.82;1.82;1.82;1.82;1.82;1.82;1.82;1.82;1.82	6.03	6.03	0.97812	EPS15 homology (EH) (2);EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.36166	0.0957	L	0.28014	0.82	0.58432	D	0.999998	B;B;B;B;B;P;B;B;B;B	0.40000	0.418;0.418;0.418;0.127;0.365;0.698;0.127;0.127;0.365;0.418	B;B;B;B;B;D;B;B;B;B	0.67231	0.353;0.353;0.353;0.159;0.24;0.95;0.118;0.118;0.24;0.353	T	0.05068	-1.0908	10	0.02654	T	1	.	16.5655	0.84588	1.0:0.0:0.0:0.0	.	211;211;211;248;248;248;248;248;248;211	A8D7D0;A7XZY7;A8CTY7;A8CTY3;F8W7U0;E7ERJ1;A8CTX8;Q15811;Q15811-3;E7ERJ0	.;.;.;.;.;.;.;ITSN1_HUMAN;.;.	V	211;248;248;248;248;248;248;248;248;248;188;248;248;248;248	ENSP00000382290:I211V;ENSP00000370719:I248V;ENSP00000370691:I248V;ENSP00000370685:I248V;ENSP00000382301:I248V;ENSP00000382289:I248V;ENSP00000382292:I248V;ENSP00000382286:I248V;ENSP00000370683:I188V;ENSP00000382275:I248V;ENSP00000387377:I248V;ENSP00000382265:I248V;ENSP00000369294:I248V	ENSP00000369294:I248V	I	+	1	0	ITSN1	34056114	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.031000	0.76491	2.302000	0.77476	0.533000	0.62120	ATT	.	.		0.433	ITSN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000140070.4	NM_003024		G	35134244	A	G	35134244	3	3	340	1	0	0	0	0	1	0	0	0	7935	449	16	2	772	2	ITSN1	21	35134244	Missense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10		35134244	12995651	134	47098										
TTC38	55020	hgsc.bcm.edu	37	chr22	46671305	46671305	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	accccttctggacacctgacAtccccctaagcaggtatgtg	8	15	1	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chr22:46671305A>G	ENST00000381031.3	+	5	602	c.526A>G	c.(526-528)Atc>Gtc	p.I176V	TTC38_ENST00000445282.2_Intron	NM_017931.2	NP_060401	Q5R3I4	TTC38_HUMAN	tetratricopeptide repeat domain 38	176						extracellular vesicular exosome (GO:0070062)				endometrium(4)|large_intestine(3)|lung(4)|ovary(1)	12						GACACCTGACATCCCCCTAAG	0.443																																					p.I176V		Atlas-SNP	.											.	TTC38	40	.	0			c.A526G						.						100	99	99					22																	46671305		1882	4098	5980	SO:0001583	missense	55020	exon5			CCTGACATCCCCC		CCDS43030.1	22q13	2013-01-11			ENSG00000075234	ENSG00000075234		"Tetratricopeptide (TTC) repeat domain containing"	26082	protein-coding gene	gene with protein product							Standard	NM_017931		Approved	FLJ20699	uc003bhi.3	Q5R3I4	OTTHUMG00000150494	ENST00000381031.3:c.526A>G	chr22.hg19:g.46671305A>G	ENSP00000370419:p.Ile176Val	90.0	0.0		28.0	11.0	NM_017931	Q8WV27|Q9NWP8	Missense_Mutation	SNP	ENST00000381031.3	hg19	CCDS43030.1	.	.	.	.	.	.	.	.	.	.	A	2.428	-0.331558	0.05314	.	.	ENSG00000075234	ENST00000381031;ENST00000421359	T	0.38240	1.15	5.93	-3.47	0.04753	.	0.605314	0.18640	N	0.135310	T	0.18551	0.0445	N	0.25485	0.75	0.29617	N	0.846493	B	0.09022	0.002	B	0.06405	0.002	T	0.20273	-1.0280	9	.	.	.	-19.539	8.1272	0.31005	0.4056:0.1836:0.4108:0.0	.	176	Q5R3I4	TTC38_HUMAN	V	176	ENSP00000370419:I176V	.	I	+	1	0	TTC38	45049969	0.001000	0.12720	0.016000	0.15963	0.829000	0.46940	0.033000	0.13754	-0.310000	0.08766	0.533000	0.62120	ATC	.	.		0.443	TTC38-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000318469.1	NM_017931		G	46671305	A	G	46671305	3	3	340	1	0	0	0	0	1	0	0	0	16721	217	8	2	544	2	TTC38	22	46671305	Missense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10		46671305	4633261	135	47099										
CCNB3	85417	hgsc.bcm.edu	37	chrX	50037976	50037976	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	cttggactggccaaaaagaaTaagcggaatctaaaatggtg	11	6	1	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chrX:50037976T>A	ENST00000376042.1	+	5	616	c.318T>A	c.(316-318)aaT>aaA	p.N106K	CCNB3_ENST00000276014.7_Missense_Mutation_p.N106K|CCNB3_ENST00000348603.2_Intron|CCNB3_ENST00000376038.1_Intron			Q8WWL7	CCNB3_HUMAN	cyclin B3	106					meiotic nuclear division (GO:0007126)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)	nucleus (GO:0005634)				breast(3)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Ovarian(276;0.236)					CCAAAAAGAATAAGCGGAATC	0.393																																					p.N106K		Atlas-SNP	.											.	CCNB3	367	.	0			c.T318A						.						121	103	109					X																	50037976		2203	4300	6503	SO:0001583	missense	85417	exon4			AAAGAATAAGCGG	AJ314764	CCDS14331.1, CCDS14332.1	Xp11	2008-07-03			ENSG00000147082	ENSG00000147082			18709	protein-coding gene	gene with protein product		300456				11846420, 12185076	Standard	XM_006724610		Approved		uc004doy.3	Q8WWL7	OTTHUMG00000021519	ENST00000376042.1:c.318T>A	chrX.hg19:g.50037976T>A	ENSP00000365210:p.Asn106Lys	107.0	0.0		31.0	16.0	NM_033031	B1AQI5|B1AQI6|Q96SB5|Q96SB6|Q96SB7|Q9NT38	Missense_Mutation	SNP	ENST00000376042.1	hg19	CCDS14331.1	.	.	.	.	.	.	.	.	.	.	T	9.444	1.088815	0.20390	.	.	ENSG00000147082	ENST00000376042;ENST00000396540;ENST00000276014	T;T	0.11063	2.81;2.81	3.83	1.31	0.21738	.	18.892400	0.00166	N	0.000002	T	0.10594	0.0259	L	0.43152	1.355	0.09310	N	1	B	0.18461	0.028	B	0.11329	0.006	T	0.27739	-1.0065	9	.	.	.	.	3.3901	0.07286	0.0:0.1305:0.2346:0.6349	.	106	Q8WWL7	CCNB3_HUMAN	K	106	ENSP00000365210:N106K;ENSP00000276014:N106K	.	N	+	3	2	CCNB3	50054716	0.003000	0.15002	0.000000	0.03702	0.001000	0.01503	0.994000	0.29693	0.065000	0.16485	0.478000	0.44815	AAT	.	.		0.393	CCNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056558.1			A	50037976	T	A	50037976	3	1	340	1	0	0	0	0	1	0	0	0	2916	1403	49	4	328	4	CCNB3	23	50037976	Missense_Mutation	SNP	T	TCGA-RC-A7SK-01A-11D-A34Z-10		50037976	105232584	136	47100										
PCDH11Y	83259	hgsc.bcm.edu	37	chrY	4968005	4968005	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0305343511450382	4	1	0.836231884057971	1.25434782608696	0.627173913043478	1	1	0	gacagcctgattctctcttcAgtgttgtaattgtcaatctg	8	9	5	1			TCGA-RC-A7SK-01A-11D-A34Z-10	TCGA-RC-A7SK-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4fd7293a-c256-40e8-a1b8-8f8b507f3441	2f8837d8-34ee-463b-bc83-36ab5067c3bd	g.chrY:4968005A>G	ENST00000333703.4	+	5	2866	c.2353A>G	c.(2353-2355)Agt>Ggt	p.S785G	PCDH11Y_ENST00000362095.5_Missense_Mutation_p.S796G|PCDH11Y_ENST00000215473.6_Missense_Mutation_p.S796G	NM_001278619.1|NM_032971.2	NP_001265548.1|NP_116753.1	Q9BZA8	PC11Y_HUMAN	protocadherin 11 Y-linked	796	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|kidney(2)|large_intestine(7)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						TTCTCTCTTCAGTGTTGTAAT	0.418																																					p.S796G		Atlas-SNP	.											.	PCDH11Y	163	.	0			c.A2386G						.																																			SO:0001583	missense	83259	exon2			CTCTTCAGTGTTG	AF332217	CCDS14776.1, CCDS14777.1, CCDS76066.1	Yp11.2	2010-01-26	2002-05-22	2002-05-24	ENSG00000099715	ENSG00000099715		"Cadherins / Protocadherins : Non-clustered"	15813	protein-coding gene	gene with protein product		400022	"protocadherin 22"	PCDH22		10644456, 11003707	Standard	NM_032971		Approved	PCDHY	uc004fqo.3	Q9BZA8	OTTHUMG00000035105	ENST00000333703.4:c.2353A>G	chrY.hg19:g.4968005A>G	ENSP00000330552:p.Ser785Gly	201.0	0.0		65.0	39.0	NM_032972	Q70LR6|Q70LR8|Q70LS0|Q70LS1|Q70LS2|Q70LS3|Q70LS4|Q70LS5|Q8WY34|Q9BZA9|Q9H4E1	Missense_Mutation	SNP	ENST00000333703.4	hg19	CCDS14776.1																																																																																			.	.		0.418	PCDH11Y-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084979.2	NM_032973		G	4968005	A	G	4968005	3	3	340	1	0	0	0	0	1	0	0	0	11518	188	7	2	2428	2	PCDH11Y	24	4968005	Missense_Mutation	SNP	A	TCGA-RC-A7SK-01A-11D-A34Z-10		4968005	54405561	137	47101										
ZNF683	257101	hgsc.bcm.edu	37	chr1	26694244	26694244	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	cagctggcacaggatgggccAtgagcatccaccatgtctgg	13	12	1	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr1:26694244A>G	ENST00000436292.1	-	3	279	c.159T>C	c.(157-159)caT>caC	p.H53H	ZNF683_ENST00000349618.3_Silent_p.H53H|ZNF683_ENST00000374204.1_Silent_p.H53H|ZNF683_ENST00000403843.1_Silent_p.H53H			Q8IZ20	ZN683_HUMAN	zinc finger protein 683	53			H -> R (in dbSNP:rs10794531).		natural killer cell differentiation (GO:0001779)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(1)|skin(1)	15		all_cancers(24;2.39e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.76e-26)|Colorectal(126;1.38e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|BRCA - Breast invasive adenocarcinoma(304;0.00099)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00793)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.159)|LUSC - Lung squamous cell carcinoma(448;0.233)		AGGATGGGCCATGAGCATCCA	0.652																																					p.H53H		Atlas-SNP	.											.	ZNF683	51	.	0			c.T159C						.						28	25	26					1																	26694244		2203	4297	6500	SO:0001819	synonymous_variant	257101	exon3			TGGGCCATGAGCA	BC029505	CCDS279.2	1p36.11	2013-01-08			ENSG00000176083	ENSG00000176083		"Zinc fingers, C2H2-type"	28495	protein-coding gene	gene with protein product	"hypothetical protein MGC33414"					12477932	Standard	NM_173574		Approved	MGC33414	uc009vsj.1	Q8IZ20	OTTHUMG00000003521	ENST00000436292.1:c.159T>C	chr1.hg19:g.26694244A>G		101.0	0.0		81.0	19.0	NM_173574	Q5T141|Q5T146|Q5T147|Q5T149|Q8NEN4	Silent	SNP	ENST00000436292.1	hg19																																																																																				.	.		0.652	ZNF683-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000009794.2	NM_173574		G	26694244	A	G	26694244	2	3	341	1	0	0	0	0	0	0	0	1	18105	214	8	2		2	ZNF683	1	26694244	Silent	SNP	A	TCGA-RG-A7D4-01A-12D-A33Q-10		26694244	222556377	1	47102										
PUM1	9698	hgsc.bcm.edu	37	chr1	31438867	31438867	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	caagggcggatcccagggtgGcgccgagagaactgctactt	15	11	0	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr1:31438867G>A	ENST00000257075.5	-	13	2141	c.2048C>T	c.(2047-2049)gCc>gTc	p.A683V	SNORD85_ENST00000363311.1_RNA|PUM1_ENST00000440538.2_Missense_Mutation_p.A657V|PUM1_ENST00000424085.2_Missense_Mutation_p.A441V|PUM1_ENST00000373742.2_Missense_Mutation_p.A624V|PUM1_ENST00000373741.4_Missense_Mutation_p.A719V|PUM1_ENST00000426105.2_Missense_Mutation_p.A683V|PUM1_ENST00000423018.2_Missense_Mutation_p.A539V|PUM1_ENST00000373747.3_Missense_Mutation_p.A684V|PUM1_ENST00000490546.1_5'Flank	NM_014676.2	NP_055491.1	Q14671	PUM1_HUMAN	pumilio RNA-binding family member 1	683	Ser-rich.				membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(17)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)		TCCCAGGGTGGCGCCGAGAGA	0.493																																					p.A683V		Atlas-SNP	.											.	PUM1	107	.	0			c.C2048T						.						74	78	77					1																	31438867		2203	4300	6503	SO:0001583	missense	9698	exon13			AGGGTGGCGCCGA	AF315592	CCDS338.1, CCDS44099.1	1p35.2	2013-09-02	2013-09-02		ENSG00000134644	ENSG00000134644			14957	protein-coding gene	gene with protein product		607204	"pumilio (Drosophila) homolog 1", "pumilio homolog 1 (Drosophila)"				Standard	NM_001020658		Approved	PUMH1, KIAA0099	uc001bsh.1	Q14671	OTTHUMG00000003795	ENST00000257075.5:c.2048C>T	chr1.hg19:g.31438867G>A	ENSP00000257075:p.Ala683Val	124.0	0.0		135.0	15.0	NM_014676	A8K6W4|B4DG92|D3DPN3|E9PCJ0|Q53HH5|Q5VXY7|Q9HAN1	Missense_Mutation	SNP	ENST00000257075.5	hg19	CCDS338.1	.	.	.	.	.	.	.	.	.	.	G	31	5.086143	0.94100	.	.	ENSG00000134644	ENST00000424085;ENST00000257075;ENST00000373747;ENST00000373749;ENST00000426105;ENST00000440538;ENST00000373741;ENST00000423018;ENST00000373742	T;T;T;T;T;T;T;T	0.18810	2.22;2.19;2.47;2.46;2.47;2.45;2.45;2.22	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.36608	0.0973	L	0.45228	1.405	0.80722	D	1	D;B;D;B;D;D;D;D	0.69078	0.997;0.084;0.997;0.137;0.982;0.994;0.982;0.982	P;B;P;B;P;P;P;P	0.59357	0.856;0.042;0.856;0.092;0.772;0.856;0.772;0.772	T	0.00500	-1.1703	10	0.25751	T	0.34	-8.5673	20.3931	0.98965	0.0:0.0:1.0:0.0	.	624;539;719;657;683;683;684;683	B4DG92;E7EWT3;Q5T1Z8;Q14671-2;Q14671;E9PCJ0;Q5T1Z4;Q53HH5	.;.;.;.;PUM1_HUMAN;.;.;.	V	441;683;684;421;683;657;719;539;624	ENSP00000400141:A441V;ENSP00000257075:A683V;ENSP00000362852:A684V;ENSP00000391723:A683V;ENSP00000401777:A657V;ENSP00000362846:A719V;ENSP00000399440:A539V;ENSP00000362847:A624V	ENSP00000257075:A683V	A	-	2	0	PUM1	31211454	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.004000	0.88535	2.824000	0.97209	0.655000	0.94253	GCC	.	.		0.493	PUM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000010671.1			A	31438867	G	A	31438867	3	1	341	1	0	0	0	0	1	0	0	0	12840	1203	42	3	1558	3	PUM1	1	31438867	Missense_Mutation	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10	4744623	31438867	217811754	2	47103										
ATG4C	84938	hgsc.bcm.edu	37	chr1	63294791	63294791	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	acaaagctgttattattctaGttcctgttagacttggtgga	9	6	1	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr1:63294791G>T	ENST00000317868.4	+	7	1084	c.877G>T	c.(877-879)Gtt>Ttt	p.V293F	ATG4C_ENST00000371120.3_Missense_Mutation_p.V293F	NM_032852.3	NP_116241.2	Q96DT6	ATG4C_HUMAN	autophagy related 4C, cysteine peptidase	293					autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|protein targeting to membrane (GO:0006612)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)		ATG4C/FBXO38(2)	NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(3)|ovary(1)|prostate(2)	19						TATTATTCTAGTTCCTGTTAG	0.338																																					p.V293F		Atlas-SNP	.											.	ATG4C	96	.	0			c.G877T						.						78	81	80					1																	63294791		2203	4300	6503	SO:0001583	missense	84938	exon7			ATTCTAGTTCCTG	AK027773	CCDS623.1	1p31.3	2014-02-12	2012-06-06	2005-09-11	ENSG00000125703	ENSG00000125703			16040	protein-coding gene	gene with protein product		611339	"AUT (S. cerevisiae)-like 1, cysteine endopeptidase; AUT-like 1, cysteine endopeptidase (S. cerevisiae)", "APG4 autophagy 4 homolog C (S. cerevisiae)", "ATG4 autophagy related 4 homolog C (S. cerevisiae)"	AUTL1, APG4C		12446702	Standard	NM_032852		Approved	FLJ14867, AUTL3	uc001dau.3	Q96DT6	OTTHUMG00000009142	ENST00000317868.4:c.877G>T	chr1.hg19:g.63294791G>T	ENSP00000322159:p.Val293Phe	107.0	0.0		116.0	27.0	NM_178221	A6NLR8|D3DQ58|Q96K04	Missense_Mutation	SNP	ENST00000317868.4	hg19	CCDS623.1	.	.	.	.	.	.	.	.	.	.	G	16.04	3.010711	0.54361	.	.	ENSG00000125703	ENST00000317868;ENST00000371120;ENST00000540025;ENST00000414558	T;T	0.50548	0.74;0.74	5.69	4.75	0.60458	.	0.169554	0.52532	D	0.000074	T	0.35068	0.0919	M	0.67625	2.065	0.52501	D	0.999957	B	0.31931	0.347	B	0.40677	0.337	T	0.36212	-0.9757	10	0.42905	T	0.14	-17.2154	7.5205	0.27624	0.1492:0.0:0.7162:0.1346	.	293	Q96DT6	ATG4C_HUMAN	F	293;293;293;37	ENSP00000322159:V293F;ENSP00000360161:V293F	ENSP00000322159:V293F	V	+	1	0	ATG4C	63067379	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.394000	0.44450	1.334000	0.45468	0.655000	0.94253	GTT	.	.		0.338	ATG4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025332.2	NM_032852		T	63294791	G	T	63294791	3	4	341	1	0	0	0	0	1	0	0	0	1098	1029	36	3	899	3	ATG4C	1	63294791	Missense_Mutation	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10	31855924	63294791	185955830	3	47104										
SLC22A15	55356	hgsc.bcm.edu	37	chr1	116574033	116574033	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	tatactcccagggtcgactgAgtgaggctgaagaggcgctg	15	9	0	4			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr1:116574033A>C	ENST00000369503.4	+	6	905	c.775A>C	c.(775-777)Agt>Cgt	p.S259R	SLC22A15_ENST00000369502.1_Nonstop_Mutation_p.*246C	NM_018420.2	NP_060890.2	Q8IZD6	S22AF_HUMAN	solute carrier family 22, member 15	259					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			endometrium(1)|large_intestine(2)|lung(12)|prostate(1)|urinary_tract(1)	17	Lung SC(450;0.184)	all_cancers(81;3.17e-06)|all_epithelial(167;2.32e-06)|all_lung(203;9.81e-06)|Lung NSC(69;5.94e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		GGGTCGACTGAGTGAGGCTGA	0.493																																					p.S259R		Atlas-SNP	.											.	SLC22A15	65	.	0			c.A775C						.						83	83	83					1																	116574033		1977	4162	6139	SO:0001583	missense	55356	exon6			CGACTGAGTGAGG	AY145501	CCDS44198.1	1p12	2013-05-22	2008-01-11		ENSG00000163393	ENSG00000163393		"Solute carriers"	20301	protein-coding gene	gene with protein product		608275	"solute carrier family 22 (organic cation transporter), member 15"			12372408	Standard	NM_018420		Approved	FLIPT1	uc001egb.4	Q8IZD6	OTTHUMG00000012008	ENST00000369503.4:c.775A>C	chr1.hg19:g.116574033A>C	ENSP00000358515:p.Ser259Arg	112.0	0.0		100.0	21.0	NM_018420	A8MUR3|Q6UXP5|Q8TAL9|Q9NSH5	Missense_Mutation	SNP	ENST00000369503.4	hg19	CCDS44198.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.50|12.50	1.956343|1.956343	0.34565|0.34565	.|.	.|.	ENSG00000163393|ENSG00000163393	ENST00000369503|ENST00000369502	T|.	0.56941|.	0.43|.	4.81|4.81	-0.816|-0.816	0.10839|0.10839	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);|.	0.535487|.	0.22852|.	N|.	0.054859|.	T|.	0.05502|.	0.0145|.	N|N	0.02412|0.02412	-0.56|-0.56	0.09310|0.09310	N|N	1|1	B|.	0.02656|.	0.0|.	B|.	0.13407|.	0.009|.	T|.	0.38950|.	-0.9637|.	10|.	0.23891|.	T|.	0.37|.	.|.	15.5677|15.5677	0.76306|0.76306	0.4101:0.5899:0.0:0.0|0.4101:0.5899:0.0:0.0	.|.	259|.	Q8IZD6|.	S22AF_HUMAN|.	R|C	259|246	ENSP00000358515:S259R|.	ENSP00000358515:S259R|.	S|X	+|+	1|3	0|0	SLC22A15|SLC22A15	116375556|116375556	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.982000|0.982000	0.71751|0.71751	1.859000|1.859000	0.39418|0.39418	-0.002000|-0.002000	0.14469|0.14469	0.533000|0.533000	0.62120|0.62120	AGT|TGA	.	.		0.493	SLC22A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033220.2	NM_018420		C	116574033	A	C	116574033	3	2	341	1	0	0	0	0	1	0	0	0	14461	304	11	5	797	5	SLC22A15	1	116574033	Missense_Mutation	SNP	A	TCGA-RG-A7D4-01A-12D-A33Q-10	53279242	116574033	132676588	4	47105										
FLG	2312	hgsc.bcm.edu	37	chr1	152279556	152279556	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	tgggacctggggtgtctggaGccatctcttagctgctcctg	14	11	2	0			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr1:152279556G>T	ENST00000368799.1	-	3	7841	c.7806C>A	c.(7804-7806)ggC>ggA	p.G2602G	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2602	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GGTGTCTGGAGCCATCTCTTA	0.547									Ichthyosis																												p.G2602G		Atlas-SNP	.											.	FLG	900	.	0			c.C7806A						.						46	52	50					1																	152279556		2199	4280	6479	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TCTGGAGCCATCT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.7806C>A	chr1.hg19:g.152279556G>T		202.0	0.0		257.0	61.0	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	hg19	CCDS30860.1																																																																																			.	.		0.547	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		T	152279556	G	T	152279556	2	4	341	1	0	0	0	0	0	0	0	1	5930	958	34	3		3	FLG	1	152279556	Silent	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10	35705523	152279556	96971065	5	47106										
FCRL5	83416	hgsc.bcm.edu	37	chr1	157516904	157516904	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	tggtgagtagaagcgaaatcCcttgcaagtgagggtcactc	13	8	1	3			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr1:157516904C>T	ENST00000361835.3	-	3	293	c.136G>A	c.(136-138)Gga>Aga	p.G46R	FCRL5_ENST00000368191.3_Intron|FCRL5_ENST00000368188.2_Missense_Mutation_p.G46R|FCRL5_ENST00000368190.3_Missense_Mutation_p.G46R|FCRL5_ENST00000356953.4_Missense_Mutation_p.G46R|FCRL5_ENST00000368189.3_Missense_Mutation_p.G46R	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	46	Ig-like C2-type 1.				negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(45)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	85	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)				AAGCGAAATCCCTTGCAAGTG	0.473																																					p.G46R		Atlas-SNP	.											.	FCRL5	177	.	0			c.G136A						.						153	142	146					1																	157516904		2203	4300	6503	SO:0001583	missense	83416	exon3			GAAATCCCTTGCA	AF369794	CCDS1165.1	1q21	2013-01-11			ENSG00000143297	ENSG00000143297		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18508	protein-coding gene	gene with protein product		605877				11027651, 11290337	Standard	NM_031281		Approved	FCRH5, IRTA2, BXMAS1, CD307e	uc009wsm.3	Q96RD9	OTTHUMG00000017481	ENST00000361835.3:c.136G>A	chr1.hg19:g.157516904C>T	ENSP00000354691:p.Gly46Arg	51.0	0.0		87.0	5.0	NM_031281	A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Missense_Mutation	SNP	ENST00000361835.3	hg19	CCDS1165.1	.	.	.	.	.	.	.	.	.	.	C	14.68	2.607894	0.46527	.	.	ENSG00000143297	ENST00000361835;ENST00000356953;ENST00000368190;ENST00000368189;ENST00000368188	T;T;T;T;T	0.12672	2.66;2.66;2.66;2.66;2.66	5.01	3.1	0.35709	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.06872	0.0175	M	0.77486	2.375	0.09310	N	1	B;B;B;B	0.28850	0.182;0.11;0.225;0.11	B;B;B;B	0.33121	0.139;0.158;0.07;0.158	T	0.38178	-0.9673	9	0.20519	T	0.43	.	8.0389	0.30511	0.0:0.8062:0.0:0.1938	.	46;46;46;46	Q96RD9-3;A6NJE8;Q96RD9-4;Q96RD9	.;.;.;FCRL5_HUMAN	R	46	ENSP00000354691:G46R;ENSP00000349434:G46R;ENSP00000357173:G46R;ENSP00000357172:G46R;ENSP00000357171:G46R	ENSP00000349434:G46R	G	-	1	0	FCRL5	155783528	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.145000	0.16157	0.496000	0.27904	0.650000	0.86243	GGA	.	.		0.473	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1	NM_031281		T	157516904	C	T	157516904	3	4	341	1	0	0	0	0	1	0	0	0	5806	632	22	3	2857	3	FCRL5	1	157516904	Missense_Mutation	SNP	C	TCGA-RG-A7D4-01A-12D-A33Q-10	5237348	157516904	91733717	6	47107										
PLEKHA6	22874	hgsc.bcm.edu	37	chr1	204192627	204192627	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	catggtatagctgctgtcggCgccccgtggggattcagacg	15	11	1	1	rs201146402		TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr1:204192627C>A	ENST00000272203.3	-	22	3434	c.3118G>T	c.(3118-3120)Gcc>Tcc	p.A1040S	PLEKHA6_ENST00000414478.1_Missense_Mutation_p.A1060S	NM_014935.4	NP_055750.2	Q9Y2H5	PKHA6_HUMAN	pleckstrin homology domain containing, family A member 6	1040										breast(2)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_cancers(21;0.0222)|Breast(84;0.179)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.229)			CTGCTGTCGGCGCCCCGTGGG	0.592																																					p.A1040S		Atlas-SNP	.											.	PLEKHA6	115	.	0			c.G3118T						.						24	23	23					1																	204192627		2039	3973	6012	SO:0001583	missense	22874	exon22			TGTCGGCGCCCCG	AB023186	CCDS1444.1	1q32	2013-01-10			ENSG00000143850	ENSG00000143850		"Pleckstrin homology (PH) domain containing"	17053	protein-coding gene	gene with protein product		607771				11001876	Standard	NM_014935		Approved	PEPP3, KIAA0969	uc001hau.4	Q9Y2H5	OTTHUMG00000036057	ENST00000272203.3:c.3118G>T	chr1.hg19:g.204192627C>A	ENSP00000272203:p.Ala1040Ser	157.0	0.0		161.0	15.0	NM_014935	A7MD51|Q5VTI6	Missense_Mutation	SNP	ENST00000272203.3	hg19	CCDS1444.1	.	.	.	.	.	.	.	.	.	.	C	14.96	2.692303	0.48202	.	.	ENSG00000143850	ENST00000272203;ENST00000414478	T;T	0.10573	2.86;3.32	4.59	1.68	0.24146	.	0.511281	0.18767	N	0.131713	T	0.06600	0.0169	N	0.22421	0.69	0.31554	N	0.658433	B	0.32862	0.387	B	0.29862	0.108	T	0.16808	-1.0390	10	0.46703	T	0.11	-7.6857	7.5934	0.28033	0.0:0.6528:0.0:0.3472	.	1040	Q9Y2H5	PKHA6_HUMAN	S	1040;1060	ENSP00000272203:A1040S;ENSP00000402046:A1060S	ENSP00000272203:A1040S	A	-	1	0	PLEKHA6	202459250	0.992000	0.36948	0.999000	0.59377	0.986000	0.74619	0.119000	0.15626	0.141000	0.18875	0.455000	0.32223	GCC	.	.		0.592	PLEKHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087889.3	NM_014935		A	204192627	C	A	204192627	3	1	341	1	0	0	0	0	1	0	0	0	12069	768	27	1	32	1	PLEKHA6	1	204192627	Missense_Mutation	SNP	C	TCGA-RG-A7D4-01A-12D-A33Q-10	46675723	204192627	45057994	7	47108										
USH2A	7399	hgsc.bcm.edu	37	chr1	215808006	215808006	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	agaactctgtgcttttgctcCgcgatcccttctttttccca	6	14	2	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr1:215808006C>A	ENST00000307340.3	-	70	15478	c.15092G>T	c.(15091-15093)cGg>cTg	p.R5031L	USH2A_ENST00000366943.2_Missense_Mutation_p.R5031L	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	5031			R -> W (in dbSNP:rs56038610). {ECO:0000269|PubMed:18273898}.		hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			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)		GCTTTTGCTCCGCGATCCCTT	0.448										HNSCC(13;0.011)																											p.R5031L		Atlas-SNP	.											.	USH2A	1168	.	0			c.G15092T						.						115	109	111					1																	215808006		2203	4300	6503	SO:0001583	missense	7399	exon70			TTGCTCCGCGATC	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.15092G>T	chr1.hg19:g.215808006C>A	ENSP00000305941:p.Arg5031Leu	94.0	0.0		155.0	18.0	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	3.441	-0.114151	0.06881	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.12774	2.65;2.65	5.82	2.87	0.33458	.	0.495526	0.16770	N	0.200241	T	0.08714	0.0216	L	0.36672	1.1	0.09310	N	1	B	0.16166	0.016	B	0.14578	0.011	T	0.44452	-0.9327	10	0.07644	T	0.81	.	6.3204	0.21215	0.0:0.5532:0.1289:0.3178	.	5031	O75445	USH2A_HUMAN	L	5031	ENSP00000305941:R5031L;ENSP00000355910:R5031L	ENSP00000305941:R5031L	R	-	2	0	USH2A	213874629	0.005000	0.15991	0.000000	0.03702	0.121000	0.20230	0.426000	0.21363	0.088000	0.17205	-0.797000	0.03246	CGG	.	.		0.448	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		A	215808006	C	A	215808006	3	1	341	1	0	0	0	0	1	0	0	0	17051	652	23	1	528	1	USH2A	1	215808006	Missense_Mutation	SNP	C	TCGA-RG-A7D4-01A-12D-A33Q-10	11615379	215808006	33442615	8	47109										
NID1	4811	hgsc.bcm.edu	37	chr1	236193033	236193033	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	cacgaaggtcacctcagcctGgcgagtgaactcaccccctg	10	16	3	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr1:236193033G>A	ENST00000264187.6	-	7	1637	c.1555C>T	c.(1555-1557)Cag>Tag	p.Q519*	NID1_ENST00000366595.3_Nonsense_Mutation_p.Q519*	NM_002508.2	NP_002499.2	P14543	NID1_HUMAN	nidogen 1	519	Nidogen G2 beta-barrel. {ECO:0000255|PROSITE-ProRule:PRU00348}.				basement membrane organization (GO:0071711)|cell-matrix adhesion (GO:0007160)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|positive regulation of cell-substrate adhesion (GO:0010811)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|cell periphery (GO:0071944)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|laminin binding (GO:0043236)|proteoglycan binding (GO:0043394)			breast(4)|endometrium(9)|kidney(1)|large_intestine(23)|lung(20)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(1)	66	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Urokinase(DB00013)	ACCTCAGCCTGGCGAGTGAAC	0.612																																					p.Q519X		Atlas-SNP	.											.	NID1	196	.	0			c.C1555T						.						42	40	40					1																	236193033		2203	4300	6503	SO:0001587	stop_gained	4811	exon7			CAGCCTGGCGAGT	BC045606	CCDS1608.1	1q43	2011-05-08	2005-06-02	2005-06-02	ENSG00000116962	ENSG00000116962			7821	protein-coding gene	gene with protein product		131390	"nidogen (enactin)"	NID		2471408, 7557988	Standard	NM_002508		Approved	entactin	uc001hxo.3	P14543	OTTHUMG00000040071	ENST00000264187.6:c.1555C>T	chr1.hg19:g.236193033G>A	ENSP00000264187:p.Gln519*	75.0	0.0		61.0	26.0	NM_002508	Q14942|Q59FL2|Q5TAF2|Q5TAF3|Q86XD7	Nonsense_Mutation	SNP	ENST00000264187.6	hg19	CCDS1608.1	.	.	.	.	.	.	.	.	.	.	G	39	7.698402	0.98441	.	.	ENSG00000116962	ENST00000264187;ENST00000366595	.	.	.	5.29	4.36	0.52297	.	0.231851	0.46758	D	0.000272	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22109	T	0.4	.	13.0934	0.59178	0.0:0.0:0.7079:0.2921	.	.	.	.	X	519	.	ENSP00000264187:Q519X	Q	-	1	0	NID1	234259656	1.000000	0.71417	0.987000	0.45799	0.974000	0.67602	4.847000	0.62867	1.417000	0.47077	0.563000	0.77884	CAG	.	.		0.612	NID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096647.2	NM_002508		A	236193033	G	A	236193033	4	1	341	1	0	0	0	0	0	1	0	0	10423	1357	47	3	2244	3	NID1	1	236193033	Nonsense_Mutation	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10	20385027	236193033	13057588	9	47110										
TCF23	150921	hgsc.bcm.edu	37	chr2	27372096	27372096	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	gttgctgccaggcgctgacaGgaagaggagccgcctcagca	15	12	1	2			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr2:27372096G>A	ENST00000296096.5	+	1	225	c.95G>A	c.(94-96)aGg>aAg	p.R32K	TCF23_ENST00000407815.3_3'UTR	NM_175769.2	NP_786951.1	Q7RTU1	TCF23_HUMAN	transcription factor 23	32					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)	nucleus (GO:0005634)				large_intestine(2)|lung(11)|prostate(1)	14	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGCGCTGACAGGAAGAGGAGC	0.642																																					p.R32K		Atlas-SNP	.											.	TCF23	28	.	0			c.G95A						.						32	26	28					2																	27372096		2176	4273	6449	SO:0001583	missense	150921	exon1			CTGACAGGAAGAG	AC013403	CCDS33163.1	2p23.3	2013-05-21			ENSG00000163792	ENSG00000163792		"Basic helix-loop-helix proteins"	18602	protein-coding gene	gene with protein product		609635				11701948, 10652346	Standard	NM_175769		Approved	OUT, bHLHa24	uc010ylg.2	Q7RTU1	OTTHUMG00000152031	ENST00000296096.5:c.95G>A	chr2.hg19:g.27372096G>A	ENSP00000296096:p.Arg32Lys	98.0	0.0		109.0	6.0	NM_175769	B2RNZ3	Missense_Mutation	SNP	ENST00000296096.5	hg19	CCDS33163.1	.	.	.	.	.	.	.	.	.	.	G	12.83	2.054589	0.36277	.	.	ENSG00000163792	ENST00000296096;ENST00000407815	D	0.97404	-4.37	4.79	1.96	0.26148	.	1.000500	0.08067	N	0.999266	D	0.93956	0.8065	L	0.49350	1.555	0.24634	N	0.993609	B	0.12013	0.005	B	0.08055	0.003	D	0.84527	0.0631	10	0.20519	T	0.43	-10.5645	6.242	0.20795	0.3154:0.0:0.6846:0.0	.	32	Q7RTU1	TCF23_HUMAN	K	32	ENSP00000296096:R32K	ENSP00000296096:R32K	R	+	2	0	TCF23	27225600	0.999000	0.42202	0.892000	0.35008	0.796000	0.44982	0.819000	0.27308	0.559000	0.29153	0.462000	0.41574	AGG	.	.		0.642	TCF23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324980.1	NM_175769		A	27372096	G	A	27372096	3	1	341	1	0	0	0	0	1	0	0	0	15707	1000	35	3	97	3	TCF23	2	27372096	Missense_Mutation	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10		27372096	215827277	10	47111										
AFTPH	54812	hgsc.bcm.edu	37	chr2	64779926	64779926	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	gtgattttggtgactttggcTctgccagtggctcaactcca	11	10	2	2			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr2:64779926T>G	ENST00000422803.1	+	2	1632	c.1318T>G	c.(1318-1320)Tct>Gct	p.S440A	AFTPH_ENST00000238856.4_Missense_Mutation_p.S440A|AFTPH_ENST00000409183.1_Missense_Mutation_p.S71A|AFTPH_ENST00000409933.1_Missense_Mutation_p.S440A|AFTPH_ENST00000238855.7_Missense_Mutation_p.S440A			Q6ULP2	AFTIN_HUMAN	aftiphilin	440					protein transport (GO:0015031)	AP-1 adaptor complex (GO:0030121)|cytosol (GO:0005829)	clathrin binding (GO:0030276)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	35						TGACTTTGGCTCTGCCAGTGG	0.378																																					p.S440A		Atlas-SNP	.											AFTPH_ENST00000238855,NS,carcinoma,0,2	AFTPH	117	.	0			c.T1318G						.						188	181	183					2																	64779926		2203	4300	6503	SO:0001583	missense	54812	exon2			TTTGGCTCTGCCA	AB073356	CCDS1878.1, CCDS46303.1	2p14	2008-02-05			ENSG00000119844	ENSG00000119844			25951	protein-coding gene	gene with protein product						14665628, 15758025, 15811338	Standard	NM_017657		Approved	MGC33965, FLJ20080, FLJ23793, Nbla10388	uc002scz.3	Q6ULP2	OTTHUMG00000129539	ENST00000422803.1:c.1318T>G	chr2.hg19:g.64779926T>G	ENSP00000397726:p.Ser440Ala	69.0	0.0		67.0	5.0	NM_017657	D6W5E9|Q6ZM66|Q86VW3|Q8TCF3|Q9H7E3|Q9HAB9|Q9NXS4	Missense_Mutation	SNP	ENST00000422803.1	hg19		.	.	.	.	.	.	.	.	.	.	A	3.296	-0.143865	0.06627	.	.	ENSG00000119844	ENST00000238856;ENST00000422803;ENST00000238855;ENST00000409933;ENST00000409183	T;T;T;T;T	0.42513	1.91;1.91;1.97;1.97;0.97	5.76	5.76	0.90799	.	0.058741	0.64402	D	0.000005	T	0.29423	0.0733	N	0.19112	0.55	0.20489	N	0.999898	B;B;B;B	0.13145	0.007;0.007;0.0;0.0	B;B;B;B	0.16289	0.015;0.015;0.003;0.001	T	0.21008	-1.0258	10	0.51188	T	0.08	-6.8951	11.0548	0.47911	0.7531:0.0:0.0:0.2469	.	440;440;440;440	Q6ULP2;Q6ULP2-2;Q6ULP2-5;Q6ULP2-4	AFTIN_HUMAN;.;.;.	A	440;440;440;440;71	ENSP00000238856:S440A;ENSP00000397726:S440A;ENSP00000238855:S440A;ENSP00000387071:S440A;ENSP00000386913:S71A	ENSP00000238855:S440A	S	+	1	0	AFTPH	64633430	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	2.013000	0.40942	1.115000	0.41800	-0.265000	0.10407	TCT	.	.		0.378	AFTPH-202	KNOWN	basic	protein_coding	protein_coding		NM_017657		G	64779926	T	G	64779926	3	3	341	1	0	0	0	0	1	0	0	0	364	1551	54	5	1320	5	AFTPH	2	64779926	Missense_Mutation	SNP	T	TCGA-RG-A7D4-01A-12D-A33Q-10	37407830	64779926	178419447	11	47112										
ASPRV1	151516	hgsc.bcm.edu	37	chr2	70188307	70188356	+	Frame_Shift_Del	DEL	AGGCCTTCAGGAGGGCCTCTTTCACAGTCCCATAGTCTCCCTGGTCCTGG	AGGCCTTCAGGAGGGCCTCTTTCACAGTCCCATAGTCTCCCTGGTCCTGG	-													0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	ggcagccccagggaccccaaAggccttcaggagggcctctt					rs139245310|rs142181991		TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	AGGCCTTCAGGAGGGCCTCTTTCACAGTCCCATAGTCTCCCTGGTCCTGG	AGGCCTTCAGGAGGGCCTCTTTCACAGTCCCATAGTCTCCCTGGTCCTGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr2:70188307_70188356delAGGCCTTCAGGAGGGCCTCTTTCACAGTCCCATAGTCTCCCTGGTCCTGG	ENST00000320256.4	-	1	1041_1090	c.465_514delCCAGGACCAGGGAGACTATGGGACTGTGAAAGAGGCCCTCCTGAAGGCCT	c.(463-516)ccccaggaccagggagactatgggactgtgaaagaggccctcctgaaggcctttfs	p.QDQGDYGTVKEALLKAF156fs	PCBP1-AS1_ENST00000435880.2_RNA|PCBP1-AS1_ENST00000419542.1_RNA|PCBP1-AS1_ENST00000457076.1_RNA|PCBP1-AS1_ENST00000413436.1_RNA|PCBP1-AS1_ENST00000418564.1_RNA|PCBP1-AS1_ENST00000596259.1_RNA	NM_152792.2	NP_690005.2			aspartic peptidase, retroviral-like 1											endometrium(3)|large_intestine(4)|lung(6)|ovary(1)	14						GGGACCCCAAAGGCCTTCAGGAGGGCCTCTTTCACAGTCCCATAGTCTCCCTGGTCCTGGGGACTGAGCC	0.552																																					p.156_172del		Pindel	.											.	ASPRV1	41	.	0			c.466_515del						.																																			SO:0001589	frameshift_variant	151516	exon1			.	AK055994	CCDS1897.1	2p13.3	2008-02-20			ENSG00000244617	ENSG00000244617			26321	protein-coding gene	gene with protein product	"Skin ASpartic Protease"	611765				16098038, 16565508	Standard	NM_152792		Approved	Taps, SASPase, FLJ25084	uc002sfz.4	Q53RT3	OTTHUMG00000129647	ENST00000320256.4:c.465_514delCCAGGACCAGGGAGACTATGGGACTGTGAAAGAGGCCCTCCTGAAGGCCT	chr2.hg19:g.70188307_70188356delAGGCCTTCAGGAGGGCCTCTTTCACAGTCCCATAGTCTCCCTGGTCCTGG	ENSP00000315383:p.Gln156fs	56.0	0.0		64.0	26.0	NM_152792		Frame_Shift_Del	DEL	ENST00000320256.4	hg19	CCDS1897.1																																																																																			.	.		0.552	ASPRV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334161.1	NM_152792		-	70188356	AGGCCTTCAGGAGGGCCTCTTTCACAGTCCCATAGTCTCCCTGGTCCTGG	-	70188307	7	5	341	1	0	1	0	1	0	0	0	0	1058	72	3	0	521	0	ASPRV1	2	70188307	Frame_Shift_Del	DEL	AGGCCTTCAGGAGGGCCTCTTTCACAGTCCCATAGTCTCCCTGGTCCTGG	TCGA-RG-A7D4-01A-12D-A33Q-10	5408381	70188307	173011066	12	47113										
TGOLN2	10618	hgsc.bcm.edu	37	chr2	85554158	85554158	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	acccgacttgctgggcccgtCtattgggccctgctcctctg	11	16	2	0			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr2:85554158C>T	ENST00000409232.3	-	2	758	c.697G>A	c.(697-699)Gac>Aac	p.D233N	TGOLN2_ENST00000282120.2_Missense_Mutation_p.D135N|TGOLN2_ENST00000377386.3_Missense_Mutation_p.D233N|TGOLN2_ENST00000444342.2_Missense_Mutation_p.D233N|TGOLN2_ENST00000398263.2_Missense_Mutation_p.D233N|TGOLN2_ENST00000409015.1_Missense_Mutation_p.D233N			O43493	TGON2_HUMAN	trans-golgi network protein 2	233	14 X 14 AA tandem repeats.					Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)											CTGGGCCCGTCTATTGGGCCC	0.577																																					p.D233N		Atlas-SNP	.											.	TGOLN2	32	.	0			c.G697A						.						114	117	116					2																	85554158		1917	4103	6020	SO:0001583	missense	10618	exon2			GCCCGTCTATTGG	AF027515	CCDS46351.1, CCDS56126.1, CCDS56127.1	2p11.2	2012-06-25			ENSG00000152291	ENSG00000152291			15450	protein-coding gene	gene with protein product	"trans-Golgi network protein (46, 48, 51kD isoforms)"	603062				9422759, 21994457	Standard	NM_001206840		Approved	TGN51, TGN46, TGN48, TGN38, TTGN2	uc021vjw.1	O43493	OTTHUMG00000153017	ENST00000409232.3:c.697G>A	chr2.hg19:g.85554158C>T	ENSP00000386443:p.Asp233Asn	78.0	0.0		58.0	7.0	NM_001206841	B2R686|B8ZZ88|D6W5K3|F8WBK2|O15282|O43492|O43499|O43500|O43501|Q53G68|Q53GV2|Q6MZV1|Q6ZTM7|Q8N6T8|Q92760|Q96QL2	Missense_Mutation	SNP	ENST00000409232.3	hg19	CCDS56126.1	.	.	.	.	.	.	.	.	.	.	C	1.878	-0.458548	0.04508	.	.	ENSG00000152291	ENST00000377386;ENST00000282120;ENST00000398263;ENST00000409232;ENST00000409015;ENST00000444342	T;T;T;T;T;T	0.12569	2.75;2.68;2.67;2.79;2.76;2.73	2.12	-4.24	0.03777	.	.	.	.	.	T	0.08980	0.0222	L	0.52573	1.65	0.09310	N	1	B;P;P;B	0.42518	0.025;0.782;0.615;0.058	B;B;B;B	0.37888	0.015;0.26;0.188;0.01	T	0.24225	-1.0166	9	0.14656	T	0.56	.	5.26	0.15567	0.0:0.2037:0.4123:0.3839	.	233;233;233;233	O43493;O43493-5;O43493-4;O43493-2	TGON2_HUMAN;.;.;.	N	233;135;233;233;233;233	ENSP00000366603:D233N;ENSP00000282120:D135N;ENSP00000381312:D233N;ENSP00000386443:D233N;ENSP00000387035:D233N;ENSP00000391190:D233N	ENSP00000282120:D135N	D	-	1	0	TGOLN2	85407669	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.362000	0.07602	-1.210000	0.02627	-0.506000	0.04501	GAC	.	.		0.577	TGOLN2-006	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000329045.2	NM_006464		T	85554158	C	T	85554158	3	4	341	1	0	0	0	0	1	0	0	0	15851	913	32	3	628	3	TGOLN2	2	85554158	Missense_Mutation	SNP	C	TCGA-RG-A7D4-01A-12D-A33Q-10	15365851	85554158	157645215	13	47114										
NCAPH	23397	hgsc.bcm.edu	37	chr2	97017638	97017638	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	cagcaggggtgtttctgtccActctccactgccaggactac	10	14	2	0			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr2:97017638A>G	ENST00000240423.4	+	7	833	c.790A>G	c.(790-792)Act>Gct	p.T264A	NCAPH_ENST00000427946.1_Missense_Mutation_p.T128A|NCAPH_ENST00000455200.1_Missense_Mutation_p.T253A	NM_001281710.1|NM_001281711.1|NM_015341.3	NP_001268639.1|NP_001268640.1|NP_056156.2	Q15003	CND2_HUMAN	non-SMC condensin I complex, subunit H	264					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Ovarian(717;0.0221)				GTTTCTGTCCACTCTCCACTG	0.493																																					p.T264A		Atlas-SNP	.											.	NCAPH	67	.	0			c.A790G						.						134	112	120					2																	97017638		2203	4300	6503	SO:0001583	missense	23397	exon7			CTGTCCACTCTCC	BC024211	CCDS2021.1, CCDS62960.1	2q11.2	2008-02-05	2006-09-04	2006-09-04	ENSG00000121152	ENSG00000121152			1112	protein-coding gene	gene with protein product		602332	"barren (Drosophila) homolog", "barren homolog (Drosophila)", "barren homolog 1 (Drosophila)"	BRRN1		9417923	Standard	NM_015341		Approved	CAP-H, hCAP-H	uc002svz.1	Q15003	OTTHUMG00000130451	ENST00000240423.4:c.790A>G	chr2.hg19:g.97017638A>G	ENSP00000240423:p.Thr264Ala	72.0	0.0		74.0	19.0	NM_015341	B4E189|Q8TB87	Missense_Mutation	SNP	ENST00000240423.4	hg19	CCDS2021.1	.	.	.	.	.	.	.	.	.	.	A	11.80	1.745670	0.30955	.	.	ENSG00000121152	ENST00000240423;ENST00000427946;ENST00000435975;ENST00000456906;ENST00000455200	T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99	5.89	5.89	0.94794	.	0.160977	0.56097	D	0.000034	T	0.48059	0.1479	M	0.65975	2.015	0.19300	N	0.999975	P;P;P;P	0.36483	0.549;0.549;0.555;0.549	B;B;B;B	0.42625	0.393;0.393;0.257;0.393	T	0.46541	-0.9184	10	0.30078	T	0.28	-19.0346	14.2643	0.66107	1.0:0.0:0.0:0.0	.	240;253;253;264	B4DRG7;E9PHA2;C9J470;Q15003	.;.;.;CND2_HUMAN	A	264;128;253;145;253	ENSP00000240423:T264A;ENSP00000400774:T128A;ENSP00000405237:T253A;ENSP00000401227:T145A;ENSP00000407308:T253A	ENSP00000240423:T264A	T	+	1	0	NCAPH	96381365	0.837000	0.29446	0.886000	0.34754	0.080000	0.17528	3.483000	0.53194	2.254000	0.74563	0.459000	0.35465	ACT	.	.		0.493	NCAPH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252842.2	NM_015341		G	97017638	A	G	97017638	3	3	341	1	0	0	0	0	1	0	0	0	10218	159	6	2	816	2	NCAPH	2	97017638	Missense_Mutation	SNP	A	TCGA-RG-A7D4-01A-12D-A33Q-10	11463480	97017638	146181735	14	47115										
TTN	7273	hgsc.bcm.edu	37	chr2	179427137	179427137	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	tgtgcaggtgctccacttttCactccctttagtctgcattt	7	12	2	0			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr2:179427137C>T	ENST00000591111.1	-	276	79023	c.78799G>A	c.(78799-78801)Gaa>Aaa	p.E26267K	TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.E19035K|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.E27908K|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.E18968K|TTN_ENST00000460472.2_Missense_Mutation_p.E18843K|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.E25340K|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586452.1_RNA			Q8WZ42	TITIN_HUMAN	titin	26267	Fibronectin type-III 91. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTCCACTTTTCACTCCCTTTA	0.433																																					p.E27908K		Atlas-SNP	.											.	TTN	18412	.	0			c.G83722A						.						100	96	98					2																	179427137		1939	4153	6092	SO:0001583	missense	7273	exon326			ACTTTTCACTCCC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.78799G>A	chr2.hg19:g.179427137C>T	ENSP00000465570:p.Glu26267Lys	33.0	0.0		64.0	17.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	16.82	3.228079	0.58777	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.58506	0.33;0.33;0.33;0.33	5.89	5.89	0.94794	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.57417	0.2052	L	0.46819	1.47	0.58432	D	0.999998	P;P;P;P	0.43231	0.801;0.801;0.801;0.684	B;B;B;B	0.40741	0.339;0.339;0.339;0.258	T	0.61802	-0.6988	9	0.87932	D	0	.	20.2618	0.98447	0.0:1.0:0.0:0.0	.	18843;18968;19035;26267	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	K	25340;18843;19035;18968;18841	ENSP00000343764:E25340K;ENSP00000434586:E18843K;ENSP00000340554:E19035K;ENSP00000352154:E18968K	ENSP00000340554:E19035K	E	-	1	0	TTN	179135383	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.361000	0.52306	2.793000	0.96121	0.655000	0.94253	GAA	.	.		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179427137	C	T	179427137	3	4	341	1	0	0	0	0	1	0	0	0	16750	835	29	3	24405	3	TTN	2	179427137	Missense_Mutation	SNP	C	TCGA-RG-A7D4-01A-12D-A33Q-10	82409499	179427137	63772236	15	47116										
MSTN	2660	hgsc.bcm.edu	37	chr2	190922105	190922105	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	tgggagtacagcaagggcctGctgaacctctggggtttgct	15	9	1	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr2:190922105G>C	ENST00000260950.4	-	3	1139	c.1007C>G	c.(1006-1008)gCa>gGa	p.A336G	C2orf88_ENST00000478197.1_Intron	NM_005259.2	NP_005250.1	O14793	GDF8_HUMAN	myostatin	336					cellular response to dexamethasone stimulus (GO:0071549)|muscle organ development (GO:0007517)|negative regulation of muscle hypertrophy (GO:0014741)|negative regulation of skeletal muscle tissue growth (GO:0048632)|ovulation cycle process (GO:0022602)|positive regulation of transcription, DNA-templated (GO:0045893)|response to electrical stimulus (GO:0051602)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to gravity (GO:0009629)|response to heat (GO:0009408)|response to muscle activity (GO:0014850)|response to testosterone (GO:0033574)|skeletal muscle atrophy (GO:0014732)|skeletal muscle tissue regeneration (GO:0043403)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)			endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|skin(1)	12			OV - Ovarian serous cystadenocarcinoma(117;0.000742)|Epithelial(96;0.0121)|all cancers(119;0.0395)			GCAAGGGCCTGCTGAACCTCT	0.378																																					p.A336G		Atlas-SNP	.											.	MSTN	46	.	0			c.C1007G						.						74	76	75					2																	190922105		2203	4299	6502	SO:0001583	missense	2660	exon3			GGGCCTGCTGAAC	AF019627	CCDS2303.1	2q32.1	2014-09-17	2007-06-21	2007-06-21	ENSG00000138379	ENSG00000138379			4223	protein-coding gene	gene with protein product		601788	"growth differentiation factor 8"	GDF8		9288100, 10610713, 17003236	Standard	NM_005259		Approved		uc002urp.3	O14793	OTTHUMG00000132663	ENST00000260950.4:c.1007C>G	chr2.hg19:g.190922105G>C	ENSP00000260950:p.Ala336Gly	55.0	0.0		79.0	18.0	NM_005259	A1C2J7|A1C2K0|Q6B0H2	Missense_Mutation	SNP	ENST00000260950.4	hg19	CCDS2303.1	.	.	.	.	.	.	.	.	.	.	G	13.78	2.340725	0.41498	.	.	ENSG00000138379	ENST00000260950	T	0.70282	-0.47	5.79	4.92	0.64577	Transforming growth factor-beta, C-terminal (3);	0.047099	0.85682	D	0.000000	T	0.60209	0.2251	N	0.25094	0.71	0.80722	D	1	B	0.14805	0.011	B	0.21917	0.037	T	0.58836	-0.7566	10	0.87932	D	0	-10.0534	14.8547	0.70326	0.0689:0.0:0.9311:0.0	.	336	O14793	GDF8_HUMAN	G	336	ENSP00000260950:A336G	ENSP00000260950:A336G	A	-	2	0	MSTN	190630350	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.937000	0.87672	1.447000	0.47661	0.585000	0.79938	GCA	.	.		0.378	MSTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255917.2	NM_005259		C	190922105	G	C	190922105	3	2	341	1	0	0	0	0	1	0	0	0	9902	1319	46	4	124	4	MSTN	2	190922105	Missense_Mutation	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10	11494968	190922105	52277268	16	47117										
ALS2CR11	151254	hgsc.bcm.edu	37	chr2	202436741	202436741	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	gtaattttctgaagaggtttTaactgaaaaaaatgtaagtg	9	2	1	3			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr2:202436741T>C	ENST00000286195.3	-	8	800	c.756A>G	c.(754-756)ttA>ttG	p.L252L	ALS2CR11_ENST00000450242.1_Silent_p.L252L|ALS2CR11_ENST00000439140.1_Silent_p.L252L|ALS2CR11_ENST00000439802.1_Silent_p.L252L	NM_152525.5	NP_689738.3	Q53TS8	AL2SA_HUMAN	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 11	252										NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(11)|ovary(1)|skin(5)|urinary_tract(3)	33						GAAGAGGTTTTAACTGAAAAA	0.328																																					p.L252L		Atlas-SNP	.											.	ALS2CR11	194	.	0			c.A756G						.						94	92	92					2																	202436741		2203	4300	6503	SO:0001819	synonymous_variant	151254	exon8			AGGTTTTAACTGA	AB053313	CCDS2349.1, CCDS54430.1, CCDS54428.1, CCDS54429.1	2q33	2007-12-07			ENSG00000155754	ENSG00000155754			14438	protein-coding gene	gene with protein product						11586298	Standard	NM_152525		Approved	FLJ25351	uc002uyf.3	Q53TS8	OTTHUMG00000132830	ENST00000286195.3:c.756A>G	chr2.hg19:g.202436741T>C		36.0	0.0		54.0	14.0	NM_001168217	C9IZH7|E9PGG4|Q8NCN6|Q96LN4	Silent	SNP	ENST00000286195.3	hg19	CCDS2349.1																																																																																			.	.		0.328	ALS2CR11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256296.2	NM_152525		C	202436741	T	C	202436741	2	2	341	1	0	0	0	0	0	0	0	1	552	1751	61	2		2	ALS2CR11	2	202436741	Silent	SNP	T	TCGA-RG-A7D4-01A-12D-A33Q-10	11514636	202436741	40762632	17	47118										
NRP2	8828	hgsc.bcm.edu	37	chr2	206581088	206581088	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	ttctctctgcgctacgagatCttcaagacaggtcagtgtgg	11	10	5	2			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr2:206581088C>A	ENST00000357785.5	+	3	454	c.423C>A	c.(421-423)atC>atA	p.I141I	NRP2_ENST00000272849.3_Silent_p.I141I|NRP2_ENST00000540178.1_Silent_p.I141I|NRP2_ENST00000412873.2_Silent_p.I141I|NRP2_ENST00000360409.3_Silent_p.I141I|NRP2_ENST00000357118.4_Silent_p.I141I|NRP2_ENST00000417189.1_Silent_p.I141I|NRP2_ENST00000355117.4_Silent_p.I141I|NRP2_ENST00000540841.1_Silent_p.I141I			Q99435	NELL2_HUMAN	neuropilin 2	0	Laminin G-like.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(14)|lung(19)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	52						GCTACGAGATCTTCAAGACAG	0.622																																					p.I141I		Atlas-SNP	.											.	NRP2	179	.	0			c.C423A						.						65	66	66					2																	206581088		2203	4300	6503	SO:0001819	synonymous_variant	8828	exon3			CGAGATCTTCAAG	AF016098	CCDS2364.1, CCDS2365.1, CCDS46496.1, CCDS46497.1, CCDS46498.1, CCDS46499.1	2q33.3	2008-05-23			ENSG00000118257	ENSG00000118257			8005	protein-coding gene	gene with protein product		602070				9529250, 9331348	Standard	NM_003872		Approved	VEGF165R2	uc002vaw.3	O60462	OTTHUMG00000132893	ENST00000357785.5:c.423C>A	chr2.hg19:g.206581088C>A		65.0	0.0		54.0	16.0	NM_201279	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Silent	SNP	ENST00000357785.5	hg19	CCDS46496.1																																																																																			.	.		0.622	NRP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000336467.1			A	206581088	C	A	206581088	2	1	341	1	0	0	0	0	0	0	0	1	10670	903	32	3		3	NRP2	2	206581088	Silent	SNP	C	TCGA-RG-A7D4-01A-12D-A33Q-10	4144347	206581088	36618285	18	47119										
PIKFYVE	200576	hgsc.bcm.edu	37	chr2	209218741	209218741	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	atggttcgagacaaccctctAtatattcgttctcattccaa	5	11	2	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr2:209218741A>G	ENST00000264380.4	+	40	6122	c.5964A>G	c.(5962-5964)ctA>ctG	p.L1988L		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	1988	Catalytic.|PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						ACAACCCTCTATATATTCGTT	0.413																																					p.L1988L		Atlas-SNP	.											.	PIKFYVE	223	.	0			c.A5964G						.						157	159	158					2																	209218741		2203	4300	6503	SO:0001819	synonymous_variant	200576	exon40			CCCTCTATATATT	AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"Zinc fingers, FYVE domain containing"	23785	protein-coding gene	gene with protein product	"zinc finger, FYVE domain containing 29"	609414	"phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	ENST00000264380.4:c.5964A>G	chr2.hg19:g.209218741A>G		99.0	0.0		95.0	22.0	NM_015040	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Silent	SNP	ENST00000264380.4	hg19	CCDS2382.1																																																																																			.	.		0.413	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040		G	209218741	A	G	209218741	2	3	341	1	0	0	0	0	0	0	0	1	11933	436	16	2		2	PIKFYVE	2	209218741	Silent	SNP	A	TCGA-RG-A7D4-01A-12D-A33Q-10	2637653	209218741	33980632	19	47120										
TRPM8	79054	hgsc.bcm.edu	37	chr2	234875362	234875362	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	tctggagctggcggtggaggCcacagaccagcatttcatcg	14	11	2	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr2:234875362C>T	ENST00000324695.4	+	15	2028	c.1988C>T	c.(1987-1989)gCc>gTc	p.A663V	TRPM8_ENST00000433712.2_Missense_Mutation_p.A351V	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8	663					calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|protein homotetramerization (GO:0051289)|protein homotrimerization (GO:0070207)|response to cold (GO:0009409)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(2)|lung(27)|prostate(2)|skin(7)|stomach(2)	66		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)	GCGGTGGAGGCCACAGACCAG	0.547																																					p.A663V		Atlas-SNP	.											.	TRPM8	146	.	0			c.C1988T						.						87	76	80					2																	234875362		2203	4300	6503	SO:0001583	missense	79054	exon15			TGGAGGCCACAGA	AC005538	CCDS33407.1	2q37	2011-12-14			ENSG00000144481	ENSG00000144481		"Voltage-gated ion channels / Transient receptor potential cation channels"	17961	protein-coding gene	gene with protein product		606678				16382100	Standard	NM_024080		Approved		uc002vvh.3	Q7Z2W7	OTTHUMG00000059129	ENST00000324695.4:c.1988C>T	chr2.hg19:g.234875362C>T	ENSP00000323926:p.Ala663Val	47.0	0.0		73.0	23.0	NM_024080	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Missense_Mutation	SNP	ENST00000324695.4	hg19	CCDS33407.1	.	.	.	.	.	.	.	.	.	.	C	19.31	3.802817	0.70682	.	.	ENSG00000144481	ENST00000324695;ENST00000433712;ENST00000456930	D;D;T	0.98455	-4.94;-4.94;-0.78	5.61	4.71	0.59529	.	0.000000	0.64402	D	0.000003	D	0.97810	0.9281	M	0.78049	2.395	0.47862	D	0.99953	D;P	0.57571	0.98;0.489	P;B	0.46389	0.515;0.177	D	0.97781	1.0232	10	0.87932	D	0	-14.6178	15.4281	0.75069	0.0:0.8604:0.1396:0.0	.	351;663	A0AVG2;Q7Z2W7	.;TRPM8_HUMAN	V	663;351;34	ENSP00000323926:A663V;ENSP00000404423:A351V;ENSP00000414198:A34V	ENSP00000323926:A663V	A	+	2	0	TRPM8	234540101	0.998000	0.40836	0.896000	0.35187	0.985000	0.73830	4.281000	0.58965	1.460000	0.47911	0.655000	0.94253	GCC	.	.		0.547	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080		T	234875362	C	T	234875362	3	4	341	1	0	0	0	0	1	0	0	0	16607	739	26	3	2042	3	TRPM8	2	234875362	Missense_Mutation	SNP	C	TCGA-RG-A7D4-01A-12D-A33Q-10	25656621	234875362	8324011	20	47121										
C3orf31	132001	hgsc.bcm.edu	37	chr3	11858718	11858718	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	cttgaggattttcctgtagtAtgctgccatagagctctcga	10	9	1	2			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr3:11858718A>G	ENST00000444133.2	-	5	798	c.656T>C	c.(655-657)aTa>aCa	p.I219T	TAMM41_ENST00000273037.5_Missense_Mutation_p.I219T|TAMM41_ENST00000455809.1_Missense_Mutation_p.I219T			Q96BW9	TAM41_HUMAN	TAM41, mitochondrial translocator assembly and maintenance protein, homolog (S. cerevisiae)	219					cardiolipin biosynthetic process (GO:0032049)|CDP-diacylglycerol biosynthetic process (GO:0016024)	extrinsic component of mitochondrial inner membrane (GO:0031314)	phosphatidate cytidylyltransferase activity (GO:0004605)										TTCCTGTAGTATGCTGCCATA	0.413																																					p.I219T		Atlas-SNP	.											.	.	.	.	0			c.T656C						.						138	136	137					3																	11858718		2203	4300	6503	SO:0001583	missense	132001	exon5			TGTAGTATGCTGC		CCDS2607.1, CCDS68345.1	3p25.2	2013-10-18	2011-08-09	2011-08-09	ENSG00000144559	ENSG00000144559			25187	protein-coding gene	gene with protein product		614948	"chromosome 3 open reading frame 31"	C3orf31		19237595	Standard	XM_005264873		Approved	MGC16471, DKFZp434E0519	uc003bwh.3	Q96BW9	OTTHUMG00000129741	ENST00000444133.2:c.656T>C	chr3.hg19:g.11858718A>G	ENSP00000388598:p.Ile219Thr	90.0	0.0		71.0	16.0	NM_138807	B4DIY7|C9J2U4	Missense_Mutation	SNP	ENST00000444133.2	hg19		.	.	.	.	.	.	.	.	.	.	A	18.10	3.547439	0.65311	.	.	ENSG00000144559	ENST00000455809;ENST00000273037;ENST00000444133	T;T;T	0.35048	1.33;1.33;1.33	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.54711	0.1875	L	0.60455	1.87	0.54753	D	0.999988	D;D;P	0.71674	0.987;0.998;0.642	D;D;P	0.70227	0.953;0.968;0.574	T	0.56492	-0.7970	10	0.54805	T	0.06	-40.35	13.9613	0.64182	1.0:0.0:0.0:0.0	.	219;219;219	B4DIY7;C9J2U4;Q96BW9	.;.;TAM41_HUMAN	T	219	ENSP00000398596:I219T;ENSP00000273037:I219T;ENSP00000388598:I219T	ENSP00000273037:I219T	I	-	2	0	TAMM41	11833718	1.000000	0.71417	0.967000	0.41034	0.994000	0.84299	9.069000	0.93967	1.898000	0.54952	0.450000	0.29827	ATA	.	.		0.413	TAMM41-008	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000339258.2	NM_138807		G	11858718	A	G	11858718	3	3	341	1	0	0	0	0	1	0	0	0	2223	449	16	2	306	2	C3orf31	3	11858718	Missense_Mutation	SNP	A	TCGA-RG-A7D4-01A-12D-A33Q-10		11858718	186163712	21	47122										
DLEC1	9940	hgsc.bcm.edu	37	chr3	38159367	38159367	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	agagatcccacactacttccGgcttatggtctccaggccct	8	15	1	1	rs370658013		TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr3:38159367G>A	ENST00000308059.6	+	33	4577	c.4556G>A	c.(4555-4557)cGg>cAg	p.R1519Q	DLEC1_ENST00000452631.2_Missense_Mutation_p.R1522Q|DLEC1_ENST00000346219.3_Missense_Mutation_p.R1519Q					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		CACTACTTCCGGCTTATGGTC	0.602											OREG0015476	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R1519Q		Atlas-SNP	.											.	DLEC1	278	.	0			c.G4556A						.	G	GLN/ARG,GLN/ARG	1,4115		0,1,2057	118	122	121		4556,4556	2	0.9	3		121	0,8428		0,0,4214	no	missense,missense	DLEC1	NM_007337.2,NM_007335.2	43,43	0,1,6271	AA,AG,GG		0.0,0.0243,0.0080	benign,benign	1519/1779,1519/1756	38159367	1,12543	2058	4214	6272	SO:0001583	missense	9940	exon33			ACTTCCGGCTTAT	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"cilia and flagella associated protein 81"	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.4556G>A	chr3.hg19:g.38159367G>A	ENSP00000308597:p.Arg1519Gln	84.0	0.0	876	80.0	19.0	NM_007337		Missense_Mutation	SNP	ENST00000308059.6	hg19	CCDS2672.2	.	.	.	.	.	.	.	.	.	.	G	15.12	2.738746	0.49045	2.43E-4	0.0	ENSG00000008226	ENST00000308059;ENST00000346219;ENST00000452631	T;T;T	0.08282	3.15;3.11;3.37	4.79	1.96	0.26148	.	0.251014	0.31167	U	0.008124	T	0.06188	0.0160	L	0.38531	1.155	0.31254	N	0.693756	B;B;B;B;B	0.33238	0.403;0.403;0.319;0.403;0.403	B;B;B;B;B	0.29598	0.059;0.059;0.018;0.104;0.059	T	0.23048	-1.0199	10	0.27082	T	0.32	-6.2763	9.2735	0.37686	0.3006:0.0:0.6994:0.0	.	1522;1519;1519;1519;1519	F8W6T4;B1B5Y4;B7ZW06;Q9Y238-3;Q9Y238	.;.;.;.;DLEC1_HUMAN	Q	1519;1519;1522	ENSP00000308597:R1519Q;ENSP00000315914:R1519Q;ENSP00000410427:R1522Q	ENSP00000308597:R1519Q	R	+	2	0	DLEC1	38134371	1.000000	0.71417	0.893000	0.35052	0.978000	0.69477	0.820000	0.27323	0.093000	0.17368	0.650000	0.86243	CGG	.	.		0.602	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337		A	38159367	G	A	38159367	3	1	341	1	0	0	0	0	1	0	0	0	4554	1116	39	1	4686	1	DLEC1	3	38159367	Missense_Mutation	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10	26300649	38159367	159863063	22	47123										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266136	41266136	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	gtgccactaccacagctcctTctctgagtggtaaaggcaat	9	12	1	1	rs121913407		TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr3:41266136T>C	ENST00000349496.5	+	3	413	c.133T>C	c.(133-135)Tct>Cct	p.S45P	CTNNB1_ENST00000405570.1_Missense_Mutation_p.S45P|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S45P|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S45P|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S38P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	45			Missing (in colorectal cancer). {ECO:0000269|PubMed:9065402}.|S -> F (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> P (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S45P(168)|p.A5_A80del(53)|p.S45del(50)|p.S45A(11)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.S45_G48del(1)|p.Q28_Q61del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.S45_L46del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.P44_N51del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.T40_L46del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.S45E(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.S45T(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.T42_K49>Q(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CACAGCTCCTTCTCTGAGTGG	0.502		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S45P	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,carcinoma,0,1	CTNNB1	4904	.	355	Substitution - Missense(181)|Deletion - In frame(149)|Complex - deletion inframe(18)|Unknown(7)	liver(151)|kidney(53)|soft_tissue(47)|large_intestine(37)|adrenal_gland(28)|endometrium(9)|stomach(7)|skin(6)|pituitary(3)|prostate(3)|thyroid(2)|small_intestine(2)|bone(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)	c.T133C						.						84	74	78					3																	41266136		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	GCTCCTTCTCTGA	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.133T>C	chr3.hg19:g.41266136T>C	ENSP00000344456:p.Ser45Pro	129.0	0.0		159.0	60.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.440246	0.83993	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.65903	0.2736	M	0.65677	2.01	0.80722	D	1	D	0.60575	0.988	P	0.62649	0.905	T	0.69083	-0.5239	10	0.87932	D	0	-13.6823	16.3453	0.83126	0.0:0.0:0.0:1.0	.	45	P35222	CTNB1_HUMAN	P	38;45;45;45;45;38;45;45;45	ENSP00000400508:S38P;ENSP00000385604:S45P;ENSP00000412219:S45P;ENSP00000379486:S45P;ENSP00000344456:S45P;ENSP00000411226:S38P;ENSP00000379488:S45P;ENSP00000409302:S45P;ENSP00000401599:S45P	ENSP00000344456:S45P	S	+	1	0	CTNNB1	41241140	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.261000	0.74972	0.533000	0.62120	TCT	.	.		0.502	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266136	T	C	41266136	3	2	341	1	0	0	0	0	1	0	0	0	4018	1783	62	2	139	2	CTNNB1	3	41266136	Missense_Mutation	SNP	T	TCGA-RG-A7D4-01A-12D-A33Q-10	3106769	41266136	156756294	23	47124										
CD200R1	131450	hgsc.bcm.edu	37	chr3	112648003	112648003	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	gtttccgtcacaaatctggtGatgtgaaatacctcaatata	7	8	3	2			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr3:112648003G>A	ENST00000440122.2	-	4	608	c.554C>T	c.(553-555)tCa>tTa	p.S185L	CD200R1_ENST00000295863.4_Intron|CD200R1_ENST00000471858.1_Intron|CD200R1_ENST00000308611.3_Intron|CD200R1_ENST00000490004.1_Missense_Mutation_p.S162L	NM_138939.2	NP_620385.1	Q8TD46	MO2R1_HUMAN	CD200 receptor 1	0	Ig-like C2-type.				regulation of immune response (GO:0050776)|viral process (GO:0016032)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	26						CAAATCTGGTGATGTGAAATA	0.393																																					p.S185L		Atlas-SNP	.											.	CD200R1	91	.	0			c.C554T						.						76	72	73					3																	112648003		2203	4300	6503	SO:0001583	missense	131450	exon4			TCTGGTGATGTGA	AK126349	CCDS2969.1, CCDS2970.1, CCDS46889.1, CCDS54623.1	3q13	2014-05-15	2004-08-31	2004-09-01	ENSG00000163606	ENSG00000163606		"Immunoglobulin superfamily / C2-set domain containing"	24235	protein-coding gene	gene with protein product		607546	"MOX2 receptor"	MOX2R		10981966, 11133863	Standard	NM_138806		Approved	OX2R, HCRTR2, CD200R	uc003dzj.1	Q8TD46	OTTHUMG00000159298	ENST00000440122.2:c.554C>T	chr3.hg19:g.112648003G>A	ENSP00000405733:p.Ser185Leu	72.0	0.0		80.0	11.0	NM_138939	B3KWZ9|E9PCM9|Q52LJ7|Q6IS95|Q6UW94|Q6WHB8|Q8TD44|Q8TD45|Q8TD52	Missense_Mutation	SNP	ENST00000440122.2	hg19	CCDS46889.1	.	.	.	.	.	.	.	.	.	.	G	10.48	1.360691	0.24598	.	.	ENSG00000163606	ENST00000440122;ENST00000490004	T;T	0.26067	1.76;1.81	4.77	0.0763	0.14402	.	.	.	.	.	T	0.17109	0.0411	.	.	.	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.06405	0.001;0.002	T	0.25606	-1.0127	8	0.87932	D	0	.	5.0056	0.14286	0.3404:0.0:0.4207:0.2389	.	162;185	Q8TD46-3;Q8TD46-2	.;.	L	185;162	ENSP00000405733:S185L;ENSP00000418801:S162L	ENSP00000405733:S185L	S	-	2	0	CD200R1	114130693	0.002000	0.14202	0.000000	0.03702	0.003000	0.03518	0.289000	0.18957	-0.138000	0.11434	-0.259000	0.10710	TCA	.	.		0.393	CD200R1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354468.1	NM_138806		A	112648003	G	A	112648003	3	1	341	1	0	0	0	0	1	0	0	0	2983	1294	45	3	559	3	CD200R1	3	112648003	Missense_Mutation	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10	71381867	112648003	85374427	24	47125										
C3orf27	23434	hgsc.bcm.edu	37	chr3	128292489	128292489	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	gagtctgggggtccctggagGcgggagacgctgagtctagg	20	8	2	2			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr3:128292489G>A	ENST00000356020.2	-	3	1050	c.84C>T	c.(82-84)cgC>cgT	p.R28R		NM_007354.2	NP_031380.1	O15544	GR6_HUMAN	chromosome 3 open reading frame 27	28										large_intestine(2)|lung(5)|prostate(1)	8				GBM - Glioblastoma multiforme(114;0.176)		GTCCCTGGAGGCGGGAGACGC	0.607																																					p.R28R		Atlas-SNP	.											.	C3orf27	23	.	0			c.C84T						.						29	30	29					3																	128292489		2203	4297	6500	SO:0001819	synonymous_variant	23434	exon3			CTGGAGGCGGGAG	AF008192	CCDS3050.1	3q21	2005-12-19			ENSG00000198685	ENSG00000198685			17099	protein-coding gene	gene with protein product						9307271	Standard	NR_125802		Approved	GR6	uc003ekq.3	O15544	OTTHUMG00000159688	ENST00000356020.2:c.84C>T	chr3.hg19:g.128292489G>A		126.0	0.0		115.0	25.0	NM_007354		Silent	SNP	ENST00000356020.2	hg19	CCDS3050.1																																																																																			.	.		0.607	C3orf27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356924.1	NM_007354		A	128292489	G	A	128292489	2	1	341	1	0	0	0	0	0	0	0	1	2221	1190	42	3		3	C3orf27	3	128292489	Silent	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10	15644486	128292489	69729941	25	47126										
OSTalpha	200931	hgsc.bcm.edu	37	chr3	195953959	195953959	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	cctttgccccatcaagaggcGgactctgctctggaagagct	11	13	3	2			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr3:195953959G>A	ENST00000296327.5	+	3	466	c.257G>A	c.(256-258)cGg>cAg	p.R86Q		NM_152672.5	NP_689885.4	Q86UW1	OSTA_HUMAN	solute carrier family 51, alpha subunit	86					bile acid and bile salt transport (GO:0015721)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)									Conjugated Estrogens(DB00286)|Digoxin(DB00390)|Dinoprostone(DB00917)	ATCAAGAGGCGGACTCTGCTC	0.597																																					p.R86Q		Atlas-SNP	.											.	.	.	.	0			c.G257A						.						95	86	89					3																	195953959		2203	4300	6503	SO:0001583	missense	200931	exon3			AGAGGCGGACTCT		CCDS3314.1	3q29	2013-05-22			ENSG00000163959	ENSG00000163959		"Solute carriers"	29955	protein-coding gene	gene with protein product	"organic solute transporter, alpha subunit"	612084				12719432, 20538072	Standard	NM_152672		Approved	OSTalpha	uc003fwd.3	Q86UW1	OTTHUMG00000155684	ENST00000296327.5:c.257G>A	chr3.hg19:g.195953959G>A	ENSP00000296327:p.Arg86Gln	43.0	0.0		51.0	5.0	NM_152672	Q6ZMC7	Missense_Mutation	SNP	ENST00000296327.5	hg19	CCDS3314.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.82|14.82	2.648913|2.648913	0.47362|0.47362	.|.	.|.	ENSG00000163959|ENSG00000163959	ENST00000428985|ENST00000296327	.|T	.|0.48522	.|0.81	5.86|5.86	-1.94|-1.94	0.07571|0.07571	.|.	.|0.384133	.|0.22351	.|N	.|0.061212	T|T	0.37785|0.37785	0.1016|0.1016	L|L	0.54323|0.54323	1.7|1.7	0.80722|0.80722	D|D	1|1	.|P;B	.|0.52577	.|0.954;0.384	.|B;B	.|0.39738	.|0.308;0.057	T|T	0.43458|0.43458	-0.9390|-0.9390	5|10	.|0.54805	.|T	.|0.06	.|.	12.2156|12.2156	0.54404|0.54404	0.6951:0.0:0.3049:0.0|0.6951:0.0:0.3049:0.0	.|.	.|86;86	.|B4DVA3;Q86UW1	.|.;OSTA_HUMAN	R|Q	57|86	.|ENSP00000296327:R86Q	.|ENSP00000296327:R86Q	G|R	+|+	1|2	0|0	AC069257.9|AC069257.9	197438356|197438356	0.981000|0.981000	0.34729|0.34729	0.947000|0.947000	0.38551|0.38551	0.306000|0.306000	0.27790|0.27790	0.130000|0.130000	0.15850|0.15850	-0.243000|-0.243000	0.09653|0.09653	0.563000|0.563000	0.77884|0.77884	GGA|CGG	.	.		0.597	SLC51A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341253.1	NM_152672		A	195953959	G	A	195953959	3	1	341	1	0	0	0	0	1	0	0	0	11309	1116	39	1	267	1	OSTalpha	3	195953959	Missense_Mutation	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10	67661470	195953959	2068471	26	47127										
DHX15	1665	hgsc.bcm.edu	37	chr4	24531241	24531241	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	taccattctggcttgatatcTgtacatgtccggatgtaatt	8	8	2	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr4:24531241T>A	ENST00000336812.4	-	13	2409	c.2253A>T	c.(2251-2253)acA>acT	p.T751T	DHX15_ENST00000508032.1_5'UTR	NM_001358.2	NP_001349.2	O43143	DHX15_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 15	751					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|U12-type spliceosomal complex (GO:0005689)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(5)|liver(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	30		Breast(46;0.0503)				GCTTGATATCTGTACATGTCC	0.393																																					p.T751T		Atlas-SNP	.											.	DHX15	69	.	0			c.A2253T						.						150	133	139					4																	24531241		2203	4300	6503	SO:0001819	synonymous_variant	1665	exon13			GATATCTGTACAT	AB001636	CCDS33966.1	4p15.3	2013-05-13	2013-05-13	2003-06-20	ENSG00000109606	ENSG00000109606		"DEAH-boxes"	2738	protein-coding gene	gene with protein product		603403	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 15", "DEAH (Asp-Glu-Ala-His) box polypeptide 15"	DDX15		9388478	Standard	NM_001358		Approved	HRH2, DBP1, PRP43, PrPp43p, PRPF43	uc003gqx.3	O43143	OTTHUMG00000160304	ENST00000336812.4:c.2253A>T	chr4.hg19:g.24531241T>A		94.0	0.0		120.0	10.0	NM_001358	Q9NQT7	Silent	SNP	ENST00000336812.4	hg19	CCDS33966.1																																																																																			.	.		0.393	DHX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360143.1	NM_001358		A	24531241	T	A	24531241	2	1	341	1	0	0	0	0	0	0	0	1	4503	1567	55	4		4	DHX15	4	24531241	Silent	SNP	T	TCGA-RG-A7D4-01A-12D-A33Q-10		24531241	166623035	27	47128										
UGT2A2	10941	hgsc.bcm.edu	37	chr4	70504723	70504723	+	Intron	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	atcctttcaccaaaggtcatCtggtcagtgagctctgataa	8	10	5	2			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr4:70504723C>T	ENST00000503640.1	-	1	771				UGT2A1_ENST00000512704.1_Intron|UGT2A1_ENST00000286604.4_Intron|UGT2A2_ENST00000457664.2_Silent_p.Q212Q|UGT2A1_ENST00000514019.1_Silent_p.Q413Q	NM_006798.3	NP_006789.2	Q9Y4X1	UD2A1_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide A1, complex locus						cellular glucuronidation (GO:0052695)|detection of chemical stimulus (GO:0009593)|metabolic process (GO:0008152)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(1)|skin(2)	30						CAAAGGTCATCTGGTCAGTGA	0.428																																					p.Q413Q		Atlas-SNP	.											.	UGT2A1	131	.	0			c.G1239A						.						49	49	49					4																	70504723		1897	4118	6015	SO:0001627	intron_variant	10941	exon3			GGTCATCTGGTCA	AJ006054	CCDS3529.1, CCDS58901.1, CCDS58902.1	4q13	2013-03-28	2010-12-02					"UDP glucuronosyltransferases"	12542	protein-coding gene	gene with protein product		604716	"UDP glycosyltransferase 2 family, polypeptide A1", "UDP glucuronosyltransferase 2 family, polypeptide A1"			10359671	Standard	NM_001252274		Approved		uc011caq.2	Q9Y4X1	OTTHUMG00000184942	ENST00000503640.1:c.715+7924G>A	chr4.hg19:g.70504723C>T		160.0	0.0		196.0	22.0	NM_001252274	B4E2F4|D3GER1|D3GER2|E9PDM7|J3KNA3	Silent	SNP	ENST00000503640.1	hg19	CCDS3529.1																																																																																			.	.		0.428	UGT2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251554.3	NM_006798		T	70504723	C	T	70504723	1	4	341	0	1	0	0	0	0	0	0	0	16969	912	32	3		3	UGT2A2	4	70504723	Intron	SNP	C	TCGA-RG-A7D4-01A-12D-A33Q-10	45973482	70504723	120649553	28	47129										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79158773	79158773	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	tcaatgtgcctttgagaaggTacggtatcctaattgtgtcc	10	8	1	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr4:79158773T>C	ENST00000325942.6	+	3	656		c.e3+2		FRAS1_ENST00000264895.6_Splice_Site|FRAS1_ENST00000264899.6_Splice_Site	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1						cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						TTTGAGAAGGTACGGTATCCT	0.413																																					.		Atlas-SNP	.											.	FRAS1	779	.	0			c.216+2T>C						.						61	59	59					4																	79158773		1936	4129	6065	SO:0001630	splice_region_variant	80144	exon3			AGAAGGTACGGTA	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.216+2T>C	chr4.hg19:g.79158773T>C		52.0	0.0		42.0	7.0	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Splice_Site	SNP	ENST00000325942.6	hg19	CCDS54772.1	.	.	.	.	.	.	.	.	.	.	T	19.95	3.922368	0.73213	.	.	ENSG00000138759	ENST00000325942;ENST00000264895;ENST00000264899;ENST00000380674	.	.	.	5.35	5.35	0.76521	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.6174	0.68558	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	FRAS1	79377797	1.000000	0.71417	0.998000	0.56505	0.912000	0.54170	5.436000	0.66538	2.156000	0.67533	0.383000	0.25322	.	.	.		0.413	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2		Intron	C	79158773	T	C	79158773	5	2	341	1	0	0	0	0	0	0	1	0	6050	1652	57	2	228	2	FRAS1	4	79158773	Splice_Site	SNP	T	TCGA-RG-A7D4-01A-12D-A33Q-10	8654050	79158773	111995503	29	47130										
DSPP	1834	hgsc.bcm.edu	37	chr4	88537513	88537513	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	gacagcagtgacagcaatgaAagcagcgacagcagtgacag	13	9	0	3	rs112275895		TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr4:88537513A>C	ENST00000282478.7	+	4	3732	c.3699A>C	c.(3697-3699)gaA>gaC	p.E1233D	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Missense_Mutation_p.E1233D			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1233	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			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)		acagcaatgaaagcagcgaca	0.547																																					p.E1233D		Atlas-SNP	.											.	DSPP	174	.	0			c.A3699C						.																																			SO:0001583	missense	1834	exon5			CAATGAAAGCAGC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3699A>C	chr4.hg19:g.88537513A>C	ENSP00000282478:p.Glu1233Asp	137.0	0.0		164.0	24.0	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	hg19	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	A	0.010	-1.785366	0.00628	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.88741	-2.42;-2.42	2.61	-5.21	0.02815	.	.	.	.	.	T	0.57213	0.2038	N	0.01048	-1.04	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.57347	-0.7827	9	0.02654	T	1	.	0.7125	0.00926	0.2623:0.1881:0.1298:0.4197	.	1233	Q9NZW4	DSPP_HUMAN	D	1233	ENSP00000382213:E1233D;ENSP00000282478:E1233D	ENSP00000282478:E1233D	E	+	3	2	DSPP	88756537	0.003000	0.15002	0.000000	0.03702	0.000000	0.00434	-2.769000	0.00780	-2.252000	0.00699	-3.496000	0.00033	GAA	.	A|0.500;C|0.500		0.547	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		C	88537513	A	C	88537513	3	2	341	1	0	0	0	0	1	0	0	0	4784	11	1	5	3713	5	DSPP	4	88537513	Missense_Mutation	SNP	A	TCGA-RG-A7D4-01A-12D-A33Q-10	9378740	88537513	102616763	30	47131										
ADH1B	125	hgsc.bcm.edu	37	chr4	100232814	100232814	+	Splice_Site	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	caacataacagggaagccatCtggaataaagtgaatattta	8	6	1	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr4:100232814C>T	ENST00000305046.8	-	7	896		c.e7-1		ADH1B_ENST00000394887.3_Splice_Site			P00325	ADH1B_HUMAN	alcohol dehydrogenase 1B (class I), beta polypeptide						ethanol oxidation (GO:0006069)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	33				OV - Ovarian serous cystadenocarcinoma(123;1.02e-07)	Ethanol(DB00898)|Fomepizole(DB01213)	GGGAAGCCATCTGGAATAAAG	0.443																																					.		Atlas-SNP	.											.	ADH1B	68	.	0			c.829-1G>A						.						182	168	173					4																	100232814		2203	4300	6503	SO:0001630	splice_region_variant	125	exon8			AGCCATCTGGAAT	AF153821	CCDS34033.1, CCDS68761.1	4q23	2008-02-05	2007-11-06		ENSG00000196616	ENSG00000196616	1.1.1.1	"Alcohol dehydrogenases"	250	protein-coding gene	gene with protein product		103720		ADH2		3006456	Standard	NM_000668		Approved		uc003hus.4	P00325	OTTHUMG00000161413	ENST00000305046.8:c.829-1G>A	chr4.hg19:g.100232814C>T		65.0	0.0		59.0	7.0	NM_000668	A8MYN5|B4DRS9|B4DVC3|Q13711|Q4ZGI9|Q96KI7	Splice_Site	SNP	ENST00000305046.8	hg19	CCDS34033.1	.	.	.	.	.	.	.	.	.	.	.	27.3	4.816068	0.90790	.	.	ENSG00000196616	ENST00000305046;ENST00000394887;ENST00000412614	.	.	.	3.66	3.66	0.41972	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3228	0.74135	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ADH1B	100451837	1.000000	0.71417	0.172000	0.22920	0.940000	0.58332	4.674000	0.61612	1.722000	0.51474	0.561000	0.74099	.	.	.		0.443	ADH1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364853.1	NM_000668	Intron	T	100232814	C	T	100232814	5	4	341	1	0	0	0	0	0	0	1	0	308	927	32	3	311	3	ADH1B	4	100232814	Splice_Site	SNP	C	TCGA-RG-A7D4-01A-12D-A33Q-10	11695301	100232814	90921462	31	47132										
ANK2	287	hgsc.bcm.edu	37	chr4	114275909	114275909	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	cagagagaagctcagaaaacAgagaatcagacaatcaaacg	9	8	3	5			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr4:114275909A>G	ENST00000357077.4	+	38	6188	c.6135A>G	c.(6133-6135)acA>acG	p.T2045T	ANK2_ENST00000264366.6_Silent_p.T2012T|ANK2_ENST00000510275.2_Intron|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000506722.1_Intron|ANK2_ENST00000394537.3_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	2045					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		CTCAGAAAACAGAGAATCAGA	0.453																																					p.T2045T		Atlas-SNP	.											.	ANK2	576	.	0			c.A6135G						.						61	71	68					4																	114275909		2203	4300	6503	SO:0001819	synonymous_variant	287	exon38			GAAAACAGAGAAT	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.6135A>G	chr4.hg19:g.114275909A>G		154.0	0.0		151.0	40.0	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Silent	SNP	ENST00000357077.4	hg19	CCDS3702.1																																																																																			.	.		0.453	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		G	114275909	A	G	114275909	2	3	341	1	0	0	0	0	0	0	0	1	621	175	7	2		2	ANK2	4	114275909	Silent	SNP	A	TCGA-RG-A7D4-01A-12D-A33Q-10	14043095	114275909	76878367	32	47133										
FAT4	79633	hgsc.bcm.edu	37	chr4	126241701	126241701	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	tttttcttgccaaaaaactgGactttgaaacacagtctttg	6	8	2	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr4:126241701G>T	ENST00000394329.3	+	1	4148	c.4135G>T	c.(4135-4137)Gac>Tac	p.D1379Y		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	1379	Cadherin 13. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						CAAAAAACTGGACTTTGAAAC	0.373																																					p.D1379Y		Atlas-SNP	.											.	FAT4	1752	.	0			c.G4135T						.						109	104	105					4																	126241701		1821	4083	5904	SO:0001583	missense	79633	exon1			AAACTGGACTTTG	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.4135G>T	chr4.hg19:g.126241701G>T	ENSP00000377862:p.Asp1379Tyr	97.0	0.0		93.0	21.0	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	hg19	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	17.54	3.414218	0.62511	.	.	ENSG00000196159	ENST00000394329	T	0.65549	-0.16	4.87	4.87	0.63330	Cadherin (4);Cadherin-like (1);	0.000000	0.36101	U	0.002792	D	0.85177	0.5637	H	0.94542	3.55	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89552	0.3800	10	0.87932	D	0	.	18.1883	0.89799	0.0:0.0:1.0:0.0	.	1379	Q6V0I7	FAT4_HUMAN	Y	1379	ENSP00000377862:D1379Y	ENSP00000377862:D1379Y	D	+	1	0	FAT4	126461151	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.454000	0.97621	2.535000	0.85469	0.655000	0.94253	GAC	.	.		0.373	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		T	126241701	G	T	126241701	3	4	341	1	0	0	0	0	1	0	0	0	5700	1174	41	3	4137	3	FAT4	4	126241701	Missense_Mutation	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10	11965792	126241701	64912575	33	47134										
FAT4	79633	hgsc.bcm.edu	37	chr4	126373179	126373179	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	ggggtacttgtgatctgaatTcccagccaaggtccacagat	11	10	1	3			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr4:126373179T>C	ENST00000394329.3	+	9	11021	c.11008T>C	c.(11008-11010)Tcc>Ccc	p.S3670P	FAT4_ENST00000335110.5_Missense_Mutation_p.S1968P	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	3670					branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						TGATCTGAATTCCCAGCCAAG	0.498																																					p.S3670P		Atlas-SNP	.											.	FAT4	1752	.	0			c.T11008C						.						130	125	127					4																	126373179		2203	4300	6503	SO:0001583	missense	79633	exon9			CTGAATTCCCAGC	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.11008T>C	chr4.hg19:g.126373179T>C	ENSP00000377862:p.Ser3670Pro	43.0	0.0		51.0	5.0	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	hg19	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	T	18.00	3.525506	0.64860	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.56611	0.45;0.45	5.77	-4.24	0.03777	.	0.000000	0.33272	U	0.005097	T	0.46483	0.1395	L	0.33485	1.01	0.46586	D	0.999111	D;D;P	0.54047	0.963;0.964;0.912	P;P;P	0.49226	0.603;0.522;0.603	T	0.53493	-0.8431	10	0.45353	T	0.12	.	18.1344	0.89614	0.0:0.0:0.6636:0.3364	.	1968;3670;3670	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	P	3670;1968	ENSP00000377862:S3670P;ENSP00000335169:S1968P	ENSP00000335169:S1968P	S	+	1	0	FAT4	126592629	1.000000	0.71417	0.023000	0.16930	0.983000	0.72400	1.299000	0.33424	-0.506000	0.06558	0.459000	0.35465	TCC	.	.		0.498	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		C	126373179	T	C	126373179	3	2	341	1	0	0	0	0	1	0	0	0	5700	1783	62	2	11042	2	FAT4	4	126373179	Missense_Mutation	SNP	T	TCGA-RG-A7D4-01A-12D-A33Q-10	131478	126373179	64781097	34	47135										
PCDH18	54510	hgsc.bcm.edu	37	chr4	138450819	138450819	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	tctggcacgtggtttgatgaGattgtcaccaaactgttgag	12	7	2	3			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr4:138450819G>C	ENST00000344876.4	-	1	2810	c.2424C>G	c.(2422-2424)atC>atG	p.I808M	PCDH18_ENST00000510305.1_Missense_Mutation_p.I19M|PCDH18_ENST00000412923.2_Missense_Mutation_p.I808M|PCDH18_ENST00000511115.1_Intron|PCDH18_ENST00000507846.1_Missense_Mutation_p.I588M	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	808					brain development (GO:0007420)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(27)|lung(21)|ovary(2)|pancreas(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86	all_hematologic(180;0.24)					GGTTTGATGAGATTGTCACCA	0.468																																					p.I808M		Atlas-SNP	.											.	PCDH18	229	.	0			c.C2424G						.						135	116	122					4																	138450819		2203	4300	6503	SO:0001583	missense	54510	exon1			TGATGAGATTGTC	AL137471	CCDS34064.1, CCDS75193.1	4q28.3	2010-01-26			ENSG00000189184	ENSG00000189184		"Cadherins / Protocadherins : Non-clustered"	14268	protein-coding gene	gene with protein product		608287				10835267, 11549318	Standard	XM_005263070		Approved	KIAA1562, PCDH68L	uc003ihe.4	Q9HCL0	OTTHUMG00000161348	ENST00000344876.4:c.2424C>G	chr4.hg19:g.138450819G>C	ENSP00000355082:p.Ile808Met	74.0	0.0		71.0	17.0	NM_019035	A8K7K3|B7ZKT1|Q52LS2	Missense_Mutation	SNP	ENST00000344876.4	hg19	CCDS34064.1	.	.	.	.	.	.	.	.	.	.	G	15.77	2.932626	0.52866	.	.	ENSG00000189184	ENST00000344876;ENST00000412923;ENST00000507846;ENST00000510305	T;T;T;T	0.55930	0.62;0.62;0.49;1.19	5.53	5.53	0.82687	.	0.000000	0.44097	D	0.000487	T	0.66317	0.2777	L	0.57536	1.79	0.80722	D	1	D;D;D	0.71674	0.998;0.998;0.998	P;D;P	0.65443	0.896;0.935;0.896	T	0.62604	-0.6819	10	0.38643	T	0.18	.	14.4949	0.67680	0.0:0.0:0.8534:0.1466	.	588;808;808	D6RIG4;Q9HCL0-2;Q9HCL0	.;.;PCD18_HUMAN	M	808;808;588;19	ENSP00000355082:I808M;ENSP00000390688:I808M;ENSP00000425903:I588M;ENSP00000424269:I19M	ENSP00000355082:I808M	I	-	3	3	PCDH18	138670269	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.815000	0.48018	2.871000	0.98454	0.655000	0.94253	ATC	.	.		0.468	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035		C	138450819	G	C	138450819	3	2	341	1	0	0	0	0	1	0	0	0	11522	932	33	4	999	4	PCDH18	4	138450819	Missense_Mutation	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10	12077640	138450819	52703457	35	47136										
EGFLAM	133584	hgsc.bcm.edu	37	chr5	38409153	38409153	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	tactgtggggagaacgaacaCgggaggggggatttcatgtc	17	6	1	1	rs375160813		TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr5:38409153C>T	ENST00000354891.3	+	10	1642	c.1296C>T	c.(1294-1296)caC>caT	p.H432H	EGFLAM_ENST00000322350.5_Silent_p.H432H|EGFLAM_ENST00000397202.2_Intron|EGFLAM_ENST00000336740.6_Silent_p.H198H	NM_001205301.1	NP_001192230.1	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G domains	432	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				extracellular matrix organization (GO:0030198)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|cell junction (GO:0030054)|interstitial matrix (GO:0005614)|synapse (GO:0045202)	glycosaminoglycan binding (GO:0005539)			NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(43)|ovary(1)|pancreas(3)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	85	all_lung(31;0.000385)					AGAACGAACACGGGAGGGGGG	0.488																																					p.H432H	Colon(62;485 1295 3347 17454)	Atlas-SNP	.											.	EGFLAM	302	.	0			c.C1296T						.	C	,,	1,4405		0,1,2202	81	77	78		1296,1296,594	-5.8	0	5		78	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	EGFLAM	NM_001205301.1,NM_152403.3,NM_182798.2	,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,	432/1018,432/1010,198/776	38409153	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	133584	exon10			CGAACACGGGAGG	AK097549	CCDS3924.1, CCDS3925.1, CCDS47199.1, CCDS56363.1	5p13.2-p13.1	2014-04-03			ENSG00000164318	ENSG00000164318		"Fibronectin type III domain containing"	26810	protein-coding gene	gene with protein product	"pikachurin", "agrin-like"					18641643, 20078962, 22760553	Standard	NM_182801		Approved	FLJ39155, AGRINL, AGRNL, PIKA	uc003jlc.2	Q63HQ2	OTTHUMG00000131139	ENST00000354891.3:c.1296C>T	chr5.hg19:g.38409153C>T		66.0	0.0		67.0	14.0	NM_001205301	A8K6D7|Q5U643|Q6P3V1|Q8N124|Q8N197|Q8N7Y0|Q8N8N5|Q8NAL2	Silent	SNP	ENST00000354891.3	hg19	CCDS56363.1																																																																																			.	.		0.488	EGFLAM-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367323.1	NM_152403		T	38409153	C	T	38409153	2	4	341	1	0	0	0	0	0	0	0	1	4968	535	19	1		1	EGFLAM	5	38409153	Silent	SNP	C	TCGA-RG-A7D4-01A-12D-A33Q-10		38409153	142506107	36	47137										
CCDC125	202243	hgsc.bcm.edu	37	chr5	68595919	68595919	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	cttctgctgtttgatatcaaGcatggcgagggcctccaaat	10	10	2	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr5:68595919G>C	ENST00000396496.2	-	8	843	c.736C>G	c.(736-738)Ctt>Gtt	p.L246V	CCDC125_ENST00000396499.1_Missense_Mutation_p.L246V|CCDC125_ENST00000383374.2_Missense_Mutation_p.L245V|CCDC125_ENST00000511257.1_Missense_Mutation_p.L121V|CCDC125_ENST00000460090.1_5'UTR			Q86Z20	CC125_HUMAN	coiled-coil domain containing 125	246						cytoplasm (GO:0005737)				breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(7)|urinary_tract(1)	19		Lung NSC(167;7.26e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.2e-56)|Epithelial(20;2.31e-52)|all cancers(19;5.85e-48)|Lung(70;0.0183)		TTGATATCAAGCATGGCGAGG	0.443																																					p.L246V		Atlas-SNP	.											CCDC125,colon,carcinoma,0,1	CCDC125	41	.	0			c.C736G						.						242	222	229					5																	68595919		2203	4300	6503	SO:0001583	missense	202243	exon7			TATCAAGCATGGC	AB024691	CCDS4000.1, CCDS75255.1	5q13.2	2008-02-05			ENSG00000183323	ENSG00000183323			28924	protein-coding gene	gene with protein product		613781					Standard	XM_005248461		Approved	KENAE	uc003jvv.1	Q86Z20	OTTHUMG00000131259	ENST00000396496.2:c.736C>G	chr5.hg19:g.68595919G>C	ENSP00000379754:p.Leu246Val	71.0	0.0		110.0	6.0	NM_176816	Q86Z19	Missense_Mutation	SNP	ENST00000396496.2	hg19	CCDS4000.1	.	.	.	.	.	.	.	.	.	.	G	19.20	3.780943	0.70222	.	.	ENSG00000183323	ENST00000396496;ENST00000396499;ENST00000383374;ENST00000511257	T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15	4.98	4.98	0.66077	.	0.000000	0.85682	D	0.000000	T	0.79975	0.4539	M	0.77103	2.36	0.45183	D	0.998191	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.996	T	0.82583	-0.0385	10	0.72032	D	0.01	-0.1671	17.3807	0.87404	0.0:0.0:1.0:0.0	.	121;246	Q86Z20-2;Q86Z20	.;CC125_HUMAN	V	246;246;245;121	ENSP00000379754:L246V;ENSP00000379756:L246V;ENSP00000372865:L245V;ENSP00000426795:L121V	ENSP00000372865:L245V	L	-	1	0	CCDC125	68631675	1.000000	0.71417	0.998000	0.56505	0.798000	0.45092	6.815000	0.75242	2.486000	0.83907	0.591000	0.81541	CTT	.	.		0.443	CCDC125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254027.4	NM_176816		C	68595919	G	C	68595919	3	2	341	1	0	0	0	0	1	0	0	0	2763	971	34	4	819	4	CCDC125	5	68595919	Missense_Mutation	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10	30186766	68595919	112319341	37	47138										
POC5	134359	hgsc.bcm.edu	37	chr5	74973679	74973679	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	tatagctaaactgctgctaaTtctattttttgaagcaaaat	5	6	1	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr5:74973679T>G	ENST00000428202.2	-	11	1693	c.1504A>C	c.(1504-1506)Att>Ctt	p.I502L	POC5_ENST00000380475.2_Intron|POC5_ENST00000446329.2_Missense_Mutation_p.I477L|POC5_ENST00000510798.1_Intron|POC5_ENST00000514838.2_Missense_Mutation_p.I474L	NM_001099271.1	NP_001092741.1	Q8NA72	POC5_HUMAN	POC5 centriolar protein	502					cell cycle (GO:0007049)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						CTGCTGCTAATTCTATTTTTT	0.418																																					p.I502L		Atlas-SNP	.											.	POC5	82	.	0			c.A1504C						.						131	117	121					5																	74973679		1842	4097	5939	SO:0001583	missense	134359	exon11			TGCTAATTCTATT	AK093098	CCDS47236.1, CCDS47237.1	5q13.3	2013-08-05	2013-08-05	2010-03-26	ENSG00000152359	ENSG00000152359			26658	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 37", "POC5 centriolar protein homolog (Chlamydomonas)"	C5orf37		19349582	Standard	NM_152408		Approved	FLJ35779, MGC120442, MGC120443, MGC120444, hPOC5	uc003keh.4	Q8NA72	OTTHUMG00000162487	ENST00000428202.2:c.1504A>C	chr5.hg19:g.74973679T>G	ENSP00000410216:p.Ile502Leu	64.0	0.0		104.0	29.0	NM_001099271	B4DJG7|Q494X7|Q494X9|Q6P085	Missense_Mutation	SNP	ENST00000428202.2	hg19	CCDS47236.1	.	.	.	.	.	.	.	.	.	.	T	12.62	1.991437	0.35131	.	.	ENSG00000152359	ENST00000428202;ENST00000514838;ENST00000446329	T;T;T	0.32023	1.88;1.47;1.87	5.92	0.828	0.18841	.	0.511853	0.23444	N	0.048106	T	0.27313	0.0670	M	0.71581	2.175	0.34221	D	0.675475	B;B	0.33940	0.433;0.433	B;B	0.29598	0.104;0.104	T	0.32981	-0.9886	10	0.23891	T	0.37	-13.1806	10.4271	0.44385	0.0:0.3387:0.0:0.6613	.	502;477	Q8NA72;Q8NA72-3	POC5_HUMAN;.	L	502;474;477	ENSP00000410216:I502L;ENSP00000420971:I474L;ENSP00000399481:I477L	ENSP00000410216:I502L	I	-	1	0	POC5	75009435	0.981000	0.34729	0.097000	0.21041	0.297000	0.27493	0.497000	0.22514	-0.070000	0.12908	-0.924000	0.02725	ATT	.	.		0.418	POC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369124.1	NM_152408		G	74973679	T	G	74973679	3	3	341	1	0	0	0	0	1	0	0	0	12186	1493	52	5	231	5	POC5	5	74973679	Missense_Mutation	SNP	T	TCGA-RG-A7D4-01A-12D-A33Q-10	6377760	74973679	105941581	38	47139										
GPR98	84059	hgsc.bcm.edu	37	chr5	89979611	89979611	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	cctcagtgtttccagtggttCtttgggagctcatattaatg	10	8	3	0			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr5:89979611C>T	ENST00000405460.2	+	28	5969	c.5873C>T	c.(5872-5874)tCt>tTt	p.S1958F		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	1958					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TCCAGTGGTTCTTTGGGAGCT	0.438																																					p.S1958F		Atlas-SNP	.											.	GPR98	605	.	0			c.C5873T						.						135	129	131					5																	89979611		1897	4131	6028	SO:0001583	missense	84059	exon28			GTGGTTCTTTGGG	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.5873C>T	chr5.hg19:g.89979611C>T	ENSP00000384582:p.Ser1958Phe	103.0	0.0		110.0	39.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	C	14.07	2.425410	0.43020	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000399043	T	0.27104	1.69	5.7	4.81	0.61882	.	0.149175	0.64402	D	0.000009	T	0.36331	0.0963	L	0.54323	1.7	0.80722	D	1	P	0.40875	0.731	P	0.49708	0.62	T	0.07028	-1.0794	10	0.62326	D	0.03	.	12.9991	0.58666	0.0:0.6071:0.3929:0.0	.	1958	Q8WXG9	GPR98_HUMAN	F	1958	ENSP00000384582:S1958F	ENSP00000296619:S1958F	S	+	2	0	GPR98	90015367	1.000000	0.71417	0.130000	0.21974	0.079000	0.17450	5.723000	0.68492	2.697000	0.92050	0.585000	0.79938	TCT	.	.		0.438	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		T	89979611	C	T	89979611	3	4	341	1	0	0	0	0	1	0	0	0	6730	913	32	3	5983	3	GPR98	5	89979611	Missense_Mutation	SNP	C	TCGA-RG-A7D4-01A-12D-A33Q-10	15005932	89979611	90935649	39	47140										
ANKRD32	84250	hgsc.bcm.edu	37	chr5	94022288	94022288	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	tgttctccagacttttcttcAcaggaattagagattttcat	6	8	4	2			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr5:94022288A>G	ENST00000265140.5	+	16	2405	c.1986A>G	c.(1984-1986)tcA>tcG	p.S662S		NM_032290.3	NP_115666.2	Q9BQI6	ANR32_HUMAN	ankyrin repeat domain 32	662						centrosome (GO:0005813)|nucleus (GO:0005634)				NS(1)|breast(2)|endometrium(2)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|skin(1)	13		all_cancers(142;1.51e-09)|all_epithelial(76;4.68e-12)|all_lung(232;5.94e-05)|Ovarian(174;0.000953)|Lung NSC(167;0.00105)|Colorectal(57;0.122)|Lung SC(612;0.152)		all cancers(79;3.88e-18)		ACTTTTCTTCACAGGAATTAG	0.363																																					p.S662S		Atlas-SNP	.											.	ANKRD32	117	.	0			c.A1986G						.						168	169	169					5																	94022288		2203	4300	6503	SO:0001819	synonymous_variant	84250	exon16			TTCTTCACAGGAA	AL136560	CCDS4071.2	5q15	2013-01-10			ENSG00000133302	ENSG00000133302		"Ankyrin repeat domain containing"	25408	protein-coding gene	gene with protein product			"BRCT domain containing 1"	BRCTD1			Standard	NM_032290		Approved	DKFZp761C121, DKFZp564C0469	uc003kkr.4	Q9BQI6	OTTHUMG00000121133	ENST00000265140.5:c.1986A>G	chr5.hg19:g.94022288A>G		34.0	0.0		67.0	14.0	NM_032290	B4DMG4|Q3B7K4|Q6NSA5|Q6PHW9|Q9Y402	Silent	SNP	ENST00000265140.5	hg19	CCDS4071.2																																																																																			.	.		0.363	ANKRD32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241610.1	NM_032290		G	94022288	A	G	94022288	2	3	341	1	0	0	0	0	0	0	0	1	660	146	6	2		2	ANKRD32	5	94022288	Silent	SNP	A	TCGA-RG-A7D4-01A-12D-A33Q-10	4042677	94022288	86892972	40	47141										
PCDHGA4	56111	hgsc.bcm.edu	37	chr5	140737153	140737153	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	agcctcttctgataactcagGatttacttgaaacaaaagga	7	8	3	2			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr5:140737153G>T	ENST00000571252.1	+	1	2386	c.2386G>T	c.(2386-2388)Gat>Tat	p.D796Y	PCDHGA1_ENST00000517417.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_5'Flank	NM_018917.2	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4	796					homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GATAACTCAGGATTTACTTGA	0.438																																					p.D796Y		Atlas-SNP	.											.	PCDHGA4	150	.	0			c.G2386T						.						53	59	57					5																	140737153		2156	4282	6438	SO:0001583	missense	56111	exon1			ACTCAGGATTTAC	AF152511	CCDS58979.1, CCDS58979.2, CCDS75331.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8702	other	protocadherin		606291				10380929	Standard	NM_018917		Approved	PCDH-GAMMA-A4		Q9Y5G9		ENST00000571252.1:c.2386G>T	chr5.hg19:g.140737153G>T	ENSP00000458570:p.Asp796Tyr	136.0	0.0		167.0	58.0	NM_018917	Q9Y5D3	Missense_Mutation	SNP	ENST00000571252.1	hg19	CCDS58979.1																																																																																			.	.		0.438	PCDHGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437959.1	NM_018917		T	140737153	G	T	140737153	3	4	341	1	0	0	0	0	1	0	0	0	11565	1174	41	3	2388	3	PCDHGA4	5	140737153	Missense_Mutation	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10	46714865	140737153	40178107	41	47142										
SLIT3	6586	hgsc.bcm.edu	37	chr5	168123358	168123358	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	ccgtccacgcaggtggcattGttttcgcagtcgttgtcctc	11	13	0	0			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr5:168123358G>A	ENST00000519560.1	-	28	3440	c.3021C>T	c.(3019-3021)aaC>aaT	p.N1007N	SLIT3_ENST00000404867.3_Silent_p.N1007N|SLIT3_ENST00000332966.8_Silent_p.N1014N	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	1007	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			AGGTGGCATTGTTTTCGCAGT	0.552																																					p.N1014N	Ovarian(29;311 847 10864 17279 24903)	Atlas-SNP	.											.	SLIT3	224	.	0			c.C3042T						.						285	230	249					5																	168123358		2203	4300	6503	SO:0001819	synonymous_variant	6586	exon28			GGCATTGTTTTCG	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"slit (Drosophila) homolog 3"	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.3021C>T	chr5.hg19:g.168123358G>A		68.0	0.0		74.0	32.0	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Silent	SNP	ENST00000519560.1	hg19	CCDS4369.1																																																																																			.	.		0.552	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062		A	168123358	G	A	168123358	2	1	341	1	0	0	0	0	0	0	0	1	14756	1368	48	3		3	SLIT3	5	168123358	Silent	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10	27386205	168123358	12791902	42	47143										
FOXI1	2299	hgsc.bcm.edu	37	chr5	169535273	169535273	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	ggcaccaccagctccccagaGaagcggccctcccctccccc	8	23	0	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr5:169535273G>A	ENST00000306268.6	+	2	856	c.795G>A	c.(793-795)gaG>gaA	p.E265E	FOXI1_ENST00000449804.2_Intron			Q12951	FOXI1_HUMAN	forkhead box I1	265					embryo development (GO:0009790)|inner ear morphogenesis (GO:0042472)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	Renal(175;0.000159)|Lung NSC(126;0.0267)|all_lung(126;0.04)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GCTCCCCAGAGAAGCGGCCCT	0.642									Pendred syndrome																												p.E265E		Atlas-SNP	.											.	FOXI1	70	.	0			c.G795A						.						49	57	54					5																	169535273		2203	4300	6503	SO:0001819	synonymous_variant	2299	exon2	Familial Cancer Database	Goiter-Deafness syndrome	CCCAGAGAAGCGG	BC029778	CCDS4372.1, CCDS47337.1	5q34	2008-02-05			ENSG00000168269	ENSG00000168269		"Forkhead boxes"	3815	protein-coding gene	gene with protein product		601093		FKHL10		7957066, 8825632	Standard	NM_144769		Approved	FREAC6	uc003mai.4	Q12951	OTTHUMG00000130436	ENST00000306268.6:c.795G>A	chr5.hg19:g.169535273G>A		110.0	0.0		161.0	19.0	NM_012188	Q14518|Q66SR7|Q8N6L8	Silent	SNP	ENST00000306268.6	hg19	CCDS4372.1																																																																																			.	.		0.642	FOXI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252827.2	NM_144769, NM_012188		A	169535273	G	A	169535273	2	1	341	1	0	0	0	0	0	0	0	1	6017	933	33	3		3	FOXI1	5	169535273	Silent	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10	1411915	169535273	11379987	43	47144										
LCP2	3937	hgsc.bcm.edu	37	chr5	169689689	169689689	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	gggctgctcctttcatgtctTtccgtggtcggtggtaaagg	14	9	2	0			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr5:169689689T>G	ENST00000046794.5	-	13	1491	c.876A>C	c.(874-876)gaA>gaC	p.E292D	LCP2_ENST00000521416.1_Missense_Mutation_p.E87D	NM_005565.3	NP_005556.1	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte protein of 76kDa)	292					blood coagulation (GO:0007596)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|innate immune response (GO:0045087)|mast cell activation (GO:0045576)|platelet activation (GO:0030168)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)				cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	23	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.247)		TTTCATGTCTTTCCGTGGTCG	0.512																																					p.E292D		Atlas-SNP	.											.	LCP2	133	.	0			c.A876C						.						75	75	75					5																	169689689		1942	4146	6088	SO:0001583	missense	3937	exon13			ATGTCTTTCCGTG		CCDS47339.1	5q35.1	2013-02-14	2002-08-29		ENSG00000043462	ENSG00000043462		"SH2 domain containing"	6529	protein-coding gene	gene with protein product	"76 kDa tyrosine phosphoprotein", "SH2 domain-containing leukocyte protein of 76kD"	601603	"lymphocyte cytosolic protein 2 (SH2 domain-containing leukocyte protein of 76kD)"	SLP76		7706237	Standard	NM_005565		Approved	SLP-76	uc003man.1	Q13094	OTTHUMG00000163121	ENST00000046794.5:c.876A>C	chr5.hg19:g.169689689T>G	ENSP00000046794:p.Glu292Asp	119.0	0.0		152.0	52.0	NM_005565	A8KA25|Q53XV4	Missense_Mutation	SNP	ENST00000046794.5	hg19	CCDS47339.1	.	.	.	.	.	.	.	.	.	.	T	7.203	0.593898	0.13875	.	.	ENSG00000043462	ENST00000046794;ENST00000521416;ENST00000520344	T;T	0.43688	0.95;0.94	5.44	-0.394	0.12434	.	0.323813	0.32970	N	0.005421	T	0.22244	0.0536	L	0.28192	0.835	0.22199	N	0.9993	B;B;B	0.11235	0.004;0.004;0.002	B;B;B	0.09377	0.004;0.002;0.002	T	0.12630	-1.0540	9	.	.	.	-9.7914	5.1887	0.15197	0.0:0.1767:0.3794:0.4439	.	87;292;292	E7ESF6;A8KA25;Q13094	.;.;LCP2_HUMAN	D	292;87;59	ENSP00000046794:E292D;ENSP00000428871:E87D	.	E	-	3	2	LCP2	169622267	0.870000	0.30015	0.070000	0.20053	0.484000	0.33280	-0.501000	0.06398	-0.302000	0.08869	0.533000	0.62120	GAA	.	.		0.512	LCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371727.1	NM_005565		G	169689689	T	G	169689689	3	3	341	1	0	0	0	0	1	0	0	0	8701	1838	64	5	761	5	LCP2	5	169689689	Missense_Mutation	SNP	T	TCGA-RG-A7D4-01A-12D-A33Q-10	154416	169689689	11225571	44	47145										
EGFL8	80864	hgsc.bcm.edu	37	chr6	32135153	32135153	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	aggcggaaaaagatgagcgcGctctgaagcaggagattcac	14	8	2	4	rs149576421		TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr6:32135153G>T	ENST00000395512.1	+	7	733	c.628G>T	c.(628-630)Gct>Tct	p.A210S	PPT2-EGFL8_ENST00000422437.1_3'UTR|AGPAT1_ENST00000490711.1_5'Flank|EGFL8_ENST00000333845.6_Missense_Mutation_p.A210S			Q99944	EGFL8_HUMAN	EGF-like-domain, multiple 8	210						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|urinary_tract(1)	10						AGATGAGCGCGCTCTGAAGCA	0.652																																					p.A210S		Atlas-SNP	.											.	EGFL8	15	.	0			c.G628T						.						44	45	45					6																	32135153		1509	2708	4217	SO:0001583	missense	80864	exon7			GAGCGCGCTCTGA	U89336	CCDS4743.1	6p21	2010-06-25	2003-05-21	2003-05-23	ENSG00000241404	ENSG00000241404			13944	protein-coding gene	gene with protein product		609897	"chromosome 6 open reading frame 8"	C6orf8			Standard	NM_030652		Approved	NG3		Q99944	OTTHUMG00000031222	ENST00000395512.1:c.628G>T	chr6.hg19:g.32135153G>T	ENSP00000378888:p.Ala210Ser	98.0	0.0		116.0	5.0	NM_030652	B0S884|G5E9Q0|Q5JP23|Q5SSX3|Q8IV30	Missense_Mutation	SNP	ENST00000395512.1	hg19	CCDS4743.1	.	.	.	.	.	.	.	.	.	.	G	0.837	-0.743096	0.03088	.	.	ENSG00000241404	ENST00000333845;ENST00000395512;ENST00000432129	D;D;T	0.89123	-2.47;-2.47;2.14	5.45	1.11	0.20524	.	.	.	.	.	T	0.62600	0.2441	L	0.37750	1.13	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.50021	-0.8876	9	0.10902	T	0.67	-6.7557	5.4355	0.16478	0.1705:0.0:0.5379:0.2916	.	210	Q99944	EGFL8_HUMAN	S	210;210;190	ENSP00000333380:A210S;ENSP00000378888:A210S;ENSP00000401694:A190S	ENSP00000333380:A210S	A	+	1	0	EGFL8	32243131	0.000000	0.05858	0.062000	0.19696	0.004000	0.04260	-0.427000	0.06999	0.270000	0.21984	-0.448000	0.05591	GCT	.	G|1.000;A|0.000		0.652	EGFL8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076463.3	NM_030652		T	32135153	G	T	32135153	3	4	341	1	0	0	0	0	1	0	0	0	4967	1087	38	1	650	1	EGFL8	6	32135153	Missense_Mutation	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10		32135153	138979914	45	47146										
LHFPL5	222662	hgsc.bcm.edu	37	chr6	35773531	35773531	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	tcgcgagccgtgggcgtgatGtggggtaccctcaccatctg	15	12	2	1	rs370902662		TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr6:35773531G>A	ENST00000373853.1	+	1	462	c.84G>A	c.(82-84)atG>atA	p.M28I	LHFPL5_ENST00000360215.1_Missense_Mutation_p.M28I			Q8TAF8	TMHS_HUMAN	lipoma HMGIC fusion partner-like 5	28					auditory receptor cell stereocilium organization (GO:0060088)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transport (GO:0006811)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)				endometrium(4)|large_intestine(4)|lung(7)|prostate(2)|skin(2)|urinary_tract(1)	20						TGGGCGTGATGTGGGGTACCC	0.607																																					p.M28I		Atlas-SNP	.											.	LHFPL5	44	.	0			c.G84A						.	G	ILE/MET	1,4405	2.1+/-5.4	0,1,2202	202	176	185		84	4.5	1	6		185	0,8600		0,0,4300	no	missense	LHFPL5	NM_182548.3	10	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	28/220	35773531	1,13005	2203	4300	6503	SO:0001583	missense	222662	exon1			CGTGATGTGGGGT	BC028630	CCDS4812.1	6p21.31	2014-01-28				ENSG00000197753			21253	protein-coding gene	gene with protein product		609427	"deafness, autosomal recessive 67"	DFNB67		16459341	Standard	NM_182548		Approved	MGC33835, dJ510O8.8, Tmhs	uc003olg.1	Q8TAF8		ENST00000373853.1:c.84G>A	chr6.hg19:g.35773531G>A	ENSP00000362960:p.Met28Ile	95.0	0.0		136.0	43.0	NM_182548	B3KX66	Missense_Mutation	SNP	ENST00000373853.1	hg19	CCDS4812.1	.	.	.	.	.	.	.	.	.	.	G	16.52	3.146510	0.57044	2.27E-4	0.0	ENSG00000197753	ENST00000373853;ENST00000360215	T;T	0.69806	-0.43;-0.43	5.33	4.47	0.54385	.	0.154695	0.64402	D	0.000013	T	0.35393	0.0930	L	0.27053	0.805	0.41178	D	0.986217	B	0.26002	0.139	B	0.25405	0.06	T	0.26573	-1.0099	10	0.33940	T	0.23	-20.5523	11.0421	0.47838	0.071:0.129:0.8:0.0	.	28	Q8TAF8	TMHS_HUMAN	I	28	ENSP00000362960:M28I;ENSP00000353346:M28I	ENSP00000353346:M28I	M	+	3	0	LHFPL5	35881509	1.000000	0.71417	1.000000	0.80357	0.773000	0.43773	4.506000	0.60428	1.252000	0.44001	-0.284000	0.09977	ATG	.	.		0.607	LHFPL5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040323.1	NM_182548		A	35773531	G	A	35773531	3	1	341	1	0	0	0	0	1	0	0	0	8777	1377	48	3	86	3	LHFPL5	6	35773531	Missense_Mutation	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10	3638378	35773531	135341536	46	47147										
KHDC1L	100129128	hgsc.bcm.edu	37	chr6	73935082	73935082	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	ttggagaatgaaagttttcgGgcagggtccaccacggctcc	13	10	0	2			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr6:73935082G>T	ENST00000370388.3	-	1	93	c.50C>A	c.(49-51)cCc>cAc	p.P17H	KHDC1L_ENST00000471312.1_5'UTR|RP11-257K9.8_ENST00000423730.3_Missense_Mutation_p.P120T	NM_001126063.2	NP_001119535.1	Q5JSQ8	KHDCL_HUMAN	KH homology domain containing 1-like	17										breast(1)|endometrium(1)|kidney(1)|lung(3)|skin(1)	7						AAAGTTTTCGGGCAGGGTCCA	0.547																																					p.P17H		Atlas-SNP	.											.	KHDC1L	22	.	0			c.C50A						.						79	74	75					6																	73935082		692	1591	2283	SO:0001583	missense	100129128	exon1			TTTTCGGGCAGGG	BC004267	CCDS47450.1	6q13	2014-05-15			ENSG00000256980	ENSG00000256980			37274	protein-coding gene	gene with protein product							Standard	NM_001126063		Approved	RP11-257K9.7	uc003pgm.4	Q5JSQ8	OTTHUMG00000132474	ENST00000370388.3:c.50C>A	chr6.hg19:g.73935082G>T	ENSP00000359415:p.Pro17His	82.0	0.0		86.0	27.0	NM_001126063	E1P535	Missense_Mutation	SNP	ENST00000370388.3	hg19	CCDS47450.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.19|14.19	2.462717|2.462717	0.43736|0.43736	.|.	.|.	ENSG00000256980|ENSG00000256980	ENST00000370388|ENST00000370385	T|.	0.64438|.	-0.1|.	1.91|1.91	1.91|1.91	0.25777|0.25777	.|.	.|.	.|.	.|.	.|.	T|T	0.16257|0.16257	0.0391|0.0391	M|M	0.63843|0.63843	1.955|1.955	0.09310|0.09310	N|N	1|1	D|.	0.89917|.	1.0|.	D|.	0.83275|.	0.996|.	T|T	0.39840|0.39840	-0.9594|-0.9594	9|6	0.87932|0.02654	D|T	0|1	.|.	7.3034|7.3034	0.26434|0.26434	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	17|.	Q5JSQ8|.	KHDCL_HUMAN|.	H|T	17|120	ENSP00000359415:P17H|.	ENSP00000359415:P17H|ENSP00000359412:P120T	P|P	-|-	2|1	0|0	RP11-257K9.7|RP11-257K9.7	73991803|73991803	0.000000|0.000000	0.05858|0.05858	0.003000|0.003000	0.11579|0.11579	0.175000|0.175000	0.22909|0.22909	-0.027000|-0.027000	0.12371|0.12371	1.374000|1.374000	0.46228|0.46228	0.205000|0.205000	0.17691|0.17691	CCC|CCG	.	.		0.547	KHDC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255640.1	NM_001126063		T	73935082	G	T	73935082	3	4	341	1	0	0	0	0	1	0	0	0	8154	1232	43	3	348	3	KHDC1L	6	73935082	Missense_Mutation	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10	38161551	73935082	97179985	47	47148										
PRDM1	639	hgsc.bcm.edu	37	chr6	106552731	106552731	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	agcagtctaaagcaaccgagCactgagaaaaatgaactctg	9	9	2	2	rs373718206		TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr6:106552731C>T	ENST00000369096.4	+	5	930	c.696C>T	c.(694-696)agC>agT	p.S232S	PRDM1_ENST00000369091.2_Silent_p.S196S|PRDM1_ENST00000369089.3_Silent_p.S98S	NM_001198.3	NP_001189.2	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain	232					cell fate commitment (GO:0045165)|eye photoreceptor cell development (GO:0042462)|germ cell development (GO:0007281)|intestinal epithelial cell development (GO:0060576)|maternal placenta development (GO:0001893)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gene expression (GO:0010628)|post-embryonic development (GO:0009791)|transcription, DNA-templated (GO:0006351)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(59)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(5)|urinary_tract(2)	94	Breast(9;0.022)	all_cancers(87;2.2e-31)|all_epithelial(87;2.03e-21)|Acute lymphoblastic leukemia(125;4.99e-11)|all_lung(197;7.55e-09)|all_hematologic(75;5.82e-08)|Lung NSC(302;1.28e-06)|Colorectal(196;0.0112)|Ovarian(999;0.0365)		all cancers(137;1.83e-46)|Epithelial(106;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(136;1.99e-20)|GBM - Glioblastoma multiforme(226;3.72e-11)|BRCA - Breast invasive adenocarcinoma(108;1.38e-05)		AGCAACCGAGCACTGAGAAAA	0.448			"D, N, Mis, F, S"		DLBCL																																p.S232S		Atlas-SNP	.		Rec	yes		6	6q21	639	"PR domain containing 1, with ZNF domain"		L	.	PRDM1	195	.	0			c.C696T						.	C	,	0,4406		0,0,2203	172	183	179		696,294	2.5	0	6		179	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	PRDM1	NM_001198.3,NM_182907.1	,	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	,	232/826,98/692	106552731	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	639	exon5			ACCGAGCACTGAG		CCDS5054.2, CCDS34505.1	6q21	2013-01-08			ENSG00000057657	ENSG00000057657		"Zinc fingers, C2H2-type"	9346	protein-coding gene	gene with protein product		603423		BLIMP1		1851123	Standard	NM_001198		Approved	PRDI-BF1	uc003prd.2	O75626	OTTHUMG00000015299	ENST00000369096.4:c.696C>T	chr6.hg19:g.106552731C>T		38.0	0.0		60.0	7.0	NM_001198	B2REA6|E1P5E0|Q86WM7	Silent	SNP	ENST00000369096.4	hg19	CCDS5054.2																																																																																			.	.		0.448	PRDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041661.3			T	106552731	C	T	106552731	2	4	341	1	0	0	0	0	0	0	0	1	12462	709	25	3		3	PRDM1	6	106552731	Silent	SNP	C	TCGA-RG-A7D4-01A-12D-A33Q-10	32617649	106552731	64562336	48	47149										
REV3L	5980	hgsc.bcm.edu	37	chr6	111732714	111732714	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	tgtaggattgtaaagatagaTcttcataaagtgtctttcct	8	5	3	2			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr6:111732714T>C	ENST00000358835.3	-	4	827	c.373A>G	c.(373-375)Atc>Gtc	p.I125V	REV3L_ENST00000368802.3_Missense_Mutation_p.I125V|REV3L_ENST00000368805.1_Missense_Mutation_p.I125V|REV3L_ENST00000435970.1_Missense_Mutation_p.I47V			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	125					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		TAAAGATAGATCTTCATAAAG	0.234								DNA polymerases (catalytic subunits)																													p.I125V		Atlas-SNP	.											.	REV3L	386	.	0			c.A373G						.						35	35	35					6																	111732714		2175	4279	6454	SO:0001583	missense	5980	exon3			GATAGATCTTCAT	AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"DNA polymerases"	9968	protein-coding gene	gene with protein product	"polymerase, DNA, zeta"	602776	"REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta", "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.373A>G	chr6.hg19:g.111732714T>C	ENSP00000351697:p.Ile125Val	131.0	0.0		234.0	56.0	NM_002912	O43214|Q5TC33	Missense_Mutation	SNP	ENST00000358835.3	hg19	CCDS5091.2	.	.	.	.	.	.	.	.	.	.	T	15.06	2.720937	0.48728	.	.	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970	T;T;T;T	0.07327	3.2;3.2;3.2;3.2	5.58	5.58	0.84498	DNA-directed DNA polymerase, family B, exonuclease domain (1);Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.04497	0.0123	L	0.60957	1.885	0.34316	D	0.685982	P	0.38129	0.619	B	0.33890	0.172	T	0.15093	-1.0449	10	0.62326	D	0.03	.	10.8914	0.46998	0.0:0.0729:0.0:0.9271	.	125	O60673	DPOLZ_HUMAN	V	125;125;125;47	ENSP00000357792:I125V;ENSP00000357795:I125V;ENSP00000351697:I125V;ENSP00000402003:I47V	ENSP00000351697:I125V	I	-	1	0	REV3L	111839407	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.823000	0.62694	2.121000	0.65114	0.533000	0.62120	ATC	.	.		0.234	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		C	111732714	T	C	111732714	3	2	341	1	0	0	0	0	1	0	0	0	13255	1435	50	2	9139	2	REV3L	6	111732714	Missense_Mutation	SNP	T	TCGA-RG-A7D4-01A-12D-A33Q-10	5179983	111732714	59382353	49	47150										
KIAA1244	57221	hgsc.bcm.edu	37	chr6	138619874	138619874	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	gaagcactcttccgacctttCgagcgcattatgcagctgga	10	12	1	0			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr6:138619874C>T	ENST00000251691.4	+	22	3946	c.3780C>T	c.(3778-3780)ttC>ttT	p.F1260F		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		TCCGACCTTTCGAGCGCATTA	0.488																																					p.F1260F		Atlas-SNP	.											.	KIAA1244	236	.	0			c.C3780T						.						119	99	105					6																	138619874		2203	4300	6503	SO:0001819	synonymous_variant	57221	exon22			ACCTTTCGAGCGC	AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	21213	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 33"		"chromosome 6 open reading frame 92"	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.3780C>T	chr6.hg19:g.138619874C>T		72.0	0.0		95.0	8.0	NM_020340		Silent	SNP	ENST00000251691.4	hg19	CCDS5189.2																																																																																			.	.		0.488	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340		T	138619874	C	T	138619874	2	4	341	1	0	0	0	0	0	0	0	1	8226	883	31	1		1	KIAA1244	6	138619874	Silent	SNP	C	TCGA-RG-A7D4-01A-12D-A33Q-10	26887160	138619874	32495193	50	47151										
CCR6	1235	hgsc.bcm.edu	37	chr6	167550515	167550515	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	ggtgcttgtgtttctggcttGtcagattcctcataacatgg	11	8	3	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr6:167550515G>A	ENST00000341935.5	+	3	1349	c.797G>A	c.(796-798)tGt>tAt	p.C266Y	CCR6_ENST00000400926.2_Missense_Mutation_p.C266Y|CCR6_ENST00000349984.4_Missense_Mutation_p.C266Y|RP11-517H2.6_ENST00000609590.1_RNA	NM_031409.3	NP_113597.2	P51684	CCR6_HUMAN	chemokine (C-C motif) receptor 6	266					cellular component movement (GO:0006928)|cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|humoral immune response (GO:0006959)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)|receptor activity (GO:0004872)			endometrium(3)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)	14		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;8.21e-20)|BRCA - Breast invasive adenocarcinoma(81;4.55e-06)|GBM - Glioblastoma multiforme(31;0.00507)		TTTCTGGCTTGTCAGATTCCT	0.438																																					p.C266Y		Atlas-SNP	.											.	CCR6	36	.	0			c.G797A						.						161	159	159					6																	167550515		2203	4300	6503	SO:0001583	missense	1235	exon3			TGGCTTGTCAGAT	U68030	CCDS5298.1	6q27	2012-08-08			ENSG00000112486	ENSG00000112486		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1607	protein-coding gene	gene with protein product		601835		STRL22		8886020	Standard	NM_031409		Approved	CKR-L3, GPR-CY4, CMKBR6, GPR29, DRY-6, DCR2, BN-1, CD196	uc010kkm.3	P51684	OTTHUMG00000016015	ENST00000341935.5:c.797G>A	chr6.hg19:g.167550515G>A	ENSP00000343952:p.Cys266Tyr	58.0	0.0		77.0	16.0	NM_004367	E1P5C6|P78553|Q92846	Missense_Mutation	SNP	ENST00000341935.5	hg19	CCDS5298.1	.	.	.	.	.	.	.	.	.	.	G	14.81	2.647476	0.47258	.	.	ENSG00000112486	ENST00000400926;ENST00000341935;ENST00000349984	T;T;T	0.54279	0.58;0.58;0.58	4.79	3.85	0.44370	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	U	0.000000	T	0.62073	0.2398	H	0.96175	3.78	0.80722	D	1	P	0.40211	0.707	P	0.49421	0.61	T	0.70389	-0.4885	10	0.11794	T	0.64	.	13.1531	0.59500	0.0:0.0:0.8397:0.1603	.	266	P51684	CCR6_HUMAN	Y	266	ENSP00000383715:C266Y;ENSP00000343952:C266Y;ENSP00000339393:C266Y	ENSP00000343952:C266Y	C	+	2	0	CCR6	167470505	1.000000	0.71417	0.876000	0.34364	0.613000	0.37349	6.894000	0.75655	2.345000	0.79718	0.655000	0.94253	TGT	.	.		0.438	CCR6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043118.1			A	167550515	G	A	167550515	3	1	341	1	0	0	0	0	1	0	0	0	2947	1377	48	3	803	3	CCR6	6	167550515	Missense_Mutation	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10	28930641	167550515	3564552	51	47152										
MTMR9	66036	hgsc.bcm.edu	37	chr8	11167038	11167038	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	ctttcttacttttaaaaggtAtcacattcttcaggagagct	6	8	4	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr8:11167038A>T	ENST00000221086.3	+	6	1285	c.812A>T	c.(811-813)tAt>tTt	p.Y271F	MTMR9_ENST00000526292.1_Missense_Mutation_p.Y186F	NM_015458.3	NP_056273.2	Q96QG7	MTMR9_HUMAN	myotubularin related protein 9	271	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.					cytoplasm (GO:0005737)	enzyme regulator activity (GO:0030234)|phosphatase activity (GO:0016791)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|urinary_tract(2)	16			STAD - Stomach adenocarcinoma(15;0.215)	COAD - Colon adenocarcinoma(149;0.0678)		TTTAAAAGGTATCACATTCTT	0.358																																					p.Y271F		Atlas-SNP	.											.	MTMR9	58	.	0			c.A812T						.						65	66	66					8																	11167038		2203	4300	6503	SO:0001583	missense	66036	exon6			AAAGGTATCACAT	AJ297823	CCDS5979.1	8p23-p22	2011-06-09	2002-09-05	2002-09-06	ENSG00000104643	ENSG00000104643		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	14596	protein-coding gene	gene with protein product		606260	"myotubularin related protein 8"	C8orf9, MTMR8		11472061, 11896452, 12890864	Standard	NM_015458		Approved	DKFZp434K171, LIP-STYX	uc003wtm.3	Q96QG7	OTTHUMG00000090647	ENST00000221086.3:c.812A>T	chr8.hg19:g.11167038A>T	ENSP00000221086:p.Tyr271Phe	45.0	0.0		44.0	15.0	NM_015458	B7Z291|Q52LU3|Q8WW11|Q96QG6|Q9NX50	Missense_Mutation	SNP	ENST00000221086.3	hg19	CCDS5979.1	.	.	.	.	.	.	.	.	.	.	A	4.479	0.088867	0.08583	.	.	ENSG00000104643	ENST00000221086;ENST00000526292	D;D	0.89810	-2.57;-2.57	5.65	4.45	0.53987	Myotubularin phosphatase domain (1);	0.387780	0.31092	N	0.008272	T	0.77039	0.4072	N	0.11201	0.11	0.35294	D	0.782445	B	0.02656	0.0	B	0.06405	0.002	T	0.76860	-0.2803	10	0.41790	T	0.15	.	9.7397	0.40411	0.6896:0.0:0.0:0.3104	.	271	Q96QG7	MTMR9_HUMAN	F	271;186	ENSP00000221086:Y271F;ENSP00000433239:Y186F	ENSP00000221086:Y271F	Y	+	2	0	MTMR9	11204448	0.973000	0.33851	0.996000	0.52242	0.659000	0.38960	1.766000	0.38491	2.153000	0.67306	0.477000	0.44152	TAT	.	.		0.358	MTMR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207307.2	NM_015458		T	11167038	A	T	11167038	3	4	341	1	0	0	0	0	1	0	0	0	9959	449	16	4	834	4	MTMR9	8	11167038	Missense_Mutation	SNP	A	TCGA-RG-A7D4-01A-12D-A33Q-10		11167038	135196984	52	47153										
CPA6	57094	hgsc.bcm.edu	37	chr8	68658304	68658304	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	cggttgcagaatcttcaaaaAgagccagcaaagaggcagga	12	8	2	3	rs147067921		TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr8:68658304A>G	ENST00000297770.4	-	1	276	c.61T>C	c.(61-63)Ttt>Ctt	p.F21L	CPA6_ENST00000297769.4_5'UTR|CPA6_ENST00000518549.1_Missense_Mutation_p.F21L	NM_020361.4	NP_065094.3	Q8N4T0	CBPA6_HUMAN	carboxypeptidase A6	21						proteinaceous extracellular matrix (GO:0005578)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(5)	26			Epithelial(68;0.04)|OV - Ovarian serous cystadenocarcinoma(28;0.0593)|all cancers(69;0.136)			ATCTTCAAAAAGAGCCAGCAA	0.502																																					p.F21L		Atlas-SNP	.											.	CPA6	69	.	0			c.T61C						.						49	48	49					8																	68658304		2203	4300	6503	SO:0001583	missense	57094	exon1			TCAAAAAGAGCCA	AF221594	CCDS6200.1	8q12.3	2012-02-10			ENSG00000165078	ENSG00000165078			17245	protein-coding gene	gene with protein product		609562				11836249	Standard	NM_020361		Approved	CPAH	uc003xxq.4	Q8N4T0	OTTHUMG00000164575	ENST00000297770.4:c.61T>C	chr8.hg19:g.68658304A>G	ENSP00000297770:p.Phe21Leu	126.0	0.0		225.0	13.0	NM_020361	Q8NEX8|Q8TDE8|Q9NRI9	Missense_Mutation	SNP	ENST00000297770.4	hg19	CCDS6200.1	.	.	.	.	.	.	.	.	.	.	A	6.770	0.511021	0.12883	.	.	ENSG00000165078	ENST00000297770;ENST00000518549	T;T	0.34072	1.38;1.38	5.62	-1.87	0.07737	.	0.549980	0.17929	N	0.157246	T	0.13372	0.0324	N	0.08118	0	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.40627	-0.9553	10	0.02654	T	1	.	10.1243	0.42641	0.4579:0.0:0.5421:0.0	.	21;21	Q8N4T0-2;Q8N4T0	.;CBPA6_HUMAN	L	21	ENSP00000297770:F21L;ENSP00000431112:F21L	ENSP00000297770:F21L	F	-	1	0	CPA6	68820858	0.953000	0.32496	0.987000	0.45799	0.997000	0.91878	-0.102000	0.10956	-0.311000	0.08754	0.533000	0.62120	TTT	.	A|1.000;T|0.000		0.502	CPA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379296.2	NM_020361		G	68658304	A	G	68658304	3	3	341	1	0	0	0	0	1	0	0	0	3796	72	3	2	1296	2	CPA6	8	68658304	Missense_Mutation	SNP	A	TCGA-RG-A7D4-01A-12D-A33Q-10	57491266	68658304	77705718	53	47154										
PREX2	80243	hgsc.bcm.edu	37	chr8	69020369	69020369	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	tcgtgtactgaagaatagggCctggcctacttttaaacagg	11	8	0	2			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr8:69020369C>T	ENST00000288368.4	+	24	3018	c.2741C>T	c.(2740-2742)gCc>gTc	p.A914V		NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	914					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						AAGAATAGGGCCTGGCCTACT	0.393																																					p.A914V		Atlas-SNP	.											.	PREX2	614	.	0			c.C2741T						.						84	74	77					8																	69020369		2203	4300	6503	SO:0001583	missense	80243	exon24			ATAGGGCCTGGCC	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.2741C>T	chr8.hg19:g.69020369C>T	ENSP00000288368:p.Ala914Val	50.0	0.0		94.0	5.0	NM_024870	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	hg19	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	C	11.74	1.730242	0.30684	.	.	ENSG00000046889	ENST00000288368;ENST00000396539	T	0.27720	1.65	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.22475	0.0542	N	0.25286	0.73	0.80722	D	1	B;B	0.26195	0.144;0.0	B;B	0.27076	0.076;0.002	T	0.07028	-1.0794	10	0.02654	T	1	.	20.1634	0.98142	0.0:1.0:0.0:0.0	.	979;914	Q70Z35-2;Q70Z35	.;PREX2_HUMAN	V	914;980	ENSP00000288368:A914V	ENSP00000288368:A914V	A	+	2	0	PREX2	69182923	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.773000	0.95371	0.655000	0.94253	GCC	.	.		0.393	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		T	69020369	C	T	69020369	3	4	341	1	0	0	0	0	1	0	0	0	12489	739	26	3	3064	3	PREX2	8	69020369	Missense_Mutation	SNP	C	TCGA-RG-A7D4-01A-12D-A33Q-10	362065	69020369	77343653	54	47155										
FAM164A	51101	hgsc.bcm.edu	37	chr8	79598833	79598833	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	cctcctcctcctccaccttcTtatgatcctggtatttggaa	5	15	1	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr8:79598833T>C	ENST00000263849.4	+	4	444	c.342T>C	c.(340-342)tcT>tcC	p.S114S	ZC2HC1A_ENST00000521176.1_3'UTR	NM_016010.2	NP_057094.2	Q96GY0	ZC21A_HUMAN	zinc finger, C2HC-type containing 1A	114							metal ion binding (GO:0046872)										CTCCACCTTCTTATGATCCTG	0.378																																					p.S114S		Atlas-SNP	.											.	.	.	.	0			c.T342C						.						55	55	55					8																	79598833		2203	4300	6503	SO:0001819	synonymous_variant	51101	exon4			ACCTTCTTATGAT		CCDS6223.1	8q21.11	2013-01-10	2012-02-03	2012-02-03	ENSG00000104427	ENSG00000104427		"Zinc fingers, C2HC-type containing"	24277	protein-coding gene	gene with protein product			"chromosome 8 open reading frame 70", "family with sequence similarity 164, member A"	C8orf70, FAM164A		10810093	Standard	NM_016010		Approved	CGI-62	uc003ybd.3	Q96GY0	OTTHUMG00000164619	ENST00000263849.4:c.342T>C	chr8.hg19:g.79598833T>C		127.0	0.0		270.0	37.0	NM_016010	Q9Y372	Silent	SNP	ENST00000263849.4	hg19	CCDS6223.1																																																																																			.	.		0.378	ZC2HC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379423.2	NM_016010		C	79598833	T	C	79598833	2	2	341	1	0	0	0	0	0	0	0	1	5483	1596	56	2		2	FAM164A	8	79598833	Silent	SNP	T	TCGA-RG-A7D4-01A-12D-A33Q-10	10578464	79598833	66765189	55	47156										
SLC25A32	81034	hgsc.bcm.edu	37	chr8	104427069	104427069	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	cgcaaggttggataagacgcCgccgctcacgcccgctatca	11	15	2	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr8:104427069C>T	ENST00000297578.4	-	1	263	c.97G>A	c.(97-99)Ggc>Agc	p.G33S	DCAF13_ENST00000519682.1_5'Flank|DCAF13_ENST00000297579.5_5'UTR|DCAF13_ENST00000521971.1_5'Flank|SLC25A32_ENST00000543107.1_5'UTR|DCAF13_ENST00000521716.1_5'Flank	NM_030780.3	NP_110407.2	Q9H2D1	MFTC_HUMAN	solute carrier family 25 (mitochondrial folate carrier), member 32	33					folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|mitochondrial transport (GO:0006839)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	folic acid transporter activity (GO:0008517)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	9			OV - Ovarian serous cystadenocarcinoma(57;2.79e-06)|STAD - Stomach adenocarcinoma(118;0.197)		Folic Acid(DB00158)	GATAAGACGCCGCCGCTCACG	0.657																																					p.G33S		Atlas-SNP	.											.	SLC25A32	36	.	0			c.G97A						.						27	31	29					8																	104427069		2203	4300	6503	SO:0001583	missense	81034	exon1			AGACGCCGCCGCT	AF283645	CCDS6300.1	8q22.3	2013-05-22	2013-03-15		ENSG00000164933	ENSG00000164933		"Solute carriers"	29683	protein-coding gene	gene with protein product		610815	"solute carrier family 25, member 32"			10978331	Standard	NM_030780		Approved	MFTC	uc003yll.4	Q9H2D1	OTTHUMG00000164790	ENST00000297578.4:c.97G>A	chr8.hg19:g.104427069C>T	ENSP00000297578:p.Gly33Ser	113.0	0.0		173.0	102.0	NM_030780	Q96JZ6|Q96SU7	Missense_Mutation	SNP	ENST00000297578.4	hg19	CCDS6300.1	.	.	.	.	.	.	.	.	.	.	C	36	5.927375	0.97110	.	.	ENSG00000164933	ENST00000297578;ENST00000424899	D	0.85171	-1.95	5.02	5.02	0.67125	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.93854	0.8034	M	0.89715	3.055	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94896	0.8052	10	0.87932	D	0	-0.8709	18.1346	0.89614	0.0:1.0:0.0:0.0	.	33	Q9H2D1	MFTC_HUMAN	S	33;17	ENSP00000297578:G33S	ENSP00000297578:G33S	G	-	1	0	SLC25A32	104496245	1.000000	0.71417	1.000000	0.80357	0.735000	0.41995	7.315000	0.78998	2.590000	0.87494	0.655000	0.94253	GGC	.	.		0.657	SLC25A32-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380290.2	NM_030780		T	104427069	C	T	104427069	3	4	341	1	0	0	0	0	1	0	0	0	14511	652	23	1	878	1	SLC25A32	8	104427069	Missense_Mutation	SNP	C	TCGA-RG-A7D4-01A-12D-A33Q-10	24828236	104427069	41936953	56	47157										
ADAMTSL1	92949	hgsc.bcm.edu	37	chr9	18888005	18888005	+	Frame_Shift_Del	DEL	G	G	-													0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	gccttgctcagaatgaggcaGgggtgctcatgcagaaggca							TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr9:18888005delG	ENST00000380548.4	+	24	4765	c.4426delG	c.(4426-4428)gggfs	p.G1476fs	ADAMTSL1_ENST00000380545.5_Frame_Shift_Del_p.G177fs	NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	1476	Ig-like C2-type 4.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(2)|lung(17)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(50;1.29e-17)		GAATGAGGCAGGGGTGCTCAT	0.493																																					p.A1475fs		Atlas-Indel,Pindel	.											.	ADAMTSL1	306	.	0			c.4425delA						.						75	70	71					9																	18888005		1936	4146	6082	SO:0001589	frameshift_variant	92949	exon24			.	AF176313	CCDS6485.1, CCDS47954.1	9p21.3	2013-01-11			ENSG00000178031	ENSG00000178031		"Immunoglobulin superfamily / I-set domain containing"	14632	protein-coding gene	gene with protein product	"punctin"	609198	"chromosome 9 open reading frame 94"	C9orf94		9628581, 11805097	Standard	NM_001040272		Approved	ADAMTSR1, FLJ35283	uc003zne.4	Q8N6G6	OTTHUMG00000019604	ENST00000380548.4:c.4426delG	chr9.hg19:g.18888005delG	ENSP00000369921:p.Gly1476fs	109.0	0.0		95.0	16.0	NM_001040272	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Frame_Shift_Del	DEL	ENST00000380548.4	hg19	CCDS47954.1																																																																																			.	.		0.493	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1			-	18888005	G	-	18888005	7	5	341	1	0	1	0	1	0	0	0	0	274	1000	35	0	4524	0	ADAMTSL1	9	18888005	Frame_Shift_Del	DEL	G	TCGA-RG-A7D4-01A-12D-A33Q-10		18888005	122325426	57	47158										
IFNA10	3446	hgsc.bcm.edu	37	chr9	21206860	21206860	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	tgctggatcatctcatggagGacagagatggcttgagcctt	13	8	2	2			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr9:21206860G>A	ENST00000357374.2	-	1	282	c.237C>T	c.(235-237)gtC>gtT	p.V79V		NM_002171.1	NP_002162.1	P01566	IFN10_HUMAN	interferon, alpha 10	79					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			endometrium(1)|large_intestine(3)|liver(1)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	16				Lung(24;1.26e-23)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.17)		TCTCATGGAGGACAGAGATGG	0.488																																					p.V79V		Atlas-SNP	.											.	IFNA10	29	.	0			c.C237T						.						54	59	57					9																	21206860		2201	4297	6498	SO:0001819	synonymous_variant	3446	exon1			ATGGAGGACAGAG		CCDS6499.1	9p22	2010-08-24			ENSG00000186803	ENSG00000186803		"Interferons"	5418	protein-coding gene	gene with protein product		147577				1385305	Standard	NM_002171		Approved	IFN-alphaC	uc003zoq.1	P01566	OTTHUMG00000019658	ENST00000357374.2:c.237C>T	chr9.hg19:g.21206860G>A		151.0	0.0		154.0	14.0	NM_002171	Q5VV13	Silent	SNP	ENST00000357374.2	hg19	CCDS6499.1																																																																																			.	.		0.488	IFNA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051887.1	NM_002171		A	21206860	G	A	21206860	2	1	341	1	0	0	0	0	0	0	0	1	7541	1161	41	3		3	IFNA10	9	21206860	Silent	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10	2318855	21206860	120006571	58	47159										
DCAF12	25853	hgsc.bcm.edu	37	chr9	34089528	34089528	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	ctcggatgtcatagaacagcAgggagccctgccctgttccc	11	14	1	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr9:34089528A>G	ENST00000361264.4	-	8	1426	c.1085T>C	c.(1084-1086)cTg>cCg	p.L362P	RP11-537H15.3_ENST00000448245.1_RNA	NM_015397.3	NP_056212.1	Q5T6F0	DCA12_HUMAN	DDB1 and CUL4 associated factor 12	362					protein ubiquitination (GO:0016567)	centrosome (GO:0005813)|Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)				breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)	11						ATAGAACAGCAGGGAGCCCTG	0.512																																					p.L362P		Atlas-SNP	.											.	DCAF12	37	.	0			c.T1085C						.						87	79	81					9																	34089528		2203	4300	6503	SO:0001583	missense	25853	exon8			AACAGCAGGGAGC	AB067479	CCDS6549.1	9p11.2	2013-01-09	2009-07-17	2009-07-17	ENSG00000198876	ENSG00000198876		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	19911	protein-coding gene	gene with protein product	"cancer/testis antigen 102"		"KIAA1892", "WD repeat domain 40A"	KIAA1892, WDR40A		11572484, 9110174	Standard	NM_015397		Approved	DKFZP434O125, MGC1058, CT102, TCC52	uc003ztt.2	Q5T6F0	OTTHUMG00000019806	ENST00000361264.4:c.1085T>C	chr9.hg19:g.34089528A>G	ENSP00000355114:p.Leu362Pro	45.0	0.0		52.0	23.0	NM_015397	A8KA70|D3DRL6|Q5T6E9|Q5T6F1|Q6P3V0|Q7L4F8|Q96PZ5|Q9NXA9|Q9UFJ1	Missense_Mutation	SNP	ENST00000361264.4	hg19	CCDS6549.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.415234	0.83449	.	.	ENSG00000198876	ENST00000361264	T	0.68624	-0.34	4.94	4.94	0.65067	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.64402	D	0.000001	T	0.81983	0.4938	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84951	0.0871	10	0.87932	D	0	-1.9753	14.2564	0.66055	1.0:0.0:0.0:0.0	.	362	Q5T6F0	DCA12_HUMAN	P	362	ENSP00000355114:L362P	ENSP00000355114:L362P	L	-	2	0	DCAF12	34079528	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.518000	0.90559	1.853000	0.53794	0.533000	0.62120	CTG	.	.		0.512	DCAF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052133.2	NM_015397		G	34089528	A	G	34089528	3	3	341	1	0	0	0	0	1	0	0	0	4265	188	7	2	284	2	DCAF12	9	34089528	Missense_Mutation	SNP	A	TCGA-RG-A7D4-01A-12D-A33Q-10	12882668	34089528	107123903	59	47160										
VPS13A	23230	hgsc.bcm.edu	37	chr9	79820239	79820239	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	aaaaatgtaggtaatcttaaActtataattccatggaaaaa	5	4	1	0			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr9:79820239A>G	ENST00000360280.3	+	4	458	c.198A>G	c.(196-198)aaA>aaG	p.K66K	VPS13A_ENST00000376634.4_Silent_p.K66K|VPS13A_ENST00000357409.5_Silent_p.K66K|VPS13A_ENST00000376636.3_Silent_p.K66K	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	66					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						GTAATCTTAAACTTATAATTC	0.289																																					p.K66K		Atlas-SNP	.											.	VPS13A	735	.	0			c.A198G						.						35	41	39					9																	79820239		2197	4275	6472	SO:0001819	synonymous_variant	23230	exon4			TCTTAAACTTATA	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"chorein"	605978	"chorea acanthocytosis", "vacuolar protein sorting 13A (yeast)"	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.198A>G	chr9.hg19:g.79820239A>G		213.0	0.0		235.0	56.0	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Silent	SNP	ENST00000360280.3	hg19	CCDS6655.1																																																																																			.	.		0.289	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		G	79820239	A	G	79820239	2	3	341	1	0	0	0	0	0	0	0	1	17204	40	2	2		2	VPS13A	9	79820239	Silent	SNP	A	TCGA-RG-A7D4-01A-12D-A33Q-10	45730711	79820239	61393192	60	47161										
LRSAM1	90678	hgsc.bcm.edu	37	chr9	130242226	130242226	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	cggaacagaacatttccagcCggatccagaagctgctgcag	11	12	0	2			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr9:130242226C>T	ENST00000323301.4	+	13	1616	c.1012C>T	c.(1012-1014)Cgg>Tgg	p.R338W	LRSAM1_ENST00000483302.1_3'UTR|LRSAM1_ENST00000373322.1_Missense_Mutation_p.R338W|LRSAM1_ENST00000373324.4_Missense_Mutation_p.R338W|LRSAM1_ENST00000300417.6_Missense_Mutation_p.R338W	NM_138361.5	NP_612370.3	Q6UWE0	LRSM1_HUMAN	leucine rich repeat and sterile alpha motif containing 1	338					cell death (GO:0008219)|negative regulation of endocytosis (GO:0045806)|protein autoubiquitination (GO:0051865)|protein catabolic process (GO:0030163)|protein polyubiquitination (GO:0000209)|ubiquitin-dependent endocytosis (GO:0070086)|viral budding (GO:0046755)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(2)	16						CATTTCCAGCCGGATCCAGAA	0.657																																					p.R338W		Atlas-SNP	.											.	LRSAM1	40	.	0			c.C1012T						.						64	68	66					9																	130242226		2203	4300	6503	SO:0001583	missense	90678	exon14			TCCAGCCGGATCC	AK056203	CCDS6873.1, CCDS55347.1	9q34.13	2014-09-17			ENSG00000148356	ENSG00000148356		"Sterile alpha motif (SAM) domain containing"	25135	protein-coding gene	gene with protein product		610933				12975309	Standard	NM_001005373		Approved	FLJ31641	uc004brd.2	Q6UWE0	OTTHUMG00000020701	ENST00000323301.4:c.1012C>T	chr9.hg19:g.130242226C>T	ENSP00000322937:p.Arg338Trp	166.0	0.0		144.0	12.0	NM_001005373	Q5VVV0|Q8NB40|Q96GT5|Q96MX5|Q96MZ7	Missense_Mutation	SNP	ENST00000323301.4	hg19	CCDS6873.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.410992	0.83340	.	.	ENSG00000148356	ENST00000300417;ENST00000373324;ENST00000323301;ENST00000373322	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	5.86	4.96	0.65561	.	0.049793	0.85682	N	0.000000	T	0.61912	0.2385	M	0.67953	2.075	0.58432	D	0.999995	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.993	T	0.62714	-0.6796	10	0.44086	T	0.13	-43.5527	14.2533	0.66035	0.15:0.85:0.0:0.0	.	338;338	Q6UWE0-2;Q6UWE0	.;LRSM1_HUMAN	W	338	ENSP00000300417:R338W;ENSP00000362421:R338W;ENSP00000322937:R338W;ENSP00000362419:R338W	ENSP00000300417:R338W	R	+	1	2	LRSAM1	129282047	0.995000	0.38212	0.925000	0.36789	0.985000	0.73830	3.379000	0.52440	1.473000	0.48159	0.655000	0.94253	CGG	.	.		0.657	LRSAM1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054164.1	NM_138361		T	130242226	C	T	130242226	3	4	341	1	0	0	0	0	1	0	0	0	9052	643	23	1	1058	1	LRSAM1	9	130242226	Missense_Mutation	SNP	C	TCGA-RG-A7D4-01A-12D-A33Q-10	50421987	130242226	10971205	61	47162										
COL5A1	1289	hgsc.bcm.edu	37	chr9	137713941	137713941	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	tgcattttctggtccttttcAgggtatcactggtccttctg	9	10	4	0			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr9:137713941A>T	ENST00000371817.3	+	59	4968		c.e59-1			NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1						axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		GGTCCTTTTCAGGGTATCACT	0.632																																					.		Atlas-SNP	.											.	COL5A1	323	.	0			c.4555-2A>T						.						103	96	99					9																	137713941		2203	4300	6503	SO:0001630	splice_region_variant	1289	exon59			CTTTTCAGGGTAT	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"Collagens"	2209	protein-coding gene	gene with protein product	"alpha 1 type V collagen"	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.4555-1A>T	chr9.hg19:g.137713941A>T		25.0	0.0		28.0	9.0	NM_000093	Q15094|Q5SUX4	Splice_Site	SNP	ENST00000371817.3	hg19	CCDS6982.1	.	.	.	.	.	.	.	.	.	.	A	19.91	3.914326	0.72983	.	.	ENSG00000130635	ENST00000371817;ENST00000355306	.	.	.	4.7	4.7	0.59300	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.8131	0.63274	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	COL5A1	136853762	1.000000	0.71417	0.883000	0.34634	0.913000	0.54294	9.171000	0.94802	1.739000	0.51704	0.448000	0.29417	.	.	.		0.632	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	Intron	T	137713941	A	T	137713941	5	4	341	1	0	0	0	0	0	0	1	0	3698	202	7	4	4787	4	COL5A1	9	137713941	Splice_Site	SNP	A	TCGA-RG-A7D4-01A-12D-A33Q-10	7471715	137713941	3499490	62	47163										
FAM171A1	221061	hgsc.bcm.edu	37	chr10	15255230	15255230	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	catccaggtacacgagctgcGtgtaggccgtgctgtctggg	15	11	1	0			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr10:15255230G>A	ENST00000378116.4	-	8	2363	c.2357C>T	c.(2356-2358)aCg>aTg	p.T786M	FAM171A1_ENST00000477161.1_5'Flank	NM_001010924.1	NP_001010924.1	Q5VUB5	F1711_HUMAN	family with sequence similarity 171, member A1	786						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(6)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	52						CACGAGCTGCGTGTAGGCCGT	0.612																																					p.T786M		Atlas-SNP	.											.	FAM171A1	252	.	0			c.C2357T						.						77	56	63					10																	15255230		2203	4300	6503	SO:0001583	missense	221061	exon8			AGCTGCGTGTAGG	AK022946	CCDS31154.1	10p13	2008-06-16	2008-06-16	2008-06-16	ENSG00000148468	ENSG00000148468			23522	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 38"	C10orf38			Standard	NM_001010924		Approved	FLJ12884	uc001iob.3	Q5VUB5	OTTHUMG00000017732	ENST00000378116.4:c.2357C>T	chr10.hg19:g.15255230G>A	ENSP00000367356:p.Thr786Met	136.0	0.0		101.0	11.0	NM_001010924	D3DRT9|Q32M49|Q8N4I0	Missense_Mutation	SNP	ENST00000378116.4	hg19	CCDS31154.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.339990	0.81911	.	.	ENSG00000148468	ENST00000378116;ENST00000396781	T	0.35421	1.31	5.25	5.25	0.73442	.	0.053602	0.64402	D	0.000001	T	0.59689	0.2212	M	0.63428	1.95	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.61073	-0.7136	10	0.72032	D	0.01	-24.5632	19.0487	0.93032	0.0:0.0:1.0:0.0	.	786	Q5VUB5	F1711_HUMAN	M	786;785	ENSP00000367356:T786M	ENSP00000367356:T786M	T	-	2	0	FAM171A1	15295236	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.002000	0.93572	2.724000	0.93272	0.563000	0.77884	ACG	.	.		0.612	FAM171A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046984.1	XM_167709		A	15255230	G	A	15255230	3	1	341	1	0	0	0	0	1	0	0	0	5495	1145	40	1	319	1	FAM171A1	10	15255230	Missense_Mutation	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10		15255230	120279517	63	47164										
RTKN2	219790	hgsc.bcm.edu	37	chr10	63976948	63976948	+	Frame_Shift_Del	DEL	G	G	-													0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	tggactgtaaaaacaatagaGtttacctcctcgcaaaacac					rs77837774		TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr10:63976948delG	ENST00000373789.3	-	9	1045	c.949delC	c.(949-951)ctcfs	p.L317fs	RTKN2_ENST00000315289.2_Frame_Shift_Del_p.L98fs|RTKN2_ENST00000395265.1_Frame_Shift_Del_p.L317fs	NM_145307.2	NP_660350.2	Q8IZC4	RTKN2_HUMAN	rhotekin 2	317	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				hemopoiesis (GO:0030097)|positive regulation of cell proliferation (GO:0008284)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Prostate(12;0.0297)|all_hematologic(501;0.215)					AAACAATAGAGTTTACCTCCT	0.328																																					p.L317fs		Atlas-Indel,Pindel	.											.	RTKN2	68	.	0			c.950delT						.						119	136	131					10																	63976948		2203	4300	6503	SO:0001589	frameshift_variant	219790	exon9			.	BC025765	CCDS7263.1, CCDS73140.1	10q21.3	2013-01-10	2007-12-14	2007-12-14	ENSG00000182010	ENSG00000182010		"Pleckstrin homology (PH) domain containing"	19364	protein-coding gene	gene with protein product			"pleckstrin homology domain containing, family K member 1"	PLEKHK1		15504364	Standard	NM_001282941		Approved	Em:AC024597.2, bA531F24.1, FLJ39352	uc001jlw.3	Q8IZC4	OTTHUMG00000018299	ENST00000373789.3:c.949delC	chr10.hg19:g.63976948delG	ENSP00000362894:p.Leu317fs	170.0	0.0		145.0	39.0	NM_145307	Q3ZCR1|Q68DZ6|Q8N8K1|Q8TAV2	Frame_Shift_Del	DEL	ENST00000373789.3	hg19	CCDS7263.1																																																																																			.	.		0.328	RTKN2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091618.1	NM_145307		-	63976948	G	-	63976948	7	5	341	1	0	1	0	1	0	0	0	0	13738	1029	36	0	896	0	RTKN2	10	63976948	Frame_Shift_Del	DEL	G	TCGA-RG-A7D4-01A-12D-A33Q-10	48721718	63976948	71557799	64	47165										
C10orf79	80217	hgsc.bcm.edu	37	chr10	105932273	105932273	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	atattttctagtttgtcattTtcttccatcatattcagaat	3	7	5	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr10:105932273T>G	ENST00000278064.2	-	20	2599	c.2274A>C	c.(2272-2274)gaA>gaC	p.E758D	WDR96_ENST00000428666.1_Missense_Mutation_p.E828D|WDR96_ENST00000357060.3_Missense_Mutation_p.E827D																NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(14)|lung(21)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						GTTTGTCATTTTCTTCCATCA	0.318																																					p.E827D		Atlas-SNP	.											.	WDR96	183	.	0			c.A2481C						.						76	68	71					10																	105932273		2202	4298	6500	SO:0001583	missense	80217	exon20			GTCATTTTCTTCC																												ENST00000278064.2:c.2274A>C	chr10.hg19:g.105932273T>G	ENSP00000278064:p.Glu758Asp	45.0	0.0		40.0	11.0	NM_025145		Missense_Mutation	SNP	ENST00000278064.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.78|14.78	2.636559|2.636559	0.47049|0.47049	.|.	.|.	ENSG00000197748|ENSG00000197748	ENST00000357060;ENST00000428666;ENST00000278064|ENST00000434629	T;T;T|.	0.16743|.	2.32;2.32;2.34|.	5.59|5.59	3.19|3.19	0.36642|0.36642	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.55924|0.55924	0.1951|0.1951	M|M	0.71581|0.71581	2.175|2.175	0.34078|0.34078	D|D	0.659268|0.659268	P;P;P|.	0.45474|.	0.707;0.859;0.859|.	B;B;B|.	0.41571|.	0.286;0.36;0.334|.	T|T	0.62158|0.62158	-0.6913|-0.6913	10|5	0.52906|.	T|.	0.07|.	.|.	4.9171|4.9171	0.13851|0.13851	0.138:0.1443:0.0:0.7177|0.138:0.1443:0.0:0.7177	.|.	828;828;827|.	G5E9L1;B4DHB6;Q8NDM7|.	.;.;WDR96_HUMAN|.	D|T	827;828;758|188	ENSP00000349568:E827D;ENSP00000400289:E828D;ENSP00000278064:E758D|.	ENSP00000278064:E758D|.	E|K	-|-	3|2	2|0	WDR96|WDR96	105922263|105922263	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.866000|0.866000	0.49608|0.49608	0.891000|0.891000	0.28309|0.28309	0.377000|0.377000	0.24735|0.24735	0.528000|0.528000	0.53228|0.53228	GAA|AAA	.	.		0.318	WDR96-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050200.1			G	105932273	T	G	105932273	3	3	341	1	0	0	0	0	1	0	0	0	1620	1838	64	5	2592	5	C10orf79	10	105932273	Missense_Mutation	SNP	T	TCGA-RG-A7D4-01A-12D-A33Q-10	41955325	105932273	29602474	65	47166										
NRAP	3026	hgsc.bcm.edu	37	chr10	115349517	115349517	+	IGR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	ggagccaggaggggtccagcCaacacctctggtcaggttca	14	12	3	0			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr10:115349517C>T	ENST00000351270.3	+	0	3009				NRAP_ENST00000360478.3_Missense_Mutation_p.G1631S|NRAP_ENST00000359988.3_Missense_Mutation_p.G1666S|NRAP_ENST00000369358.4_Missense_Mutation_p.G1674S|NRAP_ENST00000369360.3_Missense_Mutation_p.G1639S	NM_004132.3	NP_004123.1	Q14520	HABP2_HUMAN	hyaluronan binding protein 2						cell adhesion (GO:0007155)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	glycosaminoglycan binding (GO:0005539)|serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	23		Colorectal(252;0.0233)|Breast(234;0.0672)		Epithelial(162;0.00319)|all cancers(201;0.0112)	Hyaluronan(DB08818)	GGGGTCCAGCCAACACCTCTG	0.552																																					p.G1666S		Atlas-SNP	.											.	NRAP	208	.	0			c.G4996A						.						74	71	72					10																	115349517		2203	4300	6503	SO:0001628	intergenic_variant	4892	exon41			TCCAGCCAACACC		CCDS7577.1, CCDS53579.1	10q25.3	2008-08-01	2001-11-28		ENSG00000148702	ENSG00000148702			4798	protein-coding gene	gene with protein product	"plasma hyaluronan binding protein", "factor VII activating protein"	603924	"hyaluronan-binding protein 2"			8827452, 12437095	Standard	NM_004132		Approved	HABP, PHBP, HGFAL, FSAP	uc001lai.4	Q14520	OTTHUMG00000019073		chr10.hg19:g.115349517C>T		44.0	0.0		64.0	7.0	NM_001261463	A8K467|B7Z8U5|F5H5M6|O00663	Missense_Mutation	SNP	ENST00000351270.3	hg19	CCDS7577.1	.	.	.	.	.	.	.	.	.	.	C	36	5.805647	0.96967	.	.	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478;ENST00000369350	T;T;T;T	0.27720	1.83;1.83;1.78;1.65	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.58652	0.2137	M	0.70275	2.135	0.80722	D	1	B;D;D;D	0.89917	0.248;1.0;1.0;1.0	B;D;D;D	0.97110	0.206;1.0;1.0;1.0	T	0.56547	-0.7961	10	0.59425	D	0.04	.	20.3539	0.98825	0.0:1.0:0.0:0.0	.	788;1666;1631;1666	B1ANW7;A0AVL2;Q86VF7-4;Q86VF7	.;.;.;NRAP_HUMAN	S	1674;1639;1666;1631;788	ENSP00000358365:G1674S;ENSP00000358367:G1639S;ENSP00000353078:G1666S;ENSP00000353666:G1631S	ENSP00000353078:G1666S	G	-	1	0	NRAP	115339507	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.818000	0.86416	2.826000	0.97356	0.655000	0.94253	GGC	.	.		0.552	HABP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050428.1	NM_004132		T	115349517	C	T	115349517	1	4	341	0	1	0	0	0	0	0	0	0	10647	594	21	3		3	NRAP	10	115349517	IGR	SNP	C	TCGA-RG-A7D4-01A-12D-A33Q-10	9417244	115349517	20185230	66	47167										
NLRP14	338323	hgsc.bcm.edu	37	chr11	7063785	7063785	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	gtcaaaaccggtgcacagccAcagatcgtggtgcttcaggg	13	11	2	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr11:7063785A>G	ENST00000299481.4	+	4	874	c.528A>G	c.(526-528)ccA>ccG	p.P176P		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	176					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)			breast(3)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	21				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		GTGCACAGCCACAGATCGTGG	0.488																																					p.P176P		Atlas-SNP	.											.	NLRP14	187	.	0			c.A528G						.						101	106	104					11																	7063785		2201	4296	6497	SO:0001819	synonymous_variant	338323	exon4			ACAGCCACAGATC	BK001107	CCDS7776.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000158077		"Nucleotide-binding domain and leucine rich repeat containing"	22939	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 14"	609665	"NACHT, leucine rich repeat and PYD containing 14"	NALP14		12563287	Standard	NM_176822		Approved	NOD5, GC-LRR, Nalp-iota, PAN8, CLR11.2	uc001mfb.1	Q86W24		ENST00000299481.4:c.528A>G	chr11.hg19:g.7063785A>G		125.0	0.0		100.0	24.0	NM_176822	Q7RTR6	Silent	SNP	ENST00000299481.4	hg19	CCDS7776.1																																																																																			.	.		0.488	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822		G	7063785	A	G	7063785	2	3	341	1	0	0	0	0	0	0	0	1	10485	146	6	2		2	NLRP14	11	7063785	Silent	SNP	A	TCGA-RG-A7D4-01A-12D-A33Q-10		7063785	127942731	67	47168										
CTR9	9646	hgsc.bcm.edu	37	chr11	10785358	10785358	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	aagcttatcctaataattacGaaactatgaaaattctcggc	5	8	1	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr11:10785358G>A	ENST00000361367.2	+	9	1552	c.1126G>A	c.(1126-1128)Gaa>Aaa	p.E376K		NM_014633.3	NP_055448.1	Q6PD62	CTR9_HUMAN	CTR9, Paf1/RNA polymerase II complex component	376					cellular response to lipopolysaccharide (GO:0071222)|endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone H3-K4 trimethylation (GO:0080182)|histone monoubiquitination (GO:0010390)|interleukin-6-mediated signaling pathway (GO:0070102)|JAK-STAT cascade (GO:0007259)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K79 methylation (GO:2001162)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|transcriptionally active chromatin (GO:0035327)				breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(12)|ovary(2)|pancreas(1)|stomach(1)	40				all cancers(16;1.64e-07)|Epithelial(150;2.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		TAATAATTACGAAACTATGAA	0.348																																					p.E376K		Atlas-SNP	.											.	CTR9	94	.	0			c.G1126A						.						77	83	81					11																	10785358		2201	4294	6495	SO:0001583	missense	9646	exon9			AATTACGAAACTA	D63875	CCDS7805.1	11p15.3	2013-07-03	2013-07-03	2006-05-22	ENSG00000198730	ENSG00000198730		"Tetratricopeptide (TTC) repeat domain containing"	16850	protein-coding gene	gene with protein product		609366	"SH2 domain binding protein 1 (tetratricopeptide repeat containing)", "Ctr9, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)"	SH2BP1		8590280, 8636124	Standard	NM_014633		Approved	KIAA0155, TSBP, p150TSP	uc001mja.3	Q6PD62	OTTHUMG00000165789	ENST00000361367.2:c.1126G>A	chr11.hg19:g.10785358G>A	ENSP00000355013:p.Glu376Lys	55.0	0.0		64.0	8.0	NM_014633	D3DQV8|Q15015	Missense_Mutation	SNP	ENST00000361367.2	hg19	CCDS7805.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.769608	0.90020	.	.	ENSG00000198730	ENST00000361367	T	0.52057	0.68	5.62	4.71	0.59529	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.70842	0.3270	M	0.87758	2.905	0.80722	D	1	D	0.89917	1.0	D	0.66351	0.943	T	0.76846	-0.2808	10	0.56958	D	0.05	-28.0406	15.0528	0.71888	0.0687:0.0:0.9313:0.0	.	376	Q6PD62	CTR9_HUMAN	K	376	ENSP00000355013:E376K	ENSP00000355013:E376K	E	+	1	0	CTR9	10741934	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.674000	0.98633	1.513000	0.48852	0.655000	0.94253	GAA	.	.		0.348	CTR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386215.1	NM_014633		A	10785358	G	A	10785358	3	1	341	1	0	0	0	0	1	0	0	0	4026	1059	37	1	1160	1	CTR9	11	10785358	Missense_Mutation	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10	3721573	10785358	124221158	68	47169										
OR4A5	81318	hgsc.bcm.edu	37	chr11	51411561	51411561	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	cgtatatattaaaggactcaGcatgtgtgtgataatggtat	10	4	1	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr11:51411561G>A	ENST00000319760.6	-	1	887	c.835C>T	c.(835-837)Ctg>Ttg	p.L279L		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, member 5	279						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(28)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	49		all_lung(304;0.236)				AAAGGACTCAGCATGTGTGTG	0.318																																					p.L279L		Atlas-SNP	.											.	OR4A5	116	.	0			c.C835T						.						43	44	44					11																	51411561		2201	4295	6496	SO:0001819	synonymous_variant	81318	exon1			GACTCAGCATGTG	AB065506	CCDS73289.1	11p11.12	2012-08-09			ENSG00000221840	ENSG00000221840		"GPCR / Class A : Olfactory receptors"	15162	protein-coding gene	gene with protein product							Standard	NM_001005272		Approved		uc001nhi.2	Q8NH83	OTTHUMG00000166764	ENST00000319760.6:c.835C>T	chr11.hg19:g.51411561G>A		88.0	0.0		81.0	15.0	NM_001005272	Q6IF84	Silent	SNP	ENST00000319760.6	hg19	CCDS31497.1																																																																																			.	.		0.318	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272		A	51411561	G	A	51411561	2	1	341	1	0	0	0	0	0	0	0	1	11052	962	34	3		3	OR4A5	11	51411561	Silent	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10	40626203	51411561	83594955	69	47170										
GPR137	56834	hgsc.bcm.edu	37	chr11	64055851	64055851	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	tggggaacaaaggctacctgGtatttggcctcatcctcttc	10	11	2	0			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr11:64055851G>A	ENST00000313074.3	+	5	928	c.823G>A	c.(823-825)Gta>Ata	p.V275I	KCNK4_ENST00000538767.1_5'Flank|GPR137_ENST00000411458.1_Missense_Mutation_p.V333I|GPR137_ENST00000377702.4_Missense_Mutation_p.V225I|GPR137_ENST00000438980.2_Missense_Mutation_p.V275I|GPR137_ENST00000539851.1_Missense_Mutation_p.V275I	NM_020155.3	NP_064540.3	Q96N19	G137A_HUMAN	G protein-coupled receptor 137	275						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(1)|lung(4)|skin(1)	10						AGGCTACCTGGTATTTGGCCT	0.632																																					p.V333I		Atlas-SNP	.											.	GPR137	52	.	0			c.G997A						.						150	144	146					11																	64055851		2201	4297	6498	SO:0001583	missense	56834	exon7			TACCTGGTATTTG	AJ250392	CCDS8066.1, CCDS53655.1, CCDS53656.1, CCDS53657.1, CCDS53658.1	11q13.1	2014-02-12	2006-01-26		ENSG00000173264	ENSG00000173264		"GPCR / Unclassified : 7TM orphan receptors"	24300	protein-coding gene	gene with protein product						10873569, 12732197	Standard	NM_001170726		Approved	C11orf4, GPR137A, TM7SF1L1	uc010rni.2	Q96N19	OTTHUMG00000167817	ENST00000313074.3:c.823G>A	chr11.hg19:g.64055851G>A	ENSP00000321698:p.Val275Ile	50.0	0.0		31.0	7.0	NM_001170726	B4DTG7|B7Z7M1|Q4G0Y9|Q8N4K6	Missense_Mutation	SNP	ENST00000313074.3	hg19	CCDS8066.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.5|20.5	4.005876|4.005876	0.74932|0.74932	.|.	.|.	ENSG00000173264|ENSG00000173264	ENST00000536282|ENST00000411458;ENST00000539851;ENST00000377702;ENST00000438980;ENST00000313074	.|T;T;T;T	.|0.53640	.|0.61;0.68;0.66;0.64	5.0|5.0	4.08|4.08	0.47627|0.47627	.|.	.|0.164267	.|0.41605	.|D	.|0.000845	T|T	0.33614|0.33614	0.0869|0.0869	L|L	0.33339|0.33339	1.005|1.005	0.35581|0.35581	D|D	0.806303|0.806303	.|B;P;B;P;B	.|0.35745	.|0.172;0.518;0.244;0.518;0.172	.|B;B;B;B;B	.|0.32533	.|0.058;0.147;0.061;0.147;0.058	T|T	0.44190|0.44190	-0.9344|-0.9344	5|10	.|0.44086	.|T	.|0.13	-11.0226|-11.0226	9.556|9.556	0.39339|0.39339	0.0985:0.0:0.9015:0.0|0.0985:0.0:0.9015:0.0	.|.	.|275;333;275;275;225	.|B7Z7M1;B4DTG7;Q96N19-2;Q96N19;Q96N19-3	.|.;.;.;G137A_HUMAN;.	D|I	6|333;275;225;275;275	.|ENSP00000411827:V333I;ENSP00000442792:V275I;ENSP00000415698:V275I;ENSP00000321698:V275I	.|ENSP00000321698:V275I	G|V	+|+	2|1	0|0	GPR137|GPR137	63812427|63812427	1.000000|1.000000	0.71417|0.71417	0.982000|0.982000	0.44146|0.44146	0.903000|0.903000	0.53119|0.53119	7.397000|7.397000	0.79903|0.79903	1.093000|1.093000	0.41377|0.41377	0.462000|0.462000	0.41574|0.41574	GGT|GTA	.	.		0.632	GPR137-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396412.1	NM_020155		A	64055851	G	A	64055851	3	1	341	1	0	0	0	0	1	0	0	0	6653	1261	44	3	1023	3	GPR137	11	64055851	Missense_Mutation	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10	12644290	64055851	70950665	70	47171										
SNX15	29907	hgsc.bcm.edu	37	chr11	64802558	64802558	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	aggtgacccgacccttggagGtgtccagggacctacacatc	12	13	0	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr11:64802558G>T	ENST00000377244.3	+	5	530	c.400G>T	c.(400-402)Gtg>Ttg	p.V134L	RP11-399J13.3_ENST00000301886.3_3'UTR|SNX15_ENST00000352068.5_Missense_Mutation_p.V134L	NM_013306.4|NM_147777.3	NP_037438.2|NP_680086.2	Q9NRS6	SNX15_HUMAN	sorting nexin 15	134					intracellular protein transport (GO:0006886)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	14						ACCCTTGGAGGTGTCCAGGGA	0.627																																					p.V134L	Esophageal Squamous(56;269 1304 3324 8253)	Atlas-SNP	.											.	SNX15	35	.	0			c.G400T						.						31	32	31					11																	64802558		2201	4296	6497	SO:0001583	missense	29907	exon5			TTGGAGGTGTCCA	AF175267	CCDS8089.1, CCDS8090.1	11q12	2008-05-22			ENSG00000110025	ENSG00000110025		"Sorting nexins"	14978	protein-coding gene	gene with protein product		605964				11208079	Standard	NM_013306		Approved			Q9NRS6	OTTHUMG00000037387	ENST00000377244.3:c.400G>T	chr11.hg19:g.64802558G>T	ENSP00000366452:p.Val134Leu	140.0	0.0		109.0	9.0	NM_147777	E5KQS6|Q9NRS5	Missense_Mutation	SNP	ENST00000377244.3	hg19	CCDS8089.1	.	.	.	.	.	.	.	.	.	.	G	1.296	-0.606227	0.03717	.	.	ENSG00000110025	ENST00000377244;ENST00000534637;ENST00000524831;ENST00000352068;ENST00000525648	T;T;T;T	0.32515	1.89;1.45;1.47;1.88	4.77	0.393	0.16294	.	1.552840	0.03597	N	0.232706	T	0.15696	0.0378	N	0.14661	0.345	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.18429	-1.0337	10	0.02654	T	1	-9.4708	6.039	0.19724	0.2645:0.0:0.6026:0.1328	.	134;134;134	E5KQS5;E5KQS6;Q9NRS6	.;.;SNX15_HUMAN	L	134;130;122;134;54	ENSP00000366452:V134L;ENSP00000437277:V130L;ENSP00000431690:V122L;ENSP00000316410:V134L	ENSP00000316410:V134L	V	+	1	0	SNX15	64559134	0.008000	0.16893	0.000000	0.03702	0.015000	0.08874	0.038000	0.13862	-0.231000	0.09825	-1.151000	0.01829	GTG	.	.		0.627	SNX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091004.3			T	64802558	G	T	64802558	3	4	341	1	0	0	0	0	1	0	0	0	14901	1261	44	3	418	3	SNX15	11	64802558	Missense_Mutation	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10	746707	64802558	70203958	71	47172										
RELA	5970	hgsc.bcm.edu	37	chr11	65422089	65422089	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	ttcagcagctgctgaaactcGgagttgtcgacggatgccag	13	10	1	1	rs150493312		TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr11:65422089G>T	ENST00000406246.3	-	11	1677	c.1416C>A	c.(1414-1416)tcC>tcA	p.S472S	RELA_ENST00000308639.9_Silent_p.S469S|RELA_ENST00000525693.1_3'UTR	NM_001243984.1|NM_001243985.1|NM_021975.3	NP_001230913.1|NP_001230914.1|NP_068810.3	Q04206	TF65_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog A	472					acetaldehyde metabolic process (GO:0006117)|aging (GO:0007568)|cellular defense response (GO:0006968)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to tumor necrosis factor (GO:0071356)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|Fc-epsilon receptor signaling pathway (GO:0038095)|hair follicle development (GO:0001942)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|liver development (GO:0001889)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of Schwann cell differentiation (GO:0014040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|regulation of inflammatory response (GO:0050727)|response to amino acid (GO:0043200)|response to cAMP (GO:0051591)|response to cobalamin (GO:0033590)|response to drug (GO:0042493)|response to insulin (GO:0032868)|response to interleukin-1 (GO:0070555)|response to mechanical stimulus (GO:0009612)|response to morphine (GO:0043278)|response to muramyl dipeptide (GO:0032495)|response to organic substance (GO:0010033)|response to progesterone (GO:0032570)|response to UV-B (GO:0010224)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|phosphate ion binding (GO:0042301)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|repressing transcription factor binding (GO:0070491)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(11)|ovary(1)|urinary_tract(1)	19						GCTGAAACTCGGAGTTGTCGA	0.577																																					p.S472S		Atlas-SNP	.											.	RELA	44	.	0			c.C1416A						.						63	63	63					11																	65422089		2201	4297	6498	SO:0001819	synonymous_variant	5970	exon11			AAACTCGGAGTTG	Z22951	CCDS31609.1, CCDS44651.1, CCDS73322.1	11q13	2013-07-09	2013-07-09		ENSG00000173039	ENSG00000173039			9955	protein-coding gene	gene with protein product		164014	"nuclear factor of kappa light polypeptide gene enhancer in B-cells 3"	NFKB3		2001591	Standard	NM_021975		Approved	p65	uc001ofg.3	Q04206	OTTHUMG00000166566	ENST00000406246.3:c.1416C>A	chr11.hg19:g.65422089G>T		81.0	0.0		73.0	20.0	NM_021975	Q6GTV1|Q6SLK1	Silent	SNP	ENST00000406246.3	hg19	CCDS31609.1																																																																																			.	G|1.000;C|0.000		0.577	RELA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390457.2	NM_021975		T	65422089	G	T	65422089	2	4	341	1	0	0	0	0	0	0	0	1	13231	1103	39	1		1	RELA	11	65422089	Silent	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10	619531	65422089	69584427	72	47173										
KRTAP5-7	440050	hgsc.bcm.edu	37	chr11	71238737	71238737	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	ccagctgctgtaagccctgcTgctgttcctcaggctgtggg	13	13	1	0			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr11:71238737T>A	ENST00000398536.4	+	1	425	c.391T>A	c.(391-393)Tgc>Agc	p.C131S		NM_001012503.1	NP_001012521.1	Q6L8G8	KRA57_HUMAN	keratin associated protein 5-7	131	7 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				breast(1)|endometrium(1)|kidney(3)|lung(6)|ovary(1)	12						taagccctgctgctgttcctc	0.607																																					p.C131S		Atlas-SNP	.											.	KRTAP5-7	23	.	0			c.T391A						.						134	142	140					11																	71238737		2200	4294	6494	SO:0001583	missense	440050	exon1			CCCTGCTGCTGTT	AB126076	CCDS41682.1	11q13.4	2008-02-05			ENSG00000244411	ENSG00000244411		"Keratin associated proteins"	23602	protein-coding gene	gene with protein product						15144888	Standard	NM_001012503		Approved	KRTAP5.7, KRTAP5-3	uc001oqq.1	Q6L8G8	OTTHUMG00000057570	ENST00000398536.4:c.391T>A	chr11.hg19:g.71238737T>A	ENSP00000417330:p.Cys131Ser	83.0	0.0		67.0	5.0	NM_001012503	B2RNM3|Q701N5	Missense_Mutation	SNP	ENST00000398536.4	hg19	CCDS41682.1	.	.	.	.	.	.	.	.	.	.	N	10.32	1.316634	0.23908	.	.	ENSG00000244411	ENST00000398536	T	0.01871	4.59	1.69	1.69	0.24217	.	.	.	.	.	T	0.03434	0.0099	M	0.73319	2.225	0.23366	N	0.997822	B	0.16603	0.018	B	0.08055	0.003	T	0.33727	-0.9857	9	0.87932	D	0	.	4.6259	0.12477	0.0:0.0:0.3377:0.6623	.	131	Q6L8G8	KRA57_HUMAN	S	131	ENSP00000417330:C131S	ENSP00000417330:C131S	C	+	1	0	KRTAP5-7	70916385	0.104000	0.21937	0.952000	0.39060	0.009000	0.06853	0.296000	0.19083	1.040000	0.40099	0.240000	0.17902	TGC	.	.		0.607	KRTAP5-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127953.1			A	71238737	T	A	71238737	3	1	341	1	0	0	0	0	1	0	0	0	8575	1580	55	4	393	4	KRTAP5-7	11	71238737	Missense_Mutation	SNP	T	TCGA-RG-A7D4-01A-12D-A33Q-10	5816648	71238737	63767779	73	47174										
SIK3	23387	hgsc.bcm.edu	37	chr11	116728796	116728796	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	cggctggtgagcatacccgtGgggcggggtgggtgaggaag	22	7	0	2			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr11:116728796G>A	ENST00000292055.4	-	20	3102	c.3067C>T	c.(3067-3069)Cac>Tac	p.H1023Y	SIK3_ENST00000375288.1_Missense_Mutation_p.H358Y|SIK3_ENST00000375300.1_Missense_Mutation_p.H1081Y|AP006216.12_ENST00000444200.1_RNA|SIK3_ENST00000434315.2_Missense_Mutation_p.H862Y|SIK3_ENST00000542607.1_Missense_Mutation_p.H963Y|SIK3_ENST00000488337.1_5'UTR|SIK3_ENST00000446921.2_Missense_Mutation_p.H1021Y	NM_025164.3	NP_079440.3	Q9Y2K2	SIK3_HUMAN	SIK family kinase 3	1023					protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	57						GCATACCCGTGGGGCGGGGTG	0.557																																					p.H1023Y		Atlas-SNP	.											.	SIK3	112	.	0			c.C3067T						.						86	91	89					11																	116728796		2201	4296	6497	SO:0001583	missense	23387	exon20			ACCCGTGGGGCGG	AB023216	CCDS8379.1, CCDS60974.1, CCDS8379.2	11q23.3	2010-02-17			ENSG00000160584	ENSG00000160584			29165	protein-coding gene	gene with protein product		614776				10231032, 8889548	Standard	NM_025164		Approved	FLJ12240, L19, KIAA0999, QSK	uc001ppy.3	Q9Y2K2	OTTHUMG00000066628	ENST00000292055.4:c.3067C>T	chr11.hg19:g.116728796G>A	ENSP00000292055:p.His1023Tyr	124.0	0.0		80.0	22.0	NM_025164	A1A5A8|Q59FY2|Q5M9N1|Q6P3R6|Q8IYM8|Q9HA50	Missense_Mutation	SNP	ENST00000292055.4	hg19	CCDS8379.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.79|12.79	2.043583|2.043583	0.36085|0.36085	.|.	.|.	ENSG00000160584|ENSG00000160584	ENST00000375300;ENST00000292055;ENST00000375288;ENST00000542607;ENST00000434315|ENST00000445177;ENST00000446921	T;T;T;T;T|T	0.32515|0.31769	1.45;1.45;1.45;1.45;1.45|1.48	5.54|5.54	5.54|5.54	0.83059|0.83059	.|.	0.000000|.	0.42548|.	U|.	0.000685|.	T|T	0.37210|0.37210	0.0995|0.0995	N|N	0.24115|0.24115	0.695|0.695	0.38431|0.38431	D|D	0.946435|0.946435	B;B;B;B;P|.	0.34757|.	0.205;0.357;0.13;0.203;0.467|.	B;B;B;B;B|.	0.31686|.	0.126;0.081;0.033;0.052;0.134|.	T|T	0.32428|0.32428	-0.9907|-0.9907	10|7	0.87932|0.72032	D|D	0|0.01	.|.	19.4865|19.4865	0.95030|0.95030	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1023;963;862;1023;358|.	Q9Y2K2-3;A1A5A8;A1A5A9;Q9Y2K2;Q9Y2K2-2|.	.;.;.;SIK3_HUMAN;.|.	Y|L	1081;1023;358;963;862|1122;985	ENSP00000364449:H1081Y;ENSP00000292055:H1023Y;ENSP00000364437:H358Y;ENSP00000438108:H963Y;ENSP00000415873:H862Y|ENSP00000391295:P1122L	ENSP00000292055:H1023Y|ENSP00000391295:P1122L	H|P	-|-	1|2	0|0	SIK3|SIK3	116234006|116234006	1.000000|1.000000	0.71417|0.71417	0.919000|0.919000	0.36401|0.36401	0.766000|0.766000	0.43426|0.43426	4.991000|4.991000	0.63883|0.63883	2.585000|2.585000	0.87301|0.87301	0.563000|0.563000	0.77884|0.77884	CAC|CCA	.	.		0.557	SIK3-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_025164		A	116728796	G	A	116728796	3	1	341	1	0	0	0	0	1	0	0	0	14334	1348	47	3	740	3	SIK3	11	116728796	Missense_Mutation	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10	45490059	116728796	18277720	74	47175										
NCAPD3	23310	hgsc.bcm.edu	37	chr11	134027961	134027961	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	aatggtgctcagggacatggGcctgtggagaacagccacag	15	9	1	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr11:134027961G>A	ENST00000534548.2	-	31	4100	c.4036C>T	c.(4036-4038)Ccc>Tcc	p.P1346S		NM_015261.2	NP_056076.1	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3	1346					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	germinal vesicle (GO:0042585)|membrane (GO:0016020)|nuclear condensin complex (GO:0000799)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)	methylated histone binding (GO:0035064)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)		AGGGACATGGGCCTGTGGAGA	0.582																																					p.P1346S		Atlas-SNP	.											.	NCAPD3	141	.	0			c.C4036T						.						83	85	85					11																	134027961		2201	4297	6498	SO:0001630	splice_region_variant	23310	exon31			ACATGGGCCTGTG	AK124878	CCDS31723.1	11q25	2008-02-04			ENSG00000151503	ENSG00000151503			28952	protein-coding gene	gene with protein product		609276				7584044, 8619474, 14532007	Standard	NM_015261		Approved	hCAP-D3, CAP-D3, hHCP-6, KIAA0056, FLJ42888, hcp-6	uc001qhd.1	P42695	OTTHUMG00000167172	ENST00000534548.2:c.4035-1C>T	chr11.hg19:g.134027961G>A		37.0	0.0		42.0	12.0	NM_015261	A6NFS2|Q4KMQ9	Missense_Mutation	SNP	ENST00000534548.2	hg19	CCDS31723.1	.	.	.	.	.	.	.	.	.	.	G	4.218	0.039356	0.08148	.	.	ENSG00000151503	ENST00000534548	T	0.29917	1.55	5.72	2.58	0.30949	.	0.898757	0.09706	N	0.766365	T	0.28001	0.0690	L	0.56769	1.78	0.25110	N	0.990724	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.33523	-0.9865	10	0.56958	D	0.05	-0.6254	3.9509	0.09369	0.0778:0.2444:0.4269:0.2508	.	1346;406	P42695;Q96FA6	CNDD3_HUMAN;.	S	1346	ENSP00000433681:P1346S	ENSP00000433681:P1346S	P	-	1	0	NCAPD3	133533171	0.109000	0.22037	0.153000	0.22517	0.005000	0.04900	0.242000	0.18087	0.238000	0.21222	-0.314000	0.08810	CCC	.	.		0.582	NCAPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393575.2	NM_015261	Missense_Mutation	A	134027961	G	A	134027961	5	1	341	1	0	0	0	0	0	0	1	0	10215	1217	42	3	480	3	NCAPD3	11	134027961	Splice_Site	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10	17299165	134027961	978555	75	47176										
CLSTN3	9746	hgsc.bcm.edu	37	chr12	7295867	7295867	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	tgaacactctgcgctttgccAcgcccggcgtcaggcccctg	11	17	2	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr12:7295867A>G	ENST00000266546.6	+	12	2257	c.1807A>G	c.(1807-1809)Acg>Gcg	p.T603A	CLSTN3_ENST00000537408.1_Missense_Mutation_p.T615A	NM_014718.3	NP_055533.2	Q9BQT9	CSTN3_HUMAN	calsyntenin 3	603					homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(7)|prostate(1)|skin(1)	33						GCGCTTTGCCACGCCCGGCGT	0.607																																					p.T603A		Atlas-SNP	.											.	CLSTN3	84	.	0			c.A1807G						.						103	94	97					12																	7295867		2203	4300	6503	SO:0001583	missense	9746	exon12			TTTGCCACGCCCG	AB018269	CCDS8575.1	12p13.31	2011-07-01			ENSG00000139182	ENSG00000139182		"Cadherins / Cadherin-related"	18371	protein-coding gene	gene with protein product	"cadherin-related family member 14"	611324				12498782	Standard	NM_014718		Approved	CSTN3, KIAA0726, CDHR14	uc001qsr.3	Q9BQT9	OTTHUMG00000168167	ENST00000266546.6:c.1807A>G	chr12.hg19:g.7295867A>G	ENSP00000266546:p.Thr603Ala	36.0	0.0		30.0	12.0	NM_014718	D3DUT6|O94831|Q2T9J5|Q5UE57	Missense_Mutation	SNP	ENST00000266546.6	hg19	CCDS8575.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.752892	0.89753	.	.	ENSG00000139182	ENST00000266546;ENST00000537408	T;T	0.35048	1.33;1.33	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	T	0.62380	0.2423	M	0.79805	2.47	0.80722	D	1	D;D	0.89917	0.984;1.0	D;D	0.91635	0.956;0.999	T	0.66826	-0.5825	10	0.54805	T	0.06	-14.9912	15.0982	0.72253	1.0:0.0:0.0:0.0	.	615;603	Q5UE57;Q9BQT9	.;CSTN3_HUMAN	A	603;615	ENSP00000266546:T603A;ENSP00000440679:T615A	ENSP00000266546:T603A	T	+	1	0	CLSTN3	7187134	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.710000	0.91388	1.964000	0.57103	0.379000	0.24179	ACG	.	.		0.607	CLSTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398560.2	NM_014718		G	7295867	A	G	7295867	3	3	341	1	0	0	0	0	1	0	0	0	3565	159	6	2	1853	2	CLSTN3	12	7295867	Missense_Mutation	SNP	A	TCGA-RG-A7D4-01A-12D-A33Q-10		7295867	126556028	76	47177										
CD69	969	hgsc.bcm.edu	37	chr12	9906144	9906144	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	ccatgctgctgacctctgtgTttttcagaaaaacacacttg	7	11	2	2			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr12:9906144T>G	ENST00000228434.3	-	5	613	c.533A>C	c.(532-534)aAc>aCc	p.N178T		NM_001781.2	NP_001772.1	Q07108	CD69_HUMAN	CD69 molecule	178	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cellular response to drug (GO:0035690)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|large_intestine(3)|lung(4)|pancreas(1)|upper_aerodigestive_tract(1)	10						GACCTCTGTGTTTTTCAGAAA	0.318																																					p.N178T		Atlas-SNP	.											.	CD69	23	.	0			c.A533C						.						58	57	58					12																	9906144		2203	4300	6503	SO:0001583	missense	969	exon5			TCTGTGTTTTTCA	Z22576	CCDS8604.1	12p13	2011-08-30	2006-03-28		ENSG00000110848	ENSG00000110848		"C-type lectin domain containing", "CD molecules"	1694	protein-coding gene	gene with protein product		107273	"CD69 antigen (p60, early T-cell activation antigen)"			1612643	Standard	NM_001781		Approved	CLEC2C	uc001qwk.3	Q07108	OTTHUMG00000168481	ENST00000228434.3:c.533A>C	chr12.hg19:g.9906144T>G	ENSP00000228434:p.Asn178Thr	97.0	0.0		123.0	15.0	NM_001781		Missense_Mutation	SNP	ENST00000228434.3	hg19	CCDS8604.1	.	.	.	.	.	.	.	.	.	.	T	10.05	1.244243	0.22796	.	.	ENSG00000110848	ENST00000228434	T	0.18810	2.19	5.13	1.1	0.20463	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.750716	0.12665	N	0.449289	T	0.15089	0.0364	L	0.46567	1.45	0.09310	N	0.999999	B	0.12630	0.006	B	0.13407	0.009	T	0.27905	-1.0060	9	.	.	.	-6.4483	3.6254	0.08111	0.0:0.4853:0.1904:0.3243	.	178	Q07108	CD69_HUMAN	T	178	ENSP00000228434:N178T	.	N	-	2	0	CD69	9797411	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-0.033000	0.12246	0.362000	0.24319	-0.248000	0.11899	AAC	.	.		0.318	CD69-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399876.1			G	9906144	T	G	9906144	3	3	341	1	0	0	0	0	1	0	0	0	3033	1725	60	5	70	5	CD69	12	9906144	Missense_Mutation	SNP	T	TCGA-RG-A7D4-01A-12D-A33Q-10	2610277	9906144	123945751	77	47178										
CNTN1	1272	hgsc.bcm.edu	37	chr12	41422971	41422971	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	agaatacgttgtggaggttcGcgcgcacagtgatggaggag	17	6	0	2			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr12:41422971G>A	ENST00000551295.2	+	23	3047	c.2930G>A	c.(2929-2931)cGc>cAc	p.R977H	CNTN1_ENST00000347616.1_Missense_Mutation_p.R977H|CNTN1_ENST00000348761.2_Missense_Mutation_p.R966H	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	977	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.R977H(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(21)|lung(49)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				GTGGAGGTTCGCGCGCACAGT	0.448																																					p.R977H		Atlas-SNP	.											CNTN1,NS,carcinoma,0,1	CNTN1	207	.	1	Substitution - Missense(1)	kidney(1)	c.G2930A						.						229	213	218					12																	41422971		2203	4300	6503	SO:0001583	missense	1272	exon23			AGGTTCGCGCGCA	Z21488	CCDS8737.1, CCDS8738.1, CCDS58225.1	12q11-q12	2014-01-30				ENSG00000018236		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing", "Endogenous ligands"	2171	protein-coding gene	gene with protein product	"glycoprotein gP135"	600016				7959734, 8586965	Standard	NM_001843		Approved	F3, GP135	uc031qgz.1	Q12860		ENST00000551295.2:c.2930G>A	chr12.hg19:g.41422971G>A	ENSP00000447006:p.Arg977His	95.0	0.0		114.0	33.0	NM_001843	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Missense_Mutation	SNP	ENST00000551295.2	hg19	CCDS8737.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.990461	0.74589	.	.	ENSG00000018236	ENST00000551295;ENST00000347616;ENST00000348761	T;T;T	0.46063	0.88;0.88;0.88	5.18	5.18	0.71444	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.67599	0.2910	M	0.78456	2.415	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	T	0.71027	-0.4711	10	0.66056	D	0.02	.	19.0769	0.93167	0.0:0.0:1.0:0.0	.	966;977	Q12860-2;Q12860	.;CNTN1_HUMAN	H	977;977;966	ENSP00000447006:R977H;ENSP00000325660:R977H;ENSP00000261160:R966H	ENSP00000325660:R977H	R	+	2	0	CNTN1	39709238	1.000000	0.71417	0.996000	0.52242	0.298000	0.27526	8.779000	0.91792	2.588000	0.87417	0.591000	0.81541	CGC	.	.		0.448	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	NM_001843		A	41422971	G	A	41422971	3	1	341	1	0	0	0	0	1	0	0	0	3642	1087	38	1	3016	1	CNTN1	12	41422971	Missense_Mutation	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10	31516827	41422971	92428924	78	47179										
PTPRB	5787	hgsc.bcm.edu	37	chr12	70949887	70949887	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	agaacaggcaatggccgtggAgttctgaggccggcaatgca	15	9	1	2			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr12:70949887A>G	ENST00000261266.5	-	17	4131	c.4102T>C	c.(4102-4104)Tcc>Ccc	p.S1368P	PTPRB_ENST00000451516.2_Missense_Mutation_p.S1278P|PTPRB_ENST00000550857.1_Missense_Mutation_p.S1278P|PTPRB_ENST00000550358.1_Missense_Mutation_p.S1498P|PTPRB_ENST00000538708.1_Missense_Mutation_p.S1278P|PTPRB_ENST00000334414.6_Missense_Mutation_p.S1586P	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	1368	Fibronectin type-III 16. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			ATGGCCGTGGAGTTCTGAGGC	0.443																																					p.S1586P		Atlas-SNP	.											.	PTPRB	676	.	0			c.T4756C						.						45	42	43					12																	70949887		1839	4086	5925	SO:0001583	missense	5787	exon19			CCGTGGAGTTCTG	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.4102T>C	chr12.hg19:g.70949887A>G	ENSP00000261266:p.Ser1368Pro	81.0	0.0		76.0	6.0	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Missense_Mutation	SNP	ENST00000261266.5	hg19	CCDS44944.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.540052	0.85917	.	.	ENSG00000127329	ENST00000334414;ENST00000451516;ENST00000550358;ENST00000538708;ENST00000550857;ENST00000261266	T;T;T;T;T;T	0.58940	0.3;0.3;0.3;0.3;0.3;0.3	5.59	5.59	0.84812	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.64461	0.2600	L	0.27053	0.805	0.58432	D	0.999999	D;D;D;D;P	0.89917	1.0;1.0;1.0;1.0;0.898	D;D;D;D;P	0.97110	1.0;1.0;1.0;1.0;0.876	T	0.62765	-0.6785	10	0.30854	T	0.27	.	15.7577	0.78046	1.0:0.0:0.0:0.0	.	1278;1278;1586;1368;1498	P23467-2;F5H3G6;P23467-3;P23467;F8VU56	.;.;.;PTPRB_HUMAN;.	P	1586;1278;1498;1278;1278;1368	ENSP00000334928:S1586P;ENSP00000393028:S1278P;ENSP00000448058:S1498P;ENSP00000438927:S1278P;ENSP00000447302:S1278P;ENSP00000261266:S1368P	ENSP00000261266:S1368P	S	-	1	0	PTPRB	69236154	1.000000	0.71417	0.995000	0.50966	0.968000	0.65278	8.573000	0.90759	2.117000	0.64856	0.533000	0.62120	TCC	.	.		0.443	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1			G	70949887	A	G	70949887	3	3	341	1	0	0	0	0	1	0	0	0	12811	304	11	2	1955	2	PTPRB	12	70949887	Missense_Mutation	SNP	A	TCGA-RG-A7D4-01A-12D-A33Q-10	29526916	70949887	62902008	79	47180										
PPFIA2	8499	hgsc.bcm.edu	37	chr12	81747020	81747020	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	attgtttctctgtcatcatcAtcaatatcagacatttcagt	4	9	7	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr12:81747020A>T	ENST00000549396.1	-	17	2032	c.1872T>A	c.(1870-1872)gaT>gaA	p.D624E	PPFIA2_ENST00000545296.2_Intron|PPFIA2_ENST00000550584.2_Missense_Mutation_p.D624E|PPFIA2_ENST00000541570.2_Missense_Mutation_p.D191E|PPFIA2_ENST00000407050.4_Missense_Mutation_p.D550E|PPFIA2_ENST00000541017.1_5'UTR|PPFIA2_ENST00000549325.1_Missense_Mutation_p.D606E|PPFIA2_ENST00000333447.7_Missense_Mutation_p.D606E|PPFIA2_ENST00000548586.1_Missense_Mutation_p.D624E|PPFIA2_ENST00000550359.2_Missense_Mutation_p.D471E|PPFIA2_ENST00000552948.1_Missense_Mutation_p.D624E|PPFIA2_ENST00000443686.3_Missense_Mutation_p.D525E	NM_001220476.1|NM_001282536.1|NM_003625.3	NP_001207405.1|NP_001269465.1|NP_003616.2	O75334	LIPA2_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2	624	Poly-Asp.				cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|presynaptic active zone (GO:0048786)				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(37)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)	85						TGTCATCATCATCAATATCAG	0.433																																					p.D624E		Atlas-SNP	.											.	PPFIA2	207	.	0			c.T1872A						.						170	162	164					12																	81747020		1906	4140	6046	SO:0001583	missense	8499	exon16			ATCATCATCAATA	AF034799	CCDS55850.1, CCDS55851.1, CCDS55852.1, CCDS55853.1, CCDS55854.1, CCDS55855.1, CCDS55856.1, CCDS55857.1, CCDS59236.1, CCDS73503.1	12q21.31	2013-01-10						"Sterile alpha motif (SAM) domain containing"	9246	protein-coding gene	gene with protein product	"Liprin-alpha2"	603143				9624153	Standard	NM_003625		Approved		uc031qis.1	O75334		ENST00000549396.1:c.1872T>A	chr12.hg19:g.81747020A>T	ENSP00000450337:p.Asp624Glu	74.0	0.0		117.0	40.0	NM_001220476	B3KVT5|B3KXA0|B7Z2A6|B7Z3U9|B7Z663|B7ZKZ5|E7ERB8|E7ETG6|F8VP68|Q2M3G8	Missense_Mutation	SNP	ENST00000549396.1	hg19	CCDS55857.1	.	.	.	.	.	.	.	.	.	.	A	14.68	2.607943	0.46527	.	.	ENSG00000139220	ENST00000549396;ENST00000549325;ENST00000541570;ENST00000407050;ENST00000541501;ENST00000333447;ENST00000548586;ENST00000443686;ENST00000552948;ENST00000553058	T;T;T;T;T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02;1.02;1.02;1.02;1.02	5.44	3.09	0.35607	.	0.000000	0.85682	D	0.000000	T	0.47192	0.1432	L	0.41415	1.275	0.80722	D	1	D	0.58970	0.984	D	0.68192	0.956	T	0.32214	-0.9915	10	0.11794	T	0.64	-27.1628	9.6885	0.40114	0.8585:0.0:0.1415:0.0	.	624	O75334	LIPA2_HUMAN	E	624;606;191;550;635;606;624;525;624;205	ENSP00000450337:D624E;ENSP00000450298:D606E;ENSP00000438337:D191E;ENSP00000385093:D550E;ENSP00000327416:D606E;ENSP00000449338:D624E;ENSP00000388373:D525E;ENSP00000447868:D624E;ENSP00000448941:D205E	ENSP00000327416:D606E	D	-	3	2	PPFIA2	80271151	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.969000	0.49232	0.368000	0.24481	0.477000	0.44152	GAT	.	.		0.433	PPFIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408030.1			T	81747020	A	T	81747020	3	4	341	1	0	0	0	0	1	0	0	0	12319	214	8	4	1965	4	PPFIA2	12	81747020	Missense_Mutation	SNP	A	TCGA-RG-A7D4-01A-12D-A33Q-10	10797133	81747020	52104875	80	47181										
STAB2	55576	hgsc.bcm.edu	37	chr12	104157269	104157269	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	catgcttgtctttccaaacaGtcggaagaggacattaatgt	9	8	1	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr12:104157269G>C	ENST00000388887.2	+	68	7692		c.e68-1		RP11-341G23.4_ENST00000551299.1_RNA|RP11-341G23.4_ENST00000550029.1_RNA	NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						TTTCCAAACAGTCGGAAGAGG	0.527																																					.		Atlas-SNP	.											.	STAB2	370	.	0			c.7489-1G>C						.						248	241	243					12																	104157269		2203	4300	6503	SO:0001630	splice_region_variant	55576	exon68			CAAACAGTCGGAA	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"hyaluronic acid receptor for endocytosis"	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.7489-1G>C	chr12.hg19:g.104157269G>C		69.0	0.0		75.0	21.0	NM_017564		Splice_Site	SNP	ENST00000388887.2	hg19	CCDS31888.1	.	.	.	.	.	.	.	.	.	.	G	14.90	2.674513	0.47781	.	.	ENSG00000136011	ENST00000388887	.	.	.	5.32	5.32	0.75619	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.1808	0.81898	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	STAB2	102681399	1.000000	0.71417	0.967000	0.41034	0.718000	0.41266	5.912000	0.69948	2.490000	0.84030	0.561000	0.74099	.	.	.		0.527	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		Intron	C	104157269	G	C	104157269	5	2	341	1	0	0	0	0	0	0	1	0	15253	1043	36	4	7758	4	STAB2	12	104157269	Splice_Site	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10	22410249	104157269	29694626	81	47182										
TMEM132D	121256	hgsc.bcm.edu	37	chr12	129569203	129569203	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	accacgttgaccttgcctttCatttctttcccattgacaaa	4	13	2	2			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr12:129569203C>A	ENST00000422113.2	-	6	1814	c.1488G>T	c.(1486-1488)atG>atT	p.M496I	TMEM132D_ENST00000389441.4_Missense_Mutation_p.M34I	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	496					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		CCTTGCCTTTCATTTCTTTCC	0.542																																					p.M496I		Atlas-SNP	.											.	TMEM132D	299	.	0			c.G1488T						.						124	95	105					12																	129569203		2203	4300	6503	SO:0001583	missense	121256	exon6			GCCTTTCATTTCT	AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 153"	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.1488G>T	chr12.hg19:g.129569203C>A	ENSP00000408581:p.Met496Ile	109.0	0.0		95.0	19.0	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	hg19	CCDS9266.1	.	.	.	.	.	.	.	.	.	.	c	12.14	1.847441	0.32606	.	.	ENSG00000151952	ENST00000389441;ENST00000422113	T;T	0.47528	0.84;0.84	4.78	4.78	0.61160	.	0.000000	0.85682	D	0.000000	T	0.50429	0.1615	L	0.41710	1.295	0.45621	D	0.998558	D;P	0.56035	0.974;0.594	P;B	0.50659	0.647;0.39	T	0.47484	-0.9114	9	.	.	.	-70.0423	17.8083	0.88608	0.0:1.0:0.0:0.0	.	496;34	Q14C87;Q14C87-2	T132D_HUMAN;.	I	34;496	ENSP00000374092:M34I;ENSP00000408581:M496I	.	M	-	3	0	TMEM132D	128135156	1.000000	0.71417	0.998000	0.56505	0.964000	0.63967	2.559000	0.45888	2.181000	0.69327	0.556000	0.70494	ATG	.	.		0.542	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448		A	129569203	C	A	129569203	3	1	341	1	0	0	0	0	1	0	0	0	16062	826	29	3	1827	3	TMEM132D	12	129569203	Missense_Mutation	SNP	C	TCGA-RG-A7D4-01A-12D-A33Q-10	25411934	129569203	4282692	82	47183										
OR4K17	390436	hgsc.bcm.edu	37	chr14	20585954	20585954	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	ttcttttgctgggtgcttcaCtcagatatttctccttcact	6	11	5	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr14:20585954C>A	ENST00000315543.4	+	1	389	c.389C>A	c.(388-390)aCt>aAt	p.T130N		NM_001004715.1	NP_001004715.1	Q8NGC6	OR4KH_HUMAN	olfactory receptor, family 4, subfamily K, member 17	102						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(4)|lung(12)|pancreas(1)|skin(3)	21	all_cancers(95;0.00108)		Epithelial(56;7.58e-07)|all cancers(55;3.77e-06)	GBM - Glioblastoma multiforme(265;0.0144)		GGGTGCTTCACTCAGATATTT	0.428																																					p.T130N		Atlas-SNP	.											.	OR4K17	58	.	0			c.C389A						.						117	114	115					14																	20585954		2203	4300	6503	SO:0001583	missense	390436	exon1			GCTTCACTCAGAT		CCDS32030.1	14q11.2	2013-09-23			ENSG00000176230	ENSG00000176230		"GPCR / Class A : Olfactory receptors"	15355	protein-coding gene	gene with protein product							Standard	NM_001004715		Approved		uc001vwo.1	Q8NGC6	OTTHUMG00000170783	ENST00000315543.4:c.389C>A	chr14.hg19:g.20585954C>A	ENSP00000319197:p.Thr130Asn	85.0	0.0		92.0	18.0	NM_001004715	Q6IF12	Missense_Mutation	SNP	ENST00000315543.4	hg19	CCDS32030.1	.	.	.	.	.	.	.	.	.	.	.	11.60	1.687495	0.29962	.	.	ENSG00000176230	ENST00000315543	T	0.03004	4.08	2.86	1.95	0.26073	GPCR, rhodopsin-like superfamily (1);	0.229512	0.21909	U	0.067323	T	0.13841	0.0335	M	0.92649	3.33	0.09310	N	1	D	0.54601	0.967	P	0.54460	0.753	T	0.04029	-1.0983	10	0.72032	D	0.01	.	5.6902	0.17825	0.0:0.6643:0.2068:0.1289	.	102	Q8NGC6	OR4KH_HUMAN	N	130	ENSP00000319197:T130N	ENSP00000319197:T130N	T	+	2	0	OR4K17	19655794	0.000000	0.05858	0.993000	0.49108	0.615000	0.37417	-0.626000	0.05527	1.579000	0.49836	0.404000	0.27445	ACT	.	.		0.428	OR4K17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410346.1			A	20585954	C	A	20585954	3	1	341	1	0	0	0	0	1	0	0	0	11080	565	20	3	391	3	OR4K17	14	20585954	Missense_Mutation	SNP	C	TCGA-RG-A7D4-01A-12D-A33Q-10		20585954	86763586	83	47184										
NIN	51199	hgsc.bcm.edu	37	chr14	51233078	51233079	+	Missense_Mutation	DNP	GG	GG	TT													0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	tgtcagtctctcttcttgcaGgaagaactcagcactgctag							TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr14:51233078_51233079GG>TT	ENST00000382041.3	-	14	1771_1772	c.1581_1582CC>AA	c.(1579-1584)ttCCtg>ttAAtg	p.527_528FL>LM	NIN_ENST00000245441.5_Missense_Mutation_p.527_528FL>LM|NIN_ENST00000453196.1_Missense_Mutation_p.527_528FL>LM|NIN_ENST00000389868.3_Missense_Mutation_p.527_528FL>LM|NIN_ENST00000324330.9_Missense_Mutation_p.527_528FL>LM|NIN_ENST00000382043.4_Missense_Mutation_p.527_528FL>LM|NIN_ENST00000530997.2_Missense_Mutation_p.527_528FL>LM	NM_016350.4|NM_182946.1	NP_057434.4|NP_891991	Q8N4C6	NIN_HUMAN	ninein (GSK3B interacting protein)	527					centrosome localization (GO:0051642)|centrosome-templated microtubule nucleation (GO:0090222)|microtubule anchoring at centrosome (GO:0034454)	centriole (GO:0005814)|centrosome (GO:0005813)|microtubule (GO:0005874)|nucleolus (GO:0005730)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(13)|lung(16)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	71	all_epithelial(31;0.00244)|Breast(41;0.127)					TCTTCTTGCAGGAAGAACTCAG	0.49			T	PDGFRB	MPD																																p.L528M|p.F527L		Atlas-SNP	.		Dom	yes		14	14q24	51199	ninein (GSK3B interacting protein)		L	.	NIN	475	.	0			c.C1582A|c.C1581A						.																																			SO:0001583	missense	51199	exon14			CTTGCAGGAAGAA|TTGCAGGAAGAAC	AF212162	CCDS32078.1, CCDS32079.1, CCDS32078.2	14q21-q22	2013-01-10			ENSG00000100503	ENSG00000100503		"EF-hand domain containing"	14906	protein-coding gene	gene with protein product		608684				11004522, 11162463	Standard	NM_020921		Approved		uc001wyi.3	Q8N4C6	OTTHUMG00000029569	ENST00000382041.3:c.1581_1582delinsTT	chr14.hg19:g.51233078_51233079delinsTT	ENSP00000371472:p.F527_L528delinsLM	78.0|77.0	0.0		81.0|84.0	14.0|15.0	NM_020921	A6NDB8|B7WPA3|C9JSB6|C9JSG2|C9JXL2|Q5BKU3|Q6P0P6|Q9BWU6|Q9C012|Q9C013|Q9C014|Q9H5I6|Q9HAT7|Q9HBY5|Q9HCK7|Q9UH61	Missense_Mutation	SNP	ENST00000382041.3	hg19	CCDS32079.1																																																																																			.	.		0.49	NIN-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395207.2	NM_182946		TT	51233079	GG	TT	51233078	3	4	341	1	0	0	0	0	1	0	0	0	10426	991	35	3	5039	3	NIN	14	51233078	Missense_Mutation	DNP	GG	TCGA-RG-A7D4-01A-12D-A33Q-10	30647124	51233078	56116462	84	47185										
PTGER2	5732	hgsc.bcm.edu	37	chr14	52781678	52781678	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	ccctggagcgctacctctcgAtcgggcacccctacttctac	8	18	2	0			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr14:52781678A>G	ENST00000245457.5	+	1	566	c.412A>G	c.(412-414)Atc>Gtc	p.I138V	PTGER2_ENST00000557436.1_Intron	NM_000956.3	NP_000947.2	P43116	PE2R2_HUMAN	prostaglandin E receptor 2 (subtype EP2), 53kDa	138					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|cellular response to prostaglandin E stimulus (GO:0071380)|G-protein coupled receptor signaling pathway (GO:0007186)|regulation of cell proliferation (GO:0042127)|response to lipopolysaccharide (GO:0032496)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	prostaglandin E receptor activity (GO:0004957)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15	Breast(41;0.0639)|all_epithelial(31;0.0729)				Alprostadil(DB00770)|Dinoprostone(DB00917)|Misoprostol(DB00929)	CTACCTCTCGATCGGGCACCC	0.652																																					p.I138V		Atlas-SNP	.											.	PTGER2	27	.	0			c.A412G						.						60	61	60					14																	52781678		2200	4298	6498	SO:0001583	missense	5732	exon1			CTCTCGATCGGGC		CCDS9708.1	14q22	2012-08-08	2002-08-29		ENSG00000125384	ENSG00000125384		"GPCR / Class A : Prostanoid receptors"	9594	protein-coding gene	gene with protein product		176804	"prostaglandin E receptor 2 (subtype EP2), 53kD"			8250933, 7759114	Standard	NM_000956		Approved	EP2	uc001wzr.3	P43116	OTTHUMG00000140300	ENST00000245457.5:c.412A>G	chr14.hg19:g.52781678A>G	ENSP00000245457:p.Ile138Val	72.0	0.0		56.0	14.0	NM_000956	D3DSC0|Q52LG8	Missense_Mutation	SNP	ENST00000245457.5	hg19	CCDS9708.1	.	.	.	.	.	.	.	.	.	.	A	18.54	3.645913	0.67358	.	.	ENSG00000125384	ENST00000245457	T	0.76709	-1.04	5.23	2.66	0.31614	GPCR, rhodopsin-like superfamily (1);	0.050329	0.85682	D	0.000000	T	0.77405	0.4125	L	0.56769	1.78	0.43259	D	0.995192	P	0.39737	0.685	P	0.46208	0.507	T	0.78048	-0.2356	10	0.72032	D	0.01	-26.2719	10.3392	0.43868	0.6864:0.3136:0.0:0.0	.	138	P43116	PE2R2_HUMAN	V	138	ENSP00000245457:I138V	ENSP00000245457:I138V	I	+	1	0	PTGER2	51851428	1.000000	0.71417	0.998000	0.56505	0.911000	0.54048	2.186000	0.42593	0.918000	0.36919	-0.460000	0.05396	ATC	.	.		0.652	PTGER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276890.1			G	52781678	A	G	52781678	3	3	341	1	0	0	0	0	1	0	0	0	12756	333	12	2	414	2	PTGER2	14	52781678	Missense_Mutation	SNP	A	TCGA-RG-A7D4-01A-12D-A33Q-10	1548600	52781678	54567862	85	47186										
RYR3	6263	hgsc.bcm.edu	37	chr15	33825515	33825515	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	ttgctcttctttcacagtatCtaacatgcttgactacatca	4	11	5	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr15:33825515C>A	ENST00000389232.4	+	5	428	c.358C>A	c.(358-360)Cta>Ata	p.L120I	RYR3_ENST00000415757.3_Missense_Mutation_p.L120I	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	120	MIR 1. {ECO:0000255|PROSITE- ProRule:PRU00131}.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			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)		TTCACAGTATCTAACATGCTT	0.418																																					p.L120I		Atlas-SNP	.											.	RYR3	760	.	0			c.C358A						.						105	101	103					15																	33825515		1961	4159	6120	SO:0001583	missense	6263	exon5			CAGTATCTAACAT		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.358C>A	chr15.hg19:g.33825515C>A	ENSP00000373884:p.Leu120Ile	26.0	0.0		31.0	7.0	NM_001243996	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	hg19	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	C	19.05	3.752348	0.69533	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D;D	0.98437	-4.93;-4.93	4.43	4.43	0.53597	Inositol 1,4,5-trisphosphate/ryanodine receptor (1);MIR motif (2);	0.000000	0.64402	D	0.000005	D	0.98460	0.9487	M	0.73962	2.25	0.48341	D	0.999631	D;D	0.56746	0.957;0.977	D;D	0.73380	0.98;0.93	D	0.98387	1.0561	10	0.87932	D	0	.	9.2379	0.37477	0.0:0.8618:0.0:0.1382	.	120;120	Q15413-2;Q15413	.;RYR3_HUMAN	I	120	ENSP00000373884:L120I;ENSP00000399610:L120I	ENSP00000354735:L120I	L	+	1	2	RYR3	31612807	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	1.078000	0.30754	2.442000	0.82660	0.655000	0.94253	CTA	.	.		0.418	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			A	33825515	C	A	33825515	3	1	341	1	0	0	0	0	1	0	0	0	13785	912	32	3	376	3	RYR3	15	33825515	Missense_Mutation	SNP	C	TCGA-RG-A7D4-01A-12D-A33Q-10		33825515	68705877	86	47187										
LCMT2	9836	hgsc.bcm.edu	37	chr15	43621087	43621087	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	tgcaggcactgtgagaatgcCgggcttcaggtacttctccc	12	12	2	1	rs556701152		TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr15:43621087C>A	ENST00000305641.5	-	1	1716	c.1601G>T	c.(1600-1602)cGg>cTg	p.R534L	ADAL_ENST00000422466.2_5'Flank|LCMT2_ENST00000544735.1_Missense_Mutation_p.R113L|ADAL_ENST00000428046.3_5'Flank|LCMT2_ENST00000567039.1_3'UTR|ADAL_ENST00000389651.4_5'Flank	NM_014793.4	NP_055608.2	O60294	TYW4_HUMAN	leucine carboxyl methyltransferase 2	534					tRNA processing (GO:0008033)		methyltransferase activity (GO:0008168)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(2)|liver(1)|lung(9)|skin(1)|urinary_tract(1)	20		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.1e-07)	L-Leucine(DB00149)	GTGAGAATGCCGGGCTTCAGG	0.557																																					p.R534L		Atlas-SNP	.											.	LCMT2	48	.	0			c.G1601T						.						112	112	112					15																	43621087		2201	4299	6500	SO:0001583	missense	9836	exon1			GAATGCCGGGCTT	AF265443	CCDS10094.1	15q15.3	2007-01-26			ENSG00000168806	ENSG00000168806			17558	protein-coding gene	gene with protein product	"tRNA-yW synthesizing protein 4"	611246				9628581, 17150819	Standard	NM_014793		Approved	KIAA0547, MGC9534, TYW4, PPM2	uc001zrg.3	O60294	OTTHUMG00000130705	ENST00000305641.5:c.1601G>T	chr15.hg19:g.43621087C>A	ENSP00000307214:p.Arg534Leu	22.0	0.0		36.0	8.0	NM_014793	Q4JFT6|Q96B55|Q9NR10	Missense_Mutation	SNP	ENST00000305641.5	hg19	CCDS10094.1	.	.	.	.	.	.	.	.	.	.	C	19.61	3.859832	0.71834	.	.	ENSG00000168806	ENST00000305641;ENST00000544735	T;T	0.78481	-1.18;-1.18	5.61	4.69	0.59074	Kelch-type beta propeller (1);	0.142736	0.47093	D	0.000246	D	0.83027	0.5165	M	0.66939	2.045	0.45899	D	0.99874	D	0.89917	1.0	D	0.97110	1.0	T	0.80977	-0.1141	10	0.02654	T	1	0.3354	12.3058	0.54902	0.0:0.9181:0.0:0.0819	.	534	O60294	LCMT2_HUMAN	L	534;113	ENSP00000307214:R534L;ENSP00000442022:R113L	ENSP00000307214:R534L	R	-	2	0	LCMT2	41408379	0.997000	0.39634	0.735000	0.30896	0.994000	0.84299	5.834000	0.69361	1.385000	0.46445	0.655000	0.94253	CGG	.	.		0.557	LCMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253205.1	NM_014793		A	43621087	C	A	43621087	3	1	341	1	0	0	0	0	1	0	0	0	8688	652	23	1	463	1	LCMT2	15	43621087	Missense_Mutation	SNP	C	TCGA-RG-A7D4-01A-12D-A33Q-10	9795572	43621087	58910305	87	47188										
MYO5A	4644	hgsc.bcm.edu	37	chr15	52652277	52652277	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	tgtgtccaggcttaggcacaTgctgcaaggcaaataaccca	10	11	0	0			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr15:52652277T>C	ENST00000399231.3	-	25	3554	c.3311A>G	c.(3310-3312)cAt>cGt	p.H1104R	MYO5A_ENST00000553916.1_Splice_Site_p.H1104R|MYO5A_ENST00000399233.2_Splice_Site_p.H1104R|MYO5A_ENST00000358212.6_Splice_Site_p.H1104R|MYO5A_ENST00000356338.6_Splice_Site_p.H1104R	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	1104					actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		CTTAGGCACATGCTGCAAGGC	0.423																																					p.H1104R		Atlas-SNP	.											.	MYO5A	145	.	0			c.A3311G						.						95	91	93					15																	52652277		1988	4169	6157	SO:0001630	splice_region_variant	4644	exon25			GGCACATGCTGCA		CCDS42037.1, CCDS45262.1	15q21	2014-09-17	2006-09-29		ENSG00000197535	ENSG00000197535		"Myosins / Myosin superfamily : Class V"	7602	protein-coding gene	gene with protein product	"myosin, heavy polypeptide kinase", "myosin heavy chain 12", "myoxin", "myosin V"	160777	"myosin VA (heavy polypeptide 12, myoxin)"	MYH12		8188282, 8022818	Standard	NM_000259		Approved	MYO5, GS1, MYR12	uc002aby.2	Q9Y4I1	OTTHUMG00000137383	ENST00000399231.3:c.3310-1A>G	chr15.hg19:g.52652277T>C		54.0	0.0		51.0	13.0	NM_000259	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Missense_Mutation	SNP	ENST00000399231.3	hg19	CCDS42037.1	.	.	.	.	.	.	.	.	.	.	T	9.242	1.038428	0.19669	.	.	ENSG00000197535	ENST00000399231;ENST00000399229;ENST00000399233;ENST00000356338;ENST00000358212;ENST00000546028;ENST00000553916	T;T;T;T;T	0.16324	2.35;2.35;2.35;2.35;2.35	5.78	4.63	0.57726	.	0.678176	0.15560	N	0.255957	T	0.07593	0.0191	N	0.08118	0	0.23559	N	0.997419	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38045	-0.9679	10	0.18276	T	0.48	.	5.4466	0.16539	0.0:0.145:0.1557:0.6993	.	1104;1104	Q9Y4I1;Q9Y4I1-2	MYO5A_HUMAN;.	R	1104;638;1104;1104;1104;734;1104	ENSP00000382177:H1104R;ENSP00000382179:H1104R;ENSP00000348693:H1104R;ENSP00000350945:H1104R;ENSP00000451109:H1104R	ENSP00000348693:H1104R	H	-	2	0	MYO5A	50439569	1.000000	0.71417	1.000000	0.80357	0.879000	0.50718	2.473000	0.45145	0.982000	0.38575	0.533000	0.62120	CAT	.	.		0.423	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259	Missense_Mutation	C	52652277	T	C	52652277	5	2	341	1	0	0	0	0	0	0	1	0	10087	1478	51	2	2324	2	MYO5A	15	52652277	Splice_Site	SNP	T	TCGA-RG-A7D4-01A-12D-A33Q-10	9031190	52652277	49879115	88	47189										
MBTPS1	8720	hgsc.bcm.edu	37	chr16	84118684	84118684	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	tcacgccagaaccccgcacgCcagcaccataggtgacaatg	9	16	1	2			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr16:84118684C>G	ENST00000343411.3	-	10	1685	c.1190G>C	c.(1189-1191)gGc>gCc	p.G397A	MBTPS1_ENST00000569770.1_5'UTR	NM_003791.2	NP_003782.1	Q14703	MBTP1_HUMAN	membrane-bound transcription factor peptidase, site 1	397	Peptidase S8.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cholesterol metabolic process (GO:0008203)|endoplasmic reticulum unfolded protein response (GO:0030968)|lipid metabolic process (GO:0006629)|lysosome organization (GO:0007040)|proteolysis (GO:0006508)|regulation of transcription factor import into nucleus (GO:0042990)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(10)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						ACCCCGCACGCCAGCACCATA	0.557											OREG0023982	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G397A		Atlas-SNP	.											.	MBTPS1	85	.	0			c.G1190C						.						75	67	70					16																	84118684		2200	4300	6500	SO:0001583	missense	8720	exon10			CGCACGCCAGCAC	D42053	CCDS10941.1	16q24	2008-08-04	2005-08-17		ENSG00000140943	ENSG00000140943			15456	protein-coding gene	gene with protein product		603355	"membrane-bound transcription factor protease, site 1"			9809072, 10944850	Standard	NM_003791		Approved	S1P, KIAA0091, SKI-1, PCSK8	uc002fhi.3	Q14703	OTTHUMG00000137639	ENST00000343411.3:c.1190G>C	chr16.hg19:g.84118684C>G	ENSP00000344223:p.Gly397Ala	200.0	0.0	1226	123.0	11.0	NM_003791	A8K6V8|Q24JQ2|Q9UF67	Missense_Mutation	SNP	ENST00000343411.3	hg19	CCDS10941.1	.	.	.	.	.	.	.	.	.	.	C	12.86	2.063823	0.36373	.	.	ENSG00000140943	ENST00000343411	D	0.86432	-2.12	5.48	5.48	0.80851	Peptidase S8/S53, subtilisin/kexin/sedolisin (3);	0.000000	0.85682	D	0.000000	D	0.82779	0.5111	L	0.31845	0.965	0.80722	D	1	B	0.12013	0.005	B	0.24006	0.05	T	0.76528	-0.2926	10	0.21014	T	0.42	-18.8898	19.3469	0.94367	0.0:1.0:0.0:0.0	.	397	Q14703	MBTP1_HUMAN	A	397	ENSP00000344223:G397A	ENSP00000344223:G397A	G	-	2	0	MBTPS1	82676185	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	7.818000	0.86416	2.560000	0.86352	0.561000	0.74099	GGC	.	.		0.557	MBTPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269080.2	NM_003791		G	84118684	C	G	84118684	3	3	341	1	0	0	0	0	1	0	0	0	9370	739	26	4	2024	4	MBTPS1	16	84118684	Missense_Mutation	SNP	C	TCGA-RG-A7D4-01A-12D-A33Q-10		84118684	6236069	89	47190										
CYB5D2	124936	hgsc.bcm.edu	37	chr17	4058038	4058038	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	ctgacccaggtagaagctgcGatcaccagaggcttggaggc	14	11	1	3			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr17:4058038G>A	ENST00000301391.3	+	3	962	c.462G>A	c.(460-462)gcG>gcA	p.A154A	CYB5D2_ENST00000575251.1_Silent_p.A42A|CYB5D2_ENST00000575411.2_3'UTR|CYB5D2_ENST00000573984.1_Silent_p.A42A	NM_144611.3	NP_653212.1	Q8WUJ1	NEUFC_HUMAN	cytochrome b5 domain containing 2	154					nervous system development (GO:0007399)	extracellular region (GO:0005576)	heme binding (GO:0020037)			breast(1)|large_intestine(3)|liver(2)|ovary(1)	7						TAGAAGCTGCGATCACCAGAG	0.612																																					p.A154A		Atlas-SNP	.											.	CYB5D2	22	.	0			c.G462A						.						60	57	58					17																	4058038		2203	4300	6503	SO:0001819	synonymous_variant	124936	exon3			AGCTGCGATCACC	AK172844	CCDS11044.1, CCDS58501.1	17p13.2	2006-03-10							28471	protein-coding gene	gene with protein product							Standard	NM_144611		Approved	MGC32124	uc002fxm.4	Q8WUJ1		ENST00000301391.3:c.462G>A	chr17.hg19:g.4058038G>A		148.0	0.0		110.0	43.0	NM_144611	B2R7R6|D3DTJ9|I3L1K2	Silent	SNP	ENST00000301391.3	hg19	CCDS11044.1																																																																																			.	.		0.612	CYB5D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438698.1	NM_144611		A	4058038	G	A	4058038	2	1	341	1	0	0	0	0	0	0	0	1	4127	1045	37	1		1	CYB5D2	17	4058038	Silent	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10		4058038	77137172	90	47191										
TP53	7157	hgsc.bcm.edu	37	chr17	7577114	7577114	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	ggtctctcccaggacaggcaCaaacacgcacctcaaagctg	9	15	2	0			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr17:7577114C>T	ENST00000269305.4	-	8	1013	c.824G>A	c.(823-825)tGt>tAt	p.C275Y	TP53_ENST00000420246.2_Missense_Mutation_p.C275Y|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000445888.2_Missense_Mutation_p.C275Y|TP53_ENST00000359597.4_Missense_Mutation_p.C275Y|TP53_ENST00000455263.2_Missense_Mutation_p.C275Y|TP53_ENST00000413465.2_Intron	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	275	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		C -> F (in sporadic cancers; somatic mutation).|C -> G (in sporadic cancers; somatic mutation).|C -> R (in sporadic cancers; somatic mutation).|C -> S (in sporadic cancers; somatic mutation).|C -> W (in sporadic cancers; somatic mutation).|C -> Y (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:7887414}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.C275Y(53)|p.C275F(37)|p.0?(8)|p.C275fs*70(3)|p.?(2)|p.C275S(2)|p.C275fs*20(1)|p.L265_K305del41(1)|p.R273_C275delRVC(1)|p.F270_D281del12(1)|p.V274_P278del(1)|p.A276fs*29(1)|p.S269fs*21(1)|p.C275fs*67(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	AGGACAGGCACAAACACGCAC	0.552		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.C275Y	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,NS,other,0,111	TP53	33396	.	115	Substitution - Missense(92)|Whole gene deletion(8)|Deletion - Frameshift(7)|Deletion - In frame(6)|Unknown(2)	lung(14)|large_intestine(13)|breast(13)|upper_aerodigestive_tract(12)|central_nervous_system(10)|haematopoietic_and_lymphoid_tissue(10)|ovary(7)|urinary_tract(6)|stomach(5)|oesophagus(5)|bone(5)|liver(5)|skin(3)|pancreas(2)|NS(2)|prostate(2)|biliary_tract(1)	c.G824A	GRCh37	CM076568|CM951234	TP53	M		.						71	61	64					17																	7577114		2203	4300	6503	SO:0001583	missense	7157	exon8	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	CAGGCACAAACAC	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.824G>A	chr17.hg19:g.7577114C>T	ENSP00000269305:p.Cys275Tyr	84.0	0.0		52.0	15.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.605675	0.87157	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99874	-7.39;-7.39;-7.39;-7.39;-7.39;-7.39	4.92	4.92	0.64577	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99883	0.9944	M	0.92738	3.34	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.997;1.0;0.997;0.997	D	0.96317	0.9233	10	0.87932	D	0	-17.2181	15.662	0.77193	0.0:1.0:0.0:0.0	.	275;275;275;275	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	Y	275;275;275;275;275;264;143	ENSP00000352610:C275Y;ENSP00000269305:C275Y;ENSP00000398846:C275Y;ENSP00000391127:C275Y;ENSP00000391478:C275Y;ENSP00000425104:C143Y	ENSP00000269305:C275Y	C	-	2	0	TP53	7517839	1.000000	0.71417	0.999000	0.59377	0.904000	0.53231	7.587000	0.82613	2.556000	0.86216	0.462000	0.41574	TGT	.	.		0.552	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7577114	C	T	7577114	3	4	341	1	0	0	0	0	1	0	0	0	16396	478	17	3	462	3	TP53	17	7577114	Missense_Mutation	SNP	C	TCGA-RG-A7D4-01A-12D-A33Q-10	3519076	7577114	73618096	91	47192										
CNTROB	116840	hgsc.bcm.edu	37	chr17	7851880	7851898	+	Frame_Shift_Del	DEL	GGGGGGCTCTGCCTGCTGA	GGGGGGCTCTGCCTGCTGA	-													0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	actctaccaggctcggggctGgggggctctgcctgctgagg					rs541448932		TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	GGGGGGCTCTGCCTGCTGA	GGGGGGCTCTGCCTGCTGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr17:7851880_7851898delGGGGGGCTCTGCCTGCTGA	ENST00000563694.1	+	17	3381_3399	c.2456_2474delGGGGGGCTCTGCCTGCTGA	c.(2455-2475)tggggggctctgcctgctgagfs	p.WGALPAE819fs	CNTROB_ENST00000380262.3_Frame_Shift_Del_p.WGALPAE819fs|CNTROB_ENST00000565740.1_Frame_Shift_Del_p.WGALPAE819fs|CNTROB_ENST00000380255.3_3'UTR	NM_053051.3	NP_444279.2	Q8N137	CNTRB_HUMAN	centrobin, centrosomal BRCA2 interacting protein	819	Required for centrosome localization.				centriole replication (GO:0007099)|centrosome separation (GO:0051299)|cytokinesis (GO:0000910)	centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(9)	25		Prostate(122;0.173)				GCTCGGGGCTGGGGGGCTCTGCCTGCTGAGGATCTCCTG	0.575																																					p.819_825del		Atlas-Indel,Pindel	.											.	CNTROB	61	.	0			c.2455_2473del						.																																			SO:0001589	frameshift_variant	116840	exon17			.	AF331638	CCDS32557.1, CCDS11126.1	17p13.1	2006-03-15				ENSG00000170037			29616	protein-coding gene	gene with protein product	"centrobin"	611425				11984006, 16275750	Standard	NM_001037144		Approved	LIP8, PP1221	uc002gjp.3	Q8N137		ENST00000563694.1:c.2456_2474delGGGGGGCTCTGCCTGCTGA	chr17.hg19:g.7851880_7851898delGGGGGGCTCTGCCTGCTGA	ENSP00000456335:p.Trp819fs	147.0	0.0		89.0	20.0	NM_053051	A6NHQ1|Q331K3|Q69YV7|Q8NCB8|Q8WXV3|Q96CQ7|Q9C060	Frame_Shift_Del	DEL	ENST00000563694.1	hg19	CCDS11126.1																																																																																			.	.		0.575	CNTROB-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000421372.1	NM_053051		-	7851898	GGGGGGCTCTGCCTGCTGA	-	7851880	7	5	341	1	0	1	0	1	0	0	0	0	3653	1357	47	0	2522	0	CNTROB	17	7851880	Frame_Shift_Del	DEL	GGGGGGCTCTGCCTGCTGA	TCGA-RG-A7D4-01A-12D-A33Q-10	274766	7851880	73343330	92	47193										
STXBP4	252983	hgsc.bcm.edu	37	chr17	53158439	53158439	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	gagctgtgttagcttctcagActtccctcacaccactggga	9	13	2	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr17:53158439A>G	ENST00000376352.2	+	16	1591	c.1384A>G	c.(1384-1386)Act>Gct	p.T462A	STXBP4_ENST00000434978.2_Missense_Mutation_p.T440A	NM_178509.5	NP_848604.3	Q6ZWJ1	STXB4_HUMAN	syntaxin binding protein 4	462					cellular response to DNA damage stimulus (GO:0006974)|glucose transport (GO:0015758)|insulin receptor signaling pathway (GO:0008286)|positive regulation of cell cycle G1/S phase transition (GO:1902808)|positive regulation of keratinocyte proliferation (GO:0010838)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(4)|ovary(1)|upper_aerodigestive_tract(2)	19						AGCTTCTCAGACTTCCCTCAC	0.393																																					p.T462A		Atlas-SNP	.											.	STXBP4	41	.	0			c.A1384G						.						142	129	134					17																	53158439		2203	4300	6503	SO:0001583	missense	252983	exon16			TCTCAGACTTCCC	BC041485	CCDS11584.2	17q22	2008-02-05			ENSG00000166263	ENSG00000166263			19694	protein-coding gene	gene with protein product		610415				12855681	Standard	XM_005257187		Approved	Synip, MGC50337	uc002iuf.1	Q6ZWJ1	OTTHUMG00000074043	ENST00000376352.2:c.1384A>G	chr17.hg19:g.53158439A>G	ENSP00000365530:p.Thr462Ala	105.0	0.0		131.0	47.0	NM_178509	Q8IVZ5	Missense_Mutation	SNP	ENST00000376352.2	hg19	CCDS11584.2	.	.	.	.	.	.	.	.	.	.	A	8.004	0.756099	0.15846	.	.	ENSG00000166263	ENST00000376352;ENST00000434978	T;T	0.44482	0.92;0.92	5.48	3.17	0.36434	.	0.400500	0.29822	N	0.011101	T	0.26882	0.0658	L	0.50919	1.6	0.80722	D	1	B;B	0.33857	0.429;0.077	B;B	0.24006	0.05;0.026	T	0.04440	-1.0951	10	0.12103	T	0.63	-11.7525	6.2359	0.20762	0.7763:0.0:0.0804:0.1433	.	440;462	E7EPP7;Q6ZWJ1	.;STXB4_HUMAN	A	462;440	ENSP00000365530:T462A;ENSP00000391087:T440A	ENSP00000365530:T462A	T	+	1	0	STXBP4	50513438	0.999000	0.42202	0.991000	0.47740	0.035000	0.12851	2.160000	0.42348	1.053000	0.40415	0.533000	0.62120	ACT	.	.		0.393	STXBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157184.1	NM_178509		G	53158439	A	G	53158439	3	3	341	1	0	0	0	0	1	0	0	0	15370	275	10	2	1438	2	STXBP4	17	53158439	Missense_Mutation	SNP	A	TCGA-RG-A7D4-01A-12D-A33Q-10	45306559	53158439	28036771	93	47194										
USP32	84669	hgsc.bcm.edu	37	chr17	58260713	58260713	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	agagccgggtctcttggtacCaaaaaagcacttggatcaaa	10	9	2	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr17:58260713C>A	ENST00000300896.4	-	31	4130	c.3936G>T	c.(3934-3936)ttG>ttT	p.L1312F	USP32_ENST00000592339.1_Missense_Mutation_p.L982F	NM_032582.3	NP_115971.2	Q8NFA0	UBP32_HUMAN	ubiquitin specific peptidase 32	1312	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			NS(3)|breast(5)|endometrium(5)|kidney(4)|large_intestine(12)|liver(1)|lung(24)|pancreas(1)|prostate(3)|skin(3)|urinary_tract(1)	62	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			CTCTTGGTACCAAAAAAGCAC	0.458																																					p.L1312F		Atlas-SNP	.											.	USP32	128	.	0			c.G3936T						.						74	76	75					17																	58260713		2203	4300	6503	SO:0001583	missense	84669	exon31			TGGTACCAAAAAA	AF533230	CCDS32697.1	17q23.3	2013-01-10	2005-08-08		ENSG00000170832	ENSG00000170832		"Ubiquitin-specific peptidases", "EF-hand domain containing"	19143	protein-coding gene	gene with protein product		607740	"ubiquitin specific protease 32"			12838346	Standard	NM_032582		Approved	NY-REN-60, USP10	uc002iyo.1	Q8NFA0		ENST00000300896.4:c.3936G>T	chr17.hg19:g.58260713C>A	ENSP00000300896:p.Leu1312Phe	111.0	0.0		160.0	84.0	NM_032582	Q7Z5T3|Q9BX85|Q9Y591	Missense_Mutation	SNP	ENST00000300896.4	hg19	CCDS32697.1	.	.	.	.	.	.	.	.	.	.	C	19.64	3.865340	0.71949	.	.	ENSG00000170832	ENST00000300896	T	0.34072	1.38	5.78	1.07	0.20283	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.52025	0.1709	M	0.74467	2.265	0.80722	D	1	D	0.69078	0.997	D	0.65874	0.939	T	0.51896	-0.8647	10	0.72032	D	0.01	.	8.1786	0.31296	0.1198:0.676:0.0:0.2042	.	1312	Q8NFA0	UBP32_HUMAN	F	1312	ENSP00000300896:L1312F	ENSP00000300896:L1312F	L	-	3	2	USP32	55615495	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	1.826000	0.39092	0.354000	0.24105	0.650000	0.86243	TTG	.	.		0.458	USP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449235.2	NM_032582		A	58260713	C	A	58260713	3	1	341	1	0	0	0	0	1	0	0	0	17078	593	21	3	894	3	USP32	17	58260713	Missense_Mutation	SNP	C	TCGA-RG-A7D4-01A-12D-A33Q-10	5102274	58260713	22934497	94	47195										
MYOM1	8736	hgsc.bcm.edu	37	chr18	3134722	3134722	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	acgctcgcctctatgtagtaCccgaccagctctttggcatc	8	15	2	0			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr18:3134722C>A	ENST00000356443.4	-	16	2643	c.2310G>T	c.(2308-2310)ggG>ggT	p.G770G	MYOM1_ENST00000261606.7_Silent_p.G770G|MYOM1_ENST00000400569.3_Silent_p.G770G	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	770	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						CTATGTAGTACCCGACCAGCT	0.562																																					p.G770G		Atlas-SNP	.											.	MYOM1	192	.	0			c.G2310T						.						89	89	89					18																	3134722		1940	4135	6075	SO:0001819	synonymous_variant	8736	exon16			GTAGTACCCGACC	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7613	protein-coding gene	gene with protein product	"skelemin"	603508	"myomesin 1 (skelemin) (185kD)", "myomesin 1 (skelemin) 185kDa", "myomesin 1, 185kDa"			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.2310G>T	chr18.hg19:g.3134722C>A		90.0	0.0		196.0	86.0	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Silent	SNP	ENST00000356443.4	hg19	CCDS45824.1																																																																																			.	.		0.562	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803		A	3134722	C	A	3134722	2	1	341	1	0	0	0	0	0	0	0	1	10100	494	18	3		3	MYOM1	18	3134722	Silent	SNP	C	TCGA-RG-A7D4-01A-12D-A33Q-10		3134722	74942526	95	47196										
PALM	5064	hgsc.bcm.edu	37	chr19	746557	746557	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	ccccggtcacaatgatcttcAtgggttaccagaacgtggag	11	11	3	2			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr19:746557A>G	ENST00000338448.5	+	9	953	c.907A>G	c.(907-909)Atg>Gtg	p.M303V	PALM_ENST00000264560.7_Missense_Mutation_p.M259V|PALM_ENST00000593172.1_3'UTR	NM_002579.2	NP_002570.2	O75781	PALM_HUMAN	paralemmin	303					cellular component movement (GO:0006928)|cellular response to electrical stimulus (GO:0071257)|cytoskeleton organization (GO:0007010)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of dopamine receptor signaling pathway (GO:0060160)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of filopodium assembly (GO:0051491)|protein targeting to plasma membrane (GO:0072661)|regulation of cell shape (GO:0008360)|synapse maturation (GO:0060074)	apicolateral plasma membrane (GO:0016327)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cytoplasmic membrane-bounded vesicle (GO:0016023)|dendrite membrane (GO:0032590)|dendritic spine membrane (GO:0032591)|filopodium membrane (GO:0031527)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(2)|large_intestine(1)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_epithelial(18;2.19e-21)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)|Lung(535;0.201)		AATGATCTTCATGGGTTACCA	0.657																																					p.M303V		Atlas-SNP	.											.	PALM	26	.	0			c.A907G						.						39	35	37					19																	746557		2203	4300	6503	SO:0001583	missense	5064	exon9			ATCTTCATGGGTT	Y16270	CCDS32857.1, CCDS32858.1	19p13.3	2008-07-17				ENSG00000099864			8594	protein-coding gene	gene with protein product		608134				9615234, 9813098	Standard	XM_005259565		Approved	KIAA0270	uc002lpm.1	O75781		ENST00000338448.5:c.907A>G	chr19.hg19:g.746557A>G	ENSP00000341911:p.Met303Val	83.0	0.0		55.0	22.0	NM_002579	O43359|O95673|Q92559|Q9UPJ4|Q9UQS2|Q9UQS3	Missense_Mutation	SNP	ENST00000338448.5	hg19	CCDS32857.1	.	.	.	.	.	.	.	.	.	.	A	19.97	3.924688	0.73213	.	.	ENSG00000099864	ENST00000338448;ENST00000264560;ENST00000538247	T;T	0.26067	1.76;1.76	4.92	3.9	0.45041	.	0.000000	0.85682	D	0.000000	T	0.50205	0.1602	M	0.82630	2.6	0.42471	D	0.992821	D;D	0.76494	0.999;0.999	D;D	0.87578	0.997;0.998	T	0.55648	-0.8108	10	0.72032	D	0.01	-47.5939	9.2388	0.37484	0.9137:0.0:0.0863:0.0	.	259;303	O75781-2;O75781	.;PALM_HUMAN	V	303;259;168	ENSP00000341911:M303V;ENSP00000264560:M259V	ENSP00000264560:M259V	M	+	1	0	PALM	697557	1.000000	0.71417	1.000000	0.80357	0.818000	0.46254	7.091000	0.76923	1.839000	0.53478	0.379000	0.24179	ATG	.	.		0.657	PALM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457592.1	NM_002579		G	746557	A	G	746557	3	3	341	1	0	0	0	0	1	0	0	0	11417	217	8	2	941	2	PALM	19	746557	Missense_Mutation	SNP	A	TCGA-RG-A7D4-01A-12D-A33Q-10		746557	58382426	96	47197										
ZNF91	7644	hgsc.bcm.edu	37	chr19	23545412	23545412	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	tccacacttttacaacctttTcttaactgtaaattctcatg	2	11	2	0			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr19:23545412T>C	ENST00000300619.7	-	4	574	c.369A>G	c.(367-369)agA>agG	p.R123R	ZNF91_ENST00000599743.1_Intron|ZNF91_ENST00000397082.2_Silent_p.R91R	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	123					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				TACAACCTTTTCTTAACTGTA	0.358																																					p.R123R		Atlas-SNP	.											.	ZNF91	349	.	0			c.A369G						.						69	73	72					19																	23545412		2132	4273	6405	SO:0001819	synonymous_variant	7644	exon4			ACCTTTTCTTAAC	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"Zinc fingers, C2H2-type", "-"	13166	protein-coding gene	gene with protein product		603971	"zinc finger protein 91 (HPF7, HTF10)"			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.369A>G	chr19.hg19:g.23545412T>C		40.0	0.0		39.0	4.0	NM_003430	A8K5E1|B7Z6G6	Silent	SNP	ENST00000300619.7	hg19	CCDS42541.1																																																																																			.	.		0.358	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430		C	23545412	T	C	23545412	2	2	341	1	0	0	0	0	0	0	0	1	18215	1780	62	2		2	ZNF91	19	23545412	Silent	SNP	T	TCGA-RG-A7D4-01A-12D-A33Q-10	22798855	23545412	35583571	97	47198										
ZNFX1	57169	hgsc.bcm.edu	37	chr20	47864862	47864862	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	tatttgggtgacctcatccaTgtggcagatccggcatttct	10	10	2	2			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr20:47864862T>C	ENST00000396105.1	-	14	4945	c.4699A>G	c.(4699-4701)Atg>Gtg	p.M1567V	ZNFX1_ENST00000371754.4_Intron|ZNFX1_ENST00000371752.1_Missense_Mutation_p.M1567V	NM_021035.2	NP_066363.1	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1	1567							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(8)|kidney(7)|large_intestine(15)|liver(1)|lung(17)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	60			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			ACCTCATCCATGTGGCAGATC	0.542																																					p.M1567V		Atlas-SNP	.											.	ZNFX1	194	.	0			c.A4699G						.						88	92	90					20																	47864862		2203	4300	6503	SO:0001583	missense	57169	exon14			CATCCATGTGGCA	AK022641	CCDS13417.1	20q13.13	2014-02-12			ENSG00000124201	ENSG00000124201			29271	protein-coding gene	gene with protein product						10718198	Standard	NM_021035		Approved	KIAA1404, FLJ11277	uc002xui.3	Q9P2E3	OTTHUMG00000032696	ENST00000396105.1:c.4699A>G	chr20.hg19:g.47864862T>C	ENSP00000379412:p.Met1567Val	85.0	0.0		72.0	35.0	NM_021035	Q9BQM7|Q9BQM8|Q9H8C1|Q9H9S2|Q9NUM1|Q9NWW1	Missense_Mutation	SNP	ENST00000396105.1	hg19	CCDS13417.1	.	.	.	.	.	.	.	.	.	.	T	2.695	-0.272365	0.05716	.	.	ENSG00000124201	ENST00000371752;ENST00000396105	T;T	0.56103	0.48;0.48	6.04	4.02	0.46733	.	0.970787	0.08522	N	0.933342	T	0.34803	0.0910	N	0.12182	0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.24154	-1.0168	10	0.26408	T	0.33	0.3078	9.3459	0.38109	0.0:0.1749:0.5493:0.2758	.	1567	Q9P2E3	ZNFX1_HUMAN	V	1567	ENSP00000360817:M1567V;ENSP00000379412:M1567V	ENSP00000360817:M1567V	M	-	1	0	ZNFX1	47298269	0.861000	0.29849	0.845000	0.33349	0.896000	0.52359	1.830000	0.39131	0.793000	0.33875	-0.366000	0.07423	ATG	.	.		0.542	ZNFX1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079647.2	NM_021035		C	47864862	T	C	47864862	3	2	341	1	0	0	0	0	1	0	0	0	18220	1464	51	2	1061	2	ZNFX1	20	47864862	Missense_Mutation	SNP	T	TCGA-RG-A7D4-01A-12D-A33Q-10		47864862	15160658	98	47199										
DEPDC5	9681	hgsc.bcm.edu	37	chr22	32234735	32234735	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	aagagtttatttgccaacgtCtcatgcagggctaccaaatc	8	10	1	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr22:32234735C>T	ENST00000382112.3	+	26	2462	c.2392C>T	c.(2392-2394)Ctc>Ttc	p.L798F	RNU6-201P_ENST00000517100.1_RNA|DEPDC5_ENST00000382105.2_Missense_Mutation_p.L729F|DEPDC5_ENST00000266091.3_Missense_Mutation_p.L807F|DEPDC5_ENST00000382111.2_Missense_Mutation_p.L807F|DEPDC5_ENST00000400248.2_Missense_Mutation_p.L798F|DEPDC5_ENST00000400249.2_Missense_Mutation_p.L798F|DEPDC5_ENST00000535622.1_Missense_Mutation_p.L729F|DEPDC5_ENST00000400246.1_Missense_Mutation_p.L807F	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	807					intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						TTGCCAACGTCTCATGCAGGG	0.512																																					p.L807F		Atlas-SNP	.											.	DEPDC5	266	.	0			c.C2419T						.						137	141	140					22																	32234735		1988	4163	6151	SO:0001583	missense	9681	exon27			CAACGTCTCATGC	AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.2392C>T	chr22.hg19:g.32234735C>T	ENSP00000371546:p.Leu798Phe	87.0	0.0		58.0	20.0	NM_001242896	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Missense_Mutation	SNP	ENST00000382112.3	hg19	CCDS46692.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.4|25.4	4.629521|4.629521	0.87660|0.87660	.|.	.|.	ENSG00000100150|ENSG00000100150	ENST00000535622;ENST00000266091;ENST00000400249;ENST00000382109;ENST00000400246;ENST00000382105;ENST00000382112;ENST00000382111;ENST00000400248|ENST00000433147	T;T;T;T;T;T;T;T|.	0.22945|.	1.93;1.93;1.93;1.93;1.93;1.93;1.93;1.93|.	5.65|5.65	5.65|5.65	0.86999|0.86999	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.76076|0.76076	0.3937|0.3937	M|M	0.72118|0.72118	2.19|2.19	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0;0.999|.	D;D;D;D;D;D|.	0.91635|.	0.998;0.999;0.997;0.999;0.999;0.997|.	T|T	0.74472|0.74472	-0.3654|-0.3654	10|5	0.62326|.	D|.	0.03|.	.|.	18.7211|18.7211	0.91694|0.91694	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	128;807;729;807;798;798|.	B4DSS1;B9EGN9;B4DH93;O75140-4;A8MPX9;O75140|.	.;.;.;.;.;DEPD5_HUMAN|.	F|F	729;807;798;729;807;729;798;807;798|204	ENSP00000440210:L729F;ENSP00000266091:L807F;ENSP00000383108:L798F;ENSP00000383105:L807F;ENSP00000371539:L729F;ENSP00000371546:L798F;ENSP00000371545:L807F;ENSP00000383107:L798F|.	ENSP00000266091:L807F|.	L|S	+|+	1|2	0|0	DEPDC5|DEPDC5	30564735|30564735	0.975000|0.975000	0.34042|0.34042	0.999000|0.999000	0.59377|0.59377	0.996000|0.996000	0.88848|0.88848	2.349000|2.349000	0.44054|0.44054	2.663000|2.663000	0.90544|0.90544	0.655000|0.655000	0.94253|0.94253	CTC|TCT	.	.		0.512	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662		T	32234735	C	T	32234735	3	4	341	1	0	0	0	0	1	0	0	0	4444	913	32	3	2512	3	DEPDC5	22	32234735	Missense_Mutation	SNP	C	TCGA-RG-A7D4-01A-12D-A33Q-10		32234735	19069831	99	47200										
MCHR1	2847	hgsc.bcm.edu	37	chr22	41075734	41075734	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	ggccccgataacctcacttcGgcaggtgagttgactgggag	14	11	1	2	rs201514957		TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chr22:41075734G>T	ENST00000249016.4	+	1	981	c.285G>T	c.(283-285)tcG>tcT	p.S95S	MCHR1_ENST00000498400.1_Intron|MCHR1_ENST00000381433.2_Silent_p.S95S	NM_005297.3	NP_005288.3	Q99705	MCHR1_HUMAN	melanin-concentrating hormone receptor 1	95					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)|generation of precursor metabolites and energy (GO:0006091)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	integral component of plasma membrane (GO:0005887)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|hormone binding (GO:0042562)|melanin-concentrating hormone receptor activity (GO:0030273)|neuropeptide receptor activity (GO:0008188)			endometrium(5)|large_intestine(7)|lung(6)|pancreas(1)|urinary_tract(1)	20						ACCTCACTTCGGCAGGTGAGT	0.597																																					p.S95S		Atlas-SNP	.											.	MCHR1	45	.	0			c.G285T						.						58	63	61					22																	41075734		2202	4300	6502	SO:0001819	synonymous_variant	2847	exon1			CACTTCGGCAGGT		CCDS14004.1	22q13.3	2014-06-05	2006-02-15	2006-02-15	ENSG00000128285	ENSG00000128285		"GPCR / Class A : MCH receptors"	4479	protein-coding gene	gene with protein product		601751	"G protein-coupled receptor 24"	GPR24			Standard	XM_005261581		Approved	SLC1, MCH1R	uc003ayz.3	Q99705	OTTHUMG00000150256	ENST00000249016.4:c.285G>T	chr22.hg19:g.41075734G>T		65.0	0.0		63.0	21.0	NM_005297	B2RBX6|Q5R3J1|Q96S47|Q9BV08	Silent	SNP	ENST00000249016.4	hg19	CCDS14004.1																																																																																			.	.		0.597	MCHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317142.1	NM_005297		T	41075734	G	T	41075734	2	4	341	1	0	0	0	0	0	0	0	1	9391	1103	39	1		1	MCHR1	22	41075734	Silent	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10	8840999	41075734	10228832	100	47201										
MXRA5	25878	hgsc.bcm.edu	37	chrX	3239233	3239233	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	gtcccaaagacatgagaattGtggatggggacgaggatgct	15	6	0	2			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chrX:3239233G>T	ENST00000217939.6	-	5	4647	c.4493C>A	c.(4492-4494)aCa>aAa	p.T1498K		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	1498						extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				CATGAGAATTGTGGATGGGGA	0.478																																					p.T1498K		Atlas-SNP	.											.	MXRA5	815	.	0			c.C4493A						.						136	117	124					X																	3239233		2203	4300	6503	SO:0001583	missense	25878	exon5			AGAATTGTGGATG	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7539	protein-coding gene	gene with protein product	"adlican"					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.4493C>A	chrX.hg19:g.3239233G>T	ENSP00000217939:p.Thr1498Lys	75.0	0.0		106.0	5.0	NM_015419	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	hg19	CCDS14124.1	.	.	.	.	.	.	.	.	.	.	g	11.50	1.656847	0.29425	.	.	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.62364	0.03	3.18	2.27	0.28462	.	0.619297	0.13141	U	0.410657	T	0.43233	0.1238	L	0.32530	0.975	0.09310	N	1	P	0.39480	0.675	B	0.32465	0.146	T	0.16660	-1.0395	10	0.27082	T	0.32	.	7.8392	0.29389	0.1419:0.0:0.8581:0.0	.	1498	Q9NR99	MXRA5_HUMAN	K	1498	ENSP00000217939:T1498K	ENSP00000217939:T1498K	T	-	2	0	MXRA5	3249233	0.016000	0.18221	0.009000	0.14445	0.003000	0.03518	0.445000	0.21677	1.366000	0.46076	0.418000	0.28097	ACA	.	.		0.478	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		T	3239233	G	T	3239233	3	4	341	1	0	0	0	0	1	0	0	0	10012	1377	48	3	4005	3	MXRA5	23	3239233	Missense_Mutation	SNP	G	TCGA-RG-A7D4-01A-12D-A33Q-10		3239233	152031327	101	47202										
GLUD2	2747	hgsc.bcm.edu	37	chrX	120182071	120182071	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0882352941176471	9	1	1.44409937888199	1.1231884057971	1.4975845410628	0.00942253331538567	0.234306995109257	0	gtgtgcagtggttgatgtgcCgtttgggggtgctaaagctg	18	5	0	1			TCGA-RG-A7D4-01A-12D-A33Q-10	TCGA-RG-A7D4-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d11dc224-6c52-4463-837f-20d99569f8b9	473df61f-c817-4a0c-a458-934d47687fa9	g.chrX:120182071C>G	ENST00000328078.1	+	1	610	c.533C>G	c.(532-534)cCg>cGg	p.P178R		NM_012084.3	NP_036216.2	P49448	DHE4_HUMAN	glutamate dehydrogenase 2	178					glutamate biosynthetic process (GO:0006537)|glutamate catabolic process (GO:0006538)|glutamate metabolic process (GO:0006536)|oxidation-reduction process (GO:0055114)	mitochondrion (GO:0005739)	ADP binding (GO:0043531)|glutamate dehydrogenase (NAD+) activity (GO:0004352)|glutamate dehydrogenase [NAD(P)+] activity (GO:0004353)|GTP binding (GO:0005525)|leucine binding (GO:0070728)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|urinary_tract(1)	38						GTTGATGTGCCGTTTGGGGGT	0.453																																					p.P178R		Atlas-SNP	.											.	GLUD2	89	.	0			c.C533G						.						118	91	100					X																	120182071		2203	4300	6503	SO:0001583	missense	2747	exon1			ATGTGCCGTTTGG	U08997	CCDS14603.1	Xq24-q25	2008-02-05	2003-02-24	2003-02-28	ENSG00000182890	ENSG00000182890			4336	protein-coding gene	gene with protein product		300144	"glutamate dehydrogenase pseudogene 1"	GLUDP1		8207021, 9109504	Standard	NM_012084		Approved		uc004eto.3	P49448	OTTHUMG00000022320	ENST00000328078.1:c.533C>G	chrX.hg19:g.120182071C>G	ENSP00000327589:p.Pro178Arg	34.0	0.0		46.0	27.0	NM_012084	B2R8G0|Q9UDQ4	Missense_Mutation	SNP	ENST00000328078.1	hg19	CCDS14603.1	.	.	.	.	.	.	.	.	.	.	C	6.585	0.476351	0.12521	.	.	ENSG00000182890	ENST00000328078	D	0.97620	-4.46	1.62	0.69	0.18039	Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain (1);	0.000000	0.85682	D	0.000000	D	0.98544	0.9514	H	0.97315	3.98	0.54753	D	0.999989	D	0.89917	1.0	D	0.77557	0.99	D	0.96416	0.9308	10	0.87932	D	0	.	4.7803	0.13199	0.3626:0.6374:0.0:0.0	.	178	P49448	DHE4_HUMAN	R	178	ENSP00000327589:P178R	ENSP00000327589:P178R	P	+	2	0	GLUD2	120009752	0.986000	0.35501	0.370000	0.25965	0.080000	0.17528	1.818000	0.39012	0.175000	0.19841	0.472000	0.43445	CCG	.	.		0.453	GLUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058133.1	NM_012084		G	120182071	C	G	120182071	3	3	341	1	0	0	0	0	1	0	0	0	6485	652	23	4	535	4	GLUD2	23	120182071	Missense_Mutation	SNP	C	TCGA-RG-A7D4-01A-12D-A33Q-10	116942838	120182071	35088489	102	47203										
UBR4	23352	hgsc.bcm.edu	37	chr1	19513738	19513738	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	cagccgttgaatcctctgtaTggaggtgctctgggccataa	12	10	2	1			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr1:19513738T>A	ENST00000375254.3	-	13	1579	c.1552A>T	c.(1552-1554)Ata>Tta	p.I518L	UBR4_ENST00000375217.2_Missense_Mutation_p.I518L|UBR4_ENST00000375226.2_Missense_Mutation_p.I518L|UBR4_ENST00000375267.2_Missense_Mutation_p.I518L	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	518					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		ATCCTCTGTATGGAGGTGCTC	0.493																																					p.I518L		Atlas-SNP	.											.	UBR4	415	.	0			c.A1552T						.						92	80	84					1																	19513738		2203	4300	6503	SO:0001583	missense	23352	exon13			TCTGTATGGAGGT	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.1552A>T	chr1.hg19:g.19513738T>A	ENSP00000364403:p.Ile518Leu	60.0	0.0		82.0	19.0	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	hg19	CCDS189.1	.	.	.	.	.	.	.	.	.	.	T	9.020	0.984550	0.18889	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226	T;T;T;T	0.19806	2.12;2.12;2.12;2.12	5.97	4.84	0.62591	.	0.105878	0.64402	N	0.000008	T	0.08714	0.0216	N	0.05078	-0.115	0.80722	D	1	B	0.26002	0.139	B	0.16722	0.016	T	0.12142	-1.0559	10	0.02654	T	1	.	12.5388	0.56156	0.0:0.0:0.1394:0.8606	.	518	Q5T4S7	UBR4_HUMAN	L	518	ENSP00000364403:I518L;ENSP00000364416:I518L;ENSP00000364365:I518L;ENSP00000364374:I518L	ENSP00000364365:I518L	I	-	1	0	UBR4	19386325	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.756000	0.68757	1.073000	0.40885	-0.264000	0.10439	ATA	.	.		0.493	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		A	19513738	T	A	19513738	3	1	342	1	0	0	0	0	1	0	0	0	16919	1464	51	4	14375	4	UBR4	1	19513738	Missense_Mutation	SNP	T	TCGA-T1-A6J8-01A-11D-A32G-10		19513738	229736883	1	47204										
HMGB4	127540	hgsc.bcm.edu	37	chr1	34329977	34329977	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	tgaaaaggccaaatatgaagCcctggccaaactcgacaaag	9	10	0	2			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr1:34329977C>A	ENST00000522796.1	+	4	2090	c.185C>A	c.(184-186)gCc>gAc	p.A62D	HMGB4_ENST00000425537.1_3'UTR|HMGB4_ENST00000519684.1_Missense_Mutation_p.A62D|CSMD2_ENST00000373381.4_Intron			Q8WW32	HMGB4_HUMAN	high mobility group box 4	62						chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(1)|large_intestine(1)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	12		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				AAATATGAAGCCCTGGCCAAA	0.463																																					p.A62D		Atlas-SNP	.											.	HMGB4	27	.	0			c.C185A						.						120	135	130					1																	34329977		2203	4300	6503	SO:0001583	missense	127540	exon2			ATGAAGCCCTGGC		CCDS30668.1	1p35.1	2011-07-01	2011-04-05		ENSG00000176256	ENSG00000176256		"High-mobility group / Canonical"	24954	protein-coding gene	gene with protein product			"high-mobility group box 4"				Standard	NR_033264		Approved	FLJ40388	uc001bxp.3	Q8WW32	OTTHUMG00000013143	ENST00000522796.1:c.185C>A	chr1.hg19:g.34329977C>A	ENSP00000430919:p.Ala62Asp	88.0	0.0		117.0	18.0	NM_145205	B2R4X7|Q0QWA4	Missense_Mutation	SNP	ENST00000522796.1	hg19	CCDS30668.1	.	.	.	.	.	.	.	.	.	.	C	6.856	0.527267	0.13066	.	.	ENSG00000176256	ENST00000519684;ENST00000522796	T;T	0.12774	2.65;2.65	5.58	0.467	0.16721	.	0.232725	0.37053	N	0.002268	T	0.09423	0.0232	L	0.28192	0.835	0.33964	D	0.646037	P	0.47034	0.889	P	0.50896	0.653	T	0.31194	-0.9952	10	0.02654	T	1	.	4.817	0.13372	0.4359:0.4072:0.0:0.1569	.	62	B2R4X7	.	D	62	ENSP00000429214:A62D;ENSP00000430919:A62D	ENSP00000429214:A62D	A	+	2	0	HMGB4	34102564	0.991000	0.36638	0.082000	0.20525	0.854000	0.48673	2.434000	0.44802	-0.049000	0.13379	-0.192000	0.12808	GCC	.	.		0.463	HMGB4-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375773.1	NM_145205		A	34329977	C	A	34329977	3	1	342	1	0	0	0	0	1	0	0	0	7237	739	26	3	187	3	HMGB4	1	34329977	Missense_Mutation	SNP	C	TCGA-T1-A6J8-01A-11D-A32G-10	14816239	34329977	214920644	2	47205										
MSH4	4438	hgsc.bcm.edu	37	chr1	76262910	76262910	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	gcgccaaactcccggccagcTcaaggcaaggagtgattggg	14	12	1	1			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr1:76262910T>G	ENST00000263187.3	+	1	344	c.240T>G	c.(238-240)gcT>gcG	p.A80A		NM_002440.3	NP_002431.2	O15457	MSH4_HUMAN	mutS homolog 4	80					ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|female gamete generation (GO:0007292)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|ovarian follicle development (GO:0001541)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	47						CCCGGCCAGCTCAAGGCAAGG	0.647								Mismatch excision repair (MMR)																													p.A80A		Atlas-SNP	.											.	MSH4	147	.	0			c.T240G						.						9	10	10					1																	76262910		2188	4281	6469	SO:0001819	synonymous_variant	4438	exon1			GCCAGCTCAAGGC	U89293	CCDS670.1	1p31	2013-09-12	2013-09-12		ENSG00000057468	ENSG00000057468			7327	protein-coding gene	gene with protein product		602105	"mutS (E. coli) homolog 4", "mutS homolog 4 (E. coli)"			9299235	Standard	NM_002440		Approved		uc001dhd.2	O15457	OTTHUMG00000009788	ENST00000263187.3:c.240T>G	chr1.hg19:g.76262910T>G		28.0	0.0		36.0	12.0	NM_002440	Q5T4U6|Q8NEB3|Q9UNP8	Silent	SNP	ENST00000263187.3	hg19	CCDS670.1																																																																																			.	.		0.647	MSH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026983.1	NM_002440		G	76262910	T	G	76262910	2	3	342	1	0	0	0	0	0	0	0	1	9881	1538	54	5		5	MSH4	1	76262910	Silent	SNP	T	TCGA-T1-A6J8-01A-11D-A32G-10	41932933	76262910	172987711	3	47206										
BIRC6	57448	hgsc.bcm.edu	37	chr2	32842852	32842852	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	cctgccctgaaggcttggatCctgacactgacgatgcccca	10	15	0	3			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr2:32842852C>A	ENST00000421745.2	+	74	14589	c.14455C>A	c.(14455-14457)Cct>Act	p.P4819T		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	4819					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					AGGCTTGGATCCTGACACTGA	0.527																																					p.P4819T	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.C14455A						.						118	91	100					2																	32842852		2203	4300	6503	SO:0001583	missense	57448	exon74			TTGGATCCTGACA	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.14455C>A	chr2.hg19:g.32842852C>A	ENSP00000393596:p.Pro4819Thr	51.0	0.0		85.0	30.0	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	hg19	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	C	10.12	1.262068	0.23051	.	.	ENSG00000115760	ENST00000421745	T	0.73681	-0.77	5.76	5.76	0.90799	.	0.059335	0.64402	D	0.000002	T	0.62853	0.2462	L	0.34521	1.04	0.58432	D	0.999997	P	0.37781	0.608	B	0.32090	0.14	T	0.61451	-0.7060	10	0.10377	T	0.69	.	19.9664	0.97271	0.0:1.0:0.0:0.0	.	4819	Q9NR09	BIRC6_HUMAN	T	4819	ENSP00000393596:P4819T	ENSP00000393596:P4819T	P	+	1	0	BIRC6	32696356	1.000000	0.71417	0.997000	0.53966	0.466000	0.32739	5.558000	0.67319	2.718000	0.92993	0.655000	0.94253	CCT	.	.		0.527	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		A	32842852	C	A	32842852	3	1	342	1	0	0	0	0	1	0	0	0	1438	855	30	3	14749	3	BIRC6	2	32842852	Missense_Mutation	SNP	C	TCGA-T1-A6J8-01A-11D-A32G-10		32842852	210356521	4	47207										
LTBP1	4052	hgsc.bcm.edu	37	chr2	33413881	33413881	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	ccccgtggctgctaagacacAgcttggccggtgcttccagg	13	14	0	1			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr2:33413881A>G	ENST00000404816.2	+	7	2017	c.1664A>G	c.(1663-1665)cAg>cGg	p.Q555R	LTBP1_ENST00000390003.4_Missense_Mutation_p.Q229R|LTBP1_ENST00000418533.2_Missense_Mutation_p.Q229R|LTBP1_ENST00000354476.3_Missense_Mutation_p.Q555R|LTBP1_ENST00000407925.1_Missense_Mutation_p.Q229R|LTBP1_ENST00000404525.1_Missense_Mutation_p.Q229R|LTBP1_ENST00000402934.1_Missense_Mutation_p.Q229R			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	555					extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				GCTAAGACACAGCTTGGCCGG	0.502																																					p.Q555R		Atlas-SNP	.											.	LTBP1	317	.	0			c.A1664G						.						122	122	122					2																	33413881		2203	4300	6503	SO:0001583	missense	4052	exon7			AGACACAGCTTGG		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"Latent transforming growth factor, beta binding proteins"	6714	protein-coding gene	gene with protein product	"TGF-beta1-BP-1"	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.1664A>G	chr2.hg19:g.33413881A>G	ENSP00000386043:p.Gln555Arg	84.0	0.0		103.0	35.0	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	hg19	CCDS33177.2	.	.	.	.	.	.	.	.	.	.	A	16.58	3.162808	0.57368	.	.	ENSG00000049323	ENST00000404816;ENST00000354476;ENST00000390003;ENST00000418533;ENST00000402934;ENST00000404525;ENST00000407925	D;D;D;D;D;D;D	0.91577	-2.87;-2.87;-2.87;-2.87;-2.87;-2.87;-2.87	5.73	5.73	0.89815	Matrix fibril-associated (2);	.	.	.	.	D	0.92358	0.7575	L	0.44542	1.39	0.80722	D	1	D;D;B;D;D;D	0.69078	0.99;0.995;0.094;0.979;0.997;0.994	P;D;B;P;D;D	0.78314	0.844;0.991;0.07;0.798;0.99;0.925	D	0.89456	0.3733	9	0.11794	T	0.64	.	16.0283	0.80558	1.0:0.0:0.0:0.0	.	555;229;229;229;229;555	Q14766;E7EV71;Q14766-3;Q14766-2;Q14766-5;Q14766-4	LTBP1_HUMAN;.;.;.;.;.	R	555;555;229;229;229;229;229	ENSP00000386043:Q555R;ENSP00000346467:Q555R;ENSP00000374653:Q229R;ENSP00000393057:Q229R;ENSP00000384373:Q229R;ENSP00000385359:Q229R;ENSP00000384091:Q229R	ENSP00000346467:Q555R	Q	+	2	0	LTBP1	33267385	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	6.548000	0.73896	2.199000	0.70637	0.459000	0.35465	CAG	.	.		0.502	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943		G	33413881	A	G	33413881	3	3	342	1	0	0	0	0	1	0	0	0	9082	188	7	2	1745	2	LTBP1	2	33413881	Missense_Mutation	SNP	A	TCGA-T1-A6J8-01A-11D-A32G-10	571029	33413881	209785492	5	47208										
CCT7	10574	hgsc.bcm.edu	37	chr2	73479859	73479859	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	gccagctatggtgcggatcaAtgcgctgacagcagcctctg	13	12	2	1			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr2:73479859A>G	ENST00000258091.5	+	12	1643	c.1502A>G	c.(1501-1503)aAt>aGt	p.N501S	CCT7_ENST00000398422.2_Missense_Mutation_p.N297S|CCT7_ENST00000540468.1_Missense_Mutation_p.N414S|CCT7_ENST00000537131.1_Missense_Mutation_p.N401S|CCT7_ENST00000538797.1_Missense_Mutation_p.N373S|CCT7_ENST00000539919.1_Missense_Mutation_p.N457S	NM_006429.3	NP_006420.1	Q99832	TCPH_HUMAN	chaperonin containing TCP1, subunit 7 (eta)	501					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|unfolded protein binding (GO:0051082)			breast(1)|cervix(1)|endometrium(1)|lung(3)|stomach(1)	7						GTGCGGATCAATGCGCTGACA	0.542																																					p.N501S		Atlas-SNP	.											.	CCT7	60	.	0			c.A1502G						.						73	79	77					2																	73479859		2055	4198	6253	SO:0001583	missense	10574	exon12			GGATCAATGCGCT	AF026292	CCDS42696.1, CCDS46336.1, CCDS54366.1, CCDS54367.1	2p13.2	2011-09-02			ENSG00000135624	ENSG00000135624		"Heat Shock Proteins / Chaperonins"	1622	protein-coding gene	gene with protein product		605140				9819444	Standard	NM_006429		Approved	Ccth, Nip7-1	uc002siz.3	Q99832	OTTHUMG00000152765	ENST00000258091.5:c.1502A>G	chr2.hg19:g.73479859A>G	ENSP00000258091:p.Asn501Ser	119.0	0.0		198.0	83.0	NM_006429	A8K7E6|A8MWI8|B7WNW9|B7Z4T9|B7Z4Z7|O14871|Q6FI26	Missense_Mutation	SNP	ENST00000258091.5	hg19	CCDS46336.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.407098	0.83230	.	.	ENSG00000135624	ENST00000540468;ENST00000539919;ENST00000258091;ENST00000398422;ENST00000537131;ENST00000538797;ENST00000409081	T;T;T;T;T;T	0.77229	-1.08;-1.08;-1.08;-1.08;-1.08;-1.08	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	D	0.84451	0.5475	L	0.49778	1.585	0.80722	D	1	D;D;D;D;P;D	0.89917	0.999;0.96;0.982;1.0;0.835;1.0	D;P;P;D;P;D	0.91635	0.994;0.847;0.838;0.999;0.694;0.999	D	0.85659	0.1287	10	0.62326	D	0.03	-27.3315	14.2361	0.65927	1.0:0.0:0.0:0.0	.	414;373;401;459;297;501	B7Z4Z7;B7Z1C9;F5GZK5;B8ZZC9;A8MWI8;Q99832	.;.;.;.;.;TCPH_HUMAN	S	414;457;501;297;401;373;459	ENSP00000442058:N414S;ENSP00000437824:N457S;ENSP00000258091:N501S;ENSP00000381456:N297S;ENSP00000444379:N401S;ENSP00000438462:N373S	ENSP00000258091:N501S	N	+	2	0	CCT7	73333367	1.000000	0.71417	0.992000	0.48379	0.948000	0.59901	8.822000	0.92013	2.198000	0.70561	0.533000	0.62120	AAT	.	.		0.542	CCT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327714.2			G	73479859	A	G	73479859	3	3	342	1	0	0	0	0	1	0	0	0	2961	101	4	2	1548	2	CCT7	2	73479859	Missense_Mutation	SNP	A	TCGA-T1-A6J8-01A-11D-A32G-10	40065978	73479859	169719514	6	47209										
NAT8	9027	hgsc.bcm.edu	37	chr2	73868638	73868638	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	taagagtatgagggttcgagGcagcttcagcaattgccgga	14	7	1	2			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr2:73868638G>T	ENST00000272425.3	-	2	267	c.118C>A	c.(118-120)Cct>Act	p.P40T		NM_003960.3|NM_016347.2	NP_003951.3|NP_057431.2			N-acetyltransferase 8 (GCN5-related, putative)											breast(1)|endometrium(2)|kidney(2)|lung(2)|ovary(1)|prostate(1)	9						AGGGTTCGAGGCAGCTTCAGC	0.627																																					p.P40T		Atlas-SNP	.											.	NAT8	26	.	0			c.C118A						.						78	91	87					2																	73868638		2203	4300	6503	SO:0001583	missense	9027	exon2			TTCGAGGCAGCTT	AB013094	CCDS1926.1	2p13.2	2012-03-20	2008-09-24		ENSG00000144035	ENSG00000144035			18069	protein-coding gene	gene with protein product		606716	"N-acetyltransferase 8"			11397015, 9852678, 19011241	Standard	NM_003960		Approved	Hcml1, TSC501, GLA, ATase2	uc002sji.1	Q9UHE5	OTTHUMG00000129818	ENST00000272425.3:c.118C>A	chr2.hg19:g.73868638G>T	ENSP00000272425:p.Pro40Thr	68.0	0.0		86.0	36.0	NM_003960		Missense_Mutation	SNP	ENST00000272425.3	hg19	CCDS1926.1	.	.	.	.	.	.	.	.	.	.	G	18.46	3.628136	0.66901	.	.	ENSG00000144035	ENST00000272425	T	0.34472	1.36	3.86	2.87	0.33458	.	0.193112	0.43919	D	0.000504	T	0.53514	0.1801	M	0.73217	2.22	0.43628	D	0.996013	D	0.76494	0.999	D	0.66847	0.947	T	0.57046	-0.7878	10	0.56958	D	0.05	-52.0712	10.9497	0.47321	0.0:0.1925:0.8075:0.0	.	40	Q9UHE5	NAT8_HUMAN	T	40	ENSP00000272425:P40T	ENSP00000272425:P40T	P	-	1	0	NAT8	73722146	0.960000	0.32886	0.526000	0.27913	0.167000	0.22549	1.518000	0.35877	2.110000	0.64415	0.644000	0.83932	CCT	.	.		0.627	NAT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327854.1	NM_003960		T	73868638	G	T	73868638	3	4	342	1	0	0	0	0	1	0	0	0	10188	1203	42	3	569	3	NAT8	2	73868638	Missense_Mutation	SNP	G	TCGA-T1-A6J8-01A-11D-A32G-10	388779	73868638	169330735	7	47210										
C2orf68	388969	hgsc.bcm.edu	37	chr2	85836186	85836186	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	cactcacctttcctgggtcaTcaccctacgtggaggaagag	10	13	3	1			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr2:85836186T>C	ENST00000306336.5	-	4	427	c.383A>G	c.(382-384)gAt>gGt	p.D128G	C2orf68_ENST00000478626.1_5'Flank|USP39_ENST00000459775.1_Intron	NM_001013649.3	NP_001013671.2	Q2NKX9	CB068_HUMAN	chromosome 2 open reading frame 68	128										breast(1)|central_nervous_system(1)|endometrium(1)	3						TCCTGGGTCATCACCCTACGT	0.552																																					p.D128G		Atlas-SNP	.											.	C2orf68	5	.	0			c.A383G						.						75	74	74					2																	85836186		2016	4196	6212	SO:0001583	missense	388969	exon4			GGGTCATCACCCT		CCDS42704.1	2p11.2	2008-07-18			ENSG00000168887	ENSG00000168887			34353	protein-coding gene	gene with protein product							Standard	NM_001013649		Approved		uc002sqc.2	Q2NKX9	OTTHUMG00000153088	ENST00000306336.5:c.383A>G	chr2.hg19:g.85836186T>C	ENSP00000304410:p.Asp128Gly	71.0	0.0		93.0	35.0	NM_001013649	B4DT10|Q4G0J7|Q6ZVA6	Missense_Mutation	SNP	ENST00000306336.5	hg19	CCDS42704.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.974795	0.74360	.	.	ENSG00000168887	ENST00000306336	.	.	.	5.41	5.41	0.78517	.	1.609690	0.03730	N	0.253372	T	0.71333	0.3327	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.54456	-0.8291	9	0.72032	D	0.01	-8.3227	11.7613	0.51905	0.0:0.0:0.0:1.0	.	128	Q2NKX9	CB068_HUMAN	G	128	.	ENSP00000304410:D128G	D	-	2	0	C2orf68	85689697	1.000000	0.71417	0.999000	0.59377	0.916000	0.54674	4.805000	0.62561	2.281000	0.76405	0.533000	0.62120	GAT	.	.		0.552	C2orf68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329451.1	NM_001013649		C	85836186	T	C	85836186	3	2	342	1	0	0	0	0	1	0	0	0	2189	1435	50	2	121	2	C2orf68	2	85836186	Missense_Mutation	SNP	T	TCGA-T1-A6J8-01A-11D-A32G-10	11967548	85836186	157363187	8	47211										
OLA1	29789	hgsc.bcm.edu	37	chr2	175111522	175111522	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	tgggggtggtttaattccatCacctccctttttagggggca	12	9	1	0			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr2:175111522C>T	ENST00000409546.1	-	2	712	c.82G>A	c.(82-84)Gat>Aat	p.D28N	OLA1_ENST00000344357.5_Intron|OLA1_ENST00000284719.3_Missense_Mutation_p.D8N|OLA1_ENST00000428402.2_Missense_Mutation_p.D8N					Obg-like ATPase 1											breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	11						TTAATTCCATCACCTCCCTTT	0.393																																					p.D8N		Atlas-SNP	.											.	OLA1	37	.	0			c.G22A						.						63	63	63					2																	175111522		2203	4300	6503	SO:0001583	missense	29789	exon2			TTCCATCACCTCC		CCDS2255.1, CCDS42779.1	2q31.1	2014-06-24	2007-07-27	2007-07-27	ENSG00000138430	ENSG00000138430			28833	protein-coding gene	gene with protein product		611175	"GTP-binding protein 9 (putative)"	GTPBP9		17430889, 24486488	Standard	NM_013341		Approved	PTD004	uc002uih.3	Q9NTK5	OTTHUMG00000132335	ENST00000409546.1:c.82G>A	chr2.hg19:g.175111522C>T	ENSP00000386350:p.Asp28Asn	138.0	0.0		288.0	30.0	NM_013341		Missense_Mutation	SNP	ENST00000409546.1	hg19		.	.	.	.	.	.	.	.	.	.	C	19.52	3.843015	0.71488	.	.	ENSG00000138430	ENST00000284719;ENST00000428402;ENST00000409546;ENST00000427472	T;T;T;T	0.43688	0.97;0.95;0.94;0.96	5.53	4.65	0.58169	.	0.150654	0.64402	D	0.000013	T	0.30230	0.0758	N	0.19112	0.55	0.58432	D	0.999999	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.08055	0.003;0.001;0.001	T	0.07558	-1.0766	10	0.66056	D	0.02	.	13.4888	0.61382	0.0:0.923:0.0:0.0769	.	8;8;8	Q9NTK5-3;D7EHM2;Q9NTK5	.;.;OLA1_HUMAN	N	8;8;28;8	ENSP00000284719:D8N;ENSP00000410385:D8N;ENSP00000386350:D28N;ENSP00000414568:D8N	ENSP00000284719:D8N	D	-	1	0	OLA1	174819768	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.551000	0.73909	1.316000	0.45131	0.561000	0.74099	GAT	.	.		0.393	OLA1-003	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000333877.1	NM_013341		T	175111522	C	T	175111522	3	4	342	1	0	0	0	0	1	0	0	0	10859	826	29	3	1208	3	OLA1	2	175111522	Missense_Mutation	SNP	C	TCGA-T1-A6J8-01A-11D-A32G-10	89275336	175111522	68087851	9	47212										
ERBB4	2066	hgsc.bcm.edu	37	chr2	212576873	212576873	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	tccacagtctgagctgacatCaatgatcctgtgccaatgcc	8	13	2	3	rs149272231	byFrequency	TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr2:212576873C>G	ENST00000342788.4	-	9	1336	c.1026G>C	c.(1024-1026)ttG>ttC	p.L342F	ERBB4_ENST00000436443.1_Missense_Mutation_p.L342F|ERBB4_ENST00000402597.1_Missense_Mutation_p.L342F	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	342					cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	GAGCTGACATCAATGATCCTG	0.383										TSP Lung(8;0.080)																											p.L342F		Atlas-SNP	.											.	ERBB4	480	.	0			c.G1026C						.						103	94	97					2																	212576873		2203	4300	6503	SO:0001583	missense	2066	exon9			TGACATCAATGAT	L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.1026G>C	chr2.hg19:g.212576873C>G	ENSP00000342235:p.Leu342Phe	134.0	0.0		140.0	73.0	NM_001042599	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	hg19	CCDS2394.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.90|14.90	2.673978|2.673978	0.47781|0.47781	.|.	.|.	ENSG00000178568|ENSG00000178568	ENST00000342788;ENST00000436443;ENST00000402597|ENST00000260943	T;T;T|.	0.77877|.	-1.13;-1.13;-1.13|.	5.14|5.14	5.14|5.14	0.70334|0.70334	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.61173|.	0.2326|.	L|L	0.46741|0.46741	1.465|1.465	0.58432|0.58432	D|D	0.999999|0.999999	D;P;D;D;D|.	0.89917|.	1.0;0.63;1.0;1.0;1.0|.	D;B;D;D;D|.	0.91635|.	0.999;0.199;0.999;0.999;0.998|.	T|.	0.58109|.	-0.7694|.	10|.	0.33141|.	T|.	0.24|.	.|.	13.9538|13.9538	0.64135|0.64135	0.0:0.9242:0.0:0.0758|0.0:0.9242:0.0:0.0758	.|.	342;342;201;342;342|.	Q15303-4;Q15303-2;Q53QS8;Q15303-3;Q15303|.	.;.;.;.;ERBB4_HUMAN|.	F|S	342|342	ENSP00000342235:L342F;ENSP00000403204:L342F;ENSP00000385565:L342F|.	ENSP00000342235:L342F|.	L|X	-|-	3|2	2|2	ERBB4|ERBB4	212285118|212285118	1.000000|1.000000	0.71417|0.71417	0.992000|0.992000	0.48379|0.48379	0.988000|0.988000	0.76386|0.76386	0.837000|0.837000	0.27558|0.27558	2.386000|2.386000	0.81285|0.81285	0.467000|0.467000	0.42956|0.42956	TTG|TGA	.	C|1.000;T|0.000		0.383	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		G	212576873	C	G	212576873	3	3	342	1	0	0	0	0	1	0	0	0	5211	825	29	4	2980	4	ERBB4	2	212576873	Missense_Mutation	SNP	C	TCGA-T1-A6J8-01A-11D-A32G-10	37465351	212576873	30622500	10	47213										
HDAC4	9759	hgsc.bcm.edu	37	chr2	240158361	240158361	+	Splice_Site	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	gtctcggccagaaagtccatCtggagaacagagaaggcact	12	10	2	3			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr2:240158361C>G	ENST00000345617.3	-	3	814		c.e3-1			NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4						B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		GAAAGTCCATCTGGAGAACAG	0.567																																					.		Atlas-SNP	.											.	HDAC4	127	.	0			c.23-1G>C						.						50	41	44					2																	240158361		1912	3610	5522	SO:0001630	splice_region_variant	9759	exon4			GTCCATCTGGAGA	AB006626	CCDS2529.1	2q37.3	2014-02-12			ENSG00000068024	ENSG00000068024			14063	protein-coding gene	gene with protein product		605314	"brachydactyly-mental retardation syndrome"	BDMR		10206986, 10220385, 20691407	Standard	NM_006037		Approved	KIAA0288, HDAC-A, HDACA, HD4, HA6116, HDAC-4	uc002vyk.4	P56524	OTTHUMG00000133344	ENST00000345617.3:c.23-1G>C	chr2.hg19:g.240158361C>G		144.0	0.0		169.0	86.0	NM_006037	Q9UND6	Splice_Site	SNP	ENST00000345617.3	hg19	CCDS2529.1	.	.	.	.	.	.	.	.	.	.	C	15.27	2.784086	0.49997	.	.	ENSG00000068024	ENST00000345617;ENST00000544989	.	.	.	4.68	4.68	0.58851	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.479	0.61324	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	HDAC4	239823298	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	3.795000	0.55499	2.317000	0.78254	0.655000	0.94253	.	.	.		0.567	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037	Intron	G	240158361	C	G	240158361	5	3	342	1	0	0	0	0	0	0	1	0	7018	927	32	4	3332	4	HDAC4	2	240158361	Splice_Site	SNP	C	TCGA-T1-A6J8-01A-11D-A32G-10	27581488	240158361	3041012	11	47214										
TRIM71	131405	hgsc.bcm.edu	37	chr3	32932669	32932669	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	gcagttcgaccgaccagccgGcgtggcctgtgacgcctcac	13	16	1	1			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr3:32932669G>A	ENST00000383763.5	+	4	2036	c.1973G>A	c.(1972-1974)gGc>gAc	p.G658D		NM_001039111.1	NP_001034200.1	Q2Q1W2	LIN41_HUMAN	tripartite motif containing 71, E3 ubiquitin protein ligase	658					fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|miRNA metabolic process (GO:0010586)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neural tube closure (GO:0001843)|neural tube development (GO:0021915)|positive regulation of gene silencing by miRNA (GO:2000637)|protein autoubiquitination (GO:0051865)|regulation of gene silencing by miRNA (GO:0060964)|regulation of neural precursor cell proliferation (GO:2000177)|stem cell proliferation (GO:0072089)	cytoplasmic mRNA processing body (GO:0000932)	ligase activity (GO:0016874)|miRNA binding (GO:0035198)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						CGACCAGCCGGCGTGGCCTGT	0.622																																					p.G658D		Atlas-SNP	.											.	TRIM71	73	.	0			c.G1973A						.						37	40	39					3																	32932669		2085	4204	6289	SO:0001583	missense	131405	exon4			CAGCCGGCGTGGC		CCDS43060.1	3p22.3	2014-02-17	2012-02-29		ENSG00000206557	ENSG00000206557		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	32669	protein-coding gene	gene with protein product			"tripartite motif-containing 71", "tripartite motif containing 71"				Standard	NM_001039111		Approved	LIN41, LIN-41	uc003cff.3	Q2Q1W2	OTTHUMG00000155778	ENST00000383763.5:c.1973G>A	chr3.hg19:g.32932669G>A	ENSP00000373272:p.Gly658Asp	28.0	0.0		51.0	17.0	NM_001039111		Missense_Mutation	SNP	ENST00000383763.5	hg19	CCDS43060.1	.	.	.	.	.	.	.	.	.	.	G	19.97	3.924620	0.73213	.	.	ENSG00000206557	ENST00000383763	T	0.80738	-1.41	5.73	5.73	0.89815	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	D	0.89972	0.6870	M	0.80982	2.52	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.88515	0.3092	10	0.36615	T	0.2	-37.7996	18.4419	0.90669	0.0:0.0:1.0:0.0	.	658	Q2Q1W2	LIN41_HUMAN	D	658	ENSP00000373272:G658D	ENSP00000373272:G658D	G	+	2	0	TRIM71	32907673	1.000000	0.71417	0.982000	0.44146	0.875000	0.50365	9.727000	0.98787	2.708000	0.92522	0.650000	0.86243	GGC	.	.		0.622	TRIM71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341565.3	NM_001039111		A	32932669	G	A	32932669	3	1	342	1	0	0	0	0	1	0	0	0	16559	1203	42	3	1987	3	TRIM71	3	32932669	Missense_Mutation	SNP	G	TCGA-T1-A6J8-01A-11D-A32G-10		32932669	165089761	12	47215										
SLC22A14	9389	hgsc.bcm.edu	37	chr3	38347895	38347895	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	ataccccaagcacccaatggCagtttcctgacatgcttcat	6	14	1	1			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr3:38347895C>T	ENST00000273173.4	+	1	469	c.378C>T	c.(376-378)ggC>ggT	p.G126G	SLC22A14_ENST00000448498.1_Silent_p.G126G|RNU6-235P_ENST00000362644.1_RNA	NM_004803.3	NP_004794.2	Q9Y267	S22AE_HUMAN	solute carrier family 22, member 14	126					organic cation transport (GO:0015695)	integral component of plasma membrane (GO:0005887)	organic cation transmembrane transporter activity (GO:0015101)			central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(5)|prostate(2)|skin(1)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0554)|Kidney(284;0.0696)		CACCCAATGGCAGTTTCCTGA	0.527																																					p.G126G		Atlas-SNP	.											.	SLC22A14	64	.	0			c.C378T						.						142	127	132					3																	38347895		2203	4300	6503	SO:0001819	synonymous_variant	9389	exon1			CAATGGCAGTTTC	AB011082	CCDS2677.1	3p21.3	2013-05-22	2008-01-11	2003-10-15	ENSG00000144671	ENSG00000144671		"Solute carriers"	8495	protein-coding gene	gene with protein product		604048	"organic cationic transporter-like 4", "solute carrier family 22 (organic cation transporter), member 14"	ORCTL4		10072596	Standard	NM_004803		Approved	OCTL2	uc003cib.2	Q9Y267	OTTHUMG00000131082	ENST00000273173.4:c.378C>T	chr3.hg19:g.38347895C>T		122.0	0.0		114.0	24.0	NM_004803	A0AVS9|A1L4H6|B2RCX3|Q6DJT3	Silent	SNP	ENST00000273173.4	hg19	CCDS2677.1																																																																																			.	.		0.527	SLC22A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253742.3	NM_004803		T	38347895	C	T	38347895	2	4	342	1	0	0	0	0	0	0	0	1	14460	697	25	3		3	SLC22A14	3	38347895	Silent	SNP	C	TCGA-T1-A6J8-01A-11D-A32G-10	5415226	38347895	159674535	13	47216										
RAD54L2	23132	hgsc.bcm.edu	37	chr3	51661661	51661661	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	gcacttcaactacctcatctCagtctgagccttcagagcag	7	14	5	2			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr3:51661661C>G	ENST00000409535.2	+	3	357	c.232C>G	c.(232-234)Cag>Gag	p.Q78E	RAD54L2_ENST00000296477.3_5'Flank	NM_015106.2	NP_055921.2	Q9Y4B4	ARIP4_HUMAN	RAD54-like 2 (S. cerevisiae)	78						nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|transcription cofactor activity (GO:0003712)			NS(2)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|liver(2)|lung(9)|ovary(4)|skin(2)	31				BRCA - Breast invasive adenocarcinoma(193;0.000102)|Kidney(197;0.000758)|KIRC - Kidney renal clear cell carcinoma(197;0.000896)		TACCTCATCTCAGTCTGAGCC	0.567																																					p.Q78E		Atlas-SNP	.											.	RAD54L2	94	.	0			c.C232G						.						63	59	60					3																	51661661		692	1591	2283	SO:0001583	missense	23132	exon3			TCATCTCAGTCTG	AB018352	CCDS33765.2	3p21.2	2006-01-17			ENSG00000164080	ENSG00000164080			29123	protein-coding gene	gene with protein product						9872452	Standard	NM_015106		Approved	KIAA0809, SRISNF2L	uc011bdt.2	Q9Y4B4	OTTHUMG00000152936	ENST00000409535.2:c.232C>G	chr3.hg19:g.51661661C>G	ENSP00000386520:p.Gln78Glu	93.0	0.0		113.0	34.0	NM_015106	Q8TB57|Q9BV54	Missense_Mutation	SNP	ENST00000409535.2	hg19	CCDS33765.2	.	.	.	.	.	.	.	.	.	.	C	21.7	4.188590	0.78789	.	.	ENSG00000164080	ENST00000409535	T	0.18960	2.18	6.06	6.06	0.98353	.	.	.	.	.	T	0.13457	0.0326	N	0.14661	0.345	0.80722	D	1	B	0.30193	0.272	B	0.24394	0.053	T	0.16041	-1.0416	9	0.17832	T	0.49	-5.4575	17.7768	0.88511	0.0:1.0:0.0:0.0	.	78	Q9Y4B4	ARIP4_HUMAN	E	78	ENSP00000386520:Q78E	ENSP00000386520:Q78E	Q	+	1	0	RAD54L2	51636701	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.324000	0.59228	2.882000	0.98803	0.655000	0.94253	CAG	.	.		0.567	RAD54L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328700.2	NM_015106		G	51661661	C	G	51661661	3	3	342	1	0	0	0	0	1	0	0	0	13009	827	29	4	238	4	RAD54L2	3	51661661	Missense_Mutation	SNP	C	TCGA-T1-A6J8-01A-11D-A32G-10	13313766	51661661	146360769	14	47217										
ILDR1	286676	hgsc.bcm.edu	37	chr3	121712300	121712300	+	Frame_Shift_Del	DEL	C	C	-													0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	aaaggagggtggctcggccgCcagcgtgcctcactggatga							TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr3:121712300delC	ENST00000344209.5	-	7	1422	c.1296delG	c.(1294-1296)tggfs	p.W432fs	ILDR1_ENST00000393631.1_Frame_Shift_Del_p.W343fs|ILDR1_ENST00000273691.3_Frame_Shift_Del_p.W388fs|ILDR1_ENST00000462014.1_Frame_Shift_Del_p.W400fs|ILDR1_ENST00000460554.1_5'UTR	NM_001199799.1	NP_001186728.1	Q86SU0	ILDR1_HUMAN	immunoglobulin-like domain containing receptor 1	432	Arg-rich.				positive regulation of peptide hormone secretion (GO:0090277)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-density lipoprotein particle receptor activity (GO:0070506)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				GBM - Glioblastoma multiforme(114;0.156)		GGCTCGGCCGCCAGCGTGCCT	0.662																																					p.R433fs		Atlas-Indel,Pindel	.											.	ILDR1	120	.	0			c.1297delC						.						37	34	35					3																	121712300		2203	4300	6503	SO:0001589	frameshift_variant	286676	exon7			.	BC044240	CCDS3008.1, CCDS56270.1, CCDS56271.1	3q21.1	2013-10-11			ENSG00000145103	ENSG00000145103			28741	protein-coding gene	gene with protein product		609739	"deafness, autosomal recessive 42"	DFNB42		15641023, 21255762	Standard	NM_175924		Approved	MGC50831	uc003ees.3	Q86SU0	OTTHUMG00000159481	ENST00000344209.5:c.1296delG	chr3.hg19:g.121712300delC	ENSP00000345667:p.Trp432fs	66.0	0.0		109.0	47.0	NM_001199799	Q6ZP61|Q7Z578	Frame_Shift_Del	DEL	ENST00000344209.5	hg19	CCDS56271.1																																																																																			.	.		0.662	ILDR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355666.1	NM_175924		-	121712300	C	-	121712300	7	5	342	1	0	1	0	1	0	0	0	0	7718	740	26	0	352	0	ILDR1	3	121712300	Frame_Shift_Del	DEL	C	TCGA-T1-A6J8-01A-11D-A32G-10	70050639	121712300	76310130	15	47218										
BCHE	590	hgsc.bcm.edu	37	chr3	165548695	165548695	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	aaaaactgtcaagttcatccCtctgacttttccattctttg	4	11	4	1			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr3:165548695C>T	ENST00000264381.3	-	2	293	c.127G>A	c.(127-129)Ggg>Agg	p.G43R	BCHE_ENST00000540653.1_Intron	NM_000055.2	NP_000046.1	P06276	CHLE_HUMAN	butyrylcholinesterase	43					cellular protein metabolic process (GO:0044267)|choline metabolic process (GO:0019695)|cocaine metabolic process (GO:0050783)|learning (GO:0007612)|negative regulation of cell proliferation (GO:0008285)|negative regulation of synaptic transmission (GO:0050805)|neuroblast differentiation (GO:0014016)|response to alkaloid (GO:0043279)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|synaptic transmission, cholinergic (GO:0007271)	blood microparticle (GO:0072562)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)	acetylcholinesterase activity (GO:0003990)|beta-amyloid binding (GO:0001540)|catalytic activity (GO:0003824)|choline binding (GO:0033265)|cholinesterase activity (GO:0004104)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(34)|ovary(4)|pancreas(2)|stomach(1)	55					Aclidinium(DB08897)|Ambenonium(DB01122)|Bambuterol(DB01408)|Chloroprocaine(DB01161)|Chlorphenesin(DB00856)|Chlorpromazine(DB00477)|Choline(DB00122)|Cinchocaine(DB00527)|Cisplatin(DB00515)|Clevidipine(DB04920)|Cyclopentolate(DB00979)|Decamethonium(DB01245)|Demecarium(DB00944)|Diethylcarbamazine(DB00711)|Dipivefrin(DB00449)|Doxacurium chloride(DB01135)|Drospirenone(DB01395)|Echothiophate(DB01057)|Edrophonium(DB01010)|Ephedrine(DB01364)|Ethopropazine(DB00392)|Galantamine(DB00674)|Hexafluronium(DB00941)|Irinotecan(DB00762)|Isoflurophate(DB00677)|Malathion(DB00772)|Mefloquine(DB00358)|Mirabegron(DB08893)|Mivacurium(DB01226)|Neostigmine(DB01400)|Nizatidine(DB00585)|Oxybuprocaine(DB00892)|Pancuronium(DB01337)|Pegvisomant(DB00082)|Pentagastrin(DB00183)|Perindopril(DB00790)|Pipecuronium(DB01338)|Pralidoxime(DB00733)|Procainamide(DB01035)|Procaine(DB00721)|Pyridostigmine(DB00545)|Ramipril(DB00178)|Rivastigmine(DB00989)|Succinylcholine(DB00202)|Sulpiride(DB00391)|Terbutaline(DB00871)|Triamcinolone(DB00620)|Triflupromazine(DB00508)|Trimethaphan(DB01116)	AAGTTCATCCCTCTGACTTTT	0.418																																					p.G43R		Atlas-SNP	.											.	BCHE	136	.	0			c.G127A						.						104	95	98					3																	165548695		2203	4300	6503	SO:0001583	missense	590	exon2			TCATCCCTCTGAC	M16541	CCDS3198.1	3q26.1-q26.2	2013-07-10			ENSG00000114200	ENSG00000114200	3.1.1.8		983	protein-coding gene	gene with protein product		177400	"cholinesterase 1", "cholinesterase (serum) 2"	CHE1, CHE2		1769657, 2318303	Standard	NM_000055		Approved	E1	uc003fem.4	P06276	OTTHUMG00000158131	ENST00000264381.3:c.127G>A	chr3.hg19:g.165548695C>T	ENSP00000264381:p.Gly43Arg	168.0	0.0		216.0	26.0	NM_000055	A8K7P8	Missense_Mutation	SNP	ENST00000264381.3	hg19	CCDS3198.1	.	.	.	.	.	.	.	.	.	.	C	15.46	2.838994	0.51057	.	.	ENSG00000114200	ENST00000264381	D	0.99843	-7.11	5.81	5.81	0.92471	Carboxylesterase, type B (1);	0.000000	0.85682	D	0.000000	D	0.99902	0.9953	H	0.97240	3.965	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96542	0.9401	10	0.72032	D	0.01	.	19.0644	0.93104	0.0:1.0:0.0:0.0	.	43	P06276	CHLE_HUMAN	R	43	ENSP00000264381:G43R	ENSP00000264381:G43R	G	-	1	0	BCHE	167031389	1.000000	0.71417	0.993000	0.49108	0.089000	0.18198	5.627000	0.67784	2.756000	0.94617	0.655000	0.94253	GGG	.	.		0.418	BCHE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350254.1			T	165548695	C	T	165548695	3	4	342	1	0	0	0	0	1	0	0	0	1358	681	24	3	1693	3	BCHE	3	165548695	Missense_Mutation	SNP	C	TCGA-T1-A6J8-01A-11D-A32G-10	43836395	165548695	32473735	16	47219										
HES1	3280	hgsc.bcm.edu	37	chr3	193854425	193854425	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	gtcatcaaagcctattatggAgaaaagacgaagagcaagaa	10	6	2	4			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr3:193854425A>T	ENST00000232424.3	+	2	364	c.128A>T	c.(127-129)gAg>gTg	p.E43V		NM_005524.3	NP_005515.1	P30042	ES1_HUMAN	hes family bHLH transcription factor 1	0						mitochondrion (GO:0005739)				endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)	6	all_cancers(143;7.3e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;3.65e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;1.48e-05)		CCTATTATGGAGAAAAGACGA	0.438																																					p.E43V		Atlas-SNP	.											.	HES1	23	.	0			c.A128T						.						66	72	70					3																	193854425		2203	4300	6503	SO:0001583	missense	3280	exon2			TTATGGAGAAAAG	L19314	CCDS3305.1	3q28-q29	2013-10-17	2013-10-17	2003-01-10	ENSG00000114315	ENSG00000114315		"Basic helix-loop-helix proteins"	5192	protein-coding gene	gene with protein product		139605	"hairy homolog (Drosophila)", "hairy and enhancer of split 1, (Drosophila)"	HRY		8020957	Standard	NM_005524		Approved	FLJ20408, HES-1, Hes1, bHLHb39	uc003ftq.2	Q14469	OTTHUMG00000155984	ENST00000232424.3:c.128A>T	chr3.hg19:g.193854425A>T	ENSP00000232424:p.Glu43Val	137.0	0.0		190.0	87.0	NM_005524	A6NFJ6|A6NJY7|O00650|O00660|O15011|O15012|P55346|P78474|Q92505|Q92507	Missense_Mutation	SNP	ENST00000232424.3	hg19	CCDS3305.1	.	.	.	.	.	.	.	.	.	.	A	19.82	3.898497	0.72639	.	.	ENSG00000114315	ENST00000232424	D	0.99732	-6.57	5.57	4.41	0.53225	Helix-loop-helix DNA-binding (5);	0.000000	0.85682	D	0.000000	D	0.99809	0.9917	H	0.98133	4.155	0.58432	D	0.999999	D;D	0.89917	0.999;1.0	D;D	0.97110	0.981;1.0	D	0.97424	1.0011	10	0.87932	D	0	-3.8107	10.3317	0.43827	0.9219:0.0:0.078:0.0	.	43;43	B4DU36;Q14469	.;HES1_HUMAN	V	43	ENSP00000232424:E43V	ENSP00000232424:E43V	E	+	2	0	HES1	195337119	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.051000	0.93849	0.946000	0.37632	0.533000	0.62120	GAG	.	.		0.438	HES1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342632.1			T	193854425	A	T	193854425	3	4	342	1	0	0	0	0	1	0	0	0	7074	304	11	4	134	4	HES1	3	193854425	Missense_Mutation	SNP	A	TCGA-T1-A6J8-01A-11D-A32G-10	28305730	193854425	4168005	17	47220										
CDH10	1008	hgsc.bcm.edu	37	chr5	24487960	24487960	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	aagtgagtcgtaggggggtgCggtggggtcaagatcatgct	19	5	2	2			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr5:24487960C>T	ENST00000264463.4	-	12	2686	c.2179G>A	c.(2179-2181)Gca>Aca	p.A727T	CDH10_ENST00000502921.1_5'UTR	NM_006727.3	NP_006718.2	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 (T2-cadherin)	727					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(29)|lung(111)|ovary(6)|pancreas(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)	185				STAD - Stomach adenocarcinoma(35;0.0556)		TAGGGGGGTGCGGTGGGGTCA	0.458										HNSCC(23;0.051)																											p.A727T		Atlas-SNP	.											CDH10,NS,carcinoma,0,1	CDH10	391	.	0			c.G2179A						.																																			SO:0001583	missense	1008	exon12			GGGGTGCGGTGGG	AF039747	CCDS3892.1	5p14.2	2010-01-26			ENSG00000040731	ENSG00000040731		"Cadherins / Major cadherins"	1749	protein-coding gene	gene with protein product		604555				2059658	Standard	NM_006727		Approved		uc003jgr.2	Q9Y6N8	OTTHUMG00000090667	ENST00000264463.4:c.2179G>A	chr5.hg19:g.24487960C>T	ENSP00000264463:p.Ala727Thr	88.0	0.0		114.0	14.0	NM_006727	Q9ULB3	Missense_Mutation	SNP	ENST00000264463.4	hg19	CCDS3892.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657163	0.88154	.	.	ENSG00000040731	ENST00000264463	T	0.78924	-1.22	5.92	5.92	0.95590	Cadherin, cytoplasmic domain (1);	0.089346	0.85682	D	0.000000	D	0.87966	0.6311	M	0.76838	2.35	0.58432	D	0.999997	D	0.76494	0.999	D	0.63793	0.918	D	0.88078	0.2805	10	0.62326	D	0.03	.	19.3088	0.94175	0.0:1.0:0.0:0.0	.	727	Q9Y6N8	CAD10_HUMAN	T	727	ENSP00000264463:A727T	ENSP00000264463:A727T	A	-	1	0	CDH10	24523717	1.000000	0.71417	0.364000	0.25888	0.917000	0.54804	7.702000	0.84576	2.809000	0.96659	0.655000	0.94253	GCA	.	.		0.458	CDH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207345.2	NM_006727		T	24487960	C	T	24487960	3	4	342	1	0	0	0	0	1	0	0	0	3098	768	27	1	191	1	CDH10	5	24487960	Missense_Mutation	SNP	C	TCGA-T1-A6J8-01A-11D-A32G-10		24487960	156427300	18	47221										
CRHBP	1393	hgsc.bcm.edu	37	chr5	76249897	76249897	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	cagggccagttcaccttcacCgccgaccggccgcagctgca	11	18	2	0			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr5:76249897C>G	ENST00000274368.4	+	3	641	c.219C>G	c.(217-219)acC>acG	p.T73T	CRHBP_ENST00000506501.1_Silent_p.T73T	NM_001882.3	NP_001873.2	P24387	CRHBP_HUMAN	corticotropin releasing hormone binding protein	73					behavioral response to ethanol (GO:0048149)|cellular response to calcium ion (GO:0071277)|cellular response to cAMP (GO:0071320)|cellular response to cocaine (GO:0071314)|cellular response to drug (GO:0035690)|cellular response to estradiol stimulus (GO:0071392)|cellular response to estrogen stimulus (GO:0071391)|cellular response to gonadotropin-releasing hormone (GO:0097211)|cellular response to potassium ion (GO:0035865)|cellular response to stress (GO:0033554)|cellular response to tumor necrosis factor (GO:0071356)|female pregnancy (GO:0007565)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|inflammatory response (GO:0006954)|learning or memory (GO:0007611)|maternal aggressive behavior (GO:0002125)|negative regulation of corticotropin secretion (GO:0051460)|negative regulation of corticotropin-releasing hormone receptor activity (GO:1900011)|regulated secretory pathway (GO:0045055)|regulation of corticotropin secretion (GO:0051459)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|signal transduction (GO:0007165)|synaptic transmission, dopaminergic (GO:0001963)	axon terminus (GO:0043679)|dendrite (GO:0030425)|dense core granule (GO:0031045)|extracellular space (GO:0005615)|intracellular (GO:0005622)|microtubule (GO:0005874)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|perikaryon (GO:0043204)|secondary lysosome (GO:0005767)|secretory granule (GO:0030141)|varicosity (GO:0043196)	corticotropin-releasing hormone binding (GO:0051424)|peptide binding (GO:0042277)	p.T73T(1)		kidney(3)|large_intestine(4)|lung(6)|prostate(1)|skin(2)	16		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;2.17e-51)|Epithelial(54;8.79e-46)|all cancers(79;2.49e-41)		TCACCTTCACCGCCGACCGGC	0.662																																					p.T73T		Atlas-SNP	.											CRHBP,NS,carcinoma,0,1	CRHBP	46	.	1	Substitution - coding silent(1)	lung(1)	c.C219G						.						53	58	57					5																	76249897		2203	4300	6503	SO:0001819	synonymous_variant	1393	exon3			CTTCACCGCCGAC	X58022	CCDS4034.1	5q	2008-07-18	2001-11-28		ENSG00000145708	ENSG00000145708			2356	protein-coding gene	gene with protein product		122559	"corticotropin releasing hormone-binding protein"			8198617	Standard	NM_001882		Approved	CRF-BP, CRFBP	uc003ker.3	P24387	OTTHUMG00000102133	ENST00000274368.4:c.219C>G	chr5.hg19:g.76249897C>G		74.0	0.0		99.0	35.0	NM_001882	Q53F32|Q6FHT5	Silent	SNP	ENST00000274368.4	hg19	CCDS4034.1																																																																																			.	.		0.662	CRHBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219972.2	NM_001882		G	76249897	C	G	76249897	2	3	342	1	0	0	0	0	0	0	0	1	3872	639	23	4		4	CRHBP	5	76249897	Silent	SNP	C	TCGA-T1-A6J8-01A-11D-A32G-10	51761937	76249897	104665363	19	47222										
LNPEP	4012	hgsc.bcm.edu	37	chr5	96360250	96360250	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	ctactgatgtcatgacaactGtgttcaaagttggagcaaaa	9	7	2	2			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr5:96360250G>A	ENST00000231368.5	+	15	3279	c.2587G>A	c.(2587-2589)Gtg>Atg	p.V863M	LNPEP_ENST00000395770.3_Missense_Mutation_p.V849M	NM_005575.2	NP_005566.2	Q9UIQ6	LCAP_HUMAN	leucyl/cystinyl aminopeptidase	863					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-cell signaling (GO:0007267)|female pregnancy (GO:0007565)|membrane organization (GO:0061024)|protein catabolic process (GO:0030163)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|early endosome lumen (GO:0031905)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	34		all_cancers(142;7e-07)|all_epithelial(76;9.52e-10)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0269)|Breast(839;0.244)		COAD - Colon adenocarcinoma(37;0.072)		CATGACAACTGTGTTCAAAGT	0.403																																					p.V863M		Atlas-SNP	.											.	LNPEP	80	.	0			c.G2587A						.						96	90	92					5																	96360250		2203	4300	6503	SO:0001583	missense	4012	exon15			ACAACTGTGTTCA	D50810	CCDS4087.1, CCDS43346.1	5q15	2011-07-25			ENSG00000113441	ENSG00000113441	3.4.11.3		6656	protein-coding gene	gene with protein product	"cystinyl aminopeptidase", "placental leucine aminopeptidase"	151300				8550619	Standard	NM_175920		Approved	CAP, PLAP, P-LAP	uc003kmw.1	Q9UIQ6	OTTHUMG00000128719	ENST00000231368.5:c.2587G>A	chr5.hg19:g.96360250G>A	ENSP00000231368:p.Val863Met	56.0	0.0		74.0	8.0	NM_005575	O00769|Q15145|Q59H76|Q9TNQ2|Q9TNQ3|Q9UIQ7	Missense_Mutation	SNP	ENST00000231368.5	hg19	CCDS4087.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.945678	0.73672	.	.	ENSG00000113441	ENST00000231368;ENST00000395770	T;T	0.09723	2.95;2.95	5.96	5.96	0.96718	.	0.051645	0.85682	D	0.000000	T	0.31827	0.0809	M	0.74467	2.265	0.58432	D	0.999999	D	0.69078	0.997	D	0.76071	0.987	T	0.01152	-1.1435	10	0.87932	D	0	.	11.6873	0.51494	0.11:0.0:0.89:0.0	.	863	Q9UIQ6	LCAP_HUMAN	M	863;849	ENSP00000231368:V863M;ENSP00000379117:V849M	ENSP00000231368:V863M	V	+	1	0	LNPEP	96386006	1.000000	0.71417	0.998000	0.56505	0.820000	0.46376	5.380000	0.66202	2.832000	0.97577	0.655000	0.94253	GTG	.	.		0.403	LNPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250624.1	NM_005575		A	96360250	G	A	96360250	3	1	342	1	0	0	0	0	1	0	0	0	8873	1377	48	3	2645	3	LNPEP	5	96360250	Missense_Mutation	SNP	G	TCGA-T1-A6J8-01A-11D-A32G-10	20110353	96360250	84555010	20	47223										
ACSL6	23305	hgsc.bcm.edu	37	chr5	131298318	131298318	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	tcgggtgcaacatattctccCtgagcaagtttaaatatatg	8	8	1	1			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr5:131298318C>T	ENST00000379240.1	-	18	1845	c.1692G>A	c.(1690-1692)caG>caA	p.Q564Q	ACSL6_ENST00000431707.1_Silent_p.Q544Q|ACSL6_ENST00000379244.1_Silent_p.Q564Q|ACSL6_ENST00000379264.2_Silent_p.Q589Q|ACSL6_ENST00000379272.2_Silent_p.Q579Q|ACSL6_ENST00000543479.1_Silent_p.Q564Q|ACSL6_ENST00000379249.3_Silent_p.Q564Q|ACSL6_ENST00000296869.4_Silent_p.Q589Q|ACSL6_ENST00000379255.1_Silent_p.Q489Q|ACSL6_ENST00000544770.1_Silent_p.Q473Q|AC034228.4_ENST00000446275.1_RNA|ACSL6_ENST00000357096.1_Silent_p.Q489Q|ACSL6_ENST00000379246.1_Silent_p.Q575Q			Q9UKU0	ACSL6_HUMAN	acyl-CoA synthetase long-chain family member 6	564					acyl-CoA metabolic process (GO:0006637)|cellular lipid metabolic process (GO:0044255)|cellular response to insulin stimulus (GO:0032869)|fatty acid transport (GO:0015908)|long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|neuroblast proliferation (GO:0007405)|neuron development (GO:0048666)|phospholipid biosynthetic process (GO:0008654)|positive regulation of neuron projection development (GO:0010976)|positive regulation of plasma membrane long-chain fatty acid transport (GO:0010747)|positive regulation of triglyceride biosynthetic process (GO:0010867)|response to gravity (GO:0009629)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|long-chain fatty acid-CoA ligase activity (GO:0004467)|protein homodimerization activity (GO:0042803)			NS(1)|breast(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	35		all_cancers(142;0.107)|Breast(839;0.198)|Lung NSC(810;0.216)|all_lung(232;0.248)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CATATTCTCCCTGAGCAAGTT	0.438																																					p.Q589Q		Atlas-SNP	.											.	ACSL6	169	.	0			c.G1767A						.						98	92	94					5																	131298318		2203	4300	6503	SO:0001819	synonymous_variant	23305	exon18			TTCTCCCTGAGCA	AB020644	CCDS34228.1, CCDS34229.1, CCDS56381.1, CCDS56382.1, CCDS56383.1	5q31	2008-02-05	2004-02-19	2004-02-20	ENSG00000164398	ENSG00000164398		"Acyl-CoA synthetase family"	16496	protein-coding gene	gene with protein product		604443	"fatty-acid-Coenzyme A ligase, long-chain 6"	FACL6		10502316, 10548543	Standard	NM_015256		Approved	KIAA0837, ACS2, LACS5, LACS2	uc003kvy.2	Q9UKU0	OTTHUMG00000150692	ENST00000379240.1:c.1692G>A	chr5.hg19:g.131298318C>T		122.0	0.0		155.0	8.0	NM_001009185	J3KPG3|O94924|O95829|Q108M9|Q108N0|Q4G191|Q86TN7	Silent	SNP	ENST00000379240.1	hg19																																																																																				.	.		0.438	ACSL6-004	NOVEL	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000132622.1	NM_015256		T	131298318	C	T	131298318	2	4	342	1	0	0	0	0	0	0	0	1	181	680	24	3		3	ACSL6	5	131298318	Silent	SNP	C	TCGA-T1-A6J8-01A-11D-A32G-10	34938068	131298318	49616942	21	47224										
PCDHA5	56143	hgsc.bcm.edu	37	chr5	140203515	140203515	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	tcacgctgctgctgtacaccGcgctgcggtgctcggcgcag	14	15	1	0			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr5:140203515G>A	ENST00000529859.1	+	1	2155	c.2155G>A	c.(2155-2157)Gcg>Acg	p.A719T	PCDHA5_ENST00000378126.3_Missense_Mutation_p.A719T|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Missense_Mutation_p.A719T	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	719					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.A719T(4)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(3)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCTGTACACCGCGCTGCGGTG	0.667																																					p.A719T		Atlas-SNP	.											PCDHA5_ENST00000529859,NS,carcinoma,0,4	PCDHA5	361	.	4	Substitution - Missense(4)	prostate(4)	c.G2155A						.						53	51	52					5																	140203515		2203	4299	6502	SO:0001583	missense	56143	exon1			TACACCGCGCTGC	AF152483	CCDS54917.1	5q31	2010-11-26				ENSG00000204965		"Cadherins / Protocadherins : Clustered"	8671	other	complex locus constituent	"ortholog of mouse CNR6", "KIAA0345-like 9"	606311		CNRS6		10380929, 10662547	Standard	NM_018908		Approved	CNR6, CRNR6, CNRN6, PCDH-ALPHA5		Q9Y5H7		ENST00000529859.1:c.2155G>A	chr5.hg19:g.140203515G>A	ENSP00000436557:p.Ala719Thr	92.0	0.0		135.0	16.0	NM_018908	O75284|Q8N4R3	Missense_Mutation	SNP	ENST00000529859.1	hg19	CCDS54917.1	.	.	.	.	.	.	.	.	.	.	G	20.0	3.930880	0.73327	.	.	ENSG00000204965	ENST00000529619;ENST00000529859;ENST00000378126	T;T;T	0.17528	2.27;2.27;2.27	4.17	4.17	0.49024	.	.	.	.	.	T	0.49932	0.1586	M	0.92122	3.275	0.24834	N	0.992508	D;D;D	0.71674	0.994;0.998;0.998	P;P;P	0.62491	0.734;0.903;0.903	T	0.53301	-0.8458	9	0.87932	D	0	.	16.4493	0.83974	0.0:0.0:1.0:0.0	.	719;719;719	Q9Y5H7;Q9Y5H7-3;Q9Y5H7-2	PCDA5_HUMAN;.;.	T	719	ENSP00000433416:A719T;ENSP00000436557:A719T;ENSP00000367366:A719T	ENSP00000367366:A719T	A	+	1	0	PCDHA5	140183699	0.790000	0.28787	0.981000	0.43875	0.381000	0.30169	4.288000	0.59007	2.046000	0.60703	0.491000	0.48974	GCG	.	.		0.667	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908		A	140203515	G	A	140203515	3	1	342	1	0	0	0	0	1	0	0	0	11536	1087	38	1	2157	1	PCDHA5	5	140203515	Missense_Mutation	SNP	G	TCGA-T1-A6J8-01A-11D-A32G-10	8905197	140203515	40711745	22	47225										
COL23A1	91522	hgsc.bcm.edu	37	chr5	177673419	177673419	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	ccgctggggcctctctcaccCgacgcacccttctctccctt	7	21	3	0			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr5:177673419C>A	ENST00000390654.3	-	23	1689	c.1332G>T	c.(1330-1332)tcG>tcT	p.S444S		NM_173465.3	NP_775736.2	Q86Y22	CONA1_HUMAN	collagen, type XXIII, alpha 1	444	Collagen-like 4.|Gly-rich.				collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	19	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)		CTCTCTCACCCGACGCACCCT	0.547																																					p.S444S		Atlas-SNP	.											.	COL23A1	47	.	0			c.G1332T						.						24	28	27					5																	177673419		1985	4167	6152	SO:0001819	synonymous_variant	91522	exon23			CTCACCCGACGCA	AL137461	CCDS4436.1	5q35.3	2013-01-16			ENSG00000050767	ENSG00000050767		"Collagens"	22990	protein-coding gene	gene with protein product		610043				12644459	Standard	NM_173465		Approved	DKFZp434K0621	uc021yiz.1	Q86Y22	OTTHUMG00000130890	ENST00000390654.3:c.1332G>T	chr5.hg19:g.177673419C>A		60.0	0.0		87.0	35.0	NM_173465	Q8IVR4|Q9NT93	Silent	SNP	ENST00000390654.3	hg19	CCDS4436.1																																																																																			.	.		0.547	COL23A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253475.1	NM_173465		A	177673419	C	A	177673419	2	1	342	1	0	0	0	0	0	0	0	1	3684	639	23	1		1	COL23A1	5	177673419	Silent	SNP	C	TCGA-T1-A6J8-01A-11D-A32G-10	37469904	177673419	3241841	23	47226										
ADAMTS2	9509	hgsc.bcm.edu	37	chr5	178541106	178541106	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	ggggggtgcttggtgatggcCgcacctccatggctacagtg	17	10	0	1			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr5:178541106C>A	ENST00000251582.7	-	22	3499	c.3398G>T	c.(3397-3399)cGg>cTg	p.R1133L		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	1133					collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|protein processing (GO:0016485)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R1133Q(1)		breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(31)|ovary(1)|pancreas(3)|prostate(2)|skin(7)	72	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		TGGTGATGGCCGCACCTCCAT	0.582																																					p.R1133L		Atlas-SNP	.											ADAMTS2,rectum,carcinoma,0,1	ADAMTS2	190	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3398T						.						177	156	163					5																	178541106		2203	4300	6503	SO:0001583	missense	9509	exon22			GATGGCCGCACCT	AJ003125	CCDS4444.1, CCDS34311.1	5q23-q24	2008-07-18	2005-08-19		ENSG00000087116	ENSG00000087116		"ADAM metallopeptidases with thrombospondin type 1 motif"	218	protein-coding gene	gene with protein product	"procollagen I N-proteinase", "procollagen N-endopeptidase"	604539	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2"			10094461, 15373769	Standard	NM_014244		Approved	ADAMTS-3, hPCPNI, PCINP, ADAM-TS2, NPI	uc003mjw.3	O95450	OTTHUMG00000130915	ENST00000251582.7:c.3398G>T	chr5.hg19:g.178541106C>A	ENSP00000251582:p.Arg1133Leu	192.0	0.0		241.0	111.0	NM_014244		Missense_Mutation	SNP	ENST00000251582.7	hg19	CCDS4444.1	.	.	.	.	.	.	.	.	.	.	C	0.554	-0.847963	0.02651	.	.	ENSG00000087116	ENST00000251582	T	0.58940	0.3	5.05	-0.641	0.11490	.	0.828579	0.10123	N	0.713134	T	0.27832	0.0685	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16808	-1.0390	10	0.15066	T	0.55	.	2.372	0.04333	0.1227:0.2188:0.4194:0.239	.	1133	O95450	ATS2_HUMAN	L	1133	ENSP00000251582:R1133L	ENSP00000251582:R1133L	R	-	2	0	ADAMTS2	178473712	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.844000	0.04345	-0.046000	0.13446	-1.762000	0.00668	CGG	.	.		0.582	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244		A	178541106	C	A	178541106	3	1	342	1	0	0	0	0	1	0	0	0	265	652	23	1	241	1	ADAMTS2	5	178541106	Missense_Mutation	SNP	C	TCGA-T1-A6J8-01A-11D-A32G-10	867687	178541106	2374154	24	47227										
SRPK1	6732	hgsc.bcm.edu	37	chr6	35806150	35806150	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	ttccttggaatattttcctgCcacaatgagcttgcgaggca	9	10	0	1			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr6:35806150C>A	ENST00000373825.2	-	15	2032	c.1747G>T	c.(1747-1749)Gca>Tca	p.A583S	SRPK1_ENST00000373822.1_Intron|SRPK1_ENST00000423325.2_Missense_Mutation_p.A567S					SRSF protein kinase 1											endometrium(2)|large_intestine(10)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21						TATTTTCCTGCCACAATGAGC	0.388																																					p.A583S	NSCLC(31;67 978 16289 24856 26454)	Atlas-SNP	.											.	SRPK1	61	.	0			c.G1747T						.						34	35	35					6																	35806150		1833	4101	5934	SO:0001583	missense	6732	exon15			TTCCTGCCACAAT	U09564	CCDS47415.1	6p21.31	2010-06-23	2010-06-23		ENSG00000096063	ENSG00000096063			11305	protein-coding gene	gene with protein product	"SR protein kinase 1", "serine/arginine-rich splicing factor kinase 1"	601939	"SFRS protein kinase 1"			8208298, 10198174	Standard	NM_003137		Approved	SFRSK1	uc003olj.3	Q96SB4	OTTHUMG00000014583	ENST00000373825.2:c.1747G>T	chr6.hg19:g.35806150C>A	ENSP00000362931:p.Ala583Ser	64.0	0.0		98.0	38.0	NM_003137		Missense_Mutation	SNP	ENST00000373825.2	hg19	CCDS47415.1	.	.	.	.	.	.	.	.	.	.	C	6.790	0.514683	0.12944	.	.	ENSG00000096063	ENST00000373825;ENST00000361690;ENST00000423325	T;T;T	0.64618	-0.11;-0.11;-0.11	5.87	5.87	0.94306	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.27832	0.0685	N	0.01188	-0.97	0.80722	D	1	B;B	0.32051	0.001;0.354	B;P	0.44897	0.018;0.463	T	0.47711	-0.9096	9	0.02654	T	1	-13.5964	20.5827	0.99408	0.0:1.0:0.0:0.0	.	567;583	B4DS61;Q96SB4	.;SRPK1_HUMAN	S	583;599;567	ENSP00000362931:A583S;ENSP00000354674:A599S;ENSP00000391069:A567S	ENSP00000354674:A599S	A	-	1	0	SRPK1	35914128	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.707000	0.47143	2.941000	0.99782	0.655000	0.94253	GCA	.	.		0.388	SRPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040319.3	NM_003137		A	35806150	C	A	35806150	3	1	342	1	0	0	0	0	1	0	0	0	15174	739	26	3	228	3	SRPK1	6	35806150	Missense_Mutation	SNP	C	TCGA-T1-A6J8-01A-11D-A32G-10		35806150	135308917	25	47228										
MAPK14	1432	hgsc.bcm.edu	37	chr6	36075327	36075327	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	cctactttgctcagtaccacGatcctgatgatgaaccagtg	8	12	1	3			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr6:36075327G>A	ENST00000229794.4	+	11	1325	c.937G>A	c.(937-939)Gat>Aat	p.D313N	MAPK14_ENST00000310795.4_Silent_p.T286T|MAPK14_ENST00000229795.3_Missense_Mutation_p.D313N|MAPK14_ENST00000468133.1_Missense_Mutation_p.D236N	NM_139012.2|NM_139014.2	NP_620581.1|NP_620583.1	Q16539	MK14_HUMAN	mitogen-activated protein kinase 14	313					3'-UTR-mediated mRNA stabilization (GO:0070935)|activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cartilage condensation (GO:0001502)|cell morphogenesis (GO:0000902)|cell surface receptor signaling pathway (GO:0007166)|cellular component movement (GO:0006928)|cellular response to ionizing radiation (GO:0071479)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|chemotaxis (GO:0006935)|chondrocyte differentiation (GO:0002062)|DNA damage checkpoint (GO:0000077)|fatty acid oxidation (GO:0019395)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|mRNA metabolic process (GO:0016071)|muscle cell differentiation (GO:0042692)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|myoblast differentiation involved in skeletal muscle regeneration (GO:0014835)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|neurotrophin TRK receptor signaling pathway (GO:0048011)|osteoclast differentiation (GO:0030316)|p38MAPK cascade (GO:0038066)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of myoblast fusion (GO:1901741)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Ras protein signal transduction (GO:0007265)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to muramyl dipeptide (GO:0032495)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|signal transduction in response to DNA damage (GO:0042770)|skeletal muscle tissue development (GO:0007519)|stress-activated MAPK cascade (GO:0051403)|stress-induced premature senescence (GO:0090400)|striated muscle cell differentiation (GO:0051146)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|MAP kinase kinase activity (GO:0004708)|NFAT protein binding (GO:0051525)|protein serine/threonine kinase activity (GO:0004674)	p.D313N(1)		central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|stomach(1)	16						TCAGTACCACGATCCTGATGA	0.468																																					p.D313N	Pancreas(20;8 363 26997 32430 36377 43317 49243 50560 51947)|Colon(176;951 1093 20177 30266 32328 34418 35271 44052 51610)	Atlas-SNP	.											MAPK14_ENST00000229794,NS,carcinoma,0,3	MAPK14	75	.	1	Substitution - Missense(1)	large_intestine(1)	c.G937A						.						147	133	138					6																	36075327		2203	4300	6503	SO:0001583	missense	1432	exon11			TACCACGATCCTG	L35263	CCDS4815.1, CCDS4816.1, CCDS4817.1	6p21.3-p21.2	2011-06-09			ENSG00000112062	ENSG00000112062		"Mitogen-activated protein kinase cascade / Kinases"	6876	protein-coding gene	gene with protein product	"p38 MAP kinase"	600289		CSPB1, CSBP1, CSBP2		7997261	Standard	NM_139012		Approved	PRKM14, p38, Mxi2, PRKM15	uc003olq.3	Q16539	OTTHUMG00000159806	ENST00000229794.4:c.937G>A	chr6.hg19:g.36075327G>A	ENSP00000229794:p.Asp313Asn	80.0	0.0		128.0	50.0	NM_139012	A6ZJ92|A8K6P4|B0LPH0|B5TY32|O60776|Q13083|Q14084|Q8TDX0	Missense_Mutation	SNP	ENST00000229794.4	hg19	CCDS4816.1	.	.	.	.	.	.	.	.	.	.	G	36	5.785652	0.96937	.	.	ENSG00000112062	ENST00000229795;ENST00000229794;ENST00000468133	T;T;T	0.13778	2.56;2.56;2.56	5.96	5.96	0.96718	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.35770	0.0943	.	.	.	0.80722	D	1	D;P	0.89917	1.0;0.89	D;B	0.91635	0.999;0.374	T	0.09037	-1.0693	9	0.87932	D	0	-10.6888	20.4192	0.99033	0.0:0.0:1.0:0.0	.	313;313	Q16539;Q16539-2	MK14_HUMAN;.	N	313;313;236	ENSP00000229795:D313N;ENSP00000229794:D313N;ENSP00000419837:D236N	ENSP00000229794:D313N	D	+	1	0	MAPK14	36183305	1.000000	0.71417	0.943000	0.38184	0.992000	0.81027	9.869000	0.99810	2.831000	0.97527	0.650000	0.86243	GAT	.	.		0.468	MAPK14-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000357450.1	NM_001315		A	36075327	G	A	36075327	3	1	342	1	0	0	0	0	1	0	0	0	9285	1058	37	1	1116	1	MAPK14	6	36075327	Missense_Mutation	SNP	G	TCGA-T1-A6J8-01A-11D-A32G-10	269177	36075327	135039740	26	47229										
MACC1	346389	hgsc.bcm.edu	37	chr7	20198542	20198542	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	gaacacaaaaatcaaacaagTgcatctctctgtgctcaact	5	11	4	0			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr7:20198542T>C	ENST00000400331.5	-	5	1750	c.1442A>G	c.(1441-1443)cAc>cGc	p.H481R	MACC1_ENST00000589011.1_Missense_Mutation_p.H481R|MACC1_ENST00000332878.4_Missense_Mutation_p.H481R	NM_182762.3	NP_877439.3	Q6ZN28	MACC1_HUMAN	metastasis associated in colon cancer 1	481					positive regulation of cell division (GO:0051781)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(15)|lung(12)|ovary(2)|prostate(1)|skin(3)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(1)	39						ATCAAACAAGTGCATCTCTCT	0.393																																					p.H481R		Atlas-SNP	.											.	MACC1	99	.	0			c.A1442G						.						79	72	75					7																	20198542		2203	4300	6503	SO:0001583	missense	346389	exon5			AACAAGTGCATCT		CCDS5369.1	7p15.3	2008-10-14			ENSG00000183742	ENSG00000183742			30215	protein-coding gene	gene with protein product		612646					Standard	NM_182762		Approved	7A5, SH3BP4L	uc003sus.4	Q6ZN28	OTTHUMG00000128415	ENST00000400331.5:c.1442A>G	chr7.hg19:g.20198542T>C	ENSP00000383185:p.His481Arg	98.0	0.0		121.0	54.0	NM_182762	A8MUS5|B2RNR9|Q6ZQN8|Q7Z5A5	Missense_Mutation	SNP	ENST00000400331.5	hg19	CCDS5369.1	.	.	.	.	.	.	.	.	.	.	T	7.275	0.608017	0.14002	.	.	ENSG00000183742	ENST00000400331;ENST00000332878	T;T	0.09538	2.97;2.97	5.84	5.84	0.93424	.	0.204155	0.48767	D	0.000173	T	0.11707	0.0285	M	0.72118	2.19	0.32648	N	0.519819	P	0.44734	0.842	B	0.39531	0.302	T	0.04178	-1.0971	10	0.06494	T	0.89	-13.3536	10.5348	0.44998	0.0:0.0719:0.0:0.9281	.	481	Q6ZN28	MACC1_HUMAN	R	481	ENSP00000383185:H481R;ENSP00000328410:H481R	ENSP00000328410:H481R	H	-	2	0	MACC1	20165067	1.000000	0.71417	1.000000	0.80357	0.012000	0.07955	2.127000	0.42035	2.226000	0.72624	0.482000	0.46254	CAC	.	.		0.393	MACC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250202.5	NM_182762		C	20198542	T	C	20198542	3	2	342	1	0	0	0	0	1	0	0	0	9152	1696	59	2	1128	2	MACC1	7	20198542	Missense_Mutation	SNP	T	TCGA-T1-A6J8-01A-11D-A32G-10		20198542	138940121	27	47230										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48319312	48319312	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	actctgaatggataacttccAcaagaactttgtttcagcca	6	10	2	2			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr7:48319312A>G	ENST00000435803.1	+	18	8545	c.8521A>G	c.(8521-8523)Aca>Gca	p.T2841A		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	2841					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						GATAACTTCCACAAGAACTTT	0.353																																					p.T2841A		Atlas-SNP	.											.	ABCA13	1192	.	0			c.A8521G						.						92	95	94					7																	48319312		1817	4077	5894	SO:0001583	missense	154664	exon18			ACTTCCACAAGAA	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.8521A>G	chr7.hg19:g.48319312A>G	ENSP00000411096:p.Thr2841Ala	112.0	0.0		154.0	57.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	A	10.64	1.407867	0.25378	.	.	ENSG00000179869	ENST00000435803	T	0.53423	0.62	5.4	-1.31	0.09230	.	0.639625	0.13996	N	0.348493	T	0.23965	0.0580	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.09751	-1.0660	10	0.38643	T	0.18	.	4.4728	0.11720	0.4836:0.0:0.3664:0.15	.	2841	Q86UQ4	ABCAD_HUMAN	A	2841	ENSP00000411096:T2841A	ENSP00000411096:T2841A	T	+	1	0	ABCA13	48289858	0.000000	0.05858	0.000000	0.03702	0.124000	0.20399	-1.328000	0.02680	-0.490000	0.06707	-0.280000	0.10049	ACA	.	.		0.353	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		G	48319312	A	G	48319312	3	3	342	1	0	0	0	0	1	0	0	0	31	159	6	2	8420	2	ABCA13	7	48319312	Missense_Mutation	SNP	A	TCGA-T1-A6J8-01A-11D-A32G-10	28120770	48319312	110819351	28	47231										
AUTS2	26053	hgsc.bcm.edu	37	chr7	69583171	69583171	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	gacagtgaaagtgccagtggAgaatccaagggcttccaccg	13	10	0	2			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr7:69583171A>T	ENST00000342771.4	+	3	897	c.576A>T	c.(574-576)ggA>ggT	p.G192G	AUTS2_ENST00000403018.2_Silent_p.G192G|AUTS2_ENST00000406775.2_Silent_p.G192G	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	192										breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		GTGCCAGTGGAGAATCCAAGG	0.418																																					p.G192G		Atlas-SNP	.											.	AUTS2	173	.	0			c.A576T						.						57	60	59					7																	69583171		2203	4300	6503	SO:0001819	synonymous_variant	26053	exon3			CAGTGGAGAATCC	AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321			14262	protein-coding gene	gene with protein product		607270				12160723	Standard	XM_005250257		Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.576A>T	chr7.hg19:g.69583171A>T		158.0	0.0		194.0	62.0	NM_001127231	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Silent	SNP	ENST00000342771.4	hg19	CCDS5539.1																																																																																			.	.		0.418	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2			T	69583171	A	T	69583171	2	4	342	1	0	0	0	0	0	0	0	1	1225	291	11	4		4	AUTS2	7	69583171	Silent	SNP	A	TCGA-T1-A6J8-01A-11D-A32G-10	21263859	69583171	89555492	29	47232										
MLXIPL	51085	hgsc.bcm.edu	37	chr7	73009991	73009991	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	cagaacttccagttgtgcagCgtacgggttcggacgtagtc	13	10	0	1	rs370481859		TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr7:73009991C>A	ENST00000313375.3	-	15	2333	c.2286G>T	c.(2284-2286)acG>acT	p.T762T	MLXIPL_ENST00000414749.2_Silent_p.T760T|MLXIPL_ENST00000434326.1_Silent_p.T668T|MLXIPL_ENST00000354613.1_Silent_p.T741T|MLXIPL_ENST00000429400.2_Silent_p.T743T|MLXIPL_ENST00000395189.1_Silent_p.T669T	NM_032951.2|NM_032953.2	NP_116569.1|NP_116571.1	Q9NP71	MLXPL_HUMAN	MLX interacting protein-like	762					anatomical structure morphogenesis (GO:0009653)|energy reserve metabolic process (GO:0006112)|fatty acid homeostasis (GO:0055089)|glucose homeostasis (GO:0042593)|glucose mediated signaling pathway (GO:0010255)|intracellular signal transduction (GO:0035556)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of oxidative phosphorylation (GO:0090324)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular metabolic process (GO:0031325)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of glycolytic process (GO:0045821)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of energy homeostasis (GO:2000505)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride homeostasis (GO:0070328)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	carbohydrate response element binding (GO:0035538)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			cervix(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	13		Lung NSC(55;0.0659)|all_lung(88;0.152)				AGTTGTGCAGCGTACGGGTTC	0.622																																					p.T762T		Atlas-SNP	.											.	MLXIPL	54	.	0			c.G2286T						.						124	113	117					7																	73009991		2203	4300	6503	SO:0001819	synonymous_variant	51085	exon15			GTGCAGCGTACGG	AK055029	CCDS5553.1, CCDS5554.1, CCDS47605.1, CCDS47606.1	7q11.23	2013-05-21	2005-10-31	2005-10-31	ENSG00000009950	ENSG00000009950			12744	protein-coding gene	gene with protein product	"carbohydrate response element binding protein"	605678	"Williams Beuren syndrome chromosome region 14"	WBSCR14		9860302	Standard	XM_005250399		Approved	WS-bHLH, MIO, CHREBP, MONDOB, bHLHd14	uc003tyn.1	Q9NP71	OTTHUMG00000129995	ENST00000313375.3:c.2286G>T	chr7.hg19:g.73009991C>A		90.0	0.0		126.0	50.0	NM_032951	C5HU02|C5HU03|C5HU04|Q96E48|Q9BY03|Q9BY04|Q9BY05|Q9BY06|Q9Y2P3	Silent	SNP	ENST00000313375.3	hg19	CCDS5553.1																																																																																			.	.		0.622	MLXIPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252262.1	NM_032951		A	73009991	C	A	73009991	2	1	342	1	0	0	0	0	0	0	0	1	9646	755	27	1		1	MLXIPL	7	73009991	Silent	SNP	C	TCGA-T1-A6J8-01A-11D-A32G-10	3426820	73009991	86128672	30	47233										
SEMA3A	10371	hgsc.bcm.edu	37	chr7	83606504	83606504	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	catttcttatatcttgtcgtCttgtgcgtctgaagcaatta	7	8	4	1			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr7:83606504C>A	ENST00000265362.4	-	15	1975	c.1661G>T	c.(1660-1662)aGa>aTa	p.R554I	SEMA3A_ENST00000436949.1_Missense_Mutation_p.R554I	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	554					apoptotic process (GO:0006915)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|dendrite morphogenesis (GO:0048813)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of epithelial cell migration (GO:0010633)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neural crest cell migration involved in sympathetic nervous system development (GO:1903045)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of male gonad development (GO:2000020)|positive regulation of neuron migration (GO:2001224)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of heart rate (GO:0002027)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sensory system development (GO:0048880)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular region (GO:0005576)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|neuropilin binding (GO:0038191)|receptor activity (GO:0004872)			breast(3)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						ATCTTGTCGTCTTGTGCGTCT	0.343																																					p.R554I		Atlas-SNP	.											SEMA3A,colon,carcinoma,0,1	SEMA3A	121	.	0			c.G1661T						.						239	211	220					7																	83606504		2203	4300	6503	SO:0001583	missense	10371	exon15			TGTCGTCTTGTGC	L26081	CCDS5599.1	7p12.1	2013-01-11			ENSG00000075213	ENSG00000075213		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10723	protein-coding gene	gene with protein product	"sema III"	603961		SEMAD		8269517, 7748561	Standard	NM_006080		Approved	SEMA1, SemD, coll-1, Hsema-I	uc003uhz.3	Q14563	OTTHUMG00000023443	ENST00000265362.4:c.1661G>T	chr7.hg19:g.83606504C>A	ENSP00000265362:p.Arg554Ile	324.0	0.0		345.0	133.0	NM_006080		Missense_Mutation	SNP	ENST00000265362.4	hg19	CCDS5599.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.281947	0.80692	.	.	ENSG00000075213	ENST00000265362;ENST00000436949	T;T	0.21734	1.99;1.99	5.01	4.13	0.48395	.	0.043132	0.85682	D	0.000000	T	0.36552	0.0971	M	0.79693	2.465	0.80722	D	1	D	0.56035	0.974	P	0.51701	0.677	T	0.24225	-1.0166	10	0.29301	T	0.29	.	13.1439	0.59450	0.0:0.9217:0.0:0.0783	.	554	Q14563	SEM3A_HUMAN	I	554	ENSP00000265362:R554I;ENSP00000415260:R554I	ENSP00000265362:R554I	R	-	2	0	SEMA3A	83444440	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.618000	0.83043	1.110000	0.41699	0.585000	0.79938	AGA	.	.		0.343	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080		A	83606504	C	A	83606504	3	1	342	1	0	0	0	0	1	0	0	0	14039	913	32	3	666	3	SEMA3A	7	83606504	Missense_Mutation	SNP	C	TCGA-T1-A6J8-01A-11D-A32G-10	10596513	83606504	75532159	31	47234										
ZNF804B	219578	hgsc.bcm.edu	37	chr7	88847522	88847522	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	ctggaagatgtaaaggcaaaCttttactgtgaattatgtga	10	4	0	3			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr7:88847522C>A	ENST00000333190.4	+	2	771	c.162C>A	c.(160-162)aaC>aaA	p.N54K		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	54							metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			TAAAGGCAAACTTTTACTGTG	0.363										HNSCC(36;0.09)																											p.N54K		Atlas-SNP	.											.	ZNF804B	322	.	0			c.C162A						.						96	93	94					7																	88847522		2203	4300	6503	SO:0001583	missense	219578	exon2			GGCAAACTTTTAC	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"zinc finger 804B"				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.162C>A	chr7.hg19:g.88847522C>A	ENSP00000329638:p.Asn54Lys	83.0	0.0		114.0	41.0	NM_181646	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	hg19	CCDS5613.1	.	.	.	.	.	.	.	.	.	.	C	17.79	3.474955	0.63737	.	.	ENSG00000182348	ENST00000333190	T	0.06218	3.33	5.31	3.5	0.40072	.	0.071450	0.52532	D	0.000075	T	0.17746	0.0426	L	0.54323	1.7	0.44175	D	0.996989	D	0.89917	1.0	D	0.97110	1.0	T	0.00247	-1.1881	10	0.87932	D	0	-14.9041	9.3807	0.38311	0.0:0.7805:0.0:0.2195	.	54	A4D1E1	Z804B_HUMAN	K	54	ENSP00000329638:N54K	ENSP00000329638:N54K	N	+	3	2	ZNF804B	88685458	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.539000	0.36104	0.808000	0.34231	0.484000	0.47621	AAC	.	.		0.363	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646		A	88847522	C	A	88847522	3	1	342	1	0	0	0	0	1	0	0	0	18186	564	20	3	168	3	ZNF804B	7	88847522	Missense_Mutation	SNP	C	TCGA-T1-A6J8-01A-11D-A32G-10	5241018	88847522	70291141	32	47235										
RELN	5649	hgsc.bcm.edu	37	chr7	103198496	103198496	+	Splice_Site	DEL	C	C	-													0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	aataagcatccttagtccttCctgaaaataaaaacatatac							TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr7:103198496delC	ENST00000428762.1	-	37	5689	c.5530delG	c.(5530-5532)gaa>aa	p.E1844fs	RELN_ENST00000343529.5_Splice_Site_p.E1844fs|RELN_ENST00000424685.2_Splice_Site_p.E1844fs	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	1844					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		CTTAGTCCTTCCTGAAAATAA	0.274																																					p.E1844fs	NSCLC(146;835 1944 15585 22231 52158)	Atlas-Indel,Pindel	.											.	RELN	593	.	0			c.5531delA						.						61	61	61					7																	103198496		2199	4292	6491	SO:0001630	splice_region_variant	5649	exon37			.		CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.5530-1G>-	chr7.hg19:g.103198496delC		191.0	0.0		284.0	105.0	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Frame_Shift_Del	DEL	ENST00000428762.1	hg19	CCDS47680.1																																																																																			.	.		0.274	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045	Frame_Shift_Del	-	103198496	C	-	103198496	8	5	342	1	0	1	0	1	0	0	1	0	13235	869	30	0	4968	0	RELN	7	103198496	Splice_Site	DEL	C	TCGA-T1-A6J8-01A-11D-A32G-10	14350974	103198496	55940167	33	47236										
ATXN7L1	222255	hgsc.bcm.edu	37	chr7	105248313	105248313	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	gtcttgttatggaagagtccTtatcctgcccgttctgtttg	10	9	2	1			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr7:105248313T>C	ENST00000419735.3	-	12	2617	c.2572A>G	c.(2572-2574)Agg>Ggg	p.R858G	ATXN7L1_ENST00000477775.1_Missense_Mutation_p.R735G	NM_020725.1	NP_065776.1	Q9ULK2	AT7L1_HUMAN	ataxin 7-like 1	858										endometrium(1)|large_intestine(4)|lung(5)	10						GGAAGAGTCCTTATCCTGCCC	0.468																																					p.R858G		Atlas-SNP	.											.	ATXN7L1	56	.	0			c.A2572G						.						340	281	299					7																	105248313		692	1591	2283	SO:0001583	missense	222255	exon12			GAGTCCTTATCCT	AB033044	CCDS34727.1, CCDS47682.1, CCDS47683.1	7q22.1	2007-11-13			ENSG00000146776	ENSG00000146776			22210	protein-coding gene	gene with protein product			"ataxin 7-like 4"	ATXN7L4		15115762	Standard	NM_152749		Approved	KIAA1218, MGC33190	uc003vde.2	Q9ULK2	OTTHUMG00000157521	ENST00000419735.3:c.2572A>G	chr7.hg19:g.105248313T>C	ENSP00000410759:p.Arg858Gly	150.0	0.0		220.0	73.0	NM_020725	A4D0Q2|B4DTS1|Q8N2T0	Missense_Mutation	SNP	ENST00000419735.3	hg19	CCDS47682.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.200656	0.79015	.	.	ENSG00000146776	ENST00000419735;ENST00000477775	T;T	0.19250	2.19;2.16	5.69	5.69	0.88448	.	0.864252	0.10138	N	0.711273	T	0.34716	0.0907	N	0.19112	0.55	0.80722	D	1	D;D	0.67145	0.996;0.981	D;D	0.77557	0.99;0.966	T	0.08452	-1.0721	10	0.87932	D	0	.	14.5238	0.67873	0.0:0.0:0.0:1.0	.	735;858	Q9ULK2-3;Q9ULK2	.;AT7L1_HUMAN	G	858;735	ENSP00000410759:R858G;ENSP00000418476:R735G	ENSP00000410759:R858G	R	-	1	2	ATXN7L1	105035549	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.952000	0.40343	2.173000	0.68751	0.533000	0.62120	AGG	.	.		0.468	ATXN7L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349037.2			C	105248313	T	C	105248313	3	2	342	1	0	0	0	0	1	0	0	0	1216	1608	56	2	17	2	ATXN7L1	7	105248313	Missense_Mutation	SNP	T	TCGA-T1-A6J8-01A-11D-A32G-10	2049817	105248313	53890350	34	47237										
LAMB4	22798	hgsc.bcm.edu	37	chr7	107704317	107704317	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	ctcccctgttacccggctgcAggactctggatcggttacat	10	14	1	0			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr7:107704317A>G	ENST00000388781.3	-	22	3033	c.2950T>C	c.(2950-2952)Tgc>Cgc	p.C984R	LAMB4_ENST00000205386.4_Missense_Mutation_p.C984R|LAMB4_ENST00000388780.3_Missense_Mutation_p.C984R	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	984	Laminin EGF-like 10. {ECO:0000255|PROSITE-ProRule:PRU00460}.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)				NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						ACCCGGCTGCAGGACTCTGGA	0.502																																					p.C984R		Atlas-SNP	.											.	LAMB4	253	.	0			c.T2950C						.						175	160	165					7																	107704317		2203	4300	6503	SO:0001583	missense	22798	exon22			GGCTGCAGGACTC	AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"Laminins"	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.2950T>C	chr7.hg19:g.107704317A>G	ENSP00000373433:p.Cys984Arg	183.0	0.0		242.0	92.0	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Missense_Mutation	SNP	ENST00000388781.3	hg19	CCDS34732.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.963016	0.74016	.	.	ENSG00000091128	ENST00000205386;ENST00000388781;ENST00000422975;ENST00000388780	D;D;D;D	0.94330	-3.4;-3.4;-3.4;-3.4	5.11	3.97	0.46021	EGF-like, laminin (3);	0.000000	0.56097	D	0.000029	D	0.97420	0.9156	H	0.96208	3.785	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	D	0.97292	0.9925	10	0.87932	D	0	.	10.6398	0.45586	0.9251:0.0:0.0748:0.0	.	984	A4D0S4	LAMB4_HUMAN	R	984;984;10;984	ENSP00000205386:C984R;ENSP00000373433:C984R;ENSP00000416562:C10R;ENSP00000373432:C984R	ENSP00000205386:C984R	C	-	1	0	LAMB4	107491553	1.000000	0.71417	0.958000	0.39756	0.963000	0.63663	5.600000	0.67599	0.979000	0.38497	0.460000	0.39030	TGC	.	.		0.502	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857		G	107704317	A	G	107704317	3	3	342	1	0	0	0	0	1	0	0	0	8622	188	7	2	2387	2	LAMB4	7	107704317	Missense_Mutation	SNP	A	TCGA-T1-A6J8-01A-11D-A32G-10	2456004	107704317	51434346	35	47238										
ARF5	381	hgsc.bcm.edu	37	chr7	127230141	127230141	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	gcctcatctttgtggtggacAgtaatgaccgggagcgggtc	15	9	2	1			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr7:127230141A>G	ENST00000000233.5	+	4	434	c.280A>G	c.(280-282)Agt>Ggt	p.S94G	GCC1_ENST00000497650.1_Intron	NM_001662.3	NP_001653.1	P84085	ARF5_HUMAN	ADP-ribosylation factor 5	94					GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			cervix(2)|kidney(1)|lung(10)|ovary(1)	14						TGTGGTGGACAGTAATGACCG	0.542																																					p.S94G		Atlas-SNP	.											.	ARF5	20	.	0			c.A280G						.						116	123	121					7																	127230141		2203	4300	6503	SO:0001583	missense	381	exon4			GTGGACAGTAATG		CCDS34745.1	7q31.3	2008-07-18			ENSG00000004059	ENSG00000004059		"ADP-ribosylation factors"	658	protein-coding gene	gene with protein product		103188				1993656	Standard	NM_001662		Approved		uc003vmb.2	P84085	OTTHUMG00000023246	ENST00000000233.5:c.280A>G	chr7.hg19:g.127230141A>G	ENSP00000000233:p.Ser94Gly	33.0	0.0		48.0	17.0	NM_001662	P26437	Missense_Mutation	SNP	ENST00000000233.5	hg19	CCDS34745.1	.	.	.	.	.	.	.	.	.	.	A	27.4	4.828541	0.90955	.	.	ENSG00000004059	ENST00000000233;ENST00000415666	T;T	0.69306	-0.39;-0.39	5.31	5.31	0.75309	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.86986	0.6065	H	0.98238	4.18	0.58432	D	0.999996	D	0.76494	0.999	P	0.62740	0.906	D	0.91390	0.5134	10	0.87932	D	0	-11.4494	13.2158	0.59859	1.0:0.0:0.0:0.0	.	94	P84085	ARF5_HUMAN	G	94	ENSP00000000233:S94G;ENSP00000412701:S94G	ENSP00000000233:S94G	S	+	1	0	ARF5	127017377	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.222000	0.95196	2.012000	0.59069	0.397000	0.26171	AGT	.	.		0.542	ARF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059567.2	NM_001662		G	127230141	A	G	127230141	3	3	342	1	0	0	0	0	1	0	0	0	847	188	7	2	294	2	ARF5	7	127230141	Missense_Mutation	SNP	A	TCGA-T1-A6J8-01A-11D-A32G-10	19525824	127230141	31908522	36	47239										
PIP	5304	hgsc.bcm.edu	37	chr7	142836665	142836665	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	tcgggaattaggcatctgccCtgatgatgctgctgtaatcc	11	10	1	2	rs148216903	byFrequency	TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr7:142836665C>T	ENST00000291009.3	+	4	411	c.371C>T	c.(370-372)cCt>cTt	p.P124L		NM_002652.2	NP_002643.1	P12273	PIP_HUMAN	prolactin-induced protein	124					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of T cell apoptotic process (GO:0070233)|positive regulation of gene expression (GO:0010628)|proteolysis (GO:0006508)|regulation of immune system process (GO:0002682)|retina homeostasis (GO:0001895)	apical plasma membrane (GO:0016324)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	actin binding (GO:0003779)|aspartic-type endopeptidase activity (GO:0004190)|glycoprotein binding (GO:0001948)|IgG binding (GO:0019864)|protein dimerization activity (GO:0046983)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|skin(1)	18	Melanoma(164;0.059)	Ovarian(593;2.82e-05)|Breast(660;0.012)		BRCA - Breast invasive adenocarcinoma(188;0.0026)|LUSC - Lung squamous cell carcinoma(290;0.0733)|Lung(243;0.08)		GGCATCTGCCCTGATGATGCT	0.468																																					p.P124L		Atlas-SNP	.											.	PIP	34	.	0			c.C371T						.						174	168	170					7																	142836665		2203	4299	6502	SO:0001583	missense	5304	exon4			TCTGCCCTGATGA		CCDS34768.1	7q34	2013-09-19			ENSG00000159763	ENSG00000159763			8993	protein-coding gene	gene with protein product	"prolactin-inducible protein"	176720				2727805, 1955075	Standard	NM_002652		Approved	GCDFP-15, GCDFP15, GPIP4	uc003wcf.1	P12273	OTTHUMG00000152635	ENST00000291009.3:c.371C>T	chr7.hg19:g.142836665C>T	ENSP00000291009:p.Pro124Leu	158.0	0.0		240.0	18.0	NM_002652	A0A963|A0A9C3|A0A9F3|A4D2I1	Missense_Mutation	SNP	ENST00000291009.3	hg19	CCDS34768.1	.	.	.	.	.	.	.	.	.	.	C	15.49	2.847859	0.51164	.	.	ENSG00000159763	ENST00000291009	T	0.16196	2.36	4.63	4.63	0.57726	.	0.000000	0.44688	D	0.000436	T	0.40272	0.1110	M	0.71581	2.175	0.48975	D	0.999735	D	0.89917	1.0	D	0.78314	0.991	T	0.26018	-1.0115	10	0.87932	D	0	.	13.7047	0.62631	0.0:1.0:0.0:0.0	.	124	P12273	PIP_HUMAN	L	124	ENSP00000291009:P124L	ENSP00000291009:P124L	P	+	2	0	PIP	142546787	0.765000	0.28485	0.935000	0.37517	0.088000	0.18126	1.912000	0.39946	2.474000	0.83562	0.655000	0.94253	CCT	.	C|0.997;G|0.003		0.468	PIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327089.1	NM_002652		T	142836665	C	T	142836665	3	4	342	1	0	0	0	0	1	0	0	0	11944	681	24	3	385	3	PIP	7	142836665	Missense_Mutation	SNP	C	TCGA-T1-A6J8-01A-11D-A32G-10	15606524	142836665	16301998	37	47240										
SLC24A2	25769	hgsc.bcm.edu	37	chr9	19576992	19576992	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	ttcttcttggcgatcttgtgGagaattgaagccttttctct	9	8	4	2			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr9:19576992G>T	ENST00000341998.2	-	5	1219	c.1158C>A	c.(1156-1158)ctC>ctA	p.L386L	SLC24A2_ENST00000286344.3_Silent_p.L369L	NM_001193288.2|NM_020344.3	NP_001180217.1|NP_065077.1	Q9UI40	NCKX2_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 2	386					cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)	cadmium ion binding (GO:0046870)|calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium, potassium:sodium antiporter activity (GO:0008273)|manganese ion binding (GO:0030145)|nickel cation binding (GO:0016151)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|symporter activity (GO:0015293)			endometrium(3)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33				GBM - Glioblastoma multiforme(1;1.67e-55)|Lung(42;0.0443)		CGATCTTGTGGAGAATTGAAG	0.502																																					p.L386L		Atlas-SNP	.											.	SLC24A2	93	.	0			c.C1158A						.						194	166	175					9																	19576992		2203	4300	6503	SO:0001819	synonymous_variant	25769	exon5			CTTGTGGAGAATT	AF097366	CCDS6493.1, CCDS55297.1	9p22.1	2013-05-22			ENSG00000155886	ENSG00000155886		"Solute carriers"	10976	protein-coding gene	gene with protein product		609838				10662833	Standard	NM_020344		Approved	NCKX2	uc003zoa.2	Q9UI40	OTTHUMG00000019646	ENST00000341998.2:c.1158C>A	chr9.hg19:g.19576992G>T		118.0	0.0		104.0	64.0	NM_020344	B7ZLL8|Q9NTN5|Q9NZQ4	Silent	SNP	ENST00000341998.2	hg19	CCDS6493.1																																																																																			.	.		0.502	SLC24A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051866.2	NM_020344		T	19576992	G	T	19576992	2	4	342	1	0	0	0	0	0	0	0	1	14481	1161	41	3		3	SLC24A2	9	19576992	Silent	SNP	G	TCGA-T1-A6J8-01A-11D-A32G-10		19576992	121636439	38	47241										
OR13A1	79290	hgsc.bcm.edu	37	chr10	45799382	45799382	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	cagagcagccacacggctgtGgccagcccgctgcagaacac	12	16	0	2			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr10:45799382G>T	ENST00000553795.1	-	4	797	c.489C>A	c.(487-489)gcC>gcA	p.A163A	OR13A1_ENST00000374401.2_Silent_p.A163A|OR13A1_ENST00000536058.1_Silent_p.A163A	NM_001004297.2	NP_001004297.2	Q8NGR1	O13A1_HUMAN	olfactory receptor, family 13, subfamily A, member 1	163						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|skin(2)|urinary_tract(1)	19						ACACGGCTGTGGCCAGCCCGC	0.592																																					p.A163A		Atlas-SNP	.											.	OR13A1	49	.	0			c.C489A						.						33	34	34					10																	45799382		2193	4274	6467	SO:0001819	synonymous_variant	79290	exon4			GGCTGTGGCCAGC	AB065728	CCDS31188.1	10q11.21	2012-10-03			ENSG00000256574	ENSG00000256574		"GPCR / Class A : Olfactory receptors"	14772	protein-coding gene	gene with protein product							Standard	NM_001004297		Approved		uc001jcc.1	Q8NGR1	OTTHUMG00000018080	ENST00000553795.1:c.489C>A	chr10.hg19:g.45799382G>T		37.0	0.0		57.0	15.0	NM_001004297	Q2M3M4|Q5VV57|Q6IFH5|Q6ZMN6	Silent	SNP	ENST00000553795.1	hg19	CCDS31188.1																																																																																			.	.		0.592	OR13A1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047779.2	NM_001004297		T	45799382	G	T	45799382	2	4	342	1	0	0	0	0	0	0	0	1	10942	1335	47	3		3	OR13A1	10	45799382	Silent	SNP	G	TCGA-T1-A6J8-01A-11D-A32G-10		45799382	89735365	39	47242										
C10orf71	118461	hgsc.bcm.edu	37	chr10	50530973	50530973	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	agtccagaggagactggaggTgccagtttccggcctaagga	15	9	0	2			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr10:50530973T>C	ENST00000374144.3	+	3	671	c.383T>C	c.(382-384)gTg>gCg	p.V128A	C10orf71_ENST00000323868.4_Missense_Mutation_p.V128A			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	128										endometrium(1)	1						AGACTGGAGGTGCCAGTTTCC	0.542																																					p.V128A		Atlas-SNP	.											.	C10orf71	179	.	0			c.T383C						.						82	96	91					10																	50530973		1941	4135	6076	SO:0001583	missense	118461	exon3			TGGAGGTGCCAGT	AL833265	CCDS44387.1	10q11.23	2012-05-31			ENSG00000177354	ENSG00000177354			26973	protein-coding gene	gene with protein product							Standard	NM_001135196		Approved	FLJ45913	uc021pqa.2	Q711Q0	OTTHUMG00000018190	ENST00000374144.3:c.383T>C	chr10.hg19:g.50530973T>C	ENSP00000363259:p.Val128Ala	54.0	0.0		89.0	36.0	NM_001135196	A0AVL8	Missense_Mutation	SNP	ENST00000374144.3	hg19	CCDS44387.1	.	.	.	.	.	.	.	.	.	.	T	17.69	3.451858	0.63290	.	.	ENSG00000177354	ENST00000323868;ENST00000374144	T;T	0.19532	2.14;3.27	5.12	5.12	0.69794	.	0.355426	0.20380	N	0.093469	T	0.19685	0.0473	L	0.52364	1.645	0.32662	N	0.517892	B	0.32753	0.383	B	0.29716	0.106	T	0.28364	-1.0046	10	0.72032	D	0.01	.	9.4587	0.38772	0.0:0.0797:0.0:0.9203	.	128	Q711Q0-3	.	A	128	ENSP00000318713:V128A;ENSP00000363259:V128A	ENSP00000318713:V128A	V	+	2	0	C10orf71	50200979	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	3.702000	0.54800	1.936000	0.56123	0.379000	0.24179	GTG	.	.		0.542	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459		C	50530973	T	C	50530973	3	2	342	1	0	0	0	0	1	0	0	0	1616	1696	59	2	385	2	C10orf71	10	50530973	Missense_Mutation	SNP	T	TCGA-T1-A6J8-01A-11D-A32G-10	4731591	50530973	85003774	40	47243										
C10orf76	79591	hgsc.bcm.edu	37	chr10	103783452	103783452	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	ctgtaaaattgcttcaaataTgctgttgatcattacatact	5	7	2	1			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr10:103783452T>A	ENST00000370033.4	-	7	681	c.562A>T	c.(562-564)Ata>Tta	p.I188L		NM_024541.2	NP_078817.2	Q5T2E6	CJ076_HUMAN	chromosome 10 open reading frame 76	188						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(7)|prostate(2)|upper_aerodigestive_tract(2)	24		Colorectal(252;0.123)		Epithelial(162;2.41e-08)|all cancers(201;6.41e-07)		GCTTCAAATATGCTGTTGATC	0.393																																					p.I188L		Atlas-SNP	.											.	C10orf76	48	.	0			c.A562T						.						232	213	219					10																	103783452		1868	4119	5987	SO:0001583	missense	79591	exon7			CAAATATGCTGTT	AK023176	CCDS41563.1	10q24.32	2008-10-21			ENSG00000120029	ENSG00000120029			25788	protein-coding gene	gene with protein product						14702039	Standard	NM_024541		Approved	FLJ13114	uc009xwy.1	Q5T2E6	OTTHUMG00000018943	ENST00000370033.4:c.562A>T	chr10.hg19:g.103783452T>A	ENSP00000359050:p.Ile188Leu	159.0	0.0		207.0	52.0	NM_024541	Q2TB87|Q9H8Z9	Missense_Mutation	SNP	ENST00000370033.4	hg19	CCDS41563.1	.	.	.	.	.	.	.	.	.	.	T	14.78	2.636807	0.47049	.	.	ENSG00000120029	ENST00000370033	T	0.63580	-0.05	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.50377	0.1612	L	0.40543	1.245	0.80722	D	1	B	0.23540	0.087	B	0.23716	0.048	T	0.47971	-0.9075	10	0.05351	T	0.99	-17.6356	15.6377	0.76966	0.0:0.0:0.0:1.0	.	188	Q5T2E6	CJ076_HUMAN	L	188	ENSP00000359050:I188L	ENSP00000359050:I188L	I	-	1	0	C10orf76	103773442	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.663000	0.83820	2.101000	0.63845	0.460000	0.39030	ATA	.	.		0.393	C10orf76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050007.1	NM_024541		A	103783452	T	A	103783452	3	1	342	1	0	0	0	0	1	0	0	0	1618	1464	51	4	1587	4	C10orf76	10	103783452	Missense_Mutation	SNP	T	TCGA-T1-A6J8-01A-11D-A32G-10	53252479	103783452	31751295	41	47244										
OR5L2	26338	hgsc.bcm.edu	37	chr11	55594866	55594866	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	tcagctctcggctccacaccCccgtgtactttttcctcagc	6	18	3	0			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr11:55594866C>A	ENST00000378397.1	+	1	172	c.172C>A	c.(172-174)Ccc>Acc	p.P58T		NM_001004739.1	NP_001004739.1	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L, member 2	58						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			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)				GCTCCACACCCCCGTGTACTT	0.468										HNSCC(27;0.073)																											p.P58T		Atlas-SNP	.											.	OR5L2	135	.	0			c.C172A						.						254	233	240					11																	55594866		2200	4296	6496	SO:0001583	missense	26338	exon1			CACACCCCCGTGT	AB065782	CCDS31511.1	11q11	2012-08-09			ENSG00000205030	ENSG00000205030		"GPCR / Class A : Olfactory receptors"	8351	protein-coding gene	gene with protein product						1370859	Standard	NM_001004739		Approved	HTPCRX16, HSHTPCRX16	uc001nhy.1	Q8NGL0	OTTHUMG00000166812	ENST00000378397.1:c.172C>A	chr11.hg19:g.55594866C>A	ENSP00000367650:p.Pro58Thr	252.0	0.0		269.0	109.0	NM_001004739	Q6IF66|Q96RB2	Missense_Mutation	SNP	ENST00000378397.1	hg19	CCDS31511.1	.	.	.	.	.	.	.	.	.	.	.	13.55	2.271855	0.40194	.	.	ENSG00000205030	ENST00000378397	T	0.02032	4.49	5.31	4.4	0.53042	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48767	D	0.000172	T	0.21509	0.0518	H	0.97707	4.06	0.43435	D	0.995608	D	0.89917	1.0	D	0.97110	1.0	T	0.31336	-0.9947	10	0.72032	D	0.01	-36.8392	13.1571	0.59524	0.0:0.9219:0.0:0.0781	.	58	Q8NGL0	OR5L2_HUMAN	T	58	ENSP00000367650:P58T	ENSP00000367650:P58T	P	+	1	0	OR5L2	55351442	1.000000	0.71417	0.940000	0.37924	0.055000	0.15305	5.604000	0.67626	1.421000	0.47157	-0.169000	0.13324	CCC	.	.		0.468	OR5L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391516.1	NM_001004739		A	55594866	C	A	55594866	3	1	342	1	0	0	0	0	1	0	0	0	11180	623	22	3	174	3	OR5L2	11	55594866	Missense_Mutation	SNP	C	TCGA-T1-A6J8-01A-11D-A32G-10		55594866	79411650	42	47245										
LRRC55	219527	hgsc.bcm.edu	37	chr11	56949612	56949612	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	ggatgccggcaccagctgccCcgtcctttgcacatgccgta	11	16	0	0			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr11:56949612C>T	ENST00000497933.1	+	1	392	c.245C>T	c.(244-246)cCc>cTc	p.P82L		NM_001005210.2	NP_001005210.1	Q6ZSA7	LRC55_HUMAN	leucine rich repeat containing 55	52					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(13)|ovary(2)|skin(2)	25						ACCAGCTGCCCCGTCCTTTGC	0.647																																					p.P82L		Atlas-SNP	.											.	LRRC55	52	.	0			c.C245T						.						49	52	51					11																	56949612		2201	4296	6497	SO:0001583	missense	219527	exon1			GCTGCCCCGTCCT		CCDS31539.1	11q12.1	2008-02-05			ENSG00000183908	ENSG00000183908			32324	protein-coding gene	gene with protein product		615213					Standard	NM_001005210		Approved	FLJ45686	uc001njl.2	Q6ZSA7	OTTHUMG00000159309	ENST00000497933.1:c.245C>T	chr11.hg19:g.56949612C>T	ENSP00000419542:p.Pro82Leu	60.0	0.0		90.0	36.0	NM_001005210	A7E2U7|B2RN81	Missense_Mutation	SNP	ENST00000497933.1	hg19	CCDS31539.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.709813	0.89018	.	.	ENSG00000183908	ENST00000497933	D	0.98044	-4.68	5.8	5.8	0.92144	Leucine-rich repeat-containing N-terminal (2);	0.000000	0.64402	D	0.000013	D	0.98982	0.9653	M	0.91663	3.23	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.99620	1.0983	10	0.87932	D	0	.	16.9798	0.86324	0.0:1.0:0.0:0.0	.	52	Q6ZSA7	LRC55_HUMAN	L	82	ENSP00000419542:P82L	ENSP00000419542:P82L	P	+	2	0	LRRC55	56706188	1.000000	0.71417	0.953000	0.39169	0.828000	0.46876	6.640000	0.74319	2.735000	0.93741	0.655000	0.94253	CCC	.	.		0.647	LRRC55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354503.2	NM_001005210		T	56949612	C	T	56949612	3	4	342	1	0	0	0	0	1	0	0	0	9020	623	22	3	247	3	LRRC55	11	56949612	Missense_Mutation	SNP	C	TCGA-T1-A6J8-01A-11D-A32G-10	1354746	56949612	78056904	43	47246										
SPTBN2	6712	hgsc.bcm.edu	37	chr11	66475653	66475653	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	ctcgctgagccaggtctcccGcatggcagccttgcggtcga	13	15	1	1			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr11:66475653G>A	ENST00000533211.1	-	12	1640	c.1309C>T	c.(1309-1311)Cgg>Tgg	p.R437W	SPTBN2_ENST00000529997.1_Missense_Mutation_p.R437W|SPTBN2_ENST00000309996.2_Missense_Mutation_p.R437W			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	437					actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						CAGGTCTCCCGCATGGCAGCC	0.657																																					p.R437W		Atlas-SNP	.											.	SPTBN2	188	.	0			c.C1309T						.						42	44	43					11																	66475653		2200	4294	6494	SO:0001583	missense	6712	exon11			TCTCCCGCATGGC	AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"Pleckstrin homology (PH) domain containing"	11276	protein-coding gene	gene with protein product		604985	"spinocerebellar ataxia 5"	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.1309C>T	chr11.hg19:g.66475653G>A	ENSP00000432568:p.Arg437Trp	103.0	0.0		146.0	34.0	NM_006946	O14872|O14873	Missense_Mutation	SNP	ENST00000533211.1	hg19	CCDS8150.1	.	.	.	.	.	.	.	.	.	.	G	19.23	3.786587	0.70337	.	.	ENSG00000173898	ENST00000533211;ENST00000309996;ENST00000529997;ENST00000443262	T;T;T	0.50277	0.75;0.75;0.75	4.62	4.62	0.57501	.	0.000000	0.64402	D	0.000001	T	0.74321	0.3701	M	0.94021	3.485	0.58432	D	0.999997	D	0.89917	1.0	D	0.97110	1.0	T	0.80400	-0.1398	10	0.72032	D	0.01	.	11.6095	0.51052	0.0:0.0:0.8219:0.1781	.	437	O15020	SPTN2_HUMAN	W	437	ENSP00000432568:R437W;ENSP00000311489:R437W;ENSP00000433593:R437W	ENSP00000311489:R437W	R	-	1	2	SPTBN2	66232229	1.000000	0.71417	1.000000	0.80357	0.846000	0.48090	0.636000	0.24644	2.388000	0.81334	0.561000	0.74099	CGG	.	.		0.657	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946		A	66475653	G	A	66475653	3	1	342	1	0	0	0	0	1	0	0	0	15135	1086	38	1	5971	1	SPTBN2	11	66475653	Missense_Mutation	SNP	G	TCGA-T1-A6J8-01A-11D-A32G-10	9526041	66475653	68530863	44	47247										
MMP13	4322	hgsc.bcm.edu	37	chr11	102816423	102816423	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	atcaccaattcctgggaagtCttcttctattagtctcggat	7	10	5	0			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr11:102816423C>G	ENST00000260302.3	-	9	1295	c.1267G>C	c.(1267-1269)Gac>Cac	p.D423H	MMP13_ENST00000340273.4_Missense_Mutation_p.D423H	NM_002427.3	NP_002418.1	P45452	MMP13_HUMAN	matrix metallopeptidase 13 (collagenase 3)	423	Interaction with collagen.				bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cartilage development (GO:0051216)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|skin(1)|stomach(1)	27		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0144)	Marimastat(DB00786)	CCTGGGAAGTCTTCTTCTATT	0.333																																					p.D423H		Atlas-SNP	.											.	MMP13	75	.	0			c.G1267C						.						144	149	147					11																	102816423		2202	4298	6500	SO:0001583	missense	4322	exon9			GGAAGTCTTCTTC	X75308	CCDS8324.1	11q22.3	2014-01-30	2005-08-08		ENSG00000137745	ENSG00000137745		"Endogenous ligands"	7159	protein-coding gene	gene with protein product	"collagenase 3"	600108	"matrix metalloproteinase 13 (collagenase 3)"			8207000	Standard	NM_002427		Approved	CLG3	uc001phl.3	P45452	OTTHUMG00000165850	ENST00000260302.3:c.1267G>C	chr11.hg19:g.102816423C>G	ENSP00000260302:p.Asp423His	67.0	0.0		76.0	23.0	NM_002427	A8K846|B2RCZ3|Q6NWN6	Missense_Mutation	SNP	ENST00000260302.3	hg19	CCDS8324.1	.	.	.	.	.	.	.	.	.	.	C	13.86	2.363525	0.41902	.	.	ENSG00000137745	ENST00000260302;ENST00000340273	T;T	0.02606	4.23;4.23	6.16	6.16	0.99307	Hemopexin/matrixin (2);	0.317736	0.38326	N	0.001726	T	0.12518	0.0304	M	0.64404	1.975	0.20926	N	0.999828	P	0.37015	0.578	P	0.51297	0.665	T	0.00449	-1.1732	10	0.72032	D	0.01	.	20.8598	0.99761	0.0:1.0:0.0:0.0	.	423	P45452	MMP13_HUMAN	H	423	ENSP00000260302:D423H;ENSP00000339672:D423H	ENSP00000260302:D423H	D	-	1	0	MMP13	102321633	0.015000	0.18098	0.417000	0.26559	0.020000	0.10135	1.824000	0.39072	2.937000	0.99478	0.650000	0.86243	GAC	.	.		0.333	MMP13-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386648.1	NM_002427		G	102816423	C	G	102816423	3	3	342	1	0	0	0	0	1	0	0	0	9661	913	32	4	156	4	MMP13	11	102816423	Missense_Mutation	SNP	C	TCGA-T1-A6J8-01A-11D-A32G-10	36340770	102816423	32190093	45	47248			1	63		2	2	37	N	T_C	9.535435e-05
MMP13	4322	hgsc.bcm.edu	37	chr11	102816459	102816459	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	cggatagtctttatccataaTatggttagtatcatcatatc	6	7	3	0			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr11:102816459T>C	ENST00000260302.3	-	9	1259	c.1231A>G	c.(1231-1233)Att>Gtt	p.I411V	MMP13_ENST00000340273.4_Missense_Mutation_p.I411V	NM_002427.3	NP_002418.1	P45452	MMP13_HUMAN	matrix metallopeptidase 13 (collagenase 3)	411	Interaction with collagen.				bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cartilage development (GO:0051216)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|skin(1)|stomach(1)	27		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0144)	Marimastat(DB00786)	TTATCCATAATATGGTTAGTA	0.299																																					p.I411V		Atlas-SNP	.											.	MMP13	75	.	0			c.A1231G						.						108	110	109					11																	102816459		2202	4298	6500	SO:0001583	missense	4322	exon9			CCATAATATGGTT	X75308	CCDS8324.1	11q22.3	2014-01-30	2005-08-08		ENSG00000137745	ENSG00000137745		"Endogenous ligands"	7159	protein-coding gene	gene with protein product	"collagenase 3"	600108	"matrix metalloproteinase 13 (collagenase 3)"			8207000	Standard	NM_002427		Approved	CLG3	uc001phl.3	P45452	OTTHUMG00000165850	ENST00000260302.3:c.1231A>G	chr11.hg19:g.102816459T>C	ENSP00000260302:p.Ile411Val	61.0	0.0		74.0	23.0	NM_002427	A8K846|B2RCZ3|Q6NWN6	Missense_Mutation	SNP	ENST00000260302.3	hg19	CCDS8324.1	.	.	.	.	.	.	.	.	.	.	T	7.504	0.653329	0.14580	.	.	ENSG00000137745	ENST00000260302;ENST00000340273	T;T	0.02301	4.35;4.35	6.16	-3.26	0.05064	Hemopexin/matrixin (2);	1.456600	0.03973	N	0.291993	T	0.00998	0.0033	N	0.01284	-0.91	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48885	-0.8995	10	0.10111	T	0.7	.	10.1171	0.42598	0.0:0.4868:0.1092:0.404	.	411	P45452	MMP13_HUMAN	V	411	ENSP00000260302:I411V;ENSP00000339672:I411V	ENSP00000260302:I411V	I	-	1	0	MMP13	102321669	0.000000	0.05858	0.000000	0.03702	0.764000	0.43329	-0.550000	0.06034	-0.894000	0.03925	-0.256000	0.11100	ATT	.	.		0.299	MMP13-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386648.1	NM_002427		C	102816459	T	C	102816459	3	2	342	1	0	0	0	0	1	0	0	0	9661	1406	49	2	192	2	MMP13	11	102816459	Missense_Mutation	SNP	T	TCGA-T1-A6J8-01A-11D-A32G-10	36	102816459	32190057	46	47249			1	63		2	2	37	N	T_C	9.535435e-05
NTF3	4908	hgsc.bcm.edu	37	chr12	5604082	5604082	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	acttcagagaacaataaactCgtgggctggcggtggatacg	13	8	1	1			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr12:5604082C>T	ENST00000331010.6	+	1	785	c.702C>T	c.(700-702)ctC>ctT	p.L234L	NTF3_ENST00000535299.1_Intron|NTF3_ENST00000423158.3_Silent_p.L247L	NM_002527.4	NP_002518.1	P20783	NTF3_HUMAN	neurotrophin 3	234					activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell-cell signaling (GO:0007267)|enteric nervous system development (GO:0048484)|epidermis development (GO:0008544)|glial cell fate determination (GO:0007403)|induction of positive chemotaxis (GO:0050930)|mechanoreceptor differentiation (GO:0042490)|myelination (GO:0042552)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|nerve development (GO:0021675)|nervous system development (GO:0007399)|neuromuscular synaptic transmission (GO:0007274)|peripheral nervous system development (GO:0007422)|positive chemotaxis (GO:0050918)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of glial cell differentiation (GO:0045687)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of receptor internalization (GO:0002092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of synaptic transmission (GO:0050804)|signal transduction (GO:0007165)|smooth muscle cell differentiation (GO:0051145)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasmic membrane-bounded vesicle (GO:0016023)|extracellular region (GO:0005576)	chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|receptor binding (GO:0005102)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(3)|upper_aerodigestive_tract(1)	22						ACAATAAACTCGTGGGCTGGC	0.453																																					p.L247L	GBM(194;1104 2182 8339 9578 18493)	Atlas-SNP	.											.	NTF3	50	.	0			c.C741T						.						64	52	56					12																	5604082		2203	4300	6503	SO:0001819	synonymous_variant	4908	exon2			TAAACTCGTGGGC		CCDS8538.1, CCDS44806.1	12p13	2014-01-30			ENSG00000185652	ENSG00000185652		"Endogenous ligands"	8023	protein-coding gene	gene with protein product		162660				1889806	Standard	NM_002527		Approved	NGF2	uc001qnk.4	P20783	OTTHUMG00000168649	ENST00000331010.6:c.702C>T	chr12.hg19:g.5604082C>T		76.0	0.0		55.0	34.0	NM_001102654	B7Z1T5|Q6FH50	Silent	SNP	ENST00000331010.6	hg19	CCDS8538.1																																																																																			.	.		0.453	NTF3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400486.1			T	5604082	C	T	5604082	2	4	342	1	0	0	0	0	0	0	0	1	10705	871	31	1		1	NTF3	12	5604082	Silent	SNP	C	TCGA-T1-A6J8-01A-11D-A32G-10		5604082	128247813	47	47250										
PTPRO	5800	hgsc.bcm.edu	37	chr12	15739913	15739913	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	cacagcaaatgctgcagaaaGtatcctgcagtttgtacaca	8	10	0	1			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr12:15739913G>C	ENST00000281171.4	+	24	3668	c.3338G>C	c.(3337-3339)aGt>aCt	p.S1113T	PTPRO_ENST00000542557.1_Missense_Mutation_p.S274T|PTPRO_ENST00000442921.2_Missense_Mutation_p.S302T|PTPRO_ENST00000348962.2_Missense_Mutation_p.S1085T|PTPRO_ENST00000544244.1_Missense_Mutation_p.S274T|PTPRO_ENST00000445537.2_Missense_Mutation_p.S302T	NM_030667.2	NP_109592.1	Q16827	PTPRO_HUMAN	protein tyrosine phosphatase, receptor type, O	1113	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axon guidance (GO:0007411)|cell morphogenesis (GO:0000902)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|lamellipodium assembly (GO:0030032)|monocyte chemotaxis (GO:0002548)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of glomerular filtration (GO:0003105)|negative regulation of neuron projection development (GO:0010977)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of glomerular filtration (GO:0003093)|slit diaphragm assembly (GO:0036060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	phosphatase activity (GO:0016791)|protein homodimerization activity (GO:0042803)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)|Wnt-protein binding (GO:0017147)			NS(2)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(11)|lung(30)|ovary(2)|prostate(1)|skin(17)|upper_aerodigestive_tract(1)	74		Hepatocellular(102;0.244)				GCTGCAGAAAGTATCCTGCAG	0.453																																					p.S1113T		Atlas-SNP	.											.	PTPRO	148	.	0			c.G3338C						.						169	139	149					12																	15739913		2203	4300	6503	SO:0001583	missense	5800	exon24			CAGAAAGTATCCT	U20489	CCDS8674.1, CCDS8675.1, CCDS44837.1, CCDS53754.1	12p13-p12	2013-02-11			ENSG00000151490	ENSG00000151490		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9678	protein-coding gene	gene with protein product	"osteoclastic transmembrane protein-tyrosine phosphatase"	600579				7519601, 7665166, 21722858	Standard	NM_030667		Approved	PTPU2, GLEPP1, PTP-U2, PTP-oc, NPHS6	uc001rcv.2	Q16827	OTTHUMG00000168786	ENST00000281171.4:c.3338G>C	chr12.hg19:g.15739913G>C	ENSP00000281171:p.Ser1113Thr	120.0	0.0		91.0	25.0	NM_030667	A0AV39|Q13101|Q8IYG3|Q9UBF0|Q9UBT5	Missense_Mutation	SNP	ENST00000281171.4	hg19	CCDS8675.1	.	.	.	.	.	.	.	.	.	.	G	16.69	3.193564	0.58017	.	.	ENSG00000151490	ENST00000281171;ENST00000348962;ENST00000442921;ENST00000542557;ENST00000445537;ENST00000544244;ENST00000535322	D;D;D;D;D;D;D	0.84516	-1.86;-1.86;-1.86;-1.86;-1.86;-1.86;-1.86	5.07	5.07	0.68467	Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.64402	D	0.000008	D	0.85526	0.5717	N	0.17800	0.525	0.54753	D	0.999981	B;D;D	0.63046	0.196;0.99;0.992	B;D;D	0.74023	0.179;0.97;0.982	T	0.80231	-0.1468	10	0.09338	T	0.73	.	18.6382	0.91385	0.0:0.0:1.0:0.0	.	274;1085;1113	Q9UBT5;Q16827-2;Q16827	.;.;PTPRO_HUMAN	T	1113;1085;302;274;302;274;92	ENSP00000281171:S1113T;ENSP00000343434:S1085T;ENSP00000404188:S302T;ENSP00000437571:S274T;ENSP00000393449:S302T;ENSP00000439234:S274T;ENSP00000446201:S92T	ENSP00000281171:S1113T	S	+	2	0	PTPRO	15631180	1.000000	0.71417	0.177000	0.23020	0.900000	0.52787	9.456000	0.97628	2.623000	0.88846	0.650000	0.86243	AGT	.	.		0.453	PTPRO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401079.1			C	15739913	G	C	15739913	3	2	342	1	0	0	0	0	1	0	0	0	12824	1029	36	4	3432	4	PTPRO	12	15739913	Missense_Mutation	SNP	G	TCGA-T1-A6J8-01A-11D-A32G-10	10135831	15739913	118111982	48	47251										
KRT1	3848	hgsc.bcm.edu	37	chr12	53069229	53069229	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	gagccatagctgccacctccGgagccgtagctgctacctcc	10	17	0	0	rs540699806|rs267607656	byFrequency	TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr12:53069229G>A	ENST00000252244.3	-	9	1741	c.1683C>T	c.(1681-1683)tcC>tcT	p.S561S		NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1	561	Gly/Ser-rich.|Tail.		Missing (in allele 1B). {ECO:0000269|PubMed:1281859}.		complement activation, lectin pathway (GO:0001867)|establishment of skin barrier (GO:0061436)|fibrinolysis (GO:0042730)|negative regulation of inflammatory response (GO:0050728)|regulation of angiogenesis (GO:0045765)|response to oxidative stress (GO:0006979)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(7)|skin(3)	39						tgccacctccggagccgtagc	0.692																																					p.S561S		Atlas-SNP	.											.	KRT1	110	.	0			c.C1683T						.						4	4	4					12																	53069229		1797	3656	5453	SO:0001819	synonymous_variant	3848	exon9			ACCTCCGGAGCCG	X69725	CCDS8836.1	12q13.13	2014-06-05	2008-08-01		ENSG00000167768	ENSG00000167768		"-", "Intermediate filaments type II, keratins (basic)"	6412	protein-coding gene	gene with protein product		139350	"epidermolytic hyperkeratosis 1"	EHK1		2461420, 2470667, 16831889	Standard	NM_006121		Approved	KRT1A	uc001sau.1	P04264	OTTHUMG00000169749	ENST00000252244.3:c.1683C>T	chr12.hg19:g.53069229G>A		2.0	0.0		29.0	4.0	NM_006121	B2RA01|P85925|P86104|Q14720|Q6GSJ0|Q9H298	Silent	SNP	ENST00000252244.3	hg19	CCDS8836.1																																																																																			.	.		0.692	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1	NM_006121		A	53069229	G	A	53069229	2	1	342	1	0	0	0	0	0	0	0	1	8456	1103	39	1		1	KRT1	12	53069229	Silent	SNP	G	TCGA-T1-A6J8-01A-11D-A32G-10	37329316	53069229	80782666	49	47252										
GCN1L1	10985	hgsc.bcm.edu	37	chr12	120589170	120589171	+	Frame_Shift_Del	DEL	AA	AA	-													0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	tggctggcacaaggggtggcAagcagctggctacggactcc							TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr12:120589170_120589171delAA	ENST00000300648.6	-	34	4099_4100	c.4087_4088delTT	c.(4087-4089)ttgfs	p.L1363fs		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	1363					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					AAGGGGTGGCAAGCAGCTGGCT	0.604																																					p.1363_1363del		Atlas-INDEL	.											.	GCN1L1	207	.	0			c.4088_4089del						.																																			SO:0001589	frameshift_variant	10985	exon34			.	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.4087_4088delTT	chr12.hg19:g.120589170_120589171delAA	ENSP00000300648:p.Leu1363fs	65.0	0.0		69.0	22.0	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Frame_Shift_Del	DEL	ENST00000300648.6	hg19	CCDS41847.1																																																																																			.	.		0.604	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1			-	120589171	AA	-	120589170	7	5	342	1	0	1	0	1	0	0	0	0	6307	131	5	0	4027	0	GCN1L1	12	120589170	Frame_Shift_Del	DEL	AA	TCGA-T1-A6J8-01A-11D-A32G-10	67519941	120589170	13262725	50	47253	255	2								
GCN1L1	10985	hgsc.bcm.edu	37	chr12	120589173	120589174	+	Frame_Shift_Del	DEL	CA	CA	-													0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	ctggcacaaggggtggcaagCagctggctacggactcctgg							TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr12:120589173_120589174delCA	ENST00000300648.6	-	34	4096_4097	c.4084_4085delTG	c.(4084-4086)tgcfs	p.C1362fs		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	1362					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GGGTGGCAAGCAGCTGGCTACG	0.594																																					p.1362_1362del		Atlas-INDEL	.											.	GCN1L1	207	.	0			c.4085_4086del						.																																			SO:0001589	frameshift_variant	10985	exon34			.	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.4084_4085delTG	chr12.hg19:g.120589173_120589174delCA	ENSP00000300648:p.Cys1362fs	63.0	0.0		66.0	22.0	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Frame_Shift_Del	DEL	ENST00000300648.6	hg19	CCDS41847.1																																																																																			.	.		0.594	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1			-	120589174	CA	-	120589173	7	5	342	1	0	1	0	1	0	0	0	0	6307	710	25	0	4030	0	GCN1L1	12	120589173	Frame_Shift_Del	DEL	CA	TCGA-T1-A6J8-01A-11D-A32G-10	3	120589173	13262722	51	47254	255	2								
HNF1A	6927	hgsc.bcm.edu	37	chr12	121416684	121416684	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	tgagccggggccctacctccTggctggagaaggccccctgg	15	15	0	2			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr12:121416684T>C	ENST00000257555.6	+	1	339	c.113T>C	c.(112-114)cTg>cCg	p.L38P	HNF1A-AS1_ENST00000537361.1_RNA|HNF1A-AS1_ENST00000433033.2_RNA|HNF1A-AS1_ENST00000535301.1_RNA|HNF1A_ENST00000544413.1_Missense_Mutation_p.L38P|HNF1A_ENST00000541395.1_Missense_Mutation_p.L38P|HNF1A_ENST00000538626.1_Intron|HNF1A_ENST00000543427.1_Intron|HNF1A_ENST00000400024.2_Missense_Mutation_p.L38P|HNF1A_ENST00000402929.1_Missense_Mutation_p.L38P			P20823	HNF1A_HUMAN	HNF1 homeobox A	38					glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.Y36fs*107(1)|p.?(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CCCTACCTCCTGGCTGGAGAA	0.701									Hepatic Adenoma, Familial Clustering of																												p.L38P		Atlas-SNP	.											.	HNF1A	302	.	2	Unknown(1)|Complex - frameshift(1)	liver(1)|endometrium(1)	c.T113C						.						18	21	20					12																	121416684		2203	4300	6503	SO:0001583	missense	6927	exon1	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	ACCTCCTGGCTGG	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100		"Homeoboxes / HNF class"	11621	protein-coding gene	gene with protein product		142410	"transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor"	MODY3, TCF1		1535333, 7795649	Standard	NM_000545		Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	ENST00000257555.6:c.113T>C	chr12.hg19:g.121416684T>C	ENSP00000257555:p.Leu38Pro	112.0	0.0		127.0	44.0	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Missense_Mutation	SNP	ENST00000257555.6	hg19	CCDS9209.1	.	.	.	.	.	.	.	.	.	.	T	4.025	0.002126	0.07819	.	.	ENSG00000135100	ENST00000257555;ENST00000535125;ENST00000543536;ENST00000544680;ENST00000537424;ENST00000543027;ENST00000545458;ENST00000541395;ENST00000340577;ENST00000344370;ENST00000544413	D;D;D	0.98419	-4.92;-4.92;-4.92	4.45	4.45	0.53987	Hepatocyte nuclear factor 1, N-terminal (1);	0.674499	0.13192	N	0.406604	D	0.95111	0.8416	N	0.22421	0.69	0.20703	N	0.999861	B;B;B;B	0.06786	0.0;0.0;0.001;0.001	B;B;B;B	0.12156	0.002;0.002;0.007;0.003	D	0.88962	0.3394	10	0.32370	T	0.25	-1.994	12.8999	0.58119	0.0:0.0:0.0:1.0	.	38;38;38;38	F5H0K0;P20823;E7EUQ4;E7EMR0	.;HNF1A_HUMAN;.;.	P	38	ENSP00000257555:L38P;ENSP00000443112:L38P;ENSP00000438804:L38P	ENSP00000257555:L38P	L	+	2	0	HNF1A	119901067	0.999000	0.42202	0.972000	0.41901	0.473000	0.32948	3.441000	0.52893	1.637000	0.50538	0.482000	0.46254	CTG	.	.		0.701	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545		C	121416684	T	C	121416684	3	2	342	1	0	0	0	0	1	0	0	0	7260	1580	55	2	115	2	HNF1A	12	121416684	Missense_Mutation	SNP	T	TCGA-T1-A6J8-01A-11D-A32G-10	827511	121416684	12435211	52	47255										
PITPNM2	57605	hgsc.bcm.edu	37	chr12	123498529	123498529	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	gcctgggccatctgtgtacgGccggttctccaggatctcca	12	14	3	0			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr12:123498529G>A	ENST00000542749.1	-	2	202	c.139C>T	c.(139-141)Ccg>Tcg	p.P47S	PITPNM2_ENST00000320201.4_Missense_Mutation_p.P47S|PITPNM2_ENST00000546049.1_Missense_Mutation_p.P47S|PITPNM2_ENST00000451868.2_5'UTR|RN7SL133P_ENST00000585256.1_RNA|PITPNM2_ENST00000280562.5_Missense_Mutation_p.P47S|PITPNM2_ENST00000392428.1_Splice_Site_p.P47S			Q9BZ72	PITM2_HUMAN	phosphatidylinositol transfer protein, membrane-associated 2	47					metabolic process (GO:0008152)|transport (GO:0006810)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)			NS(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	39	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.55e-05)|Epithelial(86;8.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.123)		TCTGTGTACGGCCGGTTCTCC	0.592																																					p.P47S		Atlas-SNP	.											.	PITPNM2	105	.	0			c.C139T						.						132	112	119					12																	123498529		2203	4300	6503	SO:0001583	missense	57605	exon3			TGTACGGCCGGTT	AF334585	CCDS9242.1, CCDS73543.1	12q24.31	2008-02-05				ENSG00000090975			21044	protein-coding gene	gene with protein product		608920				10022914	Standard	XM_005253582		Approved	RDGBA2, RDGB2, NIR3	uc001uej.1	Q9BZ72		ENST00000542749.1:c.139C>T	chr12.hg19:g.123498529G>A	ENSP00000437611:p.Pro47Ser	115.0	0.0		141.0	64.0	NM_020845	Q9P271	Missense_Mutation	SNP	ENST00000542749.1	hg19	CCDS9242.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.027800	0.93518	.	.	ENSG00000090975	ENST00000280562;ENST00000320201;ENST00000392428;ENST00000542749	T;T;T;T	0.60171	0.21;0.21;0.21;0.21	4.42	4.42	0.53409	START-like domain (1);	0.000000	0.85682	D	0.000000	T	0.80116	0.4564	M	0.89214	3.015	0.41659	D	0.989173	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.97110	1.0;0.999;0.987	D	0.85306	0.1076	10	0.72032	D	0.01	-23.5877	17.4015	0.87461	0.0:0.0:1.0:0.0	.	47;47;47	A5D8U3;Q9BZ72-2;Q9BZ72	.;.;PITM2_HUMAN	S	47	ENSP00000280562:P47S;ENSP00000322218:P47S;ENSP00000376223:P47S;ENSP00000437611:P47S	ENSP00000280562:P47S	P	-	1	0	PITPNM2	122064482	1.000000	0.71417	0.988000	0.46212	0.944000	0.59088	9.620000	0.98373	2.168000	0.68352	0.655000	0.94253	CCG	.	.		0.592	PITPNM2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401342.1	NM_020845		A	123498529	G	A	123498529	3	1	342	1	0	0	0	0	1	0	0	0	11960	1203	42	3	4002	3	PITPNM2	12	123498529	Missense_Mutation	SNP	G	TCGA-T1-A6J8-01A-11D-A32G-10	2081845	123498529	10353366	53	47256										
AACS	65985	hgsc.bcm.edu	37	chr12	125561142	125561142	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	acaaagagaatgacagagttGccctttacattgcaagtaag	9	7	0	3			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr12:125561142G>T	ENST00000316519.6	+	3	549	c.343G>T	c.(343-345)Gcc>Tcc	p.A115S	AACS_ENST00000261686.6_Missense_Mutation_p.A115S	NM_023928.3	NP_076417.2	Q86V21	AACS_HUMAN	acetoacetyl-CoA synthetase	115					adipose tissue development (GO:0060612)|cellular response to cholesterol (GO:0071397)|cellular response to glucose stimulus (GO:0071333)|cellular response to testosterone stimulus (GO:0071394)|fatty acid metabolic process (GO:0006631)|liver development (GO:0001889)|positive regulation of insulin secretion (GO:0032024)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to nutrient (GO:0007584)|response to oleic acid (GO:0034201)|response to purine-containing compound (GO:0014074)|response to starvation (GO:0042594)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)	acetoacetate-CoA ligase activity (GO:0030729)|ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)			breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(4)|liver(1)|lung(16)|ovary(1)|stomach(1)	26	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;9.82e-05)|Epithelial(86;0.000642)|all cancers(50;0.00843)		TGACAGAGTTGCCCTTTACAT	0.502																																					p.A115S		Atlas-SNP	.											.	AACS	59	.	0			c.G343T						.						123	117	119					12																	125561142		2203	4300	6503	SO:0001583	missense	65985	exon3			AGAGTTGCCCTTT	AK022451	CCDS9263.1	12q24.31	2010-09-29			ENSG00000081760	ENSG00000081760	6.2.1.16	"Acyl-CoA synthetase family"	21298	protein-coding gene	gene with protein product	"acyl-CoA synthetase family member 1"	614364				12623130, 17762044	Standard	NM_023928		Approved	FLJ12389, SUR-5, ACSF1	uc001uhc.3	Q86V21	OTTHUMG00000168550	ENST00000316519.6:c.343G>T	chr12.hg19:g.125561142G>T	ENSP00000324842:p.Ala115Ser	60.0	0.0		78.0	31.0	NM_023928	Q49AB9|Q49AC3|Q658Q8|Q8IWD2|Q8NEW5|Q9BSJ9|Q9H829|Q9HA19	Missense_Mutation	SNP	ENST00000316519.6	hg19	CCDS9263.1	.	.	.	.	.	.	.	.	.	.	G	17.99	3.523561	0.64747	.	.	ENSG00000081760	ENST00000316519;ENST00000536752;ENST00000261686	T;T;T	0.60299	0.2;2.46;0.2	5.28	5.28	0.74379	Acyl-CoA synthase, domain of unknown function DUF3448 (1);	0.000000	0.85682	D	0.000000	D	0.84552	0.5497	H	0.96633	3.855	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	D	0.89555	0.3802	10	0.72032	D	0.01	.	18.0317	0.89286	0.0:0.0:1.0:0.0	.	115;115	Q86V21-2;Q86V21	.;AACS_HUMAN	S	115	ENSP00000324842:A115S;ENSP00000442691:A115S;ENSP00000261686:A115S	ENSP00000261686:A115S	A	+	1	0	AACS	124127095	1.000000	0.71417	0.948000	0.38648	0.079000	0.17450	8.072000	0.89496	2.632000	0.89209	0.591000	0.81541	GCC	.	.		0.502	AACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400202.1	NM_023928		T	125561142	G	T	125561142	3	4	342	1	0	0	0	0	1	0	0	0	9	1319	46	3	353	3	AACS	12	125561142	Missense_Mutation	SNP	G	TCGA-T1-A6J8-01A-11D-A32G-10	2062613	125561142	8290753	54	47257										
C13orf23	80209	hgsc.bcm.edu	37	chr13	39586338	39586338	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	acaaaaggcctggaaaaacaGaactgcctgcagcttgaagt	10	9	0	2			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr13:39586338G>T	ENST00000352251.3	-	12	3427	c.2594C>A	c.(2593-2595)tCt>tAt	p.S865Y	PROSER1_ENST00000350125.3_Missense_Mutation_p.S843Y|PROSER1_ENST00000484434.3_Intron	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	865																	TGGAAAAACAGAACTGCCTGC	0.428																																					p.S865Y		Atlas-SNP	.											.	.	.	.	0			c.C2594A						.						134	152	146					13																	39586338		2203	4300	6503	SO:0001583	missense	80209	exon12			AAAACAGAACTGC	AK022723	CCDS9368.2	13q13.2	2011-08-09	2011-08-09	2011-08-09	ENSG00000120685	ENSG00000120685			20291	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 23"	C13orf23			Standard	NM_025138		Approved	bA50D16.2, FLJ12661	uc001uwy.4	Q86XN7	OTTHUMG00000016764	ENST00000352251.3:c.2594C>A	chr13.hg19:g.39586338G>T	ENSP00000332034:p.Ser865Tyr	144.0	0.0		191.0	74.0	NM_025138	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	Missense_Mutation	SNP	ENST00000352251.3	hg19	CCDS9368.2	.	.	.	.	.	.	.	.	.	.	G	13.95	2.388781	0.42308	.	.	ENSG00000120685	ENST00000352251;ENST00000350125	T;T	0.41400	1.0;1.0	6.06	4.33	0.51752	.	.	.	.	.	T	0.23611	0.0571	N	0.08118	0	0.34830	D	0.73962	B;B	0.33212	0.009;0.402	B;B	0.33521	0.02;0.165	T	0.27020	-1.0086	8	.	.	.	-21.7819	12.5871	0.56424	0.0:0.127:0.7407:0.1323	.	843;865	A6NJ97;Q86XN7	.;PRSR1_HUMAN	Y	865;843	ENSP00000332034:S865Y;ENSP00000339123:S843Y	.	S	-	2	0	PROSER1	38484338	1.000000	0.71417	1.000000	0.80357	0.836000	0.47400	4.674000	0.61612	0.882000	0.36016	-0.156000	0.13503	TCT	.	.		0.428	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5	NM_025138		T	39586338	G	T	39586338	3	4	342	1	0	0	0	0	1	0	0	0	1723	942	33	3	248	3	C13orf23	13	39586338	Missense_Mutation	SNP	G	TCGA-T1-A6J8-01A-11D-A32G-10		39586338	75583540	55	47258										
ABCC4	10257	hgsc.bcm.edu	37	chr13	95858910	95858910	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	cgaacacgcggctggctgtgAtcacactgccgaggagcacg	14	13	1	1			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr13:95858910A>T	ENST00000376887.4	-	8	1151	c.1037T>A	c.(1036-1038)aTc>aAc	p.I346N	ABCC4_ENST00000412704.1_Missense_Mutation_p.I346N|ABCC4_ENST00000536256.1_Missense_Mutation_p.I271N|ABCC4_ENST00000538287.1_3'UTR|ABCC4_ENST00000431522.1_Missense_Mutation_p.I346N	NM_005845.3	NP_005836.2	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	346	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				blood coagulation (GO:0007596)|oxidation-reduction process (GO:0055114)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of smooth muscle cell proliferation (GO:0048661)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)	15-hydroxyprostaglandin dehydrogenase (NAD+) activity (GO:0016404)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(1)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cefazolin(DB01327)|Celecoxib(DB00482)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Flurbiprofen(DB00712)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Lamivudine(DB00709)|Leucovorin(DB00650)|Meloxicam(DB00814)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Probenecid(DB01032)|Rosuvastatin(DB01098)|Sildenafil(DB00203)|Sorafenib(DB00398)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tenofovir(DB00300)|Tioguanine(DB00352)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Zidovudine(DB00495)	GCTGGCTGTGATCACACTGCC	0.547																																					p.I346N		Atlas-SNP	.											.	ABCC4	248	.	0			c.T1037A						.						126	108	114					13																	95858910		2203	4300	6503	SO:0001583	missense	10257	exon8			GCTGTGATCACAC	U66682	CCDS9474.1	13q31	2012-03-14			ENSG00000125257	ENSG00000125257		"ATP binding cassette transporters / subfamily C"	55	protein-coding gene	gene with protein product	"canalicular multispecific organic anion transporter (ABC superfamily)", "bA464I2.1 (ATP-binding cassette, sub-family C (CFTR/MRP), member 4)", "multidrug resistance-associated protein 4", "multispecific organic anion transporter B"	605250				8894702, 9661885	Standard	NM_005845		Approved	MRP4, EST170205, MOAT-B, MOATB	uc001vmd.4	O15439	OTTHUMG00000017216	ENST00000376887.4:c.1037T>A	chr13.hg19:g.95858910A>T	ENSP00000366084:p.Ile346Asn	57.0	0.0		72.0	28.0	NM_005845	A9Z1Z7|Q8IVZ4|Q8IZN6|Q8NEW8|Q9Y6J2	Missense_Mutation	SNP	ENST00000376887.4	hg19	CCDS9474.1	.	.	.	.	.	.	.	.	.	.	A	16.98	3.270550	0.59540	.	.	ENSG00000125257	ENST00000412704;ENST00000376887;ENST00000536256;ENST00000431522	D;D;D;D	0.95447	-3.14;-3.14;-3.71;-3.14	5.34	5.34	0.76211	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.288637	0.39834	N	0.001256	D	0.98105	0.9375	M	0.92219	3.285	0.58432	D	0.999999	D;D;P;D;D	0.71674	0.967;0.997;0.942;0.998;0.977	D;D;P;D;D	0.70935	0.934;0.964;0.873;0.971;0.964	D	0.99250	1.0887	10	0.87932	D	0	.	14.9671	0.71201	1.0:0.0:0.0:0.0	.	271;346;346;346;346	B7Z3Q7;A8K2Q2;O15439-2;Q8IVZ4;O15439	.;.;.;.;MRP4_HUMAN	N	346;346;271;346	ENSP00000388657:I346N;ENSP00000366084:I346N;ENSP00000442024:I271N;ENSP00000398562:I346N	ENSP00000366084:I346N	I	-	2	0	ABCC4	94656911	1.000000	0.71417	0.995000	0.50966	0.051000	0.14879	8.579000	0.90781	1.999000	0.58509	0.533000	0.62120	ATC	.	.		0.547	ABCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045478.2	NM_005845		T	95858910	A	T	95858910	3	4	342	1	0	0	0	0	1	0	0	0	55	333	12	4	3085	4	ABCC4	13	95858910	Missense_Mutation	SNP	A	TCGA-T1-A6J8-01A-11D-A32G-10	56272572	95858910	19310968	56	47259										
CRIP2	1397	hgsc.bcm.edu	37	chr14	105945934	105945934	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	cctccacaggagtgaacaccGgtgcggtgggcagctacatc	13	13	0	1			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr14:105945934G>T	ENST00000329146.4	+	8	1284	c.571G>T	c.(571-573)Ggt>Tgt	p.G191C	CRIP2_ENST00000483017.3_Missense_Mutation_p.G265C|CRIP2_ENST00000548989.1_3'UTR	NM_001312.3	NP_001303.1	P52943	CRIP2_HUMAN	cysteine-rich protein 2	191	Gly-rich.				hemopoiesis (GO:0030097)|positive regulation of cell proliferation (GO:0008284)	cell cortex (GO:0005938)	zinc ion binding (GO:0008270)			lung(2)	2		Melanoma(154;0.226)	OV - Ovarian serous cystadenocarcinoma(23;0.00897)|Epithelial(46;0.026)	Epithelial(152;0.235)		AGTGAACACCGGTGCGGTGGG	0.657																																					p.G265C		Atlas-SNP	.											.	CRIP2	7	.	0			c.G793T						.						76	70	72					14																	105945934		2195	4292	6487	SO:0001583	missense	1397	exon8			AACACCGGTGCGG		CCDS10003.1, CCDS59246.1	14q32.3	2008-08-11			ENSG00000182809	ENSG00000182809			2361	protein-coding gene	gene with protein product		601183				8843343, 10681529	Standard	NM_001312		Approved	CRP2, ESP1	uc031qqr.1	P52943	OTTHUMG00000029906	ENST00000329146.4:c.571G>T	chr14.hg19:g.105945934G>T	ENSP00000328521:p.Gly191Cys	60.0	0.0		79.0	34.0	NM_001270837	A1A4U1|B7Z6C0|E9PD13	Missense_Mutation	SNP	ENST00000329146.4	hg19	CCDS10003.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.79|15.79	2.935998|2.935998	0.52972|0.52972	.|.	.|.	ENSG00000182809|ENSG00000182809	ENST00000483017;ENST00000329146|ENST00000550577;ENST00000538259	D;D|.	0.94931|.	-3.56;-3.56|.	4.06|4.06	4.06|4.06	0.47325|0.47325	.|.	0.000000|.	0.42682|.	U|.	0.000676|.	D|D	0.85353|0.85353	0.5677|0.5677	M|M	0.94021|0.94021	3.485|3.485	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.77557|.	0.99;0.99;0.97|.	D|D	0.89694|0.89694	0.3900|0.3900	10|5	0.87932|.	D|.	0|.	-28.7221|-28.7221	14.9374|14.9374	0.70967|0.70967	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	265;191;191|.	B7Z6C0;Q53FN1;P52943|.	.;.;CRIP2_HUMAN|.	C|L	265;191|86;174	ENSP00000426119:G265C;ENSP00000328521:G191C|.	ENSP00000328521:G191C|.	G|R	+|+	1|2	0|0	CRIP2|CRIP2	105016979|105016979	1.000000|1.000000	0.71417|0.71417	0.286000|0.286000	0.24833|0.24833	0.072000|0.072000	0.16883|0.16883	8.351000|8.351000	0.90072|0.90072	2.082000|2.082000	0.62665|0.62665	0.313000|0.313000	0.20887|0.20887	GGT|CGG	.	.		0.657	CRIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074597.3	NM_001312		T	105945934	G	T	105945934	3	4	342	1	0	0	0	0	1	0	0	0	3877	1116	39	1	601	1	CRIP2	14	105945934	Missense_Mutation	SNP	G	TCGA-T1-A6J8-01A-11D-A32G-10		105945934	1403606	57	47260										
TJP1	7082	hgsc.bcm.edu	37	chr15	30000996	30000997	+	Frame_Shift_Del	DEL	AA	AA	-													0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	ggactttcaaacttgcgttcAaatggtcgggcagaacttgt							TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr15:30000996_30000997delAA	ENST00000346128.6	-	25	5090_5091	c.4616_4617delTT	c.(4615-4617)tttfs	p.F1539fs	TJP1_ENST00000356107.6_Frame_Shift_Del_p.F1539fs|TJP1_ENST00000400011.2_Frame_Shift_Del_p.F1463fs|TJP1_ENST00000545208.2_Frame_Shift_Del_p.F1459fs	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	1539					apoptotic process (GO:0006915)|blastocyst formation (GO:0001825)|cell-cell junction assembly (GO:0007043)|cell-cell signaling involved in cell-cell junction organization (GO:1901350)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to glucose stimulus (GO:0071333)|hippo signaling (GO:0035329)|membrane organization (GO:0061024)|negative regulation of vascular permeability (GO:0043116)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to magnetism (GO:0071000)|sensory perception of sound (GO:0007605)	apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gap junction (GO:0005921)|intercalated disc (GO:0014704)|intercellular canaliculus (GO:0046581)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(4)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(1)	68		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)		ACTTGCGTTCAAATGGTCGGGC	0.401																																					p.1539_1540del	Melanoma(77;681 1843 6309 6570)	Atlas-Indel,Pindel	.											.	TJP1	140	.	0			c.4617_4618del						.																																			SO:0001589	frameshift_variant	7082	exon25			.		CCDS42007.1, CCDS45199.1, CCDS73702.1	15q13	2012-07-12	2012-07-12		ENSG00000104067	ENSG00000104067			11827	protein-coding gene	gene with protein product	"zona occludens 1", "tight junction protein ZO-1"	601009				8825647	Standard	XM_005254616		Approved	ZO-1, MGC133289, DKFZp686M05161	uc001zcr.3	Q07157	OTTHUMG00000137397	ENST00000346128.6:c.4616_4617delTT	chr15.hg19:g.30000996_30000997delAA	ENSP00000281537:p.Phe1539fs	187.0	0.0		288.0	107.0	NM_003257	B4E3K1|Q2NKP3|Q4ZGJ6	Frame_Shift_Del	DEL	ENST00000346128.6	hg19	CCDS42007.1																																																																																			.	.		0.401	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257		-	30000997	AA	-	30000996	7	5	342	1	0	1	0	1	0	0	0	0	15944	127	5	0	645	0	TJP1	15	30000996	Frame_Shift_Del	DEL	AA	TCGA-T1-A6J8-01A-11D-A32G-10		30000996	72530396	58	47261										
GABPB1	2553	hgsc.bcm.edu	37	chr15	50596296	50596296	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	ctgtggtggaataatgaccaTactgtgctgctagatgaagt	12	6	0	3			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr15:50596296T>C	ENST00000220429.8	-	3	311	c.143A>G	c.(142-144)tAt>tGt	p.Y48C	GABPB1_ENST00000396464.3_Missense_Mutation_p.Y48C|GABPB1_ENST00000380877.3_Missense_Mutation_p.Y48C|GABPB1_ENST00000359031.4_Missense_Mutation_p.Y48C|GABPB1_ENST00000429662.2_Missense_Mutation_p.Y48C|GABPB1_ENST00000543881.1_5'UTR|GABPB1_ENST00000560825.1_Missense_Mutation_p.Y48C			Q06547	GABP1_HUMAN	GA binding protein transcription factor, beta subunit 1	48					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			cervix(1)|endometrium(1)|large_intestine(7)|lung(5)	14						ATAATGACCATACTGTGCTGC	0.423																																					p.Y48C		Atlas-SNP	.											.	GABPB1	33	.	0			c.A143G						.						156	127	137					15																	50596296		2196	4295	6491	SO:0001583	missense	2553	exon3			TGACCATACTGTG	D13316	CCDS10135.1, CCDS10136.1, CCDS32239.1, CCDS45258.1	15q21.2	2013-01-10	2008-02-25	2008-02-25	ENSG00000104064	ENSG00000104064		"Ankyrin repeat domain containing"	4074	protein-coding gene	gene with protein product		600610	"GA binding protein transcription factor, beta subunit 2"	GABPB2		7958862	Standard	NM_016655		Approved	E4TF1-47, GABPB	uc001zyb.3	Q06547	OTTHUMG00000131642	ENST00000220429.8:c.143A>G	chr15.hg19:g.50596296T>C	ENSP00000220429:p.Tyr48Cys	87.0	0.0		121.0	44.0	NM_016654	A8IE52|Q06545|Q12940|Q12941|Q12942|Q8IYD0	Missense_Mutation	SNP	ENST00000220429.8	hg19	CCDS32239.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.052124	0.75960	.	.	ENSG00000104064	ENST00000220429;ENST00000380877;ENST00000396464;ENST00000429662;ENST00000359031	T;T;T;T;T	0.43688	0.94;0.94;0.94;0.94;0.94	5.45	5.45	0.79879	Ankyrin repeat-containing domain (3);	0.068964	0.64402	D	0.000011	T	0.50837	0.1639	N	0.21194	0.64	0.49798	D	0.999825	D;D;D;D;D	0.71674	0.993;0.995;0.991;0.998;0.991	D;D;P;D;P	0.87578	0.934;0.937;0.781;0.998;0.781	T	0.50857	-0.8778	10	0.40728	T	0.16	-2.9296	15.7997	0.78443	0.0:0.0:0.0:1.0	.	48;48;48;48;48	B7Z726;Q06547-3;Q06547-4;Q06547;Q06547-2	.;.;.;GABP1_HUMAN;.	C	48	ENSP00000220429:Y48C;ENSP00000370259:Y48C;ENSP00000379728:Y48C;ENSP00000395771:Y48C;ENSP00000351923:Y48C	ENSP00000220429:Y48C	Y	-	2	0	GABPB1	48383588	1.000000	0.71417	0.993000	0.49108	0.972000	0.66771	8.040000	0.89188	2.189000	0.69895	0.460000	0.39030	TAT	.	.		0.423	GABPB1-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000418294.1			C	50596296	T	C	50596296	3	2	342	1	0	0	0	0	1	0	0	0	6166	1406	49	2	1120	2	GABPB1	15	50596296	Missense_Mutation	SNP	T	TCGA-T1-A6J8-01A-11D-A32G-10	20595300	50596296	51935096	59	47262										
CGNL1	84952	hgsc.bcm.edu	37	chr15	57730244	57730244	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	acatgtgcagcaggaatatgGggtccatctgagactcgcaa	12	9	1	1			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr15:57730244G>T	ENST00000281282.5	+	2	125	c.47G>T	c.(46-48)gGg>gTg	p.G16V		NM_001252335.1|NM_032866.4	NP_001239264.1|NP_116255.2	Q0VF96	CGNL1_HUMAN	cingulin-like 1	16	Head.					myosin complex (GO:0016459)|tight junction (GO:0005923)	motor activity (GO:0003774)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(14)|ovary(4)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)	60				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)		CAGGAATATGGGGTCCATCTG	0.483																																					p.G16V		Atlas-SNP	.											.	CGNL1	125	.	0			c.G47T						.						201	210	206					15																	57730244		2192	4292	6484	SO:0001583	missense	84952	exon2			AATATGGGGTCCA	AY274808	CCDS10161.1	15q21.3	2011-06-10			ENSG00000128849	ENSG00000128849			25931	protein-coding gene	gene with protein product		607856				11214970	Standard	NM_001252335		Approved	FLJ14957, JACOP, KIAA1749, paracingulin	uc002aeg.3	Q0VF96	OTTHUMG00000166485	ENST00000281282.5:c.47G>T	chr15.hg19:g.57730244G>T	ENSP00000281282:p.Gly16Val	23.0	0.0		47.0	20.0	NM_032866	Q05BZ4|Q52LR0|Q695C7|Q7Z2L3|Q96JV2|Q96MN6|Q9C0B4	Missense_Mutation	SNP	ENST00000281282.5	hg19	CCDS10161.1	.	.	.	.	.	.	.	.	.	.	G	16.75	3.208272	0.58343	.	.	ENSG00000128849	ENST00000281282	T	0.06933	3.24	4.71	4.71	0.59529	.	0.000000	0.44285	D	0.000468	T	0.25121	0.0610	M	0.71581	2.175	0.53688	D	0.999974	D	0.76494	0.999	D	0.68353	0.957	T	0.00350	-1.1797	10	0.72032	D	0.01	-14.7537	11.7728	0.51968	0.092:0.0:0.908:0.0	.	16	Q0VF96	CGNL1_HUMAN	V	16	ENSP00000281282:G16V	ENSP00000281282:G16V	G	+	2	0	CGNL1	55517536	1.000000	0.71417	0.448000	0.26945	0.958000	0.62258	4.120000	0.57897	2.443000	0.82685	0.561000	0.74099	GGG	.	.		0.483	CGNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255482.2	NM_032866		T	57730244	G	T	57730244	3	4	342	1	0	0	0	0	1	0	0	0	3306	1232	43	3	49	3	CGNL1	15	57730244	Missense_Mutation	SNP	G	TCGA-T1-A6J8-01A-11D-A32G-10	7133948	57730244	44801148	60	47263										
HERC1	8925	hgsc.bcm.edu	37	chr15	63988457	63988457	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	ctggaagcctgaactcaatcTgcttcctgccagtgagatgc	10	12	2	2			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr15:63988457T>A	ENST00000443617.2	-	27	5074	c.4987A>T	c.(4987-4989)Aga>Tga	p.R1663*	RP11-317G6.1_ENST00000559303.2_RNA	NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	1663					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						GAACTCAATCTGCTTCCTGCC	0.478																																					p.R1663X		Atlas-SNP	.											.	HERC1	624	.	0			c.A4987T						.						88	85	86					15																	63988457		1965	4158	6123	SO:0001587	stop_gained	8925	exon27			TCAATCTGCTTCC	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.4987A>T	chr15.hg19:g.63988457T>A	ENSP00000390158:p.Arg1663*	112.0	0.0		147.0	58.0	NM_003922	Q8IW65	Nonsense_Mutation	SNP	ENST00000443617.2	hg19	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	T	44	11.006778	0.99502	.	.	ENSG00000103657	ENST00000443617;ENST00000425434	.	.	.	5.54	4.4	0.53042	.	0.065589	0.56097	D	0.000028	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.1874	0.54247	0.0:0.0:0.4533:0.5466	.	.	.	.	X	1663;647	.	ENSP00000389613:R647X	R	-	1	2	HERC1	61775510	0.773000	0.28580	0.987000	0.45799	0.917000	0.54804	0.759000	0.26461	0.900000	0.36469	0.528000	0.53228	AGA	.	.		0.478	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		A	63988457	T	A	63988457	4	1	342	1	0	0	0	0	0	1	0	0	7066	1588	55	4	9806	4	HERC1	15	63988457	Nonsense_Mutation	SNP	T	TCGA-T1-A6J8-01A-11D-A32G-10	6258213	63988457	38542935	61	47264										
CLK3	1198	hgsc.bcm.edu	37	chr15	74919878	74919878	+	Splice_Site	SNP	A	A	G													0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	gcaggcctgccttgcctttcAgagctgtgaggagaagtcag							TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr15:74919878A>G	ENST00000395066.3	+	9	1817		c.e9-1		CLK3_ENST00000348245.3_Splice_Site|CLK3_ENST00000345005.4_Splice_Site|CLK3_ENST00000352989.5_Splice_Site	NM_001130028.1	NP_001123500.1	P49761	CLK3_HUMAN	CDC-like kinase 3						protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of RNA splicing (GO:0043484)	cytoplasmic vesicle (GO:0031410)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(2)|stomach(2)|urinary_tract(1)	15						CTTGCCTTTCAGAGCTGTGAG	0.577																																					.	Ovarian(133;694 1754 28950 29027 31859)	Atlas-SNP	.											.	CLK3	78	.	0			c.913-2A>G						.						105	97	99					15																	74919878		2197	4296	6493	SO:0001630	splice_region_variant	1198	exon9			CCTTTCAGAGCTG	L29220	CCDS10265.1, CCDS45304.1	15q24	2008-05-02			ENSG00000179335	ENSG00000179335		"CDC-like kinases"	2071	protein-coding gene	gene with protein product		602990				7990150, 9856501	Standard	NM_003992		Approved	clk3	uc010uln.2	P49761	OTTHUMG00000141320	ENST00000395066.3:c.1357-1A>G	chr15.hg19:g.74919878A>G		83.0	0.0		105.0	37.0	NM_003992	D3DW59|Q53Y48|Q9BRS3|Q9BUJ7	Splice_Site	SNP	ENST00000395066.3	hg19	CCDS45304.1	.	.	.	.	.	.	.	.	.	.	A	17.63	3.438315	0.62955	.	.	ENSG00000179335	ENST00000345005;ENST00000395066;ENST00000454830;ENST00000352989	.	.	.	5.62	5.62	0.85841	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4674	0.75412	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CLK3	72706931	1.000000	0.71417	0.997000	0.53966	0.649000	0.38597	9.228000	0.95250	2.142000	0.66516	0.459000	0.35465	.	.	.		0.577	CLK3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390442.3		Intron	G	74919878	A	G	74919878	5	3	342	1	0	0	0	0	0	0	1	0	3540	202	7	2	1389	2	CLK3	15	74919878	Splice_Site	SNP	A	TCGA-T1-A6J8-01A-11D-A32G-10	10931421	74919878	27611514	62	47265	256	2								
CLK3	1198	hgsc.bcm.edu	37	chr15	74919883	74919895	+	Frame_Shift_Del	DEL	TGTGAGGAGAAGT	TGTGAGGAGAAGT	-													0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	cctgccttgcctttcagagcTgtgaggagaagtcagtgaag					rs149199059		TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	TGTGAGGAGAAGT	TGTGAGGAGAAGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr15:74919883_74919895delTGTGAGGAGAAGT	ENST00000395066.3	+	9	1821_1833	c.1360_1372delTGTGAGGAGAAGT	c.(1360-1374)tgtgaggagaagtcafs	p.CEEKS454fs	CLK3_ENST00000348245.3_3'UTR|CLK3_ENST00000345005.4_Frame_Shift_Del_p.CEEKS306fs|CLK3_ENST00000352989.5_Frame_Shift_Del_p.CEEKS283fs	NM_001130028.1	NP_001123500.1	P49761	CLK3_HUMAN	CDC-like kinase 3	454	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of RNA splicing (GO:0043484)	cytoplasmic vesicle (GO:0031410)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)	p.E308E(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(2)|stomach(2)|urinary_tract(1)	15						CTTTCAGAGCTGTGAGGAGAAGTCAGTGAAGAA	0.587																																					p.453_457del	Ovarian(133;694 1754 28950 29027 31859)	Atlas-Indel,Pindel	.											.	CLK3	78	.	1	Substitution - coding silent(1)	breast(1)	c.1359_1371del						.																																			SO:0001589	frameshift_variant	1198	exon9			.	L29220	CCDS10265.1, CCDS45304.1	15q24	2008-05-02			ENSG00000179335	ENSG00000179335		"CDC-like kinases"	2071	protein-coding gene	gene with protein product		602990				7990150, 9856501	Standard	NM_003992		Approved	clk3	uc010uln.2	P49761	OTTHUMG00000141320	ENST00000395066.3:c.1360_1372delTGTGAGGAGAAGT	chr15.hg19:g.74919883_74919895delTGTGAGGAGAAGT	ENSP00000378505:p.Cys454fs	83.0	0.0		105.0	38.0	NM_001130028	D3DW59|Q53Y48|Q9BRS3|Q9BUJ7	Frame_Shift_Del	DEL	ENST00000395066.3	hg19	CCDS45304.1																																																																																			.	.		0.587	CLK3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390442.3			-	74919895	TGTGAGGAGAAGT	-	74919883	7	5	342	1	0	1	0	1	0	0	0	0	3540	1580	55	0	1394	0	CLK3	15	74919883	Frame_Shift_Del	DEL	TGTGAGGAGAAGT	TCGA-T1-A6J8-01A-11D-A32G-10	5	74919883	27611509	63	47266	256	2								
PSTPIP1	9051	hgsc.bcm.edu	37	chr15	77310567	77310567	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	gcaggaagatgtgcaaagacAtggaggagctactgaggcag	16	6	0	3			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr15:77310567A>T	ENST00000558012.1	+	2	604	c.115A>T	c.(115-117)Atg>Ttg	p.M39L	PSTPIP1_ENST00000267939.5_Missense_Mutation_p.M38L|PSTPIP1_ENST00000379595.3_Missense_Mutation_p.M39L|PSTPIP1_ENST00000559295.1_Missense_Mutation_p.M39L	NM_003978.3	NP_003969.2	O43586	PPIP1_HUMAN	proline-serine-threonine phosphatase interacting protein 1	39	FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.				cell adhesion (GO:0007155)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|signal transduction (GO:0007165)	actomyosin contractile ring (GO:0005826)|cell projection (GO:0042995)|cleavage furrow (GO:0032154)|cytosol (GO:0005829)|membrane (GO:0016020)|stress fiber (GO:0001725)				breast(1)|endometrium(3)|lung(2)|ovary(2)|upper_aerodigestive_tract(1)	9						GTGCAAAGACATGGAGGAGCT	0.627																																					p.M39L		Atlas-SNP	.											.	PSTPIP1	50	.	0			c.A115T						.						32	38	36					15																	77310567		2158	4239	6397	SO:0001583	missense	9051	exon2			AAAGACATGGAGG	U94778	CCDS45312.1	15q24.3	2014-09-17			ENSG00000140368	ENSG00000140368			9580	protein-coding gene	gene with protein product	"CD2 cytoplasmic tail-binding protein", "CD2 antigen-binding protein 1", "PEST phosphatase-interacting protein 1"	606347				9857189	Standard	NM_003978		Approved	PSTPIP, CD2BP1L, CD2BP1, CD2BP1S, H-PIP, PAPAS	uc002bcf.2	O43586	OTTHUMG00000172594	ENST00000558012.1:c.115A>T	chr15.hg19:g.77310567A>T	ENSP00000452746:p.Met39Leu	53.0	0.0		77.0	31.0	NM_003978	B5BU74|B5BUK4|O43585|O95657	Missense_Mutation	SNP	ENST00000558012.1	hg19	CCDS45312.1	.	.	.	.	.	.	.	.	.	.	A	7.267	0.606391	0.14002	.	.	ENSG00000140368	ENST00000379595;ENST00000267939	T;T	0.32988	1.43;2.55	4.35	2.24	0.28232	Fps/Fes/Fer/CIP4 homology (3);Prismane-like (1);	0.324058	0.30020	N	0.010620	T	0.11281	0.0275	N	0.04880	-0.145	0.29385	N	0.863015	B;B;B;B	0.22909	0.0;0.023;0.077;0.001	B;B;B;B	0.22601	0.002;0.02;0.04;0.007	T	0.36601	-0.9741	10	0.02654	T	1	-12.4902	8.3338	0.32202	0.2252:0.0:0.7748:0.0	.	39;38;39;39	O43586-2;C9K004;B4E1Z9;O43586	.;.;.;PPIP1_HUMAN	L	39;38	ENSP00000368914:M39L;ENSP00000267939:M38L	ENSP00000267939:M38L	M	+	1	0	PSTPIP1	75097622	0.998000	0.40836	0.989000	0.46669	0.993000	0.82548	1.843000	0.39259	0.276000	0.22118	0.402000	0.26972	ATG	.	.		0.627	PSTPIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000419373.2	NM_003978		T	77310567	A	T	77310567	3	4	342	1	0	0	0	0	1	0	0	0	12733	217	8	4	121	4	PSTPIP1	15	77310567	Missense_Mutation	SNP	A	TCGA-T1-A6J8-01A-11D-A32G-10	2390684	77310567	25220825	64	47267										
ARNT2	9915	hgsc.bcm.edu	37	chr15	80873588	80873588	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	tcctgattgtagcaaatcccAtctcagtccagcaagactca	6	13	2	2			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr15:80873588A>T	ENST00000303329.4	+	17	1926	c.1761A>T	c.(1759-1761)ccA>ccT	p.P587P	ARNT2_ENST00000533983.1_Silent_p.P576P|ARNT2_ENST00000527771.1_Silent_p.P576P|RP11-379K22.3_ENST00000603875.1_RNA|hsa-mir-5572_ENST00000583188.1_RNA	NM_014862.3	NP_055677.3	Q9HBZ2	ARNT2_HUMAN	aryl-hydrocarbon receptor nuclear translocator 2	587					central nervous system development (GO:0007417)|in utero embryonic development (GO:0001701)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor binding (GO:0017162)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|pancreas(2)|prostate(2)|skin(1)	35			BRCA - Breast invasive adenocarcinoma(143;0.134)			AGCAAATCCCATCTCAGTCCA	0.587																																					p.P587P		Atlas-SNP	.											.	ARNT2	88	.	0			c.A1761T						.						120	94	102					15																	80873588		2203	4300	6503	SO:0001819	synonymous_variant	9915	exon17			AATCCCATCTCAG	AB002305	CCDS32307.1	15q25.1	2013-05-21			ENSG00000172379	ENSG00000172379		"Basic helix-loop-helix proteins"	16876	protein-coding gene	gene with protein product		606036				11247670	Standard	NM_014862		Approved	KIAA0307, bHLHe1	uc002bfr.3	Q9HBZ2	OTTHUMG00000165478	ENST00000303329.4:c.1761A>T	chr15.hg19:g.80873588A>T		161.0	0.0		193.0	83.0	NM_014862	B4DIS7|O15024|Q8IYC2	Silent	SNP	ENST00000303329.4	hg19	CCDS32307.1																																																																																			.	.		0.587	ARNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384389.2			T	80873588	A	T	80873588	2	4	342	1	0	0	0	0	0	0	0	1	966	204	8	4		4	ARNT2	15	80873588	Silent	SNP	A	TCGA-T1-A6J8-01A-11D-A32G-10	3563021	80873588	21657804	65	47268										
AP3B2	8120	hgsc.bcm.edu	37	chr15	83330629	83330629	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	aacacaggggccatcagctcCccaacaggtggctgaatgga	12	12	1	1			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr15:83330629C>T	ENST00000261722.3	-	24	3114	c.2907G>A	c.(2905-2907)ggG>ggA	p.G969G	RP11-752G15.3_ENST00000560650.1_RNA|AP3B2_ENST00000535359.1_Silent_p.G988G|AP3B2_ENST00000535348.1_Silent_p.G937G	NM_004644.3	NP_004635.2	Q13367	AP3B2_HUMAN	adaptor-related protein complex 3, beta 2 subunit	969					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|intracellular protein transport (GO:0006886)|post-Golgi vesicle-mediated transport (GO:0006892)	AP-3 adaptor complex (GO:0030123)|COPI-coated vesicle (GO:0030137)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(4)|endometrium(1)|kidney(1)|large_intestine(4)|lung(21)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(2)	41			BRCA - Breast invasive adenocarcinoma(143;0.229)			CCATCAGCTCCCCAACAGGTG	0.542																																					p.G969G		Atlas-SNP	.											.	AP3B2	103	.	0			c.G2907A						.						58	60	59					15																	83330629		1962	4150	6112	SO:0001819	synonymous_variant	8120	exon24			CAGCTCCCCAACA	U37673	CCDS45331.1, CCDS61736.1, CCDS61737.1	15q	2008-07-07			ENSG00000103723	ENSG00000103723			567	protein-coding gene	gene with protein product		602166				7671305, 1851215	Standard	NM_004644		Approved	NAPTB	uc010uoh.2	Q13367	OTTHUMG00000168009	ENST00000261722.3:c.2907G>A	chr15.hg19:g.83330629C>T		87.0	0.0		108.0	50.0	NM_004644	A4Z4T7|B7ZKR7|B7ZKS0|O14808|Q52LY8	Silent	SNP	ENST00000261722.3	hg19	CCDS45331.1																																																																																			.	.		0.542	AP3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397463.1			T	83330629	C	T	83330629	2	4	342	1	0	0	0	0	0	0	0	1	745	610	22	3		3	AP3B2	15	83330629	Silent	SNP	C	TCGA-T1-A6J8-01A-11D-A32G-10	2457041	83330629	19200763	66	47269										
PDZD9	255762	hgsc.bcm.edu	37	chr16	21995863	21995863	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	tattggtctccttgcagggtGatgcacagttgaccacggat	12	9	1	2			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr16:21995863G>A	ENST00000424898.2	-	4	582	c.520C>T	c.(520-522)Cac>Tac	p.H174Y	PDZD9_ENST00000537222.2_Missense_Mutation_p.H114Y|PDZD9_ENST00000286143.6_Missense_Mutation_p.H112Y			Q8IXQ8	PDZD9_HUMAN	PDZ domain containing 9	174										breast(3)|endometrium(2)|lung(3)|pancreas(1)	9						CTTGCAGGGTGATGCACAGTT	0.368																																					p.H114Y		Atlas-SNP	.											.	PDZD9	18	.	0			c.C340T						.						134	131	132					16																	21995863		2198	4300	6498	SO:0001583	missense	255762	exon3			CAGGGTGATGCAC	BC039562	CCDS10602.1, CCDS10602.2	16p12.1	2010-04-14	2010-04-14	2010-04-14	ENSG00000155714	ENSG00000155714			28740	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 65"	C16orf65		12477932	Standard	NM_173806		Approved	MGC50721	uc021ter.1	Q8IXQ8	OTTHUMG00000131586	ENST00000424898.2:c.520C>T	chr16.hg19:g.21995863G>A	ENSP00000400514:p.His174Tyr	261.0	0.0		247.0	56.0	NM_173806	F5GWW8	Missense_Mutation	SNP	ENST00000424898.2	hg19		.	.	.	.	.	.	.	.	.	.	G	2.979	-0.210741	0.06140	.	.	ENSG00000155714	ENST00000424898;ENST00000537222;ENST00000286143;ENST00000521513	T	0.44482	0.92	4.96	-4.5	0.03493	.	1.035960	0.07611	N	0.925322	T	0.17534	0.0421	N	0.10809	0.05	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.14924	-1.0455	10	0.32370	T	0.25	0.0719	1.8611	0.03189	0.435:0.1303:0.3019:0.1328	.	112	Q8IXQ8-2	.	Y	174;114;112;114	ENSP00000400514:H174Y	ENSP00000286143:H112Y	H	-	1	0	PDZD9	21903364	0.000000	0.05858	0.000000	0.03702	0.196000	0.23810	-0.147000	0.10234	-0.779000	0.04560	-0.244000	0.11960	CAC	.	.		0.368	PDZD9-003	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000381652.1	NM_173806		A	21995863	G	A	21995863	3	1	342	1	0	0	0	0	1	0	0	0	11715	1290	45	3	278	3	PDZD9	16	21995863	Missense_Mutation	SNP	G	TCGA-T1-A6J8-01A-11D-A32G-10		21995863	68358890	67	47270										
MVP	9961	hgsc.bcm.edu	37	chr16	29848051	29848051	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	gttgctctgcagacagccctGcacctccgggctcggcggaa	13	15	1	1			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr16:29848051G>C	ENST00000357402.5	+	7	819	c.681G>C	c.(679-681)ctG>ctC	p.L227L	MVP_ENST00000395353.1_Silent_p.L227L|MVP_ENST00000452209.2_Missense_Mutation_p.A42P	NM_005115.4|NM_017458.3	NP_005106.2|NP_059447.2	Q14764	MVP_HUMAN	major vault protein	227					cell proliferation (GO:0008283)|ERBB signaling pathway (GO:0038127)|mRNA transport (GO:0051028)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of protein tyrosine kinase activity (GO:0061099)|negative regulation of signaling (GO:0023057)|protein activation cascade (GO:0072376)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(7)|ovary(2)|skin(3)|soft_tissue(1)|stomach(1)	27						AGACAGCCCTGCACCTCCGGG	0.622																																					p.L227L		Atlas-SNP	.											.	MVP	80	.	0			c.G681C						.						36	41	39					16																	29848051		2197	4300	6497	SO:0001819	synonymous_variant	9961	exon7			AGCCCTGCACCTC	X79882	CCDS10656.1	16p11.2	2012-04-25			ENSG00000013364	ENSG00000013364			7531	protein-coding gene	gene with protein product	"lung resistance-related protein"	605088				7585126	Standard	NM_005115		Approved	LRP, VAULT1	uc002dui.3	Q14764	OTTHUMG00000048227	ENST00000357402.5:c.681G>C	chr16.hg19:g.29848051G>C		27.0	0.0		43.0	10.0	NM_017458	Q96BG4|Q9BPW6|Q9BQT1|Q9UBD1	Silent	SNP	ENST00000357402.5	hg19	CCDS10656.1	.	.	.	.	.	.	.	.	.	.	G	16.57	3.159666	0.57368	.	.	ENSG00000013364	ENST00000452209	.	.	.	5.47	4.51	0.55191	.	.	.	.	.	T	0.53594	0.1806	.	.	.	0.22639	N	0.998904	.	.	.	.	.	.	T	0.50268	-0.8848	5	0.87932	D	0	-9.4381	12.2321	0.54495	0.0834:0.0:0.9166:0.0	.	.	.	.	P	42	.	ENSP00000387916:A42P	A	+	1	0	MVP	29755552	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	1.125000	0.31332	1.424000	0.47217	0.462000	0.41574	GCA	.	.		0.622	MVP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109711.3	NM_005115		C	29848051	G	C	29848051	2	2	342	1	0	0	0	0	0	0	0	1	10005	1306	46	4		4	MVP	16	29848051	Silent	SNP	G	TCGA-T1-A6J8-01A-11D-A32G-10	7852188	29848051	60506702	68	47271										
ASPHD1	253982	hgsc.bcm.edu	37	chr16	29912699	29912699	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	cccagggggtcctggggatcCcggggaaggacctaggacgg	19	11	0	0			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr16:29912699C>A	ENST00000308748.5	+	1	659	c.407C>A	c.(406-408)cCc>cAc	p.P136H	ASPHD1_ENST00000483405.1_Intron|SEZ6L2_ENST00000308713.5_5'Flank|SEZ6L2_ENST00000537485.1_5'Flank|SEZ6L2_ENST00000350527.3_5'Flank|SEZ6L2_ENST00000346932.5_5'Flank	NM_181718.3	NP_859069.2	Q5U4P2	ASPH1_HUMAN	aspartate beta-hydroxylase domain containing 1	136	Gly-rich.				peptidyl-amino acid modification (GO:0018193)	integral component of membrane (GO:0016021)	dioxygenase activity (GO:0051213)			endometrium(4)|large_intestine(2)|lung(1)|prostate(1)	8						CCTGGGGATCCCGGGGAAGGA	0.706																																					p.P136H		Atlas-SNP	.											.	ASPHD1	28	.	0			c.C407A						.						19	24	22					16																	29912699		2179	4283	6462	SO:0001583	missense	253982	exon1			GGGATCCCGGGGA	AF070642	CCDS10660.1	16p11.2	2008-02-05			ENSG00000174939	ENSG00000174939			27380	protein-coding gene	gene with protein product							Standard	NM_181718		Approved		uc002dut.3	Q5U4P2	OTTHUMG00000132121	ENST00000308748.5:c.407C>A	chr16.hg19:g.29912699C>A	ENSP00000311447:p.Pro136His	31.0	0.0		35.0	16.0	NM_181718	A0AVE3|B7ZLZ3|Q8IW63|Q8N316|Q96H00	Missense_Mutation	SNP	ENST00000308748.5	hg19	CCDS10660.1	.	.	.	.	.	.	.	.	.	.	C	11.50	1.656395	0.29425	.	.	ENSG00000174939	ENST00000414952;ENST00000308748	T;T	0.42900	0.96;0.96	4.91	1.63	0.23807	.	0.442730	0.21939	N	0.066908	T	0.23926	0.0579	N	0.24115	0.695	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.15752	-1.0426	10	0.66056	D	0.02	0.7085	3.949	0.09361	0.2667:0.5394:0.0:0.1938	.	136	Q5U4P2	ASPH1_HUMAN	H	136	ENSP00000388036:P136H;ENSP00000311447:P136H	ENSP00000311447:P136H	P	+	2	0	ASPHD1	29820200	0.002000	0.14202	0.021000	0.16686	0.055000	0.15305	1.503000	0.35715	0.572000	0.29383	0.462000	0.41574	CCC	.	.		0.706	ASPHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255163.2	NM_181718		A	29912699	C	A	29912699	3	1	342	1	0	0	0	0	1	0	0	0	1054	623	22	3	409	3	ASPHD1	16	29912699	Missense_Mutation	SNP	C	TCGA-T1-A6J8-01A-11D-A32G-10	64648	29912699	60442054	69	47272										
TP53	7157	hgsc.bcm.edu	37	chr17	7578290	7578290	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	atgctgaggaggggccagacCtaagagcaatcagtgaggaa	15	7	1	4			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr17:7578290C>T	ENST00000269305.4	-	6	749		c.e6-1		TP53_ENST00000445888.2_Splice_Site|TP53_ENST00000574684.1_Intron|TP53_ENST00000455263.2_Splice_Site|TP53_ENST00000413465.2_Splice_Site|TP53_ENST00000359597.4_Splice_Site|TP53_ENST00000420246.2_Splice_Site	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53						apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.?(40)|p.0?(8)|p.G187fs*16(2)|p.D186_P191delDGLAPP(1)|p.L188fs*19(1)|p.G187_L188delGL(1)|p.G187fs*22(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGGGCCAGACCTAAGAGCAAT	0.552		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											.	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,colon,carcinoma,+2,71	TP53	33396	.	54	Unknown(40)|Whole gene deletion(8)|Deletion - Frameshift(3)|Deletion - In frame(2)|Insertion - Frameshift(1)	upper_aerodigestive_tract(11)|lung(9)|large_intestine(6)|central_nervous_system(5)|ovary(5)|haematopoietic_and_lymphoid_tissue(4)|bone(4)|liver(3)|oesophagus(2)|breast(2)|stomach(1)|genital_tract(1)|eye(1)	c.560-1G>A	GRCh37	CD043957|CS011574|CS083991	TP53	D|S		.						82	74	76					17																	7578290		2203	4300	6503	SO:0001630	splice_region_variant	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	CCAGACCTAAGAG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.560-1G>A	chr17.hg19:g.7578290C>T		87.0	0.0		71.0	41.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Splice_Site	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	9.113	1.007143	0.19199	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	.	.	.	4.67	4.67	0.58626	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.89	0.79291	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TP53	7519015	1.000000	0.71417	0.995000	0.50966	0.031000	0.12232	3.449000	0.52950	2.539000	0.85634	0.655000	0.94253	.	.	.		0.552	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	Intron	T	7578290	C	T	7578290	5	4	342	1	0	0	0	0	0	0	1	0	16396	695	24	3	735	3	TP53	17	7578290	Splice_Site	SNP	C	TCGA-T1-A6J8-01A-11D-A32G-10		7578290	73616920	70	47273										
CACNA1G	8913	hgsc.bcm.edu	37	chr17	48653551	48653551	+	Frame_Shift_Del	DEL	C	C	-													0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	tatcccaccgtgcacaccagCcctccaccggagacgctgaa							TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr17:48653551delC	ENST00000359106.5	+	8	1788	c.1788delC	c.(1786-1788)agcfs	p.S596fs	CACNA1G_ENST00000507510.2_Frame_Shift_Del_p.S596fs|CACNA1G_ENST00000514079.1_Frame_Shift_Del_p.S596fs|CACNA1G_ENST00000354983.4_Frame_Shift_Del_p.S596fs|CACNA1G_ENST00000513689.2_Frame_Shift_Del_p.S596fs|CACNA1G_ENST00000507336.1_Frame_Shift_Del_p.S596fs|CACNA1G_ENST00000507609.1_Frame_Shift_Del_p.S596fs|CACNA1G_ENST00000503485.1_Frame_Shift_Del_p.S596fs|CACNA1G_ENST00000352832.5_Frame_Shift_Del_p.S596fs|CACNA1G_ENST00000512389.1_Frame_Shift_Del_p.S596fs|CACNA1G_ENST00000360761.4_Frame_Shift_Del_p.S596fs|CACNA1G_ENST00000515411.1_Frame_Shift_Del_p.S596fs|CACNA1G_ENST00000513964.1_Frame_Shift_Del_p.S596fs|CACNA1G_ENST00000515165.1_Frame_Shift_Del_p.S596fs|CACNA1G_ENST00000510115.1_Frame_Shift_Del_p.S596fs|CACNA1G_ENST00000507896.1_Frame_Shift_Del_p.S596fs|CACNA1G_ENST00000429973.2_Frame_Shift_Del_p.S596fs|CACNA1G_ENST00000442258.2_Frame_Shift_Del_p.S596fs|CACNA1G_ENST00000514717.1_Frame_Shift_Del_p.S596fs|CACNA1G_ENST00000502264.1_Frame_Shift_Del_p.S596fs|CACNA1G_ENST00000515765.1_Frame_Shift_Del_p.S596fs|CACNA1G_ENST00000416767.4_Frame_Shift_Del_p.S596fs|CACNA1G_ENST00000510366.1_Frame_Shift_Del_p.S596fs|CACNA1G_ENST00000514181.1_Frame_Shift_Del_p.S596fs|CACNA1G_ENST00000505165.1_Frame_Shift_Del_p.S596fs|CACNA1G_ENST00000358244.5_Frame_Shift_Del_p.S596fs	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	596					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	TGCACACCAGCCCTCCACCGG	0.667																																					p.S596fs		Pindel	.											.	CACNA1G	659	.	0			c.1787delG						.						16	20	19					17																	48653551		2058	4194	6252	SO:0001589	frameshift_variant	8913	exon8			.	AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.1788delC	chr17.hg19:g.48653551delC	ENSP00000352011:p.Ser596fs	79.0	0.0		111.0	36.0	NM_001256360	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Frame_Shift_Del	DEL	ENST00000359106.5	hg19	CCDS45730.1																																																																																			.	.		0.667	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896		-	48653551	C	-	48653551	7	5	342	1	0	1	0	1	0	0	0	0	2546	738	26	0	1818	0	CACNA1G	17	48653551	Frame_Shift_Del	DEL	C	TCGA-T1-A6J8-01A-11D-A32G-10	41075261	48653551	32541659	71	47274										
MED13	9969	hgsc.bcm.edu	37	chr17	60088411	60088411	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	ctttggctggctgaatctgcGtccatgccaacatcatcact	8	13	3	1			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr17:60088411G>A	ENST00000397786.2	-	9	1543	c.1467C>T	c.(1465-1467)gaC>gaT	p.D489D		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	489					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						CTGAATCTGCGTCCATGCCAA	0.448																																					p.D489D		Atlas-SNP	.											.	MED13	181	.	0			c.C1467T						.						119	115	117					17																	60088411		2049	4203	6252	SO:0001819	synonymous_variant	9969	exon9			ATCTGCGTCCATG	AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"thyroid hormone receptor associated protein 1"	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.1467C>T	chr17.hg19:g.60088411G>A		287.0	0.0		351.0	34.0	NM_005121	B2RU05|O60334	Silent	SNP	ENST00000397786.2	hg19	CCDS42366.1																																																																																			.	.		0.448	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121		A	60088411	G	A	60088411	2	1	342	1	0	0	0	0	0	0	0	1	9439	1136	40	1		1	MED13	17	60088411	Silent	SNP	G	TCGA-T1-A6J8-01A-11D-A32G-10	11434860	60088411	21106799	72	47275										
USP36	57602	hgsc.bcm.edu	37	chr17	76814798	76814798	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	caaagcgcttgagggaaaggGttaagacgttggatgttctg	15	5	1	2			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr17:76814798G>C	ENST00000542802.3	-	10	1417	c.974C>G	c.(973-975)aCc>aGc	p.T325S	USP36_ENST00000312010.6_Missense_Mutation_p.T325S|USP36_ENST00000449938.2_Missense_Mutation_p.T25S|USP36_ENST00000588467.1_5'UTR			Q9P275	UBP36_HUMAN	ubiquitin specific peptidase 36	325	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	34			BRCA - Breast invasive adenocarcinoma(99;0.000842)|OV - Ovarian serous cystadenocarcinoma(97;0.151)			GAGGGAAAGGGTTAAGACGTT	0.522																																					p.T325S		Atlas-SNP	.											.	USP36	243	.	0			c.C974G						.						210	184	193					17																	76814798		2203	4300	6503	SO:0001583	missense	57602	exon10			GAAAGGGTTAAGA	AB040886	CCDS32755.1	17q25.3	2008-02-05	2005-08-08			ENSG00000055483		"Ubiquitin-specific peptidases"	20062	protein-coding gene	gene with protein product		612543	"ubiquitin specific protease 36"			12838346	Standard	NM_025090		Approved	KIAA1453, FLJ12851	uc002jvz.1	Q9P275		ENST00000542802.3:c.974C>G	chr17.hg19:g.76814798G>C	ENSP00000441214:p.Thr325Ser	138.0	0.0		162.0	55.0	NM_025090	Q05C98|Q05DD0|Q6IQ38|Q8NDM8|Q9NVC8	Missense_Mutation	SNP	ENST00000542802.3	hg19	CCDS32755.1	.	.	.	.	.	.	.	.	.	.	G	17.32	3.359959	0.61403	.	.	ENSG00000055483	ENST00000312010;ENST00000449938;ENST00000542802;ENST00000432878	T;T;T	0.05855	3.38;3.38;3.38	4.93	4.93	0.64822	.	0.000000	0.85682	D	0.000000	T	0.19644	0.0472	L	0.49699	1.58	0.58432	D	0.999999	D	0.60160	0.987	D	0.64595	0.927	T	0.00346	-1.1800	10	0.62326	D	0.03	-32.4734	17.7609	0.88464	0.0:0.0:1.0:0.0	.	325	Q9P275-2	.	S	325;25;325;325	ENSP00000310590:T325S;ENSP00000401119:T25S;ENSP00000441214:T325S	ENSP00000310590:T325S	T	-	2	0	USP36	74326393	1.000000	0.71417	0.042000	0.18584	0.124000	0.20399	9.064000	0.93933	2.288000	0.76882	0.563000	0.77884	ACC	.	.		0.522	USP36-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437472.3	NM_025090		C	76814798	G	C	76814798	3	2	342	1	0	0	0	0	1	0	0	0	17082	1261	44	4	2441	4	USP36	17	76814798	Missense_Mutation	SNP	G	TCGA-T1-A6J8-01A-11D-A32G-10	16726387	76814798	4380412	73	47276										
CCBE1	147372	hgsc.bcm.edu	37	chr18	57363935	57363935	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	gcgattttgctctctgagcaGatttctctatgaaaaagtgc	9	8	2	3			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr18:57363935G>A	ENST00000439986.4	-	2	175	c.138C>T	c.(136-138)atC>atT	p.I46I	RP11-2N1.2_ENST00000588946.1_RNA	NM_133459.3	NP_597716.1	Q6UXH8	CCBE1_HUMAN	collagen and calcium binding EGF domains 1	46					lymphangiogenesis (GO:0001946)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of lymphangiogenesis (GO:1901492)|positive regulation of protein processing (GO:0010954)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|positive regulation vascular endothelial growth factor production (GO:0010575)|sprouting angiogenesis (GO:0002040)|venous blood vessel morphogenesis (GO:0048845)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|protease binding (GO:0002020)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(1)|lung(6)|ovary(1)|prostate(1)|skin(3)	24		Colorectal(73;0.175)				TCTCTGAGCAGATTTCTCTAT	0.582											OREG0025022	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I46I	NSCLC(137;1340 1860 15773 39604 51087)|Esophageal Squamous(139;339 1777 2926 19691 38524)	Atlas-SNP	.											.	CCBE1	59	.	0			c.C138T						.						91	95	93					18																	57363935		2203	4300	6503	SO:0001819	synonymous_variant	147372	exon2			TGAGCAGATTTCT	AB075863	CCDS32838.1	18q21.32	2005-01-18				ENSG00000183287			29426	protein-coding gene	gene with protein product		612753				11853319, 12975309	Standard	NM_133459		Approved	FLJ30681, KIAA1983	uc002lib.3	Q6UXH8		ENST00000439986.4:c.138C>T	chr18.hg19:g.57363935G>A		113.0	0.0	1022	115.0	34.0	NM_133459	Q6MZX5|Q86SS2|Q8TF19	Silent	SNP	ENST00000439986.4	hg19	CCDS32838.1																																																																																			.	.		0.582	CCBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449685.2	NM_133459		A	57363935	G	A	57363935	2	1	342	1	0	0	0	0	0	0	0	1	2733	932	33	3		3	CCBE1	18	57363935	Silent	SNP	G	TCGA-T1-A6J8-01A-11D-A32G-10		57363935	20713313	74	47277										
CEBPA	1050	hgsc.bcm.edu	37	chr19	33792919	33792919	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	ccgtccaggtagccggcggcCgcgcagccgtagccgggcgg	18	16	0	0			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr19:33792919C>T	ENST00000498907.2	-	1	551	c.402G>A	c.(400-402)gcG>gcA	p.A134A	CEBPA-AS1_ENST00000592982.2_RNA|CTD-2540B15.7_ENST00000587312.1_RNA|CTD-2540B15.11_ENST00000589932.1_RNA	NM_004364.3	NP_004355.2	P49715	CEBPA_HUMAN	CCAAT/enhancer binding protein (C/EBP), alpha	134					acute-phase response (GO:0006953)|brown fat cell differentiation (GO:0050873)|cell maturation (GO:0048469)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|cholesterol metabolic process (GO:0008203)|cytokine-mediated signaling pathway (GO:0019221)|embryonic placenta development (GO:0001892)|generation of precursor metabolites and energy (GO:0006091)|inner ear development (GO:0048839)|liver development (GO:0001889)|lung development (GO:0030324)|macrophage differentiation (GO:0030225)|mitochondrion organization (GO:0007005)|myeloid cell differentiation (GO:0030099)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ regeneration (GO:0031100)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|response to glucocorticoid (GO:0051384)|response to vitamin B2 (GO:0033274)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|urea cycle (GO:0000050)|viral process (GO:0016032)|white fat cell differentiation (GO:0050872)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|Rb-E2F complex (GO:0035189)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A134A(2)|p.Q87fs*32(2)|p.L78_A174del(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(912)|lung(5)|prostate(1)|stomach(1)	920	Esophageal squamous(110;0.137)					AGCCGGCGGCCGCGCAGCCGT	0.811			"Mis, N, F"		"AML, MDS"				Acute Myeloid Leukemia, Familial, associated with CEBPA germline mutation																												p.A134A		Atlas-SNP	.		Dom	yes		19	19q13.1	1050	"CCAAT/enhancer binding protein (C/EBP), alpha"		L	CEBPA,NS,haematopoietic_neoplasm,0,2	CEBPA	986	.	5	Deletion - Frameshift(2)|Substitution - coding silent(2)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(5)	c.G402A						.						1	1	1					19																	33792919		103	303	406	SO:0001819	synonymous_variant	1050	exon1	Familial Cancer Database	Familial AML	GGCGGCCGCGCAG	M37197	CCDS54243.1	19q13.1	2014-09-17				ENSG00000245848		"basic leucine zipper proteins"	1833	protein-coding gene	gene with protein product		116897		CEBP		1535333, 1840554	Standard	NM_004364		Approved	C/EBP-alpha	uc002nun.3	P49715		ENST00000498907.2:c.402G>A	chr19.hg19:g.33792919C>T		4.0	1.0		14.0	9.0	NM_004364	A7LNP2|P78319|Q05CA4	Silent	SNP	ENST00000498907.2	hg19	CCDS54243.1																																																																																			.	.		0.811	CEBPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365012.1	NM_004364		T	33792919	C	T	33792919	2	4	342	1	0	0	0	0	0	0	0	1	3201	639	23	1		1	CEBPA	19	33792919	Silent	SNP	C	TCGA-T1-A6J8-01A-11D-A32G-10		33792919	25336064	75	47278										
HAMP	57817	hgsc.bcm.edu	37	chr19	35775694	35775694	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	ccccttctgctttcacagacGggacaacttgcagagctgca	9	14	2	2			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr19:35775694G>A	ENST00000598398.1	+	3	389	c.93G>A	c.(91-93)acG>acA	p.T31T	HAMP_ENST00000222304.3_Silent_p.T31T	NM_021175.2	NP_066998.1	P81172	HEPC_HUMAN	hepcidin antimicrobial peptide	31				T -> M (in Ref. 3; AAK14912). {ECO:0000305}.	cellular iron ion homeostasis (GO:0006879)|defense response to bacterium (GO:0042742)|defense response to fungus (GO:0050832)|immune response (GO:0006955)|killing of cells of other organism (GO:0031640)	apical cortex (GO:0045179)|extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|large_intestine(1)|lung(1)	4	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)		Epithelial(14;7.4e-20)|OV - Ovarian serous cystadenocarcinoma(14;6.47e-19)|all cancers(14;4.17e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			TTTCACAGACGGGACAACTTG	0.622																																					p.T31T		Atlas-SNP	.											.	HAMP	14	.	0			c.G93A						.						72	72	72					19																	35775694		2203	4300	6503	SO:0001819	synonymous_variant	57817	exon2			ACAGACGGGACAA	AF309489	CCDS12454.1	19q13.1	2014-09-17				ENSG00000105697			15598	protein-coding gene	gene with protein product		606464				11034317, 11113132	Standard	NM_021175		Approved	LEAP-1, HEPC, HFE2B, LEAP1	uc002nyw.3	P81172		ENST00000598398.1:c.93G>A	chr19.hg19:g.35775694G>A		74.0	0.0		113.0	41.0	NM_021175	Q1HE14|Q9BY68	Silent	SNP	ENST00000598398.1	hg19	CCDS12454.1																																																																																			.	.		0.622	HAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466067.1	NM_021175		A	35775694	G	A	35775694	2	1	342	1	0	0	0	0	0	0	0	1	6957	1103	39	1		1	HAMP	19	35775694	Silent	SNP	G	TCGA-T1-A6J8-01A-11D-A32G-10	1982775	35775694	23353289	76	47279										
ARHGAP33	115703	hgsc.bcm.edu	37	chr19	36273524	36273524	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	catgtcagtgcctggggaggAggagcgtctggtgcgggtgc	20	8	2	0			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr19:36273524A>G	ENST00000007510.4	+	14	1400	c.1256A>G	c.(1255-1257)gAg>gGg	p.E419G	ARHGAP33_ENST00000314737.5_Missense_Mutation_p.E419G|ARHGAP33_ENST00000378944.5_Missense_Mutation_p.E283G			O14559	RHG33_HUMAN	Rho GTPase activating protein 33	419	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|Rac GTPase activator activity (GO:0030675)			endometrium(7)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	37						CCTGGGGAGGAGGAGCGTCTG	0.657																																					p.E419G		Atlas-SNP	.											.	ARHGAP33	102	.	0			c.A1256G						.						39	35	37					19																	36273524		2203	4300	6503	SO:0001583	missense	115703	exon14			GGGAGGAGGAGCG	AY044864	CCDS12477.1, CCDS54254.1	19q13.13	2011-06-29	2010-02-19	2010-02-19		ENSG00000004777		"Rho GTPase activating proteins"	23085	protein-coding gene	gene with protein product		614902	"sorting nexin 26"	SNX26		12297274, 12461558	Standard	NM_052948		Approved	FLJ39019, TCGAP	uc002obs.2	O14559		ENST00000007510.4:c.1256A>G	chr19.hg19:g.36273524A>G	ENSP00000007510:p.Glu419Gly	38.0	0.0		53.0	20.0	NM_052948	O14552|O14560|Q6ZSP6|Q96CP3|Q9NT23	Missense_Mutation	SNP	ENST00000007510.4	hg19		.	.	.	.	.	.	.	.	.	.	a	25.4	4.638024	0.87760	.	.	ENSG00000004777	ENST00000007510;ENST00000314737;ENST00000378944	T;T;T	0.21031	2.03;2.03;2.03	5.19	5.19	0.71726	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.063750	0.64402	D	0.000014	T	0.40322	0.1112	M	0.77103	2.36	0.58432	D	0.999993	P;P;D	0.54772	0.738;0.524;0.968	B;B;P	0.53912	0.349;0.334;0.737	T	0.41980	-0.9478	10	0.87932	D	0	.	14.0346	0.64638	1.0:0.0:0.0:0.0	.	419;283;419	O14559;O14559-10;O14559-11	RHG33_HUMAN;.;.	G	419;419;283	ENSP00000007510:E419G;ENSP00000320038:E419G;ENSP00000368227:E283G	ENSP00000007510:E419G	E	+	2	0	ARHGAP33	40965364	1.000000	0.71417	0.997000	0.53966	0.984000	0.73092	6.045000	0.71020	1.976000	0.57569	0.456000	0.33151	GAG	.	.		0.657	ARHGAP33-201	KNOWN	basic	protein_coding	protein_coding		NM_052948		G	36273524	A	G	36273524	3	3	342	1	0	0	0	0	1	0	0	0	882	304	11	2	1310	2	ARHGAP33	19	36273524	Missense_Mutation	SNP	A	TCGA-T1-A6J8-01A-11D-A32G-10	497830	36273524	22855459	77	47280										
PRX	57716	hgsc.bcm.edu	37	chr19	40902988	40902988	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	ctgacactccgatgccaaggGagggcatcttgatggtgggc	15	10	1	2			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr19:40902988G>A	ENST00000324001.7	-	7	1541	c.1271C>T	c.(1270-1272)tCc>tTc	p.S424F	PRX_ENST00000291825.7_3'UTR	NM_181882.2	NP_870998.2	Q9BXM0	PRAX_HUMAN	periaxin	424					axon ensheathment (GO:0008366)|cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|ovary(2)|prostate(3)|skin(1)|urinary_tract(9)	47			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GATGCCAAGGGAGGGCATCTT	0.602																																					p.S424F		Atlas-SNP	.											.	PRX	151	.	0			c.C1271T						.						55	60	58					19																	40902988		2203	4299	6502	SO:0001583	missense	57716	exon7			CCAAGGGAGGGCA	AB046840	CCDS12556.1, CCDS33028.1	19q13.2	2014-09-17				ENSG00000105227			13797	protein-coding gene	gene with protein product		605725				10839370, 9143514	Standard	NM_181882		Approved	KIAA1620	uc002onr.3	Q9BXM0		ENST00000324001.7:c.1271C>T	chr19.hg19:g.40902988G>A	ENSP00000326018:p.Ser424Phe	85.0	0.0		139.0	52.0	NM_181882	Q9BXL9|Q9HCF2	Missense_Mutation	SNP	ENST00000324001.7	hg19	CCDS33028.1	.	.	.	.	.	.	.	.	.	.	G	19.67	3.870556	0.72065	.	.	ENSG00000105227	ENST00000324001;ENST00000341562	T	0.02345	4.33	4.65	4.65	0.58169	.	0.142496	0.32802	N	0.005639	T	0.12475	0.0303	M	0.75447	2.3	0.80722	D	1	D	0.57571	0.98	P	0.58331	0.837	T	0.00383	-1.1774	10	0.72032	D	0.01	-16.8049	16.4602	0.84033	0.0:0.0:1.0:0.0	.	424	Q9BXM0	PRAX_HUMAN	F	424	ENSP00000326018:S424F	ENSP00000326018:S424F	S	-	2	0	PRX	45594828	0.799000	0.28903	0.992000	0.48379	0.717000	0.41224	2.458000	0.45014	2.408000	0.81797	0.655000	0.94253	TCC	.	.		0.602	PRX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000462582.1	NM_020956		A	40902988	G	A	40902988	3	1	342	1	0	0	0	0	1	0	0	0	12654	1174	41	3	3118	3	PRX	19	40902988	Missense_Mutation	SNP	G	TCGA-T1-A6J8-01A-11D-A32G-10	4629464	40902988	18225995	78	47281										
CYP2A7	1549	hgsc.bcm.edu	37	chr19	41386034	41386034	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	tggaagattcctagcatcatGctcagcagtgacaggaactc	10	10	2	2			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr19:41386034G>T	ENST00000301146.4	-	4	1150	c.609C>A	c.(607-609)agC>agA	p.S203R	CTC-490E21.12_ENST00000601627.1_Intron|CYP2A7_ENST00000291764.3_Missense_Mutation_p.S152R	NM_000764.2	NP_000755.2	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 7	203						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			CTAGCATCATGCTCAGCAGTG	0.567																																					p.S203R		Atlas-SNP	.											.	CYP2A7	71	.	0			c.C609A						.						166	138	147					19																	41386034		2203	4300	6503	SO:0001583	missense	1549	exon4			CATCATGCTCAGC	NM_000764	CCDS12569.1, CCDS42570.1	19q13.2	2013-07-25	2003-01-14		ENSG00000198077	ENSG00000198077		"Cytochrome P450s"	2611	protein-coding gene	gene with protein product		608054	"cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 7"			7668294, 15128046	Standard	NM_030589		Approved	CYP2A	uc002opm.3	P20853	OTTHUMG00000182715	ENST00000301146.4:c.609C>A	chr19.hg19:g.41386034G>T	ENSP00000301146:p.Ser203Arg	74.0	0.0		108.0	46.0	NM_000764	Q13121	Missense_Mutation	SNP	ENST00000301146.4	hg19	CCDS12569.1	.	.	.	.	.	.	.	.	.	.	g	0.004	-2.362909	0.00212	.	.	ENSG00000198077	ENST00000301146;ENST00000291764	T;T	0.67698	-0.28;-0.28	1.95	-3.89	0.04193	.	0.977016	0.08403	N	0.951060	T	0.28001	0.0690	N	0.02111	-0.68	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.0;0.0;0.002	T	0.08513	-1.0718	10	0.09843	T	0.71	.	0.6051	0.00751	0.2064:0.286:0.1348:0.3728	.	203;152;203	B7ZKR0;F8W816;P20853	.;.;CP2A7_HUMAN	R	203;152	ENSP00000301146:S203R;ENSP00000291764:S152R	ENSP00000291764:S152R	S	-	3	2	CYP2A7	46077874	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-3.349000	0.00502	-2.394000	0.00583	0.175000	0.17021	AGC	.	.		0.567	CYP2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463269.2	NM_030589		T	41386034	G	T	41386034	3	4	342	1	0	0	0	0	1	0	0	0	4165	1310	46	3	899	3	CYP2A7	19	41386034	Missense_Mutation	SNP	G	TCGA-T1-A6J8-01A-11D-A32G-10	483046	41386034	17742949	79	47282										
IGFL4	444882	hgsc.bcm.edu	37	chr19	46543655	46543655	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	ccgcacctgggcgctggctgGcatagccacagtctaagatc	12	14	1	1			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr19:46543655G>A	ENST00000377697.1	-	3	143	c.90C>T	c.(88-90)tgC>tgT	p.C30C	IGFL4_ENST00000595006.1_5'UTR|IGFL4_ENST00000601672.1_5'UTR	NM_001002923.1	NP_001002923.1	Q6B9Z1	IGFL4_HUMAN	IGF-like family member 4	30						extracellular space (GO:0005615)				cervix(1)|kidney(1)|lung(1)	3		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.0036)|GBM - Glioblastoma multiforme(486;0.022)|Epithelial(262;0.208)		GCGCTGGCTGGCATAGCCACA	0.602																																					p.C30C		Atlas-SNP	.											.	IGFL4	13	.	0			c.C90T						.						84	75	78					19																	46543655		2203	4300	6503	SO:0001819	synonymous_variant	444882	exon3			TGGCTGGCATAGC	AY672114	CCDS33057.1	19q13.32	2006-07-14							32931	protein-coding gene	gene with protein product		610547				14702039	Standard	NM_001002923		Approved		uc002pdy.1	Q6B9Z1		ENST00000377697.1:c.90C>T	chr19.hg19:g.46543655G>A		65.0	0.0		101.0	45.0	NM_001002923		Silent	SNP	ENST00000377697.1	hg19	CCDS33057.1																																																																																			.	.		0.602	IGFL4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461698.1	NM_001002923		A	46543655	G	A	46543655	2	1	342	1	0	0	0	0	0	0	0	1	7598	1195	42	3		3	IGFL4	19	46543655	Silent	SNP	G	TCGA-T1-A6J8-01A-11D-A32G-10	5157621	46543655	12585328	80	47283										
NCOA6	23054	hgsc.bcm.edu	37	chr20	33329069	33329069	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	tcataacctgaattattgagGatgaattgataaagacaggt	9	4	1	5			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr20:33329069G>T	ENST00000374796.2	-	12	7561	c.4991C>A	c.(4990-4992)tCc>tAc	p.S1664Y	NCOA6_ENST00000359003.2_Missense_Mutation_p.S1664Y			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	1664	EP300/CRSP3-binding region.				brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			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						AATTATTGAGGATGAATTGAT	0.488																																					p.S1664Y		Atlas-SNP	.											.	NCOA6	219	.	0			c.C4991A						.						111	109	110					20																	33329069		2203	4300	6503	SO:0001583	missense	23054	exon11			ATTGAGGATGAAT	AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"nuclear receptor coactivator RAP250", "activating signal cointegrator-2", "peroxisome proliferator-activated receptor interacting protein"	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.4991C>A	chr20.hg19:g.33329069G>T	ENSP00000363929:p.Ser1664Tyr	82.0	0.0		113.0	31.0	NM_014071	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Missense_Mutation	SNP	ENST00000374796.2	hg19	CCDS13241.1	.	.	.	.	.	.	.	.	.	.	G	16.88	3.244413	0.59103	.	.	ENSG00000198646	ENST00000374796;ENST00000359003	T;T	0.28255	1.62;1.62	5.46	3.44	0.39384	.	0.076753	0.56097	D	0.000029	T	0.20861	0.0502	N	0.24115	0.695	0.36143	D	0.846958	B	0.24823	0.112	B	0.24541	0.054	T	0.20009	-1.0288	10	0.51188	T	0.08	-7.8052	11.341	0.49533	0.0687:0.1263:0.8051:0.0	.	1664	Q14686	NCOA6_HUMAN	Y	1664	ENSP00000363929:S1664Y;ENSP00000351894:S1664Y	ENSP00000351894:S1664Y	S	-	2	0	NCOA6	32792730	1.000000	0.71417	0.999000	0.59377	0.913000	0.54294	4.883000	0.63128	1.554000	0.49487	-0.229000	0.12294	TCC	.	.		0.488	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071		T	33329069	G	T	33329069	3	4	342	1	0	0	0	0	1	0	0	0	10242	1174	41	3	1220	3	NCOA6	20	33329069	Missense_Mutation	SNP	G	TCGA-T1-A6J8-01A-11D-A32G-10		33329069	29696451	81	47284										
BID	637	hgsc.bcm.edu	37	chr22	18256445	18256445	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	gagccatcatgaccccagcaCcgctgcacattcgtatttgt	8	14	1	1			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr22:18256445C>T	ENST00000399774.3	-	1	112				BID_ENST00000473439.1_Intron|BID_ENST00000342111.5_Intron|BID_ENST00000399765.1_Intron|BID_ENST00000551952.1_Intron|BID_ENST00000399767.1_Intron|BID_ENST00000317361.7_Missense_Mutation_p.G4D	NM_001196.3|NM_001244569.1	NP_001187.1|NP_001231498.1	P55957	BID_HUMAN	BH3 interacting domain death agonist						activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic mitochondrial changes (GO:0008637)|apoptotic process (GO:0006915)|brain development (GO:0007420)|establishment of protein localization to membrane (GO:0090150)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|glial cell apoptotic process (GO:0034349)|intrinsic apoptotic signaling pathway (GO:0097193)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of protein homooligomerization (GO:0032464)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein homooligomerization (GO:0051260)|protein targeting to mitochondrion (GO:0006626)|regulation of cell proliferation (GO:0042127)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|release of cytochrome c from mitochondria (GO:0001836)|response to estradiol (GO:0032355)|signal transduction in response to DNA damage (GO:0042770)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of mitochondrial membrane (GO:0032592)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	death receptor binding (GO:0005123)			large_intestine(2)|ovary(1)	3		all_epithelial(15;0.198)		Lung(27;0.0419)		GACCCCAGCACCGCTGCACAT	0.637																																					p.G4D		Atlas-SNP	.											.	BID	18	.	0			c.G11A						.						34	36	35					22																	18256445		2203	4300	6503	SO:0001627	intron_variant	637	exon1			CCAGCACCGCTGC	AF042083	CCDS13747.1, CCDS13748.1, CCDS13749.1	22q11.2	2014-03-07			ENSG00000015475	ENSG00000015475		"Endogenous ligands"	1050	protein-coding gene	gene with protein product		601997				8918887, 9721221	Standard	NM_001244567		Approved		uc002znc.2	P55957	OTTHUMG00000150087	ENST00000399774.3:c.57+701G>A	chr22.hg19:g.18256445C>T		72.0	0.0		31.0	24.0	NM_197966	Q549M7|Q71T04|Q7Z4M9|Q8IY86	Missense_Mutation	SNP	ENST00000399774.3	hg19	CCDS13748.1	.	.	.	.	.	.	.	.	.	.	C	10.30	1.312375	0.23908	.	.	ENSG00000015475	ENST00000317361	T	0.28255	1.62	2.66	1.54	0.23209	.	.	.	.	.	T	0.16214	0.0390	N	0.08118	0	0.18873	N	0.999989	B	0.20780	0.048	B	0.25291	0.059	T	0.26677	-1.0096	9	0.87932	D	0	.	6.9407	0.24490	0.2741:0.7259:0.0:0.0	.	4	P55957-2	.	D	4	ENSP00000318822:G4D	ENSP00000318822:G4D	G	-	2	0	BID	16636445	0.003000	0.15002	0.001000	0.08648	0.005000	0.04900	1.163000	0.31798	0.371000	0.24564	0.313000	0.20887	GGT	.	.		0.637	BID-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316178.1	NM_197966		T	18256445	C	T	18256445	1	4	342	0	1	0	0	0	0	0	0	0	1430	507	18	3		3	BID	22	18256445	Intron	SNP	C	TCGA-T1-A6J8-01A-11D-A32G-10		18256445	33048121	82	47285										
MYO18B	84700	hgsc.bcm.edu	37	chr22	26422950	26422950	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	ttcagacggtgttgggggcaCaaccctactccccgaaaagt	11	12	1	1			TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chr22:26422950C>G	ENST00000407587.2	+	43	7182	c.7013C>G	c.(7012-7014)aCa>aGa	p.T2338R	MYO18B_ENST00000536101.1_Missense_Mutation_p.T2337R|MYO18B_ENST00000335473.7_Missense_Mutation_p.T2337R			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2337						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						GTTGGGGGCACAACCCTACTC	0.557																																					p.T2337R		Atlas-SNP	.											.	MYO18B	322	.	0			c.C7010G						.						51	59	57					22																	26422950		1921	4132	6053	SO:0001583	missense	84700	exon43			GGGGCACAACCCT	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.7013C>G	chr22.hg19:g.26422950C>G	ENSP00000386096:p.Thr2338Arg	23.0	0.0		34.0	22.0	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.186|9.186	1.024779|1.024779	0.19433|0.19433	.|.	.|.	ENSG00000133454|ENSG00000133454	ENST00000543971|ENST00000536101;ENST00000335473;ENST00000407587	.|D;D;D	.|0.86956	.|-2.17;-2.17;-2.19	4.89|4.89	-2.39|-2.39	0.06602|0.06602	.|.	.|1.684560	.|0.03287	.|N	.|0.187077	D|D	0.82440|0.82440	0.5037|0.5037	L|L	0.47716|0.47716	1.5|1.5	0.09310|0.09310	N|N	1|1	.|P;P;P;P;P	.|0.49559	.|0.773;0.877;0.877;0.925;0.925	.|B;B;B;B;B	.|0.42422	.|0.387;0.216;0.216;0.387;0.387	T|T	0.73078|0.73078	-0.4096|-0.4096	5|10	.|0.52906	.|T	.|0.07	.|.	5.8496|5.8496	0.18685|0.18685	0.0:0.4647:0.1337:0.4016|0.0:0.4647:0.1337:0.4016	.|.	.|1850;2339;2337;2338;2337	.|Q8IUG5-2;B0QYF5;Q8IUG5;F5GXR6;F5GYU7	.|.;.;MY18B_HUMAN;.;.	E|R	287|2337;2337;2338	.|ENSP00000441229:T2337R;ENSP00000334563:T2337R;ENSP00000386096:T2338R	.|ENSP00000334563:T2337R	Q|T	+|+	1|2	0|0	MYO18B|MYO18B	24752950|24752950	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-0.003000|-0.003000	0.12901|0.12901	-0.119000|-0.119000	0.11830|0.11830	-0.368000|-0.368000	0.07277|0.07277	CAA|ACA	.	.		0.557	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		G	26422950	C	G	26422950	3	3	342	1	0	0	0	0	1	0	0	0	10075	478	17	4	7176	4	MYO18B	22	26422950	Missense_Mutation	SNP	C	TCGA-T1-A6J8-01A-11D-A32G-10	8166505	26422950	24881616	83	47286										
PRKX	5613	hgsc.bcm.edu	37	chrX	3533925	3533925	+	Frame_Shift_Del	DEL	C	C	-													0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	cgatgatgcttcacatcattCgccccgttcttcaaaagaaa							TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chrX:3533925delC	ENST00000262848.5	-	7	1236	c.882delG	c.(880-882)gcgfs	p.A294fs	PRKX_ENST00000425240.1_5'UTR	NM_005044.4	NP_005035.1	P51817	PRKX_HUMAN	protein kinase, X-linked	294	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|endothelial cell migration (GO:0043542)|endothelial cell proliferation (GO:0001935)|epithelial tube morphogenesis (GO:0060562)|kidney morphogenesis (GO:0060993)|myeloid cell differentiation (GO:0030099)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of epithelial cell differentiation involved in kidney development (GO:2000696)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)			kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|skin(2)	12		all_lung(23;0.000396)|Lung NSC(23;0.00123)				TCACATCATTCGCCCCGTTCT	0.438																																					p.N295fs		Atlas-INDEL	.											.	PRKX	29	.	0			c.883delA						.						119	78	92					X																	3533925		2202	4300	6502	SO:0001589	frameshift_variant	5613	exon7			.		CCDS14125.1	Xp22.3	2008-08-01			ENSG00000183943	ENSG00000183943	2.7.11.1		9441	protein-coding gene	gene with protein product		300083				7633447	Standard	NM_005044		Approved	PKX1	uc010nde.3	P51817	OTTHUMG00000021087	ENST00000262848.5:c.882delG	chrX.hg19:g.3533925delC	ENSP00000262848:p.Ala294fs	114.0	0.0		141.0	102.0	NM_005044		Frame_Shift_Del	DEL	ENST00000262848.5	hg19	CCDS14125.1																																																																																			.	.		0.438	PRKX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055659.1	NM_005044		-	3533925	C	-	3533925	7	5	342	1	0	1	0	1	0	0	0	0	12539	871	31	0	202	0	PRKX	23	3533925	Frame_Shift_Del	DEL	C	TCGA-T1-A6J8-01A-11D-A32G-10		3533925	151736635	84	47287	257	3								
PRKX	5613	hgsc.bcm.edu	37	chrX	3533926	3533926	+	Missense_Mutation	SNP	G	G	T													0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	gatgatgcttcacatcattcGccccgttcttcaaaagaaac							TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chrX:3533926G>T	ENST00000262848.5	-	7	1235	c.881C>A	c.(880-882)gCg>gAg	p.A294E	PRKX_ENST00000425240.1_5'UTR	NM_005044.4	NP_005035.1	P51817	PRKX_HUMAN	protein kinase, X-linked	294	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|endothelial cell migration (GO:0043542)|endothelial cell proliferation (GO:0001935)|epithelial tube morphogenesis (GO:0060562)|kidney morphogenesis (GO:0060993)|myeloid cell differentiation (GO:0030099)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of epithelial cell differentiation involved in kidney development (GO:2000696)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)			kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|skin(2)	12		all_lung(23;0.000396)|Lung NSC(23;0.00123)				CACATCATTCGCCCCGTTCTT	0.438																																					p.A294E		Atlas-SNP	.											.	PRKX	29	.	0			c.C881A						.						116	76	90					X																	3533926		2202	4300	6502	SO:0001583	missense	5613	exon7			TCATTCGCCCCGT		CCDS14125.1	Xp22.3	2008-08-01			ENSG00000183943	ENSG00000183943	2.7.11.1		9441	protein-coding gene	gene with protein product		300083				7633447	Standard	NM_005044		Approved	PKX1	uc010nde.3	P51817	OTTHUMG00000021087	ENST00000262848.5:c.881C>A	chrX.hg19:g.3533926G>T	ENSP00000262848:p.Ala294Glu	112.0	0.0		39.0	4.0	NM_005044		Missense_Mutation	SNP	ENST00000262848.5	hg19	CCDS14125.1	.	.	.	.	.	.	.	.	.	.	G	12.79	2.043275	0.36085	.	.	ENSG00000183943	ENST00000262848	T	0.70399	-0.48	3.69	3.69	0.42338	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.056822	0.64402	D	0.000001	D	0.83631	0.5296	M	0.85777	2.775	0.80722	D	1	D	0.65815	0.995	D	0.66602	0.945	D	0.86437	0.1764	10	0.62326	D	0.03	-13.8201	13.6885	0.62531	0.0:0.0:1.0:0.0	.	294	P51817	PRKX_HUMAN	E	294	ENSP00000262848:A294E	ENSP00000262848:A294E	A	-	2	0	PRKX	3543926	1.000000	0.71417	0.039000	0.18376	0.018000	0.09664	5.443000	0.66581	1.479000	0.48272	0.589000	0.80489	GCG	.	.		0.438	PRKX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055659.1	NM_005044		T	3533926	G	T	3533926	3	4	342	1	0	0	0	0	1	0	0	0	12539	1087	38	1	203	1	PRKX	23	3533926	Missense_Mutation	SNP	G	TCGA-T1-A6J8-01A-11D-A32G-10	1	3533926	151736634	85	47288	257	3								
PRKX	5613	hgsc.bcm.edu	37	chrX	3533930	3533930	+	Frame_Shift_Del	DEL	C	C	-													0.0853658536585366	7	1	1.60724195338513	3.46960167714885	0.936792452830189	1	1	0	atgcttcacatcattcgcccCgttcttcaaaagaaacaaca							TCGA-T1-A6J8-01A-11D-A32G-10	TCGA-T1-A6J8-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a537d6e4-82a8-4627-a88b-5173d666e2f1	b3cc3039-470f-4d68-9bd1-f2fb51d0d468	g.chrX:3533930delC	ENST00000262848.5	-	7	1231	c.877delG	c.(877-879)gggfs	p.G293fs	PRKX_ENST00000425240.1_5'UTR	NM_005044.4	NP_005035.1	P51817	PRKX_HUMAN	protein kinase, X-linked	293	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|endothelial cell migration (GO:0043542)|endothelial cell proliferation (GO:0001935)|epithelial tube morphogenesis (GO:0060562)|kidney morphogenesis (GO:0060993)|myeloid cell differentiation (GO:0030099)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of epithelial cell differentiation involved in kidney development (GO:2000696)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)			kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|skin(2)	12		all_lung(23;0.000396)|Lung NSC(23;0.00123)				TCATTCGCCCCGTTCTTCAAA	0.438																																					p.G293fs		Pindel	.											.	PRKX	29	.	0			c.878delG						.						112	75	88					X																	3533930		2202	4300	6502	SO:0001589	frameshift_variant	5613	exon7			.		CCDS14125.1	Xp22.3	2008-08-01			ENSG00000183943	ENSG00000183943	2.7.11.1		9441	protein-coding gene	gene with protein product		300083				7633447	Standard	NM_005044		Approved	PKX1	uc010nde.3	P51817	OTTHUMG00000021087	ENST00000262848.5:c.877delG	chrX.hg19:g.3533930delC	ENSP00000262848:p.Gly293fs	112.0	0.0		144.0	37.0	NM_005044		Frame_Shift_Del	DEL	ENST00000262848.5	hg19	CCDS14125.1																																																																																			.	.		0.438	PRKX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055659.1	NM_005044		-	3533930	C	-	3533930	7	5	342	1	0	1	0	1	0	0	0	0	12539	652	23	0	207	0	PRKX	23	3533930	Frame_Shift_Del	DEL	C	TCGA-T1-A6J8-01A-11D-A32G-10	4	3533930	151736630	86	47289	257	3								
HIVEP3	59269	hgsc.bcm.edu	37	chr1	42041241	42041241	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	tcgaagattttgatcctcgcCggctcccctctctgggaggc	11	14	1	2			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr1:42041241C>T	ENST00000372583.1	-	5	6066	c.5181G>A	c.(5179-5181)ccG>ccA	p.P1727P	HIVEP3_ENST00000429157.2_Silent_p.P1727P|HIVEP3_ENST00000460604.1_5'UTR|HIVEP3_ENST00000372584.1_Silent_p.P1727P|HIVEP3_ENST00000247584.5_Silent_p.P1727P	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	1727					positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				TGATCCTCGCCGGCTCCCCTC	0.557																																					p.P1727P		Atlas-SNP	.											.	HIVEP3	235	.	0			c.G5181A						.						151	161	158					1																	42041241		2203	4300	6503	SO:0001819	synonymous_variant	59269	exon5			CCTCGCCGGCTCC	AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"Zinc fingers, C2H2-type"	13561	protein-coding gene	gene with protein product	"kappabinding protein-1"	606649	"human immunodeficiency virus type I enhancer-binding protein 3"			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.5181G>A	chr1.hg19:g.42041241C>T		64.0	0.0		27.0	15.0	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Silent	SNP	ENST00000372583.1	hg19	CCDS463.1																																																																																			.	.		0.557	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503		T	42041241	C	T	42041241	2	4	343	1	0	0	0	0	0	0	0	1	7197	639	23	1		1	HIVEP3	1	42041241	Silent	SNP	C	TCGA-UB-A7MA-01A-11D-A33Q-10		42041241	207209380	1	47290										
DOCK7	85440	hgsc.bcm.edu	37	chr1	63001217	63001217	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	tctgttaacacaagtcctgcCaaataatgctgttggcggaa	9	9	1	0			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr1:63001217C>T	ENST00000340370.5	-	28	3482	c.3465G>A	c.(3463-3465)ttG>ttA	p.L1155L	DOCK7_ENST00000251157.5_Silent_p.L1186L	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	1186					activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						CAAGTCCTGCCAAATAATGCT	0.388																																					p.L1186L		Atlas-SNP	.											.	DOCK7	184	.	0			c.G3558A						.						120	114	116					1																	63001217		2203	4300	6503	SO:0001819	synonymous_variant	85440	exon29			TCCTGCCAAATAA		CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.3465G>A	chr1.hg19:g.63001217C>T		126.0	0.0		120.0	54.0	NM_001271999	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Silent	SNP	ENST00000340370.5	hg19	CCDS30734.1	.	.	.	.	.	.	.	.	.	.	C	9.420	1.082775	0.20309	.	.	ENSG00000116641	ENST00000454575	.	.	.	5.05	4.14	0.48551	.	.	.	.	.	T	0.62502	0.2433	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61008	-0.7149	4	.	.	.	.	11.5973	0.50981	0.0:0.8512:0.0:0.1488	.	.	.	.	S	358	.	.	G	-	1	0	DOCK7	62773805	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.813000	0.55636	1.349000	0.45751	0.650000	0.86243	GGC	.	.		0.388	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407		T	63001217	C	T	63001217	2	4	343	1	0	0	0	0	0	0	0	1	4694	593	21	3		3	DOCK7	1	63001217	Silent	SNP	C	TCGA-UB-A7MA-01A-11D-A33Q-10	20959976	63001217	186249404	2	47291										
ST6GALNAC3	256435	hgsc.bcm.edu	37	chr1	77093235	77093235	+	Frame_Shift_Del	DEL	C	C	-													0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	ctacgggatgataaatgacaCctactgcaagtaagatcaca							TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr1:77093235delC	ENST00000328299.3	+	4	870	c.722delC	c.(721-723)accfs	p.T241fs		NM_152996.2	NP_694541.2	Q8NDV1	SIA7C_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	241					glycoprotein metabolic process (GO:0009100)|glycosphingolipid metabolic process (GO:0006687)|glycosylceramide metabolic process (GO:0006677)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sialyltransferase activity (GO:0008373)	p.T241I(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(20)|ovary(3)|prostate(1)|skin(2)	36						ATAAATGACACCTACTGCAAG	0.403																																					p.T241fs		Atlas-Indel,Pindel	.											.	ST6GALNAC3	71	.	1	Substitution - Missense(1)	lung(1)	c.721delA						.						155	149	151					1																	77093235		2203	4300	6503	SO:0001589	frameshift_variant	256435	exon4			.		CCDS672.1	1p31.1	2013-03-01	2005-02-07	2005-02-07	ENSG00000184005	ENSG00000184005		"Sialyltransferases"	19343	protein-coding gene	gene with protein product	"ST6GALNAC III"	610133	"sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) C"	SIAT7C			Standard	NM_152996		Approved		uc001dhh.2	Q8NDV1	OTTHUMG00000009615	ENST00000328299.3:c.722delC	chr1.hg19:g.77093235delC	ENSP00000329214:p.Thr241fs	30.0	0.0		30.0	11.0	NM_152996	Q6PCE0|Q6UX29|Q8N259	Frame_Shift_Del	DEL	ENST00000328299.3	hg19	CCDS672.1																																																																																			.	.		0.403	ST6GALNAC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026501.1	NM_152996		-	77093235	C	-	77093235	7	5	343	1	0	1	0	1	0	0	0	0	15240	507	18	0	750	0	ST6GALNAC3	1	77093235	Frame_Shift_Del	DEL	C	TCGA-UB-A7MA-01A-11D-A33Q-10	14092018	77093235	172157386	3	47292										
C1orf51	148523	hgsc.bcm.edu	37	chr1	150255801	150255801	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	agagggaggacaagggggccCatgggcccaggccagacact	17	11	0	2			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr1:150255801C>A	ENST00000290363.5	+	1	573	c.124C>A	c.(124-126)Cat>Aat	p.H42N	C1orf51_ENST00000369095.1_Missense_Mutation_p.H42N|C1orf51_ENST00000369094.1_Intron|C1orf51_ENST00000469255.1_3'UTR	NM_144697.2	NP_653298.1	Q8N365	CIART_HUMAN		42					circadian regulation of gene expression (GO:0032922)|locomotor rhythm (GO:0045475)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|E-box binding (GO:0070888)			endometrium(3)|large_intestine(2)|lung(3)|urinary_tract(2)	10	Lung NSC(24;7.29e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			CAAGGGGGCCCATGGGCCCAG	0.592																																					p.H42N		Atlas-SNP	.											.	C1orf51	35	.	0			c.C124A						.						106	110	109					1																	150255801		2203	4300	6503	SO:0001583	missense	148523	exon1			GGGGCCCATGGGC																												ENST00000290363.5:c.124C>A	chr1.hg19:g.150255801C>A	ENSP00000290363:p.His42Asn	162.0	0.0		191.0	20.0	NM_144697	B2RD43|D3DV01|Q8N795|Q96MG6	Missense_Mutation	SNP	ENST00000290363.5	hg19	CCDS949.1	.	.	.	.	.	.	.	.	.	.	C	10.55	1.382243	0.24944	.	.	ENSG00000159208	ENST00000369095;ENST00000290363	.	.	.	4.57	0.571	0.17352	.	0.982616	0.08334	N	0.961898	T	0.13500	0.0327	L	0.47716	1.5	0.09310	N	1	B	0.29037	0.231	B	0.25405	0.06	T	0.30090	-0.9990	9	0.46703	T	0.11	2.389	3.3205	0.07048	0.1821:0.5235:0.0:0.2944	.	42	Q8N365	CA051_HUMAN	N	42	.	ENSP00000290363:H42N	H	+	1	0	C1orf51	148522425	0.000000	0.05858	0.000000	0.03702	0.893000	0.52053	0.316000	0.19469	-0.046000	0.13446	0.563000	0.77884	CAT	.	.		0.592	C1orf51-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035058.1			A	150255801	C	A	150255801	3	1	343	1	0	0	0	0	1	0	0	0	2045	594	21	3	126	3	C1orf51	1	150255801	Missense_Mutation	SNP	C	TCGA-UB-A7MA-01A-11D-A33Q-10	73162566	150255801	98994820	4	47293										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158637739	158637739	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	tcagaggcatagtgaccaccCtcaatcatctcttggccagt	8	13	4	2			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr1:158637739C>T	ENST00000368147.4	-	15	2127	c.1947G>A	c.(1945-1947)gaG>gaA	p.E649E		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	649					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					AGTGACCACCCTCAATCATCT	0.468																																					p.E649E		Atlas-SNP	.											.	SPTA1	720	.	0			c.G1947A						.						150	144	146					1																	158637739		1871	4099	5970	SO:0001819	synonymous_variant	6708	exon15			ACCACCCTCAATC	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.1947G>A	chr1.hg19:g.158637739C>T		79.0	0.0		106.0	72.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Silent	SNP	ENST00000368147.4	hg19	CCDS41423.1																																																																																			.	.		0.468	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		T	158637739	C	T	158637739	2	4	343	1	0	0	0	0	0	0	0	1	15131	680	24	3		3	SPTA1	1	158637739	Silent	SNP	C	TCGA-UB-A7MA-01A-11D-A33Q-10	8381938	158637739	90612882	5	47294										
COPA	1314	hgsc.bcm.edu	37	chr1	160264344	160264344	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	cttcctgtcccttgccaagaGcatcatcccccaaaccttct	4	18	2	1			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr1:160264344G>A	ENST00000241704.7	-	25	2835	c.2606C>T	c.(2605-2607)gCt>gTt	p.A869V	COPA_ENST00000368069.3_Missense_Mutation_p.A878V	NM_001098398.1|NM_004371.3	NP_001091868.1|NP_004362.2	P53621	COPA_HUMAN	coatomer protein complex, subunit alpha	869					COPI coating of Golgi vesicle (GO:0048205)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|pancreatic juice secretion (GO:0030157)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(2)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(2)	46	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			CTTGCCAAGAGCATCATCCCC	0.478																																					p.A878V		Atlas-SNP	.											.	COPA	181	.	0			c.C2633T						.						171	157	162					1																	160264344		2203	4300	6503	SO:0001583	missense	1314	exon25			CCAAGAGCATCAT	U24105	CCDS1202.1, CCDS41424.1	1q23.2	2014-01-30			ENSG00000122218	ENSG00000122218		"WD repeat domain containing", "Endogenous ligands"	2230	protein-coding gene	gene with protein product	"proxenin", "xenin"	601924				8647451	Standard	NM_004371		Approved	HEP-COP	uc001fvv.4	P53621	OTTHUMG00000033111	ENST00000241704.7:c.2606C>T	chr1.hg19:g.160264344G>A	ENSP00000241704:p.Ala869Val	212.0	0.0		234.0	133.0	NM_001098398	Q5T201|Q8IXZ9	Missense_Mutation	SNP	ENST00000241704.7	hg19	CCDS1202.1	.	.	.	.	.	.	.	.	.	.	G	12.43	1.936846	0.34189	.	.	ENSG00000122218	ENST00000368069;ENST00000241704	T;T	0.41758	0.99;0.99	5.63	-0.861	0.10676	Coatomer, alpha subunit, C-terminal (1);	0.695420	0.14586	N	0.310560	T	0.05318	0.0141	N	0.04508	-0.205	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.001	T	0.42258	-0.9462	10	0.19590	T	0.45	0.528	6.2016	0.20579	0.4413:0.1238:0.4348:0.0	.	869;878	P53621;P53621-2	COPA_HUMAN;.	V	878;869	ENSP00000357048:A878V;ENSP00000241704:A869V	ENSP00000241704:A869V	A	-	2	0	COPA	158530968	0.002000	0.14202	0.627000	0.29227	0.991000	0.79684	0.333000	0.19768	-0.149000	0.11215	0.555000	0.69702	GCT	.	.		0.478	COPA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080638.1	NM_004371		A	160264344	G	A	160264344	3	1	343	1	0	0	0	0	1	0	0	0	3729	971	34	3	1104	3	COPA	1	160264344	Missense_Mutation	SNP	G	TCGA-UB-A7MA-01A-11D-A33Q-10	1626605	160264344	88986277	6	47295										
CR2	1380	hgsc.bcm.edu	37	chr1	207651318	207651318	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	cagtatggagctgttgtaacTctggagtgtgaagatgggta	15	4	1	2			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr1:207651318T>A	ENST00000367058.3	+	15	3003	c.2814T>A	c.(2812-2814)acT>acA	p.T938T	CR2_ENST00000367057.3_Silent_p.T997T|CR2_ENST00000458541.2_Silent_p.T911T|CR2_ENST00000367059.3_Silent_p.T876T	NM_001877.4	NP_001868.2	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus) receptor 2	938	Sushi 15. {ECO:0000255|PROSITE- ProRule:PRU00302}.				B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|complement activation, classical pathway (GO:0006958)|immune response (GO:0006955)|innate immune response (GO:0045087)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	complement binding (GO:0001848)|complement receptor activity (GO:0004875)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|breast(3)|endometrium(4)|kidney(3)|large_intestine(12)|lung(26)|ovary(1)|pancreas(1)|prostate(1)|skin(12)|upper_aerodigestive_tract(3)|urinary_tract(1)	69						CTGTTGTAACTCTGGAGTGTG	0.493																																					p.T997T		Atlas-SNP	.											.	CR2	164	.	0			c.T2991A						.						125	113	117					1																	207651318		2203	4300	6503	SO:0001819	synonymous_variant	1380	exon16			TGTAACTCTGGAG	M26004	CCDS1478.1, CCDS31007.1	1q32	2014-09-17			ENSG00000117322	ENSG00000117322		"CD molecules", "Complement system"	2336	protein-coding gene	gene with protein product		120650					Standard	NM_001006658		Approved	CD21	uc001hfv.3	P20023	OTTHUMG00000036307	ENST00000367058.3:c.2814T>A	chr1.hg19:g.207651318T>A		196.0	0.0		163.0	40.0	NM_001006658	C9JHD2|Q13866|Q14212|Q53EL2|Q5BKT9|Q5SR46|Q5SR48	Silent	SNP	ENST00000367058.3	hg19	CCDS1478.1																																																																																			.	.		0.493	CR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000088274.1	NM_001877		A	207651318	T	A	207651318	2	1	343	1	0	0	0	0	0	0	0	1	3844	1538	54	4		4	CR2	1	207651318	Silent	SNP	T	TCGA-UB-A7MA-01A-11D-A33Q-10	47386974	207651318	41599303	7	47296										
RYR2	6262	hgsc.bcm.edu	37	chr1	237540701	237540702	+	Frame_Shift_Ins	INS	-	-	CA													0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	gtacgagttggagatgacctINScatcttagttagcgtgtcct							TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr1:237540701_237540702insCA	ENST00000366574.2	+	8	859_860	c.542_543insCA	c.(541-546)ctcatcfs	p.I182fs	RYR2_ENST00000360064.6_Frame_Shift_Ins_p.I180fs|RYR2_ENST00000542537.1_Frame_Shift_Ins_p.I166fs	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	182	MIR 2. {ECO:0000255|PROSITE- ProRule:PRU00131}.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GGAGATGACCTCATCTTAGTTA	0.436																																					p.L181fs		Atlas-Indel,Pindel	.											.	RYR2	1273	.	0			c.542_543insCA						.																																			SO:0001589	frameshift_variant	6262	exon8			.	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.543_544dupCA	chr1.hg19:g.237540702_237540703dupCA	ENSP00000355533:p.Ile182fs	74.0	0.0		87.0	18.0	NM_001035	Q15411|Q546N8|Q5T3P2	Frame_Shift_Ins	INS	ENST00000366574.2	hg19	CCDS55691.1																																																																																			.	.		0.436	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		CA	237540702	-	CA	237540701	7	5	343	1	0	1	1	0	0	0	0	0	13784	1551	54	0	572	0	RYR2	1	237540701	Frame_Shift_Ins	INS	-	TCGA-UB-A7MA-01A-11D-A33Q-10	29889383	237540701	11709920	8	47297										
NCKAP5	344148	hgsc.bcm.edu	37	chr2	133554289	133554289	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	cagatgaaagatccaagagaCgtgagtgaagtttctaggta	12	5	1	6			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr2:133554289C>T	ENST00000409261.1	-	12	1194	c.821G>A	c.(820-822)cGt>cAt	p.R274H	NCKAP5_ENST00000405974.3_Missense_Mutation_p.R274H|NCKAP5_ENST00000409213.1_Missense_Mutation_p.R274H|NCKAP5_ENST00000317721.6_Missense_Mutation_p.R274H	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	274										NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						ATCCAAGAGACGTGAGTGAAG	0.403																																					p.R274H		Atlas-SNP	.											.	NCKAP5	322	.	0			c.G821A						.						62	59	60					2																	133554289		1851	4103	5954	SO:0001583	missense	344148	exon12			AAGAGACGTGAGT	AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"Nck associated protein 5", "peripheral clock protein"	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.821G>A	chr2.hg19:g.133554289C>T	ENSP00000387128:p.Arg274His	62.0	0.0		48.0	10.0	NM_207481	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	hg19	CCDS46418.1	.	.	.	.	.	.	.	.	.	.	C	13.58	2.278775	0.40294	.	.	ENSG00000176771	ENST00000409261;ENST00000409213;ENST00000317721;ENST00000405974;ENST00000537661	T;T;T;T	0.51071	2.67;0.72;2.67;0.72	5.35	-0.767	0.11016	.	.	.	.	.	T	0.26955	0.0660	N	0.19112	0.55	0.09310	N	1	B;B	0.28667	0.017;0.219	B;B	0.22880	0.004;0.042	T	0.15321	-1.0441	9	0.59425	D	0.04	.	4.9132	0.13833	0.1321:0.5078:0.0:0.3601	.	274;274	O14513-2;O14513	.;NCKP5_HUMAN	H	274	ENSP00000387128:R274H;ENSP00000386952:R274H;ENSP00000380603:R274H;ENSP00000385692:R274H	ENSP00000380603:R274H	R	-	2	0	NCKAP5	133270759	0.994000	0.37717	0.023000	0.16930	0.875000	0.50365	1.593000	0.36686	-0.245000	0.09625	0.655000	0.94253	CGT	.	.		0.403	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481		T	133554289	C	T	133554289	3	4	343	1	0	0	0	0	1	0	0	0	10232	536	19	1	4944	1	NCKAP5	2	133554289	Missense_Mutation	SNP	C	TCGA-UB-A7MA-01A-11D-A33Q-10		133554289	109645084	9	47298										
NCKAP5	344148	hgsc.bcm.edu	37	chr2	133721442	133721442	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	ctcttcctctgacagcttttCctgaagcaagaaagaattac	6	11	2	4			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr2:133721442C>T	ENST00000409261.1	-	8	803	c.430G>A	c.(430-432)Gaa>Aaa	p.E144K	NCKAP5_ENST00000405974.3_Splice_Site_p.E144K|NCKAP5_ENST00000409213.1_Splice_Site_p.E144K|NCKAP5_ENST00000317721.6_Splice_Site_p.E144K	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	144										NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						GACAGCTTTTCCTGAAGCAAG	0.418																																					p.E144K		Atlas-SNP	.											.	NCKAP5	322	.	0			c.G430A						.						136	130	132					2																	133721442		1859	4093	5952	SO:0001630	splice_region_variant	344148	exon8			GCTTTTCCTGAAG	AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"Nck associated protein 5", "peripheral clock protein"	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.430-1G>A	chr2.hg19:g.133721442C>T		64.0	0.0		50.0	32.0	NM_207481	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	hg19	CCDS46418.1	.	.	.	.	.	.	.	.	.	.	C	19.18	3.777863	0.70107	.	.	ENSG00000176771	ENST00000409261;ENST00000409213;ENST00000317721;ENST00000405974;ENST00000537661;ENST00000542834	T;T;T;T	0.50813	2.71;0.73;2.71;0.73	5.0	5.0	0.66597	.	.	.	.	.	T	0.52108	0.1714	N	0.19112	0.55	0.32317	N	0.562927	B;P;D	0.67145	0.361;0.72;0.996	B;B;P	0.61874	0.308;0.423;0.895	T	0.61008	-0.7149	9	0.87932	D	0	.	15.4984	0.75677	0.0:1.0:0.0:0.0	.	119;144;144	O14513-3;O14513-2;O14513	.;.;NCKP5_HUMAN	K	144;144;144;144;144;119	ENSP00000387128:E144K;ENSP00000386952:E144K;ENSP00000380603:E144K;ENSP00000385692:E144K	ENSP00000380603:E144K	E	-	1	0	NCKAP5	133437912	1.000000	0.71417	0.993000	0.49108	0.621000	0.37620	4.934000	0.63491	2.765000	0.95021	0.650000	0.86243	GAA	.	.		0.418	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481	Missense_Mutation	T	133721442	C	T	133721442	5	4	343	1	0	0	0	0	0	0	1	0	10232	869	30	3	5351	3	NCKAP5	2	133721442	Splice_Site	SNP	C	TCGA-UB-A7MA-01A-11D-A33Q-10	167153	133721442	109477931	10	47299										
CFLAR	8837	hgsc.bcm.edu	37	chr2	201994647	201994647	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	tgatacagatgagaaggagaTgctgctctttttgtgccggg	14	6	1	4			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr2:201994647T>C	ENST00000309955.3	+	2	574	c.59T>C	c.(58-60)aTg>aCg	p.M20T	CFLAR_ENST00000342795.5_Missense_Mutation_p.M20T|CFLAR_ENST00000340870.5_Missense_Mutation_p.M20T|CFLAR_ENST00000355558.4_Missense_Mutation_p.M20T|CFLAR_ENST00000440180.1_Missense_Mutation_p.M20T|CFLAR_ENST00000341222.6_Missense_Mutation_p.M20T|CFLAR_ENST00000443227.1_Intron|CFLAR_ENST00000341582.6_Missense_Mutation_p.M20T|CFLAR_ENST00000395148.2_Missense_Mutation_p.M20T|CFLAR_ENST00000494258.1_5'Flank|CFLAR_ENST00000423241.2_Missense_Mutation_p.M20T|CFLAR_ENST00000457277.1_Missense_Mutation_p.M20T	NM_001202515.1|NM_003879.5	NP_001189444.1|NP_003870.4	O15519	CFLAR_HUMAN	CASP8 and FADD-like apoptosis regulator	20	DED 1. {ECO:0000255|PROSITE- ProRule:PRU00065}.|Interaction with FADD.|Interaction with caspase-8 propeptide.|Interaction with caspase-8.|Not proteolytically processed and involved in apoptosis inhibition.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of myoblast fusion (GO:1901740)|positive regulation of catalytic activity (GO:0043085)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of necroptotic process (GO:0060544)|regulation of satellite cell proliferation (GO:0014842)|skeletal muscle atrophy (GO:0014732)|skeletal muscle tissue development (GO:0007519)|skeletal muscle tissue regeneration (GO:0043403)|skeletal myofibril assembly (GO:0014866)|viral process (GO:0016032)	CD95 death-inducing signaling complex (GO:0031265)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|ripoptosome (GO:0097342)	cysteine-type peptidase activity (GO:0008234)|death effector domain binding (GO:0035877)|enzyme activator activity (GO:0008047)|protease binding (GO:0002020)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|stomach(1)	13						GAGAAGGAGATGCTGCTCTTT	0.473																																					p.M20T	Pancreas(16;548 657 22190 32864 42338)	Atlas-SNP	.											.	CFLAR	37	.	0			c.T59C						.						206	198	201					2																	201994647		2203	4300	6503	SO:0001583	missense	8837	exon2			AGGAGATGCTGCT	AF005774	CCDS2337.1, CCDS46487.1, CCDS56157.1, CCDS56158.1, CCDS59436.1	2q33-q34	2014-01-30			ENSG00000003402	ENSG00000003402		"Endogenous ligands"	1876	protein-coding gene	gene with protein product		603599		CASP8AP1		9208847, 9217161	Standard	NM_003879		Approved	CASH, Casper, CLARP, FLAME, FLIP, I-FLICE, MRIT, c-FLIP	uc002uxb.4	O15519	OTTHUMG00000132819	ENST00000309955.3:c.59T>C	chr2.hg19:g.201994647T>C	ENSP00000312455:p.Met20Thr	122.0	0.0		121.0	73.0	NM_001202516	B4DJE0|B7Z9F9|O14673|O14674|O14675|O15137|O15138|O15356|O15510|O43618|O43619|O43620|O60458|O60459|Q53TS6|Q54AF1|Q96TE4|Q9UEW1	Missense_Mutation	SNP	ENST00000309955.3	hg19	CCDS2337.1	.	.	.	.	.	.	.	.	.	.	T	2.837	-0.241379	0.05906	.	.	ENSG00000003402	ENST00000309955;ENST00000341222;ENST00000355558;ENST00000340870;ENST00000341582;ENST00000342795;ENST00000395148;ENST00000441224;ENST00000433445;ENST00000423241;ENST00000425030;ENST00000417748;ENST00000440180;ENST00000457277	T;T;T;T;T;T;T;T;T	0.40756	3.86;1.02;1.02;3.74;4.14;1.04;3.86;1.02;3.74	5.72	-4.07	0.03975	DEATH-like (2);Death effector (3);	0.839620	0.11140	N	0.595376	T	0.21062	0.0507	N	0.17082	0.46	0.09310	N	1	B;B;B;B;B;B;B	0.14012	0.002;0.007;0.007;0.009;0.001;0.001;0.002	B;B;B;B;B;B;B	0.17098	0.01;0.007;0.007;0.012;0.006;0.006;0.017	T	0.33420	-0.9869	10	0.13108	T	0.6	-0.4969	9.532	0.39200	0.0:0.5189:0.1257:0.3553	.	20;20;20;20;20;20;20	C9JK38;O15519-11;O15519-8;O15519;O15519-12;O15519-2;E9PAP3	.;.;.;CFLAR_HUMAN;.;.;.	T	20	ENSP00000312455:M20T;ENSP00000339335:M20T;ENSP00000347757:M20T;ENSP00000339326:M20T;ENSP00000345807:M20T;ENSP00000342809:M20T;ENSP00000399420:M20T;ENSP00000406775:M20T;ENSP00000411535:M20T	ENSP00000312455:M20T	M	+	2	0	CFLAR	201702892	0.008000	0.16893	0.001000	0.08648	0.621000	0.37620	-0.035000	0.12205	-0.768000	0.04626	0.460000	0.39030	ATG	.	.		0.473	CFLAR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256276.3	NM_003879		C	201994647	T	C	201994647	3	2	343	1	0	0	0	0	1	0	0	0	3294	1464	51	2	61	2	CFLAR	2	201994647	Missense_Mutation	SNP	T	TCGA-UB-A7MA-01A-11D-A33Q-10	68273205	201994647	41204726	11	47300										
KCNE4	23704	hgsc.bcm.edu	37	chr2	223917618	223917618	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	ccagcagccccctggagtccCgtgcggccggcggcggcagc	16	18	0	0			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr2:223917618C>T	ENST00000281830.3	+	2	554	c.223C>T	c.(223-225)Cgt>Tgt	p.R75C	KCNE4_ENST00000488477.2_Intron|KCNE4_ENST00000604125.1_Missense_Mutation_p.R24C			Q8WWG9	KCNE4_HUMAN	potassium voltage-gated channel, Isk-related family, member 4	75						apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)	voltage-gated potassium channel activity (GO:0005249)			large_intestine(2)|lung(5)|ovary(2)|skin(1)	10		Renal(207;0.0183)|Lung NSC(271;0.137)|all_lung(227;0.175)		Epithelial(121;4.48e-11)|all cancers(144;2.88e-08)|Lung(261;0.00688)|LUSC - Lung squamous cell carcinoma(224;0.008)		CCTGGAGTCCCGTGCGGCCGG	0.612																																					p.R75C		Atlas-SNP	.											.	KCNE4	21	.	0			c.C223T						.						50	47	48					2																	223917618		2203	4298	6501	SO:0001583	missense	23704	exon2			GAGTCCCGTGCGG	AY065987	CCDS2456.1, CCDS2456.2	2q36.1	2008-02-05			ENSG00000152049	ENSG00000152049		"Potassium channels"	6244	protein-coding gene	gene with protein product		607775				10219239, 12670483	Standard	NM_080671		Approved	MiRP3	uc002vnl.5	Q8WWG9	OTTHUMG00000133161	ENST00000281830.3:c.223C>T	chr2.hg19:g.223917618C>T	ENSP00000281830:p.Arg75Cys	46.0	0.0		41.0	32.0	NM_080671	B7Z275|Q53SM4|Q96CC4	Missense_Mutation	SNP	ENST00000281830.3	hg19		.	.	.	.	.	.	.	.	.	.	C	16.82	3.229551	0.58777	.	.	ENSG00000152049	ENST00000281830	.	.	.	6.17	6.17	0.99709	.	0.814657	0.11678	N	0.540137	T	0.36026	0.0952	N	0.14661	0.345	0.24173	N	0.99562	B	0.06786	0.001	B	0.06405	0.002	T	0.26950	-1.0088	9	0.66056	D	0.02	-3.963	14.9567	0.71120	0.0:0.9326:0.0:0.0674	.	24	Q8WWG9	KCNE4_HUMAN	C	24	.	ENSP00000281830:R24C	R	+	1	0	KCNE4	223625862	0.495000	0.26051	0.058000	0.19502	0.281000	0.26958	3.636000	0.54317	2.941000	0.99782	0.655000	0.94253	CGT	.	.		0.612	KCNE4-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000330997.2	NM_080671		T	223917618	C	T	223917618	3	4	343	1	0	0	0	0	1	0	0	0	8034	652	23	1	72	1	KCNE4	2	223917618	Missense_Mutation	SNP	C	TCGA-UB-A7MA-01A-11D-A33Q-10	21922971	223917618	19281755	12	47301										
CUL3	8452	hgsc.bcm.edu	37	chr2	225367700	225367700	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	acaccagttgcctgtagatgTtgcctgaattcatccatcgt	8	11	1	2	rs371616108		TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr2:225367700T>C	ENST00000264414.4	-	10	1805	c.1467A>G	c.(1465-1467)caA>caG	p.Q489Q	CUL3_ENST00000409777.1_Silent_p.Q465Q|CUL3_ENST00000344951.4_Silent_p.Q423Q|CUL3_ENST00000409096.1_Silent_p.Q465Q	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3	489					cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|COPII vesicle coating (GO:0048208)|cyclin catabolic process (GO:0008054)|embryonic cleavage (GO:0040016)|ER to Golgi vesicle-mediated transport (GO:0006888)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation (GO:0007369)|integrin-mediated signaling pathway (GO:0007229)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic metaphase plate congression (GO:0007080)|negative regulation of Rho protein signal transduction (GO:0035024)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|stem cell division (GO:0017145)|stress fiber assembly (GO:0043149)|trophectodermal cellular morphogenesis (GO:0001831)|Wnt signaling pathway (GO:0016055)	Cul3-RING ubiquitin ligase complex (GO:0031463)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|nucleus (GO:0005634)|polar microtubule (GO:0005827)	POZ domain binding (GO:0031208)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	46		all_lung(227;0.00877)|Lung NSC(271;0.011)|Renal(207;0.0112)|all_hematologic(139;0.138)		Epithelial(121;1.58e-11)|all cancers(144;1.43e-08)|Lung(261;0.00863)|LUSC - Lung squamous cell carcinoma(224;0.00902)		CCTGTAGATGTTGCCTGAATT	0.383																																					p.Q495Q		Atlas-SNP	.											.	CUL3	96	.	0			c.A1485G						.	T		1,4405	2.1+/-5.4	0,1,2202	298	276	283		1467	0.6	1	2		283	0,8600		0,0,4300	no	coding-synonymous	CUL3	NM_003590.3		0,1,6502	CC,CT,TT		0.0,0.0227,0.0077		489/769	225367700	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	8452	exon10			TAGATGTTGCCTG	U58089	CCDS2462.1, CCDS58751.1	2q36.2	2011-05-24			ENSG00000036257	ENSG00000036257			2553	protein-coding gene	gene with protein product		603136				8681378, 17192413	Standard	NM_003590		Approved		uc002vny.3	Q13618	OTTHUMG00000133167	ENST00000264414.4:c.1467A>G	chr2.hg19:g.225367700T>C		94.0	0.0		61.0	11.0	NM_001257198	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	Silent	SNP	ENST00000264414.4	hg19	CCDS2462.1																																																																																			.	.		0.383	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256871.2			C	225367700	T	C	225367700	2	2	343	1	0	0	0	0	0	0	0	1	4058	1722	60	2		2	CUL3	2	225367700	Silent	SNP	T	TCGA-UB-A7MA-01A-11D-A33Q-10	1450082	225367700	17831673	13	47302										
CHL1	10752	hgsc.bcm.edu	37	chr3	443359	443359	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	cagaaattcagtcagtaaaaGatgaaacctttggtgaatac	8	6	2	4	rs574347521		TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr3:443359G>A	ENST00000256509.2	+	27	4078	c.3436G>A	c.(3436-3438)Gat>Aat	p.D1146N	CHL1_ENST00000397491.2_Missense_Mutation_p.D1130N	NM_001253387.1|NM_001253388.1|NM_006614.3	NP_001240316.1|NP_001240317.1|NP_006605.2	Q96FC9	DDX11_HUMAN	cell adhesion molecule L1-like	0					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			NS(1)|central_nervous_system(5)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|lung(31)|ovary(1)|prostate(4)|skin(10)|stomach(1)	93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		GTCAGTAAAAGATGAAACCTT	0.303																																					p.D1146N		Atlas-SNP	.											.	CHL1	242	.	0			c.G3436A						.						90	94	93					3																	443359		2203	4300	6503	SO:0001583	missense	10752	exon27			GTAAAAGATGAAA	AF002246	CCDS2556.1, CCDS58812.1, CCDS74887.1	3p26	2013-05-01	2013-05-01		ENSG00000134121	ENSG00000134121		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	1939	protein-coding gene	gene with protein product	"neural cell adhesion molecule", "close homolog of L1"	607416	"cell adhesion molecule with homology to L1CAM (close homologue of L1)", "cell adhesion molecule with homology to L1CAM (close homolog of L1)"			9799093	Standard	NM_006614		Approved	CALL, L1CAM2, FLJ44930, MGC132578	uc003bot.3	O00533	OTTHUMG00000090601	ENST00000256509.2:c.3436G>A	chr3.hg19:g.443359G>A	ENSP00000256509:p.Asp1146Asn	85.0	0.0		57.0	16.0	NM_006614	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000256509.2	hg19	CCDS2556.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.993571	0.93167	.	.	ENSG00000134121	ENST00000256509;ENST00000397491	D;D	0.87887	-2.31;-2.31	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	D	0.93618	0.7962	M	0.77486	2.375	0.80722	D	1	D;D	0.89917	0.995;1.0	D;D	0.83275	0.958;0.996	D	0.94110	0.7370	10	0.66056	D	0.02	.	18.7377	0.91761	0.0:0.0:1.0:0.0	.	1130;1146	O00533;O00533-2	CHL1_HUMAN;.	N	1146;1130	ENSP00000256509:D1146N;ENSP00000380628:D1130N	ENSP00000256509:D1146N	D	+	1	0	CHL1	418359	1.000000	0.71417	0.963000	0.40424	0.941000	0.58515	8.702000	0.91338	2.417000	0.82017	0.585000	0.79938	GAT	.	.		0.303	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614		A	443359	G	A	443359	3	1	343	1	0	0	0	0	1	0	0	0	3351	942	33	3	3534	3	CHL1	3	443359	Missense_Mutation	SNP	G	TCGA-UB-A7MA-01A-11D-A33Q-10		443359	197579071	14	47303										
CASR	846	hgsc.bcm.edu	37	chr3	121981009	121981009	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	tgtggacacctttctgagagGtcacgaagaaagtggcgaca	13	8	2	2			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr3:121981009G>A	ENST00000490131.1	+	4	1499	c.1127G>A	c.(1126-1128)gGt>gAt	p.G376D	CASR_ENST00000296154.5_Missense_Mutation_p.G376D|CASR_ENST00000498619.1_Missense_Mutation_p.G376D	NM_000388.3	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor	376					anatomical structure morphogenesis (GO:0009653)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|chemosensory behavior (GO:0007635)|detection of calcium ion (GO:0005513)|G-protein coupled receptor signaling pathway (GO:0007186)|metabolic process (GO:0008152)|ossification (GO:0001503)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|phosphatidylinositol phospholipase C activity (GO:0004435)			NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(45)|ovary(4)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	84				GBM - Glioblastoma multiforme(114;0.226)	Cinacalcet(DB01012)	TTTCTGAGAGGTCACGAAGAA	0.498																																					p.G376D		Atlas-SNP	.											.	CASR	190	.	0			c.G1127A						.						95	88	90					3																	121981009		2203	4300	6503	SO:0001583	missense	846	exon4			TGAGAGGTCACGA	U20760	CCDS3010.1, CCDS54632.1	3q21.1	2012-08-29	2008-08-01		ENSG00000036828	ENSG00000036828		"GPCR / Class C : Calcium-sensing receptors"	1514	protein-coding gene	gene with protein product	"severe neonatal hyperparathyroidism"	601199	"hypocalciuric hypercalcemia 1"	HHC, HHC1		7677761	Standard	NM_000388		Approved	FHH, NSHPT, GPRC2A	uc003eew.4	P41180	OTTHUMG00000159491	ENST00000490131.1:c.1127G>A	chr3.hg19:g.121981009G>A	ENSP00000418685:p.Gly376Asp	139.0	0.0		104.0	47.0	NM_001178065	Q13912|Q16108|Q16109|Q16110|Q16379|Q2M1T0|Q4PJ19	Missense_Mutation	SNP	ENST00000490131.1	hg19	CCDS3010.1	.	.	.	.	.	.	.	.	.	.	G	5.693	0.312334	0.10789	.	.	ENSG00000036828	ENST00000490131;ENST00000498619;ENST00000296154	D;D;D	0.89196	-2.48;-2.48;-2.48	5.93	1.63	0.23807	Extracellular ligand-binding receptor (1);	0.593444	0.17548	N	0.170270	T	0.69351	0.3101	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.56721	-0.7932	10	0.24483	T	0.36	.	3.6669	0.08260	0.1474:0.2317:0.5025:0.1184	.	376;376	E7ENE0;P41180	.;CASR_HUMAN	D	376	ENSP00000418685:G376D;ENSP00000420194:G376D;ENSP00000296154:G376D	ENSP00000296154:G376D	G	+	2	0	CASR	123463699	0.973000	0.33851	0.343000	0.25615	0.316000	0.28119	1.549000	0.36212	0.747000	0.32809	0.655000	0.94253	GGT	.	.		0.498	CASR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355761.1	NM_000388		A	121981009	G	A	121981009	3	1	343	1	0	0	0	0	1	0	0	0	2684	1261	44	3	1137	3	CASR	3	121981009	Missense_Mutation	SNP	G	TCGA-UB-A7MA-01A-11D-A33Q-10	121537650	121981009	76041421	15	47304										
ATR	545	hgsc.bcm.edu	37	chr3	142232443	142232443	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	catgcttcatcataatgctaCagcaggtgaaaattttactg	7	8	2	1			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr3:142232443C>A	ENST00000350721.4	-	26	4662	c.4541G>T	c.(4540-4542)tGt>tTt	p.C1514F	ATR_ENST00000383101.3_Missense_Mutation_p.C1450F	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	1514					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						CATAATGCTACAGCAGGTGAA	0.363								Other conserved DNA damage response genes																													p.C1514F		Atlas-SNP	.											.	ATR	285	.	0			c.G4541T						.						106	95	98					3																	142232443		2203	4300	6503	SO:0001583	missense	545	exon26			ATGCTACAGCAGG	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.4541G>T	chr3.hg19:g.142232443C>A	ENSP00000343741:p.Cys1514Phe	297.0	0.0		209.0	65.0	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	hg19	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	C	18.11	3.549679	0.65311	.	.	ENSG00000175054	ENST00000350721;ENST00000383101	T;T	0.20738	2.05;2.05	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.52386	0.1731	M	0.82323	2.585	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.57359	-0.7825	10	0.59425	D	0.04	-14.5197	18.9138	0.92496	0.0:1.0:0.0:0.0	.	1514	Q13535	ATR_HUMAN	F	1514;1450	ENSP00000343741:C1514F;ENSP00000372581:C1450F	ENSP00000343741:C1514F	C	-	2	0	ATR	143715133	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.818000	0.86416	2.472000	0.83506	0.491000	0.48974	TGT	.	.		0.363	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		A	142232443	C	A	142232443	3	1	343	1	0	0	0	0	1	0	0	0	1204	478	17	3	3481	3	ATR	3	142232443	Missense_Mutation	SNP	C	TCGA-UB-A7MA-01A-11D-A33Q-10	20251434	142232443	55789987	16	47305										
FRYL	285527	hgsc.bcm.edu	37	chr4	48512111	48512111	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	tcttttcacattgtatgtatCcaggtgttcttgcaactcca	6	10	3	0			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr4:48512111C>T	ENST00000503238.1	-	56	8358	c.8359G>A	c.(8359-8361)Gat>Aat	p.D2787N	FRYL_ENST00000264319.7_Missense_Mutation_p.D183N|FRYL_ENST00000507873.2_Missense_Mutation_p.D183N|FRYL_ENST00000537810.1_Missense_Mutation_p.D2787N|FRYL_ENST00000358350.4_Missense_Mutation_p.D2787N			O94915	FRYL_HUMAN	FRY-like	2787					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)			p.D2787N(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						TTGTATGTATCCAGGTGTTCT	0.438																																					p.D2787N		Atlas-SNP	.											FRYL,NS,carcinoma,0,1	FRYL	242	.	1	Substitution - Missense(1)	lung(1)	c.G8359A						.						80	80	80					4																	48512111		1863	4113	5976	SO:0001583	missense	285527	exon59			ATGTATCCAGGTG	AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"KIAA0826", "furry homolog-like (Drosophila)"	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.8359G>A	chr4.hg19:g.48512111C>T	ENSP00000426064:p.Asp2787Asn	70.0	0.0		58.0	25.0	NM_015030	O95640|Q8WTZ5|Q9NT40	Missense_Mutation	SNP	ENST00000503238.1	hg19	CCDS43227.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.740223	0.89573	.	.	ENSG00000075539	ENST00000503238;ENST00000358350;ENST00000537810;ENST00000264319;ENST00000507873	T;T;T	0.30182	1.55;1.55;1.54	5.93	5.93	0.95920	.	0.000000	0.64402	U	0.000001	T	0.61800	0.2376	M	0.80028	2.48	0.80722	D	1	D;D;D	0.89917	0.997;0.999;1.0	D;D;D	0.91635	0.928;0.967;0.999	T	0.63800	-0.6555	10	0.87932	D	0	.	20.3397	0.98756	0.0:1.0:0.0:0.0	.	2787;2787;183	O94915;F5GX82;O94915-2	FRYL_HUMAN;.;.	N	2787;2787;2787;183;183	ENSP00000426064:D2787N;ENSP00000351113:D2787N;ENSP00000441114:D2787N	ENSP00000264319:D183N	D	-	1	0	FRYL	48206868	1.000000	0.71417	1.000000	0.80357	0.270000	0.26580	7.407000	0.80029	2.803000	0.96430	0.585000	0.79938	GAT	.	.		0.438	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2			T	48512111	C	T	48512111	3	4	343	1	0	0	0	0	1	0	0	0	6072	855	30	3	706	3	FRYL	4	48512111	Missense_Mutation	SNP	C	TCGA-UB-A7MA-01A-11D-A33Q-10		48512111	142642165	17	47306										
TRIM60	166655	hgsc.bcm.edu	37	chr4	165962559	165962559	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	acttttaacgattgtttcacAgaagccgtttggccttattt	7	8	1	1			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr4:165962559A>T	ENST00000512596.1	+	3	1551	c.1335A>T	c.(1333-1335)acA>acT	p.T445T	TRIM60_ENST00000508504.1_Silent_p.T445T|TRIM60_ENST00000341062.5_Silent_p.T445T	NM_152620.2	NP_689833.1	Q495X7	TRI60_HUMAN	tripartite motif containing 60	445	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.			T -> I (in Ref. 2; AAI00986). {ECO:0000305}.		intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(3)|large_intestine(6)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	29	all_hematologic(180;0.221)	Prostate(90;0.0959)|Melanoma(52;0.18)		GBM - Glioblastoma multiforme(119;0.0844)		ATTGTTTCACAGAAGCCGTTT	0.348																																					p.T445T		Atlas-SNP	.											.	TRIM60	73	.	0			c.A1335T						.						63	68	66					4																	165962559		2202	4300	6502	SO:0001819	synonymous_variant	166655	exon4			TTTCACAGAAGCC	AK093201	CCDS3808.1	4q32.3	2013-01-09	2011-01-25	2004-11-17	ENSG00000176979	ENSG00000176979		"RING-type (C3HC4) zinc fingers", "Tripartite motif containing / Tripartite motif containing"	21162	protein-coding gene	gene with protein product			"ring finger protein 129", "tripartite motif-containing 60"	RNF129, RNF33			Standard	NM_152620		Approved	FLJ35882	uc003iqy.1	Q495X7	OTTHUMG00000161262	ENST00000512596.1:c.1335A>T	chr4.hg19:g.165962559A>T		84.0	0.0		82.0	20.0	NM_001258025	Q8NA35	Silent	SNP	ENST00000512596.1	hg19	CCDS3808.1																																																																																			.	.		0.348	TRIM60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364325.1	NM_152620		T	165962559	A	T	165962559	2	4	343	1	0	0	0	0	0	0	0	1	16550	175	7	4		4	TRIM60	4	165962559	Silent	SNP	A	TCGA-UB-A7MA-01A-11D-A33Q-10	117450448	165962559	25191717	18	47307										
PDE8B	8622	hgsc.bcm.edu	37	chr5	76633096	76633096	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	attgcttgctataatgaactGattcaaatagaacatgggga	9	5	1	3			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr5:76633096G>C	ENST00000264917.5	+	6	798	c.753G>C	c.(751-753)ctG>ctC	p.L251L	PDE8B_ENST00000340978.3_Silent_p.L251L|PDE8B_ENST00000342343.4_Silent_p.L231L|PDE8B_ENST00000333194.4_Silent_p.L251L|PDE8B_ENST00000346042.3_Silent_p.L251L	NM_003719.3	NP_003710.1	O95263	PDE8B_HUMAN	phosphodiesterase 8B	251					cAMP catabolic process (GO:0006198)|cyclic nucleotide metabolic process (GO:0009187)|negative regulation of insulin secretion (GO:0046676)|negative regulation of steroid hormone biosynthetic process (GO:0090032)|phosphorelay signal transduction system (GO:0000160)	cytosol (GO:0005829)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)		GMDS/PDE8B(2)	NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(10)|lung(15)|ovary(1)|prostate(2)|skin(3)	40		all_lung(232;0.00043)|Lung NSC(167;0.00114)|Ovarian(174;0.0107)|Prostate(461;0.0605)		OV - Ovarian serous cystadenocarcinoma(54;2.21e-49)|Epithelial(54;5.82e-43)|all cancers(79;4.06e-38)	Caffeine(DB00201)|Ketotifen(DB00920)	ATAATGAACTGATTCAAATAG	0.318																																					p.L251L		Atlas-SNP	.											.	PDE8B	103	.	0			c.G753C						.						66	66	66					5																	76633096		2203	4299	6502	SO:0001819	synonymous_variant	8622	exon6			TGAACTGATTCAA	AF079529	CCDS4037.1, CCDS34190.1, CCDS34191.1, CCDS34192.1, CCDS34193.1	5q14.1	2008-05-15			ENSG00000113231	ENSG00000113231	3.1.4.17	"Phosphodiesterases"	8794	protein-coding gene	gene with protein product		603390				9784418	Standard	NM_003719		Approved		uc003kfa.3	O95263	OTTHUMG00000102170	ENST00000264917.5:c.753G>C	chr5.hg19:g.76633096G>C		162.0	0.0		130.0	18.0	NM_001029852	Q5J7V7|Q86XK8|Q8IUJ7|Q8IUJ8|Q8IUJ9|Q8IUK0|Q8N3T2	Silent	SNP	ENST00000264917.5	hg19	CCDS4037.1																																																																																			.	.		0.318	PDE8B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000220015.3	NM_003719		C	76633096	G	C	76633096	2	2	343	1	0	0	0	0	0	0	0	1	11663	1277	45	4		4	PDE8B	5	76633096	Silent	SNP	G	TCGA-UB-A7MA-01A-11D-A33Q-10		76633096	104282164	19	47308										
DMGDH	29958	hgsc.bcm.edu	37	chr5	78320120	78320120	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	taacttcacaaaatattccaGtccagcttccaaaggatttg	5	10	1	0			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr5:78320120G>A	ENST00000255189.3	-	14	2252	c.2224C>T	c.(2224-2226)Ctg>Ttg	p.L742L	DMGDH_ENST00000540686.1_Silent_p.L362L|DMGDH_ENST00000380311.4_Silent_p.L541L	NM_013391.2	NP_037523.2	Q9UI17	M2GD_HUMAN	dimethylglycine dehydrogenase	742					amino-acid betaine catabolic process (GO:0006579)|choline metabolic process (GO:0019695)|glycine catabolic process (GO:0006546)|glycine metabolic process (GO:0006544)	mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|dimethylglycine dehydrogenase activity (GO:0047865)|electron carrier activity (GO:0009055)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(2)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	34		all_lung(232;0.000638)|Lung NSC(167;0.00173)|Ovarian(174;0.0262)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;6.52e-45)|Epithelial(54;5.96e-40)|all cancers(79;3.56e-35)		AAATATTCCAGTCCAGCTTCC	0.318																																					p.L742L		Atlas-SNP	.											.	DMGDH	88	.	0			c.C2224T						.						104	102	103					5																	78320120		2202	4297	6499	SO:0001819	synonymous_variant	29958	exon14			ATTCCAGTCCAGC	AF111858	CCDS4044.1	5q14.1	2008-02-05			ENSG00000132837	ENSG00000132837	1.5.99.2		24475	protein-coding gene	gene with protein product		605849				10767172, 11231903	Standard	NM_013391		Approved		uc003kfs.3	Q9UI17	OTTHUMG00000108159	ENST00000255189.3:c.2224C>T	chr5.hg19:g.78320120G>A		292.0	0.0		239.0	88.0	NM_013391	B2RBN0|B4E1J9	Silent	SNP	ENST00000255189.3	hg19	CCDS4044.1																																																																																			.	.		0.318	DMGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226963.3	NM_013391		A	78320120	G	A	78320120	2	1	343	1	0	0	0	0	0	0	0	1	4583	1020	36	3		3	DMGDH	5	78320120	Silent	SNP	G	TCGA-UB-A7MA-01A-11D-A33Q-10	1687024	78320120	102595140	20	47309										
PCDHA3	56145	hgsc.bcm.edu	37	chr5	140181914	140181914	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	tgatcagcgtgtccgaccgcGactcaggagtcaatggacag	13	11	3	1			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr5:140181914G>A	ENST00000522353.2	+	1	1132	c.1132G>A	c.(1132-1134)Gac>Aac	p.D378N	PCDHA3_ENST00000532566.2_Missense_Mutation_p.D378N|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA2_ENST00000520672.2_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	378	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.D378N(2)		NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTCCGACCGCGACTCAGGAGT	0.493																																					p.D378N		Atlas-SNP	.											PCDHA3_ENST00000522353,colon,carcinoma,0,2	PCDHA3	396	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1132A						.						122	116	118					5																	140181914		2203	4300	6503	SO:0001583	missense	56145	exon1			GACCGCGACTCAG	AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"Cadherins / Protocadherins : Clustered"	8669	other	complex locus constituent	"KIAA0345-like 11"	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.1132G>A	chr5.hg19:g.140181914G>A	ENSP00000429808:p.Asp378Asn	116.0	0.0		81.0	10.0	NM_031497	O75286	Missense_Mutation	SNP	ENST00000522353.2	hg19	CCDS54915.1	.	.	.	.	.	.	.	.	.	.	g	16.27	3.075079	0.55646	.	.	ENSG00000255408	ENST00000522353;ENST00000532566	T;T	0.74002	-0.8;-0.8	4.79	4.79	0.61399	Cadherin (4);Cadherin-like (1);	0.000000	0.43579	U	0.000559	D	0.92721	0.7686	H	0.99391	4.545	0.46874	D	0.999235	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96159	0.9114	10	0.87932	D	0	.	18.1862	0.89793	0.0:0.0:1.0:0.0	.	378;378	Q9Y5H8-2;Q9Y5H8	.;PCDA3_HUMAN	N	378	ENSP00000429808:D378N;ENSP00000434086:D378N	ENSP00000429808:D378N	D	+	1	0	PCDHA3	140162098	1.000000	0.71417	0.656000	0.29637	0.011000	0.07611	9.869000	0.99810	2.378000	0.81104	0.467000	0.42956	GAC	.	.		0.493	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906		A	140181914	G	A	140181914	3	1	343	1	0	0	0	0	1	0	0	0	11534	1058	37	1	1134	1	PCDHA3	5	140181914	Missense_Mutation	SNP	G	TCGA-UB-A7MA-01A-11D-A33Q-10	61861794	140181914	40733346	21	47310										
ADAMTS2	9509	hgsc.bcm.edu	37	chr5	178562943	178562943	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	cgcacacagaggctgaaggcGtccttgtaggagcagcgcgt	15	11	0	2	rs370799965		TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr5:178562943G>A	ENST00000251582.7	-	13	2153	c.2052C>T	c.(2050-2052)gaC>gaT	p.D684D		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	684	Cys-rich.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|protein processing (GO:0016485)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.D684D(1)		breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(31)|ovary(1)|pancreas(3)|prostate(2)|skin(7)	72	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		GGCTGAAGGCGTCCTTGTAGG	0.637																																					p.D684D		Atlas-SNP	.											ADAMTS2,colon,carcinoma,0,3	ADAMTS2	190	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2052T						.	G		1,4405	2.1+/-5.4	0,1,2202	86	78	80		2052	-1.9	1	5		80	0,8600		0,0,4300	no	coding-synonymous	ADAMTS2	NM_014244.4		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		684/1212	178562943	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9509	exon13			GAAGGCGTCCTTG	AJ003125	CCDS4444.1, CCDS34311.1	5q23-q24	2008-07-18	2005-08-19		ENSG00000087116	ENSG00000087116		"ADAM metallopeptidases with thrombospondin type 1 motif"	218	protein-coding gene	gene with protein product	"procollagen I N-proteinase", "procollagen N-endopeptidase"	604539	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2"			10094461, 15373769	Standard	NM_014244		Approved	ADAMTS-3, hPCPNI, PCINP, ADAM-TS2, NPI	uc003mjw.3	O95450	OTTHUMG00000130915	ENST00000251582.7:c.2052C>T	chr5.hg19:g.178562943G>A		108.0	1.0		94.0	47.0	NM_014244		Silent	SNP	ENST00000251582.7	hg19	CCDS4444.1																																																																																			.	.		0.637	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244		A	178562943	G	A	178562943	2	1	343	1	0	0	0	0	0	0	0	1	265	1136	40	1		1	ADAMTS2	5	178562943	Silent	SNP	G	TCGA-UB-A7MA-01A-11D-A33Q-10	38381029	178562943	2352317	22	47311										
HIST1H1C	3006	hgsc.bcm.edu	37	chr6	26056402	26056402	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	gtgcccttgctcaccaggctCttgagaccaagtttgatacg	10	12	2	2			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr6:26056402C>G	ENST00000343677.2	-	1	297	c.255G>C	c.(253-255)aaG>aaC	p.K85N		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	85	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(4)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	34						TCACCAGGCTCTTGAGACCAA	0.542																																					p.K85N		Atlas-SNP	.											HIST1H1C,right_upper_lobe,carcinoma,0,1	HIST1H1C	80	.	0			c.G255C						.						114	118	117					6																	26056402		2203	4300	6503	SO:0001583	missense	3006	exon1			CAGGCTCTTGAGA	X57129	CCDS4577.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000187837	ENSG00000187837		"Histones / Replication-dependent"	4716	protein-coding gene	gene with protein product		142710	"H1 histone family, member 2", "histone 1, H1c"	H1F2		2759094, 12408966	Standard	NM_005319		Approved	H1.2, H1s-1, H1c	uc003nfw.3	P16403	OTTHUMG00000016140	ENST00000343677.2:c.255G>C	chr6.hg19:g.26056402C>G	ENSP00000339566:p.Lys85Asn	87.0	0.0		127.0	15.0	NM_005319	A8K4I2	Missense_Mutation	SNP	ENST00000343677.2	hg19	CCDS4577.1	.	.	.	.	.	.	.	.	.	.	C	14.92	2.680689	0.47886	.	.	ENSG00000187837	ENST00000343677	T	0.28255	1.62	5.63	2.93	0.34026	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.050070	0.85682	D	0.000000	T	0.50394	0.1613	M	0.91406	3.205	0.47214	D	0.999353	D	0.89917	1.0	D	0.87578	0.998	T	0.59941	-0.7359	10	0.87932	D	0	-6.336	10.4421	0.44472	0.0:0.7895:0.0:0.2105	.	85	P16403	H12_HUMAN	N	85	ENSP00000339566:K85N	ENSP00000339566:K85N	K	-	3	2	HIST1H1C	26164381	0.997000	0.39634	0.993000	0.49108	0.233000	0.25261	0.622000	0.24433	0.435000	0.26365	-0.136000	0.14681	AAG	.	.		0.542	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319		G	26056402	C	G	26056402	3	3	343	1	0	0	0	0	1	0	0	0	7133	912	32	4	390	4	HIST1H1C	6	26056402	Missense_Mutation	SNP	C	TCGA-UB-A7MA-01A-11D-A33Q-10		26056402	145058665	23	47312										
ZKSCAN3	80317	hgsc.bcm.edu	37	chr6	28333341	28333341	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	agaagctggtgaacaggaggGcaggctacaaagaaagcaga	15	6	0	4			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr6:28333341G>A	ENST00000377255.3	+	7	1193	c.896G>A	c.(895-897)gGc>gAc	p.G299D	ZKSCAN3_ENST00000341464.5_Missense_Mutation_p.G151D|ZKSCAN3_ENST00000252211.2_Missense_Mutation_p.G299D	NM_001242894.1	NP_001229823.1	Q9BRR0	ZKSC3_HUMAN	zinc finger with KRAB and SCAN domains 3	299					autophagy (GO:0006914)|lysosome organization (GO:0007040)|negative regulation of autophagy (GO:0010507)|negative regulation of cellular senescence (GO:2000773)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(4)|large_intestine(3)|lung(8)|pancreas(1)|skin(2)|stomach(2)|urinary_tract(1)	21						GAACAGGAGGGCAGGCTACAA	0.507																																					p.G299D		Atlas-SNP	.											.	ZKSCAN3	50	.	0			c.G896A						.						96	89	92					6																	28333341		2203	4300	6503	SO:0001583	missense	80317	exon6			AGGAGGGCAGGCT	U71601	CCDS4650.1, CCDS56408.1	6p22.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000189298		"Zinc fingers, C2H2-type", "-", "-", "-"	13853	protein-coding gene	gene with protein product		612791	"zinc finger protein 306", "zinc finger protein 309"	ZNF306, ZNF309		10520746, 22531714	Standard	NM_024493		Approved	Zfp47, ZF47, ZSCAN35	uc003nle.4	Q9BRR0	OTTHUMG00000014521	ENST00000377255.3:c.896G>A	chr6.hg19:g.28333341G>A	ENSP00000366465:p.Gly299Asp	103.0	0.0		148.0	56.0	NM_024493	B2R8W2|B3KVC0|H7BXX1|Q5VXH3|Q92972|Q9H4T3	Missense_Mutation	SNP	ENST00000377255.3	hg19	CCDS4650.1	.	.	.	.	.	.	.	.	.	.	.	14.20	2.463493	0.43736	.	.	ENSG00000189298	ENST00000252211;ENST00000341464;ENST00000377255	T;T;T	0.06218	3.43;3.33;3.43	3.26	0.255	0.15561	.	.	.	.	.	T	0.01222	0.0040	N	0.12831	0.26	0.22081	N	0.999379	B	0.22541	0.071	B	0.23716	0.048	T	0.46952	-0.9154	9	0.56958	D	0.05	.	8.0074	0.30334	0.0975:0.4585:0.444:0.0	.	299	Q9BRR0	ZKSC3_HUMAN	D	299;151;299	ENSP00000252211:G299D;ENSP00000341883:G151D;ENSP00000366465:G299D	ENSP00000252211:G299D	G	+	2	0	ZKSCAN3	28441320	0.000000	0.05858	0.965000	0.40720	0.906000	0.53458	-0.682000	0.05185	-0.088000	0.12506	0.555000	0.69702	GGC	.	.		0.507	ZKSCAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040189.3	NM_024493		A	28333341	G	A	28333341	3	1	343	1	0	0	0	0	1	0	0	0	17703	1203	42	3	914	3	ZKSCAN3	6	28333341	Missense_Mutation	SNP	G	TCGA-UB-A7MA-01A-11D-A33Q-10	2276939	28333341	142781726	24	47313										
MOCS1	4337	hgsc.bcm.edu	37	chr6	39895145	39895145	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	agctgtctgtgaggaaggcgGagaagggggccgcatgctcc	18	9	1	2			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr6:39895145G>A	ENST00000340692.5	-	2	176	c.173C>T	c.(172-174)tCc>tTc	p.S58F	MOCS1_ENST00000373188.2_Missense_Mutation_p.S58F|MOCS1_ENST00000373175.4_Missense_Mutation_p.S29F|MOCS1_ENST00000425303.2_Missense_Mutation_p.S58F|MOCS1_ENST00000308559.7_Missense_Mutation_p.S58F|MOCS1_ENST00000373195.3_Intron|MOCS1_ENST00000432280.2_Missense_Mutation_p.S29F|MOCS1_ENST00000373186.4_Missense_Mutation_p.S58F			Q9NZB8	MOCS1_HUMAN	molybdenum cofactor synthesis 1	58	Molybdenum cofactor biosynthesis protein A.				Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|molybdopterin synthase complex (GO:0019008)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|cyclic pyranopterin monophosphate synthase activity (GO:0061597)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	21	Ovarian(28;0.0355)|Colorectal(47;0.196)					GAGGAAGGCGGAGAAGGGGGC	0.652																																					p.S58F	NSCLC(84;861 1413 23785 24908 42279)|Melanoma(182;611 2047 9114 11847 26639)	Atlas-SNP	.											.	MOCS1	87	.	0			c.C173T						.						30	31	31					6																	39895145		2203	4299	6502	SO:0001583	missense	4337	exon1			AAGGCGGAGAAGG	AJ224328	CCDS4846.1, CCDS43460.1	6p21.2	2012-05-08			ENSG00000124615	ENSG00000124615			7190	protein-coding gene	gene with protein product		603707				9731530, 10053004	Standard	NM_001075098		Approved	MOCOD	uc003opb.3	Q9NZB8	OTTHUMG00000014656	ENST00000340692.5:c.173C>T	chr6.hg19:g.39895145G>A	ENSP00000344794:p.Ser58Phe	56.0	0.0		49.0	20.0	NM_005943	B3KPT7|B4DTP1|O14940|O14941|O75710|Q5J7W0|Q5TCE1|Q5TCE2|Q5TCE6|Q5TCE9|Q5TCF0|Q5TCF1|Q8N418|Q9NZB7|Q9UEM1	Missense_Mutation	SNP	ENST00000340692.5	hg19		.	.	.	.	.	.	.	.	.	.	G	25.7	4.668156	0.88348	.	.	ENSG00000124615	ENST00000373186;ENST00000308559;ENST00000373175;ENST00000373188;ENST00000340692;ENST00000425303;ENST00000432280	T;T;T	0.34859	1.34;1.35;1.35	5.44	5.44	0.79542	Aldolase-type TIM barrel (1);	0.000000	0.85682	D	0.000000	T	0.36524	0.0970	N	0.19112	0.55	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.79784	0.993;0.976;0.987;0.986	T	0.10706	-1.0618	9	.	.	.	-23.7002	19.2062	0.93730	0.0:0.0:1.0:0.0	.	58;58;58;58	Q9NZB8-5;Q9NZB8;Q9NZB8-8;Q9NZB8-6	.;MOCS1_HUMAN;.;.	F	58;58;29;58;58;58;29	ENSP00000309843:S58F;ENSP00000344794:S58F;ENSP00000416478:S58F	.	S	-	2	0	MOCS1	40003123	1.000000	0.71417	0.969000	0.41365	0.632000	0.37999	8.594000	0.90836	2.703000	0.92315	0.591000	0.81541	TCC	.	.		0.652	MOCS1-005	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000040476.2	NM_005943		A	39895145	G	A	39895145	3	1	343	1	0	0	0	0	1	0	0	0	9699	1174	41	3	1020	3	MOCS1	6	39895145	Missense_Mutation	SNP	G	TCGA-UB-A7MA-01A-11D-A33Q-10	11561804	39895145	131219922	25	47314										
TFAP2D	83741	hgsc.bcm.edu	37	chr6	50683121	50683121	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	gatccaccacggggagcccaCcgactttattaacctgcaca	8	15	0	0			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr6:50683121C>T	ENST00000008391.3	+	2	560	c.332C>T	c.(331-333)aCc>aTc	p.T111I		NM_172238.3	NP_758438.2			transcription factor AP-2 delta (activating enhancer binding protein 2 delta)											NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(26)|ovary(6)|pancreas(1)|prostate(5)|stomach(1)	60	Lung NSC(77;0.0334)					GGGGAGCCCACCGACTTTATT	0.632																																					p.T111I		Atlas-SNP	.											.	TFAP2D	144	.	0			c.C332T						.						106	98	100					6																	50683121		2203	4300	6503	SO:0001583	missense	83741	exon2			AGCCCACCGACTT	AY028376	CCDS4933.1	6p12.3	2008-02-05	2004-10-26	2004-10-27		ENSG00000008197			15581	protein-coding gene	gene with protein product		610161	"transcription factor AP-2 beta (activating enhancer-binding protein 2 beta)-like 1"	TFAP2BL1		11733187	Standard	NM_172238		Approved		uc003paf.3	Q7Z6R9		ENST00000008391.3:c.332C>T	chr6.hg19:g.50683121C>T	ENSP00000008391:p.Thr111Ile	113.0	0.0		91.0	55.0	NM_172238		Missense_Mutation	SNP	ENST00000008391.3	hg19	CCDS4933.1	.	.	.	.	.	.	.	.	.	.	C	13.25	2.180237	0.38511	.	.	ENSG00000008197	ENST00000008391	D	0.97232	-4.3	5.21	5.21	0.72293	.	0.163968	0.56097	D	0.000039	D	0.88716	0.6512	N	0.08118	0	0.48135	D	0.99959	B	0.19583	0.037	B	0.17098	0.017	D	0.85264	0.1052	10	0.39692	T	0.17	-19.3103	15.4919	0.75611	0.0:0.8614:0.1386:0.0	.	111	Q7Z6R9	AP2D_HUMAN	I	111	ENSP00000008391:T111I	ENSP00000008391:T111I	T	+	2	0	TFAP2D	50791080	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.833000	0.69349	2.590000	0.87494	0.655000	0.94253	ACC	.	.		0.632	TFAP2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040881.1	NM_172238		T	50683121	C	T	50683121	3	4	343	1	0	0	0	0	1	0	0	0	15805	507	18	3	338	3	TFAP2D	6	50683121	Missense_Mutation	SNP	C	TCGA-UB-A7MA-01A-11D-A33Q-10	10787976	50683121	120431946	26	47315										
PDE10A	10846	hgsc.bcm.edu	37	chr6	165827145	165827145	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	ggcatgcacaggatgttccgCgtggtgtagcctgtgtacaa	14	9	0	0			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr6:165827145C>T	ENST00000366882.1	-	14	1246	c.1092G>A	c.(1090-1092)acG>acA	p.T364T	PDE10A_ENST00000354448.4_Silent_p.T364T|PDE10A_ENST00000539869.2_Silent_p.T374T			Q9Y233	PDE10_HUMAN	phosphodiesterase 10A	364	GAF 2.				blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of protein kinase A signaling (GO:0010738)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|metal ion binding (GO:0046872)			breast(4)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(39)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	71		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Caffeine(DB00201)|Dipyridamole(DB00975)|Papaverine(DB01113)|Tofisopam(DB08811)|Triflusal(DB08814)	GGATGTTCCGCGTGGTGTAGC	0.483																																					p.T374T	Esophageal Squamous(22;308 615 5753 12038 40624)	Atlas-SNP	.											.	PDE10A	154	.	0			c.G1122A						.						88	71	76					6																	165827145		2203	4300	6503	SO:0001819	synonymous_variant	10846	exon13			GTTCCGCGTGGTG	AB020593	CCDS47513.1	6q26	2008-03-18			ENSG00000112541	ENSG00000112541	3.1.4.17	"Phosphodiesterases"	8772	protein-coding gene	gene with protein product		610652				10373451	Standard	NM_001130690		Approved		uc003quo.3	Q9Y233	OTTHUMG00000015986	ENST00000366882.1:c.1092G>A	chr6.hg19:g.165827145C>T		125.0	0.0		90.0	57.0	NM_001130690	Q6FHX1|Q9HCP9|Q9NTV4|Q9ULW9|Q9Y5T1	Silent	SNP	ENST00000366882.1	hg19																																																																																				.	.		0.483	PDE10A-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000043031.1			T	165827145	C	T	165827145	2	4	343	1	0	0	0	0	0	0	0	1	11639	755	27	1		1	PDE10A	6	165827145	Silent	SNP	C	TCGA-UB-A7MA-01A-11D-A33Q-10	115144024	165827145	5287922	27	47316										
ABCB5	340273	hgsc.bcm.edu	37	chr7	20738174	20738174	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	tctttgcaaaaattataaccGtaagtaaaataaatttgcta	4	5	1	0			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr7:20738174G>A	ENST00000404938.2	+	17	2806		c.e17+1		ABCB5_ENST00000258738.6_Splice_Site	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5						antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (GO:0002485)|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO:0002489)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|cell differentiation (GO:0030154)|compound eye corneal lens development (GO:0048058)|positive regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002591)|regulation of membrane potential (GO:0042391)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|efflux transmembrane transporter activity (GO:0015562)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(1)|pancreas(1)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)	77						AATTATAACCGTAAGTAAAAT	0.368																																					.		Atlas-SNP	.											.	ABCB5	357	.	0			c.2154+1G>A						.						46	45	45					7																	20738174		2202	4299	6501	SO:0001630	splice_region_variant	340273	exon17			ATAACCGTAAGTA	U66692	CCDS5371.1, CCDS55090.1, CCDS55091.1, CCDS55092.1	7p14	2012-03-14			ENSG00000004846	ENSG00000004846		"ATP binding cassette transporters / subfamily B"	46	protein-coding gene	gene with protein product	"P-glycoprotein ABCB5", "ATP-binding cassette protein"	611785				8894702, 12960149	Standard	NM_001163942		Approved	EST422562, ABCB5beta, ABCB5alpha	uc010kuh.3	Q2M3G0	OTTHUMG00000094789	ENST00000404938.2:c.2154+1G>A	chr7.hg19:g.20738174G>A		81.0	0.0		65.0	16.0	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Splice_Site	SNP	ENST00000404938.2	hg19	CCDS55090.1	.	.	.	.	.	.	.	.	.	.	G	15.84	2.953200	0.53293	.	.	ENSG00000004846	ENST00000404938;ENST00000258738	.	.	.	5.35	5.35	0.76521	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5882	0.84745	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ABCB5	20704699	1.000000	0.71417	1.000000	0.80357	0.582000	0.36321	3.288000	0.51739	2.777000	0.95525	0.591000	0.81541	.	.	.		0.368	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559	Intron	A	20738174	G	A	20738174	5	1	343	1	0	0	0	0	0	0	1	0	44	1159	40	1	2258	1	ABCB5	7	20738174	Splice_Site	SNP	G	TCGA-UB-A7MA-01A-11D-A33Q-10		20738174	138400489	28	47317										
TEX15	56154	hgsc.bcm.edu	37	chr8	30705184	30705184	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	aacagattgtgatcctgaccCctatcttcaacataagcagt	6	11	2	3			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr8:30705184C>A	ENST00000256246.2	-	1	1424	c.1350G>T	c.(1348-1350)agG>agT	p.R450S	TEX15_ENST00000523186.1_5'Flank	NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	450					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)					NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		GATCCTGACCCCTATCTTCAA	0.333																																					p.R450S		Atlas-SNP	.											.	TEX15	350	.	0			c.G1350T						.						178	176	177					8																	30705184		2203	4299	6502	SO:0001583	missense	56154	exon1			CTGACCCCTATCT	AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"cancer/testis antigen 42"	605795	"testis expressed sequence 15"			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.1350G>T	chr8.hg19:g.30705184C>A	ENSP00000256246:p.Arg450Ser	101.0	0.0		64.0	47.0	NM_031271		Missense_Mutation	SNP	ENST00000256246.2	hg19	CCDS6080.1	.	.	.	.	.	.	.	.	.	.	C	11.52	1.664268	0.29604	.	.	ENSG00000133863	ENST00000256246	T	0.10192	2.9	5.51	-4.84	0.03151	.	1.145370	0.06457	N	0.728725	T	0.04272	0.0118	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.11329	0.006	T	0.42732	-0.9434	10	0.87932	D	0	.	0.5054	0.00587	0.3815:0.1853:0.2462:0.187	.	450	Q9BXT5	TEX15_HUMAN	S	450	ENSP00000256246:R450S	ENSP00000256246:R450S	R	-	3	2	TEX15	30824726	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.172000	0.09868	-0.498000	0.06632	-0.300000	0.09419	AGG	.	.		0.333	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			A	30705184	C	A	30705184	3	1	343	1	0	0	0	0	1	0	0	0	15794	622	22	3	7035	3	TEX15	8	30705184	Missense_Mutation	SNP	C	TCGA-UB-A7MA-01A-11D-A33Q-10		30705184	115658838	29	47318										
C9orf125	84302	hgsc.bcm.edu	37	chr9	104238798	104238798	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	cagggatgactccaggcaatAgacatagtcctgcttctctt	9	11	1	2			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr9:104238798A>C	ENST00000374851.1	-	4	1724	c.577T>G	c.(577-579)Tat>Gat	p.Y193D	RP11-490D19.6_ENST00000424154.1_RNA|TMEM246_ENST00000374848.3_Missense_Mutation_p.Y193D|TMEM246_ENST00000374847.1_Missense_Mutation_p.Y193D|RP11-490D19.6_ENST00000450109.1_RNA|RP11-490D19.6_ENST00000431507.1_RNA|RP11-490D19.6_ENST00000425734.1_RNA			Q9BRR3	TM246_HUMAN	transmembrane protein 246	193						integral component of membrane (GO:0016021)											TCCAGGCAATAGACATAGTCC	0.502																																					p.Y193D		Atlas-SNP	.											.	.	.	.	0			c.T577G						.						100	80	87					9																	104238798		2203	4300	6503	SO:0001583	missense	84302	exon2			GGCAATAGACATA	BC006115	CCDS6757.1	9q31.1	2012-04-02	2012-04-02	2012-04-02	ENSG00000165152	ENSG00000165152			28180	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 125"	C9orf125		12477932	Standard	NM_032342		Approved	MGC12992	uc004bbm.3	Q9BRR3	OTTHUMG00000020381	ENST00000374851.1:c.577T>G	chr9.hg19:g.104238798A>C	ENSP00000363984:p.Tyr193Asp	94.0	0.0		81.0	19.0	NM_032342	Q49AQ4	Missense_Mutation	SNP	ENST00000374851.1	hg19	CCDS6757.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.211481	0.79240	.	.	ENSG00000165152	ENST00000374848;ENST00000374847;ENST00000374851	.	.	.	5.95	5.95	0.96441	.	0.059762	0.64402	D	0.000002	T	0.62085	0.2399	L	0.43152	1.355	0.48452	D	0.999653	D	0.60160	0.987	P	0.52217	0.693	T	0.65849	-0.6068	9	0.87932	D	0	-11.3887	15.587	0.76491	1.0:0.0:0.0:0.0	.	193	Q9BRR3	CI125_HUMAN	D	193	.	ENSP00000363980:Y193D	Y	-	1	0	C9orf125	103278619	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.005000	0.93587	2.266000	0.75297	0.528000	0.53228	TAT	.	.		0.502	TMEM246-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053444.1	NM_032342		C	104238798	A	C	104238798	3	2	343	1	0	0	0	0	1	0	0	0	2456	420	15	5	638	5	C9orf125	9	104238798	Missense_Mutation	SNP	A	TCGA-UB-A7MA-01A-11D-A33Q-10		104238798	36974633	30	47319										
LRIT1	26103	hgsc.bcm.edu	37	chr10	85994095	85994095	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	ccaaaagatgaaccaggtcaTagagtcggcagtcacatgcc	10	11	2	3			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr10:85994095T>C	ENST00000372105.3	-	3	650	c.629A>G	c.(628-630)tAt>tGt	p.Y210C		NM_015613.2	NP_056428.1	Q9P2V4	LRIT1_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 1	210	LRRCT.					integral component of endoplasmic reticulum membrane (GO:0030176)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|skin(1)	23						AACCAGGTCATAGAGTCGGCA	0.537																																					p.Y210C		Atlas-SNP	.											.	LRIT1	73	.	0			c.A629G						.						84	86	85					10																	85994095		2203	4300	6503	SO:0001583	missense	26103	exon3			AGGTCATAGAGTC	AB031547	CCDS7373.1	10q23	2013-02-11	2007-06-19	2007-06-19	ENSG00000148602	ENSG00000148602		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	23404	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 9"		"leucine rich repeat containing 21"	LRRC21		10777785	Standard	NM_015613		Approved	PAL, DKFZP434K091, FIGLER9	uc001kcz.1	Q9P2V4	OTTHUMG00000018632	ENST00000372105.3:c.629A>G	chr10.hg19:g.85994095T>C	ENSP00000361177:p.Tyr210Cys	163.0	0.0		168.0	46.0	NM_015613	Q0QD41|Q9Y4N7	Missense_Mutation	SNP	ENST00000372105.3	hg19	CCDS7373.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.983868	0.74474	.	.	ENSG00000148602	ENST00000372105	T	0.52754	0.65	5.91	5.91	0.95273	Cysteine-rich flanking region, C-terminal (1);	0.123192	0.56097	D	0.000022	T	0.62829	0.2460	M	0.69248	2.105	0.80722	D	1	D	0.69078	0.997	P	0.58928	0.848	T	0.63024	-0.6729	10	0.42905	T	0.14	.	15.3309	0.74208	0.0:0.0:0.0:1.0	.	210	Q9P2V4	LRIT1_HUMAN	C	210	ENSP00000361177:Y210C	ENSP00000361177:Y210C	Y	-	2	0	LRIT1	85984075	1.000000	0.71417	0.999000	0.59377	0.948000	0.59901	3.167000	0.50793	2.254000	0.74563	0.533000	0.62120	TAT	.	.		0.537	LRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049109.1	NM_015613		C	85994095	T	C	85994095	3	2	343	1	0	0	0	0	1	0	0	0	8956	1406	49	2	1250	2	LRIT1	10	85994095	Missense_Mutation	SNP	T	TCGA-UB-A7MA-01A-11D-A33Q-10		85994095	49540652	31	47320										
GLUD1	2746	hgsc.bcm.edu	37	chr10	88818994	88818994	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	attcttcagccactcaaagtAagatactgtcactcctccag	5	13	4	1			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr10:88818994A>G	ENST00000277865.4	-	10	1411	c.1315T>C	c.(1315-1317)Tac>Cac	p.Y439H	GLUD1_ENST00000544149.1_Missense_Mutation_p.Y306H|GLUD1_ENST00000537649.1_Missense_Mutation_p.Y272H|GLUD1_ENST00000465164.1_5'Flank	NM_005271.3	NP_005262.1	P00367	DHE3_HUMAN	glutamate dehydrogenase 1	439					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate biosynthetic process (GO:0006537)|glutamate catabolic process (GO:0006538)|glutamine metabolic process (GO:0006541)|positive regulation of insulin secretion (GO:0032024)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)|tricarboxylic acid metabolic process (GO:0072350)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|glutamate dehydrogenase (NAD+) activity (GO:0004352)|glutamate dehydrogenase [NAD(P)+] activity (GO:0004353)|GTP binding (GO:0005525)|identical protein binding (GO:0042802)|leucine binding (GO:0070728)|NAD+ binding (GO:0070403)			endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(11)|prostate(1)	22					Hexachlorophene(DB00756)	CACTCAAAGTAAGATACTGTC	0.373																																					p.Y439H		Atlas-SNP	.											.	GLUD1	30	.	0			c.T1315C						.						184	179	181					10																	88818994		2203	4299	6502	SO:0001583	missense	2746	exon10			CAAAGTAAGATAC	M20867	CCDS7382.1	10q23.2	2010-03-17			ENSG00000148672	ENSG00000148672	1.4.1.3		4335	protein-coding gene	gene with protein product		138130		GLUD		2757358	Standard	NM_005271		Approved	GDH	uc001keh.3	P00367	OTTHUMG00000018666	ENST00000277865.4:c.1315T>C	chr10.hg19:g.88818994A>G	ENSP00000277865:p.Tyr439His	165.0	0.0		141.0	15.0	NM_005271	B3KV55|B4DGN5|Q5TBU3	Missense_Mutation	SNP	ENST00000277865.4	hg19	CCDS7382.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.644235	0.87859	.	.	ENSG00000148672	ENST00000277865;ENST00000394415;ENST00000537649;ENST00000535802;ENST00000513510;ENST00000544149	D;D;D	0.96830	-4.14;-4.14;-4.14	5.66	5.66	0.87406	Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal (2);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.98548	0.9515	M	0.92317	3.295	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.99719	1.1009	10	0.87932	D	0	-9.0102	16.3294	0.83004	1.0:0.0:0.0:0.0	.	306;439	B4DGN5;P00367	.;DHE3_HUMAN	H	439;396;272;138;371;306	ENSP00000277865:Y439H;ENSP00000439291:Y272H;ENSP00000444732:Y306H	ENSP00000277865:Y439H	Y	-	1	0	GLUD1	88808974	1.000000	0.71417	0.996000	0.52242	0.982000	0.71751	8.957000	0.93082	2.317000	0.78254	0.524000	0.50904	TAC	.	.		0.373	GLUD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049188.1	NM_005271		G	88818994	A	G	88818994	3	3	343	1	0	0	0	0	1	0	0	0	6484	362	13	2	377	2	GLUD1	10	88818994	Missense_Mutation	SNP	A	TCGA-UB-A7MA-01A-11D-A33Q-10	2824899	88818994	46715753	32	47321										
SORCS3	22986	hgsc.bcm.edu	37	chr10	106976760	106976760	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	ttgctgtgtcctacgcaaacTtcagccccatcgaggacggc	10	14	1	0			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr10:106976760T>G	ENST00000369701.3	+	19	2841	c.2614T>G	c.(2614-2616)Ttc>Gtc	p.F872V	SORCS3_ENST00000369699.4_Missense_Mutation_p.F158V	NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	872	PKD. {ECO:0000255|PROSITE- ProRule:PRU00151}.				learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		CTACGCAAACTTCAGCCCCAT	0.512																																					p.F872V	NSCLC(116;1497 1690 7108 13108 14106)	Atlas-SNP	.											.	SORCS3	282	.	0			c.T2614G						.						164	124	137					10																	106976760		2203	4300	6503	SO:0001583	missense	22986	exon19			GCAAACTTCAGCC	AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.2614T>G	chr10.hg19:g.106976760T>G	ENSP00000358715:p.Phe872Val	82.0	0.0		104.0	19.0	NM_014978	Q5VXF9|Q9NQJ2	Missense_Mutation	SNP	ENST00000369701.3	hg19	CCDS7558.1	.	.	.	.	.	.	.	.	.	.	T	15.42	2.828444	0.50845	.	.	ENSG00000156395	ENST00000369701;ENST00000369699	T;T	0.60299	0.2;0.2	5.87	5.87	0.94306	PKD domain (4);	0.058143	0.64402	D	0.000001	T	0.44286	0.1286	N	0.19112	0.55	0.50039	D	0.999841	B	0.14012	0.009	B	0.20577	0.03	T	0.31779	-0.9931	9	.	.	.	.	16.5764	0.84681	0.0:0.0:0.0:1.0	.	872	Q9UPU3	SORC3_HUMAN	V	872;158	ENSP00000358715:F872V;ENSP00000358713:F158V	.	F	+	1	0	SORCS3	106966750	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	2.669000	0.46825	2.371000	0.80710	0.533000	0.62120	TTC	.	.		0.512	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978		G	106976760	T	G	106976760	3	3	343	1	0	0	0	0	1	0	0	0	14947	1609	56	5	2688	5	SORCS3	10	106976760	Missense_Mutation	SNP	T	TCGA-UB-A7MA-01A-11D-A33Q-10	18157766	106976760	28557987	33	47322										
SORCS1	114815	hgsc.bcm.edu	37	chr10	108412294	108412294	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	cgccatcagtgcaattattgGaaaccaccttcctgtaccta	6	13	1	0			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr10:108412294G>A	ENST00000263054.6	-	18	2328	c.2321C>T	c.(2320-2322)tCc>tTc	p.S774F	SORCS1_ENST00000369698.1_Missense_Mutation_p.S309F|SORCS1_ENST00000344440.6_Missense_Mutation_p.S774F	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	774					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		GCAATTATTGGAAACCACCTT	0.468																																					p.S774F		Atlas-SNP	.											.	SORCS1	534	.	0			c.C2321T						.						112	106	108					10																	108412294		2203	4300	6503	SO:0001583	missense	114815	exon18			TTATTGGAAACCA	AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.2321C>T	chr10.hg19:g.108412294G>A	ENSP00000263054:p.Ser774Phe	84.0	0.0		100.0	49.0	NM_001206572	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	hg19	CCDS7559.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.482881	0.84747	.	.	ENSG00000108018	ENST00000369698;ENST00000263054;ENST00000344440	T;T;T	0.67523	-0.27;-0.27;-0.27	5.74	5.74	0.90152	VPS10 (1);PKD domain (1);	0.000000	0.85682	D	0.000000	T	0.81735	0.4885	M	0.75777	2.31	0.45979	D	0.998792	D;D;D;D;D	0.58620	0.972;0.983;0.983;0.972;0.983	P;D;D;P;D	0.65684	0.825;0.937;0.915;0.866;0.937	T	0.80571	-0.1323	9	.	.	.	-16.8758	19.9145	0.97053	0.0:0.0:1.0:0.0	.	774;774;774;774;774	A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2	.;.;.;SORC1_HUMAN;.	F	309;774;774	ENSP00000358712:S309F;ENSP00000263054:S774F;ENSP00000345964:S774F	.	S	-	2	0	SORCS1	108402284	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.448000	0.80631	2.709000	0.92574	0.655000	0.94253	TCC	.	.		0.468	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918		A	108412294	G	A	108412294	3	1	343	1	0	0	0	0	1	0	0	0	14945	1174	41	3	1455	3	SORCS1	10	108412294	Missense_Mutation	SNP	G	TCGA-UB-A7MA-01A-11D-A33Q-10	1435534	108412294	27122453	34	47323										
ADAM12	8038	hgsc.bcm.edu	37	chr10	127797193	127797193	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	gattagcaatctctattaatCgctgcttaactttttccaga	5	9	1	1			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr10:127797193C>T	ENST00000368679.4	-	8	1028	c.719G>A	c.(718-720)cGa>cAa	p.R240Q	ADAM12_ENST00000368676.4_Missense_Mutation_p.R240Q	NM_003474.4	NP_003465.3	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12	240	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell adhesion (GO:0007155)|epidermal growth factor receptor signaling pathway (GO:0007173)|myoblast fusion (GO:0007520)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(7)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)		CTCTATTAATCGCTGCTTAAC	0.353																																					p.R240Q		Atlas-SNP	.											ADAM12_ENST00000368679,NS,carcinoma,0,3	ADAM12	388	.	0			c.G719A						.						194	172	179					10																	127797193		2203	4300	6503	SO:0001583	missense	8038	exon8			ATTAATCGCTGCT	AF023476	CCDS7653.1, CCDS7654.1	10q26	2008-07-29	2008-07-29		ENSG00000148848	ENSG00000148848		"ADAM metallopeptidase domain containing"	190	protein-coding gene	gene with protein product	"meltrin alpha"	602714	"a disintegrin and metalloproteinase domain 12 (meltrin alpha)"			9417060, 18342566	Standard	NM_003474		Approved	MCMPMltna, MLTN	uc001ljk.2	O43184	OTTHUMG00000019243	ENST00000368679.4:c.719G>A	chr10.hg19:g.127797193C>T	ENSP00000357668:p.Arg240Gln	122.0	0.0		112.0	12.0	NM_021641	O60470|Q5JRP0|Q5JRP1|Q6P9E3|Q6UWB0	Missense_Mutation	SNP	ENST00000368679.4	hg19	CCDS7653.1	.	.	.	.	.	.	.	.	.	.	C	35	5.544275	0.96488	.	.	ENSG00000148848	ENST00000368679;ENST00000368676;ENST00000448723	D;D;T	0.87256	-2.23;-2.23;-0.14	5.17	5.17	0.71159	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.64402	D	0.000001	D	0.95239	0.8456	M	0.92077	3.27	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.998;0.998;0.998;1.0	D	0.95922	0.8931	10	0.72032	D	0.01	.	18.8656	0.92290	0.0:1.0:0.0:0.0	.	237;240;237;240	O43184-3;O43184-2;O43184-4;O43184	.;.;.;ADA12_HUMAN	Q	240;240;237	ENSP00000357668:R240Q;ENSP00000357665:R240Q;ENSP00000391268:R237Q	ENSP00000357665:R240Q	R	-	2	0	ADAM12	127787183	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.651000	0.83577	2.678000	0.91216	0.655000	0.94253	CGA	.	.		0.353	ADAM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050961.1			T	127797193	C	T	127797193	3	4	343	1	0	0	0	0	1	0	0	0	236	884	31	1	2182	1	ADAM12	10	127797193	Missense_Mutation	SNP	C	TCGA-UB-A7MA-01A-11D-A33Q-10	19384899	127797193	7737554	35	47324										
BDNF	627	hgsc.bcm.edu	37	chr11	27679589	27679589	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	gaagtattgcttcagttggcCttttgatacagggacctttt	10	7	1	1			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr11:27679589C>G	ENST00000525528.1	-	1	1616	c.523G>C	c.(523-525)Ggc>Cgc	p.G175R	BDNF-AS_ENST00000502161.2_RNA|BDNF-AS_ENST00000499008.3_RNA|BDNF-AS_ENST00000532965.1_RNA|BDNF_ENST00000439476.2_Missense_Mutation_p.G175R|BDNF_ENST00000395983.3_Missense_Mutation_p.G175R|BDNF_ENST00000533131.1_Missense_Mutation_p.G175R|BDNF-AS_ENST00000501176.2_RNA|BDNF_ENST00000532997.1_Missense_Mutation_p.G175R|BDNF_ENST00000356660.4_Missense_Mutation_p.G175R|BDNF_ENST00000525950.1_Missense_Mutation_p.G175R|BDNF_ENST00000533246.1_Missense_Mutation_p.G175R|BDNF-AS_ENST00000500662.2_RNA|BDNF_ENST00000314915.6_Missense_Mutation_p.G183R|BDNF-AS_ENST00000530313.1_RNA|BDNF_ENST00000395981.3_Missense_Mutation_p.G175R|BDNF_ENST00000395986.2_Missense_Mutation_p.G190R|BDNF_ENST00000418212.1_Missense_Mutation_p.G175R|BDNF_ENST00000584049.1_5'UTR|BDNF-AS_ENST00000499568.2_RNA|BDNF_ENST00000395980.2_Missense_Mutation_p.G175R|BDNF_ENST00000420794.1_Missense_Mutation_p.G175R|BDNF_ENST00000395978.3_Missense_Mutation_p.G175R|BDNF_ENST00000438929.1_Missense_Mutation_p.G257R|BDNF_ENST00000530861.1_Missense_Mutation_p.G175R|BDNF-AS_ENST00000530686.1_RNA	NM_170735.5	NP_733931.1	P23560	BDNF_HUMAN	brain-derived neurotrophic factor	175					axon extension (GO:0048675)|axon guidance (GO:0007411)|axon target recognition (GO:0007412)|behavioral fear response (GO:0001662)|chronic inflammatory response (GO:0002544)|circadian rhythm (GO:0007623)|dendrite development (GO:0016358)|dendrite extension (GO:0097484)|feeding behavior (GO:0007631)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glutamate secretion (GO:0014047)|inner ear development (GO:0048839)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|nerve development (GO:0021675)|nervous system development (GO:0007399)|neuron recognition (GO:0008038)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of synapse assembly (GO:0051965)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of retinal cell programmed cell death (GO:0046668)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|response to anesthetic (GO:0072347)|response to fluoxetine (GO:0014076)|response to hormone (GO:0009725)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to vitamin A (GO:0033189)|taste bud development (GO:0061193)|ureteric bud development (GO:0001657)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)|synaptic vesicle (GO:0008021)	growth factor activity (GO:0008083)			breast(1)|large_intestine(3)|lung(2)	6						TTCAGTTGGCCTTTTGATACA	0.498																																					p.G257R		Atlas-SNP	.											.	BDNF	63	.	0			c.G769C						.						216	212	213					11																	27679589		2202	4299	6501	SO:0001583	missense	627	exon3			GTTGGCCTTTTGA	AB038670	CCDS7865.1, CCDS7866.1, CCDS44558.1, CCDS41628.1	11p14.1	2014-01-30			ENSG00000176697	ENSG00000176697		"Endogenous ligands"	1033	protein-coding gene	gene with protein product	"neurotrophin"	113505				2236018, 1889806, 17942328, 17493809	Standard	NM_170731		Approved		uc009yje.3	P23560	OTTHUMG00000178797	ENST00000525528.1:c.523G>C	chr11.hg19:g.27679589C>G	ENSP00000437138:p.Gly175Arg	95.0	0.0		63.0	18.0	NM_001143810	A7LA85|A7LA92|D3DQZ2|Q598Q1|Q6DN19|Q6YNR2|Q6YNR3|Q9BYY7|Q9UC24	Missense_Mutation	SNP	ENST00000525528.1	hg19	CCDS7866.1	.	.	.	.	.	.	.	.	.	.	C	15.83	2.948306	0.53186	.	.	ENSG00000176697	ENST00000439476;ENST00000525528;ENST00000395986;ENST00000533131;ENST00000356660;ENST00000418212;ENST00000533246;ENST00000530861;ENST00000395983;ENST00000438929;ENST00000395980;ENST00000532997;ENST00000395981;ENST00000395978;ENST00000525950;ENST00000314915;ENST00000420794	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26;-0.26;-0.26;-0.26;-0.26;-0.26;-0.26;-0.26;-0.26;-0.26;-0.26;-0.26;-0.26;-0.26	6.08	6.08	0.98989	Nerve growth factor-related (4);	0.000000	0.85682	D	0.000000	T	0.82213	0.4988	M	0.65498	2.005	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;0.991;1.0	D;D;D;P;D	0.97110	1.0;0.992;0.998;0.698;0.998	T	0.82043	-0.0653	10	0.87932	D	0	-11.5486	20.6721	0.99693	0.0:1.0:0.0:0.0	.	204;257;183;175;190	P23560-5;P23560-4;P23560-2;P23560;P23560-3	.;.;.;BDNF_HUMAN;.	R	175;175;190;175;175;175;175;175;175;257;175;175;175;175;175;183;175	ENSP00000389345:G175R;ENSP00000437138:G175R;ENSP00000379309:G190R;ENSP00000432727:G175R;ENSP00000349084:G175R;ENSP00000400502:G175R;ENSP00000432376:G175R;ENSP00000435564:G175R;ENSP00000379307:G175R;ENSP00000414303:G257R;ENSP00000379304:G175R;ENSP00000435805:G175R;ENSP00000379305:G175R;ENSP00000379302:G175R;ENSP00000432035:G175R;ENSP00000320002:G183R;ENSP00000389564:G175R	ENSP00000320002:G183R	G	-	1	0	BDNF	27636165	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.818000	0.86416	2.894000	0.99253	0.591000	0.81541	GGC	.	.		0.498	BDNF-016	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388135.1	NM_170735		G	27679589	C	G	27679589	3	3	343	1	0	0	0	0	1	0	0	0	1394	681	24	4	224	4	BDNF	11	27679589	Missense_Mutation	SNP	C	TCGA-UB-A7MA-01A-11D-A33Q-10		27679589	107326927	36	47325										
MRPL21	219927	hgsc.bcm.edu	37	chr11	68658837	68658837	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	aatctcaatgctgtttatccGgaggacagtctgcggggtcg	13	9	2	0			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr11:68658837G>T	ENST00000362034.2	-	7	589	c.580C>A	c.(580-582)Cgg>Agg	p.R194R	MRPL21_ENST00000450904.2_Silent_p.R109R	NM_181514.1|NM_181515.1	NP_852615.1|NP_852616.1	Q7Z2W9	RM21_HUMAN	mitochondrial ribosomal protein L21	194					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			large_intestine(1)|lung(6)|prostate(1)	8			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			CTGTTTATCCGGAGGACAGTC	0.473																																					p.R194R		Atlas-SNP	.											.	MRPL21	13	.	0			c.C580A						.						198	195	196					11																	68658837		2200	4294	6494	SO:0001819	synonymous_variant	219927	exon7			TTATCCGGAGGAC	AK096756	CCDS8186.1, CCDS44662.1	11q13.3	2012-09-13			ENSG00000197345	ENSG00000197345		"Mitochondrial ribosomal proteins / large subunits"	14479	protein-coding gene	gene with protein product		611834				11551941	Standard	NM_181514		Approved		uc001ooi.3	Q7Z2W9	OTTHUMG00000167893	ENST00000362034.2:c.580C>A	chr11.hg19:g.68658837G>T		88.0	0.0		47.0	12.0	NM_181514	A6NKU0|C9JPR2	Silent	SNP	ENST00000362034.2	hg19	CCDS8186.1																																																																																			.	.		0.473	MRPL21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396856.1	NM_181512		T	68658837	G	T	68658837	2	4	343	1	0	0	0	0	0	0	0	1	9796	1115	39	1		1	MRPL21	11	68658837	Silent	SNP	G	TCGA-UB-A7MA-01A-11D-A33Q-10	40979248	68658837	66347679	37	47326										
GRAMD1B	57476	hgsc.bcm.edu	37	chr11	123474218	123474218	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	ccagtgatgacgaggactacGtgccccctgacgacgacttc	11	14	0	3			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr11:123474218G>A	ENST00000529750.1	+	8	1033	c.706G>A	c.(706-708)Gtg>Atg	p.V236M	GRAMD1B_ENST00000456860.2_Missense_Mutation_p.V243M|GRAMD1B_ENST00000322282.7_Missense_Mutation_p.V236M	NM_020716.1	NP_065767.1	Q3KR37	GRM1B_HUMAN	GRAM domain containing 1B	236						integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394)		CGAGGACTACGTGCCCCCTGA	0.597																																					p.V236M		Atlas-SNP	.											.	GRAMD1B	122	.	0			c.G706A						.						84	79	80					11																	123474218		2004	4179	6183	SO:0001583	missense	57476	exon8			GACTACGTGCCCC	AB033027	CCDS53720.1, CCDS66253.1, CCDS66254.1	11q24.1	2005-11-02				ENSG00000023171			29214	protein-coding gene	gene with protein product						10574462	Standard	NM_001286564		Approved	KIAA1201	uc001pyx.2	Q3KR37		ENST00000529750.1:c.706G>A	chr11.hg19:g.123474218G>A	ENSP00000436500:p.Val236Met	101.0	0.0		59.0	11.0	NM_020716	Q6UW85|Q9ULL9	Missense_Mutation	SNP	ENST00000529750.1	hg19	CCDS53720.1	.	.	.	.	.	.	.	.	.	.	G	31	5.078155	0.94000	.	.	ENSG00000023171	ENST00000539133;ENST00000456860;ENST00000322282;ENST00000529750;ENST00000529432;ENST00000534764	T;T;T;T;T	0.36699	1.63;1.65;1.65;1.67;1.24	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.58250	0.2109	M	0.65498	2.005	0.80722	D	1	D;D;D;D	0.71674	0.998;0.998;0.997;0.997	P;D;P;P	0.67231	0.892;0.95;0.743;0.836	T	0.55140	-0.8187	10	0.35671	T	0.21	.	18.8312	0.92141	0.0:0.0:1.0:0.0	.	196;243;236;243	B7Z4N9;F5H572;Q3KR37;E7EPH8	.;.;GRM1B_HUMAN;.	M	243;243;236;236;196;232	ENSP00000402457:V243M;ENSP00000325628:V236M;ENSP00000436500:V236M;ENSP00000432987:V196M;ENSP00000434214:V232M	ENSP00000325628:V236M	V	+	1	0	GRAMD1B	122979428	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	9.617000	0.98361	2.436000	0.82500	0.491000	0.48974	GTG	.	.		0.597	GRAMD1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387404.2	XM_370660		A	123474218	G	A	123474218	3	1	343	1	0	0	0	0	1	0	0	0	6757	1145	40	1	736	1	GRAMD1B	11	123474218	Missense_Mutation	SNP	G	TCGA-UB-A7MA-01A-11D-A33Q-10	54815381	123474218	11532298	38	47327										
JAM3	83700	hgsc.bcm.edu	37	chr11	134014848	134014848	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	ccagagccaatcccagatttCgcaattcttctttccactta	4	14	2	2	rs549604639		TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr11:134014848C>T	ENST00000299106.4	+	5	730	c.571C>T	c.(571-573)Cgc>Tgc	p.R191C	JAM3_ENST00000529443.2_Missense_Mutation_p.R236C|JAM3_ENST00000441717.3_Missense_Mutation_p.R140C|JAM3_ENST00000524969.1_3'UTR			Q9BX67	JAM3_HUMAN	junctional adhesion molecule 3	191	Ig-like C2-type.				adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|establishment of cell polarity (GO:0030010)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|myelination (GO:0042552)|myeloid progenitor cell differentiation (GO:0002318)|neutrophil homeostasis (GO:0001780)|regulation of actin cytoskeleton organization by cell-cell adhesion (GO:0090138)|regulation of neutrophil chemotaxis (GO:0090022)|spermatid development (GO:0007286)|transmission of nerve impulse (GO:0019226)	cell-cell contact zone (GO:0044291)|desmosome (GO:0030057)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|paranodal junction (GO:0033010)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	integrin binding (GO:0005178)	p.R236C(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)	10	all_hematologic(175;0.127)	all_cancers(12;1.06e-21)|all_epithelial(12;3.37e-16)|all_lung(97;7.03e-06)|Lung NSC(97;1.67e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0506)|Esophageal squamous(93;0.0566)		Epithelial(10;1.55e-09)|BRCA - Breast invasive adenocarcinoma(10;1.35e-08)|all cancers(11;2.81e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00402)|Lung(977;0.245)		TCCCAGATTTCGCAATTCTTC	0.502																																					p.R191C		Atlas-SNP	.											JAM3,NS,carcinoma,-1,1	JAM3	41	.	1	Substitution - Missense(1)	endometrium(1)	c.C571T						.						128	108	115					11																	134014848		2201	4297	6498	SO:0001583	missense	83700	exon5			AGATTTCGCAATT	AF356518	CCDS8494.1, CCDS55799.1, CCDS8494.2	11q25	2013-01-29			ENSG00000166086	ENSG00000166086		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15532	protein-coding gene	gene with protein product		606871					Standard	NM_032801		Approved	JAM-C, JAMC	uc001qhb.3	Q9BX67	OTTHUMG00000167130	ENST00000299106.4:c.571C>T	chr11.hg19:g.134014848C>T	ENSP00000299106:p.Arg191Cys	200.0	0.0		71.0	22.0	NM_032801	B3KWG9|Q8WWL8|Q96FL1	Missense_Mutation	SNP	ENST00000299106.4	hg19	CCDS8494.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.41|12.41	1.929059|1.929059	0.34002|0.34002	.|.	.|.	ENSG00000166086|ENSG00000166086	ENST00000299106;ENST00000441717;ENST00000532165|ENST00000529443	T|T	0.63580|0.70045	-0.05|-0.45	5.06|5.06	4.16|4.16	0.48862|0.48862	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	0.799060|.	0.11759|.	N|.	0.532275|.	T|T	0.58481|0.58481	0.2125|0.2125	N|N	0.24115|0.24115	0.695|0.695	0.34201|0.34201	D|D	0.673119|0.673119	D;D|.	0.65815|.	0.995;0.995|.	P;P|.	0.54706|.	0.759;0.759|.	T|T	0.65059|0.65059	-0.6260|-0.6260	10|6	0.37606|.	T|.	0.19|.	.|.	13.4923|13.4923	0.61402|0.61402	0.0:0.9249:0.0:0.075|0.0:0.9249:0.0:0.075	.|.	140;191|.	B3KWG9;Q9BX67|.	.;JAM3_HUMAN|.	C|L	236;140;37|144	ENSP00000395742:R140C|ENSP00000431883:S144L	ENSP00000299106:R236C|.	R|S	+|+	1|2	0|0	JAM3|JAM3	133520058|133520058	0.014000|0.014000	0.17966|0.17966	0.853000|0.853000	0.33588|0.33588	0.074000|0.074000	0.17049|0.17049	0.586000|0.586000	0.23894|0.23894	1.155000|1.155000	0.42497|0.42497	-0.142000|-0.142000	0.14014|0.14014	CGC|TCG	.	.		0.502	JAM3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000393303.4	NM_032801		T	134014848	C	T	134014848	3	4	343	1	0	0	0	0	1	0	0	0	7953	884	31	1	724	1	JAM3	11	134014848	Missense_Mutation	SNP	C	TCGA-UB-A7MA-01A-11D-A33Q-10	10540630	134014848	991668	39	47328										
OR11H12	440153	hgsc.bcm.edu	37	chr14	19378493	19378493	+	Frame_Shift_Del	DEL	C	C	-													0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	gctatggtgaccccactcttCaatccccttatctatagcct							TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr14:19378493delC	ENST00000550708.1	+	1	972	c.900delC	c.(898-900)ttcfs	p.F300fs		NM_001013354.1|NM_001197287.1	NP_001013372.1|NP_001184216.1	B2RN74	O11HC_HUMAN	olfactory receptor, family 11, subfamily H, member 12	300						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	22	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		CCCCACTCTTCAATCCCCTTA	0.423																																					p.F300fs		Atlas-INDEL	.											.	OR11H12	58	.	0			c.899delT						.						6	6	6					14																	19378493		1056	2628	3684	SO:0001589	frameshift_variant	440153	exon1			.		CCDS32017.1	14q11.2	2013-01-25			ENSG00000257115	ENSG00000257115		"GPCR / Class A : Olfactory receptors"	30738	protein-coding gene	gene with protein product							Standard	NM_001013354		Approved		uc010tkp.2	B2RN74	OTTHUMG00000170298	ENST00000550708.1:c.900delC	chr14.hg19:g.19378493delC	ENSP00000449002:p.Phe300fs	326.0	0.0		265.0	19.0	NM_001013354		Frame_Shift_Del	DEL	ENST00000550708.1	hg19	CCDS32017.1																																																																																			.	.		0.423	OR11H12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408402.1	NM_001013354		-	19378493	C	-	19378493	7	5	343	1	0	1	0	1	0	0	0	0	10936	825	29	0	902	0	OR11H12	14	19378493	Frame_Shift_Del	DEL	C	TCGA-UB-A7MA-01A-11D-A33Q-10		19378493	87971047	40	47329										
PCNX	22990	hgsc.bcm.edu	37	chr14	71514665	71514666	+	Frame_Shift_Ins	INS	-	-	T													0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	ctttttcagagaccatgctgINSttggatctcttctttatgtc					rs374611988		TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr14:71514665_71514666insT	ENST00000304743.2	+	22	4748_4749	c.4302_4303insT	c.(4303-4305)ttgfs	p.L1435fs	PCNX_ENST00000238570.5_Frame_Shift_Ins_p.L1435fs|PCNX_ENST00000439984.3_Frame_Shift_Ins_p.L1324fs	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	1435						integral component of membrane (GO:0016021)				NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		AGACCATGCTGTTGGATCTCTT	0.356																																					p.L1434fs		Atlas-Indel,Pindel	.											.	PCNX	198	.	0			c.4302_4303insT						.																																			SO:0001589	frameshift_variant	22990	exon22			.	AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"pecanex-like 1 (Drosophila)"	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.4304dupT	chr14.hg19:g.71514667_71514667dupT	ENSP00000304192:p.Leu1435fs	63.0	0.0		74.0	13.0	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Frame_Shift_Ins	INS	ENST00000304743.2	hg19	CCDS9806.1																																																																																			.	.		0.356	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982		T	71514666	-	T	71514665	7	5	343	1	0	1	1	0	0	0	0	0	11600	1364	48	0	4388	0	PCNX	14	71514665	Frame_Shift_Ins	INS	-	TCGA-UB-A7MA-01A-11D-A33Q-10	52136172	71514665	35834875	41	47330										
ACAN	176	hgsc.bcm.edu	37	chr15	89401573	89401573	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	attgggagcagcctgccctcGggagcatattatggcagtgg	15	9	0	0			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr15:89401573G>A	ENST00000561243.1	+	11	5757	c.5757G>A	c.(5755-5757)tcG>tcA	p.S1919S	ACAN_ENST00000559004.1_Silent_p.S1919S|ACAN_ENST00000439576.2_Silent_p.S1919S|ACAN_ENST00000352105.7_Silent_p.S1919S			P16112	PGCA_HUMAN	aggrecan	1909	CS-2.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			GCCTGCCCTCGGGAGCATATT	0.527																																					p.S1919S		Atlas-SNP	.											.	ACAN	220	.	0			c.G5757A						.						67	71	70					15																	89401573		1975	4154	6129	SO:0001819	synonymous_variant	176	exon12			GCCCTCGGGAGCA	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	319	protein-coding gene	gene with protein product	"aggrecan proteoglycan"	155760	"chondroitin sulfate proteoglycan 1", "aggrecan 1"	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.5757G>A	chr15.hg19:g.89401573G>A		90.0	0.0		123.0	64.0	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Silent	SNP	ENST00000561243.1	hg19	CCDS53970.1																																																																																			.	.		0.527	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135		A	89401573	G	A	89401573	2	1	343	1	0	0	0	0	0	0	0	1	117	1103	39	1		1	ACAN	15	89401573	Silent	SNP	G	TCGA-UB-A7MA-01A-11D-A33Q-10		89401573	13129819	42	47331										
NOL3	8996	hgsc.bcm.edu	37	chr16	67209000	67209000	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	tgccccgcccatgctggataGgacctgggatgctgctggag	15	12	0	0			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr16:67209000G>A	ENST00000568146.1	+	4	713	c.660G>A	c.(658-660)taG>taA	p.*220*	NOL3_ENST00000268605.7_3'UTR|NOL3_ENST00000564053.1_3'UTR|NOL3_ENST00000432069.2_3'UTR|KIAA0895L_ENST00000563831.2_5'Flank			O60936	NOL3_HUMAN	nucleolar protein 3 (apoptosis repressor with CARD domain)	0					apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of gene expression (GO:0010468)|response to hypoxia (GO:0001666)|response to injury involved in regulation of muscle adaptation (GO:0014876)|RNA splicing (GO:0008380)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|sarcoplasm (GO:0016528)	identical protein binding (GO:0042802)|RNA binding (GO:0003723)			ovary(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.0335)|all cancers(182;0.184)		ATGCTGGATAGGACCTGGGAT	0.612																																					p.X220X		Atlas-SNP	.											.	NOL3	6	.	0			c.G660A						.						88	90	89					16																	67209000		2018	4190	6208	SO:0001819	synonymous_variant	8996	exon4			TGGATAGGACCTG	AF043244	CCDS42176.1, CCDS58473.1, CCDS61960.1	16q22.1	2008-08-27				ENSG00000140939			7869	protein-coding gene	gene with protein product		605235				9560245	Standard	NM_001276312		Approved	ARC, NOP30, MYP, CARD2	uc010vjd.3	O60936		ENST00000568146.1:c.660G>A	chr16.hg19:g.67209000G>A		56.0	0.0		41.0	25.0	NM_001185057	B4DFL0|O60937	Silent	SNP	ENST00000568146.1	hg19	CCDS58473.1																																																																																			.	.		0.612	NOL3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422746.1			A	67209000	G	A	67209000	2	1	343	1	0	0	0	0	0	0	0	1	10532	995	35	3		3	NOL3	16	67209000	Silent	SNP	G	TCGA-UB-A7MA-01A-11D-A33Q-10		67209000	23145753	43	47332										
MBTPS1	8720	hgsc.bcm.edu	37	chr16	84118638	84118638	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	actggagaagcaacactggtCcctgagagggcccggcaccc	13	14	0	2			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr16:84118638C>T	ENST00000343411.3	-	10	1731	c.1236G>A	c.(1234-1236)ggG>ggA	p.G412G	MBTPS1_ENST00000569770.1_5'UTR	NM_003791.2	NP_003782.1	Q14703	MBTP1_HUMAN	membrane-bound transcription factor peptidase, site 1	412	Peptidase S8.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cholesterol metabolic process (GO:0008203)|endoplasmic reticulum unfolded protein response (GO:0030968)|lipid metabolic process (GO:0006629)|lysosome organization (GO:0007040)|proteolysis (GO:0006508)|regulation of transcription factor import into nucleus (GO:0042990)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(10)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						CAACACTGGTCCCTGAGAGGG	0.602											OREG0023982	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G412G		Atlas-SNP	.											.	MBTPS1	85	.	0			c.G1236A						.						89	75	80					16																	84118638		2200	4300	6500	SO:0001819	synonymous_variant	8720	exon10			ACTGGTCCCTGAG	D42053	CCDS10941.1	16q24	2008-08-04	2005-08-17		ENSG00000140943	ENSG00000140943			15456	protein-coding gene	gene with protein product		603355	"membrane-bound transcription factor protease, site 1"			9809072, 10944850	Standard	NM_003791		Approved	S1P, KIAA0091, SKI-1, PCSK8	uc002fhi.3	Q14703	OTTHUMG00000137639	ENST00000343411.3:c.1236G>A	chr16.hg19:g.84118638C>T		206.0	0.0	1226	153.0	39.0	NM_003791	A8K6V8|Q24JQ2|Q9UF67	Silent	SNP	ENST00000343411.3	hg19	CCDS10941.1																																																																																			.	.		0.602	MBTPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269080.2	NM_003791		T	84118638	C	T	84118638	2	4	343	1	0	0	0	0	0	0	0	1	9370	842	30	3		3	MBTPS1	16	84118638	Silent	SNP	C	TCGA-UB-A7MA-01A-11D-A33Q-10	16909638	84118638	6236115	44	47333										
CTU2	9780	hgsc.bcm.edu	37	chr16	88781068	88781068	+	IGR	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	tcacccatccccctgactgaGacccggacacccccggggcc	9	21	1	2			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr16:88781068G>C	ENST00000301015.9	-	0	8072				CTU2_ENST00000312060.5_Missense_Mutation_p.E425D|CTU2_ENST00000453996.2_Missense_Mutation_p.E425D|CTU2_ENST00000567949.1_Missense_Mutation_p.E496D|CTU2_ENST00000378384.3_Missense_Mutation_p.E338D|MIR4722_ENST00000578292.1_RNA	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1						cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of mechanical stimulus (GO:0050982)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|positive regulation of integrin activation (GO:0033625)|regulation of membrane potential (GO:0042391)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|prostate(2)|skin(1)	10						CCCTGACTGAGACCCGGACAC	0.692																																					p.E425D		Atlas-SNP	.											.	CTU2	66	.	0			c.G1275C						.						32	34	34					16																	88781068		2188	4292	6480	SO:0001628	intergenic_variant	348180	exon12			GACTGAGACCCGG	D87071	CCDS54058.1	16q24.3	2011-08-31	2011-08-31	2011-08-31	ENSG00000103335	ENSG00000103335			28993	protein-coding gene	gene with protein product		611184	"family with sequence similarity 38, member A"	FAM38A		20813920, 21056836, 21299953, 21696149	Standard	NM_001142864		Approved	KIAA0233	uc010vpb.2	Q92508	OTTHUMG00000156776		chr16.hg19:g.88781068G>C		132.0	0.0		79.0	47.0	NM_001012759	A6NHT9|A7E2B7|Q0KKZ9	Missense_Mutation	SNP	ENST00000301015.9	hg19	CCDS54058.1	.	.	.	.	.	.	.	.	.	.	G	9.722	1.159838	0.21454	.	.	ENSG00000174177	ENST00000378384;ENST00000312060;ENST00000453996	T;T;T	0.17854	2.25;2.52;2.52	4.21	3.22	0.36961	.	1.163850	0.06508	U	0.737540	T	0.13628	0.0330	L	0.43152	1.355	0.09310	N	1	P;P;P	0.38922	0.589;0.589;0.651	B;B;B	0.33392	0.163;0.163;0.115	T	0.10428	-1.0630	10	0.15952	T	0.53	.	8.4764	0.33016	0.1195:0.0:0.8805:0.0	.	338;425;425	Q2VPK5-3;Q2VPK5-5;Q2VPK5	.;.;CTU2_HUMAN	D	338;425;425	ENSP00000367635:E338D;ENSP00000308617:E425D;ENSP00000388320:E425D	ENSP00000308617:E425D	E	+	3	2	CTU2	87308569	0.004000	0.15560	0.006000	0.13384	0.012000	0.07955	0.121000	0.15667	2.053000	0.61076	0.462000	0.41574	GAG	.	.		0.692	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745		C	88781068	G	C	88781068	1	2	343	0	1	0	0	0	0	0	0	0	4050	933	33	4		4	CTU2	16	88781068	IGR	SNP	G	TCGA-UB-A7MA-01A-11D-A33Q-10	4662430	88781068	1573685	45	47334										
ELAC2	60528	hgsc.bcm.edu	37	chr17	12905669	12905669	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	tgggcacactgagggtggggCcctccttctgaaagagacaa	14	10	1	3			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr17:12905669C>T	ENST00000338034.4	-	14	1465	c.1226G>A	c.(1225-1227)gGc>gAc	p.G409D	ELAC2_ENST00000395962.2_Missense_Mutation_p.G390D|ELAC2_ENST00000609345.1_5'Flank|ELAC2_ENST00000426905.3_Missense_Mutation_p.G369D	NM_018127.6|NM_173717.1	NP_060597.4|NP_776065.1	Q9BQ52	RNZ2_HUMAN	elaC ribonuclease Z 2	409					mitochondrial tRNA 3'-trailer cleavage, endonucleolytic (GO:0072684)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|skin(1)	23						GAGGGTGGGGCCCTCCTTCTG	0.562																																					p.G409D		Atlas-SNP	.											.	ELAC2	48	.	0			c.G1226A						.						77	75	76					17																	12905669		2203	4300	6503	SO:0001583	missense	60528	exon14			GTGGGGCCCTCCT	AF304370	CCDS11164.1, CCDS54093.1	17p11.2	2013-05-24	2013-05-24		ENSG00000006744	ENSG00000006744	3.1.26.11		14198	protein-coding gene	gene with protein product	"tRNase Z (long form)"	605367	"elaC (E. coli) homolog 2", "elaC homolog 2 (E. coli)"			10986046, 16636667, 21559454	Standard	NM_018127		Approved	FLJ10530, HPC2	uc010vvr.2	Q9BQ52	OTTHUMG00000058764	ENST00000338034.4:c.1226G>A	chr17.hg19:g.12905669C>T	ENSP00000337445:p.Gly409Asp	78.0	0.0		91.0	50.0	NM_018127	B4DPL9|Q6IA94|Q9HAS8|Q9HAS9|Q9NVT1	Missense_Mutation	SNP	ENST00000338034.4	hg19	CCDS11164.1	.	.	.	.	.	.	.	.	.	.	C	9.658	1.143353	0.21205	.	.	ENSG00000006744	ENST00000426905;ENST00000338034;ENST00000395962;ENST00000457438	T;T;T	0.63580	0.37;-0.05;-0.04	5.67	-3.94	0.04130	.	1.051740	0.07264	N	0.867941	T	0.44477	0.1295	L	0.48642	1.525	0.09310	N	1	B;B;B;B;B;B;B;B	0.23249	0.032;0.0;0.031;0.01;0.018;0.031;0.006;0.082	B;B;B;B;B;B;B;B	0.25140	0.013;0.002;0.047;0.017;0.021;0.013;0.014;0.058	T	0.30534	-0.9975	10	0.12430	T	0.62	-1.9754	1.6937	0.02857	0.3552:0.3366:0.095:0.2132	.	369;392;390;207;409;169;394;37	B4DPL9;E9PGJ0;G5E9D5;E7ES68;Q9BQ52;B3KSU9;B4DT15;Q9BQ52-3	.;.;.;.;RNZ2_HUMAN;.;.;.	D	369;409;390;87	ENSP00000405223:G369D;ENSP00000337445:G409D;ENSP00000379291:G390D	ENSP00000337445:G409D	G	-	2	0	ELAC2	12846394	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.194000	0.09559	-0.409000	0.07553	-0.224000	0.12420	GGC	.	.		0.562	ELAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129934.5			T	12905669	C	T	12905669	3	4	343	1	0	0	0	0	1	0	0	0	5049	739	26	3	1298	3	ELAC2	17	12905669	Missense_Mutation	SNP	C	TCGA-UB-A7MA-01A-11D-A33Q-10		12905669	68289541	46	47335										
DRG2	1819	hgsc.bcm.edu	37	chr17	18003031	18003031	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	ggatgccaccaagggagaggTgcagaggtccgcagggtggg	20	8	0	2			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr17:18003031T>C	ENST00000225729.3	+	5	599	c.461T>C	c.(460-462)gTg>gCg	p.V154A	DRG2_ENST00000583355.1_Intron|DRG2_ENST00000395726.4_Missense_Mutation_p.V154A	NM_001388.4	NP_001379.1	P55039	DRG2_HUMAN	developmentally regulated GTP binding protein 2	154	OBG-type G. {ECO:0000255|PROSITE- ProRule:PRU01047}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	14	all_neural(463;0.228)					AAGGGAGAGGTGCAGAGGTCC	0.637																																					p.V154A		Atlas-SNP	.											.	DRG2	27	.	0			c.T461C						.						45	35	38					17																	18003031		2201	4300	6501	SO:0001583	missense	1819	exon5			GAGAGGTGCAGAG	X80754	CCDS11191.1	17p13-p12	2008-07-18	2001-11-28		ENSG00000108591	ENSG00000108591			3030	protein-coding gene	gene with protein product		602986	"developmentally regulated GTP-binding protein 2"			9605870, 7929244	Standard	NM_001388		Approved		uc002gsh.2	P55039	OTTHUMG00000059399	ENST00000225729.3:c.461T>C	chr17.hg19:g.18003031T>C	ENSP00000225729:p.Val154Ala	101.0	0.0		153.0	65.0	NM_001388	B2R8G5|Q53Y50|Q9BWB2	Missense_Mutation	SNP	ENST00000225729.3	hg19	CCDS11191.1	.	.	.	.	.	.	.	.	.	.	T	27.8	4.859704	0.91433	.	.	ENSG00000108591	ENST00000395726;ENST00000225729	T;T	0.16196	2.36;2.36	5.6	5.6	0.85130	Small GTP-binding protein domain (1);GTP-binding domain, HSR1-related (1);	0.053371	0.64402	D	0.000001	T	0.09818	0.0241	N	0.02286	-0.61	0.80722	D	1	P;P	0.50066	0.931;0.879	P;P	0.48063	0.565;0.478	T	0.36720	-0.9736	10	0.09338	T	0.73	-11.3592	15.7656	0.78123	0.0:0.0:0.0:1.0	.	154;154	A8MZF9;P55039	.;DRG2_HUMAN	A	154	ENSP00000379076:V154A;ENSP00000225729:V154A	ENSP00000225729:V154A	V	+	2	0	DRG2	17943756	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.905000	0.87416	2.132000	0.65825	0.383000	0.25322	GTG	.	.		0.637	DRG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132075.3	NM_001388		C	18003031	T	C	18003031	3	2	343	1	0	0	0	0	1	0	0	0	4764	1696	59	2	479	2	DRG2	17	18003031	Missense_Mutation	SNP	T	TCGA-UB-A7MA-01A-11D-A33Q-10	5097362	18003031	63192179	47	47336										
MYCBPAP	84073	hgsc.bcm.edu	37	chr17	48586029	48586029	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	caacgtttcatggtgccgggCggcaccatgaagtctctaaa	11	11	2	1			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr17:48586029C>T	ENST00000323776.5	+	1	285	c.123C>T	c.(121-123)ggC>ggT	p.G41G	MYCBPAP_ENST00000419930.1_Silent_p.G41G|RP11-94C24.6_ENST00000502300.1_lincRNA|MYCBPAP_ENST00000436259.2_Silent_p.G4G	NM_032133.4	NP_115509.4			MYCBP associated protein											breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(8)|ovary(4)|pancreas(1)|skin(2)|urinary_tract(2)	31	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;1.23e-09)			TGGTGCCGGGCGGCACCATGA	0.617																																					p.G41G		Atlas-SNP	.											.	MYCBPAP	135	.	0			c.C123T						.						14	15	14					17																	48586029		2200	4292	6492	SO:0001819	synonymous_variant	84073	exon1			GCCGGGCGGCACC	BC028393	CCDS32680.2	17q21.33	2004-02-19			ENSG00000136449	ENSG00000136449			19677	protein-coding gene	gene with protein product		609835				12151104	Standard	NM_032133		Approved	AMAP-1, DKFZp434N1415	uc010wmr.2	Q8TBZ2	OTTHUMG00000157184	ENST00000323776.5:c.123C>T	chr17.hg19:g.48586029C>T		158.0	0.0		242.0	39.0	NM_032133		Silent	SNP	ENST00000323776.5	hg19	CCDS32680.2																																																																																			.	.		0.617	MYCBPAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347814.1	NM_032133		T	48586029	C	T	48586029	2	4	343	1	0	0	0	0	0	0	0	1	10028	755	27	1		1	MYCBPAP	17	48586029	Silent	SNP	C	TCGA-UB-A7MA-01A-11D-A33Q-10	30582998	48586029	32609181	48	47337										
PPM1E	22843	hgsc.bcm.edu	37	chr17	57046925	57046925	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	ggaagaacaagcttactttgCagtgtttgatggccatgggg	14	6	0	2			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr17:57046925C>T	ENST00000308249.2	+	4	938	c.809C>T	c.(808-810)gCa>gTa	p.A270V	RP11-579O24.3_ENST00000582080.1_RNA	NM_014906.4	NP_055721.3	Q96MI6	PPM1M_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1E	0					protein dephosphorylation (GO:0006470)	nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)|manganese ion binding (GO:0030145)			biliary_tract(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)	33	Medulloblastoma(34;0.127)|all_neural(34;0.237)		BRCA - Breast invasive adenocarcinoma(1;5.76e-11)			GCTTACTTTGCAGTGTTTGAT	0.468																																					p.A270V		Atlas-SNP	.											.	PPM1E	97	.	0			c.C809T						.						180	147	158					17																	57046925		2203	4300	6503	SO:0001583	missense	22843	exon4			ACTTTGCAGTGTT	AB028995	CCDS11613.1	17q24.2	2012-04-17	2010-03-05		ENSG00000175175	ENSG00000175175		"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	19322	protein-coding gene	gene with protein product	"partner of PIX 1", "nuclear calmodulin-dependent protein kinase phosphatase"		"protein phosphatase 1E (PP2C domain containing)"			11864573, 10470851	Standard	NR_048561		Approved	POPX1, KIAA1072, PP2CH, CaMKP-N	uc002iwx.4	Q8WY54		ENST00000308249.2:c.809C>T	chr17.hg19:g.57046925C>T	ENSP00000312411:p.Ala270Val	141.0	0.0		175.0	27.0	NM_014906	Q8N8J9|Q96DB8	Missense_Mutation	SNP	ENST00000308249.2	hg19	CCDS11613.1	.	.	.	.	.	.	.	.	.	.	C	31	5.077124	0.94000	.	.	ENSG00000175175	ENST00000308249;ENST00000443121	T	0.11277	2.79	5.49	5.49	0.81192	.	0.046830	0.85682	D	0.000000	T	0.45975	0.1369	M	0.92738	3.34	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.996	T	0.57294	-0.7836	10	0.87932	D	0	-22.1143	19.7268	0.96166	0.0:1.0:0.0:0.0	.	279;270	Q8WY54-3;Q8WY54-2	.;.	V	270;121	ENSP00000312411:A270V	ENSP00000312411:A270V	A	+	2	0	PPM1E	54401707	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.017000	0.70805	2.727000	0.93392	0.563000	0.77884	GCA	.	.		0.468	PPM1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445458.1	NM_014906		T	57046925	C	T	57046925	3	4	343	1	0	0	0	0	1	0	0	0	12350	710	25	3	823	3	PPM1E	17	57046925	Missense_Mutation	SNP	C	TCGA-UB-A7MA-01A-11D-A33Q-10	8460896	57046925	24148285	49	47338										
RNF213	57674	hgsc.bcm.edu	37	chr17	78319225	78319225	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	agagggtgcccttcaatgtcGactttgataaactgcccaga	10	10	1	3			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr17:78319225G>A	ENST00000582970.1	+	29	7233	c.7090G>A	c.(7090-7092)Gac>Aac	p.D2364N	RNF213_ENST00000508628.2_Missense_Mutation_p.D2413N|RNF213_ENST00000336301.6_Missense_Mutation_p.D437N	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	2364					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.D2413N(1)|p.D437N(1)		NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			CTTCAATGTCGACTTTGATAA	0.552																																					p.D2364N		Atlas-SNP	.											RNF213_ENST00000411702,colon,carcinoma,0,2	RNF213	766	.	2	Substitution - Missense(2)	large_intestine(2)	c.G7090A						.						68	67	68					17																	78319225		2203	4300	6503	SO:0001583	missense	57674	exon29			AATGTCGACTTTG	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.7090G>A	chr17.hg19:g.78319225G>A	ENSP00000464087:p.Asp2364Asn	67.0	1.0		82.0	31.0	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	hg19	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	G	5.617	0.298637	0.10622	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301	T	0.21361	2.01	5.01	0.769	0.18492	.	0.211870	0.38548	N	0.001643	T	0.10465	0.0256	L	0.28054	0.825	0.20926	N	0.99982	B	0.16166	0.016	B	0.20767	0.031	T	0.26258	-1.0108	10	0.16896	T	0.51	.	3.5721	0.07921	0.2694:0.106:0.5163:0.1084	.	437	Q63HN8	RN213_HUMAN	N	2364;2413;437	ENSP00000338218:D437N	ENSP00000338218:D437N	D	+	1	0	RNF213	75933820	0.096000	0.21769	0.361000	0.25849	0.086000	0.17979	0.370000	0.20433	0.372000	0.24591	0.655000	0.94253	GAC	.	.		0.552	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		A	78319225	G	A	78319225	3	1	343	1	0	0	0	0	1	0	0	0	13492	1058	37	1	7519	1	RNF213	17	78319225	Missense_Mutation	SNP	G	TCGA-UB-A7MA-01A-11D-A33Q-10	21272300	78319225	2875985	50	47339										
ASXL3	80816	hgsc.bcm.edu	37	chr18	31319066	31319066	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	gagtcagaaactgcagtagaGaccagtacccccaaaataaa	8	10	1	2			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr18:31319066G>C	ENST00000269197.5	+	11	1698	c.1698G>C	c.(1696-1698)gaG>gaC	p.E566D		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	566					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						CTGCAGTAGAGACCAGTACCC	0.418																																					p.E566D		Atlas-SNP	.											.	ASXL3	405	.	0			c.G1698C						.						72	67	69					18																	31319066		1906	4133	6039	SO:0001583	missense	80816	exon11			AGTAGAGACCAGT	AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"KIAA1713", "additional sex combs like 3 (Drosophila)"	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.1698G>C	chr18.hg19:g.31319066G>C	ENSP00000269197:p.Glu566Asp	104.0	0.0		89.0	17.0	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	hg19	CCDS45847.1	.	.	.	.	.	.	.	.	.	.	G	11.75	1.731791	0.30684	.	.	ENSG00000141431	ENST00000269197	T	0.25749	1.78	5.47	3.65	0.41850	.	0.428496	0.23638	N	0.046058	T	0.42063	0.1186	L	0.59436	1.845	0.33312	D	0.566174	D	0.69078	0.997	D	0.72625	0.978	T	0.53012	-0.8498	10	0.42905	T	0.14	.	8.8524	0.35208	0.2317:0.0:0.7683:0.0	.	566	Q9C0F0	ASXL3_HUMAN	D	566	ENSP00000269197:E566D	ENSP00000269197:E566D	E	+	3	2	ASXL3	29573064	1.000000	0.71417	0.995000	0.50966	0.218000	0.24690	3.182000	0.50910	0.760000	0.33108	0.467000	0.42956	GAG	.	.		0.418	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			C	31319066	G	C	31319066	3	2	343	1	0	0	0	0	1	0	0	0	1068	933	33	4	1740	4	ASXL3	18	31319066	Missense_Mutation	SNP	G	TCGA-UB-A7MA-01A-11D-A33Q-10		31319066	46758182	51	47340										
MUC16	94025	hgsc.bcm.edu	37	chr19	8999473	8999473	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	cagctggctcagctcccagtAtagctgctctctgtccagtc	9	15	2	0			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr19:8999473A>G	ENST00000397910.4	-	56	40905	c.40702T>C	c.(40702-40704)Tac>Cac	p.Y13568H	MUC16_ENST00000380951.5_Missense_Mutation_p.Y209H	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13570	SEA 10. {ECO:0000255|PROSITE- ProRule:PRU00188}.			Missing (in Ref. 3; AAK74120). {ECO:0000305}.	cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AGCTCCCAGTATAGCTGCTCT	0.587																																					p.Y13568H		Atlas-SNP	.											.	MUC16	4315	.	0			c.T40702C						.						185	156	165					19																	8999473		2010	4189	6199	SO:0001583	missense	94025	exon56			CCCAGTATAGCTG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.40702T>C	chr19.hg19:g.8999473A>G	ENSP00000381008:p.Tyr13568His	100.0	0.0		104.0	17.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	.	12.09	1.833078	0.32421	.	.	ENSG00000181143	ENST00000397910;ENST00000380951	T;T	0.52057	0.68;0.68	3.48	3.48	0.39840	SEA (2);	.	.	.	.	T	0.69637	0.3133	M	0.89287	3.02	.	.	.	D;D	0.89917	1.0;0.984	D;D	0.91635	0.999;0.946	T	0.79193	-0.1904	8	0.87932	D	0	-11.9353	8.5336	0.33349	1.0:0.0:0.0:0.0	.	21213;13568	Q8WXI7;B5ME49	MUC16_HUMAN;.	H	13568;209	ENSP00000381008:Y13568H;ENSP00000370338:Y209H	ENSP00000370338:Y209H	Y	-	1	0	MUC16	8860473	0.989000	0.36119	0.658000	0.29665	0.071000	0.16799	2.729000	0.47327	1.599000	0.50093	0.454000	0.30748	TAC	.	.		0.587	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	8999473	A	G	8999473	3	3	343	1	0	0	0	0	1	0	0	0	9982	449	16	2	2937	2	MUC16	19	8999473	Missense_Mutation	SNP	A	TCGA-UB-A7MA-01A-11D-A33Q-10		8999473	50129510	52	47341										
DOCK6	57572	hgsc.bcm.edu	37	chr19	11363512	11363512	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	cattcccggggctgcagcagCagctccaagtcatcagctgg	12	14	2	0	rs370478141		TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr19:11363512C>A	ENST00000294618.7	-	3	266	c.255G>T	c.(253-255)ctG>ctT	p.L85L		NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	85					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(8)|liver(2)|lung(9)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	39						GCTGCAGCAGCAGCTCCAAGT	0.632																																					p.L85L		Atlas-SNP	.											.	DOCK6	104	.	0			c.G255T						.						26	29	28					19																	11363512		1894	4109	6003	SO:0001819	synonymous_variant	57572	exon3			CAGCAGCAGCTCC		CCDS45975.1	19p13.2	2011-08-04			ENSG00000130158	ENSG00000130158			19189	protein-coding gene	gene with protein product		614194				12432077	Standard	NM_020812		Approved	KIAA1395, ZIR1	uc002mqs.5	Q96HP0		ENST00000294618.7:c.255G>T	chr19.hg19:g.11363512C>A		100.0	0.0		97.0	16.0	NM_020812	A6H8X5|Q7Z7P4|Q9P2F2	Silent	SNP	ENST00000294618.7	hg19	CCDS45975.1																																																																																			.	.		0.632	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812		A	11363512	C	A	11363512	2	1	343	1	0	0	0	0	0	0	0	1	4693	697	25	3		3	DOCK6	19	11363512	Silent	SNP	C	TCGA-UB-A7MA-01A-11D-A33Q-10	2364039	11363512	47765471	53	47342										
JUND	3727	hgsc.bcm.edu	37	chr19	18391859	18391859	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	ctggttctgcttgtgtaaatCctccagggccttgacgaagc	11	11	1	1			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr19:18391859C>T	ENST00000252818.3	-	1	573	c.436G>A	c.(436-438)Gat>Aat	p.D146N	MIR3188_ENST00000583494.1_RNA	NM_005354.4	NP_005345.3	P17535	JUND_HUMAN	jun D proto-oncogene	146					aging (GO:0007568)|cellular response to calcium ion (GO:0071277)|circadian rhythm (GO:0007623)|osteoblast development (GO:0002076)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to light stimulus (GO:0009416)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|transcription from RNA polymerase II promoter (GO:0006366)	chromatin (GO:0000785)|nucleus (GO:0005634)|protein complex (GO:0043234)	double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			lung(2)|prostate(1)	3						TTGTGTAAATCCTCCAGGGCC	0.746																																					p.D146N		Atlas-SNP	.											.	JUND	6	.	0			c.G436A						.						14	15	15					19																	18391859		2197	4290	6487	SO:0001583	missense	3727	exon1			GTAAATCCTCCAG		CCDS32959.1	19p13.2	2013-01-10				ENSG00000130522		"basic leucine zipper proteins"	6206	protein-coding gene	gene with protein product	"transcription factor jun-D", "JunD-FL isoform", "activator protein 1"	165162				2112242, 1903194	Standard	NM_005354		Approved	AP-1	uc002nip.2	P17535		ENST00000252818.3:c.436G>A	chr19.hg19:g.18391859C>T	ENSP00000252818:p.Asp146Asn	16.0	0.0		43.0	9.0	NM_005354	Q53EK9	Missense_Mutation	SNP	ENST00000252818.3	hg19	CCDS32959.1	.	.	.	.	.	.	.	.	.	.	.	31	5.098638	0.94197	.	.	ENSG00000130522	ENST00000252818	T	0.36878	1.23	3.06	3.06	0.35304	Jun-like transcription factor (1);	0.072212	0.52532	U	0.000073	T	0.43433	0.1247	L	0.34521	1.04	0.58432	D	0.999998	D	0.76494	0.999	D	0.67900	0.954	T	0.20874	-1.0262	10	0.32370	T	0.25	.	11.9982	0.53216	0.0:1.0:0.0:0.0	.	146	P17535	JUND_HUMAN	N	146	ENSP00000252818:D146N	ENSP00000252818:D146N	D	-	1	0	JUND	18252859	1.000000	0.71417	0.979000	0.43373	0.966000	0.64601	5.015000	0.64035	1.741000	0.51731	0.537000	0.68136	GAT	.	.		0.746	JUND-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466318.2	NM_005354		T	18391859	C	T	18391859	3	4	343	1	0	0	0	0	1	0	0	0	7980	855	30	3	611	3	JUND	19	18391859	Missense_Mutation	SNP	C	TCGA-UB-A7MA-01A-11D-A33Q-10	7028347	18391859	40737124	54	47343										
SFRS14	10147	hgsc.bcm.edu	37	chr19	19136612	19136612	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	gactctccttctccaaacacTctttctcaatcagcctggaa	4	15	5	0			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr19:19136612T>C	ENST00000601879.1	-	3	842	c.545A>G	c.(544-546)gAg>gGg	p.E182G	SUGP2_ENST00000452918.2_Missense_Mutation_p.E182G|SUGP2_ENST00000337018.6_Missense_Mutation_p.E182G|SUGP2_ENST00000600377.1_Missense_Mutation_p.E196G|SUGP2_ENST00000598202.1_5'UTR|SUGP2_ENST00000456085.2_Intron			Q8IX01	SUGP2_HUMAN	SURP and G patch domain containing 2	182					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						CTCCAAACACTCTTTCTCAAT	0.537																																					p.E182G		Atlas-SNP	.											.	SUGP2	107	.	0			c.A545G						.						104	92	96					19																	19136612		2203	4300	6503	SO:0001583	missense	10147	exon3			AAACACTCTTTCT	AB002363	CCDS12392.1	19p13	2013-01-28	2010-08-10	2010-08-10	ENSG00000064607	ENSG00000064607		"G patch domain containing"	18641	protein-coding gene	gene with protein product		607993	"splicing factor, arginine/serine-rich 14"	SFRS14		12594045	Standard	NM_014884		Approved	KIAA0365	uc002nkx.2	Q8IX01		ENST00000601879.1:c.545A>G	chr19.hg19:g.19136612T>C	ENSP00000472286:p.Glu182Gly	140.0	0.0		561.0	96.0	NM_014884	C9JI71|O15071|O60369|Q5JPH7|Q8WUF7	Missense_Mutation	SNP	ENST00000601879.1	hg19	CCDS12392.1	.	.	.	.	.	.	.	.	.	.	T	17.61	3.432609	0.62844	.	.	ENSG00000064607	ENST00000337018;ENST00000330854;ENST00000452918	T;T;T	0.12255	2.7;2.7;2.7	4.93	4.93	0.64822	.	0.522677	0.17456	N	0.173602	T	0.23611	0.0571	N	0.24115	0.695	0.80722	D	1	D;D	0.71674	0.998;0.964	D;P	0.78314	0.991;0.637	T	0.02728	-1.1118	10	0.87932	D	0	-15.9326	12.3088	0.54918	0.0:0.0:0.0:1.0	.	182;182	A8K5G0;Q8IX01	.;SUGP2_HUMAN	G	182	ENSP00000337926:E182G;ENSP00000332373:E182G;ENSP00000389380:E182G	ENSP00000332373:E182G	E	-	2	0	SUGP2	18997612	0.996000	0.38824	0.988000	0.46212	0.920000	0.55202	4.243000	0.58721	1.860000	0.53959	0.260000	0.18958	GAG	.	.		0.537	SUGP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464627.1	NM_001017392		C	19136612	T	C	19136612	3	2	343	1	0	0	0	0	1	0	0	0	14185	1551	54	2	2735	2	SFRS14	19	19136612	Missense_Mutation	SNP	T	TCGA-UB-A7MA-01A-11D-A33Q-10	744753	19136612	39992371	55	47344										
ARHGAP33	115703	hgsc.bcm.edu	37	chr19	36278734	36278734	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	gagaacctgtactatgagatCggggcaagtgaggggtcccc	15	9	0	3			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr19:36278734C>T	ENST00000007510.4	+	21	3411	c.3267C>T	c.(3265-3267)atC>atT	p.I1089I	ARHGAP33_ENST00000378944.5_Silent_p.I925I|AC002398.5_ENST00000433059.1_lincRNA|ARHGAP33_ENST00000314737.5_Silent_p.I928I			O14559	RHG33_HUMAN	Rho GTPase activating protein 33	1089					protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|Rac GTPase activator activity (GO:0030675)			endometrium(7)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	37						ACTATGAGATCGGGGCAAGTG	0.652																																					p.I928I		Atlas-SNP	.											.	ARHGAP33	102	.	0			c.C2784T						.						35	37	36					19																	36278734		2203	4299	6502	SO:0001819	synonymous_variant	115703	exon21			TGAGATCGGGGCA	AY044864	CCDS12477.1, CCDS54254.1	19q13.13	2011-06-29	2010-02-19	2010-02-19		ENSG00000004777		"Rho GTPase activating proteins"	23085	protein-coding gene	gene with protein product		614902	"sorting nexin 26"	SNX26		12297274, 12461558	Standard	NM_052948		Approved	FLJ39019, TCGAP	uc002obs.2	O14559		ENST00000007510.4:c.3267C>T	chr19.hg19:g.36278734C>T		225.0	0.0		638.0	30.0	NM_052948	O14552|O14560|Q6ZSP6|Q96CP3|Q9NT23	Silent	SNP	ENST00000007510.4	hg19																																																																																				.	.		0.652	ARHGAP33-201	KNOWN	basic	protein_coding	protein_coding		NM_052948		T	36278734	C	T	36278734	2	4	343	1	0	0	0	0	0	0	0	1	882	874	31	1		1	ARHGAP33	19	36278734	Silent	SNP	C	TCGA-UB-A7MA-01A-11D-A33Q-10	17142122	36278734	22850249	56	47345										
AKT2	208	hgsc.bcm.edu	37	chr19	40746009	40746009	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	ctctcggtgactgtgtgagcGacttcatcctgcagacagac	11	12	2	4			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr19:40746009G>T	ENST00000392038.2	-	7	880	c.582C>A	c.(580-582)gtC>gtA	p.V194V	AKT2_ENST00000311278.6_Silent_p.V194V|AKT2_ENST00000579047.1_Silent_p.V132V|AKT2_ENST00000424901.1_Silent_p.V194V	NM_001243027.1|NM_001243028.1|NM_001626.4	NP_001229956.1|NP_001229957.1|NP_001617.1	P31751	AKT2_HUMAN	v-akt murine thymoma viral oncogene homolog 2	194	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of Ral GTPase activity (GO:0032859)|apoptotic process (GO:0006915)|carbohydrate transport (GO:0008643)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|fat cell differentiation (GO:0045444)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|insulin receptor signaling pathway (GO:0008286)|intracellular protein transmembrane transport (GO:0065002)|mammary gland epithelial cell differentiation (GO:0060644)|membrane organization (GO:0061024)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|peripheral nervous system myelin maintenance (GO:0032287)|positive regulation of cell motility (GO:2000147)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)|protein localization to plasma membrane (GO:0072659)|regulation of cell cycle arrest (GO:0071156)|regulation of cell migration (GO:0030334)|regulation of translation (GO:0006417)|signal transduction (GO:0007165)	cell cortex (GO:0005938)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|kidney(3)|large_intestine(9)|lung(10)|prostate(2)|skin(1)	27			Lung(22;0.000499)			CTGTGTGAGCGACTTCATCCT	0.622			A		"ovarian, pancreatic "																																p.V194V		Atlas-SNP	.		Dom	yes		19	19q13.1-q13.2	208	v-akt murine thymoma viral oncogene homolog 2		E	.	AKT2	53	.	0			c.C582A						.						181	175	177					19																	40746009		2203	4300	6503	SO:0001819	synonymous_variant	208	exon7			GTGAGCGACTTCA	M77198	CCDS12552.1	19q13.1-q13.2	2013-01-10			ENSG00000105221	ENSG00000105221	2.7.11.1	"Pleckstrin homology (PH) domain containing"	392	protein-coding gene	gene with protein product		164731				1409633	Standard	NM_001626		Approved		uc002onf.3	P31751	OTTHUMG00000137375	ENST00000392038.2:c.582C>A	chr19.hg19:g.40746009G>T		90.0	0.0		158.0	123.0	NM_001626	B2RBD8|Q05BV0|Q0VAN0|Q0VAN1|Q68GC0	Silent	SNP	ENST00000392038.2	hg19	CCDS12552.1																																																																																			.	.		0.622	AKT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268029.1	NM_001626		T	40746009	G	T	40746009	2	4	343	1	0	0	0	0	0	0	0	1	480	1045	37	1		1	AKT2	19	40746009	Silent	SNP	G	TCGA-UB-A7MA-01A-11D-A33Q-10	4467275	40746009	18382974	57	47346										
MIA	8190	hgsc.bcm.edu	37	chr19	41281480	41281480	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	ctggtgtgccttggtgtcatCatcttgctgtctgccttctc	10	12	5	0			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr19:41281480C>T	ENST00000263369.3	+	1	199	c.33C>T	c.(31-33)atC>atT	p.I11I	MIA_ENST00000594436.1_Silent_p.I11I|RAB4B-EGLN2_ENST00000594136.1_5'Flank|MIA_ENST00000597784.1_Silent_p.I11I|MIA-RAB4B_ENST00000600729.1_Silent_p.I11I|RAB4B_ENST00000357052.2_5'Flank|RAB4B_ENST00000594800.1_5'Flank	NM_006533.3	NP_006524.1	Q16674	MIA_HUMAN	melanoma inhibitory activity	11					cell proliferation (GO:0008283)	extracellular space (GO:0005615)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	4			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)	GBM - Glioblastoma multiforme(1328;0.0199)		TTGGTGTCATCATCTTGCTGT	0.612																																					p.I11I		Atlas-SNP	.											.	MIA	16	.	0			c.C33T						.						185	157	166					19																	41281480		2203	4300	6503	SO:0001819	synonymous_variant	8190	exon2			TGTCATCATCTTG	X75450	CCDS12566.1	19q13.2	2012-10-15			ENSG00000261857	ENSG00000261857			7076	protein-coding gene	gene with protein product		601340				7923218, 8661134	Standard	NM_006533		Approved	CD-RAP	uc021uuu.1	Q16674		ENST00000263369.3:c.33C>T	chr19.hg19:g.41281480C>T		62.0	0.0		122.0	74.0	NM_001202553	Q6FHV3	Silent	SNP	ENST00000263369.3	hg19	CCDS12566.1																																																																																			.	.		0.612	MIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463162.1			T	41281480	C	T	41281480	2	4	343	1	0	0	0	0	0	0	0	1	9572	816	29	3		3	MIA	19	41281480	Silent	SNP	C	TCGA-UB-A7MA-01A-11D-A33Q-10	535471	41281480	17847503	58	47347										
RAB4B	53916	hgsc.bcm.edu	37	chr19	41286374	41286374	+	Frame_Shift_Del	DEL	T	T	-													0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	gaagactgtgaagctacagaTttgggacacggctggccagg							TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr19:41286374delT	ENST00000594800.1	+	3	342	c.182delT	c.(181-183)attfs	p.I61fs	RAB4B-EGLN2_ENST00000594136.1_Frame_Shift_Del_p.I61fs|MIA-RAB4B_ENST00000600729.1_3'UTR|RAB4B-EGLN2_ENST00000601949.1_Intron|RAB4B_ENST00000357052.2_Frame_Shift_Del_p.I61fs|RAB4B_ENST00000602069.1_3'UTR			P61018	RAB4B_HUMAN	RAB4B, member RAS oncogene family	61					glucose import (GO:0046323)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	insulin-responsive compartment (GO:0032593)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	GTP binding (GO:0005525)			endometrium(2)|kidney(3)|large_intestine(3)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	11			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			AAGCTACAGATTTGGGACACG	0.567																																					p.I61fs		Pindel	.											.	RAB4B	26	.	0			c.181delA						.						83	70	75					19																	41286374		2203	4300	6503	SO:0001589	frameshift_variant	53916	exon3			.	AF165522	CCDS33030.1	19q13.2	2012-10-15			ENSG00000167578	ENSG00000167578		"RAB, member RAS oncogene"	9782	protein-coding gene	gene with protein product	"ras-related GTP-binding protein 4b", "small GTP binding protein RAB4B"	612945					Standard	NM_016154		Approved	FLJ78649, MGC52123	uc002opd.2	P61018		ENST00000594800.1:c.182delT	chr19.hg19:g.41286374delT	ENSP00000470246:p.Ile61fs	131.0	0.0		331.0	111.0	NM_016154	P22750|Q7Z514|Q9HBR6	Frame_Shift_Del	DEL	ENST00000594800.1	hg19	CCDS33030.1																																																																																			.	.		0.567	RAB4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463168.1	NM_016154		-	41286374	T	-	41286374	7	5	343	1	0	1	0	1	0	0	0	0	12962	1493	52	0	192	0	RAB4B	19	41286374	Frame_Shift_Del	DEL	T	TCGA-UB-A7MA-01A-11D-A33Q-10	4894	41286374	17842609	59	47348										
PVR	5817	hgsc.bcm.edu	37	chr19	45150523	45150523	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	gtcgtgcaggcgcccacccaGgtgcccggcttcttgggcga	15	15	1	0			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr19:45150523G>C	ENST00000425690.3	+	2	407	c.108G>C	c.(106-108)caG>caC	p.Q36H	PVR_ENST00000344956.4_Missense_Mutation_p.Q36H|CTB-171A8.1_ENST00000590796.1_RNA|PVR_ENST00000406449.4_Missense_Mutation_p.Q36H|PVR_ENST00000403059.4_Missense_Mutation_p.Q36H	NM_006505.3	NP_006496.3	P15151	PVR_HUMAN	poliovirus receptor	36	Ig-like V-type.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|susceptibility to natural killer cell mediated cytotoxicity (GO:0042271)|susceptibility to T cell mediated cytotoxicity (GO:0060370)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|receptor activity (GO:0004872)			large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	6	Lung NSC(12;0.00608)|all_lung(12;0.0148)	Medulloblastoma(540;0.0425)|Ovarian(192;0.0728)|Prostate(69;0.081)|all_neural(266;0.112)		Epithelial(262;0.000601)		CGCCCACCCAGGTGCCCGGCT	0.652																																					p.Q36H		Atlas-SNP	.											.	PVR	23	.	0			c.G108C						.						12	12	12					19																	45150523		2179	4262	6441	SO:0001583	missense	5817	exon2			CACCCAGGTGCCC	BC015542	CCDS12640.1, CCDS46105.1, CCDS46106.1, CCDS46107.1	19q13.2	2013-01-29			ENSG00000073008	ENSG00000073008		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9705	protein-coding gene	gene with protein product	"nectin-like 5"	173850		PVS		2170108	Standard	XM_005259120		Approved	CD155, HVED, Necl-5, NECL5, Tage4	uc002ozm.3	P15151	OTTHUMG00000151527	ENST00000425690.3:c.108G>C	chr19.hg19:g.45150523G>C	ENSP00000402060:p.Gln36His	67.0	0.0		83.0	12.0	NM_001135769	B4DTS9|P15152|Q15267|Q15268|Q96BJ1	Missense_Mutation	SNP	ENST00000425690.3	hg19	CCDS12640.1	.	.	.	.	.	.	.	.	.	.	G	15.16	2.752036	0.49362	.	.	ENSG00000073008	ENST00000344956;ENST00000425690;ENST00000406449;ENST00000403059	T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16	4.79	-1.49	0.08718	Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.438380	0.04845	N	0.441376	T	0.70579	0.3240	M	0.66939	2.045	0.09310	N	1	D;D;D;D	0.76494	0.999;0.991;0.991;0.992	D;D;D;D	0.71870	0.972;0.972;0.958;0.975	T	0.54918	-0.8221	10	0.40728	T	0.16	.	0.7982	0.01070	0.2916:0.1557:0.3815:0.1713	.	36;36;36;36	P15151-2;P15151-3;P15151-4;P15151	.;.;.;PVR_HUMAN	H	36	ENSP00000340870:Q36H;ENSP00000402060:Q36H;ENSP00000383907:Q36H;ENSP00000385344:Q36H	ENSP00000340870:Q36H	Q	+	3	2	PVR	49842363	0.107000	0.21998	0.000000	0.03702	0.054000	0.15201	0.374000	0.20501	-0.475000	0.06852	-0.373000	0.07131	CAG	.	.		0.652	PVR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323017.2	NM_006505		C	45150523	G	C	45150523	3	2	343	1	0	0	0	0	1	0	0	0	12852	991	35	4	114	4	PVR	19	45150523	Missense_Mutation	SNP	G	TCGA-UB-A7MA-01A-11D-A33Q-10	3864149	45150523	13978460	60	47349										
MYBPC2	4606	hgsc.bcm.edu	37	chr19	50957538	50957538	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	gcagatgtcccagaccccccGgaggctgtgcgcatcacctc	11	17	1	2	rs558923030	byFrequency	TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr19:50957538G>A	ENST00000357701.5	+	18	1977	c.1926G>A	c.(1924-1926)ccG>ccA	p.P642P		NM_004533.3	NP_004524.3	Q14324	MYPC2_HUMAN	myosin binding protein C, fast type	642	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			breast(1)	1		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.0079)|GBM - Glioblastoma multiforme(134;0.0144)		CAGACCCCCCGGAGGCTGTGC	0.647													g|||	7	0.00139776	0	0	5008	,	,		14805	0		0	False		,,,				2504	0.0072				p.P642P		Atlas-SNP	.											.	MYBPC2	103	.	0			c.G1926A						.						38	40	39					19																	50957538		1994	4154	6148	SO:0001819	synonymous_variant	4606	exon18			CCCCCCGGAGGCT		CCDS46152.1	19q13.33	2013-02-11	2001-11-28		ENSG00000086967	ENSG00000086967		"Myosin binding proteins", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7550	protein-coding gene	gene with protein product	"fast-type muscle myosin-binding-protein C"	160793	"myosin-binding protein C, fast-type"			8375400	Standard	NM_004533		Approved	MYBPCF, MYBPC, MGC163408	uc002psf.2	Q14324		ENST00000357701.5:c.1926G>A	chr19.hg19:g.50957538G>A		103.0	0.0		44.0	31.0	NM_004533	A1L4G9	Silent	SNP	ENST00000357701.5	hg19	CCDS46152.1																																																																																			.	.		0.647	MYBPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464751.1	NM_004533		A	50957538	G	A	50957538	2	1	343	1	0	0	0	0	0	0	0	1	10021	1103	39	1		1	MYBPC2	19	50957538	Silent	SNP	G	TCGA-UB-A7MA-01A-11D-A33Q-10	5807015	50957538	8171445	61	47350										
HAO1	54363	hgsc.bcm.edu	37	chr20	7915180	7915180	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	tgagccatgcgctgcatggcCgtagcccccacacatattgg	11	14	0	1	rs200105698		TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr20:7915180C>A	ENST00000378789.3	-	2	291	c.240G>T	c.(238-240)acG>acT	p.T80T		NM_017545.2	NP_060015.1	Q9UJM8	HAOX1_HUMAN	hydroxyacid oxidase (glycolate oxidase) 1	80	FMN hydroxy acid dehydrogenase. {ECO:0000255|PROSITE-ProRule:PRU00683}.				cellular nitrogen compound metabolic process (GO:0034641)|fatty acid alpha-oxidation (GO:0001561)|glycolate catabolic process (GO:0046296)|glyoxylate metabolic process (GO:0046487)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	(S)-2-hydroxy-acid oxidase activity (GO:0003973)|FMN binding (GO:0010181)|glycolate oxidase activity (GO:0008891)|glyoxylate oxidase activity (GO:0047969)|long-chain-(S)-2-hydroxy-long-chain-acid oxidase activity (GO:0052853)|medium-chain-(S)-2-hydroxy-acid oxidase activity (GO:0052854)|receptor binding (GO:0005102)|very-long-chain-(S)-2-hydroxy-acid oxidase activity (GO:0052852)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36						GCTGCATGGCCGTAGCCCCCA	0.532																																					p.T80T		Atlas-SNP	.											.	HAO1	71	.	0			c.G240T						.						106	95	99					20																	7915180		2203	4300	6503	SO:0001819	synonymous_variant	54363	exon2			CATGGCCGTAGCC	AL021879	CCDS13100.1	20p12	2005-01-10			ENSG00000101323	ENSG00000101323	1.1.3.15		4809	protein-coding gene	gene with protein product		605023		GOX1		9891009	Standard	NM_017545		Approved	GOX	uc002wmw.1	Q9UJM8	OTTHUMG00000031841	ENST00000378789.3:c.240G>T	chr20.hg19:g.7915180C>A		89.0	0.0		92.0	17.0	NM_017545	Q14CQ0|Q9UPZ0|Q9Y3I7	Silent	SNP	ENST00000378789.3	hg19	CCDS13100.1																																																																																			.	C|0.999;G|0.001		0.532	HAO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077926.2			A	7915180	C	A	7915180	2	1	343	1	0	0	0	0	0	0	0	1	6960	639	23	1		1	HAO1	20	7915180	Silent	SNP	C	TCGA-UB-A7MA-01A-11D-A33Q-10		7915180	55110340	62	47351										
C20orf12	55184	hgsc.bcm.edu	37	chr20	18393405	18393405	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	agcagcttgccagatgggtaGaagaggccaacagtctgtgt	14	8	1	3			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr20:18393405G>A	ENST00000358866.6	-	12	1339	c.1317C>T	c.(1315-1317)ttC>ttT	p.F439F	DZANK1_ENST00000262547.5_Silent_p.F439F|DZANK1_ENST00000329494.5_Silent_p.F441F|DZANK1_ENST00000357236.4_Silent_p.F325F|DZANK1_ENST00000487128.1_5'UTR			Q9NVP4	DZAN1_HUMAN	double zinc ribbon and ankyrin repeat domains 1	439							zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(10)	19						CAGATGGGTAGAAGAGGCCAA	0.512																																					p.F439F		Atlas-SNP	.											.	DZANK1	65	.	0			c.C1317T						.						179	168	171					20																	18393405		1931	4132	6063	SO:0001819	synonymous_variant	55184	exon13			TGGGTAGAAGAGG	AK001462	CCDS46582.1	20p11.23	2013-01-11	2011-10-03	2011-10-03	ENSG00000089091	ENSG00000089091		"Ankyrin repeat domain containing"	15858	protein-coding gene	gene with protein product	"ankyrin repeat domain 64"		"chromosome 20 open reading frame 12"	C20orf84, C20orf12			Standard	NM_001099407		Approved	FLJ10600, dJ568F9.2, FLJ30892, bA189K21.8, ANKRD64	uc002wqq.4	Q9NVP4	OTTHUMG00000031968	ENST00000358866.6:c.1317C>T	chr20.hg19:g.18393405G>A		98.0	0.0		159.0	42.0	NM_001099407	B7ZLZ4|Q4F7X1|Q5QPD9|Q5QPE0|Q68DN8|Q6ZMX9|Q96NF0|Q9H1E0|Q9H442	Silent	SNP	ENST00000358866.6	hg19	CCDS46582.1	.	.	.	.	.	.	.	.	.	.	G	7.067	0.567605	0.13560	.	.	ENSG00000089091	ENST00000358866	.	.	.	5.51	2.18	0.27775	.	.	.	.	.	T	0.58250	0.2109	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53180	-0.8475	4	.	.	.	-19.4079	9.2005	0.37256	0.3459:0.0:0.6541:0.0	.	.	.	.	F	238	.	.	S	-	2	0	C20orf12	18341405	1.000000	0.71417	1.000000	0.80357	0.627000	0.37826	1.389000	0.34453	0.703000	0.31848	-0.143000	0.13931	TCT	.	.		0.512	DZANK1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471926.1	NM_001099407		A	18393405	G	A	18393405	2	1	343	1	0	0	0	0	0	0	0	1	2087	933	33	3		3	C20orf12	20	18393405	Silent	SNP	G	TCGA-UB-A7MA-01A-11D-A33Q-10	10478225	18393405	44632115	63	47352										
NINL	22981	hgsc.bcm.edu	37	chr20	25434223	25434223	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	gaagtgctctcaccaggtggGcgttctccacgtacagctcc	11	14	2	0			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr20:25434223G>C	ENST00000278886.6	-	24	4086	c.4013C>G	c.(4012-4014)gCc>gGc	p.A1338G	NINL_ENST00000464285.1_5'UTR|NINL_ENST00000422516.1_Missense_Mutation_p.A989G	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	1338					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|microtubule (GO:0005874)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(13)|lung(25)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	57						CACCAGGTGGGCGTTCTCCAC	0.557																																					p.A1338G		Atlas-SNP	.											.	NINL	148	.	0			c.C4013G						.						96	85	89					20																	25434223		2203	4300	6503	SO:0001583	missense	22981	exon24			AGGTGGGCGTTCT		CCDS33452.1	20p11.22-p11.1	2013-01-10			ENSG00000101004	ENSG00000101004		"EF-hand domain containing"	29163	protein-coding gene	gene with protein product	"ninein-like protein"	609580				10231032	Standard	XM_005260678		Approved	KIAA0980, NLP	uc002wux.1	Q9Y2I6	OTTHUMG00000032127	ENST00000278886.6:c.4013C>G	chr20.hg19:g.25434223G>C	ENSP00000278886:p.Ala1338Gly	126.0	0.0		115.0	26.0	NM_025176	A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	Missense_Mutation	SNP	ENST00000278886.6	hg19	CCDS33452.1	.	.	.	.	.	.	.	.	.	.	G	17.13	3.309595	0.60414	.	.	ENSG00000101004	ENST00000278886;ENST00000422516	T;T	0.48201	0.82;0.82	4.89	3.92	0.45320	.	0.152963	0.41823	N	0.000808	T	0.67477	0.2897	M	0.80183	2.485	0.24110	N	0.995841	B;D;D	0.69078	0.412;0.983;0.997	B;D;D	0.66716	0.104;0.943;0.946	T	0.62364	-0.6870	10	0.49607	T	0.09	-12.3693	14.0661	0.64831	0.0:0.1525:0.8475:0.0	.	989;1338;129	Q9Y2I6-2;Q9Y2I6;Q9HAD5	.;NINL_HUMAN;.	G	1338;989	ENSP00000278886:A1338G;ENSP00000410431:A989G	ENSP00000278886:A1338G	A	-	2	0	NINL	25382223	1.000000	0.71417	0.962000	0.40283	0.113000	0.19764	5.303000	0.65738	1.263000	0.44181	0.655000	0.94253	GCC	.	.		0.557	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078445.3	NM_025176		C	25434223	G	C	25434223	3	2	343	1	0	0	0	0	1	0	0	0	10429	1203	42	4	139	4	NINL	20	25434223	Missense_Mutation	SNP	G	TCGA-UB-A7MA-01A-11D-A33Q-10	7040818	25434223	37591297	64	47353										
XKR7	343702	hgsc.bcm.edu	37	chr20	30584708	30584708	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	atcgtcctgctggagaacgcCgcgctcaccggcttctggta	12	14	2	1			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr20:30584708C>T	ENST00000562532.2	+	3	1362	c.1188C>T	c.(1186-1188)gcC>gcT	p.A396A		NM_001011718.1	NP_001011718.1	Q5GH72	XKR7_HUMAN	XK, Kell blood group complex subunit-related family, member 7	396						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(19)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	34			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			TGGAGAACGCCGCGCTCACCG	0.597																																					p.A396A		Atlas-SNP	.											.	XKR7	62	.	0			c.C1188T						.						62	56	58					20																	30584708		2203	4300	6503	SO:0001819	synonymous_variant	343702	exon3			GAACGCCGCGCTC	AY534245	CCDS33459.1	20q11.21	2014-07-16	2006-01-12		ENSG00000260903	ENSG00000260903			23062	protein-coding gene	gene with protein product			"X Kell blood group precursor-related family, member 7", "chromosome 20 open reading frame 159"	C20orf159			Standard	NM_001011718		Approved	dJ310O13.4	uc002wxe.3	Q5GH72	OTTHUMG00000032198	ENST00000562532.2:c.1188C>T	chr20.hg19:g.30584708C>T		69.0	0.0		78.0	17.0	NM_001011718	Q9NUG5	Silent	SNP	ENST00000562532.2	hg19	CCDS33459.1																																																																																			.	.		0.597	XKR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078597.3	NM_001011718		T	30584708	C	T	30584708	2	4	343	1	0	0	0	0	0	0	0	1	17451	639	23	1		1	XKR7	20	30584708	Silent	SNP	C	TCGA-UB-A7MA-01A-11D-A33Q-10	5150485	30584708	32440812	65	47354										
ZNF334	55713	hgsc.bcm.edu	37	chr20	45130323	45130323	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	gggctgacttcctgcagtagGttctcccacattcattgcat	9	12	2	1			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr20:45130323G>C	ENST00000347606.4	-	5	1837	c.1655C>G	c.(1654-1656)aCc>aGc	p.T552S	ZNF334_ENST00000457685.2_Missense_Mutation_p.T514S|ZNF334_ENST00000593880.1_Missense_Mutation_p.T575S	NM_018102.4	NP_060572.3	Q9HCZ1	ZN334_HUMAN	zinc finger protein 334	552					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0122)				CCTGCAGTAGGTTCTCCCACA	0.458																																					p.T552S		Atlas-SNP	.											.	ZNF334	101	.	0			c.C1655G						.						167	158	161					20																	45130323		2203	4300	6503	SO:0001583	missense	55713	exon5			CAGTAGGTTCTCC	AK001331	CCDS33480.1, CCDS74736.1	20q13.12	2013-09-20			ENSG00000198185	ENSG00000198185		"Zinc fingers, C2H2-type", "-"	15806	protein-coding gene	gene with protein product							Standard	NM_018102		Approved	bA179N14.1	uc002xsc.4	Q9HCZ1	OTTHUMG00000032654	ENST00000347606.4:c.1655C>G	chr20.hg19:g.45130323G>C	ENSP00000255129:p.Thr552Ser	60.0	0.0		77.0	15.0	NM_018102	Q5T6U2|Q9NVW4	Missense_Mutation	SNP	ENST00000347606.4	hg19	CCDS33480.1	.	.	.	.	.	.	.	.	.	.	G	8.084	0.773123	0.16051	.	.	ENSG00000198185	ENST00000457685;ENST00000347606	T;T	0.27402	1.67;1.67	2.88	0.567	0.17325	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.17789	0.0427	N	0.16016	0.355	0.09310	N	1	B;B;B	0.14438	0.01;0.01;0.01	B;B;B	0.10450	0.005;0.005;0.005	T	0.24368	-1.0162	9	0.44086	T	0.13	.	9.7278	0.40342	0.0:0.5911:0.4089:0.0	.	514;552;575	B3KQ93;Q9HCZ1;Q8N3P8	.;ZN334_HUMAN;.	S	514;552	ENSP00000402582:T514S;ENSP00000255129:T552S	ENSP00000255129:T552S	T	-	2	0	ZNF334	44563730	0.000000	0.05858	0.957000	0.39632	0.912000	0.54170	-0.370000	0.07523	0.522000	0.28464	0.491000	0.48974	ACC	.	.		0.458	ZNF334-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079575.1			C	45130323	G	C	45130323	3	2	343	1	0	0	0	0	1	0	0	0	17866	1261	44	4	391	4	ZNF334	20	45130323	Missense_Mutation	SNP	G	TCGA-UB-A7MA-01A-11D-A33Q-10	14545615	45130323	17895197	66	47355										
NCOA3	8202	hgsc.bcm.edu	37	chr20	46268408	46268408	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	aaaggccggcagaatggaacCtatgaattcaaactccatgg	10	9	1	2			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr20:46268408C>G	ENST00000371998.3	+	15	2986	c.2795C>G	c.(2794-2796)cCt>cGt	p.P932R	NCOA3_ENST00000372004.3_Missense_Mutation_p.P932R|NCOA3_ENST00000371997.3_Missense_Mutation_p.P927R|NCOA3_ENST00000341724.6_Missense_Mutation_p.P862R			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	932					androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			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						AGAATGGAACCTATGAATTCA	0.493																																					p.P932R		Atlas-SNP	.											.	NCOA3	156	.	0			c.C2795G						.						126	135	132					20																	46268408		2203	4300	6503	SO:0001583	missense	8202	exon15			TGGAACCTATGAA	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7670	protein-coding gene	gene with protein product	"receptor-associated coactivator 3", "thyroid hormone receptor activator molecule 1"	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.2795C>G	chr20.hg19:g.46268408C>G	ENSP00000361066:p.Pro932Arg	102.0	0.0		161.0	46.0	NM_181659	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Missense_Mutation	SNP	ENST00000371998.3	hg19	CCDS13407.1	.	.	.	.	.	.	.	.	.	.	C	11.98	1.801183	0.31869	.	.	ENSG00000124151	ENST00000340189;ENST00000341724;ENST00000372004;ENST00000371998;ENST00000371997	T;T;T;T	0.02525	4.26;4.62;4.63;4.31	5.89	4.88	0.63580	.	0.240010	0.36409	N	0.002616	T	0.05823	0.0152	M	0.61703	1.905	0.21897	N	0.999481	B;B;B;B;B;B	0.14805	0.005;0.006;0.011;0.005;0.008;0.005	B;B;B;B;B;B	0.15870	0.005;0.01;0.014;0.006;0.014;0.006	T	0.14448	-1.0472	10	0.51188	T	0.08	-8.9246	17.7823	0.88527	0.1305:0.8695:0.0:0.0	.	932;927;936;932;932;932	A8K0W8;Q9Y6Q9-3;Q59EE8;Q0IIN7;Q9Y6Q9-5;Q9Y6Q9	.;.;.;.;.;NCOA3_HUMAN	R	932;862;932;932;927	ENSP00000342123:P862R;ENSP00000361073:P932R;ENSP00000361066:P932R;ENSP00000361065:P927R	ENSP00000345671:P932R	P	+	2	0	NCOA3	45701815	0.076000	0.21285	0.381000	0.26106	0.795000	0.44927	3.505000	0.53356	2.782000	0.95742	0.557000	0.71058	CCT	.	.		0.493	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534		G	46268408	C	G	46268408	3	3	343	1	0	0	0	0	1	0	0	0	10239	681	24	4	2875	4	NCOA3	20	46268408	Missense_Mutation	SNP	C	TCGA-UB-A7MA-01A-11D-A33Q-10	1138085	46268408	16757112	67	47356										
CRYZL1	9946	hgsc.bcm.edu	37	chr21	34994363	34994363	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	aaatcctttttcatcttcatTtctgccagaagctaaatcat	3	10	5	1			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr21:34994363T>G	ENST00000381554.3	-	4	241	c.156A>C	c.(154-156)gaA>gaC	p.E52D	CRYZL1_ENST00000381540.3_Missense_Mutation_p.E52D|CRYZL1_ENST00000413017.2_Missense_Mutation_p.E52D|CRYZL1_ENST00000445393.1_Missense_Mutation_p.E52D|AP000304.12_ENST00000429238.1_Intron|CRYZL1_ENST00000290244.5_Missense_Mutation_p.E52D|CRYZL1_ENST00000361534.2_Missense_Mutation_p.E76D	NM_145858.2	NP_665857.2	O95825	QORL1_HUMAN	crystallin, zeta (quinone reductase)-like 1	52					quinone metabolic process (GO:1901661)	cytosol (GO:0005829)	NADP binding (GO:0050661)|NADPH:quinone reductase activity (GO:0003960)|zinc ion binding (GO:0008270)			lung(1)|prostate(1)|urinary_tract(1)	3						TCATCTTCATTTCTGCCAGAA	0.328																																					p.E52D		Atlas-SNP	.											.	CRYZL1	16	.	0			c.A156C						.						78	82	81					21																	34994363		2202	4298	6500	SO:0001583	missense	9946	exon4			CTTCATTTCTGCC	AF029689	CCDS13633.2	21q22.1	2008-07-31			ENSG00000205758	ENSG00000205758			2420	protein-coding gene	gene with protein product	"quinone reductase-like 1"	603920				10191096	Standard	NM_145858		Approved	QOH-1, 4P11	uc021wio.1	O95825	OTTHUMG00000065954	ENST00000381554.3:c.156A>C	chr21.hg19:g.34994363T>G	ENSP00000370966:p.Glu52Asp	387.0	0.0		313.0	119.0	NM_145858	B2RDX1|B3KQ77|Q96DY0|Q9NVY7	Missense_Mutation	SNP	ENST00000381554.3	hg19	CCDS13633.2	.	.	.	.	.	.	.	.	.	.	T	10.78	1.446999	0.25987	.	.	ENSG00000205758	ENST00000381554;ENST00000290244;ENST00000381540;ENST00000445393;ENST00000361534;ENST00000452332;ENST00000431177;ENST00000413017	T;T;T;T;T;T;T	0.41400	3.61;1.0;3.61;1.0;3.61;3.61;3.61	4.95	2.52	0.30459	GroES-like (1);Alcohol dehydrogenase GroES-like (1);	0.052099	0.85682	D	0.000000	T	0.24353	0.0590	L	0.27944	0.81	0.80722	D	1	B;B;B	0.16396	0.017;0.003;0.017	B;B;B	0.18263	0.021;0.021;0.021	T	0.06092	-1.0846	10	0.13853	T	0.58	-17.7987	6.8537	0.24028	0.0:0.1783:0.0:0.8217	.	52;52;76	O95825;A6NND8;A6NHJ8	QORL1_HUMAN;.;.	D	52;52;52;52;76;52;52;52	ENSP00000370966:E52D;ENSP00000290244:E52D;ENSP00000370951:E52D;ENSP00000399730:E52D;ENSP00000355075:E76D;ENSP00000405510:E52D;ENSP00000389209:E52D	ENSP00000290244:E52D	E	-	3	2	CRYZL1	33916233	1.000000	0.71417	0.994000	0.49952	0.929000	0.56500	2.117000	0.41939	0.237000	0.21200	0.383000	0.25322	GAA	.	.		0.328	CRYZL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141282.2	NM_145858		G	34994363	T	G	34994363	3	3	343	1	0	0	0	0	1	0	0	0	3925	1838	64	5	933	5	CRYZL1	21	34994363	Missense_Mutation	SNP	T	TCGA-UB-A7MA-01A-11D-A33Q-10		34994363	13135532	68	47357										
OR11H1	81061	hgsc.bcm.edu	37	chr22	16448905	16448905	+	Frame_Shift_Del	DEL	G	G	-													0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	aggctatagataaggggattGaagagtggggtcaccatagc							TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr22:16448905delG	ENST00000252835.4	-	1	900	c.900delC	c.(898-900)ttcfs	p.F300fs		NM_001005239.1	NP_001005239.1	Q8NG94	O11H1_HUMAN	olfactory receptor, family 11, subfamily H, member 1	300						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)|skin(1)	11	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.208)		Kidney(3;0.00216)|KIRC - Kidney renal clear cell carcinoma(3;0.00244)|Lung(27;0.0724)|COAD - Colon adenocarcinoma(3;0.211)		TAAGGGGATTGAAGAGTGGGG	0.428																																					p.N301fs		Atlas-INDEL	.											.	OR11H1	44	.	0			c.901delA						.						1	1	1					22																	16448905		111	219	330	SO:0001589	frameshift_variant	81061	exon1			.	AP000535, AF399611	CCDS74807.1	22q11.1	2012-08-09			ENSG00000130538	ENSG00000130538		"GPCR / Class A : Olfactory receptors"	15404	protein-coding gene	gene with protein product						12213199	Standard	NM_001005239		Approved	OR22-1	uc011agd.2	Q8NG94	OTTHUMG00000030069	ENST00000252835.4:c.900delC	chr22.hg19:g.16448905delG	ENSP00000252835:p.Phe300fs	353.0	0.0		331.0	22.0	NM_001005239	Q6IEX0|Q96R32	Frame_Shift_Del	DEL	ENST00000252835.4	hg19	CCDS33594.1																																																																																			.	.		0.428	OR11H1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074923.2	NM_001005239		-	16448905	G	-	16448905	7	5	343	1	0	1	0	1	0	0	0	0	10935	1281	45	0	82	0	OR11H1	22	16448905	Frame_Shift_Del	DEL	G	TCGA-UB-A7MA-01A-11D-A33Q-10		16448905	34855661	69	47358										
GGT5	2687	hgsc.bcm.edu	37	chr22	24628913	24628913	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	ggctggaacagctgcgcccaGggcaggcggccatggcggcg	19	13	0	0			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr22:24628913G>C	ENST00000327365.4	-	4	890	c.474C>G	c.(472-474)ccC>ccG	p.P158P	GGT5_ENST00000418439.2_Missense_Mutation_p.L83V|GGT5_ENST00000398292.3_Silent_p.P158P|GGT5_ENST00000263112.7_Silent_p.P126P	NM_001099781.1|NM_004121.2	NP_001093251.1|NP_004112.2	P36269	GGT5_HUMAN	gamma-glutamyltransferase 5	158					arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|inflammatory response (GO:0006954)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)	anchored component of external side of plasma membrane (GO:0031362)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(3)|skin(3)	28						GCTGCGCCCAGGGCAGGCGGC	0.701																																					p.P158P		Atlas-SNP	.											.	GGT5	61	.	0			c.C474G						.						20	22	21					22																	24628913		2182	4269	6451	SO:0001819	synonymous_variant	2687	exon4			CGCCCAGGGCAGG	M64099	CCDS13825.1, CCDS42989.1, CCDS42990.1	22q11.23	2008-03-25	2008-03-10	2008-03-10	ENSG00000099998	ENSG00000099998		"Gamma-glutamyltransferases"	4260	protein-coding gene	gene with protein product		137168	"gamma-glutamyltransferase-like activity 1"	GGTLA1		1676842, 8095916, 18357469	Standard	NM_004121		Approved	GGT-REL	uc002zzp.4	P36269	OTTHUMG00000150796	ENST00000327365.4:c.474C>G	chr22.hg19:g.24628913G>C		84.0	0.0		78.0	36.0	NM_001099781	Q53XM9|Q6GMP0|Q96FC1|Q9UFM5	Silent	SNP	ENST00000327365.4	hg19	CCDS13825.1	.	.	.	.	.	.	.	.	.	.	G	15.12	2.738833	0.49045	.	.	ENSG00000099998	ENST00000418439	T	0.25912	1.77	4.32	0.819	0.18785	.	.	.	.	.	T	0.11623	0.0283	.	.	.	0.23704	N	0.997069	P	0.43094	0.799	B	0.37731	0.257	T	0.13469	-1.0508	8	0.17369	T	0.5	-37.4935	3.3472	0.07140	0.2141:0.0:0.4922:0.2937	.	83	E7EUG3	.	V	83	ENSP00000392146:L83V	ENSP00000392146:L83V	L	-	1	2	GGT5	22958913	0.051000	0.20477	1.000000	0.80357	0.997000	0.91878	-0.958000	0.03857	0.570000	0.29347	0.585000	0.79938	CTG	.	.		0.701	GGT5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320119.1	NM_004121		C	24628913	G	C	24628913	2	2	343	1	0	0	0	0	0	0	0	1	6370	987	35	4		4	GGT5	22	24628913	Silent	SNP	G	TCGA-UB-A7MA-01A-11D-A33Q-10	8180008	24628913	26675653	70	47359										
TCF20	6942	hgsc.bcm.edu	37	chr22	42610029	42610029	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	agcctgcagcatgagaattaGgactgggcatcattgatggg	14	7	1	2			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chr22:42610029G>C	ENST00000359486.3	-	1	1419	c.1283C>G	c.(1282-1284)cCt>cGt	p.P428R	TCF20_ENST00000335626.4_Missense_Mutation_p.P428R	NM_005650.1	NP_005641.1	Q9UGU0	TCF20_HUMAN	transcription factor 20 (AR1)	428					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(13)|lung(22)|ovary(5)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(5)	66						ATGAGAATTAGGACTGGGCAT	0.478																																					p.P428R		Atlas-SNP	.											.	TCF20	164	.	0			c.C1283G						.						129	128	128					22																	42610029		2203	4300	6503	SO:0001583	missense	6942	exon1			GAATTAGGACTGG	U19345	CCDS14032.1, CCDS14033.1	22q13.3	2011-02-08			ENSG00000100207	ENSG00000100207			11631	protein-coding gene	gene with protein product	"stromelysin-1 platelet-derived growth factor-responsive element binding protein"	603107				9730594, 10995766	Standard	NM_005650		Approved	AR1, SPBP	uc003bcj.1	Q9UGU0	OTTHUMG00000150920	ENST00000359486.3:c.1283C>G	chr22.hg19:g.42610029G>C	ENSP00000352463:p.Pro428Arg	119.0	0.0		111.0	26.0	NM_181492	A9JX12|O14528|Q13078|Q4V353|Q9H4M0	Missense_Mutation	SNP	ENST00000359486.3	hg19	CCDS14033.1	.	.	.	.	.	.	.	.	.	.	G	16.03	3.006874	0.54361	.	.	ENSG00000100207	ENST00000359486;ENST00000335626	T;T	0.32988	1.43;1.43	6.17	6.17	0.99709	.	0.000000	0.64402	D	0.000005	T	0.50548	0.1622	L	0.46157	1.445	0.80722	D	1	D;D	0.71674	0.998;0.996	D;P	0.67382	0.951;0.895	T	0.38415	-0.9662	10	0.66056	D	0.02	-14.8461	19.0599	0.93085	0.0:0.0:1.0:0.0	.	428;428	Q9UGU0-2;Q9UGU0	.;TCF20_HUMAN	R	428	ENSP00000352463:P428R;ENSP00000335561:P428R	ENSP00000335561:P428R	P	-	2	0	TCF20	40939973	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.227000	0.65305	2.941000	0.99782	0.655000	0.94253	CCT	.	.		0.478	TCF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320531.1	NM_181492		C	42610029	G	C	42610029	3	2	343	1	0	0	0	0	1	0	0	0	15705	1000	35	4	4637	4	TCF20	22	42610029	Missense_Mutation	SNP	G	TCGA-UB-A7MA-01A-11D-A33Q-10	17981116	42610029	8694537	71	47360										
FAM47A	158724	hgsc.bcm.edu	37	chrX	34149696	34149696	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	tggaggctccgggcggagatGggacactccagtctcaggag	17	10	1	1			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chrX:34149696G>A	ENST00000346193.3	-	1	751	c.700C>T	c.(700-702)Cat>Tat	p.H234Y		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	234	Pro-rich.									NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	97						GGGCGGAGATGGGACACTCCA	0.642																																					p.H234Y		Atlas-SNP	.											.	FAM47A	249	.	0			c.C700T						.						32	34	33					X																	34149696		2201	4298	6499	SO:0001583	missense	158724	exon1			GGAGATGGGACAC	BC026171	CCDS43926.1	Xp21.1	2004-08-09			ENSG00000185448	ENSG00000185448			29962	protein-coding gene	gene with protein product	"similar to hypothetical protein FLJ35782"					12477932	Standard	NM_203408		Approved	MGC27003	uc004ddg.3	Q5JRC9	OTTHUMG00000021339	ENST00000346193.3:c.700C>T	chrX.hg19:g.34149696G>A	ENSP00000345029:p.His234Tyr	101.0	0.0		101.0	22.0	NM_203408	A8K8I9|Q8TAA0	Missense_Mutation	SNP	ENST00000346193.3	hg19	CCDS43926.1	.	.	.	.	.	.	.	.	.	.	G	4.051	0.007073	0.07866	.	.	ENSG00000185448	ENST00000346193	T	0.13538	2.58	0.235	-0.47	0.12131	.	.	.	.	.	T	0.13114	0.0318	N	0.19112	0.55	0.09310	N	1	D	0.62365	0.991	P	0.59115	0.852	T	0.29671	-1.0004	8	0.59425	D	0.04	.	.	.	.	.	234	Q5JRC9	FA47A_HUMAN	Y	234	ENSP00000345029:H234Y	ENSP00000345029:H234Y	H	-	1	0	FAM47A	34059617	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-0.342000	0.07801	-2.362000	0.00609	-2.407000	0.00222	CAT	.	.		0.642	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408		A	34149696	G	A	34149696	3	1	343	1	0	0	0	0	1	0	0	0	5577	1348	47	3	1679	3	FAM47A	23	34149696	Missense_Mutation	SNP	G	TCGA-UB-A7MA-01A-11D-A33Q-10		34149696	121120864	72	47361										
GRIA3	2892	hgsc.bcm.edu	37	chrX	122598767	122598767	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	ggtcttacatgaaatcagcgGagccatctgtgtttaccaaa	9	9	3	1			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chrX:122598767G>A	ENST00000371251.1	+	13	2180	c.2128G>A	c.(2128-2130)Gag>Aag	p.E710K	GRIA3_ENST00000542149.1_Missense_Mutation_p.E710K|GRIA3_ENST00000371256.5_Missense_Mutation_p.E710K|GRIA3_ENST00000264357.5_Missense_Mutation_p.E710K|AL356213.1_ENST00000577653.1_RNA			P42263	GRIA3_HUMAN	glutamate receptor, ionotropic, AMPA 3	710					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)			breast(2)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|pancreas(2)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	57					Lithium(DB01356)	GAAATCAGCGGAGCCATCTGT	0.463																																					p.E710K		Atlas-SNP	.											.	GRIA3	386	.	0			c.G2128A						.						82	76	78					X																	122598767		2203	4300	6503	SO:0001583	missense	2892	exon13			TCAGCGGAGCCAT	U10301	CCDS14604.1, CCDS14605.1, CCDS76017.1	Xq25	2012-08-29	2012-02-03		ENSG00000125675	ENSG00000125675		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4573	protein-coding gene	gene with protein product		305915	"glutamate receptor, ionotrophic, AMPA 3"	GLUR3		1319477, 10644433	Standard	NM_007325		Approved	GluA3, GLURC, MRX94	uc004etr.4	P42263	OTTHUMG00000022685	ENST00000371251.1:c.2128G>A	chrX.hg19:g.122598767G>A	ENSP00000360297:p.Glu710Lys	317.0	0.0		233.0	104.0	NM_000828	D3DTF1|Q4VXD5|Q4VXD6|Q9HDA0|Q9HDA1|Q9HDA2|Q9P0H1	Missense_Mutation	SNP	ENST00000371251.1	hg19	CCDS14604.1	.	.	.	.	.	.	.	.	.	.	G	14.23	2.473484	0.43942	.	.	ENSG00000125675	ENST00000264357;ENST00000542149;ENST00000371256;ENST00000371251	T;T;T;T	0.37584	1.19;1.19;1.19;1.19	5.12	5.12	0.69794	Ionotropic glutamate receptor (2);	0.000000	0.85682	D	0.000000	T	0.40322	0.1112	N	0.05510	-0.035	0.80722	D	1	D;D	0.63046	0.992;0.99	D;D	0.76071	0.987;0.979	T	0.47407	-0.9120	10	0.36615	T	0.2	.	16.5308	0.84357	0.0:0.0:1.0:0.0	.	710;710	P42263;P42263-2	GRIA3_HUMAN;.	K	710	ENSP00000264357:E710K;ENSP00000446146:E710K;ENSP00000360302:E710K;ENSP00000360297:E710K	ENSP00000264357:E710K	E	+	1	0	GRIA3	122426448	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	9.864000	0.99589	2.104000	0.64026	0.415000	0.27848	GAG	.	.		0.463	GRIA3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058854.1	NM_000828		A	122598767	G	A	122598767	3	1	343	1	0	0	0	0	1	0	0	0	6778	1175	41	3	2178	3	GRIA3	23	122598767	Missense_Mutation	SNP	G	TCGA-UB-A7MA-01A-11D-A33Q-10	88449071	122598767	32671793	73	47362										
GPR50	9248	hgsc.bcm.edu	37	chrX	150348392	150348392	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0945945945945946	7	1	1.06581674958541	2.65762098597919	0.592577652279145	1	1	0	tcatcacagggctgagtgtgGtcggctccatcttcaacatc	10	12	4	1			TCGA-UB-A7MA-01A-11D-A33Q-10	TCGA-UB-A7MA-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	efb3b274-562e-4ba8-908d-6343e61e5ea8	ee2cfb72-22e3-4676-be79-889217d8dc2b	g.chrX:150348392G>T	ENST00000218316.3	+	2	406	c.337G>T	c.(337-339)Gtc>Ttc	p.V113F	GPR50-AS1_ENST00000454196.1_RNA|AF003625.3_ENST00000602313.1_lincRNA	NM_004224.3	NP_004215.2	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	113					cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|identical protein binding (GO:0042802)|melatonin receptor activity (GO:0008502)			breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	38	Acute lymphoblastic leukemia(192;6.56e-05)					GCTGAGTGTGGTCGGCTCCAT	0.542																																					p.V113F		Atlas-SNP	.											.	GPR50	195	.	0			c.G337T						.						179	173	175					X																	150348392		2202	4298	6500	SO:0001583	missense	9248	exon2			AGTGTGGTCGGCT	U52219	CCDS44012.1	Xq28	2012-08-21			ENSG00000102195	ENSG00000102195		"GPCR / Class A : Orphans"	4506	protein-coding gene	gene with protein product		300207				9933574, 18400093	Standard	NM_004224		Approved	H9, Mel1c	uc010ntg.2	Q13585	OTTHUMG00000024166	ENST00000218316.3:c.337G>T	chrX.hg19:g.150348392G>T	ENSP00000218316:p.Val113Phe	223.0	0.0		193.0	93.0	NM_004224	Q0VGG3|Q3ZAR0	Missense_Mutation	SNP	ENST00000218316.3	hg19	CCDS44012.1	.	.	.	.	.	.	.	.	.	.	G	12.22	1.873626	0.33069	.	.	ENSG00000102195	ENST00000535473;ENST00000218316	T	0.71817	-0.6	4.21	3.32	0.38043	GPCR, rhodopsin-like superfamily (1);	0.058042	0.64402	D	0.000002	T	0.72036	0.3411	L	0.42245	1.32	0.43724	D	0.996202	D;D	0.54397	0.957;0.966	P;D	0.63877	0.852;0.919	T	0.71185	-0.4667	10	0.48119	T	0.1	-23.3117	5.317	0.15860	0.2498:0.0:0.7502:0.0	.	66;113	F5H1S3;Q13585	.;MTR1L_HUMAN	F	66;113	ENSP00000218316:V113F	ENSP00000218316:V113F	V	+	1	0	GPR50	150099050	1.000000	0.71417	0.994000	0.49952	0.158000	0.22134	5.070000	0.64376	1.838000	0.53458	0.523000	0.50628	GTC	.	.		0.542	GPR50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060874.1	NM_004224		T	150348392	G	T	150348392	3	4	343	1	0	0	0	0	1	0	0	0	6705	1261	44	3	343	3	GPR50	23	150348392	Missense_Mutation	SNP	G	TCGA-UB-A7MA-01A-11D-A33Q-10	27749625	150348392	4922168	74	47363										
TNFRSF4	7293	hgsc.bcm.edu	37	chr1	1146948	1146948	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcccaggtcagatcttggccAgggtggagtgggcgtcggcc	18	11	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:1146948A>T	ENST00000379236.3	-	7	825	c.821T>A	c.(820-822)cTg>cAg	p.L274Q	TNFRSF4_ENST00000453580.1_5'Flank	NM_003327.3	NP_003318.1	P43489	TNR4_HUMAN	tumor necrosis factor receptor superfamily, member 4	274					cellular defense response (GO:0006968)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of immunoglobulin secretion (GO:0051024)|regulation of apoptotic process (GO:0042981)|regulation of protein kinase activity (GO:0045859)|T cell proliferation (GO:0042098)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	tumor necrosis factor-activated receptor activity (GO:0005031)			large_intestine(1)|lung(2)|urinary_tract(1)	4	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;3.73e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.01e-21)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		GATCTTGGCCAGGGTGGAGTG	0.697																																					p.L274Q		Atlas-SNP	.											.	TNFRSF4	12	.	0			c.T821A						.						31	37	35					1																	1146948		2202	4299	6501	SO:0001583	missense	7293	exon7			TTGGCCAGGGTGG	X75962	CCDS11.1	1p36	2008-02-05			ENSG00000186827	ENSG00000186827		"Tumor necrosis factor receptor superfamily", "CD molecules"	11918	protein-coding gene	gene with protein product		600315		TXGP1L		7510240, 2828930	Standard	NM_003327		Approved	ACT35, OX40, CD134	uc001ade.3	P43489	OTTHUMG00000001415	ENST00000379236.3:c.821T>A	chr1.hg19:g.1146948A>T	ENSP00000368538:p.Leu274Gln	85.0	0.0		52.0	23.0	NM_003327	Q13663|Q2M312|Q5T7M0	Missense_Mutation	SNP	ENST00000379236.3	hg19	CCDS11.1	.	.	.	.	.	.	.	.	.	.	A	15.61	2.885967	0.51908	.	.	ENSG00000186827	ENST00000379236	T	0.71103	-0.54	3.17	3.17	0.36434	.	0.517876	0.14050	N	0.344812	T	0.77498	0.4139	L	0.54323	1.7	0.37429	D	0.91393	D	0.64830	0.994	P	0.61328	0.887	T	0.80795	-0.1223	10	0.87932	D	0	-2.8652	11.2007	0.48739	1.0:0.0:0.0:0.0	.	274	P43489	TNR4_HUMAN	Q	274	ENSP00000368538:L274Q	ENSP00000368538:L274Q	L	-	2	0	TNFRSF4	1136811	0.998000	0.40836	0.972000	0.41901	0.296000	0.27459	1.932000	0.40143	1.686000	0.51046	0.397000	0.26171	CTG	.	.		0.697	TNFRSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004086.1			T	1146948	A	T	1146948	3	4	344	1	0	0	0	0	1	0	0	0	16312	188	7	4	16	4	TNFRSF4	1	1146948	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10		1146948	248103673	1	47364										
KIAA1751	85452	hgsc.bcm.edu	37	chr1	1888169	1888169	+	IGR	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cagcgtgatggtccgagacgTggtctctcctaccacgtagc	12	13	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:1888169T>A								TMEM52 (37457 upstream) : C1orf222 (31393 downstream)																							GTCCGAGACGTGGTCTCTCCT	0.602																																					p.T636S		Atlas-SNP	.											.	KIAA1751	92	.	0			c.A1906T						.						69	74	73					1																	1888169		2169	4272	6441	SO:0001628	intergenic_variant	85452	exon17			GAGACGTGGTCTC																													chr1.hg19:g.1888169T>A		133.0	0.0		100.0	47.0	NM_001080484		Missense_Mutation	SNP		hg19		.	.	.	.	.	.	.	.	.	.	T	7.704	0.693617	0.15039	.	.	ENSG00000142609	ENST00000270720;ENST00000461752	.	.	.	4.75	-1.44	0.08856	.	0.926256	0.09088	N	0.850224	T	0.26774	0.0655	L	0.39633	1.23	0.09310	N	0.999998	B;B	0.33171	0.4;0.167	B;B	0.30855	0.121;0.085	T	0.21552	-1.0242	9	0.06757	T	0.87	-3.2633	9.0462	0.36347	0.0:0.4884:0.0:0.5116	.	636;636	Q9C0B2-2;Q9C0B2	.;K1751_HUMAN	S	636;83	.	ENSP00000270720:T636S	T	-	1	0	C1orf222	1878029	0.004000	0.15560	0.001000	0.08648	0.003000	0.03518	-0.313000	0.08103	-0.212000	0.10109	-0.766000	0.03442	ACG	.	.	0	0.602									A	1888169	T	A	1888169	1	1	344	0	1	0	0	0	0	0	0	0	8265	1696	59	4		4	KIAA1751	1	1888169	IGR	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	741221	1888169	247362452	2	47365										
KIAA1751	85452	hgsc.bcm.edu	37	chr1	1900247	1900247	+	IGR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	actgatgatctcctgctttcTgagcttctgctcctcctcaa	6	14	4	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:1900247T>C								TMEM52 (49535 upstream) : C1orf222 (19315 downstream)																							TCCTGCTTTCTGAGCTTCTGC	0.587																																					p.R358G		Atlas-SNP	.											.	KIAA1751	92	.	0			c.A1072G						.						112	118	116					1																	1900247		2024	4178	6202	SO:0001628	intergenic_variant	85452	exon11			GCTTTCTGAGCTT																													chr1.hg19:g.1900247T>C		51.0	0.0		43.0	21.0	NM_001080484		Missense_Mutation	SNP		hg19		.	.	.	.	.	.	.	.	.	.	t	12.83	2.056999	0.36277	.	.	ENSG00000142609	ENST00000270720	.	.	.	3.67	-3.31	0.04988	.	0.166663	0.37178	N	0.002218	T	0.61438	0.2347	M	0.71581	2.175	0.09310	N	0.999999	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.59873	-0.7372	9	0.72032	D	0.01	-25.0296	12.7919	0.57539	0.0:0.0:0.3766:0.6234	.	358;358	Q9C0B2-2;Q9C0B2	.;K1751_HUMAN	G	358	.	ENSP00000270720:R358G	R	-	1	2	C1orf222	1890107	0.003000	0.15002	0.116000	0.21606	0.506000	0.33950	0.164000	0.16542	-0.398000	0.07679	-0.475000	0.04921	AGA	.	.	0	0.587									C	1900247	T	C	1900247	1	2	344	0	1	0	0	0	0	0	0	0	8265	1588	55	2		2	KIAA1751	1	1900247	IGR	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	12078	1900247	247350374	3	47366										
PLCH2	9651	hgsc.bcm.edu	37	chr1	2409915	2409915	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cgtgtctctcccgtgtccagTggagcggtgcatgggtgcca	15	12	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:2409915T>C	ENST00000419816.2	+	2	399	c.125T>C	c.(124-126)gTg>gCg	p.V42A	PLCH2_ENST00000288766.5_5'UTR|PLCH2_ENST00000378488.3_Splice_Site_p.V42A|PLCH2_ENST00000378486.3_Splice_Site_p.V42A|PLCH2_ENST00000449969.1_Splice_Site_p.V15A			O75038	PLCH2_HUMAN	phospholipase C, eta 2	42	Necessary for plasma membrane localization. {ECO:0000250}.				inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phosphatidylinositol metabolic process (GO:0046488)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(8)|ovary(1)|prostate(3)|skin(1)	20	all_cancers(77;0.000161)|all_epithelial(69;5.98e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;7.32e-16)|all_lung(118;1.15e-06)|Lung NSC(185;6.26e-05)|Renal(390;0.00571)|Breast(487;0.00832)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;1.44e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.78e-23)|GBM - Glioblastoma multiforme(42;2.8e-08)|Colorectal(212;4.19e-05)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00034)|BRCA - Breast invasive adenocarcinoma(365;0.00443)|KIRC - Kidney renal clear cell carcinoma(229;0.00548)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.2)		CCGTGTCCAGTGGAGCGGTGC	0.657																																					p.V42A		Atlas-SNP	.											.	PLCH2	131	.	0			c.T125C						.						51	58	56					1																	2409915		2198	4294	6492	SO:0001630	splice_region_variant	9651	exon2			GTCCAGTGGAGCG	AB007919	CCDS59959.1	1p36.32	2013-01-10	2006-03-16	2006-03-16	ENSG00000149527	ENSG00000149527	3.1.4.11	"EF-hand domain containing"	29037	protein-coding gene	gene with protein product		612836	"phospholipase C-like 4"	PLCL4		15899900	Standard	XM_006711054		Approved	KIAA0450, PLCeta2, RP3-395M20.1, PLC-eta2	uc001aji.1	O75038	OTTHUMG00000000719	ENST00000419816.2:c.125-1T>C	chr1.hg19:g.2409915T>C		54.0	0.0		41.0	23.0	NM_014638	A2VCM3|B9DI80|Q3LUA8|Q86XJ2|Q86XU1|Q86YU7|Q8TEH5|Q8WUS6	Missense_Mutation	SNP	ENST00000419816.2	hg19		.	.	.	.	.	.	.	.	.	.	T	12.46	1.943207	0.34283	.	.	ENSG00000149527	ENST00000449969;ENST00000378486;ENST00000378488	T;T;T	0.63417	-0.04;-0.04;-0.04	4.57	4.57	0.56435	Pleckstrin homology-type (1);	0.089852	0.44688	N	0.000436	T	0.47377	0.1442	N	0.25825	0.765	0.80722	D	1	B	0.26512	0.151	B	0.25405	0.06	T	0.39292	-0.9621	9	.	.	.	.	13.0845	0.59132	0.0:0.0:0.0:1.0	.	42	O75038	PLCH2_HUMAN	A	15;42;42	ENSP00000397289:V15A;ENSP00000367747:V42A;ENSP00000367749:V42A	.	V	+	2	0	PLCH2	2399775	1.000000	0.71417	1.000000	0.80357	0.678000	0.39670	7.722000	0.84778	1.691000	0.51100	0.459000	0.35465	GTG	.	.		0.657	PLCH2-009	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467514.1	NM_014638	Missense_Mutation	C	2409915	T	C	2409915	5	2	344	1	0	0	0	0	0	0	1	0	12047	1710	59	2	131	2	PLCH2	1	2409915	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	509668	2409915	246840706	4	47367										
PRDM16	63976	hgsc.bcm.edu	37	chr1	3102902	3102902	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cattccgatcccagcagactTcgagctccgagagtcctcca	8	16	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:3102902T>A	ENST00000270722.5	+	2	300	c.251T>A	c.(250-252)tTc>tAc	p.F84Y	PRDM16_ENST00000511072.1_Missense_Mutation_p.F84Y|PRDM16_ENST00000441472.2_Missense_Mutation_p.F84Y|PRDM16_ENST00000378391.2_Missense_Mutation_p.F84Y|PRDM16_ENST00000514189.1_Missense_Mutation_p.F84Y|PRDM16_ENST00000378398.3_Missense_Mutation_p.F84Y|PRDM16_ENST00000442529.2_Missense_Mutation_p.F84Y			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	84	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				brown fat cell differentiation (GO:0050873)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurogenesis (GO:0022008)|palate development (GO:0060021)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular respiration (GO:0043457)|somatic stem cell maintenance (GO:0035019)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(3)	59	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		CCAGCAGACTTCGAGCTCCGA	0.667			T	EVI1	"MDS, AML"																																p.F84Y		Atlas-SNP	.		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	.	PRDM16	147	.	0			c.T251A						.						44	52	50					1																	3102902		1939	4127	6066	SO:0001583	missense	63976	exon2			CAGACTTCGAGCT	AF294278	CCDS41236.1, CCDS44048.1, CCDS41236.2, CCDS44048.2	1p36.23-p33	2013-01-08			ENSG00000142611	ENSG00000142611		"Zinc fingers, C2H2-type"	14000	protein-coding gene	gene with protein product	"MDS1/EVI1-like", "PR-domain zinc finger protein 16", "transcription factor MEL1"	605557				11050005	Standard	NM_199454		Approved	MEL1, PFM13, KIAA1675, MGC166915	uc001akf.3	Q9HAZ2	OTTHUMG00000000581	ENST00000270722.5:c.251T>A	chr1.hg19:g.3102902T>A	ENSP00000270722:p.Phe84Tyr	190.0	0.0		121.0	51.0	NM_022114	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Missense_Mutation	SNP	ENST00000270722.5	hg19	CCDS41236.2	.	.	.	.	.	.	.	.	.	.	T	18.85	3.710523	0.68730	.	.	ENSG00000142611	ENST00000511072;ENST00000378398;ENST00000441472;ENST00000442529;ENST00000378391;ENST00000514189;ENST00000270722	T;T;T;T;T;T;T	0.72725	0.82;0.82;-0.68;-0.68;-0.68;0.82;-0.68	5.29	5.29	0.74685	SET domain (2);	0.000000	0.46758	U	0.000275	T	0.77274	0.4106	M	0.64170	1.965	0.36662	D	0.878003	D;D;D;D	0.63046	0.986;0.992;0.992;0.986	P;P;P;P	0.54499	0.572;0.754;0.754;0.572	T	0.81944	-0.0701	10	0.44086	T	0.13	.	15.2085	0.73198	0.0:0.0:0.0:1.0	.	84;84;84;84	Q9HAZ2;Q9HAZ2-2;F8WEV3;D3YTA5	PRD16_HUMAN;.;.;.	Y	84	ENSP00000426975:F84Y;ENSP00000367651:F84Y;ENSP00000407968:F84Y;ENSP00000405253:F84Y;ENSP00000367643:F84Y;ENSP00000421400:F84Y;ENSP00000270722:F84Y	ENSP00000270722:F84Y	F	+	2	0	PRDM16	3092762	1.000000	0.71417	1.000000	0.80357	0.677000	0.39632	7.560000	0.82277	1.999000	0.58509	0.459000	0.35465	TTC	.	.		0.667	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114		A	3102902	T	A	3102902	3	1	344	1	0	0	0	0	1	0	0	0	12469	1783	62	4	257	4	PRDM16	1	3102902	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	692987	3102902	246147719	5	47368										
PRDM16	63976	hgsc.bcm.edu	37	chr1	3319469	3319469	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggctgcgctctacgagggccTggctgaggagctcaagcccg	16	13	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:3319469T>A	ENST00000270722.5	+	6	840	c.791T>A	c.(790-792)cTg>cAg	p.L264Q	PRDM16_ENST00000378391.2_Missense_Mutation_p.L264Q|PRDM16_ENST00000511072.1_Missense_Mutation_p.L265Q|PRDM16_ENST00000441472.2_Missense_Mutation_p.L264Q|PRDM16_ENST00000514189.1_Missense_Mutation_p.L265Q|PRDM16_ENST00000378398.3_Missense_Mutation_p.L265Q|PRDM16_ENST00000442529.2_Missense_Mutation_p.L264Q|PRDM16_ENST00000512462.1_3'UTR			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	264					brown fat cell differentiation (GO:0050873)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurogenesis (GO:0022008)|palate development (GO:0060021)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular respiration (GO:0043457)|somatic stem cell maintenance (GO:0035019)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(3)	59	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		TACGAGGGCCTGGCTGAGGAG	0.637			T	EVI1	"MDS, AML"																																p.L264Q		Atlas-SNP	.		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	.	PRDM16	147	.	0			c.T791A						.						48	59	55					1																	3319469		2144	4263	6407	SO:0001583	missense	63976	exon6			AGGGCCTGGCTGA	AF294278	CCDS41236.1, CCDS44048.1, CCDS41236.2, CCDS44048.2	1p36.23-p33	2013-01-08			ENSG00000142611	ENSG00000142611		"Zinc fingers, C2H2-type"	14000	protein-coding gene	gene with protein product	"MDS1/EVI1-like", "PR-domain zinc finger protein 16", "transcription factor MEL1"	605557				11050005	Standard	NM_199454		Approved	MEL1, PFM13, KIAA1675, MGC166915	uc001akf.3	Q9HAZ2	OTTHUMG00000000581	ENST00000270722.5:c.791T>A	chr1.hg19:g.3319469T>A	ENSP00000270722:p.Leu264Gln	212.0	0.0		167.0	89.0	NM_022114	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Missense_Mutation	SNP	ENST00000270722.5	hg19	CCDS41236.2	.	.	.	.	.	.	.	.	.	.	T	26.0	4.691946	0.88735	.	.	ENSG00000142611	ENST00000511072;ENST00000378398;ENST00000441472;ENST00000442529;ENST00000378391;ENST00000514189;ENST00000270722;ENST00000512462;ENST00000408992;ENST00000509860	T;T;T;T;T;T;T;T;T	0.07114	3.28;3.31;3.32;3.31;3.31;3.3;3.3;3.27;3.22	4.32	4.32	0.51571	.	0.433888	0.16447	U	0.214050	T	0.19087	0.0458	L	0.34521	1.04	0.54753	D	0.99998	D;D;P;P	0.89917	1.0;0.989;0.666;0.883	D;P;B;P	0.87578	0.998;0.885;0.23;0.462	T	0.01330	-1.1383	10	0.62326	D	0.03	.	13.1264	0.59358	0.0:0.0:0.0:1.0	.	264;264;264;264	Q9HAZ2;Q9HAZ2-2;F8WEV3;D3YTA5	PRD16_HUMAN;.;.;.	Q	265;265;264;264;264;265;264;80;80;73	ENSP00000426975:L265Q;ENSP00000367651:L265Q;ENSP00000407968:L264Q;ENSP00000405253:L264Q;ENSP00000367643:L264Q;ENSP00000421400:L265Q;ENSP00000270722:L264Q;ENSP00000422504:L80Q;ENSP00000425796:L73Q	ENSP00000270722:L264Q	L	+	2	0	PRDM16	3309329	1.000000	0.71417	0.994000	0.49952	0.981000	0.71138	6.067000	0.71193	1.585000	0.49928	0.459000	0.35465	CTG	.	.		0.637	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114		A	3319469	T	A	3319469	3	1	344	1	0	0	0	0	1	0	0	0	12469	1580	55	4	813	4	PRDM16	1	3319469	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	216567	3319469	245931152	6	47369										
CCDC27	148870	hgsc.bcm.edu	37	chr1	3680278	3680278	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctctgtgcccaggagtgattGcgtctttacaacaacaagtg	10	10	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:3680278G>T	ENST00000294600.2	+	8	1414	c.1330G>T	c.(1330-1332)Gcg>Tcg	p.A444S		NM_152492.2	NP_689705.2	Q2M243	CCD27_HUMAN	coiled-coil domain containing 27	444										breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(2)|lung(17)|prostate(1)|skin(2)|urinary_tract(2)	36	all_cancers(77;0.0385)|Ovarian(185;0.0634)|Lung NSC(156;0.21)|all_lung(157;0.218)	all_epithelial(116;5.52e-17)|all_lung(118;1.04e-06)|Lung NSC(185;0.000214)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Lung SC(97;0.0367)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)		Epithelial(90;1.11e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.35e-22)|GBM - Glioblastoma multiforme(42;3.46e-16)|Colorectal(212;1.17e-05)|COAD - Colon adenocarcinoma(227;5.76e-05)|Kidney(185;0.00036)|BRCA - Breast invasive adenocarcinoma(365;0.000696)|KIRC - Kidney renal clear cell carcinoma(229;0.00558)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.203)		AGGAGTGATTGCGTCTTTACA	0.592																																					p.A444S		Atlas-SNP	.											.	CCDC27	79	.	0			c.G1330T						.						118	119	119					1																	3680278		2203	4300	6503	SO:0001583	missense	148870	exon8			GTGATTGCGTCTT		CCDS50.1	1p36.32	2008-02-05			ENSG00000162592	ENSG00000162592			26546	protein-coding gene	gene with protein product							Standard	NM_152492		Approved	FLJ32825	uc001akv.2	Q2M243	OTTHUMG00000003504	ENST00000294600.2:c.1330G>T	chr1.hg19:g.3680278G>T	ENSP00000294600:p.Ala444Ser	278.0	0.0		177.0	24.0	NM_152492	Q5TBV3|Q96M50	Missense_Mutation	SNP	ENST00000294600.2	hg19	CCDS50.1	.	.	.	.	.	.	.	.	.	.	G	6.720	0.501505	0.12822	.	.	ENSG00000162592	ENST00000294600	T	0.17213	2.29	4.34	-0.00366	0.14025	.	1.053250	0.07414	N	0.892837	T	0.07818	0.0196	N	0.19112	0.55	0.09310	N	1	B	0.28470	0.213	B	0.25614	0.062	T	0.37865	-0.9687	10	0.13470	T	0.59	-5.0704	0.521	0.00612	0.4492:0.2079:0.1409:0.202	.	444	Q2M243	CCD27_HUMAN	S	444	ENSP00000294600:A444S	ENSP00000294600:A444S	A	+	1	0	CCDC27	3670138	0.000000	0.05858	0.003000	0.11579	0.016000	0.09150	-0.481000	0.06552	0.197000	0.20387	0.462000	0.41574	GCG	.	.		0.592	CCDC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009740.1	NM_152492		T	3680278	G	T	3680278	3	4	344	1	0	0	0	0	1	0	0	0	2803	1319	46	3	1360	3	CCDC27	1	3680278	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	360809	3680278	245570343	7	47370										
NPHP4	261734	hgsc.bcm.edu	37	chr1	5967225	5967225	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gggtagctgtgaagtaggccTggccaagcagtgctgagtcg	17	8	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:5967225T>A	ENST00000378156.4	-	13	1826	c.1561A>T	c.(1561-1563)Agg>Tgg	p.R521W	NPHP4_ENST00000478423.2_Intron	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	521					actin cytoskeleton organization (GO:0030036)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(4)	47	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		GAAGTAGGCCTGGCCAAGCAG	0.642																																					p.R521W		Atlas-SNP	.											.	NPHP4	119	.	0			c.A1561T						.						22	28	26					1																	5967225		2017	4158	6175	SO:0001583	missense	261734	exon13			TAGGCCTGGCCAA	AB014573	CCDS44052.1	1p36	2010-03-26			ENSG00000131697	ENSG00000131697			19104	protein-coding gene	gene with protein product	"nephroretinin", "nephrocystin-4", "POC10 centriolar protein homolog (Chlamydomonas)"	607215				11920287, 12205563	Standard	XR_244787		Approved	SLSN4, KIAA0673, POC10	uc001alq.2	O75161	OTTHUMG00000000701	ENST00000378156.4:c.1561A>T	chr1.hg19:g.5967225T>A	ENSP00000367398:p.Arg521Trp	149.0	0.0		101.0	49.0	NM_015102	Q8IWC0	Missense_Mutation	SNP	ENST00000378156.4	hg19	CCDS44052.1	.	.	.	.	.	.	.	.	.	.	T	17.30	3.354257	0.61293	.	.	ENSG00000131697	ENST00000378156	D	0.87412	-2.25	5.5	1.88	0.25563	.	0.872145	0.09858	N	0.746582	D	0.84597	0.5507	L	0.36672	1.1	0.09310	N	1	D	0.58970	0.984	P	0.50192	0.634	T	0.72849	-0.4168	10	0.72032	D	0.01	.	8.0293	0.30454	0.0:0.3085:0.0:0.6915	.	521	O75161	NPHP4_HUMAN	W	521	ENSP00000367398:R521W	ENSP00000367398:R521W	R	-	1	2	NPHP4	5889812	0.064000	0.20934	0.010000	0.14722	0.052000	0.14988	0.387000	0.20718	0.064000	0.16427	0.402000	0.26972	AGG	.	.		0.642	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2			A	5967225	T	A	5967225	3	1	344	1	0	0	0	0	1	0	0	0	10590	1579	55	4	2791	4	NPHP4	1	5967225	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2286947	5967225	243283396	8	47371										
TAS1R1	80835	hgsc.bcm.edu	37	chr1	6639185	6639185	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtgatgatcagctcagcggcCcagctgcttatctgtctaac	10	12	4	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:6639185C>T	ENST00000333172.6	+	6	2260	c.2067C>T	c.(2065-2067)gcC>gcT	p.A689A	ZBTB48_ENST00000377674.4_5'Flank|TAS1R1_ENST00000328191.4_3'UTR|TAS1R1_ENST00000351136.3_Silent_p.A435A	NM_138697.3	NP_619642.2	Q7RTX1	TS1R1_HUMAN	taste receptor, type 1, member 1	689					detection of chemical stimulus involved in sensory perception of taste (GO:0050912)|sensory perception of umami taste (GO:0050917)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(13)|ovary(1)|skin(1)|urinary_tract(2)	29	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;8.73e-34)|all_epithelial(116;9.26e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Breast(487;0.000353)|Renal(390;0.0007)|Colorectal(325;0.00104)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443)		Colorectal(212;1.29e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00108)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0642)		GCTCAGCGGCCCAGCTGCTTA	0.532																																					p.A689A		Atlas-SNP	.											.	TAS1R1	76	.	0			c.C2067T						.						115	113	113					1																	6639185		2203	4300	6503	SO:0001819	synonymous_variant	80835	exon6			AGCGGCCCAGCTG		CCDS81.1, CCDS82.1	1p36.23	2012-08-22	2003-03-24		ENSG00000173662	ENSG00000173662		"Taste receptors / Type 1", "GPCR / Unclassified : Taste receptors"	14448	protein-coding gene	gene with protein product		606225	"G protein-coupled receptor 70"	GPR70			Standard	NM_138697		Approved	T1R1, TR1	uc001ant.3	Q7RTX1	OTTHUMG00000001441	ENST00000333172.6:c.2067C>T	chr1.hg19:g.6639185C>T		113.0	0.0		92.0	62.0	NM_138697	B2RMX0|Q5SY22|Q5SY24|Q8NGZ7|Q8TDJ7|Q8TDJ8|Q8TDJ9|Q8TDK0	Silent	SNP	ENST00000333172.6	hg19	CCDS81.1																																																																																			.	.		0.532	TAS1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004211.1			T	6639185	C	T	6639185	2	4	344	1	0	0	0	0	0	0	0	1	15577	610	22	3		3	TAS1R1	1	6639185	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	671960	6639185	242611436	9	47372										
SLC45A1	50651	hgsc.bcm.edu	37	chr1	8390821	8390821	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tggacttctggagggcagagAgggtgccctgacctccggct	16	11	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:8390821A>T	ENST00000471889.1	+	5	1653	c.1268A>T	c.(1267-1269)gAg>gTg	p.E423V	SLC45A1_ENST00000377479.2_Missense_Mutation_p.E457V|Y_RNA_ENST00000516445.1_RNA|SLC45A1_ENST00000481265.1_3'UTR|SLC45A1_ENST00000289877.8_Missense_Mutation_p.E423V			Q9Y2W3	S45A1_HUMAN	solute carrier family 45, member 1	423					carbohydrate transport (GO:0008643)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(2)	33	Ovarian(185;0.0661)|all_lung(157;0.127)	all_epithelial(116;1.22e-15)|all_lung(118;0.000147)|Lung NSC(185;0.000251)|Renal(390;0.000469)|Colorectal(325;0.00578)|Breast(348;0.00686)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.11)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;3.95e-66)|GBM - Glioblastoma multiforme(8;5.93e-33)|Colorectal(212;2.86e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|Kidney(185;5.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000513)|KIRC - Kidney renal clear cell carcinoma(229;0.000979)|STAD - Stomach adenocarcinoma(132;0.00199)|READ - Rectum adenocarcinoma(331;0.0649)		GAGGGCAGAGAGGGTGCCCTG	0.662																																					p.E423V		Atlas-SNP	.											.	SLC45A1	85	.	0			c.A1268T						.						36	38	37					1																	8390821		2203	4300	6503	SO:0001583	missense	50651	exon4			GCAGAGAGGGTGC	AF118274	CCDS30577.1	1p36.23	2014-01-28	2005-10-04	2005-10-04	ENSG00000162426	ENSG00000162426		"Solute carriers"	17939	protein-coding gene	gene with protein product	"H+/sugar symporter"	605763	"deleted in neuroblastoma 5"	DNB5		10729226	Standard	XM_005263467		Approved		uc001apb.3	Q9Y2W3	OTTHUMG00000000503	ENST00000471889.1:c.1268A>T	chr1.hg19:g.8390821A>T	ENSP00000418096:p.Glu423Val	98.0	0.0		73.0	23.0	NM_001080397	Q5VY46|Q5VY49	Missense_Mutation	SNP	ENST00000471889.1	hg19	CCDS30577.1	.	.	.	.	.	.	.	.	.	.	A	5.676	0.309337	0.10733	.	.	ENSG00000162426	ENST00000471889;ENST00000377479;ENST00000289877	T;T;T	0.20463	2.09;2.07;2.09	4.9	3.7	0.42460	.	0.800538	0.11945	N	0.514319	T	0.18130	0.0435	L	0.34521	1.04	0.19945	N	0.999942	B	0.29085	0.232	B	0.31614	0.133	T	0.15321	-1.0441	10	0.29301	T	0.29	-13.1484	12.2004	0.54321	0.8475:0.1525:0.0:0.0	.	423	Q9Y2W3	S45A1_HUMAN	V	423;457;423	ENSP00000418096:E423V;ENSP00000366699:E457V;ENSP00000289877:E423V	ENSP00000289877:E423V	E	+	2	0	SLC45A1	8313408	0.940000	0.31905	0.049000	0.19019	0.037000	0.13140	2.000000	0.40816	1.816000	0.52996	0.459000	0.35465	GAG	.	.		0.662	SLC45A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001245.5			T	8390821	A	T	8390821	3	4	344	1	0	0	0	0	1	0	0	0	14655	304	11	4	1282	4	SLC45A1	1	8390821	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1751636	8390821	240859800	10	47373										
CLSTN1	22883	hgsc.bcm.edu	37	chr1	9795215	9795215	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccggggggaccgaaatgcagGtggcctcgttaaaacacctg	14	11	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:9795215G>A	ENST00000377298.4	-	14	2693	c.1901C>T	c.(1900-1902)aCc>aTc	p.T634I	CLSTN1_ENST00000377288.3_Missense_Mutation_p.T615I|CLSTN1_ENST00000361311.4_Missense_Mutation_p.T624I|CLSTN1_ENST00000477264.1_5'Flank	NM_001009566.1	NP_001009566.1	O94985	CSTN1_HUMAN	calsyntenin 1	634					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	beta-amyloid binding (GO:0001540)|calcium ion binding (GO:0005509)|kinesin binding (GO:0019894)|X11-like protein binding (GO:0042988)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(9)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	36	all_lung(157;0.222)	all_lung(284;4.03e-05)|Lung NSC(185;6.93e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;8.36e-08)|COAD - Colon adenocarcinoma(227;1.93e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|STAD - Stomach adenocarcinoma(132;0.00644)|READ - Rectum adenocarcinoma(331;0.0419)		CGAAATGCAGGTGGCCTCGTT	0.582																																					p.T634I		Atlas-SNP	.											.	CLSTN1	88	.	0			c.C1901T						.						73	78	76					1																	9795215		2203	4300	6503	SO:0001583	missense	22883	exon14			ATGCAGGTGGCCT	AB020718	CCDS105.1, CCDS30580.1	1p36.22	2011-07-01			ENSG00000171603	ENSG00000171603		"Cadherins / Cadherin-related"	17447	protein-coding gene	gene with protein product	"cadherin-related family member 12"	611321				10048485	Standard	XM_005263432		Approved	CSTN1, KIAA0911, CDHR12	uc001aqh.3	O94985	OTTHUMG00000001451	ENST00000377298.4:c.1901C>T	chr1.hg19:g.9795215G>A	ENSP00000366513:p.Thr634Ile	59.0	0.0		37.0	15.0	NM_001009566	A8K183|Q5SR52|Q5UE58|Q71MN0|Q8N4K9	Missense_Mutation	SNP	ENST00000377298.4	hg19	CCDS30580.1	.	.	.	.	.	.	.	.	.	.	G	15.53	2.861282	0.51482	.	.	ENSG00000171603	ENST00000377298;ENST00000361311;ENST00000435891;ENST00000377288;ENST00000539822	T;T;T;T	0.30714	1.52;1.52;1.52;1.52	5.91	3.94	0.45596	.	0.690666	0.15711	N	0.248420	T	0.25121	0.0610	L	0.52573	1.65	0.29817	N	0.831175	B;B;B	0.27853	0.121;0.191;0.121	B;B;B	0.23275	0.02;0.045;0.02	T	0.15780	-1.0425	10	0.45353	T	0.12	-6.4901	6.6604	0.23011	0.0683:0.1278:0.6715:0.1324	.	615;624;634	B4E3Q1;O94985-2;O94985	.;.;CSTN1_HUMAN	I	634;624;435;615;615	ENSP00000366513:T634I;ENSP00000354997:T624I;ENSP00000401934:T435I;ENSP00000366502:T615I	ENSP00000354997:T624I	T	-	2	0	CLSTN1	9717802	1.000000	0.71417	0.490000	0.27465	0.975000	0.68041	5.517000	0.67061	1.504000	0.48704	0.655000	0.94253	ACC	.	.		0.582	CLSTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004239.1			A	9795215	G	A	9795215	3	1	344	1	0	0	0	0	1	0	0	0	3563	1261	44	3	1068	3	CLSTN1	1	9795215	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1404394	9795215	239455406	11	47374										
UBE4B	10277	hgsc.bcm.edu	37	chr1	10221232	10221232	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtttgttcgctatataaacaTgttgataaacgacacgacgt	8	7	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:10221232T>C	ENST00000253251.8	+	22	3538	c.2699T>C	c.(2698-2700)aTg>aCg	p.M900T	UBE4B_ENST00000377157.3_Missense_Mutation_p.M784T|RNU6-828P_ENST00000364876.1_RNA|UBE4B_ENST00000343090.6_Missense_Mutation_p.M1029T					ubiquitination factor E4B											NS(3)|breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(14)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	48		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		TATATAAACATGTTGATAAAC	0.438																																					p.M1029T		Atlas-SNP	.											.	UBE4B	233	.	0			c.T3086C						.						117	114	115					1																	10221232		2203	4300	6503	SO:0001583	missense	10277	exon23			TAAACATGTTGAT	AF091093	CCDS110.1, CCDS41245.1	1p36.1	2013-01-28	2011-05-19		ENSG00000130939	ENSG00000130939		"U-box domain containing"	12500	protein-coding gene	gene with protein product		613565	"ubiquitination factor E4B (homologous to yeast UFD2)", "ubiquitination factor E4B (UFD2 homolog, yeast)"			9734811, 10089879	Standard	NM_006048		Approved	UBOX3, E4, UFD2, KIAA0684	uc001aqs.4	O95155	OTTHUMG00000001797	ENST00000253251.8:c.2699T>C	chr1.hg19:g.10221232T>C	ENSP00000253251:p.Met900Thr	120.0	0.0		123.0	50.0	NM_001105562		Missense_Mutation	SNP	ENST00000253251.8	hg19	CCDS110.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.222094	0.79464	.	.	ENSG00000130939	ENST00000253251;ENST00000377157;ENST00000343090	T;T;T	0.46819	0.86;0.86;0.86	5.4	5.4	0.78164	Ubiquitin conjugation factor E4, core (1);	0.000000	0.85682	D	0.000000	T	0.69762	0.3147	M	0.85373	2.75	0.80722	D	1	D;D	0.61697	0.99;0.974	P;P	0.62491	0.903;0.57	T	0.75717	-0.3220	10	0.66056	D	0.02	-23.1253	15.4578	0.75330	0.0:0.0:0.0:1.0	.	1029;900	O95155;O95155-2	UBE4B_HUMAN;.	T	900;784;1029	ENSP00000253251:M900T;ENSP00000366362:M784T;ENSP00000343001:M1029T	ENSP00000253251:M900T	M	+	2	0	UBE4B	10143819	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	8.033000	0.88852	2.053000	0.61076	0.460000	0.39030	ATG	.	.		0.438	UBE4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005017.1	NM_006048		C	10221232	T	C	10221232	3	2	344	1	0	0	0	0	1	0	0	0	16898	1464	51	2	3176	2	UBE4B	1	10221232	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	426017	10221232	239029389	12	47375										
PTCHD2	57540	hgsc.bcm.edu	37	chr1	11589857	11589857	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttcgcagtgcccaaggcccgTctctcagccaccttcggctt	9	17	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:11589857T>C	ENST00000294484.6	+	15	3081	c.2943T>C	c.(2941-2943)cgT>cgC	p.R981R	PTCHD2_ENST00000389575.3_Silent_p.R981R	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	981					cholesterol homeostasis (GO:0042632)|regulation of lipid transport (GO:0032368)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hedgehog receptor activity (GO:0008158)			NS(3)|breast(2)|endometrium(9)|kidney(4)|large_intestine(5)|lung(34)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	76	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		CCAAGGCCCGTCTCTCAGCCA	0.642																																					p.R981R		Atlas-SNP	.											.	PTCHD2	193	.	0			c.T2943C						.						56	63	61					1																	11589857		2037	4179	6216	SO:0001819	synonymous_variant	57540	exon15			GGCCCGTCTCTCA	AB037758	CCDS41247.1	1p36.22	2010-02-17			ENSG00000204624	ENSG00000204624			29251	protein-coding gene	gene with protein product		611251				15738394	Standard	NM_020780		Approved	KIAA1337, DISP3	uc001ash.4	Q9P2K9	OTTHUMG00000002074	ENST00000294484.6:c.2943T>C	chr1.hg19:g.11589857T>C		79.0	0.0		63.0	35.0	NM_020780	Q5VTU9|Q9UJD6	Silent	SNP	ENST00000294484.6	hg19	CCDS41247.1																																																																																			.	.		0.642	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561		C	11589857	T	C	11589857	2	2	344	1	0	0	0	0	0	0	0	1	12745	1654	58	2		2	PTCHD2	1	11589857	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1368625	11589857	237660764	13	47376										
MIIP	60672	hgsc.bcm.edu	37	chr1	12082339	12082339	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tctcccacctgccaaatgccAgcaccaggagtccctgggcc	9	18	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:12082339A>T	ENST00000235332.4	+	3	471	c.302A>T	c.(301-303)cAg>cTg	p.Q101L	MIIP_ENST00000436478.2_Missense_Mutation_p.Q101L|MIIP_ENST00000466860.1_3'UTR|Y_RNA_ENST00000365591.1_RNA	NM_021933.3	NP_068752.2	Q5JXC2	MIIP_HUMAN	migration and invasion inhibitory protein	101										autonomic_ganglia(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(1)	15						GCCAAATGCCAGCACCAGGAG	0.692																																					p.Q101L		Atlas-SNP	.											.	MIIP	34	.	0			c.A302T						.						44	48	47					1																	12082339		2203	4298	6501	SO:0001583	missense	60672	exon3			AATGCCAGCACCA	AK022500	CCDS143.1	1p36.22	2009-07-09			ENSG00000116691	ENSG00000116691			25715	protein-coding gene	gene with protein product	"invasion inhibitory protein 45"	608772				15867349, 14617774	Standard	NM_021933		Approved	FLJ12438, IIp45	uc001ato.2	Q5JXC2	OTTHUMG00000002439	ENST00000235332.4:c.302A>T	chr1.hg19:g.12082339A>T	ENSP00000235332:p.Gln101Leu	128.0	0.0		86.0	51.0	NM_021933	C0KL22|Q96HU6|Q9H839|Q9HA00	Missense_Mutation	SNP	ENST00000235332.4	hg19	CCDS143.1	.	.	.	.	.	.	.	.	.	.	A	15.21	2.767120	0.49574	.	.	ENSG00000116691	ENST00000235332;ENST00000436478	T;T	0.18502	2.21;2.21	4.49	-1.98	0.07480	.	1.311660	0.05150	N	0.495940	T	0.11793	0.0287	L	0.36672	1.1	0.09310	N	1	B	0.18461	0.028	B	0.16722	0.016	T	0.35325	-0.9793	10	0.48119	T	0.1	-0.1853	0.786	0.01049	0.4567:0.1535:0.227:0.1627	.	101	Q5JXC2	MIIP_HUMAN	L	101	ENSP00000235332:Q101L;ENSP00000392417:Q101L	ENSP00000235332:Q101L	Q	+	2	0	MIIP	12004926	0.000000	0.05858	0.003000	0.11579	0.727000	0.41649	-0.145000	0.10265	-0.469000	0.06911	0.482000	0.46254	CAG	.	.		0.692	MIIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006941.1	NM_021933		T	12082339	A	T	12082339	3	4	344	1	0	0	0	0	1	0	0	0	9594	188	7	4	308	4	MIIP	1	12082339	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	492482	12082339	237168282	14	47377										
VPS13D	55187	hgsc.bcm.edu	37	chr1	12567012	12567012	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gatcgagaagccattttcctAgaagtcaaatacgatgacct	8	9	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:12567012A>G	ENST00000358136.3	+	69	13030	c.12900A>G	c.(12898-12900)ctA>ctG	p.L4300L	VPS13D_ENST00000356315.4_Silent_p.L4275L|VPS13D_ENST00000543710.1_Silent_p.L104L|VPS13D_ENST00000471923.1_5'UTR|VPS13D_ENST00000496628.1_3'UTR|SNORA59A_ENST00000459326.1_RNA|VPS13D_ENST00000543766.1_Silent_p.L298L	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		CCATTTTCCTAGAAGTCAAAT	0.498																																					p.L4300L		Atlas-SNP	.											.	VPS13D	316	.	0			c.A12900G						.						127	120	123					1																	12567012		2203	4300	6503	SO:0001819	synonymous_variant	55187	exon69			TTTCCTAGAAGTC	AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"vacuolar protein sorting 13D (yeast)"				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.12900A>G	chr1.hg19:g.12567012A>G		130.0	0.0		105.0	37.0	NM_015378		Silent	SNP	ENST00000358136.3	hg19	CCDS30588.1	.	.	.	.	.	.	.	.	.	.	A	10.87	1.473176	0.26423	.	.	ENSG00000048707	ENST00000011700	.	.	.	5.88	-8.95	0.00765	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.6306	0.17508	0.2103:0.2949:0.4213:0.0735	.	.	.	.	W	3122	.	.	X	+	2	0	VPS13D	12489599	0.890000	0.30428	0.766000	0.31476	0.998000	0.95712	-0.047000	0.11963	-1.582000	0.01640	0.533000	0.62120	TAG	.	.		0.498	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		G	12567012	A	G	12567012	2	3	344	1	0	0	0	0	0	0	0	1	17207	407	15	2		2	VPS13D	1	12567012	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	484673	12567012	236683609	15	47378										
PRAMEF2	65122	hgsc.bcm.edu	37	chr1	12921328	12921328	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agtgccatcctgcctggcctGagctgctgctcccagctcac	10	17	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:12921328G>C	ENST00000240189.2	+	4	1206	c.1119G>C	c.(1117-1119)ctG>ctC	p.L373L		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	373					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(22)|prostate(6)|skin(3)|upper_aerodigestive_tract(4)	42	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TGCCTGGCCTGAGCTGCTGCT	0.562																																					p.L373L		Atlas-SNP	.											.	PRAMEF2	85	.	0			c.G1119C						.						110	117	115					1																	12921328		2201	4294	6495	SO:0001819	synonymous_variant	65122	exon4			TGGCCTGAGCTGC		CCDS149.1	1p36.21	2013-01-17			ENSG00000120952	ENSG00000120952		"-"	28841	protein-coding gene	gene with protein product							Standard	NM_023014		Approved	FLJ43580	uc001aum.1	O60811	OTTHUMG00000001986	ENST00000240189.2:c.1119G>C	chr1.hg19:g.12921328G>C		207.0	0.0		161.0	16.0	NM_023014		Silent	SNP	ENST00000240189.2	hg19	CCDS149.1																																																																																			.	.		0.562	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014		C	12921328	G	C	12921328	2	2	344	1	0	0	0	0	0	0	0	1	12447	1277	45	4		4	PRAMEF2	1	12921328	Silent	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	354316	12921328	236329293	16	47379										
PADI1	29943	hgsc.bcm.edu	37	chr1	17556654	17556654	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gacattgaaagccaactgcaAgctgaccatctgccctcaag	8	13	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:17556654A>T	ENST00000375471.4	+	9	1096	c.1004A>T	c.(1003-1005)aAg>aTg	p.K335M		NM_013358.2	NP_037490.2	Q9ULC6	PADI1_HUMAN	peptidyl arginine deiminase, type I	335					protein citrullination (GO:0018101)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|skin(1)|stomach(1)|urinary_tract(1)	28		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00054)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00522)|BRCA - Breast invasive adenocarcinoma(304;1.3e-05)|COAD - Colon adenocarcinoma(227;1.31e-05)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(196;0.0069)|READ - Rectum adenocarcinoma(331;0.0681)|Lung(427;0.197)	L-Citrulline(DB00155)	GCCAACTGCAAGCTGACCATC	0.537																																					p.K335M	Esophageal Squamous(80;414 1257 4580 27746 50832)	Atlas-SNP	.											.	PADI1	77	.	0			c.A1004T						.						101	95	97					1																	17556654		2203	4300	6503	SO:0001583	missense	29943	exon9			ACTGCAAGCTGAC	AB033768	CCDS178.1	1p36.13	2008-07-18			ENSG00000142623	ENSG00000142623	3.5.3.15	"Peptidyl arginine deiminases"	18367	protein-coding gene	gene with protein product	"peptidylarginine deiminase type I", "protein-arginine deiminase type-1", "hPAD-colony 10"	607934				12416996	Standard	NM_013358		Approved	HPAD10, PDI1, PDI, PAD1	uc001bah.1	Q9ULC6	OTTHUMG00000002294	ENST00000375471.4:c.1004A>T	chr1.hg19:g.17556654A>T	ENSP00000364620:p.Lys335Met	56.0	0.0		50.0	15.0	NM_013358	A1L4K6|Q70SX6	Missense_Mutation	SNP	ENST00000375471.4	hg19	CCDS178.1	.	.	.	.	.	.	.	.	.	.	A	13.84	2.356562	0.41700	.	.	ENSG00000142623	ENST00000375471	T	0.26957	1.7	4.99	2.6	0.31112	Protein-arginine deiminase, C-terminal (1);	0.056441	0.64402	D	0.000001	T	0.50888	0.1642	M	0.87097	2.86	0.80722	D	1	D	0.76494	0.999	D	0.74348	0.983	T	0.51132	-0.8744	10	0.72032	D	0.01	-20.9056	8.7852	0.34816	0.8391:0.0:0.1609:0.0	.	335	Q9ULC6	PADI1_HUMAN	M	335	ENSP00000364620:K335M	ENSP00000364620:K335M	K	+	2	0	PADI1	17429241	0.993000	0.37304	0.988000	0.46212	0.111000	0.19643	3.010000	0.49559	0.316000	0.23135	0.383000	0.25322	AAG	.	.		0.537	PADI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006621.1	NM_013358		T	17556654	A	T	17556654	3	4	344	1	0	0	0	0	1	0	0	0	11386	72	3	4	1038	4	PADI1	1	17556654	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	4635326	17556654	231693967	17	47380										
PAX7	5081	hgsc.bcm.edu	37	chr1	19071418	19071418	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctgtggaaactggccaggccTactagggcccctggggcgac	15	13	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:19071418T>G	ENST00000420770.2	+	9	1596	c.1513T>G	c.(1513-1515)Tac>Gac	p.Y505D		NM_001135254.1	NP_001128726.1	P23759	PAX7_HUMAN	paired box 7	0					anatomical structure morphogenesis (GO:0009653)|cartilage development (GO:0051216)|chromatin remodeling (GO:0006338)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic skeletal system development (GO:0048706)|muscle tissue morphogenesis (GO:0060415)|negative regulation of apoptotic process (GO:0043066)|neuron fate commitment (GO:0048663)|positive regulation of histone methylation (GO:0031062)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell fate commitment (GO:0010453)|regulation of protein binding (GO:0043393)|skeletal muscle satellite cell commitment (GO:0014813)|skeletal muscle tissue regeneration (GO:0043403)|spinal cord association neuron differentiation (GO:0021527)	nucleus (GO:0005634)	RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)		PAX7/FOXO1(197)	breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(17)|ovary(1)|prostate(1)|skin(2)	31		Colorectal(325;3.46e-05)|all_lung(284;0.000439)|Renal(390;0.000518)|Lung NSC(340;0.000543)|Breast(348;0.00093)|Ovarian(437;0.00768)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00609)|BRCA - Breast invasive adenocarcinoma(304;4.71e-05)|Kidney(64;0.000279)|KIRC - Kidney renal clear cell carcinoma(64;0.00371)|STAD - Stomach adenocarcinoma(196;0.00658)|READ - Rectum adenocarcinoma(331;0.0576)		TGGCCAGGCCTACTAGGGCCC	0.627			T	FOXO1A	alveolar rhabdomyosarcoma																																p.Y505D		Atlas-SNP	.		Dom	yes		1	1p36.2-p36.12	5081	paired box gene 7		M	.	PAX7	127	.	0			c.T1513G						.						17	18	18					1																	19071418		1548	3517	5065	SO:0001583	missense	5081	exon9			CAGGCCTACTAGG	X96743	CCDS186.1, CCDS44074.1, CCDS44075.1	1p36.13	2011-06-20	2007-07-12		ENSG00000009709	ENSG00000009709		"Paired boxes", "Homeoboxes / PRD class"	8621	protein-coding gene	gene with protein product		167410	"paired box gene 7"			7981748, 8431641	Standard	NM_001135254		Approved	Hup1	uc001bay.3	P23759	OTTHUMG00000002433	ENST00000420770.2:c.1513T>G	chr1.hg19:g.19071418T>G	ENSP00000403389:p.Tyr505Asp	131.0	0.0		112.0	45.0	NM_001135254	E9PFV9|Q0VA99|Q2PJS5	Missense_Mutation	SNP	ENST00000420770.2	hg19	CCDS44074.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.444650	0.83993	.	.	ENSG00000009709	ENST00000420770	D	0.95690	-3.78	5.01	5.01	0.66863	.	.	.	.	.	D	0.96775	0.8947	L	0.59436	1.845	0.80722	D	1	D	0.71674	0.998	D	0.79784	0.993	D	0.97288	0.9922	9	0.87932	D	0	.	13.5514	0.61734	0.0:0.0:0.0:1.0	.	505	E9PFV9	.	D	505	ENSP00000403389:Y505D	ENSP00000403389:Y505D	Y	+	1	0	PAX7	18944005	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.206000	0.77891	1.881000	0.54492	0.533000	0.62120	TAC	.	.		0.627	PAX7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372482.1	NM_002584		G	19071418	T	G	19071418	3	3	344	1	0	0	0	0	1	0	0	0	11493	1522	53	5	1708	5	PAX7	1	19071418	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1514764	19071418	230179203	18	47381										
KIF17	57576	hgsc.bcm.edu	37	chr1	21013989	21013989	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcaaacgggtcctgcaggccTagtaacccctgcaggggcac	13	14	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:21013989T>C	ENST00000247986.2	-	8	2140	c.1830A>G	c.(1828-1830)ctA>ctG	p.L610L	KIF17_ENST00000400463.3_Silent_p.L610L|KIF17_ENST00000375044.1_Silent_p.L510L|KIF17_ENST00000490034.1_Intron			Q9P2E2	KIF17_HUMAN	kinesin family member 17	610					ATP catabolic process (GO:0006200)|cell projection organization (GO:0030030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|neurogenesis (GO:0022008)|protein complex localization (GO:0031503)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)		CCTGCAGGCCTAGTAACCCCT	0.667																																					p.L610L		Atlas-SNP	.											.	KIF17	130	.	0			c.A1830G						.						50	49	50					1																	21013989		2203	4300	6503	SO:0001819	synonymous_variant	57576	exon8			CAGGCCTAGTAAC	AB037826	CCDS213.1, CCDS44079.1, CCDS72722.1	1p36.13	2012-08-01			ENSG00000117245	ENSG00000117245		"Kinesins"	19167	protein-coding gene	gene with protein product	"kinesin-like protein KIF17", "KIF3-related motor protein", "KIF17 variant protein"	605037				10846156	Standard	XR_241202		Approved	KIAA1405, KIF3X, KIF17B, OSM-3, KLP-2	uc001bdr.4	Q9P2E2	OTTHUMG00000002863	ENST00000247986.2:c.1830A>G	chr1.hg19:g.21013989T>C		65.0	0.0		62.0	29.0	NM_001122819	A2A3Q7|A2A3Q8|O95077|Q53YS6|Q5VWA9|Q6GSA8|Q8N411	Silent	SNP	ENST00000247986.2	hg19	CCDS213.1																																																																																			.	.		0.667	KIF17-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276995.1	NM_020816		C	21013989	T	C	21013989	2	2	344	1	0	0	0	0	0	0	0	1	8288	1509	53	2		2	KIF17	1	21013989	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1942571	21013989	228236632	19	47382										
LDLRAD2	401944	hgsc.bcm.edu	37	chr1	22141096	22141096	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cccgcgcccccggcgctcaaCacctcctccccggccccggc	9	26	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:22141096C>A	ENST00000344642.2	+	2	478	c.291C>A	c.(289-291)aaC>aaA	p.N97K	LDLRAD2_ENST00000543870.1_Missense_Mutation_p.N97K	NM_001013693.2	NP_001013715.2	Q5SZI1	LRAD2_HUMAN	low density lipoprotein receptor class A domain containing 2	97						integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(1)|lung(3)	6		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.00166)|all_lung(284;0.00172)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;5.2e-26)|COAD - Colon adenocarcinoma(152;1.13e-05)|GBM - Glioblastoma multiforme(114;1.36e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00598)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.197)		CGGCGCTCAACACCTCCTCCC	0.766																																					p.N97K		Atlas-SNP	.											.	LDLRAD2	17	.	0			c.C291A						.						11	14	13					1																	22141096		2152	4223	6375	SO:0001583	missense	401944	exon2			GCTCAACACCTCC	AL590103	CCDS30624.1	1p36.12	2008-02-05	2005-10-07		ENSG00000187942	ENSG00000187942			32071	protein-coding gene	gene with protein product			"low density lipoprotein receptor A domain containing 2"				Standard	NM_001013693		Approved		uc001bfg.1	Q5SZI1	OTTHUMG00000002675	ENST00000344642.2:c.291C>A	chr1.hg19:g.22141096C>A	ENSP00000340988:p.Asn97Lys	74.0	0.0		90.0	47.0	NM_001013693	B9EJB3|Q6ZSN5	Missense_Mutation	SNP	ENST00000344642.2	hg19	CCDS30624.1	.	.	.	.	.	.	.	.	.	.	C	7.876	0.729270	0.15507	.	.	ENSG00000187942	ENST00000344642;ENST00000543870	T;T	0.45276	0.9;0.9	4.63	3.71	0.42584	CUB (2);	0.858076	0.09990	N	0.729920	T	0.29749	0.0743	L	0.40543	1.245	0.09310	N	1	B	0.29432	0.244	B	0.19666	0.026	T	0.18713	-1.0328	10	0.16896	T	0.51	-2.8124	7.4219	0.27077	0.0:0.798:0.0:0.202	.	97	Q5SZI1	LRAD2_HUMAN	K	97	ENSP00000340988:N97K;ENSP00000444097:N97K	ENSP00000340988:N97K	N	+	3	2	LDLRAD2	22013683	0.001000	0.12720	0.003000	0.11579	0.139000	0.21198	0.957000	0.29215	1.072000	0.40860	0.448000	0.29417	AAC	.	.		0.766	LDLRAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007601.1	NM_001013693		A	22141096	C	A	22141096	3	1	344	1	0	0	0	0	1	0	0	0	8715	477	17	3	297	3	LDLRAD2	1	22141096	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1127107	22141096	227109525	20	47383										
HNRNPR	10236	hgsc.bcm.edu	37	chr1	23637344	23637344	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gccctccccttcctcctcctCttcctcttactgcatagcca	3	21	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:23637344C>A	ENST00000374612.1	-	11	1628	c.1505G>T	c.(1504-1506)aGa>aTa	p.R502I	HNRNPR_ENST00000374616.3_Missense_Mutation_p.R505I|HNRNPR_ENST00000476660.1_5'UTR|HNRNPR_ENST00000426846.2_Missense_Mutation_p.R342I|HNRNPR_ENST00000302271.6_Missense_Mutation_p.R502I|HNRNPR_ENST00000478691.1_Missense_Mutation_p.R404I|HNRNPR_ENST00000427764.2_Missense_Mutation_p.R464I|HNRNPR_ENST00000606561.1_Missense_Mutation_p.R363I	NM_001102398.1|NM_005826.3	NP_001095868.1|NP_005817.1	O43390	HNRPR_HUMAN	heterogeneous nuclear ribonucleoprotein R	502	RNA-binding RGG-box.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R502T(2)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00394)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;6.83e-27)|Colorectal(126;6.01e-08)|COAD - Colon adenocarcinoma(152;3.32e-06)|GBM - Glioblastoma multiforme(114;6.69e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|KIRC - Kidney renal clear cell carcinoma(1967;0.00357)|STAD - Stomach adenocarcinoma(196;0.0131)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0875)|LUSC - Lung squamous cell carcinoma(448;0.19)		tcctcctcctcttcctcttac	0.527																																					p.R505I		Atlas-SNP	.											HNRPR,mouth,carcinoma,0,2	HNRNPR	56	.	2	Substitution - Missense(2)	upper_aerodigestive_tract(2)	c.G1514T						.						91	94	93					1																	23637344		2203	4299	6502	SO:0001583	missense	10236	exon11			CCTCCTCTTCCTC	AF000364	CCDS232.1, CCDS44085.1, CCDS60020.1, CCDS72726.1, CCDS72727.1	1p36.12	2013-02-12		2007-08-16	ENSG00000125944	ENSG00000125944		"RNA binding motif (RRM) containing"	5047	protein-coding gene	gene with protein product		607201		HNRPR		9421497	Standard	XM_005245711		Approved	hnRNP-R	uc001bgp.4	O43390	OTTHUMG00000003224	ENST00000374612.1:c.1505G>T	chr1.hg19:g.23637344C>A	ENSP00000363741:p.Arg502Ile	45.0	0.0		50.0	14.0	NM_001102398	Q2L7G6|Q5TEH1|Q9BV64|S4R3J4	Missense_Mutation	SNP	ENST00000374612.1	hg19	CCDS232.1	.	.	.	.	.	.	.	.	.	.	C	15.25	2.778884	0.49891	.	.	ENSG00000125944	ENST00000374616;ENST00000374612;ENST00000302271;ENST00000427764;ENST00000426846	T;T;T;T;T	0.22743	1.94;1.94;1.94;2.23;2.79	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.32941	0.0846	M	0.80616	2.505	0.80722	D	1	P;P;P;P;P;P	0.50943	0.842;0.842;0.842;0.842;0.94;0.902	B;B;B;B;B;P	0.44811	0.272;0.272;0.272;0.272;0.272;0.461	T	0.13282	-1.0515	10	0.26408	T	0.33	-4.0137	17.0724	0.86578	0.0:1.0:0.0:0.0	.	342;464;363;482;502;505	E7ETM7;Q2L7G6;B4DT28;Q6MZS5;O43390;O43390-2	.;.;.;.;HNRPR_HUMAN;.	I	505;502;502;464;342	ENSP00000363745:R505I;ENSP00000363741:R502I;ENSP00000304405:R502I;ENSP00000392799:R464I;ENSP00000415042:R342I	ENSP00000304405:R502I	R	-	2	0	HNRNPR	23509931	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.765000	0.85310	2.639000	0.89480	0.555000	0.69702	AGA	.	.		0.527	HNRNPR-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008889.1	NM_005826		A	23637344	C	A	23637344	3	1	344	1	0	0	0	0	1	0	0	0	7281	913	32	3	400	3	HNRNPR	1	23637344	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1496248	23637344	225613277	21	47384										
CNR2	1269	hgsc.bcm.edu	37	chr1	24201051	24201051	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atcagagaggtctagatctcTggaatctggccacggagtga	13	8	4	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:24201051T>C	ENST00000374472.4	-	2	1218	c.1057A>G	c.(1057-1059)Aga>Gga	p.R353G	CNR2_ENST00000536471.1_Missense_Mutation_p.R353G	NM_001841.2	NP_001832.1	P34972	CNR2_HUMAN	cannabinoid receptor 2 (macrophage)	353					G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation of action potential (GO:0045759)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mast cell activation (GO:0033004)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|response to amphetamine (GO:0001975)|response to lipopolysaccharide (GO:0032496)|sensory perception of pain (GO:0019233)	dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(9)|pancreas(1)|skin(2)|stomach(6)|upper_aerodigestive_tract(2)	26		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.00957)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.32e-24)|Colorectal(126;6.09e-08)|COAD - Colon adenocarcinoma(152;3.33e-06)|GBM - Glioblastoma multiforme(114;2.9e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|KIRC - Kidney renal clear cell carcinoma(1967;0.00359)|STAD - Stomach adenocarcinoma(196;0.0131)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.146)	Dronabinol(DB00470)|Nabilone(DB00486)	TCTAGATCTCTGGAATCTGGC	0.517																																					p.R353G		Atlas-SNP	.											.	CNR2	78	.	0			c.A1057G						.						86	99	94					1																	24201051		2203	4300	6503	SO:0001583	missense	1269	exon2			GATCTCTGGAATC	X74328	CCDS245.1	1p	2012-08-08			ENSG00000188822	ENSG00000188822		"GPCR / Class A : Cannabinoid receptors"	2160	protein-coding gene	gene with protein product		605051					Standard	NM_001841		Approved	CB2	uc001bif.3	P34972	OTTHUMG00000013892	ENST00000374472.4:c.1057A>G	chr1.hg19:g.24201051T>C	ENSP00000363596:p.Arg353Gly	50.0	0.0		58.0	22.0	NM_001841	C6ES44|Q4VBK8|Q5JRH7|Q6B0G7|Q6NSY0	Missense_Mutation	SNP	ENST00000374472.4	hg19	CCDS245.1	.	.	.	.	.	.	.	.	.	.	T	11.03	1.520419	0.27211	.	.	ENSG00000188822	ENST00000374472;ENST00000536471	T;T	0.79247	-1.25;-1.25	4.12	-1.36	0.09085	.	1.463340	0.04763	N	0.426559	T	0.57489	0.2057	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46721	-0.9171	10	0.02654	T	1	.	4.7693	0.13148	0.0:0.2894:0.1574:0.5533	.	353	P34972	CNR2_HUMAN	G	353	ENSP00000363596:R353G;ENSP00000442830:R353G	ENSP00000363596:R353G	R	-	1	2	CNR2	24073638	0.000000	0.05858	0.001000	0.08648	0.015000	0.08874	0.077000	0.14738	-0.044000	0.13491	-0.376000	0.06991	AGA	.	.		0.517	CNR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038949.1	NM_001841		C	24201051	T	C	24201051	3	2	344	1	0	0	0	0	1	0	0	0	3634	1588	55	2	29	2	CNR2	1	24201051	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	563707	24201051	225049570	22	47385										
SRRM1	10250	hgsc.bcm.edu	37	chr1	24996026	24996026	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggcagtccccgtctccaagtActaggcccattaggagagtc	11	13	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:24996026A>G	ENST00000323848.9	+	14	2467	c.2152A>G	c.(2152-2154)Act>Gct	p.T718A	SRRM1_ENST00000479034.1_3'UTR|SRRM1_ENST00000447431.2_Missense_Mutation_p.T730A|snoU13_ENST00000459464.1_RNA|SRRM1_ENST00000374389.4_Missense_Mutation_p.T727A	NM_005839.3	NP_005830.2	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1	718	Arg-rich.|Pro-rich.|Ser-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	36		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;1.01e-24)|Colorectal(126;5.95e-08)|COAD - Colon adenocarcinoma(152;3.24e-06)|GBM - Glioblastoma multiforme(114;0.000148)|BRCA - Breast invasive adenocarcinoma(304;0.00177)|KIRC - Kidney renal clear cell carcinoma(1967;0.00348)|STAD - Stomach adenocarcinoma(196;0.00483)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		GTCTCCAAGTACTAGGCCCAT	0.478																																					p.T718A	Ovarian(68;897 1494 3282 17478)	Atlas-SNP	.											.	SRRM1	81	.	0			c.A2152G						.						35	35	35					1																	24996026		2203	4297	6500	SO:0001583	missense	10250	exon14			CCAAGTACTAGGC	AF048977	CCDS255.1	1p36	2010-04-22			ENSG00000133226	ENSG00000133226			16638	protein-coding gene	gene with protein product	"Ser/Arg-related nuclear matrix protein", "plenty of prolines 101-like"	605975				9531537	Standard	NM_005839		Approved	SRM160, POP101, MGC39488	uc001bjm.3	Q8IYB3	OTTHUMG00000003320	ENST00000323848.9:c.2152A>G	chr1.hg19:g.24996026A>G	ENSP00000326261:p.Thr718Ala	327.0	0.0		243.0	115.0	NM_005839	O60585|Q5VVN4	Missense_Mutation	SNP	ENST00000323848.9	hg19	CCDS255.1	.	.	.	.	.	.	.	.	.	.	A	12.05	1.822716	0.32237	.	.	ENSG00000133226	ENST00000323848;ENST00000447431;ENST00000374389	T;T;T	0.37752	1.18;1.18;1.18	5.7	3.32	0.38043	.	0.291019	0.29558	N	0.011803	T	0.22322	0.0538	N	0.22421	0.69	0.80722	D	1	B;B	0.12630	0.006;0.003	B;B	0.09377	0.004;0.002	T	0.04191	-1.0970	10	0.42905	T	0.14	-2.3967	7.4256	0.27096	0.5948:0.264:0.0:0.1412	.	730;718	E9PCT1;Q8IYB3	.;SRRM1_HUMAN	A	718;730;727	ENSP00000326261:T718A;ENSP00000391430:T730A;ENSP00000363510:T727A	ENSP00000326261:T718A	T	+	1	0	SRRM1	24868613	0.999000	0.42202	0.999000	0.59377	0.825000	0.46686	2.556000	0.45862	0.397000	0.25310	0.460000	0.39030	ACT	.	.		0.478	SRRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009292.2	NM_005839		G	24996026	A	G	24996026	3	3	344	1	0	0	0	0	1	0	0	0	15183	391	14	2	2206	2	SRRM1	1	24996026	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	794975	24996026	224254595	23	47386										
ZDHHC18	84243	hgsc.bcm.edu	37	chr1	27177682	27177682	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tctgggcctctcagggtttcAcacgtacctcgtcgcctcca	9	16	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:27177682A>T	ENST00000374142.4	+	6	991	c.896A>T	c.(895-897)cAc>cTc	p.H299L	ZDHHC18_ENST00000478902.1_3'UTR	NM_032283.2	NP_115659.1	Q9NUE0	ZDH18_HUMAN	zinc finger, DHHC-type containing 18	299					cellular protein localization (GO:0034613)|protein palmitoylation (GO:0018345)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)	3		all_cancers(24;5.82e-22)|all_epithelial(13;9.91e-20)|Colorectal(325;0.000147)|Breast(348;0.000706)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;5.71e-53)|Epithelial(14;4.73e-52)|OV - Ovarian serous cystadenocarcinoma(117;1.53e-29)|Colorectal(126;1.9e-09)|COAD - Colon adenocarcinoma(152;4.2e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000548)|STAD - Stomach adenocarcinoma(196;0.00065)|KIRC - Kidney renal clear cell carcinoma(1967;0.000779)|GBM - Glioblastoma multiforme(114;0.0265)|READ - Rectum adenocarcinoma(331;0.0455)|Lung(427;0.163)|LUSC - Lung squamous cell carcinoma(448;0.237)		TCAGGGTTTCACACGTACCTC	0.572																																					p.H299L		Atlas-SNP	.											.	ZDHHC18	20	.	0			c.A896T						.						200	163	176					1																	27177682		2203	4300	6503	SO:0001583	missense	84243	exon6			GGTTTCACACGTA	AK056427	CCDS30650.1	1p36.11	2008-05-02			ENSG00000204160	ENSG00000204160		"Zinc fingers, DHHC-type"	20712	protein-coding gene	gene with protein product							Standard	NM_032283		Approved	DKFZp667O2416	uc001bnb.3	Q9NUE0	OTTHUMG00000004092	ENST00000374142.4:c.896A>T	chr1.hg19:g.27177682A>T	ENSP00000363257:p.His299Leu	111.0	0.0		95.0	38.0	NM_032283	A6NHY9|B4DQ84|Q5JYH0|Q9H020	Missense_Mutation	SNP	ENST00000374142.4	hg19	CCDS30650.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.628664	0.87560	.	.	ENSG00000204160	ENST00000374142;ENST00000374141	T;T	0.29142	1.58;1.58	4.98	3.86	0.44501	.	0.107650	0.64402	D	0.000006	T	0.70500	0.3231	H	0.99169	4.455	0.54753	D	0.999986	D	0.76494	0.999	D	0.83275	0.996	T	0.79787	-0.1656	10	0.87932	D	0	-7.9428	10.7464	0.46183	0.9255:0.0:0.0745:0.0	.	299	Q9NUE0	ZDH18_HUMAN	L	299;164	ENSP00000363257:H299L;ENSP00000363256:H164L	ENSP00000363256:H164L	H	+	2	0	ZDHHC18	27050269	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.689000	0.91265	1.038000	0.40049	0.533000	0.62120	CAC	.	.		0.572	ZDHHC18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011706.3	NM_032283		T	27177682	A	T	27177682	3	4	344	1	0	0	0	0	1	0	0	0	17623	159	6	4	918	4	ZDHHC18	1	27177682	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2181656	27177682	222072939	24	47387										
TMEM222	84065	hgsc.bcm.edu	37	chr1	27648780	27648780	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggaggcgccgacggcggccgAgacggacatgaagcaatatc	16	11	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:27648780A>T	ENST00000374076.4	+	1	130	c.92A>T	c.(91-93)gAg>gTg	p.E31V	RNU6-48P_ENST00000384161.1_RNA|TMEM222_ENST00000608611.1_5'UTR	NM_032125.2	NP_115501.2	Q9H0R3	TM222_HUMAN	transmembrane protein 222	31						integral component of membrane (GO:0016021)				biliary_tract(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	7						ACGGCGGCCGAGACGGACATG	0.687																																					p.E31V		Atlas-SNP	.											.	TMEM222	16	.	0			c.A92T						.						22	21	21					1																	27648780		2200	4296	6496	SO:0001583	missense	84065	exon1			CGGCCGAGACGGA	AL136683	CCDS297.2	1p36.11	2008-07-07	2008-07-07	2008-07-07	ENSG00000186501	ENSG00000186501			25363	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 160"	C1orf160		11230166	Standard	NM_032125		Approved	DKFZP564D0478	uc001bnr.4	Q9H0R3	OTTHUMG00000004410	ENST00000374076.4:c.92A>T	chr1.hg19:g.27648780A>T	ENSP00000363189:p.Glu31Val	196.0	0.0		182.0	101.0	NM_032125	D3DPL6|Q53HD8|Q5FVE9	Missense_Mutation	SNP	ENST00000374076.4	hg19	CCDS297.2	.	.	.	.	.	.	.	.	.	.	A	16.45	3.126051	0.56721	.	.	ENSG00000186501	ENST00000374076	.	.	.	4.41	2.02	0.26589	.	0.651645	0.13073	U	0.415936	T	0.40932	0.1137	L	0.43152	1.355	0.33437	D	0.581941	B	0.18013	0.025	B	0.20384	0.029	T	0.45991	-0.9223	9	0.37606	T	0.19	-1.5356	6.0531	0.19796	0.7842:0.0:0.2158:0.0	.	31	Q9H0R3	TM222_HUMAN	V	31	.	ENSP00000363189:E31V	E	+	2	0	TMEM222	27521367	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	2.890000	0.48609	0.744000	0.32741	-0.379000	0.06801	GAG	.	.		0.687	TMEM222-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000012809.2	NM_032125		T	27648780	A	T	27648780	3	4	344	1	0	0	0	0	1	0	0	0	16160	304	11	4	94	4	TMEM222	1	27648780	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	471098	27648780	221601841	25	47388										
RCC1	1104	hgsc.bcm.edu	37	chr1	28864505	28864505	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cagtcttattagtcaaggacAaagaacagagctgatgaagc	10	7	2	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:28864505A>G	ENST00000373833.6	+	13	1537	c.1252A>G	c.(1252-1254)Aaa>Gaa	p.K418E	RCC1_ENST00000373831.3_Missense_Mutation_p.K449E|RCC1_ENST00000398958.2_Missense_Mutation_p.K418E|RCC1_ENST00000373832.1_Missense_Mutation_p.K418E			P18754	RCC1_HUMAN	regulator of chromosome condensation 1	418					chromosome segregation (GO:0007059)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|positive regulation of Ran GTPase activity (GO:0032853)|regulation of mitosis (GO:0007088)|spindle assembly (GO:0051225)|viral process (GO:0016032)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|nucleosomal DNA binding (GO:0031492)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)			breast(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)	14		Colorectal(325;3.46e-05)|Lung NSC(340;0.000318)|all_lung(284;0.000434)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.00989)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)|Medulloblastoma(700;0.123)		Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|KIRC - Kidney renal clear cell carcinoma(1967;0.0101)|BRCA - Breast invasive adenocarcinoma(304;0.022)|READ - Rectum adenocarcinoma(331;0.0649)		AGTCAAGGACAAAGAACAGAG	0.572																																					p.K449E		Atlas-SNP	.											.	RCC1	61	.	0			c.A1345G						.						54	52	52					1																	28864505		2203	4300	6503	SO:0001583	missense	1104	exon11			AAGGACAAAGAAC	X12654	CCDS323.1, CCDS41295.1	1p35.3	2008-08-18	2005-05-09	2005-05-09	ENSG00000180198	ENSG00000180198			1913	protein-coding gene	gene with protein product		179710	"chromosome condensation 1"	CHC1		7851910	Standard	NM_001048199		Approved		uc001bqf.2	P18754	OTTHUMG00000003645	ENST00000373833.6:c.1252A>G	chr1.hg19:g.28864505A>G	ENSP00000362939:p.Lys418Glu	66.0	0.0		37.0	14.0	NM_001048194	Q16269|Q6NT97	Missense_Mutation	SNP	ENST00000373833.6	hg19	CCDS323.1	.	.	.	.	.	.	.	.	.	.	A	14.98	2.696363	0.48202	.	.	ENSG00000180198	ENST00000398958;ENST00000373833;ENST00000373832;ENST00000373831	T;T;T;T	0.80304	-1.36;-1.36;-1.36;-1.36	5.17	4.0	0.46444	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.187779	0.56097	D	0.000030	T	0.68118	0.2966	L	0.28192	0.835	0.38868	D	0.956622	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.12156	0.007;0.001;0.001	T	0.62229	-0.6898	10	0.36615	T	0.2	-15.982	9.9057	0.41375	0.8283:0.1717:0.0:0.0	.	449;435;418	P18754-2;E9PAT9;P18754	.;.;RCC1_HUMAN	E	418;418;418;449	ENSP00000381931:K418E;ENSP00000362939:K418E;ENSP00000362938:K418E;ENSP00000362937:K449E	ENSP00000362937:K449E	K	+	1	0	RCC1	28737092	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	3.455000	0.52993	0.862000	0.35528	0.460000	0.39030	AAA	.	.		0.572	RCC1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010323.3	NM_001269		G	28864505	A	G	28864505	3	3	344	1	0	0	0	0	1	0	0	0	13188	131	5	2	1383	2	RCC1	1	28864505	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1215725	28864505	220386116	26	47389										
COL16A1	1307	hgsc.bcm.edu	37	chr1	32161363	32161363	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agtccactgggaggcttaccTcatcggctgctgtctcctga	11	13	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:32161363T>A	ENST00000373672.3	-	10	1460	c.944A>T	c.(943-945)gAg>gTg	p.E315V	COL16A1_ENST00000373668.3_Splice_Site_p.E315V|COL16A1_ENST00000271069.6_Splice_Site_p.E315V	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	315	Nonhelical region 10 (NC10).				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female pregnancy (GO:0007565)|integrin-mediated signaling pathway (GO:0007229)	collagen type XVI trimer (GO:0005597)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(15)|ovary(8)|prostate(4)	48		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		GAGGCTTACCTCATCGGCTGC	0.627																																					p.E315V	Colon(143;498 1786 21362 25193 36625)	Atlas-SNP	.											.	COL16A1	137	.	0			c.A944T						.						32	37	35					1																	32161363		2041	4192	6233	SO:0001630	splice_region_variant	1307	exon10			CTTACCTCATCGG	M92642	CCDS41297.1	1p35-p34	2013-01-16			ENSG00000084636	ENSG00000084636		"Collagens"	2193	protein-coding gene	gene with protein product		120326				1631157	Standard	NM_001856		Approved		uc001btk.1	Q07092	OTTHUMG00000003883	ENST00000373672.3:c.945+1A>T	chr1.hg19:g.32161363T>A		130.0	0.0		86.0	38.0	NM_001856	Q16593|Q59F89|Q71RG9	Missense_Mutation	SNP	ENST00000373672.3	hg19	CCDS41297.1	.	.	.	.	.	.	.	.	.	.	t	18.41	3.618704	0.66787	.	.	ENSG00000084636	ENST00000373672;ENST00000271069;ENST00000373668;ENST00000373667	D;D;D;D	0.91945	-2.63;-2.66;-2.69;-2.94	4.44	4.44	0.53790	.	0.539835	0.19611	N	0.110142	D	0.90202	0.6937	N	0.13198	0.31	0.29403	N	0.861777	D;D;D	0.76494	0.997;0.998;0.999	P;D;D	0.80764	0.897;0.987;0.994	T	0.83041	-0.0157	10	0.18710	T	0.47	.	10.4222	0.44356	0.0:0.0:0.0:1.0	.	315;315;315	A6NCT7;Q07092;Q07092-2	.;COGA1_HUMAN;.	V	315;315;315;43	ENSP00000362776:E315V;ENSP00000271069:E315V;ENSP00000362772:E315V;ENSP00000362771:E43V	ENSP00000271069:E315V	E	-	2	0	COL16A1	31933950	0.993000	0.37304	0.998000	0.56505	0.460000	0.32559	1.494000	0.35616	2.233000	0.73108	0.524000	0.50904	GAG	.	.		0.627	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856	Missense_Mutation	A	32161363	T	A	32161363	5	1	344	1	0	0	0	0	0	0	1	0	3675	1565	54	4	4118	4	COL16A1	1	32161363	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	3296858	32161363	217089258	27	47390										
LCK	3932	hgsc.bcm.edu	37	chr1	32742349	32742349	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gctctacgctgtggtcacccAggagcccatctacatcatca	8	15	5	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:32742349A>T	ENST00000336890.5	+	9	1064	c.926A>T	c.(925-927)cAg>cTg	p.Q309L	LCK_ENST00000373564.3_Missense_Mutation_p.Q316L|LCK_ENST00000333070.4_Missense_Mutation_p.Q309L	NM_005356.3	NP_005347.3	P06239	LCK_HUMAN	LCK proto-oncogene, Src family tyrosine kinase	309	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|aging (GO:0007568)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular zinc ion homeostasis (GO:0006882)|dephosphorylation (GO:0016311)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hemopoiesis (GO:0030097)|innate immune response (GO:0045087)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of gene expression (GO:0010628)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|positive regulation of uterine smooth muscle contraction (GO:0070474)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of defense response to virus by virus (GO:0050690)|regulation of lymphocyte activation (GO:0051249)|release of sequestered calcium ion into cytosol (GO:0051209)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to zinc ion (GO:0010043)|T cell costimulation (GO:0031295)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|pericentriolar material (GO:0000242)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|ATP binding (GO:0005524)|ATPase binding (GO:0051117)|CD4 receptor binding (GO:0042609)|CD8 receptor binding (GO:0042610)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine kinase activity (GO:0004713)|SH2 domain binding (GO:0042169)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	37		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.212)			Dasatinib(DB01254)|Ponatinib(DB08901)	GTGGTCACCCAGGAGCCCATC	0.612			T	TRB@	T-ALL																																p.Q309L		Atlas-SNP	.		Dom	yes		1	1p35-p34.3	3932	lymphocyte-specific protein tyrosine kinase		L	.	LCK	124	.	0			c.A926T						.						42	39	40					1																	32742349		2203	4300	6503	SO:0001583	missense	3932	exon9			TCACCCAGGAGCC	M36881	CCDS359.1	1p34.3	2014-09-17	2014-06-25		ENSG00000182866	ENSG00000182866	2.7.10.1	"SH2 domain containing"	6524	protein-coding gene	gene with protein product		153390	"lymphocyte-specific protein tyrosine kinase"			2787474	Standard	XM_005270862		Approved		uc001buy.3	P06239	OTTHUMG00000007463	ENST00000336890.5:c.926A>T	chr1.hg19:g.32742349A>T	ENSP00000337825:p.Gln309Leu	60.0	0.0		45.0	31.0	NM_005356	D3DPP8|P07100|Q12850|Q13152|Q5TDH8|Q5TDH9|Q7RTZ3|Q96DW4|Q9NYT8	Missense_Mutation	SNP	ENST00000336890.5	hg19	CCDS359.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.133382	0.77662	.	.	ENSG00000182866	ENST00000336890;ENST00000398345;ENST00000495610;ENST00000333070;ENST00000436824;ENST00000373564	T;T;D;T	0.82984	2.77;2.77;-1.67;2.77	5.44	5.44	0.79542	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000005	T	0.79476	0.4452	L	0.41356	1.27	0.80722	D	1	B;B;B;B	0.27951	0.195;0.068;0.061;0.116	B;B;B;B	0.32583	0.148;0.106;0.087;0.065	T	0.79142	-0.1925	10	0.87932	D	0	.	14.8315	0.70151	1.0:0.0:0.0:0.0	.	353;316;309;309	E7EN21;Q573B4;P06239-3;P06239	.;.;.;LCK_HUMAN	L	309;49;258;309;353;316	ENSP00000337825:Q309L;ENSP00000435605:Q258L;ENSP00000328213:Q309L;ENSP00000362665:Q316L	ENSP00000328213:Q309L	Q	+	2	0	LCK	32514936	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.324000	0.79115	2.207000	0.71202	0.454000	0.30748	CAG	.	.		0.612	LCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019616.4	NM_005356		T	32742349	A	T	32742349	3	4	344	1	0	0	0	0	1	0	0	0	8685	188	7	4	956	4	LCK	1	32742349	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	580986	32742349	216508272	28	47391										
ADC	113451	hgsc.bcm.edu	37	chr1	33557811	33557811	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggcaaaggtggtaaagagccAccccagtgccaagtaagctg	13	10	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:33557811A>T	ENST00000294517.6	+	6	1027	c.440A>T	c.(439-441)cAc>cTc	p.H147L	ADC_ENST00000373440.1_Intron|ADC_ENST00000373443.3_Missense_Mutation_p.H147L|ADC_ENST00000398167.1_Missense_Mutation_p.H147L|ADC_ENST00000484656.1_3'UTR|ADC_ENST00000373441.1_Missense_Mutation_p.H147L|ADC_ENST00000358680.3_Intron	NM_052998.2	NP_443724.1	Q96A70	AZIN2_HUMAN		147					agmatine biosynthetic process (GO:0097055)|cellular nitrogen compound metabolic process (GO:0034641)|negative regulation of protein catabolic process (GO:0042177)|ornithine metabolic process (GO:0006591)|polyamine biosynthetic process (GO:0006596)|polyamine metabolic process (GO:0006595)|positive regulation of catalytic activity (GO:0043085)|positive regulation of polyamine transmembrane transport (GO:1902269)|putrescine transport (GO:0015847)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|trans-Golgi network membrane organization (GO:0098629)	axon (GO:0030424)|cis-Golgi network (GO:0005801)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum-Golgi intermediate compartment membrane (GO:0033116)|granular vesicle (GO:1990005)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)	catalytic activity (GO:0003824)|ornithine decarboxylase activator activity (GO:0042978)|putrescine transmembrane transporter activity (GO:0015489)			NS(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(2)	11		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)			L-Arginine(DB00125)	GTAAAGAGCCACCCCAGTGCC	0.587																																					p.H147L		Atlas-SNP	.											.	ADC	38	.	0			c.A440T						.						58	58	58					1																	33557811		2203	4300	6503	SO:0001583	missense	113451	exon6			AGAGCCACCCCAG																												ENST00000294517.6:c.440A>T	chr1.hg19:g.33557811A>T	ENSP00000294517:p.His147Leu	219.0	0.0		166.0	69.0	NM_052998	B2RDU5|D3DPQ9|Q5TIF4|Q5TIF5|Q5TIF6|Q8TF56|Q96L54|Q96L55|Q96L56|Q96L57|Q96MD9	Missense_Mutation	SNP	ENST00000294517.6	hg19	CCDS375.1	.	.	.	.	.	.	.	.	.	.	a	24.7	4.559838	0.86335	.	.	ENSG00000142920	ENST00000294517;ENST00000341637;ENST00000373443;ENST00000398167;ENST00000373441	T;T;T;T	0.47869	0.83;0.83;0.87;0.87	5.4	4.27	0.50696	Orn/DAP/Arg decarboxylase 2, N-terminal (1);	0.072359	0.56097	D	0.000024	T	0.66848	0.2831	M	0.81341	2.54	0.80722	D	1	D;D;D;D	0.65815	0.97;0.964;0.995;0.995	P;P;D;D	0.67900	0.736;0.796;0.954;0.927	T	0.70252	-0.4923	10	0.87932	D	0	-10.8888	11.0346	0.47793	0.926:0.0:0.074:0.0	.	147;147;52;147	Q96A70-2;Q96A70-3;D3DPR0;Q96A70	.;.;.;ADC_HUMAN	L	147	ENSP00000294517:H147L;ENSP00000362542:H147L;ENSP00000381233:H147L;ENSP00000362540:H147L	ENSP00000294517:H147L	H	+	2	0	ADC	33330398	1.000000	0.71417	0.982000	0.44146	0.996000	0.88848	9.311000	0.96282	1.004000	0.39156	0.529000	0.55759	CAC	.	.		0.587	ADC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011867.1			T	33557811	A	T	33557811	3	4	344	1	0	0	0	0	1	0	0	0	287	159	6	4	450	4	ADC	1	33557811	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	815462	33557811	215692810	29	47392										
PHC2	1912	hgsc.bcm.edu	37	chr1	33836103	33836103	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cccaagagcacagcctgctgAgcgatgcctgaggctgctgc	13	14	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:33836103A>T	ENST00000257118.5	-	4	548	c.495T>A	c.(493-495)gcT>gcA	p.A165A	PHC2_ENST00000373416.1_5'UTR|PHC2_ENST00000431992.1_Silent_p.A165A|PHC2_ENST00000419414.2_Silent_p.A165A	NM_198040.2	NP_932157.1	Q8IXK0	PHC2_HUMAN	polyhomeotic homolog 2 (Drosophila)	165					multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				CAGCCTGCTGAGCGATGCCTG	0.597																																					p.A165A		Atlas-SNP	.											.	PHC2	78	.	0			c.T495A						.						81	67	72					1																	33836103		2203	4300	6503	SO:0001819	synonymous_variant	1912	exon4			CTGCTGAGCGATG	AJ419231	CCDS378.1, CCDS379.1	1p34.3	2013-01-10	2006-09-12	2002-11-15	ENSG00000134686	ENSG00000134686		"Sterile alpha motif (SAM) domain containing"	3183	protein-coding gene	gene with protein product		602979	"early development regulator 2 (homolog of polyhomeotic 2)", "polyhomeotic-like 2 (Drosophila)"	EDR2		9121482, 12384788	Standard	NM_198040		Approved	HPH2	uc001bxg.1	Q8IXK0	OTTHUMG00000004133	ENST00000257118.5:c.495T>A	chr1.hg19:g.33836103A>T		56.0	0.0		51.0	20.0	NM_198040	A1L4Q1|A8KA40|D3DPR2|Q2TAL3|Q5T0C1|Q6NUJ6|Q6ZQR1|Q8N306|Q8TAG8|Q96BL4|Q9Y4Y7	Silent	SNP	ENST00000257118.5	hg19	CCDS378.1																																																																																			.	.		0.597	PHC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000011895.1	NM_198040		T	33836103	A	T	33836103	2	4	344	1	0	0	0	0	0	0	0	1	11826	291	11	4		4	PHC2	1	33836103	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	278292	33836103	215414518	30	47393										
CSMD2	114784	hgsc.bcm.edu	37	chr1	34123600	34123600	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cctgttctcgatcttcacacAgctgatctctgcacttccct	5	16	4	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:34123600A>T	ENST00000373380.1	-	6	1232	c.1012T>A	c.(1012-1014)Tgt>Agt	p.C338S	CSMD2_ENST00000373388.2_5'UTR|CSMD2_ENST00000373381.4_Missense_Mutation_p.C1465S			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1425						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				ATCTTCACACAGCTGATCTCT	0.587																																					p.C1425S		Atlas-SNP	.											.	CSMD2	946	.	0			c.T4273A						.						124	115	118					1																	34123600		2203	4300	6503	SO:0001583	missense	114784	exon27			TCACACAGCTGAT	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373380.1:c.1012T>A	chr1.hg19:g.34123600A>T	ENSP00000362478:p.Cys338Ser	81.0	0.0		52.0	26.0	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373380.1	hg19		.	.	.	.	.	.	.	.	.	.	a	32	5.158802	0.94686	.	.	ENSG00000121904	ENST00000373381;ENST00000373380	D;D	0.92595	-3.07;-3.07	5.78	5.78	0.91487	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.85682	D	0.000000	D	0.98112	0.9377	H	0.99740	4.74	0.80722	D	1	D;P;P	0.64830	0.994;0.926;0.942	D;P;P	0.83275	0.996;0.679;0.677	D	0.99597	1.0977	10	0.87932	D	0	.	15.2982	0.73925	1.0:0.0:0.0:0.0	.	338;1425;1465	Q7Z408-2;Q7Z408;E7EUA6	.;CSMD2_HUMAN;.	S	1465;338	ENSP00000362479:C1465S;ENSP00000362478:C338S	ENSP00000241312:C1425S	C	-	1	0	CSMD2	33896187	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.336000	0.96533	2.209000	0.71365	0.456000	0.33151	TGT	.	.		0.587	CSMD2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000030635.4	NM_052896		T	34123600	A	T	34123600	3	4	344	1	0	0	0	0	1	0	0	0	3947	188	7	4	6362	4	CSMD2	1	34123600	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	287497	34123600	215127021	31	47394										
CSMD2	114784	hgsc.bcm.edu	37	chr1	34128580	34128580	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaaggtgctatgcaggtcctTgggcagggccgggccactca	16	11	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:34128580T>A	ENST00000373380.1	-	5	1004	c.784A>T	c.(784-786)Aag>Tag	p.K262*	CSMD2_ENST00000373388.2_5'UTR|CSMD2_ENST00000373381.4_Nonsense_Mutation_p.K1389*			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1349	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				TGCAGGTCCTTGGGCAGGGCC	0.582																																					p.K1349X		Atlas-SNP	.											.	CSMD2	946	.	0			c.A4045T						.						103	96	98					1																	34128580		2203	4300	6503	SO:0001587	stop_gained	114784	exon26			GGTCCTTGGGCAG	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373380.1:c.784A>T	chr1.hg19:g.34128580T>A	ENSP00000362478:p.Lys262*	136.0	0.0		96.0	56.0	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Nonsense_Mutation	SNP	ENST00000373380.1	hg19		.	.	.	.	.	.	.	.	.	.	T	45	11.754381	0.99599	.	.	ENSG00000121904	ENST00000373381;ENST00000373380	.	.	.	5.64	1.67	0.24075	.	0.581837	0.17899	N	0.158244	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.15952	T	0.53	.	1.7038	0.02878	0.1422:0.1191:0.2931:0.4455	.	.	.	.	X	1389;262	.	ENSP00000241312:K1349X	K	-	1	0	CSMD2	33901167	0.940000	0.31905	1.000000	0.80357	0.906000	0.53458	1.172000	0.31908	0.501000	0.28013	0.459000	0.35465	AAG	.	.		0.582	CSMD2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000030635.4	NM_052896		A	34128580	T	A	34128580	4	1	344	1	0	0	0	0	0	1	0	0	3947	1821	63	4	6594	4	CSMD2	1	34128580	Nonsense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	4980	34128580	215122041	32	47395										
GJA4	2701	hgsc.bcm.edu	37	chr1	35259856	35259856	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gagaagttgctggaccaggtCcaggagcactcgaccgtggt	15	10	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:35259856C>A	ENST00000342280.4	+	2	130	c.42C>A	c.(40-42)gtC>gtA	p.V14V		NM_002060.2	NP_002051.2	P35212	CXA4_HUMAN	gap junction protein, alpha 4, 37kDa	14					blood vessel development (GO:0001568)|calcium ion transport (GO:0006816)|cell-cell junction assembly (GO:0007043)|cell-cell signaling (GO:0007267)|endothelium development (GO:0003158)|response to pain (GO:0048265)|transport (GO:0006810)	connexon complex (GO:0005922)|gap junction (GO:0005921)|integral component of plasma membrane (GO:0005887)				NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(3)|prostate(4)|stomach(1)	14		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)				TGGACCAGGTCCAGGAGCACT	0.627																																					p.V14V		Atlas-SNP	.											.	GJA4	25	.	0			c.C42A						.						85	76	79					1																	35259856		2203	4300	6503	SO:0001819	synonymous_variant	2701	exon2			CCAGGTCCAGGAG	M96789	CCDS30669.1	1p35.1	2008-02-05	2007-01-16		ENSG00000187513	ENSG00000187513		"Ion channels / Gap junction proteins (connexins)"	4278	protein-coding gene	gene with protein product	"connexin 37"	121012	"gap junction protein, alpha 4, 37kD (connexin 37)", "gap junction protein, alpha 4, 37kDa (connexin 37)"			9843209, 7680674	Standard	XM_005270750		Approved	CX37	uc001bya.3	P35212	OTTHUMG00000004050	ENST00000342280.4:c.42C>A	chr1.hg19:g.35259856C>A		84.0	0.0		79.0	30.0	NM_002060	A8K698|D3DPR4|Q9P106|Q9UBL1|Q9UNA9|Q9UNB0|Q9UNB1|Q9Y5N7	Silent	SNP	ENST00000342280.4	hg19	CCDS30669.1																																																																																			.	.		0.627	GJA4-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011556.1	NM_002060		A	35259856	C	A	35259856	2	1	344	1	0	0	0	0	0	0	0	1	6411	842	30	3		3	GJA4	1	35259856	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1131276	35259856	213990765	33	47396										
EIF2C1	26523	hgsc.bcm.edu	37	chr1	36383941	36383941	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agattgggaagagtggtaacAtcccagctgggaccacagtg	14	8	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:36383941A>G	ENST00000373204.4	+	17	2395	c.2182A>G	c.(2182-2184)Atc>Gtc	p.I728V	AGO1_ENST00000373206.1_Missense_Mutation_p.I653V	NM_012199.2	NP_036331.1	Q9UL18	AGO1_HUMAN	argonaute RISC catalytic component 1	728	Piwi. {ECO:0000255|PROSITE- ProRule:PRU00150}.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|nuclear-transcribed mRNA catabolic process (GO:0000956)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)										GAGTGGTAACATCCCAGCTGG	0.507																																					p.I728V		Atlas-SNP	.											.	.	.	.	0			c.A2182G						.						317	294	302					1																	36383941		2203	4300	6503	SO:0001583	missense	26523	exon17			GGTAACATCCCAG	AF093097	CCDS398.1	1p34.3	2013-02-15	2013-02-15	2013-02-15	ENSG00000092847	ENSG00000092847		"Argonaute/PIWI family"	3262	protein-coding gene	gene with protein product	"argonaute 1"	606228	"eukaryotic translation initiation factor 2C, 1"	EIF2C1		10534406, 12906857	Standard	NM_012199		Approved	hAGO1	uc001bzl.3	Q9UL18	OTTHUMG00000007381	ENST00000373204.4:c.2182A>G	chr1.hg19:g.36383941A>G	ENSP00000362300:p.Ile728Val	135.0	0.0		108.0	47.0	NM_012199	Q5TA57|Q6P4S0	Missense_Mutation	SNP	ENST00000373204.4	hg19	CCDS398.1	.	.	.	.	.	.	.	.	.	.	A	15.21	2.764526	0.49574	.	.	ENSG00000092847	ENST00000373206;ENST00000373204	T;T	0.28454	1.61;1.61	5.61	5.61	0.85477	Stem cell self-renewal protein Piwi (3);Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.21590	0.0520	N	0.16166	0.38	0.80722	D	1	B	0.06786	0.001	B	0.15870	0.014	T	0.03202	-1.1061	10	0.39692	T	0.17	-11.9591	16.0994	0.81158	1.0:0.0:0.0:0.0	.	728	Q9UL18	AGO1_HUMAN	V	653;728	ENSP00000362302:I653V;ENSP00000362300:I728V	ENSP00000362300:I728V	I	+	1	0	EIF2C1	36156528	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.261000	0.74972	0.533000	0.62120	ATC	.	.		0.507	AGO1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019337.3			G	36383941	A	G	36383941	3	3	344	1	0	0	0	0	1	0	0	0	5007	217	8	2	2248	2	EIF2C1	1	36383941	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1124085	36383941	212866680	34	47397										
TEKT2	27285	hgsc.bcm.edu	37	chr1	36551473	36551473	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agcaaaacctgcaggccaagAacctgcctctggatgtggcc	11	13	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:36551473A>T	ENST00000207457.3	+	4	446	c.319A>T	c.(319-321)Aac>Tac	p.N107Y		NM_014466.2	NP_055281.2	Q9UIF3	TEKT2_HUMAN	tektin 2 (testicular)	107					cell projection organization (GO:0030030)|inner dynein arm assembly (GO:0036159)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|pancreas(1)|skin(2)	13		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GCAGGCCAAGAACCTGCCTCT	0.582																																					p.N107Y		Atlas-SNP	.											.	TEKT2	32	.	0			c.A319T						.						51	49	50					1																	36551473		2203	4300	6503	SO:0001583	missense	27285	exon4			GCCAAGAACCTGC	AB033823	CCDS401.1	1p34.3	2008-02-05			ENSG00000092850	ENSG00000092850			11725	protein-coding gene	gene with protein product		608953				12029069, 11751288	Standard	NM_014466		Approved	TEKTB1	uc001bzr.3	Q9UIF3	OTTHUMG00000007629	ENST00000207457.3:c.319A>T	chr1.hg19:g.36551473A>T	ENSP00000207457:p.Asn107Tyr	154.0	0.0		115.0	43.0	NM_014466	A6NIS6|O60638	Missense_Mutation	SNP	ENST00000207457.3	hg19	CCDS401.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.133820	0.77662	.	.	ENSG00000092850	ENST00000207457	T	0.02606	4.23	5.79	4.67	0.58626	.	0.253204	0.46145	D	0.000310	T	0.10423	0.0255	M	0.65975	2.015	0.44500	D	0.997446	D	0.62365	0.991	P	0.60541	0.876	T	0.00461	-1.1725	10	0.62326	D	0.03	.	11.2519	0.49031	0.9292:0.0:0.0708:0.0	.	107	Q9UIF3	TEKT2_HUMAN	Y	107	ENSP00000207457:N107Y	ENSP00000207457:N107Y	N	+	1	0	TEKT2	36324060	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.362000	0.59467	2.207000	0.71202	0.533000	0.62120	AAC	.	.		0.582	TEKT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020200.1	NM_014466		T	36551473	A	T	36551473	3	4	344	1	0	0	0	0	1	0	0	0	15768	246	9	4	329	4	TEKT2	1	36551473	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	167532	36551473	212699148	35	47398										
MTF1	4520	hgsc.bcm.edu	37	chr1	38288109	38288109	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cctgggggtgcggaagaaacTcttgatgattagcagcaaac	13	8	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:38288109T>C	ENST00000373036.4	-	9	1591	c.1451A>G	c.(1450-1452)gAg>gGg	p.E484G		NM_005955.2	NP_005946.2	Q14872	MTF1_HUMAN	metal-regulatory transcription factor 1	484	Pro-rich.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cadmium ion (GO:0046686)|response to metal ion (GO:0010038)|response to oxidative stress (GO:0006979)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			endometrium(3)|kidney(5)|large_intestine(6)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(1)	31	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				CGGAAGAAACTCTTGATGATT	0.572																																					p.E484G		Atlas-SNP	.											.	MTF1	67	.	0			c.A1451G						.						43	41	42					1																	38288109		2203	4300	6503	SO:0001583	missense	4520	exon9			AGAAACTCTTGAT	BC014454	CCDS30676.1	1p33	2008-02-05			ENSG00000188786	ENSG00000188786			7428	protein-coding gene	gene with protein product		600172				8065932	Standard	NM_005955		Approved		uc001cce.1	Q14872	OTTHUMG00000004439	ENST00000373036.4:c.1451A>G	chr1.hg19:g.38288109T>C	ENSP00000362127:p.Glu484Gly	81.0	0.0		55.0	28.0	NM_005955	B2RAK6|Q96CB1	Missense_Mutation	SNP	ENST00000373036.4	hg19	CCDS30676.1	.	.	.	.	.	.	.	.	.	.	T	17.80	3.477573	0.63849	.	.	ENSG00000188786	ENST00000373036	T	0.10860	2.83	6.17	6.17	0.99709	.	0.096357	0.64402	D	0.000001	T	0.12817	0.0311	L	0.51422	1.61	0.41362	D	0.987435	P	0.43094	0.799	B	0.35931	0.214	T	0.01232	-1.1411	10	0.66056	D	0.02	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	484	Q14872	MTF1_HUMAN	G	484	ENSP00000362127:E484G	ENSP00000362127:E484G	E	-	2	0	MTF1	38060696	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	3.410000	0.52664	2.371000	0.80710	0.533000	0.62120	GAG	.	.		0.572	MTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012984.2	NM_005955		C	38288109	T	C	38288109	3	2	344	1	0	0	0	0	1	0	0	0	9931	1551	54	2	822	2	MTF1	1	38288109	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1736636	38288109	210962512	36	47399										
COL9A2	1298	hgsc.bcm.edu	37	chr1	40769263	40769263	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcccggccagtcctcgagggCcggggggaccagggtagccc	17	15	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:40769263C>T	ENST00000372748.3	-	28	1583	c.1487G>A	c.(1486-1488)gGc>gAc	p.G496D	COL9A2_ENST00000466267.1_5'UTR	NM_001852.3	NP_001843.1	Q14055	CO9A2_HUMAN	collagen, type IX, alpha 2	496	Triple-helical region 3 (COL3).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(4)|stomach(2)|urinary_tract(2)	22	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;2.08e-17)			TCCTCGAGGGCCGGGGGGACC	0.721																																					p.G496D		Atlas-SNP	.											COL9A2,NS,carcinoma,0,1	COL9A2	63	.	0			c.G1487A						.						8	10	9					1																	40769263		2148	4200	6348	SO:0001583	missense	1298	exon28			CGAGGGCCGGGGG	M95610	CCDS450.1	1p33-p32	2013-01-16			ENSG00000049089	ENSG00000049089		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2218	protein-coding gene	gene with protein product		120260		EDM2		8454052, 8528240, 1429648	Standard	NM_001852		Approved	MED	uc001cfh.1	Q14055	OTTHUMG00000005761	ENST00000372748.3:c.1487G>A	chr1.hg19:g.40769263C>T	ENSP00000361834:p.Gly496Asp	36.0	0.0		41.0	20.0	NM_001852	B2RMP9	Missense_Mutation	SNP	ENST00000372748.3	hg19	CCDS450.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.69|12.69	2.014876|2.014876	0.35511|0.35511	.|.	.|.	ENSG00000049089|ENSG00000049089	ENST00000427563|ENST00000372748	.|D	.|0.99619	.|-6.28	4.32|4.32	4.32|4.32	0.51571|0.51571	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.99764|0.99764	0.9904|0.9904	H|H	0.97635|0.97635	4.045|4.045	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.97110	.|1.0	D|D	0.96923|0.96923	0.9675|0.9675	6|10	0.66056|0.87932	D|D	0.02|0	.|.	14.3509|14.3509	0.66702|0.66702	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|496	.|Q14055	.|CO9A2_HUMAN	T|D	100|496	.|ENSP00000361834:G496D	ENSP00000407377:A100T|ENSP00000361834:G496D	A|G	-|-	1|2	0|0	COL9A2|COL9A2	40541850|40541850	1.000000|1.000000	0.71417|0.71417	0.935000|0.935000	0.37517|0.37517	0.146000|0.146000	0.21551|0.21551	5.846000|5.846000	0.69444|0.69444	2.247000|2.247000	0.74100|0.74100	0.462000|0.462000	0.41574|0.41574	GCC|GGC	.	.		0.721	COL9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015764.3	NM_001852		T	40769263	C	T	40769263	3	4	344	1	0	0	0	0	1	0	0	0	3710	739	26	3	602	3	COL9A2	1	40769263	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	2481154	40769263	208481358	37	47400										
COL9A2	1298	hgsc.bcm.edu	37	chr1	40777173	40777173	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cccagacctcgtctctcaccAggaaatccgcactgccttcc	6	19	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:40777173A>G	ENST00000372748.3	-	10	614	c.518T>C	c.(517-519)cTg>cCg	p.L173P		NM_001852.3	NP_001843.1	Q14055	CO9A2_HUMAN	collagen, type IX, alpha 2	173	Nonhelical region 4 (NC4).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(4)|stomach(2)|urinary_tract(2)	22	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;2.08e-17)			GTCTCTCACCAGGAAATCCGC	0.657																																					p.L173P		Atlas-SNP	.											.	COL9A2	63	.	0			c.T518C						.						57	60	59					1																	40777173		2203	4300	6503	SO:0001630	splice_region_variant	1298	exon10			CTCACCAGGAAAT	M95610	CCDS450.1	1p33-p32	2013-01-16			ENSG00000049089	ENSG00000049089		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2218	protein-coding gene	gene with protein product		120260		EDM2		8454052, 8528240, 1429648	Standard	NM_001852		Approved	MED	uc001cfh.1	Q14055	OTTHUMG00000005761	ENST00000372748.3:c.519+1T>C	chr1.hg19:g.40777173A>G		65.0	0.0		46.0	20.0	NM_001852	B2RMP9	Missense_Mutation	SNP	ENST00000372748.3	hg19	CCDS450.1	.	.	.	.	.	.	.	.	.	.	.	15.51	2.854983	0.51376	.	.	ENSG00000049089	ENST00000372748	D	0.94828	-3.53	5.56	4.42	0.53409	.	0.069694	0.64402	D	0.000020	D	0.92054	0.7482	N	0.20766	0.605	0.58432	D	0.999998	D	0.71674	0.998	P	0.59115	0.852	D	0.88558	0.3121	10	0.23302	T	0.38	.	8.9936	0.36039	0.8358:0.0:0.0:0.1642	.	173	Q14055	CO9A2_HUMAN	P	173	ENSP00000361834:L173P	ENSP00000361834:L173P	L	-	2	0	COL9A2	40549760	1.000000	0.71417	1.000000	0.80357	0.684000	0.39900	2.744000	0.47450	0.916000	0.36871	0.460000	0.39030	CTG	.	.		0.657	COL9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015764.3	NM_001852	Missense_Mutation	G	40777173	A	G	40777173	5	3	344	1	0	0	0	0	0	0	1	0	3710	202	7	2	1643	2	COL9A2	1	40777173	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	7910	40777173	208473448	38	47401										
COL9A2	1298	hgsc.bcm.edu	37	chr1	40777786	40777786	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	caacaggtccaggaggccccTggggagcagagagttgatgg	17	9	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:40777786T>A	ENST00000372748.3	-	8	460		c.e8-2			NM_001852.3	NP_001843.1	Q14055	CO9A2_HUMAN	collagen, type IX, alpha 2						axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(4)|stomach(2)|urinary_tract(2)	22	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;2.08e-17)			AGGAGGCCCCTGGGGAGCAGA	0.577																																					.		Atlas-SNP	.											.	COL9A2	63	.	0			c.364-2A>T						.						27	29	29					1																	40777786		2202	4299	6501	SO:0001630	splice_region_variant	1298	exon9			GGCCCCTGGGGAG	M95610	CCDS450.1	1p33-p32	2013-01-16			ENSG00000049089	ENSG00000049089		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2218	protein-coding gene	gene with protein product		120260		EDM2		8454052, 8528240, 1429648	Standard	NM_001852		Approved	MED	uc001cfh.1	Q14055	OTTHUMG00000005761	ENST00000372748.3:c.364-2A>T	chr1.hg19:g.40777786T>A		88.0	0.0		63.0	22.0	NM_001852	B2RMP9	Splice_Site	SNP	ENST00000372748.3	hg19	CCDS450.1	.	.	.	.	.	.	.	.	.	.	.	12.07	1.826760	0.32329	.	.	ENSG00000049089	ENST00000372748;ENST00000417105;ENST00000372736	.	.	.	5.5	4.35	0.52113	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.4426	0.38677	0.0:0.0:0.179:0.821	.	.	.	.	.	-1	.	.	.	-	.	.	COL9A2	40550373	1.000000	0.71417	0.897000	0.35233	0.259000	0.26198	5.703000	0.68340	0.885000	0.36088	0.533000	0.62120	.	.	.		0.577	COL9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015764.3	NM_001852	Intron	A	40777786	T	A	40777786	5	1	344	1	0	0	0	0	0	0	1	0	3710	1594	55	4	1807	4	COL9A2	1	40777786	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	613	40777786	208472835	39	47402										
HIVEP3	59269	hgsc.bcm.edu	37	chr1	41990547	41990547	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atatttccctcggccgcggcCtcgcacatatacatactctt	6	15	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:41990547C>T	ENST00000372583.1	-	6	6127	c.5242G>A	c.(5242-5244)Ggc>Agc	p.G1748S	HIVEP3_ENST00000429157.2_Missense_Mutation_p.G1748S|HIVEP3_ENST00000460604.1_Intron|HIVEP3_ENST00000372584.1_Missense_Mutation_p.G1748S|HIVEP3_ENST00000247584.5_Missense_Mutation_p.G1748S	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	1748					positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				CGGCCGCGGCCTCGCACATAT	0.507																																					p.G1748S		Atlas-SNP	.											.	HIVEP3	235	.	0			c.G5242A						.						131	113	119					1																	41990547		2203	4300	6503	SO:0001583	missense	59269	exon6			CGCGGCCTCGCAC	AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"Zinc fingers, C2H2-type"	13561	protein-coding gene	gene with protein product	"kappabinding protein-1"	606649	"human immunodeficiency virus type I enhancer-binding protein 3"			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.5242G>A	chr1.hg19:g.41990547C>T	ENSP00000361664:p.Gly1748Ser	108.0	0.0		93.0	46.0	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Missense_Mutation	SNP	ENST00000372583.1	hg19	CCDS463.1	.	.	.	.	.	.	.	.	.	.	C	34	5.393475	0.96009	.	.	ENSG00000127124	ENST00000372584;ENST00000372583;ENST00000247584;ENST00000429157	T;T;T;T	0.10099	2.92;2.91;2.91;2.92	4.85	4.85	0.62838	.	0.000000	0.50627	D	0.000101	T	0.36826	0.0981	M	0.80183	2.485	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.18304	-1.0341	10	0.56958	D	0.05	-19.6194	17.7486	0.88428	0.0:1.0:0.0:0.0	.	1748;1748	Q5T1R4-2;Q5T1R4	.;ZEP3_HUMAN	S	1748	ENSP00000361665:G1748S;ENSP00000361664:G1748S;ENSP00000247584:G1748S;ENSP00000410828:G1748S	ENSP00000247584:G1748S	G	-	1	0	HIVEP3	41763134	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.609000	0.82925	2.520000	0.84964	0.561000	0.74099	GGC	.	.		0.507	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503		T	41990547	C	T	41990547	3	4	344	1	0	0	0	0	1	0	0	0	7197	681	24	3	1994	3	HIVEP3	1	41990547	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1212761	41990547	207260074	40	47403										
KIAA0467	23334	hgsc.bcm.edu	37	chr1	43908181	43908181	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggccgagcgctggttcgcctGgtgcagtggcagaatgcacg	17	11	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:43908181G>T	ENST00000562955.1	+	57	7872	c.7872G>T	c.(7870-7872)ctG>ctT	p.L2624L	SZT2_ENST00000372442.1_Silent_p.L1782L	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	2681					central nervous system development (GO:0007417)|corpus callosum morphogenesis (GO:0021540)|embryo development (GO:0009790)|pigmentation (GO:0043473)|post-embryonic development (GO:0009791)|regulation of superoxide dismutase activity (GO:1901668)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)				NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						TGGTTCGCCTGGTGCAGTGGC	0.602																																					p.L2624L		Atlas-SNP	.											.	SZT2	383	.	0			c.G7872T						.						72	74	73					1																	43908181		2203	4300	6503	SO:0001819	synonymous_variant	23334	exon57			TCGCCTGGTGCAG	AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198			29040	protein-coding gene	gene with protein product	"seizure threshold 2 homolog A (mouse)", "seizure threshold 2 homolog B (mouse)"	615463	"chromosome 1 open reading frame 84", "KIAA0467"	C1orf84, KIAA0467		9455484	Standard	NM_015284		Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.7872G>T	chr1.hg19:g.43908181G>T		66.0	0.0		67.0	28.0	NM_015284	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Silent	SNP	ENST00000562955.1	hg19	CCDS30694.2																																																																																			.	.		0.602	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284		T	43908181	G	T	43908181	2	4	344	1	0	0	0	0	0	0	0	1	8187	1335	47	3		3	KIAA0467	1	43908181	Silent	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1917634	43908181	205342440	41	47404										
ERI3	79033	hgsc.bcm.edu	37	chr1	44713653	44713653	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tatgtgttgcaggctgaggcCcttgttcatgtctagaagtc	12	8	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:44713653C>A	ENST00000372257.2	-	8	1070	c.889G>T	c.(889-891)Ggc>Tgc	p.G297C	ERI3_ENST00000372259.5_Missense_Mutation_p.G182C|ERI3_ENST00000537474.1_Missense_Mutation_p.G120C	NM_024066.1	NP_076971.1	O43414	ERI3_HUMAN	ERI1 exoribonuclease family member 3	297	Exonuclease.						exonuclease activity (GO:0004527)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(2)|lung(7)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						AGGCTGAGGCCCTTGTTCATG	0.612																																					p.G297C		Atlas-SNP	.											.	ERI3	39	.	0			c.G889T						.						113	101	105					1																	44713653		2203	4300	6503	SO:0001583	missense	79033	exon8			TGAGGCCCTTGTT	AF007157	CCDS30696.1	1p34.1	2009-10-07	2009-10-07	2008-12-16	ENSG00000117419	ENSG00000117419		"Enhanced RNAi three prime mRNA exonucleases"	17276	protein-coding gene	gene with protein product	"enhanced RNAi three prime mRNA exonuclease homolog 3 (C.elegans)", "exoribonuclease 3"	609917	"prion protein interacting protein"	PRNPIP			Standard	XM_005271184		Approved	FLJ22943, PINT1	uc001clt.3	O43414	OTTHUMG00000007637	ENST00000372257.2:c.889G>T	chr1.hg19:g.44713653C>A	ENSP00000361331:p.Gly297Cys	74.0	0.0		64.0	29.0	NM_024066	B1AK98|Q5T2T7|Q5T2T9|Q5TG35|Q9BQA0|Q9UEB4	Missense_Mutation	SNP	ENST00000372257.2	hg19	CCDS30696.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.272009	0.80469	.	.	ENSG00000117419	ENST00000372257;ENST00000372259;ENST00000456170;ENST00000537474;ENST00000433471;ENST00000372253	T;T;T;T	0.23552	1.9;1.9;1.9;1.9	5.1	5.1	0.69264	Exonuclease (1);Exonuclease, RNase T/DNA polymerase III (1);Ribonuclease H-like (1);	0.278923	0.31415	N	0.007682	T	0.39989	0.1099	L	0.38175	1.15	0.50039	D	0.999847	D	0.65815	0.995	P	0.61132	0.884	T	0.18272	-1.0342	10	0.54805	T	0.06	.	18.518	0.90942	0.0:1.0:0.0:0.0	.	297	O43414	ERI3_HUMAN	C	297;182;164;120;179;191	ENSP00000361331:G297C;ENSP00000361333:G182C;ENSP00000390710:G164C;ENSP00000438360:G120C	ENSP00000361327:G191C	G	-	1	0	ERI3	44486240	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	5.222000	0.65277	2.379000	0.81126	0.655000	0.94253	GGC	.	.		0.612	ERI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020243.1	NM_024066		A	44713653	C	A	44713653	3	1	344	1	0	0	0	0	1	0	0	0	5231	623	22	3	132	3	ERI3	1	44713653	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	805472	44713653	204536968	42	47405										
STIL	6491	hgsc.bcm.edu	37	chr1	47717102	47717102	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tttctcaatactggcgtatcTgcgttggtccccacagattc	8	12	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:47717102T>C	ENST00000360380.3	-	18	3933	c.3570A>G	c.(3568-3570)gcA>gcG	p.A1190A	STIL_ENST00000371877.3_Silent_p.A1191A|STIL_ENST00000337817.5_Silent_p.A1190A|STIL_ENST00000243182.6_Silent_p.A1190A|STIL_ENST00000396221.2_Silent_p.A1173A	NM_001282936.1	NP_001269865.1	Q15468	STIL_HUMAN	SCL/TAL1 interrupting locus	1190					cell proliferation (GO:0008283)|determination of left/right symmetry (GO:0007368)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural tube closure (GO:0001843)|neural tube development (GO:0021915)|notochord development (GO:0030903)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	36		Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444)				CTGGCGTATCTGCGTTGGTCC	0.383																																					p.A1191A		Atlas-SNP	.											.	STIL	91	.	0			c.A3573G						.						95	94	94					1																	47717102		2203	4300	6503	SO:0001819	synonymous_variant	6491	exon17			CGTATCTGCGTTG	M74558	CCDS548.1, CCDS41329.1, CCDS72785.1, CCDS72786.1	1p32	2010-02-09	2005-11-29	2005-11-29	ENSG00000123473	ENSG00000123473			10879	protein-coding gene	gene with protein product		181590	"TAL1 (SCL) interrupting locus"	SIL		2209547	Standard	NM_003035		Approved	MCPH7	uc001crd.1	Q15468	OTTHUMG00000007851	ENST00000360380.3:c.3570A>G	chr1.hg19:g.47717102T>C		97.0	0.0		85.0	44.0	NM_001048166	Q5T0C5|Q68CN9	Silent	SNP	ENST00000360380.3	hg19	CCDS548.1																																																																																			.	.		0.383	STIL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021649.2	NM_003035		C	47717102	T	C	47717102	2	2	344	1	0	0	0	0	0	0	0	1	15297	1567	55	2		2	STIL	1	47717102	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	3003449	47717102	201533519	43	47406										
SPATA6	54558	hgsc.bcm.edu	37	chr1	48764441	48764441	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggcctttttgtataagttccTgtacatcttgtccatgctgt	8	9	1	0	rs374515413		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:48764441T>A	ENST00000371847.3	-	13	1575	c.1411A>T	c.(1411-1413)Agg>Tgg	p.R471W	SPATA6_ENST00000396199.3_Missense_Mutation_p.R399W|SPATA6_ENST00000371843.3_Missense_Mutation_p.R455W	NM_019073.2	NP_061946.1	Q9NWH7	SPAT6_HUMAN	spermatogenesis associated 6	471					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	21						TATAAGTTCCTGTACATCTTG	0.438																																					p.R471W		Atlas-SNP	.											.	SPATA6	45	.	0			c.A1411T						.						169	168	168					1																	48764441		2203	4300	6503	SO:0001583	missense	54558	exon13			AGTTCCTGTACAT	AK000869	CCDS551.1, CCDS65535.1, CCDS72787.1	1p32.3	2012-03-15			ENSG00000132122	ENSG00000132122			18309	protein-coding gene	gene with protein product	"spermatogenesis-related factor-1"	613947					Standard	XM_005270948		Approved	SRF1, FLJ10007, SRF-1	uc001crr.2	Q9NWH7	OTTHUMG00000007794	ENST00000371847.3:c.1411A>T	chr1.hg19:g.48764441T>A	ENSP00000360913:p.Arg471Trp	111.0	0.0		79.0	23.0	NM_019073	Q5T3N7|Q8WUE6	Missense_Mutation	SNP	ENST00000371847.3	hg19	CCDS551.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.096325	0.76870	.	.	ENSG00000132122	ENST00000371847;ENST00000371843;ENST00000396199	T;T;T	0.13089	2.63;2.62;2.62	4.78	4.78	0.61160	.	0.141252	0.50627	D	0.000107	T	0.25419	0.0618	L	0.36672	1.1	0.40543	D	0.981044	D;D;D	0.89917	1.0;0.995;0.995	D;D;D	0.77004	0.989;0.924;0.924	T	0.01844	-1.1262	10	0.72032	D	0.01	.	10.6281	0.45519	0.0:0.0:0.0:1.0	.	399;455;471	B4DX17;Q9NWH7-2;Q9NWH7	.;.;SPAT6_HUMAN	W	471;455;399	ENSP00000360913:R471W;ENSP00000360909:R455W;ENSP00000379502:R399W	ENSP00000360909:R455W	R	-	1	2	SPATA6	48537028	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	2.943000	0.49026	2.002000	0.58637	0.460000	0.39030	AGG	.	.		0.438	SPATA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021347.1	NM_019073		A	48764441	T	A	48764441	3	1	344	1	0	0	0	0	1	0	0	0	15028	1579	55	4	59	4	SPATA6	1	48764441	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1047339	48764441	200486180	44	47407										
EPS15	2060	hgsc.bcm.edu	37	chr1	51864724	51864724	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cgatgtaatactgctattgtTggctgcactgaaagggtcag	12	7	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:51864724T>C	ENST00000371733.3	-	20	2128	c.2032A>G	c.(2032-2034)Aac>Gac	p.N678D	EPS15_ENST00000371730.2_Missense_Mutation_p.N544D|EPS15_ENST00000396122.4_Missense_Mutation_p.N355D	NM_001981.2	NP_001972.1	P42566	EPS15_HUMAN	epidermal growth factor receptor pathway substrate 15	678	15 X 3 AA repeats of D-P-F.				cell proliferation (GO:0008283)|clathrin coat assembly (GO:0048268)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Golgi to endosome transport (GO:0006895)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|protein transport (GO:0015031)|vesicle organization (GO:0016050)	AP-2 adaptor complex (GO:0030122)|ciliary membrane (GO:0060170)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|polyubiquitin binding (GO:0031593)	p.0?(2)		endometrium(3)|kidney(5)|large_intestine(8)|lung(13)|prostate(2)|skin(1)|stomach(1)|urinary_tract(2)	35						CTGCTATTGTTGGCTGCACTG	0.378			T	MLL	ALL																																p.N678D		Atlas-SNP	.		Dom	yes		1	1p32	2060	epidermal growth factor receptor pathway substrate 15 (AF1p)		L	.	EPS15	72	.	2	Whole gene deletion(2)	thyroid(1)|central_nervous_system(1)	c.A2032G						.						128	119	122					1																	51864724		2203	4300	6503	SO:0001583	missense	2060	exon20			TATTGTTGGCTGC	BC054006	CCDS557.1	1p32	2013-01-10			ENSG00000085832	ENSG00000085832		"EF-hand domain containing"	3419	protein-coding gene	gene with protein product		600051				8183552	Standard	NM_001159969		Approved	AF-1P, MLLT5	uc001csq.1	P42566	OTTHUMG00000008192	ENST00000371733.3:c.2032A>G	chr1.hg19:g.51864724T>C	ENSP00000360798:p.Asn678Asp	49.0	0.0		46.0	21.0	NM_001981	B2R8J7|D3DPJ2|Q5SRH4	Missense_Mutation	SNP	ENST00000371733.3	hg19	CCDS557.1	.	.	.	.	.	.	.	.	.	.	T	5.571	0.290179	0.10567	.	.	ENSG00000085832	ENST00000371730;ENST00000371733;ENST00000396122	T;T;T	0.16743	2.32;2.32;2.32	5.34	5.34	0.76211	.	.	.	.	.	T	0.08088	0.0202	N	0.08118	0	0.23851	N	0.996663	B;B;B	0.10296	0.003;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.0	T	0.31861	-0.9928	9	0.07813	T	0.8	.	9.9886	0.41856	0.0:0.0789:0.0:0.9211	.	544;678;364	B1AUU8;P42566;P42566-2	.;EPS15_HUMAN;.	D	544;678;355	ENSP00000360795:N544D;ENSP00000360798:N678D;ENSP00000379428:N355D	ENSP00000360795:N544D	N	-	1	0	EPS15	51637312	1.000000	0.71417	0.997000	0.53966	0.846000	0.48090	1.854000	0.39368	2.026000	0.59711	0.402000	0.26972	AAC	.	.		0.378	EPS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022422.1	NM_001981		C	51864724	T	C	51864724	3	2	344	1	0	0	0	0	1	0	0	0	5194	1812	63	2	682	2	EPS15	1	51864724	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	3100283	51864724	197385897	45	47408										
C1orf175	374977	hgsc.bcm.edu	37	chr1	55119680	55119680	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcagtcagcaggatgatgccAaggacaacagcatccacact	10	12	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:55119680A>T	ENST00000421030.2	+	3	1366	c.1081A>T	c.(1081-1083)Aag>Tag	p.K361*	MROH7_ENST00000454855.2_Intron|MROH7_ENST00000472987.1_3'UTR|MROH7_ENST00000409996.1_Intron|MROH7_ENST00000395690.2_Nonsense_Mutation_p.K361*|MROH7-TTC4_ENST00000414150.2_Nonsense_Mutation_p.K361*|MROH7_ENST00000545244.1_Intron|MROH7_ENST00000339553.5_Nonsense_Mutation_p.K361*	NM_001039464.2	NP_001034553	Q68CQ1	MROH7_HUMAN	maestro heat-like repeat family member 7	361						extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											GGATGATGCCAAGGACAACAG	0.567																																					p.K361X		Atlas-SNP	.											.	.	.	.	0			c.A1081T						.						81	80	80					1																	55119680		2121	4229	6350	SO:0001587	stop_gained	374977	exon3			GATGCCAAGGACA	AL832492	CCDS41342.2	1p32.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000184313	ENSG00000184313		"maestro heat-like repeat containing"	24802	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 175", "HEAT repeat containing 8"	C1orf175, HEATR8		12477932	Standard	NM_001039464		Approved	FLJ46354	uc010ooe.1	Q68CQ1	OTTHUMG00000009890	ENST00000421030.2:c.1081A>T	chr1.hg19:g.55119680A>T	ENSP00000396622:p.Lys361*	121.0	0.0		95.0	53.0	NM_001039464	A0AUX8|Q5TA99|Q6ZP40|Q6ZRH6|Q8N311|Q8NA14	Nonsense_Mutation	SNP	ENST00000421030.2	hg19	CCDS41342.2	.	.	.	.	.	.	.	.	.	.	A	38	6.777012	0.97829	.	.	ENSG00000184313	ENST00000421030;ENST00000414867;ENST00000339553;ENST00000395690	.	.	.	3.89	2.98	0.34508	.	0.195026	0.25355	N	0.031263	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.14656	T	0.56	.	7.5019	0.27522	0.1171:0.0:0.8829:0.0	.	.	.	.	X	361	.	ENSP00000343211:K361X	K	+	1	0	HEATR8	54892268	0.991000	0.36638	0.829000	0.32907	0.307000	0.27823	1.510000	0.35790	1.237000	0.43756	-0.132000	0.14878	AAG	.	.		0.567	MROH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346978.1	NM_198547		T	55119680	A	T	55119680	4	4	344	1	0	0	0	0	0	1	0	0	2018	131	5	4	1083	4	C1orf175	1	55119680	Nonsense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3254956	55119680	194130941	46	47409										
C1orf175	374977	hgsc.bcm.edu	37	chr1	55174688	55174688	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttcttggattacgctcaaggGtccctggtcccctgcatgga	11	12	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:55174688G>A	ENST00000421030.2	+	23	3954	c.3669G>A	c.(3667-3669)ggG>ggA	p.G1223G	MROH7_ENST00000454855.2_Splice_Site_p.G741G|MROH7_ENST00000409996.1_Splice_Site_p.G791G|MROH7-TTC4_ENST00000414150.2_Splice_Site_p.G1223G	NM_001039464.2	NP_001034553	Q68CQ1	MROH7_HUMAN	maestro heat-like repeat family member 7	1223						extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											ACGCTCAAGGGTCCCTGGTCC	0.517																																					p.G1223G		Atlas-SNP	.											.	.	.	.	0			c.G3669A						.						128	124	125					1																	55174688		1906	4104	6010	SO:0001630	splice_region_variant	374977	exon23			TCAAGGGTCCCTG	AL832492	CCDS41342.2	1p32.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000184313	ENSG00000184313		"maestro heat-like repeat containing"	24802	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 175", "HEAT repeat containing 8"	C1orf175, HEATR8		12477932	Standard	NM_001039464		Approved	FLJ46354	uc010ooe.1	Q68CQ1	OTTHUMG00000009890	ENST00000421030.2:c.3668-1G>A	chr1.hg19:g.55174688G>A		76.0	0.0		46.0	28.0	NM_001039464	A0AUX8|Q5TA99|Q6ZP40|Q6ZRH6|Q8N311|Q8NA14	Silent	SNP	ENST00000421030.2	hg19	CCDS41342.2																																																																																			.	.		0.517	MROH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346978.1	NM_198547	Silent	A	55174688	G	A	55174688	5	1	344	1	0	0	0	0	0	0	1	0	2018	1275	44	3	3751	3	C1orf175	1	55174688	Splice_Site	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	55008	55174688	194075933	47	47410										
INADL	10207	hgsc.bcm.edu	37	chr1	62456026	62456026	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acgaatgcgtattggagatgAactcttagaggtgagaagca	13	5	1	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:62456026A>T	ENST00000371158.2	+	28	3971	c.3857A>T	c.(3856-3858)gAa>gTa	p.E1286V	INADL_ENST00000543708.1_Missense_Mutation_p.E70V|INADL_ENST00000545929.1_5'UTR|INADL_ENST00000316485.6_Missense_Mutation_p.E1286V	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1286	PDZ 7. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						ATTGGAGATGAACTCTTAGAG	0.448																																					p.E1286V		Atlas-SNP	.											.	INADL	179	.	0			c.A3857T						.						71	69	70					1																	62456026		2203	4300	6503	SO:0001583	missense	10207	exon28			GAGATGAACTCTT	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.3857A>T	chr1.hg19:g.62456026A>T	ENSP00000360200:p.Glu1286Val	76.0	0.0		95.0	39.0	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	hg19	CCDS617.2	.	.	.	.	.	.	.	.	.	.	A	22.5	4.294620	0.81025	.	.	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000307297;ENST00000543708	T;T;T;T	0.26067	1.76;1.76;1.76;1.76	5.73	5.73	0.89815	PDZ/DHR/GLGF (4);	0.000000	0.64402	D	0.000001	T	0.49525	0.1562	M	0.62088	1.915	0.80722	D	1	P;D;D;D;D	0.89917	0.563;0.999;1.0;1.0;1.0	P;D;D;D;D	0.97110	0.618;0.998;1.0;1.0;0.999	T	0.48043	-0.9069	10	0.56958	D	0.05	.	16.0234	0.80516	1.0:0.0:0.0:0.0	.	70;745;1286;1286;1286	B4DE90;Q8NI35-5;F8W8T2;Q8NI35;Q8NI35-4	.;.;.;INADL_HUMAN;.	V	1286;1286;1286;1286;70;70	ENSP00000360200:E1286V;ENSP00000326199:E1286V;ENSP00000307496:E70V;ENSP00000445790:E70V	ENSP00000307496:E70V	E	+	2	0	INADL	62228614	1.000000	0.71417	1.000000	0.80357	0.538000	0.34931	9.225000	0.95219	2.172000	0.68678	0.533000	0.62120	GAA	.	.		0.448	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		T	62456026	A	T	62456026	3	4	344	1	0	0	0	0	1	0	0	0	7740	246	9	4	3963	4	INADL	1	62456026	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	7281338	62456026	186794595	48	47411										
KANK4	163782	hgsc.bcm.edu	37	chr1	62733992	62733992	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agtgggggacttcttccccaGgcccactttcctgggcagca	12	14	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:62733992G>A	ENST00000371153.4	-	5	2576	c.2198C>T	c.(2197-2199)cCt>cTt	p.P733L	KANK4_ENST00000371150.1_Missense_Mutation_p.P89L|KANK4_ENST00000354381.3_Missense_Mutation_p.P105L	NM_181712.4	NP_859063.3	Q5T7N3	KANK4_HUMAN	KN motif and ankyrin repeat domains 4	733						cytoplasm (GO:0005737)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(49)|ovary(3)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	81						TTCTTCCCCAGGCCCACTTTC	0.587																																					p.P733L		Atlas-SNP	.											.	KANK4	135	.	0			c.C2198T						.						53	46	49					1																	62733992		2203	4300	6503	SO:0001583	missense	163782	exon5			TCCCCAGGCCCAC	AK096259	CCDS620.1	1p31.3	2013-10-11	2008-01-29	2008-01-29	ENSG00000132854	ENSG00000132854		"KN motif and ankyrin repeat domain containing", "Ankyrin repeat domain containing"	27263	protein-coding gene	gene with protein product		614612	"ankyrin repeat domain 38"	ANKRD38		17996375, 19554261	Standard	NM_181712		Approved	KIAA0172	uc001dah.4	Q5T7N3	OTTHUMG00000008971	ENST00000371153.4:c.2198C>T	chr1.hg19:g.62733992G>A	ENSP00000360195:p.Pro733Leu	73.0	0.0		56.0	25.0	NM_181712	B1ALP7|Q6P9A0|Q86T71|Q86VE6|Q8NAX3	Missense_Mutation	SNP	ENST00000371153.4	hg19	CCDS620.1	.	.	.	.	.	.	.	.	.	.	G	11.50	1.657672	0.29425	.	.	ENSG00000132854	ENST00000371153;ENST00000354381;ENST00000371150	T;T;T	0.48836	0.8;0.82;0.83	5.84	2.96	0.34315	.	1.118330	0.06952	N	0.814761	T	0.46444	0.1393	M	0.68952	2.095	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.35649	-0.9780	10	0.30854	T	0.27	-0.3211	8.1634	0.31211	0.1399:0.1289:0.7312:0.0	.	105;733	Q5T7N3-2;Q5T7N3	.;KANK4_HUMAN	L	733;105;89	ENSP00000360195:P733L;ENSP00000346352:P105L;ENSP00000360192:P89L	ENSP00000346352:P105L	P	-	2	0	KANK4	62506580	0.001000	0.12720	0.018000	0.16275	0.211000	0.24417	0.715000	0.25822	0.476000	0.27440	0.650000	0.86243	CCT	.	.		0.587	KANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024877.1	NM_181712		A	62733992	G	A	62733992	3	1	344	1	0	0	0	0	1	0	0	0	7988	1000	35	3	813	3	KANK4	1	62733992	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	277966	62733992	186516629	49	47412										
CACHD1	57685	hgsc.bcm.edu	37	chr1	65142576	65142576	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tccagacttacctcctgcacAgaaaccccagctgcgaggtc	8	16	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:65142576A>G	ENST00000371073.2	+	22	2975		c.e22-1		CACHD1_ENST00000290039.5_Splice_Site|CACHD1_ENST00000495994.1_Splice_Site			Q5VU97	CAHD1_HUMAN	cache domain containing 1						calcium ion transport (GO:0006816)	integral component of membrane (GO:0016021)				breast(4)|endometrium(3)|kidney(3)|large_intestine(20)|lung(14)|ovary(2)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						CCTCCTGCACAGAAACCCCAG	0.542																																					.		Atlas-SNP	.											.	CACHD1	125	.	0			c.2823-2A>G						.						134	132	133					1																	65142576		2203	4300	6503	SO:0001630	splice_region_variant	57685	exon22			CTGCACAGAAACC	AB046793	CCDS628.2	1p31.3	2008-02-05	2005-10-11	2005-10-11	ENSG00000158966	ENSG00000158966			29314	protein-coding gene	gene with protein product			"von Willebrand factor type A and cache domain containing 1"	VWCD1		10997877	Standard	NM_020925		Approved	KIAA1573	uc001dbo.1	Q5VU97	OTTHUMG00000009030	ENST00000371073.2:c.2976-1A>G	chr1.hg19:g.65142576A>G		197.0	0.0		202.0	90.0	NM_020925	Q49AE9|Q658T4|Q7Z3P2|Q9H7W4|Q9H9W3|Q9HCJ9	Splice_Site	SNP	ENST00000371073.2	hg19		.	.	.	.	.	.	.	.	.	.	A	23.5	4.421323	0.83559	.	.	ENSG00000158966	ENST00000371073;ENST00000290039	.	.	.	5.78	5.78	0.91487	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.1205	0.81351	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CACHD1	64915164	1.000000	0.71417	0.990000	0.47175	0.869000	0.49853	8.720000	0.91442	2.205000	0.71048	0.533000	0.62120	.	.	.		0.542	CACHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_020925	Intron	G	65142576	A	G	65142576	5	3	344	1	0	0	0	0	0	0	1	0	2539	202	7	2	2907	2	CACHD1	1	65142576	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2408584	65142576	184108045	50	47413										
DNAJC6	9829	hgsc.bcm.edu	37	chr1	65852603	65852603	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcaaccattgggagccggctAcaggctaaggtatggttttt	12	8	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:65852603A>G	ENST00000395325.3	+	8	1090	c.933A>G	c.(931-933)ctA>ctG	p.L311L	DNAJC6_ENST00000371069.4_Silent_p.L368L|DNAJC6_ENST00000498720.1_3'UTR|DNAJC6_ENST00000263441.7_Silent_p.L298L	NM_014787.3	NP_055602.1	O75061	AUXI_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 6	311	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				cell death (GO:0008219)|clathrin coat disassembly (GO:0072318)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of clathrin-mediated endocytosis (GO:2000369)	cytosol (GO:0005829)|synapse (GO:0045202)	protein tyrosine phosphatase activity (GO:0004725)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(22)|ovary(1)|prostate(2)|skin(1)	39						GGAGCCGGCTACAGGCTAAGG	0.433																																					p.L368L		Atlas-SNP	.											.	DNAJC6	104	.	0			c.A1104G						.						120	108	112					1																	65852603		2203	4300	6503	SO:0001819	synonymous_variant	9829	exon8			CCGGCTACAGGCT	AB007942	CCDS30739.1, CCDS58004.1, CCDS58005.1	1p31.3	2011-09-02			ENSG00000116675	ENSG00000116675		"Heat shock proteins / DNAJ (HSP40)"	15469	protein-coding gene	gene with protein product	"auxilin"	608375				9455484, 11147971	Standard	NM_001256864		Approved	KIAA0473	uc001dce.2	O75061	OTTHUMG00000009066	ENST00000395325.3:c.933A>G	chr1.hg19:g.65852603A>G		122.0	0.0		118.0	47.0	NM_001256864	B7Z3V8|D3DQ65|D3DQ66|Q32M66|Q4G0K1|Q5T614|Q5T615	Silent	SNP	ENST00000395325.3	hg19	CCDS30739.1																																																																																			.	.		0.433	DNAJC6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025134.1			G	65852603	A	G	65852603	2	3	344	1	0	0	0	0	0	0	0	1	4655	378	14	2		2	DNAJC6	1	65852603	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	710027	65852603	183398018	51	47414										
SGIP1	84251	hgsc.bcm.edu	37	chr1	67148048	67148048	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggccctggtccggggaccacCagtggtatgtcttatgcttg	14	11	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:67148048C>T	ENST00000371037.4	+	15	1388	c.1311C>T	c.(1309-1311)acC>acT	p.T437T	SGIP1_ENST00000371035.3_Intron|SGIP1_ENST00000237247.6_Silent_p.T441T|SGIP1_ENST00000371039.1_Intron|SGIP1_ENST00000371036.3_Intron	NM_032291.2	NP_115667.2	Q9BQI5	SGIP1_HUMAN	SH3-domain GRB2-like (endophilin) interacting protein 1	437	Pro-rich.				endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of feeding behavior (GO:2000253)|positive regulation of receptor-mediated endocytosis (GO:0048260)|response to dietary excess (GO:0002021)	AP-2 adaptor complex (GO:0030122)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	microtubule binding (GO:0008017)|phospholipid binding (GO:0005543)|SH3 domain binding (GO:0017124)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(43)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	71						CGGGGACCACCAGTGGTATGT	0.617																																					p.T437T		Atlas-SNP	.											.	SGIP1	272	.	0			c.C1311T						.						115	128	123					1																	67148048		2188	4284	6472	SO:0001819	synonymous_variant	84251	exon15			GACCACCAGTGGT	AL136561	CCDS30744.1	1p31.3	2008-02-05			ENSG00000118473	ENSG00000118473			25412	protein-coding gene	gene with protein product		611540				11230166	Standard	NM_032291		Approved	DKFZp761D221	uc001dcr.3	Q9BQI5	OTTHUMG00000009161	ENST00000371037.4:c.1311C>T	chr1.hg19:g.67148048C>T		162.0	0.0		159.0	60.0	NM_032291	A6NL81|A6NLD1|Q4LE32|Q5VYE2|Q5VYE3|Q5VYE4|Q68D76|Q6MZY6|Q8IWC2	Silent	SNP	ENST00000371037.4	hg19	CCDS30744.1																																																																																			.	.		0.617	SGIP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000025395.4	NM_032291		T	67148048	C	T	67148048	2	4	344	1	0	0	0	0	0	0	0	1	14221	581	21	3		3	SGIP1	1	67148048	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1295445	67148048	182102573	52	47415										
IL23R	149233	hgsc.bcm.edu	37	chr1	67666515	67666515	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	caagaagtacttggtttgggTccaagcagcaaacgcactag	11	9	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:67666515T>A	ENST00000347310.5	+	5	758	c.587T>A	c.(586-588)gTc>gAc	p.V196D	IL23R_ENST00000371002.1_Missense_Mutation_p.V196D|C1orf141_ENST00000371007.2_Intron	NM_144701.2	NP_653302.2	Q5VWK5	IL23R_HUMAN	interleukin 23 receptor	196	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|interleukin-23-mediated signaling pathway (GO:0038155)|negative regulation of interleukin-10 production (GO:0032693)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of natural killer cell proliferation (GO:0032819)|positive regulation of NK T cell activation (GO:0051135)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat4 protein (GO:0042520)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|regulation of tyrosine phosphorylation of Stat1 protein (GO:0042510)|response to interferon-gamma (GO:0034341)|response to lipopolysaccharide (GO:0032496)	interleukin-23 receptor complex (GO:0072536)|receptor complex (GO:0043235)				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	21						TTGGTTTGGGTCCAAGCAGCA	0.373																																					p.V196D		Atlas-SNP	.											.	IL23R	52	.	0			c.T587A						.						145	143	143					1																	67666515		2203	4300	6503	SO:0001583	missense	149233	exon5			TTTGGGTCCAAGC	AF461422	CCDS637.1	1p31.2	2008-02-05			ENSG00000162594	ENSG00000162594			19100	protein-coding gene	gene with protein product		607562				12023369	Standard	NM_144701		Approved	IL-23R	uc001ddo.3	Q5VWK5	OTTHUMG00000009092	ENST00000347310.5:c.587T>A	chr1.hg19:g.67666515T>A	ENSP00000321345:p.Val196Asp	203.0	0.0		196.0	101.0	NM_144701	C9JGX4|Q4VGP1|Q4VGP2|Q4VGP3|Q4VGP4|Q4VGP5|Q4VGP6|Q5VWK7|Q8IW84|Q8NFQ9|Q96AS1	Missense_Mutation	SNP	ENST00000347310.5	hg19	CCDS637.1	.	.	.	.	.	.	.	.	.	.	T	17.45	3.393858	0.62066	.	.	ENSG00000162594	ENST00000347310;ENST00000431791;ENST00000441823;ENST00000540911;ENST00000371002;ENST00000543799	T;T	0.58797	0.31;0.31	5.95	5.95	0.96441	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.72120	0.3421	M	0.83774	2.66	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	0.998;0.983;0.998;0.998;0.999;1.0;0.999	T	0.77742	-0.2474	10	0.87932	D	0	-26.2341	12.8155	0.57663	0.0:0.0:0.0:1.0	.	50;55;55;50;103;196;196	B6HY71;E9PHX4;E9PG12;B6HY79;B6VNT7;Q5VWK5-3;Q5VWK5	.;.;.;.;.;.;IL23R_HUMAN	D	196;55;55;55;196;151	ENSP00000321345:V196D;ENSP00000360041:V196D	ENSP00000321345:V196D	V	+	2	0	IL23R	67439103	0.999000	0.42202	0.953000	0.39169	0.441000	0.31987	4.051000	0.57412	2.279000	0.76181	0.533000	0.62120	GTC	.	.		0.373	IL23R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025199.2	NM_144701		A	67666515	T	A	67666515	3	1	344	1	0	0	0	0	1	0	0	0	7685	1667	58	4	601	4	IL23R	1	67666515	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	518467	67666515	181584106	53	47416										
LRRC7	57554	hgsc.bcm.edu	37	chr1	70502271	70502271	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggggtccttgcagacaacagCtaaagatgcagtacataatt	10	8	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:70502271C>T	ENST00000035383.5	+	18	2168	c.2138C>T	c.(2137-2139)gCt>gTt	p.A713V	LRRC7_ENST00000310961.5_Missense_Mutation_p.A718V|LRRC7_ENST00000415775.2_Intron	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	713						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)		p.A713V(1)		breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						CAGACAACAGCTAAAGATGCA	0.433																																					p.A713V		Atlas-SNP	.											LRRC7,NS,carcinoma,0,1	LRRC7	400	.	1	Substitution - Missense(1)	lung(1)	c.C2138T						.						135	148	144					1																	70502271		2203	4300	6503	SO:0001583	missense	57554	exon18			CAACAGCTAAAGA		CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.2138C>T	chr1.hg19:g.70502271C>T	ENSP00000035383:p.Ala713Val	115.0	1.0		132.0	61.0	NM_020794	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Missense_Mutation	SNP	ENST00000035383.5	hg19	CCDS645.1	.	.	.	.	.	.	.	.	.	.	C	16.21	3.057789	0.55325	.	.	ENSG00000033122	ENST00000310961;ENST00000035383;ENST00000370957	T;T	0.38887	1.11;1.19	5.77	5.77	0.91146	.	0.475464	0.25132	N	0.032896	T	0.27027	0.0662	L	0.47716	1.5	0.80722	D	1	B	0.18741	0.03	B	0.18561	0.022	T	0.02925	-1.1093	10	0.27082	T	0.32	.	19.335	0.94312	0.0:1.0:0.0:0.0	.	713	Q96NW7	LRRC7_HUMAN	V	718;713;536	ENSP00000309245:A718V;ENSP00000035383:A713V	ENSP00000035383:A713V	A	+	2	0	LRRC7	70274859	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.433000	0.52834	2.890000	0.99128	0.650000	0.86243	GCT	.	.		0.433	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794		T	70502271	C	T	70502271	3	4	344	1	0	0	0	0	1	0	0	0	9029	797	28	3	2208	3	LRRC7	1	70502271	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	2835756	70502271	178748350	54	47417										
LRRC40	55631	hgsc.bcm.edu	37	chr1	70616864	70616864	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	accagtgattccatttcttcTggcaaagaatttaaaaaatt	5	7	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:70616864T>G	ENST00000370952.3	-	13	1543	c.1464A>C	c.(1462-1464)ccA>ccC	p.P488P		NM_017768.4	NP_060238.3	Q9H9A6	LRC40_HUMAN	leucine rich repeat containing 40	488						membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(2)	27						CCATTTCTTCTGGCAAAGAAT	0.259																																					p.P488P		Atlas-SNP	.											.	LRRC40	66	.	0			c.A1464C						.						48	49	49					1																	70616864		2198	4289	6487	SO:0001819	synonymous_variant	55631	exon13			TTCTTCTGGCAAA		CCDS646.1	1p31.1	2008-02-05			ENSG00000066557	ENSG00000066557			26004	protein-coding gene	gene with protein product						12477932	Standard	NM_017768		Approved	FLJ20331	uc001der.2	Q9H9A6	OTTHUMG00000009348	ENST00000370952.3:c.1464A>C	chr1.hg19:g.70616864T>G		244.0	0.0		240.0	97.0	NM_017768	Q9BTR7|Q9NSK1|Q9NXC1	Silent	SNP	ENST00000370952.3	hg19	CCDS646.1																																																																																			.	.		0.259	LRRC40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025914.1	NM_017768		G	70616864	T	G	70616864	2	3	344	1	0	0	0	0	0	0	0	1	9007	1567	55	5		5	LRRC40	1	70616864	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	114593	70616864	178633757	55	47418										
PTGER3	5733	hgsc.bcm.edu	37	chr1	71418661	71418661	+	3'UTR	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gagtacctccatttcttctcTgttcagcacacgataggttt	7	11	3	0	rs568967213	byFrequency	TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:71418661T>G	ENST00000414819.1	-	0	1508				PTGER3_ENST00000460330.1_Intron|PTGER3_ENST00000354608.5_Intron|PTGER3_ENST00000351052.5_Intron|RP3-333A15.1_ENST00000426775.1_RNA|PTGER3_ENST00000370931.3_Intron|PTGER3_ENST00000370932.2_Intron|PTGER3_ENST00000356595.4_Silent_p.R396R	NM_001126044.1	NP_001119516.1	P43115	PE2R3_HUMAN	prostaglandin E receptor 3 (subtype EP3)						cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of fever generation (GO:0031622)|transcription, DNA-templated (GO:0006351)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|prostaglandin E receptor activity (GO:0004957)			endometrium(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	25					Bimatoprost(DB00905)|Dinoprostone(DB00917)|Misoprostol(DB00929)	ATTTCTTCTCTGTTCAGCACA	0.408																																					p.R396R		Atlas-SNP	.											.	PTGER3	246	.	0			c.A1186C						.						247	225	233					1																	71418661		2203	4300	6503	SO:0001624	3_prime_UTR_variant	5733	exon4			CTTCTCTGTTCAG	X83863	CCDS652.1, CCDS655.1, CCDS656.1, CCDS657.1, CCDS658.1	1p31.2	2012-08-08			ENSG00000050628	ENSG00000050628		"GPCR / Class A : Prostanoid receptors"	9595	protein-coding gene	gene with protein product		176806				7759114, 9073510	Standard	NM_001126044		Approved	EP3	uc001dfo.3	P43115	OTTHUMG00000009399	ENST00000414819.1:c.*105A>C	chr1.hg19:g.71418661T>G		55.0	0.0		42.0	13.0	NM_198718	B0AZN4|B1AK19|B5BUP5|O00326|Q12943|Q12944|Q12945|Q16546|Q5CZ59|Q5CZ61|Q5CZ62|Q5CZ63|Q5CZ64	Silent	SNP	ENST00000414819.1	hg19	CCDS656.1																																																																																			.	.		0.408	PTGER3-204	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026077.1	NM_000957		G	71418661	T	G	71418661	1	3	344	0	1	0	0	0	0	0	0	0	12757	1588	55	5		5	PTGER3	1	71418661	3'UTR	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	801797	71418661	177831960	56	47419										
C1orf173	127254	hgsc.bcm.edu	37	chr1	75065565	75065565	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atcagcctgtccttcttcatTagatttttcaccttgtttct	4	11	5	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:75065565T>C	ENST00000326665.5	-	11	1758	c.1540A>G	c.(1540-1542)Aat>Gat	p.N514D	RP4-612J11.1_ENST00000416017.1_RNA|C1orf173_ENST00000420661.2_Missense_Mutation_p.N317D	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		514	Glu-rich.									NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						CCTTCTTCATTAGATTTTTCA	0.353																																					p.N514D		Atlas-SNP	.											.	C1orf173	380	.	0			c.A1540G						.						186	193	191					1																	75065565		2203	4300	6503	SO:0001583	missense	127254	exon11			CTTCATTAGATTT																												ENST00000326665.5:c.1540A>G	chr1.hg19:g.75065565T>C	ENSP00000322609:p.Asn514Asp	123.0	0.0		110.0	54.0	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Missense_Mutation	SNP	ENST00000326665.5	hg19	CCDS30755.1	.	.	.	.	.	.	.	.	.	.	T	2.599	-0.293396	0.05568	.	.	ENSG00000178965	ENST00000326665;ENST00000420661	T;T	0.17854	2.68;2.25	6.05	3.76	0.43208	.	.	.	.	.	T	0.05593	0.0147	L	0.41824	1.3	0.24342	N	0.994952	B;B	0.33448	0.096;0.412	B;B	0.39152	0.062;0.292	T	0.41484	-0.9506	9	0.13108	T	0.6	-7.604	9.5872	0.39524	0.0:0.1438:0.0:0.8562	.	317;514	Q5RHP9-3;Q5RHP9	.;CA173_HUMAN	D	514;317	ENSP00000322609:N514D;ENSP00000398581:N317D	ENSP00000322609:N514D	N	-	1	0	C1orf173	74838153	1.000000	0.71417	0.113000	0.21522	0.001000	0.01503	2.925000	0.48884	0.551000	0.29008	-0.256000	0.11100	AAT	.	.		0.353	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1			C	75065565	T	C	75065565	3	2	344	1	0	0	0	0	1	0	0	0	2016	1754	61	2	3068	2	C1orf173	1	75065565	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	3646904	75065565	174185056	57	47420										
LPAR3	23566	hgsc.bcm.edu	37	chr1	85331282	85331282	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggggccagggaagagcaggcAgagatgttgcagaggcaatt	18	6	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:85331282A>C	ENST00000440886.1	-	1	560	c.522T>G	c.(520-522)tcT>tcG	p.S174S	LPAR3_ENST00000370611.3_Silent_p.S174S|LPAR3_ENST00000491034.1_Intron			Q9UBY5	LPAR3_HUMAN	lysophosphatidic acid receptor 3	174					activation of MAPK activity (GO:0000187)|bleb assembly (GO:0032060)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|synaptic transmission (GO:0007268)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)|lysophosphatidic acid receptor activity (GO:0070915)|phospholipid binding (GO:0005543)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|urinary_tract(1)	24						AAGAGCAGGCAGAGATGTTGC	0.537																																					p.S174S		Atlas-SNP	.											.	LPAR3	53	.	0			c.T522G						.						111	107	109					1																	85331282		2203	4300	6503	SO:0001819	synonymous_variant	23566	exon2			GCAGGCAGAGATG	AF127138	CCDS700.1	1p22.3	2012-08-08	2008-04-11	2008-04-11	ENSG00000171517	ENSG00000171517		"GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"	14298	protein-coding gene	gene with protein product		605106	"endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 7"	EDG7		10488122	Standard	NM_012152		Approved	LP-A3, Edg-7, RP4-678I3, HOFNH30, LPA3	uc009wcj.1	Q9UBY5	OTTHUMG00000009925	ENST00000440886.1:c.522T>G	chr1.hg19:g.85331282A>C		99.0	0.0		98.0	39.0	NM_012152	A0AVA3	Silent	SNP	ENST00000440886.1	hg19	CCDS700.1																																																																																			.	.		0.537	LPAR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027467.1	NM_012152		C	85331282	A	C	85331282	2	2	344	1	0	0	0	0	0	0	0	1	8915	175	7	5		5	LPAR3	1	85331282	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	10265717	85331282	163919339	58	47421										
SYDE2	84144	hgsc.bcm.edu	37	chr1	85647970	85647970	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	actttcacataaataagaccTctaggttcaagtttgacagc	6	9	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:85647970T>C	ENST00000341460.5	-	3	2404	c.2355A>G	c.(2353-2355)agA>agG	p.R785R		NM_032184.1	NP_115560.1	Q5VT97	SYDE2_HUMAN	synapse defective 1, Rho GTPase, homolog 2 (C. elegans)	785					activation of Rho GTPase activity (GO:0032862)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)	20				all cancers(265;0.0126)|Epithelial(280;0.0336)		AAATAAGACCTCTAGGTTCAA	0.368																																					p.R785R		Atlas-SNP	.											.	SYDE2	135	.	0			c.A2355G						.						92	82	85					1																	85647970		1834	4086	5920	SO:0001819	synonymous_variant	84144	exon3			AAGACCTCTAGGT	AL834286	CCDS44169.1	1p22.3	2008-02-05		2005-08-09	ENSG00000097096	ENSG00000097096			25841	protein-coding gene	gene with protein product							Standard	NM_032184		Approved	FLJ13815	uc009wcm.3	Q5VT97	OTTHUMG00000009956	ENST00000341460.5:c.2355A>G	chr1.hg19:g.85647970T>C		209.0	0.0		181.0	10.0	NM_032184	Q5VT96|Q8NDB8|Q9H8A6	Silent	SNP	ENST00000341460.5	hg19	CCDS44169.1																																																																																			.	.		0.368	SYDE2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127989.2			C	85647970	T	C	85647970	2	2	344	1	0	0	0	0	0	0	0	1	15451	1548	54	2		2	SYDE2	1	85647970	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	316688	85647970	163602651	59	47422										
CLCA1	1179	hgsc.bcm.edu	37	chr1	86961307	86961307	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttaacgcagccagacggagaGtgataccccagcagagtgga	13	10	0	4	rs566492008		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:86961307G>T	ENST00000234701.3	+	13	2413	c.2062G>T	c.(2062-2064)Gtg>Ttg	p.V688L	CLCA1_ENST00000394711.1_Missense_Mutation_p.V688L			A8K7I4	CLCA1_HUMAN	chloride channel accessory 1	688					calcium ion transport (GO:0006816)|cellular response to hypoxia (GO:0071456)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|zymogen granule membrane (GO:0042589)	chloride channel activity (GO:0005254)			NS(1)|breast(3)|endometrium(1)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Lung NSC(277;0.239)		all cancers(265;0.0249)|Epithelial(280;0.0476)		CAGACGGAGAGTGATACCCCA	0.458																																					p.V688L		Atlas-SNP	.											.	CLCA1	109	.	0			c.G2062T						.						91	89	89					1																	86961307		2203	4300	6503	SO:0001583	missense	1179	exon12			CGGAGAGTGATAC		CCDS709.1	1p22.3	2012-02-26	2009-01-29		ENSG00000016490	ENSG00000016490			2015	protein-coding gene	gene with protein product		603906	"chloride channel, calcium activated, family member 1", "chloride channel regulator 1"			9828122	Standard	NM_001285		Approved	CaCC, CLCRG1	uc001dlt.3	A8K7I4	OTTHUMG00000010254	ENST00000234701.3:c.2062G>T	chr1.hg19:g.86961307G>T	ENSP00000234701:p.Val688Leu	95.0	0.0		87.0	43.0	NM_001285	B2RAV5|O95151|Q5TDF4|Q9UNF6|Q9UPC6	Missense_Mutation	SNP	ENST00000234701.3	hg19	CCDS709.1	.	.	.	.	.	.	.	.	.	.	G	1.059	-0.673550	0.03403	.	.	ENSG00000016490	ENST00000234701;ENST00000394711	T;T	0.02763	4.17;4.17	5.45	-8.0	0.01126	.	1.930170	0.02560	N	0.096619	T	0.00300	0.0009	N	0.04203	-0.255	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.44436	-0.9328	10	0.05525	T	0.97	8.9942	2.1359	0.03762	0.415:0.0756:0.2379:0.2715	.	688	A8K7I4	CLCA1_HUMAN	L	688	ENSP00000234701:V688L;ENSP00000378200:V688L	ENSP00000234701:V688L	V	+	1	0	CLCA1	86733895	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.493000	0.06459	-1.135000	0.02895	-0.137000	0.14449	GTG	.	.		0.458	CLCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028277.1	NM_001285		T	86961307	G	T	86961307	3	4	344	1	0	0	0	0	1	0	0	0	3459	1029	36	3	2108	3	CLCA1	1	86961307	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1313337	86961307	162289314	60	47423										
ZNF644	84146	hgsc.bcm.edu	37	chr1	91403139	91403139	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgaacgaatctctttcttgcTgtctgattatggatcttttg	8	7	4	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:91403139T>A	ENST00000370440.1	-	4	3808	c.3591A>T	c.(3589-3591)acA>acT	p.T1197T	ZNF644_ENST00000347275.5_Intron|ZNF644_ENST00000467231.1_Intron|ZNF644_ENST00000337393.5_Silent_p.T1197T|ZNF644_ENST00000361321.5_Intron			Q9H582	ZN644_HUMAN	zinc finger protein 644	1197					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(2)|large_intestine(10)|lung(21)|ovary(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	47		all_lung(203;0.00206)|Lung NSC(277;0.0519)|Lung SC(238;0.101)		all cancers(265;0.00102)|Epithelial(280;0.00766)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)|OV - Ovarian serous cystadenocarcinoma(397;0.173)		TCTTTCTTGCTGTCTGATTAT	0.363																																					p.T1197T		Atlas-SNP	.											.	ZNF644	120	.	0			c.A3591T						.						104	103	103					1																	91403139		2203	4300	6503	SO:0001819	synonymous_variant	84146	exon4			TCTTGCTGTCTGA	AB033047	CCDS731.1, CCDS732.1	1p22.2	2008-02-05			ENSG00000122482	ENSG00000122482			29222	protein-coding gene	gene with protein product		614159				10574462	Standard	NM_032186		Approved	KIAA1221, BM-005, MGC60165, MGC70410	uc001dnw.3	Q9H582	OTTHUMG00000010078	ENST00000370440.1:c.3591A>T	chr1.hg19:g.91403139T>A		109.0	0.0		71.0	27.0	NM_201269	A2RU71|Q2TAM0|Q5TCC0|Q6BEP7|Q6P446|Q6PI06|Q7LG67|Q9ULJ9	Silent	SNP	ENST00000370440.1	hg19	CCDS731.1																																																																																			.	.		0.363	ZNF644-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027846.2	NM_032186		A	91403139	T	A	91403139	2	1	344	1	0	0	0	0	0	0	0	1	18075	1567	55	4		4	ZNF644	1	91403139	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	4441832	91403139	157847482	61	47424										
ZNF644	84146	hgsc.bcm.edu	37	chr1	91405810	91405810	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctctcttctccacacttatcTgggttataaattagatgttg	6	9	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:91405810T>A	ENST00000370440.1	-	3	1318	c.1101A>T	c.(1099-1101)ccA>ccT	p.P367P	ZNF644_ENST00000347275.5_Intron|ZNF644_ENST00000467231.1_Intron|ZNF644_ENST00000337393.5_Silent_p.P367P|ZNF644_ENST00000361321.5_Intron			Q9H582	ZN644_HUMAN	zinc finger protein 644	367					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(2)|large_intestine(10)|lung(21)|ovary(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	47		all_lung(203;0.00206)|Lung NSC(277;0.0519)|Lung SC(238;0.101)		all cancers(265;0.00102)|Epithelial(280;0.00766)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)|OV - Ovarian serous cystadenocarcinoma(397;0.173)		CACACTTATCTGGGTTATAAA	0.368																																					p.P367P		Atlas-SNP	.											.	ZNF644	120	.	0			c.A1101T						.						116	115	115					1																	91405810		2203	4300	6503	SO:0001819	synonymous_variant	84146	exon3			CTTATCTGGGTTA	AB033047	CCDS731.1, CCDS732.1	1p22.2	2008-02-05			ENSG00000122482	ENSG00000122482			29222	protein-coding gene	gene with protein product		614159				10574462	Standard	NM_032186		Approved	KIAA1221, BM-005, MGC60165, MGC70410	uc001dnw.3	Q9H582	OTTHUMG00000010078	ENST00000370440.1:c.1101A>T	chr1.hg19:g.91405810T>A		86.0	0.0		90.0	32.0	NM_201269	A2RU71|Q2TAM0|Q5TCC0|Q6BEP7|Q6P446|Q6PI06|Q7LG67|Q9ULJ9	Silent	SNP	ENST00000370440.1	hg19	CCDS731.1																																																																																			.	.		0.368	ZNF644-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027846.2	NM_032186		A	91405810	T	A	91405810	2	1	344	1	0	0	0	0	0	0	0	1	18075	1567	55	4		4	ZNF644	1	91405810	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2671	91405810	157844811	62	47425										
ZNF644	84146	hgsc.bcm.edu	37	chr1	91406111	91406111	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cctcattagtcataagaaatTgaatgaactctttttgggga	8	6	3	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:91406111T>A	ENST00000370440.1	-	3	1017	c.800A>T	c.(799-801)cAa>cTa	p.Q267L	ZNF644_ENST00000347275.5_Intron|ZNF644_ENST00000467231.1_Intron|ZNF644_ENST00000337393.5_Missense_Mutation_p.Q267L|ZNF644_ENST00000361321.5_Intron			Q9H582	ZN644_HUMAN	zinc finger protein 644	267					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(2)|large_intestine(10)|lung(21)|ovary(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	47		all_lung(203;0.00206)|Lung NSC(277;0.0519)|Lung SC(238;0.101)		all cancers(265;0.00102)|Epithelial(280;0.00766)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)|OV - Ovarian serous cystadenocarcinoma(397;0.173)		CATAAGAAATTGAATGAACTC	0.343																																					p.Q267L		Atlas-SNP	.											.	ZNF644	120	.	0			c.A800T						.						101	100	100					1																	91406111		2202	4300	6502	SO:0001583	missense	84146	exon3			AGAAATTGAATGA	AB033047	CCDS731.1, CCDS732.1	1p22.2	2008-02-05			ENSG00000122482	ENSG00000122482			29222	protein-coding gene	gene with protein product		614159				10574462	Standard	NM_032186		Approved	KIAA1221, BM-005, MGC60165, MGC70410	uc001dnw.3	Q9H582	OTTHUMG00000010078	ENST00000370440.1:c.800A>T	chr1.hg19:g.91406111T>A	ENSP00000359469:p.Gln267Leu	91.0	0.0		79.0	42.0	NM_201269	A2RU71|Q2TAM0|Q5TCC0|Q6BEP7|Q6P446|Q6PI06|Q7LG67|Q9ULJ9	Missense_Mutation	SNP	ENST00000370440.1	hg19	CCDS731.1	.	.	.	.	.	.	.	.	.	.	T	15.51	2.853565	0.51270	.	.	ENSG00000122482	ENST00000370440;ENST00000337393;ENST00000541557	T;T	0.00634	6.07;6.07	6.03	6.03	0.97812	.	0.062813	0.64402	D	0.000003	T	0.00328	0.0010	L	0.29908	0.895	0.51012	D	0.999908	P	0.42827	0.791	B	0.32677	0.15	T	0.79035	-0.1968	10	0.72032	D	0.01	-1.2057	15.1292	0.72507	0.0:0.0:0.0:1.0	.	267	Q9H582	ZN644_HUMAN	L	267	ENSP00000359469:Q267L;ENSP00000337008:Q267L	ENSP00000337008:Q267L	Q	-	2	0	ZNF644	91178699	1.000000	0.71417	0.992000	0.48379	0.769000	0.43574	4.302000	0.59092	2.308000	0.77769	0.533000	0.62120	CAA	.	.		0.343	ZNF644-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027846.2	NM_032186		A	91406111	T	A	91406111	3	1	344	1	0	0	0	0	1	0	0	0	18075	1812	63	4	3199	4	ZNF644	1	91406111	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	301	91406111	157844510	63	47426										
HFM1	164045	hgsc.bcm.edu	37	chr1	91859872	91859872	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tatcagaaggaaaggcaaacTggaatttttgtgttagtgaa	11	3	1	2	rs201897123		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:91859872T>A	ENST00000370425.3	-	4	370	c.272A>T	c.(271-273)cAg>cTg	p.Q91L	HFM1_ENST00000370424.3_Intron|HFM1_ENST00000294696.5_5'UTR	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	91					resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		AAAGGCAAACTGGAATTTTTG	0.313																																					p.Q91L		Atlas-SNP	.											.	HFM1	188	.	0			c.A272T						.						71	68	69					1																	91859872		2202	4298	6500	SO:0001583	missense	164045	exon4			GCAAACTGGAATT	AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"SEC63 domain containing 1"	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.272A>T	chr1.hg19:g.91859872T>A	ENSP00000359454:p.Gln91Leu	173.0	0.0		170.0	71.0	NM_001017975	B1B0B6|Q8N9Q0	Missense_Mutation	SNP	ENST00000370425.3	hg19	CCDS30769.2	.	.	.	.	.	.	.	.	.	.	T	4.837	0.155600	0.09236	.	.	ENSG00000162669	ENST00000370425;ENST00000541820;ENST00000427444;ENST00000455133	T;T;T	0.60672	0.17;1.34;1.39	4.37	4.37	0.52481	.	.	.	.	.	T	0.23926	0.0579	L	0.29908	0.895	0.48901	D	0.99972	B;B	0.16166	0.016;0.002	B;B	0.12156	0.007;0.002	T	0.09079	-1.0691	9	0.14656	T	0.56	.	10.2526	0.43377	0.0:0.0:0.0:1.0	.	91;91	B7ZM16;A2PYH4	.;HFM1_HUMAN	L	91;124;49;91	ENSP00000359454:Q91L;ENSP00000388900:Q49L;ENSP00000409827:Q91L	ENSP00000359454:Q91L	Q	-	2	0	HFM1	91632460	0.873000	0.30073	0.040000	0.18447	0.013000	0.08279	2.308000	0.43690	1.765000	0.52091	0.383000	0.25322	CAG	.	T|0.999;C|0.001		0.313	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975		A	91859872	T	A	91859872	3	1	344	1	0	0	0	0	1	0	0	0	7092	1580	55	4	4179	4	HFM1	1	91859872	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	453761	91859872	157390749	64	47427										
BRDT	676	hgsc.bcm.edu	37	chr1	92442752	92442752	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aagaatgttttgccagattcTcagcaacaatataatgttgt	7	6	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:92442752T>C	ENST00000362005.3	+	7	1189	c.771T>C	c.(769-771)tcT>tcC	p.S257S	BRDT_ENST00000399546.2_Silent_p.S257S|BRDT_ENST00000402388.1_Silent_p.S257S|BRDT_ENST00000394530.3_Silent_p.S211S|BRDT_ENST00000484781.1_3'UTR|BRDT_ENST00000370389.2_Silent_p.S184S	NM_001242805.1	NP_001229734	Q58F21	BRDT_HUMAN	bromodomain, testis-specific	257					cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|histone displacement (GO:0001207)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|mRNA processing (GO:0006397)|positive regulation of transcription during meiosis (GO:0051039)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(24)|ovary(1)|prostate(4)|skin(2)|stomach(2)|urinary_tract(2)	56		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)		TGCCAGATTCTCAGCAACAAT	0.333																																					p.S261S		Atlas-SNP	.											.	BRDT	133	.	0			c.T783C						.						69	66	67					1																	92442752		2203	4300	6503	SO:0001819	synonymous_variant	676	exon6			AGATTCTCAGCAA	AF019085	CCDS735.1, CCDS55615.1, CCDS55616.1, CCDS72820.1	1p22.1	2010-12-23			ENSG00000137948	ENSG00000137948			1105	protein-coding gene	gene with protein product	"cancer/testis antigen 9"	602144				9367677	Standard	NM_001726		Approved	BRD6, CT9	uc010osz.2	Q58F21	OTTHUMG00000010113	ENST00000362005.3:c.771T>C	chr1.hg19:g.92442752T>C		238.0	0.0		202.0	78.0	NM_001242806	A6NF68|B7Z811|B7Z890|B7ZAX7|D3DT32|O14789|Q05DQ4|Q6P5T1|Q7Z4A6|Q8IWI6	Silent	SNP	ENST00000362005.3	hg19	CCDS735.1																																																																																			.	.		0.333	BRDT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027980.2	NM_207189		C	92442752	T	C	92442752	2	2	344	1	0	0	0	0	0	0	0	1	1510	1538	54	2		2	BRDT	1	92442752	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	582880	92442752	156807869	65	47428										
LPPR4	9890	hgsc.bcm.edu	37	chr1	99771914	99771914	+	Frame_Shift_Del	DEL	C	C	-													0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcaggaaaacataagcacctCccccaaaagcagctctgctc					rs201251961		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:99771914delC	ENST00000370185.3	+	7	2137	c.1640delC	c.(1639-1641)tccfs	p.S547fs	LPPR4_ENST00000457765.1_Frame_Shift_Del_p.S489fs|LPPR4_ENST00000370184.1_Frame_Shift_Del_p.S389fs	NM_014839.4	NP_055654.2	Q7Z2D5	LPPR4_HUMAN		547					axonogenesis (GO:0007409)|inner ear development (GO:0048839)|phospholipid dephosphorylation (GO:0046839)	integral component of plasma membrane (GO:0005887)	lipid phosphatase activity (GO:0042577)|phosphatidate phosphatase activity (GO:0008195)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(39)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	72		all_epithelial(167;3.54e-06)|all_lung(203;0.00139)|Lung NSC(277;0.00202)		Epithelial(280;0.0736)|all cancers(265;0.0975)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)|Colorectal(170;0.22)		ATAAGCACCTCCCCCAAAAGC	0.537																																					p.S547fs		Atlas-Indel,Pindel	.											.	LPPR4	143	.	0			c.1639delT						.						84	90	88					1																	99771914		2203	4300	6503	SO:0001589	frameshift_variant	0	exon7			.																												ENST00000370185.3:c.1640delC	chr1.hg19:g.99771914delC	ENSP00000359204:p.Ser547fs	101.0	0.0		69.0	36.0	NM_014839	E7EPS1|O75043|Q5T9R9|Q86XQ5|Q8N3F1|Q96MP0	Frame_Shift_Del	DEL	ENST00000370185.3	hg19	CCDS757.1																																																																																			.	.		0.537	LPPR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029670.2			-	99771914	C	-	99771914	7	5	344	1	0	1	0	1	0	0	0	0	8936	855	30	0	1666	0	LPPR4	1	99771914	Frame_Shift_Del	DEL	C	TCGA-UB-A7MB-01A-11D-A33Q-10	7329162	99771914	149478707	66	47429										
VCAM1	7412	hgsc.bcm.edu	37	chr1	101186271	101186271	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcacagcaacttgtgaatctAggaaattggaaaaaggaatc	10	6	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:101186271A>T	ENST00000294728.2	+	2	405	c.304A>T	c.(304-306)Agg>Tgg	p.R102W	VCAM1_ENST00000370119.4_Intron|VCAM1_ENST00000370115.1_Missense_Mutation_p.R102W|VCAM1_ENST00000347652.2_Missense_Mutation_p.R102W	NM_001078.3	NP_001069.1	P19320	VCAM1_HUMAN	vascular cell adhesion molecule 1	102	Ig-like C2-type 1.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|amine metabolic process (GO:0009308)|B cell differentiation (GO:0030183)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-matrix adhesion (GO:0007160)|cellular response to glucose stimulus (GO:0071333)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|chorio-allantoic fusion (GO:0060710)|chronic inflammatory response (GO:0002544)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|oxidation-reduction process (GO:0055114)|positive regulation of T cell proliferation (GO:0042102)|regulation of immune response (GO:0050776)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|response to lipopolysaccharide (GO:0032496)|response to nicotine (GO:0035094)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|viral process (GO:0016032)	alpha9-beta1 integrin-vascular cell adhesion molecule-1 complex (GO:0071065)|apical part of cell (GO:0045177)|cell surface (GO:0009986)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|podosome (GO:0002102)|sarcolemma (GO:0042383)	cell adhesion molecule binding (GO:0050839)|integrin binding (GO:0005178)|primary amine oxidase activity (GO:0008131)			central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(27)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_epithelial(167;3.83e-06)|all_lung(203;0.000485)|Lung NSC(277;0.0011)		Epithelial(280;0.0227)|all cancers(265;0.0276)|COAD - Colon adenocarcinoma(174;0.149)|Colorectal(144;0.169)|Lung(183;0.196)	Carvedilol(DB01136)	TTGTGAATCTAGGAAATTGGA	0.383																																					p.R102W		Atlas-SNP	.											.	VCAM1	111	.	0			c.A304T						.						91	86	88					1																	101186271		2203	4300	6503	SO:0001583	missense	7412	exon2			GAATCTAGGAAAT	M60335	CCDS773.1, CCDS774.1, CCDS55617.1	1p32-p31	2014-01-30			ENSG00000162692	ENSG00000162692		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Endogenous ligands"	12663	protein-coding gene	gene with protein product		192225					Standard	NM_080682		Approved	CD106	uc001dti.3	P19320	OTTHUMG00000010982	ENST00000294728.2:c.304A>T	chr1.hg19:g.101186271A>T	ENSP00000294728:p.Arg102Trp	112.0	0.0		111.0	52.0	NM_001078	A8K6R7|B4DKS4|E9PDD1|Q6NUP8	Missense_Mutation	SNP	ENST00000294728.2	hg19	CCDS773.1	.	.	.	.	.	.	.	.	.	.	A	14.42	2.529938	0.45073	.	.	ENSG00000162692	ENST00000347652;ENST00000294728;ENST00000370115	T;T;T	0.67523	-0.27;-0.27;-0.27	5.82	-11.6	0.00059	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.234750	0.05058	N	0.479322	T	0.39172	0.1068	L	0.44542	1.39	0.09310	N	1	P;P	0.49185	0.915;0.92	B;P	0.47044	0.19;0.535	T	0.58891	-0.7556	9	.	.	.	11.4014	12.4172	0.55500	0.6523:0.1478:0.2:0.0	.	102;102	P19320-2;P19320	.;VCAM1_HUMAN	W	102	ENSP00000304611:R102W;ENSP00000294728:R102W;ENSP00000359133:R102W	.	R	+	1	2	VCAM1	100958859	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.372000	0.01073	-2.931000	0.00300	-0.408000	0.06270	AGG	.	.		0.383	VCAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030213.1	NM_001078		T	101186271	A	T	101186271	3	4	344	1	0	0	0	0	1	0	0	0	17152	411	15	4	310	4	VCAM1	1	101186271	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1414357	101186271	148064350	67	47430										
OLFM3	118427	hgsc.bcm.edu	37	chr1	102270334	102270334	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttgttaaaatagagtgagccAttgtagacaacatggttagt	10	4	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:102270334A>G	ENST00000338858.5	-	6	896	c.897T>C	c.(895-897)aaT>aaC	p.N299N	OLFM3_ENST00000370103.4_Silent_p.N279N|OLFM3_ENST00000462354.1_5'UTR|OLFM3_ENST00000536598.1_3'UTR			Q96PB7	NOE3_HUMAN	olfactomedin 3	299	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				eye photoreceptor cell development (GO:0042462)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)				breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(24)|ovary(3)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	43		all_epithelial(167;1.87e-06)|all_lung(203;8.12e-05)|Lung NSC(277;0.000189)		all cancers(265;0.0843)|Epithelial(280;0.0921)|COAD - Colon adenocarcinoma(174;0.145)		AGAGTGAGCCATTGTAGACAA	0.418																																					p.N279N		Atlas-SNP	.											.	OLFM3	178	.	0			c.T837C						.						98	95	96					1																	102270334		2203	4299	6502	SO:0001819	synonymous_variant	118427	exon6			TGAGCCATTGTAG	AF397392	CCDS30781.1, CCDS72832.1	1p22	2008-05-23			ENSG00000118733	ENSG00000118733			17990	protein-coding gene	gene with protein product	"optimedin"	607567				12019210, 16115881	Standard	NM_001288821		Approved	NOE3	uc001dug.2	Q96PB7	OTTHUMG00000010941	ENST00000338858.5:c.897T>C	chr1.hg19:g.102270334A>G		104.0	0.0		90.0	45.0	NM_058170	Q5T3V6|Q6IMI7|Q6IMI8|Q6IMI9|Q6IMJ1|Q8TBG1|Q96PB2|Q96PB3|Q96PB4|Q96PB5|Q96PB6	Silent	SNP	ENST00000338858.5	hg19																																																																																				.	.		0.418	OLFM3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000030142.1			G	102270334	A	G	102270334	2	3	344	1	0	0	0	0	0	0	0	1	10863	214	8	2		2	OLFM3	1	102270334	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1084063	102270334	146980287	68	47431										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103461545	103461545	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgaaaacaatttaacgttacCtttactccccgggggcccgg	9	12	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:103461545C>T	ENST00000370096.3	-	27	2607	c.2295G>A	c.(2293-2295)aaG>aaA	p.K765K	COL11A1_ENST00000358392.2_Splice_Site_p.K777K|COL11A1_ENST00000512756.1_Splice_Site_p.K649K|COL11A1_ENST00000353414.4_Splice_Site_p.K726K	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	765	Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)	p.K765N(1)|p.K777N(1)		NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		TTAACGTTACCTTTACTCCCC	0.398																																					p.K777K		Atlas-SNP	.											COL11A1_ENST00000370096,NS,carcinoma,0,2	COL11A1	972	.	2	Substitution - Missense(2)	lung(2)	c.G2331A						.						49	55	53					1																	103461545		2202	4298	6500	SO:0001630	splice_region_variant	1301	exon27			CGTTACCTTTACT	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.2295+1G>A	chr1.hg19:g.103461545C>T		181.0	0.0		153.0	64.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Silent	SNP	ENST00000370096.3	hg19	CCDS778.1																																																																																			.	.		0.398	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630	Silent	T	103461545	C	T	103461545	5	4	344	1	0	0	0	0	0	0	1	0	3669	695	24	3	3289	3	COL11A1	1	103461545	Splice_Site	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1191211	103461545	145789076	69	47432										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103484377	103484377	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttaaaacatttacatactgcAggtcctgctggtcctggtgg	10	9	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:103484377A>T	ENST00000370096.3	-	10	1659	c.1347T>A	c.(1345-1347)ccT>ccA	p.P449P	COL11A1_ENST00000358392.2_Silent_p.P461P|COL11A1_ENST00000512756.1_Silent_p.P333P|COL11A1_ENST00000353414.4_Silent_p.P410P	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	449	Collagen-like 1.|Triple-helical region (interrupted).				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		TACATACTGCAGGTCCTGCTG	0.328																																					p.P461P		Atlas-SNP	.											.	COL11A1	972	.	0			c.T1383A						.						54	56	55					1																	103484377		2203	4300	6503	SO:0001819	synonymous_variant	1301	exon10			TACTGCAGGTCCT	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.1347T>A	chr1.hg19:g.103484377A>T		547.0	1.0		506.0	252.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Silent	SNP	ENST00000370096.3	hg19	CCDS778.1																																																																																			.	.		0.328	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		T	103484377	A	T	103484377	2	4	344	1	0	0	0	0	0	0	0	1	3669	175	7	4		4	COL11A1	1	103484377	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	22832	103484377	145766244	70	47433										
FAM102B	284611	hgsc.bcm.edu	37	chr1	109171192	109171192	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gataaagaagatacagcttcAgaaaaactcagcaggtatcc	8	8	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:109171192A>T	ENST00000370035.3	+	8	1168	c.828A>T	c.(826-828)tcA>tcT	p.S276S	FAM102B_ENST00000405454.1_Silent_p.S276S	NM_001010883.2	NP_001010883.2	Q5T8I3	F102B_HUMAN	family with sequence similarity 102, member B	276										autonomic_ganglia(1)|kidney(1)|large_intestine(1)|lung(1)|skin(1)	5		all_epithelial(167;5.52e-05)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0217)|Lung(183;0.109)|COAD - Colon adenocarcinoma(174;0.141)|Epithelial(280;0.182)		ATACAGCTTCAGAAAAACTCA	0.289																																					p.S276S		Atlas-SNP	.											.	FAM102B	49	.	0			c.A828T						.						46	52	50					1																	109171192		2198	4297	6495	SO:0001819	synonymous_variant	284611	exon8			AGCTTCAGAAAAA	CR749397	CCDS30786.2	1p13.3	2012-11-05			ENSG00000162636	ENSG00000162636			27637	protein-coding gene	gene with protein product	"sym-3 homolog B (C. elegans)"						Standard	NM_001010883		Approved	DKFZp779B126, SYM-3B	uc010ouy.2	Q5T8I3	OTTHUMG00000010967	ENST00000370035.3:c.828A>T	chr1.hg19:g.109171192A>T		129.0	0.0		128.0	65.0	NM_001010883	A1L1A1|B0QZ46|B0QZ47|Q68DH7	Silent	SNP	ENST00000370035.3	hg19	CCDS30786.2																																																																																			.	.		0.289	FAM102B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030188.3	NM_001010883		T	109171192	A	T	109171192	2	4	344	1	0	0	0	0	0	0	0	1	5388	175	7	4		4	FAM102B	1	109171192	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	5686815	109171192	140079429	71	47434										
STXBP3	6814	hgsc.bcm.edu	37	chr1	109321954	109321954	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aattgatcgtggctttgatcCtgtgtccactgtcctgcatg	10	10	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:109321954C>A	ENST00000370008.3	+	9	781	c.731C>A	c.(730-732)cCt>cAt	p.P244H	STXBP3_ENST00000485167.1_3'UTR	NM_007269.2	NP_009200.2	O00186	STXB3_HUMAN	syntaxin binding protein 3	244	Mediates interaction with DOC2B. {ECO:0000250}.				blood coagulation (GO:0007596)|membrane organization (GO:0061024)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|neutrophil degranulation (GO:0043312)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein heterooligomerization (GO:0051291)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	syntaxin binding (GO:0019905)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(3)|urinary_tract(1)	13		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0386)|Lung(183;0.104)|COAD - Colon adenocarcinoma(174;0.137)|Epithelial(280;0.231)		GGCTTTGATCCTGTGTCCACT	0.373																																					p.P244H		Atlas-SNP	.											.	STXBP3	44	.	0			c.C731A						.						214	203	207					1																	109321954		2203	4300	6503	SO:0001583	missense	6814	exon9			TTGATCCTGTGTC	D63506	CCDS790.1	1p13.3	2008-02-05			ENSG00000116266	ENSG00000116266			11446	protein-coding gene	gene with protein product		608339				10194441	Standard	NM_007269		Approved	UNC-18C	uc001dvy.3	O00186	OTTHUMG00000011122	ENST00000370008.3:c.731C>A	chr1.hg19:g.109321954C>A	ENSP00000359025:p.Pro244His	90.0	0.0		96.0	42.0	NM_007269	A8K269|A8K5K7|Q53FW1|Q86YJ3|Q9UPD7	Missense_Mutation	SNP	ENST00000370008.3	hg19	CCDS790.1	.	.	.	.	.	.	.	.	.	.	C	31	5.080558	0.94050	.	.	ENSG00000116266	ENST00000370008	T	0.80033	-1.33	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	D	0.89887	0.6845	M	0.83312	2.635	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.90118	0.4197	10	0.66056	D	0.02	-15.1857	19.5865	0.95492	0.0:1.0:0.0:0.0	.	244	O00186	STXB3_HUMAN	H	244	ENSP00000359025:P244H	ENSP00000359025:P244H	P	+	2	0	STXBP3	109123477	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.772000	0.85439	2.723000	0.93209	0.655000	0.94253	CCT	.	.		0.373	STXBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030591.1	NM_007269		A	109321954	C	A	109321954	3	1	344	1	0	0	0	0	1	0	0	0	15369	681	24	3	765	3	STXBP3	1	109321954	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	150762	109321954	139928667	72	47435										
WDR47	22911	hgsc.bcm.edu	37	chr1	109553760	109553760	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcatataggcatcagctgatTgaggtcttctcattggggat	11	7	4	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:109553760T>C	ENST00000369962.3	-	5	1130	c.908A>G	c.(907-909)cAa>cGa	p.Q303R	WDR47_ENST00000361054.3_Missense_Mutation_p.Q275R|WDR47_ENST00000369965.4_Missense_Mutation_p.Q303R|WDR47_ENST00000357672.3_Missense_Mutation_p.Q275R|WDR47_ENST00000400794.3_Missense_Mutation_p.Q310R			O94967	WDR47_HUMAN	WD repeat domain 47	303					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20		all_lung(203;0.00519)|all_epithelial(167;0.00611)|Lung NSC(277;0.00822)		Colorectal(144;0.0165)|Lung(183;0.0484)|COAD - Colon adenocarcinoma(174;0.128)|Epithelial(280;0.168)|all cancers(265;0.201)|LUSC - Lung squamous cell carcinoma(189;0.244)		ATCAGCTGATTGAGGTCTTCT	0.443																																					p.Q310R		Atlas-SNP	.											.	WDR47	56	.	0			c.A929G						.						263	282	275					1																	109553760		2203	4296	6499	SO:0001583	missense	22911	exon5			GCTGATTGAGGTC	AB020700	CCDS30787.1, CCDS44186.1, CCDS44187.1	1p13.3	2013-01-09			ENSG00000085433	ENSG00000085433		"WD repeat domain containing"	29141	protein-coding gene	gene with protein product		615734				10048485	Standard	NM_014969		Approved	KIAA0893	uc001dwl.3	O94967	OTTHUMG00000011734	ENST00000369962.3:c.908A>G	chr1.hg19:g.109553760T>C	ENSP00000358979:p.Gln303Arg	101.0	0.0		77.0	29.0	NM_001142550	A8MX09|Q5TYV7|Q5TYV8|Q5TYV9|Q8IXT7|Q8IYU9	Missense_Mutation	SNP	ENST00000369962.3	hg19	CCDS44187.1	.	.	.	.	.	.	.	.	.	.	T	10.74	1.436798	0.25900	.	.	ENSG00000085433	ENST00000400794;ENST00000369962;ENST00000361054;ENST00000369965;ENST00000357672	T;T;T;T;T	0.52057	0.68;0.72;0.7;0.69;0.7	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.29914	0.0748	N	0.11313	0.125	0.80722	D	1	P;P;P;D	0.57899	0.557;0.651;0.651;0.981	B;B;B;D	0.70487	0.234;0.165;0.165;0.969	T	0.23013	-1.0200	10	0.05833	T	0.94	-10.4104	15.2955	0.73902	0.0:0.0:0.0:1.0	.	275;310;303;303	O94967-2;A8MX09;O94967;O94967-3	.;.;WDR47_HUMAN;.	R	310;303;275;303;275	ENSP00000383599:Q310R;ENSP00000358979:Q303R;ENSP00000354339:Q275R;ENSP00000358982:Q303R;ENSP00000350301:Q275R	ENSP00000350301:Q275R	Q	-	2	0	WDR47	109355283	1.000000	0.71417	0.999000	0.59377	0.736000	0.42039	7.698000	0.84413	2.005000	0.58758	0.383000	0.25322	CAA	.	.		0.443	WDR47-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000032414.2	NM_014969		C	109553760	T	C	109553760	3	2	344	1	0	0	0	0	1	0	0	0	17315	1812	63	2	1898	2	WDR47	1	109553760	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	231806	109553760	139696861	73	47436										
PSRC1	84722	hgsc.bcm.edu	37	chr1	109824547	109824547	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aggatctcctccagcttctcTggactgagggggcctaggct	13	12	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:109824547T>G	ENST00000438534.2	-	4	351	c.213A>C	c.(211-213)ccA>ccC	p.P71P	PSRC1_ENST00000369904.3_Silent_p.P71P|PSRC1_ENST00000409138.2_Silent_p.P71P|PSRC1_ENST00000369903.2_Silent_p.P71P|PSRC1_ENST00000409267.1_Silent_p.P71P|PSRC1_ENST00000369909.2_Silent_p.P71P|PSRC1_ENST00000369907.3_Silent_p.P71P	NM_001005290.3	NP_001005290.1	Q6PGN9	PSRC1_HUMAN	proline/serine-rich coiled-coil 1	71					microtubule bundle formation (GO:0001578)|mitotic metaphase plate congression (GO:0007080)|negative regulation of cell growth (GO:0030308)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mitotic spindle organization (GO:0060236)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle (GO:0005819)	microtubule binding (GO:0008017)			endometrium(1)|large_intestine(1)|lung(2)|prostate(2)|skin(1)	7		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0286)|Lung(183;0.0658)|COAD - Colon adenocarcinoma(174;0.112)|Epithelial(280;0.188)|all cancers(265;0.213)		CCAGCTTCTCTGGACTGAGGG	0.667																																					p.P71P		Atlas-SNP	.											.	PSRC1	12	.	0			c.A213C						.						22	23	22					1																	109824547		2202	4296	6498	SO:0001819	synonymous_variant	84722	exon4			CTTCTCTGGACTG		CCDS797.1, CCDS30791.1	1p13.3	2008-02-05			ENSG00000134222	ENSG00000134222			24472	protein-coding gene	gene with protein product	"differential display and activated by p53"	613126				12427559, 10618717	Standard	NM_001032291		Approved	DDA3	uc001dxd.3	Q6PGN9	OTTHUMG00000012000	ENST00000438534.2:c.213A>C	chr1.hg19:g.109824547T>G		136.0	0.0		114.0	43.0	NM_001032291	Q5T2Z3|Q6ZTI8|Q71MG3|Q9BV77	Silent	SNP	ENST00000438534.2	hg19																																																																																				.	.		0.667	PSRC1-202	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000335567.3	NM_032636		G	109824547	T	G	109824547	2	3	344	1	0	0	0	0	0	0	0	1	12731	1567	55	5		5	PSRC1	1	109824547	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	270787	109824547	139426074	74	47437										
KCNA3	3738	hgsc.bcm.edu	37	chr1	111216504	111216504	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agcgaagaaccgcaccagcaGttcgaaggagaaccagatga	12	10	0	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:111216504G>T	ENST00000369769.2	-	1	1151	c.928C>A	c.(928-930)Ctg>Atg	p.L310M		NM_002232.3	NP_002223.3	P22001	KCNA3_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 3	310					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	membrane raft (GO:0045121)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|voltage-gated ion channel activity (GO:0005244)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(7)|ovary(4)|pancreas(1)|prostate(3)|skin(1)	38		all_cancers(81;3.92e-06)|all_epithelial(167;1.28e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Lung(183;0.0235)|Colorectal(144;0.0306)|all cancers(265;0.0752)|Epithelial(280;0.0821)|COAD - Colon adenocarcinoma(174;0.132)|LUSC - Lung squamous cell carcinoma(189;0.133)	Dalfampridine(DB06637)	CGCACCAGCAGTTCGAAGGAG	0.547																																					p.L310M		Atlas-SNP	.											.	KCNA3	91	.	0			c.C928A						.						86	85	86					1																	111216504		2203	4300	6503	SO:0001583	missense	3738	exon1			CCAGCAGTTCGAA	L23499	CCDS828.2	1p13.3	2012-07-05			ENSG00000177272	ENSG00000177272		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6221	protein-coding gene	gene with protein product		176263				2251283, 16382104	Standard	NM_002232		Approved	Kv1.3, MK3, HLK3, HPCN3	uc001dzv.1	P22001	OTTHUMG00000034493	ENST00000369769.2:c.928C>A	chr1.hg19:g.111216504G>T	ENSP00000358784:p.Leu310Met	47.0	0.0		68.0	33.0	NM_002232	Q5VWN2	Missense_Mutation	SNP	ENST00000369769.2	hg19	CCDS828.2	.	.	.	.	.	.	.	.	.	.	G	16.20	3.055898	0.55325	.	.	ENSG00000177272	ENST00000369769	D	0.97378	-4.36	5.26	4.34	0.51931	Ion transport (1);	0.000000	0.64402	U	0.000006	D	0.98425	0.9476	M	0.92026	3.265	0.80722	D	1	D	0.71674	0.998	D	0.81914	0.995	D	0.99425	1.0934	10	0.87932	D	0	.	13.6853	0.62513	0.075:0.0:0.925:0.0	.	310	P22001	KCNA3_HUMAN	M	310	ENSP00000358784:L310M	ENSP00000358784:L310M	L	-	1	2	KCNA3	111018027	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.716000	0.61916	1.203000	0.43233	0.655000	0.94253	CTG	.	.		0.547	KCNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083391.1	NM_002232		T	111216504	G	T	111216504	3	4	344	1	0	0	0	0	1	0	0	0	8013	1020	36	3	803	3	KCNA3	1	111216504	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1391957	111216504	138034117	75	47438										
AMPD1	270	hgsc.bcm.edu	37	chr1	115218238	115218238	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcttttccaatgtccactccTggggcttgggactcttggag	11	11	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:115218238T>A	ENST00000520113.2	-	12	1706	c.1691A>T	c.(1690-1692)cAg>cTg	p.Q564L	AMPD1_ENST00000369538.3_Missense_Mutation_p.Q560L|AMPD1_ENST00000353928.6_Missense_Mutation_p.Q531L			P23109	AMPD1_HUMAN	adenosine monophosphate deaminase 1	564					IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(3)|pancreas(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	45	all_epithelial(7;7.83e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	Adenosine monophosphate(DB00131)	TGTCCACTCCTGGGGCTTGGG	0.463																																					p.Q564L		Atlas-SNP	.											.	AMPD1	223	.	0			c.A1691T						.						203	194	197					1																	115218238		2203	4300	6503	SO:0001583	missense	270	exon12			CACTCCTGGGGCT	M60092	CCDS876.1, CCDS876.2, CCDS53349.1	1p13	2010-02-10	2010-02-10		ENSG00000116748	ENSG00000116748	3.5.4.6		468	protein-coding gene	gene with protein product	"AMPD isoform M", "skeletal muscle AMPD"	102770	"adenosine monophosphate deaminase 1 (isoform M)"			1400401	Standard	NM_001172626		Approved	MAD, MADA	uc001efe.2	P23109	OTTHUMG00000011892	ENST00000520113.2:c.1691A>T	chr1.hg19:g.115218238T>A	ENSP00000430075:p.Gln564Leu	50.0	0.0		58.0	31.0	NM_000036	A8K5N4|B2RAM1|F2Z3B3|Q5TF00|Q5TF02	Missense_Mutation	SNP	ENST00000520113.2	hg19	CCDS876.2	.	.	.	.	.	.	.	.	.	.	T	19.55	3.848590	0.71603	.	.	ENSG00000116748	ENST00000520113;ENST00000369538;ENST00000353928	T;T;T	0.81078	-1.45;-1.45;-1.45	5.68	5.68	0.88126	Adenosine/AMP deaminase (1);	0.264640	0.43579	D	0.000541	T	0.58708	0.2141	N	0.11560	0.145	0.44619	D	0.99759	B;B	0.32653	0.379;0.052	B;B	0.37198	0.243;0.088	T	0.67818	-0.5572	10	0.52906	T	0.07	-4.8988	15.938	0.79729	0.0:0.0:0.0:1.0	.	560;531	Q5TF02;P23109	.;AMPD1_HUMAN	L	564;560;531	ENSP00000430075:Q564L;ENSP00000358551:Q560L;ENSP00000316520:Q531L	ENSP00000316520:Q531L	Q	-	2	0	AMPD1	115019761	1.000000	0.71417	1.000000	0.80357	0.871000	0.50021	6.302000	0.72788	2.167000	0.68274	0.459000	0.35465	CAG	.	.		0.463	AMPD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032860.4			A	115218238	T	A	115218238	3	1	344	1	0	0	0	0	1	0	0	0	585	1580	55	4	671	4	AMPD1	1	115218238	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	4001734	115218238	134032383	76	47439										
CSDE1	7812	hgsc.bcm.edu	37	chr1	115275369	115275369	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtcaccttggatttcgtatcTttgtctccaaagggaagttc	9	9	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:115275369T>A	ENST00000358528.4	-	10	1332	c.906A>T	c.(904-906)aaA>aaT	p.K302N	CSDE1_ENST00000530886.1_Missense_Mutation_p.K172N|CSDE1_ENST00000261443.5_Missense_Mutation_p.K271N|CSDE1_ENST00000534699.1_Missense_Mutation_p.K302N|CSDE1_ENST00000339438.6_Missense_Mutation_p.K271N|CSDE1_ENST00000438362.2_Missense_Mutation_p.K348N|CSDE1_ENST00000369530.1_Missense_Mutation_p.K317N	NM_001007553.2	NP_001007554.1	O75534	CSDE1_HUMAN	cold shock domain containing E1, RNA-binding	302	CSD 4; truncated.				male gonad development (GO:0008584)|nuclear-transcribed mRNA catabolic process, no-go decay (GO:0070966)|regulation of transcription, DNA-templated (GO:0006355)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|endometrium(11)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	51	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		ATTTCGTATCTTTGTCTCCAA	0.428																																					p.K348N		Atlas-SNP	.											.	CSDE1	145	.	0			c.A1044T						.						163	161	161					1																	115275369		2203	4300	6503	SO:0001583	missense	7812	exon11			CGTATCTTTGTCT		CCDS30811.1, CCDS30812.1, CCDS44197.1, CCDS55626.1	1p13.2	2011-11-02			ENSG00000009307	ENSG00000009307			29905	protein-coding gene	gene with protein product	"upstream of NRAS"	191510				2204029, 10048485	Standard	NM_007158		Approved	D1S155E, UNR	uc001efi.3	O75534	OTTHUMG00000012060	ENST00000358528.4:c.906A>T	chr1.hg19:g.115275369T>A	ENSP00000351329:p.Lys302Asn	237.0	0.0		220.0	106.0	NM_001242891	A8K281|E9PGZ0|G5E9Q2|O94961|Q5TF04|Q5TF05|Q68DF1|Q68DI9|Q9Y2S4	Missense_Mutation	SNP	ENST00000358528.4	hg19	CCDS30812.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.180098	0.78564	.	.	ENSG00000009307	ENST00000339438;ENST00000438362;ENST00000358528;ENST00000261443;ENST00000530886;ENST00000369530;ENST00000534699	.	.	.	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	T	0.60287	0.2257	L	0.43923	1.385	0.58432	D	0.999999	D;D;D	0.76494	0.999;0.998;0.999	D;D;D	0.78314	0.991;0.981;0.991	T	0.65730	-0.6097	9	0.62326	D	0.03	-10.8722	12.1125	0.53848	0.0:0.0686:0.0:0.9314	.	317;302;348	E9PGZ0;O75534;G5E9Q2	.;CSDE1_HUMAN;.	N	271;348;302;271;172;317;302	.	ENSP00000261443:K271N	K	-	3	2	CSDE1	115076892	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.040000	0.49799	2.247000	0.74100	0.482000	0.46254	AAA	.	.		0.428	CSDE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033397.1	NM_007158		A	115275369	T	A	115275369	3	1	344	1	0	0	0	0	1	0	0	0	3931	1606	56	4	1534	4	CSDE1	1	115275369	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	57131	115275369	133975252	77	47440										
NGF	4803	hgsc.bcm.edu	37	chr1	115829387	115829387	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgtatgccgatcagaaaagcTgtgatcagagtgtagaacaa	11	6	2	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:115829387T>A	ENST00000369512.2	-	3	198	c.30A>T	c.(28-30)acA>acT	p.T10T	RP4-663N10.1_ENST00000425449.1_RNA	NM_002506.2	NP_002497.2	P01138	NGF_HUMAN	nerve growth factor (beta polypeptide)	10					activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|adult locomotory behavior (GO:0008344)|apoptotic signaling pathway (GO:0097190)|circadian rhythm (GO:0007623)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|inflammatory response (GO:0006954)|memory (GO:0007613)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle (GO:0045786)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|nerve growth factor processing (GO:0032455)|neuron apoptotic process (GO:0051402)|neuron projection morphogenesis (GO:0048812)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axon extension (GO:0045773)|positive regulation of axonogenesis (GO:0050772)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron maturation (GO:0014042)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neurotrophin TRK receptor signaling pathway (GO:0051388)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of stem cell proliferation (GO:2000648)|Ras protein signal transduction (GO:0007265)|regulation of axonogenesis (GO:0050770)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of neurotransmitter secretion (GO:0046928)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|response to nicotine (GO:0035094)|response to ozone (GO:0010193)|response to peptide hormone (GO:0043434)|response to radiation (GO:0009314)|sensory perception of pain (GO:0019233)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)	nerve growth factor receptor binding (GO:0005163)|receptor signaling protein activity (GO:0005057)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	13	Lung SC(450;0.211)	all_cancers(81;1.07e-06)|all_epithelial(167;4.43e-06)|all_lung(203;2.86e-05)|Lung NSC(69;4.99e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|all cancers(265;0.159)|Epithelial(280;0.179)	Clenbuterol(DB01407)	TCAGAAAAGCTGTGATCAGAG	0.483																																					p.T10T		Atlas-SNP	.											.	NGF	43	.	0			c.A30T						.						130	108	116					1																	115829387		2203	4300	6503	SO:0001819	synonymous_variant	4803	exon3			AAAAGCTGTGATC		CCDS882.1	1p13.1	2014-09-17	2008-02-07	2008-02-07	ENSG00000134259	ENSG00000134259		"Endogenous ligands"	7808	protein-coding gene	gene with protein product		162030		NGFB			Standard	XM_006710663		Approved		uc001efu.1	P01138	OTTHUMG00000011880	ENST00000369512.2:c.30A>T	chr1.hg19:g.115829387T>A		85.0	0.0		63.0	31.0	NM_002506	A1A4E5|Q6FHA0|Q96P60|Q9P2Q8|Q9UKL8	Silent	SNP	ENST00000369512.2	hg19	CCDS882.1																																																																																			.	.		0.483	NGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032832.1	NM_002506		A	115829387	T	A	115829387	2	1	344	1	0	0	0	0	0	0	0	1	10404	1567	55	4		4	NGF	1	115829387	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	554018	115829387	133421234	78	47441										
CASQ2	845	hgsc.bcm.edu	37	chr1	116244009	116244009	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agctcctcagcagttggaagAtcgtcatcatctggaatctc	9	11	5	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:116244009A>T	ENST00000261448.5	-	11	1292	c.1053T>A	c.(1051-1053)gaT>gaA	p.D351E	CASQ2_ENST00000456138.2_Missense_Mutation_p.D280E	NM_001232.3	NP_001223.2	O14958	CASQ2_HUMAN	calsequestrin 2 (cardiac muscle)	351					cardiac muscle contraction (GO:0060048)|cellular response to caffeine (GO:0071313)|detection of calcium ion (GO:0005513)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|protein polymerization (GO:0051258)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of heart rate (GO:0002027)|regulation of membrane repolarization (GO:0060306)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|sequestering of calcium ion (GO:0051208)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|junctional sarcoplasmic reticulum membrane (GO:0014701)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|skin(1)	18	Lung SC(450;0.211)	all_cancers(81;1.25e-06)|all_epithelial(167;1.02e-06)|all_lung(203;8.03e-06)|Lung NSC(69;5.01e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		CAGTTGGAAGATCGTCATCAT	0.453																																					p.D351E		Atlas-SNP	.											.	CASQ2	54	.	0			c.T1053A						.						124	101	109					1																	116244009		2203	4300	6503	SO:0001583	missense	845	exon11			TGGAAGATCGTCA	BC022288	CCDS884.1	1p13.1	2014-09-17			ENSG00000118729	ENSG00000118729		"Protein disulfide isomerases"	1513	protein-coding gene	gene with protein product		114251				8406504	Standard	NM_001232		Approved	PDIB2	uc001efx.4	O14958	OTTHUMG00000011970	ENST00000261448.5:c.1053T>A	chr1.hg19:g.116244009A>T	ENSP00000261448:p.Asp351Glu	105.0	0.0		97.0	39.0	NM_001232	B2R7M6|B4DIB0|Q5T1D2|Q8TBW8	Missense_Mutation	SNP	ENST00000261448.5	hg19	CCDS884.1	.	.	.	.	.	.	.	.	.	.	A	14.27	2.484502	0.44147	.	.	ENSG00000118729	ENST00000261448;ENST00000456138;ENST00000446755	T;T	0.79454	-1.27;-1.27	6.16	4.25	0.50352	Thioredoxin-like fold (2);	0.042999	0.85682	D	0.000000	T	0.63129	0.2485	M	0.67700	2.07	0.50632	D	0.999884	B;B	0.28783	0.222;0.011	B;B	0.33620	0.167;0.059	T	0.61347	-0.7081	10	0.30854	T	0.27	-30.8445	9.8212	0.40883	0.2105:0.0:0.7895:0.0	.	280;351	B4DIB0;O14958	.;CASQ2_HUMAN	E	351;280;305	ENSP00000261448:D351E;ENSP00000403858:D280E	ENSP00000261448:D351E	D	-	3	2	CASQ2	116045532	1.000000	0.71417	0.999000	0.59377	0.270000	0.26580	2.501000	0.45389	0.934000	0.37316	-0.182000	0.12963	GAT	.	.		0.453	CASQ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033091.1	NM_001232		T	116244009	A	T	116244009	3	4	344	1	0	0	0	0	1	0	0	0	2683	330	12	4	150	4	CASQ2	1	116244009	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	414622	116244009	133006612	79	47442										
NHLH2	4808	hgsc.bcm.edu	37	chr1	116380638	116380638	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgtagcagatggccaggcgcAggatctcgatcttggagagc	15	9	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:116380638A>T	ENST00000369506.1	-	1	5900	c.356T>A	c.(355-357)cTg>cAg	p.L119Q	NHLH2_ENST00000320238.3_Missense_Mutation_p.L119Q			Q02577	HEN2_HUMAN	nescient helix loop helix 2	119	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				cell differentiation (GO:0030154)|central nervous system development (GO:0007417)|mating behavior (GO:0007617)|ovulation cycle (GO:0042698)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II activating transcription factor binding (GO:0001102)			prostate(1)	1	Lung SC(450;0.184)	all_cancers(81;1.75e-06)|all_epithelial(167;1.16e-06)|all_lung(203;9.55e-06)|Lung NSC(69;5.83e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		GGCCAGGCGCAGGATCTCGAT	0.662																																					p.L119Q		Atlas-SNP	.											.	NHLH2	8	.	0			c.T356A						.						27	31	30					1																	116380638		2203	4300	6503	SO:0001583	missense	4808	exon2			AGGCGCAGGATCT		CCDS885.1	1p12-p11	2013-05-21			ENSG00000177551	ENSG00000177551		"Basic helix-loop-helix proteins"	7818	protein-coding gene	gene with protein product		162361		HEN2		1528853	Standard	NM_005599		Approved	NSCL2, bHLHa34	uc001efy.3	Q02577	OTTHUMG00000011969	ENST00000369506.1:c.356T>A	chr1.hg19:g.116380638A>T	ENSP00000358519:p.Leu119Gln	46.0	0.0		50.0	19.0	NM_001111061	Q5T1P6	Missense_Mutation	SNP	ENST00000369506.1	hg19	CCDS885.1	.	.	.	.	.	.	.	.	.	.	A	32	5.108858	0.94292	.	.	ENSG00000177551	ENST00000320238;ENST00000369506	D;D	0.99828	-6.99;-6.99	5.14	5.14	0.70334	Helix-loop-helix DNA-binding (5);	0.000000	0.64402	D	0.000016	D	0.99854	0.9932	M	0.92412	3.305	0.80722	D	1	D	0.76494	0.999	D	0.71184	0.972	D	0.96446	0.9330	10	0.87932	D	0	-12.937	14.6357	0.68689	1.0:0.0:0.0:0.0	.	119	Q02577	HEN2_HUMAN	Q	119	ENSP00000322087:L119Q;ENSP00000358519:L119Q	ENSP00000322087:L119Q	L	-	2	0	NHLH2	116182161	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.095000	0.94175	1.936000	0.56123	0.454000	0.30748	CTG	.	.		0.662	NHLH2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033090.1	NM_005599		T	116380638	A	T	116380638	3	4	344	1	0	0	0	0	1	0	0	0	10413	188	7	4	55	4	NHLH2	1	116380638	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	136629	116380638	132869983	80	47443										
TTF2	8458	hgsc.bcm.edu	37	chr1	117618107	117618107	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aggcaaaggatggccctagcAtacaggccacccagaaaagc	11	12	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:117618107A>T	ENST00000369466.4	+	5	945	c.901A>T	c.(901-903)Ata>Tta	p.I301L		NM_003594.3	NP_003585.3	Q9UNY4	TTF2_HUMAN	transcription termination factor, RNA polymerase II	301					ATP catabolic process (GO:0006200)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(24)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	50	Lung SC(450;0.225)	all_cancers(81;4.23e-06)|all_epithelial(167;3.65e-07)|all_lung(203;2.81e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0553)|Colorectal(144;0.179)|LUSC - Lung squamous cell carcinoma(189;0.19)		TGGCCCTAGCATACAGGCCAC	0.582																																					p.I301L		Atlas-SNP	.											.	TTF2	92	.	0			c.A901T						.						52	55	54					1																	117618107		2203	4300	6503	SO:0001583	missense	8458	exon5			CCTAGCATACAGG	AF073771	CCDS892.1	1p13.1	2014-02-18			ENSG00000116830	ENSG00000116830			12398	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 6"	604718				9748214	Standard	NM_003594		Approved	HuF2, ZGRF6	uc001egy.3	Q9UNY4	OTTHUMG00000012030	ENST00000369466.4:c.901A>T	chr1.hg19:g.117618107A>T	ENSP00000358478:p.Ile301Leu	157.0	0.0		162.0	80.0	NM_003594	A8K4Q2|O75921|Q5T2K7|Q5VVU8|Q8N6I8	Missense_Mutation	SNP	ENST00000369466.4	hg19	CCDS892.1	.	.	.	.	.	.	.	.	.	.	A	10.17	1.276673	0.23307	.	.	ENSG00000116830	ENST00000369466	D	0.85955	-2.05	4.99	-9.98	0.00438	.	1.663620	0.03680	N	0.245316	T	0.32406	0.0828	N	0.03608	-0.345	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.06405	0.001;0.002	T	0.44251	-0.9340	10	0.19147	T	0.46	2.4815	0.5856	0.00719	0.2324:0.1922:0.2909:0.2845	.	301;301	Q9UNY4;Q9UNY4-2	TTF2_HUMAN;.	L	301	ENSP00000358478:I301L	ENSP00000358478:I301L	I	+	1	0	TTF2	117419630	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-2.713000	0.00816	-1.693000	0.01427	-0.496000	0.04628	ATA	.	.		0.582	TTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033277.3			T	117618107	A	T	117618107	3	4	344	1	0	0	0	0	1	0	0	0	16734	217	8	4	919	4	TTF2	1	117618107	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1237469	117618107	131632514	81	47444										
RNF115	27246	hgsc.bcm.edu	37	chr1	145663367	145663367	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cagatctccagctattgaagGgtgagttgttttattttaag	10	5	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:145663367G>C	ENST00000369291.5	+	4	632	c.428G>C	c.(427-429)gGa>gCa	p.G143A		NM_014455.2	NP_055270.1			ring finger protein 115											breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	13						GCTATTGAAGGGTGAGTTGTT	0.408																																					p.G143A		Atlas-SNP	.											.	RNF115	27	.	0			c.G428C						.						66	65	65					1																	145663367		2203	4300	6503	SO:0001630	splice_region_variant	27246	exon4			TTGAAGGGTGAGT	AF419857	CCDS72863.1	1q12	2013-01-09	2008-06-16	2008-06-16	ENSG00000121848	ENSG00000265491		"RING-type (C3HC4) zinc fingers"	18154	protein-coding gene	gene with protein product			"zinc finger protein 364"	ZNF364			Standard	NM_014455		Approved	CL469780	uc001eoj.3	Q9Y4L5	OTTHUMG00000013758	ENST00000369291.5:c.428+1G>C	chr1.hg19:g.145663367G>C		77.0	0.0		125.0	43.0	NM_014455		Missense_Mutation	SNP	ENST00000369291.5	hg19	CCDS922.1	.	.	.	.	.	.	.	.	.	.	G	15.61	2.883616	0.51908	.	.	ENSG00000121848	ENST00000369291	T	0.12879	2.64	4.99	4.08	0.47627	.	0.056732	0.64402	D	0.000001	T	0.06690	0.0171	L	0.50333	1.59	0.58432	D	0.999997	D	0.57899	0.981	P	0.48114	0.567	T	0.09840	-1.0656	10	0.06891	T	0.86	-5.5491	11.2678	0.49120	0.0881:0.0:0.9119:0.0	.	143	Q9Y4L5	RN115_HUMAN	A	143	ENSP00000358297:G143A	ENSP00000358297:G143A	G	+	2	0	RNF115	144374724	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.713000	0.68415	1.337000	0.45525	0.655000	0.94253	GGA	.	.		0.408	RNF115-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038554.2	NM_014455	Missense_Mutation	C	145663367	G	C	145663367	5	2	344	1	0	0	0	0	0	0	1	0	13445	1246	43	4	442	4	RNF115	1	145663367	Splice_Site	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	28045260	145663367	103587254	82	47445										
CHD1L	9557	hgsc.bcm.edu	37	chr1	146747893	146747893	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccattttactctgggagcccAgaaacccgctgccgatgctg	10	14	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:146747893A>T	ENST00000369258.4	+	14	1531	c.1511A>T	c.(1510-1512)cAg>cTg	p.Q504L	CHD1L_ENST00000369259.3_Missense_Mutation_p.Q300L|CHD1L_ENST00000467213.1_3'UTR|CHD1L_ENST00000431239.1_Missense_Mutation_p.Q410L|CHD1L_ENST00000361293.5_Missense_Mutation_p.Q223L	NM_001256336.1|NM_004284.4|NM_024568.2	NP_001243265.1|NP_004275.4|NP_078844.2	Q86WJ1	CHD1L_HUMAN	chromodomain helicase DNA binding protein 1-like	504	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|nucleotide binding (GO:0000166)			breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(923;0.0487)					CTGGGAGCCCAGAAACCCGCT	0.448																																					p.Q504L		Atlas-SNP	.											.	CHD1L	72	.	0			c.A1511T						.						102	103	103					1																	146747893		2203	4300	6503	SO:0001583	missense	9557	exon14			GAGCCCAGAAACC	AF054177	CCDS927.1, CCDS58021.1, CCDS58022.1, CCDS72882.1	1q21.1	2008-02-05			ENSG00000131778	ENSG00000131778			1916	protein-coding gene	gene with protein product		613039				9653160	Standard	NM_004284		Approved	ALC1	uc001epm.5	Q86WJ1	OTTHUMG00000150271	ENST00000369258.4:c.1511A>T	chr1.hg19:g.146747893A>T	ENSP00000358262:p.Gln504Leu	76.0	0.0		129.0	102.0	NM_004284	A5YM64|B4DDE1|B5MDZ7|Q53EZ3|Q5VXX7|Q6DD94|Q6PK83|Q86XH3|Q96HF7|Q96SP3|Q9BVJ1|Q9NVV8	Missense_Mutation	SNP	ENST00000369258.4	hg19	CCDS927.1	.	.	.	.	.	.	.	.	.	.	A	11.45	1.642612	0.29246	.	.	ENSG00000131778	ENST00000431239;ENST00000369259;ENST00000369258;ENST00000436230;ENST00000361293	D;T;T;T	0.89681	-2.55;-0.53;-0.53;-0.53	5.37	3.04	0.35103	Helicase, C-terminal (1);	0.292495	0.39146	N	0.001456	T	0.63141	0.2486	N	0.02181	-0.65	0.42982	D	0.994466	D;B;B	0.53151	0.958;0.004;0.0	P;B;B	0.50896	0.653;0.01;0.001	T	0.65047	-0.6263	10	0.19147	T	0.46	.	7.2942	0.26383	0.8226:0.0:0.1774:0.0	.	410;300;504	Q86WJ1-2;Q86WJ1-3;Q86WJ1	.;.;CHD1L_HUMAN	L	410;300;504;404;223	ENSP00000389031:Q410L;ENSP00000358263:Q300L;ENSP00000358262:Q504L;ENSP00000355100:Q223L	ENSP00000355100:Q223L	Q	+	2	0	CHD1L	145214517	0.273000	0.24181	0.998000	0.56505	0.836000	0.47400	0.358000	0.20216	0.431000	0.26258	0.454000	0.30748	CAG	.	.		0.448	CHD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040377.1	NM_004284		T	146747893	A	T	146747893	3	4	344	1	0	0	0	0	1	0	0	0	3326	188	7	4	1565	4	CHD1L	1	146747893	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1084526	146747893	102502728	83	47446										
GJA8	2703	hgsc.bcm.edu	37	chr1	147380840	147380840	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gattcctgagaaatccctccActccattgctgtctcctcca	5	16	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:147380840A>T	ENST00000369235.1	+	1	758	c.758A>T	c.(757-759)cAc>cTc	p.H253L	GJA8_ENST00000240986.4_Missense_Mutation_p.H253L			P48165	CXA8_HUMAN	gap junction protein, alpha 8, 50kDa	253					cell-cell signaling (GO:0007267)|lens development in camera-type eye (GO:0002088)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of plasma membrane (GO:0005887)	channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)	37	all_hematologic(923;0.0276)					AAATCCCTCCACTCCATTGCT	0.552																																					p.H253L	Melanoma(76;1255 1795 8195 52096)	Atlas-SNP	.											.	GJA8	108	.	0			c.A758T						.						50	52	51					1																	147380840		2203	4300	6503	SO:0001583	missense	2703	exon2			CCCTCCACTCCAT	U34802	CCDS30834.1	1q21.1	2008-02-05	2007-01-16		ENSG00000121634	ENSG00000121634		"Ion channels / Gap junction proteins (connexins)"	4281	protein-coding gene	gene with protein product	"connexin 50"	600897	"gap junction protein, alpha 8, 50kD (connexin 50)", "gap junction protein, alpha 8, 50kDa (connexin 50)"	CAE1, CZP1, CAE		9497259, 7796604	Standard	NM_005267		Approved	CX50	uc001epu.2	P48165	OTTHUMG00000024085	ENST00000369235.1:c.758A>T	chr1.hg19:g.147380840A>T	ENSP00000358238:p.His253Leu	91.0	0.0		184.0	136.0	NM_005267	A7L5M5|Q5VVN9|Q9NP25	Missense_Mutation	SNP	ENST00000369235.1	hg19	CCDS30834.1	.	.	.	.	.	.	.	.	.	.	a	5.829	0.337264	0.11013	.	.	ENSG00000121634	ENST00000240986;ENST00000369235	D;D	0.97430	-4.38;-4.38	4.4	4.4	0.53042	.	3.298310	0.01166	N	0.006748	D	0.91482	0.7311	L	0.27053	0.805	0.51767	D	0.999936	P	0.46064	0.872	B	0.39503	0.301	T	0.80165	-0.1496	10	0.23302	T	0.38	.	13.7607	0.62963	1.0:0.0:0.0:0.0	.	253	P48165	CXA8_HUMAN	L	253	ENSP00000240986:H253L;ENSP00000358238:H253L	ENSP00000240986:H253L	H	+	2	0	GJA8	145847464	1.000000	0.71417	0.999000	0.59377	0.957000	0.61999	2.955000	0.49121	1.837000	0.53436	0.260000	0.18958	CAC	.	.		0.552	GJA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060647.1	NM_005267		T	147380840	A	T	147380840	3	4	344	1	0	0	0	0	1	0	0	0	6413	159	6	4	760	4	GJA8	1	147380840	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	632947	147380840	101869781	84	47447										
HIST2H2AC	8338	hgsc.bcm.edu	37	chr1	149858769	149858769	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaagacgcgcatcatccctcGtcacctccagctggccatcc	8	18	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:149858769G>C	ENST00000331380.2	+	1	245	c.245G>C	c.(244-246)cGt>cCt	p.R82P	BOLA1_ENST00000369153.2_5'Flank|HIST2H2BE_ENST00000369155.2_5'Flank	NM_003517.2	NP_003508.1	Q16777	H2A2C_HUMAN	histone cluster 2, H2ac	82						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(11)|ovary(1)|skin(1)	20	Breast(34;0.0124)|all_hematologic(923;0.127)		STAD - Stomach adenocarcinoma(528;0.133)|LUSC - Lung squamous cell carcinoma(543;0.221)			ATCATCCCTCGTCACCTCCAG	0.632																																					p.R82P		Atlas-SNP	.											.	HIST2H2AC	75	.	0			c.G245C						.						53	56	55					1																	149858769		2203	4295	6498	SO:0001583	missense	8338	exon1			TCCCTCGTCACCT	AY131973	CCDS937.1	1q21.2	2011-01-27	2006-10-11	2003-02-21	ENSG00000184260	ENSG00000184260		"Histones / Replication-dependent"	4738	protein-coding gene	gene with protein product		602797	"H2A histone family, member Q", "histone 2, H2ac"	H2A, H2AFQ		1469070, 9439656, 12408966	Standard	NM_003517		Approved	H2A/q	uc001etd.3	Q16777	OTTHUMG00000035825	ENST00000331380.2:c.245G>C	chr1.hg19:g.149858769G>C	ENSP00000332194:p.Arg82Pro	220.0	0.0		406.0	125.0	NM_003517	Q6DRA7|Q8IUE5	Missense_Mutation	SNP	ENST00000331380.2	hg19	CCDS937.1	.	.	.	.	.	.	.	.	.	.	G	13.58	2.280744	0.40294	.	.	ENSG00000184260	ENST00000331380	T	0.72505	-0.66	5.56	5.56	0.83823	Histone-fold (2);Histone core (1);Histone H2A (2);	0.000000	0.44688	D	0.000431	D	0.90721	0.7088	H	0.99104	4.43	0.43145	D	0.994908	D	0.89917	1.0	D	0.97110	1.0	D	0.94356	0.7583	10	0.87932	D	0	.	18.1154	0.89553	0.0:0.0:1.0:0.0	.	82	Q16777	H2A2C_HUMAN	P	82	ENSP00000332194:R82P	ENSP00000332194:R82P	R	+	2	0	HIST2H2AC	148125393	1.000000	0.71417	0.878000	0.34440	0.407000	0.30961	7.793000	0.85851	2.629000	0.89072	0.655000	0.94253	CGT	.	.		0.632	HIST2H2AC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087128.1	NM_003517		C	149858769	G	C	149858769	3	2	344	1	0	0	0	0	1	0	0	0	7187	1145	40	4	247	4	HIST2H2AC	1	149858769	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	2477929	149858769	99391852	85	47448										
ADAMTSL4	54507	hgsc.bcm.edu	37	chr1	150526448	150526448	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gggactcctcacgggccccgCctggagcctgaccctcagca	12	18	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:150526448C>A	ENST00000369038.2	+	4	1182	c.981C>A	c.(979-981)cgC>cgA	p.R327R	MIR4257_ENST00000581735.1_RNA|RP11-54A4.2_ENST00000442435.2_RNA|ADAMTSL4_ENST00000369039.5_Silent_p.R327R|ADAMTSL4_ENST00000369041.5_Silent_p.R327R|ADAMTSL4_ENST00000271643.4_Silent_p.R327R			Q6UY14	ATL4_HUMAN	ADAMTS-like 4	327					apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|positive regulation of apoptotic process (GO:0043065)	interstitial matrix (GO:0005614)	metalloendopeptidase activity (GO:0004222)|protease binding (GO:0002020)			breast(1)|cervix(1)|endometrium(6)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(3)	32	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			ACGGGCCCCGCCTGGAGCCTG	0.701																																					p.R327R		Atlas-SNP	.											.	ADAMTSL4	101	.	0			c.C981A						.						9	12	11					1																	150526448		2176	4251	6427	SO:0001819	synonymous_variant	54507	exon6			GCCCCGCCTGGAG	BC027478	CCDS955.1, CCDS30852.1, CCDS72908.1	1q21.2	2008-02-05	2005-12-01	2005-12-01	ENSG00000143382	ENSG00000143382			19706	protein-coding gene	gene with protein product		610113	"thrombospondin repeat containing 1"	TSRC1		12706885	Standard	NM_019032		Approved	DKFZP434K1772	uc001eux.3	Q6UY14	OTTHUMG00000034863	ENST00000369038.2:c.981C>A	chr1.hg19:g.150526448C>A		44.0	0.0		102.0	27.0	NM_019032	B2RTT0|F8WAD0|Q5T5F7|Q6IPM6|Q8N643|Q9HBS6	Silent	SNP	ENST00000369038.2	hg19	CCDS955.1																																																																																			.	.		0.701	ADAMTSL4-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084395.4	NM_019032		A	150526448	C	A	150526448	2	1	344	1	0	0	0	0	0	0	0	1	277	726	26	3		3	ADAMTSL4	1	150526448	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	667679	150526448	98724173	86	47449										
BNIPL	149428	hgsc.bcm.edu	37	chr1	151018276	151018276	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctcatgttgtttttcaggctAcggaaaaacctgcgagccct	9	11	2	0	rs370988337		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:151018276A>G	ENST00000368931.3	+	8	1011	c.855A>G	c.(853-855)ctA>ctG	p.L285L	C1orf56_ENST00000368926.5_5'Flank|BNIPL_ENST00000491386.1_3'UTR|BNIPL_ENST00000295294.7_Silent_p.L203L	NM_138278.3	NP_612122.2	Q7Z465	BNIPL_HUMAN	BCL2/adenovirus E1B 19kD interacting protein like	285	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)|regulation of growth rate (GO:0040009)	cytosol (GO:0005829)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			autonomic_ganglia(1)|endometrium(3)|large_intestine(1)|lung(4)|skin(1)	10	Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			TTTTCAGGCTACGGAAAAACC	0.443																																					p.L285L		Atlas-SNP	.											.	BNIPL	45	.	0			c.A855G						.	A	,	0,4406		0,0,2203	144	128	133		609,855	-0.2	1	1		133	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	BNIPL	NM_001159642.1,NM_138278.3	,	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	,	203/276,285/358	151018276	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	149428	exon8			CAGGCTACGGAAA	AF193056	CCDS978.2, CCDS53362.1	1q21.2	2008-02-05			ENSG00000163141	ENSG00000163141			16976	protein-coding gene	gene with protein product		611275				12681488, 11741952	Standard	NM_138278		Approved	BNIPl-1, BNIPL-2, PP753	uc001ewl.2	Q7Z465	OTTHUMG00000035157	ENST00000368931.3:c.855A>G	chr1.hg19:g.151018276A>G		68.0	0.0		153.0	54.0	NM_138278	Q6DK43|Q8TCY7|Q8WYG2	Silent	SNP	ENST00000368931.3	hg19	CCDS978.2																																																																																			.	.		0.443	BNIPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085092.1	NM_138279		G	151018276	A	G	151018276	2	3	344	1	0	0	0	0	0	0	0	1	1480	378	14	2		2	BNIPL	1	151018276	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	491828	151018276	98232345	87	47450										
POGZ	23126	hgsc.bcm.edu	37	chr1	151403269	151403269	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccagacctggggctggattcTgggtcaggatgagtggctgt	17	8	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:151403269T>C	ENST00000271715.2	-	4	646	c.332A>G	c.(331-333)cAg>cGg	p.Q111R	POGZ_ENST00000409503.1_Missense_Mutation_p.Q111R|POGZ_ENST00000368863.2_Intron|POGZ_ENST00000531094.1_Missense_Mutation_p.Q58R|POGZ_ENST00000392723.1_Missense_Mutation_p.Q58R|POGZ_ENST00000361398.3_Missense_Mutation_p.Q58R|POGZ_ENST00000491586.1_Missense_Mutation_p.Q58R|POGZ_ENST00000540984.1_5'UTR	NM_001194937.1|NM_015100.3	NP_001181866.1|NP_055915.2	Q7Z3K3	POGZ_HUMAN	pogo transposable element with ZNF domain	111					kinetochore assembly (GO:0051382)|mitotic sister chromatid cohesion (GO:0007064)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(10)|kidney(3)|large_intestine(10)|liver(2)|lung(11)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	47	Lung SC(34;0.00471)|Ovarian(49;0.00672)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			GGCTGGATTCTGGGTCAGGAT	0.473																																					p.Q111R		Atlas-SNP	.											.	POGZ	211	.	0			c.A332G						.						101	101	101					1																	151403269		2203	4300	6503	SO:0001583	missense	23126	exon4			GGATTCTGGGTCA	AB007930	CCDS997.1, CCDS998.1, CCDS44222.1, CCDS44222.2, CCDS53365.1, CCDS53366.1	1q21.1	2013-07-22			ENSG00000143442	ENSG00000143442			18801	protein-coding gene	gene with protein product	"zinc finger protein 280E", "putative protein product of Nbla00003"	614787				10976766	Standard	NM_015100		Approved	KIAA0461, ZNF635m, ZNF280E	uc001eyd.2	Q7Z3K3	OTTHUMG00000012499	ENST00000271715.2:c.332A>G	chr1.hg19:g.151403269T>C	ENSP00000271715:p.Gln111Arg	61.0	0.0		128.0	47.0	NM_015100	B4DTP8|B4DYL9|B7ZBY5|E9PM80|O75049|Q3LIC4|Q5SZS1|Q5SZS2|Q5SZS3|Q5SZS4|Q8TDZ7|Q9Y4X7	Missense_Mutation	SNP	ENST00000271715.2	hg19	CCDS997.1	.	.	.	.	.	.	.	.	.	.	T	17.18	3.323163	0.60634	.	.	ENSG00000143442	ENST00000392723;ENST00000271715;ENST00000361398;ENST00000409503;ENST00000531094;ENST00000491586;ENST00000437847;ENST00000533461;ENST00000533351;ENST00000450842	T;T;T;T;T;T	0.01279	5.64;5.8;5.64;5.78;5.59;5.06	5.21	5.21	0.72293	.	0.000000	0.64402	D	0.000014	T	0.01489	0.0048	N	0.14661	0.345	0.80722	D	1	P;P;P;P;P;B	0.52316	0.851;0.596;0.952;0.718;0.908;0.396	P;B;B;B;P;B	0.61397	0.775;0.098;0.269;0.101;0.888;0.099	T	0.72047	-0.4408	10	0.62326	D	0.03	-15.1136	14.0635	0.64815	0.0:0.0:0.0:1.0	.	58;111;111;58;58;111	E9PM80;B7ZBY5;Q7Z3K3-4;Q7Z3K3-3;Q7Z3K3-2;Q7Z3K3	.;.;.;.;.;POGZ_HUMAN	R	58;111;58;111;58;58;111;111;111;58	ENSP00000376484:Q58R;ENSP00000271715:Q111R;ENSP00000354467:Q58R;ENSP00000386836:Q111R;ENSP00000431259:Q58R;ENSP00000418408:Q58R	ENSP00000271715:Q111R	Q	-	2	0	POGZ	149669893	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.956000	0.63645	2.187000	0.69744	0.477000	0.44152	CAG	.	.		0.473	POGZ-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034915.2	NM_207171		C	151403269	T	C	151403269	3	2	344	1	0	0	0	0	1	0	0	0	12195	1580	55	2	3978	2	POGZ	1	151403269	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	384993	151403269	97847352	88	47451										
FLG	2312	hgsc.bcm.edu	37	chr1	152286887	152286887	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgaatatccttttctttcttTtttttcagaactagattcat	3	7	4	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:152286887T>C	ENST00000368799.1	-	3	510	c.475A>G	c.(475-477)Aaa>Gaa	p.K159E	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	159					establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TTTCTTTCTTTTTTTTCAGAA	0.348									Ichthyosis																												p.K159E		Atlas-SNP	.											.	FLG	900	.	0			c.A475G						.						123	133	130					1																	152286887		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TTTCTTTTTTTTC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.475A>G	chr1.hg19:g.152286887T>C	ENSP00000357789:p.Lys159Glu	58.0	0.0		111.0	80.0	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	hg19	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	T	12.85	2.060701	0.36373	.	.	ENSG00000143631	ENST00000368799	T	0.00646	6.0	4.82	-7.61	0.01299	.	.	.	.	.	T	0.00109	0.0003	N	0.02539	-0.55	0.09310	N	1	D	0.53885	0.963	P	0.47299	0.543	T	0.51340	-0.8718	9	0.05351	T	0.99	-0.8351	10.092	0.42453	0.0:0.1858:0.1437:0.6705	.	159	P20930	FILA_HUMAN	E	159	ENSP00000357789:K159E	ENSP00000357789:K159E	K	-	1	0	FLG	150553511	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.333000	0.01108	-0.925000	0.03775	-0.446000	0.05623	AAA	.	.		0.348	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		C	152286887	T	C	152286887	3	2	344	1	0	0	0	0	1	0	0	0	5930	1850	64	2	11714	2	FLG	1	152286887	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	883618	152286887	96963734	89	47452										
LCE2D	353141	hgsc.bcm.edu	37	chr1	152636872	152636872	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgctgtgagagtgaaccttcTggggcctctggctgctgcca	14	11	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:152636872T>C	ENST00000368784.1	+	2	346	c.291T>C	c.(289-291)tcT>tcC	p.S97S		NM_178430.2	NP_848517.1	Q5TA82	LCE2D_HUMAN	late cornified envelope 2D	97	Cys-rich.				keratinization (GO:0031424)					large_intestine(1)|lung(7)|prostate(2)	10	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			GTGAACCTTCTGGGGCCTCTG	0.642																																					p.S97S		Atlas-SNP	.											.	LCE2D	26	.	0			c.T291C						.						41	51	48					1																	152636872		2191	4282	6473	SO:0001819	synonymous_variant	353141	exon2			ACCTTCTGGGGCC	BI670513	CCDS1018.1	1q21.3	2008-02-05	2004-10-11	2004-10-15	ENSG00000187223	ENSG00000187223		"Late cornified envelopes"	16518	protein-coding gene	gene with protein product		612612	"small proline rich-like (epidermal differentiation complex) 1A"	SPRL1A		11698679	Standard	NM_178430		Approved	LEP12	uc001fag.4	Q5TA82	OTTHUMG00000014400	ENST00000368784.1:c.291T>C	chr1.hg19:g.152636872T>C		73.0	0.0		137.0	25.0	NM_178430	A1L4M8	Silent	SNP	ENST00000368784.1	hg19	CCDS1018.1																																																																																			.	.		0.642	LCE2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040058.1	NM_178430		C	152636872	T	C	152636872	2	2	344	1	0	0	0	0	0	0	0	1	8677	1567	55	2		2	LCE2D	1	152636872	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	349985	152636872	96613749	90	47453										
SPRR4	163778	hgsc.bcm.edu	37	chr1	152944426	152944426	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccaccccagagggcccagcaGcagcaagtgaagcagccttg	12	15	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:152944426G>T	ENST00000328051.2	+	2	109	c.60G>T	c.(58-60)caG>caT	p.Q20H		NM_173080.1	NP_775103.1	Q96PI1	SPRR4_HUMAN	small proline-rich protein 4	20	Gln-rich.				keratinization (GO:0031424)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)				lung(1)|prostate(1)	2	Lung NSC(65;1.46e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			GGGCCCAGCAGCAGCAAGTGA	0.572																																					p.Q20H		Atlas-SNP	.											.	SPRR4	8	.	0			c.G60T						.						104	97	100					1																	152944426		2203	4300	6503	SO:0001583	missense	163778	exon2			CCAGCAGCAGCAA	AF335109	CCDS1031.1	1q21.3	2008-02-05	2006-11-29		ENSG00000184148	ENSG00000184148			23173	protein-coding gene	gene with protein product						11719550, 11279051	Standard	NM_173080		Approved		uc001fav.1	Q96PI1	OTTHUMG00000012450	ENST00000328051.2:c.60G>T	chr1.hg19:g.152944426G>T	ENSP00000332163:p.Gln20His	148.0	0.0		282.0	224.0	NM_173080	Q2M1Y7|Q5T522	Missense_Mutation	SNP	ENST00000328051.2	hg19	CCDS1031.1	.	.	.	.	.	.	.	.	.	.	G	8.546	0.874408	0.17395	.	.	ENSG00000184148	ENST00000328051	T	0.14893	2.47	4.75	4.75	0.60458	.	.	.	.	.	T	0.28732	0.0712	.	.	.	0.32138	N	0.585828	D	0.76494	0.999	D	0.67900	0.954	T	0.04360	-1.0957	8	0.87932	D	0	-2.064	13.1165	0.59303	0.0:0.0:1.0:0.0	.	20	Q96PI1	SPRR4_HUMAN	H	20	ENSP00000332163:Q20H	ENSP00000332163:Q20H	Q	+	3	2	SPRR4	151211050	1.000000	0.71417	1.000000	0.80357	0.311000	0.27955	2.519000	0.45546	2.461000	0.83175	0.460000	0.39030	CAG	.	.		0.572	SPRR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034663.1	NM_173080		T	152944426	G	T	152944426	3	4	344	1	0	0	0	0	1	0	0	0	15119	962	34	3	62	3	SPRR4	1	152944426	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	307554	152944426	96306195	91	47454										
SPRR2F	6705	hgsc.bcm.edu	37	chr1	153085091	153085091	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtgggcaggactgtggacacTttgatggtgggcagggctca	18	7	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:153085091T>C	ENST00000468739.1	-	2	179	c.119A>G	c.(118-120)aAg>aGg	p.K40R	SPRR2B_ENST00000368752.4_Intron	NM_001014450.1	NP_001014450.1	Q96RM1	SPR2F_HUMAN	small proline-rich protein 2F	40	3 X 9 AA tandem repeats of [PS]-K-C-P- [EQ]-[PS]-C-P-P.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)				large_intestine(1)|lung(1)|prostate(1)|urinary_tract(1)	4	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CTGTGGACACTTTGATGGTGG	0.622																																					p.K40R		Atlas-SNP	.											.	SPRR2F	12	.	0			c.A119G						.						214	188	197					1																	153085091		2203	4300	6503	SO:0001583	missense	6705	exon2			GGACACTTTGATG	AF333956	CCDS30867.1	1q21-q22	2008-02-05			ENSG00000244094	ENSG00000244094			11266	protein-coding gene	gene with protein product						8325635, 11279051	Standard	NM_001014450		Approved		uc001fbi.3	Q96RM1	OTTHUMG00000014398	ENST00000468739.1:c.119A>G	chr1.hg19:g.153085091T>C	ENSP00000418193:p.Lys40Arg	52.0	0.0		83.0	9.0	NM_001014450	Q5T9T3	Missense_Mutation	SNP	ENST00000468739.1	hg19	CCDS30867.1	.	.	.	.	.	.	.	.	.	.	T	2.131	-0.399029	0.04865	.	.	ENSG00000244094	ENST00000468739	T	0.32753	1.44	3.72	-1.45	0.08828	.	0.942785	0.08679	N	0.909641	T	0.06371	0.0164	.	.	.	0.09310	N	1	B	0.12630	0.006	B	0.12156	0.007	T	0.39522	-0.9610	9	0.87932	D	0	.	0.3353	0.00325	0.1879:0.2303:0.1936:0.3882	.	40	Q96RM1	SPR2F_HUMAN	R	40	ENSP00000418193:K40R	ENSP00000418193:K40R	K	-	2	0	SPRR2F	151351715	0.001000	0.12720	0.000000	0.03702	0.028000	0.11728	-0.001000	0.12947	-0.129000	0.11620	0.254000	0.18369	AAG	.	.		0.622	SPRR2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040056.1			C	153085091	T	C	153085091	3	2	344	1	0	0	0	0	1	0	0	0	15116	1609	56	2	103	2	SPRR2F	1	153085091	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	140665	153085091	96165530	92	47455										
NPR1	4881	hgsc.bcm.edu	37	chr1	153661567	153661567	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaggccctgctctaccagatCctgcctcagtgagtgcctga	11	14	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:153661567C>T	ENST00000368680.3	+	16	3028	c.2556C>T	c.(2554-2556)atC>atT	p.I852I		NM_000906.3	NP_000897.3	P16066	ANPRA_HUMAN	natriuretic peptide receptor 1	852					body fluid secretion (GO:0007589)|cell surface receptor signaling pathway (GO:0007166)|cGMP biosynthetic process (GO:0006182)|dopamine metabolic process (GO:0042417)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cGMP biosynthetic process (GO:0030828)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|regulation of blood vessel size (GO:0050880)|regulation of vascular permeability (GO:0043114)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|G-protein coupled peptide receptor activity (GO:0008528)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(17)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)		Amyl Nitrite(DB01612)|Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Nesiritide(DB04899)|Nitroglycerin(DB00727)|Nitroprusside(DB00325)	TCTACCAGATCCTGCCTCAGT	0.622																																					p.I852I	Pancreas(141;1349 1870 15144 15830 40702)	Atlas-SNP	.											.	NPR1	104	.	0			c.C2556T						.						110	103	105					1																	153661567		2203	4300	6503	SO:0001819	synonymous_variant	4881	exon16			CCAGATCCTGCCT	BC063304	CCDS1051.1	1q21-q22	2014-03-03	2014-03-03		ENSG00000169418	ENSG00000169418			7943	protein-coding gene	gene with protein product	"guanylate cyclase A"	108960	"atrionatriuretic peptide receptor A", "natriuretic peptide receptor A"	ANPRA, NPRA		1979052	Standard	NM_000906		Approved	GUCY2A, ANPa	uc001fcs.4	P16066	OTTHUMG00000037085	ENST00000368680.3:c.2556C>T	chr1.hg19:g.153661567C>T		90.0	0.0		168.0	125.0	NM_000906	B0ZBF0|Q5SR08|Q6P4Q3	Silent	SNP	ENST00000368680.3	hg19	CCDS1051.1																																																																																			.	.		0.622	NPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090034.1	NM_000906		T	153661567	C	T	153661567	2	4	344	1	0	0	0	0	0	0	0	1	10603	845	30	3		3	NPR1	1	153661567	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	576476	153661567	95589054	93	47456										
AQP10	89872	hgsc.bcm.edu	37	chr1	154294415	154294415	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cctcttctcagcagctcctcAcccaaggagctgtggcccag	9	17	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:154294415A>T	ENST00000324978.3	+	2	152	c.112A>T	c.(112-114)Acc>Tcc	p.T38S	AQP10_ENST00000355197.4_Intron|AQP10_ENST00000484864.1_Missense_Mutation_p.T38S	NM_080429.2	NP_536354.2	Q96PS8	AQP10_HUMAN	aquaporin 10	38					response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(14)|stomach(2)|upper_aerodigestive_tract(1)	23	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			GCAGCTCCTCACCCAAGGAGC	0.562																																					p.T38S		Atlas-SNP	.											.	AQP10	44	.	0			c.A112T						.						35	33	34					1																	154294415		2203	4298	6501	SO:0001583	missense	89872	exon2			CTCCTCACCCAAG	AF159174	CCDS1065.1	1q21.3	2008-02-05			ENSG00000143595	ENSG00000143595		"Ion channels / Aquaporins"	16029	protein-coding gene	gene with protein product		606578				11573934	Standard	NM_080429		Approved		uc001feu.3	Q96PS8	OTTHUMG00000035980	ENST00000324978.3:c.112A>T	chr1.hg19:g.154294415A>T	ENSP00000318355:p.Thr38Ser	128.0	0.0		271.0	42.0	NM_080429	Q5VYD3|Q5VYD4|Q8NG70	Missense_Mutation	SNP	ENST00000324978.3	hg19	CCDS1065.1	.	.	.	.	.	.	.	.	.	.	A	19.00	3.742219	0.69418	.	.	ENSG00000143595	ENST00000324978;ENST00000484864	D;D	0.85258	-1.96;-1.96	5.1	5.1	0.69264	Aquaporin-like (2);	0.182943	0.48286	D	0.000197	T	0.72622	0.3483	L	0.39020	1.185	0.25931	N	0.982995	B;P	0.47191	0.049;0.891	B;B	0.43225	0.037;0.412	T	0.71407	-0.4602	10	0.87932	D	0	.	13.834	0.63398	1.0:0.0:0.0:0.0	.	38;38	Q96PS8-2;Q96PS8	.;AQP10_HUMAN	S	38	ENSP00000318355:T38S;ENSP00000420341:T38S	ENSP00000318355:T38S	T	+	1	0	AQP10	152561039	1.000000	0.71417	0.984000	0.44739	0.658000	0.38924	3.957000	0.56730	2.142000	0.66516	0.418000	0.28097	ACC	.	.		0.562	AQP10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087661.1	NM_080429		T	154294415	A	T	154294415	3	4	344	1	0	0	0	0	1	0	0	0	822	159	6	4	118	4	AQP10	1	154294415	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	632848	154294415	94956206	94	47457										
ADAR	103	hgsc.bcm.edu	37	chr1	154573591	154573591	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctagcgaactgggcatattcTaacagcccgctgatggggtt	12	10	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:154573591T>C	ENST00000368474.4	-	2	1726	c.1527A>G	c.(1525-1527)ttA>ttG	p.L509L	ADAR_ENST00000471068.1_5'Flank|ADAR_ENST00000368471.3_Silent_p.L214L|ADAR_ENST00000292205.5_Silent_p.L552L	NM_001111.4|NM_015840.3|NM_015841.3	NP_001102|NP_056655.2|NP_056656.2	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific	509	DRBM 1. {ECO:0000255|PROSITE- ProRule:PRU00266}.				adenosine to inosine editing (GO:0006382)|base conversion or substitution editing (GO:0016553)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|miRNA loading onto RISC involved in gene silencing by miRNA (GO:0035280)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of viral genome replication (GO:0045071)|positive regulation of viral genome replication (GO:0045070)|pre-miRNA processing (GO:0031054)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(4)|prostate(2)|skin(2)	51	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)		GGGCATATTCTAACAGCCCGC	0.522																																					p.L509L		Atlas-SNP	.											.	ADAR	113	.	0			c.A1527G						.						99	101	100					1																	154573591		2203	4300	6503	SO:0001819	synonymous_variant	103	exon2			ATATTCTAACAGC	BC038227	CCDS1071.1, CCDS30879.1	1q21.3	2012-03-22			ENSG00000160710	ENSG00000160710	3.5.4.-		225	protein-coding gene	gene with protein product		146920	"interferon-induced protein 4"	IFI4, G1P1		7972084	Standard	NM_001111		Approved	ADAR1	uc001ffh.3	P55265	OTTHUMG00000037261	ENST00000368474.4:c.1527A>G	chr1.hg19:g.154573591T>C		83.0	0.0		204.0	65.0	NM_001111	B1AQQ9|B1AQR0|D3DV76|O15223|O43859|O43860|Q9BYM3|Q9BYM4	Silent	SNP	ENST00000368474.4	hg19	CCDS1071.1																																																																																			.	.		0.522	ADAR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090691.2	NM_001111		C	154573591	T	C	154573591	2	2	344	1	0	0	0	0	0	0	0	1	281	1519	53	2		2	ADAR	1	154573591	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	279176	154573591	94677030	95	47458										
CLK2	1196	hgsc.bcm.edu	37	chr1	155234093	155234093	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gctctctgttgtcatgggtcTgggaaacaaaaacagaactg	11	8	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:155234093T>A	ENST00000368361.4	-	11	1462		c.e11-2		CLK2_ENST00000497188.1_5'UTR|SCAMP3_ENST00000302631.3_5'Flank|CLK2_ENST00000536801.1_Splice_Site|CLK2_ENST00000355560.4_Splice_Site|CLK2_ENST00000361168.5_Splice_Site|SCAMP3_ENST00000355379.3_5'Flank			P49760	CLK2_HUMAN	CDC-like kinase 2						negative regulation of gluconeogenesis (GO:0045721)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of RNA splicing (GO:0043484)|response to ionizing radiation (GO:0010212)|response to retinoic acid (GO:0032526)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			endometrium(4)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	22	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			GTCATGGGTCTGGGAAACAAA	0.522								Other conserved DNA damage response genes																													.		Atlas-SNP	.											.	CLK2	55	.	0			c.1144-2A>T						.						88	82	84					1																	155234093		2203	4300	6503	SO:0001630	splice_region_variant	1196	exon12			TGGGTCTGGGAAA	L29218	CCDS1107.1, CCDS72939.1	1q21	2008-05-02			ENSG00000176444	ENSG00000176444		"CDC-like kinases"	2069	protein-coding gene	gene with protein product		602989				7990150, 9856501	Standard	XM_005244876		Approved	clk2	uc001fjw.3	P49760	OTTHUMG00000035873	ENST00000368361.4:c.1147-2A>T	chr1.hg19:g.155234093T>A		175.0	1.0		345.0	239.0	NM_003993	B1AVS9|B5MBX6|Q96CQ0	Splice_Site	SNP	ENST00000368361.4	hg19		.	.	.	.	.	.	.	.	.	.	T	19.45	3.830769	0.71258	.	.	ENSG00000176444	ENST00000361168;ENST00000368361;ENST00000355560;ENST00000424156;ENST00000536801	.	.	.	4.55	4.55	0.56014	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.1447	0.59454	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	CLK2	153500717	1.000000	0.71417	0.977000	0.42913	0.886000	0.51366	7.802000	0.85969	2.045000	0.60652	0.454000	0.30748	.	.	.		0.522	CLK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000087391.1	NM_003993	Intron	A	155234093	T	A	155234093	5	1	344	1	0	0	0	0	0	0	1	0	3539	1594	55	4	366	4	CLK2	1	155234093	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	660502	155234093	94016528	96	47459										
ASH1L	55870	hgsc.bcm.edu	37	chr1	155451023	155451023	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctttctcctactgcactgaaTggggatttagcggtagatac	10	9	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:155451023T>C	ENST00000368346.3	-	3	2277	c.1638A>G	c.(1636-1638)ccA>ccG	p.P546P	ASH1L_ENST00000392403.3_Silent_p.P546P			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	546					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			CTGCACTGAATGGGGATTTAG	0.448																																					p.P546P		Atlas-SNP	.											.	ASH1L	279	.	0			c.A1638G						.						115	116	115					1																	155451023		2203	4300	6503	SO:0001819	synonymous_variant	55870	exon3			ACTGAATGGGGAT	AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.1638A>G	chr1.hg19:g.155451023T>C		54.0	0.0		133.0	26.0	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Silent	SNP	ENST00000368346.3	hg19																																																																																				.	.		0.448	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		C	155451023	T	C	155451023	2	2	344	1	0	0	0	0	0	0	0	1	1041	1451	51	2		2	ASH1L	1	155451023	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	216930	155451023	93799598	97	47460										
SYT11	23208	hgsc.bcm.edu	37	chr1	155838371	155838371	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaagaccagagtgctgcggaAgaccctggaccctgtgtttg	14	10	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:155838371A>G	ENST00000368324.4	+	2	903	c.650A>G	c.(649-651)aAg>aGg	p.K217R	SYT11_ENST00000539162.1_Intron	NM_152280.4	NP_689493.3	Q9BT88	SYT11_HUMAN	synaptotagmin XI	217	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				negative regulation of neurotransmitter secretion (GO:0046929)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)			breast(2)|central_nervous_system(1)|endometrium(1)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;0.000162)			GTGCTGCGGAAGACCCTGGAC	0.557																																					p.K217R		Atlas-SNP	.											.	SYT11	55	.	0			c.A650G						.						108	90	96					1																	155838371		2203	4300	6503	SO:0001583	missense	23208	exon2			TGCGGAAGACCCT	D38522	CCDS1122.1	1q22	2013-01-21			ENSG00000132718	ENSG00000132718		"Synaptotagmins"	19239	protein-coding gene	gene with protein product		608741				11543631	Standard	NM_152280		Approved	KIAA0080, MGC10881, MGC17226, DKFZp781D015	uc001fmg.3	Q9BT88	OTTHUMG00000014105	ENST00000368324.4:c.650A>G	chr1.hg19:g.155838371A>G	ENSP00000357307:p.Lys217Arg	144.0	0.0		219.0	72.0	NM_152280	Q14998|Q5W0D4|Q68CT5|Q8IXU3|Q96SU2	Missense_Mutation	SNP	ENST00000368324.4	hg19	CCDS1122.1	.	.	.	.	.	.	.	.	.	.	A	18.77	3.695227	0.68386	.	.	ENSG00000132718	ENST00000368324	T	0.70869	-0.52	5.97	4.85	0.62838	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.53126	0.1777	L	0.33485	1.01	0.49687	D	0.999811	P	0.42203	0.773	P	0.44990	0.466	T	0.60306	-0.7289	10	0.49607	T	0.09	.	11.2541	0.49043	0.9285:0.0:0.0715:0.0	.	217	Q9BT88	SYT11_HUMAN	R	217	ENSP00000357307:K217R	ENSP00000357307:K217R	K	+	2	0	SYT11	154104995	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.341000	0.65964	2.281000	0.76405	0.533000	0.62120	AAG	.	.		0.557	SYT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039597.1	NM_152280		G	155838371	A	G	155838371	3	3	344	1	0	0	0	0	1	0	0	0	15482	72	3	2	656	2	SYT11	1	155838371	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	387348	155838371	93412250	98	47461										
BCAN	63827	hgsc.bcm.edu	37	chr1	156622305	156622305	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctgcagcctggtgcatcaccActtcctgatggagagtcaga	11	12	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:156622305A>T	ENST00000329117.5	+	8	1899	c.1563A>T	c.(1561-1563)ccA>ccT	p.P521P	BCAN_ENST00000361588.5_Silent_p.P521P|RP11-284F21.7_ENST00000448869.1_RNA	NM_021948.4	NP_068767.3	Q96GW7	PGCB_HUMAN	brevican	521	O-glycosylated at two sites.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hippocampus development (GO:0021766)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	55	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GTGCATCACCACTTCCTGATG	0.637																																					p.P521P		Atlas-SNP	.											.	BCAN	174	.	0			c.A1563T						.						24	23	24					1																	156622305		2203	4298	6501	SO:0001819	synonymous_variant	63827	exon8			ATCACCACTTCCT	BC027971	CCDS1149.1, CCDS1150.1	1q31	2013-05-07			ENSG00000132692	ENSG00000132692		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	23059	protein-coding gene	gene with protein product	"chondroitin sulfate proteoglycan 7", "brevican proteoglycan"	600347				11054543, 11873941	Standard	NM_021948		Approved	BEHAB, MGC13038, CSPG7	uc001fpp.3	Q96GW7	OTTHUMG00000033322	ENST00000329117.5:c.1563A>T	chr1.hg19:g.156622305A>T		84.0	0.0		125.0	23.0	NM_198427	D3DVC2|Q5SZ10|Q5T3I5|Q8TBB9|Q9HBK1|Q9HBK4	Silent	SNP	ENST00000329117.5	hg19	CCDS1149.1																																																																																			.	.		0.637	BCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081844.2	NM_021948		T	156622305	A	T	156622305	2	4	344	1	0	0	0	0	0	0	0	1	1345	146	6	4		4	BCAN	1	156622305	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	783934	156622305	92628316	99	47462										
FCRL5	83416	hgsc.bcm.edu	37	chr1	157488541	157488541	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggctggtacattgtgataggTgggctcttgggagtccgagt	17	6	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:157488541T>A	ENST00000361835.3	-	14	2849	c.2692A>T	c.(2692-2694)Acc>Tcc	p.T898S	FCRL5_ENST00000356953.4_Missense_Mutation_p.T898S|FCRL5_ENST00000461387.1_5'UTR	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	898					negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(45)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	85	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)				TTGTGATAGGTGGGCTCTTGG	0.507																																					p.T898S		Atlas-SNP	.											.	FCRL5	177	.	0			c.A2692T						.						110	105	107					1																	157488541		2203	4300	6503	SO:0001583	missense	83416	exon14			GATAGGTGGGCTC	AF369794	CCDS1165.1	1q21	2013-01-11			ENSG00000143297	ENSG00000143297		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18508	protein-coding gene	gene with protein product		605877				11027651, 11290337	Standard	NM_031281		Approved	FCRH5, IRTA2, BXMAS1, CD307e	uc009wsm.3	Q96RD9	OTTHUMG00000017481	ENST00000361835.3:c.2692A>T	chr1.hg19:g.157488541T>A	ENSP00000354691:p.Thr898Ser	96.0	0.0		182.0	34.0	NM_031281	A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Missense_Mutation	SNP	ENST00000361835.3	hg19	CCDS1165.1	.	.	.	.	.	.	.	.	.	.	T	14.05	2.419230	0.42918	.	.	ENSG00000143297	ENST00000361835;ENST00000356953	T;T	0.47528	0.84;0.85	4.72	1.17	0.20885	.	4.957450	0.00582	N	0.000335	T	0.22742	0.0549	L	0.46885	1.475	0.80722	D	1	B;B	0.31193	0.312;0.312	B;B	0.32090	0.14;0.14	T	0.34079	-0.9843	10	0.25106	T	0.35	.	6.3103	0.21161	0.0:0.2992:0.0:0.7008	.	898;898	A6NJE8;Q96RD9	.;FCRL5_HUMAN	S	898	ENSP00000354691:T898S;ENSP00000349434:T898S	ENSP00000349434:T898S	T	-	1	0	FCRL5	155755165	0.988000	0.35896	0.994000	0.49952	0.406000	0.30931	0.585000	0.23879	0.388000	0.25054	-0.263000	0.10527	ACC	.	.		0.507	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1	NM_031281		A	157488541	T	A	157488541	3	1	344	1	0	0	0	0	1	0	0	0	5806	1696	59	4	257	4	FCRL5	1	157488541	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	866236	157488541	91762080	100	47463										
FCRL5	83416	hgsc.bcm.edu	37	chr1	157514159	157514159	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tactccacatggcagtaatcTggaaattcggggagagactc	11	9	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:157514159T>A	ENST00000361835.3	-	5	894	c.737A>T	c.(736-738)cAg>cTg	p.Q246L	FCRL5_ENST00000368190.3_Missense_Mutation_p.Q246L|FCRL5_ENST00000356953.4_Missense_Mutation_p.Q246L|FCRL5_ENST00000368191.3_Missense_Mutation_p.Q161L|FCRL5_ENST00000368189.3_Missense_Mutation_p.Q246L	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	246	Ig-like C2-type 2.				negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(45)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	85	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)				GGCAGTAATCTGGAAATTCGG	0.522																																					p.Q246L		Atlas-SNP	.											.	FCRL5	177	.	0			c.A737T						.						135	143	140					1																	157514159		2203	4300	6503	SO:0001583	missense	83416	exon5			GTAATCTGGAAAT	AF369794	CCDS1165.1	1q21	2013-01-11			ENSG00000143297	ENSG00000143297		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18508	protein-coding gene	gene with protein product		605877				11027651, 11290337	Standard	NM_031281		Approved	FCRH5, IRTA2, BXMAS1, CD307e	uc009wsm.3	Q96RD9	OTTHUMG00000017481	ENST00000361835.3:c.737A>T	chr1.hg19:g.157514159T>A	ENSP00000354691:p.Gln246Leu	145.0	1.0		274.0	198.0	NM_031281	A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Missense_Mutation	SNP	ENST00000361835.3	hg19	CCDS1165.1	.	.	.	.	.	.	.	.	.	.	T	15.09	2.730916	0.48939	.	.	ENSG00000143297	ENST00000361835;ENST00000356953;ENST00000368190;ENST00000368191;ENST00000368189	T;T;T;T;T	0.10288	2.89;2.89;2.89;2.89;2.89	4.3	-4.43	0.03568	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	2.478390	0.01739	N	0.029316	T	0.08268	0.0206	L	0.58669	1.825	0.09310	N	1	P;P;P;D;P	0.58620	0.944;0.88;0.903;0.983;0.903	P;B;P;P;P	0.57324	0.6;0.316;0.814;0.818;0.814	T	0.21965	-1.0230	10	0.23302	T	0.38	.	8.1502	0.31137	0.0:0.5288:0.1482:0.323	.	161;246;246;246;246	F5GXJ2;Q96RD9-3;A6NJE8;Q96RD9-4;Q96RD9	.;.;.;.;FCRL5_HUMAN	L	246;246;246;161;246	ENSP00000354691:Q246L;ENSP00000349434:Q246L;ENSP00000357173:Q246L;ENSP00000357174:Q161L;ENSP00000357172:Q246L	ENSP00000349434:Q246L	Q	-	2	0	FCRL5	155780783	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.385000	0.07379	-1.173000	0.02758	-0.371000	0.07208	CAG	.	.		0.522	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1	NM_031281		A	157514159	T	A	157514159	3	1	344	1	0	0	0	0	1	0	0	0	5806	1580	55	4	2248	4	FCRL5	1	157514159	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	25618	157514159	91736462	101	47464										
CD5L	922	hgsc.bcm.edu	37	chr1	157803106	157803106	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttatccagccagatgcggccAaccccagggccatagcattt	9	14	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:157803106A>C	ENST00000368174.4	-	5	1011	c.915T>G	c.(913-915)gtT>gtG	p.V305V	CD5L_ENST00000484609.1_5'Flank	NM_005894.2	NP_005885.1	O43866	CD5L_HUMAN	CD5 molecule-like	305	SRCR 3. {ECO:0000255|PROSITE- ProRule:PRU00196}.				apoptotic process (GO:0006915)|cellular defense response (GO:0006968)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	scavenger receptor activity (GO:0005044)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	52	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			AGATGCGGCCAACCCCAGGGC	0.587																																					p.V305V		Atlas-SNP	.											.	CD5L	112	.	0			c.T915G						.						102	103	103					1																	157803106		2203	4300	6503	SO:0001819	synonymous_variant	922	exon5			GCGGCCAACCCCA	U82812	CCDS1171.1	1q21-q23	2008-02-05	2006-03-28		ENSG00000073754	ENSG00000073754			1690	protein-coding gene	gene with protein product		602592	"apoptosis inhibitor 6", "CD5 antigen-like (scavenger receptor cysteine rich family)"	API6		9045627	Standard	NM_005894		Approved	Spalpha	uc001frk.4	O43866	OTTHUMG00000022440	ENST00000368174.4:c.915T>G	chr1.hg19:g.157803106A>C		146.0	0.0		250.0	174.0	NM_005894	A8K7M5|Q6UX63	Silent	SNP	ENST00000368174.4	hg19	CCDS1171.1																																																																																			.	.		0.587	CD5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058346.1	NM_005894		C	157803106	A	C	157803106	2	2	344	1	0	0	0	0	0	0	0	1	3029	117	5	5		5	CD5L	1	157803106	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	288947	157803106	91447515	102	47465										
CD5L	922	hgsc.bcm.edu	37	chr1	157803162	157803162	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gggagagagggacttcccacAgcccagttgcttgcatacca	12	12	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:157803162A>T	ENST00000368174.4	-	5	955	c.859T>A	c.(859-861)Tgt>Agt	p.C287S	CD5L_ENST00000484609.1_5'Flank	NM_005894.2	NP_005885.1	O43866	CD5L_HUMAN	CD5 molecule-like	287	SRCR 3. {ECO:0000255|PROSITE- ProRule:PRU00196}.				apoptotic process (GO:0006915)|cellular defense response (GO:0006968)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	scavenger receptor activity (GO:0005044)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	52	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			GACTTCCCACAGCCCAGTTGC	0.587																																					p.C287S		Atlas-SNP	.											.	CD5L	112	.	0			c.T859A						.						130	133	132					1																	157803162		2203	4300	6503	SO:0001583	missense	922	exon5			TCCCACAGCCCAG	U82812	CCDS1171.1	1q21-q23	2008-02-05	2006-03-28		ENSG00000073754	ENSG00000073754			1690	protein-coding gene	gene with protein product		602592	"apoptosis inhibitor 6", "CD5 antigen-like (scavenger receptor cysteine rich family)"	API6		9045627	Standard	NM_005894		Approved	Spalpha	uc001frk.4	O43866	OTTHUMG00000022440	ENST00000368174.4:c.859T>A	chr1.hg19:g.157803162A>T	ENSP00000357156:p.Cys287Ser	144.0	0.0		227.0	160.0	NM_005894	A8K7M5|Q6UX63	Missense_Mutation	SNP	ENST00000368174.4	hg19	CCDS1171.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.033407	0.75504	.	.	ENSG00000073754	ENST00000368174	T	0.38077	1.16	4.88	4.88	0.63580	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.000000	0.85682	D	0.000000	T	0.60779	0.2295	M	0.92691	3.335	0.52099	D	0.999946	D	0.89917	1.0	D	0.85130	0.997	T	0.71616	-0.4539	10	0.87932	D	0	.	12.4752	0.55809	1.0:0.0:0.0:0.0	.	287	O43866	CD5L_HUMAN	S	287	ENSP00000357156:C287S	ENSP00000357156:C287S	C	-	1	0	CD5L	156069786	1.000000	0.71417	0.979000	0.43373	0.565000	0.35776	8.804000	0.91921	2.032000	0.59987	0.533000	0.62120	TGT	.	.		0.587	CD5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058346.1	NM_005894		T	157803162	A	T	157803162	3	4	344	1	0	0	0	0	1	0	0	0	3029	188	7	4	192	4	CD5L	1	157803162	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	56	157803162	91447459	103	47466										
OR10Z1	128368	hgsc.bcm.edu	37	chr1	158576643	158576643	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atgccagccacatgaatcctAccctctgtgcccagctggtc	8	16	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:158576643A>T	ENST00000361284.1	+	1	415	c.415A>T	c.(415-417)Acc>Tcc	p.T139S		NM_001004478.1	NP_001004478.1	Q8NGY1	O10Z1_HUMAN	olfactory receptor, family 10, subfamily Z, member 1	139						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(6)|lung(21)|pancreas(1)|prostate(3)|skin(4)	37	all_hematologic(112;0.0378)					CATGAATCCTACCCTCTGTGC	0.512																																					p.T139S		Atlas-SNP	.											.	OR10Z1	99	.	0			c.A415T						.						92	92	92					1																	158576643		2203	4300	6503	SO:0001583	missense	128368	exon1			AATCCTACCCTCT	AB065635	CCDS30901.1	1q23.1	2012-08-23			ENSG00000198967	ENSG00000198967		"GPCR / Class A : Olfactory receptors"	14996	protein-coding gene	gene with protein product							Standard	NM_001004478		Approved		uc010pio.2	Q8NGY1	OTTHUMG00000019637	ENST00000361284.1:c.415A>T	chr1.hg19:g.158576643A>T	ENSP00000354707:p.Thr139Ser	107.0	0.0		169.0	40.0	NM_001004478	Q5VYL0|Q6IFR7	Missense_Mutation	SNP	ENST00000361284.1	hg19	CCDS30901.1	.	.	.	.	.	.	.	.	.	.	A	5.648	0.304147	0.10678	.	.	ENSG00000198967	ENST00000361284	T	0.36520	1.25	5.3	2.78	0.32641	GPCR, rhodopsin-like superfamily (1);	0.543732	0.15503	N	0.258921	T	0.05777	0.0151	N	0.11064	0.09	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.42565	-0.9444	10	0.17369	T	0.5	.	7.8879	0.29661	0.7964:0.0:0.2036:0.0	.	139	Q8NGY1	O10Z1_HUMAN	S	139	ENSP00000354707:T139S	ENSP00000354707:T139S	T	+	1	0	OR10Z1	156843267	0.000000	0.05858	0.003000	0.11579	0.784000	0.44337	-1.162000	0.03141	0.373000	0.24621	-0.256000	0.11100	ACC	.	.		0.512	OR10Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051853.1	NM_001004478		T	158576643	A	T	158576643	3	4	344	1	0	0	0	0	1	0	0	0	10932	391	14	4	417	4	OR10Z1	1	158576643	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	773481	158576643	90673978	104	47467										
OR10Z1	128368	hgsc.bcm.edu	37	chr1	158576656	158576656	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaatcctaccctctgtgcccAgctggtcattacttccttcc	6	16	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:158576656A>T	ENST00000361284.1	+	1	428	c.428A>T	c.(427-429)cAg>cTg	p.Q143L		NM_001004478.1	NP_001004478.1	Q8NGY1	O10Z1_HUMAN	olfactory receptor, family 10, subfamily Z, member 1	143						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(6)|lung(21)|pancreas(1)|prostate(3)|skin(4)	37	all_hematologic(112;0.0378)					CTCTGTGCCCAGCTGGTCATT	0.502																																					p.Q143L		Atlas-SNP	.											.	OR10Z1	99	.	0			c.A428T						.						89	89	89					1																	158576656		2203	4300	6503	SO:0001583	missense	128368	exon1			GTGCCCAGCTGGT	AB065635	CCDS30901.1	1q23.1	2012-08-23			ENSG00000198967	ENSG00000198967		"GPCR / Class A : Olfactory receptors"	14996	protein-coding gene	gene with protein product							Standard	NM_001004478		Approved		uc010pio.2	Q8NGY1	OTTHUMG00000019637	ENST00000361284.1:c.428A>T	chr1.hg19:g.158576656A>T	ENSP00000354707:p.Gln143Leu	107.0	0.0		179.0	138.0	NM_001004478	Q5VYL0|Q6IFR7	Missense_Mutation	SNP	ENST00000361284.1	hg19	CCDS30901.1	.	.	.	.	.	.	.	.	.	.	A	8.808	0.934520	0.18206	.	.	ENSG00000198967	ENST00000361284	T	0.00034	8.87	5.3	5.3	0.74995	GPCR, rhodopsin-like superfamily (1);	0.192595	0.25833	N	0.028005	T	0.00039	0.0001	N	0.20483	0.58	0.34455	D	0.70113	B	0.23377	0.084	B	0.26094	0.066	T	0.00166	-1.1965	10	0.06891	T	0.86	.	8.9164	0.35585	0.9163:0.0:0.0837:0.0	.	143	Q8NGY1	O10Z1_HUMAN	L	143	ENSP00000354707:Q143L	ENSP00000354707:Q143L	Q	+	2	0	OR10Z1	156843280	0.000000	0.05858	0.994000	0.49952	0.435000	0.31806	-0.130000	0.10498	2.219000	0.72066	0.533000	0.62120	CAG	.	.		0.502	OR10Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051853.1	NM_001004478		T	158576656	A	T	158576656	3	4	344	1	0	0	0	0	1	0	0	0	10932	188	7	4	430	4	OR10Z1	1	158576656	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	13	158576656	90673965	105	47468										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158627334	158627334	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gttccttctctctgatccatGtttctgcttcatgcaggtca	7	12	5	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:158627334G>A	ENST00000368147.4	-	19	2918	c.2738C>T	c.(2737-2739)aCa>aTa	p.T913I		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	913					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TCTGATCCATGTTTCTGCTTC	0.473																																					p.T913I		Atlas-SNP	.											.	SPTA1	720	.	0			c.C2738T						.						166	167	166					1																	158627334		1998	4186	6184	SO:0001583	missense	6708	exon19			ATCCATGTTTCTG	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.2738C>T	chr1.hg19:g.158627334G>A	ENSP00000357129:p.Thr913Ile	85.0	0.0		162.0	41.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	G	17.84	3.487145	0.63962	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.51325	0.71;0.71	4.68	4.68	0.58851	.	0.265155	0.19957	N	0.102285	T	0.40522	0.1120	L	0.52011	1.625	0.35735	D	0.818194	B	0.27951	0.195	B	0.39027	0.288	T	0.50668	-0.8801	10	0.72032	D	0.01	.	16.6727	0.85271	0.0:0.0:1.0:0.0	.	913	P02549	SPTA1_HUMAN	I	913	ENSP00000357130:T913I;ENSP00000357129:T913I	ENSP00000357129:T913I	T	-	2	0	SPTA1	156893958	1.000000	0.71417	0.938000	0.37757	0.989000	0.77384	8.424000	0.90267	2.569000	0.86673	0.655000	0.94253	ACA	.	.		0.473	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		A	158627334	G	A	158627334	3	1	344	1	0	0	0	0	1	0	0	0	15131	1377	48	3	4657	3	SPTA1	1	158627334	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	50678	158627334	90623287	106	47469										
OR6K2	81448	hgsc.bcm.edu	37	chr1	158669603	158669603	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttgaagaagggagacaaaacTgcaaaggccagagcaatggc	13	7	0	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:158669603T>C	ENST00000359610.2	-	1	883	c.840A>G	c.(838-840)gcA>gcG	p.A280A		NM_001005279.1	NP_001005279.1	Q8NGY2	OR6K2_HUMAN	olfactory receptor, family 6, subfamily K, member 2	280						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	46	all_hematologic(112;0.0378)					GAGACAAAACTGCAAAGGCCA	0.398																																					p.A280A		Atlas-SNP	.											.	OR6K2	104	.	0			c.A840G						.						101	97	99					1																	158669603		2203	4300	6503	SO:0001819	synonymous_variant	81448	exon1			CAAAACTGCAAAG	BK004196	CCDS30902.1	1q23.1	2012-08-09			ENSG00000196171	ENSG00000196171		"GPCR / Class A : Olfactory receptors"	15029	protein-coding gene	gene with protein product							Standard	NM_001005279		Approved		uc001fsu.1	Q8NGY2	OTTHUMG00000022768	ENST00000359610.2:c.840A>G	chr1.hg19:g.158669603T>C		228.0	0.0		408.0	93.0	NM_001005279	B9EH33|Q6IFR6	Silent	SNP	ENST00000359610.2	hg19	CCDS30902.1																																																																																			.	.		0.398	OR6K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059061.1	NM_001005279		C	158669603	T	C	158669603	2	2	344	1	0	0	0	0	0	0	0	1	11211	1567	55	2		2	OR6K2	1	158669603	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	42269	158669603	90581018	107	47470										
OR6K2	81448	hgsc.bcm.edu	37	chr1	158669632	158669632	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cagagcaatggctatatcccAgaacaaagagtaggtggcag	12	8	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:158669632A>T	ENST00000359610.2	-	1	854	c.811T>A	c.(811-813)Tgg>Agg	p.W271R		NM_001005279.1	NP_001005279.1	Q8NGY2	OR6K2_HUMAN	olfactory receptor, family 6, subfamily K, member 2	271						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	46	all_hematologic(112;0.0378)					GCTATATCCCAGAACAAAGAG	0.418																																					p.W271R		Atlas-SNP	.											.	OR6K2	104	.	0			c.T811A						.						102	99	100					1																	158669632		2203	4300	6503	SO:0001583	missense	81448	exon1			TATCCCAGAACAA	BK004196	CCDS30902.1	1q23.1	2012-08-09			ENSG00000196171	ENSG00000196171		"GPCR / Class A : Olfactory receptors"	15029	protein-coding gene	gene with protein product							Standard	NM_001005279		Approved		uc001fsu.1	Q8NGY2	OTTHUMG00000022768	ENST00000359610.2:c.811T>A	chr1.hg19:g.158669632A>T	ENSP00000352626:p.Trp271Arg	218.0	0.0		415.0	167.0	NM_001005279	B9EH33|Q6IFR6	Missense_Mutation	SNP	ENST00000359610.2	hg19	CCDS30902.1	.	.	.	.	.	.	.	.	.	.	A	14.65	2.599223	0.46318	.	.	ENSG00000196171	ENST00000359610	T	0.00058	8.79	4.94	4.94	0.65067	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39146	N	0.001459	T	0.00073	0.0002	N	0.08118	0	0.29001	N	0.887454	D	0.63046	0.992	D	0.71184	0.972	T	0.54370	-0.8304	10	0.20046	T	0.44	-3.5061	9.1704	0.37076	0.8375:0.0:0.0:0.1625	.	271	Q8NGY2	OR6K2_HUMAN	R	271	ENSP00000352626:W271R	ENSP00000352626:W271R	W	-	1	0	OR6K2	156936256	0.212000	0.23540	1.000000	0.80357	0.984000	0.73092	1.766000	0.38491	2.053000	0.61076	0.533000	0.62120	TGG	.	.		0.418	OR6K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059061.1	NM_001005279		T	158669632	A	T	158669632	3	4	344	1	0	0	0	0	1	0	0	0	11211	188	7	4	167	4	OR6K2	1	158669632	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	29	158669632	90580989	108	47471										
AIM2	9447	hgsc.bcm.edu	37	chr1	159038418	159038418	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcgacatcatttctgatggcTgcagatgcagcaggactcat	11	10	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:159038418T>A	ENST00000368130.4	-	3	624	c.336A>T	c.(334-336)gcA>gcT	p.A112A	AIM2_ENST00000411768.1_5'UTR	NM_004833.1	NP_004824.1	O14862	AIM2_HUMAN	absent in melanoma 2	112					activation of innate immune response (GO:0002218)|apoptotic process (GO:0006915)|cellular response to drug (GO:0035690)|cellular response to interferon-beta (GO:0035458)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta secretion (GO:0050702)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein oligomerization (GO:0032461)|pyroptosis (GO:0070269)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	AIM2 inflammasome complex (GO:0097169)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)			breast(1)|large_intestine(1)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(1)	16	all_hematologic(112;0.0429)					TTCTGATGGCTGCAGATGCAG	0.423																																					p.A112A		Atlas-SNP	.											.	AIM2	70	.	0			c.A336T						.						266	211	230					1																	159038418		2203	4300	6503	SO:0001819	synonymous_variant	9447	exon3			GATGGCTGCAGAT	AF024714	CCDS1181.1	1q22	2008-07-18			ENSG00000163568	ENSG00000163568			357	protein-coding gene	gene with protein product		604578				9242382	Standard	NM_004833		Approved	PYHIN4	uc001ftj.1	O14862	OTTHUMG00000037183	ENST00000368130.4:c.336A>T	chr1.hg19:g.159038418T>A		84.0	0.0		162.0	108.0	NM_004833	A8K7M7|Q5T3V9|Q96FG9	Silent	SNP	ENST00000368130.4	hg19	CCDS1181.1																																																																																			.	.		0.423	AIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090341.1	NM_004833		A	159038418	T	A	159038418	2	1	344	1	0	0	0	0	0	0	0	1	432	1567	55	4		4	AIM2	1	159038418	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	368786	159038418	90212203	109	47472										
ATP1A2	477	hgsc.bcm.edu	37	chr1	160097597	160097597	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	caacgtgcctgaggggcttcTggccactgtcactgtgagtg	14	11	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:160097597T>A	ENST00000361216.3	+	8	1093	c.1004T>A	c.(1003-1005)cTg>cAg	p.L335Q	ATP1A2_ENST00000392233.3_Missense_Mutation_p.L335Q	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide	335					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|locomotion (GO:0040011)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of heart contraction (GO:0045822)|negative regulation of striated muscle contraction (GO:0045988)|neurotransmitter uptake (GO:0001504)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of smooth muscle contraction (GO:0006940)|regulation of striated muscle contraction (GO:0006942)|regulation of the force of heart contraction (GO:0002026)|regulation of vasoconstriction (GO:0019229)|relaxation of cardiac muscle (GO:0055119)|response to nicotine (GO:0035094)|sodium ion export from cell (GO:0036376)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	caveola (GO:0005901)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|endosome (GO:0005768)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(30)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	69	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			GAGGGGCTTCTGGCCACTGTC	0.572																																					p.L335Q		Atlas-SNP	.											.	ATP1A2	167	.	0			c.T1004A						.						76	74	75					1																	160097597		2203	4300	6503	SO:0001583	missense	477	exon8			GGCTTCTGGCCAC	AB018321	CCDS1196.1	1q23.2	2014-09-17	2010-04-20		ENSG00000018625	ENSG00000018625	3.6.3.9	"ATPases / P-type"	800	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-2", "sodium pump subunit alpha-2", "sodium-potassium ATPase catalytic subunit alpha-2"	182340	"migraine, hemiplegic 2", "ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide"	MHP2		9403481	Standard	NM_000702		Approved	FHM2	uc001fvc.3	P50993	OTTHUMG00000024080	ENST00000361216.3:c.1004T>A	chr1.hg19:g.160097597T>A	ENSP00000354490:p.Leu335Gln	56.0	0.0		107.0	77.0	NM_000702	D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Missense_Mutation	SNP	ENST00000361216.3	hg19	CCDS1196.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	21.8|21.8	4.201428|4.201428	0.79015|0.79015	.|.	.|.	ENSG00000018625|ENSG00000018625	ENST00000538123;ENST00000361216;ENST00000392233|ENST00000447527	D;D|.	0.89123|.	-2.47;-2.47|.	4.65|4.65	4.65|4.65	0.58169|0.58169	ATPase, P-type, ATPase-associated domain (1);|.	0.000000|.	0.64402|.	D|.	0.000001|.	T|T	0.81004|0.81004	0.4733|0.4733	M|M	0.92923|0.92923	3.36|3.36	0.58432|0.58432	D|D	0.999999|0.999999	D;D;D|.	0.76494|.	0.999;0.999;0.999|.	D;D;D|.	0.78314|.	0.991;0.978;0.987|.	D|D	0.86117|0.86117	0.1566|0.1566	10|5	0.87932|.	D|.	0|.	.|.	13.3483|13.3483	0.60587|0.60587	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	180;235;335|.	B4DHD7;F5GXJ7;P50993|.	.;.;AT1A2_HUMAN|.	Q|R	180;335;335|46	ENSP00000354490:L335Q;ENSP00000376066:L335Q|.	ENSP00000354490:L335Q|.	L|W	+|+	2|1	0|0	ATP1A2|ATP1A2	158364221|158364221	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.970000|7.970000	0.88000|0.88000	1.860000|1.860000	0.53959|0.53959	0.459000|0.459000	0.35465|0.35465	CTG|TGG	.	.		0.572	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060642.2	NM_000702		A	160097597	T	A	160097597	3	1	344	1	0	0	0	0	1	0	0	0	1129	1580	55	4	1034	4	ATP1A2	1	160097597	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1059179	160097597	89153024	110	47473										
ATP1A4	480	hgsc.bcm.edu	37	chr1	160144010	160144010	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcgtgtttgctcggacctccCctcagcagaagctcatcatt	8	14	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:160144010C>A	ENST00000368081.4	+	14	2572	c.2101C>A	c.(2101-2103)Cct>Act	p.P701T	ATP1A4_ENST00000418334.1_3'UTR	NM_144699.3	NP_653300.2	Q13733	AT1A4_HUMAN	ATPase, Na+/K+ transporting, alpha 4 polypeptide	701					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|fertilization (GO:0009566)|ion transmembrane transport (GO:0034220)|potassium ion transport (GO:0006813)|regulation of cellular pH (GO:0030641)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(34)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	75	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			tcgGACCTCCCCTCAGCAGAA	0.542																																					p.P701T		Atlas-SNP	.											.	ATP1A4	167	.	0			c.C2101A						.						115	102	106					1																	160144010		2203	4300	6503	SO:0001583	missense	480	exon14			ACCTCCCCTCAGC	BC028297	CCDS1197.1, CCDS44255.1	1q23.2	2012-10-22	2002-02-25		ENSG00000132681	ENSG00000132681		"ATPases / P-type"	14073	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-4", "sodium pump subunit alpha-4", "sodium-potassium ATPase catalytic subunit alpha-4"	607321	"ATPase, Na+/K+ transporting, alpha polypeptide-like 2"	ATP1AL2		1981991, 3035563	Standard	NM_144699		Approved		uc001fve.4	Q13733	OTTHUMG00000031609	ENST00000368081.4:c.2101C>A	chr1.hg19:g.160144010C>A	ENSP00000357060:p.Pro701Thr	196.0	0.0		329.0	236.0	NM_144699	Q504T2|Q7Z4I9|Q8TBN8|Q8WXA7|Q8WXH7|Q8WY13	Missense_Mutation	SNP	ENST00000368081.4	hg19	CCDS1197.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.501057	0.85176	.	.	ENSG00000132681	ENST00000368081	D	0.98987	-5.3	4.27	4.27	0.50696	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.99495	0.9820	H	0.96301	3.8	0.80722	D	1	D	0.57571	0.98	D	0.70227	0.968	D	0.98143	1.0437	10	0.87932	D	0	.	14.5908	0.68362	0.0:1.0:0.0:0.0	.	701	Q13733	AT1A4_HUMAN	T	701	ENSP00000357060:P701T	ENSP00000357060:P701T	P	+	1	0	ATP1A4	158410634	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.623000	0.83113	2.371000	0.80710	0.655000	0.94253	CCT	.	.		0.542	ATP1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077415.1	NM_144699		A	160144010	C	A	160144010	3	1	344	1	0	0	0	0	1	0	0	0	1131	623	22	3	2155	3	ATP1A4	1	160144010	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	46413	160144010	89106611	111	47474										
SLAMF1	6504	hgsc.bcm.edu	37	chr1	160582368	160582368	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gagtcaagtttcttctgaagAggctacaagagaagcaaaga	11	6	3	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:160582368A>G	ENST00000302035.6	-	6	1216	c.867T>C	c.(865-867)ccT>ccC	p.P289P	SLAMF1_ENST00000538290.1_Missense_Mutation_p.S265P|SLAMF1_ENST00000235739.5_Silent_p.P259P	NM_003037.2	NP_003028.1	Q13291	SLAF1_HUMAN	signaling lymphocytic activation molecule family member 1	289					lymphocyte activation (GO:0046649)|positive regulation of cell proliferation (GO:0008284)|regulation of catalytic activity (GO:0050790)|regulation of vesicle fusion (GO:0031338)|signal transduction (GO:0007165)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|phagocytic vesicle (GO:0045335)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(52;4.94e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			TCTTCTGAAGAGGCTACAAGA	0.502																																					p.P289P		Atlas-SNP	.											.	SLAMF1	74	.	0			c.T867C						.						51	50	50					1																	160582368		2203	4300	6503	SO:0001819	synonymous_variant	6504	exon6			CTGAAGAGGCTAC	U33017	CCDS1207.1	1q23.3	2013-01-11	2003-10-29	2003-10-31	ENSG00000117090	ENSG00000117090		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10903	protein-coding gene	gene with protein product		603492	"signaling lymphocytic activation molecule"	SLAM		7617038	Standard	XM_005245456		Approved	CD150	uc001fwl.4	Q13291	OTTHUMG00000024006	ENST00000302035.6:c.867T>C	chr1.hg19:g.160582368A>G		40.0	0.0		101.0	67.0	NM_003037	Q5W172|Q9HBE8	Silent	SNP	ENST00000302035.6	hg19	CCDS1207.1	.	.	.	.	.	.	.	.	.	.	A	12.02	1.811642	0.32053	.	.	ENSG00000117090	ENST00000538290	T	0.38560	1.13	4.21	0.389	0.16269	.	.	.	.	.	T	0.09468	0.0233	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.32161	-0.9917	5	.	.	.	-1.0383	1.3321	0.02137	0.5337:0.1862:0.101:0.1792	.	.	.	.	P	265	ENSP00000438406:S265P	.	S	-	1	0	SLAMF1	158848992	0.002000	0.14202	0.000000	0.03702	0.188000	0.23474	0.484000	0.22308	0.045000	0.15804	0.533000	0.62120	TCT	.	.		0.502	SLAMF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060454.1			G	160582368	A	G	160582368	2	3	344	1	0	0	0	0	0	0	0	1	14382	291	11	2		2	SLAMF1	1	160582368	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	438358	160582368	88668253	112	47475										
LY9	4063	hgsc.bcm.edu	37	chr1	160784286	160784286	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gagccagtcaccctgccactTgcactcccagcctgccggga	10	18	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:160784286T>G	ENST00000263285.6	+	4	837	c.807T>G	c.(805-807)ctT>ctG	p.L269L	LY9_ENST00000368037.5_Silent_p.L269L|LY9_ENST00000368041.2_Silent_p.L229L|LY9_ENST00000368040.1_5'UTR|LY9_ENST00000471816.1_3'UTR|LY9_ENST00000341032.4_Silent_p.L269L|LY9_ENST00000392203.4_Silent_p.L269L			Q9HBG7	LY9_HUMAN	lymphocyte antigen 9	269	Ig-like V-type 2.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36	all_cancers(52;2.72e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)			CCCTGCCACTTGCACTCCCAG	0.562																																					p.L269L		Atlas-SNP	.											.	LY9	115	.	0			c.T807G						.						84	81	82					1																	160784286		2203	4300	6503	SO:0001819	synonymous_variant	4063	exon4			GCCACTTGCACTC	L42621	CCDS30916.1, CCDS30917.1, CCDS65695.1, CCDS65696.1	1q23.3	2013-01-11			ENSG00000122224	ENSG00000122224		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6730	protein-coding gene	gene with protein product		600684				8537117, 7797269	Standard	NM_001261457		Approved	CD229, mLY9, SLAMF3, hly9	uc001fwu.4	Q9HBG7	OTTHUMG00000024007	ENST00000263285.6:c.807T>G	chr1.hg19:g.160784286T>G		122.0	0.0		190.0	138.0	NM_001261457	A8K7N3|Q14775|Q5VYI3|Q6P2J4|Q9H4N5|Q9NQ24	Silent	SNP	ENST00000263285.6	hg19	CCDS30916.1																																																																																			.	.		0.562	LY9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060457.3	NM_002348		G	160784286	T	G	160784286	2	3	344	1	0	0	0	0	0	0	0	1	9110	1799	63	5		5	LY9	1	160784286	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	201918	160784286	88466335	113	47476										
PVRL4	81607	hgsc.bcm.edu	37	chr1	161044159	161044159	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgcttcccagagtcttcctgGgggtctgctggagacaggcc	14	12	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:161044159G>T	ENST00000368012.3	-	6	1307	c.1005C>A	c.(1003-1005)ccC>ccA	p.P335P	PVRL4_ENST00000486694.1_5'Flank|PVRL4_ENST00000453926.2_Silent_p.P69P	NM_030916.2	NP_112178.2	Q96NY8	PVRL4_HUMAN	poliovirus receptor-related 4	335					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|viral process (GO:0016032)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|urinary_tract(1)	20	all_cancers(52;8.9e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			AGTCTTCCTGGGGGTCTGCTG	0.607																																					p.P335P	NSCLC(76;1160 1387 14476 16172 29359)	Atlas-SNP	.											.	PVRL4	48	.	0			c.C1005A						.						152	133	139					1																	161044159		2203	4300	6503	SO:0001819	synonymous_variant	81607	exon6			TTCCTGGGGGTCT	AF426163	CCDS1216.1	1q22-q23.2	2013-01-14			ENSG00000143217	ENSG00000143217		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing"	19688	protein-coding gene	gene with protein product		609607				11544254	Standard	NM_030916		Approved	nectin-4, PRR4, LNIR	uc001fxo.2	Q96NY8	OTTHUMG00000031475	ENST00000368012.3:c.1005C>A	chr1.hg19:g.161044159G>T		112.0	0.0		182.0	38.0	NM_030916	B4DQW3|Q96K15	Silent	SNP	ENST00000368012.3	hg19	CCDS1216.1																																																																																			.	.		0.607	PVRL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077074.1	NM_030916		T	161044159	G	T	161044159	2	4	344	1	0	0	0	0	0	0	0	1	12857	1219	43	3		3	PVRL4	1	161044159	Silent	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	259873	161044159	88206462	114	47477										
FCRLA	84824	hgsc.bcm.edu	37	chr1	161682966	161682966	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cctgaggaggcccctgggccTctgcctccgccgccaacccc	11	21	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:161682966T>A	ENST00000236938.6	+	5	1169	c.927T>A	c.(925-927)ccT>ccA	p.P309P	FCRLA_ENST00000367959.2_Silent_p.P315P|FCRLA_ENST00000367949.2_Silent_p.P125P|FCRLA_ENST00000367950.1_Silent_p.P85P|FCRLA_ENST00000294796.4_Silent_p.P158P|FCRLA_ENST00000540521.1_Silent_p.P175P|FCRLA_ENST00000546024.1_Silent_p.P220P|FCRLA_ENST00000367957.2_Silent_p.P169P|FCRLA_ENST00000367953.3_Silent_p.P298P|FCRLA_ENST00000350710.3_Silent_p.P74P|FCRLA_ENST00000540926.1_Silent_p.P298P|FCRLA_ENST00000349527.4_Silent_p.P197P|FCRLA_ENST00000309691.6_Silent_p.P203P|FCRLA_ENST00000470841.1_3'UTR	NM_032738.3	NP_116127.3	Q7L513	FCRLA_HUMAN	Fc receptor-like A	292	Pro-rich.				cell differentiation (GO:0030154)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)				breast(1)|kidney(12)|large_intestine(4)|lung(13)|prostate(1)|skin(2)|stomach(1)	34	all_cancers(52;2.55e-15)|all_hematologic(112;0.0359)		BRCA - Breast invasive adenocarcinoma(70;0.00301)			CCCCTGGGCCTCTGCCTCCGC	0.562																																					p.P315P		Atlas-SNP	.											.	FCRLA	101	.	0			c.T945A						.						62	68	66					1																	161682966		2203	4300	6503	SO:0001819	synonymous_variant	84824	exon6			TGGGCCTCTGCCT	AF531423	CCDS30926.1, CCDS53415.1, CCDS53416.1, CCDS53417.1, CCDS53418.1, CCDS53419.1, CCDS53420.1	1q23.3	2014-01-28	2006-09-26	2006-09-26	ENSG00000132185	ENSG00000132185		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18504	protein-coding gene	gene with protein product		606891	"Fc receptor-like and mucin-like 1"	FCRLM1		11754007	Standard	NM_001184866		Approved	MGC4595, FCRLc2, FCRLb, FCRLc1, FCRLd, FCRLe, FCRL, FCRLa, FREB, FCRLX	uc001gbe.3	Q7L513	OTTHUMG00000034537	ENST00000236938.6:c.927T>A	chr1.hg19:g.161682966T>A		91.0	0.0		161.0	118.0	NM_001184866	A0N0M1|A6NC03|A6NL20|F5H720|F8W743|G3V1J2|Q5VXA1|Q5VXA2|Q5VXA3|Q5VXA4|Q5VXB0|Q5VXB1|Q8NEW4|Q8WXH3|Q96PC6|Q96PJ0|Q96PJ1|Q96PJ2|Q96PJ4|Q9BR57	Silent	SNP	ENST00000236938.6	hg19	CCDS30926.1																																																																																			.	.		0.562	FCRLA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083574.1	NM_032738		A	161682966	T	A	161682966	2	1	344	1	0	0	0	0	0	0	0	1	5808	1538	54	4		4	FCRLA	1	161682966	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	638807	161682966	87567655	115	47478										
DUSP27	92235	hgsc.bcm.edu	37	chr1	167096996	167096996	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aagaagaagaaggtcaaggaAgatgaggatgatggtgtggg	18	1	1	6			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:167096996A>T	ENST00000361200.2	+	6	2794	c.2628A>T	c.(2626-2628)gaA>gaT	p.E876D	DUSP27_ENST00000271385.5_Missense_Mutation_p.E876D|DUSP27_ENST00000485151.1_Intron|DUSP27_ENST00000443333.1_Missense_Mutation_p.E876D			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	876					protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						AGGTCAAGGAAGATGAGGATG	0.488																																					p.E876D		Atlas-SNP	.											.	DUSP27	235	.	0			c.A2628T						.						97	81	86					1																	167096996		2203	4300	6503	SO:0001583	missense	92235	exon5			CAAGGAAGATGAG	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.2628A>T	chr1.hg19:g.167096996A>T	ENSP00000354483:p.Glu876Asp	60.0	0.0		100.0	73.0	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	hg19	CCDS30932.1	.	.	.	.	.	.	.	.	.	.	A	5.013	0.188019	0.09547	.	.	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.03358	3.96;3.96;3.96	5.4	-1.69	0.08186	.	0.795647	0.11082	N	0.601758	T	0.00580	0.0019	L	0.27053	0.805	0.26419	N	0.976136	B	0.06786	0.001	B	0.08055	0.003	T	0.47222	-0.9134	10	0.07813	T	0.8	-2.0674	2.4576	0.04533	0.2833:0.3299:0.0671:0.3197	.	876	Q5VZP5	DUS27_HUMAN	D	876	ENSP00000354483:E876D;ENSP00000271385:E876D;ENSP00000404874:E876D	ENSP00000271385:E876D	E	+	3	2	DUSP27	165363620	0.003000	0.15002	0.540000	0.28089	0.553000	0.35397	-0.953000	0.03877	-0.228000	0.09869	-0.269000	0.10298	GAA	.	.		0.488	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426		T	167096996	A	T	167096996	3	4	344	1	0	0	0	0	1	0	0	0	4826	69	3	4	2646	4	DUSP27	1	167096996	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	5414030	167096996	82153625	116	47479										
F5	2153	hgsc.bcm.edu	37	chr1	169521814	169521814	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctttgagtgtgtctctgaccTgggctctgataataggaccc	11	10	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:169521814T>A	ENST00000367797.3	-	8	1478	c.1277A>T	c.(1276-1278)cAg>cTg	p.Q426L	F5_ENST00000546081.1_Missense_Mutation_p.Q289L|F5_ENST00000367796.3_Missense_Mutation_p.Q426L	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	426	F5/8 type A 2.|Plastocyanin-like 3.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	GTCTCTGACCTGGGCTCTGAT	0.343																																					p.Q426L		Atlas-SNP	.											.	F5	301	.	0			c.A1277T						.						123	120	121					1																	169521814		2203	4300	6503	SO:0001583	missense	2153	exon8			CTGACCTGGGCTC	M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.1277A>T	chr1.hg19:g.169521814T>A	ENSP00000356771:p.Gln426Leu	116.0	0.0		184.0	138.0	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	hg19	CCDS1281.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.578911	0.86645	.	.	ENSG00000198734	ENST00000367797;ENST00000367796;ENST00000546081	D;D;D	0.98968	-5.28;-5.28;-5.28	5.65	5.65	0.86999	Cupredoxin (2);	0.000000	0.85682	D	0.000000	D	0.99089	0.9687	M	0.84326	2.69	0.43267	D	0.995219	D	0.76494	0.999	D	0.83275	0.996	D	0.99851	1.1072	9	0.87932	D	0	-14.5758	16.1566	0.81673	0.0:0.0:0.0:1.0	.	426	P12259	FA5_HUMAN	L	426;426;289	ENSP00000356771:Q426L;ENSP00000356770:Q426L;ENSP00000439664:Q289L	ENSP00000356770:Q426L	Q	-	2	0	F5	167788438	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.420000	0.80191	2.268000	0.75426	0.533000	0.62120	CAG	.	.		0.343	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130		A	169521814	T	A	169521814	3	1	344	1	0	0	0	0	1	0	0	0	5350	1580	55	4	5469	4	F5	1	169521814	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2424818	169521814	79728807	117	47480										
SELP	6403	hgsc.bcm.edu	37	chr1	169586539	169586539	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aatttcatttttattctggaTggccactaagtctgtgtagc	8	7	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:169586539T>A	ENST00000263686.6	-	3	245	c.208A>T	c.(208-210)Atc>Ttc	p.I70F	SELP_ENST00000367794.2_Missense_Mutation_p.I70F|SELP_ENST00000367786.2_Missense_Mutation_p.I70F|SELP_ENST00000367793.2_Missense_Mutation_p.I70F|SELP_ENST00000367791.2_Missense_Mutation_p.I70F|SELP_ENST00000367788.2_Missense_Mutation_p.I70F|SELP_ENST00000458599.2_Missense_Mutation_p.I70F|SELP_ENST00000367792.2_Missense_Mutation_p.I70F	NM_003005.3	NP_002996.2	P16109	LYAM3_HUMAN	selectin P (granule membrane protein 140kDa, antigen CD62)	70	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|defense response to Gram-negative bacterium (GO:0050829)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of platelet activation (GO:0010572)|regulation of integrin activation (GO:0033623)|response to lipopolysaccharide (GO:0032496)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|platelet dense granule membrane (GO:0031088)	fucose binding (GO:0042806)|glycosphingolipid binding (GO:0043208)|heparin binding (GO:0008201)|lipopolysaccharide binding (GO:0001530)|oligosaccharide binding (GO:0070492)|sialic acid binding (GO:0033691)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(32)|ovary(4)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_hematologic(923;0.208)				Dalteparin(DB06779)|Heparin(DB01109)|Nadroparin(DB08813)	TTATTCTGGATGGCCACTAAG	0.408																																					p.I70F		Atlas-SNP	.											.	SELP	132	.	0			c.A208T						.						175	162	166					1																	169586539		2203	4300	6503	SO:0001583	missense	6403	exon3			TCTGGATGGCCAC	BC068533	CCDS1282.1	1q22-q25	2008-02-05	2002-08-29		ENSG00000174175	ENSG00000174175		"CD molecules"	10721	protein-coding gene	gene with protein product		173610	"selectin P (granule membrane protein 140kD, antigen CD62)"	GRMP		1375831	Standard	NM_003005		Approved	CD62, PSEL, PADGEM, GMP140, CD62P	uc001ggi.4	P16109	OTTHUMG00000034685	ENST00000263686.6:c.208A>T	chr1.hg19:g.169586539T>A	ENSP00000263686:p.Ile70Phe	107.0	0.0		210.0	34.0	NM_003005	Q5R344|Q8IVD1	Missense_Mutation	SNP	ENST00000263686.6	hg19	CCDS1282.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.56|19.56	3.851032|3.851032	0.71719|0.71719	.|.	.|.	ENSG00000174175|ENSG00000174175	ENST00000446728|ENST00000367795;ENST00000367790;ENST00000426706;ENST00000367789;ENST00000263686;ENST00000544572;ENST00000367793;ENST00000367794;ENST00000367792;ENST00000367791;ENST00000367788;ENST00000367786;ENST00000458599	.|T;T;T;T;T;T;T;T	.|0.20200	.|2.09;2.09;2.09;2.09;2.09;2.09;2.09;2.19	5.9|5.9	5.9|5.9	0.94986|0.94986	.|C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	.|0.000000	.|0.56097	.|D	.|0.000034	T|T	0.50411|0.50411	0.1614|0.1614	H|H	0.95151|0.95151	3.63|3.63	0.58432|0.58432	D|D	0.999992|0.999992	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|1.0;1.0	T|T	0.63184|0.63184	-0.6694|-0.6694	5|10	.|0.40728	.|T	.|0.16	-27.0552|-27.0552	14.2765|14.2765	0.66184|0.66184	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|70;70	.|Q6NUL9;P16109	.|.;LYAM3_HUMAN	L|F	69|70;70;69;70;70;70;70;70;70;70;70;70;55	.|ENSP00000263686:I70F;ENSP00000356767:I70F;ENSP00000356768:I70F;ENSP00000356766:I70F;ENSP00000356765:I70F;ENSP00000356762:I70F;ENSP00000356760:I70F;ENSP00000399368:I55F	.|ENSP00000263686:I70F	H|I	-|-	2|1	0|0	SELP|SELP	167853163|167853163	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.359000|0.359000	0.29487|0.29487	7.698000|7.698000	0.84413|0.84413	2.254000|2.254000	0.74563|0.74563	0.460000|0.460000	0.39030|0.39030	CAT|ATC	.	.		0.408	SELP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083916.4	NM_003005		A	169586539	T	A	169586539	3	1	344	1	0	0	0	0	1	0	0	0	14034	1464	51	4	2340	4	SELP	1	169586539	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	64725	169586539	79664082	118	47481										
FMO2	2327	hgsc.bcm.edu	37	chr1	171174726	171174726	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccagcccctaggttccatttTcccaactgctgaacttcaag	6	15	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:171174726T>C	ENST00000209929.7	+	7	1294	c.1136T>C	c.(1135-1137)tTc>tCc	p.F379S	FMO2_ENST00000441535.1_Missense_Mutation_p.F379S|RP1-127D3.4_ENST00000445909.1_RNA|RP1-127D3.4_ENST00000422841.1_RNA|RP1-127D3.4_ENST00000445290.1_RNA|FMO2_ENST00000529935.1_3'UTR			P31512	FMO4_HUMAN	flavin containing monooxygenase 2 (non-functional)	378					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	22	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					GGTTCCATTTTCCCAACTGCT	0.463																																					p.F379S		Atlas-SNP	.											.	FMO2	66	.	0			c.T1136C						.						54	53	54					1																	171174726		2203	4300	6503	SO:0001583	missense	2327	exon7			CCATTTTCCCAAC	BC005894	CCDS1293.1	1q24.3	2011-08-04	2006-07-17		ENSG00000094963	ENSG00000094963			3770	protein-coding gene	gene with protein product		603955	"flavin containing monooxygenase 2"			1417778, 9804831	Standard	XR_426768		Approved		uc001ghk.1	Q99518	OTTHUMG00000035504	ENST00000209929.7:c.1136T>C	chr1.hg19:g.171174726T>C	ENSP00000209929:p.Phe379Ser	76.0	0.0		116.0	80.0	NM_001460	Q53XR0	Missense_Mutation	SNP	ENST00000209929.7	hg19	CCDS1293.1	.	.	.	.	.	.	.	.	.	.	T	17.24	3.338753	0.60963	.	.	ENSG00000094963	ENST00000209929;ENST00000441535	T;T	0.53857	0.6;0.6	5.55	5.55	0.83447	.	0.083924	0.85682	D	0.000000	T	0.52175	0.1718	M	0.80746	2.51	0.34366	D	0.691472	B	0.33212	0.402	B	0.41135	0.348	T	0.64402	-0.6416	10	0.87932	D	0	-25.341	14.9772	0.71283	0.0:0.0:0.0:1.0	.	379	Q99518	FMO2_HUMAN	S	379	ENSP00000209929:F379S;ENSP00000405905:F379S	ENSP00000209929:F379S	F	+	2	0	FMO2	169441350	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.349000	0.52217	2.234000	0.73211	0.533000	0.62120	TTC	.	.		0.463	FMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086216.2	NM_001460		C	171174726	T	C	171174726	3	2	344	1	0	0	0	0	1	0	0	0	5963	1783	62	2	1158	2	FMO2	1	171174726	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1588187	171174726	78075895	119	47482										
BAT2L2	23215	hgsc.bcm.edu	37	chr1	171510057	171510057	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cagcaaagaccttgttatagAgaggcctcgaccagattcaa	9	10	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:171510057A>T	ENST00000338920.4	+	16	3683	c.3446A>T	c.(3445-3447)gAg>gTg	p.E1149V	PRRC2C_ENST00000426496.2_Missense_Mutation_p.E1149V|PRRC2C_ENST00000392078.3_Missense_Mutation_p.E1151V|PRRC2C_ENST00000367742.3_Missense_Mutation_p.E1151V	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	1149					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										CTTGTTATAGAGAGGCCTCGA	0.433																																					p.E1149V		Atlas-SNP	.											.	.	.	.	0			c.A3446T						.						47	49	49					1																	171510057		2203	4300	6503	SO:0001583	missense	23215	exon16			TTATAGAGAGGCC	AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"BAT2 domain containing 1", "HLA-B associated transcript 2-like 2"	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.3446A>T	chr1.hg19:g.171510057A>T	ENSP00000343629:p.Glu1149Val	186.0	0.0		338.0	74.0	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Missense_Mutation	SNP	ENST00000338920.4	hg19	CCDS1296.2	.	.	.	.	.	.	.	.	.	.	A	9.083	0.999795	0.19121	.	.	ENSG00000117523	ENST00000392078;ENST00000451306;ENST00000426496;ENST00000367742;ENST00000338920;ENST00000392080	T;T;T;T	0.02216	4.39;4.4;4.39;4.4	5.91	5.91	0.95273	.	0.000000	0.47093	D	0.000249	T	0.01870	0.0059	L	0.29908	0.895	0.46131	D	0.998886	D	0.53462	0.96	P	0.51229	0.663	T	0.60500	-0.7251	10	0.66056	D	0.02	.	10.6452	0.45615	0.9292:0.0:0.0708:0.0	.	1149	Q9Y520-4	.	V	1151;1150;1149;1151;1149;906	ENSP00000375928:E1151V;ENSP00000410219:E1149V;ENSP00000356716:E1151V;ENSP00000343629:E1149V	ENSP00000343629:E1149V	E	+	2	0	PRRC2C	169776681	1.000000	0.71417	0.939000	0.37840	0.936000	0.57629	2.931000	0.48932	2.254000	0.74563	0.533000	0.62120	GAG	.	.		0.433	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172		T	171510057	A	T	171510057	3	4	344	1	0	0	0	0	1	0	0	0	1321	304	11	4	3504	4	BAT2L2	1	171510057	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	335331	171510057	77740564	120	47483										
MYOC	4653	hgsc.bcm.edu	37	chr1	171605647	171605647	+	Nonsense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agtatgtgaaccttagaaggGtagccctgcataaactggct	11	8	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:171605647G>C	ENST00000037502.6	-	3	1004	c.933C>G	c.(931-933)taC>taG	p.Y311*		NM_000261.1	NP_000252.1	Q99972	MYOC_HUMAN	myocilin, trabecular meshwork inducible glucocorticoid response	311	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				bone development (GO:0060348)|clustering of voltage-gated sodium channels (GO:0045162)|ERBB2-ERBB3 signaling pathway (GO:0038133)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neuron projection development (GO:0031175)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|osteoblast differentiation (GO:0001649)|positive regulation of cell migration (GO:0030335)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of MAPK cascade (GO:0043408)|skeletal muscle hypertrophy (GO:0014734)	cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|node of Ranvier (GO:0033268)|proteinaceous extracellular matrix (GO:0005578)	fibronectin binding (GO:0001968)|frizzled binding (GO:0005109)|myosin light chain binding (GO:0032027)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|prostate(1)|urinary_tract(2)	28	all_cancers(6;5.47e-10)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					CCTTAGAAGGGTAGCCCTGCA	0.552																																					p.Y311X		Atlas-SNP	.											.	MYOC	69	.	0			c.C933G						.						80	71	74					1																	171605647		2203	4300	6503	SO:0001587	stop_gained	4653	exon3			AGAAGGGTAGCCC	BC029261	CCDS1297.1	1q23-q24	2008-02-05			ENSG00000034971	ENSG00000034971			7610	protein-coding gene	gene with protein product		601652		GLC1A		9169133, 9005853	Standard	NM_000261		Approved	TIGR, JOAG1	uc001ghu.3	Q99972	OTTHUMG00000034789	ENST00000037502.6:c.933C>G	chr1.hg19:g.171605647G>C	ENSP00000037502:p.Tyr311*	71.0	0.0		138.0	22.0	NM_000261	B2RD84|O00620|Q7Z6Q9	Nonsense_Mutation	SNP	ENST00000037502.6	hg19	CCDS1297.1	.	.	.	.	.	.	.	.	.	.	G	14.20	2.463492	0.43736	.	.	ENSG00000034971	ENST00000037502;ENST00000357746;ENST00000536591;ENST00000537133	.	.	.	5.76	2.31	0.28768	.	0.436778	0.29293	N	0.012569	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.5227	0.33287	0.1686:0.133:0.6985:0.0	.	.	.	.	X	311;264;244;311	.	ENSP00000037502:Y311X	Y	-	3	2	MYOC	169872270	1.000000	0.71417	0.996000	0.52242	0.101000	0.19017	0.675000	0.25232	0.722000	0.32252	0.555000	0.69702	TAC	.	.		0.552	MYOC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084178.2	NM_000261		C	171605647	G	C	171605647	4	2	344	1	0	0	0	0	0	1	0	0	10095	1256	44	4	585	4	MYOC	1	171605647	Nonsense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	95590	171605647	77644974	121	47484										
METTL13	51603	hgsc.bcm.edu	37	chr1	171759656	171759656	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gatgcggaggacctccctgcAgccccggggcagtccattga	14	14	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:171759656A>T	ENST00000361735.3	+	5	1640	c.1374A>T	c.(1372-1374)gcA>gcT	p.A458A	METTL13_ENST00000466643.1_Intron|METTL13_ENST00000458517.1_Silent_p.A457A|METTL13_ENST00000362019.3_Silent_p.A372A|METTL13_ENST00000367737.5_Silent_p.A302A	NM_015935.4	NP_057019.3	Q8N6R0	MET13_HUMAN	methyltransferase like 13	458							methyltransferase activity (GO:0008168)			breast(3)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(8)|lung(17)|stomach(3)	41						ACCTCCCTGCAGCCCCGGGGC	0.537																																					p.A458A		Atlas-SNP	.											.	METTL13	67	.	0			c.A1374T						.						93	90	91					1																	171759656		2203	4300	6503	SO:0001819	synonymous_variant	51603	exon5			CCCTGCAGCCCCG	AF132936	CCDS1299.1, CCDS1300.1, CCDS30936.1	1q24-q25.3	2009-02-23	2009-02-23	2009-02-23	ENSG00000010165	ENSG00000010165			24248	protein-coding gene	gene with protein product			"KIAA0859"	KIAA0859		10810093, 10048485	Standard	NM_001007239		Approved	CGI-01	uc001ghz.3	Q8N6R0	OTTHUMG00000034912	ENST00000361735.3:c.1374A>T	chr1.hg19:g.171759656A>T		319.0	0.0		500.0	336.0	NM_015935	A6NFK0|A8K6S5|O94940|Q53EZ6|Q5TGP9|Q5TGQ0|Q8N2P8|Q96J11|Q96SQ0|Q9Y2Z1|Q9Y3M6	Silent	SNP	ENST00000361735.3	hg19	CCDS1299.1																																																																																			.	.		0.537	METTL13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084528.5	NM_014955		T	171759656	A	T	171759656	2	4	344	1	0	0	0	0	0	0	0	1	9506	175	7	4		4	METTL13	1	171759656	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	154009	171759656	77490965	122	47485										
ASTN1	460	hgsc.bcm.edu	37	chr1	177001594	177001594	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cctttctcccatccccacctGgtgtgaggtccatccccgac	7	19	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:177001594G>A	ENST00000367654.3	-	3	1074	c.863C>T	c.(862-864)cCa>cTa	p.P288L	ASTN1_ENST00000361833.2_Missense_Mutation_p.P288L|ASTN1_ENST00000281881.3_5'UTR|ASTN1_ENST00000424564.2_Missense_Mutation_p.P288L|ASTN1_ENST00000367657.3_Missense_Mutation_p.P288L	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	288					locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						ATCCCCACCTGGTGTGAGGTC	0.592																																					p.P288L		Atlas-SNP	.											.	ASTN1	314	.	0			c.C863T						.						102	101	102					1																	177001594		2203	4300	6503	SO:0001583	missense	460	exon3			CCACCTGGTGTGA	AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"astrotactin"	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.863C>T	chr1.hg19:g.177001594G>A	ENSP00000356626:p.Pro288Leu	32.0	0.0		68.0	23.0	NM_004319	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Missense_Mutation	SNP	ENST00000367654.3	hg19		.	.	.	.	.	.	.	.	.	.	G	21.8	4.203182	0.79127	.	.	ENSG00000152092	ENST00000367657;ENST00000361833;ENST00000367654;ENST00000424564;ENST00000541808	T;T;T;T	0.15256	2.44;2.85;2.85;2.44	5.53	5.53	0.82687	.	0.100739	0.64402	N	0.000001	T	0.16727	0.0402	N	0.24115	0.695	0.80722	D	1	P;P;P	0.42296	0.775;0.573;0.573	B;B;B	0.41412	0.356;0.272;0.272	T	0.01613	-1.1312	10	0.56958	D	0.05	-18.5904	19.0469	0.93025	0.0:0.0:1.0:0.0	.	288;288;288	O14525;O14525-2;B1AJS1	ASTN1_HUMAN;.;.	L	288	ENSP00000356629:P288L;ENSP00000354536:P288L;ENSP00000356626:P288L;ENSP00000395041:P288L	ENSP00000354536:P288L	P	-	2	0	ASTN1	175268217	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.267000	0.95665	2.563000	0.86464	0.655000	0.94253	CCA	.	.		0.592	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319		A	177001594	G	A	177001594	3	1	344	1	0	0	0	0	1	0	0	0	1064	1348	47	3	3109	3	ASTN1	1	177001594	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	5241938	177001594	72249027	123	47486										
FAM5B	57795	hgsc.bcm.edu	37	chr1	177226313	177226313	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctcgtgttgttcaccataggAgaagagtccctgaccatttt	9	10	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:177226313A>G	ENST00000361539.4	+	4	774	c.462A>G	c.(460-462)ggA>ggG	p.G154G	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	154	MACPF.				cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	extracellular region (GO:0005576)											TCACCATAGGAGAAGAGTCCC	0.493																																					p.G154G		Atlas-SNP	.											.	FAM5B	191	.	0			c.A462G						.						83	80	81					1																	177226313		2203	4300	6503	SO:0001630	splice_region_variant	57795	exon4			CATAGGAGAAGAG		CCDS1320.1	1q24	2013-08-06	2013-08-06	2013-07-31	ENSG00000198797	ENSG00000198797			13746	protein-coding gene	gene with protein product			"family with sequence similarity 5, member B"	FAM5B		15193423	Standard	NM_021165		Approved	DBCCR1L2	uc001glf.3	Q9C0B6	OTTHUMG00000034953	ENST00000361539.4:c.461-1A>G	chr1.hg19:g.177226313A>G		191.0	0.0		309.0	234.0	NM_021165	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Silent	SNP	ENST00000361539.4	hg19	CCDS1320.1																																																																																			.	.		0.493	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1	NM_021165	Silent	G	177226313	A	G	177226313	5	3	344	1	0	0	0	0	0	0	1	0	5601	318	11	2	472	2	FAM5B	1	177226313	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	224719	177226313	72024308	124	47487										
SEC16B	89866	hgsc.bcm.edu	37	chr1	177906378	177906378	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggtgtgtctgcagcatttccTcccagactgttcctccagtg	10	13	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:177906378T>C	ENST00000308284.6	-	19	2563	c.2474A>G	c.(2473-2475)gAg>gGg	p.E825G	RP4-798P15.3_ENST00000354921.3_RNA|SEC16B_ENST00000495165.1_5'Flank	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	825					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|peroxisome fission (GO:0016559)|peroxisome organization (GO:0007031)|positive regulation of gene expression (GO:0010628)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endoplasmic reticulum (GO:0070972)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)				central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)|stomach(1)	35						CAGCATTTCCTCCCAGACTGT	0.592																																					p.E825G		Atlas-SNP	.											.	SEC16B	92	.	0			c.A2474G						.						49	55	53					1																	177906378		2042	4202	6244	SO:0001583	missense	89866	exon19			ATTTCCTCCCAGA	AK090411	CCDS44281.1	1q25.2	2012-10-08	2007-06-20	2007-06-20	ENSG00000120341	ENSG00000120341			30301	protein-coding gene	gene with protein product	"regucalcin gene promotor region related protein"	612855	"leucine zipper transcription regulator 2"	LZTR2		11572484, 11605020	Standard	NM_033127		Approved	RGPR, PGPR-p117	uc001gli.1	Q96JE7	OTTHUMG00000167206	ENST00000308284.6:c.2474A>G	chr1.hg19:g.177906378T>C	ENSP00000308339:p.Glu825Gly	53.0	0.0		96.0	65.0	NM_033127	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Missense_Mutation	SNP	ENST00000308284.6	hg19	CCDS44281.1	.	.	.	.	.	.	.	.	.	.	T	12.87	2.068216	0.36470	.	.	ENSG00000120341	ENST00000308284;ENST00000414025;ENST00000239472	T	0.17691	2.26	5.11	3.97	0.46021	.	0.263692	0.32918	N	0.005492	T	0.19886	0.0478	M	0.71581	2.175	0.49130	D	0.999752	P;P;P;P	0.52463	0.953;0.483;0.483;0.78	B;B;B;B	0.42462	0.388;0.122;0.122;0.197	T	0.02398	-1.1165	10	0.38643	T	0.18	-18.5363	8.8932	0.35446	0.0:0.0:0.1887:0.8113	.	380;826;825;522	B1AM07;B1AM08;Q96JE7;Q96PW0	.;.;SC16B_HUMAN;.	G	825;509;540	ENSP00000308339:E825G	ENSP00000239472:E540G	E	-	2	0	AL359075.1	176173001	0.958000	0.32768	0.247000	0.24249	0.141000	0.21300	1.965000	0.40471	0.939000	0.37446	0.528000	0.53228	GAG	.	.		0.592	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127		C	177906378	T	C	177906378	3	2	344	1	0	0	0	0	1	0	0	0	14002	1551	54	2	740	2	SEC16B	1	177906378	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	680065	177906378	71344243	125	47488										
STX6	10228	hgsc.bcm.edu	37	chr1	180953835	180953835	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctggtcatatgagatactttTgcaagtttcttcatcacatt	6	8	4	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:180953835T>C	ENST00000258301.5	-	7	906	c.669A>G	c.(667-669)gcA>gcG	p.A223A	STX6_ENST00000469135.1_5'UTR|STX6_ENST00000542060.1_Silent_p.A122A	NM_005819.4	NP_005810.1	O43752	STX6_HUMAN	syntaxin 6	223	t-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00202}.				endosome organization (GO:0007032)|Golgi vesicle transport (GO:0048193)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147)|vesicle fusion (GO:0006906)	clathrin-coated vesicle (GO:0030136)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|SNARE complex (GO:0031201)|trans-Golgi network membrane (GO:0032588)	SNAP receptor activity (GO:0005484)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)	10						GAGATACTTTTGCAAGTTTCT	0.423																																					p.A223A		Atlas-SNP	.											.	STX6	21	.	0			c.A669G						.						101	96	97					1																	180953835		2203	4300	6503	SO:0001819	synonymous_variant	10228	exon7			TACTTTTGCAAGT	AJ002078	CCDS1341.1, CCDS65738.1	1q25.3	2008-02-05			ENSG00000135823	ENSG00000135823			11441	protein-coding gene	gene with protein product		603944				10080545	Standard	XM_005244824		Approved		uc021pfr.1	O43752	OTTHUMG00000035179	ENST00000258301.5:c.669A>G	chr1.hg19:g.180953835T>C		73.0	0.0		114.0	74.0	NM_005819	B2R652|B4DR17|Q5VY08|Q6FH83	Silent	SNP	ENST00000258301.5	hg19	CCDS1341.1																																																																																			.	.		0.423	STX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085143.1	NM_005819		C	180953835	T	C	180953835	2	2	344	1	0	0	0	0	0	0	0	1	15364	1799	63	2		2	STX6	1	180953835	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	3047457	180953835	68296786	126	47489										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181680158	181680158	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaagctgcggcgccagcagcAgattgagcgtgagctgaatg	16	9	0	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:181680158A>T	ENST00000367573.2	+	8	1124	c.1124A>T	c.(1123-1125)cAg>cTg	p.Q375L	CACNA1E_ENST00000367567.4_5'UTR|CACNA1E_ENST00000526775.1_Missense_Mutation_p.Q375L|CACNA1E_ENST00000357570.5_Missense_Mutation_p.Q326L|CACNA1E_ENST00000367570.1_Missense_Mutation_p.Q375L|CACNA1E_ENST00000360108.3_Missense_Mutation_p.Q375L|CACNA1E_ENST00000358338.5_Missense_Mutation_p.Q326L	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	375	Binding to the beta subunit. {ECO:0000250}.				calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						CGCCAGCAGCAGATTGAGCGT	0.562																																					p.Q375L		Atlas-SNP	.											.	CACNA1E	778	.	0			c.A1124T						.						70	76	74					1																	181680158		1979	4156	6135	SO:0001583	missense	777	exon8			AGCAGCAGATTGA	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.1124A>T	chr1.hg19:g.181680158A>T	ENSP00000356545:p.Gln375Leu	43.0	0.0		75.0	29.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	A	33	5.244349	0.95272	.	.	ENSG00000198216	ENST00000524607;ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.95412	-3.7;-3.7;-3.7;-3.7;-3.7;-3.7;-3.7	5.15	5.15	0.70609	.	0.358022	0.32736	N	0.005720	D	0.97467	0.9171	M	0.81341	2.54	0.80722	D	1	D;D	0.57899	0.981;0.981	D;D	0.70487	0.969;0.969	D	0.98080	1.0403	10	0.66056	D	0.02	.	14.6389	0.68708	1.0:0.0:0.0:0.0	.	375;375	Q15878-2;Q15878-3	.;.	L	375;375;375;326;326;375;375	ENSP00000432038:Q375L;ENSP00000356542:Q375L;ENSP00000434814:Q375L;ENSP00000350183:Q326L;ENSP00000351101:Q326L;ENSP00000353222:Q375L;ENSP00000356545:Q375L	ENSP00000350183:Q326L	Q	+	2	0	CACNA1E	179946781	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.197000	0.94985	1.943000	0.56356	0.533000	0.62120	CAG	.	.		0.562	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		T	181680158	A	T	181680158	3	4	344	1	0	0	0	0	1	0	0	0	2544	188	7	4	1154	4	CACNA1E	1	181680158	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	726323	181680158	67570463	127	47490										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181767600	181767600	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acctgctgatggaagcgaggAgggctccccgctgacctccc	13	15	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:181767600A>T	ENST00000367573.2	+	48	6572	c.6572A>T	c.(6571-6573)gAg>gTg	p.E2191V	CACNA1E_ENST00000367567.4_Missense_Mutation_p.E1755V|CACNA1E_ENST00000526775.1_Missense_Mutation_p.E2129V|CACNA1E_ENST00000357570.5_Missense_Mutation_p.E2142V|CACNA1E_ENST00000367570.1_Missense_Mutation_p.E2148V|CACNA1E_ENST00000360108.3_Missense_Mutation_p.E2172V|CACNA1E_ENST00000358338.5_Missense_Mutation_p.E2080V	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	2191					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						GGAAGCGAGGAGGGCTCCCCG	0.642																																					p.E2191V		Atlas-SNP	.											.	CACNA1E	778	.	0			c.A6572T						.						60	70	66					1																	181767600		2092	4221	6313	SO:0001583	missense	777	exon48			GCGAGGAGGGCTC	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.6572A>T	chr1.hg19:g.181767600A>T	ENSP00000356545:p.Glu2191Val	54.0	0.0		82.0	22.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	A	6.716	0.500795	0.12822	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.96300	-3.91;-3.91;-3.9;-3.91;-3.97;-3.9;-3.9	5.55	3.48	0.39840	.	8.129080	0.00166	N	0.000009	D	0.92967	0.7762	N	0.22421	0.69	0.21897	N	0.999487	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.82641	-0.0357	10	0.32370	T	0.25	.	9.7176	0.40284	0.0825:0.0:0.7689:0.1486	.	2129;2148	Q15878-2;Q15878-3	.;.	V	2148;2129;2142;2080;1755;2172;2191	ENSP00000356542:E2148V;ENSP00000434814:E2129V;ENSP00000350183:E2142V;ENSP00000351101:E2080V;ENSP00000356539:E1755V;ENSP00000353222:E2172V;ENSP00000356545:E2191V	ENSP00000350183:E2142V	E	+	2	0	CACNA1E	180034223	0.984000	0.35163	0.899000	0.35326	0.256000	0.26092	2.044000	0.41241	1.325000	0.45301	-0.479000	0.04858	GAG	.	.		0.642	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		T	181767600	A	T	181767600	3	4	344	1	0	0	0	0	1	0	0	0	2544	304	11	4	6629	4	CACNA1E	1	181767600	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	87442	181767600	67483021	128	47491										
LAMC1	3915	hgsc.bcm.edu	37	chr1	183102629	183102629	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaagggccggtgacaaagctGtggagatctatgccagcgtg	15	8	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:183102629G>T	ENST00000258341.4	+	22	4050	c.3793G>T	c.(3793-3795)Gtg>Ttg	p.V1265L		NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	1265	Domain II and I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						TGACAAAGCTGTGGAGATCTA	0.557																																					p.V1265L		Atlas-SNP	.											.	LAMC1	176	.	0			c.G3793T						.						134	133	133					1																	183102629		2203	4300	6503	SO:0001583	missense	3915	exon22			AAAGCTGTGGAGA	J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"Laminins"	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.3793G>T	chr1.hg19:g.183102629G>T	ENSP00000258341:p.Val1265Leu	86.0	0.0		165.0	45.0	NM_002293	Q5VYE7	Missense_Mutation	SNP	ENST00000258341.4	hg19	CCDS1351.1	.	.	.	.	.	.	.	.	.	.	G	6.372	0.436745	0.12104	.	.	ENSG00000135862	ENST00000258341	T	0.21543	2.0	5.41	5.41	0.78517	.	0.063261	0.64402	D	0.000006	T	0.07818	0.0196	N	0.02286	-0.61	0.34667	D	0.723298	B	0.02656	0.0	B	0.04013	0.001	T	0.12372	-1.0550	10	0.02654	T	1	.	13.9261	0.63964	0.0:0.2675:0.7325:0.0	.	1265	P11047	LAMC1_HUMAN	L	1265	ENSP00000258341:V1265L	ENSP00000258341:V1265L	V	+	1	0	LAMC1	181369252	0.981000	0.34729	0.979000	0.43373	0.635000	0.38103	1.965000	0.40471	2.692000	0.91855	0.563000	0.77884	GTG	.	.		0.557	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293		T	183102629	G	T	183102629	3	4	344	1	0	0	0	0	1	0	0	0	8623	1377	48	3	3879	3	LAMC1	1	183102629	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1335029	183102629	66147992	129	47492										
HMCN1	83872	hgsc.bcm.edu	37	chr1	185902889	185902889	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtgaaattcaacgatgctggAgagtatcattgtatggtttc	11	5	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:185902889A>T	ENST00000271588.4	+	11	1990	c.1761A>T	c.(1759-1761)ggA>ggT	p.G587G	HMCN1_ENST00000367492.2_Silent_p.G587G	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	587	Ig-like C2-type 2.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						ACGATGCTGGAGAGTATCATT	0.443																																					p.G587G		Atlas-SNP	.											.	HMCN1	797	.	0			c.A1761T						.						158	152	154					1																	185902889		2203	4300	6503	SO:0001819	synonymous_variant	83872	exon11			TGCTGGAGAGTAT	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.1761A>T	chr1.hg19:g.185902889A>T		72.0	0.0		134.0	31.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	hg19	CCDS30956.1																																																																																			.	.		0.443	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		T	185902889	A	T	185902889	2	4	344	1	0	0	0	0	0	0	0	1	7229	291	11	4		4	HMCN1	1	185902889	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2800260	185902889	63347732	130	47493										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186092186	186092186	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctccctccgcctgacattacAtggcataaagatgggcgtgc	10	13	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:186092186A>G	ENST00000271588.4	+	81	12562	c.12333A>G	c.(12331-12333)acA>acG	p.T4111T	HMCN1_ENST00000367492.2_Silent_p.T4111T	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	4111	Ig-like C2-type 40.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						CTGACATTACATGGCATAAAG	0.517																																					p.T4111T		Atlas-SNP	.											.	HMCN1	797	.	0			c.A12333G						.						115	91	99					1																	186092186		2203	4300	6503	SO:0001819	synonymous_variant	83872	exon81			CATTACATGGCAT	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.12333A>G	chr1.hg19:g.186092186A>G		63.0	0.0		131.0	44.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	hg19	CCDS30956.1																																																																																			.	.		0.517	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		G	186092186	A	G	186092186	2	3	344	1	0	0	0	0	0	0	0	1	7229	204	8	2		2	HMCN1	1	186092186	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	189297	186092186	63158435	131	47494										
TPR	7175	hgsc.bcm.edu	37	chr1	186291450	186291450	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tttctctttcattaacttacTgaattgcttcagcaaatcca	3	10	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:186291450T>A	ENST00000367478.4	-	45	6757	c.6461A>T	c.(6460-6462)cAt>cTt	p.H2154L		NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	2154					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		ATTAACTTACTGAATTGCTTC	0.333			T	NTRK1	papillary thyroid																																p.H2154L		Atlas-SNP	.		Dom	yes		1	1q25	7175	translocated promoter region		E	.	TPR	441	.	0			c.A6461T						.						78	73	74					1																	186291450		1853	4099	5952	SO:0001630	splice_region_variant	7175	exon45			ACTTACTGAATTG	U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"translocated promoter region (to activated MET oncogene)"			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.6461+1A>T	chr1.hg19:g.186291450T>A		252.0	0.0		459.0	98.0	NM_003292	Q15655|Q5SWY0|Q99968	Missense_Mutation	SNP	ENST00000367478.4	hg19	CCDS41446.1	.	.	.	.	.	.	.	.	.	.	T	15.57	2.872220	0.51695	.	.	ENSG00000047410	ENST00000367478	T	0.23147	1.92	5.13	5.13	0.70059	.	0.052767	0.85682	D	0.000000	T	0.30947	0.0781	M	0.72894	2.215	0.80722	D	1	B	0.28636	0.218	B	0.29440	0.102	T	0.06991	-1.0796	9	.	.	.	.	15.2344	0.73416	0.0:0.0:0.0:1.0	.	2154	P12270	TPR_HUMAN	L	2154	ENSP00000356448:H2154L	.	H	-	2	0	TPR	184558073	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.744000	0.62118	2.060000	0.61445	0.528000	0.53228	CAT	.	.		0.333	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292	Missense_Mutation	A	186291450	T	A	186291450	5	1	344	1	0	0	0	0	0	0	1	0	16431	1594	55	4	658	4	TPR	1	186291450	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	199264	186291450	62959171	132	47495										
TPR	7175	hgsc.bcm.edu	37	chr1	186324666	186324666	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	attttctgctttttctttttTgtagttctcaaaaatttcct	3	7	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:186324666T>G	ENST00000367478.4	-	17	2343	c.2047A>C	c.(2047-2049)Aaa>Caa	p.K683Q	TPR_ENST00000474852.1_5'UTR	NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	683					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		TTTTCTTTTTTGTAGTTCTCA	0.323			T	NTRK1	papillary thyroid																																p.K683Q		Atlas-SNP	.		Dom	yes		1	1q25	7175	translocated promoter region		E	.	TPR	441	.	0			c.A2047C						.						85	77	79					1																	186324666		1795	4067	5862	SO:0001583	missense	7175	exon17			CTTTTTTGTAGTT	U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"translocated promoter region (to activated MET oncogene)"			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.2047A>C	chr1.hg19:g.186324666T>G	ENSP00000356448:p.Lys683Gln	93.0	0.0		202.0	10.0	NM_003292	Q15655|Q5SWY0|Q99968	Missense_Mutation	SNP	ENST00000367478.4	hg19	CCDS41446.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.454264	0.84209	.	.	ENSG00000047410	ENST00000367478	T	0.18657	2.2	5.22	5.22	0.72569	.	0.047201	0.85682	D	0.000000	T	0.42291	0.1196	M	0.72894	2.215	0.49130	D	0.999757	D	0.69078	0.997	P	0.61874	0.895	T	0.21586	-1.0241	10	0.33940	T	0.23	.	15.3973	0.74805	0.0:0.0:0.0:1.0	.	683	P12270	TPR_HUMAN	Q	683	ENSP00000356448:K683Q	ENSP00000356448:K683Q	K	-	1	0	TPR	184591289	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.552000	0.82192	2.106000	0.64143	0.482000	0.46254	AAA	.	.		0.323	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292		G	186324666	T	G	186324666	3	3	344	1	0	0	0	0	1	0	0	0	16431	1821	63	5	5184	5	TPR	1	186324666	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	33216	186324666	62925955	133	47496										
TPR	7175	hgsc.bcm.edu	37	chr1	186327705	186327705	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agatcttttacttgtatttcCattcttcgattatctctctc	3	10	4	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:186327705C>G	ENST00000367478.4	-	13	1763	c.1467G>C	c.(1465-1467)atG>atC	p.M489I	TPR_ENST00000474852.1_5'UTR	NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	489	Necessary for association to the NPC.				carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		CTTGTATTTCCATTCTTCGAT	0.338			T	NTRK1	papillary thyroid																																p.M489I		Atlas-SNP	.		Dom	yes		1	1q25	7175	translocated promoter region		E	.	TPR	441	.	0			c.G1467C						.						180	169	172					1																	186327705		1864	4098	5962	SO:0001583	missense	7175	exon13			TATTTCCATTCTT	U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"translocated promoter region (to activated MET oncogene)"			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.1467G>C	chr1.hg19:g.186327705C>G	ENSP00000356448:p.Met489Ile	78.0	0.0		120.0	79.0	NM_003292	Q15655|Q5SWY0|Q99968	Missense_Mutation	SNP	ENST00000367478.4	hg19	CCDS41446.1	.	.	.	.	.	.	.	.	.	.	C	13.09	2.134750	0.37728	.	.	ENSG00000047410	ENST00000367478	T	0.00949	5.51	5.25	5.25	0.73442	.	0.245265	0.45126	D	0.000390	T	0.01156	0.0038	L	0.27053	0.805	0.31545	N	0.65947	B;B	0.18610	0.029;0.013	B;B	0.20384	0.029;0.004	T	0.39121	-0.9629	10	0.44086	T	0.13	.	15.2379	0.73447	0.0:0.8592:0.1408:0.0	.	489;489	Q15624;P12270	.;TPR_HUMAN	I	489	ENSP00000356448:M489I	ENSP00000356448:M489I	M	-	3	0	TPR	184594328	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.943000	0.40253	2.473000	0.83533	0.655000	0.94253	ATG	.	.		0.338	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292		G	186327705	C	G	186327705	3	3	344	1	0	0	0	0	1	0	0	0	16431	594	21	4	5780	4	TPR	1	186327705	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	3039	186327705	62922916	134	47497										
PTGS2	5743	hgsc.bcm.edu	37	chr1	186645249	186645249	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaaagtagttctgggtcaaaTttcagtttgaagtgatagcc	10	5	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:186645249T>C	ENST00000367468.5	-	8	1174	c.1038A>G	c.(1036-1038)aaA>aaG	p.K346K	PTGS2_ENST00000490885.2_5'UTR	NM_000963.2	NP_000954.1	P35354	PGH2_HUMAN	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	346					anagen (GO:0042640)|angiogenesis (GO:0001525)|arachidonic acid metabolic process (GO:0019369)|bone mineralization (GO:0030282)|brown fat cell differentiation (GO:0050873)|cellular component movement (GO:0006928)|cellular response to ATP (GO:0071318)|cellular response to hypoxia (GO:0071456)|cellular response to mechanical stimulus (GO:0071260)|cellular response to UV (GO:0034644)|cyclooxygenase pathway (GO:0019371)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|inflammatory response (GO:0006954)|learning (GO:0007612)|lipoxygenase pathway (GO:0019372)|maintenance of blood-brain barrier (GO:0035633)|memory (GO:0007613)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of smooth muscle contraction (GO:0045986)|negative regulation of synaptic transmission, dopaminergic (GO:0032227)|ovulation (GO:0030728)|positive regulation of apoptotic process (GO:0043065)|positive regulation of brown fat cell differentiation (GO:0090336)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|positive regulation of fever generation (GO:0031622)|positive regulation of fibroblast growth factor production (GO:0090271)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of platelet-derived growth factor production (GO:0090362)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transforming growth factor beta production (GO:0071636)|positive regulation of vasoconstriction (GO:0045907)|positive regulation vascular endothelial growth factor production (GO:0010575)|prostaglandin biosynthetic process (GO:0001516)|prostaglandin metabolic process (GO:0006693)|regulation of blood pressure (GO:0008217)|regulation of inflammatory response (GO:0050727)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to fatty acid (GO:0070542)|response to fructose (GO:0009750)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to lithium ion (GO:0010226)|response to manganese ion (GO:0010042)|response to oxidative stress (GO:0006979)|response to tumor necrosis factor (GO:0034612)|response to vitamin D (GO:0033280)|sensory perception of pain (GO:0019233)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|neuron projection (GO:0043005)|nucleus (GO:0005634)|protein complex (GO:0043234)	arachidonate 15-lipoxygenase activity (GO:0050473)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)|prostaglandin-endoperoxide synthase activity (GO:0004666)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	27					Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Aldesleukin(DB00041)|Aminosalicylic Acid(DB00233)|Antipyrine(DB01435)|Antrafenine(DB01419)|Balsalazide(DB01014)|Bromfenac(DB00963)|Bumetanide(DB00887)|Carprofen(DB00821)|Celecoxib(DB00482)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Clodronate(DB00720)|Dapsone(DB00250)|Desmopressin(DB00035)|Diclofenac(DB00586)|Diflunisal(DB00861)|Dihomo-gamma-linolenic acid(DB00154)|Drospirenone(DB01395)|Etanercept(DB00005)|Etodolac(DB00749)|Etoposide(DB00773)|Etoricoxib(DB01628)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|Ginseng(DB01404)|Ibuprofen(DB01050)|Icosapent(DB00159)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lenalidomide(DB00480)|Lornoxicam(DB06725)|Lumiracoxib(DB01283)|Magnesium salicylate(DB01397)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mesalazine(DB00244)|Nabumetone(DB00461)|Naproxen(DB00788)|Nepafenac(DB06802)|Niflumic Acid(DB04552)|Nonoxynol-9(DB06804)|Oxaprozin(DB00991)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pomalidomide(DB08910)|Risedronate(DB00884)|Salicylate-sodium(DB01398)|Salicylic acid(DB00936)|Salsalate(DB01399)|Sulfasalazine(DB00795)|Sulindac(DB00605)|Suprofen(DB00870)|Tafluprost(DB08819)|Tenoxicam(DB00469)|Tetrahydrobiopterin(DB00360)|Thalidomide(DB01041)|Tiaprofenic acid(DB01600)|Tolmetin(DB00500)|Triamcinolone(DB00620)|Trisalicylate-choline(DB01401)	CTGGGTCAAATTTCAGTTTGA	0.353																																					p.K346K		Atlas-SNP	.											.	PTGS2	144	.	0			c.A1038G						.						132	134	134					1																	186645249		2203	4300	6503	SO:0001819	synonymous_variant	5743	exon8			GTCAAATTTCAGT	D28235	CCDS1371.1	1q25.2-q25.3	2008-02-05			ENSG00000073756	ENSG00000073756	1.14.99.1		9605	protein-coding gene	gene with protein product		600262				1380156	Standard	NM_000963		Approved	COX2	uc001gsb.3	P35354	OTTHUMG00000035473	ENST00000367468.5:c.1038A>G	chr1.hg19:g.186645249T>C		129.0	0.0		214.0	147.0	NM_000963	A8K802|Q16876	Silent	SNP	ENST00000367468.5	hg19	CCDS1371.1																																																																																			.	.		0.353	PTGS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086157.2	NM_000963		C	186645249	T	C	186645249	2	2	344	1	0	0	0	0	0	0	0	1	12769	1490	52	2		2	PTGS2	1	186645249	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	317544	186645249	62605372	135	47498										
UCHL5	51377	hgsc.bcm.edu	37	chr1	192993077	192993077	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaatttcaccttcactgtacCtagaagaaaattatttaagt	5	7	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:192993077C>A	ENST00000367455.4	-	8	865		c.e8-1		UCHL5_ENST00000530098.2_Splice_Site|UCHL5_ENST00000367454.1_Splice_Site|UCHL5_ENST00000367448.1_Splice_Site|UCHL5_ENST00000367451.4_Splice_Site|UCHL5_ENST00000367452.4_Splice_Site|UCHL5_ENST00000367449.1_Splice_Site	NM_001199261.1|NM_015984.3	NP_001186190.1|NP_057068.1	Q9Y5K5	UCHL5_HUMAN	ubiquitin carboxyl-terminal hydrolase L5						DNA recombination (GO:0006310)|DNA repair (GO:0006281)|forebrain morphogenesis (GO:0048853)|lateral ventricle development (GO:0021670)|midbrain development (GO:0030901)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein deubiquitination (GO:0016579)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|Ino80 complex (GO:0031011)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	endopeptidase inhibitor activity (GO:0004866)|omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|proteasome binding (GO:0070628)|ubiquitin-specific protease activity (GO:0004843)	p.?(1)		NS(1)|breast(1)|cervix(1)|endometrium(5)|large_intestine(1)|lung(9)|ovary(1)	19						TTCACTGTACCTAGAAGAAAA	0.303																																					.		Atlas-SNP	.											UCHL5,NS,carcinoma,0,1	UCHL5	41	.	1	Unknown(1)	lung(1)	c.630-1G>T						.						68	70	69					1																	192993077		2202	4298	6500	SO:0001630	splice_region_variant	51377	exon9			CTGTACCTAGAAG		CCDS1378.1, CCDS55668.1, CCDS55669.1, CCDS55670.1	1q32	2011-07-06			ENSG00000116750	ENSG00000116750		"INO80 complex subunits"	19678	protein-coding gene	gene with protein product	"INO80 complex subunit R"	610667				10810093, 16027725	Standard	NM_015984		Approved	UCH37, CGI-70, INO80R	uc001gsm.3	Q9Y5K5	OTTHUMG00000035561	ENST00000367455.4:c.630-1G>T	chr1.hg19:g.192993077C>A		52.0	0.0		132.0	45.0	NM_015984	Q5LJA6|Q5LJA7|Q8TBS4|Q96BJ9|Q9H1W5|Q9P0I3|Q9UQN2	Splice_Site	SNP	ENST00000367455.4	hg19	CCDS1378.1	.	.	.	.	.	.	.	.	.	.	C	19.61	3.860595	0.71834	.	.	ENSG00000116750	ENST00000420791;ENST00000367455;ENST00000367454;ENST00000367450;ENST00000367451;ENST00000367448;ENST00000367449;ENST00000443327;ENST00000367452;ENST00000530098;ENST00000391991;ENST00000421683	.	.	.	5.07	5.07	0.68467	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.7965	0.91995	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	UCHL5	191259700	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.228000	0.78079	2.510000	0.84645	0.650000	0.86243	.	.	.		0.303	UCHL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086318.3	NM_015984	Intron	A	192993077	C	A	192993077	5	1	344	1	0	0	0	0	0	0	1	0	16937	695	24	3	376	3	UCHL5	1	192993077	Splice_Site	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	6347828	192993077	56257544	136	47499										
TROVE2	6738	hgsc.bcm.edu	37	chr1	193045014	193045014	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gttcatgaattgtataaagaAaaagcactctctgtggagac	9	6	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:193045014A>G	ENST00000367446.3	+	3	855	c.645A>G	c.(643-645)gaA>gaG	p.E215E	TROVE2_ENST00000432079.1_5'UTR|TROVE2_ENST00000367441.1_Silent_p.E215E|TROVE2_ENST00000400968.2_Silent_p.E215E|TROVE2_ENST00000367445.3_Silent_p.E215E|TROVE2_ENST00000460715.2_Intron|TROVE2_ENST00000367444.3_Silent_p.E215E|TROVE2_ENST00000367443.1_Silent_p.E215E|TROVE2_ENST00000416058.2_5'UTR	NM_004600.5	NP_004591.2	P10155	RO60_HUMAN	TROVE domain family, member 2	215	RNA-binding. {ECO:0000250}.|TROVE. {ECO:0000255|PROSITE- ProRule:PRU00343}.				cilium morphogenesis (GO:0060271)|immune system development (GO:0002520)|response to UV (GO:0009411)|smoothened signaling pathway (GO:0007224)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	metal ion binding (GO:0046872)|RNA binding (GO:0003723)|U2 snRNA binding (GO:0030620)			biliary_tract(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|urinary_tract(1)	21						TGTATAAAGAAAAAGCACTCT	0.353																																					p.E215E		Atlas-SNP	.											.	TROVE2	50	.	0			c.A645G						.						82	86	85					1																	193045014		1811	4069	5880	SO:0001819	synonymous_variant	6738	exon3			TAAAGAAAAAGCA	BC036658	CCDS41449.1, CCDS1379.1, CCDS41450.1, CCDS41450.2, CCDS53451.1	1q31	2014-08-06	2005-06-14	2005-06-14	ENSG00000116747	ENSG00000116747			11313	protein-coding gene	gene with protein product		600063	"Sjogren syndrome antigen A2 (60kDa, ribonucleoprotein autoantigen SS-A/Ro)"	SSA2		8188321	Standard	NM_001042369		Approved	Ro60	uc001gss.3	P10155	OTTHUMG00000035675	ENST00000367446.3:c.645A>G	chr1.hg19:g.193045014A>G		161.0	0.0		330.0	104.0	NM_004600	B2RBB9|Q5LJ98|Q5LJ99|Q5LJA0|Q86WL3|Q86WL4|Q92787|Q9H1W6	Silent	SNP	ENST00000367446.3	hg19	CCDS1379.1																																																																																			.	.		0.353	TROVE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086688.1	NM_004600		G	193045014	A	G	193045014	2	3	344	1	0	0	0	0	0	0	0	1	16591	11	1	2		2	TROVE2	1	193045014	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	51937	193045014	56205607	137	47500										
CFH	3075	hgsc.bcm.edu	37	chr1	196714988	196714988	+	Frame_Shift_Del	DEL	G	G	-													0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cccctccacctattgacaatGgggacattacttcattcccg							TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:196714988delG	ENST00000367429.4	+	21	3592	c.3352delG	c.(3352-3354)gggfs	p.G1118fs		NM_000186.3	NP_000177.2	P08603	CFAH_HUMAN	complement factor H	1118	Sushi 19. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)			NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						TATTGACAATGGGGACATTAC	0.398																																					p.N1117fs		Atlas-Indel,Pindel	.											.	CFH	251	.	0			c.3351delT						.						138	133	135					1																	196714988		2203	4300	6503	SO:0001589	frameshift_variant	3075	exon21			.	Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971		"Complement system"	4883	protein-coding gene	gene with protein product	"beta-1H", "H factor 2 (complement)", "age-related maculopathy susceptibility 1"	134370	"H factor 1 (complement)"	HF, HF1, HF2		2889480, 2963625	Standard	NM_000186		Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000367429.4:c.3352delG	chr1.hg19:g.196714988delG	ENSP00000356399:p.Gly1118fs	239.0	0.0		114.0	87.0	NM_000186	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Frame_Shift_Del	DEL	ENST00000367429.4	hg19	CCDS1385.1																																																																																			.	.		0.398	CFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086412.2	NM_000186		-	196714988	G	-	196714988	7	5	344	1	0	1	0	1	0	0	0	0	3285	1348	47	0	3452	0	CFH	1	196714988	Frame_Shift_Del	DEL	G	TCGA-UB-A7MB-01A-11D-A33Q-10	3669974	196714988	52535633	138	47501										
CFHR1	3078	hgsc.bcm.edu	37	chr1	196799671	196799671	+	Frame_Shift_Del	DEL	G	G	-													0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cccctccacctattgacaatGgggacattacttcattcccg							TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:196799671delG	ENST00000320493.5	+	5	737	c.649delG	c.(649-651)gggfs	p.G217fs	CFHR2_ENST00000367421.3_Intron|CFHR1_ENST00000367424.4_Frame_Shift_Del_p.G158fs	NM_002113.2	NP_002104.2	Q03591	FHR1_HUMAN	complement factor H-related 1	217	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|kidney(1)|large_intestine(2)|lung(7)	11						TATTGACAATGGGGACATTAC	0.398																																					p.N216fs		Atlas-INDEL	.											.	CFHR1	47	.	0			c.648delT						.						85	100	95					1																	196799671		1878	4132	6010	SO:0001589	frameshift_variant	3078	exon5			.	M65292	CCDS1386.1	1q32	2014-09-17	2004-08-09	2006-02-28	ENSG00000244414	ENSG00000244414		"Complement system"	4888	protein-coding gene	gene with protein product		134371	"H factor (complement)-like 1", "complement factor H-related 1 pseudogene", "H factor (complement)-like 2"	HFL1, CFHL1, CFHR1P, HFL2, CFHL1P		1711047, 1826708	Standard	NM_002113		Approved	H36-1, FHR1, CFHL, H36-2		Q03591	OTTHUMG00000036276	ENST00000320493.5:c.649delG	chr1.hg19:g.196799671delG	ENSP00000314299:p.Gly217fs	261.0	0.0		183.0	14.0	NM_002113	A8K465|Q3B774|Q9UJ17	Frame_Shift_Del	DEL	ENST00000320493.5	hg19	CCDS1386.1																																																																																			.	.		0.398	CFHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088251.2	NM_002113		-	196799671	G	-	196799671	7	5	344	1	0	1	0	1	0	0	0	0	3286	1348	47	0	667	0	CFHR1	1	196799671	Frame_Shift_Del	DEL	G	TCGA-UB-A7MB-01A-11D-A33Q-10	84683	196799671	52450950	139	47502										
NEK7	140609	hgsc.bcm.edu	37	chr1	198233311	198233311	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcattcattgaagataatgaActaaacatagttttggaact	6	5	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:198233311A>G	ENST00000367385.4	+	5	660	c.318A>G	c.(316-318)gaA>gaG	p.E106E	NEK7_ENST00000538004.1_Silent_p.E106E	NM_133494.2	NP_598001.1	Q8TDX7	NEK7_HUMAN	NIMA-related kinase 7	106	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokinesis (GO:0000910)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle (GO:0007346)|spindle assembly (GO:0051225)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			endometrium(3)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	21						AAGATAATGAACTAAACATAG	0.294																																					p.E106E		Atlas-SNP	.											.	NEK7	42	.	0			c.A318G						.						88	97	94					1																	198233311		2203	4296	6499	SO:0001819	synonymous_variant	140609	exon5			TAATGAACTAAAC	AB062450	CCDS1394.1	1q31.3	2012-11-15	2012-11-15		ENSG00000151414	ENSG00000151414			13386	protein-coding gene	gene with protein product		606848	"NIMA (never in mitosis gene a)-related kinase 7"			11701951	Standard	NM_133494		Approved		uc001gun.4	Q8TDX7	OTTHUMG00000035658	ENST00000367385.4:c.318A>G	chr1.hg19:g.198233311A>G		362.0	0.0		194.0	158.0	NM_133494	A6NGT8	Silent	SNP	ENST00000367385.4	hg19	CCDS1394.1																																																																																			.	.		0.294	NEK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086550.2	NM_133494		G	198233311	A	G	198233311	2	3	344	1	0	0	0	0	0	0	0	1	10338	40	2	2		2	NEK7	1	198233311	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1433640	198233311	51017310	140	47503										
C1orf106	55765	hgsc.bcm.edu	37	chr1	200877954	200877954	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gggtctgcagccaacaggacCtgaggctgggagcccagaac	15	12	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:200877954C>T	ENST00000367342.4	+	7	1126	c.926C>T	c.(925-927)cCt>cTt	p.P309L	C1orf106_ENST00000413687.2_Missense_Mutation_p.P224L	NM_018265.3	NP_060735.3	Q3KP66	CA106_HUMAN	chromosome 1 open reading frame 106	309	Pro-rich.									endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(2)	21						CCAACAGGACCTGAGGCTGGG	0.617																																					p.P323L		Atlas-SNP	.											.	C1orf106	59	.	0			c.C968T						.						54	63	60					1																	200877954		2203	4300	6503	SO:0001583	missense	55765	exon7			CAGGACCTGAGGC	AK001763	CCDS44292.1	1q32.1	2011-02-15			ENSG00000163362	ENSG00000163362			25599	protein-coding gene	gene with protein product						14702039	Standard	NM_018265		Approved	FLJ10901	uc001gvo.4	Q3KP66	OTTHUMG00000035789	ENST00000367342.4:c.926C>T	chr1.hg19:g.200877954C>T	ENSP00000356311:p.Pro309Leu	291.0	0.0		157.0	13.0	NM_018265	B4E1K9|E9PFY0|Q9NV65|Q9NVI0	Missense_Mutation	SNP	ENST00000367342.4	hg19		.	.	.	.	.	.	.	.	.	.	C	11.78	1.741871	0.30865	.	.	ENSG00000163362	ENST00000367342;ENST00000413687	T;T	0.44881	0.91;0.93	5.02	3.14	0.36123	.	0.754737	0.11602	N	0.547689	T	0.44138	0.1279	L	0.60455	1.87	0.18873	N	0.999982	D	0.59357	0.985	P	0.53360	0.724	T	0.23691	-1.0181	10	0.13470	T	0.59	-8.9635	4.7344	0.12981	0.1714:0.6444:0.0:0.1842	.	309	Q3KP66	CA106_HUMAN	L	309;224	ENSP00000356311:P309L;ENSP00000392105:P224L	ENSP00000356311:P309L	P	+	2	0	C1orf106	199144577	0.001000	0.12720	0.024000	0.17045	0.156000	0.22039	0.480000	0.22244	0.514000	0.28300	0.557000	0.71058	CCT	.	.		0.617	C1orf106-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000087057.2	NM_018265		T	200877954	C	T	200877954	3	4	344	1	0	0	0	0	1	0	0	0	1982	681	24	3	952	3	C1orf106	1	200877954	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	2644643	200877954	48372667	141	47504										
LGR6	59352	hgsc.bcm.edu	37	chr1	202287908	202287908	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgcctgcctcaacccactgcTgtacctgctcttcaaccccc	5	20	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:202287908T>A	ENST00000367278.3	+	18	2566	c.2477T>A	c.(2476-2478)cTg>cAg	p.L826Q	LGR6_ENST00000439764.2_Missense_Mutation_p.L687Q|LGR6_ENST00000255432.7_Missense_Mutation_p.L774Q	NM_001017403.1	NP_001017403.1	Q9HBX8	LGR6_HUMAN	leucine-rich repeat containing G protein-coupled receptor 6	826					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of Wnt signaling pathway (GO:0030177)|Wnt signaling pathway (GO:0016055)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	36						AACCCACTGCTGTACCTGCTC	0.677																																					p.L826Q		Atlas-SNP	.											.	LGR6	102	.	0			c.T2477A						.						105	101	102					1																	202287908		2203	4300	6503	SO:0001583	missense	59352	exon18			CACTGCTGTACCT	AF190501	CCDS1424.1, CCDS30971.1, CCDS30972.1	1q32.1	2012-08-21	2011-01-25		ENSG00000133067	ENSG00000133067		"GPCR / Class A : Orphans"	19719	protein-coding gene	gene with protein product		606653	"leucine-rich repeat-containing G protein-coupled receptor 6"			10935549	Standard	XM_005245404		Approved	FLJ14471	uc001gxu.3	Q9HBX8	OTTHUMG00000041383	ENST00000367278.3:c.2477T>A	chr1.hg19:g.202287908T>A	ENSP00000356247:p.Leu826Gln	50.0	0.0		16.0	15.0	NM_001017403	Q5T509|Q5T512|Q6UY15|Q86VU0|Q96K69|Q9BYD7	Missense_Mutation	SNP	ENST00000367278.3	hg19	CCDS30971.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.161088	0.78226	.	.	ENSG00000133067	ENST00000367278;ENST00000255432;ENST00000439764	T;T;T	0.44482	0.92;0.92;0.92	4.6	4.6	0.57074	.	0.000000	0.85682	D	0.000000	T	0.64182	0.2575	M	0.73598	2.24	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	T	0.69401	-0.5155	10	0.87932	D	0	.	14.4872	0.67626	0.0:0.0:0.0:1.0	.	687;774;826	Q9HBX8-1;Q9HBX8-2;Q9HBX8	.;.;LGR6_HUMAN	Q	826;774;687	ENSP00000356247:L826Q;ENSP00000255432:L774Q;ENSP00000387869:L687Q	ENSP00000255432:L774Q	L	+	2	0	LGR6	200554531	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	7.777000	0.85628	2.077000	0.62373	0.397000	0.26171	CTG	.	.		0.677	LGR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099143.1	NM_021636		A	202287908	T	A	202287908	3	1	344	1	0	0	0	0	1	0	0	0	8767	1580	55	4	2694	4	LGR6	1	202287908	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1409954	202287908	46962713	142	47505										
SLC26A9	115019	hgsc.bcm.edu	37	chr1	205884091	205884091	+	3'UTR	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggacactttttgaagcttgtAcagcaggccagcacagttgt	11	9	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:205884091A>G	ENST00000367135.3	-	0	2883				SLC26A9_ENST00000340781.4_Missense_Mutation_p.Y865H|SLC26A9_ENST00000367134.2_Missense_Mutation_p.Y865H	NM_052934.3	NP_443166.1	Q7LBE3	S26A9_HUMAN	solute carrier family 26 (anion exchanger), member 9						anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|positive regulation of gene expression (GO:0010628)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|ATPase binding (GO:0051117)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride channel activity (GO:0005254)|secondary active sulfate transmembrane transporter activity (GO:0008271)			NS(1)|breast(3)|endometrium(11)|kidney(1)|large_intestine(6)|lung(17)|ovary(1)|skin(7)|urinary_tract(5)	52	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0458)			TGAAGCTTGTACAGCAGGCCA	0.527																																					p.Y865H		Atlas-SNP	.											.	SLC26A9	176	.	0			c.T2593C						.						149	140	143					1																	205884091		2203	4300	6503	SO:0001624	3_prime_UTR_variant	115019	exon22			GCTTGTACAGCAG	AF331525	CCDS30989.1, CCDS30990.1	1q32.1	2013-07-18	2013-07-18		ENSG00000174502	ENSG00000174502		"Solute carriers"	14469	protein-coding gene	gene with protein product	"anion transporter/exchanger-9"	608481	"solute carrier family 26, member 9"			11834742	Standard	NM_134325		Approved		uc001hdp.3	Q7LBE3	OTTHUMG00000036001	ENST00000367135.3:c.*394T>C	chr1.hg19:g.205884091A>G		110.0	0.0		40.0	35.0	NM_134325	A7E2V6|B1AVM8|B1AVM9|B7ZKK2|Q96PK9|Q96RN0	Missense_Mutation	SNP	ENST00000367135.3	hg19	CCDS30990.1	.	.	.	.	.	.	.	.	.	.	A	13.87	2.365044	0.41902	.	.	ENSG00000174502	ENST00000340781;ENST00000367134	D;D	0.93659	-3.26;-3.26	4.53	-1.25	0.09405	.	9.319370	0.00166	N	0.000001	D	0.85881	0.5800	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.76217	-0.3040	10	0.87932	D	0	.	8.2911	0.31958	0.475:0.0:0.525:0.0	.	865;112	B1AVM8;Q8NAY2	.;.	H	865	ENSP00000341682:Y865H;ENSP00000356102:Y865H	ENSP00000341682:Y865H	Y	-	1	0	SLC26A9	204150714	0.000000	0.05858	0.000000	0.03702	0.380000	0.30137	-0.050000	0.11904	-0.237000	0.09739	0.379000	0.24179	TAC	.	.		0.527	SLC26A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087742.1	NM_052934		G	205884091	A	G	205884091	1	3	344	0	1	0	0	0	0	0	0	0	14539	391	14	2		2	SLC26A9	1	205884091	3'UTR	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3596183	205884091	43366530	143	47506										
SLC26A9	115019	hgsc.bcm.edu	37	chr1	205897161	205897161	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccactgtgagaccacaggcgAcaccggggtggggaacctgc	15	13	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:205897161A>T	ENST00000367135.3	-	9	1083	c.970T>A	c.(970-972)Tcg>Acg	p.S324T	SLC26A9_ENST00000340781.4_Missense_Mutation_p.S324T|SLC26A9_ENST00000367134.2_Missense_Mutation_p.S324T	NM_052934.3	NP_443166.1	Q7LBE3	S26A9_HUMAN	solute carrier family 26 (anion exchanger), member 9	324					anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|positive regulation of gene expression (GO:0010628)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|ATPase binding (GO:0051117)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride channel activity (GO:0005254)|secondary active sulfate transmembrane transporter activity (GO:0008271)			NS(1)|breast(3)|endometrium(11)|kidney(1)|large_intestine(6)|lung(17)|ovary(1)|skin(7)|urinary_tract(5)	52	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0458)			ACCACAGGCGACACCGGGGTG	0.627																																					p.S324T		Atlas-SNP	.											.	SLC26A9	176	.	0			c.T970A						.						47	44	45					1																	205897161		2203	4300	6503	SO:0001583	missense	115019	exon9			CAGGCGACACCGG	AF331525	CCDS30989.1, CCDS30990.1	1q32.1	2013-07-18	2013-07-18		ENSG00000174502	ENSG00000174502		"Solute carriers"	14469	protein-coding gene	gene with protein product	"anion transporter/exchanger-9"	608481	"solute carrier family 26, member 9"			11834742	Standard	NM_134325		Approved		uc001hdp.3	Q7LBE3	OTTHUMG00000036001	ENST00000367135.3:c.970T>A	chr1.hg19:g.205897161A>T	ENSP00000356103:p.Ser324Thr	58.0	0.0		32.0	28.0	NM_134325	A7E2V6|B1AVM8|B1AVM9|B7ZKK2|Q96PK9|Q96RN0	Missense_Mutation	SNP	ENST00000367135.3	hg19	CCDS30990.1	.	.	.	.	.	.	.	.	.	.	A	6.479	0.456480	0.12283	.	.	ENSG00000174502	ENST00000340781;ENST00000367135;ENST00000367134	D;D;D	0.92595	-3.07;-3.07;-3.07	5.08	1.45	0.22620	Sulphate transporter (1);	0.940463	0.08820	N	0.888975	T	0.75004	0.3791	N	0.02842	-0.48	0.09310	N	1	B;B	0.27791	0.014;0.189	B;B	0.25614	0.023;0.062	T	0.64952	-0.6286	10	0.12430	T	0.62	.	1.1592	0.01802	0.3407:0.289:0.2385:0.1318	.	324;324	Q7LBE3;B1AVM8	S26A9_HUMAN;.	T	324	ENSP00000341682:S324T;ENSP00000356103:S324T;ENSP00000356102:S324T	ENSP00000341682:S324T	S	-	1	0	SLC26A9	204163784	0.000000	0.05858	0.089000	0.20774	0.608000	0.37181	0.264000	0.18497	0.080000	0.16959	0.533000	0.62120	TCG	.	.		0.627	SLC26A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087742.1	NM_052934		T	205897161	A	T	205897161	3	4	344	1	0	0	0	0	1	0	0	0	14539	275	10	4	1753	4	SLC26A9	1	205897161	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	13070	205897161	43353460	144	47507										
CR1	1378	hgsc.bcm.edu	37	chr1	207741308	207741308	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acgagcttcgacctcattggAgagagcaccatccgctgcac	10	14	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:207741308A>G	ENST00000367049.4	+	25	4092	c.4092A>G	c.(4090-4092)ggA>ggG	p.G1364G	CR1_ENST00000367051.1_Silent_p.G914G|CR1_ENST00000367053.1_Silent_p.G914G|RP11-78B10.2_ENST00000596003.1_RNA|RP11-78B10.2_ENST00000597497.1_RNA|CR1_ENST00000367052.1_Intron|CR1_ENST00000400960.2_Silent_p.G914G	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	914	Sushi 21. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						ACCTCATTGGAGAGAGCACCA	0.542																																					p.G1364G		Atlas-SNP	.											.	CR1	354	.	0			c.A4092G						.						88	107	101					1																	207741308		1815	4081	5896	SO:0001819	synonymous_variant	1378	exon25			CATTGGAGAGAGC	Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"CD molecules", "Blood group antigens", "Complement system"	2334	protein-coding gene	gene with protein product		120620	"complement component (3b/4b) receptor 1, including Knops blood group system"			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.4092A>G	chr1.hg19:g.207741308A>G		258.0	0.0		143.0	108.0	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Silent	SNP	ENST00000367049.4	hg19	CCDS44308.1																																																																																			.	.		0.542	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573		G	207741308	A	G	207741308	2	3	344	1	0	0	0	0	0	0	0	1	3842	291	11	2		2	CR1	1	207741308	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1844147	207741308	41509313	145	47508										
RCOR3	55758	hgsc.bcm.edu	37	chr1	211447593	211447593	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	caaaggaaaagcatggctacAatgtggaacaggtatgtaga	12	5	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:211447593A>G	ENST00000367005.4	+	3	310	c.169A>G	c.(169-171)Aat>Gat	p.N57D	RCOR3_ENST00000419091.2_Missense_Mutation_p.N115D|RCOR3_ENST00000452621.2_Missense_Mutation_p.N115D|RCOR3_ENST00000367006.4_Missense_Mutation_p.N115D	NM_018254.3	NP_060724.1	Q9P2K3	RCOR3_HUMAN	REST corepressor 3	57	ELM2. {ECO:0000255|PROSITE- ProRule:PRU00512}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(81;0.00961)|all cancers(67;0.0999)|Epithelial(68;0.171)		GCATGGCTACAATGTGGAACA	0.338																																					p.N115D		Atlas-SNP	.											.	RCOR3	51	.	0			c.A343G						.						84	73	77					1																	211447593		2203	4300	6503	SO:0001583	missense	55758	exon4			GGCTACAATGTGG	AK001738	CCDS31016.1, CCDS44312.1, CCDS44313.1, CCDS44314.1	1q32.3	2008-02-05			ENSG00000117625	ENSG00000117625			25594	protein-coding gene	gene with protein product						10718198	Standard	NM_018254		Approved	FLJ10876	uc010psw.2	Q9P2K3	OTTHUMG00000036996	ENST00000367005.4:c.169A>G	chr1.hg19:g.211447593A>G	ENSP00000355972:p.Asn57Asp	417.0	0.0		201.0	158.0	NM_001136223	B3KYA2|B4DYY7|Q5VT47|Q7L9I5|Q8N5U3|Q9NV83	Missense_Mutation	SNP	ENST00000367005.4	hg19	CCDS31016.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.378708	0.82682	.	.	ENSG00000117625	ENST00000534478;ENST00000533469;ENST00000367006;ENST00000452621;ENST00000419091;ENST00000367005	T;T;T;T;T;T	0.46819	0.86;0.86;0.86;0.86;0.86;0.86	5.58	4.45	0.53987	ELM2 domain (1);	0.041188	0.85682	N	0.000000	T	0.64294	0.2585	M	0.74389	2.26	0.58432	D	0.999999	B;D;P;D	0.89917	0.02;1.0;0.854;1.0	B;D;P;D	0.80764	0.016;0.987;0.77;0.994	T	0.61955	-0.6956	10	0.21014	T	0.42	-20.2804	11.5871	0.50925	0.9296:0.0:0.0704:0.0	.	115;57;115;115	Q9P2K3-3;Q9P2K3;Q9P2K3-2;Q9P2K3-4	.;RCOR3_HUMAN;.;.	D	57;57;115;115;115;57	ENSP00000436057:N57D;ENSP00000436838:N57D;ENSP00000355973:N115D;ENSP00000398558:N115D;ENSP00000413929:N115D;ENSP00000355972:N57D	ENSP00000355972:N57D	N	+	1	0	RCOR3	209514216	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.236000	0.95360	1.045000	0.40225	0.477000	0.44152	AAT	.	.		0.338	RCOR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089821.1	NM_018254		G	211447593	A	G	211447593	3	3	344	1	0	0	0	0	1	0	0	0	13199	130	5	2	357	2	RCOR3	1	211447593	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3706285	211447593	37803028	146	47509										
RPS6KC1	26750	hgsc.bcm.edu	37	chr1	213303010	213303010	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cttcggattcttcagcactaGgggctgttgcttctgacagt	11	10	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:213303010G>T	ENST00000366960.3	+	6	763	c.613G>T	c.(613-615)Ggg>Tgg	p.G205W	RPS6KC1_ENST00000543354.1_Intron|RPS6KC1_ENST00000366959.3_Missense_Mutation_p.G193W|RPS6KC1_ENST00000490299.1_3'UTR|RPS6KC1_ENST00000543470.1_Missense_Mutation_p.G24W	NM_012424.3	NP_036556.2	Q96S38	KS6C1_HUMAN	ribosomal protein S6 kinase, 52kDa, polypeptide 1	205					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(6)|kidney(4)|large_intestine(8)|liver(2)|lung(15)|ovary(3)|prostate(1)|urinary_tract(3)	43				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)		TTCAGCACTAGGGGCTGTTGC	0.443																																					p.G205W		Atlas-SNP	.											.	RPS6KC1	114	.	0			c.G613T						.						87	88	87					1																	213303010		2203	4300	6503	SO:0001583	missense	26750	exon6			GCACTAGGGGCTG	AF037447	CCDS1513.1, CCDS44317.1, CCDS73028.1, CCDS73029.1, CCDS73030.1	1q41	2011-04-05	2002-08-29		ENSG00000136643	ENSG00000136643			10439	protein-coding gene	gene with protein product			"ribosomal protein S6 kinase, 52kD, polypeptide 1"			10552933	Standard	XM_005273095		Approved	humS6PKh1	uc010ptr.2	Q96S38	OTTHUMG00000036926	ENST00000366960.3:c.613G>T	chr1.hg19:g.213303010G>T	ENSP00000355927:p.Gly205Trp	89.0	0.0		39.0	27.0	NM_012424	B1APS8|B3KVM4|D3DTA4|Q8TDD3|Q9NSF4|Q9UL66	Missense_Mutation	SNP	ENST00000366960.3	hg19	CCDS1513.1	.	.	.	.	.	.	.	.	.	.	G	17.92	3.505889	0.64410	.	.	ENSG00000136643	ENST00000543470;ENST00000366960;ENST00000366959	T;T;T	0.33865	1.39;1.49;1.49	5.54	5.54	0.83059	.	0.531595	0.21576	N	0.072327	T	0.42720	0.1215	N	0.24115	0.695	0.80722	D	1	D;D;D	0.89917	1.0;0.998;0.998	D;D;D	0.69654	0.965;0.924;0.924	T	0.37430	-0.9706	10	0.87932	D	0	-24.9991	9.7173	0.40283	0.1579:0.0:0.8421:0.0	.	24;205;193	F5H7T0;Q96S38;B1APS8	.;KS6C1_HUMAN;.	W	24;205;193	ENSP00000442306:G24W;ENSP00000355927:G205W;ENSP00000355926:G193W	ENSP00000355926:G193W	G	+	1	0	RPS6KC1	211369633	0.979000	0.34478	0.996000	0.52242	0.994000	0.84299	3.138000	0.50570	2.605000	0.88082	0.591000	0.81541	GGG	.	.		0.443	RPS6KC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089690.3	NM_012424		T	213303010	G	T	213303010	3	4	344	1	0	0	0	0	1	0	0	0	13673	1000	35	3	635	3	RPS6KC1	1	213303010	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1855417	213303010	35947611	147	47510										
CENPF	1063	hgsc.bcm.edu	37	chr1	214818921	214818921	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgagtgtctccattgcattcAggtggcagaggcagaggtga	15	7	2	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:214818921A>T	ENST00000366955.3	+	13	6176	c.6008A>T	c.(6007-6009)cAg>cTg	p.Q2003L		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	2099					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		CATTGCATTCAGGTGGCAGAG	0.433																																					p.Q2003L	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.A6008T						.						77	77	77					1																	214818921		2203	4300	6503	SO:0001583	missense	1063	exon13			GCATTCAGGTGGC	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.6008A>T	chr1.hg19:g.214818921A>T	ENSP00000355922:p.Gln2003Leu	134.0	0.0		73.0	60.0	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	hg19	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	A	2.986	-0.209229	0.06140	.	.	ENSG00000117724	ENST00000366955	T	0.45276	0.9	4.98	1.38	0.22167	.	1.241830	0.06074	N	0.660694	T	0.26484	0.0647	N	0.19112	0.55	0.09310	N	1	B	0.33073	0.396	B	0.26969	0.075	T	0.18493	-1.0335	10	0.30078	T	0.28	.	8.5774	0.33607	0.5862:0.0:0.4138:0.0	.	2099	P49454	CENPF_HUMAN	L	2003	ENSP00000355922:Q2003L	ENSP00000355922:Q2003L	Q	+	2	0	CENPF	212885544	0.002000	0.14202	0.000000	0.03702	0.036000	0.12997	1.288000	0.33296	-0.009000	0.14296	0.496000	0.49642	CAG	.	.		0.433	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		T	214818921	A	T	214818921	3	4	344	1	0	0	0	0	1	0	0	0	3233	188	7	4	6054	4	CENPF	1	214818921	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1515911	214818921	34431700	148	47511										
USH2A	7399	hgsc.bcm.edu	37	chr1	216373134	216373134	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cgcctgtacagaaaaatcgtActtggcaaatggaaccagat	9	9	0	2	rs376703788		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:216373134A>T	ENST00000307340.3	-	17	4032	c.3646T>A	c.(3646-3648)Tac>Aac	p.Y1216N	RP5-1099E6.3_ENST00000420867.1_RNA|USH2A_ENST00000366943.2_Missense_Mutation_p.Y1216N|USH2A_ENST00000366942.3_Missense_Mutation_p.Y1216N	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	1216	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			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)		GAAAAATCGTACTTGGCAAAT	0.517										HNSCC(13;0.011)																											p.Y1216N		Atlas-SNP	.											.	USH2A	1168	.	0			c.T3646A						.						87	90	89					1																	216373134		2203	4300	6503	SO:0001583	missense	7399	exon17			AATCGTACTTGGC	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.3646T>A	chr1.hg19:g.216373134A>T	ENSP00000305941:p.Tyr1216Asn	147.0	1.0		83.0	67.0	NM_007123	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	A	14.64	2.594957	0.46318	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	D;D;D	0.89270	-2.49;-2.49;-2.49	5.87	5.87	0.94306	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.40818	N	0.001017	D	0.95198	0.8443	M	0.86343	2.81	0.52501	D	0.999956	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95776	0.8813	10	0.87932	D	0	.	16.5764	0.84681	1.0:0.0:0.0:0.0	.	1216;1216	O75445-2;O75445	.;USH2A_HUMAN	N	1216	ENSP00000305941:Y1216N;ENSP00000355910:Y1216N;ENSP00000355909:Y1216N	ENSP00000305941:Y1216N	Y	-	1	0	USH2A	214439757	1.000000	0.71417	0.215000	0.23724	0.068000	0.16541	4.497000	0.60367	2.371000	0.80710	0.533000	0.62120	TAC	.	.		0.517	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	216373134	A	T	216373134	3	4	344	1	0	0	0	0	1	0	0	0	17051	391	14	4	12200	4	USH2A	1	216373134	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1554213	216373134	32877487	149	47512										
ITPKB	3707	hgsc.bcm.edu	37	chr1	226835068	226835068	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aggatcctgccattggcagcTgccttgaaactccctggaga	11	12	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:226835068T>A	ENST00000272117.3	-	3	2045	c.2046A>T	c.(2044-2046)gcA>gcT	p.A682A	ITPKB_ENST00000429204.1_Silent_p.A682A			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	682					cell surface receptor signaling pathway (GO:0007166)|inositol phosphate metabolic process (GO:0043647)|MAPK cascade (GO:0000165)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of Ras protein signal transduction (GO:0046579)|positive thymic T cell selection (GO:0045059)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(1)	30		Prostate(94;0.0773)				CATTGGCAGCTGCCTTGAAAC	0.617																																					p.A682A	Colon(84;110 1851 5306 33547)	Atlas-SNP	.											.	ITPKB	158	.	0			c.A2046T						.						51	49	49					1																	226835068		2203	4300	6503	SO:0001819	synonymous_variant	3707	exon4			GGCAGCTGCCTTG	AJ242780	CCDS1555.1	1q42.12	2011-04-28	2011-04-28		ENSG00000143772	ENSG00000143772	2.7.1.127		6179	protein-coding gene	gene with protein product		147522	"inositol 1,4,5-trisphosphate 3-kinase B"			1654894, 1330886	Standard	NM_002221		Approved	IP3KB, IP3-3KB	uc010pvo.2	P27987	OTTHUMG00000037582	ENST00000272117.3:c.2046A>T	chr1.hg19:g.226835068T>A		44.0	0.0		17.0	15.0	NM_002221	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	Silent	SNP	ENST00000272117.3	hg19	CCDS1555.1																																																																																			.	.		0.617	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221		A	226835068	T	A	226835068	2	1	344	1	0	0	0	0	0	0	0	1	7927	1567	55	4		4	ITPKB	1	226835068	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	10461934	226835068	22415553	150	47513										
URB2	9816	hgsc.bcm.edu	37	chr1	229773082	229773082	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tttctgccttacagctggacAgcctcttgccaccctatcat	6	15	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:229773082A>T	ENST00000258243.2	+	4	2858	c.2722A>T	c.(2722-2724)Agc>Tgc	p.S908C		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	908						aggresome (GO:0016235)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(6)	73						ACAGCTGGACAGCCTCTTGCC	0.507																																					p.S908C		Atlas-SNP	.											.	URB2	152	.	0			c.A2722T						.						210	201	204					1																	229773082		2203	4300	6503	SO:0001583	missense	9816	exon4			CTGGACAGCCTCT	D50923	CCDS31052.1	1q42.13	2009-11-06	2008-10-01	2008-10-01	ENSG00000135763	ENSG00000135763			28967	protein-coding gene	gene with protein product	"nucleolar preribosomal-associated protein 1"		"KIAA0133"	KIAA0133		8590280	Standard	NM_014777		Approved	NPA2, NET10	uc001hts.1	Q14146	OTTHUMG00000039464	ENST00000258243.2:c.2722A>T	chr1.hg19:g.229773082A>T	ENSP00000258243:p.Ser908Cys	59.0	0.0		33.0	31.0	NM_014777	Q5VYC9	Missense_Mutation	SNP	ENST00000258243.2	hg19	CCDS31052.1	.	.	.	.	.	.	.	.	.	.	A	13.88	2.368971	0.42003	.	.	ENSG00000135763	ENST00000258243	T	0.36520	1.25	5.35	1.68	0.24146	.	0.193490	0.56097	D	0.000033	T	0.32852	0.0843	L	0.32530	0.975	0.42359	D	0.9924	D	0.64830	0.994	P	0.54401	0.751	T	0.05989	-1.0852	9	.	.	.	-12.1955	5.8712	0.18805	0.731:0.0:0.1433:0.1256	.	908	Q14146	URB2_HUMAN	C	908	ENSP00000258243:S908C	.	S	+	1	0	URB2	227839705	1.000000	0.71417	1.000000	0.80357	0.264000	0.26372	2.016000	0.40971	0.992000	0.38840	-0.334000	0.08254	AGC	.	.		0.507	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777		T	229773082	A	T	229773082	3	4	344	1	0	0	0	0	1	0	0	0	17040	188	7	4	2732	4	URB2	1	229773082	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2938014	229773082	19477539	151	47514										
SIPA1L2	57568	hgsc.bcm.edu	37	chr1	232577103	232577103	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agagctctttctttataggaAcccaggactttggaaggtgg	12	7	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:232577103A>T	ENST00000366630.1	-	13	3934	c.3576T>A	c.(3574-3576)ggT>ggA	p.G1192G	SIPA1L2_ENST00000308942.4_Silent_p.G266G|SIPA1L2_ENST00000262861.4_Silent_p.G1192G			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	1192					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				CTTTATAGGAACCCAGGACTT	0.413																																					p.G1192G		Atlas-SNP	.											.	SIPA1L2	218	.	0			c.T3576A						.						239	247	244					1																	232577103		1828	4085	5913	SO:0001819	synonymous_variant	57568	exon12			ATAGGAACCCAGG	AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.3576T>A	chr1.hg19:g.232577103A>T		32.0	0.0		20.0	20.0	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Silent	SNP	ENST00000366630.1	hg19	CCDS41474.1																																																																																			.	.		0.413	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839		T	232577103	A	T	232577103	2	4	344	1	0	0	0	0	0	0	0	1	14345	30	2	4		4	SIPA1L2	1	232577103	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2804021	232577103	16673518	152	47515										
PCNXL2	80003	hgsc.bcm.edu	37	chr1	233353792	233353792	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cttgcctttagcagggagtaCtggcagctggccatgacgag	14	10	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:233353792C>A	ENST00000258229.9	-	11	2877	c.2643G>T	c.(2641-2643)caG>caT	p.Q881H	PCNXL2_ENST00000488780.2_Missense_Mutation_p.Q14H|PCNXL2_ENST00000430153.1_Missense_Mutation_p.Q180H	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	881						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				GCAGGGAGTACTGGCAGCTGG	0.478																																					p.Q881H		Atlas-SNP	.											.	PCNXL2	204	.	0			c.G2643T						.						70	70	70					1																	233353792		2045	4214	6259	SO:0001583	missense	80003	exon11			GGAGTACTGGCAG	AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749			8736	protein-coding gene	gene with protein product			"pecanex (Drosophila)-like 2"			12477932	Standard	NM_014801		Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.2643G>T	chr1.hg19:g.233353792C>A	ENSP00000258229:p.Gln881His	153.0	0.0		79.0	69.0	NM_014801	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Missense_Mutation	SNP	ENST00000258229.9	hg19	CCDS44335.1	.	.	.	.	.	.	.	.	.	.	C	16.81	3.225557	0.58668	.	.	ENSG00000135749	ENST00000258229;ENST00000488780;ENST00000518351;ENST00000430153	T;T;T;T	0.71579	-0.58;-0.58;-0.58;-0.58	5.52	4.61	0.57282	.	.	.	.	.	T	0.79446	0.4447	L	0.56396	1.775	0.46185	D	0.998917	D;P	0.76494	0.999;0.666	D;B	0.85130	0.997;0.376	T	0.80529	-0.1342	9	0.87932	D	0	.	9.3781	0.38295	0.0:0.7834:0.0:0.2166	.	180;881	A6NKB5-2;A6NKB5	.;PCX2_HUMAN	H	881;14;61;180	ENSP00000258229:Q881H;ENSP00000430820:Q14H;ENSP00000429231:Q61H;ENSP00000394703:Q180H	ENSP00000258229:Q881H	Q	-	3	2	PCNXL2	231420415	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.105000	0.31086	1.465000	0.48006	0.650000	0.86243	CAG	.	.		0.478	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092480.3	NM_014801		A	233353792	C	A	233353792	3	1	344	1	0	0	0	0	1	0	0	0	11601	564	20	3	3866	3	PCNXL2	1	233353792	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	776689	233353792	15896829	153	47516										
GGPS1	9453	hgsc.bcm.edu	37	chr1	235505654	235505654	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaaaacaggtggactgtttgGattagcagtaggtctcatgc	13	6	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:235505654G>A	ENST00000282841.5	+	4	702	c.470G>A	c.(469-471)gGa>gAa	p.G157E	GGPS1_ENST00000358966.2_Missense_Mutation_p.G157E|GGPS1_ENST00000391855.2_Missense_Mutation_p.G103E|GGPS1_ENST00000488594.1_Missense_Mutation_p.G157E|GGPS1_ENST00000476121.1_Missense_Mutation_p.G157E			O95749	GGPPS_HUMAN	geranylgeranyl diphosphate synthase 1	157					cholesterol biosynthetic process (GO:0006695)|farnesyl diphosphate biosynthetic process (GO:0045337)|geranyl diphosphate biosynthetic process (GO:0033384)|geranylgeranyl diphosphate biosynthetic process (GO:0033386)|isoprenoid metabolic process (GO:0006720)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	dimethylallyltranstransferase activity (GO:0004161)|farnesyltranstransferase activity (GO:0004311)|geranyltranstransferase activity (GO:0004337)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)	8	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00192)|Prostate(94;0.0294)|all_epithelial(177;0.155)|Lung SC(1967;0.238)	OV - Ovarian serous cystadenocarcinoma(106;1.39e-05)		Zoledronate(DB00399)	GGACTGTTTGGATTAGCAGTA	0.393																																					p.G157E		Atlas-SNP	.											.	GGPS1	23	.	0			c.G470A						.						91	97	95					1																	235505654		2203	4300	6503	SO:0001583	missense	9453	exon4			TGTTTGGATTAGC	AB016043	CCDS1604.1	1q43	2010-04-27			ENSG00000152904	ENSG00000152904	2.5.1.1, 2.5.1.10, 2.5.1.29		4249	protein-coding gene	gene with protein product		606982				9741684, 10101267	Standard	NR_036605		Approved	GGPPS1	uc001hwv.3	O95749	OTTHUMG00000037963	ENST00000282841.5:c.470G>A	chr1.hg19:g.235505654G>A	ENSP00000282841:p.Gly157Glu	114.0	0.0		55.0	46.0	NM_001037277	A8MVQ8|Q5T2C8|Q6NW19	Missense_Mutation	SNP	ENST00000282841.5	hg19	CCDS1604.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.116305	0.77323	.	.	ENSG00000152904	ENST00000488594;ENST00000471812;ENST00000358966;ENST00000282841;ENST00000391855;ENST00000476121;ENST00000497327	T;T;T;T;T;T;T	0.61158	0.13;0.13;0.13;0.13;0.13;0.13;0.13	6.17	6.17	0.99709	Terpenoid synthase (2);	0.000000	0.85682	D	0.000000	T	0.59473	0.2196	L	0.40543	1.245	0.80722	D	1	P	0.47910	0.902	P	0.49999	0.628	T	0.47407	-0.9120	10	0.10377	T	0.69	-24.1693	20.8794	0.99867	0.0:0.0:1.0:0.0	.	157	O95749	GGPPS_HUMAN	E	157;157;157;157;103;157;157	ENSP00000418690:G157E;ENSP00000417772:G157E;ENSP00000351852:G157E;ENSP00000282841:G157E;ENSP00000375728:G103E;ENSP00000420183:G157E;ENSP00000417865:G157E	ENSP00000282841:G157E	G	+	2	0	GGPS1	233572277	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.835000	0.99442	2.941000	0.99782	0.655000	0.94253	GGA	.	.		0.393	GGPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092656.1	NM_004837		A	235505654	G	A	235505654	3	1	344	1	0	0	0	0	1	0	0	0	6368	1174	41	3	480	3	GGPS1	1	235505654	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	2151862	235505654	13744967	154	47517										
RYR2	6262	hgsc.bcm.edu	37	chr1	237872815	237872815	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggagcctaacccagaagcagAggagctcttccgcatggtgg	14	11	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:237872815A>T	ENST00000366574.2	+	70	10495	c.10178A>T	c.(10177-10179)gAg>gTg	p.E3393V	RYR2_ENST00000360064.6_Missense_Mutation_p.E3391V|RYR2_ENST00000609119.1_3'UTR|RYR2_ENST00000542537.1_Missense_Mutation_p.E3377V	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	3393					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			CCAGAAGCAGAGGAGCTCTTC	0.408																																					p.E3393V		Atlas-SNP	.											.	RYR2	1273	.	0			c.A10178T						.						94	93	93					1																	237872815		1931	4131	6062	SO:0001583	missense	6262	exon70			AAGCAGAGGAGCT	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.10178A>T	chr1.hg19:g.237872815A>T	ENSP00000355533:p.Glu3393Val	68.0	0.0		36.0	25.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	A	26.9	4.779029	0.90195	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537;ENST00000542288	T;D;T	0.97138	-0.27;-4.26;-0.27	5.5	5.5	0.81552	.	0.000000	0.64402	D	0.000005	D	0.97492	0.9179	M	0.77103	2.36	0.80722	D	1	D	0.62365	0.991	P	0.52217	0.693	D	0.98006	1.0363	10	0.87932	D	0	-17.4196	15.6035	0.76642	1.0:0.0:0.0:0.0	.	3393	Q92736	RYR2_HUMAN	V	3393;3391;3377;348	ENSP00000355533:E3393V;ENSP00000353174:E3391V;ENSP00000443798:E3377V	ENSP00000353174:E3391V	E	+	2	0	RYR2	235939438	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.288000	0.78691	2.082000	0.62665	0.533000	0.62120	GAG	.	.		0.408	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		T	237872815	A	T	237872815	3	4	344	1	0	0	0	0	1	0	0	0	13784	304	11	4	10456	4	RYR2	1	237872815	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2367161	237872815	11377806	155	47518										
SDCCAG8	10806	hgsc.bcm.edu	37	chr1	243433405	243433405	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tttcgtcaggttgttcttgcAgaacatgccagcagaagcat	10	9	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:243433405A>C	ENST00000366541.3	+	2	185		c.e2-1		SDCCAG8_ENST00000355875.4_Splice_Site|SDCCAG8_ENST00000391846.1_Splice_Site|SDCCAG8_ENST00000343783.6_Intron	NM_006642.3	NP_006633.1	Q86SQ7	SDCG8_HUMAN	serologically defined colon cancer antigen 8						establishment of cell polarity (GO:0030010)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|tube formation (GO:0035148)	cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	COAD - Colon adenocarcinoma(196;0.145)		TTGTTCTTGCAGAACATGCCA	0.443																																					.		Atlas-SNP	.											.	SDCCAG8	73	.	0			c.68-2A>C						.						89	71	77					1																	243433405		2203	4300	6503	SO:0001630	splice_region_variant	10806	exon2			TCTTGCAGAACAT	AF039690	CCDS31075.1	1q43	2011-08-02			ENSG00000054282	ENSG00000054282			10671	protein-coding gene	gene with protein product		613524				9610721, 20835237	Standard	NM_006642		Approved	NY-CO-8, CCCAP, SLSN7, NPHP10, BBS16	uc001hzw.3	Q86SQ7	OTTHUMG00000039996	ENST00000366541.3:c.68-1A>C	chr1.hg19:g.243433405A>C		69.0	0.0		30.0	27.0	NM_006642	O60527|Q3ZCR6|Q8N5F2|Q9P0F1	Splice_Site	SNP	ENST00000366541.3	hg19	CCDS31075.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.931596	0.73442	.	.	ENSG00000054282	ENST00000355875;ENST00000391846;ENST00000366541	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.8186	0.63308	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SDCCAG8	241500028	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	5.412000	0.66392	2.311000	0.77944	0.533000	0.62120	.	.	.		0.443	SDCCAG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096485.1	NM_006642	Intron	C	243433405	A	C	243433405	5	2	344	1	0	0	0	0	0	0	1	0	13974	202	7	5	72	5	SDCCAG8	1	243433405	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	5560590	243433405	5817216	156	47519										
ZNF669	79862	hgsc.bcm.edu	37	chr1	247264199	247264199	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gttcatgtattagacaagaaCcggaaacagtgaatgcttta	9	6	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr1:247264199C>A	ENST00000343381.6	-	4	1044	c.872G>T	c.(871-873)gGt>gTt	p.G291V	ZNF669_ENST00000366501.1_3'UTR|ZNF669_ENST00000358785.4_3'UTR|ZNF669_ENST00000448299.2_Missense_Mutation_p.G205V	NM_024804.2	NP_079080.2	Q96BR6	ZN669_HUMAN	zinc finger protein 669	291					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(4)|large_intestine(2)|lung(6)	17	all_cancers(71;4.09e-05)|all_epithelial(71;6.72e-06)|Breast(184;0.0226)|Ovarian(71;0.0283)|all_lung(81;0.0488)|Lung NSC(105;0.053)		OV - Ovarian serous cystadenocarcinoma(106;0.00427)			TAGACAAGAACCGGAAACAGT	0.363																																					p.G291V		Atlas-SNP	.											.	ZNF669	46	.	0			c.G872T						.						64	65	64					1																	247264199		2203	4300	6503	SO:0001583	missense	79862	exon4			CAAGAACCGGAAA		CCDS31088.1, CCDS44345.1	1q44	2013-01-08			ENSG00000188295	ENSG00000188295		"Zinc fingers, C2H2-type", "-"	25736	protein-coding gene	gene with protein product						12477932	Standard	NM_024804		Approved	FLJ12606	uc001ice.2	Q96BR6	OTTHUMG00000040869	ENST00000343381.6:c.872G>T	chr1.hg19:g.247264199C>A	ENSP00000342818:p.Gly291Val	72.0	0.0		27.0	20.0	NM_024804	B3KP94|Q5VT39|Q9H9Q6	Missense_Mutation	SNP	ENST00000343381.6	hg19	CCDS31088.1	.	.	.	.	.	.	.	.	.	.	C	9.506	1.104463	0.20632	.	.	ENSG00000188295	ENST00000535105;ENST00000448299;ENST00000343381	T;T	0.01197	5.19;5.19	0.544	-0.578	0.11724	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01800	0.0057	L	0.53671	1.685	0.09310	N	0.999999	P;P	0.48162	0.89;0.906	B;P	0.46585	0.346;0.521	T	0.44997	-0.9291	9	0.72032	D	0.01	.	4.5429	0.12067	0.0:0.696:0.0:0.304	.	205;291	B3KP94;Q96BR6	.;ZN669_HUMAN	V	205;205;291	ENSP00000404370:G205V;ENSP00000342818:G291V	ENSP00000342818:G291V	G	-	2	0	ZNF669	245330822	0.000000	0.05858	0.001000	0.08648	0.086000	0.17979	-0.514000	0.06298	-0.285000	0.09089	0.289000	0.19496	GGT	.	.		0.363	ZNF669-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000098394.4	NM_024804		A	247264199	C	A	247264199	3	1	344	1	0	0	0	0	1	0	0	0	18091	507	18	3	526	3	ZNF669	1	247264199	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	3830794	247264199	1986422	157	47520										
PXDN	7837	hgsc.bcm.edu	37	chr2	1667460	1667460	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	attcgtactggccctggtcgTggagggcaacaccagagatt	13	10	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:1667460T>A	ENST00000252804.4	-	12	1534	c.1484A>T	c.(1483-1485)cAc>cTc	p.H495L	PXDN_ENST00000483018.1_5'Flank	NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	495	Ig-like C2-type 3.				extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		GCCCTGGTCGTGGAGGGCAAC	0.622																																					p.H495L		Atlas-SNP	.											.	PXDN	255	.	0			c.A1484T						.						83	91	88					2																	1667460		2050	4170	6220	SO:0001583	missense	7837	exon12			TGGTCGTGGAGGG	AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"Immunoglobulin superfamily / I-set domain containing"	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.1484A>T	chr2.hg19:g.1667460T>A	ENSP00000252804:p.His495Leu	56.0	0.0		51.0	25.0	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Missense_Mutation	SNP	ENST00000252804.4	hg19	CCDS46221.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.7|20.7	4.039528|4.039528	0.75732|0.75732	.|.	.|.	ENSG00000130508|ENSG00000130508	ENST00000252804|ENST00000433670	T|.	0.28895|.	1.59|.	5.79|5.79	5.79|5.79	0.91817|0.91817	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	0.114935|.	0.64402|.	D|.	0.000013|.	T|T	0.46405|0.46405	0.1391|0.1391	N|N	0.11673|0.11673	0.155|0.155	0.80722|0.80722	D|D	1|1	D;D|.	0.69078|.	0.984;0.997|.	P;D|.	0.74023|.	0.839;0.982|.	T|T	0.44982|0.44982	-0.9292|-0.9292	10|5	0.59425|.	D|.	0.04|.	-37.822|-37.822	16.1224|16.1224	0.81369|0.81369	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	495;495|.	Q92626-2;Q92626|.	.;PXDN_HUMAN|.	L|S	495|491	ENSP00000252804:H495L|.	ENSP00000252804:H495L|.	H|T	-|-	2|1	0|0	PXDN|PXDN	1646467|1646467	1.000000|1.000000	0.71417|0.71417	0.306000|0.306000	0.25113|0.25113	0.329000|0.329000	0.28539|0.28539	7.706000|7.706000	0.84615|0.84615	2.208000|2.208000	0.71279|0.71279	0.533000|0.533000	0.62120|0.62120	CAC|ACG	.	.		0.622	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455		A	1667460	T	A	1667460	3	1	344	1	0	0	0	0	1	0	0	0	12862	1696	59	4	3003	4	PXDN	2	1667460	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10		1667460	241531913	158	47521										
ADAM17	6868	hgsc.bcm.edu	37	chr2	9668050	9668050	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tttataaactaacattctttTgtctttggtatcattaacaa	3	6	3	0	rs34431503	byFrequency	TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:9668050T>G	ENST00000310823.3	-	5	666	c.484A>C	c.(484-486)Aaa>Caa	p.K162Q	ADAM17_ENST00000497134.1_Missense_Mutation_p.K162Q	NM_003183.4	NP_003174.3	P78536	ADA17_HUMAN	ADAM metallopeptidase domain 17	162			K -> E (in dbSNP:rs34431503).		apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|B cell differentiation (GO:0030183)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell motility (GO:0048870)|collagen catabolic process (GO:0030574)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|germinal center formation (GO:0002467)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil mediated immunity (GO:0002446)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of chemokine production (GO:0032722)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|proteolysis (GO:0006508)|regulation of mast cell apoptotic process (GO:0033025)|response to drug (GO:0042493)|response to high density lipoprotein particle (GO:0055099)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|wound healing, spreading of epidermal cells (GO:0035313)	actin cytoskeleton (GO:0015629)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|interleukin-6 receptor binding (GO:0005138)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|Notch binding (GO:0005112)|PDZ domain binding (GO:0030165)|zinc ion binding (GO:0008270)			breast(1)|cervix(4)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)	28	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.225)		AACATTCTTTTGTCTTTGGTA	0.299																																					p.K162Q		Atlas-SNP	.											.	ADAM17	61	.	0			c.A484C						.						74	74	74					2																	9668050		2203	4300	6503	SO:0001583	missense	6868	exon5			TTCTTTTGTCTTT	U69611	CCDS1665.1	2p25	2010-08-05	2008-07-31		ENSG00000151694	ENSG00000151694		"ADAM metallopeptidase domain containing", "CD molecules"	195	protein-coding gene	gene with protein product		603639	"tumor necrosis factor, alpha, converting enzyme"	TACE		9034190, 9574564	Standard	NM_003183		Approved	cSVP, CD156B	uc002qzu.3	P78536	OTTHUMG00000090425	ENST00000310823.3:c.484A>C	chr2.hg19:g.9668050T>G	ENSP00000309968:p.Lys162Gln	83.0	0.0		75.0	41.0	NM_003183	O60226	Missense_Mutation	SNP	ENST00000310823.3	hg19	CCDS1665.1	.	.	.	.	.	.	.	.	.	.	T	14.62	2.589233	0.46110	.	.	ENSG00000151694	ENST00000310823;ENST00000497134;ENST00000538558	T;T	0.05925	3.37;3.37	5.43	5.43	0.79202	Peptidase M12B, propeptide (1);	0.381144	0.33515	N	0.004836	T	0.09291	0.0229	L	0.43152	1.355	0.24000	N	0.996219	D;B;D;B	0.55172	0.97;0.013;0.97;0.013	P;B;P;B	0.51101	0.659;0.063;0.524;0.063	T	0.29427	-1.0012	10	0.23891	T	0.37	.	8.0246	0.30430	0.0:0.1574:0.0:0.8426	.	162;162;162;162	A8K1B4;B2RNB2;Q6P5T8;P78536	.;.;.;ADA17_HUMAN	Q	162	ENSP00000309968:K162Q;ENSP00000418728:K162Q	ENSP00000309968:K162Q	K	-	1	0	ADAM17	9585501	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	3.669000	0.54561	2.187000	0.69744	0.383000	0.25322	AAA	.	T|0.996;C|0.004		0.299	ADAM17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206857.1			G	9668050	T	G	9668050	3	3	344	1	0	0	0	0	1	0	0	0	238	1821	63	5	2050	5	ADAM17	2	9668050	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	8000590	9668050	233531323	159	47522										
ROCK2	9475	hgsc.bcm.edu	37	chr2	11375944	11375944	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acccatggagtgtattgcatCcagagcaagaacaacttcag	9	10	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:11375944C>T	ENST00000315872.6	-	5	1055	c.607G>A	c.(607-609)Gat>Aat	p.D203N	ROCK2_ENST00000401753.1_5'Flank|ROCK2_ENST00000462366.1_5'Flank|RNU6-1081P_ENST00000384537.1_RNA	NM_004850.3	NP_004841.2	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein kinase 2	203	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|neural tube closure (GO:0001843)|positive regulation of centrosome duplication (GO:0010825)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of circadian rhythm (GO:0042752)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|rhythmic process (GO:0048511)|smooth muscle contraction (GO:0006939)	centrosome (GO:0005813)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole centrosome (GO:0031616)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(6)|lung(10)|prostate(1)|skin(4)|stomach(3)|urinary_tract(2)	43	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)		TGTATTGCATCCAGAGCAAGA	0.413																																					p.D203N		Atlas-SNP	.											.	ROCK2	224	.	0			c.G607A						.						143	137	139					2																	11375944		2047	4234	6281	SO:0001583	missense	9475	exon5			TTGCATCCAGAGC	D87931	CCDS42654.1	2p24	2013-01-10			ENSG00000134318	ENSG00000134318	2.7.11.1	"Pleckstrin homology (PH) domain containing"	10252	protein-coding gene	gene with protein product		604002				9933571	Standard	NM_004850		Approved		uc002rbd.1	O75116	OTTHUMG00000149916	ENST00000315872.6:c.607G>A	chr2.hg19:g.11375944C>T	ENSP00000317985:p.Asp203Asn	204.0	1.0		185.0	95.0	NM_004850	Q53QZ0|Q53SJ7|Q9UQN5	Missense_Mutation	SNP	ENST00000315872.6	hg19	CCDS42654.1	.	.	.	.	.	.	.	.	.	.	C	19.56	3.850223	0.71719	.	.	ENSG00000134318	ENST00000315872	T	0.64260	-0.09	5.84	5.84	0.93424	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.047350	0.85682	D	0.000000	T	0.55529	0.1926	L	0.27975	0.815	0.80722	D	1	P	0.34892	0.474	B	0.42319	0.383	T	0.54860	-0.8230	10	0.39692	T	0.17	.	13.3502	0.60597	0.0:0.9281:0.0:0.0719	.	203	O75116	ROCK2_HUMAN	N	203	ENSP00000317985:D203N	ENSP00000261535:D203N	D	-	1	0	ROCK2	11293395	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.965000	0.63708	2.767000	0.95098	0.591000	0.81541	GAT	.	.		0.413	ROCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313886.3			T	11375944	C	T	11375944	3	4	344	1	0	0	0	0	1	0	0	0	13533	855	30	3	3675	3	ROCK2	2	11375944	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1707894	11375944	231823429	160	47523										
NBAS	51594	hgsc.bcm.edu	37	chr2	15679482	15679482	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggtttcgggtctttcggaacTagaacaaaagaaaacaagag	11	6	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:15679482T>A	ENST00000281513.5	-	7	405		c.e7-2		NBAS_ENST00000441750.1_Splice_Site	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence						negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				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						CTTTCGGAACTAGAACAAAAG	0.398																																					.		Atlas-SNP	.											NBAS,NS,adenocarcinoma,0,1	NBAS	246	.	0			c.380-2A>T						.						69	64	66					2																	15679482		2203	4300	6503	SO:0001630	splice_region_variant	51594	exon8			CGGAACTAGAACA	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.380-2A>T	chr2.hg19:g.15679482T>A		112.0	0.0		104.0	39.0	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Splice_Site	SNP	ENST00000281513.5	hg19	CCDS1685.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.379560	0.82682	.	.	ENSG00000151779	ENST00000441750;ENST00000281513	.	.	.	5.78	5.78	0.91487	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.1095	0.81250	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	NBAS	15596933	1.000000	0.71417	1.000000	0.80357	0.812000	0.45895	7.931000	0.87625	2.210000	0.71456	0.482000	0.46254	.	.	.		0.398	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909	Intron	A	15679482	T	A	15679482	5	1	344	1	0	0	0	0	0	0	1	0	10195	1536	53	4	6921	4	NBAS	2	15679482	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	4303538	15679482	227519891	161	47524										
GEN1	348654	hgsc.bcm.edu	37	chr2	17959314	17959314	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggagttcattgttttgaaatAgaatgggaaaagcctggtat	12	3	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:17959314A>T	ENST00000381254.2	+	12	1462	c.1248A>T	c.(1246-1248)atA>atT	p.I416I	SMC6_ENST00000402989.1_Intron|GEN1_ENST00000317402.7_Silent_p.I416I	NM_001130009.1	NP_001123481.1	Q17RS7	GEN_HUMAN	GEN1 Holliday junction 5' flap endonuclease	416					DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|regulation of centrosome duplication (GO:0010824)|resolution of mitotic recombination intermediates (GO:0071140)|resolution of recombination intermediates (GO:0071139)	centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	crossover junction endodeoxyribonuclease activity (GO:0008821)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					GTTTTGAAATAGAATGGGAAA	0.254								Homologous recombination																													p.I416I		Atlas-SNP	.											.	GEN1	79	.	0			c.A1248T						.						86	93	91					2																	17959314		2198	4275	6473	SO:0001819	synonymous_variant	348654	exon12			TGAAATAGAATGG	AK098188	CCDS1691.1	2p24.2	2013-06-04	2013-06-04		ENSG00000178295	ENSG00000178295			26881	protein-coding gene	gene with protein product	"Holliday junction resolvase"	612449	"Gen endonuclease homolog 1 (Drosophila)"			15576351	Standard	NM_182625		Approved	FLJ40869, Gen	uc002rct.2	Q17RS7	OTTHUMG00000121173	ENST00000381254.2:c.1248A>T	chr2.hg19:g.17959314A>T		276.0	0.0		290.0	145.0	NM_182625	Q17RS9|Q6ZN37	Silent	SNP	ENST00000381254.2	hg19	CCDS1691.1																																																																																			.	.		0.254	GEN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241661.2	NM_182625		T	17959314	A	T	17959314	2	4	344	1	0	0	0	0	0	0	0	1	6343	410	15	4		4	GEN1	2	17959314	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2279832	17959314	225240059	162	47525										
RDH14	57665	hgsc.bcm.edu	37	chr2	18736712	18736712	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgtatgtgcctccccagattTgtccgtacaataccaggatg	9	11	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:18736712T>C	ENST00000381249.3	-	2	863	c.756A>G	c.(754-756)acA>acG	p.T252T	RDH14_ENST00000468071.1_5'UTR	NM_020905.3	NP_065956.1	Q9HBH5	RDH14_HUMAN	retinol dehydrogenase 14 (all-trans/9-cis/11-cis)	252					osteoblast differentiation (GO:0001649)	endoplasmic reticulum (GO:0005783)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	oxidoreductase activity (GO:0016491)			breast(2)|endometrium(1)|large_intestine(2)|lung(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.177)				Vitamin A(DB00162)	TCCCCAGATTTGTCCGTACAA	0.468																																					p.T566T		Atlas-SNP	.											.	.	.	.	0			c.A1698G						.						188	180	183					2																	18736712		2203	4299	6502	SO:0001819	synonymous_variant	100526794	exon9			CAGATTTGTCCGT	AF237952	CCDS1693.1	2p24.2	2011-09-14	2006-05-09		ENSG00000240857	ENSG00000240857	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	19979	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 7C, member 4"		"retinol dehydrogenase 14 (all-trans and 9-cis)"			12226107, 19027726	Standard	NM_020905		Approved	PAN2, SDR7C4		Q9HBH5	OTTHUMG00000090705	ENST00000381249.3:c.756A>G	chr2.hg19:g.18736712T>C		160.0	0.0		140.0	65.0	NM_001199103		Silent	SNP	ENST00000381249.3	hg19	CCDS1693.1																																																																																			.	.		0.468	RDH14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207394.1			C	18736712	T	C	18736712	2	2	344	1	0	0	0	0	0	0	0	1	13208	1799	63	2		2	RDH14	2	18736712	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	777398	18736712	224462661	163	47526										
APOB	338	hgsc.bcm.edu	37	chr2	21231036	21231036	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gttgcgcaggtcagcctgacTagagaagtccagtttgggga	15	8	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:21231036T>A	ENST00000233242.1	-	26	8831	c.8704A>T	c.(8704-8706)Agt>Tgt	p.S2902C		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	2902					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCAGCCTGACTAGAGAAGTCC	0.463																																					p.S2902C		Atlas-SNP	.											.	APOB	761	.	0			c.A8704T						.						174	170	171					2																	21231036		2203	4299	6502	SO:0001583	missense	338	exon26			CCTGACTAGAGAA	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.8704A>T	chr2.hg19:g.21231036T>A	ENSP00000233242:p.Ser2902Cys	106.0	0.0		107.0	49.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	T	19.25	3.791695	0.70452	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.01159	5.25	5.73	5.73	0.89815	.	0.000000	0.64402	D	0.000008	T	0.06962	0.0177	M	0.76574	2.34	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.02026	-1.1227	10	0.87932	D	0	.	15.6927	0.77466	0.0:0.0:0.0:1.0	.	2902	P04114	APOB_HUMAN	C	2902	ENSP00000233242:S2902C	ENSP00000233242:S2902C	S	-	1	0	APOB	21084541	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.067000	0.64357	2.186000	0.69663	0.454000	0.30748	AGT	.	.		0.463	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			A	21231036	T	A	21231036	3	1	344	1	0	0	0	0	1	0	0	0	785	1522	53	4	5003	4	APOB	2	21231036	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2494324	21231036	221968337	164	47527										
OTOF	9381	hgsc.bcm.edu	37	chr2	26699020	26699020	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtagaccaggctgacgggtgGgaaggcatgcaggcccaggc	18	10	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:26699020G>A	ENST00000272371.2	-	23	2968	c.2842C>T	c.(2842-2844)Cca>Tca	p.P948S	OTOF_ENST00000402415.3_Missense_Mutation_p.P258S|OTOF_ENST00000338581.6_Missense_Mutation_p.P201S|OTOF_ENST00000339598.3_Missense_Mutation_p.P201S|OTOF_ENST00000403946.3_Missense_Mutation_p.P948S	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	948	C2 3. {ECO:0000255|PROSITE- ProRule:PRU00041}.				membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			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)					CTGACGGGTGGGAAGGCATGC	0.672																																					p.P948S	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											.	OTOF	524	.	0			c.C2842T						.						34	36	35					2																	26699020		2202	4299	6501	SO:0001583	missense	9381	exon23			CGGGTGGGAAGGC	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"fer-1-like family member 2"	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.2842C>T	chr2.hg19:g.26699020G>A	ENSP00000272371:p.Pro948Ser	44.0	0.0		49.0	18.0	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Missense_Mutation	SNP	ENST00000272371.2	hg19	CCDS1725.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.973095	0.74246	.	.	ENSG00000115155	ENST00000338581;ENST00000339598;ENST00000402415;ENST00000272371;ENST00000403946	D;D;D;D;D	0.84146	-1.56;-1.57;-1.5;-1.81;-1.81	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	D	0.90947	0.7154	L	0.55834	1.745	0.80722	D	1	D;D;D;P	0.89917	1.0;0.999;1.0;0.929	D;D;D;P	0.97110	0.996;0.947;1.0;0.729	D	0.91161	0.4961	10	0.59425	D	0.04	-18.1095	18.7824	0.91939	0.0:0.0:1.0:0.0	.	948;201;258;201	Q9HC10;Q9HC10-2;Q9HC10-3;Q9HC10-4	OTOF_HUMAN;.;.;.	S	201;201;258;948;948	ENSP00000345137:P201S;ENSP00000344521:P201S;ENSP00000383906:P258S;ENSP00000272371:P948S;ENSP00000385255:P948S	ENSP00000272371:P948S	P	-	1	0	OTOF	26552524	1.000000	0.71417	0.994000	0.49952	0.284000	0.27059	9.614000	0.98353	2.546000	0.85860	0.561000	0.74099	CCA	.	.		0.672	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3			A	26699020	G	A	26699020	3	1	344	1	0	0	0	0	1	0	0	0	11312	1232	43	3	3432	3	OTOF	2	26699020	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	5467984	26699020	216500353	165	47528										
C2orf71	388939	hgsc.bcm.edu	37	chr2	29296302	29296302	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	attgagcacctgcagcttgcTgactgtgtactgtagcagct	11	10	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:29296302T>A	ENST00000331664.5	-	1	825	c.826A>T	c.(826-828)Agc>Tgc	p.S276C		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	276					response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						TGCAGCTTGCTGACTGTGTAC	0.577																																					p.S276C		Atlas-SNP	.											.	C2orf71	146	.	0			c.A826T						.						74	76	76					2																	29296302		2032	4191	6223	SO:0001583	missense	388939	exon1			GCTTGCTGACTGT		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.826A>T	chr2.hg19:g.29296302T>A	ENSP00000332809:p.Ser276Cys	60.0	0.0		53.0	22.0	NM_001029883		Missense_Mutation	SNP	ENST00000331664.5	hg19	CCDS42669.1	.	.	.	.	.	.	.	.	.	.	T	17.75	3.466188	0.63625	.	.	ENSG00000179270	ENST00000331664	T	0.22945	1.93	5.62	0.162	0.14981	.	0.536026	0.22033	N	0.065562	T	0.20780	0.0500	L	0.60455	1.87	0.28309	N	0.922755	B	0.18610	0.029	B	0.19666	0.026	T	0.17349	-1.0372	10	0.72032	D	0.01	-3.1826	3.8524	0.08960	0.2595:0.1592:0.0:0.5813	.	276	A6NGG8	CB071_HUMAN	C	276	ENSP00000332809:S276C	ENSP00000332809:S276C	S	-	1	0	C2orf71	29149806	1.000000	0.71417	0.847000	0.33407	0.965000	0.64279	1.869000	0.39519	-0.202000	0.10268	0.459000	0.35465	AGC	.	.		0.577	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883		A	29296302	T	A	29296302	3	1	344	1	0	0	0	0	1	0	0	0	2193	1580	55	4	3048	4	C2orf71	2	29296302	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2597282	29296302	213903071	166	47529										
CAPN13	92291	hgsc.bcm.edu	37	chr2	30966296	30966296	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	attcggagcaagaactccgcTgattttctccgtgtctgtgc	10	11	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:30966296T>A	ENST00000295055.8	-	13	1574	c.1398A>T	c.(1396-1398)tcA>tcT	p.S466S	CAPN13_ENST00000534090.2_Silent_p.S466S	NM_144575.2	NP_653176.2	Q6MZZ7	CAN13_HUMAN	calpain 13	466					proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	30	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					AGAACTCCGCTGATTTTCTCC	0.423																																					p.S466S		Atlas-SNP	.											.	CAPN13	70	.	0			c.A1398T						.						256	247	250					2																	30966296		1887	4133	6020	SO:0001819	synonymous_variant	92291	exon13			CTCCGCTGATTTT		CCDS46252.1	2p22-p21	2008-02-05			ENSG00000162949	ENSG00000162949			16663	protein-coding gene	gene with protein product		610228				11675017	Standard	NM_144575		Approved	FLJ23523	uc021vfm.1	Q6MZZ7	OTTHUMG00000152053	ENST00000295055.8:c.1398A>T	chr2.hg19:g.30966296T>A		132.0	0.0		104.0	44.0	NM_144575	Q17RF0|Q580X1|Q8TE80	Silent	SNP	ENST00000295055.8	hg19	CCDS46252.1																																																																																			.	.		0.423	CAPN13-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325101.2	NM_144575		A	30966296	T	A	30966296	2	1	344	1	0	0	0	0	0	0	0	1	2628	1567	55	4		4	CAPN13	2	30966296	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1669994	30966296	212233077	167	47530										
BIRC6	57448	hgsc.bcm.edu	37	chr2	32726807	32726807	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tggattacatctcactaaacAtgaaaactttcatggtgggt	8	7	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:32726807A>C	ENST00000421745.2	+	47	9193	c.9059A>C	c.(9058-9060)cAt>cCt	p.H3020P		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	3020					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					CTCACTAAACATGAAAACTTT	0.388																																					p.H3020P	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.A9059C						.						102	102	102					2																	32726807		2203	4300	6503	SO:0001583	missense	57448	exon47			CTAAACATGAAAA	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.9059A>C	chr2.hg19:g.32726807A>C	ENSP00000393596:p.His3020Pro	94.0	0.0		88.0	28.0	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	hg19	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	A	17.72	3.458620	0.63401	.	.	ENSG00000115760	ENST00000421745	T	0.74209	-0.82	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.81650	0.4867	L	0.44542	1.39	0.80722	D	1	D	0.65815	0.995	D	0.75484	0.986	T	0.80630	-0.1297	10	0.38643	T	0.18	.	16.1115	0.81266	1.0:0.0:0.0:0.0	.	3020	Q9NR09	BIRC6_HUMAN	P	3020	ENSP00000393596:H3020P	ENSP00000393596:H3020P	H	+	2	0	BIRC6	32580311	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.207000	0.71202	0.460000	0.39030	CAT	.	.		0.388	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		C	32726807	A	C	32726807	3	2	344	1	0	0	0	0	1	0	0	0	1438	217	8	5	9245	5	BIRC6	2	32726807	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1760511	32726807	210472566	168	47531										
BIRC6	57448	hgsc.bcm.edu	37	chr2	32750644	32750644	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cttcaggagcagaggctgccAacaaaataattactgtccca	8	11	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:32750644A>C	ENST00000421745.2	+	59	12003	c.11869A>C	c.(11869-11871)Aac>Cac	p.N3957H		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	3957					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					AGAGGCTGCCAACAAAATAAT	0.428																																					p.N3957H	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.A11869C						.						80	79	79					2																	32750644		2203	4300	6503	SO:0001583	missense	57448	exon59			GCTGCCAACAAAA	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.11869A>C	chr2.hg19:g.32750644A>C	ENSP00000393596:p.Asn3957His	109.0	0.0		112.0	37.0	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	hg19	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	A	15.35	2.806950	0.50421	.	.	ENSG00000115760	ENST00000421745	T	0.75938	-0.98	5.47	4.32	0.51571	.	0.533103	0.21955	N	0.066669	T	0.54447	0.1859	N	0.08118	0	0.24490	N	0.994304	B	0.25955	0.138	B	0.21917	0.037	T	0.51576	-0.8688	10	0.62326	D	0.03	.	11.0191	0.47707	0.9269:0.0:0.0731:0.0	.	3957	Q9NR09	BIRC6_HUMAN	H	3957	ENSP00000393596:N3957H	ENSP00000393596:N3957H	N	+	1	0	BIRC6	32604148	1.000000	0.71417	0.984000	0.44739	0.995000	0.86356	4.717000	0.61923	0.924000	0.37069	0.459000	0.35465	AAC	.	.		0.428	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		C	32750644	A	C	32750644	3	2	344	1	0	0	0	0	1	0	0	0	1438	130	5	5	12103	5	BIRC6	2	32750644	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	23837	32750644	210448729	169	47532										
TTC27	55622	hgsc.bcm.edu	37	chr2	32891805	32891805	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcaaattgtgaattcactccAgcacccactcctcaggaaca	5	14	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:32891805A>T	ENST00000317907.4	+	7	1140	c.909A>T	c.(907-909)ccA>ccT	p.P303P		NM_001193509.1|NM_017735.4	NP_001180438.1|NP_060205.3	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27	303										breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38						AATTCACTCCAGCACCCACTC	0.388																																					p.P303P		Atlas-SNP	.											.	TTC27	71	.	0			c.A909T						.						111	106	108					2																	32891805		2203	4300	6503	SO:0001819	synonymous_variant	55622	exon7			CACTCCAGCACCC	BC063791, AK000279	CCDS33176.1	2p22.3	2013-01-10			ENSG00000018699	ENSG00000018699		"Tetratricopeptide (TTC) repeat domain containing"	25986	protein-coding gene	gene with protein product							Standard	NM_001193509		Approved	FLJ20272	uc002rom.3	Q6P3X3	OTTHUMG00000152134	ENST00000317907.4:c.909A>T	chr2.hg19:g.32891805A>T		107.0	0.0		54.0	28.0	NM_017735	A6NKJ0|Q96SS5|Q9BVF1|Q9NWR4|Q9NXG4	Silent	SNP	ENST00000317907.4	hg19	CCDS33176.1																																																																																			.	.		0.388	TTC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325395.1	NM_017735		T	32891805	A	T	32891805	2	4	344	1	0	0	0	0	0	0	0	1	16710	175	7	4		4	TTC27	2	32891805	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	141161	32891805	210307568	170	47533										
VIT	5212	hgsc.bcm.edu	37	chr2	36982076	36982076	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cttcatagtggtgtgcttgaTaattcaggagggaaaatact	11	5	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:36982076T>A	ENST00000389975.3	+	5	590	c.288T>A	c.(286-288)gaT>gaA	p.D96E	VIT_ENST00000401530.1_Missense_Mutation_p.D96E|VIT_ENST00000404084.1_Missense_Mutation_p.D74E|VIT_ENST00000379241.3_Missense_Mutation_p.D96E|VIT_ENST00000379242.3_Missense_Mutation_p.D96E|VIT_ENST00000497382.1_5'UTR|VIT_ENST00000457137.2_Missense_Mutation_p.D96E	NM_001177969.1|NM_001177970.1	NP_001171440.1|NP_001171441.1	Q6UXI7	VITRN_HUMAN	vitrin	96	LCCL. {ECO:0000255|PROSITE- ProRule:PRU00123}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)	glycosaminoglycan binding (GO:0005539)			autonomic_ganglia(1)|breast(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_hematologic(82;0.248)				GTGTGCTTGATAATTCAGGAG	0.398																																					p.D96E		Atlas-SNP	.											.	VIT	138	.	0			c.T288A						.						157	147	150					2																	36982076		2203	4300	6503	SO:0001583	missense	5212	exon5			GCTTGATAATTCA	AF063833	CCDS33180.1, CCDS54347.1, CCDS54348.1, CCDS54349.1, CCDS54350.1	2p22.2	2008-05-15			ENSG00000205221	ENSG00000205221			12697	protein-coding gene	gene with protein product							Standard	NM_001177969		Approved		uc002rpl.3	Q6UXI7	OTTHUMG00000152149	ENST00000389975.3:c.288T>A	chr2.hg19:g.36982076T>A	ENSP00000374625:p.Asp96Glu	97.0	0.0		99.0	39.0	NM_001177969	A1A526|A6NKI9|A8K7Y4|E9PF47|Q6P7T3|Q96DM8|Q96DT1|Q9UDN0	Missense_Mutation	SNP	ENST00000389975.3	hg19	CCDS54347.1	.	.	.	.	.	.	.	.	.	.	T	16.72	3.200596	0.58126	.	.	ENSG00000205221	ENST00000379242;ENST00000389975;ENST00000402257;ENST00000457137;ENST00000404084;ENST00000379241;ENST00000401530	D;D;D;D;D;D	0.89415	-2.51;-2.51;-2.51;-2.51;-2.51;-2.51	5.63	3.26	0.37387	LCCL (5);	0.314570	0.38217	N	0.001775	D	0.90065	0.6897	L	0.58669	1.825	0.33398	D	0.577005	D;D;P;D;P;D	0.62365	0.966;0.96;0.887;0.96;0.95;0.991	P;P;P;P;P;D	0.63877	0.785;0.814;0.469;0.814;0.716;0.919	D	0.89590	0.3827	10	0.49607	T	0.09	-4.6397	4.0824	0.09932	0.1687:0.1489:0.0:0.6824	.	96;96;96;96;96;96	B4DRU4;E9PF47;Q6UXI7-2;Q6UXI7;Q6UXI7-4;Q6UXI7-3	.;.;.;VITRN_HUMAN;.;.	E	96;96;96;96;74;96;96	ENSP00000368544:D96E;ENSP00000374625:D96E;ENSP00000393561:D96E;ENSP00000384154:D74E;ENSP00000368543:D96E;ENSP00000385658:D96E	ENSP00000368543:D96E	D	+	3	2	VIT	36835580	0.999000	0.42202	0.856000	0.33681	0.932000	0.56968	0.719000	0.25881	0.949000	0.37715	0.533000	0.62120	GAT	.	.		0.398	VIT-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding				A	36982076	T	A	36982076	3	1	344	1	0	0	0	0	1	0	0	0	17186	1403	49	4	302	4	VIT	2	36982076	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	4090271	36982076	206217297	171	47534										
VIT	5212	hgsc.bcm.edu	37	chr2	37035640	37035640	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtgcagaacaaacggcttctActcgctccacgtgcagagct	10	13	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:37035640A>G	ENST00000389975.3	+	14	1672	c.1370A>G	c.(1369-1371)tAc>tGc	p.Y457C	VIT_ENST00000401530.1_Missense_Mutation_p.Y436C|VIT_ENST00000404084.1_Missense_Mutation_p.Y409C|VIT_ENST00000379241.3_Missense_Mutation_p.Y435C|VIT_ENST00000379242.3_Missense_Mutation_p.Y472C|VIT_ENST00000497382.1_Missense_Mutation_p.Y126C	NM_001177969.1|NM_001177970.1	NP_001171440.1|NP_001171441.1	Q6UXI7	VITRN_HUMAN	vitrin	457	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)	glycosaminoglycan binding (GO:0005539)			autonomic_ganglia(1)|breast(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_hematologic(82;0.248)				AACGGCTTCTACTCGCTCCAC	0.612																																					p.Y472C		Atlas-SNP	.											.	VIT	138	.	0			c.A1415G						.						35	31	32					2																	37035640		2203	4300	6503	SO:0001583	missense	5212	exon15			GCTTCTACTCGCT	AF063833	CCDS33180.1, CCDS54347.1, CCDS54348.1, CCDS54349.1, CCDS54350.1	2p22.2	2008-05-15			ENSG00000205221	ENSG00000205221			12697	protein-coding gene	gene with protein product							Standard	NM_001177969		Approved		uc002rpl.3	Q6UXI7	OTTHUMG00000152149	ENST00000389975.3:c.1370A>G	chr2.hg19:g.37035640A>G	ENSP00000374625:p.Tyr457Cys	157.0	0.0		105.0	43.0	NM_053276	A1A526|A6NKI9|A8K7Y4|E9PF47|Q6P7T3|Q96DM8|Q96DT1|Q9UDN0	Missense_Mutation	SNP	ENST00000389975.3	hg19	CCDS54347.1	.	.	.	.	.	.	.	.	.	.	A	16.43	3.120966	0.56613	.	.	ENSG00000205221	ENST00000379242;ENST00000389975;ENST00000497382;ENST00000404084;ENST00000379241;ENST00000401530	T;T;T;T;T;T	0.56941	0.43;0.43;1.15;0.43;0.43;1.15	5.12	5.12	0.69794	von Willebrand factor, type A (2);	0.055007	0.64402	D	0.000001	T	0.62036	0.2395	L	0.43152	1.355	0.53005	D	0.999963	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.81914	0.995;0.991;0.99;0.991	T	0.61983	-0.6950	10	0.45353	T	0.12	-17.7252	10.2202	0.43192	0.852:0.0:0.0:0.148	.	436;435;457;472	E9PF47;Q6UXI7-2;Q6UXI7;Q6UXI7-4	.;.;VITRN_HUMAN;.	C	472;457;126;409;435;436	ENSP00000368544:Y472C;ENSP00000374625:Y457C;ENSP00000417874:Y126C;ENSP00000384154:Y409C;ENSP00000368543:Y435C;ENSP00000385658:Y436C	ENSP00000368543:Y435C	Y	+	2	0	VIT	36889144	1.000000	0.71417	0.954000	0.39281	0.584000	0.36387	4.629000	0.61290	1.929000	0.55896	0.454000	0.30748	TAC	.	.		0.612	VIT-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding				G	37035640	A	G	37035640	3	3	344	1	0	0	0	0	1	0	0	0	17186	391	14	2	1594	2	VIT	2	37035640	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	53564	37035640	206163733	172	47535										
SIX2	10736	hgsc.bcm.edu	37	chr2	45235999	45235999	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtgccttgagccacagctgcTgcagcttggcgtggttgtgc	15	11	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:45235999T>A	ENST00000303077.6	-	1	570	c.251A>T	c.(250-252)cAg>cTg	p.Q84L		NM_016932.4	NP_058628.3	Q9NPC8	SIX2_HUMAN	SIX homeobox 2	84					anatomical structure morphogenesis (GO:0009653)|anterior/posterior axis specification (GO:0009948)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|chondrocyte differentiation (GO:0002062)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|kidney development (GO:0001822)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|mesenchymal stem cell maintenance involved in nephron morphogenesis (GO:0072038)|mesenchymal stem cell proliferation (GO:0097168)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|mesodermal cell fate specification (GO:0007501)|middle ear morphogenesis (GO:0042474)|nephron development (GO:0072006)|nephron morphogenesis (GO:0072028)|positive regulation of chondrocyte proliferation (GO:1902732)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein import into nucleus (GO:0006606)|regulation of branching involved in ureteric bud morphogenesis (GO:0090189)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(6)|large_intestine(3)|lung(8)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	22		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				CCACAGCTGCTGCAGCTTGGC	0.657																																					p.Q84L		Atlas-SNP	.											.	SIX2	39	.	0			c.A251T						.						69	67	67					2																	45235999		2203	4300	6503	SO:0001583	missense	10736	exon1			AGCTGCTGCAGCT	AF136939	CCDS1822.1	2p21	2011-06-20	2007-07-13		ENSG00000170577	ENSG00000170577		"Homeoboxes / SINE class"	10888	protein-coding gene	gene with protein product		604994	"sine oculis homeobox (Drosophila) homolog 2", "sine oculis homeobox homolog 2 (Drosophila)"				Standard	NM_016932		Approved		uc002ruo.3	Q9NPC8	OTTHUMG00000152421	ENST00000303077.6:c.251A>T	chr2.hg19:g.45235999T>A	ENSP00000304502:p.Gln84Leu	48.0	0.0		47.0	17.0	NM_016932	Q9BXH7	Missense_Mutation	SNP	ENST00000303077.6	hg19	CCDS1822.1	.	.	.	.	.	.	.	.	.	.	T	25.8	4.678746	0.88542	.	.	ENSG00000170577	ENST00000303077	D	0.91124	-2.79	4.58	4.58	0.56647	.	0.000000	0.85682	D	0.000000	D	0.96765	0.8944	H	0.96604	3.85	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.79108	0.986;0.992	D	0.97847	1.0272	10	0.87932	D	0	-21.621	13.6109	0.62078	0.0:0.0:0.0:1.0	.	84;84	Q8TBA2;Q9NPC8	.;SIX2_HUMAN	L	84	ENSP00000304502:Q84L	ENSP00000304502:Q84L	Q	-	2	0	SIX2	45089503	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.040000	0.89188	1.691000	0.51100	0.379000	0.24179	CAG	.	.		0.657	SIX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326188.2			A	45235999	T	A	45235999	3	1	344	1	0	0	0	0	1	0	0	0	14362	1580	55	4	632	4	SIX2	2	45235999	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	8200359	45235999	197963374	173	47536										
MCFD2	90411	hgsc.bcm.edu	37	chr2	47134956	47134956	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctgccagacctacctccttaTggacatgagtgatggctgtg	11	11	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:47134956T>C	ENST00000409105.1	-	4	481	c.302A>G	c.(301-303)cAt>cGt	p.H101R	MCFD2_ENST00000409218.1_Missense_Mutation_p.H101R|MCFD2_ENST00000409147.1_Missense_Mutation_p.H49R|AC016722.4_ENST00000429761.1_RNA|MCFD2_ENST00000409913.1_Missense_Mutation_p.H49R|MCFD2_ENST00000444761.2_Missense_Mutation_p.H82R|MCFD2_ENST00000493804.1_Intron|MCFD2_ENST00000409973.1_Missense_Mutation_p.H101R|MCFD2_ENST00000319466.4_Missense_Mutation_p.H101R|MCFD2_ENST00000409207.1_Missense_Mutation_p.H101R|MCFD2_ENST00000409800.1_Missense_Mutation_p.H49R	NM_001171506.2	NP_001164977.1	Q8NI22	MCFD2_HUMAN	multiple coagulation factor deficiency 2	101	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)			central_nervous_system(1)|large_intestine(1)|lung(2)	4		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)		Antihemophilic Factor(DB00025)	TACCTCCTTATGGACATGAGT	0.448																																					p.H101R		Atlas-SNP	.											.	MCFD2	13	.	0			c.A302G						.						117	101	107					2																	47134956		2203	4300	6503	SO:0001583	missense	90411	exon4			TCCTTATGGACAT	AF475284	CCDS33192.1, CCDS54354.1, CCDS54355.1	2p21	2014-09-17			ENSG00000180398	ENSG00000180398		"EF-hand domain containing"	18451	protein-coding gene	gene with protein product		607788				12717434, 2463956	Standard	NM_139279		Approved	F5F8D, LMAN1IP, SDNSF	uc021vha.1	Q8NI22	OTTHUMG00000153100	ENST00000409105.1:c.302A>G	chr2.hg19:g.47134956T>C	ENSP00000386651:p.His101Arg	46.0	0.0		36.0	18.0	NM_001171506	A8K7W2|D6W5A9|E9PD95|Q53SS3|Q68D61|Q8N3M5	Missense_Mutation	SNP	ENST00000409105.1	hg19	CCDS33192.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.501662	0.85176	.	.	ENSG00000180398	ENST00000444761;ENST00000409105;ENST00000409913;ENST00000319466;ENST00000409800;ENST00000409207;ENST00000409973;ENST00000409147;ENST00000409218;ENST00000412438;ENST00000434262	D;D;D;D;D;D;D;D;D;D;D	0.93659	-3.26;-3.26;-3.26;-3.26;-3.26;-3.26;-3.26;-3.26;-3.26;-3.26;-3.26	5.26	5.26	0.73747	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.95934	0.8676	M	0.69823	2.125	0.80722	D	1	D;D	0.89917	0.969;1.0	D;D	0.81914	0.917;0.995	D	0.95212	0.8326	10	0.36615	T	0.2	-7.4954	15.0092	0.71536	0.0:0.0:0.0:1.0	.	82;101	E9PD95;Q8NI22	.;MCFD2_HUMAN	R	82;101;49;101;49;101;101;49;101;101;68	ENSP00000394647:H82R;ENSP00000386651:H101R;ENSP00000386941:H49R;ENSP00000317271:H101R;ENSP00000387202:H49R;ENSP00000386386:H101R;ENSP00000386279:H101R;ENSP00000387082:H49R;ENSP00000386261:H101R;ENSP00000402717:H101R;ENSP00000387360:H68R	ENSP00000317271:H101R	H	-	2	0	MCFD2	46988460	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	7.466000	0.80914	2.208000	0.71279	0.533000	0.62120	CAT	.	.		0.448	MCFD2-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329518.1	NM_139279		C	47134956	T	C	47134956	3	2	344	1	0	0	0	0	1	0	0	0	9390	1464	51	2	146	2	MCFD2	2	47134956	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1898957	47134956	196064417	174	47537										
STON1	11037	hgsc.bcm.edu	37	chr2	48808054	48808054	+	Frame_Shift_Del	DEL	C	C	-													0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttcccaggttttcctggcatCcccaaagcagggactcatgt							TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:48808054delC	ENST00000406226.1	+	3	477	c.282delC	c.(280-282)atcfs	p.I94fs	STON1-GTF2A1L_ENST00000394751.3_Frame_Shift_Del_p.I94fs|STON1-GTF2A1L_ENST00000405008.1_Frame_Shift_Del_p.I94fs|STON1_ENST00000309835.3_Frame_Shift_Del_p.I94fs|STON1_ENST00000404752.1_Frame_Shift_Del_p.I94fs|STON1-GTF2A1L_ENST00000394754.1_Frame_Shift_Del_p.I94fs|STON1-GTF2A1L_ENST00000309827.2_Frame_Shift_Del_p.I94fs|STON1-GTF2A1L_ENST00000402114.2_Frame_Shift_Del_p.I94fs	NM_001198595.1	NP_001185524.1	Q9Y6Q2	STON1_HUMAN	stonin 1	94					endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)	clathrin adaptor complex (GO:0030131)		p.I94I(2)		NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(19)|prostate(3)|skin(2)	37		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TTCCTGGCATCCCCAAAGCAG	0.473																																					p.I94fs		Atlas-Indel,Pindel	.											.	STON1-GTF2A1L	180	.	2	Substitution - coding silent(2)	lung(2)	c.281delT						.						122	124	123					2																	48808054		2203	4300	6503	SO:0001589	frameshift_variant	286749	exon2			.	AF026169	CCDS1841.1	2p16.3	2008-02-05			ENSG00000243244	ENSG00000243244			17003	protein-coding gene	gene with protein product	"stoned B homolog 1 (Drosophila)"	605357				14504226, 10364255	Standard	NM_001198595		Approved	SBLF, stoned-b1		Q9Y6Q2	OTTHUMG00000129169	ENST00000406226.1:c.282delC	chr2.hg19:g.48808054delC	ENSP00000384615:p.Ile94fs	133.0	0.0		107.0	50.0	NM_001198593	A8MXJ1|B5MCF5|B7ZL16|Q96JE3|Q9BYX3	Frame_Shift_Del	DEL	ENST00000406226.1	hg19	CCDS1841.1																																																																																			.	.		0.473	STON1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323848.2	NM_006873		-	48808054	C	-	48808054	7	5	344	1	0	1	0	1	0	0	0	0	15331	845	30	0	284	0	STON1	2	48808054	Frame_Shift_Del	DEL	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1673098	48808054	194391319	175	47538										
FSHR	2492	hgsc.bcm.edu	37	chr2	49190265	49190265	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttggcgatcctggtgtcactAgaggaggacacgatgttggg	16	7	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:49190265A>G	ENST00000406846.2	-	10	1814	c.1695T>C	c.(1693-1695)tcT>tcC	p.S565S	FSHR_ENST00000541117.1_Silent_p.S301S|FSHR_ENST00000304421.4_Silent_p.S539S|FSHR_ENST00000346173.3_Silent_p.S503S	NM_000145.3	NP_000136.2	P23945	FSHR_HUMAN	follicle stimulating hormone receptor	565					female gamete generation (GO:0007292)|female gonad development (GO:0008585)|follicle-stimulating hormone signaling pathway (GO:0042699)|G-protein coupled receptor signaling pathway (GO:0007186)|gonad development (GO:0008406)|male gonad development (GO:0008584)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	follicle-stimulating hormone receptor activity (GO:0004963)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|liver(1)|lung(45)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	73		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Suramin(DB04786)|Urofollitropin(DB00094)	TGGTGTCACTAGAGGAGGACA	0.532									Gonadal Dysgenesis, 46 XX																												p.S565S		Atlas-SNP	.											.	FSHR	164	.	0			c.T1695C						.						99	84	89					2																	49190265		2203	4300	6503	SO:0001819	synonymous_variant	2492	exon10	Familial Cancer Database		GTCACTAGAGGAG		CCDS1843.1, CCDS1844.1, CCDS1844.2	2p21-p16	2014-09-17			ENSG00000170820	ENSG00000170820		"GPCR / Class A : Gonadotropin and TSH receptors"	3969	protein-coding gene	gene with protein product		136435		ODG1		8230163, 8855829	Standard	NM_000145		Approved	FSHRO, LGR1	uc002rww.3	P23945	OTTHUMG00000129259	ENST00000406846.2:c.1695T>C	chr2.hg19:g.49190265A>G		85.0	0.0		76.0	36.0	NM_000145	A8K947|G5CBS7|G5E967|J3KQ00|Q05AH0|Q16225|Q4QRJ3|Q4ZFZ2|Q53RW2	Silent	SNP	ENST00000406846.2	hg19	CCDS1843.1																																																																																			.	.		0.532	FSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251367.2			G	49190265	A	G	49190265	2	3	344	1	0	0	0	0	0	0	0	1	6081	407	15	2		2	FSHR	2	49190265	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	382211	49190265	194009108	176	47539										
NRXN1	9378	hgsc.bcm.edu	37	chr2	50463975	50463975	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cctgaagaactgtccactcgCaccaatacggcttctttctg	7	14	2	2	rs200816799		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:50463975C>A	ENST00000406316.2	-	18	4974	c.3498G>T	c.(3496-3498)gtG>gtT	p.V1166V	NRXN1_ENST00000406859.3_Silent_p.V1166V|NRXN1_ENST00000404971.1_Silent_p.V1206V|NRXN1_ENST00000401669.2_Silent_p.V1166V|NRXN1_ENST00000342183.5_Silent_p.V131V|NRXN1_ENST00000402717.3_Silent_p.V1158V|NRXN1_ENST00000331040.5_5'UTR|NRXN1_ENST00000405472.3_Silent_p.V1158V|NRXN1_ENST00000401710.1_Silent_p.V184V	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	1166	Laminin G-like 6. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			TGTCCACTCGCACCAATACGG	0.423																																					p.V1206V		Atlas-SNP	.											.	NRXN1	1118	.	0			c.G3618T						.						119	106	111					2																	50463975		2203	4300	6503	SO:0001819	synonymous_variant	9378	exon19			CACTCGCACCAAT	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.3498G>T	chr2.hg19:g.50463975C>A		144.0	0.0		139.0	56.0	NM_001135659	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Silent	SNP	ENST00000406316.2	hg19	CCDS54360.1																																																																																			.	.		0.423	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			A	50463975	C	A	50463975	2	1	344	1	0	0	0	0	0	0	0	1	10674	697	25	3		3	NRXN1	2	50463975	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1273710	50463975	192735398	177	47540										
SPTBN1	6711	hgsc.bcm.edu	37	chr2	54874335	54874335	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acaagctgtggaggactatgCagagaccgtgcatcagctct	12	10	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:54874335C>A	ENST00000356805.4	+	24	5215	c.4934C>A	c.(4933-4935)gCa>gAa	p.A1645E	SPTBN1_ENST00000333896.5_Missense_Mutation_p.A1632E	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	1645	Interaction with ANK2.				actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			GAGGACTATGCAGAGACCGTG	0.557																																					p.A1645E		Atlas-SNP	.											.	SPTBN1	378	.	0			c.C4934A						.						111	102	105					2																	54874335		2203	4300	6503	SO:0001583	missense	6711	exon24			ACTATGCAGAGAC		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"Pleckstrin homology (PH) domain containing"	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.4934C>A	chr2.hg19:g.54874335C>A	ENSP00000349259:p.Ala1645Glu	77.0	0.0		58.0	26.0	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Missense_Mutation	SNP	ENST00000356805.4	hg19	CCDS33198.1	.	.	.	.	.	.	.	.	.	.	C	32	5.113667	0.94339	.	.	ENSG00000115306	ENST00000356805;ENST00000333896	T;T	0.44083	0.93;0.93	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.48352	0.1495	L	0.56769	1.78	0.58432	D	0.999999	B;B	0.27656	0.042;0.184	B;B	0.34180	0.084;0.177	T	0.34104	-0.9842	10	0.38643	T	0.18	.	20.3334	0.98727	0.0:1.0:0.0:0.0	.	1632;1645	Q01082-3;Q01082	.;SPTB2_HUMAN	E	1645;1632	ENSP00000349259:A1645E;ENSP00000334156:A1632E	ENSP00000334156:A1632E	A	+	2	0	SPTBN1	54727839	1.000000	0.71417	0.976000	0.42696	0.990000	0.78478	7.770000	0.85390	2.818000	0.97014	0.591000	0.81541	GCA	.	.		0.557	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			A	54874335	C	A	54874335	3	1	344	1	0	0	0	0	1	0	0	0	15134	710	25	3	5137	3	SPTBN1	2	54874335	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	4410360	54874335	188325038	178	47541										
MTIF2	4528	hgsc.bcm.edu	37	chr2	55479663	55479663	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctacagtttgtttcatcactCcatcatctgcagctacaacc	4	14	4	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:55479663C>A	ENST00000263629.4	-	8	1106	c.791G>T	c.(790-792)gGa>gTa	p.G264V	MTIF2_ENST00000403721.1_Missense_Mutation_p.G264V|MTIF2_ENST00000446660.1_5'Flank|MTIF2_ENST00000394600.3_Missense_Mutation_p.G264V	NM_002453.2	NP_002444.2	P46199	IF2M_HUMAN	mitochondrial translational initiation factor 2	264	tr-type G.				formation of translation initiation complex (GO:0001732)|regulation of translational initiation (GO:0006446)|ribosome disassembly (GO:0032790)	mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	24						TTTCATCACTCCATCATCTGC	0.438																																					p.G264V		Atlas-SNP	.											.	MTIF2	64	.	0			c.G791T						.						156	134	142					2																	55479663		2203	4300	6503	SO:0001583	missense	4528	exon8			ATCACTCCATCAT	L34600	CCDS1853.1	2p16.1	2008-02-05			ENSG00000085760	ENSG00000085760			7441	protein-coding gene	gene with protein product		603766				9925935, 7829522	Standard	XM_005264335		Approved	IF-2mt	uc002ryo.3	P46199	OTTHUMG00000129338	ENST00000263629.4:c.791G>T	chr2.hg19:g.55479663C>A	ENSP00000263629:p.Gly264Val	143.0	0.0		171.0	85.0	NM_002453	D6W5D0	Missense_Mutation	SNP	ENST00000263629.4	hg19	CCDS1853.1	.	.	.	.	.	.	.	.	.	.	C	33	5.286507	0.95517	.	.	ENSG00000085760	ENST00000403721;ENST00000263629;ENST00000394600;ENST00000535023	T;T;T	0.81163	-1.46;-1.46;-1.46	6.07	6.07	0.98685	Small GTP-binding protein domain (1);Protein synthesis factor, GTP-binding (1);	0.000000	0.85682	D	0.000000	D	0.95310	0.8478	H	0.99668	4.69	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96819	0.9602	10	0.87932	D	0	-20.8143	20.6593	0.99626	0.0:1.0:0.0:0.0	.	264	P46199	IF2M_HUMAN	V	264	ENSP00000384481:G264V;ENSP00000263629:G264V;ENSP00000378099:G264V	ENSP00000263629:G264V	G	-	2	0	MTIF2	55333167	1.000000	0.71417	0.993000	0.49108	0.984000	0.73092	7.346000	0.79347	2.885000	0.99019	0.655000	0.94253	GGA	.	.		0.438	MTIF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251486.4	NM_002453		A	55479663	C	A	55479663	3	1	344	1	0	0	0	0	1	0	0	0	9943	855	30	3	1428	3	MTIF2	2	55479663	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	605328	55479663	187719710	179	47542										
PNPT1	87178	hgsc.bcm.edu	37	chr2	55910944	55910944	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtatcatagaagtagccagcTggaaagagcggtctaattga	12	6	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:55910944T>A	ENST00000447944.2	-	5	515	c.429A>T	c.(427-429)ccA>ccT	p.P143P		NM_033109.3	NP_149100.2	Q8TCS8	PNPT1_HUMAN	polyribonucleotide nucleotidyltransferase 1	143					cellular response to interferon-beta (GO:0035458)|cellular response to oxidative stress (GO:0034599)|mitochondrial mRNA catabolic process (GO:0000958)|mitochondrial mRNA polyadenylation (GO:0097222)|mitochondrial RNA 3'-end processing (GO:0000965)|mitochondrial RNA 5'-end processing (GO:0000964)|mitochondrial RNA catabolic process (GO:0000957)|mitochondrion morphogenesis (GO:0070584)|mitotic cell cycle arrest (GO:0071850)|mRNA catabolic process (GO:0006402)|negative regulation of growth (GO:0045926)|nuclear polyadenylation-dependent mRNA catabolic process (GO:0071042)|positive regulation of miRNA catabolic process (GO:2000627)|positive regulation of mitochondrial RNA catabolic process (GO:0000962)|positive regulation of mRNA catabolic process (GO:0061014)|protein homooligomerization (GO:0051260)|protein homotrimerization (GO:0070207)|regulation of cellular respiration (GO:0043457)|regulation of cellular senescence (GO:2000772)|RNA catabolic process (GO:0006401)|RNA import into mitochondrion (GO:0035927)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|RNA polyadenylation (GO:0043631)|rRNA import into mitochondrion (GO:0035928)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrial degradosome (GO:0045025)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)	3'-5'-exoribonuclease activity (GO:0000175)|miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|polyribonucleotide nucleotidyltransferase activity (GO:0004654)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(9)|skin(2)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			AGTAGCCAGCTGGAAAGAGCG	0.338																																					p.P143P		Atlas-SNP	.											.	PNPT1	68	.	0			c.A429T						.						63	65	64					2																	55910944		2203	4300	6503	SO:0001819	synonymous_variant	87178	exon5			GCCAGCTGGAAAG	BC053660	CCDS1856.1	2p15	2013-01-08			ENSG00000138035	ENSG00000138035			23166	protein-coding gene	gene with protein product	"polynucleotide phosphorylase", "3'-5' RNA exonuclease"	610316	"deafness, autosomal recessive 70"	DFNB70		12419256	Standard	NM_033109		Approved	PNPase, OLD35, old-35	uc002rzf.3	Q8TCS8	OTTHUMG00000129335	ENST00000447944.2:c.429A>T	chr2.hg19:g.55910944T>A		335.0	1.0		281.0	125.0	NM_033109	Q53SU0|Q68CN1|Q7Z7D1|Q8IWX1|Q96T05|Q9BRU3|Q9BVX0	Silent	SNP	ENST00000447944.2	hg19	CCDS1856.1																																																																																			.	.		0.338	PNPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251481.2	NM_033109		A	55910944	T	A	55910944	2	1	344	1	0	0	0	0	0	0	0	1	12182	1567	55	4		4	PNPT1	2	55910944	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	431281	55910944	187288429	180	47543										
ANTXR1	84168	hgsc.bcm.edu	37	chr2	69304560	69304560	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctggcccggattgcggacagTaaggatcatgtgtttcccgt	13	10	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:69304560T>C	ENST00000303714.4	+	8	904	c.582T>C	c.(580-582)agT>agC	p.S194S	ANTXR1_ENST00000409349.3_Silent_p.S194S|ANTXR1_ENST00000409829.3_Silent_p.S194S	NM_032208.2	NP_115584.1	Q9H6X2	ANTR1_HUMAN	anthrax toxin receptor 1	194	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				actin cytoskeleton reorganization (GO:0031532)|reproductive process (GO:0022414)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|integral component of membrane (GO:0016021)|lamellipodium membrane (GO:0031258)	actin filament binding (GO:0051015)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|transmembrane signaling receptor activity (GO:0004888)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(16)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	29						TTGCGGACAGTAAGGATCATG	0.498									Familial Infantile Hemangioma																												p.S194S		Atlas-SNP	.											.	ANTXR1	128	.	0			c.T582C						.						206	180	189					2																	69304560		2203	4300	6503	SO:0001819	synonymous_variant	84168	exon8	Familial Cancer Database	Infantile Capillary Hemangioma, HCI, Hereditary Capillary Hemangioma	GGACAGTAAGGAT	AF421380	CCDS1892.1, CCDS46313.1, CCDS46314.1	2p13.1	2006-04-12			ENSG00000169604	ENSG00000169604			21014	protein-coding gene	gene with protein product	"anthrax toxin receptor", "tumor endothelial marker 8 precursor"	606410				10947988, 11559528	Standard	NM_032208		Approved	TEM8, FLJ21776, FLJ10601, ATR	uc002sfg.3	Q9H6X2	OTTHUMG00000129575	ENST00000303714.4:c.582T>C	chr2.hg19:g.69304560T>C		78.0	0.0		63.0	26.0	NM_032208	A8K7U8|J7K7G4|J7KF88|Q4ZFV6|Q53QD8|Q96P02|Q9NVP3	Silent	SNP	ENST00000303714.4	hg19	CCDS1892.1	.	.	.	.	.	.	.	.	.	.	T	10.86	1.469983	0.26423	.	.	ENSG00000169604	ENST00000482235	.	.	.	5.39	1.81	0.25067	.	.	.	.	.	T	0.54191	0.1843	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47761	-0.9092	4	.	.	.	-15.7484	6.5138	0.22236	0.0:0.3846:0.0:0.6154	.	.	.	.	A	26	.	.	V	+	2	0	ANTXR1	69158064	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.584000	0.23864	0.883000	0.36040	0.533000	0.62120	GTA	.	.		0.498	ANTXR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251770.2	NM_032208		C	69304560	T	C	69304560	2	2	344	1	0	0	0	0	0	0	0	1	711	1635	57	2		2	ANTXR1	2	69304560	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	13393616	69304560	173894813	181	47544										
DYSF	8291	hgsc.bcm.edu	37	chr2	71780941	71780941	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cgtctctccattccagggtgCcactactactacctaccctg	6	17	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:71780941C>T	ENST00000258104.3	+	21	2212	c.1935C>T	c.(1933-1935)tgC>tgT	p.C645C	DYSF_ENST00000409744.1_Silent_p.C632C|DYSF_ENST00000409582.3_Silent_p.C662C|DYSF_ENST00000409762.1_Silent_p.C662C|DYSF_ENST00000413539.2_Silent_p.C676C|DYSF_ENST00000410020.3_Silent_p.C663C|DYSF_ENST00000429174.2_Silent_p.C645C|DYSF_ENST00000409366.1_Silent_p.C646C|DYSF_ENST00000394120.2_Silent_p.C646C|DYSF_ENST00000409651.1_Silent_p.C677C|DYSF_ENST00000410041.1_Silent_p.C663C	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	645					plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						TTCCAGGGTGCCACTACTACT	0.602																																					p.C677C		Atlas-SNP	.											.	DYSF	536	.	0			c.C2031T						.						108	83	92					2																	71780941		2203	4300	6503	SO:0001819	synonymous_variant	8291	exon22			AGGGTGCCACTAC	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"fer-1-like family member 1"	603009	"limb girdle muscular dystrophy 2B (autosomal recessive)"	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.1935C>T	chr2.hg19:g.71780941C>T		49.0	0.0		53.0	21.0	NM_001130982	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Silent	SNP	ENST00000258104.3	hg19	CCDS1918.1																																																																																			.	.		0.602	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494		T	71780941	C	T	71780941	2	4	344	1	0	0	0	0	0	0	0	1	4861	747	26	3		3	DYSF	2	71780941	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	2476381	71780941	171418432	182	47545										
SEMA4F	10505	hgsc.bcm.edu	37	chr2	74907007	74907007	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gggcccacacagtgggggcgGgactggctggcttcttcttg	17	11	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:74907007G>T	ENST00000357877.2	+	14	2133	c.1984G>T	c.(1984-1986)Gga>Tga	p.G662*	SEMA4F_ENST00000473350.1_3'UTR|SEMA4F_ENST00000339773.5_Nonsense_Mutation_p.G507*	NM_004263.3	NP_004254.2	O95754	SEM4F_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4F	662					axon guidance (GO:0007411)|cell-cell signaling (GO:0007267)|negative regulation of axon extension (GO:0030517)|nervous system development (GO:0007399)|retinal ganglion cell axon guidance (GO:0031290)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor activity (GO:0004872)			biliary_tract(1)|breast(2)|endometrium(8)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	45						AGTGGGGGCGGGACTGGCTGG	0.617																																					p.G662X		Atlas-SNP	.											.	SEMA4F	89	.	0			c.G1984T						.						37	44	42					2																	74907007		2203	4299	6502	SO:0001587	stop_gained	10505	exon14			GGGGCGGGACTGG	AF038652	CCDS1955.1, CCDS62942.1, CCDS74529.1	2p13.1	2008-05-21			ENSG00000135622	ENSG00000135622		"Semaphorins"	10734	protein-coding gene	gene with protein product	"m-Sema M"	603706		SEMAM		10051670	Standard	NM_004263		Approved	SEMAW	uc002sna.2	O95754	OTTHUMG00000129952	ENST00000357877.2:c.1984G>T	chr2.hg19:g.74907007G>T	ENSP00000350547:p.Gly662*	70.0	0.0		57.0	22.0	NM_004263	Q542Y7|Q9NS35	Nonsense_Mutation	SNP	ENST00000357877.2	hg19	CCDS1955.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.399512	0.83120	.	.	ENSG00000135622	ENST00000357877;ENST00000339773	.	.	.	5.38	5.38	0.77491	.	1.629780	0.04048	N	0.304234	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	14.6234	0.68602	0.0:0.0:1.0:0.0	.	.	.	.	X	662;507	.	ENSP00000342675:G507X	G	+	1	0	SEMA4F	74760515	1.000000	0.71417	0.983000	0.44433	0.128000	0.20619	3.733000	0.55029	2.526000	0.85167	0.467000	0.42956	GGA	.	.		0.617	SEMA4F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252214.2	NM_004263		T	74907007	G	T	74907007	4	4	344	1	0	0	0	0	0	1	0	0	14050	1233	43	3	2038	3	SEMA4F	2	74907007	Nonsense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	3126066	74907007	168292366	183	47546										
LRRTM1	347730	hgsc.bcm.edu	37	chr2	80529619	80529619	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gacacgtagagcaccaggacCacgatgaggaaggagaagat	14	8	0	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:80529619C>A	ENST00000295057.3	-	2	1982	c.1326G>T	c.(1324-1326)gtG>gtT	p.V442V	CTNNA2_ENST00000466387.1_Intron|CTNNA2_ENST00000541047.1_Intron|CTNNA2_ENST00000402739.4_Intron|LRRTM1_ENST00000409148.1_Silent_p.V442V|CTNNA2_ENST00000540488.1_Intron|CTNNA2_ENST00000496558.1_Intron|CTNNA2_ENST00000361291.4_Intron	NM_178839.4	NP_849161.2	Q86UE6	LRRT1_HUMAN	leucine rich repeat transmembrane neuronal 1	442					exploration behavior (GO:0035640)|locomotory behavior (GO:0007626)|long-term synaptic potentiation (GO:0060291)|negative regulation of receptor internalization (GO:0002091)|protein localization to synapse (GO:0035418)|synapse organization (GO:0050808)	axon (GO:0030424)|cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)		p.V442V(1)		NS(1)|breast(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(33)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	63						GCACCAGGACCACGATGAGGA	0.602										HNSCC(69;0.2)																											p.V442V		Atlas-SNP	.											LRRTM1,NS,carcinoma,0,1	LRRTM1	251	.	1	Substitution - coding silent(1)	ovary(1)	c.G1326T						.						106	93	97					2																	80529619		2203	4300	6503	SO:0001819	synonymous_variant	347730	exon2			CAGGACCACGATG	AY358310	CCDS1966.1	2p12	2004-06-22			ENSG00000162951	ENSG00000162951			19408	protein-coding gene	gene with protein product		610867				12676565	Standard	XR_244930		Approved	FLJ32082	uc002sok.1	Q86UE6	OTTHUMG00000130021	ENST00000295057.3:c.1326G>T	chr2.hg19:g.80529619C>A		37.0	0.0		27.0	10.0	NM_178839	A8K397|D6W5K1|Q96DN1	Silent	SNP	ENST00000295057.3	hg19	CCDS1966.1																																																																																			.	.		0.602	LRRTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313614.1	NM_178839		A	80529619	C	A	80529619	2	1	344	1	0	0	0	0	0	0	0	1	9048	581	21	3		3	LRRTM1	2	80529619	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	5622612	80529619	162669754	184	47547										
DNAH6	1768	hgsc.bcm.edu	37	chr2	84954900	84954900	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcttatgtcaatgtttcaagAggactttttgagcaacataa	8	6	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:84954900A>G	ENST00000237449.6	+	60	10088	c.10080A>G	c.(10078-10080)agA>agG	p.R3360R	DNAH6_ENST00000389394.3_Silent_p.R3360R			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	3360					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						ATGTTTCAAGAGGACTTTTTG	0.393																																					p.R3360R		Atlas-SNP	.											.	DNAH6	194	.	0			c.A10080G						.						180	150	159					2																	84954900		692	1591	2283	SO:0001819	synonymous_variant	1768	exon61			TTCAAGAGGACTT	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.10080A>G	chr2.hg19:g.84954900A>G		77.0	0.0		77.0	35.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	hg19	CCDS46348.1																																																																																			.	.		0.393	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		G	84954900	A	G	84954900	2	3	344	1	0	0	0	0	0	0	0	1	4607	301	11	2		2	DNAH6	2	84954900	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	4425281	84954900	158244473	185	47548										
DNAH6	1768	hgsc.bcm.edu	37	chr2	85024758	85024758	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccagaaatttttggaatgcaTgaaaatgctaatctagtctt	7	6	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:85024758T>A	ENST00000237449.6	+	69	11465	c.11457T>A	c.(11455-11457)caT>caA	p.H3819Q	DNAH6_ENST00000389394.3_Missense_Mutation_p.H3819Q			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	3819					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						TTGGAATGCATGAAAATGCTA	0.378																																					p.H3819Q		Atlas-SNP	.											.	DNAH6	194	.	0			c.T11457A						.						195	168	176					2																	85024758		692	1591	2283	SO:0001583	missense	1768	exon70			AATGCATGAAAAT	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.11457T>A	chr2.hg19:g.85024758T>A	ENSP00000237449:p.His3819Gln	65.0	0.0		57.0	33.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	hg19	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.236138	0.79800	.	.	ENSG00000115423	ENST00000389394;ENST00000237449	T;T	0.10192	2.9;2.9	5.63	4.47	0.54385	Dynein heavy chain (1);	0.000000	0.85682	D	0.000000	T	0.44685	0.1305	H	0.97158	3.95	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.55933	-0.8062	10	0.87932	D	0	.	9.7366	0.40392	0.0:0.0819:0.0:0.9181	.	3819;578	Q9C0G6;Q9C0G6-2	DYH6_HUMAN;.	Q	3819	ENSP00000374045:H3819Q;ENSP00000237449:H3819Q	ENSP00000237449:H3819Q	H	+	3	2	DNAH6	84878269	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.768000	0.62293	0.965000	0.38133	0.523000	0.50628	CAT	.	.		0.378	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		A	85024758	T	A	85024758	3	1	344	1	0	0	0	0	1	0	0	0	4607	1461	51	4	11731	4	DNAH6	2	85024758	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	69858	85024758	158174615	186	47549										
ASTL	431705	hgsc.bcm.edu	37	chr2	96795631	96795631	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggacccgggtgatgtccgagGcactcaggttccatcgctgg	15	12	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:96795631G>A	ENST00000342380.2	-	8	805	c.806C>T	c.(805-807)gCc>gTc	p.A269V		NM_001002036.3	NP_001002036.3			astacin-like metallo-endopeptidase (M12 family)											endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|prostate(1)|skin(2)	30						GATGTCCGAGGCACTCAGGTT	0.657																																					p.A269V		Atlas-SNP	.											.	ASTL	59	.	0			c.C806T						.						46	53	50					2																	96795631		2203	4300	6503	SO:0001583	missense	431705	exon8			TCCGAGGCACTCA	AJ537600	CCDS33249.1	2q11.1	2014-07-23	2006-10-10		ENSG00000188886	ENSG00000188886	3.4.24.21		31704	protein-coding gene	gene with protein product	"sperm acrosomal SLLP1 binding"	608860	"astacin-like metalloendopeptidase (M12 family)"			15087446	Standard	NM_001002036		Approved	ovastacin, SAS1B	uc010yui.2	Q6HA08	OTTHUMG00000155212	ENST00000342380.2:c.806C>T	chr2.hg19:g.96795631G>A	ENSP00000343674:p.Ala269Val	130.0	0.0		117.0	54.0	NM_001002036		Missense_Mutation	SNP	ENST00000342380.2	hg19	CCDS33249.1	.	.	.	.	.	.	.	.	.	.	G	13.11	2.139528	0.37728	.	.	ENSG00000188886	ENST00000342380	T	0.63744	-0.06	4.14	0.985	0.19779	Peptidase M12A, astacin (2);Metallopeptidase, catalytic domain (1);	0.932364	0.08949	N	0.870358	T	0.46249	0.1383	L	0.33710	1.025	0.09310	N	1	B	0.25441	0.126	B	0.28916	0.096	T	0.37009	-0.9724	10	0.31617	T	0.26	-2.213	2.4813	0.04587	0.1089:0.1879:0.5101:0.1931	.	269	Q6HA08	ASTL_HUMAN	V	269	ENSP00000343674:A269V	ENSP00000343674:A269V	A	-	2	0	ASTL	96159358	0.000000	0.05858	0.651000	0.29564	0.998000	0.95712	0.548000	0.23314	0.335000	0.23614	0.555000	0.69702	GCC	.	.		0.657	ASTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338801.1			A	96795631	G	A	96795631	3	1	344	1	0	0	0	0	1	0	0	0	1063	1203	42	3	496	3	ASTL	2	96795631	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	11770873	96795631	146403742	187	47550										
SNRNP200	23020	hgsc.bcm.edu	37	chr2	96966755	96966755	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cctcctcatcagactcaaacTgcacattcacaccgtatgtc	4	16	4	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:96966755T>C	ENST00000323853.5	-	5	688	c.611A>G	c.(610-612)cAg>cGg	p.Q204R	SNRNP200_ENST00000349783.5_Missense_Mutation_p.Q204R	NM_014014.4	NP_054733.2	O75643	U520_HUMAN	small nuclear ribonucleoprotein 200kDa (U5)	204					ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|lung(37)|ovary(7)|prostate(4)|skin(5)|stomach(1)|urinary_tract(1)	90						AGACTCAAACTGCACATTCAC	0.418																																					p.Q204R		Atlas-SNP	.											.	SNRNP200	195	.	0			c.A611G						.						244	193	210					2																	96966755		2203	4300	6503	SO:0001583	missense	23020	exon5			TCAAACTGCACAT	AL831994	CCDS2020.1	2q11.2	2013-05-13	2008-10-29	2008-10-29	ENSG00000144028	ENSG00000144028			30859	protein-coding gene	gene with protein product	"U5 snRNP specific protein, 200 KD"	601664	"activating signal cointegrator 1 complex subunit 3-like 1", "retinitis pigmentosa 33 (autosomal dominant)"	ASCC3L1, RP33		9872452, 8670905, 9774689, 9539711, 16612614, 19878916	Standard	NM_014014		Approved	U5-200KD, HELIC2, KIAA0788, BRR2	uc002svu.3	O75643	OTTHUMG00000130455	ENST00000323853.5:c.611A>G	chr2.hg19:g.96966755T>C	ENSP00000317123:p.Gln204Arg	119.0	0.0		132.0	53.0	NM_014014	O94884|Q6NZY0|Q6PX59|Q8NBE6|Q96IF2|Q9H7S0	Missense_Mutation	SNP	ENST00000323853.5	hg19	CCDS2020.1	.	.	.	.	.	.	.	.	.	.	T	11.72	1.722177	0.30503	.	.	ENSG00000144028	ENST00000323853;ENST00000349783	T;T	0.44482	0.92;0.92	5.24	5.24	0.73138	.	0.121774	0.56097	D	0.000023	T	0.42517	0.1206	M	0.69823	2.125	0.80722	D	1	B	0.12630	0.006	B	0.10450	0.005	T	0.32241	-0.9914	10	0.18710	T	0.47	-18.8126	14.4064	0.67086	0.0:0.0:0.0:1.0	.	204	O75643	U520_HUMAN	R	204	ENSP00000317123:Q204R;ENSP00000326937:Q204R	ENSP00000317123:Q204R	Q	-	2	0	SNRNP200	96330482	1.000000	0.71417	1.000000	0.80357	0.791000	0.44710	7.309000	0.78937	2.107000	0.64212	0.459000	0.35465	CAG	.	.		0.418	SNRNP200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252846.2	NM_014014		C	96966755	T	C	96966755	3	2	344	1	0	0	0	0	1	0	0	0	14867	1580	55	2	5963	2	SNRNP200	2	96966755	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	171124	96966755	146232618	188	47551										
FER1L5	0	hgsc.bcm.edu	37	chr2	97315365	97315365	+	IGR	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcctttgtcttgcagtgtacTgtcaccctacaggtggccca	10	13	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:97315365T>C								KANSL3 (11250 upstream) : FER1L5 (20589 downstream)																							TGCAGTGTACTGTCACCCTAC	0.557																																					p.T115T		Atlas-SNP	.											.	FER1L5	113	.	0			c.T345C						.						204	172	182					2																	97315365		692	1591	2283	SO:0001628	intergenic_variant	90342	exon5			GTGTACTGTCACC																													chr2.hg19:g.97315365T>C		76.0	0.0		74.0	28.0	NM_001113382		Silent	SNP		hg19																																																																																				.	.	0	0.557									C	97315365	T	C	97315365	1	2	344	0	1	0	0	0	0	0	0	0	5822	1567	55	2		2	FER1L5	2	97315365	IGR	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	348610	97315365	145884008	189	47552										
VWA3B	200403	hgsc.bcm.edu	37	chr2	98866838	98866838	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agatgacattaattaaccccCaaggagccaaactcaatatc	5	11	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:98866838C>G	ENST00000477737.1	+	20	2935	c.2731C>G	c.(2731-2733)Caa>Gaa	p.Q911E	VWA3B_ENST00000490947.2_3'UTR	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	911										NS(3)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						AATTAACCCCCAAGGAGCCAA	0.418																																					p.Q911E		Atlas-SNP	.											.	VWA3B	138	.	0			c.C2731G						.						128	123	125					2																	98866838		1884	4112	5996	SO:0001583	missense	200403	exon20			AACCCCCAAGGAG	AL832761	CCDS42718.1	2q11.2	2008-02-05			ENSG00000168658	ENSG00000168658			28385	protein-coding gene	gene with protein product						12477932	Standard	NM_144992		Approved	DKFZp686F2227, MGC26733	uc002syo.3	Q502W6	OTTHUMG00000153104	ENST00000477737.1:c.2731C>G	chr2.hg19:g.98866838C>G	ENSP00000417955:p.Gln911Glu	127.0	0.0		82.0	40.0	NM_144992	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Missense_Mutation	SNP	ENST00000477737.1	hg19	CCDS42718.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.49|12.49	1.954923|1.954923	0.34471|0.34471	.|.	.|.	ENSG00000168658|ENSG00000168658	ENST00000473149|ENST00000477737;ENST00000358269	T|T	0.16597|0.06142	2.33|3.34	4.63|4.63	3.74|3.74	0.42951|0.42951	.|.	.|0.617187	.|0.14767	.|N	.|0.299644	T|T	0.08626|0.08626	0.0214|0.0214	L|L	0.53249|0.53249	1.67|1.67	0.80722|0.80722	D|D	1|1	.|P;B;P	.|0.42871	.|0.792;0.349;0.622	.|B;B;B	.|0.40066	.|0.318;0.155;0.295	T|T	0.13602|0.13602	-1.0503|-1.0503	7|10	0.87932|0.56958	D|D	0|0.05	.|.	10.1997|10.1997	0.43075|0.43075	0.1987:0.8013:0.0:0.0|0.1987:0.8013:0.0:0.0	.|.	.|303;911;911	.|Q502W6-5;Q502W6;Q502W6-8	.|.;VWA3B_HUMAN;.	R|E	321|911;33	ENSP00000436153:P321R|ENSP00000417955:Q911E	ENSP00000436153:P321R|ENSP00000351009:Q33E	P|Q	+|+	2|1	0|0	VWA3B|VWA3B	98233270|98233270	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.890000|0.890000	0.51754|0.51754	1.987000|1.987000	0.40687|0.40687	1.271000|1.271000	0.44313|0.44313	-0.188000|-0.188000	0.12872|0.12872	CCA|CAA	.	.		0.418	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992		G	98866838	C	G	98866838	3	3	344	1	0	0	0	0	1	0	0	0	17256	595	21	4	2805	4	VWA3B	2	98866838	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1551473	98866838	144332535	190	47553										
CNGA3	1261	hgsc.bcm.edu	37	chr2	98994248	98994248	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cgggcagggctccttcaccgGccaggggatcgccaggtaac	15	14	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:98994248G>T	ENST00000272602.2	+	2	239	c.200G>T	c.(199-201)gGc>gTc	p.G67V	CNGA3_ENST00000393504.1_Missense_Mutation_p.G67V|CNGA3_ENST00000436404.2_Missense_Mutation_p.G67V|CNGA3_ENST00000409937.1_Missense_Mutation_p.G16V			Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3	67					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to magnesium ion (GO:0032026)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|photoreceptor outer segment membrane (GO:0042622)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(17)|ovary(5)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	49						TCCTTCACCGGCCAGGGGATC	0.602																																					p.G67V		Atlas-SNP	.											.	CNGA3	118	.	0			c.G200T						.						25	24	24					2																	98994248		2203	4300	6503	SO:0001583	missense	1261	exon3			TCACCGGCCAGGG	S76069	CCDS2034.1, CCDS42719.1	2q11.2	2013-01-08			ENSG00000144191	ENSG00000144191		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2150	protein-coding gene	gene with protein product		600053		CNCG3, ACHM2		7532814, 9517456, 16382102	Standard	NM_001298		Approved	CCNC1, CCNCa, CNG3	uc002syt.3	Q16281	OTTHUMG00000130561	ENST00000272602.2:c.200G>T	chr2.hg19:g.98994248G>T	ENSP00000272602:p.Gly67Val	80.0	0.0		70.0	27.0	NM_001298	E9PF93|Q4VAP7|Q53RD2|Q6ZNA7|Q9UP64	Missense_Mutation	SNP	ENST00000272602.2	hg19	CCDS2034.1	.	.	.	.	.	.	.	.	.	.	G	11.04	1.521102	0.27211	.	.	ENSG00000144191	ENST00000393504;ENST00000436404;ENST00000272602;ENST00000409937	T;T;T;D	0.99466	0.81;0.81;0.81;-5.95	5.01	1.11	0.20524	.	2.818950	0.00812	N	0.001507	D	0.97517	0.9187	L	0.39898	1.24	0.23689	N	0.997106	P;B;B	0.38250	0.624;0.013;0.007	B;B;B	0.31686	0.134;0.015;0.013	D	0.96574	0.9425	10	0.36615	T	0.2	.	3.3458	0.07134	0.145:0.1363:0.578:0.1407	.	16;67;67	E9PF93;Q4VAP7;Q16281	.;.;CNGA3_HUMAN	V	67;67;67;16	ENSP00000377140:G67V;ENSP00000410070:G67V;ENSP00000272602:G67V;ENSP00000386761:G16V	ENSP00000272602:G67V	G	+	2	0	CNGA3	98360680	0.833000	0.29383	0.011000	0.14972	0.003000	0.03518	1.775000	0.38584	0.083000	0.17047	-0.794000	0.03295	GGC	.	.		0.602	CNGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252986.1	NM_001298		T	98994248	G	T	98994248	3	4	344	1	0	0	0	0	1	0	0	0	3600	1203	42	3	206	3	CNGA3	2	98994248	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	127410	98994248	144205125	191	47554										
INPP4A	3631	hgsc.bcm.edu	37	chr2	99182502	99182502	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctttctccagcgacgggtttAacgtgcgggtccctctgccg	12	14	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:99182502A>G	ENST00000523221.1	+	20	2305	c.2305A>G	c.(2305-2307)Aac>Gac	p.N769D	INPP4A_ENST00000409016.4_Missense_Mutation_p.N730D|INPP4A_ENST00000409540.3_Missense_Mutation_p.N730D|INPP4A_ENST00000545415.1_Missense_Mutation_p.N730D|INPP4A_ENST00000467042.1_3'UTR|INPP4A_ENST00000074304.5_Missense_Mutation_p.N769D|INPP4A_ENST00000409851.3_Missense_Mutation_p.N764D|INPP4A_ENST00000409463.1_Missense_Mutation_p.N98D			Q96PE3	INP4A_HUMAN	inositol polyphosphate-4-phosphatase, type I, 107kDa	769					inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)			breast(1)|endometrium(9)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|prostate(4)|upper_aerodigestive_tract(4)	43						CGACGGGTTTAACGTGCGGGT	0.657																																					p.N769D		Atlas-SNP	.											.	INPP4A	205	.	0			c.A2305G						.						20	21	21					2																	99182502		1961	4136	6097	SO:0001583	missense	3631	exon22			GGGTTTAACGTGC	U26398	CCDS46369.1, CCDS46370.1, CCDS46371.1, CCDS46372.1	2q11.2	2008-05-27	2002-08-29		ENSG00000040933	ENSG00000040933			6074	protein-coding gene	gene with protein product		600916	"inositol polyphosphate-4-phosphatase, type I, 107kD"	INPP4		7608176, 9295334	Standard	NM_004027		Approved		uc002syy.3	Q96PE3	OTTHUMG00000153106	ENST00000523221.1:c.2305A>G	chr2.hg19:g.99182502A>G	ENSP00000427722:p.Asn769Asp	72.0	0.0		64.0	29.0	NM_001134224	O15326|Q13187|Q53TD8|Q8TC02	Missense_Mutation	SNP	ENST00000523221.1	hg19	CCDS46369.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.412649	0.83340	.	.	ENSG00000040933	ENST00000409016;ENST00000409851;ENST00000409463;ENST00000074304;ENST00000545415;ENST00000409540;ENST00000523221	T;T;T;T;T;T;T	0.41400	1.97;2.27;1.0;2.28;1.97;1.96;2.28	5.37	4.2	0.49525	.	0.000000	0.85682	D	0.000000	T	0.49813	0.1579	L	0.40543	1.245	0.58432	D	0.999995	D;D;B;D;D	0.76494	0.996;0.999;0.417;0.999;0.999	D;D;P;D;D	0.81914	0.979;0.994;0.503;0.995;0.995	T	0.37888	-0.9686	10	0.12430	T	0.62	-32.592	11.8359	0.52323	0.8534:0.1466:0.0:0.0	.	730;730;98;769;764	Q96PE3-2;Q96PE3-4;B8ZZB2;Q96PE3;Q96PE3-3	.;.;.;INP4A_HUMAN;.	D	730;764;98;769;730;730;769	ENSP00000386704:N730D;ENSP00000386777:N764D;ENSP00000386329:N98D;ENSP00000074304:N769D;ENSP00000442149:N730D;ENSP00000387294:N730D;ENSP00000427722:N769D	ENSP00000074304:N769D	N	+	1	0	INPP4A	98548934	1.000000	0.71417	0.751000	0.31187	0.898000	0.52572	9.139000	0.94554	1.042000	0.40150	0.528000	0.53228	AAC	.	.		0.657	INPP4A-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376095.1	NM_001566		G	99182502	A	G	99182502	3	3	344	1	0	0	0	0	1	0	0	0	7761	362	13	2	2383	2	INPP4A	2	99182502	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	188254	99182502	144016871	192	47555										
MRPL30	51263	hgsc.bcm.edu	37	chr2	99812077	99812077	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acaaggacttccagcagaggAgaacatgtctaacacgtgcc	10	11	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:99812077A>G	ENST00000338148.3	+	6	593	c.395A>G	c.(394-396)gAg>gGg	p.E132G	C2orf15_ENST00000512183.2_Missense_Mutation_p.E132G|MRPL30_ENST00000465432.1_3'UTR	NM_145212.3	NP_660213.1	Q8TCC3	RM30_HUMAN	mitochondrial ribosomal protein L30	132						mitochondrion (GO:0005739)|ribosome (GO:0005840)				breast(1)|endometrium(1)|kidney(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	10						CCAGCAGAGGAGAACATGTCT	0.483																																					p.E132G		Atlas-SNP	.											.	MRPL30	20	.	0			c.A395G						.						165	153	157					2																	99812077		2203	4300	6503	SO:0001583	missense	51263	exon6			CAGAGGAGAACAT	AB051342	CCDS2041.1	2q11.2	2012-09-13			ENSG00000185414	ENSG00000185414		"Mitochondrial ribosomal proteins / large subunits"	14036	protein-coding gene	gene with protein product		611838					Standard	NM_145212		Approved	MRP-L28, RPML28	uc002szv.3	Q8TCC3	OTTHUMG00000130642	ENST00000338148.3:c.395A>G	chr2.hg19:g.99812077A>G	ENSP00000338057:p.Glu132Gly	142.0	0.0		127.0	59.0	NM_145212	A6NIC6|D3DVI0|D3DVI3|Q0D2Q7|Q6ZTP4|Q96Q69|Q9P0N0	Missense_Mutation	SNP	ENST00000338148.3	hg19	CCDS2041.1	.	.	.	.	.	.	.	.	.	.	A	13.11	2.140130	0.37825	.	.	ENSG00000241962;ENSG00000241962;ENSG00000185414;ENSG00000185414	ENST00000512183;ENST00000308644;ENST00000338148;ENST00000409841	T;T;T	0.51071	0.72;0.72;0.72	4.26	3.07	0.35406	.	0.111404	0.64402	D	0.000015	T	0.44726	0.1307	M	0.70275	2.135	0.44652	D	0.99763	B	0.30511	0.282	B	0.28784	0.094	T	0.46219	-0.9207	10	0.72032	D	0.01	-18.34	9.2701	0.37666	0.8175:0.1825:0.0:0.0	.	132	Q8TCC3	RM30_HUMAN	G	132;145;132;132	ENSP00000420959:E132G;ENSP00000338057:E132G;ENSP00000386752:E132G	ENSP00000312464:E145G	E	+	2	0	C2orf15;MRPL30	99178509	1.000000	0.71417	0.994000	0.49952	0.563000	0.35712	4.151000	0.58105	0.769000	0.33313	-0.446000	0.05623	GAG	.	.		0.483	MRPL30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253130.2			G	99812077	A	G	99812077	3	3	344	1	0	0	0	0	1	0	0	0	9803	304	11	2	413	2	MRPL30	2	99812077	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	629575	99812077	143387296	193	47556										
NPAS2	4862	hgsc.bcm.edu	37	chr2	101587535	101587535	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cctccactcctcagcactaaAggtacgcccatccctgccag	6	19	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:101587535A>T	ENST00000335681.5	+	12	1424	c.1139A>T	c.(1138-1140)aAg>aTg	p.K380M	AC016738.3_ENST00000439150.1_RNA|AC016738.3_ENST00000446644.1_RNA|NPAS2_ENST00000542504.1_Splice_Site_p.K445M	NM_002518.3	NP_002509.2	Q99743	NPAS2_HUMAN	neuronal PAS domain protein 2	380					cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system development (GO:0007417)|circadian regulation of gene expression (GO:0032922)|circadian sleep/wake cycle (GO:0042745)|locomotor rhythm (GO:0045475)|negative regulation of cell death (GO:0060548)|positive regulation of DNA repair (GO:0045739)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of response to DNA damage stimulus (GO:2001020)|response to redox state (GO:0051775)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|Hsp90 protein binding (GO:0051879)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TCAGCACTAAAGGTACGCCCA	0.527																																					p.K380M		Atlas-SNP	.											.	NPAS2	88	.	0			c.A1139T						.						74	70	72					2																	101587535		2203	4300	6503	SO:0001630	splice_region_variant	4862	exon12			CACTAAAGGTACG	U77970	CCDS2048.1	2q11.2	2013-05-21			ENSG00000170485	ENSG00000170485		"Basic helix-loop-helix proteins"	7895	protein-coding gene	gene with protein product		603347				9012850, 9079689	Standard	NM_002518		Approved	MOP4, PASD4, bHLHe9	uc002tap.1	Q99743	OTTHUMG00000130675	ENST00000335681.5:c.1140+1A>T	chr2.hg19:g.101587535A>T		96.0	0.0		91.0	35.0	NM_002518	Q4ZFV9|Q53SQ3|Q86V96|Q99629	Missense_Mutation	SNP	ENST00000335681.5	hg19	CCDS2048.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.371904	0.82573	.	.	ENSG00000170485	ENST00000335681;ENST00000542504	T;T	0.07444	3.22;3.19	5.71	5.71	0.89125	.	0.289989	0.39687	N	0.001293	T	0.30103	0.0754	M	0.74258	2.255	0.58432	D	0.999993	D;D	0.89917	1.0;1.0	D;D	0.76071	0.987;0.971	T	0.01795	-1.1272	10	0.72032	D	0.01	.	15.9736	0.80040	1.0:0.0:0.0:0.0	.	445;380	F5H027;Q99743	.;NPAS2_HUMAN	M	380;445	ENSP00000338283:K380M;ENSP00000438428:K445M	ENSP00000338283:K380M	K	+	2	0	NPAS2	100953967	1.000000	0.71417	0.994000	0.49952	0.666000	0.39218	7.339000	0.79282	2.165000	0.68154	0.533000	0.62120	AAG	.	.		0.527	NPAS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253168.3		Missense_Mutation	T	101587535	A	T	101587535	5	4	344	1	0	0	0	0	0	0	1	0	10572	86	3	4	1181	4	NPAS2	2	101587535	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1775458	101587535	141611838	194	47557										
NPAS2	4862	hgsc.bcm.edu	37	chr2	101594175	101594175	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccctttctctcccacaggccCctctgccttccccatcgtcc	4	23	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:101594175C>G	ENST00000335681.5	+	15	1681	c.1396C>G	c.(1396-1398)Cct>Gct	p.P466A	AC016738.3_ENST00000439150.1_RNA|AC016738.3_ENST00000446644.1_RNA|NPAS2_ENST00000542504.1_Missense_Mutation_p.P531A|AC016738.3_ENST00000433012.1_RNA	NM_002518.3	NP_002509.2	Q99743	NPAS2_HUMAN	neuronal PAS domain protein 2	466					cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system development (GO:0007417)|circadian regulation of gene expression (GO:0032922)|circadian sleep/wake cycle (GO:0042745)|locomotor rhythm (GO:0045475)|negative regulation of cell death (GO:0060548)|positive regulation of DNA repair (GO:0045739)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of response to DNA damage stimulus (GO:2001020)|response to redox state (GO:0051775)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|Hsp90 protein binding (GO:0051879)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CCCACAGGCCCCTCTGCCTTC	0.622																																					p.P466A		Atlas-SNP	.											.	NPAS2	88	.	0			c.C1396G						.						97	101	99					2																	101594175		2203	4300	6503	SO:0001583	missense	4862	exon15			CAGGCCCCTCTGC	U77970	CCDS2048.1	2q11.2	2013-05-21			ENSG00000170485	ENSG00000170485		"Basic helix-loop-helix proteins"	7895	protein-coding gene	gene with protein product		603347				9012850, 9079689	Standard	NM_002518		Approved	MOP4, PASD4, bHLHe9	uc002tap.1	Q99743	OTTHUMG00000130675	ENST00000335681.5:c.1396C>G	chr2.hg19:g.101594175C>G	ENSP00000338283:p.Pro466Ala	75.0	0.0		61.0	15.0	NM_002518	Q4ZFV9|Q53SQ3|Q86V96|Q99629	Missense_Mutation	SNP	ENST00000335681.5	hg19	CCDS2048.1	.	.	.	.	.	.	.	.	.	.	C	1.872	-0.460100	0.04508	.	.	ENSG00000170485	ENST00000335681;ENST00000542504;ENST00000450763	T;T;T	0.28255	3.57;3.55;1.62	5.69	2.5	0.30297	.	0.798202	0.12029	N	0.506130	T	0.21103	0.0508	L	0.54323	1.7	0.25840	N	0.984064	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.10450	0.002;0.0;0.005	T	0.39375	-0.9617	10	0.05959	T	0.93	.	3.1669	0.06539	0.0:0.4858:0.228:0.2862	.	531;466;466	F5H027;A0PJF9;Q99743	.;.;NPAS2_HUMAN	A	466;531;65	ENSP00000338283:P466A;ENSP00000438428:P531A;ENSP00000392125:P65A	ENSP00000338283:P466A	P	+	1	0	NPAS2	100960607	0.969000	0.33509	0.113000	0.21522	0.026000	0.11368	2.024000	0.41049	0.735000	0.32537	0.655000	0.94253	CCT	.	.		0.622	NPAS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253168.3			G	101594175	C	G	101594175	3	3	344	1	0	0	0	0	1	0	0	0	10572	623	22	4	1450	4	NPAS2	2	101594175	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	6640	101594175	141605198	195	47558										
SH3RF3	344558	hgsc.bcm.edu	37	chr2	110053581	110053581	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cccagccaacggccagccaaGcccggagcaccatttcaaca	8	18	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:110053581G>T	ENST00000309415.6	+	7	1807	c.1807G>T	c.(1807-1809)Gcc>Tcc	p.A603S		NM_001099289.1	NP_001092759.1	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3	603							zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(5)|ovary(2)	18						GGCCAGCCAAGCCCGGAGCAC	0.647																																					p.A603S		Atlas-SNP	.											.	SH3RF3	62	.	0			c.G1807T						.						19	28	25					2																	110053581		2061	4199	6260	SO:0001583	missense	344558	exon7			AGCCAAGCCCGGA	AK074131	CCDS74557.1	2q13	2013-01-11	2008-05-14	2008-05-14	ENSG00000172985	ENSG00000172985		"RING-type (C3HC4) zinc fingers"	24699	protein-coding gene	gene with protein product			"SH3 multiple domains 4"	SH3MD4		16374509	Standard	XM_006712493		Approved	FLJ00204, POSH2	uc010ywt.1	Q8TEJ3	OTTHUMG00000153439	ENST00000309415.6:c.1807G>T	chr2.hg19:g.110053581G>T	ENSP00000309186:p.Ala603Ser	189.0	0.0		155.0	56.0	NM_001099289	A0SDZ7|A8MPR1|Q8NDU1	Missense_Mutation	SNP	ENST00000309415.6	hg19		.	.	.	.	.	.	.	.	.	.	G	12.39	1.922493	0.33908	.	.	ENSG00000172985	ENST00000418513;ENST00000309415	T;T	0.59906	0.23;2.02	5.59	4.71	0.59529	.	0.443662	0.25258	N	0.031975	T	0.46229	0.1382	.	.	.	0.31126	N	0.708265	P	0.39847	0.691	B	0.42555	0.391	T	0.53995	-0.8359	9	0.39692	T	0.17	-21.3575	2.93	0.05796	0.1557:0.1416:0.5561:0.1467	.	603	Q8TEJ3	SH3R3_HUMAN	S	603	ENSP00000414997:A603S;ENSP00000309186:A603S	ENSP00000309186:A603S	A	+	1	0	SH3RF3	109420013	0.595000	0.26857	0.988000	0.46212	0.691000	0.40173	1.317000	0.33631	1.358000	0.45922	0.650000	0.86243	GCC	.	.		0.647	SH3RF3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001099289		T	110053581	G	T	110053581	3	4	344	1	0	0	0	0	1	0	0	0	14275	971	34	3	1833	3	SH3RF3	2	110053581	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	8459406	110053581	133145792	196	47559										
SH3RF3	344558	hgsc.bcm.edu	37	chr2	110259210	110259210	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccctgcagcggaacggccgcAcaggcctcttcccgggcagc	13	18	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:110259210A>G	ENST00000309415.6	+	10	2611	c.2611A>G	c.(2611-2613)Aca>Gca	p.T871A		NM_001099289.1	NP_001092759.1	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3	871	SH3 4. {ECO:0000255|PROSITE- ProRule:PRU00192}.						zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(5)|ovary(2)	18						GAACGGCCGCACAGGCCTCTT	0.642																																					p.T871A		Atlas-SNP	.											.	SH3RF3	62	.	0			c.A2611G						.						39	42	41					2																	110259210		2047	4179	6226	SO:0001583	missense	344558	exon10			GGCCGCACAGGCC	AK074131	CCDS74557.1	2q13	2013-01-11	2008-05-14	2008-05-14	ENSG00000172985	ENSG00000172985		"RING-type (C3HC4) zinc fingers"	24699	protein-coding gene	gene with protein product			"SH3 multiple domains 4"	SH3MD4		16374509	Standard	XM_006712493		Approved	FLJ00204, POSH2	uc010ywt.1	Q8TEJ3	OTTHUMG00000153439	ENST00000309415.6:c.2611A>G	chr2.hg19:g.110259210A>G	ENSP00000309186:p.Thr871Ala	46.0	0.0		32.0	12.0	NM_001099289	A0SDZ7|A8MPR1|Q8NDU1	Missense_Mutation	SNP	ENST00000309415.6	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.27|17.27	3.348312|3.348312	0.61183|0.61183	.|.	.|.	ENSG00000172985|ENSG00000172985	ENST00000444352|ENST00000309415	.|T	.|0.51071	.|0.72	5.07|5.07	5.07|5.07	0.68467|0.68467	.|Src homology-3 domain (4);	.|0.000000	.|0.85682	.|U	.|0.000000	T|T	0.61999|0.61999	0.2392|0.2392	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|D	.|0.55385	.|0.971	.|D	.|0.65874	.|0.939	T|T	0.60357|0.60357	-0.7279|-0.7279	4|9	.|0.32370	.|T	.|0.25	-25.4388|-25.4388	10.9562|10.9562	0.47358|0.47358	0.86:0.0:0.0:0.14|0.86:0.0:0.0:0.14	.|.	.|871	.|Q8TEJ3	.|SH3R3_HUMAN	R|A	44|871	.|ENSP00000309186:T871A	.|ENSP00000309186:T871A	H|T	+|+	2|1	0|0	SH3RF3|SH3RF3	109616492|109616492	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.958000|0.958000	0.62258|0.62258	7.141000|7.141000	0.77330|0.77330	2.031000|2.031000	0.59945|0.59945	0.379000|0.379000	0.24179|0.24179	CAC|ACA	.	.		0.642	SH3RF3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001099289		G	110259210	A	G	110259210	3	3	344	1	0	0	0	0	1	0	0	0	14275	159	6	2	2313	2	SH3RF3	2	110259210	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	205629	110259210	132940163	197	47560										
CKAP2L	150468	hgsc.bcm.edu	37	chr2	113518343	113518343	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cttggattttagataaggccTataaaagacaaattaaaatt	6	4	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:113518343T>A	ENST00000302450.6	-	3	183		c.e3-2		CKAP2L_ENST00000541405.1_Splice_Site|CKAP2L_ENST00000481732.1_Splice_Site	NM_152515.3	NP_689728.3	Q8IYA6	CKP2L_HUMAN	cytoskeleton associated protein 2-like							centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	28						AGATAAGGCCTATAAAAGACA	0.269																																					.		Atlas-SNP	.											.	CKAP2L	54	.	0			c.105-2A>T						.						55	63	60					2																	113518343		2193	4271	6464	SO:0001630	splice_region_variant	150468	exon4			AAGGCCTATAAAA	AL832036	CCDS2100.1	2q13	2008-02-05			ENSG00000169607	ENSG00000169607			26877	protein-coding gene	gene with protein product						12477932	Standard	NM_152515		Approved	FLJ40629	uc002tie.2	Q8IYA6	OTTHUMG00000131313	ENST00000302450.6:c.105-2A>T	chr2.hg19:g.113518343T>A		335.0	1.0		269.0	114.0	NM_152515	A8K915|B4DZE3|B7ZAC6|F5H0M5|Q53QF8|Q53RS8|Q8N1J8	Splice_Site	SNP	ENST00000302450.6	hg19	CCDS2100.1	.	.	.	.	.	.	.	.	.	.	T	18.12	3.552404	0.65311	.	.	ENSG00000169607	ENST00000302450	.	.	.	4.8	4.8	0.61643	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.3159	0.49392	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	CKAP2L	113234814	0.997000	0.39634	0.969000	0.41365	0.982000	0.71751	3.792000	0.55476	2.096000	0.63516	0.533000	0.62120	.	.	.		0.269	CKAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254082.2	NM_152515	Intron	A	113518343	T	A	113518343	5	1	344	1	0	0	0	0	0	0	1	0	3445	1536	53	4	2162	4	CKAP2L	2	113518343	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	3259133	113518343	129681030	198	47561										
IL1B	3553	hgsc.bcm.edu	37	chr2	113593196	113593196	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	caagtcatcctcattgccacTgtaataaaaacagggacatg	7	10	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:113593196T>C	ENST00000263341.2	-	3	258		c.e3-2		IL1B_ENST00000491056.1_Splice_Site	NM_000576.2	NP_000567.1	P01584	IL1B_HUMAN	interleukin 1, beta						activation of MAPK activity (GO:0000187)|apoptotic process (GO:0006915)|cell-cell signaling (GO:0007267)|cellular response to drug (GO:0035690)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic cyclic compound (GO:0071407)|cellular response to organic substance (GO:0071310)|cytokine-mediated signaling pathway (GO:0019221)|ectopic germ cell programmed cell death (GO:0035234)|embryo implantation (GO:0007566)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fever generation (GO:0001660)|hyaluronan biosynthetic process (GO:0030213)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interleukin-1 beta production (GO:0032611)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MAPK cascade (GO:0000165)|monocyte aggregation (GO:0070487)|negative regulation of adiponectin secretion (GO:0070164)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of glucose transport (GO:0010829)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of lipid metabolic process (GO:0045833)|negative regulation of MAP kinase activity (GO:0043407)|neutrophil chemotaxis (GO:0030593)|positive regulation of angiogenesis (GO:0045766)|positive regulation of calcidiol 1-monooxygenase activity (GO:0060559)|positive regulation of cell adhesion molecule production (GO:0060355)|positive regulation of cell division (GO:0051781)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of fever generation (GO:0031622)|positive regulation of gene expression (GO:0010628)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of lipid catabolic process (GO:0050996)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of mitosis (GO:0045840)|positive regulation of monocyte chemotactic protein-1 production (GO:0071639)|positive regulation of myosin light chain kinase activity (GO:0035505)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of prostaglandin secretion (GO:0032308)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell mediated immunity (GO:0002711)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein kinase B signaling (GO:0043491)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of insulin secretion (GO:0050796)|response to ATP (GO:0033198)|response to carbohydrate (GO:0009743)|sequestering of triglyceride (GO:0030730)|signal transduction (GO:0007165)|smooth muscle adaptation (GO:0014805)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|secretory granule (GO:0030141)	cytokine activity (GO:0005125)|interleukin-1 receptor binding (GO:0005149)|protein domain specific binding (GO:0019904)			breast(2)|central_nervous_system(1)|large_intestine(1)|lung(8)	12					Canakinumab(DB06168)|Gallium nitrate(DB05260)|Minocycline(DB01017)|Rilonacept(DB06372)	TCATTGCCACTGTAATAAAAA	0.403																																					.		Atlas-SNP	.											.	IL1B	35	.	0			c.48-2A>G						.						121	105	110					2																	113593196		2203	4300	6503	SO:0001630	splice_region_variant	3553	exon4			TGCCACTGTAATA	M15330	CCDS2102.1	2q14	2014-01-30			ENSG00000125538	ENSG00000125538		"Interleukins and interleukin receptors", "Endogenous ligands"	5992	protein-coding gene	gene with protein product		147720				2954882, 2989698	Standard	NM_000576		Approved	IL1F2, IL-1B, IL1-BETA	uc002tii.1	P01584	OTTHUMG00000131344	ENST00000263341.2:c.48-2A>G	chr2.hg19:g.113593196T>C		79.0	0.0		51.0	23.0	NM_000576	Q53X59|Q53XX2|Q7M4S7|Q7RU01|Q96HE5|Q9UCT6	Splice_Site	SNP	ENST00000263341.2	hg19	CCDS2102.1	.	.	.	.	.	.	.	.	.	.	T	6.606	0.480251	0.12581	.	.	ENSG00000125538	ENST00000263341;ENST00000418817;ENST00000432018;ENST00000416750	.	.	.	4.64	3.45	0.39498	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.3138	0.32088	0.0:0.0:0.2009:0.7991	.	.	.	.	.	-1	.	.	.	-	.	.	IL1B	113309667	1.000000	0.71417	0.521000	0.27850	0.110000	0.19582	3.164000	0.50770	0.872000	0.35775	0.460000	0.39030	.	.	.		0.403	IL1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254125.2	NM_000576	Intron	C	113593196	T	C	113593196	5	2	344	1	0	0	0	0	0	0	1	0	7660	1594	55	2	783	2	IL1B	2	113593196	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	74853	113593196	129606177	199	47562										
EN1	2019	hgsc.bcm.edu	37	chr2	119600649	119600649	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cgcttgttctggaaccagatCttgatctgggactcgttgag	12	9	3	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:119600649C>A	ENST00000295206.6	-	2	1554	c.1044G>T	c.(1042-1044)aaG>aaT	p.K348N	EN1_ENST00000546667.1_5'Flank	NM_001426.3	NP_001417.3	Q05925	HME1_HUMAN	engrailed homeobox 1	348					anatomical structure morphogenesis (GO:0009653)|dorsal/ventral pattern formation (GO:0009953)|embryonic forelimb morphogenesis (GO:0035115)|hindbrain development (GO:0030902)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|multicellular organism growth (GO:0035264)|neuron development (GO:0048666)|pigmentation (GO:0043473)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|response to cocaine (GO:0042220)|skeletal system development (GO:0001501)	membrane (GO:0016020)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	9						GGAACCAGATCTTGATCTGGG	0.592																																					p.K348N		Atlas-SNP	.											.	EN1	33	.	0			c.G1044T						.						87	77	81					2																	119600649		2203	4300	6503	SO:0001583	missense	2019	exon2			CCAGATCTTGATC	L12699	CCDS2123.1	2q14.2	2011-06-20	2007-02-15		ENSG00000163064	ENSG00000163064		"Homeoboxes / ANTP class : NKL subclass"	3342	protein-coding gene	gene with protein product		131290				8094370	Standard	NM_001426		Approved		uc002tlm.3	Q05925	OTTHUMG00000131401	ENST00000295206.6:c.1044G>T	chr2.hg19:g.119600649C>A	ENSP00000295206:p.Lys348Asn	53.0	0.0		44.0	18.0	NM_001426	Q4ZG44	Missense_Mutation	SNP	ENST00000295206.6	hg19	CCDS2123.1	.	.	.	.	.	.	.	.	.	.	C	17.62	3.434177	0.62955	.	.	ENSG00000163064	ENST00000295206	D	0.96913	-4.17	4.89	2.7	0.31948	Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.98510	0.9503	H	0.96518	3.835	0.50632	D	0.999888	D	0.89917	1.0	D	0.97110	1.0	D	0.98797	1.0738	10	0.87932	D	0	-15.2674	11.8319	0.52301	0.0:0.8251:0.0:0.1749	.	348	Q05925	HME1_HUMAN	N	348	ENSP00000295206:K348N	ENSP00000295206:K348N	K	-	3	2	EN1	119317119	0.978000	0.34361	1.000000	0.80357	0.998000	0.95712	0.236000	0.17967	1.044000	0.40200	0.555000	0.69702	AAG	.	.		0.592	EN1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254191.3			A	119600649	C	A	119600649	3	1	344	1	0	0	0	0	1	0	0	0	5111	912	32	3	138	3	EN1	2	119600649	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	6007453	119600649	123598724	200	47563										
CNTNAP5	129684	hgsc.bcm.edu	37	chr2	125175023	125175023	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcctttcttctctgcagaccTttgcaggaaacatgaatgct	7	11	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:125175023T>A	ENST00000431078.1	+	4	749	c.385T>A	c.(385-387)Ttt>Att	p.F129I		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	129	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		TCTGCAGACCTTTGCAGGAAA	0.478																																					p.F129I		Atlas-SNP	.											.	CNTNAP5	405	.	0			c.T385A						.						74	73	73					2																	125175023		1997	4190	6187	SO:0001583	missense	129684	exon4			CAGACCTTTGCAG	AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.385T>A	chr2.hg19:g.125175023T>A	ENSP00000399013:p.Phe129Ile	94.0	0.0		65.0	35.0	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Missense_Mutation	SNP	ENST00000431078.1	hg19	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.387112	0.82902	.	.	ENSG00000155052	ENST00000431078	D	0.97941	-4.62	6.13	4.98	0.66077	Coagulation factor 5/8 C-terminal type domain (3);Galactose-binding domain-like (1);	0.000000	0.50627	D	0.000107	D	0.98438	0.9480	M	0.81682	2.555	0.44268	D	0.997126	D	0.89917	1.0	D	0.87578	0.998	D	0.98415	1.0574	10	0.51188	T	0.08	.	11.3882	0.49798	0.0:0.0708:0.0:0.9292	.	129	Q8WYK1	CNTP5_HUMAN	I	129	ENSP00000399013:F129I	ENSP00000399013:F129I	F	+	1	0	CNTNAP5	124891493	0.996000	0.38824	0.786000	0.31890	0.974000	0.67602	2.689000	0.46993	1.149000	0.42402	0.529000	0.55759	TTT	.	.		0.478	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			A	125175023	T	A	125175023	3	1	344	1	0	0	0	0	1	0	0	0	3652	1609	56	4	399	4	CNTNAP5	2	125175023	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	5574374	125175023	118024350	201	47564										
SMPD4	80097	hgsc.bcm.edu	37	chr2	130939136	130939136	+	5'Flank	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agcgtcgctcgcctcagagaTggaagccgccattccgccac	11	16	1	1	rs369506878		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:130939136T>A	ENST00000281871.6	+	0	0				SMPD4_ENST00000339679.7_5'UTR|SMPD4_ENST00000426662.2_5'UTR|SMPD4_ENST00000351288.6_Silent_p.P13P|SMPD4_ENST00000473720.1_5'UTR|SMPD4_ENST00000409031.1_Silent_p.P13P|MZT2B_ENST00000409255.1_5'Flank|SMPD4_ENST00000453750.1_Silent_p.P13P|SMPD4_ENST00000452225.2_5'UTR|SMPD4_ENST00000443958.2_5'UTR|AC018804.1_ENST00000578074.1_RNA|SMPD4_ENST00000431183.2_Silent_p.P13P	NM_025029.3	NP_079305.2	Q6NZ67	MZT2B_HUMAN	mitotic spindle organizing protein 2B							centrosome (GO:0005813)|gamma-tubulin ring complex (GO:0008274)|spindle (GO:0005819)				lung(1)	1						GCCTCAGAGATGGAAGCCGCC	0.706																																					p.P13P		Atlas-SNP	.											.	SMPD4	67	.	0			c.A39T						.						8	11	10					2																	130939136		1893	4074	5967	SO:0001631	upstream_gene_variant	55627	exon1			CAGAGATGGAAGC	BC066296	CCDS2157.1	2q21.1	2013-10-11	2010-07-22	2010-07-22	ENSG00000152082	ENSG00000152082			25886	protein-coding gene	gene with protein product	"mitotic-spindle organizing protein associated with a ring of gamma-tubulin 2B"	613450	"family with sequence similarity 128, member B"	FAM128B		20360068	Standard	NM_025029		Approved	FLJ14346, MOZART2B	uc002tqu.3	Q6NZ67	OTTHUMG00000131625		chr2.hg19:g.130939136T>A	Exception_encountered	82.0	0.0		63.0	32.0	NM_017751	Q96CG4	Silent	SNP	ENST00000281871.6	hg19	CCDS2157.1																																																																																			.	.		0.706	MZT2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254518.1	NM_025029		A	130939136	T	A	130939136	1	1	344	0	1	0	0	0	0	0	0	0	14822	1451	51	4		4	SMPD4	2	130939136	5'Flank	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	5764113	130939136	112260237	202	47565										
FAM168B	130074	hgsc.bcm.edu	37	chr2	131813019	131813019	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cggctgtgtgtagtacgtgcCttgctgtggggagaagagag	18	6	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:131813019C>T	ENST00000409185.1	-	5	408	c.301G>A	c.(301-303)Ggc>Agc	p.G101S	FAM168B_ENST00000389915.3_Missense_Mutation_p.G101S	NM_001009993.2	NP_001009993.2	A1KXE4	F168B_HUMAN	family with sequence similarity 168, member B	101						cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(3)|lung(2)	5						TAGTACGTGCCTTGCTGTGGG	0.597																																					p.G101S		Atlas-SNP	.											.	FAM168B	15	.	0			c.G301A						.						119	138	131					2																	131813019		2168	4262	6430	SO:0001583	missense	130074	exon5			ACGTGCCTTGCTG		CCDS42755.1	2q21.1	2008-08-08			ENSG00000152102	ENSG00000152102			27016	protein-coding gene	gene with protein product							Standard	NM_001009993		Approved	KIAA0280L	uc002tsd.3	A1KXE4	OTTHUMG00000153473	ENST00000409185.1:c.301G>A	chr2.hg19:g.131813019C>T	ENSP00000387051:p.Gly101Ser	117.0	0.0		111.0	48.0	NM_001009993	Q2TAZ6|Q6NZ40	Missense_Mutation	SNP	ENST00000409185.1	hg19	CCDS42755.1	.	.	.	.	.	.	.	.	.	.	C	31	5.065736	0.93898	.	.	ENSG00000152102	ENST00000409185;ENST00000389915	.	.	.	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.63236	0.2494	L	0.36672	1.1	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.55237	-0.8172	9	0.02654	T	1	-2.2236	16.9553	0.86257	0.0:1.0:0.0:0.0	.	101	A1KXE4	F168B_HUMAN	S	101	.	ENSP00000374565:G101S	G	-	1	0	FAM168B	131529489	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.314000	0.78988	2.666000	0.90696	0.561000	0.74099	GGC	.	.		0.597	FAM168B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331299.2	NM_001009993		T	131813019	C	T	131813019	3	4	344	1	0	0	0	0	1	0	0	0	5491	681	24	3	294	3	FAM168B	2	131813019	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	873883	131813019	111386354	203	47566										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141528495	141528495	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gagataatatcccactgtacAcatacaagtccttgtagttt	6	9	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:141528495A>T	ENST00000389484.3	-	34	6552	c.5581T>A	c.(5581-5583)Tgt>Agt	p.C1861S		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1861	EGF-like 8. {ECO:0000255|PROSITE- ProRule:PRU00076}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CCCACTGTACACATACAAGTC	0.373										TSP Lung(27;0.18)																											p.C1861S	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.T5581A						.						169	155	160					2																	141528495		2203	4300	6503	SO:0001583	missense	53353	exon34			CTGTACACATACA	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.5581T>A	chr2.hg19:g.141528495A>T	ENSP00000374135:p.Cys1861Ser	96.0	0.0		66.0	18.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.117056	0.77323	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.99966	-10.09	5.7	5.7	0.88788	Epidermal growth factor-like (1);EGF-like region, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.99981	0.9994	H	0.98701	4.305	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	D	0.98623	1.0668	10	0.87932	D	0	.	15.9467	0.79799	1.0:0.0:0.0:0.0	.	1861	Q9NZR2	LRP1B_HUMAN	S	1861;1799	ENSP00000374135:C1861S	ENSP00000374135:C1861S	C	-	1	0	LRP1B	141244965	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.717000	0.91425	2.163000	0.67991	0.477000	0.44152	TGT	.	.		0.373	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		T	141528495	A	T	141528495	3	4	344	1	0	0	0	0	1	0	0	0	8964	159	6	4	8450	4	LRP1B	2	141528495	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	9715476	141528495	101670878	204	47567										
KIF5C	3800	hgsc.bcm.edu	37	chr2	149633250	149633250	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tccggcccctcaacgaagcgGagatcctccgcggggacaaa	12	15	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:149633250G>A	ENST00000435030.1	+	1	432	c.64G>A	c.(64-66)Gag>Aag	p.E22K	AC105402.4_ENST00000601658.1_RNA|AC105402.4_ENST00000446781.2_RNA			O60282	KIF5C_HUMAN	kinesin family member 5C	22	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mRNA transport (GO:0051028)|organelle organization (GO:0006996)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(221;0.108)		CAACGAAGCGGAGATCCTCCG	0.632																																					p.E22K		Atlas-SNP	.											.	KIF5C	166	.	0			c.G64A						.						26	31	29					2																	149633250		1887	4104	5991	SO:0001583	missense	3800	exon1			GAAGCGGAGATCC	AB011103	CCDS74586.1	2q23	2008-02-05			ENSG00000168280	ENSG00000168280		"Kinesins"	6325	protein-coding gene	gene with protein product		604593				7514426	Standard	NM_004522		Approved		uc010zbu.2	O60282	OTTHUMG00000153779	ENST00000435030.1:c.64G>A	chr2.hg19:g.149633250G>A	ENSP00000393379:p.Glu22Lys	221.0	1.0		208.0	98.0	NM_004522	O95079|Q2YDC5	Missense_Mutation	SNP	ENST00000435030.1	hg19		.	.	.	.	.	.	.	.	.	.	g	36	5.817252	0.96982	.	.	ENSG00000168280	ENST00000451033;ENST00000435030	T	0.76839	-1.05	4.69	4.69	0.59074	Kinesin, motor domain (3);	.	.	.	.	D	0.88455	0.6441	.	.	.	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	D	0.90201	0.4257	8	0.87932	D	0	.	17.4709	0.87646	0.0:0.0:1.0:0.0	.	22	O60282	KIF5C_HUMAN	K	22	ENSP00000393379:E22K	ENSP00000393379:E22K	E	+	1	0	KIF5C	149349720	1.000000	0.71417	0.999000	0.59377	0.983000	0.72400	9.147000	0.94646	2.460000	0.83146	0.444000	0.29173	GAG	.	.		0.632	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000332562.3	NM_004522		A	149633250	G	A	149633250	3	1	344	1	0	0	0	0	1	0	0	0	8316	1175	41	3	66	3	KIF5C	2	149633250	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	8104755	149633250	93566123	205	47568										
NEB	4703	hgsc.bcm.edu	37	chr2	152466569	152466569	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcacacataatcttgggatcAtcttcaatgctctgggctcc	8	12	5	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:152466569A>G	ENST00000172853.10	-	77	11502	c.11355T>C	c.(11353-11355)gaT>gaC	p.D3785D	NEB_ENST00000427231.2_Silent_p.D4028D|NEB_ENST00000409198.1_Silent_p.D3785D|NEB_ENST00000603639.1_Silent_p.D4028D|NEB_ENST00000397345.3_Silent_p.D4028D|NEB_ENST00000604864.1_Silent_p.D4028D			P20929	NEBU_HUMAN	nebulin	3785					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TCTTGGGATCATCTTCAATGC	0.423																																					p.D4028D		Atlas-SNP	.											.	NEB	1697	.	0			c.T12084C						.						151	140	143					2																	152466569		1909	4134	6043	SO:0001819	synonymous_variant	4703	exon81			GGGATCATCTTCA	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.11355T>C	chr2.hg19:g.152466569A>G		78.0	0.0		64.0	26.0	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	hg19																																																																																				.	.		0.423	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		G	152466569	A	G	152466569	2	3	344	1	0	0	0	0	0	0	0	1	10311	214	8	2		2	NEB	2	152466569	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2833319	152466569	90732804	206	47569										
SLC4A10	57282	hgsc.bcm.edu	37	chr2	162813739	162813739	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gttcatcagtctttatgaccAgtattctgaaggtaacaaaa	7	7	4	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:162813739A>T	ENST00000446997.1	+	20	2875	c.2782A>T	c.(2782-2784)Agt>Tgt	p.S928C	SLC4A10_ENST00000415876.2_Missense_Mutation_p.S898C|SLC4A10_ENST00000375514.5_Missense_Mutation_p.S909C|SLC4A10_ENST00000421911.1_Missense_Mutation_p.S928C|SLC4A10_ENST00000272716.5_Missense_Mutation_p.S898C	NM_001178015.1	NP_001171486.1	Q6U841	S4A10_HUMAN	solute carrier family 4, sodium bicarbonate transporter, member 10	928					bicarbonate transport (GO:0015701)|chloride transport (GO:0006821)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|symporter activity (GO:0015293)			endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(35)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	60					Sodium bicarbonate(DB01390)	CTTTATGACCAGTATTCTGAA	0.353																																					p.S928C		Atlas-SNP	.											.	SLC4A10	309	.	0			c.A2782T						.						61	60	60					2																	162813739		1868	4114	5982	SO:0001583	missense	57282	exon20			ATGACCAGTATTC		CCDS46438.1, CCDS54411.1, CCDS54412.1	2q24.2	2013-05-22	2008-09-15		ENSG00000144290	ENSG00000144290		"Solute carriers"	13811	protein-coding gene	gene with protein product		605556	"solute carrier family 4, sodium bicarbonate transporter-like, member 10"			10964153, 18319254	Standard	NM_022058		Approved	NBCn2, NCBE	uc002ubx.4	Q6U841	OTTHUMG00000153938	ENST00000446997.1:c.2782A>T	chr2.hg19:g.162813739A>T	ENSP00000393066:p.Ser928Cys	101.0	0.0		82.0	29.0	NM_001178015	B7Z1R0|B7Z2J0|B7ZLC5|B9EG69|F8W675|Q4ZFX6|Q8TCP2|Q9HCQ6	Missense_Mutation	SNP	ENST00000446997.1	hg19	CCDS54411.1	.	.	.	.	.	.	.	.	.	.	A	18.01	3.528330	0.64860	.	.	ENSG00000144290	ENST00000375514;ENST00000415876;ENST00000272716;ENST00000449513;ENST00000446997;ENST00000421911;ENST00000415711	T;T;T;T;T	0.79749	-1.3;-1.3;-1.3;-1.3;-1.3	5.42	5.42	0.78866	Bicarbonate transporter, C-terminal (1);	0.093713	0.85682	D	0.000000	D	0.89068	0.6610	M	0.82056	2.57	0.53688	D	0.999977	P;P;D	0.65815	0.887;0.887;0.995	P;P;D	0.63283	0.823;0.823;0.913	D	0.90678	0.4603	10	0.87932	D	0	.	15.7565	0.78030	1.0:0.0:0.0:0.0	.	909;898;928	F8W675;Q6U841-2;Q6U841	.;.;S4A10_HUMAN	C	909;898;898;897;928;928;927	ENSP00000364664:S909C;ENSP00000395797:S898C;ENSP00000272716:S898C;ENSP00000393066:S928C;ENSP00000404486:S928C	ENSP00000272716:S898C	S	+	1	0	SLC4A10	162521985	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	5.790000	0.69038	2.177000	0.69029	0.533000	0.62120	AGT	.	.		0.353	SLC4A10-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333090.1	NM_022058		T	162813739	A	T	162813739	3	4	344	1	0	0	0	0	1	0	0	0	14666	188	7	4	2945	4	SLC4A10	2	162813739	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	10347170	162813739	80385634	207	47570										
DPP4	1803	hgsc.bcm.edu	37	chr2	162851476	162851476	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaagtttttctataccattgCctggaaatccactccaacat	4	11	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:162851476C>A	ENST00000360534.3	-	25	2754	c.2194G>T	c.(2194-2196)Gca>Tca	p.A732S	DPP4_ENST00000491591.1_5'UTR	NM_001935.3	NP_001926.2	P27487	DPP4_HUMAN	dipeptidyl-peptidase 4	732					cell adhesion (GO:0007155)|endothelial cell migration (GO:0043542)|negative regulation of extracellular matrix disassembly (GO:0010716)|positive regulation of cell proliferation (GO:0008284)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|response to hypoxia (GO:0001666)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intercellular canaliculus (GO:0046581)|invadopodium membrane (GO:0071438)|lamellipodium (GO:0030027)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dipeptidyl-peptidase activity (GO:0008239)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	48					Alogliptin(DB06203)|Atorvastatin(DB01076)|Linagliptin(DB08882)|Liraglutide(DB06655)|Saxagliptin(DB06335)|Sitagliptin(DB01261)|Vildagliptin(DB04876)	TATACCATTGCCTGGAAATCC	0.473																																					p.A732S		Atlas-SNP	.											.	DPP4	90	.	0			c.G2194T						.						82	76	78					2																	162851476		2203	4300	6503	SO:0001583	missense	1803	exon25			CCATTGCCTGGAA	M74777	CCDS2216.1	2q24.2	2013-09-19	2008-08-01		ENSG00000197635	ENSG00000197635	3.4.14.5	"CD molecules"	3009	protein-coding gene	gene with protein product		102720	"dipeptidylpeptidase IV (CD26, adenosine deaminase complexing protein 2)", "adenosine deaminase complexing protein 2"	CD26, ADCP2		8101391	Standard	NM_001935		Approved	DPPIV	uc002ubz.3	P27487	OTTHUMG00000132056	ENST00000360534.3:c.2194G>T	chr2.hg19:g.162851476C>A	ENSP00000353731:p.Ala732Ser	203.0	0.0		183.0	89.0	NM_001935	Q53TN1	Missense_Mutation	SNP	ENST00000360534.3	hg19	CCDS2216.1	.	.	.	.	.	.	.	.	.	.	C	13.49	2.251775	0.39797	.	.	ENSG00000197635	ENST00000360534	T	0.30448	1.53	5.66	3.85	0.44370	Peptidase S9, prolyl oligopeptidase, catalytic domain (1);	0.101945	0.64402	N	0.000002	T	0.25195	0.0612	L	0.39692	1.235	0.52501	D	0.999951	B	0.09022	0.002	B	0.29440	0.102	T	0.05517	-1.0880	10	0.36615	T	0.2	-32.2704	6.936	0.24466	0.1493:0.7089:0.0:0.1419	.	732	P27487	DPP4_HUMAN	S	732	ENSP00000353731:A732S	ENSP00000353731:A732S	A	-	1	0	DPP4	162559722	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.608000	0.54109	0.719000	0.32188	0.655000	0.94253	GCA	.	.		0.473	DPP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255079.2			A	162851476	C	A	162851476	3	1	344	1	0	0	0	0	1	0	0	0	4731	739	26	3	114	3	DPP4	2	162851476	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	37737	162851476	80347897	208	47571										
SCN7A	6332	hgsc.bcm.edu	37	chr2	167298134	167298134	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccaaacagcttcatgccgaaTgcagcagaaaagaagatgaa	9	9	1	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:167298134T>C	ENST00000409855.1	-	14	2055	c.1929A>G	c.(1927-1929)gcA>gcG	p.A643A		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	643					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	TCATGCCGAATGCAGCAGAAA	0.438																																					p.A643A		Atlas-SNP	.											.	SCN7A	410	.	0			c.A1929G						.						114	119	117					2																	167298134		2203	4300	6503	SO:0001819	synonymous_variant	6332	exon14			GCCGAATGCAGCA	M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10594	protein-coding gene	gene with protein product		182392	"sodium channel, voltage-gated, type VI, alpha", "sodium channel, voltage-gated, type VII, alpha"	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.1929A>G	chr2.hg19:g.167298134T>C		231.0	1.0		176.0	80.0	NM_002976		Silent	SNP	ENST00000409855.1	hg19	CCDS46442.1																																																																																			.	.		0.438	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1			C	167298134	T	C	167298134	2	2	344	1	0	0	0	0	0	0	0	1	13938	1451	51	2		2	SCN7A	2	167298134	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	4446658	167298134	75901239	209	47572										
LRP2	4036	hgsc.bcm.edu	37	chr2	170063518	170063518	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acttcggtccactgccaagcCccgtggtgtgacaatgccct	10	15	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:170063518C>T	ENST00000263816.3	-	39	6997	c.6712G>A	c.(6712-6714)Ggc>Agc	p.G2238S		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	2238					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	ACTGCCAAGCCCCGTGGTGTG	0.463																																					p.G2238S		Atlas-SNP	.											.	LRP2	751	.	0			c.G6712A						.						171	160	163					2																	170063518		2203	4300	6503	SO:0001583	missense	4036	exon39			CCAAGCCCCGTGG		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.6712G>A	chr2.hg19:g.170063518C>T	ENSP00000263816:p.Gly2238Ser	152.0	0.0		150.0	65.0	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	hg19	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.751932	0.89753	.	.	ENSG00000081479	ENST00000263816	D	0.97529	-4.42	5.98	5.98	0.97165	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	D	0.98333	0.9447	M	0.70787	2.145	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98400	1.0567	10	0.54805	T	0.06	.	20.4581	0.99154	0.0:1.0:0.0:0.0	.	2238	P98164	LRP2_HUMAN	S	2238	ENSP00000263816:G2238S	ENSP00000263816:G2238S	G	-	1	0	LRP2	169771764	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	6.089000	0.71384	2.835000	0.97688	0.650000	0.86243	GGC	.	.		0.463	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		T	170063518	C	T	170063518	3	4	344	1	0	0	0	0	1	0	0	0	8965	623	22	3	7419	3	LRP2	2	170063518	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	2765384	170063518	73135855	210	47573										
LRP2	4036	hgsc.bcm.edu	37	chr2	170097673	170097673	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccgcagtcattgtcccgatcAcagagccatgccctgtggat	10	14	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:170097673A>G	ENST00000263816.3	-	25	4155	c.3870T>C	c.(3868-3870)tgT>tgC	p.C1290C	LRP2_ENST00000443831.1_Silent_p.C1153C	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1290	LDL-receptor class A 14. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	TGTCCCGATCACAGAGCCATG	0.512																																					p.C1290C		Atlas-SNP	.											.	LRP2	751	.	0			c.T3870C						.						188	145	160					2																	170097673		2203	4300	6503	SO:0001819	synonymous_variant	4036	exon25			CCGATCACAGAGC		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.3870T>C	chr2.hg19:g.170097673A>G		94.0	0.0		99.0	48.0	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	hg19	CCDS2232.1																																																																																			.	.		0.512	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		G	170097673	A	G	170097673	2	3	344	1	0	0	0	0	0	0	0	1	8965	157	6	2		2	LRP2	2	170097673	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	34155	170097673	73101700	211	47574										
BBS5	129880	hgsc.bcm.edu	37	chr2	170354147	170354147	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttgtatctagcgttcaataaAgattagagattcaaaatttg	7	4	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:170354147A>G	ENST00000295240.3	+	8	1005	c.629A>G	c.(628-630)aAg>aGg	p.K210R	BBS5_ENST00000392663.2_Intron|RP11-724O16.1_ENST00000513963.1_Missense_Mutation_p.K210R|BBS5_ENST00000554017.1_Missense_Mutation_p.K210R	NM_152384.2	NP_689597.1	Q8N3I7	BBS5_HUMAN	Bardet-Biedl syndrome 5	210					cilium assembly (GO:0042384)|heart looping (GO:0001947)|melanosome transport (GO:0032402)|motile cilium assembly (GO:0044458)|protein transport (GO:0015031)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	BBSome (GO:0034464)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphatidylinositol-3-phosphate binding (GO:0032266)|RNA polymerase II repressing transcription factor binding (GO:0001103)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						CGTTCAATAAAGATTAGAGAT	0.264									Bardet-Biedl syndrome																												p.K210R		Atlas-SNP	.											.	BBS5	27	.	0			c.A629G						.						77	87	83					2																	170354147		2201	4290	6491	SO:0001583	missense	129880	exon8	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	CAATAAAGATTAG	AY604003	CCDS2233.1	2q31	2011-08-02			ENSG00000163093	ENSG00000163093			970	protein-coding gene	gene with protein product		603650				9888993, 10053027	Standard	NM_152384		Approved	DKFZp762I194		Q8N3I7	OTTHUMG00000132207	ENST00000295240.3:c.629A>G	chr2.hg19:g.170354147A>G	ENSP00000295240:p.Lys210Arg	304.0	0.0		262.0	13.0	NM_152384	D3DPC3|Q6PKN0	Missense_Mutation	SNP	ENST00000295240.3	hg19	CCDS2233.1	.	.	.	.	.	.	.	.	.	.	A	7.625	0.677621	0.14841	.	.	ENSG00000163093;ENSG00000163093;ENSG00000251569	ENST00000295240;ENST00000554017;ENST00000513963	T;T;T	0.72835	-0.69;-0.69;-0.69	5.67	5.67	0.87782	.	0.043156	0.85682	D	0.000000	T	0.44030	0.1274	N	0.02539	-0.55	0.51767	D	0.999938	B;B	0.26041	0.14;0.002	B;B	0.27380	0.079;0.017	T	0.51655	-0.8678	10	0.02654	T	1	-10.8812	15.9272	0.79628	1.0:0.0:0.0:0.0	.	210;210	E9PBE3;Q8N3I7	.;BBS5_HUMAN	R	210	ENSP00000295240:K210R;ENSP00000452313:K210R;ENSP00000424363:K210R	ENSP00000295240:K210R	K	+	2	0	BBS5;RP11-724O16.1	170062393	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.520000	0.73773	2.153000	0.67306	0.533000	0.62120	AAG	.	.		0.264	BBS5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255265.2	NM_152384		G	170354147	A	G	170354147	3	3	344	1	0	0	0	0	1	0	0	0	1340	72	3	2	659	2	BBS5	2	170354147	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	256474	170354147	72845226	212	47575										
PHOSPHO2	493911	hgsc.bcm.edu	37	chr2	170557709	170557709	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acatcattgcctttcactccAgggatggtggaactcttcaa	8	11	4	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:170557709A>T	ENST00000359744.3	+	4	616	c.228A>T	c.(226-228)ccA>ccT	p.P76P	KLHL23_ENST00000602521.1_Intron|KLHL23_ENST00000272797.4_Intron	NM_001008489.3|NM_001199285.1|NM_001199286.1|NM_001199288.1	NP_001008489.1|NP_001186214.1|NP_001186215.1|NP_001186217.1	Q8TCD6	PHOP2_HUMAN	phosphatase, orphan 2	76							metal ion binding (GO:0046872)|pyridoxal phosphatase activity (GO:0033883)			breast(1)|large_intestine(1)|lung(6)|skin(2)	10						CTTTCACTCCAGGGATGGTGG	0.353																																					p.P76P		Atlas-SNP	.											.	PHOSPHO2	27	.	0			c.A228T						.						96	97	97					2																	170557709		2203	4300	6503	SO:0001819	synonymous_variant	493911	exon4			CACTCCAGGGATG	BC022324	CCDS33319.1	2q31.1	2008-02-05			ENSG00000144362	ENSG00000144362			28316	protein-coding gene	gene with protein product						16054448	Standard	NM_001199285		Approved	MGC22679	uc021vsh.1	Q8TCD6	OTTHUMG00000153981	ENST00000359744.3:c.228A>T	chr2.hg19:g.170557709A>T		118.0	0.0		103.0	51.0	NM_001199286	B2RC30|D3DPC7	Silent	SNP	ENST00000359744.3	hg19	CCDS33319.1																																																																																			.	.		0.353	PHOSPHO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333304.1	NM_001008489		T	170557709	A	T	170557709	2	4	344	1	0	0	0	0	0	0	0	1	11866	175	7	4		4	PHOSPHO2	2	170557709	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	203562	170557709	72641664	213	47576										
UBR3	130507	hgsc.bcm.edu	37	chr2	170806488	170806488	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tagaatgaacaaacgcatcaTtgaagagatatgtagaaaag	9	4	1	5			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:170806488T>C	ENST00000272793.5	+	23	3508	c.3458T>C	c.(3457-3459)aTt>aCt	p.I1153T	UBR3_ENST00000418381.1_Missense_Mutation_p.I1153T			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	1153					embryo development (GO:0009790)|in utero embryonic development (GO:0001701)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)|suckling behavior (GO:0001967)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1)	33						AAACGCATCATTGAAGAGATA	0.368																																					p.I1153T		Atlas-SNP	.											.	UBR3	182	.	0			c.T3458C						.						75	77	76					2																	170806488		2203	4300	6503	SO:0001583	missense	130507	exon23			GCATCATTGAAGA	AL834144	CCDS2238.2	2q31.1	2008-06-23	2008-06-23	2007-11-29	ENSG00000144357	ENSG00000144357		"Ubiquitin protein ligase E3 component n-recognins"	30467	protein-coding gene	gene with protein product		613831	"zinc finger protein 650"	ZNF650		17462990	Standard	NM_172070		Approved	KIAA2024, DKFZp434P117, FLJ37422	uc010zdi.2	Q6ZT12	OTTHUMG00000132229	ENST00000272793.5:c.3458T>C	chr2.hg19:g.170806488T>C	ENSP00000272793:p.Ile1153Thr	163.0	0.0		134.0	58.0	NM_172070	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Missense_Mutation	SNP	ENST00000272793.5	hg19		.	.	.	.	.	.	.	.	.	.	T	18.86	3.712425	0.68730	.	.	ENSG00000144357	ENST00000272793;ENST00000442603;ENST00000418381	T;T	0.59772	0.24;0.24	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.53706	0.1813	L	0.47190	1.495	0.80722	D	1	B;B	0.24258	0.1;0.079	B;B	0.26770	0.073;0.051	T	0.50406	-0.8832	10	0.40728	T	0.16	.	16.0044	0.80349	0.0:0.0:0.0:1.0	.	1153;1153	Q6ZT12;E7EVK3	UBR3_HUMAN;.	T	1153	ENSP00000272793:I1153T;ENSP00000396068:I1153T	ENSP00000272793:I1153T	I	+	2	0	UBR3	170514734	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.841000	0.86834	2.191000	0.70037	0.528000	0.53228	ATT	.	.		0.368	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070		C	170806488	T	C	170806488	3	2	344	1	0	0	0	0	1	0	0	0	16918	1493	52	2	3548	2	UBR3	2	170806488	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	248779	170806488	72392885	214	47577										
MYO3B	140469	hgsc.bcm.edu	37	chr2	171243724	171243724	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	actcgagccgttttggaaaaTatctggaaatgatgtttaca	9	6	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:171243724T>C	ENST00000408978.4	+	14	1626	c.1483T>C	c.(1483-1485)Tat>Cat	p.Y495H	MYO3B_ENST00000334231.6_Missense_Mutation_p.Y504H|MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000409044.3_Missense_Mutation_p.Y495H	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	495	Myosin motor.				peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						TTTTGGAAAATATCTGGAAAT	0.438																																					p.Y495H		Atlas-SNP	.											.	MYO3B	320	.	0			c.T1483C						.						89	87	88					2																	171243724		1872	4120	5992	SO:0001583	missense	140469	exon14			GGAAAATATCTGG		CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"Myosins / Myosin superfamily : Class III"	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.1483T>C	chr2.hg19:g.171243724T>C	ENSP00000386213:p.Tyr495His	102.0	0.0		99.0	52.0	NM_001083615	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Missense_Mutation	SNP	ENST00000408978.4	hg19	CCDS42773.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.627896	0.87560	.	.	ENSG00000071909	ENST00000409044;ENST00000408978;ENST00000317915;ENST00000484338;ENST00000334231	D;D;D;D	0.89485	-2.52;-2.52;-2.52;-2.52	5.63	5.63	0.86233	Myosin head, motor domain (3);	0.000000	0.85682	D	0.000000	D	0.96210	0.8764	H	0.95611	3.695	0.58432	D	0.999992	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.997;0.999	D	0.97355	0.9966	10	0.72032	D	0.01	.	15.8361	0.78799	0.0:0.0:0.0:1.0	.	495;495;495	Q8WXR4-5;Q8WXR4-4;Q8WXR4	.;.;MYO3B_HUMAN	H	495;495;494;504;504	ENSP00000386497:Y495H;ENSP00000386213:Y495H;ENSP00000446237:Y504H;ENSP00000335100:Y504H	ENSP00000314213:Y494H	Y	+	1	0	MYO3B	170951970	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.010000	0.88615	2.145000	0.66743	0.379000	0.24179	TAT	.	.		0.438	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1			C	171243724	T	C	171243724	3	2	344	1	0	0	0	0	1	0	0	0	10086	1406	49	2	1537	2	MYO3B	2	171243724	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	437236	171243724	71955649	215	47578										
MYO3B	140469	hgsc.bcm.edu	37	chr2	171260905	171260905	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccaagcaactgaccagacccTggttggtaggtaacttctga	10	11	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:171260905T>A	ENST00000408978.4	+	20	2569	c.2426T>A	c.(2425-2427)cTg>cAg	p.L809Q	MYO3B_ENST00000334231.6_Missense_Mutation_p.L818Q|MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000409044.3_Missense_Mutation_p.L809Q	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	809	Myosin motor.				peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						GACCAGACCCTGGTTGGTAGG	0.443																																					p.L809Q		Atlas-SNP	.											.	MYO3B	320	.	0			c.T2426A						.						62	61	61					2																	171260905		1891	4122	6013	SO:0001583	missense	140469	exon20			AGACCCTGGTTGG		CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"Myosins / Myosin superfamily : Class III"	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.2426T>A	chr2.hg19:g.171260905T>A	ENSP00000386213:p.Leu809Gln	120.0	0.0		100.0	46.0	NM_001083615	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Missense_Mutation	SNP	ENST00000408978.4	hg19	CCDS42773.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.626846	0.87560	.	.	ENSG00000071909	ENST00000409044;ENST00000408978;ENST00000317915;ENST00000484338;ENST00000334231	D;D;D;D	0.89196	-2.48;-2.48;-2.48;-2.48	5.57	5.57	0.84162	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.96497	0.8857	H	0.97131	3.945	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.995;1.0	D	0.97878	1.0290	10	0.87932	D	0	.	16.0347	0.80617	0.0:0.0:0.0:1.0	.	809;809;809	Q8WXR4-5;Q8WXR4-4;Q8WXR4	.;.;MYO3B_HUMAN	Q	809;809;808;818;818	ENSP00000386497:L809Q;ENSP00000386213:L809Q;ENSP00000446237:L818Q;ENSP00000335100:L818Q	ENSP00000314213:L808Q	L	+	2	0	MYO3B	170969151	1.000000	0.71417	0.971000	0.41717	0.990000	0.78478	7.798000	0.85924	2.248000	0.74166	0.533000	0.62120	CTG	.	.		0.443	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1			A	171260905	T	A	171260905	3	1	344	1	0	0	0	0	1	0	0	0	10086	1580	55	4	2504	4	MYO3B	2	171260905	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	17181	171260905	71938468	216	47579										
HNRNPA3	220988	hgsc.bcm.edu	37	chr2	178081594	178081594	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttgtttttcctcaggaggctAtggtggtggaggtggtggca	17	5	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:178081594A>G	ENST00000392524.2	+	7	983	c.746A>G	c.(745-747)tAt>tGt	p.Y249C	HNRNPA3_ENST00000435711.1_Missense_Mutation_p.Y249C|HNRNPA3_ENST00000411529.2_Missense_Mutation_p.Y227C			P51991	ROA3_HUMAN	heterogeneous nuclear ribonucleoprotein A3	249	Gly-rich.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|urinary_tract(1)	16						TCAGGAGGCTAtggtggtgga	0.398																																					p.Y249C		Atlas-SNP	.											.	HNRNPA3	42	.	0			c.A746G						.						79	78	78					2																	178081594		2203	4300	6503	SO:0001583	missense	220988	exon7			GAGGCTATGGTGG	AF517524	CCDS2273.1	2q31.2	2013-02-12		2008-04-18	ENSG00000170144	ENSG00000170144		"RNA binding motif (RRM) containing"	24941	protein-coding gene	gene with protein product		605372		HNRPA3		11886857, 15776420	Standard	XM_005246380		Approved		uc002ulc.1	P51991	OTTHUMG00000132529	ENST00000392524.2:c.746A>G	chr2.hg19:g.178081594A>G	ENSP00000376309:p.Tyr249Cys	43.0	0.0		45.0	20.0	NM_194247	D3DPF4|Q53RW7|Q6URK5	Missense_Mutation	SNP	ENST00000392524.2	hg19	CCDS2273.1	.	.	.	.	.	.	.	.	.	.	a	11.90	1.777026	0.31411	.	.	ENSG00000170144	ENST00000392524;ENST00000411529;ENST00000435711	D;D;D	0.86865	-2.18;-2.18;-2.18	4.27	3.1	0.35709	.	0.000000	0.39083	U	0.001463	T	0.81645	0.4866	M	0.67569	2.06	0.39808	D	0.972661	P;P	0.41643	0.758;0.758	B;B	0.33846	0.171;0.171	T	0.78425	-0.2209	10	0.42905	T	0.14	.	8.2631	0.31797	0.7659:0.0:0.2341:0.0	.	227;249	B4DDB6;P51991	.;ROA3_HUMAN	C	249;227;249	ENSP00000376309:Y249C;ENSP00000408487:Y227C;ENSP00000416340:Y249C	ENSP00000376309:Y249C	Y	+	2	0	HNRNPA3	177789840	1.000000	0.71417	0.997000	0.53966	0.985000	0.73830	3.454000	0.52986	0.626000	0.30322	0.446000	0.29264	TAT	.	.		0.398	HNRNPA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255729.3	NM_194247		G	178081594	A	G	178081594	3	3	344	1	0	0	0	0	1	0	0	0	7269	449	16	2	772	2	HNRNPA3	2	178081594	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	6820689	178081594	65117779	217	47580										
TTN	7273	hgsc.bcm.edu	37	chr2	179398439	179398439	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtgtacttcttgtcattgtcAcctggtttgattttctgacc	8	9	4	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:179398439A>T	ENST00000591111.1	-	308	98204	c.97980T>A	c.(97978-97980)ggT>ggA	p.G32660G	TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000460472.2_Silent_p.G25236G|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN_ENST00000589042.1_Silent_p.G34301G|TTN-AS1_ENST00000589434.1_RNA|TTN_ENST00000359218.5_Silent_p.G25361G|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN_ENST00000342175.6_Silent_p.G25428G|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN_ENST00000342992.6_Silent_p.G31733G|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585625.1_RNA			Q8WZ42	TITIN_HUMAN	titin	32660	Ig-like 144.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGTCATTGTCACCTGGTTTGA	0.403																																					p.G34301G		Atlas-SNP	.											TTN_ENST00000359218,NS,carcinoma,0,5	TTN	18412	.	0			c.T102903A						.						146	131	136					2																	179398439		1924	4141	6065	SO:0001819	synonymous_variant	7273	exon358			ATTGTCACCTGGT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.97980T>A	chr2.hg19:g.179398439A>T		76.0	0.0		64.0	33.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179398439	A	T	179398439	2	4	344	1	0	0	0	0	0	0	0	1	16750	146	6	4		4	TTN	2	179398439	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1316845	179398439	63800934	218	47581										
TTN	7273	hgsc.bcm.edu	37	chr2	179401059	179401059	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tccattcactttccccacctAgattttcacatttcacacga	2	15	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:179401059A>T	ENST00000591111.1	-	307	95716	c.95492T>A	c.(95491-95493)cTa>cAa	p.L31831Q	TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.L24407Q|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000415561.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.L33472Q|TTN-AS1_ENST00000589434.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.L24532Q|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.L24599Q|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.L30904Q|TTN-AS1_ENST00000592630.1_RNA			Q8WZ42	TITIN_HUMAN	titin	31831	Fibronectin type-III 131. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTCCCCACCTAGATTTTCACA	0.388																																					p.L33472Q		Atlas-SNP	.											.	TTN	18412	.	0			c.T100415A						.						80	75	76					2																	179401059		1851	4097	5948	SO:0001583	missense	7273	exon357			CCACCTAGATTTT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.95492T>A	chr2.hg19:g.179401059A>T	ENSP00000465570:p.Leu31831Gln	97.0	0.0		71.0	45.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	17.94	3.510884	0.64522	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.55413	0.52;0.52;0.52;0.52	5.76	5.76	0.90799	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.61800	0.2376	N	0.25332	0.735	0.52099	D	0.999948	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.77004	0.981;0.981;0.981;0.989	T	0.66296	-0.5959	9	0.87932	D	0	.	16.0677	0.80897	1.0:0.0:0.0:0.0	.	24407;24532;24599;31831	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	Q	30904;24407;24599;24532;24404	ENSP00000343764:L30904Q;ENSP00000434586:L24407Q;ENSP00000340554:L24599Q;ENSP00000352154:L24532Q	ENSP00000340554:L24599Q	L	-	2	0	TTN	179109305	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	9.339000	0.96797	2.185000	0.69588	0.460000	0.39030	CTA	.	.		0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179401059	A	T	179401059	3	4	344	1	0	0	0	0	1	0	0	0	16750	420	15	4	7588	4	TTN	2	179401059	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2620	179401059	63798314	219	47582										
TTN	7273	hgsc.bcm.edu	37	chr2	179477140	179477140	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtgcacttggtgtccttgacAgtggtatccactgtttgcca	11	10	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:179477140A>T	ENST00000591111.1	-	216	45413	c.45189T>A	c.(45187-45189)acT>acA	p.T15063T	TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000460472.2_Silent_p.T7639T|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Silent_p.T16704T|TTN_ENST00000359218.5_Silent_p.T7764T|TTN_ENST00000342175.6_Silent_p.T7831T|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000342992.6_Silent_p.T14136T|TTN-AS1_ENST00000592630.1_RNA			Q8WZ42	TITIN_HUMAN	titin	15063	Fibronectin type-III 9. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGTCCTTGACAGTGGTATCCA	0.498																																					p.T16704T		Atlas-SNP	.											.	TTN	18412	.	0			c.T50112A						.						105	96	99					2																	179477140		1969	4143	6112	SO:0001819	synonymous_variant	7273	exon266			CTTGACAGTGGTA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.45189T>A	chr2.hg19:g.179477140A>T		84.0	0.0		69.0	37.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.498	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179477140	A	T	179477140	2	4	344	1	0	0	0	0	0	0	0	1	16750	175	7	4		4	TTN	2	179477140	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	76081	179477140	63722233	220	47583										
TTN	7273	hgsc.bcm.edu	37	chr2	179482943	179482943	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	actccttgcttctacaggatTgtcagtttctactggctcac	7	12	4	0	rs368988689		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:179482943T>A	ENST00000591111.1	-	202	42543	c.42319A>T	c.(42319-42321)Aat>Tat	p.N14107Y	TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.N6683Y|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.N15748Y|TTN_ENST00000359218.5_Missense_Mutation_p.N6808Y|TTN_ENST00000342175.6_Missense_Mutation_p.N6875Y|TTN-AS1_ENST00000589830.1_RNA|RP11-171I2.4_ENST00000605334.1_lincRNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.N13180Y|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000604956.1_RNA			Q8WZ42	TITIN_HUMAN	titin	14107	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCTACAGGATTGTCAGTTTCT	0.403																																					p.N15748Y		Atlas-SNP	.											.	TTN	18412	.	0			c.A47242T						.						167	164	165					2																	179482943		1903	4122	6025	SO:0001583	missense	7273	exon252			CAGGATTGTCAGT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.42319A>T	chr2.hg19:g.179482943T>A	ENSP00000465570:p.Asn14107Tyr	87.0	0.0		81.0	37.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	11.44	1.638370	0.29157	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.64260	-0.09;0.16;0.14;0.13	5.6	5.6	0.85130	Fibronectin, type III (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.60534	0.2276	L	0.54965	1.715	0.31660	N	0.645719	B;B;B;B	0.26876	0.162;0.162;0.162;0.162	B;B;B;B	0.24541	0.054;0.054;0.054;0.054	T	0.67252	-0.5717	9	0.87932	D	0	.	16.0832	0.81020	0.0:0.0:0.0:1.0	.	6683;6808;6875;14107	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	Y	13180;6683;6875;6808;6683	ENSP00000343764:N13180Y;ENSP00000434586:N6683Y;ENSP00000340554:N6875Y;ENSP00000352154:N6808Y	ENSP00000340554:N6875Y	N	-	1	0	TTN	179191188	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	3.358000	0.52284	2.257000	0.74773	0.528000	0.53228	AAT	.	.		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179482943	T	A	179482943	3	1	344	1	0	0	0	0	1	0	0	0	16750	1812	63	4	60895	4	TTN	2	179482943	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	5803	179482943	63716430	221	47584										
TTN	7273	hgsc.bcm.edu	37	chr2	179584711	179584711	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gctgtgctttgctactaaccTagtacagtcaagactgcaga	9	10	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:179584711T>A	ENST00000591111.1	-	79	22931	c.22707A>T	c.(22705-22707)ctA>ctT	p.L7569L	TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Splice_Site_p.L7886L|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000342992.6_Splice_Site_p.L6642L			Q8WZ42	TITIN_HUMAN	titin	13126					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCTACTAACCTAGTACAGTCA	0.388																																					p.L7886L		Atlas-SNP	.											.	TTN	18412	.	0			c.A23658T						.						51	45	47					2																	179584711		1842	4097	5939	SO:0001630	splice_region_variant	7273	exon81			CTAACCTAGTACA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.22708+1A>T	chr2.hg19:g.179584711T>A		87.0	0.0		65.0	25.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	Silent	A	179584711	T	A	179584711	5	1	344	1	0	0	0	0	0	0	1	0	16750	1536	53	4	80999	4	TTN	2	179584711	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	101768	179584711	63614662	222	47585										
TTN	7273	hgsc.bcm.edu	37	chr2	179590678	179590678	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtctttgtaccataccacctCaaacggtggtgttcccgaaa	8	12	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:179590678C>T	ENST00000591111.1	-	68	19644	c.19420G>A	c.(19420-19422)Gag>Aag	p.E6474K	TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.E6791K|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|RP11-171I2.1_ENST00000590024.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.E5547K			Q8WZ42	TITIN_HUMAN	titin	12075	Ig-like 46.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CATACCACCTCAAACGGTGGT	0.428																																					p.E6791K		Atlas-SNP	.											.	TTN	18412	.	0			c.G20371A						.						94	89	91					2																	179590678		1898	4132	6030	SO:0001583	missense	7273	exon70			CCACCTCAAACGG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.19420G>A	chr2.hg19:g.179590678C>T	ENSP00000465570:p.Glu6474Lys	167.0	0.0		125.0	56.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	13.75	2.329418	0.41197	.	.	ENSG00000155657	ENST00000342992	T	0.67698	-0.28	5.87	4.99	0.66335	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.61912	0.2385	L	0.45285	1.41	0.80722	D	1	B	0.21071	0.051	B	0.15052	0.012	T	0.60919	-0.7167	9	0.87932	D	0	.	17.4718	0.87648	0.0:0.8758:0.1242:0.0	.	6474	Q8WZ42	TITIN_HUMAN	K	5547	ENSP00000343764:E5547K	ENSP00000343764:E5547K	E	-	1	0	TTN	179298923	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	2.016000	0.40971	1.611000	0.50210	0.655000	0.94253	GAG	.	.		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179590678	C	T	179590678	3	4	344	1	0	0	0	0	1	0	0	0	16750	835	29	3	84330	3	TTN	2	179590678	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	5967	179590678	63608695	223	47586										
TTN	7273	hgsc.bcm.edu	37	chr2	179594257	179594257	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cgtcactatattttactaccTccacaggcttcagctctctg	5	14	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:179594257T>A	ENST00000591111.1	-	62	17899	c.17675A>T	c.(17674-17676)gAg>gTg	p.E5892V	TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.E6209V|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|RP11-171I2.1_ENST00000590024.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.E4965V			Q8WZ42	TITIN_HUMAN	titin	12688	Ig-like 40.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTTTACTACCTCCACAGGCTT	0.468																																					p.E6209V		Atlas-SNP	.											.	TTN	18412	.	0			c.A18626T						.						95	89	91					2																	179594257		1854	4103	5957	SO:0001583	missense	7273	exon64			ACTACCTCCACAG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.17675A>T	chr2.hg19:g.179594257T>A	ENSP00000465570:p.Glu5892Val	57.0	0.0		69.0	30.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	14.55	2.570350	0.45798	.	.	ENSG00000155657	ENST00000342992	T	0.67171	-0.25	5.92	5.92	0.95590	Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.75539	0.3863	L	0.38531	1.155	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	T	0.78076	-0.2345	9	0.87932	D	0	.	16.3526	0.83220	0.0:0.0:0.0:1.0	.	5892	Q8WZ42	TITIN_HUMAN	V	4965	ENSP00000343764:E4965V	ENSP00000343764:E4965V	E	-	2	0	TTN	179302502	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	7.698000	0.84413	2.255000	0.74692	0.533000	0.62120	GAG	.	.		0.468	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179594257	T	A	179594257	3	1	344	1	0	0	0	0	1	0	0	0	16750	1551	54	4	86099	4	TTN	2	179594257	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	3579	179594257	63605116	224	47587										
TTN	7273	hgsc.bcm.edu	37	chr2	179644181	179644181	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctctcttcaaaggaagaaatAtggaattcctatgcaaaaag	7	7	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:179644181A>T	ENST00000591111.1	-	23	3962	c.3738T>A	c.(3736-3738)caT>caA	p.H1246Q	TTN_ENST00000460472.2_Missense_Mutation_p.H1200Q|TTN_ENST00000360870.5_Missense_Mutation_p.H1246Q|TTN_ENST00000589042.1_Missense_Mutation_p.H1246Q|TTN_ENST00000359218.5_Missense_Mutation_p.H1200Q|TTN_ENST00000342175.6_Missense_Mutation_p.H1200Q|RP11-88L24.4_ENST00000582038.2_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.H1246Q			Q8WZ42	TITIN_HUMAN	titin	33451					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGGAAGAAATATGGAATTCCT	0.284																																					p.H1246Q		Atlas-SNP	.											.	TTN	18412	.	0			c.T3738A						.						17	18	17					2																	179644181		2157	4252	6409	SO:0001583	missense	7273	exon23			AGAAATATGGAAT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.3738T>A	chr2.hg19:g.179644181A>T	ENSP00000465570:p.His1246Gln	133.0	0.0		96.0	39.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	11.93	1.785685	0.31593	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.61742	0.08;0.32;0.31;0.3;0.45	5.87	-2.56	0.06268	Ribonuclease H-like (1);	.	.	.	.	T	0.35307	0.0927	N	0.12746	0.255	0.21915	N	0.999477	B;B;B;B;B	0.33637	0.005;0.005;0.005;0.005;0.42	B;B;B;B;B	0.30782	0.005;0.005;0.005;0.005;0.12	T	0.19451	-1.0305	9	0.87932	D	0	.	10.4237	0.44365	0.4349:0.1017:0.4634:0.0	.	1200;1200;1200;1246;1246	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	Q	1246;1200;1200;1200;1200;1246	ENSP00000343764:H1246Q;ENSP00000434586:H1200Q;ENSP00000340554:H1200Q;ENSP00000352154:H1200Q;ENSP00000354117:H1246Q	ENSP00000340554:H1200Q	H	-	3	2	TTN	179352426	0.015000	0.18098	0.973000	0.42090	0.994000	0.84299	-0.742000	0.04850	-0.694000	0.05113	0.533000	0.62120	CAT	.	.		0.284	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179644181	A	T	179644181	3	4	344	1	0	0	0	0	1	0	0	0	16750	446	16	4	107610	4	TTN	2	179644181	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	49924	179644181	63555192	225	47588										
ZNF385B	151126	hgsc.bcm.edu	37	chr2	180311266	180311266	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gctaacctgtgttgtgtgccTctagctgtgacagggagttc	13	9	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:180311266T>A	ENST00000410066.1	-	7	1505	c.902A>T	c.(901-903)gAg>gTg	p.E301V	ZNF385B_ENST00000409692.1_Missense_Mutation_p.E199V|ZNF385B_ENST00000336917.5_Missense_Mutation_p.E199V|ZNF385B_ENST00000466398.1_5'UTR|ZNF385B_ENST00000409343.1_Missense_Mutation_p.E225V	NM_152520.4	NP_689733.3	Q569K4	Z385B_HUMAN	zinc finger protein 385B	301	Interaction with p53/TP53.				intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|p53 binding (GO:0002039)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)	26			Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)			GTTGTGTGCCTCTAGCTGTGA	0.378																																					p.E301V	Colon(155;204 2491 32774 51842)	Atlas-SNP	.											.	ZNF385B	68	.	0			c.A902T						.						100	99	99					2																	180311266		2203	4300	6503	SO:0001583	missense	151126	exon7			TGTGCCTCTAGCT	AK057999	CCDS33339.1, CCDS46463.1, CCDS46464.1	2q31.3-q32.1	2012-10-05	2007-12-06	2007-12-06	ENSG00000144331	ENSG00000144331			26332	protein-coding gene	gene with protein product		612344	"zinc finger protein 533"	ZNF533		12477932	Standard	NM_152520		Approved	FLJ25270	uc002unn.4	Q569K4	OTTHUMG00000154559	ENST00000410066.1:c.902A>T	chr2.hg19:g.180311266T>A	ENSP00000386845:p.Glu301Val	81.0	0.0		67.0	23.0	NM_152520	Q49A04|Q6ZMZ7|Q8IY01|Q8N8H2|Q96DK4	Missense_Mutation	SNP	ENST00000410066.1	hg19	CCDS33339.1	.	.	.	.	.	.	.	.	.	.	T	27.2	4.814043	0.90790	.	.	ENSG00000144331	ENST00000410066;ENST00000336917;ENST00000409343;ENST00000409692;ENST00000457304	T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;1.79	5.83	5.83	0.93111	Zinc finger, C2H2-like (1);Zinc finger, U1-type (1);Zinc finger, C2H2 (1);	0.047874	0.85682	D	0.000000	T	0.60340	0.2261	M	0.63843	1.955	0.80722	D	1	D;D	0.67145	0.991;0.996	P;P	0.62089	0.898;0.892	T	0.63629	-0.6594	10	0.87932	D	0	0.6478	16.2127	0.82178	0.0:0.0:0.0:1.0	.	301;225	Q569K4;Q569K4-2	Z385B_HUMAN;.	V	301;199;225;199;199	ENSP00000386845:E301V;ENSP00000338225:E199V;ENSP00000386379:E225V;ENSP00000386507:E199V;ENSP00000394038:E199V	ENSP00000338225:E199V	E	-	2	0	ZNF385B	180019511	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.040000	0.89188	2.236000	0.73375	0.533000	0.62120	GAG	.	.		0.378	ZNF385B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335972.1	NM_152520		A	180311266	T	A	180311266	3	1	344	1	0	0	0	0	1	0	0	0	17892	1551	54	4	529	4	ZNF385B	2	180311266	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	667085	180311266	62888107	226	47589										
ITGA4	3676	hgsc.bcm.edu	37	chr2	182339916	182339916	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atagatggaaaaatatatttTacataaagaatgaaaataag	6	1	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:182339916T>G	ENST00000397033.2	+	4	887	c.457T>G	c.(457-459)Tac>Gac	p.Y153D	ITGA4_ENST00000478440.1_Intron|ITGA4_ENST00000339307.4_Missense_Mutation_p.Y153D	NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	153					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|chorio-allantoic fusion (GO:0060710)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|face development (GO:0060324)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|negative regulation of protein homodimerization activity (GO:0090074)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha4-beta7 complex (GO:0034669)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)|Tinzaparin(DB06822)	AAATATATTTTACATAAAGAA	0.393																																					p.Y153D		Atlas-SNP	.											.	ITGA4	142	.	0			c.T457G						.						78	79	78					2																	182339916		1822	4078	5900	SO:0001583	missense	3676	exon4			ATATTTTACATAA		CCDS42788.1	2q31-q32	2010-03-23			ENSG00000115232	ENSG00000115232		"CD molecules", "Integrins"	6140	protein-coding gene	gene with protein product		192975		CD49D		1537388	Standard	NM_000885		Approved	CD49d	uc002unu.3	P13612	OTTHUMG00000154212	ENST00000397033.2:c.457T>G	chr2.hg19:g.182339916T>G	ENSP00000380227:p.Tyr153Asp	115.0	0.0		125.0	55.0	NM_000885	D3DPG4|Q7Z4L6	Missense_Mutation	SNP	ENST00000397033.2	hg19	CCDS42788.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.326980	0.81690	.	.	ENSG00000115232	ENST00000425522;ENST00000339307;ENST00000397033;ENST00000233573	T;T;T	0.63913	-0.07;0.93;0.93	5.42	5.42	0.78866	.	0.124326	0.56097	D	0.000028	T	0.78880	0.4353	M	0.79123	2.44	0.58432	D	0.999994	D;D	0.76494	0.999;0.999	D;D	0.76071	0.987;0.955	T	0.80491	-0.1359	10	0.51188	T	0.08	.	14.9337	0.70935	0.0:0.0:0.0:1.0	.	153;153	E7EP60;P13612	.;ITA4_HUMAN	D	153	ENSP00000340149:Y153D;ENSP00000380227:Y153D;ENSP00000233573:Y153D	ENSP00000233573:Y153D	Y	+	1	0	ITGA4	182048161	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.323000	0.72891	2.176000	0.68965	0.528000	0.53228	TAC	.	.		0.393	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1			G	182339916	T	G	182339916	3	3	344	1	0	0	0	0	1	0	0	0	7887	1754	61	5	471	5	ITGA4	2	182339916	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2028650	182339916	60859457	227	47590										
CERKL	375298	hgsc.bcm.edu	37	chr2	182413408	182413408	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtttaagaaaaagacttactTaagttttgccagtgccttaa	7	6	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:182413408T>A	ENST00000339098.5	-	8	1149	c.1150A>T	c.(1150-1152)Aag>Tag	p.K384*	CERKL_ENST00000409440.3_Splice_Site_p.K340*|CERKL_ENST00000374969.2_Splice_Site_p.K245*|CERKL_ENST00000479558.1_5'UTR|CERKL_ENST00000374970.2_Splice_Site_p.K289*|CERKL_ENST00000410087.3_Splice_Site_p.K358*			Q49MI3	CERKL_HUMAN	ceramide kinase-like	384					negative regulation of apoptotic process (GO:0043066)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(13)|ovary(3)|skin(3)	32			OV - Ovarian serous cystadenocarcinoma(117;0.088)			AAGACTTACTTAAGTTTTGCC	0.368																																					p.K384X		Atlas-SNP	.											.	CERKL	138	.	0			c.A1150T						.						91	92	92					2																	182413408		2203	4300	6503	SO:0001630	splice_region_variant	375298	exon8			CTTACTTAAGTTT	BC020465	CCDS33340.1, CCDS33341.1, CCDS42789.1, CCDS46466.1, CCDS54425.1	2q31.3	2005-01-04			ENSG00000188452	ENSG00000188452			21699	protein-coding gene	gene with protein product			"retinitis pigmentosa 26 (autosomal recessive)"	RP26		14681825	Standard	NR_027689		Approved		uc002uny.3	Q49MI3	OTTHUMG00000154315	ENST00000339098.5:c.1151+1A>T	chr2.hg19:g.182413408T>A		225.0	0.0		191.0	82.0	NM_001030311	B2RPL2|B4DEY1|Q49MH9|Q49MI0|Q49MI1|Q49MI2|Q5DVJ2|Q5DVJ4|Q5DVJ5|Q6UZF6|Q6ZP59	Nonsense_Mutation	SNP	ENST00000339098.5	hg19	CCDS42789.1	.	.	.	.	.	.	.	.	.	.	T	37	6.440394	0.97568	.	.	ENSG00000188452	ENST00000410087;ENST00000409440;ENST00000374969;ENST00000339098;ENST00000374970	.	.	.	5.62	5.62	0.85841	.	0.104341	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12103	T	0.63	.	15.8317	0.78757	0.0:0.0:0.0:1.0	.	.	.	.	X	358;340;245;384;289	.	ENSP00000341159:K384X	K	-	1	0	CERKL	182121653	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	4.991000	0.63883	2.136000	0.66102	0.533000	0.62120	AAG	.	.		0.368	CERKL-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334811.1		Nonsense_Mutation	A	182413408	T	A	182413408	5	1	344	1	0	0	0	0	0	0	1	0	3270	1768	61	4	554	4	CERKL	2	182413408	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	73492	182413408	60785965	228	47591										
NEUROD1	4760	hgsc.bcm.edu	37	chr2	182543118	182543118	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctgggcttttgcctgagcgcAggatctccgacagagcccag	13	13	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:182543118A>G	ENST00000295108.3	-	2	927	c.470T>C	c.(469-471)cTg>cCg	p.L157P	NEUROD1_ENST00000496876.1_Intron|CERKL_ENST00000479558.1_Intron	NM_002500.4	NP_002491.2	Q13562	NDF1_HUMAN	neuronal differentiation 1	157				L -> S (in Ref. 1; AAA93480). {ECO:0000305}.	amacrine cell differentiation (GO:0035881)|anterior/posterior pattern specification (GO:0009952)|cellular response to glucose stimulus (GO:0071333)|cerebellum development (GO:0021549)|dentate gyrus development (GO:0021542)|embryonic organ morphogenesis (GO:0048562)|endocrine pancreas development (GO:0031018)|enteroendocrine cell differentiation (GO:0035883)|glucose homeostasis (GO:0042593)|inner ear development (GO:0048839)|insulin secretion (GO:0030073)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neurogenesis (GO:0022008)|nitric oxide mediated signal transduction (GO:0007263)|nucleocytoplasmic transport (GO:0006913)|pancreatic A cell fate commitment (GO:0003326)|pancreatic PP cell fate commitment (GO:0003329)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell differentiation (GO:0045597)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle arrest (GO:0071156)|regulation of insulin secretion (GO:0050796)|regulation of intestinal epithelial structure maintenance (GO:0060730)|response to drug (GO:0042493)|response to glucose (GO:0009749)|signal transduction involved in regulation of gene expression (GO:0023019)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|protein heterodimerization activity (GO:0046982)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25			OV - Ovarian serous cystadenocarcinoma(117;0.088)			GCCTGAGCGCAGGATCTCCGA	0.567																																					p.L157P		Atlas-SNP	.											.	NEUROD1	67	.	0			c.T470C						.						81	78	79					2																	182543118		2203	4300	6503	SO:0001583	missense	4760	exon2			GAGCGCAGGATCT	U50823	CCDS2283.1	2q32	2013-05-21	2012-02-22		ENSG00000162992	ENSG00000162992		"Basic helix-loop-helix proteins"	7762	protein-coding gene	gene with protein product	"beta-cell E-box transactivator 2", "neurogenic helix-loop-helix protein NEUROD"	601724	"neurogenic differentiation 1"	NEUROD		7754368, 8786144	Standard	NM_002500		Approved	BETA2, BHF-1, NeuroD, bHLHa3, MODY6	uc002uof.4	Q13562	OTTHUMG00000132583	ENST00000295108.3:c.470T>C	chr2.hg19:g.182543118A>G	ENSP00000295108:p.Leu157Pro	62.0	0.0		63.0	29.0	NM_002500	B2R9I8|F1T0E1|O00343|Q13340|Q5U095|Q96TH0|Q99455|Q9UEC8	Missense_Mutation	SNP	ENST00000295108.3	hg19	CCDS2283.1	.	.	.	.	.	.	.	.	.	.	A	16.69	3.192975	0.58017	.	.	ENSG00000162992	ENST00000295108	D	0.90261	-2.64	6.02	6.02	0.97574	Helix-loop-helix DNA-binding (3);	0.000000	0.64402	D	0.000001	D	0.96917	0.8993	H	0.96398	3.815	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98034	1.0378	10	0.87932	D	0	-19.2817	15.3734	0.74584	1.0:0.0:0.0:0.0	.	157	Q13562	NDF1_HUMAN	P	157	ENSP00000295108:L157P	ENSP00000295108:L157P	L	-	2	0	NEUROD1	182251363	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	9.339000	0.96797	2.299000	0.77371	0.528000	0.53228	CTG	.	.		0.567	NEUROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255792.2	NM_002500		G	182543118	A	G	182543118	3	3	344	1	0	0	0	0	1	0	0	0	10357	188	7	2	604	2	NEUROD1	2	182543118	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	129710	182543118	60656255	229	47592										
FSIP2	401024	hgsc.bcm.edu	37	chr2	186671974	186671974	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	catgtttgcctctggaatctAaggatgttgttaaaaaggtc	10	6	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:186671974A>G	ENST00000424728.1	+	17	17941	c.17941A>G	c.(17941-17943)Aag>Gag	p.K5981E	FSIP2_ENST00000343098.5_Missense_Mutation_p.K6070E			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	5981										NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						TCTGGAATCTAAGGATGTTGT	0.348																																					p.K6070E		Atlas-SNP	.											.	FSIP2	251	.	0			c.A18208G						.						127	121	123					2																	186671974		1843	4077	5920	SO:0001583	missense	401024	exon17			GAATCTAAGGATG	AK092099	CCDS54426.1	2q32.1	2010-06-18			ENSG00000188738	ENSG00000188738			21675	protein-coding gene	gene with protein product		615796				14702039	Standard	NM_173651		Approved	FLJ34780	uc002upl.3	Q5CZC0	OTTHUMG00000153874	ENST00000424728.1:c.17941A>G	chr2.hg19:g.186671974A>G	ENSP00000401306:p.Lys5981Glu	91.0	0.0		98.0	38.0	NM_173651	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Missense_Mutation	SNP	ENST00000424728.1	hg19		.	.	.	.	.	.	.	.	.	.	A	17.48	3.401071	0.62288	.	.	ENSG00000188738	ENST00000343098;ENST00000424728	T;T	0.61742	0.08;0.09	4.8	4.8	0.61643	.	0.115679	0.38663	N	0.001609	T	0.47451	0.1446	L	0.36672	1.1	0.29007	N	0.887087	.	.	.	.	.	.	T	0.40515	-0.9559	8	0.12103	T	0.63	.	10.6341	0.45554	1.0:0.0:0.0:0.0	.	.	.	.	E	6070;5981	ENSP00000344403:K6070E;ENSP00000401306:K5981E	ENSP00000344403:K6070E	K	+	1	0	FSIP2	186380219	0.501000	0.26099	0.933000	0.37362	0.947000	0.59692	2.125000	0.42016	2.002000	0.58637	0.402000	0.26972	AAG	.	.		0.348	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651		G	186671974	A	G	186671974	3	3	344	1	0	0	0	0	1	0	0	0	6083	363	13	2	18274	2	FSIP2	2	186671974	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	4128856	186671974	56527399	230	47593										
COL3A1	1281	hgsc.bcm.edu	37	chr2	189864285	189864285	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agaggaggtcttggaagtccTggtccaaagggtgacaaggt	16	6	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:189864285T>A	ENST00000304636.3	+	31	2381	c.2211T>A	c.(2209-2211)ccT>ccA	p.P737P	COL3A1_ENST00000317840.5_Silent_p.P737P	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	737	Triple-helical region.				aging (GO:0007568)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell-matrix adhesion (GO:0007160)|cellular response to amino acid stimulus (GO:0071230)|cerebral cortex development (GO:0021987)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|digestive tract development (GO:0048565)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of immune response (GO:0050777)|negative regulation of neuron migration (GO:2001223)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|positive regulation of Rho protein signal transduction (GO:0035025)|response to cytokine (GO:0034097)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	collagen type III trimer (GO:0005586)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)	TTGGAAGTCCTGGTCCAAAGG	0.463																																					p.P737P		Atlas-SNP	.											.	COL3A1	292	.	0			c.T2211A						.						83	92	89					2																	189864285		2203	4300	6503	SO:0001819	synonymous_variant	1281	exon31			AAGTCCTGGTCCA	X15332	CCDS2297.1	2q32.2	2014-09-17	2008-06-23		ENSG00000168542	ENSG00000168542		"Collagens"	2201	protein-coding gene	gene with protein product		120180	"Ehlers-Danlos syndrome type IV, autosomal dominant"	EDS4A		2780304, 2834369	Standard	NM_000090		Approved		uc002uqj.1	P02461	OTTHUMG00000132648	ENST00000304636.3:c.2211T>A	chr2.hg19:g.189864285T>A		43.0	0.0		48.0	25.0	NM_000090	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Silent	SNP	ENST00000304636.3	hg19	CCDS2297.1																																																																																			.	.		0.463	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090		A	189864285	T	A	189864285	2	1	344	1	0	0	0	0	0	0	0	1	3690	1567	55	4		4	COL3A1	2	189864285	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	3192311	189864285	53335088	231	47594										
SDPR	8436	hgsc.bcm.edu	37	chr2	192711467	192711467	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcatgttcaccagcttgtccAggagcgtgagcaccgtgact	12	12	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:192711467A>T	ENST00000304141.4	-	1	514	c.185T>A	c.(184-186)cTg>cAg	p.L62Q	AC098617.1_ENST00000424116.2_RNA	NM_004657.5	NP_004648.1			serum deprivation response											NS(1)|central_nervous_system(1)|cervix(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|urinary_tract(3)	23			OV - Ovarian serous cystadenocarcinoma(117;0.0647)			CAGCTTGTCCAGGAGCGTGAG	0.577																																					p.L62Q		Atlas-SNP	.											.	SDPR	67	.	0			c.T185A						.						117	96	103					2																	192711467		2203	4300	6503	SO:0001583	missense	8436	exon1			TTGTCCAGGAGCG	AF085481	CCDS2313.1	2q32-q33	2011-04-20	2009-09-18		ENSG00000168497	ENSG00000168497			10690	protein-coding gene	gene with protein product	"phosphatidylserine binding protein"	606728	"serum deprivation response (phosphatidylserine-binding protein)", "serum deprivation response (phosphatidylserine binding protein)"			10191091, 8241023	Standard	NM_004657		Approved	SDR, PS-p68, cavin-2, CAVIN2	uc002utb.3	O95810	OTTHUMG00000154309	ENST00000304141.4:c.185T>A	chr2.hg19:g.192711467A>T	ENSP00000305675:p.Leu62Gln	90.0	0.0		77.0	38.0	NM_004657		Missense_Mutation	SNP	ENST00000304141.4	hg19	CCDS2313.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.283522	0.80803	.	.	ENSG00000168497	ENST00000304141	T	0.78707	-1.2	4.62	4.62	0.57501	.	0.000000	0.64402	D	0.000003	D	0.88288	0.6396	M	0.83774	2.66	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90215	0.4267	10	0.87932	D	0	-25.3798	14.4766	0.67551	1.0:0.0:0.0:0.0	.	62	O95810	SDPR_HUMAN	Q	62	ENSP00000305675:L62Q	ENSP00000305675:L62Q	L	-	2	0	SDPR	192419712	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.045000	0.93812	2.073000	0.62155	0.397000	0.26171	CTG	.	.		0.577	SDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334791.2	NM_004657		T	192711467	A	T	192711467	3	4	344	1	0	0	0	0	1	0	0	0	13985	188	7	4	1100	4	SDPR	2	192711467	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2847182	192711467	50487906	232	47595										
RFTN2	130132	hgsc.bcm.edu	37	chr2	198540055	198540055	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaaaagtaccttgtagagtaAaatccagcaatacatattcg	6	7	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:198540055A>T	ENST00000295049.4	-	1	664	c.128T>A	c.(127-129)tTt>tAt	p.F43Y		NM_144629.2	NP_653230.2	Q52LD8	RFTN2_HUMAN	raftlin family member 2	43					dsRNA transport (GO:0033227)|response to exogenous dsRNA (GO:0043330)	plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(13)|urinary_tract(3)	30						TTGTAGAGTAAAATCCAGCAA	0.333																																					p.F43Y		Atlas-SNP	.											.	RFTN2	68	.	0			c.T128A						.						116	122	120					2																	198540055		2203	4300	6503	SO:0001583	missense	130132	exon1			AGAGTAAAATCCA	AK055136	CCDS2323.1	2q33.1	2008-02-05	2006-09-28	2006-09-28	ENSG00000162944	ENSG00000162944			26402	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 11"	C2orf11			Standard	NM_144629		Approved	FLJ30574, Raftlin-2	uc002uuo.4	Q52LD8	OTTHUMG00000132746	ENST00000295049.4:c.128T>A	chr2.hg19:g.198540055A>T	ENSP00000295049:p.Phe43Tyr	107.0	0.0		71.0	28.0	NM_144629	Q14DH4|Q2TA69|Q53QE0|Q53SE1|Q96NM3	Missense_Mutation	SNP	ENST00000295049.4	hg19	CCDS2323.1	.	.	.	.	.	.	.	.	.	.	A	29.8	5.037776	0.93630	.	.	ENSG00000162944	ENST00000295049;ENST00000429081	T;T	0.57752	0.38;0.38	5.83	5.83	0.93111	.	0.099528	0.64402	D	0.000001	T	0.72953	0.3525	M	0.77313	2.365	0.58432	D	0.999993	D	0.71674	0.998	D	0.81914	0.995	T	0.76769	-0.2837	10	0.87932	D	0	-15.6514	14.7678	0.69654	1.0:0.0:0.0:0.0	.	43	Q52LD8	RFTN2_HUMAN	Y	43	ENSP00000295049:F43Y;ENSP00000398128:F43Y	ENSP00000295049:F43Y	F	-	2	0	RFTN2	198248300	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.546000	0.90661	2.217000	0.71921	0.477000	0.44152	TTT	.	.		0.333	RFTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256106.2	NM_144629		T	198540055	A	T	198540055	3	4	344	1	0	0	0	0	1	0	0	0	13274	14	1	4	1413	4	RFTN2	2	198540055	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	5828588	198540055	44659318	233	47596										
AOX1	316	hgsc.bcm.edu	37	chr2	201469552	201469552	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggctcctgttatcatgggaaAcacctctgtgggtatgtaga	12	8	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:201469552A>G	ENST00000374700.2	+	9	1044	c.803A>G	c.(802-804)aAc>aGc	p.N268S		NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	268	FAD-binding PCMH-type. {ECO:0000255|PROSITE-ProRule:PRU00718}.				inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)			breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	ATCATGGGAAACACCTCTGTG	0.483																																					p.N268S		Atlas-SNP	.											.	AOX1	152	.	0			c.A803G						.						72	70	71					2																	201469552		2203	4300	6503	SO:0001583	missense	316	exon9			TGGGAAACACCTC	AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356			553	protein-coding gene	gene with protein product		602841				7570184	Standard	NM_001159		Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	ENST00000374700.2:c.803A>G	chr2.hg19:g.201469552A>G	ENSP00000363832:p.Asn268Ser	102.0	0.0		71.0	29.0	NM_001159	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	Missense_Mutation	SNP	ENST00000374700.2	hg19	CCDS33360.1	.	.	.	.	.	.	.	.	.	.	A	16.32	3.091075	0.55968	.	.	ENSG00000138356	ENST00000374700	T	0.24908	1.83	5.27	5.27	0.74061	FAD-binding, type 2, subdomain 1 (1);FAD-binding, type 2 (2);Molybdopterin dehydrogenase, FAD-binding (1);	0.158517	0.56097	D	0.000023	T	0.50034	0.1592	M	0.81112	2.525	0.58432	D	0.999999	P	0.36465	0.554	P	0.52554	0.702	T	0.53387	-0.8446	10	0.72032	D	0.01	-44.6121	15.3661	0.74523	1.0:0.0:0.0:0.0	.	268	Q06278	ADO_HUMAN	S	268	ENSP00000363832:N268S	ENSP00000363832:N268S	N	+	2	0	AOX1	201177797	1.000000	0.71417	1.000000	0.80357	0.093000	0.18481	6.689000	0.74562	2.226000	0.72624	0.459000	0.35465	AAC	.	.		0.483	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335844.1	NM_001159		G	201469552	A	G	201469552	3	3	344	1	0	0	0	0	1	0	0	0	729	43	2	2	837	2	AOX1	2	201469552	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2929497	201469552	41729821	234	47597										
CDK15	65061	hgsc.bcm.edu	37	chr2	202672587	202672587	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttcccctagagcagaggaagAgcctcccttttggggcagcc	12	13	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:202672587A>T	ENST00000374598.4	+	3	280	c.280A>T	c.(280-282)Agc>Tgc	p.S94C	Y_RNA_ENST00000365267.1_RNA|CDK15_ENST00000434439.1_Missense_Mutation_p.S94C|CDK15_ENST00000488419.1_3'UTR|CDK15_ENST00000260967.2_Missense_Mutation_p.S43C|CDK15_ENST00000450471.2_Missense_Mutation_p.S94C|CDK15_ENST00000410091.3_Missense_Mutation_p.S43C			Q96Q40	CDK15_HUMAN	cyclin-dependent kinase 15	94							ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|metal ion binding (GO:0046872)			breast(3)|endometrium(2)|kidney(5)|large_intestine(1)|lung(14)|ovary(1)	26					Adenosine triphosphate(DB00171)	GCAGAGGAAGAGCCTCCCTTT	0.473																																					p.S94C		Atlas-SNP	.											.	CDK15	66	.	0			c.A280T						.						81	82	81					2																	202672587		2203	4300	6503	SO:0001583	missense	65061	exon3			AGGAAGAGCCTCC	AB053308	CCDS2350.1, CCDS58746.1, CCDS58747.1	2q33.2	2011-11-08	2009-12-16	2009-12-16	ENSG00000138395	ENSG00000138395		"Cyclin-dependent kinases"	14434	protein-coding gene	gene with protein product			"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 7", "PFTAIRE protein kinase 2"	ALS2CR7, PFTK2		11586298, 16236519, 19884882	Standard	NM_139158		Approved	PFTAIRE2	uc002uyt.3	Q96Q40	OTTHUMG00000132838	ENST00000374598.4:c.280A>T	chr2.hg19:g.202672587A>T	ENSP00000363726:p.Ser94Cys	54.0	0.0		53.0	27.0	NM_001261435	A8K8R9|B8ZZX0|C9J1N8|C9K003|F8W6H8|Q4ZG86|Q53TV1|Q6ZMR9|Q8IUP1	Missense_Mutation	SNP	ENST00000374598.4	hg19		.	.	.	.	.	.	.	.	.	.	A	15.22	2.769870	0.49680	.	.	ENSG00000138395	ENST00000410091;ENST00000260967;ENST00000450471;ENST00000434439;ENST00000374598	T;T;T;T;T	0.70749	-0.51;-0.51;-0.51;-0.5;-0.51	5.54	4.4	0.53042	.	0.508110	0.21563	N	0.072526	T	0.60881	0.2303	N	0.14661	0.345	0.32569	N	0.530099	D;P	0.60575	0.988;0.947	P;P	0.52710	0.707;0.594	T	0.69285	-0.5185	10	0.72032	D	0.01	0.0687	7.0199	0.24908	0.784:0.0:0.216:0.0	.	94;94	Q96Q40-2;F8W6H8	.;.	C	43;43;94;94;94	ENSP00000386901:S43C;ENSP00000260967:S43C;ENSP00000406472:S94C;ENSP00000412775:S94C;ENSP00000363726:S94C	ENSP00000260967:S43C	S	+	1	0	CDK15	202380832	1.000000	0.71417	0.983000	0.44433	0.574000	0.36063	4.558000	0.60789	2.102000	0.63906	0.528000	0.53228	AGC	.	.		0.473	CDK15-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000336053.2			T	202672587	A	T	202672587	3	4	344	1	0	0	0	0	1	0	0	0	3133	304	11	4	133	4	CDK15	2	202672587	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1203035	202672587	40526786	235	47598										
ALS2CR8	79800	hgsc.bcm.edu	37	chr2	203834660	203834660	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aggatttacattaaaaaggtAcagaagtttcctgaatatag	8	4	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:203834660A>G	ENST00000402905.3	+	10	1293	c.972A>G	c.(970-972)gtA>gtG	p.V324V	CARF_ENST00000414439.1_Silent_p.V222V|CARF_ENST00000320443.8_Silent_p.V324V|CARF_ENST00000438828.2_Silent_p.V324V|CARF_ENST00000545253.1_Silent_p.V236V|WDR12_ENST00000477723.1_Intron|CARF_ENST00000456821.2_3'UTR|CARF_ENST00000545262.1_Silent_p.V248V|CARF_ENST00000428585.1_Silent_p.V248V	NM_001104586.1|NM_001282910.1|NM_001282911.1|NM_001282912.1	NP_001098056.1|NP_001269839.1|NP_001269840.1|NP_001269841.1	Q8N187	CARTF_HUMAN	calcium responsive transcription factor	324					cellular response to calcium ion (GO:0071277)|cellular response to potassium ion (GO:0035865)|positive regulation of transcription from RNA polymerase II promoter in response to calcium ion (GO:0061400)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TTAAAAAGGTACAGAAGTTTC	0.294																																					p.V324V		Atlas-SNP	.											.	ALS2CR8	56	.	0			c.A972G						.						56	50	52					2																	203834660		1785	4059	5844	SO:0001819	synonymous_variant	79800	exon11			AAAGGTACAGAAG	AB053309	CCDS42801.1, CCDS63091.1	2q33.3	2013-06-12	2013-06-12	2013-06-12	ENSG00000138380	ENSG00000138380			14435	protein-coding gene	gene with protein product	"calcium-response factor"	607586	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 8"	ALS2CR8		11586298, 11832226	Standard	XM_005246858		Approved	FLJ21579, CaRF, NYD-SP24	uc002uzo.2	Q8N187	OTTHUMG00000154528	ENST00000402905.3:c.972A>G	chr2.hg19:g.203834660A>G		256.0	0.0		200.0	108.0	NM_024744	B4E1W7|G3V1K7|Q8ND29|Q8WXC0|Q96J78|Q96Q38|Q96Q39|Q9H712	Silent	SNP	ENST00000402905.3	hg19	CCDS42801.1																																																																																			.	.		0.294	CARF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335768.5	NM_001104586		G	203834660	A	G	203834660	2	3	344	1	0	0	0	0	0	0	0	1	555	378	14	2		2	ALS2CR8	2	203834660	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1162073	203834660	39364713	236	47599										
ADAM23	8745	hgsc.bcm.edu	37	chr2	207346034	207346034	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttgacctcatactgaacaagTgagtatttagacataatctt	6	7	2	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:207346034T>C	ENST00000264377.3	+	3	837		c.e3+2		ADAM23_ENST00000374416.1_Splice_Site|ADAM23_ENST00000374415.3_Splice_Site	NM_003812.2	NP_003803.1	O75077	ADA23_HUMAN	ADAM metallopeptidase domain 23						cell adhesion (GO:0007155)|central nervous system development (GO:0007417)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|endometrium(6)|kidney(3)|large_intestine(5)|liver(2)|lung(22)|ovary(2)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	51				LUSC - Lung squamous cell carcinoma(261;0.0961)|Lung(261;0.182)|Epithelial(149;0.205)		ACTGAACAAGTGAGTATTTAG	0.363																																					.	Melanoma(194;1127 2130 19620 24042 27855)	Atlas-SNP	.											.	ADAM23	239	.	0			c.509+2T>C						.						50	50	50					2																	207346034		2203	4300	6503	SO:0001630	splice_region_variant	8745	exon3			AACAAGTGAGTAT	AB009672	CCDS2369.1	2q33	2008-06-12	2005-08-18		ENSG00000114948	ENSG00000114948		"ADAM metallopeptidase domain containing"	202	protein-coding gene	gene with protein product		603710	"a disintegrin and metalloproteinase domain 23"			9693107	Standard	NM_003812		Approved	MDC3	uc002vbq.4	O75077	OTTHUMG00000132919	ENST00000264377.3:c.509+2T>C	chr2.hg19:g.207346034T>C		238.0	0.0		241.0	112.0	NM_003812	A2RU59	Splice_Site	SNP	ENST00000264377.3	hg19	CCDS2369.1	.	.	.	.	.	.	.	.	.	.	T	15.88	2.962280	0.53400	.	.	ENSG00000114948	ENST00000264377;ENST00000374416;ENST00000431817;ENST00000374415	.	.	.	5.04	5.04	0.67666	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.0463	0.64706	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	ADAM23	207054279	1.000000	0.71417	1.000000	0.80357	0.711000	0.40976	6.454000	0.73493	2.016000	0.59253	0.528000	0.53228	.	.	.		0.363	ADAM23-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256431.2	NM_003812	Intron	C	207346034	T	C	207346034	5	2	344	1	0	0	0	0	0	0	1	0	245	1710	59	2	521	2	ADAM23	2	207346034	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	3511374	207346034	35853339	237	47600										
ADAM23	8745	hgsc.bcm.edu	37	chr2	207424750	207424750	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tggactgagaaggatcagatTgacatcaccaccaaccctgt	9	11	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:207424750T>A	ENST00000264377.3	+	11	1405	c.1077T>A	c.(1075-1077)atT>atA	p.I359I	ADAM23_ENST00000374416.1_Silent_p.I359I|ADAM23_ENST00000374415.3_Silent_p.I359I	NM_003812.2	NP_003803.1	O75077	ADA23_HUMAN	ADAM metallopeptidase domain 23	359	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell adhesion (GO:0007155)|central nervous system development (GO:0007417)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|endometrium(6)|kidney(3)|large_intestine(5)|liver(2)|lung(22)|ovary(2)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	51				LUSC - Lung squamous cell carcinoma(261;0.0961)|Lung(261;0.182)|Epithelial(149;0.205)		AGGATCAGATTGACATCACCA	0.517																																					p.I359I	Melanoma(194;1127 2130 19620 24042 27855)	Atlas-SNP	.											.	ADAM23	239	.	0			c.T1077A						.						132	110	118					2																	207424750		2203	4300	6503	SO:0001819	synonymous_variant	8745	exon11			TCAGATTGACATC	AB009672	CCDS2369.1	2q33	2008-06-12	2005-08-18		ENSG00000114948	ENSG00000114948		"ADAM metallopeptidase domain containing"	202	protein-coding gene	gene with protein product		603710	"a disintegrin and metalloproteinase domain 23"			9693107	Standard	NM_003812		Approved	MDC3	uc002vbq.4	O75077	OTTHUMG00000132919	ENST00000264377.3:c.1077T>A	chr2.hg19:g.207424750T>A		87.0	0.0		60.0	21.0	NM_003812	A2RU59	Silent	SNP	ENST00000264377.3	hg19	CCDS2369.1																																																																																			.	.		0.517	ADAM23-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256431.2	NM_003812		A	207424750	T	A	207424750	2	1	344	1	0	0	0	0	0	0	0	1	245	1800	63	4		4	ADAM23	2	207424750	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	78716	207424750	35774623	238	47601										
ADAM23	8745	hgsc.bcm.edu	37	chr2	207436495	207436495	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaatgttccctctccaacggGgctcactgcagcgacgggcc	11	15	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:207436495G>T	ENST00000264377.3	+	17	1939	c.1611G>T	c.(1609-1611)ggG>ggT	p.G537G	ADAM23_ENST00000374416.1_Silent_p.G537G|ADAM23_ENST00000374415.3_Silent_p.G537G	NM_003812.2	NP_003803.1	O75077	ADA23_HUMAN	ADAM metallopeptidase domain 23	537	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				cell adhesion (GO:0007155)|central nervous system development (GO:0007417)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|endometrium(6)|kidney(3)|large_intestine(5)|liver(2)|lung(22)|ovary(2)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	51				LUSC - Lung squamous cell carcinoma(261;0.0961)|Lung(261;0.182)|Epithelial(149;0.205)		TCTCCAACGGGGCTCACTGCA	0.438																																					p.G537G	Melanoma(194;1127 2130 19620 24042 27855)	Atlas-SNP	.											.	ADAM23	239	.	0			c.G1611T						.						131	123	126					2																	207436495		2203	4300	6503	SO:0001819	synonymous_variant	8745	exon17			CAACGGGGCTCAC	AB009672	CCDS2369.1	2q33	2008-06-12	2005-08-18		ENSG00000114948	ENSG00000114948		"ADAM metallopeptidase domain containing"	202	protein-coding gene	gene with protein product		603710	"a disintegrin and metalloproteinase domain 23"			9693107	Standard	NM_003812		Approved	MDC3	uc002vbq.4	O75077	OTTHUMG00000132919	ENST00000264377.3:c.1611G>T	chr2.hg19:g.207436495G>T		45.0	0.0		50.0	18.0	NM_003812	A2RU59	Silent	SNP	ENST00000264377.3	hg19	CCDS2369.1																																																																																			.	.		0.438	ADAM23-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256431.2	NM_003812		T	207436495	G	T	207436495	2	4	344	1	0	0	0	0	0	0	0	1	245	1219	43	3		3	ADAM23	2	207436495	Silent	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	11745	207436495	35762878	239	47602										
C2orf80	389073	hgsc.bcm.edu	37	chr2	209047758	209047758	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcaaagcaacactgatggccAagtcatagtgtgcctgggag	13	9	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:209047758A>G	ENST00000341287.4	-	4	332	c.137T>C	c.(136-138)tTg>tCg	p.L46S	C2orf80_ENST00000451346.1_Missense_Mutation_p.L27S|C2orf80_ENST00000453017.1_Missense_Mutation_p.L46S	NM_001099334.2	NP_001092804	Q0P641	CB080_HUMAN	chromosome 2 open reading frame 80	46										endometrium(2)|large_intestine(3)|lung(6)|skin(2)	13						ACTGATGGCCAAGTCATAGTG	0.493																																					p.L46S		Atlas-SNP	.											.	C2orf80	19	.	0			c.T137C						.						133	130	131					2																	209047758		1995	4172	6167	SO:0001583	missense	389073	exon4			ATGGCCAAGTCAT	AC016697, AW136505, BC035737	CCDS42809.1	2q33.3	2013-10-31			ENSG00000188674	ENSG00000188674			34352	protein-coding gene	gene with protein product	"gonad development associated 1"	615536				22080834, 24055526	Standard	NM_001099334		Approved	LOC389073, GONDA1	uc002vcr.3	Q0P641	OTTHUMG00000154751	ENST00000341287.4:c.137T>C	chr2.hg19:g.209047758A>G	ENSP00000343171:p.Leu46Ser	103.0	0.0		77.0	33.0	NM_001099334	A6NKZ3	Missense_Mutation	SNP	ENST00000341287.4	hg19	CCDS42809.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.061578	0.76187	.	.	ENSG00000188674	ENST00000341287;ENST00000451346;ENST00000453017;ENST00000449053	T;T;T	0.59224	1.18;1.06;0.28	5.43	5.43	0.79202	.	0.000000	0.44097	D	0.000489	T	0.66015	0.2747	L	0.34521	1.04	0.37976	D	0.933453	D	0.89917	1.0	D	0.91635	0.999	T	0.72171	-0.4371	10	0.87932	D	0	-10.0505	13.0967	0.59197	1.0:0.0:0.0:0.0	.	46	Q0P641	CB080_HUMAN	S	46;27;46;46	ENSP00000343171:L46S;ENSP00000405393:L27S;ENSP00000397144:L46S	ENSP00000343171:L46S	L	-	2	0	C2orf80	208756003	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	5.767000	0.68850	2.279000	0.76181	0.533000	0.62120	TTG	.	.		0.493	C2orf80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336931.1	NM_001099334		G	209047758	A	G	209047758	3	3	344	1	0	0	0	0	1	0	0	0	2199	131	5	2	468	2	C2orf80	2	209047758	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1611263	209047758	34151615	240	47603										
PTH2R	5746	hgsc.bcm.edu	37	chr2	209345825	209345825	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttctgtttctgaatacggttAgagttctagctaccaaaatc	7	8	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:209345825A>T	ENST00000272847.2	+	10	1225	c.1012A>T	c.(1012-1014)Aga>Tga	p.R338*	AC019185.4_ENST00000424628.1_RNA|PTH2R_ENST00000413482.1_3'UTR	NM_005048.2	NP_005039.1	P49190	PTH2R_HUMAN	parathyroid hormone 2 receptor	338					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	parathyroid hormone receptor activity (GO:0004991)			breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(21)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43				Epithelial(149;0.0684)|Lung(261;0.0785)|LUSC - Lung squamous cell carcinoma(261;0.0836)	Preotact(DB05829)	GAATACGGTTAGAGTTCTAGC	0.338																																					p.R338X		Atlas-SNP	.											.	PTH2R	92	.	0			c.A1012T						.						96	95	96					2																	209345825		2203	4300	6503	SO:0001587	stop_gained	5746	exon10			ACGGTTAGAGTTC	BC036811	CCDS2383.1	2q33	2012-08-10	2007-08-24	2007-08-24	ENSG00000144407	ENSG00000144407		"GPCR / Class B : Parathyroid hormone receptors"	9609	protein-coding gene	gene with protein product		601469	"parathyroid hormone receptor 2"	PTHR2			Standard	NM_005048		Approved		uc002vdb.4	P49190	OTTHUMG00000132960	ENST00000272847.2:c.1012A>T	chr2.hg19:g.209345825A>T	ENSP00000272847:p.Arg338*	181.0	0.0		178.0	69.0	NM_005048	Q8N429	Nonsense_Mutation	SNP	ENST00000272847.2	hg19	CCDS2383.1	.	.	.	.	.	.	.	.	.	.	A	39	7.591607	0.98378	.	.	ENSG00000144407	ENST00000272847	.	.	.	5.69	5.69	0.88448	.	0.000000	0.49916	D	0.000137	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.2742	0.43499	0.8342:0.1657:0.0:0.0	.	.	.	.	X	338	.	.	R	+	1	2	PTH2R	209054070	0.998000	0.40836	1.000000	0.80357	0.993000	0.82548	2.189000	0.42621	2.293000	0.77203	0.528000	0.53228	AGA	.	.		0.338	PTH2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256519.2	NM_005048		T	209345825	A	T	209345825	4	4	344	1	0	0	0	0	0	1	0	0	12773	412	15	4	1050	4	PTH2R	2	209345825	Nonsense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	298067	209345825	33853548	241	47604										
MARCH4	57574	hgsc.bcm.edu	37	chr2	217124264	217124264	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cctgggtggatgaggaggtcCgggggttggtcctgcctcct	18	10	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:217124264C>A	ENST00000273067.4	-	4	2770	c.1004G>T	c.(1003-1005)cGg>cTg	p.R335L	AC012513.6_ENST00000417481.1_RNA	NM_020814.2	NP_065865.1	Q9P2E8	MARH4_HUMAN	membrane-associated ring finger (C3HC4) 4, E3 ubiquitin protein ligase	335						Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|skin(1)	20		Renal(323;0.0854)		Epithelial(149;2.19e-05)|all cancers(144;0.00121)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0125)		TGAGGAGGTCCGGGGGTTGGT	0.617																																					p.R335L		Atlas-SNP	.											.	MARCH4	50	.	0			c.G1004T						.						79	72	75					2																	217124264		2203	4300	6503	SO:0001583	missense	57574	exon4			GAGGTCCGGGGGT	AB037820	CCDS33376.1	2q35	2013-01-09	2012-02-23		ENSG00000144583	ENSG00000144583		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	29269	protein-coding gene	gene with protein product		608208	"membrane-associated ring finger (C3HC4) 4"			10718198, 14722266	Standard	NM_020814		Approved	KIAA1399, MARCH-IV, RNF174	uc002vgb.3	Q9P2E8	OTTHUMG00000154824	ENST00000273067.4:c.1004G>T	chr2.hg19:g.217124264C>A	ENSP00000273067:p.Arg335Leu	114.0	0.0		89.0	34.0	NM_020814	Q4KMN7|Q86WR8	Missense_Mutation	SNP	ENST00000273067.4	hg19	CCDS33376.1	.	.	.	.	.	.	.	.	.	.	C	14.79	2.639412	0.47153	.	.	ENSG00000144583	ENST00000273067	T	0.15372	2.43	5.62	3.8	0.43715	.	0.752409	0.12792	N	0.438800	T	0.16642	0.0400	L	0.36672	1.1	0.29816	N	0.831278	P	0.36392	0.551	B	0.40901	0.343	T	0.11012	-1.0605	10	0.46703	T	0.11	-12.2027	8.0386	0.30508	0.0:0.7532:0.0:0.2468	.	335	Q9P2E8	MARH4_HUMAN	L	335	ENSP00000273067:R335L	ENSP00000273067:R335L	R	-	2	0	MARCH4	216832509	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.112000	0.50368	0.715000	0.32103	0.561000	0.74099	CGG	.	.		0.617	MARCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337272.2	NM_020814		A	217124264	C	A	217124264	3	1	344	1	0	0	0	0	1	0	0	0	9312	652	23	1	232	1	MARCH4	2	217124264	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	7778439	217124264	26075109	242	47605										
TNS1	7145	hgsc.bcm.edu	37	chr2	218713037	218713037	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cataccgctggggtcatgggCatagtgggaggtggtcactg	17	8	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:218713037C>A	ENST00000171887.4	-	17	2280	c.1828G>T	c.(1828-1830)Gcc>Tcc	p.A610S	TNS1_ENST00000419504.1_Missense_Mutation_p.A610S|TNS1_ENST00000480665.1_5'Flank|TNS1_ENST00000430930.1_Missense_Mutation_p.A610S	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	610					cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		GGGTCATGGGCATAGTGGGAG	0.657																																					p.A610S		Atlas-SNP	.											.	TNS1	251	.	0			c.G1828T						.						65	57	60					2																	218713037		2202	4300	6502	SO:0001583	missense	7145	exon17			CATGGGCATAGTG	AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	11973	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 155"	600076	"tensin", "matrix-remodelling associated 6"	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.1828G>T	chr2.hg19:g.218713037C>A	ENSP00000171887:p.Ala610Ser	100.0	0.0		91.0	32.0	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	hg19	CCDS2407.1	.	.	.	.	.	.	.	.	.	.	C	0.017	-1.511495	0.00984	.	.	ENSG00000079308	ENST00000171887;ENST00000419504;ENST00000430930;ENST00000446903	D;D;D;D	0.93189	-2.66;-2.7;-2.7;-3.18	4.57	1.82	0.25136	.	0.322159	0.28883	N	0.013835	T	0.77624	0.4158	N	0.02247	-0.625	0.09310	N	0.99999	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.65368	-0.6185	10	0.16896	T	0.51	.	4.7273	0.12946	0.1499:0.6103:0.0:0.2398	.	610;664;610;610;610	B2RU35;A1L0S7;Q9HBL0;E9PGF5;E9PF55	.;.;TENS1_HUMAN;.;.	S	610;610;610;735	ENSP00000171887:A610S;ENSP00000408724:A610S;ENSP00000406016:A610S;ENSP00000405460:A735S	ENSP00000171887:A610S	A	-	1	0	TNS1	218421282	0.000000	0.05858	0.579000	0.28588	0.463000	0.32649	-0.202000	0.09451	0.193000	0.20303	0.561000	0.74099	GCC	.	.		0.657	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		A	218713037	C	A	218713037	3	1	344	1	0	0	0	0	1	0	0	0	16358	710	25	3	3447	3	TNS1	2	218713037	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1588773	218713037	24486336	243	47606										
TTLL4	9654	hgsc.bcm.edu	37	chr2	219609870	219609870	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaccaaacccctttccaatcAtgagaaagttgtccgaccag	7	13	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:219609870A>T	ENST00000392102.1	+	6	2040	c.1700A>T	c.(1699-1701)cAt>cTt	p.H567L	TTLL4_ENST00000457313.1_Missense_Mutation_p.H402L|TTLL4_ENST00000442769.1_Missense_Mutation_p.H567L|TTLL4_ENST00000258398.4_Missense_Mutation_p.H567L	NM_014640.4	NP_055455.3	Q14679	TTLL4_HUMAN	tubulin tyrosine ligase-like family, member 4	567					protein polyglutamylation (GO:0018095)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)|tubulin binding (GO:0015631)			endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	39		Renal(207;0.0915)		Epithelial(149;5.03e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0101)		CTTTCCAATCATGAGAAAGTT	0.468																																					p.H567L	GBM(172;1818 2053 15407 20943 49753)	Atlas-SNP	.											.	TTLL4	96	.	0			c.A1700T						.						200	193	195					2																	219609870		2203	4300	6503	SO:0001583	missense	9654	exon6			CCAATCATGAGAA		CCDS2422.1	2p24.3-p24.1	2013-02-14			ENSG00000135912	ENSG00000135912		"Tubulin tyrosine ligase-like family"	28976	protein-coding gene	gene with protein product						11054573	Standard	NM_014640		Approved	KIAA0173	uc002viy.3	Q14679	OTTHUMG00000133081	ENST00000392102.1:c.1700A>T	chr2.hg19:g.219609870A>T	ENSP00000375951:p.His567Leu	152.0	0.0		116.0	43.0	NM_014640	A8K6V5|Q8WW29	Missense_Mutation	SNP	ENST00000392102.1	hg19	CCDS2422.1	.	.	.	.	.	.	.	.	.	.	A	14.35	2.510596	0.44660	.	.	ENSG00000135912	ENST00000457313;ENST00000392102;ENST00000442769;ENST00000258398	T;T;T;T	0.03951	3.95;4.19;3.75;4.19	3.82	2.61	0.31194	.	1.369470	0.04666	N	0.409786	T	0.04182	0.0116	N	0.22421	0.69	0.32069	N	0.594701	B;B;B	0.29432	0.003;0.244;0.02	B;B;B	0.26864	0.004;0.074;0.007	T	0.41645	-0.9497	10	0.13470	T	0.59	.	8.1458	0.31110	0.7955:0.2045:0.0:0.0	.	402;567;567	E9PH58;E7EX20;Q14679	.;.;TTLL4_HUMAN	L	402;567;567;567	ENSP00000393332:H402L;ENSP00000375951:H567L;ENSP00000396555:H567L;ENSP00000258398:H567L	ENSP00000258398:H567L	H	+	2	0	TTLL4	219318114	0.962000	0.33011	0.994000	0.49952	0.994000	0.84299	1.591000	0.36665	0.482000	0.27582	0.533000	0.62120	CAT	.	.		0.468	TTLL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256726.1	NM_014640		T	219609870	A	T	219609870	3	4	344	1	0	0	0	0	1	0	0	0	16744	217	8	4	1714	4	TTLL4	2	219609870	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	896833	219609870	23589503	244	47607										
CDK5R2	8941	hgsc.bcm.edu	37	chr2	219825484	219825484	+	Frame_Shift_Del	DEL	C	C	-													0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atgctgcggctcaacgccgaCccccacttcttcacgcaggt							TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:219825484delC	ENST00000302625.4	+	1	1108	c.942delC	c.(940-942)gacfs	p.D314fs	AC097468.7_ENST00000429343.1_RNA	NM_003936.4	NP_003927.1	Q13319	CD5R2_HUMAN	cyclin-dependent kinase 5, regulatory subunit 2 (p39)	314					cerebellum development (GO:0021549)|hippocampus development (GO:0021766)|layer formation in cerebral cortex (GO:0021819)|neuron migration (GO:0001764)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|superior olivary nucleus maturation (GO:0021722)	cyclin-dependent protein kinase 5 holoenzyme complex (GO:0016533)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	cyclin-dependent protein kinase 5 activator activity (GO:0016534)|lipid binding (GO:0008289)			central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(1)|ovary(1)	8		Renal(207;0.0474)		Epithelial(149;9.77e-07)|all cancers(144;0.000167)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCAACGCCGACCCCCACTTCT	0.711																																					p.D314fs		Atlas-Indel,Pindel	.											.	CDK5R2	17	.	0			c.941delA						.						36	38	38					2																	219825484		2203	4299	6502	SO:0001589	frameshift_variant	8941	exon1			.	U34051	CCDS2427.1	2q35	2008-05-22			ENSG00000171450	ENSG00000171450			1776	protein-coding gene	gene with protein product	"neuronal CDK5 activator isoform"	603764				7592934	Standard	NM_003936		Approved	p39nck5ai, P39, NCK5AI	uc002vjf.4	Q13319	OTTHUMG00000133083	ENST00000302625.4:c.942delC	chr2.hg19:g.219825484delC	ENSP00000304250:p.Asp314fs	71.0	0.0		76.0	32.0	NM_003936	Q4ZFW6	Frame_Shift_Del	DEL	ENST00000302625.4	hg19	CCDS2427.1																																																																																			.	.		0.711	CDK5R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256728.1	NM_003936		-	219825484	C	-	219825484	7	5	344	1	0	1	0	1	0	0	0	0	3146	506	18	0	944	0	CDK5R2	2	219825484	Frame_Shift_Del	DEL	C	TCGA-UB-A7MB-01A-11D-A33Q-10	215614	219825484	23373889	245	47608										
DES	1674	hgsc.bcm.edu	37	chr2	220285630	220285630	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gagatgatggaataccgacaCcagatccagtcctacacctg	9	12	0	3	rs375238266		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:220285630C>A	ENST00000373960.3	+	5	1064	c.978C>A	c.(976-978)caC>caA	p.H326Q		NM_001927.3	NP_001918.3	P17661	DESM_HUMAN	desmin	326	Coil 2B.|Rod.				cytoskeleton organization (GO:0007010)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart contraction (GO:0008016)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intermediate filament (GO:0005882)|neuromuscular junction (GO:0031594)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(10)|skin(1)	18		Renal(207;0.0183)		Epithelial(149;5.25e-07)|all cancers(144;0.000103)|Lung(261;0.00533)|LUSC - Lung squamous cell carcinoma(224;0.008)		AATACCGACACCAGATCCAGT	0.612																																					p.H326Q		Atlas-SNP	.											.	DES	53	.	0			c.C978A						.						98	88	91					2																	220285630		2203	4300	6503	SO:0001583	missense	1674	exon5			CCGACACCAGATC	AF521879	CCDS33383.1	2q35	2014-09-17			ENSG00000175084	ENSG00000175084		"Intermediate filaments type III"	2770	protein-coding gene	gene with protein product	"intermediate filament protein"	125660				2673923, 9736733	Standard	NM_001927		Approved	CMD1I, CSM1, CSM2	uc002vll.3	P17661	OTTHUMG00000058924	ENST00000373960.3:c.978C>A	chr2.hg19:g.220285630C>A	ENSP00000363071:p.His326Gln	68.0	0.0		61.0	26.0	NM_001927	Q15787|Q549R7|Q549R8|Q549R9|Q8IZR1|Q8IZR6|Q8NES2|Q8NEU6|Q8TAC4|Q8TCX2|Q8TD99|Q9UHN5|Q9UJ80	Missense_Mutation	SNP	ENST00000373960.3	hg19	CCDS33383.1	.	.	.	.	.	.	.	.	.	.	C	31	5.064285	0.93898	.	.	ENSG00000175084	ENST00000373960	D	0.95554	-3.74	4.91	4.91	0.64330	Filament (1);	0.000000	0.51477	D	0.000086	D	0.95573	0.8561	L	0.28274	0.84	0.58432	D	0.999999	D	0.60160	0.987	D	0.65233	0.933	D	0.96361	0.9266	10	0.66056	D	0.02	.	17.8922	0.88876	0.0:1.0:0.0:0.0	.	326	P17661	DESM_HUMAN	Q	326	ENSP00000363071:H326Q	ENSP00000363071:H326Q	H	+	3	2	DES	219993874	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.962000	0.56766	2.533000	0.85409	0.561000	0.74099	CAC	.	.		0.612	DES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130240.1	NM_001927		A	220285630	C	A	220285630	3	1	344	1	0	0	0	0	1	0	0	0	4451	506	18	3	996	3	DES	2	220285630	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	460146	220285630	22913743	246	47609										
SPEG	10290	hgsc.bcm.edu	37	chr2	220342465	220342465	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggatgaggaccatcgaggaaGgagactcagcgacttttatg	14	7	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:220342465G>T	ENST00000312358.7	+	21	4916	c.4784G>T	c.(4783-4785)aGg>aTg	p.R1595M	SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	1595					cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		CATCGAGGAAGGAGACTCAGC	0.597																																					p.R1595M		Atlas-SNP	.											.	SPEG	272	.	0			c.G4784T						.						92	100	97					2																	220342465		2038	4177	6215	SO:0001583	missense	10290	exon21			GAGGAAGGAGACT	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"Immunoglobulin superfamily / I-set domain containing"	16901	protein-coding gene	gene with protein product		615950	"aortic preferentially expressed gene 1"	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.4784G>T	chr2.hg19:g.220342465G>T	ENSP00000311684:p.Arg1595Met	91.0	0.0		75.0	29.0	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	hg19	CCDS42824.1	.	.	.	.	.	.	.	.	.	.	G	14.17	2.454963	0.43634	.	.	ENSG00000072195	ENST00000312358;ENST00000265327	T	0.40225	1.04	4.84	2.07	0.26955	Protein kinase-like domain (1);	0.602886	0.13983	N	0.349370	T	0.49081	0.1536	L	0.45470	1.425	0.80722	D	1	D	0.61697	0.99	P	0.59703	0.862	T	0.40308	-0.9570	10	0.44086	T	0.13	.	9.164	0.37041	0.2411:0.0:0.7589:0.0	.	1595	Q15772	SPEG_HUMAN	M	1595	ENSP00000311684:R1595M	ENSP00000265327:R1595M	R	+	2	0	SPEG	220050709	0.062000	0.20869	0.998000	0.56505	0.884000	0.51177	1.411000	0.34702	0.747000	0.32809	0.655000	0.94253	AGG	.	.		0.597	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		T	220342465	G	T	220342465	3	4	344	1	0	0	0	0	1	0	0	0	15051	1000	35	3	4878	3	SPEG	2	220342465	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	56835	220342465	22856908	247	47610										
CHPF	79586	hgsc.bcm.edu	37	chr2	220406616	220406616	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgccaggccgtgcgcctcggTgtaggtggtgtcaggcacca	16	12	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:220406616T>A	ENST00000243776.6	-	2	858	c.610A>T	c.(610-612)Acc>Tcc	p.T204S	TMEM198_ENST00000373883.3_5'Flank|TMEM198_ENST00000344458.2_5'Flank|CHPF_ENST00000373891.2_Missense_Mutation_p.T204S|CHPF_ENST00000535926.1_Missense_Mutation_p.T42S	NM_024536.5	NP_078812	Q8IZ52	CHSS2_HUMAN	chondroitin polymerizing factor	204					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)	21		Renal(207;0.0183)		Epithelial(149;3.02e-08)|all cancers(144;3.41e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		TGCGCCTCGGTGTAGGTGGTG	0.687											OREG0015229	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T204S		Atlas-SNP	.											.	CHPF	56	.	0			c.A610T						.						34	29	31					2																	220406616		2201	4300	6501	SO:0001583	missense	79586	exon2			CCTCGGTGTAGGT	BC008878	CCDS2443.1, CCDS56169.1	2q35	2014-02-12			ENSG00000123989	ENSG00000123989	2.4.1.175, 2.4.1.226	"Beta 3-glycosyltransferases", "Beta 4-glycosyltransferases"	24291	protein-coding gene	gene with protein product	"chondroitin sulfate synthase 2"	610405				11230166, 12716890	Standard	NM_024536		Approved	CSS2, CHSY2	uc002vmc.4	Q8IZ52	OTTHUMG00000058929	ENST00000243776.6:c.610A>T	chr2.hg19:g.220406616T>A	ENSP00000243776:p.Thr204Ser	77.0	0.0	2266	55.0	25.0	NM_024536	B4DXU0|Q6UXD6|Q7L4G1|Q9H0F8|Q9H618	Missense_Mutation	SNP	ENST00000243776.6	hg19	CCDS2443.1	.	.	.	.	.	.	.	.	.	.	T	29.0	4.964770	0.92791	.	.	ENSG00000123989	ENST00000243776;ENST00000535926;ENST00000373891	T;T	0.11604	2.76;2.77	4.29	4.29	0.51040	.	0.000000	0.85682	D	0.000000	T	0.30262	0.0759	M	0.68317	2.08	0.58432	D	0.999992	D;P	0.67145	0.996;0.82	D;B	0.77557	0.99;0.421	T	0.03717	-1.1010	10	0.72032	D	0.01	-19.8638	13.8997	0.63794	0.0:0.0:0.0:1.0	.	204;204	F8W6H2;Q8IZ52	.;CHSS2_HUMAN	S	204;42;204	ENSP00000243776:T204S;ENSP00000445571:T42S	ENSP00000243776:T204S	T	-	1	0	CHPF	220114860	1.000000	0.71417	0.995000	0.50966	0.992000	0.81027	6.128000	0.71650	1.950000	0.56595	0.448000	0.29417	ACC	.	.		0.687	CHPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130268.1	NM_024536		A	220406616	T	A	220406616	3	1	344	1	0	0	0	0	1	0	0	0	3370	1696	59	4	1729	4	CHPF	2	220406616	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	64151	220406616	22792757	248	47611										
CCDC140	151278	hgsc.bcm.edu	37	chr2	223168828	223168828	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aggcagagttgtcaggggccAagcccggcgcgatctggcca	16	12	2	1	rs567359483		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:223168828A>T	ENST00000295226.1	+	2	591	c.207A>T	c.(205-207)ccA>ccT	p.P69P		NM_153038.1	NP_694583.1	Q96MF4	CC140_HUMAN	coiled-coil domain containing 140	69										endometrium(4)|large_intestine(1)|prostate(1)	6		Renal(207;0.0376)		Epithelial(121;4.03e-10)|all cancers(144;1.8e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GTCAGGGGCCAAGCCCGGCGC	0.597																																					p.P69P		Atlas-SNP	.											.	CCDC140	20	.	0			c.A207T						.						46	50	48					2																	223168828		2203	4300	6503	SO:0001819	synonymous_variant	151278	exon2			GGGGCCAAGCCCG	AK057009	CCDS2452.1	2q36.1	2008-02-05			ENSG00000163081	ENSG00000163081			26514	protein-coding gene	gene with protein product							Standard	NM_153038		Approved	FLJ32447	uc002vnb.1	Q96MF4	OTTHUMG00000133154	ENST00000295226.1:c.207A>T	chr2.hg19:g.223168828A>T		281.0	0.0		231.0	116.0	NM_153038		Silent	SNP	ENST00000295226.1	hg19	CCDS2452.1																																																																																			.	.		0.597	CCDC140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256854.1	NM_153038		T	223168828	A	T	223168828	2	4	344	1	0	0	0	0	0	0	0	1	2776	117	5	4		4	CCDC140	2	223168828	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2762212	223168828	20030545	249	47612										
DOCK10	55619	hgsc.bcm.edu	37	chr2	225635277	225635277	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cttacctgaagatctccttcAaaagctttacttggttgtca	6	10	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:225635277A>C	ENST00000258390.7	-	54	6357	c.6290T>G	c.(6289-6291)tTg>tGg	p.L2097W	DOCK10_ENST00000409592.3_Missense_Mutation_p.L2091W	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	2097	DHR-2.				regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		GATCTCCTTCAAAAGCTTTAC	0.448																																					p.L2097W		Atlas-SNP	.											.	DOCK10	308	.	0			c.T6290G						.						120	130	127					2																	225635277		1904	4117	6021	SO:0001583	missense	55619	exon54			TCCTTCAAAAGCT	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"Pleckstrin homology (PH) domain containing"	23479	protein-coding gene	gene with protein product	"zizimin3"	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.6290T>G	chr2.hg19:g.225635277A>C	ENSP00000258390:p.Leu2097Trp	106.0	0.0		95.0	37.0	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Missense_Mutation	SNP	ENST00000258390.7	hg19	CCDS46528.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.189134	0.78789	.	.	ENSG00000135905	ENST00000409592;ENST00000258390;ENST00000373702	T;T	0.51574	0.7;0.7	5.09	5.09	0.68999	.	0.000000	0.64402	D	0.000001	T	0.75554	0.3865	M	0.93016	3.37	0.52099	D	0.999945	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.82621	-0.0367	10	0.87932	D	0	.	14.8975	0.70654	1.0:0.0:0.0:0.0	.	2097;2091;759	Q96BY6;B3FL70;B4DEY4	DOC10_HUMAN;.;.	W	2091;2097;604	ENSP00000386694:L2091W;ENSP00000258390:L2097W	ENSP00000258390:L2097W	L	-	2	0	DOCK10	225343521	1.000000	0.71417	0.974000	0.42286	0.898000	0.52572	8.962000	0.93254	1.928000	0.55862	0.533000	0.62120	TTG	.	.		0.448	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1			C	225635277	A	C	225635277	3	2	344	1	0	0	0	0	1	0	0	0	4687	131	5	5	282	5	DOCK10	2	225635277	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2466449	225635277	17564096	250	47613										
COL4A4	1286	hgsc.bcm.edu	37	chr2	227875174	227875174	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aagccaccgaggtatccaggGccaaaccctttgggcccagg	12	14	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:227875174G>T	ENST00000396625.3	-	46	4584	c.4377C>A	c.(4375-4377)ggC>ggA	p.G1459G	COL4A4_ENST00000329662.7_Silent_p.G1456G	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	1459	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		GGTATCCAGGGCCAAACCCTT	0.572																																					p.G1459G		Atlas-SNP	.											.	COL4A4	215	.	0			c.C4377A						.						28	28	28					2																	227875174		1845	4089	5934	SO:0001819	synonymous_variant	1286	exon46			TCCAGGGCCAAAC		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"Collagens"	2206	protein-coding gene	gene with protein product	"collagen of basement membrane, alpha-4 chain"	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.4377C>A	chr2.hg19:g.227875174G>T		144.0	0.0		135.0	64.0	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Silent	SNP	ENST00000396625.3	hg19	CCDS42828.1																																																																																			.	.		0.572	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092		T	227875174	G	T	227875174	2	4	344	1	0	0	0	0	0	0	0	1	3695	1190	42	3		3	COL4A4	2	227875174	Silent	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	2239897	227875174	15324199	251	47614										
AGFG1	3267	hgsc.bcm.edu	37	chr2	228398301	228398301	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agtaaatgctaattttgctcAttttgataacttccccaaat	4	8	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:228398301A>T	ENST00000310078.8	+	7	1111	c.851A>T	c.(850-852)cAt>cTt	p.H284L	AGFG1_ENST00000409979.2_Missense_Mutation_p.H308L|AGFG1_ENST00000409315.1_Missense_Mutation_p.H284L|AGFG1_ENST00000409171.1_Missense_Mutation_p.H284L|AGFG1_ENST00000373671.3_Missense_Mutation_p.H244L	NM_001135188.1|NM_001135189.1|NM_004504.4	NP_001128660.1|NP_001128661.1|NP_004495.2	P52594	AGFG1_HUMAN	ArfGAP with FG repeats 1	284					cell differentiation (GO:0030154)|mRNA export from nucleus (GO:0006406)|multicellular organismal development (GO:0007275)|regulation of ARF GTPase activity (GO:0032312)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)	ARF GTPase activator activity (GO:0008060)|DNA binding (GO:0003677)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(2)|ovary(1)|prostate(1)|skin(4)|stomach(1)	18						AATTTTGCTCATTTTGATAAC	0.393																																					p.H308L		Atlas-SNP	.											.	AGFG1	80	.	0			c.A923T						.						98	93	95					2																	228398301		2203	4300	6503	SO:0001583	missense	3267	exon8			TTGCTCATTTTGA		CCDS2467.1, CCDS46533.1, CCDS46534.1, CCDS46535.1	2q36	2009-11-30	2008-09-22	2008-09-22	ENSG00000173744	ENSG00000173744		"ADP-ribosylation factor GTPase activating proteins"	5175	protein-coding gene	gene with protein product		600862	"HIV-1 Rev binding protein"	HRB		7637788	Standard	NM_004504		Approved	RIP, RAB	uc002vpd.2	P52594	OTTHUMG00000133186	ENST00000310078.8:c.851A>T	chr2.hg19:g.228398301A>T	ENSP00000312059:p.His284Leu	109.0	0.0		86.0	39.0	NM_001135187	B3KUL1|E9PHX7|Q15277|Q4VAS0|Q4VAS1|Q4VAS3|Q53QT8|Q53R11	Missense_Mutation	SNP	ENST00000310078.8	hg19	CCDS2467.1	.	.	.	.	.	.	.	.	.	.	A	17.56	3.420784	0.62622	.	.	ENSG00000173744	ENST00000409979;ENST00000542592;ENST00000310078;ENST00000409315;ENST00000373671;ENST00000409171;ENST00000456594	T;T;T;T;T	0.23147	1.95;1.92;1.95;1.94;1.92	5.14	5.14	0.70334	.	0.169968	0.52532	D	0.000063	T	0.19406	0.0466	L	0.36672	1.1	0.47065	D	0.999308	B;B;P;B	0.34462	0.43;0.187;0.454;0.276	B;B;B;B	0.26693	0.072;0.037;0.053;0.016	T	0.03852	-1.0998	10	0.26408	T	0.33	.	14.9528	0.71088	1.0:0.0:0.0:0.0	.	244;284;308;284	P52594-2;P52594-3;E9PHX7;P52594	.;.;.;AGFG1_HUMAN	L	308;293;284;284;244;284;206	ENSP00000387282:H308L;ENSP00000312059:H284L;ENSP00000387154:H284L;ENSP00000362775:H244L;ENSP00000387218:H284L	ENSP00000312059:H284L	H	+	2	0	AGFG1	228106545	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.335000	0.90031	1.940000	0.56252	0.533000	0.62120	CAT	.	.		0.393	AGFG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256895.2	NM_004504		T	228398301	A	T	228398301	3	4	344	1	0	0	0	0	1	0	0	0	380	217	8	4	953	4	AGFG1	2	228398301	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	523127	228398301	14801072	252	47615										
WDR69	164781	hgsc.bcm.edu	37	chr2	228762991	228762991	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	accttcaggggtcatacagcAgaaatagtgagtatatttaa	9	6	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:228762991A>T	ENST00000309931.2	+	6	617	c.534A>T	c.(532-534)gcA>gcT	p.A178A	DAW1_ENST00000373666.2_Silent_p.A178A|DAW1_ENST00000545118.1_Silent_p.A163A	NM_178821.1	NP_849143.1	Q8N136	DAW1_HUMAN	dynein assembly factor with WDR repeat domains 1	178						cilium (GO:0005929)											GTCATACAGCAGAAATAGTGA	0.353																																					p.A178A		Atlas-SNP	.											.	.	.	.	0			c.A534T						.						35	36	35					2																	228762991		2201	4298	6499	SO:0001819	synonymous_variant	164781	exon6			TACAGCAGAAATA		CCDS2470.1	2q36.3	2013-09-03	2013-02-19	2013-02-19	ENSG00000123977	ENSG00000123977		"WD repeat domain containing"	26383	protein-coding gene	gene with protein product	"outer row dynein assembly 16 homolog (Chlamydomonas)"		"WD repeat domain 69"	WDR69		20568242, 21953912	Standard	NM_178821		Approved	FLJ25955, ODA16	uc002vpn.1	Q8N136	OTTHUMG00000133190	ENST00000309931.2:c.534A>T	chr2.hg19:g.228762991A>T		451.0	0.0		384.0	143.0	NM_178821	Q6ZRY1|Q8N776	Silent	SNP	ENST00000309931.2	hg19	CCDS2470.1																																																																																			.	.		0.353	DAW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331745.1	NM_178821		T	228762991	A	T	228762991	2	4	344	1	0	0	0	0	0	0	0	1	17334	175	7	4		4	WDR69	2	228762991	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	364690	228762991	14436382	253	47616										
SLC16A14	151473	hgsc.bcm.edu	37	chr2	230911189	230911189	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctttctctcctgggtcgtttGggtttttaccaggagagagg	13	8	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:230911189G>T	ENST00000295190.4	-	4	1111	c.653C>A	c.(652-654)cCa>cAa	p.P218Q		NM_152527.4	NP_689740.2	Q7RTX9	MOT14_HUMAN	solute carrier family 16, member 14	218						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			NS(1)|cervix(1)|endometrium(7)|large_intestine(7)|lung(3)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.149)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;7.31e-13)|all cancers(144;5.1e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00948)		TGGGTCGTTTGGGTTTTTACC	0.542																																					p.P218Q		Atlas-SNP	.											.	SLC16A14	75	.	0			c.C653A						.						55	61	59					2																	230911189		2203	4300	6503	SO:0001583	missense	151473	exon4			TCGTTTGGGTTTT	BN000146	CCDS2473.1	2q37.1	2013-07-18	2013-07-18		ENSG00000163053	ENSG00000163053		"Solute carriers"	26417	protein-coding gene	gene with protein product	"monocarboxylic acid transporter 14"		"solute carrier family 16 (monocarboxylic acid transporters), member 14"				Standard	NM_152527		Approved	FLJ30794, MCT14	uc002vqd.2	Q7RTX9	OTTHUMG00000133205	ENST00000295190.4:c.653C>A	chr2.hg19:g.230911189G>T	ENSP00000295190:p.Pro218Gln	114.0	0.0		107.0	51.0	NM_152527	A8KA08|Q53R92|Q96NI7	Missense_Mutation	SNP	ENST00000295190.4	hg19	CCDS2473.1	.	.	.	.	.	.	.	.	.	.	G	0.474	-0.883148	0.02530	.	.	ENSG00000163053	ENST00000295190;ENST00000457406;ENST00000412034	T;T;T	0.58060	0.36;0.36;0.36	4.94	-3.37	0.04898	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	2.381430	0.01321	N	0.010959	T	0.30070	0.0753	N	0.12569	0.235	0.09310	N	1	B;B	0.13145	0.007;0.001	B;B	0.19946	0.014;0.027	T	0.11842	-1.0571	10	0.12103	T	0.63	.	4.9684	0.14102	0.1027:0.3202:0.4283:0.1488	.	218;218	E7EMG7;Q7RTX9	.;MOT14_HUMAN	Q	218	ENSP00000295190:P218Q;ENSP00000400352:P218Q;ENSP00000395775:P218Q	ENSP00000295190:P218Q	P	-	2	0	SLC16A14	230619433	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.512000	0.06313	-0.545000	0.06224	-0.165000	0.13383	CCA	.	.		0.542	SLC16A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256918.2	NM_152527		T	230911189	G	T	230911189	3	4	344	1	0	0	0	0	1	0	0	0	14422	1348	47	3	887	3	SLC16A14	2	230911189	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	2148198	230911189	12288184	254	47617										
CAB39	51719	hgsc.bcm.edu	37	chr2	231655654	231655654	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtatggcacaaatgaaaaagAgcctcagacagaagcagtag	11	7	1	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:231655654A>T	ENST00000258418.5	+	3	611	c.182A>T	c.(181-183)gAg>gTg	p.E61V	CAB39_ENST00000410084.3_Missense_Mutation_p.E61V|CAB39_ENST00000409788.3_Missense_Mutation_p.E61V|CAB39_ENST00000484398.1_3'UTR	NM_016289.3	NP_057373.1	Q9Y376	CAB39_HUMAN	calcium binding protein 39	61					activation of protein kinase activity (GO:0032147)|cell cycle arrest (GO:0007050)|cellular hypotonic response (GO:0071476)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of rubidium ion transmembrane transporter activity (GO:2000687)|negative regulation of rubidium ion transport (GO:2000681)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein heterooligomerization (GO:0051291)|signal transduction by phosphorylation (GO:0023014)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	kinase binding (GO:0019900)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activator activity (GO:0043539)			central_nervous_system(1)|large_intestine(1)|skin(1)	3		all_lung(227;4.63e-07)|all_hematologic(139;1.83e-06)|Lung NSC(271;2.11e-05)|Acute lymphoblastic leukemia(138;5.51e-05)|Hepatocellular(293;0.0207)|Lung SC(224;0.187)		all cancers(144;1.64e-12)|Epithelial(121;5.29e-11)|LUSC - Lung squamous cell carcinoma(224;0.0154)|Lung(119;0.0177)|COAD - Colon adenocarcinoma(134;0.226)		AATGAAAAAGAGCCTCAGACA	0.418																																					p.E61V		Atlas-SNP	.											.	CAB39	30	.	0			c.A182T						.						67	73	71					2																	231655654		2203	4300	6503	SO:0001583	missense	51719	exon3			AAAAAGAGCCTCA	AF113536	CCDS2478.1	2q37.1	2008-02-05			ENSG00000135932	ENSG00000135932			20292	protein-coding gene	gene with protein product		612174					Standard	NM_016289		Approved	CGI-66, MO25	uc002vqx.3	Q9Y376	OTTHUMG00000133220	ENST00000258418.5:c.182A>T	chr2.hg19:g.231655654A>T	ENSP00000258418:p.Glu61Val	178.0	0.0		152.0	60.0	NM_001130849	A8K8L7	Missense_Mutation	SNP	ENST00000258418.5	hg19	CCDS2478.1	.	.	.	.	.	.	.	.	.	.	A	28.5	4.923420	0.92319	.	.	ENSG00000135932	ENST00000258418;ENST00000409788;ENST00000410084	T;T;T	0.36699	1.24;1.24;1.24	5.44	5.44	0.79542	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.58694	0.2140	M	0.89658	3.05	0.80722	D	1	P	0.43857	0.819	P	0.51079	0.658	T	0.67499	-0.5655	10	0.72032	D	0.01	.	13.4644	0.61245	1.0:0.0:0.0:0.0	.	61	Q9Y376	CAB39_HUMAN	V	61	ENSP00000258418:E61V;ENSP00000386238:E61V;ENSP00000386642:E61V	ENSP00000258418:E61V	E	+	2	0	CAB39	231363898	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.339000	0.96797	2.063000	0.61619	0.528000	0.53228	GAG	.	.		0.418	CAB39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256955.2	NM_016289		T	231655654	A	T	231655654	3	4	344	1	0	0	0	0	1	0	0	0	2527	304	11	4	188	4	CAB39	2	231655654	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	744465	231655654	11543719	255	47618										
PSMD1	5707	hgsc.bcm.edu	37	chr2	231944930	231944930	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctccaggatcagcctatcagGaaggtggaggtctctatgca	12	10	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:231944930G>A	ENST00000308696.6	+	12	1477	c.1315G>A	c.(1315-1317)Gaa>Aaa	p.E439K	PSMD1_ENST00000373635.4_Missense_Mutation_p.E439K|PSMD1_ENST00000409643.1_Missense_Mutation_p.E439K	NM_002807.3	NP_002798.2	Q99460	PSMD1_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	439					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)	31		Ovarian(221;0.000626)|Medulloblastoma(418;0.0109)|Renal(207;0.0112)|Lung NSC(271;0.0538)|all_lung(227;0.0713)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;4e-26)|LUSC - Lung squamous cell carcinoma(224;0.0138)|Lung(119;0.0168)	Bortezomib(DB00188)	AGCCTATCAGGAAGGTGGAGG	0.408																																					p.E439K		Atlas-SNP	.											.	PSMD1	77	.	0			c.G1315A						.						144	132	136					2																	231944930		2203	4300	6503	SO:0001583	missense	5707	exon12			TATCAGGAAGGTG	D44466	CCDS2482.1, CCDS54436.1	2q37.1	2008-05-22			ENSG00000173692	ENSG00000173692		"Proteasome (prosome, macropain) subunits"	9554	protein-coding gene	gene with protein product						8816993	Standard	NM_002807		Approved	S1, P112, Rpn2	uc002vrn.2	Q99460	OTTHUMG00000133223	ENST00000308696.6:c.1315G>A	chr2.hg19:g.231944930G>A	ENSP00000309474:p.Glu439Lys	110.0	0.0		86.0	40.0	NM_002807	B8ZZH9|Q24JU0|Q53TI2|Q6GMU5|Q6P2P4|Q6PJM7|Q6PKG9|Q86VU1|Q8IV79	Missense_Mutation	SNP	ENST00000308696.6	hg19	CCDS2482.1	.	.	.	.	.	.	.	.	.	.	G	35	5.478361	0.96291	.	.	ENSG00000173692	ENST00000308696;ENST00000373635;ENST00000409643	.	.	.	6.07	5.2	0.72013	Armadillo-type fold (1);	0.043873	0.85682	D	0.000000	T	0.66386	0.2784	L	0.59912	1.85	0.80722	D	1	P;D	0.54964	0.589;0.969	B;P	0.57101	0.222;0.813	T	0.63107	-0.6711	9	0.20519	T	0.43	-20.641	15.2523	0.73556	0.0668:0.0:0.9332:0.0	.	439;439	Q99460;Q99460-2	PSMD1_HUMAN;.	K	439	.	ENSP00000309474:E439K	E	+	1	0	PSMD1	231653174	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.629000	0.98417	1.584000	0.49913	0.655000	0.94253	GAA	.	.		0.408	PSMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256958.2			A	231944930	G	A	231944930	3	1	344	1	0	0	0	0	1	0	0	0	12704	1175	41	3	1361	3	PSMD1	2	231944930	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	289276	231944930	11254443	256	47619										
DIS3L2	129563	hgsc.bcm.edu	37	chr2	232889007	232889007	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggtgtattgagaattaatccAaagaagtttcatgaagcctt	9	5	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:232889007A>T	ENST00000409307.1	+	3	231	c.231A>T	c.(229-231)ccA>ccT	p.P77P	DIS3L2_ENST00000325385.7_Silent_p.P77P|DIS3L2_ENST00000409401.3_Silent_p.P77P|DIS3L2_ENST00000273009.6_Silent_p.P77P|DIS3L2_ENST00000470087.1_3'UTR|DIS3L2_ENST00000360410.4_Silent_p.P77P					DIS3 like 3'-5' exoribonuclease 2											breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(2)|urinary_tract(1)	40		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)		GAATTAATCCAAAGAAGTTTC	0.279																																					p.P77P		Atlas-SNP	.											.	DIS3L2	77	.	0			c.A231T						.						62	63	62					2																	232889007		1787	4050	5837	SO:0001819	synonymous_variant	129563	exon4			TAATCCAAAGAAG	BC026166	CCDS42834.1, CCDS58752.1, CCDS58753.1	2q37.1	2014-09-17	2014-03-05		ENSG00000144535	ENSG00000144535			28648	protein-coding gene	gene with protein product		614184	"family with sequence similarity 6, member A", "DIS3 mitotic control homolog (S. cerevisiae)-like 2"	FAM6A		22306653, 23503588	Standard	NM_152383		Approved	FLJ36974, MGC42174	uc010fxz.3	Q8IYB7	OTTHUMG00000153385	ENST00000409307.1:c.231A>T	chr2.hg19:g.232889007A>T		473.0	0.0		389.0	164.0	NM_001257282		Silent	SNP	ENST00000409307.1	hg19	CCDS42834.1																																																																																			.	.		0.279	DIS3L2-015	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330988.1	NM_152383		T	232889007	A	T	232889007	2	4	344	1	0	0	0	0	0	0	0	1	4539	117	5	4		4	DIS3L2	2	232889007	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	944077	232889007	10310366	257	47620										
DIS3L2	129563	hgsc.bcm.edu	37	chr2	233001416	233001416	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tggactggaaggaggactgcAattttgccctggggtaggtg	17	6	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:233001416A>G	ENST00000409307.1	+	7	937	c.937A>G	c.(937-939)Aat>Gat	p.N313D	DIS3L2_ENST00000325385.7_Missense_Mutation_p.N313D|DIS3L2_ENST00000273009.6_Missense_Mutation_p.N313D|DIS3L2_ENST00000360410.4_Silent_p.A332A					DIS3 like 3'-5' exoribonuclease 2											breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(2)|urinary_tract(1)	40		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)		GGAGGACTGCAATTTTGCCCT	0.473																																					p.N313D		Atlas-SNP	.											.	DIS3L2	77	.	0			c.A937G						.						89	86	87					2																	233001416		1929	4135	6064	SO:0001583	missense	129563	exon8			GACTGCAATTTTG	BC026166	CCDS42834.1, CCDS58752.1, CCDS58753.1	2q37.1	2014-09-17	2014-03-05		ENSG00000144535	ENSG00000144535			28648	protein-coding gene	gene with protein product		614184	"family with sequence similarity 6, member A", "DIS3 mitotic control homolog (S. cerevisiae)-like 2"	FAM6A		22306653, 23503588	Standard	NM_152383		Approved	FLJ36974, MGC42174	uc010fxz.3	Q8IYB7	OTTHUMG00000153385	ENST00000409307.1:c.937A>G	chr2.hg19:g.233001416A>G	ENSP00000386799:p.Asn313Asp	113.0	0.0		126.0	63.0	NM_152383		Missense_Mutation	SNP	ENST00000409307.1	hg19	CCDS42834.1	.	.	.	.	.	.	.	.	.	.	A	18.60	3.658084	0.67586	.	.	ENSG00000144535	ENST00000273009;ENST00000542873;ENST00000325385;ENST00000431466;ENST00000409307	T;T;T	0.29397	1.57;1.96;1.96	6.08	4.88	0.63580	.	0.101704	0.64402	D	0.000004	T	0.27241	0.0668	L	0.43152	1.355	0.80722	D	1	B	0.23316	0.083	B	0.28011	0.085	T	0.05241	-1.0897	10	0.12103	T	0.63	-23.6705	14.7279	0.69357	0.872:0.128:0.0:0.0	.	313	Q8IYB7	DI3L2_HUMAN	D	313	ENSP00000273009:N313D;ENSP00000315569:N313D;ENSP00000386799:N313D	ENSP00000273009:N313D	N	+	1	0	DIS3L2	232709660	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.073000	0.64395	2.333000	0.79357	0.482000	0.46254	AAT	.	.		0.473	DIS3L2-015	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330988.1	NM_152383		G	233001416	A	G	233001416	3	3	344	1	0	0	0	0	1	0	0	0	4539	130	5	2	963	2	DIS3L2	2	233001416	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	112409	233001416	10197957	258	47621										
UGT1A10	54575	hgsc.bcm.edu	37	chr2	234545950	234545950	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aacggactttgttttggactAtcccaaacccgtgatgccca	8	12	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:234545950A>G	ENST00000344644.5	+	1	851	c.782A>G	c.(781-783)tAt>tGt	p.Y261C	UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000373445.1_Missense_Mutation_p.Y261C	NM_019075.2	NP_061948.1	Q9HAW8	UD110_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A10	261					cellular glucuronidation (GO:0052695)|flavone metabolic process (GO:0051552)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(2)|skin(3)	32		Breast(86;0.000766)|all_lung(227;0.00271)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0334)|Lung NSC(271;0.0461)|Lung SC(224;0.128)		Epithelial(121;1.96e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000468)|Lung(119;0.00381)|LUSC - Lung squamous cell carcinoma(224;0.008)	Acetaminophen(DB00316)|Etodolac(DB00749)|Losartan(DB00678)|Mycophenolate mofetil(DB00688)|Valproic Acid(DB00313)	GTTTTGGACTATCCCAAACCC	0.443																																					p.Y261C		Atlas-SNP	.											.	UGT1A10	71	.	0			c.A782G						.						235	231	232					2																	234545950		2203	4298	6501	SO:0001583	missense	54575	exon1			TGGACTATCCCAA	U39550	CCDS33403.1	2q37	2010-03-05	2005-07-20		ENSG00000242515	ENSG00000242515		"UDP glucuronosyltransferases"	12531	other	complex locus constituent		606435	"UDP glycosyltransferase 1 family, polypeptide A10"			9295054, 9325166	Standard	NM_019075		Approved	UGT1J		Q9HAW8	OTTHUMG00000059121	ENST00000344644.5:c.782A>G	chr2.hg19:g.234545950A>G	ENSP00000343838:p.Tyr261Cys	89.0	0.0		82.0	34.0	NM_019075	O00474|Q6NT91|Q7Z6H8	Missense_Mutation	SNP	ENST00000344644.5	hg19	CCDS33403.1	.	.	.	.	.	.	.	.	.	.	A	12.34	1.908829	0.33721	.	.	ENSG00000242515	ENST00000344644;ENST00000373445	T;T	0.66460	-0.21;-0.21	3.52	0.57	0.17347	.	.	.	.	.	T	0.80597	0.4653	M	0.93720	3.45	0.19775	N	0.999954	D;D	0.54207	0.965;0.965	P;P	0.58391	0.755;0.838	T	0.68845	-0.5301	9	0.87932	D	0	.	5.8031	0.18424	0.5206:0.1332:0.0:0.3462	.	261;261	Q9HAW8;Q7Z6H8	UD110_HUMAN;.	C	261	ENSP00000343838:Y261C;ENSP00000362544:Y261C	ENSP00000343838:Y261C	Y	+	2	0	UGT1A10	234210689	0.000000	0.05858	0.901000	0.35422	0.688000	0.40055	-0.108000	0.10857	-0.014000	0.14175	-1.591000	0.00844	TAT	.	.		0.443	UGT1A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130986.1	NM_019075		G	234545950	A	G	234545950	3	3	344	1	0	0	0	0	1	0	0	0	16960	449	16	2	784	2	UGT1A10	2	234545950	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1544534	234545950	8653423	259	47622										
SPP2	6694	hgsc.bcm.edu	37	chr2	234978570	234978570	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgcttcccttttctatctttAgggatcatgagaagggtatt	9	7	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:234978570A>G	ENST00000168148.3	+	7	638		c.e7-1		SPP2_ENST00000373368.1_Splice_Site	NM_006944.2	NP_008875.1	Q13103	SPP24_HUMAN	secreted phosphoprotein 2, 24kDa						bone remodeling (GO:0046849)|negative regulation of endopeptidase activity (GO:0010951)|protein complex assembly (GO:0006461)|skeletal system development (GO:0001501)	extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	endopeptidase inhibitor activity (GO:0004866)			breast(1)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)	12		Breast(86;0.0109)|Renal(207;0.019)|all_lung(227;0.13)|all_hematologic(139;0.182)		Epithelial(121;5.73e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000166)|Lung(119;0.00539)|LUSC - Lung squamous cell carcinoma(224;0.00846)		TTCTATCTTTAGGGATCATGA	0.438																																					.		Atlas-SNP	.											.	SPP2	35	.	0			c.551-2A>G						.						98	94	96					2																	234978570		2203	4300	6503	SO:0001630	splice_region_variant	6694	exon7			ATCTTTAGGGATC		CCDS2511.1	2q37.1	2012-08-14	2002-08-29		ENSG00000072080	ENSG00000072080			11256	protein-coding gene	gene with protein product		602637	"secreted phosphoprotein 2, 24kD"			9533032	Standard	XM_005246102		Approved	SPP24	uc002vvk.1	Q13103	OTTHUMG00000059208	ENST00000168148.3:c.551-1A>G	chr2.hg19:g.234978570A>G		72.0	0.0		71.0	37.0	NM_006944	A4QMV3|Q3B892|Q546M5	Splice_Site	SNP	ENST00000168148.3	hg19	CCDS2511.1	.	.	.	.	.	.	.	.	.	.	A	11.93	1.785439	0.31593	.	.	ENSG00000072080	ENST00000373368;ENST00000168148;ENST00000425558	.	.	.	3.88	3.88	0.44766	.	.	.	.	.	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.3997	0.38424	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SPP2	234643309	0.896000	0.30565	0.154000	0.22540	0.216000	0.24613	3.418000	0.52721	1.998000	0.58463	0.528000	0.53228	.	.	.		0.438	SPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131313.3	NM_006944	Intron	G	234978570	A	G	234978570	5	3	344	1	0	0	0	0	0	0	1	0	15102	434	15	2	575	2	SPP2	2	234978570	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	432620	234978570	8220803	260	47623										
COL6A3	1293	hgsc.bcm.edu	37	chr2	238275483	238275483	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tatctttccaacctcctccgAgtcgatattcctcactccaa	3	16	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:238275483A>T	ENST00000295550.4	-	11	5799	c.5347T>A	c.(5347-5349)Tcg>Acg	p.S1783T	COL6A3_ENST00000346358.4_Missense_Mutation_p.S1583T|COL6A3_ENST00000353578.4_Missense_Mutation_p.S1577T|COL6A3_ENST00000347401.3_Missense_Mutation_p.S1582T|COL6A3_ENST00000409809.1_Missense_Mutation_p.S1577T|COL6A3_ENST00000472056.1_Missense_Mutation_p.S1176T	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1783	Nonhelical region.|VWFA 9. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		ACCTCCTCCGAGTCGATATTC	0.562																																					p.S1783T		Atlas-SNP	.											.	COL6A3	608	.	0			c.T5347A						.						88	83	85					2																	238275483		2203	4300	6503	SO:0001583	missense	1293	exon11			CCTCCGAGTCGAT	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.5347T>A	chr2.hg19:g.238275483A>T	ENSP00000295550:p.Ser1783Thr	199.0	0.0		129.0	54.0	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	hg19	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	A	15.39	2.819972	0.50633	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	D;D;D;D;D;D	0.83591	-1.74;-1.74;-1.74;-1.74;-1.74;-1.74	5.51	4.28	0.50868	von Willebrand factor, type A (3);	0.671285	0.12791	N	0.438878	T	0.77883	0.4197	N	0.25890	0.77	0.23496	N	0.997556	D;D;P	0.67145	0.996;0.984;0.6	P;P;B	0.60117	0.869;0.839;0.233	T	0.66866	-0.5815	10	0.15066	T	0.55	.	1.1162	0.01714	0.5101:0.1922:0.1139:0.1838	.	1176;1577;1783	E9PFQ6;P12111-2;P12111	.;.;CO6A3_HUMAN	T	1783;1582;1577;1176;1577;1583	ENSP00000295550:S1783T;ENSP00000315609:S1582T;ENSP00000315873:S1577T;ENSP00000418285:S1176T;ENSP00000386844:S1577T;ENSP00000295546:S1583T	ENSP00000295550:S1783T	S	-	1	0	COL6A3	237940222	0.995000	0.38212	0.996000	0.52242	0.920000	0.55202	1.099000	0.31013	2.090000	0.63153	0.528000	0.53228	TCG	.	.		0.562	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		T	238275483	A	T	238275483	3	4	344	1	0	0	0	0	1	0	0	0	3703	304	11	4	4322	4	COL6A3	2	238275483	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3296913	238275483	4923890	261	47624										
COL6A3	1293	hgsc.bcm.edu	37	chr2	238303641	238303641	+	Frame_Shift_Del	DEL	G	G	-													0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aatatgagaaaggacttcttGtttagtacgatacgtattta							TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr2:238303641delG	ENST00000295550.4	-	3	750	c.298delC	c.(298-300)caafs	p.Q100fs	COL6A3_ENST00000392004.3_Intron|COL6A3_ENST00000346358.4_Frame_Shift_Del_p.Q100fs|COL6A3_ENST00000353578.4_Intron|COL6A3_ENST00000347401.3_Frame_Shift_Del_p.Q100fs|COL6A3_ENST00000392003.2_Intron|COL6A3_ENST00000409809.1_Intron|COL6A3_ENST00000472056.1_Intron	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	100	Nonhelical region.|VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		AGGACTTCTTGTTTAGTACGA	0.403																																					p.Q100fs		Atlas-Indel,Pindel	.											.	COL6A3	608	.	0			c.299delA						.						93	96	95					2																	238303641		2203	4300	6503	SO:0001589	frameshift_variant	1293	exon3			.	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.298delC	chr2.hg19:g.238303641delG	ENSP00000295550:p.Gln100fs	156.0	0.0		129.0	63.0	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Frame_Shift_Del	DEL	ENST00000295550.4	hg19	CCDS33412.1																																																																																			.	.		0.403	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		-	238303641	G	-	238303641	7	5	344	1	0	1	0	1	0	0	0	0	3703	1386	48	0	9450	0	COL6A3	2	238303641	Frame_Shift_Del	DEL	G	TCGA-UB-A7MB-01A-11D-A33Q-10	28158	238303641	4895732	262	47625										
CHL1	10752	hgsc.bcm.edu	37	chr3	369957	369957	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaacgaggggcacatatctcActttcaagggaaataccgct	9	10	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:369957A>T	ENST00000256509.2	+	5	947	c.305A>T	c.(304-306)cAc>cTc	p.H102L	CHL1_ENST00000397491.2_Missense_Mutation_p.H102L	NM_001253387.1|NM_001253388.1|NM_006614.3	NP_001240316.1|NP_001240317.1|NP_006605.2	Q96FC9	DDX11_HUMAN	cell adhesion molecule L1-like	0	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			NS(1)|central_nervous_system(5)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|lung(31)|ovary(1)|prostate(4)|skin(10)|stomach(1)	93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		CACATATCTCACTTTCAAGGG	0.398																																					p.H102L		Atlas-SNP	.											.	CHL1	242	.	0			c.A305T						.						128	127	127					3																	369957		2203	4300	6503	SO:0001583	missense	10752	exon3			TATCTCACTTTCA	AF002246	CCDS2556.1, CCDS58812.1, CCDS74887.1	3p26	2013-05-01	2013-05-01		ENSG00000134121	ENSG00000134121		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	1939	protein-coding gene	gene with protein product	"neural cell adhesion molecule", "close homolog of L1"	607416	"cell adhesion molecule with homology to L1CAM (close homologue of L1)", "cell adhesion molecule with homology to L1CAM (close homolog of L1)"			9799093	Standard	NM_006614		Approved	CALL, L1CAM2, FLJ44930, MGC132578	uc003bot.3	O00533	OTTHUMG00000090601	ENST00000256509.2:c.305A>T	chr3.hg19:g.369957A>T	ENSP00000256509:p.His102Leu	187.0	0.0		163.0	85.0	NM_001253388	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000256509.2	hg19	CCDS2556.1	.	.	.	.	.	.	.	.	.	.	A	16.08	3.022577	0.54683	.	.	ENSG00000134121	ENST00000256509;ENST00000397491;ENST00000435603	T;T;T	0.66815	1.11;1.11;-0.23	5.02	5.02	0.67125	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.188254	0.47093	D	0.000241	T	0.59115	0.2170	L	0.41906	1.305	0.33435	D	0.581675	B;B;P	0.38455	0.355;0.355;0.632	B;B;B	0.41946	0.371;0.371;0.291	T	0.70799	-0.4774	10	0.48119	T	0.1	.	8.7575	0.34654	0.914:0.0:0.086:0.0	.	102;102;102	B3KX75;O00533;O00533-2	.;CHL1_HUMAN;.	L	102	ENSP00000256509:H102L;ENSP00000380628:H102L;ENSP00000397445:H102L	ENSP00000256509:H102L	H	+	2	0	CHL1	344957	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.087000	0.57671	1.888000	0.54679	0.533000	0.62120	CAC	.	.		0.398	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614		T	369957	A	T	369957	3	4	344	1	0	0	0	0	1	0	0	0	3351	159	6	4	315	4	CHL1	3	369957	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10		369957	197652473	263	47626										
CNTN6	27255	hgsc.bcm.edu	37	chr3	1425084	1425084	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaaacactggaagagtgctgGgctatgaggtaatccacatt	12	7	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:1425084G>T	ENST00000446702.2	+	19	3136	c.2509G>T	c.(2509-2511)Ggc>Tgc	p.G837C	CNTN6_ENST00000539053.1_Missense_Mutation_p.G765C|CNTN6_ENST00000350110.2_Missense_Mutation_p.G837C			Q9UQ52	CNTN6_HUMAN	contactin 6	837	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		AAGAGTGCTGGGCTATGAGGT	0.438																																					p.G837C		Atlas-SNP	.											.	CNTN6	245	.	0			c.G2509T						.						142	148	146					3																	1425084		2203	4300	6503	SO:0001583	missense	27255	exon19			GTGCTGGGCTATG	AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	2176	protein-coding gene	gene with protein product	"neural adhesion molecule"	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.2509G>T	chr3.hg19:g.1425084G>T	ENSP00000407822:p.Gly837Cys	52.0	0.0		42.0	24.0	NM_014461	Q2KHM2	Missense_Mutation	SNP	ENST00000446702.2	hg19	CCDS2557.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.711164	0.89112	.	.	ENSG00000134115	ENST00000446702;ENST00000539053;ENST00000350110	T;T;T	0.61742	0.08;0.08;0.08	5.74	5.74	0.90152	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000016	D	0.84338	0.5450	H	0.95611	3.695	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88360	0.2987	10	0.87932	D	0	.	19.9111	0.97025	0.0:0.0:1.0:0.0	.	837	Q9UQ52	CNTN6_HUMAN	C	837;765;837	ENSP00000407822:G837C;ENSP00000442791:G765C;ENSP00000341882:G837C	ENSP00000341882:G837C	G	+	1	0	CNTN6	1400084	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.111000	0.94308	2.728000	0.93425	0.585000	0.79938	GGC	.	.		0.438	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461		T	1425084	G	T	1425084	3	4	344	1	0	0	0	0	1	0	0	0	3647	1232	43	3	2579	3	CNTN6	3	1425084	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1055127	1425084	196597346	264	47627										
ITPR1	3708	hgsc.bcm.edu	37	chr3	4699946	4699946	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccaccactctgcgtggaggtGacagccttgtcccaaggtat	11	13	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:4699946G>T	ENST00000443694.2	+	10	1090	c.1090G>T	c.(1090-1092)Gac>Tac	p.D364Y	ITPR1_ENST00000302640.8_Missense_Mutation_p.D364Y|ITPR1_ENST00000456211.2_Missense_Mutation_p.D364Y|ITPR1_ENST00000423119.2_Missense_Mutation_p.D379Y|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000354582.6_Missense_Mutation_p.D379Y|ITPR1_ENST00000357086.4_Missense_Mutation_p.D379Y			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	379	MIR 4. {ECO:0000255|PROSITE- ProRule:PRU00131}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	GCGTGGAGGTGACAGCCTTGT	0.483																																					p.D379Y		Atlas-SNP	.											.	ITPR1	659	.	0			c.G1135T						.						103	101	102					3																	4699946		1941	4141	6082	SO:0001583	missense	3708	exon13			GGAGGTGACAGCC	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"Ion channels / Inositol triphosphate receptors"	6180	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 94"	147265	"spinocerebellar ataxia 15", "spinocerebellar ataxia 16", "spinocerebellar ataxia 29"	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.1090G>T	chr3.hg19:g.4699946G>T	ENSP00000401671:p.Asp364Tyr	100.0	0.0		80.0	39.0	NM_001099952	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	hg19	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.700238	0.88924	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000357086;ENST00000456211;ENST00000443694	D;D;D;D;D;D	0.92149	-2.98;-2.98;-2.98;-2.98;-2.98;-2.98	5.39	5.39	0.77823	MIR motif (2);MIR (2);	0.000000	0.85682	D	0.000000	D	0.96580	0.8884	M	0.84948	2.725	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.998	D	0.97010	0.9735	10	0.87932	D	0	.	19.171	0.93578	0.0:0.0:1.0:0.0	.	364;379;379	E7EPX7;Q14643;G5E9P1	.;ITPR1_HUMAN;.	Y	379;364;379;379;379;364;364	ENSP00000306253:D364Y;ENSP00000346595:D379Y;ENSP00000405934:D379Y;ENSP00000349597:D379Y;ENSP00000397885:D364Y;ENSP00000401671:D364Y	ENSP00000306253:D364Y	D	+	1	0	ITPR1	4674946	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	9.725000	0.98778	2.525000	0.85131	0.655000	0.94253	GAC	.	.		0.483	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		T	4699946	G	T	4699946	3	4	344	1	0	0	0	0	1	0	0	0	7929	1290	45	3	1177	3	ITPR1	3	4699946	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	3274862	4699946	193322484	265	47628										
C3orf32	51066	hgsc.bcm.edu	37	chr3	8661623	8661623	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tacacctggtggtcagtgccAtagatgtagtagacataagt	11	7	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:8661623A>T	ENST00000317371.4	-	19	2218	c.993T>A	c.(991-993)taT>taA	p.Y331*	SSUH2_ENST00000544814.1_Nonsense_Mutation_p.Y353*|SSUH2_ENST00000415132.1_3'UTR|SSUH2_ENST00000341795.3_Nonsense_Mutation_p.Y331*			Q9Y2M2	SSUH2_HUMAN	ssu-2 homolog (C. elegans)	331						cytoplasm (GO:0005737)											GGTCAGTGCCATAGATGTAGT	0.507																																					p.Y353X		Atlas-SNP	.											.	.	.	.	0			c.T1059A						.						172	150	157					3																	8661623		2203	4300	6503	SO:0001587	stop_gained	51066	exon12			AGTGCCATAGATG	AB024705	CCDS2568.1, CCDS58815.1	3p25.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000125046	ENSG00000125046			24809	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 32"	C3orf32		20205943	Standard	NM_001256748		Approved	fls485, ssu-2	uc011atg.3	Q9Y2M2	OTTHUMG00000122075	ENST00000317371.4:c.993T>A	chr3.hg19:g.8661623A>T	ENSP00000324551:p.Tyr331*	131.0	0.0		96.0	38.0	NM_001256748	A6NFA9|B3KS84|B7Z6E3|F5H2S5|Q7Z7K4	Nonsense_Mutation	SNP	ENST00000317371.4	hg19	CCDS2568.1	.	.	.	.	.	.	.	.	.	.	A	46	12.689718	0.99688	.	.	ENSG00000125046	ENST00000341795;ENST00000317371;ENST00000544814	.	.	.	5.07	-3.85	0.04243	.	0.078352	0.52532	D	0.000066	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.1548	11.6546	0.51311	0.4307:0.0:0.5693:0.0	.	.	.	.	X	331;331;353	.	ENSP00000324551:Y331X	Y	-	3	2	C3orf32	8636623	0.169000	0.23002	0.964000	0.40570	0.908000	0.53690	-0.894000	0.04123	-0.656000	0.05380	0.383000	0.25322	TAT	.	.		0.507	SSUH2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337900.1	NM_015931		T	8661623	A	T	8661623	4	4	344	1	0	0	0	0	0	1	0	0	2224	224	8	4	72	4	C3orf32	3	8661623	Nonsense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3961677	8661623	189360807	266	47629										
SRGAP3	9901	hgsc.bcm.edu	37	chr3	9068619	9068619	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tggcccaagatccagcttacCatataaattgatgtaacgga	8	9	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:9068619C>T	ENST00000383836.3	-	13	2027	c.1600G>A	c.(1600-1602)Gga>Aga	p.G534R	SRGAP3_ENST00000360413.3_Splice_Site_p.G510R|SRGAP3_ENST00000433332.3_5'UTR	NM_014850.3	NP_055665.1	O43295	SRGP3_HUMAN	SLIT-ROBO Rho GTPase activating protein 3	534	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)		SRGAP3/RAF1(6)	breast(1)|endometrium(2)|kidney(21)|large_intestine(7)|lung(13)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	54				OV - Ovarian serous cystadenocarcinoma(96;0.0563)		TCCAGCTTACCATATAAATTG	0.428			T	RAF1	pilocytic astrocytoma																																p.G534R		Atlas-SNP	.		Dom	yes		3	3p25.3	9901	SLIT-ROBO Rho GTPase activating protein 3		M	.	SRGAP3	146	.	0			c.G1600A						.						119	115	117					3																	9068619		2203	4300	6503	SO:0001630	splice_region_variant	9901	exon13			GCTTACCATATAA	AB007871	CCDS2572.1, CCDS33689.1	3p25.3	2011-07-04	2004-11-12	2004-11-12	ENSG00000196220	ENSG00000196220		"Rho GTPase activating proteins"	19744	protein-coding gene	gene with protein product		606525	"SLIT-ROBO Rho GTPase activating protein 2"	SRGAP2		12195014	Standard	NM_014850		Approved	KIAA0411, MEGAP, WRP, ARHGAP14	uc003brf.2	O43295	OTTHUMG00000090589	ENST00000383836.3:c.1600+1G>A	chr3.hg19:g.9068619C>T		87.0	0.0		67.0	26.0	NM_014850	Q8IX13|Q8IZV8	Missense_Mutation	SNP	ENST00000383836.3	hg19	CCDS2572.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.570746	0.86542	.	.	ENSG00000196220	ENST00000383836;ENST00000360413	T;T	0.57752	0.38;1.36	5.17	5.17	0.71159	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.82019	0.4946	H	0.96333	3.805	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.88189	0.2876	9	.	.	.	.	18.2773	0.90087	0.0:1.0:0.0:0.0	.	510;534	O43295-2;O43295	.;SRGP2_HUMAN	R	534;510	ENSP00000373347:G534R;ENSP00000353587:G510R	.	G	-	1	0	SRGAP3	9043619	1.000000	0.71417	0.962000	0.40283	0.670000	0.39368	7.576000	0.82467	2.413000	0.81919	0.655000	0.94253	GGA	.	.		0.428	SRGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207137.3		Missense_Mutation	T	9068619	C	T	9068619	5	4	344	1	0	0	0	0	0	0	1	0	15162	608	21	3	1739	3	SRGAP3	3	9068619	Splice_Site	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	406996	9068619	188953811	267	47630										
SRGAP3	9901	hgsc.bcm.edu	37	chr3	9068641	9068641	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tataaattgatgtaacggatGcagctctcgactacaagcgg	10	8	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:9068641G>C	ENST00000383836.3	-	13	2005	c.1578C>G	c.(1576-1578)tgC>tgG	p.C526W	SRGAP3_ENST00000360413.3_Missense_Mutation_p.C502W|SRGAP3_ENST00000433332.3_5'UTR	NM_014850.3	NP_055665.1	O43295	SRGP3_HUMAN	SLIT-ROBO Rho GTPase activating protein 3	526	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)		SRGAP3/RAF1(6)	breast(1)|endometrium(2)|kidney(21)|large_intestine(7)|lung(13)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	54				OV - Ovarian serous cystadenocarcinoma(96;0.0563)		TGTAACGGATGCAGCTCTCGA	0.423			T	RAF1	pilocytic astrocytoma																																p.C526W		Atlas-SNP	.		Dom	yes		3	3p25.3	9901	SLIT-ROBO Rho GTPase activating protein 3		M	.	SRGAP3	146	.	0			c.C1578G						.						135	130	132					3																	9068641		2203	4300	6503	SO:0001583	missense	9901	exon13			ACGGATGCAGCTC	AB007871	CCDS2572.1, CCDS33689.1	3p25.3	2011-07-04	2004-11-12	2004-11-12	ENSG00000196220	ENSG00000196220		"Rho GTPase activating proteins"	19744	protein-coding gene	gene with protein product		606525	"SLIT-ROBO Rho GTPase activating protein 2"	SRGAP2		12195014	Standard	NM_014850		Approved	KIAA0411, MEGAP, WRP, ARHGAP14	uc003brf.2	O43295	OTTHUMG00000090589	ENST00000383836.3:c.1578C>G	chr3.hg19:g.9068641G>C	ENSP00000373347:p.Cys526Trp	92.0	0.0		66.0	27.0	NM_014850	Q8IX13|Q8IZV8	Missense_Mutation	SNP	ENST00000383836.3	hg19	CCDS2572.1	.	.	.	.	.	.	.	.	.	.	G	16.48	3.133981	0.56828	.	.	ENSG00000196220	ENST00000383836;ENST00000360413	T;T	0.26518	1.73;1.73	5.17	0.568	0.17333	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.61652	0.2364	H	0.97783	4.075	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.998;0.998	T	0.67921	-0.5545	10	0.87932	D	0	.	9.7146	0.40268	0.4258:0.0:0.5742:0.0	.	502;526	O43295-2;O43295	.;SRGP2_HUMAN	W	526;502	ENSP00000373347:C526W;ENSP00000353587:C502W	ENSP00000353587:C502W	C	-	3	2	SRGAP3	9043641	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	0.524000	0.22940	0.043000	0.15746	0.655000	0.94253	TGC	.	.		0.423	SRGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207137.3			C	9068641	G	C	9068641	3	2	344	1	0	0	0	0	1	0	0	0	15162	1311	46	4	1761	4	SRGAP3	3	9068641	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	22	9068641	188953789	268	47631										
ATP2B2	491	hgsc.bcm.edu	37	chr3	10370618	10370618	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctgttgttcttgttgagggaTgacggcgggctcgagttctg	16	7	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:10370618T>A	ENST00000352432.4	-	22	3681	c.3612A>T	c.(3610-3612)tcA>tcT	p.S1204S	ATP2B2_ENST00000383800.4_Silent_p.S1159S|ATP2B2_ENST00000397077.1_Silent_p.S1159S|ATP2B2_ENST00000343816.4_Silent_p.S1190S|MIR378B_ENST00000578876.1_RNA|ATP2B2_ENST00000360273.2_Silent_p.S1204S|ATP2B2_ENST00000467702.2_5'UTR			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	1204					auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						TGTTGAGGGATGACGGCGGGC	0.562																																					p.S1204S	Ovarian(125;1619 1709 15675 19819 38835)	Atlas-SNP	.											.	ATP2B2	304	.	0			c.A3612T						.						125	107	113					3																	10370618		2203	4300	6503	SO:0001819	synonymous_variant	491	exon23			GAGGGATGACGGC	X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"ATPases / P-type"	815	protein-coding gene	gene with protein product	"plasma membrane Ca2+ pump 2", "plasma membrane calcium-transporting ATPase 2"	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.3612A>T	chr3.hg19:g.10370618T>A		139.0	0.0		98.0	46.0	NM_001001331	O00766|Q12994|Q16818	Silent	SNP	ENST00000352432.4	hg19	CCDS33701.1																																																																																			.	.		0.562	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683		A	10370618	T	A	10370618	2	1	344	1	0	0	0	0	0	0	0	1	1140	1451	51	4		4	ATP2B2	3	10370618	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1301977	10370618	187651812	269	47632										
C3orf20	84077	hgsc.bcm.edu	37	chr3	14813588	14813588	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctgcagtgttcccaactctgTcctgagcctggaggattctg	11	12	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:14813588T>C	ENST00000253697.3	+	16	2962	c.2510T>C	c.(2509-2511)gTc>gCc	p.V837A	C3orf20_ENST00000412910.1_Missense_Mutation_p.V715A|C3orf20_ENST00000435614.1_Missense_Mutation_p.V715A	NM_032137.4	NP_115513.4	Q8ND61	CC020_HUMAN	chromosome 3 open reading frame 20	837						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(13)|lung(11)|ovary(4)|skin(2)	40						CCCAACTCTGTCCTGAGCCTG	0.582																																					p.V837A		Atlas-SNP	.											.	C3orf20	109	.	0			c.T2510C						.						90	84	86					3																	14813588		2203	4300	6503	SO:0001583	missense	84077	exon16			ACTCTGTCCTGAG	AL136781	CCDS33706.1, CCDS54555.1	3p25.1	2011-01-25			ENSG00000131379	ENSG00000131379			25320	protein-coding gene	gene with protein product						11230166	Standard	NM_032137		Approved	DKFZP434N1817	uc003byy.3	Q8ND61	OTTHUMG00000155545	ENST00000253697.3:c.2510T>C	chr3.hg19:g.14813588T>C	ENSP00000253697:p.Val837Ala	63.0	0.0		66.0	27.0	NM_032137	Q7L0U6|Q8NCP2|Q9H0I7	Missense_Mutation	SNP	ENST00000253697.3	hg19	CCDS33706.1	.	.	.	.	.	.	.	.	.	.	T	5.701	0.313838	0.10789	.	.	ENSG00000131379	ENST00000253697;ENST00000435614;ENST00000412910	T;T;T	0.10573	3.15;2.86;2.86	2.95	-1.1	0.09872	.	1.672600	0.03657	N	0.241938	T	0.07683	0.0193	N	0.19112	0.55	0.09310	N	1	B;B	0.19200	0.034;0.034	B;B	0.22601	0.04;0.04	T	0.38436	-0.9661	10	0.48119	T	0.1	-1.2274	4.1126	0.10065	0.0:0.1287:0.4321:0.4392	.	715;837	Q8ND61-2;Q8ND61	.;CC020_HUMAN	A	837;715;715	ENSP00000253697:V837A;ENSP00000402933:V715A;ENSP00000396081:V715A	ENSP00000253697:V837A	V	+	2	0	C3orf20	14788592	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.782000	0.00772	-0.205000	0.10219	-1.430000	0.01095	GTC	.	.		0.582	C3orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340586.1	NM_032137		C	14813588	T	C	14813588	3	2	344	1	0	0	0	0	1	0	0	0	2215	1667	58	2	2564	2	C3orf20	3	14813588	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	4442970	14813588	183208842	270	47633										
KCNH8	131096	hgsc.bcm.edu	37	chr3	19492664	19492664	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cagcttttgaaagactttccAgatgaactgcgttctgacat	8	9	1	5			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:19492664A>T	ENST00000328405.2	+	10	1859	c.1593A>T	c.(1591-1593)ccA>ccT	p.P531P	KCNH8_ENST00000537696.1_3'UTR	NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	531					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(3)|lung(37)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	77						AAGACTTTCCAGATGAACTGC	0.453																																					p.P531P	NSCLC(124;1625 1765 8018 24930 42026)	Atlas-SNP	.											.	KCNH8	189	.	0			c.A1593T						.						148	151	150					3																	19492664		2203	4300	6503	SO:0001819	synonymous_variant	131096	exon10			CTTTCCAGATGAA	AY053503	CCDS2632.1	3p24.3	2012-07-05			ENSG00000183960	ENSG00000183960		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18864	protein-coding gene	gene with protein product		608260				16382104	Standard	NM_144633		Approved	Kv12.1, elk3	uc003cbk.1	Q96L42	OTTHUMG00000129891	ENST00000328405.2:c.1593A>T	chr3.hg19:g.19492664A>T		58.0	0.0		52.0	26.0	NM_144633	B7Z2I7|Q59GQ6	Silent	SNP	ENST00000328405.2	hg19	CCDS2632.1																																																																																			.	.		0.453	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	NM_144633		T	19492664	A	T	19492664	2	4	344	1	0	0	0	0	0	0	0	1	8047	175	7	4		4	KCNH8	3	19492664	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	4679076	19492664	178529766	271	47634										
EFHB	151651	hgsc.bcm.edu	37	chr3	19921298	19921298	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tacacaatatctctgcaatcTagaaaaaggcatttaaaata	4	7	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:19921298T>C	ENST00000295824.9	-	13	2490		c.e13-2		EFHB_ENST00000344838.4_Splice_Site	NM_144715.3	NP_653316.3	Q8N7U6	EFHB_HUMAN	EF-hand domain family, member B								calcium ion binding (GO:0005509)			breast(2)|endometrium(4)|kidney(1)|lung(17)|prostate(1)|urinary_tract(1)	26						CTCTGCAATCTAGAAAAAGGC	0.279																																					.		Atlas-SNP	.											.	EFHB	186	.	0			c.2329-2A>G						.						99	98	98					3																	19921298		2203	4300	6503	SO:0001630	splice_region_variant	151651	exon14			GCAATCTAGAAAA	AK122616	CCDS33715.2	3p24.3	2014-07-18			ENSG00000163576	ENSG00000163576		"EF-hand domain containing"	26330	protein-coding gene	gene with protein product	"cilia and flagella associated protein 21"					12477932	Standard	NM_144715		Approved	FLJ25200, CFAP21	uc003cbl.4	Q8N7U6	OTTHUMG00000150505	ENST00000295824.9:c.2329-2A>G	chr3.hg19:g.19921298T>C		40.0	0.0		47.0	25.0	NM_144715	A6ND25|A8MPR3|Q6ZWK9|Q8IV58|Q96LQ6	Splice_Site	SNP	ENST00000295824.9	hg19	CCDS33715.2	.	.	.	.	.	.	.	.	.	.	T	16.77	3.216178	0.58452	.	.	ENSG00000163576	ENST00000295824;ENST00000344838	.	.	.	4.77	4.77	0.60923	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4434	0.67333	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	EFHB	19896302	1.000000	0.71417	0.993000	0.49108	0.897000	0.52465	7.004000	0.76317	1.998000	0.58463	0.459000	0.35465	.	.	.		0.279	EFHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318673.2	NM_144715	Intron	C	19921298	T	C	19921298	5	2	344	1	0	0	0	0	0	0	1	0	4947	1536	53	2	178	2	EFHB	3	19921298	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	428634	19921298	178101132	272	47635										
OXSM	54995	hgsc.bcm.edu	37	chr3	25833109	25833109	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcattcgatataaactcaagGgcccaaatcatgcagtatcc	7	11	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:25833109G>T	ENST00000280701.3	+	2	697	c.598G>T	c.(598-600)Ggc>Tgc	p.G200C	NGLY1_ENST00000417874.2_5'Flank|OXSM_ENST00000420173.2_Missense_Mutation_p.G200C|OXSM_ENST00000449808.1_Intron	NM_017897.2	NP_060367.1	Q9NWU1	OXSM_HUMAN	3-oxoacyl-ACP synthase, mitochondrial	200					acyl-CoA metabolic process (GO:0006637)|medium-chain fatty acid biosynthetic process (GO:0051792)|short-chain fatty acid biosynthetic process (GO:0051790)	mitochondrion (GO:0005739)	3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	25						TAAACTCAAGGGCCCAAATCA	0.448																																					p.G200C		Atlas-SNP	.											.	OXSM	54	.	0			c.G598T						.						80	80	80					3																	25833109		2203	4300	6503	SO:0001583	missense	54995	exon2			CTCAAGGGCCCAA	BC008202	CCDS2643.1, CCDS46780.1	3p24.2	2010-03-19			ENSG00000151093	ENSG00000151093	2.3.1.41		26063	protein-coding gene	gene with protein product	"beta-ketoacyl synthase"	610324				12477932	Standard	NM_017897		Approved	KS, FLJ20604, FASN2D	uc003cdn.3	Q9NWU1	OTTHUMG00000130477	ENST00000280701.3:c.598G>T	chr3.hg19:g.25833109G>T	ENSP00000280701:p.Gly200Cys	123.0	0.0		114.0	55.0	NM_017897		Missense_Mutation	SNP	ENST00000280701.3	hg19	CCDS2643.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.822229	0.90873	.	.	ENSG00000151093	ENST00000452098;ENST00000280701;ENST00000420173;ENST00000428266	.	.	.	6.16	6.16	0.99307	Beta-ketoacyl synthase, N-terminal (1);Thiolase-like, subgroup (1);Thiolase-like (1);	0.000000	0.85682	D	0.000000	D	0.91700	0.7376	H	0.98818	4.34	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.93949	0.7230	9	0.87932	D	0	-14.5096	20.8598	0.99761	0.0:0.0:1.0:0.0	.	200;200	Q9NWU1-2;Q9NWU1	.;OXSM_HUMAN	C	200	.	ENSP00000280701:G200C	G	+	1	0	OXSM	25808113	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.827000	0.99397	2.937000	0.99478	0.650000	0.86243	GGC	.	.		0.448	OXSM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252876.2	NM_017897		T	25833109	G	T	25833109	3	4	344	1	0	0	0	0	1	0	0	0	11344	1232	43	3	600	3	OXSM	3	25833109	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	5911811	25833109	172189321	273	47636										
GADL1	339896	hgsc.bcm.edu	37	chr3	30903131	30903131	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaaccacctcttccattattAgcctacaggcctcttcaaca	3	15	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:30903131A>G	ENST00000282538.5	-	2	314	c.164T>C	c.(163-165)cTa>cCa	p.L55P	GADL1_ENST00000454381.3_Missense_Mutation_p.L55P	NM_207359.2	NP_997242.2	Q6ZQY3	GADL1_HUMAN	glutamate decarboxylase-like 1	55					carboxylic acid metabolic process (GO:0019752)		aspartate 1-decarboxylase activity (GO:0004068)|pyridoxal phosphate binding (GO:0030170)|sulfinoalanine decarboxylase activity (GO:0004782)			breast(2)|endometrium(3)|kidney(2)|lung(17)|upper_aerodigestive_tract(1)	25						TTCCATTATTAGCCTACAGGC	0.398																																					p.L55P		Atlas-SNP	.											.	GADL1	91	.	0			c.T164C						.						173	141	151					3																	30903131		692	1591	2283	SO:0001583	missense	339896	exon2			ATTATTAGCCTAC	AK128643	CCDS2649.2	3p23-p22	2009-01-14			ENSG00000144644	ENSG00000144644			27949	protein-coding gene	gene with protein product		615601					Standard	NM_207359		Approved		uc003cep.2	Q6ZQY3	OTTHUMG00000130621	ENST00000282538.5:c.164T>C	chr3.hg19:g.30903131A>G	ENSP00000282538:p.Leu55Pro	117.0	0.0		129.0	70.0	NM_207359		Missense_Mutation	SNP	ENST00000282538.5	hg19	CCDS2649.2	.	.	.	.	.	.	.	.	.	.	A	20.5	3.994732	0.74703	.	.	ENSG00000144644	ENST00000282538;ENST00000454381	T;T	0.39787	2.71;1.06	5.33	5.33	0.75918	Pyridoxal phosphate-dependent transferase, major domain (1);	.	.	.	.	T	0.39279	0.1072	N	0.19112	0.55	0.58432	D	0.999994	P	0.43352	0.804	P	0.48227	0.571	T	0.35500	-0.9786	9	0.56958	D	0.05	.	14.9431	0.71009	1.0:0.0:0.0:0.0	.	55	Q6ZQY3	GADL1_HUMAN	P	55	ENSP00000282538:L55P;ENSP00000427059:L55P	ENSP00000282538:L55P	L	-	2	0	GADL1	30878135	0.908000	0.30866	1.000000	0.80357	0.997000	0.91878	7.526000	0.81920	2.010000	0.58986	0.454000	0.30748	CTA	.	.		0.398	GADL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253106.2	NM_207359		G	30903131	A	G	30903131	3	3	344	1	0	0	0	0	1	0	0	0	6193	420	15	2	1457	2	GADL1	3	30903131	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	5070022	30903131	167119299	274	47637										
CLASP2	23122	hgsc.bcm.edu	37	chr3	33552159	33552159	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cagccagattaattgggtagTctgcagtttgaatgatagga	12	5	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:33552159T>C	ENST00000468888.2	-	37	4278	c.4232A>G	c.(4231-4233)gAc>gGc	p.D1411G	CLASP2_ENST00000307312.7_Missense_Mutation_p.D892G|CLASP2_ENST00000480013.1_Missense_Mutation_p.D1190G|CLASP2_ENST00000461133.3_Missense_Mutation_p.D1170G|CLASP2_ENST00000399362.4_Missense_Mutation_p.D1410G|CLASP2_ENST00000359576.5_Missense_Mutation_p.D1402G|CLASP2_ENST00000539981.1_3'UTR			O75122	CLAP2_HUMAN	cytoplasmic linker associated protein 2	1191					axon guidance (GO:0007411)|establishment or maintenance of cell polarity (GO:0007163)|fucosylation (GO:0036065)|microtubule anchoring (GO:0034453)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)|regulation of microtubule polymerization or depolymerization (GO:0031110)|regulation of microtubule-based process (GO:0032886)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)|microtubule plus-end binding (GO:0051010)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	48						AATTGGGTAGTCTGCAGTTTG	0.448																																					p.D1412G		Atlas-SNP	.											.	CLASP2	138	.	0			c.A4235G						.						141	124	129					3																	33552159		1921	4146	6067	SO:0001583	missense	23122	exon37			GGGTAGTCTGCAG	AB014527		3p24.3	2013-01-18			ENSG00000163539	ENSG00000163539			17078	protein-coding gene	gene with protein product		605853				9734811, 10899121	Standard	NM_015097		Approved	KIAA0627	uc021wvc.1	O75122	OTTHUMG00000156489	ENST00000468888.2:c.4232A>G	chr3.hg19:g.33552159T>C	ENSP00000419974:p.Asp1411Gly	126.0	0.0		106.0	45.0	NM_015097	Q7L8F6|Q8N6R6|Q9BQT3|Q9BQT4|Q9H7A3|Q9NSZ2	Missense_Mutation	SNP	ENST00000468888.2	hg19		.	.	.	.	.	.	.	.	.	.	T	18.57	3.652145	0.67472	.	.	ENSG00000163539	ENST00000468888;ENST00000399362;ENST00000359576;ENST00000307312;ENST00000480013;ENST00000461133	T;T;T;T;T;T	0.68624	-0.34;-0.34;-0.34;-0.34;-0.34;-0.34	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	T	0.77955	0.4208	M	0.62723	1.935	0.58432	D	0.999999	D;P	0.63880	0.993;0.947	P;P	0.60886	0.879;0.88	T	0.79266	-0.1874	10	0.56958	D	0.05	-20.6838	16.2824	0.82697	0.0:0.0:0.0:1.0	.	1402;1410	F5H604;E7ERI8	.;.	G	1411;1410;1402;892;1190;1170	ENSP00000419974:D1411G;ENSP00000382297:D1410G;ENSP00000352581:D1402G;ENSP00000304743:D892G;ENSP00000417518:D1190G;ENSP00000419305:D1170G	ENSP00000304743:D892G	D	-	2	0	CLASP2	33527163	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	5.883000	0.69721	2.250000	0.74265	0.533000	0.62120	GAC	.	.		0.448	CLASP2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000344320.4	NM_001207044		C	33552159	T	C	33552159	3	2	344	1	0	0	0	0	1	0	0	0	3457	1667	58	2	324	2	CLASP2	3	33552159	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2649028	33552159	164470271	275	47638										
STAC	6769	hgsc.bcm.edu	37	chr3	36534678	36534678	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaggttcctgaggaagccaaTgggccaggaggcgggtatga	18	7	0	2	rs199675015		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:36534678T>C	ENST00000273183.3	+	6	1023	c.723T>C	c.(721-723)aaT>aaC	p.N241N	STAC_ENST00000476388.1_3'UTR|STAC_ENST00000457375.2_Silent_p.N180N	NM_003149.1	NP_003140.1	Q99469	STAC_HUMAN	SH3 and cysteine rich domain	241					cellular response to heat (GO:0034605)|intracellular signal transduction (GO:0035556)|signal transduction (GO:0007165)	cytosol (GO:0005829)	metal ion binding (GO:0046872)			endometrium(5)|large_intestine(9)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(5)	32						AGGAAGCCAATGGGCCAGGAG	0.502																																					p.N241N		Atlas-SNP	.											.	STAC	78	.	0			c.T723C						.						108	109	109					3																	36534678		2203	4300	6503	SO:0001819	synonymous_variant	6769	exon6			AGCCAATGGGCCA	D86640	CCDS2662.1	3p22.3	2007-06-08			ENSG00000144681	ENSG00000144681			11353	protein-coding gene	gene with protein product		602317	"src homology three (SH3) and cysteine rich domain"			8954993, 10393425	Standard	XM_006713308		Approved	STAC1	uc003cgh.1	Q99469	OTTHUMG00000130798	ENST00000273183.3:c.723T>C	chr3.hg19:g.36534678T>C		100.0	0.0		69.0	36.0	NM_003149	B2R8S8	Silent	SNP	ENST00000273183.3	hg19	CCDS2662.1																																																																																			.	T|0.999;C|0.001		0.502	STAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253338.2	NM_003149		C	36534678	T	C	36534678	2	2	344	1	0	0	0	0	0	0	0	1	15254	1461	51	2		2	STAC	3	36534678	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2982519	36534678	161487752	276	47639										
TRANK1	9881	hgsc.bcm.edu	37	chr3	36897302	36897302	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcatttctacagctttatccTcctcactgtagtccccatcc	4	16	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:36897302T>A	ENST00000429976.2	-	12	4026	c.3779A>T	c.(3778-3780)gAg>gTg	p.E1260V	TRANK1_ENST00000428977.2_Missense_Mutation_p.E710V|TRANK1_ENST00000301807.6_Missense_Mutation_p.E710V	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	1260							ATP binding (GO:0005524)|hydrolase activity (GO:0016787)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(20)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	73						AGCTTTATCCTCCTCACTGTA	0.488																																					p.E1260V		Atlas-SNP	.											.	TRANK1	398	.	0			c.A3779T						.						207	211	209					3																	36897302		2089	4218	6307	SO:0001583	missense	9881	exon12			TTATCCTCCTCAC	AK096678	CCDS46789.1, CCDS46789.2	3p22.2	2013-01-11			ENSG00000168016	ENSG00000168016		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29011	protein-coding gene	gene with protein product	"lupus brain antigen 1", "KIAA0342"					9205841	Standard	NM_014831		Approved	LBA1, KIAA0342	uc003cgj.3	O15050	OTTHUMG00000155848	ENST00000429976.2:c.3779A>T	chr3.hg19:g.36897302T>A	ENSP00000416168:p.Glu1260Val	181.0	0.0		176.0	84.0	NM_014831	Q8N8K0	Missense_Mutation	SNP	ENST00000429976.2	hg19	CCDS46789.2	.	.	.	.	.	.	.	.	.	.	T	15.92	2.974303	0.53720	.	.	ENSG00000168016	ENST00000428977;ENST00000429976;ENST00000301807	T;T;T	0.35048	1.33;1.75;1.33	5.45	5.45	0.79879	.	0.096891	0.45126	D	0.000386	T	0.56688	0.2002	M	0.68593	2.085	0.47341	D	0.999392	D	0.71674	0.998	D	0.65874	0.939	T	0.55995	-0.8052	10	0.41790	T	0.15	.	15.8283	0.78730	0.0:0.0:0.0:1.0	.	1260	O15050	TRNK1_HUMAN	V	710;1260;710	ENSP00000416826:E710V;ENSP00000416168:E1260V;ENSP00000301807:E710V	ENSP00000301807:E710V	E	-	2	0	TRANK1	36872306	1.000000	0.71417	0.911000	0.35937	0.857000	0.48899	6.193000	0.72075	2.205000	0.71048	0.454000	0.30748	GAG	.	.		0.488	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831		A	36897302	T	A	36897302	3	1	344	1	0	0	0	0	1	0	0	0	16469	1551	54	4	5046	4	TRANK1	3	36897302	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	362624	36897302	161125128	277	47640										
CCR8	1237	hgsc.bcm.edu	37	chr3	39374403	39374403	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	caatcaacagactttgaagtGgaagatcttcaccaacttca	6	10	4	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:39374403G>T	ENST00000326306.4	+	2	719	c.581G>T	c.(580-582)tGg>tTg	p.W194L	CCR8_ENST00000545843.1_Missense_Mutation_p.W111L|CCR8_ENST00000414803.1_3'UTR	NM_005201.3	NP_005192.1	P51685	CCR8_HUMAN	chemokine (C-C motif) receptor 8	194					cell adhesion (GO:0007155)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)|coreceptor activity (GO:0015026)			NS(3)|breast(1)|endometrium(3)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0504)|Kidney(284;0.0635)		ACTTTGAAGTGGAAGATCTTC	0.398																																					p.W194L		Atlas-SNP	.											.	CCR8	34	.	0			c.G581T						.						136	134	134					3																	39374403		2203	4300	6503	SO:0001583	missense	1237	exon2			TGAAGTGGAAGAT	D49919	CCDS2684.1	3p22	2012-08-08			ENSG00000179934	ENSG00000179934		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1609	protein-coding gene	gene with protein product		601834		CMKBRL2, CMKBR8		8816377, 8886020	Standard	NM_005201		Approved	CY6, TER1, CKR-L1, GPR-CY6, CDw198	uc010hhr.2	P51685	OTTHUMG00000131290	ENST00000326306.4:c.581G>T	chr3.hg19:g.39374403G>T	ENSP00000326432:p.Trp194Leu	63.0	0.0		61.0	25.0	NM_005201	B2RC64|Q3KNQ8|Q3KNR3|Q9BYX5	Missense_Mutation	SNP	ENST00000326306.4	hg19	CCDS2684.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.113054	0.77210	.	.	ENSG00000179934	ENST00000326306;ENST00000545843	T;T	0.35973	1.28;1.28	4.76	4.76	0.60689	GPCR, rhodopsin-like superfamily (1);	0.152547	0.47455	D	0.000237	T	0.57301	0.2044	M	0.77486	2.375	0.80722	D	1	P;P	0.52061	0.95;0.891	P;P	0.57548	0.823;0.773	T	0.63786	-0.6558	10	0.87932	D	0	.	16.5132	0.84292	0.0:0.0:1.0:0.0	.	194;111	P51685;Q3KNR3	CCR8_HUMAN;.	L	194;111	ENSP00000326432:W194L;ENSP00000440474:W111L	ENSP00000326432:W194L	W	+	2	0	CCR8	39349407	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.778000	0.62368	2.476000	0.83614	0.655000	0.94253	TGG	.	.		0.398	CCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254058.2	NM_005201		T	39374403	G	T	39374403	3	4	344	1	0	0	0	0	1	0	0	0	2949	1357	47	3	583	3	CCR8	3	39374403	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	2477101	39374403	158648027	278	47641										
CCDC13	152206	hgsc.bcm.edu	37	chr3	42775068	42775068	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agggctgacctcgcggccacTggacccctcacccactcctt	9	19	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:42775068T>A	ENST00000310232.6	-	11	1488	c.1405A>T	c.(1405-1407)Agt>Tgt	p.S469C	CCDC13-AS1_ENST00000446950.1_RNA|CCDC13-AS1_ENST00000418161.1_RNA	NM_144719.3	NP_653320.3	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13	469										endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	25						TCGCGGCCACTGGACCCCTCA	0.602																																					p.S469C		Atlas-SNP	.											.	CCDC13	71	.	0			c.A1405T						.						60	65	63					3																	42775068		2203	4300	6503	SO:0001583	missense	152206	exon11			GGCCACTGGACCC	AK058196	CCDS2705.1	3p22.1	2005-01-25			ENSG00000244607	ENSG00000244607			26358	protein-coding gene	gene with protein product						12477932	Standard	NM_144719		Approved	FLJ25467	uc003cly.4	Q8IYE1	OTTHUMG00000133046	ENST00000310232.6:c.1405A>T	chr3.hg19:g.42775068T>A	ENSP00000309836:p.Ser469Cys	29.0	0.0		31.0	15.0	NM_144719		Missense_Mutation	SNP	ENST00000310232.6	hg19	CCDS2705.1	.	.	.	.	.	.	.	.	.	.	T	4.619	0.115054	0.08831	.	.	ENSG00000244607	ENST00000310232	T	0.25912	1.77	4.8	-9.61	0.00550	.	1.064250	0.07142	N	0.847475	T	0.18551	0.0445	L	0.57536	1.79	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.28586	-1.0039	10	0.56958	D	0.05	.	4.3336	0.11075	0.2188:0.4806:0.1124:0.1882	.	469	Q8IYE1	CCD13_HUMAN	C	469	ENSP00000309836:S469C	ENSP00000309836:S469C	S	-	1	0	CCDC13	42750072	0.000000	0.05858	0.000000	0.03702	0.145000	0.21501	-1.811000	0.01728	-2.541000	0.00485	-0.274000	0.10170	AGT	.	.		0.602	CCDC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256652.1	NM_144719		A	42775068	T	A	42775068	3	1	344	1	0	0	0	0	1	0	0	0	2767	1580	55	4	766	4	CCDC13	3	42775068	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	3400665	42775068	155247362	279	47642										
ZNF662	389114	hgsc.bcm.edu	37	chr3	42956611	42956611	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtggaactcagatctttctcAgcaccagagggtccacactg	10	12	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:42956611A>T	ENST00000541208.1	+	5	1415	c.1046A>T	c.(1045-1047)cAg>cTg	p.Q349L	ZNF662_ENST00000422021.1_Intron|ZNF662_ENST00000328199.6_Missense_Mutation_p.Q375L|KRBOX1_ENST00000426937.1_Intron|ZNF662_ENST00000440367.2_Missense_Mutation_p.Q349L			Q6ZS27	ZN662_HUMAN	zinc finger protein 662	349					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|large_intestine(6)|lung(5)|upper_aerodigestive_tract(1)	15				KIRC - Kidney renal clear cell carcinoma(284;0.217)		GATCTTTCTCAGCACCAGAGG	0.483																																					p.Q375L		Atlas-SNP	.											.	ZNF662	112	.	0			c.A1124T						.						85	82	83					3																	42956611		2203	4300	6503	SO:0001583	missense	389114	exon4			TTTCTCAGCACCA	AK127779	CCDS2708.1, CCDS46807.1	3p22.1	2013-01-08			ENSG00000182983	ENSG00000182983		"Zinc fingers, C2H2-type", "-"	31930	protein-coding gene	gene with protein product							Standard	NM_207404		Approved	FLJ45880	uc003cmk.2	Q6ZS27	OTTHUMG00000133041	ENST00000541208.1:c.1046A>T	chr3.hg19:g.42956611A>T	ENSP00000446208:p.Gln349Leu	106.0	0.0		109.0	47.0	NM_001134656	A1A4T9|F8W7S8|Q6ZNF8|Q6ZQW8	Missense_Mutation	SNP	ENST00000541208.1	hg19	CCDS2708.1	.	.	.	.	.	.	.	.	.	.	A	10.23	1.294167	0.23564	.	.	ENSG00000182983	ENST00000440367;ENST00000328199;ENST00000541208	T;T;T	0.17854	2.25;2.25;2.25	3.27	2.1	0.27182	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12732	0.0309	L	0.28504	0.86	0.09310	N	1	B;P	0.34462	0.4;0.454	B;B	0.37780	0.167;0.258	T	0.25187	-1.0139	9	0.46703	T	0.11	.	4.9413	0.13967	0.7407:0.0:0.2593:0.0	.	375;349	F8W7S8;Q6ZS27	.;ZN662_HUMAN	L	349;375;349	ENSP00000405047:Q349L;ENSP00000329264:Q375L;ENSP00000446208:Q349L	ENSP00000329264:Q375L	Q	+	2	0	ZNF662	42931615	0.000000	0.05858	0.965000	0.40720	0.992000	0.81027	-0.721000	0.04963	0.476000	0.27440	0.528000	0.53228	CAG	.	.		0.483	ZNF662-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256646.4	NM_207404		T	42956611	A	T	42956611	3	4	344	1	0	0	0	0	1	0	0	0	18086	188	7	4	1247	4	ZNF662	3	42956611	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	181543	42956611	155065819	280	47643										
C3orf39	84892	hgsc.bcm.edu	37	chr3	43122344	43122344	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	accctcgccccagccctccaTgaagaagagccgtgcctcgt	9	18	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:43122344T>A	ENST00000344697.2	-	2	925	c.580A>T	c.(580-582)Atg>Ttg	p.M194L	POMGNT2_ENST00000441964.1_Missense_Mutation_p.M194L	NM_032806.5	NP_116195.2	Q8NAT1	PMGT2_HUMAN	protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-)	194					protein O-linked glycosylation (GO:0006493)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein O-GlcNAc transferase activity (GO:0097363)										CAGCCCTCCATGAAGAAGAGC	0.642																																					p.M194L		Atlas-SNP	.											.	.	.	.	0			c.A580T						.						48	46	47					3																	43122344		2203	4300	6503	SO:0001583	missense	84892	exon2			CCTCCATGAAGAA	AK092147	CCDS2709.1	3p22.1	2014-07-15	2013-08-22	2013-08-22	ENSG00000144647	ENSG00000144647			25902	protein-coding gene	gene with protein product		614828	"chromosome 3 open reading frame 39", "glycosyltransferase-like domain containing 2"	C3orf39, GTDC2		12477932	Standard	NM_032806		Approved	FLJ14566, AGO61	uc003cmr.2	Q8NAT1	OTTHUMG00000133038	ENST00000344697.2:c.580A>T	chr3.hg19:g.43122344T>A	ENSP00000344125:p.Met194Leu	88.0	0.0		70.0	35.0	NM_032806	B3KWC3|Q96SY3	Missense_Mutation	SNP	ENST00000344697.2	hg19	CCDS2709.1	.	.	.	.	.	.	.	.	.	.	T	16.69	3.191965	0.58017	.	.	ENSG00000144647	ENST00000441964;ENST00000344697	T;T	0.75589	-0.95;-0.95	5.88	4.73	0.59995	.	0.000000	0.85682	D	0.000000	T	0.70979	0.3286	M	0.71581	2.175	0.51233	D	0.999919	B	0.09022	0.002	B	0.16722	0.016	T	0.64525	-0.6387	10	0.23891	T	0.37	-16.3798	11.0314	0.47774	0.0:0.0721:0.0:0.9279	.	194	Q8NAT1	AGO61_HUMAN	L	194	ENSP00000408992:M194L;ENSP00000344125:M194L	ENSP00000344125:M194L	M	-	1	0	C3orf39	43097348	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.139000	0.71728	1.057000	0.40506	0.533000	0.62120	ATG	.	.		0.642	POMGNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256643.1	NM_032806		A	43122344	T	A	43122344	3	1	344	1	0	0	0	0	1	0	0	0	2231	1464	51	4	1166	4	C3orf39	3	43122344	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	165733	43122344	154900086	281	47644										
SNRK	54861	hgsc.bcm.edu	37	chr3	43389366	43389366	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agggccggggctccagctgcAgtagttcggagaccagtgat	16	10	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:43389366A>G	ENST00000296088.7	+	7	1919	c.1615A>G	c.(1615-1617)Agt>Ggt	p.S539G	SNRK-AS1_ENST00000422681.1_RNA|SNRK_ENST00000454177.1_Missense_Mutation_p.S539G|RP11-188P20.3_ENST00000607513.1_RNA|SNRK_ENST00000437827.1_Missense_Mutation_p.S333G|SNRK_ENST00000429705.2_Missense_Mutation_p.S539G	NM_017719.4	NP_060189.3			SNF related kinase											breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(5)|prostate(1)|skin(2)|stomach(1)	27				KIRC - Kidney renal clear cell carcinoma(284;0.0636)|Kidney(284;0.0792)		CTCCAGCTGCAGTAGTTCGGA	0.557																																					p.S539G		Atlas-SNP	.											.	SNRK	118	.	0			c.A1615G						.						37	42	40					3																	43389366		1985	4164	6149	SO:0001583	missense	54861	exon7			AGCTGCAGTAGTT	D43636	CCDS43075.1	3p22.1	2005-08-09			ENSG00000163788	ENSG00000163788			30598	protein-coding gene	gene with protein product		612760				8654423, 7788527	Standard	NM_017719		Approved	FLJ20224, HSNFRK, KIAA0096	uc003cmt.4	Q9NRH2	OTTHUMG00000156491	ENST00000296088.7:c.1615A>G	chr3.hg19:g.43389366A>G	ENSP00000296088:p.Ser539Gly	176.0	0.0		158.0	80.0	NM_017719		Missense_Mutation	SNP	ENST00000296088.7	hg19	CCDS43075.1	.	.	.	.	.	.	.	.	.	.	A	17.93	3.510214	0.64522	.	.	ENSG00000163788	ENST00000454177;ENST00000429705;ENST00000296088;ENST00000437827	T;T;T;T	0.77489	-1.1;-1.1;-1.1;1.63	4.72	4.72	0.59763	.	0.099219	0.64402	D	0.000001	D	0.85647	0.5745	M	0.65498	2.005	0.58432	D	0.999996	D	0.58268	0.982	D	0.67548	0.952	D	0.86696	0.1926	10	0.54805	T	0.06	.	14.5039	0.67741	1.0:0.0:0.0:0.0	.	539	Q9NRH2	SNRK_HUMAN	G	539;539;539;333	ENSP00000401246:S539G;ENSP00000411375:S539G;ENSP00000296088:S539G;ENSP00000409516:S333G	ENSP00000296088:S539G	S	+	1	0	SNRK	43364370	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.263000	0.65507	1.892000	0.54788	0.460000	0.39030	AGT	.	.		0.557	SNRK-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344325.1	NM_017719		G	43389366	A	G	43389366	3	3	344	1	0	0	0	0	1	0	0	0	14866	188	7	2	1633	2	SNRK	3	43389366	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	267022	43389366	154633064	282	47645										
EXOSC7	23016	hgsc.bcm.edu	37	chr3	45046818	45046818	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agttttggaggatgaagaggGgtcgaaggacattgaattgt	16	2	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:45046818G>C	ENST00000265564.7	+	6	575	c.527G>C	c.(526-528)gGg>gCg	p.G176A	CLEC3B_ENST00000490386.1_Intron|EXOSC7_ENST00000461361.1_3'UTR	NM_015004.3	NP_055819.2	Q15024	EXOS7_HUMAN	exosome component 7	176					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA catabolic process (GO:0006401)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|RNA binding (GO:0003723)			endometrium(3)|large_intestine(1)|lung(3)	7				BRCA - Breast invasive adenocarcinoma(193;0.00911)|KIRC - Kidney renal clear cell carcinoma(197;0.0509)|Kidney(197;0.064)		GATGAAGAGGGGTCGAAGGAC	0.428																																					p.G176A		Atlas-SNP	.											.	EXOSC7	19	.	0			c.G527C						.						258	227	237					3																	45046818		2203	4300	6503	SO:0001583	missense	23016	exon6			AAGAGGGGTCGAA	BC012831	CCDS2725.1	3p21.32	2010-05-07			ENSG00000075914	ENSG00000075914	3.1.13.-		28112	protein-coding gene	gene with protein product		606488				11719186, 11812149	Standard	NR_023353		Approved	hRrp42p, Rrp42p, RRP42, EAP1, KIAA0116, p8	uc003coi.2	Q15024	OTTHUMG00000133095	ENST00000265564.7:c.527G>C	chr3.hg19:g.45046818G>C	ENSP00000265564:p.Gly176Ala	132.0	0.0		114.0	47.0	NM_015004	Q96E72	Missense_Mutation	SNP	ENST00000265564.7	hg19	CCDS2725.1	.	.	.	.	.	.	.	.	.	.	G	33	5.220455	0.95139	.	.	ENSG00000075914	ENST00000265564	T	0.35789	1.29	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	T	0.55737	0.1939	M	0.86651	2.83	0.80722	D	1	P;P	0.40602	0.723;0.723	B;P	0.44946	0.41;0.465	T	0.57556	-0.7791	10	0.42905	T	0.14	-37.2534	20.4434	0.99119	0.0:0.0:1.0:0.0	.	176;176	B2RDZ9;Q15024	.;EXOS7_HUMAN	A	176	ENSP00000265564:G176A	ENSP00000265564:G176A	G	+	2	0	EXOSC7	45021822	1.000000	0.71417	0.983000	0.44433	0.987000	0.75469	9.623000	0.98386	2.838000	0.97847	0.655000	0.94253	GGG	.	.		0.428	EXOSC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256754.2	NM_015004		C	45046818	G	C	45046818	3	2	344	1	0	0	0	0	1	0	0	0	5321	1232	43	4	549	4	EXOSC7	3	45046818	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1657452	45046818	152975612	283	47646										
FYCO1	79443	hgsc.bcm.edu	37	chr3	46011256	46011256	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agagccagtggtcagcgtccTcctgtggggccacaaaacag	13	12	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:46011256T>C	ENST00000296137.2	-	7	746	c.541A>G	c.(541-543)Agg>Ggg	p.R181G	FYCO1_ENST00000535325.1_Splice_Site_p.R181G	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	181					plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)			NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		GTCAGCGTCCTCCTGTGGGGC	0.577																																					p.R181G		Atlas-SNP	.											.	FYCO1	115	.	0			c.A541G						.						61	53	56					3																	46011256		2203	4300	6503	SO:0001630	splice_region_variant	79443	exon7			GCGTCCTCCTGTG	AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"Zinc fingers, FYVE domain containing"	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.540-1A>G	chr3.hg19:g.46011256T>C		57.0	0.0		34.0	17.0	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Missense_Mutation	SNP	ENST00000296137.2	hg19	CCDS2734.1	.	.	.	.	.	.	.	.	.	.	T	19.08	3.757179	0.69648	.	.	ENSG00000163820	ENST00000296137;ENST00000535325	T;T	0.26067	1.78;1.76	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.35566	0.0936	M	0.71581	2.175	0.58432	D	0.999999	P;P	0.45283	0.819;0.855	B;P	0.44394	0.322;0.448	T	0.28396	-1.0045	10	0.87932	D	0	-21.6977	14.4389	0.67301	0.0:0.0:0.0:1.0	.	181;181	B7ZKT7;Q9BQS8	.;FYCO1_HUMAN	G	181	ENSP00000296137:R181G;ENSP00000441178:R181G	ENSP00000296137:R181G	R	-	1	2	FYCO1	45986260	1.000000	0.71417	1.000000	0.80357	0.755000	0.42902	5.834000	0.69361	2.207000	0.71202	0.533000	0.62120	AGG	.	.		0.577	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513	Missense_Mutation	C	46011256	T	C	46011256	5	2	344	1	0	0	0	0	0	0	1	0	6133	1565	54	2	3943	2	FYCO1	3	46011256	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	964438	46011256	152011174	284	47647										
SMARCC1	6599	hgsc.bcm.edu	37	chr3	47651729	47651729	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	catgctgctgctgttccattTgctgtcgtgctcgtaattca	9	11	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:47651729T>C	ENST00000254480.5	-	26	2989	c.2870A>G	c.(2869-2871)cAa>cGa	p.Q957R	SMARCC1_ENST00000425518.1_5'UTR	NM_003074.3	NP_003065.3	Q92922	SMRC1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1	957					ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|insulin receptor signaling pathway (GO:0008286)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|XY body (GO:0001741)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|protein N-terminus binding (GO:0047485)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(5)|kidney(2)|large_intestine(3)|lung(15)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33				BRCA - Breast invasive adenocarcinoma(193;7.47e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)		CTGTTCCATTTGCTGTCGTGC	0.547																																					p.Q957R		Atlas-SNP	.											.	SMARCC1	85	.	0			c.A2870G						.						304	267	280					3																	47651729		2203	4300	6503	SO:0001583	missense	6599	exon26			TCCATTTGCTGTC	U66615	CCDS2758.1	3p21.31	2008-05-15			ENSG00000173473	ENSG00000173473			11104	protein-coding gene	gene with protein product		601732				8804307	Standard	NM_003074		Approved	BAF155, SRG3, Rsc8, CRACC1	uc003crq.2	Q92922	OTTHUMG00000133519	ENST00000254480.5:c.2870A>G	chr3.hg19:g.47651729T>C	ENSP00000254480:p.Gln957Arg	64.0	0.0		65.0	31.0	NM_003074	Q17RS0|Q6P172|Q8IWH2	Missense_Mutation	SNP	ENST00000254480.5	hg19	CCDS2758.1	.	.	.	.	.	.	.	.	.	.	T	14.56	2.571265	0.45798	.	.	ENSG00000173473	ENST00000254480	T	0.23147	1.92	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.35128	0.0921	L	0.57536	1.79	0.58432	D	0.999995	P	0.52842	0.956	P	0.47528	0.549	T	0.14035	-1.0487	10	0.72032	D	0.01	-22.1753	15.4228	0.75025	0.0:0.0:0.0:1.0	.	957	Q92922	SMRC1_HUMAN	R	957	ENSP00000254480:Q957R	ENSP00000254480:Q957R	Q	-	2	0	SMARCC1	47626733	1.000000	0.71417	1.000000	0.80357	0.087000	0.18053	8.004000	0.88535	2.229000	0.72834	0.533000	0.62120	CAA	.	.		0.547	SMARCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257491.1			C	47651729	T	C	47651729	3	2	344	1	0	0	0	0	1	0	0	0	14790	1812	63	2	459	2	SMARCC1	3	47651729	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1640473	47651729	150370701	285	47648										
MST1R	4486	hgsc.bcm.edu	37	chr3	49924915	49924915	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	caagcagtgcagacactatcTgctccacctcccccactagt	6	17	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:49924915T>A	ENST00000296474.3	-	20	4055	c.4028A>T	c.(4027-4029)cAg>cTg	p.Q1343L	MST1R_ENST00000344206.4_Missense_Mutation_p.Q1294L	NM_002447.2	NP_002438	Q04912	RON_HUMAN	macrophage stimulating 1 receptor (c-met-related tyrosine kinase)	1343	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular component movement (GO:0006928)|defense response (GO:0006952)|innate immune response (GO:0045087)|macrophage colony-stimulating factor signaling pathway (GO:0038145)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|response to virus (GO:0009615)|signal transduction (GO:0007165)|single fertilization (GO:0007338)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|macrophage colony-stimulating factor receptor activity (GO:0005011)			cervix(1)|endometrium(5)|large_intestine(3)|lung(17)|ovary(5)|prostate(2)|skin(1)|urinary_tract(3)	37				BRCA - Breast invasive adenocarcinoma(193;4.65e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)		AGACACTATCTGCTCCACCTC	0.562																																					p.Q1343L		Atlas-SNP	.											.	MST1R	205	.	0			c.A4028T						.						97	87	90					3																	49924915		2203	4300	6503	SO:0001583	missense	4486	exon20			ACTATCTGCTCCA	X70040	CCDS2807.1, CCDS58833.1	3p21	2008-08-18			ENSG00000164078	ENSG00000164078		"CD molecules"	7381	protein-coding gene	gene with protein product		600168	"PTK8 protein tyrosine kinase 8"	RON, PTK8		8386824	Standard	NM_002447		Approved	CDw136, CD136	uc003cxy.4	Q04912	OTTHUMG00000156709	ENST00000296474.3:c.4028A>T	chr3.hg19:g.49924915T>A	ENSP00000296474:p.Gln1343Leu	123.0	0.0		90.0	38.0	NM_002447	B5A944|B5A945|B5A946|B5A947	Missense_Mutation	SNP	ENST00000296474.3	hg19	CCDS2807.1	.	.	.	.	.	.	.	.	.	.	T	1.281	-0.610454	0.03690	.	.	ENSG00000164078	ENST00000296474;ENST00000344206	T;T	0.30182	1.54;1.54	5.91	-3.85	0.04243	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	1.571660	0.03232	N	0.179072	T	0.21841	0.0526	L	0.41961	1.31	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.09465	-1.0673	10	0.25751	T	0.34	0.1653	2.7135	0.05181	0.0941:0.3794:0.1893:0.3372	.	1343	Q04912	RON_HUMAN	L	1343;1294	ENSP00000296474:Q1343L;ENSP00000341325:Q1294L	ENSP00000296474:Q1343L	Q	-	2	0	MST1R	49899919	0.000000	0.05858	0.000000	0.03702	0.318000	0.28184	-0.836000	0.04382	-1.186000	0.02713	-0.250000	0.11733	CAG	.	.		0.562	MST1R-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345403.1			A	49924915	T	A	49924915	3	1	344	1	0	0	0	0	1	0	0	0	9900	1580	55	4	178	4	MST1R	3	49924915	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2273186	49924915	148097515	286	47649										
HEMK1	51409	hgsc.bcm.edu	37	chr3	50615001	50615001	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tctgacccatgagaatgctcAgaggtaggtgggggagttgc	16	7	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:50615001A>T	ENST00000232854.4	+	6	1163	c.611A>T	c.(610-612)cAg>cTg	p.Q204L	HEMK1_ENST00000434410.1_Missense_Mutation_p.Q204L|HEMK1_ENST00000455834.1_Missense_Mutation_p.Q204L	NM_016173.3	NP_057257.1	Q9Y5R4	HEMK1_HUMAN	HemK methyltransferase family member 1	204					DNA methylation (GO:0006306)	mitochondrion (GO:0005739)	DNA binding (GO:0003677)|N-methyltransferase activity (GO:0008170)|protein methyltransferase activity (GO:0008276)			lung(3)	3				BRCA - Breast invasive adenocarcinoma(193;0.000283)|KIRC - Kidney renal clear cell carcinoma(197;0.0179)|Kidney(197;0.0212)		GAGAATGCTCAGAGGTAGGTG	0.488																																					p.Q204L		Atlas-SNP	.											.	HEMK1	17	.	0			c.A611T						.						82	83	83					3																	50615001		2203	4300	6503	SO:0001583	missense	51409	exon6			ATGCTCAGAGGTA	AF172244	CCDS2830.1	3p21	2008-02-05			ENSG00000114735	ENSG00000114735			24923	protein-coding gene	gene with protein product						10690633	Standard	XM_005265218		Approved	MTQ1	uc003dav.3	Q9Y5R4	OTTHUMG00000156849	ENST00000232854.4:c.611A>T	chr3.hg19:g.50615001A>T	ENSP00000232854:p.Gln204Leu	120.0	0.0		88.0	41.0	NM_016173		Missense_Mutation	SNP	ENST00000232854.4	hg19	CCDS2830.1	.	.	.	.	.	.	.	.	.	.	A	14.53	2.562192	0.45590	.	.	ENSG00000114735	ENST00000434410;ENST00000232854;ENST00000455834;ENST00000443894	T;T;T;T	0.64085	2.56;2.56;2.56;-0.08	5.04	5.04	0.67666	Methyltransferase small (1);	0.553031	0.18635	N	0.135465	T	0.51109	0.1655	L	0.33093	0.98	0.34642	D	0.720709	B	0.18310	0.027	B	0.21546	0.035	T	0.59059	-0.7525	10	0.41790	T	0.15	-10.2583	11.089	0.48104	1.0:0.0:0.0:0.0	.	204	Q9Y5R4	HEMK1_HUMAN	L	204;204;204;42	ENSP00000404843:Q204L;ENSP00000232854:Q204L;ENSP00000404334:Q204L;ENSP00000404168:Q42L	ENSP00000232854:Q204L	Q	+	2	0	HEMK1	50590005	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	3.484000	0.53201	2.133000	0.65898	0.533000	0.62120	CAG	.	.		0.488	HEMK1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346231.1	NM_016173		T	50615001	A	T	50615001	3	4	344	1	0	0	0	0	1	0	0	0	7060	188	7	4	629	4	HEMK1	3	50615001	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	690086	50615001	147407429	287	47650										
SEMA3G	56920	hgsc.bcm.edu	37	chr3	52471561	52471561	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acctggtcaggcccctcatcCcctggcctctgcaagagcca	9	18	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:52471561C>A	ENST00000231721.2	-	15	1859	c.1860G>T	c.(1858-1860)ggG>ggT	p.G620G		NM_020163.1	NP_064548.1	Q9NS98	SEM3G_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3G	620	Ig-like C2-type.				multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)			kidney(1)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)	18				BRCA - Breast invasive adenocarcinoma(193;1.69e-05)|Kidney(197;0.00173)|KIRC - Kidney renal clear cell carcinoma(197;0.00196)|OV - Ovarian serous cystadenocarcinoma(275;0.0333)		GCCCCTCATCCCCTGGCCTCT	0.632																																					p.G620G		Atlas-SNP	.											.	SEMA3G	58	.	0			c.G1860T						.						35	37	36					3																	52471561		2203	4300	6503	SO:0001819	synonymous_variant	56920	exon15			CTCATCCCCTGGC		CCDS2856.1	3p21.1	2013-01-11			ENSG00000010319	ENSG00000010319		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	30400	protein-coding gene	gene with protein product						11214971	Standard	XM_005265327		Approved	FLJ00014, sem2	uc003dea.1	Q9NS98	OTTHUMG00000158570	ENST00000231721.2:c.1860G>T	chr3.hg19:g.52471561C>A		149.0	0.0		131.0	69.0	NM_020163	Q7L9D9|Q9H7Q3	Silent	SNP	ENST00000231721.2	hg19	CCDS2856.1																																																																																			.	.		0.632	SEMA3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351354.1	NM_020163		A	52471561	C	A	52471561	2	1	344	1	0	0	0	0	0	0	0	1	14045	610	22	3		3	SEMA3G	3	52471561	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1856560	52471561	145550869	288	47651										
SEMA3G	56920	hgsc.bcm.edu	37	chr3	52474434	52474434	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	caccttgcccccatagggccCccactggtgctgaggcccat	10	18	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:52474434C>A	ENST00000231721.2	-	10	1101	c.1102G>T	c.(1102-1104)Ggg>Tgg	p.G368W		NM_020163.1	NP_064548.1	Q9NS98	SEM3G_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3G	368	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)			kidney(1)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)	18				BRCA - Breast invasive adenocarcinoma(193;1.69e-05)|Kidney(197;0.00173)|KIRC - Kidney renal clear cell carcinoma(197;0.00196)|OV - Ovarian serous cystadenocarcinoma(275;0.0333)		CCATAGGGCCCCCACTGGTGC	0.652																																					p.G368W		Atlas-SNP	.											.	SEMA3G	58	.	0			c.G1102T						.						26	27	27					3																	52474434		2202	4299	6501	SO:0001583	missense	56920	exon10			AGGGCCCCCACTG		CCDS2856.1	3p21.1	2013-01-11			ENSG00000010319	ENSG00000010319		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	30400	protein-coding gene	gene with protein product						11214971	Standard	XM_005265327		Approved	FLJ00014, sem2	uc003dea.1	Q9NS98	OTTHUMG00000158570	ENST00000231721.2:c.1102G>T	chr3.hg19:g.52474434C>A	ENSP00000231721:p.Gly368Trp	51.0	0.0		44.0	17.0	NM_020163	Q7L9D9|Q9H7Q3	Missense_Mutation	SNP	ENST00000231721.2	hg19	CCDS2856.1	.	.	.	.	.	.	.	.	.	.	C	14.88	2.668520	0.47677	.	.	ENSG00000010319	ENST00000231721	T	0.11063	2.81	4.91	3.13	0.36017	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.128288	0.52532	D	0.000069	T	0.19967	0.0480	L	0.49350	1.555	0.52501	D	0.999958	D	0.56035	0.974	P	0.61275	0.886	T	0.00647	-1.1628	10	0.56958	D	0.05	.	7.0634	0.25139	0.1389:0.7115:0.0:0.1495	.	368	Q9NS98	SEM3G_HUMAN	W	368	ENSP00000231721:G368W	ENSP00000231721:G368W	G	-	1	0	SEMA3G	52449474	0.931000	0.31567	0.998000	0.56505	0.362000	0.29581	2.003000	0.40844	0.676000	0.31285	-0.254000	0.11334	GGG	.	.		0.652	SEMA3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351354.1	NM_020163		A	52474434	C	A	52474434	3	1	344	1	0	0	0	0	1	0	0	0	14045	623	22	3	1274	3	SEMA3G	3	52474434	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	2873	52474434	145547996	289	47652										
STAB1	23166	hgsc.bcm.edu	37	chr3	52538054	52538054	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gggagcccagctgtgtgtgcAgggaaagcgaggtgggggat	21	6	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:52538054A>T	ENST00000321725.6	+	10	1109	c.1033A>T	c.(1033-1035)Agg>Tgg	p.R345W		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	345					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)			breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		CTGTGTGTGCAGGGAAAGCGA	0.701																																					p.R345W		Atlas-SNP	.											.	STAB1	178	.	0			c.A1033T						.						23	19	20					3																	52538054		2191	4293	6484	SO:0001583	missense	23166	exon10			GTGTGCAGGGAAA	AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"MS-1 antigen", "fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1", "common lymphatic endothelial and vascular endothelial receptor-1"	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.1033A>T	chr3.hg19:g.52538054A>T	ENSP00000312946:p.Arg345Trp	56.0	0.0		52.0	27.0	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Missense_Mutation	SNP	ENST00000321725.6	hg19	CCDS33768.1	.	.	.	.	.	.	.	.	.	.	A	16.03	3.007880	0.54361	.	.	ENSG00000010327	ENST00000321725	T	0.08720	3.06	4.7	4.7	0.59300	FAS1 domain (1);	0.207467	0.41500	D	0.000873	T	0.16938	0.0407	L	0.56280	1.765	0.25588	N	0.986727	P;D	0.60575	0.929;0.988	P;P	0.55011	0.573;0.766	T	0.02950	-1.1090	10	0.72032	D	0.01	.	10.8535	0.46784	1.0:0.0:0.0:0.0	.	345;345	Q9NY15;Q9NY15-2	STAB1_HUMAN;.	W	345	ENSP00000312946:R345W	ENSP00000312946:R345W	R	+	1	2	STAB1	52513094	1.000000	0.71417	0.977000	0.42913	0.231000	0.25187	3.035000	0.49759	1.886000	0.54624	0.379000	0.24179	AGG	.	.		0.701	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136		T	52538054	A	T	52538054	3	4	344	1	0	0	0	0	1	0	0	0	15252	179	7	4	1071	4	STAB1	3	52538054	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	63620	52538054	145484376	290	47653										
ITIH4	3700	hgsc.bcm.edu	37	chr3	52860032	52860032	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcttgaaccggatgtgagccTggaggaataatccgggctga	15	8	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:52860032T>A	ENST00000266041.4	-	6	727		c.e6-2		RP5-966M1.6_ENST00000468472.1_Splice_Site|ITIH4_ENST00000485816.1_Splice_Site|ITIH4_ENST00000346281.5_Splice_Site|ITIH4_ENST00000434759.3_Splice_Site|ITIH4-AS1_ENST00000478366.1_RNA|ITIH4_ENST00000467462.1_5'Flank|ITIH4_ENST00000406595.1_Splice_Site	NM_002218.4	NP_002209.2	Q14624	ITIH4_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 4						acute-phase response (GO:0006953)|hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)|response to cytokine (GO:0034097)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)		GATGTGAGCCTGGAGGAATAA	0.517																																					.		Atlas-SNP	.											.	ITIH4	74	.	0			c.631-2A>T						.						108	91	97					3																	52860032		2203	4300	6503	SO:0001630	splice_region_variant	3700	exon7			TGAGCCTGGAGGA	D38535	CCDS2865.1, CCDS54596.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055955	ENSG00000055955			6169	protein-coding gene	gene with protein product	"plasma Kallikrein-sensitive glycoprotein"	600564	"inter-alpha (globulin) inhibitor H4 (plasma Kallikrein-sensitive glycoprotein)"	ITIHL1		9480842, 7805892	Standard	NM_002218		Approved	IHRP, H4P	uc003dfz.3	Q14624	OTTHUMG00000159023	ENST00000266041.4:c.631-2A>T	chr3.hg19:g.52860032T>A		73.0	0.0		51.0	17.0	NM_002218	B7Z545|E9PGN5|Q15135|Q9P190|Q9UQ54	Splice_Site	SNP	ENST00000266041.4	hg19	CCDS2865.1	.	.	.	.	.	.	.	.	.	.	T	15.54	2.864631	0.51482	.	.	ENSG00000055955	ENST00000266041;ENST00000346281;ENST00000485816;ENST00000406595;ENST00000538421;ENST00000434759	.	.	.	4.98	4.98	0.66077	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.6597	0.62359	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	ITIH4	52835072	1.000000	0.71417	0.977000	0.42913	0.469000	0.32828	7.005000	0.76323	1.877000	0.54381	0.459000	0.35465	.	.	.		0.517	ITIH4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317715.1	NM_002218	Intron	A	52860032	T	A	52860032	5	1	344	1	0	0	0	0	0	0	1	0	7915	1594	55	4	2239	4	ITIH4	3	52860032	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	321978	52860032	145162398	291	47654										
CADPS	8618	hgsc.bcm.edu	37	chr3	62631427	62631427	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aagcctcggcctgatcagtcTgtagtttctctcctccttcc	7	15	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:62631427T>C	ENST00000383710.4	-	6	1644	c.1295A>G	c.(1294-1296)cAg>cGg	p.Q432R	CADPS_ENST00000283269.9_Missense_Mutation_p.Q432R|CADPS_ENST00000357948.3_Missense_Mutation_p.Q432R|CADPS_ENST00000490353.2_Missense_Mutation_p.Q432R	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	432	C2.				catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		CTGATCAGTCTGTAGTTTCTC	0.453																																					p.Q432R		Atlas-SNP	.											.	CADPS	387	.	0			c.A1295G						.						225	211	216					3																	62631427		2203	4300	6503	SO:0001583	missense	8618	exon6			TCAGTCTGTAGTT	U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"Pleckstrin homology (PH) domain containing"	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.1295A>G	chr3.hg19:g.62631427T>C	ENSP00000373215:p.Gln432Arg	102.0	0.0		86.0	31.0	NM_003716	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Missense_Mutation	SNP	ENST00000383710.4	hg19	CCDS46858.1	.	.	.	.	.	.	.	.	.	.	T	18.22	3.575348	0.65878	.	.	ENSG00000163618	ENST00000383709;ENST00000383710;ENST00000357948;ENST00000283269;ENST00000490353	T;T;T;T	0.68624	-0.34;-0.34;-0.34;0.71	5.44	5.44	0.79542	C2 calcium-dependent membrane targeting (1);	0.000000	0.85682	D	0.000000	T	0.77725	0.4173	L	0.58428	1.81	0.80722	D	1	D;P;P	0.63880	0.993;0.908;0.791	D;D;B	0.65573	0.936;0.922;0.272	T	0.77446	-0.2585	10	0.42905	T	0.14	.	15.7937	0.78388	0.0:0.0:0.0:1.0	.	432;432;432	Q9ULU8-2;Q9ULU8-3;Q9ULU8	.;.;CAPS1_HUMAN	R	432	ENSP00000373215:Q432R;ENSP00000350632:Q432R;ENSP00000283269:Q432R;ENSP00000418736:Q432R	ENSP00000283269:Q432R	Q	-	2	0	CADPS	62606467	1.000000	0.71417	0.995000	0.50966	0.966000	0.64601	8.040000	0.89188	2.188000	0.69820	0.533000	0.62120	CAG	.	.		0.453	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394		C	62631427	T	C	62631427	3	2	344	1	0	0	0	0	1	0	0	0	2572	1580	55	2	2939	2	CADPS	3	62631427	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	9771395	62631427	135391003	292	47655										
PRICKLE2	166336	hgsc.bcm.edu	37	chr3	64148718	64148718	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtcatgtggcggcagctggtGtagtagctgcttgattcgca	15	8	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:64148718G>T	ENST00000295902.6	-	3	817	c.232C>A	c.(232-234)Cac>Aac	p.H78N	PRICKLE2_ENST00000564377.1_Missense_Mutation_p.H134N	NM_198859.3	NP_942559.1	Q7Z3G6	PRIC2_HUMAN	prickle homolog 2 (Drosophila)	78	PET. {ECO:0000255|PROSITE- ProRule:PRU00636}.				establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|neuron projection development (GO:0031175)	apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(9)|liver(1)|lung(10)|ovary(4)|prostate(2)|skin(2)|stomach(1)	32		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000971)|KIRC - Kidney renal clear cell carcinoma(15;0.00443)|Kidney(15;0.00497)		GGCAGCTGGTGTAGTAGCTGC	0.458																																					p.H78N		Atlas-SNP	.											.	PRICKLE2	88	.	0			c.C232A						.						217	207	211					3																	64148718		2203	4300	6503	SO:0001583	missense	166336	exon3			GCTGGTGTAGTAG	AK127839	CCDS2902.1	3p14.3	2006-09-12	2006-09-12		ENSG00000163637	ENSG00000163637			20340	protein-coding gene	gene with protein product		608501	"prickle-like 2 (Drosophila)"			12525887	Standard	NM_198859		Approved	DKFZp686D143	uc003dmf.3	Q7Z3G6	OTTHUMG00000158789	ENST00000295902.6:c.232C>A	chr3.hg19:g.64148718G>T	ENSP00000295902:p.His78Asn	68.0	0.0		68.0	25.0	NM_198859	Q0VF44	Missense_Mutation	SNP	ENST00000295902.6	hg19	CCDS2902.1	.	.	.	.	.	.	.	.	.	.	G	17.93	3.508951	0.64410	.	.	ENSG00000163637	ENST00000295902;ENST00000498162	D;D	0.85955	-2.05;-2.05	5.77	5.77	0.91146	PET domain (2);	0.000000	0.64402	D	0.000001	D	0.88145	0.6358	M	0.82056	2.57	0.80722	D	1	B	0.18461	0.028	B	0.27608	0.081	D	0.84809	0.0789	10	0.66056	D	0.02	-47.1007	19.9928	0.97374	0.0:0.0:1.0:0.0	.	78	Q7Z3G6	PRIC2_HUMAN	N	78	ENSP00000295902:H78N;ENSP00000419951:H78N	ENSP00000295902:H78N	H	-	1	0	PRICKLE2	64123758	1.000000	0.71417	0.969000	0.41365	0.848000	0.48234	6.756000	0.74919	2.745000	0.94114	0.650000	0.86243	CAC	.	.		0.458	PRICKLE2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352219.1	NM_198859		T	64148718	G	T	64148718	3	4	344	1	0	0	0	0	1	0	0	0	12499	1377	48	3	2326	3	PRICKLE2	3	64148718	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1517291	64148718	133873712	293	47656										
KBTBD8	84541	hgsc.bcm.edu	37	chr3	67054509	67054509	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	caccaatagatggctatccaAaccatccttgcttcgagcca	6	14	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:67054509A>T	ENST00000417314.2	+	3	1167	c.1118A>T	c.(1117-1119)aAa>aTa	p.K373I	KBTBD8_ENST00000295568.4_Missense_Mutation_p.K347I|KBTBD8_ENST00000460576.1_Intron			Q8NFY9	KBTB8_HUMAN	kelch repeat and BTB (POZ) domain containing 8	373						cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)				breast(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)	20		Lung NSC(201;0.0765)		BRCA - Breast invasive adenocarcinoma(55;6.02e-06)|KIRC - Kidney renal clear cell carcinoma(39;0.105)|Kidney(39;0.125)		TGGCTATCCAAACCATCCTTG	0.463																																					p.K373I		Atlas-SNP	.											.	KBTBD8	101	.	0			c.A1118T						.						133	124	127					3																	67054509		2203	4300	6503	SO:0001583	missense	84541	exon3			TATCCAAACCATC	AF385438	CCDS2906.1, CCDS2906.2	3p14	2013-01-08			ENSG00000163376	ENSG00000163376		"BTB/POZ domain containing"	30691	protein-coding gene	gene with protein product	"T-cell activation kelch repeat protein"					11347906	Standard	NM_032505		Approved	TA-KRP, KIAA1842	uc003dmy.3	Q8NFY9	OTTHUMG00000158779	ENST00000417314.2:c.1118A>T	chr3.hg19:g.67054509A>T	ENSP00000401878:p.Lys373Ile	104.0	0.0		90.0	48.0	NM_032505	B4DTW6|Q96JI5	Missense_Mutation	SNP	ENST00000417314.2	hg19	CCDS2906.2	.	.	.	.	.	.	.	.	.	.	A	13.63	2.295322	0.40594	.	.	ENSG00000163376	ENST00000295568;ENST00000417314	T;T	0.76709	-1.04;-1.04	5.36	5.36	0.76844	Kelch-type beta propeller (1);	0.088685	0.64402	D	0.000001	T	0.77980	0.4212	L	0.48642	1.525	0.39783	D	0.972325	P	0.48998	0.918	P	0.49140	0.601	T	0.78516	-0.2174	9	.	.	.	.	15.6426	0.77016	1.0:0.0:0.0:0.0	.	373	Q8NFY9	KBTB8_HUMAN	I	347;373	ENSP00000295568:K347I;ENSP00000401878:K373I	.	K	+	2	0	KBTBD8	67137199	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	4.840000	0.62817	2.161000	0.67846	0.455000	0.32223	AAA	.	.		0.463	KBTBD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352189.1	NM_032505		T	67054509	A	T	67054509	3	4	344	1	0	0	0	0	1	0	0	0	8008	14	1	4	1128	4	KBTBD8	3	67054509	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2905791	67054509	130967921	294	47657										
ROBO2	6092	hgsc.bcm.edu	37	chr3	77595492	77595492	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tttcttttaaattatagctcCcccacagtttgtggttcggc	7	10	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:77595492C>T	ENST00000461745.1	+	7	1838	c.938C>T	c.(937-939)cCc>cTc	p.P313L	ROBO2_ENST00000332191.8_Missense_Mutation_p.P313L|ROBO2_ENST00000487694.3_Missense_Mutation_p.P329L	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	313					apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)			NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		ATTATAGCTCCCCCACAGTTT	0.388																																					p.P313L		Atlas-SNP	.											.	ROBO2	527	.	0			c.C938T						.						118	113	115					3																	77595492		1815	4070	5885	SO:0001583	missense	6092	exon7			TAGCTCCCCCACA	AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10250	protein-coding gene	gene with protein product		602431	"roundabout (axon guidance receptor, Drosophila) homolog 2"			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.938C>T	chr3.hg19:g.77595492C>T	ENSP00000417164:p.Pro313Leu	51.0	0.0		58.0	22.0	NM_002942	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	hg19	CCDS43109.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.933914	0.92458	.	.	ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000343019;ENST00000461745;ENST00000332191;ENST00000398467	T;T;T	0.76578	-1.03;-1.03;-1.03	5.66	5.66	0.87406	Immunoglobulin-like fold (1);	0.000000	0.45867	D	0.000340	D	0.85737	0.5766	M	0.69523	2.12	0.47476	D	0.999433	D	0.57899	0.981	P	0.56127	0.792	D	0.86872	0.2036	9	0.87932	D	0	.	19.7452	0.96250	0.0:1.0:0.0:0.0	.	313	Q9HCK4	ROBO2_HUMAN	L	329;329;333;313;313;34	ENSP00000417335:P329L;ENSP00000417164:P313L;ENSP00000327536:P313L	ENSP00000327536:P313L	P	+	2	0	ROBO2	77678182	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	7.818000	0.86416	2.672000	0.90937	0.591000	0.81541	CCC	.	.		0.388	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		T	77595492	C	T	77595492	3	4	344	1	0	0	0	0	1	0	0	0	13529	623	22	3	966	3	ROBO2	3	77595492	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	10540983	77595492	120426938	295	47658										
CADM2	253559	hgsc.bcm.edu	37	chr3	85961527	85961527	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	catattttattttcagatgtAaaatatttaaaagaagagga	6	2	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:85961527A>T	ENST00000407528.2	+	5	569	c.507A>T	c.(505-507)gtA>gtT	p.V169V	CADM2_ENST00000405615.2_Silent_p.V171V|CADM2_ENST00000383699.3_Silent_p.V178V	NM_001167674.1	NP_001161146.1	Q8N3J6	CADM2_HUMAN	cell adhesion molecule 2	169	Ig-like C2-type 1.				adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|synapse (GO:0045202)				endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(1)|prostate(1)|skin(4)	38		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		TTTCAGATGTAAAATATTTAA	0.363																																					p.V178V		Atlas-SNP	.											.	CADM2	195	.	0			c.A534T						.						29	29	29					3																	85961527		2203	4300	6503	SO:0001819	synonymous_variant	253559	exon6			AGATGTAAAATAT	AF538973	CCDS33792.1, CCDS54613.1, CCDS54614.1	3p12.2	2013-01-11	2007-02-07	2007-02-07	ENSG00000175161	ENSG00000175161		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing"	29849	protein-coding gene	gene with protein product	"nectin-like 3"	609938	"immunoglobulin superfamily, member 4D"	IGSF4D			Standard	NM_153184		Approved	NECL3, Necl-3, SynCAM2	uc003dqj.3	Q8N3J6	OTTHUMG00000158990	ENST00000407528.2:c.507A>T	chr3.hg19:g.85961527A>T		224.0	0.0		254.0	118.0	NM_001167675	G3XHN7|G3XHN8|Q3KQY9|Q658Q7|Q8IZP8	Silent	SNP	ENST00000407528.2	hg19	CCDS54614.1																																																																																			.	.		0.363	CADM2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352822.1	NM_153184		T	85961527	A	T	85961527	2	4	344	1	0	0	0	0	0	0	0	1	2569	349	13	4		4	CADM2	3	85961527	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	8366035	85961527	112060903	296	47659										
ARL13B	200894	hgsc.bcm.edu	37	chr3	93754239	93754239	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atgtcattgaatgtctatctCtggaaaaattggtcaatgag	9	5	4	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:93754239C>G	ENST00000394222.3	+	4	720	c.445C>G	c.(445-447)Ctg>Gtg	p.L149V	ARL13B_ENST00000486562.1_3'UTR|ARL13B_ENST00000303097.7_Missense_Mutation_p.L42V|ARL13B_ENST00000535334.1_Missense_Mutation_p.L46V|ARL13B_ENST00000539730.1_5'UTR|ARL13B_ENST00000471138.1_Missense_Mutation_p.L149V	NM_001174150.1	NP_001167621.1	Q3SXY8	AR13B_HUMAN	ADP-ribosylation factor-like 13B	149					cilium assembly (GO:0042384)|dorsal/ventral pattern formation (GO:0009953)|formation of radial glial scaffolds (GO:0021943)|heart looping (GO:0001947)|interneuron migration from the subpallium to the cortex (GO:0021830)|left/right axis specification (GO:0070986)|neural tube patterning (GO:0021532)|nonmotile primary cilium assembly (GO:0035058)|small GTPase mediated signal transduction (GO:0007264)|smoothened signaling pathway (GO:0007224)	ciliary membrane (GO:0060170)|cilium (GO:0005929)|intracellular (GO:0005622)|primary cilium (GO:0072372)	GTP binding (GO:0005525)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|urinary_tract(2)	10						ATGTCTATCTCTGGAAAAATT	0.299																																					p.L149V		Atlas-SNP	.											.	ARL13B	52	.	0			c.C445G						.						115	125	122					3																	93754239		2203	4299	6502	SO:0001583	missense	200894	exon4			CTATCTCTGGAAA	AL713789	CCDS2924.1, CCDS2925.1, CCDS54615.1	3q11	2014-05-09	2005-11-18	2005-11-18	ENSG00000169379	ENSG00000169379		"ADP-ribosylation factors-like", "ADP-ribosylation factors"	25419	protein-coding gene	gene with protein product		608922	"ADP-ribosylation factor-like 2-like 1"	ARL2L1		15314642, 18674751	Standard	NR_033427		Approved	DKFZp761H079, JBTS8	uc003drf.3	Q3SXY8	OTTHUMG00000159012	ENST00000394222.3:c.445C>G	chr3.hg19:g.93754239C>G	ENSP00000377769:p.Leu149Val	153.0	0.0		156.0	67.0	NM_182896	D3DN29|G3V1S8|Q504W8|Q8TCL5	Missense_Mutation	SNP	ENST00000394222.3	hg19	CCDS2925.1	.	.	.	.	.	.	.	.	.	.	C	17.65	3.442950	0.63067	.	.	ENSG00000169379	ENST00000535334;ENST00000303097;ENST00000394222;ENST00000471138	T;T;T;T	0.78707	-0.45;-1.2;-0.45;-0.45	5.78	2.04	0.26737	.	0.000000	0.64402	D	0.000001	D	0.86347	0.5911	M	0.84082	2.675	0.80722	D	1	D;D;D	0.89917	0.998;1.0;0.998	D;D;D	0.91635	0.98;0.999;0.98	D	0.83501	0.0075	10	0.41790	T	0.15	-18.1108	10.0905	0.42445	0.0:0.7319:0.0:0.2681	.	149;42;149	B4DLH1;Q3SXY8-2;Q3SXY8	.;.;AR13B_HUMAN	V	46;42;149;149	ENSP00000445145:L46V;ENSP00000306225:L42V;ENSP00000377769:L149V;ENSP00000420780:L149V	ENSP00000306225:L42V	L	+	1	2	ARL13B	95236929	0.475000	0.25894	0.990000	0.47175	0.983000	0.72400	0.729000	0.26028	0.094000	0.17404	-0.136000	0.14681	CTG	.	.		0.299	ARL13B-005	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352904.1	NM_182896		G	93754239	C	G	93754239	3	3	344	1	0	0	0	0	1	0	0	0	929	912	32	4	459	4	ARL13B	3	93754239	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	7792712	93754239	104268191	297	47660										
IMPG2	50939	hgsc.bcm.edu	37	chr3	100964730	100964730	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cactgccggggtgacagaatGaagagtcaagctgctaacct	12	10	1	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:100964730G>A	ENST00000193391.7	-	12	1646	c.1459C>T	c.(1459-1461)Cat>Tat	p.H487Y		NM_016247.3	NP_057331.2	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2	487					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)|receptor complex (GO:0043235)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			NS(1)|breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(14)|lung(32)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64					Hyaluronan(DB08818)	GTGACAGAATGAAGAGTCAAG	0.478																																					p.H487Y		Atlas-SNP	.											.	IMPG2	164	.	0			c.C1459T						.						107	110	109					3																	100964730		2203	4300	6503	SO:0001583	missense	50939	exon12			CAGAATGAAGAGT	AF173155	CCDS2940.1	3q12.2-q12.3	2014-01-28			ENSG00000081148	ENSG00000081148			18362	protein-coding gene	gene with protein product		607056				10542133	Standard	NM_016247		Approved	IPM200, RP56	uc003duq.2	Q9BZV3	OTTHUMG00000159091	ENST00000193391.7:c.1459C>T	chr3.hg19:g.100964730G>A	ENSP00000193391:p.His487Tyr	112.0	0.0		125.0	59.0	NM_016247	A8MWT5|Q9UKD4|Q9UKK5	Missense_Mutation	SNP	ENST00000193391.7	hg19	CCDS2940.1	.	.	.	.	.	.	.	.	.	.	G	15.99	2.995495	0.54147	.	.	ENSG00000081148	ENST00000193391	T	0.25250	1.81	6.03	4.22	0.49857	.	0.636801	0.15785	N	0.244731	T	0.16642	0.0400	N	0.19112	0.55	0.26251	N	0.978726	B;B	0.21381	0.055;0.014	B;B	0.12837	0.008;0.005	T	0.12400	-1.0549	10	0.48119	T	0.1	-2.001	9.9852	0.41837	0.0695:0.2615:0.669:0.0	.	487;487	F1T0J3;Q9BZV3	.;IMPG2_HUMAN	Y	487	ENSP00000193391:H487Y	ENSP00000193391:H487Y	H	-	1	0	IMPG2	102447420	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.919000	0.40015	1.547000	0.49401	0.655000	0.94253	CAT	.	.		0.478	IMPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353256.3			A	100964730	G	A	100964730	3	1	344	1	0	0	0	0	1	0	0	0	7738	1290	45	3	2298	3	IMPG2	3	100964730	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	7210491	100964730	97057700	298	47661										
MYH15	22989	hgsc.bcm.edu	37	chr3	108149731	108149731	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctaccaggcctttctcattcTccacttttgaattcatctga	4	13	4	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:108149731T>C	ENST00000273353.3	-	27	3376	c.3320A>G	c.(3319-3321)gAg>gGg	p.E1107G		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	1107						cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						TTTCTCATTCTCCACTTTTGA	0.313																																					p.E1107G		Atlas-SNP	.											.	MYH15	223	.	0			c.A3320G						.						97	89	91					3																	108149731		1816	4084	5900	SO:0001583	missense	22989	exon27			TCATTCTCCACTT	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"Myosins / Myosin superfamily : Class II"	31073	protein-coding gene	gene with protein product		609929	"myosin, heavy polypeptide 15"			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.3320A>G	chr3.hg19:g.108149731T>C	ENSP00000273353:p.Glu1107Gly	52.0	0.0		44.0	14.0	NM_014981		Missense_Mutation	SNP	ENST00000273353.3	hg19	CCDS43127.1	.	.	.	.	.	.	.	.	.	.	T	15.72	2.916120	0.52546	.	.	ENSG00000144821	ENST00000273353	D	0.81908	-1.55	5.22	-1.98	0.07480	Myosin tail (1);	.	.	.	.	D	0.89729	0.6799	M	0.90425	3.115	0.33508	D	0.590751	D	0.89917	1.0	D	0.97110	1.0	D	0.86825	0.2007	9	0.87932	D	0	.	4.9162	0.13847	0.1016:0.0644:0.2943:0.5397	.	1107	Q9Y2K3	MYH15_HUMAN	G	1107	ENSP00000273353:E1107G	ENSP00000273353:E1107G	E	-	2	0	MYH15	109632421	1.000000	0.71417	0.000000	0.03702	0.467000	0.32768	3.162000	0.50755	-0.218000	0.10018	0.455000	0.32223	GAG	.	.		0.313	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988		C	108149731	T	C	108149731	3	2	344	1	0	0	0	0	1	0	0	0	10043	1551	54	2	2584	2	MYH15	3	108149731	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	7185001	108149731	89872699	299	47662										
DZIP3	9666	hgsc.bcm.edu	37	chr3	108396342	108396342	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atttttagtcttcttctaccAgacacagtacaatgaacaaa	4	9	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:108396342A>T	ENST00000361582.3	+	26	3011		c.e26-1		DZIP3_ENST00000463306.1_Splice_Site	NM_014648.3	NP_055463.1	Q86Y13	DZIP3_HUMAN	DAZ interacting zinc finger protein 3						protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|phosphatase binding (GO:0019902)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(21)|ovary(1)|pancreas(1)|prostate(5)|skin(1)	45						TTCTTCTACCAGACACAGTAC	0.388																																					.		Atlas-SNP	.											.	DZIP3	111	.	0			c.2782-2A>T						.						183	184	183					3																	108396342		2203	4300	6503	SO:0001630	splice_region_variant	9666	exon26			TCTACCAGACACA	AF279370	CCDS2952.1	3q13.13	2013-05-22	2013-05-22		ENSG00000198919	ENSG00000198919		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	30938	protein-coding gene	gene with protein product	"human RNA-binding ubiquitin ligase of 138 kDa", "protein phosphatase 1, regulatory subunit 66"	608672	"DAZ interacting protein 3, zinc finger"			9734811, 12538761	Standard	NM_014648		Approved	hRUL138, PPP1R66	uc003dxd.3	Q86Y13	OTTHUMG00000159232	ENST00000361582.3:c.2782-1A>T	chr3.hg19:g.108396342A>T		248.0	1.0		207.0	95.0	NM_014648	B3KN01|O75162|Q6P3R9|Q6PH82|Q86Y14|Q86Y15|Q86Y16|Q8IWI0|Q96RS9	Splice_Site	SNP	ENST00000361582.3	hg19	CCDS2952.1	.	.	.	.	.	.	.	.	.	.	A	18.92	3.725941	0.69074	.	.	ENSG00000198919	ENST00000361582;ENST00000463306	.	.	.	4.81	4.81	0.61882	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.9398	0.47266	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DZIP3	109879032	0.992000	0.36948	0.934000	0.37439	0.966000	0.64601	4.007000	0.57093	2.145000	0.66743	0.460000	0.39030	.	.	.		0.388	DZIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353968.1	NM_014648	Intron	T	108396342	A	T	108396342	5	4	344	1	0	0	0	0	0	0	1	0	4867	202	7	4	2878	4	DZIP3	3	108396342	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	246611	108396342	89626088	300	47663										
DZIP3	9666	hgsc.bcm.edu	37	chr3	108396438	108396438	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcctccaccacccagtcctgAgatactggtaagaaatacaa	6	13	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:108396438A>T	ENST00000361582.3	+	26	3106	c.2876A>T	c.(2875-2877)gAg>gTg	p.E959V	DZIP3_ENST00000463306.1_Missense_Mutation_p.E959V	NM_014648.3	NP_055463.1	Q86Y13	DZIP3_HUMAN	DAZ interacting zinc finger protein 3	959					protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|phosphatase binding (GO:0019902)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(21)|ovary(1)|pancreas(1)|prostate(5)|skin(1)	45						CCCAGTCCTGAGATACTGGTA	0.403																																					p.E959V		Atlas-SNP	.											.	DZIP3	111	.	0			c.A2876T						.						149	144	146					3																	108396438		2203	4300	6503	SO:0001583	missense	9666	exon26			GTCCTGAGATACT	AF279370	CCDS2952.1	3q13.13	2013-05-22	2013-05-22		ENSG00000198919	ENSG00000198919		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	30938	protein-coding gene	gene with protein product	"human RNA-binding ubiquitin ligase of 138 kDa", "protein phosphatase 1, regulatory subunit 66"	608672	"DAZ interacting protein 3, zinc finger"			9734811, 12538761	Standard	NM_014648		Approved	hRUL138, PPP1R66	uc003dxd.3	Q86Y13	OTTHUMG00000159232	ENST00000361582.3:c.2876A>T	chr3.hg19:g.108396438A>T	ENSP00000355028:p.Glu959Val	291.0	0.0		194.0	88.0	NM_014648	B3KN01|O75162|Q6P3R9|Q6PH82|Q86Y14|Q86Y15|Q86Y16|Q8IWI0|Q96RS9	Missense_Mutation	SNP	ENST00000361582.3	hg19	CCDS2952.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.002208	0.74932	.	.	ENSG00000198919	ENST00000361582;ENST00000463306	T;T	0.20200	2.09;2.09	4.81	4.81	0.61882	.	0.367160	0.23465	N	0.047895	T	0.30293	0.0760	L	0.44542	1.39	0.33057	D	0.533573	D;D	0.65815	0.995;0.985	P;P	0.56278	0.795;0.541	T	0.39683	-0.9602	10	0.54805	T	0.06	-3.449	10.9398	0.47266	1.0:0.0:0.0:0.0	.	577;959	D3DN61;Q86Y13	.;DZIP3_HUMAN	V	959	ENSP00000355028:E959V;ENSP00000419981:E959V	ENSP00000355028:E959V	E	+	2	0	DZIP3	109879128	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.007000	0.57093	2.145000	0.66743	0.460000	0.39030	GAG	.	.		0.403	DZIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353968.1	NM_014648		T	108396438	A	T	108396438	3	4	344	1	0	0	0	0	1	0	0	0	4867	304	11	4	2974	4	DZIP3	3	108396438	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	96	108396438	89625992	301	47664										
TRAT1	50852	hgsc.bcm.edu	37	chr3	108572586	108572586	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gatggagatgagcaactacaTgcaatagatgccagcgtttc	11	8	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:108572586T>G	ENST00000295756.6	+	6	653	c.423T>G	c.(421-423)caT>caG	p.H141Q	TRAT1_ENST00000426646.1_Missense_Mutation_p.H104Q	NM_016388.2	NP_057472.2	Q6PIZ9	TRAT1_HUMAN	T cell receptor associated transmembrane adaptor 1	141					cellular defense response (GO:0006968)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|negative regulation of receptor recycling (GO:0001920)|negative regulation of transport (GO:0051051)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of T cell receptor signaling pathway (GO:0050862)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)			endometrium(2)|kidney(2)|large_intestine(2)|lung(18)|prostate(1)|skin(3)	28						AGCAACTACATGCAATAGATG	0.463																																					p.H141Q		Atlas-SNP	.											.	TRAT1	48	.	0			c.T423G						.						107	96	100					3																	108572586		2203	4300	6503	SO:0001583	missense	50852	exon6			ACTACATGCAATA	AJ240084	CCDS33813.1	3q13	2005-05-04	2005-05-04	2005-05-04	ENSG00000163519	ENSG00000163519			30698	protein-coding gene	gene with protein product		604962	"T cell receptor interacting molecule"	TCRIM		10663578, 9687533	Standard	NM_016388		Approved	HSPC062, TRIM	uc003dxi.1	Q6PIZ9	OTTHUMG00000159198	ENST00000295756.6:c.423T>G	chr3.hg19:g.108572586T>G	ENSP00000295756:p.His141Gln	384.0	0.0		328.0	165.0	NM_016388	Q9NZX5	Missense_Mutation	SNP	ENST00000295756.6	hg19	CCDS33813.1	.	.	.	.	.	.	.	.	.	.	T	10.49	1.364422	0.24684	.	.	ENSG00000163519	ENST00000295756;ENST00000426646	T;T	0.34275	1.37;1.56	5.53	-2.98	0.05513	.	1.154570	0.06272	N	0.695795	T	0.25754	0.0627	L	0.47716	1.5	0.09310	N	1	B;B	0.16396	0.017;0.007	B;B	0.17433	0.018;0.015	T	0.27905	-1.0060	10	0.34782	T	0.22	-0.3621	1.8337	0.03135	0.1481:0.3672:0.1528:0.3319	.	104;141	C9JF66;Q6PIZ9	.;TRAT1_HUMAN	Q	141;104	ENSP00000295756:H141Q;ENSP00000410097:H104Q	ENSP00000295756:H141Q	H	+	3	2	TRAT1	110055276	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.029000	0.12329	-0.513000	0.06496	0.533000	0.62120	CAT	.	.		0.463	TRAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353794.1	NM_016388		G	108572586	T	G	108572586	3	3	344	1	0	0	0	0	1	0	0	0	16481	1461	51	5	445	5	TRAT1	3	108572586	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	176148	108572586	89449844	302	47665										
SLC9A10	285335	hgsc.bcm.edu	37	chr3	111888053	111888053	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcacttcctacctcataagaTaagtgttctctgatttttct	5	10	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:111888053T>C	ENST00000305815.5	-	24	3294	c.3042A>G	c.(3040-3042)ttA>ttG	p.L1014L	SLC9C1_ENST00000487372.1_Silent_p.L966L	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	1014					cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										CCTCATAAGATAAGTGTTCTC	0.323																																					p.L1014L		Atlas-SNP	.											.	.	.	.	0			c.A3042G						.						102	99	100					3																	111888053		2203	4300	6503	SO:0001819	synonymous_variant	285335	exon24			ATAAGATAAGTGT	AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"Solute carriers"	31401	protein-coding gene	gene with protein product	"sperm-NHE"	612738	"solute carrier family 9, isoform 10", "solute carrier family 9, member 10"	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.3042A>G	chr3.hg19:g.111888053T>C		68.0	0.0		75.0	28.0	NM_183061	Q6ZRP4|Q7RTP2	Silent	SNP	ENST00000305815.5	hg19	CCDS33817.1																																																																																			.	.		0.323	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061		C	111888053	T	C	111888053	2	2	344	1	0	0	0	0	0	0	0	1	14725	1403	49	2		2	SLC9A10	3	111888053	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	3315467	111888053	86134377	303	47666										
CCDC80	151887	hgsc.bcm.edu	37	chr3	112357721	112357721	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtggctctgggggttgagggAggttggggcaaagctggtgc	22	5	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:112357721A>T	ENST00000206423.3	-	2	1985	c.1032T>A	c.(1030-1032)ccT>ccA	p.P344P	CCDC80_ENST00000439685.2_Silent_p.P344P|CCDC80_ENST00000475181.1_5'Flank	NM_199511.1|NM_199512.1	NP_955805.1|NP_955806.1	Q76M96	CCD80_HUMAN	coiled-coil domain containing 80	344					extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(21)|ovary(3)|pancreas(2)|prostate(4)	51						GGGTTGAGGGAGGTTGGGGCA	0.602																																					p.P344P		Atlas-SNP	.											.	CCDC80	100	.	0			c.T1032A						.						77	74	75					3																	112357721		2203	4300	6503	SO:0001819	synonymous_variant	151887	exon2			TGAGGGAGGTTGG	AY333429	CCDS2968.1	3q13.2	2010-12-24			ENSG00000091986	ENSG00000091986			30649	protein-coding gene	gene with protein product	"steroid sensitive gene 1"	608298				15325258, 18178152	Standard	XM_005247135		Approved	URB, SSG1, DRO1	uc003dzf.3	Q76M96	OTTHUMG00000159265	ENST00000206423.3:c.1032T>A	chr3.hg19:g.112357721A>T		45.0	0.0		29.0	9.0	NM_199511	D3DN67|Q5PR20|Q6GPG9|Q8IVT6|Q8NBV1|Q8NHY8	Silent	SNP	ENST00000206423.3	hg19	CCDS2968.1																																																																																			.	.		0.602	CCDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354219.1	NM_199511		T	112357721	A	T	112357721	2	4	344	1	0	0	0	0	0	0	0	1	2856	291	11	4		4	CCDC80	3	112357721	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	469668	112357721	85664709	304	47667										
WDR52	55779	hgsc.bcm.edu	37	chr3	113092276	113092276	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acttgaaagtgatagtttggAtgggattgtcctctgtatcc	11	6	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:113092276A>G	ENST00000295868.2	-	18	2588	c.2426T>C	c.(2425-2427)aTc>aCc	p.I809T	WDR52_ENST00000393845.2_Missense_Mutation_p.I809T	NM_018338.3	NP_060808.2														breast(2)|central_nervous_system(3)|endometrium(3)|kidney(5)|large_intestine(7)|lung(26)|prostate(1)|urinary_tract(2)	49						GATAGTTTGGATGGGATTGTC	0.368																																					p.I809T		Atlas-SNP	.											.	WDR52	151	.	0			c.T2426C						.						145	136	139					3																	113092276		2203	4300	6503	SO:0001583	missense	55779	exon18			GTTTGGATGGGAT																												ENST00000295868.2:c.2426T>C	chr3.hg19:g.113092276A>G	ENSP00000295868:p.Ile809Thr	79.0	0.0		90.0	37.0	NM_001164496		Missense_Mutation	SNP	ENST00000295868.2	hg19	CCDS2972.1	.	.	.	.	.	.	.	.	.	.	A	15.33	2.800865	0.50315	.	.	ENSG00000206530	ENST00000393845;ENST00000295868	T;T	0.22743	1.94;1.94	5.39	5.39	0.77823	WD40 repeat-like-containing domain (1);	.	.	.	.	T	0.27765	0.0683	M	0.62723	1.935	0.80722	D	1	D	0.53619	0.961	P	0.44597	0.454	T	0.06679	-1.0813	9	0.87932	D	0	.	13.9334	0.64010	1.0:0.0:0.0:0.0	.	809	Q96MT7	WDR52_HUMAN	T	809	ENSP00000377428:I809T;ENSP00000295868:I809T	ENSP00000295868:I809T	I	-	2	0	WDR52	114574966	0.999000	0.42202	0.386000	0.26170	0.237000	0.25408	7.044000	0.76578	2.180000	0.69256	0.533000	0.62120	ATC	.	.		0.368	WDR52-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354128.3			G	113092276	A	G	113092276	3	3	344	1	0	0	0	0	1	0	0	0	17319	333	12	2	3225	2	WDR52	3	113092276	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	734555	113092276	84930154	305	47668										
ATP6V1A	523	hgsc.bcm.edu	37	chr3	113524316	113524316	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acaataaaatcacatggtccAttattcgtgagcacatggga	8	8	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:113524316A>G	ENST00000273398.3	+	14	1813	c.1705A>G	c.(1705-1707)Att>Gtt	p.I569V	ATP6V1A_ENST00000461496.1_3'UTR|ATP6V1A_ENST00000538620.1_Missense_Mutation_p.I536V	NM_001690.3	NP_001681.2	P38606	VATA_HUMAN	ATPase, H+ transporting, lysosomal 70kDa, V1 subunit A	569					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|microvillus (GO:0005902)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	ATP binding (GO:0005524)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34					Alendronate(DB00630)|Etidronic acid(DB01077)|Tiludronate(DB01133)	CACATGGTCCATTATTCGTGA	0.383																																					p.I569V		Atlas-SNP	.											.	ATP6V1A	71	.	0			c.A1705G						.						126	116	120					3																	113524316		2203	4300	6503	SO:0001583	missense	523	exon14			TGGTCCATTATTC	L09235	CCDS2976.1	3q13.31	2010-04-21	2002-08-29	2003-04-25	ENSG00000114573	ENSG00000114573	3.6.3.14	"ATPases / V-type"	851	protein-coding gene	gene with protein product		607027	"ATPase, H+ transporting, lysosomal (vacuolar proton pump), alpha polypeptide, 70kD, isoform 1"	VPP2, ATP6A1, ATP6V1A1		8463241	Standard	NM_001690		Approved	Vma1, VA68	uc003eao.3	P38606	OTTHUMG00000159295	ENST00000273398.3:c.1705A>G	chr3.hg19:g.113524316A>G	ENSP00000273398:p.Ile569Val	182.0	0.0		176.0	74.0	NM_001690	B2RBR8|B7Z1R5|D3DN75|Q53YD9|Q96DY6|Q9UHY3	Missense_Mutation	SNP	ENST00000273398.3	hg19	CCDS2976.1	.	.	.	.	.	.	.	.	.	.	A	12.66	2.005034	0.35415	.	.	ENSG00000114573	ENST00000545842;ENST00000273398;ENST00000538620	D;T	0.85339	-1.97;-1.19	5.96	3.62	0.41486	ATPase, F1/V1/A1 complex, alpha/beta subunit, C-terminal (2);	0.236343	0.49916	D	0.000139	T	0.70245	0.3202	N	0.12637	0.245	0.42169	D	0.991638	B	0.02656	0.0	B	0.04013	0.001	T	0.62723	-0.6794	10	0.27785	T	0.31	-5.6535	9.9765	0.41786	0.8644:0.0:0.1356:0.0	.	569	P38606	VATA_HUMAN	V	286;569;536	ENSP00000273398:I569V;ENSP00000439874:I536V	ENSP00000273398:I569V	I	+	1	0	ATP6V1A	115007006	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.284000	0.72652	1.081000	0.41110	0.533000	0.62120	ATT	.	.		0.383	ATP6V1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354457.1	NM_001690		G	113524316	A	G	113524316	3	3	344	1	0	0	0	0	1	0	0	0	1177	217	8	2	1755	2	ATP6V1A	3	113524316	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	432040	113524316	84498114	306	47669										
ARHGAP31	57514	hgsc.bcm.edu	37	chr3	119133814	119133814	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cttcagagagttctctggccTgaaaggggcagaggctcctc	13	11	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:119133814T>A	ENST00000264245.4	+	12	3570	c.3038T>A	c.(3037-3039)cTg>cAg	p.L1013Q		NM_020754.2	NP_065805.2	Q2M1Z3	RHG31_HUMAN	Rho GTPase activating protein 31	1013					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(3)|large_intestine(11)|lung(29)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	67						TTCTCTGGCCTGAAAGGGGCA	0.567																																					p.L1013Q	Pancreas(7;176 297 5394 51128 51241)	Atlas-SNP	.											.	ARHGAP31	175	.	0			c.T3038A						.						47	52	50					3																	119133814		1925	4141	6066	SO:0001583	missense	57514	exon12			CTGGCCTGAAAGG		CCDS43135.1	3q13.33	2011-06-29			ENSG00000031081	ENSG00000031081		"Rho GTPase activating proteins"	29216	protein-coding gene	gene with protein product		610911				9786927, 12819203, 16519628	Standard	NM_020754		Approved	CDGAP	uc003ecj.4	Q2M1Z3	OTTHUMG00000159362	ENST00000264245.4:c.3038T>A	chr3.hg19:g.119133814T>A	ENSP00000264245:p.Leu1013Gln	65.0	0.0		65.0	23.0	NM_020754	Q9ULL6	Missense_Mutation	SNP	ENST00000264245.4	hg19	CCDS43135.1	.	.	.	.	.	.	.	.	.	.	T	8.950	0.968067	0.18659	.	.	ENSG00000031081	ENST00000264245;ENST00000543280	T	0.08458	3.09	4.83	0.567	0.17325	.	0.663208	0.13049	N	0.417886	T	0.04998	0.0134	N	0.24115	0.695	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.37291	-0.9712	10	0.48119	T	0.1	.	3.3306	0.07083	0.4459:0.2839:0.0:0.2702	.	1013	Q2M1Z3	RHG31_HUMAN	Q	1013	ENSP00000264245:L1013Q	ENSP00000264245:L1013Q	L	+	2	0	ARHGAP31	120616504	0.000000	0.05858	0.855000	0.33649	0.919000	0.55068	-0.498000	0.06420	0.197000	0.20387	0.459000	0.35465	CTG	.	.		0.567	ARHGAP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354942.2			A	119133814	T	A	119133814	3	1	344	1	0	0	0	0	1	0	0	0	880	1580	55	4	3084	4	ARHGAP31	3	119133814	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	5609498	119133814	78888616	307	47670										
GPR156	165829	hgsc.bcm.edu	37	chr3	119886437	119886437	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgtagcctgctgtgtgccccAggaacagtcctgtttgcccg	12	13	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:119886437A>T	ENST00000464295.1	-	10	2332	c.1887T>A	c.(1885-1887)ccT>ccA	p.P629P	GPR156_ENST00000315843.3_Silent_p.P629P|GPR156_ENST00000461057.1_Silent_p.P625P			Q8NFN8	GP156_HUMAN	G protein-coupled receptor 156	629						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled GABA receptor activity (GO:0004965)			breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|ovary(1)|prostate(1)|skin(1)	32				GBM - Glioblastoma multiforme(114;0.19)		TGTGTGCCCCAGGAACAGTCC	0.592																																					p.P629P		Atlas-SNP	.											.	GPR156	85	.	0			c.T1887A						.						49	50	49					3																	119886437		2203	4300	6503	SO:0001819	synonymous_variant	165829	exon9			TGCCCCAGGAACA	AF488739	CCDS2997.1, CCDS54629.1	3q13.33	2012-08-21			ENSG00000175697	ENSG00000175697		"GPCR / Class C : Orphans"	20844	protein-coding gene	gene with protein product		610464				12591167	Standard	NM_153002		Approved	PGR28, GABABL	uc011bjf.2	Q8NFN8	OTTHUMG00000159406	ENST00000464295.1:c.1887T>A	chr3.hg19:g.119886437A>T		53.0	0.0		43.0	24.0	NM_153002	B7ZL66|E9PFZ4|Q14CM1|Q86SN6	Silent	SNP	ENST00000464295.1	hg19	CCDS2997.1																																																																																			.	.		0.592	GPR156-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355139.1	NM_153002		T	119886437	A	T	119886437	2	4	344	1	0	0	0	0	0	0	0	1	6669	175	7	4		4	GPR156	3	119886437	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	752623	119886437	78135993	308	47671										
STXBP5L	9515	hgsc.bcm.edu	37	chr3	120871322	120871322	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgattgttctaatgttttccAgctgctaataggttatgaaa	8	5	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:120871322A>G	ENST00000273666.6	+	8	940		c.e8-1		STXBP5L_ENST00000471454.1_Splice_Site|STXBP5L_ENST00000492541.1_Splice_Site|STXBP5L_ENST00000472879.1_Splice_Site|STXBP5L_ENST00000497029.1_Splice_Site	NM_014980.2	NP_055795.1	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like						exocytosis (GO:0006887)|glucose homeostasis (GO:0042593)|negative regulation of insulin secretion (GO:0046676)|positive regulation of protein secretion (GO:0050714)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(12)|lung(28)|ovary(7)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				GBM - Glioblastoma multiforme(114;0.0694)		AATGTTTTCCAGCTGCTAATA	0.279																																					.		Atlas-SNP	.											.	STXBP5L	159	.	0			c.670-2A>G						.						104	100	101					3																	120871322		1809	4072	5881	SO:0001630	splice_region_variant	9515	exon8			TTTTCCAGCTGCT	AB023223	CCDS43137.1	3q13.33-q21.1	2013-01-10			ENSG00000145087	ENSG00000145087		"WD repeat domain containing"	30757	protein-coding gene	gene with protein product		609381				10231032, 14767561	Standard	NM_014980		Approved	KIAA1006, LLGL4	uc003eec.4	Q9Y2K9	OTTHUMG00000159426	ENST00000273666.6:c.670-1A>G	chr3.hg19:g.120871322A>G		72.0	0.0		47.0	20.0	NM_014980	Q4G1B4|Q6PIC3	Splice_Site	SNP	ENST00000273666.6	hg19	CCDS43137.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.509066	0.85282	.	.	ENSG00000145087	ENST00000273666;ENST00000471454;ENST00000472879;ENST00000497029;ENST00000492541;ENST00000471262	.	.	.	5.58	5.58	0.84498	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7282	0.69360	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	STXBP5L	122354012	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.224000	0.89781	2.108000	0.64289	0.533000	0.62120	.	.	.		0.279	STXBP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355256.3		Intron	G	120871322	A	G	120871322	5	3	344	1	0	0	0	0	0	0	1	0	15372	202	7	2	694	2	STXBP5L	3	120871322	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	984885	120871322	77151108	309	47672										
POLQ	10721	hgsc.bcm.edu	37	chr3	121263593	121263593	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cctgaataaactaaattcttTccttccaggacttgtccaag	5	11	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:121263593T>G	ENST00000264233.5	-	2	452	c.324A>C	c.(322-324)ggA>ggC	p.G108G		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	108	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		CTAAATTCTTTCCTTCCAGGA	0.338								DNA polymerases (catalytic subunits)																													p.G108G	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.A324C						.						69	70	70					3																	121263593		2203	4300	6503	SO:0001819	synonymous_variant	10721	exon2			ATTCTTTCCTTCC	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.324A>C	chr3.hg19:g.121263593T>G		166.0	0.0		159.0	67.0	NM_199420	O95160|Q6VMB5	Silent	SNP	ENST00000264233.5	hg19	CCDS33833.1																																																																																			.	.		0.338	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		G	121263593	T	G	121263593	2	3	344	1	0	0	0	0	0	0	0	1	12217	1770	62	5		5	POLQ	3	121263593	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	392271	121263593	76758837	310	47673										
CD86	942	hgsc.bcm.edu	37	chr3	121828150	121828150	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctcccccagaccacattcctTggattacagctgtacttcca	5	16	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:121828150T>C	ENST00000330540.2	+	5	858	c.742T>C	c.(742-744)Tgg>Cgg	p.W248R	CD86_ENST00000469710.1_Missense_Mutation_p.W166R|CD86_ENST00000493101.1_Missense_Mutation_p.W136R|CD86_ENST00000393627.2_Missense_Mutation_p.W242R|CD86_ENST00000264468.5_Missense_Mutation_p.W35R	NM_175862.4	NP_787058	P42081	CD86_HUMAN	CD86 molecule	248					aging (GO:0007568)|B cell activation (GO:0042113)|cell-cell signaling (GO:0007267)|cellular response to cytokine stimulus (GO:0071345)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to metal ion (GO:0071248)|defense response to virus (GO:0051607)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|immune response (GO:0006955)|innate immune response (GO:0045087)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of T cell anergy (GO:0002668)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 biosynthetic process (GO:0045404)|positive regulation of lymphotoxin A biosynthetic process (GO:0043017)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|positive regulation of transcription, DNA-templated (GO:0045893)|response to drug (GO:0042493)|response to interferon-gamma (GO:0034341)|response to yeast (GO:0001878)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|T cell proliferation involved in immune response (GO:0002309)|toll-like receptor signaling pathway (GO:0002224)|viral process (GO:0016032)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)|receptor activity (GO:0004872)			breast(2)|endometrium(1)|kidney(1)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(3)	23				GBM - Glioblastoma multiforme(114;0.156)	Abatacept(DB01281)|Antithymocyte globulin(DB00098)|Belatacept(DB06681)	CCACATTCCTTGGATTACAGC	0.423																																					p.W248R	GBM(67;1379 1389 36064 39806)	Atlas-SNP	.											.	CD86	43	.	0			c.T742C						.						119	109	112					3																	121828150		2203	4300	6503	SO:0001583	missense	942	exon5			ATTCCTTGGATTA		CCDS3009.1, CCDS43138.1, CCDS56272.1, CCDS56273.1, CCDS74991.1	3q21	2013-01-29	2006-03-28		ENSG00000114013	ENSG00000114013		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1705	protein-coding gene	gene with protein product	"B-lymphocyte antigen B7-2"	601020	"CD86 antigen (CD28 antigen ligand 2, B7-2 antigen)"	CD28LG2		7513726	Standard	NM_006889		Approved	B7.2, B7-2	uc003eet.3	P42081	OTTHUMG00000159482	ENST00000330540.2:c.742T>C	chr3.hg19:g.121828150T>C	ENSP00000332049:p.Trp248Arg	106.0	0.0		93.0	38.0	NM_175862	A0N0P0|B7Z2F3|B7Z702|E7ETN5|E9PC27|Q13655|Q6FHB1|Q6GTS4|Q7M4L5	Missense_Mutation	SNP	ENST00000330540.2	hg19	CCDS3009.1	.	.	.	.	.	.	.	.	.	.	T	14.00	2.404570	0.42613	.	.	ENSG00000114013	ENST00000469710;ENST00000493101;ENST00000330540;ENST00000264468;ENST00000393627	T;T;T;T;T	0.44083	3.27;2.46;4.22;0.93;4.24	4.3	0.558	0.17266	.	1.112010	0.06841	N	0.795690	T	0.52996	0.1769	L	0.54323	1.7	0.09310	N	1	D;D	0.67145	0.996;0.98	D;P	0.65443	0.935;0.809	T	0.36237	-0.9756	10	0.87932	D	0	0.0976	3.7037	0.08392	0.0:0.2025:0.1913:0.6062	.	136;248	E9PC27;P42081	.;CD86_HUMAN	R	166;136;248;35;242	ENSP00000418988:W166R;ENSP00000420230:W136R;ENSP00000332049:W248R;ENSP00000264468:W35R;ENSP00000377248:W242R	ENSP00000264468:W35R	W	+	1	0	CD86	123310840	0.664000	0.27457	0.001000	0.08648	0.014000	0.08584	0.943000	0.29030	0.086000	0.17137	0.533000	0.62120	TGG	.	.		0.423	CD86-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000355671.1	NM_006889		C	121828150	T	C	121828150	3	2	344	1	0	0	0	0	1	0	0	0	3045	1812	63	2	760	2	CD86	3	121828150	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	564557	121828150	76194280	311	47674										
UROC1	131669	hgsc.bcm.edu	37	chr3	126219694	126219694	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccaagcactcccccgtcgtgTccaattcgtggaccaggcgc	10	17	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:126219694T>C	ENST00000290868.2	-	11	1042	c.989A>G	c.(988-990)gAc>gGc	p.D330G	UROC1_ENST00000383579.3_Missense_Mutation_p.D390G	NM_144639.2	NP_653240.1	Q96N76	HUTU_HUMAN	urocanate hydratase 1	330					cellular nitrogen compound metabolic process (GO:0034641)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	urocanate hydratase activity (GO:0016153)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(1)|skin(1)	39				GBM - Glioblastoma multiforme(114;0.17)		CCCCGTCGTGTCCAATTCGTG	0.642																																					p.D390G		Atlas-SNP	.											.	UROC1	150	.	0			c.A1169G						.						71	65	67					3																	126219694		2203	4300	6503	SO:0001583	missense	131669	exon12			GTCGTGTCCAATT	AK055862	CCDS3038.1, CCDS54636.1	3q21.2	2012-08-21	2012-08-21		ENSG00000159650	ENSG00000159650	4.2.1.49		26444	protein-coding gene	gene with protein product	"urocanase 1"	613012	"urocanase domain containing 1"			19304569	Standard	NM_144639		Approved	FLJ31300, HMFN0320	uc010hsi.2	Q96N76	OTTHUMG00000162753	ENST00000290868.2:c.989A>G	chr3.hg19:g.126219694T>C	ENSP00000290868:p.Asp330Gly	72.0	0.0		57.0	22.0	NM_001165974	E9PE13|Q14C64|Q68CJ7	Missense_Mutation	SNP	ENST00000290868.2	hg19	CCDS3038.1	.	.	.	.	.	.	.	.	.	.	t	14.58	2.579013	0.46006	.	.	ENSG00000159650	ENST00000290868;ENST00000383579	T;T	0.58797	0.32;0.31	4.94	3.76	0.43208	Urocanase domain (2);	0.291855	0.38837	N	0.001557	T	0.56761	0.2007	L	0.57536	1.79	0.40986	D	0.984814	B;B	0.26147	0.087;0.143	B;B	0.37198	0.158;0.243	T	0.56962	-0.7892	10	0.59425	D	0.04	-30.2383	8.7838	0.34807	0.0:0.0:0.1909:0.8091	.	390;330	E9PE13;Q96N76	.;HUTU_HUMAN	G	330;390	ENSP00000290868:D330G;ENSP00000373073:D390G	ENSP00000290868:D330G	D	-	2	0	UROC1	127702384	1.000000	0.71417	0.868000	0.34077	0.695000	0.40330	5.776000	0.68924	0.720000	0.32209	0.398000	0.26397	GAC	.	.		0.642	UROC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370325.2	NM_144639		C	126219694	T	C	126219694	3	2	344	1	0	0	0	0	1	0	0	0	17043	1667	58	2	1081	2	UROC1	3	126219694	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	4391544	126219694	71802736	312	47675										
PODXL2	50512	hgsc.bcm.edu	37	chr3	127379659	127379659	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggaccaggactccaccagccAagaggcagaggccacagtgc	13	14	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:127379659A>C	ENST00000342480.6	+	3	827	c.788A>C	c.(787-789)cAa>cCa	p.Q263P		NM_015720.2	NP_056535.1	Q9NZ53	PDXL2_HUMAN	podocalyxin-like 2	263					leukocyte tethering or rolling (GO:0050901)	integral component of plasma membrane (GO:0005887)	glycosaminoglycan binding (GO:0005539)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	26						TCCACCAGCCAAGAGGCAGAG	0.622																																					p.Q263P		Atlas-SNP	.											.	PODXL2	53	.	0			c.A788C						.						32	36	34					3																	127379659		2203	4300	6503	SO:0001583	missense	50512	exon3			CCAGCCAAGAGGC	AF219137	CCDS3044.1	3q21.3	2005-02-18			ENSG00000114631	ENSG00000114631			17936	protein-coding gene	gene with protein product	"endoglycan"					10722749	Standard	NM_015720		Approved	PODLX2, endoglycan	uc003ejq.3	Q9NZ53	OTTHUMG00000159642	ENST00000342480.6:c.788A>C	chr3.hg19:g.127379659A>C	ENSP00000345359:p.Gln263Pro	121.0	0.0		138.0	60.0	NM_015720	Q6UVY4|Q8WUV6	Missense_Mutation	SNP	ENST00000342480.6	hg19	CCDS3044.1	.	.	.	.	.	.	.	.	.	.	A	8.199	0.797645	0.16327	.	.	ENSG00000114631	ENST00000342480;ENST00000302192	T	0.24538	1.85	4.67	-2.38	0.06622	.	1.062980	0.07431	N	0.895679	T	0.13927	0.0337	N	0.24115	0.695	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.31024	-0.9958	10	0.56958	D	0.05	-0.4626	1.9353	0.03335	0.3273:0.1714:0.366:0.1353	.	263	Q9NZ53	PDXL2_HUMAN	P	263	ENSP00000345359:Q263P	ENSP00000304498:Q263P	Q	+	2	0	PODXL2	128862349	0.001000	0.12720	0.000000	0.03702	0.088000	0.18126	-0.001000	0.12947	-0.642000	0.05480	0.402000	0.26972	CAA	.	.		0.622	PODXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356638.1	NM_015720		C	127379659	A	C	127379659	3	2	344	1	0	0	0	0	1	0	0	0	12190	130	5	5	798	5	PODXL2	3	127379659	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1159965	127379659	70642771	313	47676										
CNBP	7555	hgsc.bcm.edu	37	chr3	128890513	128890513	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	accacctctgccacggcttcTcattccacgaccacggcctc	6	20	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:128890513T>A	ENST00000422453.2	-	2	248	c.88A>T	c.(88-90)Aga>Tga	p.R30*	CNBP_ENST00000504813.1_Nonsense_Mutation_p.R30*|CNBP_ENST00000451728.2_Nonsense_Mutation_p.R30*|CNBP_ENST00000441626.2_Nonsense_Mutation_p.R30*|CNBP_ENST00000500450.2_Nonsense_Mutation_p.R30*|CNBP_ENST00000502976.1_Nonsense_Mutation_p.R30*|CNBP_ENST00000446936.2_Nonsense_Mutation_p.R30*	NM_001127192.1|NM_001127193.1|NM_003418.4	NP_001120664.1|NP_001120665.1|NP_003409.1	P62633	CNBP_HUMAN	CCHC-type zinc finger, nucleic acid binding protein	30	Arg/Gly-rich.				cholesterol biosynthetic process (GO:0006695)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			biliary_tract(1)|endometrium(1)|kidney(1)|lung(2)	5						CCACGGCTTCTCATTCCACGA	0.493																																					p.R30X		Atlas-SNP	.											.	CNBP	12	.	0			c.A88T						.						57	57	57					3																	128890513		2203	4300	6503	SO:0001587	stop_gained	7555	exon2			GGCTTCTCATTCC	U19765	CCDS3056.1, CCDS46906.1, CCDS46907.1, CCDS46908.1, CCDS54637.1	3q21	2013-01-09	2006-06-29	2006-06-29				"RING-type (C3HC4) zinc fingers", "Zinc fingers, CCHC domain containing"	13164	protein-coding gene	gene with protein product		116955	"zinc finger protein 9 (a cellular retroviral nucleic acid binding protein)", "zinc finger protein 9"	DM2, ZNF9		2249857, 11486088	Standard	NM_003418		Approved	RNF163, ZCCHC22, CNBP1	uc021xdw.1	P62633		ENST00000422453.2:c.88A>T	chr3.hg19:g.128890513T>A	ENSP00000410619:p.Arg30*	367.0	1.0		293.0	141.0	NM_003418	A8K7V4|B2RAV9|B4DP17|D3DNB9|D3DNC0|D3DNC1|E9PDR7|P20694|Q4JGY0|Q4JGY1|Q5QJR0|Q5U0E9|Q6PJI7|Q96NV3	Nonsense_Mutation	SNP	ENST00000422453.2	hg19	CCDS3056.1	.	.	.	.	.	.	.	.	.	.	T	36	5.642099	0.96704	.	.	ENSG00000169714	ENST00000502976;ENST00000422453;ENST00000451728;ENST00000446936;ENST00000500450;ENST00000504813;ENST00000441626;ENST00000512338	.	.	.	5.84	4.73	0.59995	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22109	T	0.4	0.4251	11.0137	0.47677	0.0:0.0:0.1904:0.8096	.	.	.	.	X	30	.	ENSP00000410619:R30X	R	-	1	2	CNBP	130373203	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.143000	0.42187	2.243000	0.73865	0.482000	0.46254	AGA	.	.		0.493	CNBP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000358419.1	NM_003418		A	128890513	T	A	128890513	4	1	344	1	0	0	0	0	0	1	0	0	3594	1559	54	4	467	4	CNBP	3	128890513	Nonsense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1510854	128890513	69131917	314	47677										
COL6A5	256076	hgsc.bcm.edu	37	chr3	130092493	130092493	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	actaacaaaatgaagatcttGctaattatatttgtcctaat	4	6	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:130092493G>A	ENST00000432398.2	+	2	506	c.12G>A	c.(10-12)ttG>ttA	p.L4L	COL6A5_ENST00000265379.6_Silent_p.L4L	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	0					cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						TGAAGATCTTGCTAATTATAT	0.254																																					p.L4L		Atlas-SNP	.											.	COL6A5	205	.	0			c.G12A						.						54	51	52					3																	130092493		692	1583	2275	SO:0001819	synonymous_variant	256076	exon2			GATCTTGCTAATT	AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"Collagens"	26674	protein-coding gene	gene with protein product	"von Willebrand factor A domain containing 4"	611916	"collagen, type XXIX, alpha 1"	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.12G>A	chr3.hg19:g.130092493G>A		457.0	0.0		388.0	150.0	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Silent	SNP	ENST00000432398.2	hg19																																																																																				.	.		0.254	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264		A	130092493	G	A	130092493	2	1	344	1	0	0	0	0	0	0	0	1	3704	1310	46	3		3	COL6A5	3	130092493	Silent	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1201980	130092493	67929937	315	47678										
COL6A6	131873	hgsc.bcm.edu	37	chr3	130281939	130281939	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtatgcagatgttgtgttttTggtggacagctctgatcgcc	13	7	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:130281939T>C	ENST00000358511.6	+	2	123	c.92T>C	c.(91-93)tTg>tCg	p.L31S	COL6A6_ENST00000453409.2_Missense_Mutation_p.L31S	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	31	Nonhelical region.|VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						GTTGTGTTTTTGGTGGACAGC	0.413																																					p.L31S		Atlas-SNP	.											.	COL6A6	497	.	0			c.T92C						.						181	171	174					3																	130281939		1932	4132	6064	SO:0001583	missense	131873	exon2			TGTTTTTGGTGGA	AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.92T>C	chr3.hg19:g.130281939T>C	ENSP00000351310:p.Leu31Ser	104.0	0.0		87.0	46.0	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	hg19	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	T	19.38	3.817212	0.70912	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	D;D	0.87256	-2.23;-2.23	5.66	5.66	0.87406	von Willebrand factor, type A (3);	0.000000	0.46442	D	0.000300	D	0.94981	0.8376	M	0.92880	3.355	0.46499	D	0.999079	D	0.89917	1.0	D	0.91635	0.999	D	0.96041	0.9024	10	0.87932	D	0	.	15.5484	0.76126	0.0:0.0:0.0:1.0	.	31	A6NMZ7	CO6A6_HUMAN	S	31	ENSP00000351310:L31S;ENSP00000399236:L31S	ENSP00000351310:L31S	L	+	2	0	COL6A6	131764629	1.000000	0.71417	1.000000	0.80357	0.550000	0.35303	7.643000	0.83403	2.153000	0.67306	0.459000	0.35465	TTG	.	.		0.413	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		C	130281939	T	C	130281939	3	2	344	1	0	0	0	0	1	0	0	0	3705	1821	63	2	98	2	COL6A6	3	130281939	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	189446	130281939	67740491	316	47679										
COL6A6	131873	hgsc.bcm.edu	37	chr3	130284329	130284329	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tagcatcccaccctgctgagCagtatgtctccaaactgaag	8	13	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:130284329C>A	ENST00000358511.6	+	3	1184	c.1153C>A	c.(1153-1155)Cag>Aag	p.Q385K	COL6A6_ENST00000453409.2_Missense_Mutation_p.Q385K	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	385	Nonhelical region.|VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						CCCTGCTGAGCAGTATGTCTC	0.532																																					p.Q385K		Atlas-SNP	.											.	COL6A6	497	.	0			c.C1153A						.						83	95	91					3																	130284329		2058	4194	6252	SO:0001583	missense	131873	exon3			GCTGAGCAGTATG	AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"Collagens"	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.1153C>A	chr3.hg19:g.130284329C>A	ENSP00000351310:p.Gln385Lys	117.0	0.0		101.0	46.0	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	hg19	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	C	8.754	0.921883	0.17982	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	D;D	0.82526	-1.62;-1.62	5.01	4.08	0.47627	von Willebrand factor, type A (3);	0.227271	0.31199	N	0.008062	T	0.71685	0.3369	N	0.25485	0.75	0.09310	N	1	B	0.09022	0.002	B	0.15052	0.012	T	0.56685	-0.7938	10	0.25106	T	0.35	.	12.3584	0.55188	0.2913:0.7087:0.0:0.0	.	385	A6NMZ7	CO6A6_HUMAN	K	385	ENSP00000351310:Q385K;ENSP00000399236:Q385K	ENSP00000351310:Q385K	Q	+	1	0	COL6A6	131767019	0.496000	0.26059	0.957000	0.39632	0.984000	0.73092	0.258000	0.18387	2.492000	0.84095	0.561000	0.74099	CAG	.	.		0.532	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		A	130284329	C	A	130284329	3	1	344	1	0	0	0	0	1	0	0	0	3705	711	25	3	1163	3	COL6A6	3	130284329	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	2390	130284329	67738101	317	47680										
ATP2C1	27032	hgsc.bcm.edu	37	chr3	130714897	130714897	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	taaatttcaggtctgcaatcGaagagggtaaagggatttat	11	4	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:130714897G>T	ENST00000510168.1	+	23	2618	c.2068G>T	c.(2068-2070)Gaa>Taa	p.E690*	ATP2C1_ENST00000504381.1_Nonsense_Mutation_p.E635*|ATP2C1_ENST00000508532.1_Nonsense_Mutation_p.E690*|ATP2C1_ENST00000505330.1_Nonsense_Mutation_p.E674*|ATP2C1_ENST00000328560.8_Nonsense_Mutation_p.E690*|ATP2C1_ENST00000393221.4_Nonsense_Mutation_p.E724*|ATP2C1_ENST00000507488.2_Nonsense_Mutation_p.E674*|ATP2C1_ENST00000533801.2_Nonsense_Mutation_p.E685*|ATP2C1_ENST00000513801.1_Nonsense_Mutation_p.E674*|ATP2C1_ENST00000504948.1_Nonsense_Mutation_p.E674*|ATP2C1_ENST00000422190.2_Nonsense_Mutation_p.E690*|ATP2C1_ENST00000359644.3_Nonsense_Mutation_p.E690*|ATP2C1_ENST00000428331.2_Nonsense_Mutation_p.E690*			P98194	AT2C1_HUMAN	ATPase, Ca++ transporting, type 2C, member 1	690					actin cytoskeleton reorganization (GO:0031532)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cellular calcium ion homeostasis (GO:0006874)|cellular manganese ion homeostasis (GO:0030026)|epidermis development (GO:0008544)|Golgi calcium ion homeostasis (GO:0032468)|Golgi calcium ion transport (GO:0032472)|ion transmembrane transport (GO:0034220)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-transporting ATPase activity (GO:0005388)|manganese ion binding (GO:0030145)|manganese-transporting ATPase activity (GO:0015410)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)	p.E690K(1)		breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(15)|prostate(2)|skin(2)|urinary_tract(1)	39					Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	GTCTGCAATCGAAGAGGGTAA	0.299									Hailey-Hailey disease																												p.E724X	Esophageal Squamous(99;456 1443 27647 34099 42636)	Atlas-SNP	.											ATP2C1,NS,carcinoma,0,5	ATP2C1	94	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2170T						.						78	93	88					3																	130714897		2202	4297	6499	SO:0001587	stop_gained	27032	exon22	Familial Cancer Database	HHD, Familial Benign Chronic Pemphigus, Benign Familial Pemphigus	GCAATCGAAGAGG	AF181120	CCDS33856.1, CCDS46912.1, CCDS46913.1, CCDS46914.1, CCDS56278.1, CCDS56279.1, CCDS56280.1, CCDS56281.1, CCDS75006.1	3q21.3	2012-10-22			ENSG00000017260	ENSG00000017260	3.6.3.8	"ATPases / P-type"	13211	protein-coding gene	gene with protein product	"secretory pathway Ca2+/Mn2+ ATPase 1", "calcium-transporting ATPase type 2C member 1"	604384	"benign chronic pemphigus (Hailey-Hailey disease)"	BCPM		10615129, 10767338	Standard	NM_001001485		Approved	KIAA1347, ATP2C1A, PMR1, SPCA1	uc011bli.2	P98194	OTTHUMG00000136802	ENST00000510168.1:c.2068G>T	chr3.hg19:g.130714897G>T	ENSP00000427461:p.Glu690*	30.0	0.0		23.0	10.0	NM_001199181	B2RAT7|B4DSW3|B7Z3X9|G3XAH8|G8JLN9|O76005|Q86V72|Q86V73|Q8N6V1|Q8NCJ7	Nonsense_Mutation	SNP	ENST00000510168.1	hg19	CCDS46914.1	.	.	.	.	.	.	.	.	.	.	G	42	9.520463	0.99193	.	.	ENSG00000017260	ENST00000505330;ENST00000504381;ENST00000507488;ENST00000393221;ENST00000533801;ENST00000510168;ENST00000508532;ENST00000504948;ENST00000513801;ENST00000328560;ENST00000428331;ENST00000359644;ENST00000422190;ENST00000347421	.	.	.	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	.	19.9312	0.97120	0.0:0.0:1.0:0.0	.	.	.	.	X	674;635;674;724;685;690;690;674;674;690;690;690;690;689	.	ENSP00000329664:E690X	E	+	1	0	ATP2C1	132197587	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.689000	0.98673	2.720000	0.93068	0.491000	0.48974	GAA	.	.		0.299	ATP2C1-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356648.2	NM_001001486		T	130714897	G	T	130714897	4	4	344	1	0	0	0	0	0	1	0	0	1143	1059	37	1	2154	1	ATP2C1	3	130714897	Nonsense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	430568	130714897	67307533	318	47681										
DNAJC13	23317	hgsc.bcm.edu	37	chr3	132153447	132153447	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atgtttctacacaacaaaacAttcatggagggggaagtaag	10	6	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:132153447A>G	ENST00000260818.6	+	2	301	c.53A>G	c.(52-54)cAt>cGt	p.H18R	DNAJC13_ENST00000486798.1_3'UTR	NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	18					osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						ACAACAAAACATTCATGGAGG	0.318																																					p.H18R		Atlas-SNP	.											.	DNAJC13	253	.	0			c.A53G						.						98	100	99					3																	132153447		2203	4300	6503	SO:0001583	missense	23317	exon2			CAAAACATTCATG	AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"Heat shock proteins / DNAJ (HSP40)"	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.53A>G	chr3.hg19:g.132153447A>G	ENSP00000260818:p.His18Arg	43.0	0.0		26.0	15.0	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Missense_Mutation	SNP	ENST00000260818.6	hg19	CCDS33857.1	.	.	.	.	.	.	.	.	.	.	A	17.28	3.349877	0.61183	.	.	ENSG00000138246	ENST00000260818	T	0.22539	1.95	5.35	4.19	0.49359	.	0.000000	0.85682	D	0.000000	T	0.43853	0.1266	M	0.74881	2.28	0.52501	D	0.999957	D;D	0.76494	0.999;0.998	D;D	0.76071	0.972;0.987	T	0.34875	-0.9811	10	0.59425	D	0.04	.	10.6146	0.45443	0.9225:0.0:0.0775:0.0	.	18;18	A7E2Y5;O75165	.;DJC13_HUMAN	R	18	ENSP00000260818:H18R	ENSP00000260818:H18R	H	+	2	0	DNAJC13	133636137	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.237000	0.78164	0.965000	0.38133	-0.290000	0.09829	CAT	.	.		0.318	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268		G	132153447	A	G	132153447	3	3	344	1	0	0	0	0	1	0	0	0	4634	217	8	2	55	2	DNAJC13	3	132153447	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1438550	132153447	65868983	319	47682										
TMEM108	66000	hgsc.bcm.edu	37	chr3	132948183	132948183	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaagtttacaggccctctatTgccaactgttaagtaagttg	9	8	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:132948183T>C	ENST00000321871.6	+	3	238	c.28T>C	c.(28-30)Tgc>Cgc	p.C10R	TMEM108_ENST00000393130.3_Missense_Mutation_p.C10R|TMEM108_ENST00000508711.1_Missense_Mutation_p.C10R|TMEM108_ENST00000515826.1_Missense_Mutation_p.C10R	NM_001136469.1|NM_023943.2	NP_001129941.1|NP_076432.1	Q6UXF1	TM108_HUMAN	transmembrane protein 108	10						integral component of membrane (GO:0016021)				endometrium(3)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						GGCCCTCTATTGCCAACTGTT	0.373																																					p.C10R		Atlas-SNP	.											.	TMEM108	67	.	0			c.T28C						.						117	109	111					3																	132948183		2203	4300	6503	SO:0001583	missense	66000	exon3			CTCTATTGCCAAC	AL136578	CCDS33858.1, CCDS75012.1	3q22.1	2014-04-07			ENSG00000144868	ENSG00000144868			28451	protein-coding gene	gene with protein product	"cancer/testis antigen 124"					11214970	Standard	XM_005247726		Approved	MGC3040, CT124	uc003epi.3	Q6UXF1	OTTHUMG00000159685	ENST00000321871.6:c.28T>C	chr3.hg19:g.132948183T>C	ENSP00000324651:p.Cys10Arg	60.0	0.0		44.0	14.0	NM_023943	D3DNC9|Q9BQH1|Q9BW81|Q9C0H3	Missense_Mutation	SNP	ENST00000321871.6	hg19	CCDS33858.1	.	.	.	.	.	.	.	.	.	.	T	16.89	3.247445	0.59103	.	.	ENSG00000144868	ENST00000321871;ENST00000393130;ENST00000512137;ENST00000511555;ENST00000508711;ENST00000515826;ENST00000510183	T;T;T;T;T;T	0.58652	0.32;0.32;0.32;0.32;0.32;0.32	5.53	5.53	0.82687	.	0.000000	0.41605	D	0.000849	T	0.70482	0.3229	L	0.51422	1.61	0.53005	D	0.999969	D;D;D	0.89917	0.988;1.0;1.0	D;D;D	0.87578	0.983;0.997;0.998	T	0.73369	-0.4004	10	0.87932	D	0	-6.193	13.6125	0.62088	0.0:0.0:0.0:1.0	.	10;10;10	B3KT64;E9PB58;Q6UXF1	.;.;TM108_HUMAN	R	10	ENSP00000324651:C10R;ENSP00000376838:C10R;ENSP00000426301:C10R;ENSP00000422196:C10R;ENSP00000423338:C10R;ENSP00000421486:C10R	ENSP00000324651:C10R	C	+	1	0	TMEM108	134430873	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.497000	0.53295	2.112000	0.64535	0.533000	0.62120	TGC	.	.		0.373	TMEM108-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356907.2	NM_023943		C	132948183	T	C	132948183	3	2	344	1	0	0	0	0	1	0	0	0	16039	1812	63	2	30	2	TMEM108	3	132948183	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	794736	132948183	65074247	320	47683										
TMEM108	66000	hgsc.bcm.edu	37	chr3	133099726	133099726	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aagctccaacccatccctccAgggtctcagaaagcactatt	6	15	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:133099726A>T	ENST00000321871.6	+	4	1381	c.1171A>T	c.(1171-1173)Agg>Tgg	p.R391W	TMEM108_ENST00000393130.3_Missense_Mutation_p.R391W|TMEM108_ENST00000508711.1_Intron|TMEM108_ENST00000515826.1_Missense_Mutation_p.R391W	NM_001136469.1|NM_023943.2	NP_001129941.1|NP_076432.1	Q6UXF1	TM108_HUMAN	transmembrane protein 108	391						integral component of membrane (GO:0016021)				endometrium(3)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						CCATCCCTCCAGGGTCTCAGA	0.612																																					p.R391W		Atlas-SNP	.											.	TMEM108	67	.	0			c.A1171T						.						51	51	51					3																	133099726		2203	4300	6503	SO:0001583	missense	66000	exon4			CCCTCCAGGGTCT	AL136578	CCDS33858.1, CCDS75012.1	3q22.1	2014-04-07			ENSG00000144868	ENSG00000144868			28451	protein-coding gene	gene with protein product	"cancer/testis antigen 124"					11214970	Standard	XM_005247726		Approved	MGC3040, CT124	uc003epi.3	Q6UXF1	OTTHUMG00000159685	ENST00000321871.6:c.1171A>T	chr3.hg19:g.133099726A>T	ENSP00000324651:p.Arg391Trp	69.0	0.0		66.0	29.0	NM_023943	D3DNC9|Q9BQH1|Q9BW81|Q9C0H3	Missense_Mutation	SNP	ENST00000321871.6	hg19	CCDS33858.1	.	.	.	.	.	.	.	.	.	.	A	4.291	0.053236	0.08291	.	.	ENSG00000144868	ENST00000321871;ENST00000393130;ENST00000515826	T;T;T	0.46063	0.89;0.89;0.88	3.53	-1.07	0.09968	.	1.603450	0.03647	N	0.240454	T	0.16128	0.0388	N	0.02011	-0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.11591	-1.0581	10	0.37606	T	0.19	-0.1295	1.256	0.01991	0.2725:0.1614:0.4031:0.163	.	391;391	E9PB58;Q6UXF1	.;TM108_HUMAN	W	391	ENSP00000324651:R391W;ENSP00000376838:R391W;ENSP00000423338:R391W	ENSP00000324651:R391W	R	+	1	2	TMEM108	134582416	0.001000	0.12720	0.146000	0.22360	0.578000	0.36192	0.367000	0.20382	-0.022000	0.13986	-1.467000	0.01014	AGG	.	.		0.612	TMEM108-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356907.2	NM_023943		T	133099726	A	T	133099726	3	4	344	1	0	0	0	0	1	0	0	0	16039	179	7	4	1177	4	TMEM108	3	133099726	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	151543	133099726	64922704	321	47684										
BFSP2	8419	hgsc.bcm.edu	37	chr3	133169265	133169265	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aattcagtgggagagagatgTtgaaaagaaccgggtggagg	17	3	1	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:133169265T>C	ENST00000302334.2	+	4	937	c.848T>C	c.(847-849)gTt>gCt	p.V283A	BFSP2_ENST00000511434.1_3'UTR|BFSP2-AS1_ENST00000515542.1_RNA	NM_003571.2	NP_003562.1	Q13515	BFSP2_HUMAN	beaded filament structural protein 2, phakinin	283	Rod.				cell maturation (GO:0048469)|intermediate filament cytoskeleton organization (GO:0045104)|lens fiber cell development (GO:0070307)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|urinary_tract(1)	13						GAGAGAGATGTTGAAAAGAAC	0.552																																					p.V283A		Atlas-SNP	.											BFSP2,NS,lymphoid_neoplasm,0,1	BFSP2	48	.	0			c.T848C						.						115	109	111					3																	133169265		2203	4300	6503	SO:0001583	missense	8419	exon4			GAGATGTTGAAAA	U48224	CCDS33859.1	3q22.1	2013-01-16			ENSG00000170819	ENSG00000170819		"Intermediate filaments type VI, eye lens intermediate filaments"	1041	protein-coding gene	gene with protein product		603212					Standard	NM_003571		Approved	CP47, CP49, LIFL-L, phakinin	uc003epn.1	Q13515	OTTHUMG00000159719	ENST00000302334.2:c.848T>C	chr3.hg19:g.133169265T>C	ENSP00000304987:p.Val283Ala	56.0	0.0		48.0	19.0	NM_003571	Q14D32|Q9HBW5	Missense_Mutation	SNP	ENST00000302334.2	hg19	CCDS33859.1	.	.	.	.	.	.	.	.	.	.	T	1.163	-0.643225	0.03531	.	.	ENSG00000170819	ENST00000302334	D	0.87334	-2.24	5.14	3.99	0.46301	Filament (1);	0.637750	0.14156	N	0.337739	T	0.71813	0.3384	N	0.10809	0.05	0.09310	N	1	B	0.10296	0.003	B	0.18263	0.021	T	0.52749	-0.8534	10	0.02654	T	1	-9.7624	10.7718	0.46327	0.0:0.0741:0.0:0.9259	.	283	Q13515	BFSP2_HUMAN	A	283	ENSP00000304987:V283A	ENSP00000304987:V283A	V	+	2	0	BFSP2	134651955	0.872000	0.30054	0.069000	0.20011	0.959000	0.62525	2.054000	0.41335	0.997000	0.38969	0.454000	0.30748	GTT	.	.		0.552	BFSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357031.1			C	133169265	T	C	133169265	3	2	344	1	0	0	0	0	1	0	0	0	1416	1725	60	2	862	2	BFSP2	3	133169265	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	69539	133169265	64853165	322	47685										
TOPBP1	11073	hgsc.bcm.edu	37	chr3	133372268	133372268	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggtctaggttctgtcttgtaTatggattcatcctgacaaaa	9	7	4	1	rs572308153		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:133372268T>C	ENST00000260810.5	-	7	974	c.843A>G	c.(841-843)atA>atG	p.I281M	TOPBP1_ENST00000511439.1_5'UTR	NM_007027.3	NP_008958.2	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	281	BRCT 2. {ECO:0000255|PROSITE- ProRule:PRU00033}.				cellular response to DNA damage stimulus (GO:0006974)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|response to ionizing radiation (GO:0010212)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(14)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	40						CTGTCTTGTATATGGATTCAT	0.403								Other conserved DNA damage response genes					T|||	1	0.000199681	8e-04	0	5008	,	,		14780	0		0	False		,,,				2504	0				p.I281M	Ovarian(21;193 658 4424 15423 17362)	Atlas-SNP	.											.	TOPBP1	218	.	0			c.A843G						.						187	176	180					3																	133372268		1894	4117	6011	SO:0001583	missense	11073	exon7			CTTGTATATGGAT	AB019397	CCDS46919.1	3q22.1	2004-06-21			ENSG00000163781	ENSG00000163781			17008	protein-coding gene	gene with protein product		607760				9461304, 9039502	Standard	NM_007027		Approved	KIAA0259, TOP2BP1	uc003eps.3	Q92547	OTTHUMG00000159773	ENST00000260810.5:c.843A>G	chr3.hg19:g.133372268T>C	ENSP00000260810:p.Ile281Met	78.0	0.0		68.0	26.0	NM_007027	B7Z7W8|Q7LGC1|Q9UEB9	Missense_Mutation	SNP	ENST00000260810.5	hg19	CCDS46919.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.86|13.86	2.363545|2.363545	0.41902|0.41902	.|.	.|.	ENSG00000163781|ENSG00000163781	ENST00000260810|ENST00000508524	T|.	0.57273|.	0.41|.	5.78|5.78	-9.35|-9.35	0.00633|0.00633	BRCT (2);|.	0.379952|.	0.33753|.	N|.	0.004581|.	T|T	0.13243|0.13243	0.0321|0.0321	N|N	0.01482|0.01482	-0.84|-0.84	0.32048|0.32048	N|N	0.597277|0.597277	B|.	0.06786|.	0.001|.	B|.	0.08055|.	0.003|.	T|T	0.35943|0.35943	-0.9768|-0.9768	10|5	0.30078|.	T|.	0.28|.	.|.	13.4997|13.4997	0.61447|0.61447	0.0811:0.7558:0.0:0.1631|0.0811:0.7558:0.0:0.1631	.|.	281|.	Q92547|.	TOPB1_HUMAN|.	M|C	281|126	ENSP00000260810:I281M|.	ENSP00000260810:I281M|.	I|Y	-|-	3|2	3|0	TOPBP1|TOPBP1	134854958|134854958	0.067000|0.067000	0.21026|0.21026	0.617000|0.617000	0.29091|0.29091	0.938000|0.938000	0.57974|0.57974	-0.605000|-0.605000	0.05661|0.05661	-2.042000|-2.042000	0.00914|0.00914	-1.013000|-1.013000	0.02462|0.02462	ATA|TAT	.	.		0.403	TOPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357254.1	NM_007027		C	133372268	T	C	133372268	3	2	344	1	0	0	0	0	1	0	0	0	16384	1396	49	2	3813	2	TOPBP1	3	133372268	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	203003	133372268	64650162	323	47686										
CEP63	80254	hgsc.bcm.edu	37	chr3	134265095	134265095	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aagttacaagaaaaagtaaaGgcaactaacactcaacatgc	6	8	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:134265095G>T	ENST00000337090.3	+	8	1067	c.894G>T	c.(892-894)aaG>aaT	p.K298N	CEP63_ENST00000354446.3_Missense_Mutation_p.K298N|CEP63_ENST00000332047.5_Missense_Mutation_p.K298N|CEP63_ENST00000513612.2_Missense_Mutation_p.K298N|CEP63_ENST00000383229.3_Missense_Mutation_p.K298N|CEP63_ENST00000606977.1_Missense_Mutation_p.K298N			Q96MT8	CEP63_HUMAN	centrosomal protein 63kDa	298					centriole replication (GO:0007099)|DNA damage checkpoint (GO:0000077)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|signal transduction in response to DNA damage (GO:0042770)|spindle assembly (GO:0051225)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|spindle pole (GO:0000922)				kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						AAAAAGTAAAGGCAACTAACA	0.348																																					p.K298N		Atlas-SNP	.											.	CEP63	56	.	0			c.G894T						.						100	104	102					3																	134265095		2203	4300	6503	SO:0001583	missense	80254	exon8			AGTAAAGGCAACT	AK056465	CCDS3086.1, CCDS43152.1, CCDS43153.1, CCDS43154.1	3q22.1	2014-02-20			ENSG00000182923	ENSG00000182923			25815	protein-coding gene	gene with protein product		614724				14654843, 24240477	Standard	NM_001042383		Approved	FLJ13386	uc003eqo.1	Q96MT8	OTTHUMG00000159725	ENST00000337090.3:c.894G>T	chr3.hg19:g.134265095G>T	ENSP00000336524:p.Lys298Asn	403.0	0.0		424.0	210.0	NM_001042383	D3DND8|D3DND9|D3DNE0|Q96CR0|Q9H8F5|Q9H8N0	Missense_Mutation	SNP	ENST00000337090.3	hg19	CCDS3086.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.876|9.876	1.200200|1.200200	0.22121|0.22121	.|.	.|.	ENSG00000182923|ENSG00000182923	ENST00000332047;ENST00000354446;ENST00000337090;ENST00000383229;ENST00000513612|ENST00000504929	T;T;T;T;T|.	0.32988|.	1.43;1.82;2.2;1.45;2.2|.	6.1|6.1	0.885|0.885	0.19188|0.19188	.|.	0.511065|.	0.21565|.	N|.	0.072511|.	T|T	0.43233|0.43233	0.1238|0.1238	M|M	0.61703|0.61703	1.905|1.905	0.09310|0.09310	N|N	1|1	B;P;B;B|.	0.40834|.	0.034;0.73;0.003;0.003|.	B;B;B;B|.	0.39531|.	0.021;0.302;0.003;0.003|.	T|T	0.33828|0.33828	-0.9853|-0.9853	10|5	0.21014|.	T|.	0.42|.	-12.681|-12.681	6.6051|6.6051	0.22721|0.22721	0.3358:0.0:0.5417:0.1225|0.3358:0.0:0.5417:0.1225	.|.	298;298;298;298|.	Q96MT8;Q96MT8-2;Q96MT8-4;Q96MT8-3|.	CEP63_HUMAN;.;.;.|.	N|M	298|33	ENSP00000328382:K298N;ENSP00000346432:K298N;ENSP00000336524:K298N;ENSP00000372716:K298N;ENSP00000426129:K298N|.	ENSP00000328382:K298N|.	K|R	+|+	3|2	2|0	CEP63|CEP63	135747785|135747785	0.000000|0.000000	0.05858|0.05858	0.034000|0.034000	0.17996|0.17996	0.019000|0.019000	0.09904|0.09904	-0.683000|-0.683000	0.05179|0.05179	0.475000|0.475000	0.27415|0.27415	0.650000|0.650000	0.86243|0.86243	AAG|AGG	.	.		0.348	CEP63-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000470139.1	NM_025180		T	134265095	G	T	134265095	3	4	344	1	0	0	0	0	1	0	0	0	3259	991	35	3	920	3	CEP63	3	134265095	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	892827	134265095	63757335	324	47687										
SPSB4	92369	hgsc.bcm.edu	37	chr3	140785585	140785585	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aagaagctgtacccggtggtGagtgccgtgtggggccactg	17	9	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:140785585G>T	ENST00000310546.2	+	2	1383	c.639G>T	c.(637-639)gtG>gtT	p.V213V		NM_080862.1	NP_543138.1	Q96A44	SPSB4_HUMAN	splA/ryanodine receptor domain and SOCS box containing 4	213	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				biliary_tract(1)|large_intestine(1)|lung(1)|pancreas(1)	4						ACCCGGTGGTGAGTGCCGTGT	0.612																																					p.V213V		Atlas-SNP	.											.	SPSB4	19	.	0			c.G639T						.						73	70	71					3																	140785585		2203	4300	6503	SO:0001819	synonymous_variant	92369	exon2			GGTGGTGAGTGCC		CCDS3115.1	3q23	2008-02-05			ENSG00000175093	ENSG00000175093			30630	protein-coding gene	gene with protein product		611660				12076535	Standard	NM_080862		Approved	SSB-4	uc003ett.3	Q96A44	OTTHUMG00000160223	ENST00000310546.2:c.639G>T	chr3.hg19:g.140785585G>T		81.0	0.0		77.0	43.0	NM_080862		Silent	SNP	ENST00000310546.2	hg19	CCDS3115.1																																																																																			.	.		0.612	SPSB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359727.1	NM_080862		T	140785585	G	T	140785585	2	4	344	1	0	0	0	0	0	0	0	1	15130	1277	45	3		3	SPSB4	3	140785585	Silent	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	6520490	140785585	57236845	325	47688										
XRN1	54464	hgsc.bcm.edu	37	chr3	142122605	142122605	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tacttgaacaccacttttctTcaaaaaaaactttaaaagaa	2	8	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:142122605T>C	ENST00000264951.4	-	18	2131	c.2014A>G	c.(2014-2016)Aag>Gag	p.K672E	XRN1_ENST00000392981.2_Missense_Mutation_p.K672E	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	672					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA catabolic process (GO:0016075)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)	5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(6)|kidney(12)|large_intestine(11)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	61						CCACTTTTCTTCAAAAAAAAC	0.289																																					p.K672E		Atlas-SNP	.											.	XRN1	138	.	0			c.A2014G						.						68	70	69					3																	142122605		2203	4298	6501	SO:0001583	missense	54464	exon18			TTTTCTTCAAAAA	AY137776	CCDS3123.1, CCDS63801.1, CCDS75028.1	3q23	2008-02-05			ENSG00000114127	ENSG00000114127			30654	protein-coding gene	gene with protein product		607994				12515382	Standard	XM_005247544		Approved	SEP1	uc003eus.3	Q8IZH2	OTTHUMG00000159251	ENST00000264951.4:c.2014A>G	chr3.hg19:g.142122605T>C	ENSP00000264951:p.Lys672Glu	309.0	0.0		309.0	120.0	NM_001042604	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Missense_Mutation	SNP	ENST00000264951.4	hg19	CCDS3123.1	.	.	.	.	.	.	.	.	.	.	T	19.13	3.767057	0.69878	.	.	ENSG00000114127	ENST00000264951;ENST00000392981	T;T	0.39056	1.1;1.1	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.30510	0.0767	N	0.25380	0.74	0.80722	D	1	B;B;B	0.31548	0.112;0.328;0.22	B;B;B	0.32928	0.05;0.155;0.074	T	0.08638	-1.0712	10	0.08837	T	0.75	-15.9895	15.8761	0.79162	0.0:0.0:0.0:1.0	.	533;672;672	B3KW17;Q8IZH2-2;Q8IZH2	.;.;XRN1_HUMAN	E	672	ENSP00000264951:K672E;ENSP00000376707:K672E	ENSP00000264951:K672E	K	-	1	0	XRN1	143605295	1.000000	0.71417	1.000000	0.80357	0.888000	0.51559	6.957000	0.76019	2.139000	0.66308	0.533000	0.62120	AAG	.	.		0.289	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001		C	142122605	T	C	142122605	3	2	344	1	0	0	0	0	1	0	0	0	17474	1792	62	2	3206	2	XRN1	3	142122605	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1337020	142122605	55899825	326	47689										
ATR	545	hgsc.bcm.edu	37	chr3	142253962	142253962	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccttcaagcttgtaagagcaTgaatacgaacatcgacattt	7	9	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:142253962T>A	ENST00000350721.4	-	21	4026	c.3905A>T	c.(3904-3906)cAt>cTt	p.H1302L	ATR_ENST00000383101.3_Missense_Mutation_p.H1238L	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	1302					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						TGTAAGAGCATGAATACGAAC	0.348								Other conserved DNA damage response genes																													p.H1302L		Atlas-SNP	.											.	ATR	285	.	0			c.A3905T						.						77	76	77					3																	142253962		2203	4300	6503	SO:0001583	missense	545	exon21			AGAGCATGAATAC	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.3905A>T	chr3.hg19:g.142253962T>A	ENSP00000343741:p.His1302Leu	99.0	0.0		106.0	55.0	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	hg19	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	T	16.43	3.120036	0.56613	.	.	ENSG00000175054	ENST00000350721;ENST00000383101	T;T	0.04083	3.71;4.02	5.69	5.69	0.88448	Armadillo-like helical (1);Armadillo-type fold (1);	0.108901	0.64402	D	0.000007	T	0.10766	0.0263	L	0.48362	1.52	0.80722	D	1	D	0.54601	0.967	P	0.55545	0.778	T	0.33137	-0.9880	10	0.09843	T	0.71	-20.557	15.9415	0.79758	0.0:0.0:0.0:1.0	.	1302	Q13535	ATR_HUMAN	L	1302;1238	ENSP00000343741:H1302L;ENSP00000372581:H1238L	ENSP00000343741:H1302L	H	-	2	0	ATR	143736652	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.329000	0.79170	2.157000	0.67596	0.533000	0.62120	CAT	.	.		0.348	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		A	142253962	T	A	142253962	3	1	344	1	0	0	0	0	1	0	0	0	1204	1464	51	4	4137	4	ATR	3	142253962	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	131357	142253962	55768468	327	47690										
ATR	545	hgsc.bcm.edu	37	chr3	142281191	142281191	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggcacaaatttaaggaaataCtgcagtaaatggcacaaagc	9	7	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:142281191C>A	ENST00000350721.4	-	4	1174	c.1053G>T	c.(1051-1053)caG>caT	p.Q351H	ATR_ENST00000383101.3_Missense_Mutation_p.Q351H	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	351					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						TAAGGAAATACTGCAGTAAAT	0.398								Other conserved DNA damage response genes																													p.Q351H		Atlas-SNP	.											.	ATR	285	.	0			c.G1053T						.						69	69	69					3																	142281191		2203	4300	6503	SO:0001583	missense	545	exon4			GAAATACTGCAGT	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.1053G>T	chr3.hg19:g.142281191C>A	ENSP00000343741:p.Gln351His	224.0	0.0		190.0	97.0	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	hg19	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	C	10.66	1.413003	0.25465	.	.	ENSG00000175054	ENST00000350721;ENST00000383101;ENST00000515149	T;T	0.65916	-0.18;-0.18	5.67	2.49	0.30216	Armadillo-like helical (1);Armadillo-type fold (1);	0.538297	0.20497	N	0.091172	T	0.38746	0.1052	N	0.17082	0.46	0.24308	N	0.995095	B	0.10296	0.003	B	0.08055	0.003	T	0.13980	-1.0489	10	0.20519	T	0.43	-10.3408	5.9749	0.19373	0.134:0.5457:0.0:0.3203	.	351	Q13535	ATR_HUMAN	H	351;351;32	ENSP00000343741:Q351H;ENSP00000372581:Q351H	ENSP00000343741:Q351H	Q	-	3	2	ATR	143763881	0.866000	0.29940	1.000000	0.80357	0.789000	0.44602	-0.193000	0.09573	0.764000	0.33197	-0.229000	0.12294	CAG	.	.		0.398	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		A	142281191	C	A	142281191	3	1	344	1	0	0	0	0	1	0	0	0	1204	564	20	3	7057	3	ATR	3	142281191	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	27229	142281191	55741239	328	47691										
CPB1	1360	hgsc.bcm.edu	37	chr3	148558665	148558665	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgattccatttggtagatagAggcttggactcaacaagtcg	11	7	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:148558665A>T	ENST00000491148.1	+	6	711	c.377A>T	c.(376-378)gAg>gTg	p.E126V	CPB1_ENST00000282957.4_Missense_Mutation_p.E126V			P15086	CBPB1_HUMAN	carboxypeptidase B1 (tissue)	126						extracellular region (GO:0005576)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	38			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)			TGGTAGATAGAGGCTTGGACT	0.443																																					p.E126V		Atlas-SNP	.											.	CPB1	74	.	0			c.A377T						.						134	132	133					3																	148558665		2203	4300	6503	SO:0001583	missense	1360	exon5			AGATAGAGGCTTG	AJ224866	CCDS33874.1	3q24	2012-02-10			ENSG00000153002	ENSG00000153002	3.4.17.2		2299	protein-coding gene	gene with protein product	"pancreatic carboxypeptidase B", "tissue carboxypeptidase B", "protaminase"	114852					Standard	XM_005247124		Approved		uc003ewl.3	P15086	OTTHUMG00000159520	ENST00000491148.1:c.377A>T	chr3.hg19:g.148558665A>T	ENSP00000417222:p.Glu126Val	78.0	0.0		83.0	40.0	NM_001871	O60834|Q53XJ0|Q96BQ8	Missense_Mutation	SNP	ENST00000491148.1	hg19	CCDS33874.1	.	.	.	.	.	.	.	.	.	.	A	8.391	0.839742	0.16891	.	.	ENSG00000153002	ENST00000491148;ENST00000282957	T;T	0.28666	1.6;1.6	5.29	5.29	0.74685	Peptidase M14, carboxypeptidase A (2);	0.413650	0.27861	N	0.017546	T	0.23727	0.0574	L	0.28014	0.82	0.42632	D	0.993382	B	0.15473	0.013	B	0.19391	0.025	T	0.04621	-1.0938	10	0.51188	T	0.08	.	12.0893	0.53717	0.8466:0.1534:0.0:0.0	.	126	P15086	CBPB1_HUMAN	V	126	ENSP00000417222:E126V;ENSP00000282957:E126V	ENSP00000282957:E126V	E	+	2	0	CPB1	150041355	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	3.407000	0.52644	2.003000	0.58678	0.533000	0.62120	GAG	.	.		0.443	CPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355928.1	NM_001871		T	148558665	A	T	148558665	3	4	344	1	0	0	0	0	1	0	0	0	3798	304	11	4	395	4	CPB1	3	148558665	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	6277474	148558665	49463765	329	47692										
FAM194A	131831	hgsc.bcm.edu	37	chr3	150396254	150396254	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acatgttactgtttcttagtTgaaaatcaaatacaatgtca	5	6	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:150396254T>G	ENST00000295910.6	-	10	1251	c.1199A>C	c.(1198-1200)cAa>cCa	p.Q400P	FAM194A_ENST00000491361.1_Missense_Mutation_p.Q254P	NM_152394.3	NP_689607.2														NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						GTTTCTTAGTTGAAAATCAAA	0.289																																					p.Q400P		Atlas-SNP	.											.	FAM194A	91	.	0			c.A1199C						.						78	73	74					3																	150396254		2201	4289	6490	SO:0001583	missense	131831	exon10			CTTAGTTGAAAAT																												ENST00000295910.6:c.1199A>C	chr3.hg19:g.150396254T>G	ENSP00000295910:p.Gln400Pro	222.0	0.0		230.0	87.0	NM_152394		Missense_Mutation	SNP	ENST00000295910.6	hg19	CCDS3151.2	.	.	.	.	.	.	.	.	.	.	T	8.218	0.801887	0.16397	.	.	ENSG00000163645	ENST00000295910;ENST00000491361;ENST00000313811	T;T	0.14893	2.67;2.47	3.29	-2.69	0.06022	.	1.845390	0.03212	N	0.176371	T	0.16557	0.0398	L	0.47716	1.5	0.09310	N	1	P	0.35982	0.531	B	0.37833	0.259	T	0.27839	-1.0062	10	0.42905	T	0.14	2.7799	5.6877	0.17813	0.6035:0.0:0.1533:0.2431	.	400	Q7L0X2	F194A_HUMAN	P	400;254;358	ENSP00000295910:Q400P;ENSP00000419366:Q254P	ENSP00000295910:Q400P	Q	-	2	0	FAM194A	151878944	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-0.332000	0.07904	-0.506000	0.06558	0.455000	0.32223	CAA	.	.		0.289	FAM194A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257666.1			G	150396254	T	G	150396254	3	3	344	1	0	0	0	0	1	0	0	0	5531	1812	63	5	812	5	FAM194A	3	150396254	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1837589	150396254	47626176	330	47693										
P2RY1	5028	hgsc.bcm.edu	37	chr3	152554322	152554322	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgatttacaaagatctggacAactctcctctgaggagaaaa	8	8	3	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:152554322A>T	ENST00000305097.3	+	1	1587	c.751A>T	c.(751-753)Aac>Tac	p.N251Y	RP11-38P22.2_ENST00000460407.1_lincRNA	NM_002563.3	NP_002554.1	P47900	P2RY1_HUMAN	purinergic receptor P2Y, G-protein coupled, 1	251					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|aging (GO:0007568)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cell surface receptor signaling pathway (GO:0007166)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of binding (GO:0051100)|negative regulation of norepinephrine secretion (GO:0010700)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of hormone secretion (GO:0046887)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of ion transport (GO:0043270)|positive regulation of penile erection (GO:0060406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to plasma membrane (GO:0072659)|regulation of receptor activity (GO:0010469)|regulation of vasodilation (GO:0042312)|relaxation of muscle (GO:0090075)|response to growth factor (GO:0070848)|response to mechanical stimulus (GO:0009612)|sensory perception of pain (GO:0019233)|signal transduction involved in regulation of gene expression (GO:0023019)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell body (GO:0044297)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ADP binding (GO:0043531)|ADP-activated nucleotide receptor activity (GO:0045032)|ATP binding (GO:0005524)|ATP-activated nucleotide receptor activity (GO:0045031)|G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|receptor activity (GO:0004872)|scaffold protein binding (GO:0097110)			breast(1)|endometrium(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)	23			LUSC - Lung squamous cell carcinoma(72;0.0628)|Lung(72;0.11)			AGATCTGGACAACTCTCCTCT	0.438																																					p.N251Y		Atlas-SNP	.											.	P2RY1	49	.	0			c.A751T						.						105	100	102					3																	152554322		2203	4300	6503	SO:0001583	missense	5028	exon1			CTGGACAACTCTC	U42029	CCDS3169.1	3q25.2	2012-08-08			ENSG00000169860	ENSG00000169860		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	8539	protein-coding gene	gene with protein product		601167				8579591	Standard	NM_002563		Approved	P2Y1	uc003ezq.3	P47900	OTTHUMG00000159694	ENST00000305097.3:c.751A>T	chr3.hg19:g.152554322A>T	ENSP00000304767:p.Asn251Tyr	88.0	0.0		77.0	41.0	NM_002563		Missense_Mutation	SNP	ENST00000305097.3	hg19	CCDS3169.1	.	.	.	.	.	.	.	.	.	.	A	17.63	3.438213	0.62955	.	.	ENSG00000169860	ENST00000305097	T	0.20738	2.05	5.58	3.13	0.36017	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.22322	0.0538	L	0.54323	1.7	0.53688	D	0.999972	P	0.38250	0.624	B	0.41088	0.347	T	0.01748	-1.1282	10	0.72032	D	0.01	.	7.7887	0.29108	0.7886:0.1391:0.0723:0.0	.	251	P47900	P2RY1_HUMAN	Y	251	ENSP00000304767:N251Y	ENSP00000304767:N251Y	N	+	1	0	P2RY1	154037012	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.406000	0.80017	0.372000	0.24591	0.460000	0.39030	AAC	.	.		0.438	P2RY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356943.1	NM_002563		T	152554322	A	T	152554322	3	4	344	1	0	0	0	0	1	0	0	0	11355	130	5	4	753	4	P2RY1	3	152554322	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2158068	152554322	45468108	331	47694										
GPR149	344758	hgsc.bcm.edu	37	chr3	154145340	154145340	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acgccactgcatatgcgttcTgcctgcagttgatgatgcag	11	11	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:154145340T>C	ENST00000389740.2	-	2	1238	c.1139A>G	c.(1138-1140)cAg>cGg	p.Q380R		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	380					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			ATATGCGTTCTGCCTGCAGTT	0.498																																					p.Q380R		Atlas-SNP	.											.	GPR149	134	.	0			c.A1139G						.						70	73	72					3																	154145340		2010	4184	6194	SO:0001583	missense	344758	exon2			GCGTTCTGCCTGC	AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"GPCR / Class A : Orphans"	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.1139A>G	chr3.hg19:g.154145340T>C	ENSP00000374390:p.Gln380Arg	52.0	0.0		49.0	21.0	NM_001038705		Missense_Mutation	SNP	ENST00000389740.2	hg19	CCDS43162.1	.	.	.	.	.	.	.	.	.	.	T	9.864	1.197092	0.22037	.	.	ENSG00000174948	ENST00000389740	.	.	.	5.76	0.514	0.17007	.	0.313002	0.33753	N	0.004582	T	0.22627	0.0546	L	0.35723	1.085	0.26144	N	0.980238	B	0.02656	0.0	B	0.04013	0.001	T	0.20338	-1.0278	9	0.06891	T	0.86	-4.3338	4.9532	0.14025	0.0:0.263:0.2954:0.4416	.	380	Q86SP6	GP149_HUMAN	R	380	.	ENSP00000374390:Q380R	Q	-	2	0	GPR149	155628034	0.227000	0.23707	0.408000	0.26446	0.935000	0.57460	0.124000	0.15728	0.441000	0.26529	0.533000	0.62120	CAG	.	.		0.498	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580		C	154145340	T	C	154145340	3	2	344	1	0	0	0	0	1	0	0	0	6662	1580	55	2	1068	2	GPR149	3	154145340	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1591018	154145340	43877090	332	47695										
GPR149	344758	hgsc.bcm.edu	37	chr3	154145356	154145356	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gttctgcctgcagttgatgaTgcagccacagggcaagtggg	15	9	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:154145356T>C	ENST00000389740.2	-	2	1222	c.1123A>G	c.(1123-1125)Atc>Gtc	p.I375V		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	375					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			CAGTTGATGATGCAGCCACAG	0.507																																					p.I375V		Atlas-SNP	.											.	GPR149	134	.	0			c.A1123G						.						72	75	74					3																	154145356		2024	4193	6217	SO:0001583	missense	344758	exon2			TGATGATGCAGCC	AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"GPCR / Class A : Orphans"	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.1123A>G	chr3.hg19:g.154145356T>C	ENSP00000374390:p.Ile375Val	58.0	0.0		56.0	23.0	NM_001038705		Missense_Mutation	SNP	ENST00000389740.2	hg19	CCDS43162.1	.	.	.	.	.	.	.	.	.	.	T	14.03	2.415183	0.42817	.	.	ENSG00000174948	ENST00000389740	.	.	.	6.03	2.4	0.29515	.	0.099447	0.64402	N	0.000001	T	0.52597	0.1744	M	0.66939	2.045	0.35933	D	0.832662	B	0.21071	0.051	B	0.14023	0.01	T	0.56183	-0.8021	9	0.87932	D	0	-13.642	9.5231	0.39147	0.0:0.1975:0.0:0.8025	.	375	Q86SP6	GP149_HUMAN	V	375	.	ENSP00000374390:I375V	I	-	1	0	GPR149	155628050	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	2.500000	0.45381	0.184000	0.20083	-0.256000	0.11100	ATC	.	.		0.507	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580		C	154145356	T	C	154145356	3	2	344	1	0	0	0	0	1	0	0	0	6662	1464	51	2	1084	2	GPR149	3	154145356	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	16	154145356	43877074	333	47696										
MME	4311	hgsc.bcm.edu	37	chr3	154889935	154889935	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aattatattaaaaagaatggCgaagaaaaattacttcctgg	7	4	0	2	rs201494121		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:154889935C>A	ENST00000460393.1	+	21	2130	c.2010C>A	c.(2008-2010)ggC>ggA	p.G670G	MME-AS1_ENST00000484721.1_RNA|MME_ENST00000360490.2_Silent_p.G670G|MME_ENST00000493237.1_Silent_p.G670G|MME_ENST00000462745.1_Silent_p.G670G|MME_ENST00000492661.1_Silent_p.G670G	NM_000902.3|NM_007287.2	NP_000893.2|NP_009218.2	P08473	NEP_HUMAN	membrane metallo-endopeptidase	670					angiotensin maturation (GO:0002003)|beta-amyloid metabolic process (GO:0050435)|cellular protein metabolic process (GO:0044267)|cellular response to cytokine stimulus (GO:0071345)|cellular response to UV-A (GO:0071492)|cellular response to UV-B (GO:0071493)|creatinine metabolic process (GO:0046449)|kidney development (GO:0001822)|peptide metabolic process (GO:0006518)|proteolysis (GO:0006508)|replicative senescence (GO:0090399)|sensory perception of pain (GO:0019233)	axon (GO:0030424)|brush border (GO:0005903)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(31)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)|Liraglutide(DB06655)	AAAAGAATGGCGAAGAAAAAT	0.279																																					p.G670G		Atlas-SNP	.											MME,NS,carcinoma,0,1	MME	133	.	0			c.C2010A						.						80	85	84					3																	154889935		2200	4297	6497	SO:0001819	synonymous_variant	4311	exon21			GAATGGCGAAGAA		CCDS3172.1	3q25.2	2012-01-31	2007-02-21		ENSG00000196549	ENSG00000196549	3.4.24.11	"CD molecules"	7154	protein-coding gene	gene with protein product	"neutral endopeptidase", "enkephalinase", "neprilysin"	120520					Standard	NM_007287		Approved	CALLA, CD10, NEP	uc003fad.1	P08473	OTTHUMG00000158455	ENST00000460393.1:c.2010C>A	chr3.hg19:g.154889935C>A		370.0	1.0		358.0	167.0	NM_007287	A8K6U6|D3DNJ9|Q3MIX4	Silent	SNP	ENST00000460393.1	hg19	CCDS3172.1																																																																																			.	.		0.279	MME-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351076.1	NM_000902		A	154889935	C	A	154889935	2	1	344	1	0	0	0	0	0	0	0	1	9654	755	27	1		1	MME	3	154889935	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	744579	154889935	43132495	334	47697										
TRIM59	286827	hgsc.bcm.edu	37	chr3	160156798	160156798	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atttcagtaatacttctgcaAttagggcacttgagtggaat	9	6	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:160156798A>G	ENST00000309784.4	-	3	359	c.174T>C	c.(172-174)aaT>aaC	p.N58N	TRIM59_ENST00000543469.1_Silent_p.N58N|RP11-432B6.3_ENST00000483754.1_Silent_p.N58N	NM_173084.2	NP_775107.1	Q8IWR1	TRI59_HUMAN	tripartite motif containing 59	58					innate immune response (GO:0045087)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of viral entry into host cell (GO:0046597)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|urinary_tract(3)	15			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			TACTTCTGCAATTAGGGCACT	0.363																																					p.N58N		Atlas-SNP	.											.	TRIM59	42	.	0			c.T174C						.						103	105	104					3																	160156798		2203	4300	6503	SO:0001819	synonymous_variant	286827	exon3			TCTGCAATTAGGG	AY159379	CCDS3190.1	3q26	2013-01-09	2011-01-25		ENSG00000213186	ENSG00000213186		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	30834	protein-coding gene	gene with protein product			"tripartite motif-containing 57", "tripartite motif-containing 59"	TRIM57		12095697	Standard	NM_173084		Approved	TSBF1, Mrf1, RNF104	uc003fdm.3	Q8IWR1	OTTHUMG00000159034	ENST00000309784.4:c.174T>C	chr3.hg19:g.160156798A>G		132.0	0.0		120.0	46.0	NM_173084	A8K5G9|D3DNL9	Silent	SNP	ENST00000309784.4	hg19	CCDS3190.1																																																																																			.	.		0.363	TRIM59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352963.1	NM_173084		G	160156798	A	G	160156798	2	3	344	1	0	0	0	0	0	0	0	1	16547	98	4	2		2	TRIM59	3	160156798	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	5266863	160156798	37865632	335	47698										
SI	6476	hgsc.bcm.edu	37	chr3	164739156	164739156	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tggtacttcatatctcttctTttggggatcataaatctatt	6	7	5	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:164739156T>C	ENST00000264382.3	-	27	3177	c.3115A>G	c.(3115-3117)Aag>Gag	p.K1039E		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	1039	Sucrase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)			NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	TATCTCTTCTTTTGGGGATCA	0.328										HNSCC(35;0.089)																											p.K1039E		Atlas-SNP	.											.	SI	500	.	0			c.A3115G						.						200	201	201					3																	164739156		2203	4300	6503	SO:0001583	missense	6476	exon27			TCTTCTTTTGGGG	X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"Oligosaccharide alpha-1,6-glucosidase"	609845	"sucrase-isomaltase"			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.3115A>G	chr3.hg19:g.164739156T>C	ENSP00000264382:p.Lys1039Glu	106.0	0.0		91.0	41.0	NM_001041	A2RUC3|Q1JQ80|Q1RMC2	Missense_Mutation	SNP	ENST00000264382.3	hg19	CCDS3196.1	.	.	.	.	.	.	.	.	.	.	T	6.373	0.436880	0.12104	.	.	ENSG00000090402	ENST00000264382	T	0.08634	3.07	4.58	2.07	0.26955	Glycoside hydrolase-type carbohydrate-binding (1);	0.496080	0.21799	N	0.068960	T	0.07188	0.0182	L	0.33339	1.005	0.09310	N	1	B	0.12013	0.005	B	0.10450	0.005	T	0.29058	-1.0024	10	0.41790	T	0.15	.	11.1501	0.48453	0.0:0.0:0.29:0.71	.	1039	P14410	SUIS_HUMAN	E	1039	ENSP00000264382:K1039E	ENSP00000264382:K1039E	K	-	1	0	SI	166221850	0.005000	0.15991	0.004000	0.12327	0.263000	0.26337	1.582000	0.36568	0.250000	0.21479	0.477000	0.44152	AAG	.	.		0.328	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041		C	164739156	T	C	164739156	3	2	344	1	0	0	0	0	1	0	0	0	14312	1850	64	2	2456	2	SI	3	164739156	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	4582358	164739156	33283274	336	47699										
LRRIQ4	344657	hgsc.bcm.edu	37	chr3	169539921	169539921	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccaggagattcagcgtttaaAgaacatcagggtcctctacc	9	11	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:169539921A>G	ENST00000340806.6	+	1	212	c.212A>G	c.(211-213)aAg>aGg	p.K71R		NM_001080460.1	NP_001073929.1	A6NIV6	LRIQ4_HUMAN	leucine-rich repeats and IQ motif containing 4	71										breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	30						CAGCGTTTAAAGAACATCAGG	0.498																																					p.K71R		Atlas-SNP	.											.	LRRIQ4	68	.	0			c.A212G						.						89	92	91					3																	169539921		1905	4124	6029	SO:0001583	missense	344657	exon1			GTTTAAAGAACAT		CCDS46951.1	3q26.2	2008-08-08	2008-06-12	2008-06-12	ENSG00000188306	ENSG00000188306			34298	protein-coding gene	gene with protein product	"leucine rich repeat containing 64"						Standard	NM_001080460		Approved	LRRC64	uc003fgb.3	A6NIV6	OTTHUMG00000164420	ENST00000340806.6:c.212A>G	chr3.hg19:g.169539921A>G	ENSP00000342188:p.Lys71Arg	107.0	0.0		112.0	45.0	NM_001080460		Missense_Mutation	SNP	ENST00000340806.6	hg19	CCDS46951.1	.	.	.	.	.	.	.	.	.	.	A	8.770	0.925650	0.18056	.	.	ENSG00000188306	ENST00000340806	T	0.58210	0.35	5.69	0.256	0.15567	.	1.107440	0.06629	N	0.758909	T	0.32071	0.0817	N	0.15975	0.35	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.19516	-1.0303	10	0.20519	T	0.43	.	6.5895	0.22639	0.5626:0.1311:0.3063:0.0	.	71	A6NIV6	LRIQ4_HUMAN	R	71	ENSP00000342188:K71R	ENSP00000342188:K71R	K	+	2	0	LRRIQ4	171022615	0.005000	0.15991	0.001000	0.08648	0.005000	0.04900	0.051000	0.14141	0.123000	0.18342	0.459000	0.35465	AAG	.	.		0.498	LRRIQ4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378698.1	NM_001080460		G	169539921	A	G	169539921	3	3	344	1	0	0	0	0	1	0	0	0	9040	72	3	2	214	2	LRRIQ4	3	169539921	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	4800765	169539921	28482509	337	47700										
SPATA16	83893	hgsc.bcm.edu	37	chr3	172643281	172643281	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aacatgtggagtgcttgaagAtctgaaatatgacagaaaga	11	4	1	6			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:172643281A>T	ENST00000351008.3	-	7	1266	c.1083T>A	c.(1081-1083)gaT>gaA	p.D361E		NM_031955.5	NP_114161.3	Q9BXB7	SPT16_HUMAN	spermatogenesis associated 16	361					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)				breast(2)|cervix(1)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	43	Ovarian(172;0.00319)|Breast(254;0.197)		LUSC - Lung squamous cell carcinoma(14;1.48e-14)|Lung(28;6.63e-14)			GTGCTTGAAGATCTGAAATAT	0.378																																					p.D361E		Atlas-SNP	.											.	SPATA16	111	.	0			c.T1083A						.						78	75	76					3																	172643281		2203	4300	6503	SO:0001630	splice_region_variant	83893	exon7			TTGAAGATCTGAA	AF345909	CCDS3221.1	3q26.31	2009-01-05			ENSG00000144962	ENSG00000144962			29935	protein-coding gene	gene with protein product		609856				12529416, 17847006	Standard	NM_031955		Approved	NYD-SP12	uc003fin.4	Q9BXB7	OTTHUMG00000156865	ENST00000351008.3:c.1082-1T>A	chr3.hg19:g.172643281A>T		201.0	0.0		163.0	75.0	NM_031955	Q0R0N4|Q0R0S0|Q0R0W2|Q0R129|Q0R131|Q0R140|Q0R1B8|Q0R1G5|Q0R1I2|Q0R1J6|Q0R1S4|Q0R202|Q0R280|Q0R2F8|Q0R2N6|Q0R2N7|Q0R2R0|Q0R2R1|Q0R2S3|Q0R2S4|Q0R2S5|Q0R2T4|Q0R2T7|Q0R2U2|Q0R2U8|Q0R2U9|Q0R2V5|Q0R2V7|Q8NE67	Missense_Mutation	SNP	ENST00000351008.3	hg19	CCDS3221.1	.	.	.	.	.	.	.	.	.	.	A	14.25	2.479143	0.44044	.	.	ENSG00000144962	ENST00000351008	T	0.24723	1.84	5.06	-0.0959	0.13639	.	0.000000	0.64402	D	0.000001	T	0.33147	0.0853	L	0.32530	0.975	0.26284	N	0.978228	D	0.76494	0.999	D	0.80764	0.994	T	0.11227	-1.0596	10	0.87932	D	0	.	8.8598	0.35249	0.6817:0.0:0.3183:0.0	.	361	Q9BXB7	SPT16_HUMAN	E	361	ENSP00000341765:D361E	ENSP00000341765:D361E	D	-	3	2	SPATA16	174125975	0.999000	0.42202	0.378000	0.26068	0.203000	0.24098	0.540000	0.23191	0.039000	0.15632	0.379000	0.24179	GAT	.	.		0.378	SPATA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346322.1	NM_031955	Missense_Mutation	T	172643281	A	T	172643281	5	4	344	1	0	0	0	0	0	0	1	0	15016	347	12	4	646	4	SPATA16	3	172643281	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3103360	172643281	25379149	338	47701										
ECE2	9718	hgsc.bcm.edu	37	chr3	184009911	184009911	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gctggtgaccgacccccacaGccctgcccgcttccgcgtgc	11	20	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:184009911G>T	ENST00000402825.3	+	19	2537	c.2537G>T	c.(2536-2538)aGc>aTc	p.S846I	EIF2B5_ENST00000444495.1_Intron|ECE2_ENST00000404464.3_Missense_Mutation_p.S728I|ECE2_ENST00000359140.4_Missense_Mutation_p.S699I|ECE2_ENST00000357474.5_Missense_Mutation_p.S774I	NM_014693.3	NP_055508.3	O60344	ECE2_HUMAN	endothelin converting enzyme 2	846	Endothelin-converting enzyme 2 region.				brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|cell-cell signaling (GO:0007267)|heart development (GO:0007507)|peptide hormone processing (GO:0016486)	cytoplasmic vesicle membrane (GO:0030659)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|methyltransferase activity (GO:0008168)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(13)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(4)	49	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GACCCCCACAGCCCTGCCCGC	0.672																																					p.S846I		Atlas-SNP	.											.	ECE2	303	.	0			c.G2537T						.						38	40	40					3																	184009911		2203	4299	6502	SO:0001583	missense	9718	exon19			CCCACAGCCCTGC	AF428263	CCDS3255.1, CCDS33899.1, CCDS3256.2, CCDS43179.1, CCDS46969.1	3q27.1	2007-07-26			ENSG00000145194	ENSG00000145194			13275	protein-coding gene	gene with protein product		610145				11718899	Standard	NM_032331		Approved	KIAA0604, MGC2408	uc003fni.4	O60344	OTTHUMG00000150551	ENST00000402825.3:c.2537G>T	chr3.hg19:g.184009911G>T	ENSP00000384223:p.Ser846Ile	119.0	0.0		106.0	26.0	NM_014693	A5PLK8|Q6NTG7|Q6UW36|Q8NFD7|Q96NX3|Q96NX4|Q9BRZ8	Missense_Mutation	SNP	ENST00000402825.3	hg19	CCDS3256.2	.	.	.	.	.	.	.	.	.	.	G	33	5.226524	0.95173	.	.	ENSG00000145194	ENST00000402825;ENST00000359140;ENST00000404464;ENST00000357474	D;D;D;D	0.85484	-1.99;-1.99;-1.99;-1.99	5.38	5.38	0.77491	Peptidase M13, neprilysin, C-terminal (1);Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.95806	0.8635	H	0.99026	4.405	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;0.995;0.999	D	0.97587	1.0114	10	0.87932	D	0	-25.1487	16.6245	0.84952	0.0:0.0:1.0:0.0	.	728;774;699;846	O60344-2;O60344-5;O60344-3;O60344	.;.;.;ECE2_HUMAN	I	846;699;728;774	ENSP00000384223:S846I;ENSP00000352052:S699I;ENSP00000385846:S728I;ENSP00000350066:S774I	ENSP00000350066:S774I	S	+	2	0	ECE2	185492605	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.827000	0.99397	2.515000	0.84797	0.491000	0.48974	AGC	.	.		0.672	ECE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318874.3	NM_014693		T	184009911	G	T	184009911	3	4	344	1	0	0	0	0	1	0	0	0	4892	971	34	3	3175	3	ECE2	3	184009911	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	11366630	184009911	14012519	339	47702										
EPHB3	2049	hgsc.bcm.edu	37	chr3	184298263	184298263	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgctgccggcatgaagtaccTgtccgagatgaactatgtgc	12	10	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:184298263T>A	ENST00000330394.2	+	12	2698	c.2246T>A	c.(2245-2247)cTg>cAg	p.L749Q	EIF2B5_ENST00000444495.1_Intron	NM_004443.3	NP_004434.2	P54753	EPHB3_HUMAN	EPH receptor B3	749	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell migration (GO:0016477)|central nervous system projection neuron axonogenesis (GO:0021952)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|digestive tract morphogenesis (GO:0048546)|ephrin receptor signaling pathway (GO:0048013)|palate development (GO:0060021)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of axonogenesis (GO:0050770)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell-cell adhesion (GO:0022407)|regulation of Rac GTPase activity (GO:0032314)|retinal ganglion cell axon guidance (GO:0031290)|substrate adhesion-dependent cell spreading (GO:0034446)|thymus development (GO:0048538)|urogenital system development (GO:0001655)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|ephrin receptor activity (GO:0005003)			breast(5)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_cancers(143;1.89e-10)|Ovarian(172;0.0339)		Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22)			ATGAAGTACCTGTCCGAGATG	0.577																																					p.L749Q		Atlas-SNP	.											.	EPHB3	114	.	0			c.T2246A						.						167	153	158					3																	184298263		2203	4300	6503	SO:0001583	missense	2049	exon12			AGTACCTGTCCGA	X75208	CCDS3268.1	3q27.1	2013-09-19	2004-10-28		ENSG00000182580	ENSG00000182580		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3394	protein-coding gene	gene with protein product		601839	"EphB3"	ETK2		8397371	Standard	NM_004443		Approved	Hek2, Tyro6	uc003foz.3	P54753	OTTHUMG00000156710	ENST00000330394.2:c.2246T>A	chr3.hg19:g.184298263T>A	ENSP00000332118:p.Leu749Gln	105.0	0.0		80.0	35.0	NM_004443	Q7Z740	Missense_Mutation	SNP	ENST00000330394.2	hg19	CCDS3268.1	.	.	.	.	.	.	.	.	.	.	T	19.65	3.867791	0.72065	.	.	ENSG00000182580	ENST00000330394	D	0.92699	-3.09	4.06	4.06	0.47325	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000002	D	0.97520	0.9188	H	0.99726	4.73	0.80722	D	1	D	0.58268	0.982	P	0.59825	0.864	D	0.98316	1.0526	10	0.87932	D	0	.	12.9094	0.58171	0.0:0.0:0.0:1.0	.	749	P54753	EPHB3_HUMAN	Q	749	ENSP00000332118:L749Q	ENSP00000332118:L749Q	L	+	2	0	EPHB3	185780957	1.000000	0.71417	0.993000	0.49108	0.933000	0.57130	7.976000	0.88070	1.806000	0.52798	0.486000	0.48141	CTG	.	.		0.577	EPHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345413.1	NM_004443		A	184298263	T	A	184298263	3	1	344	1	0	0	0	0	1	0	0	0	5178	1580	55	4	2292	4	EPHB3	3	184298263	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	288352	184298263	13724167	340	47703										
RTP4	64108	hgsc.bcm.edu	37	chr3	187088757	187088757	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tctcctcggatagcaccatgAggattctgagcaacctggtg	11	11	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:187088757A>T	ENST00000259030.2	+	2	447	c.337A>T	c.(337-339)Agg>Tgg	p.R113W		NM_022147.2	NP_071430.2	Q96DX8	RTP4_HUMAN	receptor (chemosensory) transporter protein 4	113					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|protein targeting to membrane (GO:0006612)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	11	all_cancers(143;4.66e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.56e-18)	GBM - Glioblastoma multiforme(93;0.0269)		TAGCACCATGAGGATTCTGAG	0.507																																					p.R113W		Atlas-SNP	.											.	RTP4	20	.	0			c.A337T						.						61	60	60					3																	187088757		2203	4300	6503	SO:0001583	missense	64108	exon2			ACCATGAGGATTC	BC013161	CCDS33910.1	3q27.3	2014-02-20	2006-11-21		ENSG00000136514	ENSG00000136514		"Receptor transporter proteins"	23992	protein-coding gene	gene with protein product	"zinc finger, 3CxxC-type 4"	609350	"receptor transporter protein 4"			16271481, 15550249, 16720576	Standard	NM_022147		Approved	IFRG28, Z3CXXC4	uc003frm.3	Q96DX8	OTTHUMG00000156459	ENST00000259030.2:c.337A>T	chr3.hg19:g.187088757A>T	ENSP00000259030:p.Arg113Trp	109.0	0.0		103.0	48.0	NM_022147	Q9H4F3	Missense_Mutation	SNP	ENST00000259030.2	hg19	CCDS33910.1	.	.	.	.	.	.	.	.	.	.	A	11.67	1.707752	0.30322	.	.	ENSG00000136514	ENST00000259030	T	0.19806	2.12	4.09	2.93	0.34026	.	0.472128	0.22966	N	0.053495	T	0.43366	0.1244	M	0.81341	2.54	0.09310	N	1	D	0.89917	1.0	D	0.81914	0.995	T	0.17471	-1.0368	10	0.87932	D	0	-9.9314	7.5665	0.27881	0.7511:0.2489:0.0:0.0	.	113	Q96DX8	RTP4_HUMAN	W	113	ENSP00000259030:R113W	ENSP00000259030:R113W	R	+	1	2	RTP4	188571451	0.001000	0.12720	0.003000	0.11579	0.013000	0.08279	1.306000	0.33505	0.920000	0.36970	0.533000	0.62120	AGG	.	.		0.507	RTP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344260.1	NM_022147		T	187088757	A	T	187088757	3	4	344	1	0	0	0	0	1	0	0	0	13751	295	11	4	343	4	RTP4	3	187088757	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2790494	187088757	10933673	341	47704										
LEPREL1	55214	hgsc.bcm.edu	37	chr3	189691795	189691795	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	caccaacaagcatgattcccTggaagcaaatacaagaagat	7	10	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:189691795T>A	ENST00000319332.5	-	10	1650		c.e10-2		LEPREL1_ENST00000427335.2_Splice_Site	NM_018192.3	NP_060662.2	Q8IVL5	P3H2_HUMAN	leprecan-like 1						collagen metabolic process (GO:0032963)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|peptidyl-proline hydroxylation (GO:0019511)	basement membrane (GO:0005604)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-proline 3-dioxygenase activity (GO:0019797)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|prostate(2)|skin(5)	41	all_cancers(143;4.01e-10)|Ovarian(172;0.0925)		Lung(62;4.35e-05)	GBM - Glioblastoma multiforme(93;0.02)	L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	CATGATTCCCTGGAAGCAAAT	0.408																																					.		Atlas-SNP	.											.	LEPREL1	95	.	0			c.910-2A>T						.						161	161	161					3																	189691795		2203	4300	6503	SO:0001630	splice_region_variant	55214	exon11			ATTCCCTGGAAGC		CCDS3294.1, CCDS46981.1	3q29	2014-01-28			ENSG00000090530	ENSG00000090530	1.14.11.7		19317	protein-coding gene	gene with protein product	"prolyl 3-hydroxylase 2"	610341				15063763, 21885030	Standard	NM_018192		Approved	FLJ10718, MLAT4, P3H2	uc011bsk.2	Q8IVL5	OTTHUMG00000156312	ENST00000319332.5:c.1453-2A>T	chr3.hg19:g.189691795T>A		120.0	0.0		91.0	42.0	NM_001134418	B3KPK0|B3KWI9|D3DNV8|Q9NVI2	Splice_Site	SNP	ENST00000319332.5	hg19	CCDS3294.1	.	.	.	.	.	.	.	.	.	.	T	16.87	3.241296	0.58995	.	.	ENSG00000090530	ENST00000319332;ENST00000427335	.	.	.	5.68	5.68	0.88126	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7632	0.69619	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	LEPREL1	191174489	1.000000	0.71417	0.929000	0.37066	0.700000	0.40528	7.207000	0.77899	2.169000	0.68431	0.402000	0.26972	.	.	.		0.408	LEPREL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343855.1	NM_018192	Intron	A	189691795	T	A	189691795	5	1	344	1	0	0	0	0	0	0	1	0	8739	1594	55	4	699	4	LEPREL1	3	189691795	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2603038	189691795	8330635	342	47705										
CLDN16	10686	hgsc.bcm.edu	37	chr3	190120151	190120151	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cacaaaatgccgaggcctctGgtgggaatgcgtcacaaatg	12	10	2	0	rs104893732		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:190120151G>T	ENST00000264734.2	+	2	598	c.350G>T	c.(349-351)tGg>tTg	p.W117L	CLDN16_ENST00000468220.1_3'UTR|CLDN16_ENST00000456423.1_Intron	NM_006580.3	NP_006571.1	Q9Y5I7	CLD16_HUMAN	claudin 16	117					calcium-independent cell-cell adhesion (GO:0016338)|cellular metal ion homeostasis (GO:0006875)|excretion (GO:0007588)|magnesium ion transport (GO:0015693)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|magnesium ion transmembrane transporter activity (GO:0015095)|structural molecule activity (GO:0005198)			breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|skin(1)	19	all_cancers(143;3.61e-10)|Ovarian(172;0.0991)		Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05)	GBM - Glioblastoma multiforme(93;0.018)		CGAGGCCTCTGGTGGGAATGC	0.478																																					p.W117L		Atlas-SNP	.											.	CLDN16	59	.	0			c.G350T	GRCh37	CM001068	CLDN16	M	rs104893732	.						164	153	157					3																	190120151		2203	4300	6503	SO:0001583	missense	10686	exon2			GCCTCTGGTGGGA	AF152101	CCDS3296.1	3q28	2008-12-10			ENSG00000113946	ENSG00000113946		"Claudins"	2037	protein-coding gene	gene with protein product	"paracellin-1", "hypomagnesemia 3, with hypercalciuria and nephrocalcinosis"	603959				10390358	Standard	NM_006580		Approved	PCLN1, HOMG3	uc003fsi.3	Q9Y5I7	OTTHUMG00000156215	ENST00000264734.2:c.350G>T	chr3.hg19:g.190120151G>T	ENSP00000264734:p.Trp117Leu	83.0	0.0		65.0	20.0	NM_006580		Missense_Mutation	SNP	ENST00000264734.2	hg19	CCDS3296.1	.	.	.	.	.	.	.	.	.	.	G	29.5	5.015639	0.93404	.	.	ENSG00000113946	ENST00000264734	D	0.98455	-4.94	5.94	5.94	0.96194	Claudin, conserved site (1);	0.000000	0.64402	D	0.000001	D	0.99108	0.9693	M	0.86420	2.815	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99698	1.1003	10	0.87932	D	0	-28.1606	19.3653	0.94459	0.0:0.0:1.0:0.0	.	117	Q9Y5I7	CLD16_HUMAN	L	117	ENSP00000264734:W117L	ENSP00000264734:W117L	W	+	2	0	CLDN16	191602845	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.028000	0.76470	2.824000	0.97209	0.650000	0.86243	TGG	.	.		0.478	CLDN16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343519.1	NM_006580		T	190120151	G	T	190120151	3	4	344	1	0	0	0	0	1	0	0	0	3479	1357	47	3	356	3	CLDN16	3	190120151	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	428356	190120151	7902279	343	47706										
CCDC50	152137	hgsc.bcm.edu	37	chr3	191078935	191078935	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agagagacgacgcattcaggAgaagaaggatgaggtataac	14	5	1	5			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:191078935A>G	ENST00000392455.3	+	4	915	c.317A>G	c.(316-318)gAg>gGg	p.E106G	CCDC50_ENST00000392456.3_Missense_Mutation_p.E106G	NM_174908.3	NP_777568.1	Q8IVM0	CCD50_HUMAN	coiled-coil domain containing 50	106						cytoplasm (GO:0005737)	ubiquitin protein ligase binding (GO:0031625)			endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|stomach(1)	23	all_cancers(143;8.88e-09)|Ovarian(172;0.103)|Breast(254;0.221)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000136)		CGCATTCAGGAGAAGAAGGAT	0.448																																					p.E106G		Atlas-SNP	.											.	CCDC50	39	.	0			c.A317G						.						89	84	86					3																	191078935		2203	4300	6503	SO:0001583	missense	152137	exon4			TTCAGGAGAAGAA	AJ416916	CCDS33912.1, CCDS33913.1	3q28	2010-12-24		2005-12-23	ENSG00000152492	ENSG00000152492			18111	protein-coding gene	gene with protein product		611051	"deafness, autosomal dominant 44"	C3orf6, DFNA44		16803894, 17503326	Standard	NM_178335		Approved	Ymer	uc003fsv.3	Q8IVM0	OTTHUMG00000156177	ENST00000392455.3:c.317A>G	chr3.hg19:g.191078935A>G	ENSP00000376249:p.Glu106Gly	442.0	0.0		384.0	157.0	NM_174908	Q86VH7	Missense_Mutation	SNP	ENST00000392455.3	hg19	CCDS33913.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.586818	0.86851	.	.	ENSG00000152492	ENST00000392455;ENST00000392456	T;T	0.63255	-0.03;-0.03	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.79281	0.4419	M	0.78049	2.395	0.48975	D	0.999739	D;D	0.89917	1.0;0.997	D;D	0.91635	0.999;0.973	T	0.81551	-0.0881	10	0.66056	D	0.02	.	14.3151	0.66443	1.0:0.0:0.0:0.0	.	106;106	Q8IVM0;Q8IVM0-2	CCD50_HUMAN;.	G	106	ENSP00000376249:E106G;ENSP00000376250:E106G	ENSP00000376249:E106G	E	+	2	0	CCDC50	192561629	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.362000	0.79507	2.266000	0.75297	0.533000	0.62120	GAG	.	.		0.448	CCDC50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343315.1	NM_174908		G	191078935	A	G	191078935	3	3	344	1	0	0	0	0	1	0	0	0	2822	304	11	2	331	2	CCDC50	3	191078935	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	958784	191078935	6943495	344	47707										
ATP13A4	84239	hgsc.bcm.edu	37	chr3	193128796	193128796	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aacgtctatataattctggtAtatcagcaaatagaatgaat	6	5	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:193128796A>G	ENST00000342695.4	-	28	3594	c.3272T>C	c.(3271-3273)aTa>aCa	p.I1091T	ATP13A4_ENST00000400270.2_Missense_Mutation_p.I107T|ATP13A4_ENST00000392443.3_Missense_Mutation_p.I1072T|ATP13A4_ENST00000482964.1_5'UTR	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	1091						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(27)|ovary(2)|prostate(3)|skin(11)|upper_aerodigestive_tract(2)	71	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		TAATTCTGGTATATCAGCAAA	0.303																																					p.I1091T		Atlas-SNP	.											.	ATP13A4	154	.	0			c.T3272C						.						98	100	99					3																	193128796		2203	4290	6493	SO:0001583	missense	84239	exon28			TCTGGTATATCAG	AK095277	CCDS3304.2	3q29	2010-04-20			ENSG00000127249	ENSG00000127249		"ATPases / P-type"	25422	protein-coding gene	gene with protein product		609556				14702039, 12975309	Standard	XM_005247829		Approved	DKFZp761I1011, FLJ37958	uc003ftd.3	Q4VNC1	OTTHUMG00000074067	ENST00000342695.4:c.3272T>C	chr3.hg19:g.193128796A>G	ENSP00000339182:p.Ile1091Thr	382.0	1.0		342.0	148.0	NM_032279	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	Missense_Mutation	SNP	ENST00000342695.4	hg19	CCDS3304.2	.	.	.	.	.	.	.	.	.	.	A	18.62	3.662431	0.67700	.	.	ENSG00000127249	ENST00000400270;ENST00000392443;ENST00000342695	T;T;T	0.50813	0.73;0.73;0.73	4.71	4.71	0.59529	.	0.000000	0.64402	D	0.000005	T	0.48840	0.1522	L	0.29908	0.895	0.80722	D	1	D	0.55605	0.972	P	0.57009	0.811	T	0.40346	-0.9568	10	0.31617	T	0.26	-19.4124	12.4535	0.55691	1.0:0.0:0.0:0.0	.	1091	Q4VNC1	AT134_HUMAN	T	107;1072;1091	ENSP00000383129:I107T;ENSP00000376238:I1072T;ENSP00000339182:I1091T	ENSP00000339182:I1091T	I	-	2	0	ATP13A4	194611490	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	5.930000	0.70104	1.879000	0.54435	0.459000	0.35465	ATA	.	.		0.303	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157244.4	NM_032279		G	193128796	A	G	193128796	3	3	344	1	0	0	0	0	1	0	0	0	1126	449	16	2	330	2	ATP13A4	3	193128796	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2049861	193128796	4893634	345	47708										
ATP13A4	84239	hgsc.bcm.edu	37	chr3	193232491	193232491	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccaggtacacacttaccgttGtcctcagcaacacagtgtct	7	14	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:193232491G>T	ENST00000342695.4	-	2	552	c.230C>A	c.(229-231)aCa>aAa	p.T77K	ATP13A4_ENST00000295548.3_Missense_Mutation_p.T77K|ATP13A4_ENST00000392443.3_Missense_Mutation_p.T77K	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	77						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(27)|ovary(2)|prostate(3)|skin(11)|upper_aerodigestive_tract(2)	71	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		ACTTACCGTTGTCCTCAGCAA	0.522																																					p.T77K		Atlas-SNP	.											.	ATP13A4	154	.	0			c.C230A						.						205	181	189					3																	193232491		2203	4300	6503	SO:0001583	missense	84239	exon2			ACCGTTGTCCTCA	AK095277	CCDS3304.2	3q29	2010-04-20			ENSG00000127249	ENSG00000127249		"ATPases / P-type"	25422	protein-coding gene	gene with protein product		609556				14702039, 12975309	Standard	XM_005247829		Approved	DKFZp761I1011, FLJ37958	uc003ftd.3	Q4VNC1	OTTHUMG00000074067	ENST00000342695.4:c.230C>A	chr3.hg19:g.193232491G>T	ENSP00000339182:p.Thr77Lys	77.0	0.0		72.0	31.0	NM_032279	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	Missense_Mutation	SNP	ENST00000342695.4	hg19	CCDS3304.2	.	.	.	.	.	.	.	.	.	.	G	24.9	4.577119	0.86645	.	.	ENSG00000127249	ENST00000392443;ENST00000342695;ENST00000295548	T;T;T	0.29655	1.56;1.56;1.56	5.82	5.82	0.92795	.	0.196377	0.35936	N	0.002900	T	0.58764	0.2145	M	0.79475	2.455	0.43417	D	0.995567	D;D	0.69078	0.997;0.997	D;D	0.76071	0.984;0.987	T	0.56703	-0.7935	10	0.45353	T	0.12	-4.2854	18.6518	0.91433	0.0:0.0:1.0:0.0	.	77;77	Q4VNC1-2;Q4VNC1	.;AT134_HUMAN	K	77	ENSP00000376238:T77K;ENSP00000339182:T77K;ENSP00000295548:T77K	ENSP00000295548:T77K	T	-	2	0	ATP13A4	194715185	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.475000	0.73582	2.739000	0.93911	0.655000	0.94253	ACA	.	.		0.522	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157244.4	NM_032279		T	193232491	G	T	193232491	3	4	344	1	0	0	0	0	1	0	0	0	1126	1377	48	3	3476	3	ATP13A4	3	193232491	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	103695	193232491	4789939	346	47709										
OPA1	4976	hgsc.bcm.edu	37	chr3	193336697	193336697	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtttagagcaacagatcgtgGatctgaaagtgacaagcatt	11	6	1	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:193336697G>C	ENST00000392438.3	+	5	830	c.596G>C	c.(595-597)gGa>gCa	p.G199A	OPA1_ENST00000361715.2_Missense_Mutation_p.G181A|OPA1_ENST00000361908.3_Missense_Mutation_p.G199A|OPA1_ENST00000361828.2_Missense_Mutation_p.G217A|OPA1_ENST00000361150.2_Missense_Mutation_p.G163A|OPA1-AS1_ENST00000444085.1_RNA|OPA1_ENST00000487986.1_3'UTR|OPA1-AS1_ENST00000433105.1_RNA|OPA1_ENST00000361510.2_Missense_Mutation_p.G217A	NM_015560.2	NP_056375.2	O60313	OPA1_HUMAN	optic atrophy 1 (autosomal dominant)	199					apoptotic process (GO:0006915)|axon transport of mitochondrion (GO:0019896)|cellular senescence (GO:0090398)|GTP catabolic process (GO:0006184)|inner mitochondrial membrane organization (GO:0007007)|mitochondrial fission (GO:0000266)|mitochondrial fusion (GO:0008053)|mitochondrion organization (GO:0007005)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|neural tube closure (GO:0001843)|visual perception (GO:0007601)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial crista (GO:0030061)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)			breast(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(4)|lung(15)|upper_aerodigestive_tract(1)|urinary_tract(2)	31	all_cancers(143;9.56e-09)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;9.19e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000162)		ACAGATCGTGGATCTGAAAGT	0.358																																					p.G217A		Atlas-SNP	.											.	OPA1	79	.	0			c.G650C						.						132	133	132					3																	193336697		2203	4300	6503	SO:0001583	missense	4976	exon6			ATCGTGGATCTGA	AB011139	CCDS33917.1, CCDS43186.1	3q29	2014-09-17			ENSG00000198836	ENSG00000198836			8140	protein-coding gene	gene with protein product	"mitochondrial dynamin-like GTPase", "dynamin-like guanosine triphosphatase", "Dynamin-like 120 kDa protein, mitochondrial"	605290				9490303	Standard	NM_015560		Approved	NTG, KIAA0567, FLJ12460, NPG, MGM1	uc003ftg.3	O60313	OTTHUMG00000149897	ENST00000392438.3:c.596G>C	chr3.hg19:g.193336697G>C	ENSP00000376233:p.Gly199Ala	72.0	0.0		59.0	20.0	NM_130837	D3DNW4	Missense_Mutation	SNP	ENST00000392438.3	hg19	CCDS43186.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.404|9.404	1.078868|1.078868	0.20227|0.20227	.|.	.|.	ENSG00000198836|ENSG00000198836	ENST00000434811|ENST00000361908;ENST00000392438;ENST00000361510;ENST00000361715;ENST00000361828;ENST00000361150;ENST00000392437;ENST00000419435;ENST00000392436	.|D;D;D;D;D;D;D;T;T	.|0.94828	.|-3.06;-3.03;-3.11;-3.12;-3.06;-3.53;-2.94;1.9;-0.95	5.63|5.63	4.71|4.71	0.59529|0.59529	.|.	.|1.671300	.|0.03790	.|N	.|0.262771	D|D	0.89656|0.89656	0.6778|0.6778	N|N	0.17474|0.17474	0.49|0.49	0.39883|0.39883	D|D	0.973661|0.973661	.|B;B;B;B;B;B;B;B	.|0.06786	.|0.0;0.0;0.0;0.001;0.0;0.0;0.0;0.0	.|B;B;B;B;B;B;B;B	.|0.04013	.|0.001;0.0;0.0;0.001;0.001;0.001;0.001;0.001	T|T	0.63523|0.63523	-0.6618|-0.6618	5|10	.|0.07325	.|T	.|0.83	-23.436|-23.436	14.6908|14.6908	0.69085|0.69085	0.0:0.1441:0.8559:0.0|0.0:0.1441:0.8559:0.0	.|.	.|163;199;181;163;217;199;181;217	.|E5KLK2;O60313;E5KLK0;E5KLK1;E5KLJ6;E5KLJ7;E5KLJ9;E5KLJ5	.|.;OPA1_HUMAN;.;.;.;.;.;.	H|A	117|199;199;217;181;217;163;163;75;217	.|ENSP00000354681:G199A;ENSP00000376233:G199A;ENSP00000355324:G217A;ENSP00000355311:G181A;ENSP00000354429:G217A;ENSP00000354781:G163A;ENSP00000376232:G163A;ENSP00000399877:G75A;ENSP00000376231:G217A	.|ENSP00000354781:G163A	D|G	+|+	1|2	0|0	OPA1|OPA1	194819391|194819391	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.253000|0.253000	0.25986|0.25986	3.104000|3.104000	0.50306|0.50306	2.805000|2.805000	0.96524|0.96524	0.655000|0.655000	0.94253|0.94253	GAT|GGA	.	.		0.358	OPA1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313812.2	NM_130837		C	193336697	G	C	193336697	3	2	344	1	0	0	0	0	1	0	0	0	10880	1174	41	4	672	4	OPA1	3	193336697	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	104206	193336697	4685733	347	47710										
TNK2	10188	hgsc.bcm.edu	37	chr3	195594061	195594061	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttcagatactgggcagccctCtgcacgctccagccgtggca	11	15	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:195594061C>A	ENST00000333602.6	-	13	3578	c.2961G>T	c.(2959-2961)caG>caT	p.Q987H	TNK2_ENST00000381916.2_Intron|TNK2_ENST00000392400.1_Missense_Mutation_p.Q987H|TNK2_ENST00000428187.1_Intron	NM_005781.4	NP_005772.3	Q07912	ACK1_HUMAN	tyrosine kinase, non-receptor, 2	987	UBA.			Missing (in Ref. 4; AAH08884). {ECO:0000305}.	cell surface receptor signaling pathway (GO:0007166)|endocytosis (GO:0006897)|negative regulation of catalytic activity (GO:0043086)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of clathrin-mediated endocytosis (GO:2000369)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|endosome (GO:0005768)|Grb2-EGFR complex (GO:0070436)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|WW domain binding (GO:0050699)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(11)|ovary(3)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	29	all_cancers(143;6.48e-09)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;1.46e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.3e-19)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;0.000757)	Adenosine triphosphate(DB00171)	GGGCAGCCCTCTGCACGCTCC	0.682																																					p.Q987H		Atlas-SNP	.											.	TNK2	246	.	0			c.G2961T						.						40	45	44					3																	195594061		2202	4300	6502	SO:0001583	missense	10188	exon13			AGCCCTCTGCACG	L13738	CCDS33927.1, CCDS33928.1	3q29	2013-09-02			ENSG00000061938	ENSG00000061938			19297	protein-coding gene	gene with protein product	"activated Cdc42-associated kinase 1"	606994				8497321, 14506255	Standard	XM_006713460		Approved	p21cdc42Hs, ACK, ACK1	uc003fvt.1	Q07912	OTTHUMG00000155737	ENST00000333602.6:c.2961G>T	chr3.hg19:g.195594061C>A	ENSP00000329425:p.Gln987His	209.0	0.0		187.0	84.0	NM_005781	Q6ZMQ0|Q8N6U7|Q96H59	Missense_Mutation	SNP	ENST00000333602.6	hg19	CCDS33928.1	.	.	.	.	.	.	.	.	.	.	C	15.41	2.824029	0.50739	.	.	ENSG00000061938	ENST00000333602;ENST00000416152;ENST00000392400	T;T;T	0.75260	-0.92;1.89;-0.92	5.67	2.9	0.33743	.	.	.	.	.	T	0.78059	0.4224	L	0.57536	1.79	0.80722	D	1	P;D	0.57257	0.911;0.979	P;P	0.58331	0.594;0.837	T	0.76091	-0.3086	9	0.52906	T	0.07	.	8.1544	0.31160	0.0:0.6196:0.0:0.3804	.	987;514	Q07912;B3KXJ4	ACK1_HUMAN;.	H	987;556;987	ENSP00000329425:Q987H;ENSP00000398614:Q556H;ENSP00000376201:Q987H	ENSP00000329425:Q987H	Q	-	3	2	TNK2	197078458	0.977000	0.34250	1.000000	0.80357	0.999000	0.98932	0.893000	0.28336	0.753000	0.32945	0.655000	0.94253	CAG	.	.		0.682	TNK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341437.3	NM_005781		A	195594061	C	A	195594061	3	1	344	1	0	0	0	0	1	0	0	0	16333	912	32	3	167	3	TNK2	3	195594061	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	2257364	195594061	2428369	348	47711										
RNF168	165918	hgsc.bcm.edu	37	chr3	196199329	196199329	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccatttgtctgtgtcaccccTgatgtgggggcgcacccact	11	14	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr3:196199329T>C	ENST00000318037.3	-	6	1671	c.1077A>G	c.(1075-1077)tcA>tcG	p.S359S	CTD-2002J20.1_ENST00000610042.1_RNA	NM_152617.3	NP_689830.2	Q8IYW5	RN168_HUMAN	ring finger protein 168, E3 ubiquitin protein ligase	359					cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|histone H2A K63-linked ubiquitination (GO:0070535)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K13 ubiquitination (GO:0036351)|histone H2A-K15 ubiquitination (GO:0036352)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|negative regulation of translational elongation (GO:0045900)|positive regulation of DNA repair (GO:0045739)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)|ligase activity (GO:0016874)|nucleosome binding (GO:0031491)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)	20	all_cancers(143;1e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;5.25e-24)|all cancers(36;5.47e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00348)		GTGTCACCCCTGATGTGGGGG	0.458																																					p.S359S		Atlas-SNP	.											.	RNF168	49	.	0			c.A1077G						.						145	147	146					3																	196199329		2203	4300	6503	SO:0001819	synonymous_variant	165918	exon6			CACCCCTGATGTG	AK054732	CCDS3317.1	3q29	2014-09-17	2012-02-23		ENSG00000163961	ENSG00000163961		"RING-type (C3HC4) zinc fingers"	26661	protein-coding gene	gene with protein product		612688	"ring finger protein 168"			12477932	Standard	NM_152617		Approved	FLJ35794	uc003fwq.3	Q8IYW5	OTTHUMG00000155582	ENST00000318037.3:c.1077A>G	chr3.hg19:g.196199329T>C		93.0	0.0		98.0	45.0	NM_152617	Q8NA67|Q96NS4	Silent	SNP	ENST00000318037.3	hg19	CCDS3317.1																																																																																			.	.		0.458	RNF168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340778.1	NM_152617		C	196199329	T	C	196199329	2	2	344	1	0	0	0	0	0	0	0	1	13474	1567	55	2		2	RNF168	3	196199329	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	605268	196199329	1823101	349	47712										
ZNF721	170960	hgsc.bcm.edu	37	chr4	436177	436177	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcacatttgtaaggtttttcTccagtatgaattttcttgtg	7	6	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:436177T>C	ENST00000338977.5	-	2	2091	c.2043A>G	c.(2041-2043)ggA>ggG	p.G681G	ZNF721_ENST00000507078.1_Intron|ZNF721_ENST00000506646.1_Intron|ABCA11P_ENST00000451020.2_RNA|ZNF721_ENST00000511833.2_Silent_p.G693G			Q8TF20	ZN721_HUMAN	zinc finger protein 721	681					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(2)|large_intestine(15)|lung(6)|ovary(1)|skin(1)|stomach(5)|urinary_tract(1)	33						AAGGTTTTTCTCCAGTATGAA	0.403																																					p.K693K		Atlas-SNP	.											.	ZNF721	205	.	0			c.G2079G						.						81	86	84					4																	436177		2112	4257	6369	SO:0001819	synonymous_variant	170960	exon3			TTTTTCTCCAGTA	AK092362	CCDS46991.1	4p16.3	2013-01-08			ENSG00000182903	ENSG00000182903		"Zinc fingers, C2H2-type", "-"	29425	protein-coding gene	gene with protein product						11853319	Standard	NM_133474		Approved	KIAA1982	uc003gag.4	Q8TF20		ENST00000338977.5:c.2043A>G	chr4.hg19:g.436177T>C		119.0	0.0		93.0	31.0	NM_133474	Q69YG7	Silent	SNP	ENST00000338977.5	hg19																																																																																				.	.		0.403	ZNF721-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000357939.1	NM_133474		C	436177	T	C	436177	2	2	344	1	0	0	0	0	0	0	0	1	18137	1538	54	2		2	ZNF721	4	436177	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10		436177	190718099	350	47713										
PDE6B	5158	hgsc.bcm.edu	37	chr4	656968	656968	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agtttgggaagttcctgctcTcggaggaggttggtatactc	14	7	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:656968T>A	ENST00000496514.1	+	15	1933	c.1912T>A	c.(1912-1914)Tcg>Acg	p.S638T	PDE6B_ENST00000429163.2_Missense_Mutation_p.S359T|RP11-1191J2.5_ENST00000609172.1_RNA|PDE6B_ENST00000255622.6_Missense_Mutation_p.S638T			P35913	PDE6B_HUMAN	phosphodiesterase 6B, cGMP-specific, rod, beta	638					cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			NS(1)|breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(2)|urinary_tract(1)	30					Caffeine(DB00201)	GTTCCTGCTCTCGGAGGAGGT	0.622																																					p.S638T	GBM(71;463 1194 9848 25922 46834)	Atlas-SNP	.											.	PDE6B	80	.	0			c.T1912A						.						121	105	110					4																	656968		2203	4300	6503	SO:0001583	missense	5158	exon15			CTGCTCTCGGAGG	BC000249	CCDS33932.1, CCDS46993.1, CCDS54703.1	4p16.3	2014-01-28	2008-07-31		ENSG00000133256	ENSG00000133256	3.1.4.17	"Phosphodiesterases"	8786	protein-coding gene	gene with protein product	"congenital stationary night blindness 3, autosomal dominant"	180072		PDEB		1313787	Standard	NM_001145292		Approved	CSNB3, rd1, RP40, CSNBAD2	uc003gap.3	P35913	OTTHUMG00000159909	ENST00000496514.1:c.1912T>A	chr4.hg19:g.656968T>A	ENSP00000420295:p.Ser638Thr	129.0	0.0		87.0	27.0	NM_001145291	B7Z9T9|E7ETT3|Q53XN5|Q9BWH5|Q9UD49	Missense_Mutation	SNP	ENST00000496514.1	hg19	CCDS33932.1	.	.	.	.	.	.	.	.	.	.	T	9.884	1.202380	0.22121	.	.	ENSG00000133256	ENST00000255622;ENST00000496514;ENST00000429163	T;T;T	0.78481	-1.18;-1.18;-1.18	4.19	-1.36	0.09085	Metal-dependent phosphohydrolase, HD domain (1);5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	1.573410	0.03927	N	0.284615	T	0.65396	0.2687	N	0.12746	0.255	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.10450	0.005;0.003	T	0.50980	-0.8763	10	0.32370	T	0.25	.	15.8112	0.78565	0.0:0.0:0.8213:0.1787	.	638;638	P35913;P35913-2	PDE6B_HUMAN;.	T	638;638;359	ENSP00000255622:S638T;ENSP00000420295:S638T;ENSP00000406334:S359T	ENSP00000255622:S638T	S	+	1	0	PDE6B	646968	0.000000	0.05858	0.368000	0.25939	0.530000	0.34684	-1.181000	0.03085	-0.231000	0.09825	0.449000	0.29647	TCG	.	.		0.622	PDE6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358109.1	NM_000283		A	656968	T	A	656968	3	1	344	1	0	0	0	0	1	0	0	0	11655	1551	54	4	1970	4	PDE6B	4	656968	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	220791	656968	190497308	351	47714										
HTT	3064	hgsc.bcm.edu	37	chr4	3189596	3189596	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaacaaataaagaatttgccAgaagaaacattttcaaggta	6	5	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:3189596A>T	ENST00000355072.5	+	39	5353	c.5208A>T	c.(5206-5208)ccA>ccT	p.P1736P		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	1736					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		AGAATTTGCCAGAAGAAACAT	0.378																																					p.P1736P		Atlas-SNP	.											.	HTT	221	.	0			c.A5208T						.						86	81	83					4																	3189596		1856	4102	5958	SO:0001819	synonymous_variant	3064	exon39			TTTGCCAGAAGAA	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.5208A>T	chr4.hg19:g.3189596A>T		50.0	0.0		18.0	13.0	NM_002111	Q9UQB7	Silent	SNP	ENST00000355072.5	hg19	CCDS43206.1																																																																																			.	.		0.378	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		T	3189596	A	T	3189596	2	4	344	1	0	0	0	0	0	0	0	1	7466	175	7	4		4	HTT	4	3189596	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2532628	3189596	187964680	352	47715										
HGFAC	3083	hgsc.bcm.edu	37	chr4	3447852	3447852	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cggggcgccaggcctgcggcAggaggcacaagaagaggacg	19	11	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:3447852A>T	ENST00000382774.3	+	10	1301	c.1186A>T	c.(1186-1188)Agg>Tgg	p.R396W	HGFAC_ENST00000511533.1_Missense_Mutation_p.R403W	NM_001528.2	NP_001519.1	Q04756	HGFA_HUMAN	HGF activator	396					proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|rough endoplasmic reticulum (GO:0005791)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		GGCCTGCGGCAGGAGGCACAA	0.677																																					p.R396W		Atlas-SNP	.											.	HGFAC	69	.	0			c.A1186T						.						22	23	23					4																	3447852		2200	4291	6491	SO:0001583	missense	3083	exon10			TGCGGCAGGAGGC	D14012	CCDS3369.1, CCDS75098.1	4p16	2008-02-07			ENSG00000109758	ENSG00000109758	3.4.21.-		4894	protein-coding gene	gene with protein product		604552				7683665, 8226803	Standard	XM_005247966		Approved	HGFAP, HGFA	uc003ghc.3	Q04756	OTTHUMG00000090281	ENST00000382774.3:c.1186A>T	chr4.hg19:g.3447852A>T	ENSP00000372224:p.Arg396Trp	127.0	0.0		83.0	41.0	NM_001528	Q14726|Q2M1W7|Q53X47	Missense_Mutation	SNP	ENST00000382774.3	hg19	CCDS3369.1	.	.	.	.	.	.	.	.	.	.	A	14.03	2.415163	0.42817	.	.	ENSG00000109758	ENST00000382774;ENST00000511533	D;D	0.93247	-3.19;-3.19	3.73	-0.707	0.11245	Peptidase cysteine/serine, trypsin-like (1);	0.549223	0.17419	N	0.174883	D	0.86410	0.5926	N	0.19112	0.55	0.22435	N	0.999105	D;P	0.54772	0.968;0.907	B;B	0.43809	0.432;0.225	T	0.80243	-0.1463	10	0.72032	D	0.01	.	9.943	0.41591	0.4923:0.5077:0.0:0.0	.	403;396	D6RAR4;Q04756	.;HGFA_HUMAN	W	396;403	ENSP00000372224:R396W;ENSP00000421801:R403W	ENSP00000372224:R396W	R	+	1	2	HGFAC	3417650	0.000000	0.05858	0.043000	0.18650	0.062000	0.15995	0.381000	0.20619	-0.280000	0.09154	0.533000	0.62120	AGG	.	.		0.677	HGFAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206607.3			T	3447852	A	T	3447852	3	4	344	1	0	0	0	0	1	0	0	0	7095	179	7	4	1224	4	HGFAC	4	3447852	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	258256	3447852	187706424	353	47716										
OTOP1	133060	hgsc.bcm.edu	37	chr4	4199319	4199319	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tagcgggggtggccctcagcAcagaggatggccaagattga	16	9	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:4199319A>T	ENST00000296358.4	-	5	1266	c.1242T>A	c.(1240-1242)tgT>tgA	p.C414*		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	414					biomineral tissue development (GO:0031214)|detection of gravity (GO:0009590)|inner ear morphogenesis (GO:0042472)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		GGCCCTCAGCACAGAGGATGG	0.572																																					p.C414X		Atlas-SNP	.											.	OTOP1	118	.	0			c.T1242A						.						54	60	58					4																	4199319		2203	4300	6503	SO:0001587	stop_gained	133060	exon5			CTCAGCACAGAGG	BK000653	CCDS3372.1	4p16.2	2008-02-05			ENSG00000163982	ENSG00000163982			19656	protein-coding gene	gene with protein product		607806				12651873	Standard	NM_177998		Approved		uc003ghp.1	Q7RTM1	OTTHUMG00000090301	ENST00000296358.4:c.1242T>A	chr4.hg19:g.4199319A>T	ENSP00000296358:p.Cys414*	68.0	0.0		57.0	32.0	NM_177998	A1L476	Nonsense_Mutation	SNP	ENST00000296358.4	hg19	CCDS3372.1	.	.	.	.	.	.	.	.	.	.	A	16.07	3.018017	0.54576	.	.	ENSG00000163982	ENST00000296358	.	.	.	4.76	-7.17	0.01511	.	0.270316	0.44483	D	0.000443	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05620	T	0.96	1.1779	14.5137	0.67804	0.4532:0.0:0.5468:0.0	.	.	.	.	X	414	.	ENSP00000296358:C414X	C	-	3	2	OTOP1	4250220	0.804000	0.28969	0.008000	0.14137	0.223000	0.24884	-0.007000	0.12810	-1.451000	0.01933	0.164000	0.16699	TGT	.	.		0.572	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206661.2	NM_177998		T	4199319	A	T	4199319	4	4	344	1	0	0	0	0	0	1	0	0	11314	157	6	4	604	4	OTOP1	4	4199319	Nonsense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	751467	4199319	186954957	354	47717										
ZBTB49	166793	hgsc.bcm.edu	37	chr4	4304686	4304686	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	attgcattagtgagacggagAggcctgaagacccggctgcc	14	10	0	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:4304686A>G	ENST00000337872.4	+	3	1244	c.1123A>G	c.(1123-1125)Agg>Ggg	p.R375G	ZBTB49_ENST00000355834.3_Missense_Mutation_p.R375G|ZBTB49_ENST00000538529.1_5'UTR	NM_145291.3	NP_660334.3	Q6ZSB9	ZBT49_HUMAN	zinc finger and BTB domain containing 49	375					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	28						TGAGACGGAGAGGCCTGAAGA	0.458																																					p.R375G		Atlas-SNP	.											.	ZBTB49	63	.	0			c.A1123G						.						46	49	48					4																	4304686		2203	4300	6503	SO:0001583	missense	166793	exon3			ACGGAGAGGCCTG	AK095878	CCDS3375.1	4p16.2	2013-01-08	2010-01-26	2010-01-26	ENSG00000168826	ENSG00000168826		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	19883	protein-coding gene	gene with protein product			"zinc finger protein 509"	ZNF509		12477932	Standard	NM_145291		Approved	FLJ38559	uc003ghu.3	Q6ZSB9	OTTHUMG00000090325	ENST00000337872.4:c.1123A>G	chr4.hg19:g.4304686A>G	ENSP00000338807:p.Arg375Gly	186.0	0.0		138.0	45.0	NM_145291	Q59FJ4|Q5EBN0|Q8TB80	Missense_Mutation	SNP	ENST00000337872.4	hg19	CCDS3375.1	.	.	.	.	.	.	.	.	.	.	A	10.63	1.405189	0.25378	.	.	ENSG00000168826	ENST00000355834;ENST00000337872	T;T	0.15256	2.44;2.78	5.66	-10.1	0.00402	Aspartate carbamoyltransferase regulatory subunit, C-terminal (1);	0.655977	0.14264	N	0.330595	T	0.09512	0.0234	L	0.52364	1.645	0.09310	N	0.999998	B;B	0.28933	0.228;0.179	B;B	0.27796	0.083;0.052	T	0.06917	-1.0800	10	0.22706	T	0.39	.	6.4644	0.21973	0.2364:0.5197:0.1585:0.0853	.	375;375	Q6ZSB9-2;Q6ZSB9	.;ZBT49_HUMAN	G	375	ENSP00000348091:R375G;ENSP00000338807:R375G	ENSP00000338807:R375G	R	+	1	2	ZBTB49	4355587	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.391000	0.07323	-1.721000	0.01378	-1.271000	0.01417	AGG	.	.		0.458	ZBTB49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206688.3	NM_145291		G	4304686	A	G	4304686	3	3	344	1	0	0	0	0	1	0	0	0	17565	295	11	2	1129	2	ZBTB49	4	4304686	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	105367	4304686	186849590	355	47718										
SORCS2	57537	hgsc.bcm.edu	37	chr4	7730109	7730109	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcatgcctctgcagttttccAaggagctggatgcctacaac	9	12	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:7730109A>G	ENST00000507866.2	+	22	3011	c.2902A>G	c.(2902-2904)Aag>Gag	p.K968E	SORCS2_ENST00000329016.9_Missense_Mutation_p.K796E	NM_020777.2	NP_065828.2	Q96PQ0	SORC2_HUMAN	sortilin-related VPS10 domain containing receptor 2	968					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(8)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	42						GCAGTTTTCCAAGGAGCTGGA	0.587																																					p.K968E		Atlas-SNP	.											.	SORCS2	98	.	0			c.A2902G						.						62	68	66					4																	7730109		1962	4141	6103	SO:0001583	missense	57537	exon22			TTTTCCAAGGAGC	AB037750	CCDS47008.1	4p16.1	2008-02-05			ENSG00000184985	ENSG00000184985			16698	protein-coding gene	gene with protein product		606284				11499680	Standard	NM_020777		Approved	KIAA1329	uc003gkb.4	Q96PQ0	OTTHUMG00000159981	ENST00000507866.2:c.2902A>G	chr4.hg19:g.7730109A>G	ENSP00000422185:p.Lys968Glu	72.0	0.0		47.0	18.0	NM_020777	Q9P2L7	Missense_Mutation	SNP	ENST00000507866.2	hg19	CCDS47008.1	.	.	.	.	.	.	.	.	.	.	A	4.926	0.172121	0.09391	.	.	ENSG00000184985	ENST00000507866;ENST00000329016	T;T	0.14144	2.53;2.54	4.1	2.85	0.33270	.	2.422050	0.02388	N	0.079407	T	0.16385	0.0394	L	0.53249	1.67	0.25691	N	0.985684	B;B	0.09022	0.001;0.002	B;B	0.06405	0.002;0.002	T	0.26677	-1.0096	10	0.32370	T	0.25	.	6.268	0.20939	0.7516:0.1614:0.0869:0.0	.	796;968	B5MED8;Q96PQ0	.;SORC2_HUMAN	E	968;796	ENSP00000422185:K968E;ENSP00000329124:K796E	ENSP00000329124:K796E	K	+	1	0	SORCS2	7781009	0.512000	0.26186	0.997000	0.53966	0.135000	0.20990	1.243000	0.32767	0.501000	0.28013	0.460000	0.39030	AAG	.	.		0.587	SORCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358685.4	NM_020777		G	7730109	A	G	7730109	3	3	344	1	0	0	0	0	1	0	0	0	14946	131	5	2	2988	2	SORCS2	4	7730109	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3425423	7730109	183424167	356	47719										
CD38	952	hgsc.bcm.edu	37	chr4	15850179	15850179	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tagacctgacaagtttcttcAgtgtgtgaaaaatcctgagg	10	7	2	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:15850179A>T	ENST00000226279.3	+	8	994	c.857A>T	c.(856-858)cAg>cTg	p.Q286L		NM_001775.2	NP_001766.2	P28907	CD38_HUMAN	CD38 molecule	286					apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|female pregnancy (GO:0007565)|long term synaptic depression (GO:0060292)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone resorption (GO:0045779)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell growth (GO:0030307)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of insulin secretion (GO:0032024)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vasoconstriction (GO:0045907)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hydroperoxide (GO:0033194)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	NAD(P)+ nucleosidase activity (GO:0050135)|NAD+ nucleosidase activity (GO:0003953)|phosphorus-oxygen lyase activity (GO:0016849)|transferase activity (GO:0016740)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|stomach(1)	14						AAGTTTCTTCAGTGTGTGAAA	0.428																																					p.Q286L		Atlas-SNP	.											.	CD38	36	.	0			c.A857T						.						156	130	139					4																	15850179		2203	4300	6503	SO:0001583	missense	952	exon8			TTCTTCAGTGTGT	D84276	CCDS3417.1	4p15.32	2010-05-04	2006-03-28		ENSG00000004468	ENSG00000004468	3.2.2.5	"CD molecules"	1667	protein-coding gene	gene with protein product	"ADP-ribosyl cyclase 1", "NAD(+) nucleosidase"	107270	"CD38 antigen (p45)"			9074508, 2319135	Standard	NM_001775		Approved		uc003gol.1	P28907	OTTHUMG00000048206	ENST00000226279.3:c.857A>T	chr4.hg19:g.15850179A>T	ENSP00000226279:p.Gln286Leu	63.0	0.0		49.0	15.0	NM_001775	O00121|O00122|Q96HY4	Missense_Mutation	SNP	ENST00000226279.3	hg19	CCDS3417.1	.	.	.	.	.	.	.	.	.	.	A	10.81	1.454952	0.26161	.	.	ENSG00000004468	ENST00000226279	T	0.15372	2.43	4.95	3.78	0.43462	NAD(P)-binding domain (1);	0.247806	0.40908	D	0.001000	T	0.16385	0.0394	L	0.49513	1.565	0.09310	N	0.999995	P	0.45474	0.859	B	0.42422	0.387	T	0.10337	-1.0634	10	0.49607	T	0.09	-3.34	7.1939	0.25841	0.9013:0.0:0.0987:0.0	.	286	P28907	CD38_HUMAN	L	286	ENSP00000226279:Q286L	ENSP00000226279:Q286L	Q	+	2	0	CD38	15459277	0.929000	0.31497	0.002000	0.10522	0.002000	0.02628	3.287000	0.51732	1.032000	0.39892	0.528000	0.53228	CAG	.	.		0.428	CD38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250322.2	NM_001775		T	15850179	A	T	15850179	3	4	344	1	0	0	0	0	1	0	0	0	3011	188	7	4	887	4	CD38	4	15850179	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	8120070	15850179	175304097	357	47720										
PROM1	8842	hgsc.bcm.edu	37	chr4	16025970	16025970	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtgttgtactgggccaatatAtatttgatttgctgaaaaaa	9	4	0	2	rs368213921		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:16025970A>T	ENST00000510224.1	-	7	890	c.642T>A	c.(640-642)taT>taA	p.Y214*	PROM1_ENST00000543373.1_Nonsense_Mutation_p.Y205*|PROM1_ENST00000508167.1_Nonsense_Mutation_p.Y205*|PROM1_ENST00000502943.1_5'UTR|PROM1_ENST00000505450.1_Nonsense_Mutation_p.Y205*|PROM1_ENST00000447510.2_Nonsense_Mutation_p.Y214*|PROM1_ENST00000539194.1_Nonsense_Mutation_p.Y214*|PROM1_ENST00000540805.1_Nonsense_Mutation_p.Y214*			O43490	PROM1_HUMAN	prominin 1	214					camera-type eye photoreceptor cell differentiation (GO:0060219)|glomerular parietal epithelial cell differentiation (GO:0072139)|glomerular visceral epithelial cell differentiation (GO:0072112)|photoreceptor cell maintenance (GO:0045494)|positive regulation of nephron tubule epithelial cell differentiation (GO:2000768)|retina layer formation (GO:0010842)|retina morphogenesis in camera-type eye (GO:0060042)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actinin binding (GO:0042805)|cadherin binding (GO:0045296)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|liver(1)|lung(11)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(2)	35						GGGCCAATATATATTTGATTT	0.348																																					p.Y214X		Atlas-SNP	.											.	PROM1	91	.	0			c.T642A						.						119	109	112					4																	16025970		1834	4096	5930	SO:0001587	stop_gained	8842	exon6			CAATATATATTTG	AF027208	CCDS47029.1, CCDS54746.1, CCDS54747.1, CCDS54748.1	4p15	2013-06-06	2001-11-28	2003-03-28	ENSG00000007062	ENSG00000007062		"CD molecules"	9454	protein-coding gene	gene with protein product		604365	"prominin (mouse)-like 1", "macular dystrophy, retinal 2", "Stargardt disease 4 (autosomal dominant)"	PROML1, MCDR2, STGD4		11467842	Standard	NM_006017		Approved	AC133, CD133, RP41, CORD12	uc003goo.2	O43490	OTTHUMG00000160180	ENST00000510224.1:c.642T>A	chr4.hg19:g.16025970A>T	ENSP00000426809:p.Tyr214*	73.0	0.0		55.0	33.0	NM_006017	Q6SV49|Q6SV50|Q6SV51|Q6SV52|Q6SV53|Q96EN6	Nonsense_Mutation	SNP	ENST00000510224.1	hg19	CCDS47029.1	.	.	.	.	.	.	.	.	.	.	A	40	8.242865	0.98722	.	.	ENSG00000007062	ENST00000447510;ENST00000540805;ENST00000539194;ENST00000505450;ENST00000508167;ENST00000510224;ENST00000543373	.	.	.	4.6	-0.693	0.11298	.	0.064473	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-26.2213	9.6942	0.40147	0.6095:0.0:0.3905:0.0	.	.	.	.	X	214;214;214;205;205;214;205	.	ENSP00000415481:Y214X	Y	-	3	2	PROM1	15635068	0.117000	0.22190	0.000000	0.03702	0.234000	0.25298	0.337000	0.19841	-0.279000	0.09167	0.459000	0.35465	TAT	.	.		0.348	PROM1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359595.2	NM_006017		T	16025970	A	T	16025970	4	4	344	1	0	0	0	0	0	1	0	0	12567	456	16	4	2039	4	PROM1	4	16025970	Nonsense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	175791	16025970	175128306	358	47721										
NCAPG	64151	hgsc.bcm.edu	37	chr4	17814020	17814020	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaggaagatggtggccttttAaattatttgtttacttttct	9	4	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:17814020A>C	ENST00000251496.2	+	2	464	c.288A>C	c.(286-288)ttA>ttC	p.L96F	DCAF16_ENST00000382247.1_5'Flank|DCAF16_ENST00000507768.1_5'Flank|DCAF16_ENST00000536863.1_5'Flank	NM_022346.4	NP_071741.2	Q9BPX3	CND3_HUMAN	non-SMC condensin I complex, subunit G	96					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	27				STAD - Stomach adenocarcinoma(129;0.18)		GTGGCCTTTTAAATTATTTGT	0.368																																					p.L96F		Atlas-SNP	.											.	NCAPG	76	.	0			c.A288C						.						68	69	68					4																	17814020		2203	4300	6503	SO:0001583	missense	64151	exon2			CCTTTTAAATTAT	AF331796	CCDS3424.1	4p15.32	2014-01-15			ENSG00000109805	ENSG00000109805			24304	protein-coding gene	gene with protein product	"chromosome condensation protein G"	606280				10910072, 11136719	Standard	NM_022346		Approved	FLJ12450, hCAP-G, CAP-G, YCG1	uc003gpp.4	Q9BPX3	OTTHUMG00000128539	ENST00000251496.2:c.288A>C	chr4.hg19:g.17814020A>C	ENSP00000251496:p.Leu96Phe	70.0	0.0		47.0	20.0	NM_022346	Q3MJE0|Q96SV9|Q9BUR3|Q9BVY1|Q9H914|Q9H9Z6|Q9HBI9	Missense_Mutation	SNP	ENST00000251496.2	hg19	CCDS3424.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.133591	0.77662	.	.	ENSG00000109805	ENST00000251496	T	0.35605	1.3	5.28	2.87	0.33458	Armadillo-type fold (1);	0.160448	0.43579	D	0.000557	T	0.46718	0.1407	M	0.78456	2.415	0.50632	D	0.999881	D	0.62365	0.991	P	0.57679	0.825	T	0.44128	-0.9348	10	0.45353	T	0.12	-9.0634	2.5665	0.04784	0.517:0.0:0.286:0.197	.	96	Q9BPX3	CND3_HUMAN	F	96	ENSP00000251496:L96F	ENSP00000251496:L96F	L	+	3	2	NCAPG	17423118	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	3.220000	0.51207	0.845000	0.35118	0.533000	0.62120	TTA	.	.		0.368	NCAPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250375.1	NM_022346		C	17814020	A	C	17814020	3	2	344	1	0	0	0	0	1	0	0	0	10216	359	13	5	294	5	NCAPG	4	17814020	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1788050	17814020	173340256	359	47722										
SLIT2	9353	hgsc.bcm.edu	37	chr4	20591288	20591288	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgagttgtgtgaggagaagcTggacttctgtgcccaggacc	15	8	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:20591288T>A	ENST00000504154.1	+	30	3362	c.3110T>A	c.(3109-3111)cTg>cAg	p.L1037Q	SLIT2_ENST00000273739.5_Missense_Mutation_p.L1050Q|SLIT2_ENST00000503837.1_Missense_Mutation_p.L1033Q|SLIT2_ENST00000503823.1_Missense_Mutation_p.L1029Q	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	1037	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)			NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						GAGGAGAAGCTGGACTTCTGT	0.493																																					p.L1037Q		Atlas-SNP	.											.	SLIT2	290	.	0			c.T3110A						.						145	117	127					4																	20591288		2203	4300	6503	SO:0001583	missense	9353	exon30			AGAAGCTGGACTT	AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"slit (Drosophila) homolog 2"	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.3110T>A	chr4.hg19:g.20591288T>A	ENSP00000422591:p.Leu1037Gln	96.0	0.0		86.0	34.0	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Missense_Mutation	SNP	ENST00000504154.1	hg19	CCDS3426.1	.	.	.	.	.	.	.	.	.	.	T	26.8	4.772174	0.90108	.	.	ENSG00000145147	ENST00000503823;ENST00000504154;ENST00000273739;ENST00000382173;ENST00000503837	D;D;D;D	0.92699	-2.23;-2.23;-3.09;-2.23	5.42	5.42	0.78866	Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.89269	0.6667	L	0.41492	1.28	0.80722	D	1	P;B	0.36909	0.573;0.415	B;B	0.37601	0.254;0.096	D	0.90196	0.4253	10	0.87932	D	0	.	15.7632	0.78103	0.0:0.0:0.0:1.0	.	1029;1037	O94813-3;O94813	.;SLIT2_HUMAN	Q	1029;1037;1050;1033;1033	ENSP00000427548:L1029Q;ENSP00000422591:L1037Q;ENSP00000273739:L1050Q;ENSP00000422261:L1033Q	ENSP00000273739:L1050Q	L	+	2	0	SLIT2	20200386	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.847000	0.69451	2.179000	0.69175	0.533000	0.62120	CTG	.	.		0.493	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2			A	20591288	T	A	20591288	3	1	344	1	0	0	0	0	1	0	0	0	14755	1580	55	4	3228	4	SLIT2	4	20591288	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2777268	20591288	170562988	360	47723										
PCDH7	5099	hgsc.bcm.edu	37	chr4	30724512	30724512	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaaagtacttcttgcacaccTcgacccctctggactatgag	7	13	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:30724512T>C	ENST00000361762.2	+	1	2476	c.1468T>C	c.(1468-1470)Tcg>Ccg	p.S490P	PCDH7_ENST00000543491.1_Missense_Mutation_p.S490P	NM_002589.2	NP_002580.2	O60245	PCDH7_HUMAN	protocadherin 7	490	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(8)|liver(1)|lung(26)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	55						CTTGCACACCTCGACCCCTCT	0.612																																					p.S490P		Atlas-SNP	.											.	PCDH7	215	.	0			c.T1468C						.						96	74	81					4																	30724512		2203	4300	6503	SO:0001583	missense	5099	exon1			CACACCTCGACCC	AB006755	CCDS33971.1, CCDS75116.1	4p15	2014-06-13	2007-02-12			ENSG00000169851		"Cadherins / Protocadherins : Non-clustered"	8659	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 120"	602988	"BH-protocadherin (brain-heart)"			9615233	Standard	NM_002589		Approved	BH-Pcdh, PPP1R120	uc021xnd.1	O60245		ENST00000361762.2:c.1468T>C	chr4.hg19:g.30724512T>C	ENSP00000355243:p.Ser490Pro	57.0	0.0		45.0	22.0	NM_032457	O60246|O60247|Q4W5C4	Missense_Mutation	SNP	ENST00000361762.2	hg19	CCDS33971.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.40|16.40	3.113015|3.113015	0.56398|0.56398	.|.	.|.	ENSG00000169851|ENSG00000169851	ENST00000511884|ENST00000361762;ENST00000543491;ENST00000333135	.|T;T	.|0.52295	.|0.67;0.67	5.26|5.26	5.26|5.26	0.73747|0.73747	.|Cadherin (4);Cadherin-like (1);	.|.	.|.	.|.	.|.	T|T	0.70718|0.70718	0.3256|0.3256	M|M	0.82630|0.82630	2.6|2.6	0.52099|0.52099	D|D	0.99994|0.99994	.|D;D;D	.|0.76494	.|0.999;0.999;0.999	.|D;D;D	.|0.72982	.|0.974;0.974;0.979	T|T	0.76162|0.76162	-0.3060|-0.3060	5|9	.|0.87932	.|D	.|0	.|.	15.3401|15.3401	0.74290|0.74290	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|490;443;490	.|F5GWJ1;O60245-3;O60245	.|.;.;PCDH7_HUMAN	P|P	179|490;490;443	.|ENSP00000355243:S490P;ENSP00000441802:S490P	.|ENSP00000330302:S443P	L|S	+|+	2|1	0|0	PCDH7|PCDH7	30333610|30333610	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.866000|0.866000	0.49608|0.49608	6.093000|6.093000	0.71422|0.71422	2.208000|2.208000	0.71279|0.71279	0.533000|0.533000	0.62120|0.62120	CTC|TCG	.	.		0.612	PCDH7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360366.1	NM_032457, NM_002589		C	30724512	T	C	30724512	3	2	344	1	0	0	0	0	1	0	0	0	11525	1551	54	2	1470	2	PCDH7	4	30724512	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	10133224	30724512	160429764	361	47724										
PGM2	55276	hgsc.bcm.edu	37	chr4	37836307	37836307	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aggcatcgtgatcagttttgAcgcccgagctcatccatcca	9	13	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:37836307A>G	ENST00000381967.4	+	3	417	c.317A>G	c.(316-318)gAc>gGc	p.D106G	PGM2_ENST00000544359.1_5'UTR|PGM2_ENST00000537241.1_Intron	NM_018290.3	NP_060760.2	Q96G03	PGM2_HUMAN	phosphoglucomutase 2	106					carbohydrate metabolic process (GO:0005975)|deoxyribose phosphate catabolic process (GO:0046386)|galactose catabolic process (GO:0019388)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	magnesium ion binding (GO:0000287)|phosphoglucomutase activity (GO:0004614)|phosphopentomutase activity (GO:0008973)			breast(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(2)|urinary_tract(1)	19						ATCAGTTTTGACGCCCGAGCT	0.338																																					p.D106G		Atlas-SNP	.											.	PGM2	45	.	0			c.A317G						.						89	100	96					4																	37836307		2203	4300	6503	SO:0001583	missense	55276	exon3			GTTTTGACGCCCG	BC010087	CCDS3443.1	4p14	2012-10-02			ENSG00000169299	ENSG00000169299	5.4.2.2		8906	protein-coding gene	gene with protein product	"phosphopentomutase"	172000				9549096	Standard	NM_018290		Approved	FLJ10983	uc011byb.1	Q96G03	OTTHUMG00000097813	ENST00000381967.4:c.317A>G	chr4.hg19:g.37836307A>G	ENSP00000371393:p.Asp106Gly	426.0	0.0		377.0	182.0	NM_018290	B4E0G8|Q53FP5|Q5QTR0|Q9H0P9|Q9NV22	Missense_Mutation	SNP	ENST00000381967.4	hg19	CCDS3443.1	.	.	.	.	.	.	.	.	.	.	A	17.49	3.403745	0.62288	.	.	ENSG00000169299	ENST00000381967	D	0.97575	-4.44	6.05	6.05	0.98169	Alpha-D-phosphohexomutase, alpha/beta/alpha domain I (1);Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III (2);	0.087163	0.85682	D	0.000000	D	0.99302	0.9756	H	0.99650	4.68	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98366	1.0551	10	0.87932	D	0	-0.9632	16.5932	0.84781	1.0:0.0:0.0:0.0	.	106	Q96G03	PGM2_HUMAN	G	106	ENSP00000371393:D106G	ENSP00000371393:D106G	D	+	2	0	PGM2	37512702	1.000000	0.71417	0.979000	0.43373	0.056000	0.15407	8.875000	0.92372	2.320000	0.78422	0.528000	0.53228	GAC	.	.		0.338	PGM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215079.2	NM_018290		G	37836307	A	G	37836307	3	3	344	1	0	0	0	0	1	0	0	0	11807	275	10	2	327	2	PGM2	4	37836307	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	7111795	37836307	153317969	362	47725										
TLR10	81793	hgsc.bcm.edu	37	chr4	38774823	38774823	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gattgtagaacctcgagactCttcatttaactctgtgaatg	8	8	3	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:38774823C>G	ENST00000308973.4	-	4	2994	c.2389G>C	c.(2389-2391)Gag>Cag	p.E797Q	TLR10_ENST00000507953.1_5'Flank|TLR10_ENST00000361424.2_Missense_Mutation_p.E797Q|TLR10_ENST00000506111.1_Missense_Mutation_p.E797Q|TLR10_ENST00000508334.1_Missense_Mutation_p.E797Q	NM_001017388.2|NM_001195107.1|NM_030956.3	NP_001017388.1|NP_001182036.1|NP_112218.2	Q9BXR5	TLR10_HUMAN	toll-like receptor 10	797					immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of inflammatory response (GO:0050729)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(2)	25						CCTCGAGACTCTTCATTTAAC	0.418																																					p.E797Q		Atlas-SNP	.											.	TLR10	87	.	0			c.G2389C						.						85	83	84					4																	38774823		2203	4300	6503	SO:0001583	missense	81793	exon2			GAGACTCTTCATT	AF296673	CCDS3445.1	4p14	2009-11-23			ENSG00000174123	ENSG00000174123		"CD molecules"	15634	protein-coding gene	gene with protein product		606270				11267672	Standard	NM_030956		Approved	CD290	uc003gtk.3	Q9BXR5	OTTHUMG00000128578	ENST00000308973.4:c.2389G>C	chr4.hg19:g.38774823C>G	ENSP00000308925:p.Glu797Gln	76.0	0.0		74.0	20.0	NM_001017388	A8K7L1|B3Y668|D1CS21|D1CS22|Q32MI7|Q32MI8|Q5FWG4|Q6UXL3	Missense_Mutation	SNP	ENST00000308973.4	hg19	CCDS3445.1	.	.	.	.	.	.	.	.	.	.	C	9.620	1.133530	0.21041	.	.	ENSG00000174123	ENST00000308973;ENST00000506111;ENST00000361424;ENST00000508334	T;T;T;T	0.13196	2.61;2.61;2.61;2.61	4.99	3.23	0.37069	.	1.046150	0.07592	N	0.922093	T	0.07413	0.0187	N	0.08118	0	0.09310	N	1	B	0.12013	0.005	B	0.06405	0.002	T	0.39418	-0.9615	10	0.32370	T	0.25	.	6.1107	0.20100	0.0:0.6552:0.1719:0.1728	.	797	Q9BXR5	TLR10_HUMAN	Q	797	ENSP00000308925:E797Q;ENSP00000421483:E797Q;ENSP00000354459:E797Q;ENSP00000424923:E797Q	ENSP00000308925:E797Q	E	-	1	0	TLR10	38451218	0.000000	0.05858	0.007000	0.13788	0.024000	0.10985	0.151000	0.16283	0.583000	0.29574	0.650000	0.86243	GAG	.	.		0.418	TLR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250430.1			G	38774823	C	G	38774823	3	3	344	1	0	0	0	0	1	0	0	0	15965	922	32	4	50	4	TLR10	4	38774823	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	938516	38774823	152379453	363	47726										
SHISA3	152573	hgsc.bcm.edu	37	chr4	42403330	42403330	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgcctggtgccctcaccgccCccgccatacaccaccagcca	7	22	1	0	rs377514630		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:42403330C>A	ENST00000319234.4	+	2	797	c.579C>A	c.(577-579)ccC>ccA	p.P193P		NM_001080505.1	NP_001073974.1	A0PJX4	SHSA3_HUMAN	shisa family member 3	193	Poly-Pro.				multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	12						CCTCACCGCCCCCGCCATACA	0.657																																					p.P193P		Atlas-SNP	.											.	SHISA3	27	.	0			c.C579A						.						45	45	45					4																	42403330		2203	4300	6503	SO:0001819	synonymous_variant	152573	exon2			ACCGCCCCCGCCA	BC012029	CCDS33979.1	4p13	2013-07-31	2013-07-31		ENSG00000178343	ENSG00000178343		"Shisa homologs"	25159	protein-coding gene	gene with protein product			"shisa homolog 3 (Xenopus laevis)"				Standard	NM_001080505		Approved	hShisa3	uc003gwp.3	A0PJX4	OTTHUMG00000161043	ENST00000319234.4:c.579C>A	chr4.hg19:g.42403330C>A		57.0	0.0		63.0	32.0	NM_001080505	A0PJX3|Q96EQ5	Silent	SNP	ENST00000319234.4	hg19	CCDS33979.1																																																																																			.	.		0.657	SHISA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363539.1	NM_001080505		A	42403330	C	A	42403330	2	1	344	1	0	0	0	0	0	0	0	1	14296	610	22	3		3	SHISA3	4	42403330	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	3628507	42403330	148750946	364	47727										
ATP8A1	10396	hgsc.bcm.edu	37	chr4	42446619	42446619	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtccaatatgatgtctccaaTccagctttcaaacacacagt	5	12	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:42446619T>C	ENST00000381668.5	-	32	3222	c.2991A>G	c.(2989-2991)ggA>ggG	p.G997G	ATP8A1_ENST00000264449.10_Silent_p.G982G|AC084010.1_ENST00000582816.1_RNA	NM_006095.2	NP_006086.1	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	997					cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	51					Phosphatidylserine(DB00144)	ATGTCTCCAATCCAGCTTTCA	0.363																																					p.G997G		Atlas-SNP	.											.	ATP8A1	206	.	0			c.A2991G						.						130	117	122					4																	42446619		2203	4300	6503	SO:0001819	synonymous_variant	10396	exon32			CTCCAATCCAGCT	AF067820	CCDS3466.1, CCDS47049.1	4p13	2010-04-20	2007-09-19		ENSG00000124406	ENSG00000124406		"ATPases / P-type"	13531	protein-coding gene	gene with protein product		609542	"ATPase, aminophospholipid transporter (APLT), Class I, type 8A, member 1"			10198212, 9548971	Standard	NM_006095		Approved	ATPIA	uc003gwr.2	Q9Y2Q0	OTTHUMG00000099403	ENST00000381668.5:c.2991A>G	chr4.hg19:g.42446619T>C		95.0	0.0		58.0	26.0	NM_006095	Q32M35|Q32M36|Q4W5J7|Q4W5P2	Silent	SNP	ENST00000381668.5	hg19	CCDS3466.1																																																																																			.	.		0.363	ATP8A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216861.2	NM_006095		C	42446619	T	C	42446619	2	2	344	1	0	0	0	0	0	0	0	1	1192	1422	50	2		2	ATP8A1	4	42446619	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	43289	42446619	148707657	365	47728										
GRXCR1	389207	hgsc.bcm.edu	37	chr4	43022411	43022411	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aatgaatgaatcaggagaacTgcaagacatcctaaccaaaa	7	8	1	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:43022411T>A	ENST00000399770.2	+	3	668	c.668T>A	c.(667-669)cTg>cAg	p.L223Q		NM_001080476.2	NP_001073945.1	A8MXD5	GRCR1_HUMAN	glutaredoxin, cysteine rich 1	223	Glutaredoxin. {ECO:0000255|PROSITE- ProRule:PRU00686}.				auditory receptor cell differentiation (GO:0042491)|cell redox homeostasis (GO:0045454)|inner ear receptor cell development (GO:0060119)|inner ear receptor stereocilium organization (GO:0060122)|negative regulation of phosphatase activity (GO:0010923)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of sound (GO:0007605)|vestibular receptor cell development (GO:0060118)	kinocilium (GO:0060091)|stereocilium (GO:0032420)	electron carrier activity (GO:0009055)|protein disulfide oxidoreductase activity (GO:0015035)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(22)|ovary(1)|prostate(2)|skin(1)	32						TCAGGAGAACTGCAAGACATC	0.308																																					p.L223Q		Atlas-SNP	.											.	GRXCR1	78	.	0			c.T668A						.						84	81	82					4																	43022411		1840	4077	5917	SO:0001583	missense	389207	exon3			GAGAACTGCAAGA		CCDS43225.1	4p14	2014-06-12			ENSG00000215203	ENSG00000215203			31673	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 88"	613283	"deafness, autosomal recessive 25"	DFNB25		20137778	Standard	NM_001080476		Approved	PPP1R88	uc003gwt.3	A8MXD5	OTTHUMG00000160434	ENST00000399770.2:c.668T>A	chr4.hg19:g.43022411T>A	ENSP00000382670:p.Leu223Gln	277.0	0.0		212.0	87.0	NM_001080476		Missense_Mutation	SNP	ENST00000399770.2	hg19	CCDS43225.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.399797	0.83120	.	.	ENSG00000215203	ENST00000399770	D	0.86497	-2.13	5.79	5.79	0.91817	Glutaredoxin (1);Thioredoxin-like fold (2);	0.000000	0.56097	U	0.000027	D	0.95149	0.8428	M	0.94021	3.485	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.96228	0.9166	10	0.87932	D	0	-11.4336	15.3062	0.73992	0.0:0.0:0.0:1.0	.	223	A8MXD5	GRCR1_HUMAN	Q	223	ENSP00000382670:L223Q	ENSP00000382670:L223Q	L	+	2	0	GRXCR1	42717168	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.644000	0.83416	2.213000	0.71641	0.397000	0.26171	CTG	.	.		0.308	GRXCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360576.1	NM_001080476		A	43022411	T	A	43022411	3	1	344	1	0	0	0	0	1	0	0	0	6821	1580	55	4	678	4	GRXCR1	4	43022411	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	575792	43022411	148131865	366	47729										
GABRG1	2565	hgsc.bcm.edu	37	chr4	46066495	46066495	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggacaggaatgttcatccatGggaaagttatgaagctgaag	13	5	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:46066495G>T	ENST00000295452.4	-	5	755	c.588C>A	c.(586-588)ccC>ccA	p.P196P		NM_173536.3	NP_775807.2	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 1	196					gamma-aminobutyric acid signaling pathway (GO:0007214)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(2)|central_nervous_system(5)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(2)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	76				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GTTCATCCATGGGAAAGTTAT	0.269																																					p.P196P		Atlas-SNP	.											.	GABRG1	172	.	0			c.C588A						.						70	78	75					4																	46066495		2202	4289	6491	SO:0001819	synonymous_variant	2565	exon5			ATCCATGGGAAAG	BC031087	CCDS3470.1	4p12	2012-06-22			ENSG00000163285	ENSG00000163285		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4086	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma"	137166				1321425	Standard	NM_173536		Approved		uc003gxb.3	Q8N1C3	OTTHUMG00000128609	ENST00000295452.4:c.588C>A	chr4.hg19:g.46066495G>T		403.0	0.0		328.0	137.0	NM_173536	Q5H9T8	Silent	SNP	ENST00000295452.4	hg19	CCDS3470.1																																																																																			.	.		0.269	GABRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250470.1	NM_173536		T	46066495	G	T	46066495	2	4	344	1	0	0	0	0	0	0	0	1	6179	1335	47	3		3	GABRG1	4	46066495	Silent	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	3044084	46066495	145087781	367	47730										
GABRG1	2565	hgsc.bcm.edu	37	chr4	46099287	46099287	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cagaatttgtgtgatatctcCttcatgaatttttggggcca	9	7	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:46099287C>A	ENST00000295452.4	-	2	351	c.184G>T	c.(184-186)Gga>Tga	p.G62*		NM_173536.3	NP_775807.2	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 1	62					gamma-aminobutyric acid signaling pathway (GO:0007214)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.G62*(1)		breast(2)|central_nervous_system(5)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(2)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	76				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GTGATATCTCCTTCATGAATT	0.363																																					p.G62X		Atlas-SNP	.											.	GABRG1	172	.	1	Substitution - Nonsense(1)	lung(1)	c.G184T						.						180	180	180					4																	46099287		2203	4300	6503	SO:0001587	stop_gained	2565	exon2			TATCTCCTTCATG	BC031087	CCDS3470.1	4p12	2012-06-22			ENSG00000163285	ENSG00000163285		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4086	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma"	137166				1321425	Standard	NM_173536		Approved		uc003gxb.3	Q8N1C3	OTTHUMG00000128609	ENST00000295452.4:c.184G>T	chr4.hg19:g.46099287C>A	ENSP00000295452:p.Gly62*	204.0	1.0		126.0	66.0	NM_173536	Q5H9T8	Nonsense_Mutation	SNP	ENST00000295452.4	hg19	CCDS3470.1	.	.	.	.	.	.	.	.	.	.	C	37	6.060915	0.97246	.	.	ENSG00000163285	ENST00000295452;ENST00000540030	.	.	.	5.07	4.23	0.50019	.	0.113938	0.64402	D	0.000010	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	9.1223	0.36795	0.0:0.8361:0.0:0.1639	.	.	.	.	X	62	.	ENSP00000295452:G62X	G	-	1	0	GABRG1	45794044	1.000000	0.71417	1.000000	0.80357	0.863000	0.49368	3.522000	0.53480	1.363000	0.46019	-0.140000	0.14226	GGA	.	.		0.363	GABRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250470.1	NM_173536		A	46099287	C	A	46099287	4	1	344	1	0	0	0	0	0	1	0	0	6179	690	24	3	1245	3	GABRG1	4	46099287	Nonsense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	32792	46099287	145054989	368	47731										
SGCB	6443	hgsc.bcm.edu	37	chr4	52890300	52890300	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cgggtggtgctgaccatcacAgatccatttaggatgatact	11	9	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:52890300A>C	ENST00000381431.5	-	6	1002	c.780T>G	c.(778-780)tcT>tcG	p.S260S	SGCB_ENST00000535450.1_Silent_p.S190S	NM_000232.4	NP_000223.1	Q16585	SGCB_HUMAN	sarcoglycan, beta (43kDa dystrophin-associated glycoprotein)	260	Cys-rich.				cardiac muscle cell development (GO:0055013)|muscle fiber development (GO:0048747)|muscle organ development (GO:0007517)|vascular smooth muscle cell development (GO:0097084)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of plasma membrane (GO:0005887)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)				breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(6)|prostate(1)	17			GBM - Glioblastoma multiforme(4;7.63e-12)|LUSC - Lung squamous cell carcinoma(32;0.00204)			TGACCATCACAGATCCATTTA	0.458																																					p.S260S		Atlas-SNP	.											.	SGCB	35	.	0			c.T780G						.						92	86	88					4																	52890300		2203	4300	6503	SO:0001819	synonymous_variant	6443	exon6			CATCACAGATCCA	U29586	CCDS3488.1	4q12	2014-09-17	2002-08-29		ENSG00000163069	ENSG00000163069			10806	protein-coding gene	gene with protein product		600900	"sarcoglycan, beta (43kD dystrophin-associated glycoprotein)"	LGMD2E		8968749	Standard	NM_000232		Approved	SGC, A3b	uc003gzj.2	Q16585	OTTHUMG00000128697	ENST00000381431.5:c.780T>G	chr4.hg19:g.52890300A>C		80.0	0.0		84.0	34.0	NM_000232	B7Z635|O00661	Silent	SNP	ENST00000381431.5	hg19	CCDS3488.1																																																																																			.	.		0.458	SGCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250596.2			C	52890300	A	C	52890300	2	2	344	1	0	0	0	0	0	0	0	1	14215	175	7	5		5	SGCB	4	52890300	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	6791013	52890300	138263976	369	47732										
SCFD2	152579	hgsc.bcm.edu	37	chr4	53786893	53786893	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttaaaacgtatatacttgccTggtgggtatgatttccagga	10	6	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:53786893T>A	ENST00000401642.3	-	6	1839	c.1706A>T	c.(1705-1707)cAg>cTg	p.Q569L	SCFD2_ENST00000388940.4_Splice_Site_p.Q569L	NM_152540.3	NP_689753.2	Q8WU76	SCFD2_HUMAN	sec1 family domain containing 2	569					protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)					breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	30			GBM - Glioblastoma multiforme(3;1.07e-26)|LUSC - Lung squamous cell carcinoma(32;0.0134)			TATACTTGCCTGGTGGGTATG	0.398																																					p.Q569L		Atlas-SNP	.											.	SCFD2	78	.	0			c.A1706T						.						83	87	86					4																	53786893		2203	4300	6503	SO:0001630	splice_region_variant	152579	exon6			CTTGCCTGGTGGG	AY299407	CCDS33984.1	4q12	2004-01-15			ENSG00000184178	ENSG00000184178			30676	protein-coding gene	gene with protein product						12477932	Standard	NM_152540		Approved	STXBP1L1, FLJ39514	uc003gzu.3	Q8WU76	OTTHUMG00000160588	ENST00000401642.3:c.1707+1A>T	chr4.hg19:g.53786893T>A		58.0	0.0		41.0	12.0	NM_152540	Q8N5F3|Q8N8H0|Q96ED3	Missense_Mutation	SNP	ENST00000401642.3	hg19	CCDS33984.1	.	.	.	.	.	.	.	.	.	.	T	19.97	3.925677	0.73213	.	.	ENSG00000184178	ENST00000401642;ENST00000388940	T;T	0.79454	-0.6;-1.27	4.96	4.96	0.65561	.	0.000000	0.85682	D	0.000000	T	0.82204	0.4986	L	0.47716	1.5	0.24607	N	0.993742	D;D	0.59357	0.981;0.985	D;D	0.74023	0.969;0.982	T	0.72890	-0.4155	10	0.33141	T	0.24	.	11.1967	0.48717	0.0:0.0:0.0:1.0	.	569;569	Q8WU76-2;Q8WU76	.;SCFD2_HUMAN	L	569	ENSP00000384182:Q569L;ENSP00000373592:Q569L	ENSP00000373592:Q569L	Q	-	2	0	SCFD2	53481650	1.000000	0.71417	1.000000	0.80357	0.780000	0.44128	4.416000	0.59815	2.208000	0.71279	0.459000	0.35465	CAG	.	.		0.398	SCFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361311.3	NM_152540	Missense_Mutation	A	53786893	T	A	53786893	5	1	344	1	0	0	0	0	0	0	1	0	13905	1594	55	4	364	4	SCFD2	4	53786893	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	896593	53786893	137367383	370	47733										
PDGFRA	5156	hgsc.bcm.edu	37	chr4	55138653	55138653	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctgaaggcacgccgcttcctGatattgagtggatgatatgc	12	9	0	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:55138653G>C	ENST00000257290.5	+	9	1661	c.1330G>C	c.(1330-1332)Gat>Cat	p.D444H	FIP1L1_ENST00000507166.1_Intron	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	444	Ig-like C2-type 5.				adrenal gland development (GO:0030325)|cardiac myofibril assembly (GO:0055003)|cell activation (GO:0001775)|cell chemotaxis (GO:0060326)|cellular response to amino acid stimulus (GO:0071230)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|epidermal growth factor receptor signaling pathway (GO:0007173)|estrogen metabolic process (GO:0008210)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hematopoietic progenitor cell differentiation (GO:0002244)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|Leydig cell differentiation (GO:0033327)|lung development (GO:0030324)|luteinization (GO:0001553)|male genitalia development (GO:0030539)|metanephric glomerular capillary formation (GO:0072277)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet aggregation (GO:0070527)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-alpha signaling pathway (GO:0035790)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of chemotaxis (GO:0050920)|regulation of mesenchymal stem cell differentiation (GO:2000739)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction involved in regulation of gene expression (GO:0023019)|viral process (GO:0016032)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet-derived growth factor alpha-receptor activity (GO:0005018)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|autonomic_ganglia(1)|bone(1)|breast(4)|central_nervous_system(17)|cervix(1)|endometrium(4)|eye(1)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(22)|kidney(6)|large_intestine(26)|liver(4)|lung(48)|ovary(4)|prostate(6)|skin(11)|small_intestine(49)|soft_tissue(727)|stomach(32)|urinary_tract(1)	967	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sunitinib(DB01268)	GCCGCTTCCTGATATTGAGTG	0.453			"Mis, O, T"	FIP1L1	"GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"				Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	TSP Lung(21;0.16)																											p.D444H	Pancreas(151;208 1913 7310 23853 37092)	Atlas-SNP	.		Dom	yes		4	4q11-q13	5156	"platelet-derived growth factor, alpha-receptor"		"L, M, O"	.	PDGFRA	1583	.	0			c.G1330C						.						147	137	140					4																	55138653		2203	4300	6503	SO:0001583	missense	5156	exon9	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	CTTCCTGATATTG	D50001	CCDS3495.1	4q12	2014-09-17			ENSG00000134853	ENSG00000134853		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	8803	protein-coding gene	gene with protein product		173490					Standard	NM_006206		Approved	CD140a, PDGFR2	uc003han.4	P16234	OTTHUMG00000128699	ENST00000257290.5:c.1330G>C	chr4.hg19:g.55138653G>C	ENSP00000257290:p.Asp444His	79.0	0.0		53.0	26.0	NM_006206	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Missense_Mutation	SNP	ENST00000257290.5	hg19	CCDS3495.1	.	.	.	.	.	.	.	.	.	.	G	9.627	1.135456	0.21123	.	.	ENSG00000134853	ENST00000257290	T	0.75050	-0.9	6.17	4.44	0.53790	Immunoglobulin-like fold (1);	1.075190	0.07507	U	0.908177	T	0.69342	0.3100	L	0.46157	1.445	0.34455	D	0.701073	B;P	0.35208	0.021;0.49	B;B	0.30572	0.038;0.117	T	0.64032	-0.6502	10	0.37606	T	0.19	.	13.3275	0.60467	0.1288:0.0:0.8712:0.0	.	444;444	P16234-3;P16234	.;PGFRA_HUMAN	H	444	ENSP00000257290:D444H	ENSP00000257290:D444H	D	+	1	0	PDGFRA	54833410	0.964000	0.33143	0.016000	0.15963	0.006000	0.05464	2.632000	0.46511	0.911000	0.36747	0.655000	0.94253	GAT	.	.		0.453	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206		C	55138653	G	C	55138653	3	2	344	1	0	0	0	0	1	0	0	0	11670	1290	45	4	1360	4	PDGFRA	4	55138653	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1351760	55138653	136015623	371	47734										
KDR	3791	hgsc.bcm.edu	37	chr4	55984967	55984967	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cagtccaagtccctctgtccCctgaaaaattaatttcaggg	7	12	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:55984967C>T	ENST00000263923.4	-	3	457	c.162G>A	c.(160-162)agG>agA	p.R54R		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	54	Ig-like C2-type 1.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CCCTCTGTCCCCTGAAAAATT	0.428			Mis		"NSCLC, angiosarcoma"					TSP Lung(20;0.16)																											p.R54R		Atlas-SNP	.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	.	KDR	307	.	0			c.G162A						.						70	72	71					4																	55984967		2203	4300	6503	SO:0001630	splice_region_variant	3791	exon3			CTGTCCCCTGAAA	AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.162-1G>A	chr4.hg19:g.55984967C>T		121.0	0.0		115.0	60.0	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Silent	SNP	ENST00000263923.4	hg19	CCDS3497.1																																																																																			.	.		0.428	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1		Silent	T	55984967	C	T	55984967	5	4	344	1	0	0	0	0	0	0	1	0	8148	637	22	3	4020	3	KDR	4	55984967	Splice_Site	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	846314	55984967	135169309	372	47735										
LPHN3	23284	hgsc.bcm.edu	37	chr4	62758609	62758609	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgtgaggctgtggaagcccgAgaaatcatgtggtttaagac	14	6	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:62758609A>T	ENST00000514591.1	+	9	1841	c.1512A>T	c.(1510-1512)cgA>cgT	p.R504R	LPHN3_ENST00000506720.1_Silent_p.R572R|LPHN3_ENST00000507625.1_Silent_p.R572R|LPHN3_ENST00000506746.1_Silent_p.R572R|LPHN3_ENST00000514157.1_Silent_p.R504R|LPHN3_ENST00000504896.1_Silent_p.R504R|LPHN3_ENST00000512091.2_Silent_p.R504R|LPHN3_ENST00000506700.1_Silent_p.R504R|LPHN3_ENST00000508693.1_Silent_p.R572R|LPHN3_ENST00000545650.1_Silent_p.R504R|LPHN3_ENST00000507164.1_Silent_p.R572R|LPHN3_ENST00000511324.1_Silent_p.R572R|LPHN3_ENST00000509896.1_Silent_p.R572R|LPHN3_ENST00000508946.1_Silent_p.R504R|LPHN3_ENST00000514996.1_Silent_p.R504R			Q9HAR2	LPHN3_HUMAN	latrophilin 3	504					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						TGGAAGCCCGAGAAATCATGT	0.493																																					p.R504R		Atlas-SNP	.											.	LPHN3	800	.	0			c.A1512T						.						62	59	60					4																	62758609		1947	4148	6095	SO:0001819	synonymous_variant	23284	exon7			AGCCCGAGAAATC	AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"-", "GPCR / Class B : Orphans"	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.1512A>T	chr4.hg19:g.62758609A>T		99.0	0.0		59.0	26.0	NM_015236	E9PE04|O94867|Q9NWK5	Silent	SNP	ENST00000514591.1	hg19	CCDS54768.1																																																																																			.	.		0.493	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1			T	62758609	A	T	62758609	2	4	344	1	0	0	0	0	0	0	0	1	8926	291	11	4		4	LPHN3	4	62758609	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	6773642	62758609	128395667	373	47736										
UBA6	55236	hgsc.bcm.edu	37	chr4	68506897	68506897	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gatgaggacgaaataggaacTgtctatttaagttggatttc	11	4	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:68506897T>C	ENST00000322244.5	-	18	1585	c.1526A>G	c.(1525-1527)cAg>cGg	p.Q509R		NM_018227.5	NP_060697.4	A0AVT1	UBA6_HUMAN	ubiquitin-like modifier activating enzyme 6	509					protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|FAT10 activating enzyme activity (GO:0019780)|ligase activity (GO:0016874)			central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(6)|liver(1)|lung(23)|skin(2)|upper_aerodigestive_tract(2)	44						AAATAGGAACTGTCTATTTAA	0.279																																					p.Q509R		Atlas-SNP	.											.	UBA6	98	.	0			c.A1526G						.						168	192	184					4																	68506897		2203	4291	6494	SO:0001583	missense	55236	exon18			AGGAACTGTCTAT	AK094164	CCDS3516.1	4q13.2	2008-02-05	2007-11-30	2007-11-30	ENSG00000033178	ENSG00000033178		"Ubiquitin-like modifier activating enzymes"	25581	protein-coding gene	gene with protein product	"UBA6, ubiquitin-activating enzyme E1"	611361	"ubiquitin-activating enzyme E1-like 2"	UBE1L2		17580310	Standard	NM_018227		Approved	FLJ10808	uc003hdg.4	A0AVT1	OTTHUMG00000129299	ENST00000322244.5:c.1526A>G	chr4.hg19:g.68506897T>C	ENSP00000313454:p.Gln509Arg	96.0	0.0		85.0	46.0	NM_018227	A6N8M7|B2RAV3|Q4W5K0|Q6UV21|Q86T78|Q86TC7|Q8N5T3|Q8N9E4|Q9H3T7|Q9NVC9	Missense_Mutation	SNP	ENST00000322244.5	hg19	CCDS3516.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.7|25.7	4.662276|4.662276	0.88251|0.88251	.|.	.|.	ENSG00000033178|ENSG00000033178	ENST00000322244|ENST00000505673	T|.	0.60672|.	0.17|.	5.63|5.63	5.63|5.63	0.86233|0.86233	UBA/THIF-type NAD/FAD binding fold (1);Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.89389|0.89389	0.6701|0.6701	H|H	0.98738|0.98738	4.315|4.315	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	D|D	0.93653|0.93653	0.6975|0.6975	10|5	0.87932|.	D|.	0|.	-34.1411|-34.1411	15.8201|15.8201	0.78633|0.78633	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	509|.	A0AVT1|.	UBA6_HUMAN|.	R|G	509|43	ENSP00000313454:Q509R|.	ENSP00000313454:Q509R|.	Q|S	-|-	2|1	0|0	UBA6|UBA6	68189492|68189492	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.980000|0.980000	0.70556|0.70556	7.477000|7.477000	0.81069|0.81069	2.134000|2.134000	0.65973|0.65973	0.482000|0.482000	0.46254|0.46254	CAG|AGT	.	.		0.279	UBA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251429.2	NM_018227		C	68506897	T	C	68506897	3	2	344	1	0	0	0	0	1	0	0	0	16847	1580	55	2	1696	2	UBA6	4	68506897	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	5748288	68506897	122647379	374	47737										
TMPRSS11A	339967	hgsc.bcm.edu	37	chr4	68789885	68789885	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccctgttgatgagctcattgCtgaaaaagaagataaaacaa	8	7	1	5			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:68789885C>A	ENST00000334830.7	-	6	1237		c.e6-1		UBA6-AS1_ENST00000500538.2_RNA|TMPRSS11A_ENST00000508048.1_Splice_Site|TMPRSS11A_ENST00000396188.2_Splice_Site			Q6ZMR5	TM11A_HUMAN	transmembrane protease, serine 11A						cell cycle (GO:0007049)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|cervix(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	29						GAGCTCATTGCTGAAAAAGAA	0.338																																					.	NSCLC(26;2 894 10941 14480 22546)	Atlas-SNP	.											.	TMPRSS11A	74	.	0			c.482-1G>T						.						152	165	160					4																	68789885		2203	4300	6503	SO:0001630	splice_region_variant	339967	exon7			TCATTGCTGAAAA	AF071882	CCDS3519.1	4q13.2	2010-04-13			ENSG00000187054	ENSG00000187054		"Serine peptidases / Transmembrane"	27954	protein-coding gene	gene with protein product		611704				15328353	Standard	NM_182606		Approved	ECRG1	uc003hdr.1	Q6ZMR5	OTTHUMG00000129303	ENST00000334830.7:c.491-1G>T	chr4.hg19:g.68789885C>A		93.0	0.0		52.0	16.0	NM_001114387	J3KNQ8|Q2NKI9|Q6JE90|Q7RTY4|Q86TK8	Splice_Site	SNP	ENST00000334830.7	hg19	CCDS3519.1	.	.	.	.	.	.	.	.	.	.	C	17.87	3.494115	0.64186	.	.	ENSG00000187054	ENST00000508048;ENST00000334830;ENST00000396188	.	.	.	4.9	4.9	0.64082	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5995	0.62011	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TMPRSS11A	68472480	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	2.269000	0.43346	2.277000	0.76020	0.655000	0.94253	.	.	.		0.338	TMPRSS11A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251433.3	NM_182606	Intron	A	68789885	C	A	68789885	5	1	344	1	0	0	0	0	0	0	1	0	16254	811	28	3	795	3	TMPRSS11A	4	68789885	Splice_Site	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	282988	68789885	122364391	375	47738										
CSN3	1448	hgsc.bcm.edu	37	chr4	71113535	71113535	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cttcttctggaactccccagGctgtggaggttcaaaaccag	10	12	3	0	rs552991081	byFrequency	TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:71113535G>T	ENST00000304954.3	+	3	141	c.55G>T	c.(55-57)Gct>Tct	p.A19S		NM_005212.2	NP_005203.2	Q9UNS2	CSN3_HUMAN	casein kappa	163					cullin deneddylation (GO:0010388)|in utero embryonic development (GO:0001701)|response to light stimulus (GO:0009416)|signal transduction (GO:0007165)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18						AACTCCCCAGGCTGTGGAGGT	0.299																																					p.A19S		Atlas-SNP	.											.	CSN3	43	.	0			c.G55T						.						43	44	44					4																	71113535		2203	4297	6500	SO:0001630	splice_region_variant	1448	exon3			CCCCAGGCTGTGG	U51899	CCDS3538.1	4q21.1	2014-02-19	2003-01-24	2003-01-31	ENSG00000171209	ENSG00000171209			2446	protein-coding gene	gene with protein product		601695	"casein, kappa"	CSN10		8863730, 9050925	Standard	NM_005212		Approved		uc003hfe.4	P07498	OTTHUMG00000129399	ENST00000304954.3:c.55-1G>T	chr4.hg19:g.71113535G>T		318.0	0.0		278.0	85.0	NM_005212	B2R683|B4DY81|O43191|Q7LDR6	Missense_Mutation	SNP	ENST00000304954.3	hg19	CCDS3538.1	.	.	.	.	.	.	.	.	.	.	G	9.232	1.035999	0.19590	.	.	ENSG00000171209	ENST00000304954	T	0.30981	1.51	4.18	2.46	0.29980	.	0.263731	0.27092	N	0.020979	T	0.18718	0.0449	L	0.43152	1.355	0.28221	N	0.926521	P	0.37781	0.608	B	0.28638	0.092	T	0.10268	-1.0637	9	.	.	.	-5.5043	6.808	0.23788	0.2106:0.0:0.7894:0.0	.	19	P07498	CASK_HUMAN	S	19	ENSP00000304822:A19S	.	A	+	1	0	CSN3	71148124	1.000000	0.71417	0.999000	0.59377	0.185000	0.23345	0.988000	0.29616	0.720000	0.32209	0.585000	0.79938	GCT	.	.		0.299	CSN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251555.1	NM_005212	Missense_Mutation	T	71113535	G	T	71113535	5	4	344	1	0	0	0	0	0	0	1	0	3951	1217	42	3	61	3	CSN3	4	71113535	Splice_Site	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	2323650	71113535	120040741	376	47739										
RUFY3	22902	hgsc.bcm.edu	37	chr4	71629350	71629350	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcttgttccagaagccgcagAgataacagcaagtgttaaag	11	8	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:71629350A>T	ENST00000226328.4	+	3	997	c.434A>T	c.(433-435)gAg>gTg	p.E145V	RUFY3_ENST00000381006.3_Missense_Mutation_p.E145V|RUFY3_ENST00000417478.2_Missense_Mutation_p.E205V|RUFY3_ENST00000502653.1_Missense_Mutation_p.E92V|RUFY3_ENST00000536664.1_Missense_Mutation_p.E129V	NM_014961.3	NP_055776.1	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3	145	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.				negative regulation of axonogenesis (GO:0050771)	filopodium (GO:0030175)|growth cone (GO:0030426)				endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	16		all_hematologic(202;0.248)	Lung(101;0.235)			gaagccgcagagataacagca	0.383																																					p.E205V		Atlas-SNP	.											.	RUFY3	61	.	0			c.A614T						.						37	40	39					4																	71629350		2201	4298	6499	SO:0001583	missense	22902	exon3			CCGCAGAGATAAC	AF112221	CCDS3547.1, CCDS34001.1, CCDS47068.1, CCDS75138.1	4q13.3	2009-05-29			ENSG00000018189	ENSG00000018189		"Zinc fingers, FYVE domain containing"	30285	protein-coding gene	gene with protein product	"single axon-related 1"	611194				17439943	Standard	NM_001130709		Approved	RIPx, KIAA0871, Singar1	uc003hfr.3	Q7L099	OTTHUMG00000129910	ENST00000226328.4:c.434A>T	chr4.hg19:g.71629350A>T	ENSP00000226328:p.Glu145Val	400.0	0.0		314.0	160.0	NM_001130709	B3KM25|B4DYW7|D9N163|O94948|Q9UI00	Missense_Mutation	SNP	ENST00000226328.4	hg19	CCDS3547.1	.	.	.	.	.	.	.	.	.	.	A	18.60	3.659667	0.67586	.	.	ENSG00000018189	ENST00000503876;ENST00000417478;ENST00000381006;ENST00000226328;ENST00000536664;ENST00000513597;ENST00000502653	T;T;T;T;T;T;T	0.32753	1.44;1.44;1.44;1.44;1.44;1.44;1.44	4.77	4.77	0.60923	RUN (2);	0.094727	0.64402	D	0.000001	T	0.44519	0.1297	M	0.67397	2.05	0.80722	D	1	B;P;P;B	0.41569	0.433;0.755;0.476;0.103	B;P;B;B	0.49140	0.234;0.601;0.327;0.346	T	0.48456	-0.9034	10	0.87932	D	0	-4.216	14.5812	0.68292	1.0:0.0:0.0:0.0	.	129;145;145;205	B4DKC2;Q7L099-3;Q7L099;Q7L099-2	.;.;RUFY3_HUMAN;.	V	81;205;145;145;129;81;92	ENSP00000426734:E81V;ENSP00000399771:E205V;ENSP00000370394:E145V;ENSP00000226328:E145V;ENSP00000443652:E129V;ENSP00000425574:E81V;ENSP00000425400:E92V	ENSP00000226328:E145V	E	+	2	0	RUFY3	71848214	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.223000	0.95203	1.917000	0.55516	0.482000	0.46254	GAG	.	.		0.383	RUFY3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252161.2	NM_014961		T	71629350	A	T	71629350	3	4	344	1	0	0	0	0	1	0	0	0	13755	304	11	4	806	4	RUFY3	4	71629350	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	515815	71629350	119524926	377	47740										
NPFFR2	10886	hgsc.bcm.edu	37	chr4	72994372	72994372	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccatctggaatgtcaatgacAcaaagcatcatctgtactca	6	11	5	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:72994372A>T	ENST00000308744.6	+	2	468	c.370A>T	c.(370-372)Aca>Tca	p.T124S	NPFFR2_ENST00000344413.5_Intron|NPFFR2_ENST00000395999.1_Missense_Mutation_p.T25S|NPFFR2_ENST00000358749.3_Missense_Mutation_p.T22S	NM_004885.2	NP_004876.2	Q9Y5X5	NPFF2_HUMAN	neuropeptide FF receptor 2	124					detection of abiotic stimulus (GO:0009582)|G-protein coupled receptor signaling pathway (GO:0007186)|regulation of adenylate cyclase activity (GO:0045761)|regulation of cAMP-dependent protein kinase activity (GO:2000479)|regulation of MAPK cascade (GO:0043408)	actin cytoskeleton (GO:0015629)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide receptor activity (GO:0008188)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(24)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	43			Lung(101;0.0935)|LUSC - Lung squamous cell carcinoma(112;0.138)			TGTCAATGACACAAAGCATCA	0.363																																					p.T124S		Atlas-SNP	.											.	NPFFR2	98	.	0			c.A370T						.						124	110	115					4																	72994372		2203	4300	6503	SO:0001583	missense	10886	exon2			AATGACACAAAGC	AF236083	CCDS3551.1, CCDS3552.1, CCDS47072.1	4q21	2012-08-10	2006-02-15	2006-02-15	ENSG00000056291	ENSG00000056291		"GPCR / Class A :  Neuropeptide receptors : FF/AF", "GPCR / Class A : RF amide peptide receptors"	4525	protein-coding gene	gene with protein product	"neuropeptide FF 2"	607449	"G protein-coupled receptor 74"	GPR74		10079187, 10851242	Standard	NM_001144756		Approved	NPFF2, NPGPR	uc003hgg.2	Q9Y5X5	OTTHUMG00000129918	ENST00000308744.6:c.370A>T	chr4.hg19:g.72994372A>T	ENSP00000307822:p.Thr124Ser	83.0	0.0		79.0	36.0	NM_004885	Q96RV1|Q9NR49	Missense_Mutation	SNP	ENST00000308744.6	hg19	CCDS3551.1	.	.	.	.	.	.	.	.	.	.	A	9.583	1.124187	0.20959	.	.	ENSG00000056291	ENST00000308744;ENST00000395999;ENST00000358749	T;T;T	0.36878	1.23;1.23;1.23	5.9	5.9	0.94986	.	0.120575	0.38897	N	0.001529	T	0.19765	0.0475	N	0.05031	-0.125	0.19945	N	0.999948	B;B	0.28605	0.035;0.217	B;B	0.24974	0.041;0.057	T	0.13045	-1.0524	10	0.18710	T	0.47	.	15.9936	0.80225	1.0:0.0:0.0:0.0	.	25;124	Q9Y5X5-3;Q9Y5X5	.;NPFF2_HUMAN	S	124;25;22	ENSP00000307822:T124S;ENSP00000379321:T25S;ENSP00000351599:T22S	ENSP00000307822:T124S	T	+	1	0	NPFFR2	73213236	0.948000	0.32251	0.279000	0.24732	0.095000	0.18619	2.791000	0.47829	2.251000	0.74343	0.528000	0.53228	ACA	.	.		0.363	NPFFR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252170.2	NM_004885		T	72994372	A	T	72994372	3	4	344	1	0	0	0	0	1	0	0	0	10587	159	6	4	382	4	NPFFR2	4	72994372	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1365022	72994372	118159904	378	47741										
ADAMTS3	9508	hgsc.bcm.edu	37	chr4	73414452	73414452	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttttccaaatgccgtgatgtTaaagaacaactgctcagggt	9	8	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:73414452T>C	ENST00000286657.4	-	3	283	c.247A>G	c.(247-249)Aac>Gac	p.N83D	ADAMTS3_ENST00000505193.1_5'UTR	NM_014243.2	NP_055058.2	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 3	83					collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|protein processing (GO:0016485)|vascular endothelial growth factor production (GO:0010573)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(33)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	76			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GCCGTGATGTTAAAGAACAAC	0.478																																					p.N83D	NSCLC(168;1941 2048 2918 13048 43078)	Atlas-SNP	.											.	ADAMTS3	164	.	0			c.A247G						.						103	97	99					4																	73414452		2203	4300	6503	SO:0001583	missense	9508	exon3			TGATGTTAAAGAA	AB002364	CCDS3553.1	4q21	2008-07-29	2005-08-19		ENSG00000156140	ENSG00000156140	3.4.24.-	"ADAM metallopeptidases with thrombospondin type 1 motif"	219	protein-coding gene	gene with protein product		605011	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3"			10094461	Standard	NM_014243		Approved	KIAA0366, ADAMTS-4	uc003hgk.2	O15072	OTTHUMG00000129912	ENST00000286657.4:c.247A>G	chr4.hg19:g.73414452T>C	ENSP00000286657:p.Asn83Asp	131.0	0.0		92.0	42.0	NM_014243	A1L3U9|Q9BXZ8	Missense_Mutation	SNP	ENST00000286657.4	hg19	CCDS3553.1	.	.	.	.	.	.	.	.	.	.	T	19.35	3.811088	0.70797	.	.	ENSG00000156140	ENST00000286657	T	0.06294	3.32	5.74	5.74	0.90152	Peptidase M12B, propeptide (1);	0.000000	0.64402	D	0.000001	T	0.26666	0.0652	M	0.77103	2.36	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.00601	-1.1650	10	0.56958	D	0.05	.	15.5164	0.75828	0.0:0.0:0.0:1.0	.	83	O15072	ATS3_HUMAN	D	83	ENSP00000286657:N83D	ENSP00000286657:N83D	N	-	1	0	ADAMTS3	73633316	1.000000	0.71417	1.000000	0.80357	0.256000	0.26092	7.944000	0.87722	2.308000	0.77769	0.523000	0.50628	AAC	.	.		0.478	ADAMTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252164.2			C	73414452	T	C	73414452	3	2	344	1	0	0	0	0	1	0	0	0	267	1754	61	2	3450	2	ADAMTS3	4	73414452	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	420080	73414452	117739824	379	47742										
CXCL1	2919	hgsc.bcm.edu	37	chr4	74735406	74735406	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gagcgtccgtggccactgaaCtgcgctgccagtgcttgcag	14	13	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:74735406C>A	ENST00000395761.3	+	2	188	c.121C>A	c.(121-123)Ctg>Atg	p.L41M	CXCL1_ENST00000509101.1_3'UTR	NM_001511.3	NP_001502.1	P09341	GROA_HUMAN	chemokine (C-X-C motif) ligand 1 (melanoma growth stimulating activity, alpha)	41					actin cytoskeleton organization (GO:0030036)|cell chemotaxis (GO:0060326)|cell proliferation (GO:0008283)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|positive regulation of catalytic activity (GO:0043085)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)|enzyme activator activity (GO:0008047)|receptor binding (GO:0005102)			lung(2)	2	Breast(15;0.00102)		all cancers(17;0.00176)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)			GGCCACTGAACTGCGCTGCCA	0.642																																					p.L41M		Atlas-SNP	.											.	CXCL1	6	.	0			c.C121A						.						77	87	84					4																	74735406		2203	4300	6503	SO:0001583	missense	2919	exon2			ACTGAACTGCGCT	J03561	CCDS47074.1	4q13.3	2013-02-25	2002-08-22	2002-08-23		ENSG00000163739		"Endogenous ligands"	4602	protein-coding gene	gene with protein product		155730	"GRO1 oncogene (melanoma growth stimulating activity, alpha)", "fibroblast secretory protein"	MGSA, GRO1, FSP		2217207	Standard	NM_001511		Approved	SCYB1, GROa, MGSA-a, NAP-3	uc003hhh.3	P09341		ENST00000395761.3:c.121C>A	chr4.hg19:g.74735406C>A	ENSP00000379110:p.Leu41Met	153.0	0.0		134.0	54.0	NM_001511	Q9UCR7	Missense_Mutation	SNP	ENST00000395761.3	hg19	CCDS47074.1	.	.	.	.	.	.	.	.	.	.	C	12.80	2.045786	0.36085	.	.	ENSG00000163739	ENST00000395761	T	0.37584	1.19	5.18	4.33	0.51752	Chemokine interleukin-8-like domain (3);	0.241648	0.36703	N	0.002458	T	0.66587	0.2804	M	0.92026	3.265	0.29328	N	0.866904	D	0.89917	1.0	D	0.97110	1.0	T	0.69636	-0.5092	10	0.87932	D	0	.	12.7671	0.57399	0.0:0.9128:0.0:0.0872	.	41	P09341	GROA_HUMAN	M	41	ENSP00000379110:L41M	ENSP00000379110:L41M	L	+	1	2	CXCL1	74954270	0.996000	0.38824	0.530000	0.27963	0.008000	0.06430	1.627000	0.37050	0.584000	0.29591	-0.797000	0.03246	CTG	.	.		0.642	CXCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362734.1			A	74735406	C	A	74735406	3	1	344	1	0	0	0	0	1	0	0	0	4079	564	20	3	127	3	CXCL1	4	74735406	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1320954	74735406	116418870	380	47743										
C4orf26	152816	hgsc.bcm.edu	37	chr4	76489571	76489571	+	Nonsense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tttccattccagccattttaTtggccacaccgttaccttac	4	14	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:76489571T>G	ENST00000311623.4	+	2	350	c.315T>G	c.(313-315)taT>taG	p.Y105*	C4orf26_ENST00000435974.2_Missense_Mutation_p.I120S	NM_001257072.1|NM_178497.3	NP_001244001.1|NP_848592.2	Q17RF5	CD026_HUMAN	chromosome 4 open reading frame 26	105						extracellular region (GO:0005576)				kidney(1)|large_intestine(4)|stomach(1)	6			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			AGCCATTTTATTGGCCACACC	0.448																																					p.Y105X		Atlas-SNP	.											.	C4orf26	24	.	0			c.T315G						.						185	194	191					4																	76489571		2203	4300	6503	SO:0001587	stop_gained	152816	exon2			ATTTTATTGGCCA	AK074237	CCDS3569.1, CCDS56334.1, CCDS75142.1	4q21.1	2012-10-31			ENSG00000174792	ENSG00000174792			26300	protein-coding gene	gene with protein product		614829				22901946	Standard	NM_001206981		Approved	FLJ23657	uc011cbo.2	Q17RF5	OTTHUMG00000130104	ENST00000311623.4:c.315T>G	chr4.hg19:g.76489571T>G	ENSP00000311307:p.Tyr105*	280.0	0.0		206.0	77.0	NM_178497	B4DTI3|E7ETQ0|Q8TEC3	Nonsense_Mutation	SNP	ENST00000311623.4	hg19	CCDS3569.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.08|11.08	1.532425|1.532425	0.27387|0.27387	.|.	.|.	ENSG00000174792|ENSG00000174792	ENST00000435974|ENST00000311623	T|.	0.54675|.	0.56|.	4.72|4.72	-3.19|-3.19	0.05171|0.05171	.|.	.|3.823500	.|0.00541	.|N	.|0.000238	T|.	0.22282|.	0.0537|.	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	B|.	0.12013|.	0.005|.	B|.	0.09377|.	0.004|.	T|.	0.09684|.	-1.0663|.	7|.	.|.	.|.	.|.	.|.	4.994|4.994	0.14230|0.14230	0.0:0.4126:0.2898:0.2976|0.0:0.4126:0.2898:0.2976	.|.	120|.	E7ETQ0|.	.|.	S|X	120|105	ENSP00000406925:I120S|.	.|.	I|Y	+|+	2|3	0|2	C4orf26|C4orf26	76708595|76708595	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.093000|0.093000	0.18481|0.18481	0.072000|0.072000	0.14617|0.14617	-0.346000|-0.346000	0.08312|0.08312	-0.248000|-0.248000	0.11899|0.11899	ATT|TAT	.	.		0.448	C4orf26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252410.1	NM_178497		G	76489571	T	G	76489571	4	3	344	1	0	0	0	0	0	1	0	0	2259	1500	52	5	321	5	C4orf26	4	76489571	Nonsense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1754165	76489571	114664705	381	47744										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79229364	79229364	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	caggcagggcacctgtagcgGtgagtgctgggttgcgatgc	18	9	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:79229364G>T	ENST00000325942.6	+	15	2118		c.e15+1		FRAS1_ENST00000264899.6_Splice_Site|FRAS1_ENST00000264895.6_Splice_Site	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1						cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						ACCTGTAGCGGTGAGTGCTGG	0.502																																					.		Atlas-SNP	.											.	FRAS1	779	.	0			c.1678+1G>T						.						73	82	79					4																	79229364		2171	4264	6435	SO:0001630	splice_region_variant	80144	exon15			GTAGCGGTGAGTG	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.1678+1G>T	chr4.hg19:g.79229364G>T		115.0	0.0		75.0	27.0	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Splice_Site	SNP	ENST00000325942.6	hg19	CCDS54772.1	.	.	.	.	.	.	.	.	.	.	G	18.10	3.547451	0.65311	.	.	ENSG00000138759	ENST00000325942;ENST00000264895;ENST00000264899;ENST00000502446;ENST00000508900	.	.	.	5.57	5.57	0.84162	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.8072	0.85708	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FRAS1	79448388	1.000000	0.71417	0.998000	0.56505	0.221000	0.24807	6.193000	0.72075	2.782000	0.95742	0.591000	0.81541	.	.	.		0.502	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2		Intron	T	79229364	G	T	79229364	5	4	344	1	0	0	0	0	0	0	1	0	6050	1275	44	3	1737	3	FRAS1	4	79229364	Splice_Site	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	2739793	79229364	111924912	382	47745										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79285157	79285157	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgtcccacactggcacctgcAgcaccacctgcttccctggg	9	18	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:79285157A>T	ENST00000325942.6	+	22	3111	c.2671A>T	c.(2671-2673)Agc>Tgc	p.S891C	FRAS1_ENST00000264895.6_Missense_Mutation_p.S891C	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	891					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						TGGCACCTGCAGCACCACCTG	0.532																																					p.S891C		Atlas-SNP	.											.	FRAS1	779	.	0			c.A2671T						.						71	75	74					4																	79285157		2088	4231	6319	SO:0001583	missense	80144	exon22			ACCTGCAGCACCA	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.2671A>T	chr4.hg19:g.79285157A>T	ENSP00000326330:p.Ser891Cys	100.0	0.0		80.0	33.0	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000325942.6	hg19	CCDS54772.1	.	.	.	.	.	.	.	.	.	.	A	13.45	2.242286	0.39598	.	.	ENSG00000138759	ENST00000325942;ENST00000264895	T;T	0.30448	1.53;1.53	5.45	3.1	0.35709	.	0.729377	0.13837	N	0.359333	T	0.45196	0.1330	M	0.77313	2.365	0.19775	N	0.99995	D;P	0.59767	0.986;0.892	P;P	0.54965	0.765;0.619	T	0.27123	-1.0083	10	0.54805	T	0.06	.	7.518	0.27612	0.8203:0.0:0.1797:0.0	.	891;891	E9PHH6;A2RRR8	.;.	C	891	ENSP00000326330:S891C;ENSP00000264895:S891C	ENSP00000264895:S891C	S	+	1	0	FRAS1	79504181	0.021000	0.18746	0.916000	0.36221	0.169000	0.22640	2.232000	0.43018	2.068000	0.61886	0.528000	0.53228	AGC	.	.		0.532	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2			T	79285157	A	T	79285157	3	4	344	1	0	0	0	0	1	0	0	0	6050	188	7	4	2757	4	FRAS1	4	79285157	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	55793	79285157	111869119	383	47746										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79458286	79458286	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttgatcccacggggacaatcTacaatgaagggccccagtat	10	11	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:79458286T>A	ENST00000264895.6	+	72	11670	c.11230T>A	c.(11230-11232)Tac>Aac	p.Y3744N		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3740					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						GGGGACAATCTACAATGAAGG	0.418																																					p.Y3744N		Atlas-SNP	.											.	FRAS1	779	.	0			c.T11230A						.						103	99	100					4																	79458286		1866	4110	5976	SO:0001583	missense	80144	exon72			ACAATCTACAATG	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.11230T>A	chr4.hg19:g.79458286T>A	ENSP00000264895:p.Tyr3744Asn	119.0	0.0		87.0	31.0	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000264895.6	hg19	CCDS54771.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	22.2|22.2	4.257344|4.257344	0.80246|0.80246	.|.	.|.	ENSG00000138759|ENSG00000138759	ENST00000512123|ENST00000264895	.|T	.|0.15952	.|2.38	5.92|5.92	5.92|5.92	0.95590|0.95590	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.41328|0.41328	0.1154|0.1154	M|M	0.63428|0.63428	1.95|1.95	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.91635	.|0.999	T|T	0.21143|0.21143	-1.0254|-1.0254	5|10	.|0.87932	.|D	.|0	.|.	16.371|16.371	0.83361|0.83361	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|3744	.|E9PHH6	.|.	Q|N	1972|3744	.|ENSP00000264895:Y3744N	.|ENSP00000264895:Y3744N	L|Y	+|+	2|1	0|0	FRAS1|FRAS1	79677310|79677310	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.581000|0.581000	0.36288|0.36288	7.898000|7.898000	0.87363|0.87363	2.267000|2.267000	0.75376|0.75376	0.477000|0.477000	0.44152|0.44152	CTA|TAC	.	.		0.418	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	79458286	T	A	79458286	3	1	344	1	0	0	0	0	1	0	0	0	6050	1522	53	4	11591	4	FRAS1	4	79458286	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	173129	79458286	111695990	384	47747										
FAM190A	401145	hgsc.bcm.edu	37	chr4	91549369	91549369	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cgttattattaaagatgaagAgagttcttcaagaggtaatg	10	3	2	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:91549369A>G	ENST00000509176.1	+	6	2206	c.1918A>G	c.(1918-1920)Aga>Gga	p.R640G	CCSER1_ENST00000432775.2_Missense_Mutation_p.R640G|CCSER1_ENST00000333691.8_Missense_Mutation_p.R640G	NM_001145065.1	NP_001138537.1	Q9C0I3	CCSE1_HUMAN	coiled-coil serine-rich protein 1	640																	AAAGATGAAGAGAGTTCTTCA	0.433																																					p.R640G		Atlas-SNP	.											.	.	.	.	0			c.A1918G						.						59	59	59					4																	91549369		1888	4118	6006	SO:0001583	missense	401145	exon6			ATGAAGAGAGTTC		CCDS47099.1, CCDS47100.1	4q22.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184305	ENSG00000184305			29349	protein-coding gene	gene with protein product			"family with sequence similarity 190, member A"	FAM190A		11214970	Standard	NM_001145065		Approved	KIAA1680	uc003hsv.4	Q9C0I3	OTTHUMG00000160950	ENST00000509176.1:c.1918A>G	chr4.hg19:g.91549369A>G	ENSP00000425040:p.Arg640Gly	146.0	0.0		117.0	64.0	NM_001145065	Q4W5M0|Q86V57	Missense_Mutation	SNP	ENST00000509176.1	hg19	CCDS47099.1	.	.	.	.	.	.	.	.	.	.	A	17.79	3.474977	0.63737	.	.	ENSG00000184305	ENST00000509176;ENST00000432775;ENST00000333691;ENST00000458365	T;T;T	0.69175	1.07;-0.38;1.07	5.03	5.03	0.67393	.	0.180091	0.46442	D	0.000296	T	0.78272	0.4257	M	0.62723	1.935	0.34136	D	0.66585	D;D	0.76494	0.999;0.999	D;D	0.83275	0.996;0.996	D	0.85066	0.0937	10	0.72032	D	0.01	-21.7208	12.0696	0.53609	0.8563:0.1437:0.0:0.0	.	640;640	Q9C0I3-2;Q9C0I3	.;F190A_HUMAN	G	640	ENSP00000425040:R640G;ENSP00000389283:R640G;ENSP00000329482:R640G	ENSP00000329482:R640G	R	+	1	2	FAM190A	91768392	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	4.354000	0.59417	2.199000	0.70637	0.528000	0.53228	AGA	.	.		0.433	CCSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363109.3	NM_001145065		G	91549369	A	G	91549369	3	3	344	1	0	0	0	0	1	0	0	0	5526	296	11	2	1936	2	FAM190A	4	91549369	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	12091083	91549369	99604907	385	47748										
GRID2	2895	hgsc.bcm.edu	37	chr4	94436432	94436432	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agtcctagactctgcggtatAtgagcatgtccgcatgaaag	11	9	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:94436432A>G	ENST00000282020.4	+	13	2321	c.2063A>G	c.(2062-2064)tAt>tGt	p.Y688C	GRID2_ENST00000510992.1_Missense_Mutation_p.Y593C	NM_001510.2	NP_001501.2	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	688					cellular protein localization (GO:0034613)|cerebellar granule cell differentiation (GO:0021707)|glutamate receptor signaling pathway (GO:0007215)|heterophilic cell-cell adhesion (GO:0007157)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|ionotropic glutamate receptor complex (GO:0008328)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|PDZ domain binding (GO:0030165)|scaffold protein binding (GO:0097110)			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)		TCTGCGGTATATGAGCATGTC	0.468																																					p.Y688C		Atlas-SNP	.											.	GRID2	233	.	0			c.A2063G						.						90	81	84					4																	94436432		2203	4300	6503	SO:0001583	missense	2895	exon13			CGGTATATGAGCA	AF009014	CCDS3637.1, CCDS68758.1	4q22	2012-08-29			ENSG00000152208	ENSG00000152208		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4576	protein-coding gene	gene with protein product		602368				9465309	Standard	NM_001510		Approved	GluD2, GluR-delta-2	uc011cdt.2	O43424	OTTHUMG00000130975	ENST00000282020.4:c.2063A>G	chr4.hg19:g.94436432A>G	ENSP00000282020:p.Tyr688Cys	88.0	0.0		80.0	40.0	NM_001510	E9PH24|Q4KKU8|Q4KKU9|Q4KKV0|Q59FZ1	Missense_Mutation	SNP	ENST00000282020.4	hg19	CCDS3637.1	.	.	.	.	.	.	.	.	.	.	A	18.63	3.666051	0.67700	.	.	ENSG00000152208	ENST00000282020;ENST00000510992	T;T	0.27557	1.66;1.66	5.1	5.1	0.69264	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.000000	0.85682	D	0.000000	T	0.54727	0.1876	M	0.72353	2.195	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.995	T	0.58317	-0.7657	10	0.59425	D	0.04	.	15.1709	0.72872	1.0:0.0:0.0:0.0	.	593;688	E9PH24;O43424	.;GRID2_HUMAN	C	688;593	ENSP00000282020:Y688C;ENSP00000421257:Y593C	ENSP00000282020:Y688C	Y	+	2	0	GRID2	94655455	1.000000	0.71417	0.990000	0.47175	0.951000	0.60555	6.066000	0.71185	2.045000	0.60652	0.477000	0.44152	TAT	.	.		0.468	GRID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253588.2			G	94436432	A	G	94436432	3	3	344	1	0	0	0	0	1	0	0	0	6781	449	16	2	2113	2	GRID2	4	94436432	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2887063	94436432	96717844	386	47749										
ATOH1	474	hgsc.bcm.edu	37	chr4	94750985	94750985	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tttcgaggacagcgccctgaCagcgatgatggcgcaaaaga	13	10	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:94750985C>A	ENST00000306011.3	+	1	944	c.908C>A	c.(907-909)aCa>aAa	p.T303K		NM_005172.1	NP_005163.1	Q92858	ATOH1_HUMAN	atonal homolog 1 (Drosophila)	303					auditory receptor cell fate determination (GO:0042668)|auditory receptor cell fate specification (GO:0042667)|axon guidance (GO:0007411)|central nervous system development (GO:0007417)|cerebral cortex development (GO:0021987)|inner ear morphogenesis (GO:0042472)|negative regulation of apoptotic process (GO:0043066)|neuron migration (GO:0001764)|positive regulation of auditory receptor cell differentiation (GO:0045609)|positive regulation of neuron differentiation (GO:0045666)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	11		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;3.57e-07)		AGCGCCCTGACAGCGATGATG	0.592																																					p.T303K		Atlas-SNP	.											.	ATOH1	40	.	0			c.C908A						.						70	75	73					4																	94750985		2203	4300	6503	SO:0001583	missense	474	exon1			CCCTGACAGCGAT	U61148	CCDS3638.1	4q22	2013-05-21			ENSG00000172238	ENSG00000172238		"Basic helix-loop-helix proteins"	797	protein-coding gene	gene with protein product		601461				8872459	Standard	NM_005172		Approved	HATH1, MATH-1, Math1, bHLHa14	uc003hta.1	Q92858	OTTHUMG00000130972	ENST00000306011.3:c.908C>A	chr4.hg19:g.94750985C>A	ENSP00000302216:p.Thr303Lys	38.0	0.0		57.0	28.0	NM_005172	Q14CT9	Missense_Mutation	SNP	ENST00000306011.3	hg19	CCDS3638.1	.	.	.	.	.	.	.	.	.	.	C	15.15	2.748453	0.49257	.	.	ENSG00000172238	ENST00000306011	D	0.97665	-4.48	4.4	3.55	0.40652	.	0.309061	0.30126	N	0.010358	D	0.90160	0.6925	N	0.14661	0.345	0.27653	N	0.947315	B	0.02656	0.0	B	0.04013	0.001	T	0.77122	-0.2704	10	0.05959	T	0.93	-6.4305	9.5226	0.39145	0.3843:0.6157:0.0:0.0	.	303	Q92858	ATOH1_HUMAN	K	303	ENSP00000302216:T303K	ENSP00000302216:T303K	T	+	2	0	ATOH1	94970008	0.963000	0.33076	0.992000	0.48379	0.960000	0.62799	2.111000	0.41883	1.058000	0.40530	0.643000	0.83706	ACA	.	.		0.592	ATOH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253585.1	NM_005172		A	94750985	C	A	94750985	3	1	344	1	0	0	0	0	1	0	0	0	1112	478	17	3	910	3	ATOH1	4	94750985	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	314553	94750985	96403291	387	47750										
NHEDC1	150159	hgsc.bcm.edu	37	chr4	103822469	103822469	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gagactcttgctgtttctagAgccagaggacctaacacagc	10	11	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:103822469A>T	ENST00000296422.7	-	12	1494	c.1353T>A	c.(1351-1353)gcT>gcA	p.A451A	SLC9B1_ENST00000394789.3_Intron|SLC9B1_ENST00000512651.2_5'UTR	NM_139173.3	NP_631912	Q4ZJI4	SL9B1_HUMAN	solute carrier family 9, subfamily B (NHA1, cation proton antiporter 1), member 1	451					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										CTGTTTCTAGAGCCAGAGGAC	0.408																																					p.A451A		Atlas-SNP	.											.	.	.	.	0			c.T1353A						.						54	55	55					4																	103822469		2199	4276	6475	SO:0001819	synonymous_variant	150159	exon12			TTCTAGAGCCAGA	AF447585	CCDS34041.1, CCDS47119.1	4q24	2013-05-22	2012-03-22	2011-07-26	ENSG00000164037	ENSG00000164037		"Solute carriers"	24244	protein-coding gene	gene with protein product		611527	"Na+/H+ exchanger domain containing 1", "solute carrier family 9, subfamily B (cation proton antiporter 2), member 1"	NHEDC1		16850186	Standard	NM_139173		Approved	NHA1	uc003hww.3	Q4ZJI4	OTTHUMG00000161114	ENST00000296422.7:c.1353T>A	chr4.hg19:g.103822469A>T		213.0	0.0		202.0	49.0	NM_139173	A1KXV1|B9EH04|C9JBP7|Q49A30|Q8NCV2|Q8WVZ0	Silent	SNP	ENST00000296422.7	hg19	CCDS34041.1																																																																																			.	.		0.408	SLC9B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363841.1	NM_139173		T	103822469	A	T	103822469	2	4	344	1	0	0	0	0	0	0	0	1	10409	291	11	4		4	NHEDC1	4	103822469	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	9071484	103822469	87331807	388	47751										
TBCK	93627	hgsc.bcm.edu	37	chr4	107154797	107154797	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	caattgcatcgtacttggcaTgaatagctccctgcaaaaaa	7	10	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:107154797T>A	ENST00000273980.5	-	17	1907	c.1460A>T	c.(1459-1461)cAt>cTt	p.H487L	TBCK_ENST00000432496.2_Missense_Mutation_p.H487L|TBCK_ENST00000394706.3_Missense_Mutation_p.H448L|TBCK_ENST00000361687.4_Missense_Mutation_p.H424L|TBCK_ENST00000394708.2_Missense_Mutation_p.H487L					TBC1 domain containing kinase											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	25						GTACTTGGCATGAATAGCTCC	0.274																																					p.H487L		Atlas-SNP	.											.	TBCK	89	.	0			c.A1460T						.						58	56	56					4																	107154797		2201	4299	6500	SO:0001583	missense	93627	exon16			TTGGCATGAATAG		CCDS3673.1, CCDS54788.1, CCDS54789.1	4q24	2014-09-17			ENSG00000145348	ENSG00000145348			28261	protein-coding gene	gene with protein product						12471243	Standard	XR_427553		Approved	MGC16169, HSPC302	uc010ilv.2	Q8TEA7	OTTHUMG00000131214	ENST00000273980.5:c.1460A>T	chr4.hg19:g.107154797T>A	ENSP00000273980:p.His487Leu	281.0	0.0		244.0	117.0	NM_001163436		Missense_Mutation	SNP	ENST00000273980.5	hg19	CCDS54788.1	.	.	.	.	.	.	.	.	.	.	T	15.55	2.866012	0.51588	.	.	ENSG00000145348	ENST00000273980;ENST00000432496;ENST00000361687;ENST00000394706;ENST00000394708;ENST00000503516	T;T;T;T;T;T	0.07216	3.21;3.21;3.21;3.21;3.21;3.21	5.64	5.64	0.86602	Rab-GAP/TBC domain (4);	0.105021	0.64402	D	0.000002	T	0.05135	0.0137	N	0.11106	0.095	0.41569	D	0.988672	B;B;B	0.21309	0.001;0.054;0.0	B;B;B	0.23574	0.001;0.047;0.003	T	0.22661	-1.0210	10	0.06365	T	0.9	.	15.8714	0.79122	0.0:0.0:0.0:1.0	.	487;448;424	Q8TEA7;Q8TEA7-2;Q8TEA7-3	TBCK_HUMAN;.;.	L	487;487;424;448;487;17	ENSP00000273980:H487L;ENSP00000405847:H487L;ENSP00000355338:H424L;ENSP00000378196:H448L;ENSP00000378198:H487L;ENSP00000423834:H17L	ENSP00000273980:H487L	H	-	2	0	TBCK	107374246	1.000000	0.71417	1.000000	0.80357	0.748000	0.42578	7.034000	0.76511	2.144000	0.66660	0.533000	0.62120	CAT	.	.		0.274	TBCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253953.4	NM_033115		A	107154797	T	A	107154797	3	1	344	1	0	0	0	0	1	0	0	0	15651	1464	51	4	1265	4	TBCK	4	107154797	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	3332328	107154797	83999479	389	47752										
ALPK1	80216	hgsc.bcm.edu	37	chr4	113303587	113303587	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cgagttaaggaccctgatccAggaggcaaaggaaatgaagt	13	7	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:113303587A>T	ENST00000458497.1	+	4	434	c.155A>T	c.(154-156)cAg>cTg	p.Q52L	ALPK1_ENST00000504176.2_Intron|ALPK1_ENST00000177648.9_Missense_Mutation_p.Q52L	NM_001102406.1|NM_025144.3	NP_001095876.1|NP_079420.3	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	52							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(20)|ovary(6)|prostate(2)|urinary_tract(1)	53		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		ACCCTGATCCAGGAGGCAAAG	0.483																																					p.Q52L		Atlas-SNP	.											.	ALPK1	125	.	0			c.A155T						.						76	69	71					4																	113303587		2203	4300	6503	SO:0001583	missense	80216	exon4			TGATCCAGGAGGC	AY044164	CCDS3697.1, CCDS58923.1	4q26	2008-02-05			ENSG00000073331	ENSG00000073331			20917	protein-coding gene	gene with protein product	"lymphocyte alpha-kinase"	607347				10021370, 10819331	Standard	NM_025144		Approved	Lak, FLJ22670, KIAA1527	uc003ian.4	Q96QP1	OTTHUMG00000132911	ENST00000458497.1:c.155A>T	chr4.hg19:g.113303587A>T	ENSP00000398048:p.Gln52Leu	243.0	1.0		215.0	105.0	NM_001102406	B4E3G1|F5H138|Q68CI9|Q6P9F9|Q6ZNK4|Q9P201	Missense_Mutation	SNP	ENST00000458497.1	hg19	CCDS3697.1	.	.	.	.	.	.	.	.	.	.	A	19.71	3.878499	0.72294	.	.	ENSG00000073331	ENST00000458497;ENST00000177648;ENST00000309610	T;T	0.26810	1.71;1.71	5.63	5.63	0.86233	.	0.117523	0.64402	D	0.000016	T	0.48187	0.1486	M	0.72118	2.19	0.80722	D	1	D;P	0.65815	0.995;0.836	P;P	0.60682	0.878;0.526	T	0.51236	-0.8731	10	0.87932	D	0	-11.3802	15.839	0.78831	1.0:0.0:0.0:0.0	.	52;52	Q96QP1;B3KUH8	ALPK1_HUMAN;.	L	52;52;27	ENSP00000398048:Q52L;ENSP00000177648:Q52L	ENSP00000177648:Q52L	Q	+	2	0	ALPK1	113523036	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.638000	0.74309	2.130000	0.65690	0.533000	0.62120	CAG	.	.		0.483	ALPK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256421.2	NM_025144		T	113303587	A	T	113303587	3	4	344	1	0	0	0	0	1	0	0	0	544	188	7	4	161	4	ALPK1	4	113303587	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	6148790	113303587	77850689	390	47753										
ANK2	287	hgsc.bcm.edu	37	chr4	114278661	114278661	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cttctgaagtgtattctgttAccatcacatcccctgttgaa	6	11	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:114278661A>G	ENST00000357077.4	+	38	8940	c.8887A>G	c.(8887-8889)Acc>Gcc	p.T2963A	ANK2_ENST00000264366.6_Missense_Mutation_p.T2930A|ANK2_ENST00000506722.1_Intron|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000510275.2_Intron|ANK2_ENST00000394537.3_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	2963					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		GTATTCTGTTACCATCACATC	0.398																																					p.T2963A		Atlas-SNP	.											.	ANK2	576	.	0			c.A8887G						.						162	163	163					4																	114278661		2203	4300	6503	SO:0001583	missense	287	exon38			TCTGTTACCATCA	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.8887A>G	chr4.hg19:g.114278661A>G	ENSP00000349588:p.Thr2963Ala	114.0	0.0		87.0	39.0	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	hg19	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	A	10.43	1.347691	0.24426	.	.	ENSG00000145362	ENST00000357077;ENST00000264366	T;T	0.66460	-0.2;-0.21	5.58	1.52	0.23074	.	0.655719	0.13928	N	0.353122	T	0.56775	0.2008	L	0.50333	1.59	0.09310	N	1	B;B	0.27068	0.104;0.167	B;B	0.28011	0.039;0.085	T	0.43212	-0.9405	9	.	.	.	.	8.2285	0.31584	0.3241:0.5821:0.0938:0.0	.	2930;2963	Q01484;Q01484-4	ANK2_HUMAN;.	A	2963;2930	ENSP00000349588:T2963A;ENSP00000264366:T2930A	.	T	+	1	0	ANK2	114498110	0.000000	0.05858	0.008000	0.14137	0.084000	0.17831	-0.326000	0.07965	0.032000	0.15435	0.533000	0.62120	ACC	.	.		0.398	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		G	114278661	A	G	114278661	3	3	344	1	0	0	0	0	1	0	0	0	621	391	14	2	9102	2	ANK2	4	114278661	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	975074	114278661	76875615	391	47754										
NDST4	64579	hgsc.bcm.edu	37	chr4	115858495	115858495	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atgatgctattgtgaatgaaGccctttctgtaccgggcagg	12	8	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:115858495G>A	ENST00000264363.2	-	5	2064	c.1386C>T	c.(1384-1386)ggC>ggT	p.G462G		NM_022569.1	NP_072091.1	Q9H3R1	NDST4_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 4	462	Heparan sulfate N-deacetylase 4.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(43)|ovary(1)|prostate(7)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	81		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000562)		TGTGAATGAAGCCCTTTCTGT	0.438																																					p.G462G		Atlas-SNP	.											.	NDST4	193	.	0			c.C1386T						.						181	168	173					4																	115858495		2203	4300	6503	SO:0001819	synonymous_variant	64579	exon5			AATGAAGCCCTTT	AB036429	CCDS3706.1	4q26	2008-02-05			ENSG00000138653	ENSG00000138653		"Sulfotransferases, membrane-bound"	20779	protein-coding gene	gene with protein product		615039				11087757	Standard	NM_022569		Approved		uc003ibu.3	Q9H3R1	OTTHUMG00000132916	ENST00000264363.2:c.1386C>T	chr4.hg19:g.115858495G>A		93.0	0.0		90.0	37.0	NM_022569	Q2KHM8	Silent	SNP	ENST00000264363.2	hg19	CCDS3706.1																																																																																			.	.		0.438	NDST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256427.1	NM_022569		A	115858495	G	A	115858495	2	1	344	1	0	0	0	0	0	0	0	1	10267	958	34	3		3	NDST4	4	115858495	Silent	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1579834	115858495	75295781	392	47755										
NDST4	64579	hgsc.bcm.edu	37	chr4	115997739	115997739	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	actgtattccacacagtattTttctaaaagctctcgattcc	4	11	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:115997739T>C	ENST00000264363.2	-	2	1132	c.454A>G	c.(454-456)Aaa>Gaa	p.K152E		NM_022569.1	NP_072091.1	Q9H3R1	NDST4_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 4	152	Heparan sulfate N-deacetylase 4.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(43)|ovary(1)|prostate(7)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	81		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000562)		ACACAGTATTTTTCTAAAAGC	0.333																																					p.K152E		Atlas-SNP	.											.	NDST4	193	.	0			c.A454G						.						58	64	62					4																	115997739		2203	4300	6503	SO:0001583	missense	64579	exon2			AGTATTTTTCTAA	AB036429	CCDS3706.1	4q26	2008-02-05			ENSG00000138653	ENSG00000138653		"Sulfotransferases, membrane-bound"	20779	protein-coding gene	gene with protein product		615039				11087757	Standard	NM_022569		Approved		uc003ibu.3	Q9H3R1	OTTHUMG00000132916	ENST00000264363.2:c.454A>G	chr4.hg19:g.115997739T>C	ENSP00000264363:p.Lys152Glu	113.0	0.0		104.0	37.0	NM_022569	Q2KHM8	Missense_Mutation	SNP	ENST00000264363.2	hg19	CCDS3706.1	.	.	.	.	.	.	.	.	.	.	T	17.52	3.410340	0.62399	.	.	ENSG00000138653	ENST00000264363	T	0.41758	0.99	5.04	3.83	0.44106	.	0.046195	0.85682	D	0.000000	T	0.61999	0.2392	M	0.90145	3.09	0.49582	D	0.999803	B	0.30068	0.267	P	0.45712	0.491	T	0.62882	-0.6760	10	0.48119	T	0.1	.	11.9126	0.52747	0.0:0.0:0.146:0.854	.	152	Q9H3R1	NDST4_HUMAN	E	152	ENSP00000264363:K152E	ENSP00000264363:K152E	K	-	1	0	NDST4	116217188	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.140000	0.58031	0.734000	0.32515	0.482000	0.46254	AAA	.	.		0.333	NDST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256427.1	NM_022569		C	115997739	T	C	115997739	3	2	344	1	0	0	0	0	1	0	0	0	10267	1850	64	2	2216	2	NDST4	4	115997739	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	139244	115997739	75156537	393	47756										
NDST3	9348	hgsc.bcm.edu	37	chr4	119174753	119174753	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaataccctccaatggattcTgatgtaagcatagaccttaa	6	9	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:119174753T>A	ENST00000296499.5	+	13	2902	c.2499T>A	c.(2497-2499)tcT>tcA	p.S833S		NM_004784.2	NP_004775.1	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	833	Heparan sulfate N-sulfotransferase 3.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			NS(1)|breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	54						CAATGGATTCTGATGTAAGCA	0.328																																					p.S833S		Atlas-SNP	.											.	NDST3	107	.	0			c.T2499A						.						61	64	63					4																	119174753		2203	4298	6501	SO:0001819	synonymous_variant	9348	exon13			GGATTCTGATGTA	AF074924	CCDS3708.1	4q26	2008-08-04			ENSG00000164100	ENSG00000164100		"Sulfotransferases, membrane-bound"	7682	protein-coding gene	gene with protein product		603950				9915799	Standard	NM_004784		Approved	HSST3	uc003ibx.3	O95803	OTTHUMG00000132959	ENST00000296499.5:c.2499T>A	chr4.hg19:g.119174753T>A		318.0	0.0		271.0	103.0	NM_004784	B4DI67|Q4W5C1|Q4W5D0|Q6UWC5|Q9UP21	Silent	SNP	ENST00000296499.5	hg19	CCDS3708.1																																																																																			.	.		0.328	NDST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256517.4	NM_004784		A	119174753	T	A	119174753	2	1	344	1	0	0	0	0	0	0	0	1	10266	1567	55	4		4	NDST3	4	119174753	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	3177014	119174753	71979523	394	47757										
SEC24D	9871	hgsc.bcm.edu	37	chr4	119727008	119727008	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaacaaataccttggtcttgTatcatgcaatctgtagtgac	7	8	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:119727008T>C	ENST00000280551.6	-	7	1141	c.903A>G	c.(901-903)atA>atG	p.I301M	SEC24D_ENST00000379735.5_Missense_Mutation_p.I302M|SEC24D_ENST00000419654.2_De_novo_Start_OutOfFrame			O94855	SC24D_HUMAN	SEC24 family member D	301					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(13)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37						CTTGGTCTTGTATCATGCAAT	0.403																																					p.I301M		Atlas-SNP	.											.	SEC24D	96	.	0			c.A903G						.						165	149	154					4																	119727008		2203	4300	6503	SO:0001583	missense	9871	exon7			GTCTTGTATCATG	AB018298	CCDS3710.1	4q26	2013-10-21	2013-10-21		ENSG00000150961	ENSG00000150961			10706	protein-coding gene	gene with protein product		607186	"SEC24 (S. cerevisiae) related gene family, member D", "SEC24 family, member D (S. cerevisiae)"			9872452, 10075675	Standard	NM_014822		Approved	KIAA0755	uc003ici.4	O94855	OTTHUMG00000132957	ENST00000280551.6:c.903A>G	chr4.hg19:g.119727008T>C	ENSP00000280551:p.Ile301Met	28.0	0.0		44.0	20.0	NM_014822	Q8IYI7	Missense_Mutation	SNP	ENST00000280551.6	hg19	CCDS3710.1	.	.	.	.	.	.	.	.	.	.	T	16.55	3.153878	0.57259	.	.	ENSG00000150961	ENST00000280551;ENST00000379735	T;T	0.23348	1.91;1.91	5.2	-2.59	0.06209	.	0.105208	0.64402	D	0.000004	T	0.29223	0.0727	M	0.72894	2.215	0.80722	D	1	B;P	0.39404	0.081;0.672	B;P	0.48873	0.118;0.593	T	0.17561	-1.0365	10	0.72032	D	0.01	-10.6777	2.5766	0.04807	0.2252:0.0868:0.4597:0.2283	.	302;301	O94855-2;O94855	.;SC24D_HUMAN	M	301;302	ENSP00000280551:I301M;ENSP00000369059:I302M	ENSP00000280551:I301M	I	-	3	3	SEC24D	119946456	0.290000	0.24343	0.997000	0.53966	0.626000	0.37791	-0.774000	0.04684	-0.013000	0.14199	0.383000	0.25322	ATA	.	.		0.403	SEC24D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256514.4			C	119727008	T	C	119727008	3	2	344	1	0	0	0	0	1	0	0	0	14012	1628	57	2	2263	2	SEC24D	4	119727008	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	552255	119727008	71427268	395	47758										
BBS7	55212	hgsc.bcm.edu	37	chr4	122756329	122756329	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	caataaagtgagttctttgaTggagtgaaagaggtttgatg	13	2	1	5			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:122756329T>C	ENST00000264499.4	-	14	1664	c.1481A>G	c.(1480-1482)cAt>cGt	p.H494R	BBS7_ENST00000506636.1_Missense_Mutation_p.H494R	NM_176824.2	NP_789794.1	Q8IWZ6	BBS7_HUMAN	Bardet-Biedl syndrome 7	494					brain development (GO:0007420)|cilium morphogenesis (GO:0060271)|determination of left/right symmetry (GO:0007368)|digestive tract morphogenesis (GO:0048546)|eye development (GO:0001654)|fat cell differentiation (GO:0045444)|heart looping (GO:0001947)|limb development (GO:0060173)|melanosome transport (GO:0032402)|nonmotile primary cilium assembly (GO:0035058)|palate development (GO:0060021)|pigment granule aggregation in cell center (GO:0051877)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein transport (GO:0015031)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smoothened signaling pathway (GO:0007224)|visual perception (GO:0007601)	axoneme (GO:0005930)|BBSome (GO:0034464)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(2)|prostate(1)|skin(2)	30						AGTTCTTTGATGGAGTGAAAG	0.378									Bardet-Biedl syndrome																												p.H494R		Atlas-SNP	.											.	BBS7	61	.	0			c.A1481G						.						216	198	204					4																	122756329		2203	4300	6503	SO:0001583	missense	55212	exon14	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	CTTTGATGGAGTG	AF521644	CCDS3724.1, CCDS54799.1	4q27	2013-01-08			ENSG00000138686	ENSG00000138686			18758	protein-coding gene	gene with protein product		607590					Standard	NM_176824		Approved	FLJ10715, BBS2L1	uc003ied.3	Q8IWZ6	OTTHUMG00000133076	ENST00000264499.4:c.1481A>G	chr4.hg19:g.122756329T>C	ENSP00000264499:p.His494Arg	140.0	0.0		95.0	29.0	NM_018190	Q4W5P8|Q8N581|Q9NVI4	Missense_Mutation	SNP	ENST00000264499.4	hg19	CCDS3724.1	.	.	.	.	.	.	.	.	.	.	T	25.1	4.607781	0.87258	.	.	ENSG00000138686	ENST00000264499;ENST00000506636	D;D	0.98105	-4.72;-4.7	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	D	0.98820	0.9602	M	0.89414	3.03	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99705	1.1005	10	0.62326	D	0.03	-18.0253	15.2549	0.73576	0.0:0.0:0.0:1.0	.	494	Q8IWZ6	BBS7_HUMAN	R	494	ENSP00000264499:H494R;ENSP00000423626:H494R	ENSP00000264499:H494R	H	-	2	0	BBS7	122975779	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.945000	0.87732	1.992000	0.58205	0.528000	0.53228	CAT	.	.		0.378	BBS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256716.1			C	122756329	T	C	122756329	3	2	344	1	0	0	0	0	1	0	0	0	1341	1464	51	2	695	2	BBS7	4	122756329	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	3029321	122756329	68397947	396	47759										
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123113385	123113385	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgtatgttctggaatataggActtgttccggaagaaacaga	11	5	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:123113385A>T	ENST00000264501.4	+	11	1276	c.903A>T	c.(901-903)ggA>ggT	p.G301G	KIAA1109_ENST00000455637.1_Splice_Site_p.G301G|KIAA1109_ENST00000388738.3_Splice_Site_p.G301G			Q2LD37	K1109_HUMAN	KIAA1109	301					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						GGAATATAGGACTTGTTCCGG	0.363																																					p.G301G		Atlas-SNP	.											.	KIAA1109	424	.	0			c.A903T						.						78	73	75					4																	123113385		1821	4075	5896	SO:0001630	splice_region_variant	84162	exon9			TATAGGACTTGTT	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.902-1A>T	chr4.hg19:g.123113385A>T		95.0	0.0		110.0	54.0	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Silent	SNP	ENST00000264501.4	hg19	CCDS43267.1	.	.	.	.	.	.	.	.	.	.	A	13.62	2.290807	0.40494	.	.	ENSG00000138688	ENST00000424425	.	.	.	5.93	3.65	0.41850	.	.	.	.	.	T	0.43389	0.1245	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41070	-0.9529	4	.	.	.	.	0.621	0.00778	0.4694:0.1786:0.1741:0.1778	.	.	.	.	S	134	.	.	T	+	1	0	KIAA1109	123332835	0.997000	0.39634	1.000000	0.80357	0.983000	0.72400	0.530000	0.23036	1.081000	0.41110	0.460000	0.39030	ACT	.	.		0.363	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797	Silent	T	123113385	A	T	123113385	5	4	344	1	0	0	0	0	0	0	1	0	8217	289	10	4	937	4	KIAA1109	4	123113385	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	357056	123113385	68040891	397	47760										
ADAD1	132612	hgsc.bcm.edu	37	chr4	123336766	123336766	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggcctgagtgggaagatcacTgaaaggttaaaattactaat	11	5	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:123336766T>A	ENST00000296513.2	+	11	1667	c.1482T>A	c.(1480-1482)acT>acA	p.T494T	ADAD1_ENST00000388724.2_Silent_p.T483T|ADAD1_ENST00000388725.2_Silent_p.T476T	NM_139243.3	NP_640336.1	Q96M93	ADAD1_HUMAN	adenosine deaminase domain containing 1 (testis-specific)	494	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				multicellular organismal development (GO:0007275)|RNA processing (GO:0006396)|spermatid development (GO:0007286)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	35						GGAAGATCACTGAAAGGTTAA	0.323																																					p.T494T		Atlas-SNP	.											.	ADAD1	94	.	0			c.T1482A						.						88	89	89					4																	123336766		2203	4300	6503	SO:0001819	synonymous_variant	132612	exon11			GATCACTGAAAGG	AK057303	CCDS34058.1, CCDS54800.1, CCDS54801.1	4q27	2007-05-31			ENSG00000164113	ENSG00000164113			30713	protein-coding gene	gene with protein product		614130				7543294, 9541871	Standard	NM_139243		Approved	Tenr	uc003iep.3	Q96M93	OTTHUMG00000150128	ENST00000296513.2:c.1482T>A	chr4.hg19:g.123336766T>A		98.0	0.0		82.0	36.0	NM_139243	A6NKN4|B7WPB0|D3DNX2|Q8IWG6|Q8NA06	Silent	SNP	ENST00000296513.2	hg19	CCDS34058.1																																																																																			.	.		0.323	ADAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316452.1	NM_139243		A	123336766	T	A	123336766	2	1	344	1	0	0	0	0	0	0	0	1	231	1567	55	4		4	ADAD1	4	123336766	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	223381	123336766	67817510	398	47761										
SPATA5	166378	hgsc.bcm.edu	37	chr4	123859404	123859404	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctgatggatggcattggttcAgtaagtatagcactagtatt	11	5	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:123859404A>T	ENST00000274008.4	+	8	1527	c.1458A>T	c.(1456-1458)tcA>tcT	p.S486S	SPATA5_ENST00000422835.2_3'UTR	NM_145207.2	NP_660208.2	Q8NB90	SPAT5_HUMAN	spermatogenesis associated 5	486					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24						GCATTGGTTCAGTAAGTATAG	0.383																																					p.S486S		Atlas-SNP	.											.	SPATA5	62	.	0			c.A1458T						.						181	181	181					4																	123859404		2203	4300	6503	SO:0001630	splice_region_variant	166378	exon8			TGGTTCAGTAAGT	AF361489	CCDS3730.1	4q28.1	2010-04-21			ENSG00000145375	ENSG00000145375		"ATPases / AAA-type"	18119	protein-coding gene	gene with protein product	"ATPase family gene 2 homolog (S. cerevisiae)"	613940				16465403	Standard	NM_145207		Approved	SPAF, AFG2	uc003iez.4	Q8NB90	OTTHUMG00000133074	ENST00000274008.4:c.1458+1A>T	chr4.hg19:g.123859404A>T		80.0	0.0		52.0	17.0	NM_145207	C9JT97|Q86XW1|Q8NI20|Q8TDL7	Silent	SNP	ENST00000274008.4	hg19	CCDS3730.1																																																																																			.	.		0.383	SPATA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256714.2	NM_145207	Silent	T	123859404	A	T	123859404	5	4	344	1	0	0	0	0	0	0	1	0	15026	202	7	4	1488	4	SPATA5	4	123859404	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	522638	123859404	67294872	399	47762										
FAT4	79633	hgsc.bcm.edu	37	chr4	126328165	126328165	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccgctccaaatattcactgcTagttcgtgctgatgatggtc	9	11	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:126328165T>C	ENST00000394329.3	+	3	5451	c.5438T>C	c.(5437-5439)cTa>cCa	p.L1813P	FAT4_ENST00000335110.5_Missense_Mutation_p.L111P	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	1813	Cadherin 17. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						TATTCACTGCTAGTTCGTGCT	0.468																																					p.L1813P		Atlas-SNP	.											.	FAT4	1752	.	0			c.T5438C						.						157	146	150					4																	126328165		2203	4300	6503	SO:0001583	missense	79633	exon3			CACTGCTAGTTCG	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.5438T>C	chr4.hg19:g.126328165T>C	ENSP00000377862:p.Leu1813Pro	117.0	0.0		80.0	12.0	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	hg19	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	T	17.49	3.402048	0.62288	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.01804	4.63;4.63	5.37	5.37	0.77165	Cadherin (4);Cadherin-like (1);	0.000000	0.27861	U	0.017549	T	0.06416	0.0165	L	0.39566	1.225	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.55496	-0.8132	10	0.30078	T	0.28	.	15.6769	0.77336	0.0:0.0:0.0:1.0	.	111;1813	Q6V0I7-2;Q6V0I7	.;FAT4_HUMAN	P	1813;111	ENSP00000377862:L1813P;ENSP00000335169:L111P	ENSP00000335169:L111P	L	+	2	0	FAT4	126547615	1.000000	0.71417	0.999000	0.59377	0.880000	0.50808	5.909000	0.69923	2.157000	0.67596	0.528000	0.53228	CTA	.	.		0.468	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		C	126328165	T	C	126328165	3	2	344	1	0	0	0	0	1	0	0	0	5700	1522	53	2	5448	2	FAT4	4	126328165	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2468761	126328165	64826111	400	47763										
PCDH10	57575	hgsc.bcm.edu	37	chr4	134084265	134084265	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agcaatctgcatgttcctggCatggactctgttccagacac	9	12	2	1	rs151224823	byFrequency	TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:134084265C>A	ENST00000264360.5	+	4	3757	c.2931C>A	c.(2929-2931)ggC>ggA	p.G977G		NM_032961.1	NP_116586.1	Q9P2E7	PCD10_HUMAN	protocadherin 10	977					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(30)|liver(1)|lung(72)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(2)	136				LUSC - Lung squamous cell carcinoma(193;0.227)		ATGTTCCTGGCATGGACTCTG	0.542																																					p.G977G		Atlas-SNP	.											.	PCDH10	290	.	0			c.C2931A						.						137	121	126					4																	134084265		2203	4300	6503	SO:0001819	synonymous_variant	57575	exon4			TCCTGGCATGGAC	AB037821	CCDS34063.1, CCDS75192.1	4q28.3	2010-01-26				ENSG00000138650		"Cadherins / Protocadherins : Non-clustered"	13404	protein-coding gene	gene with protein product		608286				10835267	Standard	NM_020815		Approved	OL-PCDH, KIAA1400	uc003iha.3	Q9P2E7		ENST00000264360.5:c.2931C>A	chr4.hg19:g.134084265C>A		92.0	0.0		89.0	37.0	NM_032961	Q4W5F6|Q96SF0	Silent	SNP	ENST00000264360.5	hg19	CCDS34063.1																																																																																			.	C|0.998;G|0.002		0.542	PCDH10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000364457.2	NM_032961		A	134084265	C	A	134084265	2	1	344	1	0	0	0	0	0	0	0	1	11516	697	25	3		3	PCDH10	4	134084265	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	7756100	134084265	57070011	401	47764										
ELMOD2	255520	hgsc.bcm.edu	37	chr4	141448650	141448650	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gacatactccaagaataaggTaggataacataaaggtggta	10	5	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:141448650T>C	ENST00000323570.3	+	3	303		c.e3+2		ELMOD2_ENST00000511887.2_Missense_Mutation_p.V58A	NM_153702.3	NP_714913.1	Q8IZ81	ELMD2_HUMAN	ELMO/CED-12 domain containing 2						defense response to virus (GO:0051607)|phagocytosis (GO:0006909)|positive regulation of GTPase activity (GO:0043547)|regulation of defense response to virus (GO:0050688)	cytoskeleton (GO:0005856)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	7	all_hematologic(180;0.162)					AAGAATAAGGTAGGATAACAT	0.294																																					.		Atlas-SNP	.											.	ELMOD2	16	.	0			c.171+2T>C						.						40	43	42					4																	141448650		2199	4288	6487	SO:0001630	splice_region_variant	255520	exon3			ATAAGGTAGGATA	BX648349	CCDS3752.1	4q31.1	2006-10-24	2006-01-20		ENSG00000179387	ENSG00000179387			28111	protein-coding gene	gene with protein product		610196	"ELMO domain containing 2"			16773575	Standard	NM_153702		Approved	MGC10084	uc003iik.3	Q8IZ81	OTTHUMG00000133417	ENST00000323570.3:c.171+2T>C	chr4.hg19:g.141448650T>C		375.0	0.0		272.0	115.0	NM_153702	B2R712|D3DNZ0	Splice_Site	SNP	ENST00000323570.3	hg19	CCDS3752.1	.	.	.	.	.	.	.	.	.	.	T	19.19	3.778779	0.70107	.	.	ENSG00000179387	ENST00000323570;ENST00000502397	.	.	.	5.66	5.66	0.87406	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.1249	0.65213	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	ELMOD2	141668100	1.000000	0.71417	0.999000	0.59377	0.966000	0.64601	4.575000	0.60908	2.283000	0.76528	0.533000	0.62120	.	.	.		0.294	ELMOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257277.2	NM_153702	Intron	C	141448650	T	C	141448650	5	2	344	1	0	0	0	0	0	0	1	0	5071	1652	57	2	179	2	ELMOD2	4	141448650	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	7364385	141448650	49705626	402	47765										
INPP4B	8821	hgsc.bcm.edu	37	chr4	143007366	143007366	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atattttgaaggagattttcTagcaatgcttttaaatcatt	6	4	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:143007366T>C	ENST00000513000.1	-	25	2851	c.2418A>G	c.(2416-2418)ctA>ctG	p.L806L	INPP4B_ENST00000509777.1_Silent_p.L806L|INPP4B_ENST00000508116.1_Silent_p.L806L|INPP4B_ENST00000308502.4_Silent_p.L806L|INPP4B_ENST00000262992.4_Silent_p.L806L	NM_003866.2	NP_003857.2	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II, 105kDa	806					cellular calcium ion homeostasis (GO:0006874)|inositol phosphate metabolic process (GO:0043647)|negative regulation of osteoclast differentiation (GO:0045671)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of bone remodeling (GO:0046850)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of protein kinase B signaling (GO:0051896)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	lipid binding (GO:0008289)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(29)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58	all_hematologic(180;0.158)					GGAGATTTTCTAGCAATGCTT	0.328																																					p.L806L		Atlas-SNP	.											.	INPP4B	132	.	0			c.A2418G						.						84	87	86					4																	143007366		2201	4297	6498	SO:0001819	synonymous_variant	8821	exon25			ATTTTCTAGCAAT	U96922	CCDS3757.1	4q31.1	2008-02-05	2002-08-29			ENSG00000109452			6075	protein-coding gene	gene with protein product		607494	"inositol polyphosphate-4-phosphatase, type II, 105kD"			9295334	Standard	NM_003866		Approved		uc003iiw.4	O15327		ENST00000513000.1:c.2418A>G	chr4.hg19:g.143007366T>C		26.0	0.0		28.0	15.0	NM_003866	Q2TAI2|Q5XLE7|Q6IN59|Q6PJB4	Silent	SNP	ENST00000513000.1	hg19	CCDS3757.1																																																																																			.	.		0.328	INPP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364587.1	NM_003866		C	143007366	T	C	143007366	2	2	344	1	0	0	0	0	0	0	0	1	7762	1509	53	2		2	INPP4B	4	143007366	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1558716	143007366	48146910	403	47766										
USP38	84640	hgsc.bcm.edu	37	chr4	144133531	144133531	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gacctccatggtttactcccAgatcacagcaagactgttct	7	13	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:144133531A>T	ENST00000307017.4	+	8	2064	c.1558A>T	c.(1558-1560)Aga>Tga	p.R520*	USP38_ENST00000510377.1_Nonsense_Mutation_p.R520*	NM_032557.5	NP_115946.2	Q8NB14	UBP38_HUMAN	ubiquitin specific peptidase 38	520	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	33	all_hematologic(180;0.158)					GTTTACTCCCAGATCACAGCA	0.378																																					p.R520X		Atlas-SNP	.											.	USP38	92	.	0			c.A1558T						.						115	114	114					4																	144133531		2203	4300	6503	SO:0001587	stop_gained	84640	exon8			ACTCCCAGATCAC	AF211481	CCDS3758.1	4q31.1	2008-02-05	2005-08-08		ENSG00000170185	ENSG00000170185		"Ubiquitin-specific peptidases"	20067	protein-coding gene	gene with protein product			"ubiquitin specific protease 38"			12838346	Standard	NM_032557		Approved	KIAA1891, HP43.8KD	uc003ijb.3	Q8NB14	OTTHUMG00000161420	ENST00000307017.4:c.1558A>T	chr4.hg19:g.144133531A>T	ENSP00000303434:p.Arg520*	65.0	0.0		73.0	34.0	NM_032557	B3KX93|Q3ZCV1|Q8NDF5|Q96DK6|Q96PZ6|Q9BY55	Nonsense_Mutation	SNP	ENST00000307017.4	hg19	CCDS3758.1	.	.	.	.	.	.	.	.	.	.	A	43	10.066890	0.99329	.	.	ENSG00000170185	ENST00000510377;ENST00000307017	.	.	.	5.47	2.79	0.32731	.	0.112679	0.64402	D	0.000010	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15952	T	0.53	-11.437	13.0103	0.58727	0.5756:0.4244:0.0:0.0	.	.	.	.	X	520	.	ENSP00000303434:R520X	R	+	1	2	USP38	144352981	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.632000	0.46511	0.987000	0.38709	0.529000	0.55759	AGA	.	.		0.378	USP38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364869.1	NM_032557		T	144133531	A	T	144133531	4	4	344	1	0	0	0	0	0	1	0	0	17084	180	7	4	1588	4	USP38	4	144133531	Nonsense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1126165	144133531	47020745	404	47767										
TTC29	83894	hgsc.bcm.edu	37	chr4	147860987	147860987	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tctggaggagcaaggcagctTctgtctggctaaggctgtaa	14	8	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:147860987T>A	ENST00000325106.4	-	3	287	c.61A>T	c.(61-63)Aag>Tag	p.K21*	TTC29_ENST00000513335.1_Nonsense_Mutation_p.K47*|TTC29_ENST00000398886.4_Nonsense_Mutation_p.K47*|RP11-292D4.2_ENST00000515530.1_RNA	NM_031956.2	NP_114162.2	Q8NA56	TTC29_HUMAN	tetratricopeptide repeat domain 29	21										breast(2)|cervix(2)|endometrium(3)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	26	all_hematologic(180;0.151)					CAAGGCAGCTTCTGTCTGGCT	0.418																																					p.K21X		Atlas-SNP	.											.	TTC29	63	.	0			c.A61T						.						81	86	85					4																	147860987		1872	4096	5968	SO:0001587	stop_gained	83894	exon3			GCAGCTTCTGTCT	AF345910	CCDS47141.1, CCDS75200.1	4q31.23	2013-01-11				ENSG00000137473		"Tetratricopeptide (TTC) repeat domain containing"	29936	protein-coding gene	gene with protein product						12477932	Standard	NM_031956		Approved	NYD-SP14	uc003ikw.4	Q8NA56		ENST00000325106.4:c.61A>T	chr4.hg19:g.147860987T>A	ENSP00000316740:p.Lys21*	105.0	0.0		84.0	44.0	NM_031956	A4GU95|Q9BXB6	Nonsense_Mutation	SNP	ENST00000325106.4	hg19	CCDS47141.1	.	.	.	.	.	.	.	.	.	.	T	36	5.937785	0.97122	.	.	ENSG00000137473	ENST00000513335;ENST00000398886;ENST00000325106;ENST00000398883;ENST00000504425;ENST00000515315;ENST00000502319	.	.	.	5.3	5.3	0.74995	.	0.154112	0.42053	D	0.000774	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-24.1768	11.9333	0.52860	0.0:0.0:0.0:1.0	.	.	.	.	X	47;47;21;21;21;47;21	.	ENSP00000316740:K21X	K	-	1	0	TTC29	148080437	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	1.904000	0.39868	2.140000	0.66376	0.528000	0.53228	AAG	.	.		0.418	TTC29-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_031956		A	147860987	T	A	147860987	4	1	344	1	0	0	0	0	0	1	0	0	16711	1792	62	4	1410	4	TTC29	4	147860987	Nonsense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	3727456	147860987	43293289	405	47768										
TIGD4	201798	hgsc.bcm.edu	37	chr4	153691590	153691590	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtattggtaggtaacattcgAtaaagcagcccagtctcttt	9	8	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:153691590A>G	ENST00000304337.2	-	2	1387	c.567T>C	c.(565-567)taT>taC	p.Y189Y		NM_145720.3	NP_663772.1	Q8IY51	TIGD4_HUMAN	tigger transposable element derived 4	189	DDE.					nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	26	all_hematologic(180;0.093)					GTAACATTCGATAAAGCAGCC	0.348																																					p.Y189Y		Atlas-SNP	.											.	TIGD4	53	.	0			c.T567C						.						62	64	63					4																	153691590		2203	4296	6499	SO:0001819	synonymous_variant	201798	exon2			CATTCGATAAAGC	AK058054	CCDS34079.1	4q31.23	2008-02-05							18335	protein-coding gene	gene with protein product							Standard	NM_145720		Approved		uc003imy.3	Q8IY51		ENST00000304337.2:c.567T>C	chr4.hg19:g.153691590A>G		160.0	0.0		108.0	48.0	NM_145720	Q96LP5	Silent	SNP	ENST00000304337.2	hg19	CCDS34079.1																																																																																			.	.		0.348	TIGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365028.1	NM_145720		G	153691590	A	G	153691590	2	3	344	1	0	0	0	0	0	0	0	1	15913	340	12	2		2	TIGD4	4	153691590	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	5830603	153691590	37462686	406	47769										
FHDC1	85462	hgsc.bcm.edu	37	chr4	153897040	153897040	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgtagcaccaaagagaggctCcctgaaagaggcgtctcccg	12	12	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:153897040C>A	ENST00000511601.1	+	12	2785	c.2597C>A	c.(2596-2598)tCc>tAc	p.S866Y	FHDC1_ENST00000260008.3_Missense_Mutation_p.S866Y			Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1	866									ARFIP1/FHDC1(2)	NS(2)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	43	all_hematologic(180;0.093)					AAGAGAGGCTCCCTGAAAGAG	0.657																																					p.S866Y		Atlas-SNP	.											.	FHDC1	102	.	0			c.C2597A						.						63	77	72					4																	153897040		2200	4299	6499	SO:0001583	missense	85462	exon11			GAGGCTCCCTGAA	AB051514	CCDS34081.1	4q31.3	2014-02-12	2007-11-29		ENSG00000137460	ENSG00000137460			29363	protein-coding gene	gene with protein product						15138637	Standard	NM_033393		Approved	KIAA1727	uc003inf.2	Q9C0D6	OTTHUMG00000161452	ENST00000511601.1:c.2597C>A	chr4.hg19:g.153897040C>A	ENSP00000427567:p.Ser866Tyr	243.0	0.0		177.0	83.0	NM_033393		Missense_Mutation	SNP	ENST00000511601.1	hg19	CCDS34081.1	.	.	.	.	.	.	.	.	.	.	C	14.35	2.507860	0.44558	.	.	ENSG00000137460	ENST00000511601;ENST00000260008	T;T	0.39406	1.08;1.08	4.65	4.65	0.58169	.	1.125910	0.06249	N	0.691717	T	0.50257	0.1605	L	0.32530	0.975	0.44825	D	0.997836	D	0.56521	0.976	P	0.51016	0.656	T	0.49273	-0.8957	10	0.87932	D	0	.	17.534	0.87822	0.0:1.0:0.0:0.0	.	866	Q9C0D6	FHDC1_HUMAN	Y	866	ENSP00000427567:S866Y;ENSP00000260008:S866Y	ENSP00000260008:S866Y	S	+	2	0	FHDC1	154116490	0.195000	0.23338	0.073000	0.20177	0.077000	0.17291	2.240000	0.43088	2.119000	0.64992	0.462000	0.41574	TCC	.	.		0.657	FHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364981.2	NM_033393		A	153897040	C	A	153897040	3	1	344	1	0	0	0	0	1	0	0	0	5884	855	30	3	2639	3	FHDC1	4	153897040	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	205450	153897040	37257236	407	47770										
GRIA2	2891	hgsc.bcm.edu	37	chr4	158262575	158262575	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aagcaaacagaaattgcttaTggaacattagactctggctc	8	8	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:158262575T>C	ENST00000264426.9	+	12	2283	c.2004T>C	c.(2002-2004)taT>taC	p.Y668Y	GRIA2_ENST00000393815.2_Silent_p.Y621Y|GRIA2_ENST00000507898.1_Silent_p.Y621Y|GRIA2_ENST00000449365.1_Silent_p.Y621Y|GRIA2_ENST00000296526.7_Silent_p.Y668Y	NM_001083619.1	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2	668					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(2)|lung(32)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	79	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	AAATTGCTTATGGAACATTAG	0.403																																					p.Y668Y		Atlas-SNP	.											.	GRIA2	358	.	0			c.T2004C						.						145	140	142					4																	158262575		2203	4300	6503	SO:0001819	synonymous_variant	2891	exon12			TGCTTATGGAACA		CCDS3797.1, CCDS43274.1, CCDS43275.1	4q32.1	2012-08-29			ENSG00000120251	ENSG00000120251		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4572	protein-coding gene	gene with protein product		138247		GLUR2		1311100	Standard	NM_001083619		Approved	GluA2, GLURB	uc003ipl.4	P42262	OTTHUMG00000133836	ENST00000264426.9:c.2004T>C	chr4.hg19:g.158262575T>C		82.0	0.0		86.0	43.0	NM_000826	A8MT92|I6L997|Q96FP6	Silent	SNP	ENST00000264426.9	hg19	CCDS43274.1																																																																																			.	.		0.403	GRIA2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000258367.2			C	158262575	T	C	158262575	2	2	344	1	0	0	0	0	0	0	0	1	6777	1471	51	2		2	GRIA2	4	158262575	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	4365535	158262575	32891701	408	47771										
TMEM144	55314	hgsc.bcm.edu	37	chr4	159174638	159174638	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgatacttgcattttgcatcAtcttgactggagccttatgc	8	9	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:159174638A>G	ENST00000296529.6	+	13	1517	c.997A>G	c.(997-999)Atc>Gtc	p.I333V	TMEM144_ENST00000503404.1_3'UTR	NM_018342.4	NP_060812.2	Q7Z5S9	TM144_HUMAN	transmembrane protein 144	333						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(1)|large_intestine(7)|lung(9)|prostate(1)	19	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0539)		ATTTTGCATCATCTTGACTGG	0.383																																					p.I333V		Atlas-SNP	.											.	TMEM144	34	.	0			c.A997G						.						165	158	160					4																	159174638		2203	4300	6503	SO:0001583	missense	55314	exon13			TGCATCATCTTGA	AK002017	CCDS3799.1	4q32.1	2008-02-05			ENSG00000164124	ENSG00000164124			25633	protein-coding gene	gene with protein product						12477932	Standard	NM_018342		Approved	FLJ11155	uc003ipx.3	Q7Z5S9	OTTHUMG00000162013	ENST00000296529.6:c.997A>G	chr4.hg19:g.159174638A>G	ENSP00000296529:p.Ile333Val	55.0	0.0		43.0	15.0	NM_018342	D3DP24|Q49A05|Q9NUT3	Missense_Mutation	SNP	ENST00000296529.6	hg19	CCDS3799.1	.	.	.	.	.	.	.	.	.	.	A	6.087	0.384312	0.11524	.	.	ENSG00000164124	ENST00000296529	T	0.40756	1.02	5.49	5.49	0.81192	.	0.053649	0.85682	D	0.000000	T	0.22085	0.0532	N	0.10874	0.06	0.80722	D	1	B	0.09022	0.002	B	0.04013	0.001	T	0.10730	-1.0617	10	0.08381	T	0.77	-21.9227	12.2683	0.54691	1.0:0.0:0.0:0.0	.	333	Q7Z5S9	TM144_HUMAN	V	333	ENSP00000296529:I333V	ENSP00000296529:I333V	I	+	1	0	TMEM144	159394088	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.360000	0.52299	2.214000	0.71695	0.374000	0.22700	ATC	.	.		0.383	TMEM144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365597.1	NM_018342		G	159174638	A	G	159174638	3	3	344	1	0	0	0	0	1	0	0	0	16073	217	8	2	1039	2	TMEM144	4	159174638	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	912063	159174638	31979638	409	47772										
FSTL5	56884	hgsc.bcm.edu	37	chr4	162954782	162954782	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcaatcatttcttacctttgActcttgaactttcttgattt	4	9	4	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:162954782A>T	ENST00000306100.5	-	3	591	c.155T>A	c.(154-156)gTc>gAc	p.V52D	FSTL5_ENST00000536695.1_Missense_Mutation_p.V51D|FSTL5_ENST00000379164.4_Missense_Mutation_p.V51D|FSTL5_ENST00000427802.2_Missense_Mutation_p.V51D|RP11-497K21.1_ENST00000513093.1_RNA	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	52						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(18)|lung(43)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	91	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		CTTACCTTTGACTCTTGAACT	0.254																																					p.V52D		Atlas-SNP	.											.	FSTL5	207	.	0			c.T155A						.						31	31	31					4																	162954782		2162	4244	6406	SO:0001583	missense	56884	exon3			CCTTTGACTCTTG	BC036502	CCDS3802.1, CCDS47157.1, CCDS47158.1	4q32.3	2013-01-11			ENSG00000168843	ENSG00000168843		"EF-hand domain containing", "Immunoglobulin superfamily / I-set domain containing"	21386	protein-coding gene	gene with protein product						10574462, 15527507	Standard	NM_020116		Approved	DKFZp566D234, KIAA1263	uc003iqh.4	Q8N475	OTTHUMG00000161397	ENST00000306100.5:c.155T>A	chr4.hg19:g.162954782A>T	ENSP00000305334:p.Val52Asp	147.0	0.0		107.0	50.0	NM_020116	E9PCP6|Q9NSW7|Q9ULF7	Missense_Mutation	SNP	ENST00000306100.5	hg19	CCDS3802.1	.	.	.	.	.	.	.	.	.	.	A	13.45	2.241899	0.39598	.	.	ENSG00000168843	ENST00000306100;ENST00000379164;ENST00000427802;ENST00000536695	T;T;T;T	0.73152	-0.72;-0.69;-0.72;-0.69	4.99	0.993	0.19825	.	0.746340	0.12064	N	0.502832	T	0.42743	0.1216	N	0.08118	0	0.58432	D	0.999999	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.08055	0.003;0.0;0.0	T	0.38950	-0.9637	10	0.35671	T	0.21	.	1.4533	0.02380	0.5492:0.1785:0.1001:0.1722	.	51;51;52	E9PCP6;F8VZ90;Q8N475	.;.;FSTL5_HUMAN	D	52;51;51;51	ENSP00000305334:V52D;ENSP00000368462:V51D;ENSP00000389270:V51D;ENSP00000440409:V51D	ENSP00000305334:V52D	V	-	2	0	FSTL5	163174232	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.943000	0.29030	0.831000	0.34780	0.533000	0.62120	GTC	.	.		0.254	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116		T	162954782	A	T	162954782	3	4	344	1	0	0	0	0	1	0	0	0	6088	275	10	4	2444	4	FSTL5	4	162954782	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3780144	162954782	28199494	410	47773										
DDX60L	91351	hgsc.bcm.edu	37	chr4	169299546	169299546	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	attagcattttggaattttgCtggaatatattttcttccaa	6	5	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:169299546C>A	ENST00000511577.1	-	33	4691	c.4444G>T	c.(4444-4446)Gca>Tca	p.A1482S	DDX60L_ENST00000260184.7_Missense_Mutation_p.A1482S			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	1482							ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		TGGAATTTTGCTGGAATATAT	0.289																																					p.A1482S		Atlas-SNP	.											.	DDX60L	116	.	0			c.G4444T						.						41	36	38					4																	169299546		1779	4040	5819	SO:0001583	missense	91351	exon33			ATTTTGCTGGAAT	AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.4444G>T	chr4.hg19:g.169299546C>A	ENSP00000422423:p.Ala1482Ser	331.0	1.0		253.0	87.0	NM_001012967	Q96ND6	Missense_Mutation	SNP	ENST00000511577.1	hg19		.	.	.	.	.	.	.	.	.	.	C	2.747	-0.260984	0.05791	.	.	ENSG00000181381	ENST00000260184;ENST00000511577	T;T	0.17370	2.28;2.28	3.36	1.43	0.22495	.	.	.	.	.	T	0.11410	0.0278	M	0.65320	2	0.21105	N	0.999781	P	0.44478	0.836	B	0.30029	0.11	T	0.27739	-1.0065	9	0.08837	T	0.75	.	7.8334	0.29355	0.1729:0.4917:0.3354:0.0	.	1482	Q5H9U9	DDX6L_HUMAN	S	1482	ENSP00000260184:A1482S;ENSP00000422423:A1482S	ENSP00000260184:A1482S	A	-	1	0	DDX60L	169536121	1.000000	0.71417	0.723000	0.30687	0.533000	0.34776	2.708000	0.47152	0.025000	0.15241	0.313000	0.20887	GCA	.	.		0.289	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967		A	169299546	C	A	169299546	3	1	344	1	0	0	0	0	1	0	0	0	4381	797	28	3	700	3	DDX60L	4	169299546	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	6344764	169299546	21854730	411	47774										
GALNTL6	442117	hgsc.bcm.edu	37	chr4	173730577	173730577	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aagtgaggattgttcgcaccAagaaaagagaaggactcatc	11	7	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:173730577A>G	ENST00000506823.1	+	6	1276	c.619A>G	c.(619-621)Aag>Gag	p.K207E	GALNTL6_ENST00000508122.1_Missense_Mutation_p.K190E	NM_001034845.2	NP_001030017.2	Q49A17	GLTL6_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 6	207	Catalytic subdomain A.				protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(2)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	45						TGTTCGCACCAAGAAAAGAGA	0.483																																					p.K207E		Atlas-SNP	.											.	GALNTL6	102	.	0			c.A619G						.						102	95	98					4																	173730577		2203	4300	6503	SO:0001583	missense	442117	exon6			CGCACCAAGAAAA		CCDS34104.1	4q34.1	2014-03-13	2014-03-13		ENSG00000174473	ENSG00000174473		"Glycosyltransferase family 2 domain containing"	33844	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase-like 6"	615138	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 6"				Standard	NM_001034845		Approved	GALNT17, GalNAc-T6L	uc003isv.3	Q49A17	OTTHUMG00000160807	ENST00000506823.1:c.619A>G	chr4.hg19:g.173730577A>G	ENSP00000423313:p.Lys207Glu	104.0	0.0		85.0	27.0	NM_001034845	Q2L4S6	Missense_Mutation	SNP	ENST00000506823.1	hg19	CCDS34104.1	.	.	.	.	.	.	.	.	.	.	A	12.68	2.010985	0.35511	.	.	ENSG00000174473	ENST00000506823;ENST00000404275;ENST00000508122	T;T	0.57436	0.4;0.4	5.45	5.45	0.79879	Glycosyl transferase, family 2 (1);	0.000000	0.64402	D	0.000006	T	0.46229	0.1382	N	0.21617	0.685	0.51482	D	0.999926	P	0.42203	0.773	P	0.48063	0.565	T	0.29181	-1.0020	10	0.11182	T	0.66	.	15.7979	0.78424	1.0:0.0:0.0:0.0	.	207	Q49A17	GLTL6_HUMAN	E	207;207;190	ENSP00000423313:K207E;ENSP00000423827:K190E	ENSP00000385382:K207E	K	+	1	0	GALNTL6	173967152	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	7.277000	0.78572	2.196000	0.70406	0.402000	0.26972	AAG	.	.		0.483	GALNTL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362395.1	NM_001034845		G	173730577	A	G	173730577	3	3	344	1	0	0	0	0	1	0	0	0	6233	131	5	2	637	2	GALNTL6	4	173730577	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	4431031	173730577	17423699	412	47775										
ADAM29	11086	hgsc.bcm.edu	37	chr4	175897487	175897487	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aatctgtgcacctgtattgcAagtggaagtcggagaacatt	11	7	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:175897487A>C	ENST00000359240.3	+	5	1481	c.811A>C	c.(811-813)Aag>Cag	p.K271Q	ADAM29_ENST00000404450.4_Missense_Mutation_p.K271Q|RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000445694.1_Missense_Mutation_p.K271Q|ADAM29_ENST00000514159.1_Missense_Mutation_p.K271Q	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	271	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		CCTGTATTGCAAGTGGAAGTC	0.413																																					p.K271Q	Ovarian(140;1727 1835 21805 25838 41440)	Atlas-SNP	.											.	ADAM29	262	.	0			c.A811C						.						142	137	139					4																	175897487		2203	4300	6503	SO:0001583	missense	11086	exon4			TATTGCAAGTGGA	AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"ADAM metallopeptidase domain containing"	207	protein-coding gene	gene with protein product	"cancer/testis antigen 73"	604778	"a disintegrin and metalloproteinase domain 29"			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.811A>C	chr4.hg19:g.175897487A>C	ENSP00000352177:p.Lys271Gln	152.0	0.0		117.0	50.0	NM_001130703	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Missense_Mutation	SNP	ENST00000359240.3	hg19	CCDS3823.1	.	.	.	.	.	.	.	.	.	.	A	2.135	-0.398284	0.04865	.	.	ENSG00000168594	ENST00000359240;ENST00000445694;ENST00000404450;ENST00000514159	T;T;T;T	0.64085	-0.08;-0.08;-0.08;-0.08	4.13	-8.26	0.01021	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	4.871630	0.00822	U	0.001585	T	0.40670	0.1126	N	0.22421	0.69	0.09310	N	1	B	0.28178	0.202	B	0.27076	0.076	T	0.29518	-1.0009	9	.	.	.	.	4.2237	0.10570	0.1769:0.5099:0.2006:0.1126	.	271	Q9UKF5	ADA29_HUMAN	Q	271	ENSP00000352177:K271Q;ENSP00000414544:K271Q;ENSP00000384229:K271Q;ENSP00000423517:K271Q	.	K	+	1	0	ADAM29	176134062	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-6.754000	0.00054	-2.673000	0.00413	-1.153000	0.01818	AAG	.	.		0.413	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding				C	175897487	A	C	175897487	3	2	344	1	0	0	0	0	1	0	0	0	247	131	5	5	813	5	ADAM29	4	175897487	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2166910	175897487	15256789	413	47776										
ADAM29	11086	hgsc.bcm.edu	37	chr4	175897603	175897603	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tttagaggaatgtgtacaccAcaccgtagttgtgcaattgt	10	7	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:175897603A>T	ENST00000359240.3	+	5	1597	c.927A>T	c.(925-927)ccA>ccT	p.P309P	ADAM29_ENST00000404450.4_Silent_p.P309P|RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000445694.1_Silent_p.P309P|ADAM29_ENST00000514159.1_Silent_p.P309P	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	309	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		TGTGTACACCACACCGTAGTT	0.423																																					p.P309P	Ovarian(140;1727 1835 21805 25838 41440)	Atlas-SNP	.											.	ADAM29	262	.	0			c.A927T						.						155	152	153					4																	175897603		2203	4300	6503	SO:0001819	synonymous_variant	11086	exon4			TACACCACACCGT	AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"ADAM metallopeptidase domain containing"	207	protein-coding gene	gene with protein product	"cancer/testis antigen 73"	604778	"a disintegrin and metalloproteinase domain 29"			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.927A>T	chr4.hg19:g.175897603A>T		243.0	0.0		155.0	56.0	NM_001130703	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Silent	SNP	ENST00000359240.3	hg19	CCDS3823.1																																																																																			.	.		0.423	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding				T	175897603	A	T	175897603	2	4	344	1	0	0	0	0	0	0	0	1	247	146	6	4		4	ADAM29	4	175897603	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	116	175897603	15256673	414	47777										
ADAM29	11086	hgsc.bcm.edu	37	chr4	175899050	175899050	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agagtcatcctcagttgacgCcttcccagagtcaacctcct	7	15	3	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:175899050C>A	ENST00000359240.3	+	5	3044	c.2374C>A	c.(2374-2376)Cct>Act	p.P792T	ADAM29_ENST00000404450.4_Missense_Mutation_p.P792T|RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000445694.1_Missense_Mutation_p.P792T|ADAM29_ENST00000514159.1_Missense_Mutation_p.P792T	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	792	9 X 9 AA approximate repeats.				spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		TCAGTTGACGCCTTCCCAGAG	0.572																																					p.P792T	Ovarian(140;1727 1835 21805 25838 41440)	Atlas-SNP	.											.	ADAM29	262	.	0			c.C2374A						.						162	151	155					4																	175899050		2203	4300	6503	SO:0001583	missense	11086	exon4			TTGACGCCTTCCC	AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"ADAM metallopeptidase domain containing"	207	protein-coding gene	gene with protein product	"cancer/testis antigen 73"	604778	"a disintegrin and metalloproteinase domain 29"			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.2374C>A	chr4.hg19:g.175899050C>A	ENSP00000352177:p.Pro792Thr	174.0	0.0		108.0	28.0	NM_001130703	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Missense_Mutation	SNP	ENST00000359240.3	hg19	CCDS3823.1	.	.	.	.	.	.	.	.	.	.	C	5.659	0.306247	0.10733	.	.	ENSG00000168594	ENST00000359240;ENST00000445694;ENST00000404450;ENST00000514159	T;T;T;T	0.01963	4.53;4.53;4.53;4.53	0.727	0.727	0.18254	.	.	.	.	.	T	0.01061	0.0035	N	0.08118	0	0.09310	N	1	P	0.41232	0.743	B	0.28991	0.097	T	0.52170	-0.8611	8	.	.	.	.	7.2316	0.26046	0.0:0.9999:0.0:1.0E-4	.	792	Q9UKF5	ADA29_HUMAN	T	792	ENSP00000352177:P792T;ENSP00000414544:P792T;ENSP00000384229:P792T;ENSP00000423517:P792T	.	P	+	1	0	ADAM29	176135625	0.000000	0.05858	0.003000	0.11579	0.027000	0.11550	-0.138000	0.10374	0.675000	0.31264	0.297000	0.19635	CCT	.	.		0.572	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding				A	175899050	C	A	175899050	3	1	344	1	0	0	0	0	1	0	0	0	247	739	26	3	2376	3	ADAM29	4	175899050	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1447	175899050	15255226	415	47778										
WDR17	116966	hgsc.bcm.edu	37	chr4	177098697	177098697	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcaactttattaaagagactAaaagaagagtcactgaaagg	9	5	1	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:177098697A>G	ENST00000280190.4	+	30	3897	c.3741A>G	c.(3739-3741)ctA>ctG	p.L1247L	WDR17_ENST00000507824.2_Silent_p.L1222L|WDR17_ENST00000393643.2_Silent_p.L1223L|WDR17_ENST00000508596.1_Silent_p.L1208L			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	1247										breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(18)|lung(46)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	92		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)		TAAAGAGACTAAAAGAAGAGT	0.328																																					p.L1247L		Atlas-SNP	.											.	WDR17	198	.	0			c.A3741G						.						75	84	81					4																	177098697		2203	4298	6501	SO:0001819	synonymous_variant	116966	exon30			GAGACTAAAAGAA	AF492460	CCDS3825.1, CCDS43284.1, CCDS43284.2	4q34	2013-01-09			ENSG00000150627	ENSG00000150627		"WD repeat domain containing"	16661	protein-coding gene	gene with protein product		609005				12401215	Standard	NM_170710		Approved		uc003iuj.3	Q8IZU2	OTTHUMG00000160791	ENST00000280190.4:c.3741A>G	chr4.hg19:g.177098697A>G		120.0	0.0		96.0	50.0	NM_170710	E7EQX0|Q0QD35	Silent	SNP	ENST00000280190.4	hg19	CCDS3825.1	.	.	.	.	.	.	.	.	.	.	A	3.985	-0.005668	0.07773	.	.	ENSG00000150627	ENST00000443118	.	.	.	6.16	-2.58	0.06228	.	.	.	.	.	T	0.20129	0.0484	.	.	.	0.26957	N	0.965901	.	.	.	.	.	.	T	0.28459	-1.0043	4	.	.	.	-5.3448	2.7201	0.05198	0.4538:0.1901:0.2631:0.0931	.	.	.	.	E	482	.	.	K	+	1	0	WDR17	177335691	0.911000	0.30947	0.070000	0.20053	0.613000	0.37349	-0.008000	0.12788	-0.319000	0.08652	0.528000	0.53228	AAA	.	.		0.328	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2			G	177098697	A	G	177098697	2	3	344	1	0	0	0	0	0	0	0	1	17292	349	13	2		2	WDR17	4	177098697	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1199647	177098697	14055579	416	47779										
VEGFC	7424	hgsc.bcm.edu	37	chr4	177608644	177608644	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	catccagctccttgtttggtCcacagatgtcatggaatcca	8	12	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:177608644C>T	ENST00000280193.2	-	6	1257	c.842G>A	c.(841-843)gGa>gAa	p.G281E	VEGFC_ENST00000507638.1_5'Flank|RP11-313E19.2_ENST00000504017.1_RNA|RP11-313E19.2_ENST00000509194.1_RNA	NM_005429.2	NP_005420	P49767	VEGFC_HUMAN	vascular endothelial growth factor C	281	4 X 16 AA repeats of C-X(10)-C-X-C- X(1,3)-C.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|induction of positive chemotaxis (GO:0050930)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of lymphangiogenesis (GO:1901492)|positive regulation of mast cell chemotaxis (GO:0060754)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein secretion (GO:0050714)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)|response to drug (GO:0042493)|signal transduction (GO:0007165)|substrate-dependent cell migration (GO:0006929)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	chemoattractant activity (GO:0042056)	p.G281E(1)		biliary_tract(1)|cervix(1)|large_intestine(6)|lung(28)|pancreas(1)|prostate(2)|skin(2)	41		Breast(14;0.000223)|Renal(120;0.00988)|Prostate(90;0.00996)|Melanoma(52;0.0101)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;1.59e-18)|Epithelial(43;3.68e-16)|OV - Ovarian serous cystadenocarcinoma(60;8.52e-09)|GBM - Glioblastoma multiforme(59;0.000546)|STAD - Stomach adenocarcinoma(60;0.00308)|Colorectal(24;0.025)|COAD - Colon adenocarcinoma(29;0.0359)|LUSC - Lung squamous cell carcinoma(193;0.0397)		CTTGTTTGGTCCACAGATGTC	0.473																																					p.G281E		Atlas-SNP	.											VEGFC,NS,carcinoma,0,1	VEGFC	94	.	1	Substitution - Missense(1)	lung(1)	c.G842A						.						43	38	40					4																	177608644		1927	4136	6063	SO:0001583	missense	7424	exon6			TTTGGTCCACAGA	BC035212	CCDS43285.1	4q34.3	2013-02-18				ENSG00000150630			12682	protein-coding gene	gene with protein product	"vascular endothelial growth factor-related protein"	601528				8617204	Standard	NM_005429		Approved	VRP	uc003ius.1	P49767		ENST00000280193.2:c.842G>A	chr4.hg19:g.177608644C>T	ENSP00000280193:p.Gly281Glu	39.0	0.0		45.0	17.0	NM_005429	B2R9Q8	Missense_Mutation	SNP	ENST00000280193.2	hg19	CCDS43285.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.482970	0.84747	.	.	ENSG00000150630	ENST00000280193	.	.	.	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	D	0.82770	0.5109	M	0.74258	2.255	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.83318	-0.0019	9	0.62326	D	0.03	-18.4237	19.9099	0.97023	0.0:1.0:0.0:0.0	.	281	P49767	VEGFC_HUMAN	E	281	.	ENSP00000280193:G281E	G	-	2	0	VEGFC	177845638	1.000000	0.71417	0.996000	0.52242	0.690000	0.40134	7.201000	0.77847	2.691000	0.91804	0.650000	0.86243	GGA	.	.		0.473	VEGFC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361991.1	NM_005429		T	177608644	C	T	177608644	3	4	344	1	0	0	0	0	1	0	0	0	17167	855	30	3	428	3	VEGFC	4	177608644	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	509947	177608644	13545632	417	47780										
ODZ3	55714	hgsc.bcm.edu	37	chr4	183549876	183549876	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	accccaggatacacaatggcAtctggctctgtttattcacc	7	13	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:183549876A>T	ENST00000511685.1	+	5	945	c.822A>T	c.(820-822)gcA>gcT	p.A274A	TENM3_ENST00000406950.2_Silent_p.A274A|RN7SKP67_ENST00000515905.1_RNA			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	274	Teneurin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00694}.				camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										ACACAATGGCATCTGGCTCTG	0.423																																					p.A274A		Atlas-SNP	.											.	.	.	.	0			c.A822T						.						60	58	58					4																	183549876		1982	4173	6155	SO:0001819	synonymous_variant	55714	exon4			AATGGCATCTGGC	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.822A>T	chr4.hg19:g.183549876A>T		268.0	0.0		102.0	73.0	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Silent	SNP	ENST00000511685.1	hg19	CCDS47165.1																																																																																			.	.		0.423	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			T	183549876	A	T	183549876	2	4	344	1	0	0	0	0	0	0	0	1	10845	204	8	4		4	ODZ3	4	183549876	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	5941232	183549876	7604400	418	47781										
FAT1	2195	hgsc.bcm.edu	37	chr4	187538294	187538294	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tccctgtctagaggtttcttCacatataccttccattcatt	4	12	4	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:187538294C>T	ENST00000441802.2	-	11	9149	c.8940G>A	c.(8938-8940)gtG>gtA	p.V2980V		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2980	Cadherin 27. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						GAGGTTTCTTCACATATACCT	0.378										HNSCC(5;0.00058)																											p.V2980V	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.G8940A						.						174	158	163					4																	187538294		1864	4095	5959	SO:0001819	synonymous_variant	2195	exon11			TTTCTTCACATAT	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.8940G>A	chr4.hg19:g.187538294C>T		126.0	0.0		47.0	36.0	NM_005245		Silent	SNP	ENST00000441802.2	hg19	CCDS47177.1																																																																																			.	.		0.378	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		T	187538294	C	T	187538294	2	4	344	1	0	0	0	0	0	0	0	1	5697	813	29	3		3	FAT1	4	187538294	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	3988418	187538294	3615982	419	47782										
FAT1	2195	hgsc.bcm.edu	37	chr4	187539226	187539226	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ataacttggccgttggttccTgagtcagcatcagatgccct	10	11	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr4:187539226T>A	ENST00000441802.2	-	10	8723	c.8514A>T	c.(8512-8514)tcA>tcT	p.S2838S		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2838	Cadherin 26. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						CGTTGGTTCCTGAGTCAGCAT	0.448										HNSCC(5;0.00058)																											p.S2838S	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.A8514T						.						112	105	107					4																	187539226		1946	4163	6109	SO:0001819	synonymous_variant	2195	exon10			GGTTCCTGAGTCA	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.8514A>T	chr4.hg19:g.187539226T>A		83.0	0.0		48.0	29.0	NM_005245		Silent	SNP	ENST00000441802.2	hg19	CCDS47177.1																																																																																			.	.		0.448	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		A	187539226	T	A	187539226	2	1	344	1	0	0	0	0	0	0	0	1	5697	1567	55	4		4	FAT1	4	187539226	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	932	187539226	3615050	420	47783										
PLEKHG4B	153478	hgsc.bcm.edu	37	chr5	163383	163383	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gttcctctgagcccacccagAccctggccagccgccccagg	10	20	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:163383A>T	ENST00000283426.6	+	11	2178	c.2128A>T	c.(2128-2130)Acc>Tcc	p.T710S		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	710							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		GCCCACCCAGACCCTGGCCAG	0.622																																					p.T710S		Atlas-SNP	.											.	PLEKHG4B	167	.	0			c.A2128T						.						33	43	40					5																	163383		2201	4300	6501	SO:0001583	missense	153478	exon11			ACCCAGACCCTGG	BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"Pleckstrin homology (PH) domain containing"	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.2128A>T	chr5.hg19:g.163383A>T	ENSP00000283426:p.Thr710Ser	99.0	0.0		41.0	32.0	NM_052909		Missense_Mutation	SNP	ENST00000283426.6	hg19	CCDS34124.1	.	.	.	.	.	.	.	.	.	.	A	5.999	0.368232	0.11352	.	.	ENSG00000153404	ENST00000283426	T	0.26660	1.72	3.0	-1.34	0.09143	.	.	.	.	.	T	0.12433	0.0302	L	0.27053	0.805	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.34378	-0.9831	9	0.16420	T	0.52	.	2.4186	0.04442	0.3393:0.0:0.3855:0.2752	.	710	Q96PX9	PKH4B_HUMAN	S	710	ENSP00000283426:T710S	ENSP00000283426:T710S	T	+	1	0	PLEKHG4B	216383	0.001000	0.12720	0.008000	0.14137	0.397000	0.30659	-0.196000	0.09532	0.116000	0.18110	0.377000	0.23210	ACC	.	.		0.622	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909		T	163383	A	T	163383	3	4	344	1	0	0	0	0	1	0	0	0	12081	275	10	4	2170	4	PLEKHG4B	5	163383	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10		163383	180751877	421	47784										
BRD9	65980	hgsc.bcm.edu	37	chr5	878542	878542	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccatctcgtccgacttcaagTcgccaaatactgaattattc	5	13	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:878542T>A	ENST00000467963.1	-	11	1365	c.1199A>T	c.(1198-1200)gAc>gTc	p.D400V	BRD9_ENST00000323510.4_Missense_Mutation_p.D304V|BRD9_ENST00000435709.2_3'UTR|BRD9_ENST00000494422.1_5'UTR|BRD9_ENST00000388890.4_Missense_Mutation_p.D284V|BRD9_ENST00000483173.1_Missense_Mutation_p.D347V	NM_023924.4	NP_076413.3	Q9H8M2	BRD9_HUMAN	bromodomain containing 9	400					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		lysine-acetylated histone binding (GO:0070577)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(3)	29			Epithelial(17;0.00202)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00815)|Lung(60;0.185)			CGACTTCAAGTCGCCAAATAC	0.562																																					p.D400V		Atlas-SNP	.											.	BRD9	113	.	0			c.A1199T						.						123	103	110					5																	878542		2203	4300	6503	SO:0001583	missense	65980	exon11			TTCAAGTCGCCAA	AK023503	CCDS34127.1, CCDS34128.1, CCDS34127.2, CCDS34128.2	5p15.33	2008-02-05			ENSG00000028310	ENSG00000028310			25818	protein-coding gene	gene with protein product						12477932	Standard	NM_023924		Approved	FLJ13441	uc003jbq.3	Q9H8M2	OTTHUMG00000159258	ENST00000467963.1:c.1199A>T	chr5.hg19:g.878542T>A	ENSP00000419765:p.Asp400Val	72.0	0.0		59.0	13.0	NM_023924	A6NFY8|B4DMQ2|B4DR93|Q2XUS1|Q6UWU9|Q8IUS4|Q9H5Q5|Q9H7R9	Missense_Mutation	SNP	ENST00000467963.1	hg19	CCDS34127.2	.	.	.	.	.	.	.	.	.	.	t	19.03	3.747932	0.69533	.	.	ENSG00000028310	ENST00000323510;ENST00000388890;ENST00000323547;ENST00000483173;ENST00000467963	T;T;T;T	0.46063	0.88;0.88;0.88;0.88	5.42	5.42	0.78866	.	0.087730	0.85682	D	0.000000	T	0.54775	0.1879	M	0.68317	2.08	0.80722	D	1	D;P;P;P;P	0.52996	0.957;0.917;0.498;0.898;0.754	P;P;B;B;B	0.52646	0.705;0.684;0.199;0.426;0.297	T	0.60535	-0.7244	10	0.87932	D	0	.	15.1213	0.72443	0.0:0.0:0.0:1.0	.	347;400;78;304;284	B4DMQ2;Q9H8M2;Q8NDF4;Q9H8M2-1;Q9H8M2-3	.;BRD9_HUMAN;.;.;.	V	304;284;78;347;400	ENSP00000323557:D304V;ENSP00000373542:D284V;ENSP00000419845:D347V;ENSP00000419765:D400V	ENSP00000323557:D304V	D	-	2	0	BRD9	931542	1.000000	0.71417	0.114000	0.21550	0.427000	0.31564	6.563000	0.73964	2.052000	0.61016	0.533000	0.62120	GAC	.	.		0.562	BRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354113.1	NM_023924		A	878542	T	A	878542	3	1	344	1	0	0	0	0	1	0	0	0	1509	1667	58	4	618	4	BRD9	5	878542	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	715159	878542	180036718	422	47785										
TRIP13	9319	hgsc.bcm.edu	37	chr5	901481	901481	+	Nonsense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cgattatgtgatgacaacttTactgttttcagacaagaacg	8	7	1	4	rs375761713		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:901481T>G	ENST00000166345.3	+	5	826	c.470T>G	c.(469-471)tTa>tGa	p.L157*		NM_004237.3	NP_004228.1	Q15645	PCH2_HUMAN	thyroid hormone receptor interactor 13	157					double-strand break repair (GO:0006302)|female meiosis I (GO:0007144)|male meiosis I (GO:0007141)|oocyte maturation (GO:0001556)|oogenesis (GO:0048477)|reciprocal meiotic recombination (GO:0007131)|regulation of RNA biosynthetic process (GO:2001141)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)|transcription from RNA polymerase II promoter (GO:0006366)	male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)	ATP binding (GO:0005524)|transcription cofactor activity (GO:0003712)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	18			Epithelial(17;0.00147)|OV - Ovarian serous cystadenocarcinoma(19;0.00271)|all cancers(22;0.00622)|Lung(60;0.165)			ATGACAACTTTACTGTTTTCA	0.448																																					p.L157X		Atlas-SNP	.											.	TRIP13	41	.	0			c.T470G						.						116	110	112					5																	901481		2203	4300	6503	SO:0001587	stop_gained	9319	exon5			CAACTTTACTGTT	L40384	CCDS3858.1	5p15	2010-04-21			ENSG00000071539	ENSG00000071539		"ATPases / AAA-type"	12307	protein-coding gene	gene with protein product	"thyroid receptor interacting protein 13"	604507				7776974	Standard	NM_004237		Approved	16E1BP	uc003jbr.3	Q15645	OTTHUMG00000090349	ENST00000166345.3:c.470T>G	chr5.hg19:g.901481T>G	ENSP00000166345:p.Leu157*	129.0	0.0		77.0	33.0	NM_004237	C9K0T3|D3DTC0|O15324	Nonsense_Mutation	SNP	ENST00000166345.3	hg19	CCDS3858.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	35|35	5.484721|5.484721	0.96323|0.96323	.|.	.|.	ENSG00000071539|ENSG00000071539	ENST00000166345;ENST00000354240|ENST00000513435	.|.	.|.	.|.	5.68|5.68	4.51|4.51	0.55191|0.55191	.|.	0.186175|.	0.44902|.	D|.	0.000416|.	.|T	.|0.60945	.|0.2308	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.68224	.|-0.5465	.|3	0.02654|.	T|.	1|.	-29.7093|-29.7093	11.439|11.439	0.50086|0.50086	0.0:0.0714:0.0:0.9286|0.0:0.0714:0.0:0.9286	.|.	.|.	.|.	.|.	X|D	157|153	.|.	ENSP00000166345:L157X|.	L|Y	+|+	2|1	0|0	TRIP13|TRIP13	954481|954481	0.966000|0.966000	0.33281|0.33281	0.026000|0.026000	0.17262|0.17262	0.049000|0.049000	0.14656|0.14656	7.405000|7.405000	0.80007|0.80007	0.973000|0.973000	0.38340|0.38340	0.402000|0.402000	0.26972|0.26972	TTA|TAC	.	.		0.448	TRIP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206721.2	NM_004237		G	901481	T	G	901481	4	3	344	1	0	0	0	0	0	1	0	0	16572	1764	61	5	488	5	TRIP13	5	901481	Nonsense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	22939	901481	180013779	423	47786										
SLC12A7	10723	hgsc.bcm.edu	37	chr5	1053467	1053467	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	actgcaagaaaggatacagtTctcgtctccctgccggtttt	9	11	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:1053467T>A	ENST00000264930.5	-	23	3200	c.3157A>T	c.(3157-3159)Aac>Tac	p.N1053Y		NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	1053					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	AGGATACAGTTCTCGTCTCCC	0.602																																					p.N1053Y		Atlas-SNP	.											.	SLC12A7	97	.	0			c.A3157T						.						165	125	139					5																	1053467		2203	4300	6503	SO:0001583	missense	10723	exon23			TACAGTTCTCGTC	AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504		"Solute carriers"	10915	protein-coding gene	gene with protein product		604879				10347194	Standard	NM_006598		Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.3157A>T	chr5.hg19:g.1053467T>A	ENSP00000264930:p.Asn1053Tyr	78.0	0.0		58.0	25.0	NM_006598	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Missense_Mutation	SNP	ENST00000264930.5	hg19	CCDS34129.1	.	.	.	.	.	.	.	.	.	.	T	15.05	2.719140	0.48728	.	.	ENSG00000113504	ENST00000264930	D	0.86694	-2.16	3.88	3.88	0.44766	.	0.174503	0.48286	N	0.000185	D	0.82628	0.5078	M	0.72118	2.19	0.58432	D	0.999999	B	0.28439	0.212	B	0.28553	0.091	T	0.75025	-0.3463	10	0.05833	T	0.94	.	10.9162	0.47137	0.0:0.0:0.0:1.0	.	1053	Q9Y666	S12A7_HUMAN	Y	1053	ENSP00000264930:N1053Y	ENSP00000264930:N1053Y	N	-	1	0	SLC12A7	1106467	1.000000	0.71417	1.000000	0.80357	0.360000	0.29518	6.733000	0.74796	1.535000	0.49220	0.402000	0.26972	AAC	.	.		0.602	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598		A	1053467	T	A	1053467	3	1	344	1	0	0	0	0	1	0	0	0	14403	1783	62	4	102	4	SLC12A7	5	1053467	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	151986	1053467	179861793	424	47787										
TERT	7015	hgsc.bcm.edu	37	chr5	1254534	1254534	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggtgacacggtgtcgagtcaGcttgagcaggaatgcttggt	16	7	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:1254534G>A	ENST00000310581.5	-	15	3301	c.3244C>T	c.(3244-3246)Ctg>Ttg	p.L1082L	TERT_ENST00000296820.5_3'UTR|TERT_ENST00000334602.6_Silent_p.L1019L	NM_001193376.1|NM_198253.2	NP_001180305.1|NP_937983.2	O14746	TERT_HUMAN	telomerase reverse transcriptase	1082	CTE.				DNA strand elongation (GO:0022616)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|replicative senescence (GO:0090399)|telomere formation via telomerase (GO:0032203)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|telomerase holoenzyme complex (GO:0005697)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|telomerase activity (GO:0003720)|telomeric DNA binding (GO:0042162)|telomeric RNA binding (GO:0070034)|telomeric template RNA reverse transcriptase activity (GO:0003721)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(3)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	41	all_cancers(3;3.17e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.87e-10)		Epithelial(17;0.00105)|all cancers(22;0.00178)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)		Zidovudine(DB00495)	TGTCGAGTCAGCTTGAGCAGG	0.677									TERT Mutation-Associated Haematological Disorders;Pulmonary Fibrosis, Idiopathic;Congenital Dyskeratosis																												p.L1082L		Atlas-SNP	.											.	TERT	2594	.	0			c.C3244T						.						52	63	59					5																	1254534		2140	4252	6392	SO:0001819	synonymous_variant	7015	exon15	Familial Cancer Database	;Hamman-Rich syndrome, Fibrocystic Pulmonary Dysplasia;Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita	GAGTCAGCTTGAG	AF015950	CCDS3861.2, CCDS54831.1	5p15.33	2014-09-17			ENSG00000164362	ENSG00000164362			11730	protein-coding gene	gene with protein product		187270				9252327	Standard	NM_198253		Approved	TRT, TP2, TCS1, hEST2, EST2	uc003jcb.1	O14746	OTTHUMG00000090357	ENST00000310581.5:c.3244C>T	chr5.hg19:g.1254534G>A		78.0	0.0		56.0	25.0	NM_198253	O14783|Q2XS35|Q8N6C3|Q8NG38|Q8NG46	Silent	SNP	ENST00000310581.5	hg19	CCDS3861.2																																																																																			.	.		0.677	TERT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206729.2			A	1254534	G	A	1254534	2	1	344	1	0	0	0	0	0	0	0	1	15779	962	34	3		3	TERT	5	1254534	Silent	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	201067	1254534	179660726	425	47788										
SLC6A3	6531	hgsc.bcm.edu	37	chr5	1414820	1414820	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gctcaccgtccttggccacgTccccgatgggcacactgtgc	11	17	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:1414820T>C	ENST00000270349.9	-	8	1269	c.1142A>G	c.(1141-1143)gAc>gGc	p.D381G	SLC6A3_ENST00000453492.2_Missense_Mutation_p.D381G	NM_001044.4	NP_001035.1	Q01959	SC6A3_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 3	381					adenohypophysis development (GO:0021984)|aging (GO:0007568)|cation transmembrane transport (GO:0098655)|cell death (GO:0008219)|dopamine biosynthetic process (GO:0042416)|dopamine catabolic process (GO:0042420)|dopamine transport (GO:0015872)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|neurotransmitter biosynthetic process (GO:0042136)|positive regulation of multicellular organism growth (GO:0040018)|prepulse inhibition (GO:0060134)|regulation of dopamine metabolic process (GO:0042053)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to iron ion (GO:0010039)|response to nicotine (GO:0035094)|sensory perception of smell (GO:0007608)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	axon (GO:0030424)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine transmembrane transporter activity (GO:0005329)|dopamine:sodium symporter activity (GO:0005330)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)			breast(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(19)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38			OV - Ovarian serous cystadenocarcinoma(19;0.00928)|all cancers(22;0.0262)		Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Benzatropine(DB00245)|Benzphetamine(DB00865)|Bupropion(DB01156)|Chloroprocaine(DB01161)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Cocaine(DB00907)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Diethylpropion(DB00937)|Diphenylpyraline(DB01146)|Dopamine(DB00988)|Duloxetine(DB00476)|Ephedra(DB01363)|Escitalopram(DB01175)|Fencamfamine(DB01463)|Imipramine(DB00458)|Ioflupane I 123(DB08824)|Lisdexamfetamine(DB01255)|Loxapine(DB00408)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Mirtazapine(DB00370)|Modafinil(DB00745)|Nefazodone(DB01149)|Pethidine(DB00454)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Procaine(DB00721)|Pseudoephedrine(DB00852)|Sertraline(DB01104)|Sibutramine(DB01105)|Trimipramine(DB00726)|Venlafaxine(DB00285)	CTTGGCCACGTCCCCGATGGG	0.607																																					p.D381G		Atlas-SNP	.											.	SLC6A3	102	.	0			c.A1142G						.						74	57	63					5																	1414820		2201	4300	6501	SO:0001583	missense	6531	exon8			GCCACGTCCCCGA		CCDS3863.1	5p15.3	2013-07-19	2013-07-19		ENSG00000142319	ENSG00000142319		"Solute carriers"	11049	protein-coding gene	gene with protein product	"dopamine transporter"	126455	"solute carrier family 6 (neurotransmitter transporter, dopamine), member 3", "dopamine transporter 1"	DAT1		1406597	Standard	NM_001044		Approved	DAT	uc003jck.3	Q01959	OTTHUMG00000131016	ENST00000270349.9:c.1142A>G	chr5.hg19:g.1414820T>C	ENSP00000270349:p.Asp381Gly	56.0	0.0		40.0	18.0	NM_001044	A2RUN4|Q14996	Missense_Mutation	SNP	ENST00000270349.9	hg19	CCDS3863.1	.	.	.	.	.	.	.	.	.	.	T	18.27	3.586507	0.66105	.	.	ENSG00000142319	ENST00000270349;ENST00000453492	T;T	0.75260	-0.92;-0.92	4.09	4.09	0.47781	.	0.112351	0.64402	D	0.000012	T	0.80182	0.4576	M	0.85099	2.735	0.45914	D	0.998759	P	0.41848	0.763	P	0.46389	0.515	T	0.82944	-0.0206	10	0.72032	D	0.01	.	11.0545	0.47909	0.0:0.0:0.0:1.0	.	381	Q01959	SC6A3_HUMAN	G	381	ENSP00000270349:D381G;ENSP00000399806:D381G	ENSP00000270349:D381G	D	-	2	0	SLC6A3	1467820	0.998000	0.40836	0.994000	0.49952	0.484000	0.33280	5.594000	0.67557	1.500000	0.48636	0.454000	0.30748	GAC	.	.		0.607	SLC6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253650.3	NM_001044		C	1414820	T	C	1414820	3	2	344	1	0	0	0	0	1	0	0	0	14700	1667	58	2	752	2	SLC6A3	5	1414820	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	160286	1414820	179500440	426	47789										
ADCY2	108	hgsc.bcm.edu	37	chr5	7817092	7817092	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aacgacttcaaattgcgagtGggtacgttctgcaaaagagg	12	7	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:7817092G>C	ENST00000338316.4	+	23	3086	c.2997G>C	c.(2995-2997)gtG>gtC	p.V999V	ADCY2_ENST00000537121.1_Splice_Site_p.V819V	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	999					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						AATTGCGAGTGGGTACGTTCT	0.463											OREG0016499	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V999V		Atlas-SNP	.											.	ADCY2	337	.	0			c.G2997C						.						181	134	150					5																	7817092		2203	4300	6503	SO:0001630	splice_region_variant	108	exon23			GCGAGTGGGTACG	AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"Adenylate cyclases"	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.2998+1G>C	chr5.hg19:g.7817092G>C		169.0	0.0	644	104.0	42.0	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Silent	SNP	ENST00000338316.4	hg19	CCDS3872.2																																																																																			.	.		0.463	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546	Silent	C	7817092	G	C	7817092	5	2	344	1	0	0	0	0	0	0	1	0	294	1362	47	4	3087	4	ADCY2	5	7817092	Splice_Site	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	6402272	7817092	173098168	427	47790										
MTRR	4552	hgsc.bcm.edu	37	chr5	7878172	7878172	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cactcccggtggcatcacctGcatcctcgaggacagacctt	9	16	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:7878172G>T	ENST00000264668.2	+	5	628	c.598G>T	c.(598-600)Gca>Tca	p.A200S	MTRR_ENST00000440940.2_Missense_Mutation_p.A173S|MTRR_ENST00000341013.6_3'UTR	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	200	Hinge.				cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|DNA methylation (GO:0006306)|folic acid metabolic process (GO:0046655)|methionine biosynthetic process (GO:0009086)|methionine metabolic process (GO:0006555)|methylation (GO:0032259)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	[methionine synthase] reductase activity (GO:0030586)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|oxidoreductase activity, oxidizing metal ions, NAD or NADP as acceptor (GO:0016723)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(14)|ovary(1)|prostate(3)|stomach(1)	31					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	GGCATCACCTGCATCCTCGAG	0.512																																					p.A200S		Atlas-SNP	.											.	MTRR	74	.	0			c.G598T						.						70	66	68					5																	7878172		2203	4300	6503	SO:0001583	missense	4552	exon5			TCACCTGCATCCT	AF025794	CCDS3874.1, CCDS47190.1	5p15.31	2011-05-12			ENSG00000124275	ENSG00000124275	1.16.1.8		7473	protein-coding gene	gene with protein product		602568				9501215	Standard	NM_024010		Approved	cblE	uc003jed.3	Q9UBK8	OTTHUMG00000090477	ENST00000264668.2:c.598G>T	chr5.hg19:g.7878172G>T	ENSP00000264668:p.Ala200Ser	71.0	0.0		38.0	20.0	NM_024010	O60471|Q32MA9|Q7Z4M8	Missense_Mutation	SNP	ENST00000264668.2	hg19	CCDS3874.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	6.070|6.070	0.381292|0.381292	0.11466|0.11466	.|.	.|.	ENSG00000124275|ENSG00000124275	ENST00000264668;ENST00000440940|ENST00000514220	T;T|.	0.02121|.	4.44;4.44|.	5.72|5.72	-0.218|-0.218	0.13142|0.13142	.|.	2.011070|.	0.01682|.	N|.	0.026218|.	T|T	0.39937|0.39937	0.1097|0.1097	L|L	0.57536|0.57536	1.79|1.79	0.09310|0.09310	N|N	1|1	B|.	0.17465|.	0.022|.	B|.	0.11329|.	0.006|.	T|T	0.34403|0.34403	-0.9830|-0.9830	10|5	0.16896|.	T|.	0.51|.	-1.0779|-1.0779	5.4962|5.4962	0.16804|0.16804	0.4218:0.0:0.4291:0.149|0.4218:0.0:0.4291:0.149	.|.	200|.	Q9UBK8|.	MTRR_HUMAN|.	S|F	200;173|101	ENSP00000264668:A200S;ENSP00000402510:A173S|.	ENSP00000264668:A200S|.	A|C	+|+	1|2	0|0	MTRR|MTRR	7931172|7931172	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	0.059000|0.059000	0.14322|0.14322	-0.108000|-0.108000	0.12066|0.12066	-0.150000|-0.150000	0.13652|0.13652	GCA|TGC	.	.		0.512	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1			T	7878172	G	T	7878172	3	4	344	1	0	0	0	0	1	0	0	0	9970	1319	46	3	616	3	MTRR	5	7878172	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	61080	7878172	173037088	428	47791										
CTNND2	1501	hgsc.bcm.edu	37	chr5	11098804	11098804	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	actattgatgggtgccacagCatctggatcccttttggtgg	12	9	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:11098804C>A	ENST00000304623.8	-	15	2709	c.2520G>T	c.(2518-2520)atG>atT	p.M840I	CTNND2_ENST00000359640.2_Intron|CTNND2_ENST00000495388.2_5'UTR|CTNND2_ENST00000511377.1_Missense_Mutation_p.M749I|CTNND2_ENST00000458100.2_Missense_Mutation_p.M407I|CTNND2_ENST00000503622.1_Missense_Mutation_p.M503I	NM_001332.2	NP_001323.1	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	840					cell adhesion (GO:0007155)|learning (GO:0007612)|morphogenesis of a branching structure (GO:0001763)|multicellular organismal development (GO:0007275)|regulation of synaptic plasticity (GO:0048167)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(29)|liver(1)|lung(71)|ovary(4)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	136						GGTGCCACAGCATCTGGATCC	0.517																																					p.M840I		Atlas-SNP	.											CTNND2,colon,carcinoma,0,1	CTNND2	289	.	0			c.G2520T						.						151	137	142					5																	11098804		2203	4300	6503	SO:0001583	missense	1501	exon15			CCACAGCATCTGG	U52828	CCDS3881.1, CCDS75227.1, CCDS75228.1	5p15.2	2013-02-14	2012-08-15		ENSG00000169862	ENSG00000169862		"Armadillo repeat containing"	2516	protein-coding gene	gene with protein product	"neural plakophilin-related arm-repeat protein"	604275	"catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)"			9342840, 9223106	Standard	XM_005248251		Approved	NPRAP, GT24	uc003jfa.1	Q9UQB3	OTTHUMG00000090511	ENST00000304623.8:c.2520G>T	chr5.hg19:g.11098804C>A	ENSP00000307134:p.Met840Ile	71.0	0.0		63.0	28.0	NM_001332	B0FTZ7|O00379|O15390|O43206|O43840|Q13589|Q9UM66|Q9UPM3	Missense_Mutation	SNP	ENST00000304623.8	hg19	CCDS3881.1	.	.	.	.	.	.	.	.	.	.	C	33	5.206011	0.95033	.	.	ENSG00000169862	ENST00000304623;ENST00000511377;ENST00000458100;ENST00000503622	T;T;T;T	0.79454	-1.27;-1.27;-1.27;-1.27	6.17	6.17	0.99709	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.79522	0.4460	N	0.14661	0.345	0.80722	D	1	D;D;D	0.53885	0.959;0.959;0.963	P;P;P	0.60117	0.755;0.675;0.869	T	0.81493	-0.0908	10	0.66056	D	0.02	-28.7566	20.8794	0.99867	0.0:1.0:0.0:0.0	.	503;407;840	B4DRK2;B4DG58;Q9UQB3	.;.;CTND2_HUMAN	I	840;749;407;503	ENSP00000307134:M840I;ENSP00000426510:M749I;ENSP00000391155:M407I;ENSP00000426887:M503I	ENSP00000307134:M840I	M	-	3	0	CTNND2	11151804	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.941000	0.99782	0.655000	0.94253	ATG	.	.		0.517	CTNND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206999.1	NM_001332		A	11098804	C	A	11098804	3	1	344	1	0	0	0	0	1	0	0	0	4022	710	25	3	1189	3	CTNND2	5	11098804	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	3220632	11098804	169816456	429	47792										
CTNND2	1501	hgsc.bcm.edu	37	chr5	11117662	11117662	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tccttctgcgggcctcctctCcggccgaactaacattcctg	8	17	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:11117662C>A	ENST00000304623.8	-	13	2366	c.2177G>T	c.(2176-2178)gGa>gTa	p.G726V	CTNND2_ENST00000359640.2_Missense_Mutation_p.G726V|CTNND2_ENST00000495388.2_5'UTR|CTNND2_ENST00000511377.1_Missense_Mutation_p.G635V|CTNND2_ENST00000458100.2_Missense_Mutation_p.G293V|CTNND2_ENST00000503622.1_Missense_Mutation_p.G389V	NM_001332.2	NP_001323.1	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	726					cell adhesion (GO:0007155)|learning (GO:0007612)|morphogenesis of a branching structure (GO:0001763)|multicellular organismal development (GO:0007275)|regulation of synaptic plasticity (GO:0048167)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(29)|liver(1)|lung(71)|ovary(4)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	136						GGCCTCCTCTCCGGCCGAACT	0.527																																					p.G726V		Atlas-SNP	.											CTNND2,NS,carcinoma,0,1	CTNND2	289	.	0			c.G2177T						.						156	122	134					5																	11117662		2203	4300	6503	SO:0001583	missense	1501	exon13			TCCTCTCCGGCCG	U52828	CCDS3881.1, CCDS75227.1, CCDS75228.1	5p15.2	2013-02-14	2012-08-15		ENSG00000169862	ENSG00000169862		"Armadillo repeat containing"	2516	protein-coding gene	gene with protein product	"neural plakophilin-related arm-repeat protein"	604275	"catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)"			9342840, 9223106	Standard	XM_005248251		Approved	NPRAP, GT24	uc003jfa.1	Q9UQB3	OTTHUMG00000090511	ENST00000304623.8:c.2177G>T	chr5.hg19:g.11117662C>A	ENSP00000307134:p.Gly726Val	122.0	0.0		78.0	29.0	NM_001332	B0FTZ7|O00379|O15390|O43206|O43840|Q13589|Q9UM66|Q9UPM3	Missense_Mutation	SNP	ENST00000304623.8	hg19	CCDS3881.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.350419	0.82132	.	.	ENSG00000169862	ENST00000304623;ENST00000359640;ENST00000511377;ENST00000458100;ENST00000503622	T;T;T;T;T	0.80994	-1.44;-1.44;-1.44;-1.44;-1.44	5.6	4.73	0.59995	Armadillo-like helical (1);Armadillo-type fold (1);	0.048548	0.85682	D	0.000000	D	0.89887	0.6845	M	0.83312	2.635	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.996	D	0.91319	0.5080	10	0.87932	D	0	-12.8857	14.3949	0.67003	0.0:0.9291:0.0:0.0709	.	389;293;726	B4DRK2;B4DG58;Q9UQB3	.;.;CTND2_HUMAN	V	726;726;635;293;389	ENSP00000307134:G726V;ENSP00000352661:G726V;ENSP00000426510:G635V;ENSP00000391155:G293V;ENSP00000426887:G389V	ENSP00000307134:G726V	G	-	2	0	CTNND2	11170662	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.376000	0.79658	1.370000	0.46153	0.650000	0.86243	GGA	.	.		0.527	CTNND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206999.1	NM_001332		A	11117662	C	A	11117662	3	1	344	1	0	0	0	0	1	0	0	0	4022	855	30	3	1540	3	CTNND2	5	11117662	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	18858	11117662	169797598	430	47793										
MYO10	4651	hgsc.bcm.edu	37	chr5	16711259	16711259	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aagtcctgaaagggtcttcgGaccgcatacccagctttgcg	11	12	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:16711259G>T	ENST00000513610.1	-	20	2479	c.2025C>A	c.(2023-2025)gtC>gtA	p.V675V	MYO10_ENST00000427430.2_Silent_p.V32V|MYO10_ENST00000515803.1_Silent_p.V14V|MYO10_ENST00000512061.1_Intron|MYO10_ENST00000274203.9_Silent_p.V32V|MYO10_ENST00000505695.1_Silent_p.V14V	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	675	Myosin motor.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						AGGGTCTTCGGACCGCATACC	0.502																																					p.V675V		Atlas-SNP	.											.	MYO10	198	.	0			c.C2025A						.						44	45	45					5																	16711259		1880	4128	6008	SO:0001819	synonymous_variant	4651	exon20			TCTTCGGACCGCA	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"Myosins / Myosin superfamily : Class X", "Pleckstrin homology (PH) domain containing"	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.2025C>A	chr5.hg19:g.16711259G>T		180.0	0.0		104.0	60.0	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Silent	SNP	ENST00000513610.1	hg19	CCDS54834.1																																																																																			.	.		0.502	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		T	16711259	G	T	16711259	2	4	344	1	0	0	0	0	0	0	0	1	10071	1161	41	3		3	MYO10	5	16711259	Silent	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	5593597	16711259	164204001	431	47794										
TTC23L	153657	hgsc.bcm.edu	37	chr5	34880306	34880306	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atgctgttgagatatatttcAtaagaagtatcaatgcatat	7	4	2	2	rs528367394	byFrequency	TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:34880306A>G	ENST00000505624.1	+	9	1073	c.970A>G	c.(970-972)Ata>Gta	p.I324V	TTC23L_ENST00000514080.1_3'UTR	NM_144725.3	NP_653326.3	Q6PF05	TT23L_HUMAN	tetratricopeptide repeat domain 23-like	324										breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(9)|prostate(2)|stomach(1)|urinary_tract(1)	22						GATATATTTCATAAGAAGTAT	0.358													A|||	5	0.000998403	0	0	5008	,	,		19114	0		0	False		,,,				2504	0.0051				p.I324V		Atlas-SNP	.											.	TTC23L	47	.	0			c.A970G						.						93	90	91					5																	34880306		1825	4093	5918	SO:0001583	missense	153657	exon9			TATTTCATAAGAA		CCDS54840.1	5p13.2	2008-07-14			ENSG00000205838	ENSG00000205838			26355	protein-coding gene	gene with protein product						12477932	Standard	NM_144725		Approved	FLJ25439	uc003jiu.3	Q6PF05	OTTHUMG00000162020	ENST00000505624.1:c.970A>G	chr5.hg19:g.34880306A>G	ENSP00000422188:p.Ile324Val	186.0	0.0		198.0	94.0	NM_144725	Q6RGS4|Q8N7R3|Q96LJ2	Missense_Mutation	SNP	ENST00000505624.1	hg19	CCDS54840.1	.	.	.	.	.	.	.	.	.	.	a	1.710	-0.499209	0.04291	.	.	ENSG00000205838	ENST00000505624;ENST00000535797	T	0.11495	2.77	4.6	4.6	0.57074	.	0.405060	0.21525	U	0.073154	T	0.12347	0.0300	L	0.57536	1.79	0.23950	N	0.996376	B	0.25809	0.135	B	0.24541	0.054	T	0.10474	-1.0628	10	0.40728	T	0.16	-19.3794	10.5549	0.45112	1.0:0.0:0.0:0.0	.	324	Q6PF05	TT23L_HUMAN	V	324	ENSP00000422188:I324V	ENSP00000422188:I324V	I	+	1	0	TTC23L	34916063	0.999000	0.42202	1.000000	0.80357	0.380000	0.30137	0.626000	0.24492	2.058000	0.61347	0.473000	0.43528	ATA	.	.		0.358	TTC23L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366819.1	NM_144725		G	34880306	A	G	34880306	3	3	344	1	0	0	0	0	1	0	0	0	16706	217	8	2	1000	2	TTC23L	5	34880306	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	18169047	34880306	146034954	432	47795										
SPEF2	79925	hgsc.bcm.edu	37	chr5	35709050	35709050	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttcttatcatccttttgaagTtgagaagaaattagaagaaa	7	4	2	5			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:35709050T>A	ENST00000356031.3	+	19	2820	c.2666T>A	c.(2665-2667)gTt>gAt	p.V889D	SPEF2_ENST00000440995.2_Splice_Site_p.V884D|CTD-2113L7.1_ENST00000510433.1_RNA|SPEF2_ENST00000509059.1_Splice_Site_p.V884D	NM_024867.3	NP_079143.3	Q9C093	SPEF2_HUMAN	sperm flagellar 2	889					axoneme assembly (GO:0035082)|brain morphogenesis (GO:0048854)|embryonic neurocranium morphogenesis (GO:0048702)|fertilization (GO:0009566)|immune system development (GO:0002520)|multicellular organismal aging (GO:0010259)|respiratory system development (GO:0060541)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)|manchette (GO:0002177)|sperm midpiece (GO:0097225)				breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	37	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			CCTTTTGAAGTTGAGAAGAAA	0.378																																					p.V889D		Atlas-SNP	.											.	SPEF2	324	.	0			c.T2666A						.						43	43	43					5																	35709050		1828	4085	5913	SO:0001630	splice_region_variant	79925	exon19			TTGAAGTTGAGAA	AB051557	CCDS3910.1, CCDS43309.1	5p13.2	2010-05-04			ENSG00000152582	ENSG00000152582			26293	protein-coding gene	gene with protein product	"cancer/testis antigen 122"	610172				11214970, 16549801, 17610085	Standard	NM_024867		Approved	KPL2, FLJ23577, CT122	uc003jjo.3	Q9C093	OTTHUMG00000131111	ENST00000356031.3:c.2666-1T>A	chr5.hg19:g.35709050T>A		243.0	0.0		218.0	81.0	NM_024867	Q2TAC9|Q96LL6|Q9H5C7|Q9H5Q7	Missense_Mutation	SNP	ENST00000356031.3	hg19	CCDS43309.1	.	.	.	.	.	.	.	.	.	.	T	16.70	3.197062	0.58126	.	.	ENSG00000152582	ENST00000356031;ENST00000509059;ENST00000440995	T;T;T	0.08102	3.29;3.13;3.36	5.82	3.3	0.37823	.	0.516703	0.19831	N	0.105096	T	0.15349	0.0370	M	0.69823	2.125	0.80722	D	1	D;P;P	0.54964	0.969;0.899;0.736	P;P;B	0.53490	0.727;0.474;0.282	T	0.00880	-1.1529	9	.	.	.	.	4.4272	0.11509	0.0:0.1033:0.2037:0.693	.	884;884;889	D6REZ4;Q9C093-2;Q9C093	.;.;SPEF2_HUMAN	D	889;884;884	ENSP00000348314:V889D;ENSP00000421593:V884D;ENSP00000412125:V884D	.	V	+	2	0	SPEF2	35744807	1.000000	0.71417	0.958000	0.39756	0.857000	0.48899	1.379000	0.34340	2.222000	0.72286	0.528000	0.53228	GTT	.	.		0.378	SPEF2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367199.1	NM_144722	Missense_Mutation	A	35709050	T	A	35709050	5	1	344	1	0	0	0	0	0	0	1	0	15050	1739	60	4	2761	4	SPEF2	5	35709050	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	828744	35709050	145206210	433	47796										
C6	729	hgsc.bcm.edu	37	chr5	41143008	41143008	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cccacttcacagatgttcaaTgttttctcacttgttgatga	6	10	3	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:41143008T>A	ENST00000263413.3	-	18	2988	c.2724A>T	c.(2722-2724)acA>acT	p.T908T	C6_ENST00000337836.5_Silent_p.T908T	NM_001115131.1	NP_001108603.2	P13671	CO6_HUMAN	complement component 6	908	C5b-binding domain.|Factor I module (FIM) 2.|Kazal-like 2. {ECO:0000255|PROSITE- ProRule:PRU00798}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)				central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(7)|large_intestine(16)|liver(1)|lung(51)|ovary(3)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)	96		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)				AGATGTTCAATGTTTTCTCAC	0.453																																					p.T908T		Atlas-SNP	.											.	C6	197	.	0			c.A2724T						.						244	202	216					5																	41143008		2203	4300	6503	SO:0001819	synonymous_variant	729	exon18			GTTCAATGTTTTC	J05024	CCDS3936.1	5p13.1	2014-09-17			ENSG00000039537	ENSG00000039537		"Complement system"	1339	protein-coding gene	gene with protein product		217050					Standard	NM_001115131		Approved		uc003jmk.3	P13671	OTTHUMG00000094781	ENST00000263413.3:c.2724A>T	chr5.hg19:g.41143008T>A		89.0	0.0		82.0	34.0	NM_001115131		Silent	SNP	ENST00000263413.3	hg19	CCDS3936.1																																																																																			.	.		0.453	C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211592.1			A	41143008	T	A	41143008	2	1	344	1	0	0	0	0	0	0	0	1	2317	1451	51	4		4	C6	5	41143008	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	5433958	41143008	139772252	434	47797										
ITGA2	3673	hgsc.bcm.edu	37	chr5	52369005	52369005	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttaacattttcagtaacgctGaaaaataaaagggaaagtgc	8	5	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:52369005G>A	ENST00000296585.5	+	20	2630	c.2487G>A	c.(2485-2487)ctG>ctA	p.L829L		NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	829					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular response to hormone stimulus (GO:0032870)|collagen-activated signaling pathway (GO:0038065)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|hepatocyte differentiation (GO:0070365)|hypotonic response (GO:0006971)|integrin-mediated signaling pathway (GO:0007229)|mammary gland development (GO:0030879)|mesodermal cell differentiation (GO:0048333)|organ morphogenesis (GO:0009887)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell projection organization (GO:0031346)|positive regulation of collagen binding (GO:0033343)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA binding (GO:0043388)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|response to amine (GO:0014075)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to muscle activity (GO:0014850)|response to organic cyclic compound (GO:0014070)|skin morphogenesis (GO:0043589)|substrate-dependent cell migration (GO:0006929)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	axon terminus (GO:0043679)|basal part of cell (GO:0045178)|cell outer membrane (GO:0009279)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin alpha2-beta1 complex (GO:0034666)|integrin complex (GO:0008305)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)			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)				CAGTAACGCTGAAAAATAAAA	0.368																																					p.L829L		Atlas-SNP	.											ITGA2_ENST00000296585,NS,carcinoma,0,2	ITGA2	211	.	0			c.G2487A						.						123	118	120					5																	52369005		2203	4300	6503	SO:0001819	synonymous_variant	3673	exon20			AACGCTGAAAAAT		CCDS3957.1	5q11.2	2010-03-23			ENSG00000164171	ENSG00000164171		"CD molecules", "Integrins"	6137	protein-coding gene	gene with protein product		192974		CD49B			Standard	NM_002203		Approved	CD49b	uc003joy.3	P17301	OTTHUMG00000131165	ENST00000296585.5:c.2487G>A	chr5.hg19:g.52369005G>A		80.0	2.0		79.0	31.0	NM_002203	Q14595	Silent	SNP	ENST00000296585.5	hg19	CCDS3957.1																																																																																			.	.		0.368	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203		A	52369005	G	A	52369005	2	1	344	1	0	0	0	0	0	0	0	1	7884	1277	45	3		3	ITGA2	5	52369005	Silent	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	11225997	52369005	128546255	435	47798										
PPAP2A	8611	hgsc.bcm.edu	37	chr5	54763943	54763943	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aggaatttgagtgcaaaaggTtacagtaaacagacagggtt	12	4	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:54763943T>A	ENST00000307259.8	-	3	665	c.245A>T	c.(244-246)aAc>aTc	p.N82I	PPAP2A_ENST00000515132.1_5'UTR|PPAP2A_ENST00000264775.5_Missense_Mutation_p.N83I	NM_003711.2	NP_003702.2	O14494	LPP1_HUMAN	phosphatidic acid phosphatase type 2A	82					androgen receptor signaling pathway (GO:0030521)|germ cell migration (GO:0008354)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|lipid metabolic process (GO:0006629)|negative regulation of cell proliferation (GO:0008285)|phospholipid dephosphorylation (GO:0046839)|protein dephosphorylation (GO:0006470)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of lipid metabolic process (GO:0019216)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidate phosphatase activity (GO:0008195)			breast(2)|endometrium(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)	9		Lung NSC(810;4.08e-05)|Prostate(74;0.0181)|Breast(144;0.0544)				GTGCAAAAGGTTACAGTAAAC	0.353																																					p.N83I		Atlas-SNP	.											.	PPAP2A	42	.	0			c.A248T						.						90	97	94					5																	54763943		2203	4300	6503	SO:0001583	missense	8611	exon3			AAAAGGTTACAGT	AB000888	CCDS34159.1, CCDS34160.1	5q11	2009-05-27			ENSG00000067113	ENSG00000067113	3.1.3.4		9228	protein-coding gene	gene with protein product		607124				9305923	Standard	NM_003711		Approved	PAP-2a, LPP1	uc003jpz.4	O14494	OTTHUMG00000162240	ENST00000307259.8:c.245A>T	chr5.hg19:g.54763943T>A	ENSP00000302229:p.Asn82Ile	74.0	0.0		57.0	22.0	NM_176895	B7ZKN8|G3XA95|O60457|O60463|Q17RZ4	Missense_Mutation	SNP	ENST00000307259.8	hg19	CCDS34159.1	.	.	.	.	.	.	.	.	.	.	T	13.72	2.322377	0.41096	.	.	ENSG00000067113	ENST00000264775;ENST00000307259	T;T	0.76186	-1.0;-1.0	5.63	4.47	0.54385	.	0.642476	0.16994	N	0.191163	T	0.78848	0.4348	M	0.76574	2.34	0.44611	D	0.997588	B;P	0.44195	0.022;0.828	B;P	0.48400	0.042;0.576	T	0.76713	-0.2858	10	0.40728	T	0.16	-15.0233	11.8014	0.52128	0.0:0.0689:0.0:0.9311	.	82;83	O14494;G3XA95	LPP1_HUMAN;.	I	83;82	ENSP00000264775:N83I;ENSP00000302229:N82I	ENSP00000264775:N83I	N	-	2	0	PPAP2A	54799700	1.000000	0.71417	0.997000	0.53966	0.872000	0.50106	3.957000	0.56730	1.080000	0.41073	0.467000	0.42956	AAC	.	.		0.353	PPAP2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368073.1			A	54763943	T	A	54763943	3	1	344	1	0	0	0	0	1	0	0	0	12299	1725	60	4	625	4	PPAP2A	5	54763943	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2394938	54763943	126151317	436	47799										
PLK2	10769	hgsc.bcm.edu	37	chr5	57750786	57750786	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	attagggccttatcagatttTagccactgaaggaggtagag	12	6	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:57750786T>A	ENST00000274289.3	-	13	2118	c.1818A>T	c.(1816-1818)ctA>ctT	p.L606L	PLK2_ENST00000502671.1_Intron	NM_001252226.1|NM_006622.3	NP_001239155.1|NP_006613.2	Q9NYY3	PLK2_HUMAN	polo-like kinase 2	606	POLO box 2. {ECO:0000255|PROSITE- ProRule:PRU00154}.				G1/S transition of mitotic cell cycle (GO:0000082)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|mitotic cell cycle checkpoint (GO:0007093)|mitotic spindle organization (GO:0007052)|negative regulation of apoptotic process (GO:0043066)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein phosphorylation (GO:0006468)|Rap protein signal transduction (GO:0032486)|Ras protein signal transduction (GO:0007265)|regulation of centriole replication (GO:0046599)|regulation of synaptic plasticity (GO:0048167)	centriole (GO:0005814)|centrosome (GO:0005813)|dendrite (GO:0030425)|intracellular (GO:0005622)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			endometrium(7)|large_intestine(7)|lung(5)|ovary(3)|prostate(2)|skin(2)	26		all_cancers(5;1.76e-12)|all_epithelial(5;2.09e-13)|all_lung(5;6.64e-05)|Lung NSC(5;0.000127)|Prostate(74;0.055)|Breast(144;0.0602)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;7.03e-37)		TATCAGATTTTAGCCACTGAA	0.433																																					p.L606L		Atlas-SNP	.											.	PLK2	71	.	0			c.A1818T						.						204	209	208					5																	57750786		2203	4300	6503	SO:0001819	synonymous_variant	10769	exon13			AGATTTTAGCCAC		CCDS3974.1, CCDS75250.1	5q12.1-q13.2	2013-01-18	2010-06-24		ENSG00000145632	ENSG00000145632			19699	protein-coding gene	gene with protein product	"serum-inducible kinase"	607023	"polo-like kinase 2 (Drosophila)"				Standard	NM_006622		Approved	SNK	uc003jrn.3	Q9NYY3	OTTHUMG00000097047	ENST00000274289.3:c.1818A>T	chr5.hg19:g.57750786T>A		157.0	0.0		123.0	54.0	NM_006622	O60679|Q96CV7|Q9UE61	Silent	SNP	ENST00000274289.3	hg19	CCDS3974.1																																																																																			.	.		0.433	PLK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214150.1	NM_006622		A	57750786	T	A	57750786	2	1	344	1	0	0	0	0	0	0	0	1	12105	1741	61	4		4	PLK2	5	57750786	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2986843	57750786	123164474	437	47800										
SLC30A5	64924	hgsc.bcm.edu	37	chr5	68423913	68423913	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tattgtggcaggaacaattcAtatacaggtgacatctgatg	10	6	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:68423913A>G	ENST00000396591.3	+	15	2691	c.2081A>G	c.(2080-2082)cAt>cGt	p.H694R	CTC-498J12.3_ENST00000504129.1_RNA	NM_022902.4	NP_075053.2	Q8TAD4	ZNT5_HUMAN	solute carrier family 30 (zinc transporter), member 5	694					cellular protein metabolic process (GO:0044267)|cellular zinc ion homeostasis (GO:0006882)|cobalt ion transport (GO:0006824)|regulation of proton transport (GO:0010155)|response to zinc ion (GO:0010043)|transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	apical plasma membrane (GO:0016324)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|secretory granule (GO:0030141)|secretory granule membrane (GO:0030667)	zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Lung NSC(167;0.000986)|Prostate(74;0.00809)|Colorectal(97;0.0508)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)		GGAACAATTCATATACAGGTG	0.338																																					p.H694R		Atlas-SNP	.											.	SLC30A5	54	.	0			c.A2081G						.						130	136	134					5																	68423913		2203	4300	6503	SO:0001583	missense	64924	exon15			CAATTCATATACA	AF212235	CCDS3996.1, CCDS34173.1, CCDS58955.1	5q13.1	2013-05-22			ENSG00000145740	ENSG00000145740		"Solute carriers"	19089	protein-coding gene	gene with protein product		607819				11937503, 11904301	Standard	NM_022902		Approved	ZTL1, ZnT-5, FLJ12496, FLJ12756, ZNT5, MGC5499, ZNTL1	uc003jvh.3	Q8TAD4	OTTHUMG00000131253	ENST00000396591.3:c.2081A>G	chr5.hg19:g.68423913A>G	ENSP00000379836:p.His694Arg	73.0	0.0		66.0	27.0	NM_022902	B7ZM89|Q6UX54|Q7L4M4|Q8TDG3|Q9BVY8|Q9H9H1	Missense_Mutation	SNP	ENST00000396591.3	hg19	CCDS3996.1	.	.	.	.	.	.	.	.	.	.	A	17.05	3.290986	0.59976	.	.	ENSG00000145740	ENST00000396591;ENST00000438236	T	0.65178	-0.14	5.17	5.17	0.71159	.	0.044953	0.85682	D	0.000000	T	0.66257	0.2771	M	0.88842	2.985	0.80722	D	1	P	0.40794	0.729	B	0.34824	0.19	T	0.73418	-0.3989	10	0.46703	T	0.11	.	14.8359	0.70183	1.0:0.0:0.0:0.0	.	694	Q8TAD4	ZNT5_HUMAN	R	694;289	ENSP00000379836:H694R	ENSP00000379836:H694R	H	+	2	0	SLC30A5	68459669	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	8.909000	0.92647	2.171000	0.68590	0.402000	0.26972	CAT	.	.		0.338	SLC30A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254017.2			G	68423913	A	G	68423913	3	3	344	1	0	0	0	0	1	0	0	0	14573	217	8	2	2227	2	SLC30A5	5	68423913	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	10673127	68423913	112491347	438	47801										
MAP1B	4131	hgsc.bcm.edu	37	chr5	71494454	71494454	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccgatgttgctcctcccagaGatatgtccttatatgcctca	7	13	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:71494454G>C	ENST00000296755.7	+	5	5570	c.5272G>C	c.(5272-5274)Gat>Cat	p.D1758H		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1758					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		TCCTCCCAGAGATATGTCCTT	0.498																																					p.D1758H	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.G5272C						.						107	115	112					5																	71494454		2203	4300	6503	SO:0001583	missense	4131	exon5			CCCAGAGATATGT	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.5272G>C	chr5.hg19:g.71494454G>C	ENSP00000296755:p.Asp1758His	63.0	0.0		49.0	18.0	NM_005909	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	hg19	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	G	13.09	2.133018	0.37630	.	.	ENSG00000131711	ENST00000296755	T	0.04015	3.73	5.22	5.22	0.72569	.	0.374661	0.25619	N	0.029435	T	0.07728	0.0194	N	0.24115	0.695	0.48185	D	0.999607	P;P	0.42123	0.771;0.771	P;P	0.45946	0.498;0.498	T	0.25398	-1.0133	10	0.87932	D	0	-7.6181	19.1387	0.93439	0.0:0.0:1.0:0.0	.	1632;1758	A2BDK6;P46821	.;MAP1B_HUMAN	H	1758	ENSP00000296755:D1758H	ENSP00000296755:D1758H	D	+	1	0	MAP1B	71530210	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	5.691000	0.68249	2.608000	0.88229	0.448000	0.29417	GAT	.	.		0.498	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		C	71494454	G	C	71494454	3	2	344	1	0	0	0	0	1	0	0	0	9237	942	33	4	5290	4	MAP1B	5	71494454	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	3070541	71494454	109420806	439	47802										
RASGRF2	5924	hgsc.bcm.edu	37	chr5	80363997	80363997	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aatcgaaaggcttaaatcagAggtatttcccagtcaataga	8	7	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:80363997A>T	ENST00000265080.4	+	3	609	c.542A>T	c.(541-543)gAg>gTg	p.E181V		NM_006909.2	NP_008840.1	O14827	RGRF2_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 2	181					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			biliary_tract(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(28)|ovary(5)|prostate(3)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)		CTTAAATCAGAGGTATTTCCC	0.388																																					p.E181V		Atlas-SNP	.											.	RASGRF2	165	.	0			c.A542T						.						116	109	111					5																	80363997		2203	4300	6503	SO:0001630	splice_region_variant	5924	exon3			AATCAGAGGTATT	AF023130	CCDS4052.1	5q13	2013-01-10			ENSG00000113319	ENSG00000113319		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9876	protein-coding gene	gene with protein product		606614					Standard	NM_006909		Approved	GRF2, Ras-GRF2	uc003kha.2	O14827	OTTHUMG00000119015	ENST00000265080.4:c.543+1A>T	chr5.hg19:g.80363997A>T		79.0	0.0		61.0	42.0	NM_006909	B9EG89|Q9UK56	Missense_Mutation	SNP	ENST00000265080.4	hg19	CCDS4052.1	.	.	.	.	.	.	.	.	.	.	A	27.8	4.860871	0.91433	.	.	ENSG00000113319	ENST00000265080	T	0.51071	0.72	5.91	5.91	0.95273	.	0.159098	0.38605	U	0.001621	T	0.64416	0.2596	L	0.60455	1.87	0.80722	D	1	D	0.65815	0.995	D	0.64042	0.921	T	0.67039	-0.5771	10	0.87932	D	0	.	16.3378	0.83071	1.0:0.0:0.0:0.0	.	181	O14827	RGRF2_HUMAN	V	181	ENSP00000265080:E181V	ENSP00000265080:E181V	E	+	2	0	RASGRF2	80399753	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	9.335000	0.96500	2.255000	0.74692	0.533000	0.62120	GAG	.	.		0.388	RASGRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239215.2	NM_006909	Missense_Mutation	T	80363997	A	T	80363997	5	4	344	1	0	0	0	0	0	0	1	0	13088	318	11	4	552	4	RASGRF2	5	80363997	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	8869543	80363997	100551263	440	47803										
XRCC4	7518	hgsc.bcm.edu	37	chr5	82491711	82491711	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaaaatgagcacctgcagaaAgaaaatgaaaggcttctgag	10	6	1	5			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:82491711A>T	ENST00000511817.1	+	4	518	c.438A>T	c.(436-438)aaA>aaT	p.K146N	XRCC4_ENST00000338635.6_Missense_Mutation_p.K146N|XRCC4_ENST00000282268.3_Missense_Mutation_p.K146N|XRCC4_ENST00000509268.1_3'UTR|XRCC4_ENST00000396027.4_Missense_Mutation_p.K146N			Q13426	XRCC4_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 4	146					cellular response to lithium ion (GO:0071285)|central nervous system development (GO:0007417)|DNA ligation involved in DNA repair (GO:0051103)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|immunoglobulin V(D)J recombination (GO:0033152)|in utero embryonic development (GO:0001701)|isotype switching (GO:0045190)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of ligase activity (GO:0051351)|positive regulation of neurogenesis (GO:0050769)|pro-B cell differentiation (GO:0002328)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytosol (GO:0005829)|DNA ligase IV complex (GO:0032807)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(2)|skin(3)	17		Lung NSC(167;0.00132)|all_lung(232;0.00154)|Ovarian(174;0.034)		OV - Ovarian serous cystadenocarcinoma(54;1.44e-38)|Epithelial(54;3.72e-33)|all cancers(79;9.22e-28)		ACCTGCAGAAAGAAAATGAAA	0.383								Non-homologous end-joining																													p.K146N		Atlas-SNP	.											.	XRCC4	37	.	0			c.A438T						.						78	82	80					5																	82491711		2203	4300	6503	SO:0001583	missense	7518	exon4			GCAGAAAGAAAAT	AB017445	CCDS4058.1, CCDS4059.1	5q14.2	2008-02-05			ENSG00000152422	ENSG00000152422			12831	protein-coding gene	gene with protein product	"X-ray repair, complementing defective, repair in Chinese hamster", "DNA repair protein XRCC4"	194363				1697445, 7665175	Standard	NM_022406		Approved		uc003kib.3	Q13426	OTTHUMG00000131319	ENST00000511817.1:c.438A>T	chr5.hg19:g.82491711A>T	ENSP00000421491:p.Lys146Asn	50.0	0.0		45.0	29.0	NM_003401	A8K3X4|Q9BS72|Q9UP94	Missense_Mutation	SNP	ENST00000511817.1	hg19	CCDS4059.1	.	.	.	.	.	.	.	.	.	.	A	19.40	3.820773	0.71028	.	.	ENSG00000152422	ENST00000282268;ENST00000338635;ENST00000396027;ENST00000511817	T;T;T;T	0.15139	2.45;2.45;2.45;2.45	5.56	1.74	0.24563	DNA double-strand break repair and VJ recombination XRCC4, C-terminal (1);	0.204155	0.50627	D	0.000106	T	0.35740	0.0942	M	0.74258	2.255	0.36990	D	0.894722	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.72982	0.938;0.979;0.963	T	0.21930	-1.0231	10	0.48119	T	0.1	-24.2618	8.7384	0.34543	0.7128:0.0:0.2872:0.0	.	146;146;146	Q13426-2;Q13426;Q13426-3	.;XRCC4_HUMAN;.	N	146	ENSP00000282268:K146N;ENSP00000342011:K146N;ENSP00000379344:K146N;ENSP00000421491:K146N	ENSP00000282268:K146N	K	+	3	2	XRCC4	82527467	0.988000	0.35896	0.999000	0.59377	0.981000	0.71138	0.329000	0.19698	0.119000	0.18210	0.477000	0.44152	AAA	.	.		0.383	XRCC4-003	NOVEL	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000369624.1	NM_022550		T	82491711	A	T	82491711	3	4	344	1	0	0	0	0	1	0	0	0	17470	69	3	4	448	4	XRCC4	5	82491711	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2127714	82491711	98423549	441	47804										
GPR98	84059	hgsc.bcm.edu	37	chr5	90055290	90055290	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgaattgacagagacgttcaAtatttccttgatcagtgttg	9	6	2	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:90055290A>G	ENST00000405460.2	+	58	12101	c.12005A>G	c.(12004-12006)aAt>aGt	p.N4002S		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	4002	Calx-beta 26. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		GAGACGTTCAATATTTCCTTG	0.388																																					p.N4002S		Atlas-SNP	.											.	GPR98	605	.	0			c.A12005G						.						172	165	167					5																	90055290		2046	4209	6255	SO:0001583	missense	84059	exon58			CGTTCAATATTTC	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.12005A>G	chr5.hg19:g.90055290A>G	ENSP00000384582:p.Asn4002Ser	107.0	0.0		72.0	24.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	1.048|1.048	-0.676772|-0.676772	0.03378|0.03378	.|.	.|.	ENSG00000164199|ENSG00000164199	ENST00000509621|ENST00000405460;ENST00000296619	.|T	.|0.27104	.|1.69	4.99|4.99	-9.98|-9.98	0.00438|0.00438	.|Na-Ca exchanger/integrin-beta4 (2);	.|0.898366	.|0.09943	.|N	.|0.735694	T|T	0.07683|0.07683	0.0193|0.0193	N|N	0.05441|0.05441	-0.05|-0.05	0.49051|0.49051	D|D	0.999743|0.999743	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.08055	.|0.003;0.001	T|T	0.25328|0.25328	-1.0135|-1.0135	5|10	.|0.08381	.|T	.|0.77	.|.	7.1297|7.1297	0.25493|0.25493	0.1857:0.2436:0.4906:0.0801|0.1857:0.2436:0.4906:0.0801	.|.	.|4002;4002	.|E7ETI5;Q8WXG9	.|.;GPR98_HUMAN	V|S	1568|4002	.|ENSP00000384582:N4002S	.|ENSP00000296619:N4002S	I|N	+|+	1|2	0|0	GPR98|GPR98	90091046|90091046	0.000000|0.000000	0.05858|0.05858	0.174000|0.174000	0.22961|0.22961	0.131000|0.131000	0.20780|0.20780	-0.829000|-0.829000	0.04415|0.04415	-2.549000|-2.549000	0.00480|0.00480	-0.371000|-0.371000	0.07208|0.07208	ATA|AAT	.	.		0.388	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		G	90055290	A	G	90055290	3	3	344	1	0	0	0	0	1	0	0	0	6730	101	4	2	12235	2	GPR98	5	90055290	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	7563579	90055290	90859970	442	47805										
GPR98	84059	hgsc.bcm.edu	37	chr5	90077396	90077396	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaagtatactgccttcgaagGtaggttcagtcagctagctt	10	8	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:90077396G>T	ENST00000405460.2	+	65	13327		c.e65+1		GPR98_ENST00000425867.2_Splice_Site	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98						detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		GCCTTCGAAGGTAGGTTCAGT	0.363																																					.		Atlas-SNP	.											.	GPR98	605	.	0			c.13231+1G>T						.						51	47	48					5																	90077396		1879	4100	5979	SO:0001630	splice_region_variant	84059	exon65			TCGAAGGTAGGTT	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.13231+1G>T	chr5.hg19:g.90077396G>T		262.0	0.0		182.0	60.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Splice_Site	SNP	ENST00000405460.2	hg19	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	G	17.56	3.420352	0.62622	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	.	.	.	5.8	5.8	0.92144	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.649	0.95793	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GPR98	90113152	1.000000	0.71417	0.996000	0.52242	0.583000	0.36354	6.612000	0.74187	2.740000	0.93945	0.650000	0.86243	.	.	.		0.363	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	Intron	T	90077396	G	T	90077396	5	4	344	1	0	0	0	0	0	0	1	0	6730	1275	44	3	13490	3	GPR98	5	90077396	Splice_Site	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	22106	90077396	90837864	443	47806										
WDR36	134430	hgsc.bcm.edu	37	chr5	110430616	110430616	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	accttttttcttttttaaacAggttcagaaacttagtctgg	6	7	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:110430616A>T	ENST00000513710.2	+	2	334		c.e2-1		CTC-551A13.2_ENST00000507269.3_RNA|WDR36_ENST00000505303.1_Splice_Site|WDR36_ENST00000506538.2_Splice_Site			Q8NI36	WDR36_HUMAN	WD repeat domain 36						regulation of axon extension (GO:0030516)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|rRNA processing (GO:0006364)|visual perception (GO:0007601)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(9)|kidney(4)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(142;2.72e-05)|all_epithelial(76;4.4e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0418)|Ovarian(225;0.0443)|Colorectal(57;0.0465)|all_lung(232;0.0508)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.39e-08)|Epithelial(69;1.82e-07)|all cancers(49;2.04e-05)|COAD - Colon adenocarcinoma(37;0.111)		TTTTTTAAACAGGTTCAGAAA	0.269																																					.		Atlas-SNP	.											.	WDR36	111	.	0			c.331-2A>T						.						68	68	68					5																	110430616		2197	4291	6488	SO:0001630	splice_region_variant	134430	exon2			TTAAACAGGTTCA	AF385437	CCDS4102.1	5q22.2	2013-01-09			ENSG00000134987	ENSG00000134987		"WD repeat domain containing"	30696	protein-coding gene	gene with protein product		609669	"glaucoma 1, open angle, G"	GLC1G		15590835, 15677485	Standard	NM_139281		Approved	TA-WDRP, UTP21	uc003kpd.3	Q8NI36	OTTHUMG00000128790	ENST00000513710.2:c.331-1A>T	chr5.hg19:g.110430616A>T		77.0	0.0		50.0	28.0	NM_139281	A2RUS4|Q68E02|Q8N1Q2	Splice_Site	SNP	ENST00000513710.2	hg19	CCDS4102.1	.	.	.	.	.	.	.	.	.	.	A	18.62	3.662340	0.67700	.	.	ENSG00000134987	ENST00000506538;ENST00000513710;ENST00000505303	.	.	.	4.94	4.94	0.65067	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.4352	0.61079	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	WDR36	110458515	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	6.564000	0.73969	1.836000	0.53414	0.533000	0.62120	.	.	.		0.269	WDR36-008	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000373504.3	NM_139281	Intron	T	110430616	A	T	110430616	5	4	344	1	0	0	0	0	0	0	1	0	17305	202	7	4	335	4	WDR36	5	110430616	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	20353220	110430616	70484644	444	47807										
SNCAIP	9627	hgsc.bcm.edu	37	chr5	121780395	121780395	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acctgcatgtcgctggcctcTcaagtggtgaagttaaccaa	10	11	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:121780395T>C	ENST00000261368.8	+	8	1822	c.1560T>C	c.(1558-1560)tcT>tcC	p.S520S	SNCAIP_ENST00000379538.3_Silent_p.S154S|SNCAIP_ENST00000542191.1_Silent_p.S78S|CTC-210G5.1_ENST00000506053.1_RNA|SNCAIP_ENST00000414317.2_Silent_p.S122S|CTC-210G5.1_ENST00000505546.1_RNA|SNCAIP_ENST00000504884.2_3'UTR|SNCAIP_ENST00000503116.2_3'UTR|CTC-210G5.1_ENST00000503529.1_RNA|CTC-210G5.1_ENST00000510972.1_RNA|SNCAIP_ENST00000261367.7_Silent_p.S567S|SNCAIP_ENST00000379533.2_Silent_p.S567S|SNCAIP_ENST00000379536.2_Silent_p.S460S|CTC-210G5.1_ENST00000509993.1_RNA	NM_005460.2	NP_005451.2	Q9Y6H5	SNCAP_HUMAN	synuclein, alpha interacting protein	520					cell death (GO:0008219)|dopamine metabolic process (GO:0042417)|regulation of inclusion body assembly (GO:0090083)|regulation of neurotransmitter secretion (GO:0046928)	cytoplasm (GO:0005737)|neuronal cell body (GO:0043025)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	identical protein binding (GO:0042802)|ubiquitin protein ligase binding (GO:0031625)			NS(3)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(9)|ovary(2)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	39		all_cancers(142;0.00787)|Prostate(80;0.0327)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000625)|Epithelial(69;0.00216)|all cancers(49;0.0232)		CGCTGGCCTCTCAAGTGGTGA	0.562																																					p.S520S		Atlas-SNP	.											.	SNCAIP	308	.	0			c.T1560C						.						77	74	75					5																	121780395		2203	4300	6503	SO:0001819	synonymous_variant	9627	exon8			GGCCTCTCAAGTG	AF167306	CCDS4131.1, CCDS58964.1	5q23.2	2013-01-10	2008-07-31		ENSG00000064692	ENSG00000064692		"Ankyrin repeat domain containing"	11139	protein-coding gene	gene with protein product	"synphilin"	603779				10319874	Standard	NM_001242935		Approved	SYPH1	uc003ksw.1	Q9Y6H5	OTTHUMG00000128915	ENST00000261368.8:c.1560T>C	chr5.hg19:g.121780395T>C		113.0	0.0		80.0	29.0	NM_005460	D3DSZ1|Q05BS1|Q1PSC2|Q49AC6|Q504U9|Q6L984|Q6L985|Q6L986|Q9HC59	Silent	SNP	ENST00000261368.8	hg19	CCDS4131.1																																																																																			.	.		0.562	SNCAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250888.1			C	121780395	T	C	121780395	2	2	344	1	0	0	0	0	0	0	0	1	14856	1538	54	2		2	SNCAIP	5	121780395	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	11349779	121780395	59134865	445	47808										
ZNF608	57507	hgsc.bcm.edu	37	chr5	123983650	123983650	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttctcctttttctttttgtcTttgagtgacaccagagctgg	8	9	3	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:123983650T>C	ENST00000306315.5	-	4	2862	c.2427A>G	c.(2425-2427)aaA>aaG	p.K809K	ZNF608_ENST00000504926.1_Silent_p.K382K	NM_020747.2	NP_065798.2	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	809	Poly-Lys.						metal ion binding (GO:0046872)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(12)|ovary(3)|skin(6)|urinary_tract(1)	46		all_cancers(142;0.186)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783)		TCTTTTTGTCTTTGAGTGACA	0.478																																					p.K809K		Atlas-SNP	.											.	ZNF608	117	.	0			c.A2427G						.						130	136	134					5																	123983650		2203	4300	6503	SO:0001819	synonymous_variant	57507	exon4			TTTGTCTTTGAGT	AB033107	CCDS34219.1	5q23.2	2008-05-02			ENSG00000168916	ENSG00000168916		"Zinc fingers, C2H2-type"	29238	protein-coding gene	gene with protein product						10574462, 10508479	Standard	NM_020747		Approved	KIAA1281, DKFZp434M098, NY-REN-36	uc003ktq.1	Q9ULD9	OTTHUMG00000162999	ENST00000306315.5:c.2427A>G	chr5.hg19:g.123983650T>C		169.0	0.0		127.0	36.0	NM_020747	A7E2W9|Q3SYM6|Q68D12|Q8IY05|Q9Y5A1	Silent	SNP	ENST00000306315.5	hg19	CCDS34219.1																																																																																			.	.		0.478	ZNF608-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371300.1	XM_114432		C	123983650	T	C	123983650	2	2	344	1	0	0	0	0	0	0	0	1	18049	1606	56	2		2	ZNF608	5	123983650	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2203255	123983650	56931610	446	47809										
FBN2	2201	hgsc.bcm.edu	37	chr5	127609596	127609596	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cattcacagctgaaactgccTggagtgttttgacagattcc	9	10	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:127609596T>G	ENST00000508053.1	-	67	8750	c.7776A>C	c.(7774-7776)ccA>ccC	p.P2592P	FBN2_ENST00000262464.4_Silent_p.P2592P			P35556	FBN2_HUMAN	fibrillin 2	2592	EGF-like 44; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		TGAAACTGCCTGGAGTGTTTT	0.438																																					p.P2592P		Atlas-SNP	.											.	FBN2	858	.	0			c.A7776C						.						123	110	115					5																	127609596		2203	4300	6503	SO:0001819	synonymous_variant	2201	exon61			ACTGCCTGGAGTG	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.7776A>C	chr5.hg19:g.127609596T>G		202.0	0.0		150.0	78.0	NM_001999	B4DU01|Q59ES6	Silent	SNP	ENST00000508053.1	hg19	CCDS34222.1																																																																																			.	.		0.438	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		G	127609596	T	G	127609596	2	3	344	1	0	0	0	0	0	0	0	1	5711	1567	55	5		5	FBN2	5	127609596	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	3625946	127609596	53305664	447	47810										
FBN2	2201	hgsc.bcm.edu	37	chr5	127653902	127653902	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gggcagttacactcatagcgAccaggcgtgttgacacatag	12	10	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:127653902A>G	ENST00000508053.1	-	42	5630	c.4656T>C	c.(4654-4656)ggT>ggC	p.G1552G	FBN2_ENST00000262464.4_Silent_p.G1552G			P35556	FBN2_HUMAN	fibrillin 2	1552	EGF-like 26; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		ACTCATAGCGACCAGGCGTGT	0.403																																					p.G1552G		Atlas-SNP	.											.	FBN2	858	.	0			c.T4656C						.						190	179	183					5																	127653902		2203	4300	6503	SO:0001819	synonymous_variant	2201	exon36			ATAGCGACCAGGC	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.4656T>C	chr5.hg19:g.127653902A>G		236.0	0.0		181.0	94.0	NM_001999	B4DU01|Q59ES6	Silent	SNP	ENST00000508053.1	hg19	CCDS34222.1																																																																																			.	.		0.403	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		G	127653902	A	G	127653902	2	3	344	1	0	0	0	0	0	0	0	1	5711	262	10	2		2	FBN2	5	127653902	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	44306	127653902	53261358	448	47811										
FNIP1	96459	hgsc.bcm.edu	37	chr5	131066598	131066598	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atgacatcaatgatcttaccTggtacttaagacactggtct	7	9	3	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:131066598T>A	ENST00000510461.1	-	3	448	c.353A>T	c.(352-354)cAg>cTg	p.Q118L	FNIP1_ENST00000307954.8_Intron|CTC-432M15.3_ENST00000514667.1_Intron|FNIP1_ENST00000307968.7_Splice_Site_p.Q118L|FNIP1_ENST00000511848.1_Splice_Site_p.Q118L	NM_133372.2	NP_588613	Q8TF40	FNIP1_HUMAN	folliculin interacting protein 1	118					cellular response to starvation (GO:0009267)|immature B cell differentiation (GO:0002327)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell apoptotic process (GO:0002904)|positive regulation of GTPase activity (GO:0043547)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein phosphorylation (GO:0001934)|regulation of pro-B cell differentiation (GO:2000973)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34		all_cancers(142;0.00347)|Lung NSC(810;0.106)|all_lung(232;0.123)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0665)		TGATCTTACCTGGTACTTAAG	0.353																																					p.Q118L		Atlas-SNP	.											.	FNIP1	104	.	0			c.A353T						.						65	65	65					5																	131066598		2203	4300	6503	SO:0001630	splice_region_variant	96459	exon3			CTTACCTGGTACT	DQ145719	CCDS34226.1, CCDS34227.1	5q23.3	2014-01-28				ENSG00000217128			29418	protein-coding gene	gene with protein product		610594				11853319, 17028174	Standard	NM_001008738		Approved	KIAA1961		Q8TF40		ENST00000510461.1:c.354+1A>T	chr5.hg19:g.131066598T>A		172.0	0.0		115.0	46.0	NM_001008738	D6RJH5|Q86T47|Q9BUT0	Missense_Mutation	SNP	ENST00000510461.1	hg19	CCDS34227.1	.	.	.	.	.	.	.	.	.	.	T	18.82	3.705373	0.68615	.	.	ENSG00000217128	ENST00000307968;ENST00000510461;ENST00000511848	T;T;T	0.46451	0.87;0.87;0.87	5.27	5.27	0.74061	.	.	.	.	.	T	0.43875	0.1267	M	0.72118	2.19	0.80722	D	1	B;P;B	0.47910	0.103;0.902;0.371	B;B;B	0.39258	0.058;0.254;0.295	T	0.52253	-0.8600	9	0.52906	T	0.07	0.0281	15.4806	0.75524	0.0:0.0:0.0:1.0	.	118;118;118	Q8TF40-2;Q8TF40-3;Q8TF40	.;.;FNIP1_HUMAN	L	118	ENSP00000309266:Q118L;ENSP00000421985:Q118L;ENSP00000425619:Q118L	ENSP00000309266:Q118L	Q	-	2	0	FNIP1	131094497	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.769000	0.68865	2.124000	0.65301	0.533000	0.62120	CAG	.	.		0.353	FNIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370077.1	NM_133372	Missense_Mutation	A	131066598	T	A	131066598	5	1	344	1	0	0	0	0	0	0	1	0	5983	1594	55	4	3211	4	FNIP1	5	131066598	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	3412696	131066598	49848662	449	47812										
PDLIM4	8572	hgsc.bcm.edu	37	chr5	131607517	131607517	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcctggcggcccccggaaccTcaagcccacggccagcaagc	12	19	1	0	rs557597794		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:131607517T>A	ENST00000253754.3	+	6	768	c.704T>A	c.(703-705)cTc>cAc	p.L235H	PDLIM4_ENST00000484620.1_3'UTR|PDLIM4_ENST00000379018.3_Intron|P4HA2_ENST00000471826.1_Intron	NM_001131027.1|NM_003687.3	NP_001124499.1|NP_003678.2	P50479	PDLI4_HUMAN	PDZ and LIM domain 4	235							zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|urinary_tract(1)	10			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CCCCGGAACCTCAAGCCCACG	0.697													T|||	1	0.000199681	8e-04	0	5008	,	,		12158	0		0	False		,,,				2504	0				p.L235H		Atlas-SNP	.											.	PDLIM4	22	.	0			c.T704A						.						15	20	18					5																	131607517		2176	4265	6441	SO:0001583	missense	8572	exon6			GGAACCTCAAGCC	AF153882	CCDS4152.1, CCDS47261.1	5q31.1	2008-02-05			ENSG00000131435	ENSG00000131435			16501	protein-coding gene	gene with protein product		603422				9573374	Standard	NM_001131027		Approved	RIL	uc003kwn.3	P50479	OTTHUMG00000059645	ENST00000253754.3:c.704T>A	chr5.hg19:g.131607517T>A	ENSP00000253754:p.Leu235His	62.0	0.0		61.0	18.0	NM_003687	B2R8U1|Q53Y39|Q96AT8|Q9BTW8|Q9Y292	Missense_Mutation	SNP	ENST00000253754.3	hg19	CCDS4152.1	.	.	.	.	.	.	.	.	.	.	T	18.86	3.712660	0.68730	.	.	ENSG00000131435	ENST00000253754	T	0.13657	2.57	4.82	3.65	0.41850	.	0.376195	0.26935	N	0.021744	T	0.14356	0.0347	L	0.38175	1.15	0.80722	D	1	P	0.51791	0.948	P	0.46362	0.514	T	0.01367	-1.1373	10	0.87932	D	0	-14.9393	10.3743	0.44073	0.0:0.0787:0.0:0.9213	.	235	P50479	PDLI4_HUMAN	H	235	ENSP00000253754:L235H	ENSP00000253754:L235H	L	+	2	0	PDLIM4	131635416	1.000000	0.71417	1.000000	0.80357	0.609000	0.37215	4.056000	0.57448	0.683000	0.31428	0.379000	0.24179	CTC	.	.		0.697	PDLIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132644.2	NM_003687		A	131607517	T	A	131607517	3	1	344	1	0	0	0	0	1	0	0	0	11691	1551	54	4	726	4	PDLIM4	5	131607517	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	540919	131607517	49307743	450	47813										
TCF7	6932	hgsc.bcm.edu	37	chr5	133451714	133451714	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agggcagcacccccagccgcAgcccccgctggtaagtggac	13	17	0	0	rs570365840	byFrequency	TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:133451714A>T	ENST00000321584.4	+	3	627	c.431A>T	c.(430-432)cAg>cTg	p.Q144L	TCF7_ENST00000378560.4_Missense_Mutation_p.Q29L|TCF7_ENST00000395023.1_Missense_Mutation_p.Q29L|TCF7_ENST00000342854.5_Missense_Mutation_p.Q144L|TCF7_ENST00000395029.1_Missense_Mutation_p.Q144L|TCF7_ENST00000321603.6_Missense_Mutation_p.Q144L|TCF7_ENST00000520958.1_Missense_Mutation_p.Q29L|TCF7_ENST00000378564.1_Missense_Mutation_p.Q144L|TCF7_ENST00000518915.1_Missense_Mutation_p.Q29L|TCF7_ENST00000432532.2_Missense_Mutation_p.Q29L			P36402	TCF7_HUMAN	transcription factor 7 (T-cell specific, HMG-box)	144					alpha-beta T cell differentiation (GO:0046632)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|cellular response to interleukin-4 (GO:0071353)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|generation of neurons (GO:0048699)|immune response (GO:0006955)|neural tube development (GO:0021915)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|T cell receptor V(D)J recombination (GO:0033153)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			kidney(2)|large_intestine(7)|lung(2)|skin(1)	12		Breast(839;0.058)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CCCCAGCCGCAGCCCCCGCTG	0.642													A|||	2	0.000399361	0.0015	0	5008	,	,		14177	0		0	False		,,,				2504	0				p.Q144L		Atlas-SNP	.											.	TCF7	81	.	0			c.A431T						.						24	26	25					5																	133451714		2196	4299	6495	SO:0001583	missense	6932	exon3			AGCCGCAGCCCCC	Z47362	CCDS4169.1, CCDS4170.1, CCDS43362.1, CCDS47263.1, CCDS47263.2	5q31	2008-02-05			ENSG00000081059	ENSG00000081059			11639	protein-coding gene	gene with protein product		189908					Standard	NM_003202		Approved	TCF-1	uc003kyt.3	P36402	OTTHUMG00000129124	ENST00000321584.4:c.431A>T	chr5.hg19:g.133451714A>T	ENSP00000326540:p.Gln144Leu	149.0	0.0		76.0	35.0	NM_003202	B3KSH3|Q86WR9|Q9UKI4	Missense_Mutation	SNP	ENST00000321584.4	hg19		.	.	.	.	.	.	.	.	.	.	A	13.37	2.218150	0.39201	.	.	ENSG00000081059	ENST00000342854;ENST00000361590;ENST00000321603;ENST00000321584;ENST00000378564;ENST00000395029;ENST00000518887;ENST00000517851;ENST00000521639;ENST00000522375;ENST00000378560;ENST00000432532;ENST00000520958;ENST00000518915;ENST00000395023	D;D;D;D;D;D;D;D;D;D	0.99194	-5.48;-5.51;-5.51;-5.53;-5.49;-5.54;-5.45;-5.47;-5.49;-5.47	4.68	4.68	0.58851	CTNNB1 binding, N-teminal (1);	0.697909	0.13627	N	0.374011	D	0.95984	0.8692	L	0.34521	1.04	0.30573	N	0.763302	B;B;B;P	0.40476	0.072;0.002;0.451;0.718	B;B;B;B	0.35971	0.015;0.003;0.103;0.215	D	0.94080	0.7343	10	0.09338	T	0.73	.	10.5026	0.44815	1.0:0.0:0.0:0.0	.	144;144;144;144	P36402-9;B7WNT5;P36402;P36402-5	.;.;TCF7_HUMAN;.	L	144;144;144;144;144;144;29;29;29;29;29;29;29;29;29	ENSP00000340347:Q144L;ENSP00000326654:Q144L;ENSP00000326540:Q144L;ENSP00000367827:Q144L;ENSP00000378472:Q144L;ENSP00000367822:Q29L;ENSP00000397946:Q29L;ENSP00000429547:Q29L;ENSP00000430179:Q29L;ENSP00000378469:Q29L	ENSP00000326540:Q144L	Q	+	2	0	TCF7	133479613	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.219000	0.42899	1.969000	0.57287	0.456000	0.33151	CAG	.	.		0.642	TCF7-201	KNOWN	basic	protein_coding	protein_coding		NM_201634		T	133451714	A	T	133451714	3	4	344	1	0	0	0	0	1	0	0	0	15711	188	7	4	441	4	TCF7	5	133451714	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1844197	133451714	47463546	451	47814										
CDKL3	51265	hgsc.bcm.edu	37	chr5	133644327	133644327	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgtttttctttcatctttccTgagttcattttctttagaac	4	8	5	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:133644327T>A	ENST00000265334.4	-	8	1091	c.973A>T	c.(973-975)Agg>Tgg	p.R325W	CDKL3_ENST00000521118.1_Missense_Mutation_p.R325W|CDKL3_ENST00000521755.1_Intron|CDKL3_ENST00000523054.1_Missense_Mutation_p.R136W|CDKL3_ENST00000609383.1_Missense_Mutation_p.R30W|CTD-2410N18.4_ENST00000518409.1_RNA|CDKL3_ENST00000609654.1_Missense_Mutation_p.R136W|CDKL3_ENST00000523832.1_Missense_Mutation_p.R325W|CDKL3_ENST00000435211.1_Missense_Mutation_p.R325W|CDKL3_ENST00000435240.2_Missense_Mutation_p.R30W|CDKL3_ENST00000536186.1_Missense_Mutation_p.R30W	NM_001113575.1	NP_001107047.1	Q8IVW4	CDKL3_HUMAN	cyclin-dependent kinase-like 3	325					cellular protein modification process (GO:0006464)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|prostate(3)	11			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TCATCTTTCCTGAGTTCATTT	0.323																																					p.R325W		Atlas-SNP	.											.	CDKL3	76	.	0			c.A973T						.						63	60	61					5																	133644327		1811	4070	5881	SO:0001583	missense	51265	exon8			CTTTCCTGAGTTC	AF130372	CCDS47264.1, CCDS47265.1, CCDS75303.1	5q31.1	2014-09-09			ENSG00000006837	ENSG00000006837	2.7.11.22	"Cyclin-dependent kinases"	15483	protein-coding gene	gene with protein product	"serine-threonine protein kinase NKIAMRE"	608459				10463609	Standard	NM_016508		Approved	NKIAMRE	uc003kzf.4	Q8IVW4	OTTHUMG00000186341	ENST00000265334.4:c.973A>T	chr5.hg19:g.133644327T>A	ENSP00000265334:p.Arg325Trp	57.0	0.0		47.0	26.0	NM_001113575	D3DQA0|D3DQA1|Q9P114	Missense_Mutation	SNP	ENST00000265334.4	hg19	CCDS47264.1	.	.	.	.	.	.	.	.	.	.	T	8.321	0.824201	0.16678	.	.	ENSG00000006837	ENST00000536186;ENST00000435240;ENST00000265334;ENST00000523054;ENST00000521118;ENST00000523832;ENST00000435211	T;T;T;T;T;T;T	0.73575	0.93;0.9;-0.71;-0.48;-0.76;-0.74;-0.74	5.66	0.559	0.17272	.	0.900977	0.09696	N	0.767674	T	0.60971	0.2310	N	0.14661	0.345	0.09310	N	1	P;P;P;B;P	0.48016	0.719;0.768;0.904;0.367;0.598	B;B;P;B;B	0.48571	0.443;0.443;0.582;0.19;0.174	T	0.52275	-0.8597	10	0.62326	D	0.03	-13.2967	4.1097	0.10053	0.1438:0.2278:0.0:0.6284	.	136;30;30;136;325	B4DX41;B4DRK6;B4DGS2;B7Z2C5;Q8IVW4	.;.;.;.;CDKL3_HUMAN	W	30;30;325;136;325;325;325	ENSP00000441545:R30W;ENSP00000399807:R30W;ENSP00000265334:R325W;ENSP00000428500:R136W;ENSP00000428689:R325W;ENSP00000430496:R325W;ENSP00000395559:R325W	ENSP00000265334:R325W	R	-	1	2	CDKL3	133672226	0.002000	0.14202	0.000000	0.03702	0.090000	0.18270	0.677000	0.25262	-0.113000	0.11958	0.454000	0.30748	AGG	.	.		0.323	CDKL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377697.1	NM_001113575		A	133644327	T	A	133644327	3	1	344	1	0	0	0	0	1	0	0	0	3157	1579	55	4	833	4	CDKL3	5	133644327	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	192613	133644327	47270933	452	47815										
DDX46	9879	hgsc.bcm.edu	37	chr5	134109540	134109540	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agggaaaaagtggagtttagAggacgatgatggtatatttt	14	1	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:134109540A>G	ENST00000354283.4	+	5	737	c.602A>G	c.(601-603)gAg>gGg	p.E201G	DDX46_ENST00000452510.2_Missense_Mutation_p.E201G			Q7L014	DDX46_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	201					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TGGAGTTTAGAGGACGATGAT	0.323																																					p.E201G	Colon(13;391 453 4901 21675 24897)	Atlas-SNP	.											.	DDX46	77	.	0			c.A602G						.						131	132	132					5																	134109540		2203	4300	6503	SO:0001583	missense	9879	exon5			GTTTAGAGGACGA		CCDS34240.1, CCDS75306.1	5q31.1	2010-01-25			ENSG00000145833	ENSG00000145833		"DEAD-boxes"	18681	protein-coding gene	gene with protein product							Standard	XM_005272142		Approved	KIAA0801, FLJ25329, PRPF5, Prp5	uc003kzw.3	Q7L014	OTTHUMG00000163072	ENST00000354283.4:c.602A>G	chr5.hg19:g.134109540A>G	ENSP00000346236:p.Glu201Gly	175.0	0.0		116.0	69.0	NM_014829	O94894|Q96EI0|Q9Y658	Missense_Mutation	SNP	ENST00000354283.4	hg19	CCDS34240.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.581343	0.86748	.	.	ENSG00000145833	ENST00000452510;ENST00000537371;ENST00000354283	T;T	0.50813	0.73;0.73	4.84	4.84	0.62591	.	0.100791	0.64402	D	0.000003	T	0.61999	0.2392	L	0.55213	1.73	0.80722	D	1	D	0.57899	0.981	D	0.65140	0.932	T	0.65619	-0.6124	10	0.72032	D	0.01	-22.5969	14.3642	0.66795	1.0:0.0:0.0:0.0	.	201	Q7L014	DDX46_HUMAN	G	201	ENSP00000416534:E201G;ENSP00000346236:E201G	ENSP00000346236:E201G	E	+	2	0	DDX46	134137439	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.758000	0.91663	1.934000	0.56057	0.528000	0.53228	GAG	.	.		0.323	DDX46-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371584.1	NM_014829		G	134109540	A	G	134109540	3	3	344	1	0	0	0	0	1	0	0	0	4366	304	11	2	620	2	DDX46	5	134109540	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	465213	134109540	46805720	453	47816										
DNAJC18	202052	hgsc.bcm.edu	37	chr5	138760775	138760775	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cggtaatagtaagtgtcatcTgtcacatttgaaaacatatg	8	6	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:138760775T>C	ENST00000302060.5	-	5	668	c.588A>G	c.(586-588)acA>acG	p.T196T		NM_152686.3	NP_689899.1	Q9H819	DJC18_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 18	196						integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			AAGTGTCATCTGTCACATTTG	0.433																																					p.T196T		Atlas-SNP	.											.	DNAJC18	30	.	0			c.A588G						.						210	200	204					5																	138760775		2203	4300	6503	SO:0001819	synonymous_variant	202052	exon5			GTCATCTGTCACA	AK024054	CCDS4214.1	5q31.2	2011-09-02		2005-08-09	ENSG00000170464	ENSG00000170464		"Heat shock proteins / DNAJ (HSP40)"	28429	protein-coding gene	gene with protein product							Standard	NM_152686		Approved	MGC29463	uc003len.3	Q9H819	OTTHUMG00000129225	ENST00000302060.5:c.588A>G	chr5.hg19:g.138760775T>C		57.0	0.0		53.0	27.0	NM_152686		Silent	SNP	ENST00000302060.5	hg19	CCDS4214.1																																																																																			.	.		0.433	DNAJC18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374191.1	NM_152686		C	138760775	T	C	138760775	2	2	344	1	0	0	0	0	0	0	0	1	4639	1567	55	2		2	DNAJC18	5	138760775	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	4651235	138760775	42154485	454	47817										
PSD2	84249	hgsc.bcm.edu	37	chr5	139193135	139193135	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgggcattggggacatggcgTttgagggggacatgggggca	21	5	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:139193135T>A	ENST00000274710.3	+	3	818	c.613T>A	c.(613-615)Ttt>Att	p.F205I		NM_032289.2	NP_115665.1	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	205					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(10)|liver(2)|lung(15)|ovary(1)|prostate(2)	38			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGACATGGCGTTTGAGGGGGA	0.687																																					p.F205I		Atlas-SNP	.											.	PSD2	88	.	0			c.T613A						.						32	39	36					5																	139193135		2202	4300	6502	SO:0001583	missense	84249	exon3			ATGGCGTTTGAGG	AL136559	CCDS4216.1	5q31.3	2013-01-10			ENSG00000146005	ENSG00000146005		"Pleckstrin homology (PH) domain containing"	19092	protein-coding gene	gene with protein product							Standard	NM_032289		Approved	DKFZp761B0514	uc003leu.1	Q9BQI7	OTTHUMG00000129240	ENST00000274710.3:c.613T>A	chr5.hg19:g.139193135T>A	ENSP00000274710:p.Phe205Ile	93.0	0.0		78.0	49.0	NM_032289	D3DQD3|Q8N3J8	Missense_Mutation	SNP	ENST00000274710.3	hg19	CCDS4216.1	.	.	.	.	.	.	.	.	.	.	T	3.924	-0.017582	0.07681	.	.	ENSG00000146005	ENST00000274710	T	0.10763	2.84	4.52	-2.19	0.07015	.	1.227030	0.05868	N	0.624119	T	0.03827	0.0108	N	0.03608	-0.345	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.41610	-0.9499	10	0.24483	T	0.36	.	2.1313	0.03751	0.1191:0.2133:0.1877:0.4799	.	205	Q9BQI7	PSD2_HUMAN	I	205	ENSP00000274710:F205I	ENSP00000274710:F205I	F	+	1	0	PSD2	139173319	0.000000	0.05858	0.330000	0.25442	0.137000	0.21094	-1.332000	0.02670	-0.125000	0.11703	-0.464000	0.05259	TTT	.	.		0.687	PSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251339.1	NM_032289		A	139193135	T	A	139193135	3	1	344	1	0	0	0	0	1	0	0	0	12659	1725	60	4	619	4	PSD2	5	139193135	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	432360	139193135	41722125	455	47818										
HARS	3035	hgsc.bcm.edu	37	chr5	140056273	140056273	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccacgatggagaaaatccgcTccaccccaatgctgagcccc	8	17	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:140056273T>C	ENST00000504156.1	-	10	1879	c.1160A>G	c.(1159-1161)gAg>gGg	p.E387G	HARS_ENST00000448240.1_Missense_Mutation_p.E192G|HARS_ENST00000431330.2_Missense_Mutation_p.E273G|HARS_ENST00000415192.2_Missense_Mutation_p.E313G|HARS_ENST00000307633.3_Missense_Mutation_p.E327G|HARS_ENST00000457527.2_Missense_Mutation_p.E367G|HARS_ENST00000504366.1_Missense_Mutation_p.E318G|HARS_ENST00000438307.2_Missense_Mutation_p.E347G	NM_002109.4	NP_002100.2	P12081	SYHC_HUMAN	histidyl-tRNA synthetase	387					gene expression (GO:0010467)|histidyl-tRNA aminoacylation (GO:0006427)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|histidine-tRNA ligase activity (GO:0004821)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	19			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		L-Histidine(DB00117)	GAAAATCCGCTCCACCCCAAT	0.567																																					p.E387G		Atlas-SNP	.											.	HARS	57	.	0			c.A1160G						.						137	134	135					5																	140056273		2203	4300	6503	SO:0001583	missense	3035	exon10			ATCCGCTCCACCC	AK000498	CCDS4237.1, CCDS58976.1, CCDS58977.1, CCDS58978.1, CCDS75323.1, CCDS75324.1	5q31.3	2012-10-02			ENSG00000170445	ENSG00000170445	6.1.1.21	"Aminoacyl tRNA synthetases / Class II"	4816	protein-coding gene	gene with protein product	"histidine tRNA ligase 1, cytoplasmic"	142810					Standard	XM_005268428		Approved		uc003lgv.4	P12081	OTTHUMG00000129502	ENST00000504156.1:c.1160A>G	chr5.hg19:g.140056273T>C	ENSP00000425634:p.Glu387Gly	120.0	0.0		76.0	28.0	NM_002109	B4DHQ1|B4DY73|D6REN6|J3KNE5	Missense_Mutation	SNP	ENST00000504156.1	hg19	CCDS4237.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.168936	0.78339	.	.	ENSG00000170445	ENST00000504156;ENST00000457527;ENST00000431330;ENST00000504366;ENST00000307633;ENST00000448240;ENST00000438307;ENST00000415192;ENST00000507746	T;T;T;T;T;T;T;T;T	0.72167	-0.63;-0.63;-0.63;-0.63;-0.63;-0.63;-0.63;-0.63;-0.63	5.64	5.64	0.86602	Aminoacyl-tRNA synthetase, class II (1);	0.000000	0.85682	D	0.000000	D	0.90177	0.6930	H	0.98048	4.135	0.80722	D	1	D;D;D;D;D;D;D;D	0.76494	0.999;0.998;0.999;0.996;0.992;0.997;0.996;0.969	D;D;D;D;D;D;D;P	0.83275	0.996;0.987;0.991;0.952;0.952;0.981;0.952;0.858	D	0.93570	0.6903	10	0.66056	D	0.02	-5.3317	16.1492	0.81602	0.0:0.0:0.0:1.0	.	277;273;313;327;347;387;367;387	B4DEA2;B4E1C5;B4DDD8;B4DHQ1;B4DY73;Q52NV4;D6REN6;P12081	.;.;.;.;.;.;.;SYHC_HUMAN	G	387;367;273;318;327;192;347;313;277	ENSP00000425634:E387G;ENSP00000387893:E367G;ENSP00000393244:E273G;ENSP00000430063:E318G;ENSP00000304668:E327G;ENSP00000413605:E192G;ENSP00000411511:E347G;ENSP00000411085:E313G;ENSP00000425889:E277G	ENSP00000304668:E327G	E	-	2	0	HARS	140036457	1.000000	0.71417	1.000000	0.80357	0.084000	0.17831	7.841000	0.86834	2.272000	0.75746	0.460000	0.39030	GAG	.	.		0.567	HARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251673.2	NM_002109		C	140056273	T	C	140056273	3	2	344	1	0	0	0	0	1	0	0	0	6968	1551	54	2	385	2	HARS	5	140056273	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	863138	140056273	40858987	456	47819										
PCDHA3	56145	hgsc.bcm.edu	37	chr5	140180880	140180880	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggggagcggccagctccactActccgtctctgaggaggcca	14	14	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:140180880A>T	ENST00000522353.2	+	1	98	c.98A>T	c.(97-99)tAc>tTc	p.Y33F	PCDHA2_ENST00000520672.2_Intron|PCDHA3_ENST00000532566.2_Missense_Mutation_p.Y33F|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA1_ENST00000504120.2_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	33	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGCTCCACTACTCCGTCTCT	0.662																																					p.Y33F		Atlas-SNP	.											.	PCDHA3	396	.	0			c.A98T						.						58	64	62					5																	140180880		2203	4300	6503	SO:0001583	missense	56145	exon1			TCCACTACTCCGT	AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"Cadherins / Protocadherins : Clustered"	8669	other	complex locus constituent	"KIAA0345-like 11"	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.98A>T	chr5.hg19:g.140180880A>T	ENSP00000429808:p.Tyr33Phe	25.0	0.0		34.0	17.0	NM_031497	O75286	Missense_Mutation	SNP	ENST00000522353.2	hg19	CCDS54915.1	.	.	.	.	.	.	.	.	.	.	a	16.11	3.029917	0.54790	.	.	ENSG00000255408	ENST00000522353;ENST00000532566	T;T	0.53857	0.6;0.6	4.65	4.65	0.58169	Cadherin, N-terminal (1);Cadherin (2);Cadherin-like (1);	0.000000	0.35646	U	0.003076	T	0.78220	0.4249	M	0.92412	3.305	0.39206	D	0.963235	D;D	0.89917	1.0;0.996	D;P	0.91635	0.999;0.892	D	0.85273	0.1057	10	0.72032	D	0.01	.	14.4173	0.67158	1.0:0.0:0.0:0.0	.	33;33	Q9Y5H8-2;Q9Y5H8	.;PCDA3_HUMAN	F	33	ENSP00000429808:Y33F;ENSP00000434086:Y33F	ENSP00000429808:Y33F	Y	+	2	0	PCDHA3	140161064	1.000000	0.71417	0.998000	0.56505	0.158000	0.22134	7.116000	0.77119	1.874000	0.54306	0.477000	0.44152	TAC	.	.		0.662	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906		T	140180880	A	T	140180880	3	4	344	1	0	0	0	0	1	0	0	0	11534	391	14	4	100	4	PCDHA3	5	140180880	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	124607	140180880	40734380	457	47820										
PCDHA7	56141	hgsc.bcm.edu	37	chr5	140215472	140215472	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tggagctgcgggtgggcgagCgcgcgctgtcgagctacgtg	20	10	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:140215472C>G	ENST00000525929.1	+	1	1504	c.1504C>G	c.(1504-1506)Cgc>Ggc	p.R502G	PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA7_ENST00000378125.3_Missense_Mutation_p.R502G|PCDHA4_ENST00000530339.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron	NM_018910.2	NP_061733.1	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7	502	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|biliary_tract(1)|breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTGGGCGAGCGCGCGCTGTC	0.682																																					p.R502G	NSCLC(160;258 2013 5070 22440 28951)	Atlas-SNP	.											.	PCDHA7	367	.	0			c.C1504G						.						63	67	65					5																	140215472		2203	4297	6500	SO:0001583	missense	56141	exon1			GGCGAGCGCGCGC	AF152485	CCDS54918.1	5q31	2010-11-26				ENSG00000204963		"Cadherins / Protocadherins : Clustered"	8673	other	complex locus constituent	"KIAA0345-like 7", "ortholog to mouse CNR4"	606313		CNRS4		10380929, 10662547	Standard	NM_018910		Approved	CNR4, CRNR4		Q9UN72		ENST00000525929.1:c.1504C>G	chr5.hg19:g.140215472C>G	ENSP00000436426:p.Arg502Gly	53.0	0.0		50.0	14.0	NM_031852	O75282	Missense_Mutation	SNP	ENST00000525929.1	hg19	CCDS54918.1	.	.	.	.	.	.	.	.	.	.	C	8.512	0.866848	0.17250	.	.	ENSG00000204963	ENST00000525929;ENST00000378125	T;T	0.01034	5.42;5.42	4.01	3.11	0.35812	Cadherin (4);Cadherin-like (1);	0.000000	0.31797	U	0.007047	T	0.01489	0.0048	N	0.16656	0.425	0.22127	N	0.999346	B;B	0.30179	0.103;0.271	B;P	0.46479	0.099;0.518	T	0.47824	-0.9087	10	0.51188	T	0.08	.	11.0894	0.48106	0.3367:0.6633:0.0:0.0	.	502;502	Q9UN72-2;Q9UN72	.;PCDA7_HUMAN	G	502	ENSP00000436426:R502G;ENSP00000367365:R502G	ENSP00000367365:R502G	R	+	1	0	PCDHA7	140195656	0.000000	0.05858	0.991000	0.47740	0.317000	0.28152	-0.386000	0.07370	0.764000	0.33197	0.306000	0.20318	CGC	.	.		0.682	PCDHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372887.2	NM_018910		G	140215472	C	G	140215472	3	3	344	1	0	0	0	0	1	0	0	0	11538	768	27	4	1506	4	PCDHA7	5	140215472	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	34592	140215472	40699788	458	47821										
PCDHA10	56139	hgsc.bcm.edu	37	chr5	140237048	140237048	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaacaacccgccaggctgccAcatcttcacggtgtctgcgt	10	15	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:140237048A>T	ENST00000307360.5	+	1	1415	c.1415A>T	c.(1414-1416)cAc>cTc	p.H472L	PCDHA10_ENST00000506939.2_Missense_Mutation_p.H472L|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA8_ENST00000531613.1_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	472	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(11)|cervix(1)|endometrium(11)|kidney(5)|large_intestine(13)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	79			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCAGGCTGCCACATCTTCACG	0.657																																					p.H472L		Atlas-SNP	.											.	PCDHA10	358	.	0			c.A1415T						.						91	89	90					5																	140237048		2196	4271	6467	SO:0001583	missense	56139	exon1			GCTGCCACATCTT	AF152475	CCDS34255.1, CCDS54921.1, CCDS75325.1	5q31	2010-11-26			ENSG00000250120	ENSG00000250120		"Cadherins / Protocadherins : Clustered"	8664	other	complex locus constituent	"KIAA0345-like 4", "ortholog to mouse CNR8"	606316		CNRS8		10380929	Standard	NM_018901		Approved	CNR8, CRNR8, CNRN8, PCDH-ALPHA10		Q9Y5I2	OTTHUMG00000163372	ENST00000307360.5:c.1415A>T	chr5.hg19:g.140237048A>T	ENSP00000304234:p.His472Leu	94.0	0.0		78.0	72.0	NM_031859	A1L493|O75280|Q9NRU2	Missense_Mutation	SNP	ENST00000307360.5	hg19	CCDS54921.1	.	.	.	.	.	.	.	.	.	.	A	8.225	0.803292	0.16397	.	.	ENSG00000250120	ENST00000506939;ENST00000307360	T;T	0.49432	4.71;0.78	3.86	3.86	0.44501	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.27134	0.0665	N	0.04655	-0.195	0.09310	N	1	B;B;P	0.40638	0.332;0.095;0.725	P;B;B	0.44359	0.447;0.16;0.236	T	0.07252	-1.0782	9	0.08599	T	0.76	.	9.8241	0.40901	0.8469:0.0:0.0:0.1531	.	472;472;472	Q9Y5I2-3;Q9Y5I2;Q9Y5I2-2	.;PCDAA_HUMAN;.	L	472	ENSP00000421030:H472L;ENSP00000304234:H472L	ENSP00000304234:H472L	H	+	2	0	PCDHA10	140217232	0.000000	0.05858	1.000000	0.80357	0.558000	0.35554	-0.065000	0.11617	1.744000	0.51775	0.454000	0.30748	CAC	.	.		0.657	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901		T	140237048	A	T	140237048	3	4	344	1	0	0	0	0	1	0	0	0	11529	159	6	4	1417	4	PCDHA10	5	140237048	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	21576	140237048	40678212	459	47822										
PCDHA10	56139	hgsc.bcm.edu	37	chr5	140237342	140237342	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gctgctggcgtctcccgctgGcagcgcgggcggtgcagtca	17	14	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:140237342G>T	ENST00000307360.5	+	1	1709	c.1709G>T	c.(1708-1710)gGc>gTc	p.G570V	PCDHA10_ENST00000506939.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA8_ENST00000531613.1_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	570					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(11)|cervix(1)|endometrium(11)|kidney(5)|large_intestine(13)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	79			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTCCCGCTGGCAGCGCGGGC	0.677																																					p.G570V		Atlas-SNP	.											.	PCDHA10	358	.	0			c.G1709T						.						32	33	33					5																	140237342		1322	2288	3610	SO:0001583	missense	56139	exon1			CCGCTGGCAGCGC	AF152475	CCDS34255.1, CCDS54921.1, CCDS75325.1	5q31	2010-11-26			ENSG00000250120	ENSG00000250120		"Cadherins / Protocadherins : Clustered"	8664	other	complex locus constituent	"KIAA0345-like 4", "ortholog to mouse CNR8"	606316		CNRS8		10380929	Standard	NM_018901		Approved	CNR8, CRNR8, CNRN8, PCDH-ALPHA10		Q9Y5I2	OTTHUMG00000163372	ENST00000307360.5:c.1709G>T	chr5.hg19:g.140237342G>T	ENSP00000304234:p.Gly570Val	25.0	0.0		24.0	21.0	NM_031859	A1L493|O75280|Q9NRU2	Missense_Mutation	SNP	ENST00000307360.5	hg19	CCDS54921.1	.	.	.	.	.	.	.	.	.	.	G	0.195	-1.049638	0.01981	.	.	ENSG00000250120	ENST00000307360	T	0.54279	0.58	3.46	2.58	0.30949	Cadherin-like (1);	.	.	.	.	T	0.27419	0.0673	N	0.10916	0.065	0.09310	N	1	B;B	0.22983	0.078;0.001	B;B	0.23852	0.049;0.02	T	0.15009	-1.0452	9	0.34782	T	0.22	.	0.8384	0.01145	0.2023:0.1532:0.3869:0.2576	.	570;570	Q9Y5I2-3;Q9Y5I2	.;PCDAA_HUMAN	V	570	ENSP00000304234:G570V	ENSP00000304234:G570V	G	+	2	0	PCDHA10	140217526	0.000000	0.05858	0.003000	0.11579	0.054000	0.15201	-2.442000	0.01014	0.787000	0.33731	0.491000	0.48974	GGC	.	.		0.677	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901		T	140237342	G	T	140237342	3	4	344	1	0	0	0	0	1	0	0	0	11529	1203	42	3	1711	3	PCDHA10	5	140237342	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	294	140237342	40677918	460	47823										
PCDHA12	56137	hgsc.bcm.edu	37	chr5	140257188	140257188	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tctgtgcggtgtccagcctgCtggtgctcacgctgctgctg	14	13	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:140257188C>T	ENST00000398631.2	+	1	2131	c.2131C>T	c.(2131-2133)Ctg>Ttg	p.L711L	PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA9_ENST00000532602.1_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	711					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(4)|breast(2)|cervix(1)|endometrium(19)|kidney(8)|large_intestine(8)|liver(2)|lung(25)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTCCAGCCTGCTGGTGCTCAC	0.672																																					p.L711L	Pancreas(113;759 1672 13322 24104 50104)	Atlas-SNP	.											.	PCDHA12	196	.	0			c.C2131T						.						40	40	40					5																	140257188		2203	4299	6502	SO:0001819	synonymous_variant	56137	exon1			AGCCTGCTGGTGC	AF152477	CCDS47285.1, CCDS75327.1	5q31	2010-11-26			ENSG00000251664	ENSG00000251664		"Cadherins / Protocadherins : Clustered"	8666	other	complex locus constituent	"KIAA0345-like 2"	606318				10380929	Standard	NM_018903		Approved	PCDH-ALPHA12	uc003lic.2	Q9UN75	OTTHUMG00000163366	ENST00000398631.2:c.2131C>T	chr5.hg19:g.140257188C>T		78.0	0.0		67.0	36.0	NM_018903	O75278|Q2M1N8	Silent	SNP	ENST00000398631.2	hg19	CCDS47285.1																																																																																			.	.		0.672	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903		T	140257188	C	T	140257188	2	4	344	1	0	0	0	0	0	0	0	1	11531	796	28	3		3	PCDHA12	5	140257188	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	19846	140257188	40658072	461	47824										
PCDHA13	56136	hgsc.bcm.edu	37	chr5	140263324	140263324	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cacaggagaacgcgctggtcTcctactcgctggtggagcgg	15	12	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:140263324T>A	ENST00000289272.2	+	1	1471	c.1471T>A	c.(1471-1473)Tcc>Acc	p.S491T	PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA13_ENST00000409494.1_Missense_Mutation_p.S491T|PCDHA9_ENST00000532602.1_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	491	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|biliary_tract(2)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(18)|liver(3)|lung(23)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGCGCTGGTCTCCTACTCGCT	0.657																																					p.S491T	Melanoma(147;1739 1852 5500 27947 37288)	Atlas-SNP	.											.	PCDHA13	213	.	0			c.T1471A						.						70	72	71					5																	140263324		2203	4299	6502	SO:0001583	missense	56136	exon1			CTGGTCTCCTACT	AF152478	CCDS4240.1	5q31	2010-11-26			ENSG00000239389	ENSG00000239389		"Cadherins / Protocadherins : Clustered"	8667	other	complex locus constituent	"KIAA0345-like 1", "ortholog of mouse CNR5"	606319		CNRS5		10380929, 10662547	Standard	NM_018904		Approved	CNR5, CRNR5, CNRN5, PCDH-ALPHA13		Q9Y5I0	OTTHUMG00000129614	ENST00000289272.2:c.1471T>A	chr5.hg19:g.140263324T>A	ENSP00000289272:p.Ser491Thr	102.0	0.0		80.0	37.0	NM_031865	O75277	Missense_Mutation	SNP	ENST00000289272.2	hg19	CCDS4240.1	.	.	.	.	.	.	.	.	.	.	T	7.509	0.654214	0.14580	.	.	ENSG00000239389	ENST00000409494;ENST00000289272	T;T	0.52295	0.67;0.67	4.62	3.43	0.39272	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.35566	0.0936	N	0.17564	0.495	0.21499	N	0.999663	P;P;P	0.46457	0.878;0.593;0.852	P;B;P	0.48524	0.58;0.29;0.546	T	0.08889	-1.0700	9	0.17832	T	0.49	.	8.3569	0.32335	0.4941:0.0:0.0:0.5059	.	491;491;491	Q9Y5I0;C9JA99;Q9Y5I0-2	PCDAD_HUMAN;.;.	T	491	ENSP00000386821:S491T;ENSP00000289272:S491T	ENSP00000289272:S491T	S	+	1	0	PCDHA13	140243508	0.000000	0.05858	0.999000	0.59377	0.363000	0.29612	-0.634000	0.05477	0.768000	0.33290	0.454000	0.30748	TCC	.	.		0.657	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904		A	140263324	T	A	140263324	3	1	344	1	0	0	0	0	1	0	0	0	11532	1551	54	4	1473	4	PCDHA13	5	140263324	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	6136	140263324	40651936	462	47825										
PCDHB3	56132	hgsc.bcm.edu	37	chr5	140480277	140480277	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcttagacaaaggcaagtctTgcttctctttgtttttctgg	8	8	4	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:140480277T>C	ENST00000231130.2	+	1	44	c.44T>C	c.(43-45)tTg>tCg	p.L15S	AC005754.7_ENST00000607216.1_RNA	NM_018937.2	NP_061760.1	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3	15					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	72			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AGGCAAGTCTTGCTTCTCTTT	0.507																																					p.L15S		Atlas-SNP	.											.	PCDHB3	208	.	0			c.T44C						.						92	103	99					5																	140480277		2203	4300	6503	SO:0001583	missense	56132	exon1			AAGTCTTGCTTCT	AF152496	CCDS4245.1	5q31	2010-01-26			ENSG00000113205	ENSG00000113205		"Cadherins / Protocadherins : Clustered"	8688	other	protocadherin		606329				10380929	Standard	NM_018937		Approved	PCDH-BETA3	uc003lio.3	Q9Y5E6	OTTHUMG00000129622	ENST00000231130.2:c.44T>C	chr5.hg19:g.140480277T>C	ENSP00000231130:p.Leu15Ser	112.0	0.0		77.0	29.0	NM_018937	B2R8P2	Missense_Mutation	SNP	ENST00000231130.2	hg19	CCDS4245.1	.	.	.	.	.	.	.	.	.	.	T	15.06	2.722321	0.48728	.	.	ENSG00000113205	ENST00000231130	T	0.55234	0.53	4.77	3.6	0.41247	.	.	.	.	.	T	0.55816	0.1944	M	0.91818	3.245	0.09310	N	1	P	0.38148	0.62	B	0.28232	0.087	T	0.60203	-0.7309	9	0.66056	D	0.02	.	9.7615	0.40534	0.0:0.0833:0.0:0.9167	.	15	Q9Y5E6	PCDB3_HUMAN	S	15	ENSP00000231130:L15S	ENSP00000231130:L15S	L	+	2	0	PCDHB3	140460461	0.038000	0.19896	0.931000	0.37212	0.976000	0.68499	2.445000	0.44899	1.904000	0.55121	0.533000	0.62120	TTG	.	.		0.507	PCDHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251817.2	NM_018937		C	140480277	T	C	140480277	3	2	344	1	0	0	0	0	1	0	0	0	11552	1821	63	2	46	2	PCDHB3	5	140480277	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	216953	140480277	40434983	463	47826										
PCDHB10	56126	hgsc.bcm.edu	37	chr5	140572209	140572209	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggagtgtccttggcaggttcTgggtttggacgttattcggt	16	6	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:140572209T>C	ENST00000239446.4	+	1	268	c.84T>C	c.(82-84)tcT>tcC	p.S28S		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	28					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGGCAGGTTCTGGGTTTGGAC	0.493																																					p.S28S		Atlas-SNP	.											.	PCDHB10	177	.	0			c.T84C						.						93	105	101					5																	140572209		2203	4300	6503	SO:0001819	synonymous_variant	56126	exon1			AGGTTCTGGGTTT	AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"Cadherins / Protocadherins : Clustered"	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.84T>C	chr5.hg19:g.140572209T>C		377.0	0.0		290.0	146.0	NM_018930	Q96T99	Silent	SNP	ENST00000239446.4	hg19	CCDS4252.1																																																																																			.	.		0.493	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930		C	140572209	T	C	140572209	2	2	344	1	0	0	0	0	0	0	0	1	11544	1567	55	2		2	PCDHB10	5	140572209	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	91932	140572209	40343051	464	47827										
PCDHGA3	56112	hgsc.bcm.edu	37	chr5	140725276	140725276	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gctggaccagaacgacaacgCgcccgagatcctgtaccccg	11	16	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:140725276C>T	ENST00000253812.6	+	1	1676	c.1676C>T	c.(1675-1677)gCg>gTg	p.A559V	PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3	559	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AACGACAACGCGCCCGAGATC	0.637																																					p.A559V		Atlas-SNP	.											PCDHGA3_ENST00000253812,extremity,malignant_melanoma,+1,1	PCDHGA3	246	.	0			c.C1676T						.						124	136	132					5																	140725276		2203	4300	6503	SO:0001583	missense	56112	exon1			ACAACGCGCCCGA	AF152510	CCDS47290.1, CCDS75329.1	5q31	2010-01-26			ENSG00000254245	ENSG00000254245		"Cadherins / Protocadherins : Clustered"	8701	other	protocadherin		606290				10380929	Standard	NM_032011		Approved	PCDH-GAMMA-A3		Q9Y5H0	OTTHUMG00000163680	ENST00000253812.6:c.1676C>T	chr5.hg19:g.140725276C>T	ENSP00000253812:p.Ala559Val	92.0	0.0		68.0	26.0	NM_032011	Q9Y5D4	Missense_Mutation	SNP	ENST00000253812.6	hg19	CCDS47290.1	.	.	.	.	.	.	.	.	.	.	.	7.930	0.740437	0.15642	.	.	ENSG00000254245	ENST00000253812	T	0.61510	0.1	5.42	1.51	0.23008	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	0.262435	0.19309	U	0.117443	T	0.53769	0.1817	M	0.70275	2.135	0.09310	N	1	B;B	0.18166	0.026;0.015	B;B	0.24394	0.053;0.01	T	0.49390	-0.8945	10	0.44086	T	0.13	.	9.1398	0.36897	0.0:0.6861:0.0:0.3139	.	559;559	Q9Y5H0-2;Q9Y5H0	.;PCDG3_HUMAN	V	559	ENSP00000253812:A559V	ENSP00000253812:A559V	A	+	2	0	PCDHGA3	140705460	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	0.500000	0.22562	0.047000	0.15862	0.563000	0.77884	GCG	.	.		0.637	PCDHGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377017.1	NM_018916		T	140725276	C	T	140725276	3	4	344	1	0	0	0	0	1	0	0	0	11564	768	27	1	1678	1	PCDHGA3	5	140725276	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	153067	140725276	40189984	465	47828										
PCDHGB3	56102	hgsc.bcm.edu	37	chr5	140751344	140751344	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcctcctacaccgtgcatgtAgctgagaacaatccgcctgg	10	14	0	1	rs368442078		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:140751344A>T	ENST00000576222.1	+	1	1514	c.1383A>T	c.(1381-1383)gtA>gtT	p.V461V	PCDHGA6_ENST00000517434.1_5'Flank|PCDHGB2_ENST00000522605.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA5_ENST00000518069.1_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3	461	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCGTGCATGTAGCTGAGAACA	0.562																																					p.V461V		Atlas-SNP	.											.	PCDHGB3	168	.	0			c.A1383T						.						147	151	149					5																	140751344		2141	4252	6393	SO:0001819	synonymous_variant	56102	exon1			GCATGTAGCTGAG	AF152519	CCDS58980.1, CCDS75334.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8710	other	protocadherin		606301				10380929	Standard	NM_018924		Approved	PCDH-GAMMA-B3		Q9Y5G1		ENST00000576222.1:c.1383A>T	chr5.hg19:g.140751344A>T		93.0	0.0		64.0	33.0	NM_018924	A7E229|Q9Y5C7	Silent	SNP	ENST00000576222.1	hg19	CCDS58980.1																																																																																			.	.		0.562	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924		T	140751344	A	T	140751344	2	4	344	1	0	0	0	0	0	0	0	1	11573	407	15	4		4	PCDHGB3	5	140751344	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	26068	140751344	40163916	466	47829										
PCDHGA10	56106	hgsc.bcm.edu	37	chr5	140793269	140793269	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctccctgcagagctatcagcTcagccccaataagcacttct	6	16	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:140793269T>A	ENST00000398610.2	+	1	527	c.527T>A	c.(526-528)cTc>cAc	p.L176H	PCDHGA2_ENST00000394576.2_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018913.2|NM_032090.1	NP_061736.1|NP_114479.1	Q9Y5H3	PCDGA_HUMAN	protocadherin gamma subfamily A, 10	176	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCTATCAGCTCAGCCCCAAT	0.532																																					p.L176H		Atlas-SNP	.											.	PCDHGA10	114	.	0			c.T527A						.						33	35	34					5																	140793269		1949	4147	6096	SO:0001583	missense	56106	exon1			ATCAGCTCAGCCC		CCDS47292.1, CCDS75343.1	5q31	2010-01-26			ENSG00000253846	ENSG00000253846		"Cadherins / Protocadherins : Clustered"	8697	other	protocadherin		606297				10380929	Standard	NM_018913		Approved	PCDH-GAMMA-A10		Q9Y5H3	OTTHUMG00000163688	ENST00000398610.2:c.527T>A	chr5.hg19:g.140793269T>A	ENSP00000381611:p.Leu176His	68.0	0.0		54.0	36.0	NM_032090	Q9Y5E0	Missense_Mutation	SNP	ENST00000398610.2	hg19	CCDS47292.1	.	.	.	.	.	.	.	.	.	.	t	20.5	4.009308	0.75046	.	.	ENSG00000253846	ENST00000398610	T	0.56941	0.43	5.49	5.49	0.81192	Cadherin (4);Cadherin-like (1);	.	.	.	.	D	0.86108	0.5854	H	0.99884	4.89	0.39070	D	0.960708	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.93462	0.6811	9	0.87932	D	0	.	15.5896	0.76517	0.0:0.0:0.0:1.0	.	176;176	Q9Y5H3-2;Q9Y5H3	.;PCDGA_HUMAN	H	176	ENSP00000381611:L176H	ENSP00000381611:L176H	L	+	2	0	PCDHGA10	140773453	1.000000	0.71417	1.000000	0.80357	0.801000	0.45260	8.040000	0.89188	2.094000	0.63399	0.455000	0.32223	CTC	.	.		0.532	PCDHGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374747.1	NM_018913		A	140793269	T	A	140793269	3	1	344	1	0	0	0	0	1	0	0	0	11560	1551	54	4	529	4	PCDHGA10	5	140793269	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	41925	140793269	40121991	467	47830										
PCDHGA10	56106	hgsc.bcm.edu	37	chr5	140794504	140794504	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tggcgccccgctccgcagagCccggctacctggtgaccaag	13	17	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:140794504C>T	ENST00000398610.2	+	1	1762	c.1762C>T	c.(1762-1764)Ccc>Tcc	p.P588S	PCDHGA2_ENST00000394576.2_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB7_ENST00000398594.2_5'Flank|PCDHGA9_ENST00000573521.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018913.2|NM_032090.1	NP_061736.1|NP_114479.1	Q9Y5H3	PCDGA_HUMAN	protocadherin gamma subfamily A, 10	588	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCCGCAGAGCCCGGCTACCT	0.667																																					p.P588S		Atlas-SNP	.											.	PCDHGA10	114	.	0			c.C1762T						.						81	96	91					5																	140794504		2200	4299	6499	SO:0001583	missense	56106	exon1			GCAGAGCCCGGCT		CCDS47292.1, CCDS75343.1	5q31	2010-01-26			ENSG00000253846	ENSG00000253846		"Cadherins / Protocadherins : Clustered"	8697	other	protocadherin		606297				10380929	Standard	NM_018913		Approved	PCDH-GAMMA-A10		Q9Y5H3	OTTHUMG00000163688	ENST00000398610.2:c.1762C>T	chr5.hg19:g.140794504C>T	ENSP00000381611:p.Pro588Ser	50.0	0.0		45.0	13.0	NM_032090	Q9Y5E0	Missense_Mutation	SNP	ENST00000398610.2	hg19	CCDS47292.1	.	.	.	.	.	.	.	.	.	.	c	12.48	1.950839	0.34471	.	.	ENSG00000253846	ENST00000398610	T	0.60797	0.16	5.63	3.82	0.43975	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.63570	0.2522	M	0.74546	2.27	0.22401	N	0.999131	B;B	0.33748	0.423;0.34	B;B	0.42282	0.382;0.367	T	0.56625	-0.7948	9	0.48119	T	0.1	.	10.6324	0.45545	0.0:0.6833:0.2479:0.0688	.	588;588	Q9Y5H3-2;Q9Y5H3	.;PCDGA_HUMAN	S	588	ENSP00000381611:P588S	ENSP00000381611:P588S	P	+	1	0	PCDHGA10	140774688	0.002000	0.14202	0.920000	0.36463	0.959000	0.62525	1.148000	0.31614	0.717000	0.32145	-0.182000	0.12963	CCC	.	.		0.667	PCDHGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374747.1	NM_018913		T	140794504	C	T	140794504	3	4	344	1	0	0	0	0	1	0	0	0	11560	739	26	3	1764	3	PCDHGA10	5	140794504	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1235	140794504	40120756	468	47831										
PCDHGC3	5098	hgsc.bcm.edu	37	chr5	140856012	140856012	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttgcactgtaactctggagtTggtagtggagaacccgctgg	14	8	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:140856012T>C	ENST00000308177.3	+	1	433	c.329T>C	c.(328-330)tTg>tCg	p.L110S	PCDHGA2_ENST00000394576.2_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB4_ENST00000519479.1_Intron|RN7SL68P_ENST00000488078.2_RNA|PCDHGA10_ENST00000398610.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_002588.2|NM_032402.1	NP_002579.2|NP_115778.1	Q9UN70	PCDGK_HUMAN	protocadherin gamma subfamily C, 3	110	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(2)|urinary_tract(1)	29			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACTCTGGAGTTGGTAGTGGAG	0.532																																					p.L110S		Atlas-SNP	.											.	PCDHGC3	173	.	0			c.T329C						.						95	97	96					5																	140856012		2203	4300	6503	SO:0001583	missense	5098	exon1			TGGAGTTGGTAGT	AF152337	CCDS4261.1, CCDS75347.1, CCDS75348.1	5q31	2010-01-26			ENSG00000240184	ENSG00000240184		"Cadherins / Protocadherins : Clustered"	8716	other	protocadherin	"cadherin-like 2", "protocadherin 2", "protocadherin 43"	603627		PCDH2		9360932, 8508762	Standard	NM_032402		Approved	PC-43, PC43, PCDH-GAMMA-C3		Q9UN70	OTTHUMG00000129613	ENST00000308177.3:c.329T>C	chr5.hg19:g.140856012T>C	ENSP00000312070:p.Leu110Ser	108.0	0.0		95.0	61.0	NM_032402	O60622|Q08192|Q9Y5C4	Missense_Mutation	SNP	ENST00000308177.3	hg19	CCDS4261.1	.	.	.	.	.	.	.	.	.	.	T	15.48	2.845296	0.51164	.	.	ENSG00000240184	ENST00000308177	T	0.38887	1.11	5.65	5.65	0.86999	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.58637	0.2136	M	0.77103	2.36	0.24690	N	0.993312	P;D	0.56287	0.92;0.975	P;P	0.56343	0.578;0.796	T	0.57528	-0.7796	9	0.66056	D	0.02	.	10.362	0.44001	0.0:0.0721:0.0:0.9278	.	110;110	Q9UN70;Q9UN70-2	PCDGK_HUMAN;.	S	110	ENSP00000312070:L110S	ENSP00000312070:L110S	L	+	2	0	PCDHGC3	140836196	0.999000	0.42202	1.000000	0.80357	0.885000	0.51271	4.095000	0.57728	2.371000	0.80710	0.533000	0.62120	TTG	.	.		0.532	PCDHGC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251808.2	NM_002588		C	140856012	T	C	140856012	3	2	344	1	0	0	0	0	1	0	0	0	11578	1821	63	2	331	2	PCDHGC3	5	140856012	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	61508	140856012	40059248	469	47832										
ADRB2	154	hgsc.bcm.edu	37	chr5	148206948	148206948	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccaggaagccatcaactgctAtgccaatgagacctgctgtg	10	12	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:148206948A>G	ENST00000305988.4	+	1	793	c.554A>G	c.(553-555)tAt>tGt	p.Y185C		NM_000024.5	NP_000015	P07550	ADRB2_HUMAN	adrenoceptor beta 2, surface	185					activation of adenylate cyclase activity (GO:0007190)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|bone resorption (GO:0045453)|brown fat cell differentiation (GO:0050873)|cell surface receptor signaling pathway (GO:0007166)|desensitization of G-protein coupled receptor protein signaling pathway by arrestin (GO:0002032)|diet induced thermogenesis (GO:0002024)|endosome to lysosome transport (GO:0008333)|heat generation (GO:0031649)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of smooth muscle contraction (GO:0045986)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor-mediated endocytosis (GO:0006898)|regulation of sodium ion transport (GO:0002028)|regulation of vasodilation (GO:0042312)|response to cold (GO:0009409)|vasodilation by norepinephrine-epinephrine involved in regulation of systemic arterial blood pressure (GO:0002025)	apical plasma membrane (GO:0016324)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	beta2-adrenergic receptor activity (GO:0004941)|norepinephrine binding (GO:0051380)|potassium channel regulator activity (GO:0015459)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(1)|lung(8)|ovary(1)|prostate(3)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Acebutolol(DB01193)|Alprenolol(DB00866)|Amitriptyline(DB00321)|Amphetamine(DB00182)|Arbutamine(DB01102)|Arformoterol(DB01274)|Asenapine(DB06216)|Atenolol(DB00335)|Bambuterol(DB01408)|Betaxolol(DB00195)|Bethanidine(DB00217)|Bevantolol(DB01295)|Bisoprolol(DB00612)|Bopindolol(DB08807)|Bupranolol(DB08808)|Cabergoline(DB00248)|Carteolol(DB00521)|Carvedilol(DB01136)|Clenbuterol(DB01407)|Desipramine(DB01151)|Dipivefrin(DB00449)|Dobutamine(DB00841)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Fenoterol(DB01288)|Formoterol(DB00983)|Indacaterol(DB05039)|Isoetarine(DB00221)|Isoprenaline(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Mephentermine(DB01365)|Metipranolol(DB01214)|Metoprolol(DB00264)|Mirtazapine(DB00370)|Nadolol(DB01203)|Nebivolol(DB04861)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Orciprenaline(DB00816)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Phenoxybenzamine(DB00925)|Phenylpropanolamine(DB00397)|Pindolol(DB00960)|Pirbuterol(DB01291)|Procaterol(DB01366)|Propranolol(DB00571)|Pseudoephedrine(DB00852)|Ritodrine(DB00867)|Salbutamol(DB01001)|Salmeterol(DB00938)|Sotalol(DB00489)|Terbutaline(DB00871)|Timolol(DB00373)|Trimipramine(DB00726)	ATCAACTGCTATGCCAATGAG	0.527																																					p.Y185C		Atlas-SNP	.											.	ADRB2	42	.	0			c.A554G						.						270	228	242					5																	148206948		2203	4300	6503	SO:0001583	missense	154	exon1			ACTGCTATGCCAA	AF022953	CCDS4292.1	5q31-q32	2012-08-08	2012-05-09		ENSG00000169252	ENSG00000169252		"GPCR / Class A : Adrenoceptors : beta"	286	protein-coding gene	gene with protein product		109690	"adrenergic, beta-2-, receptor, surface"	ADRB2R			Standard	NM_000024		Approved	ADRBR, BAR, B2AR	uc003lpr.2	P07550	OTTHUMG00000129933	ENST00000305988.4:c.554A>G	chr5.hg19:g.148206948A>G	ENSP00000305372:p.Tyr185Cys	53.0	0.0		51.0	19.0	NM_000024	B0LPE4|B2R7X2|O14823|O14824|O14825|O14826|Q4JG18|Q53GA6|Q6GMT4|Q6P4D8|Q8NEQ9|Q96EC3|Q9UCZ0|Q9UCZ1|Q9UCZ2|Q9UCZ3|Q9UH95|Q9UHA1|Q9UMZ5	Missense_Mutation	SNP	ENST00000305988.4	hg19	CCDS4292.1	.	.	.	.	.	.	.	.	.	.	A	15.24	2.775355	0.49786	.	.	ENSG00000169252	ENST00000305988	T	0.37915	1.17	5.65	5.65	0.86999	GPCR, rhodopsin-like superfamily (1);	0.343376	0.31113	N	0.008223	T	0.62208	0.2409	M	0.78344	2.41	0.42057	D	0.991142	D	0.89917	1.0	D	0.81914	0.995	T	0.67177	-0.5736	10	0.87932	D	0	.	16.0399	0.80667	1.0:0.0:0.0:0.0	.	185	P07550	ADRB2_HUMAN	C	185	ENSP00000305372:Y185C	ENSP00000305372:Y185C	Y	+	2	0	ADRB2	148187141	0.994000	0.37717	0.942000	0.38095	0.942000	0.58702	2.925000	0.48884	2.371000	0.80710	0.533000	0.62120	TAT	.	.		0.527	ADRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252189.1	NM_000024		G	148206948	A	G	148206948	3	3	344	1	0	0	0	0	1	0	0	0	341	449	16	2	556	2	ADRB2	5	148206948	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	7350936	148206948	32708312	470	47833										
SH3TC2	79628	hgsc.bcm.edu	37	chr5	148406142	148406142	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaccctgactcacctggcggTatttaggttccgataaagct	10	11	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:148406142T>A	ENST00000515425.1	-	12	3147	c.3046A>T	c.(3046-3048)Acc>Tcc	p.T1016S	SH3TC2_ENST00000513340.1_5'Flank|SH3TC2_ENST00000512049.1_Missense_Mutation_p.T1009S|SH3TC2_ENST00000394358.2_3'UTR|SH3TC2_ENST00000538184.1_Missense_Mutation_p.T563S	NM_024577.3	NP_078853.2	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	1016					cell death (GO:0008219)|peripheral nervous system myelin maintenance (GO:0032287)|regulation of ERBB signaling pathway (GO:1901184)|regulation of intracellular protein transport (GO:0033157)	cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CACCTGGCGGTATTTAGGTTC	0.542																																					p.T1016S		Atlas-SNP	.											.	SH3TC2	178	.	0			c.A3046T						.						82	88	86					5																	148406142		2203	4300	6503	SO:0001583	missense	79628	exon12			TGGCGGTATTTAG	AK127248	CCDS4293.1	5q32	2014-09-17			ENSG00000169247	ENSG00000169247		"Tetratricopeptide (TTC) repeat domain containing"	29427	protein-coding gene	gene with protein product		608206				14574644	Standard	NM_024577		Approved	KIAA1985, CMT4C	uc003lpu.3	Q8TF17	OTTHUMG00000129930	ENST00000515425.1:c.3046A>T	chr5.hg19:g.148406142T>A	ENSP00000423660:p.Thr1016Ser	167.0	0.0		126.0	58.0	NM_024577	B3KWE5|Q14CC0|Q14CF5|Q9H8I5	Missense_Mutation	SNP	ENST00000515425.1	hg19	CCDS4293.1	.	.	.	.	.	.	.	.	.	.	T	16.77	3.213916	0.58452	.	.	ENSG00000169247	ENST00000538184;ENST00000515425;ENST00000512049	D;T;T	0.82255	-1.59;-1.14;-1.15	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	D	0.84871	0.5568	L	0.60845	1.875	0.80722	D	1	D;D;D	0.54397	0.966;0.966;0.966	P;P;P	0.49799	0.622;0.622;0.622	D	0.86694	0.1925	10	0.66056	D	0.02	-11.1515	15.5409	0.76048	0.0:0.0:0.0:1.0	.	1009;1016;1016	Q14CC0;E9PDF1;Q8TF17	.;.;S3TC2_HUMAN	S	563;1016;1009	ENSP00000441427:T563S;ENSP00000423660:T1016S;ENSP00000421860:T1009S	ENSP00000425627:T1016S	T	-	1	0	SH3TC2	148386335	1.000000	0.71417	0.950000	0.38849	0.005000	0.04900	5.533000	0.67160	2.254000	0.74563	0.482000	0.46254	ACC	.	.		0.542	SH3TC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252186.2	NM_024577		A	148406142	T	A	148406142	3	1	344	1	0	0	0	0	1	0	0	0	14277	1638	57	4	844	4	SH3TC2	5	148406142	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	199194	148406142	32509118	471	47834										
CAMK2A	815	hgsc.bcm.edu	37	chr5	149602599	149602599	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctgtggaagtggacgatctgCcatttgccatcccggcggtg	14	11	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:149602599C>T	ENST00000348628.6	-	17	2051	c.1386G>A	c.(1384-1386)tgG>tgA	p.W462*	CAMK2A_ENST00000398376.3_Nonsense_Mutation_p.W473*|CAMK2A_ENST00000351010.6_5'UTR	NM_015981.3|NM_171825.2	NP_057065.2|NP_741960.1	Q9UQM7	KCC2A_HUMAN	calcium/calmodulin-dependent protein kinase II alpha	462					calcium ion transport (GO:0006816)|cytokine-mediated signaling pathway (GO:0019221)|G1/S transition of mitotic cell cycle (GO:0000082)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of neurotransmitter secretion (GO:0046928)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|kinase activity (GO:0016301)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|skin(1)|stomach(1)	15		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGACGATCTGCCATTTGCCAT	0.627																																					p.W473X		Atlas-SNP	.											.	CAMK2A	42	.	0			c.G1419A						.						70	83	78					5																	149602599		2184	4293	6477	SO:0001587	stop_gained	815	exon18			GATCTGCCATTTG	AB023185	CCDS43386.1, CCDS43387.1	5q32	2013-09-20	2008-10-30		ENSG00000070808	ENSG00000070808	2.7.11.17		1460	protein-coding gene	gene with protein product	"CaM-kinase II alpha chain", "calcium/calmodulin-dependent protein kinase II alpha-B subunit", "CaM kinase II alpha subunit", "CaMK-II alpha subunit", "calcium/calmodulin-dependent protein kinase type II alpha chain"	114078	"calcium/calmodulin-dependent protein kinase (CaM kinase) II alpha"	CAMKA		10231032, 3475713	Standard	NM_015981		Approved	KIAA0968, CaMKIINalpha	uc003lrt.2	Q9UQM7	OTTHUMG00000134281	ENST00000348628.6:c.1386G>A	chr5.hg19:g.149602599C>T	ENSP00000261793:p.Trp462*	61.0	0.0		39.0	20.0	NM_015981	Q9UL21|Q9Y2H4|Q9Y352	Nonsense_Mutation	SNP	ENST00000348628.6	hg19	CCDS43386.1	.	.	.	.	.	.	.	.	.	.	C	44	10.921969	0.99489	.	.	ENSG00000070808	ENST00000348628;ENST00000398376	.	.	.	5.15	5.15	0.70609	.	0.000000	0.64402	U	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.6945	0.91596	0.0:1.0:0.0:0.0	.	.	.	.	X	462;473	.	ENSP00000261793:W462X	W	-	3	0	CAMK2A	149582792	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.487000	0.81328	2.419000	0.82065	0.555000	0.69702	TGG	.	.		0.627	CAMK2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258869.2	NM_015981		T	149602599	C	T	149602599	4	4	344	1	0	0	0	0	0	1	0	0	2601	740	26	3	58	3	CAMK2A	5	149602599	Nonsense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1196457	149602599	31312661	472	47835										
SLC36A2	153201	hgsc.bcm.edu	37	chr5	150704910	150704910	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctccaaaccgcaggtagcccAgagccgccatgccaatgtat	9	15	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:150704910A>T	ENST00000335244.4	-	8	1076	c.947T>A	c.(946-948)cTg>cAg	p.L316Q	SLC36A2_ENST00000521967.1_Missense_Mutation_p.L316Q|SLC36A2_ENST00000450886.1_Missense_Mutation_p.L40Q	NM_181776.2	NP_861441.2	Q495M3	S36A2_HUMAN	solute carrier family 36 (proton/amino acid symporter), member 2	316					amino acid transport (GO:0006865)|ion transport (GO:0006811)|proline transmembrane transport (GO:0035524)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine transmembrane transporter activity (GO:0015187)|hydrogen:amino acid symporter activity (GO:0005280)|L-alanine transmembrane transporter activity (GO:0015180)|L-proline transmembrane transporter activity (GO:0015193)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(14)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Cycloserine(DB00260)	CAGGTAGCCCAGAGCCGCCAT	0.537																																					p.L316Q		Atlas-SNP	.											.	SLC36A2	71	.	0			c.T947A						.						86	72	77					5																	150704910		2203	4300	6503	SO:0001583	missense	153201	exon8			TAGCCCAGAGCCG	AY162214	CCDS4315.1	5q33.1	2013-05-22			ENSG00000186335	ENSG00000186335		"Solute carriers"	18762	protein-coding gene	gene with protein product		608331				11959859	Standard	NM_181776		Approved	PAT2, tramdorin, TRAMD1	uc003lty.3	Q495M3	OTTHUMG00000130129	ENST00000335244.4:c.947T>A	chr5.hg19:g.150704910A>T	ENSP00000334223:p.Leu316Gln	69.0	0.0		40.0	17.0	NM_181776	Q495M4|Q495M6|Q6ZWK5|Q7Z6B5	Missense_Mutation	SNP	ENST00000335244.4	hg19	CCDS4315.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.94|18.94	3.729237|3.729237	0.69074|0.69074	.|.	.|.	ENSG00000186335|ENSG00000186335	ENST00000335244;ENST00000450886;ENST00000521967|ENST00000523044	T;T;T|.	0.02656|.	4.21;4.21;4.21|.	4.82|4.82	4.82|4.82	0.62117|0.62117	.|.	0.076390|.	0.56097|.	D|.	0.000039|.	D|D	0.86016|0.86016	0.5832|0.5832	H|H	0.94306|0.94306	3.52|3.52	0.50171|0.50171	D|D	0.999855|0.999855	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.83275|.	0.994;0.996|.	D|D	0.90122|0.90122	0.4200|0.4200	10|5	0.72032|.	D|.	0.01|.	-13.885|-13.885	14.8532|14.8532	0.70313|0.70313	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	316;316|.	E5RJJ5;Q495M3|.	.;S36A2_HUMAN|.	Q|R	316;40;316|69	ENSP00000334223:L316Q;ENSP00000399479:L40Q;ENSP00000430535:L316Q|.	ENSP00000334223:L316Q|.	L|W	-|-	2|1	0|0	SLC36A2|SLC36A2	150685103|150685103	1.000000|1.000000	0.71417|0.71417	0.950000|0.950000	0.38849|0.38849	0.416000|0.416000	0.31233|0.31233	8.727000|8.727000	0.91480|0.91480	2.150000|2.150000	0.67090|0.67090	0.383000|0.383000	0.25322|0.25322	CTG|TGG	.	.		0.537	SLC36A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252437.1			T	150704910	A	T	150704910	3	4	344	1	0	0	0	0	1	0	0	0	14609	188	7	4	516	4	SLC36A2	5	150704910	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1102311	150704910	30210350	473	47836										
FAT2	2196	hgsc.bcm.edu	37	chr5	150945854	150945854	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gctctgattcgcggtccaggTgtcctgtaacaaccagttcc	10	13	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:150945854T>G	ENST00000261800.5	-	1	2651	c.2639A>C	c.(2638-2640)cAc>cCc	p.H880P		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	880	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GCGGTCCAGGTGTCCTGTAAC	0.562																																					p.H880P		Atlas-SNP	.											.	FAT2	465	.	0			c.A2639C						.						97	93	94					5																	150945854		2203	4300	6503	SO:0001583	missense	2196	exon1			TCCAGGTGTCCTG	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.2639A>C	chr5.hg19:g.150945854T>G	ENSP00000261800:p.His880Pro	107.0	0.0		84.0	33.0	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	hg19	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	T	0.829	-0.745787	0.03065	.	.	ENSG00000086570	ENST00000261800	T	0.43294	0.95	5.67	-3.45	0.04781	Cadherin (4);Cadherin-like (1);	0.720404	0.13315	N	0.397194	T	0.09992	0.0245	N	0.00260	-1.75	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.37549	-0.9701	10	0.05525	T	0.97	.	16.3018	0.82820	0.0:0.0732:0.7722:0.1546	.	880	Q9NYQ8	FAT2_HUMAN	P	880	ENSP00000261800:H880P	ENSP00000261800:H880P	H	-	2	0	FAT2	150926047	0.002000	0.14202	0.012000	0.15200	0.819000	0.46315	0.642000	0.24735	-0.454000	0.07066	0.459000	0.35465	CAC	.	.		0.562	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		G	150945854	T	G	150945854	3	3	344	1	0	0	0	0	1	0	0	0	5698	1696	59	5	10502	5	FAT2	5	150945854	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	240944	150945854	29969406	474	47837										
FAT2	2196	hgsc.bcm.edu	37	chr5	150946124	150946124	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgcccaggtcatatactgttAcattgaggatgtagaaattg	10	6	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:150946124A>G	ENST00000261800.5	-	1	2381	c.2369T>C	c.(2368-2370)gTa>gCa	p.V790A		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	790	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ATATACTGTTACATTGAGGAT	0.517																																					p.V790A		Atlas-SNP	.											.	FAT2	465	.	0			c.T2369C						.						77	75	75					5																	150946124		2203	4300	6503	SO:0001583	missense	2196	exon1			ACTGTTACATTGA	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.2369T>C	chr5.hg19:g.150946124A>G	ENSP00000261800:p.Val790Ala	52.0	0.0		51.0	24.0	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	hg19	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	A	15.76	2.929958	0.52759	.	.	ENSG00000086570	ENST00000261800	T	0.59364	0.27	5.78	5.78	0.91487	Cadherin (4);Cadherin-like (1);	0.546274	0.17783	N	0.162145	T	0.60599	0.2281	M	0.70842	2.15	0.43199	D	0.995045	P	0.36990	0.577	B	0.36378	0.223	T	0.65813	-0.6077	10	0.87932	D	0	.	16.3979	0.83621	1.0:0.0:0.0:0.0	.	790	Q9NYQ8	FAT2_HUMAN	A	790	ENSP00000261800:V790A	ENSP00000261800:V790A	V	-	2	0	FAT2	150926317	1.000000	0.71417	0.072000	0.20136	0.900000	0.52787	7.500000	0.81588	2.333000	0.79357	0.533000	0.62120	GTA	.	.		0.517	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		G	150946124	A	G	150946124	3	3	344	1	0	0	0	0	1	0	0	0	5698	391	14	2	10772	2	FAT2	5	150946124	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	270	150946124	29969136	475	47838										
C5orf4	10826	hgsc.bcm.edu	37	chr5	154200873	154200873	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggcaggaagggaaggtggtaGccacagtgggagatggtggt	21	4	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:154200873G>A	ENST00000326080.5	-	8	1215	c.792C>T	c.(790-792)ggC>ggT	p.G264G	FAXDC2_ENST00000517938.1_Silent_p.G241G|FAXDC2_ENST00000523997.1_5'Flank	NM_032385.3	NP_115761.2	Q96IV6	FXDC2_HUMAN	fatty acid hydroxylase domain containing 2	264					fatty acid biosynthetic process (GO:0006633)	integral component of membrane (GO:0016021)	iron ion binding (GO:0005506)|oxidoreductase activity (GO:0016491)										GAAGGTGGTAGCCACAGTGGG	0.542																																					p.G264G		Atlas-SNP	.											.	.	.	.	0			c.C792T						.						211	220	217					5																	154200873		2126	4233	6359	SO:0001819	synonymous_variant	10826	exon8			GTGGTAGCCACAG	AF159165	CCDS43390.1	5q31-q32	2013-03-04	2013-03-04	2013-03-04	ENSG00000170271	ENSG00000170271		"Fatty acid hydroxylase domain containing"	1334	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 4"	C5orf4		10843801	Standard	NM_032385		Approved	FLJ13758	uc003lvs.4	Q96IV6	OTTHUMG00000164141	ENST00000326080.5:c.792C>T	chr5.hg19:g.154200873G>A		217.0	1.0		164.0	83.0	NM_032385	B4DIE1|Q9BSX6|Q9H8C7	Silent	SNP	ENST00000326080.5	hg19	CCDS43390.1																																																																																			.	.		0.542	FAXDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377429.1	NM_032385		A	154200873	G	A	154200873	2	1	344	1	0	0	0	0	0	0	0	1	2300	958	34	3		3	C5orf4	5	154200873	Silent	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	3254749	154200873	26714387	476	47839										
GEMIN5	25929	hgsc.bcm.edu	37	chr5	154287223	154287223	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttcttggtctgacacaccatTctcaacaggtcctgagttct	7	12	4	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:154287223T>C	ENST00000285873.7	-	16	2398	c.2323A>G	c.(2323-2325)Aat>Gat	p.N775D		NM_001252156.1|NM_015465.4	NP_001239085.1|NP_056280.2	Q8TEQ6	GEMI5_HUMAN	gem (nuclear organelle) associated protein 5	775					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|protein complex assembly (GO:0006461)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)	poly(A) RNA binding (GO:0044822)|snRNA binding (GO:0017069)			breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			GACACACCATTCTCAACAGGT	0.488																																					p.N775D		Atlas-SNP	.											.	GEMIN5	120	.	0			c.A2323G						.						178	160	166					5																	154287223		2203	4300	6503	SO:0001583	missense	25929	exon16			CACCATTCTCAAC	AK022748	CCDS4330.1	5q34	2013-01-10			ENSG00000082516	ENSG00000082516		"WD repeat domain containing"	20043	protein-coding gene	gene with protein product		607005				11714716	Standard	NM_015465		Approved		uc003lvx.3	Q8TEQ6	OTTHUMG00000130189	ENST00000285873.7:c.2323A>G	chr5.hg19:g.154287223T>C	ENSP00000285873:p.Asn775Asp	132.0	0.0		89.0	28.0	NM_015465	Q14CV0|Q8WWV4|Q969W4|Q9H9K3|Q9UFI5	Missense_Mutation	SNP	ENST00000285873.7	hg19	CCDS4330.1	.	.	.	.	.	.	.	.	.	.	T	16.34	3.094565	0.56075	.	.	ENSG00000082516	ENST00000285873	T	0.71698	-0.59	5.63	5.63	0.86233	.	0.160638	0.56097	D	0.000040	T	0.82038	0.4950	M	0.67953	2.075	0.41155	D	0.986053	D;D	0.69078	0.997;0.997	D;D	0.75020	0.985;0.985	T	0.83344	-0.0006	10	0.52906	T	0.07	-25.1726	14.6746	0.68969	0.0:0.0:0.0:1.0	.	774;775	B7ZLC9;Q8TEQ6	.;GEMI5_HUMAN	D	775	ENSP00000285873:N775D	ENSP00000285873:N775D	N	-	1	0	GEMIN5	154267416	1.000000	0.71417	0.952000	0.39060	0.279000	0.26890	3.072000	0.50049	2.137000	0.66172	0.460000	0.39030	AAT	.	.		0.488	GEMIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252507.1			C	154287223	T	C	154287223	3	2	344	1	0	0	0	0	1	0	0	0	6339	1783	62	2	2255	2	GEMIN5	5	154287223	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	86350	154287223	26628037	477	47840										
GEMIN5	25929	hgsc.bcm.edu	37	chr5	154317547	154317547	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cctcgaaacgggggtgtcccTggactctcgcctgcgcccgg	14	16	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:154317547T>C	ENST00000285873.7	-	1	222	c.147A>G	c.(145-147)ccA>ccG	p.P49P		NM_001252156.1|NM_015465.4	NP_001239085.1|NP_056280.2	Q8TEQ6	GEMI5_HUMAN	gem (nuclear organelle) associated protein 5	49					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|protein complex assembly (GO:0006461)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)	poly(A) RNA binding (GO:0044822)|snRNA binding (GO:0017069)			breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			GGGGTGTCCCTGGACTCTCGC	0.701																																					p.P49P		Atlas-SNP	.											.	GEMIN5	120	.	0			c.A147G						.						19	22	21					5																	154317547		2200	4299	6499	SO:0001819	synonymous_variant	25929	exon1			TGTCCCTGGACTC	AK022748	CCDS4330.1	5q34	2013-01-10			ENSG00000082516	ENSG00000082516		"WD repeat domain containing"	20043	protein-coding gene	gene with protein product		607005				11714716	Standard	NM_015465		Approved		uc003lvx.3	Q8TEQ6	OTTHUMG00000130189	ENST00000285873.7:c.147A>G	chr5.hg19:g.154317547T>C		139.0	0.0		127.0	60.0	NM_015465	Q14CV0|Q8WWV4|Q969W4|Q9H9K3|Q9UFI5	Silent	SNP	ENST00000285873.7	hg19	CCDS4330.1																																																																																			.	.		0.701	GEMIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252507.1			C	154317547	T	C	154317547	2	2	344	1	0	0	0	0	0	0	0	1	6339	1567	55	2		2	GEMIN5	5	154317547	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	30324	154317547	26597713	478	47841										
SOX30	11063	hgsc.bcm.edu	37	chr5	157065688	157065688	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtgtgacagggcttgggctcTggactgcaggtgtgggcagc	19	8	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:157065688T>A	ENST00000265007.6	-	4	1771	c.1430A>T	c.(1429-1431)cAg>cTg	p.Q477L	SOX30_ENST00000311371.5_Intron|SOX30_ENST00000519442.1_Missense_Mutation_p.Q172L	NM_178424.1	NP_848511.1	O94993	SOX30_HUMAN	SRY (sex determining region Y)-box 30	477					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to corticosteroid (GO:0031960)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	23	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GCTTGGGCTCTGGACTGCAGG	0.493																																					p.Q477L	Esophageal Squamous(31;525 799 19355 21125 41744)	Atlas-SNP	.											SOX30,NS,haematopoietic_neoplasm,0,1	SOX30	67	.	0			c.A1430T						.						62	63	63					5																	157065688		2203	4300	6503	SO:0001583	missense	11063	exon4			GGGCTCTGGACTG	AB022083	CCDS4339.1, CCDS4340.1	5q33	2010-10-21			ENSG00000039600	ENSG00000039600		"SRY (sex determining region Y)-boxes"	30635	protein-coding gene	gene with protein product		606698				15019997, 11678506	Standard	NM_178424		Approved		uc003lxb.1	O94993	OTTHUMG00000130247	ENST00000265007.6:c.1430A>T	chr5.hg19:g.157065688T>A	ENSP00000265007:p.Gln477Leu	71.0	0.0		55.0	29.0	NM_178424	O94995|Q8IYX6	Missense_Mutation	SNP	ENST00000265007.6	hg19	CCDS4339.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.183815	0.78677	.	.	ENSG00000039600	ENST00000265007;ENST00000519442	D;D	0.98105	-4.43;-4.72	5.49	5.49	0.81192	.	0.000000	0.56097	D	0.000028	D	0.97294	0.9115	L	0.27053	0.805	0.43959	D	0.996639	P;D	0.63880	0.682;0.993	B;D	0.69824	0.307;0.966	D	0.98452	1.0592	10	0.87932	D	0	.	14.1601	0.65441	0.0:0.0:0.0:1.0	.	172;477	B4DXW7;O94993	.;SOX30_HUMAN	L	477;172	ENSP00000265007:Q477L;ENSP00000427984:Q172L	ENSP00000265007:Q477L	Q	-	2	0	SOX30	156998266	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	3.497000	0.53295	2.088000	0.63022	0.528000	0.53228	CAG	.	.		0.493	SOX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252571.2	NM_007017		A	157065688	T	A	157065688	3	1	344	1	0	0	0	0	1	0	0	0	14967	1580	55	4	839	4	SOX30	5	157065688	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2748141	157065688	23849572	479	47842										
PWWP2A	114825	hgsc.bcm.edu	37	chr5	159519900	159519900	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atttcaaatcatctgtgctaTcaatgctacacactgaagca	5	10	4	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:159519900T>A	ENST00000307063.7	-	2	1791	c.1757A>T	c.(1756-1758)gAt>gTt	p.D586V	PWWP2A_ENST00000456329.3_Intron|PWWP2A_ENST00000523662.1_Intron	NM_001130864.1	NP_001124336.1	Q96N64	PWP2A_HUMAN	PWWP domain containing 2A	586	Ser-rich.									kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ATCTGTGCTATCAATGCTACA	0.413																																					p.D586V		Atlas-SNP	.											.	PWWP2A	64	.	0			c.A1757T						.						111	94	99					5																	159519900		692	1591	2283	SO:0001583	missense	114825	exon2			GTGCTATCAATGC		CCDS47331.1, CCDS47332.1, CCDS58990.1	5q33.3	2011-03-23			ENSG00000170234	ENSG00000170234			29406	protein-coding gene	gene with protein product							Standard	NM_052927		Approved	KIAA1935	uc011ded.2	Q96N64	OTTHUMG00000163546	ENST00000307063.7:c.1757A>T	chr5.hg19:g.159519900T>A	ENSP00000305151:p.Asp586Val	41.0	0.0		33.0	13.0	NM_001130864	G5EA07|Q2HJJ2|Q8IYR3|Q96PV3	Missense_Mutation	SNP	ENST00000307063.7	hg19	CCDS47332.1	.	.	.	.	.	.	.	.	.	.	T	16.80	3.223178	0.58668	.	.	ENSG00000170234	ENST00000307063	T	0.64618	-0.11	5.78	5.78	0.91487	.	.	.	.	.	T	0.70219	0.3199	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	T	0.73949	-0.3821	9	0.87932	D	0	-21.4486	15.7761	0.78220	0.0:0.0:0.0:1.0	.	586	Q96N64	PWP2A_HUMAN	V	586	ENSP00000305151:D586V	ENSP00000305151:D586V	D	-	2	0	PWWP2A	159452478	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.109000	0.71528	2.200000	0.70718	0.460000	0.39030	GAT	.	.		0.413	PWWP2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374092.1			A	159519900	T	A	159519900	3	1	344	1	0	0	0	0	1	0	0	0	12860	1435	50	4	656	4	PWWP2A	5	159519900	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2454212	159519900	21395360	480	47843										
PWWP2A	114825	hgsc.bcm.edu	37	chr5	159519933	159519933	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctgaagcactggaagagtcaGatttcttttgatttagggtc	11	6	2	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:159519933G>C	ENST00000307063.7	-	2	1758	c.1724C>G	c.(1723-1725)tCt>tGt	p.S575C	PWWP2A_ENST00000456329.3_Intron|PWWP2A_ENST00000523662.1_Intron	NM_001130864.1	NP_001124336.1	Q96N64	PWP2A_HUMAN	PWWP domain containing 2A	575	Ser-rich.									kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GGAAGAGTCAGATTTCTTTTG	0.403																																					p.S575C		Atlas-SNP	.											.	PWWP2A	64	.	0			c.C1724G						.						142	118	125					5																	159519933		692	1591	2283	SO:0001583	missense	114825	exon2			GAGTCAGATTTCT		CCDS47331.1, CCDS47332.1, CCDS58990.1	5q33.3	2011-03-23			ENSG00000170234	ENSG00000170234			29406	protein-coding gene	gene with protein product							Standard	NM_052927		Approved	KIAA1935	uc011ded.2	Q96N64	OTTHUMG00000163546	ENST00000307063.7:c.1724C>G	chr5.hg19:g.159519933G>C	ENSP00000305151:p.Ser575Cys	45.0	0.0		39.0	17.0	NM_001130864	G5EA07|Q2HJJ2|Q8IYR3|Q96PV3	Missense_Mutation	SNP	ENST00000307063.7	hg19	CCDS47332.1	.	.	.	.	.	.	.	.	.	.	G	11.47	1.648727	0.29336	.	.	ENSG00000170234	ENST00000307063	T	0.57752	0.38	5.78	4.89	0.63831	.	.	.	.	.	T	0.41373	0.1156	N	0.19112	0.55	0.38882	D	0.95693	B	0.09022	0.002	B	0.09377	0.004	T	0.33929	-0.9849	9	0.72032	D	0.01	-5.727	16.3168	0.82931	0.0:0.1326:0.8674:0.0	.	575	Q96N64	PWP2A_HUMAN	C	575	ENSP00000305151:S575C	ENSP00000305151:S575C	S	-	2	0	PWWP2A	159452511	1.000000	0.71417	0.833000	0.33012	0.986000	0.74619	7.467000	0.80930	1.402000	0.46780	0.563000	0.77884	TCT	.	.		0.403	PWWP2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374092.1			C	159519933	G	C	159519933	3	2	344	1	0	0	0	0	1	0	0	0	12860	942	33	4	689	4	PWWP2A	5	159519933	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	33	159519933	21395327	481	47844										
GABRB2	2561	hgsc.bcm.edu	37	chr5	160753450	160753450	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtagggtcccacaaggatcgAtattgggtcccattttgttt	11	8	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:160753450A>G	ENST00000393959.1	-	9	1115	c.1116T>C	c.(1114-1116)taT>taC	p.Y372Y	GABRB2_ENST00000274547.2_Silent_p.Y372Y|GABRB2_ENST00000517901.1_Intron|GABRB2_ENST00000353437.6_Intron|GABRB2_ENST00000520240.1_Intron|GABRB2_ENST00000517547.1_Intron			P47870	GBRB2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 2	372					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|GABA-A receptor activity (GO:0004890)|inhibitory extracellular ligand-gated ion channel activity (GO:0005237)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(9)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	26	Renal(175;0.00259)	Medulloblastoma(196;0.021)|all_neural(177;0.0463)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	acaaggatcgatattgggtcc	0.383																																					p.Y372Y		Atlas-SNP	.											.	GABRB2	161	.	0			c.T1116C						.						103	104	104					5																	160753450		2203	4300	6503	SO:0001819	synonymous_variant	2561	exon10			GGATCGATATTGG		CCDS4354.1, CCDS4355.1	5q34	2012-06-22			ENSG00000145864	ENSG00000145864		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4082	protein-coding gene	gene with protein product	"GABA(A) receptor, beta 2"	600232				7851879	Standard	NM_000813		Approved		uc003lys.1	P47870	OTTHUMG00000130349	ENST00000393959.1:c.1116T>C	chr5.hg19:g.160753450A>G		53.0	0.0		55.0	16.0	NM_021911	A8K115|A8K1A0|D1LYT0|D1LYT1|Q16323|Q4FZB2	Silent	SNP	ENST00000393959.1	hg19	CCDS4355.1																																																																																			.	.		0.383	GABRB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252704.1			G	160753450	A	G	160753450	2	3	344	1	0	0	0	0	0	0	0	1	6175	340	12	2		2	GABRB2	5	160753450	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1233517	160753450	20161810	482	47845										
DOCK2	1794	hgsc.bcm.edu	37	chr5	169122911	169122911	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	actggtgcaaagaagtgcacGcagggactgaggaggccctt	15	9	0	2	rs199921409		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:169122911G>T	ENST00000256935.8	+	10	1028	c.948G>T	c.(946-948)acG>acT	p.T316T		NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	316					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			AGAAGTGCACGCAGGGACTGA	0.453																																					p.T316T		Atlas-SNP	.											.	DOCK2	389	.	0			c.G948T						.						75	77	76					5																	169122911		2203	4300	6503	SO:0001819	synonymous_variant	1794	exon10			GTGCACGCAGGGA	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.948G>T	chr5.hg19:g.169122911G>T		75.0	0.0		56.0	16.0	NM_004946	Q2M3I0|Q96AK7	Silent	SNP	ENST00000256935.8	hg19	CCDS4371.1																																																																																			.	G|0.999;A|0.001		0.453	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		T	169122911	G	T	169122911	2	4	344	1	0	0	0	0	0	0	0	1	4689	1074	38	1		1	DOCK2	5	169122911	Silent	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	8369461	169122911	11792349	483	47846										
DOCK2	1794	hgsc.bcm.edu	37	chr5	169144485	169144485	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tttcagtgcgaccttggcttAcaagtaagtaattgtgcaca	9	8	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:169144485A>T	ENST00000256935.8	+	21	2209	c.2129A>T	c.(2128-2130)tAc>tTc	p.Y710F	DOCK2_ENST00000520908.1_Missense_Mutation_p.Y202F|DOCK2_ENST00000540750.1_5'UTR	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	710					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ACCTTGGCTTACAAGTAAGTA	0.448																																					p.Y710F		Atlas-SNP	.											.	DOCK2	389	.	0			c.A2129T						.						193	162	173					5																	169144485		2203	4300	6503	SO:0001583	missense	1794	exon21			TGGCTTACAAGTA	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.2129A>T	chr5.hg19:g.169144485A>T	ENSP00000256935:p.Tyr710Phe	96.0	0.0		64.0	35.0	NM_004946	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	hg19	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	A	19.56	3.850834	0.71719	.	.	ENSG00000134516	ENST00000256935;ENST00000520908	T;T	0.21191	2.02;2.02	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	T	0.39627	0.1085	L	0.56769	1.78	0.80722	D	1	D;D	0.65815	0.995;0.993	D;P	0.63113	0.911;0.753	T	0.09037	-1.0693	10	0.35671	T	0.21	.	15.1005	0.72273	1.0:0.0:0.0:0.0	.	202;710	E7ERW7;Q92608	.;DOCK2_HUMAN	F	710;202	ENSP00000256935:Y710F;ENSP00000429283:Y202F	ENSP00000256935:Y710F	Y	+	2	0	DOCK2	169077063	1.000000	0.71417	1.000000	0.80357	0.865000	0.49528	9.192000	0.94947	1.968000	0.57251	0.533000	0.62120	TAC	.	.		0.448	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		T	169144485	A	T	169144485	3	4	344	1	0	0	0	0	1	0	0	0	4689	391	14	4	2211	4	DOCK2	5	169144485	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	21574	169144485	11770775	484	47847										
DOCK2	1794	hgsc.bcm.edu	37	chr5	169188534	169188534	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgccctcagccaactcctgtAtgagttctacacctgcatcc	6	16	2	1	rs370192291		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:169188534A>C	ENST00000256935.8	+	25	2539	c.2459A>C	c.(2458-2460)tAt>tCt	p.Y820S	DOCK2_ENST00000520908.1_Missense_Mutation_p.Y312S|DOCK2_ENST00000523351.1_3'UTR|DOCK2_ENST00000540750.1_5'UTR	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	820					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CAACTCCTGTATGAGTTCTAC	0.488																																					p.Y820S		Atlas-SNP	.											.	DOCK2	389	.	0			c.A2459C						.						198	181	187					5																	169188534		2203	4300	6503	SO:0001583	missense	1794	exon25			TCCTGTATGAGTT	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.2459A>C	chr5.hg19:g.169188534A>C	ENSP00000256935:p.Tyr820Ser	77.0	0.0		52.0	20.0	NM_004946	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	hg19	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	A	11.56	1.674531	0.29693	.	.	ENSG00000134516	ENST00000256935;ENST00000343291;ENST00000520908;ENST00000519628	T;T;T	0.27402	1.67;1.67;1.67	5.67	5.67	0.87782	.	0.110120	0.64402	D	0.000005	T	0.18341	0.0440	N	0.10874	0.06	0.80722	D	1	P;P	0.38922	0.651;0.651	B;B	0.38428	0.15;0.273	T	0.10636	-1.0621	10	0.16896	T	0.51	.	15.1959	0.73088	1.0:0.0:0.0:0.0	.	312;820	E7ERW7;Q92608	.;DOCK2_HUMAN	S	820;201;312;24	ENSP00000256935:Y820S;ENSP00000429283:Y312S;ENSP00000428841:Y24S	ENSP00000256935:Y820S	Y	+	2	0	DOCK2	169121112	1.000000	0.71417	0.932000	0.37286	0.993000	0.82548	4.195000	0.58400	2.288000	0.76882	0.533000	0.62120	TAT	.	.		0.488	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		C	169188534	A	C	169188534	3	2	344	1	0	0	0	0	1	0	0	0	4689	449	16	5	2557	5	DOCK2	5	169188534	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	44049	169188534	11726726	485	47848										
STC2	8614	hgsc.bcm.edu	37	chr5	172744894	172744894	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agactgttcgtcttcccactCgctgcttccggaaggtccct	9	15	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:172744894C>A	ENST00000265087.4	-	4	2174	c.865G>T	c.(865-867)Gag>Tag	p.E289*	STC2_ENST00000520593.1_5'Flank	NM_003714.2	NP_003705.1	O76061	STC2_HUMAN	stanniocalcin 2	289					cellular calcium ion homeostasis (GO:0006874)|cellular response to hypoxia (GO:0071456)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of gene expression (GO:0010629)|negative regulation of multicellular organism growth (GO:0040015)|regulation of hormone biosynthetic process (GO:0046885)|regulation of store-operated calcium entry (GO:2001256)|response to oxidative stress (GO:0006979)|response to peptide hormone (GO:0043434)|response to vitamin D (GO:0033280)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|heme binding (GO:0020037)|protein homodimerization activity (GO:0042803)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(3)	25	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|Ovarian(839;0.223)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			TCTTCCCACTCGCTGCTTCCG	0.577																																					p.E289X		Atlas-SNP	.											STC2,lower_third,carcinoma,0,1	STC2	59	.	0			c.G865T						.						83	87	85					5																	172744894		2203	4300	6503	SO:0001587	stop_gained	8614	exon4			CCCACTCGCTGCT	AB012664	CCDS4388.1	5q35.2	2004-05-17			ENSG00000113739	ENSG00000113739			11374	protein-coding gene	gene with protein product		603665				9723890, 9753616	Standard	NM_003714		Approved	STC-2	uc003mco.1	O76061	OTTHUMG00000130542	ENST00000265087.4:c.865G>T	chr5.hg19:g.172744894C>A	ENSP00000265087:p.Glu289*	76.0	2.0		49.0	22.0	NM_003714		Nonsense_Mutation	SNP	ENST00000265087.4	hg19	CCDS4388.1	.	.	.	.	.	.	.	.	.	.	C	48	14.654425	0.99804	.	.	ENSG00000113739	ENST00000265087	.	.	.	5.3	5.3	0.74995	.	0.167000	0.52532	D	0.000068	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	-29.9991	18.9971	0.92818	0.0:1.0:0.0:0.0	.	.	.	.	X	289	.	ENSP00000265087:E289X	E	-	1	0	STC2	172677500	1.000000	0.71417	0.991000	0.47740	0.792000	0.44763	3.549000	0.53681	2.480000	0.83734	0.650000	0.86243	GAG	.	.		0.577	STC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252965.1	NM_003714		A	172744894	C	A	172744894	4	1	344	1	0	0	0	0	0	1	0	0	15291	893	31	1	47	1	STC2	5	172744894	Nonsense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	3556360	172744894	8170366	486	47849										
NSD1	64324	hgsc.bcm.edu	37	chr5	176637954	176637954	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaaccagggattcaagtgacAtagaaacagcagtggtgaaa	11	6	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:176637954A>G	ENST00000439151.2	+	5	2599	c.2554A>G	c.(2554-2556)Ata>Gta	p.I852V	NSD1_ENST00000361032.4_Missense_Mutation_p.I749V|NSD1_ENST00000347982.4_Missense_Mutation_p.I583V|NSD1_ENST00000354179.4_Missense_Mutation_p.I583V	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	852					gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		TTCAAGTGACATAGAAACAGC	0.423			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.I852V		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.A2554G						.						134	132	132					5																	176637954		2203	4300	6503	SO:0001583	missense	64324	exon5	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	AGTGACATAGAAA	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	14234	protein-coding gene	gene with protein product		606681	"Sotos syndrome"	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.2554A>G	chr5.hg19:g.176637954A>G	ENSP00000395929:p.Ile852Val	88.0	0.0		66.0	32.0	NM_022455	Q96PD8|Q96RN7	Missense_Mutation	SNP	ENST00000439151.2	hg19	CCDS4412.1	.	.	.	.	.	.	.	.	.	.	A	15.41	2.825242	0.50739	.	.	ENSG00000165671	ENST00000354179;ENST00000439151;ENST00000347982;ENST00000361032	D;D;D;D	0.95272	-3.59;-3.6;-3.59;-3.66	5.59	5.59	0.84812	.	0.000000	0.64402	D	0.000003	D	0.94225	0.8146	L	0.29908	0.895	0.26512	N	0.97459	D;D;D	0.62365	0.991;0.978;0.985	D;P;D	0.72625	0.978;0.81;0.952	D	0.88360	0.2987	9	.	.	.	.	10.1544	0.42814	0.9247:0.0:0.0753:0.0	.	583;749;852	Q96L73-2;Q96L73-3;Q96L73	.;.;NSD1_HUMAN	V	583;852;583;749	ENSP00000346111:I583V;ENSP00000395929:I852V;ENSP00000343209:I583V;ENSP00000354310:I749V	.	I	+	1	0	NSD1	176570560	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	3.652000	0.54439	2.246000	0.74042	0.533000	0.62120	ATA	.	.		0.423	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349		G	176637954	A	G	176637954	3	3	344	1	0	0	0	0	1	0	0	0	10678	217	8	2	2568	2	NSD1	5	176637954	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3893060	176637954	4277306	487	47850										
SLC34A1	6569	hgsc.bcm.edu	37	chr5	176814993	176814993	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcaatgtggcctccctgcccAgggccttcgcgggggccacg	15	16	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:176814993A>T	ENST00000324417.5	+	7	735		c.e7-1		SLC34A1_ENST00000512593.1_Splice_Site	NM_003052.4	NP_003043.3	Q06495	NPT2A_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 1						arsenate ion transmembrane transport (GO:1901684)|bone remodeling (GO:0046849)|cellular response to metal ion (GO:0071248)|cellular response to parathyroid hormone stimulus (GO:0071374)|cellular response to staurosporine (GO:0072734)|dentinogenesis (GO:0097187)|gentamycin metabolic process (GO:1901128)|glycoprotein metabolic process (GO:0009100)|indole metabolic process (GO:0042431)|ion transport (GO:0006811)|kidney development (GO:0001822)|ossification (GO:0001503)|phosphate ion homeostasis (GO:0055062)|phosphate ion transport (GO:0006817)|positive regulation of membrane potential (GO:0045838)|positive regulation of phosphate transmembrane transport (GO:2000187)|positive regulation of sodium-dependent phosphate transport (GO:2000120)|protein homooligomerization (GO:0051260)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to growth hormone (GO:0060416)|response to lead ion (GO:0010288)|response to magnesium ion (GO:0032026)|response to mercury ion (GO:0046689)|response to potassium ion (GO:0035864)|response to thyroid hormone (GO:0097066)|response to vitamin A (GO:0033189)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|tricarboxylic acid metabolic process (GO:0072350)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|membrane-bounded vesicle (GO:0031988)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|symporter activity (GO:0015293)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTCCCTGCCCAGGGCCTTCGC	0.667																																					.		Atlas-SNP	.											.	SLC34A1	73	.	0			c.645-2A>T						.						48	50	49					5																	176814993		2203	4300	6503	SO:0001630	splice_region_variant	6569	exon7			CTGCCCAGGGCCT	L13258	CCDS4418.1, CCDS54953.1	5q35.3	2013-07-17	2013-07-17		ENSG00000131183	ENSG00000131183		"Solute carriers"	11019	protein-coding gene	gene with protein product	"sodium/phosphate co-transporter", "solute carrier family 17 (sodium phosphate), member 2", "Na+-phosphate cotransporter type II"	182309	"solute carrier family 34 (sodium phosphate), member 1"	NPT2, SLC17A2		8327470, 8693007	Standard	NM_003052		Approved	NAPI-3, NPTIIa, SLC11	uc003mgk.4	Q06495	OTTHUMG00000130857	ENST00000324417.5:c.645-1A>T	chr5.hg19:g.176814993A>T		69.0	0.0		48.0	27.0	NM_001167579	B4DPE3	Splice_Site	SNP	ENST00000324417.5	hg19	CCDS4418.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.073784	0.76415	.	.	ENSG00000131183	ENST00000512593;ENST00000324417	.	.	.	5.29	5.29	0.74685	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2119	0.73230	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC34A1	176747599	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	9.170000	0.94795	2.012000	0.59069	0.454000	0.30748	.	.	.		0.667	SLC34A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253431.1	NM_003052	Intron	T	176814993	A	T	176814993	5	4	344	1	0	0	0	0	0	0	1	0	14582	202	7	4	665	4	SLC34A1	5	176814993	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	177039	176814993	4100267	488	47851										
ZFP2	80108	hgsc.bcm.edu	37	chr5	178359135	178359135	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaaaccctatgagtgtagtcAatgtggaaaagcctttagta	9	6	1	1	rs147320919	byFrequency	TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:178359135A>G	ENST00000361362.2	+	5	1351	c.821A>G	c.(820-822)cAa>cGa	p.Q274R	ZFP2_ENST00000520301.1_Missense_Mutation_p.Q274R|ZFP2_ENST00000523286.1_Missense_Mutation_p.Q274R|ZFP2_ENST00000503510.2_Missense_Mutation_p.Q274R	NM_030613.2	NP_085116.2	Q6ZN57	ZFP2_HUMAN	ZFP2 zinc finger protein	274					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	20	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.00655)|GBM - Glioblastoma multiforme(465;0.0302)|OV - Ovarian serous cystadenocarcinoma(192;0.0615)|Epithelial(171;0.111)		GAGTGTAGTCAATGTGGAAAA	0.393																																					p.Q274R		Atlas-SNP	.											.	ZFP2	70	.	0			c.A821G						.						73	74	74					5																	178359135		2203	4300	6503	SO:0001583	missense	80108	exon5			GTAGTCAATGTGG	AK025281	CCDS4440.1	5q35.3	2013-01-08	2012-11-27		ENSG00000198939	ENSG00000198939		"Zinc fingers, C2H2-type"	26138	protein-coding gene	gene with protein product			"zinc finger protein 2 homolog (mouse)"				Standard	NM_030613		Approved	FLJ21628, ZNF751	uc003mjn.1	Q6ZN57	OTTHUMG00000130885	ENST00000361362.2:c.821A>G	chr5.hg19:g.178359135A>G	ENSP00000354453:p.Gln274Arg	90.0	0.0		55.0	33.0	NM_030613	A5PLN5|B7ZM23|Q9H6Z6	Missense_Mutation	SNP	ENST00000361362.2	hg19	CCDS4440.1	.	.	.	.	.	.	.	.	.	.	a	10.88	1.475597	0.26511	.	.	ENSG00000198939	ENST00000361362;ENST00000520301;ENST00000523286;ENST00000503510	T;T;T;T	0.07327	3.2;3.2;3.2;3.2	4.79	3.59	0.41128	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.558121	0.13491	N	0.384010	T	0.08980	0.0222	L	0.39326	1.205	0.21220	N	0.999753	B	0.16802	0.019	B	0.23852	0.049	T	0.25676	-1.0125	10	0.72032	D	0.01	-2.9787	8.8763	0.35348	0.8327:0.0:0.0:0.1673	.	274	Q6ZN57	ZFP2_HUMAN	R	274	ENSP00000354453:Q274R;ENSP00000430980:Q274R;ENSP00000430531:Q274R;ENSP00000438114:Q274R	ENSP00000354453:Q274R	Q	+	2	0	ZFP2	178291741	0.001000	0.12720	0.998000	0.56505	0.810000	0.45777	1.109000	0.31135	0.818000	0.34468	0.533000	0.62120	CAA	.	A|1.000;C|0.000		0.393	ZFP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253470.2	NM_030613		G	178359135	A	G	178359135	3	3	344	1	0	0	0	0	1	0	0	0	17656	130	5	2	823	2	ZFP2	5	178359135	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1544142	178359135	2556125	489	47852										
FLT4	2324	hgsc.bcm.edu	37	chr5	180037027	180037027	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggacacccagttgtaataccTgtggggagaaatcagaaggt	13	7	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:180037027T>A	ENST00000261937.6	-	28	3765		c.e28-2		FLT4_ENST00000502649.1_Splice_Site|FLT4_ENST00000393347.3_Splice_Site	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4						blood vessel morphogenesis (GO:0048514)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|lymph vessel development (GO:0001945)|lymphangiogenesis (GO:0001946)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein autophosphorylation (GO:0046777)|regulation of blood vessel remodeling (GO:0060312)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(6)|large_intestine(5)|liver(2)|lung(37)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TTGTAATACCTGTGGGGAGAA	0.587																																					.	Colon(97;1075 1466 27033 27547 35871)	Atlas-SNP	.											FLT4_ENST00000261937,NS,carcinoma,0,2	FLT4	356	.	0			c.3687-2A>T						.						78	85	82					5																	180037027		2203	4300	6503	SO:0001630	splice_region_variant	2324	exon29			AATACCTGTGGGG	X68203	CCDS4457.1, CCDS43412.1	5q34-q35	2013-01-29			ENSG00000037280	ENSG00000037280	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3767	protein-coding gene	gene with protein product		136352				1319394	Standard	NM_002020		Approved	VEGFR3, PCL	uc003mlz.4	P35916	OTTHUMG00000130931	ENST00000261937.6:c.3687-2A>T	chr5.hg19:g.180037027T>A		62.0	1.0		47.0	17.0	NM_182925	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Splice_Site	SNP	ENST00000261937.6	hg19	CCDS4457.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.169175	0.78339	.	.	ENSG00000037280	ENST00000261937;ENST00000393347;ENST00000502649	.	.	.	4.79	4.79	0.61399	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.6296	0.68647	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	FLT4	179969633	1.000000	0.71417	0.999000	0.59377	0.972000	0.66771	7.372000	0.79612	1.938000	0.56188	0.459000	0.35465	.	.	.		0.587	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4		Intron	A	180037027	T	A	180037027	5	1	344	1	0	0	0	0	0	0	1	0	5952	1594	55	4	426	4	FLT4	5	180037027	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1677892	180037027	878233	490	47853										
TRIM41	90933	hgsc.bcm.edu	37	chr5	180661725	180661725	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcctgggcgagcgtgtctttCctttcttccgggtgctctcc	11	14	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr5:180661725C>A	ENST00000315073.5	+	6	2553	c.1843C>A	c.(1843-1845)Cct>Act	p.P615T	TRIM41_ENST00000510072.1_3'UTR|TRIM41_ENST00000351937.5_Intron	NM_033549.4	NP_291027.3	Q8WV44	TRI41_HUMAN	tripartite motif containing 41	615	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(3)|prostate(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	26	all_cancers(89;9.17e-06)|all_epithelial(37;1.19e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0684)	all_cancers(40;0.000209)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCGTGTCTTTCCTTTCTTCCG	0.622																																					p.P615T		Atlas-SNP	.											.	TRIM41	96	.	0			c.C1843A						.						84	93	90					5																	180661725		2203	4300	6503	SO:0001583	missense	90933	exon6			GTCTTTCCTTTCT	AF258579	CCDS4465.1, CCDS4466.1	5q35.3	2013-01-09	2011-01-25		ENSG00000146063	ENSG00000146063		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19013	protein-coding gene	gene with protein product	"RING-finger protein that interacts with C kinase"	610530	"tripartite motif-containing 41"			16022281	Standard	NM_033549		Approved	MGC1127, RINCK	uc003mne.2	Q8WV44	OTTHUMG00000130965	ENST00000315073.5:c.1843C>A	chr5.hg19:g.180661725C>A	ENSP00000320869:p.Pro615Thr	75.0	0.0		50.0	15.0	NM_033549	B3KNJ6|D3DWR9|Q5BKT0|Q7L484|Q96Q10|Q9BSL8	Missense_Mutation	SNP	ENST00000315073.5	hg19	CCDS4466.1	.	.	.	.	.	.	.	.	.	.	C	12.11	1.840035	0.32513	.	.	ENSG00000146063	ENST00000315073;ENST00000438174	D	0.85171	-1.95	5.06	4.19	0.49359	Concanavalin A-like lectin/glucanase (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.213333	0.33382	N	0.004967	D	0.94262	0.8157	H	0.98178	4.165	0.40053	D	0.975809	D	0.89917	1.0	D	0.97110	1.0	D	0.93890	0.7179	10	0.87932	D	0	.	6.9869	0.24733	0.0:0.7328:0.175:0.0922	.	615	Q8WV44	TRI41_HUMAN	T	615;300	ENSP00000320869:P615T	ENSP00000320869:P615T	P	+	1	0	TRIM41	180594331	1.000000	0.71417	1.000000	0.80357	0.008000	0.06430	1.752000	0.38349	1.362000	0.46000	0.455000	0.32223	CCT	.	.		0.622	TRIM41-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253574.3	NM_201627		A	180661725	C	A	180661725	3	1	344	1	0	0	0	0	1	0	0	0	16531	855	30	3	1865	3	TRIM41	5	180661725	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	624698	180661725	253535	491	47854										
PHACTR1	221692	hgsc.bcm.edu	37	chr6	12749960	12749960	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccggcggcccatccggagagTgcgctccaagagcgacacgc	14	16	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:12749960T>A	ENST00000379350.1	+	3	317	c.188T>A	c.(187-189)gTg>gAg	p.V63E	PHACTR1_ENST00000379348.2_Missense_Mutation_p.V63E|PHACTR1_ENST00000332995.7_Missense_Mutation_p.V63E			Q9C0D0	PHAR1_HUMAN	phosphatase and actin regulator 1	63					actin cytoskeleton reorganization (GO:0031532)|actomyosin structure organization (GO:0031032)|cell motility (GO:0048870)|stress fiber assembly (GO:0043149)	cell junction (GO:0030054)|cytosol (GO:0005829)|nucleus (GO:0005634)|synapse (GO:0045202)	actin binding (GO:0003779)|protein phosphatase inhibitor activity (GO:0004864)			breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	26	Breast(50;0.0427)|Ovarian(93;0.12)	all_hematologic(90;0.122)|Lung SC(78;0.195)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239)			ATCCGGAGAGTGCGCTCCAAG	0.677																																					p.V63E		Atlas-SNP	.											.	PHACTR1	94	.	0			c.T188A						.						26	33	31					6																	12749960		1900	4090	5990	SO:0001583	missense	221692	exon4			GGAGAGTGCGCTC	AB051520	CCDS75401.1	6p23	2013-01-24	2004-05-20	2004-05-21	ENSG00000112137	ENSG00000112137		"Phosphatase and actin regulators"	20990	protein-coding gene	gene with protein product		608723	"RPEL repeat containing 1"	RPEL1		11214970, 15107502	Standard	NM_030948		Approved	KIAA1733, dJ257A7.2	uc010jpc.3	Q9C0D0	OTTHUMG00000014270	ENST00000379350.1:c.188T>A	chr6.hg19:g.12749960T>A	ENSP00000368655:p.Val63Glu	40.0	0.0		38.0	17.0	NM_030948	A8K1V2|Q3MJ93|Q5JSJ2	Missense_Mutation	SNP	ENST00000379350.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.8|20.8	4.053242|4.053242	0.75960|0.75960	.|.	.|.	ENSG00000112137|ENSG00000112137	ENST00000406205|ENST00000379350;ENST00000379348;ENST00000332995;ENST00000432934	.|T;T;T	.|0.47177	.|0.85;0.85;0.85	4.6|4.6	4.6|4.6	0.57074|0.57074	.|.	.|0.233054	.|0.26704	.|U	.|0.022929	T|T	0.39600|0.39600	0.1084|0.1084	N|N	0.19112|0.19112	0.55|0.55	0.80722|0.80722	D|D	1|1	.|D;D;P;D	.|0.71674	.|0.998;0.997;0.895;0.997	.|D;D;B;P	.|0.64877	.|0.911;0.93;0.433;0.855	T|T	0.43114|0.43114	-0.9411|-0.9411	5|10	.|0.48119	.|T	.|0.1	.|.	13.1517|13.1517	0.59492|0.59492	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|63;63;63;63	.|E7ESR5;Q5R356;Q9C0D0;Q9C0D0-2	.|.;.;PHAR1_HUMAN;.	R|E	98|63	.|ENSP00000368655:V63E;ENSP00000368653:V63E;ENSP00000329880:V63E	.|ENSP00000329880:V63E	S|V	+|+	3|2	2|0	PHACTR1|PHACTR1	12857946|12857946	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	3.559000|3.559000	0.53756|0.53756	1.700000|1.700000	0.51204|0.51204	0.254000|0.254000	0.18369|0.18369	AGT|GTG	.	.		0.677	PHACTR1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039876.1	XM_166420		A	12749960	T	A	12749960	3	1	344	1	0	0	0	0	1	0	0	0	11818	1696	59	4	194	4	PHACTR1	6	12749960	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10		12749960	158365107	492	47855										
PHACTR1	221692	hgsc.bcm.edu	37	chr6	13160509	13160509	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggagtcctgaaggaaatctaTgataaaggtaaggaggattg	14	3	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:13160509T>C	ENST00000379350.1	+	5	618	c.489T>C	c.(487-489)taT>taC	p.Y163Y	PHACTR1_ENST00000457702.2_Silent_p.Y18Y|PHACTR1_ENST00000379345.2_Silent_p.Y18Y|PHACTR1_ENST00000482982.1_3'UTR|PHACTR1_ENST00000332995.7_Silent_p.Y163Y			Q9C0D0	PHAR1_HUMAN	phosphatase and actin regulator 1	163					actin cytoskeleton reorganization (GO:0031532)|actomyosin structure organization (GO:0031032)|cell motility (GO:0048870)|stress fiber assembly (GO:0043149)	cell junction (GO:0030054)|cytosol (GO:0005829)|nucleus (GO:0005634)|synapse (GO:0045202)	actin binding (GO:0003779)|protein phosphatase inhibitor activity (GO:0004864)			breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	26	Breast(50;0.0427)|Ovarian(93;0.12)	all_hematologic(90;0.122)|Lung SC(78;0.195)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239)			AGGAAATCTATGATAAAGGTA	0.443																																					p.Y163Y		Atlas-SNP	.											.	PHACTR1	94	.	0			c.T489C						.						126	126	126					6																	13160509		1955	4153	6108	SO:0001819	synonymous_variant	221692	exon6			AATCTATGATAAA	AB051520	CCDS75401.1	6p23	2013-01-24	2004-05-20	2004-05-21	ENSG00000112137	ENSG00000112137		"Phosphatase and actin regulators"	20990	protein-coding gene	gene with protein product		608723	"RPEL repeat containing 1"	RPEL1		11214970, 15107502	Standard	NM_030948		Approved	KIAA1733, dJ257A7.2	uc010jpc.3	Q9C0D0	OTTHUMG00000014270	ENST00000379350.1:c.489T>C	chr6.hg19:g.13160509T>C		67.0	0.0		88.0	24.0	NM_030948	A8K1V2|Q3MJ93|Q5JSJ2	Silent	SNP	ENST00000379350.1	hg19		.	.	.	.	.	.	.	.	.	.	T	8.535	0.871868	0.17322	.	.	ENSG00000112137	ENST00000406205	.	.	.	5.1	-0.494	0.12034	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-8.7586	9.802	0.40770	0.0:0.1314:0.0:0.8686	.	.	.	.	R	199	.	.	X	+	1	0	PHACTR1	13268495	1.000000	0.71417	0.996000	0.52242	0.917000	0.54804	1.250000	0.32850	-0.254000	0.09500	-0.408000	0.06270	TGA	.	.		0.443	PHACTR1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039876.1	XM_166420		C	13160509	T	C	13160509	2	2	344	1	0	0	0	0	0	0	0	1	11818	1471	51	2		2	PHACTR1	6	13160509	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	410549	13160509	157954558	493	47856										
CCDC90A	63933	hgsc.bcm.edu	37	chr6	13791091	13791091	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tactgttaggcacgtaaataTagaccctgtaagaaaaaaac	7	7	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:13791091T>C	ENST00000379170.4	-	9	1168	c.1030A>G	c.(1030-1032)Ata>Gta	p.I344V		NM_001031713.3	NP_001026883.1	Q96AQ8	MCUR1_HUMAN	mitochondrial calcium uniporter regulator 1	344					calcium ion import (GO:0070509)|mitochondrial calcium ion transport (GO:0006851)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)	integral component of mitochondrial inner membrane (GO:0031305)											CACGTAAATATAGACCCTGTA	0.323																																					p.I344V		Atlas-SNP	.											.	CCDC90A	15	.	0			c.A1030G						.						82	85	84					6																	13791091		2203	4300	6503	SO:0001583	missense	63933	exon9			TAAATATAGACCC	BC016850	CCDS35495.1	6p23	2013-03-13	2013-03-13	2013-03-13	ENSG00000050393	ENSG00000050393			21097	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 79", "coiled-coil domain containing 90A"	C6orf79, CCDC90A		23178883	Standard	NM_001031713		Approved	FLJ20958	uc003nbc.2	Q96AQ8	OTTHUMG00000014279	ENST00000379170.4:c.1030A>G	chr6.hg19:g.13791091T>C	ENSP00000368468:p.Ile344Val	190.0	0.0		218.0	92.0	NM_001031713	Q96JS7|Q9H7F8	Missense_Mutation	SNP	ENST00000379170.4	hg19	CCDS35495.1	.	.	.	.	.	.	.	.	.	.	T	1.092	-0.663599	0.03428	.	.	ENSG00000050393	ENST00000379170	T	0.39056	1.1	5.36	2.05	0.26809	.	0.352459	0.31709	N	0.007182	T	0.03095	0.0091	N	0.00468	-1.46	0.80722	D	1	B	0.21520	0.057	B	0.17098	0.017	T	0.46119	-0.9214	10	0.02654	T	1	-7.4092	11.178	0.48612	0.0:0.8021:0.0:0.1979	.	344	Q96AQ8	CC90A_HUMAN	V	344	ENSP00000368468:I344V	ENSP00000368468:I344V	I	-	1	0	CCDC90A	13899070	0.648000	0.27313	0.999000	0.59377	0.835000	0.47333	0.077000	0.14738	0.423000	0.26033	-0.256000	0.11100	ATA	.	.		0.323	MCUR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039909.3	NM_022102		C	13791091	T	C	13791091	3	2	344	1	0	0	0	0	1	0	0	0	2870	1406	49	2	53	2	CCDC90A	6	13791091	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	630582	13791091	157323976	494	47857										
RNF144B	255488	hgsc.bcm.edu	37	chr6	18465185	18465185	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggattctcgtaggcttgggcAtcattgccttggttacttca	11	9	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:18465185A>G	ENST00000259939.3	+	8	1116	c.799A>G	c.(799-801)Atc>Gtc	p.I267V	RNF144B_ENST00000429054.2_Missense_Mutation_p.I178V	NM_182757.3	NP_877434.2	Q7Z419	R144B_HUMAN	ring finger protein 144B	267					apoptotic process (GO:0006915)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(7)	11	Ovarian(93;0.00365)|Breast(50;0.0145)	all_hematologic(90;0.0536)	OV - Ovarian serous cystadenocarcinoma(7;0.00165)|all cancers(50;0.0102)|Epithelial(50;0.0105)			AGGCTTGGGCATCATTGCCTT	0.433																																					p.I267V		Atlas-SNP	.											.	RNF144B	18	.	0			c.A799G						.						188	152	164					6																	18465185		2203	4300	6503	SO:0001583	missense	255488	exon8			TTGGGCATCATTG	AK096832	CCDS34345.1	6p22.3	2011-05-23	2009-01-05	2007-08-20	ENSG00000137393	ENSG00000137393		"RING-type (C3HC4) zinc fingers"	21578	protein-coding gene	gene with protein product			"IBR domain containing 2"	IBRDC2			Standard	NM_182757		Approved	bA528A10.3	uc003ncs.3	Q7Z419	OTTHUMG00000014322	ENST00000259939.3:c.799A>G	chr6.hg19:g.18465185A>G	ENSP00000259939:p.Ile267Val	118.0	0.0		135.0	64.0	NM_182757	B3KUA8|B4DZI2|Q5TB85|Q6P4Q0|Q8N3R7|Q9BX38	Missense_Mutation	SNP	ENST00000259939.3	hg19	CCDS34345.1	.	.	.	.	.	.	.	.	.	.	A	13.08	2.130249	0.37630	.	.	ENSG00000137393	ENST00000429054;ENST00000259939	T;T	0.41065	1.01;1.58	5.3	4.15	0.48705	Zinc finger, RING-type (1);	0.044542	0.85682	N	0.000000	T	0.19005	0.0456	L	0.52759	1.655	0.49051	D	0.999743	B	0.10296	0.003	B	0.12156	0.007	T	0.04915	-1.0918	9	.	.	.	.	10.5182	0.44903	0.9225:0.0:0.0775:0.0	.	267	Q7Z419	R144B_HUMAN	V	178;267	ENSP00000411270:I178V;ENSP00000259939:I267V	.	I	+	1	0	RNF144B	18573164	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.148000	0.50647	0.970000	0.38263	0.528000	0.53228	ATC	.	.		0.433	RNF144B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039965.2	XM_172581		G	18465185	A	G	18465185	3	3	344	1	0	0	0	0	1	0	0	0	13461	217	8	2	825	2	RNF144B	6	18465185	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	4674094	18465185	152649882	495	47858										
TRIM38	10475	hgsc.bcm.edu	37	chr6	25983702	25983702	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaaaagaaaggctatgtagcActtacttctcccccaacttc	5	12	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:25983702A>T	ENST00000357085.3	+	8	1661	c.1185A>T	c.(1183-1185)gcA>gcT	p.A395A	TRIM38_ENST00000349458.3_Silent_p.A395A|U91328.21_ENST00000608931.1_RNA	NM_006355.3	NP_006346.1	O00635	TRI38_HUMAN	tripartite motif containing 38	395	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				negative regulation of defense response to virus (GO:0050687)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of viral entry into host cell (GO:0046598)|positive regulation of viral genome replication (GO:0045070)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|regulation of interferon-beta production (GO:0032648)|signal transduction (GO:0007165)	intracellular (GO:0005622)	signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(2)	23						GCTATGTAGCACTTACTTCTC	0.493																																					p.A395A		Atlas-SNP	.											.	TRIM38	50	.	0			c.A1185T						.						125	122	123					6																	25983702		2203	4300	6503	SO:0001819	synonymous_variant	10475	exon8			TGTAGCACTTACT	U90547	CCDS4568.1	6p21.3	2011-04-20	2011-01-25	2002-06-07	ENSG00000112343	ENSG00000112343		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	10059	protein-coding gene	gene with protein product			"ring finger protein 15", "tripartite motif-containing 38"	RNF15			Standard	XR_241880		Approved	RORET	uc003nfm.4	O00635	OTTHUMG00000014414	ENST00000357085.3:c.1185A>T	chr6.hg19:g.25983702A>T		96.0	0.0		85.0	32.0	NM_006355	B2R862	Silent	SNP	ENST00000357085.3	hg19	CCDS4568.1																																																																																			.	.		0.493	TRIM38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040076.2			T	25983702	A	T	25983702	2	4	344	1	0	0	0	0	0	0	0	1	16527	146	6	4		4	TRIM38	6	25983702	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	7518517	25983702	145131365	496	47859										
HFE	3077	hgsc.bcm.edu	37	chr6	26091582	26091582	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atcctgggctgtgaaatgcaAgaagacaacagtaccgaggg	13	8	0	3	rs28934595		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:26091582A>G	ENST00000357618.5	+	3	503	c.381A>G	c.(379-381)caA>caG	p.Q127Q	HFE_ENST00000353147.5_Intron|HFE_ENST00000470149.1_Silent_p.Q127Q|HFE_ENST00000317896.7_Intron|HFE_ENST00000397022.3_Silent_p.Q104Q|HFE_ENST00000309234.6_Silent_p.Q127Q|HFE_ENST00000352392.4_Intron|HFE_ENST00000461397.1_Silent_p.Q127Q|HFE_ENST00000349999.4_Silent_p.Q39Q|HFE_ENST00000336625.8_Intron|HFE_ENST00000488199.1_Silent_p.Q39Q	NM_000410.3|NM_139006.2	NP_000401.1|NP_620575.1	Q30201	HFE_HUMAN	hemochromatosis	127	Alpha-2.		Q -> H (in HFE1; dbSNP:rs28934595). {ECO:0000269|PubMed:10401000}.		antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular iron ion homeostasis (GO:0006879)|cellular response to iron ion starvation (GO:0010106)|female pregnancy (GO:0007565)|hormone biosynthetic process (GO:0042446)|immune response (GO:0006955)|iron ion import into cell (GO:0097459)|multicellular organismal iron ion homeostasis (GO:0060586)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein complex assembly (GO:0006461)	apical part of cell (GO:0045177)|basal part of cell (GO:0045178)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|MHC class I protein complex (GO:0042612)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	peptide antigen binding (GO:0042605)|receptor binding (GO:0005102)			endometrium(3)|large_intestine(3)|liver(2)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GTGAAATGCAAGAAGACAACA	0.517									Hemochromatosis																												p.Q127Q		Atlas-SNP	.											.	HFE	37	.	0			c.A381G	GRCh37	CM990721	HFE	M	rs28934595	.						88	73	78					6																	26091582		2203	4300	6503	SO:0001819	synonymous_variant	3077	exon3	Familial Cancer Database		AATGCAAGAAGAC		CCDS4578.1, CCDS4579.1, CCDS4580.1, CCDS4581.1, CCDS4582.1, CCDS47386.1, CCDS47387.1, CCDS54974.1, CCDS54975.1, CCDS75412.1	6p21.3	2014-09-17			ENSG00000010704	ENSG00000010704		"Immunoglobulin superfamily / C1-set domain containing"	4886	protein-coding gene	gene with protein product	"high Fe"	613609				3460331	Standard	XR_241893		Approved	HLA-H	uc003nfx.1	Q30201	OTTHUMG00000016348	ENST00000357618.5:c.381A>G	chr6.hg19:g.26091582A>G		150.0	0.0		176.0	81.0	NM_139006	B2CKL0|O75929|O75930|O75931|Q17RT0|Q96KU5|Q96KU6|Q96KU7|Q96KU8|Q9HC64|Q9HC68|Q9HC70|Q9HC83	Silent	SNP	ENST00000357618.5	hg19	CCDS4578.1																																																																																			.	.		0.517	HFE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356133.1			G	26091582	A	G	26091582	2	3	344	1	0	0	0	0	0	0	0	1	7090	69	3	2		2	HFE	6	26091582	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	107880	26091582	145023485	497	47860										
PGBD1	84547	hgsc.bcm.edu	37	chr6	28268678	28268678	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agaaaaaaagacaaagctcgAgtgagtgaactgctccaagg	11	7	0	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:28268678A>G	ENST00000405948.2	+	7	1467	c.1047A>G	c.(1045-1047)cgA>cgG	p.R349R	PGBD1_ENST00000259883.3_Silent_p.R349R	NM_001184743.1|NM_032507.3	NP_001171672.1|NP_115896.1	Q96JS3	PGBD1_HUMAN	piggyBac transposable element derived 1	349						membrane (GO:0016020)|nucleus (GO:0005634)	scavenger receptor activity (GO:0005044)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	41						ACAAAGCTCGAGTGAGTGAAC	0.478																																					p.R349R		Atlas-SNP	.											.	PGBD1	106	.	0			c.A1047G						.						89	93	92					6																	28268678		2203	4300	6503	SO:0001819	synonymous_variant	84547	exon7			AGCTCGAGTGAGT	D88259	CCDS4648.1	6p22.1	2013-01-09			ENSG00000137338	ENSG00000137338		"-"	19398	protein-coding gene	gene with protein product							Standard	NM_001184743		Approved	HUCEP-4, dJ874C20.4, SCAND4	uc003nkz.3	Q96JS3	OTTHUMG00000014520	ENST00000405948.2:c.1047A>G	chr6.hg19:g.28268678A>G		92.0	0.0		91.0	48.0	NM_001184743	Q53F43|Q6NTF5|Q8WWS4	Silent	SNP	ENST00000405948.2	hg19	CCDS4648.1																																																																																			.	.		0.478	PGBD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040188.2			G	28268678	A	G	28268678	2	3	344	1	0	0	0	0	0	0	0	1	11789	291	11	2		2	PGBD1	6	28268678	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2177096	28268678	142846389	498	47861										
OR2J3	442186	hgsc.bcm.edu	37	chr6	29080029	29080029	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtgtgtcctactggtggtgaTgtcctatgaccgttatgcag	13	8	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:29080029T>A	ENST00000377169.1	+	1	362	c.362T>A	c.(361-363)aTg>aAg	p.M121K		NM_001005216.2	NP_001005216.2	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J, member 3	121						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(5)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	24						CTGGTGGTGATGTCCTATGAC	0.507																																					p.M121K		Atlas-SNP	.											.	OR2J3	53	.	0			c.T362A						.						361	408	392					6																	29080029		1382	2648	4030	SO:0001583	missense	442186	exon1			TGGTGATGTCCTA		CCDS43433.1	6p22.2-p21.31	2012-08-09			ENSG00000204701	ENSG00000204701		"GPCR / Class A : Olfactory receptors"	8261	protein-coding gene	gene with protein product		615016					Standard	NM_001005216		Approved	OR6-6	uc011dll.2	O76001	OTTHUMG00000031092	ENST00000377169.1:c.362T>A	chr6.hg19:g.29080029T>A	ENSP00000366374:p.Met121Lys	143.0	0.0		133.0	55.0	NM_001005216	B0UY52|B9EH11|Q5SUJ7|Q6IF25|Q96R15|Q9GZK5|Q9GZL4|Q9GZL5	Missense_Mutation	SNP	ENST00000377169.1	hg19	CCDS43433.1	.	.	.	.	.	.	.	.	.	.	T	15.59	2.877435	0.51801	.	.	ENSG00000204701	ENST00000377169	T	0.01159	5.25	2.78	2.78	0.32641	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.09642	0.0237	H	0.99867	4.865	0.51767	D	0.999932	D	0.89917	1.0	D	0.85130	0.997	T	0.07731	-1.0757	9	0.87932	D	0	.	10.804	0.46507	0.0:0.0:0.0:1.0	.	121	O76001	OR2J3_HUMAN	K	121	ENSP00000366374:M121K	ENSP00000366374:M121K	M	+	2	0	OR2J3	29188008	1.000000	0.71417	1.000000	0.80357	0.447000	0.32167	4.407000	0.59754	1.268000	0.44264	0.358000	0.22013	ATG	.	.		0.507	OR2J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076132.2			A	29080029	T	A	29080029	3	1	344	1	0	0	0	0	1	0	0	0	11013	1464	51	4	364	4	OR2J3	6	29080029	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	811351	29080029	142035038	499	47862										
OR2J2	26707	hgsc.bcm.edu	37	chr6	29141976	29141976	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gttccagcacttctgcgtttAtcatgtgttgacacccatgc	8	12	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:29141976A>G	ENST00000377167.2	+	1	666	c.564A>G	c.(562-564)ttA>ttG	p.L188L		NM_030905.2	NP_112167.2	O76002	OR2J2_HUMAN	olfactory receptor, family 2, subfamily J, member 2	188						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(1)|liver(2)|lung(17)|ovary(1)|upper_aerodigestive_tract(1)	25						TTCTGCGTTTATCATGTGTTG	0.458																																					p.L188L		Atlas-SNP	.											.	OR2J2	51	.	0			c.A564G						.						167	146	153					6																	29141976		1948	4151	6099	SO:0001819	synonymous_variant	26707	exon1			GCGTTTATCATGT		CCDS43434.1	6p22.2-p21.31	2012-08-09			ENSG00000204700	ENSG00000204700		"GPCR / Class A : Olfactory receptors"	8260	protein-coding gene	gene with protein product							Standard	NM_030905		Approved	OR6-8, hs6M1-6, dJ80I19.4	uc011dlm.2	O76002	OTTHUMG00000031091	ENST00000377167.2:c.564A>G	chr6.hg19:g.29141976A>G		90.0	0.0		81.0	37.0	NM_030905	A6NCU9|A6NLD0|B0UY53|Q32N09|Q5ST39|Q5SUJ6|Q6IF24|Q9GZK2|Q9GZL3	Silent	SNP	ENST00000377167.2	hg19	CCDS43434.1																																																																																			.	.		0.458	OR2J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076131.2			G	29141976	A	G	29141976	2	3	344	1	0	0	0	0	0	0	0	1	11012	446	16	2		2	OR2J2	6	29141976	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	61947	29141976	141973091	500	47863										
OR12D3	81797	hgsc.bcm.edu	37	chr6	29343000	29343000	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaatcccaaagaagaaaggcTgcagctcctgaacaccagtc	8	12	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:29343000T>A	ENST00000396806.3	-	1	68	c.65A>T	c.(64-66)cAg>cTg	p.Q22L	OR5V1_ENST00000377154.1_Intron	NM_030959.2	NP_112221.1	Q9UGF7	O12D3_HUMAN	olfactory receptor, family 12, subfamily D, member 3	22						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)	23						GAAGAAAGGCTGCAGCTCCTG	0.383																																					p.Q22L		Atlas-SNP	.											.	OR12D3	55	.	0			c.A65T						.						42	47	45					6																	29343000		1507	2708	4215	SO:0001583	missense	81797	exon1			AAAGGCTGCAGCT		CCDS4658.1	6p22.1	2013-09-24			ENSG00000112462	ENSG00000112462		"GPCR / Class A : Olfactory receptors"	13963	protein-coding gene	gene with protein product							Standard	NM_030959		Approved	hs6M1-27	uc003nme.3	Q9UGF7	OTTHUMG00000031051	ENST00000396806.3:c.65A>T	chr6.hg19:g.29343000T>A	ENSP00000380023:p.Gln22Leu	250.0	0.0		208.0	77.0	NM_030959	A2BDZ1|Q5SQI8|Q6IF23	Missense_Mutation	SNP	ENST00000396806.3	hg19	CCDS4658.1	.	.	.	.	.	.	.	.	.	.	t	12.95	2.090152	0.36855	.	.	ENSG00000112462	ENST00000377143;ENST00000396806	T	0.00597	6.31	4.34	4.34	0.51931	.	.	.	.	.	T	0.00815	0.0027	M	0.89658	3.05	0.09310	N	1	P	0.46020	0.871	P	0.44811	0.461	T	0.30208	-0.9986	9	0.87932	D	0	-2.4275	13.3191	0.60423	0.0:0.0:0.0:1.0	.	22	Q9UGF7	O12D3_HUMAN	L	22	ENSP00000380023:Q22L	ENSP00000366348:Q22L	Q	-	2	0	OR12D3	29450979	0.045000	0.20229	0.027000	0.17364	0.858000	0.48976	1.958000	0.40402	1.808000	0.52836	0.353000	0.21931	CAG	.	.		0.383	OR12D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076056.3			A	29343000	T	A	29343000	3	1	344	1	0	0	0	0	1	0	0	0	10941	1580	55	4	889	4	OR12D3	6	29343000	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	201024	29343000	141772067	501	47864										
OR10C1	442194	hgsc.bcm.edu	37	chr6	29408614	29408614	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gccactgaccctctggtgtcCctcttctatgctgtggtcac	9	15	4	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:29408614C>A	ENST00000444197.2	+	1	1532	c.822C>A	c.(820-822)tcC>tcA	p.S274S	OR11A1_ENST00000377149.1_Intron	NM_013941.3	NP_039229.3	Q96KK4	O10C1_HUMAN	olfactory receptor, family 10, subfamily C, member 1 (gene/pseudogene)	274						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|kidney(1)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						CTCTGGTGTCCCTCTTCTATG	0.547																																					p.S274S		Atlas-SNP	.											.	OR10C1	58	.	0			c.C822A						.						195	212	206					6																	29408614		1511	2709	4220	SO:0001819	synonymous_variant	442194	exon1			GGTGTCCCTCTTC		CCDS34364.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000206474	ENSG00000206474		"GPCR / Class A : Olfactory receptors"	8165	protein-coding gene	gene with protein product			"olfactory receptor, family 10, subfamily C, member 2", "olfactory receptor, family 10, subfamily C, member 1"	OR10C2			Standard	NM_013941		Approved	hs6M1-17, OR10C1P	uc011dlp.2	Q96KK4	OTTHUMG00000031207	ENST00000444197.2:c.822C>A	chr6.hg19:g.29408614C>A		90.0	0.0		81.0	35.0	NM_013941	Q5SUN7|Q96R18	Silent	SNP	ENST00000444197.2	hg19	CCDS34364.1																																																																																			.	.		0.547	OR10C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076415.2			A	29408614	C	A	29408614	2	1	344	1	0	0	0	0	0	0	0	1	10907	610	22	3		3	OR10C1	6	29408614	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	65614	29408614	141706453	502	47865										
OR2H2	7932	hgsc.bcm.edu	37	chr6	29556136	29556136	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccatcatccacccccgcctgTgctggcagctggcatctgtg	10	17	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:29556136T>G	ENST00000383640.2	+	1	454	c.415T>G	c.(415-417)Tgc>Ggc	p.C139G	GABBR1_ENST00000355973.3_Intron	NM_007160.3	NP_009091.3	O95918	OR2H2_HUMAN	olfactory receptor, family 2, subfamily H, member 2	139					defense response (GO:0006952)|detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|mating (GO:0007618)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|urinary_tract(1)	14						CCCCCGCCTGTGCTGGCAGCT	0.612																																					p.C139G		Atlas-SNP	.											.	OR2H2	29	.	0			c.T415G						.						128	133	131					6																	29556136		1510	2709	4219	SO:0001583	missense	7932	exon1			CGCCTGTGCTGGC		CCDS34365.1	6p22.2-p21.31	2012-08-09				ENSG00000204657		"GPCR / Class A : Olfactory receptors"	8253	protein-coding gene	gene with protein product		600578					Standard	XM_005249407		Approved	hs6M1-12	uc003nmr.1	O95918		ENST00000383640.2:c.415T>G	chr6.hg19:g.29556136T>G	ENSP00000373136:p.Cys139Gly	97.0	0.0		66.0	39.0	NM_007160	Q15062|Q2M1Y3|Q5STL8|Q5SUK1|Q6IFN7|Q6NTB7|Q96R14	Missense_Mutation	SNP	ENST00000383640.2	hg19	CCDS34365.1	.	.	.	.	.	.	.	.	.	.	T	14.30	2.494225	0.44352	.	.	ENSG00000204657	ENST00000383640	T	0.00224	8.51	4.29	1.59	0.23543	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44902	D	0.000401	T	0.00440	0.0014	H	0.98682	4.3	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.37103	-0.9720	10	0.87932	D	0	.	8.2745	0.31864	0.389:0.0:0.0:0.6109	.	139	O95918	OR2H2_HUMAN	G	139	ENSP00000373136:C139G	ENSP00000373136:C139G	C	+	1	0	OR2H2	29664115	0.966000	0.33281	0.973000	0.42090	0.989000	0.77384	2.038000	0.41184	0.660000	0.30964	0.477000	0.44152	TGC	.	.		0.612	OR2H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076057.2			G	29556136	T	G	29556136	3	3	344	1	0	0	0	0	1	0	0	0	11011	1696	59	5	417	5	OR2H2	6	29556136	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	147522	29556136	141558931	503	47866										
VARS2	57176	hgsc.bcm.edu	37	chr6	30892148	30892148	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	caggaggctgtgaagcccgtGctgtggcactcgccccgccc	14	16	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:30892148G>C	ENST00000321897.5	+	25	3116	c.2484G>C	c.(2482-2484)gtG>gtC	p.V828V	VARS2_ENST00000476162.1_3'UTR|VARS2_ENST00000541562.1_Silent_p.V858V|VARS2_ENST00000542001.1_Silent_p.V688V|VARS2_ENST00000416670.2_Silent_p.V828V			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	828					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						TGAAGCCCGTGCTGTGGCACT	0.692																																					p.V858V		Atlas-SNP	.											.	VARS2	60	.	0			c.G2574C						.						29	37	34					6																	30892148		1503	2691	4194	SO:0001819	synonymous_variant	57176	exon26			GCCCGTGCTGTGG	AB067472	CCDS34387.1, CCDS54980.1	6p21.33	2012-10-26	2012-10-26	2007-02-23	ENSG00000137411	ENSG00000137411	6.1.1.9	"Aminoacyl tRNA synthetases / Class I"	21642	protein-coding gene	gene with protein product	"valine tRNA ligase 2, mitochondrial"	612802	"valyl-tRNA synthetase 2-like", "valyl-tRNA synthetase like", "valyl-tRNA synthetase 2, mitochondrial (putative)"	VARS2L, VARSL		1898367, 11572484, 18400783	Standard	NM_001167734		Approved	DKFZP434L1435, KIAA1885, G7a	uc011dmz.2	Q5ST30	OTTHUMG00000031263	ENST00000321897.5:c.2484G>C	chr6.hg19:g.30892148G>C		87.0	0.0		80.0	36.0	NM_001167734	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Silent	SNP	ENST00000321897.5	hg19	CCDS34387.1																																																																																			.	.		0.692	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442		C	30892148	G	C	30892148	2	2	344	1	0	0	0	0	0	0	0	1	17139	1306	46	4		4	VARS2	6	30892148	Silent	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1336012	30892148	140222919	504	47867										
DPCR1	135656	hgsc.bcm.edu	37	chr6	30919181	30919181	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acaccatcctcagcagagccTacagaaaatggagaaaggac	9	11	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:30919181T>A	ENST00000462446.1	+	2	2968	c.2940T>A	c.(2938-2940)ccT>ccA	p.P980P	DPCR1_ENST00000304311.2_5'UTR|HCG21_ENST00000419481.1_RNA			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	332						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						CAGCAGAGCCTACAGAAAATG	0.498																																					p.P980P		Atlas-SNP	.											.	DPCR1	99	.	0			c.T2940A						.						266	251	256					6																	30919181		692	1591	2283	SO:0001819	synonymous_variant	135656	exon2			AGAGCCTACAGAA	AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.2940T>A	chr6.hg19:g.30919181T>A		62.0	0.0		70.0	36.0	NM_080870	C9IZC0|Q658M7|Q8WYN2	Silent	SNP	ENST00000462446.1	hg19	CCDS4692.2																																																																																			.	.		0.498	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870		A	30919181	T	A	30919181	2	1	344	1	0	0	0	0	0	0	0	1	4714	1509	53	4		4	DPCR1	6	30919181	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	27033	30919181	140195886	505	47868										
MUC21	394263	hgsc.bcm.edu	37	chr6	30955029	30955029	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acctccagtggggccagcacAgccaccaactctgggtccag	11	16	1	0	rs41288693		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:30955029A>T	ENST00000376296.3	+	2	1318	c.1077A>T	c.(1075-1077)acA>acT	p.T359T	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	359	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						GGGCCAGCACAGCCACCAACT	0.642																																					p.T359T		Atlas-SNP	.											.	MUC21	98	.	0			c.A1077T						.						138	137	137					6																	30955029		2201	4298	6499	SO:0001819	synonymous_variant	394263	exon2			CAGCACAGCCACC	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"Mucins"	21661	protein-coding gene	gene with protein product	"epiglycanin"		"chromosome 6 open reading frame 205"	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.1077A>T	chr6.hg19:g.30955029A>T		29.0	0.0		35.0	13.0	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Silent	SNP	ENST00000376296.3	hg19	CCDS34388.1																																																																																			.	.		0.642	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909		T	30955029	A	T	30955029	2	4	344	1	0	0	0	0	0	0	0	1	9986	175	7	4		4	MUC21	6	30955029	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	35848	30955029	140160038	506	47869										
SKIV2L	6499	hgsc.bcm.edu	37	chr6	31935153	31935153	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cgcattgggagtgatcctacAggtgagggtgatgggaattt	16	5	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:31935153A>T	ENST00000375394.2	+	21	2695	c.2582A>T	c.(2581-2583)cAg>cTg	p.Q861L	DXO_ENST00000478221.1_5'Flank|SKIV2L_ENST00000544581.1_Splice_Site_p.Q668L	NM_006929.4	NP_008860.4	Q15477	SKIV2_HUMAN	superkiller viralicidic activity 2-like (S. cerevisiae)	861					ATP catabolic process (GO:0006200)	nucleus (GO:0005634)|Ski complex (GO:0055087)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|large_intestine(1)|ovary(1)	4						GTGATCCTACAGGTGAGGGTG	0.562																																					p.Q861L		Atlas-SNP	.											.	SKIV2L	97	.	0			c.A2582T						.						102	79	87					6																	31935153		1509	2709	4218	SO:0001630	splice_region_variant	6499	exon21			TCCTACAGGTGAG		CCDS4731.1	6p21	2010-02-17	2001-11-28		ENSG00000204351	ENSG00000204351			10898	protein-coding gene	gene with protein product		600478	"superkiller viralicidic activity 2 (S. cerevisiae homolog)-like"	SKIV2		7759100, 9799600	Standard	XM_006715168		Approved	HLP, DDX13, SKI2W, 170A	uc003nyn.1	Q15477	OTTHUMG00000031146	ENST00000375394.2:c.2583+1A>T	chr6.hg19:g.31935153A>T		83.0	0.0		108.0	46.0	NM_006929	O15005|Q12902|Q15476|Q5ST66	Missense_Mutation	SNP	ENST00000375394.2	hg19	CCDS4731.1	.	.	.	.	.	.	.	.	.	.	A	15.47	2.842793	0.51057	.	.	ENSG00000204351	ENST00000375394;ENST00000433155;ENST00000544581	T;T	0.49432	0.9;0.78	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.36413	0.0966	L	0.54323	1.7	0.80722	D	1	P	0.43542	0.81	B	0.43478	0.421	T	0.37911	-0.9685	10	0.56958	D	0.05	-22.7114	13.886	0.63708	1.0:0.0:0.0:0.0	.	861	Q15477	SKIV2_HUMAN	L	861;703;668	ENSP00000364543:Q861L;ENSP00000442645:Q668L	ENSP00000364543:Q861L	Q	+	2	0	SKIV2L	32043132	1.000000	0.71417	1.000000	0.80357	0.530000	0.34684	7.755000	0.85180	2.123000	0.65237	0.482000	0.46254	CAG	.	.		0.562	SKIV2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076264.3		Missense_Mutation	T	31935153	A	T	31935153	5	4	344	1	0	0	0	0	0	0	1	0	14374	202	7	4	2664	4	SKIV2L	6	31935153	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	980124	31935153	139179914	507	47870										
GPSM3	63940	hgsc.bcm.edu	37	chr6	32159648	32159648	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aggtccagaaggagttcagtCtgcagggagagcagggaggc	18	7	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:32159648C>A	ENST00000375040.3	-	3	575	c.183G>T	c.(181-183)caG>caT	p.Q61H	PBX2_ENST00000375050.4_5'Flank|GPSM3_ENST00000487761.1_Missense_Mutation_p.Q58H|GPSM3_ENST00000375043.3_Missense_Mutation_p.Q61H	NM_001276501.1	NP_001263430.1	Q9Y4H4	GPSM3_HUMAN	G-protein signaling modulator 3	61					regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cytoplasm (GO:0005737)	GDP-dissociation inhibitor activity (GO:0005092)			large_intestine(1)	1						GGAGTTCAGTCTGCAGGGAGA	0.677																																					p.Q61H		Atlas-SNP	.											.	GPSM3	9	.	0			c.G183T						.						33	43	39					6																	32159648		1507	2707	4214	SO:0001583	missense	63940	exon7			TTCAGTCTGCAGG	AF155657	CCDS34419.1	6p21.3	2010-06-24	2010-06-24	2004-02-04	ENSG00000213654	ENSG00000213654			13945	protein-coding gene	gene with protein product	"activator of G-protein signaling 4"		"chromosome 6 open reading frame 9", "G-protein signalling modulator 3 (AGS3-like, C. elegans)"	C6orf9		2259622, 15096500	Standard	NM_022107		Approved	NG1, G18, G18.1a, G18.1b, G18.2, AGS4	uc003oaz.3	Q9Y4H4	OTTHUMG00000031244	ENST00000375040.3:c.183G>T	chr6.hg19:g.32159648C>A	ENSP00000364180:p.Gln61His	105.0	0.0		106.0	21.0	NM_022107	A2BFJ3	Missense_Mutation	SNP	ENST00000375040.3	hg19	CCDS34419.1	.	.	.	.	.	.	.	.	.	.	C	13.89	2.371129	0.42003	.	.	ENSG00000213654	ENST00000487761;ENST00000375040;ENST00000375043	.	.	.	4.32	3.43	0.39272	.	0.000000	0.56097	U	0.000025	T	0.42653	0.1212	N	0.24115	0.695	0.40212	D	0.977633	D	0.61697	0.99	D	0.70487	0.969	T	0.38001	-0.9681	9	0.41790	T	0.15	-0.9503	8.2332	0.31610	0.0:0.8874:0.0:0.1126	.	61	Q9Y4H4	GPSM3_HUMAN	H	58;61;61	.	ENSP00000364180:Q61H	Q	-	3	2	GPSM3	32267626	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	1.969000	0.40510	2.247000	0.74100	0.460000	0.39030	CAG	.	.		0.677	GPSM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076509.1	NM_022107		A	32159648	C	A	32159648	3	1	344	1	0	0	0	0	1	0	0	0	6745	912	32	3	307	3	GPSM3	6	32159648	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	224495	32159648	138955419	508	47871										
ITPR3	3710	hgsc.bcm.edu	37	chr6	33655094	33655094	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gggccataacatctatatccTggcgctgcaggtaccagttc	10	12	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:33655094T>A	ENST00000374316.5	+	46	7227	c.6167T>A	c.(6166-6168)cTg>cAg	p.L2056Q	ITPR3_ENST00000605930.1_Missense_Mutation_p.L2056Q			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	2056					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	ATCTATATCCTGGCGCTGCAG	0.627																																					p.L2056Q		Atlas-SNP	.											.	ITPR3	409	.	0			c.T6167A						.						58	49	52					6																	33655094		2203	4300	6503	SO:0001583	missense	3710	exon45			ATATCCTGGCGCT	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"Ion channels / Inositol triphosphate receptors"	6182	protein-coding gene	gene with protein product		147267	"inositol 1,4,5-triphosphate receptor, type 3"			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.6167T>A	chr6.hg19:g.33655094T>A	ENSP00000363435:p.Leu2056Gln	51.0	0.0		55.0	28.0	NM_002224	Q14649|Q5TAQ2	Missense_Mutation	SNP	ENST00000374316.5	hg19	CCDS4783.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.703199	0.88924	.	.	ENSG00000096433	ENST00000374316	D	0.94576	-3.46	4.68	4.68	0.58851	.	0.000000	0.64402	D	0.000002	D	0.96778	0.8948	M	0.82517	2.595	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.997	D	0.97609	1.0128	10	0.87932	D	0	-15.7744	14.4245	0.67204	0.0:0.0:0.0:1.0	.	2056;1726	Q14573;Q59ES2	ITPR3_HUMAN;.	Q	2056	ENSP00000363435:L2056Q	ENSP00000363435:L2056Q	L	+	2	0	ITPR3	33763072	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.928000	0.87587	1.868000	0.54150	0.459000	0.35465	CTG	.	.		0.627	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224		A	33655094	T	A	33655094	3	1	344	1	0	0	0	0	1	0	0	0	7931	1580	55	4	6345	4	ITPR3	6	33655094	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1495446	33655094	137459973	509	47872										
DNAH8	1769	hgsc.bcm.edu	37	chr6	38816528	38816528	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agtacagaacctttgggtttAtcttgaagccgtctttgtag	10	7	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:38816528A>G	ENST00000359357.3	+	35	4753	c.4499A>G	c.(4498-4500)tAt>tGt	p.Y1500C	DNAH8_ENST00000441566.1_Missense_Mutation_p.Y1500C|DNAH8_ENST00000449981.2_Missense_Mutation_p.Y1717C			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	1500					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						CTTTGGGTTTATCTTGAAGCC	0.358																																					p.Y1717C		Atlas-SNP	.											.	DNAH8	1239	.	0			c.A5150G						.						89	96	94					6																	38816528		2203	4300	6503	SO:0001583	missense	1769	exon37			GGGTTTATCTTGA	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.4499A>G	chr6.hg19:g.38816528A>G	ENSP00000352312:p.Tyr1500Cys	107.0	0.0		107.0	48.0	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	hg19		.	.	.	.	.	.	.	.	.	.	A	25.1	4.601385	0.87055	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.72942	-0.7;-0.7;-0.7	5.78	5.78	0.91487	Dynein heavy chain, domain-2 (1);	0.130908	0.53938	D	0.000056	D	0.89781	0.6814	H	0.98849	4.35	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93890	0.7179	10	0.87932	D	0	.	16.1138	0.81283	1.0:0.0:0.0:0.0	.	1500	Q96JB1	DYH8_HUMAN	C	1705;1705;1500;1500	ENSP00000333363:Y1705C;ENSP00000352312:Y1500C;ENSP00000402294:Y1500C	ENSP00000333363:Y1705C	Y	+	2	0	DNAH8	38924506	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.122000	0.94380	2.220000	0.72140	0.533000	0.62120	TAT	.	.		0.358	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		G	38816528	A	G	38816528	3	3	344	1	0	0	0	0	1	0	0	0	4609	449	16	2	4629	2	DNAH8	6	38816528	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	5161434	38816528	132298539	510	47873										
GLP1R	2740	hgsc.bcm.edu	37	chr6	39040694	39040694	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cctgtttgcatccttcatccTgcgagcattgtccgtcttca	7	14	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:39040694T>A	ENST00000373256.4	+	6	609	c.566T>A	c.(565-567)cTg>cAg	p.L189Q		NM_002062.3	NP_002053.3	P43220	GLP1R_HUMAN	glucagon-like peptide 1 receptor	189					activation of adenylate cyclase activity (GO:0007190)|cAMP-mediated signaling (GO:0019933)|energy reserve metabolic process (GO:0006112)|learning or memory (GO:0007611)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of heart contraction (GO:0008016)|regulation of insulin secretion (GO:0050796)|response to stress (GO:0006950)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glucagon receptor activity (GO:0004967)|transmembrane signaling receptor activity (GO:0004888)			breast(5)|endometrium(3)|kidney(1)|large_intestine(8)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	31					Exenatide(DB01276)|Glucagon recombinant(DB00040)|Liraglutide(DB06655)	TCCTTCATCCTGCGAGCATTG	0.577																																					p.L189Q		Atlas-SNP	.											.	GLP1R	64	.	0			c.T566A						.						220	176	191					6																	39040694		2203	4300	6503	SO:0001583	missense	2740	exon6			TCATCCTGCGAGC		CCDS4839.1	6p21	2012-08-10			ENSG00000112164	ENSG00000112164		"GPCR / Class B : Glucagon receptors"	4324	protein-coding gene	gene with protein product		138032					Standard	NM_002062		Approved		uc003ooj.4	P43220	OTTHUMG00000014638	ENST00000373256.4:c.566T>A	chr6.hg19:g.39040694T>A	ENSP00000362353:p.Leu189Gln	62.0	0.0		71.0	43.0	NM_002062	Q2M229|Q99669	Missense_Mutation	SNP	ENST00000373256.4	hg19	CCDS4839.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.845251	0.91197	.	.	ENSG00000112164	ENST00000373256	T	0.51574	0.7	5.71	5.71	0.89125	GPCR, family 2-like (1);	0.000000	0.56097	D	0.000034	T	0.71796	0.3382	M	0.92507	3.315	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.80246	-0.1462	10	0.87932	D	0	.	15.988	0.80176	0.0:0.0:0.0:1.0	.	189	P43220	GLP1R_HUMAN	Q	189	ENSP00000362353:L189Q	ENSP00000362353:L189Q	L	+	2	0	GLP1R	39148672	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	8.015000	0.88690	2.188000	0.69820	0.533000	0.62120	CTG	.	.		0.577	GLP1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040443.1			A	39040694	T	A	39040694	3	1	344	1	0	0	0	0	1	0	0	0	6460	1580	55	4	588	4	GLP1R	6	39040694	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	224166	39040694	132074373	511	47874										
UBR2	23304	hgsc.bcm.edu	37	chr6	42562032	42562032	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acttaacacctctgaaattgAggaagaagaggtaaaaacat	8	6	1	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:42562032A>G	ENST00000372899.1	+	4	779	c.521A>G	c.(520-522)gAg>gGg	p.E174G	UBR2_ENST00000372901.1_Missense_Mutation_p.E174G|UBR2_ENST00000372903.2_Missense_Mutation_p.E174G	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	174					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			TCTGAAATTGAGGAAGAAGAG	0.363																																					p.E174G		Atlas-SNP	.											.	UBR2	134	.	0			c.A521G						.						110	107	108					6																	42562032		2203	4300	6503	SO:0001583	missense	23304	exon4			AAATTGAGGAAGA	BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"Ubiquitin protein ligase E3 component n-recognins"	21289	protein-coding gene	gene with protein product		609134	"chromosome 6 open reading frame 133"	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.521A>G	chr6.hg19:g.42562032A>G	ENSP00000361990:p.Glu174Gly	92.0	0.0		96.0	31.0	NM_001184801	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Missense_Mutation	SNP	ENST00000372899.1	hg19	CCDS4870.1	.	.	.	.	.	.	.	.	.	.	A	12.43	1.934629	0.34189	.	.	ENSG00000024048	ENST00000372903;ENST00000372899;ENST00000372901	T;T;T	0.73897	-0.79;0.21;0.21	5.21	2.69	0.31865	.	0.238301	0.40818	N	0.001007	T	0.34193	0.0889	N	0.08118	0	0.80722	D	1	B;B	0.18610	0.001;0.029	B;B	0.28916	0.01;0.096	T	0.09314	-1.0680	10	0.29301	T	0.29	-21.0842	7.6047	0.28095	0.5915:0.2801:0.0:0.1283	.	174;174	Q8IWV8;Q8IWV8-2	UBR2_HUMAN;.	G	174	ENSP00000361994:E174G;ENSP00000361990:E174G;ENSP00000361992:E174G	ENSP00000361990:E174G	E	+	2	0	UBR2	42670010	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	2.944000	0.49034	0.255000	0.21593	0.459000	0.35465	GAG	.	.		0.363	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255		G	42562032	A	G	42562032	3	3	344	1	0	0	0	0	1	0	0	0	16917	304	11	2	535	2	UBR2	6	42562032	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3521338	42562032	128553035	512	47875										
CUL9	23113	hgsc.bcm.edu	37	chr6	43155009	43155009	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccctcctgggactggaatccTatggatgggctgtacccttt	11	12	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:43155009T>A	ENST00000252050.4	+	6	1497	c.1413T>A	c.(1411-1413)ccT>ccA	p.P471P	CUL9_ENST00000354495.3_Intron|CUL9_ENST00000372647.2_Silent_p.P471P	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	471					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						ACTGGAATCCTATGGATGGGC	0.567																																					p.P471P		Atlas-SNP	.											.	CUL9	248	.	0			c.T1413A						.						154	142	146					6																	43155009		2203	4300	6503	SO:0001819	synonymous_variant	23113	exon6			GAATCCTATGGAT	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"parkin-like cytoplasmic p53 binding protein", "p53-associated parkin-like cytoplasmic protein"	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.1413T>A	chr6.hg19:g.43155009T>A		72.0	0.0		86.0	35.0	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Silent	SNP	ENST00000252050.4	hg19	CCDS4890.1																																																																																			.	.		0.567	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		A	43155009	T	A	43155009	2	1	344	1	0	0	0	0	0	0	0	1	4063	1509	53	4		4	CUL9	6	43155009	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	592977	43155009	127960058	513	47876										
MEP1A	4224	hgsc.bcm.edu	37	chr6	46801092	46801092	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	taactttatacccaaatagcAgagaaagctctggttacttg	7	8	1	1	rs12197930	byFrequency	TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:46801092A>T	ENST00000230588.4	+	11	1435	c.1426A>T	c.(1426-1428)Aga>Tga	p.R476*		NM_005588.2	NP_005579.2	Q16819	MEP1A_HUMAN	meprin A, alpha (PABA peptide hydrolase)	476	MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.		R -> G (in dbSNP:rs12197930). {ECO:0000269|PubMed:15489334}.		digestion (GO:0007586)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|meprin A complex (GO:0017090)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42			Lung(136;0.192)			CCCAAATAGCAGAGAAAGCTC	0.468																																					p.R476X		Atlas-SNP	.											.	MEP1A	93	.	0			c.A1426T						.						92	96	95					6																	46801092		2203	4300	6503	SO:0001587	stop_gained	4224	exon11			AATAGCAGAGAAA		CCDS4918.1	6p12-p11	2010-10-18			ENSG00000112818	ENSG00000112818	3.4.24.18		7015	protein-coding gene	gene with protein product		600388				7774936	Standard	NM_005588		Approved	PPHA	uc010jzh.1	Q16819	OTTHUMG00000014790	ENST00000230588.4:c.1426A>T	chr6.hg19:g.46801092A>T	ENSP00000230588:p.Arg476*	55.0	0.0		37.0	15.0	NM_005588	A2RRM4|B0AZP9|B2RCS2|Q8TDC9|Q9H1R1	Nonsense_Mutation	SNP	ENST00000230588.4	hg19	CCDS4918.1	.	.	.	.	.	.	.	.	.	.	A	14.36	2.511134	0.44660	.	.	ENSG00000112818	ENST00000230588	.	.	.	5.61	0.122	0.14702	.	0.443943	0.29631	N	0.011614	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10377	T	0.69	0.391	5.145	0.14979	0.3225:0.4882:0.0707:0.1186	.	.	.	.	X	476	.	ENSP00000230588:R476X	R	+	1	2	MEP1A	46909051	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	1.053000	0.30442	-0.189000	0.10482	-0.297000	0.09499	AGA	.	A|0.957;G|0.043		0.468	MEP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040803.1	NM_005588		T	46801092	A	T	46801092	4	4	344	1	0	0	0	0	0	1	0	0	9484	180	7	4	1468	4	MEP1A	6	46801092	Nonsense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3646083	46801092	124313975	514	47877										
DEFB113	245927	hgsc.bcm.edu	37	chr6	49937307	49937307	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaccacaagacacagtgaagAcaaaggtcagaaaaatacaa	8	8	1	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:49937307A>G	ENST00000398718.1	-	1	31	c.32T>C	c.(31-33)gTc>gCc	p.V11A		NM_001037729.1	NP_001032818.1	Q30KQ7	DB113_HUMAN	defensin, beta 113	11					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)	7	Lung NSC(77;0.042)					CACAGTGAAGACAAAGGTCAG	0.328																																					p.V11A		Atlas-SNP	.											.	DEFB113	18	.	0			c.T32C						.						106	103	104					6																	49937307		1842	4084	5926	SO:0001583	missense	245927	exon1			GTGAAGACAAAGG	DQ012017	CCDS43472.1	6p12.3	2010-03-30			ENSG00000214642	ENSG00000214642		"Defensins, beta"	18094	protein-coding gene	gene with protein product						11854508, 16033865	Standard	NM_001037729		Approved	DEFB-13	uc011dwq.2	Q30KQ7	OTTHUMG00000160210	ENST00000398718.1:c.32T>C	chr6.hg19:g.49937307A>G	ENSP00000381703:p.Val11Ala	84.0	0.0		72.0	31.0	NM_001037729		Missense_Mutation	SNP	ENST00000398718.1	hg19	CCDS43472.1	.	.	.	.	.	.	.	.	.	.	A	11.91	1.778343	0.31502	.	.	ENSG00000214642	ENST00000398718	.	.	.	4.06	4.06	0.47325	.	.	.	.	.	T	0.09335	0.0230	.	.	.	0.09310	N	1	P	0.37781	0.608	B	0.29862	0.108	T	0.06127	-1.0844	6	.	.	.	0.1889	9.5877	0.39526	1.0:0.0:0.0:0.0	.	11	Q30KQ7	DB113_HUMAN	A	11	.	.	V	-	2	0	DEFB113	50045266	0.982000	0.34865	0.083000	0.20561	0.716000	0.41182	3.461000	0.53035	1.834000	0.53371	0.482000	0.46254	GTC	.	.		0.328	DEFB113-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359666.1			G	49937307	A	G	49937307	3	3	344	1	0	0	0	0	1	0	0	0	4404	275	10	2	216	2	DEFB113	6	49937307	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3136215	49937307	121177760	515	47878										
TFAP2D	83741	hgsc.bcm.edu	37	chr6	50712859	50712859	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcgggattttggctacacttGtgaaacagagtttccagcca	10	9	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:50712859G>T	ENST00000008391.3	+	6	1151	c.923G>T	c.(922-924)tGt>tTt	p.C308F	TFAP2D_ENST00000492804.1_3'UTR	NM_172238.3	NP_758438.2			transcription factor AP-2 delta (activating enhancer binding protein 2 delta)											NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(26)|ovary(6)|pancreas(1)|prostate(5)|stomach(1)	60	Lung NSC(77;0.0334)					GGCTACACTTGTGAAACAGAG	0.453																																					p.C308F		Atlas-SNP	.											.	TFAP2D	144	.	0			c.G923T						.						109	105	107					6																	50712859		2203	4300	6503	SO:0001583	missense	83741	exon6			ACACTTGTGAAAC	AY028376	CCDS4933.1	6p12.3	2008-02-05	2004-10-26	2004-10-27		ENSG00000008197			15581	protein-coding gene	gene with protein product		610161	"transcription factor AP-2 beta (activating enhancer-binding protein 2 beta)-like 1"	TFAP2BL1		11733187	Standard	NM_172238		Approved		uc003paf.3	Q7Z6R9		ENST00000008391.3:c.923G>T	chr6.hg19:g.50712859G>T	ENSP00000008391:p.Cys308Phe	179.0	0.0		203.0	91.0	NM_172238		Missense_Mutation	SNP	ENST00000008391.3	hg19	CCDS4933.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.659370	0.88154	.	.	ENSG00000008197	ENST00000008391	D	0.97279	-4.32	5.77	5.77	0.91146	Transcription factor AP-2, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98909	0.9630	M	0.92169	3.28	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	D	0.99478	1.0947	10	0.87932	D	0	-21.7582	19.9791	0.97320	0.0:0.0:1.0:0.0	.	308	Q7Z6R9	AP2D_HUMAN	F	308	ENSP00000008391:C308F	ENSP00000008391:C308F	C	+	2	0	TFAP2D	50820818	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.733000	0.93635	0.585000	0.79938	TGT	.	.		0.453	TFAP2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040881.1	NM_172238		T	50712859	G	T	50712859	3	4	344	1	0	0	0	0	1	0	0	0	15805	1377	48	3	945	3	TFAP2D	6	50712859	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	775552	50712859	120402208	516	47879										
PKHD1	5314	hgsc.bcm.edu	37	chr6	51890688	51890688	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgctatttgtgatttctcctTgcatggcagtgactactggt	10	8	1	2	rs572226863		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:51890688T>C	ENST00000371117.3	-	32	4195	c.3920A>G	c.(3919-3921)cAa>cGa	p.Q1307R	PKHD1_ENST00000340994.4_Missense_Mutation_p.Q1307R	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	1307	IPT/TIG 8; atypical.				cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					GATTTCTCCTTGCATGGCAGT	0.522																																					p.Q1307R		Atlas-SNP	.											.	PKHD1	927	.	0			c.A3920G						.						114	101	105					6																	51890688		2203	4300	6503	SO:0001583	missense	5314	exon32			TCTCCTTGCATGG	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.3920A>G	chr6.hg19:g.51890688T>C	ENSP00000360158:p.Gln1307Arg	97.0	0.0		96.0	44.0	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	hg19	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	T	7.606	0.673860	0.14841	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.87179	-2.02;-2.22	5.87	-2.62	0.06152	.	1.410580	0.04116	N	0.315491	T	0.48677	0.1513	N	0.02391	-0.57	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	T	0.44390	-0.9331	10	0.30078	T	0.28	.	9.0846	0.36572	0.0:0.1719:0.1267:0.7015	.	1307;1307	P08F94-2;P08F94	.;PKHD1_HUMAN	R	1307	ENSP00000360158:Q1307R;ENSP00000341097:Q1307R	ENSP00000341097:Q1307R	Q	-	2	0	PKHD1	51998647	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.290000	0.08354	-0.376000	0.07943	-0.912000	0.02778	CAA	.	.		0.522	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		C	51890688	T	C	51890688	3	2	344	1	0	0	0	0	1	0	0	0	11980	1812	63	2	8487	2	PKHD1	6	51890688	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1177829	51890688	119224379	517	47880										
MCM3	4172	hgsc.bcm.edu	37	chr6	52129386	52129386	+	Nonstop_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agttcagagacgaggcctccTcagatgaggaagatgatgcc	13	9	2	5			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:52129386T>A	ENST00000229854.7	-	17	2503	c.2427A>T	c.(2425-2427)tgA>tgT	p.*809C	MCM3_ENST00000596288.1_Nonstop_Mutation_p.*854C|MCM3_ENST00000419835.2_Nonstop_Mutation_p.*763C			P25205	MCM3_HUMAN	minichromosome maintenance complex component 3	0					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	alpha DNA polymerase:primase complex (GO:0005658)|centrosome (GO:0005813)|intracellular membrane-bounded organelle (GO:0043231)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			endometrium(4)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	20	Lung NSC(77;0.0931)					CGAGGCCTCCTCAGATGAGGA	0.527																																					p.X854C		Atlas-SNP	.											.	MCM3	63	.	0			c.A2562T						.						148	125	133					6																	52129386		2203	4300	6503	SO:0001578	stop_lost	4172	exon17			GCCTCCTCAGATG	X62153	CCDS4940.1, CCDS4940.2, CCDS75468.1	6p12	2008-02-05	2007-04-04		ENSG00000112118	ENSG00000112118			6945	protein-coding gene	gene with protein product		602693	"minichromosome maintenance deficient (S. cerevisiae) 3", "MCM3 minichromosome maintenance deficient 3 (S. cerevisiae)"			1549468	Standard	NM_002388		Approved		uc011dwu.2	P25205	OTTHUMG00000014844	ENST00000229854.7:c.2427A>T	chr6.hg19:g.52129386T>A		66.0	0.0		56.0	28.0	NM_002388	B4DWW4|Q92660|Q9BTR3|Q9NUE7	Missense_Mutation	SNP	ENST00000229854.7	hg19		.	.	.	.	.	.	.	.	.	.	T	20.9	4.061521	0.76187	.	.	ENSG00000112118	ENST00000229854;ENST00000419835	.	.	.	5.39	5.39	0.77823	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.98	0.41809	0.0:0.0749:0.0:0.9251	.	.	.	.	C	809;763	.	.	X	-	3	0	MCM3	52237345	1.000000	0.71417	0.995000	0.50966	0.912000	0.54170	5.809000	0.69172	2.263000	0.75096	0.533000	0.62120	TGA	.	.		0.527	MCM3-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470784.1			A	52129386	T	A	52129386	4	1	344	1	0	0	0	0	0	0	0	0	9396	1564	54	4	3	4	MCM3	6	52129386	Nonstop_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	238698	52129386	118985681	518	47881										
HCRTR2	3062	hgsc.bcm.edu	37	chr6	55142234	55142234	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aagcccctgcagcctgtttcAcagcctcgagggccaggaca	11	15	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:55142234A>G	ENST00000370862.3	+	5	1155	c.819A>G	c.(817-819)tcA>tcG	p.S273S		NM_001526.3	NP_001517.2	O43614	OX2R_HUMAN	hypocretin (orexin) receptor 2	273					circadian sleep/wake cycle process (GO:0022410)|feeding behavior (GO:0007631)|neuropeptide signaling pathway (GO:0007218)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|orexin receptor activity (GO:0016499)			breast(3)|endometrium(2)|kidney(1)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	46	Lung NSC(77;0.107)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			AGCCTGTTTCACAGCCTCGAG	0.517																																					p.S273S		Atlas-SNP	.											.	HCRTR2	112	.	0			c.A819G						.						69	73	72					6																	55142234		2203	4300	6503	SO:0001819	synonymous_variant	3062	exon5			TGTTTCACAGCCT	AF041245	CCDS4956.1	6p12.1	2012-09-20			ENSG00000137252	ENSG00000137252		"GPCR / Class A : Hypocretin (orexin) receptors"	4849	protein-coding gene	gene with protein product		602393				9491897	Standard	NM_001526		Approved	OX2R	uc003pcl.3	O43614	OTTHUMG00000016150	ENST00000370862.3:c.819A>G	chr6.hg19:g.55142234A>G		161.0	0.0		130.0	63.0	NM_001526	Q5VTM0	Silent	SNP	ENST00000370862.3	hg19	CCDS4956.1																																																																																			.	.		0.517	HCRTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043392.1			G	55142234	A	G	55142234	2	3	344	1	0	0	0	0	0	0	0	1	7011	146	6	2		2	HCRTR2	6	55142234	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3012848	55142234	115972833	519	47882										
ZNF451	26036	hgsc.bcm.edu	37	chr6	56993604	56993604	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cattctgatacagaagcagcAagactgtgtgtggaccagtg	12	8	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:56993604A>T	ENST00000370706.4	+	5	634	c.390A>T	c.(388-390)gcA>gcT	p.A130A	ZNF451_ENST00000357489.3_Silent_p.A130A|RP11-203B9.4_ENST00000592500.1_RNA|RP11-203B9.4_ENST00000592038.1_RNA|RP11-203B9.4_ENST00000588811.1_RNA|RP11-203B9.4_ENST00000585792.1_RNA|ZNF451_ENST00000491832.2_Silent_p.A130A|RP11-203B9.4_ENST00000586432.1_RNA|RP11-203B9.4_ENST00000591553.1_RNA|RP11-203B9.4_ENST00000586053.1_RNA|RP11-203B9.4_ENST00000416069.2_RNA|RP11-203B9.4_ENST00000587815.1_RNA|RP11-203B9.4_ENST00000586668.1_RNA	NM_001031623.2	NP_001026794.1	Q9Y4E5	ZN451_HUMAN	zinc finger protein 451	130					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32	Lung NSC(77;0.145)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			CAGAAGCAGCAAGACTGTGTG	0.388																																					p.A130A		Atlas-SNP	.											.	ZNF451	181	.	0			c.A390T						.						94	89	91					6																	56993604		2203	4300	6503	SO:0001819	synonymous_variant	26036	exon5			AGCAGCAAGACTG	AB011148	CCDS4960.1, CCDS43477.1, CCDS59026.1	6p12.1	2012-08-08			ENSG00000112200	ENSG00000112200		"Zinc fingers, C2H2-type"	21091	protein-coding gene	gene with protein product		615708				9628581	Standard	NM_001031623		Approved	KIAA0576, COASTER, dJ417I1.1, KIAA1702	uc003pdm.2	Q9Y4E5	OTTHUMG00000014916	ENST00000370706.4:c.390A>T	chr6.hg19:g.56993604A>T		82.0	0.0		107.0	32.0	NM_001031623	Q5VVE9|Q5VVF1|Q86YE4|Q8N380|Q8TD15|Q9C0G1|Q9NQM1	Silent	SNP	ENST00000370706.4	hg19	CCDS43477.1																																																																																			.	.		0.388	ZNF451-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041035.2	NM_015555		T	56993604	A	T	56993604	2	4	344	1	0	0	0	0	0	0	0	1	17937	117	5	4		4	ZNF451	6	56993604	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1851370	56993604	114121463	520	47883										
EYS	346007	hgsc.bcm.edu	37	chr6	66204911	66204911	+	Frame_Shift_Del	DEL	T	T	-													0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaattaacagtgtgcattccTtttagtctgcagccaaaaag							TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:66204911delT	ENST00000370621.3	-	4	919	c.393delA	c.(391-393)aaafs	p.K131fs	EYS_ENST00000342421.5_Frame_Shift_Del_p.K131fs|EYS_ENST00000370618.3_Frame_Shift_Del_p.K131fs|EYS_ENST00000503581.1_Frame_Shift_Del_p.K131fs|EYS_ENST00000370616.2_Frame_Shift_Del_p.K131fs|EYS_ENST00000393380.2_Frame_Shift_Del_p.K131fs			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	131					detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						TGTGCATTCCTTTTAGTCTGC	0.403																																					p.G132fs		Atlas-Indel,Pindel	.											.	EYS	527	.	0			c.394delG						.						70	64	66					6																	66204911		2203	4300	6503	SO:0001589	frameshift_variant	346007	exon4			.		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.393delA	chr6.hg19:g.66204911delT	ENSP00000359655:p.Lys131fs	102.0	0.0		99.0	44.0	NM_001142801	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Frame_Shift_Del	DEL	ENST00000370621.3	hg19																																																																																				.	.		0.403	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		-	66204911	T	-	66204911	7	5	344	1	0	1	0	1	0	0	0	0	5334	1606	56	0	9163	0	EYS	6	66204911	Frame_Shift_Del	DEL	T	TCGA-UB-A7MB-01A-11D-A33Q-10	9211307	66204911	104910156	521	47884										
BAI3	577	hgsc.bcm.edu	37	chr6	69949085	69949085	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atcatctcatccaatatcctCatactggttggacagactca	5	12	4	1	rs560469400		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:69949085C>T	ENST00000370598.1	+	20	3602	c.2781C>T	c.(2779-2781)ctC>ctT	p.L927L	BAI3_ENST00000238918.8_Silent_p.L133L	NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	927					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				CCAATATCCTCATACTGGTTG	0.343													C|||	1	0.000199681	0	0	5008	,	,		14515	0		0	False		,,,				2504	0.001				p.L927L		Atlas-SNP	.											.	BAI3	451	.	0			c.C2781T						.						169	161	163					6																	69949085		2203	4298	6501	SO:0001819	synonymous_variant	577	exon20			TATCCTCATACTG	AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"-", "GPCR / Class B : Orphans"	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.2781C>T	chr6.hg19:g.69949085C>T		98.0	0.0		89.0	35.0	NM_001704	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Silent	SNP	ENST00000370598.1	hg19	CCDS4968.1																																																																																			.	.		0.343	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			T	69949085	C	T	69949085	2	4	344	1	0	0	0	0	0	0	0	1	1300	813	29	3		3	BAI3	6	69949085	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	3744174	69949085	101165982	522	47885										
COL9A1	1297	hgsc.bcm.edu	37	chr6	70935655	70935655	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctgggagacctatagctccaGgcaaaccgttgggacctctt	11	12	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:70935655G>T	ENST00000357250.6	-	37	2719	c.2561C>A	c.(2560-2562)cCt>cAt	p.P854H	COL9A1_ENST00000370499.4_Missense_Mutation_p.P611H|RP1-149L1.1_ENST00000522264.1_RNA|COL9A1_ENST00000489611.1_5'UTR|COL9A1_ENST00000320755.7_Missense_Mutation_p.P611H	NM_001851.4	NP_001842.3	P20849	CO9A1_HUMAN	collagen, type IX, alpha 1	854	Collagen-like 10.|Triple-helical region (COL1).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|organ morphogenesis (GO:0009887)|tissue homeostasis (GO:0001894)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(44)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)	80						TATAGCTCCAGGCAAACCGTT	0.428																																					p.P854H		Atlas-SNP	.											.	COL9A1	228	.	0			c.C2561A						.						79	74	75					6																	70935655		2203	4300	6503	SO:0001583	missense	1297	exon37			GCTCCAGGCAAAC		CCDS4971.1, CCDS47447.1	6q13	2013-05-07			ENSG00000112280	ENSG00000112280		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2217	protein-coding gene	gene with protein product		120210				1429648	Standard	NM_001851		Approved		uc003pfg.4	P20849	OTTHUMG00000014988	ENST00000357250.6:c.2561C>A	chr6.hg19:g.70935655G>T	ENSP00000349790:p.Pro854His	83.0	0.0		66.0	36.0	NM_001851	Q13699|Q13700|Q5TF52|Q6P467|Q96BM8|Q99225|Q9H151|Q9H152|Q9Y6P2|Q9Y6P3	Missense_Mutation	SNP	ENST00000357250.6	hg19	CCDS4971.1	.	.	.	.	.	.	.	.	.	.	G	16.40	3.113195	0.56398	.	.	ENSG00000112280	ENST00000357250;ENST00000320755;ENST00000370499	D;D;D	0.98701	-5.08;-5.08;-5.08	5.43	5.43	0.79202	.	0.051294	0.85682	D	0.000000	D	0.99477	0.9814	H	0.95539	3.685	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.98481	1.0605	10	0.66056	D	0.02	.	19.2294	0.93831	0.0:0.0:1.0:0.0	.	854;611;403	P20849;P20849-2;B3KWS8	CO9A1_HUMAN;.;.	H	854;611;611	ENSP00000349790:P854H;ENSP00000315252:P611H;ENSP00000359530:P611H	ENSP00000315252:P611H	P	-	2	0	COL9A1	70992376	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	6.149000	0.71795	2.557000	0.86248	0.591000	0.81541	CCT	.	.		0.428	COL9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041131.2			T	70935655	G	T	70935655	3	4	344	1	0	0	0	0	1	0	0	0	3709	1000	35	3	212	3	COL9A1	6	70935655	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	986570	70935655	100179412	523	47886										
MYO6	4646	hgsc.bcm.edu	37	chr6	76576647	76576647	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcctgtttgatttatttttcAgacccagtttgtggagaaaa	8	6	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:76576647A>T	ENST00000369977.3	+	18	1909		c.e18-1		snoU13_ENST00000459013.1_RNA|MYO6_ENST00000369985.4_Splice_Site|RNA5SP209_ENST00000411237.1_RNA|MYO6_ENST00000369975.1_Splice_Site|MYO6_ENST00000369981.3_Splice_Site	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI						actin filament-based movement (GO:0030048)|auditory receptor cell differentiation (GO:0042491)|cellular response to electrical stimulus (GO:0071257)|dendrite development (GO:0016358)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|endocytosis (GO:0006897)|glutamate secretion (GO:0014047)|inner ear morphogenesis (GO:0042472)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein targeting (GO:0006605)|regulation of secretion (GO:0051046)|regulation of synaptic plasticity (GO:0048167)|response to drug (GO:0042493)|sensory perception of sound (GO:0007605)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell cortex (GO:0005938)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microvillus (GO:0005902)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|unconventional myosin complex (GO:0016461)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|minus-end directed microfilament motor activity (GO:0060001)|motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(16)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	58		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		TTTATTTTTCAGACCCAGTTT	0.338																																					.		Atlas-SNP	.											.	MYO6	124	.	0			c.1771-2A>T						.						62	64	63					6																	76576647		2202	4300	6502	SO:0001630	splice_region_variant	4646	exon18			TTTTTCAGACCCA	U90236, AB002387	CCDS34487.1, CCDS75481.1	6q14.1	2014-09-17	2004-05-19		ENSG00000196586	ENSG00000196586		"Myosins / Myosin superfamily : Class VI"	7605	protein-coding gene	gene with protein product		600970	"deafness, autosomal recessive 37"	DFNA22, DFNB37		9259267, 11468689	Standard	XM_005248719		Approved	KIAA0389	uc003pih.1	Q9UM54	OTTHUMG00000015061	ENST00000369977.3:c.1771-1A>T	chr6.hg19:g.76576647A>T		63.0	0.0		64.0	35.0	NM_004999	A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	Splice_Site	SNP	ENST00000369977.3	hg19	CCDS34487.1	.	.	.	.	.	.	.	.	.	.	A	19.93	3.917409	0.73098	.	.	ENSG00000196586	ENST00000428345;ENST00000369981;ENST00000369985;ENST00000369977;ENST00000369975	.	.	.	5.61	5.61	0.85477	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.101	0.81172	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MYO6	76633367	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	8.883000	0.92426	2.263000	0.75096	0.528000	0.53228	.	.	.		0.338	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041279.2	NM_004999	Intron	T	76576647	A	T	76576647	5	4	344	1	0	0	0	0	0	0	1	0	10090	202	7	4	1835	4	MYO6	6	76576647	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	5640992	76576647	94538420	524	47887										
PHIP	55023	hgsc.bcm.edu	37	chr6	79770201	79770201	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctcaaacaactcaccaatgcTgggtgggctaccatagttaa	8	11	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:79770201T>A	ENST00000275034.4	-	6	600	c.433A>T	c.(433-435)Agc>Tgc	p.S145C		NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	145					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		TCACCAATGCTGGGTGGGCTA	0.423																																					p.S145C		Atlas-SNP	.											.	PHIP	177	.	0			c.A433T						.						80	75	77					6																	79770201		2203	4300	6503	SO:0001583	missense	55023	exon6			CAATGCTGGGTGG	AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	15673	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 14"	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.433A>T	chr6.hg19:g.79770201T>A	ENSP00000275034:p.Ser145Cys	62.0	0.0		52.0	22.0	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000275034.4	hg19	CCDS4987.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.192404	0.78902	.	.	ENSG00000146247	ENST00000275034	T	0.17854	2.25	5.15	5.15	0.70609	WD40/YVTN repeat-like-containing domain (1);	0.054903	0.85682	D	0.000000	T	0.13586	0.0329	L	0.34521	1.04	0.52501	D	0.999953	D;D	0.64830	0.994;0.994	P;P	0.54460	0.753;0.753	T	0.03139	-1.1068	9	.	.	.	-11.1752	13.9285	0.63978	0.0:0.0:0.0:1.0	.	145;145	A7J992;Q8WWQ0	.;PHIP_HUMAN	C	145	ENSP00000275034:S145C	.	S	-	1	0	PHIP	79826920	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	7.698000	0.84413	2.162000	0.67917	0.482000	0.46254	AGC	.	.		0.423	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2			A	79770201	T	A	79770201	3	1	344	1	0	0	0	0	1	0	0	0	11851	1580	55	4	5172	4	PHIP	6	79770201	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	3193554	79770201	91344866	525	47888										
LCA5	167691	hgsc.bcm.edu	37	chr6	80223068	80223068	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	attttgtcctaaatagttcaCtttctgtatcttttaccctt	3	9	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:80223068C>A	ENST00000392959.1	-	4	1192	c.581G>T	c.(580-582)aGt>aTt	p.S194I	LCA5_ENST00000467898.3_Missense_Mutation_p.S194I|LCA5_ENST00000369846.4_Missense_Mutation_p.S194I	NM_181714.3	NP_859065.2	Q86VQ0	LCA5_HUMAN	Leber congenital amaurosis 5	194					intraciliary transport (GO:0042073)|photoreceptor cell maintenance (GO:0045494)|protein transport (GO:0015031)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein complex binding (GO:0032403)			haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	32		all_cancers(76;3.32e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0176)		BRCA - Breast invasive adenocarcinoma(397;0.0657)		AAATAGTTCACTTTCTGTATC	0.358																																					p.S194I		Atlas-SNP	.											.	LCA5	71	.	0			c.G581T						.						168	163	165					6																	80223068		2203	4300	6503	SO:0001583	missense	167691	exon3			AGTTCACTTTCTG		CCDS4990.1	6q14	2014-01-28			ENSG00000135338	ENSG00000135338			31923	protein-coding gene	gene with protein product	"lebercilin"	611408	"chromosome 6 open reading frame 152"	C6orf152		10631161, 17546029	Standard	NM_181714		Approved		uc003pix.3	Q86VQ0	OTTHUMG00000015080	ENST00000392959.1:c.581G>T	chr6.hg19:g.80223068C>A	ENSP00000376686:p.Ser194Ile	187.0	0.0		148.0	64.0	NM_001122769	E1P542|Q9BWX7	Missense_Mutation	SNP	ENST00000392959.1	hg19	CCDS4990.1	.	.	.	.	.	.	.	.	.	.	C	12.11	1.840744	0.32513	.	.	ENSG00000135338	ENST00000369846;ENST00000392959	T;T	0.77620	-1.11;-1.11	6.07	5.21	0.72293	.	0.573034	0.18957	N	0.126520	T	0.46073	0.1374	N	0.24115	0.695	0.23089	N	0.998316	B;B	0.31790	0.03;0.34	B;B	0.31686	0.012;0.134	T	0.36720	-0.9736	10	0.48119	T	0.1	-0.8082	7.7401	0.28837	0.0:0.7573:0.0:0.2427	.	194;194	B4DRL2;Q86VQ0	.;LCA5_HUMAN	I	194	ENSP00000358861:S194I;ENSP00000376686:S194I	ENSP00000358861:S194I	S	-	2	0	LCA5	80279787	0.820000	0.29190	0.999000	0.59377	0.762000	0.43233	1.381000	0.34362	1.571000	0.49722	0.655000	0.94253	AGT	.	.		0.358	LCA5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259269.1	NM_181714		A	80223068	C	A	80223068	3	1	344	1	0	0	0	0	1	0	0	0	8665	565	20	3	1536	3	LCA5	6	80223068	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	452867	80223068	90891999	526	47889										
C6orf165	154313	hgsc.bcm.edu	37	chr6	88128124	88128124	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acaatatgaggtcttccttcAgatcattttggtgagttaag	9	6	3	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:88128124A>T	ENST00000507897.1	+	7	913	c.830A>T	c.(829-831)cAg>cTg	p.Q277L	C6ORF165_ENST00000369562.4_Missense_Mutation_p.Q277L			Q8IYR0	CF165_HUMAN	chromosome 6 open reading frame 165	277										NS(1)|central_nervous_system(1)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0419)		GTCTTCCTTCAGATCATTTTG	0.388																																					p.Q277L		Atlas-SNP	.											.	C6orf165	116	.	0			c.A830T						.						92	98	96					6																	88128124		2203	4300	6503	SO:0001583	missense	154313	exon7			TCCTTCAGATCAT	BC035083	CCDS34498.1	6q15	2012-02-07			ENSG00000213204	ENSG00000213204			21405	protein-coding gene	gene with protein product							Standard	NM_001031743		Approved	FLJ25974, dJ382I10.1	uc003plv.3	Q8IYR0	OTTHUMG00000015173	ENST00000507897.1:c.830A>T	chr6.hg19:g.88128124A>T	ENSP00000426769:p.Gln277Leu	71.0	0.0		61.0	28.0	NM_001031743	A8K969|E1P507|Q8N9U4	Missense_Mutation	SNP	ENST00000507897.1	hg19	CCDS34498.1	.	.	.	.	.	.	.	.	.	.	A	14.35	2.509364	0.44660	.	.	ENSG00000213204	ENST00000369562	T	0.30981	1.51	5.16	5.16	0.70880	.	0.521716	0.22690	N	0.056835	T	0.12732	0.0309	L	0.47716	1.5	0.30853	N	0.734339	P;B	0.36282	0.546;0.376	B;B	0.33960	0.173;0.124	T	0.10917	-1.0609	10	0.54805	T	0.06	.	8.4386	0.32801	0.8761:0.0:0.1239:0.0	.	277;277	Q8IYR0;E1P509	CF165_HUMAN;.	L	277	ENSP00000358575:Q277L	ENSP00000358575:Q277L	Q	+	2	0	C6orf165	88184843	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.914000	0.56401	2.082000	0.62665	0.482000	0.46254	CAG	.	.		0.388	C6orf165-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000470406.1	NM_178823		T	88128124	A	T	88128124	3	4	344	1	0	0	0	0	1	0	0	0	2343	188	7	4	852	4	C6orf165	6	88128124	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	7905056	88128124	82986943	527	47890										
MDN1	23195	hgsc.bcm.edu	37	chr6	90371171	90371171	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttctccttcttcattgtcggTgtcctcaccaccattcttgt	5	14	5	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:90371171T>C	ENST00000369393.3	-	88	14807	c.14692A>G	c.(14692-14694)Acc>Gcc	p.T4898A	MDN1_ENST00000428876.1_Missense_Mutation_p.T4898A			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	4898					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		TCATTGTCGGTGTCCTCACCA	0.458																																					p.T4898A		Atlas-SNP	.											.	MDN1	478	.	0			c.A14692G						.						222	213	216					6																	90371171		2203	4300	6503	SO:0001583	missense	23195	exon88			TGTCGGTGTCCTC	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.14692A>G	chr6.hg19:g.90371171T>C	ENSP00000358400:p.Thr4898Ala	130.0	0.0		103.0	39.0	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	hg19	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	T	11.63	1.695960	0.30052	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.02863	4.13;4.13	4.62	3.45	0.39498	.	0.342183	0.22155	N	0.063872	T	0.00906	0.0030	L	0.47716	1.5	0.20196	N	0.999924	B	0.22003	0.063	B	0.22386	0.039	T	0.48433	-0.9036	10	0.15066	T	0.55	.	5.4136	0.16361	0.0:0.2043:0.0:0.7957	.	4898	Q9NU22	MDN1_HUMAN	A	4898	ENSP00000358400:T4898A;ENSP00000413970:T4898A	ENSP00000358400:T4898A	T	-	1	0	MDN1	90427892	1.000000	0.71417	0.992000	0.48379	0.020000	0.10135	3.591000	0.53986	1.854000	0.53819	0.528000	0.53228	ACC	.	.		0.458	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			C	90371171	T	C	90371171	3	2	344	1	0	0	0	0	1	0	0	0	9424	1696	59	2	2158	2	MDN1	6	90371171	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2243047	90371171	80743896	528	47891										
MDN1	23195	hgsc.bcm.edu	37	chr6	90371808	90371808	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtttcaaatcttcattacctCatctatttgttcattaattt	2	8	6	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:90371808C>A	ENST00000369393.3	-	87	14678	c.14563G>T	c.(14563-14565)Gag>Tag	p.E4855*	MDN1_ENST00000428876.1_Nonsense_Mutation_p.E4855*			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	4855					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		TTCATTACCTCATCTATTTGT	0.388																																					p.E4855X		Atlas-SNP	.											.	MDN1	478	.	0			c.G14563T						.						376	326	343					6																	90371808		2203	4299	6502	SO:0001587	stop_gained	23195	exon87			TTACCTCATCTAT	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.14563G>T	chr6.hg19:g.90371808C>A	ENSP00000358400:p.Glu4855*	60.0	0.0		64.0	29.0	NM_014611	O15019|Q5T794	Nonsense_Mutation	SNP	ENST00000369393.3	hg19	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	C	55	25.077022	0.99963	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	.	.	.	5.62	5.62	0.85841	.	0.064498	0.64402	D	0.000013	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	.	20.0333	0.97547	0.0:1.0:0.0:0.0	.	.	.	.	X	4855	.	ENSP00000358400:E4855X	E	-	1	0	MDN1	90428529	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	3.097000	0.50251	2.810000	0.96702	0.585000	0.79938	GAG	.	.		0.388	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			A	90371808	C	A	90371808	4	1	344	1	0	0	0	0	0	1	0	0	9424	835	29	3	2291	3	MDN1	6	90371808	Nonsense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	637	90371808	80743259	529	47892										
BACH2	60468	hgsc.bcm.edu	37	chr6	90661011	90661011	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctcacttttaatctgcccccTggcaagccccggcttgaggc	9	16	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:90661011T>A	ENST00000257749.4	-	7	1521	c.814A>T	c.(814-816)Agg>Tgg	p.R272W	RP3-512E2.2_ENST00000413986.1_RNA|RP3-512E2.2_ENST00000445838.1_RNA|BACH2_ENST00000537989.1_Missense_Mutation_p.R272W|BACH2_ENST00000343122.3_Missense_Mutation_p.R272W	NM_021813.2	NP_068585.1	Q9BYV9	BACH2_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 2	272						cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	45		all_cancers(76;7.37e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.0063)		BRCA - Breast invasive adenocarcinoma(108;0.0799)		ATCTGCCCCCTGGCAAGCCCC	0.527																																					p.R272W		Atlas-SNP	.											.	BACH2	224	.	0			c.A814T						.						77	78	78					6																	90661011		2203	4300	6503	SO:0001583	missense	60468	exon7			GCCCCCTGGCAAG	AL121787	CCDS5026.1	6q15	2013-01-10			ENSG00000112182	ENSG00000112182		"BTB/POZ domain containing", "basic leucine zipper proteins"	14078	protein-coding gene	gene with protein product		605394				10949928, 12829606	Standard	NM_001170794		Approved	BTBD25	uc003pnw.3	Q9BYV9	OTTHUMG00000015216	ENST00000257749.4:c.814A>T	chr6.hg19:g.90661011T>A	ENSP00000257749:p.Arg272Trp	55.0	0.0		44.0	24.0	NM_021813	E1P518|Q59H70|Q5T793|Q9NTS5	Missense_Mutation	SNP	ENST00000257749.4	hg19	CCDS5026.1	.	.	.	.	.	.	.	.	.	.	T	6.805	0.517638	0.13005	.	.	ENSG00000112182	ENST00000257749;ENST00000537989;ENST00000343122	T;T;T	0.37584	1.19;1.19;1.19	5.03	-4.69	0.03299	.	0.868689	0.10677	N	0.646818	T	0.04998	0.0134	N	0.08118	0	0.23063	N	0.998353	B	0.22080	0.064	B	0.09377	0.004	T	0.35943	-0.9768	10	0.66056	D	0.02	-22.7857	4.9045	0.13791	0.1025:0.4521:0.1043:0.3412	.	272	Q9BYV9	BACH2_HUMAN	W	272	ENSP00000257749:R272W;ENSP00000437473:R272W;ENSP00000345642:R272W	ENSP00000257749:R272W	R	-	1	2	BACH2	90717732	0.004000	0.15560	0.414000	0.26521	0.311000	0.27955	-1.165000	0.03132	-0.733000	0.04850	0.533000	0.62120	AGG	.	.		0.527	BACH2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041522.2	NM_021813		A	90661011	T	A	90661011	3	1	344	1	0	0	0	0	1	0	0	0	1284	1579	55	4	1723	4	BACH2	6	90661011	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	289203	90661011	80454056	530	47893										
NDUFAF4	29078	hgsc.bcm.edu	37	chr6	97339048	97339048	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttcaaaagtaacaaaatattTaagaagagaattcacatctt	4	5	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:97339048T>A	ENST00000316149.7	-	3	539	c.460A>T	c.(460-462)Aaa>Taa	p.K154*	NDUFAF4_ENST00000489477.1_5'UTR	NM_014165.3	NP_054884.1	Q9P032	NDUF4_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 4	154					mitochondrial respiratory chain complex I assembly (GO:0032981)	mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)				large_intestine(5)|lung(3)|ovary(1)|skin(1)	10						ACAAAATATTTAAGAAGAGAA	0.348																																					p.K154X		Atlas-SNP	.											.	NDUFAF4	16	.	0			c.A460T						.						60	61	61					6																	97339048		2202	4298	6500	SO:0001587	stop_gained	29078	exon3			AATATTTAAGAAG	AF161474	CCDS5037.1	6q16.3	2012-10-12	2012-05-08	2009-03-18	ENSG00000123545	ENSG00000123545		"Mitochondrial respiratory chain complex assembly factors"	21034	protein-coding gene	gene with protein product		611776	"chromosome 6 open reading frame 66", "NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 4"	C6orf66		11042152, 18179882	Standard	NM_014165		Approved	HSPC125, bA22L21.1, My013, HRPAP20	uc003pow.3	Q9P032	OTTHUMG00000015246	ENST00000316149.7:c.460A>T	chr6.hg19:g.97339048T>A	ENSP00000358272:p.Lys154*	59.0	0.0		48.0	15.0	NM_014165	B2R4J5	Nonsense_Mutation	SNP	ENST00000316149.7	hg19	CCDS5037.1	.	.	.	.	.	.	.	.	.	.	T	15.01	2.704997	0.48412	.	.	ENSG00000123545	ENST00000316149	.	.	.	5.08	5.08	0.68730	.	0.213702	0.47852	D	0.000220	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08381	T	0.77	-12.7503	7.3694	0.26792	0.0:0.1702:0.0:0.8298	.	.	.	.	X	154	.	ENSP00000358272:K154X	K	-	1	0	NDUFAF4	97445769	0.999000	0.42202	0.945000	0.38365	0.439000	0.31926	1.663000	0.37429	1.916000	0.55485	0.533000	0.62120	AAA	.	.		0.348	NDUFAF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041567.1	NM_014165		A	97339048	T	A	97339048	4	1	344	1	0	0	0	0	0	1	0	0	10286	1763	61	4	71	4	NDUFAF4	6	97339048	Nonsense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	6678037	97339048	73776019	531	47894										
BVES	11149	hgsc.bcm.edu	37	chr6	105572512	105572512	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atgttatgcagaaaatgtccTcgataggagaccttcattct	8	8	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:105572512T>A	ENST00000314641.5	-	5	774	c.558A>T	c.(556-558)cgA>cgT	p.R186R	BVES_ENST00000336775.5_Silent_p.R186R|BVES_ENST00000446408.2_Silent_p.R186R	NM_001199563.1	NP_001186492.1	Q8NE79	POPD1_HUMAN	blood vessel epicardial substance	186					epithelial cell-cell adhesion (GO:0090136)|hematopoietic progenitor cell differentiation (GO:0002244)|muscle organ development (GO:0007517)|positive regulation of locomotion (GO:0040017)|positive regulation of receptor recycling (GO:0001921)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|regulation of Rac GTPase activity (GO:0032314)|sinoatrial node cell development (GO:0060931)|substrate adhesion-dependent cell spreading (GO:0034446)|vesicle-mediated transport (GO:0016192)	integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	cAMP binding (GO:0030552)|structural molecule activity (GO:0005198)			NS(2)|large_intestine(6)|lung(9)|prostate(2)|skin(1)|urinary_tract(1)	21		all_cancers(87;2.83e-05)|Acute lymphoblastic leukemia(125;1.95e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0101)|Colorectal(196;0.204)|Lung NSC(302;0.238)				GAAAATGTCCTCGATAGGAGA	0.333																																					p.R186R		Atlas-SNP	.											.	BVES	33	.	0			c.A558T						.						86	94	91					6																	105572512		2203	4299	6502	SO:0001819	synonymous_variant	11149	exon5			ATGTCCTCGATAG	AF124512	CCDS5051.1	6q21	2008-11-25			ENSG00000112276	ENSG00000112276			1152	protein-coding gene	gene with protein product	"popeye domain containing 1"	604577				10441744, 10882522	Standard	NM_147147		Approved	HBVES, POP1, POPDC1	uc003pqx.3	Q8NE79	OTTHUMG00000015291	ENST00000314641.5:c.558A>T	chr6.hg19:g.105572512T>A		45.0	0.0		30.0	10.0	NM_001199563	A8K1R4|E1P5D8|Q5T550|Q5T551|Q8IWC6|Q9HBV0|Q9UNG6	Silent	SNP	ENST00000314641.5	hg19	CCDS5051.1																																																																																			.	.		0.333	BVES-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406075.1	NM_147147		A	105572512	T	A	105572512	2	1	344	1	0	0	0	0	0	0	0	1	1577	1538	54	4		4	BVES	6	105572512	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	8233464	105572512	65542555	532	47895										
BEND3	57673	hgsc.bcm.edu	37	chr6	107390413	107390413	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgcactcagggcccggcacgTggaccttgcgctgctgctgg	15	14	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:107390413T>C	ENST00000369042.1	-	4	2172	c.1982A>G	c.(1981-1983)cAc>cGc	p.H661R	BEND3_ENST00000429433.2_Missense_Mutation_p.H661R			Q5T5X7	BEND3_HUMAN	BEN domain containing 3	661										central_nervous_system(1)|cervix(2)|endometrium(3)|large_intestine(7)|lung(10)|ovary(4)|prostate(3)	30						GCCCGGCACGTGGACCTTGCG	0.667																																					p.H661R		Atlas-SNP	.											.	BEND3	70	.	0			c.A1982G						.						30	34	33					6																	107390413		2195	4293	6488	SO:0001583	missense	57673	exon5			GGCACGTGGACCT	AB046773	CCDS34507.1	6q21	2012-11-22	2008-10-03	2008-10-03	ENSG00000178409	ENSG00000178409		"BEN domain containing"	23040	protein-coding gene	gene with protein product			"KIAA1553"	KIAA1553			Standard	NM_001080450		Approved		uc003prs.2	Q5T5X7	OTTHUMG00000015308	ENST00000369042.1:c.1982A>G	chr6.hg19:g.107390413T>C	ENSP00000358038:p.His661Arg	58.0	0.0		46.0	21.0	NM_001080450	A2RRH2|Q9HCL9	Missense_Mutation	SNP	ENST00000369042.1	hg19	CCDS34507.1	.	.	.	.	.	.	.	.	.	.	T	9.769	1.172278	0.21704	.	.	ENSG00000178409	ENST00000369042;ENST00000429433	.	.	.	4.34	3.08	0.35506	.	0.208989	0.43110	D	0.000618	T	0.22859	0.0552	N	0.14661	0.345	0.37396	D	0.912649	B	0.18461	0.028	B	0.12156	0.007	T	0.14727	-1.0462	9	0.49607	T	0.09	-2.4588	10.6919	0.45875	0.1429:0.0:0.0:0.8571	.	661	Q5T5X7	BEND3_HUMAN	R	661	.	ENSP00000358038:H661R	H	-	2	0	BEND3	107497106	0.986000	0.35501	0.995000	0.50966	0.975000	0.68041	1.808000	0.38912	1.952000	0.56665	0.374000	0.22700	CAC	.	.		0.667	BEND3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041686.1	NM_020913		C	107390413	T	C	107390413	3	2	344	1	0	0	0	0	1	0	0	0	1399	1696	59	2	508	2	BEND3	6	107390413	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1817901	107390413	63724654	533	47896										
CDC40	51362	hgsc.bcm.edu	37	chr6	110522886	110522886	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	caaaggagaacttttgcaacAtatggtaaggtgataagact	10	5	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:110522886A>G	ENST00000368932.1	+	4	503	c.402A>G	c.(400-402)acA>acG	p.T134T	CDC40_ENST00000368930.1_Silent_p.T134T|CDC40_ENST00000307731.1_Silent_p.T134T			O60508	PRP17_HUMAN	cell division cycle 40	134					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)	18		all_cancers(87;6.23e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488)		Epithelial(106;0.0221)|all cancers(137;0.0314)|OV - Ovarian serous cystadenocarcinoma(136;0.034)		CTTTTGCAACATATGGTAAGG	0.373																																					p.T134T		Atlas-SNP	.											.	CDC40	39	.	0			c.A402G						.						157	154	155					6																	110522886		2203	4300	6503	SO:0001819	synonymous_variant	51362	exon3			TGCAACATATGGT	AF015044	CCDS5081.1	6q22.1	2013-01-17	2013-01-17		ENSG00000168438	ENSG00000168438		"WD repeat domain containing"	17350	protein-coding gene	gene with protein product		605585	"cell division cycle 40 homolog (yeast)", "cell division cycle 40 homolog (S. cerevisiae)"			9769104, 9830021	Standard	NM_015891		Approved	PRP17, EHB3, PRPF17, FLJ10564	uc003pua.3	O60508	OTTHUMG00000015358	ENST00000368932.1:c.402A>G	chr6.hg19:g.110522886A>G		75.0	0.0		52.0	26.0	NM_015891	B2RBC5|O75471|Q5SRN0|Q9UPG1	Silent	SNP	ENST00000368932.1	hg19	CCDS5081.1	.	.	.	.	.	.	.	.	.	.	A	10.18	1.279650	0.23307	.	.	ENSG00000168438	ENST00000431461	.	.	.	5.72	-1.15	0.09709	.	.	.	.	.	T	0.22781	0.0550	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.27739	-1.0065	4	.	.	.	-8.9947	1.1692	0.01822	0.3801:0.2913:0.1464:0.1822	.	.	.	.	V	27	.	.	I	+	1	0	CDC40	110629579	0.153000	0.22777	0.997000	0.53966	0.959000	0.62525	-0.527000	0.06200	-0.142000	0.11354	0.528000	0.53228	ATA	.	.		0.373	CDC40-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041791.1	NM_015891		G	110522886	A	G	110522886	2	3	344	1	0	0	0	0	0	0	0	1	3072	204	8	2		2	CDC40	6	110522886	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3132473	110522886	60592181	534	47897										
KIAA1919	91749	hgsc.bcm.edu	37	chr6	111587672	111587672	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccatgattgtgttgagcaacAttggcagcctgacttcatct	9	10	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:111587672A>G	ENST00000368847.4	+	4	1260	c.907A>G	c.(907-909)Att>Gtt	p.I303V		NM_153369.2	NP_699200.2	Q5TF39	NAGT1_HUMAN	KIAA1919	303					carbohydrate transport (GO:0008643)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			large_intestine(3)|lung(2)|ovary(4)|skin(3)	12		all_cancers(87;2.35e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.0209)		OV - Ovarian serous cystadenocarcinoma(136;0.055)|all cancers(137;0.0871)|Epithelial(106;0.0884)		GTTGAGCAACATTGGCAGCCT	0.468																																					p.I303V		Atlas-SNP	.											.	KIAA1919	54	.	0			c.A907G						.						179	183	182					6																	111587672		2203	4300	6503	SO:0001583	missense	91749	exon4			AGCAACATTGGCA	BC036115	CCDS5090.1	6q22	2013-10-02			ENSG00000173214	ENSG00000173214			21053	protein-coding gene	gene with protein product							Standard	NM_153369		Approved	MGC33953, MFSD4B	uc003puv.4	Q5TF39	OTTHUMG00000015372	ENST00000368847.4:c.907A>G	chr6.hg19:g.111587672A>G	ENSP00000357840:p.Ile303Val	113.0	0.0		91.0	44.0	NM_153369	A8K9M0|Q8IYB6|Q96PW9|Q9P0D6	Missense_Mutation	SNP	ENST00000368847.4	hg19	CCDS5090.1	.	.	.	.	.	.	.	.	.	.	A	7.618	0.676219	0.14841	.	.	ENSG00000173214	ENST00000368847	T	0.57595	0.39	6.05	-0.923	0.10465	Major facilitator superfamily domain, general substrate transporter (1);	0.344054	0.35040	N	0.003491	T	0.09158	0.0226	N	0.11756	0.17	0.31285	N	0.690084	B	0.06786	0.001	B	0.15870	0.014	T	0.32481	-0.9905	10	0.06757	T	0.87	-14.9073	8.3443	0.32263	0.5562:0.1025:0.3412:0.0	.	303	Q5TF39	NAGT1_HUMAN	V	303	ENSP00000357840:I303V	ENSP00000357840:I303V	I	+	1	0	KIAA1919	111694365	0.624000	0.27102	0.992000	0.48379	0.993000	0.82548	0.016000	0.13377	-0.048000	0.13401	-0.269000	0.10298	ATT	.	.		0.468	KIAA1919-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041827.1	NM_153369		G	111587672	A	G	111587672	3	3	344	1	0	0	0	0	1	0	0	0	8271	217	8	2	921	2	KIAA1919	6	111587672	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1064786	111587672	59527395	535	47898										
RFPL4B	442247	hgsc.bcm.edu	37	chr6	112671556	112671556	+	Frame_Shift_Del	DEL	G	G	-													0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttttcctggatgctgacttaGaagaaatccagttttttgat							TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:112671556delG	ENST00000441065.2	+	3	958	c.646delG	c.(646-648)gaafs	p.E217fs	RP11-506B6.6_ENST00000590673.1_RNA|RP11-506B6.6_ENST00000585611.1_RNA|RP11-506B6.6_ENST00000587816.1_RNA	NM_001013734.2	NP_001013756.2	Q6ZWI9	RFPLB_HUMAN	ret finger protein-like 4B	217	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.						zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|skin(1)	14		all_cancers(87;9.44e-05)|all_hematologic(75;0.000114)|all_epithelial(87;0.00265)|Colorectal(196;0.0209)		all cancers(137;0.0202)|OV - Ovarian serous cystadenocarcinoma(136;0.0477)|Epithelial(106;0.0646)|GBM - Glioblastoma multiforme(226;0.0866)|BRCA - Breast invasive adenocarcinoma(108;0.244)		TGCTGACTTAGAAGAAATCCA	0.453																																					p.L215fs		Atlas-Indel,Pindel	.											.	RFPL4B	36	.	0			c.645delA						.						68	64	65					6																	112671556		2203	4300	6503	SO:0001589	frameshift_variant	442247	exon3			.	AK122906	CCDS34515.1	6q21	2007-04-24			ENSG00000251258	ENSG00000251258		"RING-type (C3HC4) zinc fingers"	33264	protein-coding gene	gene with protein product							Standard	NM_001013734		Approved	RNF211	uc003pvx.1	Q6ZWI9	OTTHUMG00000015390	ENST00000441065.2:c.646delG	chr6.hg19:g.112671556delG	ENSP00000423391:p.Glu217fs	45.0	0.0		49.0	28.0	NM_001013734	A2RU91	Frame_Shift_Del	DEL	ENST00000441065.2	hg19	CCDS34515.1																																																																																			.	.		0.453	RFPL4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041885.2	NM_001013734		-	112671556	G	-	112671556	7	5	344	1	0	1	0	1	0	0	0	0	13271	943	33	0	648	0	RFPL4B	6	112671556	Frame_Shift_Del	DEL	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1083884	112671556	58443511	536	47899										
ZUFSP	221302	hgsc.bcm.edu	37	chr6	116973312	116973312	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agccacacccgtctcacatcTgtggcagcattctgataata	7	13	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:116973312T>A	ENST00000368576.3	-	6	1248	c.1005A>T	c.(1003-1005)acA>acT	p.T335T	ZUFSP_ENST00000471919.1_5'UTR|ZUFSP_ENST00000368573.1_Missense_Mutation_p.Q279L	NM_145062.2	NP_659499.2	Q96AP4	ZUFSP_HUMAN	zinc finger with UFM1-specific peptidase domain	335							metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(6)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	21				GBM - Glioblastoma multiforme(226;0.0258)|all cancers(137;0.0368)|OV - Ovarian serous cystadenocarcinoma(136;0.0464)|Epithelial(106;0.186)		GTCTCACATCTGTGGCAGCAT	0.393																																					p.T335T		Atlas-SNP	.											.	ZUFSP	46	.	0			c.A1005T						.						94	93	93					6																	116973312		2203	4300	6503	SO:0001819	synonymous_variant	221302	exon6			CACATCTGTGGCA	AK054582	CCDS5110.1	6q22.31	2013-01-28	2008-03-25	2008-03-25	ENSG00000153975	ENSG00000153975		"Zinc fingers, C2H2-type"	21224	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 113"	C6orf113			Standard	NM_145062		Approved	dJ412I7.3	uc003pxf.2	Q96AP4	OTTHUMG00000015445	ENST00000368576.3:c.1005A>T	chr6.hg19:g.116973312T>A		97.0	0.0		75.0	23.0	NM_145062	Q5TD92|Q6PJH7|Q96NV6	Silent	SNP	ENST00000368576.3	hg19	CCDS5110.1	.	.	.	.	.	.	.	.	.	.	T	19.10	3.762065	0.69763	.	.	ENSG00000153975	ENST00000368573	.	.	.	5.69	4.53	0.55603	.	.	.	.	.	T	0.26376	0.0644	.	.	.	0.23791	N	0.99684	.	.	.	.	.	.	T	0.28038	-1.0056	5	0.87932	D	0	-1.1238	6.9542	0.24562	0.1326:0.0703:0.0:0.7971	.	.	.	.	L	279	.	ENSP00000357562:Q279L	Q	-	2	0	ZUFSP	117080005	0.955000	0.32602	1.000000	0.80357	0.990000	0.78478	0.433000	0.21477	1.089000	0.41292	0.533000	0.62120	CAG	.	.		0.393	ZUFSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041961.1	NM_145062		A	116973312	T	A	116973312	2	1	344	1	0	0	0	0	0	0	0	1	18261	1567	55	4		4	ZUFSP	6	116973312	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	4301756	116973312	54141755	537	47900										
KPNA5	3841	hgsc.bcm.edu	37	chr6	117047735	117047735	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tttcgtaccagaaaagaagcAgcttgggctataactaatgc	9	8	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:117047735A>T	ENST00000368564.1	+	12	1351	c.1203A>T	c.(1201-1203)gcA>gcT	p.A401A	KPNA5_ENST00000356348.1_Silent_p.A401A			O15131	IMA6_HUMAN	karyopherin alpha 5 (importin alpha 6)	398	NLS binding site (minor). {ECO:0000250}.				cytokine-mediated signaling pathway (GO:0019221)|NLS-bearing protein import into nucleus (GO:0006607)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)	protein transporter activity (GO:0008565)			breast(6)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0298)|all cancers(137;0.0461)|OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.212)		GAAAAGAAGCAGCTTGGGCTA	0.338																																					p.A401A		Atlas-SNP	.											.	KPNA5	57	.	0			c.A1203T						.						89	92	91					6																	117047735		2203	4300	6503	SO:0001819	synonymous_variant	3841	exon12			AGAAGCAGCTTGG	AF005361	CCDS5111.1	6q22.2	2013-02-14			ENSG00000196911	ENSG00000196911		"Importins", "Armadillo repeat containing"	6398	protein-coding gene	gene with protein product		604545				9395085	Standard	NM_002269		Approved	SRP6, IPOA6	uc003pxh.3	O15131	OTTHUMG00000015448	ENST00000368564.1:c.1203A>T	chr6.hg19:g.117047735A>T		216.0	0.0		134.0	63.0	NM_002269	B2RAI5|Q86X23	Silent	SNP	ENST00000368564.1	hg19	CCDS5111.1																																																																																			.	.		0.338	KPNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041967.1	NM_002269		T	117047735	A	T	117047735	2	4	344	1	0	0	0	0	0	0	0	1	8442	175	7	4		4	KPNA5	6	117047735	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	74423	117047735	54067332	538	47901										
GPRC6A	222545	hgsc.bcm.edu	37	chr6	117114124	117114124	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gttttacatgtgaagtcttgTggttctccaatgaaaaagct	9	6	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:117114124T>A	ENST00000310357.3	-	6	1983	c.1962A>T	c.(1960-1962)ccA>ccT	p.P654P	GPRC6A_ENST00000368549.3_Silent_p.P583P|GPRC6A_ENST00000530250.1_Silent_p.P479P	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	654					calcium-mediated signaling (GO:0019722)|response to amino acid (GO:0043200)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|liver(1)|lung(24)|ovary(5)|pancreas(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)	65		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		TGAAGTCTTGTGGTTCTCCAA	0.428																																					p.P654P		Atlas-SNP	.											.	GPRC6A	152	.	0			c.A1962T						.						108	98	101					6																	117114124		2203	4300	6503	SO:0001819	synonymous_variant	222545	exon6			GTCTTGTGGTTCT	AF502962	CCDS5112.1, CCDS69184.1, CCDS69185.1	6q22.31	2014-01-30	2014-01-30		ENSG00000173612	ENSG00000173612		"GPCR / Class C : Calcium-sensing receptors"	18510	protein-coding gene	gene with protein product			"G protein-coupled receptor, family C, group 6, member A"				Standard	NM_001286354		Approved	bA86F4.3	uc003pxj.1	Q5T6X5	OTTHUMG00000015447	ENST00000310357.3:c.1962A>T	chr6.hg19:g.117114124T>A		120.0	0.0		87.0	45.0	NM_148963	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Silent	SNP	ENST00000310357.3	hg19	CCDS5112.1																																																																																			.	.		0.428	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2			A	117114124	T	A	117114124	2	1	344	1	0	0	0	0	0	0	0	1	6737	1683	59	4		4	GPRC6A	6	117114124	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	66389	117114124	54000943	539	47902										
ROS1	6098	hgsc.bcm.edu	37	chr6	117609770	117609770	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggcagaaatctttgtctgcaTgtggttccttctcttctttc	8	10	4	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:117609770T>G	ENST00000368508.3	-	43	7127	c.6929A>C	c.(6928-6930)cAt>cCt	p.H2310P	ROS1_ENST00000368507.3_Missense_Mutation_p.H2304P	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	2310					cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		TTTGTCTGCATGTGGTTCCTT	0.483			T	"GOPC, SDC4, SLC34A2, EZR, LRIG3"	"glioblastoma, NSCLC"																																p.H2310P		Atlas-SNP	.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"O, E"	.	ROS1	728	.	0			c.A6929C						.						114	113	113					6																	117609770		2203	4300	6503	SO:0001583	missense	6098	exon43			TCTGCATGTGGTT	M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"Fibronectin type III domain containing"	10261	protein-coding gene	gene with protein product		165020	"v-ros avian UR2 sarcoma virus oncogene homolog 1", "v-ros UR2 sarcoma virus oncogene homolog 1 (avian)", "c-ros oncogene 1 , receptor tyrosine kinase"			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.6929A>C	chr6.hg19:g.117609770T>G	ENSP00000357494:p.His2310Pro	142.0	0.0		115.0	51.0	NM_002944	Q15368|Q5TDB5	Missense_Mutation	SNP	ENST00000368508.3	hg19	CCDS5116.1	.	.	.	.	.	.	.	.	.	.	T	13.38	2.221107	0.39201	.	.	ENSG00000047936	ENST00000368508;ENST00000368507	T;T	0.72051	-0.61;-0.62	4.41	3.24	0.37175	.	0.374089	0.20166	N	0.097850	T	0.33673	0.0871	N	0.24115	0.695	0.25235	N	0.989799	B	0.29909	0.261	B	0.28784	0.094	T	0.16928	-1.0386	10	0.62326	D	0.03	.	6.5849	0.22614	0.0:0.1102:0.0:0.8898	.	2310	P08922	ROS1_HUMAN	P	2310;2304	ENSP00000357494:H2310P;ENSP00000357493:H2304P	ENSP00000357493:H2304P	H	-	2	0	ROS1	117716463	0.957000	0.32711	1.000000	0.80357	0.998000	0.95712	0.923000	0.28757	0.729000	0.32403	0.460000	0.39030	CAT	.	.		0.483	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1			G	117609770	T	G	117609770	3	3	344	1	0	0	0	0	1	0	0	0	13546	1464	51	5	118	5	ROS1	6	117609770	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	495646	117609770	53505297	540	47903										
C6orf170	221322	hgsc.bcm.edu	37	chr6	121447529	121447529	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atgtttaaaatgtacctgtaTactccactgaagggaagtag	9	6	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:121447529T>C	ENST00000398212.2	-	26	3027	c.2978A>G	c.(2977-2979)tAt>tGt	p.Y993C	TBC1D32_ENST00000398197.2_5'UTR|TBC1D32_ENST00000275159.6_Missense_Mutation_p.Y1034C	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	993					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)										TGTACCTGTATACTCCACTGA	0.318																																					p.Y993C		Atlas-SNP	.											.	C6orf170	146	.	0			c.A2978G						.						100	95	97					6																	121447529		1826	4084	5910	SO:0001583	missense	221322	exon26			CCTGTATACTCCA	AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"broad-minded homolog"	615867	"chromosome 6 open reading frame 171", "chromosome 6 open reading frame 170"	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.2978A>G	chr6.hg19:g.121447529T>C	ENSP00000381270:p.Tyr993Cys	62.0	0.0		48.0	27.0	NM_152730	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Missense_Mutation	SNP	ENST00000398212.2	hg19	CCDS43501.1	.	.	.	.	.	.	.	.	.	.	T	19.13	3.768489	0.69878	.	.	ENSG00000146350	ENST00000275159;ENST00000398212	T;T	0.19394	2.15;2.15	5.15	5.15	0.70609	.	0.118478	0.64402	D	0.000015	T	0.30166	0.0756	M	0.67953	2.075	0.54753	D	0.999981	D;D	0.61080	0.985;0.989	P;P	0.58454	0.808;0.839	T	0.04454	-1.0950	10	0.52906	T	0.07	.	15.2681	0.73678	0.0:0.0:0.0:1.0	.	1034;993	Q96NH3-4;Q96NH3	.;BROMI_HUMAN	C	1034;993	ENSP00000275159:Y1034C;ENSP00000381270:Y993C	ENSP00000275159:Y1034C	Y	-	2	0	C6orf170	121489228	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	3.642000	0.54367	2.065000	0.61736	0.477000	0.44152	TAT	.	.		0.318	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730		C	121447529	T	C	121447529	3	2	344	1	0	0	0	0	1	0	0	0	2346	1406	49	2	823	2	C6orf170	6	121447529	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	3837759	121447529	49667538	541	47904										
C6orf174	387104	hgsc.bcm.edu	37	chr6	127837007	127837007	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcagactgcagacatccttcTttccagtagctccctccacc	5	17	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:127837007T>A	ENST00000525778.1	-	2	1498	c.753A>T	c.(751-753)aaA>aaT	p.K251N	SOGA3_ENST00000465909.2_Missense_Mutation_p.K251N|SOGA3_ENST00000481848.2_Missense_Mutation_p.K251N|SOGA3_ENST00000368268.2_Missense_Mutation_p.K251N|SOGA3_ENST00000556132.1_Missense_Mutation_p.K251N			Q5TF21	SOGA3_HUMAN	SOGA family member 3	251					regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											GACATCCTTCTTTCCAGTAGC	0.652																																					p.K251N		Atlas-SNP	.											.	.	.	.	0			c.A753T						.						19	24	22					6																	127837007		1923	4102	6025	SO:0001583	missense	387104	exon2			TCCTTCTTTCCAG	AK096490	CCDS43505.1	6q22.33	2013-03-28	2012-02-27	2012-02-27	ENSG00000214338	ENSG00000214338			21494	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 174"	C6orf174			Standard	NM_001012279		Approved	dJ403A15.3	uc003qbd.3	Q5TF21	OTTHUMG00000166438	ENST00000525778.1:c.753A>T	chr6.hg19:g.127837007T>A	ENSP00000434570:p.Lys251Asn	27.0	0.0		38.0	19.0	NM_001012279		Missense_Mutation	SNP	ENST00000525778.1	hg19	CCDS43505.1	.	.	.	.	.	.	.	.	.	.	C	14.10	2.433625	0.43224	.	.	ENSG00000214338	ENST00000556132;ENST00000368268;ENST00000525778;ENST00000465909	T;T;T;T	0.34667	1.35;1.35;1.35;1.35	3.68	0.884	0.19182	.	0.074138	0.50627	D	0.000119	T	0.09113	0.0225	N	0.19112	0.55	0.46521	D	0.999088	P	0.34522	0.455	B	0.32624	0.149	T	0.11155	-1.0599	10	0.37606	T	0.19	-16.7435	8.9648	0.35869	0.0:0.6358:0.0:0.3642	.	251	Q5TF21	CF174_HUMAN	N	251	ENSP00000451768:K251N;ENSP00000357251:K251N;ENSP00000434570:K251N;ENSP00000435559:K251N	ENSP00000435559:K251N	K	-	3	2	C6orf174	127878700	0.966000	0.33281	0.999000	0.59377	0.904000	0.53231	0.096000	0.15147	0.048000	0.15891	-0.994000	0.02522	AAA	.	.		0.652	SOGA3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388246.1	NM_001012279		A	127837007	T	A	127837007	3	1	344	1	0	0	0	0	1	0	0	0	2347	1606	56	4	2114	4	C6orf174	6	127837007	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	6389478	127837007	43278060	542	47905										
THEMIS	387357	hgsc.bcm.edu	37	chr6	128150865	128150865	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gagtgagtttgatgattcctTgctactgcacagctcaccat	9	10	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:128150865T>G	ENST00000368248.2	-	3	613	c.465A>C	c.(463-465)gcA>gcC	p.A155A	THEMIS_ENST00000543064.1_Silent_p.A155A|THEMIS_ENST00000537166.1_Silent_p.A120A|THEMIS_ENST00000368250.1_Silent_p.A76A	NM_001010923.2	NP_001010923.1	Q8N1K5	THMS1_HUMAN	thymocyte selection associated	155	CABIT 1.				negative T cell selection (GO:0043383)|positive T cell selection (GO:0043368)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(3)	60						GATGATTCCTTGCTACTGCAC	0.378																																					p.A155A		Atlas-SNP	.											.	THEMIS	168	.	0			c.A465C						.						157	154	155					6																	128150865		2203	4300	6503	SO:0001819	synonymous_variant	387357	exon3			ATTCCTTGCTACT	AK094863	CCDS34534.1, CCDS55055.1	6q22.33	2012-02-08	2009-06-25	2009-06-25	ENSG00000172673	ENSG00000172673			21569	protein-coding gene	gene with protein product	"thymocyte expressed molecule involved in selection"	613607	"chromosome 6 open reading frame 207", "chromosome 6 open reading frame 190", "thymocyte selection pathway associated"	C6orf207, C6orf190, TSEPA		19597499, 19597498, 19597497	Standard	NM_001010923		Approved	bA325O24.4, FLJ40584, bA325O24.3	uc011ebt.2	Q8N1K5	OTTHUMG00000015534	ENST00000368248.2:c.465A>C	chr6.hg19:g.128150865T>G		109.0	0.0		74.0	33.0	NM_001010923	A1L4F0|A8K7N1|B3KT31|B3KW32|B3KY07|F5H1J9|Q5T3C4|Q5T3C5|Q6MZT7	Silent	SNP	ENST00000368248.2	hg19	CCDS34534.1																																																																																			.	.		0.378	THEMIS-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_001010923		G	128150865	T	G	128150865	2	3	344	1	0	0	0	0	0	0	0	1	15875	1799	63	5		5	THEMIS	6	128150865	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	313858	128150865	42964202	543	47906										
LAMA2	3908	hgsc.bcm.edu	37	chr6	129498936	129498936	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aggggctacactggctacccGgactgcaaagcctgtaactg	12	12	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:129498936G>T	ENST00000421865.2	+	10	1441	c.1392G>T	c.(1390-1392)ccG>ccT	p.P464P		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	464	Laminin EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		CTGGCTACCCGGACTGCAAAG	0.488																																					p.P464P		Atlas-SNP	.											.	LAMA2	481	.	0			c.G1392T						.						104	96	99					6																	129498936		2203	4300	6503	SO:0001819	synonymous_variant	3908	exon10			CTACCCGGACTGC	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"Laminins"	6482	protein-coding gene	gene with protein product	"merosin", "congenital muscular dystrophy"	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.1392G>T	chr6.hg19:g.129498936G>T		149.0	0.0		110.0	47.0	NM_000426	Q14736|Q5VUM2|Q93022	Silent	SNP	ENST00000421865.2	hg19	CCDS5138.1																																																																																			.	.		0.488	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			T	129498936	G	T	129498936	2	4	344	1	0	0	0	0	0	0	0	1	8615	1103	39	1		1	LAMA2	6	129498936	Silent	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1348071	129498936	41616131	544	47907										
LAMA2	3908	hgsc.bcm.edu	37	chr6	129618940	129618940	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggacaatgttggtgccaaccTggagtcacagggaagaaatg	14	7	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:129618940T>A	ENST00000421865.2	+	21	3016	c.2967T>A	c.(2965-2967)ccT>ccA	p.P989P		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	989	Laminin EGF-like 10. {ECO:0000255|PROSITE-ProRule:PRU00460}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		GGTGCCAACCTGGAGTCACAG	0.478																																					p.P989P		Atlas-SNP	.											.	LAMA2	481	.	0			c.T2967A						.						92	83	86					6																	129618940		2203	4300	6503	SO:0001819	synonymous_variant	3908	exon21			CCAACCTGGAGTC	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"Laminins"	6482	protein-coding gene	gene with protein product	"merosin", "congenital muscular dystrophy"	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.2967T>A	chr6.hg19:g.129618940T>A		83.0	0.0		50.0	26.0	NM_000426	Q14736|Q5VUM2|Q93022	Silent	SNP	ENST00000421865.2	hg19	CCDS5138.1																																																																																			.	.		0.478	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			A	129618940	T	A	129618940	2	1	344	1	0	0	0	0	0	0	0	1	8615	1567	55	4		4	LAMA2	6	129618940	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	120004	129618940	41496127	545	47908										
LAMA2	3908	hgsc.bcm.edu	37	chr6	129636779	129636779	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cctttttattggaaacttccAgaacaatttgaaggaaagaa	7	6	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:129636779A>T	ENST00000421865.2	+	25	3763	c.3714A>T	c.(3712-3714)ccA>ccT	p.P1238P		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	1238	Laminin IV type A 2. {ECO:0000255|PROSITE-ProRule:PRU00458}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		GGAAACTTCCAGAACAATTTG	0.373																																					p.P1238P		Atlas-SNP	.											.	LAMA2	481	.	0			c.A3714T						.						101	99	100					6																	129636779		2203	4300	6503	SO:0001819	synonymous_variant	3908	exon25			ACTTCCAGAACAA	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"Laminins"	6482	protein-coding gene	gene with protein product	"merosin", "congenital muscular dystrophy"	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.3714A>T	chr6.hg19:g.129636779A>T		89.0	0.0		73.0	30.0	NM_000426	Q14736|Q5VUM2|Q93022	Silent	SNP	ENST00000421865.2	hg19	CCDS5138.1																																																																																			.	.		0.373	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			T	129636779	A	T	129636779	2	4	344	1	0	0	0	0	0	0	0	1	8615	175	7	4		4	LAMA2	6	129636779	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	17839	129636779	41478288	546	47909										
LAMA2	3908	hgsc.bcm.edu	37	chr6	129823895	129823895	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcacattgcaattgcatttgAtgacaccaaagttaaaaacc	5	9	1	2	rs202202014		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:129823895A>T	ENST00000421865.2	+	59	8385	c.8336A>T	c.(8335-8337)gAt>gTt	p.D2779V		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	2779	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		ATTGCATTTGATGACACCAAA	0.398																																					p.D2779V		Atlas-SNP	.											.	LAMA2	481	.	0			c.A8336T						.						90	85	87					6																	129823895		2203	4300	6503	SO:0001583	missense	3908	exon59			CATTTGATGACAC	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"Laminins"	6482	protein-coding gene	gene with protein product	"merosin", "congenital muscular dystrophy"	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.8336A>T	chr6.hg19:g.129823895A>T	ENSP00000400365:p.Asp2779Val	98.0	0.0		75.0	30.0	NM_000426	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	hg19	CCDS5138.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.621714	0.87460	.	.	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865;ENST00000443169	T	0.68025	-0.3	6.07	6.07	0.98685	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	0.000000	0.85682	D	0.000000	T	0.75982	0.3924	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.995	T	0.76116	-0.3077	9	.	.	.	.	16.6406	0.85098	1.0:0.0:0.0:0.0	.	2780;2779	A6NF00;P24043	.;LAMA2_HUMAN	V	2779;2778;2779;797	ENSP00000400365:D2779V	.	D	+	2	0	LAMA2	129865588	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.017000	0.88712	2.326000	0.78906	0.533000	0.62120	GAT	.	A|1.000;G|0.000		0.398	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			T	129823895	A	T	129823895	3	4	344	1	0	0	0	0	1	0	0	0	8615	333	12	4	8570	4	LAMA2	6	129823895	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	187116	129823895	41291172	547	47910										
SAMD3	154075	hgsc.bcm.edu	37	chr6	130497042	130497042	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atcagcaagagatttccttgTctggcctcttcggtgtccaa	9	11	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:130497042T>C	ENST00000368134.2	-	10	1374	c.766A>G	c.(766-768)Aca>Gca	p.T256A	SAMD3_ENST00000457563.2_Missense_Mutation_p.T280A|SAMD3_ENST00000437477.2_Missense_Mutation_p.T256A|SAMD3_ENST00000439090.2_Missense_Mutation_p.T256A|SAMD3_ENST00000533296.1_5'Flank|SAMD3_ENST00000532763.1_Missense_Mutation_p.T254A	NM_001258275.1	NP_001245204.1	Q8N6K7	SAMD3_HUMAN	sterile alpha motif domain containing 3	256										breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(3)|lung(15)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	29				GBM - Glioblastoma multiforme(226;0.00594)|OV - Ovarian serous cystadenocarcinoma(155;0.128)		GATTTCCTTGTCTGGCCTCTT	0.348																																					p.T256A		Atlas-SNP	.											.	SAMD3	98	.	0			c.A766G						.						108	111	110					6																	130497042		2202	4300	6502	SO:0001583	missense	154075	exon8			TCCTTGTCTGGCC	AK091351	CCDS34539.1, CCDS64525.1	6q23.1	2013-01-10			ENSG00000164483	ENSG00000164483		"Sterile alpha motif (SAM) domain containing"	21574	protein-coding gene	gene with protein product							Standard	NM_001017373		Approved	bA73O6.2, FLJ34032	uc031spp.1	Q8N6K7	OTTHUMG00000015556	ENST00000368134.2:c.766A>G	chr6.hg19:g.130497042T>C	ENSP00000357116:p.Thr256Ala	77.0	0.0		71.0	24.0	NM_001017373	B4DY20|E1P576|J3KQK4|Q4VXD8|Q8NAY1|Q8NB96	Missense_Mutation	SNP	ENST00000368134.2	hg19	CCDS34539.1	.	.	.	.	.	.	.	.	.	.	T	14.87	2.665903	0.47677	.	.	ENSG00000164483	ENST00000368134;ENST00000457563;ENST00000439090;ENST00000437477;ENST00000532763	T;T;T;T;T	0.44881	0.95;0.95;0.95;0.95;0.91	5.58	5.58	0.84498	.	0.505114	0.19833	N	0.105059	T	0.24967	0.0606	M	0.63428	1.95	0.80722	D	1	B	0.28055	0.199	B	0.27380	0.079	T	0.07790	-1.0754	10	0.16420	T	0.52	.	14.3224	0.66496	0.0:0.0:0.0:1.0	.	256	Q8N6K7	SAMD3_HUMAN	A	256;280;256;256;254	ENSP00000357116:T256A;ENSP00000402092:T280A;ENSP00000403565:T256A;ENSP00000391163:T256A;ENSP00000436088:T254A	ENSP00000357116:T256A	T	-	1	0	SAMD3	130538735	1.000000	0.71417	0.998000	0.56505	0.645000	0.38454	3.579000	0.53900	2.115000	0.64714	0.533000	0.62120	ACA	.	.		0.348	SAMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042197.3	NM_152552		C	130497042	T	C	130497042	3	2	344	1	0	0	0	0	1	0	0	0	13835	1667	58	2	816	2	SAMD3	6	130497042	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	673147	130497042	40618025	548	47911										
SGK1	6446	hgsc.bcm.edu	37	chr6	134638546	134638546	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttacccgcttcttaaaaaatTggaaggctgagcatttcttg	8	8	2	1	rs557794340		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:134638546T>C	ENST00000367858.5	-	1	650	c.53A>G	c.(52-54)cAa>cGa	p.Q18R	SGK1_ENST00000524929.1_Missense_Mutation_p.Q18R	NM_001143676.1	NP_001137148.1	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	0	Necessary for localization to the mitochondria.				apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		CTTAAAAAATTGGAAGGCTGA	0.418																																					p.Q18R		Atlas-SNP	.											.	SGK1	387	.	0			c.A53G						.						164	152	156					6																	134638546		1568	3582	5150	SO:0001583	missense	6446	exon1			AAAAATTGGAAGG	AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"serum/glucocorticoid regulated kinase"	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000367858.5:c.53A>G	chr6.hg19:g.134638546T>C	ENSP00000356832:p.Gln18Arg	138.0	0.0		93.0	37.0	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000367858.5	hg19	CCDS47476.1	.	.	.	.	.	.	.	.	.	.	T	16.08	3.020267	0.54576	.	.	ENSG00000118515	ENST00000367858;ENST00000524929;ENST00000533224	T	0.73047	-0.71	5.38	5.38	0.77491	.	0.199270	0.25014	N	0.033809	T	0.80747	0.4682	.	.	.	0.33958	D	0.645274	D;P	0.89917	1.0;0.908	D;P	0.85130	0.997;0.888	D	0.84666	0.0709	9	0.87932	D	0	.	15.3791	0.74637	0.0:0.0:0.0:1.0	.	18;18	Q7Z3I4;O00141-2	.;.	R	18	ENSP00000356832:Q18R	ENSP00000356832:Q18R	Q	-	2	0	SGK1	134680239	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.505000	0.66981	2.042000	0.60477	0.482000	0.46254	CAA	.	.		0.418	SGK1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042304.2			C	134638546	T	C	134638546	3	2	344	1	0	0	0	0	1	0	0	0	14222	1812	63	2	1949	2	SGK1	6	134638546	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	4141504	134638546	36476521	549	47912										
BCLAF1	9774	hgsc.bcm.edu	37	chr6	136599666	136599666	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atctttgagaagaaacggatCttctttttggactcctggaa	9	7	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:136599666C>T	ENST00000531224.1	-	4	605	c.353G>A	c.(352-354)aGa>aAa	p.R118K	BCLAF1_ENST00000353331.4_Missense_Mutation_p.R116K|BCLAF1_ENST00000392348.2_Missense_Mutation_p.R116K|BCLAF1_ENST00000527759.1_Missense_Mutation_p.R116K|BCLAF1_ENST00000530767.1_Missense_Mutation_p.R118K|BCLAF1_ENST00000527536.1_Missense_Mutation_p.R118K	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1	118					apoptotic process (GO:0006915)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA-templated transcription, initiation (GO:2000144)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of response to DNA damage stimulus (GO:2001022)|regulation of DNA-templated transcription in response to stress (GO:0043620)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.R118I(1)		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)		AGAAACGGATCTTCTTTTTGG	0.468																																					p.R118K	Colon(142;1534 1789 5427 7063 28491)	Atlas-SNP	.											BCLAF1_ENST00000531224,NS,carcinoma,0,1	BCLAF1	203	.	1	Substitution - Missense(1)	kidney(1)	c.G353A						.						178	184	182					6																	136599666		2203	4300	6503	SO:0001583	missense	9774	exon4			ACGGATCTTCTTT	AF249273	CCDS5177.1, CCDS47485.1, CCDS47486.1, CCDS75525.1	6q22-q23	2007-03-02			ENSG00000029363	ENSG00000029363			16863	protein-coding gene	gene with protein product		612588				8724849, 10330179	Standard	NM_001077440		Approved	KIAA0164, BTF	uc003qgx.1	Q9NYF8	OTTHUMG00000033323	ENST00000531224.1:c.353G>A	chr6.hg19:g.136599666C>T	ENSP00000435210:p.Arg118Lys	129.0	0.0		139.0	33.0	NM_014739	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Missense_Mutation	SNP	ENST00000531224.1	hg19	CCDS5177.1	.	.	.	.	.	.	.	.	.	.	C	18.95	3.732204	0.69189	.	.	ENSG00000029363	ENST00000531224;ENST00000353331;ENST00000527536;ENST00000530767;ENST00000527759;ENST00000392348;ENST00000529826	T;T;T;T;T;T;T	0.61274	0.12;0.12;0.12;0.12;0.12;0.12;0.12	5.64	5.64	0.86602	.	0.000000	0.64402	D	0.000001	T	0.68146	0.2969	M	0.64997	1.995	0.80722	D	1	P;P;P;P	0.47910	0.902;0.902;0.902;0.902	P;P;P;P	0.60173	0.87;0.87;0.87;0.87	T	0.68792	-0.5315	10	0.62326	D	0.03	-11.5288	19.6986	0.96043	0.0:1.0:0.0:0.0	.	116;116;118;118	Q9NYF8-2;Q9NYF8-3;Q9NYF8;Q9NYF8-4	.;.;BCLF1_HUMAN;.	K	118;116;118;118;116;116;118	ENSP00000435210:R118K;ENSP00000229446:R116K;ENSP00000435441:R118K;ENSP00000436501:R118K;ENSP00000434826:R116K;ENSP00000376159:R116K;ENSP00000431734:R118K	ENSP00000229446:R116K	R	-	2	0	BCLAF1	136641359	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.655000	0.67981	2.660000	0.90430	0.557000	0.71058	AGA	.	.		0.468	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739		T	136599666	C	T	136599666	3	4	344	1	0	0	0	0	1	0	0	0	1383	913	32	3	2449	3	BCLAF1	6	136599666	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1961120	136599666	34515401	550	47913										
SLC35D3	340146	hgsc.bcm.edu	37	chr6	137245642	137245642	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaaggtggggaggcagcaggTggccccgctcaggagagcag	20	9	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:137245642T>A	ENST00000331858.4	+	2	1224	c.1059T>A	c.(1057-1059)ggT>ggA	p.G353G		NM_001008783.1	NP_001008783.1	Q5M8T2	S35D3_HUMAN	solute carrier family 35, member D3	353					carbohydrate transport (GO:0008643)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)	13	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000136)|OV - Ovarian serous cystadenocarcinoma(155;0.00365)		AGGCAGCAGGTGGCCCCGCTC	0.657																																					p.G353G		Atlas-SNP	.											.	SLC35D3	33	.	0			c.T1059A						.						41	43	42					6																	137245642		2203	4300	6503	SO:0001819	synonymous_variant	340146	exon2			AGCAGGTGGCCCC		CCDS34544.1	6q23.2	2013-05-22			ENSG00000182747	ENSG00000182747		"Solute carriers"	15621	protein-coding gene	gene with protein product		612519		FRCL1			Standard	NM_001008783		Approved		uc003qhe.3	Q5M8T2	OTTHUMG00000015651	ENST00000331858.4:c.1059T>A	chr6.hg19:g.137245642T>A		51.0	0.0		39.0	14.0	NM_001008783	B4DI58|Q5QNZ6|Q6NX71	Silent	SNP	ENST00000331858.4	hg19	CCDS34544.1																																																																																			.	.		0.657	SLC35D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042389.2	XM_294017		A	137245642	T	A	137245642	2	1	344	1	0	0	0	0	0	0	0	1	14598	1683	59	4		4	SLC35D3	6	137245642	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	645976	137245642	33869425	551	47914										
ECT2L	345930	hgsc.bcm.edu	37	chr6	139164260	139164260	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cacctagggaggctgctgctActtatgggacgctgaatgaa	13	9	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:139164260A>G	ENST00000423192.1	+	5	648	c.487A>G	c.(487-489)Act>Gct	p.T163A	ECT2L_ENST00000541398.1_Missense_Mutation_p.T94A|ECT2L_ENST00000367682.2_Missense_Mutation_p.T163A			Q008S8	ECT2L_HUMAN	epithelial cell transforming 2 like	163							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			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						GGCTGCTGCTACTTATGGGAC	0.463			"N, Splice, Mis"		ETP ALL																																p.T163A		Atlas-SNP	.		Rec	yes		6	6q24.1	345930	epithelial cell transforming sequence 2 oncogene-like		L	.	ECT2L	75	.	0			c.A487G						.						126	125	125					6																	139164260		1961	4163	6124	SO:0001583	missense	345930	exon5			GCTGCTACTTATG		CCDS43508.1	6q24.1	2014-03-11	2014-03-11		ENSG00000203734	ENSG00000203734		"Rho guanine nucleotide exchange factors", "F-boxes /  "other""	21118	protein-coding gene	gene with protein product	"lung specific F-box and DH domain containing protein", "F-box protein 49"		"chromosome 6 open reading frame 91", "epithelial cell transforming sequence 2 oncogene-like"	C6orf91			Standard	NM_001077706		Approved	ARHGEF32, FBXO49, LFDH	uc021zfx.1	Q008S8	OTTHUMG00000015679	ENST00000423192.1:c.487A>G	chr6.hg19:g.139164260A>G	ENSP00000387388:p.Thr163Ala	68.0	0.0		64.0	19.0	NM_001195037	B2RUV6|Q5JWK2|Q5JWK3|Q5JWK4	Missense_Mutation	SNP	ENST00000423192.1	hg19	CCDS43508.1	.	.	.	.	.	.	.	.	.	.	A	13.28	2.189336	0.38707	.	.	ENSG00000203734	ENST00000423192;ENST00000367682;ENST00000541398	T;T;T	0.74632	0.26;0.26;-0.86	5.72	-8.41	0.00961	.	13.926100	0.01400	U	0.013544	T	0.26011	0.0634	N	0.08118	0	0.09310	N	1	B;B	0.14438	0.01;0.006	B;B	0.13407	0.009;0.002	T	0.13548	-1.0505	10	0.26408	T	0.33	4.2474	7.6495	0.28340	0.2801:0.3321:0.3879:0.0	.	94;163	F5H7S9;Q008S8	.;ECT2L_HUMAN	A	163;163;94	ENSP00000387388:T163A;ENSP00000356655:T163A;ENSP00000442307:T94A	ENSP00000356655:T163A	T	+	1	0	ECT2L	139205953	0.000000	0.05858	0.000000	0.03702	0.867000	0.49689	-1.138000	0.03216	-1.610000	0.01583	0.482000	0.46254	ACT	.	.		0.463	ECT2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042441.3	NM_001077706		G	139164260	A	G	139164260	3	3	344	1	0	0	0	0	1	0	0	0	4904	391	14	2	501	2	ECT2L	6	139164260	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1918618	139164260	31950807	552	47915										
SHPRH	257218	hgsc.bcm.edu	37	chr6	146276324	146276324	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcagaagaggtatctgaaccTgggcagggctgctcgtcatc	14	10	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:146276324T>A	ENST00000367505.2	-	2	399	c.135A>T	c.(133-135)ccA>ccT	p.P45P	SHPRH_ENST00000438092.2_Silent_p.P45P|SHPRH_ENST00000367503.3_Silent_p.P45P|SHPRH_ENST00000275233.7_Silent_p.P45P			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	45					DNA repair (GO:0006281)|nucleosome assembly (GO:0006334)|protein polyubiquitination (GO:0000209)	nucleosome (GO:0000786)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1)	79		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		TATCTGAACCTGGGCAGGGCT	0.438																																					p.P45P		Atlas-SNP	.											.	SHPRH	169	.	0			c.A135T						.						97	91	93					6																	146276324		1915	4124	6039	SO:0001819	synonymous_variant	257218	exon2			TGAACCTGGGCAG	AB095943	CCDS43513.1, CCDS47496.1, CCDS43513.2	6q24.2	2012-02-23	2012-02-23		ENSG00000146414	ENSG00000146414		"RING-type (C3HC4) zinc fingers"	19336	protein-coding gene	gene with protein product		608048	"SNF2 histone linker PHD RING helicase"			12837266	Standard	NM_001042683		Approved	FLJ90837, KIAA2023, bA545I5.2	uc003qlf.3	Q149N8	OTTHUMG00000015750	ENST00000367505.2:c.135A>T	chr6.hg19:g.146276324T>A		55.0	0.0		35.0	14.0	NM_173082	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Silent	SNP	ENST00000367505.2	hg19	CCDS43513.2																																																																																			.	.		0.438	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082		A	146276324	T	A	146276324	2	1	344	1	0	0	0	0	0	0	0	1	14306	1567	55	4		4	SHPRH	6	146276324	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	7112064	146276324	24838743	553	47916										
SASH1	23328	hgsc.bcm.edu	37	chr6	148848610	148848610	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtaaagaaggagactttgtgTacaaagaagtcatcaaatca	9	5	3	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:148848610T>C	ENST00000367467.3	+	12	1781	c.1306T>C	c.(1306-1308)Tac>Cac	p.Y436H		NM_015278.3	NP_056093.3	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	436					positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|positive regulation of p38MAPK cascade (GO:1900745)|protein polyubiquitination (GO:0000209)|regulation of protein autoubiquitination (GO:1902498)|regulation of protein K63-linked ubiquitination (GO:1900044)	membrane (GO:0016020)|protein complex (GO:0043234)	mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein C-terminus binding (GO:0008022)|protein complex scaffold (GO:0032947)|protein kinase binding (GO:0019901)			breast(4)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)		AGACTTTGTGTACAAAGAAGT	0.353																																					p.Y436H		Atlas-SNP	.											.	SASH1	123	.	0			c.T1306C						.						104	102	103					6																	148848610		2203	4300	6503	SO:0001583	missense	23328	exon12			TTTGTGTACAAAG	AB018333	CCDS5212.1	6q24.3	2013-01-10			ENSG00000111961	ENSG00000111961		"SAM and SH3 domain containing", "Sterile alpha motif (SAM) domain containing"	19182	protein-coding gene	gene with protein product		607955				9872452, 12771949	Standard	NM_015278		Approved	KIAA0790, dJ323M4.1, SH3D6A	uc003qme.1	O94885	OTTHUMG00000015773	ENST00000367467.3:c.1306T>C	chr6.hg19:g.148848610T>C	ENSP00000356437:p.Tyr436His	71.0	0.0		49.0	21.0	NM_015278	Q5TGN5|Q8TAI0|Q9H7R7	Missense_Mutation	SNP	ENST00000367467.3	hg19	CCDS5212.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.475019	0.84640	.	.	ENSG00000111961	ENST00000367467;ENST00000535767	T	0.41400	1.0	5.51	5.51	0.81932	.	0.121669	0.64402	D	0.000019	T	0.45538	0.1347	L	0.36672	1.1	0.51233	D	0.999918	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.42616	-0.9441	10	0.42905	T	0.14	-22.472	15.6579	0.77158	0.0:0.0:0.0:1.0	.	417;436	Q6P4R9;O94885	.;SASH1_HUMAN	H	436;197	ENSP00000356437:Y436H	ENSP00000356437:Y436H	Y	+	1	0	SASH1	148890303	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.751000	0.68720	2.100000	0.63781	0.523000	0.50628	TAC	.	.		0.353	SASH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042619.1	NM_015278		C	148848610	T	C	148848610	3	2	344	1	0	0	0	0	1	0	0	0	13863	1638	57	2	1352	2	SASH1	6	148848610	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2572286	148848610	22266457	554	47917										
ZBTB2	57621	hgsc.bcm.edu	37	chr6	151687080	151687080	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gttccctccagtggcttttcTggataaatttgcgtccacat	8	11	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:151687080T>G	ENST00000325144.4	-	3	1261	c.1121A>C	c.(1120-1122)cAg>cCg	p.Q374P		NM_020861.1	NP_065912.1	Q8N680	ZBTB2_HUMAN	zinc finger and BTB domain containing 2	374					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|large_intestine(2)|lung(6)|skin(1)	12			BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.63e-11)		GTGGCTTTTCTGGATAAATTT	0.527																																					p.Q374P		Atlas-SNP	.											.	ZBTB2	30	.	0			c.A1121C						.						110	108	109					6																	151687080		2203	4300	6503	SO:0001583	missense	57621	exon3			CTTTTCTGGATAA	BC020172	CCDS5231.1	6q25.1	2013-01-09			ENSG00000181472	ENSG00000181472		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	20868	protein-coding gene	gene with protein product						10819331	Standard	NM_020861		Approved	KIAA1483, ZNF437, bA351K16.2	uc003qoh.3	Q8N680	OTTHUMG00000015834	ENST00000325144.4:c.1121A>C	chr6.hg19:g.151687080T>G	ENSP00000323183:p.Gln374Pro	142.0	0.0		125.0	61.0	NM_020861	A8K7C7|Q5SZ81|Q9P245	Missense_Mutation	SNP	ENST00000325144.4	hg19	CCDS5231.1	.	.	.	.	.	.	.	.	.	.	T	19.07	3.755167	0.69648	.	.	ENSG00000181472	ENST00000325144	T	0.61158	0.13	5.76	5.76	0.90799	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.57227	0.2039	L	0.27053	0.805	0.80722	D	1	D	0.65815	0.995	D	0.70487	0.969	T	0.65026	-0.6268	10	0.72032	D	0.01	-33.5175	16.0843	0.81031	0.0:0.0:0.0:1.0	.	374	Q8N680	ZBTB2_HUMAN	P	374	ENSP00000323183:Q374P	ENSP00000323183:Q374P	Q	-	2	0	ZBTB2	151728773	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.923000	0.87546	2.191000	0.70037	0.533000	0.62120	CAG	.	.		0.527	ZBTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042715.1	NM_020861		G	151687080	T	G	151687080	3	3	344	1	0	0	0	0	1	0	0	0	17543	1580	55	5	427	5	ZBTB2	6	151687080	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2838470	151687080	19427987	555	47918										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152555815	152555815	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agacttaccaggaaagcattTagatgatcacggaccatttc	8	9	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:152555815T>C	ENST00000367255.5	-	111	21118	c.20517A>G	c.(20515-20517)ctA>ctG	p.L6839L	SYNE1_ENST00000423061.1_Silent_p.L6768L|SYNE1_ENST00000356820.4_Silent_p.L1363L|SYNE1_ENST00000265368.4_Silent_p.L6839L|SYNE1_ENST00000341594.5_Silent_p.L6451L|SYNE1_ENST00000448038.1_Silent_p.L6768L	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	6839					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GGAAAGCATTTAGATGATCAC	0.443										HNSCC(10;0.0054)																											p.L6839L		Atlas-SNP	.											.	SYNE1	3227	.	0			c.A20517G						.						143	136	138					6																	152555815		2203	4300	6503	SO:0001819	synonymous_variant	23345	exon111			AGCATTTAGATGA	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.20517A>G	chr6.hg19:g.152555815T>C		97.0	0.0		69.0	31.0	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	hg19	CCDS5236.2																																																																																			.	.		0.443	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		C	152555815	T	C	152555815	2	2	344	1	0	0	0	0	0	0	0	1	15460	1741	61	2		2	SYNE1	6	152555815	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	868735	152555815	18559252	556	47919										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152831366	152831366	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acccactttaataaagccttCttagcatttccttggatctt	4	11	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:152831366C>T	ENST00000367255.5	-	8	1144	c.543G>A	c.(541-543)aaG>aaA	p.K181K	SYNE1_ENST00000466159.2_Silent_p.K181K|SYNE1_ENST00000423061.1_Silent_p.K188K|SYNE1_ENST00000413186.2_Silent_p.K181K|SYNE1_ENST00000265368.4_Silent_p.K181K|SYNE1_ENST00000341594.5_Silent_p.K181K|SYNE1_ENST00000367253.4_Silent_p.K181K|SYNE1_ENST00000448038.1_Silent_p.K188K|SYNE1_ENST00000367248.3_Silent_p.K188K	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	181	Actin-binding.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		ATAAAGCCTTCTTAGCATTTC	0.428										HNSCC(10;0.0054)																											p.K188K		Atlas-SNP	.											.	SYNE1	3227	.	0			c.G564A						.						221	205	210					6																	152831366		2203	4300	6503	SO:0001819	synonymous_variant	23345	exon8			AGCCTTCTTAGCA	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.543G>A	chr6.hg19:g.152831366C>T		129.0	0.0		101.0	9.0	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	hg19	CCDS5236.2																																																																																			.	.		0.428	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152831366	C	T	152831366	2	4	344	1	0	0	0	0	0	0	0	1	15460	912	32	3		3	SYNE1	6	152831366	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	275551	152831366	18283701	557	47920										
MYCT1	80177	hgsc.bcm.edu	37	chr6	153043211	153043211	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctgcaatgtccaccacttccTgtggaaactgagagtcagct	9	12	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:153043211T>A	ENST00000367245.5	+	2	539	c.531T>A	c.(529-531)ccT>ccA	p.P177P	MYCT1_ENST00000529453.1_Intron	NM_025107.2	NP_079383.2	Q8N699	MYCT1_HUMAN	myc target 1	177						nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	20		Ovarian(120;0.0654)		OV - Ovarian serous cystadenocarcinoma(155;1.33e-10)|BRCA - Breast invasive adenocarcinoma(81;0.143)		CACCACTTCCTGTGGAAACTG	0.488																																					p.P177P		Atlas-SNP	.											.	MYCT1	48	.	0			c.T531A						.						90	87	88					6																	153043211		2203	4300	6503	SO:0001819	synonymous_variant	80177	exon2			ACTTCCTGTGGAA	AF527367	CCDS5239.1	6q25.1	2008-02-05			ENSG00000120279	ENSG00000120279			23172	protein-coding gene	gene with protein product						12477932	Standard	NM_025107		Approved	MTLC, FLJ21269	uc003qpc.4	Q8N699	OTTHUMG00000015850	ENST00000367245.5:c.531T>A	chr6.hg19:g.153043211T>A		85.0	0.0		77.0	32.0	NM_025107	Q8N396|Q8TBE8|Q9H763	Silent	SNP	ENST00000367245.5	hg19	CCDS5239.1	.	.	.	.	.	.	.	.	.	.	T	8.781	0.928196	0.18131	.	.	ENSG00000120279	ENST00000532295	.	.	.	5.8	-11.6	0.00059	.	.	.	.	.	T	0.16514	0.0397	.	.	.	0.58432	D	0.999996	.	.	.	.	.	.	T	0.44283	-0.9338	4	.	.	.	-24.9109	3.4935	0.07646	0.1414:0.2162:0.1408:0.5015	.	.	.	.	Q	158	.	.	L	+	2	0	MYCT1	153084904	0.000000	0.05858	0.151000	0.22473	0.953000	0.61014	-3.099000	0.00605	-2.683000	0.00407	-0.468000	0.05107	CTG	.	.		0.488	MYCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042750.2	NM_025107		A	153043211	T	A	153043211	2	1	344	1	0	0	0	0	0	0	0	1	10031	1567	55	4		4	MYCT1	6	153043211	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	211845	153043211	18071856	558	47921										
NOX3	50508	hgsc.bcm.edu	37	chr6	155776903	155776903	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttactactaatatggtggagAgaccctcattcaaaatccag	7	9	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:155776903A>G	ENST00000159060.2	-	1	134	c.32T>C	c.(31-33)cTc>cCc	p.L11P		NM_015718.2	NP_056533.1	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	11					detection of gravity (GO:0009590)|otolith development (GO:0048840)|superoxide anion generation (GO:0042554)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NADPH oxidase complex (GO:0043020)	superoxide-generating NADPH oxidase activity (GO:0016175)			cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	45		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)		TATGGTGGAGAGACCCTCATT	0.368																																					p.L11P		Atlas-SNP	.											.	NOX3	93	.	0			c.T32C						.						96	91	93					6																	155776903		2203	4300	6503	SO:0001583	missense	50508	exon1			GTGGAGAGACCCT	AF190122	CCDS5250.1	6q25.3	2008-05-15			ENSG00000074771	ENSG00000074771			7890	protein-coding gene	gene with protein product		607105				11376945	Standard	NM_015718		Approved	GP91-3	uc003qqm.3	Q9HBY0	OTTHUMG00000015883	ENST00000159060.2:c.32T>C	chr6.hg19:g.155776903A>G	ENSP00000159060:p.Leu11Pro	95.0	0.0		84.0	35.0	NM_015718	Q9HBJ9	Missense_Mutation	SNP	ENST00000159060.2	hg19	CCDS5250.1	.	.	.	.	.	.	.	.	.	.	A	4.364	0.066988	0.08388	.	.	ENSG00000074771	ENST00000159060	D	0.95821	-3.82	6.16	2.33	0.28932	.	0.235332	0.30085	N	0.010459	D	0.87834	0.6277	L	0.37850	1.14	0.19775	N	0.999956	P	0.50710	0.938	P	0.47470	0.548	T	0.82135	-0.0607	10	0.33940	T	0.23	-7.4196	8.7579	0.34656	0.6973:0.2404:0.0623:0.0	.	11	Q9HBY0	NOX3_HUMAN	P	11	ENSP00000159060:L11P	ENSP00000159060:L11P	L	-	2	0	NOX3	155818595	0.996000	0.38824	0.000000	0.03702	0.048000	0.14542	2.188000	0.42612	0.154000	0.19237	0.528000	0.53228	CTC	.	.		0.368	NOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042819.1			G	155776903	A	G	155776903	3	3	344	1	0	0	0	0	1	0	0	0	10566	304	11	2	1726	2	NOX3	6	155776903	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2733692	155776903	15338164	559	47922										
ARID1B	57492	hgsc.bcm.edu	37	chr6	157528624	157528624	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aattctatgctacattagttAggtacgttggggatcgcaaa	10	6	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:157528624A>T	ENST00000350026.5	+	19	6311	c.6310A>T	c.(6310-6312)Agg>Tgg	p.R2104W	ARID1B_ENST00000367148.1_Missense_Mutation_p.R2157W|ARID1B_ENST00000346085.5_Missense_Mutation_p.R2117W|ARID1B_ENST00000275248.4_Missense_Mutation_p.R2099W	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	2104					chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		TACATTAGTTAGGTACGTTGG	0.493																																					p.R2117W		Atlas-SNP	.											.	ARID1B	320	.	0			c.A6349T						.						187	196	193					6																	157528624		2203	4296	6499	SO:0001583	missense	57492	exon20			TTAGTTAGGTACG	AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"-"	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.6310A>T	chr6.hg19:g.157528624A>T	ENSP00000055163:p.Arg2104Trp	56.0	0.0		47.0	21.0	NM_020732	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Missense_Mutation	SNP	ENST00000350026.5	hg19	CCDS5251.2	.	.	.	.	.	.	.	.	.	.	A	13.32	2.201870	0.38905	.	.	ENSG00000049618	ENST00000346085;ENST00000350026;ENST00000367148;ENST00000275248;ENST00000414678	T;T;T;T;T	0.38240	1.15;1.15;1.15;1.15;1.15	5.26	5.26	0.73747	Armadillo-like helical (1);	0.000000	0.85682	D	0.000000	T	0.55513	0.1925	M	0.81497	2.545	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.994;0.994	T	0.63537	-0.6615	10	0.87932	D	0	.	15.477	0.75489	1.0:0.0:0.0:0.0	.	2104;2117;2099	Q8NFD5;Q8NFD5-2;G3XAA0	ARI1B_HUMAN;.;.	W	2117;2104;2157;2099;1626	ENSP00000344546:R2117W;ENSP00000055163:R2104W;ENSP00000356116:R2157W;ENSP00000275248:R2099W;ENSP00000412835:R1626W	ENSP00000275248:R2099W	R	+	1	2	ARID1B	157570316	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.742000	0.62103	2.108000	0.64289	0.533000	0.62120	AGG	.	.		0.493	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732		T	157528624	A	T	157528624	3	4	344	1	0	0	0	0	1	0	0	0	914	411	15	4	6427	4	ARID1B	6	157528624	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1751721	157528624	13586443	560	47923										
TAGAP	117289	hgsc.bcm.edu	37	chr6	159463252	159463252	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcatgagaaagggccaggacAgcaccttctttctcttctta	8	11	4	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:159463252A>C	ENST00000367066.3	-	5	504	c.173T>G	c.(172-174)cTg>cGg	p.L58R	RP1-111C20.4_ENST00000607391.1_RNA|RP1-111C20.4_ENST00000606466.1_RNA|RP1-111C20.4_ENST00000606470.1_RNA|RP1-111C20.4_ENST00000607796.1_RNA|TAGAP_ENST00000338313.5_Missense_Mutation_p.L58R|TAGAP_ENST00000326965.6_Intron	NM_001278733.1|NM_054114.3	NP_001265662.1|NP_473455.2	Q8N103	TAGAP_HUMAN	T-cell activation RhoGTPase activating protein	58					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|autonomic_ganglia(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(2)|skin(1)	23		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.16e-16)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		GGGCCAGGACAGCACCTTCTT	0.438																																					p.L58R		Atlas-SNP	.											.	TAGAP	75	.	0			c.T173G						.						142	153	149					6																	159463252		2203	4300	6503	SO:0001583	missense	117289	exon5			CAGGACAGCACCT	AF385429	CCDS5261.1, CCDS5262.1, CCDS5263.1	6q25.3	2011-09-07	2008-03-25		ENSG00000164691	ENSG00000164691		"Rho GTPase activating proteins"	15669	protein-coding gene	gene with protein product		609667	"T-cell activation GTPase activating protein"			16375659, 18311140, 18356936	Standard	NM_152133		Approved	FLJ32631, IDDM21, ARHGAP47	uc003qrz.3	Q8N103	OTTHUMG00000015923	ENST00000367066.3:c.173T>G	chr6.hg19:g.159463252A>C	ENSP00000356033:p.Leu58Arg	131.0	0.0		105.0	39.0	NM_138810	Q2NKM8|Q8NI40|Q96KZ2|Q96QA2	Missense_Mutation	SNP	ENST00000367066.3	hg19	CCDS5261.1	.	.	.	.	.	.	.	.	.	.	A	12.92	2.082557	0.36758	.	.	ENSG00000164691	ENST00000367066;ENST00000338313	T;T	0.22743	2.09;1.94	5.93	2.08	0.27032	.	0.367431	0.22908	N	0.054171	T	0.03915	0.0110	L	0.27053	0.805	0.09310	N	1	B;B	0.15473	0.006;0.013	B;B	0.14023	0.01;0.007	T	0.43893	-0.9363	10	0.23891	T	0.37	-2.9721	7.0707	0.25177	0.7426:0.1247:0.1327:0.0	.	58;58	Q8N103-4;Q8N103	.;TAGAP_HUMAN	R	58	ENSP00000356033:L58R;ENSP00000340217:L58R	ENSP00000340217:L58R	L	-	2	0	TAGAP	159383240	0.022000	0.18835	0.006000	0.13384	0.990000	0.78478	2.725000	0.47294	0.120000	0.18254	0.482000	0.46254	CTG	.	.		0.438	TAGAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042890.1	NM_054114		C	159463252	A	C	159463252	3	2	344	1	0	0	0	0	1	0	0	0	15552	188	7	5	2064	5	TAGAP	6	159463252	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1934628	159463252	11651815	561	47924										
IGF2R	3482	hgsc.bcm.edu	37	chr6	160469571	160469571	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccagatgaagtatgaaaaagAtcaggtgaatctgttttcac	9	6	3	5			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:160469571A>G	ENST00000356956.1	+	18	2658	c.2510A>G	c.(2509-2511)gAt>gGt	p.D837G		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	837					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	TATGAAAAAGATCAGGTGAAT	0.488																																					p.D837G		Atlas-SNP	.											.	IGF2R	251	.	0			c.A2510G						.						85	73	77					6																	160469571		2203	4300	6503	SO:0001583	missense	3482	exon18			AAAAAGATCAGGT	J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"CD molecules"	5467	protein-coding gene	gene with protein product	"cation-independent mannose-6 phosphate receptor"	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.2510A>G	chr6.hg19:g.160469571A>G	ENSP00000349437:p.Asp837Gly	70.0	0.0		49.0	19.0	NM_000876	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	hg19	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	A	10.30	1.310878	0.23821	.	.	ENSG00000197081	ENST00000356956	T	0.03607	3.87	5.16	1.36	0.22044	Mannose-6-phosphate receptor, binding (1);	1.255190	0.05236	N	0.511184	T	0.00998	0.0033	L	0.38838	1.175	0.09310	N	1	B	0.24317	0.101	B	0.28916	0.096	T	0.49615	-0.8921	10	0.20046	T	0.44	-7.5952	2.1463	0.03788	0.5926:0.1325:0.1473:0.1276	.	837	P11717	MPRI_HUMAN	G	837	ENSP00000349437:D837G	ENSP00000349437:D837G	D	+	2	0	IGF2R	160389561	0.001000	0.12720	0.000000	0.03702	0.064000	0.16182	1.517000	0.35867	0.001000	0.14605	0.533000	0.62120	GAT	.	.		0.488	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876		G	160469571	A	G	160469571	3	3	344	1	0	0	0	0	1	0	0	0	7585	333	12	2	2580	2	IGF2R	6	160469571	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1006319	160469571	10645496	562	47925										
PLG	5340	hgsc.bcm.edu	37	chr6	161160115	161160115	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tctaggtccccaaggccttcAtcctacaaggtcatcctggg	9	14	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:161160115A>G	ENST00000308192.9	+	16	1956	c.1893A>G	c.(1891-1893)tcA>tcG	p.S631S		NM_000301.3	NP_000292.1	P00747	PLMN_HUMAN	plasminogen	631	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of fibrinolysis (GO:0051918)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of fibrinolysis (GO:0051919)|tissue remodeling (GO:0048771)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	apolipoprotein binding (GO:0034185)|protein domain specific binding (GO:0019904)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)	59				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Alteplase(DB00009)|Aminocaproic Acid(DB00513)|Anistreplase(DB00029)|Aprotinin(DB06692)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Tranexamic Acid(DB00302)|Urokinase(DB00013)	CAAGGCCTTCATCCTACAAGG	0.498																																					p.S631S		Atlas-SNP	.											.	PLG	150	.	0			c.A1893G						.						168	156	160					6																	161160115		2203	4300	6503	SO:0001819	synonymous_variant	5340	exon16			GCCTTCATCCTAC	M74220	CCDS5279.1, CCDS55074.1	6q26	2012-10-02			ENSG00000122194	ENSG00000122194			9071	protein-coding gene	gene with protein product		173350					Standard	NM_000301		Approved		uc003qtm.4	P00747	OTTHUMG00000015957	ENST00000308192.9:c.1893A>G	chr6.hg19:g.161160115A>G		104.0	0.0		121.0	48.0	NM_000301	Q15146|Q5TEH4|Q6PA00	Silent	SNP	ENST00000308192.9	hg19	CCDS5279.1																																																																																			.	.		0.498	PLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042959.2	NM_000301		G	161160115	A	G	161160115	2	3	344	1	0	0	0	0	0	0	0	1	12095	204	8	2		2	PLG	6	161160115	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	690544	161160115	9954952	563	47926										
MAP3K4	4216	hgsc.bcm.edu	37	chr6	161523729	161523729	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtataaaaataacttcctgcAgaaccagcatatccaagagg	7	9	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:161523729A>T	ENST00000392142.4	+	19	3923		c.e19-1		MAP3K4_ENST00000348824.7_Splice_Site|MAP3K4_ENST00000366919.2_Splice_Site|MAP3K4_ENST00000366920.2_Splice_Site	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4						activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		AACTTCCTGCAGAACCAGCAT	0.373																																					.		Atlas-SNP	.											.	MAP3K4	364	.	0			c.3626-2A>T						.						35	35	35					6																	161523729		2203	4300	6503	SO:0001630	splice_region_variant	4216	exon18			TCCTGCAGAACCA	AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.3776-1A>T	chr6.hg19:g.161523729A>T		396.0	0.0		307.0	149.0	NM_006724	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Splice_Site	SNP	ENST00000392142.4	hg19	CCDS34565.1	.	.	.	.	.	.	.	.	.	.	A	19.90	3.912701	0.72983	.	.	ENSG00000085511	ENST00000366919;ENST00000392142;ENST00000540111;ENST00000366920;ENST00000348824	.	.	.	5.31	5.31	0.75309	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2821	0.73794	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MAP3K4	161443719	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	8.674000	0.91191	2.013000	0.59113	0.533000	0.62120	.	.	.		0.373	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3		Intron	T	161523729	A	T	161523729	5	4	344	1	0	0	0	0	0	0	1	0	9261	202	7	4	3848	4	MAP3K4	6	161523729	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	363614	161523729	9591338	564	47927										
PDE10A	10846	hgsc.bcm.edu	37	chr6	165863831	165863831	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttagttcatatacaactcccTgcatattcgtatcttggtac	5	10	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:165863831T>G	ENST00000366882.1	-	5	369	c.215A>C	c.(214-216)cAg>cCg	p.Q72P	PDE10A_ENST00000539869.2_Missense_Mutation_p.Q82P|PDE10A_ENST00000354448.4_Missense_Mutation_p.Q72P			Q9Y233	PDE10_HUMAN	phosphodiesterase 10A	72					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of protein kinase A signaling (GO:0010738)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|metal ion binding (GO:0046872)			breast(4)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(39)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	71		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Caffeine(DB00201)|Dipyridamole(DB00975)|Papaverine(DB01113)|Tofisopam(DB08811)|Triflusal(DB08814)	TACAACTCCCTGCATATTCGT	0.318																																					p.Q82P	Esophageal Squamous(22;308 615 5753 12038 40624)	Atlas-SNP	.											.	PDE10A	154	.	0			c.A245C						.						137	124	128					6																	165863831		2203	4300	6503	SO:0001583	missense	10846	exon4			ACTCCCTGCATAT	AB020593	CCDS47513.1	6q26	2008-03-18			ENSG00000112541	ENSG00000112541	3.1.4.17	"Phosphodiesterases"	8772	protein-coding gene	gene with protein product		610652				10373451	Standard	NM_001130690		Approved		uc003quo.3	Q9Y233	OTTHUMG00000015986	ENST00000366882.1:c.215A>C	chr6.hg19:g.165863831T>G	ENSP00000355847:p.Gln72Pro	81.0	0.0		75.0	26.0	NM_001130690	Q6FHX1|Q9HCP9|Q9NTV4|Q9ULW9|Q9Y5T1	Missense_Mutation	SNP	ENST00000366882.1	hg19		.	.	.	.	.	.	.	.	.	.	T	18.99	3.740028	0.69304	.	.	ENSG00000112541	ENST00000366882;ENST00000539869;ENST00000343842;ENST00000354448;ENST00000392126	T;T	0.71461	-0.57;-0.57	4.61	4.61	0.57282	.	0.106366	0.64402	D	0.000003	T	0.70622	0.3245	L	0.44542	1.39	0.58432	D	0.999998	D;B	0.61697	0.99;0.026	D;B	0.70487	0.969;0.018	T	0.70171	-0.4945	10	0.33141	T	0.24	.	14.3089	0.66403	0.0:0.0:0.0:1.0	.	82;72	Q9ULW9;Q9Y233	.;PDE10_HUMAN	P	72;100;82;72;71	ENSP00000355847:Q72P;ENSP00000346435:Q72P	ENSP00000341187:Q82P	Q	-	2	0	PDE10A	165783821	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.708000	0.84633	1.843000	0.53566	0.460000	0.39030	CAG	.	.		0.318	PDE10A-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000043031.1			G	165863831	T	G	165863831	3	3	344	1	0	0	0	0	1	0	0	0	11639	1580	55	5	2200	5	PDE10A	6	165863831	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	4340102	165863831	5251236	565	47928										
T	6862	hgsc.bcm.edu	37	chr6	166578331	166578331	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttttgcaaatggattgtactTaattttaagagctgtgatct	8	4	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:166578331T>A	ENST00000296946.2	-	5	1093	c.625A>T	c.(625-627)Aag>Tag	p.K209*	T_ENST00000366871.3_Nonsense_Mutation_p.K209*	NM_003181.3	NP_003172.1	O15178	BRAC_HUMAN	T, brachyury homolog (mouse)	209					anterior/posterior axis specification, embryo (GO:0008595)|BMP signaling pathway (GO:0030509)|bone morphogenesis (GO:0060349)|canonical Wnt signaling pathway (GO:0060070)|determination of heart left/right asymmetry (GO:0061371)|embryonic skeletal system development (GO:0048706)|heart morphogenesis (GO:0003007)|mesoderm development (GO:0007498)|mesoderm migration involved in gastrulation (GO:0007509)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate morphogenesis (GO:0001839)|neural tube closure (GO:0001843)|notochord formation (GO:0014028)|penetration of zona pellucida (GO:0007341)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|signal transduction (GO:0007165)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|somitogenesis (GO:0001756)|transcription from RNA polymerase II promoter (GO:0006366)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(23)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	39		Prostate(117;4.48e-07)|Ovarian(120;1.78e-06)|Breast(66;2.54e-06)|Lung SC(201;0.0225)|Esophageal squamous(34;0.0559)		OV - Ovarian serous cystadenocarcinoma(33;1.09e-113)|GBM - Glioblastoma multiforme(31;1.51e-108)|BRCA - Breast invasive adenocarcinoma(81;8.45e-09)|LUAD - Lung adenocarcinoma(999;0.0407)		GGATTGTACTTAATTTTAAGA	0.343									Chordoma, Familial Clustering of																												p.K209X		Atlas-SNP	.											.	T	77	.	0			c.A625T						.						53	57	56					6																	166578331		2203	4297	6500	SO:0001587	stop_gained	6862	exon5	Familial Cancer Database		TGTACTTAATTTT	AJ001699	CCDS5290.1, CCDS59045.1	6q27	2011-06-13	2001-11-28		ENSG00000164458	ENSG00000164458		"T-boxes"	11515	protein-coding gene	gene with protein product		601397	"T brachyury (mouse) homolog"			8963900	Standard	NM_003181		Approved		uc003quu.2	O15178	OTTHUMG00000015991	ENST00000296946.2:c.625A>T	chr6.hg19:g.166578331T>A	ENSP00000296946:p.Lys209*	108.0	0.0		59.0	34.0	NM_003181	E7ERD6|Q4KMP4	Nonsense_Mutation	SNP	ENST00000296946.2	hg19	CCDS5290.1	.	.	.	.	.	.	.	.	.	.	T	37	6.388846	0.97529	.	.	ENSG00000164458	ENST00000366876;ENST00000296946;ENST00000366871	.	.	.	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.2284	0.65875	0.0:0.0:0.0:1.0	.	.	.	.	X	209	.	ENSP00000296946:K209X	K	-	1	0	T	166498321	1.000000	0.71417	0.998000	0.56505	0.985000	0.73830	7.100000	0.76989	1.957000	0.56846	0.528000	0.53228	AAG	.	.		0.343	T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043037.2	NM_003181		A	166578331	T	A	166578331	4	1	344	1	0	0	0	0	0	1	0	0	15503	1763	61	4	702	4	T	6	166578331	Nonsense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	714500	166578331	4536736	566	47929										
CCR6	1235	hgsc.bcm.edu	37	chr6	167550197	167550197	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	attccggctccgatccagaaCactaccgcgcagcaaaatca	7	15	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr6:167550197C>A	ENST00000341935.5	+	3	1031	c.479C>A	c.(478-480)aCa>aAa	p.T160K	CCR6_ENST00000349984.4_Missense_Mutation_p.T160K|CCR6_ENST00000400926.2_Missense_Mutation_p.T160K|RP11-517H2.6_ENST00000609590.1_RNA	NM_031409.3	NP_113597.2	P51684	CCR6_HUMAN	chemokine (C-C motif) receptor 6	160					cellular component movement (GO:0006928)|cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|humoral immune response (GO:0006959)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)|receptor activity (GO:0004872)			endometrium(3)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)	14		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;8.21e-20)|BRCA - Breast invasive adenocarcinoma(81;4.55e-06)|GBM - Glioblastoma multiforme(31;0.00507)		CGATCCAGAACACTACCGCGC	0.498																																					p.T160K		Atlas-SNP	.											.	CCR6	36	.	0			c.C479A						.						78	78	78					6																	167550197		2203	4300	6503	SO:0001583	missense	1235	exon3			CCAGAACACTACC	U68030	CCDS5298.1	6q27	2012-08-08			ENSG00000112486	ENSG00000112486		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1607	protein-coding gene	gene with protein product		601835		STRL22		8886020	Standard	NM_031409		Approved	CKR-L3, GPR-CY4, CMKBR6, GPR29, DRY-6, DCR2, BN-1, CD196	uc010kkm.3	P51684	OTTHUMG00000016015	ENST00000341935.5:c.479C>A	chr6.hg19:g.167550197C>A	ENSP00000343952:p.Thr160Lys	78.0	0.0		58.0	18.0	NM_004367	E1P5C6|P78553|Q92846	Missense_Mutation	SNP	ENST00000341935.5	hg19	CCDS5298.1	.	.	.	.	.	.	.	.	.	.	C	11.54	1.670084	0.29693	.	.	ENSG00000112486	ENST00000400926;ENST00000341935;ENST00000349984	T;T;T	0.40756	1.02;1.02;1.02	4.94	4.94	0.65067	GPCR, rhodopsin-like superfamily (1);	0.083518	0.50627	U	0.000113	T	0.23766	0.0575	L	0.55481	1.735	0.39696	D	0.971116	B	0.24721	0.11	B	0.29077	0.098	T	0.13255	-1.0516	10	0.08837	T	0.75	.	17.1529	0.86782	0.0:1.0:0.0:0.0	.	160	P51684	CCR6_HUMAN	K	160	ENSP00000383715:T160K;ENSP00000343952:T160K;ENSP00000339393:T160K	ENSP00000343952:T160K	T	+	2	0	CCR6	167470187	0.360000	0.24964	0.000000	0.03702	0.002000	0.02628	2.901000	0.48695	2.264000	0.75181	0.655000	0.94253	ACA	.	.		0.498	CCR6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043118.1			A	167550197	C	A	167550197	3	1	344	1	0	0	0	0	1	0	0	0	2947	478	17	3	485	3	CCR6	6	167550197	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	971866	167550197	3564870	567	47930										
SNX8	29886	hgsc.bcm.edu	37	chr7	2317782	2317782	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cttcaggaagaggcccttctTctccggaatgagctccacct	9	14	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:2317782T>C	ENST00000222990.3	-	2	295	c.253A>G	c.(253-255)Aag>Gag	p.K85E		NM_013321.2	NP_037453.1	Q9Y5X2	SNX8_HUMAN	sorting nexin 8	85	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				early endosome to Golgi transport (GO:0034498)|intracellular protein transport (GO:0006886)	early endosome membrane (GO:0031901)	identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)			breast(2)|endometrium(5)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(2)|skin(3)	26		Ovarian(82;0.11)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0853)|OV - Ovarian serous cystadenocarcinoma(56;3.79e-14)		AGGCCCTTCTTCTCCGGAATG	0.602																																					p.K85E		Atlas-SNP	.											.	SNX8	46	.	0			c.A253G						.						100	86	91					7																	2317782		2203	4300	6503	SO:0001583	missense	29886	exon2			CCTTCTTCTCCGG	AF121858	CCDS5331.1	7p22.3	2010-08-05			ENSG00000106266	ENSG00000106266		"Sorting nexins"	14972	protein-coding gene	gene with protein product		614905					Standard	NM_013321		Approved	Mvp1	uc003slw.3	Q9Y5X2	OTTHUMG00000151512	ENST00000222990.3:c.253A>G	chr7.hg19:g.2317782T>C	ENSP00000222990:p.Lys85Glu	76.0	0.0		64.0	25.0	NM_013321	A4D207|Q96I67	Missense_Mutation	SNP	ENST00000222990.3	hg19	CCDS5331.1	.	.	.	.	.	.	.	.	.	.	T	20.5	3.999360	0.74818	.	.	ENSG00000106266	ENST00000222990;ENST00000435060;ENST00000457286;ENST00000435336;ENST00000447136;ENST00000419693	T;T;T;T;T	0.39787	1.06;1.06;1.06;1.06;1.06	5.16	5.16	0.70880	Phox homologous domain (5);	0.000000	0.85682	D	0.000000	T	0.65842	0.2730	M	0.91972	3.26	0.58432	D	0.999998	P	0.48294	0.908	P	0.53912	0.737	T	0.75158	-0.3416	10	0.72032	D	0.01	.	14.9676	0.71208	0.0:0.0:0.0:1.0	.	85	Q9Y5X2	SNX8_HUMAN	E	85;71;32;32;32;32	ENSP00000222990:K85E;ENSP00000392437:K71E;ENSP00000406954:K32E;ENSP00000406212:K32E;ENSP00000403608:K32E	ENSP00000222990:K85E	K	-	1	0	SNX8	2284308	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.363000	0.79516	1.933000	0.56026	0.533000	0.62120	AAG	.	.		0.602	SNX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322949.2			C	2317782	T	C	2317782	3	2	344	1	0	0	0	0	1	0	0	0	14923	1792	62	2	1184	2	SNX8	7	2317782	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10		2317782	156820881	568	47931										
CARD11	84433	hgsc.bcm.edu	37	chr7	2983944	2983944	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtagttgtcgtccttcacctTgaccagctcgtcattgtagc	9	12	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:2983944T>A	ENST00000396946.4	-	5	989	c.586A>T	c.(586-588)Aag>Tag	p.K196*	AC004906.3_ENST00000423194.1_RNA	NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	196					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		TCCTTCACCTTGACCAGCTCG	0.552			Mis		DLBCL																																p.K196X		Atlas-SNP	.		Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	.	CARD11	339	.	0			c.A586T						.						270	161	198					7																	2983944		2203	4300	6503	SO:0001587	stop_gained	84433	exon5			TCACCTTGACCAG	AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"card-maguk protein 1", "bcl10-interacting maguk protein 3"	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.586A>T	chr7.hg19:g.2983944T>A	ENSP00000380150:p.Lys196*	127.0	0.0		99.0	45.0	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Nonsense_Mutation	SNP	ENST00000396946.4	hg19	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	T	41	8.972946	0.99021	.	.	ENSG00000198286	ENST00000396946	.	.	.	4.16	2.96	0.34315	.	0.168937	0.47852	D	0.000214	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	-37.1486	10.7146	0.46005	0.0:0.0:0.1605:0.8395	.	.	.	.	X	196	.	ENSP00000380150:K196X	K	-	1	0	CARD11	2950470	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.728000	0.54991	0.541000	0.28827	0.459000	0.35465	AAG	.	.		0.552	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		A	2983944	T	A	2983944	4	1	344	1	0	0	0	0	0	1	0	0	2647	1821	63	4	2962	4	CARD11	7	2983944	Nonsense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	666162	2983944	156154719	569	47932										
CARD11	84433	hgsc.bcm.edu	37	chr7	2987406	2987406	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcgtctccatgtagtcatccAtctctggccctcctcctttt	6	16	3	0	rs368132142		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:2987406A>C	ENST00000396946.4	-	3	426	c.23T>G	c.(22-24)aTg>aGg	p.M8R	AC004906.3_ENST00000423194.1_RNA	NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	8					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		GTAGTCATCCATCTCTGGCCC	0.493			Mis		DLBCL																																p.M8R		Atlas-SNP	.		Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	.	CARD11	339	.	0			c.T23G						.	A	ARG/MET	0,4406		0,0,2203	188	167	174		23	4.1	1	7		174	1,8599		0,1,4299	no	missense	CARD11	NM_032415.4	91	0,1,6502	CC,CA,AA		0.0116,0.0,0.0077	possibly-damaging	8/1155	2987406	1,13005	2203	4300	6503	SO:0001583	missense	84433	exon3			TCATCCATCTCTG	AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"card-maguk protein 1", "bcl10-interacting maguk protein 3"	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.23T>G	chr7.hg19:g.2987406A>C	ENSP00000380150:p.Met8Arg	102.0	0.0		103.0	45.0	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	hg19	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	A	15.39	2.820629	0.50633	0.0	1.16E-4	ENSG00000198286	ENST00000396946;ENST00000356408	T;T	0.56275	1.45;0.47	5.21	4.05	0.47172	.	0.084546	0.85682	D	0.000000	T	0.41003	0.1140	L	0.47716	1.5	0.49798	D	0.999828	P	0.45531	0.86	B	0.35607	0.206	T	0.35051	-0.9804	10	0.62326	D	0.03	-44.657	9.6852	0.40094	0.9203:0.0:0.0797:0.0	.	8	Q9BXL7	CAR11_HUMAN	R	8	ENSP00000380150:M8R;ENSP00000348779:M8R	ENSP00000348779:M8R	M	-	2	0	CARD11	2953932	1.000000	0.71417	0.995000	0.50966	0.998000	0.95712	4.985000	0.63845	0.821000	0.34540	0.459000	0.35465	ATG	.	.		0.493	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		C	2987406	A	C	2987406	3	2	344	1	0	0	0	0	1	0	0	0	2647	217	8	5	3533	5	CARD11	7	2987406	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3462	2987406	156151257	570	47933										
FOXK1	221937	hgsc.bcm.edu	37	chr7	4794986	4794986	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	catcaccaagcattacccctActaccggacggccgacaaag	7	16	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:4794986A>G	ENST00000328914.4	+	4	1022	c.1022A>G	c.(1021-1023)tAc>tGc	p.Y341C	FOXK1_ENST00000446823.1_Missense_Mutation_p.Y178C	NM_001037165.1	NP_001032242.1			forkhead box K1											breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)		CATTACCCCTACTACCGGACG	0.612																																					p.Y341C		Atlas-SNP	.											.	FOXK1	64	.	0			c.A1022G						.						56	52	53					7																	4794986		2203	4300	6503	SO:0001583	missense	221937	exon4			ACCCCTACTACCG	BK004104	CCDS34591.1	7p22	2006-12-15			ENSG00000164916	ENSG00000164916		"Forkhead boxes"	23480	protein-coding gene	gene with protein product						15202027	Standard	NM_001037165		Approved	IMAGE:5164497	uc003snc.1	P85037	OTTHUMG00000151739	ENST00000328914.4:c.1022A>G	chr7.hg19:g.4794986A>G	ENSP00000328720:p.Tyr341Cys	105.0	0.0		99.0	29.0	NM_001037165		Missense_Mutation	SNP	ENST00000328914.4	hg19	CCDS34591.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.691281	0.88735	.	.	ENSG00000164916	ENST00000446823;ENST00000450194;ENST00000328914;ENST00000545598	D;D	0.97598	-4.45;-4.45	5.45	5.45	0.79879	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (4);	0.000000	0.85682	D	0.000000	D	0.98686	0.9559	M	0.91972	3.26	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.991	D	0.99764	1.1022	10	0.87932	D	0	.	14.7231	0.69323	1.0:0.0:0.0:0.0	.	341;178	P85037;P85037-2	FOXK1_HUMAN;.	C	178;105;341;224	ENSP00000394442:Y178C;ENSP00000328720:Y341C	ENSP00000328720:Y341C	Y	+	2	0	FOXK1	4761512	1.000000	0.71417	0.991000	0.47740	0.968000	0.65278	9.306000	0.96204	2.064000	0.61679	0.533000	0.62120	TAC	.	.		0.612	FOXK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323729.2			G	4794986	A	G	4794986	3	3	344	1	0	0	0	0	1	0	0	0	6022	391	14	2	1036	2	FOXK1	7	4794986	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1807580	4794986	154343677	571	47934										
SLC29A4	222962	hgsc.bcm.edu	37	chr7	5336593	5336593	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cgggcgtgatgatctctctgAgccgcatcctcacgaagctg	12	13	3	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:5336593A>G	ENST00000396872.3	+	7	807	c.646A>G	c.(646-648)Agc>Ggc	p.S216G	SLC29A4_ENST00000297195.4_Missense_Mutation_p.S216G|SLC29A4_ENST00000406453.3_Missense_Mutation_p.S202G			Q7RTT9	S29A4_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 4	216					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	nucleoside transmembrane transporter activity (GO:0005337)			breast(1)|cervix(2)|kidney(7)|large_intestine(1)|liver(1)|lung(7)|urinary_tract(1)	20		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0903)|OV - Ovarian serous cystadenocarcinoma(56;2.65e-15)	Metformin(DB00331)	GATCTCTCTGAGCCGCATCCT	0.706																																					p.S216G		Atlas-SNP	.											.	SLC29A4	52	.	0			c.A646G						.						13	14	14					7																	5336593		2163	4210	6373	SO:0001583	missense	222962	exon7			TCTCTGAGCCGCA	AK075422	CCDS5340.1, CCDS75561.1	7p22.2	2013-07-17	2013-07-17		ENSG00000164638	ENSG00000164638		"Solute carriers"	23097	protein-coding gene	gene with protein product		609149	"solute carrier family 29 (nucleoside transporters), member 4"			12838422	Standard	NM_153247		Approved	FLJ34923, ENT4	uc003soc.3	Q7RTT9	OTTHUMG00000023797	ENST00000396872.3:c.646A>G	chr7.hg19:g.5336593A>G	ENSP00000380081:p.Ser216Gly	18.0	0.0		24.0	10.0	NM_153247	Q6PJ08|Q86WY8|Q8NAR3|Q8NBM2	Missense_Mutation	SNP	ENST00000396872.3	hg19	CCDS5340.1	.	.	.	.	.	.	.	.	.	.	.	20.5	4.004066	0.74932	.	.	ENSG00000164638	ENST00000396872;ENST00000297195;ENST00000406453	T;T;T	0.74737	-0.87;-0.87;-0.02	3.45	3.45	0.39498	Major facilitator superfamily domain, general substrate transporter (1);	0.110120	0.64402	D	0.000016	D	0.83335	0.5232	M	0.73598	2.24	0.44515	D	0.997461	D;P	0.71674	0.998;0.938	D;P	0.76071	0.987;0.831	T	0.83131	-0.0113	10	0.45353	T	0.12	-4.2427	10.8033	0.46502	1.0:0.0:0.0:0.0	.	202;216	Q7RTT9-2;Q7RTT9	.;S29A4_HUMAN	G	216;216;202	ENSP00000380081:S216G;ENSP00000297195:S216G;ENSP00000385845:S202G	ENSP00000297195:S216G	S	+	1	0	SLC29A4	5303119	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.233000	0.72320	1.351000	0.45789	0.454000	0.30748	AGC	.	.		0.706	SLC29A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060118.6	NM_153247		G	5336593	A	G	5336593	3	3	344	1	0	0	0	0	1	0	0	0	14552	304	11	2	668	2	SLC29A4	7	5336593	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	541607	5336593	153802070	572	47935										
TNRC18	84629	hgsc.bcm.edu	37	chr7	5410083	5410083	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgatgccatgcaggaagctcTgctccaagacaaggctctcg	11	12	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:5410083T>G	ENST00000430969.1	-	11	4490	c.4142A>C	c.(4141-4143)cAg>cCg	p.Q1381P	TNRC18_ENST00000399537.4_Missense_Mutation_p.Q1381P	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1381							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		CAGGAAGCTCTGCTCCAAGAC	0.642																																					p.Q1381P		Atlas-SNP	.											.	TNRC18	311	.	0			c.A4142C						.						28	28	28					7																	5410083		2147	4251	6398	SO:0001583	missense	84629	exon11			AAGCTCTGCTCCA	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"Trinucleotide (CAG) repeat containing"	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.4142A>C	chr7.hg19:g.5410083T>G	ENSP00000395538:p.Gln1381Pro	51.0	0.0		47.0	20.0	NM_001080495	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	hg19	CCDS47534.1	.	.	.	.	.	.	.	.	.	.	T	4.795	0.147749	0.09134	.	.	ENSG00000182095	ENST00000399537;ENST00000430969;ENST00000399544;ENST00000327499	T;T	0.12255	2.7;2.7	4.72	3.54	0.40534	.	0.000000	0.31821	N	0.007007	T	0.15998	0.0385	M	0.70275	2.135	0.23620	N	0.997273	B	0.06786	0.001	B	0.04013	0.001	T	0.17167	-1.0378	10	0.30078	T	0.28	.	10.3758	0.44081	0.0:0.0:0.1643:0.8357	.	1381	O15417	TNC18_HUMAN	P	1381;1381;436;436	ENSP00000382452:Q1381P;ENSP00000395538:Q1381P	ENSP00000330383:Q436P	Q	-	2	0	TNRC18	5376609	1.000000	0.71417	0.999000	0.59377	0.341000	0.28922	3.229000	0.51278	0.636000	0.30508	0.260000	0.18958	CAG	.	.		0.642	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				G	5410083	T	G	5410083	3	3	344	1	0	0	0	0	1	0	0	0	16354	1580	55	5	4844	5	TNRC18	7	5410083	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	73490	5410083	153728580	573	47936										
USP42	84132	hgsc.bcm.edu	37	chr7	6183734	6183734	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aggtgtaaaaagatggttccAgcttcaaagaggttcactat	10	6	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:6183734A>T	ENST00000306177.5	+	9	1055	c.897A>T	c.(895-897)ccA>ccT	p.P299P		NM_032172.2	NP_115548.1	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42	299	USP.				cell differentiation (GO:0030154)|protein deubiquitination (GO:0016579)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(2)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	35		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)		AGATGGTTCCAGCTTCAAAGA	0.333																																					p.P299P		Atlas-SNP	.											.	USP42	138	.	0			c.A897T						.						135	123	127					7																	6183734		1828	4097	5925	SO:0001819	synonymous_variant	84132	exon9			GGTTCCAGCTTCA	AK022759	CCDS47535.1	7p22.2	2005-08-08	2005-08-08		ENSG00000106346	ENSG00000106346		"Ubiquitin-specific peptidases"	20068	protein-coding gene	gene with protein product			"ubiquitin specific protease 42"			12838346	Standard	NM_032172		Approved	FLJ12697	uc011jwp.2	Q9H9J4	OTTHUMG00000151888	ENST00000306177.5:c.897A>T	chr7.hg19:g.6183734A>T		73.0	0.0		64.0	25.0	NM_032172	A2RUE3|B5MDA5|Q0VIN8|Q3C166|Q6P9B4	Silent	SNP	ENST00000306177.5	hg19	CCDS47535.1																																																																																			.	.		0.333	USP42-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324262.3	XM_166526		T	6183734	A	T	6183734	2	4	344	1	0	0	0	0	0	0	0	1	17088	175	7	4		4	USP42	7	6183734	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	773651	6183734	152954929	574	47937										
COL28A1	340267	hgsc.bcm.edu	37	chr7	7530242	7530242	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgtccaattccaggagctccTggagaaccataaggaccagg	11	11	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:7530242T>A	ENST00000399429.3	-	12	1202	c.1062A>T	c.(1060-1062)ccA>ccT	p.P354P		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	354	Collagen-like 2.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		CAGGAGCTCCTGGAGAACCAT	0.458																																					p.P354P		Atlas-SNP	.											.	COL28A1	113	.	0			c.A1062T						.						48	50	49					7																	7530242		1847	4079	5926	SO:0001819	synonymous_variant	340267	exon12			AGCTCCTGGAGAA	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"Collagens"	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.1062A>T	chr7.hg19:g.7530242T>A		62.0	0.0		87.0	39.0	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Silent	SNP	ENST00000399429.3	hg19	CCDS43553.1																																																																																			.	.		0.458	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763		A	7530242	T	A	7530242	2	1	344	1	0	0	0	0	0	0	0	1	3688	1567	55	4		4	COL28A1	7	7530242	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1346508	7530242	151608421	575	47938										
MIOS	54468	hgsc.bcm.edu	37	chr7	7612424	7612424	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttcaaagatttgataggaaaAgagtttgttccaaaacatgc	8	5	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:7612424A>G	ENST00000340080.4	+	4	739	c.318A>G	c.(316-318)aaA>aaG	p.K106K	MIOS_ENST00000405785.1_Silent_p.K106K	NM_019005.3	NP_061878.3	Q9NXC5	MIO_HUMAN	missing oocyte, meiosis regulator, homolog (Drosophila)	106						lysosomal membrane (GO:0005765)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TGATAGGAAAAGAGTTTGTTC	0.423																																					p.K106K		Atlas-SNP	.											.	MIOS	68	.	0			c.A318G						.						132	122	125					7																	7612424		1889	4107	5996	SO:0001819	synonymous_variant	54468	exon4			AGGAAAAGAGTTT		CCDS43554.1	7p21.3	2011-09-12			ENSG00000164654	ENSG00000164654			21905	protein-coding gene	gene with protein product	"WD repeat-containing protein mio"	615359				14973288	Standard	NM_019005		Approved	FLJ20323	uc003srf.3	Q9NXC5	OTTHUMG00000152440	ENST00000340080.4:c.318A>G	chr7.hg19:g.7612424A>G		87.0	0.0		89.0	36.0	NM_019005	B2RTV6|O75216|Q7L551|Q9H092	Silent	SNP	ENST00000340080.4	hg19	CCDS43554.1																																																																																			.	.		0.423	MIOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326218.1	NM_019005		G	7612424	A	G	7612424	2	3	344	1	0	0	0	0	0	0	0	1	9598	69	3	2		2	MIOS	7	7612424	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	82182	7612424	151526239	576	47939										
ICA1	3382	hgsc.bcm.edu	37	chr7	8167517	8167517	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acctaccttgtagcgaggccTgtaagtctttcatattttgg	9	9	2	0	rs368311237		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:8167517T>A	ENST00000402384.3	-	13	1582	c.1316A>T	c.(1315-1317)cAg>cTg	p.Q439L	ICA1_ENST00000265577.7_Missense_Mutation_p.Q438L|ICA1_ENST00000401396.1_Missense_Mutation_p.Q427L|ICA1_ENST00000406470.2_Missense_Mutation_p.Q439L|ICA1_ENST00000422063.2_Missense_Mutation_p.Q468L|ICA1_ENST00000396675.3_Missense_Mutation_p.Q439L			Q05084	ICA69_HUMAN	islet cell autoantigen 1, 69kDa	439					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|secretory granule membrane (GO:0030667)|synaptic vesicle membrane (GO:0030672)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(8)|urinary_tract(1)	23		Ovarian(82;0.0612)		UCEC - Uterine corpus endometrioid carcinoma (126;0.246)		TAGCGAGGCCTGTAAGTCTTT	0.458																																					p.Q439L		Atlas-SNP	.											.	ICA1	65	.	0			c.A1316T						.						135	151	146					7																	8167517		2199	4300	6499	SO:0001583	missense	3382	exon13			GAGGCCTGTAAGT		CCDS34602.1, CCDS64595.1	7p22	2006-12-13	2002-08-29		ENSG00000003147	ENSG00000003147			5343	protein-coding gene	gene with protein product		147625	"islet cell autoantigen 1 (69kD)"			7918678, 8777998	Standard	NM_001276478		Approved	ICAp69	uc003srm.3	Q05084	OTTHUMG00000152008	ENST00000402384.3:c.1316A>T	chr7.hg19:g.8167517T>A	ENSP00000385570:p.Gln439Leu	68.0	0.0		58.0	29.0	NM_022307	A8K7U1|B3FTQ2|P78506|Q13824|Q96HG3	Missense_Mutation	SNP	ENST00000402384.3	hg19	CCDS34602.1	.	.	.	.	.	.	.	.	.	.	T	9.209	1.030421	0.19512	.	.	ENSG00000003147	ENST00000402384;ENST00000406470;ENST00000265577;ENST00000396675;ENST00000401396;ENST00000422063	.	.	.	5.64	5.64	0.86602	Islet cell autoantigen Ica1, C-terminal (1);	0.393296	0.27811	N	0.017752	T	0.41926	0.1180	N	0.21448	0.665	0.40857	D	0.983809	B;B;B;B	0.09022	0.002;0.001;0.001;0.002	B;B;B;B	0.13407	0.009;0.004;0.006;0.007	T	0.32640	-0.9899	9	0.25106	T	0.35	-9.6178	10.9881	0.47532	0.1393:0.0:0.0:0.8606	.	468;438;439;427	B3FTQ2;Q96HG3;Q05084;E9PDL4	.;.;ICA69_HUMAN;.	L	439;439;438;439;427;468	.	ENSP00000265577:Q438L	Q	-	2	0	ICA1	8134042	1.000000	0.71417	1.000000	0.80357	0.449000	0.32228	3.953000	0.56699	2.287000	0.76781	0.482000	0.46254	CAG	.	.		0.458	ICA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324793.1	NM_004968		A	8167517	T	A	8167517	3	1	344	1	0	0	0	0	1	0	0	0	7486	1580	55	4	143	4	ICA1	7	8167517	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	555093	8167517	150971146	577	47940										
FERD3L	222894	hgsc.bcm.edu	37	chr7	19184845	19184845	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atcctcctgggtcttccctcTcggagcgcaagggctgggtc	13	14	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:19184845T>A	ENST00000275461.3	-	1	199	c.141A>T	c.(139-141)cgA>cgT	p.R47R	AC003986.5_ENST00000452700.1_RNA	NM_152898.2	NP_690862.1	Q96RJ6	FER3L_HUMAN	Fer3-like bHLH transcription factor	47					cell development (GO:0048468)|floor plate development (GO:0033504)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of neurogenesis (GO:0050767)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(4)|large_intestine(8)|lung(16)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	35						GTCTTCCCTCTCGGAGCGCAA	0.657																																					p.R47R		Atlas-SNP	.											.	FERD3L	63	.	0			c.A141T						.						52	41	44					7																	19184845		2203	4300	6503	SO:0001819	synonymous_variant	222894	exon1			TCCCTCTCGGAGC	AF369897	CCDS5368.1	7p21.3	2013-10-17	2013-10-17		ENSG00000146618	ENSG00000146618		"Basic helix-loop-helix proteins"	16660	protein-coding gene	gene with protein product			"Fer3-like (Drosophila)"			11472856, 12217327	Standard	NM_152898		Approved	NATO3, N-TWIST, bHLHa31	uc003suo.1	Q96RJ6	OTTHUMG00000090823	ENST00000275461.3:c.141A>T	chr7.hg19:g.19184845T>A		44.0	0.0		37.0	18.0	NM_152898	Q495K0	Silent	SNP	ENST00000275461.3	hg19	CCDS5368.1																																																																																			.	.		0.657	FERD3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207627.1			A	19184845	T	A	19184845	2	1	344	1	0	0	0	0	0	0	0	1	5824	1538	54	4		4	FERD3L	7	19184845	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	11017328	19184845	139953818	578	47941										
MACC1	346389	hgsc.bcm.edu	37	chr7	20193914	20193914	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cttttcagctagttccctccAgccttttccaagcttgacag	6	14	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:20193914A>T	ENST00000400331.5	-	6	2556	c.2248T>A	c.(2248-2250)Tgg>Agg	p.W750R	MACC1_ENST00000332878.4_Missense_Mutation_p.W750R|MACC1-AS1_ENST00000439285.1_RNA|MACC1_ENST00000589011.1_Missense_Mutation_p.W750R	NM_182762.3	NP_877439.3	Q6ZN28	MACC1_HUMAN	metastasis associated in colon cancer 1	750					positive regulation of cell division (GO:0051781)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(15)|lung(12)|ovary(2)|prostate(1)|skin(3)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(1)	39						AGTTCCCTCCAGCCTTTTCCA	0.463																																					p.W750R		Atlas-SNP	.											.	MACC1	99	.	0			c.T2248A						.						134	116	122					7																	20193914		2203	4300	6503	SO:0001583	missense	346389	exon6			CCCTCCAGCCTTT		CCDS5369.1	7p15.3	2008-10-14			ENSG00000183742	ENSG00000183742			30215	protein-coding gene	gene with protein product		612646					Standard	NM_182762		Approved	7A5, SH3BP4L	uc003sus.4	Q6ZN28	OTTHUMG00000128415	ENST00000400331.5:c.2248T>A	chr7.hg19:g.20193914A>T	ENSP00000383185:p.Trp750Arg	94.0	0.0		99.0	46.0	NM_182762	A8MUS5|B2RNR9|Q6ZQN8|Q7Z5A5	Missense_Mutation	SNP	ENST00000400331.5	hg19	CCDS5369.1	.	.	.	.	.	.	.	.	.	.	A	27.8	4.865063	0.91511	.	.	ENSG00000183742	ENST00000400331;ENST00000332878	T;T	0.35048	1.33;1.33	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.63105	0.2483	M	0.82056	2.57	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.68808	-0.5311	10	0.87932	D	0	-5.7112	15.5174	0.75837	1.0:0.0:0.0:0.0	.	750	Q6ZN28	MACC1_HUMAN	R	750	ENSP00000383185:W750R;ENSP00000328410:W750R	ENSP00000328410:W750R	W	-	1	0	MACC1	20160439	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.061000	0.61500	0.533000	0.62120	TGG	.	.		0.463	MACC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250202.5	NM_182762		T	20193914	A	T	20193914	3	4	344	1	0	0	0	0	1	0	0	0	9152	188	7	4	318	4	MACC1	7	20193914	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1009069	20193914	138944749	579	47942										
ABCB5	340273	hgsc.bcm.edu	37	chr7	20683101	20683101	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cagtgacattgacaaaatcaGtgatggtattggagataaga	11	4	1	5			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:20683101G>C	ENST00000404938.2	+	7	1176	c.524G>C	c.(523-525)aGt>aCt	p.S175T		NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	175	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (GO:0002485)|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO:0002489)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|cell differentiation (GO:0030154)|compound eye corneal lens development (GO:0048058)|positive regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002591)|regulation of membrane potential (GO:0042391)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|efflux transmembrane transporter activity (GO:0015562)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(1)|pancreas(1)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)	77						GACAAAATCAGTGATGGTATT	0.373																																					p.S175T		Atlas-SNP	.											.	ABCB5	357	.	0			c.G524C						.						227	199	207					7																	20683101		1568	3582	5150	SO:0001583	missense	340273	exon7			AAATCAGTGATGG	U66692	CCDS5371.1, CCDS55090.1, CCDS55091.1, CCDS55092.1	7p14	2012-03-14			ENSG00000004846	ENSG00000004846		"ATP binding cassette transporters / subfamily B"	46	protein-coding gene	gene with protein product	"P-glycoprotein ABCB5", "ATP-binding cassette protein"	611785				8894702, 12960149	Standard	NM_001163942		Approved	EST422562, ABCB5beta, ABCB5alpha	uc010kuh.3	Q2M3G0	OTTHUMG00000094789	ENST00000404938.2:c.524G>C	chr7.hg19:g.20683101G>C	ENSP00000384881:p.Ser175Thr	102.0	0.0		96.0	11.0	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Missense_Mutation	SNP	ENST00000404938.2	hg19	CCDS55090.1	.	.	.	.	.	.	.	.	.	.	G	7.753	0.703740	0.15172	.	.	ENSG00000004846	ENST00000404938	D	0.90261	-2.64	3.85	0.51	0.16983	.	.	.	.	.	T	0.80665	0.4666	N	0.25890	0.77	0.58432	D	0.999995	P	0.35272	0.493	B	0.29440	0.102	T	0.72962	-0.4132	9	0.72032	D	0.01	.	6.9579	0.24582	0.433:0.0:0.567:0.0	.	175	A7BKA4	.	T	175	ENSP00000384881:S175T	ENSP00000384881:S175T	S	+	2	0	ABCB5	20649626	0.299000	0.24426	0.964000	0.40570	0.307000	0.27823	2.037000	0.41174	0.090000	0.17273	0.563000	0.77884	AGT	.	.		0.373	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559		C	20683101	G	C	20683101	3	2	344	1	0	0	0	0	1	0	0	0	44	1029	36	4	546	4	ABCB5	7	20683101	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	489187	20683101	138455562	580	47943										
ABCB5	340273	hgsc.bcm.edu	37	chr7	20778743	20778743	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	accaaatatagacagccgcaGtcaagaagggaaaaagccag	10	9	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:20778743G>T	ENST00000404938.2	+	24	3657	c.3005G>T	c.(3004-3006)aGt>aTt	p.S1002I	ABCB5_ENST00000258738.6_Missense_Mutation_p.S557I	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	1002					antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (GO:0002485)|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO:0002489)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|cell differentiation (GO:0030154)|compound eye corneal lens development (GO:0048058)|positive regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002591)|regulation of membrane potential (GO:0042391)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|efflux transmembrane transporter activity (GO:0015562)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(1)|pancreas(1)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)	77						GACAGCCGCAGTCAAGAAGGG	0.473																																					p.S1002I		Atlas-SNP	.											.	ABCB5	357	.	0			c.G3005T						.						45	40	41					7																	20778743		2203	4299	6502	SO:0001583	missense	340273	exon24			GCCGCAGTCAAGA	U66692	CCDS5371.1, CCDS55090.1, CCDS55091.1, CCDS55092.1	7p14	2012-03-14			ENSG00000004846	ENSG00000004846		"ATP binding cassette transporters / subfamily B"	46	protein-coding gene	gene with protein product	"P-glycoprotein ABCB5", "ATP-binding cassette protein"	611785				8894702, 12960149	Standard	NM_001163942		Approved	EST422562, ABCB5beta, ABCB5alpha	uc010kuh.3	Q2M3G0	OTTHUMG00000094789	ENST00000404938.2:c.3005G>T	chr7.hg19:g.20778743G>T	ENSP00000384881:p.Ser1002Ile	54.0	0.0		70.0	25.0	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Missense_Mutation	SNP	ENST00000404938.2	hg19	CCDS55090.1	.	.	.	.	.	.	.	.	.	.	G	11.28	1.592409	0.28357	.	.	ENSG00000004846	ENST00000404938;ENST00000258738	T;T	0.75821	-0.97;-0.97	4.58	2.62	0.31277	.	0.177869	0.38164	N	0.001793	D	0.83207	0.5204	M	0.82193	2.58	0.31994	N	0.604219	D;D	0.67145	0.996;0.982	D;D	0.66196	0.942;0.924	D	0.84257	0.0481	10	0.87932	D	0	.	7.9165	0.29820	0.0954:0.1648:0.7398:0.0	.	1002;557	A7BKA4;Q2M3G0	.;ABCB5_HUMAN	I	1002;557	ENSP00000384881:S1002I;ENSP00000258738:S557I	ENSP00000258738:S557I	S	+	2	0	ABCB5	20745268	0.993000	0.37304	0.986000	0.45419	0.169000	0.22640	1.790000	0.38734	1.308000	0.44962	0.484000	0.47621	AGT	.	.		0.473	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559		T	20778743	G	T	20778743	3	4	344	1	0	0	0	0	1	0	0	0	44	1029	36	3	3136	3	ABCB5	7	20778743	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	95642	20778743	138359920	581	47944										
DNAH11	8701	hgsc.bcm.edu	37	chr7	21630534	21630534	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tttaataattgtattttaatAgctagtggctgtattgagag	9	2	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:21630534A>T	ENST00000409508.3	+	13	2200		c.e13-1		DNAH11_ENST00000328843.6_Splice_Site	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11						microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						GTATTTTAATAGCTAGTGGCT	0.274									Kartagener syndrome																												.		Atlas-SNP	.											.	DNAH11	584	.	0			c.2170-2A>T						.						22	22	22					7																	21630534		1781	4040	5821	SO:0001630	splice_region_variant	8701	exon13	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	TTTAATAGCTAGT	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.2170-1A>T	chr7.hg19:g.21630534A>T		236.0	0.0		194.0	99.0	NM_001277115	Q9UJ82	Splice_Site	SNP	ENST00000409508.3	hg19		.	.	.	.	.	.	.	.	.	.	A	16.28	3.079675	0.55753	.	.	ENSG00000105877	ENST00000328843	.	.	.	5.9	4.72	0.59763	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.4171	0.49958	0.8487:0.1513:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DNAH11	21597059	1.000000	0.71417	0.768000	0.31515	0.752000	0.42762	7.572000	0.82409	1.017000	0.39495	0.528000	0.53228	.	.	.		0.274	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777	Intron	T	21630534	A	T	21630534	5	4	344	1	0	0	0	0	0	0	1	0	4601	434	15	4	2218	4	DNAH11	7	21630534	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	851791	21630534	137508129	582	47945										
HOXA13	3209	hgsc.bcm.edu	37	chr7	27238961	27238961	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	catatccaggtagccaggcaTgggctgatggtggtggtaag	16	7	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:27238961T>C	ENST00000222753.4	-	1	764	c.736A>G	c.(736-738)Atg>Gtg	p.M246V	HOTTIP_ENST00000472494.1_RNA|HOTTIP_ENST00000605136.1_RNA|HOTTIP_ENST00000421733.1_RNA|HOTTIP_ENST00000521028.2_RNA	NM_000522.4	NP_000513.2	P31271	HXA13_HUMAN	homeobox A13	246					artery morphogenesis (GO:0048844)|branching involved in prostate gland morphogenesis (GO:0060442)|embryonic forelimb morphogenesis (GO:0035115)|endothelial cell fate specification (GO:0060847)|endothelial cell morphogenesis (GO:0001886)|inner ear development (GO:0048839)|male genitalia development (GO:0030539)|positive regulation of mesenchymal cell apoptotic process (GO:2001055)|positive regulation of mitosis (GO:0045840)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of BMP signaling pathway (GO:0030510)|skeletal system development (GO:0001501)|tissue homeostasis (GO:0001894)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)|ventricular septum development (GO:0003281)	intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	6						TAGCCAGGCATGGGCTGATGG	0.672			T	NUP98	AML																																p.M246V		Atlas-SNP	.		Dom	yes		7	7p15-p14.2	3209	homeo box A13		L	.	HOXA13	25	.	0			c.A736G						.						40	44	43					7																	27238961		2203	4300	6503	SO:0001583	missense	3209	exon1			CAGGCATGGGCTG		CCDS5412.1	7p15.2	2011-06-20	2005-12-22		ENSG00000106031	ENSG00000106031		"Homeoboxes / ANTP class : HOXL subclass"	5102	protein-coding gene	gene with protein product		142959	"homeo box A13"	HOX1J, HOX1		1973146, 1358459	Standard	NM_000522		Approved		uc003szb.1	P31271	OTTHUMG00000023438	ENST00000222753.4:c.736A>G	chr7.hg19:g.27238961T>C	ENSP00000222753:p.Met246Val	74.0	0.0		83.0	36.0	NM_000522	A4D188|O43371	Missense_Mutation	SNP	ENST00000222753.4	hg19	CCDS5412.1	.	.	.	.	.	.	.	.	.	.	T	1.387	-0.581761	0.03854	.	.	ENSG00000106031	ENST00000222753	T	0.57107	0.42	4.43	3.54	0.40534	.	0.207707	0.39759	N	0.001277	T	0.21103	0.0508	N	0.03000	-0.44	0.24802	N	0.992695	B	0.17038	0.02	B	0.11329	0.006	T	0.28235	-1.0050	10	0.02654	T	1	.	8.0395	0.30513	0.0:0.8787:0.0:0.1213	.	246	P31271	HXA13_HUMAN	V	246	ENSP00000222753:M246V	ENSP00000222753:M246V	M	-	1	0	HOXA13	27205486	1.000000	0.71417	0.997000	0.53966	0.979000	0.70002	4.482000	0.60257	0.956000	0.37904	-0.474000	0.04947	ATG	.	.		0.672	HOXA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358752.3			C	27238961	T	C	27238961	3	2	344	1	0	0	0	0	1	0	0	0	7300	1464	51	2	438	2	HOXA13	7	27238961	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	5608427	27238961	131899702	583	47946										
TAX1BP1	8887	hgsc.bcm.edu	37	chr7	27833956	27833956	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaataggctaataataataaTgtcttcacaaagaaaacggg	8	5	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:27833956T>C	ENST00000396319.2	+	11	1513	c.1425T>C	c.(1423-1425)aaT>aaC	p.N475N	TAX1BP1_ENST00000543117.1_Silent_p.N475N|TAX1BP1_ENST00000433216.2_Silent_p.N318N|TAX1BP1_ENST00000409980.1_Silent_p.N475N|TAX1BP1_ENST00000265393.6_Silent_p.N475N	NM_006024.6	NP_006015.4	Q86VP1	TAXB1_HUMAN	Tax1 (human T-cell leukemia virus type I) binding protein 1	475					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)	cytosol (GO:0005829)	kinase binding (GO:0019900)			breast(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(8)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31			GBM - Glioblastoma multiforme(3;0.0823)			ATAATAATAATGTCTTCACAA	0.328																																					p.N475N		Atlas-SNP	.											.	TAX1BP1	71	.	0			c.T1425C						.						57	58	58					7																	27833956		2203	4300	6503	SO:0001819	synonymous_variant	8887	exon11			TAATAATGTCTTC	U33821	CCDS5415.1, CCDS43561.1, CCDS56471.1	7p15	2010-08-05			ENSG00000106052	ENSG00000106052			11575	protein-coding gene	gene with protein product		605326				10435631	Standard	NM_006024		Approved	TXBP151, CALCOCO3	uc003szl.3	Q86VP1	OTTHUMG00000023377	ENST00000396319.2:c.1425T>C	chr7.hg19:g.27833956T>C		224.0	0.0		221.0	94.0	NM_006024	B4DKU7|E7ENV2|O60398|O95770|Q13311|Q9BQG5|Q9UI88	Silent	SNP	ENST00000396319.2	hg19	CCDS5415.1																																																																																			.	.		0.328	TAX1BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214142.1	NM_006024		C	27833956	T	C	27833956	2	2	344	1	0	0	0	0	0	0	0	1	15609	1461	51	2		2	TAX1BP1	7	27833956	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	594995	27833956	131304707	584	47947										
CPVL	54504	hgsc.bcm.edu	37	chr7	29103852	29103852	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaagctgatcctcaggttccTggcagaaggggcattggaaa	13	8	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:29103852T>A	ENST00000409850.1	-	15	1610		c.e15-2		CPVL_ENST00000396276.3_Splice_Site|CPVL_ENST00000265394.5_Splice_Site			Q9H3G5	CPVL_HUMAN	carboxypeptidase, vitellogenic-like							extracellular vesicular exosome (GO:0070062)	serine-type carboxypeptidase activity (GO:0004185)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(1)	28						CTCAGGTTCCTGGCAGAAGGG	0.428																																					.		Atlas-SNP	.											.	CPVL	60	.	0			c.964-2A>T						.						64	66	65					7																	29103852		2203	4300	6503	SO:0001630	splice_region_variant	54504	exon12			GGTTCCTGGCAGA	AF106704	CCDS5419.1	7p15.1	2012-02-10			ENSG00000106066	ENSG00000106066			14399	protein-coding gene	gene with protein product	"carboxypeptidase WUG", "vitellogenic carboxypeptidase-like protein", "CP-Mac carboxypeptidase"	609780				11401439	Standard	XM_005249786		Approved		uc003szw.3	Q9H3G5	OTTHUMG00000023669	ENST00000409850.1:c.964-2A>T	chr7.hg19:g.29103852T>A		65.0	0.0		72.0	30.0	NM_019029	A4D1A4|Q6UX20|Q8NBL7|Q96AR7|Q9HB41	Splice_Site	SNP	ENST00000409850.1	hg19	CCDS5419.1	.	.	.	.	.	.	.	.	.	.	T	19.13	3.768777	0.69878	.	.	ENSG00000106066	ENST00000265394;ENST00000396276;ENST00000432534;ENST00000409850;ENST00000542995	.	.	.	5.87	4.73	0.59995	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.1348	0.48368	0.0:0.0731:0.0:0.9269	.	.	.	.	.	-1	.	.	.	-	.	.	CPVL	29070377	1.000000	0.71417	0.996000	0.52242	0.909000	0.53808	7.136000	0.77285	1.160000	0.42584	0.533000	0.62120	.	.	.		0.428	CPVL-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328305.1	NM_019029	Intron	A	29103852	T	A	29103852	5	1	344	1	0	0	0	0	0	0	1	0	3837	1594	55	4	480	4	CPVL	7	29103852	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1269896	29103852	130034811	585	47948										
WIPF3	644150	hgsc.bcm.edu	37	chr7	29915478	29915478	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acctccagcttgcgaagggcAgatccgaaaggccggagtgc	14	12	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:29915478A>C	ENST00000409290.1	+	2	123	c.123A>C	c.(121-123)gcA>gcC	p.A41A	WIPF3_ENST00000409123.1_Silent_p.A41A|WIPF3_ENST00000242140.5_Silent_p.A41A	NM_001080529.2	NP_001073998.2	A6NGB9	WIPF3_HUMAN	WAS/WASL interacting protein family, member 3	41					cell differentiation (GO:0030154)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)				breast(2)|large_intestine(3)|lung(6)|ovary(1)	12						TGCGAAGGGCAGATCCGAAAG	0.522																																					p.A41A		Atlas-SNP	.											.	WIPF3	46	.	0			c.A123C						.						64	72	69					7																	29915478		2110	4242	6352	SO:0001819	synonymous_variant	644150	exon3			AAGGGCAGATCCG	AK094250	CCDS56472.1	7p15.1	2006-10-12			ENSG00000122574	ENSG00000122574			22004	protein-coding gene	gene with protein product		612432					Standard	NM_001080529		Approved	CR16, FLJ36931	uc022aaz.1	A6NGB9	OTTHUMG00000152761	ENST00000409290.1:c.123A>C	chr7.hg19:g.29915478A>C		251.0	0.0		168.0	69.0	NM_001080529	B8ZZV2	Silent	SNP	ENST00000409290.1	hg19	CCDS56472.1																																																																																			.	.		0.522	WIPF3-002	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327705.1			C	29915478	A	C	29915478	2	2	344	1	0	0	0	0	0	0	0	1	17384	175	7	5		5	WIPF3	7	29915478	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	811626	29915478	129223185	586	47949										
C7orf16	10842	hgsc.bcm.edu	37	chr7	31732116	31732116	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aagacagactggacaagctaGaccctcgttgcagccactta	9	12	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:31732116G>T	ENST00000342032.3	+	2	689	c.61G>T	c.(61-63)Gac>Tac	p.D21Y	PPP1R17_ENST00000409146.3_Missense_Mutation_p.D21Y	NM_006658.4	NP_006649.2	O96001	PPR17_HUMAN	protein phosphatase 1, regulatory subunit 17	21					central nervous system development (GO:0007417)|intracellular signal transduction (GO:0035556)|regulation of phosphatase activity (GO:0010921)		protein serine/threonine phosphatase inhibitor activity (GO:0004865)										GGACAAGCTAGACCCTCGTTG	0.483																																					p.D21Y		Atlas-SNP	.											.	.	.	.	0			c.G61T						.						115	99	105					7																	31732116		2203	4300	6503	SO:0001583	missense	10842	exon2			AAGCTAGACCCTC	AF071789	CCDS5436.1, CCDS47570.1	7p15	2012-04-17	2011-10-11	2011-10-11	ENSG00000106341	ENSG00000106341		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	16973	protein-coding gene	gene with protein product	"G-substrate"	604088	"chromosome 7 open reading frame 16"	C7orf16		10051666, 9920894	Standard	NM_006658		Approved	GSBS	uc003tcl.3	O96001	OTTHUMG00000128629	ENST00000342032.3:c.61G>T	chr7.hg19:g.31732116G>T	ENSP00000340125:p.Asp21Tyr	87.0	0.0		90.0	40.0	NM_006658	B4DE58|Q9UDQ0	Missense_Mutation	SNP	ENST00000342032.3	hg19	CCDS5436.1	.	.	.	.	.	.	.	.	.	.	G	14.74	2.626087	0.46840	.	.	ENSG00000106341	ENST00000342032;ENST00000409146	T;T	0.40756	1.02;1.23	6.16	5.28	0.74379	.	0.272272	0.36972	N	0.002308	T	0.61160	0.2325	L	0.60455	1.87	0.43152	D	0.994925	D;D	0.89917	0.999;1.0	D;D	0.76575	0.958;0.988	T	0.65479	-0.6158	10	0.87932	D	0	-6.4603	15.0984	0.72253	0.0681:0.0:0.9319:0.0	.	21;21	B4DE58;O96001	.;PPR17_HUMAN	Y	21	ENSP00000340125:D21Y;ENSP00000386459:D21Y	ENSP00000340125:D21Y	D	+	1	0	C7orf16	31698641	1.000000	0.71417	0.599000	0.28851	0.356000	0.29392	3.904000	0.56325	1.612000	0.50221	0.650000	0.86243	GAC	.	.		0.483	PPP1R17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250498.1	NM_006658		T	31732116	G	T	31732116	3	4	344	1	0	0	0	0	1	0	0	0	2380	942	33	3	63	3	C7orf16	7	31732116	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1816638	31732116	127406547	587	47950										
BMPER	168667	hgsc.bcm.edu	37	chr7	33976943	33976943	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gagagaagtgccccgtgctgTcccgagactgtgccctggcc	14	14	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:33976943T>C	ENST00000297161.2	+	4	636	c.262T>C	c.(262-264)Tcc>Ccc	p.S88P	BMPER_ENST00000426693.1_Missense_Mutation_p.S88P	NM_133468.4	NP_597725.1	Q8N8U9	BMPER_HUMAN	BMP binding endothelial regulator	88	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.				blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|endothelial cell activation (GO:0042118)|inner ear development (GO:0048839)|negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of endothelial cell migration (GO:0010594)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|ureteric bud development (GO:0001657)	extracellular space (GO:0005615)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(24)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						CCCCGTGCTGTCCCGAGACTG	0.488																																					p.S88P		Atlas-SNP	.											.	BMPER	131	.	0			c.T262C						.						124	114	117					7																	33976943		2203	4300	6503	SO:0001583	missense	168667	exon4			GTGCTGTCCCGAG		CCDS5442.1	7p14.3	2009-02-18			ENSG00000164619	ENSG00000164619			24154	protein-coding gene	gene with protein product	"crossveinless-2"	608699				12897139, 14766204	Standard	NM_133468		Approved	Cv2, CRIM3	uc011kap.2	Q8N8U9	OTTHUMG00000128675	ENST00000297161.2:c.262T>C	chr7.hg19:g.33976943T>C	ENSP00000297161:p.Ser88Pro	106.0	0.0		61.0	25.0	NM_133468	A8K1P8|Q8TF36	Missense_Mutation	SNP	ENST00000297161.2	hg19	CCDS5442.1	.	.	.	.	.	.	.	.	.	.	T	10.35	1.324998	0.24080	.	.	ENSG00000164619	ENST00000297161;ENST00000426693	T;T	0.64991	-0.13;-0.13	5.18	2.72	0.32119	von Willebrand factor, type C (2);	0.143668	0.48767	N	0.000172	T	0.47838	0.1467	L	0.38838	1.175	0.52099	D	0.999947	B	0.09022	0.002	B	0.08055	0.003	T	0.31641	-0.9936	10	0.45353	T	0.12	.	7.6924	0.28575	0.0:0.0739:0.1407:0.7854	.	88	Q8N8U9	BMPER_HUMAN	P	88	ENSP00000297161:S88P;ENSP00000393950:S88P	ENSP00000297161:S88P	S	+	1	0	BMPER	33943468	1.000000	0.71417	0.759000	0.31340	0.236000	0.25371	3.007000	0.49536	0.262000	0.21774	0.460000	0.39030	TCC	.	.		0.488	BMPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250570.2	NM_133468		C	33976943	T	C	33976943	3	2	344	1	0	0	0	0	1	0	0	0	1468	1667	58	2	272	2	BMPER	7	33976943	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2244827	33976943	125161720	588	47951										
HERPUD2	64224	hgsc.bcm.edu	37	chr7	35733822	35733822	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tagggtaaacgttagatagaTgcgtttttagtttccccacg	10	7	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:35733822T>A	ENST00000396081.1	-	1	923	c.119A>T	c.(118-120)cAt>cTt	p.H40L	HERPUD2_ENST00000311350.3_Missense_Mutation_p.H40L|RP11-379H18.1_ENST00000605778.1_RNA	NM_022373.4	NP_071768.3	Q9BSE4	HERP2_HUMAN	HERPUD family member 2	40	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				response to unfolded protein (GO:0006986)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)				kidney(3)|large_intestine(5)|lung(6)|ovary(3)|prostate(1)	18						GTTAGATAGATGCGTTTTTAG	0.473																																					p.H40L		Atlas-SNP	.											.	HERPUD2	47	.	0			c.A119T						.						192	190	190					7																	35733822		2203	4300	6503	SO:0001583	missense	64224	exon2			GATAGATGCGTTT	BC020264	CCDS5446.1	7p14.2	2006-03-20	2006-03-20		ENSG00000122557	ENSG00000122557			21915	protein-coding gene	gene with protein product	"homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 2"						Standard	NM_022373		Approved	FLJ22313	uc003tes.4	Q9BSE4	OTTHUMG00000128687	ENST00000396081.1:c.119A>T	chr7.hg19:g.35733822T>A	ENSP00000379390:p.His40Leu	73.0	0.0		59.0	33.0	NM_022373	A4D1Y8|Q9H6F9	Missense_Mutation	SNP	ENST00000396081.1	hg19	CCDS5446.1	.	.	.	.	.	.	.	.	.	.	T	17.74	3.462991	0.63513	.	.	ENSG00000122557	ENST00000396081;ENST00000311350;ENST00000438224;ENST00000413517;ENST00000427455	T;T;T;T;T	0.72394	-0.65;-0.65;1.08;1.08;1.08	3.53	3.53	0.40419	Ubiquitin supergroup (1);Ubiquitin (2);	0.000000	0.85682	D	0.000000	T	0.70544	0.3236	L	0.39147	1.195	0.80722	D	1	D	0.60160	0.987	P	0.55749	0.783	T	0.69157	-0.5219	10	0.34782	T	0.22	-26.2328	12.0143	0.53305	0.0:0.0:0.0:1.0	.	40	Q9BSE4	HERP2_HUMAN	L	40	ENSP00000379390:H40L;ENSP00000310729:H40L;ENSP00000415475:H40L;ENSP00000391015:H40L;ENSP00000412895:H40L	ENSP00000310729:H40L	H	-	2	0	HERPUD2	35700347	1.000000	0.71417	1.000000	0.80357	0.751000	0.42716	6.938000	0.75904	1.829000	0.53265	0.383000	0.25322	CAT	.	.		0.473	HERPUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250584.1	NM_022373		A	35733822	T	A	35733822	3	1	344	1	0	0	0	0	1	0	0	0	7073	1464	51	4	1133	4	HERPUD2	7	35733822	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1756879	35733822	123404841	589	47952										
ANLN	54443	hgsc.bcm.edu	37	chr7	36436005	36436005	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	actttcagaagcaagtaaccAgcagcccctctctggtggtg	10	12	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:36436005A>T	ENST00000265748.2	+	2	370	c.149A>T	c.(148-150)cAg>cTg	p.Q50L	ANLN_ENST00000396068.2_Missense_Mutation_p.Q50L	NM_018685.2	NP_061155.2	Q9NQW6	ANLN_HUMAN	anillin, actin binding protein	50	Interaction with CD2AP.|Nuclear localization.				hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|regulation of exit from mitosis (GO:0007096)|septin ring assembly (GO:0000921)	actin cytoskeleton (GO:0015629)|actomyosin contractile ring (GO:0005826)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	actin binding (GO:0003779)			breast(2)|endometrium(5)|kidney(5)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(2)	45						GCAAGTAACCAGCAGCCCCTC	0.438																																					p.Q50L		Atlas-SNP	.											.	ANLN	101	.	0			c.A149T						.						74	76	75					7																	36436005		2203	4300	6503	SO:0001583	missense	54443	exon2			GTAACCAGCAGCC	AF273437	CCDS5447.1, CCDS64628.1	7p15-p14	2013-01-10	2006-08-22		ENSG00000011426	ENSG00000011426		"Pleckstrin homology (PH) domain containing"	14082	protein-coding gene	gene with protein product			"anillin (Drosophila Scraps homolog), actin binding protein", "anillin, actin binding protein (scraps homolog, Drosophila)"			10931866	Standard	NM_001284301		Approved	ANILLIN, Scraps, scra	uc003tff.3	Q9NQW6	OTTHUMG00000023143	ENST00000265748.2:c.149A>T	chr7.hg19:g.36436005A>T	ENSP00000265748:p.Gln50Leu	187.0	0.0		143.0	69.0	NM_018685	Q5CZ78|Q6NSK5|Q9H8Y4|Q9NVN9|Q9NVP0	Missense_Mutation	SNP	ENST00000265748.2	hg19	CCDS5447.1	.	.	.	.	.	.	.	.	.	.	A	16.23	3.063648	0.55432	.	.	ENSG00000011426	ENST00000265748;ENST00000396068;ENST00000424865;ENST00000418118	T;T;T	0.48836	0.8;0.8;3.92	5.67	1.96	0.26148	.	0.476064	0.24520	N	0.037816	T	0.32734	0.0839	L	0.55834	1.745	0.48236	D	0.999616	B;B;B	0.24882	0.113;0.014;0.113	B;B;B	0.24006	0.05;0.009;0.05	T	0.19976	-1.0289	10	0.02654	T	1	-2.6482	5.8638	0.18762	0.7407:0.0:0.1354:0.1239	.	50;50;50	A8K5D9;Q9NQW6-2;Q9NQW6	.;.;ANLN_HUMAN	L	50;50;28;28	ENSP00000265748:Q50L;ENSP00000379380:Q50L;ENSP00000404979:Q28L	ENSP00000265748:Q50L	Q	+	2	0	ANLN	36402530	1.000000	0.71417	0.994000	0.49952	0.943000	0.58893	2.742000	0.47434	0.095000	0.17434	0.482000	0.46254	CAG	.	.		0.438	ANLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218582.3	NM_018685		T	36436005	A	T	36436005	3	4	344	1	0	0	0	0	1	0	0	0	694	188	7	4	155	4	ANLN	7	36436005	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	702183	36436005	122702658	590	47953										
AMPH	273	hgsc.bcm.edu	37	chr7	38500915	38500915	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgtcacactgatttctggaaCaaagttgtcctcaaagaaac	7	9	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:38500915C>A	ENST00000356264.2	-	11	1200	c.985G>T	c.(985-987)Gtt>Ttt	p.V329F	AMPH_ENST00000325590.5_Missense_Mutation_p.V329F|AMPH_ENST00000428293.2_Missense_Mutation_p.V329F	NM_001635.3	NP_001626.1	P49418	AMPH_HUMAN	amphiphysin	329					endocytosis (GO:0006897)|learning (GO:0007612)|synaptic transmission (GO:0007268)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|leading edge membrane (GO:0031256)|synaptic vesicle (GO:0008021)	phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|kidney(3)|large_intestine(12)|liver(3)|lung(27)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)	62						ATTTCTGGAACAAAGTTGTCC	0.512																																					p.V329F		Atlas-SNP	.											.	AMPH	157	.	0			c.G985T						.						187	183	184					7																	38500915		2203	4300	6503	SO:0001583	missense	273	exon11			CTGGAACAAAGTT		CCDS5456.1, CCDS47574.1	7p14-p13	2007-06-19	2007-06-19		ENSG00000078053	ENSG00000078053			471	protein-coding gene	gene with protein product		600418	"amphiphysin (Stiff-Mann syndrome with breast cancer 128kD autoantigen)", "amphiphysin (Stiff-Man syndrome with breast cancer 128kDa autoantigen)"			8245793	Standard	NM_139316		Approved		uc003tgu.3	P49418	OTTHUMG00000023725	ENST00000356264.2:c.985G>T	chr7.hg19:g.38500915C>A	ENSP00000348602:p.Val329Phe	73.0	0.0		75.0	37.0	NM_139316	A4D1X8|A4D1X9|O43538|Q75MJ8|Q75MK5|Q75MM3|Q8N4G0	Missense_Mutation	SNP	ENST00000356264.2	hg19	CCDS5456.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.2|22.2	4.258517|4.258517	0.80246|0.80246	.|.	.|.	ENSG00000078053|ENSG00000078053	ENST00000441628|ENST00000325590;ENST00000356264;ENST00000428293;ENST00000353242;ENST00000544070	.|T;T;T	.|0.42900	.|0.96;0.96;0.96	5.77|5.77	5.77|5.77	0.91146|0.91146	.|.	.|0.171581	.|0.39687	.|N	.|0.001287	T|T	0.65217|0.65217	0.2670|0.2670	M|M	0.66939|0.66939	2.045|2.045	0.54753|0.54753	D|D	0.999981|0.999981	.|D;D;D	.|0.89917	.|0.999;0.999;1.0	.|D;D;D	.|0.74023	.|0.965;0.965;0.982	T|T	0.64398|0.64398	-0.6417|-0.6417	5|10	.|0.56958	.|D	.|0.05	-21.1308|-21.1308	19.9922|19.9922	0.97370|0.97370	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|329;329;85	.|P49418-2;P49418;Q8NFL4	.|.;AMPH_HUMAN;.	F|F	79|329;329;329;99;332	.|ENSP00000317441:V329F;ENSP00000348602:V329F;ENSP00000390734:V329F	.|ENSP00000317441:V329F	C|V	-|-	2|1	0|0	AMPH|AMPH	38467440|38467440	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	3.506000|3.506000	0.53364|0.53364	2.740000|2.740000	0.93945|0.93945	0.557000|0.557000	0.71058|0.71058	TGT|GTT	.	.		0.512	AMPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226953.2	NM_001635		A	38500915	C	A	38500915	3	1	344	1	0	0	0	0	1	0	0	0	588	478	17	3	1146	3	AMPH	7	38500915	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	2064910	38500915	120637748	591	47954										
ADCY1	107	hgsc.bcm.edu	37	chr7	45632453	45632453	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cagaggaaggcgttcctgcaGgcccggagctgcattgagga	16	10	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:45632453G>T	ENST00000297323.7	+	2	757	c.735G>T	c.(733-735)caG>caT	p.Q245H	ADCY1_ENST00000432715.1_Missense_Mutation_p.Q20H	NM_021116.2	NP_066939.1	Q08828	ADCY1_HUMAN	adenylate cyclase 1 (brain)	245					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|axonogenesis (GO:0007409)|cellular response to glucagon stimulus (GO:0071377)|circadian rhythm (GO:0007623)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of circadian rhythm (GO:0042752)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(33)|ovary(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	71					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	CGTTCCTGCAGGCCCGGAGCT	0.592																																					p.Q245H		Atlas-SNP	.											.	ADCY1	187	.	0			c.G735T						.						142	127	132					7																	45632453		2203	4300	6503	SO:0001583	missense	107	exon2			CCTGCAGGCCCGG	L05500	CCDS34631.1, CCDS75593.1	7p13-p12	2013-02-04			ENSG00000164742	ENSG00000164742	4.6.1.1	"Adenylate cyclases"	232	protein-coding gene	gene with protein product		103072				8314585	Standard	NM_021116		Approved	AC1	uc003tne.4	Q08828	OTTHUMG00000155420	ENST00000297323.7:c.735G>T	chr7.hg19:g.45632453G>T	ENSP00000297323:p.Gln245His	111.0	0.0		124.0	62.0	NM_021116	A4D2L8|Q75MI1	Missense_Mutation	SNP	ENST00000297323.7	hg19	CCDS34631.1	.	.	.	.	.	.	.	.	.	.	G	19.47	3.832750	0.71258	.	.	ENSG00000164742	ENST00000432715;ENST00000297323;ENST00000545300	D;T	0.82167	-1.58;-1.29	5.07	2.25	0.28309	.	0.065196	0.64402	D	0.000006	T	0.81418	0.4818	L	0.34521	1.04	0.49483	D	0.999793	P;D	0.56521	0.915;0.976	B;P	0.56960	0.41;0.81	T	0.79284	-0.1867	10	0.87932	D	0	.	8.6293	0.33908	0.2597:0.0:0.7403:0.0	.	245;20	Q08828;C9J1J0	ADCY1_HUMAN;.	H	20;245;245	ENSP00000392721:Q20H;ENSP00000297323:Q245H	ENSP00000297323:Q245H	Q	+	3	2	ADCY1	45598978	1.000000	0.71417	0.999000	0.59377	0.973000	0.67179	3.148000	0.50647	0.158000	0.19367	0.484000	0.47621	CAG	.	.		0.592	ADCY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340055.2	NM_021116		T	45632453	G	T	45632453	3	4	344	1	0	0	0	0	1	0	0	0	292	991	35	3	741	3	ADCY1	7	45632453	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	7131538	45632453	113506210	592	47955										
ADCY1	107	hgsc.bcm.edu	37	chr7	45717819	45717819	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccgttgtcctcaccctcatcCtggctgccttatttggcctt	7	16	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:45717819C>T	ENST00000297323.7	+	10	1877	c.1855C>T	c.(1855-1857)Ctg>Ttg	p.L619L		NM_021116.2	NP_066939.1	Q08828	ADCY1_HUMAN	adenylate cyclase 1 (brain)	619					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|axonogenesis (GO:0007409)|cellular response to glucagon stimulus (GO:0071377)|circadian rhythm (GO:0007623)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of circadian rhythm (GO:0042752)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(33)|ovary(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	71					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	CACCCTCATCCTGGCTGCCTT	0.507																																					p.L619L		Atlas-SNP	.											.	ADCY1	187	.	0			c.C1855T						.						235	219	224					7																	45717819		2203	4300	6503	SO:0001819	synonymous_variant	107	exon10			CTCATCCTGGCTG	L05500	CCDS34631.1, CCDS75593.1	7p13-p12	2013-02-04			ENSG00000164742	ENSG00000164742	4.6.1.1	"Adenylate cyclases"	232	protein-coding gene	gene with protein product		103072				8314585	Standard	NM_021116		Approved	AC1	uc003tne.4	Q08828	OTTHUMG00000155420	ENST00000297323.7:c.1855C>T	chr7.hg19:g.45717819C>T		105.0	0.0		114.0	48.0	NM_021116	A4D2L8|Q75MI1	Silent	SNP	ENST00000297323.7	hg19	CCDS34631.1																																																																																			.	.		0.507	ADCY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340055.2	NM_021116		T	45717819	C	T	45717819	2	4	344	1	0	0	0	0	0	0	0	1	292	680	24	3		3	ADCY1	7	45717819	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	85366	45717819	113420844	593	47956										
TNS3	64759	hgsc.bcm.edu	37	chr7	47408179	47408179	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atgtccagggtgggcgagccTggggaggggcctgtgctcag	20	9	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:47408179T>A	ENST00000398879.1	-	17	2430	c.2064A>T	c.(2062-2064)ccA>ccT	p.P688P	TNS3_ENST00000355730.3_Silent_p.P448P|TNS3_ENST00000311160.9_Silent_p.P688P			Q68CZ2	TENS3_HUMAN	tensin 3	688					cell migration (GO:0016477)|lung alveolus development (GO:0048286)|positive regulation of cell proliferation (GO:0008284)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(17)|endometrium(5)|kidney(4)|large_intestine(7)|liver(1)|lung(16)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	64						TGGGCGAGCCTGGGGAGGGGC	0.617																																					p.P688P		Atlas-SNP	.											.	TNS3	140	.	0			c.A2064T						.						142	162	156					7																	47408179		2048	4203	6251	SO:0001819	synonymous_variant	64759	exon17			CGAGCCTGGGGAG	AF378756	CCDS5506.2	7p12.3	2013-02-14	2005-05-13	2005-05-13	ENSG00000136205	ENSG00000136205		"SH2 domain containing"	21616	protein-coding gene	gene with protein product	"tumor endothelial marker 6"	606825	"tensin-like SH2 domain-containing 1"	TENS1		11559528	Standard	NM_022748		Approved	TEM6, H_NH0549I23.2, FLJ13732	uc003tnw.3	Q68CZ2	OTTHUMG00000074075	ENST00000398879.1:c.2064A>T	chr7.hg19:g.47408179T>A		57.0	0.0		38.0	13.0	NM_022748	B2RNV1|Q6IPQ2|Q8IZW7|Q8NAD0|Q96PE0|Q96S48	Silent	SNP	ENST00000398879.1	hg19	CCDS5506.2																																																																																			.	.		0.617	TNS3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157253.1	NM_022748		A	47408179	T	A	47408179	2	1	344	1	0	0	0	0	0	0	0	1	16359	1567	55	4		4	TNS3	7	47408179	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1690360	47408179	111730484	594	47957										
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47870899	47870899	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctgcagagctccaccaaggcTgaagggcccttgaccactgg	12	14	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:47870899T>G	ENST00000289672.2	-	42	6439	c.6389A>C	c.(6388-6390)cAg>cCg	p.Q2130P		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	2130					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						CCACCAAGGCTGAAGGGCCCT	0.562																																					p.Q2130P		Atlas-SNP	.											.	PKD1L1	328	.	0			c.A6389C						.						93	83	86					7																	47870899		2203	4300	6503	SO:0001583	missense	168507	exon42			CAAGGCTGAAGGG	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"polycystin-1L1"	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.6389A>C	chr7.hg19:g.47870899T>G	ENSP00000289672:p.Gln2130Pro	125.0	0.0		118.0	50.0	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	hg19	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	T	10.72	1.429461	0.25726	.	.	ENSG00000158683	ENST00000289672	T	0.17370	2.28	5.1	-10.2	0.00374	.	1.969070	0.02438	N	0.084314	T	0.06508	0.0167	N	0.11427	0.14	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.20605	-1.0270	10	0.23891	T	0.37	1.9044	4.1973	0.10450	0.165:0.1127:0.494:0.2283	.	2130	Q8TDX9	PK1L1_HUMAN	P	2130	ENSP00000289672:Q2130P	ENSP00000289672:Q2130P	Q	-	2	0	PKD1L1	47837424	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-1.028000	0.03589	-1.543000	0.01723	-0.445000	0.05633	CAG	.	.		0.562	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		G	47870899	T	G	47870899	3	3	344	1	0	0	0	0	1	0	0	0	11973	1580	55	5	2224	5	PKD1L1	7	47870899	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	462720	47870899	111267764	595	47958										
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47970705	47970705	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acctccttcaccgtaccttcTgggagaagtgggaaaatgtg	11	10	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:47970705T>A	ENST00000289672.2	-	6	783	c.733A>T	c.(733-735)Aga>Tga	p.R245*		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	245					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						CCGTACCTTCTGGGAGAAGTG	0.552																																					p.R245X		Atlas-SNP	.											.	PKD1L1	328	.	0			c.A733T						.						44	40	42					7																	47970705		2203	4300	6503	SO:0001587	stop_gained	168507	exon6			ACCTTCTGGGAGA	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"polycystin-1L1"	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.733A>T	chr7.hg19:g.47970705T>A	ENSP00000289672:p.Arg245*	52.0	0.0		48.0	22.0	NM_138295	Q6UWK1	Nonsense_Mutation	SNP	ENST00000289672.2	hg19	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.251848	0.80135	.	.	ENSG00000158683	ENST00000289672	.	.	.	3.06	1.91	0.25777	.	616.745000	0.00166	N	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06757	T	0.87	2.1978	4.9336	0.13930	0.0:0.1416:0.0:0.8584	.	.	.	.	X	245	.	ENSP00000289672:R245X	R	-	1	2	PKD1L1	47937230	0.000000	0.05858	0.004000	0.12327	0.001000	0.01503	0.112000	0.15479	0.580000	0.29522	-0.333000	0.08304	AGA	.	.		0.552	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		A	47970705	T	A	47970705	4	1	344	1	0	0	0	0	0	1	0	0	11973	1588	55	4	8024	4	PKD1L1	7	47970705	Nonsense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	99806	47970705	111167958	596	47959										
HUS1	3364	hgsc.bcm.edu	37	chr7	48008897	48008897	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tttcaaattcaattctccatCtaggtttgcttcaataacct	3	10	5	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:48008897C>A	ENST00000258774.5	-	6	582	c.559G>T	c.(559-561)Gat>Tat	p.D187Y	HUS1_ENST00000432325.1_Missense_Mutation_p.D166Y	NM_004507.3	NP_004498.1	O60921	HUS1_HUMAN	HUS1 checkpoint homolog (S. pombe)	187					cellular response to DNA damage stimulus (GO:0006974)|cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|embryo development (GO:0009790)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of DNA replication (GO:0008156)|protein phosphorylation (GO:0006468)|regulation of protein phosphorylation (GO:0001932)|response to UV (GO:0009411)	checkpoint clamp complex (GO:0030896)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|liver(1)|lung(3)|ovary(2)|prostate(1)	13		Breast(660;0.00139)				AATTCTCCATCTAGGTTTGCT	0.338								Direct reversal of damage;Other conserved DNA damage response genes			OREG0018063	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D187Y	Ovarian(103;466 1517 21788 34610 43890)	Atlas-SNP	.											.	HUS1	36	.	0			c.G559T						.						85	88	87					7																	48008897		2199	4298	6497	SO:0001583	missense	3364	exon6			CTCCATCTAGGTT	Y16893	CCDS34635.1	7p13-p12	2008-08-08	2001-11-28		ENSG00000136273	ENSG00000136273			5309	protein-coding gene	gene with protein product	"hus1+-like protein"	603760	"HUS1 (S. pombe) checkpoint homolog"			9878245, 9524127	Standard	NM_004507		Approved		uc003tod.2	O60921	OTTHUMG00000155645	ENST00000258774.5:c.559G>T	chr7.hg19:g.48008897C>A	ENSP00000258774:p.Asp187Tyr	42.0	0.0	951	40.0	16.0	NM_004507	B4DFI9	Missense_Mutation	SNP	ENST00000258774.5	hg19	CCDS34635.1	.	.	.	.	.	.	.	.	.	.	C	11.70	1.717435	0.30413	.	.	ENSG00000136273	ENST00000258774;ENST00000432325;ENST00000432627	T;T;T	0.11930	2.73;2.73;2.73	5.19	2.79	0.32731	.	0.456966	0.23991	N	0.042579	T	0.10423	0.0255	L	0.34521	1.04	0.23215	N	0.998104	B	0.24882	0.113	B	0.30716	0.119	T	0.25950	-1.0117	10	0.44086	T	0.13	-15.226	5.4462	0.16537	0.1538:0.0887:0.0:0.7575	.	187	O60921	HUS1_HUMAN	Y	187;166;166	ENSP00000258774:D187Y;ENSP00000416588:D166Y;ENSP00000404855:D166Y	ENSP00000258774:D187Y	D	-	1	0	HUS1	47975422	1.000000	0.71417	0.213000	0.23690	0.925000	0.55904	4.861000	0.62969	0.366000	0.24427	-0.302000	0.09304	GAT	.	.		0.338	HUS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340952.1	NM_004507		A	48008897	C	A	48008897	3	1	344	1	0	0	0	0	1	0	0	0	7468	913	32	3	295	3	HUS1	7	48008897	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	38192	48008897	111129766	597	47960										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48314790	48314790	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	caaagatagacccctgcaatGtccatgggctcatgtcttct	8	12	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:48314790G>T	ENST00000435803.1	+	17	5551	c.5527G>T	c.(5527-5529)Gtc>Ttc	p.V1843F		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1843					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						CCCCTGCAATGTCCATGGGCT	0.423																																					p.V1843F		Atlas-SNP	.											.	ABCA13	1192	.	0			c.G5527T						.						59	58	58					7																	48314790		1878	4112	5990	SO:0001583	missense	154664	exon17			TGCAATGTCCATG	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.5527G>T	chr7.hg19:g.48314790G>T	ENSP00000411096:p.Val1843Phe	84.0	0.0		66.0	27.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	G	8.118	0.780292	0.16120	.	.	ENSG00000179869	ENST00000435803	T	0.14766	2.48	5.79	-2.53	0.06326	.	1.193830	0.06290	N	0.698964	T	0.07999	0.0200	L	0.29908	0.895	0.09310	N	1	P	0.41265	0.744	B	0.39068	0.289	T	0.20739	-1.0266	9	.	.	.	.	0.2869	0.00252	0.2798:0.2014:0.2806:0.2382	.	1843	Q86UQ4	ABCAD_HUMAN	F	1843	ENSP00000411096:V1843F	.	V	+	1	0	ABCA13	48285336	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.169000	0.09911	-0.341000	0.08376	0.650000	0.86243	GTC	.	.		0.423	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		T	48314790	G	T	48314790	3	4	344	1	0	0	0	0	1	0	0	0	31	1377	48	3	5422	3	ABCA13	7	48314790	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	305893	48314790	110823873	598	47961										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48412076	48412076	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctacataaccaattaagtttTgttaatcagacatttctggt	5	7	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:48412076T>C	ENST00000435803.1	+	33	11139	c.11115T>C	c.(11113-11115)ttT>ttC	p.F3705F		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	3705					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						AATTAAGTTTTGTTAATCAGA	0.353																																					p.F3705F		Atlas-SNP	.											.	ABCA13	1192	.	0			c.T11115C						.						79	73	75					7																	48412076		1842	4080	5922	SO:0001819	synonymous_variant	154664	exon33			AAGTTTTGTTAAT	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.11115T>C	chr7.hg19:g.48412076T>C		48.0	0.0		53.0	21.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	hg19	CCDS47584.1																																																																																			.	.		0.353	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		C	48412076	T	C	48412076	2	2	344	1	0	0	0	0	0	0	0	1	31	1809	63	2		2	ABCA13	7	48412076	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	97286	48412076	110726587	599	47962										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48431709	48431709	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaaggcgcctcagtggaccaAgaaggagctgcatcagcaag	13	10	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:48431709A>T	ENST00000435803.1	+	38	11870	c.11846A>T	c.(11845-11847)aAg>aTg	p.K3949M		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	3949	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						CAGTGGACCAAGAAGGAGCTG	0.507																																					p.K3949M		Atlas-SNP	.											.	ABCA13	1192	.	0			c.A11846T						.						93	96	95					7																	48431709		2012	4170	6182	SO:0001583	missense	154664	exon38			GGACCAAGAAGGA	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.11846A>T	chr7.hg19:g.48431709A>T	ENSP00000411096:p.Lys3949Met	127.0	0.0		126.0	53.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	A	13.38	2.218996	0.39201	.	.	ENSG00000179869	ENST00000435803	D	0.93811	-3.29	5.32	-3.82	0.04281	ATPase, AAA+ type, core (1);ABC transporter-like (2);	1.674750	0.04424	U	0.368140	D	0.93148	0.7818	M	0.78916	2.43	0.09310	N	1	P;P	0.51147	0.928;0.942	P;P	0.51193	0.662;0.656	D	0.83954	0.0318	10	0.72032	D	0.01	.	1.1717	0.01826	0.3879:0.2444:0.2412:0.1266	.	1651;3949	Q86UQ4-3;Q86UQ4	.;ABCAD_HUMAN	M	3949	ENSP00000411096:K3949M	ENSP00000411096:K3949M	K	+	2	0	ABCA13	48402255	0.000000	0.05858	0.000000	0.03702	0.086000	0.17979	0.044000	0.13992	-1.012000	0.03387	0.383000	0.25322	AAG	.	.		0.507	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		T	48431709	A	T	48431709	3	4	344	1	0	0	0	0	1	0	0	0	31	72	3	4	11825	4	ABCA13	7	48431709	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	19633	48431709	110706954	600	47963										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48528889	48528889	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcctacttaaatcatctaaaCaaccttattttgtggcagca	4	10	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:48528889C>A	ENST00000435803.1	+	48	13263	c.13239C>A	c.(13237-13239)aaC>aaA	p.N4413K	ABCA13_ENST00000544596.1_Missense_Mutation_p.N143K	NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	4413					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						ATCATCTAAACAACCTTATTT	0.358																																					p.N4413K		Atlas-SNP	.											.	ABCA13	1192	.	0			c.C13239A						.						95	87	90					7																	48528889		1870	4092	5962	SO:0001583	missense	154664	exon48			TCTAAACAACCTT	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.13239C>A	chr7.hg19:g.48528889C>A	ENSP00000411096:p.Asn4413Lys	205.0	0.0		169.0	62.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	C	19.50	3.839513	0.71488	.	.	ENSG00000179869	ENST00000435803;ENST00000411975;ENST00000544596	D;D;D	0.87887	-2.31;-2.31;-2.31	5.43	4.54	0.55810	.	0.114530	0.38663	N	0.001605	D	0.93044	0.7786	M	0.88775	2.98	0.40615	D	0.981716	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.91635	0.991;0.994;0.999	D	0.93256	0.6639	10	0.87932	D	0	.	7.4333	0.27141	0.0:0.8363:0.0:0.1637	.	143;2115;4413	F5H7B7;Q86UQ4-3;Q86UQ4	.;.;ABCAD_HUMAN	K	4413;186;143	ENSP00000411096:N4413K;ENSP00000391042:N186K;ENSP00000442634:N143K	ENSP00000391042:N186K	N	+	3	2	ABCA13	48499435	1.000000	0.71417	0.995000	0.50966	0.995000	0.86356	1.629000	0.37071	2.542000	0.85734	0.650000	0.86243	AAC	.	.		0.358	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		A	48528889	C	A	48528889	3	1	344	1	0	0	0	0	1	0	0	0	31	477	17	3	13258	3	ABCA13	7	48528889	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	97180	48528889	110609774	601	47964										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48559635	48559635	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttttctttttttcactgtgcAgaatttacagaatatctatg	5	6	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:48559635A>T	ENST00000435803.1	+	53	13821		c.e53-1		ABCA13_ENST00000544596.1_Splice_Site	NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13						transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						TTCACTGTGCAGAATTTACAG	0.338																																					.		Atlas-SNP	.											.	ABCA13	1192	.	0			c.13798-2A>T						.						80	70	73					7																	48559635		1810	4065	5875	SO:0001630	splice_region_variant	154664	exon53			CTGTGCAGAATTT	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.13798-1A>T	chr7.hg19:g.48559635A>T		62.0	0.0		39.0	10.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Splice_Site	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	A	16.91	3.252653	0.59212	.	.	ENSG00000179869	ENST00000435803;ENST00000411975;ENST00000544596;ENST00000435451	.	.	.	5.35	5.35	0.76521	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.0755	0.59085	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ABCA13	48530181	1.000000	0.71417	0.976000	0.42696	0.773000	0.43773	6.374000	0.73132	2.029000	0.59856	0.528000	0.53228	.	.	.		0.338	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	Intron	T	48559635	A	T	48559635	5	4	344	1	0	0	0	0	0	0	1	0	31	202	7	4	13835	4	ABCA13	7	48559635	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	30746	48559635	110579028	602	47965										
IKZF1	10320	hgsc.bcm.edu	37	chr7	50450343	50450343	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggagaagcccttcaaatgccAcctctgcaactacgcctgcc	8	16	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:50450343A>T	ENST00000331340.3	+	5	682	c.527A>T	c.(526-528)cAc>cTc	p.H176L	IKZF1_ENST00000343574.5_Missense_Mutation_p.H89L|IKZF1_ENST00000349824.4_Intron|IKZF1_ENST00000440768.2_Missense_Mutation_p.H176L|IKZF1_ENST00000346667.4_Intron|IKZF1_ENST00000359197.5_Missense_Mutation_p.H176L|IKZF1_ENST00000357364.4_Missense_Mutation_p.H176L|IKZF1_ENST00000439701.1_Missense_Mutation_p.H176L|IKZF1_ENST00000438033.1_Missense_Mutation_p.H89L	NM_001220769.1|NM_001220772.1|NM_001220773.1|NM_001220775.1|NM_006060.4	NP_001207698.1|NP_001207701.1|NP_001207702.1|NP_001207704.1|NP_006051.1	Q13422	IKZF1_HUMAN	IKAROS family zinc finger 1 (Ikaros)	176					B cell differentiation (GO:0030183)|cell cycle (GO:0007049)|chromatin modification (GO:0016568)|forebrain development (GO:0030900)|lymph node development (GO:0048535)|mesoderm development (GO:0007498)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Peyer's patch development (GO:0048541)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neutrophil differentiation (GO:0045660)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|T cell differentiation (GO:0030217)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.?(131)		haematopoietic_and_lymphoid_tissue(275)|lung(1)	276	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;7.29e-10)|all_hematologic(4;4.8e-07)				TTCAAATGCCACCTCTGCAAC	0.647			"D,T"	BCL6	"ALL, DLBCL"																																p.H176L		Atlas-SNP	.		"Rec,Dom"	yes		7	7p12.2	10320	IKAROS family zinc finger 1		L	.	IKZF1	613	.	131	Unknown(131)	haematopoietic_and_lymphoid_tissue(131)	c.A527T						.						26	32	30					7																	50450343		2153	4269	6422	SO:0001583	missense	10320	exon5			AATGCCACCTCTG	U40462	CCDS59055.1, CCDS69299.1, CCDS75596.1, CCDS75597.1	7p12.2	2014-06-12	2006-08-25	2006-08-25	ENSG00000185811	ENSG00000185811		"Zinc fingers, C2H2-type", "IKAROS zinc fingers"	13176	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 92"	603023	"zinc finger protein, subfamily 1A, 1 (Ikaros)"	ZNFN1A1		1439790, 7935426	Standard	NM_006060		Approved	hIk-1, LyF-1, Hs.54452, IKAROS, PPP1R92	uc003tow.4	Q13422	OTTHUMG00000155907	ENST00000331340.3:c.527A>T	chr7.hg19:g.50450343A>T	ENSP00000331614:p.His176Leu	17.0	0.0		21.0	14.0	NM_006060	A4D260|B4E0Z1|D3DVM5|O00598|Q53XL2|Q69BM4|Q8WVA3	Missense_Mutation	SNP	ENST00000331340.3	hg19		.	.	.	.	.	.	.	.	.	.	A	20.5	4.001161	0.74818	.	.	ENSG00000185811	ENST00000343574;ENST00000359197;ENST00000440768;ENST00000357364;ENST00000331340;ENST00000438033;ENST00000439701	T;T;T;T;T;T;T	0.17691	2.26;2.26;2.26;2.26;2.26;2.26;2.26	5.97	5.97	0.96955	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.43765	0.1262	.	.	.	0.80722	D	1	D;D;D	0.89917	0.998;1.0;0.982	D;D;D	0.75484	0.977;0.986;0.967	T	0.31752	-0.9932	9	0.54805	T	0.06	-1.4571	16.4504	0.83984	1.0:0.0:0.0:0.0	.	89;176;176	Q13422-2;Q13422-7;Q13422	.;.;IKZF1_HUMAN	L	89;176;176;176;176;89;176	ENSP00000342750:H89L;ENSP00000352123:H176L;ENSP00000401507:H176L;ENSP00000349928:H176L;ENSP00000331614:H176L;ENSP00000396554:H89L;ENSP00000413025:H176L	ENSP00000331614:H176L	H	+	2	0	IKZF1	50417837	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.148000	0.71788	2.288000	0.76882	0.533000	0.62120	CAC	.	.		0.647	IKZF1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000342242.1	NM_006060		T	50450343	A	T	50450343	3	4	344	1	0	0	0	0	1	0	0	0	7623	159	6	4	541	4	IKZF1	7	50450343	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1890708	50450343	108688320	603	47966										
COBL	23242	hgsc.bcm.edu	37	chr7	51095619	51095619	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tctaggagaatgtggctttcTgtgccagaccctcctggagg	13	10	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:51095619T>G	ENST00000265136.7	-	10	3339	c.3174A>C	c.(3172-3174)acA>acC	p.T1058T	COBL_ENST00000395542.2_Silent_p.T1140T	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	1058					actin filament network formation (GO:0051639)|actin filament polymerization (GO:0030041)|collateral sprouting in absence of injury (GO:0048669)|digestive tract development (GO:0048565)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|liver development (GO:0001889)|neural tube closure (GO:0001843)|notochord development (GO:0030903)|positive regulation of dendrite development (GO:1900006)|somite specification (GO:0001757)	actin filament (GO:0005884)|axon (GO:0030424)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic growth cone (GO:0044294)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)			NS(2)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(26)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Glioma(55;0.08)					TGTGGCTTTCTGTGCCAGACC	0.562																																					p.T1058T	NSCLC(189;2119 2138 12223 30818 34679)	Atlas-SNP	.											.	COBL	167	.	0			c.A3174C						.						98	98	98					7																	51095619		2203	4300	6503	SO:0001819	synonymous_variant	23242	exon10			GCTTTCTGTGCCA	AB014533	CCDS34637.1, CCDS75601.1, CCDS75602.1	7p12.2-p12.1	2012-12-07	2012-12-07		ENSG00000106078	ENSG00000106078			22199	protein-coding gene	gene with protein product		610317	"cordon-bleu homolog (mouse)"				Standard	NM_015198		Approved	KIAA0633	uc003tpr.4	O75128	OTTHUMG00000155999	ENST00000265136.7:c.3174A>C	chr7.hg19:g.51095619T>G		174.0	0.0		138.0	66.0	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Silent	SNP	ENST00000265136.7	hg19	CCDS34637.1																																																																																			.	.		0.562	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198		G	51095619	T	G	51095619	2	3	344	1	0	0	0	0	0	0	0	1	3655	1567	55	5		5	COBL	7	51095619	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	645276	51095619	108043044	604	47967										
ZNF736	728927	hgsc.bcm.edu	37	chr7	63808697	63808697	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	caatgtaataaatgtggcagAggttttcagttgtgctcaat	10	5	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:63808697A>G	ENST00000423484.2	+	4	578	c.456A>G	c.(454-456)agA>agG	p.R152R	ZNF736_ENST00000355095.4_Silent_p.R152R			B4DX44	ZN736_HUMAN	zinc finger protein 736	152					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|stomach(1)|urinary_tract(1)	9						AATGTGGCAGAGGTTTTCAGT	0.398																																					p.R152R		Atlas-SNP	.											.	ZNF736	33	.	0			c.A456G						.						151	123	132					7																	63808697		692	1591	2283	SO:0001819	synonymous_variant	728927	exon5			TGGCAGAGGTTTT		CCDS55114.1	7q11.21	2013-01-08			ENSG00000234444	ENSG00000234444		"Zinc fingers, C2H2-type", "-"	32467	protein-coding gene	gene with protein product							Standard	XM_006716104		Approved		uc011kdo.2	B4DX44	OTTHUMG00000156537	ENST00000423484.2:c.456A>G	chr7.hg19:g.63808697A>G		39.0	0.0		37.0	18.0	NM_001170905		Silent	SNP	ENST00000423484.2	hg19	CCDS55114.1																																																																																			.	.		0.398	ZNF736-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000344559.2	NM_001170905		G	63808697	A	G	63808697	2	3	344	1	0	0	0	0	0	0	0	1	18140	301	11	2		2	ZNF736	7	63808697	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	12713078	63808697	95329966	605	47968										
WBSCR17	64409	hgsc.bcm.edu	37	chr7	70885934	70885934	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcatccaggaaaaccggaagCgtgtgatcctcccctccatt	9	14	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:70885934C>T	ENST00000333538.5	+	5	1439	c.805C>T	c.(805-807)Cgt>Tgt	p.R269C	WBSCR17_ENST00000498380.2_3'UTR	NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17	269					protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(5)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(7)|large_intestine(22)|lung(45)|ovary(2)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	100		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				AAACCGGAAGCGTGTGATCCT	0.542																																					p.R269C		Atlas-SNP	.											WBSCR17,right_upper_lobe,carcinoma,0,1	WBSCR17	208	.	0			c.C805T						.						201	187	192					7																	70885934		2203	4300	6503	SO:0001583	missense	64409	exon5			CGGAAGCGTGTGA	AF410457	CCDS5540.1	7q11.23	2014-03-13			ENSG00000185274	ENSG00000185274		"Glycosyltransferase family 2 domain containing"	16347	protein-coding gene	gene with protein product	"polypeptide N-acetylgalactosaminyltransferase-like 3", "polypeptide GalNAc transferase 3"	615137				12073013, 15744064, 22787146	Standard	NM_022479		Approved	GALNTL3, GalNAc-T5L	uc003tvy.4	Q6IS24	OTTHUMG00000129783	ENST00000333538.5:c.805C>T	chr7.hg19:g.70885934C>T	ENSP00000329654:p.Arg269Cys	97.0	0.0		98.0	54.0	NM_022479	Q8NFV9|Q9NTA8	Missense_Mutation	SNP	ENST00000333538.5	hg19	CCDS5540.1	.	.	.	.	.	.	.	.	.	.	C	18.32	3.598994	0.66332	.	.	ENSG00000185274	ENST00000333538	T	0.59083	0.29	5.45	3.4	0.38934	Glycosyl transferase, family 2 (1);	0.000000	0.85682	D	0.000000	T	0.79690	0.4489	M	0.91768	3.24	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.83940	0.0311	10	0.51188	T	0.08	.	14.4083	0.67099	0.319:0.681:0.0:0.0	.	269	Q6IS24	GLTL3_HUMAN	C	269	ENSP00000329654:R269C	ENSP00000329654:R269C	R	+	1	0	WBSCR17	70523870	1.000000	0.71417	0.993000	0.49108	0.997000	0.91878	2.977000	0.49297	1.258000	0.44101	0.650000	0.86243	CGT	.	.		0.542	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252006.1	NM_022479		T	70885934	C	T	70885934	3	4	344	1	0	0	0	0	1	0	0	0	17279	768	27	1	823	1	WBSCR17	7	70885934	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	7077237	70885934	88252729	606	47969										
WBSCR17	64409	hgsc.bcm.edu	37	chr7	71036347	71036347	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tggtcttctggatcctggcaTggatgtatacggaggagaaa	14	6	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:71036347T>G	ENST00000333538.5	+	6	1674	c.1040T>G	c.(1039-1041)aTg>aGg	p.M347R	WBSCR17_ENST00000498380.2_3'UTR	NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17	347	Catalytic subdomain B.				protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(5)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(7)|large_intestine(22)|lung(45)|ovary(2)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	100		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				GATCCTGGCATGGATGTATAC	0.507																																					p.M347R		Atlas-SNP	.											.	WBSCR17	208	.	0			c.T1040G						.						208	198	201					7																	71036347		2203	4300	6503	SO:0001583	missense	64409	exon6			CTGGCATGGATGT	AF410457	CCDS5540.1	7q11.23	2014-03-13			ENSG00000185274	ENSG00000185274		"Glycosyltransferase family 2 domain containing"	16347	protein-coding gene	gene with protein product	"polypeptide N-acetylgalactosaminyltransferase-like 3", "polypeptide GalNAc transferase 3"	615137				12073013, 15744064, 22787146	Standard	NM_022479		Approved	GALNTL3, GalNAc-T5L	uc003tvy.4	Q6IS24	OTTHUMG00000129783	ENST00000333538.5:c.1040T>G	chr7.hg19:g.71036347T>G	ENSP00000329654:p.Met347Arg	99.0	0.0		81.0	41.0	NM_022479	Q8NFV9|Q9NTA8	Missense_Mutation	SNP	ENST00000333538.5	hg19	CCDS5540.1	.	.	.	.	.	.	.	.	.	.	T	19.33	3.806366	0.70682	.	.	ENSG00000185274	ENST00000333538	T	0.60171	0.21	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	T	0.74344	0.3704	H	0.98199	4.17	0.80722	D	1	P	0.36027	0.533	B	0.39379	0.298	T	0.81822	-0.0756	10	0.87932	D	0	.	12.2752	0.54730	0.0:0.0:0.0:1.0	.	347	Q6IS24	GLTL3_HUMAN	R	347	ENSP00000329654:M347R	ENSP00000329654:M347R	M	+	2	0	WBSCR17	70674283	1.000000	0.71417	0.998000	0.56505	0.949000	0.60115	6.868000	0.75516	2.124000	0.65301	0.519000	0.50382	ATG	.	.		0.507	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252006.1	NM_022479		G	71036347	T	G	71036347	3	3	344	1	0	0	0	0	1	0	0	0	17279	1464	51	5	1062	5	WBSCR17	7	71036347	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	150413	71036347	88102316	607	47970										
WBSCR27	155368	hgsc.bcm.edu	37	chr7	73254767	73254767	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccgggctgggcagaggctccTggcccagggtgcagaggctg	19	12	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:73254767T>A	ENST00000297873.4	-	4	414	c.365A>T	c.(364-366)cAg>cTg	p.Q122L		NM_152559.2	NP_689772.2	Q8N6F8	WBS27_HUMAN	Williams Beuren syndrome chromosome region 27	122										NS(1)|central_nervous_system(1)|lung(2)|prostate(1)	5		Lung NSC(55;0.159)				CAGAGGCTCCTGGCCCAGGGT	0.662																																					p.Q122L		Atlas-SNP	.											.	WBSCR27	21	.	0			c.A365T						.						10	9	9					7																	73254767		2130	4186	6316	SO:0001583	missense	155368	exon4			GGCTCCTGGCCCA	AF534110	CCDS5561.1	7q11.23	2004-07-05			ENSG00000165171	ENSG00000165171			19068	protein-coding gene	gene with protein product		612546					Standard	NM_152559		Approved		uc003tzj.2	Q8N6F8	OTTHUMG00000130033	ENST00000297873.4:c.365A>T	chr7.hg19:g.73254767T>A	ENSP00000297873:p.Gln122Leu	111.0	0.0		83.0	37.0	NM_152559		Missense_Mutation	SNP	ENST00000297873.4	hg19	CCDS5561.1	.	.	.	.	.	.	.	.	.	.	T	18.86	3.712654	0.68730	.	.	ENSG00000165171	ENST00000297873	T	0.32753	1.44	4.69	3.44	0.39384	.	0.124764	0.53938	D	0.000053	T	0.27384	0.0672	N	0.15975	0.35	0.42111	D	0.99138	D	0.58620	0.983	P	0.57324	0.818	T	0.02512	-1.1148	10	0.30078	T	0.28	-23.927	8.6762	0.34181	0.0:0.0:0.1911:0.8089	.	122	Q8N6F8	WBS27_HUMAN	L	122	ENSP00000297873:Q122L	ENSP00000297873:Q122L	Q	-	2	0	WBSCR27	72892703	0.974000	0.33945	1.000000	0.80357	0.950000	0.60333	0.027000	0.13621	1.846000	0.53633	0.379000	0.24179	CAG	.	.		0.662	WBSCR27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252312.1	NM_152559		A	73254767	T	A	73254767	3	1	344	1	0	0	0	0	1	0	0	0	17281	1580	55	4	384	4	WBSCR27	7	73254767	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2218420	73254767	85883896	608	47971										
HIP1	3092	hgsc.bcm.edu	37	chr7	75192502	75192502	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcatgcttacctcaggcagcTgggggatctgaatgagccgc	14	11	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:75192502T>A	ENST00000336926.6	-	10	895	c.869A>T	c.(868-870)cAg>cTg	p.Q290L	HIP1_ENST00000434438.2_Missense_Mutation_p.Q290L	NM_005338.5	NP_005329.3	O00291	HIP1_HUMAN	huntingtin interacting protein 1	290					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell differentiation (GO:0030154)|clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|positive regulation of receptor-mediated endocytosis (GO:0048260)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|phosphatidylinositol binding (GO:0035091)|structural constituent of cytoskeleton (GO:0005200)			breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						CTCAGGCAGCTGGGGGATCTG	0.592			T	PDGFRB	CMML																																p.Q290L		Atlas-SNP	.		Dom	yes		7	7q11.23	3092	huntingtin interacting protein 1		L	.	HIP1	91	.	0			c.A869T						.						81	76	77					7																	75192502		2203	4300	6503	SO:0001583	missense	3092	exon10			GGCAGCTGGGGGA	AF052288	CCDS34669.1, CCDS59060.1	7q11.23	2008-07-18			ENSG00000127946	ENSG00000127946			4913	protein-coding gene	gene with protein product		601767				9140394, 9147654	Standard	NM_005338		Approved	ILWEQ	uc003uds.2	O00291	OTTHUMG00000156050	ENST00000336926.6:c.869A>T	chr7.hg19:g.75192502T>A	ENSP00000336747:p.Gln290Leu	74.0	0.0		72.0	31.0	NM_005338	B4E3I7|E7ES17|O00328|Q2TB58|Q8TDL4	Missense_Mutation	SNP	ENST00000336926.6	hg19	CCDS34669.1	.	.	.	.	.	.	.	.	.	.	T	15.45	2.838166	0.50951	.	.	ENSG00000127946	ENST00000336926;ENST00000434438	T;T	0.30448	1.53;1.53	5.2	5.2	0.72013	ANTH (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.24547	0.0595	N	0.17723	0.515	0.58432	D	0.999999	B;B	0.23249	0.082;0.009	B;B	0.32090	0.14;0.034	T	0.06698	-1.0812	10	0.34782	T	0.22	-30.3427	14.2615	0.66088	0.0:0.0:0.0:1.0	.	290;290	E7ES17;O00291	.;HIP1_HUMAN	L	290	ENSP00000336747:Q290L;ENSP00000410300:Q290L	ENSP00000336747:Q290L	Q	-	2	0	HIP1	75030438	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.626000	0.83164	1.958000	0.56883	0.528000	0.53228	CAG	.	.		0.592	HIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342863.2	NM_005338		A	75192502	T	A	75192502	3	1	344	1	0	0	0	0	1	0	0	0	7123	1580	55	4	2332	4	HIP1	7	75192502	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1937735	75192502	83946161	609	47972										
PHTF2	57157	hgsc.bcm.edu	37	chr7	77567113	77567113	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggtaatgattgtaagaaagcAgacatgtctgtacttgaaat	10	4	1	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:77567113A>T	ENST00000248550.7	+	12	1501	c.1425A>T	c.(1423-1425)gcA>gcT	p.A475A	PHTF2_ENST00000416283.2_Silent_p.A441A|PHTF2_ENST00000275575.7_Silent_p.A437A|PHTF2_ENST00000422959.2_Silent_p.A441A|PHTF2_ENST00000424760.1_Silent_p.A437A|PHTF2_ENST00000307305.8_Silent_p.A437A|PHTF2_ENST00000454592.1_3'UTR			Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2	475					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	19						GTAAGAAAGCAGACATGTCTG	0.318																																					p.A441A		Atlas-SNP	.											.	PHTF2	104	.	0			c.A1323T						.						60	57	58					7																	77567113		1812	4074	5886	SO:0001819	synonymous_variant	57157	exon11			GAAAGCAGACATG	AL136883	CCDS47621.1, CCDS47622.1, CCDS47623.1, CCDS47624.1	7q11.23-q21	2008-02-01			ENSG00000006576	ENSG00000006576			13411	protein-coding gene	gene with protein product						10729229	Standard	NM_020432		Approved	DKFZp434D166	uc003ugq.4	Q8N3S3	OTTHUMG00000155557	ENST00000248550.7:c.1425A>T	chr7.hg19:g.77567113A>T		289.0	0.0		276.0	119.0	NM_001127357	A0JP04|A0JP05|A4D1C2|E9PEE3|G5E9H7|Q6NW35|Q8TBW4|Q9H099	Silent	SNP	ENST00000248550.7	hg19																																																																																				.	.		0.318	PHTF2-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000340638.2	NM_020432		T	77567113	A	T	77567113	2	4	344	1	0	0	0	0	0	0	0	1	11872	175	7	4		4	PHTF2	7	77567113	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2374611	77567113	81571550	610	47973										
SEMA3C	10512	hgsc.bcm.edu	37	chr7	80457899	80457899	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctcgtgaaagtgataaacttAcactcaaagcttcttgactt	6	9	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:80457899A>G	ENST00000265361.3	-	3	826		c.e3+1		SEMA3C_ENST00000536800.1_Intron|SEMA3C_ENST00000419255.2_Splice_Site|SEMA3C_ENST00000544525.1_Splice_Site	NM_006379.3	NP_006370.1	Q99985	SEM3C_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C						axon guidance (GO:0007411)|blood vessel remodeling (GO:0001974)|cardiac right ventricle morphogenesis (GO:0003215)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|immune response (GO:0006955)|limb bud formation (GO:0060174)|neural crest cell migration (GO:0001755)|neural tube development (GO:0021915)|outflow tract morphogenesis (GO:0003151)|post-embryonic development (GO:0009791)|pulmonary myocardium development (GO:0003350)|response to drug (GO:0042493)|somitogenesis (GO:0001756)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						TGATAAACTTACACTCAAAGC	0.289																																					.		Atlas-SNP	.											.	SEMA3C	106	.	0			c.264+2T>C						.						108	108	108					7																	80457899		2203	4300	6503	SO:0001630	splice_region_variant	10512	exon4			AAACTTACACTCA	AB000220	CCDS5596.1	7q21-q31	2013-01-11			ENSG00000075223	ENSG00000075223		"Semaphorins", "Immunoglobulin superfamily / I-set domain containing"	10725	protein-coding gene	gene with protein product		602645		SEMAE		7748561, 9168980	Standard	NM_006379		Approved	SemE	uc003uhj.3	Q99985	OTTHUMG00000023447	ENST00000265361.3:c.264+1T>C	chr7.hg19:g.80457899A>G		130.0	0.0		127.0	49.0	NM_006379	B4DRL8	Splice_Site	SNP	ENST00000265361.3	hg19	CCDS5596.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.228735	0.79576	.	.	ENSG00000075223	ENST00000265361;ENST00000419255;ENST00000544525	.	.	.	5.61	5.61	0.85477	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.8155	0.78597	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SEMA3C	80295835	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	8.471000	0.90403	2.132000	0.65825	0.528000	0.53228	.	.	.		0.289	SEMA3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253279.1	NM_006379	Intron	G	80457899	A	G	80457899	5	3	344	1	0	0	0	0	0	0	1	0	14041	405	14	2	2053	2	SEMA3C	7	80457899	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2890786	80457899	78680764	611	47974										
PCLO	27445	hgsc.bcm.edu	37	chr7	82764680	82764680	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgggaggggctggcttggacAaagaatctgcctcagggggc	18	8	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:82764680A>T	ENST00000333891.9	-	3	2523	c.2186T>A	c.(2185-2187)tTg>tAg	p.L729*	PCLO_ENST00000423517.2_Nonsense_Mutation_p.L729*	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.L729S(2)|p.L675S(1)		breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TGGCTTGGACAAAGAATCTGC	0.537																																					p.L729X		Atlas-SNP	.											Q9Y6V0-3,NS,carcinoma,0,3	PCLO	1506	.	3	Substitution - Missense(3)	lung(3)	c.T2186A						.						114	110	111					7																	82764680		1921	4121	6042	SO:0001587	stop_gained	27445	exon3			TTGGACAAAGAAT	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.2186T>A	chr7.hg19:g.82764680A>T	ENSP00000334319:p.Leu729*	103.0	0.0		90.0	36.0	NM_014510		Nonsense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	G	38	7.233882	0.98154	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	.	.	.	5.83	-1.87	0.07737	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	8.5503	0.33447	0.4343:0.098:0.4677:0.0	.	.	.	.	X	675;729;729	.	ENSP00000334319:L729X	L	-	2	0	PCLO	82602616	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.304000	0.08199	-0.231000	0.09825	-0.898000	0.02899	TTG	.	.		0.537	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		T	82764680	A	T	82764680	4	4	344	1	0	0	0	0	0	1	0	0	11592	131	5	4	13351	4	PCLO	7	82764680	Nonsense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2306781	82764680	76373983	612	47975										
PCLO	27445	hgsc.bcm.edu	37	chr7	82764790	82764790	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcaggtgccttggagagatcCtgttttggtgcagcatcctt	12	9	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:82764790C>A	ENST00000333891.9	-	3	2413	c.2076G>T	c.(2074-2076)caG>caT	p.Q692H	PCLO_ENST00000423517.2_Missense_Mutation_p.Q692H	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TGGAGAGATCCTGTTTTGGTG	0.532																																					p.Q692H		Atlas-SNP	.											.	PCLO	1506	.	0			c.G2076T						.						183	188	186					7																	82764790		2077	4213	6290	SO:0001583	missense	27445	exon3			GAGATCCTGTTTT	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.2076G>T	chr7.hg19:g.82764790C>A	ENSP00000334319:p.Gln692His	114.0	0.0		95.0	45.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	C	1.942	-0.443290	0.04604	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.17370	2.29;2.28	5.7	0.199	0.15175	.	.	.	.	.	T	0.13200	0.0320	L	0.29908	0.895	0.80722	D	1	P;P	0.41569	0.755;0.755	B;P	0.44946	0.346;0.465	T	0.14090	-1.0485	9	0.87932	D	0	.	4.2422	0.10654	0.2408:0.3196:0.0:0.4395	.	692;692	Q9Y6V0-5;Q9Y6V0-6	.;.	H	638;692;692	ENSP00000334319:Q692H;ENSP00000388393:Q692H	ENSP00000334319:Q692H	Q	-	3	2	PCLO	82602726	0.976000	0.34144	0.975000	0.42487	0.091000	0.18340	0.323000	0.19593	0.344000	0.23847	0.591000	0.81541	CAG	.	.		0.532	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82764790	C	A	82764790	3	1	344	1	0	0	0	0	1	0	0	0	11592	680	24	3	13461	3	PCLO	7	82764790	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	110	82764790	76373873	613	47976										
KIAA1324L	222223	hgsc.bcm.edu	37	chr7	86571334	86571334	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggaaatacaaagagacttacAgaatgagagccccattctcc	8	10	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:86571334A>G	ENST00000450689.2	-	5	926	c.741T>C	c.(739-741)tcT>tcC	p.S247S	KIAA1324L_ENST00000444627.1_Splice_Site_p.S247S|KIAA1324L_ENST00000416314.1_Splice_Site_p.S80S|KIAA1324L_ENST00000297222.6_5'Flank	NM_001142749.2	NP_001136221.1	A8MWY0	K132L_HUMAN	KIAA1324-like	247						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(14)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44	Esophageal squamous(14;0.0058)					AGAGACTTACAGAATGAGAGC	0.403																																					p.S247S		Atlas-SNP	.											.	KIAA1324L	225	.	0			c.T741C						.						180	160	166					7																	86571334		692	1591	2283	SO:0001630	splice_region_variant	222223	exon5			ACTTACAGAATGA	AK055902	CCDS34677.1, CCDS47632.1, CCDS34677.2	7q21.12	2008-09-18			ENSG00000164659	ENSG00000164659			21945	protein-coding gene	gene with protein product	"EIG121-like"	614048					Standard	NM_001142749		Approved	FLJ31340, EIG121L	uc011kha.2	A8MWY0	OTTHUMG00000153995	ENST00000450689.2:c.741+1T>C	chr7.hg19:g.86571334A>G		106.0	0.0		85.0	34.0	NM_001142749	A4D1C9|B4DJV3|Q17RI6|Q96DP2	Silent	SNP	ENST00000450689.2	hg19	CCDS47632.1	.	.	.	.	.	.	.	.	.	.	A	12.82	2.051916	0.36181	.	.	ENSG00000164659	ENST00000423294	.	.	.	5.94	-1.25	0.09405	.	.	.	.	.	T	0.50429	0.1615	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40813	-0.9543	4	.	.	.	.	5.8694	0.18795	0.4059:0.3705:0.2236:0.0	.	.	.	.	R	208	.	.	C	-	1	0	KIAA1324L	86409270	0.976000	0.34144	0.998000	0.56505	0.974000	0.67602	0.236000	0.17967	-0.109000	0.12044	-0.263000	0.10527	TGT	.	.		0.403	KIAA1324L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333372.3	NM_152748	Silent	G	86571334	A	G	86571334	5	3	344	1	0	0	0	0	0	0	1	0	8233	202	7	2	2420	2	KIAA1324L	7	86571334	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3806544	86571334	72567329	614	47977										
C7orf63	79846	hgsc.bcm.edu	37	chr7	89917620	89917620	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	accccaggaagttacagagtGgcttaggctataatgtactt	10	8	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:89917620G>T	ENST00000389297.4	+	15	1980	c.1729G>T	c.(1729-1731)Ggc>Tgc	p.G577C	C7orf63_ENST00000497910.1_Missense_Mutation_p.G559C|C7orf63_ENST00000316089.8_Missense_Mutation_p.G577C	NM_001039706.2|NM_001160138.1	NP_001034795.2|NP_001153610.1	A5D8W1	CG063_HUMAN		577										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|prostate(3)	37						GTTACAGAGTGGCTTAGGCTA	0.348																																					p.G577C		Atlas-SNP	.											.	C7orf63	158	.	0			c.G1729T						.						134	126	129					7																	89917620		1852	4101	5953	SO:0001583	missense	79846	exon15			CAGAGTGGCTTAG																												ENST00000389297.4:c.1729G>T	chr7.hg19:g.89917620G>T	ENSP00000373948:p.Gly577Cys	116.0	0.0		94.0	34.0	NM_001039706	A3KMP9|B4DYW6|B4DZP7|B9EIM7|Q6V705|Q8IY89|Q9H7C2	Missense_Mutation	SNP	ENST00000389297.4	hg19	CCDS43613.2	.	.	.	.	.	.	.	.	.	.	G	20.7	4.035264	0.75617	.	.	ENSG00000105792	ENST00000389297;ENST00000316089;ENST00000497910;ENST00000457170;ENST00000449577	T;T;T;T;T	0.26957	2.35;2.35;2.35;1.7;1.78	5.62	5.62	0.85841	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.54791	0.1880	M	0.78801	2.425	0.52501	D	0.99995	D;D;D	0.76494	0.996;0.999;0.997	D;D;D	0.70016	0.967;0.958;0.91	T	0.57388	-0.7820	10	0.72032	D	0.01	-8.5498	19.6473	0.95784	0.0:0.0:1.0:0.0	.	559;577;577	A5D8W1-5;A5D8W1;A5D8W1-2	.;CG063_HUMAN;.	C	577;577;559;460;160	ENSP00000373948:G577C;ENSP00000321753:G577C;ENSP00000419549:G559C;ENSP00000392365:G460C;ENSP00000391571:G160C	ENSP00000321753:G577C	G	+	1	0	C7orf63	89755556	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	7.515000	0.81761	2.650000	0.89964	0.591000	0.81541	GGC	.	.		0.348	C7orf63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139891.4			T	89917620	G	T	89917620	3	4	344	1	0	0	0	0	1	0	0	0	2411	1348	47	3	1787	3	C7orf63	7	89917620	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	3346286	89917620	69221043	615	47978										
C7orf63	79846	hgsc.bcm.edu	37	chr7	89936396	89936396	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccaagacatgcaaaatgaacAaaaagtatatgcaaaagtaa	6	6	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:89936396A>G	ENST00000389297.4	+	20	2698	c.2447A>G	c.(2446-2448)cAa>cGa	p.Q816R	C7orf63_ENST00000497910.1_Missense_Mutation_p.Q798R|C7orf63_ENST00000316089.8_Missense_Mutation_p.Q770R	NM_001039706.2|NM_001160138.1	NP_001034795.2|NP_001153610.1	A5D8W1	CG063_HUMAN		816										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|prostate(3)	37						CAAAATGAACAAAAAGTATAT	0.358																																					p.Q816R		Atlas-SNP	.											.	C7orf63	158	.	0			c.A2447G						.						53	50	51					7																	89936396		1860	4098	5958	SO:0001583	missense	79846	exon20			ATGAACAAAAAGT																												ENST00000389297.4:c.2447A>G	chr7.hg19:g.89936396A>G	ENSP00000373948:p.Gln816Arg	133.0	0.0		135.0	54.0	NM_001039706	A3KMP9|B4DYW6|B4DZP7|B9EIM7|Q6V705|Q8IY89|Q9H7C2	Missense_Mutation	SNP	ENST00000389297.4	hg19	CCDS43613.2	.	.	.	.	.	.	.	.	.	.	A	14.76	2.630418	0.46944	.	.	ENSG00000105792	ENST00000389297;ENST00000316089;ENST00000497910;ENST00000449577	T;T;T;T	0.23552	2.51;2.48;2.51;1.9	5.54	1.69	0.24217	.	0.451501	0.23300	N	0.049695	T	0.18800	0.0451	L	0.53729	1.69	0.28038	N	0.933883	B;B	0.11235	0.004;0.001	B;B	0.14023	0.01;0.003	T	0.18713	-1.0328	10	0.21014	T	0.42	-6.4052	4.2621	0.10745	0.6774:0.1297:0.0687:0.1242	.	798;816	A5D8W1-5;A5D8W1	.;CG063_HUMAN	R	816;770;798;353	ENSP00000373948:Q816R;ENSP00000321753:Q770R;ENSP00000419549:Q798R;ENSP00000391571:Q353R	ENSP00000321753:Q770R	Q	+	2	0	C7orf63	89774332	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.050000	0.49877	0.326000	0.23384	0.482000	0.46254	CAA	.	.		0.358	C7orf63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139891.4			G	89936396	A	G	89936396	3	3	344	1	0	0	0	0	1	0	0	0	2411	130	5	2	2525	2	C7orf63	7	89936396	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	18776	89936396	69202267	616	47979										
AKAP9	10142	hgsc.bcm.edu	37	chr7	91724335	91724335	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttcatttgtctttctgacttAggttggaagttaaagataag	9	4	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:91724335A>T	ENST00000359028.2	+	40	9815		c.e40-1		AKAP9_ENST00000358100.2_Splice_Site|AKAP9_ENST00000356239.3_Splice_Site			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9						G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TTTCTGACTTAGGTTGGAAGT	0.348			T	BRAF	papillary thyroid																																.		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.9579-2A>T						.						57	58	57					7																	91724335		2203	4300	6503	SO:0001630	splice_region_variant	10142	exon40			TGACTTAGGTTGG	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	379	protein-coding gene	gene with protein product	"A-kinase anchoring protein 450", "AKAP9-BRAF fusion protein", "AKAP120-like protein", "centrosome- and golgi-localized protein kinase N-associated protein", "protein kinase A anchoring protein 9", "A-kinase anchor protein, 350kDa", "protein phosphatase 1, regulatory subunit 45", "yotiao"	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.9591-1A>T	chr7.hg19:g.91724335A>T		85.0	0.0		60.0	29.0	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Splice_Site	SNP	ENST00000359028.2	hg19		.	.	.	.	.	.	.	.	.	.	A	16.14	3.039940	0.55003	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394534	.	.	.	5.56	5.56	0.83823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.6715	0.77279	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	AKAP9	91562271	1.000000	0.71417	0.998000	0.56505	0.700000	0.40528	7.144000	0.77357	2.243000	0.73865	0.472000	0.43445	.	.	.		0.348	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	Intron	T	91724335	A	T	91724335	5	4	344	1	0	0	0	0	0	0	1	0	459	434	15	4	9735	4	AKAP9	7	91724335	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1787939	91724335	67414328	617	47980										
C7orf64	84060	hgsc.bcm.edu	37	chr7	92158171	92158171	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agggagtttatttgatcaccAcgtccagagggcggtatgcg	14	8	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:92158171A>T	ENST00000265732.5	+	1	85	c.44A>T	c.(43-45)cAc>cTc	p.H15L	PEX1_ENST00000248633.4_5'Flank|RBM48_ENST00000481551.1_Missense_Mutation_p.H15L|PEX1_ENST00000428214.1_5'Flank|PEX1_ENST00000438045.1_5'Flank	NM_032120.2	NP_115496.2	Q5RL73	RBM48_HUMAN	RNA binding motif protein 48	15						nucleus (GO:0005634)	RNA binding (GO:0003723)										TTTGATCACCACGTCCAGAGG	0.557																																					p.H15L		Atlas-SNP	.											.	.	.	.	0			c.A44T						.						82	85	84					7																	92158171		1995	4145	6140	SO:0001583	missense	84060	exon1			ATCACCACGTCCA	AL136619	CCDS43615.1	7q21.2	2013-02-12	2011-12-09	2011-12-09	ENSG00000127993	ENSG00000127993		"RNA binding motif (RRM) containing"	21785	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 64"	C7orf64			Standard	NM_032120		Approved	DKFZp564O0523, HSPC304	uc003ulz.3	Q5RL73	OTTHUMG00000159535	ENST00000265732.5:c.44A>T	chr7.hg19:g.92158171A>T	ENSP00000265732:p.His15Leu	131.0	0.0		108.0	50.0	NM_032120	B7Z2K5|B7ZL51|Q5H9T2|Q8IYW7|Q96NS0|Q9H0V7	Missense_Mutation	SNP	ENST00000265732.5	hg19	CCDS43615.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.543717	0.86022	.	.	ENSG00000127993	ENST00000509224;ENST00000265732;ENST00000481551;ENST00000450580	.	.	.	4.77	4.77	0.60923	.	0.000000	0.85682	D	0.000000	T	0.80204	0.4580	M	0.84082	2.675	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.997;0.997	D	0.83768	0.0218	9	0.87932	D	0	-13.9785	14.7391	0.69440	1.0:0.0:0.0:0.0	.	15;15;15	B4DGJ6;B7Z2K5;Q5RL73	.;.;CG064_HUMAN	L	17;15;15;15	.	ENSP00000265732:H15L	H	+	2	0	C7orf64	91996107	1.000000	0.71417	1.000000	0.80357	0.581000	0.36288	7.278000	0.78587	2.127000	0.65507	0.459000	0.35465	CAC	.	.		0.557	RBM48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356076.1	NM_032120		T	92158171	A	T	92158171	3	4	344	1	0	0	0	0	1	0	0	0	2412	159	6	4	46	4	C7orf64	7	92158171	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	433836	92158171	66980492	618	47981										
SAMD9L	219285	hgsc.bcm.edu	37	chr7	92763730	92763730	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gacttctgaagctctttctcTctgccataaatgtggttcta	7	10	5	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:92763730T>C	ENST00000318238.4	-	5	2771	c.1555A>G	c.(1555-1557)Aga>Gga	p.R519G	SAMD9L_ENST00000411955.1_Missense_Mutation_p.R519G|SAMD9L_ENST00000437805.1_Missense_Mutation_p.R519G	NM_152703.2	NP_689916.2	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	519					common myeloid progenitor cell proliferation (GO:0035726)|endosomal vesicle fusion (GO:0034058)|hematopoietic progenitor cell differentiation (GO:0002244)|regulation of protein catabolic process (GO:0042176)|spleen development (GO:0048536)|stem cell division (GO:0017145)	early endosome (GO:0005769)				central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(23)|liver(2)|lung(31)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	88	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)		STAD - Stomach adenocarcinoma(171;0.000302)			GCTCTTTCTCTCTGCCATAAA	0.368																																					p.R519G		Atlas-SNP	.											.	SAMD9L	227	.	0			c.A1555G						.						70	75	73					7																	92763730		2203	4300	6503	SO:0001583	missense	219285	exon5			TTTCTCTCTGCCA	AB095926	CCDS34681.1	7q21.2	2013-01-10		2005-04-26	ENSG00000177409	ENSG00000177409		"Sterile alpha motif (SAM) domain containing"	1349	protein-coding gene	gene with protein product		611170	"chromosome 7 open reading frame 6"	C7orf6			Standard	NM_152703		Approved	KIAA2005, FLJ39885	uc003umh.1	Q8IVG5	OTTHUMG00000155807	ENST00000318238.4:c.1555A>G	chr7.hg19:g.92763730T>C	ENSP00000326247:p.Arg519Gly	65.0	0.0		55.0	25.0	NM_152703	A0JP23|A0JP24|A0PJG8|A4D1G8|D6W5Q6|Q2TV71|Q2TV75|Q2UZV8|Q8IWI4|Q8N3L9|Q8N875	Missense_Mutation	SNP	ENST00000318238.4	hg19	CCDS34681.1	.	.	.	.	.	.	.	.	.	.	T	14.56	2.570468	0.45798	.	.	ENSG00000177409	ENST00000318238;ENST00000411955;ENST00000437805	T;T;T	0.13538	2.58;2.58;2.58	4.59	3.43	0.39272	.	0.376106	0.22643	N	0.057437	T	0.18551	0.0445	M	0.61703	1.905	0.33872	D	0.635011	P	0.48016	0.904	P	0.47573	0.55	T	0.25572	-1.0128	10	0.66056	D	0.02	-12.3165	6.4444	0.21867	0.0:0.0891:0.2039:0.7069	.	519	Q8IVG5	SAM9L_HUMAN	G	519	ENSP00000326247:R519G;ENSP00000405760:R519G;ENSP00000408796:R519G	ENSP00000326247:R519G	R	-	1	2	SAMD9L	92601666	0.700000	0.27796	0.981000	0.43875	0.760000	0.43138	3.368000	0.52357	0.788000	0.33755	0.377000	0.23210	AGA	.	.		0.368	SAMD9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341730.1	NM_152703		C	92763730	T	C	92763730	3	2	344	1	0	0	0	0	1	0	0	0	13842	1559	54	2	3203	2	SAMD9L	7	92763730	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	605559	92763730	66374933	619	47982										
PON3	5446	hgsc.bcm.edu	37	chr7	95023973	95023973	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	taccaagttcctcaataaggTggcagttttcaggttctact	8	9	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:95023973T>A	ENST00000265627.5	-	2	138	c.128A>T	c.(127-129)cAc>cTc	p.H43L	PON1_ENST00000542556.1_Missense_Mutation_p.H43L|PON3_ENST00000427422.1_Missense_Mutation_p.H43L|PON3_ENST00000475439.1_5'UTR|PON3_ENST00000451904.1_Missense_Mutation_p.H43L	NM_000940.2	NP_000931.1	Q15166	PON3_HUMAN	paraoxonase 3	43					aromatic compound catabolic process (GO:0019439)|carboxylic acid catabolic process (GO:0046395)|coumarin catabolic process (GO:0046226)|phenylacetate catabolic process (GO:0010124)|response to external stimulus (GO:0009605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	3,4-dihydrocoumarin hydrolase activity (GO:0018733)|aryldialkylphosphatase activity (GO:0004063)|arylesterase activity (GO:0004064)|dihydrocoumarin hydrolase activity (GO:0047856)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	24	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0151)		Edetic Acid(DB00974)|Lovastatin(DB00227)	CTCAATAAGGTGGCAGTTTTC	0.478																																					p.H43L		Atlas-SNP	.											.	PON3	59	.	0			c.A128T						.						168	132	144					7																	95023973		2203	4300	6503	SO:0001583	missense	5446	exon2			ATAAGGTGGCAGT	L48516, AF320003	CCDS5639.1	7q21.3	2014-03-14			ENSG00000105852	ENSG00000105852	3.1.1.2	"Paraoxonases"	9206	protein-coding gene	gene with protein product	"arylesterase 3"	602720				8661009	Standard	NM_000940		Approved			Q15166	OTTHUMG00000153917	ENST00000265627.5:c.128A>T	chr7.hg19:g.95023973T>A	ENSP00000265627:p.His43Leu	109.0	0.0		81.0	44.0	NM_000940	A4D1H8|O75855|O76060|Q6IRU9|Q8IX97|Q9BZH9	Missense_Mutation	SNP	ENST00000265627.5	hg19	CCDS5639.1	.	.	.	.	.	.	.	.	.	.	T	5.906	0.351256	0.11182	.	.	ENSG00000005421;ENSG00000105852;ENSG00000105852	ENST00000542556;ENST00000265627;ENST00000427422	T;T;T	0.38722	1.12;1.12;1.12	4.85	-5.46	0.02608	Six-bladed beta-propeller, TolB-like (1);	0.754074	0.13171	N	0.408311	T	0.35158	0.0922	M	0.76002	2.32	0.09310	N	1	B;B;B	0.12013	0.005;0.002;0.002	B;B;B	0.10450	0.003;0.005;0.004	T	0.33650	-0.9860	10	0.52906	T	0.07	0.6507	6.4728	0.22018	0.1199:0.3881:0.0:0.492	.	43;43;43	B4E2I0;F5H4W9;Q15166	.;.;PON3_HUMAN	L	43	ENSP00000444854:H43L;ENSP00000265627:H43L;ENSP00000413276:H43L	ENSP00000444854:H43L	H	-	2	0	PON1;PON3	94861909	0.880000	0.30214	0.036000	0.18154	0.002000	0.02628	-0.259000	0.08721	-1.124000	0.02936	-2.128000	0.00344	CAC	.	.		0.478	PON3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333007.1	NM_000940		A	95023973	T	A	95023973	3	1	344	1	0	0	0	0	1	0	0	0	12259	1696	59	4	968	4	PON3	7	95023973	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2260243	95023973	64114690	620	47983										
ARPC1A	10552	hgsc.bcm.edu	37	chr7	98946489	98946489	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcataggtgggtgagcaagcAcattaaaaagccgattcgct	11	8	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:98946489A>G	ENST00000262942.5	+	5	531	c.407A>G	c.(406-408)cAc>cGc	p.H136R	ARPC1A_ENST00000432884.2_Missense_Mutation_p.H89R	NM_001190996.1|NM_006409.3	NP_001177925.1|NP_006400.2	Q92747	ARC1A_HUMAN	actin related protein 2/3 complex, subunit 1A, 41kDa	136					actin cytoskeleton organization (GO:0030036)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|regulation of actin filament polymerization (GO:0030833)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	actin binding (GO:0003779)			endometrium(3)|large_intestine(5)|liver(2)|lung(7)|ovary(1)|prostate(1)	19	all_cancers(62;4.46e-09)|all_epithelial(64;3.44e-10)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0258)		STAD - Stomach adenocarcinoma(171;0.215)			GTGAGCAAGCACATTAAAAAG	0.463																																					p.H136R		Atlas-SNP	.											.	ARPC1A	38	.	0			c.A407G						.						135	115	122					7																	98946489		2203	4300	6503	SO:0001583	missense	10552	exon5			GCAAGCACATTAA	Y08999	CCDS5660.1	7q22.1	2013-03-14	2002-08-29		ENSG00000241685	ENSG00000241685		"Actin related protein 2/3 complex subunits", "WD repeat domain containing"	703	protein-coding gene	gene with protein product	"actin binding protein (Schizosaccharomyces pombe sop2-like)", "SOP2-like protein"	604220	"actin related protein 2/3 complex, subunit 1A (41 kD)"			8978670, 9230079	Standard	NM_006409		Approved	SOP2Hs, SOP2L, Arc40	uc003upx.2	Q92747	OTTHUMG00000154553	ENST00000262942.5:c.407A>G	chr7.hg19:g.98946489A>G	ENSP00000262942:p.His136Arg	155.0	0.0		158.0	84.0	NM_006409	A4D276|B4DLQ7|D6W5S1|Q7Z5U8|Q86WU5|Q8IXQ0	Missense_Mutation	SNP	ENST00000262942.5	hg19	CCDS5660.1	.	.	.	.	.	.	.	.	.	.	A	18.13	3.555892	0.65425	.	.	ENSG00000241685	ENST00000432884;ENST00000262942	T;T	0.59224	0.28;0.28	5.29	5.29	0.74685	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.81049	0.4742	M	0.93420	3.415	0.80722	D	1	P;D	0.61697	0.63;0.99	B;D	0.68765	0.401;0.96	D	0.84727	0.0743	10	0.44086	T	0.13	.	15.5153	0.75818	1.0:0.0:0.0:0.0	.	131;136	Q53GB6;Q92747	.;ARC1A_HUMAN	R	89;136	ENSP00000408578:H89R;ENSP00000262942:H136R	ENSP00000262942:H136R	H	+	2	0	ARPC1A	98784425	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	9.307000	0.96226	2.137000	0.66172	0.482000	0.46254	CAC	.	.		0.463	ARPC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335908.1	NM_006409		G	98946489	A	G	98946489	3	3	344	1	0	0	0	0	1	0	0	0	969	159	6	2	421	2	ARPC1A	7	98946489	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3922516	98946489	60192174	621	47984										
ZNF394	84124	hgsc.bcm.edu	37	chr7	99097607	99097607	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cttcctccactttcacgggcAaaagtccgtcgcgttgggac	10	14	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:99097607A>G	ENST00000337673.6	-	1	313	c.110T>C	c.(109-111)tTg>tCg	p.L37S	ZNF789_ENST00000493485.1_Intron|ZNF394_ENST00000426306.2_Missense_Mutation_p.L37S|ZNF789_ENST00000494186.1_Intron|ZNF394_ENST00000394177.3_Intron	NM_032164.2	NP_115540.2	Q53GI3	ZN394_HUMAN	zinc finger protein 394	37					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(5)|stomach(1)|urinary_tract(1)	16	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					TTTCACGGGCAAAAGTCCGTC	0.647																																					p.L37S	Ovarian(24;589 697 9939 12704 40742)	Atlas-SNP	.											.	ZNF394	48	.	0			c.T110C						.						51	53	52					7																	99097607		2203	4300	6503	SO:0001583	missense	84124	exon1			ACGGGCAAAAGTC	BC025241	CCDS5666.1	7q22.1	2014-01-28			ENSG00000160908	ENSG00000160908		"Zinc fingers, C2H2-type", "-", "-", "-"	18832	protein-coding gene	gene with protein product							Standard	NM_032164		Approved	ZKSCAN14, FLJ12298, ZSCAN46	uc003uqs.3	Q53GI3	OTTHUMG00000154660	ENST00000337673.6:c.110T>C	chr7.hg19:g.99097607A>G	ENSP00000337363:p.Leu37Ser	25.0	0.0		33.0	15.0	NM_032164	A4D281|Q05DA6|Q6P5X9|Q8TB27|Q9HA37|Q9UD51	Missense_Mutation	SNP	ENST00000337673.6	hg19	CCDS5666.1	.	.	.	.	.	.	.	.	.	.	A	14.13	2.442901	0.43326	.	.	ENSG00000160908	ENST00000337673;ENST00000426306	T;T	0.07567	3.18;3.65	4.04	1.58	0.23477	.	0.740871	0.11465	N	0.561338	T	0.06050	0.0157	N	0.14661	0.345	0.09310	N	1	P;P	0.48911	0.845;0.917	B;B	0.43478	0.421;0.421	T	0.36986	-0.9725	10	0.56958	D	0.05	.	8.3543	0.32321	0.5823:0.4177:0.0:0.0	.	37;37	Q05DA6;Q53GI3	.;ZN394_HUMAN	S	37	ENSP00000337363:L37S;ENSP00000409565:L37S	ENSP00000337363:L37S	L	-	2	0	ZNF394	98935543	0.000000	0.05858	0.000000	0.03702	0.058000	0.15608	0.580000	0.23803	0.341000	0.23771	0.459000	0.35465	TTG	.	.		0.647	ZNF394-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336498.1	NM_032164		G	99097607	A	G	99097607	3	3	344	1	0	0	0	0	1	0	0	0	17895	131	5	2	1587	2	ZNF394	7	99097607	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	151118	99097607	60041056	622	47985										
C7orf51	222950	hgsc.bcm.edu	37	chr7	100086259	100086259	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcccaccgccgcccagcttcAgccctcccgagccggaggga	12	20	1	0	rs140403396	byFrequency	TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:100086259A>T	ENST00000300179.2	+	4	1074	c.915A>T	c.(913-915)tcA>tcT	p.S305S	NYAP1_ENST00000454988.1_Silent_p.S248S|NYAP1_ENST00000423930.1_Silent_p.S305S	NM_173564.2	NP_775835.2	Q6ZVC0	NYAP1_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 1	305	Pro-rich.				neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												GCCCAGCTTCAGCCCTCCCGA	0.692																																					p.S305S		Atlas-SNP	.											.	.	.	.	0			c.A915T						.						48	51	50					7																	100086259		2203	4299	6502	SO:0001819	synonymous_variant	222950	exon4			AGCTTCAGCCCTC	AK094857	CCDS5696.1	7q22.1	2011-11-30	2011-11-30	2011-11-30	ENSG00000166924	ENSG00000166924			22009	protein-coding gene	gene with protein product		615477	"chromosome 7 open reading frame 51", "KIAA1486-like"	C7orf51, KIAA1486L		21946561	Standard	NM_173564		Approved	FLJ37538	uc003uvd.2	Q6ZVC0	OTTHUMG00000155290	ENST00000300179.2:c.915A>T	chr7.hg19:g.100086259A>T		69.0	0.0		57.0	30.0	NM_173564	Q6U9Y3|Q8N1V0	Silent	SNP	ENST00000300179.2	hg19	CCDS5696.1																																																																																			.	A|0.998;C|0.002		0.692	NYAP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339335.2	NM_173564		T	100086259	A	T	100086259	2	4	344	1	0	0	0	0	0	0	0	1	2402	175	7	4		4	C7orf51	7	100086259	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	988652	100086259	59052404	623	47986										
MUC17	140453	hgsc.bcm.edu	37	chr7	100674961	100674961	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tatttgagttgcagcaccaaCcctgagatgacctcgattga	9	10	0	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:100674961C>A	ENST00000306151.4	+	3	328	c.264C>A	c.(262-264)aaC>aaA	p.N88K		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	88	Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					GCAGCACCAACCCTGAGATGA	0.458																																					p.N88K		Atlas-SNP	.											.	MUC17	804	.	0			c.C264A						.						117	110	112					7																	100674961		2203	4300	6503	SO:0001583	missense	140453	exon3			CACCAACCCTGAG	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.264C>A	chr7.hg19:g.100674961C>A	ENSP00000302716:p.Asn88Lys	116.0	0.0		113.0	61.0	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	1.259	-0.616493	0.03663	.	.	ENSG00000169876	ENST00000306151	T	0.02395	4.31	0.463	0.463	0.16700	.	.	.	.	.	T	0.01353	0.0044	N	0.14661	0.345	0.09310	N	1	P	0.47604	0.898	B	0.34824	0.19	T	0.45026	-0.9289	8	0.10636	T	0.68	.	.	.	.	.	88	Q685J3	MUC17_HUMAN	K	88	ENSP00000302716:N88K	ENSP00000302716:N88K	N	+	3	2	MUC17	100461681	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.322000	0.02695	0.503000	0.28060	0.508000	0.49915	AAC	.	.		0.458	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		A	100674961	C	A	100674961	3	1	344	1	0	0	0	0	1	0	0	0	9983	506	18	3	274	3	MUC17	7	100674961	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	588702	100674961	58463702	624	47987										
MUC17	140453	hgsc.bcm.edu	37	chr7	100685847	100685847	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gggtagcaccctttcaacacCttctgttgtcaccagcacac	7	15	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:100685847C>A	ENST00000306151.4	+	3	11214	c.11150C>A	c.(11149-11151)cCt>cAt	p.P3717H		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	3717	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					CTTTCAACACCTTCTGTTGTC	0.502																																					p.P3717H		Atlas-SNP	.											.	MUC17	804	.	0			c.C11150A						.						226	205	212					7																	100685847		2203	4300	6503	SO:0001583	missense	140453	exon3			CAACACCTTCTGT	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.11150C>A	chr7.hg19:g.100685847C>A	ENSP00000302716:p.Pro3717His	32.0	0.0		29.0	12.0	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	c	10.15	1.269993	0.23221	.	.	ENSG00000169876	ENST00000306151	T	0.02121	4.44	2.12	2.12	0.27331	.	.	.	.	.	T	0.04272	0.0118	N	0.14661	0.345	0.09310	N	1	D	0.64830	0.994	D	0.73708	0.981	T	0.52801	-0.8527	9	0.33141	T	0.24	.	9.886	0.41262	0.0:1.0:0.0:0.0	.	3717	Q685J3	MUC17_HUMAN	H	3717	ENSP00000302716:P3717H	ENSP00000302716:P3717H	P	+	2	0	MUC17	100472567	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-1.280000	0.02804	1.190000	0.43042	0.423000	0.28283	CCT	.	.		0.502	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		A	100685847	C	A	100685847	3	1	344	1	0	0	0	0	1	0	0	0	9983	681	24	3	11160	3	MUC17	7	100685847	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	10886	100685847	58452816	625	47988										
TMEM168	64418	hgsc.bcm.edu	37	chr7	112407617	112407617	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tggcgggtcagcttcttcaaTatctactgtttttatcaact	7	9	5	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:112407617T>C	ENST00000312814.6	-	5	2289	c.1729A>G	c.(1729-1731)Att>Gtt	p.I577V	TMEM168_ENST00000454074.1_Missense_Mutation_p.I577V	NM_022484.4	NP_071929.3	Q9H0V1	TM168_HUMAN	transmembrane protein 168	577						integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(2)|stomach(1)	32						GCTTCTTCAATATCTACTGTT	0.413																																					p.I577V		Atlas-SNP	.											.	TMEM168	84	.	0			c.A1729G						.						97	94	95					7																	112407617		2203	4300	6503	SO:0001583	missense	64418	exon5			CTTCAATATCTAC		CCDS5757.1	7q31.32	2006-08-08			ENSG00000146802	ENSG00000146802			25826	protein-coding gene	gene with protein product						12477932	Standard	XM_005250527		Approved	DKFZp564C012,FLJ13576	uc003vgn.3	Q9H0V1	OTTHUMG00000155188	ENST00000312814.6:c.1729A>G	chr7.hg19:g.112407617T>C	ENSP00000323068:p.Ile577Val	122.0	0.0		84.0	27.0	NM_022484	A4D0T9|B4DDS0|Q8NEK4|Q9H8J2	Missense_Mutation	SNP	ENST00000312814.6	hg19	CCDS5757.1	.	.	.	.	.	.	.	.	.	.	T	0.201	-1.044389	0.01997	.	.	ENSG00000146802	ENST00000312814;ENST00000454074;ENST00000447395;ENST00000418785	.	.	.	5.71	3.32	0.38043	.	0.432949	0.27604	N	0.018639	T	0.10594	0.0259	N	0.02142	-0.665	0.28467	N	0.915617	B	0.02656	0.0	B	0.01281	0.0	T	0.32851	-0.9891	9	0.02654	T	1	0.0665	7.1602	0.25659	0.0:0.1357:0.2121:0.6522	.	577	Q9H0V1	TM168_HUMAN	V	577;577;193;138	.	ENSP00000323068:I577V	I	-	1	0	TMEM168	112194853	0.971000	0.33674	0.998000	0.56505	0.979000	0.70002	0.511000	0.22739	2.168000	0.68352	0.477000	0.44152	ATT	.	.		0.413	TMEM168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338696.4	NM_022484		C	112407617	T	C	112407617	3	2	344	1	0	0	0	0	1	0	0	0	16098	1406	49	2	368	2	TMEM168	7	112407617	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	11721770	112407617	46731046	626	47989										
GPR85	54329	hgsc.bcm.edu	37	chr7	112724069	112724069	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	caattggcagctgcctggccActggctccaggaccatgaaa	11	13	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:112724069A>T	ENST00000297146.3	-	3	1311	c.708T>A	c.(706-708)agT>agA	p.S236R	GPR85_ENST00000501255.2_Missense_Mutation_p.S236R|GPR85_ENST00000487573.1_5'Flank|GPR85_ENST00000424100.1_Missense_Mutation_p.S236R|GPR85_ENST00000449591.1_Missense_Mutation_p.S236R	NM_001146266.1	NP_001139738.1	P60893	GPR85_HUMAN	G protein-coupled receptor 85	236					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	17						CTGCCTGGCCACTGGCTCCAG	0.517																																					p.S236R		Atlas-SNP	.											.	GPR85	49	.	0			c.T708A						.						68	74	72					7																	112724069		2203	4300	6503	SO:0001583	missense	54329	exon3			CTGGCCACTGGCT	AF250237	CCDS5758.1	7q31	2012-08-21			ENSG00000164604	ENSG00000164604		"GPCR / Class A : Orphans"	4536	protein-coding gene	gene with protein product		605188				10978537, 10833454	Standard	NM_018970		Approved	SREB2	uc003vgp.1	P60893	OTTHUMG00000156933	ENST00000297146.3:c.708T>A	chr7.hg19:g.112724069A>T	ENSP00000297146:p.Ser236Arg	72.0	0.0		55.0	23.0	NM_001146265	Q9JHI6|Q9NPD1	Missense_Mutation	SNP	ENST00000297146.3	hg19	CCDS5758.1	.	.	.	.	.	.	.	.	.	.	A	12.72	2.021860	0.35701	.	.	ENSG00000164604	ENST00000501255;ENST00000297146;ENST00000424100;ENST00000449591	T;T;T;T	0.54866	0.55;0.55;0.55;0.55	5.52	1.38	0.22167	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.38026	0.1025	N	0.08118	0	0.58432	D	0.999997	P	0.43662	0.814	P	0.49887	0.625	T	0.21042	-1.0257	10	0.46703	T	0.11	.	8.9889	0.36010	0.6672:0.0:0.3328:0.0	.	236	P60893	GPR85_HUMAN	R	236	ENSP00000445808:S236R;ENSP00000297146:S236R;ENSP00000396763:S236R;ENSP00000401178:S236R	ENSP00000297146:S236R	S	-	3	2	GPR85	112511305	0.977000	0.34250	1.000000	0.80357	0.998000	0.95712	0.287000	0.18920	0.442000	0.26555	0.528000	0.53228	AGT	.	.		0.517	GPR85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346650.2			T	112724069	A	T	112724069	3	4	344	1	0	0	0	0	1	0	0	0	6723	156	6	4	408	4	GPR85	7	112724069	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	316452	112724069	46414594	627	47990										
PPP1R3A	5506	hgsc.bcm.edu	37	chr7	113519017	113519017	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gctagagaagacagttcacaGcacactgtttcttggcaggt	11	9	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:113519017G>T	ENST00000284601.3	-	4	2198	c.2130C>A	c.(2128-2130)tgC>tgA	p.C710*		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	710					glycogen metabolic process (GO:0005977)	integral component of membrane (GO:0016021)				NS(2)|breast(8)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|liver(1)|lung(43)|ovary(10)|pancreas(7)|prostate(3)|skin(15)|stomach(1)|upper_aerodigestive_tract(2)	121						ACAGTTCACAGCACACTGTTT	0.403																																					p.C710X		Atlas-SNP	.											.	PPP1R3A	317	.	0			c.C2130A						.						203	198	200					7																	113519017		2203	4300	6503	SO:0001587	stop_gained	5506	exon4			TTCACAGCACACT	AF024578	CCDS5759.1	7q31.1	2012-04-17	2011-10-04	2001-07-02	ENSG00000154415	ENSG00000154415	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9291	protein-coding gene	gene with protein product	"glycogen-associated regulatory subunit of protein phosphatase-1", "protein phosphatase 1 regulatory subunit GM"	600917	"protein phosphatase 1, regulatory (inhibitor) subunit 3A (glycogen and sarcoplasmic reticulum binding subunit, skeletal muscle)", "protein phosphatase 1, regulatory (inhibitor) subunit 3A"	PPP1R3		7926294	Standard	NM_002711		Approved	GM	uc010ljy.1	Q16821	OTTHUMG00000156944	ENST00000284601.3:c.2130C>A	chr7.hg19:g.113519017G>T	ENSP00000284601:p.Cys710*	76.0	0.0		54.0	27.0	NM_002711	A0AVQ2|A4D0T6|O43476|Q75LN8|Q7KYM8|Q86UI6	Nonsense_Mutation	SNP	ENST00000284601.3	hg19	CCDS5759.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.664661	0.88251	.	.	ENSG00000154415	ENST00000284601	.	.	.	5.81	1.55	0.23275	.	0.811921	0.11615	N	0.546346	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-2.4505	1.3849	0.02238	0.2274:0.095:0.256:0.4216	.	.	.	.	X	710	.	ENSP00000284601:C710X	C	-	3	2	PPP1R3A	113306253	0.008000	0.16893	0.133000	0.22050	0.982000	0.71751	0.104000	0.15313	0.364000	0.24374	0.650000	0.86243	TGC	.	.		0.403	PPP1R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346724.1	NM_002711		T	113519017	G	T	113519017	4	4	344	1	0	0	0	0	0	1	0	0	12383	963	34	3	1242	3	PPP1R3A	7	113519017	Nonsense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	794948	113519017	45619646	628	47991										
PPP1R3A	5506	hgsc.bcm.edu	37	chr7	113520088	113520088	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgcttcttctctaacccctcTgctttatttggaaaattgac	5	11	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:113520088T>A	ENST00000284601.3	-	4	1127	c.1059A>T	c.(1057-1059)gcA>gcT	p.A353A		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	353					glycogen metabolic process (GO:0005977)	integral component of membrane (GO:0016021)				NS(2)|breast(8)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|liver(1)|lung(43)|ovary(10)|pancreas(7)|prostate(3)|skin(15)|stomach(1)|upper_aerodigestive_tract(2)	121						CTAACCCCTCTGCTTTATTTG	0.393																																					p.A353A		Atlas-SNP	.											.	PPP1R3A	317	.	0			c.A1059T						.						173	173	173					7																	113520088		2203	4300	6503	SO:0001819	synonymous_variant	5506	exon4			CCCCTCTGCTTTA	AF024578	CCDS5759.1	7q31.1	2012-04-17	2011-10-04	2001-07-02	ENSG00000154415	ENSG00000154415	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9291	protein-coding gene	gene with protein product	"glycogen-associated regulatory subunit of protein phosphatase-1", "protein phosphatase 1 regulatory subunit GM"	600917	"protein phosphatase 1, regulatory (inhibitor) subunit 3A (glycogen and sarcoplasmic reticulum binding subunit, skeletal muscle)", "protein phosphatase 1, regulatory (inhibitor) subunit 3A"	PPP1R3		7926294	Standard	NM_002711		Approved	GM	uc010ljy.1	Q16821	OTTHUMG00000156944	ENST00000284601.3:c.1059A>T	chr7.hg19:g.113520088T>A		135.0	0.0		137.0	63.0	NM_002711	A0AVQ2|A4D0T6|O43476|Q75LN8|Q7KYM8|Q86UI6	Silent	SNP	ENST00000284601.3	hg19	CCDS5759.1																																																																																			.	.		0.393	PPP1R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346724.1	NM_002711		A	113520088	T	A	113520088	2	1	344	1	0	0	0	0	0	0	0	1	12383	1567	55	4		4	PPP1R3A	7	113520088	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1071	113520088	45618575	629	47992										
NAA38	84316	hgsc.bcm.edu	37	chr7	117828430	117828430	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggggtagaacaagtggtactAggattatacattgtaagagg	14	3	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:117828430A>T	ENST00000249299.2	+	3	363	c.171A>T	c.(169-171)ctA>ctT	p.L57L	NAA38_ENST00000424702.1_Silent_p.L57L|NAA38_ENST00000422760.1_Silent_p.L36L	NM_016200.4	NP_057284.1	Q9BRA0	LSMD1_HUMAN	N(alpha)-acetyltransferase 38, NatC auxiliary subunit	99					negative regulation of apoptotic process (GO:0043066)	cytoplasm (GO:0005737)|NatC complex (GO:0031417)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|upper_aerodigestive_tract(1)	8						AAGTGGTACTAGGATTATACA	0.368																																					p.L57L		Atlas-SNP	.											.	NAA38	16	.	0			c.A171T						.						85	85	85					7																	117828430		2203	4300	6503	SO:0001819	synonymous_variant	51691	exon3			GGTACTAGGATTA		CCDS11122.1	17p13.1	2014-01-21	2014-01-21	2014-01-21		ENSG00000183011		"N(alpha)-acetyltransferase subunits"	28212	protein-coding gene	gene with protein product			"LSM domain containing 1"	LSMD1		16484612, 19398576	Standard	NM_032356		Approved	MGC14151, PFAAP2	uc002gja.3	Q9BRA0		ENST00000249299.2:c.171A>T	chr7.hg19:g.117828430A>T		67.0	0.0		62.0	24.0	NM_016200	Q8N4M0	Silent	SNP	ENST00000249299.2	hg19	CCDS5775.1																																																																																			.	.		0.368	NAA38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346774.2	NM_032356		T	117828430	A	T	117828430	2	4	344	1	0	0	0	0	0	0	0	1	10133	407	15	4		4	NAA38	7	117828430	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	4308342	117828430	41310233	630	47993										
PTPRZ1	5803	hgsc.bcm.edu	37	chr7	121684539	121684539	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttagtaaagaaactgaggtgCtggacagtcatattcatgcc	10	7	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:121684539C>A	ENST00000393386.2	+	23	6412	c.6001C>A	c.(6001-6003)Ctg>Atg	p.L2001M	PTPRZ1_ENST00000449182.1_Missense_Mutation_p.L1134M	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	2001					axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						AACTGAGGTGCTGGACAGTCA	0.418																																					p.L2001M		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.C6001A						.						178	163	168					7																	121684539		2203	4300	6503	SO:0001583	missense	5803	exon23			GAGGTGCTGGACA	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.6001C>A	chr7.hg19:g.121684539C>A	ENSP00000377047:p.Leu2001Met	70.0	0.0		81.0	38.0	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	hg19	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	C	8.348	0.830335	0.16749	.	.	ENSG00000106278	ENST00000393386;ENST00000449182	T;T	0.11385	2.78;2.78	5.5	4.62	0.57501	.	0.400107	0.23742	N	0.045017	T	0.12475	0.0303	L	0.40543	1.245	0.09310	N	1	B;B;B	0.16166	0.004;0.016;0.016	B;B;B	0.17098	0.009;0.005;0.017	T	0.16276	-1.0408	10	0.87932	D	0	.	16.4139	0.83728	0.0:0.8683:0.1317:0.0	.	1140;1134;2001	P23471-2;C9JFM0;P23471	.;.;PTPRZ_HUMAN	M	2001;1134	ENSP00000377047:L2001M;ENSP00000410000:L1134M	ENSP00000377047:L2001M	L	+	1	2	PTPRZ1	121471775	0.000000	0.05858	0.361000	0.25849	0.475000	0.33008	0.859000	0.27858	1.314000	0.45095	-0.165000	0.13383	CTG	.	.		0.418	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		A	121684539	C	A	121684539	3	1	344	1	0	0	0	0	1	0	0	0	12829	796	28	3	6091	3	PTPRZ1	7	121684539	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	3856109	121684539	37454124	631	47994										
RNF148	378925	hgsc.bcm.edu	37	chr7	122342188	122342188	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtctccagacgcaatctaagTaaaagtaggcaattgtggca	10	8	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:122342188T>C	ENST00000434824.1	-	1	833	c.617A>G	c.(616-618)tAc>tGc	p.Y206C	CADPS2_ENST00000313070.7_Intron|CADPS2_ENST00000449022.2_Intron|RNF148_ENST00000447240.1_Intron|CADPS2_ENST00000334010.7_Intron|RNF133_ENST00000340112.2_5'Flank|CADPS2_ENST00000412584.2_Intron	NM_198085.1	NP_932351.1	Q8N7C7	RN148_HUMAN	ring finger protein 148	206						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(6)|lung(7)	16						GCAATCTAAGTAAAAGTAGGC	0.443																																					p.Y206C		Atlas-SNP	.											.	RNF148	71	.	0			c.A617G						.						108	105	106					7																	122342188		1977	4169	6146	SO:0001583	missense	378925	exon1			TCTAAGTAAAAGT	BC029264	CCDS47692.1	7q31.33	2013-01-09			ENSG00000235631	ENSG00000235631		"RING-type (C3HC4) zinc fingers"	22411	protein-coding gene	gene with protein product						8744354	Standard	NM_198085		Approved	MGC35222	uc003vkk.1	Q8N7C7	OTTHUMG00000157099	ENST00000434824.1:c.617A>G	chr7.hg19:g.122342188T>C	ENSP00000388207:p.Tyr206Cys	41.0	0.0		44.0	23.0	NM_198085	A4D0X4|Q8N308	Missense_Mutation	SNP	ENST00000434824.1	hg19	CCDS47692.1	.	.	.	.	.	.	.	.	.	.	T	1.530	-0.544547	0.04024	.	.	ENSG00000235631	ENST00000434824	T	0.04454	3.62	5.06	1.19	0.21007	.	.	.	.	.	T	0.02807	0.0084	N	0.08118	0	0.09310	N	1	B	0.31640	0.333	B	0.38921	0.285	T	0.43956	-0.9359	9	0.49607	T	0.09	.	0.4569	0.00510	0.3797:0.1618:0.1339:0.3245	.	206	Q8N7C7	RN148_HUMAN	C	206	ENSP00000388207:Y206C	ENSP00000388207:Y206C	Y	-	2	0	RNF148	122129424	.	.	0.228000	0.23943	0.093000	0.18481	.	.	0.311000	0.23014	-0.487000	0.04747	TAC	.	.		0.443	RNF148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347424.1	NM_198085		C	122342188	T	C	122342188	3	2	344	1	0	0	0	0	1	0	0	0	13464	1638	57	2	304	2	RNF148	7	122342188	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	657649	122342188	36796475	632	47995										
SPAM1	6677	hgsc.bcm.edu	37	chr7	123593884	123593884	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aataaacgccaccgggcaagGtgttacaatattttatgttg	9	7	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:123593884G>T	ENST00000439500.1	+	4	873	c.260G>T	c.(259-261)gGt>gTt	p.G87V	SPAM1_ENST00000460182.1_Missense_Mutation_p.G87V|SPAM1_ENST00000223028.7_Missense_Mutation_p.G87V|SPAM1_ENST00000402183.2_Missense_Mutation_p.G87V|SPAM1_ENST00000340011.5_Missense_Mutation_p.G87V	NM_001174045.1|NM_001174046.1	NP_001167516.1|NP_001167517.1	P38567	HYALP_HUMAN	sperm adhesion molecule 1 (PH-20 hyaluronidase, zona pellucida binding)	87					binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	hyalurononglucosaminidase activity (GO:0004415)			breast(1)|cervix(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(23)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						ACCGGGCAAGGTGTTACAATA	0.413																																					p.G87V		Atlas-SNP	.											.	SPAM1	195	.	0			c.G260T						.						54	54	54					7																	123593884		2203	4300	6503	SO:0001583	missense	6677	exon3			GGCAAGGTGTTAC	L13781	CCDS5790.1, CCDS5791.1	7q31	2008-05-02			ENSG00000106304	ENSG00000106304			11217	protein-coding gene	gene with protein product		600930				8282124, 8575780	Standard	NM_153189		Approved	HYAL5, PH-20, SPAG15	uc003vle.3	P38567	OTTHUMG00000157284	ENST00000439500.1:c.260G>T	chr7.hg19:g.123593884G>T	ENSP00000402123:p.Gly87Val	104.0	0.0		89.0	43.0	NM_153189	Q8TC30	Missense_Mutation	SNP	ENST00000439500.1	hg19	CCDS5791.1	.	.	.	.	.	.	.	.	.	.	g	16.93	3.257253	0.59321	.	.	ENSG00000106304	ENST00000402183;ENST00000460182;ENST00000340011;ENST00000439500;ENST00000223028	T;T;T;T;T	0.22945	1.93;1.93;1.93;1.93;1.93	6.03	-12.1	0.00011	Aldolase-type TIM barrel (1);Glycoside hydrolase, superfamily (1);	2.386490	0.01091	N	0.005173	T	0.19327	0.0464	L	0.32530	0.975	0.09310	N	1	P;P	0.43662	0.814;0.814	P;P	0.47915	0.561;0.561	T	0.45131	-0.9282	9	.	.	.	1.0087	4.472	0.11717	0.4111:0.2836:0.2364:0.069	.	87;87	Q8TC30;P38567	.;HYALP_HUMAN	V	87	ENSP00000386028:G87V;ENSP00000417934:G87V;ENSP00000345849:G87V;ENSP00000402123:G87V;ENSP00000223028:G87V	.	G	+	2	0	SPAM1	123381120	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-0.452000	0.06787	-2.598000	0.00452	-2.053000	0.00404	GGT	.	.		0.413	SPAM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000348309.1			T	123593884	G	T	123593884	3	4	344	1	0	0	0	0	1	0	0	0	15001	1261	44	3	262	3	SPAM1	7	123593884	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1251696	123593884	35544779	633	47996										
PAX4	5078	hgsc.bcm.edu	37	chr7	127251726	127251726	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctgtgggcacactgccagggGactgctaaaaaaaaaaagca	11	9	0	0	rs529976183		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:127251726G>T	ENST00000341640.2	-	8	957	c.752C>A	c.(751-753)tCc>tAc	p.S251Y	PAX4_ENST00000378740.2_Missense_Mutation_p.S251Y|PAX4_ENST00000463946.1_Missense_Mutation_p.S249Y|PAX4_ENST00000338516.3_Silent_p.V240V	NM_006193.2	NP_006184.2	O43316	PAX4_HUMAN	paired box 4	259					cell differentiation (GO:0030154)|circadian rhythm (GO:0007623)|endocrine pancreas development (GO:0031018)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|positive regulation of cell differentiation (GO:0045597)|response to cAMP (GO:0051591)|response to drug (GO:0042493)|retina development in camera-type eye (GO:0060041)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)			cervix(1)|kidney(2)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35						ACTGCCAGGGGACTGCTAAAA	0.567																																					p.S251Y	Ovarian(113;737 1605 7858 27720 34092)	Atlas-SNP	.											.	PAX4	66	.	0			c.C752A						.						42	48	46					7																	127251726		2203	4300	6503	SO:0001583	missense	5078	exon8			CCAGGGGACTGCT		CCDS5797.1	7q32.1	2011-06-20	2007-07-12		ENSG00000106331	ENSG00000106331		"Paired boxes", "Homeoboxes / PRD class"	8618	protein-coding gene	gene with protein product		167413	"paired box gene 4"				Standard	NM_006193		Approved	MODY9	uc010lld.1	O43316	OTTHUMG00000157562	ENST00000341640.2:c.752C>A	chr7.hg19:g.127251726G>T	ENSP00000339906:p.Ser251Tyr	27.0	0.0		22.0	12.0	NM_006193	O95161|Q6B0H0	Missense_Mutation	SNP	ENST00000341640.2	hg19	CCDS5797.1	.	.	.	.	.	.	.	.	.	.	G	11.86	1.765820	0.31228	.	.	ENSG00000106331	ENST00000341640;ENST00000378740;ENST00000463946	D;D	0.94417	-3.42;-3.27	5.38	2.45	0.29901	.	0.715682	0.12007	N	0.508274	D	0.94905	0.8353	L	0.55990	1.75	0.09310	N	0.999998	D;D;D	0.69078	0.996;0.991;0.997	P;P;D	0.69479	0.875;0.687;0.964	D	0.86178	0.1604	10	0.51188	T	0.08	.	4.1428	0.10201	0.0869:0.1583:0.5909:0.1638	.	251;259;249	O43316-4;O43316;G3V4Q1	.;PAX4_HUMAN;.	Y	251;259;249	ENSP00000339906:S251Y;ENSP00000451923:S249Y	ENSP00000339906:S251Y	S	-	2	0	PAX4	127038962	0.080000	0.21391	0.042000	0.18584	0.217000	0.24651	0.900000	0.28431	0.286000	0.22352	0.655000	0.94253	TCC	.	.		0.567	PAX4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349165.1			T	127251726	G	T	127251726	3	4	344	1	0	0	0	0	1	0	0	0	11490	1174	41	3	287	3	PAX4	7	127251726	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	3657842	127251726	31886937	634	47997										
LRRC4	64101	hgsc.bcm.edu	37	chr7	127670231	127670231	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gctttcgatggggttgttgcGaagccagagctcccgcagct	14	11	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:127670231G>A	ENST00000249363.3	-	2	720	c.463C>T	c.(463-465)Cgc>Tgc	p.R155C	SND1_ENST00000354725.3_Intron	NM_022143.4	NP_071426.1	Q9HBW1	LRRC4_HUMAN	leucine rich repeat containing 4	155					postsynaptic density protein 95 clustering (GO:0097119)|regulation of synapse organization (GO:0050807)|synapse organization (GO:0050808)	cell junction (GO:0030054)|dendritic spine (GO:0043197)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(6)|lung(4)|pancreas(1)|skin(2)	26				Lung(243;0.124)		GGGTTGTTGCGAAGCCAGAGC	0.592																																					p.R155C		Atlas-SNP	.											.	LRRC4	72	.	0			c.C463T						.						72	77	75					7																	127670231		2203	4300	6503	SO:0001583	missense	64101	exon2			TGTTGCGAAGCCA	AF196976	CCDS5799.1	7q31	2013-01-14	2003-11-19		ENSG00000128594	ENSG00000128594		"Immunoglobulin superfamily / I-set domain containing"	15586	protein-coding gene	gene with protein product		610486	"leucine-rich repeat-containing 4"			12969517	Standard	NM_022143		Approved	NAG14	uc003vmk.3	Q9HBW1	OTTHUMG00000157563	ENST00000249363.3:c.463C>T	chr7.hg19:g.127670231G>A	ENSP00000249363:p.Arg155Cys	61.0	0.0		41.0	17.0	NM_022143	A4D0Y9|Q14DU9|Q6ZMI8|Q96A85	Missense_Mutation	SNP	ENST00000249363.3	hg19	CCDS5799.1	.	.	.	.	.	.	.	.	.	.	G	16.89	3.248127	0.59103	.	.	ENSG00000128594	ENST00000249363;ENST00000494115	D;D	0.91577	-2.87;-2.66	4.56	4.56	0.56223	.	0.000000	0.64402	D	0.000001	D	0.91670	0.7367	L	0.35793	1.09	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91645	0.5330	10	0.72032	D	0.01	.	9.9972	0.41907	0.0:0.0:0.7984:0.2016	.	155	Q9HBW1	LRRC4_HUMAN	C	155;73	ENSP00000249363:R155C;ENSP00000418254:R73C	ENSP00000249363:R155C	R	-	1	0	LRRC4	127457467	0.871000	0.30034	1.000000	0.80357	0.999000	0.98932	1.307000	0.33516	2.316000	0.78162	0.655000	0.94253	CGC	.	.		0.592	LRRC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349170.1	NM_022143		A	127670231	G	A	127670231	3	1	344	1	0	0	0	0	1	0	0	0	9006	1058	37	1	1502	1	LRRC4	7	127670231	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	418505	127670231	31468432	635	47998										
CCDC136	64753	hgsc.bcm.edu	37	chr7	128449649	128449649	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcagggccagctgcaggaagAgctgcacaggctcacactgc	14	13	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:128449649A>T	ENST00000297788.4	+	11	2118	c.1751A>T	c.(1750-1752)gAg>gTg	p.E584V	CCDC136_ENST00000378685.4_Intron|CCDC136_ENST00000464832.1_Intron|CCDC136_ENST00000487361.1_Intron	NM_022742.4	NP_073579	Q96JN2	CC136_HUMAN	coiled-coil domain containing 136	584						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(3)	24						CTGCAGGAAGAGCTGCACAGG	0.597																																					p.E584V		Atlas-SNP	.											.	CCDC136	170	.	0			c.A1751T						.						23	27	26					7																	128449649		2077	4212	6289	SO:0001583	missense	64753	exon11			AGGAAGAGCTGCA		CCDS47704.1, CCDS56510.1	7q33	2007-08-01			ENSG00000128596	ENSG00000128596			22225	protein-coding gene	gene with protein product		611902				15112360	Standard	NM_022742		Approved	KIAA1793, NAG6, DKFZP434G156	uc003vnv.2	Q96JN2	OTTHUMG00000158310	ENST00000297788.4:c.1751A>T	chr7.hg19:g.128449649A>T	ENSP00000297788:p.Glu584Val	149.0	0.0		118.0	60.0	NM_022742	A4D1K1|A7MCY7|A8MYA7|Q6ZVK7|Q9H8M3|Q9UFE1	Missense_Mutation	SNP	ENST00000297788.4	hg19	CCDS47704.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	23.2|23.2	4.385031|4.385031	0.82792|0.82792	.|.	.|.	ENSG00000128596|ENSG00000128596	ENST00000297788;ENST00000397697;ENST00000320524;ENST00000464672|ENST00000494552	T|.	0.53206|.	0.63|.	5.95|5.95	5.95|5.95	0.96441|0.96441	.|.	0.000000|.	0.64402|.	D|.	0.000005|.	T|T	0.67392|0.67392	0.2888|0.2888	M|M	0.66939|0.66939	2.045|2.045	0.38759|0.38759	D|D	0.954279|0.954279	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.87578|.	0.998;0.998|.	T|T	0.69932|0.69932	-0.5011|-0.5011	10|5	0.87932|.	D|.	0|.	-31.6808|-31.6808	12.8077|12.8077	0.57622|0.57622	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	584;584|.	Q96JN2-2;Q96JN2|.	.;CC136_HUMAN|.	V|C	584;584;584;175|461	ENSP00000297788:E584V|.	ENSP00000297788:E584V|.	E|S	+|+	2|1	0|0	CCDC136|CCDC136	128236885|128236885	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.968000|0.968000	0.65278|0.65278	4.491000|4.491000	0.60326|0.60326	2.279000|2.279000	0.76181|0.76181	0.533000|0.533000	0.62120|0.62120	GAG|AGC	.	.		0.597	CCDC136-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350641.1	NM_022742		T	128449649	A	T	128449649	3	4	344	1	0	0	0	0	1	0	0	0	2772	304	11	4	1793	4	CCDC136	7	128449649	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	779418	128449649	30689014	636	47999										
FLNC	2318	hgsc.bcm.edu	37	chr7	128488063	128488063	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cacactgtccactacaccccAgccactgacgggccctacac	6	20	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:128488063A>T	ENST00000325888.8	+	26	4782	c.4521A>T	c.(4519-4521)ccA>ccT	p.P1507P	RP11-309L24.2_ENST00000469965.1_RNA|FLNC_ENST00000346177.6_Silent_p.P1507P	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	1507					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						ACTACACCCCAGCCACTGACG	0.662																																					p.P1507P		Atlas-SNP	.											.	FLNC	339	.	0			c.A4521T						.						26	35	32					7																	128488063		2123	4234	6357	SO:0001819	synonymous_variant	2318	exon26			CACCCCAGCCACT	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"actin binding protein 280"	102565	"filamin C, gamma (actin binding protein 280)"	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.4521A>T	chr7.hg19:g.128488063A>T		152.0	0.0		138.0	50.0	NM_001127487	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Silent	SNP	ENST00000325888.8	hg19	CCDS43644.1																																																																																			.	.		0.662	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3			T	128488063	A	T	128488063	2	4	344	1	0	0	0	0	0	0	0	1	5943	175	7	4		4	FLNC	7	128488063	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	38414	128488063	30650600	637	48000										
FLNC	2318	hgsc.bcm.edu	37	chr7	128494857	128494857	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agcatctggacccgggaggcTggcgctgggggcctgtccat	17	12	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:128494857T>A	ENST00000325888.8	+	42	7287	c.7026T>A	c.(7024-7026)gcT>gcA	p.A2342A	RP11-309L24.2_ENST00000469965.1_RNA|FLNC_ENST00000346177.6_Silent_p.A2309A	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	2342					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						CCCGGGAGGCTGGCGCTGGGG	0.607																																					p.A2342A		Atlas-SNP	.											.	FLNC	339	.	0			c.T7026A						.						57	68	64					7																	128494857		2058	4201	6259	SO:0001819	synonymous_variant	2318	exon42			GGAGGCTGGCGCT	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"actin binding protein 280"	102565	"filamin C, gamma (actin binding protein 280)"	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.7026T>A	chr7.hg19:g.128494857T>A		66.0	0.0		56.0	24.0	NM_001458	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Silent	SNP	ENST00000325888.8	hg19	CCDS43644.1																																																																																			.	.		0.607	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3			A	128494857	T	A	128494857	2	1	344	1	0	0	0	0	0	0	0	1	5943	1567	55	4		4	FLNC	7	128494857	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	6794	128494857	30643806	638	48001										
C7orf45	136263	hgsc.bcm.edu	37	chr7	129847933	129847933	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttctctagggcttctgtctgGgtaggatatctttttttcat	9	7	5	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:129847933G>T	ENST00000297819.3	+	1	234	c.183G>T	c.(181-183)tgG>tgT	p.W61C	TMEM209_ENST00000473456.1_5'Flank|TMEM209_ENST00000397622.2_5'Flank|TMEM209_ENST00000336804.8_5'Flank|RP11-775D22.3_ENST00000483283.1_RNA|TMEM209_ENST00000462753.1_5'Flank	NM_145268.3	NP_660311.1	Q8WWF3	SSMM1_HUMAN	serine-rich single-pass membrane protein 1	61						integral component of membrane (GO:0016021)											CTTCTGTCTGGGTAGGATATC	0.328																																					p.W61C		Atlas-SNP	.											.	.	.	.	0			c.G183T						.						163	164	164					7																	129847933		2203	4300	6503	SO:0001630	splice_region_variant	0	exon1			TGTCTGGGTAGGA	AK097635	CCDS5816.1	7q32.2	2013-03-08	2013-03-08	2013-03-08	ENSG00000165120	ENSG00000165120			29580	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 45"	C7orf45		12477932	Standard	NM_145268		Approved	FLJ40316	uc003vpp.3	Q8WWF3	OTTHUMG00000157844	ENST00000297819.3:c.183+1G>T	chr7.hg19:g.129847933G>T		57.0	0.0		70.0	37.0	NM_145268		Missense_Mutation	SNP	ENST00000297819.3	hg19	CCDS5816.1	.	.	.	.	.	.	.	.	.	.	G	18.48	3.632429	0.67015	.	.	ENSG00000165120	ENST00000297819	T	0.61859	0.07	5.84	5.84	0.93424	.	0.105473	0.43579	D	0.000545	T	0.74496	0.3724	M	0.67953	2.075	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.75777	-0.3198	10	0.72032	D	0.01	-1.8671	15.638	0.76970	0.0:0.0:1.0:0.0	.	61	Q8WWF3	CG045_HUMAN	C	61	ENSP00000297819:W61C	ENSP00000297819:W61C	W	+	3	0	C7orf45	129635169	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	3.487000	0.53222	2.779000	0.95612	0.655000	0.94253	TGG	.	.		0.328	SSMEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349768.1	NM_145268	Missense_Mutation	T	129847933	G	T	129847933	5	4	344	1	0	0	0	0	0	0	1	0	2397	1246	43	3	185	3	C7orf45	7	129847933	Splice_Site	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1353076	129847933	29290730	639	48002										
CALD1	800	hgsc.bcm.edu	37	chr7	134613624	134613624	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atccttgggacaggtgaccgAccaggtggaggtgaatgccc	15	10	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:134613624A>T	ENST00000361675.2	+	4	420	c.191A>T	c.(190-192)gAc>gTc	p.D64V	CALD1_ENST00000361901.2_Missense_Mutation_p.D64V|CALD1_ENST00000361388.2_Missense_Mutation_p.D64V|CALD1_ENST00000495522.1_Missense_Mutation_p.D58V|CALD1_ENST00000424922.1_Missense_Mutation_p.D58V|CALD1_ENST00000422748.1_Missense_Mutation_p.D64V|CALD1_ENST00000543443.1_Missense_Mutation_p.D69V|CALD1_ENST00000393118.2_Missense_Mutation_p.D58V|CALD1_ENST00000417172.1_Missense_Mutation_p.D64V			Q05682	CALD1_HUMAN	caldesmon 1	64	Myosin and calmodulin-binding. {ECO:0000250}.				cellular component movement (GO:0006928)|muscle contraction (GO:0006936)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|calmodulin binding (GO:0005516)|tropomyosin binding (GO:0005523)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(15)|lung(10)	43						CAGGTGACCGACCAGGTGGAG	0.582																																					p.D64V		Atlas-SNP	.											.	CALD1	150	.	0			c.A191T						.						77	67	71					7																	134613624		2203	4300	6503	SO:0001583	missense	800	exon4			TGACCGACCAGGT	M64110	CCDS5834.1, CCDS5835.1, CCDS5836.1, CCDS47716.1, CCDS47717.1, CCDS5836.2	7q33	2007-04-23			ENSG00000122786	ENSG00000122786			1441	protein-coding gene	gene with protein product		114213				1885618	Standard	NM_004342		Approved	CDM, H-CAD, L-CAD	uc003vrz.3	Q05682	OTTHUMG00000155407	ENST00000361675.2:c.191A>T	chr7.hg19:g.134613624A>T	ENSP00000354826:p.Asp64Val	95.0	0.0		85.0	40.0	NM_033157	A8K0X1|Q13978|Q13979|Q14741|Q14742|Q9UD91	Missense_Mutation	SNP	ENST00000361675.2	hg19	CCDS5835.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.958421	0.74016	.	.	ENSG00000122786	ENST00000417172;ENST00000436461;ENST00000361388;ENST00000422748;ENST00000454108;ENST00000361675;ENST00000361901;ENST00000445569;ENST00000435928;ENST00000393118;ENST00000424922;ENST00000495522;ENST00000543443	T;T;T;T;T;T;T;T;T;T;T;T;T	0.46819	0.86;0.86;0.86;0.86;0.86;0.86;0.86;0.86;0.86;0.86;0.86;0.86;0.86	5.55	5.55	0.83447	.	0.491893	0.16787	N	0.199531	T	0.65688	0.2715	M	0.66939	2.045	0.47547	D	0.999456	D;P;P;P;P;P;D;P	0.69078	0.979;0.942;0.928;0.928;0.928;0.928;0.997;0.863	P;P;P;P;P;P;D;P	0.65874	0.714;0.724;0.603;0.603;0.603;0.603;0.939;0.64	T	0.66428	-0.5926	10	0.56958	D	0.05	-38.7299	14.2652	0.66113	1.0:0.0:0.0:0.0	.	69;64;58;58;64;64;64;64	F5H1Z9;A8K0X1;Q05682-5;Q05682-3;Q05682-4;Q05682-2;Q05682;Q9NYG1	.;.;.;.;.;.;CALD1_HUMAN;.	V	64;64;64;64;64;64;64;78;64;58;58;58;69	ENSP00000398826:D64V;ENSP00000411476:D64V;ENSP00000355000:D64V;ENSP00000395710:D64V;ENSP00000401988:D64V;ENSP00000354826:D64V;ENSP00000354513:D64V;ENSP00000390926:D78V;ENSP00000416611:D64V;ENSP00000376826:D58V;ENSP00000393621:D58V;ENSP00000419673:D58V;ENSP00000445641:D69V	ENSP00000355000:D64V	D	+	2	0	CALD1	134264164	1.000000	0.71417	0.997000	0.53966	0.987000	0.75469	5.637000	0.67854	2.101000	0.63845	0.459000	0.35465	GAC	.	.		0.582	CALD1-005	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339939.1	NM_033138		T	134613624	A	T	134613624	3	4	344	1	0	0	0	0	1	0	0	0	2583	275	10	4	254	4	CALD1	7	134613624	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	4765691	134613624	24525039	640	48003										
SLC13A4	26266	hgsc.bcm.edu	37	chr7	135378973	135378973	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cttcttcttgctcagagagcAggtctctttaaaactgagaa	8	9	4	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:135378973A>T	ENST00000354042.4	-	10	1719	c.1030T>A	c.(1030-1032)Tgc>Agc	p.C344S		NM_012450.2	NP_036582.2	Q9UKG4	S13A4_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 4	344					sodium ion transmembrane transport (GO:0035725)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	sodium:sulfate symporter activity (GO:0015382)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	24						CTCAGAGAGCAGGTCTCTTTA	0.393																																					p.C344S		Atlas-SNP	.											.	SLC13A4	56	.	0			c.T1030A						.						155	147	150					7																	135378973		2203	4300	6503	SO:0001583	missense	26266	exon10			GAGAGCAGGTCTC	AF169301	CCDS5840.1	7q33	2013-07-18	2013-07-18		ENSG00000164707	ENSG00000164707		"Solute carriers"	15827	protein-coding gene	gene with protein product	"sulphate transporter 1"	604309	"solute carrier family 13 (sodium/sulphate symporters), member 4"			10535998	Standard	NM_012450		Approved	SUT-1, SUT1	uc003vta.3	Q9UKG4	OTTHUMG00000155539	ENST00000354042.4:c.1030T>A	chr7.hg19:g.135378973A>T	ENSP00000297282:p.Cys344Ser	31.0	0.0		53.0	29.0	NM_012450	A4D1Q4|Q8N631	Missense_Mutation	SNP	ENST00000354042.4	hg19	CCDS5840.1	.	.	.	.	.	.	.	.	.	.	A	15.71	2.914237	0.52546	.	.	ENSG00000164707	ENST00000354042	T	0.69561	-0.41	5.5	5.5	0.81552	.	0.142718	0.64402	D	0.000004	T	0.55337	0.1914	N	0.25485	0.75	0.80722	D	1	B;B	0.29378	0.243;0.088	B;B	0.32724	0.151;0.107	T	0.54009	-0.8357	10	0.32370	T	0.25	-10.7419	13.5883	0.61944	1.0:0.0:0.0:0.0	.	213;344	Q59HF0;Q9UKG4	.;S13A4_HUMAN	S	344	ENSP00000297282:C344S	ENSP00000297282:C344S	C	-	1	0	SLC13A4	135029513	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.651000	0.91078	2.090000	0.63153	0.460000	0.39030	TGC	.	.		0.393	SLC13A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340558.1	NM_012450		T	135378973	A	T	135378973	3	4	344	1	0	0	0	0	1	0	0	0	14409	188	7	4	878	4	SLC13A4	7	135378973	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	765349	135378973	23759690	641	48004										
CHRM2	1129	hgsc.bcm.edu	37	chr7	136700927	136700927	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acagcactatcaaccctgccTgctatgcactttgcaatgcc	6	15	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:136700927T>A	ENST00000445907.2	+	3	1843	c.1315T>A	c.(1315-1317)Tgc>Agc	p.C439S	CHRM2_ENST00000402486.3_Missense_Mutation_p.C439S|CHRM2_ENST00000401861.1_Missense_Mutation_p.C439S|hsa-mir-490_ENST00000425981.2_RNA|hsa-mir-490_ENST00000439694.1_RNA|hsa-mir-490_ENST00000597642.1_RNA|CHRM2_ENST00000453373.1_Missense_Mutation_p.C439S|hsa-mir-490_ENST00000586239.1_RNA|CHRM2_ENST00000320658.5_Missense_Mutation_p.C439S|hsa-mir-490_ENST00000592183.1_RNA|hsa-mir-490_ENST00000598184.1_RNA|CHRM2_ENST00000397608.3_Missense_Mutation_p.C439S|hsa-mir-490_ENST00000593789.1_RNA	NM_001006627.1|NM_001006629.1	NP_001006628.1|NP_001006630.1	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	439					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|nervous system development (GO:0007399)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|regulation of heart contraction (GO:0008016)|response to virus (GO:0009615)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(13)|liver(1)|lung(29)|ovary(4)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	68					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Bethanechol(DB01019)|Brompheniramine(DB00835)|Carbachol(DB00411)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Dimetindene(DB08801)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxacurium chloride(DB01135)|Doxepin(DB01142)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Rocuronium(DB00728)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	CAACCCTGCCTGCTATGCACT	0.418																																					p.C439S		Atlas-SNP	.											.	CHRM2	167	.	0			c.T1315A						.						233	198	210					7																	136700927		2203	4300	6503	SO:0001583	missense	1129	exon3			CCTGCCTGCTATG		CCDS5843.1	7q35-q36	2014-09-17			ENSG00000181072	ENSG00000181072		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1951	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 2"	118493					Standard	NM_000739		Approved		uc003vtl.1	P08172	OTTHUMG00000155658	ENST00000445907.2:c.1315T>A	chr7.hg19:g.136700927T>A	ENSP00000399745:p.Cys439Ser	163.0	0.0		148.0	63.0	NM_001006632	Q4VBK6|Q9P1X9	Missense_Mutation	SNP	ENST00000445907.2	hg19	CCDS5843.1	.	.	.	.	.	.	.	.	.	.	T	19.78	3.890363	0.72524	.	.	ENSG00000181072	ENST00000445907;ENST00000453373;ENST00000320658;ENST00000397608;ENST00000402486;ENST00000401861	T;T;T;T;T;T	0.37235	1.21;1.21;1.21;1.21;1.21;1.21	5.81	5.81	0.92471	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.66036	0.2749	M	0.87269	2.87	0.80722	D	1	D	0.71674	0.998	D	0.79108	0.992	T	0.72481	-0.4280	10	0.72032	D	0.01	-0.8965	16.1773	0.81862	0.0:0.0:0.0:1.0	.	439	P08172	ACM2_HUMAN	S	439	ENSP00000399745:C439S;ENSP00000415386:C439S;ENSP00000319984:C439S;ENSP00000380733:C439S;ENSP00000384937:C439S;ENSP00000384401:C439S	ENSP00000319984:C439S	C	+	1	0	CHRM2	136351467	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.991000	0.88244	2.217000	0.71921	0.482000	0.46254	TGC	.	.		0.418	CHRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341010.1			A	136700927	T	A	136700927	3	1	344	1	0	0	0	0	1	0	0	0	3379	1580	55	4	1317	4	CHRM2	7	136700927	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1321954	136700927	22437736	642	48005										
DGKI	9162	hgsc.bcm.edu	37	chr7	137170144	137170144	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	taatgaactctctgggagccAgaagaaactgactgtaggtc	11	8	1	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:137170144A>T	ENST00000288490.5	-	24	2403	c.2403T>A	c.(2401-2403)tcT>tcA	p.S801S	DGKI_ENST00000453654.2_Silent_p.S501S|DGKI_ENST00000446122.1_Silent_p.S783S|DGKI_ENST00000424189.2_Silent_p.S804S	NM_004717.2	NP_004708.1	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	801					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|positive regulation of Ras protein signal transduction (GO:0046579)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of Rap GTPase activity (GO:0032317)	cytoplasm (GO:0005737)|guanyl-nucleotide exchange factor complex (GO:0032045)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(46)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	84						TCTGGGAGCCAGAAGAAACTG	0.358																																					p.S801S		Atlas-SNP	.											.	DGKI	335	.	0			c.T2403A						.						80	80	80					7																	137170144		2202	4300	6502	SO:0001819	synonymous_variant	9162	exon24			GGAGCCAGAAGAA	AF061936	CCDS5845.1	7q32.3-q33	2013-01-10			ENSG00000157680	ENSG00000157680		"Ankyrin repeat domain containing"	2855	protein-coding gene	gene with protein product		604072				9830018	Standard	NM_004717		Approved	DGK-IOTA	uc003vtt.3	O75912	OTTHUMG00000155697	ENST00000288490.5:c.2403T>A	chr7.hg19:g.137170144A>T		237.0	0.0		190.0	97.0	NM_004717	A4D1Q9|Q9NZ49	Silent	SNP	ENST00000288490.5	hg19	CCDS5845.1																																																																																			.	.		0.358	DGKI-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341286.3	NM_004717		T	137170144	A	T	137170144	2	4	344	1	0	0	0	0	0	0	0	1	4473	175	7	4		4	DGKI	7	137170144	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	469217	137170144	21968519	643	48006										
ZC3HAV1	56829	hgsc.bcm.edu	37	chr7	138749665	138749665	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttccgtgagcccgcctgaaaTggcacaactcccctcggaca	9	16	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:138749665T>C	ENST00000242351.5	-	8	2269	c.1953A>G	c.(1951-1953)ccA>ccG	p.P651P	ZC3HAV1_ENST00000471652.1_Silent_p.P651P|ZC3HAV1_ENST00000464606.1_Silent_p.P773P	NM_020119.3	NP_064504.2	Q7Z2W4	ZCCHV_HUMAN	zinc finger CCCH-type, antiviral 1	651	WWE. {ECO:0000255|PROSITE- ProRule:PRU00248}.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of mRNA catabolic process (GO:0061014)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(4)|skin(1)	37						CCGCCTGAAATGGCACAACTC	0.453																																					p.P651P		Atlas-SNP	.											.	ZC3HAV1	75	.	0			c.A1953G						.						132	123	126					7																	138749665		2203	4300	6503	SO:0001819	synonymous_variant	56829	exon8			CTGAAATGGCACA	BX571742	CCDS5851.1, CCDS55171.1	7q34	2012-07-05			ENSG00000105939	ENSG00000105939		"Zinc fingers, CCCH-type domain containing", "Poly (ADP-ribose) polymerases"	23721	protein-coding gene	gene with protein product	"zinc finger antiviral protein", " CCCH-type zinc finger antiviral protein"	607312				12215647, 12851707	Standard	NM_024625		Approved	ZAP, FLB6421, FLJ13288, MGC48898, ZC3HDC2, ZC3H2, PARP13	uc003vun.3	Q7Z2W4	OTTHUMG00000157471	ENST00000242351.5:c.1953A>G	chr7.hg19:g.138749665T>C		58.0	0.0		72.0	36.0	NM_024625	A4D1R2|A4D1S4|Q8IW57|Q8TAJ3|Q96N79|Q9H8R9|Q9P0Y7	Silent	SNP	ENST00000242351.5	hg19	CCDS5851.1	.	.	.	.	.	.	.	.	.	.	T	4.059	0.008796	0.07912	.	.	ENSG00000105939	ENST00000460845	.	.	.	4.32	-8.63	0.00878	.	.	.	.	.	T	0.61689	0.2367	.	.	.	0.41960	D	0.990704	.	.	.	.	.	.	T	0.74904	-0.3505	4	.	.	.	.	15.1291	0.72507	0.0:0.6453:0.1928:0.162	.	.	.	.	V	216	.	.	I	-	1	0	ZC3HAV1	138400205	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-5.360000	0.00128	-3.886000	0.00095	-0.934000	0.02701	ATT	.	.		0.453	ZC3HAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348915.1	NM_020119		C	138749665	T	C	138749665	2	2	344	1	0	0	0	0	0	0	0	1	17590	1451	51	2		2	ZC3HAV1	7	138749665	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1579521	138749665	20388998	644	48007										
DENND2A	27147	hgsc.bcm.edu	37	chr7	140301960	140301961	+	Missense_Mutation	DNP	CC	CC	AA													0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atcactactcctcctctccaCcgtagaggacggcagataat					rs368178368	byFrequency	TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:140301960_140301961CC>AA	ENST00000275884.6	-	2	654_655	c.237_238GG>TT	c.(235-240)acGGtg>acTTtg	p.V80L	DENND2A_ENST00000537639.1_Missense_Mutation_p.V80L|DENND2A_ENST00000492720.1_Missense_Mutation_p.V80L|DENND2A_ENST00000496613.1_Missense_Mutation_p.V80L			Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	80					positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(22)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49	Melanoma(164;0.00956)					CTCCTCTCCACCGTAGAGGACG	0.525																																					p.V80L|p.T79T		Atlas-SNP	.											.	DENND2A	132	.	0			c.G238T|c.G237T						.																																			SO:0001583	missense	27147	exon1			TCTCCACCGTAGA|CTCCACCGTAGAG	AB033103	CCDS43659.1	7q34	2012-10-03	2005-08-17	2005-08-17	ENSG00000146966	ENSG00000146966		"DENN/MADD domain containing"	22212	protein-coding gene	gene with protein product			"KIAA1277"	KIAA1277			Standard	NM_015689		Approved	FAM31D	uc010lnj.3	Q9ULE3	OTTHUMG00000157411	ENST00000275884.6:c.237_238delinsAA	chr7.hg19:g.140301960_140301961delinsAA	ENSP00000275884:p.Val80Leu	207.0|209.0	0.0		159.0|160.0	66.0|67.0	NM_015689	C9JUI3|Q1RMD5|Q86XY0	Missense_Mutation|Silent	SNP	ENST00000275884.6	hg19	CCDS43659.1																																																																																			.	.		0.525	DENND2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348742.1	NM_015689		AA	140301961	CC	AA	140301960	3	1	344	1	0	0	0	0	1	0	0	0	4431	507	18	3	2863	3	DENND2A	7	140301960	Missense_Mutation	DNP	CC	TCGA-UB-A7MB-01A-11D-A33Q-10	1552295	140301960	18836703	645	48008										
TRYX3	136541	hgsc.bcm.edu	37	chr7	141952141	141952141	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cacatccatccgcaaaagacAggattccttgaagcatccca	6	14	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:141952141A>C	ENST00000552471.1	-	5	945	c.626T>G	c.(625-627)cTg>cGg	p.L209R	PRSS58_ENST00000547058.2_Missense_Mutation_p.L209R			Q8IYP2	PRS58_HUMAN	protease, serine, 58	209	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			kidney(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(2)|skin(2)	19						CGCAAAAGACAGGATTCCTTG	0.393																																					p.L209R		Atlas-SNP	.											.	PRSS58	41	.	0			c.T626G						.						56	59	58					7																	141952141		2203	4300	6503	SO:0001583	missense	136541	exon6			AAAGACAGGATTC		CCDS5871.1	7q34	2012-10-03			ENSG00000258223	ENSG00000258223	3.4.21.4	"Serine peptidases / Serine peptidases"	39125	protein-coding gene	gene with protein product	"trypsin X3"						Standard	NM_001001317		Approved	TRYX3	uc003vxc.4	Q8IYP2	OTTHUMG00000158565	ENST00000552471.1:c.626T>G	chr7.hg19:g.141952141A>C	ENSP00000446916:p.Leu209Arg	123.0	0.0		119.0	45.0	NM_001001317	B3KVJ6|D3DXD2	Missense_Mutation	SNP	ENST00000552471.1	hg19	CCDS5871.1	.	.	.	.	.	.	.	.	.	.	A	19.40	3.819437	0.71028	.	.	ENSG00000258223	ENST00000547058;ENST00000552471	D;D	0.82255	-1.59;-1.59	5.24	5.24	0.73138	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	D	0.90755	0.7098	M	0.83953	2.67	0.34656	D	0.722132	D	0.89917	1.0	D	0.91635	0.999	D	0.94325	0.7557	9	0.87932	D	0	.	11.4549	0.50176	1.0:0.0:0.0:0.0	.	209	Q8IYP2	PRS58_HUMAN	R	209	ENSP00000447588:L209R;ENSP00000446916:L209R	ENSP00000307206:L209R	L	-	2	0	PRSS58	141598619	0.998000	0.40836	0.381000	0.26106	0.864000	0.49448	6.520000	0.73773	2.199000	0.70637	0.533000	0.62120	CTG	.	.		0.393	PRSS58-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351328.2	NM_001001317		C	141952141	A	C	141952141	3	2	344	1	0	0	0	0	1	0	0	0	16619	188	7	5	103	5	TRYX3	7	141952141	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1650181	141952141	17186522	646	48009										
TRPV5	56302	hgsc.bcm.edu	37	chr7	142612494	142612494	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cacatgatgacatggaatggCcccccaagaatcgtctttcc	8	13	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:142612494C>A	ENST00000265310.1	-	10	1617	c.1269G>T	c.(1267-1269)ggG>ggT	p.G423G		NM_019841.4	NP_062815.2	Q9NQA5	TRPV5_HUMAN	transient receptor potential cation channel, subfamily V, member 5	423					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|ion transmembrane transport (GO:0034220)|protein tetramerization (GO:0051262)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(14)|lung(32)|ovary(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	67	Melanoma(164;0.059)					CATGGAATGGCCCCCCAAGAA	0.507																																					p.G423G		Atlas-SNP	.											.,1	TRPV5	164	.	0			c.G1269T						.						150	146	147					7																	142612494		2203	4300	6503	SO:0001819	synonymous_variant	56302	exon10			GAATGGCCCCCCA	AJ271207	CCDS5875.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000127412	ENSG00000127412		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	3145	protein-coding gene	gene with protein product		606679	"epithelial calcium channel 1"	ECAC1		10944439, 10945469, 16382100	Standard	NM_019841		Approved	CaT2	uc003wby.1	Q9NQA5	OTTHUMG00000157157	ENST00000265310.1:c.1269G>T	chr7.hg19:g.142612494C>A		264.0	0.0		188.0	83.0	NM_019841	A4D2H7|E9PBZ6|Q8N4C1|Q8NDW5|Q8NDX7|Q8NDX8|Q96PM6	Silent	SNP	ENST00000265310.1	hg19	CCDS5875.1																																																																																			.	.		0.507	TRPV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347660.1	NM_019841		A	142612494	C	A	142612494	2	1	344	1	0	0	0	0	0	0	0	1	16614	726	26	3		3	TRPV5	7	142612494	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	660353	142612494	16526169	647	48010										
FAM131B	9715	hgsc.bcm.edu	37	chr7	143054107	143054107	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tccatccatgggtgcttgagCcagggcatctggaaaaagaa	12	9	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:143054107C>A	ENST00000409408.1	-	6	2243	c.535G>T	c.(535-537)Gct>Tct	p.A179S	FAM131B_ENST00000443739.2_Missense_Mutation_p.A207S|FAM131B_ENST00000409578.1_Missense_Mutation_p.A195S|FAM131B_ENST00000409346.1_Missense_Mutation_p.A179S|FAM131B_ENST00000409222.3_Missense_Mutation_p.A179S			Q86XD5	F131B_HUMAN	family with sequence similarity 131, member B	179										breast(1)|endometrium(4)|large_intestine(3)|lung(13)|ovary(1)|skin(2)	24	Melanoma(164;0.205)					GGTGCTTGAGCCAGGGCATCT	0.547																																					p.A207S		Atlas-SNP	.											FAM131B_ENST00000443739,NS,carcinoma,0,2	FAM131B	104	.	0			c.G619T						.						40	35	36					7																	143054107		2203	4300	6503	SO:0001583	missense	9715	exon7			CTTGAGCCAGGGC	BC045611	CCDS5882.1, CCDS47734.1	7q34	2007-03-20			ENSG00000159784	ENSG00000159784			22202	protein-coding gene	gene with protein product							Standard	NM_014690		Approved	KIAA0773	uc010lpa.3	Q86XD5	OTTHUMG00000152697	ENST00000409408.1:c.535G>T	chr7.hg19:g.143054107C>A	ENSP00000387017:p.Ala179Ser	132.0	0.0		99.0	44.0	NM_001031690	A4D2H6|A6NDW3|A8K605|B8ZZN2|D3DXE3|J3KQX2|Q7L0D6|Q86T97	Missense_Mutation	SNP	ENST00000409408.1	hg19	CCDS5882.1	.	.	.	.	.	.	.	.	.	.	C	11.36	1.614637	0.28712	.	.	ENSG00000159784	ENST00000443739;ENST00000409578;ENST00000409346;ENST00000452076;ENST00000409408;ENST00000409222	T;T;T;T;T	0.24723	1.84;1.84;1.84;1.84;1.84	5.46	3.66	0.41972	.	0.204214	0.50627	D	0.000101	T	0.22551	0.0544	L	0.51422	1.61	0.52501	D	0.999955	B;B	0.22683	0.073;0.018	B;B	0.28305	0.088;0.011	T	0.03344	-1.1046	10	0.09338	T	0.73	-31.3557	11.6752	0.51425	0.0:0.8573:0.0:0.1427	.	195;179	Q86XD5-2;Q86XD5	.;F131B_HUMAN	S	207;195;179;183;179;179	ENSP00000410603:A207S;ENSP00000386568:A195S;ENSP00000386984:A179S;ENSP00000387017:A179S;ENSP00000387147:A179S	ENSP00000387147:A179S	A	-	1	0	FAM131B	142764229	0.264000	0.24093	0.605000	0.28930	0.984000	0.73092	0.711000	0.25764	0.681000	0.31386	0.655000	0.94253	GCT	.	.		0.547	FAM131B-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328057.1	NM_014690		A	143054107	C	A	143054107	3	1	344	1	0	0	0	0	1	0	0	0	5445	739	26	3	467	3	FAM131B	7	143054107	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	441613	143054107	16084556	648	48011										
NOM1	64434	hgsc.bcm.edu	37	chr7	156742760	156742760	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccccgaacagggtcccggccTgggaggccgaagcggagccg	17	15	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:156742760T>A	ENST00000275820.3	+	1	344	c.329T>A	c.(328-330)cTg>cAg	p.L110Q		NM_138400.1	NP_612409.1	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	110	Necessary for nucleolar localization and for targeting PPP1CA to the nucleolus.					nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(4)|large_intestine(9)|lung(7)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	31	Ovarian(565;0.218)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)		GGTCCCGGCCTGGGAGGCCGA	0.701																																					p.L110Q		Atlas-SNP	.											.	NOM1	73	.	0			c.T329A						.						2	3	3					7																	156742760		1586	3439	5025	SO:0001583	missense	64434	exon1			CCGGCCTGGGAGG	AF107455	CCDS34787.1	7q36.3	2014-06-13	2005-03-30	2005-03-30	ENSG00000146909	ENSG00000146909			13244	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 113"	611269	"chromosome 7 open reading frame 3"	C7orf3		10329000	Standard	XM_005249560		Approved	SGD1, PPP1R113	uc003wmy.3	Q5C9Z4	OTTHUMG00000152639	ENST00000275820.3:c.329T>A	chr7.hg19:g.156742760T>A	ENSP00000275820:p.Leu110Gln	4.0	0.0		19.0	10.0	NM_138400	Q96I08	Missense_Mutation	SNP	ENST00000275820.3	hg19	CCDS34787.1	.	.	.	.	.	.	.	.	.	.	C	6.301	0.423633	0.11928	.	.	ENSG00000146909	ENST00000275820	T	0.11277	2.79	3.37	3.37	0.38596	.	6.464470	0.01392	U	0.013265	T	0.06917	0.0176	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38887	-0.9640	10	0.13108	T	0.6	-0.0063	8.2323	0.31605	0.0:0.6603:0.246:0.0937	.	110	Q5C9Z4	NOM1_HUMAN	Q	110	ENSP00000275820:L110Q	ENSP00000275820:L110Q	L	+	2	0	NOM1	156435521	0.000000	0.05858	0.006000	0.13384	0.015000	0.08874	-0.355000	0.07671	0.412000	0.25729	-0.360000	0.07572	CTG	.	.		0.701	NOM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327098.1	NM_138400		A	156742760	T	A	156742760	3	1	344	1	0	0	0	0	1	0	0	0	10539	1580	55	4	331	4	NOM1	7	156742760	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	13688653	156742760	2395903	649	48012										
DNAJB6	10049	hgsc.bcm.edu	37	chr7	157160147	157160147	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcttcagggaattttttggtGgaagggacccattttcattt	10	6	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr7:157160147G>T	ENST00000262177.4	+	5	521	c.316G>T	c.(316-318)Gga>Tga	p.G106*	DNAJB6_ENST00000452797.2_Nonsense_Mutation_p.G57*|DNAJB6_ENST00000443280.1_Nonsense_Mutation_p.G106*|DNAJB6_ENST00000429029.2_Nonsense_Mutation_p.G106*	NM_058246.3	NP_490647.1	O75190	DNJB6_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 6	106	Gly/Phe-rich.|Interaction with HSP70.				intermediate filament organization (GO:0045109)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of ATPase activity (GO:0032781)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	ATPase activator activity (GO:0001671)|chaperone binding (GO:0051087)|heat shock protein binding (GO:0031072)|unfolded protein binding (GO:0051082)			central_nervous_system(1)|lung(1)|ovary(2)|stomach(1)	5	all_neural(206;0.181)	all_epithelial(9;0.000606)|all_hematologic(28;0.00287)|Acute lymphoblastic leukemia(9;0.0647)|Ovarian(593;0.196)	OV - Ovarian serous cystadenocarcinoma(82;0.00399)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		ATTTTTTGGTGGAAGGGACCC	0.428																																					p.G106X	Esophageal Squamous(46;195 967 1350 20350 43814)	Atlas-SNP	.											.	DNAJB6	39	.	0			c.G316T						.						138	128	132					7																	157160147		2203	4300	6503	SO:0001587	stop_gained	10049	exon5			TTTGGTGGAAGGG	AB014888	CCDS5946.1, CCDS47755.1	7q36.3	2014-02-03			ENSG00000105993	ENSG00000105993		"Heat shock proteins / DNAJ (HSP40)"	14888	protein-coding gene	gene with protein product		611332	"limb girdle muscular dystrophy 1D (autosomal dominant)"	LGMD1D		10319584, 9915854, 22366786	Standard	NM_005494		Approved	MRJ	uc003wnk.3	O75190	OTTHUMG00000157242	ENST00000262177.4:c.316G>T	chr7.hg19:g.157160147G>T	ENSP00000262177:p.Gly106*	75.0	0.0		59.0	29.0	NM_058246	A4D232|A8K7D8|A8KAG0|B4DN73|E9PCZ2|O95806|Q53EN8|Q59EF2|Q6FIC8|Q75MA2|Q9UIK6	Nonsense_Mutation	SNP	ENST00000262177.4	hg19	CCDS5946.1	.	.	.	.	.	.	.	.	.	.	G	33	5.266250	0.95399	.	.	ENSG00000105993	ENST00000441561;ENST00000429029;ENST00000262177;ENST00000417758;ENST00000452797;ENST00000443280;ENST00000421417;ENST00000412557	.	.	.	4.58	3.7	0.42460	.	0.261160	0.26404	N	0.024561	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	12.9127	0.58189	0.0793:0.0:0.9207:0.0	.	.	.	.	X	106;106;106;106;57;106;106;106	.	ENSP00000262177:G106X	G	+	1	0	DNAJB6	156852908	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	8.659000	0.91116	1.050000	0.40346	-0.140000	0.14226	GGA	.	.		0.428	DNAJB6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000348119.2			T	157160147	G	T	157160147	4	4	344	1	0	0	0	0	0	1	0	0	4626	1349	47	3	330	3	DNAJB6	7	157160147	Nonsense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	417387	157160147	1978516	650	48013										
CSMD1	64478	hgsc.bcm.edu	37	chr8	2823327	2823327	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aggtttgctcggattccaccTgccgtctttggtacagcgaa	11	11	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:2823327T>A	ENST00000520002.1	-	60	9808	c.9253A>T	c.(9253-9255)Agg>Tgg	p.R3085W	CSMD1_ENST00000537824.1_Missense_Mutation_p.R3084W|CSMD1_ENST00000400186.3_Intron|CSMD1_ENST00000542608.1_Intron|CSMD1_ENST00000602557.1_Missense_Mutation_p.R3085W|CSMD1_ENST00000602723.1_Intron			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	3085	Sushi 24. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		GGATTCCACCTGCCGTCTTTG	0.433																																					p.R3084W		Atlas-SNP	.											.	CSMD1	1469	.	0			c.A9250T						.						75	78	77					8																	2823327		2015	4195	6210	SO:0001583	missense	64478	exon59			TCCACCTGCCGTC			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.9253A>T	chr8.hg19:g.2823327T>A	ENSP00000430733:p.Arg3085Trp	134.0	0.0		61.0	43.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.14|11.14	1.549940|1.549940	0.27652|0.27652	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000335551|ENST00000520002;ENST00000318252;ENST00000537824	.|T;T	.|0.66099	.|-0.19;-0.19	5.42|5.42	2.96|2.96	0.34315|0.34315	.|Complement control module (2);Sushi/SCR/CCP (3);	.|0.145914	.|0.44483	.|D	.|0.000444	T|T	0.48696|0.48696	0.1514|0.1514	L|L	0.38175|0.38175	1.15|1.15	0.42923|0.42923	D|D	0.994298|0.994298	.|B;B	.|0.23735	.|0.09;0.03	.|B;B	.|0.22753	.|0.015;0.041	T|T	0.42344|0.42344	-0.9457|-0.9457	5|10	.|0.72032	.|D	.|0.01	.|.	7.5044|7.5044	0.27536|0.27536	0.1265:0.0695:0.0:0.804|0.1265:0.0695:0.0:0.804	.|.	.|3085;3085	.|E5RIG2;Q96PZ7	.|.;CSMD1_HUMAN	L|W	2501|3085;2946;3084	.|ENSP00000430733:R3085W;ENSP00000441462:R3084W	.|ENSP00000320445:R2946W	Q|R	-|-	2|1	0|2	CSMD1|CSMD1	2810734|2810734	0.720000|0.720000	0.27996|0.27996	0.001000|0.001000	0.08648|0.08648	0.019000|0.019000	0.09904|0.09904	1.041000|1.041000	0.30291|0.30291	0.327000|0.327000	0.23409|0.23409	0.533000|0.533000	0.62120|0.62120	CAG|AGG	.	.		0.433	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		A	2823327	T	A	2823327	3	1	344	1	0	0	0	0	1	0	0	0	3946	1579	55	4	1492	4	CSMD1	8	2823327	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10		2823327	143540695	651	48014										
CSMD1	64478	hgsc.bcm.edu	37	chr8	2944651	2944651	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcgtgagggagtcccactggTacatgccaagtgggtttcgt	15	9	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:2944651T>A	ENST00000520002.1	-	50	8000	c.7445A>T	c.(7444-7446)tAc>tTc	p.Y2482F	CSMD1_ENST00000537824.1_Missense_Mutation_p.Y2481F|CSMD1_ENST00000400186.3_Missense_Mutation_p.Y2482F|CSMD1_ENST00000542608.1_Missense_Mutation_p.Y2481F|CSMD1_ENST00000602557.1_Missense_Mutation_p.Y2482F|CSMD1_ENST00000602723.1_Missense_Mutation_p.Y2482F			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	2482	Sushi 14. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		GTCCCACTGGTACATGCCAAG	0.498																																					p.Y2481F		Atlas-SNP	.											.	CSMD1	1469	.	0			c.A7442T						.						95	97	96					8																	2944651		2035	4186	6221	SO:0001583	missense	64478	exon49			CACTGGTACATGC			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.7445A>T	chr8.hg19:g.2944651T>A	ENSP00000430733:p.Tyr2482Phe	64.0	0.0		17.0	14.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	hg19		.	.	.	.	.	.	.	.	.	.	T	7.500	0.652486	0.14580	.	.	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608	T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07	5.81	3.38	0.38709	Complement control module (2);Sushi/SCR/CCP (3);	0.159945	0.43260	D	0.000587	T	0.49287	0.1548	L	0.46741	1.465	0.80722	D	1	B;B;B	0.17038	0.005;0.02;0.014	B;B;B	0.25405	0.011;0.06;0.036	T	0.24154	-1.0168	10	0.10636	T	0.68	.	7.4321	0.27134	0.1384:0.0685:0.0:0.7931	.	2482;2482;2481	E5RIG2;Q96PZ7;F5H2I8	.;CSMD1_HUMAN;.	F	2482;2482;2343;2481;2481	ENSP00000383047:Y2482F;ENSP00000430733:Y2482F;ENSP00000441462:Y2481F;ENSP00000446243:Y2481F	ENSP00000320445:Y2343F	Y	-	2	0	CSMD1	2932058	1.000000	0.71417	0.493000	0.27502	0.029000	0.11900	2.473000	0.45145	0.423000	0.26033	0.459000	0.35465	TAC	.	.		0.498	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		A	2944651	T	A	2944651	3	1	344	1	0	0	0	0	1	0	0	0	3946	1638	57	4	3340	4	CSMD1	8	2944651	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	121324	2944651	143419371	652	48015										
CSMD1	64478	hgsc.bcm.edu	37	chr8	2964161	2964161	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcactggtacttcacaaaatCtcctagaagagtcaatgcaa	7	10	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:2964161C>A	ENST00000520002.1	-	47	7396	c.6841G>T	c.(6841-6843)Gat>Tat	p.D2281Y	CSMD1_ENST00000537824.1_Missense_Mutation_p.D2280Y|CSMD1_ENST00000400186.3_Missense_Mutation_p.D2281Y|CSMD1_ENST00000542608.1_Missense_Mutation_p.D2280Y|CSMD1_ENST00000602557.1_Missense_Mutation_p.D2281Y|CSMD1_ENST00000602723.1_Missense_Mutation_p.D2281Y			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	2281	Sushi 13. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		TTCACAAAATCTCCTAGAAGA	0.468																																					p.D2280Y		Atlas-SNP	.											.	CSMD1	1469	.	0			c.G6838T						.						45	46	46					8																	2964161		1923	4128	6051	SO:0001583	missense	64478	exon46			CAAAATCTCCTAG			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.6841G>T	chr8.hg19:g.2964161C>A	ENSP00000430733:p.Asp2281Tyr	121.0	0.0		49.0	38.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.42|17.42	3.385605|3.385605	0.61956|0.61956	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608|ENST00000335551	T;T;T;T|.	0.67171|.	-0.25;-0.25;-0.25;-0.25|.	5.31|5.31	5.31|5.31	0.75309|0.75309	Complement control module (2);Sushi/SCR/CCP (3);|.	0.062552|.	0.64402|.	D|.	0.000011|.	D|D	0.87446|0.87446	0.6179|0.6179	H|H	0.94264|0.94264	3.515|3.515	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	0.999;0.999;1.0|.	D|D	0.90900|0.90900	0.4768|0.4768	10|5	0.52906|.	T|.	0.07|.	.|.	18.9876|18.9876	0.92779|0.92779	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	2281;2281;2280|.	E5RIG2;Q96PZ7;F5H2I8|.	.;CSMD1_HUMAN;.|.	Y|I	2281;2281;2142;2280;2280|1760	ENSP00000383047:D2281Y;ENSP00000430733:D2281Y;ENSP00000441462:D2280Y;ENSP00000446243:D2280Y|.	ENSP00000320445:D2142Y|.	D|R	-|-	1|2	0|0	CSMD1|CSMD1	2951568|2951568	1.000000|1.000000	0.71417|0.71417	0.804000|0.804000	0.32291|0.32291	0.196000|0.196000	0.23810|0.23810	7.113000|7.113000	0.77095|0.77095	2.476000|2.476000	0.83614|0.83614	0.557000|0.557000	0.71058|0.71058	GAT|AGA	.	.		0.468	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		A	2964161	C	A	2964161	3	1	344	1	0	0	0	0	1	0	0	0	3946	913	32	3	3956	3	CSMD1	8	2964161	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	19510	2964161	143399861	653	48016										
CSMD1	64478	hgsc.bcm.edu	37	chr8	3216815	3216815	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaagtgaaaaccaattcttcGgctgaaggcagggactccag	11	9	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:3216815G>T	ENST00000520002.1	-	22	3721	c.3166C>A	c.(3166-3168)Cga>Aga	p.R1056R	CSMD1_ENST00000537824.1_Silent_p.R1055R|CSMD1_ENST00000539096.1_Silent_p.R1055R|CSMD1_ENST00000400186.3_Silent_p.R1056R|CSMD1_ENST00000542608.1_Silent_p.R1055R|CSMD1_ENST00000602557.1_Silent_p.R1056R|CSMD1_ENST00000602723.1_Silent_p.R1056R			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1056	Sushi 6. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CCAATTCTTCGGCTGAAGGCA	0.488																																					p.R1055R		Atlas-SNP	.											.	CSMD1	1469	.	0			c.C3163A						.						56	62	60					8																	3216815		2198	4300	6498	SO:0001819	synonymous_variant	64478	exon21			TTCTTCGGCTGAA			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.3166C>A	chr8.hg19:g.3216815G>T		110.0	0.0		59.0	48.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	hg19		.	.	.	.	.	.	.	.	.	.	g	7.119	0.577602	0.13686	.	.	ENSG00000183117	ENST00000335551	.	.	.	5.24	2.33	0.28932	.	.	.	.	.	T	0.68979	0.3060	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.66044	-0.6021	4	.	.	.	.	14.9564	0.71116	0.0:0.0:0.2929:0.7071	.	.	.	.	Q	535	.	.	P	-	2	0	CSMD1	3204222	1.000000	0.71417	0.694000	0.30210	0.770000	0.43624	3.725000	0.54970	0.163000	0.19507	-0.329000	0.08387	CCG	.	.		0.488	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		T	3216815	G	T	3216815	2	4	344	1	0	0	0	0	0	0	0	1	3946	1124	39	1		1	CSMD1	8	3216815	Silent	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	252654	3216815	143147207	654	48017										
KIAA1967	57805	hgsc.bcm.edu	37	chr8	22476767	22476767	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cggaggccgaggagaccgccCggacggcggagcgacagaag	19	12	0	2	rs201420827		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:22476767C>G	ENST00000308511.4	+	20	2875	c.2626C>G	c.(2626-2628)Cgg>Ggg	p.R876G	CCAR2_ENST00000389279.3_Missense_Mutation_p.R876G|CCAR2_ENST00000520861.1_Missense_Mutation_p.R551G|RP11-582J16.5_ENST00000521025.1_RNA|BIN3_ENST00000519335.1_5'Flank			Q8N163	CCAR2_HUMAN	cell cycle and apoptosis regulator 2	876	Interaction with NR1D1. {ECO:0000269|PubMed:23398316}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mRNA processing (GO:0006397)|negative regulation of catalytic activity (GO:0043086)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage checkpoint (GO:2000003)|regulation of circadian rhythm (GO:0042752)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of protein stability (GO:0031647)|response to UV (GO:0009411)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|DBIRD complex (GO:0044609)|mitochondrial matrix (GO:0005759)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)										GGAGACCGCCCGGACGGCGGA	0.652																																					p.R876G		Atlas-SNP	.											.	KIAA1967	72	.	0			c.C2626G						.						11	11	11					8																	22476767		2163	4241	6404	SO:0001583	missense	57805	exon20			ACCGCCCGGACGG	AL834351	CCDS34863.1	8p22	2013-08-22	2013-08-22	2013-08-22		ENSG00000158941			23360	protein-coding gene	gene with protein product	"deleted in breast cancer"	607359	"KIAA1967"	KIAA1967		12370419	Standard	NM_021174		Approved	DBC-1, DBC1, NET35	uc003xci.3	Q8N163		ENST00000308511.4:c.2626C>G	chr8.hg19:g.22476767C>G	ENSP00000310670:p.Arg876Gly	58.0	0.0		28.0	11.0	NM_021174	A6NL03|B2RB79|D3DSR6|Q6P0Q9|Q8N3G7|Q8N8M1|Q8TF34|Q9H9Q9|Q9HD12|Q9NT55	Missense_Mutation	SNP	ENST00000308511.4	hg19	CCDS34863.1	.	.	.	.	.	.	.	.	.	.	C	14.15	2.449718	0.43531	.	.	ENSG00000158941	ENST00000308511;ENST00000389279;ENST00000520861	T;T;T	0.00349	7.99;7.99;7.99	5.55	4.68	0.58851	.	0.168975	0.40818	N	0.001007	T	0.00210	0.0006	N	0.24115	0.695	0.26740	N	0.970415	P;B	0.42357	0.777;0.358	B;B	0.40982	0.345;0.122	T	0.56263	-0.8008	10	0.54805	T	0.06	-22.3026	10.18	0.42961	0.0:0.9111:0.0:0.0889	.	551;876	G3V119;Q8N163	.;K1967_HUMAN	G	876;876;551	ENSP00000310670:R876G;ENSP00000373930:R876G;ENSP00000429773:R551G	ENSP00000310670:R876G	R	+	1	2	KIAA1967	22532712	0.616000	0.27035	0.516000	0.27786	0.470000	0.32858	2.449000	0.44935	1.583000	0.49898	0.655000	0.94253	CGG	.	C|1.000;T|0.000		0.652	CCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375865.1	NM_021174		G	22476767	C	G	22476767	3	3	344	1	0	0	0	0	1	0	0	0	8274	643	23	4	2700	4	KIAA1967	8	22476767	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	19259952	22476767	123887255	655	48018										
ADAM7	8756	hgsc.bcm.edu	37	chr8	24346837	24346837	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggtgaagagtgtgactgtggCcctgctcaggtatttgcaaa	14	7	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:24346837C>T	ENST00000175238.6	+	12	1340	c.1257C>T	c.(1255-1257)ggC>ggT	p.G419G	RP11-624C23.1_ENST00000523578.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA|ADAM7_ENST00000380789.1_Silent_p.G419G|ADAM7_ENST00000520720.1_Silent_p.G191G|RP11-561E1.1_ENST00000519364.1_RNA	NM_003817.3	NP_003808.2	Q9H2U9	ADAM7_HUMAN	ADAM metallopeptidase domain 7	419	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(24)|ovary(1)|skin(15)	64		Prostate(55;0.0181)		Colorectal(74;0.0199)|COAD - Colon adenocarcinoma(73;0.0754)|BRCA - Breast invasive adenocarcinoma(99;0.182)		GTGACTGTGGCCCTGCTCAGG	0.408																																					p.G419G		Atlas-SNP	.											.	ADAM7	165	.	0			c.C1257T						.						76	68	71					8																	24346837		2203	4300	6503	SO:0001819	synonymous_variant	8756	exon12			CTGTGGCCCTGCT	AF090327	CCDS6045.1	8p21.2	2005-08-18	2005-08-18		ENSG00000069206	ENSG00000069206		"ADAM metallopeptidase domain containing"	214	protein-coding gene	gene with protein product		607310	"a disintegrin and metalloproteinase domain 7"				Standard	NM_003817		Approved	GP-83, EAPI	uc003xeb.3	Q9H2U9	OTTHUMG00000097859	ENST00000175238.6:c.1257C>T	chr8.hg19:g.24346837C>T		53.0	0.0		32.0	24.0	NM_003817	A8K8X7|O75959|Q6PEJ6	Silent	SNP	ENST00000175238.6	hg19	CCDS6045.1																																																																																			.	.		0.408	ADAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215150.1	NM_003817		T	24346837	C	T	24346837	2	4	344	1	0	0	0	0	0	0	0	1	251	726	26	3		3	ADAM7	8	24346837	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1870070	24346837	122017185	656	48019										
ZNF395	55893	hgsc.bcm.edu	37	chr8	28206270	28206270	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gctggcaggccttcttccacCggcaggccgtgcaccactgg	13	16	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:28206270C>T	ENST00000344423.5	-	10	1639	c.1508G>A	c.(1507-1509)cGg>cAg	p.R503Q	ZNF395_ENST00000523095.1_Missense_Mutation_p.R503Q|ZNF395_ENST00000523202.1_Missense_Mutation_p.R503Q	NM_018660.2	NP_061130.1	Q9H8N7	ZN395_HUMAN	zinc finger protein 395	503					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(1)|kidney(5)|large_intestine(6)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.102)|Kidney(114;0.123)|Colorectal(74;0.142)		CTTCTTCCACCGGCAGGCCGT	0.607																																					p.R503Q		Atlas-SNP	.											.	ZNF395	54	.	0			c.G1508A						.						63	63	63					8																	28206270		2203	4300	6503	SO:0001583	missense	55893	exon10			TTCCACCGGCAGG	AB044750	CCDS6067.1	8p21	2008-05-02			ENSG00000186918	ENSG00000186918		"Zinc fingers, C2H2-type"	18737	protein-coding gene	gene with protein product		609494				14625278	Standard	NM_018660		Approved	PRF-1, HDBP2, PBF, DKFZp434K1210	uc003xgr.3	Q9H8N7	OTTHUMG00000102137	ENST00000344423.5:c.1508G>A	chr8.hg19:g.28206270C>T	ENSP00000340494:p.Arg503Gln	91.0	0.0		24.0	24.0	NM_018660	B3KUY7|D3DST4|Q6F6H2|Q9BY72|Q9NPB2|Q9NS57|Q9NS58|Q9NS59	Missense_Mutation	SNP	ENST00000344423.5	hg19	CCDS6067.1	.	.	.	.	.	.	.	.	.	.	C	37	6.196366	0.97367	.	.	ENSG00000186918	ENST00000344423;ENST00000523202;ENST00000523095	T;T;T	0.37235	1.21;1.21;1.21	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.65943	0.2740	M	0.84683	2.71	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.70428	-0.4874	10	0.87932	D	0	-31.6561	17.4265	0.87527	0.0:1.0:0.0:0.0	.	503	Q9H8N7	ZN395_HUMAN	Q	503	ENSP00000340494:R503Q;ENSP00000429640:R503Q;ENSP00000428452:R503Q	ENSP00000340494:R503Q	R	-	2	0	ZNF395	28262189	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.510000	0.81708	2.720000	0.93068	0.650000	0.86243	CGG	.	.		0.607	ZNF395-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219976.1			T	28206270	C	T	28206270	3	4	344	1	0	0	0	0	1	0	0	0	17896	652	23	1	37	1	ZNF395	8	28206270	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	3859433	28206270	118157752	657	48020										
UNC5D	137970	hgsc.bcm.edu	37	chr8	35631946	35631946	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctacatttgatacccccaatGccaaaggcaaggactggcag	9	12	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:35631946G>T	ENST00000404895.2	+	16	2936	c.2608G>T	c.(2608-2610)Gcc>Tcc	p.A870S	UNC5D_ENST00000449677.1_Missense_Mutation_p.A446S|UNC5D_ENST00000287272.2_Missense_Mutation_p.A801S|UNC5D_ENST00000416672.1_Missense_Mutation_p.A875S|UNC5D_ENST00000420357.1_Missense_Mutation_p.A803S|UNC5D_ENST00000453357.2_Missense_Mutation_p.A865S	NM_080872.2	NP_543148.2	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D (C. elegans)	870	Death.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|pyramidal neuron differentiation (GO:0021859)|regulation of neuron migration (GO:2001222)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(2)|breast(7)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(56)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(6)|urinary_tract(2)	112				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)		TACCCCCAATGCCAAAGGCAA	0.473																																					p.A870S		Atlas-SNP	.											.	UNC5D	393	.	0			c.G2608T						.						119	110	113					8																	35631946		2203	4300	6503	SO:0001583	missense	137970	exon16			CCCAATGCCAAAG	AB055056	CCDS6093.2	8p12	2013-01-11			ENSG00000156687	ENSG00000156687		"Immunoglobulin superfamily / I-set domain containing"	18634	protein-coding gene	gene with protein product						18402767	Standard	NM_080872		Approved	KIAA1777, Unc5h4	uc003xjr.2	Q6UXZ4	OTTHUMG00000157145	ENST00000404895.2:c.2608G>T	chr8.hg19:g.35631946G>T	ENSP00000385143:p.Ala870Ser	103.0	0.0		58.0	47.0	NM_080872	Q8WYP7	Missense_Mutation	SNP	ENST00000404895.2	hg19	CCDS6093.2	.	.	.	.	.	.	.	.	.	.	G	6.866	0.529150	0.13127	.	.	ENSG00000156687	ENST00000404895;ENST00000420357;ENST00000287272;ENST00000416672;ENST00000453357;ENST00000449677	D;D;D;D;D;D	0.84944	-1.92;-1.92;-1.92;-1.92;-1.92;-1.92	5.95	5.95	0.96441	Death (2);DEATH-like (2);	0.099013	0.64402	D	0.000001	T	0.73822	0.3636	N	0.20807	0.61	0.58432	D	0.999997	B;B;B	0.27166	0.17;0.141;0.17	B;B;B	0.30029	0.077;0.067;0.11	T	0.68254	-0.5457	10	0.02654	T	1	-26.1272	15.1548	0.72733	0.0:0.0:0.8589:0.1411	.	446;865;870	E9PDS8;Q6UXZ4-2;Q6UXZ4	.;.;UNC5D_HUMAN	S	870;803;801;875;865;446	ENSP00000385143:A870S;ENSP00000392739:A803S;ENSP00000287272:A801S;ENSP00000412652:A875S;ENSP00000394303:A865S;ENSP00000397211:A446S	ENSP00000287272:A801S	A	+	1	0	UNC5D	35751488	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.870000	0.56070	2.827000	0.97445	0.650000	0.86243	GCC	.	.		0.473	UNC5D-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347586.2			T	35631946	G	T	35631946	3	4	344	1	0	0	0	0	1	0	0	0	17010	1319	46	3	2670	3	UNC5D	8	35631946	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	7425676	35631946	110732076	658	48021										
IDO1	3620	hgsc.bcm.edu	37	chr8	39785506	39785506	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tatgacgcctgtgtgaaagcTctggtctccctgaggagcta	12	10	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:39785506T>A	ENST00000518237.1	+	10	1653	c.1014T>A	c.(1012-1014)gcT>gcA	p.A338A	RP11-44K6.3_ENST00000517623.1_RNA|IDO1_ENST00000522495.1_Silent_p.A338A	NM_002164.5	NP_002155.1	P14902	I23O1_HUMAN	indoleamine 2,3-dioxygenase 1	338					cellular nitrogen compound metabolic process (GO:0034641)|cytokine production involved in inflammatory response (GO:0002534)|female pregnancy (GO:0007565)|kynurenic acid biosynthetic process (GO:0034276)|multicellular organismal response to stress (GO:0033555)|negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of T cell apoptotic process (GO:0070233)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chronic inflammatory response (GO:0002678)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of T cell tolerance induction (GO:0002666)|positive regulation of type 2 immune response (GO:0002830)|response to lipopolysaccharide (GO:0032496)|small molecule metabolic process (GO:0044281)|swimming behavior (GO:0036269)|tryptophan catabolic process (GO:0006569)|tryptophan catabolic process to kynurenine (GO:0019441)	cytosol (GO:0005829)|smooth muscle contractile fiber (GO:0030485)|stereocilium bundle (GO:0032421)	electron carrier activity (GO:0009055)|heme binding (GO:0020037)|indoleamine 2,3-dioxygenase activity (GO:0033754)|metal ion binding (GO:0046872)|tryptophan 2,3-dioxygenase activity (GO:0004833)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(2)	12					L-Tryptophan(DB00150)|Melatonin(DB01065)	GTGTGAAAGCTCTGGTCTCCC	0.498																																					p.A338A		Atlas-SNP	.											.	IDO1	43	.	0			c.T1014A						.						52	50	51					8																	39785506		1973	4170	6143	SO:0001819	synonymous_variant	3620	exon10			GAAAGCTCTGGTC	M34455	CCDS47847.1	8p12-p11	2009-01-07	2009-01-07	2009-01-07		ENSG00000131203	1.13.11.52		6059	protein-coding gene	gene with protein product		147435	"indoleamine-pyrrole 2,3 dioxygenase"	IDO, INDO		2109605, 8404046	Standard	NM_002164		Approved		uc003xnm.3	P14902		ENST00000518237.1:c.1014T>A	chr8.hg19:g.39785506T>A		140.0	0.0		95.0	48.0	NM_002164	Q540B4	Silent	SNP	ENST00000518237.1	hg19	CCDS47847.1																																																																																			.	.		0.498	IDO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376987.1	NM_002164		A	39785506	T	A	39785506	2	1	344	1	0	0	0	0	0	0	0	1	7510	1538	54	4		4	IDO1	8	39785506	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	4153560	39785506	106578516	659	48022										
C8orf4	56892	hgsc.bcm.edu	37	chr8	40011185	40011185	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	catctttgaaaacacagaccAagaatcactagaaaggctct	6	10	3	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:40011185A>C	ENST00000315792.3	+	1	197	c.134A>C	c.(133-135)cAa>cCa	p.Q45P		NM_020130.4	NP_064515	Q9NR00	CH004_HUMAN	chromosome 8 open reading frame 4	45					apoptotic process (GO:0006915)					breast(1)|large_intestine(1)|ovary(1)	3	Ovarian(28;0.0173)	all_cancers(7;5.34e-21)|all_epithelial(6;1.04e-14)|Lung NSC(58;9.35e-06)|all_lung(54;1.39e-05)|Hepatocellular(245;0.00745)|Breast(189;0.0334)|Colorectal(162;0.0815)|Myeloproliferative disorder(644;0.116)|Esophageal squamous(32;0.141)	LUSC - Lung squamous cell carcinoma(45;0.000149)	KIRC - Kidney renal clear cell carcinoma(67;0.0923)|Kidney(114;0.111)		AACACAGACCAAGAATCACTA	0.478																																					p.Q45P		Atlas-SNP	.											.	C8orf4	7	.	0			c.A134C						.						118	106	110					8																	40011185		2203	4300	6503	SO:0001583	missense	56892	exon1			CAGACCAAGAATC	AF268037	CCDS6115.1	8p11.2	2014-07-11			ENSG00000176907	ENSG00000176907			1357	protein-coding gene	gene with protein product	"human thyroid cancer 1"	607702				11056052, 24937306	Standard	NM_020130		Approved	TC-1, hTC-1	uc003xnq.2	Q9NR00	OTTHUMG00000164045	ENST00000315792.3:c.134A>C	chr8.hg19:g.40011185A>C	ENSP00000319914:p.Gln45Pro	102.0	0.0		70.0	39.0	NM_020130		Missense_Mutation	SNP	ENST00000315792.3	hg19	CCDS6115.1	.	.	.	.	.	.	.	.	.	.	A	12.08	1.829484	0.32329	.	.	ENSG00000176907	ENST00000315792	T	0.34667	1.35	6.08	6.08	0.98989	.	0.100173	0.64402	D	0.000001	T	0.39937	0.1097	L	0.46157	1.445	0.58432	D	0.999994	P	0.45212	0.853	P	0.44394	0.448	T	0.30504	-0.9976	10	0.87932	D	0	-5.1931	15.8241	0.78683	1.0:0.0:0.0:0.0	.	45	Q9NR00	CH004_HUMAN	P	45	ENSP00000319914:Q45P	ENSP00000319914:Q45P	Q	+	2	0	C8orf4	40130342	1.000000	0.71417	0.951000	0.38953	0.471000	0.32888	8.437000	0.90302	2.330000	0.79161	0.533000	0.62120	CAA	.	.		0.478	C8orf4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376943.1	NM_020130		C	40011185	A	C	40011185	3	2	344	1	0	0	0	0	1	0	0	0	2427	130	5	5	136	5	C8orf4	8	40011185	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	225679	40011185	106352837	660	48023										
ANK1	286	hgsc.bcm.edu	37	chr8	41519015	41519015	+	Intron	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cccttttcaggctggcccgcTtcactatctgcgcccccttc	7	19	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:41519015T>A	ENST00000347528.4	-	41	5703				RP11-930P14.1_ENST00000585088.1_RNA|MIR486_ENST00000408108.1_RNA|RP11-930P14.1_ENST00000520418.1_RNA|ANK1_ENST00000314214.8_Missense_Mutation_p.K146M|ANK1_ENST00000265709.8_Intron|ANK1_ENST00000457297.1_Intron|ANK1_ENST00000289734.7_Missense_Mutation_p.K1871M|RP11-930P14.1_ENST00000522388.1_RNA|ANK1_ENST00000396945.1_Intron|ANK1_ENST00000522231.1_Intron|ANK1_ENST00000522543.1_Intron|ANK1_ENST00000352337.4_Missense_Mutation_p.K1849M|ANK1_ENST00000379758.2_Intron|ANK1_ENST00000396942.1_Missense_Mutation_p.K1896M	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic						axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			GCTGGCCCGCTTCACTATCTG	0.617																																					p.K1871M		Atlas-SNP	.											.	ANK1	497	.	0			c.A5612T						.						82	73	76					8																	41519015		2203	4300	6503	SO:0001627	intron_variant	286	exon42			GCCCGCTTCACTA	M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"Ankyrin repeat domain containing"	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.5619+303A>T	chr8.hg19:g.41519015T>A		44.0	0.0		44.0	16.0	NM_000037	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Missense_Mutation	SNP	ENST00000347528.4	hg19	CCDS6119.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	28.6|28.6	4.931534|4.931534	0.92389|0.92389	.|.	.|.	ENSG00000029534|ENSG00000029534	ENST00000520299|ENST00000289734;ENST00000396942;ENST00000352337;ENST00000314214	.|T;T;T;D	.|0.93019	.|-1.35;-0.79;-1.12;-3.15	6.07|6.07	6.07|6.07	0.98685|0.98685	.|.	.|0.000000	.|0.41500	.|U	.|0.000876	D|D	0.96703|0.96703	0.8924|0.8924	M|M	0.80183|0.80183	2.485|2.485	0.58432|0.58432	D|D	0.999998|0.999998	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.91635	.|0.999;0.997;0.989	D|D	0.97154|0.97154	0.9833|0.9833	5|10	.|0.87932	.|D	.|0	.|.	15.81|15.81	0.78552|0.78552	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|1871;1025;146	.|P16157-3;B3KX39;Q53ER1	.|.;.;.	D|M	1030|1871;1896;1849;146	.|ENSP00000289734:K1871M;ENSP00000380147:K1896M;ENSP00000309131:K1849M;ENSP00000319123:K146M	.|ENSP00000289734:K1871M	E|K	-|-	3|2	2|0	ANK1|ANK1	41638172|41638172	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.250000|7.250000	0.78287|0.78287	2.326000|2.326000	0.78906|0.78906	0.533000|0.533000	0.62120|0.62120	GAA|AAG	.	.		0.617	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475		A	41519015	T	A	41519015	1	1	344	0	1	0	0	0	0	0	0	0	620	1609	56	4		4	ANK1	8	41519015	Intron	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1507830	41519015	104845007	661	48024										
MOS	4342	hgsc.bcm.edu	37	chr8	57026368	57026368	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctctgcagcaagcacacctgCtcccagtcaatggagcacca	8	16	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:57026368C>A	ENST00000311923.1	-	1	173	c.174G>T	c.(172-174)gaG>gaT	p.E58D		NM_005372.1	NP_005363.1	P00540	MOS_HUMAN	v-mos Moloney murine sarcoma viral oncogene homolog	58					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|chromatin organization (GO:0006325)|establishment of meiotic spindle orientation (GO:0051296)|MAPK cascade (GO:0000165)|meiotic spindle organization (GO:0000212)|negative regulation of metaphase/anaphase transition of meiotic cell cycle (GO:1902103)|protein autophosphorylation (GO:0046777)|regulation of meiosis (GO:0040020)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(12)|ovary(1)|urinary_tract(2)	22			Epithelial(17;0.00117)|all cancers(17;0.00879)			AGCACACCTGCTCCCAGTCAA	0.637																																					p.E58D	Esophageal Squamous(124;373 2870 4778)	Atlas-SNP	.											.	MOS	63	.	0			c.G174T						.						42	42	42					8																	57026368		2203	4300	6503	SO:0001583	missense	4342	exon1			CACCTGCTCCCAG		CCDS6164.1	8q11	2012-10-02			ENSG00000172680	ENSG00000172680			7199	protein-coding gene	gene with protein product		190060				9552420	Standard	NM_005372		Approved		uc011leb.2	P00540	OTTHUMG00000164299	ENST00000311923.1:c.174G>T	chr8.hg19:g.57026368C>A	ENSP00000310722:p.Glu58Asp	66.0	0.0		52.0	28.0	NM_005372	Q3KPG9|Q3KPH0	Missense_Mutation	SNP	ENST00000311923.1	hg19	CCDS6164.1	.	.	.	.	.	.	.	.	.	.	C	7.236	0.600350	0.13939	.	.	ENSG00000172680	ENST00000311923	D	0.93019	-3.15	5.14	-6.92	0.01644	Protein kinase-like domain (1);	0.444431	0.22203	N	0.063214	T	0.77778	0.4181	N	0.10629	0.01	0.26636	N	0.972385	B	0.18461	0.028	B	0.16289	0.015	T	0.71457	-0.4587	10	0.06494	T	0.89	.	10.8993	0.47043	0.1795:0.5946:0.0:0.226	.	58	P00540	MOS_HUMAN	D	58	ENSP00000310722:E58D	ENSP00000310722:E58D	E	-	3	2	MOS	57188922	0.000000	0.05858	0.983000	0.44433	0.995000	0.86356	-3.826000	0.00356	-0.666000	0.05310	0.557000	0.71058	GAG	.	.		0.637	MOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378174.1	NM_005372		A	57026368	C	A	57026368	3	1	344	1	0	0	0	0	1	0	0	0	9721	796	28	3	869	3	MOS	8	57026368	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	15507353	57026368	89337654	662	48025										
NSMAF	8439	hgsc.bcm.edu	37	chr8	59498516	59498516	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cctgtctgcacatcaatgacAttaagacagccatctgttcc	6	13	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:59498516A>G	ENST00000038176.3	-	29	2702	c.2490T>C	c.(2488-2490)aaT>aaC	p.N830N	NSMAF_ENST00000427130.2_Silent_p.N861N	NM_003580.3	NP_003571.2	Q92636	FAN_HUMAN	neutral sphingomyelinase (N-SMase) activation associated factor	830					ceramide metabolic process (GO:0006672)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	receptor signaling protein activity (GO:0005057)|sphingomyelin phosphodiesterase activator activity (GO:0016230)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	38		all_lung(136;0.174)|Lung NSC(129;0.2)				catcaatgacattaagacagc	0.463																																					p.N861N		Atlas-SNP	.											.	NSMAF	156	.	0			c.T2583C						.						147	122	130					8																	59498516		2203	4300	6503	SO:0001819	synonymous_variant	8439	exon29			AATGACATTAAGA	X96586	CCDS6173.1, CCDS47864.1	8q12-q13	2013-01-10			ENSG00000035681	ENSG00000035681		"WD repeat domain containing"	8017	protein-coding gene	gene with protein product		603043				8808629, 10640829	Standard	NM_003580		Approved	FAN	uc011lee.2	Q92636	OTTHUMG00000164352	ENST00000038176.3:c.2490T>C	chr8.hg19:g.59498516A>G		77.0	0.0		64.0	21.0	NM_001144772	B4DFB0|E9PCH0|Q8IW26	Silent	SNP	ENST00000038176.3	hg19	CCDS6173.1																																																																																			.	.		0.463	NSMAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378384.1	NM_003580		G	59498516	A	G	59498516	2	3	344	1	0	0	0	0	0	0	0	1	10683	214	8	2		2	NSMAF	8	59498516	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2472148	59498516	86865506	663	48026										
TRPA1	8989	hgsc.bcm.edu	37	chr8	72983964	72983964	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	accttccaaagaggaatctcTggtgatcttctccattagct	7	11	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:72983964T>A	ENST00000262209.4	-	2	457	c.250A>T	c.(250-252)Aga>Tga	p.R84*		NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	84					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	GAGGAATCTCTGGTGATCTTC	0.343																																					p.R84X		Atlas-SNP	.											.	TRPA1	256	.	0			c.A250T						.						130	120	124					8																	72983964		2203	4300	6503	SO:0001587	stop_gained	8989	exon2			AATCTCTGGTGAT	Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	497	protein-coding gene	gene with protein product		604775	"ankyrin-like with transmembrane domains 1"	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.250A>T	chr8.hg19:g.72983964T>A	ENSP00000262209:p.Arg84*	73.0	0.0		69.0	27.0	NM_007332	A6NIN6	Nonsense_Mutation	SNP	ENST00000262209.4	hg19	CCDS34908.1	.	.	.	.	.	.	.	.	.	.	T	20.5	3.997141	0.74818	.	.	ENSG00000104321	ENST00000262209	.	.	.	4.89	2.25	0.28309	.	0.760350	0.13067	N	0.416402	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	-1.157	4.5636	0.12172	0.0:0.1832:0.1801:0.6366	.	.	.	.	X	84	.	ENSP00000262209:R84X	R	-	1	2	TRPA1	73146518	0.181000	0.23161	0.119000	0.21687	0.011000	0.07611	0.740000	0.26188	1.833000	0.53350	0.460000	0.39030	AGA	.	.		0.343	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332		A	72983964	T	A	72983964	4	1	344	1	0	0	0	0	0	1	0	0	16592	1588	55	4	3213	4	TRPA1	8	72983964	Nonsense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	13485448	72983964	73380058	664	48027										
SLC7A13	157724	hgsc.bcm.edu	37	chr8	87229922	87229922	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcaaaggcagctggccctctTggcttgcaagatatattggt	12	9	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:87229922T>A	ENST00000297524.3	-	3	1059	c.956A>T	c.(955-957)cAa>cTa	p.Q319L	SLC7A13_ENST00000520624.1_5'UTR|SLC7A13_ENST00000419776.2_Missense_Mutation_p.Q310L	NM_138817.2	NP_620172.2	Q8TCU3	S7A13_HUMAN	solute carrier family 7 (anionic amino acid transporter), member 13	319						integral component of membrane (GO:0016021)	amino acid transmembrane transporter activity (GO:0015171)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	45						CTGGCCCTCTTGGCTTGCAAG	0.373																																					p.Q319L		Atlas-SNP	.											.	SLC7A13	97	.	0			c.A956T						.						90	103	98					8																	87229922		2203	4299	6502	SO:0001583	missense	157724	exon3			CCCTCTTGGCTTG	AJ417661	CCDS34917.1	8q21.3	2013-07-15	2011-07-12		ENSG00000164893	ENSG00000164893		"Solute carriers"	23092	protein-coding gene	gene with protein product						11907033, 11943479	Standard	XM_005250804		Approved	AGT-1, XAT2	uc003ydq.1	Q8TCU3	OTTHUMG00000163663	ENST00000297524.3:c.956A>T	chr8.hg19:g.87229922T>A	ENSP00000297524:p.Gln319Leu	134.0	0.0		116.0	55.0	NM_138817	Q05C37|Q08AH9|Q96N84	Missense_Mutation	SNP	ENST00000297524.3	hg19	CCDS34917.1	.	.	.	.	.	.	.	.	.	.	T	11.26	1.585183	0.28268	.	.	ENSG00000164893	ENST00000297524;ENST00000419776	D;D	0.89875	-2.58;-2.58	5.27	-0.265	0.12946	Amino acid permease domain (1);	1.059620	0.07423	N	0.894402	T	0.81721	0.4882	L	0.40543	1.245	0.09310	N	1	B;B	0.27140	0.169;0.016	B;B	0.27796	0.083;0.025	T	0.68307	-0.5443	10	0.62326	D	0.03	.	1.9593	0.03383	0.1308:0.1525:0.1359:0.5807	.	310;319	Q8TCU3-2;Q8TCU3	.;S7A13_HUMAN	L	319;310	ENSP00000297524:Q319L;ENSP00000410982:Q310L	ENSP00000297524:Q319L	Q	-	2	0	SLC7A13	87299038	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	0.558000	0.23469	-0.202000	0.10268	0.528000	0.53228	CAA	.	.		0.373	SLC7A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374704.1	NM_138817		A	87229922	T	A	87229922	3	1	344	1	0	0	0	0	1	0	0	0	14710	1812	63	4	464	4	SLC7A13	8	87229922	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	14245958	87229922	59134100	665	48028										
CNBD1	168975	hgsc.bcm.edu	37	chr8	88365947	88365947	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agcgtccttcttcaagttccTttcacgtgcacaatcattac	5	13	4	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:88365947T>G	ENST00000518476.1	+	10	1287	c.1236T>G	c.(1234-1236)ccT>ccG	p.P412P		NM_173538.2	NP_775809.1	Q8NA66	CNBD1_HUMAN	cyclic nucleotide binding domain containing 1	412										breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(4)|urinary_tract(1)	32						TTCAAGTTCCTTTCACGTGCA	0.328																																					p.P412P		Atlas-SNP	.											.	CNBD1	206	.	0			c.T1236G						.						95	93	94					8																	88365947		1840	4087	5927	SO:0001819	synonymous_variant	168975	exon10			AGTTCCTTTCACG	AK093121	CCDS55259.1	8q21.3	2005-08-09				ENSG00000176571			26663	protein-coding gene	gene with protein product							Standard	NM_173538		Approved	FLJ35802	uc003ydy.2	Q8NA66		ENST00000518476.1:c.1236T>G	chr8.hg19:g.88365947T>G		516.0	0.0		451.0	189.0	NM_173538		Silent	SNP	ENST00000518476.1	hg19	CCDS55259.1	.	.	.	.	.	.	.	.	.	.	T	9.990	1.230540	0.22542	.	.	ENSG00000176571	ENST00000523299;ENST00000521593	.	.	.	4.98	-2.25	0.06888	.	.	.	.	.	T	0.41511	0.1162	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.27400	-1.0075	4	.	.	.	-18.6271	2.9238	0.05778	0.3098:0.2825:0.0:0.4076	.	.	.	.	R	104;49	.	.	L	+	2	0	CNBD1	88435063	0.909000	0.30893	0.326000	0.25389	0.954000	0.61252	-0.508000	0.06344	-0.697000	0.05092	0.454000	0.30748	CTT	.	.		0.328	CNBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375113.2	NM_173538		G	88365947	T	G	88365947	2	3	344	1	0	0	0	0	0	0	0	1	3593	1596	56	5		5	CNBD1	8	88365947	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1136025	88365947	57998075	666	48029										
NBN	4683	hgsc.bcm.edu	37	chr8	90995076	90995076	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acgccagtcaaaagtctgtaTggttctcctgagataaattt	8	8	3	1	rs577332041		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:90995076T>C	ENST00000265433.3	-	2	199	c.45A>G	c.(43-45)ccA>ccG	p.P15P	NBN_ENST00000409330.1_5'UTR	NM_002485.4	NP_002476.2	O60934	NBN_HUMAN	nibrin	15					blastocyst growth (GO:0001832)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|DNA damage checkpoint (GO:0000077)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intrinsic apoptotic signaling pathway (GO:0097193)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mitotic cell cycle checkpoint (GO:0007093)|mitotic G2 DNA damage checkpoint (GO:0007095)|neuromuscular process controlling balance (GO:0050885)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|telomere maintenance (GO:0000723)	Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nuclear inclusion body (GO:0042405)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|replication fork (GO:0005657)|site of double-strand break (GO:0035861)	damaged DNA binding (GO:0003684)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(11;0.0344)			AAAGTCTGTATGGTTCTCCTG	0.353								Homologous recombination																													p.P15P		Atlas-SNP	.											.	NBN	86	.	0			c.A45G						.						88	85	86					8																	90995076		2203	4300	6503	SO:0001819	synonymous_variant	4683	exon2			TCTGTATGGTTCT	AF058696	CCDS6249.1	8q21-q24	2014-09-17	2005-06-02	2005-06-02	ENSG00000104320	ENSG00000104320			7652	protein-coding gene	gene with protein product		602667	"Nijmegen breakage syndrome 1 (nibrin)"	NBS, NBS1		9590181, 9590180	Standard	XM_005250923		Approved	ATV, AT-V2, AT-V1	uc003yej.1	O60934	OTTHUMG00000153546	ENST00000265433.3:c.45A>G	chr8.hg19:g.90995076T>C		114.0	0.0		89.0	41.0	NM_002485	B2R626|B2RNC5|O60672|Q32NF7|Q53FM6|Q63HR6|Q7LDM2	Silent	SNP	ENST00000265433.3	hg19	CCDS6249.1																																																																																			.	.		0.353	NBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331583.3	NM_001024688		C	90995076	T	C	90995076	2	2	344	1	0	0	0	0	0	0	0	1	10200	1451	51	2		2	NBN	8	90995076	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2629129	90995076	55368946	667	48030										
SLC26A7	115111	hgsc.bcm.edu	37	chr8	92401631	92401631	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tggattgcagtggatttaccTtttttgactattctggagtc	10	6	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:92401631T>A	ENST00000276609.3	+	16	1980	c.1741T>A	c.(1741-1743)Ttt>Att	p.F581I	SLC26A7_ENST00000309536.2_Missense_Mutation_p.F581I|SLC26A7_ENST00000523719.1_Missense_Mutation_p.F581I|SLC26A7_ENST00000520249.1_3'UTR	NM_001282356.1|NM_052832.2	NP_001269285.1|NP_439897.1			solute carrier family 26 (anion exchanger), member 7											breast(1)|cervix(1)|endometrium(4)|large_intestine(10)|lung(26)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	50			BRCA - Breast invasive adenocarcinoma(11;0.00802)			TGGATTTACCTTTTTTGACTA	0.403																																					p.F581I		Atlas-SNP	.											.	SLC26A7	207	.	0			c.T1741A						.						336	308	317					8																	92401631		2203	4300	6503	SO:0001583	missense	115111	exon16			TTTACCTTTTTTG	AF331521	CCDS6254.1, CCDS6255.1, CCDS75765.1	8q23	2013-07-18	2013-07-18		ENSG00000147606	ENSG00000147606		"Solute carriers"	14467	protein-coding gene	gene with protein product		608479	"solute carrier family 26, member 7"			11834742, 11829495, 16524946	Standard	NM_134266		Approved	SUT2	uc003yez.3	Q8TE54	OTTHUMG00000164062	ENST00000276609.3:c.1741T>A	chr8.hg19:g.92401631T>A	ENSP00000276609:p.Phe581Ile	113.0	0.0		71.0	34.0	NM_134266		Missense_Mutation	SNP	ENST00000276609.3	hg19	CCDS6254.1	.	.	.	.	.	.	.	.	.	.	T	18.28	3.588445	0.66105	.	.	ENSG00000147606	ENST00000523719;ENST00000276609;ENST00000309536	D;D;D	0.89939	-2.59;-2.59;-2.59	5.62	5.62	0.85841	Sulphate transporter/antisigma-factor antagonist STAS (4);	0.080536	0.53938	D	0.000059	D	0.88198	0.6372	M	0.79475	2.455	0.37465	D	0.915382	P;P	0.43578	0.775;0.811	B;B	0.40602	0.225;0.334	D	0.90365	0.4376	10	0.62326	D	0.03	.	9.647	0.39875	0.0:0.0781:0.0:0.9219	.	581;581	Q8TE54-2;Q8TE54	.;S26A7_HUMAN	I	581	ENSP00000428849:F581I;ENSP00000276609:F581I;ENSP00000309504:F581I	ENSP00000276609:F581I	F	+	1	0	SLC26A7	92470807	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.412000	0.44609	2.141000	0.66446	0.460000	0.39030	TTT	.	.		0.403	SLC26A7-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377011.1			A	92401631	T	A	92401631	3	1	344	1	0	0	0	0	1	0	0	0	14537	1609	56	4	1799	4	SLC26A7	8	92401631	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1406555	92401631	53962391	668	48031										
RUNX1T1	862	hgsc.bcm.edu	37	chr8	92983058	92983058	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccgtcatcgcctggcgcttcAcctcattgacggcctcctct	8	18	4	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:92983058A>T	ENST00000523629.1	-	11	1821	c.1367T>A	c.(1366-1368)gTg>gAg	p.V456E	RUNX1T1_ENST00000518844.1_Missense_Mutation_p.V429E|RUNX1T1_ENST00000360348.2_Missense_Mutation_p.V419E|RUNX1T1_ENST00000396218.1_Missense_Mutation_p.V429E|RUNX1T1_ENST00000265814.3_Missense_Mutation_p.V456E|RUNX1T1_ENST00000520724.1_Missense_Mutation_p.V419E|RUNX1T1_ENST00000436581.2_Missense_Mutation_p.V467E|RUNX1T1_ENST00000422361.2_Missense_Mutation_p.V419E	NM_001198626.1|NM_001198630.1|NM_001198633.1|NM_175634.2	NP_001185555.1|NP_001185559.1|NP_001185562.1|NP_783552.1	Q06455	MTG8_HUMAN	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	456					fat cell differentiation (GO:0045444)|generation of precursor metabolites and energy (GO:0006091)|regulation of DNA binding (GO:0051101)|transcription, DNA-templated (GO:0006351)	nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(54)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	86			BRCA - Breast invasive adenocarcinoma(11;0.0141)			CTGGCGCTTCACCTCATTGAC	0.547																																					p.V515E		Atlas-SNP	.											.	RUNX1T1	516	.	0			c.T1544A						.						59	48	51					8																	92983058		2203	4300	6503	SO:0001583	missense	862	exon11			CGCTTCACCTCAT	D43638	CCDS6256.1, CCDS6257.1, CCDS47891.1, CCDS56544.1, CCDS75766.1, CCDS75767.1	8q22	2007-01-29	2005-01-20	2005-01-22	ENSG00000079102	ENSG00000079102		"Zinc fingers, MYND-type"	1535	protein-coding gene	gene with protein product		133435	"core-binding factor, runt domain, alpha subunit 2; translocated to, 1; cyclin D-related"	AML1T1, CBFA2T1		1391946, 9790752	Standard	NM_004349		Approved	CDR, ETO, MTG8, ZMYND2	uc011lgi.2	Q06455	OTTHUMG00000164066	ENST00000523629.1:c.1367T>A	chr8.hg19:g.92983058A>T	ENSP00000428543:p.Val456Glu	36.0	0.0		32.0	14.0	NM_001198679	B7Z4P4|E7EPN4|O14784|Q06456|Q14873|Q16239|Q16346|Q16347|Q6IBL1|Q6NXH1|Q7Z4J5|Q92479|Q9BRZ0	Missense_Mutation	SNP	ENST00000523629.1	hg19	CCDS6256.1	.	.	.	.	.	.	.	.	.	.	A	29.0	4.965618	0.92855	.	.	ENSG00000079102	ENST00000523629;ENST00000396218;ENST00000265814;ENST00000360348;ENST00000422361;ENST00000520724;ENST00000436581;ENST00000518844	T;T;T;T;T;T;T;T	0.40225	1.04;1.04;1.04;1.04;1.04;1.04;1.04;1.04	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.69251	0.3090	M	0.84433	2.695	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.91635	0.993;0.999;0.987;0.999	T	0.74827	-0.3532	10	0.87932	D	0	-15.437	16.2806	0.82678	1.0:0.0:0.0:0.0	.	467;419;456;429	E7EPN4;Q7Z4J5;Q06455;Q06455-2	.;.;MTG8_HUMAN;.	E	456;429;456;419;419;419;467;429	ENSP00000428543:V456E;ENSP00000379520:V429E;ENSP00000265814:V456E;ENSP00000353504:V419E;ENSP00000390137:V419E;ENSP00000428742:V419E;ENSP00000402257:V467E;ENSP00000430728:V429E	ENSP00000265814:V456E	V	-	2	0	RUNX1T1	93052234	1.000000	0.71417	1.000000	0.80357	0.865000	0.49528	9.339000	0.96797	2.248000	0.74166	0.533000	0.62120	GTG	.	.		0.547	RUNX1T1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377045.3	NM_004349, NM_175635		T	92983058	A	T	92983058	3	4	344	1	0	0	0	0	1	0	0	0	13762	159	6	4	455	4	RUNX1T1	8	92983058	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	581427	92983058	53380964	669	48032										
RUNX1T1	862	hgsc.bcm.edu	37	chr8	92998408	92998408	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcctagagtggctgctgctaCtgccgccacctttttttaag	10	12	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:92998408C>T	ENST00000523629.1	-	9	1677	c.1223G>A	c.(1222-1224)aGt>aAt	p.S408N	RUNX1T1_ENST00000518844.1_Missense_Mutation_p.S381N|RUNX1T1_ENST00000360348.2_Missense_Mutation_p.S371N|RUNX1T1_ENST00000396218.1_Missense_Mutation_p.S381N|RUNX1T1_ENST00000265814.3_Missense_Mutation_p.S408N|RUNX1T1_ENST00000520724.1_Missense_Mutation_p.S371N|RUNX1T1_ENST00000436581.2_Missense_Mutation_p.S419N|RUNX1T1_ENST00000422361.2_Missense_Mutation_p.S371N	NM_001198626.1|NM_001198630.1|NM_001198633.1|NM_175634.2	NP_001185555.1|NP_001185559.1|NP_001185562.1|NP_783552.1	Q06455	MTG8_HUMAN	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	408	Poly-Ser.				fat cell differentiation (GO:0045444)|generation of precursor metabolites and energy (GO:0006091)|regulation of DNA binding (GO:0051101)|transcription, DNA-templated (GO:0006351)	nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S419I(1)|p.S371I(1)|p.S408I(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(54)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	86			BRCA - Breast invasive adenocarcinoma(11;0.0141)			GCTGCTGCTACTGCCGCCACC	0.498																																					p.S467N		Atlas-SNP	.											RUNX1T1_ENST00000436581,NS,carcinoma,0,3	RUNX1T1	516	.	3	Substitution - Missense(3)	lung(3)	c.G1400A						.						92	100	97					8																	92998408		2203	4300	6503	SO:0001583	missense	862	exon9			CTGCTACTGCCGC	D43638	CCDS6256.1, CCDS6257.1, CCDS47891.1, CCDS56544.1, CCDS75766.1, CCDS75767.1	8q22	2007-01-29	2005-01-20	2005-01-22	ENSG00000079102	ENSG00000079102		"Zinc fingers, MYND-type"	1535	protein-coding gene	gene with protein product		133435	"core-binding factor, runt domain, alpha subunit 2; translocated to, 1; cyclin D-related"	AML1T1, CBFA2T1		1391946, 9790752	Standard	NM_004349		Approved	CDR, ETO, MTG8, ZMYND2	uc011lgi.2	Q06455	OTTHUMG00000164066	ENST00000523629.1:c.1223G>A	chr8.hg19:g.92998408C>T	ENSP00000428543:p.Ser408Asn	88.0	0.0		73.0	27.0	NM_001198679	B7Z4P4|E7EPN4|O14784|Q06456|Q14873|Q16239|Q16346|Q16347|Q6IBL1|Q6NXH1|Q7Z4J5|Q92479|Q9BRZ0	Missense_Mutation	SNP	ENST00000523629.1	hg19	CCDS6256.1	.	.	.	.	.	.	.	.	.	.	C	12.23	1.876355	0.33162	.	.	ENSG00000079102	ENST00000523629;ENST00000396218;ENST00000265814;ENST00000360348;ENST00000422361;ENST00000520724;ENST00000436581;ENST00000518844	T;T;T;T;T;T;T;T	0.31510	1.5;1.49;1.5;1.49;1.49;1.49;1.5;1.49	5.44	5.44	0.79542	.	0.156586	0.56097	D	0.000028	T	0.25044	0.0608	L	0.44542	1.39	0.33826	D	0.62966	B;B;B	0.30793	0.295;0.088;0.27	B;B;B	0.26614	0.063;0.045;0.071	T	0.29336	-1.0015	10	0.19590	T	0.45	-1.156	13.5562	0.61761	0.0:0.926:0.0:0.074	.	419;408;381	E7EPN4;Q06455;Q06455-2	.;MTG8_HUMAN;.	N	408;381;408;371;371;371;419;381	ENSP00000428543:S408N;ENSP00000379520:S381N;ENSP00000265814:S408N;ENSP00000353504:S371N;ENSP00000390137:S371N;ENSP00000428742:S371N;ENSP00000402257:S419N;ENSP00000430728:S381N	ENSP00000265814:S408N	S	-	2	0	RUNX1T1	93067584	1.000000	0.71417	0.996000	0.52242	0.963000	0.63663	3.860000	0.55995	2.564000	0.86499	0.655000	0.94253	AGT	.	.		0.498	RUNX1T1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377045.3	NM_004349, NM_175635		T	92998408	C	T	92998408	3	4	344	1	0	0	0	0	1	0	0	0	13762	565	20	3	607	3	RUNX1T1	8	92998408	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	15350	92998408	53365614	670	48033										
TMEM67	91147	hgsc.bcm.edu	37	chr8	94798504	94798504	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcattttcttagtggatgcaGtaagtggacgagaaaatgac	12	5	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:94798504G>A	ENST00000453321.3	+	13	1400	c.1342G>A	c.(1342-1344)Gta>Ata	p.V448I	TMEM67_ENST00000409623.3_Missense_Mutation_p.V367I	NM_153704.5	NP_714915.3	Q5HYA8	MKS3_HUMAN	transmembrane protein 67	448					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of centrosome duplication (GO:0010826)	centrosome (GO:0005813)|ciliary membrane (GO:0060170)|cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)	filamin binding (GO:0031005)|unfolded protein binding (GO:0051082)			breast(3)|endometrium(8)|kidney(5)|large_intestine(4)|liver(2)|lung(15)|ovary(2)|skin(1)|urinary_tract(1)	41	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.00896)			AGTGGATGCAGTAAGTGGACG	0.343																																					p.V448I		Atlas-SNP	.											.	TMEM67	187	.	0			c.G1342A						.						66	68	67					8																	94798504		2203	4300	6503	SO:0001583	missense	91147	exon13			GATGCAGTAAGTG	BX648768	CCDS6258.2, CCDS47893.1	8q22.1	2014-09-17			ENSG00000164953	ENSG00000164953			28396	protein-coding gene	gene with protein product	"Meckelin"	609884	"Meckel syndrome, type 3"	MKS3		12384791, 16415887, 19508969	Standard	NM_153704		Approved	MGC26979, JBTS6, NPHP11	uc011lgk.2	Q5HYA8	OTTHUMG00000153119	ENST00000453321.3:c.1342G>A	chr8.hg19:g.94798504G>A	ENSP00000389998:p.Val448Ile	51.0	0.0		55.0	20.0	NM_153704	B3KRU5|B3KT47|G5E9H2|Q3ZCX3|Q7Z5T8|Q8IZ06	Missense_Mutation	SNP	ENST00000453321.3	hg19	CCDS6258.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.821|9.821	1.185842|1.185842	0.21870|0.21870	.|.	.|.	ENSG00000164953|ENSG00000164953	ENST00000520680|ENST00000452276;ENST00000453321;ENST00000409623;ENST00000453906	.|D;D;D;D	.|0.97114	.|-4.25;-4.25;-4.25;-4.25	5.7|5.7	0.111|0.111	0.14619|0.14619	.|.	.|0.413864	.|0.24676	.|N	.|0.036507	D|D	0.85004|0.85004	0.5598|0.5598	N|N	0.02286|0.02286	-0.61|-0.61	0.28748|0.28748	N|N	0.9016|0.9016	.|B;B;B	.|0.10296	.|0.001;0.003;0.002	.|B;B;B	.|0.10450	.|0.003;0.005;0.002	T|T	0.76830|0.76830	-0.2814|-0.2814	5|10	.|0.11485	.|T	.|0.65	-5.3407|-5.3407	1.1234|1.1234	0.01729|0.01729	0.2481:0.3592:0.1957:0.197|0.2481:0.3592:0.1957:0.197	.|.	.|448;367;367	.|Q5HYA8;B3KRU5;G5E9H2	.|MKS3_HUMAN;.;.	N|I	55|345;448;367;154	.|ENSP00000388671:V345I;ENSP00000389998:V448I;ENSP00000386966:V367I;ENSP00000403035:V154I	.|ENSP00000314488:V438I	S|V	+|+	2|1	0|0	TMEM67|TMEM67	94867680|94867680	0.244000|0.244000	0.23889|0.23889	0.998000|0.998000	0.56505|0.56505	0.991000|0.991000	0.79684|0.79684	0.220000|0.220000	0.17660|0.17660	0.343000|0.343000	0.23821|0.23821	-0.150000|-0.150000	0.13652|0.13652	AGT|GTA	.	.		0.343	TMEM67-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329641.2	NM_153704		A	94798504	G	A	94798504	3	1	344	1	0	0	0	0	1	0	0	0	16211	1029	36	3	1530	3	TMEM67	8	94798504	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1800096	94798504	51565518	671	48034										
KIAA1429	25962	hgsc.bcm.edu	37	chr8	95501074	95501074	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tctagaagcacggtcccgagGacttgggcggtaacctgtaa	13	10	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:95501074G>T	ENST00000297591.5	-	24	5374	c.5299C>A	c.(5299-5301)Cct>Act	p.P1767T	KIAA1429_ENST00000437199.1_3'UTR	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	1767					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			CGGTCCCGAGGACTTGGGCGG	0.463																																					p.P1767T		Atlas-SNP	.											.	KIAA1429	176	.	0			c.C5299A						.						96	86	90					8																	95501074		2203	4300	6503	SO:0001583	missense	25962	exon24			CCCGAGGACTTGG	AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 121"					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.5299C>A	chr8.hg19:g.95501074G>T	ENSP00000297591:p.Pro1767Thr	109.0	0.0		66.0	35.0	NM_015496	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Missense_Mutation	SNP	ENST00000297591.5	hg19	CCDS34923.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.501851	0.85176	.	.	ENSG00000164944	ENST00000297591	T	0.46451	0.87	5.71	5.71	0.89125	.	0.105837	0.64402	D	0.000004	T	0.54319	0.1851	N	0.24115	0.695	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.58352	-0.7651	10	0.87932	D	0	-15.5659	19.8632	0.96793	0.0:0.0:1.0:0.0	.	1767	Q69YN4	VIR_HUMAN	T	1767	ENSP00000297591:P1767T	ENSP00000297591:P1767T	P	-	1	0	KIAA1429	95570250	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.802000	0.85969	2.699000	0.92147	0.655000	0.94253	CCT	.	.		0.463	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496		T	95501074	G	T	95501074	3	4	344	1	0	0	0	0	1	0	0	0	8240	1174	41	3	143	3	KIAA1429	8	95501074	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	702570	95501074	50862948	672	48035										
CCNE2	9134	hgsc.bcm.edu	37	chr8	95906153	95906153	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gatgtttcttggtgacctccTctcttctttttttgacatcc	6	11	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:95906153T>A	ENST00000520509.1	-	4	383	c.131A>T	c.(130-132)gAg>gTg	p.E44V	CCNE2_ENST00000308108.4_Missense_Mutation_p.E44V|CCNE2_ENST00000523476.1_5'Flank|CCNE2_ENST00000396133.3_Missense_Mutation_p.E44V|NDUFAF6_ENST00000396113.1_5'Flank			O96020	CCNE2_HUMAN	cyclin E2	44					cell cycle checkpoint (GO:0000075)|cell division (GO:0051301)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			cervix(1)|endometrium(2)|large_intestine(3)|lung(4)|prostate(1)	11	Breast(36;8.75e-07)					GGTGACCTCCTCTCTTCTTTT	0.403																																					p.E44V		Atlas-SNP	.											.	CCNE2	29	.	0			c.A131T						.						137	140	139					8																	95906153		2203	4300	6503	SO:0001583	missense	9134	exon4			ACCTCCTCTCTTC	AF091433	CCDS6264.1	8q22.1	2005-10-18			ENSG00000175305	ENSG00000175305			1590	protein-coding gene	gene with protein product		603775				9840927, 9840943	Standard	NM_057749		Approved	CYCE2	uc003yhc.3	O96020	OTTHUMG00000164696	ENST00000520509.1:c.131A>T	chr8.hg19:g.95906153T>A	ENSP00000429089:p.Glu44Val	151.0	0.0		118.0	46.0	NM_057749	O95439	Missense_Mutation	SNP	ENST00000520509.1	hg19	CCDS6264.1	.	.	.	.	.	.	.	.	.	.	T	14.97	2.695230	0.48202	.	.	ENSG00000175305	ENST00000520509;ENST00000308108;ENST00000396133	T;T;T	0.33438	1.84;1.84;1.41	5.29	5.29	0.74685	.	0.426202	0.25114	N	0.033038	T	0.31606	0.0802	L	0.58101	1.795	0.31503	N	0.664503	B;B	0.14012	0.009;0.001	B;B	0.09377	0.004;0.001	T	0.28299	-1.0048	10	0.37606	T	0.19	.	13.7999	0.63192	0.0:0.0:0.0:1.0	.	44;44	Q8WUE3;O96020	.;CCNE2_HUMAN	V	44	ENSP00000429089:E44V;ENSP00000309181:E44V;ENSP00000379437:E44V	ENSP00000309181:E44V	E	-	2	0	CCNE2	95975329	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.613000	0.54152	2.001000	0.58596	0.459000	0.35465	GAG	.	.		0.403	CCNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379808.1	NM_057749, NM_004702		A	95906153	T	A	95906153	3	1	344	1	0	0	0	0	1	0	0	0	2923	1551	54	4	1119	4	CCNE2	8	95906153	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	405079	95906153	50457869	673	48036										
RNF19A	25897	hgsc.bcm.edu	37	chr8	101287279	101287279	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtcgagcagcatcacaggtcTggttggggtgccaaatctgt	14	9	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:101287279T>A	ENST00000519449.1	-	4	1101	c.785A>T	c.(784-786)cAg>cTg	p.Q262L	RNF19A_ENST00000341084.2_Missense_Mutation_p.Q262L	NM_001280539.1|NM_015435.3	NP_001267468.1|NP_056250.3	Q9NV58	RN19A_HUMAN	ring finger protein 19A, RBR E3 ubiquitin protein ligase	262					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	30	all_cancers(14;3.5e-05)|all_epithelial(15;8.91e-08)|Lung NSC(17;0.000615)|all_lung(17;0.00166)		Epithelial(11;3.06e-11)|all cancers(13;5.78e-09)|OV - Ovarian serous cystadenocarcinoma(57;2.24e-05)|STAD - Stomach adenocarcinoma(118;0.0525)			ATCACAGGTCTGGTTGGGGTG	0.473																																					p.Q262L		Atlas-SNP	.											.	RNF19A	67	.	0			c.A785T						.						101	97	98					8																	101287279		2203	4300	6503	SO:0001583	missense	25897	exon4			CAGGTCTGGTTGG	AB029316	CCDS6286.1	8q22	2013-10-03	2013-10-03	2007-08-20		ENSG00000034677		"RING-type (C3HC4) zinc fingers"	13432	protein-coding gene	gene with protein product		607119	"ring finger protein 19", "ring finger protein 19A", "ring finger protein 19A, E3 ubiquitin protein ligase"	RNF19		11237715, 10976766	Standard	NM_183419		Approved	dorfin, DKFZp566B1346	uc003yjj.1	Q9NV58		ENST00000519449.1:c.785A>T	chr8.hg19:g.101287279T>A	ENSP00000428968:p.Gln262Leu	128.0	0.0		112.0	55.0	NM_015435	A3KCU9|Q52LG1|Q9H5H9|Q9H8M8|Q9UFG0|Q9UFX6|Q9Y4Y1	Missense_Mutation	SNP	ENST00000519449.1	hg19	CCDS6286.1	.	.	.	.	.	.	.	.	.	.	T	28.1	4.892944	0.91889	.	.	ENSG00000034677	ENST00000519449;ENST00000341084	T;T	0.61510	0.1;0.1	5.54	5.54	0.83059	Zinc finger, C6HC-type (2);	0.000000	0.85682	D	0.000000	T	0.72195	0.3430	L	0.60067	1.865	0.80722	D	1	D	0.69078	0.997	D	0.80764	0.994	T	0.72343	-0.4322	10	0.46703	T	0.11	.	15.5127	0.75795	0.0:0.0:0.0:1.0	.	262	Q9NV58	RN19A_HUMAN	L	262	ENSP00000428968:Q262L;ENSP00000342667:Q262L	ENSP00000342667:Q262L	Q	-	2	0	RNF19A	101356455	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.868000	0.87116	2.323000	0.78572	0.528000	0.53228	CAG	.	.		0.473	RNF19A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380004.1	NM_015435		A	101287279	T	A	101287279	3	1	344	1	0	0	0	0	1	0	0	0	13485	1580	55	4	1763	4	RNF19A	8	101287279	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	5381126	101287279	45076743	674	48037										
GRHL2	79977	hgsc.bcm.edu	37	chr8	102611327	102611327	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tacgattggaaacattgaagAgattgcatataatgctgttt	9	4	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:102611327A>G	ENST00000251808.3	+	8	1384	c.1046A>G	c.(1045-1047)gAg>gGg	p.E349G	GRHL2_ENST00000395927.1_Missense_Mutation_p.E333G	NM_024915.3	NP_079191.2	Q6ISB3	GRHL2_HUMAN	grainyhead-like 2 (Drosophila)	349					brain development (GO:0007420)|camera-type eye development (GO:0043010)|cardiac ventricle morphogenesis (GO:0003208)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digit morphogenesis (GO:0042733)|face development (GO:0060324)|in utero embryonic development (GO:0001701)|lung lobe morphogenesis (GO:0060463)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	all_cancers(14;4.39e-08)|all_epithelial(15;4.09e-10)|Lung NSC(17;7.11e-06)|all_lung(17;1.44e-05)		Epithelial(11;5.81e-09)|all cancers(13;3.81e-07)|OV - Ovarian serous cystadenocarcinoma(57;0.000213)			AACATTGAAGAGATTGCATAT	0.378																																					p.E349G		Atlas-SNP	.											.	GRHL2	68	.	0			c.A1046G						.						123	113	116					8																	102611327		2203	4300	6503	SO:0001583	missense	79977	exon8			TTGAAGAGATTGC	AK023844	CCDS34931.1	8q22.3	2008-02-05	2005-07-11	2005-07-11	ENSG00000083307	ENSG00000083307			2799	protein-coding gene	gene with protein product		608576	"deafness, autosomal dominant 28", "transcription factor CP2-like 3"	DFNA28, TFCP2L3		12393799	Standard	NM_024915		Approved	FLJ13782, BOM	uc010mbu.3	Q6ISB3	OTTHUMG00000149915	ENST00000251808.3:c.1046A>G	chr8.hg19:g.102611327A>G	ENSP00000251808:p.Glu349Gly	69.0	0.0		71.0	29.0	NM_024915	A1L303|Q6NT03|Q9H8B8	Missense_Mutation	SNP	ENST00000251808.3	hg19	CCDS34931.1	.	.	.	.	.	.	.	.	.	.	A	30	5.052843	0.93793	.	.	ENSG00000083307	ENST00000251808;ENST00000395927;ENST00000395928	T;T	0.19532	2.14;2.14	5.73	5.73	0.89815	CP2 transcription factor (1);	0.000000	0.85682	D	0.000000	T	0.53110	0.1776	M	0.86502	2.82	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.59568	-0.7430	10	0.56958	D	0.05	-40.941	16.3123	0.82883	1.0:0.0:0.0:0.0	.	349	Q6ISB3	GRHL2_HUMAN	G	349;333;349	ENSP00000251808:E349G;ENSP00000379260:E333G	ENSP00000251808:E349G	E	+	2	0	GRHL2	102680503	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	9.204000	0.95041	2.308000	0.77769	0.533000	0.62120	GAG	.	.		0.378	GRHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313882.1	NM_024915		G	102611327	A	G	102611327	3	3	344	1	0	0	0	0	1	0	0	0	6773	304	11	2	1076	2	GRHL2	8	102611327	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1324048	102611327	43752695	675	48038										
RIMS2	9699	hgsc.bcm.edu	37	chr8	104924293	104924293	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aatgtcagcaccctgtaaccTggcaaccatctaaagatgga	8	11	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:104924293T>G	ENST00000436393.2	+	4	1280	c.1039T>G	c.(1039-1041)Tgg>Ggg	p.W347G	RIMS2_ENST00000262231.10_Missense_Mutation_p.W424G|RIMS2_ENST00000406091.3_Missense_Mutation_p.W569G|RIMS2_ENST00000507740.1_Missense_Mutation_p.W377G			Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	647					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			CCCTGTAACCTGGCAACCATC	0.323										HNSCC(12;0.0054)																											p.W569G		Atlas-SNP	.											.	RIMS2	1357	.	0			c.T1705G						.						104	98	100					8																	104924293		1818	4087	5905	SO:0001583	missense	9699	exon6			GTAACCTGGCAAC	AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"RAB3 interacting protein 3"	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000436393.2:c.1039T>G	chr8.hg19:g.104924293T>G	ENSP00000390665:p.Trp347Gly	53.0	0.0		57.0	26.0	NM_001100117	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Missense_Mutation	SNP	ENST00000436393.2	hg19		.	.	.	.	.	.	.	.	.	.	T	17.61	3.432138	0.62844	.	.	ENSG00000176406	ENST00000504942;ENST00000329869;ENST00000406091;ENST00000402998;ENST00000515551;ENST00000262231;ENST00000507740;ENST00000408894;ENST00000436393	T;T;T;T;T;T;T	0.28666	1.6;2.06;1.93;1.92;1.83;1.72;2.04	5.92	4.77	0.60923	PDZ/DHR/GLGF (1);	.	.	.	.	T	0.51346	0.1669	M	0.62088	1.915	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.995;1.0;0.999;0.999	D;D;D;D;D	0.91635	0.999;0.996;0.999;0.998;0.998	T	0.52888	-0.8515	9	0.87932	D	0	.	11.905	0.52705	0.0:0.0675:0.0:0.9325	.	647;347;424;377;569	Q9UQ26;D6RA03;Q9UQ26-1;Q9UQ26-3;F8WD47	RIMS2_HUMAN;.;.;.;.	G	569;600;569;647;377;424;377;377;347	ENSP00000427018:W569G;ENSP00000384892:W569G;ENSP00000425205:W377G;ENSP00000262231:W424G;ENSP00000423559:W377G;ENSP00000386228:W377G;ENSP00000390665:W347G	ENSP00000262231:W424G	W	+	1	0	RIMS2	104993469	1.000000	0.71417	0.998000	0.56505	0.884000	0.51177	8.040000	0.89188	1.084000	0.41184	-0.256000	0.11100	TGG	.	.		0.323	RIMS2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000367217.1	NM_001100117		G	104924293	T	G	104924293	3	3	344	1	0	0	0	0	1	0	0	0	13383	1580	55	5	1853	5	RIMS2	8	104924293	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2312966	104924293	41439729	676	48039										
ZFPM2	23414	hgsc.bcm.edu	37	chr8	106813460	106813461	+	Missense_Mutation	DNP	CT	CT	AC													0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agttattgcagcaccaggagCtccatgtccctagcggcaaa							TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C|T	C|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:106813460_106813461CT>AC	ENST00000407775.2	+	8	1400_1401	c.1150_1151CT>AC	c.(1150-1152)CTc>ACc	p.L384T	ZFPM2_ENST00000517361.1_Missense_Mutation_p.L252T|ZFPM2_ENST00000520492.1_Missense_Mutation_p.L252T|RP11-152P17.2_ENST00000518932.1_RNA|RP11-152P17.2_ENST00000520433.1_RNA|RP11-152P17.2_ENST00000524045.2_RNA|RP11-152P17.2_ENST00000520594.1_RNA|ZFPM2_ENST00000378472.4_Missense_Mutation_p.L115T|RP11-152P17.2_ENST00000509144.2_RNA|ZFPM2_ENST00000522296.1_3'UTR|RP11-152P17.2_ENST00000521622.1_RNA	NM_012082.3	NP_036214.2	Q8WW38	FOG2_HUMAN	zinc finger protein, FOG family member 2	384					blood coagulation (GO:0007596)|embryonic organ development (GO:0048568)|gonadal mesoderm development (GO:0007506)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of female gonad development (GO:2000195)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(4)|breast(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(11)|liver(2)|lung(48)|ovary(4)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	99			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			GCACCAGGAGCTCCATGTCCCT	0.51																																					p.L384I|p.L384P		Atlas-SNP	.											.	ZFPM2	219	.	0			c.C1150A|c.T1151C						.																																			SO:0001583	missense	23414	exon8			CAGGAGCTCCATG|AGGAGCTCCATGT	AF119334	CCDS47908.1	8q23	2013-01-10	2012-11-27		ENSG00000169946	ENSG00000169946		"Zinc fingers, C2H2-type", "Zinc fingers, C2HC-type containing"	16700	protein-coding gene	gene with protein product		603693	"zinc finger protein, multitype 2"			9927675, 10438528	Standard	NM_012082		Approved	FOG2, hFOG-2, ZNF89B, ZC2HC11B	uc003ymd.3	Q8WW38	OTTHUMG00000164818	Exception_encountered	chr8.hg19:g.106813460_106813461delinsAC	ENSP00000384179:p.Leu384Thr	137.0	0.0		106.0|105.0	48.0	NM_012082	Q32MA6|Q9NPL7|Q9NPS4|Q9UNI5	Missense_Mutation	SNP	ENST00000407775.2	hg19	CCDS47908.1																																																																																			.	.		0.51	ZFPM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380614.1			AC	106813461	CT	AC	106813460	3	1	344	1	0	0	0	0	1	0	0	0	17673	797	28	3	1180	3	ZFPM2	8	106813460	Missense_Mutation	DNP	CT	TCGA-UB-A7MB-01A-11D-A33Q-10	1889167	106813460	39550562	677	48040										
OXR1	55074	hgsc.bcm.edu	37	chr8	107691475	107691475	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	accctagacaagaaagatggAagacgaatgtcttttcagaa	9	7	2	5			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:107691475A>G	ENST00000442977.2	+	3	360	c.261A>G	c.(259-261)ggA>ggG	p.G87G	OXR1_ENST00000497705.1_Silent_p.G19G|OXR1_ENST00000517566.2_Silent_p.G86G|OXR1_ENST00000445937.1_Silent_p.G86G|OXR1_ENST00000312046.6_Silent_p.G79G|OXR1_ENST00000452423.2_5'UTR|OXR1_ENST00000531443.1_Silent_p.G86G	NM_001198532.1	NP_001185461.1	Q8N573	OXR1_HUMAN	oxidation resistance 1	87					adult walking behavior (GO:0007628)|cellular response to hydroperoxide (GO:0071447)|negative regulation of neuron apoptotic process (GO:0043524)|response to oxidative stress (GO:0006979)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)	oxidoreductase activity (GO:0016491)			NS(2)|breast(2)|endometrium(2)|large_intestine(9)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	31			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)			AGAAAGATGGAAGACGAATGT	0.338																																					p.G87G		Atlas-SNP	.											.	OXR1	190	.	0			c.A261G						.						91	95	93					8																	107691475		2203	4300	6503	SO:0001819	synonymous_variant	55074	exon3			AGATGGAAGACGA	AF309387	CCDS6304.2, CCDS47909.1, CCDS56547.1, CCDS56548.1, CCDS56549.1, CCDS56550.1	8q23	2013-03-14			ENSG00000164830	ENSG00000164830			15822	protein-coding gene	gene with protein product	"TBC/LysM-associated domain containing 3"	605609				11114193	Standard	NM_181354		Approved	TLDC3	uc011lht.2	Q8N573	OTTHUMG00000167682	ENST00000442977.2:c.261A>G	chr8.hg19:g.107691475A>G		184.0	0.0		137.0	60.0	NM_001198532	A6NK11|A8KA34|B3KXL1|B7Z402|B7Z8N5|D3HIS6|Q3LIB5|Q6ZVK9|Q8N8V0|Q9H266|Q9NWC7	Silent	SNP	ENST00000442977.2	hg19	CCDS56548.1																																																																																			.	.		0.338	OXR1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_181354		G	107691475	A	G	107691475	2	3	344	1	0	0	0	0	0	0	0	1	11343	233	9	2		2	OXR1	8	107691475	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	878015	107691475	38672547	678	48041										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113237150	113237150	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	catcctgtatactgtgttttAggtgcagtcctgttgatgag	11	7	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:113237150A>T	ENST00000297405.5	-	71	11218	c.10974T>A	c.(10972-10974)ccT>ccA	p.P3658P	CSMD3_ENST00000455883.2_Silent_p.P3489P|CSMD3_ENST00000343508.3_Silent_p.P3618P|CSMD3_ENST00000352409.3_Silent_p.P3588P	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3658						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.P3618P(1)|p.P3658P(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						ACTGTGTTTTAGGTGCAGTCC	0.393										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.P3658P		Atlas-SNP	.											CSMD3_ENST00000343508,NS,carcinoma,0,2	CSMD3	2325	.	2	Substitution - coding silent(2)	lung(2)	c.T10974A						.						279	256	264					8																	113237150		2203	4300	6503	SO:0001819	synonymous_variant	114788	exon71			TGTTTTAGGTGCA	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.10974T>A	chr8.hg19:g.113237150A>T		105.0	0.0		102.0	32.0	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	hg19	CCDS6315.1																																																																																			.	.		0.393	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	113237150	A	T	113237150	2	4	344	1	0	0	0	0	0	0	0	1	3948	407	15	4		4	CSMD3	8	113237150	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	5545675	113237150	33126872	679	48042										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113702110	113702110	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tactcacagatacagatgggTatgtttgcagaccattggtt	10	7	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:113702110T>A	ENST00000297405.5	-	14	2386	c.2142A>T	c.(2140-2142)atA>atT	p.I714I	CSMD3_ENST00000455883.2_Silent_p.I610I|CSMD3_ENST00000343508.3_Silent_p.I674I|CSMD3_ENST00000352409.3_Silent_p.I714I	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	714	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TACAGATGGGTATGTTTGCAG	0.368										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.I714I		Atlas-SNP	.											.	CSMD3	2325	.	0			c.A2142T						.						135	131	132					8																	113702110		2203	4300	6503	SO:0001819	synonymous_variant	114788	exon14			GATGGGTATGTTT	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.2142A>T	chr8.hg19:g.113702110T>A		99.0	0.0		89.0	43.0	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	hg19	CCDS6315.1																																																																																			.	.		0.368	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	113702110	T	A	113702110	2	1	344	1	0	0	0	0	0	0	0	1	3948	1628	57	4		4	CSMD3	8	113702110	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	464960	113702110	32661912	680	48043										
TNFRSF11B	4982	hgsc.bcm.edu	37	chr8	119936998	119936998	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cgctgttttcacagaggtcaAtatctgcataaagcaaaagc	8	9	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:119936998A>T	ENST00000297350.4	-	5	1199	c.821T>A	c.(820-822)aTt>aAt	p.I274N		NM_002546.3	NP_002537.3	O00300	TR11B_HUMAN	tumor necrosis factor receptor superfamily, member 11b	274	Death 2.				apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|negative regulation of bone resorption (GO:0045779)|negative regulation of odontogenesis of dentin-containing tooth (GO:0042489)|response to arsenic-containing substance (GO:0046685)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to magnesium ion (GO:0032026)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|receptor activity (GO:0004872)			breast(1)|central_nervous_system(3)|endometrium(4)|large_intestine(6)|lung(7)|prostate(3)|skin(1)	25	all_cancers(13;3.71e-26)|Lung NSC(37;1.69e-07)|Ovarian(258;0.018)|all_neural(195;0.0592)|Hepatocellular(40;0.234)		STAD - Stomach adenocarcinoma(47;0.00193)			ACAGAGGTCAATATCTGCATA	0.433																																					p.I274N		Atlas-SNP	.											.	TNFRSF11B	87	.	0			c.T821A						.						64	57	59					8																	119936998		2203	4300	6503	SO:0001583	missense	4982	exon5			AGGTCAATATCTG	U94332	CCDS6326.1	8q24	2008-07-31	2008-07-31		ENSG00000164761	ENSG00000164761		"Tumor necrosis factor receptor superfamily"	11909	protein-coding gene	gene with protein product		602643	"osteoprotegerin"	OPG		9108485	Standard	NM_002546		Approved	OCIF, TR1	uc003yon.4	O00300	OTTHUMG00000164969	ENST00000297350.4:c.821T>A	chr8.hg19:g.119936998A>T	ENSP00000297350:p.Ile274Asn	80.0	0.0		58.0	31.0	NM_002546	B2R9A8|O60236|Q53FX6|Q9UHP4	Missense_Mutation	SNP	ENST00000297350.4	hg19	CCDS6326.1	.	.	.	.	.	.	.	.	.	.	A	18.26	3.584972	0.66105	.	.	ENSG00000164761	ENST00000297350	D	0.93659	-3.26	5.74	5.74	0.90152	DEATH-like (1);	0.473189	0.25063	N	0.033432	D	0.92169	0.7517	M	0.63428	1.95	0.47778	D	0.99951	P	0.44195	0.828	B	0.40782	0.34	D	0.91716	0.5385	9	.	.	.	-18.0591	16.3426	0.83092	1.0:0.0:0.0:0.0	.	274	O00300	TR11B_HUMAN	N	274	ENSP00000297350:I274N	.	I	-	2	0	TNFRSF11B	120006179	1.000000	0.71417	1.000000	0.80357	0.780000	0.44128	7.252000	0.78309	2.317000	0.78254	0.460000	0.39030	ATT	.	.		0.433	TNFRSF11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381220.1			T	119936998	A	T	119936998	3	4	344	1	0	0	0	0	1	0	0	0	16300	101	4	4	388	4	TNFRSF11B	8	119936998	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	6234888	119936998	26427024	681	48044										
ENPP2	5168	hgsc.bcm.edu	37	chr8	120594814	120594814	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaacttccatgggtcccattAttaggagctggcttcaatcc	8	11	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:120594814A>G	ENST00000075322.6	-	18	1630	c.1572T>C	c.(1570-1572)aaT>aaC	p.N524N	ENPP2_ENST00000259486.6_Silent_p.N576N|ENPP2_ENST00000522167.1_Silent_p.N163N|ENPP2_ENST00000427067.2_Silent_p.N520N|ENPP2_ENST00000522826.1_Silent_p.N524N	NM_001040092.2	NP_001035181.1	Q13822	ENPP2_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 2	524					cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylcholine catabolic process (GO:0034638)|phospholipid catabolic process (GO:0009395)|regulation of cell migration (GO:0030334)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alkylglycerophosphoethanolamine phosphodiesterase activity (GO:0047391)|calcium ion binding (GO:0005509)|hydrolase activity (GO:0016787)|lysophospholipase activity (GO:0004622)|nucleic acid binding (GO:0003676)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(30)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)	69	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			GGGTCCCATTATTAGGAGCTG	0.408																																					p.N576N	Melanoma(20;305 879 2501 4818 31020)	Atlas-SNP	.											.	ENPP2	254	.	0			c.T1728C						.						137	143	141					8																	120594814		2203	4300	6503	SO:0001819	synonymous_variant	5168	exon19			CCCATTATTAGGA	D45421	CCDS6329.1, CCDS34936.1, CCDS47914.1	8q24.12	2014-04-09	2008-08-01		ENSG00000136960	ENSG00000136960	3.1.4.1, 3.6.1.9		3357	protein-coding gene	gene with protein product	"autotaxin"	601060		PDNP2		8586446	Standard	NM_001040092		Approved	ATX, PD-IALPHA	uc003yos.2	Q13822	OTTHUMG00000164995	ENST00000075322.6:c.1572T>C	chr8.hg19:g.120594814A>G		63.0	0.0		89.0	34.0	NM_006209	A8UHA1|E9PHP7|Q13827|Q14555|Q15117|Q9UCQ8|Q9UCR0|Q9UCR1|Q9UCR2|Q9UCR3|Q9UCR4	Silent	SNP	ENST00000075322.6	hg19	CCDS34936.1																																																																																			.	.		0.408	ENPP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000381390.1			G	120594814	A	G	120594814	2	3	344	1	0	0	0	0	0	0	0	1	5132	446	16	2		2	ENPP2	8	120594814	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	657816	120594814	25769208	682	48045										
KLHL38	340359	hgsc.bcm.edu	37	chr8	124664565	124664565	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggtcatgcttgatccaaaccAtgagggcctcaaacaccttt	8	12	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:124664565A>G	ENST00000325995.7	-	1	625	c.602T>C	c.(601-603)aTg>aCg	p.M201T	CTD-2552K11.2_ENST00000524355.1_RNA	NM_001081675.2	NP_001075144.2	Q2WGJ6	KLH38_HUMAN	kelch-like family member 38	201	BACK.									breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(16)|pancreas(1)|prostate(3)|stomach(1)	38						GATCCAAACCATGAGGGCCTC	0.562																																					p.M201T		Atlas-SNP	.											.	KLHL38	81	.	0			c.T602C						.						63	67	65					8																	124664565		2092	4203	6295	SO:0001583	missense	340359	exon1			CAAACCATGAGGG		CCDS43766.1	8q24.13	2013-02-22	2013-02-22		ENSG00000175946	ENSG00000175946		"Kelch-like", "BTB/POZ domain containing"	34435	protein-coding gene	gene with protein product			"kelch-like 38 (Drosophila)"				Standard	NM_001081675		Approved	C8ORFK36	uc003yqs.1	Q2WGJ6	OTTHUMG00000164983	ENST00000325995.7:c.602T>C	chr8.hg19:g.124664565A>G	ENSP00000321475:p.Met201Thr	88.0	0.0		80.0	36.0	NM_001081675	A0PK12	Missense_Mutation	SNP	ENST00000325995.7	hg19	CCDS43766.1	.	.	.	.	.	.	.	.	.	.	A	12.95	2.091757	0.36952	.	.	ENSG00000175946	ENST00000325995	T	0.69806	-0.43	5.84	5.84	0.93424	BTB/Kelch-associated (2);	0.082267	0.85682	D	0.000000	T	0.71576	0.3356	M	0.79805	2.47	0.41906	D	0.990442	P	0.35894	0.526	B	0.40636	0.335	T	0.75416	-0.3325	10	0.62326	D	0.03	.	12.0333	0.53410	0.9311:0.0:0.0689:0.0	.	201	Q2WGJ6	KLH38_HUMAN	T	201	ENSP00000321475:M201T	ENSP00000321475:M201T	M	-	2	0	KLHL38	124733746	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	7.473000	0.81007	2.234000	0.73211	0.459000	0.35465	ATG	.	.		0.562	KLHL38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381288.1			G	124664565	A	G	124664565	3	3	344	1	0	0	0	0	1	0	0	0	8399	217	8	2	1155	2	KLHL38	8	124664565	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	4069751	124664565	21699457	683	48046										
FER1L6	654463	hgsc.bcm.edu	37	chr8	124987506	124987506	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaaaaggtgatgtcttgaagAccagccctaaaacttctgac	9	9	2	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:124987506A>T	ENST00000522917.1	+	8	849	c.643A>T	c.(643-645)Acc>Tcc	p.T215S	FER1L6_ENST00000399018.1_Missense_Mutation_p.T215S	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	215						integral component of membrane (GO:0016021)				NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			TGTCTTGAAGACCAGCCCTAA	0.473																																					p.T215S		Atlas-SNP	.											.	FER1L6	268	.	0			c.A643T						.						126	123	124					8																	124987506		1965	4150	6115	SO:0001583	missense	654463	exon8			TTGAAGACCAGCC	AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"fer-1-like 6 (C. elegans)"				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.643A>T	chr8.hg19:g.124987506A>T	ENSP00000428280:p.Thr215Ser	323.0	0.0		216.0	95.0	NM_001039112		Missense_Mutation	SNP	ENST00000522917.1	hg19	CCDS43767.1	.	.	.	.	.	.	.	.	.	.	A	3.203	-0.163329	0.06502	.	.	ENSG00000214814	ENST00000522917;ENST00000399018	T;T	0.70869	-0.52;-0.52	5.46	-1.36	0.09085	C2 calcium/lipid-binding domain, CaLB (1);FerIin domain (1);	0.562931	0.17258	N	0.180883	T	0.44307	0.1287	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.09377	0.004	T	0.15492	-1.0435	10	0.36615	T	0.2	.	0.2357	0.00185	0.3099:0.2621:0.1921:0.2359	.	215	Q2WGJ9	FR1L6_HUMAN	S	215	ENSP00000428280:T215S;ENSP00000381982:T215S	ENSP00000381982:T215S	T	+	1	0	FER1L6	125056687	0.462000	0.25791	0.992000	0.48379	0.027000	0.11550	0.193000	0.17116	-0.119000	0.11830	-1.256000	0.01477	ACC	.	.		0.473	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112		T	124987506	A	T	124987506	3	4	344	1	0	0	0	0	1	0	0	0	5823	275	10	4	669	4	FER1L6	8	124987506	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	322941	124987506	21376516	684	48047										
FER1L6	654463	hgsc.bcm.edu	37	chr8	124998413	124998413	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccatcagctttgaagtttctAttggtaagtacagataagca	8	7	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:124998413A>G	ENST00000522917.1	+	12	1722	c.1516A>G	c.(1516-1518)Att>Gtt	p.I506V	FER1L6-AS1_ENST00000518567.1_RNA|FER1L6_ENST00000399018.1_Missense_Mutation_p.I506V	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	506						integral component of membrane (GO:0016021)				NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			TGAAGTTTCTATTGGTAAGTA	0.358																																					p.I506V		Atlas-SNP	.											.	FER1L6	268	.	0			c.A1516G						.						94	89	91					8																	124998413		1841	4097	5938	SO:0001583	missense	654463	exon12			GTTTCTATTGGTA	AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"fer-1-like 6 (C. elegans)"				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.1516A>G	chr8.hg19:g.124998413A>G	ENSP00000428280:p.Ile506Val	72.0	0.0		60.0	19.0	NM_001039112		Missense_Mutation	SNP	ENST00000522917.1	hg19	CCDS43767.1	.	.	.	.	.	.	.	.	.	.	A	8.759	0.923251	0.18056	.	.	ENSG00000214814	ENST00000522917;ENST00000399018	D;D	0.83914	-1.78;-1.78	5.47	0.662	0.17880	.	0.465278	0.18775	N	0.131510	T	0.63129	0.2485	N	0.11106	0.095	0.26714	N	0.970916	B	0.06786	0.001	B	0.06405	0.002	T	0.54470	-0.8289	10	0.51188	T	0.08	.	5.5828	0.17258	0.3729:0.1656:0.4615:0.0	.	506	Q2WGJ9	FR1L6_HUMAN	V	506	ENSP00000428280:I506V;ENSP00000381982:I506V	ENSP00000381982:I506V	I	+	1	0	FER1L6	125067594	0.013000	0.17824	0.998000	0.56505	0.329000	0.28539	0.266000	0.18534	0.396000	0.25283	-0.250000	0.11733	ATT	.	.		0.358	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112		G	124998413	A	G	124998413	3	3	344	1	0	0	0	0	1	0	0	0	5823	449	16	2	1558	2	FER1L6	8	124998413	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	10907	124998413	21365609	685	48048										
ASAP1	50807	hgsc.bcm.edu	37	chr8	131130809	131130809	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aattagtgcaagtaaatcccTggatttgatggcctcaagca	9	8	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:131130809T>A	ENST00000518721.1	-	19	1947	c.1720A>T	c.(1720-1722)Agg>Tgg	p.R574W	ASAP1_ENST00000357668.1_Missense_Mutation_p.R574W	NM_001247996.1|NM_018482.3	NP_001234925.1|NP_060952.2	Q9ULH1	ASAP1_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 1	574					cilium morphogenesis (GO:0060271)|regulation of ARF GTPase activity (GO:0032312)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|zinc ion binding (GO:0008270)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(22)|ovary(6)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	68						AGTAAATCCCTGGATTTGATG	0.408																																					p.R574W		Atlas-SNP	.											.	ASAP1	133	.	0			c.A1720T						.						122	112	115					8																	131130809		2203	4300	6503	SO:0001583	missense	50807	exon19			AATCCCTGGATTT	AB033075	CCDS6362.1, CCDS75788.1	8q24.1-q24.2	2013-01-11	2008-09-22	2008-09-22	ENSG00000153317	ENSG00000153317		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	2720	protein-coding gene	gene with protein product	"centaurin, beta 4"	605953	"development and differentiation enhancing factor 1"	DDEF1		9819391	Standard	NM_018482		Approved	PAP, KIAA1249, ZG14P, CENTB4	uc003yta.2	Q9ULH1	OTTHUMG00000164772	ENST00000518721.1:c.1720A>T	chr8.hg19:g.131130809T>A	ENSP00000429900:p.Arg574Trp	112.0	0.0		87.0	36.0	NM_018482	B2RNV3	Missense_Mutation	SNP	ENST00000518721.1	hg19	CCDS6362.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	23.4|23.4	4.409669|4.409669	0.83340|0.83340	.|.	.|.	ENSG00000153317|ENSG00000153317	ENST00000524124|ENST00000343135;ENST00000357668;ENST00000518721	.|T;T	.|0.07567	.|3.18;3.18	5.86|5.86	-3.51|-3.51	0.04696|0.04696	.|Ankyrin repeat-containing domain (1);	.|0.097526	.|0.64402	.|D	.|0.000003	T|T	0.18299|0.18299	0.0439|0.0439	M|M	0.73598|0.73598	2.24|2.24	0.58432|0.58432	D|D	0.999992|0.999992	.|D;D;D	.|0.65815	.|0.992;0.992;0.995	.|P;P;P	.|0.57502	.|0.668;0.668;0.822	T|T	0.00759|0.00759	-1.1578|-1.1578	5|10	.|0.87932	.|D	.|0	.|.	11.6756|11.6756	0.51427|0.51427	0.0:0.0606:0.552:0.3874|0.0:0.0606:0.552:0.3874	.|.	.|574;574;577	.|B2RNV3;Q9ULH1;Q9ULH1-2	.|.;ASAP1_HUMAN;.	L|W	394|577;574;574	.|ENSP00000350297:R574W;ENSP00000429900:R574W	.|ENSP00000344591:R577W	Q|R	-|-	2|1	0|2	ASAP1|ASAP1	131199991|131199991	1.000000|1.000000	0.71417|0.71417	0.948000|0.948000	0.38648|0.38648	0.989000|0.989000	0.77384|0.77384	1.346000|1.346000	0.33964|0.33964	-0.847000|-0.847000	0.04168|0.04168	-0.313000|-0.313000	0.08912|0.08912	CAG|AGG	.	.		0.408	ASAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380170.1	NM_018482		A	131130809	T	A	131130809	3	1	344	1	0	0	0	0	1	0	0	0	1010	1579	55	4	1717	4	ASAP1	8	131130809	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	6132396	131130809	15233213	686	48049										
TRAPPC9	83696	hgsc.bcm.edu	37	chr8	140898164	140898164	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcaggtgctccaggacgagcTggttcaggagtccttccaca	13	12	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:140898164T>G	ENST00000438773.2	-	21	3147	c.3014A>C	c.(3013-3015)cAg>cCg	p.Q1005P	TRAPPC9_ENST00000522504.1_5'UTR|TRAPPC9_ENST00000389328.4_Missense_Mutation_p.Q1103P|TRAPPC9_ENST00000389327.3_Missense_Mutation_p.Q996P	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	1005					cell differentiation (GO:0030154)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	47						CAGGACGAGCTGGTTCAGGAG	0.617																																					p.Q1103P		Atlas-SNP	.											.	TRAPPC9	114	.	0			c.A3308C						.						28	28	28					8																	140898164		2194	4290	6484	SO:0001583	missense	83696	exon21			ACGAGCTGGTTCA	BC006206	CCDS34946.1, CCDS55278.1	8q24.3	2010-10-22			ENSG00000167632	ENSG00000167632		"Trafficking protein particle complex"	30832	protein-coding gene	gene with protein product	"TRAPP 120 kDa subunit", "tularik gene 1"	611966				11572484	Standard	NM_031466		Approved	IKBKBBP, NIBP, KIAA1882, T1, TRS120, MRT13	uc003yvh.2	Q96Q05	OTTHUMG00000164187	ENST00000438773.2:c.3014A>C	chr8.hg19:g.140898164T>G	ENSP00000405060:p.Gln1005Pro	257.0	1.0		208.0	101.0	NM_031466	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Missense_Mutation	SNP	ENST00000438773.2	hg19	CCDS55278.1	.	.	.	.	.	.	.	.	.	.	T	16.17	3.046822	0.55110	.	.	ENSG00000167632	ENST00000389328;ENST00000389327;ENST00000438773	.	.	.	5.56	4.4	0.53042	.	0.000000	0.85682	D	0.000000	T	0.51805	0.1696	N	0.25890	0.77	0.58432	D	0.999997	B;D	0.65815	0.03;0.995	B;P	0.60541	0.034;0.876	T	0.42816	-0.9429	9	0.23891	T	0.37	.	9.6392	0.39828	0.0:0.0824:0.0:0.9176	.	1005;1103	Q96Q05;Q96Q05-2	TPPC9_HUMAN;.	P	1103;996;1005	.	ENSP00000373978:Q996P	Q	-	2	0	TRAPPC9	140967346	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.258000	0.65479	0.946000	0.37632	0.533000	0.62120	CAG	.	.		0.617	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466		G	140898164	T	G	140898164	3	3	344	1	0	0	0	0	1	0	0	0	16480	1580	55	5	444	5	TRAPPC9	8	140898164	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	9767355	140898164	5465858	687	48050										
DENND3	22898	hgsc.bcm.edu	37	chr8	142185462	142185462	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agctccgtcaagacaaacctAggcgttggcaagatcgccat	10	12	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:142185462A>T	ENST00000262585.2	+	14	2477	c.2199A>T	c.(2197-2199)ctA>ctT	p.L733L	DENND3_ENST00000424248.1_Silent_p.L681L|DENND3_ENST00000519811.1_Silent_p.L813L	NM_014957.2	NP_055772.2	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	733					cellular protein catabolic process (GO:0044257)|endosome to lysosome transport (GO:0008333)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(4)|stomach(2)|urinary_tract(1)	55	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)			AGACAAACCTAGGCGTTGGCA	0.517											OREG0019025	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L733L		Atlas-SNP	.											.	DENND3	127	.	0			c.A2199T						.						139	122	128					8																	142185462		2203	4300	6503	SO:0001819	synonymous_variant	22898	exon14			AAACCTAGGCGTT	AB020677	CCDS34947.1	8q24.3	2013-01-10				ENSG00000105339		"DENN/MADD domain containing", "WD repeat domain containing"	29134	protein-coding gene	gene with protein product						10048485	Standard	NM_014957		Approved	KIAA0870	uc003yvy.3	A2RUS2		ENST00000262585.2:c.2199A>T	chr8.hg19:g.142185462A>T		102.0	0.0	1669	76.0	32.0	NM_014957	B7ZM28|O94947|Q2TAM7|Q6ZMS6|Q96DK3	Silent	SNP	ENST00000262585.2	hg19	CCDS34947.1	.	.	.	.	.	.	.	.	.	.	A	0.978	-0.697952	0.03279	.	.	ENSG00000105339	ENST00000518668	.	.	.	4.94	-3.91	0.04168	.	.	.	.	.	T	0.47967	0.1474	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43798	-0.9369	4	.	.	.	-3.4575	6.0063	0.19549	0.2211:0.2251:0.0:0.5538	.	.	.	.	W	738	.	.	R	+	1	2	DENND3	142254644	0.000000	0.05858	0.031000	0.17742	0.103000	0.19146	-1.513000	0.02256	-0.661000	0.05345	-0.619000	0.04042	AGG	.	.		0.517	DENND3-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_014957		T	142185462	A	T	142185462	2	4	344	1	0	0	0	0	0	0	0	1	4434	407	15	4		4	DENND3	8	142185462	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1287298	142185462	4178560	688	48051										
DENND3	22898	hgsc.bcm.edu	37	chr8	142188201	142188201	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cagcaggcgctgaccaacgtCttgctgatggacgccgtcgt	13	13	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:142188201C>A	ENST00000262585.2	+	16	2780	c.2502C>A	c.(2500-2502)gtC>gtA	p.V834V	DENND3_ENST00000424248.1_Silent_p.V782V|DENND3_ENST00000518806.1_3'UTR|DENND3_ENST00000519811.1_Silent_p.V914V	NM_014957.2	NP_055772.2	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	834					cellular protein catabolic process (GO:0044257)|endosome to lysosome transport (GO:0008333)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(4)|stomach(2)|urinary_tract(1)	55	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)			TGACCAACGTCTTGCTGATGG	0.507																																					p.V834V		Atlas-SNP	.											.	DENND3	127	.	0			c.C2502A						.						76	73	74					8																	142188201		2203	4300	6503	SO:0001819	synonymous_variant	22898	exon16			CAACGTCTTGCTG	AB020677	CCDS34947.1	8q24.3	2013-01-10				ENSG00000105339		"DENN/MADD domain containing", "WD repeat domain containing"	29134	protein-coding gene	gene with protein product						10048485	Standard	NM_014957		Approved	KIAA0870	uc003yvy.3	A2RUS2		ENST00000262585.2:c.2502C>A	chr8.hg19:g.142188201C>A		51.0	0.0		38.0	25.0	NM_014957	B7ZM28|O94947|Q2TAM7|Q6ZMS6|Q96DK3	Silent	SNP	ENST00000262585.2	hg19	CCDS34947.1	.	.	.	.	.	.	.	.	.	.	C	4.741	0.137701	0.09032	.	.	ENSG00000105339	ENST00000518668	.	.	.	4.93	-4.7	0.03288	.	.	.	.	.	T	0.28632	0.0709	.	.	.	0.30804	N	0.739516	.	.	.	.	.	.	T	0.41431	-0.9509	4	.	.	.	-33.3407	6.1993	0.20567	0.0:0.2515:0.3478:0.4007	.	.	.	.	I	839	.	.	L	+	1	0	DENND3	142257383	0.000000	0.05858	0.020000	0.16555	0.494000	0.33585	-0.531000	0.06171	-0.803000	0.04415	-0.176000	0.13171	CTT	.	.		0.507	DENND3-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_014957		A	142188201	C	A	142188201	2	1	344	1	0	0	0	0	0	0	0	1	4434	900	32	3		3	DENND3	8	142188201	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	2739	142188201	4175821	689	48052										
TSNARE1	203062	hgsc.bcm.edu	37	chr8	143425368	143425368	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agccctcggagggcagggccTggcaagagaaggtcttggcc	17	11	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:143425368T>G	ENST00000307180.3	-	4	821	c.704A>C	c.(703-705)cAg>cCg	p.Q235P	TSNARE1_ENST00000520166.1_Missense_Mutation_p.Q235P|TSNARE1_ENST00000519651.1_Intron|TSNARE1_ENST00000524325.1_Missense_Mutation_p.Q235P	NM_145003.3	NP_659440.2	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1	235					intracellular protein transport (GO:0006886)|synaptic vesicle exocytosis (GO:0016079)	integral component of membrane (GO:0016021)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)			breast(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(6)|ovary(2)|stomach(2)|urinary_tract(1)	20	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					GGGCAGGGCCTGGCAAGAGAA	0.687																																					p.Q235P		Atlas-SNP	.											.	TSNARE1	59	.	0			c.A704C						.						18	19	19					8																	143425368		2172	4252	6424	SO:0001583	missense	203062	exon4			AGGGCCTGGCAAG			8q24.3	2005-08-18							26437	protein-coding gene	gene with protein product						14702039	Standard	XM_005250828		Approved	FLJ31164	uc003ywk.3	Q96NA8		ENST00000307180.3:c.704A>C	chr8.hg19:g.143425368T>G	ENSP00000303437:p.Gln235Pro	79.0	0.0		71.0	26.0	NM_145003	B7ZLB0|Q14D03	Missense_Mutation	SNP	ENST00000307180.3	hg19	CCDS6384.1	.	.	.	.	.	.	.	.	.	.	T	12.69	2.014735	0.35511	.	.	ENSG00000171045	ENST00000524325;ENST00000307180;ENST00000520166	T;T;T	0.13778	2.56;2.56;2.56	3.91	-0.372	0.12520	.	0.524577	0.13937	N	0.352477	T	0.11324	0.0276	L	0.51422	1.61	0.23168	N	0.998186	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.25813	-1.0121	10	0.87932	D	0	-0.7868	4.622	0.12460	0.0:0.1118:0.3867:0.5015	.	235;235;235	B7ZLB0;Q96NA8;A0AVG3	.;TSNA1_HUMAN;.	P	235	ENSP00000428763:Q235P;ENSP00000303437:Q235P;ENSP00000427770:Q235P	ENSP00000303437:Q235P	Q	-	2	0	TSNARE1	143423275	0.043000	0.20138	0.902000	0.35471	0.889000	0.51656	0.014000	0.13333	-0.267000	0.09325	0.491000	0.48974	CAG	.	.		0.687	TSNARE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_145003		G	143425368	T	G	143425368	3	3	344	1	0	0	0	0	1	0	0	0	16645	1580	55	5	877	5	TSNARE1	8	143425368	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1237167	143425368	2938654	690	48053										
FAM83H	286077	hgsc.bcm.edu	37	chr8	144808647	144808647	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gacgccgcgggctctcgggtTggccgttctcctgcggcact	15	15	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:144808647T>A	ENST00000388913.3	-	5	3109	c.2984A>T	c.(2983-2985)cAa>cTa	p.Q995L		NM_198488.3	NP_940890	Q6ZRV2	FA83H_HUMAN	family with sequence similarity 83, member H	995					biomineral tissue development (GO:0031214)					central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(12)|pancreas(1)|prostate(3)|urinary_tract(1)	21	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			GCTCTCGGGTTGGCCGTTCTC	0.701																																					p.Q995L		Atlas-SNP	.											.	FAM83H	68	.	0			c.A2984T						.						10	13	12					8																	144808647		1985	4132	6117	SO:0001583	missense	286077	exon5			TCGGGTTGGCCGT	AK127960	CCDS6410.2	8q24.3	2014-03-13			ENSG00000180921	ENSG00000180921			24797	protein-coding gene	gene with protein product		611927				18252228	Standard	NM_198488		Approved	FLJ46072	uc003yzk.3	Q6ZRV2	OTTHUMG00000133559	ENST00000388913.3:c.2984A>T	chr8.hg19:g.144808647T>A	ENSP00000373565:p.Gln995Leu	31.0	0.0		27.0	13.0	NM_198488	A0JLS2|Q8N4W0	Missense_Mutation	SNP	ENST00000388913.3	hg19	CCDS6410.2	.	.	.	.	.	.	.	.	.	.	t	12.83	2.056334	0.36277	.	.	ENSG00000180921	ENST00000388913	T	0.16073	2.37	5.01	2.66	0.31614	.	0.615150	0.14087	U	0.342286	T	0.13543	0.0328	L	0.32530	0.975	0.30941	N	0.725833	P	0.47409	0.895	B	0.42030	0.373	T	0.09058	-1.0692	10	0.62326	D	0.03	.	8.099	0.30846	0.0:0.1669:0.0:0.8331	.	995	Q6ZRV2	FA83H_HUMAN	L	995	ENSP00000373565:Q995L	ENSP00000373565:Q995L	Q	-	2	0	FAM83H	144880635	1.000000	0.71417	0.996000	0.52242	0.093000	0.18481	3.691000	0.54720	0.772000	0.33382	0.450000	0.29827	CAA	.	.		0.701	FAM83H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257632.2	NM_198488		A	144808647	T	A	144808647	3	1	344	1	0	0	0	0	1	0	0	0	5648	1812	63	4	559	4	FAM83H	8	144808647	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1383279	144808647	1555375	691	48054										
GPR172A	79581	hgsc.bcm.edu	37	chr8	145584307	145584307	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtgttctgtgggggctacctGatggcgctggcagtcctgag	17	9	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr8:145584307G>A	ENST00000532887.1	+	4	1642	c.1059G>A	c.(1057-1059)ctG>ctA	p.L353L	SLC52A2_ENST00000526752.1_Intron|SLC52A2_ENST00000530047.1_Silent_p.L353L|SLC52A2_ENST00000527078.1_Silent_p.L353L|SLC52A2_ENST00000540505.1_Silent_p.L265L|SLC52A2_ENST00000402965.1_Silent_p.L353L|FBXL6_ENST00000455319.2_5'Flank|SLC52A2_ENST00000329994.2_Silent_p.L353L|FBXL6_ENST00000331890.5_5'Flank			Q9HAB3	S52A2_HUMAN	solute carrier family 52 (riboflavin transporter), member 2	353					riboflavin transport (GO:0032218)	integral component of plasma membrane (GO:0005887)	riboflavin transporter activity (GO:0032217)|virus receptor activity (GO:0001618)									Gamma Hydroxybutyric Acid(DB01440)	GGGGCTACCTGATGGCGCTGG	0.697																																					p.L353L		Atlas-SNP	.											.	.	.	.	0			c.G1059A						.						59	67	64					8																	145584307		2203	4300	6503	SO:0001819	synonymous_variant	79581	exon4			CTACCTGATGGCG	AY070774	CCDS6423.1	8q24.3	2013-07-17	2013-07-17	2012-02-29		ENSG00000185803		"Solute carriers"	30224	protein-coding gene	gene with protein product		607882	"G protein-coupled receptor 172A"	GPR172A		12740431	Standard	NM_024531		Approved	FLJ11856, PAR1, GPCR41, D15Ertd747e, RFVT2, hRFT3	uc003zcd.2	Q9HAB3		ENST00000532887.1:c.1059G>A	chr8.hg19:g.145584307G>A		18.0	0.0		18.0	10.0	NM_024531	A8K6B6|D3DWL8|G1UCY1|Q86UT1	Silent	SNP	ENST00000532887.1	hg19	CCDS6423.1																																																																																			.	.		0.697	SLC52A2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382405.1	NM_024531		A	145584307	G	A	145584307	2	1	344	1	0	0	0	0	0	0	0	1	6677	1277	45	3		3	GPR172A	8	145584307	Silent	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	775660	145584307	779715	692	48055										
RANBP6	26953	hgsc.bcm.edu	37	chr9	6012662	6012662	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttcaaaatcttccctattgcTgagatacagttctctgtagc	6	10	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:6012662T>A	ENST00000259569.5	-	1	2956	c.2946A>T	c.(2944-2946)tcA>tcT	p.S982S	RANBP6_ENST00000485372.1_5'Flank	NM_001243202.1|NM_001243203.1|NM_012416.3	NP_001230131.1|NP_001230132.1|NP_036548.1	O60518	RNBP6_HUMAN	RAN binding protein 6	982					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(5)|large_intestine(8)|lung(9)|ovary(7)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	51		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00522)|Lung(218;0.101)		TCCCTATTGCTGAGATACAGT	0.363																																					p.S982S		Atlas-SNP	.											.	RANBP6	127	.	0			c.A2946T						.						112	105	107					9																	6012662		2203	4300	6503	SO:0001819	synonymous_variant	26953	exon1			TATTGCTGAGATA	AF039023	CCDS6467.1	9p24.1	2008-03-26			ENSG00000137040	ENSG00000137040			9851	protein-coding gene	gene with protein product							Standard	NM_001243202		Approved		uc003zjr.3	O60518	OTTHUMG00000019512	ENST00000259569.5:c.2946A>T	chr9.hg19:g.6012662T>A		171.0	0.0		77.0	8.0	NM_012416	Q5T7X4|Q7Z3V2|Q96E78	Silent	SNP	ENST00000259569.5	hg19	CCDS6467.1																																																																																			.	.		0.363	RANBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051650.1	NM_012416		A	6012662	T	A	6012662	2	1	344	1	0	0	0	0	0	0	0	1	13046	1567	55	4		4	RANBP6	9	6012662	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10		6012662	135200769	693	48056										
KDM4C	23081	hgsc.bcm.edu	37	chr9	7046860	7046860	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tggtattttcttttccccccAggaatgctgtctctgcaatt	7	11	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:7046860A>T	ENST00000381309.3	+	16	2824		c.e16-1		KDM4C_ENST00000428870.2_Splice_Site|KDM4C_ENST00000536108.1_Splice_Site|KDM4C_ENST00000381306.3_Splice_Site|KDM4C_ENST00000442236.2_Splice_Site|KDM4C_ENST00000543771.1_Splice_Site|KDM4C_ENST00000535193.1_Splice_Site	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C						histone H3-K9 demethylation (GO:0033169)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	androgen receptor binding (GO:0050681)|dioxygenase activity (GO:0051213)|enzyme binding (GO:0019899)|histone demethylase activity (H3-K9 specific) (GO:0032454)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43						TTTTCCCCCCAGGAATGCTGT	0.333																																					.		Atlas-SNP	.											.	KDM4C	186	.	0			c.2326-2A>T						.						181	163	169					9																	7046860		2203	4300	6503	SO:0001630	splice_region_variant	23081	exon16			CCCCCCAGGAATG	AB018323	CCDS6471.1, CCDS55285.1, CCDS55286.1, CCDS55287.1	9p24-p23	2013-01-23	2009-04-06	2009-04-06	ENSG00000107077	ENSG00000107077		"Chromatin-modifying enzymes / K-demethylases", "Tudor domain containing"	17071	protein-coding gene	gene with protein product	"tudor domain containing 14C"	605469	"jumonji domain containing 2C"	JMJD2C		9872452, 15138608	Standard	NM_015061		Approved	GASC1, KIAA0780, TDRD14C	uc003zkh.3	Q9H3R0	OTTHUMG00000019536	ENST00000381309.3:c.2260-1A>T	chr9.hg19:g.7046860A>T		90.0	0.0		29.0	27.0	NM_001146696	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Splice_Site	SNP	ENST00000381309.3	hg19	CCDS6471.1	.	.	.	.	.	.	.	.	.	.	A	15.16	2.751022	0.49257	.	.	ENSG00000107077	ENST00000535193;ENST00000543771;ENST00000381309;ENST00000381306;ENST00000442236;ENST00000536108;ENST00000428870;ENST00000420847	.	.	.	5.44	5.44	0.79542	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3102	0.74026	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	KDM4C	7036860	1.000000	0.71417	0.942000	0.38095	0.488000	0.33401	6.494000	0.73661	2.270000	0.75569	0.533000	0.62120	.	.	.		0.333	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061	Intron	T	7046860	A	T	7046860	5	4	344	1	0	0	0	0	0	0	1	0	8139	202	7	4	2386	4	KDM4C	9	7046860	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1034198	7046860	134166571	694	48057										
PTPRD	5789	hgsc.bcm.edu	37	chr9	8486105	8486105	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atctccttcaccatctcctcCccaaagcccactttgtttct	2	18	4	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:8486105C>T	ENST00000381196.4	-	25	3255	c.2712G>A	c.(2710-2712)ggG>ggA	p.G904G	PTPRD_ENST00000397606.3_Intron|PTPRD_ENST00000397611.3_Intron|PTPRD_ENST00000356435.5_Silent_p.G904G|PTPRD_ENST00000397617.3_Intron|PTPRD_ENST00000360074.4_Silent_p.G891G|PTPRD_ENST00000537002.1_Intron|PTPRD_ENST00000471274.1_5'UTR|PTPRD_ENST00000540109.1_Silent_p.G904G|PTPRD_ENST00000358503.5_Silent_p.G882G|PTPRD_ENST00000355233.5_Intron|PTPRD_ENST00000486161.1_Intron	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	904	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		CCATCTCCTCCCCAAAGCCCA	0.463										TSP Lung(15;0.13)																											p.G904G		Atlas-SNP	.											.	PTPRD	1348	.	0			c.G2712A						.						98	92	94					9																	8486105		2203	4300	6503	SO:0001819	synonymous_variant	5789	exon28			CTCCTCCCCAAAG	X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.2712G>A	chr9.hg19:g.8486105C>T		108.0	0.0		115.0	59.0	NM_002839	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Silent	SNP	ENST00000381196.4	hg19	CCDS43786.1																																																																																			.	.		0.463	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3			T	8486105	C	T	8486105	2	4	344	1	0	0	0	0	0	0	0	1	12814	610	22	3		3	PTPRD	9	8486105	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1439245	8486105	132727326	695	48058										
CER1	9350	hgsc.bcm.edu	37	chr9	14722169	14722169	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccccagaacacatacctggcTgaagggcactgtcctgcagg	11	14	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:14722169T>A	ENST00000380911.3	-	1	546	c.502A>T	c.(502-504)Agc>Tgc	p.S168C		NM_005454.2	NP_005445.1	O95813	CER1_HUMAN	cerberus 1, DAN family BMP antagonist	168	CTCK. {ECO:0000255|PROSITE- ProRule:PRU00039}.				anterior/posterior axis specification (GO:0009948)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|bone mineralization (GO:0030282)|cell migration involved in gastrulation (GO:0042074)|cellular response to BMP stimulus (GO:0071773)|determination of dorsal identity (GO:0048263)|gastrulation (GO:0007369)|growth plate cartilage chondrocyte proliferation (GO:0003419)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mesoderm development (GO:2000381)|nervous system development (GO:0007399)|sequestering of BMP in extracellular matrix (GO:0035582)|signal transduction involved in regulation of gene expression (GO:0023019)|ureteric bud development (GO:0001657)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	BMP binding (GO:0036122)|morphogen activity (GO:0016015)|protein homodimerization activity (GO:0042803)			endometrium(2)|large_intestine(3)|lung(6)	11				GBM - Glioblastoma multiforme(50;3.16e-06)		CATACCTGGCTGAAGGGCACT	0.542																																					p.S168C		Atlas-SNP	.											.	CER1	41	.	0			c.A502T						.						78	73	75					9																	14722169		2203	4300	6503	SO:0001583	missense	9350	exon1			CCTGGCTGAAGGG	AF090189	CCDS6476.1	9p23-p22	2013-02-26	2013-02-26		ENSG00000147869	ENSG00000147869			1862	protein-coding gene	gene with protein product		603777	"cerberus 1 (Xenopus laevis) homolog (cysteine knot superfamily)", "cerberus 1, cysteine knot superfamily, homolog (Xenopus laevis)"			10049596	Standard	NM_005454		Approved	DAND4	uc003zlj.3	O95813	OTTHUMG00000021022	ENST00000380911.3:c.502A>T	chr9.hg19:g.14722169T>A	ENSP00000370297:p.Ser168Cys	72.0	0.0		67.0	31.0	NM_005454	Q6ISJ1|Q6ISJ6|Q6ISQ2|Q6ISS1	Missense_Mutation	SNP	ENST00000380911.3	hg19	CCDS6476.1	.	.	.	.	.	.	.	.	.	.	T	16.12	3.033387	0.54896	.	.	ENSG00000147869	ENST00000380911	T	0.32023	1.47	5.1	-0.366	0.12545	DAN (1);Cystine knot, C-terminal (2);	0.420625	0.25050	N	0.033529	T	0.36276	0.0961	L	0.59436	1.845	0.27829	N	0.941518	D	0.71674	0.998	P	0.61533	0.89	T	0.25433	-1.0132	10	0.66056	D	0.02	-5.0552	0.5754	0.00702	0.2095:0.2674:0.136:0.387	.	168	O95813	CER1_HUMAN	C	168	ENSP00000370297:S168C	ENSP00000370297:S168C	S	-	1	0	CER1	14712169	1.000000	0.71417	0.999000	0.59377	0.843000	0.47879	0.650000	0.24858	0.082000	0.17018	-0.313000	0.08912	AGC	.	.		0.542	CER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055453.1	NM_005454		A	14722169	T	A	14722169	3	1	344	1	0	0	0	0	1	0	0	0	3267	1580	55	4	309	4	CER1	9	14722169	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	6236064	14722169	126491262	696	48059										
SNAPC3	6619	hgsc.bcm.edu	37	chr9	15447091	15447091	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttatttattctttgacttttAgcacaaagaacacaaaccat	3	8	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:15447091A>T	ENST00000380821.3	+	5	758		c.e5-1		SNAPC3_ENST00000380799.1_5'Flank	NM_001039697.1	NP_001034786.1	Q92966	SNPC3_HUMAN	small nuclear RNA activating complex, polypeptide 3, 50kDa						gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription (GO:0009301)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(3)|large_intestine(6)|lung(2)	12				GBM - Glioblastoma multiforme(50;2.15e-06)		TTTGACTTTTAGCACAAAGAA	0.353																																					.		Atlas-SNP	.											.	SNAPC3	28	.	0			c.583-2A>T						.						148	150	150					9																	15447091		2203	4300	6503	SO:0001630	splice_region_variant	6619	exon5			ACTTTTAGCACAA	U71300	CCDS6478.1	9p22.3	2008-07-21	2002-08-29		ENSG00000164975	ENSG00000164975			11136	protein-coding gene	gene with protein product		602348	"small nuclear RNA activating complex, polypeptide 3, 50kD"			9003788	Standard	XR_428427		Approved	SNAP50, PTFbeta, MGC33124, MGC132011	uc003zlt.3	Q92966	OTTHUMG00000019583	ENST00000380821.3:c.583-1A>T	chr9.hg19:g.15447091A>T		121.0	0.0		132.0	57.0	NM_001039697	D3DRI8|Q2VPI6|Q5T285	Splice_Site	SNP	ENST00000380821.3	hg19	CCDS6478.1	.	.	.	.	.	.	.	.	.	.	A	15.60	2.882884	0.51908	.	.	ENSG00000164975	ENST00000380821;ENST00000447670	.	.	.	5.9	5.9	0.94986	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9966	0.80256	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SNAPC3	15437091	1.000000	0.71417	0.977000	0.42913	0.594000	0.36715	7.084000	0.76866	2.254000	0.74563	0.482000	0.46254	.	.	.		0.353	SNAPC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051763.2	NM_001039697	Intron	T	15447091	A	T	15447091	5	4	344	1	0	0	0	0	0	0	1	0	14851	434	15	4	599	4	SNAPC3	9	15447091	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	724922	15447091	125766340	697	48060										
BNC2	54796	hgsc.bcm.edu	37	chr9	16437127	16437127	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcattctgagttgaaaggctGggttcccgcagcctcaaccc	10	13	3	2	rs183551262		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:16437127G>T	ENST00000380672.4	-	6	1122	c.1065C>A	c.(1063-1065)ccC>ccA	p.P355P	BNC2_ENST00000380666.2_Silent_p.P355P|BNC2_ENST00000380667.2_Silent_p.P288P|BNC2_ENST00000545497.1_Silent_p.P260P	NM_017637.5	NP_060107.3			basonuclin 2											NS(2)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(16)|liver(1)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(50;9.01e-08)		TTGAAAGGCTGGGTTCCCGCA	0.478																																					p.P355P		Atlas-SNP	.											.	BNC2	166	.	0			c.C1065A						.						101	104	103					9																	16437127		2203	4300	6503	SO:0001819	synonymous_variant	54796	exon6			AAGGCTGGGTTCC	AK092247	CCDS6482.2	9p22.2	2013-05-20			ENSG00000173068	ENSG00000173068		"Zinc fingers, C2H2-type"	30988	protein-coding gene	gene with protein product		608669				14702039	Standard	XM_006716784		Approved	BSN2, FLJ20043	uc003zml.3	Q6ZN30	OTTHUMG00000019593	ENST00000380672.4:c.1065C>A	chr9.hg19:g.16437127G>T		110.0	0.0		110.0	38.0	NM_017637		Silent	SNP	ENST00000380672.4	hg19	CCDS6482.2																																																																																			.	G|1.000;A|0.000		0.478	BNC2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216901.5	NM_017637		T	16437127	G	T	16437127	2	4	344	1	0	0	0	0	0	0	0	1	1475	1335	47	3		3	BNC2	9	16437127	Silent	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	990036	16437127	124776304	698	48061										
SH3GL2	6456	hgsc.bcm.edu	37	chr9	17793437	17793437	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atgagcctggagtttccaacTggagacagtactcagcccaa	10	11	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:17793437T>A	ENST00000380607.4	+	8	921	c.801T>A	c.(799-801)acT>acA	p.T267T	SH3GL2_ENST00000537391.1_Silent_p.T220T	NM_003026.2	NP_003017.1	Q99962	SH3G2_HUMAN	SH3-domain GRB2-like 2	267					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|central nervous system development (GO:0007417)|epidermal growth factor receptor signaling pathway (GO:0007173)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of receptor internalization (GO:0002090)|signal transduction (GO:0007165)|synaptic vesicle endocytosis (GO:0048488)	clathrin-coated endocytic vesicle membrane (GO:0030669)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)			NS(1)|breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(11)|skin(3)|upper_aerodigestive_tract(1)	26				GBM - Glioblastoma multiforme(50;2.71e-10)|Lung(42;0.203)		AGTTTCCAACTGGAGACAGTA	0.483																																					p.T267T		Atlas-SNP	.											.	SH3GL2	60	.	0			c.T801A						.						96	90	92					9																	17793437		2203	4300	6503	SO:0001819	synonymous_variant	6456	exon8			TCCAACTGGAGAC	X99657	CCDS6483.1	9p22	2008-02-05			ENSG00000107295	ENSG00000107295			10831	protein-coding gene	gene with protein product		604465				9169142	Standard	XM_005251549		Approved	SH3P4, SH3D2A, CNSA2, EEN-B1	uc003zna.3	Q99962	OTTHUMG00000019601	ENST00000380607.4:c.801T>A	chr9.hg19:g.17793437T>A		135.0	0.0		121.0	61.0	NM_003026	B2R618|Q9NQK5	Silent	SNP	ENST00000380607.4	hg19	CCDS6483.1																																																																																			.	.		0.483	SH3GL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051796.1	NM_003026		A	17793437	T	A	17793437	2	1	344	1	0	0	0	0	0	0	0	1	14266	1567	55	4		4	SH3GL2	9	17793437	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1356310	17793437	123419994	699	48062										
ADAMTSL1	92949	hgsc.bcm.edu	37	chr9	18892464	18892464	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccgcagggtgacctgtcaaaAgctgaaagcctctgggatct	12	11	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:18892464A>G	ENST00000380548.4	+	26	5060	c.4721A>G	c.(4720-4722)aAg>aGg	p.K1574R	ADAMTSL1_ENST00000380545.5_Missense_Mutation_p.K275R	NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	1574	TSP type-1 8. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(2)|lung(17)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(50;1.29e-17)		ACCTGTCAAAAGCTGAAAGCC	0.612																																					p.K1574R		Atlas-SNP	.											.	ADAMTSL1	306	.	0			c.A4721G						.						27	30	29					9																	18892464		1932	4128	6060	SO:0001583	missense	92949	exon26			GTCAAAAGCTGAA	AF176313	CCDS6485.1, CCDS47954.1	9p21.3	2013-01-11			ENSG00000178031	ENSG00000178031		"Immunoglobulin superfamily / I-set domain containing"	14632	protein-coding gene	gene with protein product	"punctin"	609198	"chromosome 9 open reading frame 94"	C9orf94		9628581, 11805097	Standard	NM_001040272		Approved	ADAMTSR1, FLJ35283	uc003zne.4	Q8N6G6	OTTHUMG00000019604	ENST00000380548.4:c.4721A>G	chr9.hg19:g.18892464A>G	ENSP00000369921:p.Lys1574Arg	61.0	0.0		66.0	27.0	NM_001040272	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Missense_Mutation	SNP	ENST00000380548.4	hg19	CCDS47954.1	.	.	.	.	.	.	.	.	.	.	A	12.88	2.069364	0.36470	.	.	ENSG00000178031	ENST00000380548;ENST00000380545;ENST00000316239	T;T	0.54675	0.56;0.56	5.49	5.49	0.81192	.	0.196847	0.43747	D	0.000522	T	0.24967	0.0606	N	0.03608	-0.345	0.34704	D	0.727045	B;B	0.20671	0.047;0.031	B;B	0.23419	0.021;0.046	T	0.31052	-0.9957	10	0.02654	T	1	.	10.3218	0.43771	0.9171:0.0:0.0829:0.0	.	275;1574	Q8N6G6-6;Q8N6G6	.;ATL1_HUMAN	R	1574;275;278	ENSP00000369921:K1574R;ENSP00000369918:K275R	ENSP00000325584:K278R	K	+	2	0	ADAMTSL1	18882464	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.204000	0.51082	2.093000	0.63338	0.454000	0.30748	AAG	.	.		0.612	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1			G	18892464	A	G	18892464	3	3	344	1	0	0	0	0	1	0	0	0	274	72	3	2	4827	2	ADAMTSL1	9	18892464	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1099027	18892464	122320967	700	48063										
MLLT3	4300	hgsc.bcm.edu	37	chr9	20413886	20413886	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctgttttttgtcagcagaacAagtgagtatcagtggtggtg	13	5	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:20413886A>T	ENST00000380338.4	-	5	1244	c.958T>A	c.(958-960)Tgt>Agt	p.C320S	MLLT3_ENST00000355930.6_5'UTR|MIR4473_ENST00000583731.1_RNA|MLLT3_ENST00000475957.1_5'UTR|MLLT3_ENST00000429426.2_Missense_Mutation_p.C317S	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3	320					anterior/posterior pattern specification (GO:0009952)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of transcription, DNA-templated (GO:0006355)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		TCAGCAGAACAAGTGAGTATC	0.363			T	MLL	ALL																																p.C320S		Atlas-SNP	.		Dom	yes		9	9p22	4300	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 (AF9)"		L	.	MLLT3	125	.	0			c.T958A						.						124	124	124					9																	20413886		2203	4300	6503	SO:0001583	missense	4300	exon5			CAGAACAAGTGAG	L13744	CCDS6494.1	9p22	2008-02-05	2001-11-28		ENSG00000171843	ENSG00000171843			7136	protein-coding gene	gene with protein product		159558	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 3"			8506309, 8414510	Standard	NM_001286691		Approved	AF-9, AF9, YEATS3	uc003zoe.2	P42568	OTTHUMG00000019650	ENST00000380338.4:c.958T>A	chr9.hg19:g.20413886A>T	ENSP00000369695:p.Cys320Ser	126.0	0.0		104.0	48.0	NM_004529	B1AMQ2|B2R7B3|B7Z755|D3DRJ8|Q8IVB0	Missense_Mutation	SNP	ENST00000380338.4	hg19	CCDS6494.1	.	.	.	.	.	.	.	.	.	.	A	3.928	-0.016688	0.07681	.	.	ENSG00000171843	ENST00000380338;ENST00000429426;ENST00000540751	.	.	.	6.08	6.08	0.98989	.	0.173369	0.52532	D	0.000061	T	0.38321	0.1036	N	0.15975	0.35	0.80722	D	1	B;B	0.18461	0.028;0.028	B;B	0.14023	0.01;0.01	T	0.35101	-0.9802	9	0.02654	T	1	-10.0524	16.643	0.85134	1.0:0.0:0.0:0.0	.	317;320	B7Z755;P42568	.;AF9_HUMAN	S	320;317;359	.	ENSP00000369695:C320S	C	-	1	0	MLLT3	20403886	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.607000	0.67648	2.330000	0.79161	0.533000	0.62120	TGT	.	.		0.363	MLLT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051872.1	NM_004529		T	20413886	A	T	20413886	3	4	344	1	0	0	0	0	1	0	0	0	9637	130	5	4	776	4	MLLT3	9	20413886	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1521422	20413886	120799545	701	48064										
IFNA16	3449	hgsc.bcm.edu	37	chr9	21217242	21217242	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgaggcagatcacagcccagAgaacagatggatttgtagct	12	8	1	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:21217242A>G	ENST00000380216.1	-	1	68	c.63T>C	c.(61-63)tcT>tcC	p.S21S		NM_002173.2	NP_002164.1	P05015	IFN16_HUMAN	interferon, alpha 16	21					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)	13				Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.116)		CACAGCCCAGAGAACAGATGG	0.507																																					p.S21S		Atlas-SNP	.											.	IFNA16	27	.	0			c.T63C						.						85	85	85					9																	21217242		2203	4300	6503	SO:0001819	synonymous_variant	3449	exon1			GCCCAGAGAACAG		CCDS34996.1	9p22	2010-12-10			ENSG00000147885	ENSG00000147885		"Interferons"	5421	protein-coding gene	gene with protein product		147580				1385305	Standard	NM_002173		Approved	IFN-alphaO	uc003zor.1	P05015	OTTHUMG00000019663	ENST00000380216.1:c.63T>C	chr9.hg19:g.21217242A>G		192.0	0.0		233.0	61.0	NM_002173	Q5VV12	Silent	SNP	ENST00000380216.1	hg19	CCDS34996.1																																																																																			.	.		0.507	IFNA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051892.1	NM_002173		G	21217242	A	G	21217242	2	3	344	1	0	0	0	0	0	0	0	1	7544	291	11	2		2	IFNA16	9	21217242	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	803356	21217242	119996189	702	48065										
IFNA5	3442	hgsc.bcm.edu	37	chr9	21305011	21305011	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgaaggtctgctggatcatcTcatggaggacagagatggct	14	7	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:21305011T>G	ENST00000259555.4	-	1	301	c.245A>C	c.(244-246)gAg>gCg	p.E82A		NM_002169.2	NP_002160.1	P01569	IFNA5_HUMAN	interferon, alpha 5	82					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|cytokine receptor binding (GO:0005126)|type I interferon receptor binding (GO:0005132)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)	7				Lung(24;2.34e-24)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)		CTGGATCATCTCATGGAGGAC	0.473																																					p.E82A		Atlas-SNP	.											.	IFNA5	21	.	0			c.A245C						.						125	116	119					9																	21305011		2203	4297	6500	SO:0001583	missense	3442	exon1			ATCATCTCATGGA		CCDS6502.1	9p22	2010-08-24			ENSG00000147873	ENSG00000147873		"Interferons"	5426	protein-coding gene	gene with protein product		147565				1385305	Standard	NM_002169		Approved	IFN-alphaG	uc011lnh.2	P01569	OTTHUMG00000019664	ENST00000259555.4:c.245A>C	chr9.hg19:g.21305011T>G	ENSP00000259555:p.Glu82Ala	95.0	0.0		95.0	65.0	NM_002169	Q52LX3	Missense_Mutation	SNP	ENST00000259555.4	hg19	CCDS6502.1	.	.	.	.	.	.	.	.	.	.	T	13.86	2.363005	0.41902	.	.	ENSG00000147873	ENST00000259555	T	0.04758	3.56	4.16	1.51	0.23008	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.127670	0.53938	D	0.000052	T	0.26122	0.0637	H	0.95745	3.715	0.09310	N	1	D	0.76494	0.999	D	0.87578	0.998	T	0.09907	-1.0653	10	0.87932	D	0	.	7.6131	0.28142	0.4076:0.0:0.0:0.5924	.	82	P01569	IFNA5_HUMAN	A	82	ENSP00000259555:E82A	ENSP00000259555:E82A	E	-	2	0	IFNA5	21295011	0.000000	0.05858	0.013000	0.15412	0.001000	0.01503	0.283000	0.18846	0.048000	0.15891	-0.635000	0.03985	GAG	.	.		0.473	IFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051893.1	NM_002169		G	21305011	T	G	21305011	3	3	344	1	0	0	0	0	1	0	0	0	7549	1551	54	5	328	5	IFNA5	9	21305011	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	87769	21305011	119908420	703	48066										
IFNA8	3445	hgsc.bcm.edu	37	chr9	21409216	21409216	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	actggtggccctagtggtgcTcagctacaagtcattcagct	11	11	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:21409216T>A	ENST00000380205.1	+	1	71	c.41T>A	c.(40-42)cTc>cAc	p.L14H		NM_002170.3	NP_002161.2	P32881	IFNA8_HUMAN	interferon, alpha 8	14					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|cytokine receptor binding (GO:0005126)|type I interferon receptor binding (GO:0005132)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)	9				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.0174)		CTAGTGGTGCTCAGCTACAAG	0.507																																					p.L14H		Atlas-SNP	.											.	IFNA8	19	.	0			c.T41A						.						153	146	148					9																	21409216		2203	4300	6503	SO:0001583	missense	3445	exon1			TGGTGCTCAGCTA		CCDS6507.1	9p22	2010-08-24			ENSG00000120242	ENSG00000120242		"Interferons"	5429	protein-coding gene	gene with protein product	"interferon alpha-B''", "interferon alpha type 201"	147568				1385305	Standard	NM_002170		Approved	IFN-alphaB	uc003zpc.1	P32881	OTTHUMG00000019677	ENST00000380205.1:c.41T>A	chr9.hg19:g.21409216T>A	ENSP00000369553:p.Leu14His	47.0	0.0		70.0	34.0	NM_002170	P01565|P09236|Q5VWV7|Q5VYQ3	Missense_Mutation	SNP	ENST00000380205.1	hg19	CCDS6507.1	.	.	.	.	.	.	.	.	.	.	T	12.02	1.813561	0.32053	.	.	ENSG00000120242	ENST00000380205	T	0.04317	3.65	3.43	3.43	0.39272	.	0.094776	0.44688	D	0.000430	T	0.26738	0.0654	H	0.94658	3.565	0.28700	N	0.904144	D	0.89917	1.0	D	0.72338	0.977	T	0.20840	-1.0263	10	0.87932	D	0	.	9.7942	0.40724	0.0:0.0:0.0:1.0	.	14	P32881	IFNA8_HUMAN	H	14	ENSP00000369553:L14H	ENSP00000369553:L14H	L	+	2	0	IFNA8	21399216	0.002000	0.14202	0.981000	0.43875	0.061000	0.15899	1.285000	0.33261	1.560000	0.49568	0.459000	0.35465	CTC	.	.		0.507	IFNA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051906.1	NM_002170		A	21409216	T	A	21409216	3	1	344	1	0	0	0	0	1	0	0	0	7552	1551	54	4	43	4	IFNA8	9	21409216	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	104205	21409216	119804215	704	48067										
UBAP2	55833	hgsc.bcm.edu	37	chr9	33953474	33953474	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	caaggctaccagatcaatgcTaagcagacaaaaagcaatga	8	9	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:33953474T>C	ENST00000379238.1	-	12	984		c.e12-2		SNORD121A_ENST00000459386.1_RNA|UBAP2_ENST00000360802.1_Splice_Site|UBAP2_ENST00000539807.1_Splice_Site|UBAP2_ENST00000418786.2_Splice_Site|UBAP2_ENST00000379239.4_Splice_Site|UBAP2_ENST00000449054.1_Splice_Site					ubiquitin associated protein 2											endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(13)|ovary(3)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)		AGATCAATGCTAAGCAGACAA	0.413																																					.		Atlas-SNP	.											.	UBAP2	82	.	0			c.867-2A>G						.						65	61	62					9																	33953474		2203	4300	6503	SO:0001630	splice_region_variant	55833	exon13			CAATGCTAAGCAG	AB040924	CCDS6547.1, CCDS75828.1	9p11.2	2008-02-05			ENSG00000137073	ENSG00000137073			14185	protein-coding gene	gene with protein product						8871400	Standard	NM_018449		Approved	KIAA1491, bA176F3.5, FLJ22435	uc003ztq.1	Q5T6F2	OTTHUMG00000000427	ENST00000379238.1:c.867-2A>G	chr9.hg19:g.33953474T>C		104.0	0.0		91.0	46.0	NM_018449		Splice_Site	SNP	ENST00000379238.1	hg19	CCDS6547.1	.	.	.	.	.	.	.	.	.	.	T	15.31	2.795860	0.50208	.	.	ENSG00000137073	ENST00000379238;ENST00000449054;ENST00000360802;ENST00000431417;ENST00000379260;ENST00000379239;ENST00000539807;ENST00000418786;ENST00000412543;ENST00000421278	.	.	.	5.55	5.55	0.83447	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9845	0.80142	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	UBAP2	33943474	1.000000	0.71417	0.997000	0.53966	0.571000	0.35966	6.103000	0.71492	2.230000	0.72887	0.413000	0.27773	.	.	.		0.413	UBAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001071.1	NM_018449	Intron	C	33953474	T	C	33953474	5	2	344	1	0	0	0	0	0	0	1	0	16852	1536	53	2	2566	2	UBAP2	9	33953474	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	12544258	33953474	107259957	705	48068										
CA9	768	hgsc.bcm.edu	37	chr9	35674105	35674105	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcaggaggattcccccttggGaggaggctcttctggggaag	17	9	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:35674105G>T	ENST00000378357.4	+	1	253	c.149G>T	c.(148-150)gGa>gTa	p.G50V	RN7SL22P_ENST00000471800.2_RNA	NM_001216.2	NP_001207.2	Q16790	CAH9_HUMAN	carbonic anhydrase IX	50	Proteoglycan-like (PG).				bicarbonate transport (GO:0015701)|cellular response to hypoxia (GO:0071456)|morphogenesis of an epithelium (GO:0002009)|one-carbon metabolic process (GO:0006730)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to drug (GO:0042493)|response to testosterone (GO:0033574)|secretion (GO:0046903)|small molecule metabolic process (GO:0044281)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(3)|lung(5)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	17	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)		Benzthiazide(DB00562)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Zonisamide(DB00909)	TCCCCCTTGGGAGGAGGCTCT	0.612																																					p.G50V		Atlas-SNP	.											.	CA9	48	.	0			c.G149T						.						53	51	52					9																	35674105		2203	4300	6503	SO:0001583	missense	768	exon1			CCTTGGGAGGAGG	X66839	CCDS6585.1	9p13.3	2012-08-21			ENSG00000107159	ENSG00000107159		"Carbonic anhydrases"	1383	protein-coding gene	gene with protein product	"carbonic dehydratase", "RCC-associated protein G250"	603179				8661007, 9787087	Standard	NM_001216		Approved	MN, CAIX	uc003zxo.4	Q16790	OTTHUMG00000021029	ENST00000378357.4:c.149G>T	chr9.hg19:g.35674105G>T	ENSP00000367608:p.Gly50Val	58.0	0.0		75.0	38.0	NM_001216	Q5T4R1	Missense_Mutation	SNP	ENST00000378357.4	hg19	CCDS6585.1	.	.	.	.	.	.	.	.	.	.	G	8.318	0.823561	0.16678	.	.	ENSG00000107159	ENST00000378357;ENST00000544074	T	0.67698	-0.28	4.31	2.29	0.28610	.	2.578400	0.01317	N	0.010837	T	0.72020	0.3409	L	0.34521	1.04	0.58432	D	0.999996	D;D	0.61080	0.989;0.982	D;P	0.63957	0.92;0.834	T	0.64748	-0.6334	10	0.87932	D	0	.	5.1551	0.15031	0.2693:0.0:0.7307:0.0	.	50;50	F5H404;Q16790	.;CAH9_HUMAN	V	50	ENSP00000367608:G50V	ENSP00000367608:G50V	G	+	2	0	CA9	35664105	0.999000	0.42202	0.933000	0.37362	0.044000	0.14063	0.529000	0.23019	1.045000	0.40225	0.655000	0.94253	GGA	.	.		0.612	CA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055479.1	NM_001216		T	35674105	G	T	35674105	3	4	344	1	0	0	0	0	1	0	0	0	2526	1174	41	3	151	3	CA9	9	35674105	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1720631	35674105	105539326	706	48069										
TLN1	7094	hgsc.bcm.edu	37	chr9	35724956	35724956	+	Splice_Site	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cttcctgtactccatagtgtCctgttagggcaggaagaaga	11	9	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:35724956C>A	ENST00000314888.9	-	4	582	c.229G>T	c.(229-231)Gac>Tac	p.D77Y	TLN1_ENST00000540444.1_Splice_Site_p.D77Y	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	77					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TCCATAGTGTCCTGTTAGGGC	0.502																																					p.D77Y		Atlas-SNP	.											.	TLN1	185	.	0			c.G229T						.						162	148	153					9																	35724956		2203	4300	6503	SO:0001630	splice_region_variant	7094	exon4			TAGTGTCCTGTTA	AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.229-1G>T	chr9.hg19:g.35724956C>A		86.0	0.0		62.0	21.0	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	hg19	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.150242	0.78001	.	.	ENSG00000137076	ENST00000314888;ENST00000540444	T;T	0.73047	-0.69;-0.71	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	D	0.87474	0.6186	M	0.90252	3.1	0.80722	D	1	P;D	0.89917	0.884;1.0	P;D	0.77557	0.596;0.99	D	0.88178	0.2869	10	0.49607	T	0.09	-24.0946	19.6771	0.95939	0.0:1.0:0.0:0.0	.	77;77	Q5TCU5;Q9Y490	.;TLN1_HUMAN	Y	77	ENSP00000316029:D77Y;ENSP00000442981:D77Y	ENSP00000316029:D77Y	D	-	1	0	TLN1	35714956	1.000000	0.71417	1.000000	0.80357	0.674000	0.39518	7.776000	0.85560	2.732000	0.93576	0.655000	0.94253	GAC	.	.		0.502	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289	Missense_Mutation	A	35724956	C	A	35724956	5	1	344	1	0	0	0	0	0	0	1	0	15962	869	30	3	7612	3	TLN1	9	35724956	Splice_Site	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	50851	35724956	105488475	707	48070										
RGP1	57704	hgsc.bcm.edu	37	chr9	35752015	35752015	+	5'Flank	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	taccagcggcgacgtggggcAgggggtgtcccctctgtgtc	17	12	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:35752015A>G	ENST00000378103.3	-	0	0				RGP1_ENST00000456972.2_Silent_p.A315A|RGP1_ENST00000378078.4_Silent_p.A275A|MSMP_ENST00000414286.1_5'Flank|GBA2_ENST00000545786.1_5'Flank|GBA2_ENST00000378094.4_5'Flank	NM_020944.2	NP_065995.1	Q9HCG7	GBA2_HUMAN	glucosidase, beta (bile acid) 2						bile acid metabolic process (GO:0008206)|cell death (GO:0008219)|central nervous system neuron development (GO:0021954)|glucosylceramide catabolic process (GO:0006680)|glycoside catabolic process (GO:0016139)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)	beta-glucosidase activity (GO:0008422)|glucosylceramidase activity (GO:0004348)			NS(1)|kidney(3)|large_intestine(5)|lung(5)|ovary(4)|skin(3)	21	all_epithelial(49;0.167)		Lung(28;0.00416)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			GACGTGGGGCAGGGGGTGTCC	0.577																																					p.A275A		Atlas-SNP	.											.	RGP1	60	.	0			c.A825G						.						82	84	83					9																	35752015		2095	4224	6319	SO:0001631	upstream_gene_variant	9827	exon8			TGGGGCAGGGGGT	AJ309567	CCDS6589.1	9p13.2	2013-09-11			ENSG00000070610	ENSG00000070610			18986	protein-coding gene	gene with protein product	"bile acid beta-glucosidase", "non-lysosomal glucosylceramidase"	609471	"spastic paraplegia 46 (autosomal recessive)"	SPG46		11489889, 23332916, 23332917	Standard	NM_020944		Approved	KIAA1605, AD035, DKFZp762K054	uc003zxw.3	Q9HCG7	OTTHUMG00000021024		chr9.hg19:g.35752015A>G	Exception_encountered	112.0	0.0		92.0	35.0	NM_001080496	D3DRP2|Q5TCV6|Q96A51|Q96LY1|Q96SJ2|Q9H2L8	Silent	SNP	ENST00000378103.3	hg19	CCDS6589.1																																																																																			.	.		0.577	GBA2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055456.1	NM_020944		G	35752015	A	G	35752015	1	3	344	0	1	0	0	0	0	0	0	0	13299	175	7	2		2	RGP1	9	35752015	5'Flank	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	27059	35752015	105461416	708	48071										
OR2S2	56656	hgsc.bcm.edu	37	chr9	35957519	35957519	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gctgatcacattgatggaaaTgtcagcacaggccaacttta	9	9	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:35957519T>C	ENST00000341959.2	-	1	632	c.577A>G	c.(577-579)Att>Gtt	p.I193V		NM_019897.2	NP_063950.2	Q9NQN1	OR2S1_HUMAN	olfactory receptor, family 2, subfamily S, member 2	193					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(8)|ovary(1)|skin(1)|stomach(1)	17			LUSC - Lung squamous cell carcinoma(32;0.00613)|STAD - Stomach adenocarcinoma(86;0.194)			TTGATGGAAATGTCAGCACAG	0.468																																					p.I193V	Pancreas(172;293 2036 17878 24427 30946)	Atlas-SNP	.											.	OR2S2	46	.	0			c.A577G						.						111	103	106					9																	35957519		2203	4300	6503	SO:0001583	missense	56656	exon1			TGGAAATGTCAGC	AL135841	CCDS6596.2	9p13.3	2012-08-09			ENSG00000122718	ENSG00000122718		"GPCR / Class A : Olfactory receptors"	8276	protein-coding gene	gene with protein product							Standard	NM_019897		Approved		uc011lpi.2	Q9NQN1	OTTHUMG00000019891	ENST00000341959.2:c.577A>G	chr9.hg19:g.35957519T>C	ENSP00000344040:p.Ile193Val	86.0	0.0		79.0	45.0	NM_019897	Q2M3L0|Q6IF19|Q96R42	Missense_Mutation	SNP	ENST00000341959.2	hg19	CCDS6596.2	.	.	.	.	.	.	.	.	.	.	T	10.12	1.261797	0.23051	.	.	ENSG00000122718	ENST00000341959	T	0.00107	8.72	4.17	4.17	0.49024	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	D	0.000091	T	0.00241	0.0007	L	0.58669	1.825	0.09310	N	1	B	0.33612	0.419	B	0.41691	0.364	T	0.34329	-0.9833	10	0.51188	T	0.08	.	11.8394	0.52344	0.0:0.0:0.0:1.0	.	193	Q9NQN1	OR2S1_HUMAN	V	193	ENSP00000344040:I193V	ENSP00000344040:I193V	I	-	1	0	OR2S2	35947519	0.078000	0.21339	1.000000	0.80357	0.056000	0.15407	0.792000	0.26929	2.106000	0.64143	0.533000	0.62120	ATT	.	.		0.468	OR2S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052400.2	NM_019897		C	35957519	T	C	35957519	3	2	344	1	0	0	0	0	1	0	0	0	11024	1464	51	2	386	2	OR2S2	9	35957519	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	205504	35957519	105255912	709	48072										
C9orf71	169693	hgsc.bcm.edu	37	chr9	71155621	71155621	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aggccgcaatcaggctccccTgacagtcgaatatggagccc	11	14	1	1	rs372500287		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:71155621T>A	ENST00000377311.3	-	1	162	c.110A>T	c.(109-111)cAg>cTg	p.Q37L	RP11-274B18.2_ENST00000432148.1_lincRNA|RP11-274B18.4_ENST00000413269.3_lincRNA	NM_153237.1	NP_694969.1	Q8N6L7	TM252_HUMAN	transmembrane protein 252	37						integral component of membrane (GO:0016021)											CAGGCTCCCCTGACAGTCGAA	0.527																																					p.Q37L		Atlas-SNP	.											.	.	.	.	0			c.A110T						.						60	58	59					9																	71155621		2203	4300	6503	SO:0001583	missense	169693	exon1			CTCCCCTGACAGT	BC029780	CCDS35040.1	9q21.13	2012-07-19	2012-07-19	2012-07-19	ENSG00000181778	ENSG00000181778			28537	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 71"	C9orf71		12477932	Standard	NM_153237		Approved	MGC34760	uc004agt.3	Q8N6L7	OTTHUMG00000019967	ENST00000377311.3:c.110A>T	chr9.hg19:g.71155621T>A	ENSP00000366528:p.Gln37Leu	114.0	0.0		168.0	57.0	NM_153237		Missense_Mutation	SNP	ENST00000377311.3	hg19	CCDS35040.1	.	.	.	.	.	.	.	.	.	.	T	5.938	0.357014	0.11239	.	.	ENSG00000181778	ENST00000377311	.	.	.	6.02	-2.76	0.05896	.	1.908140	0.01975	N	0.044404	T	0.33265	0.0857	L	0.47716	1.5	0.09310	N	1	B	0.32467	0.372	B	0.24394	0.053	T	0.21280	-1.0250	9	0.52906	T	0.07	2.0559	6.4752	0.22031	0.0:0.262:0.2315:0.5065	.	37	Q8N6L7	CI071_HUMAN	L	37	.	ENSP00000366528:Q37L	Q	-	2	0	C9orf71	70345441	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.009000	0.12765	-0.878000	0.04007	-0.912000	0.02778	CAG	.	.		0.527	TMEM252-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052551.1	NM_153237		A	71155621	T	A	71155621	3	1	344	1	0	0	0	0	1	0	0	0	2496	1580	55	4	410	4	C9orf71	9	71155621	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	35198102	71155621	70057810	710	48073										
TRPM6	140803	hgsc.bcm.edu	37	chr9	77418778	77418778	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	actttctgcagactcatttcTatttcctgaggagtgtctct	7	10	4	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:77418778T>C	ENST00000360774.1	-	15	1900	c.1663A>G	c.(1663-1665)Aga>Gga	p.R555G	TRPM6_ENST00000361255.3_Missense_Mutation_p.R550G|TRPM6_ENST00000376871.3_Intron|TRPM6_ENST00000451710.3_Missense_Mutation_p.R555G|TRPM6_ENST00000449912.2_Missense_Mutation_p.R550G|TRPM6_ENST00000376864.4_Missense_Mutation_p.R555G|TRPM6_ENST00000376872.3_Intron	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	555					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						GACTCATTTCTATTTCCTGAG	0.388																																					p.R555G		Atlas-SNP	.											.	TRPM6	377	.	0			c.A1663G						.						165	161	163					9																	77418778		2203	4300	6503	SO:0001583	missense	140803	exon15			CATTTCTATTTCC	AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"Voltage-gated ion channels / Transient receptor potential cation channels"	17995	protein-coding gene	gene with protein product		607009	"hypomagnesemia, secondary hypocalcemia"	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.1663A>G	chr9.hg19:g.77418778T>C	ENSP00000354006:p.Arg555Gly	71.0	0.0		95.0	31.0	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	ENST00000360774.1	hg19	CCDS6647.1	.	.	.	.	.	.	.	.	.	.	T	9.289	1.050122	0.19827	.	.	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000449912;ENST00000361255;ENST00000376864;ENST00000312449;ENST00000448641	T;T;T;T;T	0.74737	-0.87;-0.87;-0.87;-0.87;-0.87	5.51	1.46	0.22682	.	0.649355	0.15741	N	0.246924	T	0.68988	0.3061	M	0.67953	2.075	0.09310	N	1	P;P	0.43973	0.729;0.823	B;B	0.40565	0.25;0.333	T	0.61826	-0.6983	10	0.87932	D	0	.	7.4799	0.27398	0.0:0.144:0.3015:0.5545	.	555;550	Q9BX84;Q9BX84-3	TRPM6_HUMAN;.	G	555;555;550;550;555;218;218	ENSP00000354006:R555G;ENSP00000407341:R555G;ENSP00000396672:R550G;ENSP00000354962:R550G;ENSP00000366060:R555G	ENSP00000309693:R218G	R	-	1	2	TRPM6	76608598	0.001000	0.12720	0.003000	0.11579	0.058000	0.15608	0.859000	0.27858	0.368000	0.24481	0.460000	0.39030	AGA	.	.		0.388	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662		C	77418778	T	C	77418778	3	2	344	1	0	0	0	0	1	0	0	0	16605	1530	53	2	4505	2	TRPM6	9	77418778	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	6263157	77418778	63794653	711	48074										
PRUNE2	158471	hgsc.bcm.edu	37	chr9	79324425	79324425	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctttcttcatattctcctcaAaaaggttccaggaatctacc	4	12	5	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:79324425A>G	ENST00000376718.3	-	8	2888	c.2765T>C	c.(2764-2766)tTt>tCt	p.F922S	PRUNE2_ENST00000428286.1_Missense_Mutation_p.F563S	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	922					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						ATTCTCCTCAAAAAGGTTCCA	0.398																																					p.F922S		Atlas-SNP	.											.	PRUNE2	331	.	0			c.T2765C						.						229	216	220					9																	79324425		1568	3582	5150	SO:0001583	missense	158471	exon8			TCCTCAAAAAGGT	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.2765T>C	chr9.hg19:g.79324425A>G	ENSP00000365908:p.Phe922Ser	138.0	0.0		170.0	41.0	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	hg19	CCDS47982.1	.	.	.	.	.	.	.	.	.	.	A	12.88	2.069747	0.36470	.	.	ENSG00000106772	ENST00000376718;ENST00000428286;ENST00000422033	T;T	0.53206	0.63;0.65	5.83	4.65	0.58169	.	0.127954	0.36409	N	0.002614	T	0.46776	0.1410	L	0.29908	0.895	0.80722	D	1	D	0.64830	0.994	P	0.57911	0.829	T	0.49476	-0.8936	10	0.87932	D	0	-17.908	6.2135	0.20642	0.7184:0.0:0.0845:0.1971	.	922	Q8WUY3	PRUN2_HUMAN	S	922;563;921	ENSP00000365908:F922S;ENSP00000397425:F563S	ENSP00000365908:F922S	F	-	2	0	PRUNE2	78514245	1.000000	0.71417	1.000000	0.80357	0.571000	0.35966	1.530000	0.36007	2.226000	0.72624	0.459000	0.35465	TTT	.	.		0.398	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		G	79324425	A	G	79324425	3	3	344	1	0	0	0	0	1	0	0	0	12653	14	1	2	6549	2	PRUNE2	9	79324425	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1905647	79324425	61889006	712	48075										
KIF27	55582	hgsc.bcm.edu	37	chr9	86495242	86495242	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgctggtcccgcttaattacTgcatccagttgcttcctttt	7	12	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:86495242T>A	ENST00000297814.2	-	11	2756	c.2613A>T	c.(2611-2613)gcA>gcT	p.A871A	KIF27_ENST00000376347.1_Silent_p.A262A|KIF27_ENST00000334204.2_Silent_p.A871A|KIF27_ENST00000413982.1_Intron	NM_017576.1	NP_060046.1	Q86VH2	KIF27_HUMAN	kinesin family member 27	871					ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(7)|lung(17)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	43						GCTTAATTACTGCATCCAGTT	0.353																																					p.A871A		Atlas-SNP	.											.	KIF27	103	.	0			c.A2613T						.						128	105	113					9																	86495242		2203	4300	6503	SO:0001819	synonymous_variant	55582	exon11			AATTACTGCATCC	AY237536	CCDS6665.1, CCDS65071.1, CCDS65072.1	9q21.32	2008-03-03			ENSG00000165115	ENSG00000165115		"Kinesins"	18632	protein-coding gene	gene with protein product		611253					Standard	NM_017576		Approved	DKFZp434D0917	uc004ana.4	Q86VH2	OTTHUMG00000020109	ENST00000297814.2:c.2613A>T	chr9.hg19:g.86495242T>A		72.0	0.0		66.0	18.0	NM_017576	B2RTR8|Q5T6W0|Q86VH0|Q86VH1|Q9UF54	Silent	SNP	ENST00000297814.2	hg19	CCDS6665.1																																																																																			.	.		0.353	KIF27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052861.1	NM_017576		A	86495242	T	A	86495242	2	1	344	1	0	0	0	0	0	0	0	1	8305	1567	55	4		4	KIF27	9	86495242	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	7170817	86495242	54718189	713	48076										
NTRK2	4915	hgsc.bcm.edu	37	chr9	87325598	87325598	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gctcctgtgacattatgtggAtcaagactctccaagaggct	10	10	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:87325598A>T	ENST00000323115.4	+	5	828	c.475A>T	c.(475-477)Atc>Ttc	p.I159F	NTRK2_ENST00000395882.1_Missense_Mutation_p.I159F|NTRK2_ENST00000304053.6_Missense_Mutation_p.I159F|NTRK2_ENST00000376213.1_Missense_Mutation_p.I159F|NTRK2_ENST00000395866.2_Missense_Mutation_p.I3F|NTRK2_ENST00000277120.3_Missense_Mutation_p.I159F|NTRK2_ENST00000376214.1_Missense_Mutation_p.I159F|NTRK2_ENST00000376208.1_Missense_Mutation_p.I159F|NTRK2_ENST00000359847.3_Missense_Mutation_p.I159F			Q16620	NTRK2_HUMAN	neurotrophic tyrosine kinase, receptor, type 2	159	LRRCT.				activation of adenylate cyclase activity (GO:0007190)|aging (GO:0007568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|central nervous system neuron development (GO:0021954)|cerebral cortex development (GO:0021987)|circadian rhythm (GO:0007623)|feeding behavior (GO:0007631)|glutamate secretion (GO:0014047)|learning (GO:0007612)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mechanoreceptor differentiation (GO:0042490)|negative regulation of anoikis (GO:2000811)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular junction development (GO:0007528)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peripheral nervous system neuron development (GO:0048935)|positive regulation of axonogenesis (GO:0050772)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|regulation of dendrite development (GO:0050773)|regulation of neurotransmitter secretion (GO:0046928)|regulation of protein kinase B signaling (GO:0051896)|regulation of Rac GTPase activity (GO:0032314)|response to auditory stimulus (GO:0010996)|retinal rod cell development (GO:0046548)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vasculogenesis (GO:0001570)	cell surface (GO:0009986)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endosome (GO:0005768)|excitatory synapse (GO:0060076)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|receptor complex (GO:0043235)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|brain-derived neurotrophic factor binding (GO:0048403)|brain-derived neurotrophic factor-activated receptor activity (GO:0060175)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	46					Amitriptyline(DB00321)	CATTATGTGGATCAAGACTCT	0.438										TSP Lung(25;0.17)																											p.I159F		Atlas-SNP	.											.	NTRK2	331	.	0			c.A475T						.						137	121	126					9																	87325598		2203	4300	6503	SO:0001583	missense	4915	exon6			ATGTGGATCAAGA	AF410902	CCDS6671.1, CCDS35050.1, CCDS35051.1, CCDS35052.1, CCDS35053.1	9q22.1	2013-01-11			ENSG00000148053	ENSG00000148053	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing"	8032	protein-coding gene	gene with protein product		600456				7789988	Standard	NM_001018065		Approved	TRKB	uc004anz.1	Q16620	OTTHUMG00000020120	ENST00000323115.4:c.475A>T	chr9.hg19:g.87325598A>T	ENSP00000314586:p.Ile159Phe	119.0	0.0		172.0	157.0	NM_001018065	B1ANZ4|B4DFV9|Q16675|Q59GJ1|Q8WXJ5|Q8WXJ6|Q8WXJ7	Missense_Mutation	SNP	ENST00000323115.4	hg19	CCDS35050.1	.	.	.	.	.	.	.	.	.	.	A	15.34	2.805748	0.50421	.	.	ENSG00000148053	ENST00000376214;ENST00000376213;ENST00000395882;ENST00000376208;ENST00000304053;ENST00000277120;ENST00000323115;ENST00000359847;ENST00000395866	D;D;D;D;D;D;D;D;T	0.89050	-2.46;-2.46;-2.46;-2.46;-2.46;-2.46;-2.46;-2.46;-0.7	5.77	2.01	0.26516	Cysteine-rich flanking region, C-terminal (1);	0.111372	0.64402	D	0.000013	D	0.87605	0.6219	L	0.41710	1.295	0.42338	D	0.992325	P;P;P;P;B;P;P;P	0.44986	0.52;0.686;0.847;0.558;0.164;0.55;0.734;0.686	B;P;P;P;B;B;B;P	0.55222	0.221;0.771;0.771;0.594;0.224;0.35;0.319;0.771	D	0.84940	0.0865	10	0.87932	D	0	.	5.6543	0.17635	0.5726:0.2835:0.1439:0.0	.	3;159;159;159;159;159;205;159	B4DFV9;Q16620-3;Q16620-5;Q5VWE5;Q16620;Q16620-4;Q59GJ1;Q16620-2	.;.;.;.;NTRK2_HUMAN;.;.;.	F	159;159;159;159;159;159;159;159;3	ENSP00000365387:I159F;ENSP00000365386:I159F;ENSP00000379221:I159F;ENSP00000365381:I159F;ENSP00000306167:I159F;ENSP00000277120:I159F;ENSP00000314586:I159F;ENSP00000352906:I159F;ENSP00000379207:I3F	ENSP00000277120:I159F	I	+	1	0	NTRK2	86515418	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	1.484000	0.35508	0.431000	0.26258	-0.472000	0.04984	ATC	.	.		0.438	NTRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052882.1			T	87325598	A	T	87325598	3	4	344	1	0	0	0	0	1	0	0	0	10716	333	12	4	493	4	NTRK2	9	87325598	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	830356	87325598	53887833	714	48077										
C9orf153	389766	hgsc.bcm.edu	37	chr9	88842778	88842778	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	accactgtgcacctgataacAggttggagatctcctctcac	8	13	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:88842778A>T	ENST00000376001.3	-	3	314	c.234T>A	c.(232-234)ccT>ccA	p.P78P	C9orf153_ENST00000339137.3_Silent_p.P78P|C9orf153_ENST00000469914.1_Intron	NM_001276366.1	NP_001263295.1	Q5TBE3	CI153_HUMAN	chromosome 9 open reading frame 153	78										breast(1)|lung(1)	2						ACCTGATAACAGGTTGGAGAT	0.483																																					p.P78P		Atlas-SNP	.											.	C9orf153	10	.	0			c.T234A						.						198	158	172					9																	88842778		2203	4300	6503	SO:0001819	synonymous_variant	389766	exon4			GATAACAGGTTGG		CCDS35055.1, CCDS35055.2	9q22.1	2012-04-03			ENSG00000187753	ENSG00000187753			31456	protein-coding gene	gene with protein product							Standard	NM_001276366		Approved	bA507D14.1	uc031teh.1	Q5TBE3	OTTHUMG00000020134	ENST00000376001.3:c.234T>A	chr9.hg19:g.88842778A>T		97.0	0.0		99.0	43.0	NM_001276368	Q5TBE4	Silent	SNP	ENST00000376001.3	hg19	CCDS35055.1																																																																																			.	.		0.483	C9orf153-003	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052913.1	NM_001010907		T	88842778	A	T	88842778	2	4	344	1	0	0	0	0	0	0	0	1	2466	175	7	4		4	C9orf153	9	88842778	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1517180	88842778	52370653	715	48078										
C9orf79	286234	hgsc.bcm.edu	37	chr9	90501957	90501957	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcacagctggggtacagaccTccagtccctggagcccataa	11	14	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:90501957T>C	ENST00000325643.5	+	4	2621	c.2555T>C	c.(2554-2556)cTc>cCc	p.L852P		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	852					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GGTACAGACCTCCAGTCCCTG	0.577																																					p.L852P		Atlas-SNP	.											.	.	.	.	0			c.T2555C						.						47	45	45					9																	90501957		2203	4300	6503	SO:0001583	missense	286234	exon4			CAGACCTCCAGTC	AK093185	CCDS6676.1	9q22.1-q22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000177992	ENSG00000177992			26672	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 79", "family with sequence similarity 75, member E1"	C9orf79, FAM75E1			Standard	NM_178828		Approved	FLJ35866	uc004app.4	Q6ZUB1	OTTHUMG00000020157	ENST00000325643.5:c.2555T>C	chr9.hg19:g.90501957T>C	ENSP00000322640:p.Leu852Pro	79.0	0.0		63.0	21.0	NM_178828	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Missense_Mutation	SNP	ENST00000325643.5	hg19	CCDS6676.1	.	.	.	.	.	.	.	.	.	.	t	11.03	1.519447	0.27211	.	.	ENSG00000177992	ENST00000325643;ENST00000539327	T	0.06068	3.35	2.57	-0.148	0.13424	.	1.489590	0.04472	N	0.376278	T	0.13457	0.0326	L	0.41573	1.285	0.09310	N	0.999999	D;D	0.71674	0.998;0.994	D;P	0.65443	0.935;0.737	T	0.17992	-1.0351	10	0.51188	T	0.08	.	3.0452	0.06151	0.248:0.0:0.2551:0.4969	.	852;504	Q6ZUB1;Q8NA33	CI079_HUMAN;.	P	852;504	ENSP00000322640:L852P	ENSP00000322640:L852P	L	+	2	0	C9orf79	89691777	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	0.016000	0.13377	-0.032000	0.13758	0.455000	0.32223	CTC	.	.		0.577	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828		C	90501957	T	C	90501957	3	2	344	1	0	0	0	0	1	0	0	0	2499	1551	54	2	2569	2	C9orf79	9	90501957	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1659179	90501957	50711474	716	48079										
SEMA4D	10507	hgsc.bcm.edu	37	chr9	92002518	92002518	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcggcccgtgcctcgctgtcGatgcactgcagggagaaaat	14	12	0	1	rs549309784	byFrequency	TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:92002518G>C	ENST00000450295.1	-	12	1889	c.1113C>G	c.(1111-1113)atC>atG	p.I371M	SEMA4D_ENST00000422704.2_Missense_Mutation_p.I371M|SEMA4D_ENST00000420987.1_Missense_Mutation_p.I371M|SEMA4D_ENST00000339861.4_Missense_Mutation_p.I371M|SEMA4D_ENST00000343780.4_Missense_Mutation_p.I371M|SEMA4D_ENST00000356444.2_Missense_Mutation_p.I371M|SEMA4D_ENST00000455551.2_Missense_Mutation_p.I371M|SEMA4D_ENST00000438547.2_Missense_Mutation_p.I371M			Q92854	SEM4D_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	371	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|immune response (GO:0006955)|leukocyte aggregation (GO:0070486)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|ossification involved in bone maturation (GO:0043931)|positive regulation of cell migration (GO:0030335)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell projection organization (GO:0031344)|regulation of cell shape (GO:0008360)|regulation of dendrite morphogenesis (GO:0048814)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(8)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	34						CCTCGCTGTCGATGCACTGCA	0.572																																					p.I371M		Atlas-SNP	.											SEMA4D,NS,NS,0,1	SEMA4D	81	.	0			c.C1113G						.						105	110	108					9																	92002518		2203	4300	6503	SO:0001583	missense	10507	exon14			GCTGTCGATGCAC	U60800	CCDS6685.1, CCDS47991.1	9q22-q31	2013-01-11			ENSG00000187764	ENSG00000187764		"Semaphorins", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10732	protein-coding gene	gene with protein product	"M-sema G"	601866	"chromosome 9 open reading frame 164"	SEMAJ, C9orf164		8876214, 8969198	Standard	NM_006378		Approved	CD100, coll-4, FLJ39737	uc004aqo.1	Q92854	OTTHUMG00000020185	ENST00000450295.1:c.1113C>G	chr9.hg19:g.92002518G>C	ENSP00000416523:p.Ile371Met	94.0	0.0		83.0	10.0	NM_006378	B2RPM6|Q7Z5S4|Q8N8B0	Missense_Mutation	SNP	ENST00000450295.1	hg19	CCDS6685.1	.	.	.	.	.	.	.	.	.	.	G	11.68	1.711373	0.30322	.	.	ENSG00000187764	ENST00000339861;ENST00000420987;ENST00000455551;ENST00000343780;ENST00000450295;ENST00000438547;ENST00000356444;ENST00000422704	T;T;T;T;T;T;T;T	0.32023	1.47;1.47;1.47;1.47;1.47;1.47;1.47;1.47	5.36	2.58	0.30949	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.043708	0.85682	D	0.000000	T	0.53384	0.1793	M	0.88031	2.925	0.43250	D	0.995179	D;D	0.71674	0.998;0.998	D;D	0.74348	0.981;0.983	T	0.51585	-0.8687	10	0.87932	D	0	.	4.0333	0.09719	0.3202:0.0:0.4883:0.1915	.	371;371	Q92854-2;Q92854	.;SEM4D_HUMAN	M	371	ENSP00000344923:I371M;ENSP00000391733:I371M;ENSP00000411981:I371M;ENSP00000343418:I371M;ENSP00000416523:I371M;ENSP00000405102:I371M;ENSP00000348822:I371M;ENSP00000388768:I371M	ENSP00000344923:I371M	I	-	3	3	SEMA4D	91192338	1.000000	0.71417	0.937000	0.37676	0.020000	0.10135	0.924000	0.28777	0.414000	0.25790	-0.768000	0.03414	ATC	.	.		0.572	SEMA4D-018	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342411.1	NM_006378		C	92002518	G	C	92002518	3	2	344	1	0	0	0	0	1	0	0	0	14049	1048	37	4	2065	4	SEMA4D	9	92002518	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1500561	92002518	49210913	717	48080										
ROR2	4920	hgsc.bcm.edu	37	chr9	94488970	94488970	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	caagcgatgaccagtggaatTgcgatgctggggaccaagat	14	8	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:94488970T>A	ENST00000375708.3	-	8	1437	c.1239A>T	c.(1237-1239)gcA>gcT	p.A413A	ROR2_ENST00000375715.1_Silent_p.A273A|ROR2_ENST00000550066.1_5'UTR	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	413					cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|embryonic genitalia morphogenesis (GO:0030538)|inner ear morphogenesis (GO:0042472)|JNK cascade (GO:0007254)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	clathrin-coated endocytic vesicle membrane (GO:0030669)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						CCAGTGGAATTGCGATGCTGG	0.512																																					p.A413A		Atlas-SNP	.											.	ROR2	167	.	0			c.A1239T						.						113	98	103					9																	94488970		2203	4300	6503	SO:0001819	synonymous_variant	4920	exon8			TGGAATTGCGATG	M97639	CCDS6691.1	9q22	2013-01-11			ENSG00000169071	ENSG00000169071		"Immunoglobulin superfamily / I-set domain containing"	10257	protein-coding gene	gene with protein product		602337		NTRKR2, BDB, BDB1		1334494, 10700182	Standard	NM_004560		Approved		uc004arj.2	Q01974	OTTHUMG00000020211	ENST00000375708.3:c.1239A>T	chr9.hg19:g.94488970T>A		71.0	0.0		57.0	25.0	NM_004560	Q59GF5|Q5SPI5|Q9HAY7|Q9HB61	Silent	SNP	ENST00000375708.3	hg19	CCDS6691.1																																																																																			.	.		0.512	ROR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053040.1			A	94488970	T	A	94488970	2	1	344	1	0	0	0	0	0	0	0	1	13542	1799	63	4		4	ROR2	9	94488970	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2486452	94488970	46724461	718	48081										
WNK2	65268	hgsc.bcm.edu	37	chr9	96051121	96051121	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaaggaacaacccagctttcTagccagtcagcagctcctga	9	13	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:96051121T>A	ENST00000297954.4	+	20	4196	c.4196T>A	c.(4195-4197)cTa>cAa	p.L1399Q	WNK2_ENST00000349097.3_Missense_Mutation_p.L1011Q|WNK2_ENST00000427277.2_Missense_Mutation_p.L974Q|WNK2_ENST00000356055.3_5'UTR|WNK2_ENST00000395477.2_Missense_Mutation_p.L1362Q|WNK2_ENST00000395475.2_3'UTR	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	1399					intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						CCCAGCTTTCTAGCCAGTCAG	0.597																																					p.L1362Q		Atlas-SNP	.											.	WNK2	277	.	0			c.T4085A						.						14	16	15					9																	96051121		2190	4260	6450	SO:0001583	missense	65268	exon19			GCTTTCTAGCCAG	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"serologically defined colon cancer antigen 43"	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.4196T>A	chr9.hg19:g.96051121T>A	ENSP00000297954:p.Leu1399Gln	199.0	0.0		161.0	58.0	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Missense_Mutation	SNP	ENST00000297954.4	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.59|11.59	1.685315|1.685315	0.29872|0.29872	.|.	.|.	ENSG00000165238|ENSG00000165238	ENST00000297954;ENST00000395477;ENST00000349097;ENST00000427277|ENST00000432730;ENST00000448251	T;T;T;T|.	0.35789|.	1.29;1.29;1.29;1.29|.	5.83|5.83	-4.59|-4.59	0.03400|0.03400	.|.	1.418270|.	0.03859|.	N|.	0.273667|.	T|.	0.30854|.	0.0778|.	L|L	0.38175|0.38175	1.15|1.15	0.09310|0.09310	N|N	1|1	D;P;D;D|.	0.76494|.	0.998;0.744;0.999;0.974|.	P;B;D;P|.	0.67548|.	0.897;0.23;0.952;0.521|.	T|.	0.40608|.	-0.9554|.	10|.	0.18276|.	T|.	0.48|.	.|.	7.351|7.351	0.26691|0.26691	0.1196:0.2624:0.0:0.618|0.1196:0.2624:0.0:0.618	.|.	1362;965;1362;1399|.	Q9Y3S1-2;A6PVR4;F8W9F9;Q9Y3S1|.	.;.;.;WNK2_HUMAN|.	Q|K	1399;1362;1011;974|1358;159	ENSP00000297954:L1399Q;ENSP00000378860:L1362Q;ENSP00000297876:L1011Q;ENSP00000411181:L974Q|.	ENSP00000297954:L1399Q|.	L|X	+|+	2|1	0|0	WNK2|WNK2	95090942|95090942	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.023000|0.023000	0.10783|0.10783	-0.644000|-0.644000	0.05415|0.05415	-0.403000|-0.403000	0.07622|0.07622	-0.388000|-0.388000	0.06559|0.06559	CTA|TAG	.	.		0.597	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648		A	96051121	T	A	96051121	3	1	344	1	0	0	0	0	1	0	0	0	17393	1522	53	4	4159	4	WNK2	9	96051121	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1562151	96051121	45162310	719	48082										
C9orf3	84909	hgsc.bcm.edu	37	chr9	97522798	97522798	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctgactttcctcatgctatcAggatatggtacaaaactaaa	6	9	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:97522798A>T	ENST00000375315.2	+	1	733	c.733A>T	c.(733-735)Agg>Tgg	p.R245W	C9orf3_ENST00000297979.5_Missense_Mutation_p.R245W|C9orf3_ENST00000277198.2_Missense_Mutation_p.R245W	NM_001193329.1	NP_001180258.1	Q8N6M6	AMPO_HUMAN	chromosome 9 open reading frame 3	245					leukotriene biosynthetic process (GO:0019370)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(323;0.000275)		TCATGCTATCAGGATATGGTA	0.512																																					p.R245W		Atlas-SNP	.											.	C9orf3	100	.	0			c.A733T						.						63	57	59					9																	97522798		2203	4300	6503	SO:0001583	missense	84909	exon2			GCTATCAGGATAT	AF043896	CCDS6713.1, CCDS55327.1, CCDS55328.1	9q22	2013-06-27			ENSG00000148120	ENSG00000148120			1361	protein-coding gene	gene with protein product	aminopeptidase O					15687497	Standard	NM_001193329		Approved	C90RF3, FLJ14675, APO, AOPEP, AP-O	uc004ava.3	Q8N6M6	OTTHUMG00000020276	ENST00000375315.2:c.733A>T	chr9.hg19:g.97522798A>T	ENSP00000364464:p.Arg245Trp	54.0	0.0		60.0	22.0	NM_001193331	Q5T9B1|Q5T9B3|Q5T9B4|Q8WUL6|Q96M23|Q96SS1	Missense_Mutation	SNP	ENST00000375315.2	hg19	CCDS55328.1	.	.	.	.	.	.	.	.	.	.	A	18.21	3.573358	0.65765	.	.	ENSG00000148120	ENST00000277198;ENST00000297979;ENST00000375315;ENST00000427193;ENST00000424143;ENST00000428313	T;T;T;T;T;T	0.04862	4.14;4.14;4.14;3.54;4.14;3.54	4.79	3.63	0.41609	.	0.000000	0.85682	D	0.000000	T	0.21347	0.0514	M	0.66939	2.045	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;1.0;0.999	T	0.00383	-1.1774	10	0.87932	D	0	-17.1585	12.0019	0.53235	0.8551:0.1449:0.0:0.0	.	245;245;245;245	Q8N6M6;Q8N6M6-4;Q8N6M6-2;Q8N6M6-3	AMPO_HUMAN;.;.;.	W	245;245;245;119;68;27	ENSP00000277198:R245W;ENSP00000297979:R245W;ENSP00000364464:R245W;ENSP00000387736:R119W;ENSP00000402171:R68W;ENSP00000401854:R27W	ENSP00000277198:R245W	R	+	1	2	C9orf3	96562619	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	6.715000	0.74697	0.941000	0.37499	0.383000	0.25322	AGG	.	.		0.512	C9orf3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032823		T	97522798	A	T	97522798	3	4	344	1	0	0	0	0	1	0	0	0	2479	179	7	4	735	4	C9orf3	9	97522798	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1471677	97522798	43690633	720	48083										
HABP4	22927	hgsc.bcm.edu	37	chr9	99250387	99250387	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcagatggtaaaagatgactAtgaggacgattcccatgttt	10	6	1	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:99250387A>G	ENST00000375249.4	+	7	1091	c.1016A>G	c.(1015-1017)tAt>tGt	p.Y339C	HABP4_ENST00000466976.1_3'UTR|HABP4_ENST00000375251.3_Missense_Mutation_p.Y234C	NM_014282.2	NP_055097.2			hyaluronan binding protein 4											NS(1)|cervix(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	13		Acute lymphoblastic leukemia(62;0.0169)|all_hematologic(171;0.214)				AAAGATGACTATGAGGACGAT	0.498																																					p.Y339C		Atlas-SNP	.											.	HABP4	25	.	0			c.A1016G						.						177	158	165					9																	99250387		2203	4300	6503	SO:0001583	missense	22927	exon7			ATGACTATGAGGA	AF241831	CCDS6719.1	9q22.3-q31	2008-02-05			ENSG00000130956	ENSG00000130956			17062	protein-coding gene	gene with protein product						9523163, 10887182	Standard	XM_005251812		Approved	IHABP4, SERBP1L	uc010msg.3	Q5JVS0	OTTHUMG00000020298	ENST00000375249.4:c.1016A>G	chr9.hg19:g.99250387A>G	ENSP00000364398:p.Tyr339Cys	76.0	0.0		67.0	22.0	NM_014282		Missense_Mutation	SNP	ENST00000375249.4	hg19	CCDS6719.1	.	.	.	.	.	.	.	.	.	.	A	7.557	0.664000	0.14710	.	.	ENSG00000130956	ENST00000375251;ENST00000375249	T;T	0.46063	0.88;0.88	5.08	0.158	0.14942	.	1.139140	0.06144	N	0.672914	T	0.27489	0.0675	N	0.22421	0.69	0.23953	N	0.996365	B;B	0.20550	0.046;0.026	B;B	0.22386	0.039;0.007	T	0.25779	-1.0122	10	0.38643	T	0.18	0.353	4.3263	0.11041	0.4726:0.0:0.342:0.1854	.	234;339	Q5JVS0-2;Q5JVS0	.;HABP4_HUMAN	C	234;339	ENSP00000364400:Y234C;ENSP00000364398:Y339C	ENSP00000364398:Y339C	Y	+	2	0	HABP4	98290208	0.165000	0.22948	0.868000	0.34077	0.392000	0.30506	0.473000	0.22132	-0.056000	0.13221	0.528000	0.53228	TAT	.	.		0.498	HABP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053269.1	NM_014282		G	99250387	A	G	99250387	3	3	344	1	0	0	0	0	1	0	0	0	6948	449	16	2	1042	2	HABP4	9	99250387	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1727589	99250387	41963044	721	48084										
CDC14B	8555	hgsc.bcm.edu	37	chr9	99286009	99286009	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cccgtgcgaccaaggccagcTaggaaaataaagaagcacag	11	11	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:99286009T>C	ENST00000375241.1	-	10	1398		c.e10-2		CDC14B_ENST00000375236.1_Splice_Site|CDC14B_ENST00000463569.1_Splice_Site|CDC14B_ENST00000375242.3_Splice_Site|CDC14B_ENST00000481149.1_5'Flank|CDC14B_ENST00000265659.2_Splice_Site|CDC14B_ENST00000375240.3_Splice_Site	NM_003671.3|NM_033331.2	NP_003662.1|NP_201588.1	O60729	CC14B_HUMAN	cell division cycle 14B						activation of anaphase-promoting complex activity (GO:0051488)|DNA repair (GO:0006281)|G2 DNA damage checkpoint (GO:0031572)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)	15		Acute lymphoblastic leukemia(62;0.0559)				CAAGGCCAGCTAGGAAAATAA	0.478																																					.		Atlas-SNP	.											.	CDC14B	64	.	0			c.836-2A>G						.						37	34	35					9																	99286009		2203	4300	6503	SO:0001630	splice_region_variant	8555	exon11			GCCAGCTAGGAAA	AF023158	CCDS6721.1, CCDS6722.1, CCDS43853.1	9q22.3	2013-01-17	2013-01-17		ENSG00000081377	ENSG00000081377		"Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"	1719	protein-coding gene	gene with protein product		603505	"CDC14 (cell division cycle 14, S. cerevisiae) homolog B", "CDC14 cell division cycle 14 homolog B (S. cerevisiae)"			9367992	Standard	NM_003671		Approved	Cdc14B1, Cdc14B2, CDC14B3, hCDC14B	uc004awj.3	O60729	OTTHUMG00000020300	ENST00000375241.1:c.947-2A>G	chr9.hg19:g.99286009T>C		188.0	0.0		153.0	134.0	NM_001077181	A6N5X8|A8MQ20|B1AL31|B1AL32|O43183|O60730|Q5JU08	Splice_Site	SNP	ENST00000375241.1	hg19	CCDS6722.1	.	.	.	.	.	.	.	.	.	.	T	19.08	3.758761	0.69763	.	.	ENSG00000081377	ENST00000265659;ENST00000375241;ENST00000375240;ENST00000375242;ENST00000463569;ENST00000375236	.	.	.	5.34	5.34	0.76211	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7739	0.78193	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	CDC14B	98325830	1.000000	0.71417	0.965000	0.40720	0.720000	0.41350	7.825000	0.86693	2.367000	0.80283	0.528000	0.53228	.	.	.		0.478	CDC14B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053278.2	NM_033331	Intron	C	99286009	T	C	99286009	5	2	344	1	0	0	0	0	0	0	1	0	3059	1536	53	2	571	2	CDC14B	9	99286009	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	35622	99286009	41927422	722	48085										
HEMGN	55363	hgsc.bcm.edu	37	chr9	100698475	100698475	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaatagccattgtgatgtttCcttttcatgcacttcagctt	6	9	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:100698475C>A	ENST00000259456.3	-	3	294	c.151G>T	c.(151-153)Gaa>Taa	p.E51*		NM_018437.3|NM_197978.2	NP_060907.2|NP_932095.1	Q9BXL5	HEMGN_HUMAN	hemogen	51	Necessary for nuclear localization.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)	nucleus (GO:0005634)				NS(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|skin(2)|urinary_tract(1)	27		Acute lymphoblastic leukemia(62;0.0559)				TGTGATGTTTCCTTTTCATGC	0.343																																					p.E51X		Atlas-SNP	.											HEMGN,NS,malignant_melanoma,0,1	HEMGN	55	.	0			c.G151T						.						300	250	267					9																	100698475		2201	4300	6501	SO:0001587	stop_gained	55363	exon2			ATGTTTCCTTTTC	AF228713	CCDS6731.1	9q22.33	2014-01-21			ENSG00000136929	ENSG00000136929			17509	protein-coding gene	gene with protein product		610715					Standard	NM_018437		Approved	EDAG, CT155, NDR	uc004axy.4	Q9BXL5	OTTHUMG00000020336	ENST00000259456.3:c.151G>T	chr9.hg19:g.100698475C>A	ENSP00000259456:p.Glu51*	151.0	0.0		67.0	21.0	NM_197978	Q6XAR3|Q86XY5|Q9NPC0	Nonsense_Mutation	SNP	ENST00000259456.3	hg19	CCDS6731.1	.	.	.	.	.	.	.	.	.	.	C	18.23	3.578626	0.65878	.	.	ENSG00000136929	ENST00000375112;ENST00000259456	.	.	.	5.63	2.39	0.29439	.	0.224869	0.36268	N	0.002696	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-8.932	14.1732	0.65525	0.0:0.6193:0.3807:0.0	.	.	.	.	X	51	.	ENSP00000259456:E51X	E	-	1	0	HEMGN	99738296	0.371000	0.25056	0.246000	0.24233	0.018000	0.09664	0.481000	0.22260	0.791000	0.33826	-0.211000	0.12701	GAA	.	.		0.343	HEMGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053344.2	NM_197978		A	100698475	C	A	100698475	4	1	344	1	0	0	0	0	0	1	0	0	7059	864	30	3	1315	3	HEMGN	9	100698475	Nonsense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1412466	100698475	40514956	723	48086										
NR4A3	8013	hgsc.bcm.edu	37	chr9	102590707	102590707	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cagcccggaggacgaggtgcTgcccagcacctccatgtact	12	15	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:102590707T>A	ENST00000395097.2	+	3	1112	c.383T>A	c.(382-384)cTg>cAg	p.L128Q	NR4A3_ENST00000330847.1_Missense_Mutation_p.L139Q|NR4A3_ENST00000338488.4_Missense_Mutation_p.L128Q	NM_006981.3|NM_173200.2	NP_008912.2|NP_775292.1	Q92570	NR4A3_HUMAN	nuclear receptor subfamily 4, group A, member 3	128					gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|thyroid hormone receptor activity (GO:0004887)|zinc ion binding (GO:0008270)		TCF12/NR4A3(2)|TAF15/NR4A3(33)|EWSR1/NR4A3(146)|TFG/NR4A3(2)				Acute lymphoblastic leukemia(62;0.0559)|all_hematologic(171;0.189)				GACGAGGTGCTGCCCAGCACC	0.667			T	EWSR1	extraskeletal myxoid chondrosarcoma																																p.L139Q		Atlas-SNP	.		Dom	yes		9	9q22	8013	"nuclear receptor subfamily 4, group A, member 3 (NOR1)"		M	.	NR4A3	80	.	0			c.T416A						.						38	43	41					9																	102590707		2203	4296	6499	SO:0001583	missense	8013	exon4			AGGTGCTGCCCAG	U12767	CCDS6742.1, CCDS6743.1, CCDS6744.1	9q22	2013-01-16			ENSG00000119508	ENSG00000119508		"Nuclear hormone receptors"	7982	protein-coding gene	gene with protein product		600542				8614405	Standard	NM_006981		Approved	CSMF, CHN, NOR1, MINOR	uc004baf.1	Q92570	OTTHUMG00000021030	ENST00000395097.2:c.383T>A	chr9.hg19:g.102590707T>A	ENSP00000378531:p.Leu128Gln	37.0	0.0		19.0	14.0	NM_173200	A2A3I7|Q12935|Q14979|Q16420|Q4VXA8|Q4VXA9|Q9UEK2|Q9UEK3	Missense_Mutation	SNP	ENST00000395097.2	hg19	CCDS6743.1	.	.	.	.	.	.	.	.	.	.	T	16.37	3.103365	0.56291	.	.	ENSG00000119508	ENST00000395097;ENST00000338488;ENST00000330847	D;D;D	0.91577	-2.87;-2.45;-2.86	4.68	4.68	0.58851	.	2.050020	0.01617	N	0.022824	D	0.90497	0.7023	L	0.39898	1.24	0.34200	D	0.673047	P;P;P	0.47677	0.828;0.736;0.899	B;B;P	0.51355	0.299;0.221;0.667	T	0.80686	-0.1272	10	0.13470	T	0.59	.	9.1733	0.37096	0.0:0.0817:0.0:0.9183	.	139;128;128	Q92570-3;Q92570;Q92570-2	.;NR4A3_HUMAN;.	Q	128;128;139	ENSP00000378531:L128Q;ENSP00000340301:L128Q;ENSP00000333122:L139Q	ENSP00000333122:L139Q	L	+	2	0	NR4A3	101630528	1.000000	0.71417	0.998000	0.56505	0.681000	0.39784	5.987000	0.70571	2.091000	0.63221	0.455000	0.32223	CTG	.	.		0.667	NR4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055482.1			A	102590707	T	A	102590707	3	1	344	1	0	0	0	0	1	0	0	0	10643	1580	55	4	422	4	NR4A3	9	102590707	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1892232	102590707	38622724	724	48087										
CYLC2	1539	hgsc.bcm.edu	37	chr9	105767379	105767380	+	Missense_Mutation	DNP	GA	GA	TC													0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaggaaaagaagaaaagctaGatgcaaagaaagatagcaaa							TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:105767379_105767380GA>TC	ENST00000374798.3	+	5	536_537	c.466_467GA>TC	c.(466-468)GAt>TCt	p.D156S	CYLC2_ENST00000487798.1_Missense_Mutation_p.D156S	NM_001340.3	NP_001331.1	Q14093	CYLC2_HUMAN	cylicin, basic protein of sperm head cytoskeleton 2	156	31 X 3 AA repeats of K-K-X.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)	p.D156Y(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(14)|ovary(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)	41		all_hematologic(171;0.125)				agaaaagctagatgcaaagaaa	0.356																																					p.D156Y|p.D156A		Atlas-SNP	.											CYLC2,right_upper_lobe,carcinoma,0,1|.	CYLC2	109	.	1	Substitution - Missense(1)	lung(1)	c.G466T|c.A467C						.																																			SO:0001583	missense	1539	exon5			AAGCTAGATGCAA|AGCTAGATGCAAA	Z46788	CCDS35085.1	9q31.2	2008-07-21			ENSG00000155833	ENSG00000155833			2583	protein-coding gene	gene with protein product		604035				7737358	Standard	NM_001340		Approved		uc004bbs.2	Q14093	OTTHUMG00000020396	Exception_encountered	chr9.hg19:g.105767379_105767380delinsTC	ENSP00000420256:p.Asp156Ser	135.0|134.0	0.0		71.0	59.0|9.0	NM_001340	B2R8F4|Q5VVJ9	Missense_Mutation	SNP	ENST00000374798.3	hg19	CCDS35085.1																																																																																			.	.		0.356	CYLC2-001	KNOWN	alternative_3_UTR|NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053463.3	NM_001340		TC	105767380	GA	TC	105767379	3	4	344	1	0	0	0	0	1	0	0	0	4144	942	33	3	484	3	CYLC2	9	105767379	Missense_Mutation	DNP	GA	TCGA-UB-A7MB-01A-11D-A33Q-10	3176672	105767379	35446052	725	48088										
ABCA1	19	hgsc.bcm.edu	37	chr9	107620923	107620923	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccaagttgaatcatctcttcTgattttgatccattgcacag	6	10	3	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:107620923T>A	ENST00000374736.3	-	7	994	c.600A>T	c.(598-600)tcA>tcT	p.S200S	ABCA1_ENST00000423487.2_Silent_p.S200S	NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	200					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	TCATCTCTTCTGATTTTGATC	0.438																																					p.S200S		Atlas-SNP	.											.	ABCA1	244	.	0			c.A600T						.						144	138	140					9																	107620923		2203	4300	6503	SO:0001819	synonymous_variant	19	exon7			CTCTTCTGATTTT	AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"ATP binding cassette transporters / subfamily A"	29	protein-coding gene	gene with protein product	"Tangier disease"	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.600A>T	chr9.hg19:g.107620923T>A		139.0	0.0		81.0	70.0	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Silent	SNP	ENST00000374736.3	hg19	CCDS6762.1																																																																																			.	.		0.438	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502		A	107620923	T	A	107620923	2	1	344	1	0	0	0	0	0	0	0	1	28	1567	55	4		4	ABCA1	9	107620923	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1853544	107620923	33592508	726	48089										
AKNA	80709	hgsc.bcm.edu	37	chr9	117106039	117106039	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gggacaggagactgtgccatTgccttttgggaccgccttag	14	10	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:117106039T>C	ENST00000307564.4	-	19	3867	c.3706A>G	c.(3706-3708)Aat>Gat	p.N1236D	AKNA_ENST00000223791.3_Missense_Mutation_p.N696D|AKNA_ENST00000374079.4_Missense_Mutation_p.N181D|AKNA_ENST00000492875.1_5'UTR|AKNA_ENST00000374088.3_Missense_Mutation_p.N1236D|AKNA_ENST00000374075.5_Missense_Mutation_p.N1155D	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	1236					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						ACTGTGCCATTGCCTTTTGGG	0.562																																					p.N1236D		Atlas-SNP	.											.	AKNA	119	.	0			c.A3706G						.						94	90	92					9																	117106039		2203	4300	6503	SO:0001583	missense	80709	exon19			TGCCATTGCCTTT	AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.3706A>G	chr9.hg19:g.117106039T>C	ENSP00000303769:p.Asn1236Asp	113.0	0.0		63.0	44.0	NM_030767	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Missense_Mutation	SNP	ENST00000307564.4	hg19	CCDS6805.1	.	.	.	.	.	.	.	.	.	.	T	2.751	-0.259983	0.05791	.	.	ENSG00000106948	ENST00000307564;ENST00000374079;ENST00000374088;ENST00000223791;ENST00000374075	T;T;T;T;T	0.17528	2.74;2.27;2.74;2.52;2.74	4.06	-4.01	0.04045	.	1.767010	0.02524	N	0.092823	T	0.13713	0.0332	L	0.40543	1.245	0.09310	N	1	B;B	0.27732	0.118;0.187	B;B	0.27500	0.037;0.08	T	0.22208	-1.0223	10	0.22109	T	0.4	1.2622	7.576	0.27937	0.0:0.5661:0.1658:0.2681	.	1236;1155	Q7Z591;Q7Z591-2	AKNA_HUMAN;.	D	1236;181;1236;696;1155	ENSP00000303769:N1236D;ENSP00000363192:N181D;ENSP00000363201:N1236D;ENSP00000223791:N696D;ENSP00000363188:N1155D	ENSP00000223791:N696D	N	-	1	0	AKNA	116145860	0.000000	0.05858	0.000000	0.03702	0.140000	0.21249	-0.148000	0.10219	-0.816000	0.04340	0.529000	0.55759	AAT	.	.		0.562	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767		C	117106039	T	C	117106039	3	2	344	1	0	0	0	0	1	0	0	0	463	1812	63	2	629	2	AKNA	9	117106039	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	9485116	117106039	24107392	727	48090										
AKNA	80709	hgsc.bcm.edu	37	chr9	117118383	117118383	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gctccatccctgggcacagaTgcagcaaagggctgggctaa	13	12	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:117118383T>A	ENST00000307564.4	-	14	3041	c.2880A>T	c.(2878-2880)gcA>gcT	p.A960A	AKNA_ENST00000223791.3_Silent_p.A420A|AKNA_ENST00000374088.3_Silent_p.A960A|AKNA_ENST00000374075.5_Silent_p.A879A	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	960					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						TGGGCACAGATGCAGCAAAGG	0.612																																					p.A960A		Atlas-SNP	.											.	AKNA	119	.	0			c.A2880T						.						76	75	75					9																	117118383		2203	4300	6503	SO:0001819	synonymous_variant	80709	exon14			CACAGATGCAGCA	AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.2880A>T	chr9.hg19:g.117118383T>A		75.0	0.0		30.0	21.0	NM_030767	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Silent	SNP	ENST00000307564.4	hg19	CCDS6805.1																																																																																			.	.		0.612	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767		A	117118383	T	A	117118383	2	1	344	1	0	0	0	0	0	0	0	1	463	1451	51	4		4	AKNA	9	117118383	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	12344	117118383	24095048	728	48091										
DAB2IP	153090	hgsc.bcm.edu	37	chr9	124522473	124522473	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccgggcggcagttcgtggagAagtggtacccggtggtgacg	19	9	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:124522473A>C	ENST00000408936.3	+	6	1107	c.925A>C	c.(925-927)Aag>Cag	p.K309Q	DAB2IP_ENST00000259371.2_Missense_Mutation_p.K281Q|DAB2IP_ENST00000309989.1_Missense_Mutation_p.K185Q			Q5VWQ8	DAB2P_HUMAN	DAB2 interacting protein	309					activation of JUN kinase activity (GO:0007257)|activation of MAPKKK activity (GO:0000185)|angiogenesis (GO:0001525)|cell cycle (GO:0007049)|cell motility involved in cerebral cortex radial glia guided migration (GO:0021814)|cellular protein catabolic process (GO:0044257)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|layer formation in cerebral cortex (GO:0021819)|negative regulation of angiogenesis (GO:0016525)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of G0 to G1 transition (GO:0070317)|negative regulation of GTPase activity (GO:0034260)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphatidylinositol 3-kinase activity (GO:0043553)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of Ras GTPase activity (GO:0034261)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuron projection morphogenesis (GO:0048812)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of dendrite development (GO:1900006)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of synapse maturation (GO:0090129)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of ARF GTPase activity (GO:0032312)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein complex assembly (GO:0043254)|response to unfolded protein (GO:0006986)|transformed cell apoptotic process (GO:0006927)|tube formation (GO:0035148)|vascular endothelial growth factor receptor-2 signaling pathway (GO:0036324)	axon (GO:0030424)|cerebellar mossy fiber (GO:0044300)|climbing fiber (GO:0044301)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|neuronal cell body (GO:0043025)|neuronal cell body membrane (GO:0032809)|parallel fiber (GO:1990032)|plasma membrane (GO:0005886)	14-3-3 protein binding (GO:0071889)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|mitogen-activated protein kinase kinase binding (GO:0031434)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulatory subunit binding (GO:0036312)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein phosphatase 2A binding (GO:0051721)|Ras GTPase activator activity (GO:0005099)|SH3 domain binding (GO:0017124)|signaling adaptor activity (GO:0035591)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(8)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	27						GTTCGTGGAGAAGTGGTACCC	0.632																																					p.K281Q		Atlas-SNP	.											.	DAB2IP	150	.	0			c.A841C						.						65	58	61					9																	124522473		2203	4300	6503	SO:0001583	missense	153090	exon6			GTGGAGAAGTGGT	AF367051	CCDS6832.1, CCDS6833.2	9q33.1-q33.3	2008-07-21			ENSG00000136848	ENSG00000136848			17294	protein-coding gene	gene with protein product	"nGAP-like protein", "DOC-2/DAB2 interactive protein", "ASK-interacting protein", "ASK1-interacting protein 1"	609205				11944990, 11812785	Standard	XM_005251721		Approved	AF9Q34, DIP1/2, KIAA1743, AIP1	uc004bln.3	Q5VWQ8	OTTHUMG00000020595	ENST00000408936.3:c.925A>C	chr9.hg19:g.124522473A>C	ENSP00000386183:p.Lys309Gln	60.0	0.0		27.0	22.0	NM_032552	A6H8V2|A6NHI9|B0QZB1|G3XA90|Q8TDL2|Q96SE1|Q9C0C0	Missense_Mutation	SNP	ENST00000408936.3	hg19		.	.	.	.	.	.	.	.	.	.	A	17.78	3.472510	0.63737	.	.	ENSG00000136848	ENST00000394340;ENST00000436835;ENST00000259371;ENST00000408936;ENST00000373782;ENST00000309989	T;T;T;T;T;T	0.78003	-1.14;-0.47;-0.47;-0.47;-0.47;-0.47	4.72	4.72	0.59763	.	0.000000	0.85682	D	0.000000	T	0.73505	0.3595	L	0.36672	1.1	0.58432	D	0.999999	P	0.45240	0.854	P	0.47573	0.55	T	0.71020	-0.4713	10	0.25751	T	0.34	.	13.6859	0.62515	1.0:0.0:0.0:0.0	.	281	G3XA90	.	Q	281;185;281;309;218;185	ENSP00000377872:K281Q;ENSP00000409327:K185Q;ENSP00000259371:K281Q;ENSP00000386183:K309Q;ENSP00000362887:K218Q;ENSP00000310827:K185Q	ENSP00000259371:K281Q	K	+	1	0	DAB2IP	123562294	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.172000	0.65003	1.888000	0.54679	0.459000	0.35465	AAG	.	.		0.632	DAB2IP-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317857.1	NM_032552		C	124522473	A	C	124522473	3	2	344	1	0	0	0	0	1	0	0	0	4221	247	9	5	863	5	DAB2IP	9	124522473	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	7404090	124522473	16690958	729	48092										
OR1L3	26735	hgsc.bcm.edu	37	chr9	125437543	125437543	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttgatgggaaatctgctcatCatcttggctatccactctga	8	10	5	2	rs367667552		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:125437543C>T	ENST00000304820.2	+	1	229	c.135C>T	c.(133-135)atC>atT	p.I45I		NM_001005234.1	NP_001005234.1	Q8NH93	OR1L3_HUMAN	olfactory receptor, family 1, subfamily L, member 3	45						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	16						ATCTGCTCATCATCTTGGCTA	0.433																																					p.I45I		Atlas-SNP	.											.	OR1L3	51	.	0			c.C135T						.						144	140	142					9																	125437543		2203	4300	6503	SO:0001819	synonymous_variant	26735	exon1			GCTCATCATCTTG		CCDS35128.1	9q33.2	2013-09-20			ENSG00000171481	ENSG00000171481		"GPCR / Class A : Olfactory receptors"	8215	protein-coding gene	gene with protein product							Standard	NM_001005234		Approved	OR9-D	uc011lzb.2	Q8NH93	OTTHUMG00000020619	ENST00000304820.2:c.135C>T	chr9.hg19:g.125437543C>T		114.0	0.0		47.0	42.0	NM_001005234	B2RNF4|Q6IFN1	Silent	SNP	ENST00000304820.2	hg19	CCDS35128.1																																																																																			.	.		0.433	OR1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053950.1			T	125437543	C	T	125437543	2	4	344	1	0	0	0	0	0	0	0	1	10973	816	29	3		3	OR1L3	9	125437543	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	915070	125437543	15775888	730	48093										
RABGAP1	23637	hgsc.bcm.edu	37	chr9	125782674	125782674	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcttcgaggagaagtctggcAgctgctagcaggctgtcata	13	9	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:125782674A>T	ENST00000373647.4	+	13	1864	c.1730A>T	c.(1729-1731)cAg>cTg	p.Q577L		NM_012197.3	NP_036329.3	Q9Y3P9	RBGP1_HUMAN	RAB GTPase activating protein 1	577	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				cell cycle (GO:0007049)|positive regulation of GTPase activity (GO:0043547)|regulation of GTP catabolic process (GO:0033124)	centrosome (GO:0005813)|cytosol (GO:0005829)|microtubule associated complex (GO:0005875)	DNA binding (GO:0003677)|GTPase activator activity (GO:0005096)|Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)|tubulin binding (GO:0015631)			breast(3)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|prostate(4)|stomach(3)|upper_aerodigestive_tract(1)	41						GAAGTCTGGCAGCTGCTAGCA	0.453																																					p.Q577L		Atlas-SNP	.											.	RABGAP1	164	.	0			c.A1730T						.						94	89	91					9																	125782674		2203	4300	6503	SO:0001583	missense	23637	exon13			TCTGGCAGCTGCT	AJ011679	CCDS6848.2	9q34.11	2013-07-09			ENSG00000011454	ENSG00000011454			17155	protein-coding gene	gene with protein product	"rab6 GTPase activating protein (GAP and centrosome-associated)", "TBC1 domain family, member 11"	615882				10202141	Standard	NM_012197		Approved	GAPCenA, TBC1D11	uc011lzh.2	Q9Y3P9	OTTHUMG00000020633	ENST00000373647.4:c.1730A>T	chr9.hg19:g.125782674A>T	ENSP00000362751:p.Gln577Leu	59.0	0.0		27.0	23.0	NM_012197	B9A6L2|Q05CW2|Q6ZMY1|Q9HA28|Q9P0E2|Q9UG67	Missense_Mutation	SNP	ENST00000373647.4	hg19	CCDS6848.2	.	.	.	.	.	.	.	.	.	.	A	27.8	4.866514	0.91511	.	.	ENSG00000011454	ENST00000373647	T	0.77229	-1.08	5.66	5.66	0.87406	Rab-GAP/TBC domain (4);	0.000000	0.85682	D	0.000000	D	0.83294	0.5223	L	0.41356	1.27	0.80722	D	1	D	0.65815	0.995	D	0.69824	0.966	D	0.84317	0.0514	10	0.54805	T	0.06	-15.631	15.8951	0.79326	1.0:0.0:0.0:0.0	.	577	Q9Y3P9	RBGP1_HUMAN	L	577	ENSP00000362751:Q577L	ENSP00000362751:Q577L	Q	+	2	0	RABGAP1	124822495	1.000000	0.71417	0.995000	0.50966	0.962000	0.63368	8.932000	0.92897	2.147000	0.66899	0.533000	0.62120	CAG	.	.		0.453	RABGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053976.3	NM_012197		T	125782674	A	T	125782674	3	4	344	1	0	0	0	0	1	0	0	0	12979	188	7	4	1776	4	RABGAP1	9	125782674	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	345131	125782674	15430757	731	48094										
LHX2	9355	hgsc.bcm.edu	37	chr9	126794984	126794984	+	Nonstop_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cgactcttaccaaccttttcTaatgactcgcaacccctcac	3	17	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:126794984T>C	ENST00000373615.4	+	5	1958	c.1219T>C	c.(1219-1221)Taa>Caa	p.*407Q	RP11-85O21.5_ENST00000429482.1_RNA	NM_004789.3	NP_004780.3	P50458	LHX2_HUMAN	LIM homeobox 2	0					axon extension (GO:0048675)|axon guidance (GO:0007411)|cerebral cortex development (GO:0021987)|dorsal/ventral pattern formation (GO:0009953)|mesoderm development (GO:0007498)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|neural tube closure (GO:0001843)|olfactory bulb development (GO:0021772)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|retina development in camera-type eye (GO:0060041)|telencephalon regionalization (GO:0021978)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)	10						CAACCTTTTCTAATGACTCGC	0.443																																					p.X407Q		Atlas-SNP	.											.	LHX2	30	.	0			c.T1219C						.						76	74	74					9																	126794984		2203	4300	6503	SO:0001578	stop_lost	9355	exon5			CTTTTCTAATGAC	U11701	CCDS6853.1	9q33.3	2011-06-20			ENSG00000106689	ENSG00000106689		"Homeoboxes / LIM class"	6594	protein-coding gene	gene with protein product		603759				8649822, 10051612	Standard	NM_004789		Approved	LH-2, hLhx2	uc004boe.1	P50458	OTTHUMG00000020647	ENST00000373615.4:c.1219T>C	chr9.hg19:g.126794984T>C	ENSP00000362717:p.*407Glnext*1	157.0	0.0		72.0	57.0	NM_004789	O95860|Q52M57|Q8N1Z3	Missense_Mutation	SNP	ENST00000373615.4	hg19	CCDS6853.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.23|12.23	1.876370|1.876370	0.33162|0.33162	.|.	.|.	ENSG00000106689|ENSG00000106689	ENST00000446480|ENST00000373615	.|.	.|.	.|.	4.27|4.27	4.27|4.27	0.50696|0.50696	.|.	.|.	.|.	.|.	.|.	T|.	0.38348|.	0.1037|.	.|.	.|.	.|.	0.20764|0.20764	N|N	0.999853|0.999853	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.20240|.	-1.0281|.	4|.	.|.	.|.	.|.	.|.	10.0691|10.0691	0.42322|0.42322	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|.	.|.	.|.	P|Q	412|407	.|.	.|.	L|X	+|+	2|1	0|0	LHX2|LHX2	125834805|125834805	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.982000|0.982000	0.71751|0.71751	7.662000|7.662000	0.83803|0.83803	2.147000|2.147000	0.66899|0.66899	0.459000|0.459000	0.35465|0.35465	CTA|TAA	.	.		0.443	LHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054010.2			C	126794984	T	C	126794984	4	2	344	1	0	0	0	0	0	0	0	0	8780	1535	53	2	1237	2	LHX2	9	126794984	Nonstop_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1012310	126794984	14418447	732	48095										
GAPVD1	26130	hgsc.bcm.edu	37	chr9	128124887	128124887	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tatttttcacttctctaggcAaatccaccctgtttgctgtc	5	12	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:128124887A>G	ENST00000495955.1	+	28	4589	c.4299A>G	c.(4297-4299)gcA>gcG	p.A1433A	GAPVD1_ENST00000297933.6_Silent_p.A1415A|GAPVD1_ENST00000394105.2_Silent_p.A1442A|GAPVD1_ENST00000470056.1_Silent_p.A1388A|GAPVD1_ENST00000265956.4_Silent_p.A1407A|GAPVD1_ENST00000312123.9_Silent_p.A1394A|GAPVD1_ENST00000394104.2_Silent_p.A1433A|GAPVD1_ENST00000394083.2_Silent_p.A1367A			Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1	1433	VPS9. {ECO:0000255|PROSITE- ProRule:PRU00550}.				endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|regulation of protein transport (GO:0051223)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	GTPase activating protein binding (GO:0032794)|GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						TTCTCTAGGCAAATCCACCCT	0.393																																					p.A1442A		Atlas-SNP	.											.	GAPVD1	124	.	0			c.A4326G						.						142	140	141					9																	128124887		2203	4300	6503	SO:0001819	synonymous_variant	26130	exon27			CTAGGCAAATCCA		CCDS65130.1, CCDS65131.1, CCDS65132.1	9q34.11	2008-02-05			ENSG00000165219	ENSG00000165219			23375	protein-coding gene	gene with protein product		611714					Standard	XM_005251901		Approved	DKFZP434C212, KIAA1521	uc004bpr.3	Q14C86	OTTHUMG00000020678	ENST00000495955.1:c.4299A>G	chr9.hg19:g.128124887A>G		62.0	0.0		30.0	23.0	NM_015635	A8MYK3|B0QZ62|B0QZ63|B0QZ64|Q14C76|Q2Q1W1|Q8ND92|Q8WU86|Q96CZ4|Q9NXQ1|Q9P207|Q9Y4N0	Silent	SNP	ENST00000495955.1	hg19																																																																																				.	.		0.393	GAPVD1-014	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000355644.1			G	128124887	A	G	128124887	2	3	344	1	0	0	0	0	0	0	0	1	6247	117	5	2		2	GAPVD1	9	128124887	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1329903	128124887	13088544	733	48096										
QRFP	347148	hgsc.bcm.edu	37	chr9	133768976	133768976	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cctcccgaagcggaatctgcAgccagcatgctctctgcccg	10	17	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:133768976A>T	ENST00000343079.1	-	1	249	c.250T>A	c.(250-252)Tgc>Agc	p.C84S		NM_198180.1	NP_937823.1			pyroglutamylated RFamide peptide											cervix(1)|endometrium(3)|lung(1)|skin(2)	7	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.17e-05)|Epithelial(140;0.000267)		CGGAATCTGCAGCCAGCATGC	0.652																																					p.C84S		Atlas-SNP	.											.	QRFP	14	.	0			c.T250A						.						68	70	69					9																	133768976		2203	4300	6503	SO:0001583	missense	347148	exon1			ATCTGCAGCCAGC	AB109625	CCDS6936.1	9q34.12	2013-02-28			ENSG00000188710	ENSG00000188710		"Endogenous ligands"	29982	protein-coding gene	gene with protein product	"prepro-QRFP"	609795				12714592, 15808908	Standard	NM_198180		Approved	26RFa, P518	uc011mcb.2	P83859	OTTHUMG00000131663	ENST00000343079.1:c.250T>A	chr9.hg19:g.133768976A>T	ENSP00000345487:p.Cys84Ser	101.0	0.0		38.0	34.0	NM_198180		Missense_Mutation	SNP	ENST00000343079.1	hg19	CCDS6936.1	.	.	.	.	.	.	.	.	.	.	A	9.987	1.229790	0.22542	.	.	ENSG00000188710	ENST00000343079	T	0.42900	0.96	4.65	-0.566	0.11767	.	0.191853	0.35349	N	0.003263	T	0.21427	0.0516	N	0.22421	0.69	0.09310	N	1	B	0.19073	0.033	B	0.19391	0.025	T	0.14144	-1.0483	10	0.20519	T	0.43	.	4.9583	0.14054	0.599:0.1475:0.2535:0.0	.	84	P83859	OX26_HUMAN	S	84	ENSP00000345487:C84S	ENSP00000345487:C84S	C	-	1	0	QRFP	132758797	0.990000	0.36364	0.001000	0.08648	0.005000	0.04900	0.454000	0.21827	-0.301000	0.08882	-0.609000	0.04063	TGC	.	.		0.652	QRFP-001	KNOWN	mRNA_start_NF|mRNA_end_NF|cds_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254566.1	NM_198180		T	133768976	A	T	133768976	3	4	344	1	0	0	0	0	1	0	0	0	12892	188	7	4	163	4	QRFP	9	133768976	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	5644089	133768976	7444455	734	48097										
TSC1	7248	hgsc.bcm.edu	37	chr9	135779040	135779040	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cccctccccagtcctcaccaTggcagcattatgttcctcca	5	19	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:135779040T>C	ENST00000298552.3	-	17	2427	c.2206A>G	c.(2206-2208)Atg>Gtg	p.M736V	TSC1_ENST00000440111.2_Missense_Mutation_p.M736V|TSC1_ENST00000545250.1_Missense_Mutation_p.M685V	NM_000368.4|NM_001162426.1|NM_001162427.1	NP_000359.1|NP_001155898.1|NP_001155899.1	Q92574	TSC1_HUMAN	tuberous sclerosis 1	736					activation of Rho GTPase activity (GO:0032862)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|insulin receptor signaling pathway (GO:0008286)|kidney development (GO:0001822)|myelination (GO:0042552)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of TOR signaling (GO:0032007)|negative regulation of translation (GO:0017148)|neural tube closure (GO:0001843)|positive regulation of focal adhesion assembly (GO:0051894)|potassium ion transport (GO:0006813)|protein heterooligomerization (GO:0051291)|protein stabilization (GO:0050821)|regulation of cell cycle (GO:0051726)|regulation of cell-matrix adhesion (GO:0001952)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of protein kinase activity (GO:0045859)|regulation of stress fiber assembly (GO:0051492)|regulation of translation (GO:0006417)|response to insulin (GO:0032868)|rRNA export from nucleus (GO:0006407)|synapse organization (GO:0050808)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|lamellipodium (GO:0030027)|membrane (GO:0016020)|protein complex (GO:0043234)|TSC1-TSC2 complex (GO:0033596)	chaperone binding (GO:0051087)|GTPase regulator activity (GO:0030695)|protein N-terminus binding (GO:0047485)	p.?(1)		NS(1)|bone(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(9)|lung(20)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	65				OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06)		GTCCTCACCATGGCAGCATTA	0.532			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.M736V		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 1	9	9q34	7248	tuberous sclerosis 1 gene		"E, O"	.	TSC1	167	.	1	Unknown(1)	bone(1)	c.A2206G						.						70	73	72					9																	135779040		2203	4300	6503	SO:0001583	missense	7248	exon17	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	TCACCATGGCAGC	AF013168	CCDS6956.1, CCDS55350.1	9q34	2014-09-17			ENSG00000165699	ENSG00000165699			12362	protein-coding gene	gene with protein product		605284		TSC		9242607, 10806479	Standard	NM_000368		Approved	KIAA0243, LAM, hamartin	uc004cca.2	Q92574	OTTHUMG00000020844	ENST00000298552.3:c.2206A>G	chr9.hg19:g.135779040T>C	ENSP00000298552:p.Met736Val	78.0	0.0		47.0	38.0	NM_000368	B7Z897|Q5VVN5	Missense_Mutation	SNP	ENST00000298552.3	hg19	CCDS6956.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.205412	0.79127	.	.	ENSG00000165699	ENST00000298552;ENST00000440111;ENST00000545250	D;D;D	0.84223	-1.82;-1.82;-1.6	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	D	0.87838	0.6278	L	0.32530	0.975	0.80722	D	1	D;D	0.61080	0.989;0.989	D;D	0.68483	0.958;0.958	D	0.89220	0.3570	10	0.72032	D	0.01	-20.1791	14.468	0.67497	0.0:0.0:0.0:1.0	.	685;736	B7Z897;Q92574	.;TSC1_HUMAN	V	736;736;685	ENSP00000298552:M736V;ENSP00000394524:M736V;ENSP00000444017:M685V	ENSP00000298552:M736V	M	-	1	0	TSC1	134768861	1.000000	0.71417	0.949000	0.38748	0.883000	0.51084	7.992000	0.88273	2.014000	0.59158	0.528000	0.53228	ATG	.	.		0.532	TSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054799.1			C	135779040	T	C	135779040	3	2	344	1	0	0	0	0	1	0	0	0	16620	1464	51	2	1316	2	TSC1	9	135779040	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2010064	135779040	5434391	735	48098										
C9orf96	169436	hgsc.bcm.edu	37	chr9	136270407	136270407	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccggagctggtgtccagtagTatgaaggccctgctccagga	14	11	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:136270407T>C	ENST00000371957.3	+	18	2012	c.1905T>C	c.(1903-1905)agT>agC	p.S635S	C9orf96_ENST00000371955.1_Silent_p.S168S	NM_153710.3	NP_714921.4	Q8NE28	STKL1_HUMAN		635							ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			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)		TGTCCAGTAGTATGAAGGCCC	0.622																																					p.S635S		Atlas-SNP	.											.	C9orf96	77	.	0			c.T1905C						.						49	45	46					9																	136270407		2203	4300	6503	SO:0001819	synonymous_variant	169436	exon18			CAGTAGTATGAAG																												ENST00000371957.3:c.1905T>C	chr9.hg19:g.136270407T>C		23.0	0.0		12.0	10.0	NM_153710	Q5T8U8|Q6ZMP6|Q6ZMQ5	Silent	SNP	ENST00000371957.3	hg19	CCDS35169.1																																																																																			.	.		0.622	C9orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054855.1			C	136270407	T	C	136270407	2	2	344	1	0	0	0	0	0	0	0	1	2510	1635	57	2		2	C9orf96	9	136270407	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	491367	136270407	4943024	736	48099										
TMEM8C	389827	hgsc.bcm.edu	37	chr9	136384125	136384125	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acaaatgttgacctcttgggTtcgtcgaagtcggccagtgc	12	10	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:136384125T>A	ENST00000339996.3	-	3	371	c.270A>T	c.(268-270)gaA>gaT	p.E90D	TMEM8C_ENST00000413714.1_5'UTR	NM_001080483.2	NP_001073952.1	A6NI61	TMM8C_HUMAN	transmembrane protein 8C	90					muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|plasma membrane fusion (GO:0045026)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|large_intestine(2)|lung(4)	8						ACCTCTTGGGTTCGTCGAAGT	0.637																																					p.E90D		Atlas-SNP	.											.	TMEM8C	32	.	0			c.A270T						.						118	101	107					9																	136384125		2203	4300	6503	SO:0001583	missense	389827	exon3			CTTGGGTTCGTCG	BX324209	CCDS35170.1	9q34.2	2009-06-19		2009-06-19	ENSG00000187616	ENSG00000187616			33778	protein-coding gene	gene with protein product	"transmembrane protein 226"	615345					Standard	NM_001080483		Approved	TMEM226	uc011mdk.2	A6NI61	OTTHUMG00000131685	ENST00000339996.3:c.270A>T	chr9.hg19:g.136384125T>A	ENSP00000419712:p.Glu90Asp	68.0	0.0		22.0	17.0	NM_001080483		Missense_Mutation	SNP	ENST00000339996.3	hg19	CCDS35170.1	.	.	.	.	.	.	.	.	.	.	T	11.79	1.744382	0.30865	.	.	ENSG00000187616	ENST00000339996	T	0.49720	0.77	5.09	-0.235	0.13071	.	0.000000	0.85682	D	0.000000	T	0.53449	0.1797	L	0.55103	1.725	0.39448	D	0.967352	D	0.76494	0.999	D	0.69654	0.965	T	0.51466	-0.8702	10	0.18276	T	0.48	-32.0469	9.1648	0.37046	0.0:0.3954:0.0:0.6046	.	90	A6NI61	TMM8C_HUMAN	D	90	ENSP00000419712:E90D	ENSP00000419712:E90D	E	-	3	2	TMEM8C	135373946	0.054000	0.20591	0.988000	0.46212	0.215000	0.24574	-0.667000	0.05274	0.019000	0.15079	-0.765000	0.03448	GAA	.	.		0.637	TMEM8C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356200.2	NM_001080483		A	136384125	T	A	136384125	3	1	344	1	0	0	0	0	1	0	0	0	16231	1722	60	4	407	4	TMEM8C	9	136384125	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	113718	136384125	4829306	737	48100										
KCNT1	57582	hgsc.bcm.edu	37	chr9	138656968	138656968	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gacggagaagcacgtggtccTgtgtgtcagctccctcaaga	13	11	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:138656968T>A	ENST00000263604.3	+	12	1070	c.1070T>A	c.(1069-1071)cTg>cAg	p.L357Q	KCNT1_ENST00000491806.2_Missense_Mutation_p.L343Q|KCNT1_ENST00000486577.2_Missense_Mutation_p.L337Q|KCNT1_ENST00000488444.2_Missense_Mutation_p.L357Q|KCNT1_ENST00000298480.5_Missense_Mutation_p.L376Q|KCNT1_ENST00000487664.1_Missense_Mutation_p.L331Q|KCNT1_ENST00000490355.2_Missense_Mutation_p.L357Q|KCNT1_ENST00000371757.2_Missense_Mutation_p.L376Q			Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1	357					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)		CACGTGGTCCTGTGTGTCAGC	0.627																																					p.L376Q		Atlas-SNP	.											.	KCNT1	139	.	0			c.T1127A						.						204	180	188					9																	138656968		2203	4300	6503	SO:0001583	missense	57582	exon12			TGGTCCTGTGTGT	AB037843	CCDS35175.1, CCDS35175.2, CCDS65188.1	9q34.3	2012-07-05			ENSG00000107147	ENSG00000107147		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18865	protein-coding gene	gene with protein product		608167				10718198, 16382103	Standard	NM_020822		Approved	KCa4.1, KIAA1422	uc011mdq.2	Q5JUK3	OTTHUMG00000020917	ENST00000263604.3:c.1070T>A	chr9.hg19:g.138656968T>A	ENSP00000263604:p.Leu357Gln	136.0	0.0		62.0	45.0	NM_020822	B3KXF7|B7ZVY4|B9EGP2|G5E9V0|Q9P2C5	Missense_Mutation	SNP	ENST00000263604.3	hg19		.	.	.	.	.	.	.	.	.	.	T	23.0	4.366680	0.82463	.	.	ENSG00000107147	ENST00000487664;ENST00000298480;ENST00000371757;ENST00000486577;ENST00000491806;ENST00000488444;ENST00000490355;ENST00000263604	T;T;T;T	0.26223	1.75;1.75;1.75;1.75	4.35	4.35	0.52113	NAD(P)-binding domain (1);	0.000000	0.56097	U	0.000022	T	0.46210	0.1381	M	0.69358	2.11	0.58432	D	0.999999	P;D;D;D	0.67145	0.952;0.996;0.972;0.987	P;D;D;P	0.65987	0.873;0.928;0.94;0.873	T	0.49437	-0.8940	10	0.87932	D	0	-10.8422	12.853	0.57869	0.0:0.0:0.0:1.0	.	343;376;331;357	C9JYL2;B9EGP2;G5E9V0;Q5JUK3	.;.;.;KCNT1_HUMAN	Q	331;376;376;337;343;357;357;357	ENSP00000417851:L331Q;ENSP00000298480:L376Q;ENSP00000360822:L376Q;ENSP00000263604:L357Q	ENSP00000263604:L357Q	L	+	2	0	KCNT1	137796789	0.996000	0.38824	1.000000	0.80357	0.977000	0.68977	7.575000	0.82447	1.817000	0.53016	0.379000	0.24179	CTG	.	.		0.627	KCNT1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_020822		A	138656968	T	A	138656968	3	1	344	1	0	0	0	0	1	0	0	0	8100	1580	55	4	1173	4	KCNT1	9	138656968	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2272843	138656968	2556463	738	48101										
SLC34A3	142680	hgsc.bcm.edu	37	chr9	140127698	140127698	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cggtgcacgggatcttcaacTggctcacagtgctggtcctg	13	12	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:140127698T>A	ENST00000538474.1	+	7	822	c.598T>A	c.(598-600)Tgg>Agg	p.W200R	SLC34A3_ENST00000361134.2_Missense_Mutation_p.W200R	NM_001177316.1|NM_001177317.1	NP_001170787|NP_001170788	Q8N130	NPT2C_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 3	200					cellular phosphate ion homeostasis (GO:0030643)|ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|sodium:phosphate symporter activity (GO:0005436)			kidney(3)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		GATCTTCAACTGGCTCACAGT	0.701																																					p.W200R		Atlas-SNP	.											.	SLC34A3	32	.	0			c.T598A						.						13	13	13					9																	140127698		2128	4211	6339	SO:0001583	missense	142680	exon7			TTCAACTGGCTCA	AB055000	CCDS7038.1	9q34.3	2013-07-17	2013-07-17		ENSG00000198569	ENSG00000198569		"Solute carriers"	20305	protein-coding gene	gene with protein product		609826	"solute carrier family 34 (sodium phosphate), member 3"			11880379, 16358215, 16358214	Standard	NM_080877		Approved	NPTIIc, FLJ38680	uc004cmf.1	Q8N130	OTTHUMG00000131780	ENST00000538474.1:c.598T>A	chr9.hg19:g.140127698T>A	ENSP00000442397:p.Trp200Arg	59.0	0.0		26.0	22.0	NM_001177317	A2BFA1	Missense_Mutation	SNP	ENST00000538474.1	hg19	CCDS7038.1	.	.	.	.	.	.	.	.	.	.	t	18.70	3.680965	0.68042	.	.	ENSG00000198569	ENST00000538474;ENST00000361134	D;D	0.85556	-2.0;-2.0	3.59	3.59	0.41128	.	0.000000	0.52532	D	0.000062	D	0.90878	0.7134	M	0.79614	2.46	0.44937	D	0.997958	D	0.89917	1.0	D	0.85130	0.997	D	0.90971	0.4820	10	0.59425	D	0.04	-11.4777	10.4527	0.44531	0.0:0.0:0.0:1.0	.	200	Q8N130	NPT2C_HUMAN	R	200	ENSP00000442397:W200R;ENSP00000355353:W200R	ENSP00000355353:W200R	W	+	1	0	SLC34A3	139247519	1.000000	0.71417	1.000000	0.80357	0.625000	0.37756	3.047000	0.49854	1.625000	0.50366	0.449000	0.29647	TGG	.	.		0.701	SLC34A3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254712.1	NM_080877		A	140127698	T	A	140127698	3	1	344	1	0	0	0	0	1	0	0	0	14584	1580	55	4	620	4	SLC34A3	9	140127698	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1470730	140127698	1085733	739	48102										
EHMT1	79813	hgsc.bcm.edu	37	chr9	140695341	140695341	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttccctggcaggatgacggaGgctggacacccatgatctgg	14	11	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr9:140695341G>T	ENST00000460843.1	+	18	2644	c.2617G>T	c.(2617-2619)Ggc>Tgc	p.G873C		NM_024757.4	NP_079033.4	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	873					chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|embryo development (GO:0009790)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|methyltransferase activity (GO:0008168)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		GGATGACGGAGGCTGGACACC	0.587																																					p.G873C		Atlas-SNP	.											.	EHMT1	196	.	0			c.G2617T						.						162	117	132					9																	140695341		2203	4300	6503	SO:0001583	missense	79813	exon18			GACGGAGGCTGGA	AY083210	CCDS7050.1, CCDS7050.2, CCDS56595.1	9q34.3	2013-09-20			ENSG00000181090	ENSG00000181090	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases", "Ankyrin repeat domain containing"	24650	protein-coding gene	gene with protein product		607001	"euchromatic histone methyltransferase 1"			11347906, 12004135	Standard	NM_024757		Approved	Eu-HMTase1, FLJ12879, KIAA1876, bA188C12.1, KMT1D	uc011mfc.2	Q9H9B1	OTTHUMG00000020995	ENST00000460843.1:c.2617G>T	chr9.hg19:g.140695341G>T	ENSP00000417980:p.Gly873Cys	134.0	0.0		58.0	45.0	NM_024757	B1AQ58|B1AQ59|Q86X08|Q8TCN7|Q96F53|Q96JF1|Q96KH4	Missense_Mutation	SNP	ENST00000460843.1	hg19	CCDS7050.2	.	.	.	.	.	.	.	.	.	.	G	22.4	4.285174	0.80803	.	.	ENSG00000181090	ENST00000371400;ENST00000460843	T	0.74315	-0.83	5.49	5.49	0.81192	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	D	0.91466	0.7306	H	0.96720	3.87	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94009	0.7282	10	0.87932	D	0	.	19.3646	0.94456	0.0:0.0:1.0:0.0	.	873	Q9H9B1	EHMT1_HUMAN	C	842;873	ENSP00000417980:G873C	ENSP00000360453:G842C	G	+	1	0	EHMT1	139815162	1.000000	0.71417	0.977000	0.42913	0.484000	0.33280	9.604000	0.98317	2.582000	0.87167	0.561000	0.74099	GGC	.	.		0.587	EHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055371.2	NM_024757		T	140695341	G	T	140695341	3	4	344	1	0	0	0	0	1	0	0	0	4985	1000	35	3	2736	3	EHMT1	9	140695341	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	567643	140695341	518090	740	48103										
DIP2C	22982	hgsc.bcm.edu	37	chr10	395294	395294	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gggggtagaccaaggccacgTggtcgccgtcctgaaggtgg	18	10	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:395294T>A	ENST00000280886.6	-	25	3173	c.3086A>T	c.(3085-3087)cAc>cTc	p.H1029L		NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	1029						nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(8)|endometrium(6)|kidney(10)|large_intestine(13)|lung(26)|ovary(3)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	81		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		CAAGGCCACGTGGTCGCCGTC	0.652																																					p.H1029L		Atlas-SNP	.											.	DIP2C	195	.	0			c.A3086T						.						89	66	74					10																	395294		2203	4300	6503	SO:0001583	missense	22982	exon25			GCCACGTGGTCGC	BC035216	CCDS7054.1	10p15.3	2006-01-13	2006-01-13	2006-01-13	ENSG00000151240	ENSG00000151240			29150	protein-coding gene	gene with protein product		611380	"KIAA0934"	KIAA0934			Standard	NM_014974		Approved		uc001ifp.3	Q9Y2E4	OTTHUMG00000017532	ENST00000280886.6:c.3086A>T	chr10.hg19:g.395294T>A	ENSP00000280886:p.His1029Leu	29.0	0.0		33.0	16.0	NM_014974	B4DPI5|Q5SS78	Missense_Mutation	SNP	ENST00000280886.6	hg19	CCDS7054.1	.	.	.	.	.	.	.	.	.	.	T	18.33	3.600841	0.66332	.	.	ENSG00000151240	ENST00000280886	T	0.09630	2.96	5.18	4.03	0.46877	AMP-dependent synthetase/ligase (1);	0.051344	0.85682	N	0.000000	T	0.14270	0.0345	L	0.43923	1.385	0.80722	D	1	B	0.28636	0.218	B	0.39152	0.292	T	0.03957	-1.0989	10	0.62326	D	0.03	-25.8139	11.3053	0.49332	0.1366:0.0:0.0:0.8634	.	1029	Q9Y2E4	DIP2C_HUMAN	L	1029	ENSP00000280886:H1029L	ENSP00000280886:H1029L	H	-	2	0	DIP2C	385294	1.000000	0.71417	0.474000	0.27266	0.274000	0.26718	8.033000	0.88852	0.785000	0.33685	0.460000	0.39030	CAC	.	.		0.652	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974		A	395294	T	A	395294	3	1	344	1	0	0	0	0	1	0	0	0	4531	1696	59	4	1636	4	DIP2C	10	395294	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10		395294	135139453	741	48104										
PFKFB3	5209	hgsc.bcm.edu	37	chr10	6255708	6255708	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	actggattggcgtccccacaAaaggtgagactgggtctcga	13	10	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:6255708A>G	ENST00000379775.4	+	2	529	c.199A>G	c.(199-201)Aaa>Gaa	p.K67E	PFKFB3_ENST00000379782.3_Missense_Mutation_p.K67E|PFKFB3_ENST00000379785.1_Missense_Mutation_p.K67E|PFKFB3_ENST00000360521.2_Missense_Mutation_p.K67E|PFKFB3_ENST00000379789.4_Missense_Mutation_p.K47E|PFKFB3_ENST00000540253.1_Missense_Mutation_p.K81E|PFKFB3_ENST00000317350.4_Missense_Mutation_p.K67E|PFKFB3_ENST00000536985.1_Missense_Mutation_p.K47E	NM_004566.3	NP_004557.1	Q16875	F263_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	67	6-phosphofructo-2-kinase.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|liver(2)|lung(10)|ovary(3)|upper_aerodigestive_tract(1)	22						CGTCCCCACAAAAGGTGAGAC	0.612																																					p.K67E		Atlas-SNP	.											.	PFKFB3	82	.	0			c.A199G						.						112	103	106					10																	6255708		2203	4300	6503	SO:0001583	missense	5209	exon2			CCCACAAAAGGTG		CCDS7078.1, CCDS44353.1, CCDS60479.1	10p15.1	2008-05-14			ENSG00000170525	ENSG00000170525			8874	protein-coding gene	gene with protein product		605319				9146922, 10072580	Standard	NM_004566		Approved		uc001ije.3	Q16875	OTTHUMG00000017621	ENST00000379775.4:c.199A>G	chr10.hg19:g.6255708A>G	ENSP00000369100:p.Lys67Glu	45.0	0.0		55.0	29.0	NM_004566	B7Z955|O43622|O75902|Q5VX15|Q5VX18|Q5VX19	Missense_Mutation	SNP	ENST00000379775.4	hg19	CCDS7078.1	.	.	.	.	.	.	.	.	.	.	A	19.30	3.801496	0.70682	.	.	ENSG00000170525	ENST00000536985;ENST00000379789;ENST00000540253;ENST00000317350;ENST00000379785;ENST00000379782;ENST00000360521;ENST00000379775;ENST00000358499	.	.	.	5.3	5.3	0.74995	6-phosphofructo-2-kinase (1);	0.000000	0.85682	D	0.000000	T	0.76442	0.3988	M	0.78456	2.415	0.80722	D	1	D;D;P;D	0.67145	0.996;0.962;0.927;0.983	P;B;B;P	0.58970	0.849;0.354;0.335;0.64	T	0.80618	-0.1302	9	0.87932	D	0	-2.413	15.3145	0.74062	1.0:0.0:0.0:0.0	.	81;67;67;47	B7Z955;Q16875-2;Q16875;Q5VX15	.;.;F263_HUMAN;.	E	47;47;81;67;67;67;67;67;67	.	ENSP00000369105:K67E	K	+	1	0	PFKFB3	6295714	1.000000	0.71417	0.953000	0.39169	0.054000	0.15201	8.889000	0.92470	2.018000	0.59344	0.456000	0.33151	AAA	.	.		0.612	PFKFB3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046647.1			G	6255708	A	G	6255708	3	3	344	1	0	0	0	0	1	0	0	0	11771	15	1	2	225	2	PFKFB3	10	6255708	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	5860414	6255708	129279039	742	48105										
SFMBT2	57713	hgsc.bcm.edu	37	chr10	7213990	7213990	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctgagccgctccgcagggtgAcggccctccggggccgggcc	17	17	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:7213990A>G	ENST00000361972.4	-	19	2372	c.2282T>C	c.(2281-2283)gTc>gCc	p.V761A	SFMBT2_ENST00000397167.1_Missense_Mutation_p.V761A	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	761					negative regulation of gene expression (GO:0010629)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	histone binding (GO:0042393)			NS(2)|breast(3)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(26)|lung(34)|ovary(5)|pancreas(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	99						CCGCAGGGTGACGGCCCTCCG	0.746																																					p.V761A		Atlas-SNP	.											.	SFMBT2	209	.	0			c.T2282C						.						10	13	12					10																	7213990		2129	4166	6295	SO:0001583	missense	57713	exon19			AGGGTGACGGCCC	AB046837	CCDS31138.1	10p15.1	2013-01-10	2003-11-14		ENSG00000198879	ENSG00000198879		"Sterile alpha motif (SAM) domain containing"	20256	protein-coding gene	gene with protein product		615392	"Scm-related gene containing four mbt domains 2"			10997877	Standard	NM_001029880		Approved	KIAA1617	uc009xio.2	Q5VUG0	OTTHUMG00000017630	ENST00000361972.4:c.2282T>C	chr10.hg19:g.7213990A>G	ENSP00000355109:p.Val761Ala	12.0	0.0		27.0	13.0	NM_001029880	A7MD09|Q9HCF5	Missense_Mutation	SNP	ENST00000361972.4	hg19	CCDS31138.1	.	.	.	.	.	.	.	.	.	.	A	10.31	1.316073	0.23908	.	.	ENSG00000198879	ENST00000361972;ENST00000397167	T;T	0.13901	2.55;2.55	5.25	4.12	0.48240	.	0.302414	0.35407	N	0.003233	T	0.11281	0.0275	L	0.46741	1.465	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.07673	-1.0760	10	0.08179	T	0.78	.	10.8677	0.46864	0.9257:0.0:0.0743:0.0	.	761	Q5VUG0	SMBT2_HUMAN	A	761	ENSP00000355109:V761A;ENSP00000380353:V761A	ENSP00000355109:V761A	V	-	2	0	SFMBT2	7253996	0.018000	0.18449	0.177000	0.23020	0.966000	0.64601	2.259000	0.43259	0.839000	0.34971	0.459000	0.35465	GTC	.	.		0.746	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046673.1	NM_001029880		G	7213990	A	G	7213990	3	3	344	1	0	0	0	0	1	0	0	0	14173	275	10	2	414	2	SFMBT2	10	7213990	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	958282	7213990	128320757	743	48106										
MCM10	55388	hgsc.bcm.edu	37	chr10	13217598	13217598	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaacctagtgggataactagAggtcaaattgtggggacccc	12	8	1	1	rs138161730	byFrequency	TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:13217598A>T	ENST00000484800.2	+	6	787	c.684A>T	c.(682-684)agA>agT	p.R228S	MCM10_ENST00000378694.1_Missense_Mutation_p.R227S|MCM10_ENST00000378714.3_Missense_Mutation_p.R227S			Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	228					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(4)|ovary(2)|skin(1)|stomach(1)	9						GGATAACTAGAGGTCAAATTG	0.488																																					p.R228S		Atlas-SNP	.											.	MCM10	76	.	0			c.A684T						.						125	125	125					10																	13217598		2203	4300	6503	SO:0001583	missense	55388	exon6			AACTAGAGGTCAA	AB042719	CCDS7095.1, CCDS7096.1	10p13	2008-08-01	2007-04-04		ENSG00000065328	ENSG00000065328			18043	protein-coding gene	gene with protein product		609357	"MCM10 minichromosome maintenance deficient 10 (S. cerevisiae)"			11095689, 17699597	Standard	NM_018518		Approved	PRO2249, CNA43, DNA43	uc001ima.3	Q7L590	OTTHUMG00000017694	ENST00000484800.2:c.684A>T	chr10.hg19:g.13217598A>T	ENSP00000418268:p.Arg228Ser	150.0	0.0		136.0	65.0	NM_182751	A8K9I6|B7ZKZ8|Q3MIR3|Q7LD55|Q96GX4|Q96NB6|Q9H0D7|Q9H3P9|Q9P177	Missense_Mutation	SNP	ENST00000484800.2	hg19	CCDS7096.1	.	.	.	.	.	.	.	.	.	.	A	4.905	0.168207	0.09339	.	.	ENSG00000065328	ENST00000378714;ENST00000361282;ENST00000484800;ENST00000378694	T;T;T	0.15017	2.48;2.46;2.47	5.42	-1.36	0.09085	.	0.412228	0.29389	N	0.012283	T	0.12305	0.0299	L	0.57536	1.79	0.09310	N	1	B;B;B	0.27559	0.179;0.181;0.113	B;B;B	0.27380	0.077;0.079;0.036	T	0.40098	-0.9581	10	0.10377	T	0.69	-13.2441	6.7546	0.23505	0.4675:0.1315:0.401:0.0	.	227;227;228	Q5T670;Q7L590-2;Q7L590	.;.;MCM10_HUMAN	S	227;228;228;227	ENSP00000367986:R227S;ENSP00000418268:R228S;ENSP00000367966:R227S	ENSP00000354945:R228S	R	+	3	2	MCM10	13257604	0.055000	0.20627	0.000000	0.03702	0.001000	0.01503	0.349000	0.20055	-0.410000	0.07542	-0.274000	0.10170	AGA	.	A|1.000;G|0.000		0.488	MCM10-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356853.1	NM_182751		T	13217598	A	T	13217598	3	4	344	1	0	0	0	0	1	0	0	0	9394	301	11	4	702	4	MCM10	10	13217598	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	6003608	13217598	122317149	744	48107										
FAM107B	83641	hgsc.bcm.edu	37	chr10	14563994	14563994	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tccatcaccttctgcaattcTggtttgttctgaggagcaag	9	10	4	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:14563994T>A	ENST00000378470.1	-	3	439	c.153A>T	c.(151-153)ccA>ccT	p.P51P	FAM107B_ENST00000378467.4_Silent_p.P51P|FAM107B_ENST00000468747.1_Silent_p.P51P|FAM107B_ENST00000378465.3_Silent_p.P51P|FAM107B_ENST00000378458.2_Silent_p.P51P|FAM107B_ENST00000479731.1_Silent_p.P51P|FAM107B_ENST00000378462.1_Silent_p.P51P|FAM107B_ENST00000478076.1_Silent_p.P51P|FAM107B_ENST00000181796.2_Silent_p.P226P|FAM107B_ENST00000496330.1_Silent_p.P51P	NM_001282695.1|NM_001282696.1|NM_001282697.1|NM_001282698.1|NM_001282700.1|NM_001282701.1|NM_001282702.1|NM_001282703.1	NP_001269624.1|NP_001269625.1|NP_001269626.1|NP_001269627.1|NP_001269629.1|NP_001269630.1|NP_001269631.1|NP_001269632.1	Q9H098	F107B_HUMAN	family with sequence similarity 107, member B	51					sensory perception of sound (GO:0007605)					breast(7)|kidney(1)|large_intestine(4)|lung(7)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TCTGCAATTCTGGTTTGTTCT	0.353																																					p.P226P		Atlas-SNP	.											.	FAM107B	43	.	0			c.A678T						.						136	127	130					10																	14563994		2203	4300	6503	SO:0001819	synonymous_variant	83641	exon4			CAATTCTGGTTTG	AK127413	CCDS7102.1, CCDS60486.1	10p14	2006-01-17	2006-01-17	2005-11-20	ENSG00000065809	ENSG00000065809			23726	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 45"	C10orf45		11230166	Standard	XM_005252616		Approved	FLJ45505, MGC11034	uc001ina.1	Q9H098	OTTHUMG00000017709	ENST00000378470.1:c.153A>T	chr10.hg19:g.14563994T>A		73.0	0.0		59.0	26.0	NM_031453	A8K1P4|D3DRT2|Q5T9K7|Q5T9K8|Q6ZSI4	Silent	SNP	ENST00000378470.1	hg19																																																																																				.	.		0.353	FAM107B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046899.1	NM_031453		A	14563994	T	A	14563994	2	1	344	1	0	0	0	0	0	0	0	1	5395	1567	55	4		4	FAM107B	10	14563994	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1346396	14563994	120970753	745	48108										
CUBN	8029	hgsc.bcm.edu	37	chr10	17151661	17151661	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agagttgaggagcatgaggcAtctgggtggcagcctccatt	15	8	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:17151661A>T	ENST00000377833.4	-	10	1154	c.1089T>A	c.(1087-1089)gaT>gaA	p.D363E		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	363	EGF-like 5. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)	p.D363E(1)		breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	AGCATGAGGCATCTGGGTGGC	0.453																																					p.D363E		Atlas-SNP	.											CUBN,NS,carcinoma,0,1	CUBN	515	.	1	Substitution - Missense(1)	kidney(1)	c.T1089A						.						184	127	146					10																	17151661		2203	4300	6503	SO:0001583	missense	8029	exon10			TGAGGCATCTGGG	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.1089T>A	chr10.hg19:g.17151661A>T	ENSP00000367064:p.Asp363Glu	67.0	0.0		76.0	27.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	A	0.001	-3.810101	0.00004	.	.	ENSG00000107611	ENST00000377833	D	0.89875	-2.58	5.64	-11.3	0.00108	EGF domain, merozoite surface protein 1-like (1);Growth factor, receptor (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	1.079030	0.07326	N	0.878349	T	0.71013	0.3290	N	0.25426	0.745	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.68815	-0.5309	10	0.02654	T	1	.	1.5415	0.02556	0.1641:0.2739:0.2634:0.2986	.	363	O60494	CUBN_HUMAN	E	363	ENSP00000367064:D363E	ENSP00000367064:D363E	D	-	3	2	CUBN	17191667	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	-2.865000	0.00724	-8.331000	0.00000	-2.052000	0.00405	GAT	.	.		0.453	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		T	17151661	A	T	17151661	3	4	344	1	0	0	0	0	1	0	0	0	4053	214	8	4	10014	4	CUBN	10	17151661	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2587667	17151661	118383086	746	48109										
SLC39A12	221074	hgsc.bcm.edu	37	chr10	18250689	18250689	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaattttacctacacagcctActgagcctcaggcaggatga	8	11	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:18250689A>C	ENST00000377369.2	+	3	714	c.441A>C	c.(439-441)ctA>ctC	p.L147L	SLC39A12_ENST00000377371.3_Silent_p.L147L|SLC39A12_ENST00000377374.4_Silent_p.L147L|SLC39A12_ENST00000539911.1_Silent_p.L13L	NM_001145195.1|NM_001282733.1|NM_001282734.1	NP_001138667.1|NP_001269662.1|NP_001269663.1	Q504Y0	S39AC_HUMAN	solute carrier family 39 (zinc transporter), member 12	147					regulation of microtubule polymerization (GO:0031113)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)|zinc ion transmembrane import (GO:0071578)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	zinc ion transmembrane transporter activity (GO:0005385)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(5)|lung(38)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	60						TACACAGCCTACTGAGCCTCA	0.393																																					p.L147L		Atlas-SNP	.											.	SLC39A12	181	.	0			c.A441C						.						82	86	85					10																	18250689		2203	4300	6503	SO:0001819	synonymous_variant	221074	exon3			CAGCCTACTGAGC		CCDS7124.1, CCDS44362.1, CCDS60493.1, CCDS60494.1	10p12.33	2013-05-22			ENSG00000148482	ENSG00000148482		"Solute carriers"	20860	protein-coding gene	gene with protein product		608734	"solute carrier family 39 (metal ion transporter), member 12"			12659941	Standard	NM_152725		Approved	FLJ30499	uc001ipo.2	Q504Y0	OTTHUMG00000017759	ENST00000377369.2:c.441A>C	chr10.hg19:g.18250689A>C		133.0	0.0		129.0	60.0	NM_152725	B7ZL35|C9JJL4|Q49AN8|Q4G0L3|Q5VWV8|Q5VWV9|Q6NZY5|Q96NN4	Silent	SNP	ENST00000377369.2	hg19	CCDS44362.1																																																																																			.	.		0.393	SLC39A12-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_152725		C	18250689	A	C	18250689	2	2	344	1	0	0	0	0	0	0	0	1	14630	378	14	5		5	SLC39A12	10	18250689	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1099028	18250689	117284058	747	48110										
GPR158	57512	hgsc.bcm.edu	37	chr10	25887814	25887814	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccattttggaagatgagaagCttttgatttccaagactcca	8	8	0	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:25887814C>A	ENST00000376351.3	+	11	3618	c.3259C>A	c.(3259-3261)Ctt>Att	p.L1087I	GPR158_ENST00000490549.1_3'UTR	NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	1087					protein localization to plasma membrane (GO:0072659)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|cervix(1)|endometrium(9)|kidney(10)|large_intestine(20)|lung(56)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	119						AGATGAGAAGCTTTTGATTTC	0.512																																					p.L1087I		Atlas-SNP	.											.	GPR158	255	.	0			c.C3259A						.						83	88	86					10																	25887814		2203	4300	6503	SO:0001583	missense	57512	exon11			GAGAAGCTTTTGA	AB032962	CCDS31166.1	10p12.31	2012-08-21			ENSG00000151025	ENSG00000151025		"GPCR / Class C : Orphans"	23689	protein-coding gene	gene with protein product		614573					Standard	NM_020752		Approved	KIAA1136	uc001isj.3	Q5T848	OTTHUMG00000017832	ENST00000376351.3:c.3259C>A	chr10.hg19:g.25887814C>A	ENSP00000365529:p.Leu1087Ile	88.0	0.0		76.0	30.0	NM_020752	Q6QR81|Q9ULT3	Missense_Mutation	SNP	ENST00000376351.3	hg19	CCDS31166.1	.	.	.	.	.	.	.	.	.	.	C	0.127	-1.118098	0.01785	.	.	ENSG00000151025	ENST00000376351	T	0.59906	0.23	5.85	1.77	0.24775	.	1.405820	0.04219	N	0.333285	T	0.37019	0.0988	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.20672	-1.0268	10	0.35671	T	0.21	.	5.5438	0.17053	0.36:0.4576:0.1163:0.066	.	1087	Q5T848	GP158_HUMAN	I	1087	ENSP00000365529:L1087I	ENSP00000365529:L1087I	L	+	1	0	GPR158	25927820	0.053000	0.20554	0.083000	0.20561	0.004000	0.04260	0.780000	0.26760	0.051000	0.15978	-0.181000	0.13052	CTT	.	.		0.512	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	XM_166110		A	25887814	C	A	25887814	3	1	344	1	0	0	0	0	1	0	0	0	6671	797	28	3	3301	3	GPR158	10	25887814	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	7637125	25887814	109646933	748	48111										
MYO3A	53904	hgsc.bcm.edu	37	chr10	26463109	26463109	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acagcatggaaaaagaaaagAagacatctgtagttacccag	9	7	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:26463109A>G	ENST00000265944.5	+	30	4082	c.3916A>G	c.(3916-3918)Aag>Gag	p.K1306E	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	1306					ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						AAAAGAAAAGAAGACATCTGT	0.433																																					p.K1306E		Atlas-SNP	.											.	MYO3A	371	.	0			c.A3916G						.						98	106	103					10																	26463109		2203	4300	6503	SO:0001583	missense	53904	exon30			GAAAAGAAGACAT	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.3916A>G	chr10.hg19:g.26463109A>G	ENSP00000265944:p.Lys1306Glu	170.0	0.0		174.0	85.0	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	hg19	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	A	10.61	1.399552	0.25291	.	.	ENSG00000095777	ENST00000265944	T	0.79940	-1.32	5.37	3.01	0.34805	.	0.434025	0.28989	N	0.013495	T	0.58395	0.2119	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.12156	0.007	T	0.49560	-0.8927	10	0.52906	T	0.07	.	3.6825	0.08316	0.6325:0.1761:0.0763:0.1151	.	1306	Q8NEV4	MYO3A_HUMAN	E	1306	ENSP00000265944:K1306E	ENSP00000265944:K1306E	K	+	1	0	MYO3A	26503115	1.000000	0.71417	0.053000	0.19242	0.764000	0.43329	3.218000	0.51192	0.336000	0.23639	0.460000	0.39030	AAG	.	.		0.433	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		G	26463109	A	G	26463109	3	3	344	1	0	0	0	0	1	0	0	0	10085	247	9	2	4026	2	MYO3A	10	26463109	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	575295	26463109	109071638	749	48112										
ZNF33B	7582	hgsc.bcm.edu	37	chr10	43089253	43089253	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cattgcattcaaaaggtttcTcccctgtgtgtgatctctga	8	10	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:43089253T>A	ENST00000359467.3	-	5	1259	c.1145A>T	c.(1144-1146)gAg>gTg	p.E382V	ZNF33B_ENST00000486187.1_RNA	NM_006955.1	NP_008886.1	Q06732	ZN33B_HUMAN	zinc finger protein 33B	382					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(15)|skin(1)|stomach(1)	29						AAAAGGTTTCTCCCCTGTGTG	0.433																																					p.E382V	Melanoma(137;1247 1767 16772 25727 43810)	Atlas-SNP	.											.	ZNF33B	78	.	0			c.A1145T						.						102	104	104					10																	43089253		2203	4300	6503	SO:0001583	missense	7582	exon5			GGTTTCTCCCCTG	X68688, AJ491697	CCDS7198.1	10q11.2	2013-01-08	2005-03-18		ENSG00000196693	ENSG00000196693		"Zinc fingers, C2H2-type", "-"	13097	protein-coding gene	gene with protein product		194522	"zinc finger protein 33b (KOX 31)", "zinc finger protein 11B"	ZNF11B		2014798	Standard	NM_006955		Approved	KOX31, KOX2	uc001jaf.1	Q06732	OTTHUMG00000018014	ENST00000359467.3:c.1145A>T	chr10.hg19:g.43089253T>A	ENSP00000352444:p.Glu382Val	86.0	0.0		62.0	36.0	NM_006955	Q06731|Q32MA2|Q86XY8|Q8NDW3	Missense_Mutation	SNP	ENST00000359467.3	hg19	CCDS7198.1	.	.	.	.	.	.	.	.	.	.	T	17.14	3.313875	0.60414	.	.	ENSG00000196693	ENST00000359467;ENST00000395836	T	0.26810	1.71	2.28	2.28	0.28536	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.36591	N	0.002514	T	0.33644	0.0870	L	0.31578	0.945	0.35683	D	0.814267	D	0.89917	1.0	D	0.87578	0.998	T	0.42565	-0.9444	10	0.87932	D	0	.	8.5071	0.33195	0.0:0.0:0.0:1.0	.	382	Q06732	ZN33B_HUMAN	V	382;348	ENSP00000352444:E382V	ENSP00000352444:E382V	E	-	2	0	ZNF33B	42409259	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.481000	0.73608	1.324000	0.45282	0.341000	0.21757	GAG	.	.		0.433	ZNF33B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_006955		A	43089253	T	A	43089253	3	1	344	1	0	0	0	0	1	0	0	0	17870	1551	54	4	1195	4	ZNF33B	10	43089253	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	16626144	43089253	92445494	750	48113										
FXYD4	53828	hgsc.bcm.edu	37	chr10	43870979	43870979	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgcagctgagcggactgatcTgcggagggctcctggccatt	15	11	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:43870979T>G	ENST00000476166.1	+	6	464	c.130T>G	c.(130-132)Tgc>Ggc	p.C44G	FXYD4_ENST00000480834.1_3'UTR	NM_173160.2	NP_775183.1	P59646	FXYD4_HUMAN	FXYD domain containing ion transport regulator 4	44					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ion channel activity (GO:0005216)			NS(1)|large_intestine(1)|lung(3)	5						CGGACTGATCTGCGGAGGGCT	0.622																																					p.C44G	GBM(173;880 2047 13035 42390 49655)	Atlas-SNP	.											.	FXYD4	9	.	0			c.T130G						.						75	73	74					10																	43870979		2203	4300	6503	SO:0001583	missense	53828	exon6			CTGATCTGCGGAG		CCDS7203.1	10q11.21	2008-02-01	2002-01-14		ENSG00000150201	ENSG00000150201			4028	protein-coding gene	gene with protein product			"FXYD domain-containing ion transport regulator 4"			10950925, 12763854	Standard	NM_001184963		Approved	CHIF	uc001jaq.1	P59646	OTTHUMG00000018027	ENST00000476166.1:c.130T>G	chr10.hg19:g.43870979T>G	ENSP00000473361:p.Cys44Gly	88.0	0.0		83.0	38.0	NM_001184963	Q6UWZ1|Q7Z4M5	Missense_Mutation	SNP	ENST00000476166.1	hg19	CCDS7203.1	.	.	.	.	.	.	.	.	.	.	T	12.93	2.085767	0.36758	.	.	ENSG00000150201	ENST00000374451;ENST00000458363	.	.	.	4.11	1.65	0.23941	.	0.429185	0.25683	N	0.028999	T	0.27832	0.0685	.	.	.	0.09310	N	1	P	0.37176	0.586	B	0.39531	0.302	T	0.15350	-1.0440	8	0.66056	D	0.02	1.1632	4.7076	0.12856	0.1921:0.0:0.2002:0.6077	.	44	P59646	FXYD4_HUMAN	G	44	.	ENSP00000363575:C44G	C	+	1	0	FXYD4	43190985	0.470000	0.25854	0.016000	0.15963	0.050000	0.14768	0.344000	0.19962	0.337000	0.23665	-0.313000	0.08912	TGC	.	.		0.622	FXYD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047698.2	NM_173160		G	43870979	T	G	43870979	3	3	344	1	0	0	0	0	1	0	0	0	6128	1580	55	5	144	5	FXYD4	10	43870979	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	781726	43870979	91663768	751	48114										
RASSF4	83937	hgsc.bcm.edu	37	chr10	45484737	45484737	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tacagacctccgtgtttactCcagcctatggatccgtgacc	8	14	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:45484737C>G	ENST00000340258.5	+	7	660	c.547C>G	c.(547-549)Cca>Gca	p.P183A	RASSF4_ENST00000374417.2_3'UTR|RASSF4_ENST00000334940.6_Missense_Mutation_p.P192A|RASSF4_ENST00000472561.1_3'UTR	NM_032023.3	NP_114412.2	Q8WYP3	RIN2_HUMAN	Ras association (RalGDS/AF-6) domain family member 4	797	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of catalytic activity (GO:0050790)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|small GTPase regulator activity (GO:0005083)			NS(1)|endometrium(2)|large_intestine(6)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16						CGTGTTTACTCCAGCCTATGG	0.547																																					p.P183A		Atlas-SNP	.											.	RASSF4	33	.	0			c.C547G						.						108	88	95					10																	45484737		2203	4300	6503	SO:0001583	missense	83937	exon7			TTTACTCCAGCCT	BC032593	CCDS7208.1	10q11.1	2008-02-22	2008-02-22		ENSG00000107551	ENSG00000107551			20793	protein-coding gene	gene with protein product		610559					Standard	NM_032023		Approved	AD037, MGC44914	uc001jbo.3	Q9H2L5	OTTHUMG00000018060	ENST00000340258.5:c.547C>G	chr10.hg19:g.45484737C>G	ENSP00000339692:p.Pro183Ala	68.0	0.0		52.0	19.0	NM_032023	Q00425|Q5TFT8|Q9BQL3|Q9H071	Missense_Mutation	SNP	ENST00000340258.5	hg19	CCDS7208.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.411705	0.83340	.	.	ENSG00000107551	ENST00000334940;ENST00000340258;ENST00000374411	T;T	0.17213	2.29;2.29	6.03	6.03	0.97812	Ras-association (3);	0.000000	0.85682	D	0.000000	T	0.53997	0.1831	M	0.92970	3.365	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	T	0.62680	-0.6803	10	0.72032	D	0.01	-17.1966	18.0507	0.89347	0.0:1.0:0.0:0.0	.	192;274;183	Q9H2L5-2;Q59FL4;Q9H2L5	.;.;RASF4_HUMAN	A	192;183;274	ENSP00000334543:P192A;ENSP00000339692:P183A	ENSP00000334543:P192A	P	+	1	0	RASSF4	44804743	1.000000	0.71417	0.969000	0.41365	0.568000	0.35870	7.433000	0.80362	2.861000	0.98227	0.655000	0.94253	CCA	.	.		0.547	RASSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047745.2	NM_032023		G	45484737	C	G	45484737	3	3	344	1	0	0	0	0	1	0	0	0	13103	855	30	4	569	4	RASSF4	10	45484737	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1613758	45484737	90050010	752	48115										
ANUBL1	93550	hgsc.bcm.edu	37	chr10	46135397	46135397	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cctcatctgtatctgaattaTacatagaaccaccactgcaa	4	12	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:46135397T>C	ENST00000344646.5	-	6	799	c.584A>G	c.(583-585)tAt>tGt	p.Y195C	ZFAND4_ENST00000374371.2_Intron|ZFAND4_ENST00000374370.1_5'UTR|ZFAND4_ENST00000374366.3_Missense_Mutation_p.Y121C	NM_001128324.2|NM_174890.2	NP_001121796.1|NP_777550.2	Q86XD8	ZFAN4_HUMAN	zinc finger, AN1-type domain 4	195							zinc ion binding (GO:0008270)										ATCTGAATTATACATAGAACC	0.338																																					p.Y195C		Atlas-SNP	.											.	.	.	.	0			c.A584G						.						107	109	108					10																	46135397		2203	4300	6503	SO:0001583	missense	93550	exon6			GAATTATACATAG	AF311324	CCDS7214.1, CCDS60520.1	10q11.22	2013-01-09	2011-11-10	2011-11-10	ENSG00000172671	ENSG00000172671		"Zinc fingers, AN1-type domain containing"	23504	protein-coding gene	gene with protein product			"AN1, ubiquitin-like, homolog (Xenopus laevis)"	ANUBL1			Standard	XM_005271837		Approved	FLJ40185	uc001jcp.4	Q86XD8	OTTHUMG00000018085	ENST00000344646.5:c.584A>G	chr10.hg19:g.46135397T>C	ENSP00000339484:p.Tyr195Cys	54.0	0.0		51.0	17.0	NM_001128324	A8K8V4|B2RAX2|Q5VVY5	Missense_Mutation	SNP	ENST00000344646.5	hg19	CCDS7214.1	.	.	.	.	.	.	.	.	.	.	T	13.51	2.258459	0.39896	.	.	ENSG00000172671	ENST00000344646;ENST00000374366;ENST00000374370	T;T	0.27557	1.66;1.67	5.63	4.48	0.54585	.	3.911980	0.01015	N	0.003883	T	0.33702	0.0872	L	0.48642	1.525	0.46849	D	0.999225	B	0.29627	0.252	B	0.26614	0.071	T	0.32348	-0.9910	10	0.87932	D	0	-23.8925	10.1504	0.42788	0.0:0.0813:0.0:0.9187	.	195	Q86XD8	ANUB1_HUMAN	C	195;121;77	ENSP00000339484:Y195C;ENSP00000363486:Y121C	ENSP00000339484:Y195C	Y	-	2	0	ANUBL1	45455403	1.000000	0.71417	1.000000	0.80357	0.315000	0.28087	2.253000	0.43205	2.157000	0.67596	0.482000	0.46254	TAT	.	.		0.338	ZFAND4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047790.1	NM_174890		C	46135397	T	C	46135397	3	2	344	1	0	0	0	0	1	0	0	0	713	1406	49	2	1619	2	ANUBL1	10	46135397	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	650660	46135397	89399350	753	48116										
PPYR1	5540	hgsc.bcm.edu	37	chr10	47087208	47087208	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggccctggagaggcatcagcTcatcatcaacccaacaggct	10	14	4	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:47087208T>C	ENST00000395716.1	+	2	510	c.425T>C	c.(424-426)cTc>cCc	p.L142P	NPY4R_ENST00000374312.1_Missense_Mutation_p.L142P			P50391	NPY4R_HUMAN	neuropeptide Y receptor Y4	142					blood circulation (GO:0008015)|digestion (GO:0007586)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|pancreatic polypeptide receptor activity (GO:0001602)|peptide binding (GO:0042277)|peptide YY receptor activity (GO:0001601)										AGGCATCAGCTCATCATCAAC	0.587																																					p.L142P		Atlas-SNP	.											.	PPYR1	54	.	0			c.T425C						.						279	244	256					10																	47087208		2203	4300	6503	SO:0001583	missense	5540	exon3			ATCAGCTCATCAT		CCDS73100.1	10q11.2	2013-03-26	2013-03-26	2013-03-26	ENSG00000204174	ENSG00000204174		"GPCR / Class A : Neuropeptide receptors : Y"	9329	protein-coding gene	gene with protein product		601790	"pancreatic polypeptide receptor 1"	PPYR1		9417917	Standard	NM_005972		Approved	Y4, PP1	uc001jee.3	P50391	OTTHUMG00000018108	ENST00000395716.1:c.425T>C	chr10.hg19:g.47087208T>C	ENSP00000379066:p.Leu142Pro	107.0	0.0		124.0	24.0	NM_005972	Q13456|Q5ISU3|Q5T2X9|Q6FH06	Missense_Mutation	SNP	ENST00000395716.1	hg19	CCDS31193.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.079687	0.76528	.	.	ENSG00000204174	ENST00000374312;ENST00000395716	T;T	0.38077	1.16;1.16	4.93	4.93	0.64822	GPCR, rhodopsin-like superfamily (1);	0.070703	0.64402	D	0.000017	T	0.63070	0.2480	M	0.84846	2.72	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.69676	-0.5081	10	0.87932	D	0	.	12.8468	0.57833	0.0:0.0:0.0:1.0	.	142	P50391	NPY4R_HUMAN	P	142	ENSP00000363431:L142P;ENSP00000379066:L142P	ENSP00000363431:L142P	L	+	2	0	PPYR1	46507214	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.706000	0.84615	1.994000	0.58287	0.496000	0.49642	CTC	.	.		0.587	NPY4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047837.1			C	47087208	T	C	47087208	3	2	344	1	0	0	0	0	1	0	0	0	12428	1551	54	2	427	2	PPYR1	10	47087208	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	951811	47087208	88447539	754	48117										
ZNF488	118738	hgsc.bcm.edu	37	chr10	48370707	48370707	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agacgaaccgcctgggccctGaggctgctgtgggcagggcg	18	12	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:48370707G>C	ENST00000395702.2	+	2	402	c.175G>C	c.(175-177)Gag>Cag	p.E59Q	ZNF488_ENST00000494156.1_Missense_Mutation_p.E59Q|ZNF488_ENST00000586537.1_5'UTR			Q96MN9	ZN488_HUMAN	zinc finger protein 488	59					negative regulation of transcription, DNA-templated (GO:0045892)|oligodendrocyte development (GO:0014003)|positive regulation of oligodendrocyte differentiation (GO:0048714)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|ovary(2)	14						CCTGGGCCCTGAGGCTGCTGT	0.677																																					p.E59Q		Atlas-SNP	.											.	ZNF488	38	.	0			c.G175C						.						33	42	39					10																	48370707		2199	4296	6495	SO:0001583	missense	118738	exon2			GGCCCTGAGGCTG	AK056666	CCDS73120.1	10q11.22	2014-04-10			ENSG00000165388	ENSG00000265763		"Zinc fingers, C2H2-type"	23535	protein-coding gene	gene with protein product							Standard	NM_153034		Approved	FLJ32104	uc001jex.3	Q96MN9	OTTHUMG00000188322	ENST00000395702.2:c.175G>C	chr10.hg19:g.48370707G>C	ENSP00000379054:p.Glu59Gln	35.0	0.0		24.0	7.0	NM_153034	Q05CE0	Missense_Mutation	SNP	ENST00000395702.2	hg19	CCDS7217.1	.	.	.	.	.	.	.	.	.	.	G	15.24	2.775422	0.49786	.	.	ENSG00000165388	ENST00000395702;ENST00000433077;ENST00000442001;ENST00000436850;ENST00000412534;ENST00000444585;ENST00000425196	T;T;T;T;T;T	0.56275	1.69;0.59;0.55;0.47;1.16;1.18	4.9	-1.15	0.09709	.	0.368611	0.26688	N	0.023009	T	0.30978	0.0782	L	0.29908	0.895	0.09310	N	0.999998	B	0.17465	0.022	B	0.15870	0.014	T	0.08086	-1.0739	10	0.39692	T	0.17	.	3.4344	0.07440	0.082:0.2837:0.3875:0.2468	.	59	Q96MN9	ZN488_HUMAN	Q	59	ENSP00000379054:E59Q;ENSP00000401469:E59Q;ENSP00000415923:E59Q;ENSP00000406508:E59Q;ENSP00000410326:E59Q;ENSP00000412898:E59Q	ENSP00000379054:E59Q	E	+	1	0	ZNF488	47990713	0.033000	0.19621	0.002000	0.10522	0.059000	0.15707	2.064000	0.41432	0.101000	0.17610	0.561000	0.74099	GAG	.	.		0.677	ZNF488-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314632.1	NM_153034		C	48370707	G	C	48370707	3	2	344	1	0	0	0	0	1	0	0	0	17955	1291	45	4	177	4	ZNF488	10	48370707	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1283499	48370707	87164040	755	48118										
GDF2	2658	hgsc.bcm.edu	37	chr10	48416370	48416370	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tccatgctgaagctccgcacAatgttggacgctggcgtagt	12	11	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:48416370A>G	ENST00000249598.1	-	1	483	c.324T>C	c.(322-324)atT>atC	p.I108I		NM_016204.1	NP_057288.1	Q9UK05	GDF2_HUMAN	growth differentiation factor 2	108					activin receptor signaling pathway (GO:0032924)|angiogenesis (GO:0001525)|blood vessel morphogenesis (GO:0048514)|BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|cellular iron ion homeostasis (GO:0006879)|cellular response to BMP stimulus (GO:0071773)|growth (GO:0040007)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of DNA replication (GO:0008156)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|ossification (GO:0001503)|osteoblast differentiation (GO:0001649)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(2)|large_intestine(3)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	28						AGCTCCGCACAATGTTGGACG	0.597																																					p.I108I		Atlas-SNP	.											.	GDF2	77	.	0			c.T324C						.						102	78	86					10																	48416370		2203	4300	6503	SO:0001819	synonymous_variant	2658	exon1			CCGCACAATGTTG	AF156891	CCDS73118.1	10q11.22	2014-05-06			ENSG00000128802	ENSG00000263761		"Endogenous ligands"	4217	protein-coding gene	gene with protein product		605120				10849432	Standard	NM_016204		Approved	BMP-9, BMP9	uc001jfa.1	Q9UK05	OTTHUMG00000188320	ENST00000249598.1:c.324T>C	chr10.hg19:g.48416370A>G		59.0	0.0		48.0	19.0	NM_016204	Q5VSQ9|Q9Y571	Silent	SNP	ENST00000249598.1	hg19	CCDS7219.1																																																																																			.	.		0.597	GDF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047891.1	NM_016204		G	48416370	A	G	48416370	2	3	344	1	0	0	0	0	0	0	0	1	6322	126	5	2		2	GDF2	10	48416370	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	45663	48416370	87118377	756	48119										
ARHGAP22	58504	hgsc.bcm.edu	37	chr10	49687696	49687696	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tacctccgcccagcggggccCagatgactcggcggatggcc	14	16	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:49687696C>A	ENST00000249601.4	-	4	730	c.434G>T	c.(433-435)tGg>tTg	p.W145L	ARHGAP22_ENST00000417247.2_Missense_Mutation_p.W55L|ARHGAP22_ENST00000417912.2_Missense_Mutation_p.W145L|ARHGAP22_ENST00000374170.1_Missense_Mutation_p.W55L|ARHGAP22_ENST00000374172.1_Missense_Mutation_p.W20L|ARHGAP22_ENST00000435790.2_Missense_Mutation_p.W151L	NM_001256024.1|NM_021226.3	NP_001242953.1|NP_067049.2	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 22	145	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						CAGCGGGGCCCAGATGACTCG	0.667																																					p.W151L		Atlas-SNP	.											.	ARHGAP22	94	.	0			c.G452T						.						38	39	39					10																	49687696		2203	4300	6503	SO:0001583	missense	58504	exon4			GGGGCCCAGATGA	AY324801	CCDS7227.1, CCDS58079.1, CCDS58080.1, CCDS58081.1	10q11.23	2013-01-10			ENSG00000128805	ENSG00000128805		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	30320	protein-coding gene	gene with protein product		610585				8619474	Standard	NM_021226		Approved	RhoGAP2	uc010qgm.3	Q7Z5H3	OTTHUMG00000018176	ENST00000249601.4:c.434G>T	chr10.hg19:g.49687696C>A	ENSP00000249601:p.Trp145Leu	119.0	0.0		117.0	56.0	NM_001256025	A0AVP7|A5YM75|B4DED8|B9EGA0|C9JDM2|O00152|Q6ZSB0	Missense_Mutation	SNP	ENST00000249601.4	hg19	CCDS7227.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.968041	0.74131	.	.	ENSG00000128805	ENST00000249601;ENST00000374172;ENST00000374170;ENST00000417247;ENST00000435790;ENST00000417912	T;T;T;T;T;T	0.28454	1.61;2.4;2.4;2.4;1.61;1.61	4.71	4.71	0.59529	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.85682	D	0.000000	T	0.33990	0.0882	M	0.70595	2.14	0.80722	D	1	B;B;B;B	0.30686	0.054;0.29;0.108;0.003	B;B;B;B	0.32864	0.019;0.154;0.056;0.025	T	0.15925	-1.0420	10	0.10377	T	0.69	.	16.8225	0.85922	0.0:1.0:0.0:0.0	.	151;145;145;55	B4DED8;Q7Z5H3-2;Q7Z5H3;Q7Z5H3-3	.;.;RHG22_HUMAN;.	L	145;20;55;55;151;145	ENSP00000249601:W145L;ENSP00000363287:W20L;ENSP00000363285:W55L;ENSP00000410054:W55L;ENSP00000416701:W151L;ENSP00000412461:W145L	ENSP00000249601:W145L	W	-	2	0	ARHGAP22	49357702	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.763000	0.68818	2.456000	0.83038	0.655000	0.94253	TGG	.	.		0.667	ARHGAP22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358767.1	NM_021226		A	49687696	C	A	49687696	3	1	344	1	0	0	0	0	1	0	0	0	872	595	21	3	1690	3	ARHGAP22	10	49687696	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1271326	49687696	85847051	757	48120										
C10orf71	118461	hgsc.bcm.edu	37	chr10	50530956	50530956	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agccccccaccaacgccagtCcagaggagactggaggtgcc	12	16	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:50530956C>T	ENST00000374144.3	+	3	654	c.366C>T	c.(364-366)gtC>gtT	p.V122V	C10orf71_ENST00000323868.4_Silent_p.V122V			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	122										endometrium(1)	1						CAACGCCAGTCCAGAGGAGAC	0.552																																					p.V122V		Atlas-SNP	.											.	C10orf71	179	.	0			c.C366T						.						86	99	95					10																	50530956		1906	4125	6031	SO:0001819	synonymous_variant	118461	exon3			GCCAGTCCAGAGG	AL833265	CCDS44387.1	10q11.23	2012-05-31			ENSG00000177354	ENSG00000177354			26973	protein-coding gene	gene with protein product							Standard	NM_001135196		Approved	FLJ45913	uc021pqa.2	Q711Q0	OTTHUMG00000018190	ENST00000374144.3:c.366C>T	chr10.hg19:g.50530956C>T		128.0	0.0		127.0	62.0	NM_001135196	A0AVL8	Silent	SNP	ENST00000374144.3	hg19	CCDS44387.1																																																																																			.	.		0.552	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459		T	50530956	C	T	50530956	2	4	344	1	0	0	0	0	0	0	0	1	1616	842	30	3		3	C10orf71	10	50530956	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	843260	50530956	85003791	758	48121										
C10orf71	118461	hgsc.bcm.edu	37	chr10	50532101	50532101	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tagcctgctgttcaacctcaAggacgtgcggaagcgtgtta	12	10	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:50532101A>T	ENST00000374144.3	+	3	1799	c.1511A>T	c.(1510-1512)aAg>aTg	p.K504M	C10orf71_ENST00000323868.4_Missense_Mutation_p.K504M			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	504										endometrium(1)	1						TTCAACCTCAAGGACGTGCGG	0.498																																					p.K504M		Atlas-SNP	.											.	C10orf71	179	.	0			c.A1511T						.						46	49	48					10																	50532101		2060	4199	6259	SO:0001583	missense	118461	exon3			ACCTCAAGGACGT	AL833265	CCDS44387.1	10q11.23	2012-05-31			ENSG00000177354	ENSG00000177354			26973	protein-coding gene	gene with protein product							Standard	NM_001135196		Approved	FLJ45913	uc021pqa.2	Q711Q0	OTTHUMG00000018190	ENST00000374144.3:c.1511A>T	chr10.hg19:g.50532101A>T	ENSP00000363259:p.Lys504Met	85.0	0.0		58.0	32.0	NM_001135196	A0AVL8	Missense_Mutation	SNP	ENST00000374144.3	hg19	CCDS44387.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.455813	0.84209	.	.	ENSG00000177354	ENST00000323868;ENST00000374144	T;T	0.31247	1.5;2.62	5.48	5.48	0.80851	.	0.000000	0.40728	N	0.001036	T	0.53802	0.1819	M	0.64997	1.995	0.53688	D	0.999975	D	0.89917	1.0	D	0.97110	1.0	T	0.57075	-0.7873	10	0.87932	D	0	.	15.6097	0.76707	1.0:0.0:0.0:0.0	.	504	Q711Q0-3	.	M	504	ENSP00000318713:K504M;ENSP00000363259:K504M	ENSP00000318713:K504M	K	+	2	0	C10orf71	50202107	1.000000	0.71417	0.999000	0.59377	0.987000	0.75469	8.707000	0.91367	2.087000	0.62958	0.477000	0.44152	AAG	.	.		0.498	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459		T	50532101	A	T	50532101	3	4	344	1	0	0	0	0	1	0	0	0	1616	72	3	4	1513	4	C10orf71	10	50532101	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1145	50532101	85002646	759	48122										
PGBD3	267004	hgsc.bcm.edu	37	chr10	50724703	50724703	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgacaatgagttcaatgaccTcgtcatcaagaaaaagttca	7	8	4	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:50724703T>A	ENST00000374127.3	-	2	659	c.458A>T	c.(457-459)gAg>gTg	p.E153V	ERCC6_ENST00000355832.5_Intron|PGBD3_ENST00000603152.1_Missense_Mutation_p.E621V|ERCC6-PGBD3_ENST00000447839.2_Missense_Mutation_p.E621V|PGBD3_ENST00000508005.2_Missense_Mutation_p.E153V|ERCC6-PGBD3_ENST00000515869.1_Missense_Mutation_p.E621V	NM_170753.2	NP_736609.2	Q8N328	PGBD3_HUMAN	piggyBac transposable element derived 3	153										breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|lung(16)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	33						TTCAATGACCTCGTCATCAAG	0.403																																					p.P153L		Atlas-SNP	.											.	PGBD3	58	.	0			c.C458T						.						123	119	120					10																	50724703		2203	4300	6503	SO:0001583	missense	267004	exon2			ATGACCTCGTCAT	AK074682	CCDS7230.1	10q11	2011-03-24			ENSG00000243251	ENSG00000243251			19400	protein-coding gene	gene with protein product							Standard	NM_170753		Approved	FLJ90201		Q8N328	OTTHUMG00000018193	ENST00000374127.3:c.458A>T	chr10.hg19:g.50724703T>A	ENSP00000363242:p.Glu153Val	122.0	0.0		72.0	34.0	NM_170753	B3KQC4|Q5W0M0|Q6PIH0	Missense_Mutation	SNP	ENST00000374127.3	hg19	CCDS7230.1	.	.	.	.	.	.	.	.	.	.	T	15.68	2.904543	0.52333	.	.	ENSG00000243251;ENSG00000243251;ENSG00000258838;ENSG00000258838	ENST00000374127;ENST00000508005;ENST00000515869;ENST00000447839	T;T;T;T	0.20881	2.04;2.04;2.04;2.04	0.468	0.468	0.16732	.	.	.	.	.	T	0.25791	0.0628	L	0.52126	1.63	0.09310	N	1	P;D	0.54397	0.755;0.966	B;P	0.52109	0.241;0.69	T	0.12116	-1.0560	8	0.41790	T	0.15	-9.3338	.	.	.	.	621;153	E7EV46;Q8N328	.;PGBD3_HUMAN	V	153;153;621;621	ENSP00000363242:E153V;ENSP00000426963:E153V;ENSP00000423550:E621V;ENSP00000387966:E621V	ENSP00000387966:E621V	E	-	2	0	PGBD3;RP11-123B3.6	50394709	0.051000	0.20477	0.788000	0.31933	0.764000	0.43329	0.842000	0.27627	0.413000	0.25759	0.402000	0.26972	GAG	.	.		0.403	PGBD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047988.1			A	50724703	T	A	50724703	3	1	344	1	0	0	0	0	1	0	0	0	11791	1551	54	4	1327	4	PGBD3	10	50724703	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	192602	50724703	84810044	760	48123										
NCOA4	8031	hgsc.bcm.edu	37	chr10	51585413	51585413	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cttatcaggcccccatacaaAgaaggaagtcccaaggaagt	9	11	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:51585413A>G	ENST00000443446.1	+	8	1741	c.1512A>G	c.(1510-1512)aaA>aaG	p.K504K	NCOA4_ENST00000414907.2_Silent_p.K338K|NCOA4_ENST00000374087.4_Silent_p.K504K|NCOA4_ENST00000438493.1_Silent_p.K520K|NCOA4_ENST00000430396.2_Silent_p.K404K|NCOA4_ENST00000374082.1_Silent_p.K504K|NCOA4_ENST00000344348.6_Silent_p.K504K|NCOA4_ENST00000452682.1_Silent_p.K520K	NM_001145262.1	NP_001138734.1	Q13772	NCOA4_HUMAN	nuclear receptor coactivator 4	504					androgen receptor signaling pathway (GO:0030521)|male gonad development (GO:0008584)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|skin(1)	5						CCCCATACAAAGAAGGAAGTC	0.468			T	RET	papillary thyroid																																p.K520K		Atlas-SNP	.		Dom	yes		10	10q11.2	8031	nuclear receptor coactivator 4 - PTC3 (ELE1)		E	.	NCOA4	58	.	0			c.A1560G						.						79	88	85					10																	51585413		2203	4299	6502	SO:0001819	synonymous_variant	8031	exon9			ATACAAAGAAGGA	L49399	CCDS73092.1, CCDS73093.1, CCDS73094.1	10q11.2	2014-04-10			ENSG00000138293	ENSG00000266412			7671	protein-coding gene	gene with protein product	"RET-activating gene ELE1"	601984				8290261, 8643607, 24695223	Standard	NM_001145260		Approved	ARA70, RFG, ELE1, PTC3, DKFZp762E1112	uc009xon.3	Q13772	OTTHUMG00000188314	ENST00000443446.1:c.1512A>G	chr10.hg19:g.51585413A>G		70.0	0.0		82.0	41.0	NM_001145261	A8K8W5|B4E260|E9PAV7|J3KQN8|Q14239	Silent	SNP	ENST00000443446.1	hg19	CCDS7237.1																																																																																			.	.		0.468	NCOA4-204	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048052.1	NM_005437		G	51585413	A	G	51585413	2	3	344	1	0	0	0	0	0	0	0	1	10240	69	3	2		2	NCOA4	10	51585413	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	860710	51585413	83949334	761	48124										
ASAH2	56624	hgsc.bcm.edu	37	chr10	52005188	52005188	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggtggctggagggctttgggTggttgaaaaaaaatggcctc	17	5	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:52005188T>A	ENST00000395526.4	-	2	153	c.154A>T	c.(154-156)Acc>Tcc	p.T52S	ASAH2_ENST00000329428.6_Missense_Mutation_p.T33S|ASAH2_ENST00000447815.1_Missense_Mutation_p.T52S	NM_019893.2	NP_063946.2	Q9NR71	ASAH2_HUMAN	N-acylsphingosine amidohydrolase (non-lysosomal ceramidase) 2	52					apoptotic process (GO:0006915)|ceramide metabolic process (GO:0006672)|glycosphingolipid metabolic process (GO:0006687)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ceramidase activity (GO:0017040)			large_intestine(1)|lung(9)|urinary_tract(1)	11						GGGCTTTGGGTGGTTGAAAAA	0.473																																					p.T52S		Atlas-SNP	.											.	ASAH2	69	.	0			c.A154T						.						45	53	50					10																	52005188		2203	4300	6503	SO:0001583	missense	56624	exon2			TTTGGGTGGTTGA	AF250847	CCDS7239.2, CCDS44398.1	10q11.23	2008-08-11			ENSG00000188611	ENSG00000188611			18860	protein-coding gene	gene with protein product		611202				10781606	Standard	NM_019893		Approved		uc001jjd.3	Q9NR71	OTTHUMG00000018223	ENST00000395526.4:c.154A>T	chr10.hg19:g.52005188T>A	ENSP00000378897:p.Thr52Ser	105.0	0.0		83.0	35.0	NM_019893	Q3KNU1|Q5SNT7|Q5SZP6|Q5SZP7|Q5T1D5|Q71ME6	Missense_Mutation	SNP	ENST00000395526.4	hg19	CCDS7239.2	.	.	.	.	.	.	.	.	.	.	T	9.988	1.229969	0.22542	.	.	ENSG00000188611	ENST00000395526;ENST00000447815;ENST00000329428	T;T;T	0.29655	1.56;1.56;1.56	5.28	5.28	0.74379	.	0.603513	0.15960	N	0.236310	T	0.20941	0.0504	N	0.14661	0.345	0.80722	D	1	B;B	0.16802	0.019;0.011	B;B	0.20955	0.032;0.014	T	0.05022	-1.0911	10	0.38643	T	0.18	.	13.2185	0.59873	0.0:0.0:0.0:1.0	.	52;52	Q9NR71-2;Q9NR71	.;ASAH2_HUMAN	S	52;52;33	ENSP00000378897:T52S;ENSP00000388206:T52S;ENSP00000329886:T33S	ENSP00000329886:T33S	T	-	1	0	ASAH2	51675194	0.770000	0.28543	0.038000	0.18304	0.040000	0.13550	2.031000	0.41117	2.210000	0.71456	0.533000	0.62120	ACC	.	.		0.473	ASAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048061.3	NM_019893		A	52005188	T	A	52005188	3	1	344	1	0	0	0	0	1	0	0	0	1007	1696	59	4	2264	4	ASAH2	10	52005188	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	419775	52005188	83529559	762	48125										
A1CF	29974	hgsc.bcm.edu	37	chr10	52603787	52603787	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agctcatcctcaaaaaggtcTcggggaagttttccaataaa	8	9	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:52603787T>A	ENST00000373993.1	-	2	239	c.195A>T	c.(193-195)cgA>cgT	p.R65R	A1CF_ENST00000282641.2_Silent_p.R65R|A1CF_ENST00000373995.3_Silent_p.R73R|A1CF_ENST00000395489.2_Silent_p.R58R|A1CF_ENST00000373997.3_Silent_p.R65R|A1CF_ENST00000395495.1_Silent_p.R65R|A1CF_ENST00000374001.2_Silent_p.R65R			Q9NQ94	A1CF_HUMAN	APOBEC1 complementation factor	65	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cytidine to uridine editing (GO:0016554)|gene expression (GO:0010467)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|protein stabilization (GO:0050821)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			NS(1)|breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(14)|prostate(2)|skin(3)	29						CAAAAAGGTCTCGGGGAAGTT	0.398																																					p.R73R		Atlas-SNP	.											.	A1CF	190	.	0			c.A219T						.						85	99	94					10																	52603787		2203	4300	6503	SO:0001819	synonymous_variant	29974	exon5			AAGGTCTCGGGGA	AF271790	CCDS7241.1, CCDS7242.1, CCDS7243.1, CCDS73133.1	10q21.1	2013-02-12			ENSG00000148584	ENSG00000148584		"RNA binding motif (RRM) containing"	24086	protein-coding gene	gene with protein product						11815617, 11072063	Standard	NM_014576		Approved	ACF, ASP, ACF64, ACF65, APOBEC1CF	uc001jjj.3	Q9NQ94	OTTHUMG00000018240	ENST00000373993.1:c.195A>T	chr10.hg19:g.52603787T>A		185.0	0.0		133.0	55.0	NM_001198820	A1L4F2|A8K7G7|B7ZM14|Q5SZQ0|Q9NQ93|Q9NQX8|Q9NQX9|Q9NXC9|Q9NZD3	Silent	SNP	ENST00000373993.1	hg19	CCDS7242.1																																																																																			.	.		0.398	A1CF-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048086.2	NM_014576		A	52603787	T	A	52603787	2	1	344	1	0	0	0	0	0	0	0	1	2	1538	54	4		4	A1CF	10	52603787	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	598599	52603787	82930960	763	48126										
PRKG1	5592	hgsc.bcm.edu	37	chr10	53564432	53564432	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	actcatcaagcataccgagtAtatggaatttttaaaaaggt	7	6	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:53564432A>G	ENST00000401604.2	+	4	829	c.635A>G	c.(634-636)tAt>tGt	p.Y212C	PRKG1_ENST00000373980.4_Missense_Mutation_p.Y227C|PRKG1_ENST00000373985.1_Missense_Mutation_p.Y200C			Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I	212	cGMP-binding, high affinity.				actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|dendrite development (GO:0016358)|forebrain development (GO:0030900)|negative regulation of platelet aggregation (GO:0090331)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|regulation of GTPase activity (GO:0043087)|relaxation of vascular smooth muscle (GO:0060087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	53		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		CATACCGAGTATATGGAATTT	0.363																																					p.Y227C		Atlas-SNP	.											.	PRKG1	167	.	0			c.A680G						.						92	85	88					10																	53564432		2203	4300	6503	SO:0001583	missense	5592	exon4			CCGAGTATATGGA		CCDS7244.1	10q11.2	2009-07-10			ENSG00000185532	ENSG00000185532	2.7.11.1		9414	protein-coding gene	gene with protein product		176894		PRKGR1B, PRKG1B		2792381, 1544322	Standard	NM_001098512		Approved	PGK, PKG	uc001jjo.3	Q13976	OTTHUMG00000018248	ENST00000401604.2:c.635A>G	chr10.hg19:g.53564432A>G	ENSP00000384200:p.Tyr212Cys	61.0	0.0		38.0	20.0	NM_006258	A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	Missense_Mutation	SNP	ENST00000401604.2	hg19	CCDS44399.1	.	.	.	.	.	.	.	.	.	.	A	14.51	2.555548	0.45487	.	.	ENSG00000185532	ENST00000401604;ENST00000373985;ENST00000373980;ENST00000373976	T;T;T;T	0.31247	1.5;1.5;1.5;1.5	5.29	5.29	0.74685	RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (2);	0.000000	0.64402	D	0.000001	T	0.59074	0.2167	M	0.86028	2.79	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.77004	0.989;0.974	T	0.66126	-0.6001	10	0.87932	D	0	-8.7097	13.447	0.61146	1.0:0.0:0.0:0.0	.	227;212	Q13976-2;Q13976	.;KGP1_HUMAN	C	212;200;227;85	ENSP00000384200:Y212C;ENSP00000363097:Y200C;ENSP00000363092:Y227C;ENSP00000363087:Y85C	ENSP00000363087:Y85C	Y	+	2	0	PRKG1	53234438	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	8.877000	0.92386	2.124000	0.65301	0.402000	0.26972	TAT	.	.		0.363	PRKG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				G	53564432	A	G	53564432	3	3	344	1	0	0	0	0	1	0	0	0	12534	449	16	2	964	2	PRKG1	10	53564432	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	960645	53564432	81970315	764	48127										
BICC1	80114	hgsc.bcm.edu	37	chr10	60553242	60553242	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	attctattgtgacattttctAgggttgtcttcctcttgtgt	8	7	4	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:60553242A>G	ENST00000373886.3	+	9	1051		c.e9-1		BICC1_ENST00000263103.1_5'Flank	NM_001080512.1	NP_001073981.1	Q9H694	BICC1_HUMAN	BicC family RNA binding protein 1						multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)	cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	44						GACATTTTCTAGGGTTGTCTT	0.333																																					.		Atlas-SNP	.											.	BICC1	121	.	0			c.1048-2A>G						.						109	100	103					10																	60553242		2203	4300	6503	SO:0001630	splice_region_variant	80114	exon9			TTTTCTAGGGTTG	AK026129	CCDS31206.1	10q21.3	2014-09-17	2014-02-03		ENSG00000122870	ENSG00000122870		"Sterile alpha motif (SAM) domain containing"	19351	protein-coding gene	gene with protein product		614295	"bicaudal C homolog 1 (Drosophila)"				Standard	XM_005270166		Approved		uc001jki.1	Q9H694	OTTHUMG00000018271	ENST00000373886.3:c.1048-1A>G	chr10.hg19:g.60553242A>G		92.0	0.0		96.0	33.0	NM_001080512		Splice_Site	SNP	ENST00000373886.3	hg19	CCDS31206.1	.	.	.	.	.	.	.	.	.	.	A	19.32	3.804621	0.70682	.	.	ENSG00000122870	ENST00000373886	.	.	.	5.76	5.76	0.90799	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0734	0.80951	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	BICC1	60223248	1.000000	0.71417	0.994000	0.49952	0.920000	0.55202	9.210000	0.95106	2.195000	0.70347	0.533000	0.62120	.	.	.		0.333	BICC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048150.2	NM_025044	Intron	G	60553242	A	G	60553242	5	3	344	1	0	0	0	0	0	0	1	0	1427	434	15	2	1080	2	BICC1	10	60553242	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	6988810	60553242	74981505	765	48128										
ANK3	288	hgsc.bcm.edu	37	chr10	61829458	61829458	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttcatggtcatggtggatgcAgaaattcccatttttatagg	10	6	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:61829458A>C	ENST00000280772.2	-	37	11372	c.11181T>G	c.(11179-11181)tcT>tcG	p.S3727S	ANK3_ENST00000373827.2_Intron|ANK3_ENST00000503366.1_Intron|ANK3_ENST00000355288.2_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	3727					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						TGGTGGATGCAGAAATTCCCA	0.448																																					p.S3727S		Atlas-SNP	.											.	ANK3	703	.	0			c.T11181G						.						133	146	142					10																	61829458		2203	4300	6503	SO:0001819	synonymous_variant	288	exon37			GGATGCAGAAATT	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.11181T>G	chr10.hg19:g.61829458A>C		101.0	0.0		66.0	24.0	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Silent	SNP	ENST00000280772.2	hg19	CCDS7258.1																																																																																			.	.		0.448	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		C	61829458	A	C	61829458	2	2	344	1	0	0	0	0	0	0	0	1	622	175	7	5		5	ANK3	10	61829458	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1276216	61829458	73705289	766	48129										
ARID5B	84159	hgsc.bcm.edu	37	chr10	63760062	63760062	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cgactctcatagaaaacgagAgtatatgcgatgagtttggt	11	6	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:63760062A>G	ENST00000279873.7	+	4	1125	c.715A>G	c.(715-717)Agt>Ggt	p.S239G		NM_032199.2	NP_115575.1	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)	239					adipose tissue development (GO:0060612)|adrenal gland development (GO:0030325)|cell development (GO:0048468)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|fat pad development (GO:0060613)|female gonad development (GO:0008585)|fibroblast migration (GO:0010761)|kidney development (GO:0001822)|liver development (GO:0001889)|male gonad development (GO:0008584)|multicellular organism growth (GO:0035264)|muscle organ morphogenesis (GO:0048644)|negative regulation of transcription, DNA-templated (GO:0045892)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|post-embryonic development (GO:0009791)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(13)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	Prostate(12;0.016)|all_hematologic(501;0.215)					AGAAAACGAGAGTATATGCGA	0.483																																					p.S239G		Atlas-SNP	.											.	ARID5B	125	.	0			c.A715G						.						73	65	68					10																	63760062		2203	4300	6503	SO:0001583	missense	84159	exon4			AACGAGAGTATAT	M73837	CCDS31208.1, CCDS58082.1	10q11.22	2013-02-07			ENSG00000150347	ENSG00000150347		"-"	17362	protein-coding gene	gene with protein product		608538				11483573, 11478881	Standard	NM_032199		Approved	FLJ21150, MRF2	uc001jlt.2	Q14865	OTTHUMG00000018298	ENST00000279873.7:c.715A>G	chr10.hg19:g.63760062A>G	ENSP00000279873:p.Ser239Gly	91.0	0.0		71.0	29.0	NM_032199	B4DLB3|Q05DG6|Q32Q59|Q5VST4|Q6NZ42|Q7Z3M4|Q8N421|Q9H786	Missense_Mutation	SNP	ENST00000279873.7	hg19	CCDS31208.1	.	.	.	.	.	.	.	.	.	.	A	18.27	3.587724	0.66105	.	.	ENSG00000150347	ENST00000279873	T	0.22945	1.93	5.65	5.65	0.86999	.	0.159507	0.64402	D	0.000002	T	0.48624	0.1510	M	0.64997	1.995	0.80722	D	1	D;P	0.67145	0.996;0.539	D;B	0.73380	0.98;0.132	T	0.44636	-0.9315	10	0.51188	T	0.08	-13.4659	15.8734	0.79141	1.0:0.0:0.0:0.0	.	239;239	Q14865-3;Q14865	.;ARI5B_HUMAN	G	239	ENSP00000279873:S239G	ENSP00000279873:S239G	S	+	1	0	ARID5B	63430068	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.962000	0.93254	2.147000	0.66899	0.459000	0.35465	AGT	.	.		0.483	ARID5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048233.1	XM_084482		G	63760062	A	G	63760062	3	3	344	1	0	0	0	0	1	0	0	0	922	304	11	2	729	2	ARID5B	10	63760062	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1930604	63760062	71774685	767	48130										
ZNF365	22891	hgsc.bcm.edu	37	chr10	64415185	64415185	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cccttggaaagaccatctcaCcttccaacctctccatcctg	4	18	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:64415185C>T	ENST00000395251.1	+	4	519	c.185C>T	c.(184-186)aCc>aTc	p.T62I	AC067751.1_ENST00000579246.1_RNA|ZNF365_ENST00000410046.3_Intron|ZNF365_ENST00000395249.1_Intron	NM_199452.3	NP_955524	Q70YC4	TALAN_HUMAN	zinc finger protein 365	62			T -> A (in dbSNP:rs7076156). {ECO:0000269|PubMed:12740763}.							breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27	Prostate(12;0.0297)|all_hematologic(501;0.228)					GACCATCTCACCTTCCAACCT	0.502																																					p.T62I		Atlas-SNP	.											.	ZNF365	174	.	0			c.C185T						.						97	84	88					10																	64415185		2203	4300	6503	SO:0001583	missense	22891	exon4			ATCTCACCTTCCA	AB020651	CCDS7264.1, CCDS7265.1, CCDS31209.1, CCDS41531.1	10q21.2	2008-10-28			ENSG00000138311	ENSG00000138311		"Zinc fingers, C2H2-type"	18194	protein-coding gene	gene with protein product	"Talanin"	607818				10048485, 12740763	Standard	NM_199450		Approved	KIAA0844, UAN	uc001jmc.2	Q70YC4	OTTHUMG00000018302	ENST00000395251.1:c.185C>T	chr10.hg19:g.64415185C>T	ENSP00000378672:p.Thr62Ile	140.0	0.0		133.0	63.0	NM_199452		Missense_Mutation	SNP	ENST00000395251.1	hg19	CCDS7265.1	.	.	.	.	.	.	.	.	.	.	C	2.723	-0.266088	0.05754	.	.	ENSG00000138311	ENST00000395251	T	0.52983	0.64	3.86	-5.03	0.02973	.	.	.	.	.	T	0.22475	0.0542	N	0.08118	0	0.09310	N	0.999993	B	0.02656	0.0	B	0.04013	0.001	T	0.19910	-1.0291	9	0.87932	D	0	.	5.7985	0.18399	0.0:0.1967:0.2756:0.5277	.	62	Q70YC4	TALAN_HUMAN	I	62	ENSP00000378672:T62I	ENSP00000378672:T62I	T	+	2	0	ZNF365	64085191	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.625000	0.05534	-1.153000	0.02829	-1.686000	0.00732	ACC	.	.		0.502	ZNF365-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277036.1	NM_014951		T	64415185	C	T	64415185	3	4	344	1	0	0	0	0	1	0	0	0	17884	507	18	3	1673	3	ZNF365	10	64415185	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	655123	64415185	71119562	768	48131										
ZNF365	22891	hgsc.bcm.edu	37	chr10	64425949	64425949	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cttacactaggacaactccaAaattgtgtgattggtaagaa	8	7	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:64425949A>C	ENST00000395251.1	+	6	877	c.543A>C	c.(541-543)caA>caC	p.Q181H	ZNF365_ENST00000410046.3_Missense_Mutation_p.Q427H|ZNF365_ENST00000395249.1_Missense_Mutation_p.Q33H	NM_199452.3	NP_955524	Q70YC4	TALAN_HUMAN	zinc finger protein 365	181										breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27	Prostate(12;0.0297)|all_hematologic(501;0.228)					GACAACTCCAAAATTGTGTGA	0.413																																					p.Q427H		Atlas-SNP	.											.	ZNF365	174	.	0			c.A1281C						.						120	116	117					10																	64425949		2203	4300	6503	SO:0001583	missense	22891	exon7			ACTCCAAAATTGT	AB020651	CCDS7264.1, CCDS7265.1, CCDS31209.1, CCDS41531.1	10q21.2	2008-10-28			ENSG00000138311	ENSG00000138311		"Zinc fingers, C2H2-type"	18194	protein-coding gene	gene with protein product	"Talanin"	607818				10048485, 12740763	Standard	NM_199450		Approved	KIAA0844, UAN	uc001jmc.2	Q70YC4	OTTHUMG00000018302	ENST00000395251.1:c.543A>C	chr10.hg19:g.64425949A>C	ENSP00000378672:p.Gln181His	65.0	0.0		45.0	13.0	NM_199451		Missense_Mutation	SNP	ENST00000395251.1	hg19	CCDS7265.1	.	.	.	.	.	.	.	.	.	.	A	7.044	0.563189	0.13498	.	.	ENSG00000138311	ENST00000410046;ENST00000395251;ENST00000395249	T	0.53206	0.63	4.18	3.04	0.35103	.	.	.	.	.	T	0.43010	0.1228	N	0.08118	0	0.09310	N	1	D;P	0.69078	0.997;0.899	D;P	0.65684	0.937;0.466	T	0.18871	-1.0323	9	0.87932	D	0	-23.8911	6.6771	0.23100	0.8928:0.0:0.1072:0.0	.	181;427	Q70YC4;Q70YC5-3	TALAN_HUMAN;.	H	427;181;33	ENSP00000378672:Q181H	ENSP00000378670:Q33H	Q	+	3	2	ZNF365	64095955	0.000000	0.05858	0.014000	0.15608	0.060000	0.15804	0.623000	0.24447	0.921000	0.36994	0.533000	0.62120	CAA	.	.		0.413	ZNF365-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277036.1	NM_014951		C	64425949	A	C	64425949	3	2	344	1	0	0	0	0	1	0	0	0	17884	11	1	5	2039	5	ZNF365	10	64425949	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	10764	64425949	71108798	769	48132										
TET1	80312	hgsc.bcm.edu	37	chr10	70332525	70332525	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aacatgattgtgattataagAtactccctgctttgggagta	9	6	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:70332525A>G	ENST00000373644.4	+	2	639	c.430A>G	c.(430-432)Ata>Gta	p.I144V		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	144					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						TGATTATAAGATACTCCCTGC	0.428																																					p.I144V		Atlas-SNP	.											.	TET1	255	.	0			c.A430G						.						70	67	68					10																	70332525		2203	4300	6503	SO:0001583	missense	80312	exon2			TATAAGATACTCC	AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"leukemia-associated protein with a CXXC domain", "ten-eleven translocation-1"	607790	"CXXC zinc finger 6", "tet oncogene 1"	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.430A>G	chr10.hg19:g.70332525A>G	ENSP00000362748:p.Ile144Val	78.0	0.0		55.0	41.0	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	hg19	CCDS7281.1	.	.	.	.	.	.	.	.	.	.	A	0.004	-2.332159	0.00227	.	.	ENSG00000138336	ENST00000373644	T	0.05717	3.4	4.52	2.56	0.30785	.	0.961556	0.08517	N	0.934124	T	0.02418	0.0074	N	0.02916	-0.46	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43556	-0.9384	10	0.02654	T	1	.	6.5955	0.22669	0.1021:0.181:0.7169:0.0	.	144	Q8NFU7	TET1_HUMAN	V	144	ENSP00000362748:I144V	ENSP00000362748:I144V	I	+	1	0	TET1	70002531	0.000000	0.05858	0.001000	0.08648	0.651000	0.38670	0.726000	0.25984	0.283000	0.22279	-0.468000	0.05107	ATA	.	.		0.428	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		G	70332525	A	G	70332525	3	3	344	1	0	0	0	0	1	0	0	0	15784	333	12	2	432	2	TET1	10	70332525	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	5906576	70332525	65202222	770	48133										
DDX50	79009	hgsc.bcm.edu	37	chr10	70666604	70666604	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aagctaaatggagacactgaAgaaggatttaatagactttc	9	5	0	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:70666604A>G	ENST00000373585.3	+	2	332	c.225A>G	c.(223-225)gaA>gaG	p.E75E		NM_024045.1	NP_076950.1	Q9BQ39	DDX50_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 50	75						membrane (GO:0016020)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	29						GAGACACTGAAGAAGGATTTA	0.328																																					p.E75E		Atlas-SNP	.											.	DDX50	65	.	0			c.A225G						.						76	79	78					10																	70666604		2203	4300	6503	SO:0001819	synonymous_variant	79009	exon2			CACTGAAGAAGGA	AF334103	CCDS7283.1	10q22.2	2010-09-30			ENSG00000107625	ENSG00000107625		"DEAD-boxes"	17906	protein-coding gene	gene with protein product		610373				11891046	Standard	NM_024045		Approved	GU2, MGC3199, GUB, RH-II/GuB	uc001jou.3	Q9BQ39	OTTHUMG00000018362	ENST00000373585.3:c.225A>G	chr10.hg19:g.70666604A>G		231.0	0.0		212.0	81.0	NM_024045	Q5VX37|Q8WV76|Q9BWI8	Silent	SNP	ENST00000373585.3	hg19	CCDS7283.1																																																																																			.	.		0.328	DDX50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048363.1	NM_024045		G	70666604	A	G	70666604	2	3	344	1	0	0	0	0	0	0	0	1	4370	69	3	2		2	DDX50	10	70666604	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	334079	70666604	64868143	771	48134										
DDX50	79009	hgsc.bcm.edu	37	chr10	70670895	70670895	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tatatgaaggaaaagatttaAtagctcaagcacggacagga	10	5	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:70670895A>T	ENST00000373585.3	+	4	639	c.532A>T	c.(532-534)Ata>Tta	p.I178L	RNU6-571P_ENST00000384128.1_RNA	NM_024045.1	NP_076950.1	Q9BQ39	DDX50_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 50	178	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					membrane (GO:0016020)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	29						AAAAGATTTAATAGCTCAAGC	0.353																																					p.I178L		Atlas-SNP	.											.	DDX50	65	.	0			c.A532T						.						143	148	146					10																	70670895		2203	4300	6503	SO:0001583	missense	79009	exon4			GATTTAATAGCTC	AF334103	CCDS7283.1	10q22.2	2010-09-30			ENSG00000107625	ENSG00000107625		"DEAD-boxes"	17906	protein-coding gene	gene with protein product		610373				11891046	Standard	NM_024045		Approved	GU2, MGC3199, GUB, RH-II/GuB	uc001jou.3	Q9BQ39	OTTHUMG00000018362	ENST00000373585.3:c.532A>T	chr10.hg19:g.70670895A>T	ENSP00000362687:p.Ile178Leu	195.0	1.0		190.0	104.0	NM_024045	Q5VX37|Q8WV76|Q9BWI8	Missense_Mutation	SNP	ENST00000373585.3	hg19	CCDS7283.1	.	.	.	.	.	.	.	.	.	.	A	19.53	3.844485	0.71488	.	.	ENSG00000107625	ENST00000373585;ENST00000541832	T	0.12255	2.7	5.22	4.08	0.47627	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.146646	0.64402	D	0.000007	T	0.09423	0.0232	N	0.05592	-0.015	0.39725	D	0.971527	B;B	0.32939	0.391;0.334	B;B	0.42916	0.31;0.402	T	0.32295	-0.9912	10	0.34782	T	0.22	-12.4976	8.1397	0.31076	0.8472:0.0:0.1528:0.0	.	178;178	Q9BQ39;B4DED6	DDX50_HUMAN;.	L	178	ENSP00000362687:I178L	ENSP00000362687:I178L	I	+	1	0	DDX50	70340901	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.388000	0.52509	2.099000	0.63709	0.397000	0.26171	ATA	.	.		0.353	DDX50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048363.1	NM_024045		T	70670895	A	T	70670895	3	4	344	1	0	0	0	0	1	0	0	0	4370	101	4	4	546	4	DDX50	10	70670895	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	4291	70670895	64863852	772	48135										
SUPV3L1	6832	hgsc.bcm.edu	37	chr10	70968759	70968759	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggactcatccaaaagggacgAgaagaaagaagaaggaacct	12	7	1	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:70968759A>T	ENST00000359655.4	+	15	2389	c.2329A>T	c.(2329-2331)Aga>Tga	p.R777*		NM_003171.3	NP_003162.2	Q8IYB8	SUV3_HUMAN	suppressor of var1, 3-like 1 (S. cerevisiae)	777	Interaction with LAMTOR5, important for protein stability.				ATP catabolic process (GO:0006200)|chromatin maintenance (GO:0070827)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|mitochondrial mRNA catabolic process (GO:0000958)|mitochondrial mRNA surveillance (GO:0035946)|mitochondrial ncRNA surveillance (GO:0035945)|mitochondrial RNA 3'-end processing (GO:0000965)|mitochondrial RNA surveillance (GO:2000827)|mitochondrion morphogenesis (GO:0070584)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell growth (GO:0030307)|positive regulation of mitochondrial RNA catabolic process (GO:0000962)|RNA catabolic process (GO:0006401)	mitochondrial degradosome (GO:0045025)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	3'-5' RNA helicase activity (GO:0034458)|ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						AAAAGGGACGAGAAGAAAGAA	0.343																																					p.R777X		Atlas-SNP	.											.	SUPV3L1	61	.	0			c.A2329T						.						64	63	63					10																	70968759		2203	4300	6503	SO:0001587	stop_gained	6832	exon15			GGGACGAGAAGAA	AF042169	CCDS7287.1	10q22.1	2008-08-01	2001-11-28		ENSG00000156502	ENSG00000156502			11471	protein-coding gene	gene with protein product		605122	"suppressor of var1 (S.cerevisiae) 3-like 1"			9925937, 16176273	Standard	XM_005270068		Approved	SUV3	uc001jpe.1	Q8IYB8	OTTHUMG00000018375	ENST00000359655.4:c.2329A>T	chr10.hg19:g.70968759A>T	ENSP00000352678:p.Arg777*	56.0	0.0		56.0	20.0	NM_003171	A8K301|O43630	Nonsense_Mutation	SNP	ENST00000359655.4	hg19	CCDS7287.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.726700	0.89298	.	.	ENSG00000156502	ENST00000359655	.	.	.	6.16	-0.671	0.11381	.	0.164812	0.53938	D	0.000048	.	.	.	.	.	.	0.49389	D	0.999788	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.0135	5.022	0.14365	0.3461:0.4671:0.0781:0.1086	.	.	.	.	X	777	.	ENSP00000352678:R777X	R	+	1	2	SUPV3L1	70638765	0.004000	0.15560	0.002000	0.10522	0.390000	0.30446	0.157000	0.16402	-0.341000	0.08376	0.528000	0.53228	AGA	.	.		0.343	SUPV3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048396.2	NM_003171		T	70968759	A	T	70968759	4	4	344	1	0	0	0	0	0	1	0	0	15417	296	11	4	2387	4	SUPV3L1	10	70968759	Nonsense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	297864	70968759	64565988	773	48136										
CDH23	64072	hgsc.bcm.edu	37	chr10	73269837	73269837	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctctctcccttggctactccAggttcttctgtgacccagtt	7	15	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:73269837A>T	ENST00000224721.6	+	3	150		c.e3-1		CDH23_ENST00000398842.3_Splice_Site|CDH23-AS1_ENST00000428918.1_RNA|CDH23_ENST00000299366.7_Splice_Site|CDH23_ENST00000398809.4_Splice_Site|CDH23_ENST00000461841.3_Splice_Site	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23						calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						TGGCTACTCCAGGTTCTTCTG	0.562																																					.		Atlas-SNP	.											.	CDH23	365	.	0			c.146-2A>T						.						91	100	97					10																	73269837		1993	4170	6163	SO:0001630	splice_region_variant	64072	exon4			TACTCCAGGTTCT	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"Cadherins / Cadherin-related"	13733	protein-coding gene	gene with protein product	"cadherin-related family member 23"	605516	"cadherin related 23", "cadherin-like 23"	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.146-1A>T	chr10.hg19:g.73269837A>T		59.0	0.0		41.0	18.0	NM_001171931	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Splice_Site	SNP	ENST00000224721.6	hg19		.	.	.	.	.	.	.	.	.	.	A	21.7	4.185321	0.78677	.	.	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000398828;ENST00000398809;ENST00000398842;ENST00000299366;ENST00000224721	.	.	.	5.36	5.36	0.76844	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.057	0.71921	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CDH23	72939843	1.000000	0.71417	0.990000	0.47175	0.956000	0.61745	6.460000	0.73518	2.028000	0.59812	0.456000	0.33151	.	.	.		0.562	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	Intron	T	73269837	A	T	73269837	5	4	344	1	0	0	0	0	0	0	1	0	3110	202	7	4	154	4	CDH23	10	73269837	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2301078	73269837	62264910	774	48137										
NDST2	8509	hgsc.bcm.edu	37	chr10	75567441	75567441	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aagaagcactggttcatatgTactatgattggattggaaga	11	4	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:75567441T>C	ENST00000309979.6	-	3	1262	c.706A>G	c.(706-708)Aca>Gca	p.T236A	NDST2_ENST00000299641.4_Missense_Mutation_p.T113A|NDST2_ENST00000398701.2_5'Flank|RP11-574K11.31_ENST00000603027.1_Missense_Mutation_p.T236A			P52849	NDST2_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 2	236	Heparan sulfate N-deacetylase 2.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|hydrolase activity (GO:0016787)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(11)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	30	Prostate(51;0.0112)					GGTTCATATGTACTATGATTG	0.592																																					p.T236A		Atlas-SNP	.											.	NDST2	53	.	0			c.A706G						.						68	62	64					10																	75567441		2203	4300	6503	SO:0001583	missense	8509	exon3			CATATGTACTATG	U36601	CCDS7335.1	10q22	2007-03-14			ENSG00000166507	ENSG00000166507		"Sulfotransferases, membrane-bound"	7681	protein-coding gene	gene with protein product		603268				9601056	Standard	NM_003635		Approved	NST2, HSST2	uc001jvk.2	P52849	OTTHUMG00000018489	ENST00000309979.6:c.706A>G	chr10.hg19:g.75567441T>C	ENSP00000310657:p.Thr236Ala	91.0	0.0		53.0	19.0	NM_003635	Q2TB32|Q59H89	Missense_Mutation	SNP	ENST00000309979.6	hg19	CCDS7335.1	.	.	.	.	.	.	.	.	.	.	T	15.86	2.958796	0.53400	.	.	ENSG00000166507	ENST00000309979;ENST00000299641	T;T	0.47869	1.12;0.83	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.64182	0.2575	M	0.62088	1.915	0.80722	D	1	P;P	0.52692	0.882;0.955	P;P	0.61070	0.812;0.883	T	0.63839	-0.6546	10	0.48119	T	0.1	.	16.4504	0.83984	0.0:0.0:0.0:1.0	.	113;236	B4E139;P52849	.;NDST2_HUMAN	A	236;113	ENSP00000310657:T236A;ENSP00000299641:T113A	ENSP00000299641:T113A	T	-	1	0	NDST2	75237447	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.277000	0.72608	2.288000	0.76882	0.533000	0.62120	ACA	.	.		0.592	NDST2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048710.1	NM_003635		C	75567441	T	C	75567441	3	2	344	1	0	0	0	0	1	0	0	0	10265	1638	57	2	1997	2	NDST2	10	75567441	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2297604	75567441	59967306	775	48138										
MYST4	23522	hgsc.bcm.edu	37	chr10	76788413	76788413	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctgaatttgtacaccccgccAgaaacacccatggagcctga	8	14	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:76788413A>T	ENST00000287239.4	+	18	4320	c.3831A>T	c.(3829-3831)ccA>ccT	p.P1277P	KAT6B_ENST00000372725.1_Silent_p.P985P|KAT6B_ENST00000372724.1_Silent_p.P985P|KAT6B_ENST00000372714.1_Silent_p.P985P|KAT6B_ENST00000372711.1_Silent_p.P1094P	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	1277					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										ACACCCCGCCAGAAACACCCA	0.498																																					p.P1277P		Atlas-SNP	.											.	.	.	.	0			c.A3831T						.						80	78	79					10																	76788413		2203	4300	6503	SO:0001819	synonymous_variant	23522	exon18			CCCGCCAGAAACA	AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	17582	protein-coding gene	gene with protein product	"MOZ-related factor"	605880	"MYST histone acetyltransferase (monocytic leukemia) 4"	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.3831A>T	chr10.hg19:g.76788413A>T		51.0	0.0		60.0	38.0	NM_012330	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Silent	SNP	ENST00000287239.4	hg19	CCDS7345.1																																																																																			.	.		0.498	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330		T	76788413	A	T	76788413	2	4	344	1	0	0	0	0	0	0	0	1	10114	175	7	4		4	MYST4	10	76788413	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1220972	76788413	58746334	776	48139										
DLG5	9231	hgsc.bcm.edu	37	chr10	79601686	79601686	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggccgccttcttctcagatgTgctgctcttgagcttggact	11	12	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:79601686T>C	ENST00000372391.2	-	7	1395	c.1390A>G	c.(1390-1392)Aca>Gca	p.T464A	DLG5_ENST00000372388.2_Missense_Mutation_p.T464A	NM_004747.3	NP_004738.3	Q8TDM6	DLG5_HUMAN	discs, large homolog 5 (Drosophila)	464					apical protein localization (GO:0045176)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|intracellular signal transduction (GO:0035556)|metanephric collecting duct development (GO:0072205)|midbrain development (GO:0030901)|negative regulation of cell proliferation (GO:0008285)|polarized epithelial cell differentiation (GO:0030859)|protein complex assembly (GO:0006461)|protein localization to adherens junction (GO:0071896)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|zonula adherens assembly (GO:0045186)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cytoskeletal protein binding (GO:0008092)|receptor signaling complex scaffold activity (GO:0030159)			breast(9)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(17)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	60	all_cancers(46;0.0316)|all_epithelial(25;0.00147)|Breast(12;0.0015)|Prostate(51;0.0146)		Epithelial(14;0.00105)|OV - Ovarian serous cystadenocarcinoma(4;0.00151)|all cancers(16;0.00446)			TTCTCAGATGTGCTGCTCTTG	0.602																																					p.T464A		Atlas-SNP	.											.	DLG5	154	.	0			c.A1390G						.						104	83	90					10																	79601686		2203	4300	6503	SO:0001583	missense	9231	exon7			CAGATGTGCTGCT	U61843	CCDS7353.2	10q23	2008-07-09	2001-11-28		ENSG00000151208	ENSG00000151208			2904	protein-coding gene	gene with protein product		604090	"discs, large (Drosophila) homolog 5"			9738934	Standard	XM_005270276		Approved	P-dlg, KIAA0583	uc001jzk.3	Q8TDM6	OTTHUMG00000018548	ENST00000372391.2:c.1390A>G	chr10.hg19:g.79601686T>C	ENSP00000361467:p.Thr464Ala	54.0	0.0		43.0	17.0	NM_004747	A6H8Y3|Q149N1|Q5T1H7|Q5T1H8|Q6DKG3|Q86WC0|Q8TDM7|Q9UE73|Q9Y4E3	Missense_Mutation	SNP	ENST00000372391.2	hg19	CCDS7353.2	.	.	.	.	.	.	.	.	.	.	T	12.48	1.949901	0.34377	.	.	ENSG00000151208	ENST00000372391;ENST00000372388	T;T	0.04015	3.73;3.74	5.69	3.23	0.37069	.	0.000000	0.38492	N	0.001662	T	0.02156	0.0067	N	0.03608	-0.345	0.27614	N	0.94856	B;B;B	0.34290	0.447;0.319;0.004	B;B;B	0.36030	0.216;0.107;0.005	T	0.42430	-0.9452	10	0.25751	T	0.34	.	5.0616	0.14560	0.3121:0.086:0.0:0.6019	.	354;464;464	Q8TDM6-4;Q8TDM6;Q8TDM6-2	.;DLG5_HUMAN;.	A	464	ENSP00000361467:T464A;ENSP00000361464:T464A	ENSP00000361464:T464A	T	-	1	0	DLG5	79271692	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.448000	0.73469	0.995000	0.38917	0.460000	0.39030	ACA	.	.		0.602	DLG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048900.2			C	79601686	T	C	79601686	3	2	344	1	0	0	0	0	1	0	0	0	4560	1696	59	2	4473	2	DLG5	10	79601686	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2813273	79601686	55933061	777	48140										
DYDC1	143241	hgsc.bcm.edu	37	chr10	82102044	82102044	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccttgcctaattgttcttgaGctctctgtagttcttgtatt	7	9	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:82102044G>C	ENST00000372204.3	-	5	487	c.323C>G	c.(322-324)gCt>gGt	p.A108G	DYDC2_ENST00000372199.1_5'Flank|DYDC1_ENST00000372202.1_Missense_Mutation_p.A108G|DYDC2_ENST00000372198.1_5'Flank|DYDC1_ENST00000421924.2_Missense_Mutation_p.A108G|DYDC2_ENST00000372197.1_5'Flank	NM_138812.3	NP_620167.1	Q8WWB3	DYDC1_HUMAN	DPY30 domain containing 1	108										kidney(1)|large_intestine(3)|skin(1)	5			Colorectal(32;0.229)			TTGTTCTTGAGCTCTCTGTAG	0.338																																					p.A108G		Atlas-SNP	.											.	DYDC1	15	.	0			c.C323G						.						176	162	167					10																	82102044		2203	4300	6503	SO:0001583	missense	143241	exon4			TCTTGAGCTCTCT	BC019250	CCDS7366.1	10q22.3	2006-02-01			ENSG00000170788	ENSG00000170788			23460	protein-coding gene	gene with protein product		615154					Standard	NM_138812		Approved	bA36D19.5, DPY30D1	uc031pwj.1	Q8WWB3	OTTHUMG00000018609	ENST00000372204.3:c.323C>G	chr10.hg19:g.82102044G>C	ENSP00000361278:p.Ala108Gly	84.0	0.0		67.0	29.0	NM_001269053	A8K927|Q5QP03|Q5QP04|Q6WNP4|Q6ZU87	Missense_Mutation	SNP	ENST00000372204.3	hg19	CCDS7366.1	.	.	.	.	.	.	.	.	.	.	G	6.124	0.391113	0.11581	.	.	ENSG00000170788	ENST00000372204;ENST00000372202;ENST00000421924;ENST00000454362	.	.	.	3.94	-0.0574	0.13801	.	0.627980	0.15158	N	0.277327	T	0.17450	0.0419	N	0.22421	0.69	0.09310	N	1	B;B	0.10296	0.003;0.003	B;B	0.08055	0.003;0.003	T	0.13953	-1.0490	9	0.30078	T	0.28	-0.3534	1.0807	0.01642	0.2079:0.177:0.4331:0.182	.	108;108	A8K927;Q8WWB3	.;DYDC1_HUMAN	G	108	.	ENSP00000361276:A108G	A	-	2	0	DYDC1	82092024	0.000000	0.05858	0.067000	0.19924	0.989000	0.77384	-0.141000	0.10327	-0.002000	0.14469	0.655000	0.94253	GCT	.	.		0.338	DYDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049059.1	NM_138812		C	82102044	G	C	82102044	3	2	344	1	0	0	0	0	1	0	0	0	4840	971	34	4	226	4	DYDC1	10	82102044	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	2500358	82102044	53432703	778	48141										
LRIT1	26103	hgsc.bcm.edu	37	chr10	85991913	85991913	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cttctgaagagcactgcagcAgacaagcagcgtgagaggca	13	10	1	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:85991913A>T	ENST00000372105.3	-	4	1663	c.1642T>A	c.(1642-1644)Tgc>Agc	p.C548S		NM_015613.2	NP_056428.1	Q9P2V4	LRIT1_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 1	548						integral component of endoplasmic reticulum membrane (GO:0030176)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|skin(1)	23						GCACTGCAGCAGACAAGCAGC	0.537																																					p.C548S		Atlas-SNP	.											.	LRIT1	73	.	0			c.T1642A						.						110	88	96					10																	85991913		2203	4300	6503	SO:0001583	missense	26103	exon4			TGCAGCAGACAAG	AB031547	CCDS7373.1	10q23	2013-02-11	2007-06-19	2007-06-19	ENSG00000148602	ENSG00000148602		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	23404	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 9"		"leucine rich repeat containing 21"	LRRC21		10777785	Standard	NM_015613		Approved	PAL, DKFZP434K091, FIGLER9	uc001kcz.1	Q9P2V4	OTTHUMG00000018632	ENST00000372105.3:c.1642T>A	chr10.hg19:g.85991913A>T	ENSP00000361177:p.Cys548Ser	88.0	0.0		95.0	36.0	NM_015613	Q0QD41|Q9Y4N7	Missense_Mutation	SNP	ENST00000372105.3	hg19	CCDS7373.1	.	.	.	.	.	.	.	.	.	.	A	17.25	3.342176	0.61073	.	.	ENSG00000148602	ENST00000372105	T	0.38560	1.13	5.49	4.34	0.51931	.	0.047002	0.85682	D	0.000000	T	0.56396	0.1982	M	0.77313	2.365	0.80722	D	1	D	0.59357	0.985	P	0.54664	0.758	T	0.58831	-0.7567	10	0.49607	T	0.09	.	11.7523	0.51855	0.8522:0.1478:0.0:0.0	.	548	Q9P2V4	LRIT1_HUMAN	S	548	ENSP00000361177:C548S	ENSP00000361177:C548S	C	-	1	0	LRIT1	85981893	1.000000	0.71417	0.995000	0.50966	0.262000	0.26303	4.173000	0.58249	0.899000	0.36444	0.383000	0.25322	TGC	.	.		0.537	LRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049109.1	NM_015613		T	85991913	A	T	85991913	3	4	344	1	0	0	0	0	1	0	0	0	8956	188	7	4	233	4	LRIT1	10	85991913	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3889869	85991913	49542834	779	48142										
FAM190B	54462	hgsc.bcm.edu	37	chr10	86259681	86259681	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tggcagggctccttccagggGatcccacggactgttccacc	12	15	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:86259681G>A	ENST00000224756.8	+	10	2561	c.2376G>A	c.(2374-2376)ggG>ggA	p.G792G	CCSER2_ENST00000543283.1_Silent_p.G219G|CCSER2_ENST00000372088.2_Intron|CCSER2_ENST00000494144.1_Intron	NM_001284243.1|NM_018999.2	NP_001271172.1|NP_061872.2	Q9H7U1	CCSE2_HUMAN	coiled-coil serine-rich protein 2	792					microtubule bundle formation (GO:0001578)	microtubule cytoskeleton (GO:0015630)											CCTTCCAGGGGATCCCACGGA	0.542																																					p.G792G		Atlas-SNP	.											.	CCSER2	7	.	0			c.G2376A						.						129	114	119					10																	86259681		2203	4300	6503	SO:0001819	synonymous_variant	54462	exon10			CCAGGGGATCCCA		CCDS31235.1, CCDS60582.1, CCDS60583.1, CCDS73159.1	10q23.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000107771	ENSG00000107771			29197	protein-coding gene	gene with protein product			"KIAA1128", "family with sequence similarity 190, member B"	KIAA1128, FAM190B		10574461	Standard	XM_005269905		Approved		uc001kdh.1	Q9H7U1	OTTHUMG00000018641	ENST00000224756.8:c.2376G>A	chr10.hg19:g.86259681G>A		87.0	0.0		56.0	24.0	NM_018999	B4DFY4|B4DQU9|B7WPE8|D3DWE2|Q8N6E9|Q9H2S0|Q9ULU1	Silent	SNP	ENST00000224756.8	hg19	CCDS31235.1																																																																																			.	.		0.542	CCSER2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049132.2	NM_018999		A	86259681	G	A	86259681	2	1	344	1	0	0	0	0	0	0	0	1	5527	1161	41	3		3	FAM190B	10	86259681	Silent	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	267768	86259681	49275066	780	48143										
SLC16A12	387700	hgsc.bcm.edu	37	chr10	91198482	91198482	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	caaagcataaggcaccaagtAcacaaagagagggctgcagc	11	10	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:91198482A>G	ENST00000341233.4	-	6	1207	c.817T>C	c.(817-819)Tac>Cac	p.Y273H	SLC16A12_ENST00000371790.4_Missense_Mutation_p.Y303H	NM_213606.3	NP_998771.3	Q6ZSM3	MOT12_HUMAN	solute carrier family 16, member 12	273						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(4)|skin(1)|stomach(1)	14						GGCACCAAGTACACAAAGAGA	0.423																																					p.Y303H		Atlas-SNP	.											.	SLC16A12	40	.	0			c.T907C						.						90	79	83					10																	91198482		2203	4300	6503	SO:0001583	missense	387700	exon6			CCAAGTACACAAA		CCDS7404.1, CCDS7404.2	10q23.32	2013-07-18	2013-07-18		ENSG00000152779	ENSG00000152779		"Solute carriers"	23094	protein-coding gene	gene with protein product	"monocarboxylic acid transporter 12"	611910	"solute carrier family 16 (monocarboxylic acid transporters), member 12", "solute carrier family 16, member 12 (monocarboxylic acid transporter 12)"				Standard	NM_213606		Approved	MCT12	uc001kgm.3	Q6ZSM3	OTTHUMG00000018714	ENST00000341233.4:c.817T>C	chr10.hg19:g.91198482A>G	ENSP00000343022:p.Tyr273His	119.0	0.0		60.0	41.0	NM_213606	Q5M9M9|Q5T7J2|Q6ZV76	Missense_Mutation	SNP	ENST00000341233.4	hg19		.	.	.	.	.	.	.	.	.	.	A	3.946	-0.013147	0.07727	.	.	ENSG00000152779	ENST00000341233;ENST00000371790;ENST00000544887	D;D	0.82619	-1.63;-1.63	5.92	3.62	0.41486	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.103889	0.64402	N	0.000002	T	0.67571	0.2907	N	0.21448	0.665	0.48452	D	0.999656	B	0.20368	0.044	B	0.25614	0.062	T	0.56013	-0.8049	10	0.02654	T	1	.	9.5404	0.39248	0.8589:0.0:0.1411:0.0	.	273	Q6ZSM3	MOT12_HUMAN	H	273;303;80	ENSP00000343022:Y273H;ENSP00000360855:Y303H	ENSP00000343022:Y273H	Y	-	1	0	SLC16A12	91188462	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	4.527000	0.60573	0.514000	0.28300	0.459000	0.35465	TAC	.	.		0.423	SLC16A12-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_213606		G	91198482	A	G	91198482	3	3	344	1	0	0	0	0	1	0	0	0	14420	391	14	2	655	2	SLC16A12	10	91198482	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	4938801	91198482	44336265	781	48144										
KIF20B	9585	hgsc.bcm.edu	37	chr10	91469185	91469185	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cggttaagtgaaaaaagctcAgggcagatggcacagaaatt	12	6	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:91469185A>G	ENST00000371728.3	+	4	383	c.318A>G	c.(316-318)tcA>tcG	p.S106S	KIF20B_ENST00000416354.1_Silent_p.S106S|KIF20B_ENST00000260753.4_Silent_p.S106S|KIF20B_ENST00000394289.2_Silent_p.S106S	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	106	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|neural tube closure (GO:0001843)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization (GO:0070201)|regulation of mitosis (GO:0007088)|regulation of neuron migration (GO:2001222)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|WW domain binding (GO:0050699)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	58						AAAAAAGCTCAGGGCAGATGG	0.398																																					p.S106S		Atlas-SNP	.											.	KIF20B	191	.	0			c.A318G						.						98	97	97					10																	91469185		2203	4300	6503	SO:0001819	synonymous_variant	9585	exon4			AAGCTCAGGGCAG	L16782	CCDS7407.1, CCDS60590.1	10q23.31	2009-08-06	2008-07-31	2008-07-31	ENSG00000138182	ENSG00000138182			7212	protein-coding gene	gene with protein product	"cancer/testis antigen 90"	605498	"M-phase phosphoprotein 1"	MPHOSPH1		8885239, 8290587, 11470801	Standard	NM_016195		Approved	MPP1, KRMP1, CT90	uc001kgr.1	Q96Q89	OTTHUMG00000018725	ENST00000371728.3:c.318A>G	chr10.hg19:g.91469185A>G		174.0	1.0		69.0	53.0	NM_016195	A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Silent	SNP	ENST00000371728.3	hg19																																																																																				.	.		0.398	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195		G	91469185	A	G	91469185	2	3	344	1	0	0	0	0	0	0	0	1	8296	175	7	2		2	KIF20B	10	91469185	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	270703	91469185	44065562	782	48145										
CEP55	55165	hgsc.bcm.edu	37	chr10	95259889	95259889	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tccaaatccgaaactacattAgaaaaattaaagggagaaat	6	6	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:95259889A>T	ENST00000371485.3	+	2	385	c.81A>T	c.(79-81)ttA>ttT	p.L27F		NM_001127182.1|NM_018131.4	NP_001120654|NP_060601	Q53EZ4	CEP55_HUMAN	centrosomal protein 55kDa	27					establishment of protein localization (GO:0045184)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|midbody (GO:0030496)				kidney(1)|large_intestine(5)|lung(6)|stomach(1)	13		Colorectal(252;0.207)				AAACTACATTAGAAAAATTAA	0.368																																					p.L27F		Atlas-SNP	.											.	CEP55	35	.	0			c.A81T						.						137	151	147					10																	95259889		2203	4300	6503	SO:0001583	missense	55165	exon2			TACATTAGAAAAA	AK001402	CCDS7428.1	10q24.1	2014-02-20	2005-12-01	2005-12-01	ENSG00000138180	ENSG00000138180			1161	protein-coding gene	gene with protein product	"cancer/testis antigen 111"	610000	"chromosome 10 open reading frame 3"	C10orf3		16198290	Standard	NM_018131		Approved	FLJ10540, CT111	uc009xug.3	Q53EZ4	OTTHUMG00000018774	ENST00000371485.3:c.81A>T	chr10.hg19:g.95259889A>T	ENSP00000360540:p.Leu27Phe	147.0	1.0		47.0	38.0	NM_018131	B2RDG8|Q32WF5|Q3MV20|Q5VY28|Q6N034|Q96H32|Q9NVS7	Missense_Mutation	SNP	ENST00000371485.3	hg19	CCDS7428.1	.	.	.	.	.	.	.	.	.	.	A	14.15	2.448465	0.43429	.	.	ENSG00000138180	ENST00000371485;ENST00000358339	T	0.29655	1.56	5.24	4.11	0.48088	.	0.082950	0.49305	D	0.000147	T	0.45935	0.1367	M	0.62723	1.935	0.39086	D	0.960994	D	0.89917	1.0	D	0.83275	0.996	T	0.49652	-0.8917	10	0.72032	D	0.01	-7.3219	3.7919	0.08724	0.6718:0.0:0.1698:0.1583	.	27	Q53EZ4	CEP55_HUMAN	F	27	ENSP00000360540:L27F	ENSP00000351102:L27F	L	+	3	2	CEP55	95249879	1.000000	0.71417	0.995000	0.50966	0.304000	0.27724	0.922000	0.28734	0.954000	0.37851	0.455000	0.32223	TTA	.	.		0.368	CEP55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049434.1	NM_018131		T	95259889	A	T	95259889	3	4	344	1	0	0	0	0	1	0	0	0	3257	417	15	4	83	4	CEP55	10	95259889	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3790704	95259889	40274858	783	48146										
BLNK	29760	hgsc.bcm.edu	37	chr10	97976426	97976426	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tacctttttcaggtggaggtGaactgctttctgtgggatga	13	6	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:97976426G>A	ENST00000224337.5	-	7	731	c.590C>T	c.(589-591)tCa>tTa	p.S197L	BLNK_ENST00000427367.2_Missense_Mutation_p.S197L|BLNK_ENST00000413476.2_Missense_Mutation_p.S197L|BLNK_ENST00000371176.2_Missense_Mutation_p.S197L	NM_013314.3	NP_037446.1	Q8WV28	BLNK_HUMAN	B-cell linker	197	Pro-rich.				B cell differentiation (GO:0030183)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|positive regulation of signal transduction (GO:0009967)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|skin(2)|stomach(1)	14		Colorectal(252;0.083)		Epithelial(162;7.89e-08)|all cancers(201;2.27e-06)		AGGTGGAGGTGAACTGCTTTC	0.383																																					p.S197L		Atlas-SNP	.											.	BLNK	46	.	0			c.C590T						.						140	124	130					10																	97976426		2203	4300	6503	SO:0001583	missense	29760	exon7			GGAGGTGAACTGC	AF068180	CCDS7446.1, CCDS44464.1, CCDS58091.1, CCDS73171.1	10q23.2-q23.33	2014-09-17			ENSG00000095585	ENSG00000095585		"SH2 domain containing"	14211	protein-coding gene	gene with protein product	"B-cell adapter containing a SH2 domain protein", "B-cell activation", "Src homology [SH2] domain-containing leukocyte protein of 65 kD", "B cell adaptor containing SH2 domain"	604515				9697839, 10583958	Standard	NM_013314		Approved	SLP65, Ly57, SLP-65, BLNK-s, BASH, bca	uc001kls.4	Q8WV28	OTTHUMG00000018827	ENST00000224337.5:c.590C>T	chr10.hg19:g.97976426G>A	ENSP00000224337:p.Ser197Leu	156.0	0.0		68.0	49.0	NM_001114094	O75498|O75499|Q2MD49	Missense_Mutation	SNP	ENST00000224337.5	hg19	CCDS7446.1	.	.	.	.	.	.	.	.	.	.	G	13.00	2.107690	0.37242	.	.	ENSG00000095585	ENST00000224337;ENST00000371176;ENST00000427367;ENST00000413476;ENST00000428924	.	.	.	5.1	4.19	0.49359	.	0.901140	0.09577	N	0.783345	T	0.26448	0.0646	N	0.17474	0.49	0.21147	N	0.99977	B;B;B;B;B	0.09022	0.001;0.001;0.002;0.001;0.002	B;B;B;B;B	0.10450	0.002;0.005;0.003;0.001;0.002	T	0.09618	-1.0666	9	0.20519	T	0.43	-0.4666	8.5464	0.33424	0.1032:0.0:0.8968:0.0	.	197;197;197;197;197	Q2MD54;Q2MD49;Q8WV28-2;Q2MD52;Q8WV28	.;.;.;.;BLNK_HUMAN	L	197	.	ENSP00000224337:S197L	S	-	2	0	BLNK	97966416	0.981000	0.34729	0.706000	0.30403	0.898000	0.52572	3.153000	0.50685	2.375000	0.81037	0.655000	0.94253	TCA	.	.		0.383	BLNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049593.1	NM_013314		A	97976426	G	A	97976426	3	1	344	1	0	0	0	0	1	0	0	0	1447	1294	45	3	824	3	BLNK	10	97976426	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	2716537	97976426	37558321	784	48147										
TLL2	7093	hgsc.bcm.edu	37	chr10	98145897	98145897	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cctgccagacacagtttttgTttgtgggatactccttcggc	10	11	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:98145897T>G	ENST00000357947.3	-	15	2153	c.1928A>C	c.(1927-1929)aAc>aCc	p.N643T		NM_012465.3	NP_036597.1	Q9Y6L7	TLL2_HUMAN	tolloid-like 2	643	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(15)|lung(22)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	58		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)		ACAGTTTTTGTTTGTGGGATA	0.537																																					p.N643T		Atlas-SNP	.											.	TLL2	122	.	0			c.A1928C						.						116	111	113					10																	98145897		2203	4300	6503	SO:0001583	missense	7093	exon15			TTTTTGTTTGTGG	AF059516	CCDS7449.1	10q23-q24	2008-07-29			ENSG00000095587	ENSG00000095587			11844	protein-coding gene	gene with protein product		606743				10516436	Standard	NM_012465		Approved		uc001kml.2	Q9Y6L7	OTTHUMG00000018833	ENST00000357947.3:c.1928A>C	chr10.hg19:g.98145897T>G	ENSP00000350630:p.Asn643Thr	59.0	0.0		31.0	19.0	NM_012465	A6NDK0|Q2M1H1|Q6PJN5|Q9UQ00	Missense_Mutation	SNP	ENST00000357947.3	hg19	CCDS7449.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.594186	0.86953	.	.	ENSG00000095587	ENST00000357947	T	0.34472	1.36	4.98	4.98	0.66077	CUB (5);	0.000000	0.49305	D	0.000147	T	0.68842	0.3045	M	0.93507	3.425	0.58432	D	0.999998	D	0.76494	0.999	D	0.91635	0.999	T	0.77699	-0.2490	10	0.66056	D	0.02	.	14.2922	0.66286	0.0:0.0:0.0:1.0	.	643	Q9Y6L7	TLL2_HUMAN	T	643	ENSP00000350630:N643T	ENSP00000350630:N643T	N	-	2	0	TLL2	98135887	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.090000	0.71397	2.228000	0.72767	0.477000	0.44152	AAC	.	.		0.537	TLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049608.1			G	98145897	T	G	98145897	3	3	344	1	0	0	0	0	1	0	0	0	15961	1725	60	5	1147	5	TLL2	10	98145897	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	169471	98145897	37388850	785	48148										
TDRD1	56165	hgsc.bcm.edu	37	chr10	115947807	115947807	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	attttttgctttgtgagcaaAccaaacaatatttggctagt	7	6	0	1	rs540561593		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:115947807A>T	ENST00000369280.1	+	2	677	c.217A>T	c.(217-219)Acc>Tcc	p.T73S	TDRD1_ENST00000422662.1_5'UTR|TDRD1_ENST00000369282.1_Missense_Mutation_p.T73S|TDRD1_ENST00000251864.2_Missense_Mutation_p.T73S|TDRD1_ENST00000369281.2_Missense_Mutation_p.T73S			Q9BXT4	TDRD1_HUMAN	tudor domain containing 1	73					DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|germ cell development (GO:0007281)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|P granule (GO:0043186)|pi-body (GO:0071546)	metal ion binding (GO:0046872)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(5)	48		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0343)|all cancers(201;0.0754)		TTGTGAGCAAACCAAACAATA	0.388																																					p.T73S		Atlas-SNP	.											.	TDRD1	126	.	0			c.A217T						.						99	106	104					10																	115947807		2203	4300	6503	SO:0001583	missense	56165	exon2			GAGCAAACCAAAC	AF285606	CCDS7588.1	10q26.11	2013-01-23			ENSG00000095627	ENSG00000095627		"Tudor domain containing"	11712	protein-coding gene	gene with protein product	"cancer/testis antigen 41.1"	605796				11279525	Standard	NM_198795		Approved	CT41.1	uc001lbg.1	Q9BXT4	OTTHUMG00000019083	ENST00000369280.1:c.217A>T	chr10.hg19:g.115947807A>T	ENSP00000358286:p.Thr73Ser	178.0	1.0		97.0	83.0	NM_198795	A6NEN3|A6NMN2|B3KVI4|B4E2L5|D3DRC2|Q4G0Y8|Q6P518|Q9H7B3	Missense_Mutation	SNP	ENST00000369280.1	hg19		.	.	.	.	.	.	.	.	.	.	A	14.54	2.566445	0.45694	.	.	ENSG00000095627	ENST00000369282;ENST00000251864;ENST00000369281;ENST00000369280	T;T;T;T	0.36878	1.23;1.23;1.23;1.23	5.44	4.3	0.51218	.	0.208436	0.33732	N	0.004618	T	0.26702	0.0653	L	0.32530	0.975	0.80722	D	1	B;B;B;B	0.26081	0.087;0.051;0.141;0.084	B;B;B;B	0.26202	0.03;0.016;0.067;0.037	T	0.06445	-1.0826	10	0.52906	T	0.07	-4.7262	7.9624	0.30079	0.9067:0.0:0.0933:0.0	.	73;73;73;73	Q9BXT4;B7WPM2;Q9BXT4-3;Q9BXT4-2	TDRD1_HUMAN;.;.;.	S	73	ENSP00000358288:T73S;ENSP00000251864:T73S;ENSP00000358287:T73S;ENSP00000358286:T73S	ENSP00000251864:T73S	T	+	1	0	TDRD1	115937797	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	1.504000	0.35726	0.901000	0.36495	0.460000	0.39030	ACC	.	.		0.388	TDRD1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050457.2			T	115947807	A	T	115947807	3	4	344	1	0	0	0	0	1	0	0	0	15745	43	2	4	219	4	TDRD1	10	115947807	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	17801910	115947807	19586940	786	48149										
DMBT1	1755	hgsc.bcm.edu	37	chr10	124402796	124402796	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgacccctcttcccgctgctAccgaggctgtgtgttgaggt	12	13	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:124402796A>G	ENST00000338354.3	+	53	7230	c.7124A>G	c.(7123-7125)tAc>tGc	p.Y2375C	DMBT1_ENST00000368955.3_Missense_Mutation_p.Y2365C|DMBT1_ENST00000330163.4_Missense_Mutation_p.Y1747C|DMBT1_ENST00000368956.2_Missense_Mutation_p.Y1747C|DMBT1_ENST00000359586.6_Missense_Mutation_p.Y1095C|DMBT1_ENST00000344338.3_Missense_Mutation_p.Y2365C|DMBT1_ENST00000368909.3_Missense_Mutation_p.Y2375C			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	2375	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				TCCCGCTGCTACCGAGGCTGT	0.607																																					p.Y2375C	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											.	DMBT1	677	.	0			c.A7124G						.						120	123	122					10																	124402796		2082	4220	6302	SO:0001583	missense	1755	exon53			GCTGCTACCGAGG		CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.7124A>G	chr10.hg19:g.124402796A>G	ENSP00000342210:p.Tyr2375Cys	144.0	0.0		72.0	52.0	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Missense_Mutation	SNP	ENST00000338354.3	hg19		.	.	.	.	.	.	.	.	.	.	A	10.91	1.484289	0.26598	.	.	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000327438;ENST00000344338;ENST00000339712;ENST00000330163;ENST00000368909;ENST00000368955;ENST00000368956;ENST00000344467;ENST00000359586	D;D;D;D;D;D;D	0.81996	-1.56;-1.56;-1.56;-1.56;-1.56;-1.56;-1.56	5.28	-0.279	0.12890	Zona pellucida sperm-binding protein (3);	1.136700	0.07003	U	0.823658	D	0.84999	0.5597	L	0.53249	1.67	0.09310	N	1	D;D;D;D;D;D;D	0.64830	0.973;0.994;0.973;0.973;0.973;0.973;0.978	P;D;P;P;P;P;P	0.63877	0.634;0.919;0.513;0.614;0.614;0.614;0.733	T	0.69960	-0.5003	10	0.59425	D	0.04	.	1.9907	0.03445	0.4922:0.1221:0.2672:0.1186	.	1095;2355;1624;2504;1747;2365;2375	F8WEF7;Q9UGM3-5;Q9UGM3-8;Q9UGM3-6;Q9UGM3-2;Q9UGM3-3;Q9UGM3	.;.;.;.;.;.;DMBT1_HUMAN	C	2375;2504;2375;2375;2375;2374;1747;2365;1747;1747;2375;2365;1747;521;1095	ENSP00000342210:Y2375C;ENSP00000343175:Y2365C;ENSP00000327747:Y1747C;ENSP00000357905:Y2375C;ENSP00000357951:Y2365C;ENSP00000357952:Y1747C;ENSP00000352593:Y1095C	ENSP00000331522:Y1747C	Y	+	2	0	DMBT1	124392786	0.001000	0.12720	0.015000	0.15790	0.027000	0.11550	0.268000	0.18571	0.003000	0.14656	0.533000	0.62120	TAC	.	.		0.607	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406		G	124402796	A	G	124402796	3	3	344	1	0	0	0	0	1	0	0	0	4579	391	14	2	7334	2	DMBT1	10	124402796	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	8454989	124402796	11131951	787	48150										
PTPRE	5791	hgsc.bcm.edu	37	chr10	129869164	129869164	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agggtcatccagatcatcccGtgtaaggcacccgtggcgtg	13	12	2	1	rs143511195		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:129869164G>T	ENST00000254667.3	+	15	1665	c.1386G>T	c.(1384-1386)ccG>ccT	p.P462P	PTPRE_ENST00000306042.5_Splice_Site_p.P404P|PTPRE_ENST00000419012.2_Splice_Site_p.P462P	NM_006504.4	NP_006495.1	P23469	PTPRE_HUMAN	protein tyrosine phosphatase, receptor type, E	462	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of insulin receptor signaling pathway (GO:0046627)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of mast cell activation (GO:0033003)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	22		all_epithelial(44;1.66e-05)|all_lung(145;0.00456)|Lung NSC(174;0.0066)|all_neural(114;0.0936)|Colorectal(57;0.141)|Breast(234;0.166)|Melanoma(40;0.203)			Alendronate(DB00630)	AGATCATCCCGTGTAAGGCAC	0.587																																					p.P462P	Colon(52;977 1184 20575 41685)	Atlas-SNP	.											.	PTPRE	132	.	0			c.G1386T						.						56	55	55					10																	129869164		2203	4300	6503	SO:0001630	splice_region_variant	5791	exon15			CATCCCGTGTAAG	AF406557	CCDS7657.1, CCDS7658.1	10q26	2011-06-09			ENSG00000132334	ENSG00000132334		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9669	protein-coding gene	gene with protein product		600926				8595895	Standard	NM_130435		Approved	PTPE	uc001lkb.3	P23469	OTTHUMG00000019254	ENST00000254667.3:c.1387+1G>T	chr10.hg19:g.129869164G>T		68.0	0.0		34.0	23.0	NM_006504	Q13345|Q5VWH3|Q5VWH4|Q96KQ6	Silent	SNP	ENST00000254667.3	hg19	CCDS7657.1																																																																																			.	G|1.000;C|0.000		0.587	PTPRE-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050990.1		Silent	T	129869164	G	T	129869164	5	4	344	1	0	0	0	0	0	0	1	0	12815	1159	40	1	1475	1	PTPRE	10	129869164	Splice_Site	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	5466368	129869164	5665583	788	48151										
KNDC1	85442	hgsc.bcm.edu	37	chr10	135013094	135013094	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggtggtcaacgggcaggcgtCaccctccccaaggtgggtgc	16	13	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr10:135013094C>G	ENST00000304613.3	+	15	2912	c.2891C>G	c.(2890-2892)tCa>tGa	p.S964*	KNDC1_ENST00000368571.2_Nonsense_Mutation_p.S899*|KNDC1_ENST00000368572.2_Nonsense_Mutation_p.S966*			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	964					cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		GGGCAGGCGTCACCCTCCCCA	0.617																																					p.S964X		Atlas-SNP	.											.	KNDC1	155	.	0			c.C2891G						.						102	96	98					10																	135013094		2203	4300	6503	SO:0001587	stop_gained	85442	exon15			AGGCGTCACCCTC	AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"RasGEF domain family, member 2"	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.2891C>G	chr10.hg19:g.135013094C>G	ENSP00000304437:p.Ser964*	69.0	0.0		30.0	23.0	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Nonsense_Mutation	SNP	ENST00000304613.3	hg19	CCDS7674.1	.	.	.	.	.	.	.	.	.	.	C	41	8.969022	0.99019	.	.	ENSG00000171798	ENST00000304613;ENST00000368572;ENST00000368571	.	.	.	3.99	3.99	0.46301	.	0.546471	0.16936	N	0.193497	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-4.3181	13.9012	0.63804	0.0:1.0:0.0:0.0	.	.	.	.	X	964;966;899	.	ENSP00000304437:S964X	S	+	2	0	KNDC1	134863084	0.011000	0.17503	0.003000	0.11579	0.076000	0.17211	2.587000	0.46128	1.957000	0.56846	0.313000	0.20887	TCA	.	.		0.617	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643		G	135013094	C	G	135013094	4	3	344	1	0	0	0	0	0	1	0	0	8435	838	29	4	2949	4	KNDC1	10	135013094	Nonsense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	5143930	135013094	521653	789	48152										
ANO9	338440	hgsc.bcm.edu	37	chr11	430368	430368	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aggtgtaccagcccagccagAcgaagtacagggccaccttt	11	13	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:430368A>T	ENST00000332826.6	-	8	659	c.575T>A	c.(574-576)gTc>gAc	p.V192D		NM_001012302.2	NP_001012302	A1A5B4	ANO9_HUMAN	anoctamin 9	192					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|negative regulation of intracellular calcium activated chloride channel activity (GO:1902939)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)			central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|lung(5)|ovary(1)|prostate(4)|skin(4)	21						GCCCAGCCAGACGAAGTACAG	0.622																																					p.V192D		Atlas-SNP	.											.	ANO9	61	.	0			c.T575A						.						22	25	24					11																	430368		2192	4290	6482	SO:0001583	missense	338440	exon8			AGCCAGACGAAGT	U33271	CCDS31326.1	11p15.5	2014-04-09	2008-08-28	2008-08-28	ENSG00000185101	ENSG00000185101		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	20679	protein-coding gene	gene with protein product			"tumor protein p53 inducible protein 5", "transmembrane protein 16J"	TP53I5, TMEM16J		9305847, 24692353	Standard	NM_001012302		Approved	PIG5	uc001lpi.2	A1A5B4	OTTHUMG00000165446	ENST00000332826.6:c.575T>A	chr11.hg19:g.430368A>T	ENSP00000332788:p.Val192Asp	233.0	1.0		97.0	85.0	NM_001012302	B3KUC4|B4E134|Q8TEN4	Missense_Mutation	SNP	ENST00000332826.6	hg19	CCDS31326.1	.	.	.	.	.	.	.	.	.	.	A	14.35	2.508809	0.44660	.	.	ENSG00000185101	ENST00000332826	T	0.63255	-0.03	4.21	3.29	0.37713	.	0.427052	0.21377	U	0.075534	T	0.49983	0.1589	L	0.34521	1.04	0.43126	D	0.994859	B	0.32245	0.361	B	0.30251	0.113	T	0.56001	-0.8051	10	0.87932	D	0	.	12.3967	0.55389	0.083:0.0:0.917:0.0	.	192	A1A5B4	ANO9_HUMAN	D	192	ENSP00000332788:V192D	ENSP00000332788:V192D	V	-	2	0	ANO9	420368	1.000000	0.71417	1.000000	0.80357	0.512000	0.34134	4.789000	0.62446	1.158000	0.42547	-0.373000	0.07131	GTC	.	.		0.622	ANO9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384116.1	NM_001012302		T	430368	A	T	430368	3	4	344	1	0	0	0	0	1	0	0	0	704	275	10	4	1837	4	ANO9	11	430368	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10		430368	134576148	790	48153										
LRDD	55367	hgsc.bcm.edu	37	chr11	801093	801093	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaggggcccagtacaacaggTgcaggcgggagcggtccaga	18	10	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:801093T>A	ENST00000347755.5	-	10	1799	c.1658A>T	c.(1657-1659)cAc>cTc	p.H553L	PIDD_ENST00000534649.1_5'Flank|PIDD_ENST00000411829.2_Missense_Mutation_p.H553L	NM_145886.3|NM_145887.3	NP_665893.2|NP_665894.2																					GTACAACAGGTGCAGGCGGGA	0.667																																					p.H553L		Atlas-SNP	.											.	PIDD	76	.	0			c.A1658T						.						28	23	25					11																	801093		2181	4287	6468	SO:0001583	missense	55367	exon10			AACAGGTGCAGGC																												ENST00000347755.5:c.1658A>T	chr11.hg19:g.801093T>A	ENSP00000337797:p.His553Leu	64.0	0.0		21.0	14.0	NM_145887		Missense_Mutation	SNP	ENST00000347755.5	hg19	CCDS7716.1	.	.	.	.	.	.	.	.	.	.	T	11.75	1.732976	0.30684	.	.	ENSG00000177595	ENST00000411829;ENST00000347755	T;T	0.39787	1.14;1.06	4.55	4.55	0.56014	ZU5 (1);	0.000000	0.85682	D	0.000000	T	0.35682	0.0940	L	0.32530	0.975	0.42816	D	0.993974	P;P;P;P	0.48089	0.905;0.717;0.617;0.775	P;B;B;B	0.45610	0.487;0.185;0.23;0.356	T	0.24621	-1.0155	10	0.66056	D	0.02	.	9.3527	0.38149	0.1597:0.0:0.0:0.8403	.	240;553;407;553	Q9HB75-5;Q9HB75;Q9HB75-3;Q9HB75-2	.;PIDD_HUMAN;.;.	L	553	ENSP00000416801:H553L;ENSP00000337797:H553L	ENSP00000337797:H553L	H	-	2	0	PIDD	791093	1.000000	0.71417	0.977000	0.42913	0.339000	0.28857	4.652000	0.61454	1.683000	0.51011	0.459000	0.35465	CAC	.	.		0.667	PIDD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257103.1			A	801093	T	A	801093	3	1	344	1	0	0	0	0	1	0	0	0	8945	1696	59	4	1102	4	LRDD	11	801093	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	370725	801093	134205423	791	48154										
MUC2	4583	hgsc.bcm.edu	37	chr11	1083817	1083817	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcgaagccccgagccctcagCtgccagacgctggccgccgg	13	18	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:1083817C>A	ENST00000441003.2	+	18	2376	c.2349C>A	c.(2347-2349)agC>agA	p.S783R	MUC2_ENST00000359061.5_Missense_Mutation_p.S783R	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	783					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	GAGCCCTCAGCTGCCAGACGC	0.687																																					p.S783R		Atlas-SNP	.											.	MUC2	614	.	0			c.C2349A						.						14	17	16					11																	1083817		2081	4202	6283	SO:0001583	missense	4583	exon18			CCTCAGCTGCCAG	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.2349C>A	chr11.hg19:g.1083817C>A	ENSP00000415183:p.Ser783Arg	72.0	0.0		22.0	20.0	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	hg19		.	.	.	.	.	.	.	.	.	.	C	5.674	0.308911	0.10733	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.27890	1.64;1.64	4.27	3.35	0.38373	.	0.168273	0.35615	U	0.003093	T	0.41558	0.1164	M	0.74647	2.275	0.21527	N	0.999651	D	0.56968	0.978	P	0.51101	0.659	T	0.30937	-0.9961	10	0.56958	D	0.05	.	9.6366	0.39811	0.0:0.895:0.0:0.105	.	783	E7EUV1	.	R	783	ENSP00000415183:S783R;ENSP00000351956:S783R	ENSP00000351956:S783R	S	+	3	2	MUC2	1073817	0.113000	0.22115	0.934000	0.37439	0.054000	0.15201	1.144000	0.31565	1.010000	0.39314	0.455000	0.32223	AGC	.	.		0.687	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		A	1083817	C	A	1083817	3	1	344	1	0	0	0	0	1	0	0	0	9984	796	28	3	2419	3	MUC2	11	1083817	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	282724	1083817	133922699	792	48155										
KRTAP5-4	387267	hgsc.bcm.edu	37	chr11	1642911	1642911	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agggcttacagcagctgcacTgggagcagccacaagagcca	13	12	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:1642911T>C	ENST00000399682.1	-	1	457	c.413A>G	c.(412-414)cAg>cGg	p.Q138R		NM_001012709.1	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	0	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				NS(1)|endometrium(9)|kidney(2)|lung(2)|pancreas(1)|prostate(3)|skin(2)	20		all_epithelial(84;0.00819)|Breast(177;0.00832)|Ovarian(85;0.0256)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		GCAGCTGCACTGGGAGCAGCC	0.652																																					p.Q138R		Atlas-SNP	.											.	KRTAP5-4	78	.	0			c.A413G						.						15	29	25					11																	1642911		691	1587	2278	SO:0001583	missense	387267	exon1			CTGCACTGGGAGC	AB126073		11p15.5	2012-04-19			ENSG00000241598	ENSG00000241598		"Keratin associated proteins"	23599	protein-coding gene	gene with protein product						15144888	Standard	NM_001012709		Approved	KRTAP5.4	uc009ycy.1	Q6L8H1	OTTHUMG00000057553	ENST00000399682.1:c.413A>G	chr11.hg19:g.1642911T>C	ENSP00000382590:p.Gln138Arg	111.0	0.0		39.0	31.0	NM_001012709		Missense_Mutation	SNP	ENST00000399682.1	hg19		.	.	.	.	.	.	.	.	.	.	T	0.013	-1.611413	0.00835	.	.	ENSG00000241598	ENST00000399682;ENST00000328953	T	0.00760	5.73	2.54	2.54	0.30619	.	.	.	.	.	T	0.00815	0.0027	L	0.42529	1.33	0.09310	N	0.999994	B	0.18741	0.03	B	0.13407	0.009	T	0.46048	-0.9219	9	0.18710	T	0.47	.	5.7355	0.18063	0.0:0.0:0.279:0.721	.	198	Q6L8H1	KRA54_HUMAN	R	138	ENSP00000382590:Q138R	ENSP00000331603:Q138R	Q	-	2	0	KRTAP5-4	1599487	0.102000	0.21896	0.025000	0.17156	0.002000	0.02628	0.796000	0.26986	1.180000	0.42898	0.391000	0.25812	CAG	.	.		0.652	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709		C	1642911	T	C	1642911	3	2	344	1	0	0	0	0	1	0	0	0	8572	1580	55	2	277	2	KRTAP5-4	11	1642911	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	559094	1642911	133363605	793	48156										
MRGPRE	116534	hgsc.bcm.edu	37	chr11	3249418	3249418	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gggggccgctgggggcctcgCtccacccgcagcagcagcat	16	16	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:3249418C>A	ENST00000389832.5	-	2	918	c.612G>T	c.(610-612)gaG>gaT	p.E204D	MRGPRE_ENST00000436689.2_Missense_Mutation_p.E203D|AC109309.4_ENST00000418995.2_RNA			Q86SM8	MRGRE_HUMAN	MAS-related GPR, member E	204						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(6)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	19		Medulloblastoma(188;0.00106)|all_epithelial(84;0.00111)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00529)|LUSC - Lung squamous cell carcinoma(625;0.19)		GGGGGCCTCGCTCCACCCGCA	0.687																																					p.E204D		Atlas-SNP	.											.	MRGPRE	35	.	0			c.G612T						.						5	7	6					11																	3249418		2057	4121	6178	SO:0001583	missense	116534	exon2			GCCTCGCTCCACC	AY255572	CCDS41603.1, CCDS41603.2	11p15.5	2012-08-21	2004-03-25		ENSG00000184350	ENSG00000184350		"GPCR / Class A : Orphans"	30694	protein-coding gene	gene with protein product		607232	"G protein-coupled receptor 167"	GPR167		11551509	Standard	NM_001039165		Approved	mrgE	uc001lxq.5	Q86SM8	OTTHUMG00000011708	ENST00000389832.5:c.612G>T	chr11.hg19:g.3249418C>A	ENSP00000374482:p.Glu204Asp	42.0	0.0		17.0	15.0	NM_001039165	Q2M1V7	Missense_Mutation	SNP	ENST00000389832.5	hg19		.	.	.	.	.	.	.	.	.	.	c	14.24	2.474951	0.43942	.	.	ENSG00000184350	ENST00000436689;ENST00000389832	.	.	.	3.9	0.551	0.17225	GPCR, rhodopsin-like superfamily (1);	0.811019	0.10061	U	0.720971	T	0.34542	0.0901	L	0.38838	1.175	0.09310	N	1	D	0.56521	0.976	P	0.57283	0.817	T	0.23726	-1.0180	9	0.12430	T	0.62	-8.9696	3.9179	0.09231	0.1622:0.582:0.158:0.0978	.	203	Q86SM8	MRGRE_HUMAN	D	204;203	.	ENSP00000374482:E203D	E	-	3	2	MRGPRE	3205994	0.000000	0.05858	0.002000	0.10522	0.068000	0.16541	-0.619000	0.05572	0.260000	0.21731	0.462000	0.41574	GAG	.	.		0.687	MRGPRE-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000032346.5	XM_171536		A	3249418	C	A	3249418	3	1	344	1	0	0	0	0	1	0	0	0	9773	796	28	3	330	3	MRGPRE	11	3249418	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1606507	3249418	131757098	794	48157										
OR51F2	119694	hgsc.bcm.edu	37	chr11	4842970	4842970	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttgcccagatgttctttctaCacggatttactttcatggag	8	9	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:4842970C>A	ENST00000322110.5	+	1	420	c.355C>A	c.(355-357)Cac>Aac	p.H119N	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001004753.1	NP_001004753.1	Q8NH61	O51F2_HUMAN	olfactory receptor, family 51, subfamily F, member 2	119						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(4)|large_intestine(3)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|skin(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.0778)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		GTTCTTTCTACACGGATTTAC	0.468																																					p.H119N		Atlas-SNP	.											.	OR51F2	72	.	0			c.C355A						.						187	165	173					11																	4842970		2201	4298	6499	SO:0001583	missense	119694	exon1			TTTCTACACGGAT	BK004281	CCDS31361.1	11p15.4	2012-08-09			ENSG00000176925	ENSG00000176925		"GPCR / Class A : Olfactory receptors"	15197	protein-coding gene	gene with protein product							Standard	NM_001004753		Approved		uc010qyn.2	Q8NH61	OTTHUMG00000066508	ENST00000322110.5:c.355C>A	chr11.hg19:g.4842970C>A	ENSP00000323952:p.His119Asn	132.0	0.0		55.0	46.0	NM_001004753	Q6IFI1	Missense_Mutation	SNP	ENST00000322110.5	hg19	CCDS31361.1	.	.	.	.	.	.	.	.	.	.	C	18.82	3.704525	0.68615	.	.	ENSG00000176925	ENST00000322110	T	0.00547	6.66	4.43	4.43	0.53597	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42172	U	0.000756	T	0.02727	0.0082	M	0.89904	3.07	0.35542	D	0.803127	D	0.89917	1.0	D	0.91635	0.999	T	0.10245	-1.0638	10	0.87932	D	0	.	12.0721	0.53622	0.0:0.8257:0.1742:0.0	.	119	Q8NH61	O51F2_HUMAN	N	119	ENSP00000323952:H119N	ENSP00000323952:H119N	H	+	1	0	OR51F2	4799546	0.997000	0.39634	0.958000	0.39756	0.973000	0.67179	3.098000	0.50259	2.461000	0.83175	0.561000	0.74099	CAC	.	.		0.468	OR51F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142181.1	NM_001004753		A	4842970	C	A	4842970	3	1	344	1	0	0	0	0	1	0	0	0	11106	478	17	3	357	3	OR51F2	11	4842970	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1593552	4842970	130163546	795	48158										
OR51S1	119692	hgsc.bcm.edu	37	chr11	4870336	4870336	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agcaatgaggggcaatgtccAccaggagggtgcacctgata	14	9	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:4870336A>T	ENST00000322101.2	-	1	178	c.103T>A	c.(103-105)Tgg>Agg	p.W35R	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001004758.1	NP_001004758.1	Q8NGJ8	O51S1_HUMAN	olfactory receptor, family 51, subfamily S, member 1	35						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(15)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		GGCAATGTCCACCAGGAGGGT	0.577																																					p.W35R		Atlas-SNP	.											.	OR51S1	83	.	0			c.T103A						.						105	93	97					11																	4870336		2201	4298	6499	SO:0001583	missense	119692	exon1			ATGTCCACCAGGA	AB065796	CCDS31362.1	11p15.4	2012-08-09			ENSG00000176922	ENSG00000176922		"GPCR / Class A : Olfactory receptors"	15204	protein-coding gene	gene with protein product							Standard	NM_001004758		Approved		uc010qyo.2	Q8NGJ8	OTTHUMG00000066506	ENST00000322101.2:c.103T>A	chr11.hg19:g.4870336A>T	ENSP00000322754:p.Trp35Arg	120.0	0.0		67.0	56.0	NM_001004758	B9EGZ1|Q6IFI2	Missense_Mutation	SNP	ENST00000322101.2	hg19	CCDS31362.1	.	.	.	.	.	.	.	.	.	.	A	12.90	2.076117	0.36662	.	.	ENSG00000176922	ENST00000322101	T	0.00318	8.12	5.35	4.17	0.49024	.	0.000000	0.41712	D	0.000822	T	0.00210	0.0006	N	0.08118	0	0.33245	D	0.557688	D	0.67145	0.996	P	0.59703	0.862	T	0.70637	-0.4817	10	0.87932	D	0	-4.9022	2.3603	0.04306	0.602:0.161:0.083:0.1541	.	35	Q8NGJ8	O51S1_HUMAN	R	35	ENSP00000322754:W35R	ENSP00000322754:W35R	W	-	1	0	OR51S1	4826912	0.203000	0.23435	1.000000	0.80357	0.278000	0.26855	0.552000	0.23376	2.243000	0.73865	0.460000	0.39030	TGG	.	.		0.577	OR51S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142179.1	NM_001004758		T	4870336	A	T	4870336	3	4	344	1	0	0	0	0	1	0	0	0	11114	159	6	4	871	4	OR51S1	11	4870336	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	27366	4870336	130136180	796	48159										
OR51A2	401667	hgsc.bcm.edu	37	chr11	4976050	4976050	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acaactctcactctaatctgTttagtttttacacaataaac	2	10	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:4976050T>G	ENST00000380371.1	-	1	893	c.894A>C	c.(892-894)aaA>aaC	p.K298N	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001004748.1	NP_001004748.1	Q8NGJ7	O51A2_HUMAN	olfactory receptor, family 51, subfamily A, member 2	298						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			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)		CTCTAATCTGTTTAGTTTTTA	0.373																																					p.K298N		Atlas-SNP	.											.	OR51A2	40	.	0			c.A894C						.						72	60	64					11																	4976050		2022	3682	5704	SO:0001583	missense	401667	exon1			AATCTGTTTAGTT	AB065797	CCDS31368.1	11p15.4	2012-08-09			ENSG00000205496	ENSG00000205496		"GPCR / Class A : Olfactory receptors"	14764	protein-coding gene	gene with protein product							Standard	NM_001004748		Approved		uc010qyt.2	Q8NGJ7	OTTHUMG00000066602	ENST00000380371.1:c.894A>C	chr11.hg19:g.4976050T>G	ENSP00000369729:p.Lys298Asn	176.0	0.0		156.0	140.0	NM_001004748		Missense_Mutation	SNP	ENST00000380371.1	hg19	CCDS31368.1	.	.	.	.	.	.	.	.	.	.	-	9.520	1.108138	0.20714	.	.	ENSG00000205496	ENST00000380371	T	0.45668	0.89	3.45	-0.564	0.11774	.	.	.	.	.	T	0.37376	0.1001	M	0.78637	2.42	0.09310	N	1	B	0.23591	0.088	B	0.22386	0.039	T	0.48958	-0.8988	9	0.87932	D	0	.	0.849	0.01168	0.1664:0.2397:0.1641:0.4299	.	298	Q8NGJ7	O51A2_HUMAN	N	298	ENSP00000369729:K298N	ENSP00000369729:K298N	K	-	3	2	OR51A2	4932626	0.000000	0.05858	0.003000	0.11579	0.006000	0.05464	-2.275000	0.01162	0.139000	0.18822	0.412000	0.27726	AAA	.	.		0.373	OR51A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142809.1	NM_001004748		G	4976050	T	G	4976050	3	3	344	1	0	0	0	0	1	0	0	0	11095	1722	60	5	49	5	OR51A2	11	4976050	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	105714	4976050	130030466	797	48160										
OR52N5	390075	hgsc.bcm.edu	37	chr11	5799159	5799159	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agcatctgatgaagagaggcTgatcgctgccttgaggatca	13	8	2	5			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:5799159T>A	ENST00000317093.2	-	1	738	c.706A>T	c.(706-708)Agc>Tgc	p.S236C	TRIM5_ENST00000380027.1_Intron	NM_001001922.2	NP_001001922.2	Q8NH56	O52N5_HUMAN	olfactory receptor, family 52, subfamily N, member 5	236						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(3)|liver(1)|lung(17)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.05e-11)|LUSC - Lung squamous cell carcinoma(625;0.112)|BRCA - Breast invasive adenocarcinoma(625;0.135)|Lung(200;0.195)		GAAGAGAGGCTGATCGCTGCC	0.438																																					p.S236C		Atlas-SNP	.											.	OR52N5	58	.	0			c.A706T						.						116	110	112					11																	5799159		2118	4092	6210	SO:0001583	missense	390075	exon1			AGAGGCTGATCGC	AB065535	CCDS31397.1	11p15.4	2012-08-09			ENSG00000181009	ENSG00000181009		"GPCR / Class A : Olfactory receptors"	15231	protein-coding gene	gene with protein product							Standard	NM_001001922		Approved	OR52N5Q	uc010qzn.2	Q8NH56	OTTHUMG00000168799	ENST00000317093.2:c.706A>T	chr11.hg19:g.5799159T>A	ENSP00000322866:p.Ser236Cys	128.0	0.0		62.0	48.0	NM_001001922	B9EH12|Q6IFG2	Missense_Mutation	SNP	ENST00000317093.2	hg19	CCDS31397.1	.	.	.	.	.	.	.	.	.	.	T	11.15	1.553384	0.27739	.	.	ENSG00000181009	ENST00000317093	T	0.00130	8.69	3.72	3.72	0.42706	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00412	0.0013	M	0.75884	2.315	0.26563	N	0.9737	D	0.64830	0.994	D	0.67382	0.951	T	0.53129	-0.8482	9	0.46703	T	0.11	.	11.6832	0.51470	0.0:0.0:0.0:1.0	.	236	Q8NH56	O52N5_HUMAN	C	236	ENSP00000322866:S236C	ENSP00000322866:S236C	S	-	1	0	OR52N5	5755735	0.000000	0.05858	0.301000	0.25044	0.124000	0.20399	0.216000	0.17585	1.687000	0.51057	0.416000	0.27883	AGC	.	.		0.438	OR52N5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401141.1	NM_001001922		A	5799159	T	A	5799159	3	1	344	1	0	0	0	0	1	0	0	0	11139	1580	55	4	272	4	OR52N5	11	5799159	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	823109	5799159	129207357	798	48161										
DCHS1	8642	hgsc.bcm.edu	37	chr11	6644033	6644033	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctacgggcccgaacaagtccTaggaccagggctgccagtgc	13	14	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:6644033T>A	ENST00000299441.3	-	21	9285	c.8874A>T	c.(8872-8874)ctA>ctT	p.L2958L	RP11-732A19.5_ENST00000526456.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	2958					branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GAACAAGTCCTAGGACCAGGG	0.647																																					p.L2958L		Atlas-SNP	.											.	DCHS1	277	.	0			c.A8874T						.						38	36	37					11																	6644033		2196	4280	6476	SO:0001819	synonymous_variant	8642	exon21			AAGTCCTAGGACC	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"Cadherins / Cadherin-related"	13681	protein-coding gene	gene with protein product	"cadherin-related family member 6"	603057	"protocadherin 16", "dachsous 1 (Drosophila)"	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.8874A>T	chr11.hg19:g.6644033T>A		72.0	0.0		29.0	25.0	NM_003737	O15098	Silent	SNP	ENST00000299441.3	hg19	CCDS7771.1																																																																																			.	.		0.647	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		A	6644033	T	A	6644033	2	1	344	1	0	0	0	0	0	0	0	1	4289	1509	53	4		4	DCHS1	11	6644033	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	844874	6644033	128362483	799	48162										
DCHS1	8642	hgsc.bcm.edu	37	chr11	6653396	6653396	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tggtccctgggggctggttcTcagccacagccaggaaggtg	16	11	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:6653396T>A	ENST00000299441.3	-	6	3758	c.3347A>T	c.(3346-3348)gAg>gTg	p.E1116V	RP11-732A19.6_ENST00000526633.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	1116	Cadherin 11. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGGCTGGTTCTCAGCCACAGC	0.607																																					p.E1116V		Atlas-SNP	.											.	DCHS1	277	.	0			c.A3347T						.						72	69	70					11																	6653396		2201	4295	6496	SO:0001583	missense	8642	exon6			TGGTTCTCAGCCA	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"Cadherins / Cadherin-related"	13681	protein-coding gene	gene with protein product	"cadherin-related family member 6"	603057	"protocadherin 16", "dachsous 1 (Drosophila)"	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.3347A>T	chr11.hg19:g.6653396T>A	ENSP00000299441:p.Glu1116Val	58.0	0.0		30.0	29.0	NM_003737	O15098	Missense_Mutation	SNP	ENST00000299441.3	hg19	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.015749	0.75161	.	.	ENSG00000166341	ENST00000299441	T	0.76448	-1.02	4.66	4.66	0.58398	Cadherin (3);Cadherin-like (1);	0.000000	0.47093	D	0.000257	D	0.92782	0.7705	H	0.99197	4.465	0.80722	D	1	D	0.69078	0.997	D	0.80764	0.994	D	0.95176	0.8295	10	0.66056	D	0.02	.	13.7121	0.62674	0.0:0.0:0.0:1.0	.	1116	Q96JQ0	PCD16_HUMAN	V	1116	ENSP00000299441:E1116V	ENSP00000299441:E1116V	E	-	2	0	DCHS1	6609972	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.480000	0.81109	2.089000	0.63090	0.459000	0.35465	GAG	.	.		0.607	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		A	6653396	T	A	6653396	3	1	344	1	0	0	0	0	1	0	0	0	4289	1551	54	4	6613	4	DCHS1	11	6653396	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	9363	6653396	128353120	800	48163										
OR6A2	8590	hgsc.bcm.edu	37	chr11	6816315	6816315	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tggccctagaagaataaaaaTggccaggatgaaatctgtaa	10	6	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:6816315T>C	ENST00000332601.3	-	1	813	c.625A>G	c.(625-627)Att>Gtt	p.I209V		NM_003696.2	NP_003687.2	O95222	OR6A2_HUMAN	olfactory receptor, family 6, subfamily A, member 2	209					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(4)|pancreas(1)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)	29		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		AGAATAAAAATGGCCAGGATG	0.493																																					p.I209V		Atlas-SNP	.											.	OR6A2	68	.	0			c.A625G						.						106	113	110					11																	6816315		2201	4296	6497	SO:0001583	missense	8590	exon1			TAAAAATGGCCAG	AB065822	CCDS7772.1	11p15.4	2012-08-09		2004-03-10	ENSG00000184933	ENSG00000184933		"GPCR / Class A : Olfactory receptors"	15301	protein-coding gene	gene with protein product		608495		OR6A2P, OR6A1			Standard	NM_003696		Approved	OR11-55	uc001mes.1	O95222	OTTHUMG00000165736	ENST00000332601.3:c.625A>G	chr11.hg19:g.6816315T>C	ENSP00000330384:p.Ile209Val	45.0	0.0		24.0	21.0	NM_003696	Q3MJC7|Q6IF35|Q9H206	Missense_Mutation	SNP	ENST00000332601.3	hg19	CCDS7772.1	.	.	.	.	.	.	.	.	.	.	T	9.197	1.027587	0.19512	.	.	ENSG00000184933	ENST00000332601	T	0.36340	1.26	5.07	2.74	0.32292	GPCR, rhodopsin-like superfamily (1);	0.331825	0.22019	N	0.065757	T	0.22003	0.0530	N	0.17838	0.53	0.19775	N	0.99995	P	0.38129	0.619	P	0.44623	0.455	T	0.13764	-1.0497	10	0.09590	T	0.72	.	3.5549	0.07861	0.1633:0.1773:0.0:0.6594	.	209	O95222	OR6A2_HUMAN	V	209	ENSP00000330384:I209V	ENSP00000330384:I209V	I	-	1	0	OR6A2	6772891	0.000000	0.05858	0.947000	0.38551	0.129000	0.20672	-0.045000	0.12003	0.496000	0.27904	0.533000	0.62120	ATT	.	.		0.493	OR6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385981.1	NM_003696		C	6816315	T	C	6816315	3	2	344	1	0	0	0	0	1	0	0	0	11195	1464	51	2	362	2	OR6A2	11	6816315	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	162919	6816315	128190201	801	48164										
TUB	7275	hgsc.bcm.edu	37	chr11	8111646	8111646	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tggagcagaagcagaagaagAagcgccaggagcccctgatg	15	9	0	5	rs533066502	byFrequency	TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:8111646A>T	ENST00000299506.2	+	3	270	c.121A>T	c.(121-123)Aag>Tag	p.K41*	TUB_ENST00000534099.1_Nonsense_Mutation_p.K47*|TUB_ENST00000305253.4_Nonsense_Mutation_p.K96*	NM_177972.2	NP_813977.1	P50607	TUB_HUMAN	tubby bipartite transcription factor	41					multicellular organismal macromolecule metabolic process (GO:0044259)|phagocytosis (GO:0006909)|phototransduction (GO:0007602)|positive regulation of phagocytosis (GO:0050766)|response to hormone (GO:0009725)|retina development in camera-type eye (GO:0060041)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled photoreceptor activity (GO:0008020)|protein complex binding (GO:0032403)			breast(1)|cervix(1)|endometrium(9)|large_intestine(7)|lung(5)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	26		all_lung(207;6.91e-20)|Lung NSC(207;3.36e-17)		Epithelial(150;1.69e-62)|BRCA - Breast invasive adenocarcinoma(625;8.54e-06)|LUSC - Lung squamous cell carcinoma(625;0.000184)		GCAGAAGAAGAAGCGCCAGGA	0.677																																					p.K96X		Atlas-SNP	.											.	TUB	71	.	0			c.A286T						.																																			SO:0001587	stop_gained	7275	exon4			AAGAAGAAGCGCC	U54644	CCDS7786.1, CCDS7787.1	11p15.5	2013-08-06	2013-08-06		ENSG00000166402	ENSG00000166402			12406	protein-coding gene	gene with protein product		601197	"tubby (mouse) homolog", "tubby homolog (mouse)"			8612280	Standard	NM_003320		Approved	rd5	uc001mfy.3	P50607	OTTHUMG00000165690	ENST00000299506.2:c.121A>T	chr11.hg19:g.8111646A>T	ENSP00000299506:p.Lys41*	175.0	0.0		82.0	28.0	NM_003320	D3DQU4|O00293|Q6B007	Nonsense_Mutation	SNP	ENST00000299506.2	hg19	CCDS7787.1	.	.	.	.	.	.	.	.	.	.	A	37	6.491885	0.97612	.	.	ENSG00000166402	ENST00000534099;ENST00000305253;ENST00000299506	.	.	.	5.23	5.23	0.72850	.	0.149903	0.64402	D	0.000016	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-20.0894	14.0883	0.64973	1.0:0.0:0.0:0.0	.	.	.	.	X	47;96;41	.	ENSP00000299506:K41X	K	+	1	0	TUB	8068222	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.672000	0.91181	1.961000	0.56991	0.533000	0.62120	AAG	.	.		0.677	TUB-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385823.1	NM_003320		T	8111646	A	T	8111646	4	4	344	1	0	0	0	0	0	1	0	0	16757	247	9	4	342	4	TUB	11	8111646	Nonsense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1295331	8111646	126894870	802	48165										
IPO7	10527	hgsc.bcm.edu	37	chr11	9446500	9446500	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttctcctaccactgctgcccAgacacttttgtttacagcct	5	15	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:9446500A>T	ENST00000379719.3	+	11	1323	c.1181A>T	c.(1180-1182)cAg>cTg	p.Q394L		NM_006391.2	NP_006382.1	O95373	IPO7_HUMAN	importin 7	394					innate immune response (GO:0045087)|protein import into nucleus (GO:0006606)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	Ran GTPase binding (GO:0008536)|small GTPase regulator activity (GO:0005083)|transporter activity (GO:0005215)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(12)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				all cancers(16;8.29e-09)|Epithelial(150;4.76e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0217)		ACTGCTGCCCAGACACTTTTG	0.289																																					p.Q394L		Atlas-SNP	.											.	IPO7	72	.	0			c.A1181T						.						80	81	80					11																	9446500		2201	4293	6494	SO:0001583	missense	10527	exon11			CTGCCCAGACACT	AF098799	CCDS31425.1	11p15.3	2010-12-02	2003-03-11	2003-03-14	ENSG00000205339	ENSG00000205339		"Importins"	9852	protein-coding gene	gene with protein product		605586	"RAN binding protein 7"	RANBP7		9214382	Standard	NM_006391		Approved	Imp7	uc001mho.3	O95373	OTTHUMG00000165753	ENST00000379719.3:c.1181A>T	chr11.hg19:g.9446500A>T	ENSP00000369042:p.Gln394Leu	119.0	0.0		57.0	49.0	NM_006391	A6NNM5|B2R786|Q1RMF7|Q9H177|Q9NTE3	Missense_Mutation	SNP	ENST00000379719.3	hg19	CCDS31425.1	.	.	.	.	.	.	.	.	.	.	A	27.2	4.810729	0.90707	.	.	ENSG00000205339	ENST00000379719	T	0.64085	-0.08	5.19	5.19	0.71726	Armadillo-like helical (1);Armadillo-type fold (1);Exportin/Importin, Cse1-like (1);	0.000000	0.85682	D	0.000000	T	0.76471	0.3992	M	0.72576	2.205	0.80722	D	1	D	0.65815	0.995	D	0.72982	0.979	T	0.74870	-0.3517	10	0.28530	T	0.3	.	15.0432	0.71807	1.0:0.0:0.0:0.0	.	394	O95373	IPO7_HUMAN	L	394	ENSP00000369042:Q394L	ENSP00000369042:Q394L	Q	+	2	0	IPO7	9403076	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.335000	0.96500	1.927000	0.55829	0.533000	0.62120	CAG	.	.		0.289	IPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386022.1	NM_006391		T	9446500	A	T	9446500	3	4	344	1	0	0	0	0	1	0	0	0	7806	188	7	4	1223	4	IPO7	11	9446500	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1334854	9446500	125560016	803	48166										
PLEKHA7	144100	hgsc.bcm.edu	37	chr11	16816089	16816089	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggggatgtcactttcctcagCtggggtgggtgaggtcggta	18	7	2	1	rs150403598		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:16816089C>A	ENST00000355661.3	-	19	2701	c.2691G>T	c.(2689-2691)caG>caT	p.Q897H	PLEKHA7_ENST00000531066.1_Missense_Mutation_p.Q897H|PLEKHA7_ENST00000532079.1_Intron|PLEKHA7_ENST00000448080.2_Missense_Mutation_p.Q897H|PLEKHA7_ENST00000332954.4_5'Flank			Q6IQ23	PKHA7_HUMAN	pleckstrin homology domain containing, family A member 7	897	Pro-rich.				epithelial cell-cell adhesion (GO:0090136)|zonula adherens maintenance (GO:0045218)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|zonula adherens (GO:0005915)	delta-catenin binding (GO:0070097)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(1)|prostate(2)|skin(7)|urinary_tract(1)	37						CTTTCCTCAGCTGGGGTGGGT	0.567																																					p.Q897H		Atlas-SNP	.											.	PLEKHA7	120	.	0			c.G2691T						.						67	72	70					11																	16816089		2200	4294	6494	SO:0001583	missense	144100	exon19			CCTCAGCTGGGGT	BC033239	CCDS31434.1	11p15	2013-01-10			ENSG00000166689	ENSG00000166689		"Pleckstrin homology (PH) domain containing"	27049	protein-coding gene	gene with protein product		612686				12477932	Standard	NM_175058		Approved	DKFZp686M22243	uc001mmo.3	Q6IQ23	OTTHUMG00000165954	ENST00000355661.3:c.2691G>T	chr11.hg19:g.16816089C>A	ENSP00000347883:p.Gln897His	67.0	0.0		31.0	21.0	NM_175058	B4DK33|B4DWC3|Q86VZ7	Missense_Mutation	SNP	ENST00000355661.3	hg19	CCDS31434.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.88|18.88	3.717659|3.717659	0.68844|0.68844	.|.	.|.	ENSG00000166689|ENSG00000166689	ENST00000531066;ENST00000355661;ENST00000448080|ENST00000530489	T;T;T|.	0.19938|.	2.11;2.11;2.11|.	5.6|5.6	3.74|3.74	0.42951|0.42951	.|.	0.269557|.	0.38058|.	N|.	0.001830|.	T|T	0.51295|0.51295	0.1666|0.1666	L|L	0.44542|0.44542	1.39|1.39	0.34900|0.34900	D|D	0.746377|0.746377	D;P;D;D|.	0.71674|.	0.998;0.883;0.996;0.995|.	D;B;P;D|.	0.80764|.	0.994;0.438;0.862;0.912|.	T|T	0.58896|0.58896	-0.7555|-0.7555	10|5	0.56958|.	D|.	0.05|.	-21.3963|-21.3963	10.7656|10.7656	0.46292|0.46292	0.0:0.7939:0.0:0.2061|0.0:0.7939:0.0:0.2061	.|.	471;897;897;897|.	Q6IQ23-3;E9PKC0;Q6IQ23;Q6IQ23-2|.	.;.;PKHA7_HUMAN;.|.	H|I	897|528	ENSP00000435389:Q897H;ENSP00000347883:Q897H;ENSP00000416895:Q897H|.	ENSP00000347883:Q897H|.	Q|S	-|-	3|2	2|0	PLEKHA7|PLEKHA7	16772665|16772665	0.999000|0.999000	0.42202|0.42202	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	0.500000|0.500000	0.22562|0.22562	0.845000|0.845000	0.35118|0.35118	0.655000|0.655000	0.94253|0.94253	CAG|AGC	.	C|1.000;G|0.000		0.567	PLEKHA7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000387242.2	NM_175058		A	16816089	C	A	16816089	3	1	344	1	0	0	0	0	1	0	0	0	12070	796	28	3	694	3	PLEKHA7	11	16816089	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	7369589	16816089	118190427	804	48167										
IGSF22	283284	hgsc.bcm.edu	37	chr11	18743196	18743196	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttggcgttcccctgcacccgGgctcggaacacggctttgtc	12	15	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:18743196G>A	ENST00000513874.1	-	4	403	c.264C>T	c.(262-264)gcC>gcT	p.A88A	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	88	Ig-like 1.									NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						CCTGCACCCGGGCTCGGAACA	0.607											OREG0020822	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A88A		Atlas-SNP	.											.	IGSF22	211	.	0			c.C264T						.						94	94	94					11																	18743196		1992	4158	6150	SO:0001819	synonymous_variant	283284	exon4			CACCCGGGCTCGG	AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	26750	protein-coding gene	gene with protein product							Standard	NM_173588		Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.264C>T	chr11.hg19:g.18743196G>A		77.0	0.0	90	26.0	22.0	NM_173588	A6NNA0|D6RGV7	Silent	SNP	ENST00000513874.1	hg19	CCDS41625.2																																																																																			.	.		0.607	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588		A	18743196	G	A	18743196	2	1	344	1	0	0	0	0	0	0	0	1	7609	1219	43	3		3	IGSF22	11	18743196	Silent	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1927107	18743196	116263320	805	48168										
PTPN5	84867	hgsc.bcm.edu	37	chr11	18755139	18755139	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttgatgtaggaactcagaggGtcgtcagggtctggtgaggt	17	5	3	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:18755139G>T	ENST00000358540.2	-	10	1474	c.1044C>A	c.(1042-1044)gaC>gaA	p.D348E	PTPN5_ENST00000396167.2_Missense_Mutation_p.D316E|RP11-1081L13.4_ENST00000527285.1_RNA|PTPN5_ENST00000396166.3_5'Flank|PTPN5_ENST00000396170.1_Missense_Mutation_p.D316E|PTPN5_ENST00000396168.1_Missense_Mutation_p.D324E|PTPN5_ENST00000396171.4_Missense_Mutation_p.D348E|PTPN5_ENST00000477854.1_Missense_Mutation_p.D152E	NM_006906.1	NP_008837.1	P54829	PTN5_HUMAN	protein tyrosine phosphatase, non-receptor type 5 (striatum-enriched)	348	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	phosphotyrosine binding (GO:0001784)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(13)|ovary(2)|prostate(1)|skin(4)	27						AACTCAGAGGGTCGTCAGGGT	0.587																																					p.D348E		Atlas-SNP	.											.	PTPN5	163	.	0			c.C1044A						.						187	173	178					11																	18755139		2199	4293	6492	SO:0001583	missense	84867	exon10			CAGAGGGTCGTCA	BC064807	CCDS7845.1, CCDS41626.1, CCDS60746.1	11p15.1	2011-06-09			ENSG00000110786	ENSG00000110786		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9657	protein-coding gene	gene with protein product		176879				1714595	Standard	NM_001278236		Approved	STEP, PTPSTEP	uc001mpc.4	P54829	OTTHUMG00000134304	ENST00000358540.2:c.1044C>A	chr11.hg19:g.18755139G>T	ENSP00000351342:p.Asp348Glu	99.0	0.0		48.0	41.0	NM_032781	B3KXG7|B7Z386|B7ZAF5|D3DQY7|Q6P1Z2|Q8N2A1|Q8NDP8	Missense_Mutation	SNP	ENST00000358540.2	hg19	CCDS7845.1	.	.	.	.	.	.	.	.	.	.	G	17.35	3.368565	0.61624	.	.	ENSG00000110786	ENST00000477854;ENST00000358540;ENST00000396170;ENST00000396171;ENST00000396167;ENST00000396168	D;D;D;D;D;D	0.85629	-2.01;-2.01;-2.01;-2.01;-2.01;-2.01	5.67	-0.66	0.11421	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.058630	0.64402	D	0.000003	T	0.72827	0.3509	N	0.11255	0.115	0.52501	D	0.999951	B;P	0.48407	0.005;0.91	B;P	0.47864	0.026;0.559	T	0.66830	-0.5824	10	0.28530	T	0.3	.	10.8691	0.46872	0.5578:0.0:0.4422:0.0	.	348;316	P54829;B3KXG7	PTN5_HUMAN;.	E	152;348;316;348;316;324	ENSP00000435056:D152E;ENSP00000351342:D348E;ENSP00000379473:D316E;ENSP00000379474:D348E;ENSP00000379470:D316E;ENSP00000379471:D324E	ENSP00000351342:D348E	D	-	3	2	PTPN5	18711715	1.000000	0.71417	0.817000	0.32601	0.965000	0.64279	0.717000	0.25851	-0.145000	0.11294	-0.136000	0.14681	GAC	.	.		0.587	PTPN5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259196.2	NM_001039970		T	18755139	G	T	18755139	3	4	344	1	0	0	0	0	1	0	0	0	12806	1252	44	3	677	3	PTPN5	11	18755139	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	11943	18755139	116251377	806	48169										
C11orf41	25758	hgsc.bcm.edu	37	chr11	33564933	33564933	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttcagcaccggtagtgtctcAtctcccatcattacagcacc	6	15	4	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:33564933A>G	ENST00000321505.4	+	1	1113	c.933A>G	c.(931-933)tcA>tcG	p.S311S	KIAA1549L_ENST00000389726.3_Silent_p.S311S|KIAA1549L_ENST00000265654.5_Silent_p.S311S			Q6ZVL6	K154L_HUMAN	KIAA1549-like	311						integral component of membrane (GO:0016021)											GTAGTGTCTCATCTCCCATCA	0.478											OREG0020868	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S311S		Atlas-SNP	.											.	.	.	.	0			c.A933G						.						196	196	196					11																	33564933		1998	4178	6176	SO:0001819	synonymous_variant	25758	exon1			TGTCTCATCTCCC	U10991	CCDS44565.1, CCDS44565.2	11p13	2012-08-09	2012-08-09	2012-08-09	ENSG00000110427	ENSG00000110427			24836	protein-coding gene	gene with protein product		612297	"chromosome 11 open reading frame 69", "chromosome 11 open reading frame 41"	C11orf69, C11orf41			Standard	NM_012194		Approved	G2, MGC34830	uc021qfs.1	Q6ZVL6	OTTHUMG00000150410	ENST00000321505.4:c.933A>G	chr11.hg19:g.33564933A>G		185.0	0.0	841	175.0	70.0	NM_012194	B0QYU0	Silent	SNP	ENST00000321505.4	hg19	CCDS44565.2																																																																																			.	.		0.478	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194		G	33564933	A	G	33564933	2	3	344	1	0	0	0	0	0	0	0	1	1642	204	8	2		2	C11orf41	11	33564933	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	14809794	33564933	101441583	807	48170										
LDLRAD3	143458	hgsc.bcm.edu	37	chr11	36057758	36057758	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gggcgcctggcagtgtgacgGgctgcctgactgcttcgaca	16	12	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:36057758G>T	ENST00000315571.5	+	2	173	c.152G>T	c.(151-153)gGg>gTg	p.G51V	LDLRAD3_ENST00000528989.1_Intron|LDLRAD3_ENST00000524419.1_Intron	NM_174902.2	NP_777562.1	Q86YD5	LRAD3_HUMAN	low density lipoprotein receptor class A domain containing 3	51	LDL-receptor class A 1. {ECO:0000255|PROSITE-ProRule:PRU00124}.				receptor-mediated endocytosis (GO:0006898)|regulation of protein processing (GO:0070613)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(14)|prostate(7)|skin(1)	28	all_lung(20;0.089)|Lung NSC(22;0.175)|all_epithelial(35;0.177)	all_hematologic(20;0.124)				CAGTGTGACGGGCTGCCTGAC	0.622																																					p.G51V		Atlas-SNP	.											.	LDLRAD3	52	.	0			c.G152T						.						100	94	96					11																	36057758		2202	4298	6500	SO:0001583	missense	143458	exon2			GTGACGGGCTGCC	AK075546	CCDS31462.1	11p13	2014-06-05			ENSG00000179241	ENSG00000179241			27046	protein-coding gene	gene with protein product						21795536	Standard	NM_174902		Approved	LRAD3	uc001mwk.1	Q86YD5	OTTHUMG00000166313	ENST00000315571.5:c.152G>T	chr11.hg19:g.36057758G>T	ENSP00000318607:p.Gly51Val	54.0	0.0		44.0	21.0	NM_174902	B7Z1U3|B9EG81|Q8NBJ0	Missense_Mutation	SNP	ENST00000315571.5	hg19	CCDS31462.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.721872	0.89298	.	.	ENSG00000179241	ENST00000545142;ENST00000315571	D	0.96913	-4.17	5.43	5.43	0.79202	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.98191	0.9402	M	0.84082	2.675	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98931	1.0787	10	0.66056	D	0.02	.	18.2104	0.89868	0.0:0.0:1.0:0.0	.	51	Q86YD5	LRAD3_HUMAN	V	51	ENSP00000318607:G51V	ENSP00000318607:G51V	G	+	2	0	LDLRAD3	36014334	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.288000	0.78691	2.537000	0.85549	0.655000	0.94253	GGG	.	.		0.622	LDLRAD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389085.1	NM_174902		T	36057758	G	T	36057758	3	4	344	1	0	0	0	0	1	0	0	0	8716	1232	43	3	158	3	LDLRAD3	11	36057758	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	2492825	36057758	98948758	808	48171										
RAG1	5896	hgsc.bcm.edu	37	chr11	36596843	36596843	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccattgtgccttatgctggcAgatgagtctgaccacgagac	11	11	1	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:36596843A>C	ENST00000299440.5	+	2	2101	c.1989A>C	c.(1987-1989)gcA>gcC	p.A663A		NM_000448.2	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	663					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|DNA recombination (GO:0006310)|histone monoubiquitination (GO:0010390)|immune response (GO:0006955)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|pre-B cell allelic exclusion (GO:0002331)|protein autoubiquitination (GO:0051865)|regulation of T cell differentiation (GO:0045580)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	65	all_lung(20;0.226)	all_hematologic(20;0.107)				TTATGCTGGCAGATGAGTCTG	0.478									Familial Hemophagocytic Lymphohistiocytosis																												p.A663A	Pancreas(43;321 1249 3212 48200)|Esophageal Squamous(38;49 1003 17530 24363)	Atlas-SNP	.											.	RAG1	151	.	0			c.A1989C						.						71	64	66					11																	36596843		2202	4298	6500	SO:0001819	synonymous_variant	5896	exon2	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	GCTGGCAGATGAG	M29474	CCDS7902.1	11p13	2014-09-17				ENSG00000166349		"RING-type (C3HC4) zinc fingers"	9831	protein-coding gene	gene with protein product	"recombination activating protein 1", "RING finger protein 74", "V(D)J recombination-activating protein 1"	179615				1612612, 1283330	Standard	NM_000448		Approved	RNF74, MGC43321	uc001mwu.4	P15918		ENST00000299440.5:c.1989A>C	chr11.hg19:g.36596843A>C		96.0	0.0		92.0	38.0	NM_000448	E9PPC4|Q8IY72|Q8NER2	Silent	SNP	ENST00000299440.5	hg19	CCDS7902.1																																																																																			.	.		0.478	RAG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389535.1	NM_000448		C	36596843	A	C	36596843	2	2	344	1	0	0	0	0	0	0	0	1	13018	175	7	5		5	RAG1	11	36596843	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	539085	36596843	98409673	809	48172										
RAG2	5897	hgsc.bcm.edu	37	chr11	36614915	36614915	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccaacaataacaaattcatcAttgttagtttgagtcaggat	6	7	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:36614915A>G	ENST00000311485.3	-	2	965	c.804T>C	c.(802-804)aaT>aaC	p.N268N	RAG2_ENST00000528428.1_5'Flank|C11orf74_ENST00000446510.2_5'Flank|C11orf74_ENST00000334307.5_5'Flank|C11orf74_ENST00000534635.1_5'Flank|C11orf74_ENST00000347206.4_5'Flank	NM_000536.3|NM_001243785.1|NM_001243786.1	NP_000527.2|NP_001230714.1|NP_001230715.1	P55895	RAG2_HUMAN	recombination activating gene 2	268					B cell differentiation (GO:0030183)|chromatin modification (GO:0016568)|pre-B cell allelic exclusion (GO:0002331)|T cell differentiation in thymus (GO:0033077)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|pancreas(2)|prostate(1)|skin(4)	32	all_lung(20;0.226)	all_hematologic(20;0.00756)				CAAATTCATCATTGTTAGTTT	0.413									Familial Hemophagocytic Lymphohistiocytosis																												p.N268N		Atlas-SNP	.											.	RAG2	92	.	0			c.T804C						.						75	77	76					11																	36614915		2202	4298	6500	SO:0001819	synonymous_variant	5897	exon3	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	TTCATCATTGTTA	AF080577	CCDS7903.1	11p13	2014-09-17				ENSG00000175097			9832	protein-coding gene	gene with protein product		179616				1283330	Standard	NM_000536		Approved		uc001mwv.4	P55895		ENST00000311485.3:c.804T>C	chr11.hg19:g.36614915A>G		48.0	0.0		48.0	18.0	NM_001243785	A8K9E9|Q8TBL4	Silent	SNP	ENST00000311485.3	hg19	CCDS7903.1																																																																																			.	.		0.413	RAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389536.1	NM_000536		G	36614915	A	G	36614915	2	3	344	1	0	0	0	0	0	0	0	1	13020	214	8	2		2	RAG2	11	36614915	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	18072	36614915	98391601	810	48173										
ALX4	60529	hgsc.bcm.edu	37	chr11	44297157	44297157	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggtagctgctgtccatccccAcagtgtcagagtcagggggt	14	11	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:44297157A>T	ENST00000329255.3	-	2	621	c.518T>A	c.(517-519)gTg>gAg	p.V173E		NM_021926.3	NP_068745.2	Q9H161	ALX4_HUMAN	ALX homeobox 4	173					anterior/posterior pattern specification (GO:0009952)|digestive tract development (GO:0048565)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal system morphogenesis (GO:0048704)|hair follicle development (GO:0001942)|muscle organ development (GO:0007517)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of apoptotic process (GO:0042981)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	16						GTCCATCCCCACAGTGTCAGA	0.587																																					p.V173E		Atlas-SNP	.											.	ALX4	58	.	0			c.T518A						.						51	56	54					11																	44297157		2203	4299	6502	SO:0001583	missense	60529	exon2			ATCCCCACAGTGT	AF294629	CCDS31468.1	11p11.2	2011-06-20	2008-11-04		ENSG00000052850	ENSG00000052850		"Homeoboxes / PRD class"	450	protein-coding gene	gene with protein product		605420	"parietal foramina 2", "aristaless-like homeobox 4"	PFM2		11017806, 8644736	Standard	NM_021926		Approved	FPP, PFM, KIAA1788	uc001myb.3	Q9H161	OTTHUMG00000166557	ENST00000329255.3:c.518T>A	chr11.hg19:g.44297157A>T	ENSP00000332744:p.Val173Glu	45.0	0.0		52.0	26.0	NM_021926	Q96JN7|Q9H198|Q9HAY9	Missense_Mutation	SNP	ENST00000329255.3	hg19	CCDS31468.1	.	.	.	.	.	.	.	.	.	.	A	10.08	1.251265	0.22880	.	.	ENSG00000052850	ENST00000329255	D	0.90676	-2.71	3.73	3.73	0.42828	.	0.622614	0.16072	N	0.230931	T	0.81697	0.4877	L	0.50333	1.59	0.30756	N	0.744571	B	0.23806	0.091	B	0.19148	0.024	T	0.68584	-0.5370	10	0.02654	T	1	.	2.1269	0.03741	0.5847:0.0:0.1671:0.2482	.	173	Q9H161	ALX4_HUMAN	E	173	ENSP00000332744:V173E	ENSP00000332744:V173E	V	-	2	0	ALX4	44253733	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	5.758000	0.68776	1.554000	0.49487	0.374000	0.22700	GTG	.	.		0.587	ALX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390399.1			T	44297157	A	T	44297157	3	4	344	1	0	0	0	0	1	0	0	0	558	159	6	4	729	4	ALX4	11	44297157	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	7682242	44297157	90709359	811	48174										
CREB3L1	90993	hgsc.bcm.edu	37	chr11	46334468	46334468	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gagaccctggagaatgccaaCaggtgggtagtgcctcctgc	14	11	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:46334468C>A	ENST00000529193.1	+	8	1480	c.1029C>A	c.(1027-1029)aaC>aaA	p.N343K	CREB3L1_ENST00000288400.3_Missense_Mutation_p.N343K			Q96BA8	CR3L1_HUMAN	cAMP responsive element binding protein 3-like 1	343	Leucine-zipper. {ECO:0000255|PROSITE- ProRule:PRU00978}.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				regulation of bone mineralization (GO:0030500)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)	p.N343N(1)	FUS/CREB3L1(6)	NS(2)|breast(1)|large_intestine(4)|lung(2)|ovary(3)	12				GBM - Glioblastoma multiforme(35;0.0285)		AGAATGCCAACAGGTGGGTAG	0.592			T	FUS	myxofibrosarcoma																																p.N343K	Pancreas(3;159 194 19597 26278 47995)	Atlas-SNP	.		Dom	yes		11	11p11.2	90993	cAMP responsive element binding protein 3-like 1		M	CREB3L1,NS,carcinoma,0,1	CREB3L1	30	.	1	Substitution - coding silent(1)	ovary(1)	c.C1029A						.						41	45	44					11																	46334468		2038	4189	6227	SO:0001583	missense	90993	exon8			TGCCAACAGGTGG		CCDS53620.1	11q11	2013-01-10				ENSG00000157613		"basic leucine zipper proteins"	18856	protein-coding gene	gene with protein product	"BBF-2 homolog (drosophila)"						Standard	NM_052854		Approved	OASIS	uc021qil.1	Q96BA8		ENST00000529193.1:c.1029C>A	chr11.hg19:g.46334468C>A	ENSP00000434939:p.Asn343Lys	39.0	0.0		38.0	14.0	NM_052854	Q8N2D5|Q96CP0	Missense_Mutation	SNP	ENST00000529193.1	hg19	CCDS53620.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.496306	0.85069	.	.	ENSG00000157613	ENST00000529193;ENST00000288400;ENST00000446415;ENST00000530518	T;T;D	0.90133	0.55;0.55;-2.62	5.2	5.2	0.72013	Basic-leucine zipper (bZIP) transcription factor (2);bZIP transcription factor, bZIP-1 (1);	0.000000	0.85682	D	0.000000	D	0.95127	0.8421	M	0.84156	2.68	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95343	0.8440	10	0.66056	D	0.02	-1.899	13.0829	0.59123	0.0:0.9227:0.0:0.0773	.	343	Q96BA8	CR3L1_HUMAN	K	343;343;255;103	ENSP00000434939:N343K;ENSP00000288400:N343K;ENSP00000436574:N103K	ENSP00000288400:N343K	N	+	3	2	CREB3L1	46291044	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	4.684000	0.61686	2.431000	0.82371	0.561000	0.74099	AAC	.	.		0.592	CREB3L1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389702.1	NM_052854		A	46334468	C	A	46334468	3	1	344	1	0	0	0	0	1	0	0	0	3858	477	17	3	1059	3	CREB3L1	11	46334468	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	2037311	46334468	88672048	812	48175										
OR4A15	81328	hgsc.bcm.edu	37	chr11	55135489	55135489	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgactgaatttatcctcttaGggctcacacagaaccctgag	8	11	2	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:55135489G>A	ENST00000314706.3	+	1	130	c.130G>A	c.(130-132)Ggg>Agg	p.G44R		NM_001005275.1	NP_001005275.1	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A, member 15	44						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(48)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	71						TATCCTCTTAGGGCTCACACA	0.413																																					p.G44R		Atlas-SNP	.											OR4A15,NS,carcinoma,0,1	OR4A15	161	.	0			c.G130A						.						68	64	65					11																	55135489		2201	4296	6497	SO:0001583	missense	81328	exon1			CTCTTAGGGCTCA	AB065776	CCDS31500.1	11q11	2012-08-09			ENSG00000181958	ENSG00000181958		"GPCR / Class A : Olfactory receptors"	15152	protein-coding gene	gene with protein product							Standard	NM_001005275		Approved		uc010rif.2	Q8NGL6	OTTHUMG00000166711	ENST00000314706.3:c.130G>A	chr11.hg19:g.55135489G>A	ENSP00000325065:p.Gly44Arg	71.0	0.0		68.0	31.0	NM_001005275	Q6IFL4|Q96R65	Missense_Mutation	SNP	ENST00000314706.3	hg19	CCDS31500.1	.	.	.	.	.	.	.	.	.	.	g	14.78	2.636672	0.47049	.	.	ENSG00000181958	ENST00000314706	T	0.00659	5.94	3.48	3.48	0.39840	.	0.474475	0.17560	N	0.169854	T	0.06050	0.0157	H	0.95004	3.61	0.09310	N	1	D	0.76494	0.999	D	0.71184	0.972	T	0.04885	-1.0920	10	0.87932	D	0	.	10.3795	0.44104	0.0:0.0:1.0:0.0	.	44	Q8NGL6	O4A15_HUMAN	R	44	ENSP00000325065:G44R	ENSP00000325065:G44R	G	+	1	0	OR4A15	54892065	1.000000	0.71417	0.199000	0.23439	0.015000	0.08874	5.301000	0.65727	1.785000	0.52413	0.492000	0.49549	GGG	.	.		0.413	OR4A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391161.1	NM_001005275		A	55135489	G	A	55135489	3	1	344	1	0	0	0	0	1	0	0	0	11049	1000	35	3	132	3	OR4A15	11	55135489	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	8801021	55135489	79871027	813	48176										
OR4A15	81328	hgsc.bcm.edu	37	chr11	55135678	55135678	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tctattctactgcatttgctCccaaaatgattgttgacttg	6	9	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:55135678C>A	ENST00000314706.3	+	1	319	c.319C>A	c.(319-321)Ccc>Acc	p.P107T		NM_001005275.1	NP_001005275.1	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A, member 15	107						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(48)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	71						TGCATTTGCTCCCAAAATGAT	0.418																																					p.P107T		Atlas-SNP	.											.	OR4A15	161	.	0			c.C319A						.						142	140	141					11																	55135678		2201	4296	6497	SO:0001583	missense	81328	exon1			TTTGCTCCCAAAA	AB065776	CCDS31500.1	11q11	2012-08-09			ENSG00000181958	ENSG00000181958		"GPCR / Class A : Olfactory receptors"	15152	protein-coding gene	gene with protein product							Standard	NM_001005275		Approved		uc010rif.2	Q8NGL6	OTTHUMG00000166711	ENST00000314706.3:c.319C>A	chr11.hg19:g.55135678C>A	ENSP00000325065:p.Pro107Thr	43.0	0.0		35.0	16.0	NM_001005275	Q6IFL4|Q96R65	Missense_Mutation	SNP	ENST00000314706.3	hg19	CCDS31500.1	.	.	.	.	.	.	.	.	.	.	c	17.17	3.320523	0.60634	.	.	ENSG00000181958	ENST00000314706	T	0.01854	4.6	3.48	3.48	0.39840	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49916	D	0.000134	T	0.21962	0.0529	H	0.98802	4.335	0.27364	N	0.955899	D	0.76494	0.999	D	0.68621	0.959	T	0.42632	-0.9440	10	0.87932	D	0	.	12.5491	0.56216	0.0:1.0:0.0:0.0	.	107	Q8NGL6	O4A15_HUMAN	T	107	ENSP00000325065:P107T	ENSP00000325065:P107T	P	+	1	0	OR4A15	54892254	0.989000	0.36119	0.006000	0.13384	0.183000	0.23260	3.771000	0.55318	1.785000	0.52413	0.492000	0.49549	CCC	.	.		0.418	OR4A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391161.1	NM_001005275		A	55135678	C	A	55135678	3	1	344	1	0	0	0	0	1	0	0	0	11049	855	30	3	321	3	OR4A15	11	55135678	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	189	55135678	79870838	814	48177										
OR4C6	219432	hgsc.bcm.edu	37	chr11	55433038	55433038	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aagcccctgcactacacgatCatcatgagtccacgggtgtg	10	13	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:55433038C>T	ENST00000314259.3	+	1	425	c.396C>T	c.(394-396)atC>atT	p.I132I		NM_001004704.1	NP_001004704.1	Q8NH72	OR4C6_HUMAN	olfactory receptor, family 4, subfamily C, member 6	132						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|lung(49)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	71						ACTACACGATCATCATGAGTC	0.512																																					p.I132I		Atlas-SNP	.											.	OR4C6	114	.	0			c.C396T						.						105	98	100					11																	55433038		2200	4296	6496	SO:0001819	synonymous_variant	219432	exon1			CACGATCATCATG	CR593785	CCDS31506.1	11q11	2012-08-09			ENSG00000181903	ENSG00000181903		"GPCR / Class A : Olfactory receptors"	14743	protein-coding gene	gene with protein product							Standard	NM_001004704		Approved		uc010rik.2	Q8NH72	OTTHUMG00000166800	ENST00000314259.3:c.396C>T	chr11.hg19:g.55433038C>T		65.0	0.0		70.0	31.0	NM_001004704	B2RP11|Q6IFD2	Silent	SNP	ENST00000314259.3	hg19	CCDS31506.1																																																																																			.	.		0.512	OR4C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391504.1	NM_001004704		T	55433038	C	T	55433038	2	4	344	1	0	0	0	0	0	0	0	1	11061	816	29	3		3	OR4C6	11	55433038	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	297360	55433038	79573478	815	48178										
OR8J3	81168	hgsc.bcm.edu	37	chr11	55905003	55905003	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agattgatgatagctagatgTctcaggaaaaagtacatggg	12	4	1	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:55905003T>A	ENST00000301529.1	-	1	191	c.192A>T	c.(190-192)agA>agT	p.R64S		NM_001004064.1	NP_001004064.1	Q8NGG0	OR8J3_HUMAN	olfactory receptor, family 8, subfamily J, member 3	64						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(1)|lung(38)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	59	Esophageal squamous(21;0.00693)					TAGCTAGATGTCTCAGGAAAA	0.433																																					p.R64S		Atlas-SNP	.											.	OR8J3	112	.	0			c.A192T						.						143	139	140					11																	55905003		2201	4296	6497	SO:0001583	missense	81168	exon1			TAGATGTCTCAGG		CCDS31520.1	11q12.2	2012-08-09			ENSG00000167822	ENSG00000167822		"GPCR / Class A : Olfactory receptors"	15312	protein-coding gene	gene with protein product							Standard	NM_001004064		Approved		uc010riz.2	Q8NGG0	OTTHUMG00000166834	ENST00000301529.1:c.192A>T	chr11.hg19:g.55905003T>A	ENSP00000301529:p.Arg64Ser	110.0	0.0		79.0	30.0	NM_001004064	Q6IFB6|Q96RC2	Missense_Mutation	SNP	ENST00000301529.1	hg19	CCDS31520.1	.	.	.	.	.	.	.	.	.	.	T	2.806	-0.248077	0.05867	.	.	ENSG00000167822	ENST00000301529	T	0.01051	5.4	3.26	-6.53	0.01866	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000072	T	0.00608	0.0020	N	0.12887	0.27	0.09310	N	1	B	0.27117	0.168	B	0.38842	0.283	T	0.45175	-0.9279	10	0.02654	T	1	.	2.4217	0.04449	0.1025:0.2904:0.3208:0.2863	.	64	Q8NGG0	OR8J3_HUMAN	S	64	ENSP00000301529:R64S	ENSP00000301529:R64S	R	-	3	2	OR8J3	55661579	0.000000	0.05858	0.000000	0.03702	0.096000	0.18686	-1.356000	0.02609	-0.934000	0.03733	0.240000	0.17902	AGA	.	.		0.433	OR8J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391542.1	NM_001004064		A	55905003	T	A	55905003	3	1	344	1	0	0	0	0	1	0	0	0	11251	1664	58	4	757	4	OR8J3	11	55905003	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	471965	55905003	79101513	816	48179										
OR8K5	219453	hgsc.bcm.edu	37	chr11	55926969	55926969	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	attactaaagtgtaaaacacAgaagccattttatcagtatc	5	7	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:55926969A>C	ENST00000313447.1	-	1	824	c.825T>G	c.(823-825)tcT>tcG	p.S275S		NM_001004058.2	NP_001004058.2	Q8NH50	OR8K5_HUMAN	olfactory receptor, family 8, subfamily K, member 5	275						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(3)|lung(24)|ovary(2)|pancreas(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	34	Esophageal squamous(21;0.00693)	Lung NSC(402;0.197)|all_epithelial(135;0.236)				TGTAAAACACAGAAGCCATTT	0.388																																					p.S275S		Atlas-SNP	.											.	OR8K5	82	.	0			c.T825G						.						105	90	95					11																	55926969		2201	4296	6497	SO:0001819	synonymous_variant	219453	exon1			AAACACAGAAGCC	BK004347	CCDS31521.1	11q11	2012-08-09			ENSG00000181752	ENSG00000181752		"GPCR / Class A : Olfactory receptors"	15315	protein-coding gene	gene with protein product							Standard	NM_001004058		Approved		uc010rja.2	Q8NH50	OTTHUMG00000166820	ENST00000313447.1:c.825T>G	chr11.hg19:g.55926969A>C		110.0	0.0		95.0	36.0	NM_001004058	Q6IFB5	Silent	SNP	ENST00000313447.1	hg19	CCDS31521.1																																																																																			.	.		0.388	OR8K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391543.1	NM_001004058		C	55926969	A	C	55926969	2	2	344	1	0	0	0	0	0	0	0	1	11254	175	7	5		5	OR8K5	11	55926969	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	21966	55926969	79079547	817	48180										
OR5J2	282775	hgsc.bcm.edu	37	chr11	55944226	55944226	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccttgttgaggaatctgggcAtgatcctcttaatccaaatc	8	10	2	2	rs201858818		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:55944226A>G	ENST00000312298.1	+	1	133	c.133A>G	c.(133-135)Atg>Gtg	p.M45V		NM_001005492.1	NP_001005492.1	Q8NH18	OR5J2_HUMAN	olfactory receptor, family 5, subfamily J, member 2	45						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	44	Esophageal squamous(21;0.00693)					GAATCTGGGCATGATCCTCTT	0.418													.|||	1	0.000199681	0	0	5008	,	,		17938	0		0.001	False		,,,				2504	0				p.M45V		Atlas-SNP	.											.	OR5J2	98	.	0			c.A133G						.	A	VAL/MET	0,4402		0,0,2201	223	202	209		133	0.2	0.9	11		209	4,8588	3.7+/-12.6	0,4,4292	yes	missense	OR5J2	NM_001005492.1	21	0,4,6493	GG,GA,AA		0.0466,0.0,0.0308	possibly-damaging	45/313	55944226	4,12990	2201	4296	6497	SO:0001583	missense	282775	exon1			CTGGGCATGATCC	AB065595	CCDS31522.1	11q11	2012-08-09			ENSG00000174957	ENSG00000174957		"GPCR / Class A : Olfactory receptors"	19612	protein-coding gene	gene with protein product							Standard	NM_001005492		Approved		uc010rjb.2	Q8NH18	OTTHUMG00000166835	ENST00000312298.1:c.133A>G	chr11.hg19:g.55944226A>G	ENSP00000310788:p.Met45Val	74.0	0.0		72.0	36.0	NM_001005492	Q6IEU5	Missense_Mutation	SNP	ENST00000312298.1	hg19	CCDS31522.1	.	.	.	.	.	.	.	.	.	.	A	7.506	0.653603	0.14580	0.0	4.66E-4	ENSG00000174957	ENST00000312298	T	0.00421	7.46	4.57	0.237	0.15475	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000002	T	0.00271	0.0008	L	0.43554	1.36	0.21325	N	0.999724	P	0.35745	0.518	B	0.29598	0.104	T	0.50215	-0.8854	10	0.87932	D	0	.	8.1884	0.31352	0.5103:0.3697:0.0:0.12	.	45	Q8NH18	OR5J2_HUMAN	V	45	ENSP00000310788:M45V	ENSP00000310788:M45V	M	+	1	0	OR5J2	55700802	0.180000	0.23148	0.921000	0.36526	0.183000	0.23260	0.708000	0.25719	0.194000	0.20326	0.475000	0.43553	ATG	.	A|0.999;G|0.001		0.418	OR5J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391544.1	NM_001005492		G	55944226	A	G	55944226	3	3	344	1	0	0	0	0	1	0	0	0	11174	217	8	2	135	2	OR5J2	11	55944226	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	17257	55944226	79062290	818	48181										
OR8K3	219473	hgsc.bcm.edu	37	chr11	56086359	56086359	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctttgctttgttcaaatacaCatgaaattgaattgataatt	5	5	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:56086359C>A	ENST00000312711.1	+	1	577	c.577C>A	c.(577-579)Cat>Aat	p.H193N		NM_001005202.1	NP_001005202.1	Q8NH51	OR8K3_HUMAN	olfactory receptor, family 8, subfamily K, member 3	193						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(2)|endometrium(3)|large_intestine(6)|liver(2)|lung(15)|ovary(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	40	Esophageal squamous(21;0.00448)					TTCAAATACACATGAAATTGA	0.343																																					p.H193N		Atlas-SNP	.											.	OR8K3	92	.	0			c.C577A						.						97	97	97					11																	56086359		2201	4296	6497	SO:0001583	missense	219473	exon1			AATACACATGAAA	AB065541	CCDS31527.1	11q11	2012-08-09			ENSG00000181689	ENSG00000181689		"GPCR / Class A : Olfactory receptors"	15313	protein-coding gene	gene with protein product							Standard	NM_001005202		Approved		uc010rjf.2	Q8NH51	OTTHUMG00000166855	ENST00000312711.1:c.577C>A	chr11.hg19:g.56086359C>A	ENSP00000323555:p.His193Asn	85.0	0.0		75.0	29.0	NM_001005202	Q6IFC4	Missense_Mutation	SNP	ENST00000312711.1	hg19	CCDS31527.1	.	.	.	.	.	.	.	.	.	.	C	2.488	-0.318051	0.05386	.	.	ENSG00000181689	ENST00000312711	T	0.00099	8.73	4.56	3.48	0.39840	GPCR, rhodopsin-like superfamily (1);	0.717261	0.13583	N	0.377194	T	0.00178	0.0005	M	0.67700	2.07	0.09310	N	1	B	0.09022	0.002	B	0.17979	0.02	T	0.40979	-0.9534	10	0.54805	T	0.06	.	4.3093	0.10962	0.1717:0.6031:0.0:0.2253	.	193	Q8NH51	OR8K3_HUMAN	N	193	ENSP00000323555:H193N	ENSP00000323555:H193N	H	+	1	0	OR8K3	55842935	0.000000	0.05858	0.450000	0.26969	0.004000	0.04260	-0.996000	0.03709	1.014000	0.39417	0.573000	0.79308	CAT	.	.		0.343	OR8K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391602.1	NM_001005202		A	56086359	C	A	56086359	3	1	344	1	0	0	0	0	1	0	0	0	11253	478	17	3	579	3	OR8K3	11	56086359	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	142133	56086359	78920157	819	48182										
OR8K1	390157	hgsc.bcm.edu	37	chr11	56114284	56114284	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tctgacagtggtgatcatgtTctatgggacattgttattta	10	5	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:56114284T>C	ENST00000279783.2	+	1	864	c.770T>C	c.(769-771)tTc>tCc	p.F257S		NM_001002907.1	NP_001002907.1	Q8NGG5	OR8K1_HUMAN	olfactory receptor, family 8, subfamily K, member 1	257						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F257S(1)		large_intestine(8)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33	Esophageal squamous(21;0.00448)					GTGATCATGTTCTATGGGACA	0.403										HNSCC(65;0.19)																											p.F257S		Atlas-SNP	.											OR8K1,face,malignant_melanoma,0,1	OR8K1	93	.	1	Substitution - Missense(1)	skin(1)	c.T770C						.						125	109	114					11																	56114284		2201	4296	6497	SO:0001583	missense	390157	exon1			TCATGTTCTATGG	AB065835	CCDS31528.1	11q11	2012-08-09			ENSG00000150261	ENSG00000150261		"GPCR / Class A : Olfactory receptors"	14831	protein-coding gene	gene with protein product							Standard	NM_001002907		Approved		uc010rjg.2	Q8NGG5	OTTHUMG00000166858	ENST00000279783.2:c.770T>C	chr11.hg19:g.56114284T>C	ENSP00000279783:p.Phe257Ser	107.0	0.0		65.0	24.0	NM_001002907	B9EJB1|Q6IFC3|Q96RC1	Missense_Mutation	SNP	ENST00000279783.2	hg19	CCDS31528.1	.	.	.	.	.	.	.	.	.	.	T	17.86	3.492120	0.64074	.	.	ENSG00000150261	ENST00000279783	T	0.00297	8.23	5.0	5.0	0.66597	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	D	0.000087	T	0.00784	0.0026	M	0.89601	3.045	0.24841	N	0.992467	D	0.89917	1.0	D	0.81914	0.995	T	0.25152	-1.0140	10	0.87932	D	0	-27.6131	10.0256	0.42070	0.1506:0.0:0.0:0.8494	.	257	Q8NGG5	OR8K1_HUMAN	S	257	ENSP00000279783:F257S	ENSP00000279783:F257S	F	+	2	0	OR8K1	55870860	0.323000	0.24643	0.998000	0.56505	0.745000	0.42441	3.653000	0.54446	1.862000	0.54008	0.448000	0.29417	TTC	.	.		0.403	OR8K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391605.1	NM_001002907		C	56114284	T	C	56114284	3	2	344	1	0	0	0	0	1	0	0	0	11252	1783	62	2	772	2	OR8K1	11	56114284	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	27925	56114284	78892232	820	48183										
OR8K1	390157	hgsc.bcm.edu	37	chr11	56114424	56114424	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcctaaggaacaaagaagtaAaagatgctctaaagagaact	9	6	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:56114424A>T	ENST00000279783.2	+	1	1004	c.910A>T	c.(910-912)Aaa>Taa	p.K304*		NM_001002907.1	NP_001002907.1	Q8NGG5	OR8K1_HUMAN	olfactory receptor, family 8, subfamily K, member 1	304						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(8)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33	Esophageal squamous(21;0.00448)					CAAAGAAGTAAAAGATGCTCT	0.348										HNSCC(65;0.19)																											p.K304X		Atlas-SNP	.											.	OR8K1	93	.	0			c.A910T						.						68	70	70					11																	56114424		2201	4296	6497	SO:0001587	stop_gained	390157	exon1			GAAGTAAAAGATG	AB065835	CCDS31528.1	11q11	2012-08-09			ENSG00000150261	ENSG00000150261		"GPCR / Class A : Olfactory receptors"	14831	protein-coding gene	gene with protein product							Standard	NM_001002907		Approved		uc010rjg.2	Q8NGG5	OTTHUMG00000166858	ENST00000279783.2:c.910A>T	chr11.hg19:g.56114424A>T	ENSP00000279783:p.Lys304*	51.0	0.0		41.0	16.0	NM_001002907	B9EJB1|Q6IFC3|Q96RC1	Nonsense_Mutation	SNP	ENST00000279783.2	hg19	CCDS31528.1	.	.	.	.	.	.	.	.	.	.	A	15.81	2.943322	0.53079	.	.	ENSG00000150261	ENST00000279783	.	.	.	5.0	3.88	0.44766	.	0.000000	0.52532	D	0.000078	.	.	.	.	.	.	0.47094	D	0.999316	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.6608	10.2498	0.43362	0.9218:0.0:0.0782:0.0	.	.	.	.	X	304	.	ENSP00000279783:K304X	K	+	1	0	OR8K1	55871000	0.014000	0.17966	0.966000	0.40874	0.418000	0.31294	1.415000	0.34748	0.756000	0.33013	0.448000	0.29417	AAA	.	.		0.348	OR8K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391605.1	NM_001002907		T	56114424	A	T	56114424	4	4	344	1	0	0	0	0	0	1	0	0	11252	15	1	4	912	4	OR8K1	11	56114424	Nonsense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	140	56114424	78892092	821	48184										
OR5AP2	338675	hgsc.bcm.edu	37	chr11	56409824	56409824	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaaacaatgcaaagaggactCcttgtagatctggattgtcg	11	7	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:56409824C>A	ENST00000302981.1	-	1	91	c.92G>T	c.(91-93)gGa>gTa	p.G31V	OR5AP2_ENST00000544374.1_Missense_Mutation_p.G32V	NM_001002925.1	NP_001002925.1	Q8NGF4	O5AP2_HUMAN	olfactory receptor, family 5, subfamily AP, member 2	31						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	29						AAAGAGGACTCCTTGTAGATC	0.413																																					p.G31V		Atlas-SNP	.											.	OR5AP2	69	.	0			c.G92T						.						103	95	98					11																	56409824		2201	4296	6497	SO:0001583	missense	338675	exon1			AGGACTCCTTGTA	AB065854	CCDS31534.1	11q11	2012-08-09			ENSG00000172464	ENSG00000172464		"GPCR / Class A : Olfactory receptors"	15258	protein-coding gene	gene with protein product							Standard	NM_001002925		Approved		uc001njb.1	Q8NGF4	OTTHUMG00000166865	ENST00000302981.1:c.92G>T	chr11.hg19:g.56409824C>A	ENSP00000303111:p.Gly31Val	48.0	0.0		52.0	24.0	NM_001002925	B2RNM8	Missense_Mutation	SNP	ENST00000302981.1	hg19	CCDS31534.1	.	.	.	.	.	.	.	.	.	.	C	0.003	-2.481838	0.00163	.	.	ENSG00000172464	ENST00000544374;ENST00000302981	T;T	0.00380	7.64;7.64	5.19	3.05	0.35203	.	1.346700	0.05040	N	0.476107	T	0.00109	0.0003	N	0.00473	-1.45	0.18873	N	0.999986	B	0.02656	0.0	B	0.04013	0.001	T	0.23940	-1.0174	10	0.02654	T	1	.	6.4932	0.22127	0.6022:0.2852:0.0:0.1126	.	31	Q8NGF4	O5AP2_HUMAN	V	32;31	ENSP00000442701:G32V;ENSP00000303111:G31V	ENSP00000303111:G31V	G	-	2	0	OR5AP2	56166400	0.000000	0.05858	0.143000	0.22291	0.213000	0.24496	-0.800000	0.04555	0.578000	0.29487	0.637000	0.83480	GGA	.	.		0.413	OR5AP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391613.1	NM_001002925		A	56409824	C	A	56409824	3	1	344	1	0	0	0	0	1	0	0	0	11153	855	30	3	862	3	OR5AP2	11	56409824	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	295400	56409824	78596692	822	48185										
OR9G1	390174	hgsc.bcm.edu	37	chr11	56468593	56468593	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tctccacatgctcctcccacCtgacctctgtcactttatac	3	18	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:56468593C>A	ENST00000312153.1	+	1	730	c.730C>A	c.(730-732)Ctg>Atg	p.L244M		NM_001005213.1	NP_001005213.1	Q8NH87	OR9G1_HUMAN	olfactory receptor, family 9, subfamily G, member 1	244						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|kidney(1)|lung(25)|stomach(2)|upper_aerodigestive_tract(1)	31						CTCCTCCCACCTGACCTCTGT	0.458																																					p.L244M		Atlas-SNP	.											.	.	.	.	0			c.C730A						.						229	236	234					11																	56468593		2201	4296	6497	SO:0001583	missense	504191	exon1			TCCCACCTGACCT	AB065500	CCDS31536.1	11q11	2012-08-09			ENSG00000174914	ENSG00000174914		"GPCR / Class A : Olfactory receptors"	15319	protein-coding gene	gene with protein product				OR9G5			Standard	NM_001005213		Approved			Q8NH87	OTTHUMG00000167112	ENST00000312153.1:c.730C>A	chr11.hg19:g.56468593C>A	ENSP00000309012:p.Leu244Met	104.0	0.0		92.0	18.0	NM_001013358	Q6IEU9|Q8NGQ0	Missense_Mutation	SNP	ENST00000312153.1	hg19	CCDS31536.1	.	.	.	.	.	.	.	.	.	.	C	9.599	1.128252	0.21041	.	.	ENSG00000174914	ENST00000312153	T	0.50001	0.76	4.62	-4.17	0.03857	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42682	D	0.000676	T	0.60792	0.2296	M	0.87682	2.9	0.27550	N	0.950523	D	0.60160	0.987	D	0.72338	0.977	T	0.53683	-0.8404	10	0.45353	T	0.12	-21.1339	4.8763	0.13658	0.3317:0.312:0.0:0.3563	.	244	Q8NH87	OR9G1_HUMAN	M	244	ENSP00000309012:L244M	ENSP00000309012:L244M	L	+	1	2	OR9G1	56225169	0.179000	0.23135	0.147000	0.22382	0.233000	0.25261	0.111000	0.15458	-0.541000	0.06257	-2.114000	0.00352	CTG	.	.		0.458	OR9G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393253.1	NM_001005213		A	56468593	C	A	56468593	3	1	344	1	0	0	0	0	1	0	0	0	11259	680	24	3	732	3	OR9G1	11	56468593	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	58769	56468593	78537923	823	48186										
OR9G1	390174	hgsc.bcm.edu	37	chr11	56468658	56468658	+	Nonsense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gctctccccagatctagctaTtcttttgatatggacaaaat	6	10	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:56468658T>G	ENST00000312153.1	+	1	795	c.795T>G	c.(793-795)taT>taG	p.Y265*		NM_001005213.1	NP_001005213.1	Q8NH87	OR9G1_HUMAN	olfactory receptor, family 9, subfamily G, member 1	265						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|kidney(1)|lung(25)|stomach(2)|upper_aerodigestive_tract(1)	31						GATCTAGCTATTCTTTTGATA	0.428																																					p.Y265X		Atlas-SNP	.											.	.	.	.	0			c.T795G						.						198	209	205					11																	56468658		2201	4296	6497	SO:0001587	stop_gained	504191	exon1			TAGCTATTCTTTT	AB065500	CCDS31536.1	11q11	2012-08-09			ENSG00000174914	ENSG00000174914		"GPCR / Class A : Olfactory receptors"	15319	protein-coding gene	gene with protein product				OR9G5			Standard	NM_001005213		Approved			Q8NH87	OTTHUMG00000167112	ENST00000312153.1:c.795T>G	chr11.hg19:g.56468658T>G	ENSP00000309012:p.Tyr265*	94.0	0.0		72.0	11.0	NM_001013358	Q6IEU9|Q8NGQ0	Nonsense_Mutation	SNP	ENST00000312153.1	hg19	CCDS31536.1	.	.	.	.	.	.	.	.	.	.	T	4.806	0.149823	0.09185	.	.	ENSG00000174914	ENST00000312153	.	.	.	4.62	-1.62	0.08372	.	0.279150	0.25938	N	0.027326	.	.	.	.	.	.	0.53688	D	0.99997	.	.	.	.	.	.	.	.	.	.	0.08179	T	0.78	-7.5009	7.5988	0.28065	0.0:0.4569:0.1307:0.4124	.	.	.	.	X	265	.	ENSP00000309012:Y265X	Y	+	3	2	OR9G1	56225234	0.000000	0.05858	0.002000	0.10522	0.140000	0.21249	-1.013000	0.03645	-0.171000	0.10797	0.519000	0.50382	TAT	.	.		0.428	OR9G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393253.1	NM_001005213		G	56468658	T	G	56468658	4	3	344	1	0	0	0	0	0	1	0	0	11259	1500	52	5	797	5	OR9G1	11	56468658	Nonsense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	65	56468658	78537858	824	48187										
OR5B3	441608	hgsc.bcm.edu	37	chr11	58170104	58170104	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccatggagtgactggagctgGgttgtaagtacatgaagata	14	5	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:58170104G>T	ENST00000309403.2	-	1	778	c.779C>A	c.(778-780)cCc>cAc	p.P260H		NM_001005469.1	NP_001005469.1	Q8NH48	OR5B3_HUMAN	olfactory receptor, family 5, subfamily B, member 3	260						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(6)|upper_aerodigestive_tract(1)	34	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				ACTGGAGCTGGGTTGTAAGTA	0.468																																					p.P260H		Atlas-SNP	.											.	OR5B3	65	.	0			c.C779A						.						102	99	100					11																	58170104		2201	4295	6496	SO:0001583	missense	441608	exon1			GAGCTGGGTTGTA	AB065545	CCDS31549.1	11q12.1	2012-08-09			ENSG00000172769	ENSG00000172769		"GPCR / Class A : Olfactory receptors"	8324	protein-coding gene	gene with protein product				OR5B13			Standard	NM_001005469		Approved	OST129	uc010rkf.2	Q8NH48	OTTHUMG00000167516	ENST00000309403.2:c.779C>A	chr11.hg19:g.58170104G>T	ENSP00000308270:p.Pro260His	55.0	0.0		48.0	20.0	NM_001005469	Q6IEV6	Missense_Mutation	SNP	ENST00000309403.2	hg19	CCDS31549.1	.	.	.	.	.	.	.	.	.	.	g	16.96	3.267398	0.59540	.	.	ENSG00000172769	ENST00000309403	T	0.00272	8.36	4.05	4.05	0.47172	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47852	D	0.000220	T	0.00906	0.0030	M	0.91196	3.185	0.31806	N	0.627719	D	0.89917	1.0	D	0.91635	0.999	T	0.10613	-1.0622	10	0.87932	D	0	-64.5656	15.2879	0.73843	0.0:0.0:1.0:0.0	.	260	Q8NH48	OR5B3_HUMAN	H	260	ENSP00000308270:P260H	ENSP00000308270:P260H	P	-	2	0	OR5B3	57926680	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	3.630000	0.54273	2.264000	0.75181	0.650000	0.86243	CCC	.	.		0.468	OR5B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394886.1	NM_001005469		T	58170104	G	T	58170104	3	4	344	1	0	0	0	0	1	0	0	0	11161	1232	43	3	167	3	OR5B3	11	58170104	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1701446	58170104	76836412	825	48188										
DDB1	1642	hgsc.bcm.edu	37	chr11	61091480	61091480	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gagttctacacggagatcctTgagagtgacggtgccatcca	12	10	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:61091480T>A	ENST00000301764.7	-	7	1289	c.892A>T	c.(892-894)Aag>Tag	p.K298*	DDB1_ENST00000450997.2_Intron|DDB1_ENST00000545930.1_5'UTR	NM_001923.4	NP_001914.3	Q16531	DDB1_HUMAN	damage-specific DNA binding protein 1, 127kDa	298	Interaction with CDT1.|WD repeat beta-propeller A.				DNA repair (GO:0006281)|histone H2A monoubiquitination (GO:0035518)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of mitotic cell cycle phase transition (GO:1901990)|UV-damage excision repair (GO:0070914)|viral process (GO:0016032)|Wnt signaling pathway (GO:0016055)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	48						CGGAGATCCTTGAGAGTGACG	0.502								Nucleotide excision repair (NER)																													p.K298X		Atlas-SNP	.											.	DDB1	100	.	0			c.A892T						.						209	189	196					11																	61091480		2203	4299	6502	SO:0001587	stop_gained	1642	exon7			GATCCTTGAGAGT	AJ002955	CCDS31576.1	11q12-q13	2014-09-17	2002-08-29		ENSG00000167986	ENSG00000167986			2717	protein-coding gene	gene with protein product		600045	"damage-specific DNA binding protein 1 (127kD)"			8530102, 10574459	Standard	NM_001923		Approved	XPE	uc001nrc.5	Q16531	OTTHUMG00000168209	ENST00000301764.7:c.892A>T	chr11.hg19:g.61091480T>A	ENSP00000301764:p.Lys298*	169.0	0.0		170.0	75.0	NM_001923	A6NG77|B2R648|B4DG00|O15176|Q13289|Q58F96	Nonsense_Mutation	SNP	ENST00000301764.7	hg19	CCDS31576.1	.	.	.	.	.	.	.	.	.	.	T	40	8.452979	0.98817	.	.	ENSG00000167986	ENST00000301764;ENST00000535174;ENST00000541513	.	.	.	5.63	5.63	0.86233	.	0.105068	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-29.1078	15.8421	0.78857	0.0:0.0:0.0:1.0	.	.	.	.	X	298;81;113	.	ENSP00000301764:K298X	K	-	1	0	DDB1	60848056	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	6.186000	0.72026	2.157000	0.67596	0.533000	0.62120	AAG	.	.		0.502	DDB1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398816.1	NM_001923		A	61091480	T	A	61091480	4	1	344	1	0	0	0	0	0	1	0	0	4325	1821	63	4	2614	4	DDB1	11	61091480	Nonsense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2921376	61091480	73915036	826	48189										
CYBASC3	220002	hgsc.bcm.edu	37	chr11	61124109	61124109	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cacgccagtactgcatccagTagatagtgaagaggatgcac	11	10	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:61124109T>A	ENST00000294072.4	-	3	754	c.77A>T	c.(76-78)tAc>tTc	p.Y26F	CYB561A3_ENST00000546151.1_Missense_Mutation_p.Y26F|CYB561A3_ENST00000536915.1_Missense_Mutation_p.Y26F|CYB561A3_ENST00000544118.1_Missense_Mutation_p.Y26F|CYB561A3_ENST00000447532.2_Missense_Mutation_p.Y26F|CYB561A3_ENST00000539890.1_Missense_Mutation_p.Y26F|CYB561A3_ENST00000540317.1_Intron|CYB561A3_ENST00000426130.2_Missense_Mutation_p.Y43F	NM_001161452.1|NM_153611.4	NP_001154924.1|NP_705839.3	Q8NBI2	CYAC3_HUMAN	cytochrome b561 family, member A3	26	Cytochrome b561. {ECO:0000255|PROSITE- ProRule:PRU00242}.					integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)	metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)										CTGCATCCAGTAGATAGTGAA	0.522																																					p.Y43F		Atlas-SNP	.											.	CYBASC3	26	.	0			c.A128T						.						169	150	157					11																	61124109		2203	4299	6502	SO:0001583	missense	220002	exon4			ATCCAGTAGATAG	AK024953	CCDS8004.1, CCDS53639.1, CCDS73296.1	11q12.2	2013-03-14	2013-03-14	2013-03-14		ENSG00000162144		"Cytochrome b genes"	23014	protein-coding gene	gene with protein product			"cytochrome b, ascorbate dependent 3"	CYBASC3		23249217	Standard	NM_153611		Approved		uc001nrf.4	Q8NBI2		ENST00000294072.4:c.77A>T	chr11.hg19:g.61124109T>A	ENSP00000294072:p.Tyr26Phe	89.0	0.0		87.0	44.0	NM_001161454	B3KPU2|B4DLN9|J3KQH4|Q6PK96	Missense_Mutation	SNP	ENST00000294072.4	hg19	CCDS8004.1	.	.	.	.	.	.	.	.	.	.	T	10.54	1.380121	0.24944	.	.	ENSG00000162144	ENST00000426130;ENST00000294072;ENST00000447532;ENST00000546151;ENST00000544118;ENST00000536915;ENST00000539890;ENST00000542361;ENST00000537364;ENST00000539128;ENST00000545361;ENST00000537680	T;T;T;T;T;T	0.62941	0.0;0.01;-0.01;0.01;1.01;1.01	5.38	2.98	0.34508	Cytochrome b561/ferric reductase transmembrane (1);	0.538625	0.19361	N	0.116138	T	0.45357	0.1338	L	0.41906	1.305	0.09310	N	1	B;B;P;B	0.35174	0.159;0.036;0.488;0.086	B;B;B;B	0.32211	0.062;0.042;0.142;0.034	T	0.21245	-1.0251	10	0.20046	T	0.44	-12.1842	6.4702	0.22003	0.2387:0.0:0.2749:0.4864	.	43;26;26;26	B4DLN9;F5H0P5;F5H1Q2;Q8NBI2	.;.;.;CYAC3_HUMAN	F	43;26;26;26;26;26;26;26;26;26;26;26	ENSP00000398979:Y43F;ENSP00000294072:Y26F;ENSP00000389745:Y26F;ENSP00000437390:Y26F;ENSP00000443321:Y26F;ENSP00000438725:Y26F	ENSP00000294072:Y26F	Y	-	2	0	CYBASC3	60880685	0.015000	0.18098	0.034000	0.17996	0.796000	0.44982	1.047000	0.30367	0.317000	0.23160	-0.496000	0.04628	TAC	.	.		0.522	CYB561A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398714.2	NM_153611		A	61124109	T	A	61124109	3	1	344	1	0	0	0	0	1	0	0	0	4134	1638	57	4	671	4	CYBASC3	11	61124109	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	32629	61124109	73882407	827	48190										
AHNAK	79026	hgsc.bcm.edu	37	chr11	62285505	62285505	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agtggccccaaggctcccttTcacttttggtccttccaagt	8	14	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:62285505T>C	ENST00000378024.4	-	5	16658	c.16384A>G	c.(16384-16386)Aaa>Gaa	p.K5462E	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000525875.1_5'Flank	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	5462	Gly-rich.				protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				AGGCTCCCTTTCACTTTTGGT	0.547																																					p.K5462E		Atlas-SNP	.											.	AHNAK	532	.	0			c.A16384G						.						77	78	78					11																	62285505		2202	4299	6501	SO:0001583	missense	79026	exon5			TCCCTTTCACTTT	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.16384A>G	chr11.hg19:g.62285505T>C	ENSP00000367263:p.Lys5462Glu	86.0	0.0		82.0	41.0	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	hg19	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	T	11.93	1.785854	0.31593	.	.	ENSG00000124942	ENST00000378024	T	0.02552	4.25	4.88	4.88	0.63580	.	0.144874	0.30781	U	0.008887	T	0.03305	0.0096	L	0.41632	1.29	0.33695	D	0.613811	P	0.39480	0.675	B	0.42522	0.39	T	0.42766	-0.9432	10	0.23302	T	0.38	-4.8397	5.6771	0.17755	0.0:0.2296:0.0:0.7704	.	5462	Q09666	AHNK_HUMAN	E	5462	ENSP00000367263:K5462E	ENSP00000367263:K5462E	K	-	1	0	AHNAK	62042081	0.353000	0.24904	0.996000	0.52242	0.986000	0.74619	2.345000	0.44018	1.814000	0.52955	0.372000	0.22366	AAA	.	.		0.547	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		C	62285505	T	C	62285505	3	2	344	1	0	0	0	0	1	0	0	0	414	1792	62	2	1408	2	AHNAK	11	62285505	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1161396	62285505	72721011	828	48191										
AHNAK	79026	hgsc.bcm.edu	37	chr11	62288328	62288328	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	attcaaatcaatgtcactcaTggagatttgtgggcttttga	9	6	4	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:62288328T>C	ENST00000378024.4	-	5	13835	c.13561A>G	c.(13561-13563)Atg>Gtg	p.M4521V	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	4521					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				ATGTCACTCATGGAGATTTGT	0.428																																					p.M4521V		Atlas-SNP	.											.	AHNAK	532	.	0			c.A13561G						.						70	71	71					11																	62288328		2202	4299	6501	SO:0001583	missense	79026	exon5			CACTCATGGAGAT	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.13561A>G	chr11.hg19:g.62288328T>C	ENSP00000367263:p.Met4521Val	111.0	0.0		98.0	29.0	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	hg19	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	T	18.88	3.716609	0.68844	.	.	ENSG00000124942	ENST00000378024	T	0.01745	4.66	4.92	4.92	0.64577	.	0.000000	0.45606	U	0.000355	T	0.08714	0.0216	M	0.85710	2.77	0.41555	D	0.988594	P	0.42010	0.768	P	0.56514	0.8	T	0.32851	-0.9891	10	0.18276	T	0.48	.	13.1099	0.59267	0.0:0.0:0.0:1.0	.	4521	Q09666	AHNK_HUMAN	V	4521	ENSP00000367263:M4521V	ENSP00000367263:M4521V	M	-	1	0	AHNAK	62044904	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	3.157000	0.50716	1.970000	0.57323	0.523000	0.50628	ATG	.	.		0.428	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		C	62288328	T	C	62288328	3	2	344	1	0	0	0	0	1	0	0	0	414	1464	51	2	4231	2	AHNAK	11	62288328	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2823	62288328	72718188	829	48192										
AHNAK	79026	hgsc.bcm.edu	37	chr11	62289734	62289734	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcaggtgccagtctgggccaTgaacatccacatctggggca	12	12	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:62289734T>C	ENST00000378024.4	-	5	12429	c.12155A>G	c.(12154-12156)cAt>cGt	p.H4052R	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	4052					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				GTCTGGGCCATGAACATCCAC	0.502																																					p.H4052R		Atlas-SNP	.											.	AHNAK	532	.	0			c.A12155G						.						190	201	197					11																	62289734		2202	4299	6501	SO:0001583	missense	79026	exon5			GGGCCATGAACAT	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.12155A>G	chr11.hg19:g.62289734T>C	ENSP00000367263:p.His4052Arg	81.0	0.0		70.0	34.0	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	hg19	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	-	0.332	-0.955447	0.02267	.	.	ENSG00000124942	ENST00000378024	T	0.00966	5.49	4.04	4.04	0.47022	.	0.386788	0.19320	N	0.117174	T	0.01730	0.0055	M	0.75150	2.29	0.32641	N	0.520734	B	0.21606	0.058	B	0.22601	0.04	T	0.06570	-1.0819	10	0.16896	T	0.51	.	12.6376	0.56692	0.0:0.0:0.0:1.0	.	4052	Q09666	AHNK_HUMAN	R	4052	ENSP00000367263:H4052R	ENSP00000367263:H4052R	H	-	2	0	AHNAK	62046310	0.014000	0.17966	0.605000	0.28930	0.018000	0.09664	1.567000	0.36407	1.471000	0.48121	0.148000	0.16107	CAT	.	.		0.502	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		C	62289734	T	C	62289734	3	2	344	1	0	0	0	0	1	0	0	0	414	1464	51	2	5637	2	AHNAK	11	62289734	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1406	62289734	72716782	830	48193										
B3GAT3	26229	hgsc.bcm.edu	37	chr11	62384649	62384649	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gctcgccctcccgaagccgcTgggctttgggcgtgaggacc	15	15	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:62384649T>A	ENST00000265471.5	-	3	655	c.428A>T	c.(427-429)cAg>cTg	p.Q143L	B3GAT3_ENST00000534026.1_Missense_Mutation_p.Q143L|B3GAT3_ENST00000531383.1_Missense_Mutation_p.Q143L	NM_012200.3	NP_036332.2	O94766	B3GA3_HUMAN	beta-1,3-glucuronyltransferase 3	143					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|dermatan sulfate proteoglycan biosynthetic process (GO:0050651)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity (GO:0015018)|glucuronosyltransferase activity (GO:0015020)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(2)|urinary_tract(1)	12						CCGAAGCCGCTGGGCTTTGGG	0.687																																					p.Q143L		Atlas-SNP	.											.	B3GAT3	24	.	0			c.A428T						.						23	27	25					11																	62384649		2202	4297	6499	SO:0001583	missense	26229	exon3			AGCCGCTGGGCTT	AB009598	CCDS8025.1	11q12	2014-07-08	2014-07-08		ENSG00000149541	ENSG00000149541	2.4.1.135	"Beta-1,3-glucuronyltransferases"	923	protein-coding gene	gene with protein product	"glucuronosyltransferase I", "galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 3"	606374	"beta-1,3-glucuronyltransferase 3 (glucuronosyltransferase I)"			9506957	Standard	NM_012200		Approved	GlcAT-I	uc001ntw.3	O94766	OTTHUMG00000167685	ENST00000265471.5:c.428A>T	chr11.hg19:g.62384649T>A	ENSP00000265471:p.Gln143Leu	57.0	0.0		50.0	27.0	NM_012200	B7ZAB3|Q96I06|Q9UEP0	Missense_Mutation	SNP	ENST00000265471.5	hg19	CCDS8025.1	.	.	.	.	.	.	.	.	.	.	t	8.326	0.825487	0.16749	.	.	ENSG00000149541	ENST00000265471;ENST00000531383;ENST00000534026;ENST00000534715	T;T;T;T	0.62639	0.01;0.01;0.01;0.01	5.56	5.56	0.83823	.	0.227141	0.39210	N	0.001432	T	0.41673	0.1169	N	0.16656	0.425	0.42403	D	0.99257	B;B;B	0.09022	0.001;0.002;0.0	B;B;B	0.14023	0.01;0.01;0.01	T	0.34104	-0.9842	10	0.13470	T	0.59	.	9.0457	0.36345	0.164:0.0:0.0:0.8359	.	143;149;143	B7ZAB3;Q5U676;O94766	.;.;B3GA3_HUMAN	L	143;143;143;166	ENSP00000265471:Q143L;ENSP00000431359:Q143L;ENSP00000432474:Q143L;ENSP00000432854:Q166L	ENSP00000265471:Q143L	Q	-	2	0	B3GAT3	62141225	1.000000	0.71417	1.000000	0.80357	0.762000	0.43233	1.125000	0.31332	2.114000	0.64651	0.454000	0.30748	CAG	.	.		0.687	B3GAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395588.1	NM_012200		A	62384649	T	A	62384649	3	1	344	1	0	0	0	0	1	0	0	0	1255	1580	55	4	591	4	B3GAT3	11	62384649	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	94915	62384649	72621867	831	48194										
SLC22A8	9376	hgsc.bcm.edu	37	chr11	62763203	62763203	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gggaaagacagaaggtcatgCggcgcagcatgggtatccgg	17	8	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:62763203C>T	ENST00000336232.2	-	7	1109	c.974G>A	c.(973-975)cGc>cAc	p.R325H	SLC22A8_ENST00000542795.1_5'Flank|SLC22A8_ENST00000311438.8_Missense_Mutation_p.R325H|SLC22A8_ENST00000430500.2_Missense_Mutation_p.R325H|SLC22A8_ENST00000535878.1_Missense_Mutation_p.R202H|SLC22A8_ENST00000545207.1_Missense_Mutation_p.R234H	NM_001184732.1|NM_001184736.1|NM_004254.3	NP_001171661.1|NP_001171665.1|NP_004245.2	Q8TCC7	S22A8_HUMAN	solute carrier family 22 (organic anion transporter), member 8	325					glutathione transport (GO:0034635)|response to methotrexate (GO:0031427)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|organic anion transmembrane transporter activity (GO:0008514)|quaternary ammonium group transmembrane transporter activity (GO:0015651)			endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	28					Aciclovir(DB00787)|Adefovir Dipivoxil(DB00718)|Allopurinol(DB00437)|Aminohippurate(DB00345)|Aspartame(DB00168)|Baclofen(DB00181)|Benzylpenicillin(DB01053)|Bumetanide(DB00887)|Cefacetrile(DB01414)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefazolin(DB01327)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Ceftriaxone(DB01212)|Cephalexin(DB00567)|Cilastatin(DB01597)|Cimetidine(DB00501)|Conjugated Estrogens(DB00286)|Dabrafenib(DB08912)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Doxycycline(DB00254)|Enalapril(DB00584)|Estradiol(DB00783)|Famotidine(DB00927)|Furosemide(DB00695)|Ganciclovir(DB01004)|Guanidine(DB00536)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|L-Carnitine(DB00583)|Liothyronine(DB00279)|Liotrix(DB01583)|Melatonin(DB01065)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Methyltestosterone(DB06710)|Minocycline(DB01017)|Novobiocin(DB01051)|Oseltamivir(DB00198)|Ouabain(DB01092)|Oxytetracycline(DB00595)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Ranitidine(DB00863)|Salicylic acid(DB00936)|Saxagliptin(DB06335)|Succinic acid(DB00139)|Tenofovir(DB00300)|Tenoxicam(DB00469)|Testosterone(DB00624)|Tetracycline(DB00759)|Valaciclovir(DB00577)|Valproic Acid(DB00313)|Zidovudine(DB00495)	GAAGGTCATGCGGCGCAGCAT	0.582																																					p.R325H		Atlas-SNP	.											.	SLC22A8	60	.	0			c.G974A						.						156	141	146					11																	62763203		2201	4298	6499	SO:0001583	missense	9376	exon7			GTCATGCGGCGCA	AF097491, BC022387	CCDS8042.1, CCDS53643.1, CCDS53644.1	11q12.3	2013-05-22			ENSG00000149452	ENSG00000149452		"Solute carriers"	10972	protein-coding gene	gene with protein product		607581				10049739	Standard	NM_004254		Approved	OAT3	uc001nwo.3	Q8TCC7	OTTHUMG00000167768	ENST00000336232.2:c.974G>A	chr11.hg19:g.62763203C>T	ENSP00000337335:p.Arg325His	107.0	0.0		65.0	28.0	NM_001184732	B4DPH7|F5GWA8|F5H5J1|O95820|Q59EW9|Q96TC1	Missense_Mutation	SNP	ENST00000336232.2	hg19	CCDS8042.1	.	.	.	.	.	.	.	.	.	.	C	10.39	1.336433	0.24253	.	.	ENSG00000149452	ENST00000336232;ENST00000540631;ENST00000545207;ENST00000535878;ENST00000311438;ENST00000430500	T;T;T;T;T	0.76578	-1.03;-1.03;-1.03;-1.03;-1.03	5.34	2.17	0.27698	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.751400	0.12361	N	0.475671	T	0.67832	0.2935	L	0.42581	1.335	0.27474	N	0.952785	B;B	0.24920	0.093;0.114	B;B	0.30572	0.071;0.117	T	0.55780	-0.8087	10	0.25751	T	0.34	.	5.7551	0.18168	0.3726:0.5355:0.0:0.0919	.	325;325	Q8TCC7-2;Q8TCC7	.;S22A8_HUMAN	H	325;311;234;202;325;325	ENSP00000337335:R325H;ENSP00000441658:R234H;ENSP00000443368:R202H;ENSP00000311463:R325H;ENSP00000398548:R325H	ENSP00000311463:R325H	R	-	2	0	SLC22A8	62519779	0.047000	0.20315	0.338000	0.25549	0.900000	0.52787	0.126000	0.15769	0.575000	0.29434	0.555000	0.69702	CGC	.	.		0.582	SLC22A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396191.1	NM_004254		T	62763203	C	T	62763203	3	4	344	1	0	0	0	0	1	0	0	0	14475	768	27	1	674	1	SLC22A8	11	62763203	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	378554	62763203	72243313	832	48195										
SLC22A12	116085	hgsc.bcm.edu	37	chr11	64359432	64359432	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctccacaatcgtggccaaggTagggcctcccccagagccac	10	17	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:64359432T>A	ENST00000377574.1	+	1	1149		c.e1+2		SLC22A12_ENST00000336464.7_Splice_Site|SLC22A12_ENST00000473690.1_Splice_Site|SLC22A12_ENST00000377572.1_Splice_Site|SLC22A12_ENST00000377567.2_Splice_Site	NM_144585.2	NP_653186.2	Q96S37	S22AC_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 12						cellular homeostasis (GO:0019725)|response to drug (GO:0042493)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|urate transmembrane transporter activity (GO:0015143)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27					Losartan(DB00678)|Probenecid(DB01032)	GTGGCCAAGGTAGGGCCTCCC	0.627																																					.		Atlas-SNP	.											.	SLC22A12	68	.	0			c.402+2T>A						.						23	25	24					11																	64359432		2200	4297	6497	SO:0001630	splice_region_variant	116085	exon1			CCAAGGTAGGGCC	AB071863	CCDS8075.1, CCDS60835.1, CCDS60836.1	11q13.1	2013-05-22	2008-01-11		ENSG00000197891	ENSG00000197891		"Solute carriers"	17989	protein-coding gene	gene with protein product		607096	"solute carrier family 22 (organic anion/cation transporter), member 12"			12024214	Standard	NM_144585		Approved	OAT4L, RST, URAT1	uc009yps.2	Q96S37	OTTHUMG00000045213	ENST00000377574.1:c.402+2T>A	chr11.hg19:g.64359432T>A		28.0	0.0		21.0	11.0	NM_001276326	B7WPG1|G3XAN7|Q19PF7|Q19PF8|Q19PF9|Q19PG0|Q6UXW3|Q96DT2	Splice_Site	SNP	ENST00000377574.1	hg19	CCDS8075.1	.	.	.	.	.	.	.	.	.	.	T	17.21	3.332027	0.60853	.	.	ENSG00000197891	ENST00000377567;ENST00000377574;ENST00000377572;ENST00000336464	.	.	.	4.4	3.26	0.37387	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.0248	0.30430	0.0:0.1009:0.0:0.8991	.	.	.	.	.	-1	.	.	.	+	.	.	SLC22A12	64116008	1.000000	0.71417	0.227000	0.23927	0.963000	0.63663	5.532000	0.67154	0.548000	0.28955	0.397000	0.26171	.	.	.		0.627	SLC22A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104966.2	NM_144585	Intron	A	64359432	T	A	64359432	5	1	344	1	0	0	0	0	0	0	1	0	14458	1652	57	4	406	4	SLC22A12	11	64359432	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1596229	64359432	70647084	833	48196										
SF1	7536	hgsc.bcm.edu	37	chr11	64536751	64536751	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gccaactcccgaagctgcatCttccgtagatcattctggtc	8	14	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:64536751C>A	ENST00000377390.3	-	7	1060	c.723G>T	c.(721-723)aaG>aaT	p.K241N	SF1_ENST00000377387.1_Missense_Mutation_p.K366N|SF1_ENST00000433274.2_Missense_Mutation_p.K215N|SF1_ENST00000334944.5_Missense_Mutation_p.K241N|SF1_ENST00000422298.2_Missense_Mutation_p.K126N|SF1_ENST00000227503.9_Missense_Mutation_p.K241N|SF1_ENST00000489544.1_5'UTR|SF1_ENST00000377394.3_Missense_Mutation_p.K241N	NM_004630.3	NP_004621.2	Q15637	SF01_HUMAN	splicing factor 1	241					Leydig cell differentiation (GO:0033327)|male sex determination (GO:0030238)|mRNA 3'-splice site recognition (GO:0000389)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of smooth muscle cell proliferation (GO:0048662)|regulation of steroid biosynthetic process (GO:0050810)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal complex assembly (GO:0000245)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|ribosome (GO:0005840)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(12)|ovary(2)|skin(2)	31						GAAGCTGCATCTTCCGTAGAT	0.473																																					p.K366N		Atlas-SNP	.											.	SF1	124	.	0			c.G1098T						.						107	102	104					11																	64536751		2201	4297	6498	SO:0001583	missense	7536	exon7			CTGCATCTTCCGT	D26120	CCDS8080.1, CCDS8081.1, CCDS31599.1, CCDS44642.1, CCDS44642.2, CCDS53660.1, CCDS53661.1	11q13	2014-09-17	2001-12-19	2002-01-11	ENSG00000168066	ENSG00000168066		"Zinc fingers, CCHC domain containing"	12950	protein-coding gene	gene with protein product		601516	"zinc finger protein 162"	ZNF162		7912130, 9573336	Standard	NM_201997		Approved	ZFM1, ZCCHC25	uc001oaz.2	Q15637	OTTHUMG00000066833	ENST00000377390.3:c.723G>T	chr11.hg19:g.64536751C>A	ENSP00000366607:p.Lys241Asn	131.0	0.0		126.0	51.0	NM_001178030	B7Z1Q1|C9JJE2|Q14818|Q14819|Q15913|Q8IY00|Q92744|Q92745|Q969H7|Q9BW01|Q9UEI0	Missense_Mutation	SNP	ENST00000377390.3	hg19	CCDS31599.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.162973	0.78226	.	.	ENSG00000168066	ENST00000377387;ENST00000377390;ENST00000227503;ENST00000377394;ENST00000334944;ENST00000422298;ENST00000433274	T;T;T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96;0.96;0.96	6.03	4.17	0.49024	.	0.146778	0.64402	D	0.000020	T	0.58779	0.2146	M	0.75615	2.305	0.54753	D	0.999983	D;D;D;D;D;D	0.76494	0.996;0.999;0.999;0.999;0.999;0.999	P;D;D;P;D;D	0.68039	0.735;0.92;0.935;0.863;0.935;0.955	T	0.60198	-0.7310	10	0.87932	D	0	.	7.6255	0.28210	0.0:0.743:0.0:0.257	.	126;241;241;241;241;366	B4DX42;Q15637-6;Q15637-4;Q15637;Q15637-2;Q15637-5	.;.;.;SF01_HUMAN;.;.	N	366;241;241;241;241;126;215	ENSP00000366604:K366N;ENSP00000366607:K241N;ENSP00000227503:K241N;ENSP00000366611:K241N;ENSP00000334414:K241N;ENSP00000413084:K126N;ENSP00000396793:K215N	ENSP00000227503:K241N	K	-	3	2	SF1	64293327	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.873000	0.28052	0.873000	0.35799	0.557000	0.71058	AAG	.	.		0.473	SF1-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000143242.1	NM_004630		A	64536751	C	A	64536751	3	1	344	1	0	0	0	0	1	0	0	0	14160	912	32	3	1362	3	SF1	11	64536751	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	177319	64536751	70469765	834	48197										
CDC42BPG	55561	hgsc.bcm.edu	37	chr11	64601242	64601242	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gctgcgtcggccctccggccTcagatctggctctcctccat	10	18	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:64601242T>A	ENST00000342711.5	-	22	2532	c.2533A>T	c.(2533-2535)Agg>Tgg	p.R845W	CDC42BPG_ENST00000491280.1_5'Flank	NM_017525.2	NP_059995.2			CDC42 binding protein kinase gamma (DMPK-like)											central_nervous_system(1)|lung(3)	4						CCCTCCGGCCTCAGATCTGGC	0.667																																					p.R845W		Atlas-SNP	.											.	CDC42BPG	101	.	0			c.A2533T						.						45	48	47					11																	64601242		2201	4297	6498	SO:0001583	missense	55561	exon22			CCGGCCTCAGATC	AY648038	CCDS31601.1	11q13	2013-01-10			ENSG00000171219	ENSG00000171219		"Pleckstrin homology (PH) domain containing"	29829	protein-coding gene	gene with protein product		613991				9341881, 15194684	Standard	NM_017525		Approved	HSMDPKIN, MRCKgamma, DMPK2, kappa-200	uc001obs.4	Q6DT37	OTTHUMG00000045365	ENST00000342711.5:c.2533A>T	chr11.hg19:g.64601242T>A	ENSP00000345133:p.Arg845Trp	42.0	0.0		27.0	11.0	NM_017525		Missense_Mutation	SNP	ENST00000342711.5	hg19	CCDS31601.1	.	.	.	.	.	.	.	.	.	.	T	16.04	3.009772	0.54361	.	.	ENSG00000171219	ENST00000342711	T	0.68331	-0.32	5.18	2.68	0.31781	.	0.441757	0.19667	N	0.108849	T	0.60248	0.2254	N	0.08118	0	0.29738	N	0.83735	D	0.67145	0.996	P	0.62885	0.908	T	0.59563	-0.7431	10	0.66056	D	0.02	.	9.8156	0.40851	0.0:0.0:0.3265:0.6735	.	845	Q6DT37	MRCKG_HUMAN	W	845	ENSP00000345133:R845W	ENSP00000345133:R845W	R	-	1	2	CDC42BPG	64357818	0.968000	0.33430	1.000000	0.80357	0.096000	0.18686	1.141000	0.31528	0.917000	0.36895	-0.429000	0.05907	AGG	.	.		0.667	CDC42BPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105352.4	XM_290516		A	64601242	T	A	64601242	3	1	344	1	0	0	0	0	1	0	0	0	3076	1550	54	4	2186	4	CDC42BPG	11	64601242	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	64491	64601242	70405274	835	48198										
PPP2R5B	5526	hgsc.bcm.edu	37	chr11	64699068	64699068	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	caaatactggccaaaaacctGcacccagaaggaggtatgaa	9	10	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:64699068G>C	ENST00000164133.2	+	10	1605	c.983G>C	c.(982-984)tGc>tCc	p.C328S		NM_006244.3	NP_006235.1	Q15173	2A5B_HUMAN	protein phosphatase 2, regulatory subunit B', beta	328					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(9)|ovary(2)	21						CCAAAAACCTGCACCCAGAAG	0.597																																					p.C328S		Atlas-SNP	.											.	PPP2R5B	47	.	0			c.G983C						.						39	37	37					11																	64699068		2201	4297	6498	SO:0001583	missense	5526	exon10			AAACCTGCACCCA	L42374	CCDS8085.1	11q12	2010-06-18	2010-04-14		ENSG00000068971	ENSG00000068971		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9310	protein-coding gene	gene with protein product	"PP2A, B subunit, B' beta isoform", "PP2A, B subunit, B56 beta isoform", "PP2A, B subunit, PR61 beta isoform", "PP2A, B subunit, R5 beta isoform", "serine/threonine protein phosphatase 2A, 56 kDa regulatory subunit, beta isoform"	601644	"protein phosphatase 2, regulatory subunit B (B56), beta isoform", "protein phosphatase 2, regulatory subunit B', beta isoform"			7592815	Standard	NM_006244		Approved	FLJ35411, B56B, PR61B	uc001oby.3	Q15173	OTTHUMG00000150043	ENST00000164133.2:c.983G>C	chr11.hg19:g.64699068G>C	ENSP00000164133:p.Cys328Ser	59.0	0.0		49.0	16.0	NM_006244	Q13853	Missense_Mutation	SNP	ENST00000164133.2	hg19	CCDS8085.1	.	.	.	.	.	.	.	.	.	.	G	9.455	1.091616	0.20471	.	.	ENSG00000068971	ENST00000164133;ENST00000527441	.	.	.	4.79	3.88	0.44766	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.43831	0.1265	L	0.33792	1.035	0.58432	D	0.999997	B	0.21821	0.061	B	0.25614	0.062	T	0.38329	-0.9666	9	0.46703	T	0.11	-10.7544	7.2705	0.26254	0.1958:0.0:0.8042:0.0	.	328	Q15173	2A5B_HUMAN	S	328	.	ENSP00000164133:C328S	C	+	2	0	PPP2R5B	64455644	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.006000	0.57083	1.378000	0.46305	0.462000	0.41574	TGC	.	.		0.597	PPP2R5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385465.1	NM_006244		C	64699068	G	C	64699068	3	2	344	1	0	0	0	0	1	0	0	0	12405	1319	46	4	1017	4	PPP2R5B	11	64699068	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	97826	64699068	70307448	836	48199										
DRAP1	10589	hgsc.bcm.edu	37	chr11	65688799	65688799	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tctcctgccttctgccctgcAgccccccgacacccttcctg	6	22	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:65688799A>T	ENST00000312515.2	+	7	757		c.e7-1		DRAP1_ENST00000376991.2_Splice_Site|C11orf68_ENST00000449692.3_5'Flank|C11orf68_ENST00000530188.1_5'Flank|DRAP1_ENST00000532933.1_Splice_Site|C11orf68_ENST00000438576.2_5'Flank|DRAP1_ENST00000527119.1_Splice_Site	NM_006442.3	NP_006433.2	Q14919	NC2A_HUMAN	DR1-associated protein 1 (negative cofactor 2 alpha)						negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(1)	5				READ - Rectum adenocarcinoma(159;0.166)		TCTGCCCTGCAGCCCCCCGAC	0.667																																					.		Atlas-SNP	.											.	DRAP1	18	.	0			c.513-2A>T						.						55	54	54					11																	65688799		2201	4296	6497	SO:0001630	splice_region_variant	10589	exon7			CCCTGCAGCCCCC	U41843	CCDS8123.1	11q13	2010-09-29			ENSG00000175550	ENSG00000175550			3019	protein-coding gene	gene with protein product	"negative cofactor 2 alpha", "DR1-associated corepressor"	602289				8608938	Standard	NM_006442		Approved	NC2-alpha	uc001ogj.2	Q14919	OTTHUMG00000166723	ENST00000312515.2:c.513-1A>T	chr11.hg19:g.65688799A>T		168.0	0.0		148.0	80.0	NM_006442	Q13448	Splice_Site	SNP	ENST00000312515.2	hg19	CCDS8123.1	.	.	.	.	.	.	.	.	.	.	A	10.28	1.307140	0.23821	.	.	ENSG00000175550	ENST00000312515;ENST00000525501;ENST00000376991;ENST00000527119;ENST00000532933	.	.	.	4.75	4.75	0.60458	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.9426	0.47283	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DRAP1	65445375	1.000000	0.71417	0.961000	0.40146	0.095000	0.18619	3.333000	0.52090	1.921000	0.55644	0.533000	0.62120	.	.	.		0.667	DRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391197.2	NM_006442	Intron	T	65688799	A	T	65688799	5	4	344	1	0	0	0	0	0	0	1	0	4757	202	7	4	537	4	DRAP1	11	65688799	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	989731	65688799	69317717	837	48200										
FOLR1	2348	hgsc.bcm.edu	37	chr11	71907162	71907162	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccatgagtggggctgggcccTgggcagcctggcctttcctg	16	13	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:71907162T>A	ENST00000393679.1	+	5	1151	c.715T>A	c.(715-717)Tgg>Agg	p.W239R	RP11-807H22.7_ENST00000378140.3_RNA|FOLR1_ENST00000393676.3_Missense_Mutation_p.W239R|FOLR1_ENST00000393681.2_Missense_Mutation_p.W239R|FOLR1_ENST00000312293.4_Missense_Mutation_p.W239R			P15328	FOLR1_HUMAN	folate receptor 1 (adult)	239					cell death (GO:0008219)|folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|receptor-mediated endocytosis (GO:0006898)	anchored component of external side of plasma membrane (GO:0031362)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|receptor activity (GO:0004872)			cervix(2)|endometrium(1)|large_intestine(7)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	14					Methotrexate(DB00563)	GGCTGGGCCCTGGGCAGCCTG	0.607																																					p.W239R		Atlas-SNP	.											.	FOLR1	22	.	0			c.T715A						.						62	55	57					11																	71907162		2200	4293	6493	SO:0001583	missense	2348	exon4			GGGCCCTGGGCAG	J05013	CCDS8211.1	11q13.3-q14.1	2010-04-09			ENSG00000110195	ENSG00000110195			3791	protein-coding gene	gene with protein product		136430		FOLR		1717147	Standard	NM_000802		Approved		uc001osa.2	P15328		ENST00000393679.1:c.715T>A	chr11.hg19:g.71907162T>A	ENSP00000377284:p.Trp239Arg	99.0	0.0		84.0	39.0	NM_016729	Q53EW2|Q6FGT8|Q6LC90|Q9UCT2	Missense_Mutation	SNP	ENST00000393679.1	hg19	CCDS8211.1	.	.	.	.	.	.	.	.	.	.	t	6.465	0.453873	0.12283	.	.	ENSG00000110195	ENST00000312293;ENST00000393681;ENST00000393679;ENST00000393676	T;T;T;T	0.73152	-0.72;-0.72;-0.72;-0.72	4.55	-1.08	0.09936	.	4.012110	0.00357	N	0.000022	T	0.48554	0.1506	N	0.11255	0.115	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21280	-1.0250	10	0.25106	T	0.35	-27.2398	3.239	0.06774	0.2954:0.3172:0.0:0.3874	.	239	P15328	FOLR1_HUMAN	R	239	ENSP00000308137:W239R;ENSP00000377286:W239R;ENSP00000377284:W239R;ENSP00000377281:W239R	ENSP00000308137:W239R	W	+	1	0	FOLR1	71584810	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.436000	0.02421	-0.422000	0.07405	-0.468000	0.05107	TGG	.	.		0.607	FOLR1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396773.1	NM_016725		A	71907162	T	A	71907162	3	1	344	1	0	0	0	0	1	0	0	0	5989	1580	55	4	729	4	FOLR1	11	71907162	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	6218363	71907162	63099354	838	48201										
ATG16L2	89849	hgsc.bcm.edu	37	chr11	72538273	72538273	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctttcctactgtaatgacgtGgtgtgtggggaccatatcat	11	8	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:72538273G>T	ENST00000321297.5	+	14	1545	c.1407G>T	c.(1405-1407)gtG>gtT	p.V469V	ATG16L2_ENST00000534905.1_Intron	NM_033388.1	NP_203746.1	Q8NAA4	A16L2_HUMAN	autophagy related 16-like 2 (S. cerevisiae)	469					autophagy (GO:0006914)|negative stranded viral RNA replication (GO:0039689)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(2)|large_intestine(1)|lung(9)	14			BRCA - Breast invasive adenocarcinoma(5;2.73e-06)			GTAATGACGTGGTGTGTGGGG	0.597																																					p.V469V		Atlas-SNP	.											.	ATG16L2	26	.	0			c.G1407T						.						127	107	114					11																	72538273		2200	4293	6493	SO:0001819	synonymous_variant	89849	exon14			TGACGTGGTGTGT	AK024423	CCDS31634.1	11q13.4	2014-02-12	2012-06-06		ENSG00000168010	ENSG00000168010		"WD repeat domain containing"	25464	protein-coding gene	gene with protein product			"ATG16 autophagy related 16-like 2 (S. cerevisiae)"			11214971	Standard	XM_005274378		Approved	FLJ00012, WDR80, ATG16B	uc001otd.3	Q8NAA4	OTTHUMG00000167961	ENST00000321297.5:c.1407G>T	chr11.hg19:g.72538273G>T		90.0	0.0		68.0	24.0	NM_033388	A5PL30|B2RPK5|Q658V4|Q6PID3|Q8NBG0	Silent	SNP	ENST00000321297.5	hg19	CCDS31634.1	.	.	.	.	.	.	.	.	.	.	G	9.685	1.150409	0.21371	.	.	ENSG00000168010	ENST00000535830;ENST00000540222	.	.	.	5.93	5.03	0.67393	.	.	.	.	.	T	0.65585	0.2705	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.64605	-0.6368	4	.	.	.	.	12.9444	0.58364	0.0779:0.0:0.9221:0.0	.	.	.	.	C	307;247	.	.	G	+	1	0	ATG16L2	72215921	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.182000	0.42556	1.529000	0.49120	0.561000	0.74099	GGT	.	.		0.597	ATG16L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397305.1	NM_033388		T	72538273	G	T	72538273	2	4	344	1	0	0	0	0	0	0	0	1	1092	1335	47	3		3	ATG16L2	11	72538273	Silent	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	631111	72538273	62468243	839	48202										
ARHGEF17	9828	hgsc.bcm.edu	37	chr11	73066691	73066691	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cctgcctttctcaagttcctAgaggtactgtgggctagggc	12	11	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:73066691A>G	ENST00000263674.3	+	4	3917	c.3567A>G	c.(3565-3567)ctA>ctG	p.L1189L	AP002761.1_ENST00000582555.1_RNA	NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	1189	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(2)	32						TCAAGTTCCTAGAGGTACTGT	0.567																																					p.L1189L		Atlas-SNP	.											.	ARHGEF17	117	.	0			c.A3567G						.						84	82	83					11																	73066691		2200	4293	6493	SO:0001819	synonymous_variant	9828	exon4			GTTCCTAGAGGTA	AF378754	CCDS8221.1	11q13.3	2011-11-16			ENSG00000110237	ENSG00000110237		"Rho guanine nucleotide exchange factors"	21726	protein-coding gene	gene with protein product	"Rho-specific guanine-nucleotide exchange factor 164 kDa", "tumor endothelial marker 4"					11559528, 12071859	Standard	NM_014786		Approved	TEM4, KIAA0337, p164-RhoGEF	uc001otu.3	Q96PE2	OTTHUMG00000167971	ENST00000263674.3:c.3567A>G	chr11.hg19:g.73066691A>G		57.0	0.0		53.0	20.0	NM_014786	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Silent	SNP	ENST00000263674.3	hg19	CCDS8221.1																																																																																			.	.		0.567	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786		G	73066691	A	G	73066691	2	3	344	1	0	0	0	0	0	0	0	1	900	407	15	2		2	ARHGEF17	11	73066691	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	528418	73066691	61939825	840	48203										
OR2AT4	341152	hgsc.bcm.edu	37	chr11	74800166	74800166	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agcccatgagggtctgggggGtggtgtcagagcaggaggcc	20	8	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:74800166G>A	ENST00000305159.3	-	1	633	c.593C>T	c.(592-594)aCc>aTc	p.T198I		NM_001005285.1	NP_001005285.1	A6NND4	O2AT4_HUMAN	olfactory receptor, family 2, subfamily AT, member 4	198						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(2)	12						GGTCTGGGGGGTGGTGTCAGA	0.562																																					p.T198I		Atlas-SNP	.											.	OR2AT4	32	.	0			c.C593T						.						55	49	51					11																	74800166		2200	4293	6493	SO:0001583	missense	341152	exon1			TGGGGGGTGGTGT	BK004820	CCDS31639.1	11q13.4	2012-08-09			ENSG00000171561	ENSG00000171561		"GPCR / Class A : Olfactory receptors"	19620	protein-coding gene	gene with protein product							Standard	NM_001005285		Approved		uc010rro.2	A6NND4	OTTHUMG00000165370	ENST00000305159.3:c.593C>T	chr11.hg19:g.74800166G>A	ENSP00000304846:p.Thr198Ile	58.0	0.0		55.0	24.0	NM_001005285	B9EGZ8	Missense_Mutation	SNP	ENST00000305159.3	hg19	CCDS31639.1	.	.	.	.	.	.	.	.	.	.	G	10.84	1.464984	0.26335	.	.	ENSG00000171561	ENST00000305159	T	0.37584	1.19	5.26	-0.153	0.13403	GPCR, rhodopsin-like superfamily (1);	0.309092	0.18006	U	0.154745	T	0.23611	0.0571	N	0.25957	0.775	0.09310	N	1	B	0.26147	0.143	B	0.36567	0.228	T	0.23726	-1.0180	10	0.45353	T	0.12	.	2.4318	0.04473	0.1617:0.2508:0.4485:0.1391	.	198	A6NND4	O2AT4_HUMAN	I	198	ENSP00000304846:T198I	ENSP00000304846:T198I	T	-	2	0	OR2AT4	74477814	0.000000	0.05858	0.001000	0.08648	0.778000	0.44026	-3.404000	0.00482	-0.200000	0.10300	0.650000	0.86243	ACC	.	.		0.562	OR2AT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383734.1	NM_001005285		A	74800166	G	A	74800166	3	1	344	1	0	0	0	0	1	0	0	0	10996	1261	44	3	372	3	OR2AT4	11	74800166	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1733475	74800166	60206350	841	48204										
KLHL35	283212	hgsc.bcm.edu	37	chr11	75139660	75139660	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgaccacgatcacttcagctAggtccatgaatctggcgtgc	10	12	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:75139660A>G	ENST00000539798.1	-	2	892	c.893T>C	c.(892-894)cTa>cCa	p.L298P	KLHL35_ENST00000376292.4_Missense_Mutation_p.L78P	NM_001039548.2	NP_001034637.2	Q6PF15	KLH35_HUMAN	kelch-like family member 35	298										lung(2)|stomach(1)	3						CACTTCAGCTAGGTCCATGAA	0.627																																					p.L298P	Colon(77;683 1691 18820 23811)	Atlas-SNP	.											.	KLHL35	15	.	0			c.T893C						.						37	43	41					11																	75139660		2039	4170	6209	SO:0001583	missense	283212	exon2			TCAGCTAGGTCCA		CCDS44685.1, CCDS44685.2	11q13.4	2013-02-22	2013-02-22		ENSG00000149243	ENSG00000149243		"Kelch-like", "BTB/POZ domain containing"	26597	protein-coding gene	gene with protein product			"kelch-like 35 (Drosophila)"				Standard	NM_001039548		Approved	FLJ33790	uc001owm.2	Q6PF15	OTTHUMG00000133573	ENST00000539798.1:c.893T>C	chr11.hg19:g.75139660A>G	ENSP00000438526:p.Leu298Pro	37.0	0.0		31.0	17.0	NM_001039548	A2RU06|F5H412|Q86XM7|Q8NBB1	Missense_Mutation	SNP	ENST00000539798.1	hg19	CCDS44685.2	.	.	.	.	.	.	.	.	.	.	A	17.30	3.354756	0.61293	.	.	ENSG00000149243	ENST00000376292;ENST00000539798	T;T	0.72835	-0.69;-0.57	5.41	1.57	0.23409	.	0.427892	0.20925	N	0.083218	T	0.80491	0.4633	M	0.86028	2.79	0.53005	D	0.999963	D	0.69078	0.997	D	0.65010	0.931	T	0.76280	-0.3017	10	0.49607	T	0.09	.	6.0915	0.19997	0.5699:0.1473:0.0:0.2829	.	78	Q6PF15	KLH35_HUMAN	P	78;298	ENSP00000365469:L78P;ENSP00000438526:L298P	ENSP00000365469:L78P	L	-	2	0	KLHL35	74817308	0.879000	0.30193	0.878000	0.34440	0.998000	0.95712	1.535000	0.36061	0.089000	0.17243	0.459000	0.35465	CTA	.	.		0.627	KLHL35-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_173583		G	75139660	A	G	75139660	3	3	344	1	0	0	0	0	1	0	0	0	8397	420	15	2	878	2	KLHL35	11	75139660	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	339494	75139660	59866856	842	48205										
MYO7A	4647	hgsc.bcm.edu	37	chr11	76903162	76903162	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cccagtgcgagcagtacgccAaggagcagggcgcccaggag	16	13	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:76903162A>T	ENST00000409709.3	+	31	4263	c.3991A>T	c.(3991-3993)Aag>Tag	p.K1331*	MYO7A_ENST00000458637.2_Nonsense_Mutation_p.K1331*|MYO7A_ENST00000409619.2_Nonsense_Mutation_p.K1320*	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	1331	FERM 1. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						GCAGTACGCCAAGGAGCAGGG	0.672											OREG0021258	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K1331X		Atlas-SNP	.											MYO7A,NS,carcinoma,0,1	MYO7A	164	.	0			c.A3991T						.						49	57	54					11																	76903162		2107	4207	6314	SO:0001587	stop_gained	4647	exon31			TACGCCAAGGAGC	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"A-kinase anchor proteins", "Myosins / Myosin superfamily : Class VII"	7606	protein-coding gene	gene with protein product		276903	"myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.3991A>T	chr11.hg19:g.76903162A>T	ENSP00000386331:p.Lys1331*	128.0	0.0	1171	110.0	57.0	NM_000260	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Nonsense_Mutation	SNP	ENST00000409709.3	hg19	CCDS53683.1	.	.	.	.	.	.	.	.	.	.	A	38	7.194313	0.98125	.	.	ENSG00000137474	ENST00000409709;ENST00000458637;ENST00000409619;ENST00000545136;ENST00000358342;ENST00000343356;ENST00000341717;ENST00000458169	.	.	.	4.62	4.62	0.57501	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.0222	0.64563	1.0:0.0:0.0:0.0	.	.	.	.	X	1331;1331;1320;542;1330;1300;1207;512	.	ENSP00000345075:K1207X	K	+	1	0	MYO7A	76580810	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	8.953000	0.93041	1.710000	0.51325	0.386000	0.25728	AAG	.	.		0.672	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260		T	76903162	A	T	76903162	4	4	344	1	0	0	0	0	0	1	0	0	10091	131	5	4	4143	4	MYO7A	11	76903162	Nonsense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1763502	76903162	58103354	843	48206										
ODZ4	26011	hgsc.bcm.edu	37	chr11	78614413	78614413	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctctccggagagcgagtggtCcgtgggggccgggctggggt	21	10	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:78614413C>G	ENST00000278550.7	-	7	1111	c.649G>C	c.(649-651)Gac>Cac	p.D217H		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	217	Teneurin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00694}.				cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										AGCGAGTGGTCCGTGGGGGCC	0.701																																					p.D217H		Atlas-SNP	.											.	.	.	.	0			c.G649C						.						16	18	18					11																	78614413		692	1591	2283	SO:0001583	missense	26011	exon7			AGTGGTCCGTGGG	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"odz, odd Oz/ten-m homolog 4 (Drosophila)"	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.649G>C	chr11.hg19:g.78614413C>G	ENSP00000278550:p.Asp217His	39.0	0.0		19.0	10.0	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Missense_Mutation	SNP	ENST00000278550.7	hg19	CCDS44688.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.796417	0.90453	.	.	ENSG00000149256	ENST00000278550;ENST00000533074	T;T	0.47869	0.83;0.83	5.42	5.42	0.78866	Teneurin intracellular, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.64875	0.2638	L	0.50333	1.59	0.53688	D	0.999978	D	0.89917	1.0	D	0.91635	0.999	T	0.61357	-0.7079	9	.	.	.	.	19.2039	0.93722	0.0:1.0:0.0:0.0	.	217	Q6N022	TEN4_HUMAN	H	217;62	ENSP00000278550:D217H;ENSP00000432705:D62H	.	D	-	1	0	ODZ4	78292061	1.000000	0.71417	0.994000	0.49952	0.944000	0.59088	6.700000	0.74619	2.543000	0.85770	0.561000	0.74099	GAC	.	.		0.701	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			G	78614413	C	G	78614413	3	3	344	1	0	0	0	0	1	0	0	0	10846	855	30	4	7772	4	ODZ4	11	78614413	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1711251	78614413	56392103	844	48207										
SYTL2	54843	hgsc.bcm.edu	37	chr11	85436399	85436399	+	Intron	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggaacaagatgagcatcctgGggaaaaagcatatcttgggg	14	6	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:85436399G>T	ENST00000528231.1	-	7	1737				SYTL2_ENST00000525423.1_Silent_p.P367P|SYTL2_ENST00000316356.4_Intron|SYTL2_ENST00000527523.1_Intron|SYTL2_ENST00000354566.3_Silent_p.P367P|SYTL2_ENST00000524452.1_Intron|SYTL2_ENST00000389960.4_Intron|SYTL2_ENST00000359152.5_Silent_p.P891P	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2						exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		GAGCATCCTGGGGAAAAAGCA	0.493																																					p.P367P		Atlas-SNP	.											.	SYTL2	231	.	0			c.C1101A						.						49	52	51					11																	85436399		2203	4299	6502	SO:0001627	intron_variant	54843	exon1			ATCCTGGGGAAAA	AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"chromosome 11 synaptotagmin", "breast cancer-associated antigen SGA-72M", "protein phosphatase 1, regulatory subunit 151"	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.1459+2539C>A	chr11.hg19:g.85436399G>T		58.0	0.0		53.0	29.0	NM_206927	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Silent	SNP	ENST00000528231.1	hg19	CCDS53688.1																																																																																			.	.		0.493	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927		T	85436399	G	T	85436399	1	4	344	0	1	0	0	0	0	0	0	0	15498	1219	43	3		3	SYTL2	11	85436399	Intron	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	6821986	85436399	49570117	845	48208										
CCDC81	60494	hgsc.bcm.edu	37	chr11	86103710	86103710	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cgttccatttccatgaaacaAaatgtggagtttacattcaa	6	8	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:86103710A>T	ENST00000445632.2	+	4	698	c.426A>T	c.(424-426)caA>caT	p.Q142H	CCDC81_ENST00000528728.1_5'Flank|CCDC81_ENST00000278487.3_5'UTR|CCDC81_ENST00000354755.1_Intron	NM_001156474.1	NP_001149946.1	Q6ZN84	CCD81_HUMAN	coiled-coil domain containing 81	142										kidney(3)|large_intestine(8)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	20		Acute lymphoblastic leukemia(157;5.51e-06)|all_hematologic(158;0.00535)				CCATGAAACAAAATGTGGAGT	0.403																																					p.Q142H		Atlas-SNP	.											.	CCDC81	89	.	0			c.A426T						.						226	187	199					11																	86103710		692	1591	2283	SO:0001583	missense	60494	exon4			GAAACAAAATGTG	AK131331	CCDS8276.1, CCDS53691.1	11q14.2	2006-03-09			ENSG00000149201	ENSG00000149201			26281	protein-coding gene	gene with protein product							Standard	NM_001156474		Approved	FLJ16339, FLJ23514	uc001pbx.2	Q6ZN84	OTTHUMG00000167213	ENST00000445632.2:c.426A>T	chr11.hg19:g.86103710A>T	ENSP00000415528:p.Gln142His	130.0	0.0		106.0	38.0	NM_001156474	A0AVL7|Q53FW3|Q9H5E5	Missense_Mutation	SNP	ENST00000445632.2	hg19	CCDS53691.1	.	.	.	.	.	.	.	.	.	.	A	12.43	1.936381	0.34189	.	.	ENSG00000149201	ENST00000445632	T	0.49720	0.77	5.82	-2.38	0.06622	.	.	.	.	.	T	0.51669	0.1688	L	0.59436	1.845	0.22835	N	0.998676	D	0.53151	0.958	P	0.54312	0.748	T	0.50162	-0.8860	8	.	.	.	-4.9231	9.3772	0.38290	0.2676:0.144:0.5884:0.0	.	142	Q6ZN84	CCD81_HUMAN	H	142	ENSP00000415528:Q142H	.	Q	+	3	2	CCDC81	85781358	0.816000	0.29132	0.001000	0.08648	0.003000	0.03518	0.326000	0.19646	-0.422000	0.07405	-0.408000	0.06270	CAA	.	.		0.403	CCDC81-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393756.1	NM_021827		T	86103710	A	T	86103710	3	4	344	1	0	0	0	0	1	0	0	0	2857	11	1	4	440	4	CCDC81	11	86103710	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	667311	86103710	48902806	846	48209										
CCDC81	60494	hgsc.bcm.edu	37	chr11	86108753	86108753	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaaaggaagtgcaagttaaaAgaccagtcagacaaagaaga	11	5	1	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:86108753A>T	ENST00000445632.2	+	6	998	c.726A>T	c.(724-726)aaA>aaT	p.K242N	CCDC81_ENST00000528728.1_Missense_Mutation_p.K25N|CCDC81_ENST00000278487.3_Missense_Mutation_p.K25N|CCDC81_ENST00000354755.1_Missense_Mutation_p.K152N	NM_001156474.1	NP_001149946.1	Q6ZN84	CCD81_HUMAN	coiled-coil domain containing 81	242										kidney(3)|large_intestine(8)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	20		Acute lymphoblastic leukemia(157;5.51e-06)|all_hematologic(158;0.00535)				GCAAGTTAAAAGACCAGTCAG	0.448																																					p.K242N		Atlas-SNP	.											.	CCDC81	89	.	0			c.A726T						.						113	108	110					11																	86108753		2202	4299	6501	SO:0001583	missense	60494	exon6			GTTAAAAGACCAG	AK131331	CCDS8276.1, CCDS53691.1	11q14.2	2006-03-09			ENSG00000149201	ENSG00000149201			26281	protein-coding gene	gene with protein product							Standard	NM_001156474		Approved	FLJ16339, FLJ23514	uc001pbx.2	Q6ZN84	OTTHUMG00000167213	ENST00000445632.2:c.726A>T	chr11.hg19:g.86108753A>T	ENSP00000415528:p.Lys242Asn	45.0	0.0		40.0	16.0	NM_001156474	A0AVL7|Q53FW3|Q9H5E5	Missense_Mutation	SNP	ENST00000445632.2	hg19	CCDS53691.1	.	.	.	.	.	.	.	.	.	.	A	13.62	2.292792	0.40594	.	.	ENSG00000149201	ENST00000354755;ENST00000278487;ENST00000445632;ENST00000528728	T;T;T;T	0.37235	1.21;1.21;1.21;1.21	5.29	4.14	0.48551	.	0.482292	0.21359	N	0.075834	T	0.35189	0.0923	M	0.67953	2.075	0.09310	N	1	B;B;B	0.27997	0.197;0.153;0.009	B;B;B	0.28465	0.09;0.081;0.011	T	0.21759	-1.0236	9	.	.	.	-9.8979	9.4595	0.38776	0.8212:0.1788:0.0:0.0	.	25;242;152	Q6ZN84-3;Q6ZN84;Q6ZN84-2	.;CCD81_HUMAN;.	N	152;25;242;25	ENSP00000346800:K152N;ENSP00000278487:K25N;ENSP00000415528:K242N;ENSP00000437165:K25N	.	K	+	3	2	CCDC81	85786401	0.998000	0.40836	0.039000	0.18376	0.081000	0.17604	1.967000	0.40491	0.929000	0.37192	0.460000	0.39030	AAA	.	.		0.448	CCDC81-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393756.1	NM_021827		T	86108753	A	T	86108753	3	4	344	1	0	0	0	0	1	0	0	0	2857	69	3	4	748	4	CCDC81	11	86108753	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	5043	86108753	48897763	847	48210										
CTSC	1075	hgsc.bcm.edu	37	chr11	88042455	88042455	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	attgatagctttcacaaagtTgtgatcatacttgtagagcc	8	7	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:88042455T>A	ENST00000227266.5	-	4	631	c.517A>T	c.(517-519)Aac>Tac	p.N173Y		NM_001814.4	NP_001805	P53634	CATC_HUMAN	cathepsin C	173					aging (GO:0007568)|immune response (GO:0006955)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of proteolysis involved in cellular protein catabolic process (GO:1903052)|proteolysis (GO:0006508)|response to organic substance (GO:0010033)|T cell mediated cytotoxicity (GO:0001913)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)	chaperone binding (GO:0051087)|chloride ion binding (GO:0031404)|cysteine-type peptidase activity (GO:0008234)|peptidase activator activity involved in apoptotic process (GO:0016505)|phosphatase binding (GO:0019902)|serine-type endopeptidase activity (GO:0004252)			large_intestine(7)|lung(8)|ovary(2)|prostate(3)|skin(2)	22		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				TTCACAAAGTTGTGATCATAC	0.363																																					p.N173Y		Atlas-SNP	.											.	CTSC	46	.	0			c.A517T						.						161	140	147					11																	88042455		2201	4299	6500	SO:0001583	missense	1075	exon4			CAAAGTTGTGATC	AK223038	CCDS8282.1, CCDS31654.1, CCDS44693.1	11q14.2	2014-09-17			ENSG00000109861	ENSG00000109861	3.4.14.1	"Cathepsins"	2528	protein-coding gene	gene with protein product	"dipeptidyl peptidase 1"	602365		PLS, PALS		7649281, 9092576	Standard	NM_148170		Approved	DPP1	uc001pck.4	P53634	OTTHUMG00000167290	ENST00000227266.5:c.517A>T	chr11.hg19:g.88042455T>A	ENSP00000227266:p.Asn173Tyr	73.0	0.0		55.0	23.0	NM_001814	A8K7V2|B5MDD5|Q2HIY8|Q53G93|Q71E75|Q71E76|Q7M4N9|Q7Z3G7|Q7Z5U7|Q8WY99|Q8WYA7|Q8WYA8	Missense_Mutation	SNP	ENST00000227266.5	hg19	CCDS8282.1	.	.	.	.	.	.	.	.	.	.	T	15.40	2.822601	0.50739	.	.	ENSG00000109861	ENST00000393302;ENST00000227266	D	0.84298	-1.83	6.02	-1.14	0.09741	.	0.643940	0.17443	N	0.174051	T	0.79240	0.4412	L	0.43152	1.355	0.09310	N	1	B;B	0.31054	0.148;0.306	B;B	0.37198	0.163;0.243	T	0.66937	-0.5797	9	.	.	.	.	11.7393	0.51784	0.0:0.7265:0.0:0.2735	.	156;173	B4DJQ8;P53634	.;CATC_HUMAN	Y	156;173	ENSP00000227266:N173Y	.	N	-	1	0	CTSC	87682103	0.077000	0.21312	0.003000	0.11579	0.584000	0.36387	0.391000	0.20784	-0.136000	0.11475	0.528000	0.53228	AAC	.	.		0.363	CTSC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394019.2	NM_001814		A	88042455	T	A	88042455	3	1	344	1	0	0	0	0	1	0	0	0	4033	1812	63	4	890	4	CTSC	11	88042455	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1933702	88042455	46964061	848	48211										
NOX4	50507	hgsc.bcm.edu	37	chr11	89069089	89069089	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaacagtcttgaattcagtgCatgatatttttctccaatta	5	7	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:89069089C>G	ENST00000263317.4	-	17	1778	c.1540G>C	c.(1540-1542)Gca>Cca	p.A514P	NOX4_ENST00000532825.1_Missense_Mutation_p.A450P|NOX4_ENST00000424319.1_Missense_Mutation_p.A490P|NOX4_ENST00000375979.3_Missense_Mutation_p.A207P|NOX4_ENST00000527626.1_Missense_Mutation_p.A327P|NOX4_ENST00000413594.2_Missense_Mutation_p.A535P|NOX4_ENST00000528341.1_Missense_Mutation_p.A489P|NOX4_ENST00000535633.1_Missense_Mutation_p.A490P|NOX4_ENST00000343727.5_Missense_Mutation_p.A490P|NOX4_ENST00000534731.1_Missense_Mutation_p.A474P|NOX4_ENST00000531342.1_Missense_Mutation_p.A167P|NOX4_ENST00000542487.1_Missense_Mutation_p.A490P|NOX4_ENST00000525196.1_Missense_Mutation_p.A278P|NOX4_ENST00000527956.1_Missense_Mutation_p.A490P			Q9NPH5	NOX4_HUMAN	NADPH oxidase 4	514	Mediates interaction with TLR4.				bone resorption (GO:0045453)|cardiac muscle cell differentiation (GO:0055007)|cell aging (GO:0007569)|cell morphogenesis (GO:0000902)|cellular response to cAMP (GO:0071320)|cellular response to gamma radiation (GO:0071480)|cellular response to glucose stimulus (GO:0071333)|cellular response to transforming growth factor beta stimulus (GO:0071560)|homocysteine metabolic process (GO:0050667)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|oxidation-reduction process (GO:0055114)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of stress fiber assembly (GO:0051496)|reactive oxygen species metabolic process (GO:0072593)|response to hypoxia (GO:0001666)|superoxide anion generation (GO:0042554)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|modified amino acid binding (GO:0072341)|NAD(P)H oxidase activity (GO:0016174)|nucleotide binding (GO:0000166)|oxygen sensor activity (GO:0019826)|superoxide-generating NADPH oxidase activity (GO:0016175)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(20)|ovary(2)|prostate(3)|skin(2)	44		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)				GAATTCAGTGCATGATATTTT	0.333																																					p.A514P		Atlas-SNP	.											.	NOX4	101	.	0			c.G1540C						.						70	70	70					11																	89069089		2201	4296	6497	SO:0001583	missense	50507	exon17			TCAGTGCATGATA	AF254621	CCDS8285.1, CCDS44695.1, CCDS44696.1, CCDS73361.1, CCDS73362.1	11q14.2-q21	2008-02-05			ENSG00000086991	ENSG00000086991			7891	protein-coding gene	gene with protein product		605261					Standard	NM_001143837		Approved	KOX-1, KOX	uc001pct.3	Q9NPH5	OTTHUMG00000167298	ENST00000263317.4:c.1540G>C	chr11.hg19:g.89069089C>G	ENSP00000263317:p.Ala514Pro	255.0	1.0		231.0	99.0	NM_016931	A8K715|B7Z520|E7EMD7|Q5K3R4|Q5K3R5|Q5K3R6|Q5K3R8|Q7Z7G3|Q86V92	Missense_Mutation	SNP	ENST00000263317.4	hg19	CCDS8285.1	.	.	.	.	.	.	.	.	.	.	C	10.73	1.432397	0.25813	.	.	ENSG00000086991	ENST00000424319;ENST00000535633;ENST00000343727;ENST00000534731;ENST00000525196;ENST00000263317;ENST00000532825;ENST00000527956;ENST00000542487;ENST00000527626;ENST00000528341;ENST00000413594;ENST00000531342;ENST00000375979	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.95307	-3.67;-3.67;-3.67;-3.67;-3.67;-3.67;-3.67;-3.67;-3.67;-3.34;-3.67;-3.67;-3.67;-3.67	4.33	2.42	0.29668	Ferric reductase, NAD binding (1);	0.308515	0.35235	N	0.003357	D	0.85860	0.5795	N	0.11845	0.185	0.31079	N	0.712156	B;B;B;B;B;B;B;B	0.28584	0.001;0.001;0.001;0.216;0.0;0.003;0.001;0.0	B;B;B;B;B;B;B;B	0.28465	0.005;0.008;0.006;0.09;0.001;0.002;0.006;0.005	T	0.79029	-0.1970	9	.	.	.	-4.9072	9.8607	0.41112	0.0:0.8277:0.0:0.1723	.	450;327;489;278;167;207;474;514	E9PMY6;E9PR43;E9PPP2;E9PI95;Q9NPH5-3;Q9NPH5-4;Q9NPH5-6;Q9NPH5	.;.;.;.;.;.;.;NOX4_HUMAN	P	490;490;490;474;278;514;450;490;490;327;489;535;167;207	ENSP00000412446:A490P;ENSP00000440172:A490P;ENSP00000344747:A490P;ENSP00000436892:A474P;ENSP00000436716:A278P;ENSP00000263317:A514P;ENSP00000434924:A450P;ENSP00000433797:A490P;ENSP00000439373:A490P;ENSP00000436093:A327P;ENSP00000436970:A489P;ENSP00000405705:A535P;ENSP00000435039:A167P;ENSP00000365146:A207P	.	A	-	1	0	NOX4	88708737	0.995000	0.38212	0.892000	0.35008	0.899000	0.52679	2.824000	0.48088	0.379000	0.24794	-0.244000	0.11960	GCA	.	.		0.333	NOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394054.1	NM_016931		G	89069089	C	G	89069089	3	3	344	1	0	0	0	0	1	0	0	0	10567	710	25	4	204	4	NOX4	11	89069089	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1026634	89069089	45937427	849	48212										
NAALAD2	10003	hgsc.bcm.edu	37	chr11	89907042	89907042	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaatcactgtatgaaagctgGttggaaaaagacccttcacc	8	9	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:89907042G>T	ENST00000534061.1	+	14	1691	c.1461G>T	c.(1459-1461)tgG>tgT	p.W487C	NAALAD2_ENST00000321955.4_Missense_Mutation_p.W454C|NAALAD2_ENST00000375944.3_Intron	NM_005467.3	NP_005458.1	Q9Y3Q0	NALD2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	487	NAALADase.				neurotransmitter catabolic process (GO:0042135)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|dipeptidyl-peptidase activity (GO:0008239)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|N-formylglutamate deformylase activity (GO:0050129)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(32)|pancreas(1)|prostate(3)|skin(5)|stomach(2)	59		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				ATGAAAGCTGGTTGGAAAAAG	0.393																																					p.W487C		Atlas-SNP	.											.	NAALAD2	113	.	0			c.G1461T						.						117	121	120					11																	89907042		2201	4299	6500	SO:0001583	missense	10003	exon14			AAGCTGGTTGGAA	AJ012370	CCDS8288.1, CCDS73364.1	11q14.3-q21	2011-08-16			ENSG00000077616	ENSG00000077616	3.4.17.21		14526	protein-coding gene	gene with protein product	"glutamate carboxypeptidase III"	611636				10085079	Standard	NM_005467		Approved	NAALADASE2, NAADALASE2, GPCIII	uc001pdf.4	Q9Y3Q0	OTTHUMG00000166368	ENST00000534061.1:c.1461G>T	chr11.hg19:g.89907042G>T	ENSP00000432481:p.Trp487Cys	103.0	0.0		103.0	46.0	NM_005467	B3KQR4|Q4KKV4|Q4VAM9	Missense_Mutation	SNP	ENST00000534061.1	hg19	CCDS8288.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.017389	0.75161	.	.	ENSG00000077616	ENST00000534061;ENST00000321955	T;T	0.40756	1.02;1.02	5.95	5.95	0.96441	Peptidase M28 (1);	0.000000	0.64402	D	0.000001	T	0.78547	0.4300	H	0.97186	3.955	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.84920	0.0853	9	.	.	.	-5.8978	20.3931	0.98965	0.0:0.0:1.0:0.0	.	487	Q9Y3Q0	NALD2_HUMAN	C	487;454	ENSP00000432481:W487C;ENSP00000320083:W454C	.	W	+	3	0	NAALAD2	89546690	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.044000	0.76578	2.824000	0.97209	0.655000	0.94253	TGG	.	.		0.393	NAALAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389424.2	NM_005467		T	89907042	G	T	89907042	3	4	344	1	0	0	0	0	1	0	0	0	10137	1270	44	3	1515	3	NAALAD2	11	89907042	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	837953	89907042	45099474	850	48213										
FAT3	120114	hgsc.bcm.edu	37	chr11	92523226	92523226	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agatcctgcagattgaagccAcagatagagatgagaagcac	11	8	0	6			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:92523226A>T	ENST00000298047.6	+	7	4470	c.4453A>T	c.(4453-4455)Aca>Tca	p.T1485S	FAT3_ENST00000409404.2_Missense_Mutation_p.T1485S|FAT3_ENST00000525166.1_Missense_Mutation_p.T1335S			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	1485	Cadherin 14. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				GATTGAAGCCACAGATAGAGA	0.473										TCGA Ovarian(4;0.039)																											p.T1485S		Atlas-SNP	.											.	FAT3	1822	.	0			c.A4453T						.						177	172	174					11																	92523226		2074	4226	6300	SO:0001583	missense	120114	exon7			GAAGCCACAGATA	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.4453A>T	chr11.hg19:g.92523226A>T	ENSP00000298047:p.Thr1485Ser	138.0	0.0		131.0	61.0	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	hg19		.	.	.	.	.	.	.	.	.	.	A	14.18	2.459033	0.43634	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.02345	4.33;4.33;4.33	6.17	6.17	0.99709	.	.	.	.	.	T	0.04318	0.0119	L	0.45352	1.415	0.80722	D	1	B	0.15930	0.015	B	0.12837	0.008	T	0.50285	-0.8846	9	0.25106	T	0.35	.	16.8222	0.85835	1.0:0.0:0.0:0.0	.	1485	Q8TDW7-3	.	S	1485;1485;1335	ENSP00000298047:T1485S;ENSP00000387040:T1485S;ENSP00000432586:T1335S	ENSP00000298047:T1485S	T	+	1	0	FAT3	92162874	0.987000	0.35691	1.000000	0.80357	0.872000	0.50106	4.756000	0.62205	2.371000	0.80710	0.533000	0.62120	ACA	.	.		0.473	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		T	92523226	A	T	92523226	3	4	344	1	0	0	0	0	1	0	0	0	5699	159	6	4	4479	4	FAT3	11	92523226	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2616184	92523226	42483290	851	48214										
HEPHL1	341208	hgsc.bcm.edu	37	chr11	93806484	93806484	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	attttttcaggcccagtcatCaaggcagaggtgggtgatac	12	8	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:93806484C>G	ENST00000315765.9	+	8	1391	c.1383C>G	c.(1381-1383)atC>atG	p.I461M		NM_001098672.1	NP_001092142.1	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	461	Plastocyanin-like 3.				copper ion transport (GO:0006825)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	61		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				GCCCAGTCATCAAGGCAGAGG	0.438																																					p.I461M		Atlas-SNP	.											.	HEPHL1	144	.	0			c.C1383G						.						55	51	52					11																	93806484		1895	4111	6006	SO:0001583	missense	341208	exon8			AGTCATCAAGGCA	BX641008	CCDS44710.1	11q21	2008-02-05			ENSG00000181333	ENSG00000181333			30477	protein-coding gene	gene with protein product							Standard	NM_001098672		Approved	DKFZp686F22190	uc001pep.2	Q6MZM0	OTTHUMG00000167751	ENST00000315765.9:c.1383C>G	chr11.hg19:g.93806484C>G	ENSP00000313699:p.Ile461Met	85.0	0.0		70.0	34.0	NM_001098672	Q3C1W7	Missense_Mutation	SNP	ENST00000315765.9	hg19	CCDS44710.1	.	.	.	.	.	.	.	.	.	.	C	16.42	3.117797	0.56505	.	.	ENSG00000181333	ENST00000315765	D	0.99695	-6.43	5.51	3.59	0.41128	Cupredoxin (2);Multicopper oxidase, type 3 (1);	0.055403	0.64402	D	0.000002	D	0.99687	0.9882	M	0.88310	2.945	0.34529	D	0.70899	D	0.65815	0.995	D	0.72075	0.976	D	0.98045	1.0384	10	0.72032	D	0.01	.	14.3632	0.66787	0.4029:0.5971:0.0:0.0	.	461	Q6MZM0	HPHL1_HUMAN	M	461	ENSP00000313699:I461M	ENSP00000313699:I461M	I	+	3	3	HEPHL1	93446132	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	1.730000	0.38125	0.646000	0.30693	0.650000	0.86243	ATC	.	.		0.438	HEPHL1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396103.2	XM_291947		G	93806484	C	G	93806484	3	3	344	1	0	0	0	0	1	0	0	0	7064	816	29	4	1413	4	HEPHL1	11	93806484	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1283258	93806484	41200032	852	48215										
FOLR4	390243	hgsc.bcm.edu	37	chr11	94040439	94040439	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cttacacatgcaaatccaacTggcgtggtggctgggactgg	13	10	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:94040439T>A	ENST00000440961.2	+	3	480	c.436T>A	c.(436-438)Tgg>Agg	p.W146R		NM_001199206.1	NP_001186135.1	A6ND01	JUNO_HUMAN	folate receptor 4, delta (putative)	153					cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	14						CAAATCCAACTGGCGTGGTGG	0.602																																					p.W153R		Atlas-SNP	.											.	FOLR4	31	.	0			c.T457A						.						92	100	97					11																	94040439		2197	4297	6494	SO:0001583	missense	390243	exon3			TCCAACTGGCGTG			11q14	2014-07-23	2012-12-07		ENSG00000183560	ENSG00000183560			32565	protein-coding gene	gene with protein product		615737	"folate receptor 4 (delta) homolog (mouse)"			11111049, 24739963	Standard	NM_001199206		Approved	Folbp3, JUNO	uc021qou.1	A6ND01		ENST00000440961.2:c.436T>A	chr11.hg19:g.94040439T>A	ENSP00000416935:p.Trp146Arg	97.0	0.0		65.0	30.0	NM_001199206		Missense_Mutation	SNP	ENST00000440961.2	hg19		.	.	.	.	.	.	.	.	.	.	T	18.49	3.636228	0.67130	.	.	ENSG00000183560	ENST00000440961	T	0.78707	-1.2	4.43	3.28	0.37604	.	0.000000	0.85682	D	0.000000	D	0.88062	0.6336	M	0.88570	2.965	0.51012	D	0.999904	D	0.89917	1.0	D	0.85130	0.997	D	0.88114	0.2827	10	0.87932	D	0	-32.3639	9.556	0.39339	0.0:0.0:0.1774:0.8226	.	146	A6ND01-2	.	R	146	ENSP00000416935:W146R	ENSP00000416935:W146R	W	+	1	0	FOLR4	93680087	1.000000	0.71417	0.978000	0.43139	0.111000	0.19643	7.192000	0.77771	0.830000	0.34757	0.402000	0.26972	TGG	.	.		0.602	FOLR4-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000396420.1	NM_001080486		A	94040439	T	A	94040439	3	1	344	1	0	0	0	0	1	0	0	0	5992	1580	55	4	446	4	FOLR4	11	94040439	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	233955	94040439	40966077	853	48216										
GPR83	10888	hgsc.bcm.edu	37	chr11	94113896	94113896	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cttccagaagaggtcagctgGctcagggaagtctggcaggc	15	10	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:94113896G>T	ENST00000243673.2	-	4	862	c.691C>A	c.(691-693)Cca>Aca	p.P231T	GPR83_ENST00000539203.2_Missense_Mutation_p.P189T	NM_016540.3	NP_057624.3	Q9NYM4	GPR83_HUMAN	G protein-coupled receptor 83	231					response to glucocorticoid (GO:0051384)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide Y receptor activity (GO:0004983)			NS(1)|breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)	19		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				AGGTCAGCTGGCTCAGGGAAG	0.577																																					p.P231T		Atlas-SNP	.											.	GPR83	47	.	0			c.C691A						.						74	73	73					11																	94113896		2201	4298	6499	SO:0001583	missense	10888	exon4			CAGCTGGCTCAGG	AF236081	CCDS8297.1	11q21	2012-08-21	2003-07-30	2003-08-01	ENSG00000123901	ENSG00000123901		"GPCR / Class A : Orphans"	4523	protein-coding gene	gene with protein product		605569	"G protein-coupled receptor 72"	GPR72		10760605, 11060465	Standard	NM_016540		Approved		uc001pet.2	Q9NYM4	OTTHUMG00000167779	ENST00000243673.2:c.691C>A	chr11.hg19:g.94113896G>T	ENSP00000243673:p.Pro231Thr	41.0	0.0		31.0	12.0	NM_016540	B0M0K5|Q6NWR4|Q9P1Y8	Missense_Mutation	SNP	ENST00000243673.2	hg19	CCDS8297.1	.	.	.	.	.	.	.	.	.	.	G	18.76	3.692917	0.68271	.	.	ENSG00000123901	ENST00000243673;ENST00000539203	T;T	0.36520	1.25;1.25	5.41	5.41	0.78517	GPCR, rhodopsin-like superfamily (1);	0.107942	0.64402	D	0.000004	T	0.41834	0.1176	L	0.31926	0.97	0.80722	D	1	P	0.41366	0.747	P	0.49561	0.615	T	0.16041	-1.0416	10	0.44086	T	0.13	.	17.7794	0.88519	0.0:0.0:1.0:0.0	.	231	Q9NYM4	GPR83_HUMAN	T	231;189	ENSP00000243673:P231T;ENSP00000441550:P189T	ENSP00000243673:P231T	P	-	1	0	GPR83	93753544	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	9.587000	0.98229	2.535000	0.85469	0.655000	0.94253	CCA	.	.		0.577	GPR83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396232.1	NM_016540		T	94113896	G	T	94113896	3	4	344	1	0	0	0	0	1	0	0	0	6721	1203	42	3	584	3	GPR83	11	94113896	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	73457	94113896	40892620	854	48217										
PIWIL4	143689	hgsc.bcm.edu	37	chr11	94354059	94354059	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cagggcatagtcagtgtcccAgcaccatgtcagtatgctca	10	12	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:94354059A>T	ENST00000299001.6	+	20	2671	c.2460A>T	c.(2458-2460)ccA>ccT	p.P820P	RP11-867G2.8_ENST00000536540.1_RNA|RP11-867G2.8_ENST00000537874.1_RNA|PIWIL4_ENST00000537419.1_Silent_p.P171P	NM_152431.2	NP_689644.2	Q7Z3Z4	PIWL4_HUMAN	piwi-like RNA-mediated gene silencing 4	820	Piwi. {ECO:0000255|PROSITE- ProRule:PRU00150}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|piP-body (GO:0071547)	piRNA binding (GO:0034584)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|urinary_tract(2)	30		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				TCAGTGTCCCAGCACCATGTC	0.393																																					p.P820P		Atlas-SNP	.											.	PIWIL4	70	.	0			c.A2460T						.						68	61	63					11																	94354059		2201	4298	6499	SO:0001819	synonymous_variant	143689	exon20			TGTCCCAGCACCA	AB079366	CCDS31656.1	11q12	2013-02-15	2013-02-15			ENSG00000134627		"Argonaute/PIWI family"	18444	protein-coding gene	gene with protein product		610315	"piwi-like 4 (Drosophila)"			12906857	Standard	NM_152431		Approved	FLJ36156, HIWI2, Miwi2	uc001pfa.3	Q7Z3Z4		ENST00000299001.6:c.2460A>T	chr11.hg19:g.94354059A>T		82.0	0.0		86.0	40.0	NM_152431	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Silent	SNP	ENST00000299001.6	hg19	CCDS31656.1																																																																																			.	.		0.393	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396388.1	NM_152431		T	94354059	A	T	94354059	2	4	344	1	0	0	0	0	0	0	0	1	11969	175	7	4		4	PIWIL4	11	94354059	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	240163	94354059	40652457	855	48218										
MMP7	4316	hgsc.bcm.edu	37	chr11	102394039	102394039	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tttggggatctccatttccaTaggttggatacatcactgca	9	9	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:102394039T>A	ENST00000260227.4	-	5	759	c.707A>T	c.(706-708)tAt>tTt	p.Y236F		NM_002423.3	NP_002414.1	P09237	MMP7_HUMAN	matrix metallopeptidase 7 (matrilysin, uterine)	236					antibacterial peptide secretion (GO:0002779)|collagen catabolic process (GO:0030574)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|regulation of cell proliferation (GO:0042127)|response to drug (GO:0042493)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			large_intestine(6)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12	all_cancers(8;2.04e-05)|all_epithelial(12;0.00053)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0105)|all cancers(10;0.0496)|Lung(13;0.109)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0147)	Marimastat(DB00786)	TCCATTTCCATAGGTTGGATA	0.363																																					p.Y236F		Atlas-SNP	.											.	MMP7	27	.	0			c.A707T						.						91	90	90					11																	102394039		2203	4299	6502	SO:0001583	missense	4316	exon5			TTTCCATAGGTTG	Z11887	CCDS8317.1	11q21-q22	2008-02-05	2005-08-08		ENSG00000137673	ENSG00000137673	3.4.24.23		7174	protein-coding gene	gene with protein product		178990	"matrix metalloproteinase 7 (matrilysin, uterine)"	MPSL1		8978768	Standard	NM_002423		Approved	PUMP-1	uc001phb.3	P09237	OTTHUMG00000048193	ENST00000260227.4:c.707A>T	chr11.hg19:g.102394039T>A	ENSP00000260227:p.Tyr236Phe	95.0	0.0		77.0	20.0	NM_002423	Q9BTK9	Missense_Mutation	SNP	ENST00000260227.4	hg19	CCDS8317.1	.	.	.	.	.	.	.	.	.	.	T	14.64	2.595015	0.46318	.	.	ENSG00000137673	ENST00000260227	T	0.25250	1.81	5.36	5.36	0.76844	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.000000	0.53938	D	0.000060	T	0.57725	0.2073	M	0.92459	3.31	0.41216	D	0.986475	D	0.89917	1.0	D	0.91635	0.999	T	0.67288	-0.5708	10	0.87932	D	0	-18.2624	9.8139	0.40840	0.0:0.0765:0.0:0.9235	.	236	P09237	MMP7_HUMAN	F	236	ENSP00000260227:Y236F	ENSP00000260227:Y236F	Y	-	2	0	MMP7	101899249	1.000000	0.71417	0.057000	0.19452	0.079000	0.17450	4.820000	0.62671	2.036000	0.60181	0.528000	0.53228	TAT	.	.		0.363	MMP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109633.2			A	102394039	T	A	102394039	3	1	344	1	0	0	0	0	1	0	0	0	9676	1406	49	4	104	4	MMP7	11	102394039	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	8039980	102394039	32612477	856	48219										
MMP10	4319	hgsc.bcm.edu	37	chr11	102642848	102642848	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctggctattttcatcaaatcTaaaccaaatgaaagaaatac	4	8	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:102642848T>A	ENST00000279441.4	-	9	1263		c.e9-2			NM_002425.2	NP_002416.1	P09238	MMP10_HUMAN	matrix metallopeptidase 10 (stromelysin 2)						collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|regulation of cell migration (GO:0030334)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|liver(2)|lung(6)	22	all_epithelial(12;0.00961)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0303)|Lung(13;0.0828)|all cancers(10;0.116)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0145)	Marimastat(DB00786)	TCATCAAATCTAAACCAAATG	0.388																																					.		Atlas-SNP	.											.	MMP10	44	.	0			c.1227-2A>T						.						80	72	75					11																	102642848		2203	4299	6502	SO:0001630	splice_region_variant	4319	exon10			CAAATCTAAACCA	X07820	CCDS8321.1	11q22.3	2008-02-05	2005-08-08		ENSG00000166670	ENSG00000166670	3.4.24.22		7156	protein-coding gene	gene with protein product		185260	"matrix metalloproteinase 10 (stromelysin 2)"	STMY2			Standard	NM_002425		Approved		uc001phg.2	P09238	OTTHUMG00000168083	ENST00000279441.4:c.1227-2A>T	chr11.hg19:g.102642848T>A		55.0	0.0		53.0	17.0	NM_002425	B2R9X9|Q53HH9	Splice_Site	SNP	ENST00000279441.4	hg19	CCDS8321.1	.	.	.	.	.	.	.	.	.	.	T	15.40	2.822039	0.50739	.	.	ENSG00000166670	ENST00000279441	.	.	.	4.07	4.07	0.47477	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.553	0.61743	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	MMP10	102148058	1.000000	0.71417	0.988000	0.46212	0.601000	0.36947	4.289000	0.59013	1.821000	0.53095	0.524000	0.50904	.	.	.		0.388	MMP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398014.1		Intron	A	102642848	T	A	102642848	5	1	344	1	0	0	0	0	0	0	1	0	9658	1536	53	4	213	4	MMP10	11	102642848	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	248809	102642848	32363668	857	48220										
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	102984375	102984375	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcttgtttcatctatgttagAgtcacctattagttctcttt	5	8	5	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:102984375A>T	ENST00000375735.2	+	2	449	c.305A>T	c.(304-306)gAg>gTg	p.E102V	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.E102V|DYNC2H1_ENST00000334267.7_Missense_Mutation_p.E102V	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	102	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		TCTATGTTAGAGTCACCTATT	0.363																																					p.E102V		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.A305T						.						142	135	137					11																	102984375		1865	4096	5961	SO:0001583	missense	79659	exon2			TGTTAGAGTCACC	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.305A>T	chr11.hg19:g.102984375A>T	ENSP00000364887:p.Glu102Val	140.0	0.0		122.0	56.0	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	hg19	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.178855	0.78564	.	.	ENSG00000187240	ENST00000375735;ENST00000334267;ENST00000398093	T;T;T	0.32515	1.6;1.45;1.61	6.17	6.17	0.99709	.	0.353337	0.20583	U	0.089485	T	0.39384	0.1076	L	0.51422	1.61	0.54753	D	0.999985	P;B;B	0.45212	0.853;0.047;0.135	P;B;B	0.46850	0.529;0.053;0.128	T	0.10314	-1.0635	10	0.51188	T	0.08	.	16.8222	0.85835	1.0:0.0:0.0:0.0	.	102;102;102	Q8NCM8-3;Q8NCM8;Q8NCM8-2	.;DYHC2_HUMAN;.	V	102	ENSP00000364887:E102V;ENSP00000334021:E102V;ENSP00000381167:E102V	ENSP00000334021:E102V	E	+	2	0	DYNC2H1	102489585	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	8.719000	0.91436	2.371000	0.80710	0.533000	0.62120	GAG	.	.		0.363	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		T	102984375	A	T	102984375	3	4	344	1	0	0	0	0	1	0	0	0	4848	304	11	4	311	4	DYNC2H1	11	102984375	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	341527	102984375	32022141	858	48221										
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	103018556	103018556	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	accctgtgaagactgtgattGatgatctcatccagaagtta	9	8	1	6			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:103018556G>T	ENST00000375735.2	+	19	2902	c.2758G>T	c.(2758-2760)Gat>Tat	p.D920Y	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.D920Y|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	920	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		GACTGTGATTGATGATCTCAT	0.299																																					p.D920Y		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.G2758T						.						118	116	117					11																	103018556		1843	4077	5920	SO:0001583	missense	79659	exon19			GTGATTGATGATC	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.2758G>T	chr11.hg19:g.103018556G>T	ENSP00000364887:p.Asp920Tyr	49.0	0.0		43.0	21.0	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	hg19	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.746528	0.89663	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.29397	1.57;1.57	5.49	5.49	0.81192	.	0.499919	0.16053	U	0.231871	T	0.64327	0.2588	M	0.87547	2.89	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.984;0.993	T	0.66956	-0.5792	10	0.59425	D	0.04	.	19.7446	0.96247	0.0:0.0:1.0:0.0	.	920;920	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	Y	920	ENSP00000364887:D920Y;ENSP00000381167:D920Y	ENSP00000364887:D920Y	D	+	1	0	DYNC2H1	102523766	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.374000	0.97172	2.751000	0.94390	0.650000	0.86243	GAT	.	.		0.299	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		T	103018556	G	T	103018556	3	4	344	1	0	0	0	0	1	0	0	0	4848	1290	45	3	2832	3	DYNC2H1	11	103018556	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	34181	103018556	31987960	859	48222										
GRIA4	2893	hgsc.bcm.edu	37	chr11	105732861	105732861	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctataggcaacttctagaagAacttgacagaagacaagaga	9	7	1	6			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:105732861A>T	ENST00000530497.1	+	4	599	c.599A>T	c.(598-600)gAa>gTa	p.E200V	GRIA4_ENST00000428631.2_Missense_Mutation_p.E200V|GRIA4_ENST00000525187.1_Missense_Mutation_p.E200V|GRIA4_ENST00000393125.2_Missense_Mutation_p.E200V|GRIA4_ENST00000282499.5_Missense_Mutation_p.E200V|GRIA4_ENST00000393127.2_Missense_Mutation_p.E200V			P48058	GRIA4_HUMAN	glutamate receptor, ionotropic, AMPA 4	200					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(24)|liver(2)|lung(25)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	82		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)		CTTCTAGAAGAACTTGACAGA	0.348																																					p.E200V		Atlas-SNP	.											.	GRIA4	380	.	0			c.A599T						.						72	73	73					11																	105732861		2202	4299	6501	SO:0001583	missense	2893	exon5			TAGAAGAACTTGA	U16129	CCDS8333.1, CCDS41706.1, CCDS41707.1	11q22	2012-08-29	2012-02-03		ENSG00000152578	ENSG00000152578		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4574	protein-coding gene	gene with protein product		138246	"glutamate receptor, ionotrophic, AMPA 4"	GLUR4			Standard	NM_001077244		Approved	GluA4, GLURD	uc001pix.2	P48058	OTTHUMG00000166236	ENST00000530497.1:c.599A>T	chr11.hg19:g.105732861A>T	ENSP00000435775:p.Glu200Val	98.0	0.0		90.0	41.0	NM_001077244	Q86XE8	Missense_Mutation	SNP	ENST00000530497.1	hg19	CCDS8333.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.579172	0.86645	.	.	ENSG00000152578	ENST00000393125;ENST00000282499;ENST00000393127;ENST00000428631;ENST00000530497;ENST00000525187	D;D;D;D;D;D	0.83335	-1.71;-1.71;-1.71;-1.71;-1.71;-1.71	5.49	5.49	0.81192	Extracellular ligand-binding receptor (1);	0.079286	0.51477	D	0.000091	D	0.88306	0.6401	L	0.58101	1.795	0.52501	D	0.999951	P;P;P;P	0.45428	0.749;0.829;0.858;0.736	P;P;P;P	0.58454	0.839;0.642;0.756;0.595	D	0.89404	0.3698	10	0.87932	D	0	.	15.5825	0.76455	1.0:0.0:0.0:0.0	.	200;200;230;200	P48058;G3V164;Q59GL7;Q86XE8	GRIA4_HUMAN;.;.;.	V	200	ENSP00000376833:E200V;ENSP00000282499:E200V;ENSP00000376835:E200V;ENSP00000415551:E200V;ENSP00000435775:E200V;ENSP00000432180:E200V	ENSP00000282499:E200V	E	+	2	0	GRIA4	105238071	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	8.893000	0.92498	2.084000	0.62774	0.455000	0.32223	GAA	.	.		0.348	GRIA4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388593.1			T	105732861	A	T	105732861	3	4	344	1	0	0	0	0	1	0	0	0	6779	246	9	4	613	4	GRIA4	11	105732861	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2714305	105732861	29273655	860	48223										
GRIA4	2893	hgsc.bcm.edu	37	chr11	105769103	105769103	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	taatcaaactaatggatcgcTggaagaaactagatcagaga	9	6	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:105769103T>A	ENST00000530497.1	+	6	835	c.835T>A	c.(835-837)Tgg>Agg	p.W279R	GRIA4_ENST00000428631.2_Missense_Mutation_p.W279R|GRIA4_ENST00000525187.1_Missense_Mutation_p.W279R|GRIA4_ENST00000393125.2_Missense_Mutation_p.W279R|GRIA4_ENST00000282499.5_Missense_Mutation_p.W279R|GRIA4_ENST00000393127.2_Missense_Mutation_p.W279R			P48058	GRIA4_HUMAN	glutamate receptor, ionotropic, AMPA 4	279					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(24)|liver(2)|lung(25)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	82		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)		AATGGATCGCTGGAAGAAACT	0.358																																					p.W279R		Atlas-SNP	.											.	GRIA4	380	.	0			c.T835A						.						60	61	61					11																	105769103		2202	4299	6501	SO:0001583	missense	2893	exon7			GATCGCTGGAAGA	U16129	CCDS8333.1, CCDS41706.1, CCDS41707.1	11q22	2012-08-29	2012-02-03		ENSG00000152578	ENSG00000152578		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4574	protein-coding gene	gene with protein product		138246	"glutamate receptor, ionotrophic, AMPA 4"	GLUR4			Standard	NM_001077244		Approved	GluA4, GLURD	uc001pix.2	P48058	OTTHUMG00000166236	ENST00000530497.1:c.835T>A	chr11.hg19:g.105769103T>A	ENSP00000435775:p.Trp279Arg	153.0	0.0		143.0	61.0	NM_001077244	Q86XE8	Missense_Mutation	SNP	ENST00000530497.1	hg19	CCDS8333.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.303495	0.81136	.	.	ENSG00000152578	ENST00000393125;ENST00000282499;ENST00000393127;ENST00000428631;ENST00000530497;ENST00000525187	D;D;D;D;D;D	0.83755	-1.76;-1.76;-1.76;-1.76;-1.76;-1.76	5.72	5.72	0.89469	Extracellular ligand-binding receptor (1);	0.000000	0.64402	D	0.000001	D	0.89448	0.6718	L	0.60455	1.87	0.80722	D	1	D;P;D	0.89917	0.991;0.901;1.0	D;P;D	0.78314	0.947;0.695;0.991	D	0.90446	0.4435	10	0.87932	D	0	.	16.0037	0.80327	0.0:0.0:0.0:1.0	.	279;279;279	P48058;G3V164;Q86XE8	GRIA4_HUMAN;.;.	R	279	ENSP00000376833:W279R;ENSP00000282499:W279R;ENSP00000376835:W279R;ENSP00000415551:W279R;ENSP00000435775:W279R;ENSP00000432180:W279R	ENSP00000282499:W279R	W	+	1	0	GRIA4	105274313	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.668000	0.83897	2.184000	0.69523	0.533000	0.62120	TGG	.	.		0.358	GRIA4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388593.1			A	105769103	T	A	105769103	3	1	344	1	0	0	0	0	1	0	0	0	6779	1580	55	4	857	4	GRIA4	11	105769103	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	36242	105769103	29237413	861	48224										
GRIA4	2893	hgsc.bcm.edu	37	chr11	105795169	105795169	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctgacaatcactttggtacgAgaggaggtcattgacttttc	10	8	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:105795169A>G	ENST00000530497.1	+	11	1521	c.1521A>G	c.(1519-1521)cgA>cgG	p.R507R	GRIA4_ENST00000525187.1_Silent_p.R507R|GRIA4_ENST00000282499.5_Silent_p.R507R|GRIA4_ENST00000393127.2_Silent_p.R507R			P48058	GRIA4_HUMAN	glutamate receptor, ionotropic, AMPA 4	507					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(24)|liver(2)|lung(25)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	82		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)		CTTTGGTACGAGAGGAGGTCA	0.393																																					p.R507R		Atlas-SNP	.											.	GRIA4	380	.	0			c.A1521G						.						128	126	127					11																	105795169		2202	4299	6501	SO:0001819	synonymous_variant	2893	exon12			GGTACGAGAGGAG	U16129	CCDS8333.1, CCDS41706.1, CCDS41707.1	11q22	2012-08-29	2012-02-03		ENSG00000152578	ENSG00000152578		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4574	protein-coding gene	gene with protein product		138246	"glutamate receptor, ionotrophic, AMPA 4"	GLUR4			Standard	NM_001077244		Approved	GluA4, GLURD	uc001pix.2	P48058	OTTHUMG00000166236	ENST00000530497.1:c.1521A>G	chr11.hg19:g.105795169A>G		99.0	0.0		64.0	31.0	NM_001077243	Q86XE8	Silent	SNP	ENST00000530497.1	hg19	CCDS8333.1																																																																																			.	.		0.393	GRIA4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388593.1			G	105795169	A	G	105795169	2	3	344	1	0	0	0	0	0	0	0	1	6779	291	11	2		2	GRIA4	11	105795169	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	26066	105795169	29211347	862	48225										
GRIA4	2893	hgsc.bcm.edu	37	chr11	105795274	105795274	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtgttttccttcttggatccTctggcctatgagatttggat	10	8	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:105795274T>A	ENST00000530497.1	+	11	1626	c.1626T>A	c.(1624-1626)ccT>ccA	p.P542P	GRIA4_ENST00000525187.1_Silent_p.P542P|GRIA4_ENST00000282499.5_Silent_p.P542P|GRIA4_ENST00000393127.2_Silent_p.P542P			P48058	GRIA4_HUMAN	glutamate receptor, ionotropic, AMPA 4	542					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(24)|liver(2)|lung(25)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	82		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)		TCTTGGATCCTCTGGCCTATG	0.423																																					p.P542P		Atlas-SNP	.											.	GRIA4	380	.	0			c.T1626A						.						198	183	188					11																	105795274		2202	4299	6501	SO:0001819	synonymous_variant	2893	exon12			GGATCCTCTGGCC	U16129	CCDS8333.1, CCDS41706.1, CCDS41707.1	11q22	2012-08-29	2012-02-03		ENSG00000152578	ENSG00000152578		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4574	protein-coding gene	gene with protein product		138246	"glutamate receptor, ionotrophic, AMPA 4"	GLUR4			Standard	NM_001077244		Approved	GluA4, GLURD	uc001pix.2	P48058	OTTHUMG00000166236	ENST00000530497.1:c.1626T>A	chr11.hg19:g.105795274T>A		128.0	0.0		127.0	63.0	NM_001077243	Q86XE8	Silent	SNP	ENST00000530497.1	hg19	CCDS8333.1																																																																																			.	.		0.423	GRIA4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388593.1			A	105795274	T	A	105795274	2	1	344	1	0	0	0	0	0	0	0	1	6779	1538	54	4		4	GRIA4	11	105795274	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	105	105795274	29211242	863	48226										
SLC35F2	54733	hgsc.bcm.edu	37	chr11	107673871	107673871	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atacacagggcaaatgccacGaacagcagggctgtggaaaa	12	9	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:107673871G>T	ENST00000525815.1	-	7	1215	c.795C>A	c.(793-795)ttC>ttA	p.F265L	SLC35F2_ENST00000525071.1_Missense_Mutation_p.F265L|SLC35F2_ENST00000265836.7_Missense_Mutation_p.F117L|SLC35F2_ENST00000429869.1_Missense_Mutation_p.F265L|SLC35F2_ENST00000375682.4_Missense_Mutation_p.F218L	NM_017515.4	NP_059985.2	Q8IXU6	S35F2_HUMAN	solute carrier family 35, member F2	265					transport (GO:0006810)	integral component of membrane (GO:0016021)		p.F265F(1)		breast(1)|central_nervous_system(1)|endometrium(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(61;9.46e-06)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;0.000111)|all_hematologic(158;0.000315)|all_epithelial(67;0.00197)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)|Epithelial(105;0.000105)|all cancers(92;0.00217)		CAAATGCCACGAACAGCAGGG	0.443																																					p.F265L		Atlas-SNP	.											SLC35F2,NS,carcinoma,0,2	SLC35F2	29	.	1	Substitution - coding silent(1)	endometrium(1)	c.C795A						.						57	53	54					11																	107673871		1962	4145	6107	SO:0001583	missense	54733	exon7			TGCCACGAACAGC		CCDS41709.1	11q22.3	2013-05-22			ENSG00000110660	ENSG00000110660		"Solute carriers"	23615	protein-coding gene	gene with protein product						9119394	Standard	NM_017515		Approved	FLJ13018	uc001pjq.3	Q8IXU6	OTTHUMG00000166366	ENST00000525815.1:c.795C>A	chr11.hg19:g.107673871G>T	ENSP00000436785:p.Phe265Leu	242.0	0.0		191.0	77.0	NM_017515	Q14963|Q5JPA8|Q6ZRQ3|Q9H947	Missense_Mutation	SNP	ENST00000525815.1	hg19	CCDS41709.1	.	.	.	.	.	.	.	.	.	.	G	4.360	0.066285	0.08388	.	.	ENSG00000110660	ENST00000525815;ENST00000525071;ENST00000265836;ENST00000375682;ENST00000429869	T;T;T;T	0.64085	-0.08;-0.08;-0.08;-0.08	5.13	-4.21	0.03812	.	0.051897	0.85682	D	0.000000	T	0.35393	0.0930	N	0.12887	0.27	0.40400	D	0.97963	B	0.21381	0.055	B	0.26969	0.075	T	0.15009	-1.0452	10	0.13470	T	0.59	.	10.5993	0.45358	0.3688:0.108:0.5232:0.0	.	265	Q8IXU6	S35F2_HUMAN	L	265;265;117;218;265	ENSP00000436785:F265L;ENSP00000265836:F117L;ENSP00000364834:F218L;ENSP00000393571:F265L	ENSP00000265836:F117L	F	-	3	2	SLC35F2	107179081	0.984000	0.35163	0.158000	0.22627	0.438000	0.31896	0.972000	0.29409	-1.519000	0.01775	-1.641000	0.00772	TTC	.	.		0.443	SLC35F2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389417.1	NM_017515		T	107673871	G	T	107673871	3	4	344	1	0	0	0	0	1	0	0	0	14604	1049	37	1	337	1	SLC35F2	11	107673871	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1878597	107673871	27332645	864	48227										
ATM	472	hgsc.bcm.edu	37	chr11	108175446	108175446	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtacttccatacttgattcaTgatattttactccaagatac	4	9	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:108175446T>C	ENST00000452508.2	+	38	5730	c.5541T>C	c.(5539-5541)caT>caC	p.H1847H	ATM_ENST00000278616.4_Silent_p.H1847H			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1847					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			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)	Caffeine(DB00201)	ACTTGATTCATGATATTTTAC	0.343			"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)																											p.H1847H		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	.	ATM	1657	.	0			c.T5541C						.						74	71	72					11																	108175446		2201	4298	6499	SO:0001819	synonymous_variant	472	exon37	Familial Cancer Database	AT, Louis-Bar syndrome	GATTCATGATATT	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.5541T>C	chr11.hg19:g.108175446T>C		70.0	0.0		47.0	20.0	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Silent	SNP	ENST00000452508.2	hg19	CCDS31669.1																																																																																			.	.		0.343	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		C	108175446	T	C	108175446	2	2	344	1	0	0	0	0	0	0	0	1	1109	1461	51	2		2	ATM	11	108175446	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	501575	108175446	26831070	865	48228										
C11orf65	160140	hgsc.bcm.edu	37	chr11	108253873	108253873	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtctcctccatagttatataTgtttttctgtgcttgattaa	6	7	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:108253873T>G	ENST00000529391.1	-	8	826	c.817A>C	c.(817-819)Ata>Cta	p.I273L	C11orf65_ENST00000526725.1_Intron|C11orf65_ENST00000393084.1_Missense_Mutation_p.I273L|C11orf65_ENST00000525729.1_Intron			Q8NCR3	CK065_HUMAN	chromosome 11 open reading frame 65	273										endometrium(1)|large_intestine(3)|lung(4)|ovary(2)	10		all_cancers(61;1.38e-11)|all_epithelial(67;3.16e-07)|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;8.21e-06)|BRCA - Breast invasive adenocarcinoma(274;1.01e-05)|all cancers(92;0.000189)|Colorectal(284;0.114)|OV - Ovarian serous cystadenocarcinoma(223;0.144)		TAGTTATATATGTTTTTCTGT	0.313																																					p.I273L		Atlas-SNP	.											.	C11orf65	29	.	0			c.A817C						.						109	113	112					11																	108253873		2201	4294	6495	SO:0001583	missense	160140	exon9			TATATATGTTTTT	BC059411	CCDS8340.1	11q22.3	2012-05-30			ENSG00000166323	ENSG00000166323			28519	protein-coding gene	gene with protein product						12477932	Standard	NM_152587		Approved	MGC33948	uc001pkh.3	Q8NCR3	OTTHUMG00000166489	ENST00000529391.1:c.817A>C	chr11.hg19:g.108253873T>G	ENSP00000436400:p.Ile273Leu	78.0	0.0		64.0	23.0	NM_152587	B4DZU4|Q6PCA8	Missense_Mutation	SNP	ENST00000529391.1	hg19	CCDS8340.1	.	.	.	.	.	.	.	.	.	.	T	0.091	-1.167069	0.01660	.	.	ENSG00000166323	ENST00000529391;ENST00000393084	.	.	.	4.2	-0.0167	0.13971	.	0.918018	0.09153	N	0.841259	T	0.18635	0.0447	N	0.25647	0.755	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.31280	-0.9949	9	0.07813	T	0.8	-2.7239	3.5708	0.07917	0.0:0.2879:0.2128:0.4993	.	273	Q8NCR3	CK065_HUMAN	L	273	.	ENSP00000376799:I273L	I	-	1	0	C11orf65	107759083	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.221000	0.17680	-0.008000	0.14320	0.533000	0.62120	ATA	.	.		0.313	C11orf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390010.3	NM_152587		G	108253873	T	G	108253873	3	3	344	1	0	0	0	0	1	0	0	0	1657	1464	51	5	128	5	C11orf65	11	108253873	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	78427	108253873	26752643	866	48229										
CADM1	23705	hgsc.bcm.edu	37	chr11	115080321	115080321	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gatggtaaggatggtggtggTggtggtggtggtggtggtgg	25	0	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:115080321T>C	ENST00000452722.3	-	8	1071	c.1051A>G	c.(1051-1053)Acc>Gcc	p.T351A	CADM1_ENST00000536727.1_Intron|CADM1_ENST00000537058.1_Missense_Mutation_p.T351A|CADM1_ENST00000537140.1_Intron|CADM1_ENST00000542447.2_Intron|CADM1_ENST00000331581.6_Missense_Mutation_p.T351A	NM_014333.3	NP_055148.3			cell adhesion molecule 1											cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(9)|ovary(2)|skin(1)	32	all_hematologic(175;0.0628)	all_cancers(61;2.98e-14)|all_epithelial(67;2.64e-08)|all_hematologic(158;0.000154)|Melanoma(852;0.000952)|Acute lymphoblastic leukemia(157;0.00101)|Breast(348;0.0102)|Medulloblastoma(222;0.0429)|Prostate(24;0.145)|all_neural(223;0.237)		BRCA - Breast invasive adenocarcinoma(274;5.01e-06)|Epithelial(105;0.000305)|all cancers(92;0.00303)		atggtggtggtggtggtggtg	0.433																																					p.T351A		Atlas-SNP	.											.	CADM1	74	.	0			c.A1051G						.						50	55	53					11																	115080321		2201	4296	6497	SO:0001583	missense	23705	exon8			TGGTGGTGGTGGT	AB017563	CCDS8373.1, CCDS53711.1, CCDS73397.1, CCDS73398.1, CCDS73399.1	11q23.2	2013-01-29	2007-02-07	2007-02-07	ENSG00000182985	ENSG00000182985		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5951	protein-coding gene	gene with protein product	"nectin-like 2"	605686	"tumor suppressor in lung cancer 1", "immunoglobulin superfamily, member 4"	TSLC1, IGSF4		10610705	Standard	NM_014333		Approved	NECL2, ST17, BL2, SYNCAM, IGSF4A, Necl-2, SYNCAM1, RA175	uc001ppi.4	Q9BY67	OTTHUMG00000168202	ENST00000452722.3:c.1051A>G	chr11.hg19:g.115080321T>C	ENSP00000395359:p.Thr351Ala	53.0	0.0		56.0	33.0	NM_014333		Missense_Mutation	SNP	ENST00000452722.3	hg19	CCDS8373.1	.	.	.	.	.	.	.	.	.	.	T	5.061	0.196983	0.09599	.	.	ENSG00000182985	ENST00000452722;ENST00000537058;ENST00000331581;ENST00000541325	T;T;T	0.63744	-0.04;0.19;-0.06	4.29	4.29	0.51040	.	0.703928	0.13804	N	0.361575	T	0.43656	0.1257	N	0.19112	0.55	0.26262	N	0.978567	B	0.22276	0.067	B	0.15052	0.012	T	0.14839	-1.0458	10	0.09084	T	0.74	.	12.5623	0.56288	0.0:0.0:0.0:1.0	.	351	Q9BY67	CADM1_HUMAN	A	351;351;351;25	ENSP00000395359:T351A;ENSP00000439817:T351A;ENSP00000329797:T351A	ENSP00000329797:T351A	T	-	1	0	CADM1	114585531	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.814000	0.55643	1.677000	0.50941	0.533000	0.62120	ACC	.	.		0.433	CADM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398753.2	NM_014333		C	115080321	T	C	115080321	3	2	344	1	0	0	0	0	1	0	0	0	2568	1696	59	2	289	2	CADM1	11	115080321	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	6826448	115080321	19926195	867	48230										
SIDT2	51092	hgsc.bcm.edu	37	chr11	117054562	117054562	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaccgaagaccaagcctgcgGgggctccctgcctttctacc	11	16	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:117054562G>A	ENST00000324225.4	+	7	1301	c.770G>A	c.(769-771)gGg>gAg	p.G257E	SIDT2_ENST00000431081.2_Missense_Mutation_p.G257E|SIDT2_ENST00000530948.1_3'UTR	NM_001040455.1	NP_001035545.1	Q8NBJ9	SIDT2_HUMAN	SID1 transmembrane family, member 2	257					cell morphogenesis (GO:0000902)|dsRNA transport (GO:0033227)|glucose homeostasis (GO:0042593)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to glucose (GO:0009749)|type B pancreatic cell development (GO:0003323)|type B pancreatic cell proliferation (GO:0044342)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	RNA transmembrane transporter activity (GO:0051033)			NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	36	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.69e-05)|Epithelial(105;0.000219)|all cancers(92;0.00144)		CAAGCCTGCGGGGGCTCCCTG	0.532																																					p.G257E		Atlas-SNP	.											.	SIDT2	82	.	0			c.G770A						.						97	92	94					11																	117054562		2201	4296	6497	SO:0001583	missense	51092	exon7			CCTGCGGGGGCTC	AF151799	CCDS31682.1	11q23.3	2008-02-05			ENSG00000149577	ENSG00000149577			24272	protein-coding gene	gene with protein product						10810093, 12975309	Standard	NM_001040455		Approved	CGI-40	uc001pqh.1	Q8NBJ9	OTTHUMG00000167065	ENST00000324225.4:c.770G>A	chr11.hg19:g.117054562G>A	ENSP00000314023:p.Gly257Glu	81.0	0.0		44.0	21.0	NM_001040455	Q8NBY7|Q9Y357	Missense_Mutation	SNP	ENST00000324225.4	hg19	CCDS31682.1	.	.	.	.	.	.	.	.	.	.	G	33	5.204567	0.95033	.	.	ENSG00000149577	ENST00000324225;ENST00000278951;ENST00000431081;ENST00000524842	T;T;T;T	0.20881	2.04;2.04;2.04;2.04	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.52322	0.1727	M	0.82517	2.595	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.998;1.0;0.998;0.999	T	0.52624	-0.8551	10	0.52906	T	0.07	-20.2438	19.0823	0.93187	0.0:0.0:1.0:0.0	.	257;257;257;257	Q8NBJ9-2;F5H8L4;Q8NBJ9;C9JBG5	.;.;SIDT2_HUMAN;.	E	257;257;257;107	ENSP00000314023:G257E;ENSP00000278951:G257E;ENSP00000399635:G257E;ENSP00000436983:G107E	ENSP00000278951:G257E	G	+	2	0	SIDT2	116559772	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	9.016000	0.93645	2.840000	0.97914	0.596000	0.82720	GGG	.	.		0.532	SIDT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392836.1	NM_015996		A	117054562	G	A	117054562	3	1	344	1	0	0	0	0	1	0	0	0	14318	1232	43	3	796	3	SIDT2	11	117054562	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1974241	117054562	17951954	868	48231										
TMPRSS13	84000	hgsc.bcm.edu	37	chr11	117789167	117789167	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gttgctggtgctgacctggcAggagatgatcggatgggtac	17	7	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:117789167A>G	ENST00000430170.2	-	2	495	c.408T>C	c.(406-408)ccT>ccC	p.P136P	TMPRSS13_ENST00000526090.1_Silent_p.P136P|TMPRSS13_ENST00000528626.1_Silent_p.P136P|TMPRSS13_ENST00000524993.1_Silent_p.P136P|TMPRSS13_ENST00000445164.2_Silent_p.P136P	NM_001244995.1	NP_001231924.1	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	136						blood microparticle (GO:0072562)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|pancreas(1)|prostate(1)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.00106)		CTGACCTGGCAGGAGATGATC	0.612																																					p.P136P		Atlas-SNP	.											.	TMPRSS13	75	.	0			c.T408C						.						68	75	73					11																	117789167		2074	4208	6282	SO:0001819	synonymous_variant	84000	exon2			CCTGGCAGGAGAT	AB048796	CCDS41721.1, CCDS55788.1, CCDS55789.1, CCDS58185.1	11q23	2010-04-13	2005-03-11	2005-03-12	ENSG00000137747	ENSG00000137747		"Serine peptidases / Transmembrane"	29808	protein-coding gene	gene with protein product		610050	"transmembrane protease, serine 11"	TMPRSS11		11267681	Standard	NM_001077263		Approved	MSPL	uc001prs.2	Q9BYE2	OTTHUMG00000166992	ENST00000430170.2:c.408T>C	chr11.hg19:g.117789167A>G		59.0	0.0		65.0	25.0	NM_001206790	B4DTM9|E9PIJ5|F8WAJ3|Q86YM4|Q96JY8|Q9BYE1	Silent	SNP	ENST00000430170.2	hg19	CCDS58185.1																																																																																			.	.		0.612	TMPRSS13-006	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000392318.1	NM_032046		G	117789167	A	G	117789167	2	3	344	1	0	0	0	0	0	0	0	1	16260	175	7	2		2	TMPRSS13	11	117789167	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	734605	117789167	17217349	869	48232										
ARHGEF12	23365	hgsc.bcm.edu	37	chr11	120349051	120349051	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aatcgcaatcccagattcacAcctgcctgtctcagaagaac	6	14	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:120349051A>T	ENST00000397843.2	+	37	3885	c.3719A>T	c.(3718-3720)cAc>cTc	p.H1240L	ARHGEF12_ENST00000356641.3_Missense_Mutation_p.H1221L|ARHGEF12_ENST00000532993.1_Missense_Mutation_p.H1137L	NM_015313.2	NP_056128.1	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12	1240					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(5)|endometrium(6)|kidney(5)|large_intestine(13)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(2)	61		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)		CCAGATTCACACCTGCCTGTC	0.393			T	MLL	AML																																p.H1240L		Atlas-SNP	.		Dom	yes		11	11q23.3	23365	RHO guanine nucleotide exchange factor (GEF) 12 (LARG)		L	.	ARHGEF12	133	.	0			c.A3719T						.						79	74	76					11																	120349051		1927	4134	6061	SO:0001583	missense	23365	exon37			ATTCACACCTGCC	AF180681	CCDS41727.1, CCDS55794.1	11q23.3	2011-11-16			ENSG00000196914	ENSG00000196914		"Rho guanine nucleotide exchange factors"	14193	protein-coding gene	gene with protein product		604763				10681437, 9205841	Standard	NM_001198665		Approved	KIAA0382, LARG	uc001pxl.2	Q9NZN5	OTTHUMG00000166143	ENST00000397843.2:c.3719A>T	chr11.hg19:g.120349051A>T	ENSP00000380942:p.His1240Leu	73.0	0.0		60.0	25.0	NM_015313	O15086|Q6P526	Missense_Mutation	SNP	ENST00000397843.2	hg19	CCDS41727.1	.	.	.	.	.	.	.	.	.	.	A	13.59	2.281597	0.40394	.	.	ENSG00000196914	ENST00000397843;ENST00000356641;ENST00000532993	T;T;T	0.64618	-0.01;-0.11;-0.0	5.26	5.26	0.73747	.	0.000000	0.51477	D	0.000086	T	0.44159	0.1280	L	0.27053	0.805	0.27153	N	0.961351	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.23655	-1.0182	10	0.10902	T	0.67	-8.7448	9.9318	0.41528	0.8152:0.1848:0.0:0.0	.	1221;1240	Q9NZN5-2;Q9NZN5	.;ARHGC_HUMAN	L	1240;1221;1137	ENSP00000380942:H1240L;ENSP00000349056:H1221L;ENSP00000432984:H1137L	ENSP00000349056:H1221L	H	+	2	0	ARHGEF12	119854261	0.002000	0.14202	0.995000	0.50966	0.616000	0.37450	1.618000	0.36954	2.108000	0.64289	0.533000	0.62120	CAC	.	.		0.393	ARHGEF12-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388052.1	NM_015313		T	120349051	A	T	120349051	3	4	344	1	0	0	0	0	1	0	0	0	897	159	6	4	3865	4	ARHGEF12	11	120349051	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2559884	120349051	14657465	870	48233										
OR4D5	219875	hgsc.bcm.edu	37	chr11	123811185	123811185	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgctgaatcctgccatctatAccctgagaaacaaggaagtg	9	10	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:123811185A>T	ENST00000307033.2	+	1	936	c.862A>T	c.(862-864)Acc>Tcc	p.T288S		NM_001001965.1	NP_001001965.1	Q8NGN0	OR4D5_HUMAN	olfactory receptor, family 4, subfamily D, member 5	288						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		TGCCATCTATACCCTGAGAAA	0.498																																					p.T288S		Atlas-SNP	.											.	OR4D5	94	.	0			c.A862T						.						106	101	103					11																	123811185		2202	4299	6501	SO:0001583	missense	219875	exon1			ATCTATACCCTGA	BK004316	CCDS31699.1	11q24.1	2012-08-09			ENSG00000171014	ENSG00000171014		"GPCR / Class A : Olfactory receptors"	14852	protein-coding gene	gene with protein product							Standard	NM_001001965		Approved		uc001pzk.1	Q8NGN0	OTTHUMG00000165961	ENST00000307033.2:c.862A>T	chr11.hg19:g.123811185A>T	ENSP00000305970:p.Thr288Ser	94.0	0.0		86.0	45.0	NM_001001965	B9EGZ4|Q6IFE6	Missense_Mutation	SNP	ENST00000307033.2	hg19	CCDS31699.1	.	.	.	.	.	.	.	.	.	.	A	19.38	3.815986	0.70912	.	.	ENSG00000171014	ENST00000307033	T	0.36157	1.27	5.29	5.29	0.74685	.	0.000000	0.47093	D	0.000254	T	0.24431	0.0592	N	0.03209	-0.39	0.31739	N	0.636018	P	0.42961	0.795	P	0.45577	0.486	T	0.28902	-1.0029	10	0.48119	T	0.1	-15.5855	14.8805	0.70528	1.0:0.0:0.0:0.0	.	288	Q8NGN0	OR4D5_HUMAN	S	288	ENSP00000305970:T288S	ENSP00000305970:T288S	T	+	1	0	OR4D5	123316395	0.025000	0.19082	1.000000	0.80357	0.988000	0.76386	0.960000	0.29253	1.994000	0.58287	0.528000	0.53228	ACC	.	.		0.498	OR4D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387263.1	NM_001001965		T	123811185	A	T	123811185	3	4	344	1	0	0	0	0	1	0	0	0	11066	391	14	4	864	4	OR4D5	11	123811185	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3462134	123811185	11195331	871	48234										
OR8B8	26493	hgsc.bcm.edu	37	chr11	124310403	124310403	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aacactacaagctcattcacAtaggtgctggtgcaagcaca	8	11	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:124310403A>T	ENST00000328064.2	-	1	651	c.579T>A	c.(577-579)taT>taA	p.Y193*		NM_012378.1	NP_036510.1	Q15620	OR8B8_HUMAN	olfactory receptor, family 8, subfamily B, member 8	193					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		GCTCATTCACATAGGTGCTGG	0.478																																					p.Y193X		Atlas-SNP	.											.	OR8B8	76	.	0			c.T579A						.						173	139	150					11																	124310403		2201	4299	6500	SO:0001587	stop_gained	26493	exon1			ATTCACATAGGTG	AF238488	CCDS8446.1	11q24.2	2012-08-09			ENSG00000197125	ENSG00000197125		"GPCR / Class A : Olfactory receptors"	8477	protein-coding gene	gene with protein product						9119360	Standard	NM_012378		Approved	TPCR85	uc010sal.2	Q15620	OTTHUMG00000165917	ENST00000328064.2:c.579T>A	chr11.hg19:g.124310403A>T	ENSP00000330280:p.Tyr193*	179.0	0.0		161.0	72.0	NM_012378	A1L446|Q96RC8	Nonsense_Mutation	SNP	ENST00000328064.2	hg19	CCDS8446.1	.	.	.	.	.	.	.	.	.	.	A	11.60	1.687347	0.29962	.	.	ENSG00000197125	ENST00000328064	.	.	.	3.67	-1.27	0.09347	.	0.889113	0.09433	N	0.802847	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.9851	0.41837	0.4873:0.0:0.5127:0.0	.	.	.	.	X	193	.	ENSP00000330280:Y193X	Y	-	3	2	OR8B8	123815613	0.000000	0.05858	0.008000	0.14137	0.199000	0.23934	-1.613000	0.02059	-0.257000	0.09459	0.455000	0.32223	TAT	.	.		0.478	OR8B8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387056.1	NM_012378		T	124310403	A	T	124310403	4	4	344	1	0	0	0	0	0	1	0	0	11239	224	8	4	359	4	OR8B8	11	124310403	Nonsense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	499218	124310403	10696113	872	48235										
STT3A	3703	hgsc.bcm.edu	37	chr11	125489978	125489978	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctttgagcttgatgtcctggAggaagcatataccacagaac	10	9	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:125489978A>G	ENST00000529196.1	+	18	2242	c.2036A>G	c.(2035-2037)gAg>gGg	p.E679G	STT3A_ENST00000531491.1_Missense_Mutation_p.E587G|STT3A_ENST00000392708.4_Missense_Mutation_p.E679G|STT3A_ENST00000526364.1_3'UTR			P46977	STT3A_HUMAN	STT3A, subunit of the oligosaccharyltransferase complex (catalytic)	679					cellular protein metabolic process (GO:0044267)|co-translational protein modification (GO:0043686)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			NS(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	33	all_hematologic(175;0.228)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0919)|all_lung(97;0.0994)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0996)		GATGTCCTGGAGGAAGCATAT	0.428																																					p.E679G		Atlas-SNP	.											.	STT3A	52	.	0			c.A2036G						.						106	100	102					11																	125489978		2201	4299	6500	SO:0001583	missense	3703	exon17			TCCTGGAGGAAGC	BC020965	CCDS8458.1, CCDS60998.1	11q23.3	2013-03-06	2013-03-06	2006-02-07	ENSG00000134910	ENSG00000134910	2.4.99.18		6172	protein-coding gene	gene with protein product	"dolichyl-diphosphooligosaccharide protein glycotransferase"	601134	"integral membrane protein 1", "STT3, subunit of the oligosaccharyltransferase complex, homolog A (S. cerevisiae)", "STT3A, cataylic subunit of the oligosaccharyltransferase complex"	ITM1		8941377, 8634329, 10234787	Standard	NM_152713		Approved	TMC, MGC9042, STT3-A	uc001qcd.2	P46977	OTTHUMG00000165852	ENST00000529196.1:c.2036A>G	chr11.hg19:g.125489978A>G	ENSP00000436962:p.Glu679Gly	98.0	0.0		84.0	32.0	NM_152713	B4DJ24|E9PNQ1|Q86XU9|Q8TE35|Q8WUB4	Missense_Mutation	SNP	ENST00000529196.1	hg19	CCDS8458.1	.	.	.	.	.	.	.	.	.	.	A	29.9	5.046668	0.93740	.	.	ENSG00000134910	ENST00000392708;ENST00000529196;ENST00000531491	D;D;D	0.94280	-3.39;-3.39;-3.39	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	D	0.95762	0.8621	M	0.93763	3.455	0.80722	D	1	P;P	0.48998	0.717;0.918	B;P	0.45660	0.269;0.489	D	0.96582	0.9431	10	0.87932	D	0	-28.0533	15.8284	0.78733	1.0:0.0:0.0:0.0	.	587;679	B4DJ24;P46977	.;STT3A_HUMAN	G	679;679;587	ENSP00000376472:E679G;ENSP00000436962:E679G;ENSP00000432820:E587G	ENSP00000376472:E679G	E	+	2	0	STT3A	124995188	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	9.257000	0.95545	2.209000	0.71365	0.533000	0.62120	GAG	.	.		0.428	STT3A-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386691.1	NM_152713		G	125489978	A	G	125489978	3	3	344	1	0	0	0	0	1	0	0	0	15348	304	11	2	2098	2	STT3A	11	125489978	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1179575	125489978	9516538	873	48236										
ADAMTS8	11095	hgsc.bcm.edu	37	chr11	130278692	130278692	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaacactttgaactcgctccTcccccgggctcggcagaaca	9	16	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:130278692T>A	ENST00000257359.6	-	7	2600	c.1894A>T	c.(1894-1896)Agg>Tgg	p.R632W		NM_007037.4	NP_008968.4	Q9UP79	ATS8_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 8	632	Cys-rich.				negative regulation of cell proliferation (GO:0008285)|phosphate ion transmembrane transport (GO:0035435)	proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)|low-affinity phosphate transmembrane transporter activity (GO:0009673)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	10	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.039)|Lung(977;0.213)		AACTCGCTCCTCCCCCGGGCT	0.627																																					p.R632W		Atlas-SNP	.											.	ADAMTS8	172	.	0			c.A1894T						.						90	92	92					11																	130278692		1910	4124	6034	SO:0001583	missense	11095	exon7			CGCTCCTCCCCCG	AF060153	CCDS41732.1	11q25	2008-07-18	2005-08-19		ENSG00000134917	ENSG00000134917		"ADAM metallopeptidases with thrombospondin type 1 motif"	224	protein-coding gene	gene with protein product		605175	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 8"			10438512	Standard	NM_007037		Approved	METH2, FLJ41712, ADAM-TS8	uc001qgg.4	Q9UP79	OTTHUMG00000165656	ENST00000257359.6:c.1894A>T	chr11.hg19:g.130278692T>A	ENSP00000257359:p.Arg632Trp	74.0	0.0		49.0	20.0	NM_007037	Q9NZS0	Missense_Mutation	SNP	ENST00000257359.6	hg19	CCDS41732.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.380740	0.82792	.	.	ENSG00000134917	ENST00000531752;ENST00000257359;ENST00000414575	T	0.59906	0.23	5.76	3.32	0.38043	.	0.038661	0.85682	D	0.000000	T	0.66761	0.2822	M	0.71581	2.175	0.38252	D	0.941647	D;D	0.64830	0.994;0.983	P;P	0.61070	0.883;0.874	T	0.67719	-0.5598	10	0.38643	T	0.18	.	7.6952	0.28590	0.0:0.0698:0.2792:0.651	.	632;113	Q9UP79;B3KVX9	ATS8_HUMAN;.	W	30;632;661	ENSP00000257359:R632W	ENSP00000257359:R632W	R	-	1	2	ADAMTS8	129783902	0.992000	0.36948	0.963000	0.40424	0.989000	0.77384	3.976000	0.56867	1.015000	0.39444	0.533000	0.62120	AGG	.	.		0.627	ADAMTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385636.1	NM_007037		A	130278692	T	A	130278692	3	1	344	1	0	0	0	0	1	0	0	0	272	1550	54	4	787	4	ADAMTS8	11	130278692	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	4788714	130278692	4727824	874	48237										
SNX19	399979	hgsc.bcm.edu	37	chr11	130748331	130748331	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaccagctaagaggagacacCcatcctcttagagttgcctg	9	12	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:130748331C>A	ENST00000265909.4	-	11	3534	c.2965G>T	c.(2965-2967)Ggt>Tgt	p.G989C	SNX19_ENST00000426933.2_Missense_Mutation_p.G157C|SNX19_ENST00000530356.1_Missense_Mutation_p.G369C|SNX19_ENST00000545537.1_Missense_Mutation_p.G229C|SNX19_ENST00000528555.1_Missense_Mutation_p.G369C|SNX19_ENST00000533318.1_5'UTR|SNX19_ENST00000539184.1_Missense_Mutation_p.G432C|SNX19_ENST00000534726.1_Missense_Mutation_p.G229C	NM_014758.2	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19	989					protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(8)|ovary(3)|prostate(1)|skin(6)|urinary_tract(1)	35	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		GAGGAGACACCCATCCTCTTA	0.542																																					p.G989C		Atlas-SNP	.											.	SNX19	84	.	0			c.G2965T						.						125	109	115					11																	130748331		2201	4297	6498	SO:0001583	missense	399979	exon11			AGACACCCATCCT	D87443	CCDS31721.1, CCDS73416.1	11q25	2010-04-20			ENSG00000120451	ENSG00000120451		"Sorting nexins"	21532	protein-coding gene	gene with protein product							Standard	NM_014758		Approved	KIAA0254, CHET8	uc001qgk.4	Q92543	OTTHUMG00000165663	ENST00000265909.4:c.2965G>T	chr11.hg19:g.130748331C>A	ENSP00000265909:p.Gly989Cys	116.0	0.0		81.0	40.0	NM_014758	E9PKB9|Q8IV55	Missense_Mutation	SNP	ENST00000265909.4	hg19	CCDS31721.1	.	.	.	.	.	.	.	.	.	.	C	14.05	2.420386	0.42918	.	.	ENSG00000120451	ENST00000265909;ENST00000534726;ENST00000545537;ENST00000426933;ENST00000528555;ENST00000530356;ENST00000539184	T;T;T;T;T;T;T	0.38887	2.59;1.15;1.15;1.11;1.7;1.7;2.01	5.7	3.85	0.44370	.	0.313086	0.28338	N	0.015702	T	0.49253	0.1546	L	0.54323	1.7	0.09310	N	1	D;D	0.58620	0.982;0.983	P;P	0.54026	0.74;0.671	T	0.42155	-0.9468	10	0.72032	D	0.01	-1.1043	10.6571	0.45682	0.0:0.8524:0.0:0.1476	.	432;989	F5H5D1;Q92543	.;SNX19_HUMAN	C	989;229;229;157;369;369;432	ENSP00000265909:G989C;ENSP00000433699:G229C;ENSP00000437982:G229C;ENSP00000413345:G157C;ENSP00000435122:G369C;ENSP00000432307:G369C;ENSP00000443480:G432C	ENSP00000265909:G989C	G	-	1	0	SNX19	130253541	0.000000	0.05858	0.609000	0.28983	0.210000	0.24377	0.310000	0.19356	0.769000	0.33313	-0.140000	0.14226	GGT	.	.		0.542	SNX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385649.1	NM_014758		A	130748331	C	A	130748331	3	1	344	1	0	0	0	0	1	0	0	0	14905	623	22	3	17	3	SNX19	11	130748331	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	469639	130748331	4258185	875	48238										
OPCML	4978	hgsc.bcm.edu	37	chr11	133402212	133402212	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agacgacccagtaggcaggaTggtacatctcgacgctgcgg	14	11	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:133402212T>C	ENST00000524381.1	-	1	202	c.8A>G	c.(7-9)cAt>cGt	p.H3R	OPCML_ENST00000529038.1_5'UTR	NM_001012393.1	NP_001012393.1	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion molecule-like	9					cell adhesion (GO:0007155)|neuron recognition (GO:0008038)|opioid receptor signaling pathway (GO:0038003)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	opioid receptor activity (GO:0004985)			endometrium(5)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|skin(2)|urinary_tract(8)	47	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		GTAGGCAGGATGGTACATCTC	0.587																																					p.H3R		Atlas-SNP	.											.	OPCML	166	.	0			c.A8G						.						105	75	85					11																	133402212		2201	4297	6498	SO:0001583	missense	4978	exon1			GCAGGATGGTACA	BX537377	CCDS8492.1, CCDS31722.1	11q25	2013-01-11	2001-11-28		ENSG00000183715	ENSG00000183715		"Immunoglobulin superfamily / I-set domain containing"	8143	protein-coding gene	gene with protein product	"IgLON family member 1"	600632	"opioid-binding protein/cell adhesion molecule-like"			8244387	Standard	XM_005271578		Approved	OPCM, OBCAM, IGLON1	uc001qgs.3	Q14982	OTTHUMG00000163658	ENST00000524381.1:c.8A>G	chr11.hg19:g.133402212T>C	ENSP00000434750:p.His3Arg	63.0	0.0		47.0	19.0	NM_001012393	B2CZX2|B7ZLQ1|Q17RN7|Q7Z3W6	Missense_Mutation	SNP	ENST00000524381.1	hg19	CCDS31722.1	.	.	.	.	.	.	.	.	.	.	T	10.88	1.476068	0.26511	.	.	ENSG00000183715	ENST00000524381;ENST00000416724	T	0.56444	0.46	5.19	5.19	0.71726	.	.	.	.	.	T	0.34803	0.0910	N	0.14661	0.345	0.80722	D	1	B	0.12013	0.005	B	0.15484	0.013	T	0.14952	-1.0454	9	0.18710	T	0.47	.	13.6316	0.62198	0.0:0.0:0.0:1.0	.	3	Q7Z3W6	.	R	3	ENSP00000434750:H3R	ENSP00000390643:H3R	H	-	2	0	OPCML	132907422	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.722000	0.61958	1.976000	0.57569	0.528000	0.53228	CAT	.	.		0.587	OPCML-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393269.1	NM_001012393		C	133402212	T	C	133402212	3	2	344	1	0	0	0	0	1	0	0	0	10883	1464	51	2	1122	2	OPCML	11	133402212	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2653881	133402212	1604304	876	48239										
GLB1L3	112937	hgsc.bcm.edu	37	chr11	134177095	134177095	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gataagcaccatgttaaagaTgcaaagggtgagtgttttgc	12	5	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr11:134177095T>C	ENST00000431683.2	+	10	954	c.954T>C	c.(952-954)gaT>gaC	p.D318D		NM_001080407.2	NP_001073876.2	Q8NCI6	GLBL3_HUMAN	galactosidase, beta 1-like 3	318					carbohydrate metabolic process (GO:0005975)		beta-galactosidase activity (GO:0004565)			endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|pancreas(1)	13	all_hematologic(175;0.127)	all_cancers(12;5.52e-23)|all_epithelial(12;2.15e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|all_neural(223;0.0182)|Medulloblastoma(222;0.0208)|Esophageal squamous(93;0.0559)		Epithelial(10;1.3e-11)|all cancers(11;2.07e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000873)|Lung(977;0.222)		ATGTTAAAGATGCAAAGGGTG	0.438																																					p.D318D		Atlas-SNP	.											.	GLB1L3	102	.	0			c.T954C						.						139	134	136					11																	134177095		1926	4137	6063	SO:0001819	synonymous_variant	112937	exon10			TAAAGATGCAAAG		CCDS44780.1	11q25	2008-11-06	2008-01-29		ENSG00000166105	ENSG00000166105			25147	protein-coding gene	gene with protein product						12477932	Standard	NM_001080407		Approved	FLJ90231	uc009zdf.3	Q8NCI6	OTTHUMG00000133524	ENST00000431683.2:c.954T>C	chr11.hg19:g.134177095T>C		61.0	0.0		58.0	22.0	NM_001080407	A6NEM0|A6NN15|Q6P3S3|Q96FF8	Silent	SNP	ENST00000431683.2	hg19	CCDS44780.1																																																																																			.	.		0.438	GLB1L3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393625.1	NM_138416		C	134177095	T	C	134177095	2	2	344	1	0	0	0	0	0	0	0	1	6438	1461	51	2		2	GLB1L3	11	134177095	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	774883	134177095	829421	877	48240										
B4GALNT3	283358	hgsc.bcm.edu	37	chr12	660161	660161	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaacccagctatctggtggaTgggcttcctctgcagcgcta	11	12	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:660161T>C	ENST00000266383.5	+	11	1084	c.1071T>C	c.(1069-1071)gaT>gaC	p.D357D		NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	357					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			ATCTGGTGGATGGGCTTCCTC	0.602																																					p.D357D		Atlas-SNP	.											.	B4GALNT3	64	.	0			c.T1071C						.						188	160	169					12																	660161		2203	4300	6503	SO:0001819	synonymous_variant	283358	exon11			GGTGGATGGGCTT	AB089940	CCDS8504.1	12p13.33	2013-02-19			ENSG00000139044	ENSG00000139044	2.4.1.-	"Beta 4-glycosyltransferases"	24137	protein-coding gene	gene with protein product		612220				12966086	Standard	NM_173593		Approved	B4GalNac-T3, FLJ16224, FLJ40362	uc001qii.1	Q6L9W6	OTTHUMG00000129283	ENST00000266383.5:c.1071T>C	chr12.hg19:g.660161T>C		114.0	0.0		65.0	29.0	NM_173593	Q6ZNC1|Q8N7T6	Silent	SNP	ENST00000266383.5	hg19	CCDS8504.1																																																																																			.	.		0.602	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593		C	660161	T	C	660161	2	2	344	1	0	0	0	0	0	0	0	1	1268	1461	51	2		2	B4GALNT3	12	660161	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10		660161	133191734	878	48241										
B4GALNT3	283358	hgsc.bcm.edu	37	chr12	662644	662644	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agaagaggaagcaaaaacccAgccctgagcccagccaagat	10	12	0	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:662644A>G	ENST00000266383.5	+	14	1568	c.1555A>G	c.(1555-1557)Agc>Ggc	p.S519G		NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	519					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			GCAAAAACCCAGCCCTGAGCC	0.632																																					p.S519G		Atlas-SNP	.											.	B4GALNT3	64	.	0			c.A1555G						.						43	49	47					12																	662644		2203	4300	6503	SO:0001583	missense	283358	exon14			AAACCCAGCCCTG	AB089940	CCDS8504.1	12p13.33	2013-02-19			ENSG00000139044	ENSG00000139044	2.4.1.-	"Beta 4-glycosyltransferases"	24137	protein-coding gene	gene with protein product		612220				12966086	Standard	NM_173593		Approved	B4GalNac-T3, FLJ16224, FLJ40362	uc001qii.1	Q6L9W6	OTTHUMG00000129283	ENST00000266383.5:c.1555A>G	chr12.hg19:g.662644A>G	ENSP00000266383:p.Ser519Gly	78.0	0.0		51.0	23.0	NM_173593	Q6ZNC1|Q8N7T6	Missense_Mutation	SNP	ENST00000266383.5	hg19	CCDS8504.1	.	.	.	.	.	.	.	.	.	.	A	9.299	1.052660	0.19907	.	.	ENSG00000139044	ENST00000266383;ENST00000322843	T;T	0.30981	3.52;1.51	5.76	1.98	0.26296	.	0.607121	0.20062	N	0.100064	T	0.18923	0.0454	L	0.40543	1.245	0.09310	N	1	B;B	0.23442	0.085;0.049	B;B	0.19666	0.026;0.016	T	0.19778	-1.0295	10	0.23891	T	0.37	-6.1084	3.1269	0.06411	0.638:0.146:0.0764:0.1396	.	422;519	E9PHD9;Q6L9W6	.;B4GN3_HUMAN	G	519;422	ENSP00000266383:S519G;ENSP00000322953:S422G	ENSP00000266383:S519G	S	+	1	0	B4GALNT3	532905	0.009000	0.17119	0.022000	0.16811	0.005000	0.04900	0.853000	0.27777	0.085000	0.17107	-0.333000	0.08304	AGC	.	.		0.632	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593		G	662644	A	G	662644	3	3	344	1	0	0	0	0	1	0	0	0	1268	188	7	2	1609	2	B4GALNT3	12	662644	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2483	662644	133189251	879	48242										
CACNA2D4	93589	hgsc.bcm.edu	37	chr12	1987485	1987485	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaagatctgtacctaccaggGgccggaggtcgggatgggag	18	8	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:1987485G>C	ENST00000382722.5	-	16	2077	c.1715C>G	c.(1714-1716)cCc>cGc	p.P572R	CACNA2D4_ENST00000585708.1_Missense_Mutation_p.P508R|CACNA2D4_ENST00000587995.1_Intron|CACNA2D4_ENST00000585732.1_Missense_Mutation_p.P457R|CACNA2D4_ENST00000588077.1_Missense_Mutation_p.P508R|CACNA2D4_ENST00000586184.1_Missense_Mutation_p.P572R	NM_172364.4	NP_758952.4	Q7Z3S7	CA2D4_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 4	572	Cache.				calcium ion transmembrane transport (GO:0070588)|detection of light stimulus involved in visual perception (GO:0050908)	voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			endometrium(3)|kidney(2)|large_intestine(1)|liver(1)|lung(27)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	39	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		ACCTACCAGGGGCCGGAGGTC	0.512																																					p.P572R	Colon(2;101 179 21030 23310 28141)	Atlas-SNP	.											.	CACNA2D4	220	.	0			c.C1715G						.						57	62	61					12																	1987485		1959	4152	6111	SO:0001583	missense	93589	exon16			ACCAGGGGCCGGA	AF516695	CCDS44785.1	12p13.33	2003-03-05			ENSG00000151062	ENSG00000151062		"Calcium channel subunits"	20202	protein-coding gene	gene with protein product		608171				12181424	Standard	NM_172364		Approved		uc021qsx.1	Q7Z3S7	OTTHUMG00000168111	ENST00000382722.5:c.1715C>G	chr12.hg19:g.1987485G>C	ENSP00000372169:p.Pro572Arg	82.0	0.0		61.0	31.0	NM_172364	Q7Z3S8|Q86XZ5|Q8IZS9	Missense_Mutation	SNP	ENST00000382722.5	hg19	CCDS44785.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.591998	0.86953	.	.	ENSG00000151062	ENST00000456077;ENST00000280663;ENST00000382722	T	0.12255	2.7	5.6	5.6	0.85130	Cache (1);	0.000000	0.85682	D	0.000000	T	0.36303	0.0962	L	0.55990	1.75	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.968;1.0	T	0.02901	-1.1096	10	0.87932	D	0	.	19.6224	0.95663	0.0:0.0:1.0:0.0	.	572;572	Q7Z3S7-2;Q7Z3S7	.;CA2D4_HUMAN	R	508;572;572	ENSP00000372169:P572R	ENSP00000280663:P572R	P	-	2	0	CACNA2D4	1857746	1.000000	0.71417	0.967000	0.41034	0.743000	0.42351	9.869000	0.99810	2.630000	0.89119	0.655000	0.94253	CCC	.	.		0.512	CACNA2D4-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398230.2			C	1987485	G	C	1987485	3	2	344	1	0	0	0	0	1	0	0	0	2553	1232	43	4	1790	4	CACNA2D4	12	1987485	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1324841	1987485	131864410	880	48243										
CACNA2D4	93589	hgsc.bcm.edu	37	chr12	2027475	2027475	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaggtgcctagaagcagcagCcacaggagggccgaggtctt	16	10	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:2027475C>A	ENST00000382722.5	-	1	527	c.165G>T	c.(163-165)tgG>tgT	p.W55C	CACNA2D4_ENST00000587995.1_Missense_Mutation_p.W55C|CACNA2D4_ENST00000585732.1_Missense_Mutation_p.W55C|CACNA2D4_ENST00000586184.1_Missense_Mutation_p.W55C|RP5-1096D14.3_ENST00000544163.1_RNA	NM_172364.4	NP_758952.4	Q7Z3S7	CA2D4_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 4	55					calcium ion transmembrane transport (GO:0070588)|detection of light stimulus involved in visual perception (GO:0050908)	voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			endometrium(3)|kidney(2)|large_intestine(1)|liver(1)|lung(27)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	39	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		GAAGCAGCAGCCACAGGAGGG	0.622																																					p.W55C	Colon(2;101 179 21030 23310 28141)	Atlas-SNP	.											.	CACNA2D4	220	.	0			c.G165T						.						20	23	22					12																	2027475		1897	4125	6022	SO:0001583	missense	93589	exon1			CAGCAGCCACAGG	AF516695	CCDS44785.1	12p13.33	2003-03-05			ENSG00000151062	ENSG00000151062		"Calcium channel subunits"	20202	protein-coding gene	gene with protein product		608171				12181424	Standard	NM_172364		Approved		uc021qsx.1	Q7Z3S7	OTTHUMG00000168111	ENST00000382722.5:c.165G>T	chr12.hg19:g.2027475C>A	ENSP00000372169:p.Trp55Cys	71.0	0.0		47.0	20.0	NM_172364	Q7Z3S8|Q86XZ5|Q8IZS9	Missense_Mutation	SNP	ENST00000382722.5	hg19	CCDS44785.1	.	.	.	.	.	.	.	.	.	.	C	8.307	0.821185	0.16678	.	.	ENSG00000151062	ENST00000280663;ENST00000382722	T	0.06768	3.26	5.27	-1.79	0.07932	.	0.319686	0.26203	N	0.025728	T	0.04452	0.0122	N	0.16478	0.41	0.33192	D	0.55105	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.001	T	0.22138	-1.0225	10	0.37606	T	0.19	.	9.1276	0.36826	0.4037:0.4548:0.1415:0.0	.	55;55	Q7Z3S7-2;Q7Z3S7	.;CA2D4_HUMAN	C	55	ENSP00000372169:W55C	ENSP00000280663:W55C	W	-	3	0	CACNA2D4	1897736	0.535000	0.26370	0.996000	0.52242	0.313000	0.28021	-0.126000	0.10563	-0.169000	0.10834	0.555000	0.69702	TGG	.	.		0.622	CACNA2D4-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398230.2			A	2027475	C	A	2027475	3	1	344	1	0	0	0	0	1	0	0	0	2553	740	26	3	3400	3	CACNA2D4	12	2027475	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	39990	2027475	131824420	881	48244										
FKBP4	2288	hgsc.bcm.edu	37	chr12	2909266	2909266	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acagagcaccatagtgaaagAgcggggcactgtgtacttca	12	9	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:2909266A>G	ENST00000001008.4	+	7	1011	c.824A>G	c.(823-825)gAg>gGg	p.E275G	RP4-816N1.7_ENST00000547042.1_RNA|RP4-816N1.6_ENST00000547834.1_RNA	NM_002014.3	NP_002005.1	Q02790	FKBP4_HUMAN	FK506 binding protein 4, 59kDa	275	Interaction with tubulin. {ECO:0000250}.				androgen receptor signaling pathway (GO:0030521)|chaperone-mediated protein folding (GO:0061077)|copper ion transport (GO:0006825)|embryo implantation (GO:0007566)|male sex differentiation (GO:0046661)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)|negative regulation of neuron projection development (GO:0010977)|prostate gland development (GO:0030850)|protein complex localization (GO:0031503)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)|steroid hormone receptor complex assembly (GO:0006463)	axonal growth cone (GO:0044295)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|FK506 binding (GO:0005528)|GTP binding (GO:0005525)|heat shock protein binding (GO:0031072)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(1)	14			OV - Ovarian serous cystadenocarcinoma(31;0.00105)			ATAGTGAAAGAGCGGGGCACT	0.522																																					p.E275G		Atlas-SNP	.											.	FKBP4	29	.	0			c.A824G						.						110	107	108					12																	2909266		2203	4300	6503	SO:0001583	missense	2288	exon7			TGAAAGAGCGGGG	M88279	CCDS8512.1	12p13.33	2013-01-10	2002-08-29		ENSG00000004478	ENSG00000004478		"Tetratricopeptide (TTC) repeat domain containing"	3720	protein-coding gene	gene with protein product		600611	"FK506-binding protein 4 (59kD)"			1279700	Standard	NM_002014		Approved	FKBP59, FKBP52	uc001qkz.3	Q02790	OTTHUMG00000090429	ENST00000001008.4:c.824A>G	chr12.hg19:g.2909266A>G	ENSP00000001008:p.Glu275Gly	49.0	0.0		50.0	22.0	NM_002014	D3DUQ1|Q9UCP1|Q9UCV7	Missense_Mutation	SNP	ENST00000001008.4	hg19	CCDS8512.1	.	.	.	.	.	.	.	.	.	.	A	28.2	4.902327	0.92035	.	.	ENSG00000004478	ENST00000001008	T	0.74737	-0.87	5.38	5.38	0.77491	Elongated TPR repeat-containing domain (1);Tetratricopeptide repeat-containing (1);	0.095878	0.64402	D	0.000001	T	0.81545	0.4845	M	0.78285	2.405	0.80722	D	1	D	0.56287	0.975	P	0.51945	0.685	D	0.84661	0.0706	10	0.87932	D	0	-36.2317	14.2345	0.65916	1.0:0.0:0.0:0.0	.	275	Q02790	FKBP4_HUMAN	G	275	ENSP00000001008:E275G	ENSP00000001008:E275G	E	+	2	0	FKBP4	2779527	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.875000	0.92372	2.046000	0.60703	0.459000	0.35465	GAG	.	.		0.522	FKBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206861.1			G	2909266	A	G	2909266	3	3	344	1	0	0	0	0	1	0	0	0	5918	304	11	2	850	2	FKBP4	12	2909266	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	881791	2909266	130942629	882	48245										
KCNA1	3736	hgsc.bcm.edu	37	chr12	5021211	5021211	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcttcacagaccccttcttcAtcgtggaaacgctgtgtatc	7	13	4	1	rs146948558		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:5021211A>C	ENST00000382545.3	+	2	1774	c.667A>C	c.(667-669)Atc>Ctc	p.I223L	KCNA1_ENST00000543874.2_Intron	NM_000217.2	NP_000208.2	Q09470	KCNA1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 1 (episodic ataxia with myokymia)	223					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|dendrite (GO:0030425)|juxtaparanode region of axon (GO:0044224)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|potassium ion transmembrane transporter activity (GO:0015079)			NS(1)|breast(3)|cervix(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(23)|ovary(3)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63					Amitriptyline(DB00321)|Dalfampridine(DB06637)|Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Nifedipine(DB01115)|Sevoflurane(DB01236)	CCCCTTCTTCATCGTGGAAAC	0.527																																					p.I223L		Atlas-SNP	.											.	KCNA1	112	.	0			c.A667C						.						114	86	96					12																	5021211		2203	4300	6503	SO:0001583	missense	3736	exon2			TTCTTCATCGTGG	L02750	CCDS8535.1	12p13	2012-07-05			ENSG00000111262	ENSG00000111262		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6218	protein-coding gene	gene with protein product		176260		AEMK		1349297, 8821794, 16382104	Standard	NM_000217		Approved	Kv1.1, RBK1, HUK1, MBK1	uc001qnh.3	Q09470	OTTHUMG00000044398	ENST00000382545.3:c.667A>C	chr12.hg19:g.5021211A>C	ENSP00000371985:p.Ile223Leu	118.0	0.0		77.0	43.0	NM_000217	A6NM83|Q3MIQ9	Missense_Mutation	SNP	ENST00000382545.3	hg19	CCDS8535.1	.	.	.	.	.	.	.	.	.	.	A	7.147	0.582931	0.13749	.	.	ENSG00000111262	ENST00000382545;ENST00000228858	D	0.98701	-5.08	4.86	4.86	0.63082	Ion transport (1);	0.122857	0.52532	D	0.000067	D	0.94525	0.8237	N	0.21583	0.68	0.44098	D	0.996869	B	0.02656	0.0	B	0.06405	0.002	D	0.89962	0.4087	10	0.18276	T	0.48	.	5.6778	0.17759	0.8151:0.0:0.1849:0.0	.	223	Q09470	KCNA1_HUMAN	L	223	ENSP00000371985:I223L	ENSP00000228858:I223L	I	+	1	0	KCNA1	4891472	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	2.883000	0.48554	2.162000	0.67917	0.533000	0.62120	ATC	.	A|1.000;G|0.000		0.527	KCNA1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103343.2	NM_000217		C	5021211	A	C	5021211	3	2	344	1	0	0	0	0	1	0	0	0	8010	217	8	5	669	5	KCNA1	12	5021211	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2111945	5021211	128830684	883	48246										
KCNA5	3741	hgsc.bcm.edu	37	chr12	5154056	5154056	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtatccggagagctctgggtCcgcgcgggccatcgccatcg	15	14	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:5154056C>T	ENST00000252321.3	+	1	972	c.743C>T	c.(742-744)tCc>tTc	p.S248F		NM_002234.3	NP_002225.2	P22460	KCNA5_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 5	248					atrial cardiac muscle cell action potential (GO:0086014)|membrane hyperpolarization (GO:0060081)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of potassium ion transport (GO:0043267)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of myoblast proliferation (GO:2000288)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transport (GO:0043266)|regulation of vasoconstriction (GO:0019229)|response to hypoxia (GO:0001666)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|intracellular canaliculus (GO:0046691)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|potassium channel inhibitor activity (GO:0019870)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization (GO:0086089)			NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(21)|ovary(5)|prostate(2)|upper_aerodigestive_tract(2)	52					Dalfampridine(DB06637)	AGCTCTGGGTCCGCGCGGGCC	0.577																																					p.S248F		Atlas-SNP	.											.	KCNA5	138	.	0			c.C743T						.						103	113	110					12																	5154056		2203	4300	6503	SO:0001583	missense	3741	exon1			CTGGGTCCGCGCG	M83254	CCDS8536.1	12p13	2012-07-05				ENSG00000130037		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6224	protein-coding gene	gene with protein product		176267				16382104	Standard	NM_002234		Approved	Kv1.5, HK2, HPCN1	uc001qni.4	P22460		ENST00000252321.3:c.743C>T	chr12.hg19:g.5154056C>T	ENSP00000252321:p.Ser248Phe	23.0	0.0		38.0	19.0	NM_002234	Q4KKT8|Q4VAJ1|Q4VAJ2|Q9UDA4	Missense_Mutation	SNP	ENST00000252321.3	hg19	CCDS8536.1	.	.	.	.	.	.	.	.	.	.	C	15.88	2.964473	0.53507	.	.	ENSG00000130037	ENST00000252321	T	0.69040	-0.37	4.77	4.77	0.60923	.	0.077875	0.53938	U	0.000058	T	0.62648	0.2445	L	0.33245	0.995	0.51482	D	0.999921	P	0.35684	0.515	B	0.40636	0.335	T	0.68176	-0.5478	10	0.87932	D	0	.	16.9696	0.86295	0.0:1.0:0.0:0.0	.	248	P22460	KCNA5_HUMAN	F	248	ENSP00000252321:S248F	ENSP00000252321:S248F	S	+	2	0	KCNA5	5024317	0.826000	0.29277	0.157000	0.22605	0.980000	0.70556	7.584000	0.82572	2.478000	0.83669	0.561000	0.74099	TCC	.	.		0.577	KCNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398925.2	NM_002234		T	5154056	C	T	5154056	3	4	344	1	0	0	0	0	1	0	0	0	8015	855	30	3	745	3	KCNA5	12	5154056	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	132845	5154056	128697839	884	48247										
VWF	7450	hgsc.bcm.edu	37	chr12	6140731	6140731	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tccgaaaggtcccagggttaCtgccgcagtaatcctgggga	13	11	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:6140731C>T	ENST00000261405.5	-	21	2953	c.2699G>A	c.(2698-2700)aGt>aAt	p.S900N		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	900	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	CCCAGGGTTACTGCCGCAGTA	0.552																																					p.S900N		Atlas-SNP	.											.	VWF	338	.	0			c.G2699A						.						116	109	111					12																	6140731		2203	4300	6503	SO:0001583	missense	7450	exon21			GGGTTACTGCCGC		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"Endogenous ligands"	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.2699G>A	chr12.hg19:g.6140731C>T	ENSP00000261405:p.Ser900Asn	84.0	0.0		78.0	43.0	NM_000552	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	hg19	CCDS8539.1	.	.	.	.	.	.	.	.	.	.	C	6.472	0.455247	0.12283	.	.	ENSG00000110799	ENST00000261405	T	0.60548	0.18	5.58	3.74	0.42951	von Willebrand factor, type D domain (3);	1.072060	0.07297	N	0.873400	T	0.36799	0.0980	N	0.05177	-0.1	0.38996	D	0.95924	B	0.09022	0.002	B	0.10450	0.005	T	0.08310	-1.0728	10	0.16420	T	0.52	.	10.8663	0.46858	0.0:0.8416:0.0:0.1584	.	900	P04275	VWF_HUMAN	N	900	ENSP00000261405:S900N	ENSP00000261405:S900N	S	-	2	0	VWF	6010992	0.000000	0.05858	0.005000	0.12908	0.075000	0.17131	0.536000	0.23129	1.354000	0.45846	0.650000	0.86243	AGT	.	.		0.552	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		T	6140731	C	T	6140731	3	4	344	1	0	0	0	0	1	0	0	0	17261	565	20	3	5870	3	VWF	12	6140731	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	986675	6140731	127711164	885	48248										
VWF	7450	hgsc.bcm.edu	37	chr12	6143964	6143964	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggcatcacacacatggtctgTgcagttccacttccggtcct	9	14	2	0	rs371017187		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:6143964T>C	ENST00000261405.5	-	20	2829	c.2575A>G	c.(2575-2577)Aca>Gca	p.T859A		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	859					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	ACATGGTCTGTGCAGTTCCAC	0.592																																					p.T859A		Atlas-SNP	.											.	VWF	338	.	0			c.A2575G						.	T	ALA/THR	1,4405	2.1+/-5.4	0,1,2202	160	125	137		2575	4.4	1	12		137	0,8600		0,0,4300	no	missense	VWF	NM_000552.3	58	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	possibly-damaging	859/2814	6143964	1,13005	2203	4300	6503	SO:0001583	missense	7450	exon20			GGTCTGTGCAGTT		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"Endogenous ligands"	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.2575A>G	chr12.hg19:g.6143964T>C	ENSP00000261405:p.Thr859Ala	116.0	0.0		79.0	40.0	NM_000552	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	hg19	CCDS8539.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.146902	0.77888	2.27E-4	0.0	ENSG00000110799	ENST00000261405	T	0.66638	-0.22	5.56	4.38	0.52667	von Willebrand factor, type C (1);von Willebrand factor, type D domain (1);	0.000000	0.39615	N	0.001315	T	0.66771	0.2823	M	0.86178	2.8	0.80722	D	1	P	0.48294	0.908	B	0.38616	0.277	T	0.71133	-0.4681	10	0.87932	D	0	.	9.9408	0.41578	0.1523:0.0:0.0:0.8476	.	859	P04275	VWF_HUMAN	A	859	ENSP00000261405:T859A	ENSP00000261405:T859A	T	-	1	0	VWF	6014225	1.000000	0.71417	0.964000	0.40570	0.950000	0.60333	2.456000	0.44997	0.890000	0.36211	0.482000	0.46254	ACA	.	.		0.592	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		C	6143964	T	C	6143964	3	2	344	1	0	0	0	0	1	0	0	0	17261	1696	59	2	5998	2	VWF	12	6143964	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	3233	6143964	127707931	886	48249										
CLEC2B	9976	hgsc.bcm.edu	37	chr12	10005916	10005916	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aacttagtgtattcttttccTgcaaatccattttctttcgg	5	9	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:10005916T>A	ENST00000228438.2	-	5	1366	c.433A>T	c.(433-435)Agg>Tgg	p.R145W	CLEC2B_ENST00000538152.1_Missense_Mutation_p.R76W	NM_005127.2	NP_005118.2	Q92478	CLC2B_HUMAN	C-type lectin domain family 2, member B	145	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.					integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			endometrium(1)|large_intestine(3)|lung(1)	5						ATTCTTTTCCTGCAAATCCAT	0.363																																					p.R145W		Atlas-SNP	.											.	CLEC2B	19	.	0			c.A433T						.						171	144	153					12																	10005916		2203	4300	6503	SO:0001583	missense	9976	exon5			TTTTCCTGCAAAT	X96719	CCDS8605.1	12p13-p12	2005-02-09	2005-02-09	2005-02-09		ENSG00000110852		"C-type lectin domain containing"	2053	protein-coding gene	gene with protein product		603242	"C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 2 (activation-induced)"	CLECSF2		9038101	Standard	NM_005127		Approved	AICL, HP10085	uc001qwn.3	Q92478		ENST00000228438.2:c.433A>T	chr12.hg19:g.10005916T>A	ENSP00000228438:p.Arg145Trp	51.0	0.0		59.0	29.0	NM_005127	B2R9U1|Q8IZE9|Q9BS74|Q9UQB4	Missense_Mutation	SNP	ENST00000228438.2	hg19	CCDS8605.1	.	.	.	.	.	.	.	.	.	.	T	11.16	1.555914	0.27827	.	.	ENSG00000110852	ENST00000228438;ENST00000538152	T;T	0.17528	2.27;2.27	2.94	1.75	0.24633	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.425811	0.18615	N	0.136025	T	0.29556	0.0737	L	0.53249	1.67	0.09310	N	1	D	0.76494	0.999	D	0.69142	0.962	T	0.03483	-1.1032	10	0.72032	D	0.01	.	6.171	0.20416	0.0:0.0:0.2616:0.7384	.	145	Q92478	CLC2B_HUMAN	W	145;76	ENSP00000228438:R145W;ENSP00000437946:R76W	ENSP00000228438:R145W	R	-	1	2	CLEC2B	9897183	0.204000	0.23447	0.203000	0.23512	0.129000	0.20672	0.250000	0.18235	0.520000	0.28426	0.528000	0.53228	AGG	.	.		0.363	CLEC2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399881.1	NM_005127		A	10005916	T	A	10005916	3	1	344	1	0	0	0	0	1	0	0	0	3509	1579	55	4	20	4	CLEC2B	12	10005916	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	3861952	10005916	123845979	887	48250										
TAS2R7	50837	hgsc.bcm.edu	37	chr12	10954328	10954328	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccagtattaggataaatgaaTgacttgaggggtagattaga	12	3	0	5			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:10954328T>C	ENST00000240687.2	-	1	898	c.842A>G	c.(841-843)cAt>cGt	p.H281R		NM_023919.2	NP_076408.1	Q9NYW3	TA2R7_HUMAN	taste receptor, type 2, member 7	281					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			kidney(1)|large_intestine(1)|lung(3)|skin(2)|stomach(3)	10						GATAAATGAATGACTTGAGGG	0.368																																					p.H281R		Atlas-SNP	.											.	TAS2R7	35	.	0			c.A842G						.						99	99	99					12																	10954328		2203	4300	6503	SO:0001583	missense	50837	exon1			AATGAATGACTTG	AF227133	CCDS8631.1	12p13	2012-08-22			ENSG00000121377	ENSG00000121377		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14913	protein-coding gene	gene with protein product		604793				10761934, 10766242	Standard	NM_023919		Approved	T2R7, TRB4	uc001qyv.3	Q9NYW3	OTTHUMG00000168505	ENST00000240687.2:c.842A>G	chr12.hg19:g.10954328T>C	ENSP00000240687:p.His281Arg	133.0	0.0		104.0	43.0	NM_023919	Q645Y1	Missense_Mutation	SNP	ENST00000240687.2	hg19	CCDS8631.1	.	.	.	.	.	.	.	.	.	.	T	13.72	2.321970	0.41096	.	.	ENSG00000121377	ENST00000240687	T	0.03982	3.74	5.19	5.19	0.71726	GPCR, rhodopsin-like superfamily (1);	0.173105	0.36482	N	0.002570	T	0.31263	0.0791	H	0.95079	3.62	0.36709	D	0.880533	D	0.89917	1.0	D	0.97110	1.0	T	0.54702	-0.8254	10	0.87932	D	0	.	13.0838	0.59129	0.0:0.0:0.0:1.0	.	281	Q9NYW3	TA2R7_HUMAN	R	281	ENSP00000240687:H281R	ENSP00000240687:H281R	H	-	2	0	TAS2R7	10845595	1.000000	0.71417	0.666000	0.29783	0.162000	0.22319	4.708000	0.61859	2.181000	0.69327	0.524000	0.50904	CAT	.	.		0.368	TAS2R7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399931.1			C	10954328	T	C	10954328	3	2	344	1	0	0	0	0	1	0	0	0	15601	1464	51	2	118	2	TAS2R7	12	10954328	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	948412	10954328	122897567	888	48251										
GPRC5A	9052	hgsc.bcm.edu	37	chr12	13061653	13061653	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgaatatattgtcctgaccaTgaataggaccaacgtcaatg	8	8	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:13061653T>C	ENST00000014914.5	+	2	1360	c.470T>C	c.(469-471)aTg>aCg	p.M157T	GPRC5A_ENST00000542056.1_Intron	NM_003979.3	NP_003970.1	Q8NFJ5	RAI3_HUMAN	G protein-coupled receptor, class C, group 5, member A	157					signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	18		Prostate(47;0.141)		BRCA - Breast invasive adenocarcinoma(232;0.0708)	Tretinoin(DB00755)	GTCCTGACCATGAATAGGACC	0.522																																					p.M157T		Atlas-SNP	.											.	GPRC5A	38	.	0			c.T470C						.						218	203	208					12																	13061653		2203	4300	6503	SO:0001583	missense	9052	exon2			TGACCATGAATAG	AF095448	CCDS8657.1	12p13-p12.3	2014-01-30	2014-01-30	2005-05-03		ENSG00000013588		"GPCR / Class C : Orphans"	9836	protein-coding gene	gene with protein product		604138	"retinoic acid induced 3", "G protein-coupled receptor, family C, group 5, member A"	RAI3, GPCR5A		9857033	Standard	NM_003979		Approved	RAIG1	uc001rba.3	Q8NFJ5		ENST00000014914.5:c.470T>C	chr12.hg19:g.13061653T>C	ENSP00000014914:p.Met157Thr	81.0	0.0		64.0	34.0	NM_003979	B3KV45|O95357	Missense_Mutation	SNP	ENST00000014914.5	hg19	CCDS8657.1	.	.	.	.	.	.	.	.	.	.	T	18.52	3.641859	0.67244	.	.	ENSG00000013588	ENST00000014914;ENST00000534831	D;D	0.87103	-2.21;-2.21	5.63	5.63	0.86233	GPCR, family 3, C-terminal (1);	0.063209	0.64402	D	0.000003	D	0.89667	0.6781	M	0.64997	1.995	0.50467	D	0.999877	P;D	0.57257	0.912;0.979	P;P	0.54759	0.629;0.76	D	0.87615	0.2506	10	0.22706	T	0.39	-20.0187	15.8307	0.78749	0.0:0.0:0.0:1.0	.	157;157	Q8NFJ5;A8K556	RAI3_HUMAN;.	T	157	ENSP00000014914:M157T;ENSP00000441627:M157T	ENSP00000014914:M157T	M	+	2	0	GPRC5A	12952920	1.000000	0.71417	1.000000	0.80357	0.688000	0.40055	1.742000	0.38248	2.148000	0.66965	0.459000	0.35465	ATG	.	.		0.522	GPRC5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400682.1			C	13061653	T	C	13061653	3	2	344	1	0	0	0	0	1	0	0	0	6733	1464	51	2	472	2	GPRC5A	12	13061653	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2107325	13061653	120790242	889	48252										
HEBP1	50865	hgsc.bcm.edu	37	chr12	13140219	13140219	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctgcagagagccatcttcatTggggaacacagcaaaggaaa	11	9	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:13140219T>A	ENST00000014930.4	-	3	423	c.265A>T	c.(265-267)Aat>Tat	p.N89Y	HEBP1_ENST00000536942.1_Missense_Mutation_p.N89Y|RP11-392P7.6_ENST00000499948.2_RNA	NM_015987.4	NP_057071.2	Q9NRV9	HEBP1_HUMAN	heme binding protein 1	89					circadian rhythm (GO:0007623)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	heme binding (GO:0020037)			breast(1)|endometrium(1)|large_intestine(3)|lung(1)|urinary_tract(1)	7		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.153)		CCATCTTCATTGGGGAACACA	0.468																																					p.N89Y		Atlas-SNP	.											.	HEBP1	16	.	0			c.A265T						.						82	82	82					12																	13140219		2203	4300	6503	SO:0001583	missense	50865	exon3			CTTCATTGGGGAA	AF117615	CCDS31749.1	12p13.2	2014-01-30			ENSG00000013583	ENSG00000013583		"Endogenous ligands"	17176	protein-coding gene	gene with protein product		605826				10640688	Standard	NM_015987		Approved	HEBP, HBP	uc001rbd.3	Q9NRV9	OTTHUMG00000168771	ENST00000014930.4:c.265A>T	chr12.hg19:g.13140219T>A	ENSP00000014930:p.Asn89Tyr	127.0	0.0		126.0	53.0	NM_015987	A8K1G2|Q9Y5Z5	Missense_Mutation	SNP	ENST00000014930.4	hg19	CCDS31749.1	.	.	.	.	.	.	.	.	.	.	T	13.88	2.370368	0.42003	.	.	ENSG00000013583	ENST00000014930;ENST00000535636;ENST00000536942	T;T;T	0.22336	1.96;1.96;1.96	5.66	-4.11	0.03928	Regulatory factor, effector, bacterial (1);	1.181070	0.05676	N	0.589520	T	0.15912	0.0383	L	0.29908	0.895	0.09310	N	1	B	0.24651	0.108	B	0.25759	0.063	T	0.44298	-0.9337	10	0.56958	D	0.05	-21.5939	10.4353	0.44433	0.0:0.625:0.1396:0.2354	.	89	Q9NRV9	HEBP1_HUMAN	Y	89;18;89	ENSP00000014930:N89Y;ENSP00000442020:N18Y;ENSP00000441678:N89Y	ENSP00000014930:N89Y	N	-	1	0	HEBP1	13031486	0.002000	0.14202	0.002000	0.10522	0.993000	0.82548	0.002000	0.13061	-0.315000	0.08703	0.533000	0.62120	AAT	.	.		0.468	HEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401001.1			A	13140219	T	A	13140219	3	1	344	1	0	0	0	0	1	0	0	0	7045	1812	63	4	312	4	HEBP1	12	13140219	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	78566	13140219	120711676	890	48253										
ART4	420	hgsc.bcm.edu	37	chr12	14993397	14993397	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	accttttagcagctgacagtTatatgtgctcaggttcccag	9	10	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:14993397T>C	ENST00000228936.4	-	2	1216	c.835A>G	c.(835-837)Aac>Gac	p.N279D	RP11-233G1.4_ENST00000444324.2_RNA|C12orf60_ENST00000527783.1_Intron	NM_021071.2	NP_066549.2	Q93070	NAR4_HUMAN	ADP-ribosyltransferase 4 (Dombrock blood group)	279					arginine metabolic process (GO:0006525)|protein ADP-ribosylation (GO:0006471)	anchored component of membrane (GO:0031225)|membrane (GO:0016020)|plasma membrane (GO:0005886)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)			large_intestine(5)|liver(1)|lung(3)|prostate(1)|skin(2)|stomach(3)	15						AGCTGACAGTTATATGTGCTC	0.403																																					p.N279D		Atlas-SNP	.											.	ART4	27	.	0			c.A835G						.						60	59	59					12																	14993397		2203	4300	6503	SO:0001583	missense	420	exon2			GACAGTTATATGT	X95826	CCDS8668.1	12q13.2-q13.3	2014-07-18	2014-01-02	2006-01-12	ENSG00000111339	ENSG00000111339		"CD molecules", "Blood group antigens"	726	protein-coding gene	gene with protein product		110600	"Dombrock blood group", "ADP-ribosyltransferase 4 (DO blood group)", "ADP-ribosyltransferase 4"	DO		9119374	Standard	NM_021071		Approved	DOK1, CD297	uc001rcl.1	Q93070	OTTHUMG00000168738	ENST00000228936.4:c.835A>G	chr12.hg19:g.14993397T>C	ENSP00000228936:p.Asn279Asp	57.0	0.0		49.0	21.0	NM_021071	Q9BZ50|Q9BZ51|Q9HB06	Missense_Mutation	SNP	ENST00000228936.4	hg19	CCDS8668.1	.	.	.	.	.	.	.	.	.	.	T	17.92	3.505731	0.64410	.	.	ENSG00000111339	ENST00000228936;ENST00000420600	T;T	0.10192	2.9;2.9	4.07	4.07	0.47477	.	0.279897	0.31648	N	0.007284	T	0.15652	0.0377	L	0.27053	0.805	0.39380	D	0.96624	D;D	0.58620	0.983;0.983	P;P	0.57324	0.818;0.818	T	0.02307	-1.1179	10	0.72032	D	0.01	-5.3207	11.6718	0.51406	0.0:0.0:0.0:1.0	.	279;279	A8K6J7;Q93070	.;NAR4_HUMAN	D	279;262	ENSP00000228936:N279D;ENSP00000405689:N262D	ENSP00000228936:N279D	N	-	1	0	ART4	14884664	0.999000	0.42202	0.909000	0.35828	0.586000	0.36452	3.627000	0.54252	2.077000	0.62373	0.533000	0.62120	AAC	.	.		0.403	ART4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400859.1	NM_021071		C	14993397	T	C	14993397	3	2	344	1	0	0	0	0	1	0	0	0	999	1754	61	2	117	2	ART4	12	14993397	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1853178	14993397	118858498	891	48254										
KIAA0528	9847	hgsc.bcm.edu	37	chr12	22606848	22606848	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acctggtttttatttggattCtccatgaagacacactgctt	7	9	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:22606848C>T	ENST00000333957.4	-	24	3108	c.2853G>A	c.(2851-2853)gaG>gaA	p.E951E	C2CD5_ENST00000396028.2_Silent_p.E993E|C2CD5_ENST00000545552.1_Silent_p.E1005E|C2CD5_ENST00000544930.1_Silent_p.E807E|C2CD5_ENST00000536386.1_Silent_p.E1004E|C2CD5_ENST00000542676.1_Silent_p.E1002E|C2CD5_ENST00000446597.1_Silent_p.E1002E	NM_014802.1	NP_055617.1	Q86YS7	C2CD5_HUMAN	C2 calcium-dependent domain containing 5	951					cellular response to insulin stimulus (GO:0032869)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|intracellular protein transmembrane transport (GO:0065002)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)										TATTTGGATTCTCCATGAAGA	0.433																																					p.E951E		Atlas-SNP	.											KIAA0528_ENST00000544930,NS,carcinoma,0,2	.	.	.	0			c.G2853A						.						145	140	142					12																	22606848		2203	4300	6503	SO:0001819	synonymous_variant	9847	exon24			TGGATTCTCCATG	AB011100	CCDS31758.1, CCDS66337.1, CCDS66338.1, CCDS66339.1, CCDS66340.1	12p12.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000111731	ENSG00000111731			29062	protein-coding gene	gene with protein product	"138 kDa C2 domain-containing phosphoprotein"		"KIAA0528"	KIAA0528		21907143	Standard	XM_005253538		Approved	CDP138	uc001rfq.3	Q86YS7	OTTHUMG00000169100	ENST00000333957.4:c.2853G>A	chr12.hg19:g.22606848C>T		124.0	0.0		92.0	40.0	NM_014802	B4DJ03|B4DRN7|B7ZLL0|F5H2A1|F5H5R1|O60280|Q17RY7|Q7Z619|Q86SU3	Silent	SNP	ENST00000333957.4	hg19	CCDS31758.1	.	.	.	.	.	.	.	.	.	.	C	7.679	0.688568	0.14973	.	.	ENSG00000111731	ENST00000539615	.	.	.	5.31	4.22	0.49857	.	.	.	.	.	T	0.69637	0.3133	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68603	-0.5365	4	.	.	.	-17.2473	14.8287	0.70132	0.0:0.9187:0.0:0.0813	.	.	.	.	K	252	.	.	R	-	2	0	KIAA0528	22498115	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.539000	0.36104	2.475000	0.83589	0.561000	0.74099	AGA	.	.		0.433	C2CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402257.1	NM_014802		T	22606848	C	T	22606848	2	4	344	1	0	0	0	0	0	0	0	1	8191	912	32	3		3	KIAA0528	12	22606848	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	7613451	22606848	111245047	892	48255										
C12orf35	55196	hgsc.bcm.edu	37	chr12	32137547	32137547	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acagttgtaaacaaggagagAgaacttctgatagagatgtc	11	5	1	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:32137547A>T	ENST00000312561.4	+	4	4072	c.3658A>T	c.(3658-3660)Aga>Tga	p.R1220*	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	1220																	ACAAGGAGAGAGAACTTCTGA	0.388																																					p.R1220X		Atlas-SNP	.											.	.	.	.	0			c.A3658T						.						83	84	84					12																	32137547		2203	4300	6503	SO:0001587	stop_gained	55196	exon4			GGAGAGAGAACTT	AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 35"	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.3658A>T	chr12.hg19:g.32137547A>T	ENSP00000310338:p.Arg1220*	83.0	0.0		72.0	27.0	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Nonsense_Mutation	SNP	ENST00000312561.4	hg19	CCDS8725.2	.	.	.	.	.	.	.	.	.	.	A	45	11.335947	0.99548	.	.	ENSG00000174718	ENST00000312561	.	.	.	5.01	-2.31	0.06765	.	1.451400	0.04289	N	0.345144	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.1233	0.20165	0.4283:0.3232:0.2485:0.0	.	.	.	.	X	1220	.	.	R	+	1	2	C12orf35	32028814	0.000000	0.05858	0.000000	0.03702	0.488000	0.33401	0.404000	0.20999	-0.049000	0.13379	0.460000	0.39030	AGA	.	.		0.388	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169		T	32137547	A	T	32137547	4	4	344	1	0	0	0	0	0	1	0	0	1684	296	11	4	3660	4	C12orf35	12	32137547	Nonsense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	9530699	32137547	101714348	893	48256										
SYT10	341359	hgsc.bcm.edu	37	chr12	33532888	33532888	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acactcctatgacctcattgTgtcctaccctatgatttgtg	6	12	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:33532888T>C	ENST00000228567.3	-	6	1675	c.1379A>G	c.(1378-1380)cAc>cGc	p.H460R	SYT10_ENST00000535526.1_Missense_Mutation_p.H279R	NM_198992.3	NP_945343.1	Q6XYQ8	SYT10_HUMAN	synaptotagmin X	460	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				regulation of calcium ion-dependent exocytosis (GO:0017158)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(3)|skin(4)|urinary_tract(1)	42	Lung NSC(5;8.37e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0334)					GACCTCATTGTGTCCTACCCT	0.393																																					p.H460R		Atlas-SNP	.											.	SYT10	109	.	0			c.A1379G						.						211	170	184					12																	33532888		2203	4300	6503	SO:0001583	missense	341359	exon6			TCATTGTGTCCTA	AY198413	CCDS8732.1	12p11	2013-01-21			ENSG00000110975	ENSG00000110975		"Synaptotagmins"	19266	protein-coding gene	gene with protein product							Standard	NM_198992		Approved		uc001rll.1	Q6XYQ8	OTTHUMG00000169269	ENST00000228567.3:c.1379A>G	chr12.hg19:g.33532888T>C	ENSP00000228567:p.His460Arg	93.0	0.0		68.0	35.0	NM_198992	Q495U2	Missense_Mutation	SNP	ENST00000228567.3	hg19	CCDS8732.1	.	.	.	.	.	.	.	.	.	.	T	19.14	3.770379	0.69992	.	.	ENSG00000110975	ENST00000228567;ENST00000535526	T;T	0.70045	-0.45;-0.45	4.3	4.3	0.51218	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.43747	U	0.000525	T	0.53610	0.1807	N	0.01209	-0.955	0.80722	D	1	D	0.67145	0.996	D	0.73708	0.981	T	0.57388	-0.7820	10	0.12766	T	0.61	.	13.6694	0.62416	0.0:0.0:0.0:1.0	.	460	Q6XYQ8	SYT10_HUMAN	R	460;279	ENSP00000228567:H460R;ENSP00000438691:H279R	ENSP00000228567:H460R	H	-	2	0	SYT10	33424155	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.536000	0.82023	2.165000	0.68154	0.528000	0.53228	CAC	.	.		0.393	SYT10-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403222.1	NM_198992		C	33532888	T	C	33532888	3	2	344	1	0	0	0	0	1	0	0	0	15481	1696	59	2	200	2	SYT10	12	33532888	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1395341	33532888	100319007	894	48257										
KIF21A	55605	hgsc.bcm.edu	37	chr12	39727052	39727052	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tagaaccacttcttggtttcTtttttgggcttccagaagtc	8	9	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:39727052T>A	ENST00000361418.5	-	18	2464	c.2449A>T	c.(2449-2451)Aga>Tga	p.R817*	KIF21A_ENST00000541463.2_Intron|KIF21A_ENST00000395670.3_Nonsense_Mutation_p.R817*|KIF21A_ENST00000361961.3_Nonsense_Mutation_p.R804*|KIF21A_ENST00000544797.2_Nonsense_Mutation_p.R804*			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	817					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(41)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	86		Lung NSC(34;0.179)|all_lung(34;0.213)				TCTTGGTTTCTTTTTTGGGCT	0.323																																					p.R817X		Atlas-SNP	.											.,2	KIF21A	238	.	0			c.A2449T						.						202	200	200					12																	39727052		2203	4300	6503	SO:0001587	stop_gained	55605	exon18			GGTTTCTTTTTTG	AK000059	CCDS31773.1, CCDS53774.1, CCDS53775.1, CCDS53776.1	12q12	2013-01-10						"Kinesins", "WD repeat domain containing"	19349	protein-coding gene	gene with protein product		608283	"fibrosis of the extraocular muscles, congenital, 1"	FEOM1		10225949	Standard	NM_017641		Approved	FLJ20052	uc001rly.3	Q7Z4S6	OTTHUMG00000169335	ENST00000361418.5:c.2449A>T	chr12.hg19:g.39727052T>A	ENSP00000354878:p.Arg817*	111.0	0.0		126.0	41.0	NM_001173464	A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	Nonsense_Mutation	SNP	ENST00000361418.5	hg19	CCDS53776.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	23.6|23.6	4.437653|4.437653	0.83885|0.83885	.|.	.|.	ENSG00000139116|ENSG00000139116	ENST00000552961|ENST00000361961;ENST00000395670;ENST00000341813;ENST00000544797;ENST00000361418	T|.	0.19938|.	2.11|.	5.36|5.36	4.19|4.19	0.49359|0.49359	.|.	.|0.000000	.|0.56097	.|D	.|0.000025	T|.	0.22513|.	0.0543|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.31861|.	-0.9928|.	5|.	0.52906|0.02654	T|T	0.07|1	.|.	8.4439|8.4439	0.32830|0.32830	0.0:0.0702:0.1308:0.799|0.0:0.0702:0.1308:0.799	.|.	.|.	.|.	.|.	N|X	164|804;817;817;804;817	ENSP00000447765:K164N|.	ENSP00000449698:K74N|ENSP00000344501:R817X	K|R	-|-	3|1	2|2	KIF21A|KIF21A	38013319|38013319	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	3.526000|3.526000	0.53509|0.53509	0.851000|0.851000	0.35264|0.35264	0.528000|0.528000	0.53228|0.53228	AAA|AGA	.	.		0.323	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403581.1	NM_017641		A	39727052	T	A	39727052	4	1	344	1	0	0	0	0	0	1	0	0	8297	1617	56	4	2659	4	KIF21A	12	39727052	Nonsense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	6194164	39727052	94124843	895	48258										
ABCD2	225	hgsc.bcm.edu	37	chr12	40010969	40010969	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tctgaagttgtttcatttctAcctatagagaggaaaaagag	9	5	3	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:40010969A>T	ENST00000308666.3	-	2	1076	c.941T>A	c.(940-942)gTa>gAa	p.V314E		NM_005164.3	NP_005155.1	Q9UBJ2	ABCD2_HUMAN	ATP-binding cassette, sub-family D (ALD), member 2	314	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				fatty acid beta-oxidation (GO:0006635)|positive regulation of fatty acid beta-oxidation (GO:0032000)|transmembrane transport (GO:0055085)|very long-chain fatty acid catabolic process (GO:0042760)|very long-chain fatty acid metabolic process (GO:0000038)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(24)|ovary(2)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	52						TTTCATTTCTACCTATAGAGA	0.299																																					p.V314E		Atlas-SNP	.											.	ABCD2	127	.	0			c.T941A						.						92	90	91					12																	40010969		2203	4300	6503	SO:0001630	splice_region_variant	225	exon2			ATTTCTACCTATA	U28150	CCDS8734.1	12q12	2012-05-16			ENSG00000173208	ENSG00000173208		"ATP binding cassette transporters / subfamily D"	66	protein-coding gene	gene with protein product		601081		ALDL1		8577752	Standard	NM_005164		Approved	ALDR, ALDRP	uc001rmb.2	Q9UBJ2	OTTHUMG00000169337	ENST00000308666.3:c.940-1T>A	chr12.hg19:g.40010969A>T		71.0	0.0		71.0	34.0	NM_005164	B2RAM3|Q13210|Q2M3H9	Missense_Mutation	SNP	ENST00000308666.3	hg19	CCDS8734.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.207586	0.79240	.	.	ENSG00000173208	ENST00000308666	D	0.91407	-2.84	5.0	5.0	0.66597	ABC transporter, N-terminal (1);ABC transporter, integral membrane type 1 (1);	0.062472	0.64402	D	0.000005	D	0.95217	0.8449	M	0.88377	2.95	0.58432	D	0.999997	P	0.45126	0.851	P	0.57776	0.827	D	0.95532	0.8604	9	.	.	.	-11.1284	15.0052	0.71507	1.0:0.0:0.0:0.0	.	314	Q9UBJ2	ABCD2_HUMAN	E	314	ENSP00000310688:V314E	.	V	-	2	0	ABCD2	38297236	1.000000	0.71417	0.998000	0.56505	0.956000	0.61745	8.832000	0.92079	1.999000	0.58509	0.533000	0.62120	GTA	.	.		0.299	ABCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403591.1	NM_005164	Missense_Mutation	T	40010969	A	T	40010969	5	4	344	1	0	0	0	0	0	0	1	0	61	405	14	4	1317	4	ABCD2	12	40010969	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	283917	40010969	93840926	896	48259										
NELL2	4753	hgsc.bcm.edu	37	chr12	45105173	45105173	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tctcaacaagtttcatggtcTggtcctgttagacaacagaa	8	9	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:45105173T>A	ENST00000429094.2	-	11	1595	c.1091A>T	c.(1090-1092)cAg>cTg	p.Q364L	NELL2_ENST00000452445.2_Missense_Mutation_p.Q364L|NELL2_ENST00000395487.2_Missense_Mutation_p.Q363L|NELL2_ENST00000549027.1_Missense_Mutation_p.Q363L|NELL2_ENST00000437801.2_Missense_Mutation_p.Q414L|NELL2_ENST00000551601.1_Missense_Mutation_p.Q363L|NELL2_ENST00000333837.4_Missense_Mutation_p.Q387L	NM_001145108.1	NP_001138580.1	Q99435	NELL2_HUMAN	NEL-like 2 (chicken)	364						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(16)|lung(30)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	65	Lung SC(27;0.192)	Lung NSC(34;0.144)		GBM - Glioblastoma multiforme(48;0.092)		TTTCATGGTCTGGTCCTGTTA	0.398																																					p.Q414L		Atlas-SNP	.											.	NELL2	286	.	0			c.A1241T						.						102	90	94					12																	45105173		2203	4300	6503	SO:0001583	missense	4753	exon12			ATGGTCTGGTCCT	D83018	CCDS8746.1, CCDS44863.1, CCDS44864.1, CCDS53781.1	12q12	2012-01-30	2001-11-28		ENSG00000184613	ENSG00000184613			7751	protein-coding gene	gene with protein product		602320	"nel (chicken)-like 2"			19249368	Standard	NM_006159		Approved	NRP2	uc010skz.1	Q99435	OTTHUMG00000169464	ENST00000429094.2:c.1091A>T	chr12.hg19:g.45105173T>A	ENSP00000390680:p.Gln364Leu	75.0	0.0		83.0	23.0	NM_001145107	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Missense_Mutation	SNP	ENST00000429094.2	hg19	CCDS8746.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	10.68|10.68	1.419091|1.419091	0.25552|0.25552	.|.	.|.	ENSG00000184613|ENSG00000184613	ENST00000395487;ENST00000429094;ENST00000551601;ENST00000452445;ENST00000549027;ENST00000333837;ENST00000437801;ENST00000543684|ENST00000550313	T;T;T;T;T;T;T|.	0.65178|.	-0.14;-0.14;-0.14;-0.14;-0.14;-0.14;-0.14|.	5.79|5.79	5.79|5.79	0.91817|0.91817	.|.	0.405452|.	0.28853|.	N|.	0.013922|.	T|.	0.53899|.	0.1825|.	L|L	0.36672|0.36672	1.1|1.1	0.34518|0.34518	D|D	0.707848|0.707848	B;B;B;B;B;B|.	0.20887|.	0.049;0.017;0.028;0.035;0.017;0.01|.	B;B;B;B;B;B|.	0.21360|.	0.026;0.028;0.034;0.011;0.009;0.017|.	T|.	0.62515|.	-0.6838|.	10|.	0.56958|.	D|.	0.05|.	-8.0739|-8.0739	16.1415|16.1415	0.81528|0.81528	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	387;414;363;364;364;363|.	B7Z2U7;B7Z9U3;F8VVB6;B3KTI3;Q99435;Q96JS2|.	.;.;.;.;NELL2_HUMAN;.|.	L|X	363;364;363;364;363;387;414;363|108	ENSP00000378866:Q363L;ENSP00000390680:Q364L;ENSP00000449332:Q363L;ENSP00000394612:Q364L;ENSP00000447927:Q363L;ENSP00000327988:Q387L;ENSP00000416341:Q414L|.	ENSP00000327988:Q387L|.	Q|R	-|-	2|1	0|2	NELL2|NELL2	43391440|43391440	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.947000|0.947000	0.59692|0.59692	4.195000|4.195000	0.58400|0.58400	2.198000|2.198000	0.70561|0.70561	0.533000|0.533000	0.62120|0.62120	CAG|AGA	.	.		0.398	NELL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404180.1	NM_006159		A	45105173	T	A	45105173	3	1	344	1	0	0	0	0	1	0	0	0	10343	1580	55	4	1399	4	NELL2	12	45105173	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	5094204	45105173	88746722	897	48260										
SLC38A2	54407	hgsc.bcm.edu	37	chr12	46760941	46760941	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttatatcccaattgttcataTaataaagaccctacaatttg	3	8	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:46760941T>C	ENST00000256689.5	-	6	843	c.399A>G	c.(397-399)ttA>ttG	p.L133L	SLC38A2_ENST00000547252.1_5'UTR|SLC38A2_ENST00000551374.1_5'Flank	NM_018976.4	NP_061849.2	Q96QD8	S38A2_HUMAN	solute carrier family 38, member 2	133					amino acid transport (GO:0006865)|glutamate secretion (GO:0014047)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|sodium ion transport (GO:0006814)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|symporter activity (GO:0015293)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	18	Lung SC(27;0.192)|Renal(347;0.236)		OV - Ovarian serous cystadenocarcinoma(5;0.0048)|Epithelial(2;0.0374)	GBM - Glioblastoma multiforme(48;0.226)		ATTGTTCATATAATAAAGACC	0.318																																					p.L133L	Ovarian(9;448 492 8335 28722 40361)	Atlas-SNP	.											.	SLC38A2	36	.	0			c.A399G						.						87	92	91					12																	46760941		2203	4299	6502	SO:0001819	synonymous_variant	54407	exon6			TTCATATAATAAA	AB037803	CCDS8749.1	12q13.11	2014-08-12			ENSG00000134294	ENSG00000134294		"Solute carriers"	13448	protein-coding gene	gene with protein product		605180				10747860, 17237199	Standard	NM_018976		Approved	SAT2, ATA2, KIAA1382, SNAT2	uc001rpg.3	Q96QD8	OTTHUMG00000169471	ENST00000256689.5:c.399A>G	chr12.hg19:g.46760941T>C		183.0	0.0		150.0	16.0	NM_018976	Q6IA88|Q6ZMG2|Q9HAV3|Q9NVA8|Q9P2G5	Silent	SNP	ENST00000256689.5	hg19	CCDS8749.1																																																																																			.	.		0.318	SLC38A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404226.1			C	46760941	T	C	46760941	2	2	344	1	0	0	0	0	0	0	0	1	14619	1403	49	2		2	SLC38A2	12	46760941	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1655768	46760941	87090954	898	48261										
MLL2	8085	hgsc.bcm.edu	37	chr12	49420043	49420043	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tacaaactccggccgcccgtTgttctcaccaatagaacagc	7	15	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:49420043T>G	ENST00000301067.7	-	48	15705	c.15706A>C	c.(15706-15708)Aac>Cac	p.N5236H		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	5236	FYR C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00876}.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										GGCCGCCCGTTGTTCTCACCA	0.587																																					p.N5236H		Atlas-SNP	.											.	MLL2	1173	.	0			c.A15706C						.						63	67	65					12																	49420043		1969	4148	6117	SO:0001583	missense	8085	exon48			GCCCGTTGTTCTC	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.15706A>C	chr12.hg19:g.49420043T>G	ENSP00000301067:p.Asn5236His	98.0	0.0		94.0	45.0	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	hg19	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	T	11.34	1.608648	0.28623	.	.	ENSG00000167548	ENST00000301067	T	0.79454	-1.27	5.11	2.74	0.32292	.	0.000000	0.39544	N	0.001337	T	0.75347	0.3837	N	0.22421	0.69	0.36033	D	0.839544	D	0.67145	0.996	P	0.62014	0.897	T	0.79478	-0.1787	10	0.87932	D	0	.	8.3682	0.32399	0.0:0.167:0.0:0.833	.	5236	O14686	MLL2_HUMAN	H	5236	ENSP00000301067:N5236H	ENSP00000301067:N5236H	N	-	1	0	MLL2	47706310	0.996000	0.38824	1.000000	0.80357	0.996000	0.88848	1.590000	0.36654	0.901000	0.36495	0.528000	0.53228	AAC	.	.		0.587	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			G	49420043	T	G	49420043	3	3	344	1	0	0	0	0	1	0	0	0	9630	1812	63	5	935	5	MLL2	12	49420043	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2659102	49420043	84431852	899	48262										
TUBA1C	84790	hgsc.bcm.edu	37	chr12	49666554	49666554	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	accaatgcttgctttgagccAgccaaccagatggtgaaatg	10	10	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:49666554A>T	ENST00000301072.6	+	4	1169	c.894A>T	c.(892-894)ccA>ccT	p.P298P	RP11-161H23.5_ENST00000550468.2_RNA|TUBA1C_ENST00000541364.1_Silent_p.P368P	NM_032704.3	NP_116093.1	Q9BQE3	TBA1C_HUMAN	tubulin, alpha 1c	298					'de novo' posttranslational protein folding (GO:0051084)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasmic microtubule (GO:0005881)|microtubule (GO:0005874)|nucleus (GO:0005634)|vesicle (GO:0031982)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(3)|liver(1)|lung(7)|skin(1)	13						GCTTTGAGCCAGCCAACCAGA	0.512																																					p.P298P		Atlas-SNP	.											.	TUBA1C	32	.	0			c.A894T						.						62	81	74					12																	49666554		2203	4300	6503	SO:0001819	synonymous_variant	84790	exon4			TGAGCCAGCCAAC	BC004949	CCDS8782.1	12q13.12	2007-03-16	2007-02-12	2007-02-12		ENSG00000167553		"Tubulins"	20768	protein-coding gene	gene with protein product			"tubulin, alpha 6"	TUBA6		7821789	Standard	NM_032704		Approved	MGC14580, MGC10851, bcm948	uc001rtt.1	Q9BQE3		ENST00000301072.6:c.894A>T	chr12.hg19:g.49666554A>T		233.0	0.0		190.0	105.0	NM_032704		Silent	SNP	ENST00000301072.6	hg19	CCDS8782.1																																																																																			.	.		0.512	TUBA1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404424.1	NM_032704		T	49666554	A	T	49666554	2	4	344	1	0	0	0	0	0	0	0	1	16760	175	7	4		4	TUBA1C	12	49666554	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	246511	49666554	84185341	900	48263										
FAIM2	23017	hgsc.bcm.edu	37	chr12	50294962	50294962	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agaggcaccgctgtgggggcTggggggaaggcccctgcctt	19	11	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:50294962T>A	ENST00000320634.3	-	2	256	c.162A>T	c.(160-162)ccA>ccT	p.P54P	FAIM2_ENST00000550890.1_Silent_p.P8P	NM_012306.3	NP_036438.2	Q9BWQ8	LFG2_HUMAN	Fas apoptotic inhibitory molecule 2	54					apoptotic process (GO:0006915)|cerebellar granular layer development (GO:0021681)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellar Purkinje cell layer development (GO:0021680)|cerebellum development (GO:0021549)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of neuron apoptotic process (GO:0043524)|regulation of neuron apoptotic process (GO:0043523)|response to ischemia (GO:0002931)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|postsynaptic membrane (GO:0045211)				endometrium(2)|large_intestine(4)|lung(4)|ovary(2)|skin(2)	14						CTGTGGGGGCTGGGGGGAAGG	0.642																																					p.P54P		Atlas-SNP	.											.	FAIM2	32	.	0			c.A162T						.						23	24	24					12																	50294962		2203	4300	6503	SO:0001819	synonymous_variant	23017	exon2			GGGGGCTGGGGGG	AB023167	CCDS8791.1	12q13	2010-03-18				ENSG00000135472			17067	protein-coding gene	gene with protein product	"transmembrane BAX inhibitor motif containing 2"	604306				10231032, 10535980	Standard	NM_012306		Approved	KIAA0950, LFG, NMP35, LIFEGUARD, TMBIM2, LFG2	uc001rvj.2	Q9BWQ8	OTTHUMG00000169808	ENST00000320634.3:c.162A>T	chr12.hg19:g.50294962T>A		23.0	0.0		33.0	12.0	NM_012306	A8K1W6|B3KR08|Q9UJY9|Q9Y2F7	Silent	SNP	ENST00000320634.3	hg19	CCDS8791.1																																																																																			.	.		0.642	FAIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405984.1	NM_012306		A	50294962	T	A	50294962	2	1	344	1	0	0	0	0	0	0	0	1	5381	1567	55	4		4	FAIM2	12	50294962	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	628408	50294962	83556933	901	48264										
ACCN2	41	hgsc.bcm.edu	37	chr12	50473727	50473727	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggagtactgcgtgtgtgaaaTgccttgcaacctgacccgct	12	11	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:50473727T>C	ENST00000447966.2	+	8	1323	c.1094T>C	c.(1093-1095)aTg>aCg	p.M365T	ASIC1_ENST00000228468.4_Missense_Mutation_p.M365T|ASIC1_ENST00000552438.1_Missense_Mutation_p.M399T	NM_001095.3	NP_001086.2	P78348	ASIC1_HUMAN	acid-sensing (proton-gated) ion channel 1	365					associative learning (GO:0008306)|calcium ion transmembrane transport (GO:0070588)|cellular response to pH (GO:0071467)|ion transmembrane transport (GO:0034220)|memory (GO:0007613)|negative regulation of neurotransmitter secretion (GO:0046929)|protein homotrimerization (GO:0070207)|regulation of membrane potential (GO:0042391)|response to acidic pH (GO:0010447)|response to pH (GO:0009268)|sensory perception of sour taste (GO:0050915)|signal transduction (GO:0007165)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acid-sensing ion channel activity (GO:0044736)|ion gated channel activity (GO:0022839)|ligand-gated sodium channel activity (GO:0015280)									Amiloride(DB00594)|Diclofenac(DB00586)	GTGTGTGAAATGCCTTGCAAC	0.547																																					p.M399T		Atlas-SNP	.											.	.	.	.	0			c.T1196C						.						184	151	162					12																	50473727		2203	4300	6503	SO:0001583	missense	41	exon6			GTGAAATGCCTTG	U78181	CCDS8796.1, CCDS44876.1, CCDS58228.1	12q12	2012-02-23	2012-02-22	2012-02-22		ENSG00000110881		"Ion channels / Acid-sensing (proton-gated) ion channels"	100	protein-coding gene	gene with protein product		602866	"amiloride-sensitive cation channel 2, neuronal"	ACCN2		9037075	Standard	NM_001095		Approved	BNaC2, hBNaC2	uc001rvv.4	P78348	OTTHUMG00000169812	ENST00000447966.2:c.1094T>C	chr12.hg19:g.50473727T>C	ENSP00000400228:p.Met365Thr	155.0	0.0		123.0	49.0	NM_001256830	A3KN86|E5KBL7|P78349|Q96CV2	Missense_Mutation	SNP	ENST00000447966.2	hg19	CCDS44876.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	3.566|3.566	-0.088614|-0.088614	0.07097|0.07097	.|.	.|.	ENSG00000110881|ENSG00000110881	ENST00000453327|ENST00000228468;ENST00000447966;ENST00000552438	.|T;T;T	.|0.60548	.|0.18;0.18;0.18	4.74|4.74	4.74|4.74	0.60224|0.60224	.|.	.|0.050504	.|0.85682	.|D	.|0.000000	T|T	0.13286|0.13286	0.0322|0.0322	N|N	0.00053|0.00053	-2.39|-2.39	0.44469|0.44469	D|D	0.997402|0.997402	.|B;B	.|0.06786	.|0.0;0.001	.|B;B	.|0.08055	.|0.003;0.002	T|T	0.44467|0.44467	-0.9326|-0.9326	5|10	.|0.02654	.|T	.|1	-35.4779|-35.4779	9.2714|9.2714	0.37673|0.37673	0.0:0.0808:0.0:0.9192|0.0:0.0808:0.0:0.9192	.|.	.|365;365	.|P78348;P78348-1	.|ACCN2_HUMAN;.	R|T	233|365;365;399	.|ENSP00000228468:M365T;ENSP00000400228:M365T;ENSP00000450247:M399T	.|ENSP00000228468:M365T	C|M	+|+	1|2	0|0	ACCN2|ACCN2	48759994|48759994	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	3.823000|3.823000	0.55715|0.55715	2.143000|2.143000	0.66587|0.66587	0.459000|0.459000	0.35465|0.35465	TGC|ATG	.	.		0.547	ASIC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406004.2	NM_020039		C	50473727	T	C	50473727	3	2	344	1	0	0	0	0	1	0	0	0	129	1464	51	2	1120	2	ACCN2	12	50473727	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	178765	50473727	83378168	902	48265										
ACCN2	41	hgsc.bcm.edu	37	chr12	50474966	50474966	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctttgactacgcctacgaggTaagcgggggcgaggcccggc	16	12	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:50474966T>A	ENST00000447966.2	+	10	1606		c.e10+2		ASIC1_ENST00000228468.4_Splice_Site|ASIC1_ENST00000552438.1_Splice_Site	NM_001095.3	NP_001086.2	P78348	ASIC1_HUMAN	acid-sensing (proton-gated) ion channel 1						associative learning (GO:0008306)|calcium ion transmembrane transport (GO:0070588)|cellular response to pH (GO:0071467)|ion transmembrane transport (GO:0034220)|memory (GO:0007613)|negative regulation of neurotransmitter secretion (GO:0046929)|protein homotrimerization (GO:0070207)|regulation of membrane potential (GO:0042391)|response to acidic pH (GO:0010447)|response to pH (GO:0009268)|sensory perception of sour taste (GO:0050915)|signal transduction (GO:0007165)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acid-sensing ion channel activity (GO:0044736)|ion gated channel activity (GO:0022839)|ligand-gated sodium channel activity (GO:0015280)									Amiloride(DB00594)|Diclofenac(DB00586)	GCCTACGAGGTAAGCGGGGGC	0.701																																					.		Atlas-SNP	.											.	.	.	.	0			c.1377+2T>A						.						14	16	15					12																	50474966		2193	4291	6484	SO:0001630	splice_region_variant	41	exon10			ACGAGGTAAGCGG	U78181	CCDS8796.1, CCDS44876.1, CCDS58228.1	12q12	2012-02-23	2012-02-22	2012-02-22		ENSG00000110881		"Ion channels / Acid-sensing (proton-gated) ion channels"	100	protein-coding gene	gene with protein product		602866	"amiloride-sensitive cation channel 2, neuronal"	ACCN2		9037075	Standard	NM_001095		Approved	BNaC2, hBNaC2	uc001rvv.4	P78348	OTTHUMG00000169812	ENST00000447966.2:c.1377+2T>A	chr12.hg19:g.50474966T>A		65.0	0.0		69.0	33.0	NM_001095	A3KN86|E5KBL7|P78349|Q96CV2	Splice_Site	SNP	ENST00000447966.2	hg19	CCDS44876.1	.	.	.	.	.	.	.	.	.	.	T	20.5	3.999198	0.74818	.	.	ENSG00000110881	ENST00000228468;ENST00000447966;ENST00000453327;ENST00000552438	.	.	.	4.72	4.72	0.59763	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.6671	0.68915	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	ACCN2	48761233	1.000000	0.71417	0.937000	0.37676	0.941000	0.58515	6.016000	0.70798	2.110000	0.64415	0.459000	0.35465	.	.	.		0.701	ASIC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406004.2	NM_020039	Intron	A	50474966	T	A	50474966	5	1	344	1	0	0	0	0	0	0	1	0	129	1652	57	4	1551	4	ACCN2	12	50474966	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1239	50474966	83376929	903	48266										
TFCP2	7024	hgsc.bcm.edu	37	chr12	51492562	51492562	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgtactgaaaaatctacctcAtcactgatgagcacatgaat	6	9	3	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:51492562A>G	ENST00000257915.5	-	13	1874	c.1416T>C	c.(1414-1416)gaT>gaC	p.D472D	TFCP2_ENST00000307660.4_Silent_p.D421D|TFCP2_ENST00000549867.1_Silent_p.D394D|TFCP2_ENST00000548115.1_Silent_p.D421D	NM_001173452.1|NM_005653.4	NP_001166923.1|NP_005644.2	Q12800	TFCP2_HUMAN	transcription factor CP2	472					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)	23						AATCTACCTCATCACTGATGA	0.428																																					p.D472D		Atlas-SNP	.											.	TFCP2	49	.	0			c.T1416C						.						116	104	108					12																	51492562		2203	4300	6503	SO:0001819	synonymous_variant	7024	exon13			TACCTCATCACTG	U03494	CCDS8808.1, CCDS55827.1	12q13	2004-01-05				ENSG00000135457			11748	protein-coding gene	gene with protein product		189889				8157699	Standard	NM_005653		Approved	CP2, LSF, LBP-1C, TFCP2C	uc001rxw.3	Q12800	OTTHUMG00000169621	ENST00000257915.5:c.1416T>C	chr12.hg19:g.51492562A>G		46.0	0.0		55.0	24.0	NM_001173452	A8K5E9|Q12801|Q9UD75|Q9UD77	Silent	SNP	ENST00000257915.5	hg19	CCDS8808.1																																																																																			.	.		0.428	TFCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405119.1	NM_005653		G	51492562	A	G	51492562	2	3	344	1	0	0	0	0	0	0	0	1	15810	214	8	2		2	TFCP2	12	51492562	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1017596	51492562	82359333	904	48267										
SLC4A8	9498	hgsc.bcm.edu	37	chr12	51865212	51865212	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaagaagcatttgcctccctAatttgcattattttcatcta	5	9	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:51865212A>G	ENST00000453097.2	+	14	2017	c.1800A>G	c.(1798-1800)ctA>ctG	p.L600L	SLC4A8_ENST00000535225.2_Silent_p.L547L|SLC4A8_ENST00000394856.1_Silent_p.L547L|SLC4A8_ENST00000514353.3_Silent_p.L547L|SLC4A8_ENST00000358657.3_Silent_p.L627L|SLC4A8_ENST00000546663.1_3'UTR	NM_001039960.2|NM_001258401.2	NP_001035049.1|NP_001245330.1			solute carrier family 4, sodium bicarbonate cotransporter, member 8											NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(18)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(2)|urinary_tract(5)	55				BRCA - Breast invasive adenocarcinoma(357;0.15)		TTGCCTCCCTAATTTGCATTA	0.473																																					p.L600L		Atlas-SNP	.											.	SLC4A8	292	.	0			c.A1800G						.						178	161	167					12																	51865212		2203	4300	6503	SO:0001819	synonymous_variant	9498	exon14			CTCCCTAATTTGC	AB018282	CCDS44890.1, CCDS58232.1, CCDS58233.1, CCDS73470.1	12q13.13	2013-05-22			ENSG00000050438	ENSG00000050438		"Solute carriers"	11034	protein-coding gene	gene with protein product		605024				11133997	Standard	NM_001039960		Approved	NBC3	uc001rys.2	Q2Y0W8	OTTHUMG00000169489	ENST00000453097.2:c.1800A>G	chr12.hg19:g.51865212A>G		61.0	0.0		59.0	23.0	NM_001039960		Silent	SNP	ENST00000453097.2	hg19	CCDS44890.1																																																																																			.	.		0.473	SLC4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404356.1	NM_004858		G	51865212	A	G	51865212	2	3	344	1	0	0	0	0	0	0	0	1	14674	349	13	2		2	SLC4A8	12	51865212	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	372650	51865212	81986683	905	48268										
KRT81	3887	hgsc.bcm.edu	37	chr12	52682242	52682242	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggtaggcgcagtccacatccTggaaaggtggggagtgttgg	18	7	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:52682242T>C	ENST00000327741.5	-	4	708		c.e4-2		KRT86_ENST00000423955.2_Intron|KRT86_ENST00000544024.1_Intron	NM_002281.3	NP_002272.2	Q14533	KRT81_HUMAN	keratin 81							extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(2)|endometrium(3)|large_intestine(3)|lung(6)|prostate(1)|stomach(1)	16				BRCA - Breast invasive adenocarcinoma(357;0.189)		GTCCACATCCTGGAAAGGTGG	0.607																																					.		Atlas-SNP	.											.	KRT81	46	.	0			c.640-2A>G						.						109	111	110					12																	52682242		2203	4300	6503	SO:0001630	splice_region_variant	3887	exon5			ACATCCTGGAAAG	X81420	CCDS31805.1	12q13	2013-01-16	2006-07-17	2006-07-17	ENSG00000205426	ENSG00000205426		"-", "Intermediate filaments type II, keratins (basic)"	6458	protein-coding gene	gene with protein product	"hard keratin type II 1"	602153	"keratin, hair, basic, 1"	KRTHB1		7556444, 16831889	Standard	NM_002281		Approved	Hb-1	uc001sab.3	Q14533	OTTHUMG00000167574	ENST00000327741.5:c.640-2A>G	chr12.hg19:g.52682242T>C		88.0	0.0		84.0	39.0	NM_002281	Q14846|Q16274|Q17R48|Q8WU52|Q9BR74	Splice_Site	SNP	ENST00000327741.5	hg19	CCDS31805.1	.	.	.	.	.	.	.	.	.	.	.	15.09	2.731601	0.48939	.	.	ENSG00000205426	ENST00000327741;ENST00000389388	.	.	.	4.68	4.68	0.58851	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.2039	0.65721	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	KRT81	50968509	1.000000	0.71417	0.999000	0.59377	0.376000	0.30014	8.024000	0.88770	1.752000	0.51891	0.374000	0.22700	.	.	.		0.607	KRT81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395128.2	NM_002281	Intron	C	52682242	T	C	52682242	5	2	344	1	0	0	0	0	0	0	1	0	8504	1594	55	2	903	2	KRT81	12	52682242	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	817030	52682242	81169653	906	48269										
KRT6C	286887	hgsc.bcm.edu	37	chr12	52862953	52862953	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cccaatggctctgccactgcTggaactgaagccacctccaa	8	16	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:52862953T>A	ENST00000252250.6	-	9	1635	c.1588A>T	c.(1588-1590)Agc>Tgc	p.S530C		NM_173086.4	NP_775109.2	P48668	K2C6C_HUMAN	keratin 6C	530	Tail.				intermediate filament cytoskeleton organization (GO:0045104)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|prostate(2)|skin(2)	23				BRCA - Breast invasive adenocarcinoma(357;0.0828)		CTGCCACTGCTGGAACTGAAG	0.602																																					p.S530C		Atlas-SNP	.											.	KRT6C	55	.	0			c.A1588T						.						87	85	86					12																	52862953		2203	4300	6503	SO:0001583	missense	286887	exon9			CACTGCTGGAACT	L42611	CCDS8829.1	12q13.13	2013-01-16	2006-07-17	2006-07-17	ENSG00000170465	ENSG00000170465		"-", "Intermediate filaments type II, keratins (basic)"	20406	protein-coding gene	gene with protein product		612315	"keratin 6E"	KRT6E		7543104, 16831889	Standard	NM_173086		Approved		uc001sal.4	P48668	OTTHUMG00000169596	ENST00000252250.6:c.1588A>T	chr12.hg19:g.52862953T>A	ENSP00000252250:p.Ser530Cys	133.0	0.0		122.0	56.0	NM_173086	A1L4L5|P48666|Q2TAZ9|Q7RTN9	Missense_Mutation	SNP	ENST00000252250.6	hg19	CCDS8829.1	.	.	.	.	.	.	.	.	.	.	T	10.76	1.440784	0.25900	.	.	ENSG00000170465	ENST00000252250;ENST00000411979	D	0.92699	-3.09	3.56	-1.08	0.09936	.	0.441395	0.19356	N	0.116270	D	0.88032	0.6328	L	0.61218	1.895	0.21256	N	0.999745	P	0.41643	0.758	B	0.40101	0.319	T	0.79519	-0.1770	10	0.37606	T	0.19	.	8.2783	0.31885	0.0:0.6247:0.0:0.3753	.	530	P48668	K2C6C_HUMAN	C	530;515	ENSP00000252250:S530C	ENSP00000252250:S530C	S	-	1	0	KRT6C	51149220	0.007000	0.16637	0.770000	0.31555	0.488000	0.33401	0.020000	0.13466	-0.368000	0.08040	0.363000	0.22086	AGC	.	.		0.602	KRT6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404976.1	NM_173086		A	52862953	T	A	52862953	3	1	344	1	0	0	0	0	1	0	0	0	8491	1580	55	4	110	4	KRT6C	12	52862953	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	180711	52862953	80988942	907	48270										
KRT72	140807	hgsc.bcm.edu	37	chr12	52979933	52979933	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaagccagcccctcctgcccCagcattggtgctgctgatga	11	15	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:52979933C>A	ENST00000537672.2	-	9	1379	c.1369G>T	c.(1369-1371)Ggg>Tgg	p.G457W	KRT72_ENST00000293745.2_Missense_Mutation_p.G457W|KRT72_ENST00000354310.4_Missense_Mutation_p.G415W|KRT72_ENST00000398066.3_Missense_Mutation_p.G269W	NM_001146225.1	NP_001139697.1	Q14CN4	K2C72_HUMAN	keratin 72	457	Tail.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(357;0.195)		CCTCCTGCCCCAGCATTGGTG	0.597																																					p.G457W		Atlas-SNP	.											.	KRT72	70	.	0			c.G1369T						.						46	42	43					12																	52979933		2203	4300	6503	SO:0001583	missense	140807	exon9			CTGCCCCAGCATT	AY033495	CCDS8833.1, CCDS53795.1	12q13.13	2013-06-25			ENSG00000170486	ENSG00000170486		"-", "Intermediate filaments type II, keratins (basic)"	28932	protein-coding gene	gene with protein product		608246				12648212, 11703281, 16831889	Standard	NM_080747		Approved	K6IRS2, KRT6IRS2, KRT6, K6irs	uc001saq.2	Q14CN4	OTTHUMG00000169744	ENST00000537672.2:c.1369G>T	chr12.hg19:g.52979933C>A	ENSP00000441160:p.Gly457Trp	58.0	0.0		51.0	24.0	NM_001146225	B4DEI8|H9KV51|Q8NA87|Q8WWY9|Q8WWZ0	Missense_Mutation	SNP	ENST00000537672.2	hg19	CCDS8833.1	.	.	.	.	.	.	.	.	.	.	C	11.44	1.639905	0.29157	.	.	ENSG00000170486	ENST00000537672;ENST00000293745;ENST00000354310;ENST00000398066	D;D;D;T	0.83914	-1.71;-1.71;-1.78;-1.38	4.03	4.03	0.46877	.	.	.	.	.	D	0.87132	0.6101	L	0.61218	1.895	0.18873	N	0.999987	D;D	0.67145	0.996;0.992	P;P	0.60173	0.87;0.87	T	0.77619	-0.2520	9	0.38643	T	0.18	.	11.9301	0.52841	0.0:1.0:0.0:0.0	.	415;457	B4DEI8;Q14CN4	.;K2C72_HUMAN	W	457;457;415;269	ENSP00000441160:G457W;ENSP00000293745:G457W;ENSP00000346269:G415W;ENSP00000446151:G269W	ENSP00000293745:G457W	G	-	1	0	KRT72	51266200	0.012000	0.17670	0.228000	0.23943	0.108000	0.19459	1.471000	0.35365	2.254000	0.74563	0.545000	0.68477	GGG	.	.		0.597	KRT72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405693.1	NM_080747		A	52979933	C	A	52979933	3	1	344	1	0	0	0	0	1	0	0	0	8494	594	21	3	170	3	KRT72	12	52979933	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	116980	52979933	80871962	908	48271										
KRT73	319101	hgsc.bcm.edu	37	chr12	53010081	53010081	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcaaggatgggctccaggttAttcttgcagttgttcaggtc	12	8	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:53010081A>G	ENST00000305748.3	-	2	565	c.531T>C	c.(529-531)aaT>aaC	p.N177N	RP11-641A6.2_ENST00000551089.1_RNA|RP11-641A6.2_ENST00000552364.1_RNA|RP11-641A6.2_ENST00000549180.1_RNA	NM_175068.2	NP_778238.1	Q86Y46	K2C73_HUMAN	keratin 73	177	Linker 1.|Rod.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44				BRCA - Breast invasive adenocarcinoma(357;0.189)		GCTCCAGGTTATTCTTGCAGT	0.602																																					p.N177N		Atlas-SNP	.											.	KRT73	101	.	0			c.T531C						.						173	158	163					12																	53010081		2203	4300	6503	SO:0001819	synonymous_variant	319101	exon2			CAGGTTATTCTTG	AJ508776	CCDS8834.1	12q13.13	2013-06-25			ENSG00000186049	ENSG00000186049		"-", "Intermediate filaments type II, keratins (basic)"	28928	protein-coding gene	gene with protein product		608247				12648212, 16831889	Standard	NM_175068		Approved	KRT6IRS3, K6IRS3	uc001sas.3	Q86Y46	OTTHUMG00000169746	ENST00000305748.3:c.531T>C	chr12.hg19:g.53010081A>G		121.0	0.0		88.0	49.0	NM_175068	Q32MB2	Silent	SNP	ENST00000305748.3	hg19	CCDS8834.1																																																																																			.	.		0.602	KRT73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405700.1	NM_175068		G	53010081	A	G	53010081	2	3	344	1	0	0	0	0	0	0	0	1	8495	446	16	2		2	KRT73	12	53010081	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	30148	53010081	80841814	909	48272										
KRT77	374454	hgsc.bcm.edu	37	chr12	53086355	53086355	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cctccaggtcctgcagcttcTgccacgcatcctggagggcc	11	17	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:53086355T>C	ENST00000341809.3	-	7	1305	c.1277A>G	c.(1276-1278)cAg>cGg	p.Q426R	RP11-641A6.3_ENST00000547533.1_RNA|KRT77_ENST00000537195.1_Missense_Mutation_p.Q193R	NM_175078.2	NP_778253.2	Q7Z794	K2C1B_HUMAN	keratin 77	426	Coil 2.|Rod.					cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(2)|endometrium(2)|large_intestine(3)|lung(11)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25						CTGCAGCTTCTGCCACGCATC	0.602																																					p.Q426R		Atlas-SNP	.											.	KRT77	58	.	0			c.A1277G						.						45	42	43					12																	53086355		2202	4268	6470	SO:0001583	missense	374454	exon7			AGCTTCTGCCACG	BK000975	CCDS8837.1	12q13.13	2013-06-25	2006-07-17	2006-07-17	ENSG00000189182	ENSG00000189182		"-", "Intermediate filaments type II, keratins (basic)"	20411	protein-coding gene	gene with protein product		611158	"keratin 1B"	KRT1B		11683385, 16831889	Standard	NM_175078		Approved		uc001saw.3	Q7Z794	OTTHUMG00000169450	ENST00000341809.3:c.1277A>G	chr12.hg19:g.53086355T>C	ENSP00000342710:p.Gln426Arg	43.0	0.0		43.0	21.0	NM_175078	Q7RTS8	Missense_Mutation	SNP	ENST00000341809.3	hg19	CCDS8837.1	.	.	.	.	.	.	.	.	.	.	T	9.733	1.162806	0.21538	.	.	ENSG00000189182	ENST00000341809;ENST00000537195	D;D	0.82167	-1.58;-1.58	4.29	4.29	0.51040	Filament (1);	.	.	.	.	T	0.79269	0.4417	L	0.41710	1.295	0.09310	N	1	P	0.43169	0.8	P	0.45232	0.474	T	0.69300	-0.5181	9	0.41790	T	0.15	.	10.2911	0.43596	0.1475:0.0:0.0:0.8525	.	426	Q7Z794	K2C1B_HUMAN	R	426;193	ENSP00000342710:Q426R;ENSP00000440803:Q193R	ENSP00000342710:Q426R	Q	-	2	0	KRT77	51372622	0.000000	0.05858	0.609000	0.28983	0.011000	0.07611	-0.734000	0.04893	1.708000	0.51301	0.334000	0.21626	CAG	.	.		0.602	KRT77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404111.1	NM_175078		C	53086355	T	C	53086355	3	2	344	1	0	0	0	0	1	0	0	0	8499	1580	55	2	471	2	KRT77	12	53086355	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	76274	53086355	80765540	910	48273										
SOAT2	8435	hgsc.bcm.edu	37	chr12	53515148	53515148	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttggaacgtggtggtccatgActggctgtacagctacgtgt	14	8	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:53515148A>G	ENST00000301466.3	+	12	1259	c.1199A>G	c.(1198-1200)gAc>gGc	p.D400G		NM_003578.3	NP_003569.1	O75908	SOAT2_HUMAN	sterol O-acyltransferase 2	400					cholesterol efflux (GO:0033344)|cholesterol esterification (GO:0034435)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|intestinal cholesterol absorption (GO:0030299)|macrophage derived foam cell differentiation (GO:0010742)|very-low-density lipoprotein particle assembly (GO:0034379)	brush border (GO:0005903)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	cholesterol binding (GO:0015485)|cholesterol O-acyltransferase activity (GO:0034736)|fatty-acyl-CoA binding (GO:0000062)|transferase activity, transferring acyl groups (GO:0016746)			endometrium(5)|kidney(3)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|skin(1)	18					Hesperetin(DB01094)	GTGGTCCATGACTGGCTGTAC	0.567																																					p.D400G		Atlas-SNP	.											.	SOAT2	44	.	0			c.A1199G						.						156	126	136					12																	53515148		2203	4300	6503	SO:0001583	missense	8435	exon12			TCCATGACTGGCT	AF059203	CCDS8847.1	12q13.13	2012-09-20			ENSG00000167780	ENSG00000167780	2.3.1.26		11178	protein-coding gene	gene with protein product		601311				9756920	Standard	NM_003578		Approved	ACAT2	uc001sbv.3	O75908	OTTHUMG00000169774	ENST00000301466.3:c.1199A>G	chr12.hg19:g.53515148A>G	ENSP00000301466:p.Asp400Gly	91.0	0.0		92.0	34.0	NM_003578	F5H7W4|I6L9H9|Q4VB99|Q4VBA1|Q96TD4|Q9UNR2	Missense_Mutation	SNP	ENST00000301466.3	hg19	CCDS8847.1	.	.	.	.	.	.	.	.	.	.	A	18.03	3.532041	0.64972	.	.	ENSG00000167780	ENST00000301466	T	0.73681	-0.77	4.44	3.3	0.37823	.	0.056003	0.64402	N	0.000002	T	0.75443	0.3850	M	0.84585	2.705	0.80722	D	1	B	0.29162	0.235	B	0.31812	0.136	T	0.74954	-0.3488	10	0.66056	D	0.02	-22.51	9.0608	0.36433	0.9108:0.0:0.0892:0.0	.	400	O75908	SOAT2_HUMAN	G	400	ENSP00000301466:D400G	ENSP00000301466:D400G	D	+	2	0	SOAT2	51801415	1.000000	0.71417	0.989000	0.46669	0.966000	0.64601	6.860000	0.75473	0.870000	0.35726	0.379000	0.24179	GAC	.	.		0.567	SOAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405817.1			G	53515148	A	G	53515148	3	3	344	1	0	0	0	0	1	0	0	0	14926	275	10	2	1245	2	SOAT2	12	53515148	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	428793	53515148	80336747	911	48274										
RARG	5916	hgsc.bcm.edu	37	chr12	53605571	53605571	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcatcctcaaacatttcaggGttctccagcatctctcggat	6	13	5	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:53605571G>C	ENST00000425354.2	-	10	1741	c.1254C>G	c.(1252-1254)aaC>aaG	p.N418K	RARG_ENST00000394426.1_Missense_Mutation_p.N418K|RARG_ENST00000543762.1_5'UTR|RARG_ENST00000543726.1_Missense_Mutation_p.N396K|RARG_ENST00000327550.3_Missense_Mutation_p.N346K|RARG_ENST00000338561.5_Missense_Mutation_p.N407K	NM_000966.5	NP_000957.1	P13631	RARG_HUMAN	retinoic acid receptor, gamma	418	Ligand-binding.				anterior/posterior pattern specification (GO:0009952)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|embryonic camera-type eye development (GO:0031076)|embryonic eye morphogenesis (GO:0048048)|embryonic hindlimb morphogenesis (GO:0035116)|face development (GO:0060324)|gene expression (GO:0010467)|glandular epithelial cell development (GO:0002068)|growth plate cartilage chondrocyte growth (GO:0003430)|Harderian gland development (GO:0070384)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of programmed cell death (GO:0043068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of cell size (GO:0008361)|regulation of myelination (GO:0031641)|response to retinoic acid (GO:0032526)|retinal pigment epithelium development (GO:0003406)|retinoic acid receptor signaling pathway (GO:0048384)|trachea cartilage development (GO:0060534)|transcription initiation from RNA polymerase II promoter (GO:0006367)	integral component of membrane (GO:0016021)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|retinoic acid receptor activity (GO:0003708)|retinoid X receptor binding (GO:0046965)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Tazarotene(DB00799)|Tretinoin(DB00755)	ACATTTCAGGGTTCTCCAGCA	0.557																																					p.N418K		Atlas-SNP	.											.	RARG	53	.	0			c.C1254G						.						83	79	80					12																	53605571		2203	4300	6503	SO:0001583	missense	5916	exon10			TTCAGGGTTCTCC	M57707	CCDS8850.1, CCDS41790.1, CCDS58236.1, CCDS58237.1	12q13	2013-01-16			ENSG00000172819	ENSG00000172819		"Nuclear hormone receptors"	9866	protein-coding gene	gene with protein product		180190				1849262	Standard	NM_001042728		Approved	RARC, NR1B3	uc001scf.3	P13631	OTTHUMG00000048077	ENST00000425354.2:c.1254C>G	chr12.hg19:g.53605571G>C	ENSP00000388510:p.Asn418Lys	39.0	0.0		30.0	12.0	NM_000966	B7Z492|B7Z4F1|B7ZAE4|J3KNP6|P22932|Q15281|Q52LZ8|Q9BYX8|Q9H1I3|Q9UJ38	Missense_Mutation	SNP	ENST00000425354.2	hg19	CCDS8850.1	.	.	.	.	.	.	.	.	.	.	G	16.41	3.114668	0.56505	.	.	ENSG00000172819	ENST00000425354;ENST00000394426;ENST00000327550;ENST00000338561;ENST00000543726	D;D;D;D;D	0.92397	-2.86;-2.86;-3.03;-2.81;-2.91	4.35	4.35	0.52113	Nuclear hormone receptor, ligand-binding (2);	0.234953	0.40908	D	0.000981	D	0.94486	0.8225	M	0.79475	2.455	0.58432	D	0.999996	D;D;P	0.71674	0.994;0.998;0.51	D;D;B	0.68943	0.916;0.961;0.076	D	0.93882	0.7172	10	0.66056	D	0.02	.	6.745	0.23456	0.1948:0.0:0.8052:0.0	.	396;418;407	B7Z4F1;P13631;F1D8P1	.;RARG_HUMAN;.	K	418;418;346;407;396	ENSP00000388510:N418K;ENSP00000377947:N418K;ENSP00000332695:N346K;ENSP00000343698:N407K;ENSP00000444335:N396K	ENSP00000332695:N346K	N	-	3	2	RARG	51891838	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.284000	0.51708	2.416000	0.81992	0.563000	0.77884	AAC	.	.		0.557	RARG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109404.2	NM_000966		C	53605571	G	C	53605571	3	2	344	1	0	0	0	0	1	0	0	0	13069	1252	44	4	114	4	RARG	12	53605571	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	90423	53605571	80246324	912	48275										
HOXC10	3226	hgsc.bcm.edu	37	chr12	54379618	54379618	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acatctggaatcgcctcagcTggggggcaaagtgagtttcc	13	10	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:54379618T>A	ENST00000303460.4	+	1	649	c.575T>A	c.(574-576)cTg>cAg	p.L192Q	RP11-834C11.12_ENST00000513209.1_5'Flank|HOXC-AS3_ENST00000509870.1_RNA|HOXC-AS3_ENST00000513165.1_RNA|HOXC-AS3_ENST00000514702.1_RNA|HOXC-AS3_ENST00000567780.1_RNA	NM_017409.3	NP_059105.2	Q9NYD6	HXC10_HUMAN	homeobox C10	192					anterior/posterior pattern specification (GO:0009952)|embryonic limb morphogenesis (GO:0030326)|neuromuscular process (GO:0050905)|positive regulation of cell proliferation (GO:0008284)|proximal/distal pattern formation (GO:0009954)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|spinal cord motor neuron cell fate specification (GO:0021520)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|large_intestine(3)|lung(14)|pancreas(1)	20						TCGCCTCAGCTGGGGGGCAAA	0.632																																					p.L192Q		Atlas-SNP	.											.	HOXC10	42	.	0			c.T575A						.						31	36	34					12																	54379618		2203	4299	6502	SO:0001583	missense	3226	exon1			CTCAGCTGGGGGG		CCDS8868.1	12q13.13	2011-06-20	2005-12-22		ENSG00000180818	ENSG00000180818		"Homeoboxes / ANTP class : HOXL subclass"	5122	protein-coding gene	gene with protein product		605560	"homeo box C10"	HOX3I		1358459	Standard	NM_017409		Approved		uc001sen.3	Q9NYD6	OTTHUMG00000160031	ENST00000303460.4:c.575T>A	chr12.hg19:g.54379618T>A	ENSP00000307321:p.Leu192Gln	128.0	0.0		77.0	41.0	NM_017409	O15219|O15220|Q9BVD5	Missense_Mutation	SNP	ENST00000303460.4	hg19	CCDS8868.1	.	.	.	.	.	.	.	.	.	.	T	11.09	1.536306	0.27475	.	.	ENSG00000180818	ENST00000515593;ENST00000303460	D	0.92099	-2.97	4.63	4.63	0.57726	.	0.222920	0.37219	N	0.002188	T	0.81427	0.4820	N	0.19112	0.55	0.32126	N	0.587386	P	0.39964	0.697	B	0.32289	0.143	T	0.82894	-0.0231	10	0.42905	T	0.14	.	6.2259	0.20708	0.0:0.187:0.0:0.813	.	192	Q9NYD6	HXC10_HUMAN	Q	80;192	ENSP00000307321:L192Q	ENSP00000307321:L192Q	L	+	2	0	HOXC10	52665885	0.999000	0.42202	1.000000	0.80357	0.766000	0.43426	1.894000	0.39768	1.863000	0.54032	0.459000	0.35465	CTG	.	.		0.632	HOXC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358952.2			A	54379618	T	A	54379618	3	1	344	1	0	0	0	0	1	0	0	0	7318	1580	55	4	577	4	HOXC10	12	54379618	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	774047	54379618	79472277	913	48276										
NEUROD4	58158	hgsc.bcm.edu	37	chr12	55421151	55421151	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cccgttatgatgttcctataGacatgtcctatgattcctac	6	11	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:55421151G>T	ENST00000242994.3	+	2	1306	c.928G>T	c.(928-930)Gac>Tac	p.D310Y		NM_021191.2	NP_067014.2	Q9HD90	NDF4_HUMAN	neuronal differentiation 4	310					amacrine cell differentiation (GO:0035881)|cell fate commitment (GO:0045165)|glial cell differentiation (GO:0010001)|neuroblast proliferation (GO:0007405)|neuron development (GO:0048666)|neuron migration (GO:0001764)|Notch signaling pathway (GO:0007219)|positive regulation of cell differentiation (GO:0045597)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|ovary(3)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	41						TGTTCCTATAGACATGTCCTA	0.458																																					p.D310Y		Atlas-SNP	.											NEUROD4,colon,carcinoma,0,1	NEUROD4	87	.	0			c.G928T						.						418	417	418					12																	55421151		2203	4300	6503	SO:0001583	missense	58158	exon2			CCTATAGACATGT	AF203901	CCDS8886.1	12q13.13	2013-05-21	2012-02-22			ENSG00000123307		"Basic helix-loop-helix proteins"	13802	protein-coding gene	gene with protein product		611635	"neurogenic differentiation 4"				Standard	NM_021191		Approved	Atoh3, ATH-3, MATH-3, bHLHa4	uc001sgp.4	Q9HD90		ENST00000242994.3:c.928G>T	chr12.hg19:g.55421151G>T	ENSP00000242994:p.Asp310Tyr	85.0	0.0		79.0	37.0	NM_021191	B2RAC9	Missense_Mutation	SNP	ENST00000242994.3	hg19	CCDS8886.1	.	.	.	.	.	.	.	.	.	.	G	18.40	3.616429	0.66672	.	.	ENSG00000123307	ENST00000242994	D	0.96300	-3.97	5.78	4.84	0.62591	.	0.195331	0.52532	D	0.000070	D	0.96944	0.9002	L	0.59436	1.845	0.58432	D	0.999997	D	0.67145	0.996	P	0.61328	0.887	D	0.96738	0.9544	10	0.87932	D	0	-35.0092	14.3844	0.66934	0.0:0.1488:0.8512:0.0	.	310	Q9HD90	NDF4_HUMAN	Y	310	ENSP00000242994:D310Y	ENSP00000242994:D310Y	D	+	1	0	NEUROD4	53707418	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.369000	0.97156	2.906000	0.99361	0.655000	0.94253	GAC	.	.		0.458	NEUROD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406104.1			T	55421151	G	T	55421151	3	4	344	1	0	0	0	0	1	0	0	0	10359	942	33	3	930	3	NEUROD4	12	55421151	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1041533	55421151	78430744	914	48277										
OR6C3	254786	hgsc.bcm.edu	37	chr12	55726148	55726148	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acatgtacattatcaggaccAttttgagaatcccgtctgcc	7	11	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:55726148A>G	ENST00000379667.1	+	1	664	c.664A>G	c.(664-666)Att>Gtt	p.I222V		NM_054104.1	NP_473445.1	Q9NZP0	OR6C3_HUMAN	olfactory receptor, family 6, subfamily C, member 3	222					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(2)|lung(1)|prostate(1)|skin(2)	11						TATCAGGACCATTTTGAGAAT	0.358																																					p.I222V		Atlas-SNP	.											.	OR6C3	36	.	0			c.A664G						.						177	173	175					12																	55726148		2202	4300	6502	SO:0001583	missense	254786	exon1			AGGACCATTTTGA	AF179770	CCDS31819.1	12q13.2	2013-09-23			ENSG00000205329	ENSG00000205329		"GPCR / Class A : Olfactory receptors"	15437	protein-coding gene	gene with protein product							Standard	NM_054104		Approved	OST709	uc010spj.2	Q9NZP0	OTTHUMG00000169861	ENST00000379667.1:c.664A>G	chr12.hg19:g.55726148A>G	ENSP00000368989:p.Ile222Val	89.0	0.0		75.0	24.0	NM_054104		Missense_Mutation	SNP	ENST00000379667.1	hg19	CCDS31819.1	.	.	.	.	.	.	.	.	.	.	A	2.677	-0.276287	0.05679	.	.	ENSG00000205329	ENST00000379667	T	0.00024	8.98	5.13	3.98	0.46160	GPCR, rhodopsin-like superfamily (1);	0.132938	0.33712	N	0.004628	T	0.00144	0.0004	L	0.48174	1.505	0.09310	N	1	B	0.15141	0.012	B	0.26864	0.074	T	0.21518	-1.0243	10	0.59425	D	0.04	.	9.3929	0.38383	0.8495:0.0:0.1505:0.0	.	222	Q9NZP0	OR6C3_HUMAN	V	222	ENSP00000368989:I222V	ENSP00000368989:I222V	I	+	1	0	OR6C3	54012415	0.003000	0.15002	0.016000	0.15963	0.003000	0.03518	0.266000	0.18534	1.059000	0.40554	0.528000	0.53228	ATT	.	.		0.358	OR6C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406309.1			G	55726148	A	G	55726148	3	3	344	1	0	0	0	0	1	0	0	0	11201	217	8	2	666	2	OR6C3	12	55726148	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	304997	55726148	78125747	915	48278										
OBFC2B	79035	hgsc.bcm.edu	37	chr12	56619992	56619992	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggtttattctgaggttcctaActtcagtgagccaaacccag	9	10	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:56619992A>T	ENST00000380198.2	+	4	818	c.320A>T	c.(319-321)aAc>aTc	p.N107I	NABP2_ENST00000267023.4_Missense_Mutation_p.N107I|NABP2_ENST00000341463.5_Missense_Mutation_p.N107I			Q9BQ15	SOSB1_HUMAN	nucleic acid binding protein 2	107					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|mitotic cell cycle checkpoint (GO:0007093)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)|SOSS complex (GO:0070876)	single-stranded DNA binding (GO:0003697)										GAGGTTCCTAACTTCAGTGAG	0.512																																					p.N107I		Atlas-SNP	.											.	.	.	.	0			c.A320T						.						112	108	110					12																	56619992		2203	4300	6503	SO:0001583	missense	79035	exon5			TTCCTAACTTCAG	BC006171	CCDS8911.1	12q13.3	2012-06-19	2012-06-19	2012-06-19	ENSG00000139579	ENSG00000139579			28412	protein-coding gene	gene with protein product	"single strand DNA-binding protein 1", "sensor of single-strand DNA complex subunit B1"	612104	"oligonucleotide/oligosaccharide-binding fold containing 2B"	OBFC2B			Standard	NM_024068		Approved	MGC2731, SSB1, hSSB1, SOSS-B1	uc001ski.3	Q9BQ15	OTTHUMG00000152527	ENST00000380198.2:c.320A>T	chr12.hg19:g.56619992A>T	ENSP00000369545:p.Asn107Ile	152.0	0.0		116.0	58.0	NM_024068	A6NDF8|Q6XYC8	Missense_Mutation	SNP	ENST00000380198.2	hg19	CCDS8911.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.299873	0.81136	.	.	ENSG00000139579	ENST00000447747;ENST00000399713;ENST00000267023;ENST00000380198;ENST00000341463	D;D;D;D;D	0.92446	-3.04;-3.04;-3.04;-3.04;-3.04	4.32	4.32	0.51571	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);	0.000000	0.85682	D	0.000000	D	0.94771	0.8312	M	0.65498	2.005	0.58432	D	0.999992	D;D;D	0.69078	0.997;0.997;0.996	D;D;D	0.71414	0.964;0.973;0.957	D	0.95149	0.8271	10	0.87932	D	0	-16.7133	12.834	0.57763	1.0:0.0:0.0:0.0	.	107;107;107	C9JT95;C9JMP5;Q9BQ15	.;.;SOSB1_HUMAN	I	107	ENSP00000413902:N107I;ENSP00000408616:N107I;ENSP00000267023:N107I;ENSP00000369545:N107I;ENSP00000368862:N107I	ENSP00000267023:N107I	N	+	2	0	OBFC2B	54906259	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.970000	0.93415	1.741000	0.51731	0.370000	0.22315	AAC	.	.		0.512	NABP2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326610.1	NM_024068		T	56619992	A	T	56619992	3	4	344	1	0	0	0	0	1	0	0	0	10818	43	2	4	334	4	OBFC2B	12	56619992	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	893844	56619992	77231903	916	48279										
TIMELESS	8914	hgsc.bcm.edu	37	chr12	56827889	56827889	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggttccttatggtaagtgtcTccctccaagtacccaagggc	10	12	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:56827889T>C	ENST00000553532.1	-	2	216	c.66A>G	c.(64-66)ggA>ggG	p.G22G	TIMELESS_ENST00000554616.1_Silent_p.G22G|TIMELESS_ENST00000229201.4_Silent_p.G22G					timeless circadian clock											NS(1)|breast(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(8)|lung(14)|ovary(7)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	49						GGTAAGTGTCTCCCTCCAAGT	0.428																																					p.G22G		Atlas-SNP	.											.	TIMELESS	107	.	0			c.A66G						.						142	125	130					12																	56827889		2203	4300	6503	SO:0001819	synonymous_variant	8914	exon2			AGTGTCTCCCTCC	AF098162	CCDS8918.1	12q13.3	2012-12-14	2012-12-14		ENSG00000111602	ENSG00000111602			11813	protein-coding gene	gene with protein product	"Tof1 homolog (S. cerevisiae)", "timeless circadian clock 1"	603887	"timeless (Drosophila) homolog", "timeless homolog (Drosophila)"			9856465	Standard	NM_003920		Approved	hTIM, TIM, TIM1	uc001slf.2	Q9UNS1	OTTHUMG00000170600	ENST00000553532.1:c.66A>G	chr12.hg19:g.56827889T>C		147.0	0.0		96.0	38.0	NM_003920		Silent	SNP	ENST00000553532.1	hg19	CCDS8918.1																																																																																			.	.		0.428	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920		C	56827889	T	C	56827889	2	2	344	1	0	0	0	0	0	0	0	1	15919	1538	54	2		2	TIMELESS	12	56827889	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	207897	56827889	77024006	917	48280										
TAC3	6866	hgsc.bcm.edu	37	chr12	57407370	57407370	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gccgcctcctacctgtgctaGcctggctcagggctttgagc	12	15	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:57407370G>T	ENST00000458521.2	-	3	359	c.200C>A	c.(199-201)gCt>gAt	p.A67D	TAC3_ENST00000441881.1_Missense_Mutation_p.A67D|TAC3_ENST00000415231.1_Missense_Mutation_p.A67D	NM_013251.3	NP_037383.1	Q9UHF0	TKNK_HUMAN	tachykinin 3	67					female pregnancy (GO:0007565)|neuropeptide signaling pathway (GO:0007218)|tachykinin receptor signaling pathway (GO:0007217)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)			cervix(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	7						ACCTGTGCTAGCCTGGCTCAG	0.552																																					p.A67D		Atlas-SNP	.											.	TAC3	11	.	0			c.C200A						.						41	41	41					12																	57407370		2203	4300	6503	SO:0001583	missense	6866	exon3			GTGCTAGCCTGGC	AF186112	CCDS8928.1, CCDS53803.1	12q13-q21	2013-02-26	2008-07-31		ENSG00000166863	ENSG00000166863		"Endogenous ligands"	11521	protein-coding gene	gene with protein product	"preprotachykinin-B"	162330	"neuromedin K", "neurokinin beta"	NKNB		3479225, 10866201	Standard	NM_013251		Approved	ZNEUROK1, NKB	uc001smp.3	Q9UHF0	OTTHUMG00000156958	ENST00000458521.2:c.200C>A	chr12.hg19:g.57407370G>T	ENSP00000404056:p.Ala67Asp	48.0	0.0		43.0	19.0	NM_013251	Q6IAG2|Q71BC6|Q71BC9	Missense_Mutation	SNP	ENST00000458521.2	hg19	CCDS8928.1	.	.	.	.	.	.	.	.	.	.	G	12.74	2.029125	0.35797	.	.	ENSG00000166863	ENST00000458521;ENST00000441881;ENST00000415231	D;T;D	0.84146	-1.81;-1.47;-1.81	6.02	6.02	0.97574	.	0.135977	0.48767	D	0.000163	D	0.90940	0.7152	M	0.62723	1.935	0.41289	D	0.986966	D;D	0.76494	0.999;0.999	D;D	0.74023	0.96;0.982	D	0.90782	0.4680	10	0.56958	D	0.05	-15.699	16.0408	0.80680	0.0:0.0:1.0:0.0	.	67;67	Q9UHF0;Q9UHF0-3	TKNK_HUMAN;.	D	67	ENSP00000404056:A67D;ENSP00000408208:A67D;ENSP00000402995:A67D	ENSP00000300108:A67D	A	-	2	0	TAC3	55693637	0.996000	0.38824	0.954000	0.39281	0.032000	0.12392	4.839000	0.62810	2.865000	0.98341	0.655000	0.94253	GCT	.	.		0.552	TAC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346793.1	NM_001006667		T	57407370	G	T	57407370	3	4	344	1	0	0	0	0	1	0	0	0	15514	971	34	3	181	3	TAC3	12	57407370	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	579481	57407370	76444525	918	48281										
KIF5A	3798	hgsc.bcm.edu	37	chr12	57970570	57970570	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcagaagctccagttagagcTagagaagcttcaggctgact	11	9	2	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:57970570T>A	ENST00000455537.2	+	20	2499	c.2225T>A	c.(2224-2226)cTa>cAa	p.L742Q	KIF5A_ENST00000286452.5_Missense_Mutation_p.L653Q	NM_004984.2	NP_004975.2	Q12840	KIF5A_HUMAN	kinesin family member 5A	742					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein localization (GO:0008104)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(32)|ovary(2)|prostate(2)|skin(2)	62						CAGTTAGAGCTAGAGAAGCTT	0.498																																					p.L742Q		Atlas-SNP	.											.	KIF5A	143	.	0			c.T2225A						.						88	79	82					12																	57970570		2203	4300	6503	SO:0001583	missense	3798	exon20			TAGAGCTAGAGAA	U06698	CCDS8945.1	12q13.13	2011-07-15	2004-02-13			ENSG00000155980		"Kinesins"	6323	protein-coding gene	gene with protein product		602821	"spastic paraplegia 10 (autosomal dominant)"	SPG10		9858832, 10441583, 16489470	Standard	NM_004984		Approved	D12S1889, NKHC, MY050	uc001sor.1	Q12840	OTTHUMG00000170143	ENST00000455537.2:c.2225T>A	chr12.hg19:g.57970570T>A	ENSP00000408979:p.Leu742Gln	72.0	0.0		61.0	25.0	NM_004984	A6H8M5|Q4LE26	Missense_Mutation	SNP	ENST00000455537.2	hg19	CCDS8945.1	.	.	.	.	.	.	.	.	.	.	T	9.232	1.036080	0.19590	.	.	ENSG00000155980	ENST00000455537;ENST00000286452	D;D	0.84660	-1.88;-1.88	4.4	4.4	0.53042	.	0.000000	0.64402	D	0.000010	T	0.71213	0.3313	N	0.13098	0.295	0.52099	D	0.999946	B;B	0.14438	0.01;0.004	B;B	0.15484	0.013;0.007	T	0.65323	-0.6196	10	0.10902	T	0.67	.	13.0832	0.59125	0.0:0.0:0.0:1.0	.	653;742	B7Z2M7;Q12840	.;KIF5A_HUMAN	Q	742;653	ENSP00000408979:L742Q;ENSP00000286452:L653Q	ENSP00000286452:L653Q	L	+	2	0	KIF5A	56256837	0.995000	0.38212	0.998000	0.56505	0.983000	0.72400	2.034000	0.41145	1.999000	0.58509	0.459000	0.35465	CTA	.	.		0.498	KIF5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407634.1	NM_004984		A	57970570	T	A	57970570	3	1	344	1	0	0	0	0	1	0	0	0	8314	1522	53	4	2303	4	KIF5A	12	57970570	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	563200	57970570	75881325	919	48282										
DTX3	196403	hgsc.bcm.edu	37	chr12	58001020	58001020	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccgcgcaggcccaccccctcTccgagcagccccacttctgc	8	23	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:58001020T>A	ENST00000548198.1	+	3	1878	c.374T>A	c.(373-375)cTc>cAc	p.L125H	ARHGEF25_ENST00000333972.7_5'Flank|DTX3_ENST00000548804.1_Missense_Mutation_p.L125H|DTX3_ENST00000337737.3_Missense_Mutation_p.L125H|DTX3_ENST00000551632.1_Missense_Mutation_p.L128H			Q8N9I9	DTX3_HUMAN	deltex 3, E3 ubiquitin ligase	125	Pro-rich.				Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(6)|urinary_tract(1)	12	Melanoma(17;0.122)					CCACCCCCTCTCCGAGCAGCC	0.706																																					p.L125H		Atlas-SNP	.											.	DTX3	27	.	0			c.T374A						.						10	12	12					12																	58001020		1824	4064	5888	SO:0001583	missense	196403	exon5			CCCCTCTCCGAGC	AK094385	CCDS41800.1, CCDS66410.1	12q13.2	2014-01-28	2014-01-28			ENSG00000178498		"RING-type (C3HC4) zinc fingers"	24457	protein-coding gene	gene with protein product		613142	"deltex 3 homolog (Drosophila)", "deltex homolog 3 (Drosophila)"			12670957	Standard	XM_005268697		Approved	FLJ34766, RNF154	uc001sow.1	Q8N9I9		ENST00000548198.1:c.374T>A	chr12.hg19:g.58001020T>A	ENSP00000447873:p.Leu125His	50.0	0.0		44.0	21.0	NM_178502	Q53ZZ2|Q8NAU6|Q8NDS8	Missense_Mutation	SNP	ENST00000548198.1	hg19	CCDS41800.1	.	.	.	.	.	.	.	.	.	.	T	10.91	1.483366	0.26598	.	.	ENSG00000178498	ENST00000548804;ENST00000549583;ENST00000337737;ENST00000548198;ENST00000551632;ENST00000548478	T;T;T;T;T;T	0.47177	1.4;0.85;1.4;1.4;1.39;0.88	3.47	2.32	0.28847	.	0.161017	0.26895	N	0.021941	T	0.21509	0.0518	N	0.08118	0	0.22982	N	0.998478	B	0.02656	0.0	B	0.01281	0.0	T	0.08785	-1.0705	10	0.37606	T	0.19	-0.0795	2.9399	0.05826	0.2152:0.1212:0.0:0.6635	.	125	Q8N9I9	DTX3_HUMAN	H	125;128;125;125;128;118	ENSP00000449294:L125H;ENSP00000449688:L128H;ENSP00000338050:L125H;ENSP00000447873:L125H;ENSP00000448696:L128H;ENSP00000448224:L118H	ENSP00000338050:L125H	L	+	2	0	DTX3	56287287	0.357000	0.24938	0.997000	0.53966	0.975000	0.68041	1.071000	0.30666	0.542000	0.28846	0.368000	0.22195	CTC	.	.		0.706	DTX3-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000407848.1	NM_178502		A	58001020	T	A	58001020	3	1	344	1	0	0	0	0	1	0	0	0	4797	1551	54	4	380	4	DTX3	12	58001020	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	30450	58001020	75850875	920	48283										
AGAP2	116986	hgsc.bcm.edu	37	chr12	58121778	58121778	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggatctgactctcgatggccTggacccaggcatcccgctcc	11	16	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:58121778T>A	ENST00000547588.1	-	15	2707	c.2708A>T	c.(2707-2709)cAg>cTg	p.Q903L	AGAP2-AS1_ENST00000542466.2_3'UTR|RP11-571M6.8_ENST00000548410.2_RNA|AGAP2_ENST00000257897.3_Missense_Mutation_p.Q547L	NM_001122772.2	NP_001116244.1	Q99490	AGAP2_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	903	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				axon guidance (GO:0007411)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|large_intestine(7)|lung(20)|prostate(3)|skin(1)|stomach(1)	48						CTCGATGGCCTGGACCCAGGC	0.567																																					p.Q903L		Atlas-SNP	.											.	AGAP2	167	.	0			c.A2708T						.						160	147	152					12																	58121778		2203	4300	6503	SO:0001583	missense	116986	exon15			ATGGCCTGGACCC	AF413077	CCDS8951.1, CCDS44932.1	12q13.2	2013-05-30	2008-09-22	2008-09-22	ENSG00000135439	ENSG00000135439		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16921	protein-coding gene	gene with protein product		605476	"centaurin, gamma 1"	CENTG1			Standard	NM_001122772		Approved		uc001spq.3	Q99490	OTTHUMG00000170285	ENST00000547588.1:c.2708A>T	chr12.hg19:g.58121778T>A	ENSP00000449241:p.Gln903Leu	49.0	0.0		59.0	26.0	NM_001122772	A8K9F7|O00578|Q548E0|Q8IWU3	Missense_Mutation	SNP	ENST00000547588.1	hg19	CCDS44932.1	.	.	.	.	.	.	.	.	.	.	T	15.37	2.812142	0.50527	.	.	ENSG00000135439	ENST00000257897;ENST00000547588	T;T	0.18502	2.21;2.21	5.0	5.0	0.66597	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.128620	0.52532	D	0.000067	T	0.19406	0.0466	L	0.45352	1.415	0.80722	D	1	B;B;B	0.33345	0.409;0.011;0.292	B;B;B	0.37780	0.258;0.016;0.184	T	0.02797	-1.1109	10	0.49607	T	0.09	.	13.9938	0.64382	0.0:0.0:0.0:1.0	.	547;903;903	Q99490-2;F8VVT9;Q99490	.;.;AGAP2_HUMAN	L	547;903	ENSP00000257897:Q547L;ENSP00000449241:Q903L	ENSP00000257897:Q547L	Q	-	2	0	AGAP2	56408045	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.057000	0.41365	2.007000	0.58848	0.533000	0.62120	CAG	.	.		0.567	AGAP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408367.1	NM_014770		A	58121778	T	A	58121778	3	1	344	1	0	0	0	0	1	0	0	0	368	1580	55	4	890	4	AGAP2	12	58121778	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	120758	58121778	75730117	921	48284										
PPM1H	57460	hgsc.bcm.edu	37	chr12	63083571	63083571	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcccctggtcactccaatagTtgccattacccgggcctagg	9	15	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:63083571T>C	ENST00000228705.6	-	8	1453	c.1153A>G	c.(1153-1155)Act>Gct	p.T385A	PPM1H_ENST00000551214.1_5'UTR	NM_020700.1	NP_065751.1	Q9ULR3	PPM1H_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1H	385	PP2C-like.						phosphoprotein phosphatase activity (GO:0004721)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)	18			GBM - Glioblastoma multiforme(1;0.000443)|BRCA - Breast invasive adenocarcinoma(9;0.209)	GBM - Glioblastoma multiforme(28;0.0126)		ACTCCAATAGTTGCCATTACC	0.522																																					p.T385A		Atlas-SNP	.											.	PPM1H	42	.	0			c.A1153G						.						73	74	74					12																	63083571		1948	4153	6101	SO:0001583	missense	57460	exon8			CAATAGTTGCCAT	AB032983	CCDS44934.1	12q14.1	2012-04-17	2010-03-05	2004-03-26	ENSG00000111110	ENSG00000111110	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	18583	protein-coding gene	gene with protein product	"neurite extension-related protein phosphatase related to PP2C"		"ras homolog gene family, member C like 1", "protein phosphatase 1H (PP2C domain containing)"	ARHCL1			Standard	NM_020700		Approved	KIAA1157, FLJ13253, NERPP-2C	uc001srk.3	Q9ULR3	OTTHUMG00000169990	ENST00000228705.6:c.1153A>G	chr12.hg19:g.63083571T>C	ENSP00000228705:p.Thr385Ala	62.0	0.0		52.0	22.0	NM_020700	B1Q2A9|B2RXG4|Q6PI86	Missense_Mutation	SNP	ENST00000228705.6	hg19	CCDS44934.1	.	.	.	.	.	.	.	.	.	.	T	28.7	4.939127	0.92526	.	.	ENSG00000111110	ENST00000228705	T	0.16324	2.35	5.84	5.84	0.93424	Protein phosphatase 2C-like (5);	0.000000	0.85682	D	0.000000	T	0.40322	0.1112	M	0.62266	1.93	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.07712	-1.0758	9	.	.	.	1.17	16.2167	0.82231	0.0:0.0:0.0:1.0	.	385	Q9ULR3	PPM1H_HUMAN	A	385	ENSP00000228705:T385A	.	T	-	1	0	PPM1H	61369838	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.633000	0.83260	2.231000	0.72958	0.533000	0.62120	ACT	.	.		0.522	PPM1H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406760.2	NM_020700		C	63083571	T	C	63083571	3	2	344	1	0	0	0	0	1	0	0	0	12353	1725	60	2	403	2	PPM1H	12	63083571	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	4961793	63083571	70768324	922	48285										
CAND1	55832	hgsc.bcm.edu	37	chr12	67703830	67703830	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tttacaatgaaacaaaagttAgaaaggagcttataagagag	9	3	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:67703830A>T	ENST00000545606.1	+	12	3612	c.3175A>T	c.(3175-3177)Aga>Tga	p.R1059*		NM_018448.3	NP_060918.2	Q86VP6	CAND1_HUMAN	cullin-associated and neddylation-dissociated 1	1059					cell differentiation (GO:0030154)|negative regulation of catalytic activity (GO:0043086)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|protein ubiquitination (GO:0016567)|SCF complex assembly (GO:0010265)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				NS(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)	35			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)		AACAAAAGTTAGAAAGGAGCT	0.338																																					p.R1059X		Atlas-SNP	.											.	CAND1	100	.	0			c.A3175T						.						127	128	127					12																	67703830		2203	4299	6502	SO:0001587	stop_gained	55832	exon12			AAAGTTAGAAAGG		CCDS8977.1	12q14	2008-02-05			ENSG00000111530	ENSG00000111530			30688	protein-coding gene	gene with protein product	"TBP interacting protein"	607727				10048485, 8954946	Standard	NM_018448		Approved	TIP120A, DKFZp434M1414, KIAA0829, TIP120	uc001stn.2	Q86VP6	OTTHUMG00000169060	ENST00000545606.1:c.3175A>T	chr12.hg19:g.67703830A>T	ENSP00000442318:p.Arg1059*	121.0	0.0		112.0	44.0	NM_018448	B2RAU3|O94918|Q6PIY4|Q8NDJ4|Q96JZ9|Q96T19|Q9BTC4|Q9H0G2|Q9P0H7|Q9UF85	Nonsense_Mutation	SNP	ENST00000545606.1	hg19	CCDS8977.1	.	.	.	.	.	.	.	.	.	.	A	41	8.906242	0.98998	.	.	ENSG00000111530	ENST00000545606;ENST00000299218;ENST00000544619	.	.	.	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-15.3867	11.0205	0.47715	0.7137:0.2863:0.0:0.0	.	.	.	.	X	1059;1059;599	.	.	R	+	1	2	CAND1	65990097	1.000000	0.71417	1.000000	0.80357	0.660000	0.38997	2.280000	0.43443	2.086000	0.62901	0.533000	0.62120	AGA	.	.		0.338	CAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402105.1	NM_018448		T	67703830	A	T	67703830	4	4	344	1	0	0	0	0	0	1	0	0	2617	412	15	4	3221	4	CAND1	12	67703830	Nonsense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	4620259	67703830	66148065	923	48286										
YEATS4	8089	hgsc.bcm.edu	37	chr12	69759665	69759665	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttgaccctaatgaaagacctGtgagtagcattaatctttgt	8	7	1	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:69759665G>T	ENST00000247843.2	+	4	603		c.e4+1		YEATS4_ENST00000548020.1_Intron	NM_006530.2	NP_006521.1	O95619	YETS4_HUMAN	YEATS domain containing 4						chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic nuclear division (GO:0007067)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|protein C-terminus binding (GO:0008022)|sequence-specific DNA binding transcription factor activity (GO:0003700)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(1)	5	all_epithelial(5;9.25e-35)|Breast(13;9.83e-07)|Esophageal squamous(21;0.187)		Epithelial(6;6.89e-18)|BRCA - Breast invasive adenocarcinoma(5;3.14e-09)|Lung(24;9.68e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|OV - Ovarian serous cystadenocarcinoma(12;0.00691)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.24)|Kidney(9;0.241)			TGAAAGACCTGTGAGTAGCAT	0.274																																					.		Atlas-SNP	.											.	YEATS4	15	.	0			c.333+1G>T						.						49	53	52					12																	69759665		2202	4292	6494	SO:0001630	splice_region_variant	8089	exon4			AGACCTGTGAGTA	AJ245746	CCDS8990.1, CCDS73495.1	12q13-q15	2008-02-05				ENSG00000127337			24859	protein-coding gene	gene with protein product		602116				9302258, 11903063	Standard	XM_005269163		Approved	NuBI-1, GAS41, YAF9	uc001sux.3	O95619	OTTHUMG00000169358	ENST00000247843.2:c.333+1G>T	chr12.hg19:g.69759665G>T		257.0	0.0		263.0	99.0	NM_006530	Q9NQD0	Splice_Site	SNP	ENST00000247843.2	hg19	CCDS8990.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.942740	0.73672	.	.	ENSG00000127337	ENST00000247843;ENST00000549685;ENST00000552955	.	.	.	5.48	4.6	0.57074	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4403	0.67311	0.071:0.0:0.929:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	YEATS4	68045932	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	9.146000	0.94640	1.453000	0.47775	0.555000	0.69702	.	.	.		0.274	YEATS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403663.1	NM_006530	Intron	T	69759665	G	T	69759665	5	4	344	1	0	0	0	0	0	0	1	0	17488	1391	48	3	348	3	YEATS4	12	69759665	Splice_Site	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	2055835	69759665	64092230	924	48287										
LRRC10	376132	hgsc.bcm.edu	37	chr12	70004105	70004105	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccggttgcccgagagccagaTggtcctcagctcctggaggc	14	14	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:70004105T>C	ENST00000361484.3	-	1	837	c.514A>G	c.(514-516)Atc>Gtc	p.I172V		NM_201550.2	NP_963844.2	Q5BKY1	LRC10_HUMAN	leucine rich repeat containing 10	172					cardiac muscle cell development (GO:0055013)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|sarcomere (GO:0030017)				large_intestine(2)|lung(6)	8	all_cancers(2;2.83e-105)|Breast(13;9.83e-07)|Esophageal squamous(21;0.187)		Epithelial(6;1.98e-18)|GBM - Glioblastoma multiforme(2;7.43e-12)|Lung(24;0.000185)|OV - Ovarian serous cystadenocarcinoma(12;0.00126)|STAD - Stomach adenocarcinoma(21;0.00501)|Kidney(9;0.143)|LUSC - Lung squamous cell carcinoma(43;0.24)			GAGAGCCAGATGGTCCTCAGC	0.587																																					p.I172V		Atlas-SNP	.											.	LRRC10	26	.	0			c.A514G						.						65	61	62					12																	70004105		2203	4300	6503	SO:0001583	missense	376132	exon1			GCCAGATGGTCCT	AK095935	CCDS31856.1	12q15	2009-09-08				ENSG00000198812			20264	protein-coding gene	gene with protein product		610846				14751244	Standard	NM_201550		Approved	HRLRRP, LRRC10A	uc001svc.3	Q5BKY1		ENST00000361484.3:c.514A>G	chr12.hg19:g.70004105T>C	ENSP00000355166:p.Ile172Val	44.0	0.0		48.0	21.0	NM_201550	Q6ZVY4	Missense_Mutation	SNP	ENST00000361484.3	hg19	CCDS31856.1	.	.	.	.	.	.	.	.	.	.	T	16.29	3.082500	0.55861	.	.	ENSG00000198812	ENST00000361484	T	0.25414	1.8	5.62	5.62	0.85841	.	0.043908	0.85682	D	0.000000	T	0.17831	0.0428	N	0.13272	0.32	0.44719	D	0.997712	B	0.32409	0.37	B	0.30316	0.114	T	0.06075	-1.0847	10	0.62326	D	0.03	.	16.1209	0.81357	0.0:0.0:0.0:1.0	.	172	Q5BKY1	LRC10_HUMAN	V	172	ENSP00000355166:I172V	ENSP00000355166:I172V	I	-	1	0	LRRC10	68290372	1.000000	0.71417	1.000000	0.80357	0.798000	0.45092	5.008000	0.63991	2.268000	0.75426	0.454000	0.30748	ATC	.	.		0.587	LRRC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403834.1	NM_201550		C	70004105	T	C	70004105	3	2	344	1	0	0	0	0	1	0	0	0	8976	1464	51	2	323	2	LRRC10	12	70004105	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	244440	70004105	63847790	925	48288										
PTPRB	5787	hgsc.bcm.edu	37	chr12	70983979	70983979	+	Frame_Shift_Del	DEL	A	A	-													0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agagacctcatcctgccattAttgtttgcctccaggtttgc							TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:70983979delA	ENST00000261266.5	-	6	1190	c.1161delT	c.(1159-1161)aatfs	p.N388fs	PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000451516.2_Intron|PTPRB_ENST00000551525.1_Frame_Shift_Del_p.N605fs|PTPRB_ENST00000550358.1_Frame_Shift_Del_p.N606fs|PTPRB_ENST00000550857.1_Intron|PTPRB_ENST00000538708.1_Frame_Shift_Del_p.N388fs|PTPRB_ENST00000334414.6_Frame_Shift_Del_p.N606fs	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	388	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			TCCTGCCATTATTGTTTGCCT	0.448											OREG0021990	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N606fs		Atlas-Indel,Pindel	.											.	PTPRB	676	.	0			c.1816delA						.						118	116	117					12																	70983979		1932	4151	6083	SO:0001589	frameshift_variant	5787	exon8			.	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.1161delT	chr12.hg19:g.70983979delA	ENSP00000261266:p.Asn388fs	152.0	0.0	1126	111.0	38.0	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Frame_Shift_Del	DEL	ENST00000261266.5	hg19	CCDS44944.1																																																																																			.	.		0.448	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1			-	70983979	A	-	70983979	7	5	344	1	0	1	0	1	0	0	0	0	12811	446	16	0	4940	0	PTPRB	12	70983979	Frame_Shift_Del	DEL	A	TCGA-UB-A7MB-01A-11D-A33Q-10	979874	70983979	62867916	926	48289										
TRHDE	29953	hgsc.bcm.edu	37	chr12	73012775	73012775	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cagccgagctctttatcctcTagataaattactggaccgca	7	12	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:73012775T>C	ENST00000261180.4	+	13	2387	c.2291T>C	c.(2290-2292)cTa>cCa	p.L764P		NM_013381.2	NP_037513.1	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme	764					cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(8)|kidney(3)|large_intestine(13)|lung(38)|ovary(2)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	79						CTTTATCCTCTAGATAAATTA	0.353																																					p.L764P		Atlas-SNP	.											.	TRHDE	194	.	0			c.T2291C						.						49	53	52					12																	73012775		2202	4300	6502	SO:0001583	missense	29953	exon13			ATCCTCTAGATAA	AF126372	CCDS9004.1	12q15-q21	2012-07-25		2005-08-09		ENSG00000072657	3.4.19.6		30748	protein-coding gene	gene with protein product	"pyroglutamyl-peptidase II", "pyroglutamyl aminopeptidase II", "TRH-specific aminopeptidase"	606950				10491199, 12975309	Standard	NM_013381		Approved	PGPEP2, TRH-DE, PAP-II	uc001sxa.3	Q9UKU6		ENST00000261180.4:c.2291T>C	chr12.hg19:g.73012775T>C	ENSP00000261180:p.Leu764Pro	295.0	0.0		254.0	120.0	NM_013381	A5PL19|Q6UWJ4	Missense_Mutation	SNP	ENST00000261180.4	hg19	CCDS9004.1	.	.	.	.	.	.	.	.	.	.	T	19.01	3.743592	0.69418	.	.	ENSG00000072657	ENST00000261180	T	0.07908	3.15	5.77	4.61	0.57282	.	0.000000	0.64402	D	0.000001	T	0.30070	0.0753	M	0.83223	2.63	0.80722	D	1	D	0.71674	0.998	D	0.71184	0.972	T	0.05852	-1.0860	10	0.87932	D	0	.	12.6445	0.56728	0.1239:0.0:0.0:0.8761	.	764	Q9UKU6	TRHDE_HUMAN	P	764	ENSP00000261180:L764P	ENSP00000261180:L764P	L	+	2	0	TRHDE	71299042	1.000000	0.71417	0.993000	0.49108	0.990000	0.78478	5.625000	0.67770	1.077000	0.40990	0.533000	0.62120	CTA	.	.		0.353	TRHDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405380.1	NM_013381		C	73012775	T	C	73012775	3	2	344	1	0	0	0	0	1	0	0	0	16494	1522	53	2	2341	2	TRHDE	12	73012775	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2028796	73012775	60839120	927	48290										
CAPS2	84698	hgsc.bcm.edu	37	chr12	75716791	75716791	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	actgagtatatggagtttgaCatggtgtgacccagccaaga	12	7	0	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:75716791C>A	ENST00000409445.3	-	5	507	c.311G>T	c.(310-312)tGt>tTt	p.C104F	CAPS2_ENST00000393284.3_5'UTR|CAPS2_ENST00000442339.2_Intron|CAPS2_ENST00000409799.1_Intron	NM_032606.3	NP_115995.2	Q9BXY5	CAYP2_HUMAN	calcyphosine 2	104							calcium ion binding (GO:0005509)			endometrium(2)|large_intestine(1)|lung(4)|ovary(2)|skin(1)	10						TGGAGTTTGACATGGTGTGAC	0.279																																					p.C104F		Atlas-SNP	.											.	CAPS2	96	.	0			c.G311T						.						37	33	34					12																	75716791		692	1588	2280	SO:0001583	missense	84698	exon5			GTTTGACATGGTG	AF251056	CCDS9008.2, CCDS66424.1, CCDS73497.1	12q14.1	2013-01-10	2005-05-09		ENSG00000180881	ENSG00000180881		"EF-hand domain containing"	16471	protein-coding gene	gene with protein product		607724	"calcyphosphine 2"			11846421	Standard	NM_032606		Approved		uc001sxk.4	Q9BXY5	OTTHUMG00000152787	ENST00000409445.3:c.311G>T	chr12.hg19:g.75716791C>A	ENSP00000386959:p.Cys104Phe	282.0	0.0		278.0	95.0	NM_032606	Q6PH84|Q8N242|Q8NAY5	Missense_Mutation	SNP	ENST00000409445.3	hg19	CCDS9008.2	.	.	.	.	.	.	.	.	.	.	C	0.373	-0.932866	0.02359	.	.	ENSG00000180881	ENST00000409445	T	0.52526	0.66	4.75	1.82	0.25136	.	1.082800	0.07004	N	0.823820	T	0.32406	0.0828	L	0.29908	0.895	0.09310	N	1	B	0.26002	0.139	B	0.16289	0.015	T	0.20306	-1.0279	10	0.25106	T	0.35	-0.0152	6.158	0.20348	0.4798:0.4319:0.0:0.0883	.	104	Q9BXY5	CAYP2_HUMAN	F	104	ENSP00000386959:C104F	ENSP00000386959:C104F	C	-	2	0	CAPS2	74003058	0.935000	0.31712	0.000000	0.03702	0.005000	0.04900	0.308000	0.19314	0.280000	0.22209	0.561000	0.74099	TGT	.	.		0.279	CAPS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000327880.2			A	75716791	C	A	75716791	3	1	344	1	0	0	0	0	1	0	0	0	2640	478	17	3	1418	3	CAPS2	12	75716791	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	2704016	75716791	58135104	928	48291										
CAPS2	84698	hgsc.bcm.edu	37	chr12	75720286	75720286	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cctctaaatccatttgagttCctgtgtttatcatgcagtat	6	9	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:75720286C>G	ENST00000409445.3	-	2	246	c.50G>C	c.(49-51)gGa>gCa	p.G17A	CAPS2_ENST00000393284.3_5'Flank|CAPS2_ENST00000442339.2_Intron|CAPS2_ENST00000409799.1_Missense_Mutation_p.G5A	NM_032606.3	NP_115995.2	Q9BXY5	CAYP2_HUMAN	calcyphosine 2	17							calcium ion binding (GO:0005509)			endometrium(2)|large_intestine(1)|lung(4)|ovary(2)|skin(1)	10						CATTTGAGTTCCTGTGTTTAT	0.343																																					p.G17A		Atlas-SNP	.											CAPS2_ENST00000409445,NS,carcinoma,0,1	CAPS2	96	.	0			c.G50C						.						110	100	103					12																	75720286		692	1591	2283	SO:0001583	missense	84698	exon2			TGAGTTCCTGTGT	AF251056	CCDS9008.2, CCDS66424.1, CCDS73497.1	12q14.1	2013-01-10	2005-05-09		ENSG00000180881	ENSG00000180881		"EF-hand domain containing"	16471	protein-coding gene	gene with protein product		607724	"calcyphosphine 2"			11846421	Standard	NM_032606		Approved		uc001sxk.4	Q9BXY5	OTTHUMG00000152787	ENST00000409445.3:c.50G>C	chr12.hg19:g.75720286C>G	ENSP00000386959:p.Gly17Ala	69.0	0.0		53.0	14.0	NM_032606	Q6PH84|Q8N242|Q8NAY5	Missense_Mutation	SNP	ENST00000409445.3	hg19	CCDS9008.2	.	.	.	.	.	.	.	.	.	.	C	9.564	1.119323	0.20877	.	.	ENSG00000180881	ENST00000409799;ENST00000409445	T;T	0.35236	1.32;1.74	4.41	2.05	0.26809	.	.	.	.	.	T	0.14874	0.0359	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.27262	-1.0079	9	0.15499	T	0.54	.	3.4664	0.07552	0.0:0.4252:0.1959:0.379	.	17	Q9BXY5	CAYP2_HUMAN	A	5;17	ENSP00000386977:G5A;ENSP00000386959:G17A	ENSP00000386959:G17A	G	-	2	0	CAPS2	74006553	0.153000	0.22777	0.009000	0.14445	0.006000	0.05464	-0.076000	0.11412	0.850000	0.35239	0.462000	0.41574	GGA	.	.		0.343	CAPS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000327880.2			G	75720286	C	G	75720286	3	3	344	1	0	0	0	0	1	0	0	0	2640	855	30	4	1691	4	CAPS2	12	75720286	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	3495	75720286	58131609	929	48292										
GLIPR1L1	256710	hgsc.bcm.edu	37	chr12	75728612	75728612	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cactgacccacactttatagAcaactgcatagaagcccaca	5	14	0	3	rs143627655	byFrequency	TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:75728612A>T	ENST00000378695.4	+	1	194	c.104A>T	c.(103-105)gAc>gTc	p.D35V	GLIPR1L1_ENST00000312442.2_Missense_Mutation_p.D35V|CAPS2_ENST00000442339.2_Intron			Q6UWM5	GPRL1_HUMAN	GLI pathogenesis-related 1 like 1	35					binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|extracellular region (GO:0005576)|sperm connecting piece (GO:0097224)				endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)	10						CACTTTATAGACAACTGCATA	0.468											OREG0021998	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D35V		Atlas-SNP	.											.	GLIPR1L1	28	.	0			c.A104T						.						137	127	131					12																	75728612		2203	4300	6503	SO:0001583	missense	256710	exon1			TTATAGACAACTG	BC014603	CCDS9009.1	12q21.1	2014-06-03				ENSG00000173401			28392	protein-coding gene	gene with protein product		610395				12477932	Standard	NM_152779		Approved	MGC26856	uc001sxn.3	Q6UWM5	OTTHUMG00000169755	ENST00000378695.4:c.104A>T	chr12.hg19:g.75728612A>T	ENSP00000367967:p.Asp35Val	109.0	0.0	1162	107.0	48.0	NM_152779	Q96L06	Missense_Mutation	SNP	ENST00000378695.4	hg19		.	.	.	.	.	.	.	.	.	.	A	13.03	2.116432	0.37339	.	.	ENSG00000173401	ENST00000378695;ENST00000312442	T;T	0.44083	0.93;0.93	4.81	4.81	0.61882	CAP domain (2);	0.966554	0.08581	N	0.924526	T	0.36608	0.0973	N	0.19112	0.55	0.09310	N	0.999998	B;B	0.34372	0.449;0.451	B;B	0.39660	0.303;0.306	T	0.38023	-0.9680	10	0.59425	D	0.04	.	11.8737	0.52536	1.0:0.0:0.0:0.0	.	35;35	Q6UWM5;Q6UWM5-2	GPRL1_HUMAN;.	V	35	ENSP00000367967:D35V;ENSP00000310770:D35V	ENSP00000310770:D35V	D	+	2	0	GLIPR1L1	74014879	0.031000	0.19500	0.003000	0.11579	0.002000	0.02628	3.497000	0.53295	1.804000	0.52760	0.460000	0.39030	GAC	.	A|0.999;G|0.001		0.468	GLIPR1L1-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000405714.1	NM_152779		T	75728612	A	T	75728612	3	4	344	1	0	0	0	0	1	0	0	0	6450	275	10	4	106	4	GLIPR1L1	12	75728612	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	8326	75728612	58123283	930	48293										
MGAT4C	25834	hgsc.bcm.edu	37	chr12	86373569	86373569	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgtatgatgaataatagcccAtgtgctgaaagagagatggt	12	4	0	5			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:86373569A>T	ENST00000604798.1	-	8	2139	c.935T>A	c.(934-936)aTg>aAg	p.M312K	MGAT4C_ENST00000393205.2_Missense_Mutation_p.M341K|MGAT4C_ENST00000552435.2_Missense_Mutation_p.H100Q|MGAT4C_ENST00000332156.1_Missense_Mutation_p.M312K|MGAT4C_ENST00000552808.2_Missense_Mutation_p.M312K|MGAT4C_ENST00000549405.2_Missense_Mutation_p.M312K|MGAT4C_ENST00000548651.1_Missense_Mutation_p.M312K			Q9UBM8	MGT4C_HUMAN	MGAT4 family, member C	312					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						ATAATAGCCCATGTGCTGAAA	0.408																																					p.M312K		Atlas-SNP	.											.	MGAT4C	110	.	0			c.T935A						.						80	78	78					12																	86373569		2203	4300	6503	SO:0001583	missense	25834	exon7			TAGCCCATGTGCT		CCDS9030.1	12q21	2014-07-14	2014-07-14		ENSG00000182050	ENSG00000182050		"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	30871	protein-coding gene	gene with protein product		607385	"mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme C (putative)"			10570912	Standard	NM_013244		Approved	HGNT-IV-H	uc001tal.4	Q9UBM8	OTTHUMG00000169846	ENST00000604798.1:c.935T>A	chr12.hg19:g.86373569A>T	ENSP00000474896:p.Met312Lys	81.0	0.0		68.0	24.0	NM_013244	B4DRH2|Q4G199|Q9UIU5	Missense_Mutation	SNP	ENST00000604798.1	hg19	CCDS9030.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.25|16.25	3.070742|3.070742	0.55539|0.55539	.|.	.|.	ENSG00000182050|ENSG00000182050	ENST00000552435|ENST00000332156;ENST00000393205;ENST00000549405;ENST00000550460;ENST00000552808;ENST00000548651;ENST00000547225	.|T;T;T;T;T;T	.|0.49432	.|0.78;0.78;0.78;0.78;0.78;0.78	5.75|5.75	5.75|5.75	0.90469|0.90469	.|.	.|0.041776	.|0.85682	.|D	.|0.000000	T|T	0.67268|0.67268	0.2875|0.2875	M|M	0.81802|0.81802	2.56|2.56	0.80722|0.80722	D|D	1|1	.|D;D	.|0.56746	.|0.977;0.959	.|P;P	.|0.58873	.|0.847;0.847	T|T	0.70905|0.70905	-0.4745|-0.4745	6|10	0.72032|0.52906	D|T	0.01|0.07	-24.5606|-24.5606	16.1254|16.1254	0.81392|0.81392	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|341;312	.|B4DRH2;Q9UBM8	.|.;MGT4C_HUMAN	Q|K	100|312;341;312;312;312;312;312	.|ENSP00000331664:M312K;ENSP00000376900:M341K;ENSP00000449022:M312K;ENSP00000446647:M312K;ENSP00000447253:M312K;ENSP00000449172:M312K	ENSP00000448093:H100Q|ENSP00000331664:M312K	H|M	-|-	3|2	2|0	MGAT4C|MGAT4C	84897700|84897700	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.360000|0.360000	0.29518|0.29518	9.332000|9.332000	0.96446|0.96446	2.195000|2.195000	0.70347|0.70347	0.529000|0.529000	0.55759|0.55759	CAT|ATG	.	.		0.408	MGAT4C-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406212.2	NM_013244		T	86373569	A	T	86373569	3	4	344	1	0	0	0	0	1	0	0	0	9556	217	8	4	505	4	MGAT4C	12	86373569	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	10644957	86373569	47478326	931	48294										
CEP290	80184	hgsc.bcm.edu	37	chr12	88513944	88513944	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggaaatcactgatcttcaatTcaagtttattgatttccttt	5	7	4	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:88513944T>C	ENST00000552810.1	-	15	1812	c.1469A>G	c.(1468-1470)gAa>gGa	p.E490G	CEP290_ENST00000309041.7_Missense_Mutation_p.E490G|CEP290_ENST00000397838.3_5'UTR	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	490					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						GATCTTCAATTCAAGTTTATT	0.328																																					p.E490G		Atlas-SNP	.											.	CEP290	195	.	0			c.A1469G						.						81	73	75					12																	88513944		1825	4059	5884	SO:0001583	missense	80184	exon15			TTCAATTCAAGTT	AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"Joubert syndrome 5", "nephrocystin-6", "cancer/testis antigen 87", "POC3 centriolar protein homolog (Chlamydomonas)", "Meckel syndrome, type 4"	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.1469A>G	chr12.hg19:g.88513944T>C	ENSP00000448012:p.Glu490Gly	311.0	0.0		274.0	119.0	NM_025114	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Missense_Mutation	SNP	ENST00000552810.1	hg19	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	T	16.37	3.104406	0.56291	.	.	ENSG00000198707	ENST00000552810;ENST00000309041;ENST00000536998;ENST00000545139	T;T	0.69175	-0.38;-0.38	5.67	4.53	0.55603	.	0.132878	0.48767	D	0.000161	T	0.59932	0.2230	L	0.49350	1.555	0.80722	D	1	B;B	0.19583	0.01;0.037	B;B	0.22386	0.004;0.039	T	0.60182	-0.7313	10	0.49607	T	0.09	.	11.0569	0.47925	0.0:0.0724:0.0:0.9276	.	490;490	Q05BJ6;O15078	.;CE290_HUMAN	G	490;490;490;392	ENSP00000448012:E490G;ENSP00000308021:E490G	ENSP00000308021:E490G	E	-	2	0	CEP290	87038075	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	2.819000	0.48049	2.156000	0.67533	0.528000	0.53228	GAA	.	.		0.328	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		C	88513944	T	C	88513944	3	2	344	1	0	0	0	0	1	0	0	0	3255	1783	62	2	6130	2	CEP290	12	88513944	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2140375	88513944	45337951	932	48295										
LUM	4060	hgsc.bcm.edu	37	chr12	91502590	91502590	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttggtacacttttcaatttcAgctcatcacagtacatggca	6	10	4	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:91502590A>T	ENST00000266718.4	-	2	621	c.167T>A	c.(166-168)cTg>cAg	p.L56Q	LUM_ENST00000548071.1_Intron	NM_002345.3	NP_002336.1	P51884	LUM_HUMAN	lumican	56	LRRNT.				carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to growth factor (GO:0070848)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrillar collagen trimer (GO:0005583)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	24						TTTCAATTTCAGCTCATCACA	0.403																																					p.L56Q		Atlas-SNP	.											.	LUM	65	.	0			c.T167A						.						114	111	112					12																	91502590		2203	4300	6503	SO:0001583	missense	4060	exon2			AATTTCAGCTCAT	BT006707	CCDS9038.1	12q21.33	2014-06-13			ENSG00000139329			"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	6724	protein-coding gene	gene with protein product	"lumican proteoglycan"	600616		LDC		7558030	Standard	NM_002345		Approved	SLRR2D	uc001tbm.3	P51884	OTTHUMG00000170074	ENST00000266718.4:c.167T>A	chr12.hg19:g.91502590A>T	ENSP00000266718:p.Leu56Gln	82.0	0.0		59.0	24.0	NM_002345	B2R6R5|Q96QM7	Missense_Mutation	SNP	ENST00000266718.4	hg19	CCDS9038.1	.	.	.	.	.	.	.	.	.	.	A	18.27	3.587601	0.66105	.	.	ENSG00000139329	ENST00000266718	D	0.96587	-4.06	5.66	5.66	0.87406	Leucine-rich repeat-containing N-terminal (2);	0.063431	0.64402	D	0.000008	D	0.95589	0.8566	L	0.41236	1.265	0.47441	D	0.99942	P	0.47191	0.891	P	0.54889	0.763	D	0.94247	0.7490	10	0.31617	T	0.26	-6.7817	12.0999	0.53776	0.8568:0.1432:0.0:0.0	.	56	P51884	LUM_HUMAN	Q	56	ENSP00000266718:L56Q	ENSP00000266718:L56Q	L	-	2	0	LUM	90026721	1.000000	0.71417	0.955000	0.39395	0.769000	0.43574	6.423000	0.73361	2.284000	0.76573	0.528000	0.53228	CTG	.	.		0.403	LUM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407150.2	NM_002345		T	91502590	A	T	91502590	3	4	344	1	0	0	0	0	1	0	0	0	9094	188	7	4	857	4	LUM	12	91502590	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2988646	91502590	42349305	933	48296										
BTG1	694	hgsc.bcm.edu	37	chr12	92539312	92539324	+	5'UTR	DEL	GGGGGCGGCGTGC	GGGGGCGGCGTGC	-													0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cgggtgtagaagggatgcatGggggcggcgtgcgggggcgg					rs377332794|rs576191276		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	GGGGGCGGCGTGC	GGGGGCGGCGTGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:92539312_92539324delGGGGGCGGCGTGC	ENST00000256015.3	-	0	349_361				RP11-796E2.4_ENST00000499685.2_RNA|C12orf79_ENST00000549802.1_5'Flank|C12orf79_ENST00000551563.2_5'Flank|RP11-796E2.4_ENST00000501008.2_RNA|C12orf79_ENST00000546975.1_5'Flank	NM_001731.2	NP_001722.1	P62324	BTG1_HUMAN	B-cell translocation gene 1, anti-proliferative						cell migration (GO:0016477)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of myoblast differentiation (GO:0045663)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|transcription cofactor activity (GO:0003712)			haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(1)|lung(2)	16		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)				AGGGATGCATgggggcggcgtgcgggggcggcc	0.732			T	MYC	BCLL																																.		Atlas-Indel,Pindel	.		Dom	yes		12	12q22	694	"B-cell translocation gene 1, anti-proliferative"		L	.	BTG1	30	.	0			.						.																																			SO:0001623	5_prime_UTR_variant	694	wholegene			.		CCDS9043.1	12q21.33	2012-10-02			ENSG00000133639	ENSG00000133639			1130	protein-coding gene	gene with protein product		109580				15033446	Standard	NM_001731		Approved		uc001tby.3	P62324	OTTHUMG00000170092	ENST00000256015.3:c.-13GCACGCCGCCCCC>-	chr12.hg19:g.92539312_92539324delGGGGGCGGCGTGC		43.0	0.0		44.0	19.0	NM_001731	P31607	Frame_Shift_Del	DEL	ENST00000256015.3	hg19	CCDS9043.1																																																																																			.	.		0.732	BTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407227.1			-	92539324	GGGGGCGGCGTGC	-	92539312	6	5	344	0	1	1	0	1	0	0	0	0	1555	1363	47	0		0	BTG1	12	92539312	5'UTR	DEL	GGGGGCGGCGTGC	TCGA-UB-A7MB-01A-11D-A33Q-10	1036722	92539312	41312583	934	48297										
UBE2N	7334	hgsc.bcm.edu	37	chr12	93804888	93804888	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cattaggatgataaattttgGtcatgaaacgtactttaggg	10	4	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:93804888G>A	ENST00000318066.2	-	2	595	c.218C>T	c.(217-219)aCc>aTc	p.T73I	UBE2N_ENST00000549833.1_Missense_Mutation_p.T10I|UBE2N_ENST00000550657.1_Missense_Mutation_p.T73I|UBE2N_ENST00000552442.1_Missense_Mutation_p.T73I	NM_003348.3	NP_003339.1	P61088	UBE2N_HUMAN	ubiquitin-conjugating enzyme E2N	73					cellular protein modification process (GO:0006464)|cytokine-mediated signaling pathway (GO:0019221)|DNA double-strand break processing (GO:0000729)|double-strand break repair via homologous recombination (GO:0000724)|Fc-epsilon receptor signaling pathway (GO:0038095)|histone ubiquitination (GO:0016574)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of DNA repair (GO:0045739)|positive regulation of histone modification (GO:0031058)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|postreplication repair (GO:0006301)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of DNA repair (GO:0006282)|regulation of histone ubiquitination (GO:0033182)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|protein complex (GO:0043234)|UBC13-MMS2 complex (GO:0031372)|UBC13-UEV1A complex (GO:0035370)|ubiquitin ligase complex (GO:0000151)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|liver(2)|lung(5)	10						ATAAATTTTGGTCATGAAACG	0.378								Direct reversal of damage;Rad6 pathway																													p.T73I	Pancreas(197;738 2228 30225 32034 33454)	Atlas-SNP	.											.	UBE2N	20	.	0			c.C218T						.						91	92	92					12																	93804888		2203	4300	6503	SO:0001583	missense	7334	exon2			ATTTTGGTCATGA	D83004	CCDS31875.1	12q22	2011-05-19	2011-05-19			ENSG00000177889		"Ubiquitin-conjugating enzymes E2"	12492	protein-coding gene	gene with protein product		603679	"ubiquitin-conjugating enzyme E2N (homologous to yeast UBC13)", "ubiquitin-conjugating enzyme E2N (UBC13 homolog, yeast)"			8902611	Standard	NM_003348		Approved	UbcH-ben, UBC13, MGC8489	uc001tcp.3	P61088	OTTHUMG00000170156	ENST00000318066.2:c.218C>T	chr12.hg19:g.93804888G>A	ENSP00000316176:p.Thr73Ile	195.0	0.0		186.0	84.0	NM_003348	Q16781|Q53Y81	Missense_Mutation	SNP	ENST00000318066.2	hg19	CCDS31875.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.756077	0.89843	.	.	ENSG00000177889	ENST00000318066;ENST00000550657;ENST00000549833;ENST00000552442	T;T;T;T	0.77489	-1.1;-1.1;-1.1;-1.1	5.94	5.94	0.96194	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.000000	0.44097	U	0.000485	D	0.93772	0.8009	H	0.98802	4.335	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95571	0.8638	10	0.87932	D	0	.	20.3736	0.98901	0.0:0.0:1.0:0.0	.	73	P61088	UBE2N_HUMAN	I	73;73;10;73	ENSP00000316176:T73I;ENSP00000449352:T73I;ENSP00000450260:T10I;ENSP00000448352:T73I	ENSP00000316176:T73I	T	-	2	0	UBE2N	92329019	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.660000	0.98599	2.820000	0.97059	0.650000	0.86243	ACC	.	.		0.378	UBE2N-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407710.1	NM_003348		A	93804888	G	A	93804888	3	1	344	1	0	0	0	0	1	0	0	0	16881	1261	44	3	252	3	UBE2N	12	93804888	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1265576	93804888	40047007	935	48298										
METAP2	10988	hgsc.bcm.edu	37	chr12	95905678	95905678	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttttttataacagtgaaaccAatccgtaatctaaatggaca	5	7	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:95905678A>C	ENST00000323666.5	+	9	1201	c.972A>C	c.(970-972)ccA>ccC	p.P324P	METAP2_ENST00000551840.1_Silent_p.P323P|METAP2_ENST00000550777.1_Silent_p.P288P|METAP2_ENST00000546753.1_Silent_p.P301P|METAP2_ENST00000261220.9_Silent_p.P301P	NM_006838.3	NP_006829.1			methionyl aminopeptidase 2											endometrium(3)|large_intestine(2)|lung(7)|prostate(1)	13						CAGTGAAACCAATCCGTAATC	0.358																																					p.P324P		Atlas-SNP	.											.	METAP2	28	.	0			c.A972C						.						92	84	87					12																	95905678		2203	4300	6503	SO:0001819	synonymous_variant	10988	exon9			GAAACCAATCCGT	U13261	CCDS9052.1	12q22	2014-09-04			ENSG00000111142		3.4.11.18		16672	protein-coding gene	gene with protein product	"Peptidase M"	601870				7644482, 8858118	Standard	NM_006838		Approved	MNPEP, p67, MAP2	uc001tec.3	P50579	OTTHUMG00000170280	ENST00000323666.5:c.972A>C	chr12.hg19:g.95905678A>C		69.0	0.0		55.0	17.0	NM_006838		Silent	SNP	ENST00000323666.5	hg19	CCDS9052.1																																																																																			.	.		0.358	METAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408296.1	NM_006838		C	95905678	A	C	95905678	2	2	344	1	0	0	0	0	0	0	0	1	9496	117	5	5		5	METAP2	12	95905678	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2100790	95905678	37946217	936	48299										
GAS2L3	283431	hgsc.bcm.edu	37	chr12	101018227	101018227	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggagccccacaagcaaagccAgtcccagcacagaaacttaa	8	14	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:101018227A>C	ENST00000539410.1	+	9	2030	c.1644A>C	c.(1642-1644)ccA>ccC	p.P548P	GAS2L3_ENST00000266754.5_Silent_p.P548P|GAS2L3_ENST00000537247.1_Silent_p.P444P|GAS2L3_ENST00000547754.1_Silent_p.P548P			Q86XJ1	GA2L3_HUMAN	growth arrest-specific 2 like 3	548					actin cytoskeleton organization (GO:0030036)|cell cycle arrest (GO:0007050)|microtubule cytoskeleton organization (GO:0000226)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	actin binding (GO:0003779)|microtubule binding (GO:0008017)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(15)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35						AAGCAAAGCCAGTCCCAGCAC	0.448																																					p.P548P		Atlas-SNP	.											.	GAS2L3	76	.	0			c.A1644C						.						48	48	48					12																	101018227		2203	4300	6503	SO:0001819	synonymous_variant	283431	exon10			AAAGCCAGTCCCA	AK095594	CCDS9079.1	12q23.1	2014-09-11			ENSG00000139354	ENSG00000139354			27475	protein-coding gene	gene with protein product							Standard	NM_174942		Approved		uc001thu.3	Q86XJ1	OTTHUMG00000170439	ENST00000539410.1:c.1644A>C	chr12.hg19:g.101018227A>C		102.0	0.0		95.0	37.0	NM_174942	B2RCN2	Silent	SNP	ENST00000539410.1	hg19	CCDS9079.1																																																																																			.	.		0.448	GAS2L3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409143.1	NM_174942		C	101018227	A	C	101018227	2	2	344	1	0	0	0	0	0	0	0	1	6256	175	7	5		5	GAS2L3	12	101018227	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	5112549	101018227	32833668	937	48300										
SLC5A8	160728	hgsc.bcm.edu	37	chr12	101551063	101551063	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtatcagagcagcttcacaaAcgagtcccattgctcttgcc	8	13	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:101551063A>T	ENST00000536262.2	-	15	2385	c.1827T>A	c.(1825-1827)cgT>cgA	p.R609R		NM_145913.3	NP_666018.3			solute carrier family 5 (sodium/monocarboxylate cotransporter), member 8											breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(29)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						AGCTTCACAAACGAGTCCCAT	0.378																																					p.R609R	GBM(60;420 1056 13605 22380 47675)	Atlas-SNP	.											.	SLC5A8	102	.	0			c.T1827A						.						135	118	124					12																	101551063		2203	4300	6503	SO:0001819	synonymous_variant	160728	exon15			TCACAAACGAGTC	AY081220	CCDS9080.1	12q23.1	2013-07-19	2013-07-19		ENSG00000256870	ENSG00000256870		"Solute carriers"	19119	protein-coding gene	gene with protein product		608044	"solute carrier family 5 (iodide transporter), member 8"			12107270, 12829793	Standard	NM_145913		Approved	AIT	uc001thz.4	Q8N695	OTTHUMG00000170499	ENST00000536262.2:c.1827T>A	chr12.hg19:g.101551063A>T		101.0	0.0		73.0	8.0	NM_145913		Silent	SNP	ENST00000536262.2	hg19	CCDS9080.1																																																																																			.	.		0.378	SLC5A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409401.1	NM_145913		T	101551063	A	T	101551063	2	4	344	1	0	0	0	0	0	0	0	1	14686	30	2	4		4	SLC5A8	12	101551063	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	532836	101551063	32300832	938	48301										
UTP20	27340	hgsc.bcm.edu	37	chr12	101748808	101748808	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctctttccttcctcaaaacaAggaagaaatagagagaacaa	6	9	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:101748808A>G	ENST00000261637.4	+	41	5480	c.5306A>G	c.(5305-5307)aAg>aGg	p.K1769R		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	1769					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						CCTCAAAACAAGGAAGAAATA	0.428																																					p.K1769R		Atlas-SNP	.											UTP20,bladder,carcinoma,0,1	UTP20	222	.	0			c.A5306G						.						56	54	55					12																	101748808		2203	4300	6503	SO:0001583	missense	27340	exon41			AAAACAAGGAAGA	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"down regulated in metastasis"	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.5306A>G	chr12.hg19:g.101748808A>G	ENSP00000261637:p.Lys1769Arg	176.0	0.0		147.0	9.0	NM_014503	Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	hg19	CCDS9081.1	.	.	.	.	.	.	.	.	.	.	A	7.458	0.644125	0.14451	.	.	ENSG00000120800	ENST00000261637	T	0.19105	2.17	5.79	5.79	0.91817	Armadillo-type fold (1);	0.203901	0.50627	D	0.000107	T	0.20292	0.0488	L	0.52364	1.645	0.49798	D	0.99982	B	0.26512	0.151	B	0.23275	0.045	T	0.04268	-1.0964	10	0.19147	T	0.46	-21.0544	14.0875	0.64968	1.0:0.0:0.0:0.0	.	1769	O75691	UTP20_HUMAN	R	1769	ENSP00000261637:K1769R	ENSP00000261637:K1769R	K	+	2	0	UTP20	100272939	1.000000	0.71417	1.000000	0.80357	0.067000	0.16453	4.724000	0.61972	2.207000	0.71202	0.533000	0.62120	AAG	.	.		0.428	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		G	101748808	A	G	101748808	3	3	344	1	0	0	0	0	1	0	0	0	17114	72	3	2	5468	2	UTP20	12	101748808	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	197745	101748808	32103087	939	48302										
STAB2	55576	hgsc.bcm.edu	37	chr12	104107485	104107485	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gctgactgtaagagaaccacCccaggaaggcgagtgtgcac	13	11	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:104107485C>A	ENST00000388887.2	+	42	4680	c.4476C>A	c.(4474-4476)acC>acA	p.T1492T		NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						AGAGAACCACCCCAGGAAGGC	0.532																																					p.T1492T		Atlas-SNP	.											.	STAB2	370	.	0			c.C4476A						.						277	251	260					12																	104107485		2203	4300	6503	SO:0001819	synonymous_variant	55576	exon42			AACCACCCCAGGA	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"hyaluronic acid receptor for endocytosis"	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.4476C>A	chr12.hg19:g.104107485C>A		89.0	0.0		93.0	36.0	NM_017564		Silent	SNP	ENST00000388887.2	hg19	CCDS31888.1																																																																																			.	.		0.532	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			A	104107485	C	A	104107485	2	1	344	1	0	0	0	0	0	0	0	1	15253	610	22	3		3	STAB2	12	104107485	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	2358677	104107485	29744410	940	48303										
TCP11L2	255394	hgsc.bcm.edu	37	chr12	106734764	106734764	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aagaggaggacaatcctatcTggtccttgattggtgagtcc	12	8	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:106734764T>A	ENST00000299045.3	+	9	1477	c.1303T>A	c.(1303-1305)Tgg>Agg	p.W435R		NM_152772.1	NP_689985.1	Q8N4U5	T11L2_HUMAN	t-complex 11, testis-specific-like 2	435										endometrium(2)|kidney(2)|large_intestine(5)|ovary(3)|prostate(1)|urinary_tract(2)	15						CAATCCTATCTGGTCCTTGAT	0.358																																					p.W435R		Atlas-SNP	.											.	TCP11L2	59	.	0			c.T1303A						.						167	163	165					12																	106734764		2203	4300	6503	SO:0001583	missense	255394	exon9			CCTATCTGGTCCT	BC033617	CCDS9104.1, CCDS66456.1	12q23.3	2014-08-12	2012-09-20		ENSG00000166046	ENSG00000166046			28627	protein-coding gene	gene with protein product			"t-complex 11 (mouse) like 2", "t-complex 11 (mouse)-like 2"				Standard	XM_005268769		Approved	MGC40368	uc001tln.3	Q8N4U5	OTTHUMG00000170087	ENST00000299045.3:c.1303T>A	chr12.hg19:g.106734764T>A	ENSP00000299045:p.Trp435Arg	81.0	0.0		66.0	39.0	NM_152772	B2RA65|G3V1Y9	Missense_Mutation	SNP	ENST00000299045.3	hg19	CCDS9104.1	.	.	.	.	.	.	.	.	.	.	T	1.935	-0.445026	0.04604	.	.	ENSG00000166046	ENST00000299045	T	0.09723	2.95	5.58	-2.54	0.06307	.	0.591918	0.20480	N	0.091501	T	0.01558	0.0050	N	0.00108	-2.11	0.29274	N	0.870505	B	0.02656	0.0	B	0.01281	0.0	T	0.42498	-0.9448	10	0.25106	T	0.35	-3.2136	4.8987	0.13764	0.2754:0.3182:0.0:0.4064	.	435	Q8N4U5	T11L2_HUMAN	R	435	ENSP00000299045:W435R	ENSP00000299045:W435R	W	+	1	0	TCP11L2	105258894	0.685000	0.27652	0.088000	0.20740	0.995000	0.86356	-0.356000	0.07661	-0.754000	0.04715	0.455000	0.32223	TGG	.	.		0.358	TCP11L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407206.1	NM_152772		A	106734764	T	A	106734764	3	1	344	1	0	0	0	0	1	0	0	0	15730	1580	55	4	1333	4	TCP11L2	12	106734764	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2627279	106734764	27117131	941	48304										
DAO	1610	hgsc.bcm.edu	37	chr12	109286766	109286766	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgatcatcccaggttaactgAgaggggagtgaagttcttcc	12	8	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:109286766A>T	ENST00000228476.3	+	6	665	c.461A>T	c.(460-462)gAg>gTg	p.E154V	DAO_ENST00000551281.1_Intron	NM_001917.4	NP_001908.3	P14920	OXDA_HUMAN	D-amino-acid oxidase	154					cellular nitrogen compound metabolic process (GO:0034641)|D-alanine catabolic process (GO:0055130)|D-serine catabolic process (GO:0036088)|D-serine metabolic process (GO:0070178)|dopamine biosynthetic process (GO:0042416)|glyoxylate metabolic process (GO:0046487)|leucine metabolic process (GO:0006551)|proline catabolic process (GO:0006562)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	cofactor binding (GO:0048037)|D-amino-acid oxidase activity (GO:0003884)|FAD binding (GO:0071949)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|prostate(2)|skin(1)	26					Flavin adenine dinucleotide(DB03147)	AGGTTAACTGAGAGGGGAGTG	0.542																																					p.E154V		Atlas-SNP	.											.	DAO	58	.	0			c.A461T						.						177	145	156					12																	109286766		2203	4300	6503	SO:0001583	missense	1610	exon6			TAACTGAGAGGGG	D11370	CCDS9122.1	12q24.11	2013-09-20			ENSG00000110887	ENSG00000110887	1.4.3.3		2671	protein-coding gene	gene with protein product		124050				1356107, 8182053	Standard	NM_001917		Approved	DAMOX	uc001tnr.4	P14920	OTTHUMG00000169360	ENST00000228476.3:c.461A>T	chr12.hg19:g.109286766A>T	ENSP00000228476:p.Glu154Val	68.0	0.0		53.0	21.0	NM_001917	B2R7I5|Q16758|Q8N6R2	Missense_Mutation	SNP	ENST00000228476.3	hg19	CCDS9122.1	.	.	.	.	.	.	.	.	.	.	A	13.71	2.318326	0.40996	.	.	ENSG00000110887	ENST00000228476;ENST00000547768;ENST00000547166	D;D;D	0.83335	-1.71;-1.71;-1.71	5.82	4.69	0.59074	FAD dependent oxidoreductase (1);NAD(P)-binding domain (1);	0.303860	0.39341	N	0.001381	D	0.83207	0.5204	M	0.74647	2.275	0.48571	D	0.999677	P	0.45348	0.856	P	0.46975	0.533	T	0.81675	-0.0825	10	0.32370	T	0.25	-16.0708	8.9302	0.35666	0.916:0.0:0.084:0.0	.	154	P14920	OXDA_HUMAN	V	154;31;154	ENSP00000228476:E154V;ENSP00000449967:E31V;ENSP00000447104:E154V	ENSP00000228476:E154V	E	+	2	0	DAO	107810895	1.000000	0.71417	0.999000	0.59377	0.485000	0.33311	4.782000	0.62396	2.223000	0.72356	0.482000	0.46254	GAG	.	.		0.542	DAO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403682.1			T	109286766	A	T	109286766	3	4	344	1	0	0	0	0	1	0	0	0	4233	304	11	4	479	4	DAO	12	109286766	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2552002	109286766	24565129	942	48305										
C12orf51	283450	hgsc.bcm.edu	37	chr12	112717077	112717077	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tccaccaaaaagagatcgggTggcagagctgcctgatcccc	11	13	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:112717077T>G	ENST00000430131.2	-	9	1605	c.460A>C	c.(460-462)Acc>Ccc	p.T154P	HECTD4_ENST00000550722.1_Missense_Mutation_p.T404P|HECTD4_ENST00000377560.5_Missense_Mutation_p.T404P			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	154					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										AGAGATCGGGTGGCAGAGCTG	0.458																																					p.T404P		Atlas-SNP	.											.	.	.	.	0			c.A1210C						.						78	78	78					12																	112717077		1872	4106	5978	SO:0001583	missense	283450	exon9			ATCGGGTGGCAGA	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 51"	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.460A>C	chr12.hg19:g.112717077T>G	ENSP00000404379:p.Thr154Pro	65.0	0.0		43.0	18.0	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Missense_Mutation	SNP	ENST00000430131.2	hg19		.	.	.	.	.	.	.	.	.	.	T	20.2	3.956954	0.73902	.	.	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722	T;T;T	0.53857	0.69;0.6;0.66	5.54	5.54	0.83059	.	.	.	.	.	T	0.54255	0.1847	N	0.08118	0	0.80722	D	1	D	0.65815	0.995	D	0.72982	0.979	T	0.65429	-0.6170	9	0.87932	D	0	.	15.6803	0.77364	0.0:0.0:0.0:1.0	.	154	Q9Y4D8	K0614_HUMAN	P	404;154;404	ENSP00000366783:T404P;ENSP00000404379:T154P;ENSP00000449784:T404P	ENSP00000366783:T404P	T	-	1	0	C12orf51	111201460	1.000000	0.71417	0.998000	0.56505	0.973000	0.67179	7.629000	0.83207	2.115000	0.64714	0.482000	0.46254	ACC	.	.		0.458	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		G	112717077	T	G	112717077	3	3	344	1	0	0	0	0	1	0	0	0	1698	1696	59	5	11798	5	C12orf51	12	112717077	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	3430311	112717077	21134818	943	48306										
RASAL1	8437	hgsc.bcm.edu	37	chr12	113557018	113557018	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gggcacctggcatctcccgcAgctccagcacttcatcccag	9	18	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:113557018A>T	ENST00000261729.5	-	8	872	c.557T>A	c.(556-558)cTg>cAg	p.L186Q	RASAL1_ENST00000548055.1_Missense_Mutation_p.L186Q|RASAL1_ENST00000418411.2_5'UTR|RASAL1_ENST00000546530.1_Missense_Mutation_p.L186Q|RASAL1_ENST00000446861.3_Missense_Mutation_p.L186Q			O95294	RASL1_HUMAN	RAS protein activator like 1 (GAP1 like)	186	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|phospholipid binding (GO:0005543)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(3)|prostate(2)|skin(2)	43						CATCTCCCGCAGCTCCAGCAC	0.617																																					p.L186Q		Atlas-SNP	.											.	RASAL1	89	.	0			c.T557A						.						68	59	62					12																	113557018		2203	4300	6503	SO:0001583	missense	8437	exon8			TCCCGCAGCTCCA	AF086713	CCDS9165.1, CCDS55888.1, CCDS55889.1, CCDS73529.1	12q23-q24	2013-01-10			ENSG00000111344	ENSG00000111344		"Pleckstrin homology (PH) domain containing"	9873	protein-coding gene	gene with protein product		604118				9751798	Standard	NM_001193520		Approved	RASAL	uc001tul.3	O95294	OTTHUMG00000169705	ENST00000261729.5:c.557T>A	chr12.hg19:g.113557018A>T	ENSP00000261729:p.Leu186Gln	63.0	0.0		50.0	22.0	NM_004658	B7ZKM4|C9JFK5|F8VQX1|Q52M03|Q59H24|Q96CC7	Missense_Mutation	SNP	ENST00000261729.5	hg19	CCDS9165.1	.	.	.	.	.	.	.	.	.	.	A	27.2	4.812995	0.90707	.	.	ENSG00000111344	ENST00000546530;ENST00000261729;ENST00000446861;ENST00000548055	T;T;T;T	0.71103	-0.54;-0.54;-0.54;-0.54	5.46	5.46	0.80206	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.082956	0.50627	D	0.000119	D	0.85164	0.5634	M	0.85945	2.785	0.41541	D	0.98851	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.993;1.0;1.0	D;D;D;D;D;D;D	0.80764	0.994;0.994;0.989;0.994;0.967;0.992;0.983	D	0.87972	0.2737	10	0.87932	D	0	.	14.5106	0.67784	1.0:0.0:0.0:0.0	.	186;186;186;198;186;186;186	B7ZKM4;B4DG06;F8VRH9;Q59H24;F8VQX1;O95294;O95294-2	.;.;.;.;.;RASL1_HUMAN;.	Q	186	ENSP00000450244:L186Q;ENSP00000261729:L186Q;ENSP00000395920:L186Q;ENSP00000448510:L186Q	ENSP00000261729:L186Q	L	-	2	0	RASAL1	112041401	1.000000	0.71417	0.990000	0.47175	0.978000	0.69477	8.840000	0.92125	2.085000	0.62840	0.402000	0.26972	CTG	.	.		0.617	RASAL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405522.2	NM_004658		T	113557018	A	T	113557018	3	4	344	1	0	0	0	0	1	0	0	0	13078	188	7	4	1917	4	RASAL1	12	113557018	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	839941	113557018	20294877	944	48307										
NOS1	4842	hgsc.bcm.edu	37	chr12	117680507	117680507	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gctttttgtggacattggatAgacctgtggggagaaaaaca	13	5	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:117680507A>G	ENST00000338101.4	-	20	3072	c.3068T>C	c.(3067-3069)cTa>cCa	p.L1023P	NOS1_ENST00000317775.6_Missense_Mutation_p.L989P|NOS1_ENST00000344089.3_3'UTR			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		GACATTGGATAGACCTGTGGG	0.512																																					p.L1023P	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											.	NOS1	240	.	0			c.T3068C						.						110	108	108					12																	117680507		1894	4109	6003	SO:0001583	missense	4842	exon21			TTGGATAGACCTG		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.3068T>C	chr12.hg19:g.117680507A>G	ENSP00000337459:p.Leu1023Pro	76.0	0.0		60.0	31.0	NM_001204218		Missense_Mutation	SNP	ENST00000338101.4	hg19	CCDS55890.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.206962	0.79127	.	.	ENSG00000089250	ENST00000397605;ENST00000317775;ENST00000541241;ENST00000338101	T;T	0.35973	1.28;1.28	4.47	4.47	0.54385	Riboflavin synthase-like beta-barrel (1);	0.261054	0.30269	N	0.010018	T	0.59376	0.2189	M	0.75615	2.305	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.65067	-0.6258	10	0.87932	D	0	-13.694	13.9206	0.63928	1.0:0.0:0.0:0.0	.	989	P29475	NOS1_HUMAN	P	884;989;989;1023	ENSP00000320758:L989P;ENSP00000337459:L1023P	ENSP00000320758:L989P	L	-	2	0	NOS1	116164890	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.391000	0.90177	1.857000	0.53885	0.377000	0.23210	CTA	.	.		0.512	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1			G	117680507	A	G	117680507	3	3	344	1	0	0	0	0	1	0	0	0	10550	420	15	2	1378	2	NOS1	12	117680507	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	4123489	117680507	16171388	945	48308										
NOS1	4842	hgsc.bcm.edu	37	chr12	117703310	117703310	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tggtcaacaatggtcactttGtcactctgtgggaggagagg	14	7	4	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:117703310G>T	ENST00000338101.4	-	11	1951	c.1947C>A	c.(1945-1947)gaC>gaA	p.D649E	NOS1_ENST00000317775.6_Missense_Mutation_p.D649E|NOS1_ENST00000344089.3_3'UTR			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		TGGTCACTTTGTCACTCTGTG	0.577																																					p.D649E	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											.	NOS1	240	.	0			c.C1947A						.						43	43	43					12																	117703310		2059	4219	6278	SO:0001583	missense	4842	exon12			CACTTTGTCACTC		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.1947C>A	chr12.hg19:g.117703310G>T	ENSP00000337459:p.Asp649Glu	50.0	0.0		52.0	26.0	NM_000620		Missense_Mutation	SNP	ENST00000338101.4	hg19	CCDS55890.1	.	.	.	.	.	.	.	.	.	.	G	9.474	1.096323	0.20552	.	.	ENSG00000089250	ENST00000397605;ENST00000317775;ENST00000541241;ENST00000338101	T;T	0.21191	2.02;2.02	5.37	4.47	0.54385	Nitric oxide synthase, oxygenase domain (2);	0.139018	0.64402	D	0.000004	T	0.13243	0.0321	L	0.31294	0.92	0.80722	D	1	B	0.34313	0.448	B	0.36134	0.218	T	0.03503	-1.1030	10	0.02654	T	1	-46.7229	10.2563	0.43399	0.1496:0.0:0.8504:0.0	.	649	P29475	NOS1_HUMAN	E	544;649;649;649	ENSP00000320758:D649E;ENSP00000337459:D649E	ENSP00000320758:D649E	D	-	3	2	NOS1	116187693	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	3.505000	0.53356	1.489000	0.48450	0.655000	0.94253	GAC	.	.		0.577	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1			T	117703310	G	T	117703310	3	4	344	1	0	0	0	0	1	0	0	0	10550	1368	48	3	2429	3	NOS1	12	117703310	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	22803	117703310	16148585	946	48309										
KSR2	283455	hgsc.bcm.edu	37	chr12	118298200	118298200	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	caaggctaccttctttttgcAggacagctgccggctgaagt	11	11	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:118298200A>G	ENST00000339824.5	-	2	944	c.217T>C	c.(217-219)Tgc>Cgc	p.C73R	KSR2_ENST00000425217.1_Missense_Mutation_p.C44R			Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2	73					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(25)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TTCTTTTTGCAGGACAGCTGC	0.587																																					p.C44R		Atlas-SNP	.											.	KSR2	208	.	0			c.T130C						.						39	42	41					12																	118298200		1568	3582	5150	SO:0001583	missense	283455	exon2			TTTTGCAGGACAG	AY345972	CCDS61250.1	12q24.22-q24.23	2014-08-12			ENSG00000171435	ENSG00000171435			18610	protein-coding gene	gene with protein product		610737				12471243	Standard	NM_173598		Approved	FLJ25965	uc001two.2	Q6VAB6	OTTHUMG00000169020	ENST00000339824.5:c.217T>C	chr12.hg19:g.118298200A>G	ENSP00000339952:p.Cys73Arg	43.0	0.0		34.0	17.0	NM_173598	A0PJT2|Q3B828|Q8N775	Missense_Mutation	SNP	ENST00000339824.5	hg19		.	.	.	.	.	.	.	.	.	.	A	16.77	3.215483	0.58452	.	.	ENSG00000171435	ENST00000425217;ENST00000339824	T;T	0.78595	-1.19;-1.18	4.96	4.96	0.65561	.	.	.	.	.	T	0.76828	0.4042	L	0.43923	1.385	0.80722	D	1	P	0.48998	0.918	P	0.49140	0.601	T	0.78285	-0.2263	9	0.49607	T	0.09	.	13.9028	0.63815	1.0:0.0:0.0:0.0	.	73	Q6VAB6	KSR2_HUMAN	R	44;73	ENSP00000389715:C44R;ENSP00000339952:C73R	ENSP00000339952:C73R	C	-	1	0	KSR2	116782583	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	9.257000	0.95545	1.989000	0.58080	0.260000	0.18958	TGC	.	.		0.587	KSR2-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401987.2	NM_173598		G	118298200	A	G	118298200	3	3	344	1	0	0	0	0	1	0	0	0	8591	188	7	2	2711	2	KSR2	12	118298200	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	594890	118298200	15553695	947	48310										
SRRM4	84530	hgsc.bcm.edu	37	chr12	119588876	119588876	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtgaagaagtccagtttggtCccatccacagcccggagctc	11	13	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:119588876C>A	ENST00000267260.4	+	10	1519	c.1131C>A	c.(1129-1131)gtC>gtA	p.V377V		NM_194286.3	NP_919262.2	A7MD48	SRRM4_HUMAN	serine/arginine repetitive matrix 4	377	Ser-rich.				cell differentiation (GO:0030154)|mRNA processing (GO:0006397)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	mRNA binding (GO:0003729)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	24						CCAGTTTGGTCCCATCCACAG	0.577																																					p.V377V		Atlas-SNP	.											.	SRRM4	131	.	0			c.C1131A						.						75	81	79					12																	119588876		1992	4177	6169	SO:0001819	synonymous_variant	84530	exon10			TTTGGTCCCATCC	AB058756	CCDS44994.1	12q24.23	2009-09-22	2009-09-21	2009-09-21	ENSG00000139767	ENSG00000139767			29389	protein-coding gene	gene with protein product	"neural-specific SR-related protein of 100 kDa"	613103	"KIAA1853"	KIAA1853		19737518	Standard	NM_194286		Approved	nSR100	uc001txa.2	A7MD48	OTTHUMG00000168928	ENST00000267260.4:c.1131C>A	chr12.hg19:g.119588876C>A		86.0	0.0		92.0	42.0	NM_194286	A8K5P6|B2RZH7|Q7Z5F0|Q96JH4	Silent	SNP	ENST00000267260.4	hg19	CCDS44994.1																																																																																			.	.		0.577	SRRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401640.2	NM_194286		A	119588876	C	A	119588876	2	1	344	1	0	0	0	0	0	0	0	1	15186	842	30	3		3	SRRM4	12	119588876	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1290676	119588876	14263019	948	48311										
GCN1L1	10985	hgsc.bcm.edu	37	chr12	120594786	120594786	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tggccacgcgaggcagcaacTccgggccattctaggagaga	14	12	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:120594786T>A	ENST00000300648.6	-	27	3110	c.3098A>T	c.(3097-3099)gAg>gTg	p.E1033V	MIR4498_ENST00000577599.1_RNA	NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	1033					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					AGGCAGCAACTCCGGGCCATT	0.612																																					p.E1033V		Atlas-SNP	.											.	GCN1L1	207	.	0			c.A3098T						.						45	53	51					12																	120594786		2076	4203	6279	SO:0001583	missense	10985	exon27			AGCAACTCCGGGC	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.3098A>T	chr12.hg19:g.120594786T>A	ENSP00000300648:p.Glu1033Val	73.0	0.0		56.0	18.0	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Missense_Mutation	SNP	ENST00000300648.6	hg19	CCDS41847.1	.	.	.	.	.	.	.	.	.	.	T	15.97	2.988639	0.53934	.	.	ENSG00000089154	ENST00000300648	T	0.48836	0.8	5.79	5.79	0.91817	Armadillo-type fold (2);	0.050794	0.85682	D	0.000000	T	0.49167	0.1541	M	0.68317	2.08	0.80722	D	1	P	0.49961	0.93	B	0.41236	0.351	T	0.54153	-0.8336	10	0.45353	T	0.12	.	16.1164	0.81306	0.0:0.0:0.0:1.0	.	1033	Q92616	GCN1L_HUMAN	V	1033	ENSP00000300648:E1033V	ENSP00000300648:E1033V	E	-	2	0	GCN1L1	119079169	1.000000	0.71417	0.814000	0.32528	0.315000	0.28087	6.868000	0.75516	2.198000	0.70561	0.482000	0.46254	GAG	.	.		0.612	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1			A	120594786	T	A	120594786	3	1	344	1	0	0	0	0	1	0	0	0	6307	1551	54	4	5045	4	GCN1L1	12	120594786	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1005910	120594786	13257109	949	48312										
COX6A1	1337	hgsc.bcm.edu	37	chr12	120875944	120875944	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcaaaaatggcggtagttggTgtgtcctcggtttctcggct	13	8	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:120875944T>C	ENST00000229379.2	+	1	52	c.15T>C	c.(13-15)ggT>ggC	p.G5G	AL021546.6_ENST00000551806.1_5'Flank	NM_004373.3	NP_004364.2	P12074	CX6A1_HUMAN	cytochrome c oxidase subunit VIa polypeptide 1	5					cellular metabolic process (GO:0044237)|generation of precursor metabolites and energy (GO:0006091)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex IV (GO:0005751)	cytochrome-c oxidase activity (GO:0004129)					all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CGGTAGTTGGTGTGTCCTCGG	0.617																																					p.G5G		Atlas-SNP	.											.	COX6A1	5	.	0			c.T15C						.						24	25	24					12																	120875944		2202	4299	6501	SO:0001819	synonymous_variant	1337	exon1			AGTTGGTGTGTCC	X15341	CCDS9197.1	12q24	2011-07-04			ENSG00000111775	ENSG00000111775	1.9.3.1	"Mitochondrial respiratory chain complex / Complex IV"	2277	protein-coding gene	gene with protein product		602072		COX6A		9284905	Standard	NM_004373		Approved		uc001tyf.2	P12074	OTTHUMG00000047791	ENST00000229379.2:c.15T>C	chr12.hg19:g.120875944T>C		58.0	0.0		37.0	20.0	NM_004373	B2R500|O43714|Q32Q37	Silent	SNP	ENST00000229379.2	hg19	CCDS9197.1																																																																																			.	.		0.617	COX6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108984.3	NM_004373		C	120875944	T	C	120875944	2	2	344	1	0	0	0	0	0	0	0	1	3776	1683	59	2		2	COX6A1	12	120875944	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	281158	120875944	12975951	950	48313										
PITPNM2	57605	hgsc.bcm.edu	37	chr12	123498472	123498472	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccagctgggaatgtgcatgcCcacatgatacaccttgtgtg	11	11	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:123498472C>A	ENST00000542749.1	-	2	259	c.196G>T	c.(196-198)Ggc>Tgc	p.G66C	PITPNM2_ENST00000392428.1_Intron|PITPNM2_ENST00000280562.5_Missense_Mutation_p.G66C|PITPNM2_ENST00000546049.1_Missense_Mutation_p.G66C|RN7SL133P_ENST00000585256.1_RNA|PITPNM2_ENST00000451868.2_5'UTR|PITPNM2_ENST00000320201.4_Missense_Mutation_p.G66C			Q9BZ72	PITM2_HUMAN	phosphatidylinositol transfer protein, membrane-associated 2	66					metabolic process (GO:0008152)|transport (GO:0006810)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)			NS(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	39	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.55e-05)|Epithelial(86;8.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.123)		ATGTGCATGCCCACATGATAC	0.617																																					p.G66C		Atlas-SNP	.											.	PITPNM2	105	.	0			c.G196T						.						148	119	129					12																	123498472		2203	4300	6503	SO:0001583	missense	57605	exon3			GCATGCCCACATG	AF334585	CCDS9242.1, CCDS73543.1	12q24.31	2008-02-05				ENSG00000090975			21044	protein-coding gene	gene with protein product		608920				10022914	Standard	XM_005253582		Approved	RDGBA2, RDGB2, NIR3	uc001uej.1	Q9BZ72		ENST00000542749.1:c.196G>T	chr12.hg19:g.123498472C>A	ENSP00000437611:p.Gly66Cys	80.0	0.0		72.0	30.0	NM_020845	Q9P271	Missense_Mutation	SNP	ENST00000542749.1	hg19	CCDS9242.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.925287	0.92319	.	.	ENSG00000090975	ENST00000280562;ENST00000320201;ENST00000542749	T;T;T	0.47177	0.85;0.85;0.85	4.42	4.42	0.53409	START-like domain (1);	0.000000	0.85682	D	0.000000	T	0.76241	0.3960	M	0.92169	3.28	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.999	D	0.83929	0.0305	10	0.87932	D	0	-46.6565	17.4015	0.87461	0.0:1.0:0.0:0.0	.	66;66;66	A5D8U3;Q9BZ72-2;Q9BZ72	.;.;PITM2_HUMAN	C	66	ENSP00000280562:G66C;ENSP00000322218:G66C;ENSP00000437611:G66C	ENSP00000280562:G66C	G	-	1	0	PITPNM2	122064425	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.585000	0.82584	2.168000	0.68352	0.655000	0.94253	GGC	.	.		0.617	PITPNM2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401342.1	NM_020845		A	123498472	C	A	123498472	3	1	344	1	0	0	0	0	1	0	0	0	11960	623	22	3	3945	3	PITPNM2	12	123498472	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	2622528	123498472	10353423	951	48314										
DNAH10	196385	hgsc.bcm.edu	37	chr12	124285839	124285839	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	catgtgcaggtacacagctgGgatacagcgcatgttggatc	13	9	0	0	rs571838812		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:124285839G>A	ENST00000409039.3	+	15	2145	c.2120G>A	c.(2119-2121)gGg>gAg	p.G707E		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	707	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		TACACAGCTGGGATACAGCGC	0.463													G|||	1	0.000199681	0	0	5008	,	,		19431	0		0	False		,,,				2504	0.001				p.G707E		Atlas-SNP	.											.	DNAH10	888	.	0			c.G2120A						.						280	246	258					12																	124285839		2203	4300	6503	SO:0001583	missense	196385	exon15			CAGCTGGGATACA	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.2120G>A	chr12.hg19:g.124285839G>A	ENSP00000386770:p.Gly707Glu	76.0	0.0		74.0	38.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	hg19	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	G	3.796	-0.042686	0.07452	.	.	ENSG00000197653	ENST00000409039	T	0.54279	0.58	5.49	5.49	0.81192	Dynein heavy chain, domain-1 (1);	0.109402	0.36338	N	0.002659	T	0.45175	0.1329	L	0.58583	1.82	0.09310	N	0.999999	B;B;B	0.30361	0.199;0.277;0.045	B;B;B	0.35899	0.124;0.213;0.063	T	0.44436	-0.9328	10	0.05525	T	0.97	.	9.3321	0.38027	0.1995:0.0:0.8005:0.0	.	707;582;707	Q8IVF4-2;C4IXU6;Q8IVF4	.;.;DYH10_HUMAN	E	707	ENSP00000386770:G707E	ENSP00000386770:G707E	G	+	2	0	DNAH10	122851792	0.988000	0.35896	0.036000	0.18154	0.024000	0.10985	2.195000	0.42677	2.571000	0.86741	0.655000	0.94253	GGG	.	.		0.463	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			A	124285839	G	A	124285839	3	1	344	1	0	0	0	0	1	0	0	0	4600	1232	43	3	2178	3	DNAH10	12	124285839	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	787367	124285839	9566056	952	48315										
DNAH10	196385	hgsc.bcm.edu	37	chr12	124383215	124383215	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctcagctcagtgcaagcgtcTggatgggggactggacaagc	15	10	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:124383215T>A	ENST00000409039.3	+	55	9165	c.9140T>A	c.(9139-9141)cTg>cAg	p.L3047Q		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	3047	Stalk. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		TGCAAGCGTCTGGATGGGGGA	0.562																																					p.L3047Q		Atlas-SNP	.											.	DNAH10	888	.	0			c.T9140A						.						14	17	16					12																	124383215		2021	4190	6211	SO:0001583	missense	196385	exon55			AGCGTCTGGATGG	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.9140T>A	chr12.hg19:g.124383215T>A	ENSP00000386770:p.Leu3047Gln	92.0	0.0		92.0	44.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	hg19	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	T	21.6	4.167450	0.78339	.	.	ENSG00000197653	ENST00000409039	D	0.81821	-1.54	4.66	4.66	0.58398	Dynein heavy chain, coiled coil stalk (1);	0.079027	0.52532	D	0.000063	D	0.92606	0.7651	H	0.96301	3.8	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.94775	0.7948	10	0.87932	D	0	.	14.2582	0.66065	0.0:0.0:0.0:1.0	.	3047	Q8IVF4	DYH10_HUMAN	Q	3047	ENSP00000386770:L3047Q	ENSP00000386770:L3047Q	L	+	2	0	DNAH10	122949168	1.000000	0.71417	0.979000	0.43373	0.791000	0.44710	7.864000	0.87037	1.952000	0.56665	0.379000	0.24179	CTG	.	.		0.562	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			A	124383215	T	A	124383215	3	1	344	1	0	0	0	0	1	0	0	0	4600	1580	55	4	9358	4	DNAH10	12	124383215	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	97376	124383215	9468680	953	48316										
NCOR2	9612	hgsc.bcm.edu	37	chr12	124886995	124886995	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccacctccggcttctcctccTccttctccgcctccttttcc	3	23	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:124886995T>A	ENST00000405201.1	-	14	1595	c.1595A>T	c.(1594-1596)gAg>gTg	p.E532V	NCOR2_ENST00000404121.2_Missense_Mutation_p.E102V|NCOR2_ENST00000356219.3_Missense_Mutation_p.E532V|NCOR2_ENST00000429285.2_Missense_Mutation_p.E531V|NCOR2_ENST00000404621.1_Missense_Mutation_p.E531V|NCOR2_ENST00000397355.1_Missense_Mutation_p.E532V			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	532					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		cttctcctcctccttctccgc	0.642																																					p.E532V		Atlas-SNP	.											.	NCOR2	475	.	0			c.A1595T						.						86	104	98					12																	124886995		2148	4243	6391	SO:0001583	missense	9612	exon16			TCCTCCTCCTTCT	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"nuclear receptor co-repressor 2"			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.1595A>T	chr12.hg19:g.124886995T>A	ENSP00000384018:p.Glu532Val	70.0	0.0		56.0	26.0	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	hg19	CCDS41858.2	.	.	.	.	.	.	.	.	.	.	T	12.31	1.898391	0.33535	.	.	ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000429285;ENST00000458234	T;T;T;T;T;T;T	0.66815	-0.23;-0.21;-0.23;1.93;3.26;1.93;0.51	4.25	4.25	0.50352	.	1.156430	0.06472	N	0.731335	T	0.78509	0.4294	L	0.50333	1.59	0.45342	D	0.998338	D;D;D	0.76494	0.998;0.998;0.999	D;D;D	0.78314	0.981;0.981;0.991	T	0.67749	-0.5590	10	0.59425	D	0.04	-6.829	11.0327	0.47783	0.0:0.0:0.0:1.0	.	531;532;532	C9J0Q5;C9J239;C9JFD3	.;.;.	V	532;531;532;532;532;102;531;532	ENSP00000384018:E532V;ENSP00000384202:E531V;ENSP00000348551:E532V;ENSP00000380513:E532V;ENSP00000385618:E102V;ENSP00000400281:E531V;ENSP00000402808:E532V	ENSP00000348551:E532V	E	-	2	0	NCOR2	123452948	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.147000	0.58078	1.695000	0.51148	0.402000	0.26972	GAG	.	.		0.642	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312		A	124886995	T	A	124886995	3	1	344	1	0	0	0	0	1	0	0	0	10245	1551	54	4	6109	4	NCOR2	12	124886995	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	503780	124886995	8964900	954	48317										
TMEM132D	121256	hgsc.bcm.edu	37	chr12	130184613	130184613	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cgtcttccctgacgcagtccCctctctcaccccctgggtgc	8	20	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr12:130184613C>A	ENST00000422113.2	-	2	1036	c.710G>T	c.(709-711)gGg>gTg	p.G237V	RP11-174M13.2_ENST00000544036.1_lincRNA	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	237					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		GACGCAGTCCCCTCTCTCACC	0.667																																					p.G237V		Atlas-SNP	.											.	TMEM132D	299	.	0			c.G710T						.						80	74	76					12																	130184613		2203	4300	6503	SO:0001583	missense	121256	exon2			CAGTCCCCTCTCT	AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 153"	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.710G>T	chr12.hg19:g.130184613C>A	ENSP00000408581:p.Gly237Val	81.0	0.0		97.0	39.0	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	hg19	CCDS9266.1	.	.	.	.	.	.	.	.	.	.	C	16.12	3.032281	0.54790	.	.	ENSG00000151952	ENST00000422113	T	0.12984	2.63	5.35	4.45	0.53987	.	0.000000	0.64402	D	0.000004	T	0.39784	0.1091	M	0.87180	2.865	0.45439	D	0.998415	D	0.76494	0.999	D	0.63033	0.91	T	0.46317	-0.9200	9	.	.	.	-27.7105	14.4464	0.67352	0.0:0.7196:0.2804:0.0	.	237	Q14C87	T132D_HUMAN	V	237	ENSP00000408581:G237V	.	G	-	2	0	TMEM132D	128750566	0.960000	0.32886	0.043000	0.18650	0.033000	0.12548	2.514000	0.45503	1.218000	0.43458	0.650000	0.86243	GGG	.	.		0.667	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448		A	130184613	C	A	130184613	3	1	344	1	0	0	0	0	1	0	0	0	16062	623	22	3	2621	3	TMEM132D	12	130184613	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	5297618	130184613	3667282	955	48318										
MPHOSPH8	54737	hgsc.bcm.edu	37	chr13	20220900	20220900	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaaacaaaagaattaaagaaAgttaaaaagggtgaaataag	9	1	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr13:20220900A>T	ENST00000361479.5	+	3	755	c.687A>T	c.(685-687)aaA>aaT	p.K229N	MPHOSPH8_ENST00000414242.2_Missense_Mutation_p.K229N	NM_017520.3	NP_059990.2	Q99549	MPP8_HUMAN	M-phase phosphoprotein 8	229	Lys-rich.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of DNA methylation (GO:0044030)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear heterochromatin (GO:0005720)|nuclear nucleosome (GO:0000788)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	methylated histone binding (GO:0035064)			breast(2)|endometrium(1)|large_intestine(2)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		all_cancers(29;2.83e-16)|all_lung(29;1.16e-17)|all_epithelial(30;8.13e-16)|Lung NSC(5;6.91e-15)|Lung SC(185;0.0367)		all cancers(112;8.43e-05)|Epithelial(112;0.000426)|OV - Ovarian serous cystadenocarcinoma(117;0.00596)|Lung(94;0.015)|LUSC - Lung squamous cell carcinoma(192;0.0795)		aattaaagaaagttaaaaagg	0.299																																					p.K229N		Atlas-SNP	.											.	MPHOSPH8	58	.	0			c.A687T						.						19	21	20					13																	20220900		2151	4266	6417	SO:0001583	missense	54737	exon3			AAAGAAAGTTAAA	AK056785, AJ293409	CCDS9287.1	13q12.11	2013-01-10			ENSG00000196199	ENSG00000196199		"Ankyrin repeat domain containing"	29810	protein-coding gene	gene with protein product		611626				8885239	Standard	NM_017520		Approved	mpp8, HSMPP8	uc001umh.3	Q99549	OTTHUMG00000016498	ENST00000361479.5:c.687A>T	chr13.hg19:g.20220900A>T	ENSP00000355388:p.Lys229Asn	169.0	0.0		152.0	57.0	NM_017520	B7Z6F9|Q5JPE5|Q5JTQ0|Q86TK3|Q96MK4|Q9BTP1	Missense_Mutation	SNP	ENST00000361479.5	hg19	CCDS9287.1	.	.	.	.	.	.	.	.	.	.	A	16.35	3.097574	0.56075	.	.	ENSG00000196199	ENST00000414242;ENST00000361479;ENST00000538024	T;T	0.45276	0.9;0.9	5.93	4.72	0.59763	.	3.271500	0.00674	N	0.000655	T	0.64843	0.2635	M	0.68952	2.095	0.33530	D	0.593464	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79784	0.976;0.993;0.989	T	0.33343	-0.9872	10	0.23302	T	0.38	.	9.8709	0.41172	0.8137:0.0:0.1863:0.0	.	229;229;229	Q99549;Q99549-2;B3KS10	MPP8_HUMAN;.;.	N	229	ENSP00000414663:K229N;ENSP00000355388:K229N	ENSP00000355388:K229N	K	+	3	2	MPHOSPH8	19118900	1.000000	0.71417	0.918000	0.36340	0.686000	0.39977	1.840000	0.39230	1.029000	0.39812	0.528000	0.53228	AAA	.	.		0.299	MPHOSPH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044028.2	NM_017520		T	20220900	A	T	20220900	3	4	344	1	0	0	0	0	1	0	0	0	9736	69	3	4	697	4	MPHOSPH8	13	20220900	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10		20220900	94948978	956	48319										
EFHA1	221154	hgsc.bcm.edu	37	chr13	22113457	22113457	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttacctttatcgccaaggtcTctgaaaaaagttgatccaca	6	10	1	2	rs371935367		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr13:22113457T>A	ENST00000382374.4	-	4	515	c.450A>T	c.(448-450)agA>agT	p.R150S		NM_152726.2	NP_689939.1	Q8IYU8	MICU2_HUMAN	mitochondrial calcium uptake 2	150					mitochondrial calcium ion transport (GO:0006851)|negative regulation of mitochondrial calcium ion concentration (GO:0051562)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)	calcium channel complex (GO:0034704)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|uniplex complex (GO:1990246)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)										CGCCAAGGTCTCTGAAAAAAG	0.313																																					p.R150S		Atlas-SNP	.											.	EFHA1	33	.	0			c.A450T						.						61	61	61					13																	22113457		2203	4300	6503	SO:0001583	missense	221154	exon4			AAGGTCTCTGAAA	AK091907	CCDS9297.1	13q12.11	2013-03-13	2013-03-13	2013-03-13	ENSG00000165487	ENSG00000165487		"EF-hand domain containing"	31830	protein-coding gene	gene with protein product		610632	"EF hand domain family A1", "EF-hand domain family, member A1"	EFHA1		23409044	Standard	NM_152726		Approved		uc001uof.3	Q8IYU8	OTTHUMG00000067414	ENST00000382374.4:c.450A>T	chr13.hg19:g.22113457T>A	ENSP00000371811:p.Arg150Ser	197.0	0.0		182.0	84.0	NM_152726	Q8N0T6|Q8NAX8	Missense_Mutation	SNP	ENST00000382374.4	hg19	CCDS9297.1	.	.	.	.	.	.	.	.	.	.	T	18.90	3.721802	0.68959	.	.	ENSG00000165487	ENST00000382374	T	0.39056	1.1	4.02	4.02	0.46733	.	0.000000	0.85682	D	0.000000	T	0.56963	0.2021	M	0.64260	1.97	0.58432	D	0.999997	D	0.76494	0.999	D	0.80764	0.994	T	0.54543	-0.8278	10	0.33141	T	0.24	-21.7224	10.7094	0.45973	0.0:0.0:0.0:1.0	.	150	Q8IYU8	EFHA1_HUMAN	S	150	ENSP00000371811:R150S	ENSP00000371811:R150S	R	-	3	2	EFHA1	21011457	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.451000	0.44952	1.819000	0.53055	0.402000	0.26972	AGA	.	.		0.313	MICU2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144355.1	NM_152726		A	22113457	T	A	22113457	3	1	344	1	0	0	0	0	1	0	0	0	4945	1548	54	4	890	4	EFHA1	13	22113457	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1892557	22113457	93056421	957	48320										
SGCG	6445	hgsc.bcm.edu	37	chr13	23898515	23898515	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tctcccaaccagcttgtgctTgatgctgaaactgtgtgctt	9	11	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr13:23898515T>A	ENST00000218867.3	+	8	835	c.711T>A	c.(709-711)ctT>ctA	p.L237L	SGCG_ENST00000545013.1_Silent_p.L237L|SGCG_ENST00000537476.1_Silent_p.L237L	NM_000231.2	NP_000222	Q13326	SGCG_HUMAN	sarcoglycan, gamma (35kDa dystrophin-associated glycoprotein)	237					muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		all_cancers(29;4.34e-23)|all_epithelial(30;4.4e-19)|all_lung(29;2.45e-18)|Lung SC(185;0.0228)|Breast(139;0.188)		all cancers(112;0.00255)|Epithelial(112;0.0129)|OV - Ovarian serous cystadenocarcinoma(117;0.0365)|Lung(94;0.205)		AGCTTGTGCTTGATGCTGAAA	0.522																																					p.L237L		Atlas-SNP	.											.	SGCG	64	.	0			c.T711A						.						94	77	82					13																	23898515		2203	4300	6503	SO:0001819	synonymous_variant	6445	exon8			TGTGCTTGATGCT	U34976	CCDS9299.1	13q12-q13	2014-09-17	2002-08-29		ENSG00000102683	ENSG00000102683			10809	protein-coding gene	gene with protein product	"Maghrebian myopathy (autosomal recessive)", "35kD dystrophin-associated glycoprotein", "limb girdle muscular dystrophy 2C (Duchenne-like muscular dystrophy, autosomal recessive)", "gamma sarcoglycan"	608896	"sarcoglycan, gamma (35kD dystrophin-associated glycoprotein)"	DMDA1, MAM, LGMD2C		8968757	Standard	NM_000231		Approved	SCARMD2, DAGA4, SCG3, DMDA, TYPE, A4, MGC130048	uc001uom.2	Q13326	OTTHUMG00000016563	ENST00000218867.3:c.711T>A	chr13.hg19:g.23898515T>A		48.0	0.0		38.0	17.0	NM_000231	Q32M32|Q5T9J6	Silent	SNP	ENST00000218867.3	hg19	CCDS9299.1																																																																																			.	.		0.522	SGCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044151.1	NM_000231		A	23898515	T	A	23898515	2	1	344	1	0	0	0	0	0	0	0	1	14218	1799	63	4		4	SGCG	13	23898515	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1785058	23898515	91271363	958	48321										
FLT3	2322	hgsc.bcm.edu	37	chr13	28601380	28601380	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaaatcaagtaaattggtccTgaaatagttacagtttcaat	6	5	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr13:28601380T>C	ENST00000241453.7	-	17	2135		c.e17-2		FLT3_ENST00000537084.1_Splice_Site|FLT3_ENST00000380982.4_Splice_Site	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3						B cell differentiation (GO:0030183)|cellular response to cytokine stimulus (GO:0071345)|common myeloid progenitor cell proliferation (GO:0035726)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell differentiation (GO:0097028)|hemopoiesis (GO:0030097)|leukocyte homeostasis (GO:0001776)|lymphocyte proliferation (GO:0046651)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|pro-B cell differentiation (GO:0002328)|pro-T cell differentiation (GO:0002572)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor signaling pathway (GO:0038084)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|cytokine receptor activity (GO:0004896)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(12329)|kidney(2)|large_intestine(8)|lung(30)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12390	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Ponatinib(DB08901)|Sorafenib(DB00398)|Sunitinib(DB01268)	AAATTGGTCCTGAAATAGTTA	0.348			"Mis, O"		"AML, ALL"																																.		Atlas-SNP	.		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	.	FLT3	15525	.	0			c.2054-2A>G						.						69	68	68					13																	28601380		2203	4300	6503	SO:0001630	splice_region_variant	2322	exon18			TGGTCCTGAAATA	U02687	CCDS31953.1	13q12	2014-09-17			ENSG00000122025	ENSG00000122025	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3765	protein-coding gene	gene with protein product		136351				8394751	Standard	NM_004119		Approved	STK1, FLK2, CD135	uc001urw.3	P36888	OTTHUMG00000016646	ENST00000241453.7:c.2054-2A>G	chr13.hg19:g.28601380T>C		67.0	0.0		52.0	29.0	NM_004119	A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	Splice_Site	SNP	ENST00000241453.7	hg19	CCDS31953.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.388144	0.82902	.	.	ENSG00000122025	ENST00000241453;ENST00000380982;ENST00000537084	.	.	.	6.03	6.03	0.97812	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5582	0.84512	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	FLT3	27499380	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	7.841000	0.86834	2.308000	0.77769	0.533000	0.62120	.	.	.		0.348	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044319.2		Intron	C	28601380	T	C	28601380	5	2	344	1	0	0	0	0	0	0	1	0	5950	1594	55	2	961	2	FLT3	13	28601380	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	4702865	28601380	86568498	959	48322										
FRY	10129	hgsc.bcm.edu	37	chr13	32812069	32812069	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acctgaccctgcagctcttcAgtctgctgacaccagtgtcc	8	16	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr13:32812069A>T	ENST00000380250.3	+	44	6860	c.6364A>T	c.(6364-6366)Agt>Tgt	p.S2122C		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	2122						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		GCAGCTCTTCAGTCTGCTGAC	0.552																																					p.S2122C		Atlas-SNP	.											.	FRY	312	.	0			c.A6364T						.						87	89	88					13																	32812069		2069	4224	6293	SO:0001583	missense	10129	exon44			CTCTTCAGTCTGC	AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"chromosome 13 open reading frame 14"	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.6364A>T	chr13.hg19:g.32812069A>T	ENSP00000369600:p.Ser2122Cys	88.0	0.0		55.0	27.0	NM_023037	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	hg19	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	A	15.58	2.876250	0.51801	.	.	ENSG00000073910	ENST00000380250;ENST00000380257	T	0.26810	1.71	5.96	5.96	0.96718	.	0.037974	0.85682	D	0.000000	T	0.20007	0.0481	N	0.16368	0.405	0.80722	D	1	B	0.17038	0.02	B	0.23150	0.044	T	0.03221	-1.1059	10	0.46703	T	0.11	.	16.4381	0.83884	1.0:0.0:0.0:0.0	.	2122	Q5TBA9	FRY_HUMAN	C	2122;959	ENSP00000369600:S2122C	ENSP00000369600:S2122C	S	+	1	0	FRY	31710069	1.000000	0.71417	0.998000	0.56505	0.954000	0.61252	5.788000	0.69020	2.280000	0.76307	0.533000	0.62120	AGT	.	.		0.552	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037		T	32812069	A	T	32812069	3	4	344	1	0	0	0	0	1	0	0	0	6071	188	7	4	6538	4	FRY	13	32812069	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	4210689	32812069	82357809	960	48323										
FRY	10129	hgsc.bcm.edu	37	chr13	32841436	32841436	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agccacatcaaccagcttatGtgtgactcagatggctcctg	9	12	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr13:32841436G>C	ENST00000380250.3	+	55	8572	c.8076G>C	c.(8074-8076)atG>atC	p.M2692I	FRY_ENST00000542859.1_Missense_Mutation_p.M62I	NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	2692						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		ACCAGCTTATGTGTGACTCAG	0.537																																					p.M2692I		Atlas-SNP	.											.	FRY	312	.	0			c.G8076C						.						124	130	128					13																	32841436		2077	4229	6306	SO:0001583	missense	10129	exon55			GCTTATGTGTGAC	AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"chromosome 13 open reading frame 14"	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.8076G>C	chr13.hg19:g.32841436G>C	ENSP00000369600:p.Met2692Ile	51.0	0.0		36.0	15.0	NM_023037	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	hg19	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	G	16.01	3.001495	0.54254	.	.	ENSG00000073910	ENST00000380250;ENST00000380235;ENST00000542859	T	0.21734	1.99	5.52	5.52	0.82312	.	0.042128	0.85682	D	0.000000	T	0.24236	0.0587	L	0.51422	1.61	0.58432	D	0.999999	B;B	0.09022	0.002;0.0	B;B	0.04013	0.001;0.0	T	0.02424	-1.1161	10	0.30854	T	0.27	.	19.4344	0.94785	0.0:0.0:1.0:0.0	.	473;2692	Q8NB82;Q5TBA9	.;FRY_HUMAN	I	2692;336;62	ENSP00000369600:M2692I	ENSP00000369567:M336I	M	+	3	0	FRY	31739436	1.000000	0.71417	1.000000	0.80357	0.715000	0.41141	5.231000	0.65327	2.600000	0.87896	0.650000	0.86243	ATG	.	.		0.537	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037		C	32841436	G	C	32841436	3	2	344	1	0	0	0	0	1	0	0	0	6071	1377	48	4	8294	4	FRY	13	32841436	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	29367	32841436	82328442	961	48324										
NBEA	26960	hgsc.bcm.edu	37	chr13	35731383	35731383	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggctggagagtctgggtggaTaccctctcaatagcccattc	12	11	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr13:35731383T>C	ENST00000400445.3	+	21	3354	c.2820T>C	c.(2818-2820)gaT>gaC	p.D940D	NBEA_ENST00000310336.4_Silent_p.D940D|NBEA_ENST00000540320.1_Silent_p.D940D|NBEA_ENST00000379939.2_Silent_p.D940D	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	940					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		TCTGGGTGGATACCCTCTCAA	0.408																																					p.D940D		Atlas-SNP	.											.	NBEA	340	.	0			c.T2820C						.						63	63	63					13																	35731383		1865	4108	5973	SO:0001819	synonymous_variant	26960	exon21			GGTGGATACCCTC	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.2820T>C	chr13.hg19:g.35731383T>C		58.0	0.0		61.0	19.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Silent	SNP	ENST00000400445.3	hg19	CCDS45026.1																																																																																			.	.		0.408	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		C	35731383	T	C	35731383	2	2	344	1	0	0	0	0	0	0	0	1	10196	1403	49	2		2	NBEA	13	35731383	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2889947	35731383	79438495	962	48325										
FREM2	341640	hgsc.bcm.edu	37	chr13	39262741	39262741	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtagtggatctagaaggagcAgcttcagacccttttgcctt	11	9	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr13:39262741A>T	ENST00000280481.7	+	1	1476	c.1260A>T	c.(1258-1260)gcA>gcT	p.A420A		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	420					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		TAGAAGGAGCAGCTTCAGACC	0.527																																					p.A420A		Atlas-SNP	.											.	FREM2	385	.	0			c.A1260T						.						75	84	81					13																	39262741		2203	4300	6503	SO:0001819	synonymous_variant	341640	exon1			AGGAGCAGCTTCA	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.1260A>T	chr13.hg19:g.39262741A>T		77.0	0.0		60.0	28.0	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	hg19	CCDS31960.1																																																																																			.	.		0.527	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		T	39262741	A	T	39262741	2	4	344	1	0	0	0	0	0	0	0	1	6053	175	7	4		4	FREM2	13	39262741	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3531358	39262741	75907137	963	48326										
FREM2	341640	hgsc.bcm.edu	37	chr13	39357294	39357294	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	catcaggaggagcggagatgTgagccaggagttgatggtgg	19	5	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr13:39357294T>A	ENST00000280481.7	+	5	5945	c.5729T>A	c.(5728-5730)gTg>gAg	p.V1910E		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1910	Calx-beta 2.				cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		AGCGGAGATGTGAGCCAGGAG	0.433																																					p.V1910E		Atlas-SNP	.											.	FREM2	385	.	0			c.T5729A						.						200	182	188					13																	39357294		2203	4300	6503	SO:0001583	missense	341640	exon5			GAGATGTGAGCCA	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.5729T>A	chr13.hg19:g.39357294T>A	ENSP00000280481:p.Val1910Glu	104.0	0.0		103.0	42.0	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	hg19	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	T	15.07	2.724867	0.48833	.	.	ENSG00000150893	ENST00000280481	T	0.32988	1.43	5.84	3.4	0.38934	Na-Ca exchanger/integrin-beta4 (2);	0.339678	0.30800	N	0.008842	T	0.35770	0.0943	M	0.67397	2.05	0.40479	D	0.980425	P	0.36909	0.573	B	0.41813	0.367	T	0.16424	-1.0403	10	0.62326	D	0.03	.	9.6982	0.40169	0.0:0.1455:0.0:0.8545	.	1910	Q5SZK8	FREM2_HUMAN	E	1910	ENSP00000280481:V1910E	ENSP00000280481:V1910E	V	+	2	0	FREM2	38255294	0.167000	0.22975	0.765000	0.31456	0.327000	0.28475	0.636000	0.24644	0.455000	0.26910	0.421000	0.28195	GTG	.	.		0.433	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		A	39357294	T	A	39357294	3	1	344	1	0	0	0	0	1	0	0	0	6053	1696	59	4	5747	4	FREM2	13	39357294	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	94553	39357294	75812584	964	48327										
LRCH1	23143	hgsc.bcm.edu	37	chr13	47302989	47302989	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atttccccaacagagcattgAgatgagattgaaggtcagtc	10	8	1	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr13:47302989A>G	ENST00000389798.3	+	17	1969	c.1772A>G	c.(1771-1773)gAg>gGg	p.E591G	LRCH1_ENST00000311191.6_Missense_Mutation_p.E591G|LRCH1_ENST00000389797.3_Missense_Mutation_p.E626G	NM_015116.2	NP_055931	Q9Y2L9	LRCH1_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 1	591	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.									breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)		CAGAGCATTGAGATGAGATTG	0.478																																					p.E626G		Atlas-SNP	.											.	LRCH1	104	.	0			c.A1877G						.						138	127	131					13																	47302989		2203	4300	6503	SO:0001583	missense	23143	exon18			GCATTGAGATGAG	AB023233	CCDS31972.1, CCDS53865.1, CCDS53866.1	13q14.11	2008-02-05	2004-05-27	2004-05-28	ENSG00000136141	ENSG00000136141			20309	protein-coding gene	gene with protein product		610368	"calponin homology (CH) domain containing 1"	CHDC1		10231032	Standard	NM_015116		Approved	KIAA1016	uc001vbk.3	Q9Y2L9	OTTHUMG00000016877	ENST00000389798.3:c.1772A>G	chr13.hg19:g.47302989A>G	ENSP00000374448:p.Glu591Gly	81.0	0.0		58.0	23.0	NM_001164211	B7ZLL5|F8W6F0|Q17R43|Q2KHR1|Q5TBU9|Q7Z5F6|Q7Z5F7	Missense_Mutation	SNP	ENST00000389798.3	hg19	CCDS31972.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.726427	0.89298	.	.	ENSG00000136141	ENST00000311191;ENST00000389798;ENST00000389797	T;T;T	0.70631	-0.33;-0.5;-0.42	5.81	5.81	0.92471	Calponin homology domain (5);	0.000000	0.85682	D	0.000000	D	0.86590	0.5969	M	0.90705	3.14	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.89215	0.3567	10	0.87932	D	0	-0.9429	14.1039	0.65075	1.0:0.0:0.0:0.0	.	591;626;591	Q9Y2L9-2;F8W6F0;Q9Y2L9	.;.;LRCH1_HUMAN	G	591;591;626	ENSP00000308493:E591G;ENSP00000374448:E591G;ENSP00000374447:E626G	ENSP00000308493:E591G	E	+	2	0	LRCH1	46200990	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.556000	0.90697	2.216000	0.71823	0.533000	0.62120	GAG	.	.		0.478	LRCH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044824.2	NM_015116		G	47302989	A	G	47302989	3	3	344	1	0	0	0	0	1	0	0	0	8941	304	11	2	1947	2	LRCH1	13	47302989	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	7945695	47302989	67866889	965	48328										
RB1	5925	hgsc.bcm.edu	37	chr13	48953748	48953748	+	Frame_Shift_Del	DEL	C	C	-													0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agcgatacaaacttggagttCgcttgtattaccgagtaatg							TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr13:48953748delC	ENST00000267163.4	+	14	1489	c.1351delC	c.(1351-1353)cgcfs	p.R451fs		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	451	Domain A.|Pocket; binds T and E1A.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(8)|p.R451C(3)		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(DB00071)|Insulin Regular(DB00030)"	ACTTGGAGTTCGCTTGTATTA	0.343		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)																											p.V450fs		Atlas-Indel,Pindel	.	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	.	RB1	1068	.	26	Whole gene deletion(15)|Unknown(8)|Substitution - Missense(3)	bone(11)|breast(5)|central_nervous_system(2)|lung(2)|adrenal_gland(1)|large_intestine(1)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	c.1350delT						.						21	22	22					13																	48953748		2201	4300	6501	SO:0001589	frameshift_variant	5925	exon14	Familial Cancer Database		.	M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1351delC	chr13.hg19:g.48953748delC	ENSP00000267163:p.Arg451fs	276.0	0.0		211.0	191.0	NM_000321	A8K5E3|P78499|Q5VW46|Q8IZL4	Frame_Shift_Del	DEL	ENST00000267163.4	hg19	CCDS31973.1																																																																																			.	.		0.343	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			-	48953748	C	-	48953748	7	5	344	1	0	1	0	1	0	0	0	0	13113	884	31	0	1405	0	RB1	13	48953748	Frame_Shift_Del	DEL	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1650759	48953748	66216130	966	48329										
RB1	5925	hgsc.bcm.edu	37	chr13	49030437	49030437	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aagcaacctcagccttccagAcccagaagccattgaaatct	6	14	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr13:49030437A>T	ENST00000267163.4	+	19	2050	c.1912A>T	c.(1912-1914)Acc>Tcc	p.T638S		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	638	Pocket; binds T and E1A.|Spacer.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(10)		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(DB00071)|Insulin Regular(DB00030)"	AGCCTTCCAGACCCAGAAGCC	0.398		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)																											p.T638S		Atlas-SNP	.	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	.	RB1	1068	.	25	Whole gene deletion(15)|Unknown(10)	bone(10)|haematopoietic_and_lymphoid_tissue(4)|breast(4)|adrenal_gland(1)|eye(1)|soft_tissue(1)|endometrium(1)|urinary_tract(1)|lung(1)|liver(1)	c.A1912T						.						80	76	77					13																	49030437		2203	4300	6503	SO:0001583	missense	5925	exon19	Familial Cancer Database		TTCCAGACCCAGA	M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1912A>T	chr13.hg19:g.49030437A>T	ENSP00000267163:p.Thr638Ser	279.0	0.0		275.0	116.0	NM_000321	A8K5E3|P78499|Q5VW46|Q8IZL4	Missense_Mutation	SNP	ENST00000267163.4	hg19	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	A	14.69	2.610765	0.46527	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	D	0.91843	-2.92	5.97	5.97	0.96955	Cyclin-like (1);	0.228456	0.45606	D	0.000358	D	0.87924	0.6300	L	0.60455	1.87	0.37381	D	0.912036	B	0.16166	0.016	B	0.10450	0.005	T	0.82257	-0.0547	10	0.13470	T	0.59	.	8.1931	0.31381	0.729:0.1385:0.0:0.1325	.	638	P06400	RB_HUMAN	S	617;638	ENSP00000267163:T638S	ENSP00000267163:T638S	T	+	1	0	RB1	47928438	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.419000	0.34793	2.275000	0.75901	0.533000	0.62120	ACC	.	.		0.398	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			T	49030437	A	T	49030437	3	4	344	1	0	0	0	0	1	0	0	0	13113	275	10	4	1986	4	RB1	13	49030437	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	76689	49030437	66139441	967	48330										
FNDC3A	22862	hgsc.bcm.edu	37	chr13	49781371	49781371	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cacagtgctcttcatctctcAgaggactgaaccaccagcca	7	15	4	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr13:49781371A>T	ENST00000492622.2	+	26	3742	c.3437A>T	c.(3436-3438)cAg>cTg	p.Q1146L	FNDC3A_ENST00000541916.1_Missense_Mutation_p.Q1146L|FNDC3A_ENST00000398316.3_Missense_Mutation_p.Q1090L	NM_001079673.1	NP_001073141.1	Q9Y2H6	FND3A_HUMAN	fibronectin type III domain containing 3A	1146	Fibronectin type-III 9. {ECO:0000255|PROSITE-ProRule:PRU00316}.				fertilization (GO:0009566)|Sertoli cell development (GO:0060009)|single organismal cell-cell adhesion (GO:0016337)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|prostate(5)|skin(2)|urinary_tract(1)	41		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)		TTCATCTCTCAGAGGACTGAA	0.567																																					p.Q1146L		Atlas-SNP	.											.	FNDC3A	93	.	0			c.A3437T						.						114	94	101					13																	49781371		2203	4300	6503	SO:0001583	missense	22862	exon26			TCTCTCAGAGGAC	AB023187	CCDS9413.2, CCDS41886.1	13q14.12	2013-02-11	2005-01-20	2005-01-22	ENSG00000102531	ENSG00000102531		"Fibronectin type III domain containing"	20296	protein-coding gene	gene with protein product		615794	"fibronectin type III domain containing 3"	FNDC3			Standard	NM_001079673		Approved	bA203I16.5, KIAA0970	uc001vcm.3	Q9Y2H6	OTTHUMG00000016911	ENST00000492622.2:c.3437A>T	chr13.hg19:g.49781371A>T	ENSP00000417257:p.Gln1146Leu	158.0	0.0		136.0	126.0	NM_001079673	B4DYG1|Q5HYC9|Q5JVF8|Q5JVF9|Q6EVH3|Q6EVH4|Q6N020|Q6P9D5|Q6ZME4|Q9H1W1	Missense_Mutation	SNP	ENST00000492622.2	hg19	CCDS41886.1	.	.	.	.	.	.	.	.	.	.	A	15.94	2.982190	0.53827	.	.	ENSG00000102531	ENST00000492622;ENST00000337156;ENST00000541916;ENST00000398316	T;T;T	0.37058	1.22;1.22;1.23	5.38	5.38	0.77491	.	0.100347	0.43579	D	0.000558	T	0.37320	0.0999	L	0.56769	1.78	0.50039	D	0.999841	B;B	0.33512	0.336;0.415	B;B	0.38500	0.275;0.25	T	0.13045	-1.0524	10	0.10111	T	0.7	-4.3017	14.5761	0.68249	1.0:0.0:0.0:0.0	.	1090;1146	Q9Y2H6-2;Q9Y2H6	.;FND3A_HUMAN	L	1146;1082;1146;1090	ENSP00000417257:Q1146L;ENSP00000441831:Q1146L;ENSP00000381362:Q1090L	ENSP00000338579:Q1082L	Q	+	2	0	FNDC3A	48679372	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.351000	0.66022	2.035000	0.60131	0.528000	0.53228	CAG	.	.		0.567	FNDC3A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354845.2	NM_014923		T	49781371	A	T	49781371	3	4	344	1	0	0	0	0	1	0	0	0	5977	188	7	4	3546	4	FNDC3A	13	49781371	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	750934	49781371	65388507	968	48331										
SUGT1	10910	hgsc.bcm.edu	37	chr13	53227239	53227239	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acccccaggcggcgttagagGtgagagagcccatttctgct	13	12	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr13:53227239G>A	ENST00000343788.6	+	2	178		c.e2+1		SUGT1_ENST00000535397.1_Splice_Site|SUGT1_ENST00000483074.1_Splice_Site|SUGT1_ENST00000310528.8_Splice_Site	NM_001130912.1	NP_001124384.1	Q9Y2Z0	SUGT1_HUMAN	SGT1, suppressor of G2 allele of SKP1 (S. cerevisiae)						innate immune response (GO:0045087)|mitotic nuclear division (GO:0007067)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				kidney(3)|large_intestine(3)|lung(2)	8		Lung NSC(96;0.00212)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.25e-08)		GGCGTTAGAGGTGAGAGAGCC	0.612											OREG0022432	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.		Atlas-SNP	.											.	SUGT1	37	.	0			c.96+1G>A						.						98	106	104					13																	53227239		2203	4300	6503	SO:0001630	splice_region_variant	10910	exon2			TTAGAGGTGAGAG	AF068289	CCDS9436.1, CCDS45050.1	13q14.3	2014-03-20			ENSG00000165416	ENSG00000165416			16987	protein-coding gene	gene with protein product		604098				10445024	Standard	NM_006704		Approved	SGT1	uc001vhc.2	Q9Y2Z0	OTTHUMG00000016977	ENST00000343788.6:c.96+1G>A	chr13.hg19:g.53227239G>A		84.0	0.0	991	69.0	23.0	NM_001130912	A2A303|Q5JAK5|Q5TAM6|Q6VXY6	Splice_Site	SNP	ENST00000343788.6	hg19	CCDS45050.1	.	.	.	.	.	.	.	.	.	.	G	17.49	3.402523	0.62288	.	.	ENSG00000165416	ENST00000343788;ENST00000310528	.	.	.	3.16	3.16	0.36331	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.0597	0.42266	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SUGT1	52125240	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.436000	0.59948	2.052000	0.61016	0.467000	0.42956	.	.	.		0.612	SUGT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045104.2		Intron	A	53227239	G	A	53227239	5	1	344	1	0	0	0	0	0	0	1	0	15384	1275	44	3	103	3	SUGT1	13	53227239	Splice_Site	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	3445868	53227239	61942639	969	48332										
DIAPH3	81624	hgsc.bcm.edu	37	chr13	60490362	60490362	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgatttcctcatatggcaccCgaaaagagctcaggaagatt	9	9	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr13:60490362C>G	ENST00000400324.4	-	19	2412	c.2192G>C	c.(2191-2193)cGg>cCg	p.R731P	DIAPH3_ENST00000400330.1_Missense_Mutation_p.R731P|DIAPH3_ENST00000465066.1_5'UTR|DIAPH3_ENST00000400320.1_Missense_Mutation_p.R685P|DIAPH3_ENST00000377908.2_Missense_Mutation_p.R720P|DIAPH3_ENST00000400319.1_Missense_Mutation_p.R661P|DIAPH3_ENST00000267215.4_Missense_Mutation_p.R731P	NM_001042517.1|NM_001258366.1	NP_001035982.1|NP_001245295.1	Q9NSV4	DIAP3_HUMAN	diaphanous-related formin 3	731	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|liver(1)|lung(20)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		ATATGGCACCCGAAAAGAGCT	0.338																																					p.R731P		Atlas-SNP	.											.	DIAPH3	139	.	0			c.G2192C						.						116	102	106					13																	60490362		1822	4086	5908	SO:0001583	missense	81624	exon19			GGCACCCGAAAAG	AL137718	CCDS41898.1, CCDS58294.1, CCDS58295.1, CCDS58296.1, CCDS58297.1, CCDS73579.1, CCDS73580.1	13q21.2	2013-05-24	2013-05-24		ENSG00000139734	ENSG00000139734			15480	protein-coding gene	gene with protein product		614567	"diaphanous (Drosophila, homolog) 3", "auditory neuropathy, autosomal dominant 1", "diaphanous homolog 3 (Drosophila)"	AUNA1		14767582, 20624953	Standard	NM_030932		Approved	DRF3, FLJ34705, AN, NSDAN	uc001vht.4	Q9NSV4	OTTHUMG00000017004	ENST00000400324.4:c.2192G>C	chr13.hg19:g.60490362C>G	ENSP00000383178:p.Arg731Pro	81.0	0.0		66.0	32.0	NM_001042517	A2A3B8|A2A3B9|A2A3C0|Q18P99|Q18PA0|Q18PA1|Q2KPB6|Q3ZK23|Q5JTP8|Q5T2S7|Q5XKF6|Q6MZF0|Q6NUP0|Q86VS4|Q8NAV4	Missense_Mutation	SNP	ENST00000400324.4	hg19	CCDS41898.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.736571	0.89482	.	.	ENSG00000139734	ENST00000400324;ENST00000400330;ENST00000400327;ENST00000413168;ENST00000400329;ENST00000377908;ENST00000400319;ENST00000400320;ENST00000267215;ENST00000267214;ENST00000453990	T;T;T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06;-0.06;1.04	5.87	5.87	0.94306	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.000000	0.85682	D	0.000000	D	0.84092	0.5396	M	0.89715	3.055	0.52099	D	0.999942	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.91635	0.97;0.996;0.999	D	0.86408	0.1746	10	0.87932	D	0	.	19.8113	0.96547	0.0:1.0:0.0:0.0	.	468;468;731	Q9NSV4-2;Q9NSV4-1;Q9NSV4	.;.;DIAP3_HUMAN	P	731;731;720;685;661;720;661;685;731;468;731	ENSP00000383178:R731P;ENSP00000383184:R731P;ENSP00000367141:R720P;ENSP00000383173:R661P;ENSP00000383174:R685P;ENSP00000267215:R731P	ENSP00000267214:R468P	R	-	2	0	DIAPH3	59388363	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.755000	0.68750	2.767000	0.95098	0.591000	0.81541	CGG	.	.		0.338	DIAPH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045166.3	NM_001042517		G	60490362	C	G	60490362	3	3	344	1	0	0	0	0	1	0	0	0	4522	652	23	4	1449	4	DIAPH3	13	60490362	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	7263123	60490362	54679516	970	48333										
KLHL1	57626	hgsc.bcm.edu	37	chr13	70535471	70535471	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aattggacaaggtcccagagAgcattggggtctatgccttc	12	9	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr13:70535471A>G	ENST00000377844.4	-	3	1545	c.786T>C	c.(784-786)gcT>gcC	p.A262A	KLHL1_ENST00000545028.1_Silent_p.A69A	NM_020866.2	NP_065917.1	Q9NR64	KLHL1_HUMAN	kelch-like family member 1	262	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				actin cytoskeleton organization (GO:0030036)|adult walking behavior (GO:0007628)|cerebellar Purkinje cell layer development (GO:0021680)|dendrite development (GO:0016358)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	actin binding (GO:0003779)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(56)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	84		Breast(118;0.000162)		COAD - Colon adenocarcinoma(199;0.000193)|GBM - Glioblastoma multiforme(99;0.000211)		GGTCCCAGAGAGCATTGGGGT	0.388																																					p.A262A		Atlas-SNP	.											.	KLHL1	164	.	0			c.T786C						.						158	139	145					13																	70535471		2203	4300	6503	SO:0001819	synonymous_variant	57626	exon3			CCAGAGAGCATTG	AB040923	CCDS9445.1, CCDS73582.1	13q21	2013-01-30	2013-01-30		ENSG00000150361	ENSG00000150361		"Kelch-like", "BTB/POZ domain containing"	6352	protein-coding gene	gene with protein product	"Kelch-like protein 1", "Mayven-related protein 2"	605332	"kelch (Drosophila)-like 1", "kelch-like 1 (Drosophila)"			10888605	Standard	NM_020866		Approved	KIAA1490, MRP2, FLJ30047	uc001vip.3	Q9NR64	OTTHUMG00000017056	ENST00000377844.4:c.786T>C	chr13.hg19:g.70535471A>G		92.0	0.0		77.0	29.0	NM_020866	A8K5X0|Q5VZ64|Q9H4X4|Q9NR65|Q9P238	Silent	SNP	ENST00000377844.4	hg19	CCDS9445.1																																																																																			.	.		0.388	KLHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045231.3	NM_020866		G	70535471	A	G	70535471	2	3	344	1	0	0	0	0	0	0	0	1	8374	291	11	2		2	KLHL1	13	70535471	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	10045109	70535471	44634407	971	48334										
MYCBP2	23077	hgsc.bcm.edu	37	chr13	77844588	77844588	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttaaagctgctttcttaatgCcattactaaaccagtcctga	5	10	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr13:77844588C>T	ENST00000544440.2	-	6	934	c.917G>A	c.(916-918)gGc>gAc	p.G306D	MYCBP2_ENST00000357337.6_Missense_Mutation_p.G306D|MYCBP2_ENST00000407578.2_Missense_Mutation_p.G344D|MYCBP2_ENST00000360084.5_5'UTR					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		TTTCTTAATGCCATTACTAAA	0.343																																					p.G344D		Atlas-SNP	.											.	MYCBP2	1029	.	0			c.G1031A						.						88	87	87					13																	77844588		2203	4299	6502	SO:0001583	missense	23077	exon6			TTAATGCCATTAC	AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"MYC binding protein 2"			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.917G>A	chr13.hg19:g.77844588C>T	ENSP00000444596:p.Gly306Asp	155.0	0.0		148.0	62.0	NM_015057		Missense_Mutation	SNP	ENST00000544440.2	hg19		.	.	.	.	.	.	.	.	.	.	C	31	5.104462	0.94245	.	.	ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440	T;T;T	0.32272	1.47;1.46;1.47	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.56572	0.1994	M	0.69358	2.11	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.58418	-0.7640	10	0.87932	D	0	.	19.0683	0.93122	0.0:1.0:0.0:0.0	.	306	O75592	MYCB2_HUMAN	D	306;344;306	ENSP00000349892:G306D;ENSP00000384288:G344D;ENSP00000444596:G306D	ENSP00000349892:G306D	G	-	2	0	MYCBP2	76742589	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.794000	0.85869	2.588000	0.87417	0.563000	0.77884	GGC	.	.		0.343	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057		T	77844588	C	T	77844588	3	4	344	1	0	0	0	0	1	0	0	0	10027	739	26	3	13317	3	MYCBP2	13	77844588	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	7309117	77844588	37325290	972	48335										
SLITRK5	26050	hgsc.bcm.edu	37	chr13	88330290	88330290	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aatatcccaaattcccgtgcAgccccgctgcttacactttc	5	16	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr13:88330290A>C	ENST00000325089.6	+	2	2866	c.2647A>C	c.(2647-2649)Agc>Cgc	p.S883R	SLITRK5_ENST00000400028.3_Missense_Mutation_p.S642R	NM_015567.1	NP_056382.1	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5	883					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|cardiovascular system development (GO:0072358)|dendrite morphogenesis (GO:0048813)|grooming behavior (GO:0007625)|response to xenobiotic stimulus (GO:0009410)|skin development (GO:0043588)|striatum development (GO:0021756)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(14)|lung(40)|ovary(2)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(4)	81	all_neural(89;0.101)|Medulloblastoma(90;0.163)					ATTCCCGTGCAGCCCCGCTGC	0.602																																					p.S883R		Atlas-SNP	.											.	SLITRK5	192	.	0			c.A2647C						.						52	55	54					13																	88330290		2203	4300	6503	SO:0001583	missense	26050	exon2			CCGTGCAGCCCCG	AB020725	CCDS9465.1	13q31.1	2004-04-16	2004-01-08		ENSG00000165300	ENSG00000165300			20295	protein-coding gene	gene with protein product		609680	"leucine rich repeat containing 11"	LRRC11		10048485, 14557068	Standard	NM_015567		Approved	bA364G4.2, KIAA0918	uc001vln.3	O94991	OTTHUMG00000017167	ENST00000325089.6:c.2647A>C	chr13.hg19:g.88330290A>C	ENSP00000366283:p.Ser883Arg	139.0	0.0		132.0	58.0	NM_015567	B3KNB8|B4DSH5|Q5VT81	Missense_Mutation	SNP	ENST00000325089.6	hg19	CCDS9465.1	.	.	.	.	.	.	.	.	.	.	A	11.97	1.796210	0.31777	.	.	ENSG00000165300	ENST00000325089;ENST00000400028	T;T	0.58797	0.31;0.66	5.57	4.41	0.53225	.	0.301301	0.36444	N	0.002592	T	0.31104	0.0786	N	0.08118	0	0.36300	D	0.856976	B;B	0.33413	0.411;0.068	B;B	0.28849	0.095;0.026	T	0.36383	-0.9750	9	.	.	.	-20.0065	9.0073	0.36120	0.9139:0.0:0.0861:0.0	.	642;883	B4DSH5;O94991	.;SLIK5_HUMAN	R	883;642	ENSP00000366283:S883R;ENSP00000442244:S642R	.	S	+	1	0	SLITRK5	87128291	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.330000	0.52068	2.117000	0.64856	0.459000	0.35465	AGC	.	.		0.602	SLITRK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045416.3			C	88330290	A	C	88330290	3	2	344	1	0	0	0	0	1	0	0	0	14761	188	7	5	2649	5	SLITRK5	13	88330290	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	10485702	88330290	26839588	973	48336										
ITGBL1	9358	hgsc.bcm.edu	37	chr13	102250520	102250520	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaggtcatggacagtgtaatTgcggaagatgtgactgcaaa	13	5	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr13:102250520T>G	ENST00000376180.3	+	7	1105	c.886T>G	c.(886-888)Tgc>Ggc	p.C296G	ITGBL1_ENST00000376162.3_Missense_Mutation_p.C203G|ITGBL1_ENST00000545560.2_Missense_Mutation_p.C155G	NM_001271756.1|NM_004791.1	NP_001258685.1|NP_004782.1	O95965	ITGBL_HUMAN	integrin, beta-like 1 (with EGF-like repeat domains)	296	Cysteine-rich tandem repeats.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)				breast(1)|large_intestine(6)|lung(16)|ovary(1)|prostate(4)|skin(3)	31	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					ACAGTGTAATTGCGGAAGATG	0.448																																					p.C296G		Atlas-SNP	.											.	ITGBL1	83	.	0			c.T886G						.						147	126	133					13																	102250520		2203	4300	6503	SO:0001583	missense	9358	exon7			TGTAATTGCGGAA	AF072752	CCDS9499.1, CCDS61361.1, CCDS61362.1, CCDS73594.1	13q33	2008-07-18			ENSG00000198542	ENSG00000198542			6164	protein-coding gene	gene with protein product	"ten integrin EGF-like repeat domains protein", "ITGBL1, integrin beta-like 1"	604234				10051402	Standard	NM_004791		Approved	TIED, OSCP	uc001vpb.4	O95965	OTTHUMG00000017296	ENST00000376180.3:c.886T>G	chr13.hg19:g.102250520T>G	ENSP00000365351:p.Cys296Gly	65.0	0.0		56.0	50.0	NM_004791	A8K5M5|B3KTP1|B4DQ02|Q8N172|Q9NPR0	Missense_Mutation	SNP	ENST00000376180.3	hg19	CCDS9499.1	.	.	.	.	.	.	.	.	.	.	T	18.17	3.564972	0.65651	.	.	ENSG00000198542	ENST00000376180;ENST00000537118;ENST00000539955;ENST00000545560;ENST00000376162	D;D;D	0.96459	-4.02;-4.02;-4.02	5.42	5.42	0.78866	EGF, extracellular (1);Epidermal growth factor-like (1);	0.000000	0.85682	D	0.000000	D	0.98134	0.9384	M	0.88377	2.95	0.80722	D	1	P;D	0.89917	0.947;1.0	D;D	0.97110	0.953;1.0	D	0.98505	1.0616	10	0.22706	T	0.39	.	15.4567	0.75321	0.0:0.0:0.0:1.0	.	155;296	B3KTP1;O95965	.;ITGBL_HUMAN	G	296;204;155;155;203	ENSP00000365351:C296G;ENSP00000439903:C155G;ENSP00000365332:C203G	ENSP00000365332:C203G	C	+	1	0	ITGBL1	101048521	1.000000	0.71417	1.000000	0.80357	0.664000	0.39144	7.603000	0.82811	2.045000	0.60652	0.533000	0.62120	TGC	.	.		0.448	ITGBL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045669.2	NM_004791		G	102250520	T	G	102250520	3	3	344	1	0	0	0	0	1	0	0	0	7911	1812	63	5	912	5	ITGBL1	13	102250520	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	13920230	102250520	12919358	974	48337										
C13orf39	196541	hgsc.bcm.edu	37	chr13	103343193	103343193	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	accaccgctccgtaactctcTatggattcctggatgacaat	7	13	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr13:103343193T>C	ENST00000267273.6	-	2	257	c.252A>G	c.(250-252)atA>atG	p.I84M		NM_001010977.1	NP_001010977.1	Q5VZV1	MT21C_HUMAN	methyltransferase like 21C	84					peptidyl-lysine methylation (GO:0018022)|protein methylation (GO:0006479)	nucleus (GO:0005634)	protein-lysine N-methyltransferase activity (GO:0016279)			breast(1)|large_intestine(3)|lung(2)|skin(1)	7						CGTAACTCTCTATGGATTCCT	0.463																																					p.I84M		Atlas-SNP	.											.	METTL21C	23	.	0			c.A252G						.						153	129	137					13																	103343193		2203	4300	6503	SO:0001583	missense	196541	exon2			ACTCTCTATGGAT		CCDS32003.1	13q33.1	2011-03-03	2011-03-03	2011-03-03	ENSG00000139780	ENSG00000139780			33717	protein-coding gene	gene with protein product		615259	"chromosome 13 open reading frame 39"	C13orf39			Standard	NM_001010977		Approved	LOC196541	uc001vpj.4	Q5VZV1	OTTHUMG00000017304	ENST00000267273.6:c.252A>G	chr13.hg19:g.103343193T>C	ENSP00000267273:p.Ile84Met	105.0	0.0		125.0	114.0	NM_001010977		Missense_Mutation	SNP	ENST00000267273.6	hg19	CCDS32003.1	.	.	.	.	.	.	.	.	.	.	T	15.73	2.918856	0.52546	.	.	ENSG00000139780	ENST00000267273	T	0.06449	3.3	6.16	-0.812	0.10853	.	0.176177	0.64402	D	0.000008	T	0.10078	0.0247	L	0.42632	1.34	0.39491	D	0.968057	D	0.64830	0.994	D	0.64410	0.925	T	0.36138	-0.9760	10	0.33141	T	0.24	-4.7417	3.0091	0.06038	0.2296:0.0654:0.3645:0.3405	.	84	Q5VZV1	MT21C_HUMAN	M	84	ENSP00000267273:I84M	ENSP00000267273:I84M	I	-	3	3	METTL21C	102141194	0.993000	0.37304	0.790000	0.31976	0.947000	0.59692	0.185000	0.16958	-0.318000	0.08665	0.528000	0.53228	ATA	.	.		0.463	METTL21C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045682.2	NM_001010977		C	103343193	T	C	103343193	3	2	344	1	0	0	0	0	1	0	0	0	1734	1512	53	2	554	2	C13orf39	13	103343193	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1092673	103343193	11826685	975	48338										
GRK1	6011	hgsc.bcm.edu	37	chr13	114324036	114324036	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaagaagattctgatgaaagTacacagcaggttcatcgtgt	11	6	2	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr13:114324036T>A	ENST00000335678.6	+	2	966	c.734T>A	c.(733-735)gTa>gAa	p.V245E		NM_002929.2	NP_002920.1	Q15835	RK_HUMAN	G protein-coupled receptor kinase 1	245	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of apoptotic process (GO:0043066)|photoreceptor cell morphogenesis (GO:0008594)|phototransduction, visible light (GO:0007603)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)|protein autophosphorylation (GO:0046777)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|protein kinase activity (GO:0004672)|rhodopsin kinase activity (GO:0050254)			ovary(2)	2	Lung NSC(43;0.0113)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.00696)|all_epithelial(44;0.00347)|all_lung(25;0.0221)|Breast(118;0.0411)|Lung NSC(25;0.0839)	all cancers(43;0.234)			CTGATGAAAGTACACAGCAGG	0.498																																					p.V245E		Atlas-SNP	.											.	GRK1	41	.	0			c.T734A						.						234	241	239					13																	114324036		2109	4227	6336	SO:0001583	missense	6011	exon2			TGAAAGTACACAG			13q34	2013-09-02	2004-03-23	2004-03-24	ENSG00000185974	ENSG00000185974	2.7.11.14		10013	protein-coding gene	gene with protein product		180381	"rhodopsin kinase"	RHOK		8812493, 15057823	Standard	NM_002929		Approved	GPRK1, RK	uc010tkf.2	Q15835	OTTHUMG00000185528	ENST00000335678.6:c.734T>A	chr13.hg19:g.114324036T>A	ENSP00000334876:p.Val245Glu	58.0	0.0		55.0	32.0	NM_002929	Q53X14	Missense_Mutation	SNP	ENST00000335678.6	hg19		.	.	.	.	.	.	.	.	.	.	t	14.51	2.558287	0.45590	.	.	ENSG00000185974	ENST00000335678	T	0.26518	1.73	4.36	4.36	0.52297	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.127206	0.52532	D	0.000074	T	0.50274	0.1606	.	.	.	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.55554	-0.8123	9	0.87932	D	0	-18.6425	11.8052	0.52150	0.0:0.0:0.0:1.0	.	245	Q15835	RK_HUMAN	E	245	ENSP00000334876:V245E	ENSP00000334876:V245E	V	+	2	0	GRK1	113372037	1.000000	0.71417	0.089000	0.20774	0.038000	0.13279	7.081000	0.76844	1.731000	0.51592	0.418000	0.28097	GTA	.	.		0.498	GRK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470655.1	NM_002929		A	114324036	T	A	114324036	3	1	344	1	0	0	0	0	1	0	0	0	6799	1638	57	4	740	4	GRK1	13	114324036	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	10980843	114324036	845842	976	48339										
OR4K2	390431	hgsc.bcm.edu	37	chr14	20344887	20344887	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttcctggattatgggagttaTgcattcaatgagtcaggtca	11	6	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:20344887T>C	ENST00000298642.2	+	1	497	c.461T>C	c.(460-462)aTg>aCg	p.M154T		NM_001005501.1	NP_001005501.1	Q8NGD2	OR4K2_HUMAN	olfactory receptor, family 4, subfamily K, member 2	154						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(16)|ovary(2)|skin(9)|upper_aerodigestive_tract(2)	43	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		ATGGGAGTTATGCATTCAATG	0.473																																					p.M154T		Atlas-SNP	.											.	OR4K2	97	.	0			c.T461C						.						353	344	347					14																	20344887		2203	4300	6503	SO:0001583	missense	390431	exon1			GAGTTATGCATTC		CCDS32023.1	14q11.2	2013-09-23			ENSG00000165762	ENSG00000165762		"GPCR / Class A : Olfactory receptors"	14728	protein-coding gene	gene with protein product							Standard	NM_001005501		Approved		uc001vwh.1	Q8NGD2	OTTHUMG00000170624	ENST00000298642.2:c.461T>C	chr14.hg19:g.20344887T>C	ENSP00000298642:p.Met154Thr	110.0	0.0		116.0	22.0	NM_001005501	B2RNK8|Q6IFA5	Missense_Mutation	SNP	ENST00000298642.2	hg19	CCDS32023.1	.	.	.	.	.	.	.	.	.	.	.	6.485	0.457625	0.12342	.	.	ENSG00000165762	ENST00000298642	T	0.36520	1.25	5.12	3.95	0.45737	GPCR, rhodopsin-like superfamily (1);	0.099316	0.44483	D	0.000441	T	0.19087	0.0458	N	0.05383	-0.06	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.16100	-1.0414	10	0.49607	T	0.09	.	9.2432	0.37509	0.0:0.0871:0.0:0.9129	.	154	Q8NGD2	OR4K2_HUMAN	T	154	ENSP00000298642:M154T	ENSP00000298642:M154T	M	+	2	0	OR4K2	19414727	0.369000	0.25039	0.999000	0.59377	0.697000	0.40408	2.999000	0.49473	0.934000	0.37316	0.460000	0.39030	ATG	.	.		0.473	OR4K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409864.1			C	20344887	T	C	20344887	3	2	344	1	0	0	0	0	1	0	0	0	11081	1464	51	2	463	2	OR4K2	14	20344887	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10		20344887	87004653	977	48340										
OR4K15	81127	hgsc.bcm.edu	37	chr14	20444394	20444394	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agttcctttctcctcttggtTgtctcctacactgtaatact	5	12	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:20444394T>C	ENST00000305051.5	+	1	792	c.717T>C	c.(715-717)gtT>gtC	p.V239V		NM_001005486.1	NP_001005486.1	Q8NH41	OR4KF_HUMAN	olfactory receptor, family 4, subfamily K, member 15	239						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|ovary(1)|prostate(2)|skin(1)|stomach(1)	39	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;3.58e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TCCTCTTGGTTGTCTCCTACA	0.458																																					p.V239V		Atlas-SNP	.											.	OR4K15	82	.	0			c.T717C						.						111	108	109					14																	20444394		2203	4298	6501	SO:0001819	synonymous_variant	81127	exon1			CTTGGTTGTCTCC		CCDS32026.1	14q11.2	2013-09-23			ENSG00000169488	ENSG00000169488		"GPCR / Class A : Olfactory receptors"	15353	protein-coding gene	gene with protein product							Standard	NM_001005486		Approved	OR4K15Q	uc010tkx.2	Q8NH41	OTTHUMG00000170635	ENST00000305051.5:c.717T>C	chr14.hg19:g.20444394T>C		68.0	0.0		86.0	52.0	NM_001005486	B9EIL3|Q6IEZ4	Silent	SNP	ENST00000305051.5	hg19	CCDS32026.1																																																																																			.	.		0.458	OR4K15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409883.1			C	20444394	T	C	20444394	2	2	344	1	0	0	0	0	0	0	0	1	11079	1799	63	2		2	OR4K15	14	20444394	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	99507	20444394	86905146	978	48341										
OR11G2	390439	hgsc.bcm.edu	37	chr14	20666491	20666491	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgatatatagtcttaggaacAaagatatgagaaaagctctg	9	4	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:20666491A>T	ENST00000357366.3	+	1	997	c.997A>T	c.(997-999)Aaa>Taa	p.K333*		NM_001005503.1	NP_001005503.1	Q8NGC1	O11G2_HUMAN	olfactory receptor, family 11, subfamily G, member 2	333						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	22	all_cancers(95;0.00108)		Epithelial(56;9.76e-07)|all cancers(55;5.61e-06)	GBM - Glioblastoma multiforme(265;0.0144)		tCTTAGGAACAAAGATATGAG	0.353																																					p.K333X		Atlas-SNP	.											.	OR11G2	73	.	0			c.A997T						.						91	98	96					14																	20666491		2203	4300	6503	SO:0001587	stop_gained	390439	exon1			AGGAACAAAGATA		CCDS32032.1	14q11.2	2013-09-24			ENSG00000196832	ENSG00000196832		"GPCR / Class A : Olfactory receptors"	15346	protein-coding gene	gene with protein product							Standard	NM_001005503		Approved		uc010tlb.2	Q8NGC1	OTTHUMG00000167700	ENST00000357366.3:c.997A>T	chr14.hg19:g.20666491A>T	ENSP00000349930:p.Lys333*	97.0	0.0		76.0	25.0	NM_001005503	Q6IF09|Q96R33	Nonsense_Mutation	SNP	ENST00000357366.3	hg19	CCDS32032.1	.	.	.	.	.	.	.	.	.	.	a	23.9	4.469285	0.84533	.	.	ENSG00000196832	ENST00000357366	.	.	.	4.94	4.94	0.65067	.	0.128718	0.34879	N	0.003604	.	.	.	.	.	.	0.38836	D	0.955963	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.1253	0.14880	0.7239:0.1848:0.0913:0.0	.	.	.	.	X	333	.	ENSP00000349930:K333X	K	+	1	0	OR11G2	19736331	0.021000	0.18746	1.000000	0.80357	0.985000	0.73830	0.725000	0.25970	2.077000	0.62373	0.533000	0.62120	AAA	.	.		0.353	OR11G2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395722.1			T	20666491	A	T	20666491	4	4	344	1	0	0	0	0	0	1	0	0	10934	131	5	4	999	4	OR11G2	14	20666491	Nonsense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	222097	20666491	86683049	979	48342										
TEP1	7011	hgsc.bcm.edu	37	chr14	20851687	20851687	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tccagtctgaaatcagctgcCcattctggtccactaaccta	6	14	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:20851687C>A	ENST00000262715.5	-	26	3867	c.3827G>T	c.(3826-3828)gGg>gTg	p.G1276V	TEP1_ENST00000545983.1_5'Flank|TEP1_ENST00000556935.1_Missense_Mutation_p.G1168V	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1276	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		AATCAGCTGCCCATTCTGGTC	0.597																																					p.G1276V		Atlas-SNP	.											.	TEP1	224	.	0			c.G3827T						.						85	77	80					14																	20851687		2203	4300	6503	SO:0001583	missense	7011	exon26			AGCTGCCCATTCT		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"WD repeat domain containing"	11726	protein-coding gene	gene with protein product	"TROVE domain family, member 1"	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.3827G>T	chr14.hg19:g.20851687C>A	ENSP00000262715:p.Gly1276Val	99.0	0.0		91.0	47.0	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	hg19	CCDS9548.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.319991	0.81469	.	.	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935	D;D	0.81579	-1.51;-1.51	5.51	5.51	0.81932	NACHT nucleoside triphosphatase (1);	0.051670	0.85682	D	0.000000	D	0.89234	0.6657	M	0.72894	2.215	0.80722	D	1	D;D;D	0.76494	0.999;0.998;0.999	D;D;D	0.80764	0.975;0.964;0.994	D	0.89561	0.3806	10	0.59425	D	0.04	-16.5151	18.1892	0.89802	0.0:1.0:0.0:0.0	.	1168;626;1276	G3V5X7;G3V2A4;Q99973	.;.;TEP1_HUMAN	V	1276;1276;1168	ENSP00000262715:G1276V;ENSP00000452574:G1168V	ENSP00000262715:G1276V	G	-	2	0	TEP1	19921527	0.994000	0.37717	0.976000	0.42696	0.998000	0.95712	5.568000	0.67385	2.571000	0.86741	0.655000	0.94253	GGG	.	.		0.597	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		A	20851687	C	A	20851687	3	1	344	1	0	0	0	0	1	0	0	0	15774	623	22	3	4176	3	TEP1	14	20851687	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	185196	20851687	86497853	980	48343										
TEP1	7011	hgsc.bcm.edu	37	chr14	20871535	20871535	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	accccagaagaagggactcaCctttctctgctcttctctga	7	14	4	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:20871535C>A	ENST00000262715.5	-	7	1307		c.e7+1		TEP1_ENST00000556935.1_Splice_Site	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1						RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		AAGGGACTCACCTTTCTCTGC	0.408																																					.		Atlas-SNP	.											.	TEP1	224	.	0			c.1266+1G>T						.						180	176	177					14																	20871535		2203	4300	6503	SO:0001630	splice_region_variant	7011	exon8			GACTCACCTTTCT		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"WD repeat domain containing"	11726	protein-coding gene	gene with protein product	"TROVE domain family, member 1"	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.1266+1G>T	chr14.hg19:g.20871535C>A		121.0	0.0		106.0	51.0	NM_007110	A0AUV9	Splice_Site	SNP	ENST00000262715.5	hg19	CCDS9548.1	.	.	.	.	.	.	.	.	.	.	C	8.379	0.837166	0.16891	.	.	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935	.	.	.	4.8	4.8	0.61643	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.0862	0.64957	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TEP1	19941375	1.000000	0.71417	0.994000	0.49952	0.018000	0.09664	3.290000	0.51755	2.601000	0.87937	0.563000	0.77884	.	.	.		0.408	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	Intron	A	20871535	C	A	20871535	5	1	344	1	0	0	0	0	0	0	1	0	15774	521	18	3	6812	3	TEP1	14	20871535	Splice_Site	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	19848	20871535	86478005	981	48344										
OXA1L	5018	hgsc.bcm.edu	37	chr14	23237247	23237247	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tctggagagactgcagatgtAgtccaaactgctgcagagca	12	9	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:23237247A>T	ENST00000604262.1	+	3	329	c.306A>T	c.(304-306)gtA>gtT	p.V102V	OXA1L_ENST00000358043.5_Silent_p.V86V|CTD-2555K7.2_ENST00000554857.1_RNA|CTD-2555K7.2_ENST00000553792.1_RNA|CTD-2555K7.2_ENST00000554730.1_RNA|OXA1L_ENST00000412791.1_Silent_p.V102V|OXA1L_ENST00000285848.5_Silent_p.V162V			Q15070	OXA1L_HUMAN	oxidase (cytochrome c) assembly 1-like	102					aerobic respiration (GO:0009060)|mitochondrial proton-transporting ATP synthase complex assembly (GO:0033615)|mitochondrial respiratory chain complex I assembly (GO:0032981)|mitochondrial respiratory chain complex I biogenesis (GO:0097031)|negative regulation of ATPase activity (GO:0032780)|negative regulation of oxidoreductase activity (GO:0051354)|oxidation-reduction process (GO:0055114)|protein complex assembly (GO:0006461)|protein insertion into membrane (GO:0051205)|protein tetramerization (GO:0051262)	integral component of mitochondrial membrane (GO:0032592)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	mitochondrial ribosome binding (GO:0097177)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(5)|skin(2)	19	all_cancers(95;8.44e-05)			GBM - Glioblastoma multiforme(265;0.0096)		CTGCAGATGTAGTCCAAACTG	0.527																																					p.V162V		Atlas-SNP	.											.	OXA1L	49	.	0			c.A486T						.						55	53	53					14																	23237247		2203	4300	6503	SO:0001819	synonymous_variant	5018	exon3			AGATGTAGTCCAA		CCDS9573.1	14q11.2	2009-05-26			ENSG00000155463	ENSG00000155463			8526	protein-coding gene	gene with protein product		601066				8586451, 19349278	Standard	NM_005015		Approved	MGC133129, OXA1	uc001wgn.2	Q15070	OTTHUMG00000028691	ENST00000604262.1:c.306A>T	chr14.hg19:g.23237247A>T		82.0	0.0		80.0	35.0	NM_005015	B4DPA2	Silent	SNP	ENST00000604262.1	hg19																																																																																				.	.		0.527	OXA1L-012	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000468876.1	NM_005015		T	23237247	A	T	23237247	2	4	344	1	0	0	0	0	0	0	0	1	11337	407	15	4		4	OXA1L	14	23237247	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2365712	23237247	84112293	982	48345										
MMP14	4323	hgsc.bcm.edu	37	chr14	23312529	23312529	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cctggggctcgagcattccaGtgacccctcggccatcatgg	12	15	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:23312529G>T	ENST00000311852.6	+	5	1013	c.752G>T	c.(751-753)aGt>aTt	p.S251I	MMP14_ENST00000548162.1_3'UTR	NM_004995.2	NP_004986.1	P50281	MMP14_HUMAN	matrix metallopeptidase 14 (membrane-inserted)	251					angiogenesis (GO:0001525)|astrocyte cell migration (GO:0043615)|branching morphogenesis of an epithelial tube (GO:0048754)|chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|endodermal cell differentiation (GO:0035987)|endothelial cell proliferation (GO:0001935)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|male gonad development (GO:0008584)|negative regulation of focal adhesion assembly (GO:0051895)|ovarian follicle development (GO:0001541)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|proteolysis (GO:0006508)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to oxidative stress (GO:0006979)|tissue remodeling (GO:0048771)|zymogen activation (GO:0031638)	extracellular matrix (GO:0031012)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|peptidase activator activity (GO:0016504)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	20	all_cancers(95;9.47e-05)			GBM - Glioblastoma multiforme(265;0.00551)	Marimastat(DB00786)	GAGCATTCCAGTGACCCCTCG	0.582																																					p.S251I		Atlas-SNP	.											.	MMP14	40	.	0			c.G752T						.						95	85	88					14																	23312529		2203	4300	6503	SO:0001583	missense	4323	exon5			ATTCCAGTGACCC		CCDS9577.1	14q11-q12	2011-06-29	2005-08-08		ENSG00000157227	ENSG00000157227			7160	protein-coding gene	gene with protein product	"membrane type 1 metalloprotease"	600754	"matrix metalloproteinase 14 (membrane-inserted)"			8015608	Standard	NM_004995		Approved	MT1-MMP	uc001whc.3	P50281	OTTHUMG00000028704	ENST00000311852.6:c.752G>T	chr14.hg19:g.23312529G>T	ENSP00000308208:p.Ser251Ile	53.0	0.0		44.0	15.0	NM_004995	A8K5L0|Q6GSF3|Q92678	Missense_Mutation	SNP	ENST00000311852.6	hg19	CCDS9577.1	.	.	.	.	.	.	.	.	.	.	G	19.85	3.903582	0.72754	.	.	ENSG00000157227	ENST00000311852	T	0.24151	1.87	5.66	-1.86	0.07760	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.460849	0.26328	N	0.025011	T	0.39600	0.1084	M	0.90082	3.085	0.27922	N	0.938195	P	0.42757	0.789	P	0.46758	0.526	T	0.45789	-0.9237	10	0.72032	D	0.01	.	10.4148	0.44316	0.6276:0.0:0.3724:0.0	.	251	P50281	MMP14_HUMAN	I	251	ENSP00000308208:S251I	ENSP00000308208:S251I	S	+	2	0	MMP14	22382369	0.999000	0.42202	0.960000	0.40013	0.963000	0.63663	2.205000	0.42770	-0.455000	0.07054	-0.794000	0.03295	AGT	.	.		0.582	MMP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071660.3	NM_004995		T	23312529	G	T	23312529	3	4	344	1	0	0	0	0	1	0	0	0	9662	1029	36	3	770	3	MMP14	14	23312529	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	75282	23312529	84037011	983	48346										
CEBPE	1053	hgsc.bcm.edu	37	chr14	23587945	23587945	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cccggggctcctccttcaccGccacagccctggggtcgtag	12	18	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:23587945G>T	ENST00000206513.5	-	1	880	c.356C>A	c.(355-357)gCg>gAg	p.A119E		NM_001805.3	NP_001796.2	Q15744	CEBPE_HUMAN	CCAAT/enhancer binding protein (C/EBP), epsilon	119					cellular response to lipopolysaccharide (GO:0071222)|cytokine biosynthetic process (GO:0042089)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|macrophage differentiation (GO:0030225)|phagocytosis (GO:0006909)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			large_intestine(2)|lung(3)|ovary(2)|prostate(1)|skin(1)	9	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.0064)		CTCCTTCACCGCCACAGCCCT	0.677																																					p.A119E	NSCLC(63;1230 1818 14565 22565)	Atlas-SNP	.											.	CEBPE	34	.	0			c.C356A						.						20	22	21					14																	23587945		2202	4298	6500	SO:0001583	missense	1053	exon1			TTCACCGCCACAG		CCDS9589.1	14q11.2	2014-09-17			ENSG00000092067	ENSG00000092067		"basic leucine zipper proteins"	1836	protein-coding gene	gene with protein product		600749				8661101	Standard	NM_001805		Approved	CRP1	uc001wiv.2	Q15744	OTTHUMG00000028719	ENST00000206513.5:c.356C>A	chr14.hg19:g.23587945G>T	ENSP00000206513:p.Ala119Glu	39.0	0.0		42.0	18.0	NM_001805	Q15745|Q8IYI2|Q99803	Missense_Mutation	SNP	ENST00000206513.5	hg19	CCDS9589.1	.	.	.	.	.	.	.	.	.	.	G	14.91	2.675656	0.47781	.	.	ENSG00000092067	ENST00000206513	T	0.32023	1.47	5.22	5.22	0.72569	.	0.429650	0.23362	N	0.049003	T	0.19046	0.0457	L	0.27053	0.805	0.36601	D	0.87466	B	0.32160	0.358	B	0.29176	0.099	T	0.15983	-1.0418	10	0.13853	T	0.58	-11.7292	11.106	0.48203	0.0864:0.0:0.9136:0.0	.	119	Q15744	CEBPE_HUMAN	E	119	ENSP00000206513:A119E	ENSP00000206513:A119E	A	-	2	0	CEBPE	22657785	0.975000	0.34042	0.950000	0.38849	0.752000	0.42762	1.730000	0.38125	2.421000	0.82119	0.561000	0.74099	GCG	.	.		0.677	CEBPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071716.2	NM_001805		T	23587945	G	T	23587945	3	4	344	1	0	0	0	0	1	0	0	0	3204	1087	38	1	497	1	CEBPE	14	23587945	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	275416	23587945	83761595	984	48347										
MYH6	4624	hgsc.bcm.edu	37	chr14	23858850	23858850	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggtggtgaaatcattgagggAgcgttgggcctcttctagct	15	7	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:23858850A>T	ENST00000356287.3	-	26	3840	c.3811T>A	c.(3811-3813)Tcc>Acc	p.S1271T	MYH6_ENST00000405093.3_Missense_Mutation_p.S1271T|MIR208A_ENST00000362287.1_RNA			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	1271					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)			breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		TCATTGAGGGAGCGTTGGGCC	0.567																																					p.S1271T		Atlas-SNP	.											.	MYH6	274	.	0			c.T3811A						.						119	97	104					14																	23858850		2203	4300	6503	SO:0001583	missense	4624	exon27			TGAGGGAGCGTTG	D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"Myosins / Myosin superfamily : Class II"	7576	protein-coding gene	gene with protein product	"cardiomyopathy, hypertrophic 1"	160710	"myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.3811T>A	chr14.hg19:g.23858850A>T	ENSP00000348634:p.Ser1271Thr	139.0	0.0		126.0	55.0	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Missense_Mutation	SNP	ENST00000356287.3	hg19	CCDS9600.1	.	.	.	.	.	.	.	.	.	.	a	7.225	0.598121	0.13939	.	.	ENSG00000197616	ENST00000405093;ENST00000356287	T;T	0.77877	-1.13;-1.13	4.82	4.82	0.62117	Myosin tail (1);	.	.	.	.	T	0.49762	0.1576	N	0.04148	-0.265	0.30858	N	0.733842	B	0.02656	0.0	B	0.09377	0.004	T	0.49624	-0.8920	9	0.06236	T	0.91	.	5.6867	0.17807	0.5546:0.1325:0.0:0.313	.	1271	P13533	MYH6_HUMAN	T	1271	ENSP00000386041:S1271T;ENSP00000348634:S1271T	ENSP00000348634:S1271T	S	-	1	0	MYH6	22928690	0.000000	0.05858	1.000000	0.80357	0.748000	0.42578	-0.355000	0.07671	1.932000	0.55993	0.459000	0.35465	TCC	.	.		0.567	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3			T	23858850	A	T	23858850	3	4	344	1	0	0	0	0	1	0	0	0	10047	304	11	4	2060	4	MYH6	14	23858850	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	270905	23858850	83490690	985	48348										
MYH7	4625	hgsc.bcm.edu	37	chr14	23892879	23892879	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agagctttcttctccttggtCagcttggcaatgatctcatc	8	11	4	2	rs368728770		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:23892879C>A	ENST00000355349.3	-	24	3138	c.2976G>T	c.(2974-2976)ctG>ctT	p.L992L		NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	992					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		TCTCCTTGGTCAGCTTGGCAA	0.537																																					p.L992L		Atlas-SNP	.											.	MYH7	349	.	0			c.G2976T						.						156	150	152					14																	23892879		2203	4300	6503	SO:0001819	synonymous_variant	4625	exon24			CTTGGTCAGCTTG	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.2976G>T	chr14.hg19:g.23892879C>A		102.0	0.0		91.0	39.0	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Silent	SNP	ENST00000355349.3	hg19	CCDS9601.1																																																																																			.	.		0.537	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257		A	23892879	C	A	23892879	2	1	344	1	0	0	0	0	0	0	0	1	10048	813	29	3		3	MYH7	14	23892879	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	34029	23892879	83456661	986	48349										
MYH7	4625	hgsc.bcm.edu	37	chr14	23900689	23900689	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aatgaattcgaatgaatttcCcctggagagatggaagagag	12	5	0	4	rs397516267		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:23900689C>A	ENST00000355349.3	-	9	896	c.734G>T	c.(733-735)gGg>gTg	p.G245V		NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	245	Myosin motor.				adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		AATGAATTTCCCCTGGAGAGA	0.512																																					p.G245V		Atlas-SNP	.											.	MYH7	349	.	0			c.G734T						.						136	136	136					14																	23900689		2203	4300	6503	SO:0001630	splice_region_variant	4625	exon9			AATTTCCCCTGGA	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.733-1G>T	chr14.hg19:g.23900689C>A		70.0	0.0		67.0	27.0	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Missense_Mutation	SNP	ENST00000355349.3	hg19	CCDS9601.1	.	.	.	.	.	.	.	.	.	.	C	15.23	2.771113	0.49680	.	.	ENSG00000092054	ENST00000355349;ENST00000544444	D	0.97888	-4.59	3.47	3.47	0.39725	Myosin head, motor domain (3);	.	.	.	.	D	0.99378	0.9781	H	0.99855	4.85	0.80722	D	1	D	0.71674	0.998	D	0.80764	0.994	D	0.97754	1.0216	9	0.87932	D	0	.	15.4877	0.75578	0.0:1.0:0.0:0.0	.	245	P12883	MYH7_HUMAN	V	245	ENSP00000347507:G245V	ENSP00000347507:G245V	G	-	2	0	MYH7	22970529	1.000000	0.71417	1.000000	0.80357	0.235000	0.25334	7.440000	0.80464	1.946000	0.56461	0.305000	0.20034	GGG	.	.		0.512	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257	Missense_Mutation	A	23900689	C	A	23900689	5	1	344	1	0	0	0	0	0	0	1	0	10048	637	22	3	5201	3	MYH7	14	23900689	Splice_Site	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	7810	23900689	83448851	987	48350										
DCAF11	80344	hgsc.bcm.edu	37	chr14	24586232	24586232	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gagcttgggatggtcgtcttGgggatcgatacaacccacct	13	10	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:24586232G>T	ENST00000446197.3	+	3	989	c.262G>T	c.(262-264)Ggg>Tgg	p.G88W	DCAF11_ENST00000396936.1_Missense_Mutation_p.L9F|NRL_ENST00000561028.1_5'Flank|DCAF11_ENST00000560171.1_Intron|DCAF11_ENST00000559115.1_Missense_Mutation_p.G88W|DCAF11_ENST00000396941.4_Missense_Mutation_p.G62W	NM_025230.4	NP_079506.3	Q8TEB1	DCA11_HUMAN	DDB1 and CUL4 associated factor 11	88					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)											TGGTCGTCTTGGGGATCGATA	0.443																																					p.G88W		Atlas-SNP	.											.	.	.	.	0			c.G262T						.						114	111	112					14																	24586232		2203	4300	6503	SO:0001583	missense	80344	exon3			CGTCTTGGGGATC	AF130070	CCDS9610.1, CCDS41929.1	14q11.2	2013-01-09	2009-07-17	2009-07-17	ENSG00000100897	ENSG00000100897		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	20258	protein-coding gene	gene with protein product		613317	"WD repeat domain 23"	WDR23			Standard	NM_025230		Approved	PRO2389, GL014	uc001wlv.3	Q8TEB1	OTTHUMG00000028793	ENST00000446197.3:c.262G>T	chr14.hg19:g.24586232G>T	ENSP00000415556:p.Gly88Trp	186.0	0.0		147.0	69.0	NM_025230	B3KQ83|D3DS56|Q5D039|Q86U00|Q86U39|Q8NDN2|Q9H2J0|Q9H3A3|Q9H5C9	Missense_Mutation	SNP	ENST00000446197.3	hg19	CCDS9610.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	22.5|22.5	4.302290|4.302290	0.81136|0.81136	.|.	.|.	ENSG00000100897|ENSG00000100897	ENST00000326009;ENST00000446197;ENST00000396941|ENST00000396936	T;T|T	0.50001|0.56275	0.76;0.87|0.47	5.22|5.22	5.22|5.22	0.72569|0.72569	.|.	0.048773|.	0.85682|.	D|.	0.000000|.	T|T	0.51856|0.51856	0.1699|0.1699	L|L	0.57536|0.57536	1.79|1.79	0.33970|0.33970	D|D	0.646678|0.646678	D;D;D|B;B	0.89917|0.17038	0.999;0.998;1.0|0.012;0.02	D;P;D|B;B	0.97110|0.16722	0.989;0.87;1.0|0.014;0.016	T|T	0.58962|0.58962	-0.7543|-0.7543	10|9	0.87932|0.41790	D|T	0|0.15	-28.7435|-28.7435	16.3214|16.3214	0.82952|0.82952	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	62;88;88|32;9	Q8TEB1-2;A8K9T2;Q8TEB1|Q59GN6;Q8TEB1-3	.;.;DCA11_HUMAN|.;.	W|F	88;62;62|9	ENSP00000415556:G62W;ENSP00000380146:G62W|ENSP00000380142:L9F	ENSP00000323680:G88W|ENSP00000380142:L9F	G|L	+|+	1|3	0|2	DCAF11|DCAF11	23656072|23656072	1.000000|1.000000	0.71417|0.71417	0.976000|0.976000	0.42696|0.42696	0.929000|0.929000	0.56500|0.56500	7.434000|7.434000	0.80377|0.80377	2.720000|2.720000	0.93068|0.93068	0.563000|0.563000	0.77884|0.77884	GGG|TTG	.	.		0.443	DCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071907.4			T	24586232	G	T	24586232	3	4	344	1	0	0	0	0	1	0	0	0	4264	1348	47	3	268	3	DCAF11	14	24586232	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	685543	24586232	82763308	988	48351										
ADCY4	196883	hgsc.bcm.edu	37	chr14	24792119	24792119	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gctgtgcacacctggagtccAaggggcccagatagaggcgg	16	11	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:24792119A>T	ENST00000310677.4	-	19	2446	c.2333T>A	c.(2332-2334)tTg>tAg	p.L778*	ADCY4_ENST00000418030.2_Nonsense_Mutation_p.L778*|ADCY4_ENST00000554068.2_Nonsense_Mutation_p.L778*	NM_001198568.1|NM_001198592.1|NM_139247.3	NP_001185497.1|NP_001185521.1|NP_640340.2	Q8NFM4	ADCY4_HUMAN	adenylate cyclase 4	778					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(265;0.0192)		CCTGGAGTCCAAGGGGCCCAG	0.642																																					p.L778X		Atlas-SNP	.											.	ADCY4	86	.	0			c.T2333A						.						19	20	20					14																	24792119		2196	4296	6492	SO:0001587	stop_gained	196883	exon19			GAGTCCAAGGGGC	AF497516	CCDS9627.1	14q11.2	2013-02-04			ENSG00000129467	ENSG00000129467	4.6.1.1	"Adenylate cyclases"	235	protein-coding gene	gene with protein product		600292				7766992	Standard	NM_001198592		Approved	AC4	uc001woy.3	Q8NFM4	OTTHUMG00000029347	ENST00000310677.4:c.2333T>A	chr14.hg19:g.24792119A>T	ENSP00000312126:p.Leu778*	55.0	0.0		68.0	41.0	NM_001198592	B3KV74|D3DS75|Q17R40|Q6ZTM6|Q96ML7	Nonsense_Mutation	SNP	ENST00000310677.4	hg19	CCDS9627.1	.	.	.	.	.	.	.	.	.	.	A	39	7.378070	0.98245	.	.	ENSG00000129467	ENST00000310677;ENST00000554068;ENST00000418030	.	.	.	4.41	-6.55	0.01854	.	2.065940	0.02472	N	0.087674	.	.	.	.	.	.	0.19300	N	0.999971	.	.	.	.	.	.	.	.	.	.	0.08179	T	0.78	.	1.0086	0.01492	0.2871:0.2779:0.2834:0.1516	.	.	.	.	X	778	.	ENSP00000312126:L778X	L	-	2	0	ADCY4	23861959	0.000000	0.05858	0.054000	0.19295	0.883000	0.51084	-1.588000	0.02106	-0.839000	0.04212	0.460000	0.39030	TTG	.	.		0.642	ADCY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073200.4			T	24792119	A	T	24792119	4	4	344	1	0	0	0	0	0	1	0	0	296	131	5	4	932	4	ADCY4	14	24792119	Nonsense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	205887	24792119	82557421	989	48352										
NFATC4	4776	hgsc.bcm.edu	37	chr14	24841727	24841727	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaggatcgaggtacagcctaGagcccaccaccgggcccact	12	15	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:24841727G>T	ENST00000250373.4	+	3	1418	c.1277G>T	c.(1276-1278)aGa>aTa	p.R426I	NFATC4_ENST00000554661.1_Missense_Mutation_p.R356I|NFATC4_ENST00000553708.1_Missense_Mutation_p.R426I|NFATC4_ENST00000555802.1_5'Flank|NFATC4_ENST00000556279.1_Missense_Mutation_p.R458I|NFATC4_ENST00000553469.1_Missense_Mutation_p.R458I|NFATC4_ENST00000556169.1_Missense_Mutation_p.R414I|NFATC4_ENST00000413692.2_Missense_Mutation_p.R489I|NFATC4_ENST00000539237.2_Missense_Mutation_p.R458I|NFATC4_ENST00000554473.1_5'Flank|NFATC4_ENST00000555590.1_Missense_Mutation_p.R439I|NFATC4_ENST00000554591.1_Missense_Mutation_p.R489I|NFATC4_ENST00000557767.1_5'Flank|NFATC4_ENST00000554344.1_Missense_Mutation_p.R356I|NFATC4_ENST00000555167.1_5'Flank|NFATC4_ENST00000556759.1_5'Flank|NFATC4_ENST00000553879.1_Missense_Mutation_p.R356I|NFATC4_ENST00000557451.1_Missense_Mutation_p.R356I|NFATC4_ENST00000422617.3_Missense_Mutation_p.R414I|NFATC4_ENST00000555453.1_Missense_Mutation_p.R414I|NFATC4_ENST00000424781.2_Missense_Mutation_p.R439I|NFATC4_ENST00000554050.1_Missense_Mutation_p.R426I|NFATC4_ENST00000555393.1_5'Flank|NFATC4_ENST00000554966.1_Missense_Mutation_p.R439I	NM_004554.4	NP_004545.2	Q14934	NFAC4_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4	426	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				cellular respiration (GO:0045333)|cellular response to lithium ion (GO:0071285)|cellular response to UV (GO:0034644)|heart development (GO:0007507)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of synaptic plasticity (GO:0048167)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription coactivator activity (GO:0003713)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(7)|liver(4)|lung(12)|ovary(1)|skin(2)	34				GBM - Glioblastoma multiforme(265;0.018)		GTACAGCCTAGAGCCCACCAC	0.617																																					p.R489I		Atlas-SNP	.											.	NFATC4	115	.	0			c.G1466T						.						50	50	50					14																	24841727		2203	4300	6503	SO:0001583	missense	4776	exon4			AGCCTAGAGCCCA	BC053855	CCDS9629.1, CCDS45089.1, CCDS55909.1, CCDS55910.1, CCDS55911.1, CCDS73625.1	14q11.2	2009-11-24			ENSG00000100968	ENSG00000100968		"Nuclear factor of activated T-cells"	7778	protein-coding gene	gene with protein product		602699				7749981	Standard	NM_004554		Approved	NFAT3	uc010tok.2	Q14934	OTTHUMG00000029351	ENST00000250373.4:c.1277G>T	chr14.hg19:g.24841727G>T	ENSP00000250373:p.Arg426Ile	47.0	0.0		56.0	32.0	NM_001198967	B4DDG5|B4DY55|B5B2U7|B5B2U8|B5B2U9|B5B2V0|B5B2V1|B5B2V2|B5B2V3|B5B2V4|B5B2V5|B5B2V7|B5B2V8|B5B2V9|B5B2W0|B5B2W1|B5B2W2|B5B2W3|B5B2W4|B5B2W5|B5B2W6|B5B2W7|B5B2W8|B5B2W9|B5B2X0|Q7Z598|Q96H68	Missense_Mutation	SNP	ENST00000250373.4	hg19	CCDS9629.1	.	.	.	.	.	.	.	.	.	.	G	16.62	3.173541	0.57584	.	.	ENSG00000100968	ENST00000413692;ENST00000554591;ENST00000555590;ENST00000554966;ENST00000424781;ENST00000539237;ENST00000556279;ENST00000553469;ENST00000554050;ENST00000554779;ENST00000250373;ENST00000553708;ENST00000553879;ENST00000554344;ENST00000554661;ENST00000556169;ENST00000557451;ENST00000422617;ENST00000555453	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.45668	0.89;0.89;0.89;0.89;0.89;0.89;0.89;0.89;0.89;1.77;0.89;0.89;0.89;0.89;0.89;0.89;0.89;0.89;0.89	5.01	5.01	0.66863	Rel homology (3);p53-like transcription factor, DNA-binding (1);	0.053425	0.64402	D	0.000001	T	0.61702	0.2368	M	0.63428	1.95	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.76494	0.997;0.999;0.994;0.999;0.994;0.997;0.999;0.999;0.999;0.999;0.997;0.997;0.999;0.997;0.998	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.75020	0.931;0.961;0.935;0.974;0.935;0.964;0.974;0.974;0.974;0.974;0.964;0.964;0.985;0.964;0.979	T	0.64537	-0.6384	10	0.87932	D	0	-4.2966	15.8646	0.79055	0.0:0.0:1.0:0.0	.	414;414;458;458;439;439;439;489;489;414;356;458;403;489;426	Q14934-17;Q14934-9;Q14934-14;Q14934-4;Q14934-15;Q14934-6;Q14934-7;Q14934-2;Q14934-3;Q14934-10;Q14934-12;Q14934-5;B4DU09;Q14934-11;Q14934	.;.;.;.;.;.;.;.;.;.;.;.;.;.;NFAC4_HUMAN	I	489;489;439;439;439;458;458;458;426;118;426;426;356;356;356;414;356;414;414	ENSP00000388910:R489I;ENSP00000452039:R489I;ENSP00000451224:R439I;ENSP00000450644:R439I;ENSP00000388668:R439I;ENSP00000439350:R458I;ENSP00000452270:R458I;ENSP00000451502:R458I;ENSP00000451151:R426I;ENSP00000451992:R118I;ENSP00000250373:R426I;ENSP00000450590:R426I;ENSP00000452349:R356I;ENSP00000450469:R356I;ENSP00000450733:R356I;ENSP00000451454:R414I;ENSP00000451284:R356I;ENSP00000396788:R414I;ENSP00000450686:R414I	ENSP00000250373:R426I	R	+	2	0	NFATC4	23911567	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.377000	0.52425	2.603000	0.88011	0.655000	0.94253	AGA	.	.		0.617	NFATC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073206.6	NM_004554		T	24841727	G	T	24841727	3	4	344	1	0	0	0	0	1	0	0	0	10374	942	33	3	1480	3	NFATC4	14	24841727	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	49608	24841727	82507813	990	48353										
NFATC4	4776	hgsc.bcm.edu	37	chr14	24843545	24843545	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tctgcagcccagcgctcagcCcaggagctgccccaggtgga	13	16	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:24843545C>A	ENST00000250373.4	+	6	1887	c.1746C>A	c.(1744-1746)gcC>gcA	p.A582A	NFATC4_ENST00000554661.1_Silent_p.A512A|NFATC4_ENST00000553708.1_Silent_p.A582A|NFATC4_ENST00000555802.1_5'UTR|NFATC4_ENST00000556279.1_Silent_p.A614A|NFATC4_ENST00000553469.1_Silent_p.A614A|NFATC4_ENST00000556169.1_Silent_p.A570A|NFATC4_ENST00000413692.2_Silent_p.A645A|NFATC4_ENST00000539237.2_Silent_p.A614A|NFATC4_ENST00000554473.1_Silent_p.A117A|NFATC4_ENST00000555590.1_Silent_p.A595A|NFATC4_ENST00000554591.1_Silent_p.A645A|NFATC4_ENST00000557767.1_5'UTR|NFATC4_ENST00000554344.1_Silent_p.A512A|NFATC4_ENST00000555167.1_Silent_p.A117A|NFATC4_ENST00000556759.1_Silent_p.A117A|NFATC4_ENST00000553879.1_Silent_p.A512A|NFATC4_ENST00000557451.1_Silent_p.A512A|NFATC4_ENST00000422617.3_Silent_p.A570A|NFATC4_ENST00000555453.1_Silent_p.A570A|NFATC4_ENST00000424781.2_Silent_p.A595A|NFATC4_ENST00000554050.1_Silent_p.A582A|NFATC4_ENST00000555393.1_5'UTR|NFATC4_ENST00000554966.1_Silent_p.A595A	NM_004554.4	NP_004545.2	Q14934	NFAC4_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4	582	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				cellular respiration (GO:0045333)|cellular response to lithium ion (GO:0071285)|cellular response to UV (GO:0034644)|heart development (GO:0007507)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of synaptic plasticity (GO:0048167)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription coactivator activity (GO:0003713)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(7)|liver(4)|lung(12)|ovary(1)|skin(2)	34				GBM - Glioblastoma multiforme(265;0.018)		AGCGCTCAGCCCAGGAGCTGC	0.642																																					p.A645A		Atlas-SNP	.											.	NFATC4	115	.	0			c.C1935A						.						36	31	33					14																	24843545		2203	4300	6503	SO:0001819	synonymous_variant	4776	exon7			CTCAGCCCAGGAG	BC053855	CCDS9629.1, CCDS45089.1, CCDS55909.1, CCDS55910.1, CCDS55911.1, CCDS73625.1	14q11.2	2009-11-24			ENSG00000100968	ENSG00000100968		"Nuclear factor of activated T-cells"	7778	protein-coding gene	gene with protein product		602699				7749981	Standard	NM_004554		Approved	NFAT3	uc010tok.2	Q14934	OTTHUMG00000029351	ENST00000250373.4:c.1746C>A	chr14.hg19:g.24843545C>A		45.0	0.0		44.0	21.0	NM_001198967	B4DDG5|B4DY55|B5B2U7|B5B2U8|B5B2U9|B5B2V0|B5B2V1|B5B2V2|B5B2V3|B5B2V4|B5B2V5|B5B2V7|B5B2V8|B5B2V9|B5B2W0|B5B2W1|B5B2W2|B5B2W3|B5B2W4|B5B2W5|B5B2W6|B5B2W7|B5B2W8|B5B2W9|B5B2X0|Q7Z598|Q96H68	Silent	SNP	ENST00000250373.4	hg19	CCDS9629.1																																																																																			.	.		0.642	NFATC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073206.6	NM_004554		A	24843545	C	A	24843545	2	1	344	1	0	0	0	0	0	0	0	1	10374	610	22	3		3	NFATC4	14	24843545	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1818	24843545	82505995	991	48354										
NKX2-8	26257	hgsc.bcm.edu	37	chr14	37051488	37051488	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aggcggcgcaggggtcgggcTggggggcgcgtggttctggc	24	9	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:37051488T>A	ENST00000258829.5	-	1	324	c.107A>T	c.(106-108)cAg>cTg	p.Q36L		NM_014360.2	NP_055175.2	O15522	NKX28_HUMAN	NK2 homeobox 8	36					axonogenesis (GO:0007409)|liver development (GO:0001889)|lung development (GO:0030324)|negative regulation of epithelial cell proliferation (GO:0050680)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			upper_aerodigestive_tract(1)	1	Breast(36;0.143)|Hepatocellular(127;0.158)|Esophageal squamous(585;0.164)		Lung(8;1.12e-09)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.00357)|all cancers(34;0.0113)|LUSC - Lung squamous cell carcinoma(13;0.0189)	GBM - Glioblastoma multiforme(112;0.0171)		GGGGTCGGGCTGGGGGGCGCG	0.687																																					p.Q36L		Atlas-SNP	.											.	NKX2-8	13	.	0			c.A107T						.						16	18	18					14																	37051488		2198	4292	6490	SO:0001583	missense	26257	exon1			TCGGGCTGGGGGG		CCDS9660.1	14q13.3	2012-03-09	2007-07-09	2002-10-04	ENSG00000136327	ENSG00000136327		"Homeoboxes / ANTP class : NKL subclass"	16364	protein-coding gene	gene with protein product		603245	"NK-2 homolog H (Drosophila)", "NK2 transcription factor related, locus 8 (Drosophila)"	NKX2H		9446603	Standard	NM_014360		Approved	NKX2.8, Nkx2-9	uc001wtx.3	O15522	OTTHUMG00000028772	ENST00000258829.5:c.107A>T	chr14.hg19:g.37051488T>A	ENSP00000258829:p.Gln36Leu	102.0	0.0		73.0	31.0	NM_014360	Q8IUT7	Missense_Mutation	SNP	ENST00000258829.5	hg19	CCDS9660.1	.	.	.	.	.	.	.	.	.	.	T	9.718	1.158856	0.21454	.	.	ENSG00000136327	ENST00000258829	D	0.90069	-2.61	4.44	-4.55	0.03441	.	2.387170	0.01947	N	0.042373	T	0.78966	0.4367	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.66333	-0.5950	10	0.37606	T	0.19	.	8.8062	0.34938	0.1142:0.23:0.0:0.6558	.	36	O15522	NKX28_HUMAN	L	36	ENSP00000258829:Q36L	ENSP00000258829:Q36L	Q	-	2	0	NKX2-8	36121239	0.000000	0.05858	0.000000	0.03702	0.817000	0.46193	-0.283000	0.08433	-0.818000	0.04329	0.449000	0.29647	CAG	.	.		0.687	NKX2-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071844.6			A	37051488	T	A	37051488	3	1	344	1	0	0	0	0	1	0	0	0	10463	1580	55	4	620	4	NKX2-8	14	37051488	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	12207943	37051488	70298052	992	48355										
KLHL28	54813	hgsc.bcm.edu	37	chr14	45414552	45414552	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ataaaaaacagtctcttcggTagctacattcaaacagtcat	5	9	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:45414552T>A	ENST00000396128.4	-	2	699	c.580A>T	c.(580-582)Acc>Tcc	p.T194S	KLHL28_ENST00000355081.2_Missense_Mutation_p.T208S	NM_017658.3	NP_060128.2	Q9NXS3	KLH28_HUMAN	kelch-like family member 28	194										breast(2)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						GTCTCTTCGGTAGCTACATTC	0.378																																					p.T194S		Atlas-SNP	.											.	KLHL28	53	.	0			c.A580T						.						102	101	102					14																	45414552		2203	4300	6503	SO:0001583	missense	54813	exon2			CTTCGGTAGCTAC	AK000088	CCDS9680.1	14q21.1	2013-02-22	2013-02-22	2007-01-09	ENSG00000179454	ENSG00000179454		"Kelch-like", "BTB/POZ domain containing"	19741	protein-coding gene	gene with protein product			"BTB (POZ) domain containing 5", "kelch-like 28 (Drosophila)"	BTBD5			Standard	NM_017658		Approved	FLJ20081	uc001wvr.3	Q9NXS3	OTTHUMG00000140263	ENST00000396128.4:c.580A>T	chr14.hg19:g.45414552T>A	ENSP00000379434:p.Thr194Ser	97.0	0.0		108.0	49.0	NM_017658	Q0VAL5	Missense_Mutation	SNP	ENST00000396128.4	hg19	CCDS9680.1	.	.	.	.	.	.	.	.	.	.	T	7.032	0.560896	0.13498	.	.	ENSG00000179454	ENST00000396128;ENST00000355081	T;T	0.65916	-0.18;-0.18	5.85	5.85	0.93711	BTB/Kelch-associated (2);	0.042865	0.85682	D	0.000000	T	0.30039	0.0752	N	0.00890	-1.11	0.45747	D	0.998648	B;B	0.27264	0.0;0.173	B;B	0.28011	0.002;0.085	T	0.47522	-0.9111	10	0.02654	T	1	.	15.897	0.79341	0.0:0.0:0.0:1.0	.	194;194	Q9NXS3-2;Q9NXS3	.;KLH28_HUMAN	S	194;208	ENSP00000379434:T194S;ENSP00000347193:T208S	ENSP00000347193:T208S	T	-	1	0	KLHL28	44484302	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	5.796000	0.69080	2.238000	0.73509	0.533000	0.62120	ACC	.	.		0.378	KLHL28-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276790.3			A	45414552	T	A	45414552	3	1	344	1	0	0	0	0	1	0	0	0	8391	1638	57	4	1151	4	KLHL28	14	45414552	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	8363064	45414552	61934988	993	48356										
FANCM	57697	hgsc.bcm.edu	37	chr14	45658267	45658267	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgaggaggagaacaatgtaaAtgataaaagagaatctaata	10	2	1	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:45658267A>T	ENST00000267430.5	+	20	5127	c.5042A>T	c.(5041-5043)aAt>aTt	p.N1681I	FANCM_ENST00000542564.2_Missense_Mutation_p.N1655I	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1681					DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						AACAATGTAAATGATAAAAGA	0.338								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.N1681I		Atlas-SNP	.											.	FANCM	225	.	0			c.A5042T						.						73	76	75					14																	45658267		2203	4300	6503	SO:0001583	missense	57697	exon20	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	ATGTAAATGATAA	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"Fanconi anemia, complementation groups"	23168	protein-coding gene	gene with protein product		609644	"KIAA1596"	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.5042A>T	chr14.hg19:g.45658267A>T	ENSP00000267430:p.Asn1681Ile	111.0	0.0		106.0	44.0	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	hg19	CCDS32070.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.45|13.45	2.239444|2.239444	0.39598|0.39598	.|.	.|.	ENSG00000187790|ENSG00000187790	ENST00000554809|ENST00000267430;ENST00000542564;ENST00000556250	.|T;T;T	.|0.19532	.|2.72;2.72;2.14	5.02|5.02	3.84|3.84	0.44239|0.44239	.|.	.|0.755219	.|0.13314	.|N	.|0.397248	T|T	0.18002|0.18002	0.0432|0.0432	L|L	0.47716|0.47716	1.5|1.5	0.09310|0.09310	N|N	1|1	.|P;P	.|0.41265	.|0.744;0.744	.|B;B	.|0.35859	.|0.212;0.212	T|T	0.09079|0.09079	-1.0691|-1.0691	5|10	.|0.49607	.|T	.|0.09	.|.	9.1624|9.1624	0.37030|0.37030	0.8158:0.1842:0.0:0.0|0.8158:0.1842:0.0:0.0	.|.	.|1655;1681	.|B2RTQ9;Q8IYD8	.|.;FANCM_HUMAN	N|I	613|1681;1655;1197	.|ENSP00000267430:N1681I;ENSP00000442493:N1655I;ENSP00000452033:N1197I	.|ENSP00000267430:N1681I	K|N	+|+	3|2	2|0	FANCM|FANCM	44728017|44728017	0.002000|0.002000	0.14202|0.14202	0.021000|0.021000	0.16686|0.16686	0.363000|0.363000	0.29612|0.29612	0.901000|0.901000	0.28445|0.28445	0.972000|0.972000	0.38314|0.38314	0.528000|0.528000	0.53228|0.53228	AAA|AAT	.	.		0.338	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		T	45658267	A	T	45658267	3	4	344	1	0	0	0	0	1	0	0	0	5679	101	4	4	5120	4	FANCM	14	45658267	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	243715	45658267	61691273	994	48357										
POLE2	5427	hgsc.bcm.edu	37	chr14	50140842	50140842	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cgccccctaccaaacttaccTggtgcaaaatggtatatcgc	7	14	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:50140842T>A	ENST00000216367.5	-	5	515	c.416A>T	c.(415-417)cAg>cTg	p.Q139L	POLE2_ENST00000554396.1_Splice_Site_p.Q139L|POLE2_ENST00000556584.1_5'UTR|POLE2_ENST00000539565.2_Splice_Site_p.Q113L	NM_002692.3	NP_002683.2	P56282	DPOE2_HUMAN	polymerase (DNA directed), epsilon 2, accessory subunit	139					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	epsilon DNA polymerase complex (GO:0008622)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)			kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	10	all_epithelial(31;0.0021)|Breast(41;0.0124)				Cladribine(DB00242)	CAAACTTACCTGGTGCAAAAT	0.418																																					p.Q139L		Atlas-SNP	.											.	POLE2	36	.	0			c.A416T						.						228	242	237					14																	50140842		2203	4300	6503	SO:0001630	splice_region_variant	5427	exon5			CTTACCTGGTGCA	AF025840	CCDS32073.1, CCDS55914.1, CCDS55915.1	14q21-q22	2012-05-18	2012-05-18		ENSG00000100479	ENSG00000100479		"DNA polymerases"	9178	protein-coding gene	gene with protein product	"DNA polymerase epsilon subunit B"	602670	"polymerase (DNA directed), epsilon 2 (p59 subunit)"			9405441, 9443964	Standard	NM_002692		Approved	DPE2	uc001wwu.3	P56282	OTTHUMG00000170813	ENST00000216367.5:c.417+1A>T	chr14.hg19:g.50140842T>A		89.0	0.0		93.0	39.0	NM_001197331	A0AV55|A4FU92|A4LBB7|A6NH58|B4DDE6|O43560	Missense_Mutation	SNP	ENST00000216367.5	hg19	CCDS32073.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.481451	0.84747	.	.	ENSG00000100479	ENST00000216367;ENST00000539565;ENST00000554396	T;T;T	0.37235	1.63;1.65;1.21	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.65249	0.2673	M	0.88241	2.94	0.80722	D	1	D	0.71674	0.998	D	0.68483	0.958	T	0.73430	-0.3985	10	0.87932	D	0	-10.0145	14.9498	0.71064	0.0:0.0:0.0:1.0	.	139	P56282	DPOE2_HUMAN	L	139;113;139	ENSP00000216367:Q139L;ENSP00000446313:Q113L;ENSP00000451621:Q139L	ENSP00000216367:Q139L	Q	-	2	0	POLE2	49210592	1.000000	0.71417	1.000000	0.80357	0.871000	0.50021	6.995000	0.76257	1.996000	0.58369	0.528000	0.53228	CAG	.	.		0.418	POLE2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410512.1	NM_002692	Missense_Mutation	A	50140842	T	A	50140842	5	1	344	1	0	0	0	0	0	0	1	0	12206	1594	55	4	1227	4	POLE2	14	50140842	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	4482575	50140842	57208698	995	48358										
SDCCAG1	9147	hgsc.bcm.edu	37	chr14	50318359	50318359	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	attcgtatgccagattcaagTaaaagtgtagctttaaagtc	8	6	1	1	rs548635945		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:50318359T>C	ENST00000298310.5	-	3	602	c.153A>G	c.(151-153)ttA>ttG	p.L51L	RN7SL3_ENST00000578231.1_RNA|NEMF_ENST00000556672.1_Silent_p.L51L|NEMF_ENST00000545773.1_Silent_p.L51L|NEMF_ENST00000546046.1_Silent_p.L51L			O60524	NEMF_HUMAN	nuclear export mediator factor	51					nuclear export (GO:0051168)	nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(13)|liver(1)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	36						CAGATTCAAGTAAAAGTGTAG	0.368													T|||	1	0.000199681	8e-04	0	5008	,	,		17297	0		0	False		,,,				2504	0				p.L51L		Atlas-SNP	.											.	NEMF	79	.	0			c.A153G						.						106	106	106					14																	50318359		2203	4300	6503	SO:0001819	synonymous_variant	9147	exon3			TTCAAGTAAAAGT	AF039687	CCDS9694.1	14q21.3	2012-11-19	2011-01-31	2011-01-31	ENSG00000165525	ENSG00000165525			10663	protein-coding gene	gene with protein product		608378	"serologically defined colon cancer antigen 1"	SDCCAG1		9610721, 10575219	Standard	XR_429334		Approved	NY-CO-1, FLJ10051	uc001wxc.3	O60524	OTTHUMG00000170857	ENST00000298310.5:c.153A>G	chr14.hg19:g.50318359T>C		53.0	0.0		63.0	26.0	NM_004713	A0JLQ3|B3KSK1|B4DDL3|B4DHA9|B4E3F3|Q32Q66|Q8WW70|Q9NWG1	Silent	SNP	ENST00000298310.5	hg19	CCDS9694.1																																																																																			.	.		0.368	NEMF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410798.1	NM_004713		C	50318359	T	C	50318359	2	2	344	1	0	0	0	0	0	0	0	1	13972	1635	57	2		2	SDCCAG1	14	50318359	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	177517	50318359	57031181	996	48359										
NID2	22795	hgsc.bcm.edu	37	chr14	52481921	52481921	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcacgtactggtcatcccggGgggtgccaccgtagtgctcc	14	14	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:52481921G>C	ENST00000216286.5	-	15	3100	c.3101C>G	c.(3100-3102)cCc>cGc	p.P1034R	NID2_ENST00000541773.1_Missense_Mutation_p.P933R	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	1034	Thyroglobulin type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00500}.				basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					GTCATCCCGGGGGGTGCCACC	0.617																																					p.P1034R		Atlas-SNP	.											.	NID2	201	.	0			c.C3101G						.						50	47	48					14																	52481921		2203	4300	6503	SO:0001583	missense	22795	exon15			TCCCGGGGGGTGC	AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.3101C>G	chr14.hg19:g.52481921G>C	ENSP00000216286:p.Pro1034Arg	127.0	0.0		119.0	58.0	NM_007361	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	hg19	CCDS9706.1	.	.	.	.	.	.	.	.	.	.	G	19.37	3.813751	0.70912	.	.	ENSG00000087303	ENST00000216286;ENST00000316204;ENST00000541773;ENST00000395707	T;T	0.61859	0.07;0.07	5.67	5.67	0.87782	Thyroglobulin type-1 (4);	0.095044	0.85682	D	0.000000	T	0.70945	0.3282	L	0.45228	1.405	0.47308	D	0.999386	D;D;D;D	0.76494	0.998;0.973;0.994;0.999	D;D;D;D	0.75484	0.979;0.918;0.954;0.986	T	0.69551	-0.5115	10	0.48119	T	0.1	.	19.3726	0.94495	0.0:0.0:1.0:0.0	.	628;933;1036;1034	E7EPP3;Q14112-2;Q5CZI2;Q14112	.;.;.;NID2_HUMAN	R	1034;628;933;1036	ENSP00000216286:P1034R;ENSP00000443730:P933R	ENSP00000216286:P1034R	P	-	2	0	NID2	51551671	1.000000	0.71417	0.067000	0.19924	0.370000	0.29829	9.339000	0.96797	2.680000	0.91292	0.655000	0.94253	CCC	.	.		0.617	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1			C	52481921	G	C	52481921	3	2	344	1	0	0	0	0	1	0	0	0	10424	1232	43	4	1058	4	NID2	14	52481921	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	2163562	52481921	54867619	997	48360										
GPR137C	283554	hgsc.bcm.edu	37	chr14	53100355	53100355	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtactgtttttccgggcacaGagattaaaccagaatttggt	10	7	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:53100355G>T	ENST00000321662.6	+	5	975	c.975G>T	c.(973-975)caG>caT	p.Q325H		NM_001099652.1	NP_001093122.1	Q8N3F9	G137C_HUMAN	G protein-coupled receptor 137C	325						integral component of membrane (GO:0016021)				NS(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	8	Breast(41;0.0716)					TCCGGGCACAGAGATTAAACC	0.358																																					p.Q325H		Atlas-SNP	.											.	GPR137C	24	.	0			c.G975T						.						101	94	96					14																	53100355		1831	4087	5918	SO:0001583	missense	283554	exon5			GGCACAGAGATTA	BX647179	CCDS45106.1	14q22.1	2012-08-10				ENSG00000180998			25445	protein-coding gene	gene with protein product							Standard	NM_001099652		Approved	DKFZp762F0713, TM7SF1L2	uc001wzu.4	Q8N3F9		ENST00000321662.6:c.975G>T	chr14.hg19:g.53100355G>T	ENSP00000315106:p.Gln325His	75.0	0.0		69.0	30.0	NM_001099652	Q86SM2	Missense_Mutation	SNP	ENST00000321662.6	hg19	CCDS45106.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.96|14.96	2.692640|2.692640	0.48202|0.48202	.|.	.|.	ENSG00000180998|ENSG00000180998	ENST00000542169|ENST00000321662	.|T	.|0.48522	.|0.81	5.55|5.55	4.66|4.66	0.58398|0.58398	.|.	.|0.048957	.|0.85682	.|D	.|0.000000	.|T	.|0.52677	.|0.1749	L|L	0.32530|0.32530	0.975|0.975	0.58432|0.58432	D|D	0.999999|0.999999	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.73380	.|0.98;0.98	.|T	.|0.45542	.|-0.9254	.|10	.|0.22109	.|T	.|0.4	-25.1548|-25.1548	10.6219|10.6219	0.45484|0.45484	0.1462:0.0:0.8538:0.0|0.1462:0.0:0.8538:0.0	.|.	.|325;154	.|Q8N3F9;B3KW22	.|G137C_HUMAN;.	X|H	295|325	.|ENSP00000315106:Q325H	.|ENSP00000315106:Q325H	E|Q	+|+	1|3	0|2	GPR137C|GPR137C	52170105|52170105	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	4.136000|4.136000	0.58004|0.58004	1.486000|1.486000	0.48398|0.48398	0.655000|0.655000	0.94253|0.94253	GAG|CAG	.	.		0.358	GPR137C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411685.1	XM_290615		T	53100355	G	T	53100355	3	4	344	1	0	0	0	0	1	0	0	0	6655	933	33	3	993	3	GPR137C	14	53100355	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	618434	53100355	54249185	998	48361										
DDHD1	80821	hgsc.bcm.edu	37	chr14	53521180	53521180	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agaatcgaggaagccagaacTgctatgtggaagggtctgtg	15	6	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:53521180T>A	ENST00000323669.5	-	11	2412	c.2413A>T	c.(2413-2415)Agt>Tgt	p.S805C	DDHD1_ENST00000555621.1_5'Flank|DDHD1_ENST00000357758.3_Missense_Mutation_p.S805C|DDHD1_ENST00000395606.1_Missense_Mutation_p.S812C	NM_001160148.1	NP_001153620.1	Q8NEL9	DDHD1_HUMAN	DDHD domain containing 1	805	DDHD. {ECO:0000255|PROSITE- ProRule:PRU00378}.				cell death (GO:0008219)|lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)	25	Breast(41;0.037)					AAGCCAGAACTGCTATGTGGA	0.423																																					p.S812C		Atlas-SNP	.											.	DDHD1	202	.	0			c.A2434T						.						206	154	171					14																	53521180		2203	4300	6503	SO:0001583	missense	80821	exon12			CAGAACTGCTATG	AB051492	CCDS9714.1, CCDS53895.1, CCDS53896.1	14q21	2012-11-23			ENSG00000100523	ENSG00000100523			19714	protein-coding gene	gene with protein product	"phosphatidic acid-preferring phospholipase A1"	614603	"spastic paraplegia 28 (autosomal recessive)"	SPG28		11214970, 20359546	Standard	NM_030637		Approved	KIAA1705, PA-PLA1	uc001xai.3	Q8NEL9	OTTHUMG00000140305	ENST00000323669.5:c.2413A>T	chr14.hg19:g.53521180T>A	ENSP00000327104:p.Ser805Cys	218.0	0.0		134.0	65.0	NM_001160147	G5E9D1|Q8WVH3|Q96LL2|Q9C0F8	Missense_Mutation	SNP	ENST00000323669.5	hg19	CCDS53895.1	.	.	.	.	.	.	.	.	.	.	T	17.30	3.355968	0.61293	.	.	ENSG00000100523	ENST00000323669;ENST00000395606;ENST00000357758;ENST00000395610	.	.	.	5.71	3.31	0.37934	DDHD (2);	0.306880	0.44688	D	0.000433	T	0.51975	0.1706	L	0.29908	0.895	0.37229	D	0.905598	P;P;P;P	0.50528	0.822;0.936;0.878;0.852	P;P;P;P	0.56343	0.645;0.694;0.796;0.584	T	0.57183	-0.7855	9	0.49607	T	0.09	-7.6271	9.9161	0.41434	0.0:0.1398:0.0:0.8602	.	201;812;805;805	Q2VYF2;G5E9D1;Q8NEL9;Q8NEL9-2	.;.;DDHD1_HUMAN;.	C	805;812;805;676	.	ENSP00000327104:S805C	S	-	1	0	DDHD1	52590930	1.000000	0.71417	1.000000	0.80357	0.478000	0.33099	1.941000	0.40233	0.938000	0.37419	0.528000	0.53228	AGT	.	.		0.423	DDHD1-003	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276901.1			A	53521180	T	A	53521180	3	1	344	1	0	0	0	0	1	0	0	0	4328	1580	55	4	301	4	DDHD1	14	53521180	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	420825	53521180	53828360	999	48362										
DDHD1	80821	hgsc.bcm.edu	37	chr14	53521253	53521253	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggcttcttctcatcttccatTgagtcttttgatgtttcaga	7	9	5	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:53521253T>C	ENST00000323669.5	-	11	2339	c.2340A>G	c.(2338-2340)tcA>tcG	p.S780S	DDHD1_ENST00000555621.1_5'Flank|DDHD1_ENST00000357758.3_Silent_p.S780S|DDHD1_ENST00000395606.1_Silent_p.S787S	NM_001160148.1	NP_001153620.1	Q8NEL9	DDHD1_HUMAN	DDHD domain containing 1	780	DDHD. {ECO:0000255|PROSITE- ProRule:PRU00378}.				cell death (GO:0008219)|lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)	25	Breast(41;0.037)					CATCTTCCATTGAGTCTTTTG	0.468																																					p.S787S		Atlas-SNP	.											.	DDHD1	202	.	0			c.A2361G						.						240	172	195					14																	53521253		2203	4300	6503	SO:0001819	synonymous_variant	80821	exon12			TTCCATTGAGTCT	AB051492	CCDS9714.1, CCDS53895.1, CCDS53896.1	14q21	2012-11-23			ENSG00000100523	ENSG00000100523			19714	protein-coding gene	gene with protein product	"phosphatidic acid-preferring phospholipase A1"	614603	"spastic paraplegia 28 (autosomal recessive)"	SPG28		11214970, 20359546	Standard	NM_030637		Approved	KIAA1705, PA-PLA1	uc001xai.3	Q8NEL9	OTTHUMG00000140305	ENST00000323669.5:c.2340A>G	chr14.hg19:g.53521253T>C		222.0	0.0		178.0	78.0	NM_001160147	G5E9D1|Q8WVH3|Q96LL2|Q9C0F8	Silent	SNP	ENST00000323669.5	hg19	CCDS53895.1																																																																																			.	.		0.468	DDHD1-003	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276901.1			C	53521253	T	C	53521253	2	2	344	1	0	0	0	0	0	0	0	1	4328	1799	63	2		2	DDHD1	14	53521253	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	73	53521253	53828287	1000	48363										
C14orf105	55195	hgsc.bcm.edu	37	chr14	57960276	57960276	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcccttccaaggctttattcTggtcctgcagtcttgccagt	9	13	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:57960276T>C	ENST00000216445.3	-	1	294	c.158A>G	c.(157-159)cAg>cGg	p.Q53R	C14orf105_ENST00000534126.1_Missense_Mutation_p.Q53R|C14orf105_ENST00000422976.2_Missense_Mutation_p.Q53R|C14orf105_ENST00000526336.1_Missense_Mutation_p.Q53R	NM_001283057.1|NM_018168.2	NP_001269986.1|NP_060638.2	Q9NVL8	CN105_HUMAN	chromosome 14 open reading frame 105	53										breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)	11						GGCTTTATTCTGGTCCTGCAG	0.438																																					p.Q53R		Atlas-SNP	.											.	C14orf105	26	.	0			c.A158G						.						130	132	132					14																	57960276		2203	4300	6503	SO:0001583	missense	55195	exon1			TTATTCTGGTCCT	AK001512	CCDS9730.1, CCDS61458.1, CCDS61459.1	14q22.2	2012-09-25			ENSG00000100557	ENSG00000100557			20189	protein-coding gene	gene with protein product							Standard	XM_005267806		Approved	FLJ10650	uc001xcy.2	Q9NVL8	OTTHUMG00000140317	ENST00000216445.3:c.158A>G	chr14.hg19:g.57960276T>C	ENSP00000216445:p.Gln53Arg	43.0	0.0		47.0	20.0	NM_018168	Q53G04	Missense_Mutation	SNP	ENST00000216445.3	hg19	CCDS9730.1	.	.	.	.	.	.	.	.	.	.	T	2.002	-0.429156	0.04701	.	.	ENSG00000100557	ENST00000216445;ENST00000422976;ENST00000534126;ENST00000526336	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	5.16	-10.3	0.00346	.	0.855302	0.10195	N	0.704114	T	0.12646	0.0307	N	0.04203	-0.255	0.09310	N	1	B;B;B	0.11235	0.004;0.001;0.001	B;B;B	0.13407	0.009;0.001;0.001	T	0.16988	-1.0384	10	0.10636	T	0.68	1.6089	6.5085	0.22208	0.0867:0.0951:0.0869:0.7313	.	53;53;53	F5GWJ3;E9PSE9;Q9NVL8	.;.;CN105_HUMAN	R	53	ENSP00000216445:Q53R;ENSP00000392368:Q53R;ENSP00000434003:Q53R;ENSP00000436517:Q53R	ENSP00000216445:Q53R	Q	-	2	0	C14orf105	57030029	0.000000	0.05858	0.001000	0.08648	0.989000	0.77384	-2.572000	0.00912	-2.287000	0.00669	0.455000	0.32223	CAG	.	.		0.438	C14orf105-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276921.2	NM_018168		C	57960276	T	C	57960276	3	2	344	1	0	0	0	0	1	0	0	0	1739	1580	55	2	756	2	C14orf105	14	57960276	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	4439023	57960276	49389264	1001	48364										
KIAA0586	9786	hgsc.bcm.edu	37	chr14	58924599	58924599	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aagattttgagaggagtacaAaacaataaaaaagtacttga	8	3	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:58924599A>G	ENST00000556134.1	+	12	1714	c.1440A>G	c.(1438-1440)caA>caG	p.Q480Q	KIAA0586_ENST00000261244.5_Silent_p.Q495Q|KIAA0586_ENST00000538571.2_3'UTR|KIAA0586_ENST00000423743.3_Silent_p.Q451Q|KIAA0586_ENST00000354386.6_Silent_p.Q548Q	NM_001244190.1|NM_001244193.1	NP_001231119.1|NP_001231122.1	Q9BVV6	TALD3_HUMAN	KIAA0586	480	Required for centrosomal localization. {ECO:0000250}.				cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|regulation of establishment of protein localization (GO:0070201)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				endometrium(4)|kidney(6)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GAGGAGTACAAAACAATAAAA	0.363																																					p.Q548Q		Atlas-SNP	.											.	KIAA0586	180	.	0			c.A1644G						.						66	62	63					14																	58924599		1819	4074	5893	SO:0001819	synonymous_variant	9786	exon13			AGTACAAAACAAT	AB011158	CCDS45115.1, CCDS58320.1, CCDS58321.1, CCDS58322.1, CCDS73639.1	14q23.1	2012-12-06			ENSG00000100578	ENSG00000100578			19960	protein-coding gene	gene with protein product		610178				16702409	Standard	NM_014749		Approved	Talpid3	uc010trr.2	Q9BVV6	OTTHUMG00000171141	ENST00000556134.1:c.1440A>G	chr14.hg19:g.58924599A>G		100.0	0.0		71.0	33.0	NM_001244189	B4DZB6|E7EWM8|J3KQH9|O60328|Q6NYC6|Q6UV20	Silent	SNP	ENST00000556134.1	hg19	CCDS58321.1																																																																																			.	.		0.363	KIAA0586-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000411887.1	NM_014749		G	58924599	A	G	58924599	2	3	344	1	0	0	0	0	0	0	0	1	8195	11	1	2		2	KIAA0586	14	58924599	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	964323	58924599	48424941	1002	48365										
MTHFD1	4522	hgsc.bcm.edu	37	chr14	64886605	64886605	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aggggagtggatcaaacctgGggcaatagtcatcgactgtg	15	7	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:64886605G>T	ENST00000545908.1	+	8	1086	c.857G>T	c.(856-858)gGg>gTg	p.G286V	MTHFD1_ENST00000216605.8_Missense_Mutation_p.G230V			P11586	C1TC_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase	230	Methylenetetrahydrofolate dehydrogenase and cyclohydrolase.				folic acid metabolic process (GO:0046655)|folic acid-containing compound biosynthetic process (GO:0009396)|histidine biosynthetic process (GO:0000105)|methionine biosynthetic process (GO:0009086)|one-carbon metabolic process (GO:0006730)|purine nucleotide biosynthetic process (GO:0006164)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|formate-tetrahydrofolate ligase activity (GO:0004329)|methenyltetrahydrofolate cyclohydrolase activity (GO:0004477)|methylenetetrahydrofolate dehydrogenase (NADP+) activity (GO:0004488)|methylenetetrahydrofolate dehydrogenase [NAD(P)+] activity (GO:0004486)			endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	30				OV - Ovarian serous cystadenocarcinoma(108;8.7e-12)|all cancers(60;3.29e-11)|BRCA - Breast invasive adenocarcinoma(234;0.0488)	Tetrahydrofolic acid(DB00116)	ATCAAACCTGGGGCAATAGTC	0.473																																					p.G230V	Colon(18;220 581 13419 18191 31512)|GBM(126;343 1658 28700 44425 52519)	Atlas-SNP	.											.	MTHFD1	61	.	0			c.G689T						.						127	114	118					14																	64886605		2203	4300	6503	SO:0001583	missense	4522	exon8			AACCTGGGGCAAT	J04031	CCDS9763.1	14q24	2004-12-13			ENSG00000100714	ENSG00000100714	1.5.1.15, 3.5.4.-		7432	protein-coding gene	gene with protein product		172460		MTHFC, MTHFD		3053686, 2786332	Standard	NM_005956		Approved		uc001xhb.3	P11586	OTTHUMG00000141309	ENST00000545908.1:c.857G>T	chr14.hg19:g.64886605G>T	ENSP00000438588:p.Gly286Val	106.0	0.0		87.0	47.0	NM_005956	B2R5Y2|G3V2B8|Q86VC9|Q9BVP5	Missense_Mutation	SNP	ENST00000545908.1	hg19		.	.	.	.	.	.	.	.	.	.	G	29.1	4.977851	0.92982	.	.	ENSG00000100714	ENST00000545908;ENST00000555709;ENST00000216605;ENST00000555252	T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04	5.74	5.74	0.90152	Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.89966	0.6868	H	0.99927	4.965	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.996;0.995;1.0	D	0.94492	0.7702	10	0.87932	D	0	-19.1945	18.1027	0.89510	0.0:0.0:1.0:0.0	.	286;230;230	F5H2F4;P11586;G3V2B8	.;C1TC_HUMAN;.	V	286;230;286;210	ENSP00000438588:G286V;ENSP00000450560:G230V;ENSP00000216605:G286V;ENSP00000451309:G210V	ENSP00000216605:G230V	G	+	2	0	MTHFD1	63956358	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.869000	0.99810	2.716000	0.92895	0.650000	0.86243	GGG	.	.		0.473	MTHFD1-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000412167.1			T	64886605	G	T	64886605	3	4	344	1	0	0	0	0	1	0	0	0	9936	1232	43	3	719	3	MTHFD1	14	64886605	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	5962006	64886605	42462935	1003	48366										
PLEK2	26499	hgsc.bcm.edu	37	chr14	67857415	67857415	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtaatgcaggaaagctggatCcttccttagaacaaagcgac	10	9	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:67857415C>T	ENST00000216446.4	-	7	960	c.820G>A	c.(820-822)Gat>Aat	p.D274N		NM_016445.1	NP_057529.1	Q9NYT0	PLEK2_HUMAN	pleckstrin 2	274	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|intracellular signal transduction (GO:0035556)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	15				all cancers(60;0.000728)|OV - Ovarian serous cystadenocarcinoma(108;0.00593)|BRCA - Breast invasive adenocarcinoma(234;0.00953)		AAAGCTGGATCCTTCCTTAGA	0.512																																					p.D274N		Atlas-SNP	.											.	PLEK2	23	.	0			c.G820A						.						215	183	194					14																	67857415		2203	4300	6503	SO:0001583	missense	26499	exon7			CTGGATCCTTCCT	AF228603	CCDS9782.1	14q23.3	2014-08-12			ENSG00000100558	ENSG00000100558		"Pleckstrin homology (PH) domain containing"	19238	protein-coding gene	gene with protein product		608007				11911883, 17658464	Standard	NM_016445		Approved		uc001xjh.1	Q9NYT0	OTTHUMG00000171247	ENST00000216446.4:c.820G>A	chr14.hg19:g.67857415C>T	ENSP00000216446:p.Asp274Asn	115.0	0.0		92.0	36.0	NM_016445	Q96JT0	Missense_Mutation	SNP	ENST00000216446.4	hg19	CCDS9782.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.973162	0.74246	.	.	ENSG00000100558	ENST00000216446;ENST00000554395	T;T	0.30182	2.98;1.54	5.78	5.78	0.91487	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.430079	0.28203	N	0.016213	T	0.29684	0.0741	L	0.42632	1.34	0.49798	D	0.999822	B	0.14012	0.009	B	0.23150	0.044	T	0.07028	-1.0794	10	0.15952	T	0.53	-23.8295	18.1919	0.89809	0.0:1.0:0.0:0.0	.	274	Q9NYT0	PLEK2_HUMAN	N	274;174	ENSP00000216446:D274N;ENSP00000450892:D174N	ENSP00000216446:D274N	D	-	1	0	PLEK2	66927168	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	4.172000	0.58243	2.724000	0.93272	0.555000	0.69702	GAT	.	.		0.512	PLEK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412547.2			T	67857415	C	T	67857415	3	4	344	1	0	0	0	0	1	0	0	0	12063	855	30	3	253	3	PLEK2	14	67857415	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	2970810	67857415	39492125	1004	48367										
RAD51L1	5890	hgsc.bcm.edu	37	chr14	68758622	68758622	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttatcttgacgaatcagattAcaacccatctgagtggagcc	8	10	3	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:68758622A>G	ENST00000487270.1	+	8	826	c.778A>G	c.(778-780)Aca>Gca	p.T260A	RAD51B_ENST00000471583.1_Missense_Mutation_p.T260A|RAD51B_ENST00000469165.2_3'UTR|RAD51B_ENST00000487861.1_Missense_Mutation_p.T260A|RAD51B_ENST00000488612.1_Missense_Mutation_p.T260A|RAD51B_ENST00000390683.3_Missense_Mutation_p.T260A	NM_133509.3	NP_598193.2	O15315	RA51B_HUMAN	RAD51 paralog B	260					ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|reciprocal meiotic recombination (GO:0007131)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Rad51B-Rad51C-Rad51D-XRCC2 complex (GO:0033063)|replication fork (GO:0005657)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|single-stranded DNA binding (GO:0003697)		HMGA2/RAD51B(11)	breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	11						GAATCAGATTACAACCCATCT	0.493								Direct reversal of damage																													p.T260A		Atlas-SNP	.											.	RAD51B	80	.	0			c.A778G						.						130	122	124					14																	68758622		2203	4300	6503	SO:0001583	missense	5890	exon8			CAGATTACAACCC	U84138	CCDS9789.1, CCDS9790.1	14q23-q24.2	2013-07-02	2013-07-02	2011-07-01	ENSG00000182185	ENSG00000182185			9822	protein-coding gene	gene with protein product		602948	"RAD51 (S. cerevisiae)-like 1", "RAD51-like 1 (S. cerevisiae)", "RAD51 homolog B (S. cerevisiae)"	RAD51L1		6261043, 9207106	Standard	NM_002877		Approved	REC2, hREC2, R51H2	uc001xkf.2	O15315	OTTHUMG00000157530	ENST00000487270.1:c.778A>G	chr14.hg19:g.68758622A>G	ENSP00000419471:p.Thr260Ala	47.0	0.0		44.0	20.0	NM_133509	O60914|O75210|Q3Y4F8|Q6FHX8|Q86SY3|Q86SY4|Q86TR0|Q86U92|Q86U93|Q86U94|Q8N6H4|Q9UPL5	Missense_Mutation	SNP	ENST00000487270.1	hg19	CCDS9789.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.363562	0.82353	.	.	ENSG00000182185	ENST00000487861;ENST00000471583;ENST00000487270;ENST00000488612;ENST00000390683;ENST00000402498;ENST00000342389	T;T;T;T;T	0.38401	1.14;1.14;1.14;1.14;1.14	5.57	5.57	0.84162	DNA recombination/repair protein RecA/RadB, ATP-binding domain (1);ATPase, AAA+ type, core (1);DNA recombination and repair protein Rad51, C-terminal (1);	0.000000	0.52532	D	0.000075	T	0.51500	0.1678	L	0.39692	1.235	0.32850	D	0.506519	P;D;D;D;D	0.76494	0.91;0.995;0.999;0.981;0.987	P;D;D;P;D	0.83275	0.74;0.91;0.996;0.814;0.944	T	0.63211	-0.6688	10	0.66056	D	0.02	-31.5054	14.606	0.68478	1.0:0.0:0.0:0.0	.	260;260;260;260;260	C9JYJ0;O15315-4;O15315;O15315-1;O15315-2	.;.;RA51B_HUMAN;.;.	A	260	ENSP00000419881:T260A;ENSP00000418859:T260A;ENSP00000419471:T260A;ENSP00000420061:T260A;ENSP00000375101:T260A	ENSP00000343531:T260A	T	+	1	0	RAD51B	67828375	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.993000	0.70616	2.244000	0.73946	0.533000	0.62120	ACA	.	.		0.493	RAD51B-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000349063.1			G	68758622	A	G	68758622	3	3	344	1	0	0	0	0	1	0	0	0	13004	391	14	2	804	2	RAD51L1	14	68758622	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	901207	68758622	38590918	1005	48368										
GALNTL1	57452	hgsc.bcm.edu	37	chr14	69727044	69727044	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccaatgccatcgccatcctgAccgtagcctggatcctgggc	10	16	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:69727044A>T	ENST00000337827.4	+	1	364	c.37A>T	c.(37-39)Acc>Tcc	p.T13S	GALNT16_ENST00000448469.3_Missense_Mutation_p.T13S|GALNT16_ENST00000554858.1_3'UTR|GALNT16_ENST00000553669.1_Missense_Mutation_p.T13S|RP11-363J20.2_ENST00000556316.1_lincRNA	NM_001168368.1|NM_020692.2	NP_001161840.1|NP_065743.2	Q8N428	GLT16_HUMAN	polypeptide N-acetylgalactosaminyltransferase 16	13					protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)										CGCCATCCTGACCGTAGCCTG	0.706																																					p.T13S		Atlas-SNP	.											.	GALNT16	8	.	0			c.A37T						.						95	72	80					14																	69727044		2203	4300	6503	SO:0001583	missense	57452	exon1			ATCCTGACCGTAG	AB032956	CCDS32107.1	14q24.1	2014-03-13	2014-03-13	2013-01-25	ENSG00000100626	ENSG00000100626	2.4.1.41	"Glycosyltransferase family 2 domain containing"	23233	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 16"	615132	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 1", "UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 16"	GALNTL1		10574461, 22186971	Standard	NM_020692		Approved	KIAA1130, GalNAc-T16	uc010aqu.2	Q8N428	OTTHUMG00000171231	ENST00000337827.4:c.37A>T	chr14.hg19:g.69727044A>T	ENSP00000336729:p.Thr13Ser	68.0	0.0		49.0	26.0	NM_001168368	Q4KMG3|Q58A55|Q9ULT9	Missense_Mutation	SNP	ENST00000337827.4	hg19	CCDS32107.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.017454	0.75161	.	.	ENSG00000100626	ENST00000337827;ENST00000448469;ENST00000553669	T;T;T	0.56103	0.61;0.61;0.48	3.72	3.72	0.42706	.	0.172006	0.40144	N	0.001171	T	0.50820	0.1638	L	0.27053	0.805	0.52501	D	0.999955	D;D	0.63880	0.993;0.993	D;D	0.65443	0.935;0.935	T	0.47459	-0.9116	10	0.02654	T	1	.	12.513	0.56015	1.0:0.0:0.0:0.0	.	13;13	Q8N428;Q58A55	GLTL1_HUMAN;.	S	13	ENSP00000336729:T13S;ENSP00000402970:T13S;ENSP00000451200:T13S	ENSP00000336729:T13S	T	+	1	0	GALNTL1	68796797	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.820000	0.69250	1.672000	0.50884	0.374000	0.22700	ACC	.	.		0.706	GALNT16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412434.1	NM_001168368		T	69727044	A	T	69727044	3	4	344	1	0	0	0	0	1	0	0	0	6229	275	10	4	39	4	GALNTL1	14	69727044	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	968422	69727044	37622496	1006	48369										
SIPA1L1	26037	hgsc.bcm.edu	37	chr14	72200517	72200517	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccaacctggtagatgctgccAaagcctatgagggtgagtcc	12	11	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:72200517A>G	ENST00000555818.1	+	19	5407	c.5059A>G	c.(5059-5061)Aaa>Gaa	p.K1687E	SIPA1L1_ENST00000381232.3_Missense_Mutation_p.K1666E|SIPA1L1_ENST00000537413.1_Missense_Mutation_p.K1141E|SIPA1L1_ENST00000358550.2_Missense_Mutation_p.K1666E|SIPA1L1_ENST00000554874.1_3'UTR	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	1687					actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		AGATGCTGCCAAAGCCTATGA	0.582																																					p.K1687E		Atlas-SNP	.											.	SIPA1L1	219	.	0			c.A5059G						.						87	68	74					14																	72200517		2203	4300	6503	SO:0001583	missense	26037	exon19			GCTGCCAAAGCCT	AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.5059A>G	chr14.hg19:g.72200517A>G	ENSP00000450832:p.Lys1687Glu	31.0	0.0		34.0	13.0	NM_015556	J3KP19|O95321|Q9UDU4|Q9UNU4	Missense_Mutation	SNP	ENST00000555818.1	hg19	CCDS9807.1	.	.	.	.	.	.	.	.	.	.	A	29.7	5.028872	0.93518	.	.	ENSG00000197555	ENST00000381232;ENST00000555818;ENST00000358550;ENST00000537413	T;T;T;T	0.36878	1.23;1.23;1.23;1.23	5.09	5.09	0.68999	.	0.088505	0.85682	D	0.000000	T	0.57666	0.2069	L	0.61218	1.895	0.58432	D	0.999997	P;P;P;P;D	0.89917	0.792;0.789;0.955;0.885;1.0	B;P;P;P;D	0.87578	0.318;0.507;0.88;0.57;0.998	T	0.61118	-0.7127	10	0.66056	D	0.02	-23.3941	15.1848	0.72993	1.0:0.0:0.0:0.0	.	1141;1687;1141;1666;1687	F5GYF8;A6H8W6;B4DYX7;O43166-2;O43166	.;.;.;.;SI1L1_HUMAN	E	1666;1687;1666;1141	ENSP00000370630:K1666E;ENSP00000450832:K1687E;ENSP00000351352:K1666E;ENSP00000440682:K1141E	ENSP00000351352:K1687E	K	+	1	0	SIPA1L1	71270270	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.928000	0.70088	2.044000	0.60594	0.459000	0.35465	AAA	.	.		0.582	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556		G	72200517	A	G	72200517	3	3	344	1	0	0	0	0	1	0	0	0	14344	131	5	2	5129	2	SIPA1L1	14	72200517	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2473473	72200517	35149023	1007	48370										
C14orf45	80127	hgsc.bcm.edu	37	chr14	74514746	74514757	+	In_Frame_Del	DEL	AAGAGAGTCATA	AAGAGAGTCATA	-													0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaaaaactcccagaagttgcAagagagtcatactttacttt							TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	AAGAGAGTCATA	AAGAGAGTCATA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:74514746_74514757delAAGAGAGTCATA	ENST00000394009.3	+	7	884_895	c.761_772delAAGAGAGTCATA	c.(760-774)caagagagtcatact>cct	p.254_258QESHT>P	AC005484.5_ENST00000492026.1_RNA|CCDC176_ENST00000553773.1_5'UTR|CCDC176_ENST00000489323.1_3'UTR	NM_025057.2	NP_079333.2	Q8ND07	BBOF1_HUMAN	coiled-coil domain containing 176	254					motile cilium assembly (GO:0044458)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)											CAGAAGTTGCAAGAGAGTCATACTTTACTTTT	0.354																																					p.254_257del		Atlas-Indel,Pindel	.											.	.	.	.	0			c.760_771del						.																																			SO:0001651	inframe_deletion	80127	exon7			.	BI457605	CCDS32119.2	14q24.3	2013-01-04	2012-09-25	2012-09-25	ENSG00000119636	ENSG00000119636			19855	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 45"	C14orf45			Standard	NM_025057		Approved		uc010tup.2	Q8ND07	OTTHUMG00000152786	ENST00000394009.3:c.761_772delAAGAGAGTCATA	chr14.hg19:g.74514746_74514757delAAGAGAGTCATA	ENSP00000377577:p.Gln254_Thr258delinsPro	227.0	0.0		149.0	24.0	NM_025057	Q0P604|Q9H5P8	In_Frame_Del	DEL	ENST00000394009.3	hg19	CCDS32119.2																																																																																			.	.		0.354	CCDC176-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327863.1	NM_025057		-	74514757	AAGAGAGTCATA	-	74514746	7	5	344	1	0	1	0	1	0	0	0	0	1777	130	5	0	787	0	C14orf45	14	74514746	In_Frame_Del	DEL	AAGAGAGTCATA	TCGA-UB-A7MB-01A-11D-A33Q-10	2314229	74514746	32834794	1008	48371										
LTBP2	4053	hgsc.bcm.edu	37	chr14	75019087	75019087	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctccgttcaggcaggggatcTggcagaaatctgcaacatca	11	11	4	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:75019087T>A	ENST00000261978.4	-	6	1588	c.1202A>T	c.(1201-1203)cAg>cTg	p.Q401L	LTBP2_ENST00000557425.1_Intron|CTD-2207P18.1_ENST00000554552.1_lincRNA|LTBP2_ENST00000556690.1_Missense_Mutation_p.Q401L	NM_000428.2	NP_000419.1	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding protein 2	401	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				protein secretion (GO:0009306)|protein targeting (GO:0006605)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|liver(1)|lung(29)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)		GCAGGGGATCTGGCAGAAATC	0.622																																					p.Q401L		Atlas-SNP	.											.	LTBP2	158	.	0			c.A1202T						.						29	30	30					14																	75019087		2203	4300	6503	SO:0001583	missense	4053	exon6			GGGATCTGGCAGA		CCDS9831.1	14q24.3	2011-10-20	2001-12-04			ENSG00000119681		"Latent transforming growth factor, beta binding proteins"	6715	protein-coding gene	gene with protein product		602091	"chromosome 14 open reading frame 141"	LTBP3, C14orf141		7798248	Standard	NM_000428		Approved		uc001xqa.3	Q14767		ENST00000261978.4:c.1202A>T	chr14.hg19:g.75019087T>A	ENSP00000261978:p.Gln401Leu	26.0	0.0		23.0	12.0	NM_000428	Q99907|Q9NS51	Missense_Mutation	SNP	ENST00000261978.4	hg19	CCDS9831.1	.	.	.	.	.	.	.	.	.	.	t	21.9	4.213831	0.79352	.	.	ENSG00000119681	ENST00000261978;ENST00000556690	T;T	0.32988	1.43;1.43	4.9	4.9	0.64082	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.37906	N	0.001885	T	0.38506	0.1043	N	0.22421	0.69	0.34902	D	0.746568	D	0.64830	0.994	D	0.74348	0.983	T	0.46952	-0.9154	10	0.27082	T	0.32	.	13.127	0.59360	0.0:0.0:0.0:1.0	.	401	Q14767	LTBP2_HUMAN	L	401	ENSP00000261978:Q401L;ENSP00000451477:Q401L	ENSP00000261978:Q401L	Q	-	2	0	LTBP2	74088840	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.458000	0.66679	1.822000	0.53115	0.449000	0.29647	CAG	.	.		0.622	LTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413595.1	NM_000428		A	75019087	T	A	75019087	3	1	344	1	0	0	0	0	1	0	0	0	9083	1580	55	4	4387	4	LTBP2	14	75019087	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	504341	75019087	32330453	1009	48372										
MLH3	27030	hgsc.bcm.edu	37	chr14	75516322	75516322	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tatggccaaaccagaacgcaAtttggcttgtacttcaactg	8	10	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:75516322A>G	ENST00000556740.1	-	1	72	c.37T>C	c.(37-39)Ttg>Ctg	p.L13L	MLH3_ENST00000544985.1_5'Flank|MLH3_ENST00000555671.1_5'Flank|MLH3_ENST00000238662.7_Silent_p.L13L|MLH3_ENST00000556257.1_Silent_p.L13L|MLH3_ENST00000380968.2_5'UTR|MLH3_ENST00000355774.2_Silent_p.L13L			Q9UHC1	MLH3_HUMAN	mutL homolog 3	13					ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44				BRCA - Breast invasive adenocarcinoma(234;0.00688)		CCAGAACGCAATTTGGCTTGT	0.463								Mismatch excision repair (MMR)																													p.L13L		Atlas-SNP	.											.	MLH3	200	.	0			c.T37C						.						56	53	54					14																	75516322		2203	4300	6503	SO:0001819	synonymous_variant	27030	exon2			AACGCAATTTGGC	AF195657	CCDS9837.1, CCDS32123.1	14q24.3	2014-09-17	2013-09-12			ENSG00000119684			7128	protein-coding gene	gene with protein product		604395	"mutL (E. coli) homolog 3", "mutL homolog 3 (E. coli)"			10615123	Standard	XR_245681		Approved		uc001xrd.1	Q9UHC1		ENST00000556740.1:c.37T>C	chr14.hg19:g.75516322A>G		79.0	0.0		64.0	36.0	NM_014381	P49751|Q56DK9|Q9P292|Q9UHC0	Silent	SNP	ENST00000556740.1	hg19	CCDS32123.1																																																																																			.	.		0.463	MLH3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415006.1	NM_014381		G	75516322	A	G	75516322	2	3	344	1	0	0	0	0	0	0	0	1	9627	98	4	2		2	MLH3	14	75516322	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	497235	75516322	31833218	1010	48373										
FOS	2353	hgsc.bcm.edu	37	chr14	75747981	75747981	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cggtggtcacctgtactcccAgctgcactgcttacacgtct	9	15	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:75747981A>T	ENST00000303562.4	+	4	1206	c.997A>T	c.(997-999)Agc>Tgc	p.S333C	FOS_ENST00000535987.1_Missense_Mutation_p.S297C|FOS_ENST00000555686.1_Missense_Mutation_p.S219C|FOS_ENST00000555347.1_Missense_Mutation_p.S185C	NM_005252.3	NP_005243.1	P01100	FOS_HUMAN	FBJ murine osteosarcoma viral oncogene homolog	333					aging (GO:0007568)|cellular response to calcium ion (GO:0071277)|cellular response to extracellular stimulus (GO:0031668)|cellular response to hormone stimulus (GO:0032870)|cellular response to reactive oxygen species (GO:0034614)|conditioned taste aversion (GO:0001661)|DNA methylation (GO:0006306)|Fc-epsilon receptor signaling pathway (GO:0038095)|female pregnancy (GO:0007565)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nervous system development (GO:0007399)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to cold (GO:0009409)|response to corticosterone (GO:0051412)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to gravity (GO:0009629)|response to light stimulus (GO:0009416)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to toxic substance (GO:0009636)|skeletal muscle cell differentiation (GO:0035914)|sleep (GO:0030431)|SMAD protein signal transduction (GO:0060395)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	double-stranded DNA binding (GO:0003690)|R-SMAD binding (GO:0070412)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	12		all_lung(585;0.0138)|all_epithelial(191;0.0263)|all_neural(303;0.112)		BRCA - Breast invasive adenocarcinoma(234;0.0117)	Nadroparin(DB08813)|Pseudoephedrine(DB00852)	CTGTACTCCCAGCTGCACTGC	0.637																																					p.S333C		Atlas-SNP	.											.	FOS	30	.	0			c.A997T						.						77	81	79					14																	75747981		2203	4300	6503	SO:0001583	missense	2353	exon4			ACTCCCAGCTGCA	K00650	CCDS9841.1	14q24.3	2013-01-10	2009-07-23			ENSG00000170345		"basic leucine zipper proteins"	3796	protein-coding gene	gene with protein product		164810	"v-fos FBJ murine osteosarcoma viral oncogene homolog"			16123044, 16055710, 15926923	Standard	NM_005252		Approved	c-fos, AP-1	uc001xrn.3	P01100		ENST00000303562.4:c.997A>T	chr14.hg19:g.75747981A>T	ENSP00000306245:p.Ser333Cys	39.0	0.0		34.0	16.0	NM_005252	A8K4E2|B4DQ65|P18849	Missense_Mutation	SNP	ENST00000303562.4	hg19	CCDS9841.1	.	.	.	.	.	.	.	.	.	.	A	7.828	0.719199	0.15372	.	.	ENSG00000170345	ENST00000303562;ENST00000535987;ENST00000555686;ENST00000555347	T;T;T	0.67345	0.3;0.74;-0.26	5.51	3.1	0.35709	.	0.642369	0.17200	N	0.183154	T	0.45756	0.1358	N	0.16368	0.405	0.27049	N	0.963831	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.34054	-0.9844	10	0.48119	T	0.1	-28.1479	5.1648	0.15079	0.688:0.0:0.149:0.163	.	297;333	B4DQ65;P01100	.;FOS_HUMAN	C	333;297;219;185	ENSP00000306245:S333C;ENSP00000442268:S297C;ENSP00000452590:S219C	ENSP00000306245:S333C	S	+	1	0	FOS	74817734	0.806000	0.28996	0.993000	0.49108	0.869000	0.49853	1.398000	0.34554	0.365000	0.24400	-0.371000	0.07208	AGC	.	.		0.637	FOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415044.1	NM_005252		T	75747981	A	T	75747981	3	4	344	1	0	0	0	0	1	0	0	0	5993	188	7	4	1011	4	FOS	14	75747981	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	231659	75747981	31601559	1011	48374										
C14orf174	161394	hgsc.bcm.edu	37	chr14	77844096	77844096	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agaggtaaagtcggaaacatCcagagagatgggagagtttt	14	4	0	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:77844096C>G	ENST00000216471.4	+	1	621	c.335C>G	c.(334-336)tCc>tGc	p.S112C	TMED8_ENST00000216468.7_5'Flank|SAMD15_ENST00000533095.2_Intron	NM_001010860.1	NP_001010860.1	Q9P1V8	SAM15_HUMAN	sterile alpha motif domain containing 15	112										breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						TCGGAAACATCCAGAGAGATG	0.498																																					p.S112C		Atlas-SNP	.											.	SAMD15	60	.	0			c.C335G						.						146	158	154					14																	77844096		2203	4300	6503	SO:0001583	missense	161394	exon1			AAACATCCAGAGA	AK093282	CCDS32126.1	14q24.3	2013-01-10	2010-10-20	2010-10-20	ENSG00000100583	ENSG00000100583		"Sterile alpha motif (SAM) domain containing"	18631	protein-coding gene	gene with protein product			"family with sequence similarity 15, member A", "chromosome 14 open reading frame 174"	FAM15A, C14orf174			Standard	XM_006720069		Approved	FLJ35963	uc001xtq.1	Q9P1V8		ENST00000216471.4:c.335C>G	chr14.hg19:g.77844096C>G	ENSP00000216471:p.Ser112Cys	85.0	0.0		61.0	24.0	NM_001010860	Q2M3P3	Missense_Mutation	SNP	ENST00000216471.4	hg19	CCDS32126.1	.	.	.	.	.	.	.	.	.	.	C	12.38	1.921277	0.33908	.	.	ENSG00000100583	ENST00000216471	T	0.35605	1.3	4.82	-3.41	0.04839	.	3.816370	0.01056	N	0.004544	T	0.32194	0.0821	L	0.40543	1.245	0.09310	N	1	P	0.52316	0.952	P	0.44447	0.45	T	0.41840	-0.9486	10	0.54805	T	0.06	11.1824	6.8559	0.24040	0.1277:0.2842:0.0:0.5881	.	112	Q9P1V8	SAM15_HUMAN	C	112	ENSP00000216471:S112C	ENSP00000216471:S112C	S	+	2	0	SAMD15	76913849	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.355000	0.07671	-0.776000	0.04578	-0.349000	0.07799	TCC	.	.		0.498	SAMD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394587.2	NM_001010860		G	77844096	C	G	77844096	3	3	344	1	0	0	0	0	1	0	0	0	1761	855	30	4	337	4	C14orf174	14	77844096	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	2096115	77844096	29505444	1012	48375										
FLRT2	23768	hgsc.bcm.edu	37	chr14	86089087	86089087	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaaacttcccacgattcctgActgggatggcagagaaagag	12	9	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:86089087A>G	ENST00000330753.4	+	2	1996	c.1229A>G	c.(1228-1230)gAc>gGc	p.D410G	FLRT2_ENST00000554746.1_Missense_Mutation_p.D410G	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	410					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		ACGATTCCTGACTGGGATGGC	0.507																																					p.D410G		Atlas-SNP	.											.	FLRT2	168	.	0			c.A1229G						.						71	72	71					14																	86089087		2203	4300	6503	SO:0001583	missense	23768	exon2			TTCCTGACTGGGA	AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070		"Fibronectin type III domain containing"	3761	protein-coding gene	gene with protein product		604807				10644439, 16872596	Standard	XM_005267490		Approved		uc001xvr.3	O43155		ENST00000330753.4:c.1229A>G	chr14.hg19:g.86089087A>G	ENSP00000332879:p.Asp410Gly	211.0	0.0		189.0	75.0	NM_013231	A0AV84|B7ZLP3	Missense_Mutation	SNP	ENST00000330753.4	hg19	CCDS9877.1	.	.	.	.	.	.	.	.	.	.	A	10.30	1.312314	0.23908	.	.	ENSG00000185070	ENST00000330753;ENST00000554746;ENST00000535800	T;T	0.56776	0.44;0.44	6.17	5.02	0.67125	.	0.529823	0.22337	N	0.061396	T	0.32346	0.0826	N	0.08118	0	0.32321	N	0.562389	B	0.19817	0.039	B	0.15052	0.012	T	0.30268	-0.9984	10	0.22109	T	0.4	-11.0571	13.779	0.63071	0.872:0.1279:0.0:0.0	.	410	O43155	FLRT2_HUMAN	G	410;410;63	ENSP00000332879:D410G;ENSP00000451050:D410G	ENSP00000332879:D410G	D	+	2	0	FLRT2	85158840	0.986000	0.35501	0.587000	0.28692	0.981000	0.71138	1.821000	0.39041	1.132000	0.42129	0.533000	0.62120	GAC	.	.		0.507	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1			G	86089087	A	G	86089087	3	3	344	1	0	0	0	0	1	0	0	0	5947	275	10	2	1231	2	FLRT2	14	86089087	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	8244991	86089087	21260453	1013	48376										
GALC	2581	hgsc.bcm.edu	37	chr14	88401194	88401194	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgtctgtccacagagacttgTcattcagcatgccagaggtg	11	10	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:88401194T>A	ENST00000261304.2	-	17	2046	c.1940A>T	c.(1939-1941)gAc>gTc	p.D647V	GALC_ENST00000393568.4_Missense_Mutation_p.D624V|GALC_ENST00000393569.2_Missense_Mutation_p.D621V|GALC_ENST00000544807.2_Intron	NM_000153.3|NM_001201401.1	NP_000144.2|NP_001188330.1	P54803	GALC_HUMAN	galactosylceramidase	647					carbohydrate metabolic process (GO:0005975)|galactosylceramide catabolic process (GO:0006683)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	galactosylceramidase activity (GO:0004336)			endometrium(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						CAGAGACTTGTCATTCAGCAT	0.413																																					p.D647V		Atlas-SNP	.											.	GALC	48	.	0			c.A1940T						.						81	78	79					14																	88401194		1893	4122	6015	SO:0001583	missense	2581	exon17			GACTTGTCATTCA	L23116	CCDS9878.2, CCDS55936.1, CCDS55937.1	14q31	2009-01-06	2005-11-29		ENSG00000054983	ENSG00000054983	3.2.1.46		4115	protein-coding gene	gene with protein product	"Krabbe disease"	606890	"galactosylceramidase (Krabbe disease)"				Standard	NM_000153		Approved		uc001xvt.3	P54803	OTTHUMG00000028646	ENST00000261304.2:c.1940A>T	chr14.hg19:g.88401194T>A	ENSP00000261304:p.Asp647Val	70.0	0.0		61.0	21.0	NM_000153	B4DKE8|B4DYN1|B4DZJ8|B7Z7Z2|J3KN25|J3KPP8|Q8J030	Missense_Mutation	SNP	ENST00000261304.2	hg19	CCDS9878.2	.	.	.	.	.	.	.	.	.	.	T	11.60	1.686075	0.29962	.	.	ENSG00000054983	ENST00000261304;ENST00000393569;ENST00000539620;ENST00000393568	D;D;D	0.93547	-3.24;-3.24;-3.24	5.53	0.779	0.18550	.	0.296256	0.42053	D	0.000772	D	0.89022	0.6597	L	0.36672	1.1	0.45676	D	0.998593	B;B;B	0.30741	0.293;0.134;0.283	B;B;B	0.34652	0.187;0.137;0.187	D	0.84382	0.0550	10	0.87932	D	0	-4.3802	11.2612	0.49085	0.0:0.7239:0.0:0.2761	.	624;621;647	E7EPA4;P54803-4;P54803	.;.;GALC_HUMAN	V	647;621;436;624	ENSP00000261304:D647V;ENSP00000377199:D621V;ENSP00000377198:D624V	ENSP00000261304:D647V	D	-	2	0	GALC	87470947	0.997000	0.39634	0.429000	0.26710	0.392000	0.30506	2.003000	0.40844	0.162000	0.19483	-0.297000	0.09499	GAC	.	.		0.413	GALC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071559.2			A	88401194	T	A	88401194	3	1	344	1	0	0	0	0	1	0	0	0	6209	1667	58	4	121	4	GALC	14	88401194	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2312107	88401194	18948346	1014	48377										
GPR65	8477	hgsc.bcm.edu	37	chr14	88478190	88478190	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acaaaagatactatggaattAgaggtccttgagtagaacca	9	6	0	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:88478190A>T	ENST00000267549.3	+	2	1557	c.999A>T	c.(997-999)ttA>ttT	p.L333F	RP11-300J18.2_ENST00000554433.1_RNA	NM_003608.3	NP_003599.2	Q8IYL9	PSYR_HUMAN	G protein-coupled receptor 65	333					actin cytoskeleton reorganization (GO:0031532)|activation of Rho GTPase activity (GO:0032862)|apoptotic process (GO:0006915)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|multicellular organismal development (GO:0007275)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of stress fiber assembly (GO:0051496)|response to acidic pH (GO:0010447)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|prostate(1)	16						CTATGGAATTAGAGGTCCTTG	0.328																																					p.L333F		Atlas-SNP	.											.	GPR65	48	.	0			c.A999T						.						53	55	54					14																	88478190		2201	4299	6500	SO:0001583	missense	8477	exon2			GGAATTAGAGGTC	U95218	CCDS9879.1	14q31-q32.1	2012-08-21			ENSG00000140030	ENSG00000140030		"GPCR / Class A : Orphans"	4517	protein-coding gene	gene with protein product		604620				9655242	Standard	NM_003608		Approved	hTDAG8, TDAG8	uc001xvv.3	Q8IYL9	OTTHUMG00000028648	ENST00000267549.3:c.999A>T	chr14.hg19:g.88478190A>T	ENSP00000267549:p.Leu333Phe	92.0	0.0		80.0	37.0	NM_003608	O75819	Missense_Mutation	SNP	ENST00000267549.3	hg19	CCDS9879.1	.	.	.	.	.	.	.	.	.	.	A	18.13	3.554486	0.65425	.	.	ENSG00000140030	ENST00000267549	T	0.61158	0.13	5.64	4.47	0.54385	.	0.825823	0.10172	N	0.707050	T	0.56321	0.1977	N	0.08118	0	0.33381	D	0.574897	D	0.89917	1.0	D	0.83275	0.996	T	0.57124	-0.7865	10	0.32370	T	0.25	.	9.6499	0.39890	0.9188:0.0:0.0812:0.0	.	333	Q8IYL9	PSYR_HUMAN	F	333	ENSP00000267549:L333F	ENSP00000267549:L333F	L	+	3	2	GPR65	87547943	1.000000	0.71417	0.976000	0.42696	0.955000	0.61496	1.420000	0.34804	0.931000	0.37242	0.528000	0.53228	TTA	.	.		0.328	GPR65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071564.4			T	88478190	A	T	88478190	3	4	344	1	0	0	0	0	1	0	0	0	6714	417	15	4	1001	4	GPR65	14	88478190	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	76996	88478190	18871350	1015	48378										
KCNK10	54207	hgsc.bcm.edu	37	chr14	88707163	88707163	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cattgtcagcatcaagagcaTgctgcaaagaaagggaaaaa	10	7	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:88707163T>C	ENST00000340700.5	-	3	840	c.389A>G	c.(388-390)cAt>cGt	p.H130R	KCNK10_ENST00000312350.5_Splice_Site_p.H135R|KCNK10_ENST00000319231.5_Splice_Site_p.H135R	NM_021161.4	NP_066984.1	P57789	KCNKA_HUMAN	potassium channel, subfamily K, member 10	130					signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	47						ATCAAGAGCATGCTGCAAAGA	0.398																																					p.H135R		Atlas-SNP	.											.	KCNK10	273	.	0			c.A404G						.						76	69	72					14																	88707163		2203	4300	6503	SO:0001630	splice_region_variant	54207	exon3			AGAGCATGCTGCA	AF279890	CCDS9880.1, CCDS9881.1, CCDS9882.1	14q31	2014-06-12						"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6273	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 97"	605873				10880510, 16382106	Standard	NM_021161		Approved	K2p10.1, TREK-2, TREK2, PPP1R97	uc001xwn.3	P57789		ENST00000340700.5:c.388-1A>G	chr14.hg19:g.88707163T>C		25.0	0.0		32.0	19.0	NM_138318	B2R8T4|B2RCT3|B5TJL4|Q6B014|Q8TDK7|Q8TDK8|Q9HB59	Missense_Mutation	SNP	ENST00000340700.5	hg19	CCDS9880.1	.	.	.	.	.	.	.	.	.	.	T	11.19	1.565038	0.27915	.	.	ENSG00000100433	ENST00000340700;ENST00000312350;ENST00000319231;ENST00000556282	D;D;D;T	0.90732	-2.71;-2.72;-2.72;1.0	6.03	6.03	0.97812	.	0.050045	0.85682	D	0.000000	T	0.81735	0.4885	N	0.22421	0.69	0.51012	D	0.999904	B;B;B	0.14012	0.009;0.002;0.002	B;B;B	0.17979	0.02;0.013;0.006	T	0.74565	-0.3623	10	0.13853	T	0.58	.	8.5531	0.33465	0.0:0.1434:0.0:0.8566	.	130;135;135	P57789;B2R8T4;Q6B014	KCNKA_HUMAN;.;.	R	130;135;135;118	ENSP00000343104:H130R;ENSP00000310568:H135R;ENSP00000312811:H135R;ENSP00000452587:H118R	ENSP00000310568:H135R	H	-	2	0	KCNK10	87776916	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	4.819000	0.62664	2.308000	0.77769	0.533000	0.62120	CAT	.	.		0.398	KCNK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410167.1	NM_021161	Missense_Mutation	C	88707163	T	C	88707163	5	2	344	1	0	0	0	0	0	0	1	0	8068	1478	51	2	1247	2	KCNK10	14	88707163	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	228973	88707163	18642377	1016	48379										
ZC3H14	79882	hgsc.bcm.edu	37	chr14	89044335	89044335	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cttttatgtgaaagttccacAgaaacagacacttccagttg	7	9	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:89044335A>C	ENST00000251038.5	+	9	1355	c.1130A>C	c.(1129-1131)cAg>cCg	p.Q377P	ZC3H14_ENST00000555755.1_Missense_Mutation_p.Q377P|ZC3H14_ENST00000557607.1_Missense_Mutation_p.Q222P|ZC3H14_ENST00000393514.5_Missense_Mutation_p.Q377P|ZC3H14_ENST00000359301.3_Missense_Mutation_p.Q343P|ZC3H14_ENST00000302216.8_Missense_Mutation_p.Q377P|ZC3H14_ENST00000336693.4_Missense_Mutation_p.Q343P|ZC3H14_ENST00000556945.1_Missense_Mutation_p.Q377P|ZC3H14_ENST00000557605.1_3'UTR	NM_001160103.1|NM_001160104.1|NM_024824.4	NP_001153575.1|NP_001153576.1|NP_079100.2	Q6PJT7	ZC3HE_HUMAN	zinc finger CCCH-type containing 14	377						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(2)	21						AAAGTTCCACAGAAACAGACA	0.398																																					p.Q377P		Atlas-SNP	.											.	ZC3H14	71	.	0			c.A1130C						.						94	99	97					14																	89044335		2203	4300	6503	SO:0001583	missense	79882	exon9			TTCCACAGAAACA	AF155107	CCDS32133.1, CCDS32134.1, CCDS32135.1, CCDS32136.1, CCDS55938.1	14q31.3	2014-08-12			ENSG00000100722	ENSG00000100722		"Zinc fingers, CCCH-type domain containing"	20509	protein-coding gene	gene with protein product		613279				10508479	Standard	NM_024824		Approved	FLJ11806, UKp68, NY-REN-37	uc001xww.3	Q6PJT7	OTTHUMG00000170803	ENST00000251038.5:c.1130A>C	chr14.hg19:g.89044335A>C	ENSP00000251038:p.Gln377Pro	331.0	0.0		255.0	96.0	NM_001160104	A8MY46|B4DXU8|B4DZW7|B4E2H4|G3V5R4|Q6MZU4|Q6PJ32|Q6PUI6|Q6PUI8|Q86TQ5|Q86TW0|Q86TW1|Q8NCT6|Q8NCZ3|Q8TDE2|Q9HAC9|Q9Y5A0	Missense_Mutation	SNP	ENST00000251038.5	hg19	CCDS32133.1	.	.	.	.	.	.	.	.	.	.	A	19.07	3.756835	0.69648	.	.	ENSG00000100722	ENST00000251038;ENST00000393530;ENST00000353091;ENST00000359301;ENST00000302216;ENST00000380684;ENST00000556945;ENST00000557607;ENST00000555755;ENST00000393514;ENST00000336693	.	.	.	5.51	5.51	0.81932	.	0.057130	0.64402	D	0.000001	T	0.75199	0.3817	M	0.68952	2.095	0.46586	D	0.999116	D;B;D;D;B;D	0.76494	0.999;0.023;0.999;0.999;0.021;0.999	D;B;D;D;B;D	0.76575	0.977;0.015;0.951;0.988;0.013;0.988	T	0.76299	-0.3010	9	0.51188	T	0.08	-2.4362	11.2029	0.48751	0.8469:0.1531:0.0:0.0	.	377;358;377;377;377;377	G3V256;F8W848;G3V5R4;Q6PJT7-2;Q6PJT7-3;Q6PJT7	.;.;.;.;.;ZC3HE_HUMAN	P	377;377;377;343;377;358;377;222;377;377;343	.	ENSP00000251038:Q377P	Q	+	2	0	ZC3H14	88114088	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.323000	0.65858	2.218000	0.71995	0.528000	0.53228	CAG	.	.		0.398	ZC3H14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410387.1	NM_024824		C	89044335	A	C	89044335	3	2	344	1	0	0	0	0	1	0	0	0	17581	188	7	5	1164	5	ZC3H14	14	89044335	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	337172	89044335	18305205	1017	48380										
EML5	161436	hgsc.bcm.edu	37	chr14	89154769	89154769	+	Frame_Shift_Del	DEL	T	T	-													0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctgcacacatcattgtgtcaTttttccccagtgtgcctatg							TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:89154769delT	ENST00000380664.5	-	18	2587	c.2588delA	c.(2587-2589)aatfs	p.N863fs	EML5_ENST00000554922.1_Frame_Shift_Del_p.N863fs|EML5_ENST00000352093.5_Intron			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	863						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)			breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						CATTGTGTCATTTTTCCCCAG	0.393																																					p.N863fs		Atlas-Indel,Pindel	.											.	EML5	141	.	0			c.2589delT						.						265	253	257					14																	89154769		1932	4144	6076	SO:0001589	frameshift_variant	161436	exon18			.	AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"WD repeat domain containing"	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.2588delA	chr14.hg19:g.89154769delT	ENSP00000370039:p.Asn863fs	60.0	0.0		56.0	23.0	NM_183387	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Frame_Shift_Del	DEL	ENST00000380664.5	hg19	CCDS45148.1																																																																																			.	.		0.393	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1			-	89154769	T	-	89154769	7	5	344	1	0	1	0	1	0	0	0	0	5102	1493	52	0	3449	0	EML5	14	89154769	Frame_Shift_Del	DEL	T	TCGA-UB-A7MB-01A-11D-A33Q-10	110434	89154769	18194771	1018	48381										
KCNK13	56659	hgsc.bcm.edu	37	chr14	90650791	90650791	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccccattgaaggctggagctActttgactcactctacttct	7	13	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:90650791A>T	ENST00000282146.4	+	2	1112	c.671A>T	c.(670-672)tAc>tTc	p.Y224F		NM_022054.2	NP_071337.2	Q9HB14	KCNKD_HUMAN	potassium channel, subfamily K, member 13	224					synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(12)|prostate(1)|skin(4)	25		all_cancers(154;0.186)				GGCTGGAGCTACTTTGACTCA	0.537																																					p.Y224F		Atlas-SNP	.											.	KCNK13	76	.	0			c.A671T						.						158	136	143					14																	90650791		2203	4300	6503	SO:0001583	missense	56659	exon2			GGAGCTACTTTGA	AF287303	CCDS9889.1	14q32.11	2012-03-07				ENSG00000152315		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6275	protein-coding gene	gene with protein product		607367				11060316, 16382106	Standard	NM_022054		Approved	K2p13.1, THIK-1, THIK1	uc001xye.1	Q9HB14		ENST00000282146.4:c.671A>T	chr14.hg19:g.90650791A>T	ENSP00000282146:p.Tyr224Phe	105.0	0.0		92.0	39.0	NM_022054	B5TJL8|Q96E79	Missense_Mutation	SNP	ENST00000282146.4	hg19	CCDS9889.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.980554	0.74474	.	.	ENSG00000152315	ENST00000282146	T	0.23147	1.92	5.31	4.13	0.48395	Ion transport 2 (1);	0.000000	0.37437	N	0.002088	T	0.41373	0.1156	L	0.49571	1.57	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.07927	-1.0747	10	0.27082	T	0.32	.	11.3329	0.49487	0.8636:0.0:0.0:0.1364	.	224	Q9HB14	KCNKD_HUMAN	F	224	ENSP00000282146:Y224F	ENSP00000282146:Y224F	Y	+	2	0	KCNK13	89720544	1.000000	0.71417	0.998000	0.56505	0.883000	0.51084	6.102000	0.71486	0.811000	0.34303	0.533000	0.62120	TAC	.	.		0.537	KCNK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411251.1	NM_022054		T	90650791	A	T	90650791	3	4	344	1	0	0	0	0	1	0	0	0	8070	391	14	4	677	4	KCNK13	14	90650791	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1496022	90650791	16698749	1019	48382										
FAM181A	90050	hgsc.bcm.edu	37	chr14	94395161	94395161	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttgcaagggcttggagccccTgggacctgagactaccctgg	14	12	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:94395161T>A	ENST00000267594.5	+	3	1023	c.716T>A	c.(715-717)cTg>cAg	p.L239Q	FAM181A-AS1_ENST00000554742.1_RNA|FAM181A_ENST00000557719.1_Missense_Mutation_p.L177Q|FAM181A_ENST00000556222.1_Missense_Mutation_p.L177Q|FAM181A_ENST00000557000.2_Missense_Mutation_p.L177Q	NM_001207073.1|NM_001207074.1|NM_138344.4	NP_001194002.1|NP_001194003.1|NP_612353.3	Q8N9Y4	F181A_HUMAN	family with sequence similarity 181, member A	239										cervix(1)|endometrium(2)|large_intestine(8)|lung(4)|prostate(1)|skin(2)	18						TTGGAGCCCCTGGGACCTGAG	0.632																																					p.L239Q		Atlas-SNP	.											.	FAM181A	42	.	0			c.T716A						.						42	41	42					14																	94395161		2203	4300	6503	SO:0001583	missense	90050	exon3			AGCCCCTGGGACC	BC009073	CCDS9914.1, CCDS55939.1	14q32.12	2011-11-30	2008-07-22	2008-07-22	ENSG00000140067	ENSG00000140067			20491	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 152"	C14orf152			Standard	NM_138344		Approved		uc021saz.1	Q8N9Y4	OTTHUMG00000171297	ENST00000267594.5:c.716T>A	chr14.hg19:g.94395161T>A	ENSP00000267594:p.Leu239Gln	42.0	0.0		22.0	15.0	NM_138344	B2RD39|Q96GY1	Missense_Mutation	SNP	ENST00000267594.5	hg19	CCDS9914.1	.	.	.	.	.	.	.	.	.	.	T	10.39	1.336830	0.24253	.	.	ENSG00000140067	ENST00000557719;ENST00000267594;ENST00000556222;ENST00000554404;ENST00000557000	T;T;T;T;T	0.37235	1.21;1.21;1.21;1.21;1.34	4.74	3.6	0.41247	.	1.301940	0.05701	N	0.594008	T	0.40247	0.1109	L	0.51422	1.61	0.09310	N	1	P	0.44946	0.846	P	0.44990	0.466	T	0.32561	-0.9902	10	0.87932	D	0	-3.0385	7.8741	0.29584	0.0:0.2012:0.0:0.7988	.	239	Q8N9Y4	F181A_HUMAN	Q	177;239;177;177;228	ENSP00000451802:L177Q;ENSP00000267594:L239Q;ENSP00000451678:L177Q;ENSP00000452393:L177Q;ENSP00000451445:L228Q	ENSP00000267594:L239Q	L	+	2	0	FAM181A	93464914	0.000000	0.05858	0.751000	0.31187	0.325000	0.28411	0.147000	0.16202	1.784000	0.52394	0.459000	0.35465	CTG	.	.		0.632	FAM181A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412840.1	NM_138344		A	94395161	T	A	94395161	3	1	344	1	0	0	0	0	1	0	0	0	5513	1580	55	4	722	4	FAM181A	14	94395161	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	3744370	94395161	12954379	1020	48383										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105413692	105413692	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccagttgggcagaggggggcTgaatgctgatgtcagtggtc	18	7	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:105413692T>A	ENST00000333244.5	-	7	8215	c.8096A>T	c.(8095-8097)cAg>cTg	p.Q2699L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2699						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				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)			AGAGGGGGGCTGAATGCTGAT	0.622																																					p.Q2699L		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A8096T						.						147	162	157					14																	105413692		1985	4165	6150	SO:0001583	missense	113146	exon7			GGGGGCTGAATGC	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.8096A>T	chr14.hg19:g.105413692T>A	ENSP00000353114:p.Gln2699Leu	214.0	0.0		120.0	49.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	hg19	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	N	12.02	1.813201	0.32053	.	.	ENSG00000185567	ENST00000333244	T	0.01572	4.76	3.47	0.681	0.17986	.	.	.	.	.	T	0.07593	0.0191	M	0.76838	2.35	0.09310	N	1	D	0.63046	0.992	D	0.72982	0.979	T	0.17653	-1.0362	9	0.40728	T	0.16	-16.6091	7.0504	0.25069	0.0:0.0:0.4722:0.5278	.	2699	Q8IVF2	AHNK2_HUMAN	L	2699	ENSP00000353114:Q2699L	ENSP00000353114:Q2699L	Q	-	2	0	AHNAK2	104484737	0.005000	0.15991	0.001000	0.08648	0.014000	0.08584	0.018000	0.13422	0.233000	0.21120	0.254000	0.18369	CAG	.	.		0.622	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105413692	T	A	105413692	3	1	344	1	0	0	0	0	1	0	0	0	415	1580	55	4	9295	4	AHNAK2	14	105413692	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	11018531	105413692	1935848	1021	48384										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105420987	105420987	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cccggcccccgcttgctcttTatggattgaaattttggcca	9	13	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr14:105420987T>C	ENST00000333244.5	-	7	920	c.801A>G	c.(799-801)atA>atG	p.I267M	AHNAK2_ENST00000557457.1_5'Flank	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	267						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				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)			GCTTGCTCTTTATGGATTGAA	0.577																																					p.I267M		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A801G						.						29	31	30					14																	105420987		1913	4116	6029	SO:0001583	missense	113146	exon7			GCTCTTTATGGAT	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.801A>G	chr14.hg19:g.105420987T>C	ENSP00000353114:p.Ile267Met	48.0	0.0		24.0	19.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	hg19	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	t	14.58	2.576992	0.45902	.	.	ENSG00000185567	ENST00000333244	T	0.03386	3.95	5.23	-10.5	0.00291	.	0.764756	0.10362	U	0.683829	T	0.03220	0.0094	L	0.53249	1.67	0.09310	N	1	B	0.25955	0.138	B	0.24701	0.055	T	0.21109	-1.0255	10	0.66056	D	0.02	.	5.7909	0.18359	0.1448:0.4862:0.2906:0.0785	.	267	Q8IVF2	AHNK2_HUMAN	M	267	ENSP00000353114:I267M	ENSP00000353114:I267M	I	-	3	3	AHNAK2	104492032	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-2.472000	0.00989	-3.002000	0.00275	0.528000	0.53228	ATA	.	.		0.577	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		C	105420987	T	C	105420987	3	2	344	1	0	0	0	0	1	0	0	0	415	1744	61	2	16590	2	AHNAK2	14	105420987	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	7295	105420987	1928553	1022	48385										
C15orf2	23742	hgsc.bcm.edu	37	chr15	24923872	24923872	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agagttaacatcaccatataCtgcattgggcacacctgtta	7	10	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:24923872C>A	ENST00000329468.2	+	1	3332	c.2858C>A	c.(2857-2859)aCt>aAt	p.T953N		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	953					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											TCACCATATACTGCATTGGGC	0.483																																					p.T953N		Atlas-SNP	.											.	.	.	.	0			c.C2858A						.						78	79	79					15																	24923872		2203	4300	6503	SO:0001583	missense	23742	exon1			CATATACTGCATT	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"chromosome 15 open reading frame 2"	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.2858C>A	chr15.hg19:g.24923872C>A	ENSP00000333735:p.Thr953Asn	54.0	0.0		42.0	22.0	NM_018958		Missense_Mutation	SNP	ENST00000329468.2	hg19	CCDS10015.1	.	.	.	.	.	.	.	.	.	.	.	9.390	1.075291	0.20227	.	.	ENSG00000185823	ENST00000329468	T	0.06218	3.33	2.04	2.04	0.26737	.	.	.	.	.	T	0.03608	0.0103	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36163	-0.9759	9	0.62326	D	0.03	.	7.595	0.28044	0.0:1.0:0.0:0.0	.	953	Q9NZP6	CO002_HUMAN	N	953	ENSP00000333735:T953N	ENSP00000333735:T953N	T	+	2	0	C15orf2	22474965	0.001000	0.12720	0.001000	0.08648	0.173000	0.22820	1.296000	0.33389	1.443000	0.47586	0.313000	0.20887	ACT	.	.		0.483	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		A	24923872	C	A	24923872	3	1	344	1	0	0	0	0	1	0	0	0	1786	565	20	3	2860	3	C15orf2	15	24923872	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10		24923872	77607520	1023	48386										
GABRG3	2567	hgsc.bcm.edu	37	chr15	27777744	27777744	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtgtcatttttgttgcttgcAgaactattccctcctggaca	8	10	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:27777744A>T	ENST00000333743.6	+	10	1376		c.e10-1		RP11-100M12.3_ENST00000556642.1_RNA	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3						gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(23)|skin(1)|upper_aerodigestive_tract(4)	42		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TGTTGCTTGCAGAACTATTCC	0.408																																					.	NSCLC(114;800 1656 7410 37729 45293)	Atlas-SNP	.											.	GABRG3	115	.	0			c.1123-2A>T						.						83	80	81					15																	27777744		1972	4161	6133	SO:0001630	splice_region_variant	2567	exon10			GCTTGCAGAACTA		CCDS45195.1, CCDS59251.1	15q12	2012-06-22			ENSG00000182256	ENSG00000182256		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4088	protein-coding gene	gene with protein product	"GABA(G) receptor, gamma 3"	600233				7601451	Standard	NM_033223		Approved		uc001zbg.2	Q99928	OTTHUMG00000044462	ENST00000333743.6:c.1123-1A>T	chr15.hg19:g.27777744A>T		72.0	0.0		57.0	29.0	NM_033223	G3V594|Q9HD46|Q9NYT2	Splice_Site	SNP	ENST00000333743.6	hg19	CCDS45195.1	.	.	.	.	.	.	.	.	.	.	A	19.27	3.794589	0.70452	.	.	ENSG00000182256	ENST00000333743	.	.	.	5.85	5.85	0.93711	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4129	0.74941	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GABRG3	25451339	1.000000	0.71417	0.999000	0.59377	0.713000	0.41058	8.906000	0.92626	2.237000	0.73441	0.528000	0.53228	.	.	.		0.408	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2		Intron	T	27777744	A	T	27777744	5	4	344	1	0	0	0	0	0	0	1	0	6181	202	7	4	1159	4	GABRG3	15	27777744	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2853872	27777744	74753648	1024	48387										
MTMR15	22909	hgsc.bcm.edu	37	chr15	31197069	31197069	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgaaatgtgtgctaacaatgActtcgttcaagtggatccag	10	7	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:31197069A>T	ENST00000362065.4	+	2	494	c.203A>T	c.(202-204)gAc>gTc	p.D68V	FAN1_ENST00000561607.1_Missense_Mutation_p.D68V|FAN1_ENST00000561594.1_Missense_Mutation_p.D68V|FAN1_ENST00000565466.1_Missense_Mutation_p.D68V	NM_014967.4	NP_055782.3	Q9Y2M0	FAN1_HUMAN	FANCD2/FANCI-associated nuclease 1	68					DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA incision (GO:0033683)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|5'-flap endonuclease activity (GO:0017108)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|phosphodiesterase I activity (GO:0004528)|ubiquitin binding (GO:0043130)			autonomic_ganglia(2)|breast(2)|cervix(2)|endometrium(7)|kidney(1)|large_intestine(6)|lung(8)|skin(1)	29						GCTAACAATGACTTCGTTCAA	0.418								Direct reversal of damage																													p.D68V		Atlas-SNP	.											.	FAN1	77	.	0			c.A203T						.						83	82	82					15																	31197069		2202	4300	6502	SO:0001583	missense	22909	exon2			ACAATGACTTCGT		CCDS32186.1, CCDS58344.1	15q13.2-q13.3	2010-08-04	2010-08-04	2010-08-04		ENSG00000198690			29170	protein-coding gene	gene with protein product		613534	"KIAA1018", "myotubularin related protein 15"	KIAA1018, MTMR15		20603015, 20603016, 20603073	Standard	NM_014967		Approved		uc001zff.3	Q9Y2M0		ENST00000362065.4:c.203A>T	chr15.hg19:g.31197069A>T	ENSP00000354497:p.Asp68Val	140.0	0.0		157.0	63.0	NM_001146095	A8K4M2|Q86WU8	Missense_Mutation	SNP	ENST00000362065.4	hg19	CCDS32186.1	.	.	.	.	.	.	.	.	.	.	A	15.87	2.961488	0.53400	.	.	ENSG00000198690	ENST00000362065	T	0.80994	-1.44	5.15	1.5	0.22942	.	0.876889	0.09872	N	0.744753	T	0.76314	0.3970	L	0.36672	1.1	0.09310	N	0.999999	P;D	0.53151	0.651;0.958	B;P	0.48704	0.109;0.587	T	0.63180	-0.6695	10	0.42905	T	0.14	-6.6987	9.1715	0.37083	0.7031:0.0:0.2969:0.0	.	68;68	Q9Y2M0;Q9Y2M0-2	FAN1_HUMAN;.	V	68	ENSP00000354497:D68V	ENSP00000354497:D68V	D	+	2	0	FAN1	28984361	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	0.241000	0.18065	0.061000	0.16311	0.374000	0.22700	GAC	.	.		0.418	FAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430740.1	NM_014967		T	31197069	A	T	31197069	3	4	344	1	0	0	0	0	1	0	0	0	9952	275	10	4	205	4	MTMR15	15	31197069	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3419325	31197069	71334323	1025	48388										
FMN1	342184	hgsc.bcm.edu	37	chr15	33091016	33091016	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaaccttacctttctttagaTatgtttttactctcccgttt	4	10	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:33091016T>C	ENST00000559047.1	-	16	4118	c.4119A>G	c.(4117-4119)atA>atG	p.I1373M	FMN1_ENST00000561249.1_Missense_Mutation_p.I1275M|FMN1_ENST00000334528.9_Missense_Mutation_p.I1150M			Q68DA7	FMN1_HUMAN	formin 1	1373	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		TTTCTTTAGATATGTTTTTAC	0.403																																					p.I1150M		Atlas-SNP	.											.	FMN1	174	.	0			c.A3450G						.						124	111	115					15																	33091016		1833	4087	5920	SO:0001583	missense	342184	exon15			TTTAGATATGTTT	AH002864	CCDS45209.1, CCDS61581.1, CCDS61582.1	15q13.3	2013-06-13	2005-01-20	2005-01-22	ENSG00000248905	ENSG00000248905			3768	protein-coding gene	gene with protein product	"limb deformity protein"	136535	"formin (limb deformity)"	LD, FMN		1673046	Standard	NM_001277313		Approved	DKFZP686C2281, FLJ45135, MGC125288, MGC125289	uc031qrh.1	Q68DA7	OTTHUMG00000172201	ENST00000559047.1:c.4119A>G	chr15.hg19:g.33091016T>C	ENSP00000454047:p.Ile1373Met	77.0	0.0		62.0	27.0	NM_001103184	Q3B7I6|Q3ZAR4|Q6ZSY1	Missense_Mutation	SNP	ENST00000559047.1	hg19		.	.	.	.	.	.	.	.	.	.	T	13.63	2.295018	0.40594	.	.	ENSG00000248905	ENST00000334528	T	0.63255	-0.03	6.08	2.37	0.29283	.	0.144593	0.64402	D	0.000009	T	0.67767	0.2928	L	0.59436	1.845	.	.	.	D	0.53885	0.963	P	0.62813	0.907	T	0.72516	-0.4269	9	0.46703	T	0.11	.	5.8974	0.18947	0.2228:0.0:0.3433:0.4339	.	1150	Q68DA7-5	.	M	1150	ENSP00000333950:I1150M	ENSP00000333950:I1150M	I	-	3	3	FMN1	30878308	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.978000	0.40598	1.095000	0.41419	0.533000	0.62120	ATA	.	.		0.403	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184		C	33091016	T	C	33091016	3	2	344	1	0	0	0	0	1	0	0	0	5957	1396	49	2	152	2	FMN1	15	33091016	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1893947	33091016	69440376	1026	48389										
RYR3	6263	hgsc.bcm.edu	37	chr15	33954785	33954785	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcaccaaaagcagagccccgAgattcccttggagagtctca	9	13	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:33954785A>T	ENST00000389232.4	+	35	5124	c.5054A>T	c.(5053-5055)gAg>gTg	p.E1685V	RYR3_ENST00000415757.3_Missense_Mutation_p.E1685V	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	1685	4 X approximate repeats.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			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)		CAGAGCCCCGAGATTCCCTTG	0.597																																					p.E1685V		Atlas-SNP	.											.	RYR3	760	.	0			c.A5054T						.						70	74	73					15																	33954785		1994	4170	6164	SO:0001583	missense	6263	exon35			GCCCCGAGATTCC		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.5054A>T	chr15.hg19:g.33954785A>T	ENSP00000373884:p.Glu1685Val	81.0	0.0		74.0	35.0	NM_001243996	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	hg19	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	A	8.686	0.906304	0.17760	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	T;T	0.74315	-0.83;-0.83	5.41	5.41	0.78517	.	0.134088	0.51477	D	0.000094	T	0.64046	0.2563	N	0.17082	0.46	0.37874	D	0.930152	B;P	0.46578	0.045;0.88	B;P	0.47786	0.023;0.557	T	0.66368	-0.5941	10	0.30078	T	0.28	.	10.7948	0.46453	0.8589:0.0:0.0:0.1411	.	1685;1685	Q15413-2;Q15413	.;RYR3_HUMAN	V	1685	ENSP00000373884:E1685V;ENSP00000399610:E1685V	ENSP00000354735:E1685V	E	+	2	0	RYR3	31742077	1.000000	0.71417	1.000000	0.80357	0.090000	0.18270	7.092000	0.76930	2.281000	0.76405	0.533000	0.62120	GAG	.	.		0.597	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			T	33954785	A	T	33954785	3	4	344	1	0	0	0	0	1	0	0	0	13785	304	11	4	5192	4	RYR3	15	33954785	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	863769	33954785	68576607	1027	48390										
RYR3	6263	hgsc.bcm.edu	37	chr15	34080457	34080457	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcagcaaagccaggcccgacCtgctgagaagccacttcatc	9	15	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:34080457C>G	ENST00000389232.4	+	67	9698	c.9628C>G	c.(9628-9630)Ctg>Gtg	p.L3210V	RYR3_ENST00000415757.3_Missense_Mutation_p.L3210V	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3210					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			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)		CAGGCCCGACCTGCTGAGAAG	0.502																																					p.L3210V		Atlas-SNP	.											.	RYR3	760	.	0			c.C9628G						.						109	116	114					15																	34080457		2010	4201	6211	SO:0001583	missense	6263	exon67			CCCGACCTGCTGA		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.9628C>G	chr15.hg19:g.34080457C>G	ENSP00000373884:p.Leu3210Val	99.0	0.0		95.0	47.0	NM_001243996	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	hg19	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	C	17.93	3.509343	0.64522	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D;D	0.97430	-4.37;-4.38	4.55	3.63	0.41609	.	0.000000	0.64402	D	0.000007	D	0.98090	0.9370	M	0.83603	2.65	0.47621	D	0.999474	D;D	0.89917	0.998;1.0	D;D	0.85130	0.99;0.997	D	0.98262	1.0499	10	0.72032	D	0.01	.	10.2646	0.43447	0.0:0.839:0.0:0.161	.	3210;3210	Q15413-2;Q15413	.;RYR3_HUMAN	V	3210	ENSP00000373884:L3210V;ENSP00000399610:L3210V	ENSP00000354735:L3210V	L	+	1	2	RYR3	31867749	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	3.856000	0.55964	1.274000	0.44362	-0.136000	0.14681	CTG	.	.		0.502	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			G	34080457	C	G	34080457	3	3	344	1	0	0	0	0	1	0	0	0	13785	680	24	4	9894	4	RYR3	15	34080457	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	125672	34080457	68450935	1028	48391										
RYR3	6263	hgsc.bcm.edu	37	chr15	34105180	34105180	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cagagaatttcagcagctgtCttccacctggaacaggtaag	10	10	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:34105180C>T	ENST00000389232.4	+	73	10444	c.10374C>T	c.(10372-10374)gtC>gtT	p.V3458V	RYR3_ENST00000415757.3_Silent_p.V3453V	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3458					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			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)		CAGCAGCTGTCTTCCACCTGG	0.493																																					p.V3458V		Atlas-SNP	.											.	RYR3	760	.	0			c.C10374T						.						75	75	75					15																	34105180		1962	4152	6114	SO:0001819	synonymous_variant	6263	exon73			AGCTGTCTTCCAC		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.10374C>T	chr15.hg19:g.34105180C>T		65.0	0.0		57.0	36.0	NM_001036	O15175|Q15412	Silent	SNP	ENST00000389232.4	hg19	CCDS45210.1																																																																																			.	.		0.493	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			T	34105180	C	T	34105180	2	4	344	1	0	0	0	0	0	0	0	1	13785	900	32	3		3	RYR3	15	34105180	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	24723	34105180	68426212	1029	48392										
RASGRP1	10125	hgsc.bcm.edu	37	chr15	38804991	38804991	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	accagttattcacctgagccAcctggatgaacttgatgaag	9	10	1	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:38804991A>G	ENST00000310803.5	-	7	1019	c.842T>C	c.(841-843)gTg>gCg	p.V281A	RASGRP1_ENST00000558164.1_Missense_Mutation_p.V281A|RASGRP1_ENST00000561180.1_Missense_Mutation_p.V332A|RASGRP1_ENST00000539159.1_Missense_Mutation_p.V233A|RASGRP1_ENST00000450598.2_Missense_Mutation_p.V281A|RASGRP1_ENST00000559830.1_Missense_Mutation_p.V281A	NM_001128602.1|NM_005739.3	NP_001122074.1|NP_005730.2	O95267	GRP1_HUMAN	RAS guanyl releasing protein 1 (calcium and DAG-regulated)	281	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				activation of Rho GTPase activity (GO:0032862)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response to antigenic stimulus (GO:0002437)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|platelet activation (GO:0030168)|Ras protein signal transduction (GO:0007265)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)|secretory granule localization (GO:0032252)|signal transduction (GO:0007165)|vesicle transport along microtubule (GO:0047496)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|lipid binding (GO:0008289)			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)		CACCTGAGCCACCTGGATGAA	0.478																																					p.V281A		Atlas-SNP	.											.	RASGRP1	50	.	0			c.T842C						.						52	57	55					15																	38804991		2000	4168	6168	SO:0001583	missense	10125	exon7			TGAGCCACCTGGA	AF106071	CCDS45221.1, CCDS45222.1	15q15	2013-01-10				ENSG00000172575		"EF-hand domain containing"	9878	protein-coding gene	gene with protein product		603962				10087292, 9789079	Standard	NM_005739		Approved	CalDAG-GEFII, RASGRP	uc001zke.4	O95267		ENST00000310803.5:c.842T>C	chr15.hg19:g.38804991A>G	ENSP00000310244:p.Val281Ala	78.0	0.0		68.0	27.0	NM_001128602	Q56CZ0|Q58G75|Q59HB1|Q5I3A8|Q6GV31|Q6NX39|Q7LDG6|Q9UI94|Q9UNN9	Missense_Mutation	SNP	ENST00000310803.5	hg19	CCDS45222.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.600388	0.87055	.	.	ENSG00000172575	ENST00000310803;ENST00000450598;ENST00000415523;ENST00000431814;ENST00000539159;ENST00000414708;ENST00000541438	T;T;T;T	0.41758	0.99;0.99;0.99;0.99	5.21	5.21	0.72293	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	T	0.70518	0.3233	M	0.90483	3.12	0.80722	D	1	D;D;D;D	0.89917	0.997;0.999;1.0;1.0	D;D;D;D	0.80764	0.992;0.991;0.994;0.99	T	0.77996	-0.2377	10	0.87932	D	0	-22.0175	15.2514	0.73549	1.0:0.0:0.0:0.0	.	281;281;281;281	C9JM27;C9JCE5;O95267;O95267-2	.;.;GRP1_HUMAN;.	A	281;281;281;281;233;281;281	ENSP00000310244:V281A;ENSP00000388540:V281A;ENSP00000444762:V233A;ENSP00000413105:V281A	ENSP00000310244:V281A	V	-	2	0	RASGRP1	36592283	1.000000	0.71417	1.000000	0.80357	0.853000	0.48598	9.139000	0.94554	2.189000	0.69895	0.528000	0.53228	GTG	.	.		0.478	RASGRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418223.1	NM_005739		G	38804991	A	G	38804991	3	3	344	1	0	0	0	0	1	0	0	0	13089	159	6	2	1595	2	RASGRP1	15	38804991	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	4699811	38804991	63726401	1030	48393										
BUB1B	701	hgsc.bcm.edu	37	chr15	40491906	40491906	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaaagaaatccaaactactcAgcaagaaagaacaggtgatc	7	8	1	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:40491906A>T	ENST00000287598.6	+	10	1574	c.1379A>T	c.(1378-1380)cAg>cTg	p.Q460L	BUB1B_ENST00000412359.3_Missense_Mutation_p.Q474L	NM_001211.5	NP_001202	O60566	BUB1B_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase B	460					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|protein localization to chromosome, centromeric region (GO:0071459)|protein localization to kinetochore (GO:0034501)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|condensed chromosome kinetochore (GO:0000777)|condensed chromosome outer kinetochore (GO:0000940)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|perinuclear region of cytoplasm (GO:0048471)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(1)|stomach(2)|urinary_tract(2)	36		all_cancers(109;1.12e-18)|all_epithelial(112;1.61e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0556)		CAAACTACTCAGCAAGAAAGA	0.323			"Mis, N, F, S"			rhabdomyosarcoma			Mosaic Variegated Aneuploidy Syndrome																												p.Q460L		Atlas-SNP	.	yes	Rec		Mosaic variegated aneuploidy	15	15q15	701	BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast)		M	.	BUB1B	71	.	0			c.A1379T						.						111	118	116					15																	40491906		2203	4300	6503	SO:0001583	missense	701	exon10	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	CTACTCAGCAAGA	AF107297	CCDS10053.1	15q15	2014-09-17	2013-01-17		ENSG00000156970	ENSG00000156970			1149	protein-coding gene	gene with protein product		602860	"budding uninhibited by benzimidazoles 1 (yeast homolog), beta", "budding uninhibited by benzimidazoles 1 homolog beta (yeast)"			9889005	Standard	NM_001211		Approved	BUBR1, MAD3L, Bub1A, SSK1	uc001zkx.4	O60566	OTTHUMG00000129877	ENST00000287598.6:c.1379A>T	chr15.hg19:g.40491906A>T	ENSP00000287598:p.Gln460Leu	320.0	0.0		285.0	122.0	NM_001211	B2R6U0|B4DL09|B4DLG3|O60501|O60627|O60758|O75389|Q59HH6|Q8WV50|Q96KM4	Missense_Mutation	SNP	ENST00000287598.6	hg19	CCDS10053.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.243663	0.79912	.	.	ENSG00000156970	ENST00000287598;ENST00000412359;ENST00000442874	T;T	0.44881	0.91;0.91	5.48	5.48	0.80851	.	0.251821	0.34460	N	0.003949	T	0.54598	0.1868	M	0.62723	1.935	0.30493	N	0.771224	D;D	0.62365	0.991;0.965	P;P	0.59424	0.857;0.65	T	0.61168	-0.7117	10	0.56958	D	0.05	-11.8265	9.7305	0.40359	0.9221:0.0:0.0779:0.0	.	474;460	O60566-3;O60566	.;BUB1B_HUMAN	L	460;474;406	ENSP00000287598:Q460L;ENSP00000398470:Q474L	ENSP00000287598:Q460L	Q	+	2	0	BUB1B	38279198	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.825000	0.48096	2.073000	0.62155	0.533000	0.62120	CAG	.	.		0.323	BUB1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252122.4			T	40491906	A	T	40491906	3	4	344	1	0	0	0	0	1	0	0	0	1573	188	7	4	1417	4	BUB1B	15	40491906	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1686915	40491906	62039486	1031	48394										
PLCB2	5330	hgsc.bcm.edu	37	chr15	40591344	40591344	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctcactaagaagtgaagatcTcatctatttctggccgagga	9	9	4	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:40591344T>A	ENST00000260402.3	-	8	917	c.668A>T	c.(667-669)gAg>gTg	p.E223V	PLCB2-AS1_ENST00000559520.1_RNA|PLCB2_ENST00000557821.1_Missense_Mutation_p.E223V|PLCB2_ENST00000456256.2_Missense_Mutation_p.E223V	NM_001284297.1|NM_004573.2	NP_001271226.1|NP_004564.2	Q00722	PLCB2_HUMAN	phospholipase C, beta 2	223					activation of phospholipase C activity (GO:0007202)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|sensory perception of bitter taste (GO:0050913)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(3)	39		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0508)		AGTGAAGATCTCATCTATTTC	0.512																																					p.E223V		Atlas-SNP	.											.	PLCB2	177	.	0			c.A668T						.						104	110	108					15																	40591344		2001	4164	6165	SO:0001583	missense	5330	exon8			AAGATCTCATCTA		CCDS42020.1, CCDS61591.1, CCDS61592.1, CCDS73704.1	15q15.1	2012-01-23			ENSG00000137841	ENSG00000137841	3.1.4.11		9055	protein-coding gene	gene with protein product		604114				1644792, 9925923	Standard	XM_005254448		Approved	FLJ38135	uc001zld.3	Q00722	OTTHUMG00000172412	ENST00000260402.3:c.668A>T	chr15.hg19:g.40591344T>A	ENSP00000260402:p.Glu223Val	71.0	0.0		43.0	18.0	NM_004573	A8K6J2|B9EGH5	Missense_Mutation	SNP	ENST00000260402.3	hg19	CCDS42020.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.091549	0.76756	.	.	ENSG00000137841	ENST00000260402;ENST00000456256	T;T	0.20069	2.1;2.1	5.51	5.51	0.81932	Phospholipase C, phosphoinositol-specific, EF-hand-like (1);EF-hand-like domain (1);	0.052187	0.85682	D	0.000000	T	0.46347	0.1388	M	0.72118	2.19	0.80722	D	1	D;P;P	0.89917	1.0;0.865;0.594	D;P;P	0.80764	0.994;0.506;0.472	T	0.42732	-0.9434	10	0.52906	T	0.07	.	15.6206	0.76802	0.0:0.0:0.0:1.0	.	223;223;223	B9EGH5;Q00722-2;Q00722	.;.;PLCB2_HUMAN	V	223	ENSP00000260402:E223V;ENSP00000411991:E223V	ENSP00000260402:E223V	E	-	2	0	PLCB2	38378636	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.751000	0.68720	2.080000	0.62538	0.533000	0.62120	GAG	.	.		0.512	PLCB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418430.1			A	40591344	T	A	40591344	3	1	344	1	0	0	0	0	1	0	0	0	12037	1551	54	4	2989	4	PLCB2	15	40591344	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	99438	40591344	61940048	1032	48395										
DISP2	85455	hgsc.bcm.edu	37	chr15	40660858	40660858	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agcgctggatggagagccccAgctgcgcccgcctggggcct	16	15	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:40660858A>T	ENST00000267889.3	+	8	2632	c.2545A>T	c.(2545-2547)Agc>Tgc	p.S849C	RP11-64K12.4_ENST00000558421.1_RNA	NM_033510.1	NP_277045.1	A7MBM2	DISP2_HUMAN	dispatched homolog 2 (Drosophila)	849					smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)	30		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.39e-06)|Colorectal(105;0.0114)|READ - Rectum adenocarcinoma(2;0.0649)|BRCA - Breast invasive adenocarcinoma(123;0.0798)|Lung(196;0.15)|LUAD - Lung adenocarcinoma(183;0.247)		GGAGAGCCCCAGCTGCGCCCG	0.652																																					p.S849C		Atlas-SNP	.											.	DISP2	86	.	0			c.A2545T						.						18	21	20					15																	40660858		2201	4297	6498	SO:0001583	missense	85455	exon8			AGCCCCAGCTGCG	AB051529	CCDS10056.1	15q14	2004-01-15			ENSG00000140323	ENSG00000140323			19712	protein-coding gene	gene with protein product		607503				11214970, 10619433	Standard	NM_033510		Approved	DISPB, KIAA1742, HsT16908	uc001zlk.1	A7MBM2	OTTHUMG00000129983	ENST00000267889.3:c.2545A>T	chr15.hg19:g.40660858A>T	ENSP00000267889:p.Ser849Cys	28.0	0.0		33.0	14.0	NM_033510	Q6AHW3|Q9C0C1	Missense_Mutation	SNP	ENST00000267889.3	hg19	CCDS10056.1	.	.	.	.	.	.	.	.	.	.	G	1.930	-0.446243	0.04604	.	.	ENSG00000140323	ENST00000267889	T	0.11712	2.75	4.99	-7.01	0.01594	.	1.052620	0.07293	N	0.872860	T	0.07324	0.0185	N	0.22421	0.69	0.09310	N	1	B	0.14438	0.01	B	0.13407	0.009	T	0.33497	-0.9866	10	0.37606	T	0.19	-0.0026	13.1494	0.59480	0.675:0.2049:0.1201:0.0	.	849	A7MBM2	DISP2_HUMAN	C	849	ENSP00000267889:S849C	ENSP00000267889:S849C	S	+	1	0	DISP2	38448150	0.000000	0.05858	0.000000	0.03702	0.104000	0.19210	0.279000	0.18771	-1.935000	0.01049	-2.025000	0.00428	AGC	.	.		0.652	DISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252249.1	NM_033510		T	40660858	A	T	40660858	3	4	344	1	0	0	0	0	1	0	0	0	4542	188	7	4	2575	4	DISP2	15	40660858	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	69514	40660858	61870534	1033	48396										
JMJD7-PLA2G4B	100137049	hgsc.bcm.edu	37	chr15	42134021	42134021	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tggttcctgtttccagcctcAgagcacagagttcagcttgt	10	11	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:42134021A>T	ENST00000452633.1	+	9	847	c.495A>T	c.(493-495)tcA>tcT	p.S165S	JMJD7-PLA2G4B_ENST00000382448.4_Silent_p.S396S|PLA2G4B_ENST00000458483.1_Silent_p.S165S|PLA2G4B_ENST00000542534.2_Silent_p.S396S|JMJD7-PLA2G4B_ENST00000342159.4_Silent_p.S396S			P0C869	PA24B_HUMAN	phospholipase A2, group IVB (cytosolic)	165					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|arachidonic acid metabolic process (GO:0019369)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|parturition (GO:0007567)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular region (GO:0005576)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|calcium-dependent phospholipid binding (GO:0005544)|lysophospholipase activity (GO:0004622)						all_cancers(109;1.84e-13)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		all cancers(2;1.08e-30)|Epithelial(2;1.43e-22)|OV - Ovarian serous cystadenocarcinoma(18;1.13e-17)|GBM - Glioblastoma multiforme(94;9.77e-07)|Colorectal(2;0.0129)|COAD - Colon adenocarcinoma(120;0.0371)		TTCCAGCCTCAGAGCACAGAG	0.642																																					p.S396S		Atlas-SNP	.											.	JMJD7-PLA2G4B	90	.	0			c.A1188T						.						34	33	33					15																	42134021		2203	4300	6503	SO:0001819	synonymous_variant	8681	exon13			AGCCTCAGAGCAC	AF065215	CCDS45241.1	15q11.2-q21.3	2010-08-17			ENSG00000243708	ENSG00000243708	3.1.1.4		9036	protein-coding gene	gene with protein product		606088				9705332	Standard	NM_001114633		Approved	cPLA2-beta, HsT16992		P0C869	OTTHUMG00000156809	ENST00000452633.1:c.495A>T	chr15.hg19:g.42134021A>T		77.0	0.0		78.0	35.0	NM_005090	B4DRT9|O95712|Q19KD5|Q19KD6|Q59GF9|Q8TB10|Q9UKV7	Silent	SNP	ENST00000452633.1	hg19	CCDS45241.1																																																																																			.	.		0.642	PLA2G4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000345969.1	NM_001114633		T	42134021	A	T	42134021	2	4	344	1	0	0	0	0	0	0	0	1	7964	175	7	4		4	JMJD7-PLA2G4B	15	42134021	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1473163	42134021	60397371	1034	48397										
PLA2G4D	283748	hgsc.bcm.edu	37	chr15	42364510	42364510	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tccagattgttctctttgacAttgaggctcaagtagagggg	12	7	2	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:42364510A>G	ENST00000290472.3	-	14	1492	c.1398T>C	c.(1396-1398)aaT>aaC	p.N466N		NM_178034.3	NP_828848.3	Q86XP0	PA24D_HUMAN	phospholipase A2, group IVD (cytosolic)	466	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(7)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(109;6.37e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.019)|Ovarian(310;0.143)|Colorectal(260;0.245)		OV - Ovarian serous cystadenocarcinoma(18;4.9e-17)|GBM - Glioblastoma multiforme(94;1.02e-06)		TCTCTTTGACATTGAGGCTCA	0.577																																					p.N466N		Atlas-SNP	.											.	PLA2G4D	72	.	0			c.T1398C						.						198	187	191					15																	42364510		2203	4299	6502	SO:0001819	synonymous_variant	283748	exon14			TTTGACATTGAGG	AB090876	CCDS32203.1	15q14	2008-09-19				ENSG00000159337	3.1.1.4		30038	protein-coding gene	gene with protein product		612864				14709560	Standard	NM_178034		Approved	cPLA2delta	uc001zox.3	Q86XP0		ENST00000290472.3:c.1398T>C	chr15.hg19:g.42364510A>G		51.0	0.0		42.0	20.0	NM_178034	Q8N176	Silent	SNP	ENST00000290472.3	hg19	CCDS32203.1																																																																																			.	.		0.577	PLA2G4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419317.1	NM_178034		G	42364510	A	G	42364510	2	3	344	1	0	0	0	0	0	0	0	1	12013	214	8	2		2	PLA2G4D	15	42364510	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	230489	42364510	60166882	1035	48398										
LRRC57	255252	hgsc.bcm.edu	37	chr15	42839595	42839595	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggggaggtaatgctcccagtTggttcccagagaggctcagg	16	9	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:42839595T>A	ENST00000323443.2	-	3	723	c.356A>T	c.(355-357)cAa>cTa	p.Q119L	HAUS2_ENST00000568876.1_5'Flank|LRRC57_ENST00000563454.1_Missense_Mutation_p.Q119L|HAUS2_ENST00000568846.2_5'Flank|LRRC57_ENST00000397130.3_Missense_Mutation_p.Q119L|HAUS2_ENST00000260372.3_5'Flank			Q8N9N7	LRC57_HUMAN	leucine rich repeat containing 57	119						extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|lung(5)|prostate(1)	8		all_cancers(109;1.99e-12)|all_epithelial(112;5.11e-11)|Lung NSC(122;4.53e-07)|all_lung(180;1.64e-06)|Melanoma(134;0.0262)		GBM - Glioblastoma multiforme(94;6.87e-07)		TGCTCCCAGTTGGTTCCCAGA	0.507																																					p.Q119L		Atlas-SNP	.											.	LRRC57	20	.	0			c.A356T						.						89	79	82					15																	42839595		2203	4299	6502	SO:0001583	missense	255252	exon4			CCCAGTTGGTTCC	AK094891	CCDS10089.1	15q15.1	2006-02-13			ENSG00000180979	ENSG00000180979			26719	protein-coding gene	gene with protein product							Standard	NM_153260		Approved	FLJ36812	uc001zqc.3	Q8N9N7	OTTHUMG00000130679	ENST00000323443.2:c.356A>T	chr15.hg19:g.42839595T>A	ENSP00000326817:p.Gln119Leu	89.0	0.0		80.0	42.0	NM_153260	Q7Z2Z6|Q8N1T6	Missense_Mutation	SNP	ENST00000323443.2	hg19	CCDS10089.1	.	.	.	.	.	.	.	.	.	.	T	15.48	2.844831	0.51164	.	.	ENSG00000180979	ENST00000323443;ENST00000397130	T;T	0.56941	0.43;0.43	5.41	1.8	0.24995	.	0.344931	0.35207	N	0.003370	T	0.33702	0.0872	N	0.17278	0.47	0.48762	D	0.999705	B	0.09022	0.002	B	0.10450	0.005	T	0.12192	-1.0557	10	0.59425	D	0.04	.	9.2621	0.37619	0.0:0.2087:0.0:0.7913	.	119	Q8N9N7	LRC57_HUMAN	L	119	ENSP00000326817:Q119L;ENSP00000380319:Q119L	ENSP00000326817:Q119L	Q	-	2	0	LRRC57	40626887	1.000000	0.71417	0.963000	0.40424	0.958000	0.62258	2.021000	0.41020	0.428000	0.26173	-0.256000	0.11100	CAA	.	.		0.507	LRRC57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253174.1	NM_153260		A	42839595	T	A	42839595	3	1	344	1	0	0	0	0	1	0	0	0	9022	1812	63	4	375	4	LRRC57	15	42839595	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	475085	42839595	59691797	1036	48399										
EPB42	2038	hgsc.bcm.edu	37	chr15	43500883	43500883	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tctgaagtccctcctcattaTagtattcatctatgagaaga	6	9	4	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:43500883T>C	ENST00000441366.2	-	7	1148	c.923A>G	c.(922-924)tAt>tGt	p.Y308C	EPB42_ENST00000540029.1_Missense_Mutation_p.Y230C|EPB42_ENST00000300215.3_Missense_Mutation_p.Y338C|EPB42_ENST00000563128.1_5'Flank	NM_000119.2|NM_001114134.1	NP_000110.2|NP_001107606.1	P16452	EPB42_HUMAN	erythrocyte membrane protein band 4.2	308					cell morphogenesis (GO:0000902)|erythrocyte maturation (GO:0043249)|hemoglobin metabolic process (GO:0020027)|iron ion homeostasis (GO:0055072)|peptide cross-linking (GO:0018149)|regulation of cell shape (GO:0008360)|spleen development (GO:0048536)	cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)|structural constituent of cytoskeleton (GO:0005200)			endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.7e-07)		CTCCTCATTATAGTATTCATC	0.572																																					p.Y338C		Atlas-SNP	.											.	EPB42	53	.	0			c.A1013G						.						140	145	143					15																	43500883		2203	4299	6502	SO:0001583	missense	2038	exon7			TCATTATAGTATT	M60298	CCDS10093.1, CCDS45249.1	15q15-q21	2013-05-02			ENSG00000166947	ENSG00000166947		"Transglutaminases"	3381	protein-coding gene	gene with protein product	"Erythrocyte surface protein band 4.2"	177070				1284644	Standard	NM_000119		Approved	PA, MGC116735, MGC116737	uc001zrb.4	P16452	OTTHUMG00000130701	ENST00000441366.2:c.923A>G	chr15.hg19:g.43500883T>C	ENSP00000396616:p.Tyr308Cys	120.0	0.0		139.0	65.0	NM_000119	Q4KKX0|Q4VB97	Missense_Mutation	SNP	ENST00000441366.2	hg19	CCDS45249.1	.	.	.	.	.	.	.	.	.	.	T	18.38	3.612266	0.66672	.	.	ENSG00000166947	ENST00000300215;ENST00000540029;ENST00000441366;ENST00000397027	T;T;T	0.53423	0.62;0.62;0.62	5.15	5.15	0.70609	Transglutaminase-like (2);	0.000000	0.85682	D	0.000000	T	0.73125	0.3547	M	0.90082	3.085	0.46749	D	0.999186	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.998;0.999	T	0.79298	-0.1861	10	0.87932	D	0	-20.394	12.9755	0.58534	0.0:0.0:0.0:1.0	.	230;308;338;308	F5H563;B7Z4C3;P16452-2;P16452	.;.;.;EPB42_HUMAN	C	338;230;308;308	ENSP00000300215:Y338C;ENSP00000444699:Y230C;ENSP00000396616:Y308C	ENSP00000300215:Y338C	Y	-	2	0	EPB42	41288175	0.937000	0.31787	1.000000	0.80357	0.638000	0.38207	1.565000	0.36386	2.163000	0.67991	0.459000	0.35465	TAT	.	.		0.572	EPB42-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432219.1	NM_000119		C	43500883	T	C	43500883	3	2	344	1	0	0	0	0	1	0	0	0	5160	1406	49	2	1180	2	EPB42	15	43500883	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	661288	43500883	59030509	1037	48400										
TGM7	116179	hgsc.bcm.edu	37	chr15	43571862	43571862	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	catccgcactgtgtgcctccAgaagggcttctgggtaccac	11	14	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:43571862A>C	ENST00000452443.2	-	10	1643	c.1639T>G	c.(1639-1641)Tgg>Ggg	p.W547G		NM_052955.2	NP_443187.1	Q96PF1	TGM7_HUMAN	transglutaminase 7	547					peptide cross-linking (GO:0018149)		metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(2)|prostate(4)|skin(1)	39		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.14e-07)	L-Glutamine(DB00130)	GTGTGCCTCCAGAAGGGCTTC	0.637																																					p.W547G		Atlas-SNP	.											.	TGM7	86	.	0			c.T1639G						.						106	107	107					15																	43571862		2202	4299	6501	SO:0001583	missense	116179	exon10			GCCTCCAGAAGGG	AF363393	CCDS32213.1	15q15.2	2004-07-01				ENSG00000159495		"Transglutaminases"	30790	protein-coding gene	gene with protein product	"transglutaminase Z"	606776				11390390	Standard	NM_052955		Approved	TGMZ	uc001zrf.1	Q96PF1		ENST00000452443.2:c.1639T>G	chr15.hg19:g.43571862A>C	ENSP00000389466:p.Trp547Gly	49.0	0.0		37.0	11.0	NM_052955		Missense_Mutation	SNP	ENST00000452443.2	hg19	CCDS32213.1	.	.	.	.	.	.	.	.	.	.	A	10.06	1.247070	0.22796	.	.	ENSG00000159495	ENST00000452443	T	0.32023	1.47	4.69	3.55	0.40652	Transglutaminase, C-terminal (1);Immunoglobulin-like fold (1);	0.066277	0.64402	N	0.000004	T	0.21881	0.0527	L	0.39326	1.205	0.35313	D	0.784082	B	0.12630	0.006	B	0.09377	0.004	T	0.17623	-1.0363	10	0.22109	T	0.4	-11.164	8.3372	0.32221	0.8002:0.1998:0.0:0.0	.	547	Q96PF1	TGM7_HUMAN	G	547	ENSP00000389466:W547G	ENSP00000389466:W547G	W	-	1	0	TGM7	41359154	1.000000	0.71417	0.975000	0.42487	0.513000	0.34164	4.364000	0.59479	0.805000	0.34159	0.533000	0.62120	TGG	.	.		0.637	TGM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432489.1	NM_052955		C	43571862	A	C	43571862	3	2	344	1	0	0	0	0	1	0	0	0	15850	188	7	5	509	5	TGM7	15	43571862	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	70979	43571862	58959530	1038	48401										
WDR76	79968	hgsc.bcm.edu	37	chr15	44158449	44158449	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtagaaatcttccatgagacAggaaagagggtgcattcgtt	12	6	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:44158449A>C	ENST00000263795.6	+	13	1810	c.1740A>C	c.(1738-1740)acA>acC	p.T580T	WDR76_ENST00000478130.1_3'UTR|Y_RNA_ENST00000363521.1_RNA|WDR76_ENST00000381246.2_Silent_p.T516T	NM_001167941.1|NM_024908.3	NP_001161413.1|NP_079184.2	Q9H967	WDR76_HUMAN	WD repeat domain 76	580										breast(1)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)	20		all_cancers(109;3.26e-11)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.61e-06)|all_lung(180;1.5e-05)|Melanoma(134;0.0417)		all cancers(107;3.78e-21)|GBM - Glioblastoma multiforme(94;5.04e-07)		TCCATGAGACAGGAAAGAGGG	0.493																																					p.T580T		Atlas-SNP	.											.	WDR76	34	.	0			c.A1740C						.						197	157	171					15																	44158449		2198	4298	6496	SO:0001819	synonymous_variant	79968	exon13			TGAGACAGGAAAG	AK023035	CCDS10106.1, CCDS53938.1	15q15.3	2013-01-09			ENSG00000092470	ENSG00000092470		"WD repeat domain containing"	25773	protein-coding gene	gene with protein product						12860291	Standard	NM_024908		Approved	FLJ12973	uc001zti.2	Q9H967	OTTHUMG00000060143	ENST00000263795.6:c.1740A>C	chr15.hg19:g.44158449A>C		126.0	0.0		141.0	57.0	NM_024908	A0MNP5|Q05CI4	Silent	SNP	ENST00000263795.6	hg19	CCDS10106.1																																																																																			.	.		0.493	WDR76-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133482.2	NM_024908		C	44158449	A	C	44158449	2	2	344	1	0	0	0	0	0	0	0	1	17341	175	7	5		5	WDR76	15	44158449	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	586587	44158449	58372943	1039	48402										
SEMA6D	80031	hgsc.bcm.edu	37	chr15	48058822	48058822	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cataaccacagtgctgaaggAtatgaacaagacacagaatt	8	8	0	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:48058822A>G	ENST00000316364.5	+	16	2095	c.1656A>G	c.(1654-1656)ggA>ggG	p.G552G	SEMA6D_ENST00000558816.1_Silent_p.G552G|SEMA6D_ENST00000537942.1_Silent_p.G565G|SEMA6D_ENST00000355997.3_Silent_p.G552G|SEMA6D_ENST00000389428.3_Silent_p.G552G|SEMA6D_ENST00000389433.2_Silent_p.G552G|SEMA6D_ENST00000358066.4_Silent_p.G565G|SEMA6D_ENST00000389432.2_Silent_p.G565G|SEMA6D_ENST00000536845.2_Silent_p.G552G|SEMA6D_ENST00000354744.4_Silent_p.G552G|SEMA6D_ENST00000558014.1_Silent_p.G565G	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	552	PSI.				axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		GTGCTGAAGGATATGAACAAG	0.453																																					p.G565G		Atlas-SNP	.											.	SEMA6D	322	.	0			c.A1695G						.						153	128	136					15																	48058822		2198	4297	6495	SO:0001819	synonymous_variant	80031	exon16			TGAAGGATATGAA	AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"Semaphorins"	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.1656A>G	chr15.hg19:g.48058822A>G		105.0	0.0		88.0	44.0	NM_020858	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Silent	SNP	ENST00000316364.5	hg19	CCDS32225.1																																																																																			.	.		0.453	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966		G	48058822	A	G	48058822	2	3	344	1	0	0	0	0	0	0	0	1	14057	320	12	2		2	SEMA6D	15	48058822	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3900373	48058822	54472570	1040	48403										
FBN1	2200	hgsc.bcm.edu	37	chr15	48756135	48756135	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	attcacttgcatgtagtctgGaggacagatacaggtgtagt	12	6	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:48756135G>T	ENST00000316623.5	-	41	5481	c.5026C>A	c.(5026-5028)Cca>Aca	p.P1676T		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	1676	EGF-like 28; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		atgtagTCTGGAGGACAGATA	0.433																																					p.P1676T		Atlas-SNP	.											.	FBN1	310	.	0			c.C5026A						.						159	136	144					15																	48756135		2198	4296	6494	SO:0001583	missense	2200	exon41			AGTCTGGAGGACA	X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.5026C>A	chr15.hg19:g.48756135G>T	ENSP00000325527:p.Pro1676Thr	77.0	0.0		57.0	24.0	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	hg19	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.260324	0.80246	.	.	ENSG00000166147	ENST00000316623;ENST00000389087;ENST00000544030	D	0.92099	-2.97	5.73	5.73	0.89815	EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.098441	0.64402	D	0.000001	D	0.94381	0.8193	L	0.41415	1.275	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93330	0.6700	10	0.41790	T	0.15	.	19.8579	0.96771	0.0:0.0:1.0:0.0	.	1676	P35555	FBN1_HUMAN	T	1676;244;566	ENSP00000325527:P1676T	ENSP00000325527:P1676T	P	-	1	0	FBN1	46543427	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.321000	0.72881	2.868000	0.98415	0.555000	0.69702	CCA	.	.		0.433	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			T	48756135	G	T	48756135	3	4	344	1	0	0	0	0	1	0	0	0	5710	1174	41	3	3693	3	FBN1	15	48756135	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	697313	48756135	53775257	1041	48404										
C15orf33	196951	hgsc.bcm.edu	37	chr15	49867301	49867301	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtcttccagattttaaaaacTctttcctatggaaaaaaaca	4	8	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:49867301T>G	ENST00000299338.6	-	8	855	c.552A>C	c.(550-552)agA>agC	p.R184S	FAM227B_ENST00000561064.1_Missense_Mutation_p.R184S	NM_152647.2	NP_689860.2	Q96M60	F227B_HUMAN	family with sequence similarity 227, member B	184																	TTTTAAAAACTCTTTCCTATG	0.328																																					p.R184S		Atlas-SNP	.											.	.	.	.	0			c.A552C						.						42	46	45					15																	49867301		2196	4293	6489	SO:0001583	missense	196951	exon8			AAAAACTCTTTCC		CCDS32237.1	15q21.2	2012-07-04	2012-07-04	2012-07-04	ENSG00000166262	ENSG00000166262			26543	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 33"	C15orf33			Standard	NM_152647		Approved	FLJ32800	uc001zxl.2	Q96M60	OTTHUMG00000172328	ENST00000299338.6:c.552A>C	chr15.hg19:g.49867301T>G	ENSP00000299338:p.Arg184Ser	329.0	0.0		271.0	115.0	NM_152647	Q86WS2	Missense_Mutation	SNP	ENST00000299338.6	hg19	CCDS32237.1	.	.	.	.	.	.	.	.	.	.	T	12.71	2.020484	0.35606	.	.	ENSG00000166262	ENST00000299338;ENST00000354658	.	.	.	4.55	-0.417	0.12347	.	0.278625	0.25642	N	0.029271	T	0.19927	0.0479	N	0.08118	0	0.09310	N	1	B;B	0.15473	0.013;0.001	B;B	0.19391	0.025;0.003	T	0.17198	-1.0377	9	0.44086	T	0.13	-11.4846	8.2466	0.31693	0.0:0.4278:0.0:0.5722	.	184;184	Q96M60-2;Q96M60	.;CO033_HUMAN	S	184	.	ENSP00000299338:R184S	R	-	3	2	C15orf33	47654593	0.000000	0.05858	0.019000	0.16419	0.471000	0.32888	-0.011000	0.12721	0.005000	0.14708	-0.609000	0.04063	AGA	.	.		0.328	FAM227B-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417872.1	NM_152647		G	49867301	T	G	49867301	3	3	344	1	0	0	0	0	1	0	0	0	1793	1548	54	5	1010	5	C15orf33	15	49867301	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1111166	49867301	52664091	1042	48405										
AP4E1	23431	hgsc.bcm.edu	37	chr15	51289653	51289653	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttctttgtcaaatgtggcatAtgaagatgattattattcga	8	4	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:51289653A>G	ENST00000261842.5	+	18	2583	c.2477A>G	c.(2476-2478)tAt>tGt	p.Y826C	AP4E1_ENST00000560508.1_Missense_Mutation_p.Y751C	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	826					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	coated pit (GO:0005905)|Golgi apparatus (GO:0005794)|membrane coat (GO:0030117)				breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(5)|skin(2)	27				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		AATGTGGCATATGAAGATGAT	0.348																																					p.Y826C		Atlas-SNP	.											.	AP4E1	78	.	0			c.A2477G						.						134	129	131					15																	51289653		2196	4294	6490	SO:0001583	missense	23431	exon18			TGGCATATGAAGA	AB030653	CCDS32240.1, CCDS58362.1	15q21.2	2014-09-17			ENSG00000081014	ENSG00000081014			573	protein-coding gene	gene with protein product		607244				10436028, 21620353	Standard	NM_007347		Approved	AP-4-EPSILON, SPG51	uc001zyx.2	Q9UPM8	OTTHUMG00000172458	ENST00000261842.5:c.2477A>G	chr15.hg19:g.51289653A>G	ENSP00000261842:p.Tyr826Cys	74.0	0.0		88.0	31.0	NM_007347	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	Missense_Mutation	SNP	ENST00000261842.5	hg19	CCDS32240.1	.	.	.	.	.	.	.	.	.	.	A	8.426	0.847508	0.17034	.	.	ENSG00000081014	ENST00000261842	T	0.17213	2.29	5.47	0.369	0.16151	.	0.879637	0.10114	N	0.714282	T	0.10723	0.0262	N	0.19112	0.55	0.09310	N	1	D	0.55800	0.973	B	0.43754	0.43	T	0.22871	-1.0204	10	0.39692	T	0.17	-0.4456	5.4812	0.16725	0.6491:0.1424:0.2084:0.0	.	826	Q9UPM8	AP4E1_HUMAN	C	826	ENSP00000261842:Y826C	ENSP00000261842:Y826C	Y	+	2	0	AP4E1	49076945	0.032000	0.19561	0.073000	0.20177	0.230000	0.25150	1.112000	0.31172	0.033000	0.15463	0.383000	0.25322	TAT	.	.		0.348	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418656.1			G	51289653	A	G	51289653	3	3	344	1	0	0	0	0	1	0	0	0	752	449	16	2	2547	2	AP4E1	15	51289653	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1422352	51289653	51241739	1043	48406										
KIAA1370	56204	hgsc.bcm.edu	37	chr15	52879347	52879347	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgtaggctataaaacacataCcacttgtattgttcctgaag	7	8	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:52879347C>T	ENST00000261844.7	-	11	3030		c.e11+1		RP11-23N2.4_ENST00000566344.1_RNA|RP11-23N2.4_ENST00000562062.1_RNA|FAM214A_ENST00000546305.2_Splice_Site	NM_019600.2	NP_062546.2	Q32MH5	F214A_HUMAN	family with sequence similarity 214, member A																		AAAACACATACCACTTGTATT	0.378																																					.		Atlas-SNP	.											.	.	.	.	0			c.2877+1G>A						.						142	132	135					15																	52879347		1866	4116	5982	SO:0001630	splice_region_variant	56204	exon12			CACATACCACTTG	AB037791	CCDS45263.1, CCDS66773.1	15q21.2-q21.3	2011-12-01	2011-12-01	2011-12-01	ENSG00000047346	ENSG00000047346			25609	protein-coding gene	gene with protein product			"KIAA1370"	KIAA1370		10718198	Standard	XM_005254547		Approved	FLJ10980	uc002acg.4	Q32MH5		ENST00000261844.7:c.2877+1G>A	chr15.hg19:g.52879347C>T		114.0	0.0		63.0	25.0	NM_019600	A8KA52|B4DEP5|B4DF40|F5H8G0|Q32MH6|Q4G0R7|Q5XJ16|Q6PDA3|Q9NV24|Q9P2H7	Splice_Site	SNP	ENST00000261844.7	hg19	CCDS45263.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.306491	0.81247	.	.	ENSG00000047346	ENST00000261844;ENST00000399202;ENST00000546305	.	.	.	5.17	5.17	0.71159	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.7072	0.91643	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	KIAA1370	50666639	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.429000	0.80309	2.405000	0.81733	0.650000	0.86243	.	.	.		0.378	FAM214A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419914.1	NM_019600	Intron	T	52879347	C	T	52879347	5	4	344	1	0	0	0	0	0	0	1	0	8235	521	18	3	364	3	KIAA1370	15	52879347	Splice_Site	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1589694	52879347	49652045	1044	48407										
RNF111	54778	hgsc.bcm.edu	37	chr15	59373264	59373264	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcatcctgtacatgctttccAttctcaaatatcttctcatg	3	12	4	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:59373264A>G	ENST00000557998.1	+	8	2365	c.2078A>G	c.(2077-2079)cAt>cGt	p.H693R	RNF111_ENST00000434298.1_Missense_Mutation_p.H693R|RNF111_ENST00000561186.1_Missense_Mutation_p.H693R|RNF111_ENST00000559209.1_Missense_Mutation_p.H693R|RNF111_ENST00000348370.4_Missense_Mutation_p.H693R	NM_001270530.1	NP_001257459.1	Q6ZNA4	RN111_HUMAN	ring finger protein 111	693	Pro-rich.				gene expression (GO:0010467)|pattern specification process (GO:0007389)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein polyubiquitination (GO:0000209)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|SUMO polymer binding (GO:0032184)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35				all cancers(107;0.194)		CATGCTTTCCATTCTCAAATA	0.512																																					p.H693R	NSCLC(72;983 1365 10746 34387 47081)	Atlas-SNP	.											.	RNF111	179	.	0			c.A2078G						.						281	247	259					15																	59373264		2192	4291	6483	SO:0001583	missense	54778	exon8			CTTTCCATTCTCA	AL157474	CCDS10169.1, CCDS58365.1, CCDS58366.1	15q21	2013-01-09			ENSG00000157450	ENSG00000157450		"RING-type (C3HC4) zinc fingers"	17384	protein-coding gene	gene with protein product		605840				11298452	Standard	NM_017610		Approved	ARK, Arkadia, FLJ38008, DKFZP761D081	uc002aft.4	Q6ZNA4	OTTHUMG00000132716	ENST00000557998.1:c.2078A>G	chr15.hg19:g.59373264A>G	ENSP00000452732:p.His693Arg	202.0	0.0		199.0	91.0	NM_017610	C9JUS4|H0YN55|Q6P9A4|Q6ZMU2|Q7L428|Q7Z346|Q8N1P9|Q8WUA3|Q9NSR1	Missense_Mutation	SNP	ENST00000557998.1	hg19	CCDS58366.1	.	.	.	.	.	.	.	.	.	.	A	17.69	3.451784	0.63290	.	.	ENSG00000157450	ENST00000348370;ENST00000434298	T;T	0.15952	2.4;2.38	5.31	5.31	0.75309	.	0.163774	0.53938	D	0.000055	T	0.27731	0.0682	L	0.44542	1.39	0.58432	D	0.999994	D;D;D	0.65815	0.995;0.989;0.993	P;P;P	0.60473	0.875;0.688;0.835	T	0.01225	-1.1413	10	0.37606	T	0.19	-11.4673	10.5124	0.44870	0.8555:0.0:0.0:0.1445	.	693;693;693	Q6ZNA4-3;Q6ZNA4;Q6ZNA4-2	.;RN111_HUMAN;.	R	693	ENSP00000288199:H693R;ENSP00000393641:H693R	ENSP00000288199:H693R	H	+	2	0	RNF111	57160556	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.495000	0.66912	2.021000	0.59480	0.383000	0.25322	CAT	.	.		0.512	RNF111-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000416012.1	NM_017610		G	59373264	A	G	59373264	3	3	344	1	0	0	0	0	1	0	0	0	13440	217	8	2	2104	2	RNF111	15	59373264	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	6493917	59373264	43158128	1045	48408										
VPS13C	54832	hgsc.bcm.edu	37	chr15	62223325	62223325	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	caattccttctctgagatcaTcaagggtgcatgtcttaagt	8	9	4	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:62223325T>G	ENST00000261517.5	-	50	6075	c.6002A>C	c.(6001-6003)gAt>gCt	p.D2001A	VPS13C_ENST00000395896.4_Missense_Mutation_p.D2001A|VPS13C_ENST00000395898.3_Missense_Mutation_p.D1958A|VPS13C_ENST00000249837.3_Missense_Mutation_p.D1958A	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						TCTGAGATCATCAAGGGTGCA	0.438																																					p.D2001A		Atlas-SNP	.											.	VPS13C	506	.	0			c.A6002C						.						154	131	139					15																	62223325		2203	4300	6503	SO:0001583	missense	54832	exon50			AGATCATCAAGGG	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"vacuolar protein sorting 13C (yeast)"				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.6002A>C	chr15.hg19:g.62223325T>G	ENSP00000261517:p.Asp2001Ala	96.0	0.0		91.0	41.0	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	hg19	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.588936	0.86851	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.51325	0.71;0.71;0.9	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.69860	0.3158	M	0.78637	2.42	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.997;0.998;0.997;0.996	T	0.74241	-0.3729	10	0.72032	D	0.01	.	15.7481	0.77962	0.0:0.0:0.0:1.0	.	1958;2001;1958;2001	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	A	1958;2001;2001;2001	ENSP00000249837:D1958A;ENSP00000261517:D2001A;ENSP00000379233:D2001A	ENSP00000249837:D1958A	D	-	2	0	VPS13C	60010617	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.669000	0.74462	2.168000	0.68352	0.528000	0.53228	GAT	.	.		0.438	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		G	62223325	T	G	62223325	3	3	344	1	0	0	0	0	1	0	0	0	17206	1435	50	5	5431	5	VPS13C	15	62223325	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2850061	62223325	40308067	1046	48409										
TLN2	83660	hgsc.bcm.edu	37	chr15	63102125	63102125	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cattcctttctctctccagcAagcatccttccaccccgatg	4	18	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:63102125A>C	ENST00000561311.1	+	51	6895	c.6665A>C	c.(6664-6666)cAa>cCa	p.Q2222P	TLN2_ENST00000306829.6_Splice_Site_p.Q2222P			Q9Y4G6	TLN2_HUMAN	talin 2	2222					cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						TCTCTCCAGCAAGCATCCTTC	0.547																																					p.Q2222P		Atlas-SNP	.											.	TLN2	253	.	0			c.A6665C						.						101	73	83					15																	63102125		2203	4300	6503	SO:0001630	splice_region_variant	83660	exon49			TCCAGCAAGCATC	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.6664-1A>C	chr15.hg19:g.63102125A>C		119.0	0.0		88.0	46.0	NM_015059	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	hg19	CCDS32261.1	.	.	.	.	.	.	.	.	.	.	A	15.30	2.792369	0.50102	.	.	ENSG00000171914	ENST00000306829	T	0.68331	-0.32	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.64670	0.2619	L	0.57536	1.79	0.80722	D	1	B	0.17268	0.021	B	0.17098	0.017	T	0.60632	-0.7225	10	0.38643	T	0.18	-10.3349	15.9649	0.79961	1.0:0.0:0.0:0.0	.	2222	Q9Y4G6	TLN2_HUMAN	P	2222	ENSP00000303476:Q2222P	ENSP00000303476:Q2222P	Q	+	2	0	TLN2	60889178	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	9.287000	0.95975	2.178000	0.69098	0.459000	0.35465	CAA	.	.		0.547	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2		Missense_Mutation	C	63102125	A	C	63102125	5	2	344	1	0	0	0	0	0	0	1	0	15963	144	5	5	6859	5	TLN2	15	63102125	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	878800	63102125	39429267	1047	48410										
MEGF11	84465	hgsc.bcm.edu	37	chr15	66222097	66222097	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtgtctcccagccagccaggAgtgcaggagcaggagccgtc	15	13	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:66222097A>T	ENST00000409699.2	-	12	1705	c.1533T>A	c.(1531-1533)acT>acA	p.T511T	MEGF11_ENST00000422354.1_Silent_p.T511T|MEGF11_ENST00000395625.2_Silent_p.T436T|MEGF11_ENST00000288745.3_Silent_p.T436T|MEGF11_ENST00000360698.4_Silent_p.T511T|MEGF11_ENST00000395614.1_5'UTR			A6BM72	MEG11_HUMAN	multiple EGF-like-domains 11	511	EGF-like 9. {ECO:0000255|PROSITE- ProRule:PRU00076}.				homotypic cell-cell adhesion (GO:0034109)|retina layer formation (GO:0010842)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	19						GCCAGCCAGGAGTGCAGGAGC	0.667																																					p.T511T		Atlas-SNP	.											.	MEGF11	70	.	0			c.T1533A						.						35	26	29					15																	66222097		2184	4250	6434	SO:0001819	synonymous_variant	84465	exon12			GCCAGGAGTGCAG	AB058677	CCDS10213.2	15q22.31	2006-03-31			ENSG00000157890	ENSG00000157890			29635	protein-coding gene	gene with protein product		612454				11347906	Standard	NM_032445		Approved	KIAA1781, DKFZp434L121	uc002apm.2	A6BM72	OTTHUMG00000133175	ENST00000409699.2:c.1533T>A	chr15.hg19:g.66222097A>T		105.0	0.0		98.0	36.0	NM_032445	Q17R86|Q6UXS5|Q8ND91|Q96KG6	Silent	SNP	ENST00000409699.2	hg19	CCDS10213.2																																																																																			.	.		0.667	MEGF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329307.2	NM_032445		T	66222097	A	T	66222097	2	4	344	1	0	0	0	0	0	0	0	1	9470	291	11	4		4	MEGF11	15	66222097	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3119972	66222097	36309295	1048	48411										
RPL4	6124	hgsc.bcm.edu	37	chr15	66795504	66795504	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcagcactagtctgatgaccTaaaattgagaagagataaaa	8	6	2	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:66795504T>A	ENST00000307961.6	-	3	268		c.e3-2		SNORD16_ENST00000362803.1_RNA|ZWILCH_ENST00000307897.5_5'Flank|RPL4_ENST00000564517.1_5'Flank|ZWILCH_ENST00000535141.2_5'Flank|SNORD18A_ENST00000363753.1_RNA|RPL4_ENST00000568588.1_Splice_Site|SNORD18B_ENST00000365659.1_RNA|ZWILCH_ENST00000565627.1_5'Flank|SNORD18C_ENST00000362704.1_RNA|ZWILCH_ENST00000446801.2_5'Flank	NM_000968.3	NP_000959.2	P36578	RL4_HUMAN	ribosomal protein L4						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|stomach(1)|urinary_tract(1)	17						TCTGATGACCTAAAATTGAGA	0.478																																					.		Atlas-SNP	.											.	RPL4	29	.	0			c.176-2A>T						.						40	40	40					15																	66795504		2201	4299	6500	SO:0001630	splice_region_variant	6124	exon4			ATGACCTAAAATT	AB007167	CCDS10218.1	15q22	2011-04-06			ENSG00000174444	ENSG00000174444		"L ribosomal proteins"	10353	protein-coding gene	gene with protein product	"60S ribosomal protein L4"	180479				9582194, 8268230	Standard	NM_000968		Approved	L4	uc002apv.3	P36578	OTTHUMG00000133193	ENST00000307961.6:c.176-2A>T	chr15.hg19:g.66795504T>A		110.0	0.0		115.0	44.0	NM_000968	A8K502|P39029|Q4VBR0|Q969Z9	Splice_Site	SNP	ENST00000307961.6	hg19	CCDS10218.1	.	.	.	.	.	.	.	.	.	.	T	17.77	3.471942	0.63737	.	.	ENSG00000174444	ENST00000307961;ENST00000449253;ENST00000432669	.	.	.	4.75	4.75	0.60458	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4518	0.67389	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	RPL4	64582558	1.000000	0.71417	0.932000	0.37286	0.768000	0.43524	7.668000	0.83897	2.000000	0.58554	0.454000	0.30748	.	.	.		0.478	RPL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256903.2	NM_000968	Intron	A	66795504	T	A	66795504	5	1	344	1	0	0	0	0	0	0	1	0	13610	1536	53	4	1141	4	RPL4	15	66795504	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	573407	66795504	35735888	1049	48412										
ITGA11	22801	hgsc.bcm.edu	37	chr15	68624266	68624266	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atggctcctgcgtggttgtcCtccaggggggctcccaccac	13	15	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:68624266C>T	ENST00000315757.7	-	14	1787	c.1701G>A	c.(1699-1701)gaG>gaA	p.E567E	ITGA11_ENST00000423218.2_Silent_p.E567E	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	567					cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|collagen-activated signaling pathway (GO:0038065)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|osteoblast differentiation (GO:0001649)|substrate-dependent cell migration (GO:0006929)	focal adhesion (GO:0005925)|integrin alpha11-beta1 complex (GO:0034681)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(6)|lung(22)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	52						CGTGGTTGTCCTCCAGGGGGG	0.577																																					p.E567E		Atlas-SNP	.											.	ITGA11	110	.	0			c.G1701A						.						57	56	56					15																	68624266		1983	4152	6135	SO:0001819	synonymous_variant	22801	exon14			GTTGTCCTCCAGG	AF109681	CCDS45291.1	15q22.3-q23	2010-03-23				ENSG00000137809		"Integrins"	6136	protein-coding gene	gene with protein product		604789				10486209	Standard	NM_001004439		Approved	HsT18964	uc002ari.3	Q9UKX5		ENST00000315757.7:c.1701G>A	chr15.hg19:g.68624266C>T		100.0	0.0		104.0	57.0	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Silent	SNP	ENST00000315757.7	hg19	CCDS45291.1																																																																																			.	.		0.577	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211		T	68624266	C	T	68624266	2	4	344	1	0	0	0	0	0	0	0	1	7883	680	24	3		3	ITGA11	15	68624266	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1828762	68624266	33907126	1050	48413										
ITGA11	22801	hgsc.bcm.edu	37	chr15	68624312	68624312	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cattgtaggaatcctggttgAggtctcgaactgaggcaatg	13	7	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:68624312A>T	ENST00000315757.7	-	14	1741	c.1655T>A	c.(1654-1656)cTc>cAc	p.L552H	ITGA11_ENST00000423218.2_Missense_Mutation_p.L552H	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	552					cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|collagen-activated signaling pathway (GO:0038065)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|osteoblast differentiation (GO:0001649)|substrate-dependent cell migration (GO:0006929)	focal adhesion (GO:0005925)|integrin alpha11-beta1 complex (GO:0034681)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(6)|lung(22)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	52						ATCCTGGTTGAGGTCTCGAAC	0.532																																					p.L552H		Atlas-SNP	.											.	ITGA11	110	.	0			c.T1655A						.						62	60	61					15																	68624312		1971	4161	6132	SO:0001583	missense	22801	exon14			TGGTTGAGGTCTC	AF109681	CCDS45291.1	15q22.3-q23	2010-03-23				ENSG00000137809		"Integrins"	6136	protein-coding gene	gene with protein product		604789				10486209	Standard	NM_001004439		Approved	HsT18964	uc002ari.3	Q9UKX5		ENST00000315757.7:c.1655T>A	chr15.hg19:g.68624312A>T	ENSP00000327290:p.Leu552His	123.0	0.0		127.0	52.0	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Missense_Mutation	SNP	ENST00000315757.7	hg19	CCDS45291.1	.	.	.	.	.	.	.	.	.	.	A	18.44	3.624455	0.66901	.	.	ENSG00000137809	ENST00000315757;ENST00000423218;ENST00000535491;ENST00000537153	T;T	0.12984	2.63;2.63	4.67	4.67	0.58626	.	0.140675	0.49305	D	0.000156	T	0.48995	0.1531	H	0.97103	3.94	0.45490	D	0.99845	D;D	0.69078	0.997;0.992	D;D	0.64506	0.926;0.926	T	0.67047	-0.5769	10	0.87932	D	0	.	13.3244	0.60450	1.0:0.0:0.0:0.0	.	552;552	A8K8T0;Q9UKX5	.;ITA11_HUMAN	H	552;552;187;552	ENSP00000327290:L552H;ENSP00000403392:L552H	ENSP00000327290:L552H	L	-	2	0	ITGA11	66411366	1.000000	0.71417	1.000000	0.80357	0.477000	0.33069	8.882000	0.92420	1.747000	0.51819	0.374000	0.22700	CTC	.	.		0.532	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211		T	68624312	A	T	68624312	3	4	344	1	0	0	0	0	1	0	0	0	7883	304	11	4	1979	4	ITGA11	15	68624312	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	46	68624312	33907080	1051	48414										
CORO2B	10391	hgsc.bcm.edu	37	chr15	69006317	69006317	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtggtgttcctggggaacatGaagcggctcctcacgacagg	15	10	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:69006317G>T	ENST00000566799.1	+	6	731	c.702G>T	c.(700-702)atG>atT	p.M234I	CORO2B_ENST00000543950.1_Missense_Mutation_p.M229I|CORO2B_ENST00000540068.1_Missense_Mutation_p.M229I|CORO2B_ENST00000261861.5_Missense_Mutation_p.M229I			Q9UQ03	COR2B_HUMAN	coronin, actin binding protein, 2B	234					actin cytoskeleton organization (GO:0030036)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|membrane (GO:0016020)	actin binding (GO:0003779)|actin filament binding (GO:0051015)	p.M234I(1)		kidney(3)|large_intestine(13)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36						TGGGGAACATGAAGCGGCTCC	0.597																																					p.M234I		Atlas-SNP	.											CORO2B,NS,carcinoma,0,1	CORO2B	68	.	1	Substitution - Missense(1)	lung(1)	c.G702T						.						81	63	69					15																	69006317		2200	4298	6498	SO:0001583	missense	10391	exon6			GAACATGAAGCGG	AB010098	CCDS53952.1, CCDS10229.2	15q22.31	2013-01-10	2001-11-28		ENSG00000103647	ENSG00000103647		"Coronins", "WD repeat domain containing"	2256	protein-coding gene	gene with protein product	"clipin C", "coronin, actin-binding, 2B"	605002	"coronin, actin-binding protein, 2B"			10224093, 10231032	Standard	NM_001190456		Approved	ClipinC, KIAA0925	uc021spj.1	Q9UQ03	OTTHUMG00000133288	ENST00000566799.1:c.702G>T	chr15.hg19:g.69006317G>T	ENSP00000454783:p.Met234Ile	94.0	0.0		61.0	20.0	NM_006091	A8K0W3|O94767|Q8TAN1	Missense_Mutation	SNP	ENST00000566799.1	hg19	CCDS10229.2	.	.	.	.	.	.	.	.	.	.	G	11.98	1.800776	0.31869	.	.	ENSG00000103647	ENST00000261861;ENST00000540068;ENST00000543950	T;T	0.57595	0.39;0.39	5.34	3.34	0.38264	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.236530	0.49305	D	0.000159	T	0.44498	0.1296	M	0.62723	1.935	0.43453	D	0.995647	B	0.02656	0.0	B	0.04013	0.001	T	0.30268	-0.9984	10	0.19147	T	0.46	-27.8533	8.4511	0.32871	0.0863:0.1563:0.7574:0.0	.	234	Q9UQ03	COR2B_HUMAN	I	234;229;229	ENSP00000446250:M229I;ENSP00000443819:M229I	ENSP00000261861:M234I	M	+	3	0	CORO2B	66793371	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.664000	0.46783	1.241000	0.43820	0.655000	0.94253	ATG	.	.		0.597	CORO2B-203	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_006091		T	69006317	G	T	69006317	3	4	344	1	0	0	0	0	1	0	0	0	3759	1290	45	3	724	3	CORO2B	15	69006317	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	382005	69006317	33525075	1052	48415										
GRAMD2	196996	hgsc.bcm.edu	37	chr15	72455799	72455799	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcccaccattttctgaagctActtgggctcttgacttttct	6	12	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:72455799A>G	ENST00000309731.7	-	10	777	c.764T>C	c.(763-765)gTa>gCa	p.V255A	GRAMD2_ENST00000564184.1_5'UTR	NM_001012642.2	NP_001012660.1	Q8IUY3	GRAM2_HUMAN	GRAM domain containing 2	255						integral component of membrane (GO:0016021)				cervix(2)|endometrium(1)|large_intestine(4)|lung(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	13						TTCTGAAGCTACTTGGGCTCT	0.512																																					p.V255A		Atlas-SNP	.											.	GRAMD2	31	.	0			c.T764C						.						88	94	92					15																	72455799		2199	4297	6496	SO:0001583	missense	196996	exon10			GAAGCTACTTGGG	AK002016	CCDS32283.1	15q23	2006-11-29	2005-11-03	2005-11-03					27287	protein-coding gene	gene with protein product						12477932	Standard	NM_001012642		Approved		uc002atq.3	Q8IUY3		ENST00000309731.7:c.764T>C	chr15.hg19:g.72455799A>G	ENSP00000311657:p.Val255Ala	87.0	0.0		85.0	38.0	NM_001012642	B3KT68	Missense_Mutation	SNP	ENST00000309731.7	hg19	CCDS32283.1	.	.	.	.	.	.	.	.	.	.	A	1.877	-0.458878	0.04508	.	.	ENSG00000175318	ENST00000309731	T	0.29917	1.55	3.38	-0.764	0.11027	.	.	.	.	.	T	0.16896	0.0406	L	0.36672	1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35176	-0.9799	9	0.08599	T	0.76	.	4.018	0.09652	0.3381:0.3468:0.3151:0.0	.	255	Q8IUY3	GRAM2_HUMAN	A	255	ENSP00000311657:V255A	ENSP00000311657:V255A	V	-	2	0	GRAMD2	70242853	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.144000	0.03197	-0.139000	0.11414	-0.242000	0.12053	GTA	.	.		0.512	GRAMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420040.1	NM_001012642		G	72455799	A	G	72455799	3	3	344	1	0	0	0	0	1	0	0	0	6759	391	14	2	312	2	GRAMD2	15	72455799	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3449482	72455799	30075593	1053	48416										
HCN4	10021	hgsc.bcm.edu	37	chr15	73614832	73614832	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agggcccagctcatagattgGatggcagtttggagcgcact	14	9	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:73614832G>T	ENST00000261917.3	-	8	4595	c.3602C>A	c.(3601-3603)tCc>tAc	p.S1201Y		NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	1201					blood circulation (GO:0008015)|cation transport (GO:0006812)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)	cAMP binding (GO:0030552)|cation channel activity (GO:0005261)|identical protein binding (GO:0042802)|intracellular cAMP activated cation channel activity (GO:0005222)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(13)|liver(1)|lung(18)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				COAD - Colon adenocarcinoma(1;0.142)		TCATAGATTGGATGGCAGTTT	0.542																																					p.S1201Y		Atlas-SNP	.											.	HCN4	150	.	0			c.C3602A						.						14	15	15					15																	73614832		2192	4284	6476	SO:0001583	missense	10021	exon8			AGATTGGATGGCA	AJ132429	CCDS10248.1	15q24.1	2011-07-05			ENSG00000138622	ENSG00000138622		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	16882	protein-coding gene	gene with protein product		605206				10228147, 10430953, 16382102	Standard	NM_005477		Approved		uc002avp.3	Q9Y3Q4	OTTHUMG00000137563	ENST00000261917.3:c.3602C>A	chr15.hg19:g.73614832G>T	ENSP00000261917:p.Ser1201Tyr	175.0	0.0		143.0	65.0	NM_005477	Q9UMQ7	Missense_Mutation	SNP	ENST00000261917.3	hg19	CCDS10248.1	.	.	.	.	.	.	.	.	.	.	G	13.86	2.364469	0.41902	.	.	ENSG00000138622	ENST00000261917	D	0.98978	-5.29	3.52	3.52	0.40303	.	.	.	.	.	D	0.98710	0.9567	L	0.46157	1.445	0.53688	D	0.999977	D	0.71674	0.998	D	0.77557	0.99	D	0.99250	1.0887	9	0.87932	D	0	.	13.1926	0.59719	0.0:0.0:1.0:0.0	.	1201	Q9Y3Q4	HCN4_HUMAN	Y	1201	ENSP00000261917:S1201Y	ENSP00000261917:S1201Y	S	-	2	0	HCN4	71401885	1.000000	0.71417	0.992000	0.48379	0.347000	0.29111	5.285000	0.65633	1.660000	0.50760	0.305000	0.20034	TCC	.	.		0.542	HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268900.2	NM_005477		T	73614832	G	T	73614832	3	4	344	1	0	0	0	0	1	0	0	0	7008	1174	41	3	13	3	HCN4	15	73614832	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1159033	73614832	28916560	1054	48417										
CD276	80381	hgsc.bcm.edu	37	chr15	73994758	73994758	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gctggtgcacagctttgctgAgggccaggaccagggcagcg	17	11	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:73994758A>G	ENST00000318443.5	+	3	544	c.242A>G	c.(241-243)gAg>gGg	p.E81G	CD276_ENST00000318424.5_Missense_Mutation_p.E81G|CD276_ENST00000564751.1_Missense_Mutation_p.E81G|CD276_ENST00000561213.1_Missense_Mutation_p.E81G|CD276_ENST00000537340.2_5'UTR	NM_001024736.1	NP_001019907.1	Q5ZPR3	CD276_HUMAN	CD276 molecule	81	Ig-like V-type 1.				cell proliferation (GO:0008283)|immune response (GO:0006955)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of bone mineralization (GO:0030501)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|regulation of immune response (GO:0050776)|T cell activation (GO:0042110)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			endometrium(3)|lung(5)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	13						AGCTTTGCTGAGGGCCAGGAC	0.642																																					p.E81G		Atlas-SNP	.											.	CD276	29	.	0			c.A242G						.						56	48	50					15																	73994758		2198	4297	6495	SO:0001583	missense	80381	exon3			TTGCTGAGGGCCA	AF302102	CCDS10251.1, CCDS32288.1	15q23-q24	2013-01-11	2006-03-28		ENSG00000103855	ENSG00000103855		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing"	19137	protein-coding gene	gene with protein product		605715	"CD276 antigen"			11224528, 12055244	Standard	XM_005254699		Approved	B7-H3, B7H3, B7RP-2	uc002avv.1	Q5ZPR3	OTTHUMG00000137585	ENST00000318443.5:c.242A>G	chr15.hg19:g.73994758A>G	ENSP00000320084:p.Glu81Gly	67.0	0.0		58.0	28.0	NM_025240	Q6P5Y4|Q6UXI2|Q8NBI8|Q8NC34|Q8NCB6|Q9BXR1	Missense_Mutation	SNP	ENST00000318443.5	hg19	CCDS32288.1	.	.	.	.	.	.	.	.	.	.	A	2.399	-0.337986	0.05278	.	.	ENSG00000103855	ENST00000318424;ENST00000318443;ENST00000379823;ENST00000543481	T;T	0.65916	-0.18;-0.18	2.84	2.84	0.33178	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.46737	0.1408	L	0.34521	1.04	0.31794	N	0.629227	B;B;B;B	0.09022	0.0;0.002;0.001;0.0	B;B;B;B	0.08055	0.0;0.003;0.002;0.001	T	0.48703	-0.9012	9	0.30078	T	0.28	-3.3593	7.3886	0.26897	0.8049:0.0:0.0:0.195	.	27;81;81;81	B4DK26;Q5ZPR3-2;Q5ZPR3;Q5ZPR3-4	.;.;CD276_HUMAN;.	G	81	ENSP00000320058:E81G;ENSP00000320084:E81G	ENSP00000320058:E81G	E	+	2	0	CD276	71781811	0.950000	0.32346	0.922000	0.36590	0.052000	0.14988	2.737000	0.47393	1.537000	0.49254	0.260000	0.18958	GAG	.	.		0.642	CD276-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268979.1	NM_025240		G	73994758	A	G	73994758	3	3	344	1	0	0	0	0	1	0	0	0	2994	304	11	2	248	2	CD276	15	73994758	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	379926	73994758	28536634	1055	48418										
SEMA7A	8482	hgsc.bcm.edu	37	chr15	74707046	74707046	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctgggtgacggtcagccaccTggaaggtctctgtgggtatc	15	10	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:74707046T>A	ENST00000261918.4	-	10	1684	c.1136A>T	c.(1135-1137)cAg>cTg	p.Q379L	SEMA7A_ENST00000542748.1_Missense_Mutation_p.Q214L|SEMA7A_ENST00000543145.2_Missense_Mutation_p.Q365L	NM_003612.3	NP_003603.1	O75326	SEM7A_HUMAN	semaphorin 7A, GPI membrane anchor (John Milton Hagen blood group)	379	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon extension (GO:0048675)|axon guidance (GO:0007411)|immune response (GO:0006955)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|olfactory lobe development (GO:0021988)|osteoblast differentiation (GO:0001649)|positive regulation of axon extension (GO:0045773)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of protein phosphorylation (GO:0001934)|regulation of inflammatory response (GO:0050727)	anchored component of membrane (GO:0031225)|external side of plasma membrane (GO:0009897)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(3)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(3)|lung(12)|upper_aerodigestive_tract(1)	30						GTCAGCCACCTGGAAGGTCTC	0.627																																					p.Q379L		Atlas-SNP	.											.	SEMA7A	58	.	0			c.A1136T						.						63	71	68					15																	74707046		2197	4296	6493	SO:0001583	missense	8482	exon10			GCCACCTGGAAGG	AF069493	CCDS10262.1, CCDS53958.1, CCDS53959.1	15q22.3-q23	2014-07-18	2006-02-23		ENSG00000138623	ENSG00000138623		"Semaphorins", "CD molecules", "Blood group antigens", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10741	protein-coding gene	gene with protein product	"John Milton Hagen blood group", "H-Sema K1"	607961	"sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A", "sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A (JMH blood group)"	SEMAL		9721204	Standard	NM_003612		Approved	H-Sema-L, CD108	uc002axv.3	O75326	OTTHUMG00000139000	ENST00000261918.4:c.1136A>T	chr15.hg19:g.74707046T>A	ENSP00000261918:p.Gln379Leu	79.0	0.0		61.0	37.0	NM_003612	B4DDP7|F5H1S0|Q1XE81|Q1XE82|Q1XE83|Q1XE84|Q3MIY5	Missense_Mutation	SNP	ENST00000261918.4	hg19	CCDS10262.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.286583	0.80803	.	.	ENSG00000138623	ENST00000261918;ENST00000543145;ENST00000542748	T;T;T	0.23348	1.91;1.91;1.91	5.67	5.67	0.87782	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.246806	0.40064	N	0.001185	T	0.38134	0.1029	M	0.76574	2.34	0.37416	D	0.913449	P;D	0.60160	0.953;0.987	P;P	0.51777	0.55;0.679	T	0.46679	-0.9174	10	0.41790	T	0.15	-25.0977	9.425	0.38574	0.0:0.0808:0.0:0.9192	.	365;379	F5H1S0;O75326	.;SEM7A_HUMAN	L	379;365;214	ENSP00000261918:Q379L;ENSP00000438966:Q365L;ENSP00000441493:Q214L	ENSP00000261918:Q379L	Q	-	2	0	SEMA7A	72494099	0.977000	0.34250	1.000000	0.80357	0.932000	0.56968	2.671000	0.46842	2.166000	0.68216	0.454000	0.30748	CAG	.	.		0.627	SEMA7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272904.3	NM_003612		A	74707046	T	A	74707046	3	1	344	1	0	0	0	0	1	0	0	0	14058	1580	55	4	884	4	SEMA7A	15	74707046	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	712288	74707046	27824346	1056	48419										
CYP1A1	1543	hgsc.bcm.edu	37	chr15	75013936	75013936	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aatggggtaaccataccagcTccaaagaggtccaagacgat	10	10	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:75013936T>C	ENST00000379727.3	-	3	1146	c.948A>G	c.(946-948)ggA>ggG	p.G316G	CYP1A1_ENST00000564596.1_Silent_p.G55G|CYP1A1_ENST00000395049.4_Silent_p.G316G|CYP1A1_ENST00000395048.2_Silent_p.G316G|CYP1A1_ENST00000567032.1_Silent_p.G316G			P04798	CP1A1_HUMAN	cytochrome P450, family 1, subfamily A, polypeptide 1	316					9-cis-retinoic acid biosynthetic process (GO:0042904)|aging (GO:0007568)|amine metabolic process (GO:0009308)|arachidonic acid metabolic process (GO:0019369)|camera-type eye development (GO:0043010)|cell proliferation (GO:0008283)|cellular lipid metabolic process (GO:0044255)|cellular response to organic cyclic compound (GO:0071407)|coumarin metabolic process (GO:0009804)|dibenzo-p-dioxin catabolic process (GO:0019341)|digestive tract development (GO:0048565)|drug metabolic process (GO:0017144)|embryo development ending in birth or egg hatching (GO:0009792)|epoxygenase P450 pathway (GO:0019373)|flavonoid metabolic process (GO:0009812)|hepatocyte differentiation (GO:0070365)|hydrogen peroxide biosynthetic process (GO:0050665)|insecticide metabolic process (GO:0017143)|maternal process involved in parturition (GO:0060137)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound metabolic process (GO:0006778)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|response to antibiotic (GO:0046677)|response to arsenic-containing substance (GO:0046685)|response to drug (GO:0042493)|response to food (GO:0032094)|response to herbicide (GO:0009635)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to iron(III) ion (GO:0010041)|response to lipopolysaccharide (GO:0032496)|response to nematode (GO:0009624)|response to virus (GO:0009615)|response to vitamin A (GO:0033189)|response to wounding (GO:0009611)|small molecule metabolic process (GO:0044281)|vitamin D metabolic process (GO:0042359)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|demethylase activity (GO:0032451)|flavonoid 3'-monooxygenase activity (GO:0016711)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on diphenols and related substances as donors (GO:0016679)|oxygen binding (GO:0019825)|steroid hydroxylase activity (GO:0008395)|vitamin D 24-hydroxylase activity (GO:0070576)			autonomic_ganglia(1)|breast(2)|endometrium(1)|large_intestine(7)|lung(13)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34					Acetaminophen(DB00316)|Albendazole(DB00518)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Arsenic trioxide(DB01169)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bezafibrate(DB01393)|Bortezomib(DB00188)|Caffeine(DB00201)|Carvedilol(DB01136)|Chloroquine(DB00608)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Cinnarizine(DB00568)|Clenbuterol(DB01407)|Clobetasol propionate(DB01013)|Clofibrate(DB00636)|Clomifene(DB00882)|Clonidine(DB00575)|Clozapine(DB00363)|Dacarbazine(DB00851)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Dexamethasone(DB01234)|Dexmedetomidine(DB00633)|Diclofenac(DB00586)|Dicyclomine(DB00804)|Dronabinol(DB00470)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Ethanol(DB00898)|Flunarizine(DB04841)|Fluorescein(DB00693)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Granisetron(DB00889)|Haloperidol(DB00502)|Isoprenaline(DB01064)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Lorcaserin(DB04871)|Mebendazole(DB00643)|Melatonin(DB01065)|Menadione(DB00170)|Methoxsalen(DB00553)|Nicotine(DB00184)|Nifedipine(DB01115)|Nitroprusside(DB00325)|Norfloxacin(DB01059)|Omeprazole(DB00338)|Ouabain(DB01092)|Oxaliplatin(DB00526)|Pentamidine(DB00738)|Phenobarbital(DB01174)|Prazosin(DB00457)|Primaquine(DB01087)|Progesterone(DB00396)|Propofol(DB00818)|Propranolol(DB00571)|Pyridoxine(DB00165)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Riluzole(DB00740)|Sildenafil(DB00203)|Streptozocin(DB00428)|Sulindac(DB00605)|Tamoxifen(DB00675)|Testosterone(DB00624)|Thalidomide(DB01041)|Theophylline(DB00277)|Thiabendazole(DB00730)|Ticlopidine(DB00208)|Toremifene(DB00539)|Tretinoin(DB00755)|Vitamin A(DB00162)|Warfarin(DB00682)	CCATACCAGCTCCAAAGAGGT	0.512									Endometrial Cancer, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia																												p.G316G		Atlas-SNP	.											.	CYP1A1	60	.	0			c.A948G						.						189	140	157					15																	75013936		2197	4296	6493	SO:0001819	synonymous_variant	1543	exon3	Familial Cancer Database	;AIMAH, Cushing disease, Adrenal, Familial	ACCAGCTCCAAAG	BC023019	CCDS10268.1	15q24.1	2007-12-14	2003-01-14		ENSG00000140465	ENSG00000140465	1.14.14.1	"Cytochrome P450s"	2595	protein-coding gene	gene with protein product		108330	"cytochrome P450, subfamily I (aromatic compound-inducible), polypeptide 1"	CYP1		15128046	Standard	NM_000499		Approved	P450DX, P1-450, P450-C, CP11	uc002ayp.4	P04798	OTTHUMG00000142812	ENST00000379727.3:c.948A>G	chr15.hg19:g.75013936T>C		80.0	0.0		62.0	26.0	NM_000499	A4F3V9|A4F3W0|Q53G18	Silent	SNP	ENST00000379727.3	hg19	CCDS10268.1																																																																																			.	.		0.512	CYP1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286396.1	NM_000499		C	75013936	T	C	75013936	2	2	344	1	0	0	0	0	0	0	0	1	4151	1538	54	2		2	CYP1A1	15	75013936	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	306890	75013936	27517456	1057	48420										
LMAN1L	79748	hgsc.bcm.edu	37	chr15	75111520	75111520	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgaacagtggcctcactcccAgtgatccaggtgagttctgt	11	11	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:75111520A>T	ENST00000309664.5	+	6	764	c.625A>T	c.(625-627)Agt>Tgt	p.S209C	RP11-414J4.2_ENST00000564823.1_RNA|LMAN1L_ENST00000379709.3_Missense_Mutation_p.S209C	NM_021819.2	NP_068591.2	Q9HAT1	LMA1L_HUMAN	lectin, mannose-binding, 1 like	209	L-type lectin-like. {ECO:0000255|PROSITE- ProRule:PRU00658}.					integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(2)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						CCTCACTCCCAGTGATCCAGG	0.622																																					p.S209C		Atlas-SNP	.											.	LMAN1L	43	.	0			c.A625T						.						202	177	185					15																	75111520		2197	4296	6493	SO:0001583	missense	79748	exon6			ACTCCCAGTGATC	AF303398	CCDS10270.1	15q24.1	2005-08-05			ENSG00000140506	ENSG00000140506			6632	protein-coding gene	gene with protein product		609548				11255007	Standard	NM_021819		Approved	ERGL, ERGIC-53L	uc002ayt.1	Q9HAT1	OTTHUMG00000142813	ENST00000309664.5:c.625A>T	chr15.hg19:g.75111520A>T	ENSP00000310431:p.Ser209Cys	69.0	0.0		56.0	20.0	NM_021819	Q6UWN2	Missense_Mutation	SNP	ENST00000309664.5	hg19	CCDS10270.1	.	.	.	.	.	.	.	.	.	.	A	12.04	1.819864	0.32145	.	.	ENSG00000140506	ENST00000309664;ENST00000456603;ENST00000379709	T;T	0.65178	-0.14;-0.14	5.67	-0.627	0.11541	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	1.733160	0.02348	N	0.075627	T	0.68577	0.3016	M	0.61703	1.905	0.09310	N	0.999997	D;D;D;D	0.60160	0.987;0.973;0.987;0.978	P;P;P;P	0.57371	0.819;0.634;0.75;0.75	T	0.51244	-0.8730	10	0.66056	D	0.02	.	1.1069	0.01696	0.3905:0.3003:0.1645:0.1447	.	101;209;137;209	B4DGW5;Q9HAT1-3;B4DU67;Q9HAT1	.;.;.;LMA1L_HUMAN	C	209;101;209	ENSP00000310431:S209C;ENSP00000369031:S209C	ENSP00000310431:S209C	S	+	1	0	LMAN1L	72898573	0.334000	0.24739	0.040000	0.18447	0.100000	0.18952	0.790000	0.26900	-0.126000	0.11682	-1.345000	0.01243	AGT	.	.		0.622	LMAN1L-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286397.4			T	75111520	A	T	75111520	3	4	344	1	0	0	0	0	1	0	0	0	8846	188	7	4	647	4	LMAN1L	15	75111520	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	97584	75111520	27419872	1058	48421										
C15orf39	56905	hgsc.bcm.edu	37	chr15	75499850	75499850	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cgggagtgccagtctcttccAcagaaggagggcgcaaggcc	15	12	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:75499850A>T	ENST00000360639.2	+	2	1781	c.1461A>T	c.(1459-1461)ccA>ccT	p.P487P	C15orf39_ENST00000394987.4_Silent_p.P487P|C15orf39_ENST00000567617.1_Silent_p.P487P			Q6ZRI6	CO039_HUMAN	chromosome 15 open reading frame 39	487						cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(2)|endometrium(3)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	16						AGTCTCTTCCACAGAAGGAGG	0.627																																					p.P487P		Atlas-SNP	.											.	C15orf39	64	.	0			c.A1461T						.						57	59	58					15																	75499850		2197	4295	6492	SO:0001819	synonymous_variant	56905	exon2			TCTTCCACAGAAG	AK128205	CCDS10276.1	15q23	2013-03-14	2005-10-24		ENSG00000167173	ENSG00000167173			24497	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 38~Name Same As HGNC:28782"				Standard	NM_015492		Approved	DKFZP434H132, FLJ46337	uc002azq.4	Q6ZRI6	OTTHUMG00000142820	ENST00000360639.2:c.1461A>T	chr15.hg19:g.75499850A>T		66.0	0.0		43.0	18.0	NM_015492	B3KWI3|C9J888|Q71JB1|Q7L3S0|Q8N3F2|Q96FB6|Q9NTU5	Silent	SNP	ENST00000360639.2	hg19	CCDS10276.1																																																																																			.	.		0.627	C15orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286410.1	NM_015492		T	75499850	A	T	75499850	2	4	344	1	0	0	0	0	0	0	0	1	1795	146	6	4		4	C15orf39	15	75499850	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	388330	75499850	27031542	1059	48422										
UBE2Q2	92912	hgsc.bcm.edu	37	chr15	76152229	76152229	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgttttgtagcttcgtcagcAattgaagtggttgatatgtg	12	4	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:76152229A>T	ENST00000267938.4	+	3	675	c.293A>T	c.(292-294)cAa>cTa	p.Q98L	UBE2Q2_ENST00000561851.1_Missense_Mutation_p.Q82L|UBE2Q2_ENST00000569423.1_Intron|UBE2Q2_ENST00000338677.4_Missense_Mutation_p.Q98L	NM_173469.2	NP_775740.1	Q8WVN8	UB2Q2_HUMAN	ubiquitin-conjugating enzyme E2Q family member 2	98					protein K48-linked ubiquitination (GO:0070936)	cytoplasm (GO:0005737)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)	12						CTTCGTCAGCAATTGAAGTGG	0.383																																					p.Q98L		Atlas-SNP	.											.	UBE2Q2	26	.	0			c.A293T						.						81	69	73					15																	76152229		2197	4294	6491	SO:0001583	missense	92912	exon3			GTCAGCAATTGAA	BC017708	CCDS10286.1, CCDS45309.1, CCDS66839.1	15q24.2	2010-05-12	2008-05-02		ENSG00000140367	ENSG00000140367		"Ubiquitin-conjugating enzymes E2"	19248	protein-coding gene	gene with protein product		612501	"ubiquitin-conjugating enzyme E2Q (putative) 2"			16300736	Standard	NM_001145335		Approved	DKFZp762C143	uc002bbg.2	Q8WVN8	OTTHUMG00000142839	ENST00000267938.4:c.293A>T	chr15.hg19:g.76152229A>T	ENSP00000267938:p.Gln98Leu	100.0	0.0		75.0	38.0	NM_173469	B7Z3Q2|H3BRG2|Q8N4G6|Q96J08	Missense_Mutation	SNP	ENST00000267938.4	hg19	CCDS10286.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.485285	0.84854	.	.	ENSG00000140367	ENST00000338677;ENST00000267938;ENST00000426727	T;T	0.39997	1.05;1.05	5.17	5.17	0.71159	Ubiquitin-conjugating enzyme/RWD-like (1);RWD domain (1);	0.000000	0.85682	D	0.000000	T	0.43188	0.1236	L	0.52011	1.625	0.80722	D	1	B;B	0.32382	0.212;0.368	B;B	0.38327	0.086;0.271	T	0.46582	-0.9181	10	0.87932	D	0	.	12.9562	0.58430	1.0:0.0:0.0:0.0	.	82;98	E9PHD0;Q8WVN8	.;UB2Q2_HUMAN	L	98;98;82	ENSP00000340187:Q98L;ENSP00000267938:Q98L	ENSP00000267938:Q98L	Q	+	2	0	UBE2Q2	73939284	1.000000	0.71417	0.977000	0.42913	0.988000	0.76386	7.871000	0.87180	1.968000	0.57251	0.519000	0.50382	CAA	.	.		0.383	UBE2Q2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286475.1	NM_173469		T	76152229	A	T	76152229	3	4	344	1	0	0	0	0	1	0	0	0	16885	130	5	4	439	4	UBE2Q2	15	76152229	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	652379	76152229	26379163	1060	48423										
UBE2Q2	92912	hgsc.bcm.edu	37	chr15	76183352	76183352	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agagtgcagtttggagcaaaTaaggtacttctgttaagaat	11	4	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:76183352T>C	ENST00000267938.4	+	11	1408	c.1026T>C	c.(1024-1026)aaT>aaC	p.N342N	UBE2Q2_ENST00000561851.1_Silent_p.N326N|UBE2Q2_ENST00000569423.1_Silent_p.N307N|UBE2Q2_ENST00000338677.4_Intron	NM_173469.2	NP_775740.1	Q8WVN8	UB2Q2_HUMAN	ubiquitin-conjugating enzyme E2Q family member 2	342					protein K48-linked ubiquitination (GO:0070936)	cytoplasm (GO:0005737)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)	12						TTGGAGCAAATAAGGTACTTC	0.353																																					p.N342N		Atlas-SNP	.											.	UBE2Q2	26	.	0			c.T1026C						.						82	85	84					15																	76183352		2197	4294	6491	SO:0001819	synonymous_variant	92912	exon11			AGCAAATAAGGTA	BC017708	CCDS10286.1, CCDS45309.1, CCDS66839.1	15q24.2	2010-05-12	2008-05-02		ENSG00000140367	ENSG00000140367		"Ubiquitin-conjugating enzymes E2"	19248	protein-coding gene	gene with protein product		612501	"ubiquitin-conjugating enzyme E2Q (putative) 2"			16300736	Standard	NM_001145335		Approved	DKFZp762C143	uc002bbg.2	Q8WVN8	OTTHUMG00000142839	ENST00000267938.4:c.1026T>C	chr15.hg19:g.76183352T>C		105.0	0.0		82.0	32.0	NM_173469	B7Z3Q2|H3BRG2|Q8N4G6|Q96J08	Silent	SNP	ENST00000267938.4	hg19	CCDS10286.1																																																																																			.	.		0.353	UBE2Q2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286475.1	NM_173469		C	76183352	T	C	76183352	2	2	344	1	0	0	0	0	0	0	0	1	16885	1403	49	2		2	UBE2Q2	15	76183352	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	31123	76183352	26348040	1061	48424										
SCAPER	49855	hgsc.bcm.edu	37	chr15	77021006	77021006	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctgttgttcaattcgggcttCttgttctttcctcttcatta	6	10	5	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:77021006C>G	ENST00000563290.1	-	17	2190	c.2095G>C	c.(2095-2097)Gaa>Caa	p.E699Q	SCAPER_ENST00000538941.2_Missense_Mutation_p.E453Q|SCAPER_ENST00000324767.7_Missense_Mutation_p.E699Q			Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER	699	Glu-rich.					endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(16)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	39						ATTCGGGCTTCTTGTTCTTTC	0.433																																					p.E699Q		Atlas-SNP	.											.	SCAPER	160	.	0			c.G2095C						.						146	138	141					15																	77021006		1828	4077	5905	SO:0001583	missense	49855	exon16			GGGCTTCTTGTTC	AB040887, AF242528	CCDS53961.1, CCDS53962.1	15q24.3	2012-10-05	2009-03-11	2007-08-20	ENSG00000140386	ENSG00000140386		"Zinc fingers, C2H2-type"	13081	protein-coding gene	gene with protein product		611611	"zinc finger protein 291"	ZNF291		17698606	Standard	NM_020843		Approved	Zfp291	uc002bby.3	Q9BY12	OTTHUMG00000172655	ENST00000563290.1:c.2095G>C	chr15.hg19:g.77021006C>G	ENSP00000454973:p.Glu699Gln	103.0	0.0		77.0	32.0	NM_020843	F5H7X8|H3BNR7|Q3B7X7|Q96BS9|Q9H3D8|Q9NT03|Q9P274	Missense_Mutation	SNP	ENST00000563290.1	hg19	CCDS53962.1	.	.	.	.	.	.	.	.	.	.	C	28.7	4.942254	0.92526	.	.	ENSG00000140386	ENST00000324767;ENST00000538941;ENST00000303521	T;T	0.27256	1.7;1.68	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.43656	0.1257	L	0.38531	1.155	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.982;0.997;0.994	T	0.27331	-1.0077	10	0.51188	T	0.08	.	18.9347	0.92580	0.0:1.0:0.0:0.0	.	698;720;453	Q9BY12;Q9BY12-2;F5H7X8	SCAPE_HUMAN;.;.	Q	699;453;721	ENSP00000326924:E699Q;ENSP00000442190:E453Q	ENSP00000303560:E721Q	E	-	1	0	SCAPER	74808061	1.000000	0.71417	0.993000	0.49108	0.975000	0.68041	7.295000	0.78780	2.554000	0.86153	0.563000	0.77884	GAA	.	.		0.433	SCAPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419698.1	NM_020843		G	77021006	C	G	77021006	3	3	344	1	0	0	0	0	1	0	0	0	13893	922	32	4	2171	4	SCAPER	15	77021006	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	837654	77021006	25510386	1062	48425										
KIAA1024	23251	hgsc.bcm.edu	37	chr15	79749742	79749742	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cccaacttaccttgtgccaaAggatcaacagccaattctcc	5	15	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:79749742A>G	ENST00000305428.3	+	2	1328	c.1253A>G	c.(1252-1254)aAg>aGg	p.K418R		NM_015206.2	NP_056021.1	Q9UPX6	K1024_HUMAN	KIAA1024	418						integral component of membrane (GO:0016021)				central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(2)|pancreas(2)|prostate(1)	49						CTTGTGCCAAAGGATCAACAG	0.488																																					p.K418R		Atlas-SNP	.											.	KIAA1024	146	.	0			c.A1253G						.						65	72	70					15																	79749742		2196	4293	6489	SO:0001583	missense	23251	exon2			TGCCAAAGGATCA	AB028947	CCDS32306.1	15q25.1	2007-12-12				ENSG00000169330			29172	protein-coding gene	gene with protein product						10470851	Standard	NM_015206		Approved		uc002bew.1	Q9UPX6		ENST00000305428.3:c.1253A>G	chr15.hg19:g.79749742A>G	ENSP00000307461:p.Lys418Arg	216.0	0.0		191.0	86.0	NM_015206	A7MD43	Missense_Mutation	SNP	ENST00000305428.3	hg19	CCDS32306.1	.	.	.	.	.	.	.	.	.	.	A	5.585	0.292666	0.10567	.	.	ENSG00000169330	ENST00000305428	T	0.33654	1.4	5.14	4.01	0.46588	.	0.338473	0.34750	N	0.003718	T	0.33030	0.0849	L	0.60455	1.87	0.32009	N	0.602276	B	0.20052	0.041	B	0.24155	0.051	T	0.34650	-0.9820	9	.	.	.	.	9.2707	0.37670	0.917:0.0:0.083:0.0	.	418	Q9UPX6	K1024_HUMAN	R	418	ENSP00000307461:K418R	.	K	+	2	0	KIAA1024	77536797	0.991000	0.36638	0.126000	0.21872	0.048000	0.14542	3.558000	0.53749	0.801000	0.34066	0.402000	0.26972	AAG	.	.		0.488	KIAA1024-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416718.1	NM_015206		G	79749742	A	G	79749742	3	3	344	1	0	0	0	0	1	0	0	0	8214	72	3	2	1255	2	KIAA1024	15	79749742	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2728736	79749742	22781650	1063	48426										
MEX3B	84206	hgsc.bcm.edu	37	chr15	82336831	82336831	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agtgctcggcagcagagatgAtctccctccgagccatggcc	12	14	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:82336831A>G	ENST00000329713.4	-	2	815	c.380T>C	c.(379-381)aTc>aCc	p.I127T	MEX3B_ENST00000558133.1_3'UTR|AC026956.1_ENST00000410589.1_RNA	NM_032246.4	NP_115622.2	Q6ZN04	MEX3B_HUMAN	mex-3 RNA binding family member B	127	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.				protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|upper_aerodigestive_tract(1)	19						AGCAGAGATGATCTCCCTCCG	0.622																																					p.I127T		Atlas-SNP	.											.	MEX3B	50	.	0			c.T380C						.						54	53	53					15																	82336831		2203	4300	6503	SO:0001583	missense	84206	exon2			GAGATGATCTCCC	AK131424	CCDS10319.1	15q25.1	2013-08-21	2013-08-21	2007-07-18	ENSG00000183496	ENSG00000183496		"RING-type (C3HC4) zinc fingers", "Mex-3 homologs"	25297	protein-coding gene	gene with protein product		611008	"ring finger and KH domain containing 3", "mex-3 homolog B (C. elegans)"	RKHD3		11230166, 17267406	Standard	NM_032246		Approved	DKFZp434J0617, RNF195	uc002bgq.2	Q6ZN04	OTTHUMG00000147356	ENST00000329713.4:c.380T>C	chr15.hg19:g.82336831A>G	ENSP00000329918:p.Ile127Thr	34.0	0.0		31.0	14.0	NM_032246	Q4G0W1|Q8IVG2|Q9H0J0	Missense_Mutation	SNP	ENST00000329713.4	hg19	CCDS10319.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.227673	0.79576	.	.	ENSG00000183496	ENST00000329713	T	0.46451	0.87	4.41	4.41	0.53225	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.128586	0.51477	D	0.000091	T	0.62829	0.2460	M	0.76170	2.325	0.80722	D	1	D	0.71674	0.998	D	0.79108	0.992	T	0.67833	-0.5568	10	0.87932	D	0	-25.1565	12.7441	0.57270	1.0:0.0:0.0:0.0	.	127	Q6ZN04	MEX3B_HUMAN	T	127	ENSP00000329918:I127T	ENSP00000329918:I127T	I	-	2	0	MEX3B	80123886	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.373000	0.90131	1.857000	0.53885	0.402000	0.26972	ATC	.	.		0.622	MEX3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304000.1	XM_290645		G	82336831	A	G	82336831	3	3	344	1	0	0	0	0	1	0	0	0	9519	333	12	2	1333	2	MEX3B	15	82336831	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2587089	82336831	20194561	1064	48427										
EFTUD1	79631	hgsc.bcm.edu	37	chr15	82444096	82444096	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctccttgttcctcaaatttaCttaggtcccatttttccaga	4	12	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:82444096C>T	ENST00000268206.7	-	18	2867	c.2699G>A	c.(2698-2700)aGt>aAt	p.S900N	EFTUD1_ENST00000359445.3_Missense_Mutation_p.S849N	NM_024580.5	NP_078856.4	Q7Z2Z2	ETUD1_HUMAN	elongation factor Tu GTP binding domain containing 1	900					GTP catabolic process (GO:0006184)|mature ribosome assembly (GO:0042256)		GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ribosome binding (GO:0043022)|translation elongation factor activity (GO:0003746)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(14)|ovary(1)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32						CTCAAATTTACTTAGGTCCCA	0.463																																					p.S900N		Atlas-SNP	.											.	EFTUD1	74	.	0			c.G2699A						.						96	95	96					15																	82444096		1870	4104	5974	SO:0001583	missense	79631	exon18			AATTTACTTAGGT	AK056656	CCDS42070.1, CCDS42071.1	15q25.2	2012-07-04			ENSG00000140598	ENSG00000140598			25789	protein-coding gene	gene with protein product	"ribosome assembly 1 homolog (yeast)"					14702039	Standard	NM_024580		Approved	FLJ13119, FAM42A, HsT19294, RIA1	uc002bgt.1	Q7Z2Z2	OTTHUMG00000172573	ENST00000268206.7:c.2699G>A	chr15.hg19:g.82444096C>T	ENSP00000268206:p.Ser900Asn	84.0	0.0		98.0	41.0	NM_024580	A6NKY5|B7Z6I0|Q9H8Z6	Missense_Mutation	SNP	ENST00000268206.7	hg19	CCDS42071.1	.	.	.	.	.	.	.	.	.	.	C	7.926	0.739619	0.15642	.	.	ENSG00000140598	ENST00000268206;ENST00000359445	T;T	0.62941	-0.01;-0.01	5.44	2.56	0.30785	Ribosomal protein S5 domain 2-type fold (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);	0.537282	0.16462	N	0.213362	T	0.44498	0.1296	L	0.31420	0.93	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.001	T	0.22906	-1.0203	10	0.13108	T	0.6	2.3643	9.1368	0.36879	0.0:0.6772:0.0:0.3228	.	849;900	Q7Z2Z2-2;Q7Z2Z2	.;ETUD1_HUMAN	N	900;849	ENSP00000268206:S900N;ENSP00000352418:S849N	ENSP00000268206:S900N	S	-	2	0	EFTUD1	80231151	0.912000	0.30974	0.004000	0.12327	0.979000	0.70002	0.429000	0.21412	0.420000	0.25954	0.585000	0.79938	AGT	.	.		0.463	EFTUD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419252.1	NM_024580		T	82444096	C	T	82444096	3	4	344	1	0	0	0	0	1	0	0	0	4962	565	20	3	675	3	EFTUD1	15	82444096	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	107265	82444096	20087296	1065	48428										
BTBD1	53339	hgsc.bcm.edu	37	chr15	83718868	83718868	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tctgcacttattgcatccatTgtgcttttgtctattgtatc	6	9	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:83718868T>C	ENST00000261721.4	-	3	823	c.621A>G	c.(619-621)acA>acG	p.T207T	RP11-382A20.7_ENST00000570202.1_RNA|BTBD1_ENST00000379403.2_Silent_p.T207T|RP11-382A20.6_ENST00000568441.1_RNA|RP11-382A20.5_ENST00000566841.1_RNA	NM_001011885.1|NM_025238.3	NP_001011885.1|NP_079514.1	Q9H0C5	BTBD1_HUMAN	BTB (POZ) domain containing 1	207					protein ubiquitination (GO:0016567)|regulation of protein binding (GO:0043393)	cytoplasmic mRNA processing body (GO:0000932)|protein complex (GO:0043234)				central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)	10				all cancers(203;0.000186)		TTGCATCCATTGTGCTTTTGT	0.318																																					p.T207T		Atlas-SNP	.											.	BTBD1	32	.	0			c.A621G						.						123	116	118					15																	83718868		2203	4300	6503	SO:0001819	synonymous_variant	53339	exon3			ATCCATTGTGCTT	AF355402	CCDS10322.1, CCDS32313.1	15q24	2013-01-08			ENSG00000064726	ENSG00000064726		"BTB/POZ domain containing"	1120	protein-coding gene	gene with protein product		608530					Standard	XM_006720573		Approved		uc002bjn.3	Q9H0C5	OTTHUMG00000147364	ENST00000261721.4:c.621A>G	chr15.hg19:g.83718868T>C		79.0	0.0		60.0	31.0	NM_025238	A6NMI8|Q9BX71|Q9NWN4	Silent	SNP	ENST00000261721.4	hg19	CCDS10322.1																																																																																			.	.		0.318	BTBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304008.1			C	83718868	T	C	83718868	2	2	344	1	0	0	0	0	0	0	0	1	1539	1799	63	2		2	BTBD1	15	83718868	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1274772	83718868	18812524	1066	48429										
AKAP13	11214	hgsc.bcm.edu	37	chr15	86286977	86286977	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcgtccacctctgcctctacCcgcctgtttgggttaacaaa	8	15	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:86286977C>A	ENST00000394518.2	+	36	8408	c.8313C>A	c.(8311-8313)acC>acA	p.T2771T	AKAP13_ENST00000361243.2_Silent_p.T2775T|AKAP13_ENST00000394510.2_Silent_p.T1016T|RP11-158M2.3_ENST00000558375.1_RNA|AKAP13_ENST00000560579.1_3'UTR	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	2771	Interaction with ESR1.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						CTGCCTCTACCCGCCTGTTTG	0.522																																					p.T2775T	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.C8325A						.						56	60	59					15																	86286977		2202	4299	6501	SO:0001819	synonymous_variant	11214	exon36			CTCTACCCGCCTG	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"A-kinase anchor proteins", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	371	protein-coding gene	gene with protein product		604686	"lymphoid blast crisis oncogene"	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.8313C>A	chr15.hg19:g.86286977C>A		138.0	0.0		101.0	15.0	NM_006738	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Silent	SNP	ENST00000394518.2	hg19	CCDS32319.1																																																																																			.	.		0.522	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200		A	86286977	C	A	86286977	2	1	344	1	0	0	0	0	0	0	0	1	449	610	22	3		3	AKAP13	15	86286977	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	2568109	86286977	16244415	1067	48430										
AGBL1	123624	hgsc.bcm.edu	37	chr15	86702252	86702252	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acccgaaagcgcacccaagcAatcaggtacagagtgccatg	10	13	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:86702252A>C	ENST00000441037.2	+	4	440	c.345A>C	c.(343-345)gcA>gcC	p.A115A	AGBL1_ENST00000421325.2_Silent_p.A115A	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	115					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						GCACCCAAGCAATCAGGTACA	0.448																																					p.A115A		Atlas-SNP	.											.	AGBL1	151	.	0			c.A345C						.						111	103	105					15																	86702252		1938	4141	6079	SO:0001819	synonymous_variant	123624	exon4			CCAAGCAATCAGG	AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 4"	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.345A>C	chr15.hg19:g.86702252A>C		86.0	0.0		81.0	41.0	NM_152336	A1A4X5|A6NJH6|C9JHL5	Silent	SNP	ENST00000441037.2	hg19	CCDS58398.1																																																																																			.	.		0.448	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336		C	86702252	A	C	86702252	2	2	344	1	0	0	0	0	0	0	0	1	375	117	5	5		5	AGBL1	15	86702252	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	415275	86702252	15829140	1068	48431										
AGBL1	123624	hgsc.bcm.edu	37	chr15	86823010	86823010	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tccctatacctacacagcccTcatggtaacttcctctttat	3	15	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:86823010T>A	ENST00000441037.2	+	15	2173	c.2078T>A	c.(2077-2079)cTc>cAc	p.L693H	AGBL1_ENST00000421325.2_Missense_Mutation_p.L693H|AGBL1_ENST00000389298.3_Missense_Mutation_p.L424H	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	693					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						TACACAGCCCTCATGGTAACT	0.512																																					p.L693H		Atlas-SNP	.											.	AGBL1	151	.	0			c.T2078A						.						320	296	304					15																	86823010		1980	4170	6150	SO:0001583	missense	123624	exon15			CAGCCCTCATGGT	AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 4"	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.2078T>A	chr15.hg19:g.86823010T>A	ENSP00000413001:p.Leu693His	106.0	0.0		110.0	54.0	NM_152336	A1A4X5|A6NJH6|C9JHL5	Missense_Mutation	SNP	ENST00000441037.2	hg19	CCDS58398.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.503655	0.85176	.	.	ENSG00000166748	ENST00000441037;ENST00000421325;ENST00000389298	T;T	0.17054	2.3;2.31	5.3	5.3	0.74995	.	0.168121	0.39274	N	0.001412	T	0.45756	0.1358	M	0.83774	2.66	0.47123	D	0.999326	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.994;0.98	T	0.50972	-0.8764	10	0.87932	D	0	-23.891	14.5795	0.68278	0.0:0.0:0.0:1.0	.	392;424;693	Q96MI9-2;Q96MI9-3;Q96MI9	.;.;CBPC4_HUMAN	H	722;693;424	ENSP00000397173:L693H;ENSP00000373949:L424H	ENSP00000373949:L424H	L	+	2	0	AGBL1	84624014	1.000000	0.71417	0.998000	0.56505	0.960000	0.62799	7.600000	0.82769	2.230000	0.72887	0.533000	0.62120	CTC	.	.		0.512	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336		A	86823010	T	A	86823010	3	1	344	1	0	0	0	0	1	0	0	0	375	1551	54	4	2132	4	AGBL1	15	86823010	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	120758	86823010	15708382	1069	48432										
AGBL1	123624	hgsc.bcm.edu	37	chr15	87097675	87097675	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtggagaaatctcgagcttcCacggcccgggtggtggtgtg	17	9	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:87097675C>A	ENST00000441037.2	+	20	2858	c.2763C>A	c.(2761-2763)tcC>tcA	p.S921S	AGBL1_ENST00000389298.3_Silent_p.S652S|AGBL1_ENST00000421325.2_Silent_p.S921S	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	921					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						CTCGAGCTTCCACGGCCCGGG	0.512																																					p.S921S		Atlas-SNP	.											.	AGBL1	151	.	0			c.C2763A						.						31	32	32					15																	87097675		1894	4113	6007	SO:0001819	synonymous_variant	123624	exon20			AGCTTCCACGGCC	AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 4"	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.2763C>A	chr15.hg19:g.87097675C>A		77.0	0.0		63.0	30.0	NM_152336	A1A4X5|A6NJH6|C9JHL5	Silent	SNP	ENST00000441037.2	hg19	CCDS58398.1																																																																																			.	.		0.512	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336		A	87097675	C	A	87097675	2	1	344	1	0	0	0	0	0	0	0	1	375	581	21	3		3	AGBL1	15	87097675	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	274665	87097675	15433717	1070	48433										
ACAN	176	hgsc.bcm.edu	37	chr15	89388804	89388804	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aggaggacatcaccgtccagAcagtgacctggcctgacatg	12	12	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:89388804A>G	ENST00000561243.1	+	6	1120	c.1120A>G	c.(1120-1122)Aca>Gca	p.T374A	ACAN_ENST00000559004.1_Missense_Mutation_p.T374A|ACAN_ENST00000558207.1_Missense_Mutation_p.T374A|ACAN_ENST00000439576.2_Missense_Mutation_p.T374A|ACAN_ENST00000352105.7_Missense_Mutation_p.T374A			P16112	PGCA_HUMAN	aggrecan	374					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			CACCGTCCAGACAGTGACCTG	0.557																																					p.T374A		Atlas-SNP	.											.	ACAN	220	.	0			c.A1120G						.						65	74	71					15																	89388804		2164	4261	6425	SO:0001583	missense	176	exon7			GTCCAGACAGTGA	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	319	protein-coding gene	gene with protein product	"aggrecan proteoglycan"	155760	"chondroitin sulfate proteoglycan 1", "aggrecan 1"	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.1120A>G	chr15.hg19:g.89388804A>G	ENSP00000453342:p.Thr374Ala	92.0	0.0		75.0	36.0	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	hg19	CCDS53970.1	.	.	.	.	.	.	.	.	.	.	A	17.55	3.418181	0.62622	.	.	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	T;T	0.02763	4.41;4.17	5.61	5.61	0.85477	.	0.000000	0.33553	N	0.004786	T	0.13970	0.0338	M	0.78801	2.425	0.38200	D	0.940152	D;D;P	0.76494	0.999;0.999;0.874	D;D;B	0.76071	0.987;0.987;0.391	T	0.01767	-1.1278	10	0.39692	T	0.17	-9.1083	12.4865	0.55877	1.0:0.0:0.0:0.0	.	374;374;374	E7ENV9;E7EX88;Q6PID9	.;.;.	A	374	ENSP00000387356:T374A;ENSP00000341615:T374A	ENSP00000268134:T374A	T	+	1	0	ACAN	87189808	1.000000	0.71417	0.998000	0.56505	0.965000	0.64279	4.956000	0.63645	2.266000	0.75297	0.533000	0.62120	ACA	.	.		0.557	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135		G	89388804	A	G	89388804	3	3	344	1	0	0	0	0	1	0	0	0	117	275	10	2	1142	2	ACAN	15	89388804	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2291129	89388804	13142588	1071	48434										
ABHD2	11057	hgsc.bcm.edu	37	chr15	89694906	89694906	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acctcccttgtcctttctttAgatacattccaccgttgatc	4	14	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:89694906A>G	ENST00000352732.5	+	4	714		c.e4-1		ABHD2_ENST00000355100.3_Splice_Site|ABHD2_ENST00000565973.1_Splice_Site	NM_152924.4	NP_690888.1	P08910	ABHD2_HUMAN	abhydrolase domain containing 2						negative regulation of cell migration (GO:0030336)|response to wounding (GO:0009611)	integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|soft_tissue(1)	23	Lung NSC(78;0.0472)|all_lung(78;0.089)					TCCTTTCTTTAGATACATTCC	0.448																																					.	Colon(11;252 417 24570 33239 41878)	Atlas-SNP	.											.	ABHD2	55	.	0			c.195-2A>G						.						105	98	100					15																	89694906		2200	4299	6499	SO:0001630	splice_region_variant	11057	exon4			TTCTTTAGATACA	X12433	CCDS10348.1	15q26.1	2006-10-06			ENSG00000140526	ENSG00000140526		"Abhydrolase domain containing"	18717	protein-coding gene	gene with protein product		612196					Standard	NM_152924		Approved	LABH2	uc002bnk.2	P08910	OTTHUMG00000148684	ENST00000352732.5:c.195-1A>G	chr15.hg19:g.89694906A>G		81.0	0.0		64.0	32.0	NM_152924	Q53G48|Q53GU0|Q5FVD9|Q8TC79	Splice_Site	SNP	ENST00000352732.5	hg19	CCDS10348.1	.	.	.	.	.	.	.	.	.	.	A	16.03	3.008552	0.54361	.	.	ENSG00000140526	ENST00000352732;ENST00000355100	.	.	.	6.03	6.03	0.97812	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5655	0.84588	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ABHD2	87495910	1.000000	0.71417	0.901000	0.35422	0.341000	0.28922	8.934000	0.92915	2.302000	0.77476	0.533000	0.62120	.	.	.		0.448	ABHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309074.2		Intron	G	89694906	A	G	89694906	5	3	344	1	0	0	0	0	0	0	1	0	82	434	15	2	199	2	ABHD2	15	89694906	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	306102	89694906	12836486	1072	48435										
WDR93	56964	hgsc.bcm.edu	37	chr15	90246187	90246187	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctttgttttcccagctcaacAaaatgccaaattgtatggct	6	10	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:90246187A>C	ENST00000268130.7	+	3	411	c.310A>C	c.(310-312)Aaa>Caa	p.K104Q	WDR93_ENST00000558000.1_Missense_Mutation_p.K104Q|RP11-300G22.2_ENST00000557964.1_RNA|WDR93_ENST00000560294.1_Missense_Mutation_p.K104Q	NM_020212.1	NP_064597.1	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	104					electron transport chain (GO:0022900)		oxidoreductase activity, acting on NAD(P)H (GO:0016651)			NS(1)|breast(3)|endometrium(2)|kidney(4)|large_intestine(5)|liver(2)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	33	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)			CCAGCTCAACAAAATGCCAAA	0.358																																					p.K104Q		Atlas-SNP	.											.	WDR93	63	.	0			c.A310C						.						59	58	58					15																	90246187		2200	4299	6499	SO:0001583	missense	56964	exon3			CTCAACAAAATGC		CCDS32326.1, CCDS66862.1, CCDS73779.1	15q26.1	2012-11-02						"WD repeat domain containing"	26924	protein-coding gene	gene with protein product							Standard	NM_020212		Approved		uc002boj.3	Q6P2C0		ENST00000268130.7:c.310A>C	chr15.hg19:g.90246187A>C	ENSP00000268130:p.Lys104Gln	101.0	0.0		85.0	41.0	NM_020212	Q8N7Y8|Q9NP89	Missense_Mutation	SNP	ENST00000268130.7	hg19	CCDS32326.1	.	.	.	.	.	.	.	.	.	.	A	9.180	1.023334	0.19433	.	.	ENSG00000140527	ENST00000268130	T	0.29655	1.56	5.62	3.22	0.36961	WD40 repeat-like-containing domain (1);	0.815256	0.11195	N	0.589518	T	0.28764	0.0713	M	0.67953	2.075	0.09310	N	0.999999	B;B;B	0.20261	0.043;0.017;0.043	B;B;B	0.18561	0.018;0.022;0.018	T	0.28138	-1.0053	10	0.22109	T	0.4	-1.6312	5.9281	0.19124	0.7471:0.1655:0.0874:0.0	.	104;104;104	Q6P2C0-2;B4E3E2;Q6P2C0	.;.;WDR93_HUMAN	Q	104	ENSP00000268130:K104Q	ENSP00000268130:K104Q	K	+	1	0	WDR93	88047191	0.001000	0.12720	0.197000	0.23402	0.702000	0.40608	1.036000	0.30228	0.917000	0.36895	0.533000	0.62120	AAA	.	.		0.358	WDR93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416369.1	NM_020212		C	90246187	A	C	90246187	3	2	344	1	0	0	0	0	1	0	0	0	17355	131	5	5	316	5	WDR93	15	90246187	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	551281	90246187	12285205	1073	48436										
MCTP2	55784	hgsc.bcm.edu	37	chr15	94913364	94913364	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aagacgtcggcattctacaaGtgaaggttttaaaggcagca	11	7	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:94913364G>A	ENST00000357742.4	+	11	1537	c.1537G>A	c.(1537-1539)Gtg>Atg	p.V513M	MCTP2_ENST00000331706.4_Missense_Mutation_p.V101M|MCTP2_ENST00000557742.1_Missense_Mutation_p.V101M|MCTP2_ENST00000451018.3_Missense_Mutation_p.V513M	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2	513	C2 3. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|liver(1)|lung(12)|ovary(1)|pancreas(1)|skin(9)|stomach(2)	49	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)			CATTCTACAAGTGAAGGTTTT	0.363																																					p.V513M		Atlas-SNP	.											.	MCTP2	122	.	0			c.G1537A						.						97	94	95					15																	94913364		2197	4298	6495	SO:0001583	missense	55784	exon11			CTACAAGTGAAGG	AK002037	CCDS32338.1, CCDS53975.1, CCDS53976.1	15q26.2	2006-02-08				ENSG00000140563			25636	protein-coding gene	gene with protein product						15528213	Standard	NM_018349		Approved	FLJ11175, FLJ33303	uc002btj.3	Q6DN12		ENST00000357742.4:c.1537G>A	chr15.hg19:g.94913364G>A	ENSP00000350377:p.Val513Met	119.0	0.0		106.0	20.0	NM_001159643	A2RRC2|C6G483|C6G484|Q49AB0|Q8TAX2|Q9NUS2|Q9NUW7	Missense_Mutation	SNP	ENST00000357742.4	hg19	CCDS32338.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.423026	0.83559	.	.	ENSG00000140563	ENST00000451018;ENST00000331706;ENST00000357742	T;T;T	0.75938	-0.98;-0.98;-0.98	5.84	5.84	0.93424	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.052097	0.85682	D	0.000000	D	0.88492	0.6451	M	0.85041	2.73	0.80722	D	1	P;D;D	0.89917	0.927;0.999;1.0	D;D;D	0.85130	0.919;0.992;0.997	D	0.88848	0.3317	10	0.62326	D	0.03	.	20.1454	0.98074	0.0:0.0:1.0:0.0	.	513;101;513	Q6DN12-2;Q6DN12-4;Q6DN12	.;.;MCTP2_HUMAN	M	513;101;513	ENSP00000395109:V513M;ENSP00000329646:V101M;ENSP00000350377:V513M	ENSP00000329646:V101M	V	+	1	0	MCTP2	92714368	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	7.769000	0.85360	2.748000	0.94277	0.650000	0.86243	GTG	.	.		0.363	MCTP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415060.3	NM_018349		A	94913364	G	A	94913364	3	1	344	1	0	0	0	0	1	0	0	0	9410	1029	36	3	1579	3	MCTP2	15	94913364	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	4667177	94913364	7618028	1074	48437										
IGF1R	3480	hgsc.bcm.edu	37	chr15	99478555	99478555	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttcctcccaggtgcgattgcTgggtgtggtgtcccaaggcc	14	12	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:99478555T>A	ENST00000268035.6	+	17	3808	c.3197T>A	c.(3196-3198)cTg>cAg	p.L1066Q	IGF1R_ENST00000558762.1_Missense_Mutation_p.L1065Q	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	1066	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"	GTGCGATTGCTGGGTGTGGTG	0.547																																					p.L1066Q		Atlas-SNP	.											.	IGF1R	147	.	0			c.T3197A						.						77	65	69					15																	99478555		1941	3777	5718	SO:0001583	missense	3480	exon17			GATTGCTGGGTGT	M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"CD molecules", "Fibronectin type III domain containing"	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.3197T>A	chr15.hg19:g.99478555T>A	ENSP00000268035:p.Leu1066Gln	87.0	0.0		75.0	35.0	NM_000875	B1B5Y2|Q14CV2|Q9UCC0	Missense_Mutation	SNP	ENST00000268035.6	hg19	CCDS10378.1	.	.	.	.	.	.	.	.	.	.	T	26.9	4.783494	0.90282	.	.	ENSG00000140443	ENST00000268035	D	0.90620	-2.7	5.3	5.3	0.74995	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.42821	D	0.000651	D	0.96204	0.8762	M	0.91972	3.26	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.97127	0.9815	10	0.87932	D	0	.	15.2481	0.73521	0.0:0.0:0.0:1.0	.	1065;1066	C9J5X1;P08069	.;IGF1R_HUMAN	Q	1066	ENSP00000268035:L1066Q	ENSP00000268035:L1066Q	L	+	2	0	IGF1R	97296078	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	8.040000	0.89188	2.015000	0.59207	0.533000	0.62120	CTG	.	.		0.547	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875		A	99478555	T	A	99478555	3	1	344	1	0	0	0	0	1	0	0	0	7580	1580	55	4	3263	4	IGF1R	15	99478555	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	4565191	99478555	3052837	1075	48438										
LRRK1	79705	hgsc.bcm.edu	37	chr15	101598240	101598240	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gccagatgaaggacccgactTttgccaccttcatgtatgaa	9	11	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:101598240T>A	ENST00000388948.3	+	29	4932	c.4573T>A	c.(4573-4575)Ttt>Att	p.F1525I	LRRK1_ENST00000284395.5_Missense_Mutation_p.F1522I|RP11-505E24.2_ENST00000559857.1_RNA	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1											breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			GGACCCGACTTTTGCCACCTT	0.557																																					p.F1525I		Atlas-SNP	.											.	LRRK1	310	.	0			c.T4573A						.						97	98	98					15																	101598240		1994	4157	6151	SO:0001583	missense	79705	exon29			CCGACTTTTGCCA	AB058693	CCDS42086.1	15q26.3	2007-01-29			ENSG00000154237	ENSG00000154237			18608	protein-coding gene	gene with protein product		610986				11347906, 14654223	Standard	XM_005254979		Approved	FLJ23119, KIAA1790, Roco1, RIPK6	uc002bwr.3	Q38SD2	OTTHUMG00000165514	ENST00000388948.3:c.4573T>A	chr15.hg19:g.101598240T>A	ENSP00000373600:p.Phe1525Ile	80.0	0.0		55.0	24.0	NM_024652		Missense_Mutation	SNP	ENST00000388948.3	hg19	CCDS42086.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.134767	0.77662	.	.	ENSG00000154237	ENST00000388948;ENST00000284395;ENST00000529762;ENST00000542170	T;T	0.75477	-0.92;-0.94	4.57	4.57	0.56435	Protein kinase, catalytic domain (1);	0.207715	0.43747	D	0.000534	D	0.83608	0.5291	M	0.61703	1.905	0.54753	D	0.999981	D	0.89917	1.0	D	0.83275	0.996	D	0.84993	0.0895	10	0.56958	D	0.05	.	14.2612	0.66085	0.0:0.0:0.0:1.0	.	1525	Q38SD2	LRRK1_HUMAN	I	1525;1522;216;79	ENSP00000373600:F1525I;ENSP00000284395:F1522I	ENSP00000284395:F1522I	F	+	1	0	LRRK1	99415763	1.000000	0.71417	0.953000	0.39169	0.555000	0.35460	6.938000	0.75904	1.835000	0.53391	0.459000	0.35465	TTT	.	.		0.557	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652		A	101598240	T	A	101598240	3	1	344	1	0	0	0	0	1	0	0	0	9041	1841	64	4	4683	4	LRRK1	15	101598240	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2119685	101598240	933152	1076	48439										
LRRK1	79705	hgsc.bcm.edu	37	chr15	101605833	101605833	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcaggcggctggagccctacAtggccccctccatggttacg	13	15	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:101605833A>G	ENST00000388948.3	+	32	5550	c.5191A>G	c.(5191-5193)Atg>Gtg	p.M1731V	LRRK1_ENST00000284395.5_Missense_Mutation_p.M1728V|LRRK1_ENST00000532145.1_3'UTR|RP11-505E24.2_ENST00000559857.1_RNA	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1											breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			GGAGCCCTACATGGCCCCCTC	0.617																																					p.M1731V		Atlas-SNP	.											.	LRRK1	310	.	0			c.A5191G						.						66	78	74					15																	101605833		2088	4215	6303	SO:0001583	missense	79705	exon32			CCCTACATGGCCC	AB058693	CCDS42086.1	15q26.3	2007-01-29			ENSG00000154237	ENSG00000154237			18608	protein-coding gene	gene with protein product		610986				11347906, 14654223	Standard	XM_005254979		Approved	FLJ23119, KIAA1790, Roco1, RIPK6	uc002bwr.3	Q38SD2	OTTHUMG00000165514	ENST00000388948.3:c.5191A>G	chr15.hg19:g.101605833A>G	ENSP00000373600:p.Met1731Val	71.0	0.0		55.0	27.0	NM_024652		Missense_Mutation	SNP	ENST00000388948.3	hg19	CCDS42086.1	.	.	.	.	.	.	.	.	.	.	G	0.082	-1.182567	0.01620	.	.	ENSG00000154237	ENST00000388948;ENST00000284395;ENST00000529762;ENST00000542170	T;T	0.69685	-0.42;-0.42	5.7	-6.66	0.01789	WD40 repeat-like-containing domain (1);	1.871250	0.02048	N	0.049842	T	0.37517	0.1006	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.29971	-0.9994	10	0.27082	T	0.32	.	5.0728	0.14615	0.4641:0.0578:0.3406:0.1375	.	1731	Q38SD2	LRRK1_HUMAN	V	1731;1728;422;285	ENSP00000373600:M1731V;ENSP00000284395:M1728V	ENSP00000284395:M1728V	M	+	1	0	LRRK1	99423356	0.000000	0.05858	0.000000	0.03702	0.055000	0.15305	-1.304000	0.02741	-2.243000	0.00707	-2.208000	0.00301	ATG	.	.		0.617	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652		G	101605833	A	G	101605833	3	3	344	1	0	0	0	0	1	0	0	0	9041	217	8	2	5313	2	LRRK1	15	101605833	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	7593	101605833	925559	1077	48440										
TARSL2	123283	hgsc.bcm.edu	37	chr15	102252089	102252089	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	attcagtgtgttacctgtctTcaatgaacatgtcataataa	6	7	4	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr15:102252089T>C	ENST00000335968.3	-	5	1022	c.806A>G	c.(805-807)gAa>gGa	p.E269G		NM_152334.2	NP_689547.2	A2RTX5	SYTC2_HUMAN	threonyl-tRNA synthetase-like 2	269					threonyl-tRNA aminoacylation (GO:0006435)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|threonine-tRNA ligase activity (GO:0004829)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(14)|ovary(2)|skin(1)|urinary_tract(1)	29	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000268)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			TTACCTGTCTTCAATGAACAT	0.428																																					p.E269G		Atlas-SNP	.											.	TARSL2	63	.	0			c.A806G						.						94	85	88					15																	102252089		2203	4300	6503	SO:0001583	missense	123283	exon5			CTGTCTTCAATGA	AL833188	CCDS10394.1	15q26.3	2008-02-05			ENSG00000185418	ENSG00000185418			24728	protein-coding gene	gene with protein product							Standard	NM_152334		Approved	FLJ25005	uc002bxm.3	A2RTX5	OTTHUMG00000149869	ENST00000335968.3:c.806A>G	chr15.hg19:g.102252089T>C	ENSP00000338093:p.Glu269Gly	74.0	0.0		67.0	15.0	NM_152334	B2RMP7|Q6B0A1|Q6IS76|Q96LW3|Q96MP4	Missense_Mutation	SNP	ENST00000335968.3	hg19	CCDS10394.1	.	.	.	.	.	.	.	.	.	.	T	9.102	1.004479	0.19199	.	.	ENSG00000185418	ENST00000335968;ENST00000539112	.	.	.	5.49	1.63	0.23807	Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain (1);	0.276251	0.41396	N	0.000888	T	0.24236	0.0587	N	0.05280	-0.08	0.42438	D	0.9927	B	0.10296	0.003	B	0.12837	0.008	T	0.04153	-1.0973	9	0.15499	T	0.54	-5.3897	5.8254	0.18550	0.0:0.1559:0.1406:0.7034	.	269	A2RTX5	SYTC2_HUMAN	G	269	.	ENSP00000338093:E269G	E	-	2	0	TARSL2	100069612	0.993000	0.37304	0.185000	0.23176	0.855000	0.48748	1.710000	0.37920	0.016000	0.14998	0.433000	0.28618	GAA	.	.		0.428	TARSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313619.3	NM_152334		C	102252089	T	C	102252089	3	2	344	1	0	0	0	0	1	0	0	0	15576	1783	62	2	1662	2	TARSL2	15	102252089	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	646256	102252089	279303	1078	48441										
RHBDF1	64285	hgsc.bcm.edu	37	chr16	114754	114754	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcaccggccgccggagctcaTggtggggtgaagagatgtgg	19	9	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:114754T>C	ENST00000262316.6	-	3	333	c.191A>G	c.(190-192)cAt>cGt	p.H64R	RHBDF1_ENST00000454039.2_Missense_Mutation_p.H64R	NM_022450.3	NP_071895.3	Q96CC6	RHDF1_HUMAN	rhomboid 5 homolog 1 (Drosophila)	64					cell migration (GO:0016477)|cell proliferation (GO:0008283)|negative regulation of protein secretion (GO:0050709)|protein transport (GO:0015031)|proteolysis (GO:0006508)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of protein secretion (GO:0050708)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	18		all_cancers(16;2.56e-05)|all_epithelial(16;0.000116)|Hepatocellular(780;0.0068)|Lung NSC(18;0.0795)|all_lung(18;0.159)				CCGGAGCTCATGGTGGGGTGA	0.642																																					p.H64R		Atlas-SNP	.											.	RHBDF1	54	.	0			c.A191G						.						101	106	104					16																	114754		2203	4300	6503	SO:0001583	missense	64285	exon3			AGCTCATGGTGGG	BC014425	CCDS32344.1	16p13.3	2008-02-05	2006-02-22		ENSG00000007384	ENSG00000007384			20561	protein-coding gene	gene with protein product		614403	"chromosome 16 open reading frame 8", "rhomboid family 1 (Drosophila)"	C16orf8		8318735, 15965977	Standard	NM_022450		Approved	EGFR-RS, FLJ2235, Dist1	uc002cfl.4	Q96CC6	OTTHUMG00000060719	ENST00000262316.6:c.191A>G	chr16.hg19:g.114754T>C	ENSP00000262316:p.His64Arg	66.0	0.0		44.0	20.0	NM_022450	Q04842|Q1W6H2|Q4TT59|Q96S34|Q9H6E1	Missense_Mutation	SNP	ENST00000262316.6	hg19	CCDS32344.1	.	.	.	.	.	.	.	.	.	.	.	5.691	0.311967	0.10789	.	.	ENSG00000007384	ENST00000262316;ENST00000454039;ENST00000338527;ENST00000450643;ENST00000420545;ENST00000419764	T;T;D	0.85339	0.84;-0.02;-1.97	5.62	-3.8	0.04307	.	0.764923	0.13222	N	0.404326	T	0.69278	0.3093	N	0.08118	0	0.20307	N	0.999912	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.09377	0.004;0.002;0.0	T	0.44862	-0.9300	10	0.16420	T	0.52	2.0E-4	19.1641	0.93546	0.0:0.0:0.7182:0.2817	.	64;87;64	F5GWL4;B4E3Q0;Q96CC6	.;.;RHDF1_HUMAN	R	64	ENSP00000262316:H64R;ENSP00000392133:H64R;ENSP00000408915:H64R	ENSP00000262316:H64R	H	-	2	0	RHBDF1	54754	0.992000	0.36948	0.006000	0.13384	0.247000	0.25773	0.813000	0.27225	-0.570000	0.06022	-0.331000	0.08364	CAT	.	.		0.642	RHBDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134178.2	NM_022450		C	114754	T	C	114754	3	2	344	1	0	0	0	0	1	0	0	0	13334	1464	51	2	2440	2	RHBDF1	16	114754	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10		114754	90239999	1079	48442										
PDIA2	64714	hgsc.bcm.edu	37	chr16	333349	333349	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctggccctgcgggagcacccTgccctgctggtggaattctg	14	14	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:333349T>A	ENST00000219406.6	+	1	198	c.180T>A	c.(178-180)ccT>ccA	p.P60P	PDIA2_ENST00000404312.1_Silent_p.P60P	NM_006849.2	NP_006840.2	Q13087	PDIA2_HUMAN	protein disulfide isomerase family A, member 2	60	Thioredoxin 1. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|peptidyl-proline hydroxylation (GO:0019511)|protein folding (GO:0006457)|protein retention in ER lumen (GO:0006621)|regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902175)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)	protein disulfide isomerase activity (GO:0003756)|steroid binding (GO:0005496)			breast(1)|central_nervous_system(4)|kidney(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	17		all_cancers(16;6.71e-07)|all_epithelial(16;1.59e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00769)|all_lung(18;0.0186)				GGGAGCACCCTGCCCTGCTGG	0.701																																					p.P60P		Atlas-SNP	.											.	PDIA2	51	.	0			c.T180A						.						24	32	29					16																	333349		1941	4135	6076	SO:0001819	synonymous_variant	64714	exon1			GCACCCTGCCCTG	U19948	CCDS42089.1	16p13.3	2009-11-20	2005-06-29	2005-03-03	ENSG00000185615	ENSG00000185615	5.3.4.1	"Protein disulfide isomerases"	14180	protein-coding gene	gene with protein product		608012	"protein disulfide isomerase, pancreatic", "protein disulfide isomerase-associated 2"	PDIP		8561901	Standard	NM_006849		Approved	PDA2, PDI, PDIR	uc002cgo.1	Q13087	OTTHUMG00000064891	ENST00000219406.6:c.180T>A	chr16.hg19:g.333349T>A		67.0	0.0		47.0	27.0	NM_006849	A6ZJ64|B4DI27|Q2WGM4|Q4TT67|Q6B010|Q96KJ6|Q9BW95	Silent	SNP	ENST00000219406.6	hg19	CCDS42089.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	0.243|0.243	-1.012534|-1.012534	0.02095|0.02095	.|.	.|.	ENSG00000185615|ENSG00000185615	ENST00000455994|ENST00000456379	.|.	.|.	.|.	3.82|3.82	-7.63|-7.63	0.01290|0.01290	.|.	.|.	.|.	.|.	.|.	T|T	0.16896|0.16896	0.0406|0.0406	.|.	.|.	.|.	0.09310|0.09310	N|N	0.999999|0.999999	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.15292|0.15292	-1.0442|-1.0442	5|4	0.87932|.	D|.	0|.	.|.	2.8748|2.8748	0.05628|0.05628	0.2254:0.296:0.3667:0.1119|0.2254:0.296:0.3667:0.1119	.|.	.|.	.|.	.|.	S|Q	42|57	.|.	ENSP00000415084:C42S|.	C|L	+|+	1|2	0|0	PDIA2|PDIA2	273350|273350	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.847000|0.847000	0.48162|0.48162	-2.182000|-2.182000	0.01256|0.01256	-2.542000|-2.542000	0.00485|0.00485	-0.373000|-0.373000	0.07131|0.07131	TGC|CTG	.	.		0.701	PDIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139315.3	NM_006849		A	333349	T	A	333349	2	1	344	1	0	0	0	0	0	0	0	1	11677	1567	55	4		4	PDIA2	16	333349	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	218595	333349	90021404	1080	48443										
CCDC78	124093	hgsc.bcm.edu	37	chr16	774367	774367	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcctgcggctcagatccaccAgcctcttgtggtagctgcgg	13	14	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:774367A>T	ENST00000293889.6	-	9	1013	c.908T>A	c.(907-909)cTg>cAg	p.L303Q	HAGHL_ENST00000564537.1_5'Flank|HAGHL_ENST00000389703.3_5'Flank|HAGHL_ENST00000561546.1_5'Flank|HAGHL_ENST00000341413.4_5'Flank|HAGHL_ENST00000549114.1_5'Flank|HAGHL_ENST00000564545.1_5'Flank	NM_001031737.2	NP_001026907.2	A2IDD5	CCD78_HUMAN	coiled-coil domain containing 78	303					cell projection organization (GO:0030030)|de novo centriole assembly (GO:0098535)|skeletal muscle contraction (GO:0003009)	centriole (GO:0005814)|deuterosome (GO:0098536)|perinuclear region of cytoplasm (GO:0048471)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|lung(2)|skin(3)	9		Hepatocellular(780;0.0218)				CAGATCCACCAGCCTCTTGTG	0.652																																					p.L303Q		Atlas-SNP	.											.	CCDC78	26	.	0			c.T908A						.						64	73	70					16																	774367		2198	4295	6493	SO:0001583	missense	124093	exon9			TCCACCAGCCTCT	BC042110	CCDS32353.1	16p13.3	2014-07-15		2006-02-20	ENSG00000162004	ENSG00000162004			14153	protein-coding gene	gene with protein product		614666		C16orf25		24075808	Standard	NM_001031737		Approved	FLJ34512	uc002cjg.3	A2IDD5	OTTHUMG00000121176	ENST00000293889.6:c.908T>A	chr16.hg19:g.774367A>T	ENSP00000293889:p.Leu303Gln	37.0	0.0		41.0	20.0	NM_001031737	B4DNY4|B4E1U6|Q05BY7|Q05CA0|Q6T2V5|Q6ZR33|Q8IUR3|Q8NAY7|Q96S12	Missense_Mutation	SNP	ENST00000293889.6	hg19	CCDS32353.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	a|a	15.03|15.03	2.710942|2.710942	0.48517|0.48517	.|.	.|.	ENSG00000162004|ENSG00000162004	ENST00000293889|ENST00000345165	T|.	0.36699|.	1.24|.	5.38|5.38	4.3|4.3	0.51218|0.51218	.|.	0.137793|.	0.45606|.	D|.	0.000342|.	T|T	0.47002|0.47002	0.1422|0.1422	L|L	0.48642|0.48642	1.525|1.525	0.32213|0.32213	N|N	0.57623|0.57623	D;D;D|.	0.76494|.	0.998;0.999;0.999|.	D;D;D|.	0.71656|.	0.962;0.974;0.962|.	T|T	0.55211|0.55211	-0.8176|-0.8176	10|5	0.72032|.	D|.	0.01|.	-14.134|-14.134	8.7357|8.7357	0.34528|0.34528	0.9101:0.0:0.0899:0.0|0.9101:0.0:0.0899:0.0	.|.	62;303;152|.	D3DU63;A2IDD5;D3DU61|.	.;CCD78_HUMAN;.|.	Q|R	303|152	ENSP00000293889:L303Q|.	ENSP00000293889:L303Q|.	L|W	-|-	2|1	0|0	CCDC78|CCDC78	714368|714368	0.004000|0.004000	0.15560|0.15560	0.995000|0.995000	0.50966|0.50966	0.014000|0.014000	0.08584|0.08584	1.645000|1.645000	0.37238|0.37238	2.038000|2.038000	0.60285|0.60285	0.444000|0.444000	0.29173|0.29173	CTG|TGG	.	.		0.652	CCDC78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241665.3	NM_173476		T	774367	A	T	774367	3	4	344	1	0	0	0	0	1	0	0	0	2854	188	7	4	432	4	CCDC78	16	774367	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	441018	774367	89580386	1081	48444										
CACNA1H	8912	hgsc.bcm.edu	37	chr16	1270071	1270071	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctggtgagaaaaccccggtgAggccggtgacccaggggggc	18	11	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:1270071A>G	ENST00000348261.5	+	35	6387	c.6139A>G	c.(6139-6141)Agg>Ggg	p.R2047G	CACNA1H_ENST00000358590.4_Missense_Mutation_p.R2041G|CACNA1H_ENST00000565831.1_Missense_Mutation_p.R2041G	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	2047					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	AACCCCGGTGAGGCCGGTGAC	0.662																																					p.R2047G		Atlas-SNP	.											.	CACNA1H	317	.	0			c.A6139G						.						15	19	18					16																	1270071		1928	4108	6036	SO:0001583	missense	8912	exon35			CCGGTGAGGCCGG	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.6139A>G	chr16.hg19:g.1270071A>G	ENSP00000334198:p.Arg2047Gly	109.0	0.0		84.0	39.0	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	hg19	CCDS45375.1	.	.	.	.	.	.	.	.	.	.	A	10.60	1.396197	0.25205	.	.	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.96491	-4.03;-3.98	4.62	0.818	0.18778	.	3.663200	0.00810	N	0.001492	D	0.90277	0.6959	N	0.08118	0	0.09310	N	1	B;B;B;B;B	0.29716	0.075;0.036;0.255;0.0;0.02	B;B;B;B;B	0.20184	0.027;0.028;0.023;0.001;0.018	T	0.83200	-0.0079	10	0.23891	T	0.37	.	10.4864	0.44724	0.5792:0.4208:0.0:0.0	.	793;771;777;2041;2047	A2SX38;A2SX35;A2SX37;O95180-2;O95180	.;.;.;.;CAC1H_HUMAN	G	2047;2041	ENSP00000334198:R2047G;ENSP00000351401:R2041G	ENSP00000334198:R2047G	R	+	1	2	CACNA1H	1210072	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-0.131000	0.10482	-0.032000	0.13758	0.254000	0.18369	AGG	.	.		0.662	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407		G	1270071	A	G	1270071	3	3	344	1	0	0	0	0	1	0	0	0	2547	295	11	2	6273	2	CACNA1H	16	1270071	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	495704	1270071	89084682	1082	48445										
TELO2	9894	hgsc.bcm.edu	37	chr16	1551726	1551726	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccccgcagagatcgtggatgGcggcgtcccccaagcacagc	13	16	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:1551726G>A	ENST00000262319.6	+	11	1703	c.1424G>A	c.(1423-1425)gGc>gAc	p.G475D	TELO2_ENST00000564507.1_3'UTR	NM_016111.3	NP_057195.2	Q9Y4R8	TELO2_HUMAN	telomere maintenance 2	475					regulation of TOR signaling (GO:0032006)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	protein complex binding (GO:0032403)			NS(1)|endometrium(1)|kidney(5)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	19		Hepatocellular(780;0.219)				ATCGTGGATGGCGGCGTCCCC	0.652																																					p.G475D		Atlas-SNP	.											.	TELO2	44	.	0			c.G1424A						.						45	55	51					16																	1551726		2199	4300	6499	SO:0001583	missense	9894	exon11			TGGATGGCGGCGT	AL080126	CCDS32363.1	16p13.3	2013-08-06	2013-08-06		ENSG00000100726	ENSG00000100726			29099	protein-coding gene	gene with protein product		611140	"TEL2, telomere maintenance 2, homolog (S. cerevisiae)"			9734811, 11230166, 12670948	Standard	NM_016111		Approved	KIAA0683, hCLK2, TEL2	uc002cly.3	Q9Y4R8	OTTHUMG00000044471	ENST00000262319.6:c.1424G>A	chr16.hg19:g.1551726G>A	ENSP00000262319:p.Gly475Asp	24.0	0.0		20.0	11.0	NM_016111	D3DU73|O75168|Q7LDV4|Q9BR21	Missense_Mutation	SNP	ENST00000262319.6	hg19	CCDS32363.1	.	.	.	.	.	.	.	.	.	.	G	4.336	0.061679	0.08339	.	.	ENSG00000100726	ENST00000437914;ENST00000262319	T	0.13307	2.6	4.45	0.133	0.14766	.	1.473200	0.03126	N	0.164575	T	0.09468	0.0233	L	0.36672	1.1	0.09310	N	1	B	0.28233	0.204	B	0.24006	0.05	T	0.23084	-1.0198	10	0.14252	T	0.57	0.7029	1.5534	0.02580	0.1929:0.1643:0.4736:0.1691	.	475	Q9Y4R8	TELO2_HUMAN	D	89;475	ENSP00000262319:G475D	ENSP00000262319:G475D	G	+	2	0	TELO2	1491727	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.175000	0.16762	-0.007000	0.14345	0.655000	0.94253	GGC	.	.		0.652	TELO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103602.2	NM_016111		A	1551726	G	A	1551726	3	1	344	1	0	0	0	0	1	0	0	0	15772	1203	42	3	1462	3	TELO2	16	1551726	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	281655	1551726	88803027	1083	48446										
TBL3	10607	hgsc.bcm.edu	37	chr16	2026270	2026270	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccaggtgatgtgcgtggctcAgggttccggtcacacacaca	13	12	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:2026270A>T	ENST00000568546.1	+	13	1375	c.1247A>T	c.(1246-1248)cAg>cTg	p.Q416L		NM_006453.2	NP_006444.2	Q12788	TBL3_HUMAN	transducin (beta)-like 3	416					G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|intracellular signal transduction (GO:0035556)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)			breast(1)|endometrium(2)|kidney(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	18						TGCGTGGCTCAGGGTTCCGGT	0.637																																					p.Q416L	Melanoma(118;616 1651 35077 38081 48633)	Atlas-SNP	.											.	TBL3	54	.	0			c.A1247T						.						117	80	92					16																	2026270		2198	4299	6497	SO:0001583	missense	10607	exon13			TGGCTCAGGGTTC	U02609	CCDS10453.1	16p13.3	2013-01-10			ENSG00000183751	ENSG00000183751		"WD repeat domain containing"	11587	protein-coding gene	gene with protein product		605915				8307582	Standard	NM_006453		Approved	SAZD, UTP13	uc002cnu.1	Q12788	OTTHUMG00000128710	ENST00000568546.1:c.1247A>T	chr16.hg19:g.2026270A>T	ENSP00000454836:p.Gln416Leu	87.0	0.0		63.0	29.0	NM_006453	Q59GD6|Q8IVB7|Q96A78	Missense_Mutation	SNP	ENST00000568546.1	hg19	CCDS10453.1	.	.	.	.	.	.	.	.	.	.	A	5.834	0.338180	0.11069	.	.	ENSG00000183751	ENST00000332704	.	.	.	4.99	3.82	0.43975	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.435265	0.19833	N	0.105047	T	0.22399	0.0540	N	0.04132	-0.27	0.51233	D	0.999917	B;P	0.35527	0.005;0.507	B;B	0.33568	0.038;0.166	T	0.05903	-1.0857	9	0.37606	T	0.19	-14.9031	7.3119	0.26479	0.8043:0.0:0.0:0.1957	.	178;416	A0JLS5;Q12788	.;TBL3_HUMAN	L	416	.	ENSP00000331815:Q416L	Q	+	2	0	TBL3	1966271	0.985000	0.35326	1.000000	0.80357	0.284000	0.27059	1.606000	0.36826	1.874000	0.54306	0.459000	0.35465	CAG	.	.		0.637	TBL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250615.3	NM_006453		T	2026270	A	T	2026270	3	4	344	1	0	0	0	0	1	0	0	0	15658	188	7	4	1297	4	TBL3	16	2026270	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	474544	2026270	88328483	1084	48447										
ZNF598	90850	hgsc.bcm.edu	37	chr16	2048704	2048704	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctccccgggcccgcctgaccTgtctgaactcccctgagtgg	11	18	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:2048704T>A	ENST00000563630.1	-	11	2437	c.2195A>T	c.(2194-2196)cAg>cTg	p.Q732L	AC005606.15_ENST00000567515.1_lincRNA|ZNF598_ENST00000562103.1_Splice_Site_p.Q732L|ZNF598_ENST00000431526.1_Splice_Site_p.Q787L			Q86UK7	ZN598_HUMAN	zinc finger protein 598	787	Pro-rich.						poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|skin(1)|urinary_tract(1)	16						CCGCCTGACCTGTCTGAACTC	0.672																																					p.Q787L		Atlas-SNP	.											.	ZNF598	55	.	0			c.A2360T						.						10	11	10					16																	2048704		1860	4076	5936	SO:0001630	splice_region_variant	90850	exon13			CTGACCTGTCTGA	BC029270		16p13.3	2008-05-02				ENSG00000167962		"Zinc fingers, C2H2-type"	28079	protein-coding gene	gene with protein product							Standard	NM_178167		Approved	FLJ00086	uc002cof.2	Q86UK7		ENST00000563630.1:c.2196+1A>T	chr16.hg19:g.2048704T>A		73.0	0.0		64.0	27.0	NM_178167	Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	Missense_Mutation	SNP	ENST00000563630.1	hg19		.	.	.	.	.	.	.	.	.	.	.	14.51	2.557353	0.45590	.	.	ENSG00000167962	ENST00000431526	T	0.20881	2.04	4.73	4.73	0.59995	.	0.058623	0.64402	D	0.000001	T	0.47801	0.1465	M	0.83012	2.62	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.69479	0.943;0.964	T	0.54070	-0.8348	10	0.62326	D	0.03	-28.0265	13.5873	0.61940	0.0:0.0:0.0:1.0	.	787;779	Q86UK7;Q86UK7-2	ZN598_HUMAN;.	L	787	ENSP00000411409:Q787L	ENSP00000411409:Q787L	Q	-	2	0	ZNF598	1988705	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	4.561000	0.60809	1.996000	0.58369	0.374000	0.22700	CAG	.	.		0.672	ZNF598-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000434439.1	NM_178167	Missense_Mutation	A	2048704	T	A	2048704	5	1	344	1	0	0	0	0	0	0	1	0	18043	1594	55	4	362	4	ZNF598	16	2048704	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	22434	2048704	88306049	1085	48448										
E4F1	1877	hgsc.bcm.edu	37	chr16	2282755	2282755	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gctgactaggttctctctgcAgatgagcgcccctacaagtg	11	12	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:2282755A>C	ENST00000301727.4	+	6	778		c.e6-1		E4F1_ENST00000564139.1_Splice_Site|RP11-304L19.12_ENST00000564055.1_lincRNA|E4F1_ENST00000565090.1_Splice_Site	NM_004424.3	NP_004415.2	Q66K89	E4F1_HUMAN	E4F transcription factor 1						cell proliferation (GO:0008283)|DNA replication (GO:0006260)|mitotic cell cycle arrest (GO:0071850)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|regulation of cell cycle process (GO:0010564)|regulation of growth (GO:0040008)|regulation of mitotic cell cycle, embryonic (GO:0009794)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	cAMP response element binding (GO:0035497)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			ovary(1)	1						TTCTCTCTGCAGATGAGCGCC	0.637																																					.		Atlas-SNP	.											.	E4F1	53	.	0			c.731-2A>C						.						52	61	58					16																	2282755		2196	4300	6496	SO:0001630	splice_region_variant	1877	exon6			CTCTGCAGATGAG	U87269	CCDS32370.1, CCDS73809.1, CCDS73810.1	16p13.3	2013-01-08				ENSG00000167967		"Zinc fingers, C2H2-type"	3121	protein-coding gene	gene with protein product		603022				9763670, 8828041	Standard	XM_005255155		Approved	E4F	uc002cpm.3	Q66K89		ENST00000301727.4:c.731-1A>C	chr16.hg19:g.2282755A>C		56.0	0.0		36.0	21.0	NM_004424	A8K2R4|O00146	Splice_Site	SNP	ENST00000301727.4	hg19	CCDS32370.1	.	.	.	.	.	.	.	.	.	.	A	11.36	1.616415	0.28801	.	.	ENSG00000167967	ENST00000301727	.	.	.	5.65	5.65	0.86999	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7005	0.69152	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	E4F1	2222756	1.000000	0.71417	0.819000	0.32651	0.398000	0.30690	9.109000	0.94291	2.154000	0.67381	0.459000	0.35465	.	.	.		0.637	E4F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435225.1	NM_004424	Intron	C	2282755	A	C	2282755	5	2	344	1	0	0	0	0	0	0	1	0	4876	202	7	5	751	5	E4F1	16	2282755	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	234051	2282755	88071998	1086	48449										
ABCA3	21	hgsc.bcm.edu	37	chr16	2348543	2348543	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctggtggggggaaagagaccTggggcccagcaggagacccc	18	11	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:2348543T>C	ENST00000301732.5	-	15	2442		c.e15-2		ABCA3_ENST00000382381.3_Splice_Site	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3						response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	alveolar lamellar body (GO:0097208)|alveolar lamellar body membrane (GO:0097233)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(7)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(7)|prostate(5)|skin(6)|upper_aerodigestive_tract(1)	70		Ovarian(90;0.17)			Imatinib(DB00619)	GAAAGAGACCTGGGGCCCAGC	0.602																																					.		Atlas-SNP	.											.	ABCA3	176	.	0			c.1742-2A>G						.						53	53	53					16																	2348543		2198	4300	6498	SO:0001630	splice_region_variant	21	exon16			GAGACCTGGGGCC	U78735	CCDS10466.1	16p13.3	2012-03-14			ENSG00000167972	ENSG00000167972		"ATP binding cassette transporters / subfamily A"	33	protein-coding gene	gene with protein product		601615		ABC3		8706931	Standard	NM_001089		Approved	ABC-C, EST111653, LBM180	uc002cpy.1	Q99758	OTTHUMG00000128845	ENST00000301732.5:c.1742-2A>G	chr16.hg19:g.2348543T>C		62.0	0.0		74.0	31.0	NM_001089	B2RU09|Q54A95|Q6P5P9|Q92473	Splice_Site	SNP	ENST00000301732.5	hg19	CCDS10466.1	.	.	.	.	.	.	.	.	.	.	T	11.66	1.703639	0.30232	.	.	ENSG00000167972	ENST00000301732;ENST00000382381	.	.	.	5.93	5.93	0.95920	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2293	0.73374	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	ABCA3	2288544	1.000000	0.71417	0.760000	0.31359	0.145000	0.21501	2.991000	0.49409	2.281000	0.76405	0.533000	0.62120	.	.	.		0.602	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089	Intron	C	2348543	T	C	2348543	5	2	344	1	0	0	0	0	0	0	1	0	33	1594	55	2	3450	2	ABCA3	16	2348543	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	65788	2348543	88006210	1087	48450										
C16orf89	146556	hgsc.bcm.edu	37	chr16	5112500	5112500	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cagcctccagcttctcccccAgcatccccacgcgcaggctc	7	22	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:5112500A>T	ENST00000315997.5	-	2	485	c.284T>A	c.(283-285)cTg>cAg	p.L95Q	C16orf89_ENST00000350219.4_Missense_Mutation_p.L133Q|C16orf89_ENST00000472572.3_Missense_Mutation_p.L95Q|ALG1_ENST00000588623.1_Intron|C16orf89_ENST00000474471.3_Missense_Mutation_p.L95Q|C16orf89_ENST00000422873.1_Missense_Mutation_p.L133Q	NM_152459.4	NP_689672.4	Q6UX73	CP089_HUMAN	chromosome 16 open reading frame 89	95						cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	12						CTTCTCCCCCAGCATCCCCAC	0.587																																					p.L95Q		Atlas-SNP	.											.	C16orf89	64	.	0			c.T284A						.						60	63	62					16																	5112500		1992	4173	6165	SO:0001583	missense	146556	exon2			TCCCCCAGCATCC		CCDS42116.1, CCDS45404.1, CCDS42116.2, CCDS45404.2	16p13.3	2011-12-12			ENSG00000153446	ENSG00000153446			28687	protein-coding gene	gene with protein product						12975309, 20578903	Standard	NM_001098514		Approved	MGC45438	uc010bud.3	Q6UX73	OTTHUMG00000159314	ENST00000315997.5:c.284T>A	chr16.hg19:g.5112500A>T	ENSP00000324672:p.Leu95Gln	61.0	0.0		60.0	30.0	NM_001098514	B4DUM5|Q8N2I3|Q8N4T1	Missense_Mutation	SNP	ENST00000315997.5	hg19	CCDS42116.2	.	.	.	.	.	.	.	.	.	.	A	12.97	2.097164	0.37048	.	.	ENSG00000153446	ENST00000474471;ENST00000472572;ENST00000477550;ENST00000422873;ENST00000350219;ENST00000315997	T;T;T;T;T	0.45668	0.89;0.89;0.89;0.89;0.89	4.98	4.98	0.66077	.	0.378221	0.22649	N	0.057359	T	0.56688	0.2002	L	0.56769	1.78	0.09310	N	0.999999	D;D	0.76494	0.999;0.996	D;D	0.66196	0.942;0.931	T	0.50906	-0.8772	10	0.56958	D	0.05	-28.942	11.0561	0.47920	1.0:0.0:0.0:0.0	.	95;133	Q6UX73;G3V0F0	CP089_HUMAN;.	Q	95;95;95;133;133;95	ENSP00000417158:L95Q;ENSP00000420566:L95Q;ENSP00000390402:L133Q;ENSP00000283478:L133Q;ENSP00000324672:L95Q	ENSP00000324672:L95Q	L	-	2	0	C16orf89	5052501	0.395000	0.25254	0.341000	0.25589	0.005000	0.04900	4.352000	0.59404	1.880000	0.54463	0.379000	0.24179	CTG	.	.		0.587	C16orf89-001	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354524.1	NM_152459		T	5112500	A	T	5112500	3	4	344	1	0	0	0	0	1	0	0	0	1844	188	7	4	1087	4	C16orf89	16	5112500	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2763957	5112500	85242253	1088	48451										
CLEC16A	23274	hgsc.bcm.edu	37	chr16	11076808	11076808	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tctgaatggtgatctgtctgAgatgtacgctaagactgaac	11	7	3	5			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:11076808A>T	ENST00000409790.1	+	10	1261	c.1031A>T	c.(1030-1032)gAg>gTg	p.E344V	CLEC16A_ENST00000409552.3_Missense_Mutation_p.E342V	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A											breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						GATCTGTCTGAGATGTACGCT	0.413																																					p.E344V		Atlas-SNP	.											.	CLEC16A	101	.	0			c.A1031T						.						108	102	104					16																	11076808		1912	4139	6051	SO:0001583	missense	23274	exon9			TGTCTGAGATGTA	AB002348	CCDS45409.1, CCDS58423.1	16p13.13	2010-04-27	2007-07-17	2007-07-17	ENSG00000038532	ENSG00000038532		"C-type lectin domain containing"	29013	protein-coding gene	gene with protein product		611303	"KIAA0350"	KIAA0350		9205841, 17632545	Standard	NM_015226		Approved	Gop-1	uc002dao.3	Q2KHT3	OTTHUMG00000152915	ENST00000409790.1:c.1031A>T	chr16.hg19:g.11076808A>T	ENSP00000387122:p.Glu344Val	51.0	0.0		57.0	25.0	NM_015226		Missense_Mutation	SNP	ENST00000409790.1	hg19	CCDS45409.1	.	.	.	.	.	.	.	.	.	.	A	13.16	2.153373	0.38021	.	.	ENSG00000038532	ENST00000409790;ENST00000542102;ENST00000409552	T	0.41758	0.99	5.64	4.52	0.55395	.	0.054680	0.64402	D	0.000001	T	0.09335	0.0230	N	0.00082	-2.215	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.12656	-1.0539	10	0.27082	T	0.32	-26.626	8.1531	0.31152	0.6438:0.0:0.0:0.3562	.	344;342	Q2KHT3;Q2KHT3-2	CL16A_HUMAN;.	V	344;344;342	ENSP00000387122:E344V	ENSP00000386495:E342V	E	+	2	0	CLEC16A	10984309	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	4.044000	0.57361	2.144000	0.66660	0.533000	0.62120	GAG	.	.		0.413	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226		T	11076808	A	T	11076808	3	4	344	1	0	0	0	0	1	0	0	0	3502	304	11	4	1065	4	CLEC16A	16	11076808	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	5964308	11076808	79277945	1089	48452										
MKL2	57496	hgsc.bcm.edu	37	chr16	14340581	14340581	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaggcagaattgccacctacAggaaccagcaacgcaacccg	9	14	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:14340581A>T	ENST00000341243.5	+	10	1431	c.1431A>T	c.(1429-1431)acA>acT	p.T477T	MKL2_ENST00000574045.1_Silent_p.T488T|MKL2_ENST00000571589.1_Silent_p.T488T|MKL2_ENST00000318282.5_Silent_p.T488T			Q9ULH7	MKL2_HUMAN	MKL/myocardin-like 2	477					blood vessel morphogenesis (GO:0048514)|cardiac muscle tissue development (GO:0048738)|embryonic organ development (GO:0048568)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|muscle organ development (GO:0007517)|positive regulation of striated muscle tissue development (GO:0045844)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(6)|liver(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						TGCCACCTACAGGAACCAGCA	0.502																																					p.T488T		Atlas-SNP	.											.	MKL2	103	.	0			c.A1464T						.						213	193	200					16																	14340581		2197	4300	6497	SO:0001819	synonymous_variant	57496	exon12			ACCTACAGGAACC	AB033069	CCDS32391.1	16p13.12	2012-11-29			ENSG00000186260	ENSG00000186260			29819	protein-coding gene	gene with protein product		609463				10574462	Standard	NM_014048		Approved	MRTF-B, FLJ31823	uc002dcg.3	Q9ULH7	OTTHUMG00000177379	ENST00000341243.5:c.1431A>T	chr16.hg19:g.14340581A>T		83.0	0.0		68.0	36.0	NM_014048	A6ND53|B4DGT8|Q68CT1|Q6UB16|Q86WW2|Q8N226	Silent	SNP	ENST00000341243.5	hg19																																																																																				.	.		0.502	MKL2-202	KNOWN	basic	protein_coding	protein_coding		NM_014048		T	14340581	A	T	14340581	2	4	344	1	0	0	0	0	0	0	0	1	9611	175	7	4		4	MKL2	16	14340581	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3263773	14340581	76014172	1090	48453										
XYLT1	64131	hgsc.bcm.edu	37	chr16	17353092	17353092	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tggctgctgttggctgcggcTctgtccccgggaggcagcac	16	13	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:17353092T>C	ENST00000261381.6	-	3	750	c.666A>G	c.(664-666)agA>agG	p.R222R		NM_022166.3	NP_071449.1	Q86Y38	XYLT1_HUMAN	xylosyltransferase I	222					cellular response to heat (GO:0034605)|chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						TGGCTGCGGCTCTGTCCCCGG	0.592																																					p.R222R		Atlas-SNP	.											.	XYLT1	147	.	0			c.A666G						.						105	117	113					16																	17353092		2197	4300	6497	SO:0001819	synonymous_variant	64131	exon3			TGCGGCTCTGTCC	AJ277441	CCDS10569.1	16p12	2013-02-25			ENSG00000103489	ENSG00000103489	2.4.2.26	"Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	15516	protein-coding gene	gene with protein product	"protein xylosyltransferase 1"	608124				11099377	Standard	NM_022166		Approved	XT-I, PXYLT1	uc002dfa.3	Q86Y38	OTTHUMG00000129975	ENST00000261381.6:c.666A>G	chr16.hg19:g.17353092T>C		87.0	0.0		86.0	40.0	NM_022166	Q9H1B6	Silent	SNP	ENST00000261381.6	hg19	CCDS10569.1																																																																																			.	.		0.592	XYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252241.2	NM_022166		C	17353092	T	C	17353092	2	2	344	1	0	0	0	0	0	0	0	1	17478	1548	54	2		2	XYLT1	16	17353092	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	3012511	17353092	73001661	1091	48454										
TMC7	79905	hgsc.bcm.edu	37	chr16	19033071	19033071	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cccagtcttactcacgaaatAcaagatcaccaacagcagct	5	14	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:19033071A>G	ENST00000304381.5	+	4	711	c.581A>G	c.(580-582)tAc>tGc	p.Y194C	TMC7_ENST00000421369.3_Missense_Mutation_p.Y84C|TMC7_ENST00000569532.1_Missense_Mutation_p.Y194C	NM_024847.3	NP_079123.3	Q7Z402	TMC7_HUMAN	transmembrane channel-like 7	194					ion transport (GO:0006811)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	28						CTCACGAAATACAAGATCACC	0.423																																					p.Y194C		Atlas-SNP	.											.	TMC7	75	.	0			c.A581G						.						169	138	148					16																	19033071		2197	4300	6497	SO:0001583	missense	79905	exon4			CGAAATACAAGAT	AY263165	CCDS10573.1, CCDS53992.1, CCDS73837.1	16p13.11	2008-02-05			ENSG00000170537	ENSG00000170537			23000	protein-coding gene	gene with protein product						12812529, 12906855	Standard	XM_005255597		Approved	FLJ21240	uc002dfq.3	Q7Z402	OTTHUMG00000131456	ENST00000304381.5:c.581A>G	chr16.hg19:g.19033071A>G	ENSP00000304710:p.Tyr194Cys	109.0	0.0		103.0	37.0	NM_024847	E7ERB6|Q5H9Q8|Q7Z5M4|Q86WX0|Q9H766	Missense_Mutation	SNP	ENST00000304381.5	hg19	CCDS10573.1	.	.	.	.	.	.	.	.	.	.	A	12.38	1.919639	0.33908	.	.	ENSG00000170537	ENST00000304381;ENST00000421369	T;T	0.51574	0.7;0.7	5.04	3.93	0.45458	.	0.289586	0.29838	N	0.011073	T	0.55878	0.1948	L	0.43152	1.355	0.40671	D	0.982216	D;P;D	0.76494	0.999;0.887;0.957	D;P;P	0.66847	0.947;0.593;0.719	T	0.53394	-0.8445	10	0.39692	T	0.17	.	10.4775	0.44674	0.854:0.0:0.0:0.146	.	194;194;194	B4DF02;Q7Z402;B3KSZ3	.;TMC7_HUMAN;.	C	194;84	ENSP00000304710:Y194C;ENSP00000397081:Y84C	ENSP00000304710:Y194C	Y	+	2	0	TMC7	18940572	1.000000	0.71417	1.000000	0.80357	0.190000	0.23558	6.440000	0.73435	0.851000	0.35264	-0.509000	0.04479	TAC	.	.		0.423	TMC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254276.3	NM_024847		G	19033071	A	G	19033071	3	3	344	1	0	0	0	0	1	0	0	0	16005	391	14	2	595	2	TMC7	16	19033071	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1679979	19033071	71321682	1092	48455										
GPR139	124274	hgsc.bcm.edu	37	chr16	20084903	20084903	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggggaccaccaagacagcgaGctgttggctgcgaggtgggc	18	10	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:20084903G>C	ENST00000570682.1	-	1	336	c.36C>G	c.(34-36)agC>agG	p.S12R		NM_001002911.2	NP_001002911.1	Q6DWJ6	GP139_HUMAN	G protein-coupled receptor 139	12					G-protein coupled receptor signaling pathway (GO:0007186)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	30						AAGACAGCGAGCTGTTGGCTG	0.701																																					p.S12R		Atlas-SNP	.											.	GPR139	75	.	0			c.C36G						.						33	34	34					16																	20084903		2203	4299	6502	SO:0001583	missense	124274	exon1			CAGCGAGCTGTTG	AY255545	CCDS32398.1	16p13.11	2012-08-21						"GPCR / Class A : Orphans"	19995	protein-coding gene	gene with protein product						12679517	Standard	XM_005255114		Approved	PGR3	uc002dgu.1	Q6DWJ6		ENST00000570682.1:c.36C>G	chr16.hg19:g.20084903G>C	ENSP00000458791:p.Ser12Arg	126.0	0.0		115.0	52.0	NM_001002911	A8K5R9|Q86SP2|Q8TDU8	Missense_Mutation	SNP	ENST00000570682.1	hg19	CCDS32398.1	.	.	.	.	.	.	.	.	.	.	G	16.00	2.999051	0.54147	.	.	ENSG00000180269	ENST00000326571	.	.	.	4.32	4.32	0.51571	.	0.429903	0.19621	N	0.109902	T	0.31231	0.0790	N	0.08118	0	0.35835	D	0.825609	B	0.06786	0.001	B	0.08055	0.003	T	0.30119	-0.9989	9	0.27082	T	0.32	-18.8853	12.1817	0.54216	0.0:0.0:1.0:0.0	.	12	Q6DWJ6	GP139_HUMAN	R	12	.	ENSP00000370779:S12R	S	-	3	2	GPR139	19992404	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.205000	0.42770	2.216000	0.71823	0.455000	0.32223	AGC	.	.		0.701	GPR139-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438522.1	NM_001002911		C	20084903	G	C	20084903	3	2	344	1	0	0	0	0	1	0	0	0	6656	962	34	4	1033	4	GPR139	16	20084903	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1051832	20084903	70269850	1093	48456										
ACSM3	6296	hgsc.bcm.edu	37	chr16	20788756	20788756	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gacattctctacagactacaAtcttcaaaagcaaactgcat	4	11	3	1	rs545664454		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:20788756A>T	ENST00000289416.5	+	4	967	c.492A>T	c.(490-492)caA>caT	p.Q164H	ACSM3_ENST00000440284.2_Missense_Mutation_p.Q164H|ACSM3_ENST00000450120.2_Missense_Mutation_p.Q119H	NM_005622.3	NP_005613.2	Q53FZ2	ACSM3_HUMAN	acyl-CoA synthetase medium-chain family member 3	164					cholesterol homeostasis (GO:0042632)|fatty acid biosynthetic process (GO:0006633)|regulation of blood pressure (GO:0008217)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty acid ligase activity (GO:0015645)|metal ion binding (GO:0046872)			breast(1)|endometrium(5)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)	21						ACAGACTACAATCTTCAAAAG	0.408																																					p.Q164H		Atlas-SNP	.											.	ACSM3	113	.	0			c.A492T						.						93	90	91					16																	20788756		2201	4300	6501	SO:0001583	missense	6296	exon4			ACTACAATCTTCA	D16350	CCDS10589.1, CCDS45435.1	16p13.11	2006-02-08	2005-09-08	2005-09-08	ENSG00000005187	ENSG00000005187		"Acyl-CoA synthetase family"	10522	protein-coding gene	gene with protein product		145505	"SA (rat hypertension-associated) homolog", "SA hypertension-associated homolog (rat)"	SAH		7843754, 7907320, 11470804	Standard	NM_005622		Approved	SA	uc002dhr.3	Q53FZ2	OTTHUMG00000131552	ENST00000289416.5:c.492A>T	chr16.hg19:g.20788756A>T	ENSP00000289416:p.Gln164His	107.0	0.0		91.0	46.0	NM_005622	O60363|Q13732|Q15425|Q7KYM6|Q9BUA2	Missense_Mutation	SNP	ENST00000289416.5	hg19	CCDS10589.1	.	.	.	.	.	.	.	.	.	.	A	9.010	0.982226	0.18889	.	.	ENSG00000005187	ENST00000289416;ENST00000440284;ENST00000450120	T;T;T	0.42900	0.96;0.96;0.96	6.05	-4.53	0.03462	AMP-dependent synthetase/ligase (1);	0.130941	0.52532	D	0.000062	T	0.28300	0.0699	L	0.33189	0.99	0.18873	N	0.999987	B;B;P	0.45212	0.234;0.154;0.853	B;B;B	0.37451	0.25;0.149;0.196	T	0.27971	-1.0058	10	0.66056	D	0.02	-8.6757	17.251	0.87042	0.3899:0.0:0.6101:0.0	.	119;164;164	E7ETR5;Q53FZ2;Q53FZ2-2	.;ACSM3_HUMAN;.	H	164;164;119	ENSP00000289416:Q164H;ENSP00000394565:Q164H;ENSP00000395297:Q119H	ENSP00000289416:Q164H	Q	+	3	2	ACSM3	20696257	0.000000	0.05858	0.261000	0.24466	0.001000	0.01503	-0.372000	0.07504	-1.314000	0.02300	-1.867000	0.00556	CAA	.	.		0.408	ACSM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254414.2	NM_005622		T	20788756	A	T	20788756	3	4	344	1	0	0	0	0	1	0	0	0	185	98	4	4	502	4	ACSM3	16	20788756	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	703853	20788756	69565997	1094	48457										
DNAH3	55567	hgsc.bcm.edu	37	chr16	21136500	21136500	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	caggtccctgacttactttgTgtatcatgaaaagggaaacg	10	8	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:21136500T>G	ENST00000261383.3	-	9	1399	c.1400A>C	c.(1399-1401)cAc>cCc	p.H467P	CTC-508F8.1_ENST00000575612.1_RNA|DNAH3_ENST00000415178.1_Missense_Mutation_p.H467P	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	467	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			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)		ACTTACTTTGTGTATCATGAA	0.468																																					p.H467P		Atlas-SNP	.											.	DNAH3	1142	.	0			c.A1400C						.						95	91	92					16																	21136500		2201	4300	6501	SO:0001583	missense	55567	exon9			ACTTTGTGTATCA	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"Axonemal dyneins"	2949	protein-coding gene	gene with protein product		603334	"dynein, axonemal, heavy polypeptide 3"			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.1400A>C	chr16.hg19:g.21136500T>G	ENSP00000261383:p.His467Pro	51.0	0.0		68.0	35.0	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	hg19	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	T	12.35	1.911241	0.33721	.	.	ENSG00000158486	ENST00000261383;ENST00000415178;ENST00000396036	T;T	0.22539	1.95;2.1	5.63	4.54	0.55810	.	0.181972	0.36778	N	0.002415	T	0.33876	0.0878	L	0.47016	1.485	0.48762	D	0.999704	B;D	0.63046	0.025;0.992	B;D	0.65010	0.014;0.931	T	0.02184	-1.1199	10	0.31617	T	0.26	.	10.692	0.45877	0.0:0.0759:0.0:0.9241	.	467;438	Q8TD57;Q8TD57-2	DYH3_HUMAN;.	P	467;467;438	ENSP00000261383:H467P;ENSP00000394245:H467P	ENSP00000261383:H467P	H	-	2	0	DNAH3	21044001	1.000000	0.71417	0.999000	0.59377	0.619000	0.37552	6.229000	0.72294	0.980000	0.38523	0.533000	0.62120	CAC	.	.		0.468	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		G	21136500	T	G	21136500	3	3	344	1	0	0	0	0	1	0	0	0	4605	1696	59	5	11165	5	DNAH3	16	21136500	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	347744	21136500	69218253	1095	48458										
ZP2	7783	hgsc.bcm.edu	37	chr16	21215496	21215496	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcccaggaaactctggtatgGtgagagtcatgtgtgtggca	14	7	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:21215496G>A	ENST00000574002.1	-	10	1309	c.827C>T	c.(826-828)aCc>aTc	p.T276I	ZP2_ENST00000574091.1_Missense_Mutation_p.T276I|ZP2_ENST00000219593.4_Missense_Mutation_p.T276I|AF001550.7_ENST00000572747.1_RNA			Q05996	ZP2_HUMAN	zona pellucida glycoprotein 2 (sperm receptor)	276					binding of sperm to zona pellucida (GO:0007339)|intracellular protein transport (GO:0006886)|multicellular organism reproduction (GO:0032504)|prevention of polyspermy (GO:0060468)|signal transduction (GO:0007165)|single fertilization (GO:0007338)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|coreceptor activity (GO:0015026)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(16)|ovary(1)|prostate(1)|stomach(1)	41				GBM - Glioblastoma multiforme(48;0.0573)		CTCTGGTATGGTGAGAGTCAT	0.448																																					p.T276I		Atlas-SNP	.											.	ZP2	92	.	0			c.C827T						.						102	91	95					16																	21215496		2200	4300	6500	SO:0001583	missense	7783	exon9			GGTATGGTGAGAG	M90366	CCDS10596.1, CCDS73843.1	16p12	2014-07-04			ENSG00000103310	ENSG00000103310		"Zona pellucida glycoproteins"	13188	protein-coding gene	gene with protein product		182888				8385033	Standard	XM_005255562		Approved	ZPA	uc002dii.2	Q05996	OTTHUMG00000090681	ENST00000574002.1:c.827C>T	chr16.hg19:g.21215496G>A	ENSP00000460971:p.Thr276Ile	78.0	0.0		42.0	18.0	NM_003460	B2R7J2|Q4VAN9|Q4VAP0|Q4VAP1	Missense_Mutation	SNP	ENST00000574002.1	hg19	CCDS10596.1	.	.	.	.	.	.	.	.	.	.	G	12.78	2.041156	0.35989	.	.	ENSG00000103310	ENST00000219593	T	0.48836	0.8	6.08	2.55	0.30701	.	0.577135	0.18492	N	0.139620	T	0.54224	0.1845	L	0.54908	1.71	0.24118	N	0.995814	D;B;B	0.89917	1.0;0.059;0.027	D;B;B	0.68943	0.961;0.024;0.018	T	0.36601	-0.9741	10	0.28530	T	0.3	-2.4717	4.9809	0.14164	0.1301:0.1293:0.608:0.1326	.	276;276;276	B4DEV1;Q4VAP1;Q05996	.;.;ZP2_HUMAN	I	276	ENSP00000219593:T276I	ENSP00000219593:T276I	T	-	2	0	ZP2	21122997	0.969000	0.33509	0.958000	0.39756	0.993000	0.82548	1.670000	0.37502	0.862000	0.35528	0.655000	0.94253	ACC	.	.		0.448	ZP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207365.2			A	21215496	G	A	21215496	3	1	344	1	0	0	0	0	1	0	0	0	18231	1261	44	3	1454	3	ZP2	16	21215496	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	78996	21215496	69139257	1096	48459										
POLR3E	55718	hgsc.bcm.edu	37	chr16	22316495	22316495	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agatcgatgtgtacttggccAagagtctggcggaaaagctg	14	7	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:22316495A>G	ENST00000299853.5	+	3	222	c.55A>G	c.(55-57)Aag>Gag	p.K19E	POLR3E_ENST00000564256.1_3'UTR|POLR3E_ENST00000359210.4_Missense_Mutation_p.K19E|POLR3E_ENST00000564209.1_Missense_Mutation_p.K19E|POLR3E_ENST00000418581.2_Intron	NM_001258033.1|NM_001258035.1|NM_018119.3	NP_001244962.1|NP_001244964.1|NP_060589.1	Q9NVU0	RPC5_HUMAN	polymerase (RNA) III (DNA directed) polypeptide E (80kD)	19					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	centrosome (GO:0005813)|cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA-directed RNA polymerase activity (GO:0003899)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27				GBM - Glioblastoma multiforme(48;0.012)		GTACTTGGCCAAGAGTCTGGC	0.532																																					p.K19E		Atlas-SNP	.											.	POLR3E	62	.	0			c.A55G						.						191	178	182					16																	22316495		2197	4300	6497	SO:0001583	missense	55718	exon3			TTGGCCAAGAGTC	AY092085	CCDS10605.1, CCDS58432.1, CCDS58433.1, CCDS58434.1, CCDS73845.1	16p12	2013-01-21			ENSG00000058600	ENSG00000058600		"RNA polymerase subunits"	30347	protein-coding gene	gene with protein product						10819331, 10521666	Standard	NM_018119		Approved	RPC5, SIN, FLJ10509	uc002dkk.4	Q9NVU0	OTTHUMG00000094779	ENST00000299853.5:c.55A>G	chr16.hg19:g.22316495A>G	ENSP00000299853:p.Lys19Glu	76.0	0.0		71.0	29.0	NM_001258033	B4DL24|B4DUP6|H3BT11|Q9BWF7|Q9H8W8|Q9H907|Q9P276	Missense_Mutation	SNP	ENST00000299853.5	hg19	CCDS10605.1	.	.	.	.	.	.	.	.	.	.	A	31	5.099329	0.94197	.	.	ENSG00000058600	ENST00000299853;ENST00000359210	T;T	0.46819	0.86;0.86	5.51	5.51	0.81932	.	0.097108	0.64402	D	0.000001	T	0.66287	0.2774	M	0.79011	2.435	0.58432	D	0.999995	D;D;D;D	0.63046	0.992;0.99;0.992;0.99	P;P;P;P	0.60415	0.874;0.731;0.825;0.801	T	0.71586	-0.4548	10	0.87932	D	0	-12.7431	14.614	0.68534	1.0:0.0:0.0:0.0	.	19;19;19;19	B4DUP6;Q9NVU0-2;Q9NVU0;Q9NVU0-3	.;.;RPC5_HUMAN;.	E	19	ENSP00000299853:K19E;ENSP00000352140:K19E	ENSP00000299853:K19E	K	+	1	0	POLR3E	22223996	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.271000	0.78506	2.094000	0.63399	0.459000	0.35465	AAG	.	.		0.532	POLR3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211590.1	NM_018119		G	22316495	A	G	22316495	3	3	344	1	0	0	0	0	1	0	0	0	12241	131	5	2	61	2	POLR3E	16	22316495	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1100999	22316495	68038258	1097	48460										
USP31	57478	hgsc.bcm.edu	37	chr16	23080584	23080584	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtccgattcgtctttgaacaCgccttccatgacagccagag	9	13	1	3	rs34435034		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:23080584C>A	ENST00000219689.7	-	16	2841	c.2842G>T	c.(2842-2844)Gtg>Ttg	p.V948L	USP31_ENST00000567975.1_Missense_Mutation_p.V241L	NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	0	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	57				GBM - Glioblastoma multiforme(48;0.0187)		TCTTTGAACACGCCTTCCATG	0.577																																					p.V948L		Atlas-SNP	.											.	USP31	122	.	0			c.G2842T						.						86	88	87					16																	23080584		2197	4300	6497	SO:0001583	missense	57478	exon16			TGAACACGCCTTC	AB033029	CCDS10607.1	16p12.3	2008-02-05	2005-08-08		ENSG00000103404	ENSG00000103404		"Ubiquitin-specific peptidases"	20060	protein-coding gene	gene with protein product			"ubiquitin specific protease 31"			12838346	Standard	NM_020718		Approved	KIAA1203	uc002dll.3	Q70CQ4	OTTHUMG00000094793	ENST00000219689.7:c.2842G>T	chr16.hg19:g.23080584C>A	ENSP00000219689:p.Val948Leu	79.0	0.0		52.0	23.0	NM_020718	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Missense_Mutation	SNP	ENST00000219689.7	hg19	CCDS10607.1	.	.	.	.	.	.	.	.	.	.	C	13.59	2.282242	0.40394	.	.	ENSG00000103404	ENST00000219689;ENST00000381162	T	0.08193	3.12	6.06	4.13	0.48395	.	1.277350	0.05869	N	0.624252	T	0.07728	0.0194	N	0.22421	0.69	0.29065	N	0.88364	B;B;B	0.25441	0.102;0.061;0.126	B;B;B	0.28011	0.085;0.01;0.044	T	0.38802	-0.9644	10	0.09590	T	0.72	-11.5201	11.8951	0.52652	0.0:0.8609:0.0:0.1391	.	251;948;241	Q70CQ4-2;Q70CQ4;B3KS48	.;UBP31_HUMAN;.	L	948;251	ENSP00000219689:V948L	ENSP00000219689:V948L	V	-	1	0	USP31	22988085	0.669000	0.27502	0.996000	0.52242	0.978000	0.69477	1.460000	0.35244	0.903000	0.36546	0.650000	0.86243	GTG	.	C|0.999;T|0.001		0.577	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718		A	23080584	C	A	23080584	3	1	344	1	0	0	0	0	1	0	0	0	17077	536	19	1	1220	1	USP31	16	23080584	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	764089	23080584	67274169	1098	48461										
CACNG3	10368	hgsc.bcm.edu	37	chr16	24373102	24373102	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cgaccgggaccacgcttttcTacagttccacaattccacac	6	16	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:24373102T>A	ENST00000005284.3	+	4	2068	c.866T>A	c.(865-867)cTa>cAa	p.L289Q		NM_006539.3	NP_006530.1	O60359	CCG3_HUMAN	calcium channel, voltage-dependent, gamma subunit 3	289					calcium ion transport (GO:0006816)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|prostate(4)|skin(2)	40				GBM - Glioblastoma multiforme(48;0.0809)		CACGCTTTTCTACAGTTCCAC	0.552																																					p.L289Q		Atlas-SNP	.											.	CACNG3	112	.	0			c.T866A						.						83	89	87					16																	24373102		2197	4300	6497	SO:0001583	missense	10368	exon4			CTTTTCTACAGTT	AF131911	CCDS10620.1	16p12.1	2008-05-14			ENSG00000006116	ENSG00000006116		"Calcium channel subunits"	1407	protein-coding gene	gene with protein product		606403				10221464, 10493829	Standard	NM_006539		Approved		uc002dmf.3	O60359	OTTHUMG00000131651	ENST00000005284.3:c.866T>A	chr16.hg19:g.24373102T>A	ENSP00000005284:p.Leu289Gln	96.0	0.0		94.0	40.0	NM_006539		Missense_Mutation	SNP	ENST00000005284.3	hg19	CCDS10620.1	.	.	.	.	.	.	.	.	.	.	t	19.26	3.792955	0.70452	.	.	ENSG00000006116	ENST00000005284	T	0.61040	0.14	4.93	4.93	0.64822	.	0.159575	0.42682	D	0.000672	T	0.73567	0.3603	M	0.73962	2.25	0.49213	D	0.999768	D	0.67145	0.996	D	0.64595	0.927	T	0.77902	-0.2414	10	0.87932	D	0	-2.8647	14.3047	0.66377	0.0:0.0:0.0:1.0	.	289	O60359	CCG3_HUMAN	Q	289	ENSP00000005284:L289Q	ENSP00000005284:L289Q	L	+	2	0	CACNG3	24280603	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.695000	0.84257	1.839000	0.53478	0.524000	0.50904	CTA	.	.		0.552	CACNG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254548.1	NM_006539		A	24373102	T	A	24373102	3	1	344	1	0	0	0	0	1	0	0	0	2560	1522	53	4	880	4	CACNG3	16	24373102	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1292518	24373102	65981651	1099	48462										
HS3ST4	9951	hgsc.bcm.edu	37	chr16	26147136	26147136	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cgagatccccacctttgaggTgctggccttcaaaaaccgga	10	13	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:26147136T>G	ENST00000331351.5	+	2	1330	c.938T>G	c.(937-939)gTg>gGg	p.V313G	HS3ST4_ENST00000475436.1_3'UTR	NM_006040.2	NP_006031.2	Q9Y661	HS3S4_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	313					heparan sulfate proteoglycan metabolic process (GO:0030201)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)			breast(2)|endometrium(3)|large_intestine(1)|lung(9)	15				GBM - Glioblastoma multiforme(48;0.0988)		ACCTTTGAGGTGCTGGCCTTC	0.532																																					p.V313G		Atlas-SNP	.											.	HS3ST4	120	.	0			c.T938G						.						167	159	161					16																	26147136		1568	3582	5150	SO:0001583	missense	9951	exon2			TTGAGGTGCTGGC	AF105378	CCDS53995.1	16p11.2	2008-03-12			ENSG00000182601	ENSG00000182601	2.8.2.23	"Sulfotransferases, membrane-bound"	5200	protein-coding gene	gene with protein product		604059				9988767	Standard	NM_006040		Approved	3OST4	uc002dof.3	Q9Y661	OTTHUMG00000059978	ENST00000331351.5:c.938T>G	chr16.hg19:g.26147136T>G	ENSP00000330606:p.Val313Gly	97.0	0.0		110.0	43.0	NM_006040	Q5QI42|Q8NDC2	Missense_Mutation	SNP	ENST00000331351.5	hg19	CCDS53995.1	.	.	.	.	.	.	.	.	.	.	T	12.35	1.910367	0.33721	.	.	ENSG00000182601	ENST00000331351	T	0.52983	0.64	5.35	5.35	0.76521	Sulfotransferase domain (1);	0.000000	0.64402	U	0.000013	T	0.26810	0.0656	N	0.04508	-0.205	0.80722	D	1	B	0.13145	0.007	B	0.15870	0.014	T	0.09378	-1.0677	10	0.22706	T	0.39	.	14.5047	0.67746	0.0:0.0:0.0:1.0	.	313	Q9Y661	HS3S4_HUMAN	G	313	ENSP00000330606:V313G	ENSP00000330606:V313G	V	+	2	0	HS3ST4	26054637	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.036000	0.64164	2.015000	0.59207	0.533000	0.62120	GTG	.	.		0.532	HS3ST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133286.2	NM_006040		G	26147136	T	G	26147136	3	3	344	1	0	0	0	0	1	0	0	0	7376	1696	59	5	944	5	HS3ST4	16	26147136	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1774034	26147136	64207617	1100	48463										
IL4R	3566	hgsc.bcm.edu	37	chr16	27374493	27374493	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggctggttacaaggccttctCaagcctgcttgccagcagtg	12	12	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:27374493C>G	ENST00000395762.2	+	11	2079	c.1820C>G	c.(1819-1821)tCa>tGa	p.S607*	IL4R_ENST00000380922.3_Nonsense_Mutation_p.S592*|IL4R_ENST00000170630.2_Nonsense_Mutation_p.S607*|IL4R_ENST00000543915.2_Nonsense_Mutation_p.S607*	NM_000418.3	NP_000409.1	P24394	IL4RA_HUMAN	interleukin 4 receptor	607	Required for IL4-induced gene expression.				defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|ovulation (GO:0030728)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|production of molecular mediator involved in inflammatory response (GO:0002532)|regulation of cell proliferation (GO:0042127)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	interleukin-4 receptor activity (GO:0004913)|receptor signaling protein activity (GO:0005057)	p.S607*(1)		breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	33						AAGGCCTTCTCAAGCCTGCTT	0.597																																					p.S607X		Atlas-SNP	.											IL4R,NS,carcinoma,0,1	IL4R	70	.	1	Substitution - Nonsense(1)	lung(1)	c.C1820G						.						36	39	38					16																	27374493		2196	4300	6496	SO:0001587	stop_gained	3566	exon11			CCTTCTCAAGCCT	X52425	CCDS10629.1, CCDS58441.1	16p12.1-p11.2	2008-05-14			ENSG00000077238	ENSG00000077238		"Interleukins and interleukin receptors", "CD molecules"	6015	protein-coding gene	gene with protein product		147781				1679753	Standard	NM_000418		Approved	CD124	uc010bxy.4	P24394	OTTHUMG00000097015	ENST00000395762.2:c.1820C>G	chr16.hg19:g.27374493C>G	ENSP00000379111:p.Ser607*	34.0	0.0		40.0	20.0	NM_000418	B4E076|B9EKU8|H3BSY5|Q96P01|Q9H181|Q9H182|Q9H183|Q9H184|Q9H185|Q9H186|Q9H187|Q9H188	Nonsense_Mutation	SNP	ENST00000395762.2	hg19	CCDS10629.1	.	.	.	.	.	.	.	.	.	.	C	38	6.908099	0.97928	.	.	ENSG00000077238	ENST00000395762;ENST00000543915;ENST00000380922;ENST00000170630	.	.	.	5.09	4.13	0.48395	.	2.792480	0.00951	N	0.002962	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-17.9719	11.6839	0.51474	0.0:0.8212:0.1788:0.0	.	.	.	.	X	607;607;592;607	.	ENSP00000170630:S607X	S	+	2	0	IL4R	27281994	0.341000	0.24801	0.841000	0.33234	0.192000	0.23643	0.933000	0.28897	1.139000	0.42245	0.555000	0.69702	TCA	.	.		0.597	IL4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214104.4			G	27374493	C	G	27374493	4	3	344	1	0	0	0	0	0	1	0	0	7707	838	29	4	1872	4	IL4R	16	27374493	Nonsense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1227357	27374493	62980260	1101	48464										
IL21R	50615	hgsc.bcm.edu	37	chr16	27448852	27448852	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aggacgaggccacctcctgcAgcctccacaggtcggcccac	11	18	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:27448852A>T	ENST00000337929.3	+	4	669	c.196A>T	c.(196-198)Agc>Tgc	p.S66C	IL21R_ENST00000395755.1_Missense_Mutation_p.S66C|IL21R_ENST00000564089.1_Missense_Mutation_p.S66C|IL21R_ENST00000395754.4_Missense_Mutation_p.S66C	NM_181078.2	NP_851564.1	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor	66	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				interleukin-21-mediated signaling pathway (GO:0038114)|natural killer cell activation (GO:0030101)	integral component of membrane (GO:0016021)	interleukin-21 receptor activity (GO:0001532)			breast(2)|large_intestine(3)|lung(1)|ovary(2)	8						CACCTCCTGCAGCCTCCACAG	0.577			T	BCL6	NHL																																p.S88C		Atlas-SNP	.		Dom	yes		16	16p11	50615	interleukin 21 receptor		L	.	IL21R	95	.	0			c.A262T						.						118	92	101					16																	27448852		2197	4300	6497	SO:0001583	missense	50615	exon5			TCCTGCAGCCTCC	AF254067	CCDS10630.1	16p11	2014-09-17			ENSG00000103522	ENSG00000103522		"Interleukins and interleukin receptors", "CD molecules"	6006	protein-coding gene	gene with protein product		605383				11081504	Standard	NM_181078		Approved	CD360	uc002dos.2	Q9HBE5	OTTHUMG00000131675	ENST00000337929.3:c.196A>T	chr16.hg19:g.27448852A>T	ENSP00000338010:p.Ser66Cys	72.0	0.0		65.0	31.0	NM_181079	A8K9E8|D3DWF7|Q96HZ1|Q9HB91	Missense_Mutation	SNP	ENST00000337929.3	hg19	CCDS10630.1	.	.	.	.	.	.	.	.	.	.	A	12.71	2.020343	0.35606	.	.	ENSG00000103522	ENST00000337929;ENST00000395755;ENST00000395754	D;D;D	0.96619	-4.07;-4.07;-4.07	4.65	2.15	0.27550	Fibronectin, type III (1);	0.260360	0.39274	N	0.001420	D	0.96744	0.8937	M	0.69823	2.125	0.39204	D	0.963209	D	0.76494	0.999	D	0.72338	0.977	D	0.95199	0.8315	10	0.59425	D	0.04	-24.1159	4.8747	0.13650	0.6165:0.1954:0.0:0.188	.	66	Q9HBE5	IL21R_HUMAN	C	66	ENSP00000338010:S66C;ENSP00000379104:S66C;ENSP00000379103:S66C	ENSP00000338010:S66C	S	+	1	0	IL21R	27356353	1.000000	0.71417	0.999000	0.59377	0.032000	0.12392	1.284000	0.33249	0.704000	0.31869	-0.341000	0.08007	AGC	.	.		0.577	IL21R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254578.2	NM_181078		T	27448852	A	T	27448852	3	4	344	1	0	0	0	0	1	0	0	0	7680	188	7	4	206	4	IL21R	16	27448852	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	74359	27448852	62905901	1102	48465										
GTF3C1	2975	hgsc.bcm.edu	37	chr16	27509073	27509073	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgagagtcccctgatccactTgggccctcttttccttgact	8	14	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:27509073T>C	ENST00000356183.4	-	14	2250	c.2235A>G	c.(2233-2235)ccA>ccG	p.P745P	GTF3C1_ENST00000561623.1_Silent_p.P745P	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	745					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						CTGATCCACTTGGGCCCTCTT	0.458																																					p.P745P		Atlas-SNP	.											.	GTF3C1	210	.	0			c.A2235G						.						136	125	129					16																	27509073		2197	4300	6497	SO:0001819	synonymous_variant	2975	exon14			TCCACTTGGGCCC	U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"General transcription factors"	4664	protein-coding gene	gene with protein product		603246	"general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.2235A>G	chr16.hg19:g.27509073T>C		125.0	0.0		116.0	53.0	NM_001520	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Silent	SNP	ENST00000356183.4	hg19	CCDS32414.1																																																																																			.	.		0.458	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520		C	27509073	T	C	27509073	2	2	344	1	0	0	0	0	0	0	0	1	6881	1799	63	2		2	GTF3C1	16	27509073	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	60221	27509073	62845680	1103	48466										
KIAA0556	23247	hgsc.bcm.edu	37	chr16	27760972	27760972	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gagcaggagcacacacttcaCgagtcatggagctccctcag	11	13	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:27760972C>G	ENST00000261588.4	+	16	2710	c.2691C>G	c.(2689-2691)caC>caG	p.H897Q		NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	897						extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						ACACACTTCACGAGTCATGGA	0.617																																					p.H897Q		Atlas-SNP	.											KIAA0556_ENST00000261588,colon,carcinoma,0,2	KIAA0556	348	.	0			c.C2691G						.						91	86	88					16																	27760972		2197	4300	6497	SO:0001583	missense	23247	exon16			ACTTCACGAGTCA	AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.2691C>G	chr16.hg19:g.27760972C>G	ENSP00000261588:p.His897Gln	143.0	1.0		108.0	54.0	NM_015202	A7E2C2	Missense_Mutation	SNP	ENST00000261588.4	hg19	CCDS32415.1	.	.	.	.	.	.	.	.	.	.	C	12.63	1.995013	0.35226	.	.	ENSG00000047578	ENST00000261588	T	0.08458	3.09	4.7	-9.19	0.00685	.	0.302883	0.33572	N	0.004766	T	0.04407	0.0121	L	0.42245	1.32	0.32250	N	0.571539	B	0.15930	0.015	B	0.14023	0.01	T	0.49835	-0.8897	10	0.06625	T	0.88	-10.1703	10.6601	0.45698	0.0:0.1709:0.1767:0.6524	.	897	O60303	K0556_HUMAN	Q	897	ENSP00000261588:H897Q	ENSP00000261588:H897Q	H	+	3	2	KIAA0556	27668473	0.001000	0.12720	0.050000	0.19076	0.958000	0.62258	-2.635000	0.00868	-1.401000	0.02058	0.655000	0.94253	CAC	.	.		0.617	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202		G	27760972	C	G	27760972	3	3	344	1	0	0	0	0	1	0	0	0	8192	535	19	4	2753	4	KIAA0556	16	27760972	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	251899	27760972	62593781	1104	48467										
C16orf54	283897	hgsc.bcm.edu	37	chr16	29755668	29755668	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gctccaaggtgacccgtggcTggaggccccactcaggatcc	13	15	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:29755668T>A	ENST00000329410.3	-	2	700	c.605A>T	c.(604-606)cAg>cTg	p.Q202L	AC009133.17_ENST00000565600.1_RNA	NM_175900.3	NP_787096.2	Q6UWD8	CP054_HUMAN	chromosome 16 open reading frame 54	202						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|lung(2)|prostate(1)|urinary_tract(1)	6						GACCCGTGGCTGGAGGCCCCA	0.667																																					p.Q202L		Atlas-SNP	.											.	C16orf54	18	.	0			c.A605T						.						13	15	14					16																	29755668		2082	4148	6230	SO:0001583	missense	283897	exon2			CGTGGCTGGAGGC	AK093000	CCDS10652.1	16p11.2	2012-10-10		2005-08-09	ENSG00000185905	ENSG00000185905			26649	protein-coding gene	gene with protein product						12975309	Standard	NM_175900		Approved	FLJ35681	uc002dtp.2	Q6UWD8	OTTHUMG00000132116	ENST00000329410.3:c.605A>T	chr16.hg19:g.29755668T>A	ENSP00000327506:p.Gln202Leu	93.0	0.0		99.0	52.0	NM_175900	A6NJR6|Q8NAB0	Missense_Mutation	SNP	ENST00000329410.3	hg19	CCDS10652.1	.	.	.	.	.	.	.	.	.	.	T	17.75	3.466213	0.63625	.	.	ENSG00000185905	ENST00000329410	T	0.65732	-0.17	5.22	5.22	0.72569	.	0.000000	0.39544	U	0.001323	T	0.68016	0.2955	L	0.29908	0.895	0.40662	D	0.98213	D	0.76494	0.999	D	0.83275	0.996	T	0.72384	-0.4310	10	0.87932	D	0	-13.6752	11.4916	0.50383	0.0:0.0:0.0:1.0	.	202	Q6UWD8	CP054_HUMAN	L	202	ENSP00000327506:Q202L	ENSP00000327506:Q202L	Q	-	2	0	C16orf54	29663169	1.000000	0.71417	1.000000	0.80357	0.314000	0.28054	2.252000	0.43196	1.971000	0.57363	0.260000	0.18958	CAG	.	.		0.667	C16orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255158.1	NM_175900		A	29755668	T	A	29755668	3	1	344	1	0	0	0	0	1	0	0	0	1821	1580	55	4	73	4	C16orf54	16	29755668	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1994696	29755668	60599085	1105	48468										
SEZ6L2	26470	hgsc.bcm.edu	37	chr16	29906726	29906726	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggggggccaggcctggggatCccccaccagccagcaccagg	16	16	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:29906726C>A	ENST00000308713.5	-	5	1234	c.707G>T	c.(706-708)gGa>gTa	p.G236V	SEZ6L2_ENST00000537485.1_Missense_Mutation_p.G192V|SEZ6L2_ENST00000350527.3_Missense_Mutation_p.G166V|SEZ6L2_ENST00000346932.5_Intron|SEZ6L2_ENST00000562159.1_5'UTR	NM_001114099.2|NM_201575.3	NP_001107571.1|NP_963869.2	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2	236	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)		p.G236A(1)|p.G166A(1)		breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GCCTGGGGATCCCCCACCAGC	0.627																																					p.G236V		Atlas-SNP	.											SEZ6L2_ENST00000350527,NS,carcinoma,0,2	SEZ6L2	137	.	2	Substitution - Missense(2)	lung(2)	c.G707T						.						41	50	47					16																	29906726		2197	4300	6497	SO:0001583	missense	26470	exon5			GGGGATCCCCCAC	AY358404	CCDS10658.1, CCDS10659.1, CCDS45458.1, CCDS58447.1, CCDS73865.1	16p12.1	2008-02-05			ENSG00000174938	ENSG00000174938			30844	protein-coding gene	gene with protein product	"type I transmembrane receptor (seizure related protein)"					12975309	Standard	NM_012410		Approved	PSK-1, FLJ90517	uc010vec.2	Q6UXD5	OTTHUMG00000132112	ENST00000308713.5:c.707G>T	chr16.hg19:g.29906726C>A	ENSP00000312550:p.Gly236Val	80.0	0.0		74.0	34.0	NM_001243332	B7Z1N0|F5H293|H7BXQ6|Q9BW82|Q9UJ45|Q9UJ46|Q9UJ47	Missense_Mutation	SNP	ENST00000308713.5	hg19	CCDS10659.1	.	.	.	.	.	.	.	.	.	.	c	16.73	3.205329	0.58234	.	.	ENSG00000174938	ENST00000350527;ENST00000308713;ENST00000537485	T;T;T	0.43294	0.95;0.95;0.95	5.22	5.22	0.72569	CUB (5);	0.000000	0.48767	D	0.000179	T	0.59376	0.2189	M	0.62723	1.935	0.80722	D	1	D;D;D;D;D	0.89917	0.995;0.992;1.0;1.0;0.99	D;D;D;D;P	0.77557	0.953;0.94;0.99;0.99;0.901	T	0.60037	-0.7341	10	0.52906	T	0.07	.	11.7866	0.52045	0.0:0.9146:0.0:0.0854	.	192;236;166;236;166	F5H293;B7Z5L4;Q6UXD5-2;Q6UXD5;Q6UXD5-3	.;.;.;SE6L2_HUMAN;.	V	166;236;192	ENSP00000310206:G166V;ENSP00000312550:G236V;ENSP00000439412:G192V	ENSP00000312550:G236V	G	-	2	0	SEZ6L2	29814227	0.925000	0.31364	0.954000	0.39281	0.377000	0.30045	3.354000	0.52254	2.434000	0.82447	0.586000	0.80456	GGA	.	.		0.627	SEZ6L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255154.2	NM_012410		A	29906726	C	A	29906726	3	1	344	1	0	0	0	0	1	0	0	0	14159	855	30	3	2120	3	SEZ6L2	16	29906726	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	151058	29906726	60448027	1106	48469										
FBRS	64319	hgsc.bcm.edu	37	chr16	30680873	30680873	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cttctcagcaagaccccaccGggagcccttttgggggcacc	11	16	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:30680873G>C	ENST00000287468.5	+	12	1553	c.1290G>C	c.(1288-1290)ccG>ccC	p.P430P	FBRS_ENST00000356166.6_Silent_p.P950P|FBRS_ENST00000568722.1_Silent_p.P342P|FBRS_ENST00000395073.2_Intron	NM_001105079.1	NP_001098549.1	Q9HAH7	FBRS_HUMAN	fibrosin	430								p.P430P(1)|p.?(1)		ovary(1)	1			Colorectal(24;0.103)			AGACCCCACCGGGAGCCCTTT	0.697																																					p.P430P		Atlas-SNP	.											.	FBRS	39	.	2	Unknown(1)|Substitution - coding silent(1)	lung(2)	c.G1290C						.						65	79	75					16																	30680873		1970	4149	6119	SO:0001819	synonymous_variant	64319	exon12			CCCACCGGGAGCC	AK021680		16p11.2	2008-02-05	2007-04-18	2007-04-18	ENSG00000156860	ENSG00000156860			20442	protein-coding gene	gene with protein product		608601	"fibrosin 1"	FBS1		7892239, 9809749	Standard	NM_001105079		Approved	FBS, FLJ11618	uc002dzd.4	Q9HAH7	OTTHUMG00000132390	ENST00000287468.5:c.1290G>C	chr16.hg19:g.30680873G>C		64.0	0.0		72.0	32.0	NM_001105079	B4DP86|Q96CI9|Q9H9X4	Silent	SNP	ENST00000287468.5	hg19																																																																																				.	.		0.697	FBRS-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_022452		C	30680873	G	C	30680873	2	2	344	1	0	0	0	0	0	0	0	1	5715	1103	39	4		4	FBRS	16	30680873	Silent	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	774147	30680873	59673880	1107	48470										
PHKG2	5261	hgsc.bcm.edu	37	chr16	30764551	30764551	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cctatgcccctccttcccttAggatgcggaagggagagctg	12	13	0	1	rs34885557		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:30764551A>T	ENST00000563588.1	+	5	565		c.e5-1		RP11-2C24.4_ENST00000483578.1_lincRNA|PHKG2_ENST00000328273.7_Splice_Site|PHKG2_ENST00000424889.3_Splice_Site	NM_000294.2	NP_000285.1	P15735	PHKG2_HUMAN	phosphorylase kinase, gamma 2 (testis)						carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|positive regulation of glycogen catabolic process (GO:0045819)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)	ATP binding (GO:0005524)|phosphorylase kinase activity (GO:0004689)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			ovary(1)|skin(1)	2			Colorectal(24;0.198)			TCCTTCCCTTAGGATGCGGAA	0.532																																					.		Atlas-SNP	.											.	PHKG2	29	.	0			c.327-2A>T						.						41	40	40					16																	30764551		2197	4300	6497	SO:0001630	splice_region_variant	5261	exon5			TCCCTTAGGATGC	S73483, M31606	CCDS10690.1, CCDS54002.1	16p11.2	2008-02-05			ENSG00000156873	ENSG00000156873			8931	protein-coding gene	gene with protein product		172471				2915644, 8020963	Standard	NM_000294		Approved		uc021tgo.1	P15735	OTTHUMG00000132400	ENST00000563588.1:c.327-1A>T	chr16.hg19:g.30764551A>T		57.0	0.0		42.0	20.0	NM_001172432	A8K0C7|B4DEB7|E9PEU3|P11800	Splice_Site	SNP	ENST00000563588.1	hg19	CCDS10690.1	.	.	.	.	.	.	.	.	.	.	A	19.49	3.836871	0.71373	.	.	ENSG00000156873	ENST00000328273;ENST00000424889	.	.	.	5.47	5.47	0.80525	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5455	0.68027	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PHKG2	30672052	1.000000	0.71417	0.998000	0.56505	0.971000	0.66376	9.339000	0.96797	2.065000	0.61736	0.533000	0.62120	.	.	.		0.532	PHKG2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255531.2	NM_000294	Intron	T	30764551	A	T	30764551	5	4	344	1	0	0	0	0	0	0	1	0	11856	434	15	4	339	4	PHKG2	16	30764551	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	83678	30764551	59590202	1108	48471										
ORAI3	93129	hgsc.bcm.edu	37	chr16	30965031	30965031	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccatggcctccacagccatcAtggtacccgtggggctcgtg	12	15	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:30965031A>G	ENST00000318663.4	+	2	978	c.754A>G	c.(754-756)Atg>Gtg	p.M252V	ORAI3_ENST00000566237.1_Missense_Mutation_p.M252V|AC135048.13_ENST00000566056.1_RNA|ORAI3_ENST00000562699.1_Intron	NM_152288.2	NP_689501.1	Q9BRQ5	ORAI3_HUMAN	ORAI calcium release-activated calcium modulator 3	252					store-operated calcium entry (GO:0002115)	integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)	6						CACAGCCATCATGGTACCCGT	0.627											OREG0023742	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.M252V		Atlas-SNP	.											.	ORAI3	19	.	0			c.A754G						.						55	62	59					16																	30965031		2197	4300	6497	SO:0001583	missense	93129	exon2			GCCATCATGGTAC	BC006126	CCDS10697.1	16p11.2	2007-08-14	2007-08-14	2007-08-14	ENSG00000175938	ENSG00000175938		"ORAI calcium release-activated calcium modulators"	28185	protein-coding gene	gene with protein product		610930	"transmembrane protein 142C"	TMEM142C		16582901	Standard	NM_152288		Approved	MGC13024	uc002eac.3	Q9BRQ5	OTTHUMG00000132409	ENST00000318663.4:c.754A>G	chr16.hg19:g.30965031A>G	ENSP00000322249:p.Met252Val	57.0	0.0	821	47.0	25.0	NM_152288	Q96BI8	Missense_Mutation	SNP	ENST00000318663.4	hg19	CCDS10697.1	.	.	.	.	.	.	.	.	.	.	a	23.5	4.422990	0.83559	.	.	ENSG00000175938	ENST00000318663	T	0.42513	0.97	5.64	5.64	0.86602	.	0.085873	0.51477	D	0.000097	T	0.51160	0.1658	N	0.26042	0.785	0.80722	D	1	D	0.59357	0.985	D	0.72338	0.977	T	0.50491	-0.8822	10	0.42905	T	0.14	-20.3393	14.8628	0.70394	1.0:0.0:0.0:0.0	.	252	Q9BRQ5	ORAI3_HUMAN	V	252	ENSP00000322249:M252V	ENSP00000322249:M252V	M	+	1	0	ORAI3	30872532	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.962000	0.93254	2.158000	0.67659	0.524000	0.50904	ATG	.	.		0.627	ORAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255545.20	NM_152288		G	30965031	A	G	30965031	3	3	344	1	0	0	0	0	1	0	0	0	11268	217	8	2	760	2	ORAI3	16	30965031	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	200480	30965031	59389722	1109	48472										
PYDC1	260434	hgsc.bcm.edu	37	chr16	31228226	31228226	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atctagctgcccgagcgcgcCccgcgggatgcgctcaaagc	13	16	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:31228226C>A	ENST00000302964.3	-	1	454	c.124G>T	c.(124-126)Ggc>Tgc	p.G42C	PYDC1_ENST00000568383.1_5'Flank|TRIM72_ENST00000322122.3_Intron	NM_152901.2	NP_690865.1	Q8WXC3	PYDC1_HUMAN	PYD (pyrin domain) containing 1	42	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.				innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of interleukin-1 beta secretion (GO:0050718)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(2)|lung(1)	5						CCGAGCGCGCCCCGCGGGATG	0.647																																					p.G42C		Atlas-SNP	.											.	PYDC1	7	.	0			c.G124T						.						63	58	60					16																	31228226		2197	4299	6496	SO:0001583	missense	260434	exon1			GCGCGCCCCGCGG		CCDS10710.1	16p11.2	2008-02-05	2005-12-02		ENSG00000169900	ENSG00000169900			30261	protein-coding gene	gene with protein product		615700	"pyrin domain containing 1"			11786556, 16905547	Standard	NM_152901		Approved	ASC2, POP1	uc002ebo.3	Q8WXC3	OTTHUMG00000132407	ENST00000302964.3:c.124G>T	chr16.hg19:g.31228226C>A	ENSP00000304336:p.Gly42Cys	97.0	0.0		86.0	44.0	NM_152901	B2R8L4|Q8NFP8	Missense_Mutation	SNP	ENST00000302964.3	hg19	CCDS10710.1	.	.	.	.	.	.	.	.	.	.	C	16.27	3.077048	0.55753	.	.	ENSG00000169900	ENST00000302964	T	0.50277	0.75	3.84	2.88	0.33553	Pyrin (2);DEATH-like (2);	0.000000	0.40728	U	0.001021	T	0.61949	0.2388	.	.	.	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.50591	-0.8810	9	0.56958	D	0.05	.	7.0736	0.25191	0.0:0.873:0.0:0.127	.	42	Q8WXC3	PYDC1_HUMAN	C	42	ENSP00000304336:G42C	ENSP00000304336:G42C	G	-	1	0	PYDC1	31135727	0.171000	0.23029	0.001000	0.08648	0.033000	0.12548	3.870000	0.56070	0.809000	0.34255	0.561000	0.74099	GGC	.	.		0.647	PYDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255543.2	NM_152901		A	31228226	C	A	31228226	3	1	344	1	0	0	0	0	1	0	0	0	12873	623	22	3	149	3	PYDC1	16	31228226	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	263195	31228226	59126527	1110	48473										
ITGAD	3681	hgsc.bcm.edu	37	chr16	31419776	31419776	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cagggcaagcagctccttccAgcacgagatgtcccaagaag	11	13	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:31419776A>T	ENST00000389202.2	+	10	1089	c.1040A>T	c.(1039-1041)cAg>cTg	p.Q347L		NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	347					activated T cell proliferation (GO:0050798)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)	cell surface (GO:0009986)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(43)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						AGCTCCTTCCAGCACGAGATG	0.557																																					p.Q347L		Atlas-SNP	.											.	ITGAD	154	.	0			c.A1040T						.						81	72	75					16																	31419776		2197	4300	6497	SO:0001583	missense	3681	exon10			CCTTCCAGCACGA	U40274	CCDS32438.1	16p13.1-p11	2010-03-23				ENSG00000156886		"CD molecules", "Integrins"	6146	protein-coding gene	gene with protein product		602453				8666289, 9598326	Standard	NM_005353		Approved	CD11d, ADB2	uc002ebv.1	Q13349		ENST00000389202.2:c.1040A>T	chr16.hg19:g.31419776A>T	ENSP00000373854:p.Gln347Leu	60.0	0.0		58.0	32.0	NM_005353	Q15575|Q15576	Missense_Mutation	SNP	ENST00000389202.2	hg19	CCDS32438.1	.	.	.	.	.	.	.	.	.	.	A	18.78	3.697393	0.68386	.	.	ENSG00000156886	ENST00000444228;ENST00000389202	T	0.41758	0.99	5.47	3.2	0.36748	.	.	.	.	.	T	0.55210	0.1906	M	0.72624	2.21	0.29096	N	0.881795	D;D	0.67145	0.996;0.996	P;P	0.58660	0.843;0.843	T	0.52223	-0.8604	9	0.72032	D	0.01	.	8.5239	0.33293	0.8346:0.0:0.1654:0.0	.	363;347	Q59H14;Q13349	.;ITAD_HUMAN	L	363;347	ENSP00000373854:Q347L	ENSP00000373854:Q347L	Q	+	2	0	ITGAD	31327277	1.000000	0.71417	0.418000	0.26571	0.876000	0.50452	2.753000	0.47524	0.909000	0.36697	0.524000	0.50904	CAG	.	.		0.557	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353		T	31419776	A	T	31419776	3	4	344	1	0	0	0	0	1	0	0	0	7893	188	7	4	1078	4	ITGAD	16	31419776	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	191550	31419776	58934977	1111	48474										
ARMC5	79798	hgsc.bcm.edu	37	chr16	31477974	31477974	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tggaagaggccgtgggccgcAtccacctgggaccccagggt	16	13	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:31477974A>T	ENST00000563544.1	+	7	3118	c.2572A>T	c.(2572-2574)Atc>Ttc	p.I858F	ARMC5_ENST00000538189.1_Missense_Mutation_p.I890F|ARMC5_ENST00000457010.2_3'UTR|ARMC5_ENST00000412665.2_Missense_Mutation_p.I502F|ARMC5_ENST00000268314.4_Missense_Mutation_p.I858F|ARMC5_ENST00000408912.3_Missense_Mutation_p.I953F			Q96C12	ARMC5_HUMAN	armadillo repeat containing 5	858										central_nervous_system(1)|endometrium(4)|large_intestine(3)|liver(2)|lung(12)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						CGTGGGCCGCATCCACCTGGG	0.716																																					p.I858F		Atlas-SNP	.											.	ARMC5	94	.	0			c.A2572T						.						16	26	22					16																	31477974		2164	4267	6431	SO:0001583	missense	79798	exon6			GGCCGCATCCACC	AY217348	CCDS42155.1, CCDS45472.1, CCDS73874.1	16p11	2013-02-14			ENSG00000140691	ENSG00000140691		"Armadillo repeat containing"	25781	protein-coding gene	gene with protein product		615549					Standard	NM_024742		Approved	FLJ13063	uc002ecc.3	Q96C12	OTTHUMG00000176618	ENST00000563544.1:c.2572A>T	chr16.hg19:g.31477974A>T	ENSP00000456877:p.Ile858Phe	50.0	0.0		47.0	20.0	NM_001105247	Q86WM9|Q9H7P8|Q9H925	Missense_Mutation	SNP	ENST00000563544.1	hg19	CCDS45472.1	.	.	.	.	.	.	.	.	.	.	A	15.36	2.809743	0.50421	.	.	ENSG00000140691	ENST00000408912;ENST00000538189;ENST00000268314;ENST00000412665	T;T;T;T	0.46063	2.16;2.18;2.2;0.88	5.07	2.79	0.32731	.	0.427059	0.23481	N	0.047719	T	0.21801	0.0525	N	0.08118	0	0.36530	D	0.8707	P;P;P;P	0.43701	0.815;0.815;0.815;0.703	B;B;B;B	0.42422	0.299;0.299;0.387;0.299	T	0.12553	-1.0543	10	0.46703	T	0.11	-25.2642	5.3445	0.16002	0.7708:0.0:0.2292:0.0	.	890;890;953;858	B4DH27;F5H156;B4DIU9;Q96C12	.;.;.;ARMC5_HUMAN	F	953;890;858;502	ENSP00000386125:I953F;ENSP00000443995:I890F;ENSP00000268314:I858F;ENSP00000400183:I502F	ENSP00000268314:I858F	I	+	1	0	ARMC5	31385475	0.000000	0.05858	0.995000	0.50966	0.929000	0.56500	0.185000	0.16958	0.967000	0.38186	0.368000	0.22195	ATC	.	.		0.716	ARMC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432847.1	NM_024742		T	31477974	A	T	31477974	3	4	344	1	0	0	0	0	1	0	0	0	954	217	8	4	2908	4	ARMC5	16	31477974	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	58198	31477974	58876779	1112	48475										
PHKB	5257	hgsc.bcm.edu	37	chr16	47622970	47622970	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agatgggtatagaacatcatTggaagatcccaacagatgct	10	7	1	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:47622970T>C	ENST00000323584.5	+	10	1049	c.1025T>C	c.(1024-1026)tTg>tCg	p.L342S	PHKB_ENST00000566044.1_Missense_Mutation_p.L335S|PHKB_ENST00000299167.8_Missense_Mutation_p.L342S|PHKB_ENST00000567402.1_3'UTR|PHKB_ENST00000455779.1_Missense_Mutation_p.L335S	NM_000293.2	NP_000284.1	Q93100	KPBB_HUMAN	phosphorylase kinase, beta	342					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|liver(1)|lung(18)|ovary(1)|skin(1)	41		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				AGAACATCATTGGAAGATCCC	0.338																																					p.L342S		Atlas-SNP	.											.	PHKB	298	.	0			c.T1025C						.						68	73	71					16																	47622970		2201	4300	6501	SO:0001583	missense	5257	exon10			CATCATTGGAAGA		CCDS10729.1, CCDS42161.1	16q12-q13	2009-07-10			ENSG00000102893	ENSG00000102893	2.7.11.19		8927	protein-coding gene	gene with protein product		172490					Standard	NM_000293		Approved		uc002eev.4	Q93100	OTTHUMG00000133102	ENST00000323584.5:c.1025T>C	chr16.hg19:g.47622970T>C	ENSP00000313504:p.Leu342Ser	72.0	0.0		26.0	23.0	NM_000293	Q8N4T5	Missense_Mutation	SNP	ENST00000323584.5	hg19	CCDS10729.1	.	.	.	.	.	.	.	.	.	.	T	19.70	3.877135	0.72180	.	.	ENSG00000102893	ENST00000299167;ENST00000455779;ENST00000323584	D;D	0.94092	-3.35;-3.35	5.83	5.83	0.93111	Six-hairpin glycosidase-like (1);Glycoside hydrolase 15-related (1);	0.153364	0.46145	D	0.000317	D	0.96448	0.8841	M	0.86268	2.805	0.48696	D	0.999691	D;P	0.53151	0.958;0.702	P;B	0.59825	0.864;0.444	D	0.96629	0.9465	10	0.56958	D	0.05	-4.9254	16.2071	0.82135	0.0:0.0:0.0:1.0	.	342;335	Q93100;Q93100-4	KPBB_HUMAN;.	S	335;335;342	ENSP00000414345:L335S;ENSP00000313504:L342S	ENSP00000299167:L335S	L	+	2	0	PHKB	46180471	1.000000	0.71417	0.976000	0.42696	0.840000	0.47671	5.040000	0.64191	2.240000	0.73641	0.477000	0.44152	TTG	.	.		0.338	PHKB-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000430413.1			C	47622970	T	C	47622970	3	2	344	1	0	0	0	0	1	0	0	0	11854	1821	63	2	1122	2	PHKB	16	47622970	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	16144996	47622970	42731783	1113	48476										
PHKB	5257	hgsc.bcm.edu	37	chr16	47727355	47727355	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cccaccgggttctatgaccgAgtgtggcagattctggagcg	14	11	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:47727355A>T	ENST00000323584.5	+	28	2856	c.2832A>T	c.(2830-2832)cgA>cgT	p.R944R	PHKB_ENST00000566044.1_Silent_p.R937R|PHKB_ENST00000299167.8_Silent_p.R944R|PHKB_ENST00000455779.1_Silent_p.R937R	NM_000293.2	NP_000284.1	Q93100	KPBB_HUMAN	phosphorylase kinase, beta	944	Calmodulin-binding. {ECO:0000255}.				carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|liver(1)|lung(18)|ovary(1)|skin(1)	41		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				TCTATGACCGAGTGTGGCAGA	0.488																																					p.R944R		Atlas-SNP	.											.	PHKB	298	.	0			c.A2832T						.						73	67	69					16																	47727355		2201	4300	6501	SO:0001819	synonymous_variant	5257	exon28			TGACCGAGTGTGG		CCDS10729.1, CCDS42161.1	16q12-q13	2009-07-10			ENSG00000102893	ENSG00000102893	2.7.11.19		8927	protein-coding gene	gene with protein product		172490					Standard	NM_000293		Approved		uc002eev.4	Q93100	OTTHUMG00000133102	ENST00000323584.5:c.2832A>T	chr16.hg19:g.47727355A>T		148.0	0.0		70.0	59.0	NM_000293	Q8N4T5	Silent	SNP	ENST00000323584.5	hg19	CCDS10729.1																																																																																			.	.		0.488	PHKB-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000430413.1			T	47727355	A	T	47727355	2	4	344	1	0	0	0	0	0	0	0	1	11854	291	11	4		4	PHKB	16	47727355	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	104385	47727355	42627398	1114	48477										
ZNF423	23090	hgsc.bcm.edu	37	chr16	49764842	49764842	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttcctgtcttccagcgcacgGctggttttctgatcgcactc	9	14	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:49764842G>A	ENST00000561648.1	-	3	170	c.117C>T	c.(115-117)agC>agT	p.S39S	ZNF423_ENST00000562520.1_5'UTR|ZNF423_ENST00000563137.2_5'UTR|ZNF423_ENST00000262383.2_Silent_p.S39S|ZNF423_ENST00000562871.1_5'UTR	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	39					cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				CCAGCGCACGGCTGGTTTTCT	0.493																																					p.S39S		Atlas-SNP	.											.	ZNF423	463	.	0			c.C117T						.						321	273	289					16																	49764842		2198	4300	6498	SO:0001819	synonymous_variant	23090	exon3			CGCACGGCTGGTT	AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"Zinc fingers, C2H2-type"	16762	protein-coding gene	gene with protein product	"OLF-1/EBF associated zinc finger gene", " Smad- and Olf-interacting zinc finger protein", "early B-cell factor associated zinc finger protein"	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.117C>T	chr16.hg19:g.49764842G>A		101.0	0.0		45.0	38.0	NM_015069	O94860|Q76N04|Q9NZ13	Silent	SNP	ENST00000561648.1	hg19	CCDS32445.1																																																																																			.	.		0.493	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069		A	49764842	G	A	49764842	2	1	344	1	0	0	0	0	0	0	0	1	17913	1194	42	3		3	ZNF423	16	49764842	Silent	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	2037487	49764842	40589911	1115	48478										
RBL2	5934	hgsc.bcm.edu	37	chr16	53498136	53498136	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgctaataactttattttatAgggtattctggaacaagatg	8	4	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:53498136A>G	ENST00000262133.6	+	12	1697		c.e12-1		RBL2_ENST00000379935.4_Splice_Site|RBL2_ENST00000544545.1_Splice_Site	NM_005611.3	NP_005602.3	Q08999	RBL2_HUMAN	retinoblastoma-like 2						chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						TTTATTTTATAGGGTATTCTG	0.353																																					.		Atlas-SNP	.											.	RBL2	115	.	0			c.1561-2A>G						.						66	69	68					16																	53498136		2198	4300	6498	SO:0001630	splice_region_variant	5934	exon12			TTTTATAGGGTAT	X74594	CCDS10748.1	16q12.2	2014-03-11	2014-03-11		ENSG00000103479	ENSG00000103479			9894	protein-coding gene	gene with protein product		180203				8361765, 8643454	Standard	NM_005611		Approved	Rb2, p130	uc002ehi.4	Q08999	OTTHUMG00000133198	ENST00000262133.6:c.1561-1A>G	chr16.hg19:g.53498136A>G		50.0	0.0		30.0	25.0	NM_005611	B7Z913|Q15073|Q16084|Q8NE70|Q92812	Splice_Site	SNP	ENST00000262133.6	hg19	CCDS10748.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.117580	0.77323	.	.	ENSG00000103479	ENST00000262133;ENST00000544405;ENST00000379935;ENST00000544545	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9995	0.80280	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	RBL2	52055637	1.000000	0.71417	0.996000	0.52242	0.984000	0.73092	9.129000	0.94430	2.186000	0.69663	0.528000	0.53228	.	.	.		0.353	RBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256908.3	NM_005611	Intron	G	53498136	A	G	53498136	5	3	344	1	0	0	0	0	0	0	1	0	13125	434	15	2	1605	2	RBL2	16	53498136	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3733294	53498136	36856617	1116	48479										
SLC12A3	6559	hgsc.bcm.edu	37	chr16	56936357	56936357	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaggatgaggccactgtcaaCgagatgcggcgggactgccc	15	11	1	2	rs13306666	byFrequency	TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:56936357C>A	ENST00000563236.1	+	24	2818	c.2793C>A	c.(2791-2793)aaC>aaA	p.N931K	SLC12A3_ENST00000566786.1_Missense_Mutation_p.N939K|SLC12A3_ENST00000438926.2_Missense_Mutation_p.N940K|SLC12A3_ENST00000262502.5_Missense_Mutation_p.N930K			P55017	S12A3_HUMAN	solute carrier family 12 (sodium/chloride transporter), member 3	931					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:chloride symporter activity (GO:0015378)|transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(28)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50					Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325)	CCACTGTCAACGAGATGCGGC	0.562																																					p.N940K		Atlas-SNP	.											SLC12A3,caecum,carcinoma,0,1	SLC12A3	99	.	0			c.C2820A						.						111	92	99					16																	56936357		2198	4300	6498	SO:0001583	missense	6559	exon24			TGTCAACGAGATG		CCDS10770.1, CCDS45491.1, CCDS58464.1	16q13	2013-07-18	2013-07-18		ENSG00000070915	ENSG00000070915		"Solute carriers"	10912	protein-coding gene	gene with protein product		600968				8812482	Standard	NM_000339		Approved	NCCT	uc002ekd.4	P55017	OTTHUMG00000133284	ENST00000563236.1:c.2793C>A	chr16.hg19:g.56936357C>A	ENSP00000456149:p.Asn931Lys	89.0	0.0		27.0	24.0	NM_000339	A8MSJ2|C9JNN9	Missense_Mutation	SNP	ENST00000563236.1	hg19	CCDS58464.1	.	.	.	.	.	.	.	.	.	.	C	7.845	0.722675	0.15439	.	.	ENSG00000070915	ENST00000438926;ENST00000262502	.	.	.	5.07	-10.1	0.00402	.	1.104770	0.06615	N	0.756285	T	0.24353	0.0590	N	0.25647	0.755	0.20638	N	0.999871	B;B;B	0.15141	0.004;0.007;0.012	B;B;B	0.26310	0.017;0.031;0.068	T	0.34900	-0.9810	9	0.46703	T	0.11	.	6.1675	0.20398	0.333:0.2396:0.0:0.4274	.	939;931;940	P55017-3;P55017;P55017-2	.;S12A3_HUMAN;.	K	939;940	.	ENSP00000262502:N940K	N	+	3	2	SLC12A3	55493858	0.000000	0.05858	0.000000	0.03702	0.414000	0.31173	-2.268000	0.01169	-2.460000	0.00537	-0.284000	0.09977	AAC	.	C|0.998;T|0.002		0.562	SLC12A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432337.1			A	56936357	C	A	56936357	3	1	344	1	0	0	0	0	1	0	0	0	14399	535	19	1	2914	1	SLC12A3	16	56936357	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	3438221	56936357	33418396	1117	48480										
CNGB1	1258	hgsc.bcm.edu	37	chr16	57935438	57935438	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	accaaaaggtgtacctgaaaGagtgcgactttgctaacgat	10	8	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:57935438G>A	ENST00000251102.8	-	28	2946	c.2886C>T	c.(2884-2886)ctC>ctT	p.L962L	CNGB1_ENST00000564448.1_Silent_p.L956L	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	962					cation transport (GO:0006812)|cytosolic calcium ion homeostasis (GO:0051480)|detection of light stimulus involved in visual perception (GO:0050908)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|protein heterotetramerization (GO:0051290)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina homeostasis (GO:0001895)|rhodopsin mediated signaling pathway (GO:0016056)|sensory perception of smell (GO:0007608)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|intracellular cyclic nucleotide activated cation channel complex (GO:0017071)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)|transmembrane transporter complex (GO:1902495)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(7)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(11)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	54						GTACCTGAAAGAGTGCGACTT	0.537																																					p.L962L	Colon(156;1293 1853 16336 28962 38659)	Atlas-SNP	.											.	CNGB1	105	.	0			c.C2886T						.						108	112	110					16																	57935438		2056	4201	6257	SO:0001819	synonymous_variant	1258	exon28			CTGAAAGAGTGCG	AF042498	CCDS42169.1, CCDS45495.1, CCDS67042.1	16q13	2013-02-14			ENSG00000070729	ENSG00000070729		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2151	protein-coding gene	gene with protein product	"glutamic acid-rich protein"	600724		CNCG2, CNCG3L		8766832, 7590744, 16382102	Standard	NM_001297		Approved	RCNC2, RCNCb, GARP, GAR1, CNGB1B, RP45	uc002emt.2	Q14028	OTTHUMG00000154810	ENST00000251102.8:c.2886C>T	chr16.hg19:g.57935438G>A		59.0	0.0		37.0	32.0	NM_001297	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Silent	SNP	ENST00000251102.8	hg19	CCDS42169.1																																																																																			.	.		0.537	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297		A	57935438	G	A	57935438	2	1	344	1	0	0	0	0	0	0	0	1	3602	929	33	3		3	CNGB1	16	57935438	Silent	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	999081	57935438	32419315	1118	48481										
CCDC113	29070	hgsc.bcm.edu	37	chr16	58293762	58293762	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgcctttatgttttaggataAtatgaaggagaaattacgtt	9	3	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:58293762A>T	ENST00000219299.4	+	5	630	c.551A>T	c.(550-552)aAt>aTt	p.N184I	CCDC113_ENST00000443128.2_Missense_Mutation_p.N130I	NM_014157.3	NP_054876.2	Q9H0I3	CC113_HUMAN	coiled-coil domain containing 113	184						cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)				large_intestine(4)|lung(6)|ovary(1)|urinary_tract(1)	12						TTTTAGGATAATATGAAGGAG	0.348																																					p.N184I		Atlas-SNP	.											.	CCDC113	30	.	0			c.A551T						.						76	79	78					16																	58293762		2197	4300	6497	SO:0001583	missense	29070	exon5			AGGATAATATGAA	AL136785	CCDS10795.1, CCDS45497.1	16q21	2008-02-05			ENSG00000103021	ENSG00000103021			25002	protein-coding gene	gene with protein product						11230166, 11042152	Standard	NM_014157		Approved	HSPC065, DKFZp434N1418	uc002ene.3	Q9H0I3	OTTHUMG00000133489	ENST00000219299.4:c.551A>T	chr16.hg19:g.58293762A>T	ENSP00000219299:p.Asn184Ile	190.0	0.0		89.0	81.0	NM_014157	B2RAQ7|B4DR20|Q9NZX2	Missense_Mutation	SNP	ENST00000219299.4	hg19	CCDS10795.1	.	.	.	.	.	.	.	.	.	.	A	7.973	0.749445	0.15778	.	.	ENSG00000103021	ENST00000443128;ENST00000219299	T;T	0.31510	1.49;1.5	5.1	-3.26	0.05064	.	1.406200	0.03978	N	0.292758	T	0.20251	0.0487	L	0.33485	1.01	0.09310	N	1	B;B	0.20550	0.036;0.046	B;B	0.21546	0.025;0.035	T	0.22871	-1.0204	10	0.38643	T	0.18	-2.7455	2.4403	0.04492	0.2272:0.2797:0.3685:0.1246	.	130;184	B4DR20;Q9H0I3	.;CC113_HUMAN	I	130;184	ENSP00000402588:N130I;ENSP00000219299:N184I	ENSP00000219299:N184I	N	+	2	0	CCDC113	56851263	0.000000	0.05858	0.917000	0.36280	0.362000	0.29581	-0.010000	0.12743	-0.288000	0.09051	-0.338000	0.08134	AAT	.	.		0.348	CCDC113-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257387.2	NM_014157		T	58293762	A	T	58293762	3	4	344	1	0	0	0	0	1	0	0	0	2752	101	4	4	569	4	CCDC113	16	58293762	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	358324	58293762	32060991	1119	48482										
PRSS54	221191	hgsc.bcm.edu	37	chr16	58320072	58320072	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttgctaggatccatgttactTatacccactataacgacaat	5	10	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:58320072T>G	ENST00000219301.4	-	5	685	c.291A>C	c.(289-291)atA>atC	p.I97I	PRSS54_ENST00000543437.1_5'UTR|PRSS54_ENST00000567164.1_Silent_p.I97I|PRSS54_ENST00000563336.1_5'Flank	NM_001080492.1	NP_001073961.1	Q6PEW0	PRS54_HUMAN	protease, serine, 54	97	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					cytoplasm (GO:0005737)|extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						CCATGTTACTTATACCCACTA	0.438																																					p.I97I		Atlas-SNP	.											.	PRSS54	48	.	0			c.A291C						.						215	173	187					16																	58320072		2198	4300	6498	SO:0001819	synonymous_variant	221191	exon5			GTTACTTATACCC	AK058068	CCDS32463.1	16q21	2010-05-07			ENSG00000103023	ENSG00000103023		"Serine peptidases / Serine peptidases"	26336	protein-coding gene	gene with protein product	"cancer/testis antigen 67"					17521433	Standard	NM_001080492		Approved	FLJ25339, KLKBL4, CT67	uc002enf.3	Q6PEW0		ENST00000219301.4:c.291A>C	chr16.hg19:g.58320072T>G		115.0	0.0		49.0	38.0	NM_001080492	Q96LN9|Q9NT77	Silent	SNP	ENST00000219301.4	hg19	CCDS32463.1																																																																																			.	.		0.438	PRSS54-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422556.1	NM_001080492		G	58320072	T	G	58320072	2	3	344	1	0	0	0	0	0	0	0	1	12645	1744	61	5		5	PRSS54	16	58320072	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	26310	58320072	32034681	1120	48483										
CDH5	1003	hgsc.bcm.edu	37	chr16	66431975	66431975	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggagtttgccaagccctaccAgcccaaagtgtgtgagaacg	12	11	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:66431975A>T	ENST00000341529.3	+	9	1599	c.1451A>T	c.(1450-1452)cAg>cTg	p.Q484L	CDH5_ENST00000539168.1_5'UTR	NM_001795.3	NP_001786.2	P33151	CADH5_HUMAN	cadherin 5, type 2 (vascular endothelium)	484	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|blood vessel maturation (GO:0001955)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|negative regulation of cell proliferation (GO:0008285)|regulation of establishment of cell polarity (GO:2000114)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|kidney(18)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	54		Ovarian(137;0.0955)		OV - Ovarian serous cystadenocarcinoma(108;0.107)	Lenalidomide(DB00480)	AAGCCCTACCAGCCCAAAGTG	0.577																																					p.Q484L		Atlas-SNP	.											.	CDH5	111	.	0			c.A1451T						.						174	160	165					16																	66431975		2201	4300	6501	SO:0001583	missense	1003	exon9			CCTACCAGCCCAA	X79981	CCDS10804.1	16q22.1	2010-01-26	2008-07-25		ENSG00000179776	ENSG00000179776		"CD molecules", "Cadherins / Major cadherins"	1764	protein-coding gene	gene with protein product	"VE-cadherin"	601120	"cadherin 5, type 2, VE-cadherin (vascular epithelium)"			2059658	Standard	NM_001795		Approved	7B4, CD144	uc002eom.4	P33151	OTTHUMG00000137495	ENST00000341529.3:c.1451A>T	chr16.hg19:g.66431975A>T	ENSP00000344115:p.Gln484Leu	128.0	0.0		51.0	43.0	NM_001795	Q4VAI5|Q4VAI6	Missense_Mutation	SNP	ENST00000341529.3	hg19	CCDS10804.1	.	.	.	.	.	.	.	.	.	.	A	15.43	2.832444	0.50845	.	.	ENSG00000179776	ENST00000341529;ENST00000539262	T	0.14391	2.51	4.5	4.5	0.54988	Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.10766	0.0263	L	0.29908	0.895	0.58432	D	0.999999	B	0.06786	0.001	B	0.06405	0.002	T	0.06144	-1.0843	9	0.87932	D	0	.	9.185	0.37165	0.8168:0.1832:0.0:0.0	.	484	P33151	CADH5_HUMAN	L	484;225	ENSP00000344115:Q484L	ENSP00000344115:Q484L	Q	+	2	0	CDH5	64989476	0.999000	0.42202	0.900000	0.35374	0.879000	0.50718	6.134000	0.71689	1.899000	0.54978	0.459000	0.35465	CAG	.	.		0.577	CDH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268767.1	NM_001795		T	66431975	A	T	66431975	3	4	344	1	0	0	0	0	1	0	0	0	3115	188	7	4	1481	4	CDH5	16	66431975	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	8111903	66431975	23922778	1121	48484										
CMTM4	146223	hgsc.bcm.edu	37	chr16	66670433	66670433	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaagtagaggccttcacacgGggagcatgccatgatggtct	13	9	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:66670433G>A	ENST00000330687.4	-	2	419	c.238C>T	c.(238-240)Ccg>Tcg	p.P80S	CMTM4_ENST00000563952.1_Missense_Mutation_p.P51S|CMTM4_ENST00000394106.2_Missense_Mutation_p.P80S	NM_178818.2|NM_181521.2	NP_848933.1|NP_852662.1	Q8IZR5	CKLF4_HUMAN	CKLF-like MARVEL transmembrane domain containing 4	80	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				chemotaxis (GO:0006935)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				cervix(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|pancreas(1)|stomach(1)	9		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0811)|Epithelial(162;0.214)		CCTTCACACGGGGAGCATGCC	0.433																																					p.P80S		Atlas-SNP	.											.	CMTM4	19	.	0			c.C238T						.						113	99	104					16																	66670433		2201	4300	6501	SO:0001583	missense	146223	exon2			CACACGGGGAGCA	AF479814	CCDS10817.1, CCDS42170.1	16q22.1-q22.3	2008-02-05	2005-11-08	2005-11-08	ENSG00000183723	ENSG00000183723			19175	protein-coding gene	gene with protein product		607887	"chemokine-like factor super family 4", "chemokine-like factor superfamily 4"	CKLFSF4		12782130	Standard	NM_178818		Approved		uc002epz.3	Q8IZR5	OTTHUMG00000137500	ENST00000330687.4:c.238C>T	chr16.hg19:g.66670433G>A	ENSP00000333833:p.Pro80Ser	62.0	0.0		34.0	29.0	NM_178818	Q52M40|Q8IZR4|Q8IZV1	Missense_Mutation	SNP	ENST00000330687.4	hg19	CCDS10817.1	.	.	.	.	.	.	.	.	.	.	G	17.61	3.432003	0.62844	.	.	ENSG00000183723	ENST00000330687;ENST00000394106	T;T	0.26373	1.74;1.74	5.73	5.73	0.89815	Marvel (1);MARVEL-like domain (1);	0.000000	0.85682	D	0.000000	T	0.38480	0.1042	N	0.22421	0.69	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.06373	-1.0830	10	0.21014	T	0.42	.	19.9133	0.97031	0.0:0.0:1.0:0.0	.	80	Q8IZR5	CKLF4_HUMAN	S	80	ENSP00000333833:P80S;ENSP00000377666:P80S	ENSP00000333833:P80S	P	-	1	0	CMTM4	65227934	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	9.382000	0.97209	2.721000	0.93114	0.655000	0.94253	CCG	.	.		0.433	CMTM4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268807.1			A	66670433	G	A	66670433	3	1	344	1	0	0	0	0	1	0	0	0	3587	1232	43	3	486	3	CMTM4	16	66670433	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	238458	66670433	23684320	1122	48485										
KCTD19	146212	hgsc.bcm.edu	37	chr16	67325322	67325322	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcagtgacatttctgtgcatAaaacatctcttcccaggaca	7	11	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:67325322A>G	ENST00000304372.5	-	14	2510	c.2455T>C	c.(2455-2457)Tat>Cat	p.Y819H		NM_001100915.1	NP_001094385.1	Q17RG1	KCD19_HUMAN	potassium channel tetramerization domain containing 19	819					protein homooligomerization (GO:0051260)					endometrium(3)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)	23		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0311)|Epithelial(162;0.0906)		TTCTGTGCATAAAACATCTCT	0.502																																					p.Y819H		Atlas-SNP	.											.	KCTD19	82	.	0			c.T2455C						.						72	70	70					16																	67325322		1967	4165	6132	SO:0001583	missense	146212	exon14			GTGCATAAAACAT	AK097481	CCDS42179.1	16q22.1	2013-06-20	2013-06-20			ENSG00000168676			24753	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 19"				Standard	NM_001100915		Approved	FLJ40162	uc002esu.2	Q17RG1		ENST00000304372.5:c.2455T>C	chr16.hg19:g.67325322A>G	ENSP00000305702:p.Tyr819His	136.0	0.0		50.0	46.0	NM_001100915	B4DZ49|Q8N804	Missense_Mutation	SNP	ENST00000304372.5	hg19	CCDS42179.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.051870	0.75960	.	.	ENSG00000168676	ENST00000304372	T	0.73152	-0.72	5.63	5.63	0.86233	.	0.000000	0.49916	D	0.000121	T	0.75250	0.3824	L	0.27053	0.805	0.35604	D	0.808141	D	0.76494	0.999	D	0.83275	0.996	T	0.82508	-0.0422	10	0.87932	D	0	-10.8343	13.221	0.59887	1.0:0.0:0.0:0.0	.	819	Q17RG1	KCD19_HUMAN	H	819	ENSP00000305702:Y819H	ENSP00000305702:Y819H	Y	-	1	0	KCTD19	65882823	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	5.991000	0.70602	2.157000	0.67596	0.374000	0.22700	TAT	.	.		0.502	KCTD19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422061.1	XM_085367		G	67325322	A	G	67325322	3	3	344	1	0	0	0	0	1	0	0	0	8115	362	13	2	337	2	KCTD19	16	67325322	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	654889	67325322	23029431	1123	48486										
LRRC36	55282	hgsc.bcm.edu	37	chr16	67375858	67375858	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tctactgatgatctcttttcAgaactggtggagtctctttc	8	9	4	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:67375858A>C	ENST00000329956.6	+	2	89		c.e2-1		LRRC36_ENST00000563303.1_Intron	NM_018296.5	NP_060766.5	Q1X8D7	LRC36_HUMAN	leucine rich repeat containing 36											endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	24		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0669)|Epithelial(162;0.161)		ATCTCTTTTCAGAACTGGTGG	0.413																																					.		Atlas-SNP	.											.	LRRC36	68	.	0			c.71-2A>C						.						104	101	102					16																	67375858		2198	4300	6498	SO:0001630	splice_region_variant	55282	exon2			CTTTTCAGAACTG	BC026156	CCDS32467.1, CCDS58474.1	16q22.1	2008-02-05				ENSG00000159708			25615	protein-coding gene	gene with protein product						12477932	Standard	NM_001161575		Approved	FLJ11004	uc002esv.3	Q1X8D7		ENST00000329956.6:c.71-1A>C	chr16.hg19:g.67375858A>C		68.0	0.0		34.0	30.0	NM_018296	A4FTV6|A6NDE9|A8K8E6|Q7Z5K5	Splice_Site	SNP	ENST00000329956.6	hg19	CCDS32467.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.962108	0.74016	.	.	ENSG00000159708	ENST00000329956	.	.	.	5.55	5.55	0.83447	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.1001	0.53778	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	LRRC36	65933359	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.504000	0.60414	2.113000	0.64589	0.460000	0.39030	.	.	.		0.413	LRRC36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421770.1	NM_018296	Intron	C	67375858	A	C	67375858	5	2	344	1	0	0	0	0	0	0	1	0	8999	202	7	5	75	5	LRRC36	16	67375858	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	50536	67375858	22978895	1124	48487										
EDC4	23644	hgsc.bcm.edu	37	chr16	67909967	67909967	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	caaacaagactggtcttcggAccatgccacccattaacctg	7	14	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:67909967A>G	ENST00000358933.5	+	2	441	c.202A>G	c.(202-204)Acc>Gcc	p.T68A	AC040162.1_ENST00000408599.1_RNA	NM_014329.4	NP_055144.3	Q6P2E9	EDC4_HUMAN	enhancer of mRNA decapping 4	68					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	41		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)		TGGTCTTCGGACCATGCCACC	0.532																																					p.T68A		Atlas-SNP	.											.	EDC4	101	.	0			c.A202G						.						119	102	108					16																	67909967		2198	4300	6498	SO:0001583	missense	23644	exon2			CTTCGGACCATGC	U17474	CCDS10849.1	16q22.1	2008-02-05			ENSG00000038358	ENSG00000038358			17157	protein-coding gene	gene with protein product		606030				9067524	Standard	NM_014329		Approved	RCD-8, Ge-1, HEDLS	uc002eur.3	Q6P2E9	OTTHUMG00000137543	ENST00000358933.5:c.202A>G	chr16.hg19:g.67909967A>G	ENSP00000351811:p.Thr68Ala	96.0	0.0		30.0	25.0	NM_014329	A6NGM1|A8K4T4|Q13025|Q13826|Q6ZR12|Q7Z6H7	Missense_Mutation	SNP	ENST00000358933.5	hg19	CCDS10849.1	.	.	.	.	.	.	.	.	.	.	A	11.54	1.668018	0.29604	.	.	ENSG00000038358	ENST00000358933	.	.	.	5.91	-0.238	0.13055	.	0.818985	0.11618	N	0.546070	T	0.13415	0.0325	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.23013	-1.0200	9	0.20519	T	0.43	-4.0825	0.6508	0.00826	0.4217:0.141:0.1574:0.2799	.	68	Q6P2E9	EDC4_HUMAN	A	68	.	ENSP00000351811:T68A	T	+	1	0	EDC4	66467468	0.000000	0.05858	0.983000	0.44433	0.948000	0.59901	0.247000	0.18179	-0.019000	0.14055	0.533000	0.62120	ACC	.	.		0.532	EDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268874.2	NM_014329		G	67909967	A	G	67909967	3	3	344	1	0	0	0	0	1	0	0	0	4910	275	10	2	208	2	EDC4	16	67909967	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	534109	67909967	22444786	1125	48488										
HYDIN	54768	hgsc.bcm.edu	37	chr16	70995883	70995883	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttggaaaatgattttttccaGgctttcctcatcctcctctt	5	11	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:70995883G>T	ENST00000393567.2	-	38	6097	c.5947C>A	c.(5947-5949)Ctg>Atg	p.L1983M		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	1983					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				ATTTTTTCCAGGCTTTCCTCA	0.448																																					p.L1983M		Atlas-SNP	.											.	HYDIN	788	.	0			c.C5947A						.						19	47	38					16																	70995883		1752	4040	5792	SO:0001583	missense	54768	exon38			TTTCCAGGCTTTC	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.5947C>A	chr16.hg19:g.70995883G>T	ENSP00000377197:p.Leu1983Met	110.0	0.0		62.0	34.0	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	hg19	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	G	10.80	1.451706	0.26074	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.40756	1.02	4.32	-0.201	0.13212	.	0.000000	0.27891	U	0.017431	T	0.38506	0.1043	L	0.34521	1.04	0.80722	D	1	D	0.61080	0.989	P	0.58928	0.848	T	0.18618	-1.0331	10	0.31617	T	0.26	.	4.8069	0.13325	0.2971:0.1627:0.5402:0.0	.	1982	F8WD23	.	M	1983;1982	ENSP00000377197:L1983M	ENSP00000310485:L274M	L	-	1	2	HYDIN	69553384	0.996000	0.38824	0.996000	0.52242	0.139000	0.21198	0.061000	0.14366	0.054000	0.16065	-0.430000	0.05897	CTG	.	.		0.448	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			T	70995883	G	T	70995883	3	4	344	1	0	0	0	0	1	0	0	0	7476	991	35	3	9614	3	HYDIN	16	70995883	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	3085916	70995883	19358870	1126	48489										
KIAA0174	9798	hgsc.bcm.edu	37	chr16	71957226	71957226	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctgccaatggggacttatcaGgcctttcccaatattcatcc	7	13	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:71957226G>A	ENST00000378799.6	+	8	1151	c.795G>A	c.(793-795)caG>caA	p.Q265Q	IST1_ENST00000606369.1_Silent_p.Q117Q|IST1_ENST00000538565.1_3'UTR|IST1_ENST00000378798.5_Intron|IST1_ENST00000535424.1_Silent_p.Q278Q|IST1_ENST00000538850.1_Silent_p.Q117Q|RP11-498D10.5_ENST00000567146.1_RNA|IST1_ENST00000544564.1_Silent_p.Q265Q|IST1_ENST00000329908.8_Silent_p.Q265Q|IST1_ENST00000541571.2_Silent_p.Q265Q			P53990	IST1_HUMAN	increased sodium tolerance 1 homolog (yeast)	263	Interaction with VPS37B.|Interaction with VTA1.				abscission (GO:0009838)|cell division (GO:0051301)|cytokinesis (GO:0000910)|establishment of protein localization (GO:0045184)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of proteolysis (GO:0045862)|protein localization (GO:0008104)|viral capsid secondary envelopment (GO:0046745)|viral release from host cell (GO:0019076)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|Flemming body (GO:0090543)|midbody (GO:0030496)	MIT domain binding (GO:0090541)|protein complex binding (GO:0032403)|protein domain specific binding (GO:0019904)										GGACTTATCAGGCCTTTCCCA	0.463																																					p.Q278Q		Atlas-SNP	.											.	.	.	.	0			c.G834A						.						113	103	106					16																	71957226		2198	4300	6498	SO:0001819	synonymous_variant	9798	exon9			TTATCAGGCCTTT	BC004359	CCDS10905.1, CCDS59271.1, CCDS59272.1, CCDS59273.1, CCDS59274.1	16q22.2	2011-08-18	2011-08-18	2011-08-18	ENSG00000182149	ENSG00000182149			28977	protein-coding gene	gene with protein product			"KIAA0174"	KIAA0174		8724849, 19129480	Standard	NM_001270975		Approved		uc002fbm.2	P53990	OTTHUMG00000137597	ENST00000378799.6:c.795G>A	chr16.hg19:g.71957226G>A		97.0	0.0		63.0	53.0	NM_001270976	A8KAH5|J3QLU7|Q3SYM4|Q9BQ81|Q9BWN2	Silent	SNP	ENST00000378799.6	hg19	CCDS59272.1																																																																																			.	.		0.463	IST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269005.2	NM_014761		A	71957226	G	A	71957226	2	1	344	1	0	0	0	0	0	0	0	1	8167	991	35	3		3	KIAA0174	16	71957226	Silent	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	961343	71957226	18397527	1127	48490										
CNTNAP4	85445	hgsc.bcm.edu	37	chr16	76523604	76523604	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aactgcatggaccatcatacAgcacaacggctctgacttaa	7	12	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:76523604A>T	ENST00000476707.1	+	12	2052	c.1913A>T	c.(1912-1914)cAg>cTg	p.Q638L	CNTNAP4_ENST00000307431.8_Missense_Mutation_p.Q634L|CNTNAP4_ENST00000478060.1_Missense_Mutation_p.Q562L|CNTNAP4_ENST00000469589.1_3'UTR|CNTNAP4_ENST00000377504.4_Missense_Mutation_p.Q586L			Q9C0A0	CNTP4_HUMAN	contactin associated protein-like 4	635	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				cell adhesion (GO:0007155)|regulation of grooming behavior (GO:2000821)|regulation of synaptic transmission, dopaminergic (GO:0032225)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|presynaptic membrane (GO:0042734)				breast(4)|central_nervous_system(1)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(33)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	64						ACCATCATACAGCACAACGGC	0.423																																					p.Q562L		Atlas-SNP	.											.	CNTNAP4	600	.	0			c.A1685T						.						41	36	38					16																	76523604		2198	4300	6498	SO:0001583	missense	85445	exon12			TCATACAGCACAA	AB051550	CCDS10924.1, CCDS10924.2, CCDS73915.1	16q23.1	2008-02-05			ENSG00000152910	ENSG00000152910			18747	protein-coding gene	gene with protein product		610518				12093160	Standard	NM_033401		Approved	CASPR4, KIAA1763	uc010chb.1	Q9C0A0	OTTHUMG00000137617	ENST00000476707.1:c.1913A>T	chr16.hg19:g.76523604A>T	ENSP00000417628:p.Gln638Leu	119.0	0.0		49.0	40.0	NM_138994	E9PFZ6|Q86YZ7	Missense_Mutation	SNP	ENST00000476707.1	hg19		.	.	.	.	.	.	.	.	.	.	A	13.44	2.238303	0.39598	.	.	ENSG00000152910	ENST00000307431;ENST00000377504;ENST00000478060;ENST00000476707	T;T;T;T	0.28895	1.59;1.59;1.59;1.59	4.55	4.55	0.56014	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (3);	.	.	.	.	T	0.25791	0.0628	.	.	.	0.35631	D	0.810189	B;B;B;B	0.16396	0.007;0.017;0.001;0.008	B;B;B;B	0.23275	0.021;0.04;0.015;0.045	T	0.25779	-1.0122	8	0.59425	D	0.04	.	8.717	0.34416	0.9136:0.0:0.0864:0.0	.	562;638;610;635	E9PFZ6;E9PDN6;Q96M80;Q9C0A0	.;.;.;CNTP4_HUMAN	L	634;586;562;638	ENSP00000306893:Q634L;ENSP00000439733:Q586L;ENSP00000418741:Q562L;ENSP00000417628:Q638L	ENSP00000306893:Q634L	Q	+	2	0	CNTNAP4	75081105	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.100000	0.50275	2.045000	0.60652	0.455000	0.32223	CAG	.	.		0.423	CNTNAP4-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000348216.1	NM_033401		T	76523604	A	T	76523604	3	4	344	1	0	0	0	0	1	0	0	0	3651	188	7	4	1967	4	CNTNAP4	16	76523604	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	4566378	76523604	13831149	1128	48491										
PKD1L2	114780	hgsc.bcm.edu	37	chr16	81248727	81248727	+	RNA	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcccgtagacggcatcctggAcctggatgacctgccccaag	12	15	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:81248727A>T	ENST00000525539.1	-	0	535				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						GGCATCCTGGACCTGGATGAC	0.622											OREG0023964	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V179D		Atlas-SNP	.											.	PKD1L2	361	.	0			c.T536A						.						18	24	22					16																	81248727		1956	4136	6092			114780	exon3			TCCTGGACCTGGA	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		chr16.hg19:g.81248727A>T		107.0	0.0	1204	37.0	29.0	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	hg19		.	.	.	.	.	.	.	.	.	.	A	17.34	3.364965	0.61513	.	.	ENSG00000166473	ENST00000337114	T	0.28454	1.61	4.77	4.77	0.60923	D-galactoside/L-rhamnose binding SUEL lectin domain (2);	0.298098	0.29389	N	0.012292	T	0.52158	0.1717	.	.	.	0.45139	D	0.998158	D;D	0.59767	0.986;0.984	P;P	0.60609	0.656;0.877	T	0.58668	-0.7596	9	0.87932	D	0	-2.8932	14.3633	0.66787	1.0:0.0:0.0:0.0	.	179;179	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	D	179	ENSP00000337397:V179D	ENSP00000337397:V179D	V	-	2	0	PKD1L2	79806228	1.000000	0.71417	0.503000	0.27626	0.152000	0.21847	7.666000	0.83877	1.781000	0.52344	0.529000	0.55759	GTC	.	.		0.622	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2			T	81248727	A	T	81248727	1	4	344	0	1	0	0	0	0	0	0	0	11974	275	10	4		4	PKD1L2	16	81248727	RNA	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	4725123	81248727	9106026	1129	48492										
ADAD2	161931	hgsc.bcm.edu	37	chr16	84230327	84230327	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcaccaggcggccagggctgTggggaagccctacctcctgg	15	14	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:84230327T>C	ENST00000315906.5	+	9	1653	c.1601T>C	c.(1600-1602)gTg>gCg	p.V534A	RP11-486L19.2_ENST00000569834.1_RNA|ADAD2_ENST00000268624.3_Missense_Mutation_p.V616A|RP11-486L19.2_ENST00000536986.1_RNA|RP11-486L19.2_ENST00000561900.1_RNA|RP11-486L19.2_ENST00000565643.1_RNA	NM_001145400.1	NP_001138872.1	Q8NCV1	ADAD2_HUMAN	adenosine deaminase domain containing 2	534	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				RNA processing (GO:0006396)		adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(1)	13						GCCAGGGCTGTGGGGAAGCCC	0.667																																					p.V616A		Atlas-SNP	.											ADAD2,NS,carcinoma,0,1	ADAD2	46	.	0			c.T1847C						.						59	61	60					16																	84230327		2200	4300	6500	SO:0001583	missense	161931	exon10			GGGCTGTGGGGAA	AF447586	CCDS10944.1, CCDS45536.1	16q24.1	2007-05-31			ENSG00000140955	ENSG00000140955			30714	protein-coding gene	gene with protein product							Standard	NM_139174		Approved	TENRL, FLJ00337	uc002fhr.2	Q8NCV1	OTTHUMG00000137637	ENST00000315906.5:c.1601T>C	chr16.hg19:g.84230327T>C	ENSP00000325153:p.Val534Ala	58.0	0.0		26.0	24.0	NM_139174	B2RCL6|Q8NA94	Missense_Mutation	SNP	ENST00000315906.5	hg19	CCDS45536.1	.	.	.	.	.	.	.	.	.	.	T	0.106	-1.144585	0.01728	.	.	ENSG00000140955	ENST00000315906;ENST00000268624	D;D	0.93604	-3.25;-3.25	5.27	4.18	0.49190	Adenosine deaminase/editase (2);	0.320112	0.25619	N	0.029435	T	0.81992	0.4940	N	0.08118	0	0.09310	N	1	B;B	0.12630	0.003;0.006	B;B	0.12837	0.007;0.008	T	0.66712	-0.5854	10	0.15066	T	0.55	-17.2826	7.0084	0.24849	0.0:0.1003:0.0:0.8997	.	534;616	Q8NCV1;Q8NCV1-2	ADAD2_HUMAN;.	A	534;616	ENSP00000325153:V534A;ENSP00000268624:V616A	ENSP00000268624:V616A	V	+	2	0	ADAD2	82787828	0.053000	0.20554	0.032000	0.17829	0.307000	0.27823	2.082000	0.41605	1.975000	0.57531	0.477000	0.44152	GTG	.	.		0.667	ADAD2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433385.1	NM_139174		C	84230327	T	C	84230327	3	2	344	1	0	0	0	0	1	0	0	0	232	1696	59	2	1885	2	ADAD2	16	84230327	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2981600	84230327	6124426	1130	48493										
CDH15	1013	hgsc.bcm.edu	37	chr16	89246648	89246648	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gctgggcagcgtcatctacaGcatccagggacccggcgtgg	15	13	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:89246648G>C	ENST00000289746.2	+	3	307	c.242G>C	c.(241-243)aGc>aCc	p.S81T	CDH15_ENST00000521087.1_Intron	NM_004933.2	NP_004924.1	P55291	CAD15_HUMAN	cadherin 15, type 1, M-cadherin (myotubule)	81	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)	caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(80;0.0261)		GTCATCTACAGCATCCAGGGA	0.622																																					p.S81T		Atlas-SNP	.											.	CDH15	54	.	0			c.G242C						.						46	43	44					16																	89246648		2197	4300	6497	SO:0001583	missense	1013	exon3			TCTACAGCATCCA	D83542	CCDS10976.1	16q24.3	2010-01-26	2008-10-30		ENSG00000129910	ENSG00000129910		"Cadherins / Major cadherins"	1754	protein-coding gene	gene with protein product		114019	"cadherin 15, M-cadherin (myotubule)"	CDH3, CDH14		1427864	Standard	NM_004933		Approved		uc002fmt.3	P55291	OTTHUMG00000138045	ENST00000289746.2:c.242G>C	chr16.hg19:g.89246648G>C	ENSP00000289746:p.Ser81Thr	84.0	0.0		37.0	27.0	NM_004933		Missense_Mutation	SNP	ENST00000289746.2	hg19	CCDS10976.1	.	.	.	.	.	.	.	.	.	.	G	17.52	3.408955	0.62399	.	.	ENSG00000129910	ENST00000289746	T	0.54866	0.55	4.77	4.77	0.60923	Cadherin (4);Cadherin-like (1);	0.000000	0.64402	D	0.000004	T	0.45935	0.1367	L	0.53780	1.695	0.35365	D	0.788539	B	0.34255	0.445	B	0.33254	0.16	T	0.52975	-0.8503	10	0.07990	T	0.79	.	16.5579	0.84491	0.0:0.0:1.0:0.0	.	81	P55291	CAD15_HUMAN	T	81	ENSP00000289746:S81T	ENSP00000289746:S81T	S	+	2	0	CDH15	87774149	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	4.784000	0.62411	2.209000	0.71365	0.561000	0.74099	AGC	.	.		0.622	CDH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269920.1	NM_004933		C	89246648	G	C	89246648	3	2	344	1	0	0	0	0	1	0	0	0	3102	971	34	4	252	4	CDH15	16	89246648	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	5016321	89246648	1108105	1131	48494										
ANKRD11	29123	hgsc.bcm.edu	37	chr16	89350278	89350278	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcttctcccgggcccggctgTcccgcctcctctccttgctg	10	20	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr16:89350278T>C	ENST00000301030.4	-	9	3132	c.2672A>G	c.(2671-2673)gAc>gGc	p.D891G	ANKRD11_ENST00000378330.2_Missense_Mutation_p.D891G	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	891	Lys-rich.				bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		GGCCCGGCTGTCCCGCCTCCT	0.557																																					p.D891G		Atlas-SNP	.											.	ANKRD11	195	.	0			c.A2672G						.						59	64	62					16																	89350278		2198	4300	6498	SO:0001583	missense	29123	exon9			CGGCTGTCCCGCC	AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"Ankyrin repeat domain containing"	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.2672A>G	chr16.hg19:g.89350278T>C	ENSP00000301030:p.Asp891Gly	79.0	0.0		41.0	38.0	NM_001256183	Q6NTG1|Q6QMF8	Missense_Mutation	SNP	ENST00000301030.4	hg19	CCDS32513.1	.	.	.	.	.	.	.	.	.	.	T	7.481	0.648710	0.14516	.	.	ENSG00000167522	ENST00000301030;ENST00000378330;ENST00000330736	T;T	0.44881	0.91;0.91	5.44	5.44	0.79542	.	0.385891	0.25329	N	0.031445	T	0.37758	0.1015	L	0.47716	1.5	0.80722	D	1	P;P	0.38504	0.634;0.501	B;B	0.35971	0.215;0.107	T	0.19712	-1.0297	10	0.37606	T	0.19	.	15.1653	0.72818	0.0:0.0:0.0:1.0	.	510;891	Q7Z5E5;Q6UB99	.;ANR11_HUMAN	G	891;891;510	ENSP00000301030:D891G;ENSP00000367581:D891G	ENSP00000301030:D891G	D	-	2	0	ANKRD11	87877779	1.000000	0.71417	0.255000	0.24374	0.009000	0.06853	5.840000	0.69402	2.058000	0.61347	0.482000	0.46254	GAC	.	.		0.557	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		C	89350278	T	C	89350278	3	2	344	1	0	0	0	0	1	0	0	0	639	1667	58	2	5339	2	ANKRD11	16	89350278	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	103630	89350278	1004475	1132	48495										
SCARF1	8578	hgsc.bcm.edu	37	chr17	1538573	1538573	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgggggccgccggtggccagTggctgaatccccgggactgg	19	12	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:1538573T>G	ENST00000263071.4	-	11	2021	c.1972A>C	c.(1972-1974)Act>Cct	p.T658P	SCARF1_ENST00000348987.3_Missense_Mutation_p.T572P|SCARF1_ENST00000571272.1_3'UTR	NM_003693.2|NM_145350.1	NP_003684.2|NP_663325.1	Q14162	SREC_HUMAN	scavenger receptor class F, member 1	658	Gly-rich.				cell adhesion (GO:0007155)|cholesterol catabolic process (GO:0006707)|dendrite development (GO:0016358)|neuron remodeling (GO:0016322)|positive regulation of axon regeneration (GO:0048680)|positive regulation of neuron projection development (GO:0010976)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	endocytic vesicle membrane (GO:0030666)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	low-density lipoprotein particle binding (GO:0030169)|scavenger receptor activity (GO:0005044)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(3)|kidney(2)|lung(9)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		CGGTGGCCAGTGGCTGAATCC	0.687																																					p.T658P		Atlas-SNP	.											.	SCARF1	46	.	0			c.A1972C						.						15	18	17					17																	1538573		2058	4080	6138	SO:0001583	missense	8578	exon11			GGCCAGTGGCTGA	D63483	CCDS11007.1, CCDS45564.1	17p13.3	2008-07-18			ENSG00000074660	ENSG00000074660			16820	protein-coding gene	gene with protein product	"scavenger receptor expressed by endothelial cells", "acetyl LDL receptor"	607873				9395444, 8590280	Standard	NM_003693		Approved	SREC, KIAA0149	uc002fsz.2	Q14162	OTTHUMG00000090555	ENST00000263071.4:c.1972A>C	chr17.hg19:g.1538573T>G	ENSP00000263071:p.Thr658Pro	71.0	0.0		46.0	39.0	NM_003693	A8MQ05|O43701|Q8NHD2|Q8NHD3|Q8NHD4|Q8NHD5	Missense_Mutation	SNP	ENST00000263071.4	hg19	CCDS11007.1	.	.	.	.	.	.	.	.	.	.	T	7.944	0.743414	0.15642	.	.	ENSG00000074660	ENST00000263071;ENST00000348987	T;T	0.35236	1.32;1.32	5.0	-3.74	0.04385	.	1.677830	0.03425	N	0.206831	T	0.32041	0.0816	L	0.51422	1.61	0.09310	N	1	P;P	0.41265	0.744;0.682	B;B	0.40825	0.341;0.163	T	0.32534	-0.9903	10	0.23891	T	0.37	8.1697	7.8658	0.29537	0.1276:0.5076:0.0:0.3648	.	572;658	Q14162-2;Q14162	.;SREC_HUMAN	P	658;572	ENSP00000263071:T658P;ENSP00000323964:T572P	ENSP00000263071:T658P	T	-	1	0	SCARF1	1485323	0.000000	0.05858	0.001000	0.08648	0.330000	0.28571	-0.588000	0.05774	-0.769000	0.04620	0.454000	0.30748	ACT	.	.		0.687	SCARF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207081.4	NM_003693		G	1538573	T	G	1538573	3	3	344	1	0	0	0	0	1	0	0	0	13898	1696	59	5	524	5	SCARF1	17	1538573	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10		1538573	79656637	1133	48496										
OR1D2	4991	hgsc.bcm.edu	37	chr17	2996103	2996103	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cagtgaaggagaggttggccAggaagaagtacacgggggtg	19	5	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:2996103A>T	ENST00000331459.1	-	1	187	c.188T>A	c.(187-189)cTg>cAg	p.L63Q		NM_002548.2	NP_002539.2	P34982	OR1D2_HUMAN	olfactory receptor, family 1, subfamily D, member 2	63					cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|G-protein coupled receptor signaling pathway (GO:0007186)|protein import into nucleus, translocation (GO:0000060)|sensory perception of smell (GO:0007608)|single fertilization (GO:0007338)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(2)|large_intestine(2)|lung(10)|ovary(1)	15						GAGGTTGGCCAGGAAGAAGTA	0.537																																					p.L63Q		Atlas-SNP	.											.	OR1D2	39	.	0			c.T188A						.						153	150	151					17																	2996103		2203	4300	6503	SO:0001583	missense	4991	exon1			TTGGCCAGGAAGA	U04678	CCDS11019.1	17p13.3	2012-08-09			ENSG00000184166	ENSG00000184166		"GPCR / Class A : Olfactory receptors"	8183	protein-coding gene	gene with protein product		164342		OLFR1		1370859, 1840504	Standard	NM_002548		Approved	OR17-4	uc010vrb.2	P34982	OTTHUMG00000090619	ENST00000331459.1:c.188T>A	chr17.hg19:g.2996103A>T	ENSP00000327585:p.Leu63Gln	174.0	0.0		110.0	91.0	NM_002548	Q6IFL8|Q96RA4|Q9UM78	Missense_Mutation	SNP	ENST00000331459.1	hg19	CCDS11019.1	.	.	.	.	.	.	.	.	.	.	a	18.73	3.685733	0.68157	.	.	ENSG00000184166	ENST00000331459	T	0.14893	2.47	3.0	3.0	0.34707	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.58581	0.2132	H	0.99659	4.685	0.32194	N	0.578732	D	0.69078	0.997	D	0.67548	0.952	T	0.74705	-0.3575	9	0.87932	D	0	.	10.0639	0.42292	1.0:0.0:0.0:0.0	.	63	P34982	OR1D2_HUMAN	Q	63	ENSP00000327585:L63Q	ENSP00000327585:L63Q	L	-	2	0	OR1D2	2942853	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.643000	0.91040	1.221000	0.43506	0.443000	0.29094	CTG	.	.		0.537	OR1D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207207.1	NM_002548		T	2996103	A	T	2996103	3	4	344	1	0	0	0	0	1	0	0	0	10962	188	7	4	753	4	OR1D2	17	2996103	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1457530	2996103	78199107	1134	48497										
OR1A2	26189	hgsc.bcm.edu	37	chr17	3100889	3100889	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcagcaagaacagaataatgTcttctttgtgatttttttgt	7	5	3	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:3100889T>A	ENST00000381951.1	+	1	77	c.77T>A	c.(76-78)gTc>gAc	p.V26D		NM_012352.1	NP_036484.1	Q9Y585	OR1A2_HUMAN	olfactory receptor, family 1, subfamily A, member 2	26					positive regulation of cytokinesis (GO:0032467)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|large_intestine(2)|lung(5)|skin(4)|stomach(2)	18						CAGAATAATGTCTTCTTTGTG	0.418																																					p.V26D		Atlas-SNP	.											.	OR1A2	52	.	0			c.T77A						.						178	161	167					17																	3100889		2203	4300	6503	SO:0001583	missense	26189	exon1			ATAATGTCTTCTT	AF155225	CCDS11021.1	17p13.3	2012-08-09			ENSG00000172150	ENSG00000172150		"GPCR / Class A : Olfactory receptors"	8180	protein-coding gene	gene with protein product						10673334	Standard	NM_012352		Approved	OR17-6	uc002fvd.1	Q9Y585	OTTHUMG00000090638	ENST00000381951.1:c.77T>A	chr17.hg19:g.3100889T>A	ENSP00000371377:p.Val26Asp	96.0	0.0		49.0	36.0	NM_012352	Q3KPH3|Q6IFM0|Q6NTD8|Q96R86	Missense_Mutation	SNP	ENST00000381951.1	hg19	CCDS11021.1	.	.	.	.	.	.	.	.	.	.	T	6.778	0.512487	0.12944	.	.	ENSG00000172150	ENST00000381951	T	0.03689	3.84	3.68	3.68	0.42216	.	0.482987	0.17512	N	0.171591	T	0.09024	0.0223	M	0.83692	2.655	0.20764	N	0.999858	P	0.41041	0.736	B	0.41271	0.352	T	0.07328	-1.0778	10	0.87932	D	0	.	11.5786	0.50879	0.0:0.0:0.0:1.0	.	26	Q9Y585	OR1A2_HUMAN	D	26	ENSP00000371377:V26D	ENSP00000371377:V26D	V	+	2	0	OR1A2	3047639	0.001000	0.12720	0.700000	0.30305	0.019000	0.09904	1.042000	0.30303	1.672000	0.50884	0.491000	0.48974	GTC	.	.		0.418	OR1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207293.1	NM_012352		A	3100889	T	A	3100889	3	1	344	1	0	0	0	0	1	0	0	0	10959	1667	58	4	79	4	OR1A2	17	3100889	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	104786	3100889	78094321	1135	48498										
SLC2A4	6517	hgsc.bcm.edu	37	chr17	7189182	7189182	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gctgtggctggtttctccaaCtggacgagcaacttcatcat	10	11	3	0	rs375934415		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:7189182C>T	ENST00000317370.8	+	10	1549	c.1281C>T	c.(1279-1281)aaC>aaT	p.N427N	SLC2A4_ENST00000571308.1_Silent_p.N427N|SLC2A4_ENST00000424875.2_Silent_p.N417N|RP1-4G17.2_ENST00000576271.1_RNA	NM_001042.2	NP_001033.1	P14672	GTR4_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 4	427					amylopectin biosynthetic process (GO:0010021)|brown fat cell differentiation (GO:0050873)|carbohydrate metabolic process (GO:0005975)|cellular response to insulin stimulus (GO:0032869)|cellular response to osmotic stress (GO:0071470)|glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|membrane organization (GO:0061024)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|endomembrane system (GO:0012505)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|insulin-responsive compartment (GO:0032593)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|multivesicular body (GO:0005771)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|trans-Golgi network transport vesicle (GO:0030140)|vesicle membrane (GO:0012506)	D-glucose transmembrane transporter activity (GO:0055056)|glucose transmembrane transporter activity (GO:0005355)			breast(1)|endometrium(3)|large_intestine(7)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	17						GTTTCTCCAACTGGACGAGCA	0.607																																					p.N427N		Atlas-SNP	.											.	SLC2A4	44	.	0			c.C1281T						.	C		0,4406		0,0,2203	79	68	72		1281	5.1	1	17		72	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SLC2A4	NM_001042.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		427/510	7189182	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	6517	exon10			CTCCAACTGGACG	M20747	CCDS11097.1	17p13	2013-05-22			ENSG00000181856	ENSG00000181856		"Solute carriers"	11009	protein-coding gene	gene with protein product		138190		GLUT4			Standard	NM_001042		Approved		uc002gfp.3	P14672	OTTHUMG00000102181	ENST00000317370.8:c.1281C>T	chr17.hg19:g.7189182C>T		111.0	0.0		50.0	44.0	NM_001042	Q05BQ3|Q14CX2	Silent	SNP	ENST00000317370.8	hg19	CCDS11097.1																																																																																			.	.		0.607	SLC2A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220031.3			T	7189182	C	T	7189182	2	4	344	1	0	0	0	0	0	0	0	1	14561	564	20	3		3	SLC2A4	17	7189182	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	4088293	7189182	74006028	1136	48499										
TP53	7157	hgsc.bcm.edu	37	chr17	7578235	7578235	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aagtgtttctgtcatccaaaTactccacacgcaaatttcct	4	12	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:7578235T>C	ENST00000269305.4	-	6	803	c.614A>G	c.(613-615)tAt>tGt	p.Y205C	TP53_ENST00000420246.2_Missense_Mutation_p.Y205C|TP53_ENST00000455263.2_Missense_Mutation_p.Y205C|TP53_ENST00000445888.2_Missense_Mutation_p.Y205C|TP53_ENST00000574684.1_Intron|TP53_ENST00000413465.2_Missense_Mutation_p.Y205C|TP53_ENST00000359597.4_Missense_Mutation_p.Y205C	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	205	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		Y -> C (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1459726}.|Y -> D (in sporadic cancers; somatic mutation).|Y -> F (in sporadic cancers; somatic mutation).|Y -> H (in sporadic cancers; somatic mutation).|Y -> N (in sporadic cancers; somatic mutation).|Y -> S (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Y205C(68)|p.Y205S(14)|p.Y205F(8)|p.0?(8)|p.Y112C(5)|p.?(5)|p.Y73C(5)|p.Y73S(1)|p.Y112S(1)|p.E204fs*39(1)|p.E204_N210delEYLDDRN(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GTCATCCAAATACTCCACACG	0.542		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.Y205C	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,temporoparietal,glioma,0,24	TP53	33396	.	117	Substitution - Missense(102)|Whole gene deletion(8)|Unknown(5)|Deletion - In frame(1)|Deletion - Frameshift(1)	lung(20)|upper_aerodigestive_tract(19)|central_nervous_system(10)|large_intestine(9)|biliary_tract(8)|breast(6)|ovary(6)|haematopoietic_and_lymphoid_tissue(5)|endometrium(5)|urinary_tract(5)|bone(5)|soft_tissue(4)|oesophagus(4)|stomach(3)|liver(3)|pancreas(2)|vulva(1)|skin(1)|prostate(1)	c.A614G						.						136	121	126					17																	7578235		2203	4300	6503	SO:0001583	missense	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	TCCAAATACTCCA	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.614A>G	chr17.hg19:g.7578235T>C	ENSP00000269305:p.Tyr205Cys	133.0	0.0		73.0	60.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	17.85	3.490024	0.64074	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99872	-7.36;-7.36;-7.36;-7.36;-7.36;-7.36;-7.36;-7.36	5.41	4.33	0.51752	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99840	0.9927	M	0.88906	2.99	0.58432	D	0.999999	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.91635	0.995;0.998;0.995;0.997;0.999;0.997;0.996	D	0.97320	0.9943	10	0.87932	D	0	-5.8058	9.707	0.40222	0.0:0.0827:0.0:0.9173	.	166;205;205;112;205;205;205	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	C	205;205;205;205;205;205;194;112;73;112;73	ENSP00000410739:Y205C;ENSP00000352610:Y205C;ENSP00000269305:Y205C;ENSP00000398846:Y205C;ENSP00000391127:Y205C;ENSP00000391478:Y205C;ENSP00000425104:Y73C;ENSP00000423862:Y112C	ENSP00000269305:Y205C	Y	-	2	0	TP53	7518960	1.000000	0.71417	0.137000	0.22149	0.045000	0.14185	7.996000	0.88334	1.001000	0.39076	-0.256000	0.11100	TAT	.	.		0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7578235	T	C	7578235	3	2	344	1	0	0	0	0	1	0	0	0	16396	1406	49	2	680	2	TP53	17	7578235	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	389053	7578235	73616975	1137	48500										
MFSD6L	162387	hgsc.bcm.edu	37	chr17	8700730	8700730	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	caagccagtcctgttctgtcCcctgctcagagtcactggtg	10	14	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:8700730C>T	ENST00000329805.4	-	1	1937	c.1709G>A	c.(1708-1710)gGg>gAg	p.G570E		NM_152599.3	NP_689812.3	Q8IWD5	MFS6L_HUMAN	major facilitator superfamily domain containing 6-like	570						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(7)|skin(4)	17						CTGTTCTGTCCCCTGCTCAGA	0.547																																					p.G570E		Atlas-SNP	.											.	MFSD6L	46	.	0			c.G1709A						.						103	89	93					17																	8700730		2203	4300	6503	SO:0001583	missense	162387	exon1			TCTGTCCCCTGCT	AK093092	CCDS11146.1	17p13.1	2014-05-30			ENSG00000185156	ENSG00000185156			26656	protein-coding gene	gene with protein product							Standard	NM_152599		Approved	FLJ35773	uc002glp.2	Q8IWD5	OTTHUMG00000178584	ENST00000329805.4:c.1709G>A	chr17.hg19:g.8700730C>T	ENSP00000330051:p.Gly570Glu	45.0	0.0		28.0	27.0	NM_152599	Q6YL34|Q8NA76	Missense_Mutation	SNP	ENST00000329805.4	hg19	CCDS11146.1	.	.	.	.	.	.	.	.	.	.	C	2.889	-0.229988	0.06022	.	.	ENSG00000185156	ENST00000329805	D	0.95137	-3.62	5.03	3.07	0.35406	.	0.325810	0.27826	N	0.017693	D	0.84465	0.5478	L	0.27053	0.805	0.34810	D	0.737653	P	0.34864	0.473	B	0.24848	0.056	T	0.81885	-0.0727	10	0.02654	T	1	-13.8239	7.7331	0.28797	0.0:0.7419:0.0:0.2581	.	570	Q8IWD5	MFS6L_HUMAN	E	570	ENSP00000330051:G570E	ENSP00000330051:G570E	G	-	2	0	MFSD6L	8641455	0.997000	0.39634	0.646000	0.29493	0.891000	0.51852	3.094000	0.50227	0.722000	0.32252	0.557000	0.71058	GGG	.	.		0.547	MFSD6L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442554.1	NM_152599		T	8700730	C	T	8700730	3	4	344	1	0	0	0	0	1	0	0	0	9545	623	22	3	55	3	MFSD6L	17	8700730	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1122495	8700730	72494480	1138	48501										
DHRS7C	201140	hgsc.bcm.edu	37	chr17	9674809	9674809	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atttggcctcctgcagttacCcctcctccgggacattgagc	9	15	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:9674809C>A	ENST00000330255.5	-	6	947	c.935G>T	c.(934-936)gGg>gTg	p.G312V	DHRS7C_ENST00000571134.1_Missense_Mutation_p.G311V	NM_001105571.2|NM_001220493.1	NP_001099041.1|NP_001207422.1	A6NNS2	DRS7C_HUMAN	dehydrogenase/reductase (SDR family) member 7C	312					regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	extracellular region (GO:0005576)|longitudinal sarcoplasmic reticulum (GO:0014801)|sarcoplasmic reticulum membrane (GO:0033017)	retinol dehydrogenase activity (GO:0004745)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)	15						CTGCAGTTACCCCTCCTCCGG	0.602																																					p.G312V		Atlas-SNP	.											.	DHRS7C	34	.	0			c.G935T						.						34	38	37					17																	9674809		1984	4147	6131	SO:0001583	missense	201140	exon6			AGTTACCCCTCCT		CCDS56020.1, CCDS58517.1	17p13.1	2011-09-20				ENSG00000184544		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	32423	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 32C, member 2"					19027726	Standard	NM_001105571		Approved	SDR32C2	uc010vvb.2	A6NNS2		ENST00000330255.5:c.935G>T	chr17.hg19:g.9674809C>A	ENSP00000327975:p.Gly312Val	42.0	0.0		27.0	17.0	NM_001220493	B7ZW74|B9EJH3	Missense_Mutation	SNP	ENST00000330255.5	hg19	CCDS56020.1	.	.	.	.	.	.	.	.	.	.	C	3.517	-0.098582	0.07010	.	.	ENSG00000184544	ENST00000330255	D	0.86956	-2.19	5.5	3.48	0.39840	.	.	.	.	.	T	0.72606	0.3481	N	0.08118	0	0.35704	D	0.815886	B;B	0.18166	0.026;0.026	B;B	0.14023	0.01;0.01	T	0.70368	-0.4891	9	0.87932	D	0	.	6.6553	0.22984	0.0:0.6418:0.0:0.3582	.	312;308	A6NNS2;B9EJH3	DRS7C_HUMAN;.	V	312	ENSP00000327975:G312V	ENSP00000327975:G312V	G	-	2	0	DHRS7C	9615534	0.002000	0.14202	0.506000	0.27664	0.128000	0.20619	0.325000	0.19628	0.822000	0.34565	0.655000	0.94253	GGG	.	.		0.602	DHRS7C-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439863.1	XM_113912		A	9674809	C	A	9674809	3	1	344	1	0	0	0	0	1	0	0	0	4499	623	22	3	7	3	DHRS7C	17	9674809	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	974079	9674809	71520401	1139	48502										
GLP2R	9340	hgsc.bcm.edu	37	chr17	9774103	9774103	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgaaaattctcaagcttctcAtttctaagctcaaagctcat	4	10	5	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:9774103A>G	ENST00000262441.5	+	10	1609	c.1096A>G	c.(1096-1098)Att>Gtt	p.I366V	GLP2R_ENST00000574745.1_Missense_Mutation_p.I186V	NM_004246.1	NP_004237.1	O95838	GLP2R_HUMAN	glucagon-like peptide 2 receptor	366					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|positive regulation of cell proliferation (GO:0008284)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|glucagon receptor activity (GO:0004967)			endometrium(4)|large_intestine(7)|lung(22)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	44					Glucagon recombinant(DB00040)|Teduglutide(DB08900)	CAAGCTTCTCATTTCTAAGCT	0.388																																					p.I366V		Atlas-SNP	.											.	GLP2R	90	.	0			c.A1096G						.						176	188	184					17																	9774103		2203	4299	6502	SO:0001583	missense	9340	exon10			CTTCTCATTTCTA	AF105367	CCDS11150.1	17p13.3	2012-08-10			ENSG00000065325	ENSG00000065325		"GPCR / Class B : Glucagon receptors"	4325	protein-coding gene	gene with protein product		603659				9990065	Standard	NM_004246		Approved		uc002gmd.1	O95838	OTTHUMG00000130269	ENST00000262441.5:c.1096A>G	chr17.hg19:g.9774103A>G	ENSP00000262441:p.Ile366Val	134.0	0.0		48.0	34.0	NM_004246	Q4VAT3	Missense_Mutation	SNP	ENST00000262441.5	hg19	CCDS11150.1	.	.	.	.	.	.	.	.	.	.	A	11.12	1.545543	0.27652	.	.	ENSG00000065325	ENST00000396206;ENST00000262441	T	0.36878	1.23	6.17	3.98	0.46160	GPCR, family 2-like (1);	0.000000	0.40469	N	0.001091	T	0.15349	0.0370	N	0.14661	0.345	0.25154	N	0.990402	B	0.06786	0.001	B	0.13407	0.009	T	0.32771	-0.9894	10	0.02654	T	1	.	4.8724	0.13639	0.6841:0.1579:0.158:0.0	.	366	O95838	GLP2R_HUMAN	V	366	ENSP00000262441:I366V	ENSP00000262441:I366V	I	+	1	0	GLP2R	9714828	0.999000	0.42202	1.000000	0.80357	0.995000	0.86356	1.538000	0.36094	1.142000	0.42291	0.533000	0.62120	ATT	.	.		0.388	GLP2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252601.4			G	9774103	A	G	9774103	3	3	344	1	0	0	0	0	1	0	0	0	6461	217	8	2	1134	2	GLP2R	17	9774103	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	99294	9774103	71421107	1140	48503										
MYH1	4619	hgsc.bcm.edu	37	chr17	10416941	10416941	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tttaggaggtcctgttactcAcatgtttcaatatcagcaga	8	8	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:10416941A>T	ENST00000226207.5	-	9	900		c.e9+1		RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult						muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						CCTGTTACTCACATGTTTCAA	0.408																																					.		Atlas-SNP	.											.	MYH1	403	.	0			c.805+2T>A						.						107	105	106					17																	10416941		2203	4300	6503	SO:0001630	splice_region_variant	4619	exon10			TTACTCACATGTT		CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"Myosins / Myosin superfamily : Class II"	7567	protein-coding gene	gene with protein product	"myosin heavy chain IIx/d"	160730	"myosin, heavy polypeptide 1, skeletal muscle, adult"			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.805+1T>A	chr17.hg19:g.10416941A>T		106.0	0.0		44.0	39.0	NM_005963	Q14CA4|Q9Y622	Splice_Site	SNP	ENST00000226207.5	hg19	CCDS11155.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.492895	0.84962	.	.	ENSG00000109061	ENST00000226207;ENST00000379814	.	.	.	5.33	5.33	0.75918	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.5967	0.76587	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MYH1	10357666	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.247000	0.72411	2.138000	0.66242	0.459000	0.35465	.	.	.		0.408	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963	Intron	T	10416941	A	T	10416941	5	4	344	1	0	0	0	0	0	0	1	0	10038	173	6	4	5140	4	MYH1	17	10416941	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	642838	10416941	70778269	1141	48504										
MYH2	4620	hgsc.bcm.edu	37	chr17	10432930	10432930	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tagctttggtcagggtgttgActttgtcctcctctgcctgc	11	11	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:10432930A>G	ENST00000245503.5	-	24	3452	c.3068T>C	c.(3067-3069)gTc>gCc	p.V1023A	MYH2_ENST00000397183.2_Missense_Mutation_p.V1023A|RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA|MYH2_ENST00000532183.2_Intron|RP11-799N11.1_ENST00000581304.1_RNA	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	1023					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|plasma membrane repair (GO:0001778)|response to activity (GO:0014823)	A band (GO:0031672)|actomyosin contractile ring (GO:0005826)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|protein complex (GO:0043234)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(99)|ovary(6)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(4)	176						CAGGGTGTTGACTTTGTCCTC	0.468																																					p.V1023A		Atlas-SNP	.											.	MYH2	390	.	0			c.T3068C						.						202	192	196					17																	10432930		2203	4297	6500	SO:0001583	missense	4620	exon24			GTGTTGACTTTGT		CCDS11156.1	17p13.1	2014-02-04	2006-09-29		ENSG00000125414	ENSG00000125414		"Myosins / Myosin superfamily : Class II"	7572	protein-coding gene	gene with protein product		160740	"myosin, heavy polypeptide 2, skeletal muscle, adult", "inclusion body myopathy 3, autosomal dominant"	IBM3		7545970, 11889243	Standard	NM_001100112		Approved	MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A	uc010coi.3	Q9UKX2	OTTHUMG00000130363	ENST00000245503.5:c.3068T>C	chr17.hg19:g.10432930A>G	ENSP00000245503:p.Val1023Ala	128.0	0.0		52.0	40.0	NM_017534	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Missense_Mutation	SNP	ENST00000245503.5	hg19	CCDS11156.1	.	.	.	.	.	.	.	.	.	.	A	16.37	3.104523	0.56291	.	.	ENSG00000125414	ENST00000245503;ENST00000397183	D;D	0.91011	-2.77;-2.77	5.24	5.24	0.73138	.	0.000000	0.35466	U	0.003193	D	0.88537	0.6463	L	0.54323	1.7	0.58432	D	0.999993	P	0.37663	0.604	B	0.36845	0.234	D	0.89171	0.3537	10	0.56958	D	0.05	.	15.3006	0.73949	1.0:0.0:0.0:0.0	.	1023	Q9UKX2	MYH2_HUMAN	A	1023	ENSP00000245503:V1023A;ENSP00000380367:V1023A	ENSP00000245503:V1023A	V	-	2	0	MYH2	10373655	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.713000	0.91408	2.194000	0.70268	0.482000	0.46254	GTC	.	.		0.468	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534		G	10432930	A	G	10432930	3	3	344	1	0	0	0	0	1	0	0	0	10044	275	10	2	2825	2	MYH2	17	10432930	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	15989	10432930	70762280	1142	48505										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11809030	11809030	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acgtggtgggaagagccctaGattttgcaacctcatttgaa	11	8	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:11809030G>A	ENST00000262442.4	+	61	11721	c.11653G>A	c.(11653-11655)Gat>Aat	p.D3885N	DNAH9_ENST00000608377.1_Missense_Mutation_p.D197N|DNAH9_ENST00000454412.2_Missense_Mutation_p.D3885N|DNAH9_ENST00000396001.2_3'UTR	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	3885	AAA 6. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		AAGAGCCCTAGATTTTGCAAC	0.428																																					p.D3885N		Atlas-SNP	.											.	DNAH9	695	.	0			c.G11653A						.						91	91	91					17																	11809030		2203	4300	6503	SO:0001583	missense	1770	exon61			GCCCTAGATTTTG	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.11653G>A	chr17.hg19:g.11809030G>A	ENSP00000262442:p.Asp3885Asn	84.0	0.0		39.0	32.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	hg19	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.745864	0.89663	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703;ENST00000396001;ENST00000361801	T;T;T	0.10960	2.82;2.82;2.82	4.81	4.81	0.61882	Dynein heavy chain (1);	0.143656	0.64402	N	0.000009	T	0.21347	0.0514	L	0.43598	1.365	0.80722	D	1	P;P	0.41569	0.566;0.755	B;P	0.53809	0.285;0.735	T	0.00704	-1.1602	10	0.29301	T	0.29	.	18.4172	0.90574	0.0:0.0:1.0:0.0	.	238;3885	B7Z7H0;Q9NYC9	.;DYH9_HUMAN	N	3885;3885;2467;197;238	ENSP00000262442:D3885N;ENSP00000414874:D3885N;ENSP00000379323:D197N	ENSP00000262442:D3885N	D	+	1	0	DNAH9	11749755	1.000000	0.71417	0.969000	0.41365	0.478000	0.33099	7.711000	0.84669	2.665000	0.90641	0.655000	0.94253	GAT	.	.		0.428	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		A	11809030	G	A	11809030	3	1	344	1	0	0	0	0	1	0	0	0	4610	942	33	3	11895	3	DNAH9	17	11809030	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1376100	11809030	69386180	1143	48506										
CENPV	201161	hgsc.bcm.edu	37	chr17	16253335	16253335	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctgtgtgcttcaccaggcccTggtattcactaaatgaaaca	8	11	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:16253335T>C	ENST00000299736.4	-	2	481	c.419A>G	c.(418-420)cAg>cGg	p.Q140R	CENPV_ENST00000476243.1_5'UTR	NM_181716.2	NP_859067.2	Q7Z7K6	CENPV_HUMAN	centromere protein V	143					ameboidal cell migration (GO:0001667)|centromere complex assembly (GO:0034508)|mitotic nuclear division (GO:0007067)|pericentric heterochromatin assembly (GO:0031508)|positive regulation of cytokinesis (GO:0032467)|regulation of chromosome organization (GO:0033044)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|spindle midzone (GO:0051233)	carbon-sulfur lyase activity (GO:0016846)			endometrium(1)|large_intestine(2)	3						CACCAGGCCCTGGTATTCACT	0.413																																					p.Q140R		Atlas-SNP	.											.	CENPV	14	.	0			c.A419G						.						55	59	58					17																	16253335		2203	4300	6503	SO:0001583	missense	201161	exon2			AGGCCCTGGTATT	AF514992	CCDS32575.1	17p11.2	2013-11-05	2008-10-29	2008-10-29	ENSG00000166582	ENSG00000166582			29920	protein-coding gene	gene with protein product		608139	"proline rich 6"	PRR6		12196509, 18772885	Standard	NM_181716		Approved	p30, CENP-V	uc002gpw.3	Q7Z7K6	OTTHUMG00000059345	ENST00000299736.4:c.419A>G	chr17.hg19:g.16253335T>C	ENSP00000299736:p.Gln140Arg	302.0	1.0		132.0	111.0	NM_181716	B2RPK2|Q3L8N5|Q8NFH6	Missense_Mutation	SNP	ENST00000299736.4	hg19	CCDS32575.1	.	.	.	.	.	.	.	.	.	.	T	14.93	2.683120	0.47991	.	.	ENSG00000166582	ENST00000299736	.	.	.	5.17	5.17	0.71159	.	0.436886	0.24879	N	0.034878	T	0.23806	0.0576	N	0.08118	0	0.28623	N	0.908075	B	0.29188	0.236	B	0.23716	0.048	T	0.15235	-1.0444	9	0.42905	T	0.14	.	13.2422	0.60004	0.0:0.0:0.0:1.0	.	140	Q7Z7K6-3	.	R	140	.	ENSP00000299736:Q140R	Q	-	2	0	CENPV	16194060	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.333000	0.43912	2.078000	0.62432	0.482000	0.46254	CAG	.	.		0.413	CENPV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131877.1	NM_181716		C	16253335	T	C	16253335	3	2	344	1	0	0	0	0	1	0	0	0	3245	1580	55	2	415	2	CENPV	17	16253335	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	4444305	16253335	64941875	1144	48507										
TRPV2	51393	hgsc.bcm.edu	37	chr17	16332223	16332223	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcttgtgtctgcgctggtgcTgggctggctgaacctgcttt	15	10	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:16332223T>A	ENST00000338560.7	+	10	1913	c.1514T>A	c.(1513-1515)cTg>cAg	p.L505Q	TRPV2_ENST00000577397.1_Missense_Mutation_p.L75Q|AC093484.4_ENST00000441875.1_RNA|TRPV2_ENST00000583241.1_3'UTR	NM_016113.4	NP_057197.2	Q9Y5S1	TRPV2_HUMAN	transient receptor potential cation channel, subfamily V, member 2	505					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|positive regulation of axon extension (GO:0045773)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|response to temperature stimulus (GO:0009266)|sensory perception (GO:0007600)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axonal growth cone (GO:0044295)|cell body (GO:0044297)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|growth cone membrane (GO:0032584)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|ion channel activity (GO:0005216)|ion transmembrane transporter activity (GO:0015075)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|stomach(3)	28				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		GCGCTGGTGCTGGGCTGGCTG	0.597																																					p.L505Q		Atlas-SNP	.											.	TRPV2	74	.	0			c.T1514A						.						140	124	129					17																	16332223		2203	4300	6503	SO:0001583	missense	51393	exon10			TGGTGCTGGGCTG	AF129112	CCDS32576.1	17p11.2	2013-01-10			ENSG00000187688	ENSG00000187688		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	18082	protein-coding gene	gene with protein product		606676				10201375, 16382100	Standard	NM_016113		Approved	VRL, VRL-1, VRL1	uc002gpy.3	Q9Y5S1	OTTHUMG00000058989	ENST00000338560.7:c.1514T>A	chr17.hg19:g.16332223T>A	ENSP00000342222:p.Leu505Gln	47.0	0.0		28.0	24.0	NM_016113	A6NML2|A8K0Z0|Q9Y670	Missense_Mutation	SNP	ENST00000338560.7	hg19	CCDS32576.1	.	.	.	.	.	.	.	.	.	.	T	15.93	2.976798	0.53720	.	.	ENSG00000187688	ENST00000338560	D	0.99113	-5.44	5.58	5.58	0.84498	Ion transport (1);	0.139205	0.49305	D	0.000157	D	0.99287	0.9751	M	0.85462	2.755	0.58432	D	0.999996	D	0.89917	1.0	D	0.85130	0.997	D	0.99180	1.0867	10	0.72032	D	0.01	-12.8692	14.9328	0.70929	0.0:0.0:0.0:1.0	.	505	Q9Y5S1	TRPV2_HUMAN	Q	505	ENSP00000342222:L505Q	ENSP00000342222:L505Q	L	+	2	0	TRPV2	16272948	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.559000	0.82265	2.131000	0.65755	0.533000	0.62120	CTG	.	.		0.597	TRPV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130464.2	NM_016113		A	16332223	T	A	16332223	3	1	344	1	0	0	0	0	1	0	0	0	16611	1580	55	4	1548	4	TRPV2	17	16332223	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	78888	16332223	64862987	1145	48508										
ZNF287	57336	hgsc.bcm.edu	37	chr17	16455335	16455335	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctaaaatccttatcacattcAttacatttatagggtctctc	3	10	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:16455335A>T	ENST00000395824.1	-	6	2738	c.2121T>A	c.(2119-2121)aaT>aaA	p.N707K	ZNF287_ENST00000395825.3_Missense_Mutation_p.N707K			Q9HBT7	ZN287_HUMAN	zinc finger protein 287	700					positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(5)|prostate(1)|urinary_tract(1)	20				UCEC - Uterine corpus endometrioid carcinoma (92;0.083)		TATCACATTCATTACATTTAT	0.368																																					p.N707K		Atlas-SNP	.											.	ZNF287	60	.	0			c.T2121A						.						143	144	144					17																	16455335		2203	4300	6503	SO:0001583	missense	57336	exon6			ACATTCATTACAT	AF217227	CCDS11179.2	17p11.2	2013-01-09			ENSG00000141040	ENSG00000141040		"Zinc fingers, C2H2-type", "-", "-", "-"	13502	protein-coding gene	gene with protein product							Standard	NM_020653		Approved	ZKSCAN13, ZSCAN45	uc002gqi.2	Q9HBT7	OTTHUMG00000058993	ENST00000395824.1:c.2121T>A	chr17.hg19:g.16455335A>T	ENSP00000379168:p.Asn707Lys	101.0	0.0		217.0	76.0	NM_020653	Q6IAG1	Missense_Mutation	SNP	ENST00000395824.1	hg19	CCDS11179.2	.	.	.	.	.	.	.	.	.	.	A	8.541	0.873220	0.17322	.	.	ENSG00000141040	ENST00000395825;ENST00000395824	T;T	0.07021	3.23;3.23	4.89	-1.37	0.09056	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.378699	0.22825	N	0.055177	T	0.02533	0.0077	N	0.02202	-0.64	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.42258	-0.9462	10	0.25751	T	0.34	.	6.0826	0.19950	0.4411:0.1501:0.4088:0.0	.	700	Q9HBT7	ZN287_HUMAN	K	707	ENSP00000379169:N707K;ENSP00000379168:N707K	ENSP00000379168:N707K	N	-	3	2	ZNF287	16396060	0.000000	0.05858	0.972000	0.41901	0.998000	0.95712	-1.371000	0.02573	-0.393000	0.07739	0.454000	0.30748	AAT	.	.		0.368	ZNF287-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130504.1			T	16455335	A	T	16455335	3	4	344	1	0	0	0	0	1	0	0	0	17840	214	8	4	168	4	ZNF287	17	16455335	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	123112	16455335	64739875	1146	48509										
MAPK7	5598	hgsc.bcm.edu	37	chr17	19286534	19286534	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggctgacctgcctgacctccAggacccctgaggcccccagc	11	19	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:19286534A>T	ENST00000308406.5	+	7	2827	c.2441A>T	c.(2440-2442)cAg>cTg	p.Q814L	MAPK7_ENST00000395604.3_Missense_Mutation_p.Q814L|MAPK7_ENST00000571657.1_3'UTR|MFAP4_ENST00000574313.2_5'Flank|MAPK7_ENST00000395602.4_Missense_Mutation_p.Q814L|MAPK7_ENST00000299612.7_Missense_Mutation_p.Q675L	NM_139033.2	NP_620602.2	Q13164	MK07_HUMAN	mitogen-activated protein kinase 7	814					cAMP-mediated signaling (GO:0019933)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to transforming growth factor beta stimulus (GO:0071560)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cAMP catabolic process (GO:0030821)|negative regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051344)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NFAT protein import into nucleus (GO:0051534)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of response to cytokine stimulus (GO:0060761)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|regulation of angiogenesis (GO:0045765)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|mitogen-activated protein kinase binding (GO:0051019)			autonomic_ganglia(1)|central_nervous_system(4)|endometrium(5)|kidney(2)|large_intestine(4)|lung(9)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	30	all_cancers(12;2.87e-05)|all_epithelial(12;0.00114)|Hepatocellular(7;0.00345)|Breast(13;0.206)					CCTGACCTCCAGGACCCCTGA	0.602																																					p.Q814L		Atlas-SNP	.											.	MAPK7	72	.	0			c.A2441T						.						46	45	46					17																	19286534		2203	4300	6503	SO:0001583	missense	5598	exon7			ACCTCCAGGACCC	U25278	CCDS11206.1, CCDS11207.1	17p11.2	2011-06-09			ENSG00000166484	ENSG00000166484	2.7.11.24	"Mitogen-activated protein kinase cascade / Kinases"	6880	protein-coding gene	gene with protein product	"BMK1 kinase", "extracellular-signal-regulated kinase 5"	602521		PRKM7		10072598, 7759517	Standard	NM_139032		Approved	BMK1, ERK5	uc002gvp.3	Q13164	OTTHUMG00000059587	ENST00000308406.5:c.2441A>T	chr17.hg19:g.19286534A>T	ENSP00000311005:p.Gln814Leu	61.0	0.0		36.0	17.0	NM_002749	Q16634|Q59F50|Q6QLU7|Q7L4P4|Q969G1|Q96G51	Missense_Mutation	SNP	ENST00000308406.5	hg19	CCDS11206.1	.	.	.	.	.	.	.	.	.	.	A	15.94	2.980735	0.53827	.	.	ENSG00000166484	ENST00000308406;ENST00000299612;ENST00000395604;ENST00000395602	T;T;T;T	0.75260	-0.66;-0.92;-0.66;-0.66	4.91	4.91	0.64330	.	0.136830	0.49916	D	0.000128	T	0.68174	0.2972	L	0.47716	1.5	0.33226	D	0.555299	B	0.14438	0.01	B	0.14023	0.01	T	0.74548	-0.3629	10	0.87932	D	0	-15.4878	12.5144	0.56024	1.0:0.0:0.0:0.0	.	814	Q13164	MK07_HUMAN	L	814;675;814;814	ENSP00000311005:Q814L;ENSP00000299612:Q675L;ENSP00000378968:Q814L;ENSP00000378966:Q814L	ENSP00000299612:Q675L	Q	+	2	0	MAPK7	19227127	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.178000	0.42519	1.841000	0.53522	0.402000	0.26972	CAG	.	.		0.602	MAPK7-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132506.1	NM_139033		T	19286534	A	T	19286534	3	4	344	1	0	0	0	0	1	0	0	0	9291	188	7	4	2463	4	MAPK7	17	19286534	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2831199	19286534	61908676	1147	48510										
USP22	23326	hgsc.bcm.edu	37	chr17	20919135	20919135	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcgtcctgctgctcgtagccTgctaggtgcctcgcgtgggt	15	13	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:20919135T>A	ENST00000261497.4	-	6	971	c.768A>T	c.(766-768)gcA>gcT	p.A256A	USP22_ENST00000455117.2_Intron|USP22_ENST00000537526.2_Silent_p.A244A	NM_015276.1	NP_056091.1	Q9UPT9	UBP22_HUMAN	ubiquitin specific peptidase 22	256	USP.				cell cycle (GO:0007049)|chromatin organization (GO:0006325)|embryo development (GO:0009790)|histone deubiquitination (GO:0016578)|histone H4 acetylation (GO:0043967)|histone ubiquitination (GO:0016574)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|protein deubiquitination (GO:0016579)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	SAGA complex (GO:0000124)	enzyme binding (GO:0019899)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|transcription coactivator activity (GO:0003713)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)	15						GCTCGTAGCCTGCTAGGTGCC	0.637																																					p.A256A		Atlas-SNP	.											.	USP22	45	.	0			c.A768T						.						51	60	57					17																	20919135		2051	4187	6238	SO:0001819	synonymous_variant	23326	exon6			GTAGCCTGCTAGG	AB028986	CCDS42285.1	17p11.2	2006-11-24	2005-08-08		ENSG00000124422	ENSG00000124422		"Ubiquitin-specific peptidases"	12621	protein-coding gene	gene with protein product		612116	"ubiquitin specific protease 22", "ubiquitin specific peptidase 3-like"	USP3L		12838346	Standard	NM_015276		Approved	KIAA1063	uc002gym.4	Q9UPT9	OTTHUMG00000133621	ENST00000261497.4:c.768A>T	chr17.hg19:g.20919135T>A		46.0	0.0		41.0	16.0	NM_015276	A0JNS3|Q2NLE2|Q6MZY4|Q8TBS8|Q96IW5	Silent	SNP	ENST00000261497.4	hg19	CCDS42285.1																																																																																			.	.		0.637	USP22-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444169.1			A	20919135	T	A	20919135	2	1	344	1	0	0	0	0	0	0	0	1	17069	1567	55	4		4	USP22	17	20919135	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1632601	20919135	60276075	1148	48511										
KCNJ12	3768	hgsc.bcm.edu	37	chr17	21319679	21319679	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaaccagtacaagattgactActcgcacttccacaagacct	6	13	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:21319679A>G	ENST00000583088.1	+	3	1920	c.1025A>G	c.(1024-1026)tAc>tGc	p.Y342C	KCNJ12_ENST00000331718.5_Missense_Mutation_p.Y342C	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	342					muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	AAGATTGACTACTCGCACTTC	0.582										Prostate(3;0.18)																											p.Y342C		Atlas-SNP	.											.	.	.	.	0			c.A1025G						.						157	155	156					17																	21319679		2203	4300	6503	SO:0001583	missense	100134444	exon3			TTGACTACTCGCA	L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6258	protein-coding gene	gene with protein product		602323	"potassium inwardly-rectifying channel, subfamily J, inhibitor 1"	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.1025A>G	chr17.hg19:g.21319679A>G	ENSP00000463778:p.Tyr342Cys	90.0	0.0		67.0	10.0	NM_001194958	O43401|Q15756|Q8NG63	Missense_Mutation	SNP	ENST00000583088.1	hg19	CCDS11219.1	.	.	.	.	.	.	.	.	.	.	A	17.43	3.388784	0.61956	.	.	ENSG00000184185	ENST00000331718	D	0.95238	-3.65	5.76	5.76	0.90799	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (2);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.000000	0.85682	D	0.000000	D	0.97717	0.9251	M	0.89715	3.055	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	D	0.98628	1.0670	10	0.87932	D	0	.	16.0796	0.80995	1.0:0.0:0.0:0.0	.	342	Q14500	IRK12_HUMAN	C	342	ENSP00000328150:Y342C	ENSP00000328150:Y342C	Y	+	2	0	KCNJ12	21260272	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	9.179000	0.94861	2.206000	0.71126	0.533000	0.62120	TAC	.	.		0.582	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012		G	21319679	A	G	21319679	3	3	344	1	0	0	0	0	1	0	0	0	8055	391	14	2	1027	2	KCNJ12	17	21319679	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	400544	21319679	59875531	1149	48512										
NLK	51701	hgsc.bcm.edu	37	chr17	26499544	26499544	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtattttatttccttgtagtTggatttgatcacggatctgt	9	5	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:26499544T>A	ENST00000407008.3	+	7	1767	c.1049T>A	c.(1048-1050)tTg>tAg	p.L350*		NM_016231.4	NP_057315.3	Q9UBE8	NLK_HUMAN	nemo-like kinase	350	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|Sufficient for interaction with DAPK3.				intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of Wnt signaling pathway (GO:0030178)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|serine phosphorylation of STAT3 protein (GO:0033136)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase activity (GO:0004707)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|SH2 domain binding (GO:0042169)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(1)	14	all_lung(13;0.000343)|Lung NSC(42;0.00184)			UCEC - Uterine corpus endometrioid carcinoma (53;0.168)		TCCTTGTAGTTGGATTTGATC	0.413																																					p.L350X		Atlas-SNP	.											.	NLK	88	.	0			c.T1049A						.						89	80	83					17																	26499544		2202	4300	6502	SO:0001630	splice_region_variant	51701	exon7			TGTAGTTGGATTT	AF197898	CCDS11224.2	17q11.2	2005-12-22	2005-12-22		ENSG00000087095	ENSG00000087095			29858	protein-coding gene	gene with protein product		609476	"nemo like kinase"			9448268, 10863097	Standard	NM_016231		Approved		uc010crj.3	Q9UBE8	OTTHUMG00000132451	ENST00000407008.3:c.1048-1T>A	chr17.hg19:g.26499544T>A		73.0	0.0		61.0	25.0	NM_016231	B2RCX1|Q2PNI9|Q6P2A3	Nonsense_Mutation	SNP	ENST00000407008.3	hg19	CCDS11224.2	.	.	.	.	.	.	.	.	.	.	T	37	6.371926	0.97515	.	.	ENSG00000087095	ENST00000407008	.	.	.	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.5408	15.7393	0.77876	0.0:0.0:0.0:1.0	.	.	.	.	X	350	.	ENSP00000384625:L350X	L	+	2	0	NLK	23523671	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.499000	0.81566	2.308000	0.77769	0.533000	0.62120	TTG	.	.		0.413	NLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255607.3	NM_016231	Nonsense_Mutation	A	26499544	T	A	26499544	5	1	344	1	0	0	0	0	0	0	1	0	10475	1826	63	4	1075	4	NLK	17	26499544	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	5179865	26499544	54695666	1150	48513										
CCL11	6356	hgsc.bcm.edu	37	chr17	32612882	32612882	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcatagcagctgccttcagcCcccaggggctcgctgggcca	12	16	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:32612882C>A	ENST00000305869.3	+	1	196	c.55C>A	c.(55-57)Ccc>Acc	p.P19T		NM_002986.2	NP_002977.1	P51671	CCL11_HUMAN	chemokine (C-C motif) ligand 11	19					actin filament organization (GO:0007015)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|chronic inflammatory response (GO:0002544)|cytoskeleton organization (GO:0007010)|eosinophil chemotaxis (GO:0048245)|ERK1 and ERK2 cascade (GO:0070371)|immune response (GO:0006955)|inflammatory response (GO:0006954)|mammary duct terminal end bud growth (GO:0060763)|mast cell chemotaxis (GO:0002551)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of Rac GTPase activity (GO:0032855)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|response to interleukin-4 (GO:0070670)|response to radiation (GO:0009314)|response to virus (GO:0009615)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)			breast(1)|lung(1)|prostate(1)	3	Breast(3;0.00224)	Breast(31;0.151)|Ovarian(249;0.17)		BRCA - Breast invasive adenocarcinoma(366;0.155)		TGCCTTCAGCCCCCAGGGGCT	0.562																																					p.P19T		Atlas-SNP	.											.	CCL11	12	.	0			c.C55A						.						114	113	114					17																	32612882		2203	4300	6503	SO:0001583	missense	6356	exon1			TTCAGCCCCCAGG	AB063614	CCDS11279.1	17q21.1-q21.2	2013-02-25	2002-08-22	2002-08-23	ENSG00000172156	ENSG00000172156		"Chemokine ligands", "Endogenous ligands"	10610	protein-coding gene	gene with protein product	"eotaxin-1"	601156	"small inducible cytokine subfamily A (Cys-Cys), member 11 (eotaxin)"	SCYA11		9169149	Standard	NM_002986		Approved	eotaxin, MGC22554	uc002hia.1	P51671	OTTHUMG00000132884	ENST00000305869.3:c.55C>A	chr17.hg19:g.32612882C>A	ENSP00000302234:p.Pro19Thr	44.0	0.0		43.0	21.0	NM_002986	P50877|Q92490|Q92491	Missense_Mutation	SNP	ENST00000305869.3	hg19	CCDS11279.1	.	.	.	.	.	.	.	.	.	.	C	2.604	-0.292243	0.05568	.	.	ENSG00000172156	ENST00000305869	T	0.02472	4.28	4.48	-4.72	0.03269	.	1.482540	0.04225	N	0.334269	T	0.00998	0.0033	.	.	.	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.41910	-0.9482	9	0.02654	T	1	.	0.8354	0.01139	0.3226:0.1627:0.1061:0.4086	.	19	P51671	CCL11_HUMAN	T	19	ENSP00000302234:P19T	ENSP00000302234:P19T	P	+	1	0	CCL11	29636995	0.002000	0.14202	0.066000	0.19879	0.114000	0.19823	-0.527000	0.06200	-0.766000	0.04639	0.462000	0.41574	CCC	.	.		0.562	CCL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256377.2	NM_002986		A	32612882	C	A	32612882	3	1	344	1	0	0	0	0	1	0	0	0	2885	623	22	3	57	3	CCL11	17	32612882	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	6113338	32612882	48582328	1151	48514										
NLE1	54475	hgsc.bcm.edu	37	chr17	33462285	33462285	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cacttgcccgtcctgccatcCcacagcttgatggacttgtc	8	16	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:33462285C>A	ENST00000442241.4	-	10	1236	c.1197G>T	c.(1195-1197)tgG>tgT	p.W399C	NLE1_ENST00000360831.5_Missense_Mutation_p.W357C|NLE1_ENST00000586869.1_Missense_Mutation_p.W107C|NLE1_ENST00000593176.1_5'Flank	NM_001014445.1|NM_018096.3	NP_001014445.1|NP_060566.2	Q9NVX2	NLE1_HUMAN	notchless homolog 1 (Drosophila)	399					hematopoietic stem cell homeostasis (GO:0061484)|inner cell mass cell differentiation (GO:0001826)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:2001268)|negative regulation of mitotic cell cycle (GO:0045930)|Notch signaling pathway (GO:0007219)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|ribosomal large subunit biogenesis (GO:0042273)	nucleolus (GO:0005730)|nucleus (GO:0005634)				NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)	22		Ovarian(249;0.17)				TCCTGCCATCCCACAGCTTGA	0.562																																					p.W399C		Atlas-SNP	.											.	NLE1	42	.	0			c.G1197T						.						173	140	151					17																	33462285		2203	4300	6503	SO:0001583	missense	54475	exon10			GCCATCCCACAGC		CCDS11291.1, CCDS45647.1	17q12	2013-01-10		2005-08-09	ENSG00000073536	ENSG00000073536		"WD repeat domain containing"	19889	protein-coding gene	gene with protein product	"Notchless gene homolog, (Drosophila)"						Standard	XM_005257989		Approved	FLJ10458	uc002hiy.1	Q9NVX2	OTTHUMG00000132928	ENST00000442241.4:c.1197G>T	chr17.hg19:g.33462285C>A	ENSP00000413572:p.Trp399Cys	108.0	0.0		90.0	46.0	NM_018096	O60868|Q59GJ8|Q9BU54	Missense_Mutation	SNP	ENST00000442241.4	hg19	CCDS11291.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.5|20.5	3.996042|3.996042	0.74703|0.74703	.|.	.|.	ENSG00000073536|ENSG00000073536	ENST00000436188|ENST00000442241;ENST00000360831;ENST00000537697	.|D	.|0.83506	.|-1.73	5.11|5.11	5.11|5.11	0.69529|0.69529	.|WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.94138|0.94138	0.8120|0.8120	H|H	0.97077|0.97077	3.935|3.935	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|1.0;0.999	D|D	0.95742|0.95742	0.8784|0.8784	5|10	.|0.87932	.|D	.|0	-12.2759|-12.2759	16.0884|16.0884	0.81073|0.81073	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|375;399	.|B4E074;Q9NVX2	.|.;NLE1_HUMAN	V|C	179|399;107;375	.|ENSP00000413572:W399C	.|ENSP00000354075:W107C	G|W	-|-	2|3	0|0	NLE1|NLE1	30486398|30486398	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.122000|7.122000	0.77169|0.77169	2.637000|2.637000	0.89404|0.89404	0.650000|0.650000	0.86243|0.86243	GGG|TGG	.	.		0.562	NLE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256441.2	NM_018096		A	33462285	C	A	33462285	3	1	344	1	0	0	0	0	1	0	0	0	10469	624	22	3	276	3	NLE1	17	33462285	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	849403	33462285	47732925	1152	48515										
UNC45B	146862	hgsc.bcm.edu	37	chr17	33495163	33495163	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cctgcagggcccctttgaccTgggcaaccagctgctgggac	13	15	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:33495163T>A	ENST00000268876.5	+	10	1332	c.1235T>A	c.(1234-1236)cTg>cAg	p.L412Q	UNC45B_ENST00000591048.1_Missense_Mutation_p.L412Q|UNC45B_ENST00000378449.1_Missense_Mutation_p.L412Q|RP11-799D4.3_ENST00000585646.1_RNA|UNC45B_ENST00000433649.1_Missense_Mutation_p.L412Q|UNC45B_ENST00000394570.2_Missense_Mutation_p.L412Q	NM_173167.2	NP_775259.1	Q8IWX7	UN45B_HUMAN	unc-45 homolog B (C. elegans)	412					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(10)|lung(24)|ovary(3)|prostate(2)|skin(1)|stomach(1)|urinary_tract(3)	59		Ovarian(249;0.17)				CCCTTTGACCTGGGCAACCAG	0.577																																					p.L412Q		Atlas-SNP	.											.	UNC45B	133	.	0			c.T1235A						.						99	81	87					17																	33495163		2203	4300	6503	SO:0001583	missense	146862	exon10			TTGACCTGGGCAA	AW755253	CCDS11292.1, CCDS45648.1	17q12	2008-02-05	2005-11-17	2005-11-17	ENSG00000141161	ENSG00000141161			14304	protein-coding gene	gene with protein product		611220	"cardiomyopathy associated 4"	CMYA4		12356907	Standard	NM_001267052		Approved	UNC45	uc002hja.3	Q8IWX7	OTTHUMG00000132931	ENST00000268876.5:c.1235T>A	chr17.hg19:g.33495163T>A	ENSP00000268876:p.Leu412Gln	114.0	0.0		101.0	44.0	NM_001267052	Q495Q8|Q495Q9	Missense_Mutation	SNP	ENST00000268876.5	hg19	CCDS11292.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.475812	0.84640	.	.	ENSG00000141161	ENST00000394570;ENST00000268876;ENST00000433649;ENST00000378449	T;T;T;T	0.49432	0.78;0.78;0.78;0.78	5.02	5.02	0.67125	Armadillo-like helical (1);Armadillo-type fold (1);	0.068819	0.64402	D	0.000019	T	0.59555	0.2202	L	0.44542	1.39	0.36609	D	0.875097	D;D;D	0.69078	0.997;0.991;0.971	D;P;P	0.67725	0.953;0.804;0.824	T	0.68511	-0.5389	10	0.87932	D	0	-15.046	14.3661	0.66807	0.0:0.0:0.0:1.0	.	412;412;412	Q8IWX7-2;Q8IWX7-3;Q8IWX7	.;.;UN45B_HUMAN	Q	412	ENSP00000378071:L412Q;ENSP00000268876:L412Q;ENSP00000412840:L412Q;ENSP00000367710:L412Q	ENSP00000268876:L412Q	L	+	2	0	UNC45B	30519276	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.085000	0.71343	2.233000	0.73108	0.533000	0.62120	CTG	.	.		0.577	UNC45B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256458.2	NM_173167		A	33495163	T	A	33495163	3	1	344	1	0	0	0	0	1	0	0	0	17004	1580	55	4	1269	4	UNC45B	17	33495163	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	32878	33495163	47700047	1153	48516										
CCL18	6362	hgsc.bcm.edu	37	chr17	34398401	34398401	+	Nonstop_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gacctgaagctgaatgcctgAggggcctggaagctgcgagg	17	9	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:34398401A>T	ENST00000004921.3	+	3	333	c.270A>T	c.(268-270)tgA>tgT	p.*90C	AC069363.1_ENST00000590992.1_RNA|AC069363.1_ENST00000588864.1_RNA	NM_002988.2	NP_002979.1	P55774	CCL18_HUMAN	chemokine (C-C motif) ligand 18 (pulmonary and activation-regulated)	0					cell chemotaxis (GO:0060326)|cell communication (GO:0007154)|cell-cell signaling (GO:0007267)|chemotaxis (GO:0006935)|immune response (GO:0006955)|inflammatory response (GO:0006954)|response to biotic stimulus (GO:0009607)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	chemokine activity (GO:0008009)			endometrium(1)|large_intestine(2)|lung(1)	4		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		TGAATGCCTGAGGGGCCTGGA	0.607																																					p.X90C		Atlas-SNP	.											.	CCL18	9	.	0			c.A270T						.						46	45	45					17																	34398401		2203	4300	6503	SO:0001578	stop_lost	6362	exon3			TGCCTGAGGGGCC	Y13710	CCDS11306.1	17q11.2	2014-05-06	2002-08-22	2002-08-23	ENSG00000006074	ENSG00000275385		"Chemokine ligands"	10616	protein-coding gene	gene with protein product		603757	"small inducible cytokine subfamily A (Cys-Cys), member 18, pulmonary and activation-regulated"	SCYA18		9233607, 10049593	Standard	NM_002988		Approved	DC-CK1, PARC, AMAC-1, DCCK1, MIP-4, CKb7	uc002hku.3	P55774	OTTHUMG00000188410	ENST00000004921.3:c.270A>T	chr17.hg19:g.34398401A>T	ENSP00000004921:p.*90Cysext*35	146.0	0.0		130.0	72.0	NM_002988	B5BUM2|Q53X71	Missense_Mutation	SNP	ENST00000004921.3	hg19	CCDS11306.1	.	.	.	.	.	.	.	.	.	.	.	5.623	0.299699	0.10622	.	.	ENSG00000006074	ENST00000004921	.	.	.	4.64	2.32	0.28847	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.1728	0.10337	0.6805:0.2089:0.1106:0.0	.	.	.	.	C	90	.	.	X	+	3	0	CCL18	31422514	0.004000	0.15560	0.000000	0.03702	0.002000	0.02628	1.204000	0.32296	0.343000	0.23821	0.533000	0.62120	TGA	.	.		0.607	CCL18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256583.1	NM_002988		T	34398401	A	T	34398401	4	4	344	1	0	0	0	0	0	0	0	0	2891	317	11	4	280	4	CCL18	17	34398401	Nonstop_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	903238	34398401	46796809	1154	48517										
GPR179	440435	hgsc.bcm.edu	37	chr17	36485679	36485679	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agatttcggccttgttgccaCtgtctggctgacgcgtttct	11	11	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:36485679C>A	ENST00000342292.4	-	11	3793	c.3773G>T	c.(3772-3774)aGt>aTt	p.S1258I	GPR179_ENST00000584976.1_5'Flank	NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	1258					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				CTTGTTGCCACTGTCTGGCTG	0.602																																					p.S1258I		Atlas-SNP	.											.	GPR179	170	.	0			c.G3773T						.						64	67	66					17																	36485679		1963	4156	6119	SO:0001583	missense	440435	exon11			TTGCCACTGTCTG		CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"GPCR / Class C : Orphans"	31371	protein-coding gene	gene with protein product		614515	"GPR158-like 1", "GPR179"	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.3773G>T	chr17.hg19:g.36485679C>A	ENSP00000345060:p.Ser1258Ile	43.0	0.0		44.0	20.0	NM_001004334		Missense_Mutation	SNP	ENST00000342292.4	hg19	CCDS42308.1	.	.	.	.	.	.	.	.	.	.	C	10.22	1.290562	0.23564	.	.	ENSG00000188888	ENST00000342292	T	0.61040	0.14	5.38	3.41	0.39046	.	0.835586	0.10912	N	0.620472	T	0.52613	0.1745	L	0.55481	1.735	0.09310	N	1	P	0.49961	0.93	B	0.41571	0.36	T	0.44298	-0.9337	10	0.72032	D	0.01	-0.1392	9.1095	0.36718	0.0:0.8303:0.0:0.1697	.	1258	Q6PRD1	GP179_HUMAN	I	1258	ENSP00000345060:S1258I	ENSP00000345060:S1258I	S	-	2	0	GPR179	33739205	0.001000	0.12720	0.001000	0.08648	0.034000	0.12701	0.730000	0.26043	0.841000	0.35020	0.462000	0.41574	AGT	.	.		0.602	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2			A	36485679	C	A	36485679	3	1	344	1	0	0	0	0	1	0	0	0	6682	565	20	3	3334	3	GPR179	17	36485679	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	2087278	36485679	44709531	1155	48518										
PCGF2	7703	hgsc.bcm.edu	37	chr17	36891668	36891668	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctgggagagccatgggatggGgtggctgggctgggcaggga	23	6	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:36891668G>T	ENST00000580830.1	-	12	1544	c.843C>A	c.(841-843)acC>acA	p.T281T	PCGF2_ENST00000579882.1_3'UTR|PCGF2_ENST00000581345.1_Silent_p.T281T|PCGF2_ENST00000578109.1_3'UTR|PCGF2_ENST00000360797.2_Silent_p.T281T|PCGF2_ENST00000585100.1_3'UTR			P35227	PCGF2_HUMAN	polycomb group ring finger 2	281	Pro/Ser-rich.				anterior/posterior pattern specification (GO:0009952)|cellular response to hydrogen peroxide (GO:0070301)|embryonic skeletal system morphogenesis (GO:0048704)|histone acetylation (GO:0016573)|in utero embryonic development (GO:0001701)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	10	Breast(7;9.07e-22)					CATGGGATGGGGTGGCTGGGC	0.692											OREG0024367	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T281T		Atlas-SNP	.											.	PCGF2	24	.	0			c.C843A						.						18	14	15					17																	36891668		2190	4282	6472	SO:0001819	synonymous_variant	7703	exon11			GGATGGGGTGGCT	D13969	CCDS32638.1	17q12	2013-01-09	2005-01-17	2005-01-19		ENSG00000277258		"RING-type (C3HC4) zinc fingers", "Polycomb group ring fingers"	12929	protein-coding gene	gene with protein product		600346	"ring finger protein 110"	ZNF144, RNF110		8325509	Standard	NM_007144		Approved	MEL-18	uc002hqp.1	P35227		ENST00000580830.1:c.843C>A	chr17.hg19:g.36891668G>T		50.0	0.0	866	55.0	25.0	NM_007144	A6NGD8	Silent	SNP	ENST00000580830.1	hg19	CCDS32638.1																																																																																			.	.		0.692	PCGF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442246.2	NM_007144		T	36891668	G	T	36891668	2	4	344	1	0	0	0	0	0	0	0	1	11584	1219	43	3		3	PCGF2	17	36891668	Silent	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	405989	36891668	44303542	1156	48519										
CCR7	1236	hgsc.bcm.edu	37	chr17	38721654	38721654	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atgaagaggctcactcacccAggtccatgacgctctctggg	11	13	3	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:38721654A>T	ENST00000246657.2	-	1	70	c.8T>A	c.(7-9)cTg>cAg	p.L3Q		NM_001838.3	NP_001829.1	P32248	CCR7_HUMAN	chemokine (C-C motif) receptor 7	3					activation of Rho GTPase activity (GO:0032862)|cellular response to cytokine stimulus (GO:0071345)|chemokine (C-C motif) ligand 19 signaling pathway (GO:0038115)|chemokine (C-C motif) ligand 21 signaling pathway (GO:0038116)|chemokine-mediated signaling pathway (GO:0070098)|dendritic cell chemotaxis (GO:0002407)|establishment of T cell polarity (GO:0001768)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interleukin-12 secretion (GO:0072610)|lymphocyte migration into lymph node (GO:0097022)|mature dendritic cell differentiation (GO:0097029)|myeloid dendritic cell chemotaxis (GO:0002408)|negative regulation of leukocyte apoptotic process (GO:2000107)|negative thymic T cell selection (GO:0045060)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell motility (GO:2000147)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of glycoprotein biosynthetic process involved in immunological synapse formation (GO:2000526)|positive regulation of humoral immune response (GO:0002922)|positive regulation of hypersensitivity (GO:0002885)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of immunological synapse formation (GO:2000522)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of T cell costimulation (GO:2000525)|positive regulation of T cell receptor signaling pathway (GO:0050862)|regulation of dendritic cell dendrite assembly (GO:2000547)|regulation of interferon-gamma production (GO:0032649)|regulation of interleukin-1 beta secretion (GO:0050706)|release of sequestered calcium ion into cytosol (GO:0051209)|response to lipopolysaccharide (GO:0032496)|response to nitric oxide (GO:0071731)|response to prostaglandin E (GO:0034695)|ruffle organization (GO:0031529)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|C-C motif chemokine 19 receptor activity (GO:0038117)|C-C motif chemokine 21 receptor activity (GO:0038121)|chemokine (C-C motif) ligand 19 binding (GO:0035757)|chemokine (C-C motif) ligand 21 binding (GO:0035758)|G-protein coupled receptor activity (GO:0004930)			breast(1)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		Breast(137;0.000496)				TCACTCACCCAGGTCCATGAC	0.592																																					p.L3Q		Atlas-SNP	.											CCR7,NS,carcinoma,0,1	CCR7	31	.	0			c.T8A						.						144	113	124					17																	38721654		2203	4300	6503	SO:0001583	missense	1236	exon1			TCACCCAGGTCCA		CCDS11369.1	17q12-q21.2	2012-08-08			ENSG00000126353	ENSG00000126353		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1608	protein-coding gene	gene with protein product		600242		CMKBR7, EBI1		8383238	Standard	NM_001838		Approved	BLR2, CDw197, CD197	uc002huw.3	P32248	OTTHUMG00000133375	ENST00000246657.2:c.8T>A	chr17.hg19:g.38721654A>T	ENSP00000246657:p.Leu3Gln	71.0	0.0		58.0	15.0	NM_001838		Missense_Mutation	SNP	ENST00000246657.2	hg19	CCDS11369.1	.	.	.	.	.	.	.	.	.	.	A	12.25	1.882786	0.33255	.	.	ENSG00000126353	ENST00000246657	T	0.61510	0.1	4.59	3.48	0.39840	.	6.654570	0.00481	N	0.000125	T	0.47340	0.1440	N	0.22421	0.69	0.80722	D	1	B	0.19583	0.037	B	0.15484	0.013	T	0.31888	-0.9927	10	0.51188	T	0.08	.	7.3185	0.26513	0.898:0.0:0.102:0.0	.	3	P32248	CCR7_HUMAN	Q	3	ENSP00000246657:L3Q	ENSP00000246657:L3Q	L	-	2	0	CCR7	35975180	1.000000	0.71417	0.994000	0.49952	0.653000	0.38743	0.763000	0.26517	0.847000	0.35167	0.450000	0.29827	CTG	.	.		0.592	CCR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257222.1			T	38721654	A	T	38721654	3	4	344	1	0	0	0	0	1	0	0	0	2948	188	7	4	1140	4	CCR7	17	38721654	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1829986	38721654	42473556	1157	48520										
KRT24	192666	hgsc.bcm.edu	37	chr17	38855854	38855854	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctgatctgcgtttgaatttcTgacagctgagccacgtagcc	10	11	2	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:38855854T>C	ENST00000264651.2	-	6	1259	c.1203A>G	c.(1201-1203)tcA>tcG	p.S401S		NM_019016.2	NP_061889.2	Q2M2I5	K1C24_HUMAN	keratin 24	401	Coil 2.|Rod.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Breast(137;0.00526)				TTTGAATTTCTGACAGCTGAG	0.463																																					p.S401S	GBM(61;380 1051 14702 23642 31441)	Atlas-SNP	.											.	KRT24	60	.	0			c.A1203G						.						104	101	102					17																	38855854		2203	4300	6503	SO:0001819	synonymous_variant	192666	exon6			AATTTCTGACAGC		CCDS11372.1	17q21.2	2013-06-25			ENSG00000167916	ENSG00000167916		"-", "Intermediate filaments type I, keratins (acidic)"	18527	protein-coding gene	gene with protein product		607742				16831889	Standard	NM_019016		Approved	FLJ20261, MGC138169, MGC138173	uc002hvd.3	Q2M2I5	OTTHUMG00000133372	ENST00000264651.2:c.1203A>G	chr17.hg19:g.38855854T>C		68.0	0.0		73.0	29.0	NM_019016	Q9NXG7	Silent	SNP	ENST00000264651.2	hg19	CCDS11372.1																																																																																			.	.		0.463	KRT24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257217.1	NM_019016		C	38855854	T	C	38855854	2	2	344	1	0	0	0	0	0	0	0	1	8470	1567	55	2		2	KRT24	17	38855854	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	134200	38855854	42339356	1158	48521										
KRT40	125115	hgsc.bcm.edu	37	chr17	39137242	39137242	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttttcaatctgggtactgacCtgaacagccaaccattcttc	6	12	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:39137242C>T	ENST00000398486.2	-	6	1009	c.849G>A	c.(847-849)caG>caA	p.Q283Q	KRT40_ENST00000377755.4_Splice_Site_p.Q283Q	NM_182497.3	NP_872303.2	Q6A162	K1C40_HUMAN	keratin 40	283	Coil 2.|Rod.					intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9		Breast(137;0.00043)				GGGTACTGACCTGAACAGCCA	0.473																																					p.Q283Q		Atlas-SNP	.											.	KRT40	27	.	0			c.G849A						.						196	193	194					17																	39137242		1955	4171	6126	SO:0001630	splice_region_variant	125115	exon6			ACTGACCTGAACA	AK093919	CCDS42320.1	17q21.2	2013-01-16			ENSG00000204889	ENSG00000204889		"-", "Intermediate filaments type I, keratins (acidic)"	26707	protein-coding gene	gene with protein product						16831889	Standard	NM_182497		Approved	FLJ36600, KA36	uc010cxh.1	Q6A162	OTTHUMG00000133596	ENST00000398486.2:c.849+1G>A	chr17.hg19:g.39137242C>T		85.0	0.0		103.0	48.0	NM_182497	Q6IFU5	Silent	SNP	ENST00000398486.2	hg19	CCDS42320.1																																																																																			.	.		0.473	KRT40-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257701.3	NM_182497	Silent	T	39137242	C	T	39137242	5	4	344	1	0	0	0	0	0	0	1	0	8487	695	24	3	462	3	KRT40	17	39137242	Splice_Site	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	281388	39137242	42057968	1159	48522										
KRT40	125115	hgsc.bcm.edu	37	chr17	39140425	39140425	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atgtagcacaggtaccggggAgacaagctgtttccacggag	14	9	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:39140425A>T	ENST00000398486.2	-	3	261	c.101T>A	c.(100-102)cTc>cAc	p.L34H	KRT40_ENST00000377755.4_Missense_Mutation_p.L34H	NM_182497.3	NP_872303.2	Q6A162	K1C40_HUMAN	keratin 40	34	Head.					intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9		Breast(137;0.00043)				GGTACCGGGGAGACAAGCTGT	0.577																																					p.L34H		Atlas-SNP	.											.	KRT40	27	.	0			c.T101A						.						47	54	52					17																	39140425		2080	4210	6290	SO:0001583	missense	125115	exon3			CCGGGGAGACAAG	AK093919	CCDS42320.1	17q21.2	2013-01-16			ENSG00000204889	ENSG00000204889		"-", "Intermediate filaments type I, keratins (acidic)"	26707	protein-coding gene	gene with protein product						16831889	Standard	NM_182497		Approved	FLJ36600, KA36	uc010cxh.1	Q6A162	OTTHUMG00000133596	ENST00000398486.2:c.101T>A	chr17.hg19:g.39140425A>T	ENSP00000381500:p.Leu34His	110.0	0.0		83.0	36.0	NM_182497	Q6IFU5	Missense_Mutation	SNP	ENST00000398486.2	hg19	CCDS42320.1	.	.	.	.	.	.	.	.	.	.	A	12.05	1.822064	0.32237	.	.	ENSG00000204889	ENST00000377755;ENST00000398486	D;D	0.83335	-1.71;-1.71	4.92	2.65	0.31530	.	0.293395	0.18722	N	0.133000	T	0.76702	0.4024	M	0.75264	2.295	0.21740	N	0.99956	B	0.23854	0.092	B	0.24269	0.052	T	0.59010	-0.7534	10	0.15066	T	0.55	.	3.4011	0.07324	0.588:0.0:0.2498:0.1622	.	34	Q6A162	K1C40_HUMAN	H	34	ENSP00000366984:L34H;ENSP00000381500:L34H	ENSP00000366984:L34H	L	-	2	0	KRT40	36393951	0.876000	0.30132	0.067000	0.19924	0.022000	0.10575	1.198000	0.32223	0.297000	0.22615	0.482000	0.46254	CTC	.	.		0.577	KRT40-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257701.3	NM_182497		T	39140425	A	T	39140425	3	4	344	1	0	0	0	0	1	0	0	0	8487	304	11	4	1222	4	KRT40	17	39140425	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3183	39140425	42054785	1160	48523										
KRTAP9-9	81870	hgsc.bcm.edu	37	chr17	39411764	39411764	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cctgctgtgtgtctagctgcTgccagccttgctgccgccca	11	16	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:39411764T>A	ENST00000394008.1	+	1	129	c.127T>A	c.(127-129)Tgc>Agc	p.C43S		NM_030975.2	NP_112237.2	Q9BYP9	KRA99_HUMAN	keratin associated protein 9-9	48	14 X 5 AA repeats of C-C-[RQVGE]- [SPSTNQ]-[TASL].					keratin filament (GO:0045095)				endometrium(3)|skin(2)|upper_aerodigestive_tract(1)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			GTCTAGCTGCTGCCAGCCTTG	0.642																																					p.C43S		Atlas-SNP	.											.	KRTAP9-9	24	.	0			c.T127A						.																																			SO:0001583	missense	81870	exon1			AGCTGCTGCCAGC	AJ406951	CCDS54127.1	17q21.2	2010-06-03			ENSG00000198083	ENSG00000198083		"Keratin associated proteins"	16773	protein-coding gene	gene with protein product			"keratin associated protein 9-5"	KRTAP9-5		11279113	Standard	NM_030975		Approved	KAP9.9, KAP9.5	uc021txh.1	Q9BYP9	OTTHUMG00000133602	ENST00000394008.1:c.127T>A	chr17.hg19:g.39411764T>A	ENSP00000377576:p.Cys43Ser	49.0	0.0		37.0	18.0	NM_030975	B5MDD6|Q9BYQ1	Missense_Mutation	SNP	ENST00000394008.1	hg19	CCDS54127.1	.	.	.	.	.	.	.	.	.	.	.	11.76	1.733500	0.30684	.	.	ENSG00000198083	ENST00000394008	T	0.05025	3.51	4.07	1.74	0.24563	.	.	.	.	.	T	0.09774	0.0240	M	0.77616	2.38	0.09310	N	1	B	0.18968	0.032	B	0.19946	0.027	T	0.24333	-1.0163	9	0.62326	D	0.03	.	5.817	0.18497	0.1442:0.0:0.4649:0.3909	.	48	Q9BYP9	KRA99_HUMAN	S	43	ENSP00000377576:C43S	ENSP00000377576:C43S	C	+	1	0	KRTAP9-9	36665290	0.998000	0.40836	0.476000	0.27291	0.849000	0.48306	1.110000	0.31147	0.228000	0.21019	0.374000	0.22700	TGC	.	.		0.642	KRTAP9-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257710.1	NM_030975		A	39411764	T	A	39411764	3	1	344	1	0	0	0	0	1	0	0	0	8586	1580	55	4	129	4	KRTAP9-9	17	39411764	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	271339	39411764	41783446	1161	48524										
KRT32	3882	hgsc.bcm.edu	37	chr17	39619248	39619248	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	catgcactgcatctgggccaGctgggagctgtagcgggcct	15	12	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:39619248G>C	ENST00000225899.3	-	6	1154	c.1051C>G	c.(1051-1053)Ctg>Gtg	p.L351V		NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	351	Coil 2.|Rod.				epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(137;0.000812)				ATCTGGGCCAGCTGGGAGCTG	0.587																																					p.L351V		Atlas-SNP	.											.	KRT32	57	.	0			c.C1051G						.						74	74	74					17																	39619248		2203	4300	6503	SO:0001583	missense	3882	exon6			GGGCCAGCTGGGA	X90761	CCDS11393.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000108759	ENSG00000108759		"-", "Intermediate filaments type I, keratins (acidic)"	6449	protein-coding gene	gene with protein product	"hard keratin type I"	602760	"keratin, hair, acidic, 2"	KRTHA2		7556444, 8823373, 16831889	Standard	NM_002278		Approved	Ha-2	uc002hwr.3	Q14532	OTTHUMG00000133430	ENST00000225899.3:c.1051C>G	chr17.hg19:g.39619248G>C	ENSP00000225899:p.Leu351Val	71.0	0.0		76.0	39.0	NM_002278		Missense_Mutation	SNP	ENST00000225899.3	hg19	CCDS11393.1	.	.	.	.	.	.	.	.	.	.	G	14.33	2.503365	0.44558	.	.	ENSG00000108759	ENST00000225899	D	0.89746	-2.56	4.98	2.96	0.34315	Filament (1);	0.000000	0.30109	N	0.010382	D	0.93229	0.7843	M	0.80508	2.5	0.40915	D	0.984267	D	0.57257	0.979	D	0.66084	0.941	D	0.93795	0.7096	10	0.87932	D	0	.	11.5181	0.50534	0.1559:0.0:0.8441:0.0	.	351	Q14532	K1H2_HUMAN	V	351	ENSP00000225899:L351V	ENSP00000225899:L351V	L	-	1	2	KRT32	36872774	0.726000	0.28059	0.999000	0.59377	0.127000	0.20565	1.028000	0.30128	1.219000	0.43474	-0.333000	0.08304	CTG	.	.		0.587	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257293.1	NM_002278		C	39619248	G	C	39619248	3	2	344	1	0	0	0	0	1	0	0	0	8477	962	34	4	303	4	KRT32	17	39619248	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	207484	39619248	41575962	1162	48525										
KRT15	3866	hgsc.bcm.edu	37	chr17	39673060	39673060	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgatgggggccagctctcacCtcttcgtggttcttcttcag	11	12	5	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:39673060C>A	ENST00000254043.3	-	3	4323	c.738G>T	c.(736-738)gaG>gaT	p.E246D	KRT15_ENST00000393976.2_Splice_Site_p.E246D|KRT15_ENST00000393974.3_Splice_Site_p.E81D|KRT15_ENST00000393981.3_Splice_Site_p.E81D	NM_002275.3	NP_002266	P19012	K1C15_HUMAN	keratin 15	246	Coil 1B.|Rod.				epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16		Breast(137;0.000286)				CAGCTCTCACCTCTTCGTGGT	0.577																																					p.E246D		Atlas-SNP	.											.	KRT15	60	.	0			c.G738T						.						84	73	77					17																	39673060		2203	4300	6503	SO:0001630	splice_region_variant	3866	exon3			TCTCACCTCTTCG		CCDS11398.1	17q21.2	2013-06-20			ENSG00000171346	ENSG00000171346		"-", "Intermediate filaments type I, keratins (acidic)"	6421	protein-coding gene	gene with protein product	"keratin-15, basic", "keratin-15, beta", "type I cytoskeletal 15", "cytokeratin 15"	148030				16831889	Standard	NM_002275		Approved	K15, CK15, K1CO	uc002hwy.3	P19012	OTTHUMG00000133435	ENST00000254043.3:c.738+1G>T	chr17.hg19:g.39673060C>A		45.0	0.0		40.0	14.0	NM_002275	B3KQY1|B3KRA2|E0CX14|Q53XV8|Q9BUG4	Missense_Mutation	SNP	ENST00000254043.3	hg19	CCDS11398.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.776217	0.90195	.	.	ENSG00000171346	ENST00000254043;ENST00000393974;ENST00000393976;ENST00000393981;ENST00000458290	T;T;T;T;T	0.79033	-1.23;-1.23;-1.23;-1.23;-1.23	4.67	3.69	0.42338	Filament (1);	0.000000	0.47093	D	0.000255	D	0.89217	0.6652	M	0.89904	3.07	0.58432	D	0.999991	D;D;D	0.89917	1.0;0.993;0.993	D;D;D	0.91635	0.999;0.951;0.951	D	0.90751	0.4657	9	.	.	.	.	13.2354	0.59967	0.0:0.9223:0.0:0.0777	.	81;246;246	A8MT21;B3KVF5;P19012	.;.;K1C15_HUMAN	D	246;81;246;81;81	ENSP00000254043:E246D;ENSP00000377544:E81D;ENSP00000377546:E246D;ENSP00000377550:E81D;ENSP00000409282:E81D	.	E	-	3	2	KRT15	36926586	1.000000	0.71417	1.000000	0.80357	0.801000	0.45260	2.632000	0.46511	1.169000	0.42739	0.655000	0.94253	GAG	.	.		0.577	KRT15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257301.1	NM_002275	Missense_Mutation	A	39673060	C	A	39673060	5	1	344	1	0	0	0	0	0	0	1	0	8461	695	24	3	656	3	KRT15	17	39673060	Splice_Site	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	53812	39673060	41522150	1163	48526										
KRT9	3857	hgsc.bcm.edu	37	chr17	39728014	39728014	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctggcactaaaaccacccccAgatcctccgccgtagctgta	7	17	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:39728014A>G	ENST00000246662.4	-	1	296	c.231T>C	c.(229-231)tcT>tcC	p.S77S	KRT9_ENST00000588431.1_Intron	NM_000226.3	NP_000217.2	P35527	K1C9_HUMAN	keratin 9	77	Head.				epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		Breast(137;0.000307)				AACCACCCCCAGATCCTCCGC	0.582																																					p.S77S		Atlas-SNP	.											.	KRT9	78	.	0			c.T231C						.						106	94	98					17																	39728014		2203	4300	6503	SO:0001819	synonymous_variant	3857	exon1			ACCCCCAGATCCT		CCDS32654.1	17q21.2	2013-06-20	2008-08-01		ENSG00000171403	ENSG00000171403		"-", "Intermediate filaments type I, keratins (acidic)"	6447	protein-coding gene	gene with protein product	"cytokeratin 9", "type I cytoskeletal 9", "epidermolytic palmoplantar keratoderma"	607606				7512862, 16831889	Standard	NM_000226		Approved	EPPK, K9, CK-9	uc002hxe.4	P35527	OTTHUMG00000133599	ENST00000246662.4:c.231T>C	chr17.hg19:g.39728014A>G		162.0	0.0		151.0	52.0	NM_000226	O00109|Q0IJ47|Q14665	Silent	SNP	ENST00000246662.4	hg19	CCDS32654.1																																																																																			.	.		0.582	KRT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257707.1	NM_000226		G	39728014	A	G	39728014	2	3	344	1	0	0	0	0	0	0	0	1	8510	175	7	2		2	KRT9	17	39728014	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	54954	39728014	41467196	1164	48527										
GHDC	84514	hgsc.bcm.edu	37	chr17	40345476	40345476	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggctgcccagaccagggcccCccatgccactcggtgctgga	13	17	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:40345476C>A	ENST00000301671.8	-	2	565	c.124G>T	c.(124-126)Ggg>Tgg	p.G42W	GHDC_ENST00000414034.3_Missense_Mutation_p.G42W|GHDC_ENST00000436923.2_Missense_Mutation_p.G42W|GHDC_ENST00000428494.2_Missense_Mutation_p.G42W|GHDC_ENST00000590520.1_5'UTR|GHDC_ENST00000593209.1_Missense_Mutation_p.G42W|GHDC_ENST00000587427.1_Missense_Mutation_p.G42W			Q8N2G8	GHDC_HUMAN	GH3 domain containing	42						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		all_cancers(22;0.000229)|Breast(137;0.00104)|all_epithelial(22;0.00304)		BRCA - Breast invasive adenocarcinoma(366;0.124)		ACCAGGGCCCCCCATGCCACT	0.682																																					p.G42W		Atlas-SNP	.											.	GHDC	63	.	0			c.G124T						.						9	9	9					17																	40345476		2159	4221	6380	SO:0001583	missense	84514	exon3			GGGCCCCCCATGC	AF316997, BC011056	CCDS11422.1, CCDS45682.1	17q21.2	2006-08-02				ENSG00000167925			24438	protein-coding gene	gene with protein product		608587				11161808, 11735219	Standard	NR_024573		Approved	LGP1	uc002hzf.4	Q8N2G8		ENST00000301671.8:c.124G>T	chr17.hg19:g.40345476C>A	ENSP00000301671:p.Gly42Trp	33.0	0.0		29.0	12.0	NM_001142622	B4DQS4|E9PDB5|Q9BXM6	Missense_Mutation	SNP	ENST00000301671.8	hg19	CCDS11422.1	.	.	.	.	.	.	.	.	.	.	C	18.07	3.541967	0.65198	.	.	ENSG00000167925	ENST00000428494;ENST00000414034;ENST00000301671;ENST00000436923	.	.	.	5.7	-4.38	0.03622	.	0.740503	0.12512	N	0.462409	T	0.30262	0.0759	N	0.19112	0.55	0.09310	N	1	P;D;D	0.60575	0.876;0.988;0.979	B;P;P	0.59115	0.299;0.852;0.514	T	0.26985	-1.0087	8	.	.	.	-0.2479	7.271	0.26256	0.0:0.2577:0.1373:0.605	.	42;42;42	E9PDB5;Q8N2G8-2;Q8N2G8	.;.;GHDC_HUMAN	W	42	.	.	G	-	1	0	GHDC	37599002	0.000000	0.05858	0.000000	0.03702	0.126000	0.20510	-1.514000	0.02254	-0.348000	0.08286	-0.137000	0.14449	GGG	.	.		0.682	GHDC-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449794.1	NM_032484		A	40345476	C	A	40345476	3	1	344	1	0	0	0	0	1	0	0	0	6377	623	22	3	1589	3	GHDC	17	40345476	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	617462	40345476	40849734	1165	48528										
AOC3	8639	hgsc.bcm.edu	37	chr17	41004309	41004309	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cagctccccctctacagttcTatccccaaggcccccgcttc	5	21	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:41004309T>A	ENST00000308423.2	+	1	1109	c.949T>A	c.(949-951)Tat>Aat	p.Y317N	AOC3_ENST00000591562.1_5'Flank	NM_003734.2	NP_003725.1	Q16853	AOC3_HUMAN	amine oxidase, copper containing 3	317			Y -> H (in dbSNP:rs438287).		amine metabolic process (GO:0009308)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell adhesion (GO:0007155)|inflammatory response (GO:0006954)|response to antibiotic (GO:0046677)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	aliphatic-amine oxidase activity (GO:0052595)|aminoacetone:oxygen oxidoreductase(deaminating) activity (GO:0052594)|calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|phenethylamine:oxygen oxidoreductase (deaminating) activity (GO:0052596)|primary amine oxidase activity (GO:0008131)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|tryptamine:oxygen oxidoreductase (deaminating) activity (GO:0052593)			breast(1)|central_nervous_system(4)|endometrium(4)|kidney(1)|large_intestine(8)|lung(14)|ovary(1)|skin(8)	41		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)	Hydralazine(DB01275)|Phenelzine(DB00780)	TCTACAGTTCTATCCCCAAGG	0.612																																					p.Y317N	NSCLC(3;192 220 10664 11501 16477)	Atlas-SNP	.											.	AOC3	88	.	0			c.T949A						.						39	44	43					17																	41004309		2197	4298	6495	SO:0001583	missense	8639	exon1			CAGTTCTATCCCC	AF067406	CCDS11444.1, CCDS62198.1, CCDS74071.1	17q21	2013-05-08	2013-05-08			ENSG00000131471	1.4.3.21		550	protein-coding gene	gene with protein product	"vascular adhesion protein 1"	603735				9653080, 8972912	Standard	NM_003734		Approved	VAP1, HPAO, VAP-1	uc002ibv.4	Q16853		ENST00000308423.2:c.949T>A	chr17.hg19:g.41004309T>A	ENSP00000312326:p.Tyr317Asn	42.0	0.0		55.0	26.0	NM_003734	B2RCI5|K7ESB3|L0L8N9|Q45F94	Missense_Mutation	SNP	ENST00000308423.2	hg19	CCDS11444.1	.	.	.	.	.	.	.	.	.	.	T	3.689	-0.063922	0.07273	.	.	ENSG00000131471	ENST00000308423	T	0.03663	3.85	4.79	-0.566	0.11767	Copper amine oxidase, C-terminal (3);	0.821470	0.11194	N	0.589528	T	0.03220	0.0094	N	0.19112	0.55	0.09310	N	0.999998	B	0.18461	0.028	B	0.31495	0.131	T	0.45818	-0.9235	10	0.72032	D	0.01	.	6.3467	0.21353	0.0:0.2341:0.248:0.5179	.	317	Q16853	AOC3_HUMAN	N	317	ENSP00000312326:Y317N	ENSP00000312326:Y317N	Y	+	1	0	AOC3	38257835	0.123000	0.22298	0.174000	0.22961	0.451000	0.32288	0.273000	0.18662	-0.044000	0.13491	-1.471000	0.01009	TAT	.	T|0.720;C|0.280		0.612	AOC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452444.1	NM_003734		A	41004309	T	A	41004309	3	1	344	1	0	0	0	0	1	0	0	0	728	1522	53	4	951	4	AOC3	17	41004309	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	658833	41004309	40190901	1166	48529										
NBR1	4077	hgsc.bcm.edu	37	chr17	41341610	41341610	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgctccatattctagttcagAgaacaagtggttaacgaaac	8	8	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:41341610A>T	ENST00000422280.1	+	8	945	c.486A>T	c.(484-486)agA>agT	p.R162S	NBR1_ENST00000589872.1_Missense_Mutation_p.R162S|NBR1_ENST00000389312.4_Missense_Mutation_p.R162S|NBR1_ENST00000542611.1_Missense_Mutation_p.R141S|NBR1_ENST00000341165.6_Missense_Mutation_p.R162S|NBR1_ENST00000590996.1_Missense_Mutation_p.R162S	NM_031858.2	NP_114064.1	Q14596	NBR1_HUMAN	neighbor of BRCA1 gene 1	162					macroautophagy (GO:0016236)|negative regulation of osteoblast differentiation (GO:0045668)|protein oligomerization (GO:0051259)|regulation of bone mineralization (GO:0030500)|regulation of stress-activated MAPK cascade (GO:0032872)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)	mitogen-activated protein kinase binding (GO:0051019)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(1)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	24		Breast(137;0.00086)		BRCA - Breast invasive adenocarcinoma(366;0.0934)		TCTAGTTCAGAGAACAAGTGG	0.398																																					p.R162S		Atlas-SNP	.											.	NBR1	55	.	0			c.A486T						.						63	61	62					17																	41341610		1839	4089	5928	SO:0001583	missense	4077	exon8			GTTCAGAGAACAA	X76952	CCDS45694.1	17q21.31	2008-02-01	2005-02-15	2005-02-16		ENSG00000188554			6746	protein-coding gene	gene with protein product		166945	"membrane component, chromosome 17, surface marker 2 (ovarian carcinoma antigen CA125)"	M17S2		8069304	Standard	XM_006721903		Approved	CA125, KIAA0049, 1A1-3B	uc010whv.2	Q14596		ENST00000422280.1:c.486A>T	chr17.hg19:g.41341610A>T	ENSP00000411250:p.Arg162Ser	115.0	0.0		99.0	49.0	NM_031862	Q13173|Q15026|Q5J7Q8|Q96GB6|Q9NRF7	Missense_Mutation	SNP	ENST00000422280.1	hg19	CCDS45694.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.382993	0.82792	.	.	ENSG00000188554	ENST00000422280;ENST00000542611;ENST00000341165;ENST00000389312;ENST00000389311	T;T;T;T	0.54279	1.37;0.58;1.37;1.21	5.87	4.79	0.61399	.	0.054253	0.85682	D	0.000000	T	0.63663	0.2530	M	0.67953	2.075	0.44880	D	0.997896	D;D;D	0.76494	0.999;0.992;0.999	D;D;D	0.66847	0.947;0.921;0.942	T	0.67405	-0.5679	10	0.87932	D	0	-11.6239	4.7675	0.13139	0.7421:0.0:0.2579:0.0	.	141;162;162	B7Z5R6;Q14596-2;Q14596	.;.;NBR1_HUMAN	S	162;141;162;162;162	ENSP00000411250:R162S;ENSP00000437545:R141S;ENSP00000343479:R162S;ENSP00000373963:R162S	ENSP00000343479:R162S	R	+	3	2	NBR1	38595136	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	3.089000	0.50183	2.248000	0.74166	0.533000	0.62120	AGA	.	.		0.398	NBR1-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453461.1	NM_005899		T	41341610	A	T	41341610	3	4	344	1	0	0	0	0	1	0	0	0	10209	301	11	4	512	4	NBR1	17	41341610	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	337301	41341610	39853600	1167	48530										
NBR1	4077	hgsc.bcm.edu	37	chr17	41352594	41352594	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaacagtgcccctaatcccaGaggtagtggagcttccaccg	10	13	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:41352594G>C	ENST00000422280.1	+	17	2896	c.2437G>C	c.(2437-2439)Gag>Cag	p.E813Q	NBR1_ENST00000589872.1_Missense_Mutation_p.E813Q|NBR1_ENST00000389312.4_Missense_Mutation_p.E813Q|NBR1_ENST00000542611.1_Missense_Mutation_p.E792Q|NBR1_ENST00000341165.6_Missense_Mutation_p.E813Q|NBR1_ENST00000590996.1_Missense_Mutation_p.E813Q	NM_031858.2	NP_114064.1	Q14596	NBR1_HUMAN	neighbor of BRCA1 gene 1	813					macroautophagy (GO:0016236)|negative regulation of osteoblast differentiation (GO:0045668)|protein oligomerization (GO:0051259)|regulation of bone mineralization (GO:0030500)|regulation of stress-activated MAPK cascade (GO:0032872)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)	mitogen-activated protein kinase binding (GO:0051019)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(1)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	24		Breast(137;0.00086)		BRCA - Breast invasive adenocarcinoma(366;0.0934)		CCTAATCCCAGAGGTAGTGGA	0.557																																					p.E813Q		Atlas-SNP	.											.	NBR1	55	.	0			c.G2437C						.						65	57	59					17																	41352594		1568	3582	5150	SO:0001583	missense	4077	exon17			ATCCCAGAGGTAG	X76952	CCDS45694.1	17q21.31	2008-02-01	2005-02-15	2005-02-16		ENSG00000188554			6746	protein-coding gene	gene with protein product		166945	"membrane component, chromosome 17, surface marker 2 (ovarian carcinoma antigen CA125)"	M17S2		8069304	Standard	XM_006721903		Approved	CA125, KIAA0049, 1A1-3B	uc010whv.2	Q14596		ENST00000422280.1:c.2437G>C	chr17.hg19:g.41352594G>C	ENSP00000411250:p.Glu813Gln	207.0	0.0		180.0	75.0	NM_031862	Q13173|Q15026|Q5J7Q8|Q96GB6|Q9NRF7	Missense_Mutation	SNP	ENST00000422280.1	hg19	CCDS45694.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.218390	0.79464	.	.	ENSG00000188554	ENST00000422280;ENST00000542611;ENST00000537493;ENST00000341165;ENST00000389312;ENST00000389311	T;T;T;T	0.51574	1.32;0.7;1.32;1.32	5.66	4.63	0.57726	.	.	.	.	.	T	0.66839	0.2830	M	0.71581	2.175	0.46521	D	0.999087	D;D;D	0.69078	0.997;0.981;0.977	D;P;P	0.75484	0.986;0.845;0.732	T	0.67852	-0.5563	9	0.51188	T	0.08	-5.3917	15.4539	0.75297	0.0:0.2453:0.7547:0.0	.	792;813;813	B7Z5R6;Q14596-2;Q14596	.;.;NBR1_HUMAN	Q	813;792;64;813;813;813	ENSP00000411250:E813Q;ENSP00000437545:E792Q;ENSP00000343479:E813Q;ENSP00000373963:E813Q	ENSP00000343479:E813Q	E	+	1	0	NBR1	38708120	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	5.879000	0.69690	2.676000	0.91093	0.591000	0.81541	GAG	.	.		0.557	NBR1-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453461.1	NM_005899		C	41352594	G	C	41352594	3	2	344	1	0	0	0	0	1	0	0	0	10209	943	33	4	2499	4	NBR1	17	41352594	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	10984	41352594	39842616	1168	48531										
FZD2	2535	hgsc.bcm.edu	37	chr17	42635241	42635241	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	catcatgcccaaccttctggGccacacgaaccaggaggacg	10	15	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:42635241G>T	ENST00000315323.3	+	1	317	c.185G>T	c.(184-186)gGc>gTc	p.G62V		NM_001466.3	NP_001457.1	Q14332	FZD2_HUMAN	frizzled class receptor 2	62	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cell-cell signaling (GO:0007267)|cochlea morphogenesis (GO:0090103)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hard palate development (GO:0060022)|inner ear receptor cell development (GO:0060119)|membranous septum morphogenesis (GO:0003149)|muscular septum morphogenesis (GO:0003150)|neuron differentiation (GO:0030182)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of cGMP metabolic process (GO:0030825)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|sensory perception of smell (GO:0007608)|vasculature development (GO:0001944)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	apical part of cell (GO:0045177)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(8)	33		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.189)		AACCTTCTGGGCCACACGAAC	0.612																																					p.G62V		Atlas-SNP	.											.	FZD2	81	.	0			c.G185T						.						174	150	158					17																	42635241		2203	4300	6503	SO:0001583	missense	2535	exon1			TTCTGGGCCACAC	L37882	CCDS11484.1	17q21.1	2014-01-29	2014-01-29			ENSG00000180340		"GPCR / Class F : Frizzled receptors"	4040	protein-coding gene	gene with protein product		600667	"frizzled (Drosophila) homolog 2", "frizzled homolog 2 (Drosophila)", "frizzled 2, seven transmembrane spanning receptor", "frizzled family receptor 2"			7558010, 9813155	Standard	NM_001466		Approved		uc002igx.2	Q14332		ENST00000315323.3:c.185G>T	chr17.hg19:g.42635241G>T	ENSP00000323901:p.Gly62Val	85.0	0.0		69.0	36.0	NM_001466	Q0VG82	Missense_Mutation	SNP	ENST00000315323.3	hg19	CCDS11484.1	.	.	.	.	.	.	.	.	.	.	g	18.64	3.667518	0.67814	.	.	ENSG00000180340	ENST00000541149;ENST00000315323	D	0.81659	-1.52	4.14	4.14	0.48551	Frizzled domain (5);	0.000000	0.85682	D	0.000000	D	0.92211	0.7530	H	0.94385	3.53	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	D	0.94697	0.7879	10	0.87932	D	0	.	16.0247	0.80536	0.0:0.0:1.0:0.0	.	62	Q14332	FZD2_HUMAN	V	138;62	ENSP00000323901:G62V	ENSP00000323901:G62V	G	+	2	0	FZD2	39990767	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.656000	0.83736	1.848000	0.53677	0.462000	0.41574	GGC	.	.		0.612	FZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457806.1	NM_001466		T	42635241	G	T	42635241	3	4	344	1	0	0	0	0	1	0	0	0	6138	1203	42	3	187	3	FZD2	17	42635241	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1282647	42635241	38559969	1169	48532										
C17orf104	284071	hgsc.bcm.edu	37	chr17	42750732	42750732	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaatttaaaatgcttccctcAggttgtgactttactaggca	7	8	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:42750732A>C	ENST00000409122.2	+	7	2599		c.e7-1		RP11-1072C15.4_ENST00000591628.1_RNA	NM_001145080.2	NP_001138552.2	A2RUB1	CQ104_HUMAN	chromosome 17 open reading frame 104											autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|pancreas(1)|skin(1)	24						TGCTTCCCTCAGGTTGTGACT	0.368																																					.		Atlas-SNP	.											.	C17orf104	75	.	0			c.2458-2A>C						.						208	175	185					17																	42750732		692	1591	2283	SO:0001630	splice_region_variant	284071	exon7			TCCCTCAGGTTGT		CCDS45703.1, CCDS45703.2	17q21.31	2009-09-08			ENSG00000180336	ENSG00000180336			26670	protein-coding gene	gene with protein product							Standard	NM_001145080		Approved	FLJ35848	uc002iha.3	A2RUB1	OTTHUMG00000153039	ENST00000409122.2:c.2458-1A>C	chr17.hg19:g.42750732A>C		49.0	0.0		63.0	24.0	NM_001145080	B4DXJ2|B5MD93|B9EGQ6|C4AM97|Q4G0Y1|Q8IVZ7|Q8NA45	Splice_Site	SNP	ENST00000409122.2	hg19	CCDS45703.2	.	.	.	.	.	.	.	.	.	.	A	21.2	4.110358	0.77210	.	.	ENSG00000180336	ENST00000409122	.	.	.	5.67	5.67	0.87782	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9161	0.79521	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	C17orf104	40106258	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	8.071000	0.89494	2.171000	0.68590	0.528000	0.53228	.	.	.		0.368	C17orf104-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329171.2	NM_001145080	Intron	C	42750732	A	C	42750732	5	2	344	1	0	0	0	0	0	0	1	0	1853	202	7	5	2482	5	C17orf104	17	42750732	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	115491	42750732	38444478	1170	48533										
HOXB6	3216	hgsc.bcm.edu	37	chr17	46675506	46675506	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggtggagttcacgaaataggAactcattgggaggggaggcg	18	5	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:46675506A>T	ENST00000484302.2	-	2	629	c.7T>A	c.(7-9)Tcc>Acc	p.S3T	HOXB-AS3_ENST00000487849.3_RNA|HOXB-AS3_ENST00000477144.1_RNA|HOXB-AS3_ENST00000474324.1_RNA|HOXB-AS3_ENST00000480872.1_RNA|HOXB3_ENST00000552000.2_Intron|HOXB6_ENST00000225648.3_Missense_Mutation_p.S3T|HOXB-AS3_ENST00000465846.2_RNA|HOXB-AS3_ENST00000474040.1_RNA|HOXB-AS3_ENST00000466037.2_RNA|HOXB-AS3_ENST00000467155.2_RNA|HOXB6_ENST00000490419.1_5'Flank|HOXB-AS3_ENST00000460041.1_RNA|HOXB-AS3_ENST00000481995.1_RNA|HOXB-AS3_ENST00000492897.3_RNA|HOXB-AS3_ENST00000476204.1_RNA|HOXB-AS3_ENST00000429755.4_RNA			P17509	HXB6_HUMAN	homeobox B6	3					anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|erythrocyte homeostasis (GO:0034101)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(1)|lung(4)	7						ACGAAATAGGAACTCATTGGG	0.597																																					p.S3T		Atlas-SNP	.											.	HOXB6	13	.	0			c.T7A						.						8	10	9					17																	46675506		2158	4218	6376	SO:0001583	missense	3216	exon3			AATAGGAACTCAT		CCDS11531.1	17q21.32	2011-06-20	2005-12-22		ENSG00000108511	ENSG00000108511		"Homeoboxes / ANTP class : HOXL subclass"	5117	protein-coding gene	gene with protein product		142961	"homeo box B6"	HOX2, HOX2B		1973146, 1358459	Standard	XM_005257284		Approved		uc002ins.1	P17509	OTTHUMG00000159912	ENST00000484302.2:c.7T>A	chr17.hg19:g.46675506A>T	ENSP00000420009:p.Ser3Thr	68.0	0.0		67.0	31.0	NM_018952	A8K835|D3DTV5|P09068|Q9HB11|Q9UGH2	Missense_Mutation	SNP	ENST00000484302.2	hg19	CCDS11531.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.756445	0.89843	.	.	ENSG00000108511	ENST00000484302;ENST00000225648	D;D	0.94537	-3.45;-3.45	5.26	5.26	0.73747	.	0.000000	0.64402	D	0.000001	D	0.96873	0.8979	M	0.76170	2.325	0.58432	D	0.999999	D;D	0.89917	0.974;1.0	D;D	0.83275	0.953;0.996	D	0.97462	1.0035	10	0.87932	D	0	.	15.007	0.71519	1.0:0.0:0.0:0.0	.	3;3	P17509-2;P17509	.;HXB6_HUMAN	T	3	ENSP00000420009:S3T;ENSP00000225648:S3T	ENSP00000225648:S3T	S	-	1	0	HOXB6	44030505	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.592000	0.90828	2.208000	0.71279	0.459000	0.35465	TCC	.	.		0.597	HOXB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358146.2			T	46675506	A	T	46675506	3	4	344	1	0	0	0	0	1	0	0	0	7314	246	9	4	675	4	HOXB6	17	46675506	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3924774	46675506	34519704	1171	48534										
SPOP	8405	hgsc.bcm.edu	37	chr17	47679227	47679227	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctttgaagatgccaactcacTagttgatgaaatccactgcc	7	11	1	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:47679227T>C	ENST00000393328.2	-	10	1345	c.980A>G	c.(979-981)tAt>tGt	p.Y327C	SPOP_ENST00000504102.1_Splice_Site_p.Y327C|SPOP_ENST00000347630.2_Splice_Site_p.Y327C|SPOP_ENST00000503676.1_Splice_Site_p.Y327C|SPOP_ENST00000393331.3_Splice_Site_p.Y327C	NM_003563.3	NP_003554.1	O43791	SPOP_HUMAN	speckle-type POZ protein	327	Important for homodimerization.				glucose homeostasis (GO:0042593)|positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902237)|positive regulation of type B pancreatic cell apoptotic process (GO:2000676)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	Cul3-RING ubiquitin ligase complex (GO:0031463)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	ubiquitin protein ligase binding (GO:0031625)			endometrium(18)|kidney(1)|large_intestine(3)|liver(1)|lung(4)|ovary(3)|prostate(33)	63						GCCAACTCACTAGTTGATGAA	0.438										Prostate(2;0.17)																											p.Y327C		Atlas-SNP	.											.	SPOP	91	.	0			c.A980G						.						95	96	96					17																	47679227		2203	4300	6503	SO:0001630	splice_region_variant	8405	exon9			ACTCACTAGTTGA	AJ000644	CCDS11551.1	17q21.33	2013-01-09			ENSG00000121067	ENSG00000121067		"BTB/POZ domain containing"	11254	protein-coding gene	gene with protein product		602650				9414087	Standard	NM_001007227		Approved	TEF2, BTBD32	uc002ipg.3	O43791	OTTHUMG00000161496	ENST00000393328.2:c.980+1A>G	chr17.hg19:g.47679227T>C		99.0	0.0		76.0	37.0	NM_001007228	B2R6S3|D3DTW7|Q53HJ1	Missense_Mutation	SNP	ENST00000393328.2	hg19	CCDS11551.1	.	.	.	.	.	.	.	.	.	.	T	13.54	2.269140	0.40095	.	.	ENSG00000121067	ENST00000393328;ENST00000393331;ENST00000347630;ENST00000504102;ENST00000503536;ENST00000503676;ENST00000513872	T;T;T;T;T	0.68624	-0.34;-0.34;-0.34;-0.34;-0.34	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.57533	0.2060	L	0.34521	1.04	0.80722	D	1	B	0.09022	0.002	B	0.04013	0.001	T	0.55036	-0.8203	10	0.52906	T	0.07	-0.0427	15.2499	0.73536	0.0:0.0:0.0:1.0	.	327	O43791	SPOP_HUMAN	C	327;327;327;327;211;327;280	ENSP00000377001:Y327C;ENSP00000377004:Y327C;ENSP00000240327:Y327C;ENSP00000425905:Y327C;ENSP00000420908:Y327C	ENSP00000240327:Y327C	Y	-	2	0	SPOP	45034226	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.080000	0.50112	2.273000	0.75805	0.482000	0.46254	TAT	.	.		0.438	SPOP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365154.2	NM_003563	Missense_Mutation	C	47679227	T	C	47679227	5	2	344	1	0	0	0	0	0	0	1	0	15099	1536	53	2	152	2	SPOP	17	47679227	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1003721	47679227	33515983	1172	48535										
SPOP	8405	hgsc.bcm.edu	37	chr17	47699405	47699405	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaagttattgatggtccacaTgtaggagaatttcactacct	8	7	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:47699405T>A	ENST00000393328.2	-	4	468	c.103A>T	c.(103-105)Atg>Ttg	p.M35L	SPOP_ENST00000504102.1_Missense_Mutation_p.M35L|SPOP_ENST00000513080.1_5'UTR|SPOP_ENST00000347630.2_Missense_Mutation_p.M35L|SPOP_ENST00000503676.1_Missense_Mutation_p.M35L|SPOP_ENST00000393331.3_Missense_Mutation_p.M35L	NM_003563.3	NP_003554.1	O43791	SPOP_HUMAN	speckle-type POZ protein	35	MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.				glucose homeostasis (GO:0042593)|positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902237)|positive regulation of type B pancreatic cell apoptotic process (GO:2000676)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	Cul3-RING ubiquitin ligase complex (GO:0031463)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	ubiquitin protein ligase binding (GO:0031625)			endometrium(18)|kidney(1)|large_intestine(3)|liver(1)|lung(4)|ovary(3)|prostate(33)	63						ATGGTCCACATGTAGGAGAAT	0.373										Prostate(2;0.17)																											p.M35L		Atlas-SNP	.											.	SPOP	91	.	0			c.A103T						.						55	53	54					17																	47699405		2203	4300	6503	SO:0001583	missense	8405	exon3			TCCACATGTAGGA	AJ000644	CCDS11551.1	17q21.33	2013-01-09			ENSG00000121067	ENSG00000121067		"BTB/POZ domain containing"	11254	protein-coding gene	gene with protein product		602650				9414087	Standard	NM_001007227		Approved	TEF2, BTBD32	uc002ipg.3	O43791	OTTHUMG00000161496	ENST00000393328.2:c.103A>T	chr17.hg19:g.47699405T>A	ENSP00000377001:p.Met35Leu	148.0	0.0		120.0	55.0	NM_001007228	B2R6S3|D3DTW7|Q53HJ1	Missense_Mutation	SNP	ENST00000393328.2	hg19	CCDS11551.1	.	.	.	.	.	.	.	.	.	.	T	17.02	3.282096	0.59867	.	.	ENSG00000121067	ENST00000393328;ENST00000393331;ENST00000347630;ENST00000504102;ENST00000503676;ENST00000509079;ENST00000505581;ENST00000507970;ENST00000514121;ENST00000515508;ENST00000510476;ENST00000508805	T;T;T;T;T;T;T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91	5.48	5.48	0.80851	TRAF-type (1);TRAF-like (1);MATH (1);	0.000000	0.85682	D	0.000000	T	0.17619	0.0423	N	0.01242	-0.935	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.15983	-1.0418	10	0.15499	T	0.54	-0.9742	15.4048	0.74868	0.0:0.0:0.0:1.0	.	35	O43791	SPOP_HUMAN	L	35	ENSP00000377001:M35L;ENSP00000377004:M35L;ENSP00000240327:M35L;ENSP00000425905:M35L;ENSP00000420908:M35L;ENSP00000426986:M35L;ENSP00000420960:M35L;ENSP00000426262:M35L;ENSP00000424119:M35L;ENSP00000426537:M35L;ENSP00000425410:M35L	ENSP00000240327:M35L	M	-	1	0	SPOP	45054404	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.868000	0.87116	2.307000	0.77673	0.528000	0.53228	ATG	.	.		0.373	SPOP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365154.2	NM_003563		A	47699405	T	A	47699405	3	1	344	1	0	0	0	0	1	0	0	0	15099	1464	51	4	1053	4	SPOP	17	47699405	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	20178	47699405	33495805	1173	48536										
MYCBPAP	84073	hgsc.bcm.edu	37	chr17	48597032	48597032	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cagtgggttctggagtcgacTggaatacttgggagatgaga	16	5	1	2	rs183786523		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:48597032T>A	ENST00000323776.5	+	7	1091	c.929T>A	c.(928-930)cTg>cAg	p.L310Q	MYCBPAP_ENST00000436259.2_Missense_Mutation_p.L273Q|MYCBPAP_ENST00000468821.1_3'UTR	NM_032133.4	NP_115509.4			MYCBP associated protein											breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(8)|ovary(4)|pancreas(1)|skin(2)|urinary_tract(2)	31	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;1.23e-09)			TGGAGTCGACTGGAATACTTG	0.537																																					p.L310Q		Atlas-SNP	.											.	MYCBPAP	135	.	0			c.T929A						.						92	83	86					17																	48597032		2203	4300	6503	SO:0001583	missense	84073	exon7			GTCGACTGGAATA	BC028393	CCDS32680.2	17q21.33	2004-02-19			ENSG00000136449	ENSG00000136449			19677	protein-coding gene	gene with protein product		609835				12151104	Standard	NM_032133		Approved	AMAP-1, DKFZp434N1415	uc010wmr.2	Q8TBZ2	OTTHUMG00000157184	ENST00000323776.5:c.929T>A	chr17.hg19:g.48597032T>A	ENSP00000323184:p.Leu310Gln	109.0	0.0		82.0	45.0	NM_032133		Missense_Mutation	SNP	ENST00000323776.5	hg19	CCDS32680.2	.	.	.	.	.	.	.	.	.	.	T	18.95	3.732647	0.69189	.	.	ENSG00000136449	ENST00000323776;ENST00000436259	T;T	0.40756	1.02;1.02	5.86	3.56	0.40772	.	0.141462	0.46758	D	0.000264	T	0.51058	0.1652	M	0.72479	2.2	0.36170	D	0.848702	D;D	0.71674	0.998;0.998	D;D	0.65443	0.935;0.935	T	0.59423	-0.7457	10	0.11182	T	0.66	-5.2915	4.6699	0.12683	0.0:0.4328:0.0:0.5672	.	273;310	Q8TBZ2;B4DZQ1	MYBPP_HUMAN;.	Q	310;273	ENSP00000323184:L310Q;ENSP00000397209:L273Q	ENSP00000323184:L310Q	L	+	2	0	MYCBPAP	45952031	0.994000	0.37717	0.967000	0.41034	0.936000	0.57629	2.892000	0.48625	1.035000	0.39972	0.460000	0.39030	CTG	.	T|1.000;C|0.000		0.537	MYCBPAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347814.1	NM_032133		A	48597032	T	A	48597032	3	1	344	1	0	0	0	0	1	0	0	0	10028	1580	55	4	955	4	MYCBPAP	17	48597032	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	897627	48597032	32598178	1174	48537										
AKAP1	8165	hgsc.bcm.edu	37	chr17	55187406	55187406	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gttctgacaggaacagcatgGattccgtggatagctgttgc	13	8	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:55187406G>T	ENST00000337714.3	+	3	1968	c.1735G>T	c.(1735-1737)Gat>Tat	p.D579Y	AKAP1_ENST00000572557.1_Missense_Mutation_p.D579Y|AKAP1_ENST00000539273.1_Missense_Mutation_p.D579Y|AKAP1_ENST00000571629.1_Missense_Mutation_p.D579Y	NM_003488.3	NP_003479.1	Q92667	AKAP1_HUMAN	A kinase (PRKA) anchor protein 1	579					blood coagulation (GO:0007596)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(2)|liver(1)|lung(7)|ovary(2)|pancreas(1)|skin(1)	14	Breast(9;5.46e-08)					GAACAGCATGGATTCCGTGGA	0.532																																					p.D579Y		Atlas-SNP	.											.	AKAP1	73	.	0			c.G1735T						.						93	87	89					17																	55187406		2203	4300	6503	SO:0001583	missense	8165	exon4			AGCATGGATTCCG	X97335	CCDS11594.1	17q22	2013-01-23			ENSG00000121057	ENSG00000121057		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Tudor domain containing"	367	protein-coding gene	gene with protein product	"protein kinase anchoring protein 1", "dual specificity A-kinase-anchoring protein 1", "protein phosphatase 1, regulatory subunit 43", "tudor domain containing 17"	602449		PRKA1		8769136, 7499250	Standard	NM_003488		Approved	AKAP121, AKAP149, SAKAP84, S-AKAP84, AKAP84, D-AKAP1, PPP1R43, TDRD17	uc002iux.3	Q92667	OTTHUMG00000140369	ENST00000337714.3:c.1735G>T	chr17.hg19:g.55187406G>T	ENSP00000337736:p.Asp579Tyr	77.0	0.0		77.0	27.0	NM_001242902	A8K8Q1|D3DTZ0|Q13320|Q9BW14	Missense_Mutation	SNP	ENST00000337714.3	hg19	CCDS11594.1	.	.	.	.	.	.	.	.	.	.	G	16.44	3.124410	0.56613	.	.	ENSG00000121057	ENST00000337714;ENST00000427138;ENST00000539273	T;T	0.27256	1.68;1.68	5.18	5.18	0.71444	.	0.049094	0.85682	D	0.000000	T	0.52289	0.1725	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.55897	-0.8068	10	0.87932	D	0	-18.2913	17.7148	0.88333	0.0:0.0:1.0:0.0	.	579	Q92667	AKAP1_HUMAN	Y	579;621;579	ENSP00000337736:D579Y;ENSP00000443139:D579Y	ENSP00000337736:D579Y	D	+	1	0	AKAP1	52542405	1.000000	0.71417	1.000000	0.80357	0.083000	0.17756	9.303000	0.96183	2.426000	0.82243	0.655000	0.94253	GAT	.	.		0.532	AKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277069.1			T	55187406	G	T	55187406	3	4	344	1	0	0	0	0	1	0	0	0	445	1174	41	3	1741	3	AKAP1	17	55187406	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	6590374	55187406	26007804	1175	48538										
USP32	84669	hgsc.bcm.edu	37	chr17	58260585	58260585	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggcttttgctcaggagcacgTcctcttccccagccgaactc	9	16	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:58260585T>A	ENST00000300896.4	-	31	4258	c.4064A>T	c.(4063-4065)gAc>gTc	p.D1355V	USP32_ENST00000592339.1_Missense_Mutation_p.D1025V	NM_032582.3	NP_115971.2	Q8NFA0	UBP32_HUMAN	ubiquitin specific peptidase 32	1355	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			NS(3)|breast(5)|endometrium(5)|kidney(4)|large_intestine(12)|liver(1)|lung(24)|pancreas(1)|prostate(3)|skin(3)|urinary_tract(1)	62	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			CAGGAGCACGTCCTCTTCCCC	0.577																																					p.D1355V		Atlas-SNP	.											.	USP32	128	.	0			c.A4064T						.						75	69	71					17																	58260585		2203	4300	6503	SO:0001583	missense	84669	exon31			AGCACGTCCTCTT	AF533230	CCDS32697.1	17q23.3	2013-01-10	2005-08-08		ENSG00000170832	ENSG00000170832		"Ubiquitin-specific peptidases", "EF-hand domain containing"	19143	protein-coding gene	gene with protein product		607740	"ubiquitin specific protease 32"			12838346	Standard	NM_032582		Approved	NY-REN-60, USP10	uc002iyo.1	Q8NFA0		ENST00000300896.4:c.4064A>T	chr17.hg19:g.58260585T>A	ENSP00000300896:p.Asp1355Val	137.0	0.0		130.0	70.0	NM_032582	Q7Z5T3|Q9BX85|Q9Y591	Missense_Mutation	SNP	ENST00000300896.4	hg19	CCDS32697.1	.	.	.	.	.	.	.	.	.	.	T	13.19	2.163053	0.38217	.	.	ENSG00000170832	ENST00000300896	T	0.46063	0.88	5.79	2.3	0.28687	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.293915	0.35870	N	0.002929	T	0.24005	0.0581	N	0.24115	0.695	0.36937	D	0.89218	B	0.02656	0.0	B	0.06405	0.002	T	0.08806	-1.0704	10	0.56958	D	0.05	.	3.4903	0.07636	0.1347:0.0724:0.1412:0.6517	.	1355	Q8NFA0	UBP32_HUMAN	V	1355	ENSP00000300896:D1355V	ENSP00000300896:D1355V	D	-	2	0	USP32	55615367	0.673000	0.27539	0.159000	0.22649	0.961000	0.63080	1.170000	0.31883	0.107000	0.17824	0.455000	0.32223	GAC	.	.		0.577	USP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449235.2	NM_032582		A	58260585	T	A	58260585	3	1	344	1	0	0	0	0	1	0	0	0	17078	1667	58	4	766	4	USP32	17	58260585	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	3073179	58260585	22934625	1176	48539										
BRIP1	83990	hgsc.bcm.edu	37	chr17	59793426	59793426	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	attgtcgttttagttcaaccTaataattttaaaatatattt	3	4	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:59793426T>A	ENST00000259008.2	-	17	2647		c.e17-2		BRIP1_ENST00000577598.1_Splice_Site	NM_032043.2	NP_114432.2	Q9BX63	FANCJ_HUMAN	BRCA1 interacting protein C-terminal helicase 1						DNA damage checkpoint (GO:0000077)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(9)|kidney(5)|large_intestine(9)|liver(2)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	55						TAGTTCAACCtaataatttta	0.289			"F, N, Mis"			"AML, leukemia, breast"		Involved in tolerance or repair of DNA crosslinks																													.		Atlas-SNP	.	yes	Rec		"Fanconi anaemia J, breast cancer susceptiblity"	17	17q22	83990	BRCA1 interacting protein C-terminal helicase 1		"L, E"	.	BRIP1	237	.	0			c.2380-2A>T						.						29	28	28					17																	59793426		2203	4299	6502	SO:0001630	splice_region_variant	83990	exon18			TCAACCTAATAAT	AF360549	CCDS11631.1	17q22.2	2014-09-17				ENSG00000136492		"Fanconi anemia, complementation groups"	20473	protein-coding gene	gene with protein product	"BRCA1/BRCA2-associated helicase 1"	605882				11595410, 11301010	Standard	NM_032043		Approved	OF, BACH1, FANCJ	uc002izk.2	Q9BX63		ENST00000259008.2:c.2380-2A>T	chr17.hg19:g.59793426T>A		54.0	0.0		39.0	16.0	NM_032043	Q3MJE2|Q8NCI5	Splice_Site	SNP	ENST00000259008.2	hg19	CCDS11631.1																																																																																			.	.		0.289	BRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445362.1	NM_032043	Intron	A	59793426	T	A	59793426	5	1	344	1	0	0	0	0	0	0	1	0	1516	1536	53	4	1387	4	BRIP1	17	59793426	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1532841	59793426	21401784	1177	48540										
MRC2	9902	hgsc.bcm.edu	37	chr17	60744225	60744225	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccctcaagtacctcaactggGagagtggtgaggcacaaggt	13	10	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:60744225G>T	ENST00000303375.5	+	5	1369	c.967G>T	c.(967-969)Gag>Tag	p.E323*		NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	323	C-type lectin 1. {ECO:0000255|PROSITE- ProRule:PRU00040}.				collagen catabolic process (GO:0030574)|endocytosis (GO:0006897)|osteoblast differentiation (GO:0001649)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|collagen binding (GO:0005518)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(11)|lung(28)|ovary(2)|prostate(1)|skin(3)	53						CCTCAACTGGGAGAGTGGTGA	0.637																																					p.E323X		Atlas-SNP	.											.	MRC2	126	.	0			c.G967T						.						56	58	58					17																	60744225		2203	4300	6503	SO:0001587	stop_gained	9902	exon5			AACTGGGAGAGTG	AB014609	CCDS11634.1	17q23	2011-08-30				ENSG00000011028		"CD molecules", "C-type lectin domain containing"	16875	protein-coding gene	gene with protein product		612264				9734811, 8702911	Standard	NM_006039		Approved	KIAA0709, ENDO180, CLEC13E, CD280	uc002jad.4	Q9UBG0		ENST00000303375.5:c.967G>T	chr17.hg19:g.60744225G>T	ENSP00000307513:p.Glu323*	98.0	0.0		79.0	37.0	NM_006039	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	Nonsense_Mutation	SNP	ENST00000303375.5	hg19	CCDS11634.1	.	.	.	.	.	.	.	.	.	.	G	41	8.802297	0.98960	.	.	ENSG00000011028	ENST00000303375	.	.	.	3.77	3.77	0.43336	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07990	T	0.79	-13.1823	15.7977	0.78424	0.0:0.0:1.0:0.0	.	.	.	.	X	323	.	ENSP00000307513:E323X	E	+	1	0	MRC2	58097957	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	9.657000	0.98554	1.939000	0.56221	0.462000	0.41574	GAG	.	.		0.637	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1			T	60744225	G	T	60744225	4	4	344	1	0	0	0	0	0	1	0	0	9767	1175	41	3	985	3	MRC2	17	60744225	Nonsense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	950799	60744225	20450985	1178	48541										
BPTF	2186	hgsc.bcm.edu	37	chr17	65907751	65907751	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccattgtttcttcttccaagAgtgctttacattcatcagtg	6	10	4	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:65907751A>G	ENST00000321892.4	+	13	4190	c.4129A>G	c.(4129-4131)Agt>Ggt	p.S1377G	BPTF_ENST00000306378.6_Missense_Mutation_p.S1251G|BPTF_ENST00000424123.3_Missense_Mutation_p.S1238G|BPTF_ENST00000335221.5_Missense_Mutation_p.S1377G			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	1377					anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			TTCTTCCAAGAGTGCTTTACA	0.418																																					p.S1377G		Atlas-SNP	.											.	BPTF	415	.	0			c.A4129G						.						94	90	91					17																	65907751		2203	4300	6503	SO:0001583	missense	2186	exon13			TCCAAGAGTGCTT	AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"Zinc fingers, PHD-type"	3581	protein-coding gene	gene with protein product		601819	"fetal Alzheimer antigen"	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.4129A>G	chr17.hg19:g.65907751A>G	ENSP00000315454:p.Ser1377Gly	126.0	0.0		122.0	49.0	NM_004459	Q6NX67|Q7Z7D6|Q9UIG2	Missense_Mutation	SNP	ENST00000321892.4	hg19		.	.	.	.	.	.	.	.	.	.	A	4.645	0.119989	0.08881	.	.	ENSG00000171634	ENST00000306378;ENST00000335221;ENST00000321892	T;T;T	0.63580	-0.05;-0.05;-0.05	5.72	4.64	0.57946	.	.	.	.	.	T	0.49440	0.1557	L	0.29908	0.895	0.09310	N	1	B;B	0.33940	0.372;0.433	B;B	0.33454	0.114;0.164	T	0.43015	-0.9417	9	0.54805	T	0.06	-0.116	9.2717	0.37675	0.8434:0.0:0.1566:0.0	.	1251;1377	Q12830-2;Q12830-4	.;.	G	1251;1377;1377	ENSP00000307208:S1251G;ENSP00000334351:S1377G;ENSP00000315454:S1377G	ENSP00000307208:S1251G	S	+	1	0	BPTF	63338213	0.500000	0.26091	0.200000	0.23457	0.702000	0.40608	1.892000	0.39748	0.991000	0.38814	0.528000	0.53228	AGT	.	.		0.418	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459		G	65907751	A	G	65907751	3	3	344	1	0	0	0	0	1	0	0	0	1497	304	11	2	4179	2	BPTF	17	65907751	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	5163526	65907751	15287459	1179	48542										
RNF157	114804	hgsc.bcm.edu	37	chr17	74151646	74151646	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cccgtcccttcccttacctcTccttcttctgagggggccct	7	19	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:74151646T>C	ENST00000269391.6	-	15	1827	c.1695A>G	c.(1693-1695)ggA>ggG	p.G565G	RNF157-AS1_ENST00000585542.1_RNA|RNF157-AS1_ENST00000590137.1_RNA|RNF157-AS1_ENST00000586661.1_RNA|RNF157-AS1_ENST00000586627.1_RNA|RNF157-AS1_ENST00000592748.1_RNA|RNF157_ENST00000319945.6_Silent_p.G565G	NM_052916.2	NP_443148.1	Q96PX1	RN157_HUMAN	ring finger protein 157	565							zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	25			LUSC - Lung squamous cell carcinoma(166;0.187)			CCCTTACCTCTCCTTCTTCTG	0.587																																					p.G565G	GBM(186;507 2120 27388 27773 52994)	Atlas-SNP	.											.	RNF157	66	.	0			c.A1695G						.						42	44	44					17																	74151646		2202	4299	6501	SO:0001819	synonymous_variant	114804	exon15			TACCTCTCCTTCT	AK091467	CCDS32740.1	17q25.3	2004-02-27			ENSG00000141576	ENSG00000141576		"RING-type (C3HC4) zinc fingers"	29402	protein-coding gene	gene with protein product						11572484	Standard	NM_052916		Approved	KIAA1917	uc002jqz.3	Q96PX1	OTTHUMG00000132627	ENST00000269391.6:c.1695A>G	chr17.hg19:g.74151646T>C		52.0	0.0		55.0	17.0	NM_052916	Q8NB72|Q96N56	Silent	SNP	ENST00000269391.6	hg19	CCDS32740.1																																																																																			.	.		0.587	RNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255874.2	XM_290732		C	74151646	T	C	74151646	2	2	344	1	0	0	0	0	0	0	0	1	13469	1538	54	2		2	RNF157	17	74151646	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	8243895	74151646	7043564	1180	48543										
SEC14L1	6397	hgsc.bcm.edu	37	chr17	75196640	75196640	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gacaaagccagagagatcatGtgtcagtctttgacgtggag	13	7	3	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:75196640G>T	ENST00000413679.2	+	9	1197	c.894G>T	c.(892-894)atG>atT	p.M298I	SEC14L1_ENST00000443798.4_Missense_Mutation_p.M298I|SEC14L1_ENST00000431431.2_Missense_Mutation_p.M264I|SEC14L1_ENST00000585618.1_Missense_Mutation_p.M298I|SEC14L1_ENST00000591437.1_Missense_Mutation_p.M264I|SEC14L1_ENST00000436233.4_Missense_Mutation_p.M298I|SEC14L1_ENST00000392476.2_Missense_Mutation_p.M298I|SEC14L1_ENST00000430767.4_Missense_Mutation_p.M298I	NM_001143998.1|NM_001143999.1|NM_003003.3	NP_001137470|NP_001137471|NP_002994	Q92503	S14L1_HUMAN	SEC14-like 1 (S. cerevisiae)	298					transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(2)	31						GAGAGATCATGTGTCAGTCTT	0.448																																					p.M298I		Atlas-SNP	.											.	SEC14L1	81	.	0			c.G894T						.						147	141	143					17																	75196640		2203	4300	6503	SO:0001583	missense	6397	exon11			GATCATGTGTCAG	D67029	CCDS11752.1, CCDS42385.1, CCDS45789.1	17q25.2	2008-02-01	2001-11-28			ENSG00000129657			10698	protein-coding gene	gene with protein product		601504	"SEC14 (S. cerevisiae)-like 1"	SEC14L		8697811	Standard	NM_001143998		Approved	PRELID4A	uc002jto.3	Q92503		ENST00000413679.2:c.894G>T	chr17.hg19:g.75196640G>T	ENSP00000394716:p.Met298Ile	92.0	0.0		60.0	25.0	NM_001204408	A8K4E8|B4DDI5|D5G3K1|Q99780	Missense_Mutation	SNP	ENST00000413679.2	hg19	CCDS11752.1	.	.	.	.	.	.	.	.	.	.	G	14.90	2.674621	0.47781	.	.	ENSG00000129657	ENST00000392476;ENST00000443798;ENST00000436233;ENST00000430767;ENST00000413679;ENST00000431431	T;T;T;T;T;T	0.69306	-0.28;-0.28;-0.28;-0.28;-0.28;-0.39	5.4	3.22	0.36961	Phosphatidylinositol transfer protein-like, N-terminal (1);	0.148106	0.64402	D	0.000008	T	0.49525	0.1562	N	0.22421	0.69	0.35984	D	0.836204	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.55515	-0.8129	10	0.52906	T	0.07	-36.1981	9.3747	0.38275	0.0:0.3855:0.4608:0.1537	.	298;298	Q92503-2;Q92503	.;S14L1_HUMAN	I	298;298;298;298;298;264	ENSP00000376268:M298I;ENSP00000406030:M298I;ENSP00000390392:M298I;ENSP00000408169:M298I;ENSP00000394716:M298I;ENSP00000389838:M264I	ENSP00000376268:M298I	M	+	3	0	SEC14L1	72708235	1.000000	0.71417	0.999000	0.59377	0.986000	0.74619	1.242000	0.32755	1.368000	0.46115	0.650000	0.86243	ATG	.	.		0.448	SEC14L1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000436240.1	NM_003003		T	75196640	G	T	75196640	3	4	344	1	0	0	0	0	1	0	0	0	13996	1377	48	3	920	3	SEC14L1	17	75196640	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1044994	75196640	5998570	1181	48544										
TK1	7083	hgsc.bcm.edu	37	chr17	76170929	76170929	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tggctttcctggcactgggcAgttctctttgttgtccggcc	12	12	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:76170929A>G	ENST00000301634.7	-	7	854	c.616T>C	c.(616-618)Tgc>Cgc	p.C206R	TK1_ENST00000405273.1_Missense_Mutation_p.C206R|TK1_ENST00000588734.1_Missense_Mutation_p.C239R|TK1_ENST00000590862.1_Intron|TK1_ENST00000590430.1_3'UTR	NM_003258.4	NP_003249.3	P04183	KITH_HUMAN	thymidine kinase 1, soluble	206					deoxyribonucleoside monophosphate biosynthetic process (GO:0009157)|digestive tract development (GO:0048565)|DNA replication (GO:0006260)|fetal process involved in parturition (GO:0060138)|liver development (GO:0001889)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide biosynthetic process (GO:0009165)|protein homotetramerization (GO:0051289)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|response to copper ion (GO:0046688)|response to cortisol (GO:0051414)|response to nutrient levels (GO:0031667)|response to toxic substance (GO:0009636)|skeletal muscle cell proliferation (GO:0014856)|small molecule metabolic process (GO:0044281)|thymidine metabolic process (GO:0046104)	cytosol (GO:0005829)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|nucleoside kinase activity (GO:0019206)|thymidine kinase activity (GO:0004797)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|urinary_tract(2)	4			BRCA - Breast invasive adenocarcinoma(99;0.00269)|OV - Ovarian serous cystadenocarcinoma(97;0.0804)|Lung(188;0.23)		Trifluridine(DB00432)|Zidovudine(DB00495)	GGCACTGGGCAGTTCTCTTTG	0.612																																					p.C206R		Atlas-SNP	.											.	TK1	23	.	0			c.T616C						.						43	42	42					17																	76170929		2203	4300	6503	SO:0001583	missense	7083	exon7			CTGGGCAGTTCTC		CCDS11754.1	17q23.2-q25.3	2012-10-02			ENSG00000167900	ENSG00000167900	2.7.1.21		11830	protein-coding gene	gene with protein product		188300					Standard	NM_003258		Approved		uc002juw.2	P04183	OTTHUMG00000150674	ENST00000301634.7:c.616T>C	chr17.hg19:g.76170929A>G	ENSP00000301634:p.Cys206Arg	65.0	0.0		49.0	22.0	NM_003258	B2RC58|Q969V0|Q9UMG9	Missense_Mutation	SNP	ENST00000301634.7	hg19	CCDS11754.1	.	.	.	.	.	.	.	.	.	.	A	11.40	1.628987	0.28978	.	.	ENSG00000167900	ENST00000301634;ENST00000405273	.	.	.	5.7	4.61	0.57282	.	0.640586	0.17349	N	0.177448	T	0.41143	0.1146	L	0.27053	0.805	0.58432	D	0.999998	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.20140	-1.0284	9	0.35671	T	0.21	-12.3596	6.6955	0.23197	0.5999:0.3222:0.0779:0.0	.	206;206	B5BU32;P04183	.;KITH_HUMAN	R	206	.	ENSP00000301634:C206R	C	-	1	0	TK1	73682524	0.970000	0.33590	0.991000	0.47740	0.926000	0.56050	0.667000	0.25112	0.957000	0.37930	0.533000	0.62120	TGC	.	.		0.612	TK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319577.1	NM_003258		G	76170929	A	G	76170929	3	3	344	1	0	0	0	0	1	0	0	0	15947	188	7	2	92	2	TK1	17	76170929	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	974289	76170929	5024281	1182	48545										
TMEM105	284186	hgsc.bcm.edu	37	chr17	79287489	79287489	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgcaccccggccccacagccCcttcatcctcaccaccccgc	5	25	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:79287489C>T	ENST00000332900.1	-	3	901	c.352G>A	c.(352-354)Ggg>Agg	p.G118R		NM_178520.3	NP_848615.1	Q8N8V8	TM105_HUMAN	transmembrane protein 105	118						integral component of membrane (GO:0016021)				NS(1)|large_intestine(3)|lung(1)|ovary(2)	7	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.0892)			CCCCACAGCCCCTTCATCCTC	0.602																																					p.G118R		Atlas-SNP	.											.	TMEM105	19	.	0			c.G352A						.						53	58	57					17																	79287489		2203	4300	6503	SO:0001583	missense	284186	exon3			ACAGCCCCTTCAT	AK096111	CCDS11781.1	17q25.3	2008-04-21	2008-04-21	2008-04-21		ENSG00000185332			26794	protein-coding gene	gene with protein product							Standard	NM_178520		Approved	FLJ38792	uc002kad.2	Q8N8V8		ENST00000332900.1:c.352G>A	chr17.hg19:g.79287489C>T	ENSP00000329795:p.Gly118Arg	138.0	0.0		65.0	52.0	NM_178520		Missense_Mutation	SNP	ENST00000332900.1	hg19	CCDS11781.1	.	.	.	.	.	.	.	.	.	.	C	9.348	1.064680	0.20067	.	.	ENSG00000185332	ENST00000332900	T	0.58797	0.31	1.76	-0.629	0.11533	.	.	.	.	.	T	0.33147	0.0853	N	0.08118	0	0.09310	N	1	P	0.39094	0.659	B	0.40134	0.32	T	0.22765	-1.0207	9	0.87932	D	0	.	3.1892	0.06612	0.0:0.5348:0.2781:0.1871	.	118	Q8N8V8	TM105_HUMAN	R	118	ENSP00000329795:G118R	ENSP00000329795:G118R	G	-	1	0	TMEM105	76902084	0.000000	0.05858	0.000000	0.03702	0.083000	0.17756	-0.416000	0.07097	-0.106000	0.12110	0.313000	0.20887	GGG	.	.		0.602	TMEM105-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439607.1	NM_178520		T	79287489	C	T	79287489	3	4	344	1	0	0	0	0	1	0	0	0	16034	623	22	3	41	3	TMEM105	17	79287489	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	3116560	79287489	1907721	1183	48546										
TBCD	6904	hgsc.bcm.edu	37	chr17	80887026	80887026	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gctgtgtggcccagcaggccAgtgagaagattgaccgtttc	14	10	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr17:80887026A>T	ENST00000355528.4	+	31	2861	c.2731A>T	c.(2731-2733)Agt>Tgt	p.S911C	TBCD_ENST00000539345.2_Missense_Mutation_p.S911C	NM_005993.4	NP_005984.3	Q9BTW9	TBCD_HUMAN	tubulin folding cofactor D	911					'de novo' posttranslational protein folding (GO:0051084)|adherens junction assembly (GO:0034333)|cellular protein metabolic process (GO:0044267)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of microtubule polymerization (GO:0031115)|positive regulation of GTPase activity (GO:0043547)|post-chaperonin tubulin folding pathway (GO:0007023)|protein folding (GO:0006457)|tight junction assembly (GO:0070830)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|tight junction (GO:0005923)	beta-tubulin binding (GO:0048487)|chaperone binding (GO:0051087)|GTPase activator activity (GO:0005096)					Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)			CCAGCAGGCCAGTGAGAAGAT	0.607																																					p.S911C		Atlas-SNP	.											.	TBCD	94	.	0			c.A2731T						.						69	75	73					17																	80887026		2175	4264	6439	SO:0001583	missense	6904	exon31			CAGGCCAGTGAGA	BC003094	CCDS45818.1	17q25.3	2006-11-21	2006-11-21			ENSG00000141556			11581	protein-coding gene	gene with protein product		604649	"tubulin-specific chaperone d"				Standard	NM_005993		Approved		uc002kfz.3	Q9BTW9		ENST00000355528.4:c.2731A>T	chr17.hg19:g.80887026A>T	ENSP00000347719:p.Ser911Cys	32.0	0.0		18.0	15.0	NM_005993	O95458|Q7L8K1|Q8IXP6|Q8NAX0|Q8WYH4|Q96E74|Q9UF82|Q9UG46|Q9Y2J3	Missense_Mutation	SNP	ENST00000355528.4	hg19	CCDS45818.1	.	.	.	.	.	.	.	.	.	.	A	13.08	2.130845	0.37630	.	.	ENSG00000141556	ENST00000355528;ENST00000334614	T	0.30981	1.51	5.27	5.27	0.74061	Armadillo-like helical (1);Armadillo-type fold (1);Tubulin-specific chaperone D, C-terminal (1);	0.128422	0.53938	D	0.000051	T	0.25827	0.0629	L	0.50333	1.59	0.80722	D	1	B;B;B	0.27910	0.077;0.044;0.193	B;B;B	0.27170	0.077;0.055;0.077	T	0.07888	-1.0749	9	.	.	.	.	7.8514	0.29457	0.908:0.0:0.092:0.0	.	662;911;911	F8WC00;Q9BTW9;Q9BTW9-4	.;TBCD_HUMAN;.	C	911;662	ENSP00000347719:S911C	.	S	+	1	0	TBCD	78480315	1.000000	0.71417	0.458000	0.27068	0.556000	0.35491	4.036000	0.57304	2.001000	0.58596	0.533000	0.62120	AGT	.	.		0.607	TBCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439415.1	NM_005993		T	80887026	A	T	80887026	3	4	344	1	0	0	0	0	1	0	0	0	15648	188	7	4	2853	4	TBCD	17	80887026	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1599537	80887026	308184	1184	48547										
EPB41L3	23136	hgsc.bcm.edu	37	chr18	5396213	5396213	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atctcacctgtgatgattcaTatgtgatggttttggtttcg	10	6	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr18:5396213T>C	ENST00000341928.2	-	19	3300	c.2960A>G	c.(2959-2961)tAt>tGt	p.Y987C	EPB41L3_ENST00000400111.3_Missense_Mutation_p.Y765C|EPB41L3_ENST00000542652.2_5'UTR|EPB41L3_ENST00000542146.1_Missense_Mutation_p.Y292C|EPB41L3_ENST00000427684.2_Missense_Mutation_p.Y284C|EPB41L3_ENST00000544123.1_Missense_Mutation_p.Y818C|EPB41L3_ENST00000342933.3_Missense_Mutation_p.Y987C|EPB41L3_ENST00000540638.2_Missense_Mutation_p.Y765C	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	987	C-terminal (CTD).				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						TGATGATTCATATGTGATGGT	0.443																																					p.Y987C		Atlas-SNP	.											.	EPB41L3	222	.	0			c.A2960G						.						295	284	288					18																	5396213		2203	4300	6503	SO:0001583	missense	23136	exon19			GATTCATATGTGA	AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.2960A>G	chr18.hg19:g.5396213T>C	ENSP00000343158:p.Tyr987Cys	80.0	0.0		36.0	31.0	NM_012307	B7Z4I5|F5GX05|O95713|Q9BRP5	Missense_Mutation	SNP	ENST00000341928.2	hg19	CCDS11838.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.572307	0.86542	.	.	ENSG00000082397	ENST00000341928;ENST00000540638;ENST00000544123;ENST00000545076;ENST00000427684;ENST00000542146;ENST00000342933;ENST00000400111	T;T;T;T;T;T	0.77750	-1.12;-1.12;-1.12;-1.12;-1.12;-1.12	5.84	5.84	0.93424	Band 4.1, C-terminal (1);	0.385314	0.25321	N	0.031519	D	0.88584	0.6476	M	0.80028	2.48	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.97110	0.998;0.999;0.993;0.998;0.999;0.973;1.0;0.998	D	0.89322	0.3641	10	0.56958	D	0.05	.	16.226	0.82293	0.0:0.0:0.0:1.0	.	818;284;292;379;656;765;987;222	F5GX05;E7EUF8;F5H7W5;B7Z8M8;A8K968;Q9Y2J2-2;Q9Y2J2;B3KT50	.;.;.;.;.;.;E41L3_HUMAN;.	C	987;656;818;656;284;292;987;765	ENSP00000343158:Y987C;ENSP00000441174:Y818C;ENSP00000392195:Y284C;ENSP00000442233:Y292C;ENSP00000341138:Y987C;ENSP00000382981:Y765C	ENSP00000343158:Y987C	Y	-	2	0	EPB41L3	5386213	1.000000	0.71417	0.971000	0.41717	0.983000	0.72400	7.973000	0.88032	2.230000	0.72887	0.528000	0.53228	TAT	.	.		0.443	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307		C	5396213	T	C	5396213	3	2	344	1	0	0	0	0	1	0	0	0	5156	1406	49	2	319	2	EPB41L3	18	5396213	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10		5396213	72681035	1185	48548										
EPB41L3	23136	hgsc.bcm.edu	37	chr18	5416315	5416315	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctacggagctctgtgggagaTgtgggggcacaatgggtgga	19	6	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr18:5416315T>C	ENST00000341928.2	-	13	1909	c.1569A>G	c.(1567-1569)acA>acG	p.T523T	EPB41L3_ENST00000400111.3_Intron|EPB41L3_ENST00000542652.2_Intron|EPB41L3_ENST00000542146.1_Intron|EPB41L3_ENST00000427684.2_Intron|EPB41L3_ENST00000544123.1_Intron|EPB41L3_ENST00000342933.3_Silent_p.T523T|EPB41L3_ENST00000540638.2_Intron	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	523	Spectrin--actin-binding. {ECO:0000255}.				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						CTGTGGGAGATGTGGGGGCAC	0.562																																					p.T523T		Atlas-SNP	.											.	EPB41L3	222	.	0			c.A1569G						.						50	50	50					18																	5416315		2203	4300	6503	SO:0001819	synonymous_variant	23136	exon13			GGGAGATGTGGGG	AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.1569A>G	chr18.hg19:g.5416315T>C		35.0	0.0		26.0	19.0	NM_012307	B7Z4I5|F5GX05|O95713|Q9BRP5	Silent	SNP	ENST00000341928.2	hg19	CCDS11838.1																																																																																			.	.		0.562	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307		C	5416315	T	C	5416315	2	2	344	1	0	0	0	0	0	0	0	1	5156	1451	51	2		2	EPB41L3	18	5416315	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	20102	5416315	72660933	1186	48549										
TUBB6	84617	hgsc.bcm.edu	37	chr18	12325366	12325366	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	actgtcggtgcaccagctggTggagaatacagacgagacct	13	10	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr18:12325366T>A	ENST00000317702.5	+	4	812	c.578T>A	c.(577-579)gTg>gAg	p.V193E	TUBB6_ENST00000590967.1_Intron|TUBB6_ENST00000591909.1_Intron|TUBB6_ENST00000591208.1_3'UTR			Q9BUF5	TBB6_HUMAN	tubulin, beta 6 class V	193					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)	14				READ - Rectum adenocarcinoma(1;0.0649)		CACCAGCTGGTGGAGAATACA	0.592																																					p.V193E		Atlas-SNP	.											.	TUBB6	35	.	0			c.T578A						.						183	148	160					18																	12325366		2203	4300	6503	SO:0001583	missense	84617	exon4			AGCTGGTGGAGAA	AK001295	CCDS11858.1	18p11.21	2011-10-10	2011-10-10		ENSG00000176014	ENSG00000176014		"Tubulins"	20776	protein-coding gene	gene with protein product	"tubulin beta MGC4083", "class V beta-tubulin"	615103	"tubulin, beta 6"			12477932	Standard	NM_032525		Approved	MGC4083, HsT1601	uc002kqw.3	Q9BUF5	OTTHUMG00000131692	ENST00000317702.5:c.578T>A	chr18.hg19:g.12325366T>A	ENSP00000318697:p.Val193Glu	111.0	0.0		45.0	36.0	NM_032525	B3KM76|Q9HA42	Missense_Mutation	SNP	ENST00000317702.5	hg19	CCDS11858.1	.	.	.	.	.	.	.	.	.	.	T	16.50	3.141666	0.57044	.	.	ENSG00000176014	ENST00000317702;ENST00000417736;ENST00000445717	T	0.69306	-0.39	5.03	5.03	0.67393	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.85682	D	0.000000	D	0.88753	0.6522	H	0.98295	4.195	0.80722	D	1	D;D	0.89917	0.993;1.0	D;D	0.87578	0.969;0.998	D	0.93087	0.6496	10	0.87932	D	0	.	15.0606	0.71951	0.0:0.0:0.0:1.0	.	165;193	B4DP54;Q9BUF5	.;TBB6_HUMAN	E	193;121;165	ENSP00000318697:V193E	ENSP00000318697:V193E	V	+	2	0	TUBB6	12315366	1.000000	0.71417	1.000000	0.80357	0.888000	0.51559	6.146000	0.71777	2.025000	0.59659	0.374000	0.22700	GTG	.	.		0.592	TUBB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254600.2	NM_032525		A	12325366	T	A	12325366	3	1	344	1	0	0	0	0	1	0	0	0	16775	1696	59	4	592	4	TUBB6	18	12325366	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	6909051	12325366	65751882	1187	48550										
ROCK1	6093	hgsc.bcm.edu	37	chr18	18559965	18559965	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tacctgggttttataaagtgTctgcaaaacaagtgacaagg	10	6	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr18:18559965T>C	ENST00000399799.2	-	22	3500	c.2560A>G	c.(2560-2562)Aca>Gca	p.T854A		NM_005406.2	NP_005397.1	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein kinase 1	854	Glu-rich.				actin cytoskeleton organization (GO:0030036)|apical constriction (GO:0003383)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|bleb assembly (GO:0032060)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of focal adhesion assembly (GO:0051894)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(4)|central_nervous_system(1)|large_intestine(8)|lung(2)	16	Melanoma(1;0.165)					TTATAAAGTGTCTGCAAAACA	0.269																																					p.T854A		Atlas-SNP	.											.	ROCK1	162	.	0			c.A2560G						.						40	38	38					18																	18559965		2185	4284	6469	SO:0001630	splice_region_variant	6093	exon22			AAAGTGTCTGCAA		CCDS11870.2	18q11.2	2013-01-10			ENSG00000067900	ENSG00000067900	2.7.11.1	"Pleckstrin homology (PH) domain containing"	10251	protein-coding gene	gene with protein product		601702				8617235	Standard	NM_005406		Approved	p160ROCK	uc002kte.3	Q13464	OTTHUMG00000131723	ENST00000399799.2:c.2560-1A>G	chr18.hg19:g.18559965T>C		60.0	0.0		47.0	20.0	NM_005406	B0YJ91|Q2KHM4|Q59GZ4	Missense_Mutation	SNP	ENST00000399799.2	hg19	CCDS11870.2	.	.	.	.	.	.	.	.	.	.	T	22.2	4.256131	0.80246	.	.	ENSG00000067900	ENST00000399799	T	0.65549	-0.16	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.68760	0.3036	M	0.76170	2.325	0.58432	D	0.999996	P	0.50066	0.931	P	0.48089	0.566	T	0.71517	-0.4569	10	0.42905	T	0.14	.	14.7008	0.69154	0.0:0.0:0.0:1.0	.	854	Q13464	ROCK1_HUMAN	A	854	ENSP00000382697:T854A	ENSP00000382697:T854A	T	-	1	0	ROCK1	16813963	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.203000	0.77864	2.134000	0.65973	0.460000	0.39030	ACA	.	.		0.269	ROCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254641.2	NM_005406	Missense_Mutation	C	18559965	T	C	18559965	5	2	344	1	0	0	0	0	0	0	1	0	13532	1681	58	2	1552	2	ROCK1	18	18559965	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	6234599	18559965	59517283	1188	48551										
MIB1	57534	hgsc.bcm.edu	37	chr18	19345790	19345790	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccagcaaccaatcattggcaTtcgatggaagtgtgcagagt	11	9	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr18:19345790T>A	ENST00000261537.6	+	2	551	c.287T>A	c.(286-288)aTt>aAt	p.I96N	MIB1_ENST00000578646.1_3'UTR	NM_020774.2	NP_065825.1	Q86YT6	MIB1_HUMAN	mindbomb E3 ubiquitin protein ligase 1	96					blood vessel development (GO:0001568)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|negative regulation of neuron differentiation (GO:0045665)|neural tube formation (GO:0001841)|Notch signaling pathway (GO:0007219)|positive regulation of endocytosis (GO:0045807)|somitogenesis (GO:0001756)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(13)|ovary(5)	27			STAD - Stomach adenocarcinoma(5;0.212)			ATCATTGGCATTCGATGGAAG	0.383																																					p.I96N		Atlas-SNP	.											.	MIB1	87	.	0			c.T287A						.						145	129	135					18																	19345790		2203	4300	6503	SO:0001583	missense	57534	exon2			TTGGCATTCGATG	AB037744	CCDS11871.1	18q11.2	2014-09-17	2012-02-23		ENSG00000101752	ENSG00000101752		"Zinc fingers, ZZ-type", "Ankyrin repeat domain containing"	21086	protein-coding gene	gene with protein product		608677	"mindbomb homolog 1 (Drosophila)"				Standard	NM_020774		Approved	DIP-1, MIB, KIAA1323, ZZANK2, ZZZ6	uc002ktq.3	Q86YT6	OTTHUMG00000131753	ENST00000261537.6:c.287T>A	chr18.hg19:g.19345790T>A	ENSP00000261537:p.Ile96Asn	59.0	0.0		49.0	32.0	NM_020774	B0YJ38|Q2TB37|Q68D01|Q6YI51|Q8NBY0|Q8TCB5|Q8TCL7|Q9P2M3	Missense_Mutation	SNP	ENST00000261537.6	hg19	CCDS11871.1	.	.	.	.	.	.	.	.	.	.	T	27.7	4.852564	0.91355	.	.	ENSG00000101752	ENST00000261537	D	0.91124	-2.79	5.79	5.79	0.91817	Zinc finger, ZZ-type (4);	0.000000	0.85682	D	0.000000	D	0.93996	0.8077	L	0.61036	1.89	0.80722	D	1	P	0.49961	0.93	P	0.62298	0.9	D	0.94512	0.7719	10	0.87932	D	0	-7.2449	16.1113	0.81266	0.0:0.0:0.0:1.0	.	96	Q86YT6	MIB1_HUMAN	N	96	ENSP00000261537:I96N	ENSP00000261537:I96N	I	+	2	0	MIB1	17599788	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.759000	0.85235	2.213000	0.71641	0.482000	0.46254	ATT	.	.		0.383	MIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254675.1	NM_020774		A	19345790	T	A	19345790	3	1	344	1	0	0	0	0	1	0	0	0	9575	1493	52	4	293	4	MIB1	18	19345790	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	785825	19345790	58731458	1189	48552										
CABLES1	91768	hgsc.bcm.edu	37	chr18	20774494	20774494	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acatgcggcaacacgataccAggaatggcaggtactacatt	10	10	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr18:20774494A>G	ENST00000256925.7	+	3	1000	c.1000A>G	c.(1000-1002)Agg>Ggg	p.R334G	CABLES1_ENST00000400473.2_Missense_Mutation_p.R7G|CABLES1_ENST00000585061.1_Intron|CABLES1_ENST00000420687.2_Missense_Mutation_p.R69G	NM_001100619.2	NP_001094089.1	Q8TDN4	CABL1_HUMAN	Cdk5 and Abl enzyme substrate 1	334	Interacts with CDK3. {ECO:0000250}.				blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|nervous system development (GO:0007399)|regulation of cell cycle (GO:0051726)|regulation of cell division (GO:0051302)	cytosol (GO:0005829)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			breast(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|stomach(1)	11	all_cancers(21;0.000102)|all_epithelial(16;2.48e-06)|Lung NSC(20;0.00696)|all_lung(20;0.0197)|Colorectal(14;0.0202)|Ovarian(20;0.127)					ACACGATACCAGGAATGGCAG	0.463																																					p.R334G		Atlas-SNP	.											.	CABLES1	32	.	0			c.A1000G						.						67	64	65					18																	20774494		1940	4153	6093	SO:0001583	missense	91768	exon3			GATACCAGGAATG	BC037218	CCDS42417.1, CCDS42418.1, CCDS58615.1	18q11.2	2005-08-16				ENSG00000134508			25097	protein-coding gene	gene with protein product		609194				12477932	Standard	NM_138375		Approved	HsT2563, FLJ35924	uc002kuc.2	Q8TDN4		ENST00000256925.7:c.1000A>G	chr18.hg19:g.20774494A>G	ENSP00000256925:p.Arg334Gly	62.0	0.0		53.0	29.0	NM_001100619	B4DK60|Q8N3Y8|Q8NA22|Q9BTG1	Missense_Mutation	SNP	ENST00000256925.7	hg19	CCDS42417.1	.	.	.	.	.	.	.	.	.	.	A	17.70	3.454910	0.63290	.	.	ENSG00000134508	ENST00000400473;ENST00000256925;ENST00000420687	T;T;T	0.53857	0.6;0.63;0.68	5.77	5.77	0.91146	.	0.131649	0.64402	D	0.000003	T	0.54287	0.1849	M	0.65975	2.015	0.47511	D	0.999442	B;P	0.42871	0.096;0.792	B;B	0.40329	0.073;0.326	T	0.57057	-0.7876	10	0.40728	T	0.16	-0.2103	16.1024	0.81184	1.0:0.0:0.0:0.0	.	69;334	Q8TDN4-2;Q8TDN4	.;CABL1_HUMAN	G	7;334;69	ENSP00000383321:R7G;ENSP00000256925:R334G;ENSP00000413851:R69G	ENSP00000256925:R334G	R	+	1	2	CABLES1	19028492	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	5.375000	0.66173	2.200000	0.70718	0.459000	0.35465	AGG	.	.		0.463	CABLES1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445198.2	NM_138375		G	20774494	A	G	20774494	3	3	344	1	0	0	0	0	1	0	0	0	2531	179	7	2	1064	2	CABLES1	18	20774494	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1428704	20774494	57302754	1190	48553										
C18orf8	29919	hgsc.bcm.edu	37	chr18	21104400	21104400	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctataacatgtggattcttcAtcttggattgtctttcaacc	6	9	5	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr18:21104400A>G	ENST00000269221.3	+	12	1124	c.1014A>G	c.(1012-1014)tcA>tcG	p.S338S	C18orf8_ENST00000590868.1_Silent_p.S290S	NM_013326.3	NP_037458.3	Q96DM3	MIC1_HUMAN	chromosome 18 open reading frame 8	338						lysosomal membrane (GO:0005765)				endometrium(9)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	21	all_cancers(21;0.000122)|all_epithelial(16;8.08e-07)|Lung NSC(20;0.00206)|all_lung(20;0.00659)|Colorectal(14;0.0202)|Ovarian(20;0.127)					TGGATTCTTCATCTTGGATTG	0.453																																					p.S338S		Atlas-SNP	.											.	C18orf8	58	.	0			c.A1014G						.						131	120	124					18																	21104400		2203	4300	6503	SO:0001819	synonymous_variant	29919	exon12			TTCTTCATCTTGG	AK057192	CCDS32803.1, CCDS74199.1	18q11.2	2013-12-13			ENSG00000141452	ENSG00000141452			24326	protein-coding gene	gene with protein product	"colon cancer associated protein Mic1", "macrophage inhibitory cytokine 1"					12477932	Standard	NM_013326		Approved	MIC1, MIC-1, HsT2591	uc021uie.2	Q96DM3		ENST00000269221.3:c.1014A>G	chr18.hg19:g.21104400A>G		64.0	0.0		55.0	21.0	NM_013326	Q9BU17|Q9Y5M0	Silent	SNP	ENST00000269221.3	hg19	CCDS32803.1																																																																																			.	.		0.453	C18orf8-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445386.1	NM_013326		G	21104400	A	G	21104400	2	3	344	1	0	0	0	0	0	0	0	1	1909	204	8	2		2	C18orf8	18	21104400	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	329906	21104400	56972848	1191	48554										
ZNF521	25925	hgsc.bcm.edu	37	chr18	22669533	22669533	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atgctgctgcaacttgtttgCttgaacaaatactgaaatga	8	7	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr18:22669533C>A	ENST00000361524.3	-	7	3950	c.3802G>T	c.(3802-3804)Gca>Tca	p.A1268S	ZNF521_ENST00000538137.2_Missense_Mutation_p.A1268S|ZNF521_ENST00000584787.1_Missense_Mutation_p.A1048S	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	1268					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					AACTTGTTTGCTTGAACAAAT	0.413			T	PAX5	ALL																																p.A1268S		Atlas-SNP	.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	.	ZNF521	269	.	0			c.G3802T						.						150	139	142					18																	22669533		2203	4300	6503	SO:0001583	missense	25925	exon7			TGTTTGCTTGAAC	AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"Zinc fingers, C2H2-type"	24605	protein-coding gene	gene with protein product	"early hematopoietic zinc finger"	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.3802G>T	chr18.hg19:g.22669533C>A	ENSP00000354794:p.Ala1268Ser	110.0	0.0		102.0	40.0	NM_015461	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Missense_Mutation	SNP	ENST00000361524.3	hg19	CCDS32806.1	.	.	.	.	.	.	.	.	.	.	C	18.14	3.558155	0.65538	.	.	ENSG00000198795	ENST00000361524;ENST00000538137;ENST00000399425	T	0.27402	1.67	5.79	5.79	0.91817	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.000000	0.64402	D	0.000002	T	0.37758	0.1015	N	0.12527	0.23	0.53005	D	0.999969	D	0.76494	0.999	D	0.91635	0.999	T	0.16600	-1.0397	10	0.12103	T	0.63	-14.2605	20.0132	0.97467	0.0:1.0:0.0:0.0	.	1268	Q96K83	ZN521_HUMAN	S	1268;1302;1268	ENSP00000354794:A1268S	ENSP00000354794:A1268S	A	-	1	0	ZNF521	20923531	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.484000	0.81180	2.708000	0.92522	0.650000	0.86243	GCA	.	.		0.413	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461		A	22669533	C	A	22669533	3	1	344	1	0	0	0	0	1	0	0	0	17980	797	28	3	141	3	ZNF521	18	22669533	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1565133	22669533	55407715	1192	48555										
ZNF521	25925	hgsc.bcm.edu	37	chr18	22806527	22806527	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cttgcttaagatgttcatttAggttatagagtgagggcagg	13	4	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr18:22806527A>T	ENST00000361524.3	-	4	1503	c.1355T>A	c.(1354-1356)cTa>cAa	p.L452Q	ZNF521_ENST00000538137.2_Missense_Mutation_p.L452Q|ZNF521_ENST00000579111.1_5'Flank|ZNF521_ENST00000584787.1_Missense_Mutation_p.L232Q	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	452					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					ATGTTCATTTAGGTTATAGAG	0.453			T	PAX5	ALL																																p.L452Q		Atlas-SNP	.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	.	ZNF521	269	.	0			c.T1355A						.						89	89	89					18																	22806527		2203	4300	6503	SO:0001583	missense	25925	exon4			TCATTTAGGTTAT	AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"Zinc fingers, C2H2-type"	24605	protein-coding gene	gene with protein product	"early hematopoietic zinc finger"	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.1355T>A	chr18.hg19:g.22806527A>T	ENSP00000354794:p.Leu452Gln	91.0	0.0		69.0	41.0	NM_015461	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Missense_Mutation	SNP	ENST00000361524.3	hg19	CCDS32806.1	.	.	.	.	.	.	.	.	.	.	A	10.36	1.329747	0.24167	.	.	ENSG00000198795	ENST00000361524;ENST00000538137;ENST00000399425	T;T	0.22336	1.96;2.17	6.06	6.06	0.98353	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.000000	0.64402	D	0.000001	T	0.46034	0.1372	M	0.61703	1.905	0.42541	D	0.993072	D	0.89917	1.0	D	0.97110	1.0	T	0.41858	-0.9485	10	0.87932	D	0	-10.5503	16.6127	0.84892	1.0:0.0:0.0:0.0	.	452	Q96K83	ZN521_HUMAN	Q	452;486;452	ENSP00000354794:L452Q;ENSP00000382352:L452Q	ENSP00000354794:L452Q	L	-	2	0	ZNF521	21060525	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.322000	0.78497	0.528000	0.53228	CTA	.	.		0.453	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461		T	22806527	A	T	22806527	3	4	344	1	0	0	0	0	1	0	0	0	17980	420	15	4	2600	4	ZNF521	18	22806527	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	136994	22806527	55270721	1193	48556										
ZNF521	25925	hgsc.bcm.edu	37	chr18	22807425	22807425	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcgcttgtgtttgaacagccTactgcagtaggtgcatttga	12	8	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr18:22807425T>A	ENST00000361524.3	-	4	605	c.457A>T	c.(457-459)Agg>Tgg	p.R153W	ZNF521_ENST00000538137.2_Missense_Mutation_p.R153W|ZNF521_ENST00000579111.1_5'Flank|ZNF521_ENST00000584787.1_5'UTR	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	153					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					TTGAACAGCCTACTGCAGTAG	0.498			T	PAX5	ALL																																p.R153W		Atlas-SNP	.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	.	ZNF521	269	.	0			c.A457T						.						134	123	126					18																	22807425		2203	4300	6503	SO:0001583	missense	25925	exon4			ACAGCCTACTGCA	AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"Zinc fingers, C2H2-type"	24605	protein-coding gene	gene with protein product	"early hematopoietic zinc finger"	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.457A>T	chr18.hg19:g.22807425T>A	ENSP00000354794:p.Arg153Trp	143.0	0.0		119.0	62.0	NM_015461	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Missense_Mutation	SNP	ENST00000361524.3	hg19	CCDS32806.1	.	.	.	.	.	.	.	.	.	.	T	10.33	1.319805	0.23994	.	.	ENSG00000198795	ENST00000361524;ENST00000538137;ENST00000399425	T;T	0.30182	1.54;1.54	5.93	-6.18	0.02085	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.52451	0.1735	L	0.56769	1.78	0.27090	N	0.962862	D	0.89917	1.0	D	0.91635	0.999	T	0.64132	-0.6479	10	0.87932	D	0	-27.9206	27.849	0.99998	0.0:0.0:0.884:0.1159	.	153	Q96K83	ZN521_HUMAN	W	153;187;153	ENSP00000354794:R153W;ENSP00000382352:R153W	ENSP00000354794:R153W	R	-	1	2	ZNF521	21061423	0.892000	0.30473	0.240000	0.24138	0.999000	0.98932	0.419000	0.21247	-0.847000	0.04168	0.533000	0.62120	AGG	.	.		0.498	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461		A	22807425	T	A	22807425	3	1	344	1	0	0	0	0	1	0	0	0	17980	1521	53	4	3498	4	ZNF521	18	22807425	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	898	22807425	55269823	1194	48557										
TAF4B	6875	hgsc.bcm.edu	37	chr18	23854702	23854702	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctgtaactaccctgaagcctTcaagtttgggagcatcatcc	8	12	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr18:23854702T>C	ENST00000269142.5	+	4	1671	c.673T>C	c.(673-675)Tca>Cca	p.S225P	TAF4B_ENST00000400466.2_Missense_Mutation_p.S225P|TAF4B_ENST00000578121.1_Missense_Mutation_p.S225P	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	225					gene expression (GO:0010467)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|NF-kappaB binding (GO:0051059)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|prostate(1)|skin(1)	29	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			CCTGAAGCCTTCAAGTTTGGG	0.418																																					p.S225P		Atlas-SNP	.											.	TAF4B	71	.	0			c.T673C						.						158	151	153					18																	23854702		1891	4120	6011	SO:0001583	missense	6875	exon4			AAGCCTTCAAGTT	Y09321	CCDS42421.1	18q11.1	2008-08-01	2002-08-29	2001-12-07		ENSG00000141384			11538	protein-coding gene	gene with protein product	"TATA box binding protein (TBP)-associated factor 4B"	601689	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, C2, 105kD"	TAF2C2		8858156, 10849440	Standard	XM_005258339		Approved	TAFII105	uc002kvu.4	Q92750		ENST00000269142.5:c.673T>C	chr18.hg19:g.23854702T>C	ENSP00000269142:p.Ser225Pro	186.0	0.0		164.0	71.0	NM_005640	Q29YA4|Q29YA5	Missense_Mutation	SNP	ENST00000269142.5	hg19	CCDS42421.1	.	.	.	.	.	.	.	.	.	.	T	10.63	1.404905	0.25378	.	.	ENSG00000141384	ENST00000418698;ENST00000269142;ENST00000400466	T;T;T	0.25250	1.81;1.83;1.81	5.81	4.64	0.57946	.	0.417829	0.23912	N	0.043339	T	0.17152	0.0412	L	0.40543	1.245	0.35289	D	0.782017	B;B	0.15719	0.001;0.014	B;B	0.15484	0.001;0.013	T	0.18524	-1.0334	10	0.20046	T	0.44	-3.1267	4.1337	0.10160	0.1758:0.1123:0.0:0.7119	.	225;225	Q92750;A4PBF7	TAF4B_HUMAN;.	P	225	ENSP00000389365:S225P;ENSP00000269142:S225P;ENSP00000383314:S225P	ENSP00000269142:S225P	S	+	1	0	TAF4B	22108700	1.000000	0.71417	0.999000	0.59377	0.601000	0.36947	1.845000	0.39279	1.015000	0.39444	-0.301000	0.09380	TCA	.	.		0.418	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000446260.3	NM_005640		C	23854702	T	C	23854702	3	2	344	1	0	0	0	0	1	0	0	0	15542	1783	62	2	687	2	TAF4B	18	23854702	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1047277	23854702	54222546	1195	48558										
DSG3	1830	hgsc.bcm.edu	37	chr18	29039011	29039011	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cctagatcacatgtcgggctCtaaatgcccaaggactagat	9	11	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr18:29039011C>A	ENST00000257189.4	+	5	471	c.388C>A	c.(388-390)Cta>Ata	p.L130I		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	130	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(28)|ovary(4)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			ATGTCGGGCTCTAAATGCCCA	0.348																																					p.L130I		Atlas-SNP	.											.	DSG3	172	.	0			c.C388A						.						69	68	68					18																	29039011		2203	4300	6503	SO:0001583	missense	1830	exon5			CGGGCTCTAAATG	M76482	CCDS11898.1	18q12.1	2010-06-24	2010-06-24		ENSG00000134757	ENSG00000134757		"Cadherins / Major cadherins"	3050	protein-coding gene	gene with protein product	"pemphigus vulgaris antigen"	169615	"desmoglein 3 (pemphigus vulgaris antigen)"			1601426	Standard	NM_001944		Approved	CDHF6	uc002kws.3	P32926	OTTHUMG00000131985	ENST00000257189.4:c.388C>A	chr18.hg19:g.29039011C>A	ENSP00000257189:p.Leu130Ile	176.0	0.0		165.0	67.0	NM_001944	A8K2V2	Missense_Mutation	SNP	ENST00000257189.4	hg19	CCDS11898.1	.	.	.	.	.	.	.	.	.	.	C	18.54	3.646709	0.67358	.	.	ENSG00000134757	ENST00000257189	T	0.52526	0.66	5.39	-1.15	0.09709	Cadherin (4);Cadherin-like (1);	0.411769	0.17743	N	0.163498	T	0.50171	0.1600	M	0.72118	2.19	0.09310	N	1	D	0.56521	0.976	P	0.57283	0.817	T	0.38286	-0.9668	10	0.35671	T	0.21	.	1.574	0.02621	0.1236:0.3576:0.2423:0.2765	.	130	P32926	DSG3_HUMAN	I	130	ENSP00000257189:L130I	ENSP00000257189:L130I	L	+	1	2	DSG3	27293009	0.002000	0.14202	0.006000	0.13384	0.464000	0.32679	-0.516000	0.06282	0.048000	0.15891	-0.165000	0.13383	CTA	.	.		0.348	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944		A	29039011	C	A	29039011	3	1	344	1	0	0	0	0	1	0	0	0	4780	912	32	3	406	3	DSG3	18	29039011	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	5184309	29039011	49038237	1196	48559										
C18orf34	374864	hgsc.bcm.edu	37	chr18	30672732	30672732	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaaaaaccaatacctgtttcTtatctctaattgaagtatca	4	8	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr18:30672732T>A	ENST00000383096.3	-	21	2563	c.2381A>T	c.(2380-2382)aAg>aTg	p.K794M	CCDC178_ENST00000403303.1_Missense_Mutation_p.K794M|CCDC178_ENST00000579947.1_Missense_Mutation_p.K794M|CCDC178_ENST00000579916.1_Intron|CCDC178_ENST00000402325.1_Intron|CCDC178_ENST00000300227.8_Missense_Mutation_p.K756M|CCDC178_ENST00000581852.1_Intron|CCDC178_ENST00000583930.1_Missense_Mutation_p.K794M|CCDC178_ENST00000406524.2_Missense_Mutation_p.K794M			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178	794																	TACCTGTTTCTTATCTCTAAT	0.299																																					p.K794M		Atlas-SNP	.											.	.	.	.	0			c.A2381T						.						49	57	54					18																	30672732		2198	4281	6479	SO:0001583	missense	374864	exon20			TGTTTCTTATCTC	AK126038	CCDS11906.1, CCDS42424.1	18q12.1	2012-10-15	2012-10-15	2012-10-15	ENSG00000166960	ENSG00000166960			29588	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 34"	C18orf34			Standard	NM_198995		Approved	FLJ44050	uc002kxn.2	Q5BJE1	OTTHUMG00000132279	ENST00000383096.3:c.2381A>T	chr18.hg19:g.30672732T>A	ENSP00000372576:p.Lys794Met	254.0	0.0		200.0	104.0	NM_001105528	A6NDC6|J3KS92|Q6ZP67|Q6ZU20	Missense_Mutation	SNP	ENST00000383096.3	hg19	CCDS42424.1	.	.	.	.	.	.	.	.	.	.	T	6.211	0.407143	0.11754	.	.	ENSG00000166960	ENST00000403303;ENST00000383096;ENST00000300227;ENST00000406524	T;T;T;T	0.17528	2.34;2.34;2.35;2.27	5.6	5.6	0.85130	.	.	.	.	.	T	0.32882	0.0844	L	0.40543	1.245	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.70016	0.948;0.967;0.943;0.912	T	0.03008	-1.1083	9	0.66056	D	0.02	-9.7934	14.7771	0.69738	0.0:0.0:0.0:1.0	.	794;794;756;794	F8W7A7;B5MD75;Q5BJE1-2;Q5BJE1	.;.;.;CR034_HUMAN	M	794;794;756;794	ENSP00000385591:K794M;ENSP00000372576:K794M;ENSP00000300227:K756M;ENSP00000385867:K794M	ENSP00000300227:K756M	K	-	2	0	C18orf34	28926730	0.005000	0.15991	0.582000	0.28627	0.141000	0.21300	0.802000	0.27069	2.145000	0.66743	0.528000	0.53228	AAG	.	.		0.299	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255373.2	NM_198995		A	30672732	T	A	30672732	3	1	344	1	0	0	0	0	1	0	0	0	1904	1609	56	4	234	4	C18orf34	18	30672732	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1633721	30672732	47404516	1197	48560										
DTNA	1837	hgsc.bcm.edu	37	chr18	32444004	32444004	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agagctaatggtccagttggAgggtctcatgaagctactaa	12	7	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr18:32444004A>T	ENST00000399113.3	+	16	1640	c.1640A>T	c.(1639-1641)gAg>gTg	p.E547V	DTNA_ENST00000444659.1_Missense_Mutation_p.E547V|DTNA_ENST00000596745.1_Missense_Mutation_p.E297V|DTNA_ENST00000556414.3_Missense_Mutation_p.E199V|DTNA_ENST00000399121.5_Missense_Mutation_p.E487V|DTNA_ENST00000598334.1_Missense_Mutation_p.E487V|DTNA_ENST00000601125.1_Missense_Mutation_p.E169V|DTNA_ENST00000269191.6_Missense_Mutation_p.E547V|DTNA_ENST00000598774.1_Missense_Mutation_p.E490V|DTNA_ENST00000599844.1_3'UTR|DTNA_ENST00000269192.7_Missense_Mutation_p.E256V|DTNA_ENST00000597599.1_Missense_Mutation_p.E487V|DTNA_ENST00000283365.9_Missense_Mutation_p.E490V|DTNA_ENST00000269190.7_Missense_Mutation_p.E548V|DTNA_ENST00000595022.1_Missense_Mutation_p.E487V|DTNA_ENST00000399097.3_Missense_Mutation_p.E195V|DTNA_ENST00000598142.1_Missense_Mutation_p.E490V|DTNA_ENST00000597674.1_Missense_Mutation_p.E169V|DTNA_ENST00000591182.1_Missense_Mutation_p.E195V|DTNA_ENST00000348997.5_Missense_Mutation_p.E544V			Q9Y4J8	DTNA_HUMAN	dystrobrevin, alpha	547					neuromuscular synaptic transmission (GO:0007274)|signal transduction (GO:0007165)|striated muscle contraction (GO:0006941)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(2)|lung(19)|prostate(1)|upper_aerodigestive_tract(1)	29						GTCCAGTTGGAGGGTCTCATG	0.443																																					p.E547V		Atlas-SNP	.											.	DTNA	321	.	0			c.A1640T						.						75	77	77					18																	32444004		2203	4299	6502	SO:0001583	missense	1837	exon16			AGTTGGAGGGTCT	U84540	CCDS11908.1, CCDS11909.1, CCDS42426.1, CCDS45848.1, CCDS56060.1, CCDS56061.1, CCDS56062.1, CCDS56063.1, CCDS59309.1, CCDS59310.1, CCDS59311.1, CCDS59312.1, CCDS59313.1, CCDS59314.1	18q12	2014-09-17			ENSG00000134769	ENSG00000134769			3057	protein-coding gene	gene with protein product	"dystrophin-related protein 3"	601239				8081380, 15834686	Standard	NM_001390		Approved	D18S892E, DTN, DTN-1, DTN-2, DTN-3, DRP3	uc010dmn.1	Q9Y4J8	OTTHUMG00000132309	ENST00000399113.3:c.1640A>T	chr18.hg19:g.32444004A>T	ENSP00000382064:p.Glu547Val	35.0	0.0		35.0	19.0	NM_001390	A8K541|A8MSZ0|A8MUY4|B4DGS6|B4DIR0|B4DIU8|M0QYX6|M0R397|O15332|O15333|O75697|Q13197|Q13198|Q13199|Q13498|Q13499|Q13500|Q59GK7|Q9BS59	Missense_Mutation	SNP	ENST00000399113.3	hg19	CCDS59311.1	.	.	.	.	.	.	.	.	.	.	A	28.9	4.956498	0.92726	.	.	ENSG00000134769	ENST00000399119;ENST00000283365;ENST00000399114;ENST00000269190;ENST00000399097;ENST00000348997;ENST00000399121;ENST00000444659;ENST00000269191;ENST00000399113;ENST00000269192;ENST00000450377;ENST00000556414	T;T;T;T;T;T	0.22539	1.96;1.95;2.02;1.95;2.02;1.95	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	T	0.48624	0.1510	M	0.76328	2.33	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.999;1.0;0.994;0.998;0.999;0.999;0.998;1.0;0.997;0.999;1.0;1.0;1.0;0.999	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.91635	0.999;0.996;0.983;0.981;0.997;0.994;0.987;0.996;0.995;0.994;0.994;0.994;0.994;0.994	T	0.50849	-0.8779	10	0.87932	D	0	-18.4609	16.2453	0.82441	1.0:0.0:0.0:0.0	.	199;256;237;297;547;547;487;490;195;544;487;498;490;490	B4DIU8;B4DIR0;B7Z3X3;B4DGS6;Q9Y4J8;Q9Y4J8-3;A8K541;F5H5C1;Q9Y4J8-6;Q9Y4J8-4;E9PEH8;Q59GK7;Q9Y4J8-2;Q9Y4J8-5	.;.;.;.;DTNA_HUMAN;.;.;.;.;.;.;.;.;.	V	490;490;487;548;195;544;547;547;547;547;256;195;199	ENSP00000283365:E490V;ENSP00000269190:E548V;ENSP00000336682:E544V;ENSP00000405819:E547V;ENSP00000269191:E547V;ENSP00000382064:E547V	ENSP00000269190:E548V	E	+	2	0	DTNA	30698002	1.000000	0.71417	0.996000	0.52242	0.906000	0.53458	9.328000	0.96403	2.241000	0.73720	0.533000	0.62120	GAG	.	.		0.443	DTNA-005	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255422.2	NM_001390		T	32444004	A	T	32444004	3	4	344	1	0	0	0	0	1	0	0	0	4790	304	11	4	1737	4	DTNA	18	32444004	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1771272	32444004	45633244	1198	48561										
RIT2	6014	hgsc.bcm.edu	37	chr18	40554045	40554045	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agaacatcacctacctggccAgcagtgtccaagatgtccaa	8	13	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr18:40554045A>T	ENST00000326695.5	-	3	399	c.228T>A	c.(226-228)gcT>gcA	p.A76A	RIT2_ENST00000282028.4_Silent_p.A76A|RIT2_ENST00000589109.1_Silent_p.A76A|RIT2_ENST00000590910.1_Silent_p.A76A	NM_002930.2	NP_002921.1	Q99578	RIT2_HUMAN	Ras-like without CAAX 2	76				A -> D (in Ref. 1; AAB42214). {ECO:0000305}.	neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(2)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						CTACCTGGCCAGCAGTGTCCA	0.363																																					p.A76A		Atlas-SNP	.											.	RIT2	56	.	0			c.T228A						.						75	65	68					18																	40554045		2203	4300	6503	SO:0001819	synonymous_variant	6014	exon3			CTGGCCAGCAGTG	BC018060	CCDS11921.1, CCDS62431.1	18q12.3	2014-05-09	2002-09-11	2002-09-13	ENSG00000152214	ENSG00000152214			10017	protein-coding gene	gene with protein product		609592	"Ric (Drosophila)-like, expressed in neurons"	RIN		8824319, 8918462	Standard	NM_002930		Approved	RIBA	uc002lav.4	Q99578	OTTHUMG00000132611	ENST00000326695.5:c.228T>A	chr18.hg19:g.40554045A>T		296.0	1.0		252.0	134.0	NM_001272077	B2R9L1|O15295|Q8TD69|Q8WVF6|Q92964	Silent	SNP	ENST00000326695.5	hg19	CCDS11921.1																																																																																			.	.		0.363	RIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255852.1	NM_002930		T	40554045	A	T	40554045	2	4	344	1	0	0	0	0	0	0	0	1	13402	175	7	4		4	RIT2	18	40554045	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	8110041	40554045	37523203	1199	48562										
HAUS1	115106	hgsc.bcm.edu	37	chr18	43703286	43703286	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agcaactttcagccagaggcAtggatgcttctctgtctcat	9	11	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr18:43703286A>G	ENST00000282058.6	+	6	702	c.622A>G	c.(622-624)Atg>Gtg	p.M208V	HAUS1_ENST00000588704.1_3'UTR|RNU6-1278P_ENST00000516130.1_RNA|HAUS1_ENST00000585518.1_Missense_Mutation_p.H76R	NM_138443.3	NP_612452.1	Q96CS2	HAUS1_HUMAN	HAUS augmin-like complex, subunit 1	208					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)				endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	7						AGCCAGAGGCATGGATGCTTC	0.338																																					p.M208V	NSCLC(79;183 1423 5813 15597 38427)	Atlas-SNP	.											.	HAUS1	22	.	0			c.A622G						.						97	104	102					18																	43703286		2203	4300	6503	SO:0001583	missense	115106	exon6			AGAGGCATGGATG	AY360137	CCDS11928.1	18q21.1	2013-10-11	2009-04-20	2009-04-20	ENSG00000152240	ENSG00000152240		"HAUS augmin-like complex subunits"	25174	protein-coding gene	gene with protein product		608775	"coiled-coil domain containing 5 (spindle associated)"	CCDC5		19427217	Standard	NR_026978		Approved	HEI-C, HsT1461, FLJ40084	uc002lbu.3	Q96CS2	OTTHUMG00000132638	ENST00000282058.6:c.622A>G	chr18.hg19:g.43703286A>G	ENSP00000282058:p.Met208Val	258.0	0.0		190.0	82.0	NM_138443	B2RDM7|Q8N837	Missense_Mutation	SNP	ENST00000282058.6	hg19	CCDS11928.1	.	.	.	.	.	.	.	.	.	.	A	12.40	1.925668	0.34002	.	.	ENSG00000152240	ENST00000282058	.	.	.	5.28	4.1	0.47936	.	0.124345	0.64402	D	0.000001	T	0.56499	0.1989	M	0.74258	2.255	0.38240	D	0.941305	B	0.15930	0.015	B	0.10450	0.005	T	0.53365	-0.8449	9	0.24483	T	0.36	4.9293	6.3455	0.21347	0.6765:0.1652:0.0:0.1583	.	208	Q96CS2	HAUS1_HUMAN	V	208	.	ENSP00000282058:M208V	M	+	1	0	HAUS1	41957284	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.914000	0.48797	0.925000	0.37094	0.460000	0.39030	ATG	.	.		0.338	HAUS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255885.1	NM_138443		G	43703286	A	G	43703286	3	3	344	1	0	0	0	0	1	0	0	0	6974	217	8	2	644	2	HAUS1	18	43703286	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3149241	43703286	34373962	1200	48563										
KATNAL2	83473	hgsc.bcm.edu	37	chr18	44589401	44589401	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	catcaagggagcaaccagtgAacttgccttgaacaccttcg	9	12	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr18:44589401A>T	ENST00000245121.5	+	6	586	c.392A>T	c.(391-393)gAa>gTa	p.E131V	KATNAL2_ENST00000356157.7_Missense_Mutation_p.E203V|KATNAL2_ENST00000592005.1_Intron	NM_031303.2	NP_112593.2			katanin p60 subunit A-like 2											central_nervous_system(2)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	27						GCAACCAGTGAACTTGCCTTG	0.458																																					p.E131V		Atlas-SNP	.											.	KATNAL2	64	.	0			c.A392T						.						143	126	132					18																	44589401		2203	4300	6503	SO:0001583	missense	83473	exon6			CCAGTGAACTTGC	BC034999	CCDS32828.1	18q21.1	2010-04-21			ENSG00000167216	ENSG00000167216		"ATPases / AAA-type"	25387	protein-coding gene	gene with protein product		614697				12477932	Standard	NM_031303		Approved	MGC33211, DKFZP667C165	uc002lco.3	Q8IYT4		ENST00000245121.5:c.392A>T	chr18.hg19:g.44589401A>T	ENSP00000245121:p.Glu131Val	62.0	0.0		56.0	22.0	NM_031303		Missense_Mutation	SNP	ENST00000245121.5	hg19	CCDS32828.1	.	.	.	.	.	.	.	.	.	.	A	15.35	2.808556	0.50421	.	.	ENSG00000167216	ENST00000356157;ENST00000245121	D;D	0.94497	-3.44;-3.44	6.01	6.01	0.97437	.	0.278041	0.39544	N	0.001338	D	0.91603	0.7347	L	0.29908	0.895	0.39865	D	0.973438	P	0.48503	0.911	P	0.48270	0.572	D	0.91325	0.5085	10	0.44086	T	0.13	-14.9125	9.954	0.41655	0.9179:0.0:0.0821:0.0	.	203	Q8IYT4	KATL2_HUMAN	V	203;131	ENSP00000348478:E203V;ENSP00000245121:E131V	ENSP00000245121:E131V	E	+	2	0	KATNAL2	42843399	1.000000	0.71417	0.077000	0.20336	0.112000	0.19704	5.171000	0.64996	2.307000	0.77673	0.528000	0.53228	GAA	.	.		0.458	KATNAL2-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446138.2	NM_031303		T	44589401	A	T	44589401	3	4	344	1	0	0	0	0	1	0	0	0	7995	246	9	4	410	4	KATNAL2	18	44589401	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	886115	44589401	33487847	1201	48564										
ATP8B1	5205	hgsc.bcm.edu	37	chr18	55338765	55338765	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	taaccgttcataaataacagTgtcagcacctttacagtaaa	5	9	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr18:55338765T>G	ENST00000283684.4	-	16	1866	c.1867A>C	c.(1867-1869)Act>Cct	p.T623P	ATP8B1_ENST00000536015.1_Missense_Mutation_p.T623P|RP11-35G9.3_ENST00000599199.1_RNA|RP11-35G9.5_ENST00000588925.1_RNA|RP11-35G9.3_ENST00000592201.1_RNA			O43520	AT8B1_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 1	623					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|drug transmembrane transport (GO:0006855)|inner ear receptor cell development (GO:0060119)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|phospholipid translocation (GO:0045332)|regulation of microvillus assembly (GO:0032534)|sensory perception of sound (GO:0007605)|transmembrane transport (GO:0055085)|vestibulocochlear nerve formation (GO:0021650)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|cardiolipin binding (GO:1901612)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(6)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(19)|ovary(3)|prostate(1)	53		Colorectal(73;0.229)				TAAATAACAGTGTCAGCACCT	0.348																																					p.T623P		Atlas-SNP	.											.	ATP8B1	126	.	0			c.A1867C						.						172	148	156					18																	55338765		2203	4300	6503	SO:0001583	missense	5205	exon17			TAACAGTGTCAGC	AF038007	CCDS11965.1	18q21	2010-04-28	2010-04-28		ENSG00000081923	ENSG00000081923		"ATPases / P-type"	3706	protein-coding gene	gene with protein product		602397	"ATPase, Class I, type 8B, member 1", "ATPase, class I, type 8B, member 1"	FIC1, BRIC, PFIC1		9500542, 7655458	Standard	NM_005603		Approved	ATPIC, PFIC	uc002lgw.3	O43520	OTTHUMG00000132739	ENST00000283684.4:c.1867A>C	chr18.hg19:g.55338765T>G	ENSP00000283684:p.Thr623Pro	154.0	0.0		130.0	54.0	NM_005603	Q9BTP8	Missense_Mutation	SNP	ENST00000283684.4	hg19	CCDS11965.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.409808	0.83340	.	.	ENSG00000081923	ENST00000283684;ENST00000536015	T;T	0.70045	-0.45;-0.45	6.02	6.02	0.97574	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.85682	D	0.000000	D	0.87795	0.6267	H	0.95982	3.75	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.91482	0.5205	10	0.87932	D	0	.	16.2061	0.82131	0.0:0.0:0.0:1.0	.	623	O43520	AT8B1_HUMAN	P	623	ENSP00000283684:T623P;ENSP00000445359:T623P	ENSP00000283684:T623P	T	-	1	0	ATP8B1	53489763	1.000000	0.71417	1.000000	0.80357	0.643000	0.38383	8.018000	0.88722	2.311000	0.77944	0.533000	0.62120	ACT	.	.		0.348	ATP8B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256097.1	NM_005603		G	55338765	T	G	55338765	3	3	344	1	0	0	0	0	1	0	0	0	1194	1696	59	5	1936	5	ATP8B1	18	55338765	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	10749364	55338765	22738483	1202	48565										
RAX	30062	hgsc.bcm.edu	37	chr18	56936364	56936364	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtccccgaagccgggcccgcAcgggtaggagggcggcggcg	20	14	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr18:56936364A>T	ENST00000334889.3	-	3	1099	c.913T>A	c.(913-915)Tgc>Agc	p.C305S	RAX_ENST00000256852.7_3'UTR	NM_013435.2	NP_038463.2	Q9Y2V3	RX_HUMAN	retina and anterior neural fold homeobox	305					camera-type eye development (GO:0043010)|hypothalamus development (GO:0021854)|limb development (GO:0060173)|pattern specification process (GO:0007389)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|visual perception (GO:0007601)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|prostate(1)	6		Lung NSC(161;0.0804)|Colorectal(73;0.0946)		STAD - Stomach adenocarcinoma(84;0.18)		CCGGGCCCGCACGGGTAGGAG	0.731																																					p.C305S	GBM(150;770 1898 17679 24325 37807)	Atlas-SNP	.											.	RAX	19	.	0			c.T913A						.						6	8	7					18																	56936364		2046	4100	6146	SO:0001583	missense	30062	exon3			GCCCGCACGGGTA	AF115392	CCDS11972.1	18q21.31	2011-06-20			ENSG00000134438	ENSG00000134438		"Homeoboxes / PRD class"	18662	protein-coding gene	gene with protein product		601881				10625658, 10766016, 14662654	Standard	NM_013435		Approved	RX	uc002lhx.3	Q9Y2V3	OTTHUMG00000132757	ENST00000334889.3:c.913T>A	chr18.hg19:g.56936364A>T	ENSP00000334813:p.Cys305Ser	51.0	0.0		42.0	15.0	NM_013435	Q86V11	Missense_Mutation	SNP	ENST00000334889.3	hg19	CCDS11972.1	.	.	.	.	.	.	.	.	.	.	A	29.2	4.987880	0.93106	.	.	ENSG00000134438	ENST00000334889	D	0.88818	-2.43	3.98	3.98	0.46160	.	0.099413	0.64402	D	0.000001	D	0.92672	0.7671	M	0.76574	2.34	0.80722	D	1	D	0.71674	0.998	D	0.78314	0.991	D	0.90698	0.4618	10	0.21540	T	0.41	.	11.8646	0.52486	1.0:0.0:0.0:0.0	.	305	Q9Y2V3	RX_HUMAN	S	305	ENSP00000334813:C305S	ENSP00000334813:C305S	C	-	1	0	RAX	55087344	1.000000	0.71417	0.989000	0.46669	0.993000	0.82548	6.695000	0.74593	1.439000	0.47511	0.454000	0.30748	TGC	.	.		0.731	RAX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256128.2			T	56936364	A	T	56936364	3	4	344	1	0	0	0	0	1	0	0	0	13111	159	6	4	131	4	RAX	18	56936364	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1597599	56936364	21140884	1203	48566										
CCBE1	147372	hgsc.bcm.edu	37	chr18	57122130	57122130	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cttcatctggtagaactcctTgcatgtggcacagcaagttc	9	11	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr18:57122130T>A	ENST00000439986.4	-	6	644	c.607A>T	c.(607-609)Aag>Tag	p.K203*	CCBE1_ENST00000398179.2_5'UTR	NM_133459.3	NP_597716.1	Q6UXH8	CCBE1_HUMAN	collagen and calcium binding EGF domains 1	203					lymphangiogenesis (GO:0001946)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of lymphangiogenesis (GO:1901492)|positive regulation of protein processing (GO:0010954)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|positive regulation vascular endothelial growth factor production (GO:0010575)|sprouting angiogenesis (GO:0002040)|venous blood vessel morphogenesis (GO:0048845)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|protease binding (GO:0002020)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(1)|lung(6)|ovary(1)|prostate(1)|skin(3)	24		Colorectal(73;0.175)				TAGAACTCCTTGCATGTGGCA	0.557																																					p.K203X	NSCLC(137;1340 1860 15773 39604 51087)|Esophageal Squamous(139;339 1777 2926 19691 38524)	Atlas-SNP	.											.	CCBE1	59	.	0			c.A607T						.						156	112	127					18																	57122130		2203	4300	6503	SO:0001587	stop_gained	147372	exon6			ACTCCTTGCATGT	AB075863	CCDS32838.1	18q21.32	2005-01-18				ENSG00000183287			29426	protein-coding gene	gene with protein product		612753				11853319, 12975309	Standard	NM_133459		Approved	FLJ30681, KIAA1983	uc002lib.3	Q6UXH8		ENST00000439986.4:c.607A>T	chr18.hg19:g.57122130T>A	ENSP00000404464:p.Lys203*	76.0	0.0		64.0	27.0	NM_133459	Q6MZX5|Q86SS2|Q8TF19	Nonsense_Mutation	SNP	ENST00000439986.4	hg19	CCDS32838.1	.	.	.	.	.	.	.	.	.	.	T	36	5.885371	0.97068	.	.	ENSG00000183287	ENST00000439986	.	.	.	5.48	5.48	0.80851	.	0.145275	0.64402	D	0.000008	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-22.1422	14.567	0.68185	0.0:0.0:0.0:1.0	.	.	.	.	X	203	.	ENSP00000404464:K203X	K	-	1	0	CCBE1	55273110	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	4.166000	0.58203	2.059000	0.61396	0.459000	0.35465	AAG	.	.		0.557	CCBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449685.2	NM_133459		A	57122130	T	A	57122130	4	1	344	1	0	0	0	0	0	1	0	0	2733	1821	63	4	637	4	CCBE1	18	57122130	Nonsense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	185766	57122130	20955118	1204	48567										
CDH20	28316	hgsc.bcm.edu	37	chr18	59166656	59166656	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttcaagacatcaatgacaatGagcccaagttcctggacgga	9	10	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr18:59166656G>T	ENST00000262717.4	+	3	882	c.484G>T	c.(484-486)Gag>Tag	p.E162*	CDH20_ENST00000538374.1_Nonsense_Mutation_p.E162*|CDH20_ENST00000536675.2_Nonsense_Mutation_p.E162*			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2	162	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|skin(3)	61		Colorectal(73;0.186)				CAATGACAATGAGCCCAAGTT	0.512																																					p.E162X		Atlas-SNP	.											.	CDH20	117	.	0			c.G484T						.						73	75	74					18																	59166656		2203	4300	6503	SO:0001587	stop_gained	28316	exon2			GACAATGAGCCCA	AF217289	CCDS11977.1	18q21.33	2010-01-26			ENSG00000101542	ENSG00000101542		"Cadherins / Major cadherins"	1760	protein-coding gene	gene with protein product		605807				10995570	Standard	NM_031891		Approved	CDH7L3, Cdh7	uc010dps.1	Q9HBT6	OTTHUMG00000132768	ENST00000262717.4:c.484G>T	chr18.hg19:g.59166656G>T	ENSP00000262717:p.Glu162*	114.0	0.0		101.0	54.0	NM_031891	Q495S3	Nonsense_Mutation	SNP	ENST00000262717.4	hg19	CCDS11977.1	.	.	.	.	.	.	.	.	.	.	G	41	9.016063	0.99037	.	.	ENSG00000101542	ENST00000536675;ENST00000538374;ENST00000262717	.	.	.	6.06	6.06	0.98353	.	0.117279	0.64402	D	0.000009	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	.	20.6397	0.99537	0.0:0.0:1.0:0.0	.	.	.	.	X	162	.	ENSP00000262717:E162X	E	+	1	0	CDH20	57317636	1.000000	0.71417	0.998000	0.56505	0.978000	0.69477	7.881000	0.87252	2.880000	0.98712	0.650000	0.86243	GAG	.	.		0.512	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256141.2	NM_031891		T	59166656	G	T	59166656	4	4	344	1	0	0	0	0	0	1	0	0	3108	1291	45	3	490	3	CDH20	18	59166656	Nonsense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	2044526	59166656	18910592	1205	48568										
SERPINB2	5055	hgsc.bcm.edu	37	chr18	61562574	61562574	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctttaccagctgtgggttcaTgcagcagatccagaagggta	12	9	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr18:61562574T>C	ENST00000299502.4	+	3	325	c.245T>C	c.(244-246)aTg>aCg	p.M82T	SERPINB2_ENST00000457692.1_Missense_Mutation_p.M82T|SERPINB2_ENST00000482254.1_3'UTR	NM_002575.2	NP_002566.1	P05120	PAI2_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 2	82					blood coagulation (GO:0007596)|fibrinolysis (GO:0042730)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|liver(1)|lung(12)|prostate(2)|skin(2)|stomach(1)	32		Esophageal squamous(42;0.131)			Tenecteplase(DB00031)|Urokinase(DB00013)	TGTGGGTTCATGCAGCAGATC	0.433																																					p.M82T		Atlas-SNP	.											.	SERPINB2	63	.	0			c.T245C						.						189	185	186					18																	61562574		2203	4300	6503	SO:0001583	missense	5055	exon3			GGTTCATGCAGCA	Y00630	CCDS11989.1	18q21.3	2014-02-18	2005-08-18		ENSG00000197632	ENSG00000197632		"Serine (or cysteine) peptidase inhibitors"	8584	protein-coding gene	gene with protein product		173390	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2"	PLANH2, PAI2		24172014	Standard	NM_002575		Approved	HsT1201	uc002ljo.3	P05120	OTTHUMG00000060592	ENST00000299502.4:c.245T>C	chr18.hg19:g.61562574T>C	ENSP00000299502:p.Met82Thr	69.0	0.0		75.0	24.0	NM_002575	Q96E96	Missense_Mutation	SNP	ENST00000299502.4	hg19	CCDS11989.1	.	.	.	.	.	.	.	.	.	.	T	4.329	0.060439	0.08339	.	.	ENSG00000197632	ENST00000404622;ENST00000299502;ENST00000457692;ENST00000413956;ENST00000443281	D;D;D;D;T	0.83591	-1.57;-1.74;-1.74;-1.55;-1.07	5.93	-7.49	0.01355	Serpin domain (3);	433.424000	0.00654	U	0.000566	T	0.69196	0.3084	L	0.41027	1.25	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.57148	-0.7861	10	0.12766	T	0.61	.	3.3198	0.07047	0.1155:0.4126:0.2358:0.2361	.	82	P05120	PAI2_HUMAN	T	82	ENSP00000385397:M82T;ENSP00000299502:M82T;ENSP00000401645:M82T;ENSP00000402386:M82T;ENSP00000397096:M82T	ENSP00000299502:M82T	M	+	2	0	SERPINB2	59713554	0.000000	0.05858	0.001000	0.08648	0.234000	0.25298	-2.068000	0.01382	-1.714000	0.01390	-0.408000	0.06270	ATG	.	.		0.433	SERPINB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134009.1	NM_002575		C	61562574	T	C	61562574	3	2	344	1	0	0	0	0	1	0	0	0	14116	1464	51	2	251	2	SERPINB2	18	61562574	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2395918	61562574	16514674	1206	48569										
DSEL	92126	hgsc.bcm.edu	37	chr18	65180193	65180193	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gacacggcttccccactcacAaataccatttccccatgttg	5	16	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr18:65180193A>G	ENST00000310045.7	-	2	3156	c.1683T>C	c.(1681-1683)ttT>ttC	p.F561F	CTD-2541J13.2_ENST00000583493.1_RNA|CTD-2541J13.2_ENST00000581951.1_RNA	NM_032160.2	NP_115536.1	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	551					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	isomerase activity (GO:0016853)|sulfotransferase activity (GO:0008146)			NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(25)|lung(23)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)				CCCCACTCACAAATACCATTT	0.468																																					p.F561F		Atlas-SNP	.											.	DSEL	196	.	0			c.T1683C						.						90	83	85					18																	65180193		2203	4300	6503	SO:0001819	synonymous_variant	92126	exon2			ACTCACAAATACC	AF480435	CCDS11995.1	18q22.1	2007-01-29	2007-01-29	2007-01-29	ENSG00000171451	ENSG00000171451			18144	protein-coding gene	gene with protein product		611125	"chromosome 18 open reading frame 4"	C18orf4		16505484	Standard	NM_032160		Approved	NCAG1, FLJ11477	uc002lke.1	Q8IZU8	OTTHUMG00000132804	ENST00000310045.7:c.1683T>C	chr18.hg19:g.65180193A>G		105.0	0.0		109.0	44.0	NM_032160	Q17RH1|Q6P5Z3	Silent	SNP	ENST00000310045.7	hg19	CCDS11995.1																																																																																			.	.		0.468	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160		G	65180193	A	G	65180193	2	3	344	1	0	0	0	0	0	0	0	1	4777	127	5	2		2	DSEL	18	65180193	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3617619	65180193	12897055	1207	48570										
CCDC102B	79839	hgsc.bcm.edu	37	chr18	66678301	66678301	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaagaaactaagattacgagTggaagaactaaagcagggac	11	5	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr18:66678301T>C	ENST00000360242.5	+	7	1511	c.1394T>C	c.(1393-1395)gTg>gCg	p.V465A	CCDC102B_ENST00000584156.1_Missense_Mutation_p.V465A|CCDC102B_ENST00000319445.6_Missense_Mutation_p.V465A	NM_024781.2	NP_079057	Q68D86	C102B_HUMAN	coiled-coil domain containing 102B	465										breast(2)|endometrium(3)|large_intestine(5)|lung(19)|ovary(1)|skin(5)|stomach(1)	36		Esophageal squamous(42;0.0559)|Colorectal(73;0.0604)				AGATTACGAGTGGAAGAACTA	0.373																																					p.V465A		Atlas-SNP	.											.	CCDC102B	92	.	0			c.T1394C						.						111	106	108					18																	66678301		2203	4300	6503	SO:0001583	missense	79839	exon9			TACGAGTGGAAGA	AK027247	CCDS11996.2	18q22.1	2007-11-14	2006-04-10	2006-04-10	ENSG00000150636	ENSG00000150636			26295	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 14", "aminoacylase 1-like"	C18orf14, ACY1L		14702039	Standard	NM_001093729		Approved	FLJ23594, HsT1731, AN	uc002lkk.2	Q68D86	OTTHUMG00000132808	ENST00000360242.5:c.1394T>C	chr18.hg19:g.66678301T>C	ENSP00000353377:p.Val465Ala	159.0	0.0		135.0	50.0	NM_001093729	Q7Z467|Q8NDK7|Q9H5C1	Missense_Mutation	SNP	ENST00000360242.5	hg19	CCDS11996.2	.	.	.	.	.	.	.	.	.	.	T	9.891	1.204337	0.22205	.	.	ENSG00000150636	ENST00000319445;ENST00000360242	T;T	0.25912	1.77;1.77	5.29	5.29	0.74685	.	0.171467	0.27691	N	0.018247	T	0.42426	0.1202	M	0.71036	2.16	0.80722	D	1	D	0.55385	0.971	P	0.55615	0.78	T	0.37753	-0.9692	10	0.59425	D	0.04	-5.1028	11.6135	0.51074	0.0:0.0:0.0:1.0	.	465	Q68D86	C102B_HUMAN	A	465	ENSP00000316237:V465A;ENSP00000353377:V465A	ENSP00000316237:V465A	V	+	2	0	CCDC102B	64829281	1.000000	0.71417	0.846000	0.33378	0.276000	0.26787	5.958000	0.70330	1.994000	0.58287	0.533000	0.62120	GTG	.	.		0.373	CCDC102B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256225.2	NM_024781		C	66678301	T	C	66678301	3	2	344	1	0	0	0	0	1	0	0	0	2739	1696	59	2	1416	2	CCDC102B	18	66678301	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1498108	66678301	11398947	1208	48571										
FAM69C	125704	hgsc.bcm.edu	37	chr18	72114218	72114218	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cggccaccacggccccaggcTgctgttggacaactccaggc	12	17	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr18:72114218T>A	ENST00000343998.6	-	2	507	c.499A>T	c.(499-501)Agc>Tgc	p.S167C	FAM69C_ENST00000400291.2_Intron	NM_001044369.2	NP_001037834.2	Q0P6D2	FA69C_HUMAN	family with sequence similarity 69, member C	167						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	transferase activity, transferring phosphorus-containing groups (GO:0016772)			breast(1)|large_intestine(2)|ovary(2)	5						GGCCCCAGGCTGCTGTTGGAC	0.701																																					p.S167C		Atlas-SNP	.											.	FAM69C	45	.	0			c.A499T						.						2	4	3					18																	72114218		578	1428	2006	SO:0001583	missense	125704	exon2			CCAGGCTGCTGTT	BC019628	CCDS42445.2	18q22.3	2012-08-03	2009-07-23	2009-07-23	ENSG00000187773	ENSG00000187773			31729	protein-coding gene	gene with protein product		614544	"chromosome 18 open reading frame 51"	C18orf51		21334309	Standard	NM_001044369		Approved		uc002llk.3	Q0P6D2	OTTHUMG00000156984	ENST00000343998.6:c.499A>T	chr18.hg19:g.72114218T>A	ENSP00000344331:p.Ser167Cys	60.0	0.0		61.0	32.0	NM_001044369		Missense_Mutation	SNP	ENST00000343998.6	hg19	CCDS42445.2	.	.	.	.	.	.	.	.	.	.	T	13.94	2.386954	0.42308	.	.	ENSG00000187773	ENST00000343998	.	.	.	3.59	1.04	0.20106	.	0.377645	0.28482	N	0.015200	T	0.47116	0.1428	L	0.38175	1.15	0.38321	D	0.943539	D	0.65815	0.995	P	0.52672	0.706	T	0.46414	-0.9193	9	0.54805	T	0.06	-5.4831	5.8663	0.18777	0.0:0.0942:0.1658:0.74	.	167	Q0P6D2	FA69C_HUMAN	C	167	.	ENSP00000344331:S167C	S	-	1	0	FAM69C	70265198	0.828000	0.29307	0.874000	0.34290	0.442000	0.32017	0.693000	0.25497	0.091000	0.17302	0.402000	0.26972	AGC	.	.		0.701	FAM69C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346971.2	XM_058931		A	72114218	T	A	72114218	3	1	344	1	0	0	0	0	1	0	0	0	5612	1580	55	4	772	4	FAM69C	18	72114218	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	5435917	72114218	5963030	1209	48572										
THEG	51298	hgsc.bcm.edu	37	chr19	362299	362299	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctgtcgtatccctcgttgagGcccttgcgcactttgggctt	11	13	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:362299G>A	ENST00000342640.4	-	8	1083	c.1041C>T	c.(1039-1041)ggC>ggT	p.G347G	THEG_ENST00000346878.2_Silent_p.G323G	NM_016585.4	NP_057669.1	Q9P2T0	THEG_HUMAN	theg spermatid protein	347					cell differentiation (GO:0030154)|chaperone-mediated protein complex assembly (GO:0051131)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)				NS(1)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(2)|soft_tissue(1)	29		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCTCGTTGAGGCCCTTGCGCA	0.602																																					p.G347G		Atlas-SNP	.											.	THEG	58	.	0			c.C1041T						.						153	150	151					19																	362299		2203	4300	6503	SO:0001819	synonymous_variant	51298	exon8			GTTGAGGCCCTTG	AF268610	CCDS12025.1, CCDS12026.1	19p13.3	2012-02-24	2012-02-24		ENSG00000105549	ENSG00000105549			13706	protein-coding gene	gene with protein product	"cancer/testis antigen 56"	609503	"Theg homolog (mouse)"			11173852	Standard	NM_016585		Approved	CT56, THEG1	uc002lol.3	Q9P2T0	OTTHUMG00000165491	ENST00000342640.4:c.1041C>T	chr19.hg19:g.362299G>A		96.0	0.0		54.0	21.0	NM_016585	A6NMJ8	Silent	SNP	ENST00000342640.4	hg19	CCDS12025.1	.	.	.	.	.	.	.	.	.	.	G	2.420	-0.333431	0.05278	.	.	ENSG00000105549	ENST00000530711	.	.	.	3.98	0.308	0.15815	.	.	.	.	.	T	0.38348	0.1037	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.38802	-0.9644	5	0.87932	D	0	-10.5385	5.0232	0.14372	0.129:0.4317:0.4393:0.0	.	.	.	.	V	125	.	ENSP00000431699:A125V	A	-	2	0	THEG	313299	0.001000	0.12720	0.010000	0.14722	0.059000	0.15707	0.247000	0.18179	0.315000	0.23110	-0.230000	0.12252	GCC	.	.		0.602	THEG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384431.2			A	362299	G	A	362299	2	1	344	1	0	0	0	0	0	0	0	1	15872	1190	42	3		3	THEG	19	362299	Silent	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10		362299	58766684	1210	48573										
C19orf21	126353	hgsc.bcm.edu	37	chr19	758534	758534	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cccatgtctggggctgggagGtggctggggcccctgcactg	18	12	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:758534G>T	ENST00000215582.6	+	2	1691	c.1588G>T	c.(1588-1590)Gtg>Ttg	p.V530L		NM_173481.2	NP_775752.1	Q8IVT2	MISP_HUMAN	mitotic spindle positioning	530					mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											GGGCTGGGAGGTGGCTGGGGC	0.667																																					p.V530L		Atlas-SNP	.											.	C19orf21	56	.	0			c.G1588T						.						31	38	35					19																	758534		2201	4298	6499	SO:0001583	missense	126353	exon2			TGGGAGGTGGCTG	BC052236	CCDS12042.1	19p13.3	2014-06-25	2013-05-03	2013-05-03	ENSG00000099812	ENSG00000099812			27000	protein-coding gene	gene with protein product	"mitotic interactor and substrate of Plk1"	615289	"chromosome 19 open reading frame 21"	C19orf21		23574715, 23509069, 24475924	Standard	NM_173481		Approved	DKFZp686H18209, Caprice		Q8IVT2	OTTHUMG00000181786	ENST00000215582.6:c.1588G>T	chr19.hg19:g.758534G>T	ENSP00000215582:p.Val530Leu	86.0	0.0		77.0	33.0	NM_173481		Missense_Mutation	SNP	ENST00000215582.6	hg19	CCDS12042.1	.	.	.	.	.	.	.	.	.	.	G	9.589	1.125617	0.20959	.	.	ENSG00000099812	ENST00000215582	T	0.33216	1.42	3.24	2.15	0.27550	.	0.954746	0.08645	N	0.914884	T	0.22898	0.0553	L	0.60455	1.87	0.09310	N	1	P	0.46512	0.879	B	0.38755	0.281	T	0.12167	-1.0558	10	0.09590	T	0.72	-9.8294	4.0192	0.09657	0.1415:0.2549:0.6036:0.0	.	530	Q8IVT2	CS021_HUMAN	L	530	ENSP00000215582:V530L	ENSP00000215582:V530L	V	+	1	0	C19orf21	709534	0.013000	0.17824	0.015000	0.15790	0.004000	0.04260	0.419000	0.21247	0.879000	0.35944	0.561000	0.74099	GTG	.	.		0.667	MISP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457600.2	NM_173481		T	758534	G	T	758534	3	4	344	1	0	0	0	0	1	0	0	0	1915	1261	44	3	1590	3	C19orf21	19	758534	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	396235	758534	58370449	1211	48574										
C19orf21	126353	hgsc.bcm.edu	37	chr19	758601	758601	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tctgctggaaagggagagggAgagtgtcctgcgccgggagc	19	8	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:758601A>T	ENST00000215582.6	+	2	1758	c.1655A>T	c.(1654-1656)gAg>gTg	p.E552V		NM_173481.2	NP_775752.1	Q8IVT2	MISP_HUMAN	mitotic spindle positioning	552					mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											AGGGAGAGGGAGAGTGTCCTG	0.617																																					p.E552V		Atlas-SNP	.											.	C19orf21	56	.	0			c.A1655T						.						50	57	54					19																	758601		2203	4300	6503	SO:0001583	missense	126353	exon2			AGAGGGAGAGTGT	BC052236	CCDS12042.1	19p13.3	2014-06-25	2013-05-03	2013-05-03	ENSG00000099812	ENSG00000099812			27000	protein-coding gene	gene with protein product	"mitotic interactor and substrate of Plk1"	615289	"chromosome 19 open reading frame 21"	C19orf21		23574715, 23509069, 24475924	Standard	NM_173481		Approved	DKFZp686H18209, Caprice		Q8IVT2	OTTHUMG00000181786	ENST00000215582.6:c.1655A>T	chr19.hg19:g.758601A>T	ENSP00000215582:p.Glu552Val	153.0	0.0		129.0	58.0	NM_173481		Missense_Mutation	SNP	ENST00000215582.6	hg19	CCDS12042.1	.	.	.	.	.	.	.	.	.	.	A	13.39	2.222775	0.39300	.	.	ENSG00000099812	ENST00000215582	T	0.34859	1.34	3.69	1.35	0.21983	.	0.452377	0.19429	N	0.114487	T	0.29028	0.0721	M	0.62723	1.935	0.25105	N	0.990754	B	0.32968	0.392	B	0.28638	0.092	T	0.20605	-1.0270	10	0.62326	D	0.03	-17.6222	5.0176	0.14345	0.4799:0.4061:0.1141:0.0	.	552	Q8IVT2	CS021_HUMAN	V	552	ENSP00000215582:E552V	ENSP00000215582:E552V	E	+	2	0	C19orf21	709601	0.998000	0.40836	0.719000	0.30619	0.316000	0.28119	1.410000	0.34691	0.060000	0.16281	0.459000	0.35465	GAG	.	.		0.617	MISP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457600.2	NM_173481		T	758601	A	T	758601	3	4	344	1	0	0	0	0	1	0	0	0	1915	304	11	4	1657	4	C19orf21	19	758601	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	67	758601	58370382	1212	48575										
APC2	10297	hgsc.bcm.edu	37	chr19	1460853	1460853	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tccgacagtgaggagctccaCcaggtacagggcggggtgct	16	11	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:1460853C>G	ENST00000535453.1	+	11	3231	c.1518C>G	c.(1516-1518)caC>caG	p.H506Q	APC2_ENST00000233607.2_Missense_Mutation_p.H506Q|APC2_ENST00000238483.4_Missense_Mutation_p.H232Q|CTB-25B13.12_ENST00000588225.1_RNA			P02655	APOC2_HUMAN	adenomatosis polyposis coli 2	0					cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|chylomicron remnant clearance (GO:0034382)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle clearance (GO:0034384)|lipid catabolic process (GO:0016042)|lipoprotein metabolic process (GO:0042157)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of lipid metabolic process (GO:0045833)|negative regulation of receptor-mediated endocytosis (GO:0048261)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipid catabolic process (GO:0060697)|positive regulation of triglyceride catabolic process (GO:0010898)|positive regulation of very-low-density lipoprotein particle remodeling (GO:0010902)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)|triglyceride-rich lipoprotein particle remodeling (GO:0034370)|very-low-density lipoprotein particle remodeling (GO:0034372)	chylomicron (GO:0042627)|early endosome (GO:0005769)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate-density lipoprotein particle (GO:0034363)|low-density lipoprotein particle (GO:0034362)|spherical high-density lipoprotein particle (GO:0034366)|very-low-density lipoprotein particle (GO:0034361)	lipase inhibitor activity (GO:0055102)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|kidney(4)|large_intestine(2)|lung(5)|pancreas(1)|skin(2)	18		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AGGAGCTCCACCAGGTACAGG	0.701																																					p.H506Q		Atlas-SNP	.											APC2,NS,malignant_melanoma,0,1	APC2	50	.	0			c.C1518G						.						23	27	26					19																	1460853		2200	4293	6493	SO:0001583	missense	10297	exon12			GCTCCACCAGGTA		CCDS12068.1	19p13.3	2013-02-14			ENSG00000115266	ENSG00000115266		"Armadillo repeat containing"	24036	protein-coding gene	gene with protein product	"adenomatous polyposis coli like"	612034				9823329, 10021369	Standard	XM_005259475		Approved	APCL	uc002lsr.1	O95996		ENST00000535453.1:c.1518C>G	chr19.hg19:g.1460853C>G	ENSP00000442954:p.His506Gln	109.0	0.0		81.0	11.0	NM_005883	C0JYY4|Q9BS39|Q9UDE3|Q9UNK3	Missense_Mutation	SNP	ENST00000535453.1	hg19	CCDS12068.1	.	.	.	.	.	.	.	.	.	.	C	5.077	0.199913	0.09652	.	.	ENSG00000115266	ENST00000233607;ENST00000238483;ENST00000535453	T;T;T	0.62498	0.02;1.04;0.02	4.07	3.02	0.34903	Armadillo-like helical (1);Armadillo-type fold (1);	0.063724	0.64402	D	0.000007	T	0.43100	0.1232	N	0.01576	-0.805	0.35386	D	0.79032	D;D	0.65815	0.96;0.995	D;D	0.70487	0.944;0.969	T	0.52909	-0.8512	10	0.06236	T	0.91	-39.0196	6.0903	0.19991	0.0:0.6978:0.1923:0.1099	.	505;506	O95996-3;O95996	.;APC2_HUMAN	Q	506;232;506	ENSP00000233607:H506Q;ENSP00000238483:H232Q;ENSP00000442954:H506Q	ENSP00000233607:H506Q	H	+	3	2	APC2	1411853	0.994000	0.37717	1.000000	0.80357	0.684000	0.39900	0.132000	0.15891	0.897000	0.36392	0.563000	0.77884	CAC	.	.		0.701	APC2-004	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449539.2	NM_005883		G	1460853	C	G	1460853	3	3	344	1	0	0	0	0	1	0	0	0	764	506	18	4	1560	4	APC2	19	1460853	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	702252	1460853	57668130	1213	48576										
MAP2K2	5605	hgsc.bcm.edu	37	chr19	4117490	4117490	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cgccgttgcccgcgcccagcTctgagatcctttcgaagtca	10	16	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:4117490T>C	ENST00000262948.5	-	2	483	c.230A>G	c.(229-231)gAg>gGg	p.E77G	MAP2K2_ENST00000394867.4_5'UTR|MAP2K2_ENST00000599345.1_5'UTR	NM_030662.3	NP_109587.1	P36507	MP2K2_HUMAN	mitogen-activated protein kinase kinase 2	77	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|MAPK cascade (GO:0000165)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine autophosphorylation (GO:0036289)|positive regulation of cell motility (GO:2000147)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|Ras protein signal transduction (GO:0007265)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of stress-activated MAPK cascade (GO:0032872)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisomal membrane (GO:0005778)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|scaffold protein binding (GO:0097110)						Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)	Bosutinib(DB06616)|Trametinib(DB08911)	CGCGCCCAGCTCTGAGATCCT	0.612																																					p.E77G		Atlas-SNP	.											.	MAP2K2	72	.	0			c.A230G						.						73	68	69					19																	4117490		2203	4300	6503	SO:0001583	missense	5605	exon2			CCCAGCTCTGAGA	L11285	CCDS12120.1	19p13.3	2014-09-17			ENSG00000126934	ENSG00000126934	2.7.12.2	"Mitogen-activated protein kinase cascade / Kinase kinases"	6842	protein-coding gene	gene with protein product		601263		PRKMK2		8388392	Standard	NM_030662		Approved	MEK2	uc002lzk.3	P36507	OTTHUMG00000134286	ENST00000262948.5:c.230A>G	chr19.hg19:g.4117490T>C	ENSP00000262948:p.Glu77Gly	70.0	0.0		55.0	16.0	NM_030662		Missense_Mutation	SNP	ENST00000262948.5	hg19	CCDS12120.1	.	.	.	.	.	.	.	.	.	.	t	22.0	4.229875	0.79688	.	.	ENSG00000126934	ENST00000262948	D	0.93659	-3.26	4.67	3.65	0.41850	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.95532	0.8548	M	0.76433	2.335	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95150	0.8272	10	0.87932	D	0	-33.5457	8.6127	0.33813	0.0:0.0931:0.0:0.9069	.	77	P36507	MP2K2_HUMAN	G	77	ENSP00000262948:E77G	ENSP00000262948:E77G	E	-	2	0	MAP2K2	4068490	1.000000	0.71417	0.974000	0.42286	0.849000	0.48306	7.892000	0.87324	1.738000	0.51689	0.454000	0.30748	GAG	.	.		0.612	MAP2K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258957.2			C	4117490	T	C	4117490	3	2	344	1	0	0	0	0	1	0	0	0	9246	1551	54	2	1012	2	MAP2K2	19	4117490	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2656637	4117490	55011493	1214	48577										
SIRT6	51548	hgsc.bcm.edu	37	chr19	4175099	4175099	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agccagcggcaggttcccgcTgggccggatctgcagcgatg	16	13	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:4175099T>A	ENST00000337491.2	-	7	728	c.664A>T	c.(664-666)Agc>Tgc	p.S222C	SIRT6_ENST00000381935.3_Missense_Mutation_p.S150C|SIRT6_ENST00000594279.1_Silent_p.P136P|SIRT6_ENST00000305232.6_Missense_Mutation_p.S195C|SIRT6_ENST00000601488.1_Silent_p.P147P	NM_016539.2	NP_057623.2	Q8N6T7	SIR6_HUMAN	sirtuin 6	222	Deacetylase sirtuin-type. {ECO:0000255|PROSITE-ProRule:PRU00236}.				histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|protein ADP-ribosylation (GO:0006471)|regulation of double-strand break repair via homologous recombination (GO:0010569)	nuclear telomeric heterochromatin (GO:0005724)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (GO:0017136)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(1)|lung(4)|ovary(1)|skin(1)	8		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.023)|STAD - Stomach adenocarcinoma(1328;0.18)		AGGTTCCCGCTGGGCCGGATC	0.682																																					p.S222C		Atlas-SNP	.											.	SIRT6	16	.	0			c.A664T						.						22	20	21					19																	4175099		2194	4282	6476	SO:0001583	missense	51548	exon7			TCCCGCTGGGCCG	AF233396	CCDS12122.1, CCDS54199.1	19p13.3	2010-06-25	2010-06-25			ENSG00000077463			14934	protein-coding gene	gene with protein product		606211	"sirtuin (silent mating type information regulation 2, S. cerevisiae, homolog) 6", "sirtuin (silent mating type information regulation 2 homolog) 6 (S. cerevisiae)"			10873683	Standard	NM_016539		Approved		uc002lzo.3	Q8N6T7		ENST00000337491.2:c.664A>T	chr19.hg19:g.4175099T>A	ENSP00000337332:p.Ser222Cys	58.0	0.0		35.0	19.0	NM_016539	B2RCD0|O75291|Q6IAF5|Q6PK99|Q8NCD2|Q9BSI5|Q9BWP3|Q9NRC7|Q9UQD1	Missense_Mutation	SNP	ENST00000337491.2	hg19	CCDS12122.1	.	.	.	.	.	.	.	.	.	.	T	14.98	2.698439	0.48307	.	.	ENSG00000077463	ENST00000337491;ENST00000305232;ENST00000381935	T;T;T	0.17370	2.28;2.28;2.28	4.49	4.49	0.54785	.	0.041854	0.85682	D	0.000000	T	0.26085	0.0636	L	0.50993	1.605	0.58432	D	0.999992	B;P	0.36599	0.389;0.56	B;P	0.47075	0.359;0.536	T	0.02698	-1.1122	10	0.54805	T	0.06	-29.4814	12.5915	0.56445	0.0:0.0:0.0:1.0	.	195;222	Q8N6T7-2;Q8N6T7	.;SIRT6_HUMAN	C	222;195;150	ENSP00000337332:S222C;ENSP00000305310:S195C;ENSP00000371360:S150C	ENSP00000305310:S195C	S	-	1	0	SIRT6	4126099	1.000000	0.71417	1.000000	0.80357	0.219000	0.24729	4.333000	0.59285	1.652000	0.50683	0.379000	0.24179	AGC	.	.		0.682	SIRT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457931.2			A	4175099	T	A	4175099	3	1	344	1	0	0	0	0	1	0	0	0	14357	1580	55	4	411	4	SIRT6	19	4175099	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	57609	4175099	54953884	1215	48578										
ANKRD24	170961	hgsc.bcm.edu	37	chr19	4207906	4207906	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcactatggcgccctggcggGggacaaactcatcctgcacc	11	15	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:4207906G>A	ENST00000600132.1	+	10	1049	c.773G>A	c.(772-774)gGg>gAg	p.G258E	ANKRD24_ENST00000318934.4_Missense_Mutation_p.G258E|RN7SL84P_ENST00000578969.1_RNA|ANKRD24_ENST00000262970.5_Missense_Mutation_p.G348E	NM_133475.1	NP_597732.1	Q8TF21	ANR24_HUMAN	ankyrin repeat domain 24	258										endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)	21				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0233)|STAD - Stomach adenocarcinoma(1328;0.181)		GCCCTGGCGGGGGACAAACTC	0.677											OREG0025162	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G258E		Atlas-SNP	.											.	ANKRD24	180	.	0			c.G773A						.						13	17	16					19																	4207906		1956	4134	6090	SO:0001583	missense	170961	exon10			TGGCGGGGGACAA	AB075861	CCDS45925.1	19p13.3	2013-01-10				ENSG00000089847		"Ankyrin repeat domain containing"	29424	protein-coding gene	gene with protein product						11853319	Standard	NM_133475		Approved	KIAA1981	uc010dtt.1	Q8TF21		ENST00000600132.1:c.773G>A	chr19.hg19:g.4207906G>A	ENSP00000471252:p.Gly258Glu	88.0	0.0	617	82.0	38.0	NM_133475	O75268|O95781	Missense_Mutation	SNP	ENST00000600132.1	hg19	CCDS45925.1	.	.	.	.	.	.	.	.	.	.	G	14.91	2.676017	0.47886	.	.	ENSG00000089847	ENST00000318934;ENST00000262970	T;T	0.34859	1.34;1.34	4.89	4.89	0.63831	Ankyrin repeat-containing domain (3);	0.000000	0.34386	N	0.004017	T	0.52338	0.1728	L	0.45581	1.43	0.50313	D	0.999867	D;P	0.89917	1.0;0.664	D;P	0.91635	0.999;0.876	T	0.53781	-0.8390	10	0.66056	D	0.02	-51.6963	13.5487	0.61719	0.0:0.0:1.0:0.0	.	258;348	Q8TF21;Q8TF21-2	ANR24_HUMAN;.	E	258;348	ENSP00000321731:G258E;ENSP00000262970:G348E	ENSP00000262970:G348E	G	+	2	0	ANKRD24	4158906	1.000000	0.71417	0.978000	0.43139	0.621000	0.37620	6.349000	0.73013	2.266000	0.75297	0.462000	0.41574	GGG	.	.		0.677	ANKRD24-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458188.1	XM_114000		A	4207906	G	A	4207906	3	1	344	1	0	0	0	0	1	0	0	0	653	1232	43	3	807	3	ANKRD24	19	4207906	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	32807	4207906	54921077	1216	48579										
CCDC94	55702	hgsc.bcm.edu	37	chr19	4249223	4249223	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acgtttccttcctcccctgcAgaaatactacccgccggact	6	17	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:4249223A>G	ENST00000262962.7	+	2	92		c.e2-1			NM_018074.4	NP_060544.2	Q9BW85	CCD94_HUMAN	coiled-coil domain containing 94											NS(1)|endometrium(1)|lung(2)|ovary(1)|stomach(2)	7				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0348)|STAD - Stomach adenocarcinoma(1328;0.183)		CCTCCCCTGCAGAAATACTAC	0.587																																					.		Atlas-SNP	.											.	CCDC94	28	.	0			c.25-2A>G						.						59	48	51					19																	4249223		2203	4300	6503	SO:0001630	splice_region_variant	55702	exon2			CCCTGCAGAAATA	AK001236	CCDS12124.1	19p13.3	2008-02-05				ENSG00000105248			25518	protein-coding gene	gene with protein product						12477932	Standard	NM_018074		Approved	FLJ10374	uc002lzv.4	Q9BW85		ENST00000262962.7:c.25-1A>G	chr19.hg19:g.4249223A>G		86.0	0.0		72.0	34.0	NM_018074	O75270|Q9H862|Q9NW16	Splice_Site	SNP	ENST00000262962.7	hg19	CCDS12124.1	.	.	.	.	.	.	.	.	.	.	.	17.11	3.305640	0.60305	.	.	ENSG00000105248	ENST00000262962	.	.	.	5.18	5.18	0.71444	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.1594	0.65436	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CCDC94	4200223	1.000000	0.71417	0.985000	0.45067	0.644000	0.38419	7.061000	0.76699	2.076000	0.62316	0.528000	0.53228	.	.	.		0.587	CCDC94-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458007.2	NM_018074	Intron	G	4249223	A	G	4249223	5	3	344	1	0	0	0	0	0	0	1	0	2875	202	7	2	29	2	CCDC94	19	4249223	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	41317	4249223	54879760	1217	48580										
STAP2	55620	hgsc.bcm.edu	37	chr19	4333984	4333984	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccttacctggaagtcccgatTgctattgtagaaataaatgg	9	8	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:4333984T>A	ENST00000594605.1	-	2	283	c.160A>T	c.(160-162)Aat>Tat	p.N54Y	STAP2_ENST00000600324.1_Missense_Mutation_p.N54Y	NM_001013841.1	NP_001013863.1	Q9UGK3	STAP2_HUMAN	signal transducing adaptor family member 2	54	PH.					cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0339)|STAD - Stomach adenocarcinoma(1328;0.18)		AAGTCCCGATTGCTATTGTAG	0.527																																					p.N54Y		Atlas-SNP	.											.	STAP2	38	.	0			c.A160T						.						65	66	66					19																	4333984		2203	4300	6503	SO:0001583	missense	55620	exon2			CCCGATTGCTATT	AJ245719	CCDS12128.1, CCDS45926.1	19p13.3	2011-05-03	2007-08-09		ENSG00000178078	ENSG00000178078			30430	protein-coding gene	gene with protein product		607881				10980601, 11441184	Standard	XM_005259592		Approved	STAP-2, BKS	uc002mac.3	Q9UGK3		ENST00000594605.1:c.160A>T	chr19.hg19:g.4333984T>A	ENSP00000471052:p.Asn54Tyr	65.0	0.0		68.0	37.0	NM_001013841	A6NKK3|Q9NXI2	Missense_Mutation	SNP	ENST00000594605.1	hg19	CCDS45926.1	.	.	.	.	.	.	.	.	.	.	T	17.01	3.278640	0.59758	.	.	ENSG00000178078	ENST00000314714;ENST00000424810	.	.	.	5.05	5.05	0.67936	Pleckstrin homology-type (1);Pleckstrin homology domain (1);	0.411506	0.25538	N	0.029993	T	0.54127	0.1839	L	0.57536	1.79	0.28246	N	0.925476	P;D	0.58620	0.873;0.983	P;P	0.58331	0.46;0.837	T	0.54091	-0.8345	9	0.87932	D	0	-3.9828	11.2648	0.49104	0.0:0.0:0.0:1.0	.	54;54	Q9UGK3-2;Q9UGK3	.;STAP2_HUMAN	Y	54	.	ENSP00000317912:N54Y	N	-	1	0	STAP2	4284984	0.352000	0.24895	0.949000	0.38748	0.532000	0.34746	1.738000	0.38207	1.921000	0.55644	0.510000	0.49958	AAT	.	.		0.527	STAP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458114.2	NM_001013841		A	4333984	T	A	4333984	3	1	344	1	0	0	0	0	1	0	0	0	15268	1812	63	4	1237	4	STAP2	19	4333984	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	84761	4333984	54794999	1218	48581										
ARRDC5	645432	hgsc.bcm.edu	37	chr19	4902726	4902726	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gagctccaccttcactatggGgtccaccagggtgctgttca	11	13	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:4902726G>T	ENST00000381781.2	-	1	153	c.154C>A	c.(154-156)Ccc>Acc	p.P52T	UHRF1_ENST00000592666.1_RNA	NM_001080523.1	NP_001073992.1	A6NEK1	ARRD5_HUMAN	arrestin domain containing 5	52										endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0257)		TTCACTATGGGGTCCACCAGG	0.507																																					p.P52T		Atlas-SNP	.											.	ARRDC5	19	.	0			c.C154A						.						150	138	142					19																	4902726		1894	4121	6015	SO:0001583	missense	645432	exon1			CTATGGGGTCCAC		CCDS45929.1	19p13.3	2007-10-05				ENSG00000205784			31407	protein-coding gene	gene with protein product						12886014	Standard	NM_001080523		Approved		uc002mbm.3	A6NEK1		ENST00000381781.2:c.154C>A	chr19.hg19:g.4902726G>T	ENSP00000371200:p.Pro52Thr	139.0	0.0		120.0	62.0	NM_001080523		Missense_Mutation	SNP	ENST00000381781.2	hg19	CCDS45929.1	.	.	.	.	.	.	.	.	.	.	G	19.94	3.920626	0.73213	.	.	ENSG00000205784	ENST00000381781	T	0.12672	2.66	5.37	5.37	0.77165	Immunoglobulin E-set (1);Arrestin-like, N-terminal (1);	0.000000	0.47093	D	0.000253	T	0.27933	0.0688	L	0.41236	1.265	0.40766	D	0.983044	D	0.89917	1.0	D	0.97110	1.0	T	0.00382	-1.1775	10	0.36615	T	0.2	-38.8905	14.4683	0.67499	0.0:0.0:1.0:0.0	.	52	A6NEK1	ARRD5_HUMAN	T	52	ENSP00000371200:P52T	ENSP00000371200:P52T	P	-	1	0	ARRDC5	4853726	1.000000	0.71417	0.999000	0.59377	0.975000	0.68041	4.859000	0.62954	2.796000	0.96246	0.650000	0.86243	CCC	.	.		0.507	ARRDC5-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450443.1	XM_292803		T	4902726	G	T	4902726	3	4	344	1	0	0	0	0	1	0	0	0	986	1232	43	3	886	3	ARRDC5	19	4902726	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	568742	4902726	54226257	1219	48582										
ZNRF4	148066	hgsc.bcm.edu	37	chr19	5456001	5456001	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgatccgccgctacgactgcAccttcgacctcaaggtgctg	10	15	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:5456001A>T	ENST00000222033.4	+	1	576	c.499A>T	c.(499-501)Acc>Tcc	p.T167S		NM_181710.3	NP_859061.3	Q8WWF5	ZNRF4_HUMAN	zinc and ring finger 4	167	PA.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			NS(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (162;0.0002)		CTACGACTGCACCTTCGACCT	0.662																																					p.T167S		Atlas-SNP	.											.	ZNRF4	59	.	0			c.A499T						.						38	40	39					19																	5456001		2147	4244	6391	SO:0001583	missense	148066	exon1			GACTGCACCTTCG	AK098722	CCDS42475.1	19p13.3	2013-01-09				ENSG00000105428		"RING-type (C3HC4) zinc fingers"	17726	protein-coding gene	gene with protein product		612063					Standard	NM_181710		Approved	spzn, Ssrzf1, RNF204	uc002mca.4	Q8WWF5		ENST00000222033.4:c.499A>T	chr19.hg19:g.5456001A>T	ENSP00000222033:p.Thr167Ser	14.0	0.0		13.0	9.0	NM_181710	A8K886|O75866	Missense_Mutation	SNP	ENST00000222033.4	hg19	CCDS42475.1	.	.	.	.	.	.	.	.	.	.	A	7.017	0.557858	0.13436	.	.	ENSG00000105428	ENST00000222033	T	0.06528	3.29	4.65	1.19	0.21007	Protease-associated domain, PA (1);	0.126722	0.49916	N	0.000130	T	0.03434	0.0099	L	0.28740	0.885	0.21675	N	0.999599	B	0.30179	0.271	B	0.27380	0.079	T	0.39840	-0.9594	10	0.23891	T	0.37	-12.3359	1.0194	0.01514	0.414:0.1595:0.0957:0.3308	.	167	Q8WWF5	ZNRF4_HUMAN	S	167	ENSP00000222033:T167S	ENSP00000222033:T167S	T	+	1	0	ZNRF4	5407001	0.024000	0.19004	0.064000	0.19789	0.253000	0.25986	0.140000	0.16056	-0.133000	0.11537	-0.669000	0.03829	ACC	.	.		0.662	ZNRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450924.1	NM_181710		T	5456001	A	T	5456001	3	4	344	1	0	0	0	0	1	0	0	0	18229	159	6	4	501	4	ZNRF4	19	5456001	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	553275	5456001	53672982	1220	48583										
RANBP3	8498	hgsc.bcm.edu	37	chr19	5918611	5918611	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	catctgggcccacagcttggTgttgaggatcagtcgcaggc	14	11	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:5918611T>A	ENST00000340578.6	-	15	1426	c.1369A>T	c.(1369-1371)Acc>Tcc	p.T457S	RANBP3_ENST00000034275.8_Missense_Mutation_p.T389S|RANBP3_ENST00000541471.1_Missense_Mutation_p.T329S|RANBP3_ENST00000591092.1_Missense_Mutation_p.T384S|RANBP3_ENST00000439268.2_Missense_Mutation_p.T452S	NM_003624.2|NM_007320.2|NM_007322.2	NP_003615.2|NP_015559.2|NP_015561.1	Q9H6Z4	RANB3_HUMAN	RAN binding protein 3	457	RanBD1. {ECO:0000255|PROSITE- ProRule:PRU00164}.				intracellular transport (GO:0046907)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	R-SMAD binding (GO:0070412)|Ran GTPase binding (GO:0008536)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)	18						CACAGCTTGGTGTTGAGGATC	0.612																																					p.T457S		Atlas-SNP	.											.	RANBP3	36	.	0			c.A1369T						.						136	153	148					19																	5918611		2135	4237	6372	SO:0001583	missense	8498	exon15			GCTTGGTGTTGAG	Y08698	CCDS42477.1, CCDS42478.1, CCDS45935.1, CCDS74268.1	19p13.3	2008-02-05							9850	protein-coding gene	gene with protein product		603327				9637251	Standard	NM_007322		Approved		uc002mdw.3	Q9H6Z4		ENST00000340578.6:c.1369A>T	chr19.hg19:g.5918611T>A	ENSP00000341483:p.Thr457Ser	118.0	0.0		96.0	49.0	NM_007322	B2RAT8|O60405|O75759|O75760|Q9BT47|Q9UG74	Missense_Mutation	SNP	ENST00000340578.6	hg19	CCDS42478.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.166370	0.78339	.	.	ENSG00000031823	ENST00000340578;ENST00000439268;ENST00000034275;ENST00000541471	T;T;T;T	0.41065	1.01;1.01;1.01;1.01	4.98	4.98	0.66077	Pleckstrin homology-type (1);Ran binding protein 1 (3);	0.000000	0.85682	D	0.000000	T	0.47710	0.1460	L	0.27944	0.81	0.80722	D	1	D;D;D;D;D;D;D	0.76494	0.997;0.999;0.999;0.999;0.999;0.999;0.999	D;D;D;D;D;D;D	0.91635	0.997;0.999;0.999;0.999;0.998;0.998;0.999	T	0.33059	-0.9883	10	0.17369	T	0.5	-31.6078	12.635	0.56679	0.0:0.0:0.0:1.0	.	329;452;329;384;389;452;457	F5H4C2;Q53GE1;B7Z5P4;B7Z7F3;Q9H6Z4-3;Q9H6Z4-2;Q9H6Z4	.;.;.;.;.;.;RANB3_HUMAN	S	457;452;389;329	ENSP00000341483:T457S;ENSP00000404837:T452S;ENSP00000034275:T389S;ENSP00000445071:T329S	ENSP00000034275:T389S	T	-	1	0	RANBP3	5869611	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	7.600000	0.82769	1.859000	0.53934	0.459000	0.35465	ACC	.	.		0.612	RANBP3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452304.1	NM_007322		A	5918611	T	A	5918611	3	1	344	1	0	0	0	0	1	0	0	0	13044	1696	59	4	346	4	RANBP3	19	5918611	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	462610	5918611	53210372	1221	48584										
DENND1C	79958	hgsc.bcm.edu	37	chr19	6478804	6478804	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctggtctcacttggtcctggGctaggaggtctcccactgtg	13	12	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:6478804G>A	ENST00000381480.2	-	6	468	c.356C>T	c.(355-357)gCc>gTc	p.A119V	DENND1C_ENST00000591030.1_5'UTR|DENND1C_ENST00000543576.1_Missense_Mutation_p.A75V	NM_024898.2	NP_079174.2	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	119	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of Rab GTPase activity (GO:0032851)	cytoplasmic vesicle (GO:0031410)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(3)|kidney(3)|large_intestine(1)|lung(3)	10						TTGGTCCTGGGCTAGGAGGTC	0.597																																					p.A119V		Atlas-SNP	.											.	DENND1C	93	.	0			c.C356T						.						60	69	66					19																	6478804		2017	4162	6179	SO:0001583	missense	79958	exon6			TCCTGGGCTAGGA	AL713770	CCDS45938.1	19p13.3	2014-02-06	2005-08-17	2005-08-17	ENSG00000205744	ENSG00000205744		"DENN/MADD domain containing"	26225	protein-coding gene	gene with protein product		613634	"family with sequence similarity 31, member C"	FAM31C		12477932	Standard	XM_005259646		Approved	FLJ22757	uc002mfe.3	Q8IV53	OTTHUMG00000180853	ENST00000381480.2:c.356C>T	chr19.hg19:g.6478804G>A	ENSP00000370889:p.Ala119Val	179.0	0.0		119.0	51.0	NM_024898	B4E051|D3PFD4|Q8NDB1|Q9H5Z2	Missense_Mutation	SNP	ENST00000381480.2	hg19	CCDS45938.1	.	.	.	.	.	.	.	.	.	.	G	11.43	1.636240	0.29068	.	.	ENSG00000205744	ENST00000381480;ENST00000543576	T;T	0.11604	2.76;2.76	4.98	4.98	0.66077	DENN (3);	0.179445	0.48286	D	0.000199	T	0.12092	0.0294	L	0.46819	1.47	0.30962	N	0.723577	B	0.29188	0.236	B	0.30401	0.115	T	0.05289	-1.0894	10	0.21014	T	0.42	-12.8762	15.7122	0.77641	0.0:0.0:1.0:0.0	.	119	Q8IV53	DEN1C_HUMAN	V	119;75	ENSP00000370889:A119V;ENSP00000437805:A75V	ENSP00000370889:A119V	A	-	2	0	DENND1C	6429804	0.995000	0.38212	0.913000	0.36048	0.086000	0.17979	3.513000	0.53414	2.313000	0.78055	0.313000	0.20887	GCC	.	.		0.597	DENND1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453332.2	NM_024898		A	6478804	G	A	6478804	3	1	344	1	0	0	0	0	1	0	0	0	4430	1203	42	3	2121	3	DENND1C	19	6478804	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	560193	6478804	52650179	1222	48585										
C3	718	hgsc.bcm.edu	37	chr19	6710810	6710810	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccaccaggtcctggccgggcTctcgcacctggcgtcccgcc	12	20	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:6710810T>C	ENST00000245907.6	-	13	1618	c.1526A>G	c.(1525-1527)gAg>gGg	p.E509G		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	509					complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	CTGGCCGGGCTCTCGCACCTG	0.662																																					p.E509G		Atlas-SNP	.											.	C3	192	.	0			c.A1526G						.						50	51	51					19																	6710810		2203	4300	6503	SO:0001583	missense	718	exon13			CCGGGCTCTCGCA	J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"Complement system", "Endogenous ligands"	1318	protein-coding gene	gene with protein product	"C3a anaphylatoxin", "complement component C3a", "complement component C3b", "prepro-C3"	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.1526A>G	chr19.hg19:g.6710810T>C	ENSP00000245907:p.Glu509Gly	85.0	0.0		100.0	44.0	NM_000064	A7E236	Missense_Mutation	SNP	ENST00000245907.6	hg19	CCDS32883.1	.	.	.	.	.	.	.	.	.	.	T	7.936	0.741733	0.15642	.	.	ENSG00000125730	ENST00000245907	T	0.66280	-0.2	5.17	4.15	0.48705	Alpha-2-macroglobulin, N-terminal 2 (1);	0.613743	0.17905	N	0.158071	T	0.40322	0.1112	N	0.17901	0.54	0.09310	N	1	B	0.09022	0.002	B	0.17979	0.02	T	0.18650	-1.0330	10	0.27082	T	0.32	.	2.311	0.04186	0.1528:0.0858:0.1585:0.6028	.	509	P01024	CO3_HUMAN	G	509	ENSP00000245907:E509G	ENSP00000245907:E509G	E	-	2	0	C3	6661810	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	0.047000	0.14056	0.823000	0.34589	0.533000	0.62120	GAG	.	.		0.662	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064		C	6710810	T	C	6710810	3	2	344	1	0	0	0	0	1	0	0	0	2206	1551	54	2	3581	2	C3	19	6710810	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	232006	6710810	52418173	1223	48586										
FBN3	84467	hgsc.bcm.edu	37	chr19	8175948	8175948	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gggcccaaccttaccctggcAggcccggtggtcctcggtgg	15	15	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:8175948A>T	ENST00000600128.1	-	33	4618	c.4204T>A	c.(4204-4206)Tgc>Agc	p.C1402S	FBN3_ENST00000601739.1_Missense_Mutation_p.C1402S|FBN3_ENST00000270509.2_Missense_Mutation_p.C1402S			Q75N90	FBN3_HUMAN	fibrillin 3	1402	EGF-like 21; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						TTACCCTGGCAGGCCCGGTGG	0.667																																					p.C1402S		Atlas-SNP	.											.	FBN3	300	.	0			c.T4204A						.						54	52	53					19																	8175948		2203	4300	6503	SO:0001583	missense	84467	exon32			CCTGGCAGGCCCG		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.4204T>A	chr19.hg19:g.8175948A>T	ENSP00000470498:p.Cys1402Ser	63.0	0.0		50.0	17.0	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	hg19	CCDS12196.1	.	.	.	.	.	.	.	.	.	.	A	16.73	3.203206	0.58234	.	.	ENSG00000142449	ENST00000270509	D	0.99429	-5.89	3.67	3.67	0.42095	EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	U	0.000000	D	0.99560	0.9842	M	0.92970	3.365	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.98231	1.0483	10	0.59425	D	0.04	.	12.5776	0.56373	1.0:0.0:0.0:0.0	.	1402	Q75N90	FBN3_HUMAN	S	1402	ENSP00000270509:C1402S	ENSP00000270509:C1402S	C	-	1	0	FBN3	8081948	1.000000	0.71417	0.983000	0.44433	0.128000	0.20619	8.443000	0.90320	1.434000	0.47414	0.379000	0.24179	TGC	.	.		0.667	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447		T	8175948	A	T	8175948	3	4	344	1	0	0	0	0	1	0	0	0	5712	188	7	4	4353	4	FBN3	19	8175948	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1465138	8175948	50953035	1224	48587										
MUC16	94025	hgsc.bcm.edu	37	chr19	9062263	9062263	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaagaagtcagaagtggataTggaaacactcgtttccccca	9	9	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:9062263T>C	ENST00000397910.4	-	3	25386	c.25183A>G	c.(25183-25185)Ata>Gta	p.I8395V		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	8397	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GAAGTGGATATGGAAACACTC	0.483																																					p.I8395V		Atlas-SNP	.											.	MUC16	4315	.	0			c.A25183G						.						133	126	128					19																	9062263		2000	4173	6173	SO:0001583	missense	94025	exon3			TGGATATGGAAAC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.25183A>G	chr19.hg19:g.9062263T>C	ENSP00000381008:p.Ile8395Val	52.0	0.0		54.0	30.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	3.445	-0.113300	0.06881	.	.	ENSG00000181143	ENST00000397910	T	0.23147	1.92	2.69	-5.38	0.02673	.	.	.	.	.	T	0.12263	0.0298	N	0.22421	0.69	.	.	.	B	0.11235	0.004	B	0.12156	0.007	T	0.29274	-1.0017	8	0.87932	D	0	.	0.4557	0.00508	0.2815:0.226:0.2982:0.1943	.	8395	B5ME49	.	V	8395	ENSP00000381008:I8395V	ENSP00000381008:I8395V	I	-	1	0	MUC16	8923263	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.963000	0.01513	-1.915000	0.01077	0.324000	0.21423	ATA	.	.		0.483	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	9062263	T	C	9062263	3	2	344	1	0	0	0	0	1	0	0	0	9982	1464	51	2	18668	2	MUC16	19	9062263	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	886315	9062263	50066720	1225	48588										
MUC16	94025	hgsc.bcm.edu	37	chr19	9067175	9067175	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gttcctgccctggaggatgtAgttggtgtgtccaaggtaaa	14	7	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:9067175A>T	ENST00000397910.4	-	3	20474	c.20271T>A	c.(20269-20271)acT>acA	p.T6757T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	6759	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGGAGGATGTAGTTGGTGTGT	0.478																																					p.T6757T		Atlas-SNP	.											.	MUC16	4315	.	0			c.T20271A						.						273	268	270					19																	9067175		2199	4295	6494	SO:0001819	synonymous_variant	94025	exon3			GGATGTAGTTGGT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.20271T>A	chr19.hg19:g.9067175A>T		84.0	0.0		58.0	27.0	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9067175	A	T	9067175	2	4	344	1	0	0	0	0	0	0	0	1	9982	407	15	4		4	MUC16	19	9067175	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	4912	9067175	50061808	1226	48589										
MUC16	94025	hgsc.bcm.edu	37	chr19	9067507	9067507	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaatgttgactccatctcaaTccttgtaatctcagaggagc	8	10	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:9067507T>C	ENST00000397910.4	-	3	20142	c.19939A>G	c.(19939-19941)Att>Gtt	p.I6647V		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	6649	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TCCATCTCAATCCTTGTAATC	0.502																																					p.I6647V		Atlas-SNP	.											.	MUC16	4315	.	0			c.A19939G						.						104	102	103					19																	9067507		2022	4181	6203	SO:0001583	missense	94025	exon3			TCTCAATCCTTGT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.19939A>G	chr19.hg19:g.9067507T>C	ENSP00000381008:p.Ile6647Val	96.0	0.0		90.0	42.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	7.155	0.584604	0.13749	.	.	ENSG00000181143	ENST00000397910	T	0.25250	1.81	2.57	-3.36	0.04913	.	.	.	.	.	T	0.14830	0.0358	L	0.38175	1.15	.	.	.	B	0.16603	0.018	B	0.11329	0.006	T	0.34004	-0.9846	8	0.87932	D	0	.	0.3985	0.00422	0.3637:0.1247:0.1862:0.3253	.	6647	B5ME49	.	V	6647	ENSP00000381008:I6647V	ENSP00000381008:I6647V	I	-	1	0	MUC16	8928507	0.000000	0.05858	0.000000	0.03702	0.579000	0.36224	-1.351000	0.02622	-0.919000	0.03803	0.138000	0.15974	ATT	.	.		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	9067507	T	C	9067507	3	2	344	1	0	0	0	0	1	0	0	0	9982	1435	50	2	23912	2	MUC16	19	9067507	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	332	9067507	50061476	1227	48590										
MUC16	94025	hgsc.bcm.edu	37	chr19	9069194	9069194	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtagttgagttcatcaccagGgcggtgctgtcctctttcag	12	10	4	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:9069194G>A	ENST00000397910.4	-	3	18455	c.18252C>T	c.(18250-18252)gcC>gcT	p.A6084A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	6086	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TCATCACCAGGGCGGTGCTGT	0.483																																					p.A6084A		Atlas-SNP	.											.	MUC16	4315	.	0			c.C18252T						.						77	85	83					19																	9069194		2120	4246	6366	SO:0001819	synonymous_variant	94025	exon3			CACCAGGGCGGTG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.18252C>T	chr19.hg19:g.9069194G>A		111.0	0.0		111.0	56.0	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.483	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9069194	G	A	9069194	2	1	344	1	0	0	0	0	0	0	0	1	9982	1219	43	3		3	MUC16	19	9069194	Silent	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1687	9069194	50059789	1228	48591										
MUC16	94025	hgsc.bcm.edu	37	chr19	9071260	9071260	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tctctcatgagtgatgctgcTcaaatttggaggtgaactgg	12	7	3	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:9071260T>A	ENST00000397910.4	-	3	16389	c.16186A>T	c.(16186-16188)Agc>Tgc	p.S5396C		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5398	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTGATGCTGCTCAAATTTGGA	0.502																																					p.S5396C		Atlas-SNP	.											.	MUC16	4315	.	0			c.A16186T						.						350	328	335					19																	9071260		2073	4219	6292	SO:0001583	missense	94025	exon3			TGCTGCTCAAATT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.16186A>T	chr19.hg19:g.9071260T>A	ENSP00000381008:p.Ser5396Cys	100.0	0.0		96.0	42.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	3.710	-0.059692	0.07317	.	.	ENSG00000181143	ENST00000397910	T	0.30448	1.53	2.38	-1.08	0.09936	.	.	.	.	.	T	0.28167	0.0695	L	0.27053	0.805	.	.	.	D	0.61697	0.99	P	0.54460	0.753	T	0.36962	-0.9726	8	0.87932	D	0	.	5.859	0.18736	0.0:0.4604:0.0:0.5396	.	5396	B5ME49	.	C	5396	ENSP00000381008:S5396C	ENSP00000381008:S5396C	S	-	1	0	MUC16	8932260	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.423000	0.21313	-0.376000	0.07943	-0.736000	0.03550	AGC	.	.		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9071260	T	A	9071260	3	1	344	1	0	0	0	0	1	0	0	0	9982	1551	54	4	27665	4	MUC16	19	9071260	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2066	9071260	50057723	1229	48592										
MUC16	94025	hgsc.bcm.edu	37	chr19	9077042	9077042	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtgaggcttgtaatgccttgGtctccagagggcagagacac	14	9	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:9077042G>T	ENST00000397910.4	-	3	10607	c.10404C>A	c.(10402-10404)gaC>gaA	p.D3468E		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3469	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TAATGCCTTGGTCTCCAGAGG	0.502																																					p.D3468E		Atlas-SNP	.											.	MUC16	4315	.	0			c.C10404A						.						118	115	116					19																	9077042		2102	4221	6323	SO:0001583	missense	94025	exon3			GCCTTGGTCTCCA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.10404C>A	chr19.hg19:g.9077042G>T	ENSP00000381008:p.Asp3468Glu	55.0	0.0		47.0	27.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	6.223	0.409355	0.11812	.	.	ENSG00000181143	ENST00000397910	T	0.02763	4.17	2.13	-4.26	0.03755	.	.	.	.	.	T	0.01870	0.0059	N	0.08118	0	.	.	.	P	0.34977	0.478	B	0.41236	0.351	T	0.44329	-0.9335	8	0.87932	D	0	.	3.7188	0.08448	0.5467:0.0:0.2655:0.1879	.	3468	B5ME49	.	E	3468	ENSP00000381008:D3468E	ENSP00000381008:D3468E	D	-	3	2	MUC16	8938042	0.000000	0.05858	0.000000	0.03702	0.188000	0.23474	-0.822000	0.04448	-1.238000	0.02535	0.313000	0.20887	GAC	.	.		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9077042	G	T	9077042	3	4	344	1	0	0	0	0	1	0	0	0	9982	1252	44	3	33447	3	MUC16	19	9077042	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	5782	9077042	50051941	1230	48593										
OR7G1	125962	hgsc.bcm.edu	37	chr19	9226012	9226012	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acatggagagaagaatcagcAagccccagaaatggacattc	10	9	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:9226012A>T	ENST00000541538.1	-	1	427	c.428T>A	c.(427-429)tTg>tAg	p.L143*	OR7G1_ENST00000293614.1_Nonsense_Mutation_p.L143*	NM_001005192.2	NP_001005192.2	Q8NGA0	OR7G1_HUMAN	olfactory receptor, family 7, subfamily G, member 1	143						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|skin(2)	20						AAGAATCAGCAAGCCCCAGAA	0.483																																					p.L143X		Atlas-SNP	.											.	OR7G1	53	.	0			c.T428A						.						84	87	86					19																	9226012		2203	4300	6503	SO:0001587	stop_gained	125962	exon1			ATCAGCAAGCCCC		CCDS32898.1, CCDS32898.2	19p13.2	2013-09-24			ENSG00000161807	ENSG00000161807		"GPCR / Class A : Olfactory receptors"	8465	protein-coding gene	gene with protein product				OR7G1P			Standard	NM_001005192		Approved	OR19-15	uc021uoi.1	Q8NGA0	OTTHUMG00000168067	ENST00000541538.1:c.428T>A	chr19.hg19:g.9226012A>T	ENSP00000444134:p.Leu143*	92.0	0.0		89.0	32.0	NM_001005192	Q6IFJ5|Q96RA1	Nonsense_Mutation	SNP	ENST00000541538.1	hg19	CCDS32898.2	.	.	.	.	.	.	.	.	.	.	a	12.96	2.093750	0.36952	.	.	ENSG00000161807	ENST00000293614;ENST00000541538	.	.	.	3.78	-3.53	0.04667	.	0.620307	0.12078	U	0.501552	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.8569	0.13564	0.1973:0.0:0.2747:0.528	.	.	.	.	X	143	.	ENSP00000293614:L143X	L	-	2	0	OR7G1	9087012	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.867000	0.01646	-0.515000	0.06479	0.410000	0.27636	TTG	.	.		0.483	OR7G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397912.1			T	9226012	A	T	9226012	4	4	344	1	0	0	0	0	0	1	0	0	11231	131	5	4	581	4	OR7G1	19	9226012	Nonsense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	148970	9226012	49902971	1231	48594										
S1PR5	53637	hgsc.bcm.edu	37	chr19	10624587	10624587	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tccagcccgtcgcgctggggCgatgagcgctccgagccgct	15	16	0	1	rs544821498		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:10624587C>T	ENST00000439028.3	-	2	1226	c.1101G>A	c.(1099-1101)tcG>tcA	p.S367S	S1PR5_ENST00000333430.4_Silent_p.S367S	NM_001166215.1	NP_001159687.1	Q9H228	S1PR5_HUMAN	sphingosine-1-phosphate receptor 5	367					regulation of neuron differentiation (GO:0045664)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sphingosine-1-phosphate receptor activity (GO:0038036)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	12					Fingolimod(DB08868)	CGCGCTGGGGCGATGAGCGCT	0.731													C|||	1	0.000199681	0	0	5008	,	,		11295	0		0	False		,,,				2504	0.001				p.S367S		Atlas-SNP	.											.	S1PR5	33	.	0			c.G1101A						.						11	15	14					19																	10624587		2158	4218	6376	SO:0001819	synonymous_variant	53637	exon2			CTGGGGCGATGAG	AK074661	CCDS12240.1	19p13.2	2012-08-08	2008-04-30	2008-04-30		ENSG00000180739		"GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"	14299	protein-coding gene	gene with protein product		605146	"endothelial differentiation, sphingolipid G-protein-coupled receptor, 8"	EDG8		10799507	Standard	NM_030760		Approved	Edg-8	uc002mou.2	Q9H228		ENST00000439028.3:c.1101G>A	chr19.hg19:g.10624587C>T		33.0	0.0		36.0	18.0	NM_030760	Q6NW11	Silent	SNP	ENST00000439028.3	hg19	CCDS12240.1																																																																																			.	.		0.731	S1PR5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452015.1	NM_030760		T	10624587	C	T	10624587	2	4	344	1	0	0	0	0	0	0	0	1	13812	755	27	1		1	S1PR5	19	10624587	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1398575	10624587	48504396	1232	48595										
S1PR5	53637	hgsc.bcm.edu	37	chr19	10625481	10625481	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cccaggagcaggaacatgggAgcgtggaagcgcgggtggcg	20	9	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:10625481A>G	ENST00000439028.3	-	2	332	c.207T>C	c.(205-207)gcT>gcC	p.A69A	S1PR5_ENST00000333430.4_Silent_p.A69A	NM_001166215.1	NP_001159687.1	Q9H228	S1PR5_HUMAN	sphingosine-1-phosphate receptor 5	69					regulation of neuron differentiation (GO:0045664)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sphingosine-1-phosphate receptor activity (GO:0038036)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	12					Fingolimod(DB08868)	GGAACATGGGAGCGTGGAAGC	0.662																																					p.A69A		Atlas-SNP	.											S1PR5,colon,carcinoma,-2,1	S1PR5	33	.	0			c.T207C						.						39	32	35					19																	10625481		2195	4297	6492	SO:0001819	synonymous_variant	53637	exon2			CATGGGAGCGTGG	AK074661	CCDS12240.1	19p13.2	2012-08-08	2008-04-30	2008-04-30		ENSG00000180739		"GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"	14299	protein-coding gene	gene with protein product		605146	"endothelial differentiation, sphingolipid G-protein-coupled receptor, 8"	EDG8		10799507	Standard	NM_030760		Approved	Edg-8	uc002mou.2	Q9H228		ENST00000439028.3:c.207T>C	chr19.hg19:g.10625481A>G		70.0	0.0		70.0	17.0	NM_030760	Q6NW11	Silent	SNP	ENST00000439028.3	hg19	CCDS12240.1																																																																																			.	.		0.662	S1PR5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452015.1	NM_030760		G	10625481	A	G	10625481	2	3	344	1	0	0	0	0	0	0	0	1	13812	291	11	2		2	S1PR5	19	10625481	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	894	10625481	48503502	1233	48596										
SMARCA4	6597	hgsc.bcm.edu	37	chr19	11101907	11101907	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctaaggcctacaagcgcagcAagcgccagtccctgcgcgag	12	15	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:11101907A>C	ENST00000429416.3	+	9	1608	c.1327A>C	c.(1327-1329)Aag>Cag	p.K443Q	SMARCA4_ENST00000358026.2_Missense_Mutation_p.K443Q|SMARCA4_ENST00000589677.1_Missense_Mutation_p.K443Q|SMARCA4_ENST00000413806.3_Missense_Mutation_p.K443Q|SMARCA4_ENST00000444061.3_Missense_Mutation_p.K443Q|SMARCA4_ENST00000344626.4_Missense_Mutation_p.K443Q|SMARCA4_ENST00000590574.1_Missense_Mutation_p.K443Q|SMARCA4_ENST00000541122.2_Missense_Mutation_p.K443Q|SMARCA4_ENST00000450717.3_Missense_Mutation_p.K443Q	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	443					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				CAAGCGCAGCAAGCGCCAGTC	0.637			"F, N, Mis"		NSCLC																																p.K443Q		Atlas-SNP	.		Rec	yes		19	19p13.2	6597	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"		E	.	SMARCA4	502	.	1	Unknown(1)	lung(1)	c.A1327C						.						46	44	45					19																	11101907		2203	4300	6503	SO:0001583	missense	6597	exon8			CGCAGCAAGCGCC	D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"SNF2-like 4", "global transcription activator homologous sequence", "sucrose nonfermenting-like 4", "mitotic growth and transcription activator", "BRM/SWI2-related gene 1", "homeotic gene regulator", "nuclear protein GRB1", "brahma protein-like 1", "ATP-dependent helicase SMARCA4"	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.1327A>C	chr19.hg19:g.11101907A>C	ENSP00000395654:p.Lys443Gln	94.0	0.0		90.0	33.0	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	hg19	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	A	26.9	4.785314	0.90282	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	T;T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97;0.97	4.86	4.86	0.63082	.	0.056734	0.64402	D	0.000002	T	0.69611	0.3130	M	0.89601	3.045	0.58432	D	0.999995	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;1.0;1.0;1.0	D;D;D;D;D;D;D	0.80764	0.99;0.994;0.994;0.99;0.968;0.994;0.994	T	0.77064	-0.2726	10	0.87932	D	0	-49.5151	13.8602	0.63554	1.0:0.0:0.0:0.0	.	443;443;443;443;443;443;443	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;A7E2E1;P51532	.;.;.;.;.;.;SMCA4_HUMAN	Q	443	ENSP00000395654:K443Q;ENSP00000350720:K443Q;ENSP00000343896:K443Q;ENSP00000445036:K443Q;ENSP00000392837:K443Q;ENSP00000397783:K443Q;ENSP00000414727:K443Q	ENSP00000343896:K443Q	K	+	1	0	SMARCA4	10962907	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.053000	0.93860	2.177000	0.69029	0.533000	0.62120	AAG	.	.		0.637	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		C	11101907	A	C	11101907	3	2	344	1	0	0	0	0	1	0	0	0	14785	131	5	5	1353	5	SMARCA4	19	11101907	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	476426	11101907	48027076	1234	48597										
NFIX	4784	hgsc.bcm.edu	37	chr19	13136064	13136064	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcgcaaggacatccggcccgAgttccgcgaggacttcgtgc	14	14	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:13136064A>T	ENST00000592199.1	+	2	257	c.257A>T	c.(256-258)gAg>gTg	p.E86V	NFIX_ENST00000587260.1_Missense_Mutation_p.E85V|NFIX_ENST00000358552.3_Missense_Mutation_p.E85V|NFIX_ENST00000587760.1_Missense_Mutation_p.E78V|NFIX_ENST00000397661.2_Missense_Mutation_p.E86V|NFIX_ENST00000585575.1_Missense_Mutation_p.E78V|NFIX_ENST00000588228.1_Missense_Mutation_p.E39V|NFIX_ENST00000360105.4_Missense_Mutation_p.E89V			Q14938	NFIX_HUMAN	nuclear factor I/X (CCAAT-binding transcription factor)	86					astrocyte differentiation (GO:0048708)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell layer development (GO:0021680)|DNA replication (GO:0006260)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(1)|skin(1)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(19;8.2e-22)			ATCCGGCCCGAGTTCCGCGAG	0.657																																					p.E94V		Atlas-SNP	.											.	NFIX	61	.	0			c.A281T						.						54	55	54					19																	13136064		2203	4300	6503	SO:0001583	missense	4784	exon2			GGCCCGAGTTCCG	U18761	CCDS45996.1, CCDS59359.1	19p13.3	2008-02-05				ENSG00000008441			7788	protein-coding gene	gene with protein product		164005				8340106, 7590749	Standard	NM_001271043		Approved	NF1A	uc010xmx.2	Q14938		ENST00000592199.1:c.257A>T	chr19.hg19:g.13136064A>T	ENSP00000467512:p.Glu86Val	66.0	0.0		61.0	28.0	NM_001271043	B4DM25|O60413|Q0VG09|Q12859|Q13050|Q13052|Q5U094|Q9UPH1|Q9Y6R8	Missense_Mutation	SNP	ENST00000592199.1	hg19		.	.	.	.	.	.	.	.	.	.	A	21.1	4.092373	0.76756	.	.	ENSG00000008441	ENST00000397661;ENST00000360105;ENST00000264825;ENST00000438869;ENST00000358552	T;T	0.77877	-1.13;-1.13	5.26	5.26	0.73747	MAD homology 1, Dwarfin-type (2);CTF transcription factor/nuclear factor 1, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.87257	0.6132	M	0.76002	2.32	0.80722	D	1	D;D;D;D;D	0.89917	0.997;0.997;0.996;1.0;0.997	D;D;D;D;D	0.87578	0.996;0.993;0.99;0.998;0.993	D	0.88828	0.3303	10	0.87932	D	0	.	14.1503	0.65378	1.0:0.0:0.0:0.0	.	94;85;89;86;86	B4DHW2;Q14938-5;F8W8H9;Q14938;Q14938-3	.;.;.;NFIX_HUMAN;.	V	86;86;89;39;85	ENSP00000380781:E86V;ENSP00000351354:E85V	ENSP00000264825:E89V	E	+	2	0	NFIX	12997064	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.283000	0.95860	1.992000	0.58205	0.533000	0.62120	GAG	.	.		0.657	NFIX-013	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000452763.1	NM_002501		T	13136064	A	T	13136064	3	4	344	1	0	0	0	0	1	0	0	0	10383	304	11	4	263	4	NFIX	19	13136064	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2034157	13136064	45992919	1235	48598										
CACNA1A	773	hgsc.bcm.edu	37	chr19	13411364	13411364	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cagggattaggggcacttacAcagctatagacatgttggcc	12	9	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:13411364A>T	ENST00000360228.5	-	18	2278	c.2279T>A	c.(2278-2280)gTg>gAg	p.V760E	CACNA1A_ENST00000573710.2_Splice_Site_p.V761E	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	761					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	GGGCACTTACACAGCTATAGA	0.547																																					p.V761E		Atlas-SNP	.											.	CACNA1A	715	.	0			c.T2282A						.						170	179	176					19																	13411364		2027	4190	6217	SO:0001630	splice_region_variant	773	exon18			ACTTACACAGCTA	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.2279+1T>A	chr19.hg19:g.13411364A>T		87.0	0.0		74.0	23.0	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	hg19	CCDS45998.1	.	.	.	.	.	.	.	.	.	.	A	12.16	1.853333	0.32791	.	.	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084	D	0.95690	-3.78	5.19	5.19	0.71726	.	4.557950	0.00846	N	0.001790	D	0.92257	0.7544	L	0.29908	0.895	0.42082	D	0.991257	B;B;B	0.31153	0.09;0.145;0.31	B;B;B	0.29176	0.031;0.099;0.092	T	0.77305	-0.2637	9	.	.	.	.	8.712	0.34389	0.9129:0.0:0.0871:0.0	.	761;764;760	O00555;E9PD31;Q9NS88	CAC1A_HUMAN;.;.	E	760;764;761;761	ENSP00000353362:V760E	.	V	-	2	0	CACNA1A	13272364	1.000000	0.71417	0.996000	0.52242	0.743000	0.42351	3.198000	0.51035	1.959000	0.56917	0.402000	0.26972	GTG	.	.		0.547	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068	Missense_Mutation	T	13411364	A	T	13411364	5	4	344	1	0	0	0	0	0	0	1	0	2540	173	6	4	5463	4	CACNA1A	19	13411364	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	275300	13411364	45717619	1236	48599										
EMR3	84658	hgsc.bcm.edu	37	chr19	14749129	14749129	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aggtagagatagtgcaaagcAccggcgatgatggagcacag	15	7	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:14749129A>T	ENST00000253673.5	-	11	1372	c.1272T>A	c.(1270-1272)ggT>ggA	p.G424G	EMR3_ENST00000344373.4_Silent_p.G372G|EMR3_ENST00000443157.2_Silent_p.G298G|EMR3_ENST00000599900.1_Silent_p.G209G	NM_032571.3	NP_115960.2	Q9BY15	EMR3_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 3	424					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(14)|ovary(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	50						AGTGCAAAGCACCGGCGATGA	0.577																																					p.G424G		Atlas-SNP	.											.	EMR3	99	.	0			c.T1272A						.						89	71	77					19																	14749129		2203	4300	6503	SO:0001819	synonymous_variant	84658	exon11			CAAAGCACCGGCG	AF239764	CCDS12315.1, CCDS74296.1, CCDS74297.1	19p13.1	2014-08-08				ENSG00000131355		"-", "GPCR / Class B : Orphans"	23647	protein-coding gene	gene with protein product		606101				11279179, 12975309	Standard	XM_005260118		Approved		uc002mzi.4	Q9BY15		ENST00000253673.5:c.1272T>A	chr19.hg19:g.14749129A>T		78.0	0.0		55.0	30.0	NM_032571		Silent	SNP	ENST00000253673.5	hg19	CCDS12315.1																																																																																			.	.		0.577	EMR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466488.1	NM_032571		T	14749129	A	T	14749129	2	4	344	1	0	0	0	0	0	0	0	1	5108	146	6	4		4	EMR3	19	14749129	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1337765	14749129	44379854	1237	48600										
EMR3	84658	hgsc.bcm.edu	37	chr19	14755018	14755018	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tatcaggaagcagccatcccTggaccactggctgccctgcc	10	16	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:14755018T>A	ENST00000253673.5	-	9	1052	c.952A>T	c.(952-954)Agg>Tgg	p.R318W	EMR3_ENST00000344373.4_Missense_Mutation_p.R266W|EMR3_ENST00000443157.2_Missense_Mutation_p.R192W|EMR3_ENST00000599900.1_Missense_Mutation_p.R103W	NM_032571.3	NP_115960.2	Q9BY15	EMR3_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 3	318	GPS. {ECO:0000255|PROSITE- ProRule:PRU00098}.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(14)|ovary(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	50						CAGCCATCCCTGGACCACTGG	0.517																																					p.R318W		Atlas-SNP	.											EMR3,ear,carcinoma,+1,1	EMR3	99	.	0			c.A952T						.						107	91	96					19																	14755018		2203	4300	6503	SO:0001583	missense	84658	exon9			CATCCCTGGACCA	AF239764	CCDS12315.1, CCDS74296.1, CCDS74297.1	19p13.1	2014-08-08				ENSG00000131355		"-", "GPCR / Class B : Orphans"	23647	protein-coding gene	gene with protein product		606101				11279179, 12975309	Standard	XM_005260118		Approved		uc002mzi.4	Q9BY15		ENST00000253673.5:c.952A>T	chr19.hg19:g.14755018T>A	ENSP00000253673:p.Arg318Trp	75.0	0.0		66.0	30.0	NM_032571		Missense_Mutation	SNP	ENST00000253673.5	hg19	CCDS12315.1	.	.	.	.	.	.	.	.	.	.	t	20.7	4.034925	0.75617	.	.	ENSG00000131355	ENST00000443157;ENST00000253673;ENST00000344373	T;T;T	0.69561	-0.41;-0.41;-0.41	3.3	3.3	0.37823	GPS domain (3);	.	.	.	.	T	0.71392	0.3334	L	0.52126	1.63	0.09310	N	1	D;P;P	0.52996	0.957;0.947;0.952	P;P;P	0.58520	0.84;0.649;0.762	T	0.59968	-0.7354	9	0.87932	D	0	.	8.3393	0.32235	0.0:0.0:0.0:1.0	.	192;266;318	E7EW83;Q9BY15-2;Q9BY15	.;.;EMR3_HUMAN	W	192;318;266	ENSP00000396208:R192W;ENSP00000253673:R318W;ENSP00000340758:R266W	ENSP00000253673:R318W	R	-	1	2	EMR3	14616018	0.000000	0.05858	0.383000	0.26132	0.747000	0.42532	-0.646000	0.05403	1.531000	0.49152	0.520000	0.50463	AGG	.	.		0.517	EMR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466488.1	NM_032571		A	14755018	T	A	14755018	3	1	344	1	0	0	0	0	1	0	0	0	5108	1579	55	4	1038	4	EMR3	19	14755018	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	5889	14755018	44373965	1238	48601										
ZNF333	84449	hgsc.bcm.edu	37	chr19	14828536	14828536	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acagagatcctgtccattgaTgtgaaaggggtaaggctcac	12	8	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:14828536T>C	ENST00000292530.6	+	11	982	c.891T>C	c.(889-891)gaT>gaC	p.D297D	ZNF333_ENST00000536363.1_Silent_p.D188D|ZNF333_ENST00000540689.2_Silent_p.D297D	NM_032433.2	NP_115809.1	Q96JL9	ZN333_HUMAN	zinc finger protein 333	297					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|pancreas(1)|prostate(1)	21						TGTCCATTGATGTGAAAGGGG	0.438																																					p.D297D	NSCLC(60;75 1281 16985 25154 29885)	Atlas-SNP	.											.	ZNF333	76	.	0			c.T891C						.						135	120	125					19																	14828536		2203	4300	6503	SO:0001819	synonymous_variant	84449	exon11			CATTGATGTGAAA		CCDS12316.1, CCDS74298.1	19p13	2013-01-08				ENSG00000160961		"Zinc fingers, C2H2-type", "-"	15624	protein-coding gene	gene with protein product		611811				12151103	Standard	XM_005260098		Approved	KIAA1806	uc002mzn.3	Q96JL9		ENST00000292530.6:c.891T>C	chr19.hg19:g.14828536T>C		73.0	0.0		60.0	30.0	NM_032433	Q6P2E6|Q86WS6|Q8TDL0	Silent	SNP	ENST00000292530.6	hg19	CCDS12316.1																																																																																			.	.		0.438	ZNF333-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466496.1	NM_032433		C	14828536	T	C	14828536	2	2	344	1	0	0	0	0	0	0	0	1	17865	1461	51	2		2	ZNF333	19	14828536	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	73518	14828536	44300447	1239	48602										
NOTCH3	4854	hgsc.bcm.edu	37	chr19	15290991	15290991	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tggctaccagtacggccctcTgggcacacgcagtagtggga	14	12	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:15290991T>G	ENST00000263388.2	-	20	3294	c.3219A>C	c.(3217-3219)ccA>ccC	p.P1073P		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	1073	EGF-like 27. {ECO:0000255|PROSITE- ProRule:PRU00076}.				forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			TACGGCCCTCTGGGCACACGC	0.652																																					p.P1073P		Atlas-SNP	.											.	NOTCH3	340	.	0			c.A3219C						.						59	51	54					19																	15290991		2203	4300	6503	SO:0001819	synonymous_variant	4854	exon20			GCCCTCTGGGCAC	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"Ankyrin repeat domain containing"	7883	protein-coding gene	gene with protein product		600276	"Notch (Drosophila) homolog 3", "Notch homolog 3 (Drosophila)"	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.3219A>C	chr19.hg19:g.15290991T>G		55.0	0.0		52.0	25.0	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Silent	SNP	ENST00000263388.2	hg19	CCDS12326.1																																																																																			.	.		0.652	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435		G	15290991	T	G	15290991	2	3	344	1	0	0	0	0	0	0	0	1	10559	1567	55	5		5	NOTCH3	19	15290991	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	462455	15290991	43837992	1240	48603										
NOTCH3	4854	hgsc.bcm.edu	37	chr19	15299987	15299987	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgctcgcaggggttggcgccTgccggatggagtgcgatcgg	19	10	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:15299987T>A	ENST00000263388.2	-	8	1268		c.e8-2			NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3						forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			GGTTGGCGCCTGCCGGATGGA	0.667																																					.		Atlas-SNP	.											.	NOTCH3	340	.	0			c.1193-2A>T						.						55	50	52					19																	15299987		2203	4300	6503	SO:0001630	splice_region_variant	4854	exon9			GGCGCCTGCCGGA	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"Ankyrin repeat domain containing"	7883	protein-coding gene	gene with protein product		600276	"Notch (Drosophila) homolog 3", "Notch homolog 3 (Drosophila)"	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.1193-2A>T	chr19.hg19:g.15299987T>A		79.0	0.0		66.0	25.0	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Splice_Site	SNP	ENST00000263388.2	hg19	CCDS12326.1	.	.	.	.	.	.	.	.	.	.	T	11.41	1.629605	0.28978	.	.	ENSG00000074181	ENST00000263388;ENST00000539383	.	.	.	4.77	4.77	0.60923	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.2963	0.60298	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	NOTCH3	15160987	1.000000	0.71417	0.571000	0.28486	0.003000	0.03518	7.529000	0.81952	1.789000	0.52484	0.459000	0.35465	.	.	.		0.667	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435	Intron	A	15299987	T	A	15299987	5	1	344	1	0	0	0	0	0	0	1	0	10559	1594	55	4	5878	4	NOTCH3	19	15299987	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	8996	15299987	43828996	1241	48604										
F2RL3	9002	hgsc.bcm.edu	37	chr19	17000522	17000522	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	caccaggctggtgcccgcccTctatgggctggtcctggtgg	15	14	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:17000522T>A	ENST00000248076.3	+	2	578	c.248T>A	c.(247-249)cTc>cAc	p.L83H	F2RL3_ENST00000599210.1_Missense_Mutation_p.S82T	NM_003950.2	NP_003941.2	Q96RI0	PAR4_HUMAN	coagulation factor II (thrombin) receptor-like 3	83					blood coagulation (GO:0007596)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|platelet activation (GO:0030168)|platelet dense granule organization (GO:0060155)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|response to wounding (GO:0009611)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	thrombin receptor activity (GO:0015057)			cervix(1)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	7						GTGCCCGCCCTCTATGGGCTG	0.687																																					p.L83H		Atlas-SNP	.											.	F2RL3	20	.	0			c.T248A						.						14	15	15					19																	17000522		2188	4273	6461	SO:0001583	missense	9002	exon2			CCGCCCTCTATGG	AF055917	CCDS12350.1	19p12	2012-08-08						"GPCR / Class A : Protease activated receptors"	3540	protein-coding gene	gene with protein product	"proteinase-activated receptor-4"	602779				9618465	Standard	XM_005260139		Approved	PAR4	uc002nfa.3	Q96RI0		ENST00000248076.3:c.248T>A	chr19.hg19:g.17000522T>A	ENSP00000248076:p.Leu83His	20.0	0.0		25.0	13.0	NM_003950	O76067|Q6DK42	Missense_Mutation	SNP	ENST00000248076.3	hg19	CCDS12350.1	.	.	.	.	.	.	.	.	.	.	T	16.95	3.262985	0.59431	.	.	ENSG00000127533	ENST00000248076	T	0.46063	0.88	4.0	4.0	0.46444	.	0.179139	0.36740	U	0.002433	T	0.43523	0.1251	N	0.19112	0.55	0.45806	D	0.998688	D	0.67145	0.996	P	0.61201	0.885	T	0.34800	-0.9814	10	0.40728	T	0.16	.	12.1057	0.53811	0.0:0.0:0.0:1.0	.	83	Q96RI0	PAR4_HUMAN	H	83	ENSP00000248076:L83H	ENSP00000248076:L83H	L	+	2	0	F2RL3	16861522	1.000000	0.71417	0.031000	0.17742	0.286000	0.27126	7.553000	0.82203	1.466000	0.48025	0.402000	0.26972	CTC	.	.		0.687	F2RL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462875.1			A	17000522	T	A	17000522	3	1	344	1	0	0	0	0	1	0	0	0	5348	1551	54	4	254	4	F2RL3	19	17000522	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1700535	17000522	42128461	1242	48605										
IL12RB1	3594	hgsc.bcm.edu	37	chr19	18171954	18171954	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccttccctccagggaactcaAtggcggagctggcacagggt	13	13	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:18171954A>G	ENST00000600835.2	-	16	2067	c.1769T>C	c.(1768-1770)aTt>aCt	p.I590T	IL12RB1_ENST00000593993.2_Missense_Mutation_p.I590T			P42701	I12R1_HUMAN	interleukin 12 receptor, beta 1	590					cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-23-mediated signaling pathway (GO:0038155)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|interleukin-12 receptor complex (GO:0042022)|interleukin-23 receptor complex (GO:0072536)	cytokine receptor activity (GO:0004896)			endometrium(1)|kidney(1)|lung(3)|pancreas(1)|skin(2)	8						AGGGAACTCAATGGCGGAGCT	0.537																																					p.I590T		Atlas-SNP	.											.	IL12RB1	92	.	0			c.T1769C						.						36	39	38					19																	18171954		1926	4126	6052	SO:0001583	missense	3594	exon15			AACTCAATGGCGG	U03187	CCDS32957.1, CCDS54232.1	19p13.1	2014-09-17						"Interleukins and interleukin receptors", "CD molecules", "Fibronectin type III domain containing"	5971	protein-coding gene	gene with protein product		601604		IL12RB		9284929	Standard	XM_005259893		Approved	CD212	uc002nhw.1	P42701		ENST00000600835.2:c.1769T>C	chr19.hg19:g.18171954A>G	ENSP00000470788:p.Ile590Thr	307.0	0.0		268.0	122.0	NM_005535	A8K308|B2RPF1|B7ZKK3|Q8N6Q7	Missense_Mutation	SNP	ENST00000600835.2	hg19	CCDS54232.1	.	.	.	.	.	.	.	.	.	.	A	0.015	-1.548783	0.00926	.	.	ENSG00000096996	ENST00000430026	T	0.80480	-1.38	2.47	2.47	0.30058	.	0.972993	0.08343	N	0.960587	T	0.57621	0.2066	N	0.11427	0.14	0.20196	N	0.999927	P;B	0.36535	0.557;0.421	B;B	0.30495	0.116;0.054	T	0.47699	-0.9097	10	0.11794	T	0.64	-10.6607	6.8551	0.24036	1.0:0.0:0.0:0.0	.	590;590	P42701-2;P42701	.;I12R1_HUMAN	T	590	ENSP00000403103:I590T	ENSP00000403103:I590T	I	-	2	0	IL12RB1	18032954	0.013000	0.17824	0.002000	0.10522	0.055000	0.15305	3.466000	0.53071	1.407000	0.46875	0.240000	0.17902	ATT	.	.		0.537	IL12RB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466525.3			G	18171954	A	G	18171954	3	3	344	1	0	0	0	0	1	0	0	0	7635	101	4	2	231	2	IL12RB1	19	18171954	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1171432	18171954	40957029	1243	48606										
KIAA1683	80726	hgsc.bcm.edu	37	chr19	18377981	18377982	+	Missense_Mutation	DNP	CA	CA	AG													0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gccgccatcatctgggaaatCagcttctgccggagccaata					rs61740692	byFrequency	TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C|A	C|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:18377981_18377982CA>AG	ENST00000600328.3	-	3	561_562	c.368_369TG>CT	c.(367-369)cTG>cCT	p.L123P	KIAA1683_ENST00000392413.4_Missense_Mutation_p.L123P|KIAA1683_ENST00000600359.3_Missense_Mutation_p.L77P			Q9H0B3	K1683_HUMAN	KIAA1683	123	IQ 1. {ECO:0000255|PROSITE- ProRule:PRU00116}.					mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						TCTGGGAAATCAGCTTCTGCCG	0.564																																					p.L123L|p.L123P		Atlas-SNP	.											.	KIAA1683	190	.	0			c.G369T|c.T368C						.																																			SO:0001583	missense	80726	exon3			GGAAATCAGCTTC|GAAATCAGCTTCT	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.368_369delinsAG	chr19.hg19:g.18377981_18377982delinsAG	ENSP00000470780:p.Leu123Pro	77.0	0.0		74.0|72.0	33.0|31.0	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Silent|Missense_Mutation	SNP	ENST00000600328.3	hg19	CCDS32958.1																																																																																			.	C|0.984;G|0.016|.		0.564	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3			AG	18377982	CA	AG	18377981	3	1	344	1	0	0	0	0	1	0	0	0	8260	813	29	3	3742	3	KIAA1683	19	18377981	Missense_Mutation	DNP	CA	TCGA-UB-A7MB-01A-11D-A33Q-10	206027	18377981	40751002	1244	48607										
TMEM161A	54929	hgsc.bcm.edu	37	chr19	19243552	19243552	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtggcttctcctcactaaggCcattggcccacctgggagga	12	13	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:19243552C>T	ENST00000162044.9	-	4	264	c.200G>A	c.(199-201)gGc>gAc	p.G67D	TMEM161A_ENST00000450333.2_Missense_Mutation_p.G67D|TMEM161A_ENST00000592147.1_5'UTR|TMEM161A_ENST00000587583.2_Missense_Mutation_p.G67D	NM_017814.2	NP_060284.1	Q9NX61	T161A_HUMAN	transmembrane protein 161A	67					cellular response to oxidative stress (GO:0034599)|cellular response to UV (GO:0034644)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|positive regulation of DNA repair (GO:0045739)|response to retinoic acid (GO:0032526)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	15			OV - Ovarian serous cystadenocarcinoma(5;1.19e-05)|Epithelial(12;0.0011)			CTCACTAAGGCCATTGGCCCA	0.632																																					p.G67D		Atlas-SNP	.											.	TMEM161A	37	.	0			c.G200A						.						73	49	57					19																	19243552		2203	4300	6503	SO:0001583	missense	54929	exon4			CTAAGGCCATTGG	BC005210	CCDS12393.1, CCDS58656.1	19p13.11	2008-02-05				ENSG00000064545			26020	protein-coding gene	gene with protein product						12975309	Standard	NM_017814		Approved	FLJ39645, FLJ20422	uc002nlg.4	Q9NX61		ENST00000162044.9:c.200G>A	chr19.hg19:g.19243552C>T	ENSP00000162044:p.Gly67Asp	98.0	0.0		86.0	35.0	NM_001256766	B3KUE0|G5E9M6|Q7L2Y1	Missense_Mutation	SNP	ENST00000162044.9	hg19	CCDS12393.1	.	.	.	.	.	.	.	.	.	.	C	17.71	3.457575	0.63401	.	.	ENSG00000064545	ENST00000450333;ENST00000162044	.	.	.	3.86	3.86	0.44501	.	0.285572	0.38381	N	0.001716	T	0.73644	0.3613	M	0.69823	2.125	0.80722	D	1	D;D;D	0.69078	0.992;0.994;0.997	P;P;P	0.61940	0.767;0.851;0.896	T	0.74185	-0.3747	9	0.36615	T	0.2	.	13.6353	0.62219	0.0:1.0:0.0:0.0	.	67;67;67	G5E9M6;B3KUE0;Q9NX61	.;.;T161A_HUMAN	D	67	.	ENSP00000162044:G67D	G	-	2	0	TMEM161A	19104552	0.982000	0.34865	0.814000	0.32528	0.671000	0.39405	3.843000	0.55865	1.868000	0.54150	0.462000	0.41574	GGC	.	.		0.632	TMEM161A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460089.2	NM_017814		T	19243552	C	T	19243552	3	4	344	1	0	0	0	0	1	0	0	0	16091	739	26	3	1275	3	TMEM161A	19	19243552	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	865571	19243552	39885431	1245	48608										
CILP2	148113	hgsc.bcm.edu	37	chr19	19651056	19651056	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttcaacgtggaccaccccggAggcgacggcgacttcgagag	14	13	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:19651056A>T	ENST00000291495.5	+	3	292	c.207A>T	c.(205-207)ggA>ggT	p.G69G	CILP2_ENST00000586018.1_Silent_p.G75G	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	69						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				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						ACCACCCCGGAGGCGACGGCG	0.721																																					p.G69G		Atlas-SNP	.											.	CILP2	84	.	0			c.A207T						.						22	24	23					19																	19651056		2192	4297	6489	SO:0001819	synonymous_variant	148113	exon3			CCCCGGAGGCGAC	AF542080	CCDS12405.1	19p13.11	2013-01-14				ENSG00000160161		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	24213	protein-coding gene	gene with protein product		612419				12477932	Standard	NM_153221		Approved	MGC45771	uc002nmv.4	Q8IUL8		ENST00000291495.5:c.207A>T	chr19.hg19:g.19651056A>T		27.0	0.0		30.0	15.0	NM_153221	Q6NV88|Q8N4A6|Q8WV21	Silent	SNP	ENST00000291495.5	hg19	CCDS12405.1																																																																																			.	.		0.721	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221		T	19651056	A	T	19651056	2	4	344	1	0	0	0	0	0	0	0	1	3432	291	11	4		4	CILP2	19	19651056	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	407504	19651056	39477927	1246	48609										
CILP2	148113	hgsc.bcm.edu	37	chr19	19655120	19655120	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cgagctggtcctgccttctgGcgctttccgcagagccgacg	13	15	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:19655120G>T	ENST00000291495.5	+	8	1851	c.1766G>T	c.(1765-1767)gGc>gTc	p.G589V	CILP2_ENST00000586018.1_Missense_Mutation_p.G595V	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	589						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				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						CTGCCTTCTGGCGCTTTCCGC	0.667																																					p.G589V		Atlas-SNP	.											.	CILP2	84	.	0			c.G1766T						.						66	74	71					19																	19655120		2203	4300	6503	SO:0001583	missense	148113	exon8			CTTCTGGCGCTTT	AF542080	CCDS12405.1	19p13.11	2013-01-14				ENSG00000160161		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	24213	protein-coding gene	gene with protein product		612419				12477932	Standard	NM_153221		Approved	MGC45771	uc002nmv.4	Q8IUL8		ENST00000291495.5:c.1766G>T	chr19.hg19:g.19655120G>T	ENSP00000291495:p.Gly589Val	71.0	0.0		56.0	33.0	NM_153221	Q6NV88|Q8N4A6|Q8WV21	Missense_Mutation	SNP	ENST00000291495.5	hg19	CCDS12405.1	.	.	.	.	.	.	.	.	.	.	G	3.212	-0.161451	0.06502	.	.	ENSG00000160161	ENST00000291495	T	0.46063	0.88	3.77	2.62	0.31277	.	0.598723	0.17292	N	0.179616	T	0.27524	0.0676	L	0.34521	1.04	0.21386	N	0.999707	B;B	0.29936	0.262;0.262	B;B	0.32533	0.081;0.147	T	0.08827	-1.0703	10	0.31617	T	0.26	-6.6907	3.9515	0.09371	0.1268:0.0:0.6356:0.2376	.	589;589	B2RAJ0;Q8IUL8	.;CILP2_HUMAN	V	589	ENSP00000291495:G589V	ENSP00000291495:G589V	G	+	2	0	CILP2	19516120	0.059000	0.20769	0.004000	0.12327	0.097000	0.18754	2.799000	0.47892	1.658000	0.50742	0.430000	0.28490	GGC	.	.		0.667	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221		T	19655120	G	T	19655120	3	4	344	1	0	0	0	0	1	0	0	0	3432	1203	42	3	1796	3	CILP2	19	19655120	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	4064	19655120	39473863	1247	48610										
PBX4	80714	hgsc.bcm.edu	37	chr19	19675781	19675781	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcagctggcgtggttccctgGgaccccaacttccgtggtat	13	13	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:19675781G>A	ENST00000251203.9	-	6	1172	c.886C>T	c.(886-888)Cca>Tca	p.P296S		NM_025245.2	NP_079521.1	Q9BYU1	PBX4_HUMAN	pre-B-cell leukemia homeobox 4	296					positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|XY body (GO:0001741)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(1)|lung(4)|ovary(1)|prostate(3)	9						TGGTTCCCTGGGACCCCAACT	0.537																																					p.P296S		Atlas-SNP	.											.	PBX4	34	.	0			c.C886T						.						235	233	234					19																	19675781		2203	4300	6503	SO:0001583	missense	80714	exon6			TCCCTGGGACCCC	AJ300182	CCDS12406.1	19p13.11	2014-09-11	2007-01-30		ENSG00000105717			"Homeoboxes / TALE class"	13403	protein-coding gene	gene with protein product		608127	"pre-B-cell leukemia transcription factor 4"				Standard	NM_025245		Approved		uc002nmy.3	Q9BYU1	OTTHUMG00000172310	ENST00000251203.9:c.886C>T	chr19.hg19:g.19675781G>A	ENSP00000251203:p.Pro296Ser	107.0	0.0		94.0	47.0	NM_025245	A5D8Y0|B3KUK9	Missense_Mutation	SNP	ENST00000251203.9	hg19	CCDS12406.1	.	.	.	.	.	.	.	.	.	.	G	3.920	-0.018396	0.07681	.	.	ENSG00000105717	ENST00000251203	D	0.90444	-2.67	3.67	0.0742	0.14394	.	0.446039	0.21782	N	0.069191	T	0.67655	0.2916	N	0.02539	-0.55	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.60520	-0.7247	10	0.02654	T	1	-30.8686	4.7298	0.12959	0.2038:0.0:0.6254:0.1708	.	296	Q9BYU1	PBX4_HUMAN	S	296	ENSP00000251203:P296S	ENSP00000251203:P296S	P	-	1	0	PBX4	19536781	0.387000	0.25188	0.001000	0.08648	0.300000	0.27592	2.243000	0.43115	-0.045000	0.13468	0.505000	0.49811	CCA	.	.		0.537	PBX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417784.6			A	19675781	G	A	19675781	3	1	344	1	0	0	0	0	1	0	0	0	11504	1232	43	3	250	3	PBX4	19	19675781	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	20661	19675781	39453202	1248	48611										
GMIP	51291	hgsc.bcm.edu	37	chr19	19749243	19749243	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctccttcatccactgctcctTgaactccttccgccacttct	3	19	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:19749243T>C	ENST00000203556.4	-	8	723	c.586A>G	c.(586-588)Aag>Gag	p.K196E	GMIP_ENST00000586269.1_5'Flank|GMIP_ENST00000587238.1_Missense_Mutation_p.K196E|GMIP_ENST00000445806.2_Missense_Mutation_p.K196E	NM_016573.2	NP_057657.2	Q9P107	GMIP_HUMAN	GEM interacting protein	196					intracellular signal transduction (GO:0035556)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|Rho GTPase activator activity (GO:0005100)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24						CACTGCTCCTTGAACTCCTTC	0.597																																					p.K196E		Atlas-SNP	.											.	GMIP	55	.	0			c.A586G						.						156	110	126					19																	19749243		2203	4300	6503	SO:0001583	missense	51291	exon8			GCTCCTTGAACTC	AF132541	CCDS12408.1, CCDS74318.1	19p13.11	2011-09-07				ENSG00000089639		"Rho GTPase activating proteins"	24852	protein-coding gene	gene with protein product		609694				12093360, 16086184	Standard	XM_005259927		Approved	ARHGAP46	uc002nnd.3	Q9P107		ENST00000203556.4:c.586A>G	chr19.hg19:g.19749243T>C	ENSP00000203556:p.Lys196Glu	113.0	0.0		92.0	33.0	NM_016573	A0AVN9|B7ZLZ0	Missense_Mutation	SNP	ENST00000203556.4	hg19	CCDS12408.1	.	.	.	.	.	.	.	.	.	.	T	25.4	4.634589	0.87660	.	.	ENSG00000089639	ENST00000203556;ENST00000445806	T;T	0.42131	0.98;0.98	4.18	4.18	0.49190	.	0.000000	0.45606	D	0.000343	T	0.54902	0.1887	M	0.84219	2.685	0.47905	D	0.99954	D;D;D	0.60160	0.987;0.987;0.987	P;P;P	0.53549	0.729;0.729;0.729	T	0.61461	-0.7058	10	0.87932	D	0	-34.4022	7.7174	0.28712	0.0:0.0:0.2142:0.7858	.	196;196;196	E7ERB7;B7ZLZ0;Q9P107	.;.;GMIP_HUMAN	E	196	ENSP00000203556:K196E;ENSP00000397075:K196E	ENSP00000203556:K196E	K	-	1	0	GMIP	19610243	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.422000	0.80217	1.751000	0.51876	0.402000	0.26972	AAG	.	.		0.597	GMIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460551.1	NM_016573		C	19749243	T	C	19749243	3	2	344	1	0	0	0	0	1	0	0	0	6499	1821	63	2	2382	2	GMIP	19	19749243	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	73462	19749243	39379740	1249	48612										
ZNF93	81931	hgsc.bcm.edu	37	chr19	20026109	20026109	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggaccattgcaatttagagaTgtggccatagaattctctct	9	8	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:20026109T>C	ENST00000343769.5	+	2	52	c.24T>C	c.(22-24)gaT>gaC	p.D8D	ZNF93_ENST00000591366.1_Silent_p.D8D|AC007204.2_ENST00000592245.1_lincRNA|ZNF93_ENST00000592160.1_Silent_p.D8D	NM_031218.3	NP_112495.2	P35789	ZNF93_HUMAN	zinc finger protein 93	8	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(2)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	24						AATTTAGAGATGTGGCCATAG	0.418																																					p.D8D		Atlas-SNP	.											.	ZNF93	81	.	0			c.T24C						.						107	116	113					19																	20026109		2203	4300	6503	SO:0001819	synonymous_variant	81931	exon2			TAGAGATGTGGCC	M61873	CCDS32973.1	19p12	2014-02-12	2006-05-12		ENSG00000184635	ENSG00000184635		"Zinc fingers, C2H2-type", "-"	13169	protein-coding gene	gene with protein product		603975	"zinc finger protein 505", "zinc finger protein 93 (HTF34)"	ZNF505		8467795, 2023909	Standard	NM_031218		Approved	HPF34, TF34, FLJ12488	uc002non.3	P35789	OTTHUMG00000182371	ENST00000343769.5:c.24T>C	chr19.hg19:g.20026109T>C		35.0	0.0		40.0	22.0	NM_031218	A6NMY2|B9EGT2|Q8N8Q4|Q9H9X5|Q9Y2N8	Silent	SNP	ENST00000343769.5	hg19	CCDS32973.1																																																																																			.	.		0.418	ZNF93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460808.2	NM_031218		C	20026109	T	C	20026109	2	2	344	1	0	0	0	0	0	0	0	1	18217	1461	51	2		2	ZNF93	19	20026109	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	276866	20026109	39102874	1250	48613										
ZNF430	80264	hgsc.bcm.edu	37	chr19	21239855	21239855	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtctttaactggttctcaacCcttactagacacagaagaat	6	10	2	3	rs148853343		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:21239855C>T	ENST00000261560.5	+	5	922	c.741C>T	c.(739-741)acC>acT	p.T247T	AC012627.1_ENST00000578233.1_RNA	NM_001172671.1|NM_025189.3	NP_001166142.1|NP_079465.3	Q9H8G1	ZN430_HUMAN	zinc finger protein 430	247					regulation of transcription, DNA-templated (GO:0006355)|substantia nigra development (GO:0021762)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T247T(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	23						GGTTCTCAACCCTTACTAGAC	0.358																																					p.T247T		Atlas-SNP	.											ZNF430,abdomen,malignant_melanoma,0,1	ZNF430	59	.	1	Substitution - coding silent(1)	skin(1)	c.C741T						.						53	59	57					19																	21239855		2203	4300	6503	SO:0001819	synonymous_variant	80264	exon5			CTCAACCCTTACT	AK023721	CCDS32978.1	19p12	2013-01-08				ENSG00000118620		"Zinc fingers, C2H2-type", "-"	20808	protein-coding gene	gene with protein product							Standard	NM_025189		Approved	FLJ13659	uc002npj.3	Q9H8G1		ENST00000261560.5:c.741C>T	chr19.hg19:g.21239855C>T		221.0	0.0		182.0	81.0	NM_025189	Q86V70	Silent	SNP	ENST00000261560.5	hg19	CCDS32978.1																																																																																			.	.		0.358	ZNF430-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463539.1	NM_025189		T	21239855	C	T	21239855	2	4	344	1	0	0	0	0	0	0	0	1	17919	610	22	3		3	ZNF430	19	21239855	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1213746	21239855	37889128	1251	48614										
ZNF431	170959	hgsc.bcm.edu	37	chr19	21365902	21365902	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccttcaaatgtgaagaatgtGgcaaagcttttaagcagtcc	9	8	1	2	rs571315156		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:21365902G>T	ENST00000311048.7	+	5	940	c.796G>T	c.(796-798)Ggc>Tgc	p.G266C	ZNF431_ENST00000600692.1_3'UTR|ZNF431_ENST00000594425.1_Intron	NM_133473.2	NP_597730.2	Q8TF32	ZN431_HUMAN	zinc finger protein 431	266					cell differentiation (GO:0030154)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23						TGAAGAATGTGGCAAAGCTTT	0.398																																					p.G266C		Atlas-SNP	.											.	ZNF431	71	.	0			c.G796T						.						45	49	47					19																	21365902		2201	4296	6497	SO:0001583	missense	170959	exon5			GAATGTGGCAAAG	AB075849	CCDS32979.1	19p12	2013-01-08				ENSG00000196705		"Zinc fingers, C2H2-type", "-"	20809	protein-coding gene	gene with protein product						11853319	Standard	NM_133473		Approved	KIAA1969	uc002npp.2	Q8TF32		ENST00000311048.7:c.796G>T	chr19.hg19:g.21365902G>T	ENSP00000308578:p.Gly266Cys	67.0	0.0		78.0	39.0	NM_133473	A8KAK7|Q8IWC4	Missense_Mutation	SNP	ENST00000311048.7	hg19	CCDS32979.1	.	.	.	.	.	.	.	.	.	.	.	16.09	3.025085	0.54683	.	.	ENSG00000196705	ENST00000311048	T	0.07800	3.16	1.0	1.0	0.19881	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.34048	0.0884	H	0.94183	3.505	0.37630	D	0.921655	D	0.76494	0.999	D	0.76575	0.988	T	0.44112	-0.9349	9	0.87932	D	0	.	8.8725	0.35325	0.0:0.0:1.0:0.0	.	266	Q8TF32	ZN431_HUMAN	C	266	ENSP00000308578:G266C	ENSP00000308578:G266C	G	+	1	0	ZNF431	21157742	1.000000	0.71417	0.912000	0.35992	0.907000	0.53573	2.316000	0.43761	0.446000	0.26666	0.449000	0.29647	GGC	.	.		0.398	ZNF431-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463943.1	XM_086098		T	21365902	G	T	21365902	3	4	344	1	0	0	0	0	1	0	0	0	17920	1348	47	3	814	3	ZNF431	19	21365902	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	126047	21365902	37763081	1252	48615										
ZNF429	353088	hgsc.bcm.edu	37	chr19	21719234	21719234	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	taggtgattgtaagctatacAaaggaggttataatggactt	11	3	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:21719234A>G	ENST00000358491.4	+	4	587	c.379A>G	c.(379-381)Aaa>Gaa	p.K127E	ZNF429_ENST00000594022.1_3'UTR|ZNF429_ENST00000597078.1_Intron	NM_001001415.2	NP_001001415.2	Q86V71	ZN429_HUMAN	zinc finger protein 429	127					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(13)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	34						TAAGCTATACAAAGGAGGTTA	0.328																																					p.K127E		Atlas-SNP	.											.	ZNF429	338	.	0			c.A379G						.						70	75	73					19																	21719234		2147	4264	6411	SO:0001583	missense	353088	exon4			CTATACAAAGGAG	AY269786	CCDS42537.1	19p12	2014-02-14			ENSG00000197013	ENSG00000197013		"Zinc fingers, C2H2-type", "-"	20817	protein-coding gene	gene with protein product							Standard	NM_001001415		Approved		uc002nqd.1	Q86V71	OTTHUMG00000182848	ENST00000358491.4:c.379A>G	chr19.hg19:g.21719234A>G	ENSP00000351280:p.Lys127Glu	138.0	0.0		113.0	45.0	NM_001001415	A6NLV7|Q9BZE6	Missense_Mutation	SNP	ENST00000358491.4	hg19	CCDS42537.1	.	.	.	.	.	.	.	.	.	.	.	9.783	1.175721	0.21704	.	.	ENSG00000197013	ENST00000358491	T	0.06608	3.28	1.17	-0.026	0.13932	.	.	.	.	.	T	0.07863	0.0197	M	0.79805	2.47	0.09310	N	1	B	0.25719	0.132	B	0.20184	0.028	T	0.35500	-0.9786	9	0.32370	T	0.25	.	2.1397	0.03772	0.4071:0.3336:0.2593:0.0	.	127	Q86V71	ZN429_HUMAN	E	127	ENSP00000351280:K127E	ENSP00000351280:K127E	K	+	1	0	ZNF429	21511074	0.000000	0.05858	0.012000	0.15200	0.039000	0.13416	-0.314000	0.08092	0.486000	0.27676	0.248000	0.18094	AAA	.	.		0.328	ZNF429-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463981.1	NM_001001415		G	21719234	A	G	21719234	3	3	344	1	0	0	0	0	1	0	0	0	17917	131	5	2	393	2	ZNF429	19	21719234	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	353332	21719234	37409749	1253	48616										
ZNF681	148213	hgsc.bcm.edu	37	chr19	23926975	23926975	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtaaggtttgagaactggttAaaggctttcccacattcttc	9	8	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:23926975A>G	ENST00000402377.3	-	4	1518	c.1377T>C	c.(1375-1377)ttT>ttC	p.F459F	ZNF681_ENST00000395385.3_Silent_p.F390F	NM_138286.2	NP_612143.2	Q96N22	ZN681_HUMAN	zinc finger protein 681	459					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(3)	21		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				AGAACTGGTTAAAGGCTTTCC	0.368																																					p.F459F		Atlas-SNP	.											.	ZNF681	76	.	0			c.T1377C						.						51	53	53					19																	23926975		2203	4299	6502	SO:0001819	synonymous_variant	148213	exon4			CTGGTTAAAGGCT	AK056088	CCDS12414.2	19p12	2013-01-08			ENSG00000196172	ENSG00000196172		"Zinc fingers, C2H2-type", "-"	26457	protein-coding gene	gene with protein product	"hypothetical protein FLJ31526"						Standard	NM_138286		Approved	FLJ31526	uc002nrk.4	Q96N22	OTTHUMG00000150831	ENST00000402377.3:c.1377T>C	chr19.hg19:g.23926975A>G		38.0	0.0		21.0	8.0	NM_138286	B3KVF7	Silent	SNP	ENST00000402377.3	hg19	CCDS12414.2																																																																																			.	.		0.368	ZNF681-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320248.2	NM_138286		G	23926975	A	G	23926975	2	3	344	1	0	0	0	0	0	0	0	1	18103	359	13	2		2	ZNF681	19	23926975	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2207741	23926975	35202008	1254	48617										
ZNF536	9745	hgsc.bcm.edu	37	chr19	30935770	30935770	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctccaggtacctctcctgccTgcagagtggcttcatgaccc	9	16	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:30935770T>G	ENST00000355537.3	+	2	1448	c.1301T>G	c.(1300-1302)cTg>cGg	p.L434R		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	434					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					CTCTCCTGCCTGCAGAGTGGC	0.652																																					p.L434R		Atlas-SNP	.											.	ZNF536	424	.	0			c.T1301G						.						30	32	31					19																	30935770		2202	4294	6496	SO:0001583	missense	9745	exon2			CCTGCCTGCAGAG		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"Zinc fingers, C2H2-type"	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.1301T>G	chr19.hg19:g.30935770T>G	ENSP00000347730:p.Leu434Arg	69.0	0.0		62.0	21.0	NM_014717	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	hg19	CCDS32984.1	.	.	.	.	.	.	.	.	.	.	T	13.43	2.235969	0.39498	.	.	ENSG00000198597	ENST00000355537	T	0.10382	2.88	5.44	5.44	0.79542	.	0.000000	0.64402	D	0.000001	T	0.21103	0.0508	L	0.32530	0.975	0.54753	D	0.999982	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.994	T	0.06716	-1.0811	10	0.16896	T	0.51	-19.0498	15.4838	0.75548	0.0:0.0:0.0:1.0	.	434;434	A7E228;O15090	.;ZN536_HUMAN	R	434	ENSP00000347730:L434R	ENSP00000347730:L434R	L	+	2	0	ZNF536	35627610	1.000000	0.71417	1.000000	0.80357	0.828000	0.46876	7.667000	0.83888	2.049000	0.60858	0.482000	0.46254	CTG	.	.		0.652	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		G	30935770	T	G	30935770	3	3	344	1	0	0	0	0	1	0	0	0	17989	1580	55	5	1303	5	ZNF536	19	30935770	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	7008795	30935770	28193213	1255	48618										
ZNF507	22847	hgsc.bcm.edu	37	chr19	32843894	32843894	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgttatccagaagttaagcaAgatagtggaaaatgaaaagt	10	3	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:32843894A>G	ENST00000311921.4	+	2	350	c.158A>G	c.(157-159)aAg>aGg	p.K53R	ZNF507_ENST00000544431.1_Missense_Mutation_p.K53R|ZNF507_ENST00000355898.5_Missense_Mutation_p.K53R	NM_001136156.1|NM_014910.4	NP_001129628.1|NP_055725.2	Q8TCN5	ZN507_HUMAN	zinc finger protein 507	53					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	31	Esophageal squamous(110;0.162)					AAGTTAAGCAAGATAGTGGAA	0.363																																					p.K53R		Atlas-SNP	.											.	ZNF507	92	.	0			c.A158G						.						68	67	67					19																	32843894		2203	4300	6503	SO:0001583	missense	22847	exon3			TAAGCAAGATAGT	AB029007	CCDS32985.1	19q13.12	2008-02-05				ENSG00000168813		"Zinc fingers, C2H2-type"	23783	protein-coding gene	gene with protein product							Standard	NM_014910		Approved	KIAA1084	uc002ntd.3	Q8TCN5		ENST00000311921.4:c.158A>G	chr19.hg19:g.32843894A>G	ENSP00000312277:p.Lys53Arg	74.0	0.0		78.0	36.0	NM_001136156	A8K911|Q2TBF1|Q6MZU0|Q9UPR8	Missense_Mutation	SNP	ENST00000311921.4	hg19	CCDS32985.1	.	.	.	.	.	.	.	.	.	.	A	16.17	3.046418	0.55110	.	.	ENSG00000168813	ENST00000355898;ENST00000311921;ENST00000544431	T;T;T	0.10668	3.14;3.14;2.85	5.5	4.49	0.54785	.	0.000000	0.85682	D	0.000000	T	0.22399	0.0540	M	0.63843	1.955	0.33723	D	0.617236	D;D	0.89917	0.999;1.0	D;D	0.74023	0.941;0.982	T	0.28681	-1.0036	10	0.11794	T	0.64	.	7.462	0.27300	0.7848:0.1429:0.0723:0.0	.	53;53	Q8TCN5;Q8TCN5-2	ZN507_HUMAN;.	R	53	ENSP00000348162:K53R;ENSP00000312277:K53R;ENSP00000441549:K53R	ENSP00000312277:K53R	K	+	2	0	ZNF507	37535734	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.472000	0.73567	1.027000	0.39758	0.402000	0.26972	AAG	.	.		0.363	ZNF507-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450301.3	NM_014910		G	32843894	A	G	32843894	3	3	344	1	0	0	0	0	1	0	0	0	17968	72	3	2	160	2	ZNF507	19	32843894	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1908124	32843894	26285089	1256	48619										
RGS9BP	388531	hgsc.bcm.edu	37	chr19	33167237	33167237	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gactgcgtgctaccaccaccTggtgctgaccgtcggtggct	13	14	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:33167237T>A	ENST00000334176.3	+	1	925	c.68T>A	c.(67-69)cTg>cAg	p.L23Q	ANKRD27_ENST00000587352.1_5'Flank|ANKRD27_ENST00000306065.4_5'Flank	NM_207391.2	NP_997274.2	Q6ZS82	R9BP_HUMAN	regulator of G protein signaling 9 binding protein	23					detection of light stimulus involved in visual perception (GO:0050908)|negative regulation of signal transduction (GO:0009968)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)	integral component of membrane (GO:0016021)				central_nervous_system(1)|lung(2)	3	Esophageal squamous(110;0.137)					TACCACCACCTGGTGCTGACC	0.711																																					p.L23Q		Atlas-SNP	.											.	RGS9BP	9	.	0			c.T68A						.						34	27	29					19																	33167237		2145	4235	6380	SO:0001583	missense	388531	exon1			ACCACCTGGTGCT	AW302149	CCDS12424.1	19q13.11	2008-02-05	2007-08-14			ENSG00000186326			30304	protein-coding gene	gene with protein product		607814	"regulator of G protein signalling 9 binding protein"			12119397, 8889548	Standard	NM_207391		Approved	FLJ45744, PERRS, R9AP, RGS9	uc002ntp.1	Q6ZS82		ENST00000334176.3:c.68T>A	chr19.hg19:g.33167237T>A	ENSP00000334134:p.Leu23Gln	34.0	0.0		50.0	22.0	NM_207391	Q6ZVJ6	Missense_Mutation	SNP	ENST00000334176.3	hg19	CCDS12424.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.250804	0.80135	.	.	ENSG00000186326	ENST00000334176	T	0.31769	1.48	4.63	3.59	0.41128	.	0.181976	0.37530	U	0.002054	T	0.32376	0.0827	M	0.76328	2.33	0.53688	D	0.99997	P	0.40211	0.707	B	0.36244	0.22	T	0.20042	-1.0287	10	0.87932	D	0	-23.8121	10.5762	0.45229	0.1445:0.0:0.0:0.8555	.	23	Q6ZS82	R9BP_HUMAN	Q	23	ENSP00000334134:L23Q	ENSP00000334134:L23Q	L	+	2	0	RGS9BP	37859077	1.000000	0.71417	0.997000	0.53966	0.755000	0.42902	6.034000	0.70933	0.773000	0.33404	0.254000	0.18369	CTG	.	.		0.711	RGS9BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450337.1	NM_207391		A	33167237	T	A	33167237	3	1	344	1	0	0	0	0	1	0	0	0	13329	1580	55	4	70	4	RGS9BP	19	33167237	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	323343	33167237	25961746	1257	48620										
MLL4	9757	hgsc.bcm.edu	37	chr19	36221017	36221017	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cagaaacacactgatctcctGgatggcaaggtgggccagaa	12	10	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:36221017G>C	ENST00000222270.7	+	23	5067	c.5067G>C	c.(5065-5067)ctG>ctC	p.L1689L	KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000420124.1_Silent_p.L1689L	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	1689					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										CTGATCTCCTGGATGGCAAGG	0.587																																					p.L1689L		Atlas-SNP	.											.	MLL4	229	.	0			c.G5067C						.						54	59	57					19																	36221017		2066	4210	6276	SO:0001819	synonymous_variant	8085	exon23			TCTCCTGGATGGC	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"Chromatin-modifying enzymes / K-methyltransferases"	15840	protein-coding gene	gene with protein product	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.5067G>C	chr19.hg19:g.36221017G>C		157.0	0.0		113.0	55.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Silent	SNP	ENST00000222270.7	hg19	CCDS46055.1																																																																																			.	.		0.587	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727		C	36221017	G	C	36221017	2	2	344	1	0	0	0	0	0	0	0	1	9632	1335	47	4		4	MLL4	19	36221017	Silent	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	3053780	36221017	22907966	1258	48621										
ARHGAP33	115703	hgsc.bcm.edu	37	chr19	36276186	36276186	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gggccccagtgtccctcgaaAgaagcccctgccctggctgg	13	16	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:36276186A>T	ENST00000007510.4	+	18	1961	c.1817A>T	c.(1816-1818)aAg>aTg	p.K606M	ARHGAP33_ENST00000378944.5_Missense_Mutation_p.K470M|ARHGAP33_ENST00000314737.5_Missense_Mutation_p.K606M			O14559	RHG33_HUMAN	Rho GTPase activating protein 33	606					protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|Rac GTPase activator activity (GO:0030675)			endometrium(7)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	37						GTCCCTCGAAAGAAGCCCCTG	0.687																																					p.K606M		Atlas-SNP	.											.	ARHGAP33	102	.	0			c.A1817T						.						28	36	33					19																	36276186		2200	4293	6493	SO:0001583	missense	115703	exon18			CTCGAAAGAAGCC	AY044864	CCDS12477.1, CCDS54254.1	19q13.13	2011-06-29	2010-02-19	2010-02-19		ENSG00000004777		"Rho GTPase activating proteins"	23085	protein-coding gene	gene with protein product		614902	"sorting nexin 26"	SNX26		12297274, 12461558	Standard	NM_052948		Approved	FLJ39019, TCGAP	uc002obs.2	O14559		ENST00000007510.4:c.1817A>T	chr19.hg19:g.36276186A>T	ENSP00000007510:p.Lys606Met	98.0	0.0		92.0	43.0	NM_052948	O14552|O14560|Q6ZSP6|Q96CP3|Q9NT23	Missense_Mutation	SNP	ENST00000007510.4	hg19		.	.	.	.	.	.	.	.	.	.	A	13.28	2.188802	0.38609	.	.	ENSG00000004777	ENST00000007510;ENST00000314737;ENST00000378944	T;T;T	0.13420	2.88;2.59;2.92	4.34	3.29	0.37713	.	0.409870	0.22740	N	0.056209	T	0.12220	0.0297	L	0.29908	0.895	0.34292	D	0.683363	B;P;B	0.36599	0.038;0.56;0.022	B;B;B	0.40825	0.053;0.341;0.046	T	0.17961	-1.0352	10	0.59425	D	0.04	.	9.1418	0.36908	0.8362:0.0:0.0:0.1638	.	606;470;606	O14559;O14559-10;O14559-11	RHG33_HUMAN;.;.	M	606;606;470	ENSP00000007510:K606M;ENSP00000320038:K606M;ENSP00000368227:K470M	ENSP00000007510:K606M	K	+	2	0	ARHGAP33	40968026	0.892000	0.30473	0.996000	0.52242	0.997000	0.91878	0.912000	0.28597	0.679000	0.31345	0.379000	0.24179	AAG	.	.		0.687	ARHGAP33-201	KNOWN	basic	protein_coding	protein_coding		NM_052948		T	36276186	A	T	36276186	3	4	344	1	0	0	0	0	1	0	0	0	882	72	3	4	1887	4	ARHGAP33	19	36276186	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	55169	36276186	22852797	1259	48622										
ZNF585A	199704	hgsc.bcm.edu	37	chr19	37644045	37644045	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atcttgagtgtggacttttgTgtgaatgctttgccacagtc	11	7	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:37644045T>G	ENST00000356958.4	-	5	1014	c.756A>C	c.(754-756)acA>acC	p.T252T	ZNF585A_ENST00000292841.5_Silent_p.T197T|ZNF585A_ENST00000355533.2_Silent_p.T197T|ZNF585A_ENST00000392157.2_Silent_p.T197T|ZNF585A_ENST00000588723.1_Intron			Q6P3V2	Z585A_HUMAN	zinc finger protein 585A	252					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(4)|central_nervous_system(1)|endometrium(2)|large_intestine(17)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TGGACTTTTGTGTGAATGCTT	0.433																																					p.T197T		Atlas-SNP	.											.	ZNF585A	117	.	0			c.A591C						.						155	154	154					19																	37644045		2203	4300	6503	SO:0001819	synonymous_variant	199704	exon6			CTTTTGTGTGAAT	AK074345	CCDS12499.1, CCDS74353.1	19q13.13	2013-01-08				ENSG00000196967		"Zinc fingers, C2H2-type", "-"	26305	protein-coding gene	gene with protein product						12477932	Standard	NM_199126		Approved	FLJ23765	uc002ofn.1	Q6P3V2		ENST00000356958.4:c.756A>C	chr19.hg19:g.37644045T>G		71.0	0.0		72.0	37.0	NM_199126	Q8TE95|Q96MV3	Silent	SNP	ENST00000356958.4	hg19																																																																																				.	.		0.433	ZNF585A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000457980.2	NM_152655		G	37644045	T	G	37644045	2	3	344	1	0	0	0	0	0	0	0	1	18032	1683	59	5		5	ZNF585A	19	37644045	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1367859	37644045	21484938	1260	48623										
RYR1	6261	hgsc.bcm.edu	37	chr19	39076640	39076640	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agcaagtgaaggaggatatgGaggtaggtcatgtctggggg	19	3	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:39076640G>T	ENST00000359596.3	+	103	14866	c.14866G>T	c.(14866-14868)Gag>Tag	p.E4956*	RYR1_ENST00000355481.4_Nonsense_Mutation_p.E4951*|RYR1_ENST00000360985.3_Nonsense_Mutation_p.E4951*			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	4956					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GGAGGATATGGAGGTAGGTCA	0.562																																					p.E4956X		Atlas-SNP	.											.	RYR1	708	.	0			c.G14866T						.						98	91	93					19																	39076640		2203	4300	6503	SO:0001587	stop_gained	6261	exon103			GATATGGAGGTAG	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.14866G>T	chr19.hg19:g.39076640G>T	ENSP00000352608:p.Glu4956*	69.0	0.0		56.0	25.0	NM_000540	Q16314|Q16368|Q9NPK1|Q9P1U4	Nonsense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	G	55	24.841755	0.99962	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	.	.	.	4.67	4.67	0.58626	.	0.000000	0.64402	U	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	17.4182	0.87506	0.0:0.0:1.0:0.0	.	.	.	.	X	4956;4951;4951	.	ENSP00000347667:E4951X	E	+	1	0	RYR1	43768480	1.000000	0.71417	1.000000	0.80357	0.718000	0.41266	9.647000	0.98478	2.423000	0.82170	0.650000	0.86243	GAG	.	.		0.562	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			T	39076640	G	T	39076640	4	4	344	1	0	0	0	0	0	1	0	0	13783	1175	41	3	15276	3	RYR1	19	39076640	Nonsense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1432595	39076640	20052343	1261	48624										
FBXO27	126433	hgsc.bcm.edu	37	chr19	39517611	39517611	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tagaagttggacgaggagtcTgtacatacagccgctgtcgt	13	8	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:39517611T>A	ENST00000292853.4	-	5	726	c.607A>T	c.(607-609)Aga>Tga	p.R203*	FBXO27_ENST00000509137.2_Nonsense_Mutation_p.R203*|FBXO27_ENST00000600828.1_Nonsense_Mutation_p.R202*	NM_178820.3	NP_849142.1	Q8NI29	FBX27_HUMAN	F-box protein 27	203	FBA. {ECO:0000255|PROSITE- ProRule:PRU00482}.					SCF ubiquitin ligase complex (GO:0019005)	glycoprotein binding (GO:0001948)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|ovary(1)|urinary_tract(2)	17	all_cancers(60;3.79e-07)|all_lung(34;1.26e-07)|Lung NSC(34;1.46e-07)|all_epithelial(25;4.69e-07)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			ACGAGGAGTCTGTACATACAG	0.557																																					p.R203X		Atlas-SNP	.											.	FBXO27	26	.	0			c.A607T						.						155	146	149					19																	39517611		2203	4300	6503	SO:0001587	stop_gained	126433	exon5			GGAGTCTGTACAT	AF436061	CCDS12527.1	19q13.2	2008-02-05	2004-06-15			ENSG00000161243		"F-boxes /  "other""	18753	protein-coding gene	gene with protein product		609099	"F-box only protein 27"			126433	Standard	NM_178820		Approved	Fbg5, Fbx27	uc002okh.3	Q8NI29		ENST00000292853.4:c.607A>T	chr19.hg19:g.39517611T>A	ENSP00000292853:p.Arg203*	88.0	0.0		85.0	26.0	NM_178820	Q96C87	Nonsense_Mutation	SNP	ENST00000292853.4	hg19	CCDS12527.1	.	.	.	.	.	.	.	.	.	.	T	16.96	3.265772	0.59540	.	.	ENSG00000161243	ENST00000292853;ENST00000509137	.	.	.	3.97	-0.938	0.10412	.	1.130880	0.06812	N	0.790508	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11182	T	0.66	-2.8285	1.1537	0.01791	0.2076:0.1699:0.4398:0.1827	.	.	.	.	X	203	.	ENSP00000292853:R203X	R	-	1	2	FBXO27	44209451	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.189000	0.09629	-0.126000	0.11682	-1.525000	0.00928	AGA	.	.		0.557	FBXO27-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463281.1			A	39517611	T	A	39517611	4	1	344	1	0	0	0	0	0	1	0	0	5745	1588	55	4	252	4	FBXO27	19	39517611	Nonsense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	440971	39517611	19611372	1262	48625										
TTC9B	148014	hgsc.bcm.edu	37	chr19	40724111	40724111	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cacggcggcacgcaggctgcTgtcgagcgccgcgcccaggc	16	17	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:40724111T>A	ENST00000311308.6	-	1	195	c.178A>T	c.(178-180)Agc>Tgc	p.S60C		NM_152479.5	NP_689692.2	Q8N6N2	TTC9B_HUMAN	tetratricopeptide repeat domain 9B	60					chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)	FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)	5						CGCAGGCTGCTGTCGAGCGCC	0.721																																					p.S60C		Atlas-SNP	.											.	TTC9B	8	.	0			c.A178T						.						21	18	19					19																	40724111		2201	4295	6496	SO:0001583	missense	148014	exon1			GGCTGCTGTCGAG	BC029539	CCDS12550.1	19q13.2	2013-01-11				ENSG00000174521		"Tetratricopeptide (TTC) repeat domain containing"	26395	protein-coding gene	gene with protein product							Standard	NM_152479		Approved	FLJ30373	uc002onc.3	Q8N6N2		ENST00000311308.6:c.178A>T	chr19.hg19:g.40724111T>A	ENSP00000311760:p.Ser60Cys	22.0	0.0		30.0	17.0	NM_152479	A8K0I5|Q96NP9	Missense_Mutation	SNP	ENST00000311308.6	hg19	CCDS12550.1	.	.	.	.	.	.	.	.	.	.	T	16.77	3.213691	0.58452	.	.	ENSG00000174521	ENST00000311308	T	0.19250	2.16	4.46	3.41	0.39046	.	0.560619	0.18353	N	0.143823	T	0.16599	0.0399	L	0.47190	1.495	0.28992	N	0.888	B	0.06786	0.001	B	0.04013	0.001	T	0.19679	-1.0298	10	0.72032	D	0.01	-13.6359	3.7149	0.08434	0.192:0.1037:0.0:0.7043	.	60	Q8N6N2	TTC9B_HUMAN	C	60	ENSP00000311760:S60C	ENSP00000311760:S60C	S	-	1	0	TTC9B	45415951	1.000000	0.71417	1.000000	0.80357	0.829000	0.46940	1.196000	0.32198	0.552000	0.29026	0.241000	0.17934	AGC	.	.		0.721	TTC9B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462604.1	NM_152479		A	40724111	T	A	40724111	3	1	344	1	0	0	0	0	1	0	0	0	16731	1580	55	4	553	4	TTC9B	19	40724111	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1206500	40724111	18404872	1263	48626										
PRX	57716	hgsc.bcm.edu	37	chr19	40903671	40903671	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgagcctcttcggccacttcTcgtacacgcagccgaggcag	11	15	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:40903671T>A	ENST00000324001.7	-	7	858	c.588A>T	c.(586-588)cgA>cgT	p.R196R	PRX_ENST00000291825.7_3'UTR	NM_181882.2	NP_870998.2	Q9BXM0	PRAX_HUMAN	periaxin	196	Arg/Lys-rich (basic).				axon ensheathment (GO:0008366)|cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|ovary(2)|prostate(3)|skin(1)|urinary_tract(9)	47			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)			CGGCCACTTCTCGTACACGCA	0.711																																					p.R196R		Atlas-SNP	.											.	PRX	151	.	0			c.A588T						.						4	5	5					19																	40903671		2009	3972	5981	SO:0001819	synonymous_variant	57716	exon7			CACTTCTCGTACA	AB046840	CCDS12556.1, CCDS33028.1	19q13.2	2014-09-17				ENSG00000105227			13797	protein-coding gene	gene with protein product		605725				10839370, 9143514	Standard	NM_181882		Approved	KIAA1620	uc002onr.3	Q9BXM0		ENST00000324001.7:c.588A>T	chr19.hg19:g.40903671T>A		23.0	0.0		19.0	10.0	NM_181882	Q9BXL9|Q9HCF2	Silent	SNP	ENST00000324001.7	hg19	CCDS33028.1																																																																																			.	.		0.711	PRX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000462582.1	NM_020956		A	40903671	T	A	40903671	2	1	344	1	0	0	0	0	0	0	0	1	12654	1538	54	4		4	PRX	19	40903671	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	179560	40903671	18225312	1264	48627										
CEACAM6	4680	hgsc.bcm.edu	37	chr19	42265920	42265920	+	Nonsense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tccccctcaaaggccaattaCcgtccaggggaaaatctgaa	8	13	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:42265920C>G	ENST00000199764.6	+	4	965	c.747C>G	c.(745-747)taC>taG	p.Y249*	AC011513.4_ENST00000601409.1_RNA	NM_002483.4	NP_002474.3	P40199	CEAM6_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 6 (non-specific cross reacting antigen)	249	Ig-like C2-type 2.				cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|kidney(4)|large_intestine(1)|lung(4)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	18				OV - Ovarian serous cystadenocarcinoma(3;0.00575)|all cancers(3;0.0352)|Epithelial(262;0.0797)		AGGCCAATTACCGTCCAGGGG	0.517																																					p.Y249X		Atlas-SNP	.											.	CEACAM6	52	.	0			c.C747G						.						92	91	91					19																	42265920		2203	4300	6503	SO:0001587	stop_gained	4680	exon4			CAATTACCGTCCA	M29541	CCDS12585.1	19q13.1-q13.2	2013-01-29			ENSG00000086548	ENSG00000086548		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1818	protein-coding gene	gene with protein product		163980		NCA			Standard	NM_002483		Approved	CD66c	uc002orm.2	P40199	OTTHUMG00000151064	ENST00000199764.6:c.747C>G	chr19.hg19:g.42265920C>G	ENSP00000199764:p.Tyr249*	130.0	0.0		110.0	44.0	NM_002483	Q13774|Q14920|Q53XP7	Nonsense_Mutation	SNP	ENST00000199764.6	hg19	CCDS12585.1	.	.	.	.	.	.	.	.	.	.	C	34	5.392338	0.95988	.	.	ENSG00000086548	ENST00000199764	.	.	.	1.87	0.662	0.17880	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.17832	T	0.49	.	5.8308	0.18579	0.0:0.6345:0.3655:0.0	.	.	.	.	X	249	.	ENSP00000199764:Y249X	Y	+	3	2	CEACAM6	46957760	0.000000	0.05858	0.046000	0.18839	0.794000	0.44872	-0.311000	0.08124	0.076000	0.16826	0.305000	0.20034	TAC	.	.		0.517	CEACAM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321147.1			G	42265920	C	G	42265920	4	3	344	1	0	0	0	0	0	1	0	0	3198	518	18	4	761	4	CEACAM6	19	42265920	Nonsense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1362249	42265920	16863063	1265	48628										
LYPD4	147719	hgsc.bcm.edu	37	chr19	42342129	42342129	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cacacaggtcgggcagctacAggacgcagatgtgatagact	13	10	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:42342129A>C	ENST00000330743.3	-	4	1629	c.418T>G	c.(418-420)Tgt>Ggt	p.C140G	LYPD4_ENST00000343055.4_Missense_Mutation_p.C105G|AC020956.3_ENST00000593354.1_lincRNA|LYPD4_ENST00000601246.1_Missense_Mutation_p.C105G	NM_173506.4	NP_775777.3	Q6UWN0	LYPD4_HUMAN	LY6/PLAUR domain containing 4	140						anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(2)	12						GGGCAGCTACAGGACGCAGAT	0.512																																					p.C140G		Atlas-SNP	.											.	LYPD4	30	.	0			c.T418G						.						123	106	111					19																	42342129		2203	4300	6503	SO:0001583	missense	147719	exon4			AGCTACAGGACGC	AY358726	CCDS12587.1	19q13.2	2008-02-05				ENSG00000273111			28659	protein-coding gene	gene with protein product						12975309	Standard	XM_005278383		Approved	MGC42718	uc002orp.1	Q6UWN0		ENST00000330743.3:c.418T>G	chr19.hg19:g.42342129A>C	ENSP00000328737:p.Cys140Gly	117.0	0.0		97.0	45.0	NM_173506	Q8IYW0	Missense_Mutation	SNP	ENST00000330743.3	hg19	CCDS12587.1	.	.	.	.	.	.	.	.	.	.	N	4.636	0.118245	0.08881	.	.	ENSG00000183103	ENST00000330743;ENST00000343055	T;T	0.68903	-0.36;-0.36	4.13	0.51	0.16983	.	1.693900	0.02980	N	0.145524	T	0.45175	0.1329	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.23726	-1.0180	10	0.25106	T	0.35	0.6212	5.5958	0.17327	0.0988:0.0:0.3812:0.52	.	105;140	Q6UWN0-2;Q6UWN0	.;LYPD4_HUMAN	G	140;105	ENSP00000328737:C140G;ENSP00000339568:C105G	ENSP00000328737:C140G	C	-	1	0	LYPD4	47033969	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	0.215000	0.17562	-0.013000	0.14199	-0.370000	0.07254	TGT	.	.		0.512	LYPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463039.1	NM_173506		C	42342129	A	C	42342129	3	2	344	1	0	0	0	0	1	0	0	0	9121	188	7	5	330	5	LYPD4	19	42342129	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	76209	42342129	16786854	1266	48629										
POU2F2	5452	hgsc.bcm.edu	37	chr19	42621499	42621499	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctgctggggctgaatcgccaCtggggtcttcagccttgatc	13	12	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:42621499C>A	ENST00000526816.2	-	5	221	c.206G>T	c.(205-207)aGt>aTt	p.S69I	POU2F2_ENST00000529952.1_Missense_Mutation_p.S69I|POU2F2_ENST00000342301.4_Missense_Mutation_p.S69I|POU2F2_ENST00000389341.5_Missense_Mutation_p.S69I|POU2F2_ENST00000529067.1_Missense_Mutation_p.S69I|POU2F2_ENST00000533720.1_Missense_Mutation_p.S69I|POU2F2_ENST00000560558.1_Intron|POU2F2_ENST00000524801.2_5'UTR|POU2F2_ENST00000560398.1_Missense_Mutation_p.S91I			P09086	PO2F2_HUMAN	POU class 2 homeobox 2	69					cell maturation (GO:0048469)|humoral immune response (GO:0006959)|immunoglobulin secretion involved in immune response (GO:0002380)|mature B cell differentiation (GO:0002335)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(5)|lung(4)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Prostate(69;0.059)			Dolutegravir(DB08930)	TGAATCGCCACTGGGGTCTTC	0.637																																					p.S69I		Atlas-SNP	.											.	POU2F2	106	.	0			c.G206T						.						44	46	45					19																	42621499		2203	4299	6502	SO:0001583	missense	5452	exon5			TCGCCACTGGGGT		CCDS33035.1, CCDS56094.1, CCDS56095.1, CCDS58665.1	19q13.2	2011-06-20	2007-07-13					"Homeoboxes / POU class"	9213	protein-coding gene	gene with protein product		164176	"POU domain class 2, transcription factor 2"	OTF2			Standard	NM_001207026		Approved	OCT2	uc002osp.3	P09086		ENST00000526816.2:c.206G>T	chr19.hg19:g.42621499C>A	ENSP00000431603:p.Ser69Ile	26.0	0.0		34.0	21.0	NM_002698	Q16648|Q7M4M8|Q9BRS4	Missense_Mutation	SNP	ENST00000526816.2	hg19	CCDS56095.1	.	.	.	.	.	.	.	.	.	.	C	15.59	2.878207	0.51801	.	.	ENSG00000028277	ENST00000389341;ENST00000342301;ENST00000292077;ENST00000533720;ENST00000526816;ENST00000529067;ENST00000529952;ENST00000531773	D;D;D;D;D	0.85013	-1.86;-1.75;-1.93;-1.64;-1.69	3.97	3.97	0.46021	.	4.182530	0.00633	U	0.000485	D	0.84320	0.5446	L	0.39898	1.24	0.32974	D	0.522724	P;P;P	0.46512	0.589;0.879;0.804	B;B;B	0.43680	0.122;0.427;0.256	T	0.76971	-0.2761	10	0.72032	D	0.01	.	11.3907	0.49813	0.0:0.8157:0.1843:0.0	.	69;69;69	P09086-4;P09086;P09086-3	.;PO2F2_HUMAN;.	I	69;69;69;69;68;69;69;57	ENSP00000373992:S69I;ENSP00000339369:S69I;ENSP00000437221:S69I;ENSP00000437224:S69I;ENSP00000436988:S69I	ENSP00000292077:S69I	S	-	2	0	POU2F2	47313339	0.998000	0.40836	0.995000	0.50966	0.706000	0.40770	1.762000	0.38451	2.216000	0.71823	0.305000	0.20034	AGT	.	.		0.637	POU2F2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387329.3			A	42621499	C	A	42621499	3	1	344	1	0	0	0	0	1	0	0	0	12281	565	20	3	1225	3	POU2F2	19	42621499	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	279370	42621499	16507484	1267	48630										
CIC	23152	hgsc.bcm.edu	37	chr19	42793207	42793207	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tacacagcctggacggcggaGaagtagacagtcaggcgcta	14	10	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:42793207G>C	ENST00000575354.2	+	7	1139	c.1099G>C	c.(1099-1101)Gaa>Caa	p.E367Q	CIC_ENST00000572681.2_Missense_Mutation_p.E1276Q|CIC_ENST00000160740.3_Missense_Mutation_p.E367Q	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	367					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				GGACGGCGGAGAAGTAGACAG	0.667			"Mis, F, S"		oligodendroglioma																																p.E367Q		Atlas-SNP	.		Rec	yes		19	19q13.2	23152	capicua homolog		O	.	CIC	249	.	0			c.G1099C						.						46	51	49					19																	42793207		2203	4297	6500	SO:0001583	missense	23152	exon7			GGCGGAGAAGTAG	AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"capicua (Drosophila) homolog", "capicua homolog (Drosophila)"			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.1099G>C	chr19.hg19:g.42793207G>C	ENSP00000458663:p.Glu367Gln	34.0	0.0		31.0	18.0	NM_015125	Q7LGI1|Q9UEG5|Q9Y6T1	Missense_Mutation	SNP	ENST00000575354.2	hg19	CCDS12601.1	.	.	.	.	.	.	.	.	.	.	G	10.93	1.489945	0.26686	.	.	ENSG00000079432	ENST00000160740	.	.	.	4.76	3.73	0.42828	.	.	.	.	.	T	0.53126	0.1777	L	0.27053	0.805	0.37514	D	0.917255	D	0.61697	0.99	P	0.57204	0.815	T	0.62343	-0.6874	8	0.87932	D	0	-10.5508	12.2832	0.54776	0.0:0.0:0.8292:0.1708	.	367	Q96RK0	CIC_HUMAN	Q	367	.	ENSP00000160740:E367Q	E	+	1	0	CIC	47485047	1.000000	0.71417	0.839000	0.33178	0.017000	0.09413	4.791000	0.62460	1.242000	0.43836	-0.234000	0.12200	GAA	.	.		0.667	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			C	42793207	G	C	42793207	3	2	344	1	0	0	0	0	1	0	0	0	3426	943	33	4	1125	4	CIC	19	42793207	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	171708	42793207	16335776	1268	48631										
CXCL17	284340	hgsc.bcm.edu	37	chr19	42937971	42937971	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccttcctggagccatctcctAgaagcctggcctcggtccct	9	17	1	1	rs545020215	byFrequency	TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:42937971A>G	ENST00000601181.1	-	2	332	c.117T>C	c.(115-117)tcT>tcC	p.S39S	LIPE-AS1_ENST00000594688.1_RNA|LIPE-AS1_ENST00000457234.2_RNA|LIPE-AS1_ENST00000594624.2_RNA|LIPE-AS1_ENST00000597203.1_RNA|LIPE-AS1_ENST00000593740.2_RNA	NM_198477.1	NP_940879.1	Q6UXB2	VCC1_HUMAN	chemokine (C-X-C motif) ligand 17	39					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|chemotaxis (GO:0006935)	extracellular region (GO:0005576)				large_intestine(2)|skin(1)	3		Prostate(69;0.00899)				GCCATCTCCTAGAAGCCTGGC	0.567											OREG0025504	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	7	0.00139776	0	0	5008	,	,		16897	0		0	False		,,,				2504	0.0072				p.S39S		Atlas-SNP	.											.	CXCL17	8	.	0			c.T117C						.						132	114	120					19																	42937971		2203	4300	6503	SO:0001819	synonymous_variant	284340	exon2			TCTCCTAGAAGCC		CCDS12608.1	19q13.2	2007-10-15				ENSG00000189377			19232	protein-coding gene	gene with protein product		611387				17201934	Standard	NM_198477		Approved	Dcip1, UNQ473, DMC, VCC1	uc002otu.3	Q6UXB2		ENST00000601181.1:c.117T>C	chr19.hg19:g.42937971A>G		46.0	0.0	912	31.0	18.0	NM_198477	A8KAC0	Silent	SNP	ENST00000601181.1	hg19	CCDS12608.1																																																																																			.	.		0.567	CXCL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463872.1			G	42937971	A	G	42937971	2	3	344	1	0	0	0	0	0	0	0	1	4086	407	15	2		2	CXCL17	19	42937971	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	144764	42937971	16191012	1269	48632										
PSG6	5675	hgsc.bcm.edu	37	chr19	43412004	43412004	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gatgtaaggcatgggcagctTcgctgtgtggataacagaag	15	6	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:43412004T>C	ENST00000292125.2	-	4	753	c.709A>G	c.(709-711)Aag>Gag	p.K237E	PSG6_ENST00000187910.2_Missense_Mutation_p.K237E|PSG6_ENST00000402603.4_Intron	NM_002782.4	NP_002773.1	Q00889	PSG6_HUMAN	pregnancy specific beta-1-glycoprotein 6	237					female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(19)|ovary(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	44		Prostate(69;0.00899)				ATGGGCAGCTTCGCTGTGTGG	0.493																																					p.K237E		Atlas-SNP	.											.	PSG6	89	.	0			c.A709G						.						224	216	218					19																	43412004		2201	4299	6500	SO:0001583	missense	5675	exon4			GCAGCTTCGCTGT		CCDS12613.1, CCDS33038.1	19q13.2	2013-01-29			ENSG00000170848	ENSG00000170848		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9523	protein-coding gene	gene with protein product		176395				1690992	Standard	NM_002782		Approved			Q00889	OTTHUMG00000151127	ENST00000292125.2:c.709A>G	chr19.hg19:g.43412004T>C	ENSP00000292125:p.Lys237Glu	39.0	0.0		40.0	24.0	NM_001031850	O75244|Q15224|Q15235|Q549K1	Missense_Mutation	SNP	ENST00000292125.2	hg19	CCDS12613.1	.	.	.	.	.	.	.	.	.	.	N	2.564	-0.301221	0.05495	.	.	ENSG00000170848	ENST00000187910;ENST00000292125	T;T	0.30714	1.52;1.54	1.42	-2.12	0.07165	.	.	.	.	.	T	0.07999	0.0200	N	0.00801	-1.175	0.09310	N	1	B;B	0.12013	0.002;0.005	B;B	0.17979	0.004;0.02	T	0.27054	-1.0085	9	0.40728	T	0.16	.	2.4016	0.04402	0.0:0.4139:0.328:0.2581	.	237;237	Q00889;Q00889-2	PSG6_HUMAN;.	E	237	ENSP00000187910:K237E;ENSP00000292125:K237E	ENSP00000187910:K237E	K	-	1	0	PSG6	48103844	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	-1.550000	0.02180	-0.042000	0.13535	0.113000	0.15668	AAG	.	.		0.493	PSG6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321436.1	NM_002782		C	43412004	T	C	43412004	3	2	344	1	0	0	0	0	1	0	0	0	12671	1792	62	2	649	2	PSG6	19	43412004	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	474033	43412004	15716979	1270	48633										
ZNF221	7638	hgsc.bcm.edu	37	chr19	44470227	44470227	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tttgatcttcatcaacaatcAcactcaggagagaaatctca	5	10	6	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:44470227A>T	ENST00000251269.5	+	6	901	c.573A>T	c.(571-573)tcA>tcT	p.S191S	ZNF221_ENST00000592350.1_Silent_p.S191S|ZNF221_ENST00000587682.1_Silent_p.S191S	NM_013359.2	NP_037491	Q9UK13	ZN221_HUMAN	zinc finger protein 221	191					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(11)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	30		Prostate(69;0.0352)				ATCAACAATCACACTCAGGAG	0.398																																					p.S191S		Atlas-SNP	.											.	ZNF221	59	.	0			c.A573T						.						132	125	127					19																	44470227		2203	4300	6503	SO:0001819	synonymous_variant	7638	exon6			ACAATCACACTCA	AF187987	CCDS12633.1	19q13.31	2013-01-08				ENSG00000159905		"Zinc fingers, C2H2-type", "-"	13014	protein-coding gene	gene with protein product							Standard	NM_013359		Approved		uc002oxx.2	Q9UK13		ENST00000251269.5:c.573A>T	chr19.hg19:g.44470227A>T		86.0	0.0		55.0	23.0	NM_013359	B2RAI6|Q2M2H2|Q9P1U8	Silent	SNP	ENST00000251269.5	hg19	CCDS12633.1																																																																																			.	.		0.398	ZNF221-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460068.1			T	44470227	A	T	44470227	2	4	344	1	0	0	0	0	0	0	0	1	17790	146	6	4		4	ZNF221	19	44470227	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1058223	44470227	14658756	1271	48634										
ZNF230	7773	hgsc.bcm.edu	37	chr19	44515114	44515114	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccacacagcagagaaactgtAcaaatctgaggagtgtggaa	11	8	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:44515114A>G	ENST00000429154.2	+	5	1151	c.923A>G	c.(922-924)tAc>tGc	p.Y308C		NM_006300.3	NP_006291.2	Q9UIE0	ZN230_HUMAN	zinc finger protein 230	308				YKS -> SKC (in Ref. 1; AAB62180). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(10)|skin(1)|stomach(3)|urinary_tract(2)	22		Prostate(69;0.0352)				GAGAAACTGTACAAATCTGAG	0.418																																					p.Y308C	GBM(175;914 2069 22996 47111 52600)	Atlas-SNP	.											.	ZNF230	44	.	0			c.A923G						.						142	138	139					19																	44515114		2203	4300	6503	SO:0001583	missense	7773	exon5			AACTGTACAAATC	U95044	CCDS33044.1	19q13.31	2013-01-08				ENSG00000159882		"Zinc fingers, C2H2-type", "-"	13024	protein-coding gene	gene with protein product							Standard	NM_006300		Approved	FDZF2	uc002oyb.1	Q9UIE0		ENST00000429154.2:c.923A>G	chr19.hg19:g.44515114A>G	ENSP00000409318:p.Tyr308Cys	86.0	0.0		55.0	24.0	NM_006300	O15322|Q504X7|Q86W84|Q9P1U6	Missense_Mutation	SNP	ENST00000429154.2	hg19	CCDS33044.1	.	.	.	.	.	.	.	.	.	.	A	13.64	2.298105	0.40694	.	.	ENSG00000159882	ENST00000429154	T	0.35973	1.28	2.55	1.5	0.22942	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.51958	0.1705	M	0.74647	2.275	0.26113	N	0.98065	D	0.89917	1.0	D	0.75484	0.986	T	0.40496	-0.9560	9	0.87932	D	0	.	2.4498	0.04515	0.4714:0.0:0.1425:0.3861	.	308	Q9UIE0	ZN230_HUMAN	C	308	ENSP00000409318:Y308C	ENSP00000409318:Y308C	Y	+	2	0	ZNF230	49206954	0.000000	0.05858	0.001000	0.08648	0.576000	0.36127	0.321000	0.19558	0.217000	0.20800	0.172000	0.16884	TAC	.	.		0.418	ZNF230-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460456.1			G	44515114	A	G	44515114	3	3	344	1	0	0	0	0	1	0	0	0	17799	391	14	2	937	2	ZNF230	19	44515114	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	44887	44515114	14613869	1272	48635										
ZNF224	7767	hgsc.bcm.edu	37	chr19	44610721	44610721	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttcccctgccagactgaggcAggactatctgtaattcacac	8	13	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:44610721A>T	ENST00000336976.6	+	6	662	c.408A>T	c.(406-408)gcA>gcT	p.A136A	AC084219.4_ENST00000592946.1_RNA	NM_013398.2	NP_037530.2	Q9NZL3	ZN224_HUMAN	zinc finger protein 224	136					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nuclear membrane (GO:0031965)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	19		Prostate(69;0.0435)				AGACTGAGGCAGGACTATCTG	0.408																																					p.A136A		Atlas-SNP	.											.	ZNF224	70	.	0			c.A408T						.						96	95	95					19																	44610721		2203	4300	6503	SO:0001819	synonymous_variant	7767	exon6			TGAGGCAGGACTA	AF187990	CCDS33046.1	19q13.2	2013-01-08	2004-02-13			ENSG00000267680		"Zinc fingers, C2H2-type", "-"	13017	protein-coding gene	gene with protein product		194555	"zinc finger protein 255", "zinc finger protein 27"	ZNF255, ZNF27			Standard	NM_013398		Approved	BMZF-2, KOX22	uc002oyh.2	Q9NZL3		ENST00000336976.6:c.408A>T	chr19.hg19:g.44610721A>T		71.0	0.0		77.0	38.0	NM_013398	A6NFW9|P17033|Q86V10|Q8IZC8|Q9UID9|Q9Y2P6	Silent	SNP	ENST00000336976.6	hg19	CCDS33046.1																																																																																			.	.		0.408	ZNF224-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460477.1	NM_013398		T	44610721	A	T	44610721	2	4	344	1	0	0	0	0	0	0	0	1	17793	175	7	4		4	ZNF224	19	44610721	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	95607	44610721	14518262	1273	48636										
ZFP112	7771	hgsc.bcm.edu	37	chr19	44832441	44832441	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggtttttctccagtgtggacTctctgatggccttgaaggtg	13	8	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:44832441T>A	ENST00000337401.4	-	5	1975	c.1887A>T	c.(1885-1887)agA>agT	p.R629S	ZNF112_ENST00000354340.4_Missense_Mutation_p.R623S|ZNF112_ENST00000536500.1_Missense_Mutation_p.R646S	NM_001083335.1	NP_001076804.1	Q9UJU3	ZN112_HUMAN	zinc finger protein 112	629					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										CAGTGTGGACTCTCTGATGGC	0.463																																					p.R629S		Atlas-SNP	.											.	ZFP112	219	.	0			c.A1887T						.						132	131	131					19																	44832441		2203	4300	6503	SO:0001583	missense	7771	exon5			GTGGACTCTCTGA	AF198358		19q13.2	2014-02-06	2012-11-27		ENSG00000062370	ENSG00000062370		"Zinc fingers, C2H2-type"	12892	protein-coding gene	gene with protein product		603994	"zinc finger protein 112 homolog (mouse)", "zinc finger protein 228"	ZFP112, ZNF228			Standard	NM_013380		Approved			Q9UJU3	OTTHUMG00000182357	ENST00000337401.4:c.1887A>T	chr19.hg19:g.44832441T>A	ENSP00000337081:p.Arg629Ser	146.0	0.0		113.0	49.0	NM_001083335	A4FU53|Q9HCA7	Missense_Mutation	SNP	ENST00000337401.4	hg19	CCDS54276.1	.	.	.	.	.	.	.	.	.	.	t	16.84	3.235048	0.58886	.	.	ENSG00000062370	ENST00000337401;ENST00000412927;ENST00000354340;ENST00000536500;ENST00000253426	T;T;T	0.24151	1.87;1.87;1.87	5.0	0.0326	0.14176	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.36002	N	0.002854	T	0.37237	0.0996	L	0.58969	1.84	0.29605	N	0.847398	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.74023	0.982;0.969;0.982	T	0.19910	-1.0291	10	0.59425	D	0.04	-29.812	4.7691	0.13146	0.0:0.2399:0.2866:0.4735	.	628;646;629	B4DYT4;F5GWS7;Q9UJU3	.;.;ZF112_HUMAN	S	629;629;623;646;628	ENSP00000337081:R629S;ENSP00000346305:R623S;ENSP00000441990:R646S	ENSP00000253426:R628S	R	-	3	2	ZNF285	49524281	0.000000	0.05858	0.998000	0.56505	0.996000	0.88848	-0.478000	0.06575	0.016000	0.14998	-0.253000	0.11424	AGA	.	.		0.463	ZNF112-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460744.1	NM_013380		A	44832441	T	A	44832441	3	1	344	1	0	0	0	0	1	0	0	0	17653	1548	54	4	858	4	ZFP112	19	44832441	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	221720	44832441	14296542	1274	48637										
ZFP112	7771	hgsc.bcm.edu	37	chr19	44833042	44833042	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccctatgctgaatgtcaagaTttgaactacaaatgaaactc	6	9	1	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:44833042T>G	ENST00000337401.4	-	5	1374	c.1286A>C	c.(1285-1287)aAt>aCt	p.N429T	ZNF112_ENST00000354340.4_Missense_Mutation_p.N423T|ZNF112_ENST00000536500.1_Missense_Mutation_p.N446T	NM_001083335.1	NP_001076804.1	Q9UJU3	ZN112_HUMAN	zinc finger protein 112	429					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										AATGTCAAGATTTGAACTACA	0.368																																					p.N429T		Atlas-SNP	.											.	ZFP112	219	.	0			c.A1286C						.						88	86	87					19																	44833042		2203	4300	6503	SO:0001583	missense	7771	exon5			TCAAGATTTGAAC	AF198358		19q13.2	2014-02-06	2012-11-27		ENSG00000062370	ENSG00000062370		"Zinc fingers, C2H2-type"	12892	protein-coding gene	gene with protein product		603994	"zinc finger protein 112 homolog (mouse)", "zinc finger protein 228"	ZFP112, ZNF228			Standard	NM_013380		Approved			Q9UJU3	OTTHUMG00000182357	ENST00000337401.4:c.1286A>C	chr19.hg19:g.44833042T>G	ENSP00000337081:p.Asn429Thr	76.0	0.0		82.0	26.0	NM_001083335	A4FU53|Q9HCA7	Missense_Mutation	SNP	ENST00000337401.4	hg19	CCDS54276.1	.	.	.	.	.	.	.	.	.	.	T	3.032	-0.199420	0.06219	.	.	ENSG00000062370	ENST00000337401;ENST00000412927;ENST00000354340;ENST00000536500;ENST00000253426	T;T;T	0.15603	2.41;2.41;2.41	4.73	2.59	0.31030	.	0.682943	0.12076	N	0.501709	T	0.12135	0.0295	L	0.42632	1.34	0.09310	N	1	P;P;B	0.38078	0.483;0.617;0.335	B;B;B	0.31101	0.058;0.124;0.058	T	0.16897	-1.0387	10	0.21540	T	0.41	-5.9597	8.9986	0.36068	0.0:0.1684:0.0:0.8316	.	428;446;429	B4DYT4;F5GWS7;Q9UJU3	.;.;ZF112_HUMAN	T	429;429;423;446;428	ENSP00000337081:N429T;ENSP00000346305:N423T;ENSP00000441990:N446T	ENSP00000253426:N428T	N	-	2	0	ZNF285	49524882	0.000000	0.05858	0.010000	0.14722	0.077000	0.17291	0.246000	0.18160	0.894000	0.36317	0.459000	0.35465	AAT	.	.		0.368	ZNF112-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460744.1	NM_013380		G	44833042	T	G	44833042	3	3	344	1	0	0	0	0	1	0	0	0	17653	1493	52	5	1459	5	ZFP112	19	44833042	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	601	44833042	14295941	1275	48638										
RSPH6A	81492	hgsc.bcm.edu	37	chr19	46318016	46318016	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccaaggggttgactgggggcTcctggaaggtggggtccagt	19	8	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:46318016T>A	ENST00000221538.3	-	1	561	c.419A>T	c.(418-420)gAg>gTg	p.E140V	RSPH6A_ENST00000597055.1_Missense_Mutation_p.E140V|SYMPK_ENST00000598155.1_5'Flank	NM_030785.3	NP_110412.1	Q9H0K4	RSH6A_HUMAN	radial spoke head 6 homolog A (Chlamydomonas)	140						intracellular (GO:0005622)				central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	32						GACTGGGGGCTCCTGGAAGGT	0.612																																					p.E140V		Atlas-SNP	.											.	RSPH6A	70	.	0			c.A419T						.						41	45	43					19																	46318016		2203	4300	6503	SO:0001583	missense	81492	exon1			GGGGGCTCCTGGA	AL136761	CCDS12675.1	19q13.3	2010-02-17	2009-11-18	2009-11-18	ENSG00000104941	ENSG00000104941			14241	protein-coding gene	gene with protein product		607548	"radial spokehead-like 1"	RSHL1		11237735	Standard	NM_030785		Approved	RSP4, RSP6, RSPH4B	uc002pdm.3	Q9H0K4		ENST00000221538.3:c.419A>T	chr19.hg19:g.46318016T>A	ENSP00000221538:p.Glu140Val	74.0	0.0		52.0	23.0	NM_030785	Q53FE2|Q6PEZ9	Missense_Mutation	SNP	ENST00000221538.3	hg19	CCDS12675.1	.	.	.	.	.	.	.	.	.	.	T	12.29	1.895000	0.33442	.	.	ENSG00000104941	ENST00000221538	T	0.17054	2.3	4.17	0.703	0.18116	.	2.063930	0.02016	N	0.047438	T	0.12347	0.0300	L	0.27053	0.805	0.09310	N	1	B	0.33073	0.396	B	0.26310	0.068	T	0.22661	-1.0210	10	0.35671	T	0.21	-14.1801	6.8589	0.24056	0.0:0.3047:0.0:0.6953	.	140	Q9H0K4	RSH6A_HUMAN	V	140	ENSP00000221538:E140V	ENSP00000221538:E140V	E	-	2	0	RSPH6A	51009856	0.003000	0.15002	0.031000	0.17742	0.020000	0.10135	0.861000	0.27885	-0.055000	0.13244	0.392000	0.25879	GAG	.	.		0.612	RSPH6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461657.1			A	46318016	T	A	46318016	3	1	344	1	0	0	0	0	1	0	0	0	13722	1551	54	4	1758	4	RSPH6A	19	46318016	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1484974	46318016	12810967	1276	48639										
ARHGAP35	2909	hgsc.bcm.edu	37	chr19	47425269	47425269	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccgtgccccatgacagcaccCaaggcaaaatcatcaccatt	6	16	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:47425269C>T	ENST00000404338.3	+	1	3337	c.3337C>T	c.(3337-3339)Caa>Taa	p.Q1113*		NM_004491.4	NP_004482.4	Q9NRY4	RHG35_HUMAN	Rho GTPase activating protein 35	1113					axon guidance (GO:0007411)|camera-type eye development (GO:0043010)|forebrain development (GO:0030900)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular permeability (GO:0043116)|neural tube closure (GO:0001843)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|GTP binding (GO:0005525)|Rho GTPase activator activity (GO:0005100)|transcription corepressor activity (GO:0003714)										TGACAGCACCCAAGGCAAAAT	0.498																																					p.Q1113X		Atlas-SNP	.											.	.	.	.	0			c.C3337T						.						58	56	56					19																	47425269		2043	4188	6231	SO:0001587	stop_gained	2909	exon1			AGCACCCAAGGCA	M73077	CCDS46127.1	19q13.32	2011-06-29	2011-06-07	2011-06-07	ENSG00000160007	ENSG00000160007		"Rho GTPase activating proteins"	4591	protein-coding gene	gene with protein product		605277	"glucocorticoid receptor DNA binding factor 1"	GRLF1		1894621, 20675588	Standard	NM_004491		Approved	GRF-1, p190ARhoGAP, P190A, KIAA1722, p190RhoGAP	uc010ekv.3	Q9NRY4		ENST00000404338.3:c.3337C>T	chr19.hg19:g.47425269C>T	ENSP00000385720:p.Gln1113*	154.0	0.0		101.0	43.0	NM_004491	A7E2A4|Q14452|Q9C0E1	Nonsense_Mutation	SNP	ENST00000404338.3	hg19	CCDS46127.1	.	.	.	.	.	.	.	.	.	.	C	42	9.404450	0.99161	.	.	ENSG00000160007	ENST00000317082;ENST00000404338	.	.	.	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	-26.9041	18.7132	0.91666	0.0:1.0:0.0:0.0	.	.	.	.	X	1113	.	ENSP00000324820:Q1113X	Q	+	1	0	ARHGAP35	52117109	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	7.818000	0.86416	2.720000	0.93068	0.655000	0.94253	CAA	.	.		0.498	ARHGAP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466652.1	NM_004491		T	47425269	C	T	47425269	4	4	344	1	0	0	0	0	0	1	0	0	6804	595	21	3	3339	3	ARHGAP35	19	47425269	Nonsense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1107253	47425269	11703714	1277	48640										
KPTN	11133	hgsc.bcm.edu	37	chr19	47986778	47986778	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccttgatgaacgtgatccccAcaaccagaccccgcttgggg	10	15	0	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:47986778A>T	ENST00000338134.3	-	2	397	c.290T>A	c.(289-291)gTg>gAg	p.V97E	KPTN_ENST00000536339.1_5'UTR|NAPA-AS1_ENST00000593284.1_RNA|NAPA-AS1_ENST00000594367.1_RNA|KPTN_ENST00000595484.1_5'UTR	NM_007059.2	NP_008990.2	Q9Y664	KPTN_HUMAN	kaptin (actin binding protein)	97					actin filament organization (GO:0007015)|cellular component movement (GO:0006928)|sensory perception of sound (GO:0007605)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	actin binding (GO:0003779)			breast(1)|lung(3)|ovary(2)|pancreas(2)	8		all_cancers(25;1.55e-10)|all_epithelial(76;3.4e-08)|all_lung(116;1.73e-07)|Lung NSC(112;3.95e-07)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		OV - Ovarian serous cystadenocarcinoma(262;0.000428)|all cancers(93;0.000631)|Epithelial(262;0.0153)|GBM - Glioblastoma multiforme(486;0.0694)		CGTGATCCCCACAACCAGACC	0.582											OREG0025593	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V97E		Atlas-SNP	.											.	KPTN	34	.	0			c.T290A						.						31	37	35					19																	47986778		1968	4145	6113	SO:0001583	missense	11133	exon2			ATCCCCACAACCA	AF105369	CCDS42583.1	19q13.32	2014-08-13	2001-11-28		ENSG00000118162	ENSG00000118162			6404	protein-coding gene	gene with protein product		615620	"kaptin (actin-binding protein)"			10099934	Standard	XM_005258467		Approved	2E4	uc002pgy.3	Q9Y664	OTTHUMG00000183443	ENST00000338134.3:c.290T>A	chr19.hg19:g.47986778A>T	ENSP00000337850:p.Val97Glu	110.0	0.0	951	80.0	27.0	NM_007059	B3KN86|B4DQ76|Q96GT1	Missense_Mutation	SNP	ENST00000338134.3	hg19	CCDS42583.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.625165	0.87560	.	.	ENSG00000118162	ENST00000338134	.	.	.	4.67	4.67	0.58626	.	0.000000	0.85682	D	0.000000	T	0.76737	0.4029	M	0.76574	2.34	0.80722	D	1	D	0.76494	0.999	D	0.67548	0.952	T	0.80296	-0.1442	9	0.87932	D	0	-1.2341	13.3858	0.60795	1.0:0.0:0.0:0.0	.	97	Q9Y664	KPTN_HUMAN	E	97	.	ENSP00000337850:V97E	V	-	2	0	KPTN	52678590	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	8.438000	0.90305	1.881000	0.54492	0.398000	0.26397	GTG	.	.		0.582	KPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466672.2			T	47986778	A	T	47986778	3	4	344	1	0	0	0	0	1	0	0	0	8446	159	6	4	1064	4	KPTN	19	47986778	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	561509	47986778	11142205	1278	48641										
ELSPBP1	64100	hgsc.bcm.edu	37	chr19	48519284	48519284	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agaaacagcagtggaaattcTgtgaaacgaatggtgagccc	12	7	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:48519284T>G	ENST00000339841.2	+	4	521	c.343T>G	c.(343-345)Tgt>Ggt	p.C115G	ELSPBP1_ENST00000597519.1_Intron	NM_022142.4	NP_071425.3	Q96BH3	ESPB1_HUMAN	epididymal sperm binding protein 1	115	Fibronectin type-II 2. {ECO:0000255|PROSITE-ProRule:PRU00479}.				single fertilization (GO:0007338)	extracellular region (GO:0005576)				NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(6)	10		all_cancers(25;8.7e-09)|all_lung(116;1.15e-06)|all_epithelial(76;1.17e-06)|Lung NSC(112;2.56e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000253)|all cancers(93;0.00129)|Epithelial(262;0.0314)|GBM - Glioblastoma multiforme(486;0.0606)		GTGGAAATTCTGTGAAACGAA	0.547																																					p.C115G		Atlas-SNP	.											.	ELSPBP1	29	.	0			c.T343G						.						131	111	118					19																	48519284		2203	4300	6503	SO:0001583	missense	64100	exon4			AAATTCTGTGAAA	AJ278478	CCDS12708.1	19q13.33	2009-09-17							14417	protein-coding gene	gene with protein product	"epididymal protein 12"	607443					Standard	NM_022142		Approved	HE12, E12, EDDM12	uc002pht.3	Q96BH3		ENST00000339841.2:c.343T>G	chr19.hg19:g.48519284T>G	ENSP00000340660:p.Cys115Gly	82.0	0.0		57.0	19.0	NM_022142	Q96RT0|Q9H4C8	Missense_Mutation	SNP	ENST00000339841.2	hg19	CCDS12708.1	.	.	.	.	.	.	.	.	.	.	T	13.51	2.258236	0.39896	.	.	ENSG00000169393	ENST00000339841	D	0.91996	-2.95	3.55	3.55	0.40652	Fibronectin, type II, collagen-binding (4);Kringle-like fold (1);	0.000000	0.50627	D	0.000110	D	0.96781	0.8949	H	0.96111	3.77	0.38260	D	0.94185	D	0.89917	1.0	D	0.87578	0.998	D	0.97225	0.9880	10	0.72032	D	0.01	.	9.0552	0.36401	0.0:0.0:0.0:1.0	.	115	Q96BH3	ESPB1_HUMAN	G	115	ENSP00000340660:C115G	ENSP00000340660:C115G	C	+	1	0	ELSPBP1	53211096	0.992000	0.36948	0.980000	0.43619	0.459000	0.32528	1.295000	0.33377	1.549000	0.49425	0.443000	0.29094	TGT	.	.		0.547	ELSPBP1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465207.1			G	48519284	T	G	48519284	3	3	344	1	0	0	0	0	1	0	0	0	5085	1580	55	5	353	5	ELSPBP1	19	48519284	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	532506	48519284	10609699	1279	48642										
PLA2G4C	8605	hgsc.bcm.edu	37	chr19	48551611	48551611	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaggctcatctatgccaagcAgcaacttcgggcactatcct	9	13	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:48551611A>C	ENST00000599921.1	-	17	1972	c.1615T>G	c.(1615-1617)Tgc>Ggc	p.C539G	PLA2G4C_ENST00000599111.1_Missense_Mutation_p.C549G|PLA2G4C_ENST00000413144.2_Missense_Mutation_p.C539G|PLA2G4C_ENST00000354276.3_3'UTR			Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC (cytosolic, calcium-independent)	539	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid metabolic process (GO:0019369)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|parturition (GO:0007567)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(12)|lung(13)|ovary(2)|prostate(1)|skin(3)	38		all_cancers(25;2.84e-05)|all_lung(116;4.62e-05)|Lung NSC(112;7.61e-05)|all_epithelial(76;0.000192)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;8.09e-05)|all cancers(93;0.000517)|Epithelial(262;0.0135)|GBM - Glioblastoma multiforme(486;0.0717)		TATGCCAAGCAGCAACTTCGG	0.532																																					p.C549G		Atlas-SNP	.											.	PLA2G4C	76	.	0			c.T1645G						.						107	82	90					19																	48551611		2203	4300	6503	SO:0001583	missense	8605	exon17			CCAAGCAGCAACT	AF065214	CCDS12710.1, CCDS54286.1, CCDS59403.1	19q13.3	2008-09-19					3.1.1.4		9037	protein-coding gene	gene with protein product		603602				9705332	Standard	NM_003706		Approved	cPLA2-gamma	uc002phx.3	Q9UP65		ENST00000599921.1:c.1615T>G	chr19.hg19:g.48551611A>C	ENSP00000469473:p.Cys539Gly	44.0	0.0		40.0	24.0	NM_001159322	B2RB71|B4DI40|O75457|Q6IBI8|Q9UG68	Missense_Mutation	SNP	ENST00000599921.1	hg19	CCDS12710.1	.	.	.	.	.	.	.	.	.	.	A	1.059	-0.673604	0.03403	.	.	ENSG00000105499	ENST00000413144	T	0.02369	4.32	1.66	0.579	0.17397	Lysophospholipase, catalytic domain (1);	.	.	.	.	T	0.01558	0.0050	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46952	-0.9154	9	0.46703	T	0.11	1.5938	3.0786	0.06254	0.7175:0.0:0.2825:0.0	.	549;539	B4DI40;Q9UP65	.;PA24C_HUMAN	G	539	ENSP00000400036:C539G	ENSP00000400036:C539G	C	-	1	0	PLA2G4C	53243423	0.188000	0.23250	0.011000	0.14972	0.032000	0.12392	0.256000	0.18351	0.124000	0.18369	0.332000	0.21555	TGC	.	.		0.532	PLA2G4C-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465551.1			C	48551611	A	C	48551611	3	2	344	1	0	0	0	0	1	0	0	0	12012	188	7	5	14	5	PLA2G4C	19	48551611	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	32327	48551611	10577372	1280	48643										
FGF21	26291	hgsc.bcm.edu	37	chr19	49261303	49261303	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctgccagggaacaagtccccAcaccgggaccctgcaccccg	10	19	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:49261303A>T	ENST00000593756.1	+	4	1028	c.456A>T	c.(454-456)ccA>ccT	p.P152P	FGF21_ENST00000222157.3_Silent_p.P152P|FUT1_ENST00000310160.3_5'Flank			Q9NSA1	FGF21_HUMAN	fibroblast growth factor 21	152					cell-cell signaling (GO:0007267)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of glucose import (GO:0046326)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|regulation of low-density lipoprotein particle clearance (GO:0010988)|signal transduction (GO:0007165)	extracellular region (GO:0005576)				breast(1)|cervix(2)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	8		all_lung(116;1.7e-06)|all_epithelial(76;3.52e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000348)|Epithelial(262;0.019)|GBM - Glioblastoma multiforme(486;0.022)		ACAAGTCCCCACACCGGGACC	0.682																																					p.P152P		Atlas-SNP	.											.	FGF21	21	.	0			c.A456T						.						42	50	47					19																	49261303		2203	4298	6501	SO:0001819	synonymous_variant	26291	exon3			GTCCCCACACCGG	AB021975	CCDS12734.1	19q13.33	2012-09-20			ENSG00000105550	ENSG00000105550			3678	protein-coding gene	gene with protein product		609436				10858549	Standard	XM_005258731		Approved		uc002pko.1	Q9NSA1		ENST00000593756.1:c.456A>T	chr19.hg19:g.49261303A>T		188.0	0.0		164.0	59.0	NM_019113	Q8N683	Silent	SNP	ENST00000593756.1	hg19	CCDS12734.1																																																																																			.	.		0.682	FGF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466200.1			T	49261303	A	T	49261303	2	4	344	1	0	0	0	0	0	0	0	1	5858	146	6	4		4	FGF21	19	49261303	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	709692	49261303	9867680	1281	48644										
GYS1	2997	hgsc.bcm.edu	37	chr19	49473817	49473817	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcctacccggcctaggtattTccagtccagaaggtcggaga	11	12	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:49473817T>C	ENST00000323798.3	-	14	1991	c.1795A>G	c.(1795-1797)Aaa>Gaa	p.K599E	GYS1_ENST00000263276.6_Missense_Mutation_p.K535E|GYS1_ENST00000544287.1_Missense_Mutation_p.K232E|GYS1_ENST00000541188.1_Missense_Mutation_p.K519E	NM_002103.4	NP_002094.2	P13807	GYS1_HUMAN	glycogen synthase 1 (muscle)	599					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|heart development (GO:0007507)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|inclusion body (GO:0016234)|membrane (GO:0016020)	glucose binding (GO:0005536)|glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein kinase binding (GO:0019901)			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)		CCTAGGTATTTCCAGTCCAGA	0.602											OREG0025611	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K599E		Atlas-SNP	.											.	GYS1	59	.	0			c.A1795G						.						31	36	34					19																	49473817		2203	4300	6503	SO:0001583	missense	2997	exon14			GGTATTTCCAGTC		CCDS12747.1, CCDS54292.1	19q13.3	2013-02-22			ENSG00000104812	ENSG00000104812	2.4.1.11	"Glycosyltransferase group 1 domain containing"	4706	protein-coding gene	gene with protein product		138570		GYS			Standard	NM_002103		Approved	GSY	uc002plp.3	P13807	OTTHUMG00000150723	ENST00000323798.3:c.1795A>G	chr19.hg19:g.49473817T>C	ENSP00000317904:p.Lys599Glu	59.0	0.0	962	51.0	27.0	NM_002103	Q9BTT9	Missense_Mutation	SNP	ENST00000323798.3	hg19	CCDS12747.1	.	.	.	.	.	.	.	.	.	.	T	17.33	3.361226	0.61403	.	.	ENSG00000104812	ENST00000323798;ENST00000263276;ENST00000541188;ENST00000544287	T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3	5.19	5.19	0.71726	.	0.045321	0.85682	D	0.000000	T	0.61565	0.2357	L	0.31926	0.97	0.80722	D	1	B;B;P	0.50066	0.021;0.128;0.931	B;B;P	0.46510	0.033;0.099;0.519	T	0.66791	-0.5834	10	0.72032	D	0.01	-19.5254	13.2988	0.60313	0.0:0.0:0.0:1.0	.	519;535;599	B7Z806;Q9BTT9;P13807	.;.;GYS1_HUMAN	E	599;535;519;232	ENSP00000317904:K599E;ENSP00000263276:K535E;ENSP00000437922:K519E;ENSP00000444004:K232E	ENSP00000263276:K535E	K	-	1	0	GYS1	54165629	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.896000	0.69822	2.109000	0.64355	0.459000	0.35465	AAA	.	.		0.602	GYS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319791.1	NM_002103		C	49473817	T	C	49473817	3	2	344	1	0	0	0	0	1	0	0	0	6921	1792	62	2	430	2	GYS1	19	49473817	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	212514	49473817	9655166	1282	48645										
TRPM4	54795	hgsc.bcm.edu	37	chr19	49703938	49703938	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctatggcgtggccacggaggGgctcctgaggccacgggaca	17	12	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:49703938G>T	ENST00000252826.5	+	19	2975	c.2849G>T	c.(2848-2850)gGg>gTg	p.G950V	TRPM4_ENST00000427978.2_Missense_Mutation_p.G805V|TRPM4_ENST00000355712.5_Missense_Mutation_p.G596V	NM_017636.3	NP_060106.2	Q8TD43	TRPM4_HUMAN	transient receptor potential cation channel, subfamily M, member 4	950					calcium ion transmembrane transport (GO:0070588)|cardiac conduction (GO:0061337)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|protein sumoylation (GO:0016925)|regulation of membrane potential (GO:0042391)|regulation of T cell cytokine production (GO:0002724)|transmembrane transport (GO:0055085)|vasoconstriction (GO:0042310)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)			breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(18)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	49		all_lung(116;8.54e-05)|Lung NSC(112;0.000139)|all_neural(266;0.0506)|Ovarian(192;0.15)		all cancers(93;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000222)|GBM - Glioblastoma multiforme(486;0.00339)|Epithelial(262;0.00751)		GCCACGGAGGGGCTCCTGAGG	0.612																																					p.G950V		Atlas-SNP	.											.	TRPM4	119	.	0			c.G2849T						.						54	52	53					19																	49703938		2203	4300	6503	SO:0001583	missense	54795	exon19			CGGAGGGGCTCCT	AK000048	CCDS33073.1, CCDS56098.1	19q13.3	2011-12-14				ENSG00000130529		"Voltage-gated ion channels / Transient receptor potential cation channels"	17993	protein-coding gene	gene with protein product		606936				11535825, 16382100	Standard	NM_017636		Approved	FLJ20041	uc002pmw.3	Q8TD43		ENST00000252826.5:c.2849G>T	chr19.hg19:g.49703938G>T	ENSP00000252826:p.Gly950Val	45.0	0.0		41.0	17.0	NM_017636	A2RU25|Q7Z5D9|Q96L84|Q9NXV1	Missense_Mutation	SNP	ENST00000252826.5	hg19	CCDS33073.1	.	.	.	.	.	.	.	.	.	.	G	16.25	3.069144	0.55539	.	.	ENSG00000130529	ENST00000252826;ENST00000427978;ENST00000355712	T;T;T	0.64803	-0.12;-0.12;-0.12	4.57	3.54	0.40534	.	0.060880	0.64402	D	0.000005	T	0.69993	0.3173	L	0.42245	1.32	0.80722	D	1	D;D;D;D	0.76494	0.993;0.992;0.992;0.999	D;P;P;D	0.72982	0.955;0.856;0.856;0.979	T	0.71961	-0.4434	10	0.87932	D	0	-27.9137	11.4642	0.50227	0.0907:0.0:0.9092:0.0	.	596;776;805;950	B4DIX5;Q8TD43-2;Q8TD43-3;Q8TD43	.;.;.;TRPM4_HUMAN	V	950;805;596	ENSP00000252826:G950V;ENSP00000407492:G805V;ENSP00000347944:G596V	ENSP00000252826:G950V	G	+	2	0	TRPM4	54395750	1.000000	0.71417	0.996000	0.52242	0.494000	0.33585	3.411000	0.52672	1.061000	0.40601	0.313000	0.20887	GGG	.	.		0.612	TRPM4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465543.2	NM_017636		T	49703938	G	T	49703938	3	4	344	1	0	0	0	0	1	0	0	0	16603	1232	43	3	2923	3	TRPM4	19	49703938	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	230121	49703938	9425045	1283	48646										
SCAF1	58506	hgsc.bcm.edu	37	chr19	50154181	50154181	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cccgtcacctcaccttgggcAcgggagacgggggccctgcc	14	17	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:50154181A>C	ENST00000360565.3	+	7	659	c.535A>C	c.(535-537)Acg>Ccg	p.T179P		NM_021228.2	NP_067051.2	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	179					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	20		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00113)|GBM - Glioblastoma multiforme(134;0.0204)		CACCTTGGGCACGGGAGACGG	0.667																																					p.T179P		Atlas-SNP	.											.	SCAF1	78	.	0			c.A535C						.						33	25	28					19																	50154181		2203	4299	6502	SO:0001583	missense	58506	exon7			TTGGGCACGGGAG	AK024444	CCDS33074.1	19q13.3-q13.4	2011-01-10			ENSG00000126461	ENSG00000126461			30403	protein-coding gene	gene with protein product						11461075	Standard	NM_021228		Approved	SR-A1, FLJ00034	uc002poq.3	Q9H7N4		ENST00000360565.3:c.535A>C	chr19.hg19:g.50154181A>C	ENSP00000353769:p.Thr179Pro	76.0	0.0		65.0	20.0	NM_021228	Q7Z5V7|Q8WVA1|Q9NR59	Missense_Mutation	SNP	ENST00000360565.3	hg19	CCDS33074.1	.	.	.	.	.	.	.	.	.	.	a	10.87	1.471260	0.26423	.	.	ENSG00000126461	ENST00000360565;ENST00000447618	T	0.37584	1.19	4.42	4.42	0.53409	.	0.547159	0.15489	N	0.259696	T	0.35941	0.0949	N	0.19112	0.55	0.23776	N	0.99687	D	0.64830	0.994	P	0.59889	0.865	T	0.09271	-1.0682	10	0.35671	T	0.21	-2.173	7.529	0.27672	0.8087:0.0:0.0:0.1913	.	179	Q9H7N4	SFR19_HUMAN	P	179	ENSP00000353769:T179P	ENSP00000353769:T179P	T	+	1	0	SCAF1	54845993	0.999000	0.42202	1.000000	0.80357	0.973000	0.67179	2.225000	0.42954	2.002000	0.58637	0.525000	0.51046	ACG	.	.		0.667	SCAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465764.1	NM_021228		C	50154181	A	C	50154181	3	2	344	1	0	0	0	0	1	0	0	0	13883	159	6	5	557	5	SCAF1	19	50154181	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	450243	50154181	8974802	1284	48647										
SIGLEC11	114132	hgsc.bcm.edu	37	chr19	50453266	50453266	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gacatctccctctccaattgAagcccaaagcctgggcccct	7	17	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:50453266A>T	ENST00000447370.2	-	11	2148	c.2058T>A	c.(2056-2058)ctT>ctA	p.L686L	SIGLEC11_ENST00000426971.2_Silent_p.L590L|U3_ENST00000408198.1_RNA|CTC-326K19.6_ENST00000451973.1_Intron	NM_052884.2	NP_443116.2	Q96RL6	SIG11_HUMAN	sialic acid binding Ig-like lectin 11	686					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(6)|pancreas(1)|prostate(1)|skin(1)	32		all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17)		GBM - Glioblastoma multiforme(134;0.00107)|OV - Ovarian serous cystadenocarcinoma(262;0.00517)		TCTCCAATTGAAGCCCAAAGC	0.612																																					p.L686L		Atlas-SNP	.											.	SIGLEC11	70	.	0			c.T2058A						.						33	30	31					19																	50453266		2202	4300	6502	SO:0001819	synonymous_variant	114132	exon11			CAATTGAAGCCCA	AF337818	CCDS12790.2, CCDS46150.1	19q13.3	2013-01-29			ENSG00000161640	ENSG00000161640		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15622	protein-coding gene	gene with protein product		607157				11986327	Standard	NM_052884		Approved		uc010ybi.2	Q96RL6	OTTHUMG00000157077	ENST00000447370.2:c.2058T>A	chr19.hg19:g.50453266A>T		99.0	0.0		71.0	27.0	NM_052884		Silent	SNP	ENST00000447370.2	hg19	CCDS12790.2	.	.	.	.	.	.	.	.	.	.	A	2.794	-0.250723	0.05867	.	.	ENSG00000161640	ENST00000426971	.	.	.	2.38	2.38	0.29361	.	.	.	.	.	T	0.32852	0.0843	.	.	.	0.20926	N	0.999821	.	.	.	.	.	.	T	0.20009	-1.0288	4	.	.	.	.	6.9775	0.24683	1.0:0.0:0.0:0.0	.	.	.	.	Y	580	.	.	F	-	2	0	SIGLEC11	55145078	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-0.576000	0.05854	1.044000	0.40200	0.459000	0.35465	TTC	.	.		0.612	SIGLEC11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347382.1	NM_052884		T	50453266	A	T	50453266	2	4	344	1	0	0	0	0	0	0	0	1	14322	233	9	4		4	SIGLEC11	19	50453266	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	299085	50453266	8675717	1285	48648										
NAPSA	9476	hgsc.bcm.edu	37	chr19	50861904	50861904	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccacccgggcgctgctcttcAtgtccccgcggtcgaagacg	12	17	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:50861904A>C	ENST00000253719.2	-	9	1377	c.1169T>G	c.(1168-1170)aTg>aGg	p.M390R	NR1H2_ENST00000600978.1_Intron|NR1H2_ENST00000542413.1_Intron	NM_004851.1	NP_004842.1	O96009	NAPSA_HUMAN	napsin A aspartic peptidase	390					membrane protein proteolysis (GO:0033619)|proteolysis (GO:0006508)|surfactant homeostasis (GO:0043129)	alveolar lamellar body (GO:0097208)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	aspartic-type endopeptidase activity (GO:0004190)|endopeptidase activity (GO:0004175)|peptidase activity (GO:0008233)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|skin(3)	12		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00743)|GBM - Glioblastoma multiforme(134;0.0183)		GCTGCTCTTCATGTCCCCGCG	0.697																																					p.M390R		Atlas-SNP	.											.	NAPSA	38	.	0			c.T1169G						.						19	20	20					19																	50861904		2200	4299	6499	SO:0001583	missense	9476	exon9			CTCTTCATGTCCC	AF090386	CCDS12794.1	19q13.33	2011-08-25				ENSG00000131400			13395	protein-coding gene	gene with protein product	"kidney-derived aspartic protease-like protein"	605631					Standard	NM_004851		Approved	NAP1, NAPA, Kdap, KAP	uc002prx.3	O96009		ENST00000253719.2:c.1169T>G	chr19.hg19:g.50861904A>C	ENSP00000253719:p.Met390Arg	108.0	0.0		68.0	30.0	NM_004851	Q8WWD9	Missense_Mutation	SNP	ENST00000253719.2	hg19	CCDS12794.1	.	.	.	.	.	.	.	.	.	.	A	0.007	-1.935602	0.00484	.	.	ENSG00000131400	ENST00000253719	T	0.27890	1.64	2.58	-5.17	0.02849	Peptidase aspartic (1);Peptidase aspartic, catalytic (1);	1.002540	0.08040	N	0.995041	T	0.07954	0.0199	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.09796	-1.0658	10	0.15952	T	0.53	.	0.3384	0.00329	0.2436:0.2486:0.1487:0.359	.	390	O96009	NAPSA_HUMAN	R	390	ENSP00000253719:M390R	ENSP00000253719:M390R	M	-	2	0	NAPSA	55553716	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-1.727000	0.01860	-3.659000	0.00125	-2.160000	0.00327	ATG	.	.		0.697	NAPSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464714.1	NM_004851		C	50861904	A	C	50861904	3	2	344	1	0	0	0	0	1	0	0	0	10175	217	8	5	97	5	NAPSA	19	50861904	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	408638	50861904	8267079	1286	48649										
SHANK1	50944	hgsc.bcm.edu	37	chr19	51189492	51189492	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctccccacaccaggccgcctAcctcagtggcaaagaaacct	7	18	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:51189492A>G	ENST00000293441.1	-	20	2596		c.e20+1		SHANK1_ENST00000359082.3_Splice_Site|SHANK1_ENST00000391814.1_Splice_Site|SHANK1_ENST00000391813.1_Splice_Site	NM_016148.2	NP_057232.2	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1						adult behavior (GO:0030534)|associative learning (GO:0008306)|cytoskeletal anchoring at plasma membrane (GO:0007016)|dendritic spine morphogenesis (GO:0060997)|determination of affect (GO:0050894)|habituation (GO:0046959)|long-term memory (GO:0007616)|negative regulation of actin filament bundle assembly (GO:0032232)|neuromuscular process controlling balance (GO:0050885)|olfactory behavior (GO:0042048)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|protein complex assembly (GO:0006461)|protein localization to synapse (GO:0035418)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|righting reflex (GO:0060013)|social behavior (GO:0035176)|synapse maturation (GO:0060074)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|excitatory synapse (GO:0060076)|intracellular (GO:0005622)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ankyrin repeat binding (GO:0071532)|GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|somatostatin receptor binding (GO:0031877)			breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	64		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)		CAGGCCGCCTACCTCAGTGGC	0.612																																					.		Atlas-SNP	.											.	SHANK1	210	.	0			c.2577+2T>C						.						58	51	54					19																	51189492		2203	4300	6503	SO:0001630	splice_region_variant	50944	exon21			CCGCCTACCTCAG	AF163302	CCDS12799.1	19q13.3	2013-01-10			ENSG00000161681	ENSG00000161681		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	15474	protein-coding gene	gene with protein product	"somatostatin receptor-interacting protein"	604999				10551867	Standard	NM_016148		Approved	SSTRIP, SPANK-1, synamon	uc002psx.1	Q9Y566	OTTHUMG00000137380	ENST00000293441.1:c.2577+1T>C	chr19.hg19:g.51189492A>G		45.0	0.0		19.0	9.0	NM_016148	A8MXP5|B7WNY6|Q9NYW9	Splice_Site	SNP	ENST00000293441.1	hg19	CCDS12799.1	.	.	.	.	.	.	.	.	.	.	A	15.84	2.953199	0.53293	.	.	ENSG00000161681	ENST00000293441;ENST00000391813;ENST00000359082;ENST00000391814	.	.	.	3.75	3.75	0.43078	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.8749	0.52541	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SHANK1	55881304	1.000000	0.71417	0.999000	0.59377	0.583000	0.36354	6.734000	0.74801	1.725000	0.51514	0.247000	0.18012	.	.	.		0.612	SHANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268071.1	NM_016148	Intron	G	51189492	A	G	51189492	5	3	344	1	0	0	0	0	0	0	1	0	14279	405	14	2	3922	2	SHANK1	19	51189492	Splice_Site	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	327588	51189492	7939491	1287	48650										
C19orf75	284369	hgsc.bcm.edu	37	chr19	51768725	51768725	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tctgtgcagtggtggatgggAggagtccccgtgggtgtgga	20	6	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:51768725A>T	ENST00000316401.7	+	3	507	c.126A>T	c.(124-126)ggA>ggT	p.G42G	SIGLECL1_ENST00000597824.1_Intron|SIGLECL1_ENST00000593968.1_Intron|CTD-3187F8.2_ENST00000597569.1_RNA	NM_173635.1	NP_775906.1	Q96PQ1	SIG12_HUMAN	SIGLEC family like 1	416	Ig-like V-type 1.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)										GGTGGATGGGAGGAGTCCCCG	0.577																																					p.G42G		Atlas-SNP	.											.	.	.	.	0			c.A126T						.						80	72	75					19																	51768725		2203	4300	6503	SO:0001819	synonymous_variant	284369	exon3			GATGGGAGGAGTC	AK097554	CCDS12827.1	19q13.33	2013-03-20	2012-07-20	2012-07-20	ENSG00000179213	ENSG00000179213			26856	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 75", "sialic acid binding Ig-like lectin 23, pseudogene", "sialic acid binding Ig-like lectin, pseudogene 7"	C19orf75, SIGLEC23P, SIGLECP7			Standard	NM_173635		Approved	FLJ40235	uc002pwb.1	Q8N7X8	OTTHUMG00000182881	ENST00000316401.7:c.126A>T	chr19.hg19:g.51768725A>T		116.0	0.0		87.0	34.0	NM_173635	Q8IYH7	Silent	SNP	ENST00000316401.7	hg19	CCDS12827.1																																																																																			.	.		0.577	SIGLECL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464161.2	NM_173635		T	51768725	A	T	51768725	2	4	344	1	0	0	0	0	0	0	0	1	1951	291	11	4		4	C19orf75	19	51768725	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	579233	51768725	7360258	1288	48651										
IGLON5	402665	hgsc.bcm.edu	37	chr19	51828607	51828607	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccgctgcccgcagtccctgcCcgcattgtgaacatctcgtc	9	18	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:51828607C>A	ENST00000270642.8	+	4	399	c.399C>A	c.(397-399)gcC>gcA	p.A133A		NM_001101372.1	NP_001094842.1	A6NGN9	IGLO5_HUMAN	IgLON family member 5	133	Ig-like C2-type 2.					extracellular region (GO:0005576)				large_intestine(5)|lung(6)|prostate(1)	12						CAGTCCCTGCCCGCATTGTGA	0.652																																					p.A133A		Atlas-SNP	.											.	IGLON5	31	.	0			c.C399A						.						29	33	31					19																	51828607		2103	4221	6324	SO:0001819	synonymous_variant	402665	exon4			CCCTGCCCGCATT		CCDS46158.1	19q13.33	2013-01-29			ENSG00000142549	ENSG00000142549		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	34550	protein-coding gene	gene with protein product							Standard	NM_001101372		Approved	LOC402665	uc002pwc.2	A6NGN9	OTTHUMG00000154422	ENST00000270642.8:c.399C>A	chr19.hg19:g.51828607C>A		61.0	0.0		46.0	21.0	NM_001101372		Silent	SNP	ENST00000270642.8	hg19	CCDS46158.1																																																																																			.	.		0.652	IGLON5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335149.1	NM_001101372		A	51828607	C	A	51828607	2	1	344	1	0	0	0	0	0	0	0	1	7604	610	22	3		3	IGLON5	19	51828607	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	59882	51828607	7300376	1289	48652										
SIGLEC8	27181	hgsc.bcm.edu	37	chr19	51958812	51958812	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cagggtttgaggaccgtgagGggcacagggtcaggctcccc	17	11	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:51958812G>A	ENST00000321424.3	-	4	977	c.911C>T	c.(910-912)cCc>cTc	p.P304L	SIGLEC8_ENST00000340550.5_Missense_Mutation_p.P211L|SIGLEC8_ENST00000597352.1_5'UTR|SIGLEC8_ENST00000430817.1_Missense_Mutation_p.P195L	NM_014442.2	NP_055257.2	Q9NYZ4	SIGL8_HUMAN	sialic acid binding Ig-like lectin 8	304	Ig-like C2-type 2.				cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(11)|liver(3)|lung(15)|ovary(2)|skin(4)|stomach(3)|urinary_tract(2)	50		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000627)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		GGACCGTGAGGGGCACAGGGT	0.642																																					p.P304L		Atlas-SNP	.											.	SIGLEC8	130	.	0			c.C911T						.						50	49	49					19																	51958812		2203	4300	6503	SO:0001583	missense	27181	exon4			CGTGAGGGGCACA	AF195092	CCDS33086.1	19q13.33-q13.41	2013-01-29			ENSG00000105366	ENSG00000105366		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10877	protein-coding gene	gene with protein product		605639				10625619	Standard	XR_243922		Approved	SIGLEC-8, SAF2, SIGLEC8L, MGC59785	uc002pwt.3	Q9NYZ4		ENST00000321424.3:c.911C>T	chr19.hg19:g.51958812G>A	ENSP00000321077:p.Pro304Leu	73.0	0.0		46.0	26.0	NM_014442	Q7Z728	Missense_Mutation	SNP	ENST00000321424.3	hg19	CCDS33086.1	.	.	.	.	.	.	.	.	.	.	.	13.81	2.347646	0.41599	.	.	ENSG00000105366	ENST00000430817;ENST00000321424;ENST00000340550	T;T;T	0.13538	2.58;2.58;2.58	2.19	2.19	0.27852	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.673556	0.12250	N	0.485707	T	0.15003	0.0362	L	0.55743	1.74	0.09310	N	0.999997	P;P;P	0.40731	0.728;0.537;0.624	B;B;B	0.40901	0.223;0.343;0.3	T	0.12578	-1.0542	10	0.66056	D	0.02	.	7.9807	0.30181	0.0:0.0:1.0:0.0	.	195;211;304	C9JT30;Q9NYZ4-2;Q9NYZ4	.;.;SIGL8_HUMAN	L	195;304;211	ENSP00000389142:P195L;ENSP00000321077:P304L;ENSP00000339448:P211L	ENSP00000321077:P304L	P	-	2	0	SIGLEC8	56650624	0.001000	0.12720	0.053000	0.19242	0.125000	0.20455	0.575000	0.23729	1.533000	0.49186	0.502000	0.49764	CCC	.	.		0.642	SIGLEC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463648.2	NM_014442		A	51958812	G	A	51958812	3	1	344	1	0	0	0	0	1	0	0	0	14329	1232	43	3	604	3	SIGLEC8	19	51958812	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	130205	51958812	7170171	1290	48653										
SIGLEC12	89858	hgsc.bcm.edu	37	chr19	52003208	52003208	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gagagcttgtcatatatgtaGttccatttcctgcttcctct	7	10	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:52003208G>T	ENST00000291707.3	-	2	829	c.774C>A	c.(772-774)aaC>aaA	p.N258K	SIGLEC12_ENST00000598614.1_Missense_Mutation_p.N140K	NM_053003.2	NP_443729.1	Q96PQ1	SIG12_HUMAN	sialic acid binding Ig-like lectin 12 (gene/pseudogene)	258	Ig-like V-type 2.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(2)|biliary_tract(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(1)|lung(23)|ovary(4)|prostate(2)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)	61		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.0102)		CATATATGTAGTTCCATTTCC	0.552																																					p.N258K		Atlas-SNP	.											.	SIGLEC12	243	.	0			c.C774A						.						91	77	82					19																	52003208		2203	4300	6503	SO:0001583	missense	89858	exon2			TATGTAGTTCCAT	AF282256	CCDS12833.1, CCDS59416.1	19q13.41	2013-01-29	2011-06-29	2004-10-20	ENSG00000254521	ENSG00000254521		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15482	protein-coding gene	gene with protein product		606094	"SIGLEC-like 1", "sialic acid binding Ig-like lectin 12"	SIGLECL1		11409877, 11328818, 21555517	Standard	NM_053003		Approved	SLG, S2V, Siglec-XII, Siglec-12, Siglec-L1	uc002pwx.1	Q96PQ1	OTTHUMG00000165524	ENST00000291707.3:c.774C>A	chr19.hg19:g.52003208G>T	ENSP00000291707:p.Asn258Lys	85.0	0.0		60.0	29.0	NM_053003	Q8IYH7	Missense_Mutation	SNP	ENST00000291707.3	hg19	CCDS12833.1	.	.	.	.	.	.	.	.	.	.	.	8.740	0.918641	0.17982	.	.	ENSG00000254521	ENST00000291707	T	0.68025	-0.3	0.673	-0.465	0.12157	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	0.618720	0.13110	U	0.413012	T	0.77116	0.4083	M	0.84082	2.675	0.09310	N	1	D;P	0.89917	1.0;0.941	D;P	0.64237	0.923;0.608	T	0.65274	-0.6208	9	0.66056	D	0.02	.	.	.	.	.	258;140	Q96PQ1;Q96PQ1-2	SIG12_HUMAN;.	K	258	ENSP00000291707:N258K	ENSP00000291707:N258K	N	-	3	2	SIGLEC12	56695020	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-0.079000	0.11357	-0.134000	0.11516	0.503000	0.49774	AAC	.	.		0.552	SIGLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384641.2	NM_053003		T	52003208	G	T	52003208	3	4	344	1	0	0	0	0	1	0	0	0	14323	1020	36	3	1041	3	SIGLEC12	19	52003208	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	44396	52003208	7125775	1291	48654										
SIGLEC12	89858	hgsc.bcm.edu	37	chr19	52004872	52004872	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aggagcaaagcacagagacaCacaggccctcctgcaccgtc	10	15	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:52004872C>A	ENST00000291707.3	-	1	171	c.116G>T	c.(115-117)tGt>tTt	p.C39F	SIGLEC12_ENST00000598614.1_5'Flank	NM_053003.2	NP_443729.1	Q96PQ1	SIG12_HUMAN	sialic acid binding Ig-like lectin 12 (gene/pseudogene)	39	Ig-like V-type 1.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(2)|biliary_tract(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(1)|lung(23)|ovary(4)|prostate(2)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)	61		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.0102)		CACAGAGACACACAGGCCCTC	0.587																																					p.C39F		Atlas-SNP	.											.	SIGLEC12	243	.	0			c.G116T						.						111	83	93					19																	52004872		2203	4300	6503	SO:0001583	missense	89858	exon1			GAGACACACAGGC	AF282256	CCDS12833.1, CCDS59416.1	19q13.41	2013-01-29	2011-06-29	2004-10-20	ENSG00000254521	ENSG00000254521		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15482	protein-coding gene	gene with protein product		606094	"SIGLEC-like 1", "sialic acid binding Ig-like lectin 12"	SIGLECL1		11409877, 11328818, 21555517	Standard	NM_053003		Approved	SLG, S2V, Siglec-XII, Siglec-12, Siglec-L1	uc002pwx.1	Q96PQ1	OTTHUMG00000165524	ENST00000291707.3:c.116G>T	chr19.hg19:g.52004872C>A	ENSP00000291707:p.Cys39Phe	88.0	0.0		50.0	22.0	NM_053003	Q8IYH7	Missense_Mutation	SNP	ENST00000291707.3	hg19	CCDS12833.1	.	.	.	.	.	.	.	.	.	.	.	17.37	3.371512	0.61624	.	.	ENSG00000254521	ENST00000291707	T	0.65178	-0.14	2.09	2.09	0.27110	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.82742	0.5103	H	0.96080	3.765	0.26366	N	0.976962	D	0.89917	1.0	D	0.80764	0.994	T	0.70400	-0.4882	9	0.87932	D	0	.	7.6643	0.28421	0.0:1.0:0.0:0.0	.	39	Q96PQ1	SIG12_HUMAN	F	39	ENSP00000291707:C39F	ENSP00000291707:C39F	C	-	2	0	SIGLEC12	56696684	0.390000	0.25213	0.942000	0.38095	0.723000	0.41478	0.691000	0.25467	1.173000	0.42796	0.503000	0.49774	TGT	.	.		0.587	SIGLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384641.2	NM_053003		A	52004872	C	A	52004872	3	1	344	1	0	0	0	0	1	0	0	0	14323	478	17	3	1776	3	SIGLEC12	19	52004872	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1664	52004872	7124111	1292	48655										
SIGLEC6	946	hgsc.bcm.edu	37	chr19	52023460	52023460	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cttctgagatggggccagccTcagcagggtggtctgaaact	14	10	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:52023460T>A	ENST00000425629.3	-	8	1392	c.1238A>T	c.(1237-1239)gAg>gTg	p.E413V	CTD-3073N11.9_ENST00000598220.1_RNA|SIGLEC6_ENST00000359982.4_3'UTR|SIGLEC6_ENST00000474054.1_5'UTR|SIGLEC6_ENST00000343300.4_Nonstop_Mutation_p.*354C|SIGLEC6_ENST00000346477.3_Missense_Mutation_p.E397V|SIGLEC6_ENST00000436458.1_Missense_Mutation_p.E361V|SIGLEC6_ENST00000391797.3_Nonstop_Mutation_p.*343C	NM_001245.5	NP_001236.4	O43699	SIGL6_HUMAN	sialic acid binding Ig-like lectin 6	413					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(15)|ovary(1)|stomach(1)	28		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00115)|OV - Ovarian serous cystadenocarcinoma(262;0.0165)		GGGGCCAGCCTCAGCAGGGTG	0.507																																					p.X354C		Atlas-SNP	.											.	SIGLEC6	142	.	0			c.A1062T						.						206	198	200					19																	52023460		1984	4166	6150	SO:0001583	missense	946	exon6			CCAGCCTCAGCAG	D86358	CCDS12834.3, CCDS12835.3, CCDS12836.3, CCDS54307.1, CCDS54308.1, CCDS59417.1	19q13.3	2013-01-29			ENSG00000105492	ENSG00000105492		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10875	protein-coding gene	gene with protein product		604405		CD33L, CD33L1		9465907	Standard	NM_001245		Approved	OB-BP1, SIGLEC-6, CD327	uc002pwy.3	O43699	OTTHUMG00000133571	ENST00000425629.3:c.1238A>T	chr19.hg19:g.52023460T>A	ENSP00000401502:p.Glu413Val	73.0	0.0		49.0	17.0	NM_198846	A8MV71|B2RTS8|C9JBE5|F8WA78|O15388|O43700	Missense_Mutation	SNP	ENST00000425629.3	hg19	CCDS12834.3	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.023|0.023	-1.404729|-1.404729	0.01155|0.01155	.|.	.|.	ENSG00000105492|ENSG00000105492	ENST00000346477;ENST00000391797;ENST00000425629;ENST00000436458|ENST00000343300	T;T|.	0.50548|.	1.17;0.74|.	2.57|2.57	-5.13|-5.13	0.02884|0.02884	.|.	.|.	.|.	.|.	.|.	T|.	0.18299|.	0.0439|.	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	B;B;B|.	0.31837|.	0.001;0.342;0.005|.	B;B;B|.	0.34385|.	0.002;0.181;0.005|.	T|.	0.24190|.	-1.0167|.	8|.	0.54805|.	T|.	0.06|.	.|.	2.9982|2.9982	0.06005|0.06005	0.3171:0.2772:0.0:0.4056|0.3171:0.2772:0.0:0.4056	.|.	361;397;413|.	C9JBE5;O43699-3;O43699|.	.;.;SIGL6_HUMAN|.	V|C	386;397;413;361|354	ENSP00000401502:E413V;ENSP00000410679:E361V|.	ENSP00000344064:E386V|.	E|X	-|-	2|3	0|0	SIGLEC6|SIGLEC6	56715272|56715272	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.009000|0.009000	0.06853|0.06853	-1.266000|-1.266000	0.02842|0.02842	-1.398000|-1.398000	0.02066|0.02066	-1.333000|-1.333000	0.01266|0.01266	GAG|TGA	.	.		0.507	SIGLEC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257670.3	NM_001245		A	52023460	T	A	52023460	3	1	344	1	0	0	0	0	1	0	0	0	14327	1564	54	4	127	4	SIGLEC6	19	52023460	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	18588	52023460	7105523	1293	48656										
FPR1	2357	hgsc.bcm.edu	37	chr19	52249744	52249744	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gctactgtccccgttttaccAggtactgtagtcacacgaat	8	12	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:52249744A>T	ENST00000595042.1	-	3	645	c.504T>A	c.(502-504)ccT>ccA	p.P168P	FPR1_ENST00000304748.4_Silent_p.P168P	NM_001193306.1	NP_001180235.1	P21462	FPR1_HUMAN	formyl peptide receptor 1	168					activation of MAPK activity (GO:0000187)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|nitric oxide mediated signal transduction (GO:0007263)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	N-formyl peptide receptor activity (GO:0004982)|receptor activity (GO:0004872)			endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(3)	20		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00106)|OV - Ovarian serous cystadenocarcinoma(262;0.018)	Nedocromil(DB00716)	CCGTTTTACCAGGTACTGTAG	0.532																																					p.P168P		Atlas-SNP	.											.	FPR1	64	.	0			c.T504A						.						83	78	80					19																	52249744		2203	4300	6503	SO:0001819	synonymous_variant	2357	exon3			TTTACCAGGTACT	M60627	CCDS12839.1	19q13.41	2014-09-17				ENSG00000171051		"GPCR / Class A : Formyl peptide receptors"	3826	protein-coding gene	gene with protein product		136537				2161213, 12595898	Standard	NM_001193306		Approved	FPR, FMLP	uc002pxq.3	P21462		ENST00000595042.1:c.504T>A	chr19.hg19:g.52249744A>T		54.0	0.0		48.0	24.0	NM_001193306	Q14939|Q7Z6A4|Q86U52|Q9NS48	Silent	SNP	ENST00000595042.1	hg19	CCDS12839.1																																																																																			.	.		0.532	FPR1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466905.1	NM_002029		T	52249744	A	T	52249744	2	4	344	1	0	0	0	0	0	0	0	1	6046	175	7	4		4	FPR1	19	52249744	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	226284	52249744	6879239	1294	48657										
ZNF347	84671	hgsc.bcm.edu	37	chr19	53644359	53644359	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttctgagtgaagaccttgccAcactcattacatttgtaagg	8	9	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:53644359A>G	ENST00000334197.7	-	5	1790	c.1722T>C	c.(1720-1722)tgT>tgC	p.C574C	ZNF347_ENST00000601469.2_Silent_p.C575C|ZNF347_ENST00000452676.2_Silent_p.C575C|ZNF347_ENST00000601804.1_Intron	NM_032584.2	NP_115973.2	Q96SE7	ZN347_HUMAN	zinc finger protein 347	574					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|prostate(3)|skin(1)	23				GBM - Glioblastoma multiforme(134;0.0179)		AGACCTTGCCACACTCATTAC	0.418																																					p.C575C	Melanoma(64;205 1597 17324 45721)	Atlas-SNP	.											.	ZNF347	87	.	0			c.T1725C						.						153	145	148					19																	53644359		2203	4298	6501	SO:0001819	synonymous_variant	84671	exon5			CTTGCCACACTCA	AY029765	CCDS33097.1, CCDS54314.1	19q13.3	2013-01-08				ENSG00000197937		"Zinc fingers, C2H2-type", "-"	16447	protein-coding gene	gene with protein product							Standard	NM_032584		Approved	ZNF1111	uc010eql.2	Q96SE7		ENST00000334197.7:c.1722T>C	chr19.hg19:g.53644359A>G		66.0	0.0		37.0	17.0	NM_001172675	B3KU77|B9EG59|G5E9N4|Q8TCN1	Silent	SNP	ENST00000334197.7	hg19	CCDS33097.1																																																																																			.	.		0.418	ZNF347-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464170.1	NM_032584		G	53644359	A	G	53644359	2	3	344	1	0	0	0	0	0	0	0	1	17876	157	6	2		2	ZNF347	19	53644359	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1394615	53644359	5484624	1295	48658										
ZNF677	342926	hgsc.bcm.edu	37	chr19	53741010	53741010	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttgactacagaccttgccacAtatattacattgatatggtt	6	8	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:53741010A>C	ENST00000598513.1	-	5	1120	c.970T>G	c.(970-972)Tgt>Ggt	p.C324G	CTD-2245F17.6_ENST00000596041.1_RNA|ZNF677_ENST00000333952.4_Missense_Mutation_p.C324G	NM_182609.2	NP_872415.1	Q86XU0	ZN677_HUMAN	zinc finger protein 677	324					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(13)|lung(6)|ovary(1)|pancreas(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				GBM - Glioblastoma multiforme(134;0.00352)		ACCTTGCCACATATATTACAT	0.388																																					p.C324G		Atlas-SNP	.											.	ZNF677	94	.	0			c.T970G						.						113	104	107					19																	53741010		2203	4300	6503	SO:0001583	missense	342926	exon5			TGCCACATATATT	BC050038	CCDS12861.1	19q13.42	2013-01-08				ENSG00000197928		"Zinc fingers, C2H2-type", "-"	28730	protein-coding gene	gene with protein product	"hypothetical protein MGC48625"					12477932	Standard	NM_182609		Approved	MGC48625	uc002qbg.1	Q86XU0		ENST00000598513.1:c.970T>G	chr19.hg19:g.53741010A>C	ENSP00000469391:p.Cys324Gly	99.0	0.0		72.0	40.0	NM_182609		Missense_Mutation	SNP	ENST00000598513.1	hg19	CCDS12861.1	.	.	.	.	.	.	.	.	.	.	A	15.48	2.845002	0.51164	.	.	ENSG00000197928	ENST00000333952	D	0.85861	-2.04	2.21	1.16	0.20824	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.36409	N	0.002611	D	0.89945	0.6862	H	0.98883	4.36	0.30915	N	0.728634	B	0.23249	0.082	B	0.30029	0.11	D	0.86334	0.1700	10	0.66056	D	0.02	.	6.6411	0.22909	0.7561:0.2439:0.0:0.0	.	324	Q86XU0	ZN677_HUMAN	G	324	ENSP00000334394:C324G	ENSP00000334394:C324G	C	-	1	0	ZNF677	58432822	1.000000	0.71417	0.448000	0.26945	0.892000	0.51952	5.974000	0.70465	0.288000	0.22398	0.533000	0.62120	TGT	.	.		0.388	ZNF677-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464189.1	NM_182609		C	53741010	A	C	53741010	3	2	344	1	0	0	0	0	1	0	0	0	18099	217	8	5	788	5	ZNF677	19	53741010	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	96651	53741010	5387973	1296	48659										
BIRC8	112401	hgsc.bcm.edu	37	chr19	53793261	53793261	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cttaacgtccttgaaatcaaAtcccattcgtatagcttctt	4	11	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:53793261A>T	ENST00000426466.1	-	1	1614	c.367T>A	c.(367-369)Ttt>Att	p.F123I		NM_033341.4	NP_203127.3	Q96P09	BIRC8_HUMAN	baculoviral IAP repeat containing 8	123					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(10)|urinary_tract(1)	19				GBM - Glioblastoma multiforme(134;0.00304)		TTGAAATCAAATCCCATTCGT	0.388																																					p.F123I		Atlas-SNP	.											.	BIRC8	54	.	0			c.T367A						.						185	181	182					19																	53793261		2203	4300	6503	SO:0001583	missense	112401	exon1			AATCAAATCCCAT	AF164682	CCDS12863.1	19q13.3-q13.4	2011-01-25	2011-01-25			ENSG00000163098		"Baculoviral IAP repeat containing"	14878	protein-coding gene	gene with protein product	"IAP-like protein 2", "inhibitor of apoptosis-like protein 2"		"baculoviral IAP repeat-containing 8"			11390657	Standard	NM_033341		Approved	ILP-2, hILP2	uc002qbk.3	Q96P09		ENST00000426466.1:c.367T>A	chr19.hg19:g.53793261A>T	ENSP00000412957:p.Phe123Ile	118.0	0.0		93.0	39.0	NM_033341	Q6IPY1|Q96RW5	Missense_Mutation	SNP	ENST00000426466.1	hg19	CCDS12863.1	.	.	.	.	.	.	.	.	.	.	A	15.17	2.754010	0.49362	.	.	ENSG00000163098	ENST00000426466	T	0.39406	1.08	0.502	0.502	0.16932	.	.	.	.	.	T	0.52629	0.1746	M	0.79475	2.455	0.45791	D	0.998673	D	0.65815	0.995	P	0.59221	0.854	T	0.51702	-0.8672	9	0.44086	T	0.13	-5.0451	5.4107	0.16346	0.9999:0.0:1.0E-4:0.0	.	123	Q96P09	BIRC8_HUMAN	I	123	ENSP00000412957:F123I	ENSP00000412957:F123I	F	-	1	0	BIRC8	58485073	0.934000	0.31675	0.016000	0.15963	0.010000	0.07245	1.909000	0.39917	0.486000	0.27676	0.344000	0.21773	TTT	.	.		0.388	BIRC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464357.1	NM_033341		T	53793261	A	T	53793261	3	4	344	1	0	0	0	0	1	0	0	0	1440	101	4	4	347	4	BIRC8	19	53793261	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	52251	53793261	5335722	1297	48660										
DPRX	503834	hgsc.bcm.edu	37	chr19	54139945	54139945	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	caaccgccaataccagagggTggggtctccaccagtgtcgg	13	13	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:54139945T>A	ENST00000376650.1	+	3	330	c.279T>A	c.(277-279)ggT>ggA	p.G93G		NM_001012728.1	NP_001012746.1	A6NFQ7	DPRX_HUMAN	divergent-paired related homeobox	93					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.G93G(1)		endometrium(4)|large_intestine(1)|lung(7)	12	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.013)		TACCAGAGGGTGGGGTCTCCA	0.512																																					p.G93G		Atlas-SNP	.											DPRX,NS,carcinoma,0,1	DPRX	34	.	1	Substitution - coding silent(1)	endometrium(1)	c.T279A						.						97	87	91					19																	54139945		2203	4300	6503	SO:0001819	synonymous_variant	503834	exon3			AGAGGGTGGGGTC		CCDS33103.1	19q13.42	2011-06-20			ENSG00000204595	ENSG00000204595		"Homeoboxes / PRD class"	32166	protein-coding gene	gene with protein product		611165					Standard	NM_001012728		Approved		uc002qcf.1	A6NFQ7		ENST00000376650.1:c.279T>A	chr19.hg19:g.54139945T>A		98.0	0.0		65.0	25.0	NM_001012728		Silent	SNP	ENST00000376650.1	hg19	CCDS33103.1																																																																																			.	.		0.512	DPRX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409880.1	NM_001012728		A	54139945	T	A	54139945	2	1	344	1	0	0	0	0	0	0	0	1	4740	1683	59	4		4	DPRX	19	54139945	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	346684	54139945	4989038	1298	48661										
PRKCG	5582	hgsc.bcm.edu	37	chr19	54401219	54401219	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tctcctttccacagcgggtgCggatgggcccctcttcctct	10	16	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:54401219C>A	ENST00000263431.3	+	10	1228	c.946C>A	c.(946-948)Cgg>Agg	p.R316R	PRKCG_ENST00000542049.1_Silent_p.R203R|PRKCG_ENST00000540413.1_Silent_p.R316R|PRKCG_ENST00000536044.1_Nonsense_Mutation_p.C286*	NM_002739.3	NP_002730.1	P05129	KPCG_HUMAN	protein kinase C, gamma	316				RVRM -> VSRT (in Ref. 5; AAA60102). {ECO:0000305}.	activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cell death (GO:0008219)|chemosensory behavior (GO:0007635)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein ubiquitination (GO:0031397)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of mismatch repair (GO:0032425)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to morphine (GO:0043278)|response to pain (GO:0048265)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic membrane (GO:0097060)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(4)|ovary(2)|pancreas(2)|skin(1)	10	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)	Tamoxifen(DB00675)	ACAGCGGGTGCGGATGGGccc	0.587																																					p.R316R		Atlas-SNP	.											.	PRKCG	246	.	0			c.C946A						.						108	111	110					19																	54401219		2203	4300	6503	SO:0001819	synonymous_variant	5582	exon10			CGGGTGCGGATGG	M13977	CCDS12867.1	19q13.4	2014-09-17			ENSG00000126583	ENSG00000126583	2.7.11.1		9402	protein-coding gene	gene with protein product	"PKC-gamma"	176980		PKCG, SCA14		8432525, 3755548	Standard	NM_002739		Approved	PKCC, MGC57564	uc002qcq.1	P05129	OTTHUMG00000064846	ENST00000263431.3:c.946C>A	chr19.hg19:g.54401219C>A		57.0	0.0		38.0	22.0	NM_002739	B7Z8Q0	Silent	SNP	ENST00000263431.3	hg19	CCDS12867.1	.	.	.	.	.	.	.	.	.	.	C	38	7.112960	0.98070	.	.	ENSG00000126583	ENST00000536044	.	.	.	5.06	5.06	0.68205	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.26408	T	0.33	.	14.2693	0.66143	0.0:1.0:0.0:0.0	.	.	.	.	X	286	.	ENSP00000440541:C286X	C	+	3	2	PRKCG	59093031	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	1.618000	0.36954	2.530000	0.85305	0.484000	0.47621	TGC	.	.		0.587	PRKCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139233.3	NM_002739		A	54401219	C	A	54401219	2	1	344	1	0	0	0	0	0	0	0	1	12524	759	27	1		1	PRKCG	19	54401219	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	261274	54401219	4727764	1299	48662										
CACNG7	59284	hgsc.bcm.edu	37	chr19	54444786	54444786	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcaacgacgaggtcatgaacAggcccagcagctctgagcag	12	12	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:54444786A>C	ENST00000391767.1	+	5	699	c.487A>C	c.(487-489)Agg>Cgg	p.R163R	CACNG7_ENST00000468076.1_3'UTR|CACNG7_ENST00000391766.1_Silent_p.R163R|CACNG7_ENST00000222212.2_Silent_p.R163R			P62955	CCG7_HUMAN	calcium channel, voltage-dependent, gamma subunit 7	163					calcium ion transport (GO:0006816)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0711)		GGTCATGAACAGGCCCAGCAG	0.557																																					p.R163R		Atlas-SNP	.											.	CACNG7	58	.	0			c.A487C						.						161	137	145					19																	54444786		2203	4300	6503	SO:0001819	synonymous_variant	59284	exon4			ATGAACAGGCCCA	AF288387	CCDS12868.1	19q13.4	2008-05-02			ENSG00000105605	ENSG00000105605		"Calcium channel subunits"	13626	protein-coding gene	gene with protein product		606899				11170751	Standard	NM_031896		Approved		uc002qcr.2	P62955	OTTHUMG00000064852	ENST00000391767.1:c.487A>C	chr19.hg19:g.54444786A>C		67.0	0.0		55.0	30.0	NM_031896	Q52LL8|Q8VBX3|Q8WXS6|Q9BXT1	Silent	SNP	ENST00000391767.1	hg19	CCDS12868.1																																																																																			.	.		0.557	CACNG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139240.2			C	54444786	A	C	54444786	2	2	344	1	0	0	0	0	0	0	0	1	2564	179	7	5		5	CACNG7	19	54444786	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	43567	54444786	4684197	1300	48663										
NLRP2	55655	hgsc.bcm.edu	37	chr19	55497556	55497556	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cagctgatgctcatcggaacCtctgcctagctcttcgaggt	10	13	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:55497556C>A	ENST00000543010.1	+	8	2382	c.2239C>A	c.(2239-2241)Ctc>Atc	p.L747I	NLRP2_ENST00000448584.2_Missense_Mutation_p.L747I|NLRP2_ENST00000538819.1_Missense_Mutation_p.L723I|NLRP2_ENST00000263437.6_Missense_Mutation_p.L744I|NLRP2_ENST00000391721.4_Missense_Mutation_p.L723I|NLRP2_ENST00000339757.7_Missense_Mutation_p.L725I|NLRP2_ENST00000427260.2_Missense_Mutation_p.L724I|NLRP2_ENST00000537859.1_Missense_Mutation_p.L725I	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	747					positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|Pyrin domain binding (GO:0032090)			large_intestine(4)|liver(1)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	11			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		TCATCGGAACCTCTGCCTAGC	0.443																																					p.L747I		Atlas-SNP	.											.	NLRP2	161	.	0			c.C2239A						.						119	94	103					19																	55497556		2203	4300	6503	SO:0001583	missense	55655	exon8			CGGAACCTCTGCC	AK000517	CCDS12913.1, CCDS54318.1, CCDS54319.1	19q13.42	2008-02-05	2006-12-08	2006-12-08	ENSG00000022556	ENSG00000022556		"Nucleotide-binding domain and leucine rich repeat containing"	22948	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2"	609364	"NACHT, leucine rich repeat and PYD containing 2"	NALP2		12563287, 11270363	Standard	NM_001174081		Approved	FLJ20510, PYPAF2, NBS1, PAN1, CLR19.9	uc021vbq.1	Q9NX02	OTTHUMG00000167763	ENST00000543010.1:c.2239C>A	chr19.hg19:g.55497556C>A	ENSP00000445135:p.Leu747Ile	97.0	0.0		91.0	38.0	NM_017852	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Missense_Mutation	SNP	ENST00000543010.1	hg19	CCDS12913.1	.	.	.	.	.	.	.	.	.	.	C	8.799	0.932335	0.18131	.	.	ENSG00000022556	ENST00000543010;ENST00000391721;ENST00000339757;ENST00000448584;ENST00000537859;ENST00000427260;ENST00000538819;ENST00000263437	T;T;T;T;T;T;T;T	0.60171	0.21;0.21;0.21;0.21;0.21;0.21;0.21;0.21	2.65	-2.22	0.06952	.	0.768134	0.10716	N	0.642357	T	0.60599	0.2281	M	0.65975	2.015	0.09310	N	0.999997	P;D;P;D;P	0.58268	0.945;0.982;0.945;0.982;0.945	P;P;P;P;P	0.56751	0.643;0.805;0.643;0.805;0.643	T	0.51756	-0.8665	10	0.41790	T	0.15	.	3.3665	0.07206	0.2098:0.4303:0.0:0.3599	.	724;725;744;723;747	B4DZL7;Q9NX02-2;A8K9G6;Q9NX02-4;Q9NX02	.;.;.;.;NALP2_HUMAN	I	747;723;725;747;725;724;723;744	ENSP00000445135:L747I;ENSP00000375601:L723I;ENSP00000344074:L725I;ENSP00000409370:L747I;ENSP00000440601:L725I;ENSP00000402474:L724I;ENSP00000441133:L723I;ENSP00000263437:L744I	ENSP00000263437:L744I	L	+	1	0	NLRP2	60189368	0.041000	0.20044	0.014000	0.15608	0.008000	0.06430	-0.144000	0.10280	-0.652000	0.05408	-0.312000	0.09012	CTC	.	.		0.443	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852		A	55497556	C	A	55497556	3	1	344	1	0	0	0	0	1	0	0	0	10486	681	24	3	2265	3	NLRP2	19	55497556	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1052770	55497556	3631427	1301	48664										
NLRP2	55655	hgsc.bcm.edu	37	chr19	55505725	55505725	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcctgttgtgtttggatctgGggctgaatcacataggagtt	14	6	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:55505725G>T	ENST00000543010.1	+	11	2940	c.2797G>T	c.(2797-2799)Ggg>Tgg	p.G933W	NLRP2_ENST00000448584.2_Missense_Mutation_p.G933W|NLRP2_ENST00000538819.1_Missense_Mutation_p.G909W|NLRP2_ENST00000263437.6_Missense_Mutation_p.G930W|NLRP2_ENST00000391721.4_Missense_Mutation_p.G909W|NLRP2_ENST00000339757.7_Missense_Mutation_p.G911W|NLRP2_ENST00000427260.2_Missense_Mutation_p.G910W|NLRP2_ENST00000537859.1_Missense_Mutation_p.G911W	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	933					positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|Pyrin domain binding (GO:0032090)			large_intestine(4)|liver(1)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	11			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		TTTGGATCTGGGGCTGAATCA	0.443																																					p.G933W		Atlas-SNP	.											.	NLRP2	161	.	0			c.G2797T						.						197	169	179					19																	55505725		2203	4300	6503	SO:0001583	missense	55655	exon11			GATCTGGGGCTGA	AK000517	CCDS12913.1, CCDS54318.1, CCDS54319.1	19q13.42	2008-02-05	2006-12-08	2006-12-08	ENSG00000022556	ENSG00000022556		"Nucleotide-binding domain and leucine rich repeat containing"	22948	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2"	609364	"NACHT, leucine rich repeat and PYD containing 2"	NALP2		12563287, 11270363	Standard	NM_001174081		Approved	FLJ20510, PYPAF2, NBS1, PAN1, CLR19.9	uc021vbq.1	Q9NX02	OTTHUMG00000167763	ENST00000543010.1:c.2797G>T	chr19.hg19:g.55505725G>T	ENSP00000445135:p.Gly933Trp	107.0	0.0		95.0	52.0	NM_017852	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Missense_Mutation	SNP	ENST00000543010.1	hg19	CCDS12913.1	.	.	.	.	.	.	.	.	.	.	G	12.39	1.922669	0.33908	.	.	ENSG00000022556	ENST00000543010;ENST00000391721;ENST00000339757;ENST00000448584;ENST00000537859;ENST00000427260;ENST00000538819;ENST00000263437	T;T;T;T;T;T;T;T	0.55052	0.54;0.54;0.54;0.54;0.54;0.54;0.54;0.54	2.48	1.43	0.22495	.	.	.	.	.	T	0.69196	0.3084	M	0.84948	2.725	0.09310	N	0.999998	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.997;0.999;0.998;0.999;0.998	T	0.54186	-0.8331	9	0.42905	T	0.14	.	5.1988	0.15252	0.1695:0.0:0.8305:0.0	.	910;911;930;909;933	B4DZL7;Q9NX02-2;A8K9G6;Q9NX02-4;Q9NX02	.;.;.;.;NALP2_HUMAN	W	933;909;911;933;911;910;909;930	ENSP00000445135:G933W;ENSP00000375601:G909W;ENSP00000344074:G911W;ENSP00000409370:G933W;ENSP00000440601:G911W;ENSP00000402474:G910W;ENSP00000441133:G909W;ENSP00000263437:G930W	ENSP00000263437:G930W	G	+	1	0	NLRP2	60197537	0.981000	0.34729	0.147000	0.22382	0.012000	0.07955	0.923000	0.28757	0.595000	0.29777	0.561000	0.74099	GGG	.	.		0.443	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852		T	55505725	G	T	55505725	3	4	344	1	0	0	0	0	1	0	0	0	10486	1232	43	3	2835	3	NLRP2	19	55505725	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	8169	55505725	3623258	1302	48665										
NLRP2	55655	hgsc.bcm.edu	37	chr19	55505788	55505788	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aggctttgaggaaaccactgTgcaacttgagatgtctgtgg	13	7	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:55505788T>C	ENST00000543010.1	+	11	3003	c.2860T>C	c.(2860-2862)Tgc>Cgc	p.C954R	NLRP2_ENST00000448584.2_Missense_Mutation_p.C954R|NLRP2_ENST00000538819.1_Missense_Mutation_p.C930R|NLRP2_ENST00000263437.6_Missense_Mutation_p.C951R|NLRP2_ENST00000391721.4_Missense_Mutation_p.C930R|NLRP2_ENST00000339757.7_Missense_Mutation_p.C932R|NLRP2_ENST00000427260.2_Missense_Mutation_p.C931R|NLRP2_ENST00000537859.1_Missense_Mutation_p.C932R	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	954					positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|Pyrin domain binding (GO:0032090)			large_intestine(4)|liver(1)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	11			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		GAAACCACTGTGCAACTTGAG	0.413																																					p.C954R		Atlas-SNP	.											.	NLRP2	161	.	0			c.T2860C						.						180	150	161					19																	55505788		2203	4300	6503	SO:0001583	missense	55655	exon11			CCACTGTGCAACT	AK000517	CCDS12913.1, CCDS54318.1, CCDS54319.1	19q13.42	2008-02-05	2006-12-08	2006-12-08	ENSG00000022556	ENSG00000022556		"Nucleotide-binding domain and leucine rich repeat containing"	22948	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2"	609364	"NACHT, leucine rich repeat and PYD containing 2"	NALP2		12563287, 11270363	Standard	NM_001174081		Approved	FLJ20510, PYPAF2, NBS1, PAN1, CLR19.9	uc021vbq.1	Q9NX02	OTTHUMG00000167763	ENST00000543010.1:c.2860T>C	chr19.hg19:g.55505788T>C	ENSP00000445135:p.Cys954Arg	84.0	0.0		87.0	44.0	NM_017852	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Missense_Mutation	SNP	ENST00000543010.1	hg19	CCDS12913.1	.	.	.	.	.	.	.	.	.	.	T	12.32	1.901200	0.33535	.	.	ENSG00000022556	ENST00000543010;ENST00000391721;ENST00000339757;ENST00000448584;ENST00000537859;ENST00000427260;ENST00000538819;ENST00000263437	T;T;T;T;T;T;T;T	0.52526	0.66;0.66;0.66;0.66;0.66;0.66;0.66;0.66	2.47	2.47	0.30058	.	.	.	.	.	T	0.71022	0.3291	M	0.92691	3.335	0.09310	N	0.999991	D;D;D;D;D	0.89917	0.999;1.0;0.996;1.0;0.999	D;D;D;D;D	0.80764	0.985;0.994;0.969;0.994;0.985	T	0.57849	-0.7740	9	0.62326	D	0.03	.	6.8412	0.23963	0.0:0.0:0.0:1.0	.	931;932;951;930;954	B4DZL7;Q9NX02-2;A8K9G6;Q9NX02-4;Q9NX02	.;.;.;.;NALP2_HUMAN	R	954;930;932;954;932;931;930;951	ENSP00000445135:C954R;ENSP00000375601:C930R;ENSP00000344074:C932R;ENSP00000409370:C954R;ENSP00000440601:C932R;ENSP00000402474:C931R;ENSP00000441133:C930R;ENSP00000263437:C951R	ENSP00000263437:C951R	C	+	1	0	NLRP2	60197600	0.027000	0.19231	0.011000	0.14972	0.176000	0.22953	1.154000	0.31688	1.370000	0.46153	0.454000	0.30748	TGC	.	.		0.413	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852		C	55505788	T	C	55505788	3	2	344	1	0	0	0	0	1	0	0	0	10486	1696	59	2	2898	2	NLRP2	19	55505788	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	63	55505788	3623195	1303	48666										
GP6	51206	hgsc.bcm.edu	37	chr19	55538983	55538983	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agggggtcgctgggggctgaCcacaggtatgggtccctgct	18	10	0	1	rs41301959		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:55538983C>A	ENST00000417454.1	-	4	600	c.573G>T	c.(571-573)tgG>tgT	p.W191C	GP6_ENST00000333884.2_Missense_Mutation_p.W191C|CTC-550B14.7_ENST00000593060.1_RNA|CTC-550B14.7_ENST00000586961.1_RNA|CTC-550B14.7_ENST00000586845.1_RNA|GP6_ENST00000310373.3_Missense_Mutation_p.W191C|CTC-550B14.6_ENST00000585492.1_RNA	NM_016363.4	NP_057447	Q9HCN6	GPVI_HUMAN	glycoprotein VI (platelet)	191	Ig-like C2-type 2.				blood coagulation (GO:0007596)|enzyme linked receptor protein signaling pathway (GO:0007167)|leukocyte migration (GO:0050900)|platelet activation (GO:0030168)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	collagen binding (GO:0005518)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19			BRCA - Breast invasive adenocarcinoma(297;0.156)	GBM - Glioblastoma multiforme(193;0.0515)		TGGGGGCTGACCACAGGTATG	0.572																																					p.W191C		Atlas-SNP	.											.	GP6	55	.	0			c.G573T						.						54	60	58					19																	55538983		1952	4182	6134	SO:0001583	missense	51206	exon4			GGCTGACCACAGG	AB035073	CCDS42626.1, CCDS46184.1, CCDS58678.1	19q13.4	2013-01-29			ENSG00000088053	ENSG00000088053		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14388	protein-coding gene	gene with protein product		605546				11027634	Standard	NM_001083899		Approved	GPVI	uc002qil.3	Q9HCN6	OTTHUMG00000159709	ENST00000417454.1:c.573G>T	chr19.hg19:g.55538983C>A	ENSP00000394922:p.Trp191Cys	78.0	0.0		56.0	34.0	NM_016363	Q9HCN7|Q9UIF2	Missense_Mutation	SNP	ENST00000417454.1	hg19	CCDS46184.1	.	.	.	.	.	.	.	.	.	.	C	14.61	2.585543	0.46110	.	.	ENSG00000088053	ENST00000417454;ENST00000310373;ENST00000333884	T;T;T	0.00902	5.56;5.56;5.56	3.99	3.99	0.46301	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.07188	0.0182	M	0.92077	3.27	0.49915	D	0.999839	D;D;D	0.89917	0.999;1.0;1.0	P;D;D	0.77004	0.892;0.983;0.989	T	0.00409	-1.1757	9	0.66056	D	0.02	.	11.8426	0.52364	0.0:1.0:0.0:0.0	.	191;191;191	Q9HCN6-2;Q9HCN6-3;Q9HCN6	.;.;GPVI_HUMAN	C	191	ENSP00000394922:W191C;ENSP00000308782:W191C;ENSP00000334552:W191C	ENSP00000308782:W191C	W	-	3	0	GP6	60230795	0.998000	0.40836	0.998000	0.56505	0.153000	0.21895	2.109000	0.41863	2.262000	0.75019	0.555000	0.69702	TGG	.	.		0.572	GP6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357006.1			A	55538983	C	A	55538983	3	1	344	1	0	0	0	0	1	0	0	0	6592	508	18	3	1309	3	GP6	19	55538983	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	33195	55538983	3590000	1304	48667										
RDH13	112724	hgsc.bcm.edu	37	chr19	55556516	55556516	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggcactttcagcccaaagccTccgggccacctcctcatcct	7	19	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:55556516T>C	ENST00000415061.3	-	7	1065	c.922A>G	c.(922-924)Agg>Ggg	p.R308G	CTC-550B14.7_ENST00000593060.1_RNA|CTC-550B14.7_ENST00000586961.1_RNA|CTC-550B14.7_ENST00000586845.1_RNA|RDH13_ENST00000396247.3_Missense_Mutation_p.R237G|CTC-550B14.6_ENST00000585492.1_RNA|RDH13_ENST00000592423.1_5'Flank	NM_001145971.1	NP_001139443.1	Q8NBN7	RDH13_HUMAN	retinol dehydrogenase 13 (all-trans/9-cis)	308					eye photoreceptor cell development (GO:0042462)|response to high light intensity (GO:0009644)|retina layer formation (GO:0010842)	mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)			endometrium(2)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	12			BRCA - Breast invasive adenocarcinoma(297;0.199)	GBM - Glioblastoma multiforme(193;0.0504)	Vitamin A(DB00162)	GCCCAAAGCCTCCGGGCCACC	0.627																																					p.R308G		Atlas-SNP	.											.	RDH13	43	.	0			c.A922G						.						29	34	32					19																	55556516		1881	4102	5983	SO:0001583	missense	112724	exon7			AAAGCCTCCGGGC		CCDS42627.1, CCDS54320.1	19q13.42	2011-09-14	2006-05-09			ENSG00000160439	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	19978	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 7C, member 3"		"retinol dehydrogenase 13 (all-trans and 9-cis)"			12226107, 19027726	Standard	NM_138412		Approved	SDR7C3	uc002qio.3	Q8NBN7		ENST00000415061.3:c.922A>G	chr19.hg19:g.55556516T>C	ENSP00000391121:p.Arg308Gly	119.0	0.0		80.0	21.0	NM_001145971	Q6UX79|Q96G88	Missense_Mutation	SNP	ENST00000415061.3	hg19	CCDS54320.1	.	.	.	.	.	.	.	.	.	.	T	11.54	1.669286	0.29604	.	.	ENSG00000160439	ENST00000415061;ENST00000396247	T;T	0.68624	-0.34;-0.34	4.61	2.46	0.29980	NAD(P)-binding domain (1);	0.095561	0.64402	D	0.000001	T	0.60599	0.2281	M	0.70903	2.155	0.29053	N	0.884387	P	0.38922	0.651	B	0.33521	0.165	T	0.59595	-0.7425	10	0.62326	D	0.03	.	10.0938	0.42462	0.0:0.0:0.3226:0.6773	.	308	Q8NBN7	RDH13_HUMAN	G	308;237	ENSP00000391121:R308G;ENSP00000379547:R237G	ENSP00000379547:R237G	R	-	1	2	RDH13	60248328	0.800000	0.28916	0.988000	0.46212	0.593000	0.36681	1.257000	0.32932	0.342000	0.23796	-0.940000	0.02684	AGG	.	.		0.627	RDH13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451470.1	NM_138412		C	55556516	T	C	55556516	3	2	344	1	0	0	0	0	1	0	0	0	13207	1550	54	2	77	2	RDH13	19	55556516	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	17533	55556516	3572467	1305	48668										
SYT5	6861	hgsc.bcm.edu	37	chr19	55689571	55689571	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggctgggccacaccttgtctAtgtaactctggcccagcccc	10	16	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:55689571A>G	ENST00000354308.3	-	3	614	c.245T>C	c.(244-246)aTa>aCa	p.I82T	SYT5_ENST00000590851.1_Intron|SYT5_ENST00000537500.1_Missense_Mutation_p.I82T|CTD-2587H24.5_ENST00000591665.1_RNA	NM_003180.2	NP_003171.2	O00445	SYT5_HUMAN	synaptotagmin V	82					calcium ion-dependent exocytosis (GO:0017156)|energy reserve metabolic process (GO:0006112)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|dense core granule (GO:0031045)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|metal ion binding (GO:0046872)|transporter activity (GO:0005215)			kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	18			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0452)		CACCTTGTCTATGTAACTCTG	0.642																																					p.I82T		Atlas-SNP	.											.	SYT5	45	.	0			c.T245C						.						22	21	22					19																	55689571		2198	4300	6498	SO:0001583	missense	6861	exon3			TTGTCTATGTAAC	X96783	CCDS12919.1, CCDS74455.1	19q13.42	2014-07-02			ENSG00000129990	ENSG00000129990		"Synaptotagmins"	11513	protein-coding gene	gene with protein product	"synaptotagmin 5"	600782				9177789	Standard	XM_006723338		Approved		uc002qjn.1	O00445	OTTHUMG00000180669	ENST00000354308.3:c.245T>C	chr19.hg19:g.55689571A>G	ENSP00000346265:p.Ile82Thr	37.0	0.0		21.0	13.0	NM_003180	B3KWJ8|B7Z300|Q86X72	Missense_Mutation	SNP	ENST00000354308.3	hg19	CCDS12919.1	.	.	.	.	.	.	.	.	.	.	A	8.450	0.852859	0.17106	.	.	ENSG00000129990	ENST00000537500;ENST00000354308	T;T	0.52057	0.68;0.68	4.06	4.06	0.47325	.	0.379657	0.29799	N	0.011178	T	0.20577	0.0495	N	0.03608	-0.345	0.37593	D	0.920254	B;B	0.34015	0.435;0.0	B;B	0.29353	0.101;0.004	T	0.18999	-1.0319	10	0.09338	T	0.73	.	12.7052	0.57058	1.0:0.0:0.0:0.0	.	82;82	Q4FD32;O00445	.;SYT5_HUMAN	T	82	ENSP00000442896:I82T;ENSP00000346265:I82T	ENSP00000346265:I82T	I	-	2	0	SYT5	60381383	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.733000	0.55029	1.797000	0.52628	0.459000	0.35465	ATA	.	.		0.642	SYT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452501.1	NM_003180		G	55689571	A	G	55689571	3	3	344	1	0	0	0	0	1	0	0	0	15492	449	16	2	943	2	SYT5	19	55689571	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	133055	55689571	3439412	1306	48669										
ZNF471	57573	hgsc.bcm.edu	37	chr19	57036782	57036782	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcatgcatcactcactcagcAtcaaagagtacattctggag	7	11	6	1	rs372005205		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:57036782A>C	ENST00000308031.5	+	5	1479	c.1346A>C	c.(1345-1347)cAt>cCt	p.H449P	ZNF471_ENST00000593197.1_Intron|ZNF471_ENST00000591537.1_3'UTR	NM_020813.2	NP_065864.2	Q9BX82	ZN471_HUMAN	zinc finger protein 471	449					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(8)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0307)		CTCACTCAGCATCAAAGAGTA	0.393																																					p.H449P	Colon(65;957 1402 6678 10163)|Esophageal Squamous(159;2295 2541 15408 21211)	Atlas-SNP	.											.	ZNF471	99	.	0			c.A1346C						.						94	91	92					19																	57036782		2203	4300	6503	SO:0001583	missense	57573	exon5			CTCAGCATCAAAG	AB037817	CCDS12945.1	19q13.43	2013-01-08				ENSG00000196263		"Zinc fingers, C2H2-type", "-"	23226	protein-coding gene	gene with protein product						10718198	Standard	NM_020813		Approved	KIAA1396, Z1971	uc002qnh.3	Q9BX82		ENST00000308031.5:c.1346A>C	chr19.hg19:g.57036782A>C	ENSP00000309161:p.His449Pro	91.0	0.0		38.0	32.0	NM_020813	B4DF32|O75260|Q08AD6|Q08AD7|Q8N3V1|Q9P2F1	Missense_Mutation	SNP	ENST00000308031.5	hg19	CCDS12945.1	.	.	.	.	.	.	.	.	.	.	A	16.94	3.260819	0.59431	.	.	ENSG00000196263	ENST00000308031	D	0.86865	-2.18	3.66	3.66	0.41972	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.95130	0.8422	H	0.96861	3.895	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	D	0.95741	0.8783	9	0.87932	D	0	.	11.4245	0.50003	1.0:0.0:0.0:0.0	.	449	Q9BX82	ZN471_HUMAN	P	449	ENSP00000309161:H449P	ENSP00000309161:H449P	H	+	2	0	ZNF471	61728594	0.866000	0.29940	0.707000	0.30419	0.951000	0.60555	3.671000	0.54576	1.536000	0.49237	0.379000	0.24179	CAT	.	.		0.393	ZNF471-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458405.1	NM_020813		C	57036782	A	C	57036782	3	2	344	1	0	0	0	0	1	0	0	0	17945	217	8	5	1360	5	ZNF471	19	57036782	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1347211	57036782	2092201	1307	48670										
ZNF71	58491	hgsc.bcm.edu	37	chr19	57132817	57132817	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccgcggggagatgcaggtgcAgagtgggagccattgggaat	19	7	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:57132817A>T	ENST00000328070.6	+	3	396	c.162A>T	c.(160-162)gcA>gcT	p.A54A		NM_021216.4	NP_067039.1	Q9NQZ8	ZNF71_HUMAN	zinc finger protein 71	54					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			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)		ATGCAGGTGCAGAGTGGGAGC	0.617																																					p.A54A		Atlas-SNP	.											.	ZNF71	69	.	0			c.A162T						.						43	42	43					19																	57132817		2203	4300	6503	SO:0001819	synonymous_variant	58491	exon3			AGGTGCAGAGTGG	X60074	CCDS12947.1	19q13.4	2013-01-08	2006-05-12			ENSG00000197951		"Zinc fingers, C2H2-type"	13141	protein-coding gene	gene with protein product		194545	"zinc finger protein 71 (Cos26)"			1639391	Standard	NM_021216		Approved	Cos26, EZFIT	uc002qnm.4	Q9NQZ8		ENST00000328070.6:c.162A>T	chr19.hg19:g.57132817A>T		125.0	0.0		42.0	37.0	NM_021216	Q15919|Q9UC09|Q9UQD3	Silent	SNP	ENST00000328070.6	hg19	CCDS12947.1																																																																																			.	.		0.617	ZNF71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459798.2	NM_021216		T	57132817	A	T	57132817	2	4	344	1	0	0	0	0	0	0	0	1	18129	175	7	4		4	ZNF71	19	57132817	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	96035	57132817	1996166	1308	48671										
ZNF460	10794	hgsc.bcm.edu	37	chr19	57803168	57803168	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccacactggagagaagccctAtgagtgtttacagtgtggaa	12	8	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:57803168A>G	ENST00000360338.3	+	3	1581	c.1259A>G	c.(1258-1260)tAt>tGt	p.Y420C	ZNF460_ENST00000537645.1_Missense_Mutation_p.Y379C	NM_006635.3	NP_006626.3	Q14592	ZN460_HUMAN	zinc finger protein 460	420					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		GAGAAGCCCTATGAGTGTTTA	0.463																																					p.Y420C		Atlas-SNP	.											.	ZNF460	59	.	0			c.A1259G						.						71	73	72					19																	57803168		2203	4300	6503	SO:0001583	missense	10794	exon3			AGCCCTATGAGTG	X78931	CCDS12949.1	19q13.4	2013-01-08				ENSG00000197714		"Zinc fingers, C2H2-type", "-"	21628	protein-coding gene	gene with protein product		604755	"zinc finger protein 272"	ZNF272		15004467	Standard	NM_006635		Approved	HZF8	uc002qog.2	Q14592		ENST00000360338.3:c.1259A>G	chr19.hg19:g.57803168A>G	ENSP00000353491:p.Tyr420Cys	91.0	0.0		54.0	51.0	NM_006635	A4FU64|B4DNX9|Q2VPC7|Q6VSF8	Missense_Mutation	SNP	ENST00000360338.3	hg19	CCDS12949.1	.	.	.	.	.	.	.	.	.	.	A	11.64	1.698945	0.30142	.	.	ENSG00000197714	ENST00000537645;ENST00000360338	T;T	0.25414	1.8;1.8	1.68	0.52	0.17040	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.29749	0.0743	M	0.84219	2.685	0.09310	N	1	P	0.52061	0.95	B	0.43809	0.432	T	0.27400	-1.0075	9	0.87932	D	0	.	3.0136	0.06052	0.5806:0.259:0.1604:0.0	.	420	Q14592	ZN460_HUMAN	C	379;420	ENSP00000446167:Y379C;ENSP00000353491:Y420C	ENSP00000353491:Y420C	Y	+	2	0	ZNF460	62494980	0.003000	0.15002	0.144000	0.22314	0.803000	0.45373	0.730000	0.26043	0.080000	0.16959	0.528000	0.53228	TAT	.	.		0.463	ZNF460-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465727.1	NM_006635		G	57803168	A	G	57803168	3	3	344	1	0	0	0	0	1	0	0	0	17939	449	16	2	1269	2	ZNF460	19	57803168	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	670351	57803168	1325815	1309	48672										
ZNF549	256051	hgsc.bcm.edu	37	chr19	58048776	58048776	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcagaaaccttatacgtctgTggccagtgggaaatggtttt	12	7	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:58048776T>G	ENST00000376233.3	+	4	585	c.404T>G	c.(403-405)gTg>gGg	p.V135G	ZNF549_ENST00000602149.1_Intron|ZNF550_ENST00000601415.1_Intron|ZNF549_ENST00000240719.3_Missense_Mutation_p.V122G|ZNF549_ENST00000594943.1_Intron	NM_001199295.1	NP_001186224	Q6P9A3	ZN549_HUMAN	zinc finger protein 549	135	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	21		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TATACGTCTGTGGCCAGTGGG	0.473																																					p.V135G		Atlas-SNP	.											.	ZNF549	118	.	0			c.T404G						.						122	103	109					19																	58048776		2203	4300	6503	SO:0001583	missense	256051	exon4			CGTCTGTGGCCAG	AK092236	CCDS12952.1, CCDS56106.1	19q13.43	2013-01-08				ENSG00000121406		"Zinc fingers, C2H2-type", "-"	26632	protein-coding gene	gene with protein product						12477932	Standard	NM_153263		Approved	FLJ34917	uc002qpb.2	Q6P9A3		ENST00000376233.3:c.404T>G	chr19.hg19:g.58048776T>G	ENSP00000365407:p.Val135Gly	159.0	0.0		93.0	68.0	NM_001199295	B3KV91|O43336|Q8NAR4	Missense_Mutation	SNP	ENST00000376233.3	hg19	CCDS56106.1	.	.	.	.	.	.	.	.	.	.	T	0.003	-2.424625	0.00186	.	.	ENSG00000121406	ENST00000240719;ENST00000376233	T;T	0.59364	0.27;0.27	2.28	-3.41	0.04839	Krueppel-associated box (1);	.	.	.	.	T	0.15998	0.0385	N	0.00595	-1.35	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.19095	-1.0316	9	0.11182	T	0.66	.	1.9729	0.03409	0.1366:0.1345:0.1793:0.5496	.	135;122	Q6P9A3;Q6P9A3-2	ZN549_HUMAN;.	G	122;135	ENSP00000240719:V122G;ENSP00000365407:V135G	ENSP00000240719:V122G	V	+	2	0	ZNF549	62740588	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.957000	0.01521	-0.862000	0.04089	-1.122000	0.02009	GTG	.	.		0.473	ZNF549-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466780.1	NM_153263		G	58048776	T	G	58048776	3	3	344	1	0	0	0	0	1	0	0	0	17996	1696	59	5	375	5	ZNF549	19	58048776	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	245608	58048776	1080207	1310	48673										
ZSCAN18	65982	hgsc.bcm.edu	37	chr19	58598367	58598367	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgagggtcctctggaaaggaCttcagcttctgaaacattag	11	8	3	2	rs368736992	byFrequency	TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:58598367C>G	ENST00000240727.6	-	5	1050	c.651G>C	c.(649-651)aaG>aaC	p.K217N	ZSCAN18_ENST00000601144.1_Missense_Mutation_p.K217N|ZSCAN18_ENST00000600404.1_Missense_Mutation_p.K273N|ZSCAN18_ENST00000421612.2_Missense_Mutation_p.K82N	NM_023926.4	NP_076415.3	Q8TBC5	ZSC18_HUMAN	zinc finger and SCAN domain containing 18	217					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|skin(3)	19		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.114)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)		CTGGAAAGGACTTCAGCTTCT	0.632																																					p.K273N		Atlas-SNP	.											.	ZSCAN18	104	.	0			c.G819C						.						60	53	55					19																	58598367		2203	4300	6503	SO:0001583	missense	65982	exon5			AAAGGACTTCAGC	AY280799, AY279352	CCDS12971.1, CCDS46214.1, CCDS46215.1	19q13.43	2013-01-09	2007-02-20	2007-02-20		ENSG00000121413		"-", "Zinc fingers, C2H2-type"	21037	protein-coding gene	gene with protein product			"zinc finger protein 447"	ZNF447			Standard	NM_001145542		Approved	FLJ12895	uc010yht.1	Q8TBC5		ENST00000240727.6:c.651G>C	chr19.hg19:g.58598367C>G	ENSP00000240727:p.Lys217Asn	27.0	0.0		17.0	16.0	NM_001145542	B4DG23|E9PBI0|Q9BRK7|Q9H9A0	Missense_Mutation	SNP	ENST00000240727.6	hg19	CCDS12971.1	.	.	.	.	.	.	.	.	.	.	C	7.607	0.674005	0.14841	.	.	ENSG00000121413	ENST00000433686;ENST00000240727;ENST00000421612	T;T	0.02656	4.52;4.21	3.06	2.0	0.26442	.	0.923172	0.08891	N	0.878662	T	0.01870	0.0059	N	0.08118	0	0.09310	N	1	P;D;P;P	0.54964	0.675;0.969;0.782;0.675	B;B;B;B	0.42959	0.228;0.403;0.279;0.145	T	0.49634	-0.8919	10	0.38643	T	0.18	-0.1177	5.4555	0.16588	0.0:0.8352:0.0:0.1648	.	273;82;217;217	B4DG23;E9PBI0;Q8TBC5-2;Q8TBC5	.;.;.;ZSC18_HUMAN	N	273;217;82	ENSP00000240727:K217N;ENSP00000392653:K82N	ENSP00000240727:K217N	K	-	3	2	ZSCAN18	63290179	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.295000	0.19065	0.807000	0.34208	0.561000	0.74099	AAG	.	.		0.632	ZSCAN18-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466706.1	NM_023926		G	58598367	C	G	58598367	3	3	344	1	0	0	0	0	1	0	0	0	18245	564	20	4	893	4	ZSCAN18	19	58598367	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	549591	58598367	530616	1311	48674										
ZSCAN18	65982	hgsc.bcm.edu	37	chr19	58601546	58601546	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tggtctcgggttcttcctgcTggactccggctgctgacccc	12	15	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr19:58601546T>A	ENST00000240727.6	-	2	488	c.89A>T	c.(88-90)cAg>cTg	p.Q30L	ZSCAN18_ENST00000601144.1_Missense_Mutation_p.Q30L|ZSCAN18_ENST00000600404.1_Missense_Mutation_p.Q86L|ZSCAN18_ENST00000421612.2_Intron	NM_023926.4	NP_076415.3	Q8TBC5	ZSC18_HUMAN	zinc finger and SCAN domain containing 18	30					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|skin(3)	19		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.114)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)		TTCTTCCTGCTGGACTCCGGC	0.647																																					p.Q86L		Atlas-SNP	.											.	ZSCAN18	104	.	0			c.A257T						.						36	40	39					19																	58601546		2203	4300	6503	SO:0001583	missense	65982	exon2			TCCTGCTGGACTC	AY280799, AY279352	CCDS12971.1, CCDS46214.1, CCDS46215.1	19q13.43	2013-01-09	2007-02-20	2007-02-20		ENSG00000121413		"-", "Zinc fingers, C2H2-type"	21037	protein-coding gene	gene with protein product			"zinc finger protein 447"	ZNF447			Standard	NM_001145542		Approved	FLJ12895	uc010yht.1	Q8TBC5		ENST00000240727.6:c.89A>T	chr19.hg19:g.58601546T>A	ENSP00000240727:p.Gln30Leu	215.0	1.0		81.0	62.0	NM_001145542	B4DG23|E9PBI0|Q9BRK7|Q9H9A0	Missense_Mutation	SNP	ENST00000240727.6	hg19	CCDS12971.1	.	.	.	.	.	.	.	.	.	.	T	12.02	1.813444	0.32053	.	.	ENSG00000121413	ENST00000433686;ENST00000240727	T	0.01998	4.51	3.52	-2.2	0.06994	.	.	.	.	.	T	0.01254	0.0041	N	0.24115	0.695	0.18873	N	0.999984	B;B;B;B	0.18310	0.027;0.0;0.011;0.006	B;B;B;B	0.12837	0.004;0.001;0.008;0.004	T	0.49062	-0.8978	9	0.08837	T	0.75	-1.0345	1.0985	0.01679	0.1836:0.1323:0.3748:0.3093	.	86;100;30;30	B4DG23;Q6ZMK6;Q8TBC5-2;Q8TBC5	.;.;.;ZSC18_HUMAN	L	86;30	ENSP00000240727:Q30L	ENSP00000240727:Q30L	Q	-	2	0	ZSCAN18	63293358	0.002000	0.14202	0.007000	0.13788	0.042000	0.13812	0.430000	0.21428	-0.638000	0.05509	0.379000	0.24179	CAG	.	.		0.647	ZSCAN18-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466706.1	NM_023926		A	58601546	T	A	58601546	3	1	344	1	0	0	0	0	1	0	0	0	18245	1580	55	4	1467	4	ZSCAN18	19	58601546	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	3179	58601546	527437	1312	48675										
C20orf54	113278	hgsc.bcm.edu	37	chr20	744623	744623	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgcttccattccggggagggCggacaccaaagctctgggaa	14	11	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr20:744623C>A	ENST00000217254.7	-	3	833	c.592G>T	c.(592-594)Gcc>Tcc	p.A198S	SLC52A3_ENST00000473664.1_Intron|SLC52A3_ENST00000381944.3_Missense_Mutation_p.A198S	NM_033409.3	NP_212134.3	Q9NQ40	S52A3_HUMAN	solute carrier family 52 (riboflavin transporter), member 3	198					cellular response to heat (GO:0034605)|riboflavin metabolic process (GO:0006771)|riboflavin transport (GO:0032218)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	riboflavin transporter activity (GO:0032217)										CCGGGGAGGGCGGACACCAAA	0.567																																					p.A198S		Atlas-SNP	.											.	.	.	.	0			c.G592T						.						26	24	24					20																	744623		2197	4294	6491	SO:0001583	missense	113278	exon3			GGAGGGCGGACAC	AL118502	CCDS13007.1	20p13	2013-07-17	2013-07-17	2012-02-29	ENSG00000101276	ENSG00000101276		"Solute carriers"	16187	protein-coding gene	gene with protein product	"hypothetical protein LOC113278"	613350	"chromosome 20 open reading frame 54"	C20orf54		11780052, 19122205	Standard	NM_033409		Approved	bA371L19.1, hRFT2, RFVT3	uc002wed.4	Q9NQ40	OTTHUMG00000031647	ENST00000217254.7:c.592G>T	chr20.hg19:g.744623C>A	ENSP00000217254:p.Ala198Ser	52.0	0.0		63.0	17.0	NM_033409	A8K6P1|Q5W1A0|Q5W1A1|Q8NCL7|Q96GD5	Missense_Mutation	SNP	ENST00000217254.7	hg19	CCDS13007.1	.	.	.	.	.	.	.	.	.	.	C	0.299	-0.975106	0.02215	.	.	ENSG00000101276	ENST00000217254;ENST00000381944	T;T	0.73258	-0.73;-0.73	2.92	-2.63	0.06133	.	4.686180	0.00999	N	0.003646	T	0.46795	0.1411	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42189	-0.9466	10	0.08837	T	0.75	.	7.6215	0.28187	0.0:0.3991:0.0:0.6009	.	198;198	Q9NQ40-2;Q9NQ40	.;RFT2_HUMAN	S	198	ENSP00000217254:A198S;ENSP00000371370:A198S	ENSP00000217254:A198S	A	-	1	0	C20orf54	692623	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.441000	0.02409	-0.612000	0.05701	-0.254000	0.11334	GCC	.	.		0.567	SLC52A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077482.2	NM_033409		A	744623	C	A	744623	3	1	344	1	0	0	0	0	1	0	0	0	2116	768	27	1	829	1	C20orf54	20	744623	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10		744623	62280897	1313	48676										
SIRPB1	10326	hgsc.bcm.edu	37	chr20	1551660	1551660	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aagctgtttctgtccgggacAcatttccattctccaaccag	7	13	2	0	rs201191774		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr20:1551660A>T	ENST00000381605.4	-	4	939	c.875T>A	c.(874-876)gTg>gAg	p.V292E	SIRPB1_ENST00000262929.5_Intron|RP4-576H24.4_ENST00000564763.1_Intron|SIRPB1_ENST00000381603.3_Intron	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1	292	Ig-like C1-type 2.				cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				central_nervous_system(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	31						TGTCCGGGACACATTTCCATT	0.557																																					p.V292E		Atlas-SNP	.											.	SIRPB1	83	.	0			c.T875A						.						187	169	175					20																	1551660		2203	4300	6503	SO:0001583	missense	10326	exon4			CGGGACACATTTC	Y10376	CCDS13019.1, CCDS42850.1, CCDS46571.1	20p13	2013-01-11			ENSG00000101307	ENSG00000101307		"Signal-regulatory proteins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C1-set domain containing"	15928	protein-coding gene	gene with protein product		603889				9062191, 16339511	Standard	NM_001083910		Approved	SIRP-BETA-1, CD172b	uc010gai.3	O00241	OTTHUMG00000031676	ENST00000381605.4:c.875T>A	chr20.hg19:g.1551660A>T	ENSP00000371018:p.Val292Glu	96.0	0.0		145.0	40.0	NM_006065	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Missense_Mutation	SNP	ENST00000381605.4	hg19	CCDS13019.1	.	.	.	.	.	.	.	.	.	.	.	6.022	0.372502	0.11409	.	.	ENSG00000101307	ENST00000381605	T	0.02258	4.37	2.39	2.39	0.29439	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	1.188170	0.06119	N	0.668564	T	0.02418	0.0074	N	0.25890	0.77	0.19775	N	0.999951	P	0.39964	0.697	B	0.42138	0.377	T	0.43750	-0.9372	10	0.13853	T	0.58	.	6.5862	0.22622	1.0:0.0:0.0:0.0	.	292	O00241	SIRB1_HUMAN	E	292	ENSP00000371018:V292E	ENSP00000371018:V292E	V	-	2	0	SIRPB1	1499660	0.000000	0.05858	0.009000	0.14445	0.026000	0.11368	0.313000	0.19415	1.095000	0.41419	0.260000	0.18958	GTG	.	A|1.000;G|0.000		0.557	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065		T	1551660	A	T	1551660	3	4	344	1	0	0	0	0	1	0	0	0	14348	159	6	4	329	4	SIRPB1	20	1551660	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	807037	1551660	61473860	1314	48677										
C20orf141	128653	hgsc.bcm.edu	37	chr20	2796253	2796253	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agtcagggggccggtgaaggTcctggacagcaggaggctct	18	9	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr20:2796253T>A	ENST00000380589.4	+	2	504	c.330T>A	c.(328-330)ggT>ggA	p.G110G	TMEM239_ENST00000380585.1_5'Flank|C20orf141_ENST00000603872.1_Silent_p.G110G|TMEM239_ENST00000380593.4_Intron|TMEM239_ENST00000361033.1_5'Flank|TMEM239_ENST00000554164.1_Intron	NM_080739.2	NP_542777.1	Q9NUB4	CT141_HUMAN	chromosome 20 open reading frame 141	110	Leu-rich.					integral component of membrane (GO:0016021)				endometrium(4)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)	10						CCGGTGAAGGTCCTGGACAGC	0.627																																					p.G110G		Atlas-SNP	.											.	C20orf141	21	.	0			c.T330A						.						45	44	44					20																	2796253		2203	4300	6503	SO:0001819	synonymous_variant	128653	exon2			TGAAGGTCCTGGA		CCDS13034.1	20p13	2012-10-30			ENSG00000258713	ENSG00000258713			16134	protein-coding gene	gene with protein product							Standard	NM_001256538		Approved	dJ860F19.4	uc002wgw.3	Q9NUB4	OTTHUMG00000031707	ENST00000380589.4:c.330T>A	chr20.hg19:g.2796253T>A		87.0	0.0		77.0	30.0	NM_080739		Silent	SNP	ENST00000380589.4	hg19	CCDS13034.1																																																																																			.	.		0.627	C20orf141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077644.2	NM_080739		A	2796253	T	A	2796253	2	1	344	1	0	0	0	0	0	0	0	1	2091	1654	58	4		4	C20orf141	20	2796253	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1244593	2796253	60229267	1315	48678										
DDRGK1	65992	hgsc.bcm.edu	37	chr20	3180750	3180750	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cacgttcagcctcctctgccTggagagaggtcttcataggg	12	12	4	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr20:3180750T>G	ENST00000354488.3	-	4	466		c.e4-2		DDRGK1_ENST00000380201.2_Splice_Site	NM_023935.1	NP_076424.1	Q96HY6	DDRGK_HUMAN	DDRGK domain containing 1							endoplasmic reticulum (GO:0005783)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|skin(2)|urinary_tract(1)	7						CTCCTCTGCCTGGAGAGAGGT	0.637																																					.		Atlas-SNP	.											.	DDRGK1	21	.	0			c.409-2A>C						.						72	58	62					20																	3180750		2203	4299	6502	SO:0001630	splice_region_variant	65992	exon5			TCTGCCTGGAGAG	AL121891	CCDS13050.1	20p13	2011-08-18	2008-10-03	2008-10-03	ENSG00000198171	ENSG00000198171			16110	protein-coding gene	gene with protein product	"Dashurin"		"chromosome 20 open reading frame 116"	C20orf116		20036718, 20228063, 21494687	Standard	NM_023935		Approved	dJ1187M17.3	uc002wic.3	Q96HY6	OTTHUMG00000031732	ENST00000354488.3:c.409-2A>C	chr20.hg19:g.3180750T>G		62.0	0.0		71.0	29.0	NM_023935	A6NIU5|C9JSZ5|Q9BW47	Splice_Site	SNP	ENST00000354488.3	hg19	CCDS13050.1	.	.	.	.	.	.	.	.	.	.	T	13.63	2.294045	0.40594	.	.	ENSG00000198171	ENST00000354488;ENST00000380213;ENST00000380201	.	.	.	5.35	5.35	0.76521	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.7287	0.51724	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	DDRGK1	3128750	1.000000	0.71417	0.907000	0.35723	0.377000	0.30045	4.510000	0.60455	2.025000	0.59659	0.533000	0.62120	.	.	.		0.637	DDRGK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077709.2	NM_023935	Intron	G	3180750	T	G	3180750	5	3	344	1	0	0	0	0	0	0	1	0	4340	1594	55	5	561	5	DDRGK1	20	3180750	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	384497	3180750	59844770	1316	48679										
SMOX	54498	hgsc.bcm.edu	37	chr20	4168039	4168039	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gagatgtaccgagacctcttCcagcaggggacctgagggct	14	11	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr20:4168039C>T	ENST00000305958.4	+	7	1878	c.1653C>T	c.(1651-1653)ttC>ttT	p.F551F	SMOX_ENST00000379460.2_Silent_p.F551F|SMOX_ENST00000339123.6_Silent_p.F498F|SMOX_ENST00000278795.3_Silent_p.F528F|SMOX_ENST00000346595.2_Silent_p.F186F	NM_175839.2	NP_787033.1	Q9NWM0	SMOX_HUMAN	spermine oxidase	551					cellular nitrogen compound metabolic process (GO:0034641)|oxidation-reduction process (GO:0055114)|polyamine biosynthetic process (GO:0006596)|polyamine catabolic process (GO:0006598)|polyamine metabolic process (GO:0006595)|small molecule metabolic process (GO:0044281)|spermine catabolic process (GO:0046208)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	N1-acetylspermine:oxygen oxidoreductase (N1-acetylspermidine-forming) activity (GO:0052895)|norspermine:oxygen oxidoreductase activity (GO:0052894)|polyamine oxidase activity (GO:0046592)|spermine:oxygen oxidoreductase (spermidine-forming) activity (GO:0052901)			breast(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(7)|lung(5)|skin(2)|urinary_tract(1)	26					Spermine(DB00127)	GAGACCTCTTCCAGCAGGGGA	0.632																																					p.F581F		Atlas-SNP	.											.	SMOX	119	.	0			c.C1743T						.						62	56	58					20																	4168039		2203	4300	6503	SO:0001819	synonymous_variant	54498	exon8			CCTCTTCCAGCAG	AK000753	CCDS13075.1, CCDS13076.1, CCDS13077.1, CCDS13078.1, CCDS74702.1	20p13	2003-10-15	2003-10-15	2003-10-15	ENSG00000088826	ENSG00000088826			15862	protein-coding gene	gene with protein product		615854	"chromosome 20 open reading frame 16"	C20orf16		11454677, 12398765	Standard	NM_175839		Approved	FLJ20746, dJ779E11.1, PAO, PAOh1, MGC1010, SMO	uc002wkp.3	Q9NWM0	OTTHUMG00000031777	ENST00000305958.4:c.1653C>T	chr20.hg19:g.4168039C>T		107.0	0.0		72.0	33.0	NM_001270691	A2A2P5|A2A2P6|A8BE87|D3DVZ4|Q5TE26|Q5TE27|Q6UY28|Q8IX00|Q96LC3|Q96LC4|Q96QT3|Q9BW38|Q9H6H1|Q9NP51|Q9NPY1|Q9NPY2	Silent	SNP	ENST00000305958.4	hg19	CCDS13075.1																																																																																			.	.		0.632	SMOX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077806.1	NM_175842		T	4168039	C	T	4168039	2	4	344	1	0	0	0	0	0	0	0	1	14818	854	30	3		3	SMOX	20	4168039	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	987289	4168039	58857481	1317	48680										
SLC23A2	9962	hgsc.bcm.edu	37	chr20	4913132	4913132	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agaaagctgggtgctttgccTcgtcttcgtatttgccttct	10	10	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr20:4913132T>A	ENST00000379333.1	-	3	469	c.77A>T	c.(76-78)gAg>gTg	p.E26V	SLC23A2_ENST00000424750.2_Missense_Mutation_p.E26V|SLC23A2_ENST00000338244.1_Missense_Mutation_p.E26V|SLC23A2_ENST00000468355.1_5'UTR	NM_203327.1	NP_976072.1	Q9UGH3	S23A2_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 2	26					L-ascorbic acid metabolic process (GO:0019852)|L-ascorbic acid transport (GO:0015882)|molecular hydrogen transport (GO:0015993)|nucleobase transport (GO:0015851)|nucleobase-containing compound metabolic process (GO:0006139)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|transepithelial L-ascorbic acid transport (GO:0070904)|vitamin metabolic process (GO:0006766)|vitamin transmembrane transport (GO:0035461)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-ascorbate:sodium symporter activity (GO:0008520)|L-ascorbic acid transporter activity (GO:0015229)|nucleobase transmembrane transporter activity (GO:0015205)|sodium-dependent L-ascorbate transmembrane transporter activity (GO:0070890)|sodium-dependent multivitamin transmembrane transporter activity (GO:0008523)			endometrium(1)|kidney(3)|large_intestine(9)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						GTGCTTTGCCTCGTCTTCGTA	0.403																																					p.E26V		Atlas-SNP	.											.	SLC23A2	62	.	0			c.A77T						.						217	179	192					20																	4913132		2203	4300	6503	SO:0001583	missense	9962	exon3			TTTGCCTCGTCTT	AF058319	CCDS13085.1	20p13	2013-07-18	2013-07-18	2003-03-21	ENSG00000089057	ENSG00000089057		"Solute carriers"	10973	protein-coding gene	gene with protein product		603791	"solute carrier family 23 (nucleobase transporters), member 1"	SLC23A1		9804989, 10331392	Standard	NM_005116		Approved	SVCT2, KIAA0238, YSPL2	uc002wlh.1	Q9UGH3	OTTHUMG00000031793	ENST00000379333.1:c.77A>T	chr20.hg19:g.4913132T>A	ENSP00000368637:p.Glu26Val	81.0	0.0		83.0	30.0	NM_203327	B4DJZ1|Q8WWR4|Q92512|Q96D54|Q9UNU1|Q9UP85	Missense_Mutation	SNP	ENST00000379333.1	hg19	CCDS13085.1	.	.	.	.	.	.	.	.	.	.	T	15.01	2.706180	0.48412	.	.	ENSG00000089057	ENST00000379333;ENST00000338244;ENST00000424750	T;T;T	0.54866	0.55;0.55;0.55	5.14	5.14	0.70334	.	0.210797	0.43110	D	0.000613	T	0.38852	0.1056	N	0.19112	0.55	0.24168	N	0.995639	P;P;P	0.48911	0.917;0.596;0.917	B;B;B	0.41135	0.348;0.143;0.348	T	0.38993	-0.9635	10	0.66056	D	0.02	-9.7838	12.9483	0.58386	0.0:0.0:0.0:1.0	.	26;26;26	B4DJZ1;A0MSJ5;Q9UGH3	.;.;S23A2_HUMAN	V	26	ENSP00000368637:E26V;ENSP00000344322:E26V;ENSP00000406601:E26V	ENSP00000344322:E26V	E	-	2	0	SLC23A2	4861132	0.989000	0.36119	0.146000	0.22360	0.764000	0.43329	4.687000	0.61708	1.954000	0.56735	0.450000	0.29827	GAG	.	.		0.403	SLC23A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077832.1			A	4913132	T	A	4913132	3	1	344	1	0	0	0	0	1	0	0	0	14478	1551	54	4	1935	4	SLC23A2	20	4913132	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	745093	4913132	58112388	1318	48681										
PLCB4	5332	hgsc.bcm.edu	37	chr20	9449299	9449299	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agccaagataaatctatcaaGaataaagcagaacgggaaag	9	6	2	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr20:9449299G>A	ENST00000378493.1	+	32	3309	c.3294G>A	c.(3292-3294)aaG>aaA	p.K1098K	PLCB4_ENST00000492632.1_3'UTR|PLCB4_ENST00000334005.3_Silent_p.K1098K|PLCB4_ENST00000378473.3_Silent_p.K1110K|PLCB4_ENST00000378501.2_Silent_p.K1098K|PLCB4_ENST00000278655.4_Silent_p.K1098K|PLCB4_ENST00000414679.2_Silent_p.K1110K			Q15147	PLCB4_HUMAN	phospholipase C, beta 4	1098					inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|smooth endoplasmic reticulum (GO:0005790)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(2)|breast(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(11)|liver(4)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(19)|upper_aerodigestive_tract(1)	87						AATCTATCAAGAATAAAGCAG	0.398																																					p.K1110K		Atlas-SNP	.											.	PLCB4	204	.	0			c.G3330A						.						122	114	117					20																	9449299		2203	4300	6503	SO:0001819	synonymous_variant	5332	exon35			TATCAAGAATAAA		CCDS13104.1, CCDS13105.1, CCDS54447.1	20p12	2008-03-18			ENSG00000101333	ENSG00000101333	3.1.4.11		9059	protein-coding gene	gene with protein product		600810				8530101	Standard	NM_000933		Approved		uc021wam.1	Q15147	OTTHUMG00000031853	ENST00000378493.1:c.3294G>A	chr20.hg19:g.9449299G>A		35.0	0.0		37.0	11.0	NM_001172646	B7ZLK6|E2QRH8|Q17R56|Q5JYS8|Q5JYS9|Q5JYT0|Q5JYT3|Q5JYT4|Q9BQW5|Q9BQW6|Q9BQW8|Q9UJQ2	Silent	SNP	ENST00000378493.1	hg19	CCDS13105.1																																																																																			.	.		0.398	PLCB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077948.2			A	9449299	G	A	9449299	2	1	344	1	0	0	0	0	0	0	0	1	12039	933	33	3		3	PLCB4	20	9449299	Silent	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	4536167	9449299	53576221	1319	48682										
PAK7	57144	hgsc.bcm.edu	37	chr20	9546811	9546811	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aggtgctggatgagaggctgAgggagctcaggtaggaagcc	19	6	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr20:9546811A>T	ENST00000378429.3	-	6	1757	c.1211T>A	c.(1210-1212)cTc>cAc	p.L404H	PAK7_ENST00000378423.1_Missense_Mutation_p.L404H|PAK7_ENST00000353224.5_Missense_Mutation_p.L404H	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	404	Linker.				apoptotic process (GO:0006915)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|learning (GO:0007612)|locomotory behavior (GO:0007626)|memory (GO:0007613)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(44)|ovary(2)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)	81			COAD - Colon adenocarcinoma(9;0.194)			TGAGAGGCTGAGGGAGCTCAG	0.637																																					p.L404H		Atlas-SNP	.											.	PAK7	194	.	0			c.T1211A						.						91	88	89					20																	9546811		2203	4300	6503	SO:0001583	missense	57144	exon5			AGGCTGAGGGAGC	AB033090	CCDS13107.1	20p12	2008-06-17	2008-06-17		ENSG00000101349	ENSG00000101349			15916	protein-coding gene	gene with protein product		608038	"p21(CDKN1A)-activated kinase 7"			11756552, 10574462	Standard	NM_020341		Approved	KIAA1264, PAK5	uc002wnk.2	Q9P286	OTTHUMG00000031857	ENST00000378429.3:c.1211T>A	chr20.hg19:g.9546811A>T	ENSP00000367686:p.Leu404His	67.0	0.0		46.0	21.0	NM_177990	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Missense_Mutation	SNP	ENST00000378429.3	hg19	CCDS13107.1	.	.	.	.	.	.	.	.	.	.	A	18.27	3.587403	0.66105	.	.	ENSG00000101349	ENST00000378429;ENST00000353224;ENST00000378423;ENST00000439520	T;T;T	0.34472	1.36;1.36;1.36	5.94	4.83	0.62350	.	0.103207	0.64402	D	0.000002	T	0.16471	0.0396	N	0.08118	0	0.49213	D	0.999767	P;P	0.51791	0.948;0.948	B;B	0.43155	0.41;0.41	T	0.02736	-1.1117	9	.	.	.	.	3.4129	0.07365	0.6842:0.0:0.3158:0.0	.	404;404	B0AZM9;Q9P286	.;PAK7_HUMAN	H	404;404;404;352	ENSP00000367686:L404H;ENSP00000322957:L404H;ENSP00000367679:L404H	.	L	-	2	0	PAK7	9494811	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	3.849000	0.55910	2.265000	0.75225	0.482000	0.46254	CTC	.	.		0.637	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1			T	9546811	A	T	9546811	3	4	344	1	0	0	0	0	1	0	0	0	11414	304	11	4	972	4	PAK7	20	9546811	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	97512	9546811	53478709	1320	48683										
PAK7	57144	hgsc.bcm.edu	37	chr20	9561478	9561478	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tggggtgggtgggctttcttTccttagggagttggagcgag	19	5	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr20:9561478T>C	ENST00000378429.3	-	5	850	c.304A>G	c.(304-306)Aaa>Gaa	p.K102E	PAK7_ENST00000378423.1_Missense_Mutation_p.K102E|PAK7_ENST00000353224.5_Missense_Mutation_p.K102E	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	102	Linker.				apoptotic process (GO:0006915)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|learning (GO:0007612)|locomotory behavior (GO:0007626)|memory (GO:0007613)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(44)|ovary(2)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)	81			COAD - Colon adenocarcinoma(9;0.194)			GGGCTTTCTTTCCTTAGGGAG	0.537																																					p.K102E		Atlas-SNP	.											.	PAK7	194	.	0			c.A304G						.						129	131	131					20																	9561478		2203	4300	6503	SO:0001583	missense	57144	exon4			TTTCTTTCCTTAG	AB033090	CCDS13107.1	20p12	2008-06-17	2008-06-17		ENSG00000101349	ENSG00000101349			15916	protein-coding gene	gene with protein product		608038	"p21(CDKN1A)-activated kinase 7"			11756552, 10574462	Standard	NM_020341		Approved	KIAA1264, PAK5	uc002wnk.2	Q9P286	OTTHUMG00000031857	ENST00000378429.3:c.304A>G	chr20.hg19:g.9561478T>C	ENSP00000367686:p.Lys102Glu	72.0	0.0		65.0	22.0	NM_177990	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Missense_Mutation	SNP	ENST00000378429.3	hg19	CCDS13107.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.934958	0.73442	.	.	ENSG00000101349	ENST00000378429;ENST00000353224;ENST00000378423;ENST00000439520	T;T;T	0.44083	0.93;0.93;0.93	5.82	5.82	0.92795	.	0.085006	0.85682	D	0.000000	T	0.42449	0.1203	L	0.55481	1.735	0.53688	D	0.999976	P;P	0.49090	0.842;0.919	B;B	0.42087	0.324;0.375	T	0.33369	-0.9871	9	.	.	.	.	16.1729	0.81831	0.0:0.0:0.0:1.0	.	102;102	B0AZM9;Q9P286	.;PAK7_HUMAN	E	102;102;102;50	ENSP00000367686:K102E;ENSP00000322957:K102E;ENSP00000367679:K102E	.	K	-	1	0	PAK7	9509478	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	6.231000	0.72307	2.214000	0.71695	0.533000	0.62120	AAA	.	.		0.537	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1			C	9561478	T	C	9561478	3	2	344	1	0	0	0	0	1	0	0	0	11414	1792	62	2	1883	2	PAK7	20	9561478	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	14667	9561478	53464042	1321	48684										
PAK7	57144	hgsc.bcm.edu	37	chr20	9624845	9624845	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tttggcctgttggccgtatcTgctaacaggctgtgccactg	12	11	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr20:9624845T>A	ENST00000378429.3	-	4	678	c.132A>T	c.(130-132)gcA>gcT	p.A44A	PAK7_ENST00000378423.1_Silent_p.A44A|PAK7_ENST00000353224.5_Silent_p.A44A	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	44	Linker.				apoptotic process (GO:0006915)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|learning (GO:0007612)|locomotory behavior (GO:0007626)|memory (GO:0007613)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.A44A(1)		NS(1)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(44)|ovary(2)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)	81			COAD - Colon adenocarcinoma(9;0.194)			TGGCCGTATCTGCTAACAGGC	0.542																																					p.A44A		Atlas-SNP	.											PAK7,mouth,carcinoma,0,1	PAK7	194	.	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.A132T						.						128	116	120					20																	9624845		2203	4300	6503	SO:0001819	synonymous_variant	57144	exon3			CGTATCTGCTAAC	AB033090	CCDS13107.1	20p12	2008-06-17	2008-06-17		ENSG00000101349	ENSG00000101349			15916	protein-coding gene	gene with protein product		608038	"p21(CDKN1A)-activated kinase 7"			11756552, 10574462	Standard	NM_020341		Approved	KIAA1264, PAK5	uc002wnk.2	Q9P286	OTTHUMG00000031857	ENST00000378429.3:c.132A>T	chr20.hg19:g.9624845T>A		107.0	0.0		87.0	35.0	NM_177990	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Silent	SNP	ENST00000378429.3	hg19	CCDS13107.1																																																																																			.	.		0.542	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1			A	9624845	T	A	9624845	2	1	344	1	0	0	0	0	0	0	0	1	11414	1567	55	4		4	PAK7	20	9624845	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	63367	9624845	53400675	1322	48685										
KIF16B	55614	hgsc.bcm.edu	37	chr20	16485049	16485049	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agcaagcagcgttttcagtcTggctatttcagctcgcagct	10	11	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr20:16485049T>A	ENST00000354981.2	-	10	1301	c.1144A>T	c.(1144-1146)Aga>Tga	p.R382*	KIF16B_ENST00000408042.1_Nonsense_Mutation_p.R382*|KIF16B_ENST00000355755.3_Nonsense_Mutation_p.R382*|KIF16B_ENST00000378003.2_5'UTR	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	382					ATP catabolic process (GO:0006200)|early endosome to late endosome transport (GO:0045022)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|formation of primary germ layer (GO:0001704)|Golgi to endosome transport (GO:0006895)|microtubule-based movement (GO:0007018)|receptor catabolic process (GO:0032801)|regulation of receptor recycling (GO:0001919)	early endosome (GO:0005769)|endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(24)|ovary(1)|prostate(15)|skin(3)|upper_aerodigestive_tract(2)	74						GTTTTCAGTCTGGCTATTTCA	0.398																																					p.R382X		Atlas-SNP	.											.	KIF16B	305	.	0			c.A1144T						.						229	211	217					20																	16485049		2203	4300	6503	SO:0001587	stop_gained	55614	exon10			TCAGTCTGGCTAT	AK000142	CCDS13122.1, CCDS56178.1	20p11.23	2008-03-03	2008-03-03	2008-03-03	ENSG00000089177	ENSG00000089177		"Kinesins"	15869	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 23"	C20orf23		16084724, 16782399	Standard	NM_024704		Approved	FLJ20135, dJ971B4.1, SNX23	uc010gci.2	Q96L93	OTTHUMG00000031927	ENST00000354981.2:c.1144A>T	chr20.hg19:g.16485049T>A	ENSP00000347076:p.Arg382*	143.0	0.0		114.0	51.0	NM_001199865	A6NKJ9|A7E2A8|B1AKG3|B1AKT7|C9JDN5|C9JI52|C9JSM8|C9JWJ7|Q2TBF5|Q5HYC0|Q5HYK1|Q5JWW3|Q5TFK5|Q86VL9|Q86YS5|Q8IYU0|Q9BQJ8|Q9BQM0|Q9BQM1|Q9BQM5|Q9H5U0|Q9HCI2|Q9NXN9	Nonsense_Mutation	SNP	ENST00000354981.2	hg19	CCDS13122.1	.	.	.	.	.	.	.	.	.	.	T	39	7.662869	0.98419	.	.	ENSG00000089177	ENST00000354981;ENST00000355755;ENST00000377997;ENST00000408042	.	.	.	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.7762	0.57451	0.0:0.0:0.1725:0.8275	.	.	.	.	X	382	.	ENSP00000347076:R382X	R	-	1	2	KIF16B	16433049	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.148000	0.50647	2.371000	0.80710	0.533000	0.62120	AGA	.	.		0.398	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683		A	16485049	T	A	16485049	4	1	344	1	0	0	0	0	0	1	0	0	8287	1588	55	4	2877	4	KIF16B	20	16485049	Nonsense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	6860204	16485049	46540471	1323	48686										
CST9	128822	hgsc.bcm.edu	37	chr20	23586297	23586297	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	actcaggacgcgcaacagccTgtaggcatgctcctccttgc	10	15	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr20:23586297T>G	ENST00000376971.3	-	1	216	c.205A>C	c.(205-207)Agg>Cgg	p.R69R		NM_001008693.2	NP_001008693.2	Q5W186	CST9_HUMAN	cystatin 9 (testatin)	69						extracellular region (GO:0005576)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			central_nervous_system(2)|large_intestine(4)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	12	Colorectal(13;0.0993)					CGCAACAGCCTGTAGGCATGC	0.517																																					p.R69R		Atlas-SNP	.											.	CST9	26	.	0			c.A205C						.						257	196	217					20																	23586297		2203	4300	6503	SO:0001819	synonymous_variant	128822	exon1			ACAGCCTGTAGGC	AF494536	CCDS33450.1	20p11.21	2012-08-14			ENSG00000173335	ENSG00000173335			13261	protein-coding gene	gene with protein product						20565543	Standard	NM_001008693		Approved	CLM, CTES7A	uc002wtl.3	Q5W186	OTTHUMG00000032076	ENST00000376971.3:c.205A>C	chr20.hg19:g.23586297T>G		107.0	0.0		121.0	56.0	NM_001008693	B2RP76|Q8TD53	Silent	SNP	ENST00000376971.3	hg19	CCDS33450.1																																																																																			.	.		0.517	CST9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078341.1	NM_001008693.1		G	23586297	T	G	23586297	2	3	344	1	0	0	0	0	0	0	0	1	3981	1579	55	5		5	CST9	20	23586297	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	7101248	23586297	39439223	1324	48687										
HM13	81502	hgsc.bcm.edu	37	chr20	30102430	30102430	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccaacagcactacgcggccgCcttccacgcccgagggcatc	10	19	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr20:30102430C>T	ENST00000340852.5	+	1	200	c.76C>T	c.(76-78)Cct>Tct	p.P26S	HM13_ENST00000398174.3_Missense_Mutation_p.P26S|HM13_ENST00000335574.5_Missense_Mutation_p.P26S|HM13_ENST00000376127.3_Missense_Mutation_p.P26S	NM_030789.2	NP_110416.1	Q8TCT9	HM13_HUMAN	histocompatibility (minor) 13	26					membrane protein proteolysis (GO:0033619)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	aspartic endopeptidase activity, intramembrane cleaving (GO:0042500)|peptidase activity (GO:0008233)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(2)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	12	all_cancers(5;3.44e-05)|Lung NSC(7;4.38e-06)|all_lung(7;7.65e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		all cancers(5;0.000479)|Colorectal(19;0.00202)|COAD - Colon adenocarcinoma(19;0.0264)			TACGCGGCCGCCTTCCACGCC	0.711																																					p.P26S		Atlas-SNP	.											.	HM13	52	.	0			c.C76T						.						11	12	11					20																	30102430		2170	4252	6422	SO:0001583	missense	81502	exon1			CGGCCGCCTTCCA	AL110115	CCDS13182.1, CCDS13183.1, CCDS42861.1	20q11.21	2012-02-21			ENSG00000101294	ENSG00000101294			16435	protein-coding gene	gene with protein product	"signal peptide peptidase beta", "presenilin-like protein 3", "intramembrane protease", "signal peptide peptidase like 1"	607106				12077416, 14704149	Standard	NM_030789		Approved	H13, dJ324O17.1, SPP, PSL3, IMP1, IMPAS, PSENL3, SPPL1	uc002wwc.3	Q8TCT9	OTTHUMG00000032175	ENST00000340852.5:c.76C>T	chr20.hg19:g.30102430C>T	ENSP00000343032:p.Pro26Ser	68.0	0.0		79.0	29.0	NM_178581	B2RAY5|E1P5L3|Q15K36|Q540H8|Q5JWP2|Q5JWP3|Q5JWP4|Q5JWP5|Q7Z4F2|Q86Y35|Q95H87|Q9H110|Q9H111	Missense_Mutation	SNP	ENST00000340852.5	hg19	CCDS13182.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.305057	0.81247	.	.	ENSG00000101294	ENST00000335574;ENST00000340852;ENST00000398174;ENST00000376127;ENST00000344042	T;T;T;T;T	0.23348	1.97;1.96;1.97;1.91;1.91	4.06	4.06	0.47325	.	0.234366	0.44902	D	0.000407	T	0.36248	0.0960	L	0.58510	1.815	0.39586	D	0.969503	P;D;D;D	0.59767	0.889;0.986;0.986;0.965	B;P;P;P	0.53593	0.444;0.73;0.73;0.647	T	0.26608	-1.0098	10	0.56958	D	0.05	-11.8579	11.4548	0.50176	0.0:0.8177:0.1822:0.0	.	26;26;26;26	Q8TCT9;Q8TCT9-4;Q8TCT9-2;Q8TCT9-5	HM13_HUMAN;.;.;.	S	26	ENSP00000335294:P26S;ENSP00000343032:P26S;ENSP00000381237:P26S;ENSP00000365296:P26S;ENSP00000341347:P26S	ENSP00000335294:P26S	P	+	1	0	HM13	29566091	1.000000	0.71417	0.999000	0.59377	0.965000	0.64279	2.071000	0.41500	2.091000	0.63221	0.555000	0.69702	CCT	.	.		0.711	HM13-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078527.2	NM_178580		T	30102430	C	T	30102430	3	4	344	1	0	0	0	0	1	0	0	0	7226	739	26	3	78	3	HM13	20	30102430	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	6516133	30102430	32923090	1325	48688										
FOXS1	2307	hgsc.bcm.edu	37	chr20	30432970	30432970	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tccacggcgtgccttggcggGgccccgggtgccctcagcac	15	17	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr20:30432970G>A	ENST00000375978.3	-	1	450	c.376C>T	c.(376-378)Ccc>Tcc	p.P126S		NM_004118.3	NP_004109.1	O43638	FOXS1_HUMAN	forkhead box S1	126					blood vessel development (GO:0001568)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|neuromuscular process controlling balance (GO:0050885)|positive regulation of multicellular organism growth (GO:0040018)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(3)|lung(3)|ovary(1)|urinary_tract(1)	9						GCCTTGGCGGGGCCCCGGGTG	0.706																																					p.P126S		Atlas-SNP	.											.	FOXS1	29	.	0			c.C376T						.						12	14	14					20																	30432970		2193	4281	6474	SO:0001583	missense	2307	exon1			TGGCGGGGCCCCG	AF042831	CCDS13192.1	20q11.1-q11.2	2008-04-10	2008-04-10	2008-04-10	ENSG00000179772	ENSG00000179772		"Forkhead boxes"	3735	protein-coding gene	gene with protein product		602939	"forkhead (Drosophila)-like 18", "forkhead-like 18 (Drosophila)"	FKHL18		9325056, 17062144	Standard	NM_004118		Approved	FREAC10	uc002wwt.1	O43638	OTTHUMG00000032183	ENST00000375978.3:c.376C>T	chr20.hg19:g.30432970G>A	ENSP00000365145:p.Pro126Ser	27.0	0.0		27.0	13.0	NM_004118	Q96D28	Missense_Mutation	SNP	ENST00000375978.3	hg19	CCDS13192.1	.	.	.	.	.	.	.	.	.	.	G	6.655	0.489429	0.12641	.	.	ENSG00000179772	ENST00000375978	D	0.93247	-3.19	4.5	1.14	0.20703	.	0.381500	0.18351	N	0.143881	D	0.83931	0.5361	L	0.27053	0.805	0.28440	N	0.916861	B	0.06786	0.001	B	0.06405	0.002	T	0.68439	-0.5408	10	0.12430	T	0.62	.	5.3393	0.15974	0.0996:0.0:0.4654:0.435	.	126	O43638	FOXS1_HUMAN	S	126	ENSP00000365145:P126S	ENSP00000365145:P126S	P	-	1	0	FOXS1	29896631	0.946000	0.32159	0.618000	0.29105	0.130000	0.20726	1.445000	0.35079	0.601000	0.29879	0.555000	0.69702	CCC	.	.		0.706	FOXS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078560.2	NM_004118		A	30432970	G	A	30432970	3	1	344	1	0	0	0	0	1	0	0	0	6043	1232	43	3	620	3	FOXS1	20	30432970	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	330540	30432970	32592550	1326	48689										
XKR7	343702	hgsc.bcm.edu	37	chr20	30585087	30585087	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgcggacagaggggcctgtcAtccggattgacttgcctcgc	14	12	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr20:30585087A>T	ENST00000562532.2	+	3	1741	c.1567A>T	c.(1567-1569)Atc>Ttc	p.I523F		NM_001011718.1	NP_001011718.1	Q5GH72	XKR7_HUMAN	XK, Kell blood group complex subunit-related family, member 7	523						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(19)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	34			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			GGGGCCTGTCATCCGGATTGA	0.642																																					p.I523F		Atlas-SNP	.											.	XKR7	62	.	0			c.A1567T						.						44	50	48					20																	30585087		2203	4299	6502	SO:0001583	missense	343702	exon3			CCTGTCATCCGGA	AY534245	CCDS33459.1	20q11.21	2014-07-16	2006-01-12		ENSG00000260903	ENSG00000260903			23062	protein-coding gene	gene with protein product			"X Kell blood group precursor-related family, member 7", "chromosome 20 open reading frame 159"	C20orf159			Standard	NM_001011718		Approved	dJ310O13.4	uc002wxe.3	Q5GH72	OTTHUMG00000032198	ENST00000562532.2:c.1567A>T	chr20.hg19:g.30585087A>T	ENSP00000477059:p.Ile523Phe	29.0	0.0		29.0	16.0	NM_001011718	Q9NUG5	Missense_Mutation	SNP	ENST00000562532.2	hg19	CCDS33459.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.184979	0.78677	.	.	ENSG00000101321	ENST00000217299	.	.	.	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	T	0.77772	0.4180	M	0.74467	2.265	0.58432	D	0.999999	D	0.76494	0.999	D	0.85130	0.997	T	0.80480	-0.1364	9	0.66056	D	0.02	-4.5707	13.404	0.60900	1.0:0.0:0.0:0.0	.	523	Q5GH72	XKR7_HUMAN	F	523	.	ENSP00000217299:I523F	I	+	1	0	XKR7	30048748	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.139000	0.94554	2.037000	0.60232	0.459000	0.35465	ATC	.	.		0.642	XKR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078597.3	NM_001011718		T	30585087	A	T	30585087	3	4	344	1	0	0	0	0	1	0	0	0	17451	217	8	4	1577	4	XKR7	20	30585087	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	152117	30585087	32440433	1327	48690										
PLUNC	51297	hgsc.bcm.edu	37	chr20	31827623	31827623	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggacagcataaaggtcactgAcccccagctgctggaacttg	11	12	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr20:31827623A>G	ENST00000354297.4	+	4	406	c.335A>G	c.(334-336)gAc>gGc	p.D112G	BPIFA1_ENST00000375413.4_Missense_Mutation_p.D112G|BPIFA1_ENST00000375422.2_Missense_Mutation_p.D112G	NM_130852.2	NP_570913.1	Q9NP55	BPIA1_HUMAN	BPI fold containing family A, member 1	112					antibacterial humoral response (GO:0019731)|innate immune response (GO:0045087)|multicellular organismal water homeostasis (GO:0050891)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|regulation of liquid surface tension (GO:0050828)|regulation of sodium ion transmembrane transport (GO:1902305)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	lipid binding (GO:0008289)										AAGGTCACTGACCCCCAGCTG	0.512																																					p.D112G		Atlas-SNP	.											.	.	.	.	0			c.A335G						.						174	163	167					20																	31827623		2203	4300	6503	SO:0001583	missense	51297	exon4			TCACTGACCCCCA	AB024937	CCDS13217.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000198183	ENSG00000198183		"BPI fold containing"	15749	protein-coding gene	gene with protein product		607412	"palate, lung and nasal epithelium carcinoma associated", "palate, lung and nasal epithelium associated"	PLUNC		11018263, 11251963, 21787333	Standard	NM_130852		Approved	LUNX, bA49G10.5, SPLUNC1	uc002wyv.3	Q9NP55	OTTHUMG00000032243	ENST00000354297.4:c.335A>G	chr20.hg19:g.31827623A>G	ENSP00000346251:p.Asp112Gly	104.0	0.0		104.0	34.0	NM_016583	A8K9R3|E1P5M9|Q9NZT0	Missense_Mutation	SNP	ENST00000354297.4	hg19	CCDS13217.1	.	.	.	.	.	.	.	.	.	.	A	11.82	1.752326	0.31046	.	.	ENSG00000198183	ENST00000375422;ENST00000354297;ENST00000375413;ENST00000544328	T;T;T	0.04317	3.65;3.65;3.65	5.44	5.44	0.79542	.	0.565880	0.18004	N	0.154800	T	0.05273	0.0140	L	0.29908	0.895	0.09310	N	1	B	0.09022	0.002	B	0.14578	0.011	T	0.26052	-1.0114	10	0.62326	D	0.03	-0.0574	11.8174	0.52218	1.0:0.0:0.0:0.0	.	112	Q9NP55	BPIA1_HUMAN	G	112;112;112;98	ENSP00000364571:D112G;ENSP00000346251:D112G;ENSP00000364562:D112G	ENSP00000346251:D112G	D	+	2	0	BPIFA1	31291284	0.137000	0.22531	0.058000	0.19502	0.678000	0.39670	4.007000	0.57093	2.288000	0.76882	0.533000	0.62120	GAC	.	.		0.512	BPIFA1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078667.2	NM_130852		G	31827623	A	G	31827623	3	3	344	1	0	0	0	0	1	0	0	0	12124	275	10	2	345	2	PLUNC	20	31827623	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1242536	31827623	31197897	1328	48691										
EDEM2	55741	hgsc.bcm.edu	37	chr20	33714169	33714169	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gggtgtagttccggatggctTtgttatactctgcagtgggg	16	6	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr20:33714169T>C	ENST00000374492.3	-	8	959	c.854A>G	c.(853-855)aAa>aGa	p.K285R	EDEM2_ENST00000374491.3_Missense_Mutation_p.K248R|EDEM2_ENST00000542871.1_Missense_Mutation_p.K9R|EDEM2_ENST00000540582.1_Missense_Mutation_p.K244R|EDEM2_ENST00000541621.1_Missense_Mutation_p.K64R	NM_018217.2	NP_060687.2	Q9BV94	EDEM2_HUMAN	ER degradation enhancer, mannosidase alpha-like 2	285					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	22			BRCA - Breast invasive adenocarcinoma(18;0.00936)			CCGGATGGCTTTGTTATACTC	0.517																																					p.K285R	Esophageal Squamous(51;906 1021 24535 36410 39145)	Atlas-SNP	.											.	EDEM2	46	.	0			c.A854G						.						159	144	149					20																	33714169		2203	4300	6503	SO:0001583	missense	55741	exon8			ATGGCTTTGTTAT	AK001645	CCDS13247.1, CCDS46592.1	20q11.22	2006-03-31	2006-03-31	2006-03-31	ENSG00000088298	ENSG00000088298			15877	protein-coding gene	gene with protein product		610302	"chromosome 20 open reading frame 31"	C20orf49, C20orf31		15537790, 15579471	Standard	NM_018217		Approved	FLJ10783, bA4204.1	uc002xbo.2	Q9BV94	OTTHUMG00000032322	ENST00000374492.3:c.854A>G	chr20.hg19:g.33714169T>C	ENSP00000363616:p.Lys285Arg	99.0	0.0		68.0	26.0	NM_018217	B4DTG9|Q6GU33|Q6IA89|Q6UWZ4|Q9H4U0|Q9H886|Q9NTL9|Q9NVE6	Missense_Mutation	SNP	ENST00000374492.3	hg19	CCDS13247.1	.	.	.	.	.	.	.	.	.	.	T	12.40	1.925567	0.34002	.	.	ENSG00000088298	ENST00000374491;ENST00000374492;ENST00000541621;ENST00000542871;ENST00000540582	T;T;T;T;T	0.72167	-0.63;-0.63;-0.63;-0.63;-0.63	5.18	5.18	0.71444	.	0.155762	0.56097	D	0.000030	T	0.62441	0.2428	L	0.41710	1.295	0.45554	D	0.998502	B;B;B;B	0.12630	0.006;0.0;0.002;0.001	B;B;B;B	0.14023	0.01;0.004;0.004;0.006	T	0.57757	-0.7756	10	0.27785	T	0.31	-13.361	15.0331	0.71723	0.0:0.0:0.0:1.0	.	244;64;248;285	F5GZ44;G3V1Q0;Q9BV94-2;Q9BV94	.;.;.;EDEM2_HUMAN	R	248;285;64;9;244	ENSP00000363615:K248R;ENSP00000363616:K285R;ENSP00000443528:K64R;ENSP00000441642:K9R;ENSP00000441548:K244R	ENSP00000363615:K248R	K	-	2	0	EDEM2	33177830	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.737000	0.38197	1.954000	0.56735	0.460000	0.39030	AAA	.	.		0.517	EDEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078842.2	NM_018217		C	33714169	T	C	33714169	3	2	344	1	0	0	0	0	1	0	0	0	4914	1841	64	2	898	2	EDEM2	20	33714169	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1886546	33714169	29311351	1329	48692										
MMP24	10893	hgsc.bcm.edu	37	chr20	33839777	33839777	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cgtaggcggagaaacaagcgCtatgccctgactggacagaa	13	10	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr20:33839777C>A	ENST00000246186.6	+	3	550	c.465C>A	c.(463-465)cgC>cgA	p.R155R	MMP24-AS1_ENST00000438751.1_RNA|EDEM2_ENST00000540582.1_Intron|MMP24-AS1_ENST00000433764.1_RNA|MMP24-AS1_ENST00000454184.1_RNA|MMP24-AS1_ENST00000456350.1_RNA|MMP24-AS1_ENST00000566203.2_RNA	NM_006690.3	NP_006681.1	Q9Y5R2	MMP24_HUMAN	matrix metallopeptidase 24 (membrane-inserted)	155					cell-cell adhesion (GO:0098609)|cell-cell adhesion mediated by cadherin (GO:0044331)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|glial cell differentiation (GO:0010001)|neuronal stem cell maintenance (GO:0097150)|positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)|trans-Golgi network membrane (GO:0032588)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|large_intestine(1)|lung(2)|prostate(2)|skin(5)	14			BRCA - Breast invasive adenocarcinoma(18;0.00252)		Marimastat(DB00786)	GAAACAAGCGCTATGCCCTGA	0.557																																					p.R155R		Atlas-SNP	.											.	MMP24	35	.	0			c.C465A						.						142	151	148					20																	33839777		2042	4192	6234	SO:0001819	synonymous_variant	10893	exon3			CAAGCGCTATGCC	AF131284	CCDS46593.1	20q11.2	2008-07-16	2005-08-08		ENSG00000125966	ENSG00000125966			7172	protein-coding gene	gene with protein product	"membrane-type 5 matrix metalloproteinase"	604871	"matrix metalloproteinase 24 (membrane-inserted)"			10363975	Standard	NM_006690		Approved	MT5-MMP	uc002xbu.2	Q9Y5R2	OTTHUMG00000032330	ENST00000246186.6:c.465C>A	chr20.hg19:g.33839777C>A		87.0	0.0		67.0	33.0	NM_006690	B7ZBG8|Q9H440	Silent	SNP	ENST00000246186.6	hg19	CCDS46593.1																																																																																			.	.		0.557	MMP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078851.4	NM_006690		A	33839777	C	A	33839777	2	1	344	1	0	0	0	0	0	0	0	1	9670	784	28	3		3	MMP24	20	33839777	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	125608	33839777	29185743	1330	48693										
CEP250	11190	hgsc.bcm.edu	37	chr20	34065725	34065725	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gagaaccagtctgtgtgcagCagaatggaggccgcagagca	15	9	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr20:34065725C>G	ENST00000397527.1	+	17	2613	c.1893C>G	c.(1891-1893)agC>agG	p.S631R	RP3-477O4.14_ENST00000453914.1_RNA|RP3-477O4.14_ENST00000444933.1_RNA|RP3-477O4.14_ENST00000416260.1_RNA|CEP250_ENST00000342580.4_Missense_Mutation_p.S631R	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	631	Gln/Glu-rich.				centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of centriole-centriole cohesion (GO:0030997)	centriole (GO:0005814)|centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)|spindle pole centrosome (GO:0031616)	protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			CTGTGTGCAGCAGAATGGAGG	0.512																																					p.S631R		Atlas-SNP	.											.	CEP250	141	.	0			c.C1893G						.						45	45	45					20																	34065725		2202	4297	6499	SO:0001583	missense	11190	exon17			GTGCAGCAGAATG	AF022655	CCDS13255.1	20q11.22	2014-02-20	2006-01-11	2006-01-11	ENSG00000126001	ENSG00000126001			1859	protein-coding gene	gene with protein product		609689	"centrosomal protein 2"	CEP2		9506584, 9647649	Standard	NM_007186		Approved	C-NAP1	uc021wco.1	Q9BV73	OTTHUMG00000032343	ENST00000397527.1:c.1893C>G	chr20.hg19:g.34065725C>G	ENSP00000380661:p.Ser631Arg	118.0	0.0		97.0	48.0	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Missense_Mutation	SNP	ENST00000397527.1	hg19	CCDS13255.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.79|13.79	2.341751|2.341751	0.41498|0.41498	.|.	.|.	ENSG00000126001|ENSG00000126001	ENST00000425096|ENST00000397527;ENST00000342580;ENST00000425934	.|T;T;T	.|0.24151	.|2.82;2.83;1.87	5.6|5.6	3.3|3.3	0.37823|0.37823	.|.	.|0.616834	.|0.16353	.|N	.|0.218126	T|T	0.18130|0.18130	0.0435|0.0435	L|L	0.36672|0.36672	1.1|1.1	0.29753|0.29753	N|N	0.836141|0.836141	.|B	.|0.10296	.|0.003	.|B	.|0.14023	.|0.01	T|T	0.14008|0.14008	-1.0488|-1.0488	5|10	.|0.19590	.|T	.|0.45	.|.	8.6188|8.6188	0.33849|0.33849	0.0:0.7125:0.164:0.1235|0.0:0.7125:0.164:0.1235	.|.	.|631	.|Q9BV73	.|CP250_HUMAN	E|R	145|631;631;630	.|ENSP00000380661:S631R;ENSP00000341541:S631R;ENSP00000413827:S630R	.|ENSP00000341541:S631R	Q|S	+|+	1|3	0|2	CEP250|CEP250	33529139|33529139	0.878000|0.878000	0.30173|0.30173	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	0.711000|0.711000	0.25764|0.25764	1.338000|1.338000	0.45544|0.45544	0.650000|0.650000	0.86243|0.86243	CAG|AGC	.	.		0.512	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186		G	34065725	C	G	34065725	3	3	344	1	0	0	0	0	1	0	0	0	3254	709	25	4	1947	4	CEP250	20	34065725	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	225948	34065725	28959795	1331	48694										
C20orf117	140710	hgsc.bcm.edu	37	chr20	35406236	35406236	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaggaagggcagcttctggcTctcttcccagctgctggggg	16	11	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr20:35406236T>C	ENST00000279034.6	-	15	3320		c.e15-2		SOGA1_ENST00000237536.4_3'UTR	NM_199181.2	NP_954650.2	O94964	SOGA1_HUMAN	suppressor of glucose, autophagy associated 1						insulin receptor signaling pathway (GO:0008286)|negative regulation of gluconeogenesis (GO:0045721)|regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				endometrium(5)|kidney(1)|lung(21)|urinary_tract(1)	28						AGCTTCTGGCTCTCTTCCCAG	0.592																																					.		Atlas-SNP	.											.	SOGA1	136	.	0			c.2994-2A>G						.						28	32	30					20																	35406236		1612	3572	5184	SO:0001630	splice_region_variant	140710	exon16			TCTGGCTCTCTTC	AK126630	CCDS46598.1, CCDS54459.1	20q11.23	2012-03-01	2012-02-27	2012-02-27	ENSG00000149639	ENSG00000149639			16111	protein-coding gene	gene with protein product	"suppressor of glucose by autophagy", "suppressor of glucose from autophagy"		"chromosome 20 open reading frame 117", "KIAA0889"	C20orf117, KIAA0889		20813965	Standard	NM_080627		Approved	dJ132F21.1, FLJ44670, SOGA	uc021wcx.1	O94964	OTTHUMG00000032395	ENST00000279034.6:c.2994-2A>G	chr20.hg19:g.35406236T>C		58.0	0.0		53.0	15.0	NM_199181	A6NK10|Q14DB2|Q5JW51|Q6ZTG8	Splice_Site	SNP	ENST00000279034.6	hg19	CCDS46598.1	.	.	.	.	.	.	.	.	.	.	T	15.09	2.731593	0.48939	.	.	ENSG00000149639	ENST00000279034	.	.	.	2.96	-0.626	0.11544	.	.	.	.	.	.	.	.	.	.	.	0.38337	D	0.943955	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.6122	0.17412	0.0:0.4509:0.0:0.5491	.	.	.	.	.	-1	.	.	.	-	.	.	KIAA0889	34839650	1.000000	0.71417	0.352000	0.25734	0.910000	0.53928	1.258000	0.32944	-0.014000	0.14175	-0.456000	0.05471	.	.	.		0.592	SOGA1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276634.3	NM_199181	Intron	C	35406236	T	C	35406236	5	2	344	1	0	0	0	0	0	0	1	0	2085	1565	54	2	62	2	C20orf117	20	35406236	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1340511	35406236	27619284	1332	48695										
C20orf117	140710	hgsc.bcm.edu	37	chr20	35423004	35423004	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggaagaaacagatttggttcTgcgaaggacagaggaggaaa	15	4	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr20:35423004T>A	ENST00000357779.3	-	14	3095		c.e14-2		SOGA1_ENST00000279034.6_Splice_Site|SOGA1_ENST00000456801.2_Splice_Site|SOGA1_ENST00000237536.4_Splice_Site			O94964	SOGA1_HUMAN	suppressor of glucose, autophagy associated 1						insulin receptor signaling pathway (GO:0008286)|negative regulation of gluconeogenesis (GO:0045721)|regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				endometrium(5)|kidney(1)|lung(21)|urinary_tract(1)	28						GATTTGGTTCTGCGAAGGACA	0.522																																					.		Atlas-SNP	.											.	SOGA1	136	.	0			c.2769-2A>T						.						67	67	67					20																	35423004		2010	4163	6173	SO:0001630	splice_region_variant	140710	exon15			TGGTTCTGCGAAG	AK126630	CCDS46598.1, CCDS54459.1	20q11.23	2012-03-01	2012-02-27	2012-02-27	ENSG00000149639	ENSG00000149639			16111	protein-coding gene	gene with protein product	"suppressor of glucose by autophagy", "suppressor of glucose from autophagy"		"chromosome 20 open reading frame 117", "KIAA0889"	C20orf117, KIAA0889		20813965	Standard	NM_080627		Approved	dJ132F21.1, FLJ44670, SOGA	uc021wcx.1	O94964	OTTHUMG00000032395	ENST00000357779.3:c.2769-2A>T	chr20.hg19:g.35423004T>A		77.0	0.0		66.0	35.0	NM_199181	A6NK10|Q14DB2|Q5JW51|Q6ZTG8	Splice_Site	SNP	ENST00000357779.3	hg19		.	.	.	.	.	.	.	.	.	.	T	13.94	2.386488	0.42308	.	.	ENSG00000149639	ENST00000237536;ENST00000279034;ENST00000456801;ENST00000357779	.	.	.	5.38	5.38	0.77491	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5192	0.67840	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	KIAA0889	34856418	1.000000	0.71417	0.992000	0.48379	0.552000	0.35366	7.489000	0.81451	2.254000	0.74563	0.533000	0.62120	.	.	.		0.522	SOGA1-201	KNOWN	basic	protein_coding	protein_coding		NM_199181	Intron	A	35423004	T	A	35423004	5	1	344	1	0	0	0	0	0	0	1	0	2085	1594	55	4	1574	4	C20orf117	20	35423004	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	16768	35423004	27602516	1333	48696										
LPIN3	64900	hgsc.bcm.edu	37	chr20	39978721	39978721	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agagctgagcggcccgagtcCtcagtggtccttgaaggcag	15	11	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr20:39978721C>G	ENST00000373257.3	+	7	877	c.786C>G	c.(784-786)tcC>tcG	p.S262S		NM_022896.1	NP_075047.1	Q9BQK8	LPIN3_HUMAN	lipin 3	262					fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(7)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		Myeloproliferative disorder(115;0.000739)				GGCCCGAGTCCTCAGTGGTCC	0.627																																					p.S262S		Atlas-SNP	.											.	LPIN3	69	.	0			c.C786G						.						25	20	22					20																	39978721		2201	4299	6500	SO:0001819	synonymous_variant	64900	exon7			CGAGTCCTCAGTG	AL132654	CCDS33469.1	20q11.2-q12	2006-04-04	2002-05-23		ENSG00000132793	ENSG00000132793			14451	protein-coding gene	gene with protein product		605520	"lipin 3-like"	LIPN3L		11138012	Standard	XM_005260515		Approved	SMP2	uc002xjx.3	Q9BQK8	OTTHUMG00000033056	ENST00000373257.3:c.786C>G	chr20.hg19:g.39978721C>G		82.0	0.0		81.0	29.0	NM_022896	B2RTT5|Q5TDB9|Q9NPY8|Q9UJE5	Silent	SNP	ENST00000373257.3	hg19	CCDS33469.1																																																																																			.	.		0.627	LPIN3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080393.1	NM_022896		G	39978721	C	G	39978721	2	3	344	1	0	0	0	0	0	0	0	1	8929	668	24	4		4	LPIN3	20	39978721	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	4555717	39978721	23046799	1334	48697										
STK4	6789	hgsc.bcm.edu	37	chr20	43607128	43607128	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tattcataaagagaccggccAgattgttgctattaagcaag	9	7	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr20:43607128A>T	ENST00000372806.3	+	3	256	c.161A>T	c.(160-162)cAg>cTg	p.Q54L	STK4_ENST00000499879.2_Missense_Mutation_p.Q54L|STK4_ENST00000372801.1_Missense_Mutation_p.Q54L|STK4_ENST00000396731.4_Missense_Mutation_p.Q54L	NM_006282.2	NP_006273.1	Q13043	STK4_HUMAN	serine/threonine kinase 4	54	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell differentiation involved in embryonic placenta development (GO:0060706)|cell morphogenesis (GO:0000902)|central nervous system development (GO:0007417)|endocardium development (GO:0003157)|hepatocyte apoptotic process (GO:0097284)|hippo signaling (GO:0035329)|intracellular signal transduction (GO:0035556)|keratinocyte differentiation (GO:0030216)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of organ growth (GO:0046621)|neural tube formation (GO:0001841)|patterning of blood vessels (GO:0001569)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|primitive hemopoiesis (GO:0060215)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(2)|lung(5)|ovary(1)|prostate(1)|skin(2)	20		Myeloproliferative disorder(115;0.0122)				GAGACCGGCCAGATTGTTGCT	0.403																																					p.Q54L	GBM(187;1039 2137 11798 21916 33213)	Atlas-SNP	.											.	STK4	84	.	0			c.A161T						.						81	82	82					20																	43607128		2203	4300	6503	SO:0001583	missense	6789	exon3			CCGGCCAGATTGT		CCDS13341.1	20q11.2-q13.2	2014-09-17			ENSG00000101109	ENSG00000101109			11408	protein-coding gene	gene with protein product	"mammalian sterile 20-like 1", "yeast Ste20-like", "kinase responsive to stress 2"	604965				8816758, 9545236, 11517310	Standard	NM_006282		Approved	MST1, KRS2, YSK3	uc002xnb.3	Q13043	OTTHUMG00000033059	ENST00000372806.3:c.161A>T	chr20.hg19:g.43607128A>T	ENSP00000361892:p.Gln54Leu	72.0	0.0		60.0	24.0	NM_006282	B2RCR8|Q15802|Q4G156|Q5H982|Q6PD60|Q9BR32|Q9NTZ4	Missense_Mutation	SNP	ENST00000372806.3	hg19	CCDS13341.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.304719	0.81247	.	.	ENSG00000101109	ENST00000372806;ENST00000396731;ENST00000372801;ENST00000499879	T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21	5.63	5.63	0.86233	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.054356	0.85682	D	0.000000	T	0.75824	0.3902	L	0.50993	1.605	0.58432	D	0.999998	D;B;B;B	0.56287	0.975;0.1;0.04;0.122	P;B;B;B	0.60473	0.875;0.039;0.046;0.106	T	0.77958	-0.2392	10	0.66056	D	0.02	.	15.8431	0.78864	1.0:0.0:0.0:0.0	.	54;54;54;54	F5H5B4;Q13043-2;A0PJ51;Q13043	.;.;.;STK4_HUMAN	L	54	ENSP00000361892:Q54L;ENSP00000379957:Q54L;ENSP00000361887:Q54L;ENSP00000443514:Q54L	ENSP00000361887:Q54L	Q	+	2	0	STK4	43040542	1.000000	0.71417	0.998000	0.56505	0.924000	0.55760	9.335000	0.96500	2.136000	0.66102	0.533000	0.62120	CAG	.	.		0.403	STK4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080401.4	NM_006282		T	43607128	A	T	43607128	3	4	344	1	0	0	0	0	1	0	0	0	15321	188	7	4	171	4	STK4	20	43607128	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3628407	43607128	19418392	1335	48698										
SEMG2	6407	hgsc.bcm.edu	37	chr20	43851485	43851485	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gagtatggccataaggaaaaTaaaatatcataccaatcttc	6	7	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr20:43851485T>C	ENST00000372769.3	+	2	1302	c.1212T>C	c.(1210-1212)aaT>aaC	p.N404N		NM_003008.2	NP_002999.1	Q02383	SEMG2_HUMAN	semenogelin II	404	4 X 60 AA tandem repeats, type I.|Repeat-rich region.				sexual reproduction (GO:0019953)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|secretory granule (GO:0030141)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(6)|lung(9)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Myeloproliferative disorder(115;0.0122)				ATAAGGAAAATAAAATATCAT	0.383																																					p.N404N		Atlas-SNP	.											.	SEMG2	92	.	0			c.T1212C						.						71	68	69					20																	43851485		2203	4300	6503	SO:0001819	synonymous_variant	6407	exon2			GGAAAATAAAATA		CCDS13346.1	20q12-q13.1	2008-07-02			ENSG00000124157	ENSG00000124157			10743	protein-coding gene	gene with protein product	"Semenogelin 2"	182141				1517240, 9523691	Standard	NM_003008		Approved	SGII	uc002xnk.3	Q02383	OTTHUMG00000032566	ENST00000372769.3:c.1212T>C	chr20.hg19:g.43851485T>C		109.0	0.0		105.0	45.0	NM_003008	Q53ZU2|Q6X2M5|Q6X2M6	Silent	SNP	ENST00000372769.3	hg19	CCDS13346.1																																																																																			.	.		0.383	SEMG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079417.1	NM_003008		C	43851485	T	C	43851485	2	2	344	1	0	0	0	0	0	0	0	1	14060	1403	49	2		2	SEMG2	20	43851485	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	244357	43851485	19174035	1336	48699										
SLC12A5	57468	hgsc.bcm.edu	37	chr20	44684872	44684872	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctccgcctgaacgtcccagaAgagacggctggtgacagtga	13	12	0	5			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr20:44684872A>G	ENST00000454036.2	+	22	2989	c.2940A>G	c.(2938-2940)gaA>gaG	p.E980E	SLC12A5_ENST00000243964.3_Silent_p.E957E	NM_001134771.1	NP_001128243.1	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 5	980					cellular ion homeostasis (GO:0006873)|chloride transmembrane transport (GO:1902476)|ion transport (GO:0006811)|learning (GO:0007612)|multicellular organism growth (GO:0035264)|potassium ion transport (GO:0006813)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|thermosensory behavior (GO:0040040)|transmembrane transport (GO:0055085)|transport (GO:0006810)	dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(1)|lung(38)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	80		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)	ACGTCCCAGAAGAGACGGCTG	0.577																																					p.E980E		Atlas-SNP	.											.	SLC12A5	181	.	0			c.A2940G						.						77	74	75					20																	44684872		2203	4300	6503	SO:0001819	synonymous_variant	57468	exon22			CCCAGAAGAGACG	AB033002	CCDS13391.1, CCDS46610.1	20q13.12	2013-05-22	2010-04-20		ENSG00000124140	ENSG00000124140		"Solute carriers"	13818	protein-coding gene	gene with protein product		606726					Standard	NM_020708		Approved	KIAA1176, KCC2	uc010zxl.1	Q9H2X9	OTTHUMG00000032638	ENST00000454036.2:c.2940A>G	chr20.hg19:g.44684872A>G		99.0	0.0		88.0	33.0	NM_001134771	A2RTX2|Q5VZ41|Q9H4Z0|Q9ULP4	Silent	SNP	ENST00000454036.2	hg19	CCDS46610.1																																																																																			.	.		0.577	SLC12A5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471538.1			G	44684872	A	G	44684872	2	3	344	1	0	0	0	0	0	0	0	1	14401	69	3	2		2	SLC12A5	20	44684872	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	833387	44684872	18340648	1337	48700										
CSE1L	1434	hgsc.bcm.edu	37	chr20	47675054	47675054	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acagaatatttaaagaaaacActtgatcctgatcctgccat	5	9	0	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr20:47675054A>G	ENST00000262982.2	+	2	177	c.54A>G	c.(52-54)acA>acG	p.T18T	CSE1L_ENST00000396192.3_Silent_p.T18T|CSE1L_ENST00000542325.1_5'UTR	NM_001256135.1|NM_001316.3	NP_001243064.1|NP_001307.2	P55060	XPO2_HUMAN	CSE1 chromosome segregation 1-like (yeast)	18					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	importin-alpha export receptor activity (GO:0008262)			breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(11)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	35			BRCA - Breast invasive adenocarcinoma(12;0.000491)|Colorectal(8;0.198)			TAAAGAAAACACTTGATCCTG	0.358																																					p.T18T		Atlas-SNP	.											.	CSE1L	83	.	0			c.A54G						.						110	119	116					20																	47675054		2203	4300	6503	SO:0001819	synonymous_variant	1434	exon2			GAAAACACTTGAT	U33286	CCDS13412.1, CCDS58773.1	20q13	2013-05-01	2001-11-28		ENSG00000124207	ENSG00000124207		"Exportins"	2431	protein-coding gene	gene with protein product	"cellular apoptosis susceptibility"	601342	"chromosome segregation 1 (yeast homolog)-like"			8963895, 7479798	Standard	NM_001316		Approved	CAS, XPO2, CSE1	uc002xty.4	P55060	OTTHUMG00000033046	ENST00000262982.2:c.54A>G	chr20.hg19:g.47675054A>G		68.0	0.0		52.0	29.0	NM_001256135	A3RLL6|B2R5T4|E1P5Y0|F8W904|O75432|Q32M40|Q9H5B7|Q9NTS0|Q9UP98|Q9UP99|Q9UPA0	Silent	SNP	ENST00000262982.2	hg19	CCDS13412.1																																																																																			.	.		0.358	CSE1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080345.2	NM_001316		G	47675054	A	G	47675054	2	3	344	1	0	0	0	0	0	0	0	1	3932	146	6	2		2	CSE1L	20	47675054	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2990182	47675054	15350466	1338	48701										
STX16	8675	hgsc.bcm.edu	37	chr20	57246218	57246218	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctgtcttgctagggttttacAgaggaccagttagttctggt	12	7	2	1	rs546565420		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr20:57246218A>G	ENST00000371141.4	+	7	1381	c.657A>G	c.(655-657)acA>acG	p.T219T	STX16-NPEPL1_ENST00000530122.1_Silent_p.T219T|STX16_ENST00000358029.4_Silent_p.T215T|STX16_ENST00000361830.3_Silent_p.T219T|STX16_ENST00000355957.5_Silent_p.T202T|STX16_ENST00000496003.1_Intron|STX16_ENST00000361770.5_Silent_p.T202T|STX16_ENST00000359617.4_Silent_p.T166T|STX16_ENST00000371132.4_Silent_p.T198T	NM_001001433.2	NP_001001433.1	O14662	STX16_HUMAN	syntaxin 16	219					intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)			breast(1)|cervix(1)|large_intestine(3)|lung(9)|ovary(1)|pancreas(1)|urinary_tract(1)	17	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;3.73e-09)|Epithelial(14;8.54e-06)|all cancers(14;6.89e-05)			AGGGTTTTACAGAGGACCAGT	0.418																																					p.T219T		Atlas-SNP	.											.	STX16	36	.	0			c.A657G						.						102	97	99					20																	57246218		2203	4300	6503	SO:0001819	synonymous_variant	8675	exon7			TTTTACAGAGGAC	AF038897	CCDS13468.1, CCDS13469.1, CCDS46619.1, CCDS46620.1, CCDS56199.1	20q13.32	2008-07-02			ENSG00000124222	ENSG00000124222			11431	protein-coding gene	gene with protein product		603666				9464276, 9587053, 15800843	Standard	NM_003763		Approved	hsyn16, SYN16	uc002xzi.3	O14662	OTTHUMG00000033084	ENST00000371141.4:c.657A>G	chr20.hg19:g.57246218A>G		87.0	0.0		72.0	27.0	NM_001001433	A6NK32|A6NN69|A8MPP0|B7ZBN1|B7ZBN2|B7ZBN3|E1P5M0|E1P607|O14661|O14663|O60517|Q5W084|Q5W086|Q5W087|Q5XKI6|Q6GMS8|Q9H0Z0|Q9H1T7|Q9H1T8|Q9UIX5	Silent	SNP	ENST00000371141.4	hg19	CCDS13468.1																																																																																			.	.		0.418	STX16-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080517.2	NM_001001433		G	57246218	A	G	57246218	2	3	344	1	0	0	0	0	0	0	0	1	15354	175	7	2		2	STX16	20	57246218	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	9571164	57246218	5779302	1339	48702										
PHACTR3	116154	hgsc.bcm.edu	37	chr20	58349384	58349384	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cagcgtggagcggggcaaggAgagggaggaggcttggagct	22	6	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr20:58349384A>T	ENST00000371015.1	+	7	1480	c.1013A>T	c.(1012-1014)gAg>gTg	p.E338V	PHACTR3_ENST00000395639.4_Missense_Mutation_p.E227V|PHACTR3_ENST00000395636.2_Missense_Mutation_p.E297V|PHACTR3_ENST00000541461.1_Missense_Mutation_p.E297V|PHACTR3_ENST00000355648.4_Missense_Mutation_p.E297V|PHACTR3_ENST00000361300.4_Missense_Mutation_p.E227V|PHACTR3_ENST00000359926.3_Missense_Mutation_p.E335V	NM_001281507.1|NM_080672.3	NP_001268436.1|NP_542403.1	Q96KR7	PHAR3_HUMAN	phosphatase and actin regulator 3	338						nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|liver(2)|lung(32)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	59	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)			CGGGGCAAGGAGAGGGAGGAG	0.507																																					p.E338V		Atlas-SNP	.											.	PHACTR3	104	.	0			c.A1013T						.						106	103	104					20																	58349384		2203	4300	6503	SO:0001583	missense	116154	exon7			GCAAGGAGAGGGA	AJ311122	CCDS13480.1, CCDS13481.1, CCDS42895.1, CCDS56202.1	20q13.32-q13.33	2014-06-13	2004-05-20	2004-05-20	ENSG00000087495	ENSG00000087495		"Phosphatase and actin regulators"	15833	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 123"	608725	"chromosome 20 open reading frame 101"	C20orf101		15107502	Standard	NM_001199505		Approved	PPP1R123	uc002yau.3	Q96KR7	OTTHUMG00000032869	ENST00000371015.1:c.1013A>T	chr20.hg19:g.58349384A>T	ENSP00000360054:p.Glu338Val	85.0	0.0		99.0	36.0	NM_080672	B1AKX0|B1AN68|B1AN69|B2RB46|Q32P33|Q707P6|Q9H4T4	Missense_Mutation	SNP	ENST00000371015.1	hg19	CCDS13480.1	.	.	.	.	.	.	.	.	.	.	A	12.58	1.981029	0.34942	.	.	ENSG00000087495	ENST00000359926;ENST00000371015;ENST00000395639;ENST00000541461;ENST00000355648;ENST00000395636;ENST00000361300	T;T;T;T;T;T;T	0.31769	1.87;1.85;1.48;1.88;1.88;1.88;1.48	5.06	5.06	0.68205	.	0.467536	0.26510	N	0.023967	T	0.31670	0.0804	L	0.57536	1.79	0.47621	D	0.999471	B;B;B	0.26902	0.163;0.008;0.008	B;B;B	0.26969	0.075;0.011;0.007	T	0.07177	-1.0786	10	0.33141	T	0.24	-15.4158	13.9996	0.64424	1.0:0.0:0.0:0.0	.	227;338;335	Q96KR7-3;Q96KR7;B1AKX0	.;PHAR3_HUMAN;.	V	335;338;227;297;297;297;227	ENSP00000353002:E335V;ENSP00000360054:E338V;ENSP00000379001:E227V;ENSP00000442483:E297V;ENSP00000347866:E297V;ENSP00000378998:E297V;ENSP00000354555:E227V	ENSP00000347866:E297V	E	+	2	0	PHACTR3	57782779	1.000000	0.71417	0.997000	0.53966	0.249000	0.25844	6.175000	0.71949	1.893000	0.54813	0.533000	0.62120	GAG	.	.		0.507	PHACTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079923.3	NM_080672		T	58349384	A	T	58349384	3	4	344	1	0	0	0	0	1	0	0	0	11820	304	11	4	1039	4	PHACTR3	20	58349384	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1103166	58349384	4676136	1340	48703										
CDH26	60437	hgsc.bcm.edu	37	chr20	58563998	58563998	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcccagcgcaaagcctcatcAttgtcgtggagaatgaggag	13	10	2	2	rs547604097		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr20:58563998A>G	ENST00000244047.5	+	9	1374	c.1063A>G	c.(1063-1065)Att>Gtt	p.I355V	CDH26_ENST00000348616.4_Missense_Mutation_p.I355V			Q8IXH8	CAD26_HUMAN	cadherin 26	355	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(11)|lung(14)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	44	all_lung(29;0.00963)		BRCA - Breast invasive adenocarcinoma(7;5.58e-09)			AAGCCTCATCATTGTCGTGGA	0.567																																					p.I355V		Atlas-SNP	.											.	CDH26	229	.	0			c.A1063G						.						58	63	61					20																	58563998		2203	4300	6503	SO:0001583	missense	60437	exon9			CTCATCATTGTCG	AF169690, AK055202	CCDS13485.1, CCDS13486.1	20q13.33	2010-01-26	2009-11-20		ENSG00000124215	ENSG00000124215		"Cadherins / Major cadherins"	15902	protein-coding gene	gene with protein product			"cadherin-like 26"				Standard	NM_177980		Approved	VR20	uc002ybe.3	Q8IXH8	OTTHUMG00000032874	ENST00000244047.5:c.1063A>G	chr20.hg19:g.58563998A>G	ENSP00000244047:p.Ile355Val	64.0	0.0		70.0	29.0	NM_177980	A2A2M5|B3KNX3|Q6P5Y6|Q8TCH3|Q9BQN4|Q9NRU1	Missense_Mutation	SNP	ENST00000244047.5	hg19		.	.	.	.	.	.	.	.	.	.	A	3.222	-0.159347	0.06544	.	.	ENSG00000124215	ENST00000244047;ENST00000348616	T;T	0.56103	0.48;0.48	5.19	-1.44	0.08856	.	0.622919	0.16780	N	0.199840	T	0.26557	0.0649	N	0.11023	0.085	0.09310	N	1	P	0.35383	0.498	B	0.40066	0.318	T	0.34304	-0.9834	10	0.08179	T	0.78	.	5.6053	0.17377	0.5488:0.1366:0.3147:0.0	.	355	Q8IXH8-4	.	V	355	ENSP00000244047:I355V;ENSP00000339390:I355V	ENSP00000244047:I355V	I	+	1	0	CDH26	57997393	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	0.321000	0.19558	-0.498000	0.06632	0.533000	0.62120	ATT	.	.		0.567	CDH26-201	KNOWN	basic	protein_coding	protein_coding		NM_177980		G	58563998	A	G	58563998	3	3	344	1	0	0	0	0	1	0	0	0	3112	217	8	2	1097	2	CDH26	20	58563998	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	214614	58563998	4461522	1341	48704										
USP25	29761	hgsc.bcm.edu	37	chr21	17196476	17196476	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agaatttccccaagttttatAtttggacaggtatggtttga	9	5	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr21:17196476A>G	ENST00000285679.6	+	11	1568	c.1199A>G	c.(1198-1200)tAt>tGt	p.Y400C	USP25_ENST00000285681.2_Missense_Mutation_p.Y400C|USP25_ENST00000400183.2_Missense_Mutation_p.Y400C|USP25_ENST00000351097.5_Intron	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	400	USP.				cellular protein modification process (GO:0006464)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|proteolysis (GO:0006508)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|SUMO binding (GO:0032183)|ubiquitin-specific protease activity (GO:0004843)			breast(4)|endometrium(6)|kidney(2)|large_intestine(13)|liver(5)|lung(14)|ovary(4)|prostate(1)|skin(1)|urinary_tract(2)	52				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)		CAAGTTTTATATTTGGACAGG	0.313																																					p.Y400C		Atlas-SNP	.											.	USP25	156	.	0			c.A1199G						.						62	64	63					21																	17196476		2201	4298	6499	SO:0001583	missense	29761	exon11			TTTTATATTTGGA	AF170562	CCDS33515.1, CCDS63336.1, CCDS63337.1	21q11.2	2011-02-24	2005-08-08		ENSG00000155313	ENSG00000155313		"Ubiquitin-specific peptidases"	12624	protein-coding gene	gene with protein product		604736	"ubiquitin specific protease 25"			12838346, 10612803	Standard	NM_013396		Approved	USP21	uc002yjy.1	Q9UHP3	OTTHUMG00000074343	ENST00000285679.6:c.1199A>G	chr21.hg19:g.17196476A>G	ENSP00000285679:p.Tyr400Cys	28.0	0.0		28.0	15.0	NM_013396	C0LSZ0|Q6DHZ9|Q9H9W1	Missense_Mutation	SNP	ENST00000285679.6	hg19	CCDS33515.1	.	.	.	.	.	.	.	.	.	.	A	19.65	3.868062	0.72065	.	.	ENSG00000155313	ENST00000285681;ENST00000285679;ENST00000400183	T;T;T	0.74315	-0.83;-0.83;-0.83	4.67	4.67	0.58626	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	D	0.83801	0.5333	M	0.64567	1.98	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.997;0.997;0.998	D	0.85314	0.1080	10	0.59425	D	0.04	.	14.8212	0.70074	1.0:0.0:0.0:0.0	.	400;400;400	Q9UHP3-3;Q9UHP3-1;Q9UHP3	.;.;UBP25_HUMAN	C	400	ENSP00000285681:Y400C;ENSP00000285679:Y400C;ENSP00000383044:Y400C	ENSP00000285679:Y400C	Y	+	2	0	USP25	16118347	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	8.901000	0.92560	2.063000	0.61619	0.528000	0.53228	TAT	.	.		0.313	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1			G	17196476	A	G	17196476	3	3	344	1	0	0	0	0	1	0	0	0	17071	449	16	2	1241	2	USP25	21	17196476	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10		17196476	30933419	1342	48705										
TMPRSS15	5651	hgsc.bcm.edu	37	chr21	19732132	19732132	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tctaatatatctgtataataTgtattaaaatcatcgaagct	4	5	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr21:19732132T>C	ENST00000284885.3	-	8	855	c.822A>G	c.(820-822)acA>acG	p.T274T		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	274	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.					brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						CTGTATAATATGTATTAAAAT	0.244																																					p.T274T		Atlas-SNP	.											.	TMPRSS15	189	.	0			c.A822G						.						28	34	32					21																	19732132		2177	4249	6426	SO:0001819	synonymous_variant	5651	exon8			ATAATATGTATTA		CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"Serine peptidases / Transmembrane"	9490	protein-coding gene	gene with protein product	"proenterokinase", "enteropeptidase"	606635	"protease, serine, 7 (enterokinase)"	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.822A>G	chr21.hg19:g.19732132T>C		188.0	0.0		188.0	86.0	NM_002772	Q2NKL7	Silent	SNP	ENST00000284885.3	hg19	CCDS13571.1																																																																																			.	.		0.244	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772		C	19732132	T	C	19732132	2	2	344	1	0	0	0	0	0	0	0	1	16261	1451	51	2		2	TMPRSS15	21	19732132	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2535656	19732132	28397763	1343	48706										
NCAM2	4685	hgsc.bcm.edu	37	chr21	22782650	22782650	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	actcttgggaaggaaatcctAtcaatataagttgtgatgtg	10	5	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr21:22782650A>G	ENST00000400546.1	+	10	1501	c.1252A>G	c.(1252-1254)Atc>Gtc	p.I418V	NCAM2_ENST00000284894.7_Missense_Mutation_p.I276V	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	418	Ig-like C2-type 5.				axonal fasciculation (GO:0007413)|neuron cell-cell adhesion (GO:0007158)|sensory perception of smell (GO:0007608)	axon (GO:0030424)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(4)|cervix(2)|endometrium(8)|kidney(6)|large_intestine(22)|liver(4)|lung(49)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	108		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		AGGAAATCCTATCAATATAAG	0.313																																					p.I418V		Atlas-SNP	.											.	NCAM2	220	.	0			c.A1252G						.						54	52	53					21																	22782650		1817	4067	5884	SO:0001583	missense	4685	exon10			AATCCTATCAATA		CCDS42910.1	21q21	2013-02-11			ENSG00000154654	ENSG00000154654		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7657	protein-coding gene	gene with protein product		602040				9226371	Standard	NM_004540		Approved	NCAM21, MGC51008	uc002yld.2	O15394	OTTHUMG00000078121	ENST00000400546.1:c.1252A>G	chr21.hg19:g.22782650A>G	ENSP00000383392:p.Ile418Val	353.0	0.0		322.0	144.0	NM_004540	A8MQ06|B7Z841|Q7Z7F2	Missense_Mutation	SNP	ENST00000400546.1	hg19	CCDS42910.1	.	.	.	.	.	.	.	.	.	.	A	3.053	-0.195039	0.06259	.	.	ENSG00000154654	ENST00000400546;ENST00000284894	T;T	0.25085	1.82;1.82	4.91	4.91	0.64330	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.050564	0.85682	D	0.000000	T	0.09949	0.0244	N	0.02751	-0.505	0.80722	D	1	B;B	0.21147	0.052;0.052	B;B	0.17722	0.018;0.019	T	0.13019	-1.0525	10	0.02654	T	1	-14.9905	13.6486	0.62297	1.0:0.0:0.0:0.0	.	276;418	B7Z5K2;O15394	.;NCAM2_HUMAN	V	418;276	ENSP00000383392:I418V;ENSP00000284894:I276V	ENSP00000284894:I276V	I	+	1	0	NCAM2	21704521	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.106000	0.71511	1.961000	0.56991	0.482000	0.46254	ATC	.	.		0.313	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540		G	22782650	A	G	22782650	3	3	344	1	0	0	0	0	1	0	0	0	10212	449	16	2	1290	2	NCAM2	21	22782650	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3050518	22782650	25347245	1344	48707										
JAM2	58494	hgsc.bcm.edu	37	chr21	27062262	27062262	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gggtcggagtgtctcctttgTctactatcaacagactcttc	9	11	4	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr21:27062262T>A	ENST00000480456.1	+	3	768	c.218T>A	c.(217-219)gTc>gAc	p.V73D	JAM2_ENST00000400532.1_Missense_Mutation_p.V73D|JAM2_ENST00000312957.5_Missense_Mutation_p.V73D|JAM2_ENST00000425221.2_Intron	NM_001270407.1|NM_021219.3	NP_001257336.1|NP_067042.1	P57087	JAM2_HUMAN	junctional adhesion molecule 2	73	Ig-like V-type.				blood coagulation (GO:0007596)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|single organismal cell-cell adhesion (GO:0016337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(12)|prostate(1)|stomach(1)|urinary_tract(1)	19						GTCTCCTTTGTCTACTATCAA	0.438																																					p.V73D		Atlas-SNP	.											.	JAM2	33	.	0			c.T218A						.						120	122	122					21																	27062262		1866	4089	5955	SO:0001583	missense	58494	exon3			CCTTTGTCTACTA	AF255910	CCDS42911.1, CCDS58787.1, CCDS58788.1	21q21.2	2013-01-11			ENSG00000154721	ENSG00000154721		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing"	14686	protein-coding gene	gene with protein product		606870		C21orf43		10779521, 10945976	Standard	NM_021219		Approved	VE-JAM, JAM-B, JAMB, CD322	uc031rvc.1	P57087	OTTHUMG00000078441	ENST00000480456.1:c.218T>A	chr21.hg19:g.27062262T>A	ENSP00000420419:p.Val73Asp	35.0	0.0		25.0	19.0	NM_021219	B2R6T9|B4DGT9|Q6UXG6|Q6YNC1	Missense_Mutation	SNP	ENST00000480456.1	hg19	CCDS42911.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.105952	0.77096	.	.	ENSG00000154721	ENST00000480456;ENST00000400533;ENST00000400532;ENST00000400537;ENST00000312957	T;T;T	0.69040	-0.37;-0.37;-0.37	5.13	5.13	0.70059	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.057005	0.64402	D	0.000001	T	0.81019	0.4736	M	0.82056	2.57	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.998;0.995;0.997	T	0.82922	-0.0217	10	0.62326	D	0.03	.	11.4919	0.50385	0.0:0.0:0.0:1.0	.	73;73;73;73	A8MQ45;A8MXS1;A8MTB0;P57087	.;.;.;JAM2_HUMAN	D	73	ENSP00000420419:V73D;ENSP00000383376:V73D;ENSP00000318416:V73D	ENSP00000318416:V73D	V	+	2	0	JAM2	25984133	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.827000	0.55745	2.279000	0.76181	0.528000	0.53228	GTC	.	.		0.438	JAM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171347.1			A	27062262	T	A	27062262	3	1	344	1	0	0	0	0	1	0	0	0	7952	1667	58	4	228	4	JAM2	21	27062262	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	4279612	27062262	21067633	1345	48708										
APP	351	hgsc.bcm.edu	37	chr21	27277345	27277345	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggttctgatacctggtcgagTggtcagtcctcggtcggcag	15	10	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr21:27277345T>C	ENST00000346798.3	-	15	1987	c.1954A>G	c.(1954-1956)Act>Gct	p.T652A	APP_ENST00000354192.3_Missense_Mutation_p.T521A|APP_ENST00000359726.3_Missense_Mutation_p.T596A|APP_ENST00000448388.2_Missense_Mutation_p.T542A|APP_ENST00000357903.3_Missense_Mutation_p.T633A|APP_ENST00000440126.3_Missense_Mutation_p.T628A|APP_ENST00000439274.2_Missense_Mutation_p.T596A|APP_ENST00000348990.5_Missense_Mutation_p.T577A|APP_ENST00000358918.3_Intron	NM_000484.3	NP_000475.1	P05067	A4_HUMAN	amyloid beta (A4) precursor protein	652					adult locomotory behavior (GO:0008344)|axon cargo transport (GO:0008088)|axon midline choice point recognition (GO:0016199)|axonogenesis (GO:0007409)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|collateral sprouting in absence of injury (GO:0048669)|dendrite development (GO:0016358)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|ionotropic glutamate receptor signaling pathway (GO:0035235)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|mRNA polyadenylation (GO:0006378)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron differentiation (GO:0045665)|neuromuscular process controlling balance (GO:0050885)|neuron apoptotic process (GO:0051402)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of multicellular organism growth (GO:0040014)|regulation of protein binding (GO:0043393)|regulation of synapse structure and activity (GO:0050803)|regulation of translation (GO:0006417)|response to oxidative stress (GO:0006979)|smooth endoplasmic reticulum calcium ion homeostasis (GO:0051563)|suckling behavior (GO:0001967)|synaptic growth at neuromuscular junction (GO:0051124)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|ciliary rootlet (GO:0035253)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endosome (GO:0005768)|ER to Golgi transport vesicle (GO:0030134)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|receptor complex (GO:0043235)|spindle midzone (GO:0051233)|synapse (GO:0045202)	acetylcholine receptor binding (GO:0033130)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|peptidase activator activity (GO:0016504)|PTB domain binding (GO:0051425)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)			endometrium(5)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(209;0.00295)				CCTGGTCGAGTGGTCAGTCCT	0.532																																					p.T652A		Atlas-SNP	.											APP,NS,carcinoma,0,1	APP	90	.	0			c.A1954G						.						150	133	139					21																	27277345		2203	4300	6503	SO:0001583	missense	351	exon15			GTCGAGTGGTCAG	M15533	CCDS13576.1, CCDS13577.1, CCDS33523.1, CCDS46638.1, CCDS46639.1, CCDS56211.1, CCDS56212.1, CCDS56213.1	21q21.2	2014-01-30	2008-07-31		ENSG00000142192	ENSG00000142192		"Endogenous ligands"	620	protein-coding gene	gene with protein product	"peptidase nexin-II"	104760	"Alzheimer disease"	AD1		1679289	Standard	NM_001136130		Approved		uc002ylz.3	P05067	OTTHUMG00000078438	ENST00000346798.3:c.1954A>G	chr21.hg19:g.27277345T>C	ENSP00000284981:p.Thr652Ala	104.0	0.0		98.0	34.0	NM_000484	B2R5V1|B4DII8|D3DSD1|D3DSD2|D3DSD3|P09000|P78438|Q13764|Q13778|Q13793|Q16011|Q16014|Q16019|Q16020|Q6GSC0|Q8WZ99|Q9BT38|Q9UC33|Q9UCA9|Q9UCB6|Q9UCC8|Q9UCD1|Q9UQ58	Missense_Mutation	SNP	ENST00000346798.3	hg19	CCDS13576.1	.	.	.	.	.	.	.	.	.	.	T	16.46	3.129933	0.56721	.	.	ENSG00000142192	ENST00000346798;ENST00000354192;ENST00000348990;ENST00000357903;ENST00000359726;ENST00000448388;ENST00000440126;ENST00000439274	D;D;D;D;D;D;D;D	0.96073	-1.96;-3.89;-3.89;-1.97;-3.9;-3.89;-1.97;-1.96	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	D	0.96670	0.8913	L	0.50333	1.59	0.80722	D	1	D;D;P;D;D;D;D	0.76494	0.999;0.998;0.956;0.999;0.974;0.974;0.998	D;D;P;D;D;D;D	0.85130	0.993;0.993;0.899;0.997;0.953;0.953;0.993	D	0.96799	0.9588	10	0.52906	T	0.07	-17.7823	15.3268	0.74172	0.0:0.0:0.0:1.0	.	542;596;628;521;577;633;652	E9PEV0;E9PG40;B4DII8;P05067-10;P05067-4;P05067-8;P05067	.;.;.;.;.;.;A4_HUMAN	A	652;521;577;633;596;542;628;596	ENSP00000284981:T652A;ENSP00000346129:T521A;ENSP00000345463:T577A;ENSP00000350578:T633A;ENSP00000352760:T596A;ENSP00000388538:T542A;ENSP00000387483:T628A;ENSP00000398879:T596A	ENSP00000284981:T652A	T	-	1	0	APP	26199216	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.093000	0.71422	2.288000	0.76882	0.533000	0.62120	ACT	.	.		0.532	APP-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171340.1	NM_000484		C	27277345	T	C	27277345	3	2	344	1	0	0	0	0	1	0	0	0	815	1696	59	2	374	2	APP	21	27277345	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	215083	27277345	20852550	1346	48709										
ADAMTS5	11096	hgsc.bcm.edu	37	chr21	28306845	28306845	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgcaggcagattctccccttTccacaaggcgtcccttccac	7	17	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr21:28306845T>A	ENST00000284987.5	-	4	1750	c.1629A>T	c.(1627-1629)ggA>ggT	p.G543G	AP001601.2_ENST00000426771.1_RNA	NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 5	543	Disintegrin.				defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	72						TTCTCCCCTTTCCACAAGGCG	0.522																																					p.G543G	Esophageal Squamous(53;683 1080 10100 14424 45938)	Atlas-SNP	.											.	ADAMTS5	184	.	0			c.A1629T						.						93	86	88					21																	28306845		2203	4300	6503	SO:0001819	synonymous_variant	11096	exon4			CCCCTTTCCACAA	AF142099	CCDS13579.1	21q21.3	2008-07-31	2008-07-31		ENSG00000154736	ENSG00000154736		"ADAM metallopeptidases with thrombospondin type 1 motif"	221	protein-coding gene	gene with protein product	"aggrecanase-2"	605007	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"			10438522	Standard	NM_007038		Approved	ADMP-2, ADAMTS11	uc002ymg.3	Q9UNA0	OTTHUMG00000078686	ENST00000284987.5:c.1629A>T	chr21.hg19:g.28306845T>A		114.0	0.0		83.0	38.0	NM_007038	Q52LV4|Q9UKP2	Silent	SNP	ENST00000284987.5	hg19	CCDS13579.1																																																																																			.	.		0.522	ADAMTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171648.1			A	28306845	T	A	28306845	2	1	344	1	0	0	0	0	0	0	0	1	269	1770	62	4		4	ADAMTS5	21	28306845	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1029500	28306845	19823050	1347	48710										
KRTAP11-1	337880	hgsc.bcm.edu	37	chr21	32253723	32253723	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctggaaggaactgggcaaacAgatgccgcccaggcagtcag	14	11	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr21:32253723A>C	ENST00000332378.4	-	1	151	c.121T>G	c.(121-123)Tgt>Ggt	p.C41G		NM_175858.2	NP_787054.1	Q8IUC1	KR111_HUMAN	keratin associated protein 11-1	41						keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(12)|pancreas(1)	18						CTGGGCAAACAGATGCCGCCC	0.572																																					p.C41G		Atlas-SNP	.											.	KRTAP11-1	46	.	0			c.T121G						.						76	73	74					21																	32253723		2203	4300	6503	SO:0001583	missense	337880	exon1			GCAAACAGATGCC	AJ457065	CCDS13608.1	21q22.1	2003-03-11			ENSG00000182591	ENSG00000182591		"Keratin associated proteins"	18922	protein-coding gene	gene with protein product		600064				12359730	Standard	NM_175858		Approved	KAP11.1	uc002yov.3	Q8IUC1	OTTHUMG00000057773	ENST00000332378.4:c.121T>G	chr21.hg19:g.32253723A>C	ENSP00000330720:p.Cys41Gly	113.0	0.0		109.0	45.0	NM_175858	A1L4I8	Missense_Mutation	SNP	ENST00000332378.4	hg19	CCDS13608.1	.	.	.	.	.	.	.	.	.	.	A	11.55	1.673384	0.29693	.	.	ENSG00000182591	ENST00000332378	T	0.04654	3.58	5.4	1.74	0.24563	.	0.689891	0.13918	N	0.353780	T	0.06826	0.0174	M	0.63843	1.955	0.19775	N	0.999955	B	0.27316	0.175	B	0.26693	0.072	T	0.23691	-1.0181	10	0.62326	D	0.03	-0.4836	8.1465	0.31115	0.7592:0.0:0.2408:0.0	.	41	Q8IUC1	KR111_HUMAN	G	41	ENSP00000330720:C41G	ENSP00000330720:C41G	C	-	1	0	KRTAP11-1	31175594	0.729000	0.28090	0.715000	0.30552	0.816000	0.46133	0.481000	0.22260	0.130000	0.18549	0.529000	0.55759	TGT	.	.		0.572	KRTAP11-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128225.1			C	32253723	A	C	32253723	3	2	344	1	0	0	0	0	1	0	0	0	8526	188	7	5	374	5	KRTAP11-1	21	32253723	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3946878	32253723	15876172	1348	48711										
SETD4	54093	hgsc.bcm.edu	37	chr21	37408515	37408515	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccaccaaagttagttggtttAtcagggcctctttttcatcc	7	11	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr21:37408515A>G	ENST00000399215.1	-	10	2595	c.1223T>C	c.(1222-1224)aTa>aCa	p.I408T	SETD4_ENST00000399212.1_Missense_Mutation_p.I384T|SETD4_ENST00000332131.4_Missense_Mutation_p.I408T|SETD4_ENST00000481477.1_5'UTR|AP000688.1_ENST00000600312.1_Intron			Q9NVD3	SETD4_HUMAN	SET domain containing 4	408				EILVKYLPSTDKQMDKKISILKDHGYIENLTFGWDGPSWRL LTALKLLCLEAEKFTCWKKVLLGEVISDTNEKTSLDIAQKI CYYFIEETNAVLQKVSHMKDEKEALINQLTLVESLWTEELK ILRASAETLHSLQTAFT -> GWNQLCS (in Ref. 5; AAH02898). {ECO:0000305}.			methyltransferase activity (GO:0008168)			autonomic_ganglia(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)	15						TAGTTGGTTTATCAGGGCCTC	0.378																																					p.I408T		Atlas-SNP	.											.	SETD4	37	.	0			c.T1223C						.						123	122	122					21																	37408515		2203	4300	6503	SO:0001583	missense	54093	exon11			TGGTTTATCAGGG	AK001660	CCDS13640.1, CCDS42923.1, CCDS74791.1, CCDS74792.1	21q22.13	2006-02-15	2006-02-15	2006-02-15	ENSG00000185917	ENSG00000185917			1258	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 27", "chromosome 21 open reading frame 18"	C21orf27, C21orf18			Standard	XM_005261000		Approved		uc021wiy.1	Q9NVD3	OTTHUMG00000086483	ENST00000399215.1:c.1223T>C	chr21.hg19:g.37408515A>G	ENSP00000382163:p.Ile408Thr	100.0	0.0		86.0	35.0	NM_017438	B4DT14|D3DSG2|D3DSG4|Q8NE19|Q9BU46	Missense_Mutation	SNP	ENST00000399215.1	hg19	CCDS13640.1	.	.	.	.	.	.	.	.	.	.	A	3.542	-0.093530	0.07053	.	.	ENSG00000185917	ENST00000399215;ENST00000399212;ENST00000332131	T;T;T	0.15952	2.38;2.38;2.38	5.63	-3.12	0.05282	Rubisco LS methyltransferase, substrate-binding domain (1);	0.938409	0.09149	N	0.841874	T	0.10121	0.0248	L	0.44542	1.39	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.12156	0.004;0.007	T	0.42498	-0.9448	10	0.13470	T	0.59	-36.9396	2.206	0.03935	0.2357:0.4258:0.1637:0.1749	.	384;408	Q9NVD3-3;Q9NVD3	.;SETD4_HUMAN	T	408;384;408	ENSP00000382163:I408T;ENSP00000382161:I384T;ENSP00000329189:I408T	ENSP00000329189:I408T	I	-	2	0	SETD4	36330385	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.253000	0.08794	-0.160000	0.11002	0.460000	0.39030	ATA	.	.		0.378	SETD4-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194456.1	NM_017438		G	37408515	A	G	37408515	3	3	344	1	0	0	0	0	1	0	0	0	14148	449	16	2	103	2	SETD4	21	37408515	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	5154792	37408515	10721380	1349	48712										
DOPEY2	9980	hgsc.bcm.edu	37	chr21	37572789	37572789	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gccttgaagagggctccgagAtctccgacaggtgcgtgggc	16	11	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr21:37572789A>T	ENST00000399151.3	+	4	566	c.481A>T	c.(481-483)Atc>Ttc	p.I161F	DOPEY2_ENST00000492760.1_Intron	NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	161					cognition (GO:0050890)|endoplasmic reticulum organization (GO:0007029)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(6)|lung(25)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						GGGCTCCGAGATCTCCGACAG	0.622																																					p.I161F		Atlas-SNP	.											.	DOPEY2	184	.	0			c.A481T						.						45	45	45					21																	37572789		2203	4300	6503	SO:0001583	missense	9980	exon4			TCCGAGATCTCCG	AJ237839	CCDS13643.1	21q22.2	2013-03-05	2006-02-02	2006-02-02	ENSG00000142197	ENSG00000142197			1291	protein-coding gene	gene with protein product		604803	"chromosome 21 open reading frame 5"	C21orf5		16301316, 16303751, 10931277	Standard	NM_005128		Approved	KIAA0933	uc002yvg.3	Q9Y3R5	OTTHUMG00000086619	ENST00000399151.3:c.481A>T	chr21.hg19:g.37572789A>T	ENSP00000382104:p.Ile161Phe	27.0	0.0		31.0	14.0	NM_005128	D3DSG5|Q6PJQ7|Q9UEZ3	Missense_Mutation	SNP	ENST00000399151.3	hg19	CCDS13643.1	.	.	.	.	.	.	.	.	.	.	A	15.44	2.834308	0.50951	.	.	ENSG00000142197	ENST00000399151	T	0.11169	2.8	5.42	5.42	0.78866	Dopey, N-terminal (1);	0.047232	0.85682	D	0.000000	T	0.15349	0.0370	N	0.11364	0.135	0.46725	D	0.99917	D;D	0.71674	0.995;0.998	D;D	0.70935	0.933;0.971	T	0.33752	-0.9856	9	.	.	.	.	14.923	0.70854	1.0:0.0:0.0:0.0	.	161;161	Q9Y3R5-2;Q9Y3R5	.;DOP2_HUMAN	F	161	ENSP00000382104:I161F	.	I	+	1	0	DOPEY2	36494659	1.000000	0.71417	1.000000	0.80357	0.494000	0.33585	5.649000	0.67936	2.180000	0.69256	0.482000	0.46254	ATC	.	.		0.622	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	NM_005128		T	37572789	A	T	37572789	3	4	344	1	0	0	0	0	1	0	0	0	4710	333	12	4	491	4	DOPEY2	21	37572789	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	164274	37572789	10557106	1350	48713										
DOPEY2	9980	hgsc.bcm.edu	37	chr21	37605269	37605269	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acaagatgaaacgctataagAgctctggacacaaccctttt	7	10	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr21:37605269A>G	ENST00000399151.3	+	15	2603	c.2518A>G	c.(2518-2520)Agc>Ggc	p.S840G		NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	840					cognition (GO:0050890)|endoplasmic reticulum organization (GO:0007029)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(6)|lung(25)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						ACGCTATAAGAGCTCTGGACA	0.473																																					p.S840G		Atlas-SNP	.											.	DOPEY2	184	.	0			c.A2518G						.						119	113	115					21																	37605269		2203	4300	6503	SO:0001583	missense	9980	exon15			TATAAGAGCTCTG	AJ237839	CCDS13643.1	21q22.2	2013-03-05	2006-02-02	2006-02-02	ENSG00000142197	ENSG00000142197			1291	protein-coding gene	gene with protein product		604803	"chromosome 21 open reading frame 5"	C21orf5		16301316, 16303751, 10931277	Standard	NM_005128		Approved	KIAA0933	uc002yvg.3	Q9Y3R5	OTTHUMG00000086619	ENST00000399151.3:c.2518A>G	chr21.hg19:g.37605269A>G	ENSP00000382104:p.Ser840Gly	191.0	0.0		158.0	74.0	NM_005128	D3DSG5|Q6PJQ7|Q9UEZ3	Missense_Mutation	SNP	ENST00000399151.3	hg19	CCDS13643.1	.	.	.	.	.	.	.	.	.	.	A	10.90	1.481459	0.26598	.	.	ENSG00000142197	ENST00000399151	T	0.13778	2.56	5.98	0.879	0.19155	.	0.590844	0.20063	N	0.100031	T	0.09774	0.0240	L	0.44542	1.39	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.002	T	0.32561	-0.9902	10	0.23302	T	0.38	-9.8206	6.3183	0.21202	0.6105:0.1243:0.2652:0.0	.	840;840	Q9Y3R5-2;Q9Y3R5	.;DOP2_HUMAN	G	840	ENSP00000382104:S840G	ENSP00000382104:S840G	S	+	1	0	DOPEY2	36527139	1.000000	0.71417	0.035000	0.18076	0.930000	0.56654	3.496000	0.53288	0.128000	0.18479	0.528000	0.53228	AGC	.	.		0.473	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	NM_005128		G	37605269	A	G	37605269	3	3	344	1	0	0	0	0	1	0	0	0	4710	304	11	2	2572	2	DOPEY2	21	37605269	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	32480	37605269	10524626	1351	48714										
HMGN1	3150	hgsc.bcm.edu	37	chr21	40720227	40720227	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcgaggcttaccttcgctgcTgcctttttcggcttcgcttc	9	14	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr21:40720227T>A	ENST00000380749.5	-	4	399	c.117A>T	c.(115-117)gcA>gcT	p.A39A	HMGN1_ENST00000361263.4_5'Flank|snoU13_ENST00000459446.1_RNA|HMGN1_ENST00000380747.1_Silent_p.A55A|HMGN1_ENST00000489072.1_5'UTR|HMGN1_ENST00000380748.1_Silent_p.A29A	NM_004965.6	NP_004956.5	P05114	HMGN1_HUMAN	high mobility group nucleosome binding domain 1	39					chromatin organization (GO:0006325)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|post-embryonic camera-type eye morphogenesis (GO:0048597)|pyrimidine dimer repair by nucleotide-excision repair (GO:0000720)|regulation of development, heterochronic (GO:0040034)|regulation of epithelial cell proliferation (GO:0050678)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to UV-B (GO:0010224)|response to UV-C (GO:0010225)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(2)|lung(1)	3		Prostate(19;8.69e-07)				CCTTCGCTGCTGCCTTTTTCG	0.547																																					p.A39A		Atlas-SNP	.											.	HMGN1	8	.	0			c.A117T						.						89	87	88					21																	40720227		2203	4300	6503	SO:0001819	synonymous_variant	3150	exon4			CGCTGCTGCCTTT		CCDS33559.1	21q22.3	2011-07-01	2011-04-05	2002-08-16	ENSG00000205581	ENSG00000205581		"High-mobility group / Canonical"	4984	protein-coding gene	gene with protein product	"high-mobility group nucleosome binding 1", "nonhistone chromosomal protein HMG-14"	163920	"high-mobility group (nonhistone chromosomal) protein 14", "high-mobility group nucleosome binding domain 1"	HMG14		3782107, 2563381	Standard	NM_004965		Approved	FLJ27265, FLJ31471, MGC104230, MGC117425	uc002yxo.3	P05114	OTTHUMG00000066178	ENST00000380749.5:c.117A>T	chr21.hg19:g.40720227T>A		102.0	0.0		80.0	33.0	NM_004965	Q3KQR8	Silent	SNP	ENST00000380749.5	hg19	CCDS33559.1																																																																																			.	.		0.547	HMGN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141645.2	NM_004965		A	40720227	T	A	40720227	2	1	344	1	0	0	0	0	0	0	0	1	7243	1567	55	4		4	HMGN1	21	40720227	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	3114958	40720227	7409668	1352	48715										
PRDM15	63977	hgsc.bcm.edu	37	chr21	43281737	43281737	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gtggtttaggaaagtgtgcaTgctggcacttcttgaatgct	13	6	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr21:43281737T>G	ENST00000269844.3	-	7	936	c.826A>C	c.(826-828)Atg>Ctg	p.M276L	PRDM15_ENST00000422911.1_Intron|PRDM15_ENST00000398548.1_Intron|PRDM15_ENST00000538201.1_Intron|PRDM15_ENST00000447207.2_5'Flank	NM_022115.3	NP_071398.3	P57071	PRD15_HUMAN	PR domain containing 15	276					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(3)|skin(2)|stomach(2)|urinary_tract(1)	43						AAAGTGTGCATGCTGGCACTT	0.562																																					p.M276L		Atlas-SNP	.											.	PRDM15	110	.	0			c.A826C						.						132	107	116					21																	43281737		2203	4300	6503	SO:0001583	missense	63977	exon7			TGTGCATGCTGGC	AF276513	CCDS13676.1, CCDS42932.1, CCDS63370.1	21q22.3	2013-01-08	2002-07-31		ENSG00000141956	ENSG00000141956		"Zinc fingers, C2H2-type"	13999	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 83"	ZNF298, C21orf83		12036297, 12036298	Standard	NM_022115		Approved		uc002yzq.1	P57071	OTTHUMG00000086781	ENST00000269844.3:c.826A>C	chr21.hg19:g.43281737T>G	ENSP00000269844:p.Met276Leu	75.0	0.0		59.0	21.0	NM_022115	E9PDJ6|E9PF37|E9PGL3|Q4W8S0|Q4W8S3|Q4W8S4|Q4W8S5|Q8N0X3|Q8NEX0|Q9NQV3	Missense_Mutation	SNP	ENST00000269844.3	hg19	CCDS13676.1	.	.	.	.	.	.	.	.	.	.	T	7.481	0.648763	0.14516	.	.	ENSG00000141956	ENST00000269844	T	0.06933	3.24	2.16	-3.48	0.04739	.	.	.	.	.	T	0.03178	0.0093	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41448	-0.9508	9	0.62326	D	0.03	.	0.5087	0.00591	0.1665:0.2405:0.2397:0.3532	.	276	P57071	PRD15_HUMAN	L	276	ENSP00000269844:M276L	ENSP00000269844:M276L	M	-	1	0	PRDM15	42154806	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.553000	0.06012	-0.764000	0.04651	-0.337000	0.08149	ATG	.	.		0.562	PRDM15-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022115		G	43281737	T	G	43281737	3	3	344	1	0	0	0	0	1	0	0	0	12468	1464	51	5	3797	5	PRDM15	21	43281737	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2561510	43281737	4848158	1353	48716										
KRTAP10-4	386672	hgsc.bcm.edu	37	chr21	45994365	45994365	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tctgctgcaagcctgtgtgcTctgaggattcctcttcatgc	10	12	4	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr21:45994365T>C	ENST00000400374.3	+	1	760	c.730T>C	c.(730-732)Tct>Cct	p.S244P	TSPEAR_ENST00000397916.1_5'Flank|TSPEAR_ENST00000323084.4_Intron	NM_198687.1	NP_941960.1	P60372	KR104_HUMAN	keratin associated protein 10-4	244	36 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|prostate(1)	18						GCCTGTGTGCTCTGAGGATTC	0.632																																					p.S244P		Atlas-SNP	.											.	KRTAP10-4	44	.	0			c.T730C						.						105	107	107					21																	45994365		2203	4300	6503	SO:0001583	missense	386672	exon1			GTGTGCTCTGAGG	AB076351	CCDS42957.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000215454	ENSG00000215454		"Keratin associated proteins"	20521	protein-coding gene	gene with protein product			"keratin associated protein 18-4"	KRTAP18-4			Standard	NM_198687		Approved	KRTAP18.4, KAP10.4	uc002zfk.1	P60372	OTTHUMG00000057641	ENST00000400374.3:c.730T>C	chr21.hg19:g.45994365T>C	ENSP00000383225:p.Ser244Pro	33.0	0.0		34.0	14.0	NM_198687	Q08AS0	Missense_Mutation	SNP	ENST00000400374.3	hg19	CCDS42957.1	.	.	.	.	.	.	.	.	.	.	N	1.107	-0.659226	0.03454	.	.	ENSG00000215454	ENST00000400374	T	0.00892	5.57	2.13	0.969	0.19686	.	.	.	.	.	T	0.01695	0.0054	M	0.84082	2.675	0.09310	N	1	B	0.12013	0.005	B	0.12837	0.008	T	0.39375	-0.9617	9	0.66056	D	0.02	.	3.8286	0.08865	0.0:0.1934:0.0:0.8066	.	244	P60372	KR104_HUMAN	P	244	ENSP00000383225:S244P	ENSP00000383225:S244P	S	+	1	0	KRTAP10-4	44818793	0.000000	0.05858	0.024000	0.17045	0.139000	0.21198	0.046000	0.14035	0.275000	0.22094	0.413000	0.27773	TCT	.	.		0.632	KRTAP10-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128045.1	NM_198687		C	45994365	T	C	45994365	3	2	344	1	0	0	0	0	1	0	0	0	8520	1551	54	2	732	2	KRTAP10-4	21	45994365	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2712628	45994365	2135530	1354	48717										
KRTAP12-2	353323	hgsc.bcm.edu	37	chr21	46086475	46086475	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccgcatacacgacaggcctgCagctcacaggcacgcacagg	11	16	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr21:46086475C>A	ENST00000360770.3	-	1	369	c.329G>T	c.(328-330)tGc>tTc	p.C110F	TSPEAR_ENST00000323084.4_Intron	NM_181684.2	NP_859012.1	P59991	KR122_HUMAN	keratin associated protein 12-2	110	23 X 5 AA approximate repeats.					keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(1)|lung(3)	5						GACAGGCCTGCAGCTCACAGG	0.637																																					p.C110F		Atlas-SNP	.											.	KRTAP12-2	10	.	0			c.G329T						.						58	66	64					21																	46086475		2166	4252	6418	SO:0001583	missense	353323	exon1			GGCCTGCAGCTCA	AJ566389	CCDS42965.1	21q22.3	2006-03-13			ENSG00000221864	ENSG00000221864		"Keratin associated proteins"	20530	protein-coding gene	gene with protein product							Standard	NM_181684		Approved	KRTAP12.2, KAP12.2	uc002zfu.3	P59991	OTTHUMG00000057636	ENST00000360770.3:c.329G>T	chr21.hg19:g.46086475C>A	ENSP00000354001:p.Cys110Phe	88.0	0.0		68.0	23.0	NM_181684	A6NIS1|A6NMS9|Q0VAS4	Missense_Mutation	SNP	ENST00000360770.3	hg19	CCDS42965.1	.	.	.	.	.	.	.	.	.	.	c	14.56	2.572082	0.45798	.	.	ENSG00000221864	ENST00000360770;ENST00000539483	T	0.07114	3.22	3.55	2.64	0.31445	.	.	.	.	.	T	0.35364	0.0929	M	0.93150	3.385	0.20764	N	0.999854	D	0.76494	0.999	D	0.71870	0.975	T	0.19224	-1.0312	9	0.87932	D	0	.	10.4991	0.44796	0.0:0.8001:0.1999:0.0	.	110	P59991	KR122_HUMAN	F	110;60	ENSP00000354001:C110F	ENSP00000354001:C110F	C	-	2	0	KRTAP12-2	44910903	0.957000	0.32711	0.339000	0.25562	0.073000	0.16967	0.370000	0.20433	0.442000	0.26555	0.407000	0.27541	TGC	.	.		0.637	KRTAP12-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128039.1	NM_181684		A	46086475	C	A	46086475	3	1	344	1	0	0	0	0	1	0	0	0	8528	710	25	3	115	3	KRTAP12-2	21	46086475	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	92110	46086475	2043420	1355	48718										
COL6A2	1292	hgsc.bcm.edu	37	chr21	47552138	47552138	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gctggagaccacacaataccTgaactccttctcgcacgtgg	9	14	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr21:47552138T>A	ENST00000300527.4	+	28	2836	c.2732T>A	c.(2731-2733)cTg>cAg	p.L911Q		NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	911	Nonhelical region.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)				NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		ACACAATACCTGAACTCCTTC	0.682																																					p.L911Q		Atlas-SNP	.											.	COL6A2	351	.	0			c.T2732A						.						18	19	19					21																	47552138		2192	4296	6488	SO:0001583	missense	1292	exon28			AATACCTGAACTC	M20777	CCDS13728.1, CCDS13729.1, CCDS13730.1	21q22.3	2014-09-17			ENSG00000142173	ENSG00000142173		"Collagens"	2212	protein-coding gene	gene with protein product		120240					Standard	NM_001849		Approved		uc002zia.1	P12110	OTTHUMG00000090489	ENST00000300527.4:c.2732T>A	chr21.hg19:g.47552138T>A	ENSP00000300527:p.Leu911Gln	41.0	0.0		23.0	21.0	NM_001849	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Missense_Mutation	SNP	ENST00000300527.4	hg19	CCDS13728.1	.	.	.	.	.	.	.	.	.	.	T	10.94	1.493590	0.26774	.	.	ENSG00000142173	ENST00000300527	T	0.79033	-1.23	4.18	4.18	0.49190	von Willebrand factor, type A (3);	0.440483	0.22437	U	0.060061	D	0.84474	0.5480	M	0.65975	2.015	0.80722	D	1	D	0.71674	0.998	D	0.74023	0.982	D	0.84998	0.0898	10	0.87932	D	0	-28.1939	8.7972	0.34887	0.1681:0.0:0.0:0.8319	.	911	P12110	CO6A2_HUMAN	Q	911	ENSP00000300527:L911Q	ENSP00000300527:L911Q	L	+	2	0	COL6A2	46376566	1.000000	0.71417	1.000000	0.80357	0.101000	0.19017	5.900000	0.69853	1.541000	0.49316	0.260000	0.18958	CTG	.	.		0.682	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1			A	47552138	T	A	47552138	3	1	344	1	0	0	0	0	1	0	0	0	3702	1580	55	4	3168	4	COL6A2	21	47552138	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	1465663	47552138	577757	1356	48719										
C21orf58	54058	hgsc.bcm.edu	37	chr21	47735441	47735441	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cagagcagtctgcagggcatCgtccggccggtcctcatttc	12	14	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr21:47735441C>T	ENST00000291691.7	-	4	1527	c.391G>A	c.(391-393)Gat>Aat	p.D131N	C21orf58_ENST00000397682.3_5'UTR|C21orf58_ENST00000397685.4_Missense_Mutation_p.D48N|C21orf58_ENST00000397680.1_5'UTR|C21orf58_ENST00000397683.1_5'UTR|C21orf58_ENST00000397679.1_5'UTR	NM_058180.3	NP_478060.2	P58505	CU058_HUMAN	chromosome 21 open reading frame 58	131										breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(1)|pancreas(1)	9	Breast(49;0.112)			Colorectal(79;0.239)		TGCAGGGCATCGTCCGGCCGG	0.597																																					p.D131N		Atlas-SNP	.											.	C21orf58	25	.	0			c.G391A						.						109	81	90					21																	47735441		2203	4300	6503	SO:0001583	missense	54058	exon4			GGGCATCGTCCGG		CCDS13735.1, CCDS68229.1	21q22.3	2008-07-07			ENSG00000160298	ENSG00000160298			1300	protein-coding gene	gene with protein product							Standard	XM_005261149		Approved		uc002zjf.3	P58505	OTTHUMG00000090634	ENST00000291691.7:c.391G>A	chr21.hg19:g.47735441C>T	ENSP00000291691:p.Asp131Asn	77.0	0.0		35.0	28.0	NM_058180	B3KPI1	Missense_Mutation	SNP	ENST00000291691.7	hg19	CCDS13735.1	.	.	.	.	.	.	.	.	.	.	C	16.29	3.082236	0.55861	.	.	ENSG00000160298	ENST00000417060;ENST00000291691;ENST00000397685	T;T;T	0.21543	2.0;2.0;2.0	4.98	-0.15	0.13416	.	1.246520	0.06189	N	0.680903	T	0.19248	0.0462	L	0.52573	1.65	0.09310	N	1	B;B	0.10296	0.003;0.003	B;B	0.06405	0.001;0.002	T	0.34725	-0.9817	10	0.62326	D	0.03	0.0	4.6313	0.12502	0.0:0.4345:0.3015:0.264	.	131;131	P58505;P58505-2	CU058_HUMAN;.	N	93;131;48	ENSP00000402356:D93N;ENSP00000291691:D131N;ENSP00000380801:D48N	ENSP00000291691:D131N	D	-	1	0	C21orf58	46559869	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.998000	0.03701	-0.380000	0.07894	-0.126000	0.14955	GAT	.	.		0.597	C21orf58-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207283.1	NM_058180		T	47735441	C	T	47735441	3	4	344	1	0	0	0	0	1	0	0	0	2131	884	31	1	597	1	C21orf58	21	47735441	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	183303	47735441	394454	1357	48720										
GNB1L	54584	hgsc.bcm.edu	37	chr22	19808139	19808139	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acctgaggagctggcgccccTggggcagcgtctgcagccag	16	14	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr22:19808139T>A	ENST00000329517.6	-	4	472	c.236A>T	c.(235-237)cAg>cTg	p.Q79L	GNB1L_ENST00000405009.1_Missense_Mutation_p.Q79L|GNB1L_ENST00000403325.1_Missense_Mutation_p.Q79L|GNB1L_ENST00000460402.1_Intron	NM_053004.2	NP_443730.1	Q9BYB4	GNB1L_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 1-like	79					G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|social behavior (GO:0035176)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)		p.Q79P(1)		breast(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(3)|skin(1)	12	Colorectal(54;0.0993)					CTGGCGCCCCTGGGGCAGCGT	0.657																																					p.Q79L		Atlas-SNP	.											GNB1L,NS,carcinoma,0,1	GNB1L	34	.	1	Substitution - Missense(1)	prostate(1)	c.A236T						.						28	33	32					22																	19808139		2203	4299	6502	SO:0001583	missense	54584	exon4			CGCCCCTGGGGCA	AF238328	CCDS13768.1	22q11.2	2013-05-21			ENSG00000185838	ENSG00000185838		"WD repeat domain containing"	4397	protein-coding gene	gene with protein product		610778				11072084	Standard	NM_053004		Approved	GY2, WDR14	uc002zqf.1	Q9BYB4	OTTHUMG00000150279	ENST00000329517.6:c.236A>T	chr22.hg19:g.19808139T>A	ENSP00000331313:p.Gln79Leu	107.0	0.0		82.0	32.0	NM_053004	Q9H2S2|Q9H4M4	Missense_Mutation	SNP	ENST00000329517.6	hg19	CCDS13768.1	.	.	.	.	.	.	.	.	.	.	T	11.33	1.605604	0.28623	.	.	ENSG00000185838	ENST00000329517;ENST00000403325;ENST00000405009	T;T;T	0.37058	1.22;1.22;5.0	5.57	2.2	0.27929	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.771754	0.11573	U	0.550516	T	0.24967	0.0606	L	0.46157	1.445	0.19775	N	0.999957	B	0.32160	0.358	B	0.23716	0.048	T	0.33266	-0.9875	10	0.87932	D	0	-16.2102	1.8293	0.03127	0.1681:0.0893:0.1757:0.5669	.	79	Q9BYB4	GNB1L_HUMAN	L	79	ENSP00000331313:Q79L;ENSP00000385154:Q79L;ENSP00000384626:Q79L	ENSP00000331313:Q79L	Q	-	2	0	GNB1L	18188139	0.348000	0.24861	0.734000	0.30879	0.972000	0.66771	0.530000	0.23036	0.356000	0.24157	0.455000	0.32223	CAG	.	.		0.657	GNB1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075202.1			A	19808139	T	A	19808139	3	1	344	1	0	0	0	0	1	0	0	0	6524	1580	55	4	767	4	GNB1L	22	19808139	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10		19808139	31496427	1358	48721										
P2RX6	9127	hgsc.bcm.edu	37	chr22	21380894	21380894	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acccacttgccaacccattcCgggagcctgtagccgttccc	8	18	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr22:21380894C>A	ENST00000413302.2	+	12	1462	c.1314C>A	c.(1312-1314)tcC>tcA	p.S438S	P2RX6_ENST00000402329.3_3'UTR|P2RX6_ENST00000401443.1_Silent_p.S412S|P2RX6_ENST00000443995.3_Silent_p.S385S|P2RX6_ENST00000336296.2_Silent_p.S428S			O15547	P2RX6_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 6	438					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|muscle contraction (GO:0006936)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|channel activity (GO:0015267)|extracellular ATP-gated cation channel activity (GO:0004931)|identical protein binding (GO:0042802)|purinergic nucleotide receptor activity (GO:0001614)|transmembrane signaling receptor activity (GO:0004888)										CAACCCATTCCGGGAGCCTGT	0.637																																					p.S438S		Atlas-SNP	.											.	.	.	.	0			c.C1314A						.						34	29	31					22																	21380894		2200	4287	6487	SO:0001819	synonymous_variant	9127	exon12			CCATTCCGGGAGC		CCDS13788.2, CCDS54504.1	22q11.21	2012-01-17	2008-03-28	2008-03-28	ENSG00000099957	ENSG00000099957		"Purinergic receptors", "Ligand-gated ion channels / Purinergic receptors, ionotropic"	8538	protein-coding gene	gene with protein product		608077	"purinergic receptor P2X-like 1, orphan receptor"	P2RXL1		9242461, 10591208, 8786426	Standard	NM_005446		Approved	P2XM, MGC129625, P2X6	uc010gsu.1	O15547	OTTHUMG00000150689	ENST00000413302.2:c.1314C>A	chr22.hg19:g.21380894C>A		96.0	0.0		72.0	26.0	NM_005446	F6V3D7|Q32MB6|Q58F04|Q6IC33|Q9UL50	Silent	SNP	ENST00000413302.2	hg19	CCDS13788.2																																																																																			.	.		0.637	P2RX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319625.2	NM_005446		A	21380894	C	A	21380894	2	1	344	1	0	0	0	0	0	0	0	1	11353	639	23	1		1	P2RX6	22	21380894	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1572755	21380894	29923672	1359	48722										
PRAME	23532	hgsc.bcm.edu	37	chr22	22892325	22892325	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggagtctacgcagattaatcAtctggcccaggtaaggagaa	12	8	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr22:22892325A>G	ENST00000398741.1	-	5	1082	c.776T>C	c.(775-777)aTg>aCg	p.M259T	PRAME_ENST00000402697.1_Missense_Mutation_p.M259T|PRAME_ENST00000398743.2_Missense_Mutation_p.M259T|PRAME_ENST00000485532.1_5'Flank|PRAME_ENST00000424204.2_Missense_Mutation_p.M243T|PRAME_ENST00000405655.3_Missense_Mutation_p.M259T|PRAME_ENST00000539862.1_Missense_Mutation_p.M243T|PRAME_ENST00000543184.1_Missense_Mutation_p.M259T	NM_206955.1	NP_996838.1	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma	259					apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	retinoic acid receptor binding (GO:0042974)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05)		READ - Rectum adenocarcinoma(21;0.0649)		CAGATTAATCATCTGGCCCAG	0.483																																					p.M259T	Melanoma(73;1707 1838 15168 27201)	Atlas-SNP	.											.	PRAME	78	.	0			c.T776C						.						98	91	93					22																	22892325		2203	4300	6503	SO:0001583	missense	23532	exon5			TTAATCATCTGGC	U65011	CCDS13801.1	22q11.22	2013-01-17			ENSG00000185686	ENSG00000185686		"-"	9336	protein-coding gene	gene with protein product	"cancer/testis antigen 130"	606021		MAPE		9047241, 10591208	Standard	XM_006725402		Approved	CT130	uc002zwj.3	P78395	OTTHUMG00000151172	ENST00000398741.1:c.776T>C	chr22.hg19:g.22892325A>G	ENSP00000381726:p.Met259Thr	75.0	0.0		80.0	32.0	NM_206954	B2R6Y7|O43481|Q8IXN8	Missense_Mutation	SNP	ENST00000398741.1	hg19	CCDS13801.1	.	.	.	.	.	.	.	.	.	.	A	12.04	1.819437	0.32145	.	.	ENSG00000185686	ENST00000398743;ENST00000543184;ENST00000398741;ENST00000405655;ENST00000539862;ENST00000402697;ENST00000424204	T;T;T;T;T;T;T	0.00986	5.47;5.47;5.47;5.47;5.47;5.47;5.47	3.78	3.78	0.43462	.	0.115233	0.64402	D	0.000014	T	0.05456	0.0144	M	0.89030	3	0.26454	N	0.975553	D	0.71674	0.998	D	0.68192	0.956	T	0.02942	-1.1091	10	0.87932	D	0	.	9.1966	0.37231	1.0:0.0:0.0:0.0	.	259	P78395	PRAME_HUMAN	T	259;259;259;259;243;259;243	ENSP00000381728:M259T;ENSP00000445675:M259T;ENSP00000381726:M259T;ENSP00000384343:M259T;ENSP00000445097:M243T;ENSP00000385198:M259T;ENSP00000407342:M243T	ENSP00000381726:M259T	M	-	2	0	PRAME	21222325	0.996000	0.38824	0.990000	0.47175	0.022000	0.10575	2.845000	0.48254	1.944000	0.56390	0.533000	0.62120	ATG	.	.		0.483	PRAME-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321644.1	NM_206953		G	22892325	A	G	22892325	3	3	344	1	0	0	0	0	1	0	0	0	12436	217	8	2	761	2	PRAME	22	22892325	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1511431	22892325	28412241	1360	48723										
SUSD2	56241	hgsc.bcm.edu	37	chr22	24584255	24584255	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcgcggtggtggcggcggttGcgctcgtctatgtgctgctg	18	10	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr22:24584255G>A	ENST00000358321.3	+	14	2665	c.2404G>A	c.(2404-2406)Gcg>Acg	p.A802T		NM_019601.3	NP_062547.1	Q9UGT4	SUSD2_HUMAN	sushi domain containing 2	802					immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	26						GGCGGCGGTTGCGCTCGTCTA	0.677																																					p.A802T		Atlas-SNP	.											.	SUSD2	68	.	0			c.G2404A						.						57	60	59					22																	24584255		2203	4299	6502	SO:0001583	missense	56241	exon14			GCGGTTGCGCTCG	AK026431	CCDS13824.1	22q11-q12	2005-08-16			ENSG00000099994	ENSG00000099994			30667	protein-coding gene	gene with protein product		615825				12477932	Standard	NM_019601		Approved	BK65A6.2, FLJ22778	uc002zzn.1	Q9UGT4	OTTHUMG00000150792	ENST00000358321.3:c.2404G>A	chr22.hg19:g.24584255G>A	ENSP00000351075:p.Ala802Thr	36.0	0.0		31.0	18.0	NM_019601	Q9H5Y6	Missense_Mutation	SNP	ENST00000358321.3	hg19	CCDS13824.1	.	.	.	.	.	.	.	.	.	.	G	10.70	1.424638	0.25639	.	.	ENSG00000099994	ENST00000358321	T	0.20598	2.06	4.71	-8.18	0.01053	.	0.772302	0.11865	N	0.521959	T	0.06325	0.0163	N	0.14661	0.345	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.31586	-0.9938	10	0.18276	T	0.48	-5.8995	0.1339	0.00076	0.3238:0.2287:0.2035:0.244	.	802	Q9UGT4	SUSD2_HUMAN	T	802	ENSP00000351075:A802T	ENSP00000351075:A802T	A	+	1	0	SUSD2	22914255	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.219000	0.09228	-1.172000	0.02762	-1.297000	0.01338	GCG	.	.		0.677	SUSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320088.1	NM_019601		A	24584255	G	A	24584255	3	1	344	1	0	0	0	0	1	0	0	0	15423	1319	46	3	2458	3	SUSD2	22	24584255	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	1691930	24584255	26720311	1361	48724										
GGT5	2687	hgsc.bcm.edu	37	chr22	24629889	24629889	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgacccctccgcccaggcccAtgctctgagggttgacgacg	12	16	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr22:24629889A>T	ENST00000327365.4	-	2	673	c.257T>A	c.(256-258)aTg>aAg	p.M86K	GGT5_ENST00000398292.3_Missense_Mutation_p.M86K|GGT5_ENST00000263112.7_Missense_Mutation_p.M86K|GGT5_ENST00000418439.2_Intron	NM_001099781.1|NM_004121.2	NP_001093251.1|NP_004112.2	P36269	GGT5_HUMAN	gamma-glutamyltransferase 5	86					arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|inflammatory response (GO:0006954)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)	anchored component of external side of plasma membrane (GO:0031362)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(3)|skin(3)	28						GCCCAGGCCCATGCTCTGAGG	0.612																																					p.M86K		Atlas-SNP	.											.	GGT5	61	.	0			c.T257A						.						114	92	100					22																	24629889		2203	4300	6503	SO:0001583	missense	2687	exon2			AGGCCCATGCTCT	M64099	CCDS13825.1, CCDS42989.1, CCDS42990.1	22q11.23	2008-03-25	2008-03-10	2008-03-10	ENSG00000099998	ENSG00000099998		"Gamma-glutamyltransferases"	4260	protein-coding gene	gene with protein product		137168	"gamma-glutamyltransferase-like activity 1"	GGTLA1		1676842, 8095916, 18357469	Standard	NM_004121		Approved	GGT-REL	uc002zzp.4	P36269	OTTHUMG00000150796	ENST00000327365.4:c.257T>A	chr22.hg19:g.24629889A>T	ENSP00000330080:p.Met86Lys	101.0	0.0		111.0	54.0	NM_001099782	Q53XM9|Q6GMP0|Q96FC1|Q9UFM5	Missense_Mutation	SNP	ENST00000327365.4	hg19	CCDS13825.1	.	.	.	.	.	.	.	.	.	.	A	19.77	3.889803	0.72524	.	.	ENSG00000099998	ENST00000327365;ENST00000263112;ENST00000438024;ENST00000398292	T;T;T	0.06371	3.31;3.31;3.31	4.87	2.68	0.31781	.	0.128752	0.64402	D	0.000002	T	0.22085	0.0532	M	0.91406	3.205	0.80722	D	1	P;P;B;P	0.35575	0.454;0.51;0.336;0.51	B;P;B;P	0.48982	0.36;0.597;0.222;0.597	T	0.00307	-1.1830	10	0.62326	D	0.03	-12.8913	8.8518	0.35203	0.864:0.0:0.136:0.0	.	86;86;86;86	P36269-2;Q53XM9;Q6GMP0;P36269	.;.;.;GGT5_HUMAN	K	86;86;1;86	ENSP00000330080:M86K;ENSP00000263112:M86K;ENSP00000381340:M86K	ENSP00000263112:M86K	M	-	2	0	GGT5	22959889	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	3.327000	0.52045	0.315000	0.23110	0.254000	0.18369	ATG	.	.		0.612	GGT5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320119.1	NM_004121		T	24629889	A	T	24629889	3	4	344	1	0	0	0	0	1	0	0	0	6370	217	8	4	1550	4	GGT5	22	24629889	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	45634	24629889	26674677	1362	48725										
TMEM211	255349	hgsc.bcm.edu	37	chr22	25334227	25334227	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	attgaaggccaacaggagccAgcctccgaggagcatcacag	12	12	1	1	rs112354981		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr22:25334227A>T	ENST00000423535.1	-	2	228	c.229T>A	c.(229-231)Tgg>Agg	p.W77R	TMEM211_ENST00000382744.1_Missense_Mutation_p.W6R|TMEM211_ENST00000407886.1_Missense_Mutation_p.W6R			Q6ICI0	TM211_HUMAN	transmembrane protein 211	77						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	8						AACAGGAGCCAGCCTCCGAGG	0.577																																					p.W6R		Atlas-SNP	.											.	TMEM211	16	.	0			c.T16A						.						64	59	61					22																	25334227		2203	4300	6503	SO:0001583	missense	255349	exon2			GGAGCCAGCCTCC		CCDS33624.1	22q11.23	2009-01-12			ENSG00000206069	ENSG00000206069			33725	protein-coding gene	gene with protein product							Standard	NM_001001663		Approved	bA9F11.1	uc003abk.1	Q6ICI0	OTTHUMG00000150790	ENST00000423535.1:c.229T>A	chr22.hg19:g.25334227A>T	ENSP00000387813:p.Trp77Arg	26.0	0.0		33.0	16.0	NM_001001663		Missense_Mutation	SNP	ENST00000423535.1	hg19		.	.	.	.	.	.	.	.	.	.	A	17.74	3.464111	0.63513	.	.	ENSG00000206069	ENST00000407886;ENST00000423535;ENST00000382744	T;T;T	0.78126	-1.15;-0.56;-1.15	4.06	4.06	0.47325	.	0.000000	0.45126	D	0.000395	D	0.85465	0.5703	M	0.69823	2.125	0.44162	D	0.99696	D	0.76494	0.999	D	0.72338	0.977	D	0.86752	0.1961	10	0.72032	D	0.01	-29.1687	11.4718	0.50272	1.0:0.0:0.0:0.0	.	77	Q6ICI0	TM211_HUMAN	R	6;77;6	ENSP00000385494:W6R;ENSP00000387813:W77R;ENSP00000372192:W6R	ENSP00000372192:W6R	W	-	1	0	TMEM211	23664227	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	2.917000	0.48821	1.872000	0.54250	0.440000	0.28878	TGG	.	A|0.500;G|0.500		0.577	TMEM211-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001001663		T	25334227	A	T	25334227	3	4	344	1	0	0	0	0	1	0	0	0	16150	188	7	4	381	4	TMEM211	22	25334227	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	704338	25334227	25970339	1363	48726										
MYO18B	84700	hgsc.bcm.edu	37	chr22	26423048	26423048	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaaaactgagctctccgaccAcacccagggacatgctgttg	10	13	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr22:26423048A>T	ENST00000407587.2	+	43	7280	c.7111A>T	c.(7111-7113)Aca>Tca	p.T2371S	MYO18B_ENST00000335473.7_Missense_Mutation_p.T2370S|MYO18B_ENST00000536101.1_Missense_Mutation_p.T2370S			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2370						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						CTCTCCGACCACACCCAGGGA	0.582																																					p.T2370S		Atlas-SNP	.											.	MYO18B	322	.	0			c.A7108T						.						91	99	97					22																	26423048		1994	4167	6161	SO:0001583	missense	84700	exon43			CCGACCACACCCA	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.7111A>T	chr22.hg19:g.26423048A>T	ENSP00000386096:p.Thr2371Ser	56.0	0.0		56.0	25.0	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	hg19		.	.	.	.	.	.	.	.	.	.	A	4.875	0.162662	0.09287	.	.	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.87179	-2.2;-2.2;-2.22	4.86	-8.03	0.01114	.	2.664100	0.01326	N	0.011097	T	0.71126	0.3303	N	0.08118	0	0.09310	N	1	B;B;B;B;B	0.09022	0.001;0.0;0.0;0.002;0.001	B;B;B;B;B	0.08055	0.002;0.001;0.001;0.003;0.001	T	0.64744	-0.6335	10	0.10636	T	0.68	.	11.9263	0.52820	0.1335:0.2192:0.6473:0.0	.	1883;2372;2370;2371;2370	Q8IUG5-2;B0QYF5;Q8IUG5;F5GXR6;F5GYU7	.;.;MY18B_HUMAN;.;.	S	2370;2370;2371	ENSP00000441229:T2370S;ENSP00000334563:T2370S;ENSP00000386096:T2371S	ENSP00000334563:T2370S	T	+	1	0	MYO18B	24753048	0.000000	0.05858	0.000000	0.03702	0.353000	0.29299	-0.685000	0.05167	-1.742000	0.01342	-0.464000	0.05259	ACA	.	.		0.582	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		T	26423048	A	T	26423048	3	4	344	1	0	0	0	0	1	0	0	0	10075	159	6	4	7274	4	MYO18B	22	26423048	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1088821	26423048	24881518	1364	48727										
SEZ6L	23544	hgsc.bcm.edu	37	chr22	26688929	26688929	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tggcccacacactcccccagAggccagaacccggggagcct	11	18	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr22:26688929A>T	ENST00000248933.6	+	2	747	c.652A>T	c.(652-654)Agg>Tgg	p.R218W	SEZ6L_ENST00000360929.3_Missense_Mutation_p.R218W|SEZ6L_ENST00000529632.2_Missense_Mutation_p.R218W|SEZ6L_ENST00000402979.1_De_novo_Start_InFrame|SEZ6L_ENST00000404234.3_Missense_Mutation_p.R218W|SEZ6L_ENST00000403121.1_De_novo_Start_InFrame|SEZ6L_ENST00000343706.4_Missense_Mutation_p.R218W			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	218					adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)				breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	80						ACTCCCCCAGAGGCCAGAACC	0.642																																					p.R218W		Atlas-SNP	.											.	SEZ6L	174	.	0			c.A652T						.						39	44	42					22																	26688929		2199	4293	6492	SO:0001583	missense	23544	exon2			CCCCAGAGGCCAG	AL050253	CCDS13833.1, CCDS54508.1, CCDS54510.1, CCDS54511.1, CCDS74837.1	22q12.1	2008-05-14	2001-11-28		ENSG00000100095	ENSG00000100095			10763	protein-coding gene	gene with protein product		607021	"seizure related gene 6 (mouse)-like"				Standard	NM_021115		Approved		uc003acb.3	Q9BYH1	OTTHUMG00000150870	ENST00000248933.6:c.652A>T	chr22.hg19:g.26688929A>T	ENSP00000248933:p.Arg218Trp	156.0	0.0		84.0	38.0	NM_021115	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Missense_Mutation	SNP	ENST00000248933.6	hg19	CCDS13833.1	.	.	.	.	.	.	.	.	.	.	A	13.39	2.221691	0.39300	.	.	ENSG00000100095	ENST00000404234;ENST00000529632;ENST00000360929;ENST00000248933;ENST00000343706	T;T;T;T;T	0.27557	1.9;2.01;2.1;1.9;1.66	3.84	0.415	0.16411	.	0.857165	0.09894	U	0.741905	T	0.24470	0.0593	N	0.08118	0	0.21064	N	0.999792	P;P;D;D;P;P	0.63046	0.953;0.953;0.992;0.992;0.953;0.953	B;B;P;P;B;B	0.58970	0.43;0.315;0.849;0.849;0.315;0.315	T	0.13335	-1.0513	10	0.38643	T	0.18	.	4.2931	0.10888	0.6277:0.1733:0.199:0.0	.	218;218;218;218;218;218	B7ZLJ8;B7ZLJ6;Q9BYH1-5;Q9BYH1-4;B0QYG3;Q9BYH1	.;.;.;.;.;SE6L1_HUMAN	W	218	ENSP00000384772:R218W;ENSP00000437037:R218W;ENSP00000354185:R218W;ENSP00000248933:R218W;ENSP00000342661:R218W	ENSP00000248933:R218W	R	+	1	2	SEZ6L	25018929	0.000000	0.05858	0.159000	0.22649	0.448000	0.32197	0.170000	0.16663	-0.082000	0.12640	0.333000	0.21579	AGG	.	.		0.642	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3			T	26688929	A	T	26688929	3	4	344	1	0	0	0	0	1	0	0	0	14158	295	11	4	658	4	SEZ6L	22	26688929	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	265881	26688929	24615637	1365	48728										
HPS4	89781	hgsc.bcm.edu	37	chr22	26849269	26849269	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agaggctgaaggcgccatccTgagggtttgggaagccggag	18	8	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr22:26849269T>G	ENST00000398145.2	-	14	2673	c.2057A>C	c.(2056-2058)cAg>cCg	p.Q686P	HPS4_ENST00000493455.2_Intron|HPS4_ENST00000398141.1_Missense_Mutation_p.Q699P|HPS4_ENST00000336873.5_Missense_Mutation_p.Q686P|HPS4_ENST00000402105.3_Missense_Mutation_p.Q681P	NM_022081.5	NP_071364.4	Q9NQG7	HPS4_HUMAN	Hermansky-Pudlak syndrome 4	686					blood coagulation (GO:0007596)|hemostasis (GO:0007599)|lysosome organization (GO:0007040)|melanocyte differentiation (GO:0030318)|positive regulation of eye pigmentation (GO:0048075)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)	BLOC-3 complex (GO:0031085)|cytoplasm (GO:0005737)|lysosome (GO:0005764)|melanosome (GO:0042470)|membrane (GO:0016020)|platelet dense granule (GO:0042827)	protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(3)|kidney(5)|large_intestine(4)|lung(12)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	32						GGCGCCATCCTGAGGGTTTGG	0.592									Hermansky-Pudlak syndrome																												p.Q686P		Atlas-SNP	.											.	HPS4	123	.	0			c.A2057C						.						128	129	129					22																	26849269		2203	4300	6503	SO:0001583	missense	89781	exon14	Familial Cancer Database	HPS, HPS1-8	CCATCCTGAGGGT		CCDS13835.1, CCDS46677.1	22q12.1	2014-09-17			ENSG00000100099	ENSG00000100099			15844	protein-coding gene	gene with protein product		606682				11836498, 12663659	Standard	NM_022081		Approved	KIAA1667, LE	uc003aci.4	Q9NQG7	OTTHUMG00000030459	ENST00000398145.2:c.2057A>C	chr22.hg19:g.26849269T>G	ENSP00000381213:p.Gln686Pro	67.0	0.0		41.0	20.0	NM_022081	B1AHQ4|Q5H8V6|Q96LX6|Q9BY93|Q9UH37|Q9UH38	Missense_Mutation	SNP	ENST00000398145.2	hg19	CCDS13835.1	.	.	.	.	.	.	.	.	.	.	T	13.79	2.341917	0.41498	.	.	ENSG00000100099	ENST00000398145;ENST00000398141;ENST00000402105;ENST00000336873	T;T;T;T	0.20881	2.04;2.04;2.04;2.04	4.46	3.42	0.39159	.	0.134270	0.52532	D	0.000075	T	0.44030	0.1274	M	0.77103	2.36	0.41815	D	0.989993	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.999	T	0.38972	-0.9636	10	0.87932	D	0	-9.7599	9.2347	0.37459	0.0:0.0856:0.0:0.9144	.	686;686;686;699;681	Q6P1K3;Q9NQG7;A8K2E6;Q9NQG7-4;Q9NQG7-3	.;HPS4_HUMAN;.;.;.	P	686;699;681;686	ENSP00000381213:Q686P;ENSP00000381210:Q699P;ENSP00000384185:Q681P;ENSP00000338457:Q686P	ENSP00000338457:Q686P	Q	-	2	0	HPS4	25179269	1.000000	0.71417	0.809000	0.32408	0.047000	0.14425	5.048000	0.64238	0.748000	0.32831	0.454000	0.30748	CAG	.	.		0.592	HPS4-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320778.1	NM_022081		G	26849269	T	G	26849269	3	3	344	1	0	0	0	0	1	0	0	0	7350	1580	55	5	73	5	HPS4	22	26849269	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	160340	26849269	24455297	1366	48729										
CRYBB1	1414	hgsc.bcm.edu	37	chr22	26995533	26995533	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cacgcaggcgacgcagggacTgcatctgtggctggaaggct	16	11	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr22:26995533T>A	ENST00000215939.2	-	6	810	c.680A>T	c.(679-681)cAg>cTg	p.Q227L	TPST2_ENST00000403880.1_5'Flank	NM_001887.3	NP_001878.1	P53674	CRBB1_HUMAN	crystallin, beta B1	227	Beta/gamma crystallin 'Greek key' 4. {ECO:0000255|PROSITE-ProRule:PRU00028}.				visual perception (GO:0007601)		structural constituent of eye lens (GO:0005212)			breast(1)|endometrium(4)|large_intestine(8)|lung(8)|ovary(1)|prostate(3)|skin(2)|urinary_tract(4)	31						ACGCAGGGACTGCATCTGTGG	0.617																																					p.Q227L		Atlas-SNP	.											.	CRYBB1	49	.	0			c.A680T						.						69	59	62					22																	26995533		2203	4300	6503	SO:0001583	missense	1414	exon6			AGGGACTGCATCT		CCDS13840.1	22q12.1	2008-06-10			ENSG00000100122	ENSG00000100122			2397	protein-coding gene	gene with protein product		600929				8575764, 12360425	Standard	NM_001887		Approved		uc003acy.1	P53674	OTTHUMG00000150980	ENST00000215939.2:c.680A>T	chr22.hg19:g.26995533T>A	ENSP00000215939:p.Gln227Leu	112.0	0.0		97.0	40.0	NM_001887		Missense_Mutation	SNP	ENST00000215939.2	hg19	CCDS13840.1	.	.	.	.	.	.	.	.	.	.	T	25.4	4.637910	0.87760	.	.	ENSG00000100122	ENST00000215939	T	0.76709	-1.04	4.22	4.22	0.49857	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.000000	0.85682	D	0.000000	D	0.87394	0.6166	M	0.81179	2.53	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.88888	0.3344	10	0.66056	D	0.02	.	12.9201	0.58226	0.0:0.0:0.0:1.0	.	227	P53674	CRBB1_HUMAN	L	227	ENSP00000215939:Q227L	ENSP00000215939:Q227L	Q	-	2	0	CRYBB1	25325533	1.000000	0.71417	0.999000	0.59377	0.918000	0.54935	5.541000	0.67212	1.904000	0.55121	0.460000	0.39030	CAG	.	.		0.617	CRYBB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320767.1	NM_001887		A	26995533	T	A	26995533	3	1	344	1	0	0	0	0	1	0	0	0	3912	1580	55	4	82	4	CRYBB1	22	26995533	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	146264	26995533	24309033	1367	48730										
CRYBA4	1413	hgsc.bcm.edu	37	chr22	27026355	27026355	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggatttcagtatgtgctggaAtgcgatcaccattccggtga	12	8	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr22:27026355A>T	ENST00000354760.3	+	6	530	c.495A>T	c.(493-495)gaA>gaT	p.E165D	CRYBA4_ENST00000466315.1_3'UTR	NM_001886.2	NP_001877.1	P53673	CRBA4_HUMAN	crystallin, beta A4	165	Beta/gamma crystallin 'Greek key' 4. {ECO:0000255|PROSITE-ProRule:PRU00028}.				camera-type eye development (GO:0043010)|visual perception (GO:0007601)		structural constituent of eye lens (GO:0005212)			large_intestine(6)|liver(1)|lung(6)|skin(3)|urinary_tract(2)	18						ATGTGCTGGAATGCGATCACC	0.542																																					p.E165D		Atlas-SNP	.											.	CRYBA4	33	.	0			c.A495T						.						121	97	105					22																	27026355		2203	4300	6503	SO:0001583	missense	1413	exon6			GCTGGAATGCGAT		CCDS13841.1	22q12.1	2008-06-10			ENSG00000196431	ENSG00000196431			2396	protein-coding gene	gene with protein product		123631				8999933, 960806	Standard	NM_001886		Approved		uc003acz.4	P53673	OTTHUMG00000150983	ENST00000354760.3:c.495A>T	chr22.hg19:g.27026355A>T	ENSP00000346805:p.Glu165Asp	53.0	0.0		45.0	15.0	NM_001886	Q4VB22|Q6ICE4	Missense_Mutation	SNP	ENST00000354760.3	hg19	CCDS13841.1	.	.	.	.	.	.	.	.	.	.	A	14.60	2.582644	0.46006	.	.	ENSG00000196431	ENST00000354760	T	0.78246	-1.16	4.4	2.01	0.26516	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.000000	0.64402	D	0.000005	D	0.87107	0.6095	M	0.91459	3.21	0.49389	D	0.999785	D	0.76494	0.999	D	0.97110	1.0	D	0.84807	0.0788	10	0.49607	T	0.09	.	5.0367	0.14438	0.3553:0.0:0.6447:0.0	.	165	P53673	CRBA4_HUMAN	D	165	ENSP00000346805:E165D	ENSP00000346805:E165D	E	+	3	2	CRYBA4	25356355	1.000000	0.71417	0.806000	0.32338	0.001000	0.01503	3.578000	0.53892	1.064000	0.40671	-0.364000	0.07487	GAA	.	.		0.542	CRYBA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320793.1	NM_001886		T	27026355	A	T	27026355	3	4	344	1	0	0	0	0	1	0	0	0	3911	98	4	4	513	4	CRYBA4	22	27026355	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	30822	27026355	24278211	1368	48731										
CHEK2	11200	hgsc.bcm.edu	37	chr22	29130640	29130640	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gccttgggactgggtaacgcTgccatggggctgtgaacagg	17	9	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr22:29130640T>A	ENST00000405598.1	-	3	261	c.70A>T	c.(70-72)Agc>Tgc	p.S24C	CHEK2_ENST00000382566.1_Missense_Mutation_p.S24C|CHEK2_ENST00000403642.1_Missense_Mutation_p.S24C|CHEK2_ENST00000382578.1_Missense_Mutation_p.S24C|CHEK2_ENST00000328354.6_Missense_Mutation_p.S24C|CHEK2_ENST00000404276.1_Missense_Mutation_p.S24C|CHEK2_ENST00000348295.3_Missense_Mutation_p.S24C|CHEK2_ENST00000402731.1_Missense_Mutation_p.S24C|CHEK2_ENST00000382580.2_Missense_Mutation_p.S24C|CHEK2_ENST00000382565.1_Missense_Mutation_p.S24C|CHEK2_ENST00000544772.1_5'UTR			O96017	CHK2_HUMAN	checkpoint kinase 2	24					cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						TGGGTAACGCTGCCATGGGGC	0.567			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																													p.S24C		Atlas-SNP	.	yes	Rec		familial breast cancer	22	22q12.1	11200	CHK2 checkpoint homolog (S. pombe)		E	.	CHEK2	438	.	0			c.A70T						.						128	106	113					22																	29130640		2203	4300	6503	SO:0001583	missense	11200	exon2			TAACGCTGCCATG	AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"CHK2 (checkpoint, S.pombe) homolog", "CHK2 checkpoint homolog (S. pombe)"	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.70A>T	chr22.hg19:g.29130640T>A	ENSP00000386087:p.Ser24Cys	110.0	0.0		94.0	33.0	NM_145862	A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Missense_Mutation	SNP	ENST00000405598.1	hg19	CCDS13843.1	.	.	.	.	.	.	.	.	.	.	T	11.12	1.546427	0.27652	.	.	ENSG00000183765	ENST00000348295;ENST00000382578;ENST00000382565;ENST00000382563;ENST00000382566;ENST00000328354;ENST00000404276;ENST00000405598;ENST00000382580;ENST00000403642;ENST00000402731;ENST00000447421;ENST00000439200;ENST00000398017	T;T;T;D;T;T;T;T;T;T;T;D;D	0.94376	0.62;-0.28;-0.18;-3.41;-0.34;-0.34;-0.34;-0.29;-0.28;0.62;0.17;-3.35;-2.4	4.63	-9.27	0.00659	.	1.412880	0.04396	N	0.363279	T	0.82217	0.4989	N	0.14661	0.345	0.09310	N	1	B;B;B;B;B;P	0.45827	0.0;0.0;0.0;0.0;0.0;0.867	B;B;B;B;B;B	0.41202	0.001;0.001;0.0;0.001;0.0;0.35	T	0.80037	-0.1550	10	0.36615	T	0.2	11.8626	2.8334	0.05507	0.1094:0.1871:0.1963:0.5072	.	24;24;24;24;24;24	O96017-7;O96017-4;A8JZZ5;O96017-12;O96017;O96017-9	.;.;.;.;CHK2_HUMAN;.	C	24;24;24;24;24;24;24;24;24;24;24;24;24;34	ENSP00000329012:S24C;ENSP00000372021:S24C;ENSP00000372006:S24C;ENSP00000372007:S24C;ENSP00000329178:S24C;ENSP00000385747:S24C;ENSP00000386087:S24C;ENSP00000372023:S24C;ENSP00000384919:S24C;ENSP00000384835:S24C;ENSP00000397478:S24C;ENSP00000408065:S24C;ENSP00000381099:S34C	ENSP00000329178:S24C	S	-	1	0	CHEK2	27460640	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-1.432000	0.02430	-2.458000	0.00538	-0.408000	0.06270	AGC	.	.		0.567	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735		A	29130640	T	A	29130640	3	1	344	1	0	0	0	0	1	0	0	0	3337	1580	55	4	1750	4	CHEK2	22	29130640	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2104285	29130640	22173926	1369	48732										
MORC2	22880	hgsc.bcm.edu	37	chr22	31333654	31333654	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gggctggttccagttggcagAgaggtagccaaactcatccc	13	11	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr22:31333654A>G	ENST00000397641.3	-	15	1822	c.1414T>C	c.(1414-1416)Tct>Cct	p.S472P	MORC2_ENST00000215862.4_Missense_Mutation_p.S410P|MORC2_ENST00000469915.1_Intron			Q9Y6X9	MORC2_HUMAN	MORC family CW-type zinc finger 2	472						cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	21						CAGTTGGCAGAGAGGTAGCCA	0.547																																					p.S410P		Atlas-SNP	.											.	MORC2	78	.	0			c.T1228C						.						69	65	66					22																	31333654		2203	4300	6503	SO:0001583	missense	22880	exon16			TGGCAGAGAGGTA	AB020659	CCDS33636.1	22q12.2	2005-06-15	2005-06-15	2005-06-15	ENSG00000133422	ENSG00000133422			23573	protein-coding gene	gene with protein product			"zinc finger, CW-type with coiled-coil domain 1", "zinc finger, CW type with coiled-coil domain 1"	ZCWCC1		14607086	Standard	XM_005261391		Approved	ZCW3, KIAA0852, AC004542.C22.1	uc003aje.1	Q9Y6X9	OTTHUMG00000151193	ENST00000397641.3:c.1414T>C	chr22.hg19:g.31333654A>G	ENSP00000380763:p.Ser472Pro	38.0	0.0		44.0	19.0	NM_014941	B2RNB1|Q9UF28|Q9Y6V2	Missense_Mutation	SNP	ENST00000397641.3	hg19		.	.	.	.	.	.	.	.	.	.	A	29.0	4.968457	0.92855	.	.	ENSG00000133422	ENST00000397641;ENST00000215862	T;T	0.14144	2.53;2.53	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.38772	0.1053	M	0.74881	2.28	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.21518	-1.0243	10	0.72032	D	0.01	.	15.8945	0.79325	1.0:0.0:0.0:0.0	.	472	Q9Y6X9	MORC2_HUMAN	P	472;410	ENSP00000380763:S472P;ENSP00000215862:S410P	ENSP00000215862:S410P	S	-	1	0	MORC2	29663654	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.905000	0.92613	2.210000	0.71456	0.454000	0.30748	TCT	.	.		0.547	MORC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000321710.2	NM_014941		G	31333654	A	G	31333654	3	3	344	1	0	0	0	0	1	0	0	0	9711	304	11	2	1732	2	MORC2	22	31333654	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	2203014	31333654	19970912	1370	48733										
BPIL2	254240	hgsc.bcm.edu	37	chr22	32828474	32828474	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgtagattgattatgggaggCtctgtggccatgatcctcac	12	8	2	3	rs374301481		TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr22:32828474C>A	ENST00000397452.1	-	11	1145	c.1035G>T	c.(1033-1035)gaG>gaT	p.E345D	BPIFC_ENST00000432451.2_Intron|BPIFC_ENST00000300399.3_Missense_Mutation_p.E345D|BPIFC_ENST00000534972.1_Missense_Mutation_p.E69D			Q8NFQ6	BPIFC_HUMAN	BPI fold containing family C	345						extracellular region (GO:0005576)	lipopolysaccharide binding (GO:0001530)|phospholipid binding (GO:0005543)										TTATGGGAGGCTCTGTGGCCA	0.493																																					p.E345D		Atlas-SNP	.											.	.	.	.	0			c.G1035T						.						261	242	248					22																	32828474		2203	4300	6503	SO:0001583	missense	254240	exon10			GGGAGGCTCTGTG	AF465766	CCDS13906.1	22q12.3	2011-08-04	2011-08-01	2011-08-01	ENSG00000184459	ENSG00000184459		"BPI fold containing"	16503	protein-coding gene	gene with protein product		614109	"bactericidal/permeability-increasing protein-like 2"	BPIL2			Standard	NM_174932		Approved	dJ149A16.7	uc003amn.2	Q8NFQ6	OTTHUMG00000058273	ENST00000397452.1:c.1035G>T	chr22.hg19:g.32828474C>A	ENSP00000380594:p.Glu345Asp	111.0	0.0		99.0	46.0	NM_174932	A2RRF1	Missense_Mutation	SNP	ENST00000397452.1	hg19	CCDS13906.1	.	.	.	.	.	.	.	.	.	.	C	11.42	1.633996	0.29068	.	.	ENSG00000184459	ENST00000397452;ENST00000300399;ENST00000534972	T;T;T	0.07216	3.21;3.21;3.21	6.07	-1.39	0.08997	.	0.403397	0.29466	N	0.012069	T	0.08670	0.0215	M	0.76838	2.35	0.22127	N	0.999344	P	0.36354	0.549	B	0.37198	0.243	T	0.30268	-0.9984	10	0.15499	T	0.54	-7.3211	5.3781	0.16176	0.1339:0.4605:0.0:0.4056	.	345	Q8NFQ6	BPIFC_HUMAN	D	345;345;69	ENSP00000380594:E345D;ENSP00000300399:E345D;ENSP00000439123:E69D	ENSP00000300399:E345D	E	-	3	2	BPIFC	31158474	0.700000	0.27796	0.979000	0.43373	0.115000	0.19883	0.077000	0.14738	0.159000	0.19401	0.650000	0.86243	GAG	.	.		0.493	BPIFC-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129029.2	NM_174932		A	32828474	C	A	32828474	3	1	344	1	0	0	0	0	1	0	0	0	1494	796	28	3	512	3	BPIL2	22	32828474	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	1494820	32828474	18476092	1371	48734										
SYN3	8224	hgsc.bcm.edu	37	chr22	32914296	32914296	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cttccagatctctggggctgAggagactgagcttggcgagg	16	9	1	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr22:32914296A>G	ENST00000358763.2	-	13	1586	c.1344T>C	c.(1342-1344)ccT>ccC	p.P448P	SYN3_ENST00000332840.5_Silent_p.P448P|SYN3_ENST00000467095.1_5'UTR	NM_001135774.1	NP_001129246.1	O14994	SYN3_HUMAN	synapsin III	448	J; Pro-rich linker.				neurotransmitter secretion (GO:0007269)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33						TCTGGGGCTGAGGAGACTGAG	0.527																																					p.P448P		Atlas-SNP	.											.	SYN3	77	.	0			c.T1344C						.						45	56	52					22																	32914296		2203	4300	6503	SO:0001819	synonymous_variant	8224	exon12			GGGCTGAGGAGAC	AF046873	CCDS13908.1	22q12.3	2008-05-14			ENSG00000185666	ENSG00000185666			11496	protein-coding gene	gene with protein product		602705				9539796	Standard	NM_003490		Approved		uc003amx.3	O14994	OTTHUMG00000031004	ENST00000358763.2:c.1344T>C	chr22.hg19:g.32914296A>G		22.0	0.0		25.0	12.0	NM_003490	B1B1F9	Silent	SNP	ENST00000358763.2	hg19	CCDS13908.1																																																																																			.	.		0.527	SYN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075892.4			G	32914296	A	G	32914296	2	3	344	1	0	0	0	0	0	0	0	1	15457	291	11	2		2	SYN3	22	32914296	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	85822	32914296	18390270	1372	48735										
MYH9	4627	hgsc.bcm.edu	37	chr22	36684453	36684453	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctccagctctgcctccatctCccgcacctgggggaaggaac	10	17	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr22:36684453C>A	ENST00000216181.5	-	34	5007	c.4777G>T	c.(4777-4779)Gag>Tag	p.E1593*	MYH9_ENST00000475726.1_5'Flank	NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	1593					actin cytoskeleton reorganization (GO:0031532)|actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|angiogenesis (GO:0001525)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood vessel endothelial cell migration (GO:0043534)|cytokinesis (GO:0000910)|establishment of meiotic spindle localization (GO:0051295)|establishment of T cell polarity (GO:0001768)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|meiotic spindle organization (GO:0000212)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte differentiation (GO:0030224)|myoblast fusion (GO:0007520)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of cell shape (GO:0008360)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|uropod organization (GO:0032796)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|actomyosin contractile ring (GO:0005826)|cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|cleavage furrow (GO:0032154)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|spindle (GO:0005819)|stress fiber (GO:0001725)|uropod (GO:0001931)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3)	86						GCCTCCATCTCCCGCACCTGG	0.622			T	ALK	ALCL		"Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"		Hereditary Macrothrombocytopenia, MYH9-associated																												p.E1593X		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"myosin, heavy polypeptide 9, non-muscle"	yes	L	.	MYH9	225	.	0			c.G4777T						.						67	57	61					22																	36684453		2203	4300	6503	SO:0001587	stop_gained	4627	exon34	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	CCATCTCCCGCAC		CCDS13927.1	22q13.1	2014-09-17	2006-09-29		ENSG00000100345	ENSG00000100345		"Myosins / Myosin superfamily : Class II"	7579	protein-coding gene	gene with protein product	"nonmuscle myosin heavy chain II-A"	160775	"myosin, heavy polypeptide 9, non-muscle"	DFNA17		1860190, 11023810	Standard	NM_002473		Approved	NMMHCA, NMHC-II-A, MHA, FTNS, EPSTS	uc003apg.3	P35579	OTTHUMG00000030429	ENST00000216181.5:c.4777G>T	chr22.hg19:g.36684453C>A	ENSP00000216181:p.Glu1593*	25.0	0.0		26.0	11.0	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Nonsense_Mutation	SNP	ENST00000216181.5	hg19	CCDS13927.1	.	.	.	.	.	.	.	.	.	.	C	47	13.370925	0.99738	.	.	ENSG00000100345	ENST00000337818;ENST00000397231;ENST00000216181	.	.	.	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.7664	0.96346	0.0:1.0:0.0:0.0	.	.	.	.	X	1015;195;1593	.	ENSP00000216181:E1593X	E	-	1	0	MYH9	35014399	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.776000	0.85560	2.735000	0.93741	0.655000	0.94253	GAG	.	.		0.622	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473		A	36684453	C	A	36684453	4	1	344	1	0	0	0	0	0	1	0	0	10051	864	30	3	1137	3	MYH9	22	36684453	Nonsense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	3770157	36684453	14620113	1373	48736										
EIF3D	8664	hgsc.bcm.edu	37	chr22	36920644	36920644	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttgctggctcttggcctaccTgggcaaatctcattcgattc	9	12	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr22:36920644T>A	ENST00000216190.8	-	4	675	c.305A>T	c.(304-306)cAg>cTg	p.Q102L	EIF3D_ENST00000541106.1_Intron|EIF3D_ENST00000405442.1_Splice_Site_p.Q102L	NM_003753.3	NP_003744.1			eukaryotic translation initiation factor 3, subunit D											cervix(1)|endometrium(2)|large_intestine(6)|lung(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	15						TTGGCCTACCTGGGCAAATCT	0.507																																					p.Q102L		Atlas-SNP	.											.	EIF3D	37	.	0			c.A305T						.						125	104	111					22																	36920644		2203	4300	6503	SO:0001630	splice_region_variant	8664	exon4			CCTACCTGGGCAA	U54558	CCDS13930.1	22q13.1	2007-07-27	2007-07-27	2007-07-27	ENSG00000100353	ENSG00000100353			3278	protein-coding gene	gene with protein product		603915	"eukaryotic translation initiation factor 3, subunit 7 zeta, 66/67kDa"	EIF3S7		9341143	Standard	NM_003753		Approved	eIF3-p66, eIF3-zeta, eIF3d	uc003apr.3	O15371	OTTHUMG00000150599	ENST00000216190.8:c.306+1A>T	chr22.hg19:g.36920644T>A		75.0	0.0		56.0	28.0	NM_003753		Missense_Mutation	SNP	ENST00000216190.8	hg19	CCDS13930.1	.	.	.	.	.	.	.	.	.	.	T	15.45	2.838548	0.51057	.	.	ENSG00000100353	ENST00000216190;ENST00000397177;ENST00000405442;ENST00000455547;ENST00000457241;ENST00000432675;ENST00000402116	.	.	.	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.55242	0.1908	L	0.43757	1.38	0.80722	D	1	B	0.12630	0.006	B	0.14023	0.01	T	0.50224	-0.8853	9	0.19590	T	0.45	-0.2562	16.5582	0.84512	0.0:0.0:0.0:1.0	.	102	O15371	EIF3D_HUMAN	L	102	.	ENSP00000216190:Q102L	Q	-	2	0	EIF3D	35250590	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	7.755000	0.85180	2.308000	0.77769	0.533000	0.62120	CAG	.	.		0.507	EIF3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319026.1		Missense_Mutation	A	36920644	T	A	36920644	5	1	344	1	0	0	0	0	0	0	1	0	5016	1594	55	4	1389	4	EIF3D	22	36920644	Splice_Site	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	236191	36920644	14383922	1374	48737										
ELFN2	114794	hgsc.bcm.edu	37	chr22	37769351	37769351	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gggggagagctgcgagtaggTggagtcacgcttggagcggg	22	6	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr22:37769351T>A	ENST00000402918.2	-	3	3009	c.2224A>T	c.(2224-2226)Acc>Tcc	p.T742S	RP1-63G5.8_ENST00000609322.1_RNA|RP1-63G5.5_ENST00000430883.1_RNA|ELFN2_ENST00000435824.1_5'Flank	NM_052906.3	NP_443138.2	Q5R3F8	PPR29_HUMAN	extracellular leucine-rich repeat and fibronectin type III domain containing 2	742					negative regulation of phosphatase activity (GO:0010923)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	35	Melanoma(58;0.0574)					TGCGAGTAGGTGGAGTCACGC	0.642																																					p.T742S		Atlas-SNP	.											.	ELFN2	89	.	0			c.A2224T						.						67	62	64					22																	37769351		2203	4300	6503	SO:0001583	missense	114794	exon3			AGTAGGTGGAGTC	BC041596	CCDS33642.1	22q13.1	2013-02-11	2011-10-27	2011-10-27	ENSG00000166897	ENSG00000166897		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Fibronectin type III domain containing"	29396	protein-coding gene	gene with protein product			"leucine rich repeat containing 62", "extracellular leucine-rich repeat and fibronectin type III containing 2", "extracellular leucine-rich repeat and fibronectin type III domain containing 2", "protein phosphatase 1, regulatory subunit 29"	LRRC62, PPP1R29		17868438	Standard	XR_244427		Approved	dJ63G5.3, KIAA1904	uc003asq.4	Q5R3F8	OTTHUMG00000150558	ENST00000402918.2:c.2224A>T	chr22.hg19:g.37769351T>A	ENSP00000385277:p.Thr742Ser	51.0	0.0		44.0	18.0	NM_052906	Q96PY3	Missense_Mutation	SNP	ENST00000402918.2	hg19	CCDS33642.1	.	.	.	.	.	.	.	.	.	.	T	9.270	1.045446	0.19748	.	.	ENSG00000166897	ENST00000349653;ENST00000402918	T;T	0.49139	0.79;0.79	4.63	-4.34	0.03666	.	0.512774	0.22551	N	0.058585	T	0.18299	0.0439	N	0.02011	-0.69	0.09310	N	0.999998	B	0.06786	0.001	B	0.04013	0.001	T	0.11036	-1.0604	10	0.42905	T	0.14	-24.9305	12.5652	0.56306	0.0:0.4851:0.0:0.5149	.	742	Q5R3F8	PPR29_HUMAN	S	742	ENSP00000300147:T742S;ENSP00000385277:T742S	ENSP00000300147:T742S	T	-	1	0	ELFN2	36099297	1.000000	0.71417	0.758000	0.31321	0.982000	0.71751	0.632000	0.24583	-1.053000	0.03218	-0.372000	0.07161	ACC	.	.		0.642	ELFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318900.2	NM_052906		A	37769351	T	A	37769351	3	1	344	1	0	0	0	0	1	0	0	0	5060	1696	59	4	242	4	ELFN2	22	37769351	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	848707	37769351	13535215	1375	48738										
MICALL1	85377	hgsc.bcm.edu	37	chr22	38318312	38318312	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agcccccctgcgggccgcccCacccctgcccccaggaaggc	11	23	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr22:38318312C>A	ENST00000215957.6	+	6	1029	c.903C>A	c.(901-903)ccC>ccA	p.P301P		NM_033386.3	NP_203744.1	Q8N3F8	MILK1_HUMAN	MICAL-like 1	301	Pro-rich.				endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|neuron projection development (GO:0031175)|protein localization to endosome (GO:0036010)|protein targeting to membrane (GO:0006612)|receptor-mediated endocytosis (GO:0006898)|retrograde transport, endosome to plasma membrane (GO:1990126)|slow endocytic recycling (GO:0032458)	extrinsic component of membrane (GO:0019898)|late endosome (GO:0005770)|recycling endosome membrane (GO:0055038)	identical protein binding (GO:0042802)|phosphatidic acid binding (GO:0070300)|Rab GTPase binding (GO:0017137)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	24	Melanoma(58;0.045)					CGGGCCGCCCCACCCCTGCCC	0.721																																					p.P301P		Atlas-SNP	.											.	MICALL1	53	.	0			c.C903A						.						2	3	3					22																	38318312		1601	3463	5064	SO:0001819	synonymous_variant	85377	exon6			CCGCCCCACCCCT	BK000466	CCDS13961.1	22q13.1	2006-11-24			ENSG00000100139	ENSG00000100139			29804	protein-coding gene	gene with protein product	"molecule interacting with Rab13"					11258795, 12110185	Standard	NM_033386		Approved	MIRAB13, KIAA1668, MICAL-L1	uc003aui.3	Q8N3F8	OTTHUMG00000150670	ENST00000215957.6:c.903C>A	chr22.hg19:g.38318312C>A		20.0	0.0		23.0	12.0	NM_033386	Q5TI16|Q7RTP5|Q8N3N8|Q9BVL9|Q9BY92|Q9UH43|Q9UH44|Q9UH45	Silent	SNP	ENST00000215957.6	hg19	CCDS13961.1																																																																																			.	.		0.721	MICALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319545.4	NM_033386		A	38318312	C	A	38318312	2	1	344	1	0	0	0	0	0	0	0	1	9582	581	21	3		3	MICALL1	22	38318312	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	548961	38318312	12986254	1376	48739										
APOBEC3D	140564	hgsc.bcm.edu	37	chr22	39421150	39421150	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gcaaccgactgcctgctaacAggcgcttccagatcacctgg	10	15	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr22:39421150A>C	ENST00000216099.8	+	3	693	c.286A>C	c.(286-288)Agg>Cgg	p.R96R	APOBEC3D_ENST00000427494.2_Intron|APOBEC3D_ENST00000381568.4_Silent_p.R96R	NM_152426.3	NP_689639.2	Q96AK3	ABC3D_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3D	96	CMP/dCMP deaminase zinc-binding 1.				defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines (GO:0016814)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)	11	Melanoma(58;0.04)					GCCTGCTAACAGGCGCTTCCA	0.547																																					p.R96R		Atlas-SNP	.											.	APOBEC3D	61	.	0			c.A286C						.						102	100	101					22																	39421150		2202	4300	6502	SO:0001819	synonymous_variant	140564	exon3			GCTAACAGGCGCT	BF832090	CCDS46709.1	22q13.1	2012-10-19	2008-05-01		ENSG00000243811	ENSG00000243811		"Apolipoprotein B mRNA editing enzymes"	17354	protein-coding gene	gene with protein product		609900	"apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3D (putative)", "apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3E pseudogene"	APOBEC3E		11863358	Standard	NM_152426		Approved	ARP6, APOBEC3DE	uc003awt.4	Q96AK3	OTTHUMG00000151084	ENST00000216099.8:c.286A>C	chr22.hg19:g.39421150A>C		97.0	0.0		77.0	28.0	NM_152426	Q5JZ91|Q7Z2N2|Q7Z2N5|Q7Z2N6	Silent	SNP	ENST00000216099.8	hg19	CCDS46709.1																																																																																			.	.		0.547	APOBEC3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321232.2	NM_152426		C	39421150	A	C	39421150	2	2	344	1	0	0	0	0	0	0	0	1	792	179	7	5		5	APOBEC3D	22	39421150	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1102838	39421150	11883416	1377	48740										
TTLL1	25809	hgsc.bcm.edu	37	chr22	43459928	43459928	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ggcaaaacccaagcttgtacCtaggagggaatgtagattaa	11	7	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr22:43459928C>A	ENST00000266254.7	-	7	879		c.e7-1		TTLL1_ENST00000331018.7_Splice_Site	NM_012263.4	NP_036395.1	O95922	TTLL1_HUMAN	tubulin tyrosine ligase-like family, member 1						axoneme assembly (GO:0035082)|epithelial cilium movement (GO:0003351)|protein polyglutamylation (GO:0018095)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	tubulin-glutamic acid ligase activity (GO:0070740)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(1)	23		Ovarian(80;0.0694)		BRCA - Breast invasive adenocarcinoma(115;0.00461)		AAGCTTGTACCTAGGAGGGAA	0.438																																					.		Atlas-SNP	.											.	TTLL1	41	.	0			c.639-1G>T						.						159	153	155					22																	43459928		2203	4300	6503	SO:0001630	splice_region_variant	25809	exon8			TTGTACCTAGGAG	AL096886	CCDS14043.1	22q13.1	2013-02-14			ENSG00000100271	ENSG00000100271		"Tubulin tyrosine ligase-like family"	1312	protein-coding gene	gene with protein product		608955	"tubulin tyrosine ligase-like 1"	C22orf7		10591208, 11054573	Standard	NM_012263		Approved		uc003bdi.3	O95922	OTTHUMG00000150699	ENST00000266254.7:c.639-1G>T	chr22.hg19:g.43459928C>A		100.0	0.0		80.0	35.0	NM_012263	B2RDS7|Q9BR27|Q9NRS9|Q9UMU0	Splice_Site	SNP	ENST00000266254.7	hg19	CCDS14043.1	.	.	.	.	.	.	.	.	.	.	C	15.23	2.770617	0.49680	.	.	ENSG00000100271	ENST00000495814;ENST00000331018;ENST00000266254	.	.	.	5.44	4.42	0.53409	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.9128	0.58189	0.0:0.9244:0.0:0.0756	.	.	.	.	.	-1	.	.	.	-	.	.	TTLL1	41789872	1.000000	0.71417	0.996000	0.52242	0.533000	0.34776	4.526000	0.60566	1.437000	0.47472	0.591000	0.81541	.	.	.		0.438	TTLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319659.1	NM_012263	Intron	A	43459928	C	A	43459928	5	1	344	1	0	0	0	0	0	0	1	0	16737	695	24	3	653	3	TTLL1	22	43459928	Splice_Site	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	4038778	43459928	7844638	1378	48741										
ARHGAP8	23779	hgsc.bcm.edu	37	chr22	45218295	45218295	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctatttcaactacctgagtgAgctccacgaacaccttaaat	5	12	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr22:45218295A>T	ENST00000389774.2	+	7	665	c.524A>T	c.(523-525)gAg>gTg	p.E175V	ARHGAP8_ENST00000389773.5_Missense_Mutation_p.E266V|PRR5-ARHGAP8_ENST00000352766.7_Missense_Mutation_p.E354V|ARHGAP8_ENST00000356099.6_Missense_Mutation_p.E144V|ARHGAP8_ENST00000517296.3_Missense_Mutation_p.E354V|PRR5-ARHGAP8_ENST00000361473.5_Missense_Mutation_p.E275V|ARHGAP8_ENST00000336963.4_Missense_Mutation_p.E144V	NM_001017526.1	NP_001017526.1	P85298	RHG08_HUMAN	Rho GTPase activating protein 8	175	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(9)|prostate(1)|skin(7)	29		all_neural(38;0.00409)|Ovarian(80;0.00976)|Glioma(61;0.0649)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0204)		TACCTGAGTGAGCTCCACGAA	0.478																																					p.E266V		Atlas-SNP	.											.	PRR5-ARHGAP8	53	.	0			c.A797T						.						137	134	135					22																	45218295		2203	4300	6503	SO:0001583	missense	553158	exon9			TGAGTGAGCTCCA	AF177331	CCDS14060.2, CCDS33664.1, CCDS56233.1	22q13.3	2010-05-11			ENSG00000241484	ENSG00000241484		"Rho GTPase activating proteins"	677	protein-coding gene	gene with protein product		609405				10591208	Standard	NM_001198726		Approved	FLJ20185, BPGAP1		P85298	OTTHUMG00000030234	ENST00000389774.2:c.524A>T	chr22.hg19:g.45218295A>T	ENSP00000374424:p.Glu175Val	118.0	0.0		66.0	26.0	NM_181334	A6ZJ79|A6ZJ80|O75983|O95695|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Missense_Mutation	SNP	ENST00000389774.2	hg19	CCDS33664.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.75|13.75	2.331317|2.331317	0.41297|0.41297	.|.	.|.	ENSG00000248405;ENSG00000248405;ENSG00000241484;ENSG00000241484;ENSG00000241484;ENSG00000241484;ENSG00000241484|ENSG00000248405	ENST00000361473;ENST00000352766;ENST00000517296;ENST00000389773;ENST00000389774;ENST00000336963;ENST00000356099|ENST00000515632	T;T;T;T;T;T;T|.	0.70631|.	-0.5;-0.5;-0.5;-0.5;-0.5;-0.5;-0.5|.	4.26|4.26	4.26|4.26	0.50523|0.50523	Cellular retinaldehyde-binding/triple function, C-terminal (5);|.	0.000000|.	0.33272|.	U|.	0.005096|.	T|T	0.72938|0.72938	0.3523|0.3523	M|M	0.78223|0.78223	2.4|2.4	0.47153|0.47153	D|D	0.999336|0.999336	D;P;D;D;D;D;D|.	0.76494|.	0.99;0.948;0.998;0.999;0.971;0.992;0.995|.	D;P;D;D;P;P;D|.	0.79784|.	0.92;0.859;0.939;0.993;0.816;0.906;0.934|.	T|T	0.74569|0.74569	-0.3622|-0.3622	10|5	0.87932|.	D|.	0|.	.|.	11.7684|11.7684	0.51943|0.51943	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	180;144;180;175;185;354;275|.	B7ZMA4;A6ZJ79;A2RU51;P85298;Q6PCC7;B1AHC4;B1AHC3|.	.;.;.;RHG08_HUMAN;.;.;.|.	V|C	275;354;354;266;175;144;144|198	ENSP00000354732:E275V;ENSP00000262731:E354V;ENSP00000429240:E354V;ENSP00000374423:E266V;ENSP00000374424:E175V;ENSP00000337287:E144V;ENSP00000348407:E144V|.	ENSP00000337287:E144V|.	E|S	+|+	2|1	0|0	PRR5-ARHGAP8;ARHGAP8|PRR5-ARHGAP8	43596959|43596959	1.000000|1.000000	0.71417|0.71417	0.512000|0.512000	0.27736|0.27736	0.010000|0.010000	0.07245|0.07245	7.116000|7.116000	0.77119|0.77119	1.771000|1.771000	0.52183|0.52183	0.383000|0.383000	0.25322|0.25322	GAG|AGC	.	.		0.478	ARHGAP8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000075088.4	NM_017701		T	45218295	A	T	45218295	3	4	344	1	0	0	0	0	1	0	0	0	888	304	11	4	546	4	ARHGAP8	22	45218295	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1758367	45218295	6086271	1379	48742										
PKDREJ	10343	hgsc.bcm.edu	37	chr22	46657787	46657787	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aatttgtgcaatttaggaacAaagaaaatctatcagagaca	7	5	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr22:46657787A>G	ENST00000253255.5	-	1	1432	c.1433T>C	c.(1432-1434)tTg>tCg	p.L478S		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	478	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		ATTTAGGAACAAAGAAAATCT	0.398																																					p.L478S		Atlas-SNP	.											.	PKDREJ	195	.	0			c.T1433C						.						98	106	103					22																	46657787		2203	4300	6503	SO:0001583	missense	10343	exon1			AGGAACAAAGAAA	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like", "polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like", "polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.1433T>C	chr22.hg19:g.46657787A>G	ENSP00000253255:p.Leu478Ser	73.0	0.0		54.0	26.0	NM_006071	B1AJY3|O95850	Missense_Mutation	SNP	ENST00000253255.5	hg19	CCDS14073.1	.	.	.	.	.	.	.	.	.	.	A	13.70	2.314310	0.40996	.	.	ENSG00000130943	ENST00000253255	T	0.80994	-1.44	5.18	5.18	0.71444	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	0.000000	0.46442	D	0.000294	D	0.88254	0.6387	M	0.66939	2.045	0.36331	D	0.858856	D	0.89917	1.0	D	0.83275	0.996	D	0.91832	0.5476	10	0.87932	D	0	-17.7051	14.5202	0.67844	1.0:0.0:0.0:0.0	.	478	Q9NTG1	PKDRE_HUMAN	S	478	ENSP00000253255:L478S	ENSP00000253255:L478S	L	-	2	0	PKDREJ	45036451	0.923000	0.31300	0.339000	0.25562	0.003000	0.03518	6.507000	0.73717	2.082000	0.62665	0.533000	0.62120	TTG	.	.		0.398	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071		G	46657787	A	G	46657787	3	3	344	1	0	0	0	0	1	0	0	0	11979	131	5	2	5332	2	PKDREJ	22	46657787	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1439492	46657787	4646779	1380	48743										
TBC1D22A	25771	hgsc.bcm.edu	37	chr22	47189485	47189485	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gagtttgagagcaataccagCgatgcctgggacgctgggga	16	8	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr22:47189485C>A	ENST00000337137.4	+	3	373	c.207C>A	c.(205-207)agC>agA	p.S69R	TBC1D22A_ENST00000406733.1_Missense_Mutation_p.S22R|TBC1D22A_ENST00000355704.3_Missense_Mutation_p.S50R|TBC1D22A_ENST00000380995.1_Missense_Mutation_p.S22R|TBC1D22A_ENST00000407381.3_Missense_Mutation_p.S69R|TBC1D22A_ENST00000472791.1_3'UTR	NM_001284304.1|NM_001284305.1|NM_014346.2	NP_001271233.1|NP_001271234.1|NP_055161.1	Q8WUA7	TB22A_HUMAN	TBC1 domain family, member 22A	69							protein homodimerization activity (GO:0042803)|Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(3)|large_intestine(10)|lung(5)|ovary(2)|prostate(1)	22		all_cancers(38;4.44e-05)|all_epithelial(38;0.000507)|Breast(42;0.0488)|all_lung(38;0.0682)|Ovarian(80;0.0731)|all_neural(38;0.0966)|Glioma(61;0.222)|Lung SC(80;0.236)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0347)|BRCA - Breast invasive adenocarcinoma(115;0.231)		GCAATACCAGCGATGCCTGGG	0.612																																					p.S69R		Atlas-SNP	.											.	TBC1D22A	54	.	0			c.C207A						.						67	62	63					22																	47189485		2203	4300	6503	SO:0001583	missense	25771	exon3			TACCAGCGATGCC	AK125705	CCDS14078.1, CCDS63511.1, CCDS63512.1, CCDS74877.1	22q13	2008-01-22	2005-01-05	2005-01-05	ENSG00000054611	ENSG00000054611			1309	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 4"	C22orf4			Standard	XM_005261496		Approved		uc003bib.3	Q8WUA7	OTTHUMG00000150332	ENST00000337137.4:c.207C>A	chr22.hg19:g.47189485C>A	ENSP00000336724:p.Ser69Arg	82.0	0.0		66.0	37.0	NM_014346	B0QYI2|B0QYI3|B9A6M3|Q5TE47|Q6ZUH2|Q92680|Q9BVD6|Q9UGG0|Q9UGT2|Q9UGU6|Q9UH25|Q9Y4W5	Missense_Mutation	SNP	ENST00000337137.4	hg19	CCDS14078.1	.	.	.	.	.	.	.	.	.	.	C	19.94	3.919073	0.73098	.	.	ENSG00000054611	ENST00000337137;ENST00000380995;ENST00000407381;ENST00000355704;ENST00000406733	T;T;T;T;T	0.51574	1.69;0.7;1.54;1.62;1.76	4.7	-4.9	0.03094	.	0.000000	0.85682	D	0.000000	T	0.62134	0.2403	M	0.78049	2.395	0.51012	D	0.999904	D;D;D;D	0.76494	0.998;0.999;0.999;0.998	D;D;D;D	0.77004	0.957;0.988;0.989;0.957	T	0.67256	-0.5716	10	0.66056	D	0.02	-12.6946	12.9514	0.58403	0.0:0.6093:0.0:0.3907	.	69;50;69;69	B9A6M3;Q8WUA7-2;B0QYI1;Q8WUA7	.;.;.;TB22A_HUMAN	R	69;22;69;50;22	ENSP00000336724:S69R;ENSP00000370383:S22R;ENSP00000384036:S69R;ENSP00000347932:S50R;ENSP00000385634:S22R	ENSP00000336724:S69R	S	+	3	2	TBC1D22A	45568149	0.143000	0.22626	0.833000	0.33012	0.968000	0.65278	-0.612000	0.05616	-0.734000	0.04843	-0.639000	0.03973	AGC	.	.		0.612	TBC1D22A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317600.3	NM_014346		A	47189485	C	A	47189485	3	1	344	1	0	0	0	0	1	0	0	0	15626	767	27	1	217	1	TBC1D22A	22	47189485	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	531698	47189485	4115081	1381	48744										
MOV10L1	54456	hgsc.bcm.edu	37	chr22	50599429	50599429	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctttgctggaatacagtattAcaaacggtgtttacatggga	10	6	0	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chr22:50599429A>G	ENST00000262794.5	+	26	3582	c.3499A>G	c.(3499-3501)Aca>Gca	p.T1167A	MOV10L1_ENST00000395858.3_Missense_Mutation_p.T1121A|MOV10L1_ENST00000540615.1_Intron|MOV10L1_ENST00000395852.1_Missense_Mutation_p.T294A|MOV10L1_ENST00000545383.1_Missense_Mutation_p.T1167A	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	1167					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		ATACAGTATTACAAACGGTGT	0.498																																					p.T1167A		Atlas-SNP	.											.	MOV10L1	238	.	0			c.A3499G						.						266	245	252					22																	50599429		2203	4300	6503	SO:0001583	missense	54456	exon26			AGTATTACAAACG	AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"cardiac helicase activated by MEF2C protein"	605794	"Mov10 (mouse)-like 1", "Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.3499A>G	chr22.hg19:g.50599429A>G	ENSP00000262794:p.Thr1167Ala	147.0	0.0		115.0	41.0	NM_018995	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Missense_Mutation	SNP	ENST00000262794.5	hg19	CCDS14084.1	.	.	.	.	.	.	.	.	.	.	.	0.027	-1.360565	0.01245	.	.	ENSG00000073146	ENST00000545383;ENST00000262794;ENST00000395858;ENST00000395852	D;D;T;D	0.92149	-1.72;-1.72;-1.35;-2.98	5.14	2.96	0.34315	.	0.516685	0.23291	N	0.049795	T	0.80507	0.4636	N	0.17082	0.46	0.20764	N	0.99985	B;B;B	0.09022	0.0;0.002;0.001	B;B;B	0.08055	0.002;0.003;0.002	T	0.62511	-0.6839	10	0.09338	T	0.73	-14.3664	5.7805	0.18304	0.7378:0.1717:0.0906:0.0	.	294;1121;1167	Q9BXT6-2;A8MXC6;Q9BXT6	.;.;M10L1_HUMAN	A	1167;1167;1121;294	ENSP00000438978:T1167A;ENSP00000262794:T1167A;ENSP00000379199:T1121A;ENSP00000379193:T294A	ENSP00000262794:T1167A	T	+	1	0	MOV10L1	48941556	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	1.128000	0.31369	0.764000	0.33197	0.408000	0.27601	ACA	.	.		0.498	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995		G	50599429	A	G	50599429	3	3	344	1	0	0	0	0	1	0	0	0	9728	391	14	2	3654	2	MOV10L1	22	50599429	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3409944	50599429	705137	1382	48745										
NLGN4X	57502	hgsc.bcm.edu	37	chrX	5810965	5810965	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccccgtcagtgtgtttggaaTcatggtgatggtgtttggcg	15	7	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chrX:5810965T>A	ENST00000381095.3	-	6	2971	c.2344A>T	c.(2344-2346)Att>Ttt	p.I782F	NLGN4X_ENST00000275857.6_Missense_Mutation_p.I782F|NLGN4X_ENST00000381093.2_Missense_Mutation_p.I802F|NLGN4X_ENST00000538097.1_Missense_Mutation_p.I782F|NLGN4X_ENST00000381092.1_Missense_Mutation_p.I782F	NM_001282145.1|NM_001282146.1|NM_181332.1	NP_001269074.1|NP_001269075.1|NP_851849.1	Q8N0W4	NLGNX_HUMAN	neuroligin 4, X-linked	782					adult behavior (GO:0030534)|brainstem development (GO:0003360)|cell-cell junction organization (GO:0045216)|cerebellum development (GO:0021549)|learning (GO:0007612)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|neuron cell-cell adhesion (GO:0007158)|neuron differentiation (GO:0030182)|organ growth (GO:0035265)|presynaptic membrane assembly (GO:0097105)|social behavior (GO:0035176)|synapse organization (GO:0050808)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|chloride ion binding (GO:0031404)|neurexin family protein binding (GO:0042043)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)			breast(1)|cervix(2)|endometrium(4)|large_intestine(21)|lung(39)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	81						GTGTTTGGAATCATGGTGATG	0.532																																					p.I782F		Atlas-SNP	.											.	NLGN4X	191	.	0			c.A2344T						.						308	253	271					X																	5810965		2203	4300	6503	SO:0001583	missense	57502	exon6			TTGGAATCATGGT	AB033086	CCDS14126.1	Xp22.33	2008-02-05	2004-05-21	2004-05-26	ENSG00000146938	ENSG00000146938			14287	protein-coding gene	gene with protein product		300427	"neuroligin 4"	NLGN4		10574462	Standard	XM_005274564		Approved	KIAA1260, NLGN, HLNX	uc004crr.3	Q8N0W4	OTTHUMG00000021093	ENST00000381095.3:c.2344A>T	chrX.hg19:g.5810965T>A	ENSP00000370485:p.Ile782Phe	118.0	0.0		68.0	59.0	NM_181332	Q6UX10|Q9ULG0	Missense_Mutation	SNP	ENST00000381095.3	hg19	CCDS14126.1	.	.	.	.	.	.	.	.	.	.	T	19.43	3.825517	0.71143	.	.	ENSG00000146938	ENST00000381095;ENST00000381093;ENST00000275857;ENST00000381092;ENST00000538097	T;T;T;T;T	0.19250	2.16;2.16;2.16;2.16;2.16	3.82	3.82	0.43975	.	0.268763	0.19869	N	0.104233	T	0.35480	0.0933	M	0.74881	2.28	0.58432	D	0.999997	D;P;P	0.54601	0.967;0.911;0.947	P;P;P	0.52267	0.694;0.459;0.66	T	0.25363	-1.0134	10	0.87932	D	0	.	11.2516	0.49028	0.0:0.0:0.0:1.0	.	839;782;802	A6NMU8;Q8N0W4;Q8N0W4-2	.;NLGNX_HUMAN;.	F	782;802;782;782;782	ENSP00000370485:I782F;ENSP00000370483:I802F;ENSP00000275857:I782F;ENSP00000370482:I782F;ENSP00000439203:I782F	ENSP00000275857:I782F	I	-	1	0	NLGN4X	5820965	1.000000	0.71417	0.950000	0.38849	0.966000	0.64601	6.912000	0.75753	1.222000	0.43521	0.417000	0.27973	ATT	.	.		0.532	NLGN4X-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055673.1	NM_020742		A	5810965	T	A	5810965	3	1	344	1	0	0	0	0	1	0	0	0	10473	1435	50	4	110	4	NLGN4X	23	5810965	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10		5810965	149459595	1383	48746										
FAM9A	171482	hgsc.bcm.edu	37	chrX	8767070	8767070	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctgagctttggcagccttccTgctgcgcttcctgcccacgg	11	16	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chrX:8767070T>A	ENST00000543214.1	-	3	292	c.157A>T	c.(157-159)Agg>Tgg	p.R53W	FAM9A_ENST00000381003.3_Missense_Mutation_p.R53W	NM_001171186.1	NP_001164657.1	Q8IZU1	FAM9A_HUMAN	family with sequence similarity 9, member A	53						nucleus (GO:0005634)		p.R53G(1)		endometrium(11)|kidney(2)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	18		Hepatocellular(5;0.219)				GCAGCCTTCCTGCTGCGCTTC	0.562																																					p.R53W		Atlas-SNP	.											.	FAM9A	57	.	1	Substitution - Missense(1)	endometrium(1)	c.A157T						.						107	76	86					X																	8767070		2203	4300	6503	SO:0001583	missense	171482	exon3			CCTTCCTGCTGCG		CCDS14131.1	Xp22.32	2012-11-29			ENSG00000183304	ENSG00000183304			18403	protein-coding gene	gene with protein product	"testis expressed 39A"	300477					Standard	NM_174951		Approved	TEX39A	uc004csg.3	Q8IZU1	OTTHUMG00000021110	ENST00000543214.1:c.157A>T	chrX.hg19:g.8767070T>A	ENSP00000440163:p.Arg53Trp	106.0	0.0		72.0	62.0	NM_174951	B7ZLH5|Q2M2D1	Missense_Mutation	SNP	ENST00000543214.1	hg19	CCDS14131.1	.	.	.	.	.	.	.	.	.	.	t	8.214	0.800994	0.16397	.	.	ENSG00000183304	ENST00000381003;ENST00000543214	.	.	.	0.207	0.207	0.15214	.	.	.	.	.	T	0.26810	0.0656	L	0.34521	1.04	0.09310	N	1	P	0.50819	0.939	B	0.43680	0.427	T	0.14643	-1.0465	7	0.66056	D	0.02	.	.	.	.	.	53	Q8IZU1	FAM9A_HUMAN	W	53	.	ENSP00000370391:R53W	R	-	1	2	FAM9A	8727070	0.002000	0.14202	0.003000	0.11579	0.003000	0.03518	-0.238000	0.08977	0.234000	0.21139	0.231000	0.17811	AGG	.	.		0.562	FAM9A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055697.1	NM_174951		A	8767070	T	A	8767070	3	1	344	1	0	0	0	0	1	0	0	0	5667	1579	55	4	869	4	FAM9A	23	8767070	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2956105	8767070	146503490	1384	48747										
TLR7	51284	hgsc.bcm.edu	37	chrX	12905637	12905637	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttcttgccttctggagttttTgatggtatgcctccaaatct	8	9	3	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chrX:12905637T>G	ENST00000380659.3	+	3	2149	c.2010T>G	c.(2008-2010)ttT>ttG	p.F670L		NM_016562.3	NP_057646.1	Q9NYK1	TLR7_HUMAN	toll-like receptor 7	670					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of chemokine production (GO:0032722)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|toll-like receptor 7 signaling pathway (GO:0034154)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	cytoplasm (GO:0005737)|early phagosome (GO:0032009)|endolysosome membrane (GO:0036020)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|single-stranded RNA binding (GO:0003727)|siRNA binding (GO:0035197)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(4)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	44					Hydroxychloroquine(DB01611)|Imiquimod(DB00724)	CTGGAGTTTTTGATGGTATGC	0.353																																					p.F670L		Atlas-SNP	.											.	TLR7	125	.	0			c.T2010G						.						78	85	82					X																	12905637		2203	4299	6502	SO:0001583	missense	51284	exon3			AGTTTTTGATGGT	AF240467	CCDS14151.1	Xp22.3	2008-02-05			ENSG00000196664	ENSG00000196664			15631	protein-coding gene	gene with protein product		300365				11022119	Standard	NM_016562		Approved		uc004cvc.3	Q9NYK1	OTTHUMG00000021137	ENST00000380659.3:c.2010T>G	chrX.hg19:g.12905637T>G	ENSP00000370034:p.Phe670Leu	61.0	0.0		46.0	32.0	NM_016562	D1CS69|Q9NR98	Missense_Mutation	SNP	ENST00000380659.3	hg19	CCDS14151.1	.	.	.	.	.	.	.	.	.	.	T	15.98	2.991315	0.54041	.	.	ENSG00000196664	ENST00000380659	T	0.78003	-1.14	5.46	4.29	0.51040	.	0.060847	0.64402	D	0.000003	T	0.76205	0.3955	L	0.37850	1.14	0.51233	D	0.999918	P	0.39551	0.678	P	0.50109	0.631	T	0.72730	-0.4205	10	0.40728	T	0.16	.	10.547	0.45066	0.0:0.077:0.0:0.923	.	670	Q9NYK1	TLR7_HUMAN	L	670	ENSP00000370034:F670L	ENSP00000370034:F670L	F	+	3	2	TLR7	12815558	1.000000	0.71417	0.951000	0.38953	0.951000	0.60555	1.073000	0.30691	0.725000	0.32318	0.430000	0.28490	TTT	.	.		0.353	TLR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055769.1	NM_016562		G	12905637	T	G	12905637	3	3	344	1	0	0	0	0	1	0	0	0	15971	1809	63	5	2016	5	TLR7	23	12905637	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	4138567	12905637	142364923	1385	48748										
TLR8	51311	hgsc.bcm.edu	37	chrX	12938413	12938413	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aaacttttccaaaatttctcCaatctggaaattatttactt	2	8	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chrX:12938413C>A	ENST00000218032.6	+	2	1341	c.1254C>A	c.(1252-1254)tcC>tcA	p.S418S	TLR8_ENST00000311912.5_Silent_p.S436S	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	418					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)	p.S436S(1)		breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	AAAATTTCTCCAATCTGGAAA	0.353																																					p.S418S		Atlas-SNP	.											.	TLR8	134	.	1	Substitution - coding silent(1)	lung(1)	c.C1254A						.						49	54	52					X																	12938413		2199	4296	6495	SO:0001819	synonymous_variant	51311	exon2			TTTCTCCAATCTG	AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"CD molecules"	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.1254C>A	chrX.hg19:g.12938413C>A		55.0	0.0		40.0	38.0	NM_138636	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Silent	SNP	ENST00000218032.6	hg19	CCDS14152.1																																																																																			.	.		0.353	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610		A	12938413	C	A	12938413	2	1	344	1	0	0	0	0	0	0	0	1	15972	581	21	3		3	TLR8	23	12938413	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	32776	12938413	142332147	1386	48749										
DDX53	168400	hgsc.bcm.edu	37	chrX	23019627	23019627	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atattgctgatgacttgtcaAgcgacttcaatatccaaggc	8	9	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chrX:23019627A>G	ENST00000327968.5	+	1	1541	c.1453A>G	c.(1453-1455)Agc>Ggc	p.S485G	RP11-40F8.2_ENST00000455399.1_lincRNA	NM_182699.3	NP_874358.2	Q86TM3	DDX53_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 53	485	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|RNA binding (GO:0003723)			breast(2)|endometrium(5)|kidney(4)|large_intestine(3)|lung(15)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	35						TGACTTGTCAAGCGACTTCAA	0.418																																					p.S485G		Atlas-SNP	.											.	DDX53	76	.	0			c.A1453G						.						116	102	107					X																	23019627		2203	4300	6503	SO:0001583	missense	168400	exon1			TTGTCAAGCGACT	AY039237	CCDS35214.1	Xp22.13	2009-03-25			ENSG00000184735	ENSG00000184735		"DEAD-boxes"	20083	protein-coding gene	gene with protein product	"cancer associated gene", "cancer/testis antigen 26"						Standard	NM_182699		Approved	CAGE, CT26	uc004daj.3	Q86TM3	OTTHUMG00000021248	ENST00000327968.5:c.1453A>G	chrX.hg19:g.23019627A>G	ENSP00000368667:p.Ser485Gly	115.0	0.0		80.0	74.0	NM_182699	Q0D2N2|Q6NVV4	Missense_Mutation	SNP	ENST00000327968.5	hg19	CCDS35214.1	.	.	.	.	.	.	.	.	.	.	A	17.73	3.461223	0.63513	.	.	ENSG00000184735	ENST00000327968	T	0.04758	3.56	4.32	4.32	0.51571	Helicase, C-terminal (2);	0.043818	0.85682	D	0.000000	T	0.14227	0.0344	L	0.47190	1.495	0.49798	D	0.999822	D	0.89917	1.0	D	0.91635	0.999	T	0.00601	-1.1650	10	0.72032	D	0.01	-8.6362	10.8846	0.46960	1.0:0.0:0.0:0.0	.	485	Q86TM3	DDX53_HUMAN	G	485	ENSP00000368667:S485G	ENSP00000368667:S485G	S	+	1	0	DDX53	22929548	1.000000	0.71417	0.021000	0.16686	0.019000	0.09904	7.219000	0.78000	1.532000	0.49169	0.486000	0.48141	AGC	.	.		0.418	DDX53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056043.1	NM_182699		G	23019627	A	G	23019627	3	3	344	1	0	0	0	0	1	0	0	0	4373	72	3	2	1455	2	DDX53	23	23019627	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	10081214	23019627	132250933	1387	48750										
FAM47C	442444	hgsc.bcm.edu	37	chrX	37027900	37027900	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ctcctgagactggagtgtccCatctctgcccggagcctcca	10	16	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chrX:37027900C>T	ENST00000358047.3	+	1	1469	c.1417C>T	c.(1417-1419)Cat>Tat	p.H473Y		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	473										breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	120						TGGAGTGTCCCATCTCTGCCC	0.637																																					p.H473Y		Atlas-SNP	.											.	FAM47C	267	.	0			c.C1417T						.						65	62	63					X																	37027900		2202	4300	6502	SO:0001583	missense	442444	exon1			GTGTCCCATCTCT	AK125992	CCDS35227.1	Xp21.1	2006-07-04			ENSG00000198173	ENSG00000198173			25301	protein-coding gene	gene with protein product							Standard	NM_001013736		Approved		uc004ddl.2	Q5HY64	OTTHUMG00000024025	ENST00000358047.3:c.1417C>T	chrX.hg19:g.37027900C>T	ENSP00000367913:p.His473Tyr	54.0	0.0		50.0	46.0	NM_001013736	Q6ZU46	Missense_Mutation	SNP	ENST00000358047.3	hg19	CCDS35227.1	.	.	.	.	.	.	.	.	.	.	c	9.290	1.050486	0.19827	.	.	ENSG00000198173	ENST00000358047	T	0.18960	2.18	1.44	-2.89	0.05665	.	.	.	.	.	T	0.35970	0.0950	M	0.76574	2.34	0.09310	N	1	D	0.69078	0.997	D	0.68483	0.958	T	0.19353	-1.0308	9	0.62326	D	0.03	.	3.5628	0.07889	0.2386:0.572:0.0:0.1894	.	473	Q5HY64	FA47C_HUMAN	Y	473	ENSP00000367913:H473Y	ENSP00000367913:H473Y	H	+	1	0	FAM47C	36937821	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	0.387000	0.20718	-0.998000	0.03446	-0.572000	0.04151	CAT	.	.		0.637	FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060508.1	NM_001013736		T	37027900	C	T	37027900	3	4	344	1	0	0	0	0	1	0	0	0	5579	594	21	3	1419	3	FAM47C	23	37027900	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	14008273	37027900	118242660	1388	48751										
UBA1	7317	hgsc.bcm.edu	37	chrX	47074244	47074244	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cgaaagctgggccgccacgtGcgggcgctggtgcttgagct	17	12	0	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chrX:47074244G>A	ENST00000335972.6	+	26	3276	c.3093G>A	c.(3091-3093)gtG>gtA	p.V1031V	UBA1_ENST00000377351.4_Silent_p.V1031V|UBA1_ENST00000377269.3_Silent_p.V479V	NM_003334.3	NP_003325.2	P22314	UBA1_HUMAN	ubiquitin-like modifier activating enzyme 1	1031					cell death (GO:0008219)|cellular response to DNA damage stimulus (GO:0006974)|modification-dependent protein catabolic process (GO:0019941)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin activating enzyme activity (GO:0004839)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						GCCGCCACGTGCGGGCGCTGG	0.602																																					p.V1031V		Atlas-SNP	.											.	UBA1	89	.	0			c.G3093A						.						99	72	81					X																	47074244		2203	4300	6503	SO:0001819	synonymous_variant	7317	exon26			CCACGTGCGGGCG	AF258566	CCDS14275.1	Xp11.23	2014-08-13	2007-11-30	2007-11-30	ENSG00000130985	ENSG00000130985	6.3.2.19	"Ubiquitin-like modifier activating enzymes"	12469	protein-coding gene	gene with protein product	"UBA1, ubiquitin-activating enzyme E1 homolog (yeast)", "POC20 centriolar protein homolog (Chlamydomonas)"	314370	"ubiquitin-activating enzyme E1 (A1S9T and BN75 temperature sensitivity complementing)", "ubiquitin-activating enzyme E1"	A1S9T, GXP1, UBE1		1845793	Standard	NM_153280		Approved	UBE1X, POC20, CFAP124	uc004dhj.4	P22314	OTTHUMG00000021436	ENST00000335972.6:c.3093G>A	chrX.hg19:g.47074244G>A		34.0	0.0		25.0	24.0	NM_153280	Q5JRR8|Q96E13	Silent	SNP	ENST00000335972.6	hg19	CCDS14275.1																																																																																			.	.		0.602	UBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056389.1	NM_003334		A	47074244	G	A	47074244	2	1	344	1	0	0	0	0	0	0	0	1	16842	1306	46	3		3	UBA1	23	47074244	Silent	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	10046344	47074244	108196316	1389	48752										
SUV39H1	6839	hgsc.bcm.edu	37	chrX	48558575	48558575	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tcaagtgtgtgcgtatcctcAagcagttccacaaggactta	9	10	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chrX:48558575A>T	ENST00000376687.3	+	3	449	c.259A>T	c.(259-261)Aag>Tag	p.K87*	SUV39H1_ENST00000337852.6_Nonsense_Mutation_p.K98*|AF196970.3_ENST00000416061.1_RNA|SUV39H1_ENST00000453214.2_Missense_Mutation_p.Q24L	NM_003173.2	NP_003164.1	O43463	SUV91_HUMAN	suppressor of variegation 3-9 homolog 1 (Drosophila)	87	Chromo. {ECO:0000255|PROSITE- ProRule:PRU00053}.|Interaction with SIRT1.				cell cycle (GO:0007049)|cell differentiation (GO:0030154)|chromatin organization (GO:0006325)|chromatin silencing at rDNA (GO:0000183)|histone H3-K9 dimethylation (GO:0036123)|histone H3-K9 trimethylation (GO:0036124)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|rRNA processing (GO:0006364)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin silencing complex (GO:0005677)|chromosome, centromeric region (GO:0000775)|condensed nuclear chromosome (GO:0000794)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|rDNA heterochromatin (GO:0033553)	chromatin binding (GO:0003682)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|protein N-terminus binding (GO:0047485)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	14						GCGTATCCTCAAGCAGTTCCA	0.567																																					p.K87X		Atlas-SNP	.											.	SUV39H1	36	.	0			c.A259T						.						30	22	24					X																	48558575		2199	4298	6497	SO:0001587	stop_gained	6839	exon3			ATCCTCAAGCAGT	AF019968	CCDS14304.1, CCDS65252.1	Xp11.23	2011-07-01	2001-11-28		ENSG00000101945	ENSG00000101945		"Chromatin-modifying enzymes / K-methyltransferases"	11479	protein-coding gene	gene with protein product		300254	"suppressor of variegation 3-9 (Drosophila) homolog 1"	SUV39H		10202156	Standard	NM_001282166		Approved	KMT1A	uc004dkn.3	O43463	OTTHUMG00000022701	ENST00000376687.3:c.259A>T	chrX.hg19:g.48558575A>T	ENSP00000365877:p.Lys87*	135.0	1.0		115.0	104.0	NM_003173	B2R6E8|B4DST0|Q53G60|Q6FHK6	Nonsense_Mutation	SNP	ENST00000376687.3	hg19	CCDS14304.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	37|37	6.309281|6.309281	0.97462|0.97462	.|.	.|.	ENSG00000101945|ENSG00000101945	ENST00000337852;ENST00000376687|ENST00000448548;ENST00000453214	.|.	.|.	.|.	4.82|4.82	4.82|4.82	0.62117|0.62117	.|.	0.134893|.	0.49916|.	D|.	0.000136|.	.|T	.|0.41373	.|0.1156	.|.	.|.	.|.	0.24671|0.24671	N|N	0.993417|0.993417	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.28235	.|-1.0050	.|5	0.02654|0.34782	T|T	1|0.22	.|.	11.3805|11.3805	0.49754|0.49754	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|.	.|.	.|.	X|L	98;87|86;24	.|.	ENSP00000337976:K98X|ENSP00000410043:Q86L	K|Q	+|+	1|2	0|0	SUV39H1|SUV39H1	48443519|48443519	0.995000|0.995000	0.38212|0.38212	0.998000|0.998000	0.56505|0.56505	0.815000|0.815000	0.46073|0.46073	2.367000|2.367000	0.44213|0.44213	1.584000|1.584000	0.49913|0.49913	0.409000|0.409000	0.27619|0.27619	AAG|CAA	.	.		0.567	SUV39H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058909.1	NM_003173		T	48558575	A	T	48558575	4	4	344	1	0	0	0	0	0	1	0	0	15427	131	5	4	269	4	SUV39H1	23	48558575	Nonsense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1484331	48558575	106711985	1390	48753										
HDAC6	10013	hgsc.bcm.edu	37	chrX	48681555	48681555	+	Frame_Shift_Del	DEL	G	G	-													0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agccctcagaggcagccacaGggggagccactctggcccag							TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chrX:48681555delG	ENST00000334136.5	+	25	2924	c.2746delG	c.(2746-2748)gggfs	p.G917fs	HDAC6_ENST00000444343.2_Frame_Shift_Del_p.G931fs|HDAC6_ENST00000376619.2_Frame_Shift_Del_p.G917fs			Q9UBN7	HDAC6_HUMAN	histone deacetylase 6	917					aggresome assembly (GO:0070842)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to misfolded protein (GO:0071218)|cellular response to topologically incorrect protein (GO:0035967)|histone deacetylation (GO:0016575)|Hsp90 deacetylation (GO:0070846)|intracellular protein transport (GO:0006886)|lysosome localization (GO:0032418)|macroautophagy (GO:0016236)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of oxidoreductase activity (GO:0051354)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of proteolysis (GO:0045861)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of chaperone-mediated protein complex assembly (GO:0090035)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of hydrogen peroxide-mediated programmed cell death (GO:1901300)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of signal transduction (GO:0009967)|protein complex disassembly (GO:0043241)|protein deacetylation (GO:0006476)|protein polyubiquitination (GO:0000209)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of establishment of protein localization (GO:0070201)|regulation of gene expression, epigenetic (GO:0040029)|regulation of microtubule-based movement (GO:0060632)|regulation of receptor activity (GO:0010469)|response to growth factor (GO:0070848)|response to misfolded protein (GO:0051788)|response to organic substance (GO:0010033)|response to toxic substance (GO:0009636)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	aggresome (GO:0016235)|axon (GO:0030424)|caveola (GO:0005901)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|dendrite (GO:0030425)|histone deacetylase complex (GO:0000118)|inclusion body (GO:0016234)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)	alpha-tubulin binding (GO:0043014)|beta-catenin binding (GO:0008013)|core promoter binding (GO:0001047)|dynein complex binding (GO:0070840)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|Hsp90 protein binding (GO:0051879)|microtubule binding (GO:0008017)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|polyubiquitin binding (GO:0031593)|tau protein binding (GO:0048156)|tubulin deacetylase activity (GO:0042903)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|kidney(5)|large_intestine(8)|lung(9)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	40					Vorinostat(DB02546)	GGCAGCCACAGGGGGAGCCAC	0.637																																					p.T915fs	Pancreas(112;205 1675 2305 8976 15959)	Pindel	.											.	HDAC6	111	.	0			c.2745delA						.						19	18	18					X																	48681555		2199	4294	6493	SO:0001589	frameshift_variant	10013	exon25			.	AF132609	CCDS14306.1	Xp11.23	2014-06-12			ENSG00000094631	ENSG00000094631			14064	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 90"	300272				10220385, 10048485	Standard	NM_006044		Approved	KIAA0901, JM21, HD6, FLJ16239, PPP1R90	uc004dks.1	Q9UBN7	OTTHUMG00000034496	ENST00000334136.5:c.2746delG	chrX.hg19:g.48681555delG	ENSP00000334061:p.Gly917fs	70.0	0.0		67.0	31.0	NM_006044	O94975|Q6NT75|Q7L3E5|Q96CY0	Frame_Shift_Del	DEL	ENST00000334136.5	hg19	CCDS14306.1																																																																																			.	.		0.637	HDAC6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083394.2	NM_006044		-	48681555	G	-	48681555	7	5	344	1	0	1	0	1	0	0	0	0	7020	1000	35	0	2840	0	HDAC6	23	48681555	Frame_Shift_Del	DEL	G	TCGA-UB-A7MB-01A-11D-A33Q-10	122980	48681555	106589005	1391	48754										
GPR173	54328	hgsc.bcm.edu	37	chrX	53106453	53106453	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cgagtatcgtcaccgcaagaTgaagccagtgcagatggtgc	13	10	1	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chrX:53106453T>C	ENST00000332582.4	+	2	1141	c.650T>C	c.(649-651)aTg>aCg	p.M217T		NM_018969.5	NP_061842.1	Q9NS66	GP173_HUMAN	G protein-coupled receptor 173	217					negative regulation of neuron migration (GO:2001223)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|gonadotropin-releasing hormone receptor activity (GO:0004968)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)	16						CACCGCAAGATGAAGCCAGTG	0.592																																					p.M217T		Atlas-SNP	.											.	GPR173	66	.	0			c.T650C						.						23	22	22					X																	53106453		2196	4288	6484	SO:0001583	missense	54328	exon2			GCAAGATGAAGCC	AB040801	CCDS14349.1	Xp11	2012-08-21	2006-02-15		ENSG00000184194	ENSG00000184194		"GPCR / Class A : Orphans"	18186	protein-coding gene	gene with protein product		300253	"G-protein coupled receptor 173", "G protein coupled receptor 173"			10833454	Standard	NM_018969		Approved	SREB3	uc004dru.3	Q9NS66	OTTHUMG00000021596	ENST00000332582.4:c.650T>C	chrX.hg19:g.53106453T>C	ENSP00000331600:p.Met217Thr	20.0	0.0		30.0	27.0	NM_018969	B1B0A5	Missense_Mutation	SNP	ENST00000332582.4	hg19	CCDS14349.1	.	.	.	.	.	.	.	.	.	.	T	16.39	3.109921	0.56398	.	.	ENSG00000184194	ENST00000332582	T	0.71103	-0.54	4.85	4.85	0.62838	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.81029	0.4738	M	0.77820	2.39	0.58432	D	0.999996	D	0.89917	1.0	D	0.91635	0.999	T	0.78723	-0.2093	10	0.12766	T	0.61	-11.4851	11.4995	0.50428	0.0:0.0:0.0:1.0	.	217	Q9NS66	GP173_HUMAN	T	217	ENSP00000331600:M217T	ENSP00000331600:M217T	M	+	2	0	GPR173	53123178	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.040000	0.89188	1.614000	0.50241	0.430000	0.28490	ATG	.	.		0.592	GPR173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056717.2	NM_018969		C	53106453	T	C	53106453	3	2	344	1	0	0	0	0	1	0	0	0	6679	1464	51	2	652	2	GPR173	23	53106453	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	4424898	53106453	102164107	1392	48755										
TRO	7216	hgsc.bcm.edu	37	chrX	54955840	54955840	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gctttggaggcatactcagcAccagtgtctgttttggtggc	13	9	2	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chrX:54955840A>T	ENST00000173898.7	+	12	2795	c.2683A>T	c.(2683-2685)Acc>Tcc	p.T895S	TRO_ENST00000375041.2_Missense_Mutation_p.T498S|TRO_ENST00000375022.4_Intron|TRO_ENST00000399736.1_Intron|SNORA11_ENST00000408823.1_RNA|TRO_ENST00000319167.8_Intron|TRO_ENST00000420798.2_Missense_Mutation_p.T426S	NM_001039705.2	NP_001034794.1	Q12816	TROP_HUMAN	trophinin	895	62 X 10 AA approximate tandem repeats.				embryo implantation (GO:0007566)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|skin(2)|urinary_tract(1)	37						CATACTCAGCACCAGTGTCTG	0.557																																					p.T895S		Atlas-SNP	.											.	TRO	246	.	0			c.A2683T						.						69	63	65					X																	54955840		2087	4200	6287	SO:0001583	missense	7216	exon12			CTCAGCACCAGTG	U04811	CCDS43958.1, CCDS43959.1, CCDS59527.1, CCDS59528.1, CCDS59529.1	Xp11.22-p11.21	2008-02-05			ENSG00000067445	ENSG00000067445			12326	protein-coding gene	gene with protein product		300132				9533028, 11454705	Standard	NM_001039705		Approved	MAGE-D3, KIAA1114, MAGED3	uc004dtq.4	Q12816	OTTHUMG00000021640	ENST00000173898.7:c.2683A>T	chrX.hg19:g.54955840A>T	ENSP00000173898:p.Thr895Ser	55.0	0.0		43.0	43.0	NM_001039705	B1AKE9|B1AKF1|F5GY27|Q96SX2|Q9NU89|Q9UPN8	Missense_Mutation	SNP	ENST00000173898.7	hg19	CCDS43959.1	.	.	.	.	.	.	.	.	.	.	A	7.125	0.578684	0.13686	.	.	ENSG00000067445	ENST00000173898;ENST00000420798;ENST00000375041	T;T;T	0.13196	2.61;2.61;2.61	2.81	2.81	0.32909	.	.	.	.	.	T	0.27594	0.0678	L	0.50333	1.59	0.09310	N	1	D;D	0.76494	0.999;0.999	D;D	0.73708	0.981;0.981	T	0.03051	-1.1078	9	0.56958	D	0.05	.	8.5314	0.33337	1.0:0.0:0.0:0.0	.	498;895	B1AKE9;Q12816	.;TROP_HUMAN	S	895;426;498	ENSP00000173898:T895S;ENSP00000405126:T426S;ENSP00000364181:T498S	ENSP00000173898:T895S	T	+	1	0	TRO	54972565	0.000000	0.05858	0.539000	0.28077	0.095000	0.18619	0.033000	0.13754	1.355000	0.45865	0.443000	0.29094	ACC	.	.		0.557	TRO-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056837.3	NM_016157		T	54955840	A	T	54955840	3	4	344	1	0	0	0	0	1	0	0	0	16589	159	6	4	2725	4	TRO	23	54955840	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1849387	54955840	100314720	1393	48756										
MTMR8	55613	hgsc.bcm.edu	37	chrX	63490847	63490847	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cttttctagttcatgcacatCtgtctccagcattgctctct	5	13	5	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chrX:63490847C>G	ENST00000374852.3	-	13	1655	c.1588G>C	c.(1588-1590)Gat>Cat	p.D530H	MTMR8_ENST00000453546.1_Intron	NM_017677.3	NP_060147.2	Q96EF0	MTMR8_HUMAN	myotubularin related protein 8	530						nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)	p.0?(2)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|skin(3)	37						TCATGCACATCTGTCTCCAGC	0.478																																					p.D530H		Atlas-SNP	.											.	MTMR8	178	.	2	Whole gene deletion(2)	ovary(1)|large_intestine(1)	c.G1588C						.						121	100	107					X																	63490847		2203	4300	6503	SO:0001583	missense	55613	exon13			GCACATCTGTCTC	AK000133	CCDS14379.1	Xq11.2-q12	2013-01-11			ENSG00000102043	ENSG00000102043		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	16825	protein-coding gene	gene with protein product						11275328	Standard	NM_017677		Approved	FLJ20126	uc004dvs.3	Q96EF0	OTTHUMG00000021707	ENST00000374852.3:c.1588G>C	chrX.hg19:g.63490847C>G	ENSP00000363985:p.Asp530His	120.0	0.0		91.0	86.0	NM_017677	Q5JT99|Q9NXP6	Missense_Mutation	SNP	ENST00000374852.3	hg19	CCDS14379.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.99|10.99	1.506647|1.506647	0.26949|0.26949	.|.	.|.	ENSG00000102043|ENSG00000102043	ENST00000374852;ENST00000247400|ENST00000442913	D|.	0.94330|.	-3.4|.	3.75|3.75	1.87|1.87	0.25490|0.25490	.|.	0.314036|.	0.20770|.	U|.	0.086009|.	T|T	0.09423|0.09423	0.0232|0.0232	N|N	0.02129|0.02129	-0.67|-0.67	0.09310|0.09310	N|N	1|1	B|.	0.02656|.	0.0|.	B|.	0.06405|.	0.002|.	T|T	0.31420|0.31420	-0.9944|-0.9944	10|5	0.08599|.	T|.	0.76|.	.|.	5.3298|5.3298	0.15926|0.15926	0.0:0.6106:0.0:0.3894|0.0:0.6106:0.0:0.3894	.|.	530|.	Q96EF0|.	MTMR8_HUMAN|.	H|T	530;416|333	ENSP00000363985:D530H|.	ENSP00000247400:D416H|.	D|R	-|-	1|2	0|0	MTMR8|MTMR8	63407572|63407572	0.009000|0.009000	0.17119|0.17119	0.008000|0.008000	0.14137|0.14137	0.989000|0.989000	0.77384|0.77384	0.350000|0.350000	0.20079|0.20079	0.523000|0.523000	0.28482|0.28482	0.594000|0.594000	0.82650|0.82650	GAT|AGA	.	.		0.478	MTMR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056949.2	NM_017677		G	63490847	C	G	63490847	3	3	344	1	0	0	0	0	1	0	0	0	9958	913	32	4	534	4	MTMR8	23	63490847	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	8535007	63490847	91779713	1394	48757										
AR	367	hgsc.bcm.edu	37	chrX	66937427	66937427	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ccttcaccaatgtcaactccAggatgctctacttcgcccct	5	17	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chrX:66937427A>C	ENST00000374690.3	+	5	2805	c.2281A>C	c.(2281-2283)Agg>Cgg	p.R761R	AR_ENST00000396043.2_Silent_p.R229R|AR_ENST00000396044.3_Intron	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	760	Interaction with KAT7.|Interaction with LPXN.|Ligand-binding.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	TGTCAACTCCAGGATGCTCTA	0.537									Androgen Insensitivity Syndrome																												p.R761R		Atlas-SNP	.											.	AR	249	.	0			c.A2281C	GRCh37	CX034080	AR	X		.						134	95	108					X																	66937427		2203	4300	6503	SO:0001819	synonymous_variant	367	exon5	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	AACTCCAGGATGC	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.2281A>C	chrX.hg19:g.66937427A>C		58.0	0.0		58.0	52.0	NM_000044	A2RUN2|B1AKD7|Q9UD95	Silent	SNP	ENST00000374690.3	hg19	CCDS14387.1																																																																																			.	.		0.537	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		C	66937427	A	C	66937427	2	2	344	1	0	0	0	0	0	0	0	1	836	179	7	5		5	AR	23	66937427	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3446580	66937427	88333133	1395	48758										
RLIM	51132	hgsc.bcm.edu	37	chrX	73812565	73812565	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acctctgttaacgcttcagtTgaatttcgttctgatctaga	7	9	4	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chrX:73812565T>A	ENST00000332687.6	-	4	803	c.585A>T	c.(583-585)tcA>tcT	p.S195S	RLIM_ENST00000349225.2_Silent_p.S195S	NM_016120.3	NP_057204.2	Q9NVW2	RNF12_HUMAN	ring finger protein, LIM domain interacting	195					negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|random inactivation of X chromosome (GO:0060816)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	ligase activity (GO:0016874)|transcription corepressor activity (GO:0003714)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						ACGCTTCAGTTGAATTTCGTT	0.483																																					p.S195S	Esophageal Squamous(169;1899 1923 14997 18818 32118)	Atlas-SNP	.											.	RLIM	90	.	0			c.A585T						.						183	156	165					X																	73812565		2203	4300	6503	SO:0001819	synonymous_variant	51132	exon5			TTCAGTTGAATTT	AF155109	CCDS14427.1	Xq13-q21	2013-01-09	2009-02-17	2009-02-17	ENSG00000131263	ENSG00000131263		"RING-type (C3HC4) zinc fingers"	13429	protein-coding gene	gene with protein product	"ring zinc finger protein NY-REN-43antigen", "LIM domain interacting ring finger protein"	300379	"ring finger protein 12"	RNF12		10508479	Standard	NM_016120		Approved	NY-REN-43, MGC15161	uc004ebw.3	Q9NVW2	OTTHUMG00000021859	ENST00000332687.6:c.585A>T	chrX.hg19:g.73812565T>A		47.0	0.0		43.0	33.0	NM_183353	B2RBQ1|D3DTE0|Q96D38|Q9Y598	Silent	SNP	ENST00000332687.6	hg19	CCDS14427.1																																																																																			.	.		0.483	RLIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057268.1	NM_016120		A	73812565	T	A	73812565	2	1	344	1	0	0	0	0	0	0	0	1	13405	1799	63	4		4	RLIM	23	73812565	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	6875138	73812565	81457995	1396	48759										
ATRX	546	hgsc.bcm.edu	37	chrX	76938245	76938245	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aattctttttttggtggttcTggcagcaccaattttactca	7	8	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chrX:76938245T>A	ENST00000373344.5	-	9	2717	c.2503A>T	c.(2503-2505)Aga>Tga	p.R835*	ATRX_ENST00000395603.3_Nonsense_Mutation_p.R797*|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	835					ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						TTGGTGGTTCTGGcagcacca	0.323			"Mis, F, N"		"Pancreatic neuroendocrine tumors, paediatric GBM"		ATR-X (alpha thalassemia/mental retardation) syndrome																														p.R835X		Atlas-SNP	.		Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	.	ATRX	833	.	1	Unknown(1)	bone(1)	c.A2503T						.						130	142	138					X																	76938245		2202	4293	6495	SO:0001587	stop_gained	546	exon9			TGGTTCTGGCAGC	U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"RAD54 homolog (S. cerevisiae)"	300032	"alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)", "Juberg-Marsidi syndrome"	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.2503A>T	chrX.hg19:g.76938245T>A	ENSP00000362441:p.Arg835*	54.0	0.0		53.0	52.0	NM_000489	D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Nonsense_Mutation	SNP	ENST00000373344.5	hg19	CCDS14434.1	.	.	.	.	.	.	.	.	.	.	T	39	7.446328	0.98289	.	.	ENSG00000085224	ENST00000373344;ENST00000395603;ENST00000400862	.	.	.	5.73	5.73	0.89815	.	0.401292	0.26816	N	0.022360	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.0166	8.8438	0.35157	0.0:0.0846:0.0:0.9154	.	.	.	.	X	835;797;762	.	ENSP00000362441:R835X	R	-	1	2	ATRX	76824901	1.000000	0.71417	0.744000	0.31058	0.463000	0.32649	4.988000	0.63863	1.917000	0.55516	0.380000	0.24917	AGA	.	.		0.323	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		A	76938245	T	A	76938245	4	1	344	1	0	0	0	0	0	1	0	0	1208	1588	55	4	5083	4	ATRX	23	76938245	Nonsense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	3125680	76938245	78332315	1397	48760										
BRWD3	254065	hgsc.bcm.edu	37	chrX	79979304	79979304	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agcaaatgtccatgagaatcTgtgcaggcaaaatggtttcc	10	8	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chrX:79979304T>C	ENST00000373275.4	-	16	1809	c.1593A>G	c.(1591-1593)acA>acG	p.T531T	BRWD3_ENST00000473691.1_5'Flank	NM_153252.4	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	531					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)					breast(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(39)|ovary(4)|prostate(2)|skin(3)	87						CATGAGAATCTGTGCAGGCAA	0.378																																					p.T531T		Atlas-SNP	.											.	BRWD3	251	.	0			c.A1593G						.						93	82	86					X																	79979304		2203	4300	6503	SO:0001819	synonymous_variant	254065	exon16			AGAATCTGTGCAG		CCDS14447.1	Xq21.1	2013-01-09			ENSG00000165288	ENSG00000165288		"WD repeat domain containing"	17342	protein-coding gene	gene with protein product		300553				15543602, 16094372	Standard	NM_153252		Approved	FLJ38568, MRX93	uc004edt.3	Q6RI45	OTTHUMG00000021908	ENST00000373275.4:c.1593A>G	chrX.hg19:g.79979304T>C		52.0	0.0		47.0	45.0	NM_153252	C9IZ39|C9J3F3|Q2T9J6|Q5JRN1|Q6RI37|Q6RI42|Q6RI44|Q8N916	Silent	SNP	ENST00000373275.4	hg19	CCDS14447.1																																																																																			.	.		0.378	BRWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057344.1	NM_153252		C	79979304	T	C	79979304	2	2	344	1	0	0	0	0	0	0	0	1	1528	1567	55	2		2	BRWD3	23	79979304	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	3041059	79979304	75291256	1398	48761										
RPS6KA6	27330	hgsc.bcm.edu	37	chrX	83390124	83390124	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	agctttacttttctggcttcAggtctctataaacaattcct	5	10	3	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chrX:83390124A>C	ENST00000262752.2	-	7	603	c.596T>G	c.(595-597)cTg>cGg	p.L199R	RPS6KA6_ENST00000543399.1_Missense_Mutation_p.L199R	NM_014496.4	NP_055311.1	Q9UK32	KS6A6_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 6	199	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|central nervous system development (GO:0007417)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|negative regulation of embryonic development (GO:0045992)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of mesoderm development (GO:2000381)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(26)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	46						TTCTGGCTTCAGGTCTCTATA	0.363																																					p.L199R		Atlas-SNP	.											.	RPS6KA6	116	.	0			c.T596G						.						50	45	47					X																	83390124		2203	4297	6500	SO:0001583	missense	27330	exon7			GGCTTCAGGTCTC	AF184965	CCDS14451.1	Xq21.1	2011-04-05	2002-08-29		ENSG00000072133	ENSG00000072133			10435	protein-coding gene	gene with protein product		300303	"ribosomal protein S6 kinase, 90kD, polypeptide 6"			10644430	Standard	NM_014496		Approved	RSK4	uc004eej.2	Q9UK32	OTTHUMG00000021923	ENST00000262752.2:c.596T>G	chrX.hg19:g.83390124A>C	ENSP00000262752:p.Leu199Arg	301.0	0.0		260.0	233.0	NM_014496	B2R854|B7ZL90|Q6FHX2|Q8WX28|Q9H4S6	Missense_Mutation	SNP	ENST00000262752.2	hg19	CCDS14451.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.026606	0.75390	.	.	ENSG00000072133	ENST00000262752;ENST00000543399	T;T	0.43294	0.95;0.95	4.82	4.82	0.62117	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000001	T	0.77445	0.4131	H	0.98446	4.235	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	D	0.86094	0.1552	10	0.87932	D	0	.	13.5737	0.61862	1.0:0.0:0.0:0.0	.	199;199	B7ZL90;Q9UK32	.;KS6A6_HUMAN	R	199	ENSP00000262752:L199R;ENSP00000440830:L199R	ENSP00000262752:L199R	L	-	2	0	RPS6KA6	83276780	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.126000	0.94411	1.577000	0.49804	0.437000	0.28790	CTG	.	.		0.363	RPS6KA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057372.1	NM_014496		C	83390124	A	C	83390124	3	2	344	1	0	0	0	0	1	0	0	0	13670	188	7	5	1705	5	RPS6KA6	23	83390124	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3410820	83390124	71880436	1399	48762										
DACH2	117154	hgsc.bcm.edu	37	chrX	85769362	85769362	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tctgacccatgcagtcccagGcctcttatcgccaggactta	8	15	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chrX:85769362G>T	ENST00000373125.4	+	3	608	c.608G>T	c.(607-609)gGc>gTc	p.G203V	DACH2_ENST00000508860.1_Missense_Mutation_p.G36V|DACH2_ENST00000373131.1_Missense_Mutation_p.G190V|DACH2_ENST00000510272.1_5'UTR	NM_053281.3	NP_444511.1	Q96NX9	DACH2_HUMAN	dachshund family transcription factor 2	203					development of primary female sexual characteristics (GO:0046545)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(14)|lung(28)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	71						GCAGTCCCAGGCCTCTTATCG	0.478																																					p.G203V		Atlas-SNP	.											.	DACH2	263	.	0			c.G608T						.						49	41	44					X																	85769362		2203	4300	6503	SO:0001583	missense	117154	exon3			TCCCAGGCCTCTT	AF428101	CCDS14455.1, CCDS48140.1, CCDS55457.1	Xq21.3	2014-02-03	2014-02-03		ENSG00000126733	ENSG00000126733			16814	protein-coding gene	gene with protein product		300608	"dachshund homolog 2 (Drosophila)"				Standard	NM_053281		Approved		uc004eew.2	Q96NX9	OTTHUMG00000021944	ENST00000373125.4:c.608G>T	chrX.hg19:g.85769362G>T	ENSP00000362217:p.Gly203Val	224.0	0.0		197.0	176.0	NM_053281	B1AJV3|B4DQG3|Q8NAY3|Q8ND17|Q96N55	Missense_Mutation	SNP	ENST00000373125.4	hg19	CCDS14455.1	.	.	.	.	.	.	.	.	.	.	G	16.74	3.206840	0.58343	.	.	ENSG00000126733	ENST00000344497;ENST00000373131;ENST00000373125;ENST00000508860;ENST00000400297	D;D	0.87029	-2.19;-2.2	4.88	4.01	0.46588	.	0.163605	0.41938	D	0.000782	D	0.91054	0.7185	L	0.59436	1.845	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.974;0.994;0.987	D	0.90175	0.4238	10	0.51188	T	0.08	.	12.126	0.53917	0.0857:0.0:0.9143:0.0	.	69;190;203	Q1RMF5;Q96NX9-2;Q96NX9	.;.;DACH2_HUMAN	V	203;190;203;36;36	ENSP00000362223:G190V;ENSP00000362217:G203V	ENSP00000345134:G203V	G	+	2	0	DACH2	85656018	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	6.572000	0.74005	0.834000	0.34852	0.506000	0.49869	GGC	.	.		0.478	DACH2-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359266.1	NM_053281		T	85769362	G	T	85769362	3	4	344	1	0	0	0	0	1	0	0	0	4223	1203	42	3	618	3	DACH2	23	85769362	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	2379238	85769362	69501198	1400	48763										
PCDH11X	27328	hgsc.bcm.edu	37	chrX	91873834	91873834	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atgtctgaaagacttcatccCagtgatgattcaattaaagt	7	7	3	4			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chrX:91873834C>T	ENST00000373094.1	+	7	4784	c.3939C>T	c.(3937-3939)ccC>ccT	p.P1313P	PCDH11X_ENST00000504220.2_3'UTR|PCDH11X_ENST00000406881.1_Silent_p.P1305P|PCDH11X_ENST00000298274.8_Silent_p.P1276P|PCDH11X_ENST00000361655.2_Silent_p.P1295P|PCDH11X_ENST00000373097.1_Silent_p.P1303P|PCDH11X_ENST00000373088.1_Silent_p.P1276P	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	1313					homophilic cell adhesion (GO:0007156)|negative regulation of phosphatase activity (GO:0010923)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						GACTTCATCCCAGTGATGATT	0.478																																					p.P1313P	NSCLC(38;925 1092 2571 38200 45895)	Atlas-SNP	.											.	PCDH11X	714	.	0			c.C3939T						.						182	166	171					X																	91873834		2203	4300	6503	SO:0001819	synonymous_variant	27328	exon7			TCATCCCAGTGAT	AB026187	CCDS14461.1, CCDS14462.1, CCDS55458.1, CCDS55459.1, CCDS55460.1, CCDS55461.1	Xq21.3	2014-06-13	2002-05-22	2002-05-24	ENSG00000102290	ENSG00000102290		"Cadherins / Protocadherins : Non-clustered"	8656	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 119"	300246	"protocadherin 11"	PCDH11		10644456	Standard	NM_001168360		Approved	PCDH-X, PCDHX, PPP1R119	uc004efm.2	Q9BZA7	OTTHUMG00000021965	ENST00000373094.1:c.3939C>T	chrX.hg19:g.91873834C>T		172.0	0.0		162.0	151.0	NM_032968	A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	Silent	SNP	ENST00000373094.1	hg19	CCDS14461.1																																																																																			.	.		0.478	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969		T	91873834	C	T	91873834	2	4	344	1	0	0	0	0	0	0	0	1	11517	581	21	3		3	PCDH11X	23	91873834	Silent	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	6104472	91873834	63396726	1401	48764										
ARMCX3	51566	hgsc.bcm.edu	37	chrX	100880234	100880234	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttgggactgaagctggaaccAgagctagggccagggcaagg	17	8	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chrX:100880234A>T	ENST00000341189.4	+	5	1131	c.265A>T	c.(265-267)Aga>Tga	p.R89*	ARMCX3-AS1_ENST00000454228.1_RNA|RP4-545K15.5_ENST00000564612.1_RNA|ARMCX3_ENST00000537169.1_Nonsense_Mutation_p.R89*|ARMCX3_ENST00000471229.2_Nonsense_Mutation_p.R89*	NM_016607.3	NP_057691.1	Q9UH62	ARMX3_HUMAN	armadillo repeat containing, X-linked 3	89					cellular protein localization (GO:0034613)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	integral component of mitochondrial outer membrane (GO:0031307)				endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)	11						AGCTGGAACCagagctagggc	0.547																																					p.R89X		Atlas-SNP	.											.	ARMCX3	33	.	0			c.A265T						.						70	69	70					X																	100880234		2203	4300	6503	SO:0001587	stop_gained	51566	exon5			GGAACCAGAGCTA	AY359079	CCDS14489.1	Xq22.1	2014-03-21			ENSG00000102401	ENSG00000102401		"Armadillo repeat containing"	24065	protein-coding gene	gene with protein product		300364				11162520, 11042152, 19304657, 16221301, 22569362	Standard	NM_016607		Approved	ALEX3, GASP6	uc004eia.1	Q9UH62	OTTHUMG00000022035	ENST00000341189.4:c.265A>T	chrX.hg19:g.100880234A>T	ENSP00000340672:p.Arg89*	37.0	0.0		30.0	29.0	NM_016607	Q53HC6|Q7LCF5|Q9NPE4	Nonsense_Mutation	SNP	ENST00000341189.4	hg19	CCDS14489.1	.	.	.	.	.	.	.	.	.	.	A	38	7.035055	0.98017	.	.	ENSG00000102401	ENST00000341189;ENST00000537169	.	.	.	4.22	4.22	0.49857	.	0.611666	0.16813	N	0.198462	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-10.0219	8.7431	0.34569	1.0:0.0:0.0:0.0	.	.	.	.	X	89	.	.	R	+	1	2	ARMCX3	100766890	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	3.612000	0.54142	1.885000	0.54596	0.481000	0.45027	AGA	.	.		0.547	ARMCX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057568.2	NM_016607		T	100880234	A	T	100880234	4	4	344	1	0	0	0	0	0	1	0	0	961	180	7	4	267	4	ARMCX3	23	100880234	Nonsense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	9006400	100880234	54390326	1402	48765										
COL4A5	1287	hgsc.bcm.edu	37	chrX	107821343	107821343	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	aatttccagggacccaaaggTgaaaaagtgagtaaagaaag	11	5	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chrX:107821343T>A	ENST00000361603.2	+	12	925	c.681T>A	c.(679-681)ggT>ggA	p.G227G	COL4A5_ENST00000328300.6_Silent_p.G227G	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5	227	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|neuromuscular junction (GO:0031594)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(32)|ovary(4)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	99						GACCCAAAGGTGAAAAAGTGA	0.378									Alport syndrome with Diffuse Leiomyomatosis																												p.G227G		Atlas-SNP	.											.	COL4A5	262	.	0			c.T681A						.						37	37	37					X																	107821343		2185	4289	6474	SO:0001819	synonymous_variant	1287	exon12	Familial Cancer Database		CAAAGGTGAAAAA	M90464	CCDS14543.1, CCDS35366.1	Xq22	2014-09-17	2008-07-28		ENSG00000188153	ENSG00000188153		"Collagens"	2207	protein-coding gene	gene with protein product		303630	"Alport syndrome"	ASLN, ATS			Standard	NM_000495		Approved		uc004enz.2	P29400	OTTHUMG00000022182	ENST00000361603.2:c.681T>A	chrX.hg19:g.107821343T>A		192.0	0.0		159.0	145.0	NM_000495	Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Silent	SNP	ENST00000361603.2	hg19	CCDS14543.1																																																																																			.	.		0.378	COL4A5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057880.2			A	107821343	T	A	107821343	2	1	344	1	0	0	0	0	0	0	0	1	3696	1683	59	4		4	COL4A5	23	107821343	Silent	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	6941109	107821343	47449217	1403	48766										
PAK3	5063	hgsc.bcm.edu	37	chrX	110391047	110391047	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gaagaacccacaagctgttcTagatgttctcaaattctatg	7	9	3	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chrX:110391047T>C	ENST00000372010.1	+	8	846	c.404T>C	c.(403-405)cTa>cCa	p.L135P	PAK3_ENST00000425146.1_Missense_Mutation_p.L120P|PAK3_ENST00000360648.4_Missense_Mutation_p.L156P|PAK3_ENST00000372007.5_Missense_Mutation_p.L120P|PAK3_ENST00000262836.4_Missense_Mutation_p.L135P|PAK3_ENST00000518291.1_Missense_Mutation_p.L156P|PAK3_ENST00000519681.1_Missense_Mutation_p.L141P|PAK3_ENST00000446737.1_Missense_Mutation_p.L120P|PAK3_ENST00000417227.1_Missense_Mutation_p.L141P			O75914	PAK3_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 3	135	Autoregulatory region. {ECO:0000250}.|Linker.			VLDV -> CSRC (in Ref. 2; AAF67008). {ECO:0000305}.	activation of MAPK activity (GO:0000187)|axonogenesis (GO:0007409)|dendrite development (GO:0016358)|dendritic spine morphogenesis (GO:0060997)|MAPK cascade (GO:0000165)|regulation of actin filament polymerization (GO:0030833)|synapse organization (GO:0050808)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(15)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	41						CAAGCTGTTCTAGATGTTCTC	0.413										TSP Lung(19;0.15)																											p.L156P		Atlas-SNP	.											.	PAK3	179	.	0			c.T467C						.						116	100	105					X																	110391047		2203	4300	6503	SO:0001583	missense	5063	exon5			CTGTTCTAGATGT	AF068864	CCDS14554.1, CCDS48151.1, CCDS48152.1, CCDS48153.1	Xq22.3	2008-06-17	2008-06-17		ENSG00000077264	ENSG00000077264			8592	protein-coding gene	gene with protein product		300142	"mental retardation, X-linked 47", "p21 (CDKN1A)-activated kinase 3"	MRX30, MRX47		8826460, 9731525	Standard	NM_002578		Approved	hPAK3, bPAK	uc010npv.1	O75914	OTTHUMG00000022202	ENST00000372010.1:c.404T>C	chrX.hg19:g.110391047T>C	ENSP00000361080:p.Leu135Pro	244.0	0.0		250.0	223.0	NM_001128168	A8K389|B1GX77|B1GX78|B1GX79|Q5JWX1|Q5JWX2|Q7Z2D6|Q7Z2E4|Q7Z3Z8|Q8WWK5|Q8WX23|Q9P0J8	Missense_Mutation	SNP	ENST00000372010.1	hg19	CCDS48153.1	.	.	.	.	.	.	.	.	.	.	T	15.95	2.983683	0.53827	.	.	ENSG00000077264	ENST00000446737;ENST00000425146;ENST00000372010;ENST00000519681;ENST00000372007;ENST00000518291;ENST00000429193;ENST00000360648;ENST00000417227;ENST00000262836	D;D;D;D;D;D;D;D;D;D	0.87256	-2.23;-2.23;-2.23;-2.23;-2.23;-2.23;-2.23;-2.23;-2.23;-2.23	5.74	5.74	0.90152	PAK-box/P21-Rho-binding (1);	0.076673	0.53938	D	0.000055	D	0.94499	0.8229	M	0.89968	3.075	0.80722	D	1	D;D;D;D	0.89917	0.998;0.999;1.0;0.995	D;D;D;D	0.79784	0.981;0.993;0.993;0.981	D	0.95449	0.8532	10	0.87932	D	0	.	15.039	0.71774	0.0:0.0:0.0:1.0	.	141;156;135;120	O75914-4;O75914-3;O75914;O75914-2	.;.;PAK3_HUMAN;.	P	120;120;135;141;120;156;156;156;141;135	ENSP00000410853:L120P;ENSP00000401982:L120P;ENSP00000361080:L135P;ENSP00000429113:L141P;ENSP00000361077:L120P;ENSP00000428921:L156P;ENSP00000405642:L156P;ENSP00000353864:L156P;ENSP00000389172:L141P;ENSP00000262836:L135P	ENSP00000262836:L135P	L	+	2	0	PAK3	110277703	0.997000	0.39634	0.639000	0.29394	0.938000	0.57974	7.698000	0.84413	1.935000	0.56089	0.437000	0.28790	CTA	.	.		0.413	PAK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057918.1	NM_002578		C	110391047	T	C	110391047	3	2	344	1	0	0	0	0	1	0	0	0	11411	1522	53	2	485	2	PAK3	23	110391047	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	2569704	110391047	44879513	1404	48767										
DOCK11	139818	hgsc.bcm.edu	37	chrX	117722105	117722105	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttttccctgctatagattgtAttacttcttcatatgtgccc	5	10	2	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chrX:117722105A>G	ENST00000276202.7	+	17	1864	c.1801A>G	c.(1801-1803)Att>Gtt	p.I601V	DOCK11_ENST00000276204.6_Missense_Mutation_p.I601V	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	601					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(4)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(17)|liver(1)|lung(35)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	84						TATAGATTGTATTACTTCTTC	0.308																																					p.I601V		Atlas-SNP	.											.	DOCK11	185	.	0			c.A1801G						.						94	91	92					X																	117722105		2201	4291	6492	SO:0001583	missense	139818	exon17			GATTGTATTACTT	AK125641	CCDS35373.1	Xq24	2013-10-25			ENSG00000147251	ENSG00000147251		"Pleckstrin homology (PH) domain containing"	23483	protein-coding gene	gene with protein product	"zizimin2"	300681				12432077, 16968698	Standard	NM_144658		Approved	FLJ32122, FLJ43653, ZIZ2, ACG	uc004eqp.2	Q5JSL3	OTTHUMG00000022256	ENST00000276202.7:c.1801A>G	chrX.hg19:g.117722105A>G	ENSP00000276202:p.Ile601Val	54.0	0.0		47.0	45.0	NM_144658	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Missense_Mutation	SNP	ENST00000276202.7	hg19	CCDS35373.1	.	.	.	.	.	.	.	.	.	.	A	1.728	-0.494854	0.04322	.	.	ENSG00000147251	ENST00000276204;ENST00000276202	T;T	0.14144	2.53;2.53	5.92	4.79	0.61399	.	0.107463	0.64402	D	0.000005	T	0.02342	0.0072	N	0.00335	-1.625	0.30442	N	0.776079	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.31392	-0.9945	10	0.10377	T	0.69	-3.4468	1.66	0.02789	0.4573:0.0:0.2675:0.2752	.	601;601	A6NIW2;Q5JSL3	.;DOC11_HUMAN	V	601	ENSP00000276204:I601V;ENSP00000276202:I601V	ENSP00000276202:I601V	I	+	1	0	DOCK11	117606133	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	3.396000	0.52565	2.000000	0.58554	0.481000	0.45027	ATT	.	.		0.308	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658		G	117722105	A	G	117722105	3	3	344	1	0	0	0	0	1	0	0	0	4688	449	16	2	1867	2	DOCK11	23	117722105	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	7331058	117722105	37548455	1405	48768										
DOCK11	139818	hgsc.bcm.edu	37	chrX	117722147	117722147	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgaagccttttgaaaagaatTgccaaaatattactgtggag	9	5	0	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chrX:117722147T>G	ENST00000276202.7	+	17	1906	c.1843T>G	c.(1843-1845)Tgc>Ggc	p.C615G	DOCK11_ENST00000276204.6_Missense_Mutation_p.C615G	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	615					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(4)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(17)|liver(1)|lung(35)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	84						TGAAAAGAATTGCCAAAATAT	0.313																																					p.C615G		Atlas-SNP	.											.	DOCK11	185	.	0			c.T1843G						.						96	93	94					X																	117722147		2201	4296	6497	SO:0001583	missense	139818	exon17			AAGAATTGCCAAA	AK125641	CCDS35373.1	Xq24	2013-10-25			ENSG00000147251	ENSG00000147251		"Pleckstrin homology (PH) domain containing"	23483	protein-coding gene	gene with protein product	"zizimin2"	300681				12432077, 16968698	Standard	NM_144658		Approved	FLJ32122, FLJ43653, ZIZ2, ACG	uc004eqp.2	Q5JSL3	OTTHUMG00000022256	ENST00000276202.7:c.1843T>G	chrX.hg19:g.117722147T>G	ENSP00000276202:p.Cys615Gly	57.0	0.0		46.0	41.0	NM_144658	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Missense_Mutation	SNP	ENST00000276202.7	hg19	CCDS35373.1	.	.	.	.	.	.	.	.	.	.	T	12.48	1.950089	0.34377	.	.	ENSG00000147251	ENST00000276204;ENST00000276202	T;T	0.16196	2.36;2.36	5.82	5.82	0.92795	.	0.086103	0.85682	D	0.000000	T	0.12092	0.0294	N	0.25144	0.715	0.51767	D	0.999938	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.15607	-1.0431	10	0.20046	T	0.44	-6.5108	12.7932	0.57545	0.0:0.0:0.0:1.0	.	615;615	A6NIW2;Q5JSL3	.;DOC11_HUMAN	G	615	ENSP00000276204:C615G;ENSP00000276202:C615G	ENSP00000276202:C615G	C	+	1	0	DOCK11	117606175	0.549000	0.26481	0.995000	0.50966	0.961000	0.63080	0.858000	0.27845	1.958000	0.56883	0.481000	0.45027	TGC	.	.		0.313	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658		G	117722147	T	G	117722147	3	3	344	1	0	0	0	0	1	0	0	0	4688	1812	63	5	1909	5	DOCK11	23	117722147	Missense_Mutation	SNP	T	TCGA-UB-A7MB-01A-11D-A33Q-10	42	117722147	37548413	1406	48769										
IGSF1	3547	hgsc.bcm.edu	37	chrX	130419759	130419759	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	acctggtgcctccaactctaGaactttactgggctttgacc	8	13	1	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chrX:130419759G>T	ENST00000361420.3	-	4	440	c.361C>A	c.(361-363)Cta>Ata	p.L121I	IGSF1_ENST00000370910.1_Missense_Mutation_p.L112I|IGSF1_ENST00000370901.4_Missense_Mutation_p.L121I|IGSF1_ENST00000370904.1_Missense_Mutation_p.L112I|IGSF1_ENST00000370903.3_Missense_Mutation_p.L121I|IGSF1_ENST00000370900.1_Missense_Mutation_p.L121I			Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1	121	Ig-like C2-type 1.				regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	coreceptor activity (GO:0015026)|inhibin binding (GO:0034711)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|liver(1)|lung(37)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)	78						TCCAACTCTAGAACTTTACTG	0.473																																					p.L121I		Atlas-SNP	.											.	IGSF1	231	.	0			c.C361A						.						75	72	73					X																	130419759		2203	4300	6503	SO:0001583	missense	3547	exon4			ACTCTAGAACTTT	AF034198	CCDS14629.1, CCDS14630.1, CCDS55490.1, CCDS55491.1	Xq25	2013-01-11			ENSG00000147255	ENSG00000147255		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5948	protein-coding gene	gene with protein product		300137				9521868, 9729118	Standard	NM_001555		Approved	KIAA0364, IGDC1, IGCD1, INHBP, MGC75490, PGSF2	uc004ewe.4	Q8N6C5	OTTHUMG00000022406	ENST00000361420.3:c.361C>A	chrX.hg19:g.130419759G>T	ENSP00000355010:p.Leu121Ile	35.0	0.0		40.0	38.0	NM_001555	B5MEG2|H9KV64|O15070|Q9NTC8	Missense_Mutation	SNP	ENST00000361420.3	hg19	CCDS14629.1	.	.	.	.	.	.	.	.	.	.	G	15.37	2.814960	0.50527	.	.	ENSG00000147255	ENST00000370910;ENST00000361420;ENST00000370904;ENST00000370903;ENST00000370901;ENST00000370900	T;T;T;T;T;T	0.12465	2.68;2.68;2.68;2.68;2.68;2.68	4.76	3.81	0.43845	Immunoglobulin-like fold (1);	0.211844	0.23789	N	0.044544	T	0.40522	0.1120	M	0.91038	3.17	0.31199	N	0.699974	P;D;D	0.63046	0.942;0.99;0.992	P;D;D	0.76071	0.638;0.979;0.987	T	0.52011	-0.8632	10	0.72032	D	0.01	.	6.6331	0.22867	0.1635:0.0:0.8365:0.0	.	121;112;121	Q8N6C5-3;Q8N6C5-2;Q8N6C5	.;.;IGSF1_HUMAN	I	112;121;112;121;121;121	ENSP00000359947:L112I;ENSP00000355010:L121I;ENSP00000359941:L112I;ENSP00000359940:L121I;ENSP00000359938:L121I;ENSP00000359937:L121I	ENSP00000355010:L121I	L	-	1	2	IGSF1	130247440	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	1.346000	0.33964	0.908000	0.36671	0.600000	0.82982	CTA	.	.		0.473	IGSF1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058288.1			T	130419759	G	T	130419759	3	4	344	1	0	0	0	0	1	0	0	0	7605	933	33	3	3794	3	IGSF1	23	130419759	Missense_Mutation	SNP	G	TCGA-UB-A7MB-01A-11D-A33Q-10	12697612	130419759	24850801	1407	48770										
PLAC1	10761	hgsc.bcm.edu	37	chrX	133700330	133700330	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tgctggctactctcatggagCagggcttggtgagccatggg	16	9	1	1			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chrX:133700330C>A	ENST00000359237.4	-	3	668	c.383G>T	c.(382-384)tGc>tTc	p.C128F	PLAC1_ENST00000476971.1_5'UTR	NM_021796.3	NP_068568.1			placenta-specific 1											large_intestine(4)|lung(1)|pancreas(1)	6	Acute lymphoblastic leukemia(192;0.000127)					TCTCATGGAGCAGGGCTTGGT	0.542																																					p.C128F		Atlas-SNP	.											.	PLAC1	17	.	0			c.G383T						.						127	106	113					X																	133700330		2203	4300	6503	SO:0001583	missense	10761	exon3			ATGGAGCAGGGCT	AF234654	CCDS14642.1	Xq26.3	2013-10-14			ENSG00000170965	ENSG00000170965			9044	protein-coding gene	gene with protein product	"cancer/testis antigen 92"	300296				10995572	Standard	NM_021796		Approved	CT92, OOSP2L	uc004exo.1	Q9HBJ0	OTTHUMG00000022457	ENST00000359237.4:c.383G>T	chrX.hg19:g.133700330C>A	ENSP00000352173:p.Cys128Phe	70.0	0.0		76.0	70.0	NM_021796		Missense_Mutation	SNP	ENST00000359237.4	hg19	CCDS14642.1	.	.	.	.	.	.	.	.	.	.	C	2.809	-0.247387	0.05867	.	.	ENSG00000170965	ENST00000359237	D	0.81499	-1.5	4.64	-3.64	0.04515	.	0.989692	0.08194	N	0.983304	T	0.59649	0.2209	L	0.31294	0.92	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.44065	-0.9352	10	0.11485	T	0.65	-2.6072	0.4916	0.00565	0.2732:0.1665:0.1494:0.411	.	128	Q9HBJ0	PLAC1_HUMAN	F	128	ENSP00000352173:C128F	ENSP00000352173:C128F	C	-	2	0	PLAC1	133527996	0.000000	0.05858	0.000000	0.03702	0.251000	0.25915	-1.161000	0.03144	-0.886000	0.03966	-0.224000	0.12420	TGC	.	.		0.542	PLAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058375.1	NM_021796		A	133700330	C	A	133700330	3	1	344	1	0	0	0	0	1	0	0	0	12021	710	25	3	259	3	PLAC1	23	133700330	Missense_Mutation	SNP	C	TCGA-UB-A7MB-01A-11D-A33Q-10	3280571	133700330	21570230	1408	48771										
SAGE1	55511	hgsc.bcm.edu	37	chrX	134993960	134993960	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	atttgcggtaggcaccaaaaActacagtgtctctgcaggtg	11	9	1	0			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chrX:134993960A>C	ENST00000370709.3	+	17	2369	c.2369A>C	c.(2368-2370)aAc>aCc	p.N790T	SAGE1_ENST00000324447.3_Missense_Mutation_p.N790T|SAGE1_ENST00000537770.1_Missense_Mutation_p.N414T|SAGE1_ENST00000535938.1_Missense_Mutation_p.N790T			Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	790						nucleus (GO:0005634)				breast(5)|endometrium(5)|large_intestine(10)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	55	Acute lymphoblastic leukemia(192;0.000127)					GGCACCAAAAACTACAGTGTC	0.428																																					p.N790T		Atlas-SNP	.											.	SAGE1	160	.	0			c.A2369C						.						128	118	121					X																	134993960		2203	4300	6503	SO:0001583	missense	55511	exon18			CCAAAAACTACAG	AJ278111	CCDS14652.1	Xq26	2009-03-25			ENSG00000181433	ENSG00000181433			30369	protein-coding gene	gene with protein product	"cancer/testis antigen 14"	300359				10919659	Standard	NM_018666		Approved	SAGE, CT14	uc004ezh.3	Q9NXZ1	OTTHUMG00000022496	ENST00000370709.3:c.2369A>C	chrX.hg19:g.134993960A>C	ENSP00000359743:p.Asn790Thr	84.0	0.0		75.0	68.0	NM_018666	Q5JNW0	Missense_Mutation	SNP	ENST00000370709.3	hg19	CCDS14652.1	.	.	.	.	.	.	.	.	.	.	A	9.436	1.086860	0.20390	.	.	ENSG00000181433	ENST00000324447;ENST00000535938;ENST00000537770;ENST00000370709	T;T;T;T	0.34072	1.38;1.38;1.41;1.38	2.45	-4.9	0.03094	.	0.395989	0.26935	N	0.021753	T	0.27731	0.0682	N	0.16743	0.435	0.09310	N	1	B;D	0.64830	0.095;0.994	B;P	0.60173	0.124;0.87	T	0.34304	-0.9834	10	0.32370	T	0.25	.	6.0703	0.19885	0.6642:0.2183:0.1175:0.0	.	414;790	F5H2Z8;Q9NXZ1	.;SAGE1_HUMAN	T	790;790;414;790	ENSP00000323191:N790T;ENSP00000445959:N790T;ENSP00000438276:N414T;ENSP00000359743:N790T	ENSP00000323191:N790T	N	+	2	0	SAGE1	134821626	0.000000	0.05858	0.000000	0.03702	0.171000	0.22731	-1.511000	0.02260	-1.840000	0.01184	0.150000	0.16122	AAC	.	.		0.428	SAGE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058448.1	NM_018666		C	134993960	A	C	134993960	3	2	344	1	0	0	0	0	1	0	0	0	13824	43	2	5	2435	5	SAGE1	23	134993960	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1293630	134993960	20276600	1409	48772										
MAGEC2	51438	hgsc.bcm.edu	37	chrX	141291576	141291576	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gagggcacctcctcctcctcAggaccaccaagaatcagaga	9	15	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chrX:141291576A>T	ENST00000247452.3	-	3	545	c.198T>A	c.(196-198)ccT>ccA	p.P66P		NM_016249.3	NP_057333.1	Q9UBF1	MAGC2_HUMAN	melanoma antigen family C, 2	66					cellular protein catabolic process (GO:0044257)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin protein ligase binding (GO:0031625)			NS(2)|breast(3)|endometrium(3)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)	47	Acute lymphoblastic leukemia(192;6.56e-05)					CCTCCTCCTCAGGACCACCAA	0.532										HNSCC(46;0.14)																											p.P66P		Atlas-SNP	.											.	MAGEC2	102	.	0			c.T198A						.						73	71	71					X																	141291576		2203	4300	6503	SO:0001819	synonymous_variant	51438	exon3			CTCCTCAGGACCA	AF116195	CCDS14678.1	Xq27	2009-03-25	2004-06-08	2004-06-09	ENSG00000046774	ENSG00000046774			13574	protein-coding gene	gene with protein product	"cancer/testis antigen 10"	300468	"melanoma antigen, family E, 1, cancer/testis specific"	MAGEE1		10699956	Standard	NM_016249		Approved	CT10, MAGE-C2	uc004fbu.2	Q9UBF1	OTTHUMG00000022574	ENST00000247452.3:c.198T>A	chrX.hg19:g.141291576A>T		44.0	0.0		37.0	34.0	NM_016249	Q5JZ00|Q96D45|Q9P1M6|Q9P1M7	Silent	SNP	ENST00000247452.3	hg19	CCDS14678.1																																																																																			.	.		0.532	MAGEC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058611.1	NM_016249		T	141291576	A	T	141291576	2	4	344	1	0	0	0	0	0	0	0	1	9190	175	7	4		4	MAGEC2	23	141291576	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	6297616	141291576	13978984	1410	48773										
SLITRK2	84631	hgsc.bcm.edu	37	chrX	144904336	144904336	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	ttgagggaggacaccttcctAggcctggagagcctggagta	15	9	0	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chrX:144904336A>T	ENST00000370490.1	+	1	4648	c.393A>T	c.(391-393)ctA>ctT	p.L131L	SLITRK2_ENST00000428560.2_Silent_p.L131L|SLITRK2_ENST00000434188.2_Silent_p.L131L|SLITRK2_ENST00000413937.2_Silent_p.L131L|SLITRK2_ENST00000447897.2_Silent_p.L131L			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	131					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					ACACCTTCCTAGGCCTGGAGA	0.502																																					p.L131L		Atlas-SNP	.											.	SLITRK2	221	.	0			c.A393T						.						77	61	67					X																	144904336		2203	4300	6503	SO:0001819	synonymous_variant	84631	exon5			CTTCCTAGGCCTG	Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"slit-like 1 (Drosophila)"	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.393A>T	chrX.hg19:g.144904336A>T		102.0	0.0		58.0	52.0	NM_001144005	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Silent	SNP	ENST00000370490.1	hg19	CCDS14680.1																																																																																			.	.		0.502	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539		T	144904336	A	T	144904336	2	4	344	1	0	0	0	0	0	0	0	1	14758	407	15	4		4	SLITRK2	23	144904336	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3612760	144904336	10366224	1411	48774										
AFF2	2334	hgsc.bcm.edu	37	chrX	147967466	147967466	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	cagtgatgaagatgaccttgAgcctgtgaagaccttgacca	11	9	0	8			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chrX:147967466A>T	ENST00000370460.2	+	8	1789	c.1310A>T	c.(1309-1311)gAg>gTg	p.E437V	AFF2_ENST00000286437.5_Missense_Mutation_p.E78V|AFF2_ENST00000342251.3_Missense_Mutation_p.E404V|AFF2_ENST00000370457.5_Missense_Mutation_p.E404V|AFF2_ENST00000370458.1_Missense_Mutation_p.E398V	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	437					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)			breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					GATGACCTTGAGCCTGTGAAG	0.473																																					p.E437V		Atlas-SNP	.											.	AFF2	679	.	0			c.A1310T						.						327	275	293					X																	147967466		2203	4300	6503	SO:0001583	missense	2334	exon8			ACCTTGAGCCTGT	U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"fragile X mental retardation 2"	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.1310A>T	chrX.hg19:g.147967466A>T	ENSP00000359489:p.Glu437Val	55.0	0.0		48.0	43.0	NM_002025	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Missense_Mutation	SNP	ENST00000370460.2	hg19	CCDS14684.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.253834	0.80135	.	.	ENSG00000155966	ENST00000370460;ENST00000370457;ENST00000342251;ENST00000370458;ENST00000286437	T;T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23;-0.23	5.45	5.45	0.79879	.	0.060479	0.64402	D	0.000007	T	0.77246	0.4102	L	0.50333	1.59	0.48632	D	0.999686	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.87578	0.974;0.955;0.955;0.955;0.955;0.974;0.998	T	0.77710	-0.2486	10	0.48119	T	0.1	.	14.5211	0.67851	1.0:0.0:0.0:0.0	.	78;402;404;398;427;437;398	B4DXD5;P51816-6;P51816-3;P51816-2;P51816-5;P51816;P51816-4	.;.;.;.;.;AFF2_HUMAN;.	V	437;404;404;398;78	ENSP00000359489:E437V;ENSP00000359486:E404V;ENSP00000345459:E404V;ENSP00000359487:E398V;ENSP00000286437:E78V	ENSP00000286437:E78V	E	+	2	0	AFF2	147775159	1.000000	0.71417	0.995000	0.50966	0.995000	0.86356	4.973000	0.63763	1.808000	0.52836	0.481000	0.45027	GAG	.	.		0.473	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025		T	147967466	A	T	147967466	3	4	344	1	0	0	0	0	1	0	0	0	357	304	11	4	1395	4	AFF2	23	147967466	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	3063130	147967466	7303094	1412	48775										
MTMR1	8776	hgsc.bcm.edu	37	chrX	149867740	149867740	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	tctagtcagatttcaggttcAgtgacatcagaaaatgtgtc	9	7	5	3			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chrX:149867740A>G	ENST00000370390.3	+	2	376	c.219A>G	c.(217-219)tcA>tcG	p.S73S	MTMR1_ENST00000544228.1_Silent_p.S73S|MTMR1_ENST00000451863.2_Silent_p.S73S|MTMR1_ENST00000541925.1_5'UTR|MTMR1_ENST00000445323.2_Silent_p.S73S|MTMR1_ENST00000542156.1_Silent_p.S73S	NM_003828.2	NP_003819.1	Q13613	MTMR1_HUMAN	myotubularin related protein 1	73					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(5)|ovary(2)|prostate(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					TTTCAGGTTCAGTGACATCAG	0.353																																					p.S73S		Atlas-SNP	.											.	MTMR1	82	.	0			c.A219G						.						143	134	137					X																	149867740		2203	4300	6503	SO:0001819	synonymous_variant	8776	exon2			AGGTTCAGTGACA	U58032	CCDS14695.1	Xq28	2011-06-09			ENSG00000063601	ENSG00000063601		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7449	protein-coding gene	gene with protein product		300171				9828128	Standard	XM_005274765		Approved		uc004fei.3	Q13613	OTTHUMG00000024159	ENST00000370390.3:c.219A>G	chrX.hg19:g.149867740A>G		45.0	0.0		32.0	30.0	NM_003828	A0A024RC07|Q9UBX6|Q9UEM0|Q9UQD5	Silent	SNP	ENST00000370390.3	hg19	CCDS14695.1																																																																																			.	.		0.353	MTMR1-013	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060863.2	NM_003828, NM_176789		G	149867740	A	G	149867740	2	3	344	1	0	0	0	0	0	0	0	1	9947	175	7	2		2	MTMR1	23	149867740	Silent	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	1900274	149867740	5402820	1413	48776										
PDZD4	57595	hgsc.bcm.edu	37	chrX	153073936	153073936	+	Frame_Shift_Del	DEL	C	C	-													0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	caggtcgtgacaggagctgtCcccccggaggcgggggctgc							TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chrX:153073936delC	ENST00000164640.4	-	2	366	c.175delG	c.(175-177)gacfs	p.D59fs	PDZD4_ENST00000544474.1_Intron|PDZD4_ENST00000475140.1_5'UTR|PDZD4_ENST00000393758.2_5'UTR	NM_032512.2	NP_115901.2	Q76G19	PDZD4_HUMAN	PDZ domain containing 4	59						cytoplasm (GO:0005737)				breast(3)|cervix(1)|endometrium(5)|lung(13)|skin(1)	23	all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CAGGAGCTGTCCCCCCGGAGG	0.657																																					p.D59fs		Atlas-Indel,Pindel	.											.	PDZD4	67	.	0			c.176delA						.						44	34	38					X																	153073936		2202	4296	6498	SO:0001589	frameshift_variant	57595	exon2			.	AK091444	CCDS14732.1	Xq28	2008-02-05		2006-01-24	ENSG00000067840	ENSG00000067840			21167	protein-coding gene	gene with protein product		300634		PDZK4		10819331, 15077175	Standard	NM_032512		Approved	KIAA1444, LU1, FLJ34125, PDZRN4L	uc004fiz.1	Q76G19	OTTHUMG00000024209	ENST00000164640.4:c.175delG	chrX.hg19:g.153073936delC	ENSP00000164640:p.Asp59fs	99.0	0.0		46.0	40.0	NM_032512	B3KXB1|B7ZKY3|Q8NB75|Q9BUH9|Q9P284	Frame_Shift_Del	DEL	ENST00000164640.4	hg19	CCDS14732.1																																																																																			.	.		0.657	PDZD4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061013.3	NM_032512		-	153073936	C	-	153073936	7	5	344	1	0	1	0	1	0	0	0	0	11712	855	30	0	2162	0	PDZD4	23	153073936	Frame_Shift_Del	DEL	C	TCGA-UB-A7MB-01A-11D-A33Q-10	3206196	153073936	2196624	1414	48777										
DKC1	1736	hgsc.bcm.edu	37	chrX	153996705	153996705	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0212014134275618	30	1	1.355246640941	1.87347931873479	1.09114729552686	0.828228411406117	1	0	gttctggagtcatgagtgaaAaggtatgtgttacggggcta	15	4	2	2			TCGA-UB-A7MB-01A-11D-A33Q-10	TCGA-UB-A7MB-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7af114d-6f4d-4bf8-978c-4eebf696b12e	2cff442a-ea76-4fbd-9c30-57cc414c49bd	g.chrX:153996705A>G	ENST00000369550.5	+	8	979	c.769A>G	c.(769-771)Aag>Gag	p.K257E	SNORA36A_ENST00000384221.1_RNA	NM_001142463.1|NM_001363.3	NP_001135935.1|NP_001354.1	O60832	DKC1_HUMAN	dyskeratosis congenita 1, dyskerin	257					cell proliferation (GO:0008283)|pseudouridine synthesis (GO:0001522)|RNA processing (GO:0006396)|rRNA processing (GO:0006364)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)|telomerase activity (GO:0003720)			breast(2)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|prostate(1)	15	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					CATGAGTGAAAAGGTATGTGT	0.483									Congenital Dyskeratosis																												p.K257E		Atlas-SNP	.											.	DKC1	41	.	0			c.A769G						.						255	216	229					X																	153996705		2203	4300	6503	SO:0001583	missense	1736	exon8	Familial Cancer Database	Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita	AGTGAAAAGGTAT	AJ224481	CCDS14761.1, CCDS76062.1	Xq28	2014-09-17			ENSG00000130826	ENSG00000130826			2890	protein-coding gene	gene with protein product		300126		DKC		9590285, 9888995	Standard	NM_001142463		Approved	XAP101, dyskerin, NAP57, NOLA4	uc004fmm.3	O60832	OTTHUMG00000024242	ENST00000369550.5:c.769A>G	chrX.hg19:g.153996705A>G	ENSP00000358563:p.Lys257Glu	40.0	0.0		30.0	27.0	NM_001363	F5BSB3|O43845|Q96G67|Q9Y505	Missense_Mutation	SNP	ENST00000369550.5	hg19	CCDS14761.1	.	.	.	.	.	.	.	.	.	.	A	17.75	3.466126	0.63625	.	.	ENSG00000130826	ENST00000369550	D	0.87571	-2.27	5.88	5.88	0.94601	Pseudouridine synthase, catalytic domain (1);	0.044317	0.85682	D	0.000000	T	0.79667	0.4485	N	0.20881	0.62	0.54753	D	0.99998	B;B	0.11235	0.004;0.004	B;B	0.09377	0.002;0.004	T	0.74160	-0.3755	10	0.35671	T	0.21	-26.7131	13.9652	0.64205	1.0:0.0:0.0:0.0	.	257;257	A8MUT5;O60832	.;DKC1_HUMAN	E	257	ENSP00000358563:K257E	ENSP00000358563:K257E	K	+	1	0	DKC1	153649899	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	6.947000	0.75959	1.979000	0.57680	0.486000	0.48141	AAG	.	.		0.483	DKC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061180.5	NM_001363		G	153996705	A	G	153996705	3	3	344	1	0	0	0	0	1	0	0	0	4544	15	1	2	799	2	DKC1	23	153996705	Missense_Mutation	SNP	A	TCGA-UB-A7MB-01A-11D-A33Q-10	922769	153996705	1273855	1415	48778										
ZBTB8OS	339487	hgsc.bcm.edu	37	chr1	33087489	33087489	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	gtcaatgatcacaaaaacttCcgggttctcttcattataga	6	9	4	2			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr1:33087489C>A	ENST00000468695.1	-	7	532	c.514G>T	c.(514-516)Gaa>Taa	p.E172*	ZBTB8OS_ENST00000341885.5_Intron|ZBTB8OS_ENST00000373501.2_3'UTR|ZBTB8OS_ENST00000492007.1_5'UTR	NM_178547.2	NP_848642.1	Q8IWT0	ARCH_HUMAN	zinc finger and BTB domain containing 8 opposite strand	160					tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	extracellular vesicular exosome (GO:0070062)|tRNA-splicing ligase complex (GO:0072669)	metal ion binding (GO:0046872)			endometrium(1)|lung(4)|upper_aerodigestive_tract(1)	6		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				ACAAAAACTTCCGGGTTCTCT	0.328																																					p.E172X		Atlas-SNP	.											.	ZBTB8OS	9	.	0			c.G514T						.						100	102	101					1																	33087489		2203	4299	6502	SO:0001587	stop_gained	339487	exon7			AAACTTCCGGGTT	AY151084	CCDS365.1	1p35.1	2010-09-30			ENSG00000176261	ENSG00000176261			24094	protein-coding gene	gene with protein product	"archease"	615891				12477932	Standard	NM_178547		Approved	ARCH	uc001bvp.3	Q8IWT0	OTTHUMG00000007856	ENST00000468695.1:c.514G>T	chr1.hg19:g.33087489C>A	ENSP00000417677:p.Glu172*	74.0	0.0		47.0	24.0	NM_178547	Q5TGK5|Q6PDA1|Q8IWS9|Q8NEV6|Q8NEV7	Nonsense_Mutation	SNP	ENST00000468695.1	hg19	CCDS365.1	.	.	.	.	.	.	.	.	.	.	C	19.59	3.856230	0.71834	.	.	ENSG00000176261	ENST00000468695	.	.	.	5.38	5.38	0.77491	.	0.141058	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.22109	T	0.4	-13.4102	18.5807	0.91170	0.0:1.0:0.0:0.0	.	.	.	.	X	172	.	ENSP00000417677:E172X	E	-	1	0	ZBTB8OS	32860076	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.493000	0.66899	2.906000	0.99361	0.655000	0.94253	GAA	.	.		0.328	ZBTB8OS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021669.3	NM_178547		A	33087489	C	A	33087489	4	1	345	1	0	0	0	0	0	1	0	0	17572	864	30	3	29	3	ZBTB8OS	1	33087489	Nonsense_Mutation	SNP	C	TCGA-UB-A7MC-01A-11D-A33Q-10		33087489	216163132	1	48779										
SERBP1	26135	hgsc.bcm.edu	37	chr1	67895954	67895954	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	aatcggttggtgaccacgcaGccgaagccttcctgtaagtg	12	11	0	1			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr1:67895954G>T	ENST00000370995.2	-	1	115	c.30C>A	c.(28-30)ggC>ggA	p.G10G	SERBP1_ENST00000361219.6_Silent_p.G10G|SERBP1_ENST00000370990.5_Silent_p.G10G|SERBP1_ENST00000370994.4_Silent_p.G10G			Q8NC51	PAIRB_HUMAN	SERPINE1 mRNA binding protein 1	10					regulation of apoptotic process (GO:0042981)|regulation of mRNA stability (GO:0043488)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(2)	13						TGACCACGCAGCCGAAGCCTT	0.617																																					p.G10G		Atlas-SNP	.											.	SERBP1	31	.	0			c.C30A						.						53	59	57					1																	67895954		2195	4269	6464	SO:0001819	synonymous_variant	26135	exon1			CACGCAGCCGAAG	AF151813	CCDS639.1, CCDS30746.1, CCDS30747.1, CCDS30748.1	1p31	2009-12-17			ENSG00000142864	ENSG00000142864			17860	protein-coding gene	gene with protein product		607378				11001948, 10810093, 18440126, 17698176	Standard	NM_001018067		Approved	PAI-RBP1, DKFZP564M2423, CGI-55, HABP4L, PAIRBP1, CHD3IP	uc001ddv.3	Q8NC51	OTTHUMG00000009372	ENST00000370995.2:c.30C>A	chr1.hg19:g.67895954G>T		186.0	0.0		134.0	50.0	NM_001018067	Q5VU19|Q5VU20|Q5VU22|Q8WUH0|Q96SE2|Q9BTY3|Q9BUM4|Q9Y367|Q9Y4S3	Silent	SNP	ENST00000370995.2	hg19	CCDS30746.1																																																																																			.	.		0.617	SERBP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025984.2	NM_001018067		T	67895954	G	T	67895954	2	4	345	1	0	0	0	0	0	0	0	1	14090	958	34	3		3	SERBP1	1	67895954	Silent	SNP	G	TCGA-UB-A7MC-01A-11D-A33Q-10	34808465	67895954	181354667	2	48780										
CELSR2	1952	hgsc.bcm.edu	37	chr1	109794350	109794350	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	ccttgctggggtgggacatgActtccccttcaccatcaaca	9	14	2	1			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr1:109794350A>G	ENST00000271332.3	+	1	1710	c.1649A>G	c.(1648-1650)gAc>gGc	p.D550G		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	550	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		GTGGGACATGACTTCCCCTTC	0.557																																					p.D550G	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-SNP	.											.	CELSR2	228	.	0			c.A1649G						.						118	99	105					1																	109794350		2203	4300	6503	SO:0001583	missense	1952	exon1			GACATGACTTCCC	D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3231	protein-coding gene	gene with protein product		604265	"cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.1649A>G	chr1.hg19:g.109794350A>G	ENSP00000271332:p.Asp550Gly	147.0	0.0		68.0	26.0	NM_001408	Q5T2Y7|Q92566	Missense_Mutation	SNP	ENST00000271332.3	hg19	CCDS796.1	.	.	.	.	.	.	.	.	.	.	N	11.05	1.524698	0.27299	.	.	ENSG00000143126	ENST00000271332	T	0.50548	0.74	4.78	3.66	0.41972	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.14442	0.0349	N	0.17564	0.495	0.37407	D	0.913078	B	0.09022	0.002	B	0.17433	0.018	T	0.04386	-1.0955	9	0.32370	T	0.25	.	8.91	0.35548	0.8442:0.0:0.1558:0.0	.	550	Q9HCU4	CELR2_HUMAN	G	550	ENSP00000271332:D550G	ENSP00000271332:D550G	D	+	2	0	CELSR2	109595873	0.849000	0.29639	0.992000	0.48379	0.877000	0.50540	2.250000	0.43178	0.900000	0.36469	0.529000	0.55759	GAC	.	.		0.557	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408		G	109794350	A	G	109794350	3	3	345	1	0	0	0	0	1	0	0	0	3224	275	10	2	1651	2	CELSR2	1	109794350	Missense_Mutation	SNP	A	TCGA-UB-A7MC-01A-11D-A33Q-10	41898396	109794350	139456271	3	48781										
LCE1F	353137	hgsc.bcm.edu	37	chr1	152748923	152748923	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	agtgccctcccaagtgccccAcaccgaagtgccccccaaag	8	19	0	0	rs554010131	byFrequency	TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr1:152748923A>G	ENST00000334371.2	+	1	76	c.76A>G	c.(76-78)Aca>Gca	p.T26A		NM_178354.2	NP_848131.1	Q5T754	LCE1F_HUMAN	late cornified envelope 1F	26	Pro-rich.				keratinization (GO:0031424)					kidney(1)|large_intestine(2)|lung(7)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			caagtgccccacaccgaagtg	0.657																																					p.T26A		Atlas-SNP	.											.	LCE1F	42	.	0			c.A76G						.						57	60	59					1																	152748923		2203	4300	6503	SO:0001583	missense	353137	exon1			TGCCCCACACCGA		CCDS1023.1	1q21.3	2008-02-05			ENSG00000240386	ENSG00000240386		"Late cornified envelopes"	29467	protein-coding gene	gene with protein product		612608				11698679	Standard	NM_178354		Approved	LEP6	uc010pdv.2	Q5T754	OTTHUMG00000012403	ENST00000334371.2:c.76A>G	chr1.hg19:g.152748923A>G	ENSP00000334187:p.Thr26Ala	481.0	0.0		695.0	114.0	NM_178354		Missense_Mutation	SNP	ENST00000334371.2	hg19	CCDS1023.1	.	.	.	.	.	.	.	.	.	.	A	0.058	-1.230932	0.01518	.	.	ENSG00000240386	ENST00000334371	T	0.03553	3.89	3.56	-7.12	0.01537	.	.	.	.	.	T	0.00906	0.0030	N	0.25647	0.755	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.43032	-0.9416	9	0.87932	D	0	.	12.1466	0.54026	0.571:0.0:0.429:0.0	.	26	Q5T754	LCE1F_HUMAN	A	26	ENSP00000334187:T26A	ENSP00000334187:T26A	T	+	1	0	LCE1F	151015547	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.225000	0.01212	-2.384000	0.00591	-1.259000	0.01468	ACA	.	.		0.657	LCE1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034523.2	NM_178354		G	152748923	A	G	152748923	3	3	345	1	0	0	0	0	1	0	0	0	8673	159	6	2	78	2	LCE1F	1	152748923	Missense_Mutation	SNP	A	TCGA-UB-A7MC-01A-11D-A33Q-10	42954573	152748923	96501698	4	48782										
NTRK1	4914	hgsc.bcm.edu	37	chr1	156849827	156849827	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	tgctgcccattcgctggatgCcgcccgagagcatcctgtac	11	15	0	1			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr1:156849827C>T	ENST00000524377.1	+	16	2124	c.2083C>T	c.(2083-2085)Ccg>Tcg	p.P695S	NTRK1_ENST00000392302.2_Missense_Mutation_p.P659S|NTRK1_ENST00000358660.3_Missense_Mutation_p.P692S|NTRK1_ENST00000531606.1_3'UTR|NTRK1_ENST00000368196.3_Missense_Mutation_p.P689S	NM_002529.3	NP_002520.2	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	695	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		P -> L (in CIPA). {ECO:0000269|PubMed:10861667}.		activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|axon guidance (GO:0007411)|axonogenesis involved in innervation (GO:0060385)|B cell differentiation (GO:0030183)|cellular response to nerve growth factor stimulus (GO:1990090)|cellular response to nicotine (GO:0071316)|circadian rhythm (GO:0007623)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|developmental programmed cell death (GO:0010623)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory nerve development (GO:0021553)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of angiogenesis (GO:0045766)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|response to activity (GO:0014823)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to ethanol (GO:0045471)|response to hydrostatic pressure (GO:0051599)|response to nutrient levels (GO:0031667)|response to radiation (GO:0009314)|Sertoli cell development (GO:0060009)|small GTPase mediated signal transduction (GO:0007264)|sympathetic nervous system development (GO:0048485)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome (GO:0005769)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.P695S(3)|p.P659S(2)		breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(35)|ovary(8)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	74	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Amitriptyline(DB00321)|Imatinib(DB00619)|Regorafenib(DB08896)	TCGCTGGATGCCGCCCGAGAG	0.647			T	"TPM3, TPR, TFG"	papillary thyroid					TSP Lung(10;0.080)																											p.P695S		Atlas-SNP	.		Dom	yes		1	1q21-q22	4914	"neurotrophic tyrosine kinase, receptor, type 1"		E	NTRK1_ENST00000392302,NS,carcinoma,0,4	NTRK1	287	.	5	Substitution - Missense(5)	prostate(3)|kidney(2)	c.C2083T						.						62	60	61					1																	156849827		2203	4300	6503	SO:0001583	missense	4914	exon16			TGGATGCCGCCCG	Y09028	CCDS1161.1, CCDS30890.1, CCDS30891.1	1q21-q22	2014-09-17			ENSG00000198400	ENSG00000198400	2.7.10.1	"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	8031	protein-coding gene	gene with protein product	"high affinity nerve growth factor receptor"	191315				2869410	Standard	NM_001007792		Approved	TRK, TRKA, MTC	uc001fqh.1	P04629	OTTHUMG00000041304	ENST00000524377.1:c.2083C>T	chr1.hg19:g.156849827C>T	ENSP00000431418:p.Pro695Ser	124.0	0.0		185.0	12.0	NM_002529	B2R6T5|B7ZM34|P08119|Q15655|Q15656|Q5D056|Q5VZS2|Q7Z5C3|Q9UIU7	Missense_Mutation	SNP	ENST00000524377.1	hg19	CCDS1161.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.817037	0.90790	.	.	ENSG00000198400	ENST00000392302;ENST00000368196;ENST00000524377;ENST00000358660	D;D;D;D	0.88046	-2.33;-2.33;-2.33;-2.33	4.23	4.23	0.50019	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.56097	D	0.000034	T	0.82226	0.4991	N	0.04275	-0.24	0.80722	D	1	D;D;D;D	0.89917	0.995;0.972;0.998;1.0	D;B;P;D	0.78314	0.946;0.29;0.852;0.991	D	0.88267	0.2927	10	0.87932	D	0	.	15.7052	0.77573	0.0:1.0:0.0:0.0	.	692;689;695;659	A8K3Z4;P04629-2;P04629;A6NF12	.;.;NTRK1_HUMAN;.	S	659;689;695;692	ENSP00000376120:P659S;ENSP00000357179:P689S;ENSP00000431418:P695S;ENSP00000351486:P692S	ENSP00000351486:P692S	P	+	1	0	NTRK1	155116451	1.000000	0.71417	0.997000	0.53966	0.961000	0.63080	7.388000	0.79795	2.362000	0.80069	0.561000	0.74099	CCG	.	.		0.647	NTRK1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392279.1	NM_002529		T	156849827	C	T	156849827	3	4	345	1	0	0	0	0	1	0	0	0	10715	739	26	3	2275	3	NTRK1	1	156849827	Missense_Mutation	SNP	C	TCGA-UB-A7MC-01A-11D-A33Q-10	4100904	156849827	92400794	5	48783										
SLC30A1	7779	hgsc.bcm.edu	37	chr1	211749002	211749002	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	tacactagcaaattcaggctGaatggtagtagcgtgaattc	10	7	1	2			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr1:211749002G>T	ENST00000367001.4	-	2	1381	c.1252C>A	c.(1252-1254)Cag>Aag	p.Q418K		NM_021194.2	NP_067017.2	Q9Y6M5	ZNT1_HUMAN	solute carrier family 30 (zinc transporter), member 1	418					cadmium ion transmembrane transport (GO:0070574)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|cellular zinc ion homeostasis (GO:0006882)|detoxification of cadmium ion (GO:0071585)|in utero embryonic development (GO:0001701)|negative regulation of calcium ion import (GO:0090281)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of zinc ion transmembrane import (GO:0071584)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)	calcium channel inhibitor activity (GO:0019855)|zinc ion transmembrane transporter activity (GO:0005385)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(1)|ovary(3)|prostate(1)	11				OV - Ovarian serous cystadenocarcinoma(81;0.00535)|GBM - Glioblastoma multiforme(131;0.051)|all cancers(67;0.0604)|Epithelial(68;0.0978)		AATTCAGGCTGAATGGTAGTA	0.428																																					p.Q418K		Atlas-SNP	.											.	SLC30A1	27	.	0			c.C1252A						.						112	103	106					1																	211749002		2203	4299	6502	SO:0001583	missense	7779	exon2			CAGGCTGAATGGT	AF323590	CCDS1499.1	1q32.3	2013-05-22			ENSG00000170385	ENSG00000170385		"Solute carriers"	11012	protein-coding gene	gene with protein product		609521		ZNT1			Standard	NM_021194		Approved	ZRC1	uc001hio.1	Q9Y6M5	OTTHUMG00000036995	ENST00000367001.4:c.1252C>A	chr1.hg19:g.211749002G>T	ENSP00000355968:p.Gln418Lys	107.0	1.0		125.0	120.0	NM_021194	Q0VAK9|Q9BZF6	Missense_Mutation	SNP	ENST00000367001.4	hg19	CCDS1499.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.541156	0.85917	.	.	ENSG00000170385	ENST00000367001	T	0.55413	0.52	5.69	5.69	0.88448	.	0.124150	0.56097	D	0.000022	D	0.84234	0.5427	H	0.98333	4.205	0.80722	D	1	D	0.56521	0.976	D	0.69824	0.966	D	0.90002	0.4115	10	0.87932	D	0	-12.0654	19.8182	0.96579	0.0:0.0:1.0:0.0	.	418	Q9Y6M5	ZNT1_HUMAN	K	418	ENSP00000355968:Q418K	ENSP00000355968:Q418K	Q	-	1	0	SLC30A1	209815625	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.502000	0.97981	2.687000	0.91594	0.563000	0.77884	CAG	.	.		0.428	SLC30A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104738.2			T	211749002	G	T	211749002	3	4	345	1	0	0	0	0	1	0	0	0	14568	1299	45	3	275	3	SLC30A1	1	211749002	Missense_Mutation	SNP	G	TCGA-UB-A7MC-01A-11D-A33Q-10	54899175	211749002	37501619	6	48784										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228494331	228494331	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	ggccaccagtgccaccctcaCtgtcacaggtgggctcccag	11	17	2	0			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr1:228494331C>T	ENST00000422127.1	+	44	11962	c.11918C>T	c.(11917-11919)aCt>aTt	p.T3973I	OBSCN_ENST00000366707.4_Missense_Mutation_p.T1607I|OBSCN_ENST00000570156.2_Missense_Mutation_p.T4930I|OBSCN_ENST00000284548.11_Missense_Mutation_p.T3973I|OBSCN_ENST00000366709.4_Missense_Mutation_p.T1092I	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3973	Ig-like 40.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GCCACCCTCACTGTCACAGGT	0.632																																					p.T4930I		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C14789T						.						19	22	21					1																	228494331		2104	4213	6317	SO:0001583	missense	84033	exon55			CCCTCACTGTCAC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.11918C>T	chr1.hg19:g.228494331C>T	ENSP00000409493:p.Thr3973Ile	91.0	0.0		91.0	50.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	C	13.04	2.119446	0.37436	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.68624	-0.34;-0.34;-0.34;-0.34	5.22	3.33	0.38152	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.711645	0.13144	N	0.410406	T	0.75671	0.3881	L	0.60904	1.88	0.09310	N	1	D;P	0.89917	1.0;0.798	D;P	0.91635	0.999;0.454	T	0.62464	-0.6849	10	0.22109	T	0.4	.	10.0964	0.42478	0.0:0.771:0.0:0.229	.	3973;3973	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	I	3973;3973;1607;1092	ENSP00000284548:T3973I;ENSP00000409493:T3973I;ENSP00000355668:T1607I;ENSP00000355670:T1092I	ENSP00000284548:T3973I	T	+	2	0	OBSCN	226560954	0.000000	0.05858	0.017000	0.16124	0.293000	0.27360	-0.227000	0.09126	0.582000	0.29556	0.407000	0.27541	ACT	.	.		0.632	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228494331	C	T	228494331	3	4	345	1	0	0	0	0	1	0	0	0	10821	565	20	3	12088	3	OBSCN	1	228494331	Missense_Mutation	SNP	C	TCGA-UB-A7MC-01A-11D-A33Q-10	16745329	228494331	20756290	7	48785										
OSR1	130497	hgsc.bcm.edu	37	chr2	19553505	19553505	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	tcactgcctgaaggaaggagTagttggtgagctgcagggaa	16	6	1	2			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr2:19553505T>C	ENST00000272223.2	-	2	406	c.62A>G	c.(61-63)tAc>tGc	p.Y21C	OSR1_ENST00000536433.1_Missense_Mutation_p.Y21C	NM_145260.2	NP_660303.1	Q8TAX0	OSR1_HUMAN	odd-skipped related transciption factor 1	21					cell differentiation (GO:0030154)|cell proliferation involved in kidney development (GO:0072111)|cellular response to retinoic acid (GO:0071300)|chondrocyte differentiation (GO:0002062)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal joint development (GO:0072498)|embryonic skeletal joint morphogenesis (GO:0060272)|embryonic skeletal limb joint morphogenesis (GO:0036023)|gonad development (GO:0008406)|heart development (GO:0007507)|intermediate mesoderm development (GO:0048389)|mesangial cell development (GO:0072143)|mesonephric duct morphogenesis (GO:0072180)|mesonephros development (GO:0001823)|metanephric cap mesenchymal cell proliferation involved in metanephros development (GO:0090094)|metanephric epithelium development (GO:0072207)|metanephric glomerulus vasculature development (GO:0072239)|metanephric interstitial fibroblast development (GO:0072259)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchyme development (GO:0072075)|metanephric mesenchyme morphogenesis (GO:0072133)|metanephric nephron tubule development (GO:0072234)|metanephric smooth muscle tissue development (GO:0072208)|middle ear morphogenesis (GO:0042474)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of nephron tubule epithelial cell differentiation (GO:0072183)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis (GO:0042476)|palate development (GO:0060021)|pattern specification involved in metanephros development (GO:0072268)|positive regulation of bone mineralization (GO:0030501)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gastrulation (GO:2000543)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posterior mesonephric tubule development (GO:0072166)|pronephros development (GO:0048793)|renal vesicle progenitor cell differentiation (GO:0072184)|specification of anterior mesonephric tubule identity (GO:0072168)|specification of posterior mesonephric tubule identity (GO:0072169)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351)|ureter urothelium development (GO:0072190)|ureteric bud development (GO:0001657)|urogenital system development (GO:0001655)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(1)|large_intestine(2)|lung(4)|ovary(1)	8	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)	Acute lymphoblastic leukemia(84;0.221)				AAGGAAGGAGTAGTTGGTGAG	0.582																																					p.Y21C		Atlas-SNP	.											.	OSR1	29	.	0			c.A62G						.						56	53	54					2																	19553505		2203	4300	6503	SO:0001583	missense	130497	exon2			AAGGAGTAGTTGG	BC025712	CCDS1694.1	2p24.1	2013-10-17	2013-10-17	2004-11-26	ENSG00000143867	ENSG00000143867		"Zinc fingers, C2H2-type"	8111	protein-coding gene	gene with protein product		608891	"odd-skipped (Drosophila) homolog", "odd-skipped related 1 (Drosophila)"	ODD		2120051, 12119563	Standard	XM_006711942		Approved		uc002rdc.3	Q8TAX0	OTTHUMG00000088793	ENST00000272223.2:c.62A>G	chr2.hg19:g.19553505T>C	ENSP00000272223:p.Tyr21Cys	138.0	0.0		126.0	16.0	NM_145260	B3KV97|D6W521	Missense_Mutation	SNP	ENST00000272223.2	hg19	CCDS1694.1	.	.	.	.	.	.	.	.	.	.	T	15.08	2.727856	0.48833	.	.	ENSG00000143867	ENST00000272223;ENST00000536433	T;T	0.08807	3.05;3.05	5.5	5.5	0.81552	.	0.054794	0.85682	D	0.000000	T	0.11196	0.0273	L	0.59436	1.845	0.50171	D	0.999853	B	0.21520	0.057	B	0.15870	0.014	T	0.07083	-1.0791	9	.	.	.	-30.654	15.6005	0.76620	0.0:0.0:0.0:1.0	.	21	Q8TAX0	OSR1_HUMAN	C	21	ENSP00000272223:Y21C;ENSP00000441801:Y21C	.	Y	-	2	0	OSR1	19416986	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.176000	0.58269	2.223000	0.72356	0.454000	0.30748	TAC	.	.		0.582	OSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000201432.2	NM_145260		C	19553505	T	C	19553505	3	2	345	1	0	0	0	0	1	0	0	0	11302	1638	57	2	746	2	OSR1	2	19553505	Missense_Mutation	SNP	T	TCGA-UB-A7MC-01A-11D-A33Q-10		19553505	223645868	8	48786										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168104195	168104195	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	taatctaacaactaaagaatCagacagggcagtgagagagc	10	7	2	4			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr2:168104195C>T	ENST00000409195.1	+	9	6382	c.6293C>T	c.(6292-6294)tCa>tTa	p.S2098L	XIRP2_ENST00000295237.9_Missense_Mutation_p.S2098L|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.S1876L|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409756.2_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1923					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						ACTAAAGAATCAGACAGGGCA	0.378																																					p.S2098L		Atlas-SNP	.											.	XIRP2	914	.	0			c.C6293T						.						55	51	52					2																	168104195		1921	4147	6068	SO:0001583	missense	129446	exon9			AAGAATCAGACAG	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.6293C>T	chr2.hg19:g.168104195C>T	ENSP00000386840:p.Ser2098Leu	221.0	0.0		212.0	60.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	hg19	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	C	15.45	2.837223	0.50951	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.20069	2.1;2.1;2.1	5.92	5.92	0.95590	.	0.458938	0.18502	N	0.139318	T	0.27933	0.0688	L	0.60455	1.87	0.50467	D	0.999876	P;P;P	0.45986	0.87;0.649;0.775	B;B;B	0.42282	0.36;0.295;0.382	T	0.01464	-1.1348	10	0.30078	T	0.28	-2.4455	19.1058	0.93294	0.0:1.0:0.0:0.0	.	1923;1923;1876	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	L	2098;2098;1876	ENSP00000386840:S2098L;ENSP00000295237:S2098L;ENSP00000387255:S1876L	ENSP00000295237:S2098L	S	+	2	0	XIRP2	167812441	1.000000	0.71417	0.997000	0.53966	0.259000	0.26198	4.519000	0.60517	2.822000	0.97130	0.650000	0.86243	TCA	.	.		0.378	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		T	168104195	C	T	168104195	3	4	345	1	0	0	0	0	1	0	0	0	17445	838	29	3	6323	3	XIRP2	2	168104195	Missense_Mutation	SNP	C	TCGA-UB-A7MC-01A-11D-A33Q-10	148550690	168104195	75095178	9	48787										
COL3A1	1281	hgsc.bcm.edu	37	chr2	189871670	189871670	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	gttttcatcttagggccctgCtggccctgctggtgctcccg	12	14	2	0			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr2:189871670C>A	ENST00000304636.3	+	44	3379	c.3209C>A	c.(3208-3210)gCt>gAt	p.A1070D	COL3A1_ENST00000317840.5_Intron	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	1070	Triple-helical region.			A -> P (in Ref. 15; AA sequence). {ECO:0000305}.	aging (GO:0007568)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell-matrix adhesion (GO:0007160)|cellular response to amino acid stimulus (GO:0071230)|cerebral cortex development (GO:0021987)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|digestive tract development (GO:0048565)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of immune response (GO:0050777)|negative regulation of neuron migration (GO:2001223)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|positive regulation of Rho protein signal transduction (GO:0035025)|response to cytokine (GO:0034097)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	collagen type III trimer (GO:0005586)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)	TAGGGCCCTGCTGGCCCTGCT	0.373																																					p.A1070D		Atlas-SNP	.											.	COL3A1	292	.	0			c.C3209A						.						89	94	93					2																	189871670		2203	4300	6503	SO:0001583	missense	1281	exon44			GCCCTGCTGGCCC	X15332	CCDS2297.1	2q32.2	2014-09-17	2008-06-23		ENSG00000168542	ENSG00000168542		"Collagens"	2201	protein-coding gene	gene with protein product		120180	"Ehlers-Danlos syndrome type IV, autosomal dominant"	EDS4A		2780304, 2834369	Standard	NM_000090		Approved		uc002uqj.1	P02461	OTTHUMG00000132648	ENST00000304636.3:c.3209C>A	chr2.hg19:g.189871670C>A	ENSP00000304408:p.Ala1070Asp	187.0	0.0		186.0	98.0	NM_000090	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Missense_Mutation	SNP	ENST00000304636.3	hg19	CCDS2297.1	.	.	.	.	.	.	.	.	.	.	C	14.71	2.618143	0.46736	.	.	ENSG00000168542	ENST00000304636	D	0.93426	-3.22	4.99	4.99	0.66335	.	0.475449	0.17935	N	0.157026	D	0.94374	0.8191	L	0.56199	1.76	0.80722	D	1	D	0.53462	0.96	P	0.57371	0.819	D	0.91715	0.5384	10	0.11794	T	0.64	.	18.6397	0.91390	0.0:1.0:0.0:0.0	.	1070	P02461	CO3A1_HUMAN	D	1070	ENSP00000304408:A1070D	ENSP00000304408:A1070D	A	+	2	0	COL3A1	189579915	0.344000	0.24827	1.000000	0.80357	0.260000	0.26232	1.002000	0.29796	2.476000	0.83614	0.655000	0.94253	GCT	.	.		0.373	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090		A	189871670	C	A	189871670	3	1	345	1	0	0	0	0	1	0	0	0	3690	797	28	3	3383	3	COL3A1	2	189871670	Missense_Mutation	SNP	C	TCGA-UB-A7MC-01A-11D-A33Q-10	21767475	189871670	53327703	10	48788										
XIRP1	165904	hgsc.bcm.edu	37	chr3	39226567	39226567	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	gactgtcagggctctcagggGccccttggtgggaaccttcc	14	13	2	0			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr3:39226567G>T	ENST00000340369.3	-	2	4598	c.4370C>A	c.(4369-4371)gCc>gAc	p.A1457D	XIRP1_ENST00000396251.1_3'UTR|XIRP1_ENST00000421646.1_Missense_Mutation_p.A140D	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	1457					cardiac muscle cell development (GO:0055013)|negative regulation of cell proliferation (GO:0008285)|regulation of membrane potential (GO:0042391)|sarcomere organization (GO:0045214)	fascia adherens (GO:0005916)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(14)|lung(22)|ovary(4)|pancreas(1)|prostate(2)|skin(6)	71				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		GCTCTCAGGGGCCCCTTGGTG	0.632																																					p.A1457D		Atlas-SNP	.											.	XIRP1	173	.	0			c.C4370A						.						48	59	55					3																	39226567		2199	4300	6499	SO:0001583	missense	165904	exon2			TCAGGGGCCCCTT	AW755250	CCDS2683.1, CCDS56245.1	3p21.33	2008-02-05	2007-06-27	2007-06-27	ENSG00000168334	ENSG00000168334			14301	protein-coding gene	gene with protein product		609777	"cardiomyopathy associated 1"	CMYA1		12203715, 15454575	Standard	NM_001198621		Approved	DKFZp451D042, Xin	uc003cjk.2	Q702N8	OTTHUMG00000131297	ENST00000340369.3:c.4370C>A	chr3.hg19:g.39226567G>T	ENSP00000343140:p.Ala1457Asp	83.0	0.0		54.0	23.0	NM_194293	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Missense_Mutation	SNP	ENST00000340369.3	hg19	CCDS2683.1	.	.	.	.	.	.	.	.	.	.	G	13.48	2.250691	0.39797	.	.	ENSG00000168334	ENST00000340369;ENST00000421646	T;T	0.25085	3.61;1.82	4.42	0.297	0.15762	.	2.810620	0.01497	N	0.017338	T	0.28034	0.0691	M	0.63843	1.955	0.36424	D	0.864469	B	0.12013	0.005	B	0.12156	0.007	T	0.25813	-1.0121	10	0.62326	D	0.03	.	3.9964	0.09559	0.1882:0.0:0.4896:0.3222	.	1457	Q702N8	XIRP1_HUMAN	D	1457;140	ENSP00000343140:A1457D;ENSP00000391645:A140D	ENSP00000343140:A1457D	A	-	2	0	XIRP1	39201571	0.507000	0.26146	0.000000	0.03702	0.001000	0.01503	1.886000	0.39688	-0.064000	0.13043	-0.181000	0.13052	GCC	.	.		0.632	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522		T	39226567	G	T	39226567	3	4	345	1	0	0	0	0	1	0	0	0	17444	1203	42	3	1165	3	XIRP1	3	39226567	Missense_Mutation	SNP	G	TCGA-UB-A7MC-01A-11D-A33Q-10		39226567	158795863	11	48789										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266113	41266113	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	cctggactctggaatccattCtggtgccactaccacagctc	8	15	2	0	rs121913416|rs121913403		TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr3:41266113C>G	ENST00000349496.5	+	3	390	c.110C>G	c.(109-111)tCt>tGt	p.S37C	CTNNB1_ENST00000396183.3_Missense_Mutation_p.S37C|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S37C|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S37C|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S30C	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	37			S -> A (in MDB and hepatocellular carcinoma; enhances transactivation of target genes). {ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10666372}.|S -> C (in PTR, hepatoblastoma and ovarian cancer). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10391090, ECO:0000269|PubMed:9927029}.|S -> F (in PTR). {ECO:0000269|PubMed:10192393}.|S -> Y (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|SG -> W (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S37F(172)|p.S37C(141)|p.A5_A80del(53)|p.S37Y(31)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.I35_K170del(1)|p.H24_G38del(1)|p.I35_T41del(1)|p.I35_G38del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.D32fs*9(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.GIHS34?(1)|p.S37_G38>W(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GGAATCCATTCTGGTGCCACT	0.498	S37C(JHUEM2_ENDOMETRIUM)|S37C(SNU398_LIVER)|S37F(HUTU80_SMALL_INTESTINE)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S37C	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,0,1	CTNNB1	4904	.	474	Substitution - Missense(344)|Deletion - In frame(102)|Complex - deletion inframe(18)|Unknown(7)|Deletion - Frameshift(3)	liver(145)|endometrium(64)|stomach(38)|skin(34)|ovary(33)|central_nervous_system(28)|pancreas(28)|large_intestine(22)|pituitary(22)|lung(21)|biliary_tract(15)|thyroid(4)|soft_tissue(4)|urinary_tract(4)|small_intestine(3)|oesophagus(3)|adrenal_gland(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|bone(1)|breast(1)	c.C110G						.						93	78	83					3																	41266113		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	TCCATTCTGGTGC	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.110C>G	chr3.hg19:g.41266113C>G	ENSP00000344456:p.Ser37Cys	181.0	0.0		115.0	49.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.407996	0.83340	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.51325	0.71;0.71;0.71;0.71;0.71;0.71;0.71;0.71;0.71	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.72819	0.3508	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75297	-0.3367	10	0.87932	D	0	-15.9763	19.9596	0.97236	0.0:1.0:0.0:0.0	.	37	P35222	CTNB1_HUMAN	C	30;37;37;37;37;30;37;37;37	ENSP00000400508:S30C;ENSP00000385604:S37C;ENSP00000412219:S37C;ENSP00000379486:S37C;ENSP00000344456:S37C;ENSP00000411226:S30C;ENSP00000379488:S37C;ENSP00000409302:S37C;ENSP00000401599:S37C	ENSP00000344456:S37C	S	+	2	0	CTNNB1	41241117	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.726000	0.93360	0.655000	0.94253	TCT	.	.		0.498	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266113	C	G	41266113	3	3	345	1	0	0	0	0	1	0	0	0	4018	913	32	4	116	4	CTNNB1	3	41266113	Missense_Mutation	SNP	C	TCGA-UB-A7MC-01A-11D-A33Q-10	2039546	41266113	156756317	12	48790										
COL7A1	1294	hgsc.bcm.edu	37	chr3	48624098	48624098	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	tgggaacagtggggagggccGatgactgtaagacagcaggc	18	7	0	2			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr3:48624098G>A	ENST00000328333.8	-	25	3408	c.3301C>T	c.(3301-3303)Cgg>Tgg	p.R1101W	COL7A1_ENST00000454817.1_Missense_Mutation_p.R1101W	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	1101	Nonhelical region (NC1).|VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		GGGGAGGGCCGATGACTGTAA	0.562																																					p.R1101W		Atlas-SNP	.											.	COL7A1	320	.	0			c.C3301T						.						35	27	30					3																	48624098		2203	4300	6503	SO:0001583	missense	1294	exon25			AGGGCCGATGACT	L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"Collagens", "Fibronectin type III domain containing"	2214	protein-coding gene	gene with protein product	"collagen VII, alpha-1 polypeptide", "LC collagen"	120120	"epidermolysis bullosa, dystrophic, dominant and recessive"	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.3301C>T	chr3.hg19:g.48624098G>A	ENSP00000332371:p.Arg1101Trp	140.0	0.0		90.0	4.0	NM_000094	Q14054|Q16507	Missense_Mutation	SNP	ENST00000328333.8	hg19	CCDS2773.1	.	.	.	.	.	.	.	.	.	.	G	12.09	1.832814	0.32421	.	.	ENSG00000114270	ENST00000328333;ENST00000454817	D;D	0.83914	-1.78;-1.78	4.98	4.98	0.66077	von Willebrand factor, type A (2);	0.000000	0.42294	D	0.000723	D	0.86230	0.5883	L	0.29908	0.895	0.43133	D	0.994878	D	0.89917	1.0	D	0.97110	1.0	D	0.88171	0.2864	10	0.87932	D	0	.	15.7613	0.78082	0.0:0.0:1.0:0.0	.	1101	Q02388	CO7A1_HUMAN	W	1101	ENSP00000332371:R1101W;ENSP00000412569:R1101W	ENSP00000332371:R1101W	R	-	1	2	COL7A1	48599102	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.644000	0.61397	2.463000	0.83235	0.561000	0.74099	CGG	.	.		0.562	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094		A	48624098	G	A	48624098	3	1	345	1	0	0	0	0	1	0	0	0	3706	1057	37	1	5909	1	COL7A1	3	48624098	Missense_Mutation	SNP	G	TCGA-UB-A7MC-01A-11D-A33Q-10	7357985	48624098	149398332	13	48791										
ACOX2	8309	hgsc.bcm.edu	37	chr3	58517052	58517052	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	caggaagccattgtctgtttGatcaaagtccatcttgggtc	10	9	3	1	rs75760511		TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr3:58517052G>T	ENST00000302819.5	-	7	1036	c.745C>A	c.(745-747)Caa>Aaa	p.Q249K	ACOX2_ENST00000459701.2_Missense_Mutation_p.Q249K	NM_003500.3	NP_003491.1	Q99424	ACOX2_HUMAN	acyl-CoA oxidase 2, branched chain	249					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA 24-hydroxylase activity (GO:0033791)|acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)|flavin adenine dinucleotide binding (GO:0050660)|pristanoyl-CoA oxidase activity (GO:0016402)|receptor binding (GO:0005102)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(1)|skin(3)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(55;0.000194)|Kidney(10;0.00255)|KIRC - Kidney renal clear cell carcinoma(10;0.00268)|OV - Ovarian serous cystadenocarcinoma(275;0.156)		TTGTCTGTTTGATCAAAGTCC	0.532																																					p.Q249K		Atlas-SNP	.											.	ACOX2	53	.	0			c.C745A						.						156	130	139					3																	58517052		2203	4300	6503	SO:0001583	missense	8309	exon7			CTGTTTGATCAAA	X95190	CCDS33775.1	3p14.3	2012-07-13	2010-04-30		ENSG00000168306	ENSG00000168306	1.17.99.3		120	protein-coding gene	gene with protein product	"trihydroxycoprostanoyl-CoA oxidase", "3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholestanoyl-CoA 24-hydroxylase"	601641	"acyl-Coenzyme A oxidase 2, branched chain"			8943006, 9070889	Standard	NM_003500		Approved	BRCACOX, BRCOX, THCCox	uc003dkl.3	Q99424	OTTHUMG00000159154	ENST00000302819.5:c.745C>A	chr3.hg19:g.58517052G>T	ENSP00000307697:p.Gln249Lys	99.0	0.0		65.0	26.0	NM_003500	A6NF16|B2R8U5	Missense_Mutation	SNP	ENST00000302819.5	hg19	CCDS33775.1	.	.	.	.	.	.	.	.	.	.	G	1.940	-0.443906	0.04604	.	.	ENSG00000168306	ENST00000459701;ENST00000302819	T;T	0.62788	-0.0;-0.0	5.06	-0.654	0.11443	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA oxidase/dehydrogenase, central domain (1);	1.021070	0.07774	N	0.952337	T	0.42245	0.1194	L	0.29908	0.895	0.09310	N	1	B	0.19200	0.034	B	0.20184	0.028	T	0.22173	-1.0224	10	0.10377	T	0.69	-11.0312	3.9363	0.09307	0.1326:0.0978:0.4994:0.2701	.	249	Q99424	ACOX2_HUMAN	K	249	ENSP00000418562:Q249K;ENSP00000307697:Q249K	ENSP00000307697:Q249K	Q	-	1	0	ACOX2	58492092	0.001000	0.12720	0.000000	0.03702	0.093000	0.18481	0.469000	0.22067	-0.398000	0.07679	-0.165000	0.13383	CAA	.	.		0.532	ACOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353541.1			T	58517052	G	T	58517052	3	4	345	1	0	0	0	0	1	0	0	0	159	1299	45	3	1336	3	ACOX2	3	58517052	Missense_Mutation	SNP	G	TCGA-UB-A7MC-01A-11D-A33Q-10	9892954	58517052	139505378	14	48792										
SENP7	57337	hgsc.bcm.edu	37	chr3	101136470	101136470	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	taaggctttggcgaagaggtTctaatttttgacatgtctct	10	6	2	2			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr3:101136470T>C	ENST00000394095.2	-	5	502	c.449A>G	c.(448-450)gAa>gGa	p.E150G	SENP7_ENST00000314261.7_Intron|SENP7_ENST00000348610.3_Missense_Mutation_p.E117G|SENP7_ENST00000358203.3_Intron|SENP7_ENST00000394094.2_Missense_Mutation_p.E150G|SENP7_ENST00000394091.1_Intron	NM_001282802.1|NM_020654.3	NP_001269731.1|NP_065705.3	Q9BQF6	SENP7_HUMAN	SUMO1/sentrin specific peptidase 7	150						intracellular (GO:0005622)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)			breast(2)|endometrium(1)|kidney(1)|large_intestine(16)|lung(15)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						GCGAAGAGGTTCTAATTTTTG	0.373																																					p.E150G		Atlas-SNP	.											.	SENP7	170	.	0			c.A449G						.						180	167	171					3																	101136470		1865	4117	5982	SO:0001583	missense	57337	exon5			AGAGGTTCTAATT		CCDS2941.2, CCDS43121.1, CCDS63704.1, CCDS63705.1, CCDS63706.1	3q12	2008-02-05	2005-08-17		ENSG00000138468	ENSG00000138468			30402	protein-coding gene	gene with protein product		612846	"SUMO1/sentrin specific protease 7"			11214970, 11230166	Standard	NM_001282802		Approved		uc003dut.3	Q9BQF6	OTTHUMG00000149927	ENST00000394095.2:c.449A>G	chr3.hg19:g.101136470T>C	ENSP00000377655:p.Glu150Gly	91.0	0.0		129.0	34.0	NM_020654	A1L3A5|A8MW39|B7WNW8|Q7Z3F4|Q96PS5|Q9C0F6|Q9HBT5	Missense_Mutation	SNP	ENST00000394095.2	hg19	CCDS2941.2	.	.	.	.	.	.	.	.	.	.	T	15.38	2.816145	0.50527	.	.	ENSG00000138468	ENST00000394095;ENST00000394094;ENST00000348610	T;T;T	0.49139	0.79;0.79;0.79	5.67	5.67	0.87782	.	0.387118	0.24922	N	0.034526	T	0.36248	0.0960	L	0.51422	1.61	0.80722	D	1	P;B	0.36837	0.571;0.435	B;B	0.30855	0.121;0.078	T	0.27088	-1.0084	10	0.36615	T	0.2	-6.6264	7.2314	0.26045	0.0:0.1232:0.0:0.8768	.	117;150	Q9BQF6-2;Q9BQF6	.;SENP7_HUMAN	G	150;150;117	ENSP00000377655:E150G;ENSP00000377654:E150G;ENSP00000342159:E117G	ENSP00000342159:E117G	E	-	2	0	SENP7	102619160	0.991000	0.36638	1.000000	0.80357	0.997000	0.91878	1.217000	0.32455	2.285000	0.76669	0.528000	0.53228	GAA	.	.		0.373	SENP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313957.2	NM_020654		C	101136470	T	C	101136470	3	2	345	1	0	0	0	0	1	0	0	0	14066	1783	62	2	2783	2	SENP7	3	101136470	Missense_Mutation	SNP	T	TCGA-UB-A7MC-01A-11D-A33Q-10	42619418	101136470	96885960	15	48793										
ZNF518B	85460	hgsc.bcm.edu	37	chr4	10445315	10445315	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	tatagaaagacttctggaaaGcagtctcccttgcttattta	7	8	2	2			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr4:10445315G>C	ENST00000326756.3	-	3	3076	c.2638C>G	c.(2638-2640)Ctt>Gtt	p.L880V		NM_053042.2	NP_444270.2	Q9C0D4	Z518B_HUMAN	zinc finger protein 518B	880					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	42						CTTCTGGAAAGCAGTCTCCCT	0.403																																					p.L880V		Atlas-SNP	.											.	ZNF518B	116	.	0			c.C2638G						.						67	71	70					4																	10445315		2203	4300	6503	SO:0001583	missense	85460	exon3			TGGAAAGCAGTCT	AB051516	CCDS33960.1	4p16.1	2007-12-07				ENSG00000178163		"Zinc fingers, C2H2-type"	29365	protein-coding gene	gene with protein product						11214970	Standard	XM_005248193		Approved	KIAA1729	uc003gmn.3	Q9C0D4		ENST00000326756.3:c.2638C>G	chr4.hg19:g.10445315G>C	ENSP00000317614:p.Leu880Val	82.0	0.0		39.0	5.0	NM_053042	Q96LN8	Missense_Mutation	SNP	ENST00000326756.3	hg19	CCDS33960.1	.	.	.	.	.	.	.	.	.	.	G	0.884	-0.727841	0.03158	.	.	ENSG00000178163	ENST00000326756	T	0.01538	4.79	6.02	0.754	0.18410	.	1.652120	0.03340	N	0.194653	T	0.01061	0.0035	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.47724	-0.9095	10	0.16896	T	0.51	-1.2574	0.2586	0.00215	0.2704:0.2443:0.2593:0.2261	.	880	Q9C0D4	Z518B_HUMAN	V	880	ENSP00000317614:L880V	ENSP00000317614:L880V	L	-	1	0	ZNF518B	10054413	0.000000	0.05858	0.001000	0.08648	0.097000	0.18754	-0.002000	0.12924	0.386000	0.24997	0.655000	0.94253	CTT	.	.		0.403	ZNF518B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359040.1	NM_053042		C	10445315	G	C	10445315	3	2	345	1	0	0	0	0	1	0	0	0	17978	971	34	4	590	4	ZNF518B	4	10445315	Missense_Mutation	SNP	G	TCGA-UB-A7MC-01A-11D-A33Q-10		10445315	180708961	16	48794										
SLIT2	9353	hgsc.bcm.edu	37	chr4	20490566	20490566	+	Frame_Shift_Del	DEL	A	A	-													0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	cctcccacctgagaggccatAatgtagccgaggttcaaaaa							TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr4:20490566delA	ENST00000504154.1	+	8	988	c.736delA	c.(736-738)aatfs	p.N246fs	SLIT2_ENST00000503823.1_Frame_Shift_Del_p.N246fs|SLIT2_ENST00000503837.1_Frame_Shift_Del_p.N246fs|SLIT2_ENST00000273739.5_Frame_Shift_Del_p.N246fs	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	246	LRRCT 1.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)			NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						GAGAGGCCATAATGTAGCCGA	0.498																																					p.H245fs		Atlas-Indel,Pindel	.											.	SLIT2	290	.	0			c.735delT						.						158	155	156					4																	20490566		2203	4300	6503	SO:0001589	frameshift_variant	9353	exon8			.	AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"slit (Drosophila) homolog 2"	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.736delA	chr4.hg19:g.20490566delA	ENSP00000422591:p.Asn246fs	189.0	0.0		101.0	38.0	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Frame_Shift_Del	DEL	ENST00000504154.1	hg19	CCDS3426.1																																																																																			.	.		0.498	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2			-	20490566	A	-	20490566	7	5	345	1	0	1	0	1	0	0	0	0	14755	362	13	0	766	0	SLIT2	4	20490566	Frame_Shift_Del	DEL	A	TCGA-UB-A7MC-01A-11D-A33Q-10	10045251	20490566	170663710	17	48795										
POC5	134359	hgsc.bcm.edu	37	chr5	74998430	74998430	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	gaagaactgctgtaccgtacCttaagacctgaactccaaag	8	11	0	3			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr5:74998430C>T	ENST00000428202.2	-	5	702	c.513G>A	c.(511-513)aaG>aaA	p.K171K	POC5_ENST00000446329.2_Splice_Site_p.K146K|POC5_ENST00000510798.1_Splice_Site_p.K54K|POC5_ENST00000514838.2_Splice_Site_p.K143K|POC5_ENST00000504862.1_5'UTR|POC5_ENST00000380475.2_Splice_Site_p.K54K	NM_001099271.1	NP_001092741.1	Q8NA72	POC5_HUMAN	POC5 centriolar protein	171					cell cycle (GO:0007049)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						TGTACCGTACCTTAAGACCTG	0.323																																					p.K171K		Atlas-SNP	.											.	POC5	82	.	0			c.G513A						.						77	71	73					5																	74998430		1868	4092	5960	SO:0001630	splice_region_variant	134359	exon5			CCGTACCTTAAGA	AK093098	CCDS47236.1, CCDS47237.1	5q13.3	2013-08-05	2013-08-05	2010-03-26	ENSG00000152359	ENSG00000152359			26658	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 37", "POC5 centriolar protein homolog (Chlamydomonas)"	C5orf37		19349582	Standard	NM_152408		Approved	FLJ35779, MGC120442, MGC120443, MGC120444, hPOC5	uc003keh.4	Q8NA72	OTTHUMG00000162487	ENST00000428202.2:c.513+1G>A	chr5.hg19:g.74998430C>T		69.0	0.0		92.0	27.0	NM_001099271	B4DJG7|Q494X7|Q494X9|Q6P085	Silent	SNP	ENST00000428202.2	hg19	CCDS47236.1																																																																																			.	.		0.323	POC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369124.1	NM_152408	Silent	T	74998430	C	T	74998430	5	4	345	1	0	0	0	0	0	0	1	0	12186	695	24	3	1246	3	POC5	5	74998430	Splice_Site	SNP	C	TCGA-UB-A7MC-01A-11D-A33Q-10		74998430	105916830	18	48796										
PCDHA1	56147	hgsc.bcm.edu	37	chr5	140167835	140167835	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	ttctggtgctagtgaaggatCacggtgagccggcgctgaca	15	9	2	3			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr5:140167835C>G	ENST00000504120.2	+	1	1960	c.1960C>G	c.(1960-1962)Cac>Gac	p.H654D	PCDHA1_ENST00000378133.3_Missense_Mutation_p.H654D|PCDHA1_ENST00000394633.3_Intron	NM_018900.2	NP_061723.1	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1	654	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(34)|prostate(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(3)	70			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGTGAAGGATCACGGTGAGCC	0.662																																					p.H654D		Atlas-SNP	.											.	PCDHA1	387	.	0			c.C1960G						.						50	56	54					5																	140167835		2203	4300	6503	SO:0001583	missense	56147	exon1			AAGGATCACGGTG	AF152479	CCDS54912.1, CCDS54913.1	5q31	2010-11-26				ENSG00000204970		"Cadherins / Protocadherins : Clustered"	8663	other	complex locus constituent	"KIAA0345-like 13"	606307				10380929	Standard	NM_018900		Approved			Q9Y5I3		ENST00000504120.2:c.1960C>G	chr5.hg19:g.140167835C>G	ENSP00000420840:p.His654Asp	58.0	0.0		61.0	38.0	NM_031410	O75288|Q9NRT7	Missense_Mutation	SNP	ENST00000504120.2	hg19	CCDS54913.1	.	.	.	.	.	.	.	.	.	.	c	12.01	1.810365	0.32053	.	.	ENSG00000204970	ENST00000504120;ENST00000378133	T;T	0.51817	0.69;0.69	3.89	3.89	0.44902	Cadherin (4);Cadherin-like (1);	0.000000	0.41396	U	0.000888	T	0.67202	0.2868	M	0.78456	2.415	0.29879	N	0.826163	D;D	0.76494	0.999;0.985	D;D	0.73380	0.98;0.92	T	0.67945	-0.5539	10	0.87932	D	0	.	13.2056	0.59793	0.0:0.8261:0.1739:0.0	.	654;654	Q9Y5I3;Q9Y5I3-3	PCDA1_HUMAN;.	D	654	ENSP00000420840:H654D;ENSP00000367373:H654D	ENSP00000367373:H654D	H	+	1	0	PCDHA1	140148019	0.000000	0.05858	1.000000	0.80357	0.122000	0.20287	0.064000	0.14437	1.876000	0.54355	0.650000	0.86243	CAC	.	.		0.662	PCDHA1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389127.1	NM_018900		G	140167835	C	G	140167835	3	3	345	1	0	0	0	0	1	0	0	0	11528	826	29	4	1962	4	PCDHA1	5	140167835	Missense_Mutation	SNP	C	TCGA-UB-A7MC-01A-11D-A33Q-10	65169405	140167835	40747425	19	48797										
PCDHB16	57717	hgsc.bcm.edu	37	chr5	140562669	140562669	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	tcagcccaagctctcatttcCgggttctaatccatgaattc	6	13	3	1			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr5:140562669C>T	ENST00000361016.2	+	1	1690	c.535C>T	c.(535-537)Cgg>Tgg	p.R179W		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	179	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTCTCATTTCCGGGTTCTAAT	0.448																																					p.R179W		Atlas-SNP	.											.	PCDHB16	159	.	0			c.C535T						.						45	48	47					5																	140562669		2202	4300	6502	SO:0001583	missense	57717	exon1			CATTTCCGGGTTC	AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"Cadherins / Protocadherins : Clustered"	14546	other	protocadherin	"cadherin ME1", "protocadherin-3x", "PCDHbeta 16"	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325	ENST00000361016.2:c.535C>T	chr5.hg19:g.140562669C>T	ENSP00000354293:p.Arg179Trp	64.0	0.0		78.0	16.0	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	hg19	CCDS4251.1	.	.	.	.	.	.	.	.	.	.	C	15.31	2.795997	0.50208	.	.	ENSG00000196963	ENST00000361016	T	0.20598	2.06	4.69	0.829	0.18847	Cadherin (4);Cadherin-like (1);	1.494410	0.04967	N	0.463091	T	0.35508	0.0934	M	0.84433	2.695	0.09310	N	1	P	0.47191	0.891	P	0.48488	0.579	T	0.19549	-1.0302	10	0.72032	D	0.01	.	3.0352	0.06119	0.2003:0.4988:0.103:0.1979	.	179	Q9NRJ7	PCDBG_HUMAN	W	179	ENSP00000354293:R179W	ENSP00000354293:R179W	R	+	1	2	PCDHB16	140542853	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-1.712000	0.01885	0.085000	0.17107	-0.789000	0.03336	CGG	.	.		0.448	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957		T	140562669	C	T	140562669	3	4	345	1	0	0	0	0	1	0	0	0	11550	643	23	1	537	1	PCDHB16	5	140562669	Missense_Mutation	SNP	C	TCGA-UB-A7MC-01A-11D-A33Q-10	394834	140562669	40352591	20	48798										
ATP10B	23120	hgsc.bcm.edu	37	chr5	160047535	160047535	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	tggggcaggcgcacagtcacCtgctcaggtgtccgggacac	15	13	2	0			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr5:160047535C>A	ENST00000327245.5	-	15	3081	c.2235G>T	c.(2233-2235)caG>caT	p.Q745H	CTC-348L5.1_ENST00000523598.1_RNA	NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	745					phospholipid translocation (GO:0045332)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1)	75	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GCACAGTCACCTGCTCAGGTG	0.617																																					p.Q745H		Atlas-SNP	.											.	ATP10B	201	.	0			c.G2235T						.						33	37	35					5																	160047535		2109	4220	6329	SO:0001583	missense	23120	exon15			AGTCACCTGCTCA	AB018258	CCDS43394.1	5q34	2010-04-20	2007-09-19		ENSG00000118322	ENSG00000118322		"ATPases / P-type"	13543	protein-coding gene	gene with protein product			"ATPase, Class V, type 10B"			9872452, 11015572	Standard	NM_025153		Approved	ATPVB, KIAA0715, FLJ21477	uc003lym.1	O94823	OTTHUMG00000163551	ENST00000327245.5:c.2235G>T	chr5.hg19:g.160047535C>A	ENSP00000313600:p.Gln745His	198.0	0.0		179.0	50.0	NM_025153	Q9H725	Missense_Mutation	SNP	ENST00000327245.5	hg19	CCDS43394.1	.	.	.	.	.	.	.	.	.	.	C	19.29	3.799211	0.70567	.	.	ENSG00000118322	ENST00000327245;ENST00000520108	T;T	0.58940	0.3;0.3	5.36	1.08	0.20341	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.143106	0.51477	D	0.000086	T	0.58366	0.2117	L	0.31752	0.955	0.39672	D	0.970765	D;D	0.64830	0.994;0.994	D;D	0.66497	0.944;0.944	T	0.54649	-0.8262	9	.	.	.	.	10.7446	0.46172	0.0:0.6901:0.0:0.3099	.	353;745	Q2YDW8;O94823	.;AT10B_HUMAN	H	745;353	ENSP00000313600:Q745H;ENSP00000431081:Q353H	.	Q	-	3	2	ATP10B	159980113	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	0.539000	0.23175	0.277000	0.22141	0.655000	0.94253	CAG	.	.		0.617	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374127.1	NM_025153		A	160047535	C	A	160047535	3	1	345	1	0	0	0	0	1	0	0	0	1117	680	24	3	2198	3	ATP10B	5	160047535	Missense_Mutation	SNP	C	TCGA-UB-A7MC-01A-11D-A33Q-10	19484866	160047535	20867725	21	48799										
HLA-DMB	3109	hgsc.bcm.edu	37	chr6	32906517	32906518	+	Frame_Shift_Ins	INS	-	-	GCCCATT													0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	gtgtgtggcacaattctgaaINSgcccattgcgcaagcgctgc							TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr6:32906517_32906518insGCCCATT	ENST00000418107.2	-	2	542_543	c.280_281insAATGGGC	c.(280-282)cttfs	p.L94fs	HLA-DMB_ENST00000416244.2_Frame_Shift_Ins_p.L94fs|XXbac-BPG181M17.5_ENST00000429234.1_Frame_Shift_Ins_p.L126fs|AL645941.1_ENST00000390777.1_RNA	NM_002118.4	NP_002109.2	P28068	DMB_HUMAN	major histocompatibility complex, class II, DM beta	94	Beta-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|immune response (GO:0006955)|MHC class II protein complex assembly (GO:0002399)|peptide antigen assembly with MHC class II protein complex (GO:0002503)|positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001190)|positive regulation of T cell proliferation (GO:0042102)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)	MHC class II protein complex binding (GO:0023026)			breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13						ACAATTCTGAAGCCCATTGCGC	0.559																																					p.L94fs		Atlas-Indel,Pindel	.											.	HLA-DMB	38	.	0			c.281_282insAATGGGC						.																																			SO:0001589	frameshift_variant	3109	exon2			.		CCDS4760.1	6p21.3	2014-05-16			ENSG00000242574	ENSG00000242574		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4935	protein-coding gene	gene with protein product		142856				1922365	Standard	NM_002118		Approved	D6S221E, RING7	uc003ocl.2	P28068	OTTHUMG00000031176	ENST00000418107.2:c.274_280dupAATGGGC	chr6.hg19:g.32906518_32906524dupGCCCATT	ENSP00000398890:p.Leu94fs	150.0	0.0		153.0	45.0	NM_002118	O77936|Q13012|Q29751|Q58ZE2|Q5SNZ8|Q5STC4|Q9XRX2	Frame_Shift_Ins	INS	ENST00000418107.2	hg19	CCDS4760.1																																																																																			.	.		0.559	HLA-DMB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076340.2	NM_002118		GCCCATT	32906518	-	GCCCATT	32906517	7	5	345	1	0	1	1	0	0	0	0	0	7208	72	3	0	530	0	HLA-DMB	6	32906517	Frame_Shift_Ins	INS	-	TCGA-UB-A7MC-01A-11D-A33Q-10		32906517	138208550	22	48800										
PHF3	23469	hgsc.bcm.edu	37	chr6	64401788	64401788	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	tgaaatactagatccagataCtttggaaaaccaagctacag	7	8	0	3			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr6:64401788C>G	ENST00000262043.3	+	5	2691	c.2351C>G	c.(2350-2352)aCt>aGt	p.T784S	PHF3_ENST00000393387.1_Missense_Mutation_p.T784S			Q92576	PHF3_HUMAN	PHD finger protein 3	784					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(7)|cervix(2)|endometrium(8)|kidney(7)|large_intestine(18)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(6)	75	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			GATCCAGATACTTTGGAAAAC	0.368																																					p.T784S	GBM(135;136 1820 29512 34071 46235)	Atlas-SNP	.											.	PHF3	191	.	0			c.C2351G						.						109	107	107					6																	64401788		2203	4300	6503	SO:0001583	missense	23469	exon4			CAGATACTTTGGA	AF091622	CCDS4966.1	6q12	2013-09-24			ENSG00000118482	ENSG00000118482		"Zinc fingers, PHD-type"	8921	protein-coding gene	gene with protein product		607789				11856869	Standard	XM_005248701		Approved		uc003pep.1	Q92576	OTTHUMG00000014952	ENST00000262043.3:c.2351C>G	chr6.hg19:g.64401788C>G	ENSP00000262043:p.Thr784Ser	142.0	0.0		215.0	104.0	NM_015153	A3KFI8|Q14CR5|Q5CZI1|Q5T1T6|Q9NQ16|Q9UI45	Missense_Mutation	SNP	ENST00000262043.3	hg19	CCDS4966.1	.	.	.	.	.	.	.	.	.	.	C	9.361	1.068130	0.20067	.	.	ENSG00000118482	ENST00000506783;ENST00000481385;ENST00000515594;ENST00000262043;ENST00000494284;ENST00000393387	T;T;T;T;T;T	0.45668	2.22;1.91;0.89;2.25;1.91;2.25	4.96	-3.18	0.05186	.	1.105820	0.07078	N	0.836602	T	0.08358	0.0208	N	0.22421	0.69	0.09310	N	0.99999	B	0.15141	0.012	B	0.12156	0.007	T	0.30387	-0.9980	10	0.20519	T	0.43	0.007	5.5428	0.17047	0.1153:0.2751:0.0:0.6096	.	784	Q92576	PHF3_HUMAN	S	598;696;53;784;737;784	ENSP00000424694:T598S;ENSP00000425227:T696S;ENSP00000425338:T53S;ENSP00000262043:T784S;ENSP00000424078:T737S;ENSP00000377048:T784S	ENSP00000262043:T784S	T	+	2	0	PHF3	64459747	0.083000	0.21467	0.675000	0.29917	0.963000	0.63663	0.288000	0.18939	-0.631000	0.05560	-0.438000	0.05819	ACT	.	.		0.368	PHF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041086.2			G	64401788	C	G	64401788	3	3	345	1	0	0	0	0	1	0	0	0	11845	565	20	4	2365	4	PHF3	6	64401788	Missense_Mutation	SNP	C	TCGA-UB-A7MC-01A-11D-A33Q-10	31495271	64401788	106713279	23	48801										
TAAR2	9287	hgsc.bcm.edu	37	chr6	132938951	132938951	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	ggccactgagcaaagatgaaAaatggatgttatgctaagca	11	6	0	3			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr6:132938951A>C	ENST00000367931.1	-	2	393	c.394T>G	c.(394-396)Ttt>Gtt	p.F132V	TAAR2_ENST00000537809.1_Missense_Mutation_p.F87V|TAAR2_ENST00000275191.2_Missense_Mutation_p.F87V			Q9P1P5	TAAR2_HUMAN	trace amine associated receptor 2	132					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|trace-amine receptor activity (GO:0001594)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|skin(1)	23	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00608)|GBM - Glioblastoma multiforme(226;0.0151)		CAAAGATGAAAAATGGATGTT	0.333																																					p.F132V		Atlas-SNP	.											.	TAAR2	45	.	0			c.T394G						.						71	70	71					6																	132938951		2203	4300	6503	SO:0001583	missense	9287	exon2			GATGAAAAATGGA	AF112460	CCDS34541.1, CCDS5157.1	6q24	2012-08-08	2005-02-23	2005-02-24	ENSG00000146378	ENSG00000146378		"GPCR / Class A : Trace amine associated receptors"	4514	protein-coding gene	gene with protein product		604849	"G protein-coupled receptor 58"	GPR58		10684976, 15718104	Standard	NM_014626		Approved		uc003qdl.1	Q9P1P5	OTTHUMG00000015585	ENST00000367931.1:c.394T>G	chr6.hg19:g.132938951A>C	ENSP00000356908:p.Phe132Val	122.0	0.0		143.0	9.0	NM_001033080	Q5QD02|Q6NWS1|Q6NWS2|Q6NWS3	Missense_Mutation	SNP	ENST00000367931.1	hg19	CCDS34541.1	.	.	.	.	.	.	.	.	.	.	A	16.40	3.112965	0.56398	.	.	ENSG00000146378	ENST00000275191;ENST00000367931;ENST00000537809	T;T;T	0.40756	1.02;1.02;1.02	6.0	6.0	0.97389	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.60314	0.2259	M	0.77486	2.375	0.39819	D	0.972806	D	0.89917	1.0	D	0.91635	0.999	T	0.66376	-0.5939	10	0.72032	D	0.01	-52.8563	16.5044	0.84266	1.0:0.0:0.0:0.0	.	132	Q9P1P5	TAAR2_HUMAN	V	87;132;87	ENSP00000275191:F87V;ENSP00000356908:F132V;ENSP00000441263:F87V	ENSP00000275191:F87V	F	-	1	0	TAAR2	132980644	0.871000	0.30034	1.000000	0.80357	0.652000	0.38707	1.881000	0.39638	2.295000	0.77249	0.528000	0.53228	TTT	.	.		0.333	TAAR2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390735.1	NM_014626		C	132938951	A	C	132938951	3	2	345	1	0	0	0	0	1	0	0	0	15505	14	1	5	665	5	TAAR2	6	132938951	Missense_Mutation	SNP	A	TCGA-UB-A7MC-01A-11D-A33Q-10	68537163	132938951	38176116	24	48802										
IL6	3569	hgsc.bcm.edu	37	chr7	22767222	22767222	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	tgacaaacaaattcggtacaTcctcgacggcatctcagccc	7	14	1	1			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr7:22767222T>A	ENST00000404625.1	+	3	638	c.179T>A	c.(178-180)aTc>aAc	p.I60N	IL6_ENST00000407492.1_Intron|IL6_ENST00000401651.1_Intron|IL6_ENST00000406575.1_Missense_Mutation_p.I60N|AC073072.5_ENST00000325042.2_RNA|IL6_ENST00000420258.2_Missense_Mutation_p.I114N|IL6_ENST00000258743.5_Missense_Mutation_p.I60N|IL6_ENST00000401630.3_Missense_Mutation_p.I37N			P05231	IL6_HUMAN	interleukin 6	60					acute-phase response (GO:0006953)|aging (GO:0007568)|bone remodeling (GO:0046849)|branching involved in salivary gland morphogenesis (GO:0060445)|cell growth (GO:0016049)|cell redox homeostasis (GO:0045454)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endocrine pancreas development (GO:0031018)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|glucagon secretion (GO:0070091)|hepatic immune response (GO:0002384)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|interleukin-6-mediated signaling pathway (GO:0070102)|monocyte chemotaxis (GO:0002548)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine biosynthetic process (GO:0045079)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of hormone secretion (GO:0046888)|negative regulation of lipid storage (GO:0010888)|negative regulation of muscle organ development (GO:0048635)|negative regulation of neuron death (GO:1901215)|negative regulation of protein kinase activity (GO:0006469)|neuron projection development (GO:0031175)|neutrophil apoptotic process (GO:0001781)|neutrophil mediated immunity (GO:0002446)|platelet activation (GO:0030168)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell activation (GO:0050871)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine production (GO:0032722)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|positive regulation of type B pancreatic cell apoptotic process (GO:2000676)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of angiogenesis (GO:0045765)|regulation of cell shape (GO:0008360)|regulation of circadian sleep/wake cycle, non-REM sleep (GO:0045188)|regulation of vascular endothelial growth factor production (GO:0010574)|response to amino acid (GO:0043200)|response to antibiotic (GO:0046677)|response to caffeine (GO:0031000)|response to calcium ion (GO:0051592)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to glucocorticoid (GO:0051384)|response to heat (GO:0009408)|response to insulin (GO:0032868)|response to mechanical stimulus (GO:0009612)|response to nutrient levels (GO:0031667)|response to peptidoglycan (GO:0032494)|T-helper 17 cell lineage commitment (GO:0072540)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|interleukin-6 receptor complex (GO:0005896)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|interleukin-6 receptor binding (GO:0005138)			breast(1)|endometrium(2)|large_intestine(4)|lung(1)	8					Ginseng(DB01404)	ATTCGGTACATCCTCGACGGC	0.592																																					p.I60N	Esophageal Squamous(47;342 1214 13936 33513)	Atlas-SNP	.											.	IL6	30	.	0			c.T179A						.						103	98	100					7																	22767222		2203	4300	6503	SO:0001583	missense	3569	exon2			GGTACATCCTCGA	M18403	CCDS5375.1	7p21-p15	2014-04-04	2014-04-04		ENSG00000136244	ENSG00000136244		"Interleukins and interleukin receptors", "Interferons"	6018	protein-coding gene	gene with protein product	"interferon, beta 2"	147620	"interleukin 6 (interferon, beta 2)"	IFNB2		3294161	Standard	NM_000600		Approved	IL-6, BSF2, HGF, HSF	uc003svj.4	P05231	OTTHUMG00000023178	ENST00000404625.1:c.179T>A	chr7.hg19:g.22767222T>A	ENSP00000385675:p.Ile60Asn	122.0	0.0		84.0	56.0	NM_000600	Q9UCU2|Q9UCU3|Q9UCU4	Missense_Mutation	SNP	ENST00000404625.1	hg19	CCDS5375.1	.	.	.	.	.	.	.	.	.	.	T	16.88	3.244650	0.59103	.	.	ENSG00000136244	ENST00000404625;ENST00000426291;ENST00000258743;ENST00000420258;ENST00000401630;ENST00000406575	T;T;T;T;T;T	0.28069	1.63;1.63;1.63;1.63;1.63;1.63	5.73	4.58	0.56647	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.529823	0.22030	N	0.065612	T	0.49338	0.1551	M	0.62723	1.935	0.09310	N	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.994;0.995;0.997	T	0.39603	-0.9606	10	0.87932	D	0	-12.0626	8.6145	0.33822	0.0:0.0866:0.0:0.9134	.	114;60;60	B4DNQ5;B5MC14;P05231	.;.;IL6_HUMAN	N	60;60;60;114;37;60	ENSP00000385675:I60N;ENSP00000405150:I60N;ENSP00000258743:I60N;ENSP00000405994:I114N;ENSP00000384928:I37N;ENSP00000385227:I60N	ENSP00000258743:I60N	I	+	2	0	IL6	22733747	0.061000	0.20836	0.001000	0.08648	0.004000	0.04260	3.470000	0.53100	1.112000	0.41740	0.454000	0.30748	ATC	.	.		0.592	IL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250225.2	NM_000600		A	22767222	T	A	22767222	3	1	345	1	0	0	0	0	1	0	0	0	7710	1435	50	4	185	4	IL6	7	22767222	Missense_Mutation	SNP	T	TCGA-UB-A7MC-01A-11D-A33Q-10		22767222	136371441	25	48803										
ZSCAN21	7589	hgsc.bcm.edu	37	chr7	99662023	99662023	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	gagcttcagtcagcatgcggGcctcagctcccaccagagac	11	15	3	1			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr7:99662023G>C	ENST00000292450.4	+	4	1369	c.1205G>C	c.(1204-1206)gGc>gCc	p.G402A	ZSCAN21_ENST00000543588.1_Missense_Mutation_p.A368P|ZNF3_ENST00000413658.2_3'UTR|ZSCAN21_ENST00000456748.2_Missense_Mutation_p.A368P	NM_145914.2	NP_666019.1	Q9Y5A6	ZSC21_HUMAN	zinc finger and SCAN domain containing 21	402					positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|skin(1)	21	Lung NSC(181;0.0211)|all_lung(186;0.0323)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)			CAGCATGCGGGCCTCAGCTCC	0.522																																					p.G402A		Atlas-SNP	.											.	ZSCAN21	29	.	0			c.G1205C						.						85	81	82					7																	99662023		2203	4300	6503	SO:0001583	missense	7589	exon4			ATGCGGGCCTCAG	AL136865	CCDS5681.1	7q11.1	2013-01-08	2006-10-06	2006-10-06	ENSG00000166529	ENSG00000166529		"-", "Zinc fingers, C2H2-type"	13104	protein-coding gene	gene with protein product		601261	"zinc finger protein 38 (KOX 25)", "zinc finger protein 38"	ZNF38		2288909, 2014798	Standard	NM_145914		Approved	DKFZp434L134, NY-REN-21, Zipro1	uc003uso.3	Q9Y5A6	OTTHUMG00000154583	ENST00000292450.4:c.1205G>C	chr7.hg19:g.99662023G>C	ENSP00000292450:p.Gly402Ala	60.0	0.0		62.0	19.0	NM_145914	A4D2A6|D6W5T9|Q9H0B5	Missense_Mutation	SNP	ENST00000292450.4	hg19	CCDS5681.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.850|7.850	0.723758|0.723758	0.15439|0.15439	.|.	.|.	ENSG00000166529|ENSG00000166529	ENST00000543588;ENST00000456748|ENST00000292450;ENST00000379635	T;T|T	0.02258|0.06768	4.37;4.37|3.26	4.52|4.52	4.52|4.52	0.55395|0.55395	.|Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.|0.000000	.|0.42821	.|D	.|0.000644	T|T	0.05364|0.05364	0.0142|0.0142	N|N	0.02985|0.02985	-0.445|-0.445	0.80722|0.80722	D|D	1|1	D|P	0.56035|0.39094	0.974|0.659	P|P	0.48030|0.45971	0.564|0.499	T|T	0.49943|0.49943	-0.8885|-0.8885	9|10	0.87932|0.07990	D|T	0|0.79	.|.	15.1433|15.1433	0.72626|0.72626	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	368|402	G3V1M0|Q9Y5A6	.|ZSC21_HUMAN	P|A	368|402;377	ENSP00000441212:A368P;ENSP00000390960:A368P|ENSP00000292450:G402A	ENSP00000390960:A368P|ENSP00000292450:G402A	A|G	+|+	1|2	0|0	ZSCAN21|ZSCAN21	99499959|99499959	0.000000|0.000000	0.05858|0.05858	0.992000|0.992000	0.48379|0.48379	0.393000|0.393000	0.30537|0.30537	0.238000|0.238000	0.18004|0.18004	2.524000|2.524000	0.85096|0.85096	0.655000|0.655000	0.94253|0.94253	GCC|GGC	.	.		0.522	ZSCAN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336166.1	NM_145914		C	99662023	G	C	99662023	3	2	345	1	0	0	0	0	1	0	0	0	18248	1203	42	4	1215	4	ZSCAN21	7	99662023	Missense_Mutation	SNP	G	TCGA-UB-A7MC-01A-11D-A33Q-10	76894801	99662023	59476640	26	48804										
CSMD1	64478	hgsc.bcm.edu	37	chr8	3216738	3216738	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	cccaggcaggtaagcttggtGgcaccttctaaacgatatcc	10	12	1	0			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr8:3216738G>A	ENST00000520002.1	-	22	3798	c.3243C>T	c.(3241-3243)gcC>gcT	p.A1081A	CSMD1_ENST00000602723.1_Silent_p.A1081A|CSMD1_ENST00000400186.3_Silent_p.A1081A|CSMD1_ENST00000542608.1_Silent_p.A1080A|CSMD1_ENST00000602557.1_Silent_p.A1081A|CSMD1_ENST00000539096.1_Silent_p.A1080A|CSMD1_ENST00000537824.1_Silent_p.A1080A			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1081	Sushi 6. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		TAAGCTTGGTGGCACCTTCTA	0.542																																					p.A1080A		Atlas-SNP	.											.	CSMD1	1469	.	0			c.C3240T						.						71	77	75					8																	3216738		2203	4300	6503	SO:0001819	synonymous_variant	64478	exon21			CTTGGTGGCACCT			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.3243C>T	chr8.hg19:g.3216738G>A		118.0	0.0		156.0	41.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	hg19		.	.	.	.	.	.	.	.	.	.	t	14.13	2.442437	0.43326	.	.	ENSG00000183117	ENST00000335551	.	.	.	5.18	-7.27	0.01461	.	.	.	.	.	T	0.44973	0.1319	.	.	.	0.41715	D	0.989474	.	.	.	.	.	.	T	0.46898	-0.9158	4	.	.	.	.	5.3646	0.16107	0.1842:0.1181:0.5163:0.1814	.	.	.	.	Y	561	.	.	H	-	1	0	CSMD1	3204145	0.157000	0.22836	0.098000	0.21074	0.814000	0.46013	-0.481000	0.06552	-2.368000	0.00604	-1.692000	0.00727	CAC	.	.		0.542	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		A	3216738	G	A	3216738	2	1	345	1	0	0	0	0	0	0	0	1	3946	1335	47	3		3	CSMD1	8	3216738	Silent	SNP	G	TCGA-UB-A7MC-01A-11D-A33Q-10		3216738	143147284	27	48805										
ANK1	286	hgsc.bcm.edu	37	chr8	41554074	41554074	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	acttcctctcatggaaccacCccgggcgtcaaccatgaagc	8	16	2	1			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr8:41554074C>G	ENST00000347528.4	-	26	2850	c.2767G>C	c.(2767-2769)Ggt>Cgt	p.G923R	ANK1_ENST00000379758.2_Missense_Mutation_p.G923R|ANK1_ENST00000289734.7_Missense_Mutation_p.G923R|ANK1_ENST00000352337.4_Missense_Mutation_p.G923R|ANK1_ENST00000396942.1_Missense_Mutation_p.G923R|ANK1_ENST00000396945.1_Missense_Mutation_p.G923R|ANK1_ENST00000265709.8_Missense_Mutation_p.G964R	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	923	ZU5 1. {ECO:0000255|PROSITE- ProRule:PRU00485}.				axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			ATGGAACCACCCCGGGCGTCA	0.647																																					p.G964R		Atlas-SNP	.											.	ANK1	497	.	0			c.G2890C						.						49	45	46					8																	41554074		2202	4300	6502	SO:0001583	missense	286	exon27			AACCACCCCGGGC	M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"Ankyrin repeat domain containing"	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.2767G>C	chr8.hg19:g.41554074C>G	ENSP00000339620:p.Gly923Arg	90.0	0.0		69.0	23.0	NM_001142446	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Missense_Mutation	SNP	ENST00000347528.4	hg19	CCDS6119.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	32|32	5.180926|5.180926	0.94846|0.94846	.|.	.|.	ENSG00000029534|ENSG00000029534	ENST00000520299|ENST00000347528;ENST00000289734;ENST00000379758;ENST00000396945;ENST00000396942;ENST00000352337;ENST00000265709;ENST00000358820	.|T;T;T;T;T;T;T	.|0.68181	.|-0.31;-0.31;-0.31;-0.31;-0.31;-0.31;-0.31	5.67|5.67	5.67|5.67	0.87782|0.87782	.|ZU5 (3);	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	D|D	0.84243|0.84243	0.5429|0.5429	M|M	0.83118|0.83118	2.625|2.625	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D;D	.|0.97110	.|0.999;0.998;1.0;1.0;0.999;1.0	D|D	0.85809|0.85809	0.1378|0.1378	6|10	.|0.87932	.|D	.|0	.|.	19.7607|19.7607	0.96316|0.96316	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|964;923;923;923;923;239	.|P16157-21;P16157-4;P16157;P16157-5;P16157-3;B3KX39	.|.;.;ANK1_HUMAN;.;.;.	A|R	244|923;923;923;923;923;923;964;923	.|ENSP00000339620:G923R;ENSP00000289734:G923R;ENSP00000369082:G923R;ENSP00000380149:G923R;ENSP00000380147:G923R;ENSP00000309131:G923R;ENSP00000265709:G964R	.|ENSP00000265709:G964R	G|G	-|-	2|1	0|0	ANK1|ANK1	41673231|41673231	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.865000|0.865000	0.49528|0.49528	7.785000|7.785000	0.85724|0.85724	2.686000|2.686000	0.91538|0.91538	0.561000|0.561000	0.74099|0.74099	GGG|GGT	.	.		0.647	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475		G	41554074	C	G	41554074	3	3	345	1	0	0	0	0	1	0	0	0	620	623	22	4	3272	4	ANK1	8	41554074	Missense_Mutation	SNP	C	TCGA-UB-A7MC-01A-11D-A33Q-10	38337336	41554074	104809948	28	48806										
ATAD2	29028	hgsc.bcm.edu	37	chr8	124340448	124340448	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	accttttccttcattttcatCagaaatatgtattatctgag	4	8	4	2			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr8:124340448C>T	ENST00000287394.5	-	25	3957	c.3850G>A	c.(3850-3852)Gat>Aat	p.D1284N	ATAD2_ENST00000521903.1_Missense_Mutation_p.D602N	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	1284					ATP catabolic process (GO:0006200)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	48	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			TCATTTTCATCAGAAATATGT	0.308																																					p.D1284N		Atlas-SNP	.											.	ATAD2	160	.	0			c.G3850A						.						50	48	49					8																	124340448		2202	4299	6501	SO:0001583	missense	29028	exon25			TTTCATCAGAAAT	BC019909	CCDS6343.1	8q24.13	2014-01-21		2007-02-08	ENSG00000156802	ENSG00000156802		"ATPases / AAA-type"	30123	protein-coding gene	gene with protein product		611941				12477932	Standard	NM_014109		Approved	PRO2000, DKFZp667N1320, MGC5254, MGC29843, CT137	uc003yqh.4	Q6PL18	OTTHUMG00000165090	ENST00000287394.5:c.3850G>A	chr8.hg19:g.124340448C>T	ENSP00000287394:p.Asp1284Asn	53.0	0.0		67.0	17.0	NM_014109	Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	Missense_Mutation	SNP	ENST00000287394.5	hg19	CCDS6343.1	.	.	.	.	.	.	.	.	.	.	C	2.482	-0.319418	0.05386	.	.	ENSG00000156802	ENST00000287394;ENST00000521903	D;T	0.92048	-2.96;1.48	5.01	2.22	0.28083	.	12.131900	0.00166	N	0.000000	D	0.86066	0.5844	N	0.22421	0.69	0.23341	N	0.997879	B	0.02656	0.0	B	0.01281	0.0	T	0.71097	-0.4691	10	0.25751	T	0.34	-5.7908	5.7605	0.18196	0.1543:0.6797:0.0:0.166	.	1284	Q6PL18	ATAD2_HUMAN	N	1284;602	ENSP00000287394:D1284N;ENSP00000429213:D602N	ENSP00000287394:D1284N	D	-	1	0	ATAD2	124409629	0.993000	0.37304	0.256000	0.24389	0.116000	0.19942	1.279000	0.33191	0.240000	0.21263	-0.158000	0.13435	GAT	.	.		0.308	ATAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381766.2	NM_014109		T	124340448	C	T	124340448	3	4	345	1	0	0	0	0	1	0	0	0	1071	826	29	3	338	3	ATAD2	8	124340448	Missense_Mutation	SNP	C	TCGA-UB-A7MC-01A-11D-A33Q-10	82786374	124340448	22023574	29	48807										
PHF2	5253	hgsc.bcm.edu	37	chr9	96416768	96416768	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	tgagcgctggcggtctgcctCtaaccacagcgagatgttct	12	12	3	2			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr9:96416768C>G	ENST00000359246.4	+	7	1230	c.863C>G	c.(862-864)tCt>tGt	p.S288C	PHF2_ENST00000375376.4_Intron	NM_005392.3	NP_005383.3	O75151	PHF2_HUMAN	PHD finger protein 2	288	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				liver development (GO:0001889)|negative regulation of chromatin silencing at rDNA (GO:0061188)|protein demethylation (GO:0006482)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K9 specific) (GO:0032454)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)		CGGTCTGCCTCTAACCACAGC	0.587																																					p.S288C		Atlas-SNP	.											.	PHF2	113	.	0			c.C863G						.						106	95	98					9																	96416768		2203	4300	6503	SO:0001583	missense	5253	exon7			CTGCCTCTAACCA	AF043725	CCDS35069.1	9q22	2013-01-28			ENSG00000197724	ENSG00000197724		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	8920	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 1E", "centromere protein 35"	604351				10051327, 20129925	Standard	NM_005392		Approved	KIAA0662, JHDM1E, CENP-35	uc004aub.3	O75151	OTTHUMG00000020253	ENST00000359246.4:c.863C>G	chr9.hg19:g.96416768C>G	ENSP00000352185:p.Ser288Cys	80.0	0.0		59.0	40.0	NM_005392	Q4VXG0|Q8N3K2|Q9Y6N4	Missense_Mutation	SNP	ENST00000359246.4	hg19	CCDS35069.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.490545	0.84962	.	.	ENSG00000197724	ENST00000359246	T	0.72282	-0.64	5.12	5.12	0.69794	Transcription factor jumonji/aspartyl beta-hydroxylase (2);Transcription factor jumonji (1);	0.186594	0.47852	D	0.000203	T	0.75946	0.3919	M	0.82923	2.615	0.80722	D	1	P	0.44986	0.847	B	0.41510	0.359	T	0.81193	-0.1044	10	0.59425	D	0.04	-10.5597	18.7374	0.91761	0.0:1.0:0.0:0.0	.	288	O75151	PHF2_HUMAN	C	288	ENSP00000352185:S288C	ENSP00000352185:S288C	S	+	2	0	PHF2	95456589	1.000000	0.71417	0.588000	0.28705	0.994000	0.84299	7.543000	0.82106	2.644000	0.89710	0.585000	0.79938	TCT	.	.		0.587	PHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053162.1	NM_005392		G	96416768	C	G	96416768	3	3	345	1	0	0	0	0	1	0	0	0	11839	913	32	4	889	4	PHF2	9	96416768	Missense_Mutation	SNP	C	TCGA-UB-A7MC-01A-11D-A33Q-10		96416768	44796663	30	48808										
SFMBT2	57713	hgsc.bcm.edu	37	chr10	7205790	7205790	+	Frame_Shift_Del	DEL	T	T	-													0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	tctcgatctggtggcataacTtgatggcaggccccagcttc							TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr10:7205790delT	ENST00000361972.4	-	21	2717	c.2627delA	c.(2626-2628)aagfs	p.K876fs	SFMBT2_ENST00000397167.1_Frame_Shift_Del_p.K876fs	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	876	SAM.				negative regulation of gene expression (GO:0010629)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	histone binding (GO:0042393)			NS(2)|breast(3)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(26)|lung(34)|ovary(5)|pancreas(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	99						GTGGCATAACTTGATGGCAGG	0.572																																					p.K876fs		Atlas-Indel,Pindel	.											.	SFMBT2	209	.	0			c.2628delG						.						108	90	96					10																	7205790		2203	4300	6503	SO:0001589	frameshift_variant	57713	exon21			.	AB046837	CCDS31138.1	10p15.1	2013-01-10	2003-11-14		ENSG00000198879	ENSG00000198879		"Sterile alpha motif (SAM) domain containing"	20256	protein-coding gene	gene with protein product		615392	"Scm-related gene containing four mbt domains 2"			10997877	Standard	NM_001029880		Approved	KIAA1617	uc009xio.2	Q5VUG0	OTTHUMG00000017630	ENST00000361972.4:c.2627delA	chr10.hg19:g.7205790delT	ENSP00000355109:p.Lys876fs	94.0	0.0		68.0	37.0	NM_001029880	A7MD09|Q9HCF5	Frame_Shift_Del	DEL	ENST00000361972.4	hg19	CCDS31138.1																																																																																			.	.		0.572	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046673.1	NM_001029880		-	7205790	T	-	7205790	7	5	345	1	0	1	0	1	0	0	0	0	14173	1609	56	0	61	0	SFMBT2	10	7205790	Frame_Shift_Del	DEL	T	TCGA-UB-A7MC-01A-11D-A33Q-10		7205790	128328957	31	48809										
ARID5B	84159	hgsc.bcm.edu	37	chr10	63851284	63851284	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	ggggcaacccaggcatcatgTccccactggccaagaaaaag	11	13	1	1			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr10:63851284T>C	ENST00000279873.7	+	10	2472	c.2062T>C	c.(2062-2064)Tcc>Ccc	p.S688P	ARID5B_ENST00000309334.5_Missense_Mutation_p.S445P	NM_032199.2	NP_115575.1	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)	688					adipose tissue development (GO:0060612)|adrenal gland development (GO:0030325)|cell development (GO:0048468)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|fat pad development (GO:0060613)|female gonad development (GO:0008585)|fibroblast migration (GO:0010761)|kidney development (GO:0001822)|liver development (GO:0001889)|male gonad development (GO:0008584)|multicellular organism growth (GO:0035264)|muscle organ morphogenesis (GO:0048644)|negative regulation of transcription, DNA-templated (GO:0045892)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|post-embryonic development (GO:0009791)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(13)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	Prostate(12;0.016)|all_hematologic(501;0.215)					AGGCATCATGTCCCCACTGGC	0.527																																					p.S688P		Atlas-SNP	.											.	ARID5B	125	.	0			c.T2062C						.						59	57	57					10																	63851284		2203	4300	6503	SO:0001583	missense	84159	exon10			ATCATGTCCCCAC	M73837	CCDS31208.1, CCDS58082.1	10q11.22	2013-02-07			ENSG00000150347	ENSG00000150347		"-"	17362	protein-coding gene	gene with protein product		608538				11483573, 11478881	Standard	NM_032199		Approved	FLJ21150, MRF2	uc001jlt.2	Q14865	OTTHUMG00000018298	ENST00000279873.7:c.2062T>C	chr10.hg19:g.63851284T>C	ENSP00000279873:p.Ser688Pro	143.0	0.0		159.0	10.0	NM_032199	B4DLB3|Q05DG6|Q32Q59|Q5VST4|Q6NZ42|Q7Z3M4|Q8N421|Q9H786	Missense_Mutation	SNP	ENST00000279873.7	hg19	CCDS31208.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.215448	0.79352	.	.	ENSG00000150347	ENST00000279873;ENST00000309334	T;T	0.69175	-0.29;-0.38	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.80884	0.4709	M	0.67953	2.075	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.82772	-0.0292	10	0.87932	D	0	-18.4042	16.2674	0.82597	0.0:0.0:0.0:1.0	.	688	Q14865	ARI5B_HUMAN	P	688;445	ENSP00000279873:S688P;ENSP00000308862:S445P	ENSP00000279873:S688P	S	+	1	0	ARID5B	63521290	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.499000	0.81566	2.242000	0.73789	0.533000	0.62120	TCC	.	.		0.527	ARID5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048233.1	XM_084482		C	63851284	T	C	63851284	3	2	345	1	0	0	0	0	1	0	0	0	922	1667	58	2	2100	2	ARID5B	10	63851284	Missense_Mutation	SNP	T	TCGA-UB-A7MC-01A-11D-A33Q-10	56645494	63851284	71683463	32	48810										
C10orf76	79591	hgsc.bcm.edu	37	chr10	103766310	103766310	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	ggctcaccatcagaggaaggCggtgtggtcccaagtggtgt	16	9	2	1			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr10:103766310C>T	ENST00000370033.4	-	14	1154	c.1035G>A	c.(1033-1035)ccG>ccA	p.P345P		NM_024541.2	NP_078817.2	Q5T2E6	CJ076_HUMAN	chromosome 10 open reading frame 76	345						integral component of membrane (GO:0016021)		p.P345P(1)		autonomic_ganglia(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(7)|prostate(2)|upper_aerodigestive_tract(2)	24		Colorectal(252;0.123)		Epithelial(162;2.41e-08)|all cancers(201;6.41e-07)		CAGAGGAAGGCGGTGTGGTCC	0.488																																					p.P345P		Atlas-SNP	.											C10orf76,colon,carcinoma,0,1	C10orf76	48	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1035A						.						125	133	131					10																	103766310		1949	4140	6089	SO:0001819	synonymous_variant	79591	exon14			GGAAGGCGGTGTG	AK023176	CCDS41563.1	10q24.32	2008-10-21			ENSG00000120029	ENSG00000120029			25788	protein-coding gene	gene with protein product						14702039	Standard	NM_024541		Approved	FLJ13114	uc009xwy.1	Q5T2E6	OTTHUMG00000018943	ENST00000370033.4:c.1035G>A	chr10.hg19:g.103766310C>T		88.0	1.0		60.0	3.0	NM_024541	Q2TB87|Q9H8Z9	Silent	SNP	ENST00000370033.4	hg19	CCDS41563.1																																																																																			.	.		0.488	C10orf76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050007.1	NM_024541		T	103766310	C	T	103766310	2	4	345	1	0	0	0	0	0	0	0	1	1618	755	27	1		1	C10orf76	10	103766310	Silent	SNP	C	TCGA-UB-A7MC-01A-11D-A33Q-10	39915026	103766310	31768437	33	48811										
SLC29A2	3177	hgsc.bcm.edu	37	chr11	66135014	66135014	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	ttggccaggtagtagcgggcAaacttctgcagaaggacagg	15	8	1	1			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr11:66135014A>G	ENST00000357440.2	-	7	882	c.654T>C	c.(652-654)ttT>ttC	p.F218F	SLC29A2_ENST00000544554.1_Silent_p.F218F|SLC29A2_ENST00000546034.1_Silent_p.F218F|SLC29A2_ENST00000311161.7_Silent_p.F218F	NM_001532.2	NP_001523.2	Q14542	S29A2_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 2	218					cell proliferation (GO:0008283)|nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	nucleoside transmembrane transporter activity (GO:0005337)			breast(1)|kidney(2)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	10					Didanosine(DB00900)|Gemcitabine(DB00441)|Mercaptopurine(DB01033)|Zalcitabine(DB00943)|Zidovudine(DB00495)	AGTAGCGGGCAAACTTCTGCA	0.597																																					p.F218F		Atlas-SNP	.											.	SLC29A2	24	.	0			c.T654C						.						122	110	114					11																	66135014		2200	4295	6495	SO:0001819	synonymous_variant	3177	exon7			GCGGGCAAACTTC	X86681	CCDS8137.1, CCDS73326.1	11q13	2013-07-17	2013-07-17		ENSG00000174669	ENSG00000174669		"Solute carriers"	11004	protein-coding gene	gene with protein product		602110	"solute carrier family 29 (nucleoside transporters), member 2"	ENT2, HNP36		9192854, 9478986	Standard	NM_001532		Approved	DER12	uc001oht.3	Q14542	OTTHUMG00000169056	ENST00000357440.2:c.654T>C	chr11.hg19:g.66135014A>G		131.0	0.0		62.0	56.0	NM_001532	B3KPY7|O43530|Q52M84|Q96R00|Q9UPE0	Silent	SNP	ENST00000357440.2	hg19	CCDS8137.1																																																																																			.	.		0.597	SLC29A2-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402093.1	NM_001532		G	66135014	A	G	66135014	2	3	345	1	0	0	0	0	0	0	0	1	14550	127	5	2		2	SLC29A2	11	66135014	Silent	SNP	A	TCGA-UB-A7MC-01A-11D-A33Q-10		66135014	68871502	34	48812										
SLCO1C1	53919	hgsc.bcm.edu	37	chr12	20858984	20858984	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	tcatgggagttggaacactgCtcattgcaatgcctcagttc	10	10	3	0			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr12:20858984C>T	ENST00000266509.2	+	4	741	c.373C>T	c.(373-375)Ctc>Ttc	p.L125F	SLCO1C1_ENST00000381552.1_Missense_Mutation_p.L125F|SLCO1C1_ENST00000545604.1_Missense_Mutation_p.L125F|SLCO1C1_ENST00000545102.1_Missense_Mutation_p.L7F|SLCO1C1_ENST00000540354.1_Missense_Mutation_p.L125F	NM_017435.4	NP_059131.1	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family, member 1C1	125					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			NS(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	60	Esophageal squamous(101;0.149)				Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Meclofenamic acid(DB00939)|Methotrexate(DB00563)|Ouabain(DB01092)|Phenytoin(DB00252)|Probenecid(DB01032)	TGGAACACTGCTCATTGCAAT	0.393																																					p.L125F		Atlas-SNP	.											.	SLCO1C1	216	.	0			c.C373T						.						210	207	208					12																	20858984		2203	4300	6503	SO:0001583	missense	53919	exon4			ACACTGCTCATTG	AF260704	CCDS8683.1, CCDS53757.1, CCDS53758.1, CCDS53759.1	12p12.2	2013-05-22	2003-11-25	2003-11-26	ENSG00000139155	ENSG00000139155		"Solute carriers"	13819	protein-coding gene	gene with protein product		613389	"solute carrier family 21 (organic anion transporter), member 14"	SLC21A14			Standard	NM_017435		Approved	OATP-F, OATP1C1, OATP1	uc010sii.2	Q9NYB5	OTTHUMG00000168966	ENST00000266509.2:c.373C>T	chr12.hg19:g.20858984C>T	ENSP00000266509:p.Leu125Phe	57.0	0.0		89.0	19.0	NM_017435	B7Z251|B7Z3Q3|B7Z8P1|F5GZD6|Q5JPA4	Missense_Mutation	SNP	ENST00000266509.2	hg19	CCDS8683.1	.	.	.	.	.	.	.	.	.	.	C	18.19	3.569373	0.65765	.	.	ENSG00000139155	ENST00000545604;ENST00000540354;ENST00000266509;ENST00000381552;ENST00000545102	T;T;T;T;T	0.50813	0.73;0.73;0.73;0.73;0.73	5.11	3.26	0.37387	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.167532	0.39985	N	0.001215	T	0.64057	0.2564	M	0.87097	2.86	0.44402	D	0.99731	P;B;P;B	0.48764	0.915;0.434;0.866;0.434	P;P;P;P	0.53549	0.519;0.62;0.729;0.539	T	0.69308	-0.5179	10	0.66056	D	0.02	.	11.75	0.51843	0.0:0.8612:0.0:0.1388	.	7;125;125;125	F5GZD6;B7Z3Q3;Q5JPA4;Q9NYB5	.;.;.;SO1C1_HUMAN	F	125;125;125;125;7	ENSP00000444149:L125F;ENSP00000438665:L125F;ENSP00000266509:L125F;ENSP00000370964:L125F;ENSP00000444527:L7F	ENSP00000266509:L125F	L	+	1	0	SLCO1C1	20750251	0.191000	0.23288	0.928000	0.36995	0.949000	0.60115	0.045000	0.14013	0.714000	0.32081	0.655000	0.94253	CTC	.	.		0.393	SLCO1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401765.1	NM_017435		T	20858984	C	T	20858984	3	4	345	1	0	0	0	0	1	0	0	0	14740	797	28	3	383	3	SLCO1C1	12	20858984	Missense_Mutation	SNP	C	TCGA-UB-A7MC-01A-11D-A33Q-10		20858984	112992911	35	48813										
SMUG1	23583	hgsc.bcm.edu	37	chr12	54576393	54576393	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	cagtcccggaccatgcttacTtccccaaagggcacctgtga	9	15	0	1			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr12:54576393T>G	ENST00000508394.2	-	3	362	c.300A>C	c.(298-300)gaA>gaC	p.E100D	SMUG1_ENST00000506595.1_Missense_Mutation_p.E100D|SMUG1_ENST00000243112.5_Missense_Mutation_p.E100D|SMUG1_ENST00000514196.1_Missense_Mutation_p.E100D|SMUG1_ENST00000513838.1_Missense_Mutation_p.E100D|SMUG1_ENST00000514685.1_Missense_Mutation_p.E100D|SMUG1_ENST00000337581.3_Missense_Mutation_p.E100D|SMUG1_ENST00000505662.1_5'UTR|SMUG1_ENST00000505128.1_3'UTR|SMUG1_ENST00000401977.2_Missense_Mutation_p.E100D	NM_001243787.1|NM_001243788.1|NM_014311.2	NP_001230716.1|NP_001230717.1|NP_055126.1	Q53HV7	SMUG1_HUMAN	single-strand-selective monofunctional uracil-DNA glycosylase 1	100				Missing (in Ref. 3; BAC03670). {ECO:0000305}.	base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depyrimidination (GO:0045008)|DNA repair (GO:0006281)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA N-glycosylase activity (GO:0019104)|oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity (GO:0000703)|single-strand selective uracil DNA N-glycosylase activity (GO:0017065)|uracil DNA N-glycosylase activity (GO:0004844)			kidney(1)|large_intestine(4)|lung(1)	6						CCATGCTTACTTCCCCAAAGG	0.567								Base excision repair (BER), DNA glycosylases																													p.E100D		Atlas-SNP	.											.	SMUG1	18	.	0			c.A300C						.						80	84	83					12																	54576393		2203	4300	6503	SO:0001583	missense	23583	exon4			GCTTACTTCCCCA	AF125182	CCDS8874.1, CCDS58239.1	12q13.13	2013-10-28			ENSG00000123415	ENSG00000123415			17148	protein-coding gene	gene with protein product		607753				10074426, 11526119	Standard	NM_014311		Approved	UNG3, FDG, HMUDG	uc009znf.2	Q53HV7	OTTHUMG00000160068	ENST00000508394.2:c.300A>C	chr12.hg19:g.54576393T>G	ENSP00000424191:p.Glu100Asp	74.0	0.0		73.0	20.0	NM_001243790	A8K2K9|O95862|Q0D2M0|Q8NB71|Q9BWC8	Missense_Mutation	SNP	ENST00000508394.2	hg19	CCDS8874.1	.	.	.	.	.	.	.	.	.	.	T	9.903	1.207332	0.22205	.	.	ENSG00000123415	ENST00000506595;ENST00000514685;ENST00000337581;ENST00000508394;ENST00000513838;ENST00000243112;ENST00000401977;ENST00000514196;ENST00000504338;ENST00000507904	T;T;T;T;T;T;T;T;T;T	0.54279	0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58	4.13	2.62	0.31277	Uracil-DNA glycosylase-like (3);	0.000000	0.85682	D	0.000000	T	0.54127	0.1839	L	0.37897	1.145	0.80722	D	1	B;D	0.76494	0.195;0.999	B;D	0.66716	0.03;0.946	T	0.49523	-0.8931	10	0.35671	T	0.21	.	5.9245	0.19101	0.0:0.274:0.0:0.726	.	100;100	Q53HV7;Q53HV7-2	SMUG1_HUMAN;.	D	100	ENSP00000421206:E100D;ENSP00000421139:E100D;ENSP00000338606:E100D;ENSP00000424191:E100D;ENSP00000423629:E100D;ENSP00000243112:E100D;ENSP00000384828:E100D;ENSP00000425974:E100D;ENSP00000423083:E100D;ENSP00000423457:E100D	ENSP00000243112:E100D	E	-	3	2	SMUG1	52862660	1.000000	0.71417	1.000000	0.80357	0.792000	0.44763	1.483000	0.35497	0.801000	0.34066	0.460000	0.39030	GAA	.	.		0.567	SMUG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359074.3	NM_014311		G	54576393	T	G	54576393	3	3	345	1	0	0	0	0	1	0	0	0	14833	1606	56	5	516	5	SMUG1	12	54576393	Missense_Mutation	SNP	T	TCGA-UB-A7MC-01A-11D-A33Q-10	33717409	54576393	79275502	36	48814										
CCDC41	10154	hgsc.bcm.edu	37	chr12	94703723	94703723	+	IGR	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	aggaggaaatggtagttccaTgcttggaaccatggctgatg	14	6	0	1			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr12:94703723T>A	ENST00000258526.4	+	0	7346				CCDC41_ENST00000339839.5_Missense_Mutation_p.M658L|CCDC41_ENST00000397809.5_Missense_Mutation_p.M658L	NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(12)|lung(30)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						GGTAGTTCCATGCTTGGAACC	0.363																																					p.M658L		Atlas-SNP	.											.	CCDC41	59	.	0			c.A1972T						.						182	169	173					12																	94703723		1879	4107	5986	SO:0001628	intergenic_variant	51134	exon16			GTTCCATGCTTGG	AF030339	CCDS9049.1	12q23	2009-04-17				ENSG00000136040		"CD molecules", "Plexins"	9106	protein-coding gene	gene with protein product		604259					Standard	NR_037687		Approved	VESPR, CD232	uc001tdc.3	O60486	OTTHUMG00000170235		chr12.hg19:g.94703723T>A		170.0	0.0		147.0	57.0	NM_016122	Q59H25	Missense_Mutation	SNP	ENST00000258526.4	hg19	CCDS9049.1	.	.	.	.	.	.	.	.	.	.	T	5.027	0.190655	0.09547	.	.	ENSG00000173588	ENST00000552632;ENST00000339839;ENST00000397809	T;T	0.40756	1.02;1.02	5.94	-2.11	0.07187	.	.	.	.	.	T	0.19886	0.0478	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.23476	-1.0187	9	0.25106	T	0.35	3.714	9.2095	0.37309	0.0:0.5051:0.3138:0.1811	.	650	Q9Y592	CCD41_HUMAN	L	122;658;658	ENSP00000344655:M658L;ENSP00000380911:M658L	ENSP00000344655:M658L	M	-	1	0	CCDC41	93227854	0.089000	0.21612	0.038000	0.18304	0.002000	0.02628	-0.071000	0.11505	-0.295000	0.08960	-0.472000	0.04984	ATG	.	.		0.363	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2			A	94703723	T	A	94703723	1	1	345	0	1	0	0	0	0	0	0	0	2815	1464	51	4		4	CCDC41	12	94703723	IGR	SNP	T	TCGA-UB-A7MC-01A-11D-A33Q-10	40127330	94703723	39148172	37	48815										
SLC5A8	160728	hgsc.bcm.edu	37	chr12	101561932	101561932	+	Frame_Shift_Del	DEL	C	C	-													0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	acaggcccataagtggtccaCcaaccataccaaatacgctg							TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr12:101561932delC	ENST00000536262.2	-	11	1820	c.1262delG	c.(1261-1263)ggtfs	p.G422fs		NM_145913.3	NP_666018.3			solute carrier family 5 (sodium/monocarboxylate cotransporter), member 8											breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(29)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						AAGTGGTCCACCAACCATACC	0.378																																					p.G421fs	GBM(60;420 1056 13605 22380 47675)	Atlas-Indel,Pindel	.											.	SLC5A8	102	.	0			c.1263delT						.						93	78	83					12																	101561932		2203	4300	6503	SO:0001589	frameshift_variant	160728	exon11			.	AY081220	CCDS9080.1	12q23.1	2013-07-19	2013-07-19		ENSG00000256870	ENSG00000256870		"Solute carriers"	19119	protein-coding gene	gene with protein product		608044	"solute carrier family 5 (iodide transporter), member 8"			12107270, 12829793	Standard	NM_145913		Approved	AIT	uc001thz.4	Q8N695	OTTHUMG00000170499	ENST00000536262.2:c.1262delG	chr12.hg19:g.101561932delC	ENSP00000445340:p.Gly422fs	232.0	0.0		204.0	59.0	NM_145913		Frame_Shift_Del	DEL	ENST00000536262.2	hg19	CCDS9080.1																																																																																			.	.		0.378	SLC5A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409401.1	NM_145913		-	101561932	C	-	101561932	7	5	345	1	0	1	0	1	0	0	0	0	14686	507	18	0	590	0	SLC5A8	12	101561932	Frame_Shift_Del	DEL	C	TCGA-UB-A7MC-01A-11D-A33Q-10	6858209	101561932	32289963	38	48816										
CCDC53	51019	hgsc.bcm.edu	37	chr12	102439885	102439885	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	ttgttggatacgaagtgaaaGgtctgccagtttctgtaaaa	11	5	2	1			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr12:102439885G>C	ENST00000240079.6	-	3	324	c.163C>G	c.(163-165)Ctt>Gtt	p.L55V	CCDC53_ENST00000539515.1_5'UTR|CCDC53_ENST00000545679.1_Missense_Mutation_p.L55V	NM_016053.2	NP_057137.1	Q9Y3C0	CCD53_HUMAN	coiled-coil domain containing 53	55						actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|WASH complex (GO:0071203)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4						CGAAGTGAAAGGTCTGCCAGT	0.279																																					p.L55V		Atlas-SNP	.											.	CCDC53	14	.	0			c.C163G						.						46	42	43					12																	102439885		1796	4062	5858	SO:0001583	missense	51019	exon3			GTGAAAGGTCTGC	AF151874	CCDS44959.1, CCDS73512.1	12q23.3	2014-05-09			ENSG00000120860	ENSG00000120860			24256	protein-coding gene	gene with protein product						10810093, 20498093	Standard	XM_005268939		Approved	CGI-116	uc010svw.2	Q9Y3C0	OTTHUMG00000168187	ENST00000240079.6:c.163C>G	chr12.hg19:g.102439885G>C	ENSP00000240079:p.Leu55Val	248.0	0.0		194.0	108.0	NM_016053	B2RC74|Q53FF0|Q6IAI4|Q96QK0	Missense_Mutation	SNP	ENST00000240079.6	hg19	CCDS44959.1	.	.	.	.	.	.	.	.	.	.	G	10.76	1.441377	0.25900	.	.	ENSG00000120860	ENST00000240079;ENST00000545679;ENST00000542923	.	.	.	5.37	5.37	0.77165	.	0.107337	0.64402	D	0.000006	T	0.43122	0.1233	N	0.25485	0.75	0.39799	D	0.97254	P;P	0.42827	0.566;0.791	B;B	0.43155	0.212;0.41	T	0.25606	-1.0127	9	0.14252	T	0.57	-21.5529	16.3866	0.83507	0.0:0.0:1.0:0.0	.	55;55	F5GZ97;Q9Y3C0	.;CCD53_HUMAN	V	55;55;5	.	ENSP00000240079:L55V	L	-	1	0	CCDC53	100964015	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	3.617000	0.54181	2.659000	0.90383	0.655000	0.94253	CTT	.	.		0.279	CCDC53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398685.1	NM_016053		C	102439885	G	C	102439885	3	2	345	1	0	0	0	0	1	0	0	0	2825	1000	35	4	372	4	CCDC53	12	102439885	Missense_Mutation	SNP	G	TCGA-UB-A7MC-01A-11D-A33Q-10	877953	102439885	31412010	39	48817										
STAB2	55576	hgsc.bcm.edu	37	chr12	104048376	104048376	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	ccatggaggcaaaaagaaggTaaaaattatacaaggggaca	11	5	0	1			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr12:104048376T>C	ENST00000388887.2	+	13	1655	c.1451T>C	c.(1450-1452)gTa>gCa	p.V484A	RP11-341G23.2_ENST00000551905.1_RNA	NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						AAAAAGAAGGTAAAAATTATA	0.398																																					p.V484A		Atlas-SNP	.											.	STAB2	370	.	0			c.T1451C						.						71	69	69					12																	104048376		2203	4300	6503	SO:0001583	missense	55576	exon13			AGAAGGTAAAAAT	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"hyaluronic acid receptor for endocytosis"	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.1451T>C	chr12.hg19:g.104048376T>C	ENSP00000373539:p.Val484Ala	158.0	0.0		140.0	41.0	NM_017564		Missense_Mutation	SNP	ENST00000388887.2	hg19	CCDS31888.1	.	.	.	.	.	.	.	.	.	.	T	6.830	0.522352	0.13066	.	.	ENSG00000136011	ENST00000388887	D	0.87571	-2.27	5.8	3.52	0.40303	FAS1 domain (5);	0.269718	0.34531	N	0.003884	T	0.74160	0.3680	N	0.16066	0.365	0.35383	D	0.790061	P	0.38617	0.64	B	0.40602	0.334	T	0.72561	-0.4256	10	0.16896	T	0.51	.	7.1107	0.25388	0.0:0.09:0.3474:0.5626	.	484	Q8WWQ8	STAB2_HUMAN	A	484	ENSP00000373539:V484A	ENSP00000373539:V484A	V	+	2	0	STAB2	102572506	1.000000	0.71417	0.951000	0.38953	0.039000	0.13416	1.848000	0.39309	1.027000	0.39758	0.460000	0.39030	GTA	.	.		0.398	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			C	104048376	T	C	104048376	3	2	345	1	0	0	0	0	1	0	0	0	15253	1638	57	2	1501	2	STAB2	12	104048376	Missense_Mutation	SNP	T	TCGA-UB-A7MC-01A-11D-A33Q-10	1608491	104048376	29803519	40	48818										
TCHP	84260	hgsc.bcm.edu	37	chr12	110353220	110353220	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	gcactcaggttgcagagcgcCggctgcaggcatgggaagca	16	11	1	1			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr12:110353220C>T	ENST00000312777.5	+	12	1547	c.1333C>T	c.(1333-1335)Cgg>Tgg	p.R445W	TCHP_ENST00000405876.4_Missense_Mutation_p.R445W	NM_032300.4	NP_115676.1			trichoplein, keratin filament binding											NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|skin(2)	22						TGCAGAGCGCCGGCTGCAGGC	0.652																																					p.R445W		Atlas-SNP	.											.	TCHP	45	.	0			c.C1333T						.						52	54	53					12																	110353220		2203	4300	6503	SO:0001583	missense	84260	exon12			GAGCGCCGGCTGC	AK092736	CCDS9137.1	12q24.11	2011-08-25	2006-01-27			ENSG00000139437			28135	protein-coding gene	gene with protein product	"mitostatin"	612654				15731013, 20930847	Standard	NM_032300		Approved	MGC10854, TpMs	uc001tpn.3	Q9BT92		ENST00000312777.5:c.1333C>T	chr12.hg19:g.110353220C>T	ENSP00000324404:p.Arg445Trp	110.0	0.0		98.0	4.0	NM_001143852		Missense_Mutation	SNP	ENST00000312777.5	hg19	CCDS9137.1	.	.	.	.	.	.	.	.	.	.	C	17.20	3.329774	0.60743	.	.	ENSG00000139437	ENST00000405876;ENST00000312777;ENST00000551627	T;T	0.11930	2.73;2.73	5.84	3.87	0.44632	.	0.692081	0.14740	N	0.301220	T	0.12135	0.0295	L	0.38175	1.15	0.24743	N	0.993022	D	0.60575	0.988	P	0.44394	0.448	T	0.13710	-1.0499	10	0.87932	D	0	-20.3914	6.999	0.24799	0.1716:0.7405:0.0:0.0878	.	445	Q9BT92	TCHP_HUMAN	W	445;445;89	ENSP00000384520:R445W;ENSP00000324404:R445W	ENSP00000324404:R445W	R	+	1	2	TCHP	108837603	0.042000	0.20092	1.000000	0.80357	0.391000	0.30476	1.470000	0.35354	2.763000	0.94921	0.650000	0.86243	CGG	.	.		0.652	TCHP-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403289.1	NM_032300		T	110353220	C	T	110353220	3	4	345	1	0	0	0	0	1	0	0	0	15717	643	23	1	1375	1	TCHP	12	110353220	Missense_Mutation	SNP	C	TCGA-UB-A7MC-01A-11D-A33Q-10	6304844	110353220	23498675	41	48819										
STX2	2054	hgsc.bcm.edu	37	chr12	131285985	131285985	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	aagtgaagatggatggcttcCcgctctccagcatctcttct	9	12	3	2			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr12:131285985C>G	ENST00000392373.2	-	7	606	c.512G>C	c.(511-513)gGg>gCg	p.G171A	STX2_ENST00000261653.6_Missense_Mutation_p.G171A	NM_194356.2	NP_919337.1	P32856	STX2_HUMAN	syntaxin 2	171					acrosome reaction (GO:0007340)|cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|intracellular protein transport (GO:0006886)|organ morphogenesis (GO:0009887)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|signal transduction (GO:0007165)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)	calcium-dependent protein binding (GO:0048306)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)	16	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.79e-06)|all cancers(50;5.27e-05)|Epithelial(86;5.29e-05)		GGATGGCTTCCCGCTCTCCAG	0.522																																					p.G171A		Atlas-SNP	.											.	STX2	66	.	0			c.G512C						.						73	74	74					12																	131285985		2203	4300	6503	SO:0001583	missense	2054	exon7			GGCTTCCCGCTCT	D14582	CCDS9269.1, CCDS9270.1	12q24	2008-02-05	2006-04-25	2006-04-25	ENSG00000111450	ENSG00000111450			3403	protein-coding gene	gene with protein product		132350	"epimorphin"	STX2B, STX2C, STX2A, EPIM		8938452, 15943887	Standard	NM_001980		Approved	EPM	uc001uio.4	P32856	OTTHUMG00000168365	ENST00000392373.2:c.512G>C	chr12.hg19:g.131285985C>G	ENSP00000376178:p.Gly171Ala	165.0	0.0		150.0	12.0	NM_194356	Q86VW8	Missense_Mutation	SNP	ENST00000392373.2	hg19	CCDS9270.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.655577	0.88056	.	.	ENSG00000111450	ENST00000261653;ENST00000392373	T;T	0.27104	1.69;1.69	5.3	5.3	0.74995	t-SNARE (1);	0.000000	0.85682	D	0.000000	T	0.60625	0.2283	M	0.92268	3.29	0.80722	D	1	D;D;D	0.71674	0.997;0.997;0.998	P;P;D	0.65573	0.82;0.82;0.936	T	0.71272	-0.4642	10	0.66056	D	0.02	-27.634	17.9754	0.89126	0.0:1.0:0.0:0.0	.	171;171;171	P32856-3;P32856-2;P32856	.;.;STX2_HUMAN	A	171	ENSP00000261653:G171A;ENSP00000376178:G171A	ENSP00000261653:G171A	G	-	2	0	STX2	129851938	0.999000	0.42202	0.965000	0.40720	0.810000	0.45777	4.154000	0.58125	2.478000	0.83669	0.650000	0.86243	GGG	.	.		0.522	STX2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399455.2	NM_194356		G	131285985	C	G	131285985	3	3	345	1	0	0	0	0	1	0	0	0	15360	623	22	4	452	4	STX2	12	131285985	Missense_Mutation	SNP	C	TCGA-UB-A7MC-01A-11D-A33Q-10	20932765	131285985	2565910	42	48820										
PCCA	5095	hgsc.bcm.edu	37	chr13	100925472	100925472	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	tttttttggatgcggagactCgaagagcgatgggagaacaa	14	5	0	3	rs138149179		TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr13:100925472C>A	ENST00000376285.1	+	12	975	c.937C>A	c.(937-939)Cga>Aga	p.R313R	PCCA_ENST00000376279.3_Silent_p.R313R|PCCA_ENST00000376286.4_Silent_p.R287R	NM_000282.3	NP_000273.2	P05165	PCCA_HUMAN	propionyl CoA carboxylase, alpha polypeptide	313	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.|Biotin carboxylation.				biotin metabolic process (GO:0006768)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|propionyl-CoA carboxylase activity (GO:0004658)			breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(8)|prostate(1)|skin(2)	26	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)	TGCGGAGACTCGAAGAGCGAT	0.378																																					p.R313R		Atlas-SNP	.											.	PCCA	59	.	0			c.C937A	GRCh37	CM991019	PCCA	M	rs138149179	.						80	83	82					13																	100925472		2203	4300	6503	SO:0001819	synonymous_variant	5095	exon12			GAGACTCGAAGAG	X14608	CCDS9496.2, CCDS45065.1, CCDS53878.1	13q32	2011-01-14	2010-04-30		ENSG00000175198	ENSG00000175198	6.4.1.3		8653	protein-coding gene	gene with protein product		232000	"propionyl Coenzyme A carboxylase, alpha polypeptide"			1427880	Standard	NM_000282		Approved		uc001voo.3	P05165	OTTHUMG00000017284	ENST00000376285.1:c.937C>A	chr13.hg19:g.100925472C>A		88.0	0.0		179.0	57.0	NM_001178004	B4DKY8|B4DPF9|C9JPQ8|Q15979|Q8WXQ7	Silent	SNP	ENST00000376285.1	hg19	CCDS9496.2																																																																																			.	C|1.000;T|0.000		0.378	PCCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045627.2			A	100925472	C	A	100925472	2	1	345	1	0	0	0	0	0	0	0	1	11513	876	31	1		1	PCCA	13	100925472	Silent	SNP	C	TCGA-UB-A7MC-01A-11D-A33Q-10		100925472	14244406	43	48821										
MYO16	23026	hgsc.bcm.edu	37	chr13	109707405	109707405	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	ttattacagttattaaaaaaGaaaggaacttctacatttct	4	5	2	1			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr13:109707405G>A	ENST00000357550.2	+	25	3035	c.2994G>A	c.(2992-2994)aaG>aaA	p.K998K	MYO16_ENST00000356711.2_Silent_p.K998K|MYO16_ENST00000457511.2_Silent_p.K510K	NM_001198950.1	NP_001185879.1			myosin XVI											NS(3)|breast(4)|central_nervous_system(2)|endometrium(10)|kidney(8)|large_intestine(27)|lung(51)|ovary(9)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	121	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			TATTAAAAAAGAAAGGAACTT	0.378																																					p.K1020K		Atlas-SNP	.											.	MYO16	285	.	0			c.G3060A						.						45	46	46					13																	109707405		2203	4299	6502	SO:0001819	synonymous_variant	23026	exon26			AAAAAAGAAAGGA		CCDS32008.1, CCDS73598.1	13q33.3	2014-06-12			ENSG00000041515	ENSG00000041515		"Myosins / Myosin superfamily : Class XVI", "Ankyrin repeat domain containing"	29822	protein-coding gene	gene with protein product	"neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 3", "protein phosphatase 1, regulatory subunit 107"	615479				11588169, 17029291, 21946561	Standard	NM_001198950		Approved	MYR8, KIAA0865, Myo16b, NYAP3, PPP1R107	uc001vqt.1	Q9Y6X6	OTTHUMG00000017333	ENST00000357550.2:c.2994G>A	chr13.hg19:g.109707405G>A		336.0	0.0		570.0	366.0	NM_001198950		Silent	SNP	ENST00000357550.2	hg19	CCDS32008.1																																																																																			.	.		0.378	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011		A	109707405	G	A	109707405	2	1	345	1	0	0	0	0	0	0	0	1	10073	933	33	3		3	MYO16	13	109707405	Silent	SNP	G	TCGA-UB-A7MC-01A-11D-A33Q-10	8781933	109707405	5462473	44	48822										
RASA3	22821	hgsc.bcm.edu	37	chr13	114751254	114751254	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	ccgggccgtcatacacagatTtgctcccacaggcctctgtg	10	15	2	1			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr13:114751254T>G	ENST00000334062.7	-	23	2382	c.2261A>C	c.(2260-2262)aAa>aCa	p.K754T	RASA3_ENST00000389544.4_Missense_Mutation_p.K722T	NM_007368.2	NP_031394.2	Q14644	RASA3_HUMAN	RAS p21 protein activator 3	754					calcium ion transmembrane transport (GO:0070588)|intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	calcium-release channel activity (GO:0015278)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|Ras GTPase activator activity (GO:0005099)	p.K754T(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(20)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	47	Lung NSC(43;0.00814)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.016)|all_epithelial(44;0.00577)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.188)	BRCA - Breast invasive adenocarcinoma(86;0.128)			ATACACAGATTTGCTCCCACA	0.642																																					p.K754T		Atlas-SNP	.											RASA3,NS,carcinoma,0,1	RASA3	83	.	1	Substitution - Missense(1)	ovary(1)	c.A2261C						.						78	72	74					13																	114751254		2203	4300	6503	SO:0001583	missense	22821	exon23			ACAGATTTGCTCC		CCDS32016.1	13q34	2013-01-10			ENSG00000185989	ENSG00000185989		"Pleckstrin homology (PH) domain containing"	20331	protein-coding gene	gene with protein product		605182				7637787, 9382842	Standard	NM_007368		Approved	GAP1IP4BP, GAPIII	uc001vui.3	Q14644	OTTHUMG00000017399	ENST00000334062.7:c.2261A>C	chr13.hg19:g.114751254T>G	ENSP00000335029:p.Lys754Thr	117.0	0.0		149.0	89.0	NM_007368	A6NL15|F8W6X8|Q8IUY2	Missense_Mutation	SNP	ENST00000334062.7	hg19	CCDS32016.1	.	.	.	.	.	.	.	.	.	.	T	5.198	0.222060	0.09863	.	.	ENSG00000185989	ENST00000334062;ENST00000389544	D;D	0.86164	-1.97;-2.08	4.78	2.5	0.30297	.	0.097591	0.64402	D	0.000002	T	0.82185	0.4982	L	0.51422	1.61	0.80722	D	1	B	0.14438	0.01	B	0.31495	0.131	T	0.70174	-0.4944	9	.	.	.	.	6.9812	0.24704	0.0:0.1998:0.0:0.8002	.	754	Q14644	RASA3_HUMAN	T	754;722	ENSP00000335029:K754T;ENSP00000374195:K722T	.	K	-	2	0	RASA3	113769356	1.000000	0.71417	0.973000	0.42090	0.311000	0.27955	2.172000	0.42463	0.276000	0.22118	-0.415000	0.06103	AAA	.	.		0.642	RASA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045957.2	NM_007368		G	114751254	T	G	114751254	3	3	345	1	0	0	0	0	1	0	0	0	13077	1841	64	5	251	5	RASA3	13	114751254	Missense_Mutation	SNP	T	TCGA-UB-A7MC-01A-11D-A33Q-10	5043849	114751254	418624	45	48823										
OR4M1	441670	hgsc.bcm.edu	37	chr14	20249255	20249255	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	atgtttgggccatccatctaCatttatgctcgcccatttga	7	11	1	1			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr14:20249255C>A	ENST00000315957.4	+	1	855	c.774C>A	c.(772-774)taC>taA	p.Y258*		NM_001005500.1	NP_001005500.1	Q8NGD0	OR4M1_HUMAN	olfactory receptor, family 4, subfamily M, member 1	258						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(32)|prostate(1)|skin(2)	42	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		CATCCATCTACATTTATGCTC	0.408																																					p.Y258X		Atlas-SNP	.											.	OR4M1	104	.	0			c.C774A						.						223	210	214					14																	20249255		2203	4300	6503	SO:0001587	stop_gained	441670	exon1			CATCTACATTTAT		CCDS32021.1	14q11.2	2013-09-23			ENSG00000176299	ENSG00000176299		"GPCR / Class A : Olfactory receptors"	14735	protein-coding gene	gene with protein product							Standard	NM_001005500		Approved		uc010tku.2	Q8NGD0	OTTHUMG00000170599	ENST00000315957.4:c.774C>A	chr14.hg19:g.20249255C>A	ENSP00000319654:p.Tyr258*	355.0	0.0		368.0	82.0	NM_001005500	B9EH18|Q6IFA3	Nonsense_Mutation	SNP	ENST00000315957.4	hg19	CCDS32021.1	.	.	.	.	.	.	.	.	.	.	.	24.2	4.503729	0.85176	.	.	ENSG00000176299	ENST00000315957	.	.	.	4.42	1.6	0.23607	.	0.000000	0.45126	D	0.000398	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.26408	T	0.33	-12.9251	7.8655	0.29535	0.0:0.7092:0.0:0.2908	.	.	.	.	X	258	.	ENSP00000319654:Y258X	Y	+	3	2	OR4M1	19319095	0.595000	0.26857	1.000000	0.80357	0.979000	0.70002	0.075000	0.14686	0.616000	0.30141	0.506000	0.49869	TAC	.	.		0.408	OR4M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409770.1			A	20249255	C	A	20249255	4	1	345	1	0	0	0	0	0	1	0	0	11084	489	17	3	776	3	OR4M1	14	20249255	Nonsense_Mutation	SNP	C	TCGA-UB-A7MC-01A-11D-A33Q-10		20249255	87100285	46	48824										
C15orf24	56851	hgsc.bcm.edu	37	chr15	34376643	34376643	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	atgaactcagaaacatcaggCaactcatggttggaattcag	9	8	4	2			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr15:34376643C>T	ENST00000256545.4	-	5	729	c.621G>A	c.(619-621)ttG>ttA	p.L207L		NM_020154.2	NP_064539.1	Q9NPA0	EMC7_HUMAN	ER membrane protein complex subunit 7	207						ER membrane protein complex (GO:0072546)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)										AAACATCAGGCAACTCATGGT	0.428																																					p.L207L		Atlas-SNP	.											.	.	.	.	0			c.G621A						.						155	134	141					15																	34376643		2201	4298	6499	SO:0001819	synonymous_variant	56851	exon5			ATCAGGCAACTCA	AJ245874	CCDS10032.1	15q14	2012-05-30	2012-05-30	2012-05-30	ENSG00000134153	ENSG00000134153			24301	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 24"	C15orf24		10873569, 22119785	Standard	NM_020154		Approved	C11orf3	uc001zhm.3	Q9NPA0	OTTHUMG00000129367	ENST00000256545.4:c.621G>A	chr15.hg19:g.34376643C>T		154.0	0.0		151.0	44.0	NM_020154	B2RC00|Q96ED5	Silent	SNP	ENST00000256545.4	hg19	CCDS10032.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.298|8.298	0.819278|0.819278	0.16607|0.16607	.|.	.|.	ENSG00000134153|ENSG00000134153	ENST00000527822|ENST00000528949	.|.	.|.	.|.	5.19|5.19	4.27|4.27	0.50696|0.50696	.|.	.|.	.|.	.|.	.|.	T|T	0.69504|0.69504	0.3118|0.3118	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.68953|0.68953	-0.5273|-0.5273	4|4	.|.	.|.	.|.	-13.7048|-13.7048	13.7651|13.7651	0.62990|0.62990	0.0:0.926:0.0:0.074|0.0:0.926:0.0:0.074	.|.	.|.	.|.	.|.	T|Y	157|143	.|.	.|.	A|C	-|-	1|2	0|0	C15orf24|C15orf24	32163935|32163935	0.999000|0.999000	0.42202|0.42202	0.997000|0.997000	0.53966|0.53966	0.984000|0.984000	0.73092|0.73092	0.665000|0.665000	0.25083|0.25083	1.410000|1.410000	0.46936|0.46936	0.557000|0.557000	0.71058|0.71058	GCC|TGC	.	.		0.428	EMC7-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251519.1	NM_020154		T	34376643	C	T	34376643	2	4	345	1	0	0	0	0	0	0	0	1	1788	709	25	3		3	C15orf24	15	34376643	Silent	SNP	C	TCGA-UB-A7MC-01A-11D-A33Q-10		34376643	68154749	47	48825										
PLA2G4D	283748	hgsc.bcm.edu	37	chr15	42378519	42378519	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	tccgtgactgagtcctcatcAtagatgctaagctccagaac	8	12	2	4			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr15:42378519A>G	ENST00000290472.3	-	4	373	c.279T>C	c.(277-279)taT>taC	p.Y93Y		NM_178034.3	NP_828848.3	Q86XP0	PA24D_HUMAN	phospholipase A2, group IVD (cytosolic)	93	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(7)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(109;6.37e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.019)|Ovarian(310;0.143)|Colorectal(260;0.245)		OV - Ovarian serous cystadenocarcinoma(18;4.9e-17)|GBM - Glioblastoma multiforme(94;1.02e-06)		AGTCCTCATCATAGATGCTAA	0.488																																					p.Y93Y		Atlas-SNP	.											.	PLA2G4D	72	.	0			c.T279C						.						118	101	107					15																	42378519		2203	4299	6502	SO:0001819	synonymous_variant	283748	exon4			CTCATCATAGATG	AB090876	CCDS32203.1	15q14	2008-09-19				ENSG00000159337	3.1.1.4		30038	protein-coding gene	gene with protein product		612864				14709560	Standard	NM_178034		Approved	cPLA2delta	uc001zox.3	Q86XP0		ENST00000290472.3:c.279T>C	chr15.hg19:g.42378519A>G		65.0	0.0		50.0	30.0	NM_178034	Q8N176	Silent	SNP	ENST00000290472.3	hg19	CCDS32203.1																																																																																			.	.		0.488	PLA2G4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419317.1	NM_178034		G	42378519	A	G	42378519	2	3	345	1	0	0	0	0	0	0	0	1	12013	224	8	2		2	PLA2G4D	15	42378519	Silent	SNP	A	TCGA-UB-A7MC-01A-11D-A33Q-10	8001876	42378519	60152873	48	48826										
ISG20	3669	hgsc.bcm.edu	37	chr15	89182609	89182609	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	ccaaggaacatggctgggagCcgtgaggtggtggccatgga	18	8	0	1			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr15:89182609C>T	ENST00000306072.5	+	2	370	c.12C>T	c.(10-12)agC>agT	p.S4S	ISG20_ENST00000379224.5_Silent_p.S4S|ISG20_ENST00000560741.1_Silent_p.S4S	NM_002201.4	NP_002192.2	Q96AZ6	ISG20_HUMAN	interferon stimulated exonuclease gene 20kDa	4					cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|DNA catabolic process, exonucleolytic (GO:0000738)|negative regulation of viral genome replication (GO:0045071)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)|type I interferon signaling pathway (GO:0060337)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	3'-5'-exoribonuclease activity (GO:0000175)|exonuclease activity (GO:0004527)|exoribonuclease II activity (GO:0008859)|metal ion binding (GO:0046872)|single-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008310)|U1 snRNA binding (GO:0030619)|U2 snRNA binding (GO:0030620)|U3 snoRNA binding (GO:0034511)			large_intestine(1)|lung(3)|prostate(1)	5	Lung NSC(78;0.0554)|all_lung(78;0.103)		BRCA - Breast invasive adenocarcinoma(143;0.12)			TGGCTGGGAGCCGTGAGGTGG	0.662											OREG0023441	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S4S		Atlas-SNP	.											.	ISG20	17	.	0			c.C12T						.						26	25	25					15																	89182609		2199	4298	6497	SO:0001819	synonymous_variant	3669	exon2			TGGGAGCCGTGAG	X89773	CCDS10345.1	15q26	2006-02-22	2002-08-29		ENSG00000172183	ENSG00000172183			6130	protein-coding gene	gene with protein product		604533	"interferon stimulated gene (20kD)"			9235947, 9605874	Standard	NM_002201		Approved	HEM45, CD25	uc002bmv.1	Q96AZ6	OTTHUMG00000148679	ENST00000306072.5:c.12C>T	chr15.hg19:g.89182609C>T		52.0	0.0	1265	41.0	29.0	NM_002201	O00441|O00586	Silent	SNP	ENST00000306072.5	hg19	CCDS10345.1																																																																																			.	.		0.662	ISG20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309069.2	NM_002201		T	89182609	C	T	89182609	2	4	345	1	0	0	0	0	0	0	0	1	7863	738	26	3		3	ISG20	15	89182609	Silent	SNP	C	TCGA-UB-A7MC-01A-11D-A33Q-10	46804090	89182609	13348783	49	48827										
HSD3B7	80270	hgsc.bcm.edu	37	chr16	30997473	30997473	+	Frame_Shift_Del	DEL	A	A	-													0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	atccacacggctgggctggtAgacgtgtttggcagggccag							TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr16:30997473delA	ENST00000297679.5	+	3	363	c.270delA	c.(268-270)gtafs	p.V90fs	AC135048.1_ENST00000602217.1_Frame_Shift_Del_p.Y21fs|HSD3B7_ENST00000262520.6_Frame_Shift_Del_p.V90fs|HSD3B7_ENST00000353250.5_Frame_Shift_Del_p.V90fs	NM_025193.3	NP_079469.2	Q9H2F3	3BHS7_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 7	90					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|cholest-5-ene-3-beta,7-alpha-diol 3-beta-dehydrogenase activity (GO:0047016)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						CTGGGCTGGTAGACGTGTTTG	0.627																																					p.V90fs		Atlas-Indel,Pindel	.											.	HSD3B7	33	.	0			c.269delT						.						65	53	57					16																	30997473		2197	4300	6497	SO:0001589	frameshift_variant	80270	exon3			.	AF277719	CCDS10698.1, CCDS45466.1	16p11.2	2011-09-14			ENSG00000099377	ENSG00000099377	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Extended SDR fold"	18324	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 11E, member 3"	607764				11067870, 19027726	Standard	NM_001142777		Approved	C(27)-3BETA-HSD, SDR11E3	uc002eaf.2	Q9H2F3	OTTHUMG00000132417	ENST00000297679.5:c.270delA	chr16.hg19:g.30997473delA	ENSP00000297679:p.Val90fs	215.0	0.0		160.0	43.0	NM_001142778	Q96M28|Q9BSN9	Frame_Shift_Del	DEL	ENST00000297679.5	hg19	CCDS10698.1																																																																																			.	.		0.627	HSD3B7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255554.2			-	30997473	A	-	30997473	7	5	345	1	0	1	0	1	0	0	0	0	7401	407	15	0	276	0	HSD3B7	16	30997473	Frame_Shift_Del	DEL	A	TCGA-UB-A7MC-01A-11D-A33Q-10		30997473	59357280	50	48828										
ANKRD11	29123	hgsc.bcm.edu	37	chr16	89350329	89350329	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	ccgtctccaagatgagcttgGccacagagtcgctcttcatg	10	13	3	3			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr16:89350329G>A	ENST00000301030.4	-	9	3081	c.2621C>T	c.(2620-2622)gCc>gTc	p.A874V	ANKRD11_ENST00000378330.2_Missense_Mutation_p.A874V	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	874	Lys-rich.				bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		GATGAGCTTGGCCACAGAGTC	0.562																																					p.A874V		Atlas-SNP	.											.	ANKRD11	195	.	0			c.C2621T						.						68	74	72					16																	89350329		2198	4300	6498	SO:0001583	missense	29123	exon9			AGCTTGGCCACAG	AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"Ankyrin repeat domain containing"	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.2621C>T	chr16.hg19:g.89350329G>A	ENSP00000301030:p.Ala874Val	74.0	0.0		81.0	21.0	NM_001256183	Q6NTG1|Q6QMF8	Missense_Mutation	SNP	ENST00000301030.4	hg19	CCDS32513.1	.	.	.	.	.	.	.	.	.	.	G	17.30	3.353671	0.61293	.	.	ENSG00000167522	ENST00000301030;ENST00000378330;ENST00000330736	T;T	0.37235	1.21;1.21	5.51	5.51	0.81932	.	0.074531	0.53938	D	0.000048	T	0.34048	0.0884	L	0.50919	1.6	0.80722	D	1	P;B	0.37731	0.607;0.132	B;B	0.32465	0.146;0.038	T	0.08207	-1.0733	10	0.25751	T	0.34	.	19.4153	0.94694	0.0:0.0:1.0:0.0	.	493;874	Q7Z5E5;Q6UB99	.;ANR11_HUMAN	V	874;874;493	ENSP00000301030:A874V;ENSP00000367581:A874V	ENSP00000301030:A874V	A	-	2	0	ANKRD11	87877830	1.000000	0.71417	1.000000	0.80357	0.733000	0.41908	7.017000	0.76399	2.595000	0.87683	0.561000	0.74099	GCC	.	.		0.562	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		A	89350329	G	A	89350329	3	1	345	1	0	0	0	0	1	0	0	0	639	1203	42	3	5390	3	ANKRD11	16	89350329	Missense_Mutation	SNP	G	TCGA-UB-A7MC-01A-11D-A33Q-10	58352856	89350329	1004424	51	48829										
C16orf55	124045	hgsc.bcm.edu	37	chr16	89724816	89724816	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	gccaagcacccgccgccggcAgcttcgctggaaggtaggag	15	14	0	0			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr16:89724816A>T	ENST00000301031.4	+	2	195	c.195A>T	c.(193-195)gcA>gcT	p.A65A	CHMP1A_ENST00000550102.1_5'Flank|SPATA33_ENST00000579310.1_Silent_p.A66A|CHMP1A_ENST00000397901.3_5'Flank|CHMP1A_ENST00000535997.2_5'Flank|SPATA33_ENST00000568929.1_Silent_p.A35A|CHMP1A_ENST00000547614.1_5'Flank|CHMP1A_ENST00000253475.5_5'Flank	NM_001271908.1|NM_153025.1	NP_001258837.1|NP_694570.1	Q96N06	SPT33_HUMAN	spermatogenesis associated 33	65						cytoplasm (GO:0005737)|nucleus (GO:0005634)											CGCCGCCGGCAGCTTCGCTGG	0.667																																					p.A66A		Atlas-SNP	.											.	C16orf55	6	.	0			c.A198T						.						10	13	12					16																	89724816		2187	4275	6462	SO:0001819	synonymous_variant	124045	exon2			GCCGGCAGCTTCG	AK056168	CCDS10983.1, CCDS62012.1, CCDS73929.1	16q24.3	2013-07-16	2013-07-05	2013-07-05	ENSG00000167523	ENSG00000167523			26463	protein-coding gene	gene with protein product		615409	"chromosome 16 open reading frame 55"	C16orf55		23844118	Standard	NM_153025		Approved	FLJ31606	uc010vpk.2	Q96N06	OTTHUMG00000138048	ENST00000301031.4:c.195A>T	chr16.hg19:g.89724816A>T		72.0	0.0		39.0	24.0	NM_001271910	A8WFL2|B4DZN8	Silent	SNP	ENST00000301031.4	hg19	CCDS10983.1																																																																																			.	.		0.667	SPATA33-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000269924.2	NM_153025		T	89724816	A	T	89724816	2	4	345	1	0	0	0	0	0	0	0	1	1822	175	7	4		4	C16orf55	16	89724816	Silent	SNP	A	TCGA-UB-A7MC-01A-11D-A33Q-10	374487	89724816	629937	52	48830										
NUP88	4927	hgsc.bcm.edu	37	chr17	5290351	5290351	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	aagttgatcaggtatcagctGtaattctttcttcatgtctc	7	8	6	1			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr17:5290351G>T	ENST00000573584.1	-	15	2505	c.1996C>A	c.(1996-1998)Cag>Aag	p.Q666K	NUP88_ENST00000573169.1_5'Flank	NM_002532.4	NP_002523.2	Q99567	NUP88_HUMAN	nucleoporin 88kDa	666					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	transporter activity (GO:0005215)			endometrium(4)|kidney(4)|large_intestine(4)|lung(3)	15						GGTATCAGCTGTAATTCTTTC	0.378																																					p.Q666K		Atlas-SNP	.											.	NUP88	47	.	0			c.C1996A						.						107	107	107					17																	5290351		2203	4300	6503	SO:0001583	missense	4927	exon15			TCAGCTGTAATTC	Y08612	CCDS11070.1	17p13	2004-02-18	2002-08-29		ENSG00000108559	ENSG00000108559			8067	protein-coding gene	gene with protein product		602552	"nucleoporin 88kD"			9049309	Standard	NM_002532		Approved	MGC8530	uc002gbo.2	Q99567	OTTHUMG00000099453	ENST00000573584.1:c.1996C>A	chr17.hg19:g.5290351G>T	ENSP00000458954:p.Gln666Lys	74.0	0.0		46.0	43.0	NM_002532	D3DTM2|Q9BWE5	Missense_Mutation	SNP	ENST00000573584.1	hg19	CCDS11070.1	.	.	.	.	.	.	.	.	.	.	G	17.30	3.353546	0.61293	.	.	ENSG00000108559	ENST00000225696;ENST00000543132	.	.	.	4.63	3.64	0.41730	.	0.121851	0.56097	D	0.000024	T	0.49457	0.1558	L	0.45137	1.4	0.44214	D	0.997046	B;B	0.31125	0.067;0.309	B;B	0.31946	0.044;0.138	T	0.47142	-0.9140	9	0.31617	T	0.26	-10.4131	14.1283	0.65235	0.0:0.1512:0.8488:0.0	.	551;666	B4DP20;Q99567	.;NUP88_HUMAN	K	666;551	.	ENSP00000225696:Q666K	Q	-	1	0	NUP88	5231075	1.000000	0.71417	0.981000	0.43875	0.994000	0.84299	5.248000	0.65421	1.284000	0.44531	0.557000	0.71058	CAG	.	.		0.378	NUP88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216918.3	NM_002532		T	5290351	G	T	5290351	3	4	345	1	0	0	0	0	1	0	0	0	10780	1386	48	3	241	3	NUP88	17	5290351	Missense_Mutation	SNP	G	TCGA-UB-A7MC-01A-11D-A33Q-10		5290351	75904859	53	48831										
TP53	7157	hgsc.bcm.edu	37	chr17	7577538	7577538	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	tgatggtgaggatgggcctcCggttcatgccgcccatgcag	15	11	1	2	rs11540652		TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr17:7577538C>T	ENST00000269305.4	-	7	932	c.743G>A	c.(742-744)cGg>cAg	p.R248Q	TP53_ENST00000455263.2_Missense_Mutation_p.R248Q|TP53_ENST00000420246.2_Missense_Mutation_p.R248Q|TP53_ENST00000445888.2_Missense_Mutation_p.R248Q|TP53_ENST00000413465.2_Missense_Mutation_p.R248Q|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.R248Q	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	248	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.		NR -> IP (in a sporadic cancer; somatic mutation).|NR -> KW (in sporadic cancers; somatic mutation).|R -> C (in a sporadic cancer; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:7682763}.|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs11540652). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:2263646, ECO:0000269|PubMed:7682763, ECO:0000269|PubMed:7887414}.|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:8829627}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R248Q(580)|p.R248L(75)|p.R248P(19)|p.R155Q(18)|p.0?(8)|p.?(5)|p.R155L(3)|p.R155P(2)|p.N247_R248delNR(2)|p.R248fs*16(2)|p.M246_P250delMNRRP(2)|p.R248_P250delRRP(1)|p.unknown(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*96(1)|p.R248fs*>39(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GATGGGCCTCCGGTTCATGCC	0.572	R248Q(BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(HCC1143_BREAST)|R248Q(HCC70_BREAST)|R248Q(HEC1A_ENDOMETRIUM)|R248Q(HS683_CENTRAL_NERVOUS_SYSTEM)|R248Q(HSC4_UPPER_AERODIGESTIVE_TRACT)|R248Q(KASUMI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KYSE150_OESOPHAGUS)|R248Q(MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NAMALWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NCIH211_LUNG)|R248Q(NCIN87_STOMACH)|R248Q(NIHOVCAR3_OVARY)|R248Q(NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(P12ICHIKAWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(PANC0203_PANCREAS)|R248Q(PC14_LUNG)|R248Q(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(RT112_URINARY_TRACT)|R248Q(SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SF295_CENTRAL_NERVOUS_SYSTEM)|R248Q(SKUT1_SOFT_TISSUE)|R248Q(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SW1463_LARGE_INTESTINE)|R248Q(WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.R248Q	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,adenocarcinoma,0,4	TP53	33396	.	725	Substitution - Missense(698)|Whole gene deletion(8)|Deletion - In frame(7)|Unknown(6)|Insertion - Frameshift(3)|Deletion - Frameshift(2)|Complex - compound substitution(1)	large_intestine(138)|breast(83)|haematopoietic_and_lymphoid_tissue(74)|lung(71)|upper_aerodigestive_tract(63)|central_nervous_system(46)|oesophagus(37)|urinary_tract(37)|ovary(36)|stomach(35)|endometrium(23)|skin(18)|prostate(11)|bone(10)|biliary_tract(9)|liver(9)|pancreas(7)|vulva(3)|kidney(3)|cervix(3)|peritoneum(2)|thyroid(2)|soft_tissue(1)|pituitary(1)|adrenal_gland(1)|small_intestine(1)|thymus(1)	c.G743A	GRCh37	CM920675	TP53	M	rs11540652	.	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	152	112	126	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	743,743,743,743,347,347,347	3.7	1	17	dbSNP_120	126	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense,missense	TP53	NM_000546.4,NM_001126112.1,NM_001126113.1,NM_001126114.1,NM_001126115.1,NM_001126116.1,NM_001126117.1	43,43,43,43,43,43,43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	248/394,248/394,248/347,248/342,116/262,116/210,116/215	7577538	1,13005	2203	4300	6503	SO:0001583	missense	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GGCCTCCGGTTCA	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.743G>A	chr17.hg19:g.7577538C>T	ENSP00000269305:p.Arg248Gln	102.0	0.0		46.0	42.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.822907	0.90873	0.0	1.16E-4	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99864	-7.28;-7.28;-7.28;-7.28;-7.28;-7.28;-7.28;-7.28	4.62	3.65	0.41850	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99840	0.9927	M	0.88640	2.97	0.58432	A	0.999994	D;D;D;D;D;D	0.89917	1.0;0.994;1.0;1.0;1.0;1.0	D;P;D;D;D;D	0.91635	0.996;0.882;0.999;0.995;0.996;0.995	D	0.96819	0.9602	9	0.72032	D	0.01	-9.5643	10.6687	0.45745	0.0:0.9059:0.0:0.0941	rs11540652;rs11540652	248;248;155;248;248;248	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	Q	248;248;248;248;248;248;237;155;116;155	ENSP00000410739:R248Q;ENSP00000352610:R248Q;ENSP00000269305:R248Q;ENSP00000398846:R248Q;ENSP00000391127:R248Q;ENSP00000391478:R248Q;ENSP00000425104:R116Q;ENSP00000423862:R155Q	ENSP00000269305:R248Q	R	-	2	0	TP53	7518263	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	5.884000	0.69729	1.305000	0.44909	0.462000	0.41574	CGG	.	.		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7577538	C	T	7577538	3	4	345	1	0	0	0	0	1	0	0	0	16396	652	23	1	547	1	TP53	17	7577538	Missense_Mutation	SNP	C	TCGA-UB-A7MC-01A-11D-A33Q-10	2287187	7577538	73617672	54	48832										
KIAA1267	284058	hgsc.bcm.edu	37	chr17	44109414	44109414	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	caaaggctgcgtcccttaccTgttcatccagccccagctct	7	17	2	0			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr17:44109414T>C	ENST00000262419.6	-	14	3559	c.3089A>G	c.(3088-3090)cAg>cGg	p.Q1030R	KANSL1_ENST00000393476.3_Splice_Site_p.Q324R|KANSL1_ENST00000574590.1_Splice_Site_p.Q1030R|KANSL1_ENST00000575318.1_Splice_Site_p.Q966R|KANSL1_ENST00000572904.1_Splice_Site_p.Q1030R|KANSL1_ENST00000432791.1_Splice_Site_p.Q1030R	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	1030	Sufficient for interaction with KAT8.				chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											GTCCCTTACCTGTTCATCCAG	0.622																																					p.Q1030R		Atlas-SNP	.											.	.	.	.	0			c.A3089G						.						55	49	51					17																	44109414		2203	4300	6503	SO:0001630	splice_region_variant	284058	exon14			CTTACCTGTTCAT	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"centromere protein 36"	612452	"KIAA1267"	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.3090+1A>G	chr17.hg19:g.44109414T>C		64.0	0.0		88.0	30.0	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Missense_Mutation	SNP	ENST00000262419.6	hg19	CCDS11503.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.149417	0.78001	.	.	ENSG00000120071	ENST00000262419;ENST00000432791;ENST00000393476	T;T;T	0.24538	2.64;2.64;1.85	5.72	5.72	0.89469	.	0.130718	0.53938	D	0.000059	T	0.17789	0.0427	L	0.27053	0.805	0.33088	D	0.537555	B;B;B;B	0.15141	0.01;0.01;0.012;0.012	B;B;B;B	0.13407	0.009;0.009;0.006;0.006	T	0.16571	-1.0398	10	0.29301	T	0.29	-9.9329	10.1399	0.42730	0.1491:0.0:0.0:0.8509	.	298;361;1030;1030	B3KT49;Q7Z3B3-2;C9JHY2;Q7Z3B3	.;.;.;K1267_HUMAN	R	1030;1030;324	ENSP00000262419:Q1030R;ENSP00000387393:Q1030R;ENSP00000377117:Q324R	ENSP00000262419:Q1030R	Q	-	2	0	KIAA1267	41465261	1.000000	0.71417	0.999000	0.59377	0.892000	0.51952	2.838000	0.48199	2.185000	0.69588	0.459000	0.35465	CAG	.	.		0.622	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	Missense_Mutation	C	44109414	T	C	44109414	5	2	345	1	0	0	0	0	0	0	1	0	8228	1594	55	2	236	2	KIAA1267	17	44109414	Splice_Site	SNP	T	TCGA-UB-A7MC-01A-11D-A33Q-10	36531876	44109414	37085796	55	48833										
OTOP2	92736	hgsc.bcm.edu	37	chr17	72926856	72926856	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	tggccctgctgatgggtgccGccctgggtcagtacgccatc	14	14	1	1			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr17:72926856G>C	ENST00000580223.1	+	5	1156	c.1126G>C	c.(1126-1128)Gcc>Ccc	p.A376P	OTOP2_ENST00000331427.4_Missense_Mutation_p.A376P			Q7RTS6	OTOP2_HUMAN	otopetrin 2	376						integral component of membrane (GO:0016021)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|ovary(3)|prostate(4)|skin(1)|urinary_tract(2)	39	all_lung(278;0.172)|Lung NSC(278;0.207)					GATGGGTGCCGCCCTGGGTCA	0.637																																					p.A376P		Atlas-SNP	.											.	OTOP2	81	.	0			c.G1126C						.						76	67	70					17																	72926856		2203	4300	6503	SO:0001583	missense	92736	exon6			GGTGCCGCCCTGG	BK000567	CCDS11708.1	17q25.3	2006-09-20				ENSG00000183034			19657	protein-coding gene	gene with protein product		607827				12651873	Standard	NM_178160		Approved		uc010wrp.2	Q7RTS6		ENST00000580223.1:c.1126G>C	chr17.hg19:g.72926856G>C	ENSP00000463837:p.Ala376Pro	122.0	0.0		130.0	68.0	NM_178160		Missense_Mutation	SNP	ENST00000580223.1	hg19	CCDS11708.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.449374	0.84101	.	.	ENSG00000183034	ENST00000331427	T	0.25250	1.81	5.47	5.47	0.80525	.	0.062767	0.64402	D	0.000003	T	0.54532	0.1864	M	0.79011	2.435	0.58432	D	0.999992	D	0.89917	1.0	D	0.83275	0.996	T	0.52170	-0.8611	10	0.40728	T	0.16	-18.7953	19.3792	0.94525	0.0:0.0:1.0:0.0	.	376	Q7RTS6	OTOP2_HUMAN	P	376	ENSP00000332528:A376P	ENSP00000332528:A376P	A	+	1	0	OTOP2	70438451	1.000000	0.71417	0.997000	0.53966	0.942000	0.58702	6.164000	0.71885	2.581000	0.87130	0.456000	0.33151	GCC	.	.		0.637	OTOP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445306.1	NM_178160		C	72926856	G	C	72926856	3	2	345	1	0	0	0	0	1	0	0	0	11315	1087	38	4	1144	4	OTOP2	17	72926856	Missense_Mutation	SNP	G	TCGA-UB-A7MC-01A-11D-A33Q-10	28817442	72926856	8268354	56	48834										
DNM2	1785	hgsc.bcm.edu	37	chr19	10906053	10906053	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	tttgtctcttctcagatggaGtttgacgagaaggacttacg	11	7	2	3			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr19:10906053G>T	ENST00000355667.6	+	9	1214	c.1134G>T	c.(1132-1134)gaG>gaT	p.E378D	DNM2_ENST00000389253.4_Missense_Mutation_p.E378D|DNM2_ENST00000314646.5_Missense_Mutation_p.E378D|DNM2_ENST00000359692.6_Missense_Mutation_p.E378D|DNM2_ENST00000408974.4_Missense_Mutation_p.E378D|DNM2_ENST00000585892.1_Missense_Mutation_p.E378D	NM_001005360.2|NM_001190716.1	NP_001005360.1|NP_001177645.1	P50570	DYN2_HUMAN	dynamin 2	378					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|endocytosis (GO:0006897)|G2/M transition of mitotic cell cycle (GO:0000086)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|nitric oxide metabolic process (GO:0046209)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic vesicle transport (GO:0048489)|transferrin transport (GO:0033572)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	enzyme binding (GO:0019899)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|microtubule binding (GO:0008017)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	42			Epithelial(33;4.17e-05)|all cancers(31;8.48e-05)			CTCAGATGGAGTTTGACGAGA	0.562			"F, N, Splice, Mis, O"		ETP ALL																																p.E378D		Atlas-SNP	.		Rec	yes		19	19p13.2	1785	dynamin 2		L	.	DNM2	175	.	0			c.G1134T						.						172	129	143					19																	10906053		2203	4300	6503	SO:0001583	missense	1785	exon9			GATGGAGTTTGAC		CCDS32907.1, CCDS32908.1, CCDS45968.1, CCDS45969.1, CCDS59351.1	19p	2014-09-17						"Pleckstrin homology (PH) domain containing"	2974	protein-coding gene	gene with protein product	"dynamin II", "cytoskeletal protein"	602378				7590285, 9143510	Standard	NM_001190716		Approved	DYNII, DYN2, CMTDIB, CMTDI1, DI-CMTB	uc002mps.2	P50570		ENST00000355667.6:c.1134G>T	chr19.hg19:g.10906053G>T	ENSP00000347890:p.Glu378Asp	53.0	0.0		45.0	29.0	NM_001005361	A8K1B6|E7EV30|E9PEQ4|K7ESI9|Q5I0Y0|Q7Z5S3|Q9UPH4	Missense_Mutation	SNP	ENST00000355667.6	hg19	CCDS45968.1	.	.	.	.	.	.	.	.	.	.	G	11.62	1.694089	0.30052	.	.	ENSG00000079805	ENST00000389252;ENST00000408974;ENST00000355667;ENST00000359692;ENST00000389253;ENST00000314646	T;T;T;T;T	0.72725	-0.68;-0.68;-0.68;-0.68;-0.68	5.29	3.03	0.35002	Dynamin central domain (1);	0.441600	0.25938	N	0.027333	T	0.47507	0.1449	N	0.16066	0.365	0.49389	D	0.999787	B;B;B;B;P	0.39576	0.31;0.004;0.002;0.024;0.679	B;B;B;B;B	0.40066	0.248;0.029;0.012;0.033;0.318	T	0.37384	-0.9708	10	0.09590	T	0.72	-6.6102	6.9382	0.24478	0.327:0.0:0.673:0.0	.	111;378;378;378;378	B4DJ53;A8K1B6;P50570-2;P50570;E9PEQ4	.;.;.;DYN2_HUMAN;.	D	367;378;378;378;378;378	ENSP00000386192:E378D;ENSP00000347890:E378D;ENSP00000352721:E378D;ENSP00000373905:E378D;ENSP00000313164:E378D	ENSP00000313164:E378D	E	+	3	2	DNM2	10767053	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	2.032000	0.41127	1.249000	0.43950	-0.140000	0.14226	GAG	.	.		0.562	DNM2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452592.1	NM_004945		T	10906053	G	T	10906053	3	4	345	1	0	0	0	0	1	0	0	0	4674	1020	36	3	1168	3	DNM2	19	10906053	Missense_Mutation	SNP	G	TCGA-UB-A7MC-01A-11D-A33Q-10		10906053	48222930	57	48835										
PRNP	5621	hgsc.bcm.edu	37	chr20	4680289	4680289	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	agcaggcccatcatacatttCggcagtgactatgaggaccg	11	11	1	2			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr20:4680289C>T	ENST00000379440.4	+	2	710	c.423C>T	c.(421-423)ttC>ttT	p.F141F	PRNP_ENST00000430350.2_Silent_p.F141F	NM_000311.3|NM_001080121.1|NM_001080122.1|NM_001080123.1|NM_001271561.1|NM_183079.2	NP_000302.1|NP_001073590.1|NP_001073591.1|NP_001073592.1|NP_001258490.1|NP_898902.1	F7VJQ1	APRIO_HUMAN	prion protein	0						integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)				central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|skin(1)	14						TCATACATTTCGGCAGTGACT	0.547																																					p.F141F		Atlas-SNP	.											PRNP,NS,carcinoma,0,2	PRNP	31	.	0			c.C423T						.						98	73	82					20																	4680289		2203	4300	6503	SO:0001819	synonymous_variant	5621	exon2			ACATTTCGGCAGT	M13899	CCDS13080.1	20p13	2014-06-05	2008-07-28		ENSG00000171867	ENSG00000171867		"CD molecules"	9449	protein-coding gene	gene with protein product	"Creutzfeldt-Jakob disease", "Gerstmann-Strausler-Scheinker syndrome", "fatal familial insomnia", "p27-30"	176640	"prion protein (p27-30)"	PRIP, GSS, CJD			Standard	NM_000311		Approved	CD230, PRP, AltPrP	uc002wkw.4	F7VJQ1	OTTHUMG00000031786	ENST00000379440.4:c.423C>T	chr20.hg19:g.4680289C>T		115.0	0.0		92.0	23.0	NM_000311		Silent	SNP	ENST00000379440.4	hg19	CCDS13080.1																																																																																			.	.		0.547	PRNP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077820.2	NM_000311		T	4680289	C	T	4680289	2	4	345	1	0	0	0	0	0	0	0	1	12556	883	31	1		1	PRNP	20	4680289	Silent	SNP	C	TCGA-UB-A7MC-01A-11D-A33Q-10		4680289	58345231	58	48836										
PDRG1	81572	hgsc.bcm.edu	37	chr20	30538175	30538175	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	tcgattctgattccttttagTgtccaggtccacaatctgaa	7	10	2	2			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr20:30538175T>C	ENST00000202017.4	-	2	233	c.103A>G	c.(103-105)Act>Gct	p.T35A		NM_030815.2	NP_110442.1	Q9NUG6	PDRG1_HUMAN	p53 and DNA-damage regulated 1	35					protein folding (GO:0006457)	cytoplasm (GO:0005737)|prefoldin complex (GO:0016272)				endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|skin(1)|stomach(1)	8			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			TTCCTTTTAGTGTCCAGGTCC	0.522																																					p.T35A		Atlas-SNP	.											.	PDRG1	17	.	0			c.A103G						.						82	81	81					20																	30538175		2203	4300	6503	SO:0001583	missense	81572	exon2			TTTTAGTGTCCAG	AL031658	CCDS13194.1	20q11.21	2009-06-12	2009-06-12	2004-10-07	ENSG00000088356	ENSG00000088356			16119	protein-coding gene	gene with protein product		610789	"chromosome 20 open reading frame 126"	C20orf126		14562055	Standard	NM_030815		Approved	dJ310O13.3	uc002wxd.3	Q9NUG6	OTTHUMG00000032196	ENST00000202017.4:c.103A>G	chr20.hg19:g.30538175T>C	ENSP00000202017:p.Thr35Ala	66.0	0.0		66.0	44.0	NM_030815	B2R511|Q96GP3|Q9BUW8	Missense_Mutation	SNP	ENST00000202017.4	hg19	CCDS13194.1	.	.	.	.	.	.	.	.	.	.	T	2.667	-0.278482	0.05679	.	.	ENSG00000088356	ENST00000202017	T	0.42131	0.98	4.18	1.74	0.24563	Prefoldin beta-like (1);	0.936195	0.09135	N	0.843835	T	0.27866	0.0686	L	0.36672	1.1	0.25358	N	0.988807	B	0.06786	0.001	B	0.09377	0.004	T	0.24190	-1.0167	10	0.23891	T	0.37	-5.0751	2.9713	0.05924	0.2145:0.1161:0.0:0.6694	.	35	Q9NUG6	PDRG1_HUMAN	A	35	ENSP00000202017:T35A	ENSP00000202017:T35A	T	-	1	0	PDRG1	30001836	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	0.529000	0.23019	0.758000	0.33059	0.460000	0.39030	ACT	.	.		0.522	PDRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078593.2	NM_030815		C	30538175	T	C	30538175	3	2	345	1	0	0	0	0	1	0	0	0	11699	1696	59	2	314	2	PDRG1	20	30538175	Missense_Mutation	SNP	T	TCGA-UB-A7MC-01A-11D-A33Q-10	25857886	30538175	32487345	59	48837										
ZSWIM1	90204	hgsc.bcm.edu	37	chr20	44511960	44511960	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	gaccgcatctggctggctcaCcgctggagaagccgagctga	14	13	2	2			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr20:44511960C>A	ENST00000372523.1	+	2	824	c.729C>A	c.(727-729)caC>caA	p.H243Q	ZSWIM1_ENST00000372520.1_Missense_Mutation_p.H243Q	NM_080603.4	NP_542170.3	Q9BR11	ZSWM1_HUMAN	zinc finger, SWIM-type containing 1	243						nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	13		Myeloproliferative disorder(115;0.028)				GGCTGGCTCACCGCTGGAGAA	0.572																																					p.H243Q		Atlas-SNP	.											.	ZSWIM1	35	.	0			c.C729A						.						52	46	48					20																	44511960		2203	4300	6503	SO:0001583	missense	90204	exon2			GGCTCACCGCTGG	AL008726	CCDS13382.2	20q13.12	2013-09-20	2003-12-17	2003-12-19	ENSG00000168612	ENSG00000168612		"Zinc fingers, SWIM-type"	16155	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 162"	C20orf162			Standard	NM_080603		Approved	dJ337O18.5	uc010ghi.3	Q9BR11	OTTHUMG00000074023	ENST00000372523.1:c.729C>A	chr20.hg19:g.44511960C>A	ENSP00000361601:p.His243Gln	70.0	0.0		41.0	10.0	NM_080603	Q5JZH2|Q9BR12|Q9BV30	Missense_Mutation	SNP	ENST00000372523.1	hg19	CCDS13382.2	.	.	.	.	.	.	.	.	.	.	C	16.89	3.246615	0.59103	.	.	ENSG00000168612	ENST00000372523;ENST00000372520	T;T	0.32753	1.44;1.44	5.26	2.25	0.28309	.	0.000000	0.56097	U	0.000031	T	0.36936	0.0985	L	0.36672	1.1	0.34155	D	0.668035	D	0.63880	0.993	P	0.58721	0.844	T	0.52638	-0.8549	10	0.66056	D	0.02	-22.8742	10.8481	0.46754	0.0:0.7335:0.0:0.2665	.	243	Q9BR11	ZSWM1_HUMAN	Q	243	ENSP00000361601:H243Q;ENSP00000361598:H243Q	ENSP00000361598:H243Q	H	+	3	2	ZSWIM1	43945367	0.963000	0.33076	1.000000	0.80357	0.994000	0.84299	0.056000	0.14256	0.800000	0.34041	0.650000	0.86243	CAC	.	.		0.572	ZSWIM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157064.2	NM_080603		A	44511960	C	A	44511960	3	1	345	1	0	0	0	0	1	0	0	0	18255	506	18	3	731	3	ZSWIM1	20	44511960	Missense_Mutation	SNP	C	TCGA-UB-A7MC-01A-11D-A33Q-10	13973785	44511960	18513560	60	48838										
NCOA3	8202	hgsc.bcm.edu	37	chr20	46265070	46265070	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	ccccctagattcaagttgtaAagaatcttctgttagtgtca	7	9	4	2			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr20:46265070A>G	ENST00000371998.3	+	12	2131	c.1940A>G	c.(1939-1941)aAa>aGa	p.K647R	NCOA3_ENST00000372004.3_Missense_Mutation_p.K647R|NCOA3_ENST00000371997.3_Missense_Mutation_p.K657R|NCOA3_ENST00000341724.6_Missense_Mutation_p.K657R			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	647	Ser-rich.				androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			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						TCAAGTTGTAAAGAATCTTCT	0.453																																					p.K657R		Atlas-SNP	.											.	NCOA3	156	.	0			c.A1970G						.						80	75	77					20																	46265070		2203	4300	6503	SO:0001583	missense	8202	exon12			GTTGTAAAGAATC	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7670	protein-coding gene	gene with protein product	"receptor-associated coactivator 3", "thyroid hormone receptor activator molecule 1"	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.1940A>G	chr20.hg19:g.46265070A>G	ENSP00000361066:p.Lys647Arg	126.0	0.0		93.0	58.0	NM_001174088	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Missense_Mutation	SNP	ENST00000371998.3	hg19	CCDS13407.1	.	.	.	.	.	.	.	.	.	.	A	17.55	3.418007	0.62622	.	.	ENSG00000124151	ENST00000340189;ENST00000341724;ENST00000372004;ENST00000371998;ENST00000371997	T;T;T;T	0.58210	0.35;0.35;0.35;0.35	5.4	5.4	0.78164	Steroid receptor coactivator (1);	0.000000	0.85682	D	0.000000	T	0.69106	0.3074	L	0.58428	1.81	0.43803	D	0.996352	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;0.999;1.0;1.0;0.999;1.0	T	0.70483	-0.4859	10	0.52906	T	0.07	-29.9474	15.7123	0.77641	1.0:0.0:0.0:0.0	.	647;657;651;647;647;647	A8K0W8;Q9Y6Q9-3;Q59EE8;Q0IIN7;Q9Y6Q9-5;Q9Y6Q9	.;.;.;.;.;NCOA3_HUMAN	R	647;657;647;647;657	ENSP00000342123:K657R;ENSP00000361073:K647R;ENSP00000361066:K647R;ENSP00000361065:K657R	ENSP00000345671:K647R	K	+	2	0	NCOA3	45698477	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	8.678000	0.91211	2.165000	0.68154	0.459000	0.35465	AAA	.	.		0.453	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534		G	46265070	A	G	46265070	3	3	345	1	0	0	0	0	1	0	0	0	10239	14	1	2	2008	2	NCOA3	20	46265070	Missense_Mutation	SNP	A	TCGA-UB-A7MC-01A-11D-A33Q-10	1753110	46265070	16760450	61	48839										
ZNF831	128611	hgsc.bcm.edu	37	chr20	57829551	57829551	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	ttttccttccagaggccagtAtgggtgtggggaaatgactg	14	7	0	2			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr20:57829551A>G	ENST00000371030.2	+	5	4787	c.4787A>G	c.(4786-4788)tAt>tGt	p.Y1596C		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	1596							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					AGAGGCCAGTATGGGTGTGGG	0.473																																					p.Y1596C		Atlas-SNP	.											.	ZNF831	287	.	0			c.A4787G						.						83	79	80					20																	57829551		1906	4130	6036	SO:0001583	missense	128611	exon5			GCCAGTATGGGTG	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 174"	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.4787A>G	chr20.hg19:g.57829551A>G	ENSP00000360069:p.Tyr1596Cys	233.0	0.0		194.0	62.0	NM_178457	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	hg19	CCDS42894.1	.	.	.	.	.	.	.	.	.	.	A	9.600	1.128458	0.21041	.	.	ENSG00000124203	ENST00000371030	T	0.07216	3.21	5.66	-0.773	0.10995	.	0.902716	0.09374	N	0.810868	T	0.08179	0.0204	M	0.61703	1.905	0.09310	N	1	B	0.15473	0.013	B	0.12156	0.007	T	0.42481	-0.9449	10	0.41790	T	0.15	0.1695	1.0782	0.01637	0.4309:0.1638:0.2653:0.1399	.	1596	Q5JPB2	ZN831_HUMAN	C	1596	ENSP00000360069:Y1596C	ENSP00000360069:Y1596C	Y	+	2	0	ZNF831	57262946	0.000000	0.05858	0.000000	0.03702	0.062000	0.15995	-0.070000	0.11523	-0.427000	0.07350	-0.340000	0.08031	TAT	.	.		0.473	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		G	57829551	A	G	57829551	3	3	345	1	0	0	0	0	1	0	0	0	18200	449	16	2	4805	2	ZNF831	20	57829551	Missense_Mutation	SNP	A	TCGA-UB-A7MC-01A-11D-A33Q-10	11564481	57829551	5195969	62	48840										
TMPRSS15	5651	hgsc.bcm.edu	37	chr21	19704474	19704474	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	tttggctcccacagctcaaaAggtcctccacagtccgctga	8	15	1	1			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chr21:19704474A>G	ENST00000284885.3	-	14	1614	c.1581T>C	c.(1579-1581)ccT>ccC	p.P527P		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	527	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.					brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						ACAGCTCAAAAGGTCCTCCAC	0.398																																					p.P527P		Atlas-SNP	.											.	TMPRSS15	189	.	0			c.T1581C						.						124	123	123					21																	19704474		2203	4300	6503	SO:0001819	synonymous_variant	5651	exon14			CTCAAAAGGTCCT		CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"Serine peptidases / Transmembrane"	9490	protein-coding gene	gene with protein product	"proenterokinase", "enteropeptidase"	606635	"protease, serine, 7 (enterokinase)"	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.1581T>C	chr21.hg19:g.19704474A>G		93.0	0.0		87.0	5.0	NM_002772	Q2NKL7	Silent	SNP	ENST00000284885.3	hg19	CCDS13571.1																																																																																			.	.		0.398	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772		G	19704474	A	G	19704474	2	3	345	1	0	0	0	0	0	0	0	1	16261	59	3	2		2	TMPRSS15	21	19704474	Silent	SNP	A	TCGA-UB-A7MC-01A-11D-A33Q-10		19704474	28425421	63	48841										
IQSEC2	23096	hgsc.bcm.edu	37	chrX	53277343	53277343	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.09375	6	1	1.48587127158556	2.08021978021978	1.15567765567766	1	1	0	ttctgggcctcaccctgaacCcggatatgggactggaactt	11	12	2	1			TCGA-UB-A7MC-01A-11D-A33Q-10	TCGA-UB-A7MC-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7021c007-2dca-4528-a727-24cc186289b5	0856f8bb-d4eb-4f86-9bae-e349845c39dc	g.chrX:53277343C>T	ENST00000375368.5	-	6	2705	c.2505G>A	c.(2503-2505)cgG>cgA	p.R835R	IQSEC2_ENST00000375365.2_Silent_p.R640R|IQSEC2_ENST00000396435.3_Silent_p.R845R			Q5JU85	IQEC2_HUMAN	IQ motif and Sec7 domain 2	835	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(10)|ovary(4)|skin(1)	29						CACCCTGAACCCGGATATGGG	0.587																																					p.R845R		Atlas-SNP	.											.	IQSEC2	195	.	0			c.G2535A						.						95	56	69					X																	53277343		2203	4300	6503	SO:0001819	synonymous_variant	23096	exon7			CTGAACCCGGATA	AB011094	CCDS35298.1, CCDS48130.1	Xp11.23	2014-01-31			ENSG00000124313	ENSG00000124313			29059	protein-coding gene	gene with protein product		300522	"mental retardation, X-linked 1 (non-dysmorphic)"	MRX1		9628581, 20473311	Standard	NM_001243197		Approved	KIAA0522	uc004dsd.3	Q5JU85	OTTHUMG00000021608	ENST00000375368.5:c.2505G>A	chrX.hg19:g.53277343C>T		121.0	0.0		88.0	79.0	NM_001111125	B3KT97|C7SDG1|O60275|Q5JUX1	Silent	SNP	ENST00000375368.5	hg19																																																																																				.	.		0.587	IQSEC2-201	KNOWN	basic	protein_coding	protein_coding		XM_291345		T	53277343	C	T	53277343	2	4	345	1	0	0	0	0	0	0	0	1	7827	610	22	3		3	IQSEC2	23	53277343	Silent	SNP	C	TCGA-UB-A7MC-01A-11D-A33Q-10		53277343	101993217	64	48842										
ZNF436	80818	hgsc.bcm.edu	37	chr1	23689096	23689096	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	gagctaggtgagagctccggCtgaagcttttcccacactcc	11	13	0	2			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr1:23689096C>T	ENST00000314011.4	-	4	915	c.779G>A	c.(778-780)aGc>aAc	p.S260N	ZNF436_ENST00000374608.3_Missense_Mutation_p.S260N	NM_001077195.1	NP_001070663.1	Q9C0F3	ZN436_HUMAN	zinc finger protein 436	260					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	19		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;5.97e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000977)|KIRC - Kidney renal clear cell carcinoma(1967;0.00336)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		AGAGCTCCGGCTGAAGCTTTT	0.512																																					p.S260N		Atlas-SNP	.											.	ZNF436	49	.	0			c.G779A						.						95	102	100					1																	23689096		2203	4300	6503	SO:0001583	missense	80818	exon4			CTCCGGCTGAAGC	AB051497	CCDS233.1	1p36	2013-01-08			ENSG00000125945	ENSG00000125945		"Zinc fingers, C2H2-type", "-"	20814	protein-coding gene	gene with protein product		611703				11214970	Standard	NM_001077195		Approved	KIAA1710, Zfp46	uc001bgt.3	Q9C0F3	OTTHUMG00000003232	ENST00000314011.4:c.779G>A	chr1.hg19:g.23689096C>T	ENSP00000313582:p.Ser260Asn	115.0	0.0		87.0	36.0	NM_001077195	Q658I9	Missense_Mutation	SNP	ENST00000314011.4	hg19	CCDS233.1	.	.	.	.	.	.	.	.	.	.	C	12.43	1.934183	0.34096	.	.	ENSG00000125945	ENST00000314011;ENST00000374609;ENST00000374608	T;T;T	0.33216	1.42;3.18;1.42	5.79	4.85	0.62838	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.079820	0.53938	D	0.000041	T	0.20292	0.0488	L	0.28274	0.84	0.29159	N	0.877876	B	0.16166	0.016	B	0.14023	0.01	T	0.04900	-1.0919	10	0.46703	T	0.11	-27.5095	8.2953	0.31982	0.0:0.7601:0.1576:0.0822	.	260	Q9C0F3	ZN436_HUMAN	N	260	ENSP00000313582:S260N;ENSP00000363737:S260N;ENSP00000363736:S260N	ENSP00000313582:S260N	S	-	2	0	ZNF436	23561683	0.001000	0.12720	1.000000	0.80357	0.984000	0.73092	0.017000	0.13399	2.739000	0.93911	0.655000	0.94253	AGC	.	.		0.512	ZNF436-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008908.1	NM_030634		T	23689096	C	T	23689096	3	4	346	1	0	0	0	0	1	0	0	0	17924	797	28	3	637	3	ZNF436	1	23689096	Missense_Mutation	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10		23689096	225561525	1	48843										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27106592	27106592	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	ggttacactcgccaacatctCggggcagttggacctatctc	10	13	2	0			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr1:27106592C>G	ENST00000324856.7	+	20	6574	c.6203C>G	c.(6202-6204)tCg>tGg	p.S2068W	ARID1A_ENST00000540690.1_Missense_Mutation_p.S396W|ARID1A_ENST00000457599.2_Missense_Mutation_p.S1851W|ARID1A_ENST00000374152.2_Missense_Mutation_p.S1685W	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	2068					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		GCCAACATCTCGGGGCAGTTG	0.577			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.S2068W		Atlas-SNP	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.C6203G						.						122	123	122					1																	27106592		2203	4300	6503	SO:0001583	missense	8289	exon20			ACATCTCGGGGCA	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.6203C>G	chr1.hg19:g.27106592C>G	ENSP00000320485:p.Ser2068Trp	32.0	0.0		38.0	17.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Missense_Mutation	SNP	ENST00000324856.7	hg19	CCDS285.1	.	.	.	.	.	.	.	.	.	.	C	18.69	3.677301	0.68042	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000374152;ENST00000540690	T;T;T;T	0.54071	1.21;1.21;1.21;0.59	5.1	4.19	0.49359	.	0.000000	0.85682	D	0.000000	T	0.72153	0.3425	M	0.78049	2.395	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.994;0.998;0.987	T	0.77091	-0.2716	10	0.87932	D	0	-1.431	14.2014	0.65707	0.0:0.9277:0.0:0.0723	.	1685;2068;1851	O14497-3;O14497;O14497-2	.;ARI1A_HUMAN;.	W	2068;1851;1685;396	ENSP00000320485:S2068W;ENSP00000387636:S1851W;ENSP00000363267:S1685W;ENSP00000442437:S396W	ENSP00000320485:S2068W	S	+	2	0	ARID1A	26979179	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.464000	0.80887	1.521000	0.48983	0.591000	0.81541	TCG	.	.		0.577	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		G	27106592	C	G	27106592	3	3	346	1	0	0	0	0	1	0	0	0	913	893	31	4	6281	4	ARID1A	1	27106592	Missense_Mutation	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	3417496	27106592	222144029	2	48844										
FGR	2268	hgsc.bcm.edu	37	chr1	27942229	27942229	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	catccccgaagcagccggtgCccagccggcgctccagcgtg	13	18	0	0			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr1:27942229C>G	ENST00000374005.3	-	8	1097	c.809G>C	c.(808-810)gGc>gCc	p.G270A	FGR_ENST00000545953.1_Missense_Mutation_p.G204A|FGR_ENST00000374004.1_Missense_Mutation_p.G270A|FGR_ENST00000399173.1_Missense_Mutation_p.G270A	NM_005248.2	NP_005239.1	P09769	FGR_HUMAN	FGR proto-oncogene, Src family tyrosine kinase	270	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood coagulation (GO:0007596)|defense response to Gram-positive bacterium (GO:0050830)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response-regulating cell surface receptor signaling pathway (GO:0002768)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of innate immune response (GO:0045088)|regulation of phagocytosis (GO:0050764)|regulation of protein kinase activity (GO:0045859)|response to virus (GO:0009615)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|Fc-gamma receptor I complex binding (GO:0034988)|immunoglobulin receptor binding (GO:0034987)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphotyrosine binding (GO:0001784)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(4)	16		all_lung(284;2.05e-05)|Colorectal(325;3.46e-05)|Lung NSC(340;3.67e-05)|Renal(390;0.00121)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.25e-24)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00244)|KIRC - Kidney renal clear cell carcinoma(1967;0.0027)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		GCAGCCGGTGCCCAGCCGGCG	0.706																																					p.G270A		Atlas-SNP	.											.	FGR	39	.	0			c.G809C						.						12	14	13					1																	27942229		2190	4288	6478	SO:0001583	missense	2268	exon8			CCGGTGCCCAGCC	BC064382	CCDS305.1	1p36.2-p36.1	2014-06-25	2014-06-25		ENSG00000000938	ENSG00000000938		"SH2 domain containing"	3697	protein-coding gene	gene with protein product		164940	"Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog", "v-fgr feline Gardner-Rasheed sarcoma viral oncogene homolog", "feline Gardner-Rasheed sarcoma viral oncogene homolog"	SRC2		3922831	Standard	NM_001042729		Approved	c-fgr, p55c-fgr	uc001bom.3	P09769	OTTHUMG00000003516	ENST00000374005.3:c.809G>C	chr1.hg19:g.27942229C>G	ENSP00000363117:p.Gly270Ala	67.0	0.0		71.0	20.0	NM_001042729	D3DPL7|Q9UIQ3	Missense_Mutation	SNP	ENST00000374005.3	hg19	CCDS305.1	.	.	.	.	.	.	.	.	.	.	C	32	5.165854	0.94768	.	.	ENSG00000000938	ENST00000374005;ENST00000545953;ENST00000399173;ENST00000374004;ENST00000374003;ENST00000457296	D;D;D;D;D;D	0.90504	-2.68;-2.68;-2.68;-2.68;-2.68;-2.68	4.62	4.62	0.57501	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);SH2 motif (1);Protein kinase, catalytic domain (1);	0.094831	0.43747	D	0.000525	D	0.95987	0.8693	M	0.90369	3.11	0.53688	D	0.999976	D	0.65815	0.995	D	0.70935	0.971	D	0.96799	0.9588	10	0.87932	D	0	.	16.9239	0.86170	0.0:1.0:0.0:0.0	.	270	P09769	FGR_HUMAN	A	270;204;270;270;270;270	ENSP00000363117:G270A;ENSP00000445302:G204A;ENSP00000382126:G270A;ENSP00000363116:G270A;ENSP00000363115:G270A;ENSP00000407670:G270A	ENSP00000363115:G270A	G	-	2	0	FGR	27814816	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.813000	0.86123	2.508000	0.84585	0.561000	0.74099	GGC	.	.		0.706	FGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009772.1	NM_005248		G	27942229	C	G	27942229	3	3	346	1	0	0	0	0	1	0	0	0	5882	739	26	4	804	4	FGR	1	27942229	Missense_Mutation	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	835637	27942229	221308392	3	48845										
BAI2	576	hgsc.bcm.edu	37	chr1	32207460	32207460	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	cggtgccctcgcaggggtagCcctgcgtgcccgtggcctgg	17	15	0	0			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr1:32207460C>G	ENST00000373658.3	-	9	1867	c.1526G>C	c.(1525-1527)gGc>gCc	p.G509A	BAI2_ENST00000398547.1_Missense_Mutation_p.G442A|BAI2_ENST00000373655.2_Missense_Mutation_p.G509A|BAI2_ENST00000257070.4_Missense_Mutation_p.G509A|BAI2_ENST00000398542.1_Missense_Mutation_p.G442A|BAI2_ENST00000398556.3_Missense_Mutation_p.G457A|BAI2_ENST00000398538.1_Missense_Mutation_p.G497A|BAI2_ENST00000527361.1_Missense_Mutation_p.G509A|BAI2_ENST00000440175.2_Missense_Mutation_p.G151A	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	509	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.				G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(2)|endometrium(1)|large_intestine(7)|liver(2)|lung(24)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	55		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)		GCAGGGGTAGCCCTGCGTGCC	0.647																																					p.G509A		Atlas-SNP	.											.	BAI2	128	.	0			c.G1526C						.						72	77	75					1																	32207460		2203	4299	6502	SO:0001583	missense	576	exon9			GGGTAGCCCTGCG	AB005298	CCDS72746.1, CCDS72747.1	1p35	2014-08-08			ENSG00000121753	ENSG00000121753		"-", "GPCR / Class B : Orphans"	944	protein-coding gene	gene with protein product		602683				9533023	Standard	XM_006710783		Approved		uc001btn.3	O60241	OTTHUMG00000003885	ENST00000373658.3:c.1526G>C	chr1.hg19:g.32207460C>G	ENSP00000362762:p.Gly509Ala	62.0	0.0		50.0	16.0	NM_001703	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Missense_Mutation	SNP	ENST00000373658.3	hg19	CCDS346.2	.	.	.	.	.	.	.	.	.	.	C	24.7	4.563253	0.86335	.	.	ENSG00000121753	ENST00000398556;ENST00000398547;ENST00000373658;ENST00000373655;ENST00000398542;ENST00000257070;ENST00000527361;ENST00000440175;ENST00000398538;ENST00000420125;ENST00000533175	T;T;T;T;T;T;T;T;T;T;T	0.23950	1.88;1.88;1.88;1.88;1.88;1.88;1.88;1.88;1.88;1.88;1.88	4.95	4.95	0.65309	.	0.000000	0.39759	N	0.001273	T	0.58148	0.2102	M	0.88241	2.94	0.58432	D	0.999999	D;D;D;D;D;D;D	0.71674	0.998;0.993;0.997;0.993;0.998;0.993;0.998	D;P;D;D;D;P;D	0.72982	0.979;0.873;0.965;0.979;0.979;0.873;0.979	T	0.66606	-0.5881	10	0.62326	D	0.03	.	17.3262	0.87248	0.0:1.0:0.0:0.0	.	442;509;497;151;442;509;509	A2A3C3;O60241-4;O60241-3;B4DKC3;A2A3C1;O60241-2;O60241	.;.;.;.;.;.;BAI2_HUMAN	A	457;442;509;509;442;509;509;151;497;447;488	ENSP00000381564:G457A;ENSP00000381555:G442A;ENSP00000362762:G509A;ENSP00000362759:G509A;ENSP00000381550:G442A;ENSP00000257070:G509A;ENSP00000435397:G509A;ENSP00000391071:G151A;ENSP00000381548:G497A;ENSP00000410921:G447A;ENSP00000437219:G488A	ENSP00000257070:G509A	G	-	2	0	BAI2	31980047	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	7.434000	0.80377	2.457000	0.83068	0.561000	0.74099	GGC	.	.		0.647	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703		G	32207460	C	G	32207460	3	3	346	1	0	0	0	0	1	0	0	0	1299	739	26	4	3331	4	BAI2	1	32207460	Missense_Mutation	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	4265231	32207460	217043161	4	48846										
SLC44A3	126969	hgsc.bcm.edu	37	chr1	95357851	95357859	+	In_Frame_Del	DEL	TTTCACTGT	TTTCACTGT	-													0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	gcacaggtgttagtggtgtgTttcactgtttttggaggact					rs200876036		TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	TTTCACTGT	TTTCACTGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr1:95357851_95357859delTTTCACTGT	ENST00000271227.6	+	14	1737_1745	c.1635_1643delTTTCACTGT	c.(1633-1644)tgtttcactgtt>tgt	p.FTV546del	SLC44A3_ENST00000446120.2_In_Frame_Del_p.FTV510del|SLC44A3_ENST00000529450.1_In_Frame_Del_p.FTV513del|SLC44A3_ENST00000467909.1_In_Frame_Del_p.FTV498del|SLC44A3_ENST00000527077.1_In_Frame_Del_p.FTV478del|SLC44A3_ENST00000532427.1_In_Frame_Del_p.FTV466del	NM_001114106.2|NM_001258340.1|NM_001258341.1	NP_001107578.1|NP_001245269.1|NP_001245270.1	Q8N4M1	CTL3_HUMAN	solute carrier family 44, member 3	546					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(6)|prostate(2)|stomach(1)|urinary_tract(1)	23		all_lung(203;0.000712)|Lung NSC(277;0.00316)		all cancers(265;0.039)|Epithelial(280;0.124)	Choline(DB00122)	TAGTGGTGTGTTTCACTGTTTTTGGAGGA	0.388																																					p.545_548del		Atlas-Indel,Pindel	.											.	SLC44A3	109	.	0			c.1634_1642del						.																																			SO:0001651	inframe_deletion	126969	exon14			.	BC033858	CCDS751.1, CCDS44176.1, CCDS58011.1, CCDS58012.1, CCDS58013.1, CCDS72827.1	1p22.1	2013-05-22	2005-09-06		ENSG00000143036	ENSG00000143036		"Solute carriers"	28689	protein-coding gene	gene with protein product			"solute carrier family, member 3"			15715662, 12975309	Standard	NM_001114106		Approved	MGC45474, CTL3	uc001dqv.5	Q8N4M1	OTTHUMG00000010700	ENST00000271227.6:c.1635_1643delTTTCACTGT	chr1.hg19:g.95357851_95357859delTTTCACTGT	ENSP00000271227:p.Phe546_Val548del	327.0	0.0		231.0	49.0	NM_001114106	B4DVY4|B4E1M4|B7ZA08|E9PJH2|E9PJY8|Q6UWT1|Q7Z6C5|Q9BWY7	In_Frame_Del	DEL	ENST00000271227.6	hg19	CCDS44176.1																																																																																			.	.		0.388	SLC44A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029544.3	NM_152369		-	95357859	TTTCACTGT	-	95357851	7	5	346	1	0	1	0	1	0	0	0	0	14652	1731	60	0	1689	0	SLC44A3	1	95357851	In_Frame_Del	DEL	TTTCACTGT	TCGA-UB-A7MD-01A-12D-A34Z-10	63150391	95357851	153892770	5	48847										
FASLG	356	hgsc.bcm.edu	37	chr1	172633481	172633481	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	ctctatgatacaggccacccCagtccaccccctgaaaaaaa	5	16	1	2	rs143306673		TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr1:172633481C>T	ENST00000367721.2	+	3	586	c.402C>T	c.(400-402)ccC>ccT	p.P134P	FASLG_ENST00000340030.3_Missense_Mutation_p.P119L	NM_000639.1	NP_000630.1	P48023	TNFL6_HUMAN	Fas ligand (TNF superfamily, member 6)	134					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell-cell signaling (GO:0007267)|cellular chloride ion homeostasis (GO:0030644)|endosomal lumen acidification (GO:0048388)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|immune response (GO:0006955)|inflammatory cell apoptotic process (GO:0006925)|necroptotic process (GO:0070266)|necroptotic signaling pathway (GO:0097527)|negative regulation of angiogenesis (GO:0016525)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to growth factor (GO:0070848)|response to lipopolysaccharide (GO:0032496)|retinal cell programmed cell death (GO:0046666)|signal transduction (GO:0007165)|T cell apoptotic process (GO:0070231)|transcription, DNA-templated (GO:0006351)	caveola (GO:0005901)|cytoplasmic membrane-bounded vesicle (GO:0016023)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	receptor binding (GO:0005102)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(12)|prostate(1)|skin(1)	19						CAGGCCACCCCAGTCCACCCC	0.378																																					p.P134P	Ovarian(28;486 876 30334 44033)	Atlas-SNP	.											.	FASLG	44	.	0			c.C402T						.	C		1,4405	2.1+/-5.4	0,1,2202	52	52	52		402	0.4	0	1	dbSNP_134	52	0,8600		0,0,4300	no	coding-synonymous	FASLG	NM_000639.1		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		134/282	172633481	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	356	exon3			CCACCCCAGTCCA	U11821	CCDS1304.1	1q23	2014-09-17	2005-01-07	2005-01-07	ENSG00000117560	ENSG00000117560		"Tumor necrosis factor (ligand) superfamily", "CD molecules", "Endogenous ligands"	11936	protein-coding gene	gene with protein product		134638	"tumor necrosis factor (ligand) superfamily, member 6"	APT1LG1, TNFSF6		7826947, 9022072	Standard	NM_000639		Approved	FasL, CD178	uc001gis.3	P48023	OTTHUMG00000034841	ENST00000367721.2:c.402C>T	chr1.hg19:g.172633481C>T		121.0	0.0		196.0	43.0	NM_000639	Q9BZP9	Silent	SNP	ENST00000367721.2	hg19	CCDS1304.1	.	.	.	.	.	.	.	.	.	.	C	0.261	-0.999569	0.02128	2.27E-4	0.0	ENSG00000117560	ENST00000340030	.	.	.	4.78	0.362	0.16113	.	0.572869	0.17490	N	0.172362	T	0.18299	0.0439	.	.	.	0.39723	D	0.971497	B	0.33238	0.403	B	0.25405	0.06	T	0.06041	-1.0849	8	0.72032	D	0.01	-7.6123	3.5259	0.07759	0.161:0.4346:0.3133:0.0911	.	119	P48023-2	.	L	119	.	ENSP00000344739:P119L	P	+	2	0	FASLG	170900104	0.000000	0.05858	0.025000	0.17156	0.080000	0.17528	-1.570000	0.02140	0.174000	0.19809	-0.143000	0.13931	CCA	.	C|1.000;T|0.000		0.378	FASLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084276.1			T	172633481	C	T	172633481	2	4	346	1	0	0	0	0	0	0	0	1	5690	581	21	3		3	FASLG	1	172633481	Silent	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	77275630	172633481	76617140	6	48848										
CAPN9	10753	hgsc.bcm.edu	37	chr1	230914797	230914797	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	cccgatgccctggaggaagaCgcgatccacaaatgggaggt	14	11	0	1	rs200401992		TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr1:230914797C>A	ENST00000271971.2	+	9	1145	c.1032C>A	c.(1030-1032)gaC>gaA	p.D344E	CAPN9_ENST00000366666.2_Missense_Mutation_p.D281E|RP11-99J16__A.2_ENST00000452640.1_RNA|RP11-99J16__A.2_ENST00000428480.1_RNA|RP11-99J16__A.2_ENST00000412344.1_RNA|CAPN9_ENST00000354537.1_Missense_Mutation_p.D318E	NM_006615.2	NP_006606.1	O14815	CAN9_HUMAN	calpain 9	344	Domain III.				digestion (GO:0007586)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	25	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)				TGGAGGAAGACGCGATCCACA	0.582																																					p.D344E		Atlas-SNP	.											.	CAPN9	116	.	0			c.C1032A						.						86	73	77					1																	230914797		2203	4300	6503	SO:0001583	missense	10753	exon9			GGAAGACGCGATC	AF022799	CCDS1586.1, CCDS31053.1	1q42.11-q42.3	2013-01-10	2004-11-11		ENSG00000135773	ENSG00000135773		"EF-hand domain containing"	1486	protein-coding gene	gene with protein product	"novel calpain large subunit-4"	606401	"calpain 9 (nCL-4)"			9524069, 10835488	Standard	XM_005273010		Approved	nCL-4, GC36	uc001htz.1	O14815	OTTHUMG00000037779	ENST00000271971.2:c.1032C>A	chr1.hg19:g.230914797C>A	ENSP00000271971:p.Asp344Glu	41.0	0.0		68.0	27.0	NM_006615	B1APS1|B1AQI0|Q9NS74	Missense_Mutation	SNP	ENST00000271971.2	hg19	CCDS1586.1	.	.	.	.	.	.	.	.	.	.	C	7.552	0.662995	0.14710	.	.	ENSG00000135773	ENST00000271971;ENST00000354537;ENST00000366666	T;T;T	0.15603	2.41;2.41;2.41	5.24	-10.5	0.00291	Peptidase C2, calpain, catalytic domain (1);	0.561206	0.20326	N	0.094523	T	0.09379	0.0231	L	0.35644	1.08	0.09310	N	1	B;P;B	0.37636	0.086;0.603;0.02	B;B;B	0.33846	0.012;0.171;0.007	T	0.03493	-1.1031	10	0.23302	T	0.38	.	16.2695	0.82607	0.0:0.7222:0.1565:0.1213	.	281;318;344	E7ESS6;O14815-2;O14815	.;.;CAN9_HUMAN	E	344;318;281	ENSP00000271971:D344E;ENSP00000346538:D318E;ENSP00000355626:D281E	ENSP00000271971:D344E	D	+	3	2	CAPN9	228981420	0.000000	0.05858	0.000000	0.03702	0.061000	0.15899	-0.547000	0.06055	-2.499000	0.00511	-1.119000	0.02030	GAC	.	C|0.999;T|0.001		0.582	CAPN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092179.1	NM_006615		A	230914797	C	A	230914797	3	1	346	1	0	0	0	0	1	0	0	0	2634	535	19	1	1066	1	CAPN9	1	230914797	Missense_Mutation	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	58281316	230914797	18335824	7	48849										
OR2T12	127064	hgsc.bcm.edu	37	chr1	248458788	248458789	+	Missense_Mutation	DNP	GG	GG	TA													0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	aacagggaggtcaaaacggtGgccagaagcatcatgaagag					rs570331659	byFrequency	TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr1:248458788_248458789GG>TA	ENST00000317996.1	-	1	91_92	c.92_93CC>TA	c.(91-93)gCC>gTA	p.A31V		NM_001004692.1	NP_001004692.1	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T, member 12	31						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(3)|large_intestine(3)|lung(25)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0201)			TCAAAACGGTGGCCAGAAGCAT	0.495																																					p.A31A|p.A31V		Atlas-SNP	.											.|OR2T12,NS,carcinoma,0,1	OR2T12	113	.	0			c.C93A|c.C92T						.																																			SO:0001583	missense	127064	exon1			AACGGTGGCCAGA|ACGGTGGCCAGAA	BK004485	CCDS31110.1	1q44	2012-08-09			ENSG00000177201	ENSG00000177201		"GPCR / Class A : Olfactory receptors"	19592	protein-coding gene	gene with protein product							Standard	NM_001004692		Approved		uc010pzj.2	Q8NG77	OTTHUMG00000040457	ENST00000317996.1:c.92_93delinsTA	chr1.hg19:g.248458788_248458789delinsTA	ENSP00000324583:p.Ala31Val	221.0|222.0	0.0		202.0	51.0	NM_001004692		Silent|Missense_Mutation	SNP	ENST00000317996.1	hg19	CCDS31110.1																																																																																			.	.		0.495	OR2T12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097353.1	NM_001004692		TA	248458789	GG	TA	248458788	3	4	346	1	0	0	0	0	1	0	0	0	11028	1335	47	3	872	3	OR2T12	1	248458788	Missense_Mutation	DNP	GG	TCGA-UB-A7MD-01A-12D-A34Z-10	17543991	248458788	791833	8	48850										
CAD	790	hgsc.bcm.edu	37	chr2	27460247	27460247	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	ctgcttccattttctcccagGattgattgatgtccatgtgc	8	11	1	2			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr2:27460247G>T	ENST00000403525.1	+	27	4352	c.4208G>T	c.(4207-4209)gGa>gTa	p.G1403V	CAD_ENST00000264705.4_Splice_Site_p.G1466V			O76075	DFFB_HUMAN	carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	0					apoptotic chromosome condensation (GO:0030263)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			NS(1)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(40)|ovary(6)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	92	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTTCTCCCAGGATTGATTGAT	0.532																																					p.G1466V		Atlas-SNP	.											.	CAD	199	.	0			c.G4397T						.						77	78	77					2																	27460247		2203	4300	6503	SO:0001630	splice_region_variant	790	exon28			TCCCAGGATTGAT	D78586	CCDS1742.1	2p22-p21	2012-10-02			ENSG00000084774	ENSG00000084774	2.1.3.2, 3.5.2.-		1424	protein-coding gene	gene with protein product		114010				8619816, 2565865	Standard	NM_004341		Approved		uc002rji.3	P27708	OTTHUMG00000097070	ENST00000403525.1:c.4208-1G>T	chr2.hg19:g.27460247G>T		62.0	0.0		43.0	18.0	NM_004341	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Missense_Mutation	SNP	ENST00000403525.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.1|25.1	4.598426|4.598426	0.87055|0.87055	.|.	.|.	ENSG00000084774|ENSG00000084774	ENST00000458503|ENST00000264705;ENST00000403525	.|T;T	.|0.69806	.|-0.43;-0.43	5.09|5.09	5.09|5.09	0.68999|0.68999	.|Methylglyoxal synthase-like domain (1);Amidohydrolase 1 (1);	.|0.047590	.|0.85682	.|D	.|0.000000	D|D	0.89798|0.89798	0.6819|0.6819	H|H	0.99130|0.99130	4.44|4.44	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|1.0;1.0	D|D	0.94202|0.94202	0.7451|0.7451	5|9	.|.	.|.	.|.	.|.	17.0773|17.0773	0.86590|0.86590	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1403;1466	.|F8VPD4;P27708	.|.;PYR1_HUMAN	Y|V	118|1466;1403	.|ENSP00000264705:G1466V;ENSP00000384510:G1403V	.|.	D|G	+|+	1|2	0|0	CAD|CAD	27313751|27313751	1.000000|1.000000	0.71417|0.71417	0.942000|0.942000	0.38095|0.38095	0.931000|0.931000	0.56810|0.56810	9.255000|9.255000	0.95524|0.95524	2.365000|2.365000	0.80145|0.80145	0.561000|0.561000	0.74099|0.74099	GAT|GGA	.	.		0.532	CAD-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000324970.1		Missense_Mutation	T	27460247	G	T	27460247	5	4	346	1	0	0	0	0	0	0	1	0	2567	1188	41	3	4507	3	CAD	2	27460247	Splice_Site	SNP	G	TCGA-UB-A7MD-01A-12D-A34Z-10		27460247	215739126	9	48851										
SMEK2	57223	hgsc.bcm.edu	37	chr2	55825809	55825809	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	atattcaaggcatcccacgaCatccatgatacactcatcag	5	13	3	1			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr2:55825809C>T	ENST00000345102.5	-	4	965	c.664G>A	c.(664-666)Gtc>Atc	p.V222I	SMEK2_ENST00000407823.3_Missense_Mutation_p.V222I|SMEK2_ENST00000272313.5_Missense_Mutation_p.V222I	NM_001122964.1	NP_001116436	Q5MIZ7	P4R3B_HUMAN	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	222					positive regulation of gluconeogenesis (GO:0045722)|protein dephosphorylation (GO:0006470)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)				kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	16			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			CATCCCACGACATCCATGATA	0.368																																					p.V222I		Atlas-SNP	.											.	SMEK2	86	.	0			c.G664A						.						96	94	95					2																	55825809		2203	4300	6503	SO:0001583	missense	57223	exon4			CCACGACATCCAT	AB037808	CCDS1855.1, CCDS46289.1, CCDS62913.1	2p16.1	2008-09-15			ENSG00000138041				29267	protein-coding gene	gene with protein product		610352				16085932, 18614045	Standard	NM_001122964		Approved	PSY2, FLFL2, KIAA1387, FLJ31474	uc002rzc.3	Q5MIZ7	OTTHUMG00000129336	ENST00000345102.5:c.664G>A	chr2.hg19:g.55825809C>T	ENSP00000339769:p.Val222Ile	94.0	0.0		137.0	46.0	NM_001122964	Q6P9B0|Q86XB8|Q9BQJ0|Q9BRK2|Q9H913|Q9P2G0	Missense_Mutation	SNP	ENST00000345102.5	hg19	CCDS46289.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.889305	0.91889	.	.	ENSG00000138041	ENST00000272313;ENST00000407823;ENST00000345102	T;T;T	0.47528	0.84;0.84;0.84	5.59	5.59	0.84812	Domain of unknown function DUF625 (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.57917	0.2086	M	0.62266	1.93	0.80722	D	1	B;B;B;P	0.39551	0.282;0.329;0.154;0.678	B;P;B;B	0.47075	0.247;0.536;0.249;0.437	T	0.52563	-0.8559	10	0.33141	T	0.24	-6.6529	19.5832	0.95478	0.0:1.0:0.0:0.0	.	222;222;222;222	Q5MIZ7-2;Q5MIZ7;Q5MIZ7-3;B4DKA9	.;P4R3B_HUMAN;.;.	I	222	ENSP00000272313:V222I;ENSP00000385912:V222I;ENSP00000339769:V222I	ENSP00000272313:V222I	V	-	1	0	SMEK2	55679313	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.814000	0.86154	2.621000	0.88768	0.655000	0.94253	GTC	.	.		0.368	SMEK2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251483.1	NM_020463		T	55825809	C	T	55825809	3	4	346	1	0	0	0	0	1	0	0	0	14809	478	17	3	1941	3	SMEK2	2	55825809	Missense_Mutation	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	28365562	55825809	187373564	10	48852										
PCDP1	200373	hgsc.bcm.edu	37	chr2	120385299	120385299	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	accagccggttctctgtgtcGcccaaggaggtgctgccctt	12	14	1	0	rs202085071	byFrequency	TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr2:120385299G>A	ENST00000413369.3	+	16	1674	c.1587G>A	c.(1585-1587)tcG>tcA	p.S529S	PCDP1_ENST00000597189.1_3'UTR|PCDP1_ENST00000602047.1_Silent_p.S243S	NM_001271049.1	NP_001257978																Colorectal(110;0.196)					TCTCTGTGTCGCCCAAGGAGG	0.557													G|||	2	0.000399361	0	0	5008	,	,		13612	0.002		0	False		,,,				2504	0				p.S529S		Atlas-SNP	.											.	.	.	.	0			c.G1587A						.	G		0,4406		0,0,2203	110	113	112		729	-8.5	0	2		112	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PCDP1	NM_001029996.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		243/555	120385299	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	0	exon16			TGTGTCGCCCAAG																												ENST00000413369.3:c.1587G>A	chr2.hg19:g.120385299G>A		126.0	0.0		134.0	45.0	NM_001271049		Silent	SNP	ENST00000413369.3	hg19	CCDS33282.2	.	.	.	.	.	.	.	.	.	.	G	4.090	0.014659	0.07959	0.0	1.16E-4	ENSG00000163075	ENST00000443972;ENST00000413057	.	.	.	4.27	-8.54	0.00912	.	.	.	.	.	T	0.25195	0.0612	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.20042	-1.0287	4	.	.	.	2.1415	7.6382	0.28277	0.1542:0.0953:0.6558:0.0946	.	.	.	.	H	88;77	.	.	R	+	2	0	AC069154.2	120101769	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.881000	0.00715	-2.657000	0.00421	-0.140000	0.14226	CGC	.	G|0.999;A|0.001		0.557	PCDP1-006	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464236.1			A	120385299	G	A	120385299	2	1	346	1	0	0	0	0	0	0	0	1	11581	1074	38	1		1	PCDP1	2	120385299	Silent	SNP	G	TCGA-UB-A7MD-01A-12D-A34Z-10	64559490	120385299	122814074	11	48853										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168098387	168098387	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	gaaaagatcctttattctgaCaaagagatgacaaccccagc	7	10	1	4			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr2:168098387C>A	ENST00000409728.1	+	9	1331	c.1242C>A	c.(1240-1242)gaC>gaA	p.D414E	XIRP2_ENST00000409043.1_Missense_Mutation_p.D381E|XIRP2_ENST00000409605.1_Missense_Mutation_p.D159E|XIRP2_ENST00000409273.1_Missense_Mutation_p.D159E|XIRP2_ENST00000295237.9_Missense_Mutation_p.D381E|XIRP2_ENST00000409195.1_Missense_Mutation_p.D381E|XIRP2_ENST00000420519.1_Missense_Mutation_p.D414E|XIRP2_ENST00000409756.2_Missense_Mutation_p.D381E	NM_001199143.1	NP_001186072.1	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	206					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TTTATTCTGACAAAGAGATGA	0.368																																					p.D414E		Atlas-SNP	.											.	XIRP2	914	.	0			c.C1242A						.						123	117	119					2																	168098387		1834	4078	5912	SO:0001583	missense	129446	exon9			TTCTGACAAAGAG	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409728.1:c.1242C>A	chr2.hg19:g.168098387C>A	ENSP00000386619:p.Asp414Glu	50.0	0.0		57.0	19.0	NM_001199143	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409728.1	hg19	CCDS56143.1	.	.	.	.	.	.	.	.	.	.	C	18.17	3.564919	0.65651	.	.	ENSG00000163092	ENST00000409043;ENST00000409728;ENST00000409195;ENST00000409756;ENST00000420519;ENST00000295237;ENST00000409273;ENST00000409605	T;T;T;T;T;T;T;T	0.77489	-1.1;-1.1;4.13;-1.1;-1.1;4.13;4.17;-1.09	5.27	3.44	0.39384	.	0.292782	0.36815	N	0.002394	D	0.83294	0.5223	M	0.62723	1.935	0.27451	N	0.953436	D;D;D;P;P	0.71674	0.957;0.998;0.998;0.947;0.933	P;D;D;P;P	0.65573	0.526;0.913;0.936;0.673;0.597	T	0.75673	-0.3236	10	0.59425	D	0.04	-6.5178	9.7168	0.40278	0.0:0.8356:0.0:0.1644	.	206;381;414;206;159	A4UGR9;A4UGR9-4;A4UGR9-6;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.;.;.	E	381;414;381;381;414;381;159;159	ENSP00000386454:D381E;ENSP00000386619:D414E;ENSP00000386840:D381E;ENSP00000386724:D381E;ENSP00000415541:D414E;ENSP00000295237:D381E;ENSP00000387255:D159E;ENSP00000386981:D159E	ENSP00000295237:D381E	D	+	3	2	XIRP2	167806633	0.998000	0.40836	0.996000	0.52242	0.781000	0.44180	0.342000	0.19926	0.700000	0.31782	0.591000	0.81541	GAC	.	.		0.368	XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333552.1	NM_152381		A	168098387	C	A	168098387	3	1	346	1	0	0	0	0	1	0	0	0	17445	477	17	3	1169	3	XIRP2	2	168098387	Missense_Mutation	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	47713088	168098387	75100986	12	48854										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168106758	168106758	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	gaattcttgagaaaacgtgaAgaactgcaacagattttgtc	9	6	1	4			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr2:168106758A>G	ENST00000409195.1	+	9	8945	c.8856A>G	c.(8854-8856)gaA>gaG	p.E2952E	XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409273.1_Silent_p.E2730E|XIRP2_ENST00000295237.9_Silent_p.E2952E|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409756.2_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2777					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						GAAAACGTGAAGAACTGCAAC	0.373																																					p.E2952E		Atlas-SNP	.											.	XIRP2	914	.	0			c.A8856G						.						93	91	91					2																	168106758		1826	4085	5911	SO:0001819	synonymous_variant	129446	exon9			ACGTGAAGAACTG	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.8856A>G	chr2.hg19:g.168106758A>G		177.0	0.0		136.0	37.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent	SNP	ENST00000409195.1	hg19	CCDS42769.1																																																																																			.	.		0.373	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		G	168106758	A	G	168106758	2	3	346	1	0	0	0	0	0	0	0	1	17445	69	3	2		2	XIRP2	2	168106758	Silent	SNP	A	TCGA-UB-A7MD-01A-12D-A34Z-10	8371	168106758	75092615	13	48855										
FSIP2	401024	hgsc.bcm.edu	37	chr2	186671281	186671281	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	ctgccaaagaaaaagaagagGaagagagagaaaaagagaaa	12	3	0	6			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr2:186671281G>C	ENST00000424728.1	+	17	17248	c.17248G>C	c.(17248-17250)Gaa>Caa	p.E5750Q	FSIP2_ENST00000343098.5_Missense_Mutation_p.E5839Q			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	5750										NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						aaaagaagaggaagagagaga	0.368																																					p.E5839Q		Atlas-SNP	.											.	FSIP2	251	.	0			c.G17515C						.						54	51	52					2																	186671281		1815	4069	5884	SO:0001583	missense	401024	exon17			GAAGAGGAAGAGA	AK092099	CCDS54426.1	2q32.1	2010-06-18			ENSG00000188738	ENSG00000188738			21675	protein-coding gene	gene with protein product		615796				14702039	Standard	NM_173651		Approved	FLJ34780	uc002upl.3	Q5CZC0	OTTHUMG00000153874	ENST00000424728.1:c.17248G>C	chr2.hg19:g.186671281G>C	ENSP00000401306:p.Glu5750Gln	70.0	0.0		61.0	5.0	NM_173651	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Missense_Mutation	SNP	ENST00000424728.1	hg19		.	.	.	.	.	.	.	.	.	.	G	12.36	1.915401	0.33815	.	.	ENSG00000188738	ENST00000343098;ENST00000424728	T;T	0.49139	0.79;0.79	4.66	-2.92	0.05615	.	.	.	.	.	T	0.26593	0.0650	N	0.19112	0.55	0.09310	N	1	.	.	.	.	.	.	T	0.21690	-1.0238	7	0.46703	T	0.11	.	1.1887	0.01860	0.4679:0.1467:0.242:0.1433	.	.	.	.	Q	5839;5750	ENSP00000344403:E5839Q;ENSP00000401306:E5750Q	ENSP00000344403:E5839Q	E	+	1	0	FSIP2	186379526	0.000000	0.05858	0.000000	0.03702	0.347000	0.29111	-1.723000	0.01866	-0.807000	0.04393	-0.216000	0.12614	GAA	.	.		0.368	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651		C	186671281	G	C	186671281	3	2	346	1	0	0	0	0	1	0	0	0	6083	1175	41	4	17581	4	FSIP2	2	186671281	Missense_Mutation	SNP	G	TCGA-UB-A7MD-01A-12D-A34Z-10	18564523	186671281	56528092	14	48856										
ALS2CR8	79800	hgsc.bcm.edu	37	chr2	203834763	203834763	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	acatgctaaagaagaacttgGtagatgctggtggtgttctt	12	5	1	3			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr2:203834763G>A	ENST00000402905.3	+	10	1396	c.1075G>A	c.(1075-1077)Gta>Ata	p.V359I	CARF_ENST00000428585.1_Missense_Mutation_p.V283I|CARF_ENST00000545262.1_Missense_Mutation_p.V283I|CARF_ENST00000438828.2_Missense_Mutation_p.V359I|CARF_ENST00000414439.1_Missense_Mutation_p.V257I|CARF_ENST00000456821.2_3'UTR|CARF_ENST00000545253.1_Missense_Mutation_p.V271I|CARF_ENST00000320443.8_Missense_Mutation_p.V359I|WDR12_ENST00000477723.1_Intron	NM_001104586.1|NM_001282910.1|NM_001282911.1|NM_001282912.1	NP_001098056.1|NP_001269839.1|NP_001269840.1|NP_001269841.1	Q8N187	CARTF_HUMAN	calcium responsive transcription factor	359					cellular response to calcium ion (GO:0071277)|cellular response to potassium ion (GO:0035865)|positive regulation of transcription from RNA polymerase II promoter in response to calcium ion (GO:0061400)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)										GAAGAACTTGGTAGATGCTGG	0.313																																					p.V359I		Atlas-SNP	.											.	ALS2CR8	56	.	0			c.G1075A						.						116	109	111					2																	203834763		1823	4074	5897	SO:0001583	missense	79800	exon11			AACTTGGTAGATG	AB053309	CCDS42801.1, CCDS63091.1	2q33.3	2013-06-12	2013-06-12	2013-06-12	ENSG00000138380	ENSG00000138380			14435	protein-coding gene	gene with protein product	"calcium-response factor"	607586	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 8"	ALS2CR8		11586298, 11832226	Standard	XM_005246858		Approved	FLJ21579, CaRF, NYD-SP24	uc002uzo.2	Q8N187	OTTHUMG00000154528	ENST00000402905.3:c.1075G>A	chr2.hg19:g.203834763G>A	ENSP00000384006:p.Val359Ile	275.0	0.0		262.0	60.0	NM_024744	B4E1W7|G3V1K7|Q8ND29|Q8WXC0|Q96J78|Q96Q38|Q96Q39|Q9H712	Missense_Mutation	SNP	ENST00000402905.3	hg19	CCDS42801.1	.	.	.	.	.	.	.	.	.	.	G	7.620	0.676562	0.14841	.	.	ENSG00000138380	ENST00000402905;ENST00000414439;ENST00000428585;ENST00000545253;ENST00000545262;ENST00000320443;ENST00000438828	.	.	.	5.26	3.14	0.36123	.	0.358910	0.26499	N	0.024038	T	0.13927	0.0337	N	0.03608	-0.345	0.20563	N	0.999884	B;B;B	0.09022	0.002;0.002;0.002	B;B;B	0.14578	0.011;0.011;0.005	T	0.22277	-1.0221	9	0.17369	T	0.5	-6.165	6.8921	0.24234	0.3049:0.0:0.6951:0.0	.	271;283;359	B4DIA7;G3V1K7;Q8N187	.;.;AL2S8_HUMAN	I	359;257;283;271;283;359;359	.	ENSP00000316224:V359I	V	+	1	0	ALS2CR8	203543008	1.000000	0.71417	0.943000	0.38184	0.995000	0.86356	1.754000	0.38369	1.175000	0.42826	0.650000	0.86243	GTA	.	.		0.313	CARF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335768.5	NM_001104586		A	203834763	G	A	203834763	3	1	346	1	0	0	0	0	1	0	0	0	555	1261	44	3	1105	3	ALS2CR8	2	203834763	Missense_Mutation	SNP	G	TCGA-UB-A7MD-01A-12D-A34Z-10	17163482	203834763	39364610	15	48857										
ZDBF2	57683	hgsc.bcm.edu	37	chr2	207174747	207174747	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	ttcatttgtggggaaaacatGgtctcagataatgagagaag	12	4	2	3			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr2:207174747G>A	ENST00000374423.3	+	5	5881	c.5495G>A	c.(5494-5496)tGg>tAg	p.W1832*		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1832							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						GGGAAAACATGGTCTCAGATA	0.413																																					p.W1832X		Atlas-SNP	.											.	ZDBF2	531	.	0			c.G5495A						.						79	78	78					2																	207174747		1881	4107	5988	SO:0001587	stop_gained	57683	exon5			AAACATGGTCTCA	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"Zinc fingers, DBF-type"	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.5495G>A	chr2.hg19:g.207174747G>A	ENSP00000363545:p.Trp1832*	96.0	0.0		74.0	20.0	NM_020923	Q6ZNP7|Q6ZSN8	Nonsense_Mutation	SNP	ENST00000374423.3	hg19	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	G	48	14.249833	0.99786	.	.	ENSG00000204186	ENST00000374423	.	.	.	5.61	4.72	0.59763	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.7862	0.85575	0.0:0.1287:0.8713:0.0	.	.	.	.	X	1832	.	ENSP00000363545:W1832X	W	+	2	0	ZDBF2	206882992	0.999000	0.42202	0.998000	0.56505	0.998000	0.95712	1.491000	0.35583	1.360000	0.45960	0.644000	0.83932	TGG	.	.		0.413	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		A	207174747	G	A	207174747	4	1	346	1	0	0	0	0	0	1	0	0	17614	1357	47	3	5505	3	ZDBF2	2	207174747	Nonsense_Mutation	SNP	G	TCGA-UB-A7MD-01A-12D-A34Z-10	3339984	207174747	36024626	16	48858										
EPHA4	2043	hgsc.bcm.edu	37	chr2	222347339	222347339	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	gcggccacctgtattctgagGgctactccattccaagttca	9	13	2	1			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr2:222347339G>T	ENST00000281821.2	-	5	1092	c.1051C>A	c.(1051-1053)Cct>Act	p.P351T	EPHA4_ENST00000392071.4_Missense_Mutation_p.P300T|EPHA4_ENST00000409854.1_Missense_Mutation_p.P351T|EPHA4_ENST00000409938.1_Missense_Mutation_p.P351T	NM_004438.3	NP_004429.1	P54764	EPHA4_HUMAN	EPH receptor A4	351	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult walking behavior (GO:0007628)|cell adhesion (GO:0007155)|corticospinal tract morphogenesis (GO:0021957)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|glial cell migration (GO:0008347)|motor neuron axon guidance (GO:0008045)|negative regulation of axon regeneration (GO:0048681)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001108)|protein autophosphorylation (GO:0046777)|regulation of astrocyte differentiation (GO:0048710)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rap GTPase activity (GO:0032317)	axon (GO:0030424)|axon terminus (GO:0043679)|axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|DH domain binding (GO:0097161)|GPI-linked ephrin receptor activity (GO:0005004)|PH domain binding (GO:0042731)|protein kinase activity (GO:0004672)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		GTATTCTGAGGGCTACTCCAT	0.502																																					p.P351T		Atlas-SNP	.											.	EPHA4	263	.	0			c.C1051A						.						133	146	141					2																	222347339		2203	4300	6503	SO:0001583	missense	2043	exon5			TCTGAGGGCTACT	L36645	CCDS2447.1	2q36.3	2013-02-11	2004-10-28		ENSG00000116106	ENSG00000116106	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3388	protein-coding gene	gene with protein product		602188	"EphA4"	TYRO1		9267020	Standard	NM_004438		Approved	Hek8	uc002vmq.3	P54764	OTTHUMG00000133142	ENST00000281821.2:c.1051C>A	chr2.hg19:g.222347339G>T	ENSP00000281821:p.Pro351Thr	71.0	0.0		83.0	31.0	NM_004438	A8K2P1|B2R601|B7Z6Q8|Q2M380	Missense_Mutation	SNP	ENST00000281821.2	hg19	CCDS2447.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.990779	0.93106	.	.	ENSG00000116106	ENST00000281821;ENST00000409854;ENST00000409938;ENST00000392071;ENST00000443796	T;T;T;T;T	0.63096	0.02;0.02;0.02;0.02;-0.02	5.91	5.91	0.95273	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.86497	0.5947	H	0.95780	3.72	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89505	0.3767	10	0.87932	D	0	.	20.2983	0.98569	0.0:0.0:1.0:0.0	.	351	P54764	EPHA4_HUMAN	T	351;351;351;300;55	ENSP00000281821:P351T;ENSP00000386276:P351T;ENSP00000386829:P351T;ENSP00000375923:P300T;ENSP00000395917:P55T	ENSP00000281821:P351T	P	-	1	0	EPHA4	222055583	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.869000	0.99810	2.802000	0.96397	0.655000	0.94253	CCT	.	.		0.502	EPHA4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256836.3			T	222347339	G	T	222347339	3	4	346	1	0	0	0	0	1	0	0	0	5171	1232	43	3	1961	3	EPHA4	2	222347339	Missense_Mutation	SNP	G	TCGA-UB-A7MD-01A-12D-A34Z-10	15172592	222347339	20852034	17	48859										
SPHKAP	80309	hgsc.bcm.edu	37	chr2	228855885	228855885	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	ggctggctgttcccgtaggcGgtccagatgcaggtgctgag	17	10	0	2			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr2:228855885G>A	ENST00000392056.3	-	11	4836	c.4790C>T	c.(4789-4791)cCg>cTg	p.P1597L	SPHKAP_ENST00000344657.5_Missense_Mutation_p.P1568L	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	1597						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)			NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		TCCCGTAGGCGGTCCAGATGC	0.572																																					p.P1597L		Atlas-SNP	.											.	SPHKAP	750	.	0			c.C4790T						.						59	58	58					2																	228855885		2203	4300	6503	SO:0001583	missense	80309	exon11			GTAGGCGGTCCAG		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"A-kinase anchor proteins"	30619	protein-coding gene	gene with protein product	"sphingosine kinase type 1-interacting protein"	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.4790C>T	chr2.hg19:g.228855885G>A	ENSP00000375909:p.Pro1597Leu	100.0	0.0		92.0	24.0	NM_001142644	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	hg19	CCDS46537.1	.	.	.	.	.	.	.	.	.	.	A	0.114	-1.134243	0.01742	.	.	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.12255	2.7;2.7	6.17	-4.12	0.03916	A-kinase anchor 110kDa, C-terminal (1);	1.207290	0.05787	N	0.609652	T	0.02304	0.0071	N	0.00197	-1.87	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39187	-0.9626	10	0.12766	T	0.61	.	4.0356	0.09729	0.4099:0.1064:0.3807:0.103	.	1597;1568	Q2M3C7;Q2M3C7-2	SPKAP_HUMAN;.	L	1597;1568	ENSP00000375909:P1597L;ENSP00000339886:P1568L	ENSP00000339886:P1568L	P	-	2	0	SPHKAP	228564129	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	0.269000	0.18589	-0.926000	0.03770	-0.254000	0.11334	CCG	.	.		0.572	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623		A	228855885	G	A	228855885	3	1	346	1	0	0	0	0	1	0	0	0	15063	1116	39	1	320	1	SPHKAP	2	228855885	Missense_Mutation	SNP	G	TCGA-UB-A7MD-01A-12D-A34Z-10	6508546	228855885	14343488	18	48860										
DNER	92737	hgsc.bcm.edu	37	chr2	230411752	230411752	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	cacacaggtgctgaccttcaCcaccagagttaagcgcaaag	9	13	1	2			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr2:230411752C>T	ENST00000341772.4	-	5	1038	c.904G>A	c.(904-906)Gtg>Atg	p.V302M		NM_139072.3	NP_620711.3	Q8NFT8	DNER_HUMAN	delta/notch-like EGF repeat containing	302					central nervous system development (GO:0007417)|endocytosis (GO:0006897)|glial cell differentiation (GO:0010001)|neuron migration (GO:0001764)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|skeletal muscle fiber development (GO:0048741)|synapse assembly (GO:0007416)	dendrite (GO:0030425)|early endosome (GO:0005769)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|clathrin binding (GO:0030276)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	63		all_lung(227;0.00413)|Renal(207;0.0113)|Lung NSC(271;0.0211)|all_hematologic(139;0.105)|Acute lymphoblastic leukemia(138;0.175)		Epithelial(121;1.4e-11)|all cancers(144;7.7e-09)|LUSC - Lung squamous cell carcinoma(224;0.034)|Lung(119;0.0375)		CTGACCTTCACCACCAGAGTT	0.468																																					p.V302M		Atlas-SNP	.											.	DNER	129	.	0			c.G904A						.						141	119	126					2																	230411752		2203	4300	6503	SO:0001583	missense	92737	exon5			CCTTCACCACCAG	AY358891	CCDS33390.1	2q36.3	2006-10-26			ENSG00000187957	ENSG00000187957			24456	protein-coding gene	gene with protein product		607299				11950833, 11997712	Standard	NM_139072		Approved	UNQ26, bet	uc002vpv.3	Q8NFT8	OTTHUMG00000153637	ENST00000341772.4:c.904G>A	chr2.hg19:g.230411752C>T	ENSP00000345229:p.Val302Met	34.0	0.0		54.0	21.0	NM_139072	A6NP39|Q53R88|Q53TP7|Q53TQ5|Q8IYT0|Q8TB42|Q9NTF1|Q9UDM2	Missense_Mutation	SNP	ENST00000341772.4	hg19	CCDS33390.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.523852	0.85600	.	.	ENSG00000187957	ENST00000341772;ENST00000543700	D	0.87729	-2.29	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	D	0.90669	0.7073	L	0.34521	1.04	0.58432	D	0.999998	D	0.76494	0.999	D	0.80764	0.994	D	0.90652	0.4583	10	0.54805	T	0.06	.	20.0518	0.97629	0.0:1.0:0.0:0.0	.	302	Q8NFT8	DNER_HUMAN	M	302;30	ENSP00000345229:V302M	ENSP00000345229:V302M	V	-	1	0	DNER	230119996	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.427000	0.66483	2.744000	0.94065	0.650000	0.86243	GTG	.	.		0.468	DNER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331902.1	NM_139072		T	230411752	C	T	230411752	3	4	346	1	0	0	0	0	1	0	0	0	4669	507	18	3	1345	3	DNER	2	230411752	Missense_Mutation	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	1555867	230411752	12787621	19	48861										
KCNJ13	3769	hgsc.bcm.edu	37	chr2	233632998	233632998	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	tgtttgggcttttagaaaccAgaggagttggaaattcaggg	14	4	1	2			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr2:233632998A>G	ENST00000233826.3	-	3	1125	c.986T>C	c.(985-987)cTg>cCg	p.L329P	KCNJ13_ENST00000409779.1_3'UTR|GIGYF2_ENST00000409451.3_Intron|AC064852.4_ENST00000427571.1_RNA|GIGYF2_ENST00000409547.1_Intron|GIGYF2_ENST00000373563.4_Intron|KCNJ13_ENST00000410029.1_Missense_Mutation_p.L329P|GIGYF2_ENST00000373566.3_Intron|GIGYF2_ENST00000409196.3_Intron|GIGYF2_ENST00000409480.1_Intron|GIGYF2_ENST00000452341.2_Intron	NM_002242.4	NP_002233.2	O60928	KCJ13_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 13	329					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)	integral component of membrane (GO:0016021)	inward rectifier potassium channel activity (GO:0005242)			endometrium(3)|large_intestine(2)|lung(2)|stomach(1)|urinary_tract(1)	9		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0306)|Lung NSC(271;0.0908)		Epithelial(121;5.9e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0617)		TTTAGAAACCAGAGGAGTTGG	0.413																																					p.L329P		Atlas-SNP	.											.	KCNJ13	18	.	0			c.T986C						.						130	132	131					2																	233632998		2203	4300	6503	SO:0001583	missense	3769	exon3			GAAACCAGAGGAG	AJ006128	CCDS2498.1, CCDS54437.1	2q37	2014-01-28			ENSG00000115474	ENSG00000115474		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6259	protein-coding gene	gene with protein product		603208				9878260, 9620703, 16382105	Standard	NM_002242		Approved	Kir7.1, Kir1.4, LCA16	uc002vtp.3	O60928	OTTHUMG00000153292	ENST00000233826.3:c.986T>C	chr2.hg19:g.233632998A>G	ENSP00000233826:p.Leu329Pro	193.0	0.0		153.0	54.0	NM_002242	A0PGH1|O76023|Q53SA1|Q8N3Y4	Missense_Mutation	SNP	ENST00000233826.3	hg19	CCDS2498.1	.	.	.	.	.	.	.	.	.	.	A	12.02	1.812597	0.32053	.	.	ENSG00000115474	ENST00000233826;ENST00000410029	D;D	0.92048	-2.96;-2.96	6.17	3.87	0.44632	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.772320	0.12006	N	0.508323	D	0.89104	0.6620	L	0.51422	1.61	0.42359	D	0.992407	B	0.26041	0.14	B	0.34346	0.18	D	0.84729	0.0744	10	0.35671	T	0.21	.	6.5608	0.22485	0.8333:0.0:0.1667:0.0	.	329	O60928	IRK13_HUMAN	P	329	ENSP00000233826:L329P;ENSP00000386251:L329P	ENSP00000233826:L329P	L	-	2	0	KCNJ13	233341242	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.375000	0.52410	2.371000	0.80710	0.533000	0.62120	CTG	.	.		0.413	KCNJ13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257036.1	NM_002242		G	233632998	A	G	233632998	3	3	346	1	0	0	0	0	1	0	0	0	8056	188	7	2	100	2	KCNJ13	2	233632998	Missense_Mutation	SNP	A	TCGA-UB-A7MD-01A-12D-A34Z-10	3221246	233632998	9566375	20	48862										
COL6A3	1293	hgsc.bcm.edu	37	chr2	238256451	238256451	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	aaggcccacgcaaacttaccCttcggcctctgatgcctttg	8	15	1	1			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr2:238256451C>G	ENST00000295550.4	-	31	7480	c.7028G>C	c.(7027-7029)aGg>aCg	p.R2343T	COL6A3_ENST00000346358.4_Splice_Site_p.R2143T|COL6A3_ENST00000409809.1_Splice_Site_p.R2137T|COL6A3_ENST00000472056.1_Splice_Site_p.R1736T|COL6A3_ENST00000347401.3_Splice_Site_p.R2142T|COL6A3_ENST00000353578.4_Splice_Site_p.R2137T	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2343	Collagen-like 5.|Triple-helical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		CAAACTTACCCTTCGGCCTCT	0.507																																					p.R2343T		Atlas-SNP	.											.	COL6A3	608	.	0			c.G7028C						.						146	113	124					2																	238256451		2203	4300	6503	SO:0001630	splice_region_variant	1293	exon31			CTTACCCTTCGGC	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.7029+1G>C	chr2.hg19:g.238256451C>G		55.0	0.0		43.0	10.0	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	hg19	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	17.86	3.492166	0.64074	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	D;D;D;D;D;D	0.93488	-3.23;-3.17;-3.17;-2.88;-3.17;-3.17	4.56	4.56	0.56223	.	0.000000	0.52532	D	0.000077	D	0.93871	0.8039	L	0.28054	0.825	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;0.999	D;D;D;D	0.91635	0.999;0.998;0.999;0.976	D	0.93711	0.7024	10	0.40728	T	0.16	.	16.5242	0.84326	0.0:1.0:0.0:0.0	.	1736;1736;2137;2343	E9PFQ6;B7ZMJ7;P12111-2;P12111	.;.;.;CO6A3_HUMAN	T	2343;2142;2137;1736;2137;2143	ENSP00000295550:R2343T;ENSP00000315609:R2142T;ENSP00000315873:R2137T;ENSP00000418285:R1736T;ENSP00000386844:R2137T;ENSP00000295546:R2143T	ENSP00000295550:R2343T	R	-	2	0	COL6A3	237921190	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	4.008000	0.57103	2.374000	0.81015	0.655000	0.94253	AGG	.	.		0.507	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	Missense_Mutation	G	238256451	C	G	238256451	5	3	346	1	0	0	0	0	0	0	1	0	3703	695	24	4	2561	4	COL6A3	2	238256451	Splice_Site	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	4623453	238256451	4942922	21	48863										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266097	41266097	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	ggcagcaacagtcttacctgGactctggaatccattctggt	10	11	3	0	rs28931588|rs121913416|rs121913417		TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr3:41266097G>A	ENST00000349496.5	+	3	374	c.94G>A	c.(94-96)Gac>Aac	p.D32N	CTNNB1_ENST00000453024.1_Missense_Mutation_p.D25N|CTNNB1_ENST00000396183.3_Missense_Mutation_p.D32N|CTNNB1_ENST00000396185.3_Missense_Mutation_p.D32N|CTNNB1_ENST00000405570.1_Missense_Mutation_p.D32N	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	32			D -> A (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|D -> G (in PTR and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629}.|D -> Y (in PTR, hepatoblastoma and hepatocellular carcinoma; dbSNP:rs28931588). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:11703283, ECO:0000269|PubMed:9927029}.|Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.D32Y(128)|p.D32N(82)|p.A5_A80del(53)|p.D32H(40)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.WQQQSYLD25?(5)|p.W25_D32del(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.S29_H36del(1)|p.D32del(1)|p.M14_S45del(1)|p.Q28_D32>H(1)|p.Q28fs*20(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.D32fs*9(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GTCTTACCTGGACTCTGGAAT	0.478	D32N(KE39_STOMACH)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.D32N	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,0,2	CTNNB1	4904	.	397	Substitution - Missense(250)|Deletion - In frame(120)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)|Complex - frameshift(1)	liver(155)|central_nervous_system(55)|endometrium(40)|stomach(36)|pancreas(28)|large_intestine(22)|pituitary(22)|skin(11)|ovary(9)|soft_tissue(4)|prostate(4)|small_intestine(2)|haematopoietic_and_lymphoid_tissue(2)|bone(2)|adrenal_gland(1)|biliary_tract(1)|urinary_tract(1)|lung(1)|NS(1)	c.G94A						.						92	77	82					3																	41266097		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	TACCTGGACTCTG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.94G>A	chr3.hg19:g.41266097G>A	ENSP00000344456:p.Asp32Asn	147.0	0.0		124.0	37.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	G	30	5.054970	0.93793	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.49432	0.78;0.78;0.78;0.78;0.78;0.78;0.78;0.78;0.78	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.71567	0.3355	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.72982	0.979	T	0.73824	-0.3861	10	0.87932	D	0	0.3843	19.9596	0.97236	0.0:0.0:1.0:0.0	.	32	P35222	CTNB1_HUMAN	N	25;32;32;32;32;25;32;32;32	ENSP00000400508:D25N;ENSP00000385604:D32N;ENSP00000412219:D32N;ENSP00000379486:D32N;ENSP00000344456:D32N;ENSP00000411226:D25N;ENSP00000379488:D32N;ENSP00000409302:D32N;ENSP00000401599:D32N	ENSP00000344456:D32N	D	+	1	0	CTNNB1	41241101	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.726000	0.93360	0.655000	0.94253	GAC	.	.		0.478	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		A	41266097	G	A	41266097	3	1	346	1	0	0	0	0	1	0	0	0	4018	1174	41	3	100	3	CTNNB1	3	41266097	Missense_Mutation	SNP	G	TCGA-UB-A7MD-01A-12D-A34Z-10		41266097	156756333	22	48864										
GSK3B	2932	hgsc.bcm.edu	37	chr3	119631579	119631579	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	gaggtataatcagtggctccAaagatcaactctggtgccct	10	10	3	1			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr3:119631579A>C	ENST00000264235.8	-	6	1669	c.687T>G	c.(685-687)ttT>ttG	p.F229L	GSK3B_ENST00000316626.5_Missense_Mutation_p.F229L	NM_001146156.1|NM_002093.3	NP_001139628.1|NP_002084.2	P49841	GSK3B_HUMAN	glycogen synthase kinase 3 beta	229	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell migration (GO:0016477)|cellular response to interleukin-3 (GO:0036016)|cellular response to mechanical stimulus (GO:0071260)|circadian rhythm (GO:0007623)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial to mesenchymal transition (GO:0001837)|ER overload response (GO:0006983)|establishment of cell polarity (GO:0030010)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fat cell differentiation (GO:0045444)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glycogen metabolic process (GO:0005977)|hippocampus development (GO:0021766)|hypermethylation of CpG island (GO:0044027)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|myoblast fusion (GO:0007520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of neuron maturation (GO:0014043)|negative regulation of neuron projection development (GO:0010977)|negative regulation of NFAT protein import into nucleus (GO:0051534)|negative regulation of protein binding (GO:0032091)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of type B pancreatic cell development (GO:2000077)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein binding (GO:0032092)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of stem cell differentiation (GO:2000738)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|protein localization to microtubule (GO:0035372)|protein phosphorylation (GO:0006468)|re-entry into mitotic cell cycle (GO:0000320)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of microtubule-based process (GO:0032886)|regulation of neuronal synaptic plasticity (GO:0048168)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|superior temporal gyrus development (GO:0071109)	beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|kinase activity (GO:0016301)|NF-kappaB binding (GO:0051059)|p53 binding (GO:0002039)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II transcription factor binding (GO:0001085)|tau-protein kinase activity (GO:0050321)|ubiquitin protein ligase binding (GO:0031625)			endometrium(1)|large_intestine(8)|lung(7)|prostate(2)	18				GBM - Glioblastoma multiforme(114;0.24)	Lithium(DB01356)	CAGTGGCTCCAAAGATCAACT	0.343																																					p.F229L		Atlas-SNP	.											.	GSK3B	119	.	0			c.T687G						.						69	69	69					3																	119631579		2203	4299	6502	SO:0001583	missense	2932	exon6			GGCTCCAAAGATC	BC012760	CCDS2996.1, CCDS54628.1	3q13.3	2008-02-15			ENSG00000082701	ENSG00000082701			4617	protein-coding gene	gene with protein product		605004				10486203	Standard	NM_002093		Approved		uc003edm.3	P49841	OTTHUMG00000133765	ENST00000264235.8:c.687T>G	chr3.hg19:g.119631579A>C	ENSP00000264235:p.Phe229Leu	66.0	0.0		85.0	21.0	NM_002093	D3DN89|Q9BWH3|Q9UL47	Missense_Mutation	SNP	ENST00000264235.8	hg19	CCDS54628.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.648256	0.87958	.	.	ENSG00000082701	ENST00000264235;ENST00000316626	T;T	0.62639	0.01;0.01	5.27	5.27	0.74061	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.52224	0.1721	N	0.00652	-1.29	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.74914	-0.3502	10	0.87932	D	0	-8.6308	15.347	0.74346	1.0:0.0:0.0:0.0	.	229;229	P49841;P49841-2	GSK3B_HUMAN;.	L	229	ENSP00000264235:F229L;ENSP00000324806:F229L	ENSP00000264235:F229L	F	-	3	2	GSK3B	121114269	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.003000	0.57061	2.212000	0.71576	0.460000	0.39030	TTT	.	.		0.343	GSK3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258240.2			C	119631579	A	C	119631579	3	2	346	1	0	0	0	0	1	0	0	0	6833	127	5	5	642	5	GSK3B	3	119631579	Missense_Mutation	SNP	A	TCGA-UB-A7MD-01A-12D-A34Z-10	78365482	119631579	78390851	23	48865										
PCDH7	5099	hgsc.bcm.edu	37	chr4	30724818	30724818	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	atcccgattctggggacatcCtggtcaataccgtgctggac	11	12	2	0			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr4:30724818C>A	ENST00000361762.2	+	1	2782	c.1774C>A	c.(1774-1776)Ctg>Atg	p.L592M	PCDH7_ENST00000543491.1_Missense_Mutation_p.L592M	NM_002589.2	NP_002580.2	O60245	PCDH7_HUMAN	protocadherin 7	592	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(8)|liver(1)|lung(26)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	55						TGGGGACATCCTGGTCAATAC	0.567																																					p.L592M		Atlas-SNP	.											.	PCDH7	215	.	0			c.C1774A						.						67	62	64					4																	30724818		2203	4300	6503	SO:0001583	missense	5099	exon1			GACATCCTGGTCA	AB006755	CCDS33971.1, CCDS75116.1	4p15	2014-06-13	2007-02-12			ENSG00000169851		"Cadherins / Protocadherins : Non-clustered"	8659	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 120"	602988	"BH-protocadherin (brain-heart)"			9615233	Standard	NM_002589		Approved	BH-Pcdh, PPP1R120	uc021xnd.1	O60245		ENST00000361762.2:c.1774C>A	chr4.hg19:g.30724818C>A	ENSP00000355243:p.Leu592Met	54.0	0.0		38.0	11.0	NM_032457	O60246|O60247|Q4W5C4	Missense_Mutation	SNP	ENST00000361762.2	hg19	CCDS33971.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.17|14.17	2.456135|2.456135	0.43634|0.43634	.|.	.|.	ENSG00000169851|ENSG00000169851	ENST00000361762;ENST00000543491;ENST00000333135|ENST00000511884	T;T|.	0.51574|.	0.7;0.7|.	5.37|5.37	5.37|5.37	0.77165|0.77165	Cadherin (4);Cadherin-like (1);|.	.|.	.|.	.|.	.|.	T|T	0.43590|0.43590	0.1254|0.1254	L|L	0.27053|0.27053	0.805|0.805	0.36509|0.36509	D|D	0.869479|0.869479	P;P;P|.	0.47604|.	0.898;0.898;0.783|.	P;P;P|.	0.50314|.	0.601;0.601;0.637|.	T|T	0.46048|0.46048	-0.9219|-0.9219	9|5	0.52906|.	T|.	0.07|.	.|.	8.0026|8.0026	0.30306|0.30306	0.1614:0.7539:0.0:0.0847|0.1614:0.7539:0.0:0.0847	.|.	592;545;592|.	F5GWJ1;O60245-3;O60245|.	.;.;PCDH7_HUMAN|.	M|H	592;592;545|281	ENSP00000355243:L592M;ENSP00000441802:L592M|.	ENSP00000330302:L545M|.	L|P	+|+	1|2	2|0	PCDH7|PCDH7	30333916|30333916	0.997000|0.997000	0.39634|0.39634	0.999000|0.999000	0.59377|0.59377	0.989000|0.989000	0.77384|0.77384	2.457000|2.457000	0.45005|0.45005	2.793000|2.793000	0.96121|0.96121	0.655000|0.655000	0.94253|0.94253	CTG|CCT	.	.		0.567	PCDH7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360366.1	NM_032457, NM_002589		A	30724818	C	A	30724818	3	1	346	1	0	0	0	0	1	0	0	0	11525	680	24	3	1776	3	PCDH7	4	30724818	Missense_Mutation	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10		30724818	160429458	24	48866										
DCAF4L1	285429	hgsc.bcm.edu	37	chr4	41984023	41984023	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	atccctcctctttggcgagcGaccgatttaacttcattctg	7	13	3	0			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr4:41984023G>T	ENST00000333141.5	+	1	311	c.214G>T	c.(214-216)Gac>Tac	p.D72Y		NM_001029955.3	NP_001025126.2	Q3SXM0	DC4L1_HUMAN	DDB1 and CUL4 associated factor 4-like 1	72								p.D72N(1)		breast(1)|endometrium(5)|kidney(6)|large_intestine(11)|lung(12)|prostate(1)|skin(1)	37						TTTGGCGAGCGACCGATTTAA	0.547																																					p.D72Y		Atlas-SNP	.											DCAF4L1,colon,carcinoma,0,1	DCAF4L1	70	.	1	Substitution - Missense(1)	large_intestine(1)	c.G214T						.						96	81	86					4																	41984023		2203	4300	6503	SO:0001583	missense	285429	exon1			GCGAGCGACCGAT	BC035027	CCDS33978.1	4p13	2013-01-09	2009-07-17	2009-07-17		ENSG00000182308		"WD repeat domain containing"	27723	protein-coding gene	gene with protein product			"WD repeat domain 21B"	WDR21B			Standard	NM_001029955		Approved		uc003gwk.2	Q3SXM0		ENST00000333141.5:c.214G>T	chr4.hg19:g.41984023G>T	ENSP00000327796:p.Asp72Tyr	107.0	0.0		96.0	4.0	NM_001029955	B3KVI3|Q3ZCW8|Q499Y5|Q9UFI0	Missense_Mutation	SNP	ENST00000333141.5	hg19	CCDS33978.1	.	.	.	.	.	.	.	.	.	.	G	4.057	0.008362	0.07912	.	.	ENSG00000182308	ENST00000333141	T	0.45668	0.89	0.688	-0.52	0.11935	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.182934	0.64402	D	0.000015	T	0.30293	0.0760	M	0.61703	1.905	0.19775	N	0.999956	B	0.29253	0.239	B	0.16289	0.015	T	0.12941	-1.0528	9	0.45353	T	0.12	.	.	.	.	.	72	Q3SXM0	DC4L1_HUMAN	Y	72	ENSP00000327796:D72Y	ENSP00000327796:D72Y	D	+	1	0	DCAF4L1	41678780	0.993000	0.37304	0.023000	0.16930	0.003000	0.03518	0.617000	0.24359	-0.335000	0.08451	-0.657000	0.03884	GAC	.	.		0.547	DCAF4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360958.1	NM_001029955		T	41984023	G	T	41984023	3	4	346	1	0	0	0	0	1	0	0	0	4273	1058	37	1	216	1	DCAF4L1	4	41984023	Missense_Mutation	SNP	G	TCGA-UB-A7MD-01A-12D-A34Z-10	11259205	41984023	149170253	25	48867										
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123267816	123267816	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	ctgcctcctttaaatatgatAtgcgccgactcagtgaaatt	7	10	1	2			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr4:123267816A>G	ENST00000264501.4	+	75	13145	c.12772A>G	c.(12772-12774)Atg>Gtg	p.M4258V	KIAA1109_ENST00000388738.3_Missense_Mutation_p.M4258V			Q2LD37	K1109_HUMAN	KIAA1109	4258					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						TAAATATGATATGCGCCGACT	0.358																																					p.M4258V		Atlas-SNP	.											.	KIAA1109	424	.	0			c.A12772G						.						169	153	158					4																	123267816		1852	4094	5946	SO:0001583	missense	84162	exon73			TATGATATGCGCC	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.12772A>G	chr4.hg19:g.123267816A>G	ENSP00000264501:p.Met4258Val	52.0	0.0		63.0	21.0	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	23.8|23.8	4.462346|4.462346	0.84425|0.84425	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000306802|ENST00000264501;ENST00000388738;ENST00000438707	.|T;T;T	.|0.39406	.|2.06;2.06;1.08	5.84|5.84	5.84|5.84	0.93424|0.93424	.|.	.|0.041700	.|0.85682	.|N	.|0.000000	T|T	0.63046|0.63046	0.2478|0.2478	M|M	0.72894|0.72894	2.215|2.215	0.80722|0.80722	D|D	1|1	.|P;P	.|0.45715	.|0.811;0.865	.|P;P	.|0.60789	.|0.879;0.824	T|T	0.64719|0.64719	-0.6341|-0.6341	5|10	.|0.62326	.|D	.|0.03	.|.	16.2302|16.2302	0.82332|0.82332	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|4257;4258	.|Q2LD37-4;Q2LD37	.|.;K1109_HUMAN	M|V	633|4258;4258;927	.|ENSP00000264501:M4258V;ENSP00000373390:M4258V;ENSP00000410874:M927V	.|ENSP00000264501:M4258V	I|M	+|+	3|1	3|0	KIAA1109|KIAA1109	123487266|123487266	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.339000|9.339000	0.96797|0.96797	2.228000|2.228000	0.72767|0.72767	0.533000|0.533000	0.62120|0.62120	ATA|ATG	.	.		0.358	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		G	123267816	A	G	123267816	3	3	346	1	0	0	0	0	1	0	0	0	8217	449	16	2	13062	2	KIAA1109	4	123267816	Missense_Mutation	SNP	A	TCGA-UB-A7MD-01A-12D-A34Z-10	81283793	123267816	67886460	26	48868										
SLC1A3	6507	hgsc.bcm.edu	37	chr5	36686198	36686198	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	ggaccaccaccaacgtactgGgagactccctgggagctggg	14	13	0	1			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr5:36686198G>A	ENST00000265113.4	+	10	1932	c.1456G>A	c.(1456-1458)Gga>Aga	p.G486R	CTD-2353F22.1_ENST00000510740.1_RNA|SLC1A3_ENST00000381918.3_Missense_Mutation_p.G441R	NM_004172.4	NP_004163.3	P43003	EAA1_HUMAN	solute carrier family 1 (glial high affinity glutamate transporter), member 3	486					auditory behavior (GO:0031223)|cell morphogenesis involved in neuron differentiation (GO:0048667)|cranial nerve development (GO:0021545)|D-aspartate import (GO:0070779)|gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate biosynthetic process (GO:0006537)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|neuromuscular process controlling balance (GO:0050885)|neurotransmitter uptake (GO:0001504)|positive regulation of synaptic transmission (GO:0050806)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|response to light stimulus (GO:0009416)|response to wounding (GO:0009611)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell projection (GO:0042995)|cell surface (GO:0009986)|fibril (GO:0043205)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	glutamate binding (GO:0016595)|high-affinity glutamate transmembrane transporter activity (GO:0005314)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(23)|skin(1)	41	all_lung(31;0.000245)		Epithelial(62;0.0444)|Lung(74;0.111)|all cancers(62;0.128)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			CAACGTACTGGGAGACTCCCT	0.512																																					p.G486R		Atlas-SNP	.											.	SLC1A3	88	.	0			c.G1456A						.						91	91	91					5																	36686198		2203	4300	6503	SO:0001583	missense	6507	exon10			GTACTGGGAGACT		CCDS3919.1, CCDS54844.1	5p13	2013-05-22			ENSG00000079215	ENSG00000079215		"Solute carriers"	10941	protein-coding gene	gene with protein product	"glutamate transporter variant EAAT1ex9skip"	600111				7521911, 7698014	Standard	NM_004172		Approved	EAAT1, GLAST, EA6	uc003jkj.4	P43003	OTTHUMG00000090793	ENST00000265113.4:c.1456G>A	chr5.hg19:g.36686198G>A	ENSP00000265113:p.Gly486Arg	89.0	0.0		81.0	6.0	NM_004172	B2R5T3|Q4JCQ8	Missense_Mutation	SNP	ENST00000265113.4	hg19	CCDS3919.1	.	.	.	.	.	.	.	.	.	.	G	36	5.598926	0.96614	.	.	ENSG00000079215	ENST00000265113;ENST00000427100;ENST00000381918	T;T	0.68765	-0.35;-0.29	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	D	0.89770	0.6811	H	0.98370	4.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.93402	0.6761	10	0.87932	D	0	-13.2793	19.6689	0.95903	0.0:0.0:1.0:0.0	.	441;486	Q4JCQ8;P43003	.;EAA1_HUMAN	R	486;434;441	ENSP00000265113:G486R;ENSP00000371343:G441R	ENSP00000265113:G486R	G	+	1	0	SLC1A3	36721955	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.776000	0.99001	2.642000	0.89623	0.655000	0.94253	GGA	.	.		0.512	SLC1A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207579.2	NM_004172		A	36686198	G	A	36686198	3	1	346	1	0	0	0	0	1	0	0	0	14448	1233	43	3	1507	3	SLC1A3	5	36686198	Missense_Mutation	SNP	G	TCGA-UB-A7MD-01A-12D-A34Z-10		36686198	144229062	27	48869										
EPB41L4A	64097	hgsc.bcm.edu	37	chr5	111600696	111600696	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	tgcagtatgtttatatgggtCataatctccaagctccgcta	8	9	2	0			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr5:111600696C>A	ENST00000261486.5	-	6	727	c.451G>T	c.(451-453)Gac>Tac	p.D151Y		NM_022140.3	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte membrane protein band 4.1 like 4A	151	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(2)|skin(1)	34		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		TTATATGGGTCATAATCTCCA	0.328																																					p.D151Y		Atlas-SNP	.											.	EPB41L4A	130	.	0			c.G451T						.						137	125	129					5																	111600696		1819	4078	5897	SO:0001583	missense	64097	exon6			ATGGGTCATAATC	AB030240	CCDS43350.1	5q21.3	2008-02-05			ENSG00000129595	ENSG00000129595			13278	protein-coding gene	gene with protein product		612141				10874211	Standard	XM_005272043		Approved	NBL4	uc003kpv.1	Q9HCS5	OTTHUMG00000162902	ENST00000261486.5:c.451G>T	chr5.hg19:g.111600696C>A	ENSP00000261486:p.Asp151Tyr	86.0	0.0		78.0	17.0	NM_022140	A4FUI6	Missense_Mutation	SNP	ENST00000261486.5	hg19	CCDS43350.1	.	.	.	.	.	.	.	.	.	.	C	18.74	3.687873	0.68271	.	.	ENSG00000129595	ENST00000261486	T	0.74002	-0.8	5.46	4.59	0.56863	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.000000	0.85682	D	0.000000	D	0.89996	0.6877	H	0.96430	3.82	0.40568	D	0.981277	D	0.89917	1.0	D	0.97110	1.0	D	0.92928	0.6361	10	0.87932	D	0	.	13.3554	0.60625	0.0:0.9224:0.0:0.0776	.	151	Q9HCS5	E41LA_HUMAN	Y	151	ENSP00000261486:D151Y	ENSP00000261486:D151Y	D	-	1	0	EPB41L4A	111628595	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	6.052000	0.71080	1.308000	0.44962	0.650000	0.86243	GAC	.	.		0.328	EPB41L4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370969.1			A	111600696	C	A	111600696	3	1	346	1	0	0	0	0	1	0	0	0	5157	826	29	3	1681	3	EPB41L4A	5	111600696	Missense_Mutation	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	74914498	111600696	69314564	28	48870										
ACSL6	23305	hgsc.bcm.edu	37	chr5	131324528	131324528	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	gatgtagcggatagccccagGgcccagggtgtcatagagcg	16	10	1	1			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr5:131324528G>A	ENST00000379240.1	-	6	700	c.547C>T	c.(547-549)Cct>Tct	p.P183S	ACSL6_ENST00000544770.1_Missense_Mutation_p.P92S|ACSL6_ENST00000379246.1_Missense_Mutation_p.P194S|ACSL6_ENST00000379249.3_Missense_Mutation_p.P183S|ACSL6_ENST00000543479.1_Missense_Mutation_p.P183S|ACSL6_ENST00000379255.1_Missense_Mutation_p.P148S|ACSL6_ENST00000431707.1_Missense_Mutation_p.P148S|ACSL6_ENST00000296869.4_Missense_Mutation_p.P208S|ACSL6_ENST00000379264.2_Missense_Mutation_p.P208S|ACSL6_ENST00000357096.1_Missense_Mutation_p.P148S|ACSL6_ENST00000379272.2_Missense_Mutation_p.P183S|ACSL6_ENST00000379244.1_Missense_Mutation_p.P183S			Q9UKU0	ACSL6_HUMAN	acyl-CoA synthetase long-chain family member 6	183					acyl-CoA metabolic process (GO:0006637)|cellular lipid metabolic process (GO:0044255)|cellular response to insulin stimulus (GO:0032869)|fatty acid transport (GO:0015908)|long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|neuroblast proliferation (GO:0007405)|neuron development (GO:0048666)|phospholipid biosynthetic process (GO:0008654)|positive regulation of neuron projection development (GO:0010976)|positive regulation of plasma membrane long-chain fatty acid transport (GO:0010747)|positive regulation of triglyceride biosynthetic process (GO:0010867)|response to gravity (GO:0009629)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|long-chain fatty acid-CoA ligase activity (GO:0004467)|protein homodimerization activity (GO:0042803)			NS(1)|breast(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	35		all_cancers(142;0.107)|Breast(839;0.198)|Lung NSC(810;0.216)|all_lung(232;0.248)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			ATAGCCCCAGGGCCCAGGGTG	0.602																																					p.P208S		Atlas-SNP	.											.	ACSL6	169	.	0			c.C622T						.						125	122	123					5																	131324528		2203	4300	6503	SO:0001583	missense	23305	exon6			CCCCAGGGCCCAG	AB020644	CCDS34228.1, CCDS34229.1, CCDS56381.1, CCDS56382.1, CCDS56383.1	5q31	2008-02-05	2004-02-19	2004-02-20	ENSG00000164398	ENSG00000164398		"Acyl-CoA synthetase family"	16496	protein-coding gene	gene with protein product		604443	"fatty-acid-Coenzyme A ligase, long-chain 6"	FACL6		10502316, 10548543	Standard	NM_015256		Approved	KIAA0837, ACS2, LACS5, LACS2	uc003kvy.2	Q9UKU0	OTTHUMG00000150692	ENST00000379240.1:c.547C>T	chr5.hg19:g.131324528G>A	ENSP00000368542:p.Pro183Ser	42.0	0.0		35.0	10.0	NM_001009185	J3KPG3|O94924|O95829|Q108M9|Q108N0|Q4G191|Q86TN7	Missense_Mutation	SNP	ENST00000379240.1	hg19		.	.	.	.	.	.	.	.	.	.	G	12.86	2.064624	0.36470	.	.	ENSG00000164398	ENST00000379249;ENST00000379264;ENST00000379272;ENST00000357096;ENST00000379255;ENST00000296869;ENST00000379246;ENST00000379244;ENST00000544770;ENST00000379240;ENST00000431707;ENST00000543479;ENST00000434099;ENST00000430403	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.40225	1.04;1.04;1.04;1.04;1.04;1.04;1.04;1.04;1.04;1.04;1.04;1.04;1.04;1.04	5.79	5.79	0.91817	AMP-dependent synthetase/ligase (1);	0.156891	0.64402	D	0.000016	T	0.43545	0.1252	L	0.46670	1.46	0.51767	D	0.999936	B;B;B;B;B;B;B	0.19445	0.014;0.029;0.036;0.01;0.029;0.029;0.029	B;B;B;B;B;B;B	0.25405	0.025;0.036;0.06;0.042;0.02;0.053;0.036	T	0.20874	-1.0262	10	0.46703	T	0.11	.	20.0263	0.97523	0.0:0.0:1.0:0.0	.	183;183;173;183;148;208;208	Q9UKU0-3;Q9UKU0-6;B4DFW3;Q9UKU0;Q9UKU0-7;Q9UKU0-1;Q9UKU0-8	.;.;.;ACSL6_HUMAN;.;.;.	S	183;208;183;148;148;208;194;183;92;183;148;183;148;183	ENSP00000368551:P183S;ENSP00000368566:P208S;ENSP00000368574:P183S;ENSP00000349608:P148S;ENSP00000368557:P148S;ENSP00000296869:P208S;ENSP00000368548:P194S;ENSP00000368546:P183S;ENSP00000445154:P92S;ENSP00000368542:P183S;ENSP00000413329:P148S;ENSP00000442124:P183S;ENSP00000397507:P148S;ENSP00000398423:P183S	ENSP00000296869:P208S	P	-	1	0	ACSL6	131352427	1.000000	0.71417	0.999000	0.59377	0.447000	0.32167	4.936000	0.63506	2.735000	0.93741	0.655000	0.94253	CCT	.	.		0.602	ACSL6-004	NOVEL	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000132622.1	NM_015256		A	131324528	G	A	131324528	3	1	346	1	0	0	0	0	1	0	0	0	181	1232	43	3	1692	3	ACSL6	5	131324528	Missense_Mutation	SNP	G	TCGA-UB-A7MD-01A-12D-A34Z-10	19723832	131324528	49590732	29	48871										
SPOCK1	6695	hgsc.bcm.edu	37	chr5	136314459	136314459	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	gtcctttggtcccagctcccGttcatattctaggtcatcca	7	14	3	0			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr5:136314459G>A	ENST00000394945.1	-	11	1373	c.1204C>T	c.(1204-1206)Cgg>Tgg	p.R402W	SPOCK1_ENST00000509978.1_5'Flank|SPOCK1_ENST00000282223.7_Missense_Mutation_p.R402W	NM_004598.3	NP_004589.1	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 1	402					cell adhesion (GO:0007155)|central nervous system neuron differentiation (GO:0021953)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron projection development (GO:0010977)|nervous system development (GO:0007399)|neurogenesis (GO:0022008)|neuron migration (GO:0001764)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|postsynaptic density (GO:0014069)|proteinaceous extracellular matrix (GO:0005578)|sarcoplasm (GO:0016528)	calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(2)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CCCAGCTCCCGTTCATATTCT	0.517																																					p.R402W		Atlas-SNP	.											.	SPOCK1	58	.	0			c.C1204T						.						145	126	133					5																	136314459		2203	4300	6503	SO:0001583	missense	6695	exon11			GCTCCCGTTCATA	AF231124	CCDS4191.1	5q31.2	2008-02-05	2005-11-04	2005-11-04	ENSG00000152377	ENSG00000152377			11251	protein-coding gene	gene with protein product		602264	"sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican)"	TIC1, SPOCK		9545645	Standard	NM_004598		Approved	testican-1	uc003lbp.3	Q08629	OTTHUMG00000129157	ENST00000394945.1:c.1204C>T	chr5.hg19:g.136314459G>A	ENSP00000378401:p.Arg402Trp	143.0	0.0		139.0	30.0	NM_004598	B3KSW3|Q59EW0|Q8N630|Q9UCL8	Missense_Mutation	SNP	ENST00000394945.1	hg19	CCDS4191.1	.	.	.	.	.	.	.	.	.	.	G	12.09	1.834025	0.32421	.	.	ENSG00000152377	ENST00000394945;ENST00000282223	T;T	0.47177	0.85;0.85	5.16	1.3	0.21679	.	0.370343	0.27622	N	0.018560	T	0.28797	0.0714	N	0.22421	0.69	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.18304	-1.0341	10	0.72032	D	0.01	.	5.4803	0.16719	0.1505:0.0:0.5737:0.2758	.	402	Q08629	TICN1_HUMAN	W	402	ENSP00000378401:R402W;ENSP00000282223:R402W	ENSP00000282223:R402W	R	-	1	2	SPOCK1	136342358	1.000000	0.71417	0.131000	0.22000	0.884000	0.51177	4.144000	0.58057	-0.056000	0.13221	0.557000	0.71058	CGG	.	.		0.517	SPOCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251222.1	NM_004598		A	136314459	G	A	136314459	3	1	346	1	0	0	0	0	1	0	0	0	15094	1144	40	1	119	1	SPOCK1	5	136314459	Missense_Mutation	SNP	G	TCGA-UB-A7MD-01A-12D-A34Z-10	4989931	136314459	44600801	30	48872										
PCDHA1	56147	hgsc.bcm.edu	37	chr5	140167891	140167891	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	cttgtatctctggtggagagCggccaggcgccaaaggcgtc	15	11	1	1	rs540450492		TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr5:140167891C>T	ENST00000504120.2	+	1	2016	c.2016C>T	c.(2014-2016)agC>agT	p.S672S	PCDHA1_ENST00000378133.3_Silent_p.S672S|PCDHA1_ENST00000394633.3_Intron	NM_018900.2	NP_061723.1	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1	672	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(34)|prostate(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(3)	70			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGTGGAGAGCGGCCAGGCGC	0.652													.|||	1	0.000199681	0	0	5008	,	,		16720	0		0.001	False		,,,				2504	0				p.S672S		Atlas-SNP	.											PCDHA1_ENST00000504120,NS,carcinoma,0,2	PCDHA1	387	.	0			c.C2016T						.						42	47	45					5																	140167891		2201	4300	6501	SO:0001819	synonymous_variant	56147	exon1			GGAGAGCGGCCAG	AF152479	CCDS54912.1, CCDS54913.1	5q31	2010-11-26				ENSG00000204970		"Cadherins / Protocadherins : Clustered"	8663	other	complex locus constituent	"KIAA0345-like 13"	606307				10380929	Standard	NM_018900		Approved			Q9Y5I3		ENST00000504120.2:c.2016C>T	chr5.hg19:g.140167891C>T		51.0	0.0		57.0	12.0	NM_031410	O75288|Q9NRT7	Silent	SNP	ENST00000504120.2	hg19	CCDS54913.1																																																																																			.	.		0.652	PCDHA1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389127.1	NM_018900		T	140167891	C	T	140167891	2	4	346	1	0	0	0	0	0	0	0	1	11528	767	27	1		1	PCDHA1	5	140167891	Silent	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	3853432	140167891	40747369	31	48873										
EBF1	1879	hgsc.bcm.edu	37	chr5	158158108	158158108	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	gctcagggtcaccagggtgcCgaggaatgaccttctgtaac	13	11	3	1			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr5:158158108C>G	ENST00000313708.6	-	11	1376	c.1094G>C	c.(1093-1095)cGg>cCg	p.R365P	EBF1_ENST00000517373.1_Missense_Mutation_p.R357P|EBF1_ENST00000518836.1_5'UTR|EBF1_ENST00000380654.4_Missense_Mutation_p.R334P	NM_024007.3	NP_076870.1	Q9UH73	COE1_HUMAN	early B-cell factor 1	365					multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)		HMGA2/EBF1(2)	breast(3)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(18)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42	Renal(175;0.00196)	Acute lymphoblastic leukemia(3;2.99e-06)|all_hematologic(3;0.000772)|Medulloblastoma(196;0.037)|all_neural(177;0.143)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ACCAGGGTGCCGAGGAATGAC	0.438			T	HMGA2	lipoma																																p.R365P		Atlas-SNP	.		Dom	yes		5	5q34	1879	early B-cell factor 1		M	.	EBF1	110	.	0			c.G1094C						.						69	68	68					5																	158158108		2203	4300	6503	SO:0001583	missense	1879	exon11			GGGTGCCGAGGAA	AF208502	CCDS4343.1	5q34	2008-02-05	2006-09-26	2006-09-26	ENSG00000164330	ENSG00000164330			3126	protein-coding gene	gene with protein product		164343	"early B-cell factor"	EBF		8012110	Standard	NM_024007		Approved	OLF1	uc010jip.3	Q9UH73	OTTHUMG00000130304	ENST00000313708.6:c.1094G>C	chr5.hg19:g.158158108C>G	ENSP00000322898:p.Arg365Pro	29.0	0.0		34.0	8.0	NM_024007	Q8IW11	Missense_Mutation	SNP	ENST00000313708.6	hg19	CCDS4343.1	.	.	.	.	.	.	.	.	.	.	C	33	5.236483	0.95240	.	.	ENSG00000164330	ENST00000318060;ENST00000313708;ENST00000380654;ENST00000517373	T;T;T	0.44881	0.91;0.91;0.91	5.51	5.51	0.81932	Helix-loop-helix DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.70002	0.3174	M	0.85197	2.74	0.58432	D	0.999999	D;D;D;D	0.76494	0.998;0.998;0.999;0.999	D;D;D;D	0.74674	0.934;0.975;0.963;0.984	T	0.73448	-0.3979	10	0.62326	D	0.03	-5.5481	19.7818	0.96418	0.0:1.0:0.0:0.0	.	365;352;365;334	A8K0Z7;B4E2U8;Q9UH73;Q9UH73-2	.;.;COE1_HUMAN;.	P	365;365;334;357	ENSP00000322898:R365P;ENSP00000370029:R334P;ENSP00000428020:R357P	ENSP00000322898:R365P	R	-	2	0	EBF1	158090686	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.445000	0.80570	2.736000	0.93811	0.655000	0.94253	CGG	.	.		0.438	EBF1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000252649.1	NM_024007		G	158158108	C	G	158158108	3	3	346	1	0	0	0	0	1	0	0	0	4882	652	23	4	705	4	EBF1	5	158158108	Missense_Mutation	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	17990217	158158108	22757152	32	48874										
NPM1	4869	hgsc.bcm.edu	37	chr5	170837534	170837534	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	tttttttttttttccaggctAttcaagatctctggcagtgg	8	7	2	1			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr5:170837534A>G	ENST00000296930.5	+	11	1151	c.850A>G	c.(850-852)Att>Gtt	p.I284V	NPM1_ENST00000351986.6_Missense_Mutation_p.I255V|NPM1_ENST00000517671.1_Missense_Mutation_p.I284V	NM_002520.6	NP_002511.1	P06748	NPM_HUMAN	nucleophosmin (nucleolar phosphoprotein B23, numatrin)	284	Required for nucleolar localization.				cell aging (GO:0007569)|CENP-A containing nucleosome assembly (GO:0034080)|centrosome cycle (GO:0007098)|DNA repair (GO:0006281)|intracellular protein transport (GO:0006886)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of centrosome duplication (GO:0010826)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|nucleocytoplasmic transport (GO:0006913)|nucleosome assembly (GO:0006334)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of translation (GO:0045727)|protein localization (GO:0008104)|protein oligomerization (GO:0051259)|regulation of centriole replication (GO:0046599)|regulation of eIF2 alpha phosphorylation by dsRNA (GO:0060735)|regulation of endodeoxyribonuclease activity (GO:0032071)|regulation of endoribonuclease activity (GO:0060699)|response to stress (GO:0006950)|ribosome assembly (GO:0042255)|signal transduction (GO:0007165)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle pole centrosome (GO:0031616)	histone binding (GO:0042393)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)|ribosomal large subunit binding (GO:0043023)|ribosomal small subunit binding (GO:0043024)|RNA binding (GO:0003723)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|unfolded protein binding (GO:0051082)		NPM1/ALK(632)	central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4261)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	4269	Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TTTCCAGGCTATTCAAGATCT	0.289			"T, F "	"ALK, RARA, MLF1"	"NHL, APL, AML"																																p.I284V		Atlas-SNP	.		Dom	yes		5	5q35	4869	"nucleophosmin (nucleolar phosphoprotein B23, numatrin)"		L	.	NPM1	5003	.	0			c.A850G						.						105	101	102					5																	170837534		1811	4077	5888	SO:0001583	missense	4869	exon11			CAGGCTATTCAAG	M26697	CCDS4376.1, CCDS4377.1, CCDS43399.1	5q35.1	2014-09-17			ENSG00000181163	ENSG00000181163			7910	protein-coding gene	gene with protein product	"nucleolar phosphoprotein B23", "numatrin", "nucleophosmin/nucleoplasmin family, member 1"	164040				8471164, 8122112	Standard	NM_002520		Approved	B23, NPM	uc003mbi.3	P06748	OTTHUMG00000130465	ENST00000296930.5:c.850A>G	chr5.hg19:g.170837534A>G	ENSP00000296930:p.Ile284Val	29.0	0.0		28.0	9.0	NM_002520	A8K3N7|B5BU00|D3DQL6|P08693|Q12826|Q13440|Q13441|Q14115|Q5EU94|Q5EU95|Q5EU96|Q5EU97|Q5EU98|Q5EU99|Q6V962|Q8WTW5|Q96AT6|Q96DC4|Q96EA5|Q9BYG9|Q9UDJ7	Missense_Mutation	SNP	ENST00000296930.5	hg19	CCDS4376.1	.	.	.	.	.	.	.	.	.	.	A	12.37	1.918739	0.33908	.	.	ENSG00000181163	ENST00000517671;ENST00000296930;ENST00000351986	T;T;T	0.50001	0.76;0.76;0.76	4.75	4.75	0.60458	.	0.313249	0.29730	U	0.011343	T	0.43233	0.1238	L	0.50919	1.6	0.80722	D	1	B;B	0.22080	0.01;0.064	B;B	0.23716	0.024;0.048	T	0.34976	-0.9807	10	0.39692	T	0.17	.	12.8646	0.57932	1.0:0.0:0.0:0.0	.	255;284	P06748-2;P06748	.;NPM_HUMAN	V	284;284;255	ENSP00000428755:I284V;ENSP00000296930:I284V;ENSP00000341168:I255V	ENSP00000296930:I284V	I	+	1	0	NPM1	170770139	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	5.601000	0.67606	1.916000	0.55485	0.397000	0.26171	ATT	.	.		0.289	NPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252858.2	NM_002520		G	170837534	A	G	170837534	3	3	346	1	0	0	0	0	1	0	0	0	10596	449	16	2	905	2	NPM1	5	170837534	Missense_Mutation	SNP	A	TCGA-UB-A7MD-01A-12D-A34Z-10	12679426	170837534	10077726	33	48875										
TRIM26	7726	hgsc.bcm.edu	37	chr6	30156977	30156977	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	caagtctctcagcagcttccCtggggagaaaaaaggacagc	11	11	2	1			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr6:30156977C>A	ENST00000454678.2	-	9	1341		c.e9-1		TRIM26_ENST00000437089.1_Splice_Site|TRIM26_ENST00000453195.1_Splice_Site	NM_003449.4	NP_003440.1	Q12899	TRI26_HUMAN	tripartite motif containing 26						innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)	cytoplasm (GO:0005737)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			lung(1)|ovary(2)	3						AGCAGCTTCCCTGGGGAGAAA	0.448																																					.		Atlas-SNP	.											.	TRIM26	74	.	0			c.905-1G>T						.						120	133	128					6																	30156977		1511	2709	4220	SO:0001630	splice_region_variant	7726	exon10			GCTTCCCTGGGGA	AB088090	CCDS4678.1	6p21.3	2013-01-09	2011-01-25	2001-11-23	ENSG00000234127	ENSG00000234127		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	12962	protein-coding gene	gene with protein product		600830	"tripartite motif-containing 26"	ZNF173		8530076	Standard	NM_003449		Approved	RNF95	uc003npt.3	Q12899	OTTHUMG00000031041	ENST00000454678.2:c.905-1G>T	chr6.hg19:g.30156977C>A		39.0	0.0		30.0	7.0	NM_003449	A6NG96|Q5SRL2	Splice_Site	SNP	ENST00000454678.2	hg19	CCDS4678.1	.	.	.	.	.	.	.	.	.	.	C	17.43	3.388320	0.61956	.	.	ENSG00000234127	ENST00000453195;ENST00000454678;ENST00000437089	.	.	.	5.76	5.76	0.90799	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4618	0.75363	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TRIM26	30264956	1.000000	0.71417	0.666000	0.29783	0.992000	0.81027	2.566000	0.45948	2.713000	0.92767	0.453000	0.30009	.	.	.		0.448	TRIM26-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253442.1	NM_003449	Intron	A	30156977	C	A	30156977	5	1	346	1	0	0	0	0	0	0	1	0	16515	695	24	3	723	3	TRIM26	6	30156977	Splice_Site	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10		30156977	140958090	34	48876										
DNAH8	1769	hgsc.bcm.edu	37	chr6	38795995	38795995	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	ttaaacagatttgaagttgaAgtaaccaaagaagaatcaga	8	4	1	6	rs368262519		TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr6:38795995A>G	ENST00000359357.3	+	28	3722	c.3468A>G	c.(3466-3468)gaA>gaG	p.E1156E	DNAH8_ENST00000441566.1_Silent_p.E1156E|DNAH8_ENST00000449981.2_Silent_p.E1373E			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	1156					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						TTGAAGTTGAAGTAACCAAAG	0.343																																					p.E1373E		Atlas-SNP	.											.	DNAH8	1239	.	0			c.A4119G						.	A		0,4406		0,0,2203	119	120	120		4119	3.2	1	6		120	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	DNAH8	NM_001206927.1		0,1,6502	GG,GA,AA		0.0116,0.0,0.0077		1373/4708	38795995	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	1769	exon30			AGTTGAAGTAACC	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.3468A>G	chr6.hg19:g.38795995A>G		44.0	0.0		55.0	13.0	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Silent	SNP	ENST00000359357.3	hg19																																																																																				.	.		0.343	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		G	38795995	A	G	38795995	2	3	346	1	0	0	0	0	0	0	0	1	4609	69	3	2		2	DNAH8	6	38795995	Silent	SNP	A	TCGA-UB-A7MD-01A-12D-A34Z-10	8639018	38795995	132319072	35	48877										
TREM1	54210	hgsc.bcm.edu	37	chr6	41250178	41250178	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	atcgaacagcatgtgaggctCcttgggaggctggtagatca	14	8	1	2	rs565227078		TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr6:41250178C>G	ENST00000244709.4	-	2	424	c.361G>C	c.(361-363)Gag>Cag	p.E121Q	TREM1_ENST00000334475.6_Missense_Mutation_p.E121Q|TREM1_ENST00000591620.1_Missense_Mutation_p.E121Q|TREM1_ENST00000589614.1_Missense_Mutation_p.E121Q	NM_018643.3	NP_061113.1	Q9NP99	TREM1_HUMAN	triggering receptor expressed on myeloid cells 1	121	Ig-like V-type.				blood coagulation (GO:0007596)|chemokine metabolic process (GO:0050755)|cytokine secretion involved in immune response (GO:0002374)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|neutrophil mediated killing of gram-negative bacterium (GO:0070945)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|scaffold protein binding (GO:0097110)			NS(1)|breast(2)|endometrium(2)|large_intestine(5)|lung(5)|skin(1)	16	Ovarian(28;0.0327)|Colorectal(47;0.196)					ATGTGAGGCTCCTTGGGAGGC	0.547																																					p.E121Q		Atlas-SNP	.											.	TREM1	38	.	0			c.G361C						.						75	58	64					6																	41250178		2203	4300	6503	SO:0001583	missense	54210	exon2			GAGGCTCCTTGGG	AF196329	CCDS4854.1, CCDS56427.1, CCDS59499.1	6p21.1	2013-01-11			ENSG00000124731	ENSG00000124731		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	17760	protein-coding gene	gene with protein product		605085				11922939, 10799849	Standard	NM_018643		Approved	TREM-1, CD354	uc003oqf.2	Q9NP99	OTTHUMG00000014674	ENST00000244709.4:c.361G>C	chr6.hg19:g.41250178C>G	ENSP00000244709:p.Glu121Gln	95.0	0.0		84.0	22.0	NM_001242590	B4DWG2|K7EJW1|Q53FL8|Q5T2C9|Q86YU1	Missense_Mutation	SNP	ENST00000244709.4	hg19	CCDS4854.1	.	.	.	.	.	.	.	.	.	.	C	9.740	1.164583	0.21538	.	.	ENSG00000124731	ENST00000244709;ENST00000334475	T;T	0.66099	-0.19;-0.19	4.37	0.483	0.16820	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	1.214900	0.05966	N	0.641400	T	0.28532	0.0706	L	0.40543	1.245	0.09310	N	1	B;B	0.25390	0.103;0.125	B;B	0.19391	0.015;0.025	T	0.28681	-1.0036	10	0.54805	T	0.06	-2.4557	4.262	0.10745	0.0:0.5478:0.1687:0.2835	.	121;121	Q9NP99-2;Q9NP99	.;TREM1_HUMAN	Q	121	ENSP00000244709:E121Q;ENSP00000334284:E121Q	ENSP00000244709:E121Q	E	-	1	0	TREM1	41358156	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.410000	0.21098	-0.024000	0.13941	0.591000	0.81541	GAG	.	.		0.547	TREM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040505.2	NM_018643		G	41250178	C	G	41250178	3	3	346	1	0	0	0	0	1	0	0	0	16485	864	30	4	355	4	TREM1	6	41250178	Missense_Mutation	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	2454183	41250178	129864889	36	48878										
COL9A1	1297	hgsc.bcm.edu	37	chr6	71009833	71009833	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	ctactctctggatagctcttCtagatgctgctttatctacc	6	12	4	1			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr6:71009833C>T	ENST00000357250.6	-	4	370	c.212G>A	c.(211-213)aGa>aAa	p.R71K	COL9A1_ENST00000370496.3_Missense_Mutation_p.R71K	NM_001851.4	NP_001842.3	P20849	CO9A1_HUMAN	collagen, type IX, alpha 1	71	Laminin G-like.|Nonhelical region (NC4).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|organ morphogenesis (GO:0009887)|tissue homeostasis (GO:0001894)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(44)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)	80						GATAGCTCTTCTAGATGCTGC	0.373																																					p.R71K		Atlas-SNP	.											.	COL9A1	228	.	0			c.G212A						.						90	86	87					6																	71009833		2203	4300	6503	SO:0001583	missense	1297	exon4			GCTCTTCTAGATG		CCDS4971.1, CCDS47447.1	6q13	2013-05-07			ENSG00000112280	ENSG00000112280		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2217	protein-coding gene	gene with protein product		120210				1429648	Standard	NM_001851		Approved		uc003pfg.4	P20849	OTTHUMG00000014988	ENST00000357250.6:c.212G>A	chr6.hg19:g.71009833C>T	ENSP00000349790:p.Arg71Lys	129.0	0.0		144.0	51.0	NM_001851	Q13699|Q13700|Q5TF52|Q6P467|Q96BM8|Q99225|Q9H151|Q9H152|Q9Y6P2|Q9Y6P3	Missense_Mutation	SNP	ENST00000357250.6	hg19	CCDS4971.1	.	.	.	.	.	.	.	.	.	.	C	9.851	1.193720	0.22037	.	.	ENSG00000112280	ENST00000357250;ENST00000370496	T;T	0.02067	4.47;4.47	5.66	4.8	0.61643	Concanavalin A-like lectin/glucanase (1);Laminin G, thrombospondin-type, N-terminal (1);	0.693949	0.15450	N	0.261729	T	0.00552	0.0018	N	0.11892	0.195	0.80722	D	1	B	0.06786	0.001	B	0.08055	0.003	T	0.49418	-0.8942	10	0.18276	T	0.48	.	6.5798	0.22588	0.1466:0.6955:0.0:0.1579	.	71	P20849	CO9A1_HUMAN	K	71	ENSP00000349790:R71K;ENSP00000359527:R71K	ENSP00000349790:R71K	R	-	2	0	COL9A1	71066554	0.972000	0.33761	0.990000	0.47175	0.984000	0.73092	1.310000	0.33551	1.538000	0.49270	0.650000	0.86243	AGA	.	.		0.373	COL9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041131.2			T	71009833	C	T	71009833	3	4	346	1	0	0	0	0	1	0	0	0	3709	913	32	3	2769	3	COL9A1	6	71009833	Missense_Mutation	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	29759655	71009833	100105234	37	48879										
EEF1A1	1915	hgsc.bcm.edu	37	chr6	74227627	74227628	+	Missense_Mutation	DNP	GT	GT	AA													0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	tgatgacacccaccgcaactGtctgtctcatatcacgaaca							TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	G|T	G|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr6:74227627_74227628GT>AA	ENST00000316292.9	-	7	2285_2286	c.1294_1295AC>TT	c.(1294-1296)ACa>TTa	p.T432L	EEF1A1_ENST00000331523.2_Missense_Mutation_p.T432L|EEF1A1_ENST00000491404.1_Intron|EEF1A1_ENST00000309268.6_Missense_Mutation_p.T432L	NM_001402.5	NP_001393.1	P68104	EF1A1_HUMAN	eukaryotic translation elongation factor 1 alpha 1	432					cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation elongation factor activity (GO:0003746)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(6)|prostate(2)|skin(3)	18						CACCGCAACTGTCTGTCTCATA	0.401											OREG0003893	type=REGULATORY REGION|Gene=BC038897|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.T432I|p.T432S		Atlas-SNP	.											.	EEF1A1	56	.	0			c.C1295T|c.A1294T						.																																			SO:0001583	missense	1915	exon8			GCAACTGTCTGTC|CAACTGTCTGTCT	BC019669	CCDS4980.1	6q14.1	2010-06-30	2004-11-19		ENSG00000156508	ENSG00000156508			3189	protein-coding gene	gene with protein product		130590	"leukocyte receptor cluster (LRC) member 7"	EF1A, EEF1A, LENG7		8812466, 10941842	Standard	NM_001402		Approved	EE1A1	uc003phj.3	P68104	OTTHUMG00000015031	ENST00000316292.9:c.1294_1295delinsAA	chr6.hg19:g.74227627_74227628delinsAA	ENSP00000339063:p.Thr432Leu	106.0	0.0	1151	96.0	28.0|29.0	NM_001402	P04719|P04720|Q6IQ15	Missense_Mutation	SNP	ENST00000316292.9	hg19	CCDS4980.1																																																																																			.	.		0.401	EEF1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041210.2	NM_001402		AA	74227628	GT	AA	74227627	3	1	346	1	0	0	0	0	1	0	0	0	4925	1377	48	3	97	3	EEF1A1	6	74227627	Missense_Mutation	DNP	GT	TCGA-UB-A7MD-01A-12D-A34Z-10	3217794	74227627	96887440	38	48880										
MDN1	23195	hgsc.bcm.edu	37	chr6	90452952	90452952	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	tcctccttcatggcctgaacCagaggcccatcatgccactc	7	17	2	2			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr6:90452952C>G	ENST00000369393.3	-	31	4480	c.4365G>C	c.(4363-4365)ctG>ctC	p.L1455L	MDN1_ENST00000428876.1_Silent_p.L1455L			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	1455					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		TGGCCTGAACCAGAGGCCCAT	0.468																																					p.L1455L		Atlas-SNP	.											.	MDN1	478	.	0			c.G4365C						.						102	97	99					6																	90452952		2203	4300	6503	SO:0001819	synonymous_variant	23195	exon31			CTGAACCAGAGGC	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.4365G>C	chr6.hg19:g.90452952C>G		123.0	0.0		129.0	38.0	NM_014611	O15019|Q5T794	Silent	SNP	ENST00000369393.3	hg19	CCDS5024.1																																																																																			.	.		0.468	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			G	90452952	C	G	90452952	2	3	346	1	0	0	0	0	0	0	0	1	9424	581	21	4		4	MDN1	6	90452952	Silent	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	16225325	90452952	80662115	39	48881										
IGF2R	3482	hgsc.bcm.edu	37	chr6	160454117	160454117	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	ctcaagtcaaagcagcaggaAgataccacaatcagaccctc	7	13	3	2			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr6:160454117A>C	ENST00000356956.1	+	9	1337	c.1189A>C	c.(1189-1191)Aga>Cga	p.R397R		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	397					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	AGCAGCAGGAAGATACCACAA	0.438																																					p.R397R		Atlas-SNP	.											.	IGF2R	251	.	0			c.A1189C						.						96	87	90					6																	160454117		2203	4300	6503	SO:0001819	synonymous_variant	3482	exon9			GCAGGAAGATACC	J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"CD molecules"	5467	protein-coding gene	gene with protein product	"cation-independent mannose-6 phosphate receptor"	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.1189A>C	chr6.hg19:g.160454117A>C		48.0	0.0		27.0	16.0	NM_000876	Q7Z7G9|Q96PT5	Silent	SNP	ENST00000356956.1	hg19	CCDS5273.1																																																																																			.	.		0.438	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876		C	160454117	A	C	160454117	2	2	346	1	0	0	0	0	0	0	0	1	7585	64	3	5		5	IGF2R	6	160454117	Silent	SNP	A	TCGA-UB-A7MD-01A-12D-A34Z-10	70001165	160454117	10660950	40	48882										
OSBPL3	26031	hgsc.bcm.edu	37	chr7	24904971	24904971	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	gtcactctacctttggagcaTttttccatgtcctctgaaga	7	11	3	2			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr7:24904971T>G	ENST00000313367.2	-	7	1114	c.663A>C	c.(661-663)aaA>aaC	p.K221N	OSBPL3_ENST00000353930.1_Missense_Mutation_p.K221N|OSBPL3_ENST00000396431.1_Missense_Mutation_p.K221N|OSBPL3_ENST00000396429.1_Missense_Mutation_p.K221N|OSBPL3_ENST00000431825.2_Missense_Mutation_p.K221N|OSBPL3_ENST00000409069.1_Missense_Mutation_p.K221N|OSBPL3_ENST00000352860.1_Missense_Mutation_p.K221N	NM_015550.2	NP_056365.1	Q9H4L5	OSBL3_HUMAN	oxysterol binding protein-like 3	221					lipid transport (GO:0006869)	cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(19)|prostate(1)|skin(3)|urinary_tract(1)	43						CTTTGGAGCATTTTTCCATGT	0.393																																					p.K221N		Atlas-SNP	.											.	OSBPL3	100	.	0			c.A663C						.						262	242	249					7																	24904971		2203	4300	6503	SO:0001583	missense	26031	exon7			GGAGCATTTTTCC	AB014604	CCDS5390.1, CCDS5391.1, CCDS5392.1, CCDS47564.1	7p15.3	2013-01-10			ENSG00000070882	ENSG00000070882		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16370	protein-coding gene	gene with protein product		606732		OSBP3		9734811	Standard	XM_005249698		Approved	ORP-3, ORP3, KIAA0704	uc003sxf.3	Q9H4L5	OTTHUMG00000023277	ENST00000313367.2:c.663A>C	chr7.hg19:g.24904971T>G	ENSP00000315410:p.Lys221Asn	118.0	0.0		106.0	21.0	NM_145321	A4D167|A4D168|A4D169|A4D170|A4D171|A4D172|B8ZZ79|B8ZZP0|O14591|O43357|O43358|Q8N702|Q8N703|Q8N704|Q8NFH0|Q8NFH1|Q8NI12|Q8NI13|Q9BZF4|Q9UED6	Missense_Mutation	SNP	ENST00000313367.2	hg19	CCDS5390.1	.	.	.	.	.	.	.	.	.	.	T	18.75	3.689770	0.68271	.	.	ENSG00000070882	ENST00000313367;ENST00000352860;ENST00000353930;ENST00000431825;ENST00000396431;ENST00000396429;ENST00000409069	T;T;T;T;T;T;T	0.48522	2.15;0.84;0.81;2.16;0.84;0.81;2.16	5.75	1.99	0.26369	.	0.097834	0.64402	D	0.000001	T	0.49813	0.1579	M	0.71581	2.175	0.42308	D	0.992203	P;P;B;P	0.43909	0.821;0.682;0.38;0.726	P;P;B;B	0.47299	0.543;0.462;0.343;0.342	T	0.40365	-0.9567	10	0.27082	T	0.32	-7.1484	9.6826	0.40078	0.0:0.1999:0.0:0.8001	.	221;221;221;221	Q9H4L5-4;Q9H4L5-2;Q9H4L5-3;Q9H4L5	.;.;.;OSBL3_HUMAN	N	221	ENSP00000315410:K221N;ENSP00000315331:K221N;ENSP00000315277:K221N;ENSP00000389779:K221N;ENSP00000379708:K221N;ENSP00000379706:K221N;ENSP00000386953:K221N	ENSP00000315410:K221N	K	-	3	2	OSBPL3	24871496	0.997000	0.39634	1.000000	0.80357	0.997000	0.91878	0.345000	0.19979	0.093000	0.17368	0.533000	0.62120	AAA	.	.		0.393	OSBPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214085.2			G	24904971	T	G	24904971	3	3	346	1	0	0	0	0	1	0	0	0	11288	1490	52	5	2068	5	OSBPL3	7	24904971	Missense_Mutation	SNP	T	TCGA-UB-A7MD-01A-12D-A34Z-10		24904971	134233692	41	48883										
STEAP4	79689	hgsc.bcm.edu	37	chr7	87910335	87910335	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	ccaagtattcccaaagccacAtatgaatcactgagccaggc	7	13	1	2			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr7:87910335A>G	ENST00000380079.4	-	4	1145	c.1044T>C	c.(1042-1044)taT>taC	p.Y348Y	STEAP4_ENST00000301959.5_Silent_p.Y172Y|AC003991.3_ENST00000434733.1_RNA|AC003991.3_ENST00000595121.1_RNA|AC003991.3_ENST00000600908.1_RNA|AC003991.3_ENST00000447758.1_RNA	NM_001205315.1|NM_024636.3	NP_001192244.1|NP_078912.2	Q687X5	STEA4_HUMAN	STEAP family member 4	348	Ferric oxidoreductase.				copper ion import (GO:0015677)|fat cell differentiation (GO:0045444)|ferric iron import into cell (GO:0097461)|iron ion homeostasis (GO:0055072)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cupric reductase activity (GO:0008823)|ferric-chelate reductase (NADPH) activity (GO:0052851)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(3)	15	Esophageal squamous(14;0.00802)					CCAAAGCCACATATGAATCAC	0.388																																					p.Y348Y		Atlas-SNP	.											.	STEAP4	54	.	0			c.T1044C						.						91	89	89					7																	87910335		1881	4112	5993	SO:0001819	synonymous_variant	79689	exon5			AGCCACATATGAA	AK026806	CCDS43611.1, CCDS56494.1	7q21.13	2014-01-28	2005-06-15	2005-06-15	ENSG00000127954	ENSG00000127954			21923	protein-coding gene	gene with protein product		611098	"tumor necrosis factor, alpha-induced protein 9"	TNFAIP9		11443137, 15897894	Standard	NM_024636		Approved	FLJ23153, TIARP, STAMP2	uc003ujs.3	Q687X5	OTTHUMG00000153853	ENST00000380079.4:c.1044T>C	chr7.hg19:g.87910335A>G		97.0	0.0		112.0	30.0	NM_001205315	Q658Q9|Q687X4|Q8WWB0|Q9H5R1	Silent	SNP	ENST00000380079.4	hg19	CCDS43611.1																																																																																			.	.		0.388	STEAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332712.4	NM_024636		G	87910335	A	G	87910335	2	3	346	1	0	0	0	0	0	0	0	1	15295	224	8	2		2	STEAP4	7	87910335	Silent	SNP	A	TCGA-UB-A7MD-01A-12D-A34Z-10	63005364	87910335	71228328	42	48884										
MLL3	58508	hgsc.bcm.edu	37	chr7	151878921	151878922	+	Missense_Mutation	DNP	AG	AG	TA													0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	tctgccctaggagatggtttAgtaaagtgatcactggttcc					rs369706450		TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	A|G	A|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr7:151878921_151878922AG>TA	ENST00000262189.6	-	36	6241_6242	c.6023_6024CT>TA	c.(6022-6024)aCT>aTA	p.T2008I	KMT2C_ENST00000355193.2_Missense_Mutation_p.T2008I	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	2008	Pro-rich.		T -> A (in dbSNP:rs6951159).		histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										GAGATGGTTTAGTAAAGTGATC	0.47																																					p.T2008T|p.T2008I		Atlas-SNP	.											.	MLL3	1564	.	0			c.T6024A|c.C6023T						.																																			SO:0001583	missense	58508	exon36			TGGTTTAGTAAAG|GGTTTAGTAAAGT	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.6023_6024delinsTA	chr7.hg19:g.151878921_151878922delinsTA	ENSP00000262189:p.Thr2008Ile	75.0|76.0	0.0		92.0|90.0	35.0	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Silent|Missense_Mutation	SNP	ENST00000262189.6	hg19	CCDS5931.1																																																																																			.	.		0.47	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			TA	151878922	AG	TA	151878921	3	4	346	1	0	0	0	0	1	0	0	0	9631	407	15	4	8807	4	MLL3	7	151878921	Missense_Mutation	DNP	AG	TCGA-UB-A7MD-01A-12D-A34Z-10	63968586	151878921	7259742	43	48885										
ZBTB10	65986	hgsc.bcm.edu	37	chr8	81412438	81412438	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	aacaaaagtgtttatttggaAtaatatgggctcccagggaa	10	5	0	0			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr8:81412438A>G	ENST00000430430.1	+	3	2461	c.1682A>G	c.(1681-1683)aAt>aGt	p.N561S	ZBTB10_ENST00000455036.3_Missense_Mutation_p.N561S|ZBTB10_ENST00000426744.2_Missense_Mutation_p.N561S|ZBTB10_ENST00000379091.4_Missense_Mutation_p.N269S	NM_001277145.1	NP_001264074.1	Q96DT7	ZBT10_HUMAN	zinc finger and BTB domain containing 10	561					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(4)	20	all_cancers(3;1.68e-09)|all_epithelial(4;5.13e-11)|Lung NSC(7;1.75e-07)|all_lung(9;7.38e-07)|Breast(3;2.96e-06)		BRCA - Breast invasive adenocarcinoma(6;0.000434)|Epithelial(68;0.00486)|all cancers(69;0.0296)			TTTATTTGGAATAATATGGGC	0.353																																					p.N561S		Atlas-SNP	.											.	ZBTB10	51	.	0			c.A1682G						.						35	34	34					8																	81412438		1815	4070	5885	SO:0001583	missense	65986	exon2			TTTGGAATAATAT	AK022814	CCDS47880.1, CCDS64920.1	8q13-q21.1	2013-01-09			ENSG00000205189	ENSG00000205189		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	30953	protein-coding gene	gene with protein product						12477932	Standard	NM_001105539		Approved	RINZF, FLJ12752	uc003ybx.5	Q96DT7	OTTHUMG00000155016	ENST00000430430.1:c.1682A>G	chr8.hg19:g.81412438A>G	ENSP00000387462:p.Asn561Ser	110.0	0.0		121.0	55.0	NM_023929	A4FVD0|Q86W96|Q8IXI9|Q96MH9	Missense_Mutation	SNP	ENST00000430430.1	hg19	CCDS47880.1	.	.	.	.	.	.	.	.	.	.	A	19.06	3.754300	0.69648	.	.	ENSG00000205189	ENST00000379091;ENST00000430430;ENST00000455036;ENST00000426744;ENST00000519370	T;T;T;T	0.15372	2.53;2.46;2.46;2.43	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.29716	0.0742	L	0.29908	0.895	0.47037	D	0.999299	D;D;D;D	0.76494	0.985;0.997;0.998;0.999	P;D;D;D	0.85130	0.834;0.97;0.994;0.997	T	0.02966	-1.1088	10	0.24483	T	0.36	.	15.9836	0.80130	1.0:0.0:0.0:0.0	.	417;561;561;269	A8E4L4;Q96DT7;Q96DT7-2;Q96DT7-4	.;ZBT10_HUMAN;.;.	S	269;561;561;561;389	ENSP00000368384:N269S;ENSP00000387462:N561S;ENSP00000412036:N561S;ENSP00000416134:N561S	ENSP00000368384:N269S	N	+	2	0	ZBTB10	81574993	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.366000	0.90111	2.185000	0.69588	0.528000	0.53228	AAT	.	.		0.353	ZBTB10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338055.2	NM_023929		G	81412438	A	G	81412438	3	3	346	1	0	0	0	0	1	0	0	0	17538	101	4	2	1688	2	ZBTB10	8	81412438	Missense_Mutation	SNP	A	TCGA-UB-A7MD-01A-12D-A34Z-10		81412438	64951584	44	48886										
LRRC6	23639	hgsc.bcm.edu	37	chr8	133634904	133634904	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	ccatcttcagtgatcaaagtCctgggtggtttcactttctt	8	10	5	1			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr8:133634904C>T	ENST00000519595.1	-	7	965	c.867G>A	c.(865-867)agG>agA	p.R289R	LRRC6_ENST00000520446.1_5'Flank|LRRC6_ENST00000250173.1_Silent_p.R289R|LRRC6_ENST00000518642.1_Silent_p.R289R			Q86X45	TILB_HUMAN	leucine rich repeat containing 6	289					cilium movement (GO:0003341)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|inner dynein arm assembly (GO:0036159)|male gonad development (GO:0008584)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)|reproductive system development (GO:0061458)|sperm motility (GO:0030317)	cilium (GO:0005929)|cytoplasm (GO:0005737)				breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|prostate(1)|urinary_tract(2)	34	Ovarian(258;0.00352)|Esophageal squamous(12;0.00507)|all_neural(3;0.0052)|Medulloblastoma(3;0.0922)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)			TGATCAAAGTCCTGGGTGGTT	0.403																																					p.R289R		Atlas-SNP	.											.	LRRC6	58	.	0			c.G867A						.						303	287	293					8																	133634904		2203	4300	6503	SO:0001819	synonymous_variant	23639	exon7			CAAAGTCCTGGGT	U60666	CCDS6365.1	8q24	2013-02-22			ENSG00000129295	ENSG00000129295			16725	protein-coding gene	gene with protein product	"leucine rich testes protein"	614930				10775177, 23122586	Standard	NM_012472		Approved	TSLRP, LRTP, CILD19	uc003ytk.4	Q86X45	OTTHUMG00000164646	ENST00000519595.1:c.867G>A	chr8.hg19:g.133634904C>T		162.0	0.0		236.0	61.0	NM_012472	Q13648|Q4G183	Silent	SNP	ENST00000519595.1	hg19		.	.	.	.	.	.	.	.	.	.	C	5.057	0.196109	0.09599	.	.	ENSG00000129295	ENST00000519085	.	.	.	5.54	2.74	0.32292	.	.	.	.	.	T	0.31389	0.0795	.	.	.	0.25614	N	0.986468	.	.	.	.	.	.	T	0.21965	-1.0230	4	.	.	.	-18.665	5.3498	0.16030	0.0:0.6092:0.1472:0.2435	.	.	.	.	N	11	.	.	D	-	1	0	LRRC6	133704086	1.000000	0.71417	0.485000	0.27403	0.645000	0.38454	1.946000	0.40283	0.283000	0.22279	0.637000	0.83480	GAC	.	.		0.403	LRRC6-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379578.1	NM_012472		T	133634904	C	T	133634904	2	4	346	1	0	0	0	0	0	0	0	1	9025	854	30	3		3	LRRC6	8	133634904	Silent	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	52222466	133634904	12729118	45	48887										
PTK2	5747	hgsc.bcm.edu	37	chr8	141756887	141756887	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	gtgtgcacagctccatgattAtccagacaggattctctgtg	10	10	1	2			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr8:141756887A>G	ENST00000522684.1	-	18	1719	c.1490T>C	c.(1489-1491)aTa>aCa	p.I497T	PTK2_ENST00000517887.1_Missense_Mutation_p.I541T|PTK2_ENST00000519419.1_Missense_Mutation_p.I541T|PTK2_ENST00000520151.1_Intron|PTK2_ENST00000538769.1_Missense_Mutation_p.I165T|PTK2_ENST00000395218.2_Missense_Mutation_p.I497T|PTK2_ENST00000521059.1_Missense_Mutation_p.I497T|PTK2_ENST00000519465.1_Missense_Mutation_p.I125T|PTK2_ENST00000535192.1_Missense_Mutation_p.I497T|PTK2_ENST00000340930.3_Missense_Mutation_p.I497T	NM_153831.3	NP_722560.1	Q05397	FAK1_HUMAN	protein tyrosine kinase 2	497	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell motility (GO:0048870)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|central nervous system neuron axonogenesis (GO:0021955)|embryo development (GO:0009790)|endothelial cell migration (GO:0043542)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|establishment of nucleus localization (GO:0040023)|extracellular matrix organization (GO:0030198)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|growth hormone receptor signaling pathway (GO:0060396)|heart morphogenesis (GO:0003007)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of organ growth (GO:0046621)|negative regulation of synapse assembly (GO:0051964)|netrin-activated signaling pathway (GO:0038007)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|placenta development (GO:0001890)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|regulation of endothelial cell migration (GO:0010594)|regulation of focal adhesion assembly (GO:0051893)|regulation of osteoblast differentiation (GO:0045667)|regulation of Rho GTPase activity (GO:0032319)|signal complex assembly (GO:0007172)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)	apical plasma membrane (GO:0016324)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|stress fiber (GO:0001725)	actin binding (GO:0003779)|ATP binding (GO:0005524)|JUN kinase binding (GO:0008432)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(6)|lung(23)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	48	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)			CTCCATGATTATCCAGACAGG	0.398																																					p.I519T		Atlas-SNP	.											.	PTK2	311	.	0			c.T1556C						.						124	103	110					8																	141756887		2203	4300	6503	SO:0001583	missense	5747	exon18			ATGATTATCCAGA	L13616	CCDS6381.1, CCDS56557.1	8q24.3	2013-02-18	2013-02-18		ENSG00000169398	ENSG00000169398	2.7.10.1	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9611	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 71"	600758	"PTK2 protein tyrosine kinase 2"			8422239	Standard	NM_153831		Approved	FAK, FADK, FAK1, PPP1R71	uc003yvt.3	Q05397	OTTHUMG00000067438	ENST00000522684.1:c.1490T>C	chr8.hg19:g.141756887A>G	ENSP00000429911:p.Ile497Thr	64.0	0.0		84.0	9.0	NM_005607	B4E2N6|F5H4S4|Q14291|Q9UD85	Missense_Mutation	SNP	ENST00000522684.1	hg19	CCDS6381.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.604267	0.87157	.	.	ENSG00000169398	ENST00000522684;ENST00000535192;ENST00000519465;ENST00000517887;ENST00000521059;ENST00000395214;ENST00000395218;ENST00000354438;ENST00000395221;ENST00000523539;ENST00000340930;ENST00000538769;ENST00000519419;ENST00000521986;ENST00000342207;ENST00000519024	D;D;D;D;D;D;D;D;D;D;D;D	0.85861	-2.04;-2.04;-2.04;-2.04;-2.04;-2.04;-2.04;-2.04;-2.04;-2.04;-2.04;-2.04	5.63	5.63	0.86233	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.087685	0.85682	D	0.000000	D	0.92958	0.7759	M	0.84948	2.725	0.80722	D	1	D;P;D;D;D;D;P;B;P;P	0.89917	0.994;0.492;0.96;0.993;1.0;0.993;0.931;0.274;0.898;0.866	D;P;P;D;D;D;D;P;D;P	0.81914	0.942;0.851;0.885;0.919;0.995;0.912;0.922;0.557;0.949;0.837	D	0.93978	0.7255	10	0.87932	D	0	.	16.1825	0.81920	1.0:0.0:0.0:0.0	.	497;192;417;497;519;497;449;345;165;125	B4E2N6;B4DH13;Q59GN8;Q05397;Q658W2;Q8IYN9;Q59GM6;Q05397-2;Q8N9D7;E9PEI4	.;.;.;FAK1_HUMAN;.;.;.;.;.;.	T	497;497;125;541;497;449;497;418;192;169;497;165;541;195;343;132	ENSP00000429911:I497T;ENSP00000438009:I497T;ENSP00000429170:I125T;ENSP00000429082:I541T;ENSP00000429474:I497T;ENSP00000378644:I497T;ENSP00000428492:I169T;ENSP00000341189:I497T;ENSP00000445742:I165T;ENSP00000429129:I541T;ENSP00000430603:I195T;ENSP00000428232:I132T	ENSP00000341189:I497T	I	-	2	0	PTK2	141826069	1.000000	0.71417	0.994000	0.49952	0.993000	0.82548	8.950000	0.93019	2.281000	0.76405	0.524000	0.50904	ATA	.	.		0.398	PTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378054.5	NM_005607		G	141756887	A	G	141756887	3	3	346	1	0	0	0	0	1	0	0	0	12775	449	16	2	1728	2	PTK2	8	141756887	Missense_Mutation	SNP	A	TCGA-UB-A7MD-01A-12D-A34Z-10	8121983	141756887	4607135	46	48888										
MELK	9833	hgsc.bcm.edu	37	chr9	36630339	36630339	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	gtggctctctcccagtagcaTtctgcttcttcaacaaatgc	7	13	4	0			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr9:36630339T>G	ENST00000298048.2	+	9	894	c.710T>G	c.(709-711)aTt>aGt	p.I237S	MELK_ENST00000536329.1_Missense_Mutation_p.I166S|MELK_ENST00000541717.1_Missense_Mutation_p.I237S|MELK_ENST00000543751.1_Missense_Mutation_p.I205S|MELK_ENST00000536860.1_Missense_Mutation_p.I189S|MELK_ENST00000487398.1_3'UTR|MELK_ENST00000536987.1_Missense_Mutation_p.I106S|MELK_ENST00000545008.1_Missense_Mutation_p.I166S|MELK_ENST00000538311.1_Missense_Mutation_p.I43S	NM_014791.3	NP_055606.1	Q14680	MELK_HUMAN	maternal embryonic leucine zipper kinase	237	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|hemopoiesis (GO:0030097)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|neural precursor cell proliferation (GO:0061351)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)	cell cortex (GO:0005938)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)	29		Acute lymphoblastic leukemia(2;1.09e-08)|all_hematologic(2;8.15e-06)	STAD - Stomach adenocarcinoma(86;0.228)			CCCAGTAGCATTCTGCTTCTT	0.348																																					p.I237S	Ovarian(82;980 1317 7225 14391 18624)	Atlas-SNP	.											.	MELK	74	.	0			c.T710G						.						195	205	202					9																	36630339		2203	4300	6503	SO:0001583	missense	9833	exon9			GTAGCATTCTGCT	D79997	CCDS6606.1, CCDS59123.1, CCDS59124.1, CCDS59125.1, CCDS59126.1, CCDS59127.1, CCDS59128.1	9p13.1	2008-02-05			ENSG00000165304	ENSG00000165304			16870	protein-coding gene	gene with protein product		607025				8724849, 9136115	Standard	NM_001256689		Approved	KIAA0175	uc003zzn.4	Q14680	OTTHUMG00000019906	ENST00000298048.2:c.710T>G	chr9.hg19:g.36630339T>G	ENSP00000298048:p.Ile237Ser	59.0	0.0		61.0	20.0	NM_014791	A6P3A7|A6P3A8|B1AMQ6|B7Z1E6|B7Z5M5|B7Z6Q7|B7Z6R8|B7Z6Y0|B7Z7Q1|D3DRP8|F5H0Y0|F5H2R4|F5H689|Q7L3C3	Missense_Mutation	SNP	ENST00000298048.2	hg19	CCDS6606.1	.	.	.	.	.	.	.	.	.	.	T	13.09	2.132096	0.37630	.	.	ENSG00000165304	ENST00000298048;ENST00000538311;ENST00000536987;ENST00000545008;ENST00000536860;ENST00000536329;ENST00000541717;ENST00000543751	T;T;T;T;T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14;-0.14;-0.14;-0.14;-0.14	5.41	3.08	0.35506	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.423208	0.29451	N	0.012116	T	0.52677	0.1749	N	0.20766	0.605	0.21290	N	0.99973	B;B;B;B;B;P;B	0.35307	0.343;0.321;0.053;0.053;0.149;0.494;0.066	P;B;B;B;B;B;B	0.46389	0.515;0.138;0.062;0.06;0.174;0.297;0.155	T	0.46803	-0.9165	10	0.48119	T	0.1	-1.4603	7.2153	0.25957	0.0:0.2437:0.0:0.7563	.	157;166;189;237;166;205;237	B7Z1G6;F5H2R4;F5H0Y0;F5H689;A6P3A8;A6P3A7;Q14680	.;.;.;.;.;.;MELK_HUMAN	S	237;43;106;166;189;166;237;205	ENSP00000298048:I237S;ENSP00000438226:I43S;ENSP00000439184:I106S;ENSP00000445452:I166S;ENSP00000439792:I189S;ENSP00000443550:I166S;ENSP00000437804:I237S;ENSP00000441596:I205S	ENSP00000298048:I237S	I	+	2	0	MELK	36620339	0.003000	0.15002	0.543000	0.28128	0.987000	0.75469	0.554000	0.23407	0.881000	0.35993	0.533000	0.62120	ATT	.	.		0.348	MELK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052428.3	NM_014791		G	36630339	T	G	36630339	3	3	346	1	0	0	0	0	1	0	0	0	9479	1493	52	5	740	5	MELK	9	36630339	Missense_Mutation	SNP	T	TCGA-UB-A7MD-01A-12D-A34Z-10		36630339	104583092	47	48889										
SYK	6850	hgsc.bcm.edu	37	chr9	93650155	93650155	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	gtgggaagcattctcctatgGgcagaagccatatcgagtga	13	8	1	2			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr9:93650155G>T	ENST00000375754.4	+	12	1854	c.1706G>T	c.(1705-1707)gGg>gTg	p.G569V	SYK_ENST00000375747.1_Missense_Mutation_p.G546V|SYK_ENST00000375746.1_Missense_Mutation_p.G569V|SYK_ENST00000375751.4_Missense_Mutation_p.G546V	NM_003177.5	NP_003168.2	P43405	KSYK_HUMAN	spleen tyrosine kinase	569	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|B cell receptor signaling pathway (GO:0050853)|beta selection (GO:0043366)|blood coagulation (GO:0007596)|blood vessel morphogenesis (GO:0048514)|cell proliferation (GO:0008283)|cellular response to molecule of fungal origin (GO:0071226)|defense response to bacterium (GO:0042742)|enzyme linked receptor protein signaling pathway (GO:0007167)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte activation involved in immune response (GO:0002366)|leukocyte cell-cell adhesion (GO:0007159)|leukotriene biosynthetic process (GO:0019370)|lymph vessel development (GO:0001945)|macrophage activation involved in immune response (GO:0002281)|neutrophil activation involved in immune response (GO:0002283)|neutrophil chemotaxis (GO:0030593)|organ morphogenesis (GO:0009887)|platelet activation (GO:0030168)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of bone resorption (GO:0045780)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045425)|positive regulation of interleukin-3 biosynthetic process (GO:0045401)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of arachidonic acid secretion (GO:0090237)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of neutrophil degranulation (GO:0043313)|regulation of phagocytosis (GO:0050764)|regulation of platelet activation (GO:0010543)|regulation of platelet aggregation (GO:0090330)|regulation of superoxide anion generation (GO:0032928)|serotonin secretion by platelet (GO:0002554)|viral process (GO:0016032)	B cell receptor complex (GO:0019815)|cytosol (GO:0005829)|early phagosome (GO:0032009)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	ATP binding (GO:0005524)|integrin binding (GO:0005178)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)	p.G546V(1)|p.G569V(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(3)|skin(2)|stomach(2)	26						TTCTCCTATGGGCAGAAGCCA	0.468			T	"ETV6, ITK"	"MDS, peripheral T-cell lymphoma"																																p.G569V		Atlas-SNP	.		Dom	yes		9	9q22	6850	spleen tyrosine kinase		L	SYK_ENST00000375754,NS,carcinoma,0,2	SYK	132	.	2	Substitution - Missense(2)	lung(2)	c.G1706T						.						119	115	117					9																	93650155		2203	4300	6503	SO:0001583	missense	6850	exon12			CCTATGGGCAGAA	L28824	CCDS6688.1, CCDS47992.1	9q22	2013-02-14			ENSG00000165025	ENSG00000165025		"SH2 domain containing"	11491	protein-coding gene	gene with protein product		600085				8082894, 1423621	Standard	XM_005252147		Approved		uc004aqz.3	P43405	OTTHUMG00000020200	ENST00000375754.4:c.1706G>T	chr9.hg19:g.93650155G>T	ENSP00000364907:p.Gly569Val	118.0	0.0		107.0	8.0	NM_003177		Missense_Mutation	SNP	ENST00000375754.4	hg19	CCDS6688.1	.	.	.	.	.	.	.	.	.	.	G	16.83	3.231238	0.58777	.	.	ENSG00000165025	ENST00000375754;ENST00000375751;ENST00000375747;ENST00000375746	T;T;T;T	0.72394	-0.65;-0.65;-0.65;-0.65	4.77	4.77	0.60923	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.90937	0.7151	H	0.98754	4.32	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.94746	0.7923	10	0.87932	D	0	.	17.9801	0.89138	0.0:0.0:1.0:0.0	.	546;569	P43405-2;P43405	.;KSYK_HUMAN	V	569;546;546;569	ENSP00000364907:G569V;ENSP00000364904:G546V;ENSP00000364899:G546V;ENSP00000364898:G569V	ENSP00000364898:G569V	G	+	2	0	SYK	92689976	1.000000	0.71417	0.981000	0.43875	0.182000	0.23217	9.037000	0.93765	2.459000	0.83118	0.455000	0.32223	GGG	.	.		0.468	SYK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053018.1			T	93650155	G	T	93650155	3	4	346	1	0	0	0	0	1	0	0	0	15453	1232	43	3	1748	3	SYK	9	93650155	Missense_Mutation	SNP	G	TCGA-UB-A7MD-01A-12D-A34Z-10	57019816	93650155	47563276	48	48890										
NCBP1	4686	hgsc.bcm.edu	37	chr9	100425320	100425320	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	atgtttgaggtctggaggaaCcatccacaggtaaaaattat	10	6	1	1	rs200307901		TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr9:100425320C>G	ENST00000375147.3	+	18	2044	c.1788C>G	c.(1786-1788)aaC>aaG	p.N596K		NM_002486.4	NP_002477.1	Q09161	NCBP1_HUMAN	nuclear cap binding protein subunit 1, 80kDa	596					7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA cis splicing, via spliceosome (GO:0045292)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of viral transcription (GO:0050434)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|spliceosomal snRNP assembly (GO:0000387)|termination of RNA polymerase II transcription (GO:0006369)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|mRNA cap binding complex (GO:0005845)|nuclear cap binding complex (GO:0005846)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA cap binding (GO:0000339)			NS(1)|central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)	19		Acute lymphoblastic leukemia(62;0.158)				TCTGGAGGAACCATCCACAGG	0.343																																					p.N596K	Ovarian(36;879 898 2893 44212 50307)	Atlas-SNP	.											.	NCBP1	64	.	0			c.C1788G						.						96	101	99					9																	100425320		2203	4299	6502	SO:0001583	missense	4686	exon18			GAGGAACCATCCA	BC001450	CCDS6728.1	9q34.1	2010-01-26	2002-08-29		ENSG00000136937	ENSG00000136937			7658	protein-coding gene	gene with protein product		600469	"nuclear cap binding protein subunit 1, 80kD"	NCBP		7937105, 8812508	Standard	NM_002486		Approved	CBP80, Sto1	uc004axq.3	Q09161	OTTHUMG00000020332	ENST00000375147.3:c.1788C>G	chr9.hg19:g.100425320C>G	ENSP00000364289:p.Asn596Lys	89.0	0.0		65.0	14.0	NM_002486	B2R718|Q59G76|Q5T1V0|Q5T7X2	Missense_Mutation	SNP	ENST00000375147.3	hg19	CCDS6728.1	.	.	.	.	.	.	.	.	.	.	C	13.73	2.323188	0.41096	.	.	ENSG00000136937	ENST00000375147	.	.	.	5.55	3.31	0.37934	MIF4G-like, type 2 (1);Armadillo-type fold (1);MIF4-like, type 1/2/3 (1);	0.000000	0.85682	D	0.000000	T	0.52108	0.1714	L	0.61218	1.895	0.80722	D	1	B	0.30526	0.283	B	0.38156	0.266	T	0.38436	-0.9661	9	0.12430	T	0.62	-22.1877	7.546	0.27768	0.0:0.6654:0.0:0.3346	.	596	Q09161	NCBP1_HUMAN	K	596	.	ENSP00000364289:N596K	N	+	3	2	NCBP1	99465141	0.985000	0.35326	1.000000	0.80357	0.998000	0.95712	0.163000	0.16520	1.465000	0.48006	0.655000	0.94253	AAC	.	C|1.000;A|0.000		0.343	NCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053337.1	NM_002486		G	100425320	C	G	100425320	3	3	346	1	0	0	0	0	1	0	0	0	10220	506	18	4	1858	4	NCBP1	9	100425320	Missense_Mutation	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	6775165	100425320	40788111	49	48891										
LAMC3	10319	hgsc.bcm.edu	37	chr9	133914252	133914252	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	tccccactcctgcccatagcCtgcaactgcagtggccgctc	8	19	0	0			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr9:133914252C>T	ENST00000361069.4	+	5	1111	c.978C>T	c.(976-978)ccC>ccT	p.P326P	LAMC3_ENST00000480883.1_3'UTR	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	326	Laminin EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00460}.				astrocyte development (GO:0014002)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|extracellular matrix organization (GO:0030198)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	structural molecule activity (GO:0005198)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(31)|ovary(3)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	69	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		TGCCCATAGCCTGCAACTGCA	0.612																																					p.P326P		Atlas-SNP	.											.	LAMC3	167	.	0			c.C978T						.						76	80	79					9																	133914252		2203	4296	6499	SO:0001630	splice_region_variant	10319	exon5			CATAGCCTGCAAC	AF041835	CCDS6938.1	9q31-q34	2013-03-01			ENSG00000050555	ENSG00000050555		"Laminins"	6494	protein-coding gene	gene with protein product		604349				10225960	Standard	NM_006059		Approved	DKFZp434E202	uc004caa.1	Q9Y6N6	OTTHUMG00000020819	ENST00000361069.4:c.977-1C>T	chr9.hg19:g.133914252C>T		24.0	0.0		25.0	11.0	NM_006059	B1APX9|B1APY0|Q59H72	Silent	SNP	ENST00000361069.4	hg19	CCDS6938.1																																																																																			.	.		0.612	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3	NM_006059	Silent	T	133914252	C	T	133914252	5	4	346	1	0	0	0	0	0	0	1	0	8625	695	24	3	996	3	LAMC3	9	133914252	Splice_Site	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	33488932	133914252	7299179	50	48892										
OLFM1	10439	hgsc.bcm.edu	37	chr9	138011380	138011380	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	tggacggctatcacaacaacCgcttcgtacgtgagtacaag	10	11	1	1			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr9:138011380C>T	ENST00000371793.3	+	6	1065	c.814C>T	c.(814-816)Cgc>Tgc	p.R272C	OLFM1_ENST00000371796.3_Missense_Mutation_p.R245C|OLFM1_ENST00000252854.4_Missense_Mutation_p.R254C	NM_001282611.1	NP_001269540.1	Q99784	NOE1_HUMAN	olfactomedin 1	272	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of neuron migration (GO:2001223)|nervous system development (GO:0007399)|protein oligomerization (GO:0051259)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(2)	21		Myeloproliferative disorder(178;0.0333)		Epithelial(140;5.49e-08)|OV - Ovarian serous cystadenocarcinoma(145;9.68e-08)|all cancers(34;1.88e-07)		TCACAACAACCGCTTCGTACG	0.572																																					p.R254C		Atlas-SNP	.											.	OLFM1	57	.	0			c.C760T						.						121	108	113					9																	138011380		2203	4300	6503	SO:0001583	missense	10439	exon6			AACAACCGCTTCG	AF035301	CCDS6986.1, CCDS6987.1, CCDS65183.1, CCDS65184.1	9q34.3	2014-01-20			ENSG00000130558	ENSG00000130558			17187	protein-coding gene	gene with protein product	"pancortin"	605366				9039501	Standard	NM_006334		Approved	NOE1, OlfA, AMY, NOELIN	uc004cfl.4	Q99784	OTTHUMG00000020897	ENST00000371793.3:c.814C>T	chr9.hg19:g.138011380C>T	ENSP00000360858:p.Arg272Cys	71.0	0.0		42.0	11.0	NM_014279	Q53XZ8|Q6IMJ4|Q6IMJ5|Q8N8R0|Q969S7|Q99452	Missense_Mutation	SNP	ENST00000371793.3	hg19		.	.	.	.	.	.	.	.	.	.	C	25.7	4.665111	0.88251	.	.	ENSG00000130558	ENST00000252854;ENST00000371796;ENST00000371793;ENST00000539877	D;D;D;D	0.88664	-2.41;-2.41;-2.41;-2.13	5.07	5.07	0.68467	Olfactomedin-like (3);	0.000000	0.85682	D	0.000000	D	0.95411	0.8510	M	0.89214	3.015	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76071	0.98;0.987	D	0.96221	0.9160	10	0.87932	D	0	.	18.4324	0.90630	0.0:1.0:0.0:0.0	.	272;254	Q99784;Q6IMJ8	NOE1_HUMAN;.	C	254;245;272;169	ENSP00000252854:R254C;ENSP00000360861:R245C;ENSP00000360858:R272C;ENSP00000443806:R169C	ENSP00000252854:R254C	R	+	1	0	OLFM1	137151201	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.590000	0.82653	2.357000	0.79964	0.561000	0.74099	CGC	.	.		0.572	OLFM1-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000054974.1	NM_014279		T	138011380	C	T	138011380	3	4	346	1	0	0	0	0	1	0	0	0	10861	652	23	1	792	1	OLFM1	9	138011380	Missense_Mutation	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	4097128	138011380	3202051	51	48893										
UBAC1	10422	hgsc.bcm.edu	37	chr9	138837090	138837090	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	cactccatggcctgaggcacCgacatgctgcaaggcaagag	12	13	0	2			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr9:138837090C>A	ENST00000371756.3	-	7	877	c.660G>T	c.(658-660)tcG>tcT	p.S220S	UBAC1_ENST00000465873.1_5'UTR	NM_016172.2	NP_057256.2	Q9BSL1	UBAC1_HUMAN	UBA domain containing 1	220	UBA 1. {ECO:0000255|PROSITE- ProRule:PRU00212}.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				NS(1)|biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(6)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	25		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.1e-06)|Epithelial(140;7.79e-06)		CCTGAGGCACCGACATGCTGC	0.592																																					p.S220S	NSCLC(78;973 1398 27381 29552 42415)	Atlas-SNP	.											.	UBAC1	40	.	0			c.G660T						.						53	46	49					9																	138837090		2203	4300	6503	SO:0001819	synonymous_variant	10422	exon7			AGGCACCGACATG	AF176796	CCDS35177.1	9q34.3	2008-02-05	2007-04-20	2007-04-20	ENSG00000130560	ENSG00000130560			30221	protein-coding gene	gene with protein product		608129	"ubiquitin associated domain containing 1"	UBADC1		10857748, 8619474	Standard	NM_016172		Approved	GBDR1	uc004cgt.3	Q9BSL1	OTTHUMG00000020920	ENST00000371756.3:c.660G>T	chr9.hg19:g.138837090C>A		31.0	0.0		39.0	17.0	NM_016172	O75500|Q9UMW7	Silent	SNP	ENST00000371756.3	hg19	CCDS35177.1																																																																																			.	.		0.592	UBAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055034.1	NM_016172		A	138837090	C	A	138837090	2	1	346	1	0	0	0	0	0	0	0	1	16849	639	23	1		1	UBAC1	9	138837090	Silent	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	825710	138837090	2376341	52	48894										
CCAR1	55749	hgsc.bcm.edu	37	chr10	70507323	70507323	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	tacagcagcctcagcaaaaaGgtatctttgcttttgtttca	7	9	3	0			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr10:70507323G>A	ENST00000265872.6	+	8	945	c.826G>A	c.(826-828)Gct>Act	p.A276T	CCAR1_ENST00000543719.1_Splice_Site_p.A261T|CCAR1_ENST00000535016.1_Splice_Site_p.A261T	NM_001282959.1|NM_001282960.1|NM_018237.2	NP_001269888.1|NP_001269889.1|NP_060707.2	Q8IX12	CCAR1_HUMAN	cell division cycle and apoptosis regulator 1	276					apoptotic process (GO:0006915)|cell cycle (GO:0007049)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|lung(13)|ovary(7)|skin(3)	56						TCAGCAAAAAGGTATCTTTGC	0.393																																					p.A276T		Atlas-SNP	.											.	CCAR1	118	.	0			c.G826A						.						104	103	103					10																	70507323		2203	4300	6503	SO:0001630	splice_region_variant	55749	exon8			CAAAAAGGTATCT	AY249140	CCDS7282.1, CCDS60547.1	10q22.1	2004-02-19			ENSG00000060339	ENSG00000060339			24236	protein-coding gene	gene with protein product		612569				12816952	Standard	NM_018237		Approved	FLJ10590, CARP-1, CARP1	uc001joo.3	Q8IX12	OTTHUMG00000018361	ENST00000265872.6:c.826+1G>A	chr10.hg19:g.70507323G>A		60.0	0.0		44.0	7.0	NM_018237	A0JLT7|A1L4P7|A8K9D4|B4DNP8|B4DRK8|Q32NE3|Q5EBM3|Q5VUP6|Q6PIZ0|Q6X935|Q9H8N4|Q9NVA7|Q9NVQ0|Q9NWM6	Missense_Mutation	SNP	ENST00000265872.6	hg19	CCDS7282.1	.	.	.	.	.	.	.	.	.	.	G	18.96	3.732951	0.69189	.	.	ENSG00000060339	ENST00000265872;ENST00000535016;ENST00000543719;ENST00000539539;ENST00000543225;ENST00000536012	T;T;T;T;T;T	0.29655	1.56;1.85;1.85;1.87;1.89;1.9	5.06	5.06	0.68205	.	0.183837	0.48286	D	0.000182	T	0.19046	0.0457	N	0.08118	0	0.45676	D	0.99859	B;B;B	0.25609	0.02;0.034;0.13	B;B;B	0.26969	0.003;0.011;0.075	T	0.07888	-1.0749	10	0.19590	T	0.45	-12.2394	18.781	0.91932	0.0:0.0:1.0:0.0	.	261;276;250	Q8IX12-2;Q8IX12;F5H2E6	.;CCAR1_HUMAN;.	T	276;261;261;261;250;81	ENSP00000265872:A276T;ENSP00000441820:A261T;ENSP00000445254:A261T;ENSP00000439252:A261T;ENSP00000438610:A250T;ENSP00000439642:A81T	ENSP00000265872:A276T	A	+	1	0	CCAR1	70177329	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.160000	0.77495	2.526000	0.85167	0.655000	0.94253	GCT	.	.		0.393	CCAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048356.2	NM_018237	Missense_Mutation	A	70507323	G	A	70507323	5	1	346	1	0	0	0	0	0	0	1	0	2732	1014	35	3	852	3	CCAR1	10	70507323	Splice_Site	SNP	G	TCGA-UB-A7MD-01A-12D-A34Z-10		70507323	65027424	53	48895										
DUSP13	51207	hgsc.bcm.edu	37	chr10	76865548	76865548	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	ccgcctggcgcagggacagcCgctggtgcagcatgaggtag	17	12	0	1	rs200574063	byFrequency	TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr10:76865548C>T	ENST00000372702.3	-	3	509	c.446G>A	c.(445-447)cGg>cAg	p.R149Q	DUSP13_ENST00000491677.2_5'UTR|DUSP13_ENST00000607131.1_Intron|DUSP13_ENST00000372700.3_Intron|DUSP13_ENST00000607009.1_Intron			Q9UII6	DS13B_HUMAN	dual specificity phosphatase 13	158	Tyrosine-protein phosphatase.				meiotic nuclear division (GO:0007126)|protein dephosphorylation (GO:0006470)|spermatogenesis (GO:0007283)		protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			large_intestine(3)|lung(3)|prostate(1)|urinary_tract(1)	8	all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348)					CAGGGACAGCCGCTGGTGCAG	0.647													C|||	5	0.000998403	0.0038	0	5008	,	,		17110	0		0	False		,,,				2504	0				p.R149Q	NSCLC(174;1655 2059 12324 40663 42963)	Atlas-SNP	.											.	DUSP13	82	.	0			c.G446A						.	C	GLN/ARG,,	12,4280		0,12,2134	13	18	17		446,,	-0.6	1	10		17	0,8374		0,0,4187	yes	missense,intron,intron	DUSP13	NM_001007271.1,NM_001007272.1,NM_001007273.1	43,,	0,12,6321	TT,TC,CC		0.0,0.2796,0.0947	,,	149/189,,	76865548	12,12654	2146	4187	6333	SO:0001583	missense	51207	exon3			GACAGCCGCTGGT	AB027004	CCDS7346.1, CCDS31224.1, CCDS53542.1	10q23.1	2013-10-25			ENSG00000079393	ENSG00000079393		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	19681	protein-coding gene	gene with protein product		613191				10585869	Standard	XM_005269883		Approved	BEDP, TMDP, FLJ32450, DUSP13A, DUSP13B	uc001jwu.3	Q6B8I1	OTTHUMG00000018516	ENST00000372702.3:c.446G>A	chr10.hg19:g.76865548C>T	ENSP00000361787:p.Arg149Gln	50.0	0.0		52.0	25.0	NM_001007271	A8K776|A8K782|B3KPY1|B3KXT0|B4DUK0|Q5JSC6|Q6IAR0|Q96GC2	Missense_Mutation	SNP	ENST00000372702.3	hg19	CCDS53542.1	.	.	.	.	.	.	.	.	.	.	C	11.44	1.640526	0.29157	0.002796	0.0	ENSG00000079393	ENST00000372702	T	0.60171	0.21	4.81	-0.652	0.11450	Dual specificity phosphatase, catalytic domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	.	.	.	.	T	0.37919	0.1021	N	0.20574	0.59	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.21621	-1.0240	9	0.27785	T	0.31	.	9.3275	0.38001	0.0:0.3962:0.0:0.6038	.	149	Q6B8I1	MDSP_HUMAN	Q	149	ENSP00000361787:R149Q	ENSP00000361787:R149Q	R	-	2	0	DUSP13	76535554	0.000000	0.05858	0.996000	0.52242	0.468000	0.32798	-0.170000	0.09897	0.027000	0.15297	-0.672000	0.03802	CGG	.	.		0.647	DUSP13-012	KNOWN	NMD_exception|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000401503.3			T	76865548	C	T	76865548	3	4	346	1	0	0	0	0	1	0	0	0	4815	652	23	1	1020	1	DUSP13	10	76865548	Missense_Mutation	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	6358225	76865548	58669199	54	48896										
SLC1A2	6506	hgsc.bcm.edu	37	chr11	35308464	35308464	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	atcaatccccagattttcttCcaggcaacgaaaggtgacag	8	11	2	2			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr11:35308464C>G	ENST00000278379.3	-	8	1408	c.1126G>C	c.(1126-1128)Gaa>Caa	p.E376Q	SLC1A2_ENST00000606205.1_Missense_Mutation_p.E376Q|SLC1A2_ENST00000395750.1_Missense_Mutation_p.E367Q|RP1-68D18.3_ENST00000532760.1_RNA|SLC1A2_ENST00000479543.1_5'Flank|SLC1A2_ENST00000395753.1_Missense_Mutation_p.E367Q	NM_004171.3	NP_004162.2	P43004	EAA2_HUMAN	solute carrier family 1 (glial high affinity glutamate transporter), member 2	376					adult behavior (GO:0030534)|cellular response to extracellular stimulus (GO:0031668)|D-aspartate import (GO:0070779)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|positive regulation of glucose import (GO:0046326)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to wounding (GO:0009611)|synaptic transmission (GO:0007268)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)|visual behavior (GO:0007632)	axolemma (GO:0030673)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glutamate:sodium symporter activity (GO:0015501)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|urinary_tract(1)	24	all_lung(20;0.211)|all_epithelial(35;0.234)	all_hematologic(20;0.109)	STAD - Stomach adenocarcinoma(6;0.00731)			AGATTTTCTTCCAGGCAACGA	0.463																																					p.E376Q	NSCLC(100;1273 1575 12993 16869 47409)|Ovarian(164;45 1946 8965 30452 48454)	Atlas-SNP	.											.	SLC1A2	54	.	0			c.G1126C						.						155	149	151					11																	35308464		2202	4298	6500	SO:0001583	missense	6506	exon8			TTTCTTCCAGGCA	AB209444	CCDS31459.1, CCDS55756.1	11p13-p12	2013-05-22			ENSG00000110436	ENSG00000110436		"Solute carriers"	10940	protein-coding gene	gene with protein product		600300				1448170	Standard	NM_004171		Approved	GLT-1, EAAT2	uc001mwd.3	P43004	OTTHUMG00000044391	ENST00000278379.3:c.1126G>C	chr11.hg19:g.35308464C>G	ENSP00000278379:p.Glu376Gln	61.0	0.0		60.0	24.0	NM_004171	B4DQE9|Q14417|Q541G6|U3KQQ4	Missense_Mutation	SNP	ENST00000278379.3	hg19	CCDS31459.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.1|28.1	4.889942|4.889942	0.91889|0.91889	.|.	.|.	ENSG00000110436|ENSG00000110436	ENST00000278379;ENST00000395750;ENST00000395753|ENST00000531628	T;T;T|.	0.61980|.	0.06;0.06;0.06|.	5.62|5.62	4.71|4.71	0.59529|0.59529	.|.	0.086454|.	0.85682|.	D|.	0.000000|.	T|T	0.72669|0.72669	0.3489|0.3489	M|M	0.70842|0.70842	2.15|2.15	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.995;0.999|.	T|T	0.73269|0.73269	-0.4036|-0.4036	10|5	0.72032|.	D|.	0.01|.	-18.6683|-18.6683	14.8568|14.8568	0.70344|0.70344	0.0:0.9308:0.0:0.0692|0.0:0.9308:0.0:0.0692	.|.	376;376|.	B4DQE9;P43004|.	.;EAA2_HUMAN|.	Q|C	376;367;367|93	ENSP00000278379:E376Q;ENSP00000379099:E367Q;ENSP00000379102:E367Q|.	ENSP00000278379:E376Q|.	E|W	-|-	1|3	0|0	SLC1A2|SLC1A2	35265040|35265040	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	7.776000|7.776000	0.85560|0.85560	1.517000|1.517000	0.48917|0.48917	0.561000|0.561000	0.74099|0.74099	GAA|TGG	.	.		0.463	SLC1A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258181.1	NM_004171		G	35308464	C	G	35308464	3	3	346	1	0	0	0	0	1	0	0	0	14447	864	30	4	614	4	SLC1A2	11	35308464	Missense_Mutation	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10		35308464	99698052	55	48897										
OR5D18	219438	hgsc.bcm.edu	37	chr11	55587559	55587559	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	tggttgtgggatcctatgccTggggagtctcatgttccttg	14	8	1	0			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr11:55587559T>A	ENST00000333976.4	+	1	474	c.454T>A	c.(454-456)Tgg>Agg	p.W152R		NM_001001952.1	NP_001001952.1	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D, member 18	152						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(3)|large_intestine(6)|lung(33)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		all_epithelial(135;0.208)				ATCCTATGCCTGGGGAGTCTC	0.478																																					p.W152R		Atlas-SNP	.											.	OR5D18	121	.	0			c.T454A						.						189	178	182					11																	55587559		2200	4296	6496	SO:0001583	missense	219438	exon1			TATGCCTGGGGAG	AB065781	CCDS31510.1	11q11	2012-08-09			ENSG00000186119	ENSG00000186119		"GPCR / Class A : Olfactory receptors"	15285	protein-coding gene	gene with protein product							Standard	NM_001001952		Approved		uc010rin.2	Q8NGL1	OTTHUMG00000166811	ENST00000333976.4:c.454T>A	chr11.hg19:g.55587559T>A	ENSP00000335025:p.Trp152Arg	206.0	0.0		177.0	58.0	NM_001001952	Q6IF67|Q6IFD3|Q96RB3	Missense_Mutation	SNP	ENST00000333976.4	hg19	CCDS31510.1	.	.	.	.	.	.	.	.	.	.	.	8.973	0.973516	0.18736	.	.	ENSG00000186119	ENST00000333976	T	0.36520	1.25	4.85	0.776	0.18532	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36628	N	0.002487	T	0.50531	0.1621	M	0.75447	2.3	0.09310	N	0.999994	D	0.71674	0.998	D	0.73708	0.981	T	0.35992	-0.9766	10	0.27785	T	0.31	-7.4768	7.165	0.25685	0.0:0.0835:0.371:0.5456	.	152	Q8NGL1	OR5DI_HUMAN	R	152	ENSP00000335025:W152R	ENSP00000335025:W152R	W	+	1	0	OR5D18	55344135	0.000000	0.05858	0.022000	0.16811	0.010000	0.07245	-0.220000	0.09215	0.298000	0.22638	0.462000	0.41574	TGG	.	.		0.478	OR5D18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391515.1	NM_001001952		A	55587559	T	A	55587559	3	1	346	1	0	0	0	0	1	0	0	0	11166	1580	55	4	456	4	OR5D18	11	55587559	Missense_Mutation	SNP	T	TCGA-UB-A7MD-01A-12D-A34Z-10	20279095	55587559	79418957	56	48898										
GAL	51083	hgsc.bcm.edu	37	chr11	68455540	68455540	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	ggcctcaccagcaagcgggaGctgcggcccgaagatgacat	14	13	1	2			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr11:68455540G>A	ENST00000265643.3	+	4	453	c.195G>A	c.(193-195)gaG>gaA	p.E65E		NM_015973.3	NP_057057.2	P22466	GALA_HUMAN	galanin/GMAP prepropeptide	65					cAMP-mediated signaling (GO:0019933)|feeding behavior (GO:0007631)|inflammatory response (GO:0006954)|insulin secretion (GO:0030073)|negative regulation of lymphocyte proliferation (GO:0050672)|negative regulation of root hair elongation (GO:1902891)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catagen (GO:0051795)|positive regulation of cortisol secretion (GO:0051464)|positive regulation of large conductance calcium-activated potassium channel activity (GO:1902608)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein kinase A signaling (GO:0010737)|regulation of glucocorticoid metabolic process (GO:0031943)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to insulin (GO:0032868)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|neuronal cell body (GO:0043025)|secretory granule (GO:0030141)	neuropeptide hormone activity (GO:0005184)|type 1 galanin receptor binding (GO:0031764)|type 2 galanin receptor binding (GO:0031765)|type 3 galanin receptor binding (GO:0031766)			lung(4)	4	Esophageal squamous(3;7.33e-10)	Melanoma(852;0.0749)	LUAD - Lung adenocarcinoma(13;0.0514)	Kidney(183;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(183;3.23e-08)|Lung(977;0.000152)|LUSC - Lung squamous cell carcinoma(976;0.00154)		GCAAGCGGGAGCTGCGGCCCG	0.602																																					p.E65E		Atlas-SNP	.											.	GAL	11	.	0			c.G195A						.						87	78	81					11																	68455540		2200	4294	6494	SO:0001819	synonymous_variant	51083	exon4			GCGGGAGCTGCGG	L11144	CCDS8183.1	11q13.2	2013-02-26	2012-10-23		ENSG00000069482	ENSG00000069482		"Endogenous ligands"	4114	protein-coding gene	gene with protein product	"galanin-message-associated peptide", "galanin/GMAP prepropeptide"	137035	"galanin", "galanin prepropeptide"	GALN		7508413	Standard	XM_006718580		Approved	GMAP, GAL-GMAP, GLNN	uc001oob.3	P22466	OTTHUMG00000167890	ENST00000265643.3:c.195G>A	chr11.hg19:g.68455540G>A		62.0	0.0		67.0	24.0	NM_015973	Q14413	Silent	SNP	ENST00000265643.3	hg19	CCDS8183.1																																																																																			.	.		0.602	GAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396843.2	NM_001479		A	68455540	G	A	68455540	2	1	346	1	0	0	0	0	0	0	0	1	6204	962	34	3		3	GAL	11	68455540	Silent	SNP	G	TCGA-UB-A7MD-01A-12D-A34Z-10	12867981	68455540	66550976	57	48899										
GPR84	53831	hgsc.bcm.edu	37	chr12	54757494	54757494	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	tcgggtacggagcttgggctGgatggccaaggccagtaggg	19	8	0	0			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr12:54757494G>T	ENST00000551809.1	-	1	777	c.142C>A	c.(142-144)Cag>Aag	p.Q48K	GPR84_ENST00000267015.3_Missense_Mutation_p.Q48K|RP11-753H16.5_ENST00000552785.1_RNA|RP11-753H16.3_ENST00000550474.1_RNA			Q9NQS5	GPR84_HUMAN	G protein-coupled receptor 84	48						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(2)|kidney(2)|large_intestine(6)|lung(5)|skin(1)|urinary_tract(1)	18						AGCTTGGGCTGGATGGCCAAG	0.582																																					p.Q48K		Atlas-SNP	.											.	GPR84	38	.	0			c.C142A						.						187	156	167					12																	54757494		2203	4300	6503	SO:0001583	missense	53831	exon2			TGGGCTGGATGGC	AF237762	CCDS8878.1	12q13.13	2012-08-20						"GPCR / Class A : Fatty acid receptors"	4535	protein-coding gene	gene with protein product		606383				11273702	Standard	NM_020370		Approved	EX33	uc001sfu.3	Q9NQS5		ENST00000551809.1:c.142C>A	chr12.hg19:g.54757494G>T	ENSP00000450310:p.Gln48Lys	55.0	0.0		50.0	14.0	NM_020370	B6V9G7	Missense_Mutation	SNP	ENST00000551809.1	hg19	CCDS8878.1	.	.	.	.	.	.	.	.	.	.	G	9.510	1.105459	0.20632	.	.	ENSG00000139572	ENST00000267015;ENST00000551809	T;T	0.71461	-0.57;-0.57	4.81	3.84	0.44239	GPCR, rhodopsin-like superfamily (1);	0.370724	0.19734	N	0.107286	T	0.59376	0.2189	L	0.40543	1.245	0.31811	N	0.627181	B	0.20164	0.042	B	0.22753	0.041	T	0.58685	-0.7593	10	0.25106	T	0.35	-3.7216	10.9202	0.47161	0.0:0.3044:0.6955:0.0	.	48	Q9NQS5	GPR84_HUMAN	K	48	ENSP00000267015:Q48K;ENSP00000450310:Q48K	ENSP00000267015:Q48K	Q	-	1	0	GPR84	53043761	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	4.497000	0.60367	2.602000	0.87976	0.555000	0.69702	CAG	.	.		0.582	GPR84-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406156.1			T	54757494	G	T	54757494	3	4	346	1	0	0	0	0	1	0	0	0	6722	1357	47	3	1052	3	GPR84	12	54757494	Missense_Mutation	SNP	G	TCGA-UB-A7MD-01A-12D-A34Z-10		54757494	79094401	58	48900										
MON2	23041	hgsc.bcm.edu	37	chr12	62979151	62979151	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	tactccagttttccttcagtAataaagtcacaacacctcaa	3	12	3	0			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr12:62979151A>T	ENST00000393632.2	+	33	5168	c.4777A>T	c.(4777-4779)Aat>Tat	p.N1593Y	MON2_ENST00000280379.6_Missense_Mutation_p.N1594Y|MON2_ENST00000552738.1_Missense_Mutation_p.N1564Y|MON2_ENST00000393630.3_Missense_Mutation_p.N1594Y|MON2_ENST00000551397.1_5'Flank|MON2_ENST00000393629.2_Missense_Mutation_p.N1587Y|MON2_ENST00000546600.1_Missense_Mutation_p.N1593Y	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	1593					actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		TTCCTTCAGTAATAAAGTCAC	0.353																																					p.N1593Y		Atlas-SNP	.											.	MON2	160	.	0			c.A4777T						.						91	86	88					12																	62979151		2203	4300	6503	SO:0001583	missense	23041	exon33			TTCAGTAATAAAG		CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987			29177	protein-coding gene	gene with protein product			"MON2 homolog (yeast)"			16301316, 24285343	Standard	NM_015026		Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000393632.2:c.4777A>T	chr12.hg19:g.62979151A>T	ENSP00000377252:p.Asn1593Tyr	162.0	0.0		148.0	47.0	NM_015026	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Missense_Mutation	SNP	ENST00000393632.2	hg19	CCDS31849.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.384753	0.82792	.	.	ENSG00000061987	ENST00000393632;ENST00000393630;ENST00000280379;ENST00000546600;ENST00000552738;ENST00000393629	T;T;T;T;T;T	0.58210	0.36;0.36;0.36;0.36;0.35;0.36	5.31	5.31	0.75309	.	0.092243	0.64402	D	0.000001	T	0.64472	0.2601	L	0.42245	1.32	0.80722	D	1	D;D;D;D;D	0.76494	0.997;0.996;0.994;0.999;0.998	P;D;P;D;D	0.72075	0.854;0.93;0.846;0.976;0.93	T	0.62595	-0.6821	9	.	.	.	-17.5848	15.5557	0.76189	1.0:0.0:0.0:0.0	.	1587;1564;1593;462;1593	B9EGP5;F8VWA6;F8W1Z6;Q7Z3U7-3;Q7Z3U7-4	.;.;.;.;.	Y	1593;1594;1594;1593;1564;1587	ENSP00000377252:N1593Y;ENSP00000377250:N1594Y;ENSP00000280379:N1594Y;ENSP00000447407:N1593Y;ENSP00000449215:N1564Y;ENSP00000377249:N1587Y	.	N	+	1	0	MON2	61265418	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.481000	0.81124	2.123000	0.65237	0.460000	0.39030	AAT	.	.		0.353	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026		T	62979151	A	T	62979151	3	4	346	1	0	0	0	0	1	0	0	0	9709	362	13	4	4907	4	MON2	12	62979151	Missense_Mutation	SNP	A	TCGA-UB-A7MD-01A-12D-A34Z-10	8221657	62979151	70872744	59	48901										
ZFC3H1	196441	hgsc.bcm.edu	37	chr12	72030765	72030766	+	Frame_Shift_Ins	INS	-	-	ATTA													0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	caggtgggagaggtggtaatINSggtggtagaggaggtagagg							TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr12:72030765_72030766insATTA	ENST00000378743.3	-	8	2157_2158	c.1799_1800insTAAT	c.(1798-1800)ccafs	p.-600fs	SNORA17_ENST00000391159.1_RNA	NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing						RNA processing (GO:0006396)	extracellular space (GO:0005615)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						GAGGTGGTAATGGTGGTAGAGG	0.441																																					p.P600fs		Atlas-Indel,Pindel	.											.	ZFC3H1	172	.	0			c.1800_1801insTAAT						.																																			SO:0001589	frameshift_variant	196441	exon8			.	AB011118	CCDS41813.1	12q21.1	2013-01-25	2008-10-01	2008-10-01		ENSG00000133858		"Zinc finger, C3H1-type containing"	28328	protein-coding gene	gene with protein product			"proline/serine-rich coiled-coil 2", "coiled-coil domain containing 131"	PSRC2, CCDC131		9628581	Standard	NM_144982		Approved	MGC23401, KIAA0546	uc001swo.2	O60293	OTTHUMG00000169545	ENST00000378743.3:c.1799_1800insTAAT	chr12.hg19:g.72030765_72030766insATTA	ENSP00000368017:p.Pro600fs	91.0	0.0		141.0	23.0	NM_144982	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Frame_Shift_Ins	INS	ENST00000378743.3	hg19	CCDS41813.1																																																																																			.	.		0.441	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982		ATTA	72030766	-	ATTA	72030765	7	5	346	1	0	1	1	0	0	0	0	0	17648	1451	51	0	4281	0	ZFC3H1	12	72030765	Frame_Shift_Ins	INS	-	TCGA-UB-A7MD-01A-12D-A34Z-10	9051614	72030765	61821130	60	48902										
EEA1	8411	hgsc.bcm.edu	37	chr12	93236314	93236314	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	gtacatatacagcaacttccTgggggcctttggcaagttca	10	10	1	0			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr12:93236314T>A	ENST00000322349.8	-	10	1106	c.842A>T	c.(841-843)cAg>cTg	p.Q281L		NM_003566.3	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1	281					early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|synaptic vesicle to endosome fusion (GO:0016189)|vesicle fusion (GO:0006906)	axonal spine (GO:0044308)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|recycling endosome (GO:0055037)|serine-pyruvate aminotransferase complex (GO:0005969)	1-phosphatidylinositol binding (GO:0005545)|calmodulin binding (GO:0005516)|GTP-dependent protein binding (GO:0030742)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(5)|large_intestine(11)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	36						AGCAACTTCCTGGGGGCCTTT	0.308																																					p.Q281L		Atlas-SNP	.											.	EEA1	104	.	0			c.A842T						.						39	40	40					12																	93236314		2203	4299	6502	SO:0001583	missense	8411	exon10			ACTTCCTGGGGGC	L40157	CCDS31874.1	12q22	2007-02-23	2007-02-23			ENSG00000102189		"Zinc fingers, FYVE domain containing"	3185	protein-coding gene	gene with protein product		605070	"early endosome antigen 1, 162kD"			7768953, 9697774	Standard	NM_003566		Approved	ZFYVE2	uc001tck.3	Q15075	OTTHUMG00000170110	ENST00000322349.8:c.842A>T	chr12.hg19:g.93236314T>A	ENSP00000317955:p.Gln281Leu	230.0	0.0		345.0	99.0	NM_003566	Q14221	Missense_Mutation	SNP	ENST00000322349.8	hg19	CCDS31874.1	.	.	.	.	.	.	.	.	.	.	T	25.1	4.599645	0.87055	.	.	ENSG00000102189	ENST00000322349;ENST00000540777	D	0.83419	-1.72	5.51	5.51	0.81932	.	0.000000	0.48767	D	0.000169	D	0.86024	0.5834	L	0.34521	1.04	0.80722	D	1	D	0.60160	0.987	D	0.67725	0.953	D	0.86690	0.1922	10	0.49607	T	0.09	.	15.6229	0.76820	0.0:0.0:0.0:1.0	.	281	Q15075	EEA1_HUMAN	L	281;280	ENSP00000317955:Q281L	ENSP00000317955:Q281L	Q	-	2	0	EEA1	91760445	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.560000	0.73950	2.094000	0.63399	0.460000	0.39030	CAG	.	.		0.308	EEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407304.1	NM_003566		A	93236314	T	A	93236314	3	1	346	1	0	0	0	0	1	0	0	0	4923	1580	55	4	3473	4	EEA1	12	93236314	Missense_Mutation	SNP	T	TCGA-UB-A7MD-01A-12D-A34Z-10	21205549	93236314	40615581	61	48903										
HCFC2	29915	hgsc.bcm.edu	37	chr12	104474603	104474604	+	Frame_Shift_Del	DEL	AA	AA	-													0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	catacagccagtgttataggAaacaagtatggtggtttttt							TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr12:104474603_104474604delAA	ENST00000229330.4	+	5	866_867	c.762_763delAA	c.(760-765)ggaaacfs	p.N255fs		NM_013320.2	NP_037452.1	Q9Y5Z7	HCFC2_HUMAN	host cell factor C2	255					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	35						GTGTTATAGGAAACAAGTATGG	0.322																																					p.254_254del	Esophageal Squamous(184;1814 2036 4771 6974 15702)	Atlas-Indel,Pindel	.											.	HCFC2	94	.	0			c.761_762del						.																																			SO:0001589	frameshift_variant	29915	exon5			.	AF117210	CCDS9097.1	12q23.3	2011-03-30			ENSG00000111727	ENSG00000111727			24972	protein-coding gene	gene with protein product		607926				10196288	Standard	NM_013320		Approved	HCF-2	uc001tkj.4	Q9Y5Z7	OTTHUMG00000170175	ENST00000229330.4:c.762_763delAA	chr12.hg19:g.104474603_104474604delAA	ENSP00000229330:p.Asn255fs	99.0	0.0		94.0	33.0	NM_013320	B2R8Q5|C0H5X3	Frame_Shift_Del	DEL	ENST00000229330.4	hg19	CCDS9097.1																																																																																			.	.		0.322	HCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407780.1	NM_013320		-	104474604	AA	-	104474603	7	5	346	1	0	1	0	1	0	0	0	0	7002	233	9	0	780	0	HCFC2	12	104474603	Frame_Shift_Del	DEL	AA	TCGA-UB-A7MD-01A-12D-A34Z-10	11238289	104474603	29377292	62	48904										
DAO	1610	hgsc.bcm.edu	37	chr12	109283278	109283278	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	aggacacagttctgggatttCggaagctgacccccagagag	13	10	1	2	rs201583577		TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr12:109283278C>T	ENST00000228476.3	+	4	547	c.343C>T	c.(343-345)Cgg>Tgg	p.R115W	DAO_ENST00000551281.1_Intron	NM_001917.4	NP_001908.3	P14920	OXDA_HUMAN	D-amino-acid oxidase	115					cellular nitrogen compound metabolic process (GO:0034641)|D-alanine catabolic process (GO:0055130)|D-serine catabolic process (GO:0036088)|D-serine metabolic process (GO:0070178)|dopamine biosynthetic process (GO:0042416)|glyoxylate metabolic process (GO:0046487)|leucine metabolic process (GO:0006551)|proline catabolic process (GO:0006562)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	cofactor binding (GO:0048037)|D-amino-acid oxidase activity (GO:0003884)|FAD binding (GO:0071949)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|prostate(2)|skin(1)	26					Flavin adenine dinucleotide(DB03147)	TCTGGGATTTCGGAAGCTGAC	0.532																																					p.R115W		Atlas-SNP	.											.	DAO	58	.	0			c.C343T						.	C	TRP/ARG	0,4406		0,0,2203	88	81	83		343	5.2	1	12		83	1,8599	1.2+/-3.3	0,1,4299	yes	missense	DAO	NM_001917.4	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	115/348	109283278	1,13005	2203	4300	6503	SO:0001583	missense	1610	exon4			GGATTTCGGAAGC	D11370	CCDS9122.1	12q24.11	2013-09-20			ENSG00000110887	ENSG00000110887	1.4.3.3		2671	protein-coding gene	gene with protein product		124050				1356107, 8182053	Standard	NM_001917		Approved	DAMOX	uc001tnr.4	P14920	OTTHUMG00000169360	ENST00000228476.3:c.343C>T	chr12.hg19:g.109283278C>T	ENSP00000228476:p.Arg115Trp	48.0	0.0		49.0	9.0	NM_001917	B2R7I5|Q16758|Q8N6R2	Missense_Mutation	SNP	ENST00000228476.3	hg19	CCDS9122.1	.	.	.	.	.	.	.	.	.	.	C	17.49	3.402537	0.62288	0.0	1.16E-4	ENSG00000110887	ENST00000228476;ENST00000547166	D;D	0.83163	-1.69;-1.69	6.06	5.17	0.71159	FAD dependent oxidoreductase (1);	0.049288	0.85682	D	0.000000	D	0.93736	0.7998	H	0.95917	3.74	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95339	0.8436	10	0.87932	D	0	-14.6652	13.984	0.64321	0.2751:0.7249:0.0:0.0	.	115	P14920	OXDA_HUMAN	W	115	ENSP00000228476:R115W;ENSP00000447104:R115W	ENSP00000228476:R115W	R	+	1	2	DAO	107807407	1.000000	0.71417	1.000000	0.80357	0.531000	0.34715	2.461000	0.45040	1.562000	0.49601	0.655000	0.94253	CGG	.	.		0.532	DAO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403682.1			T	109283278	C	T	109283278	3	4	346	1	0	0	0	0	1	0	0	0	4233	875	31	1	353	1	DAO	12	109283278	Missense_Mutation	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	4808675	109283278	24568617	63	48905										
FAM48A	55578	hgsc.bcm.edu	37	chr13	37605935	37605935	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	tgcttttctttcctttctttTttgtaagaaatcaagtaacc	4	8	3	1			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr13:37605935T>C	ENST00000350612.6	-	11	1025	c.805A>G	c.(805-807)Aaa>Gaa	p.K269E	SUPT20H_ENST00000475892.1_Missense_Mutation_p.K269E|SUPT20H_ENST00000542180.1_Missense_Mutation_p.K257E|SUPT20H_ENST00000464744.1_Missense_Mutation_p.K270E|AL138706.1_ENST00000408173.1_RNA|SUPT20H_ENST00000356185.3_Missense_Mutation_p.K270E|SUPT20H_ENST00000360252.4_Missense_Mutation_p.K270E	NM_001014286.2	NP_001014308.2	Q8NEM7	SP20H_HUMAN	suppressor of Ty 20 homolog (S. cerevisiae)	269					autophagy (GO:0006914)|chromatin organization (GO:0006325)|gastrulation (GO:0007369)	SAGA complex (GO:0000124)|SAGA-type complex (GO:0070461)	transcription cofactor activity (GO:0003712)										TCCTTTCTTTTTTGTAAGAAA	0.373																																					p.K270E		Atlas-SNP	.											.	.	.	.	0			c.A808G						.						61	67	65					13																	37605935		2203	4300	6503	SO:0001583	missense	55578	exon11			TTCTTTTTTGTAA	AF093250	CCDS9362.1, CCDS31959.1, CCDS61311.1	13q13	2012-11-29	2012-11-29	2012-11-29	ENSG00000102710	ENSG00000102710			20596	protein-coding gene	gene with protein product	"p38 interacting protein", "transcription factor (p38 interacting protein)"	613417	"chromosome 13 open reading frame 19", "family with sequence similarity 48, member A"	C13orf19, FAM48A		12070015 , 16685401	Standard	NM_001278480		Approved	SPT20, bA421P11.4, P38IP	uc001uwg.3	Q8NEM7	OTTHUMG00000016747	ENST00000350612.6:c.805A>G	chr13.hg19:g.37605935T>C	ENSP00000218894:p.Lys269Glu	179.0	0.0		218.0	63.0	NM_017569	E7ER46|Q71RF3|Q9Y6A6	Missense_Mutation	SNP	ENST00000350612.6	hg19	CCDS31959.1	.	.	.	.	.	.	.	.	.	.	T	16.15	3.040872	0.55003	.	.	ENSG00000102710	ENST00000360252;ENST00000475892;ENST00000350612;ENST00000356185;ENST00000536874;ENST00000464744;ENST00000542180	T;T;T;T;T;T	0.55052	0.56;0.54;1.14;0.56;0.56;0.75	5.94	5.94	0.96194	.	0.101865	0.64402	D	0.000002	T	0.54334	0.1852	L	0.50333	1.59	0.49483	D	0.999799	B;P;P;B;B;B	0.36753	0.212;0.568;0.568;0.235;0.199;0.126	B;B;B;B;B;B	0.40636	0.086;0.175;0.311;0.18;0.335;0.137	T	0.57969	-0.7719	10	0.72032	D	0.01	-10.7368	16.4075	0.83691	0.0:0.0:0.0:1.0	.	257;269;269;270;270;269	B4E2D5;B3KNI1;E7ER46;A8K8L1;Q8NEM7-2;Q8NEM7	.;.;.;.;.;FA48A_HUMAN	E	270;269;269;270;269;270;257	ENSP00000353388:K270E;ENSP00000417510:K269E;ENSP00000218894:K269E;ENSP00000348512:K270E;ENSP00000419754:K270E;ENSP00000439000:K257E	ENSP00000218894:K269E	K	-	1	0	FAM48A	36503935	1.000000	0.71417	0.990000	0.47175	0.349000	0.29174	5.850000	0.69473	2.275000	0.75901	0.528000	0.53228	AAA	.	.		0.373	SUPT20H-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354766.1	NM_017569		C	37605935	T	C	37605935	3	2	346	1	0	0	0	0	1	0	0	0	5580	1850	64	2	1598	2	FAM48A	13	37605935	Missense_Mutation	SNP	T	TCGA-UB-A7MD-01A-12D-A34Z-10		37605935	77563943	64	48906										
DOCK9	23348	hgsc.bcm.edu	37	chr13	99533811	99533811	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	agaacagtgtgttttacataCcttaacatatgacctcaagt	6	8	1	2			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr13:99533811C>T	ENST00000376460.1	-	25	2826		c.e25+1		DOCK9_ENST00000339416.2_Splice_Site|DOCK9_ENST00000448493.2_Splice_Site|DOCK9_ENST00000442173.1_Splice_Site	NM_001130048.1|NM_015296.2	NP_001123520.1|NP_056111.1	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9						blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(18)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					GTTTTACATACCTTAACATAT	0.423																																					.		Atlas-SNP	.											.	DOCK9	311	.	0			c.2748+1G>A						.						96	90	92					13																	99533811		1945	4133	6078	SO:0001630	splice_region_variant	23348	exon26			TACATACCTTAAC	AF527605	CCDS45062.1	13q32.3	2013-01-10			ENSG00000088387	ENSG00000088387		"Pleckstrin homology (PH) domain containing"	14132	protein-coding gene	gene with protein product	"zizimin1"	607325				12172552, 12432077	Standard	NM_015296		Approved	KIAA1058, ZIZ1	uc001vnt.2	Q9BZ29	OTTHUMG00000017260	ENST00000376460.1:c.2745+1G>A	chr13.hg19:g.99533811C>T		53.0	0.0		52.0	15.0	NM_015296	B3KX25|E9PFM9|Q5JUD4|Q5JUD6|Q5T2Q1|Q5TAN8|Q9BZ25|Q9BZ26|Q9BZ27|Q9BZ28|Q9UPU4	Splice_Site	SNP	ENST00000376460.1	hg19	CCDS45062.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.886544	0.91814	.	.	ENSG00000088387	ENST00000376460;ENST00000357329;ENST00000376455;ENST00000400235;ENST00000428223;ENST00000339416;ENST00000448493;ENST00000442173	.	.	.	5.46	5.46	0.80206	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.6793	0.95956	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DOCK9	98331812	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.427000	0.80284	2.713000	0.92767	0.655000	0.94253	.	.	.		0.423	DOCK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045566.1	NM_015296	Intron	T	99533811	C	T	99533811	5	4	346	1	0	0	0	0	0	0	1	0	4696	521	18	3	3649	3	DOCK9	13	99533811	Splice_Site	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	61927876	99533811	15636067	65	48907										
ANKRD10	55608	hgsc.bcm.edu	37	chr13	111532383	111532383	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	atcccactgagcggggtcgtGgaggggaagtccaaatgtcc	15	10	0	1			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr13:111532383G>C	ENST00000267339.2	-	6	998	c.864C>G	c.(862-864)tcC>tcG	p.S288S	ANKRD10_ENST00000375758.5_3'UTR	NM_017664.2	NP_060134.2	Q9NXR5	ANR10_HUMAN	ankyrin repeat domain 10	288										central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(3)	9	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		all cancers(43;0.0882)|BRCA - Breast invasive adenocarcinoma(86;0.188)|Lung(89;0.208)			GCGGGGTCGTGGAGGGGAAGT	0.473																																					p.S288S		Atlas-SNP	.											.	ANKRD10	24	.	0			c.C864G						.						72	74	73					13																	111532383		2203	4300	6503	SO:0001819	synonymous_variant	55608	exon6			GGTCGTGGAGGGG	AK000100	CCDS9520.1, CCDS66580.1	13q33.3	2013-01-10			ENSG00000088448	ENSG00000088448		"Ankyrin repeat domain containing"	20265	protein-coding gene	gene with protein product							Standard	NM_017664		Approved	FLJ20093	uc001vrn.3	Q9NXR5	OTTHUMG00000017349	ENST00000267339.2:c.864C>G	chr13.hg19:g.111532383G>C		82.0	0.0		64.0	22.0	NM_017664	Q5VW12|Q9BV12	Silent	SNP	ENST00000267339.2	hg19	CCDS9520.1																																																																																			.	.		0.473	ANKRD10-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045783.1			C	111532383	G	C	111532383	2	2	346	1	0	0	0	0	0	0	0	1	638	1335	47	4		4	ANKRD10	13	111532383	Silent	SNP	G	TCGA-UB-A7MD-01A-12D-A34Z-10	11998572	111532383	3637495	66	48908										
PSMB5	5693	hgsc.bcm.edu	37	chr14	23495455	23495455	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	tggctcgacgggccagatcaTaggcctgctccacttccagg	12	14	1	1	rs60224002		TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr14:23495455T>C	ENST00000361611.6	-	3	898	c.635A>G	c.(634-636)tAt>tGt	p.Y212C	PSMB5_ENST00000425762.2_Missense_Mutation_p.Y109C|PSMB5_ENST00000460922.2_3'UTR|PSMB5_ENST00000493471.2_3'UTR	NM_002797.3	NP_002788.1	P28074	PSB5_HUMAN	proteasome (prosome, macropain) subunit, beta type, 5	212					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to oxidative stress (GO:0006979)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)			kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	7	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.0121)	Bortezomib(DB00188)|Carfilzomib(DB08889)	GGCCAGATCATAGGCCTGCTC	0.567																																					p.Y212C		Atlas-SNP	.											.	PSMB5	31	.	0			c.A635G						.						160	139	147					14																	23495455		2203	4300	6503	SO:0001583	missense	5693	exon3			AGATCATAGGCCT	D29011	CCDS9584.1, CCDS45083.1, CCDS45084.1	14q11.2	2008-08-29			ENSG00000100804	ENSG00000100804		"Proteasome (prosome, macropain) subunits"	9542	protein-coding gene	gene with protein product		600306				8066462, 8811196	Standard	NM_001130725		Approved	X, MB1	uc001wii.3	P28074	OTTHUMG00000028713	ENST00000361611.6:c.635A>G	chr14.hg19:g.23495455T>C	ENSP00000355325:p.Tyr212Cys	79.0	0.0		60.0	14.0	NM_002797	B2R4N9|B4DUM9|D3DS43|E9PAV2|Q16242|Q6PEW2|Q7Z3B5|Q86T01|Q9TNN9	Missense_Mutation	SNP	ENST00000361611.6	hg19	CCDS9584.1	.	.	.	.	.	.	.	.	.	.	T	10.96	1.499269	0.26861	.	.	ENSG00000100804	ENST00000361611;ENST00000425762	T;T	0.22134	1.97;1.97	5.25	5.25	0.73442	.	0.180201	0.50627	D	0.000106	T	0.20536	0.0494	L	0.41492	1.28	0.34311	D	0.685429	B	0.18968	0.032	B	0.25405	0.06	T	0.16719	-1.0393	10	0.37606	T	0.19	-2.4825	14.1432	0.65334	0.0:0.0:0.0:1.0	rs60224002	212	P28074	PSB5_HUMAN	C	212;109	ENSP00000355325:Y212C;ENSP00000395206:Y109C	ENSP00000355325:Y212C	Y	-	2	0	PSMB5	22565295	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.206000	0.42779	1.988000	0.58038	0.392000	0.25879	TAT	.	T|0.998;C|0.002		0.567	PSMB5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071695.4	NM_002797		C	23495455	T	C	23495455	3	2	346	1	0	0	0	0	1	0	0	0	12692	1406	49	2	160	2	PSMB5	14	23495455	Missense_Mutation	SNP	T	TCGA-UB-A7MD-01A-12D-A34Z-10		23495455	83854085	67	48909										
CHURC1	91612	hgsc.bcm.edu	37	chr14	65398907	65398907	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	aagccgaagatactatcagtAttctccctgatgacccccga	7	13	2	3			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr14:65398907A>G	ENST00000549115.1	+	4	433	c.379A>G	c.(379-381)Att>Gtt	p.I127V	FNTB_ENST00000447296.2_Intron|CHURC1_ENST00000359118.2_Missense_Mutation_p.I101V|CHURC1_ENST00000552002.2_Missense_Mutation_p.I100V|CHURC1-FNTB_ENST00000549987.1_Intron|FNTB_ENST00000542227.1_Intron|CHURC1_ENST00000548752.2_Missense_Mutation_p.Y103C|CHURC1_ENST00000607599.1_Missense_Mutation_p.I128V			Q8WUH1	CHUR_HUMAN	churchill domain containing 1	127					multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)		zinc ion binding (GO:0008270)			breast(1)|pancreas(1)	2				all cancers(60;0.00119)|OV - Ovarian serous cystadenocarcinoma(108;0.0056)|BRCA - Breast invasive adenocarcinoma(234;0.00976)		TACTATCAGTATTCTCCCTGA	0.398																																					p.I128V		Atlas-SNP	.											.	CHURC1	6	.	0			c.A382G						.						144	131	135					14																	65398907		2203	4300	6503	SO:0001583	missense	91612	exon4			ATCAGTATTCTCC	AF060510	CCDS32101.1, CCDS32101.2, CCDS55921.1, CCDS55922.1	14q23.3	2011-09-28	2004-05-05	2004-05-07	ENSG00000258289	ENSG00000258289			20099	protein-coding gene	gene with protein product		608577		C14orf52			Standard	NM_145165		Approved	My015, FLJ33064		Q8WUH1	OTTHUMG00000170218	ENST00000549115.1:c.379A>G	chr14.hg19:g.65398907A>G	ENSP00000448050:p.Ile127Val	101.0	0.0		115.0	35.0	NM_145165	B3KQ81|G3V1X3|G3V214|Q9H3K7	Missense_Mutation	SNP	ENST00000549115.1	hg19	CCDS55921.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.889|9.889	1.203766|1.203766	0.22121|0.22121	.|.	.|.	ENSG00000258289|ENSG00000258289	ENST00000552002;ENST00000549115;ENST00000359118|ENST00000548752	.|.	.|.	.|.	6.11|6.11	3.75|3.75	0.43078|0.43078	.|.	0.190860|.	0.45867|.	D|.	0.000336|.	T|T	0.15565|0.15565	0.0375|0.0375	N|N	0.01576|0.01576	-0.805|-0.805	0.80722|0.80722	D|D	1|1	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.04013|.	0.0;0.001|.	T|T	0.04522|0.04522	-1.0945|-1.0945	9|5	0.09084|.	T|.	0.74|.	.|.	2.377|2.377	0.04345|0.04345	0.6102:0.0:0.1534:0.2364|0.6102:0.0:0.1534:0.2364	.|.	100;128|.	Q8WUH1;G3V214|.	CHUR_HUMAN;.|.	V|C	128;127;101|103	.|.	ENSP00000352026:I101V|.	I|Y	+|+	1|2	0|0	CHURC1|CHURC1	64468660|64468660	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	4.446000|4.446000	0.60014|0.60014	1.108000|1.108000	0.41662|0.41662	0.533000|0.533000	0.62120|0.62120	ATT|TAT	.	.		0.398	CHURC1-002	KNOWN	NAGNAG_splice_site|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000408062.1	NM_145165		G	65398907	A	G	65398907	3	3	346	1	0	0	0	0	1	0	0	0	3419	449	16	2	315	2	CHURC1	14	65398907	Missense_Mutation	SNP	A	TCGA-UB-A7MD-01A-12D-A34Z-10	41903452	65398907	41950633	68	48910										
C15orf2	23742	hgsc.bcm.edu	37	chr15	24923800	24923800	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	agcaccagttataggcttaaCatctccttcagtccagccac	6	14	2	0			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr15:24923800C>A	ENST00000329468.2	+	1	3260	c.2786C>A	c.(2785-2787)aCa>aAa	p.T929K		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	929			T -> P (in dbSNP:rs34413216).		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											ATAGGCTTAACATCTCCTTCA	0.483																																					p.T929K		Atlas-SNP	.											.	.	.	.	0			c.C2786A						.						88	91	90					15																	24923800		2203	4300	6503	SO:0001583	missense	23742	exon1			GCTTAACATCTCC	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"chromosome 15 open reading frame 2"	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.2786C>A	chr15.hg19:g.24923800C>A	ENSP00000333735:p.Thr929Lys	33.0	0.0		35.0	8.0	NM_018958		Missense_Mutation	SNP	ENST00000329468.2	hg19	CCDS10015.1	.	.	.	.	.	.	.	.	.	.	.	5.606	0.296622	0.10622	.	.	ENSG00000185823	ENST00000329468	T	0.09911	2.93	2.04	1.07	0.20283	.	1.446920	0.04526	N	0.385475	T	0.09335	0.0230	N	0.24115	0.695	0.09310	N	1	B	0.24920	0.114	B	0.32022	0.139	T	0.42481	-0.9449	10	0.28530	T	0.3	.	6.4327	0.21807	0.0:0.6495:0.3505:0.0	.	929	Q9NZP6	CO002_HUMAN	K	929	ENSP00000333735:T929K	ENSP00000333735:T929K	T	+	2	0	C15orf2	22474893	0.001000	0.12720	0.000000	0.03702	0.010000	0.07245	1.363000	0.34159	0.388000	0.25054	0.313000	0.20887	ACA	.	.		0.483	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		A	24923800	C	A	24923800	3	1	346	1	0	0	0	0	1	0	0	0	1786	478	17	3	2788	3	C15orf2	15	24923800	Missense_Mutation	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10		24923800	77607592	69	48911										
SPTBN5	51332	hgsc.bcm.edu	37	chr15	42178394	42178394	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	agccggggtggcttctcctgGgtgcggaagatggtgaatgc	18	8	1	2			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr15:42178394G>A	ENST00000320955.6	-	7	1286	c.1059C>T	c.(1057-1059)acC>acT	p.T353T		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	353					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		GCTTCTCCTGGGTGCGGAAGA	0.647																																					p.T318T		Atlas-SNP	.											.	SPTBN5	171	.	0			c.C954T						.						24	27	26					15																	42178394		2009	4192	6201	SO:0001819	synonymous_variant	51332	exon7			CTCCTGGGTGCGG	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"beta V spectrin"	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.1059C>T	chr15.hg19:g.42178394G>A		60.0	0.0		69.0	19.0	NM_016642		Silent	SNP	ENST00000320955.6	hg19																																																																																				.	.		0.647	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642		A	42178394	G	A	42178394	2	1	346	1	0	0	0	0	0	0	0	1	15137	1219	43	3		3	SPTBN5	15	42178394	Silent	SNP	G	TCGA-UB-A7MD-01A-12D-A34Z-10	17254594	42178394	60352998	70	48912										
PLA2G4E	123745	hgsc.bcm.edu	37	chr15	42280320	42280320	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	tgtgacaggttccaggcatcCagcaggttcagggagaagat	14	8	1	3			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr15:42280320C>A	ENST00000399518.3	-	16	2244	c.1758G>T	c.(1756-1758)ctG>ctT	p.L586L	PLA2G4E_ENST00000413860.2_Silent_p.L557L|CTD-2382E5.1_ENST00000499478.2_RNA	NM_001206670.1	NP_001193599.1	Q3MJ16	PA24E_HUMAN	phospholipase A2, group IVE	574	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|stomach(1)	16		all_cancers(109;8.09e-13)|all_epithelial(112;2.03e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.0273)		OV - Ovarian serous cystadenocarcinoma(18;7.61e-18)|GBM - Glioblastoma multiforme(94;3.07e-06)		TCCAGGCATCCAGCAGGTTCA	0.607																																					p.L586L		Atlas-SNP	.											.	PLA2G4E	60	.	0			c.G1758T						.						42	50	48					15																	42280320		2116	4252	6368	SO:0001819	synonymous_variant	123745	exon16			GGCATCCAGCAGG		CCDS55962.1	15q15.1	2008-09-19			ENSG00000188089	ENSG00000188089	3.1.1.4		24791	protein-coding gene	gene with protein product						15866882	Standard	NM_001206670		Approved	FLJ45651	uc021sjp.1	Q3MJ16	OTTHUMG00000130371	ENST00000399518.3:c.1758G>T	chr15.hg19:g.42280320C>A		41.0	0.0		32.0	14.0	NM_001206670	Q6ZSC0	Silent	SNP	ENST00000399518.3	hg19	CCDS55962.1																																																																																			.	.		0.607	PLA2G4E-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252738.2	NM_198442		A	42280320	C	A	42280320	2	1	346	1	0	0	0	0	0	0	0	1	12014	581	21	3		3	PLA2G4E	15	42280320	Silent	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	101926	42280320	60251072	71	48913										
SEMA6D	80031	hgsc.bcm.edu	37	chr15	48060868	48060868	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	tacctggagacctaaactgaCaagctctcggaaatttgtag	9	9	1	2			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr15:48060868C>A	ENST00000316364.5	+	18	2295	c.1856C>A	c.(1855-1857)aCa>aAa	p.T619K	SEMA6D_ENST00000389433.2_Missense_Mutation_p.T600K|SEMA6D_ENST00000354744.4_Intron|SEMA6D_ENST00000358066.4_Intron|SEMA6D_ENST00000558014.1_Intron|SEMA6D_ENST00000389432.2_Intron|SEMA6D_ENST00000536845.2_Missense_Mutation_p.T619K|SEMA6D_ENST00000558816.1_Intron|SEMA6D_ENST00000355997.3_Intron|SEMA6D_ENST00000537942.1_Intron|SEMA6D_ENST00000389428.3_Intron	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	619					axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		CCTAAACTGACAAGCTCTCGG	0.443																																					p.T619K		Atlas-SNP	.											.	SEMA6D	322	.	0			c.C1856A						.						115	108	111					15																	48060868		2198	4297	6495	SO:0001583	missense	80031	exon18			AACTGACAAGCTC	AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"Semaphorins"	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.1856C>A	chr15.hg19:g.48060868C>A	ENSP00000324857:p.Thr619Lys	62.0	0.0		61.0	15.0	NM_153618	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Missense_Mutation	SNP	ENST00000316364.5	hg19	CCDS32225.1	.	.	.	.	.	.	.	.	.	.	C	12.24	1.879792	0.33162	.	.	ENSG00000137872	ENST00000536845;ENST00000316364;ENST00000389433	T;T;T	0.16073	2.38;2.38;2.37	5.49	5.49	0.81192	.	0.000000	0.64402	D	0.000017	T	0.09555	0.0235	N	0.08118	0	0.80722	D	1	B	0.24186	0.099	B	0.19946	0.027	T	0.12016	-1.0564	10	0.05959	T	0.93	.	19.7433	0.96241	0.0:1.0:0.0:0.0	.	619	Q8NFY4	SEM6D_HUMAN	K	619;619;600	ENSP00000446152:T619K;ENSP00000324857:T619K;ENSP00000374084:T600K	ENSP00000324857:T619K	T	+	2	0	SEMA6D	45848160	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.590000	0.53979	2.733000	0.93635	0.655000	0.94253	ACA	.	.		0.443	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966		A	48060868	C	A	48060868	3	1	346	1	0	0	0	0	1	0	0	0	14057	478	17	3	1965	3	SEMA6D	15	48060868	Missense_Mutation	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	5780548	48060868	54470524	72	48914										
BNC1	646	hgsc.bcm.edu	37	chr15	83932654	83932654	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	ggtagctgggaggaggcctaCagtctggggacgtcactgtg	18	8	2	0			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr15:83932654C>T	ENST00000345382.2	-	4	1434	c.1349G>A	c.(1348-1350)tGt>tAt	p.C450Y	BNC1_ENST00000569704.1_Missense_Mutation_p.C443Y|RP11-382A20.4_ENST00000565495.1_RNA	NM_001717.3	NP_001708.3	Q01954	BNC1_HUMAN	basonuclin 1	450					chromosome organization (GO:0051276)|epidermis development (GO:0008544)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	56						AGGAGGCCTACAGTCTGGGGA	0.522																																					p.C450Y		Atlas-SNP	.											.	BNC1	149	.	0			c.G1349A						.						111	102	105					15																	83932654		2203	4300	6503	SO:0001583	missense	646	exon4			GGCCTACAGTCTG	L03427	CCDS10324.1, CCDS73771.1	15q25.1	2013-05-20	2004-04-30	2004-05-04	ENSG00000169594	ENSG00000169594		"Zinc fingers, C2H2-type"	1081	protein-coding gene	gene with protein product		601930	"basonuclin"	BNC		1332044	Standard	NM_001717		Approved	HsT19447	uc002bjt.1	Q01954	OTTHUMG00000147362	ENST00000345382.2:c.1349G>A	chr15.hg19:g.83932654C>T	ENSP00000307041:p.Cys450Tyr	120.0	0.0		103.0	28.0	NM_001717	Q15840	Missense_Mutation	SNP	ENST00000345382.2	hg19	CCDS10324.1	.	.	.	.	.	.	.	.	.	.	C	0.018	-1.467134	0.01053	.	.	ENSG00000169594	ENST00000345382;ENST00000541809	T	0.42900	0.96	4.98	3.12	0.35913	.	0.136514	0.64402	N	0.000004	T	0.32585	0.0834	L	0.60455	1.87	0.28465	N	0.915674	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.33292	-0.9874	10	0.06494	T	0.89	-6.0256	9.874	0.41191	0.0:0.7786:0.0:0.2214	.	443;450	F5GY04;Q01954	.;BNC1_HUMAN	Y	450;443	ENSP00000307041:C450Y	ENSP00000307041:C450Y	C	-	2	0	BNC1	81723658	0.640000	0.27243	0.854000	0.33618	0.259000	0.26198	0.856000	0.27818	0.701000	0.31803	-0.137000	0.14449	TGT	.	.		0.522	BNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304006.1	NM_001717		T	83932654	C	T	83932654	3	4	346	1	0	0	0	0	1	0	0	0	1474	478	17	3	1643	3	BNC1	15	83932654	Missense_Mutation	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	35871786	83932654	18598738	73	48915										
PDE8A	5151	hgsc.bcm.edu	37	chr15	85664189	85664189	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	gagagccaccatgcggccttGgccttccagctgaccactgg	12	15	0	2			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr15:85664189G>A	ENST00000310298.4	+	19	2148	c.1896G>A	c.(1894-1896)ttG>ttA	p.L632L	PDE8A_ENST00000394553.1_Silent_p.L632L|PDE8A_ENST00000557957.1_Silent_p.L560L|PDE8A_ENST00000339708.5_Silent_p.L586L			O60658	PDE8A_HUMAN	phosphodiesterase 8A	632	Catalytic. {ECO:0000250}.				cAMP catabolic process (GO:0006198)|cyclic nucleotide metabolic process (GO:0009187)|phosphorelay signal transduction system (GO:0000160)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	25	Colorectal(223;0.227)		BRCA - Breast invasive adenocarcinoma(143;0.0608)		Caffeine(DB00201)|Ketotifen(DB00920)	ATGCGGCCTTGGCCTTCCAGC	0.463																																					p.L632L		Atlas-SNP	.											.	PDE8A	50	.	0			c.G1896A						.						93	79	84					15																	85664189		2203	4299	6502	SO:0001819	synonymous_variant	5151	exon18			GGCCTTGGCCTTC	AF056490	CCDS10336.1, CCDS10337.1, CCDS58397.1	15q25.3	2008-05-14			ENSG00000073417	ENSG00000073417	3.1.4.17	"Phosphodiesterases"	8793	protein-coding gene	gene with protein product		602972				9618252	Standard	NM_001243137		Approved	HsT19550	uc002blh.3	O60658	OTTHUMG00000148670	ENST00000310298.4:c.1896G>A	chr15.hg19:g.85664189G>A		60.0	0.0		68.0	28.0	NM_002605	B3KXE6|H0YMZ7|Q6P9H3|Q969I1|Q96PC9|Q96PD0|Q96PD1|Q96T71|Q9UMB7|Q9UMC3	Silent	SNP	ENST00000310298.4	hg19	CCDS10336.1																																																																																			.	.		0.463	PDE8A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000309018.1	NM_002605		A	85664189	G	A	85664189	2	1	346	1	0	0	0	0	0	0	0	1	11662	1339	47	3		3	PDE8A	15	85664189	Silent	SNP	G	TCGA-UB-A7MD-01A-12D-A34Z-10	1731535	85664189	16867203	74	48916										
C16orf13	84326	hgsc.bcm.edu	37	chr16	684899	684899	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	tagctctgacctgcatctgaGcatcaggtcaaagtccacgt	9	12	4	2			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr16:684899G>A	ENST00000301686.8	-	4	489	c.478C>T	c.(478-480)Ctc>Ttc	p.L160F	C16orf13_ENST00000397664.4_Intron|C16orf13_ENST00000397665.2_Intron|C16orf13_ENST00000338401.4_Intron|C16orf13_ENST00000397666.2_Intron	NM_032366.3	NP_115742.3	Q96S19	CP013_HUMAN	chromosome 16 open reading frame 13	160										large_intestine(1)	1		Hepatocellular(780;0.00335)				CTGCATCTGAGCATCAGGTCA	0.627																																					p.L160F		Atlas-SNP	.											.	C16orf13	11	.	0			c.C478T						.						30	35	33					16																	684899		2162	4259	6421	SO:0001583	missense	84326	exon4			ATCTGAGCATCAG		CCDS32352.1, CCDS42090.1, CCDS42091.1, CCDS45367.1, CCDS45368.1, CCDS73798.1	16p13.3	2012-10-09			ENSG00000130731	ENSG00000130731			14141	protein-coding gene	gene with protein product							Standard	NM_001040160		Approved	MGC13114	uc002chw.1	Q96S19	OTTHUMG00000047855	ENST00000301686.8:c.478C>T	chr16.hg19:g.684899G>A	ENSP00000445926:p.Leu160Phe	23.0	0.0		21.0	9.0	NM_032366	A8MTR1|A8MWJ8|A8MZA1|B4DG95|B4DIJ3|D6REA6|F6TF62|F6VM53|Q96IW1|Q96MD6	Missense_Mutation	SNP	ENST00000301686.8	hg19	CCDS45368.1	.	.	.	.	.	.	.	.	.	.	G	16.27	3.077205	0.55753	.	.	ENSG00000130731	ENST00000301686	T	0.65178	-0.14	4.6	4.6	0.57074	.	0.084173	0.49916	D	0.000125	D	0.84042	0.5385	M	0.94101	3.495	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88648	0.3180	10	0.87932	D	0	.	16.1476	0.81580	0.0:0.0:1.0:0.0	.	160	Q96S19	CP013_HUMAN	F	160	ENSP00000445926:L160F	ENSP00000445926:L160F	L	-	1	0	Z84479.1	624900	0.994000	0.37717	0.915000	0.36163	0.618000	0.37518	3.832000	0.55783	2.379000	0.81126	0.561000	0.74099	CTC	.	.		0.627	C16orf13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109081.2	NM_001040160		A	684899	G	A	684899	3	1	346	1	0	0	0	0	1	0	0	0	1813	971	34	3	219	3	C16orf13	16	684899	Missense_Mutation	SNP	G	TCGA-UB-A7MD-01A-12D-A34Z-10		684899	89669854	75	48917										
WDR90	197335	hgsc.bcm.edu	37	chr16	709346	709346	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	catctccaccacggctgggcGtctgtgccaggcctcccgaa	11	17	2	0			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr16:709346G>A	ENST00000293879.4	+	26	3154	c.3154G>A	c.(3154-3156)Gtc>Atc	p.V1052I	WDR90_ENST00000549091.1_Missense_Mutation_p.V1052I			Q96KV7	WDR90_HUMAN	WD repeat domain 90	1052										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				ACGGCTGGGCGTCTGTGCCAG	0.711																																					p.V1052I		Atlas-SNP	.											.	WDR90	107	.	0			c.G3154A						.						14	20	18					16																	709346		2094	4201	6295	SO:0001583	missense	197335	exon26			CTGGGCGTCTGTG	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"WD repeat domain containing"	26960	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 17", "chromosome 16 open reading frame 15", "chromosome 16 open reading frame 16", "chromosome 16 open reading frame 19", "chromosome 16 open reading frame 18"	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.3154G>A	chr16.hg19:g.709346G>A	ENSP00000293879:p.Val1052Ile	92.0	0.0		50.0	13.0	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Missense_Mutation	SNP	ENST00000293879.4	hg19	CCDS42092.1	.	.	.	.	.	.	.	.	.	.	G	2.289	-0.362831	0.05103	.	.	ENSG00000161996	ENST00000549091;ENST00000293879	T;T	0.26660	1.76;1.72	4.38	-8.76	0.00830	.	3.312490	0.01911	N	0.039832	T	0.09379	0.0231	N	0.03154	-0.405	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.17806	-1.0357	10	0.13470	T	0.59	.	8.2669	0.31819	0.1956:0.3681:0.4362:0.0	.	1052;1052	F8VUX9;Q96KV7	.;WDR90_HUMAN	I	1052	ENSP00000448122:V1052I;ENSP00000293879:V1052I	ENSP00000293879:V1052I	V	+	1	0	WDR90	649347	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.053000	0.01400	-2.553000	0.00478	-1.434000	0.01081	GTC	.	.		0.711	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294		A	709346	G	A	709346	3	1	346	1	0	0	0	0	1	0	0	0	17352	1145	40	1	3256	1	WDR90	16	709346	Missense_Mutation	SNP	G	TCGA-UB-A7MD-01A-12D-A34Z-10	24447	709346	89645407	76	48918										
TPSD1	23430	hgsc.bcm.edu	37	chr16	1306673	1306673	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	ccagtgggtgctaaccgcggCgcactgcgtggaaccgtgag	16	12	0	1			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr16:1306673C>T	ENST00000211076.3	+	2	387	c.239C>T	c.(238-240)gCg>gTg	p.A80V	TPSD1_ENST00000397534.2_Missense_Mutation_p.A73V|RP11-616M22.5_ENST00000566997.1_RNA	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	80	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				CTAACCGCGGCGCACTGCGTG	0.701																																					p.A80V		Atlas-SNP	.											TPSD1,NS,carcinoma,0,1	TPSD1	47	.	0			c.C239T						.						42	51	48					16																	1306673		2199	4298	6497	SO:0001583	missense	23430	exon2			CCGCGGCGCACTG	AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"mMCP-7-like II", "mMCP-7-like I", "MMCP-7-LIKE-2"	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.239C>T	chr16.hg19:g.1306673C>T	ENSP00000211076:p.Ala80Val	65.0	0.0		67.0	22.0	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Missense_Mutation	SNP	ENST00000211076.3	hg19	CCDS10432.1	.	.	.	.	.	.	.	.	.	.	-	15.31	2.795139	0.50208	.	.	ENSG00000095917	ENST00000397534;ENST00000211076	D;D	0.89746	-2.56;-2.56	3.0	1.98	0.26296	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.143335	0.32175	N	0.006466	D	0.92244	0.7540	H	0.95917	3.74	0.38830	D	0.95582	P;P	0.50617	0.937;0.937	B;P	0.45577	0.352;0.486	D	0.92167	0.5740	10	0.72032	D	0.01	.	9.5188	0.39122	0.0:0.7372:0.2628:0.0	.	73;80	C9JJL5;Q9BZJ3	.;TRYD_HUMAN	V	73;80	ENSP00000380668:A73V;ENSP00000211076:A80V	ENSP00000211076:A80V	A	+	2	0	TPSD1	1246674	0.996000	0.38824	0.004000	0.12327	0.012000	0.07955	3.480000	0.53172	0.510000	0.28216	0.185000	0.17295	GCG	.	.		0.701	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2			T	1306673	C	T	1306673	3	4	346	1	0	0	0	0	1	0	0	0	16440	768	27	1	245	1	TPSD1	16	1306673	Missense_Mutation	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	597327	1306673	89048080	77	48919										
EME2	197342	hgsc.bcm.edu	37	chr16	1826218	1826218	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	accacagccaaccctgatctCctgctggacctgggctcctg	9	17	1	1			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr16:1826218C>T	ENST00000568449.1	+	8	1140	c.1119C>T	c.(1117-1119)ctC>ctT	p.L373L	EME2_ENST00000307394.7_Silent_p.L438L	NM_001257370.1	NP_001244299.1	A4GXA9	EME2_HUMAN	essential meiotic structure-specific endonuclease subunit 2	373					DNA recombination (GO:0006310)|DNA repair (GO:0006281)	nucleus (GO:0005634)	DNA binding (GO:0003677)|endonuclease activity (GO:0004519)			central_nervous_system(1)|kidney(2)|lung(5)|pancreas(1)	9						ACCCTGATCTCCTGCTGGACC	0.687								Direct reversal of damage;Homologous recombination																													p.L373L		Atlas-SNP	.											.	EME2	40	.	0			c.C1119T						.						72	62	65					16																	1826218		2174	4258	6432	SO:0001819	synonymous_variant	197342	exon8			TGATCTCCTGCTG	AK074080	CCDS58404.1	16p13.3	2013-07-03	2013-07-03			ENSG00000197774			27289	protein-coding gene	gene with protein product	"SLX2 structure-specific endonuclease subunit homolog B (S. cerevisiae)"	610886	"essential meiotic endonuclease 1 homolog 2 (S. pombe)"			12721304	Standard	NM_001257370		Approved	FLJ00151, SLX2B	uc010brw.1	A4GXA9		ENST00000568449.1:c.1119C>T	chr16.hg19:g.1826218C>T		35.0	0.0		39.0	14.0	NM_001257370	Q8TEP2|Q96RY3	Silent	SNP	ENST00000568449.1	hg19	CCDS58404.1																																																																																			.	.		0.687	EME2-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000433185.2	NM_001010865		T	1826218	C	T	1826218	2	4	346	1	0	0	0	0	0	0	0	1	5091	842	30	3		3	EME2	16	1826218	Silent	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	519545	1826218	88528535	78	48920										
TIGD7	91151	hgsc.bcm.edu	37	chr16	3350103	3350103	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	ccccactgtatagctgagctAgacacagtttctcctctttg	7	13	2	2			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr16:3350103A>T	ENST00000396862.1	-	2	2340	c.512T>A	c.(511-513)cTa>cAa	p.L171Q	TIGD7_ENST00000574598.1_5'Flank|TIGD7_ENST00000268674.2_Missense_Mutation_p.L171Q	NM_033208.3	NP_149985.2	Q6NT04	TIGD7_HUMAN	tigger transposable element derived 7	171	DDE.					nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	12						tagctgAGCTAGACACAGTTT	0.418																																					p.L171Q		Atlas-SNP	.											.	TIGD7	41	.	0			c.T512A						.						161	157	159					16																	3350103		2197	4300	6497	SO:0001583	missense	91151	exon2			TGAGCTAGACACA	AF251050	CCDS10500.1	16p13.11	2008-02-05			ENSG00000140993	ENSG00000140993			18331	protein-coding gene	gene with protein product		612969					Standard	NM_033208		Approved	Sancho	uc002cus.3	Q6NT04	OTTHUMG00000129325	ENST00000396862.1:c.512T>A	chr16.hg19:g.3350103A>T	ENSP00000380071:p.Leu171Gln	136.0	0.0		157.0	54.0	NM_033208	Q9BXZ0	Missense_Mutation	SNP	ENST00000396862.1	hg19	CCDS10500.1	.	.	.	.	.	.	.	.	.	.	A	12.24	1.878217	0.33162	.	.	ENSG00000140993	ENST00000426381;ENST00000396862;ENST00000268674	T;T	0.33438	1.41;1.41	5.22	5.22	0.72569	.	0.293724	0.17915	U	0.157710	T	0.44498	0.1296	L	0.50333	1.59	0.29096	N	0.881769	D	0.56287	0.975	P	0.62298	0.9	T	0.32613	-0.9900	10	0.30854	T	0.27	.	11.4827	0.50335	1.0:0.0:0.0:0.0	.	171	Q6NT04	TIGD7_HUMAN	Q	171	ENSP00000380071:L171Q;ENSP00000268674:L171Q	ENSP00000268674:L171Q	L	-	2	0	TIGD7	3290104	0.945000	0.32115	0.758000	0.31321	0.918000	0.54935	2.781000	0.47750	1.977000	0.57605	0.533000	0.62120	CTA	.	.		0.418	TIGD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251465.1	NM_033208		T	3350103	A	T	3350103	3	4	346	1	0	0	0	0	1	0	0	0	15916	420	15	4	1141	4	TIGD7	16	3350103	Missense_Mutation	SNP	A	TCGA-UB-A7MD-01A-12D-A34Z-10	1523885	3350103	87004650	79	48921										
NLRC3	197358	hgsc.bcm.edu	37	chr16	3613898	3613898	+	RNA	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	gctctgcatcctggggccccGtcctgctgcgccacaggtgg	14	16	1	0			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr16:3613898G>T	ENST00000301749.7	-	0	1445				NLRC3_ENST00000324659.8_RNA|NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000603507.1_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CTGGGGCCCCGTCCTGCTGCG	0.667																																					p.T347K		Atlas-SNP	.											.	NLRC3	103	.	0			c.C1040A						.						30	34	33					16																	3613898		1994	4146	6140			197358	exon5			GGCCCCGTCCTGC	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"Nucleotide-binding domain and leucine rich repeat containing"	29889	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3", "NOD-like receptor C3"	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		chr16.hg19:g.3613898G>T		13.0	0.0		17.0	7.0	NM_178844	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Missense_Mutation	SNP	ENST00000301749.7	hg19		.	.	.	.	.	.	.	.	.	.	G	0.006	-2.070469	0.00379	.	.	ENSG00000167984	ENST00000419350;ENST00000301749;ENST00000359128;ENST00000448023;ENST00000324659	D;D;D;D	0.83755	-1.76;-1.76;-1.76;-1.76	5.15	-10.3	0.00346	.	1.039180	0.07631	N	0.928641	T	0.49881	0.1583	.	.	.	0.09310	N	1	B	0.13594	0.008	B	0.12156	0.007	T	0.49293	-0.8955	9	0.05833	T	0.94	.	1.3184	0.02112	0.44:0.1678:0.1654:0.2268	.	394	C9JLH9	.	K	347;347;347;394;329	ENSP00000301749:T347K;ENSP00000352039:T347K;ENSP00000414415:T394K;ENSP00000323897:T329K	ENSP00000301749:T347K	T	-	2	0	NLRC3	3553899	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.069000	0.01381	-2.458000	0.00538	-0.119000	0.15052	ACG	.	.		0.667	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844		T	3613898	G	T	3613898	1	4	346	0	1	0	0	0	0	0	0	0	10477	1145	40	1		1	NLRC3	16	3613898	RNA	SNP	G	TCGA-UB-A7MD-01A-12D-A34Z-10	263795	3613898	86740855	80	48922										
A2BP1	54715	hgsc.bcm.edu	37	chr16	7760685	7760685	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	atgctgatgatgtgggtctcGttctttcttcattgcaggct	11	8	4	2	rs369122393		TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr16:7760685G>T	ENST00000550418.1	+	16	2120	c.1132G>T	c.(1132-1134)Gtt>Ttt	p.V378F	RBFOX1_ENST00000547372.1_3'UTR|RBFOX1_ENST00000547338.1_Missense_Mutation_p.V378F|RBFOX1_ENST00000552089.1_3'UTR|RBFOX1_ENST00000340209.4_Missense_Mutation_p.V383F|RBFOX1_ENST00000355637.4_3'UTR|RBFOX1_ENST00000311745.5_Missense_Mutation_p.V399F|RBFOX1_ENST00000436368.2_Intron|RBFOX1_ENST00000553186.1_Missense_Mutation_p.V351F	NM_018723.3	NP_061193.2	Q9NWB1	RFOX1_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 1	378					mRNA processing (GO:0006397)|neuromuscular process controlling balance (GO:0050885)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|RNA transport (GO:0050658)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	nucleotide binding (GO:0000166)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|lung(17)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)	55						TGTGGGTCTCGTTCTTTCTTC	0.413																																					p.V399F	Ovarian(157;934 2567 15163 39509)	Atlas-SNP	.											.	RBFOX1	341	.	0			c.G1195T						.						226	198	208					16																	7760685		2197	4300	6497	SO:0001583	missense	54715	exon13			GGTCTCGTTCTTT	AF107203	CCDS10531.1, CCDS10532.1, CCDS45405.1, CCDS55983.1, CCDS55984.1	16p13.3	2013-02-12			ENSG00000078328	ENSG00000078328		"RNA binding motif (RRM) containing"	18222	protein-coding gene	gene with protein product	"ataxin 2-binding protein 1", "hexaribonucleotide binding protein 1"	605104				10814712, 16260614	Standard	NM_018723		Approved	A2BP1, FOX-1, HRNBP1	uc002cyy.2	Q9NWB1	OTTHUMG00000129551	ENST00000550418.1:c.1132G>T	chr16.hg19:g.7760685G>T	ENSP00000450031:p.Val378Phe	116.0	0.0		112.0	27.0	NM_145891	Q7Z7I7|Q8TAE3|Q8TAF2|Q8WYB2|Q9NS20	Missense_Mutation	SNP	ENST00000550418.1	hg19	CCDS55983.1	.	.	.	.	.	.	.	.	.	.	G	14.93	2.681620	0.47991	.	.	ENSG00000078328	ENST00000550418;ENST00000553186;ENST00000547338;ENST00000311745;ENST00000352951;ENST00000340209	T;T;T;T;T	0.33216	1.42;1.69;1.42;1.74;1.43	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.34483	0.0899	N	0.08118	0	0.80722	D	1	D;D;P;P	0.76494	0.999;0.999;0.454;0.553	D;D;B;B	0.68943	0.961;0.961;0.176;0.121	T	0.16012	-1.0417	10	0.10636	T	0.68	-9.0665	20.3923	0.98948	0.0:0.0:1.0:0.0	.	372;399;351;378	F8WAC5;Q9NWB1-2;Q9NWB1-3;Q9NWB1	.;.;.;RFOX1_HUMAN	F	378;351;378;399;372;383	ENSP00000450031:V378F;ENSP00000447753:V351F;ENSP00000447717:V378F;ENSP00000309117:V399F;ENSP00000344196:V383F	ENSP00000309117:V399F	V	+	1	0	RBFOX1	7700686	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.850000	0.92190	2.831000	0.97527	0.609000	0.83330	GTT	.	.		0.413	RBFOX1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409492.2	NM_145891		T	7760685	G	T	7760685	3	4	346	1	0	0	0	0	1	0	0	0	3	1145	40	1	1377	1	A2BP1	16	7760685	Missense_Mutation	SNP	G	TCGA-UB-A7MD-01A-12D-A34Z-10	4146787	7760685	82594068	81	48923										
ZNF267	10308	hgsc.bcm.edu	37	chr16	31927163	31927163	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	tgtgctaaaccttttacttgTttctcaaatcttattgtgca	5	8	2	0			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr16:31927163T>G	ENST00000300870.10	+	4	1802	c.1593T>G	c.(1591-1593)tgT>tgG	p.C531W		NM_001265588.1|NM_003414.5	NP_001252517.1|NP_003405	Q14586	ZN267_HUMAN	zinc finger protein 267	531					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(5)|kidney(1)|large_intestine(14)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	41						CTTTTACTTGTTTCTCAAATC	0.353																																					p.C531W		Atlas-SNP	.											.	ZNF267	94	.	0			c.T1593G						.						38	42	41					16																	31927163		2196	4298	6494	SO:0001583	missense	10308	exon4			TACTTGTTTCTCA	X78925	CCDS32440.1	16p11.2	2013-01-08			ENSG00000185947	ENSG00000185947		"Zinc fingers, C2H2-type", "-"	13060	protein-coding gene	gene with protein product		604752				7865130	Standard	NM_003414		Approved	HZF2	uc002ecs.5	Q14586		ENST00000300870.10:c.1593T>G	chr16.hg19:g.31927163T>G	ENSP00000300870:p.Cys531Trp	52.0	0.0		56.0	14.0	NM_003414	A0JNZ9|Q8NE41|Q9NRJ0	Missense_Mutation	SNP	ENST00000300870.10	hg19	CCDS32440.1	.	.	.	.	.	.	.	.	.	.	.	4.640	0.118900	0.08881	.	.	ENSG00000185947	ENST00000300870	T	0.26518	1.73	0.458	0.458	0.16670	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.15435	0.0372	N	0.25144	0.715	0.09310	N	1	P	0.47106	0.89	B	0.41894	0.369	T	0.15321	-1.0441	8	0.33141	T	0.24	.	.	.	.	.	531	Q14586	ZN267_HUMAN	W	531	ENSP00000300870:C531W	ENSP00000300870:C531W	C	+	3	2	ZNF267	31834664	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-4.545000	0.00218	0.407000	0.25591	0.397000	0.26171	TGT	.	.		0.353	ZNF267-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432446.2	NM_003414		G	31927163	T	G	31927163	3	3	346	1	0	0	0	0	1	0	0	0	17821	1731	60	5	1607	5	ZNF267	16	31927163	Missense_Mutation	SNP	T	TCGA-UB-A7MD-01A-12D-A34Z-10	24166478	31927163	58427590	82	48924										
GPR97	222487	hgsc.bcm.edu	37	chr16	57717987	57717987	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	tgctgcctgctgggcccgggGggctgtcttccactacttcc	13	15	1	0			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr16:57717987G>T	ENST00000333493.4	+	9	1186	c.1025G>T	c.(1024-1026)gGg>gTg	p.G342V	RP11-405F3.4_ENST00000563062.1_RNA|GPR97_ENST00000450388.3_Missense_Mutation_p.G222V|GPR97_ENST00000327655.6_Missense_Mutation_p.G132V	NM_170776.4	NP_740746.4	Q86Y34	GPR97_HUMAN	G protein-coupled receptor 97	342					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						TGGGCCCGGGGGGCTGTCTTC	0.602																																					p.G342V		Atlas-SNP	.											.	GPR97	74	.	0			c.G1025T						.						99	97	98					16																	57717987		2198	4300	6498	SO:0001583	missense	222487	exon9			CCCGGGGGGCTGT	AY140959	CCDS10786.1	16q13	2014-08-08			ENSG00000182885	ENSG00000182885		"-", "GPCR / Class B : Orphans"	13728	protein-coding gene	gene with protein product						12435584, 222487	Standard	NM_170776		Approved	Pb99, PGR26	uc002emh.3	Q86Y34	OTTHUMG00000133458	ENST00000333493.4:c.1025G>T	chr16.hg19:g.57717987G>T	ENSP00000332900:p.Gly342Val	57.0	0.0		66.0	19.0	NM_170776	Q6ZMF4|Q86SL9|Q8IZF1	Missense_Mutation	SNP	ENST00000333493.4	hg19	CCDS10786.1	.	.	.	.	.	.	.	.	.	.	G	15.54	2.864908	0.51482	.	.	ENSG00000182885	ENST00000333493;ENST00000327655;ENST00000450388	T;T;T	0.38887	1.11;1.11;1.11	4.99	4.03	0.46877	GPCR, family 2-like (1);	0.102172	0.43110	D	0.000611	T	0.61702	0.2368	M	0.73962	2.25	0.29777	N	0.834341	D	0.69078	0.997	D	0.67103	0.949	T	0.64433	-0.6409	10	0.87932	D	0	.	12.8778	0.57999	0.0:0.3919:0.6081:0.0	.	342	Q86Y34	GPR97_HUMAN	V	342;132;222	ENSP00000332900:G342V;ENSP00000331199:G132V;ENSP00000404803:G222V	ENSP00000331199:G132V	G	+	2	0	GPR97	56275488	0.408000	0.25360	0.015000	0.15790	0.010000	0.07245	0.757000	0.26433	1.074000	0.40909	0.591000	0.81541	GGG	.	.		0.602	GPR97-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257333.2	NM_170776		T	57717987	G	T	57717987	3	4	346	1	0	0	0	0	1	0	0	0	6729	1232	43	3	1059	3	GPR97	16	57717987	Missense_Mutation	SNP	G	TCGA-UB-A7MD-01A-12D-A34Z-10	25790824	57717987	32636766	83	48925										
FANCA	2175	hgsc.bcm.edu	37	chr16	89813065	89813065	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	agtcgaccatcagggaggggTctctgctccgcagacaggcg	15	12	2	1			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr16:89813065T>A	ENST00000389301.3	-	35	3470	c.3440A>T	c.(3439-3441)gAc>gTc	p.D1147V	FANCA_ENST00000568369.1_Missense_Mutation_p.D1147V	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	1147					DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		CAGGGAGGGGTCTCTGCTCCG	0.552			"D, Mis, N, F, S"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.D1147V		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"Fanconi anemia, complementation group A"		L	.	FANCA	99	.	0			c.A3440T						.						71	70	70					16																	89813065		2198	4300	6498	SO:0001583	missense	2175	exon35	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GAGGGGTCTCTGC	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"Fanconi anemia, complementation groups"	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.3440A>T	chr16.hg19:g.89813065T>A	ENSP00000373952:p.Asp1147Val	39.0	0.0		31.0	7.0	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Missense_Mutation	SNP	ENST00000389301.3	hg19	CCDS32515.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.284325	0.80803	.	.	ENSG00000187741	ENST00000389301;ENST00000305699	D	0.85013	-1.93	5.39	5.39	0.77823	.	0.296333	0.28706	N	0.014413	D	0.90851	0.7126	M	0.67953	2.075	0.80722	D	1	D;D;D	0.76494	0.999;0.993;0.993	D;P;P	0.68765	0.96;0.844;0.844	D	0.91836	0.5479	10	0.87932	D	0	-16.6636	14.5788	0.68271	0.0:0.0:0.0:1.0	.	124;1147;1147	B7Z6Y4;B4DRI7;O15360	.;.;FANCA_HUMAN	V	1147;124	ENSP00000373952:D1147V	ENSP00000306281:D124V	D	-	2	0	FANCA	88340566	0.696000	0.27757	0.533000	0.28001	0.006000	0.05464	2.413000	0.44618	2.045000	0.60652	0.459000	0.35465	GAC	.	.		0.552	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1			A	89813065	T	A	89813065	3	1	346	1	0	0	0	0	1	0	0	0	5670	1667	58	4	963	4	FANCA	16	89813065	Missense_Mutation	SNP	T	TCGA-UB-A7MD-01A-12D-A34Z-10	32095078	89813065	541688	84	48926										
DVL2	1856	hgsc.bcm.edu	37	chr17	7137468	7137468	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	ctcttgaaatcgccgagggtGatgcgctcggcggggacagg	17	10	1	2			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr17:7137468G>A	ENST00000005340.5	-	1	396	c.114C>T	c.(112-114)atC>atT	p.I38I	DVL2_ENST00000575458.1_Silent_p.I38I|PHF23_ENST00000570753.1_5'Flank	NM_004422.2	NP_004413.1	O14641	DVL2_HUMAN	dishevelled segment polarity protein 2	38	DIX. {ECO:0000255|PROSITE- ProRule:PRU00069}.				canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration in hindbrain (GO:0021535)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|convergent extension involved in neural plate elongation (GO:0022007)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hippo signaling (GO:0035329)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|segment specification (GO:0007379)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|clathrin-coated endocytic vesicle (GO:0045334)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|identical protein binding (GO:0042802)			breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(7)|skin(1)	25						CGCCGAGGGTGATGCGCTCGG	0.597																																					p.I38I		Atlas-SNP	.											.	DVL2	49	.	0			c.C114T						.						104	112	110					17																	7137468		2203	4300	6503	SO:0001819	synonymous_variant	1856	exon1			GAGGGTGATGCGC	BC014844	CCDS11091.1	17p13.1	2013-05-22	2013-05-22		ENSG00000004975	ENSG00000004975		"Dishevelled homologs"	3086	protein-coding gene	gene with protein product		602151	"dishevelled 2 (homologous to Drosophila dsh)", "dishevelled, dsh homolog 2 (Drosophila)"			8662242	Standard	NM_004422		Approved		uc002gez.1	O14641	OTTHUMG00000102155	ENST00000005340.5:c.114C>T	chr17.hg19:g.7137468G>A		78.0	0.0		38.0	12.0	NM_004422	D3DTN3|Q53XM0	Silent	SNP	ENST00000005340.5	hg19	CCDS11091.1																																																																																			.	.		0.597	DVL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219999.2	NM_004422		A	7137468	G	A	7137468	2	1	346	1	0	0	0	0	0	0	0	1	4838	1280	45	3		3	DVL2	17	7137468	Silent	SNP	G	TCGA-UB-A7MD-01A-12D-A34Z-10		7137468	74057742	85	48927										
TP53	7157	hgsc.bcm.edu	37	chr17	7579591	7579591	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	gcttgggacggcaagggggaCtgtagatgggtgaaaagagc	19	5	0	3			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr17:7579591C>T	ENST00000269305.4	-	4	286		c.e4-1		TP53_ENST00000359597.4_Splice_Site|TP53_ENST00000445888.2_Splice_Site|TP53_ENST00000420246.2_Splice_Site|TP53_ENST00000455263.2_Splice_Site|TP53_ENST00000413465.2_Splice_Site|TP53_ENST00000574684.1_5'Flank	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53						apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.?(8)|p.0?(8)|p.L35fs*10(3)|p.S33fs*10(1)|p.P13fs*18(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCAAGGGGGACTGTAGATGGG	0.592		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											.	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000413465,NS,carcinoma,0,31	TP53	33396	.	21	Unknown(11)|Whole gene deletion(8)|Insertion - Frameshift(1)|Deletion - Frameshift(1)	bone(4)|large_intestine(3)|central_nervous_system(3)|lung(3)|pancreas(3)|upper_aerodigestive_tract(2)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)	c.97-1G>A	GRCh37	CS971912	TP53	S		.						141	137	138					17																	7579591		2203	4300	6503	SO:0001630	splice_region_variant	7157	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GGGGGACTGTAGA	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.97-1G>A	chr17.hg19:g.7579591C>T		30.0	0.0		30.0	9.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Splice_Site	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	6.702	0.498192	0.12762	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000508793;ENST00000503591	.	.	.	2.49	2.49	0.30216	.	.	.	.	.	.	.	.	.	.	.	0.40380	D	0.979434	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.6143	0.33822	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TP53	7520316	0.879000	0.30193	0.021000	0.16686	0.027000	0.11550	1.937000	0.40193	1.730000	0.51580	0.561000	0.74099	.	.	.		0.592	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	Intron	T	7579591	C	T	7579591	5	4	346	1	0	0	0	0	0	0	1	0	16396	579	20	3	1206	3	TP53	17	7579591	Splice_Site	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	442123	7579591	73615619	86	48928										
SREBF1	6720	hgsc.bcm.edu	37	chr17	17721042	17721042	+	Frame_Shift_Del	DEL	C	C	-													0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	aaagactgggctgtcaggctCcgagtcactgccactgccac							TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr17:17721042delC	ENST00000261646.5	-	7	1556	c.1372delG	c.(1372-1374)gagfs	p.E458fs	SREBF1_ENST00000355815.4_Frame_Shift_Del_p.E488fs|SREBF1_ENST00000395757.1_Frame_Shift_Del_p.E204fs|SREBF1_ENST00000583732.1_5'Flank|SREBF1_ENST00000338854.5_Frame_Shift_Del_p.E458fs|SREBF1_ENST00000435530.2_Frame_Shift_Del_p.E458fs	NM_004176.4	NP_004167.3	P36956	SRBP1_HUMAN	sterol regulatory element binding transcription factor 1	458	Gly/Pro/Ser-rich.|Interaction with LMNA. {ECO:0000250}.				aging (GO:0007568)|cellular lipid metabolic process (GO:0044255)|cellular response to fatty acid (GO:0071398)|cellular response to starvation (GO:0009267)|cholesterol metabolic process (GO:0008203)|circadian rhythm (GO:0007623)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|lipid metabolic process (GO:0006629)|lung development (GO:0030324)|negative regulation of insulin secretion (GO:0046676)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of fatty acid metabolic process (GO:0019217)|regulation of heart rate by chemical signal (GO:0003062)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to drug (GO:0042493)|response to food (GO:0032094)|response to glucagon (GO:0033762)|response to glucose (GO:0009749)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|sterol response element binding (GO:0032810)			cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	14						CTGTCAGGCTCCGAGTCACTG	0.657																																					p.E488fs		Atlas-INDEL	.											.	SREBF1	47	.	0			c.1463delA						.						46	36	39					17																	17721042		2203	4297	6500	SO:0001589	frameshift_variant	6720	exon8			.	BC057388	CCDS11189.1, CCDS32583.1	17p11.2	2013-05-21			ENSG00000072310	ENSG00000072310		"Basic helix-loop-helix proteins"	11289	protein-coding gene	gene with protein product		184756				8402897, 7759101	Standard	NM_001005291		Approved	SREBP1, bHLHd1, SREBP-1c	uc002grt.2	P36956	OTTHUMG00000059313	ENST00000261646.5:c.1372delG	chr17.hg19:g.17721042delC	ENSP00000261646:p.Glu458fs	52.0	0.0		28.0	12.0	NM_001005291	B0I4X3|B0I4X4|D3DXC4|Q16062|Q59F52|Q6P4R7|Q6PFW7|Q6PJ36|Q8TAK9	Frame_Shift_Del	DEL	ENST00000261646.5	hg19	CCDS11189.1																																																																																			.	.		0.657	SREBF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131771.1	NM_004176		-	17721042	C	-	17721042	7	5	346	1	0	1	0	1	0	0	0	0	15156	864	30	0	2123	0	SREBF1	17	17721042	Frame_Shift_Del	DEL	C	TCGA-UB-A7MD-01A-12D-A34Z-10	10141451	17721042	63474168	87	48929										
UNC45B	146862	hgsc.bcm.edu	37	chr17	33495177	33495177	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	ttgacctgggcaaccagctgCtgggactgaaaggtgtgatg	15	8	0	3			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr17:33495177C>G	ENST00000268876.5	+	10	1346	c.1249C>G	c.(1249-1251)Ctg>Gtg	p.L417V	UNC45B_ENST00000378449.1_Missense_Mutation_p.L417V|RP11-799D4.3_ENST00000585646.1_RNA|UNC45B_ENST00000433649.1_Missense_Mutation_p.L417V|UNC45B_ENST00000394570.2_Missense_Mutation_p.L417V|UNC45B_ENST00000591048.1_Missense_Mutation_p.L417V	NM_173167.2	NP_775259.1	Q8IWX7	UN45B_HUMAN	unc-45 homolog B (C. elegans)	417					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(10)|lung(24)|ovary(3)|prostate(2)|skin(1)|stomach(1)|urinary_tract(3)	59		Ovarian(249;0.17)				CAACCAGCTGCTGGGACTGAA	0.592																																					p.L417V		Atlas-SNP	.											.	UNC45B	133	.	0			c.C1249G						.						110	86	94					17																	33495177		2203	4300	6503	SO:0001583	missense	146862	exon10			CAGCTGCTGGGAC	AW755253	CCDS11292.1, CCDS45648.1	17q12	2008-02-05	2005-11-17	2005-11-17	ENSG00000141161	ENSG00000141161			14304	protein-coding gene	gene with protein product		611220	"cardiomyopathy associated 4"	CMYA4		12356907	Standard	NM_001267052		Approved	UNC45	uc002hja.3	Q8IWX7	OTTHUMG00000132931	ENST00000268876.5:c.1249C>G	chr17.hg19:g.33495177C>G	ENSP00000268876:p.Leu417Val	86.0	0.0		82.0	29.0	NM_001267052	Q495Q8|Q495Q9	Missense_Mutation	SNP	ENST00000268876.5	hg19	CCDS11292.1	.	.	.	.	.	.	.	.	.	.	C	13.88	2.369898	0.42003	.	.	ENSG00000141161	ENST00000394570;ENST00000268876;ENST00000433649;ENST00000378449	T;T;T;T	0.46819	0.86;0.86;0.86;0.86	5.02	5.02	0.67125	Armadillo-like helical (1);Armadillo-type fold (1);	0.135277	0.50627	D	0.000107	T	0.45538	0.1347	L	0.35341	1.055	0.24841	N	0.992463	P;B;B	0.40083	0.702;0.278;0.208	P;B;B	0.45449	0.481;0.199;0.39	T	0.32771	-0.9894	10	0.23891	T	0.37	-15.1686	17.8675	0.88800	0.0:1.0:0.0:0.0	.	417;417;417	Q8IWX7-2;Q8IWX7-3;Q8IWX7	.;.;UN45B_HUMAN	V	417	ENSP00000378071:L417V;ENSP00000268876:L417V;ENSP00000412840:L417V;ENSP00000367710:L417V	ENSP00000268876:L417V	L	+	1	2	UNC45B	30519290	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.339000	0.52135	2.767000	0.95098	0.655000	0.94253	CTG	.	.		0.592	UNC45B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256458.2	NM_173167		G	33495177	C	G	33495177	3	3	346	1	0	0	0	0	1	0	0	0	17004	796	28	4	1283	4	UNC45B	17	33495177	Missense_Mutation	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	15774135	33495177	47700033	88	48930										
KLHL11	55175	hgsc.bcm.edu	37	chr17	40010438	40010438	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	cttgggacaacatgatgctgTctgataaaagtttgaattga	10	5	1	4			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr17:40010438T>C	ENST00000319121.3	-	2	1741	c.1681A>G	c.(1681-1683)Aca>Gca	p.T561A	RP11-156E6.1_ENST00000560400.1_RNA	NM_018143.1	NP_060613.1	Q9NVR0	KLH11_HUMAN	kelch-like family member 11	561										NS(2)|breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	17		Breast(137;0.00156)				CATGATGCTGTCTGATAAAAG	0.408																																					p.T561A		Atlas-SNP	.											.	KLHL11	44	.	0			c.A1681G						.						100	103	102					17																	40010438		2203	4300	6503	SO:0001583	missense	55175	exon2			ATGCTGTCTGATA		CCDS11411.1	17q21	2013-01-30	2013-01-30		ENSG00000178502	ENSG00000178502		"Kelch-like", "BTB/POZ domain containing"	19008	protein-coding gene	gene with protein product			"kelch-like 11 (Drosophila)"				Standard	NM_018143		Approved	FLJ10572	uc002hyf.1	Q9NVR0	OTTHUMG00000133506	ENST00000319121.3:c.1681A>G	chr17.hg19:g.40010438T>C	ENSP00000314608:p.Thr561Ala	67.0	0.0		55.0	16.0	NM_018143		Missense_Mutation	SNP	ENST00000319121.3	hg19	CCDS11411.1	.	.	.	.	.	.	.	.	.	.	T	17.70	3.454141	0.63290	.	.	ENSG00000178502	ENST00000319121;ENST00000540254	T	0.65549	-0.16	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.51924	0.1703	L	0.32530	0.975	0.80722	D	1	P	0.38565	0.637	B	0.37047	0.24	T	0.52102	-0.8620	10	0.32370	T	0.25	0.1393	15.4567	0.75321	0.0:0.0:0.0:1.0	.	561	Q9NVR0	KLH11_HUMAN	A	561;424	ENSP00000314608:T561A	ENSP00000314608:T561A	T	-	1	0	KLHL11	37263964	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	7.559000	0.82265	2.106000	0.64143	0.477000	0.44152	ACA	.	.		0.408	KLHL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257464.2	NM_018143		C	40010438	T	C	40010438	3	2	346	1	0	0	0	0	1	0	0	0	8376	1667	58	2	449	2	KLHL11	17	40010438	Missense_Mutation	SNP	T	TCGA-UB-A7MD-01A-12D-A34Z-10	6515261	40010438	41184772	89	48931										
TMUB2	79089	hgsc.bcm.edu	37	chr17	42266396	42266396	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	ctttgttcctgcagcgtggaCcctgccagcagccaggccat	11	15	0	0			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr17:42266396C>T	ENST00000587989.1	+	3	195	c.42C>T	c.(40-42)gaC>gaT	p.D14D	TMUB2_ENST00000589856.1_5'UTR|ASB16-AS1_ENST00000591166.1_RNA|TMUB2_ENST00000590235.1_5'UTR|TMUB2_ENST00000587172.1_5'UTR|TMUB2_ENST00000592825.1_5'UTR|TMUB2_ENST00000589184.1_5'UTR|ASB16-AS1_ENST00000585457.1_RNA|TMUB2_ENST00000589785.1_5'UTR|TMUB2_ENST00000538716.2_Silent_p.D14D|TMUB2_ENST00000446571.3_5'UTR|TMUB2_ENST00000319511.6_5'UTR|ASB16-AS1_ENST00000592897.1_RNA|TMUB2_ENST00000357984.3_5'UTR|ASB16-AS1_ENST00000588785.1_RNA			Q71RG4	TMUB2_HUMAN	transmembrane and ubiquitin-like domain containing 2	14						integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(1)|lung(3)	8		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.113)		GCAGCGTGGACCCTGCCAGCA	0.557																																					p.D14D		Atlas-SNP	.											.	TMUB2	29	.	0			c.C42T						.						66	58	61					17																	42266396		2203	4300	6503	SO:0001819	synonymous_variant	79089	exon3			CGTGGACCCTGCC		CCDS11479.1, CCDS54134.1	17q21	2006-06-27				ENSG00000168591			28459	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_177441		Approved	MGC3123	uc002ifo.3	Q71RG4		ENST00000587989.1:c.42C>T	chr17.hg19:g.42266396C>T		60.0	0.0		79.0	20.0	NM_001076674	B3KU81|Q8NDI2|Q9BPZ5|Q9HAG3	Silent	SNP	ENST00000587989.1	hg19	CCDS54134.1																																																																																			.	.		0.557	TMUB2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457711.1	NM_177441		T	42266396	C	T	42266396	2	4	346	1	0	0	0	0	0	0	0	1	16280	506	18	3		3	TMUB2	17	42266396	Silent	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	2255958	42266396	38928814	90	48932										
TTLL6	284076	hgsc.bcm.edu	37	chr17	46878909	46878909	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	ggtaacttttcatttccatcAcccgctccagtgacactgag	7	13	2	2			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr17:46878909A>T	ENST00000393382.3	-	4	599	c.458T>A	c.(457-459)gTg>gAg	p.V153E		NM_001130918.1	NP_001124390.1			tubulin tyrosine ligase-like family, member 6											endometrium(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)	18						CATTTCCATCACCCGCTCCAG	0.522																																					p.V153E		Atlas-SNP	.											.	TTLL6	113	.	0			c.T458A						.						154	123	133					17																	46878909		692	1591	2283	SO:0001583	missense	284076	exon4			TCCATCACCCGCT	AK093127	CCDS11537.2, CCDS45724.1	17q21.32	2013-02-14			ENSG00000170703	ENSG00000170703		"Tubulin tyrosine ligase-like family"	26664	protein-coding gene	gene with protein product		610849				15890843	Standard	NM_173623		Approved	FLJ35808	uc021tzm.1	Q8N841	OTTHUMG00000156978	ENST00000393382.3:c.458T>A	chr17.hg19:g.46878909A>T	ENSP00000377043:p.Val153Glu	96.0	0.0		68.0	29.0	NM_001130918		Missense_Mutation	SNP	ENST00000393382.3	hg19	CCDS45724.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.638671	0.87760	.	.	ENSG00000170703	ENST00000440941;ENST00000393382	.	.	.	4.39	4.39	0.52855	.	0.000000	0.46758	U	0.000276	T	0.80297	0.4597	M	0.87547	2.89	0.51012	D	0.999901	D	0.76494	0.999	D	0.75484	0.986	D	0.83736	0.0201	9	0.66056	D	0.02	.	12.7456	0.57280	1.0:0.0:0.0:0.0	.	105	Q8N841	TTLL6_HUMAN	E	153;105	.	ENSP00000377043:V105E	V	-	2	0	TTLL6	44233908	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.736000	0.91554	1.834000	0.53371	0.477000	0.44152	GTG	.	.		0.522	TTLL6-003	KNOWN	downstream_ATG|non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346939.3	NM_173623		T	46878909	A	T	46878909	3	4	346	1	0	0	0	0	1	0	0	0	16746	159	6	4	2346	4	TTLL6	17	46878909	Missense_Mutation	SNP	A	TCGA-UB-A7MD-01A-12D-A34Z-10	4612513	46878909	34316301	91	48933										
UBE2Z	65264	hgsc.bcm.edu	37	chr17	46988176	46988176	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	ttggtgttatacagggatatCatgtccatttataaggagcc	10	6	1	0			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr17:46988176C>T	ENST00000360943.5	+	2	459	c.324C>T	c.(322-324)atC>atT	p.I108I	RP11-463M16.4_ENST00000508743.1_RNA	NM_023079.4	NP_075567.2	Q9H832	UBE2Z_HUMAN	ubiquitin-conjugating enzyme E2Z	108					apoptotic process (GO:0006915)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)										ACAGGGATATCATGTCCATTT	0.488																																					p.I108I		Atlas-SNP	.											.	.	.	.	0			c.C324T						.						148	145	146					17																	46988176		2203	4300	6503	SO:0001819	synonymous_variant	65264	exon2			GGATATCATGTCC	BC015890	CCDS11540.2	17q21.32	2010-01-14	2007-07-18		ENSG00000159202	ENSG00000159202		"Ubiquitin-conjugating enzymes E2"	25847	protein-coding gene	gene with protein product	"UBA6-specific enzyme E2"	611362				17597759	Standard	NM_023079		Approved	FLJ13855, USE1	uc002ioi.3	Q9H832	OTTHUMG00000150521	ENST00000360943.5:c.324C>T	chr17.hg19:g.46988176C>T		67.0	0.0		78.0	20.0	NM_023079	A6N8M6|A6NC60|Q7L354|Q8TCM4|Q9H893	Silent	SNP	ENST00000360943.5	hg19	CCDS11540.2																																																																																			.	.		0.488	UBE2Z-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318724.2	NM_023079		T	46988176	C	T	46988176	2	4	346	1	0	0	0	0	0	0	0	1	16893	816	29	3		3	UBE2Z	17	46988176	Silent	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	109267	46988176	34207034	92	48934										
TTYH2	94015	hgsc.bcm.edu	37	chr17	72233606	72233606	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	gtgtggagggaggtcaccatGgagctgaccaagctatccga	15	9	1	1			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr17:72233606G>T	ENST00000269346.4	+	4	662	c.588G>T	c.(586-588)atG>atT	p.M196I	TTYH2_ENST00000529107.1_Missense_Mutation_p.M175I	NM_032646.5	NP_116035.5	Q9BSA4	TTYH2_HUMAN	tweety family member 2	196						chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(14)|ovary(3)|pancreas(1)|stomach(3)|upper_aerodigestive_tract(1)	36						AGGTCACCATGGAGCTGACCA	0.602																																					p.M196I		Atlas-SNP	.											.	TTYH2	63	.	0			c.G588T						.						73	67	69					17																	72233606		2203	4300	6503	SO:0001583	missense	94015	exon4			CACCATGGAGCTG		CCDS32717.1, CCDS45770.1	17q25.1	2013-09-02	2013-09-02		ENSG00000141540	ENSG00000141540			13877	protein-coding gene	gene with protein product		608855	"tweety (Drosophila) homolog 2", "tweety homolog 2 (Drosophila)"			11597145	Standard	XM_005257824		Approved	C17orf29	uc002jkc.3	Q9BSA4	OTTHUMG00000166018	ENST00000269346.4:c.588G>T	chr17.hg19:g.72233606G>T	ENSP00000269346:p.Met196Ile	41.0	0.0		36.0	12.0	NM_032646	B3KX97|Q3B7H8|Q3B7R9|Q6AWB4|Q8NBB7|Q96PK1	Missense_Mutation	SNP	ENST00000269346.4	hg19	CCDS32717.1	.	.	.	.	.	.	.	.	.	.	G	3.862	-0.029754	0.07589	.	.	ENSG00000141540	ENST00000269346;ENST00000529107	T;T	0.09538	2.97;2.97	5.52	-11.0	0.00169	.	1.194220	0.05715	N	0.596697	T	0.05777	0.0151	N	0.16368	0.405	0.09310	N	1	B;B	0.17268	0.016;0.021	B;B	0.21151	0.033;0.027	T	0.35943	-0.9768	10	0.37606	T	0.19	4.6593	9.4911	0.38960	0.1344:0.3812:0.4265:0.0579	.	175;196	B4DKD1;Q9BSA4	.;TTYH2_HUMAN	I	196;175	ENSP00000269346:M196I;ENSP00000433089:M175I	ENSP00000269346:M196I	M	+	3	0	TTYH2	69745201	0.000000	0.05858	0.000000	0.03702	0.133000	0.20885	-2.116000	0.01327	-4.242000	0.00062	-0.302000	0.09304	ATG	.	.		0.602	TTYH2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387459.1			T	72233606	G	T	72233606	3	4	346	1	0	0	0	0	1	0	0	0	16755	1348	47	3	602	3	TTYH2	17	72233606	Missense_Mutation	SNP	G	TCGA-UB-A7MD-01A-12D-A34Z-10	25245430	72233606	8961604	93	48935										
ITGB4	3691	hgsc.bcm.edu	37	chr17	73727379	73727379	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	agacagcccccgaggccttcGgacagaggtcacctccaaga	11	15	1	3			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr17:73727379G>A	ENST00000200181.3	+	10	1332	c.1145G>A	c.(1144-1146)cGg>cAg	p.R382Q	ITGB4_ENST00000339591.3_Missense_Mutation_p.R382Q|ITGB4_ENST00000579662.1_Missense_Mutation_p.R382Q|ITGB4_ENST00000450894.3_Missense_Mutation_p.R382Q|ITGB4_ENST00000449880.2_Missense_Mutation_p.R382Q|ITGB4_ENST00000584558.1_3'UTR	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	382					amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			CGAGGCCTTCGGACAGAGGTC	0.642																																					p.R382Q		Atlas-SNP	.											ITGB4,colon,carcinoma,0,1	ITGB4	165	.	0			c.G1145A						.						62	58	59					17																	73727379		2203	4300	6503	SO:0001583	missense	3691	exon10			GCCTTCGGACAGA		CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"CD molecules", "Integrins", "Fibronectin type III domain containing"	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.1145G>A	chr17.hg19:g.73727379G>A	ENSP00000200181:p.Arg382Gln	37.0	0.0		37.0	14.0	NM_001005731	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Missense_Mutation	SNP	ENST00000200181.3	hg19	CCDS11727.1	.	.	.	.	.	.	.	.	.	.	G	13.47	2.246796	0.39697	.	.	ENSG00000132470	ENST00000450894;ENST00000200181;ENST00000339591;ENST00000449880	D;D;D	0.92249	-3.0;-3.0;-3.0	4.97	1.92	0.25849	Integrin beta subunit, N-terminal (2);	0.368522	0.25526	N	0.030061	D	0.84880	0.5570	L	0.28344	0.845	0.25903	N	0.983322	B;B;P;P	0.50943	0.066;0.055;0.484;0.94	B;B;B;B	0.43950	0.027;0.02;0.184;0.437	T	0.77869	-0.2427	10	0.54805	T	0.06	.	5.8834	0.18868	0.5183:0.0:0.4817:0.0	.	382;382;382;382	P16144-5;P16144-3;A0AVL6;P16144	.;.;.;ITB4_HUMAN	Q	298;382;382;382	ENSP00000200181:R382Q;ENSP00000344079:R382Q;ENSP00000400217:R382Q	ENSP00000200181:R382Q	R	+	2	0	ITGB4	71238974	1.000000	0.71417	0.996000	0.52242	0.817000	0.46193	2.241000	0.43097	0.513000	0.28278	0.455000	0.32223	CGG	.	.		0.642	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1			A	73727379	G	A	73727379	3	1	346	1	0	0	0	0	1	0	0	0	7906	1116	39	1	1179	1	ITGB4	17	73727379	Missense_Mutation	SNP	G	TCGA-UB-A7MD-01A-12D-A34Z-10	1493773	73727379	7467831	94	48936										
QRICH2	84074	hgsc.bcm.edu	37	chr17	74290071	74290071	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	ttaaggaagtgaaccctccgTgcttagaaaatcccataagt	8	9	0	2			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr17:74290071T>A	ENST00000262765.5	-	4	418	c.239A>T	c.(238-240)cAc>cTc	p.H80L		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	80										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4)	62						GAACCCTCCGTGCTTAGAAAA	0.448																																					p.H80L		Atlas-SNP	.											.	QRICH2	143	.	0			c.A239T						.						85	93	90					17																	74290071		2203	4300	6503	SO:0001583	missense	84074	exon4			CCTCCGTGCTTAG	AK058102	CCDS32741.1	17q25.1	2009-03-19			ENSG00000129646	ENSG00000129646			25326	protein-coding gene	gene with protein product							Standard	NM_032134		Approved	DKFZP434P0316	uc002jrd.1	Q9H0J4	OTTHUMG00000167578	ENST00000262765.5:c.239A>T	chr17.hg19:g.74290071T>A	ENSP00000262765:p.His80Leu	42.0	0.0		29.0	12.0	NM_032134	A2RRE1|Q96LM3	Missense_Mutation	SNP	ENST00000262765.5	hg19	CCDS32741.1	.	.	.	.	.	.	.	.	.	.	t	4.333	0.061163	0.08339	.	.	ENSG00000129646	ENST00000262765;ENST00000301613	T	0.08458	3.09	3.74	-6.9	0.01655	.	.	.	.	.	T	0.05593	0.0147	N	0.22421	0.69	0.09310	N	1	B;B	0.30281	0.275;0.144	B;B	0.28232	0.087;0.025	T	0.29336	-1.0015	9	0.66056	D	0.02	0.0271	12.4132	0.55480	0.0:0.3246:0.0:0.6754	.	80;80	B5MD94;Q9H0J4	.;QRIC2_HUMAN	L	80	ENSP00000262765:H80L	ENSP00000262765:H80L	H	-	2	0	QRICH2	71801666	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-5.378000	0.00127	-1.610000	0.01583	-1.987000	0.00451	CAC	.	.		0.448	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134		A	74290071	T	A	74290071	3	1	346	1	0	0	0	0	1	0	0	0	12895	1696	59	4	4816	4	QRICH2	17	74290071	Missense_Mutation	SNP	T	TCGA-UB-A7MD-01A-12D-A34Z-10	562692	74290071	6905139	95	48937										
DNAH17	8632	hgsc.bcm.edu	37	chr17	76433836	76433836	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	ggggatgatgtgggtctcggGgctgggggcaggctccgcgc	22	9	1	1			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr17:76433836G>T	ENST00000585328.1	-	74	12029	c.11905C>A	c.(11905-11907)Ccc>Acc	p.P3969T	DNAH17_ENST00000586052.1_5'UTR|DNAH17_ENST00000389840.5_Missense_Mutation_p.P3968T	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	3968	AAA 6. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			TGGGTCTCGGGGCTGGGGGCA	0.642																																					p.P3974T		Atlas-SNP	.											.	DNAH17	347	.	0			c.C11920A						.						55	52	53					17																	76433836		2203	4299	6502	SO:0001583	missense	8632	exon74			TCTCGGGGCTGGG	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"Axonemal dyneins"	2946	protein-coding gene	gene with protein product		610063	"dynein, axonemal, heavy polypeptide 17", "dynein, axonemal, heavy chain like 1", "dynein, axonemal, heavy like 1"	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.11905C>A	chr17.hg19:g.76433836G>T	ENSP00000465516:p.Pro3969Thr	42.0	0.0		47.0	16.0	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Missense_Mutation	SNP	ENST00000585328.1	hg19		.	.	.	.	.	.	.	.	.	.	G	17.16	3.319484	0.60524	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.24151	1.87	5.22	4.23	0.50019	.	0.972289	0.08438	N	0.945875	T	0.59046	0.2165	M	0.92555	3.32	0.44316	D	0.997193	P	0.37015	0.578	P	0.51550	0.673	T	0.57394	-0.7819	10	0.66056	D	0.02	.	15.41	0.74911	0.0:0.1446:0.8554:0.0	.	3969	E7EUM8	.	T	3969;3968	ENSP00000374490:P3968T	ENSP00000300671:P3969T	P	-	1	0	DNAH17	73945431	1.000000	0.71417	1.000000	0.80357	0.400000	0.30750	6.490000	0.73645	1.154000	0.42482	0.561000	0.74099	CCC	.	.		0.642	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		T	76433836	G	T	76433836	3	4	346	1	0	0	0	0	1	0	0	0	4603	1232	43	3	1500	3	DNAH17	17	76433836	Missense_Mutation	SNP	G	TCGA-UB-A7MD-01A-12D-A34Z-10	2143765	76433836	4761374	96	48938										
ANKRD30B	374860	hgsc.bcm.edu	37	chr18	14764069	14764069	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	atgtcctacaaaagaaacatCtacaaaagcaagtacaaatg	5	8	1	1			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr18:14764069C>A	ENST00000358984.4	+	7	1385	c.1205C>A	c.(1204-1206)tCt>tAt	p.S402Y	ANKRD30B_ENST00000579292.1_Intron|ANKRD30B_ENST00000447268.2_Missense_Mutation_p.S402Y	NM_001145029.1	NP_001138501.1	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B	402										breast(3)|endometrium(4)|kidney(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	22						AAAGAAACATCTACAAAAGCA	0.373																																					p.S402Y		Atlas-SNP	.											.	ANKRD30B	237	.	0			c.C1205A						.						15	12	13					18																	14764069		691	1589	2280	SO:0001583	missense	374860	exon7			AAACATCTACAAA	BC028407	CCDS54182.1	18p11.21	2013-01-10			ENSG00000180777	ENSG00000180777		"Ankyrin repeat domain containing"	24165	protein-coding gene	gene with protein product						11280766	Standard	NM_001145029		Approved	NY-BR-1.1	uc010dlo.2	Q9BXX2		ENST00000358984.4:c.1205C>A	chr18.hg19:g.14764069C>A	ENSP00000351875:p.Ser402Tyr	43.0	0.0		35.0	13.0	NM_001145029	B4DGP1|F8WAG3|Q4G175	Missense_Mutation	SNP	ENST00000358984.4	hg19	CCDS54182.1	.	.	.	.	.	.	.	.	.	.	N	9.117	1.007960	0.19199	.	.	ENSG00000180777	ENST00000358984;ENST00000447268	T;T	0.41758	0.99;1.0	0.64	0.64	0.17752	.	.	.	.	.	T	0.42017	0.1184	L	0.47716	1.5	0.09310	N	1	D	0.58268	0.982	P	0.50231	0.635	T	0.28332	-1.0047	8	0.72032	D	0.01	.	.	.	.	.	402	F8WAG3	.	Y	402	ENSP00000351875:S402Y;ENSP00000399031:S402Y	ENSP00000351875:S402Y	S	+	2	0	ANKRD30B	14754069	0.000000	0.05858	0.004000	0.12327	0.055000	0.15305	-1.014000	0.03641	0.609000	0.30018	0.313000	0.20887	TCT	.	.		0.373	ANKRD30B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443557.1	NM_001145029		A	14764069	C	A	14764069	3	1	346	1	0	0	0	0	1	0	0	0	659	913	32	3	1231	3	ANKRD30B	18	14764069	Missense_Mutation	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10		14764069	63313179	97	48939										
CHST9	83539	hgsc.bcm.edu	37	chr18	24496571	24496571	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	tggataaactctttgaacttGactccagatccattaattaa	5	8	1	3			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr18:24496571G>A	ENST00000284224.8	-	6	1261	c.984C>T	c.(982-984)gtC>gtT	p.V328V	AQP4-AS1_ENST00000582605.1_RNA|AQP4-AS1_ENST00000568797.1_RNA|CHST9_ENST00000581714.1_Silent_p.V328V|AQP4-AS1_ENST00000578701.1_RNA|CHST9_ENST00000580774.1_3'UTR|AQP4-AS1_ENST00000579964.1_RNA	NM_031422.5	NP_113610.2	Q7L1S5	CHST9_HUMAN	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 9	328					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|hormone biosynthetic process (GO:0042446)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|skin(3)	28	all_lung(6;0.0145)|Ovarian(20;0.124)					CTTTGAACTTGACTCCAGATC	0.413																																					p.V328V		Atlas-SNP	.											CHST9_ENST00000284224,NS,carcinoma,0,2	CHST9	114	.	0			c.C984T						.						143	138	139					18																	24496571		1907	4111	6018	SO:0001819	synonymous_variant	83539	exon6			GAACTTGACTCCA	AF239821	CCDS42422.1, CCDS58618.1	18q11.2	2011-04-28			ENSG00000154080	ENSG00000154080		"Sulfotransferases, membrane-bound"	19898	protein-coding gene	gene with protein product		610191				11139592, 11445554	Standard	NM_031422		Approved	GALNAC4ST-2, GALNAC-4-ST2	uc002kwe.4	Q7L1S5		ENST00000284224.8:c.984C>T	chr18.hg19:g.24496571G>A		146.0	0.0		105.0	23.0	NM_031422	Q6UX69|Q9BXH3|Q9BXH4|Q9BZW9	Silent	SNP	ENST00000284224.8	hg19	CCDS42422.1																																																																																			.	.		0.413	CHST9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446549.1	NM_031422		A	24496571	G	A	24496571	2	1	346	1	0	0	0	0	0	0	0	1	3413	1277	45	3		3	CHST9	18	24496571	Silent	SNP	G	TCGA-UB-A7MD-01A-12D-A34Z-10	9732502	24496571	53580677	98	48940										
TCEB3B	51224	hgsc.bcm.edu	37	chr18	44560133	44560133	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	actctgcgtccagggaaagcAgcttcctcccggaactttgg	11	13	1	0			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr18:44560133A>T	ENST00000332567.4	-	1	1855	c.1503T>A	c.(1501-1503)gcT>gcA	p.A501A	KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000592005.1_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	501	Activation domain. {ECO:0000250}.				regulation of DNA-templated transcription, elongation (GO:0032784)|transcription from RNA polymerase II promoter (GO:0006366)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|lung(24)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						CAGGGAAAGCAGCTTCCTCCC	0.607																																					p.A501A		Atlas-SNP	.											.	TCEB3B	141	.	0			c.T1503A						.						70	79	76					18																	44560133		2203	4300	6503	SO:0001819	synonymous_variant	51224	exon1			GAAAGCAGCTTCC	BC036022	CCDS11932.1	18q21.1	2009-08-04			ENSG00000206181	ENSG00000206181			30771	protein-coding gene	gene with protein product	"transcription elongation factor (SIII) elongin A2", "elongin A2"	609522				7660129, 8244996	Standard	NM_016427		Approved	HsT832, TCEB3L	uc002lcr.1	Q8IYF1	OTTHUMG00000132649	ENST00000332567.4:c.1503T>A	chr18.hg19:g.44560133A>T		52.0	0.0		60.0	14.0	NM_016427	Q9P2V9	Silent	SNP	ENST00000332567.4	hg19	CCDS11932.1																																																																																			.	.		0.607	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427		T	44560133	A	T	44560133	2	4	346	1	0	0	0	0	0	0	0	1	15697	175	7	4		4	TCEB3B	18	44560133	Silent	SNP	A	TCGA-UB-A7MD-01A-12D-A34Z-10	20063562	44560133	33517115	99	48941										
CCDC11	220136	hgsc.bcm.edu	37	chr18	47788414	47788414	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	cttgcacagcatccttgattCttgctcgcacaaggctgtcc	8	14	1	1			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr18:47788414C>A	ENST00000398545.4	-	2	362	c.245G>T	c.(244-246)aGa>aTa	p.R82I		NM_145020.3	NP_659457.2														endometrium(1)|kidney(4)|large_intestine(6)|lung(6)|ovary(1)|pancreas(1)|skin(1)	20				STAD - Stomach adenocarcinoma(97;2.66e-05)|Colorectal(21;7.57e-05)|Lung(128;0.00932)|READ - Rectum adenocarcinoma(32;0.164)		ATCCTTGATTCTTGCTCGCAC	0.423																																					p.R82I		Atlas-SNP	.											.	CCDC11	59	.	0			c.G245T						.						173	158	163					18																	47788414		1917	4136	6053	SO:0001583	missense	220136	exon2			TTGATTCTTGCTC																												ENST00000398545.4:c.245G>T	chr18.hg19:g.47788414C>A	ENSP00000381553:p.Arg82Ile	148.0	0.0		122.0	45.0	NM_145020		Missense_Mutation	SNP	ENST00000398545.4	hg19	CCDS11940.2	.	.	.	.	.	.	.	.	.	.	C	17.77	3.471679	0.63737	.	.	ENSG00000172361	ENST00000398545	T	0.43688	0.94	5.12	4.24	0.50183	.	0.357634	0.18120	U	0.151099	T	0.57315	0.2045	M	0.65498	2.005	0.46167	D	0.998902	D	0.76494	0.999	D	0.66716	0.946	T	0.57376	-0.7822	10	0.66056	D	0.02	-9.6961	8.8334	0.35098	0.0:0.9014:0.0:0.0986	.	82	Q96M91	CCD11_HUMAN	I	82	ENSP00000381553:R82I	ENSP00000381553:R82I	R	-	2	0	CCDC11	46042412	0.998000	0.40836	0.997000	0.53966	0.552000	0.35366	1.497000	0.35649	2.817000	0.96982	0.563000	0.77884	AGA	.	.		0.423	CCDC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255922.3			A	47788414	C	A	47788414	3	1	346	1	0	0	0	0	1	0	0	0	2748	913	32	3	1327	3	CCDC11	18	47788414	Missense_Mutation	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	3228281	47788414	30288834	100	48942										
C3	718	hgsc.bcm.edu	37	chr19	6681964	6681966	+	In_Frame_Del	DEL	GAT	GAT	-													0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	agccttaccttgtccaggtaGatgatgagggtgttcctatc							TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	GAT	GAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr19:6681964_6681966delGAT	ENST00000245907.6	-	35	4428_4430	c.4336_4338delATC	c.(4336-4338)atcdel	p.I1446del	C3_ENST00000599668.1_5'Flank	NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	1446	Properdin-binding.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	TGTCCAGGTAGATGATGAGGGTG	0.522																																					p.1446_1447del		Atlas-Indel,Pindel	.											C3,NS,carcinoma,0,1	C3	192	.	0			c.4337_4339del						.																																			SO:0001651	inframe_deletion	718	exon35			.	J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"Complement system", "Endogenous ligands"	1318	protein-coding gene	gene with protein product	"C3a anaphylatoxin", "complement component C3a", "complement component C3b", "prepro-C3"	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.4336_4338delATC	chr19.hg19:g.6681967_6681969delGAT	ENSP00000245907:p.Ile1446del	66.0	0.0		50.0	15.0	NM_000064	A7E236	In_Frame_Del	DEL	ENST00000245907.6	hg19	CCDS32883.1																																																																																			.	.		0.522	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064		-	6681966	GAT	-	6681964	7	5	346	1	0	1	0	1	0	0	0	0	2206	932	33	0	681	0	C3	19	6681964	In_Frame_Del	DEL	GAT	TCGA-UB-A7MD-01A-12D-A34Z-10		6681964	52447019	101	48943										
ECSIT	51295	hgsc.bcm.edu	37	chr19	11624014	11624014	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	agggaaccacagcttcaggcGcaccaacttgagcatggggt	13	11	1	1	rs373672064		TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr19:11624014G>A	ENST00000270517.7	-	4	730	c.595C>T	c.(595-597)Cgc>Tgc	p.R199C	ECSIT_ENST00000591352.1_Intron|ECSIT_ENST00000592312.1_Missense_Mutation_p.R83C|ECSIT_ENST00000591104.1_Missense_Mutation_p.R199C|ECSIT_ENST00000252440.7_Missense_Mutation_p.R199C|ECSIT_ENST00000417981.2_Intron|RN7SL833P_ENST00000498758.2_RNA|ECSIT_ENST00000588998.1_Intron	NM_016581.4	NP_057665.2	Q9BQ95	ECSIT_HUMAN	ECSIT signalling integrator	199					BMP signaling pathway (GO:0030509)|innate immune response (GO:0045087)|mesoderm formation (GO:0001707)|oxidation-reduction process (GO:0055114)|regulation of oxidoreductase activity (GO:0051341)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	oxidoreductase activity, acting on NAD(P)H (GO:0016651)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	11						AGCTTCAGGCGCACCAACTTG	0.592																																					p.R199C		Atlas-SNP	.											.	ECSIT	32	.	0			c.C595T						.		CYS/ARG,CYS/ARG,	0,4406		0,0,2203	132	95	108		595,595,	4.9	0.9	19		108	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,intron	ECSIT	NM_001142464.2,NM_016581.4,NM_001142465.2	180,180,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,	199/297,199/432,	11624014	1,13005	2203	4300	6503	SO:0001583	missense	51295	exon4			TCAGGCGCACCAA	BC005119	CCDS12262.1, CCDS45979.1, CCDS45980.1, CCDS59353.1	19p13.2	2013-05-24	2013-05-24			ENSG00000130159		"Mitochondrial respiratory chain complex assembly factors"	29548	protein-coding gene	gene with protein product	"signaling intermediate in Toll pathway evolutionarily conserved ortholog (mouse)"	608388	"ECSIT homolog (Drosophila)"			10465784, 22982022	Standard	NM_001142464		Approved	SITPEC	uc002msb.3	Q9BQ95		ENST00000270517.7:c.595C>T	chr19.hg19:g.11624014G>A	ENSP00000270517:p.Arg199Cys	35.0	0.0		48.0	16.0	NM_001142464	E9PAN9|K7EMM0|Q96HQ7|Q9NYI1	Missense_Mutation	SNP	ENST00000270517.7	hg19	CCDS12262.1	.	.	.	.	.	.	.	.	.	.	g	15.87	2.959959	0.53400	0.0	1.16E-4	ENSG00000130159	ENST00000270517;ENST00000252440	D;D	0.88046	-2.33;-2.33	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	D	0.93693	0.7985	M	0.87180	2.865	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.94393	0.7616	10	0.87932	D	0	-28.7658	13.0287	0.58829	0.0:0.0:0.8382:0.1618	.	199;199	Q9BQ95-2;Q9BQ95	.;ECSIT_HUMAN	C	199	ENSP00000270517:R199C;ENSP00000252440:R199C	ENSP00000252440:R199C	R	-	1	0	ECSIT	11485014	1.000000	0.71417	0.933000	0.37362	0.008000	0.06430	6.854000	0.75440	2.453000	0.82957	0.639000	0.83563	CGC	.	.		0.592	ECSIT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442603.2	NM_016581		A	11624014	G	A	11624014	3	1	346	1	0	0	0	0	1	0	0	0	4902	1087	38	1	720	1	ECSIT	19	11624014	Missense_Mutation	SNP	G	TCGA-UB-A7MD-01A-12D-A34Z-10	4942050	11624014	47504969	102	48944										
ZNF28	7576	hgsc.bcm.edu	37	chr19	53304474	53304474	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	aaagatttttctctcatgtgTacattccgtttttgtgtgag	8	6	2	2	rs372999948		TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr19:53304474T>A	ENST00000457749.2	-	4	743	c.624A>T	c.(622-624)gtA>gtT	p.V208V	ZNF28_ENST00000360272.4_Silent_p.V155V|ZNF28_ENST00000438150.2_Silent_p.V155V|ZNF28_ENST00000414252.2_Silent_p.V155V	NM_006969.3	NP_008900.3	P17035	ZNF28_HUMAN	zinc finger protein 28	208					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|liver(1)|lung(10)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(134;0.0386)|Lung(386;0.145)		CTCTCATGTGTACATTCCGTT	0.338																																					p.V208V		Atlas-SNP	.											.	ZNF28	191	.	0			c.A624T						.						129	136	134					19																	53304474		2203	4300	6503	SO:0001819	synonymous_variant	7576	exon4			CATGTGTACATTC	X52355	CCDS33093.1, CCDS33093.2	19q13.41	2013-01-08	2006-05-10		ENSG00000198538	ENSG00000198538		"Zinc fingers, C2H2-type", "-"	13073	protein-coding gene	gene with protein product			"zinc finger protein 28 (KOX 24)"				Standard	NR_036599		Approved	KOX24, DKFZp781D0275	uc002qad.3	P17035	OTTHUMG00000154564	ENST00000457749.2:c.624A>T	chr19.hg19:g.53304474T>A		64.0	0.0		66.0	22.0	NM_006969	A8KAK9|B4E3G0|B9EIK7|Q5H9V1|Q5HYM9|Q6ZML9|Q6ZN56	Silent	SNP	ENST00000457749.2	hg19	CCDS33093.2																																																																																			.	.		0.338	ZNF28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336038.2	NM_006969		A	53304474	T	A	53304474	2	1	346	1	0	0	0	0	0	0	0	1	17828	1625	57	4		4	ZNF28	19	53304474	Silent	SNP	T	TCGA-UB-A7MD-01A-12D-A34Z-10	41680460	53304474	5824509	103	48945										
ZNF415	55786	hgsc.bcm.edu	37	chr19	53612425	53612425	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	ttctctccagtgtgaactctCcgatgtagtgcaaggcatga	10	10	2	2			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr19:53612425C>T	ENST00000500065.4	-	4	1206	c.873G>A	c.(871-873)cgG>cgA	p.R291R	ZNF415_ENST00000455735.2_Silent_p.R339R|ZNF415_ENST00000440291.1_Silent_p.R278R|ZNF415_ENST00000597748.1_3'UTR|ZNF415_ENST00000243643.4_Silent_p.R291R|ZNF415_ENST00000448501.1_Silent_p.R339R|ZNF415_ENST00000421033.1_Silent_p.R303R|ZNF415_ENST00000597503.1_3'UTR|ZNF415_ENST00000594011.1_3'UTR|ZNF415_ENST00000595193.1_3'UTR|ZNF415_ENST00000601493.1_Silent_p.R61R	NM_001136038.2	NP_001129510.2	Q09FC8	ZN415_HUMAN	zinc finger protein 415	339					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				GBM - Glioblastoma multiforme(134;0.0191)		TGTGAACTCTCCGATGTAGTG	0.423																																					p.R291R		Atlas-SNP	.											.	ZNF415	68	.	0			c.G873A						.						101	89	93					19																	53612425		2203	4300	6503	SO:0001819	synonymous_variant	55786	exon4			AACTCTCCGATGT	AK002053	CCDS12860.1, CCDS54313.1	19q13.42	2014-03-18			ENSG00000170954	ENSG00000170954		"Zinc fingers, C2H2-type", "-"	20636	protein-coding gene	gene with protein product						14702039	Standard	NM_001136038		Approved		uc002qaw.3	Q09FC8	OTTHUMG00000182865	ENST00000500065.4:c.873G>A	chr19.hg19:g.53612425C>T		58.0	0.0		65.0	19.0	NM_018355	F5H287|Q09FC7|Q09FC9|Q09FD0|Q6NSZ2|Q6P3S0|Q9NUR2	Silent	SNP	ENST00000500065.4	hg19	CCDS54313.1																																																																																			.	.		0.423	ZNF415-025	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464043.1	NM_018355		T	53612425	C	T	53612425	2	4	346	1	0	0	0	0	0	0	0	1	17907	842	30	3		3	ZNF415	19	53612425	Silent	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	307951	53612425	5516558	104	48946										
POLR3F	10621	hgsc.bcm.edu	37	chr20	18464200	18464200	+	Nonstop_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	tgacagagtggctcgaatttTaatagagagctatgaacttt	10	5	0	4			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr20:18464200T>C	ENST00000377603.4	+	9	1329	c.949T>C	c.(949-951)Taa>Caa	p.*317Q	POLR3F_ENST00000462997.1_3'UTR	NM_006466.2	NP_006457.2	Q9H1D9	RPC6_HUMAN	polymerase (RNA) III (DNA directed) polypeptide F, 39 kDa	0					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			breast(2)	2						GCTCGAATTTTAATAGAGAGC	0.323																																					p.X317Q	GBM(69;898 1468 19907 52011)	Atlas-SNP	.											.	POLR3F	14	.	0			c.T949C						.						30	32	31					20																	18464200		2203	4298	6501	SO:0001578	stop_lost	10621	exon9			GAATTTTAATAGA	U93869	CCDS13135.1	20p11.23	2013-01-21	2002-08-29		ENSG00000132664	ENSG00000132664		"RNA polymerase subunits"	15763	protein-coding gene	gene with protein product	"RNA polymerase III C39 subunit"		"polymerase (RNA) III (DNA directed) polypeptide F (39 kDa)"			9171375	Standard	NM_006466		Approved	RPC39, RPC6	uc002wqv.3	Q9H1D9	OTTHUMG00000031971	ENST00000377603.4:c.949T>C	chr20.hg19:g.18464200T>C	ENSP00000366828:p.*317Glnext*1	36.0	0.0		36.0	8.0	NM_006466	A8K4C7|O15319	Missense_Mutation	SNP	ENST00000377603.4	hg19	CCDS13135.1	.	.	.	.	.	.	.	.	.	.	T	16.92	3.256406	0.59321	.	.	ENSG00000132664	ENST00000377603	.	.	.	5.57	5.57	0.84162	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.99999	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.74	0.77887	0.0:0.0:0.0:1.0	.	.	.	.	Q	317	.	.	X	+	1	0	POLR3F	18412200	1.000000	0.71417	0.994000	0.49952	0.339000	0.28857	7.668000	0.83897	2.133000	0.65898	0.533000	0.62120	TAA	.	.		0.323	POLR3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078170.2	NM_006466		C	18464200	T	C	18464200	4	2	346	1	0	0	0	0	0	0	0	0	12242	1767	61	2	983	2	POLR3F	20	18464200	Nonstop_Mutation	SNP	T	TCGA-UB-A7MD-01A-12D-A34Z-10		18464200	44561320	105	48947										
ZNF335	63925	hgsc.bcm.edu	37	chr20	44592256	44592256	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	cagatgcggcacaggaagggCctcaaaagtggtttgggcga	16	8	1	1			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr20:44592256C>A	ENST00000322927.2	-	9	1489	c.1389G>T	c.(1387-1389)agG>agT	p.R463S	ZNF335_ENST00000426788.1_Missense_Mutation_p.R308S	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	463					brain development (GO:0007420)|brain morphogenesis (GO:0048854)|cerebral cortex neuron differentiation (GO:0021895)|histone H3-K4 trimethylation (GO:0080182)|in utero embryonic development (GO:0001701)|neuron projection morphogenesis (GO:0048812)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of neurogenesis (GO:0050769)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(13)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	51		Myeloproliferative disorder(115;0.0122)				ACAGGAAGGGCCTCAAAAGTG	0.572																																					p.R463S		Atlas-SNP	.											.	ZNF335	115	.	0			c.G1389T						.						237	219	225					20																	44592256		2203	4300	6503	SO:0001583	missense	63925	exon9			GAAGGGCCTCAAA	AK026157	CCDS13389.1	20q13.12	2011-09-12			ENSG00000198026	ENSG00000198026		"Zinc fingers, C2H2-type"	15807	protein-coding gene	gene with protein product	"NRC-interacting factor 1"	610827				12215545, 19131338	Standard	NM_022095		Approved	bA465L10.2, NIF-1	uc002xqw.3	Q9H4Z2	OTTHUMG00000032637	ENST00000322927.2:c.1389G>T	chr20.hg19:g.44592256C>A	ENSP00000325326:p.Arg463Ser	78.0	0.0		58.0	18.0	NM_022095	B4DLG7|Q548D0|Q9H684	Missense_Mutation	SNP	ENST00000322927.2	hg19	CCDS13389.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.937453	0.73557	.	.	ENSG00000198026	ENST00000322927;ENST00000243961;ENST00000426788	T;T	0.30182	1.54;1.54	5.16	0.878	0.19150	.	0.104089	0.64402	D	0.000005	T	0.38665	0.1049	L	0.34521	1.04	0.58432	D	0.999993	D;D	0.89917	1.0;0.999	D;D	0.83275	0.996;0.991	T	0.15378	-1.0439	10	0.87932	D	0	-32.8936	8.7232	0.34454	0.0:0.596:0.0:0.404	.	308;463	Q9H4Z2-2;Q9H4Z2	.;ZN335_HUMAN	S	463;240;308	ENSP00000325326:R463S;ENSP00000397098:R308S	ENSP00000243961:R240S	R	-	3	2	ZNF335	44025663	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	0.847000	0.27696	0.349000	0.23975	0.655000	0.94253	AGG	.	.		0.572	ZNF335-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079553.1	NM_022095		A	44592256	C	A	44592256	3	1	346	1	0	0	0	0	1	0	0	0	17867	738	26	3	2719	3	ZNF335	20	44592256	Missense_Mutation	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	26128056	44592256	18433264	106	48948										
PRAME	23532	hgsc.bcm.edu	37	chr22	22892516	22892516	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	tttcgcttcactttctcaatGaggtaggagaacaattcatc	7	9	3	2			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chr22:22892516G>A	ENST00000398741.1	-	5	891	c.585C>T	c.(583-585)ctC>ctT	p.L195L	PRAME_ENST00000539862.1_Silent_p.L179L|PRAME_ENST00000402697.1_Silent_p.L195L|PRAME_ENST00000543184.1_Silent_p.L195L|PRAME_ENST00000398743.2_Silent_p.L195L|PRAME_ENST00000424204.2_Silent_p.L179L|PRAME_ENST00000485532.1_5'Flank|PRAME_ENST00000405655.3_Silent_p.L195L	NM_206955.1	NP_996838.1	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma	195					apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	retinoic acid receptor binding (GO:0042974)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05)		READ - Rectum adenocarcinoma(21;0.0649)		CTTTCTCAATGAGGTAGGAGA	0.453																																					p.L195L	Melanoma(73;1707 1838 15168 27201)	Atlas-SNP	.											.	PRAME	78	.	0			c.C585T						.						154	146	149					22																	22892516		2203	4300	6503	SO:0001819	synonymous_variant	23532	exon5			CTCAATGAGGTAG	U65011	CCDS13801.1	22q11.22	2013-01-17			ENSG00000185686	ENSG00000185686		"-"	9336	protein-coding gene	gene with protein product	"cancer/testis antigen 130"	606021		MAPE		9047241, 10591208	Standard	XM_006725402		Approved	CT130	uc002zwj.3	P78395	OTTHUMG00000151172	ENST00000398741.1:c.585C>T	chr22.hg19:g.22892516G>A		57.0	0.0		70.0	18.0	NM_206954	B2R6Y7|O43481|Q8IXN8	Silent	SNP	ENST00000398741.1	hg19	CCDS13801.1																																																																																			.	.		0.453	PRAME-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321644.1	NM_206953		A	22892516	G	A	22892516	2	1	346	1	0	0	0	0	0	0	0	1	12436	1277	45	3		3	PRAME	22	22892516	Silent	SNP	G	TCGA-UB-A7MD-01A-12D-A34Z-10		22892516	28412050	107	48949										
ACOT9	23597	hgsc.bcm.edu	37	chrX	23731290	23731290	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	cgagccaccattacaaatgtTgcatccaaaacaggacaaaa	6	11	0	0			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chrX:23731290T>C	ENST00000336430.7	-	8	728	c.597A>G	c.(595-597)gcA>gcG	p.A199A	ACOT9_ENST00000379295.1_Silent_p.A139A|ACOT9_ENST00000492081.1_Intron|ACOT9_ENST00000379303.5_Silent_p.A208A	NM_001033583.2	NP_001028755.2	Q9Y305	ACOT9_HUMAN	acyl-CoA thioesterase 9	199					acyl-CoA metabolic process (GO:0006637)	mitochondrion (GO:0005739)	acetyl-CoA hydrolase activity (GO:0003986)|carboxylic ester hydrolase activity (GO:0052689)			breast(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(4)|pancreas(1)|skin(1)	15						TTACAAATGTTGCATCCAAAA	0.328																																					p.A208A		Atlas-SNP	.											.	ACOT9	33	.	0			c.A624G						.						85	72	76					X																	23731290		2203	4300	6503	SO:0001819	synonymous_variant	23597	exon9			AAATGTTGCATCC	AF132950	CCDS35216.1, CCDS43924.1	Xp22.11	2008-02-05			ENSG00000123130	ENSG00000123130		"Acyl CoA thioesterases"	17152	protein-coding gene	gene with protein product		300862				10383425, 10810093, 16103133, 16940157	Standard	XM_005274471		Approved	CGI-16, MT-ACT48, ACATE2	uc004dao.3	Q9Y305	OTTHUMG00000021257	ENST00000336430.7:c.597A>G	chrX.hg19:g.23731290T>C		145.0	0.0		189.0	131.0	NM_001037171	B3KNC9|B7ZM94	Silent	SNP	ENST00000336430.7	hg19	CCDS35216.1																																																																																			.	.		0.328	ACOT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056065.1	NM_012332		C	23731290	T	C	23731290	2	2	346	1	0	0	0	0	0	0	0	1	157	1799	63	2		2	ACOT9	23	23731290	Silent	SNP	T	TCGA-UB-A7MD-01A-12D-A34Z-10		23731290	131539270	108	48950										
FAM123B	139285	hgsc.bcm.edu	37	chrX	63410478	63410478	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	ctccagggtctctgcagtgtCgagagagcggcttctcctgt	13	12	2	1			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chrX:63410478C>T	ENST00000330258.3	-	2	2961	c.2689G>A	c.(2689-2691)Gac>Aac	p.D897N	AMER1_ENST00000403336.1_Intron|AMER1_ENST00000374869.3_Intron	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	897					adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)									TCTGCAGTGTCGAGAGAGCGG	0.602																																					p.D897N		Atlas-SNP	.											.	.	.	.	67	Whole gene deletion(67)	kidney(65)|ovary(1)|large_intestine(1)	c.G2689A						.						41	40	41					X																	63410478		2069	4192	6261	SO:0001583	missense	139285	exon2			CAGTGTCGAGAGA	AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"-"	26837	protein-coding gene	gene with protein product	"Wilms Tumor on the X", "adenomatous polyposis coli membrane recruitment 1"	300647	"family with sequence similarity 123B"	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.2689G>A	chrX.hg19:g.63410478C>T	ENSP00000329117:p.Asp897Asn	64.0	0.0		72.0	44.0	NM_152424	A2IB86|Q8N885	Missense_Mutation	SNP	ENST00000330258.3	hg19	CCDS14377.2	.	.	.	.	.	.	.	.	.	.	C	21.0	4.082665	0.76528	.	.	ENSG00000184675	ENST00000330258	T	0.71222	-0.55	4.79	4.79	0.61399	.	.	.	.	.	T	0.71074	0.3297	N	0.19112	0.55	0.80722	D	1	D	0.76494	0.999	P	0.62813	0.907	T	0.70146	-0.4952	8	.	.	.	-12.3048	15.8198	0.78631	0.0:1.0:0.0:0.0	.	897	Q5JTC6	F123B_HUMAN	N	897	ENSP00000329117:D897N	.	D	-	1	0	FAM123B	63327203	1.000000	0.71417	0.997000	0.53966	0.972000	0.66771	6.856000	0.75450	2.385000	0.81259	0.529000	0.55759	GAC	.	.		0.602	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		T	63410478	C	T	63410478	3	4	346	1	0	0	0	0	1	0	0	0	5428	884	31	1	722	1	FAM123B	23	63410478	Missense_Mutation	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	39679188	63410478	91860082	109	48951										
AFF2	2334	hgsc.bcm.edu	37	chrX	148037267	148037267	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	ctgcctcctccaatcatccaAccaatggaagtccagatgaa	6	14	1	2			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chrX:148037267A>T	ENST00000370460.2	+	11	2171	c.1692A>T	c.(1690-1692)caA>caT	p.Q564H	AFF2_ENST00000370457.5_Missense_Mutation_p.Q531H|AFF2_ENST00000342251.3_Missense_Mutation_p.Q531H|AFF2_ENST00000286437.5_Missense_Mutation_p.Q205H	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	564					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)			breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					CAATCATCCAACCAATGGAAG	0.458																																					p.Q564H		Atlas-SNP	.											.	AFF2	679	.	0			c.A1692T						.						191	200	197					X																	148037267		2203	4300	6503	SO:0001583	missense	2334	exon11			CATCCAACCAATG	U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"fragile X mental retardation 2"	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.1692A>T	chrX.hg19:g.148037267A>T	ENSP00000359489:p.Gln564His	58.0	0.0		71.0	37.0	NM_002025	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Missense_Mutation	SNP	ENST00000370460.2	hg19	CCDS14684.1	.	.	.	.	.	.	.	.	.	.	A	16.23	3.065278	0.55432	.	.	ENSG00000155966	ENST00000370460;ENST00000370457;ENST00000342251;ENST00000286437	T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11	5.56	-5.73	0.02398	.	0.270973	0.36893	N	0.002352	T	0.63105	0.2483	L	0.41236	1.265	0.25746	N	0.985106	D;D;D;D;D;D	0.71674	0.998;0.998;0.998;0.998;0.998;0.998	D;P;P;P;P;D	0.66196	0.942;0.904;0.904;0.904;0.904;0.942	T	0.64076	-0.6492	10	0.45353	T	0.12	.	13.3874	0.60803	0.195:0.088:0.717:0.0	.	205;529;531;525;554;564	B4DXD5;P51816-6;P51816-3;P51816-2;P51816-5;P51816	.;.;.;.;.;AFF2_HUMAN	H	564;531;531;205	ENSP00000359489:Q564H;ENSP00000359486:Q531H;ENSP00000345459:Q531H;ENSP00000286437:Q205H	ENSP00000286437:Q205H	Q	+	3	2	AFF2	147844967	0.129000	0.22400	0.262000	0.24481	0.952000	0.60782	-0.537000	0.06128	-1.286000	0.02384	-0.335000	0.08231	CAA	.	.		0.458	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025		T	148037267	A	T	148037267	3	4	346	1	0	0	0	0	1	0	0	0	357	40	2	4	1789	4	AFF2	23	148037267	Missense_Mutation	SNP	A	TCGA-UB-A7MD-01A-12D-A34Z-10	84626789	148037267	7233293	110	48952										
PASD1	139135	hgsc.bcm.edu	37	chrX	150842573	150842573	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0540540540540541	6	1	0.874933687002653	0.583289124668435	0.972148541114058	0.131221719457014	0.709357990687916	0	ccggctttggcaagagttgtCtgattcactcggtcctgttg	12	10	2	2			TCGA-UB-A7MD-01A-12D-A34Z-10	TCGA-UB-A7MD-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d48970c7-b709-4f1b-99d3-3a4d1654738b	d3214cb5-374d-4e2f-b712-07dfcb82966a	g.chrX:150842573C>G	ENST00000370357.4	+	15	2335	c.2090C>G	c.(2089-2091)tCt>tGt	p.S697C		NM_173493.2	NP_775764.2	Q8IV76	PASD1_HUMAN	PAS domain containing 1	697						nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(3)|liver(1)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	48	Acute lymphoblastic leukemia(192;6.56e-05)					CAAGAGTTGTCTGATTCACTC	0.527																																					p.S697C		Atlas-SNP	.											.	PASD1	286	.	0			c.C2090G						.						124	115	118					X																	150842573		2203	4300	6503	SO:0001583	missense	139135	exon15			AGTTGTCTGATTC	AY270020	CCDS35431.1	Xq28	2009-08-06			ENSG00000166049	ENSG00000166049			20686	protein-coding gene	gene with protein product	"cancer/testis antigen 63"					15122589, 15162151	Standard	NM_173493		Approved	CT63	uc004fev.4	Q8IV76	OTTHUMG00000024169	ENST00000370357.4:c.2090C>G	chrX.hg19:g.150842573C>G	ENSP00000359382:p.Ser697Cys	69.0	0.0		47.0	29.0	NM_173493	Q3MNE0|Q69HD7|Q8N7X9	Missense_Mutation	SNP	ENST00000370357.4	hg19	CCDS35431.1	.	.	.	.	.	.	.	.	.	.	C	11.21	1.572103	0.28092	.	.	ENSG00000166049	ENST00000370357	T	0.34275	1.37	3.25	0.239	0.15484	.	.	.	.	.	T	0.23846	0.0577	N	0.14661	0.345	0.09310	N	1	P	0.52463	0.953	P	0.47705	0.555	T	0.11299	-1.0593	9	0.51188	T	0.08	-8.0E-4	5.0809	0.14656	0.4461:0.3644:0.1895:0.0	.	697	Q8IV76	PASD1_HUMAN	C	697	ENSP00000359382:S697C	ENSP00000359382:S697C	S	+	2	0	PASD1	150593229	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.403000	0.07214	-0.063000	0.13065	-0.237000	0.12165	TCT	.	.		0.527	PASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060879.2	NM_173493		G	150842573	C	G	150842573	3	3	346	1	0	0	0	0	1	0	0	0	11480	913	32	4	2144	4	PASD1	23	150842573	Missense_Mutation	SNP	C	TCGA-UB-A7MD-01A-12D-A34Z-10	2805306	150842573	4427987	111	48953										
USP48	84196	hgsc.bcm.edu	37	chr1	22021689	22021689	+	Frame_Shift_Del	DEL	T	T	-													0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	tataattttgatgggatatcTtttgccgctttgttccacca							TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr1:22021689delT	ENST00000308271.9	-	23	3401	c.2753delA	c.(2752-2754)aagfs	p.K918fs	USP48_ENST00000374732.3_Intron|USP48_ENST00000400301.1_Intron|USP48_ENST00000529637.1_Frame_Shift_Del_p.K930fs	NM_032236.5	NP_115612.4	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 48	918					ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			NS(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(14)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)		ATGGGATATCTTTTGCCGCTT	0.388																																					p.K918fs		Atlas-Indel,Pindel	.											.	USP48	91	.	0			c.2754delG						.						142	135	137					1																	22021689		2202	4300	6502	SO:0001589	frameshift_variant	84196	exon23			.	AF502942	CCDS30623.1, CCDS44084.1	1p36.12	2008-02-05	2005-08-08	2004-04-07	ENSG00000090686	ENSG00000090686		"Ubiquitin-specific peptidases"	18533	protein-coding gene	gene with protein product			"ubiquitin specific protease 31", "ubiquitin specific protease 48"	USP31		12838346	Standard	XM_005246009		Approved	FLJ23277, FLJ11328, FLJ20103, FLJ23054, MGC14879	uc001bfb.3	Q86UV5	OTTHUMG00000007798	ENST00000308271.9:c.2753delA	chr1.hg19:g.22021689delT	ENSP00000309262:p.Lys918fs	50.0	0.0		55.0	16.0	NM_032236	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Frame_Shift_Del	DEL	ENST00000308271.9	hg19	CCDS30623.1																																																																																			.	.		0.388	USP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021372.1	NM_032236		-	22021689	T	-	22021689	7	5	347	1	0	1	0	1	0	0	0	0	17094	1609	56	0	374	0	USP48	1	22021689	Frame_Shift_Del	DEL	T	TCGA-UB-A7ME-01A-11D-A33K-10		22021689	227228932	1	48954										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27094294	27094294	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	cttccagaaatccagttcttCtactacaaccaatgagaaga	5	11	2	3			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr1:27094294C>G	ENST00000324856.7	+	11	3373	c.3002C>G	c.(3001-3003)tCt>tGt	p.S1001C	ARID1A_ENST00000457599.2_Missense_Mutation_p.S1001C|ARID1A_ENST00000374152.2_Missense_Mutation_p.S618C	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1001	Poly-Ser.				androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		TCCAGTTCTTCTACTACAACC	0.478			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.S1001C		Atlas-SNP	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.C3002G						.						88	79	82					1																	27094294		2203	4300	6503	SO:0001583	missense	8289	exon11			GTTCTTCTACTAC	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.3002C>G	chr1.hg19:g.27094294C>G	ENSP00000320485:p.Ser1001Cys	76.0	0.0		69.0	33.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Missense_Mutation	SNP	ENST00000324856.7	hg19	CCDS285.1	.	.	.	.	.	.	.	.	.	.	C	19.76	3.888226	0.72524	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000374152	T;T;T	0.03152	4.26;4.03;4.07	5.17	3.29	0.37713	ARID/BRIGHT DNA-binding domain (2);	0.000000	0.85682	D	0.000000	T	0.12518	0.0304	L	0.59436	1.845	0.80722	D	1	D;B;B	0.71674	0.998;0.017;0.005	D;B;B	0.71414	0.973;0.008;0.002	T	0.00431	-1.1743	10	0.66056	D	0.02	-10.562	10.6932	0.45884	0.0:0.7963:0.1324:0.0713	.	1001;1001;655	O14497;O14497-2;Q4LE49	ARI1A_HUMAN;.;.	C	1001;1001;618	ENSP00000320485:S1001C;ENSP00000387636:S1001C;ENSP00000363267:S618C	ENSP00000320485:S1001C	S	+	2	0	ARID1A	26966881	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.651000	0.83577	0.749000	0.32854	-0.175000	0.13238	TCT	.	.		0.478	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		G	27094294	C	G	27094294	3	3	347	1	0	0	0	0	1	0	0	0	913	913	32	4	3044	4	ARID1A	1	27094294	Missense_Mutation	SNP	C	TCGA-UB-A7ME-01A-11D-A33K-10	5072605	27094294	222156327	2	48955										
LRRC41	10489	hgsc.bcm.edu	37	chr1	46746117	46746117	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	tcctggggagaggcaaaggtGgcactatccagggacagctg	16	9	0	1			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr1:46746117G>A	ENST00000343304.6	-	6	2157	c.1872C>T	c.(1870-1872)gcC>gcT	p.A624A	LRRC41_ENST00000472710.1_5'UTR	NM_006369.4	NP_006360.3	Q15345	LRC41_HUMAN	leucine rich repeat containing 41	624					protein ubiquitination (GO:0016567)	membrane (GO:0016020)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(7)|ovary(3)|pancreas(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Acute lymphoblastic leukemia(166;0.155)					AGGCAAAGGTGGCACTATCCA	0.577																																					p.A624A		Atlas-SNP	.											.	LRRC41	74	.	0			c.C1872T						.						93	100	98					1																	46746117		2203	4300	6503	SO:0001819	synonymous_variant	10489	exon6			AAAGGTGGCACTA	AK024051	CCDS533.1	1p34.1	2008-02-05			ENSG00000132128	ENSG00000132128			16917	protein-coding gene	gene with protein product						11384984	Standard	XM_005270376		Approved	MUF1	uc001cpn.3	Q15345	OTTHUMG00000007810	ENST00000343304.6:c.1872C>T	chr1.hg19:g.46746117G>A		309.0	0.0		308.0	65.0	NM_006369	A8K5G8|Q3MJ96|Q5TDF5|Q71RA8|Q9BSM0	Silent	SNP	ENST00000343304.6	hg19	CCDS533.1																																																																																			.	.		0.577	LRRC41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021438.1	NM_006369		A	46746117	G	A	46746117	2	1	347	1	0	0	0	0	0	0	0	1	9008	1335	47	3		3	LRRC41	1	46746117	Silent	SNP	G	TCGA-UB-A7ME-01A-11D-A33K-10	19651823	46746117	202504504	3	48956										
KIAA0494	9813	hgsc.bcm.edu	37	chr1	47154101	47154101	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	tttctatcaggttgactctcTgggtaagattactgactgtc	9	8	3	3			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr1:47154101T>A	ENST00000371933.3	-	7	1887	c.911A>T	c.(910-912)cAg>cTg	p.Q304L	EFCAB14-AS1_ENST00000418985.1_RNA|EFCAB14-AS1_ENST00000442839.1_RNA|EFCAB14_ENST00000544071.1_Intron|EFCAB14_ENST00000484461.1_5'UTR	NM_014774.2	NP_055589.1	O75071	EFC14_HUMAN	EF-hand calcium binding domain 14	304							calcium ion binding (GO:0005509)										GTTGACTCTCTGGGTAAGATT	0.443																																					p.Q304L		Atlas-SNP	.											.	.	.	.	0			c.A911T						.						293	230	251					1																	47154101		2203	4300	6503	SO:0001583	missense	9813	exon7			ACTCTCTGGGTAA	AB007963	CCDS30706.1	1p33	2013-01-10	2012-11-29	2012-11-29	ENSG00000159658	ENSG00000159658		"EF-hand domain containing"	29051	protein-coding gene	gene with protein product			"KIAA0494"	KIAA0494		9455484	Standard	NM_014774		Approved		uc001cqk.4	O75071	OTTHUMG00000007992	ENST00000371933.3:c.911A>T	chr1.hg19:g.47154101T>A	ENSP00000361001:p.Gln304Leu	131.0	0.0		130.0	21.0	NM_014774	D3DQ23|Q5SXB8	Missense_Mutation	SNP	ENST00000371933.3	hg19	CCDS30706.1	.	.	.	.	.	.	.	.	.	.	T	15.22	2.769092	0.49680	.	.	ENSG00000159658	ENST00000371933	D	0.94280	-3.39	5.3	5.3	0.74995	.	0.055882	0.64402	D	0.000001	D	0.89832	0.6829	L	0.55481	1.735	0.80722	D	1	P	0.35272	0.493	B	0.33042	0.157	D	0.89126	0.3506	10	0.72032	D	0.01	-5.2602	8.1634	0.31211	0.0:0.1332:0.0:0.8668	.	304	O75071	K0494_HUMAN	L	304	ENSP00000361001:Q304L	ENSP00000361001:Q304L	Q	-	2	0	KIAA0494	46926688	0.849000	0.29639	1.000000	0.80357	0.990000	0.78478	0.234000	0.17930	2.231000	0.72958	0.459000	0.35465	CAG	.	.		0.443	EFCAB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021931.1	NM_014774		A	47154101	T	A	47154101	3	1	347	1	0	0	0	0	1	0	0	0	8188	1580	55	4	596	4	KIAA0494	1	47154101	Missense_Mutation	SNP	T	TCGA-UB-A7ME-01A-11D-A33K-10	407984	47154101	202096520	4	48957										
GFI1	2672	hgsc.bcm.edu	37	chr1	92946582	92946582	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	ccaggccgctccatgagtacGgtttgaaaggcagggggaag	16	9	0	2			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr1:92946582G>A	ENST00000370332.1	-	4	680	c.362C>T	c.(361-363)cCg>cTg	p.P121L	GFI1_ENST00000294702.5_Missense_Mutation_p.P121L|GFI1_ENST00000427103.1_Missense_Mutation_p.P121L|GFI1_ENST00000483490.1_5'Flank	NM_001127215.1	NP_001120687.1	Q99684	GFI1_HUMAN	growth factor independent 1 transcription repressor	121					auditory receptor cell differentiation (GO:0042491)|cell fate commitment (GO:0045165)|cellular response to lipopolysaccharide (GO:0071222)|inner ear morphogenesis (GO:0042472)|mechanosensory behavior (GO:0007638)|negative regulation of calcidiol 1-monooxygenase activity (GO:0010956)|negative regulation of cell fate specification (GO:0009996)|negative regulation of neuron projection development (GO:0010977)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vitamin D biosynthetic process (GO:0010957)|positive regulation of cell fate specification (GO:0042660)|positive regulation of interleukin-6-mediated signaling pathway (GO:0070105)|regulation of toll-like receptor signaling pathway (GO:0034121)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|viral process (GO:0016032)	nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.P121L(1)		autonomic_ganglia(1)|endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	15		all_lung(203;0.00292)|Lung NSC(277;0.0115)|all_neural(321;0.185)|Glioma(108;0.203)		OV - Ovarian serous cystadenocarcinoma(397;9.04e-07)|Epithelial(280;1.17e-05)|all cancers(265;5.61e-05)|GBM - Glioblastoma multiforme(16;0.0191)		CCATGAGTACGGTTTGAAAGG	0.662																																					p.P121L		Atlas-SNP	.											GFI1,mouth,carcinoma,0,1	GFI1	41	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.C362T						.						23	24	24					1																	92946582		2203	4300	6503	SO:0001583	missense	2672	exon4			GAGTACGGTTTGA	U67369	CCDS30773.1	1p22	2014-09-17	2007-10-04		ENSG00000162676	ENSG00000162676		"Zinc fingers, C2H2-type"	4237	protein-coding gene	gene with protein product		600871	"growth factor independent 1"	ZNF163		7789186	Standard	NM_005263		Approved	GFI1A, GFI-1	uc001dov.4	Q99684	OTTHUMG00000010897	ENST00000370332.1:c.362C>T	chr1.hg19:g.92946582G>A	ENSP00000359357:p.Pro121Leu	164.0	0.0		152.0	29.0	NM_005263	Q8N564	Missense_Mutation	SNP	ENST00000370332.1	hg19	CCDS30773.1	.	.	.	.	.	.	.	.	.	.	g	24.5	4.543632	0.86022	.	.	ENSG00000162676	ENST00000370332;ENST00000427103;ENST00000294702	T;T;T	0.18016	2.24;2.24;2.24	4.37	2.44	0.29823	.	0.183997	0.48767	D	0.000168	T	0.09512	0.0234	M	0.68952	2.095	0.80722	D	1	P	0.51240	0.943	B	0.38194	0.267	T	0.09292	-1.0681	10	0.59425	D	0.04	-14.4336	13.2094	0.59815	0.0:0.0:0.7104:0.2896	.	121	Q99684	GFI1_HUMAN	L	121	ENSP00000359357:P121L;ENSP00000399719:P121L;ENSP00000294702:P121L	ENSP00000294702:P121L	P	-	2	0	GFI1	92719170	1.000000	0.71417	0.881000	0.34555	0.961000	0.63080	6.102000	0.71486	0.564000	0.29238	0.556000	0.70494	CCG	.	.		0.662	GFI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030054.1	NM_005263		A	92946582	G	A	92946582	3	1	347	1	0	0	0	0	1	0	0	0	6347	1116	39	1	922	1	GFI1	1	92946582	Missense_Mutation	SNP	G	TCGA-UB-A7ME-01A-11D-A33K-10	45792481	92946582	156304039	5	48958										
ARNT	405	hgsc.bcm.edu	37	chr1	150788840	150788840	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	aacatctgtcctgcagaagcTgatggctggacaatggttac	11	9	1	2			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr1:150788840T>A	ENST00000358595.5	-	19	2045	c.1845A>T	c.(1843-1845)tcA>tcT	p.S615S	ARNT_ENST00000515192.1_Silent_p.S601S|ARNT_ENST00000354396.2_Silent_p.S613S|ARNT_ENST00000505755.1_Silent_p.S600S	NM_001197325.1|NM_001668.3|NM_178427.2	NP_001184254.1|NP_001659.1|NP_848514.1	P27540	ARNT_HUMAN	aryl hydrocarbon receptor nuclear translocator	615					cell differentiation (GO:0030154)|cellular response to hypoxia (GO:0071456)|embryonic placenta development (GO:0001892)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of glycolytic process (GO:0045821)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor activity (GO:0004874)|aryl hydrocarbon receptor binding (GO:0017162)|enhancer binding (GO:0035326)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|prostate(2)|skin(4)|stomach(1)	34	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.02)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211)			CTGCAGAAGCTGATGGCTGGA	0.502			T	ETV6	AML																																p.S615S		Atlas-SNP	.		Dom	yes		1	1q21	405	aryl hydrocarbon receptor nuclear translocator		L	.	ARNT	68	.	0			c.A1845T						.						69	71	70					1																	150788840		2203	4300	6503	SO:0001819	synonymous_variant	405	exon19			AGAAGCTGATGGC	AF001307	CCDS970.1, CCDS971.1, CCDS65641.1, CCDS65642.1	1q21	2013-05-21			ENSG00000143437	ENSG00000143437		"Basic helix-loop-helix proteins"	700	protein-coding gene	gene with protein product		126110					Standard	NM_001668		Approved	HIF-1beta, bHLHe2	uc001evr.2	P27540	OTTHUMG00000035011	ENST00000358595.5:c.1845A>T	chr1.hg19:g.150788840T>A		66.0	0.0		124.0	21.0	NM_001668	B2R9H1|C4AMA1|F8WAP6|Q59ED4|Q5QP39|Q8NDC7	Silent	SNP	ENST00000358595.5	hg19	CCDS970.1																																																																																			.	.		0.502	ARNT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084741.2			A	150788840	T	A	150788840	2	1	347	1	0	0	0	0	0	0	0	1	965	1567	55	4		4	ARNT	1	150788840	Silent	SNP	T	TCGA-UB-A7ME-01A-11D-A33K-10	57842258	150788840	98461781	6	48959										
FLG	2312	hgsc.bcm.edu	37	chr1	152278842	152278842	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	gattgttcctcattacgtgtTgttctgcttgcacttctgga	9	9	3	0			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr1:152278842T>A	ENST00000368799.1	-	3	8555	c.8520A>T	c.(8518-8520)acA>acT	p.T2840T	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2840	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CATTACGTGTTGTTCTGCTTG	0.562									Ichthyosis																												p.T2840T		Atlas-SNP	.											.	FLG	900	.	0			c.A8520T						.						323	481	428					1																	152278842		2162	4299	6461	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	ACGTGTTGTTCTG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.8520A>T	chr1.hg19:g.152278842T>A		187.0	0.0		350.0	80.0	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	hg19	CCDS30860.1																																																																																			.	.		0.562	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152278842	T	A	152278842	2	1	347	1	0	0	0	0	0	0	0	1	5930	1799	63	4		4	FLG	1	152278842	Silent	SNP	T	TCGA-UB-A7ME-01A-11D-A33K-10	1490002	152278842	96971779	7	48960										
SH3YL1	26751	hgsc.bcm.edu	37	chr2	234273	234273	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	attatcaccaagtctgatacCtaaagtgtagaaacccatgg	7	9	2	2			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr2:234273C>T	ENST00000405430.1	-	7	668		c.e7-1		SH3YL1_ENST00000415006.2_Splice_Site|SH3YL1_ENST00000468321.1_Splice_Site|SH3YL1_ENST00000403658.1_Splice_Site|SH3YL1_ENST00000403712.2_Splice_Site|SH3YL1_ENST00000403657.1_Splice_Site|SH3YL1_ENST00000356150.5_Splice_Site			Q96HL8	SH3Y1_HUMAN	SH3 and SYLF domain containing 1						phosphatidylinositol biosynthetic process (GO:0006661)|regulation of ruffle assembly (GO:1900027)	ruffle membrane (GO:0032587)	phosphatase binding (GO:0019902)|phosphatidylinositol binding (GO:0035091)			large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)	7	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.034)		all cancers(51;0.000647)|Epithelial(75;0.0043)|OV - Ovarian serous cystadenocarcinoma(76;0.00871)|GBM - Glioblastoma multiforme(21;0.148)		AGTCTGATACCTAAAGTGTAG	0.388																																					.		Atlas-SNP	.											.	SH3YL1	49	.	0			c.292-1G>A						.						76	74	75					2																	234273		1826	4078	5904	SO:0001630	splice_region_variant	26751	exon6			TGATACCTAAAGT		CCDS42646.1, CCDS42646.2, CCDS54332.1, CCDS62841.1	2p25.3	2013-10-18	2013-10-18		ENSG00000035115	ENSG00000035115			29546	protein-coding gene	gene with protein product			"SH3 domain containing, Ysc84-like 1 (S. cerevisiae)"			21624956	Standard	NM_001282687		Approved	Ray, DKFZP586F1318	uc002qvx.3	Q96HL8	OTTHUMG00000151359	ENST00000405430.1:c.292-1G>A	chr2.hg19:g.234273C>T		63.0	0.0		83.0	17.0	NM_001159597	A8K8E7|B7WNJ4|B7WPL6|Q8NEL2|Q9H5X4|Q9Y3V5	Splice_Site	SNP	ENST00000405430.1	hg19		.	.	.	.	.	.	.	.	.	.	C	10.45	1.354440	0.24512	.	.	ENSG00000035115	ENST00000415006;ENST00000403712;ENST00000403657;ENST00000405430;ENST00000356150;ENST00000403658;ENST00000451005;ENST00000431160;ENST00000454318	.	.	.	5.92	5.92	0.95590	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.809	0.78543	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SH3YL1	224273	1.000000	0.71417	0.991000	0.47740	0.048000	0.14542	7.318000	0.79029	2.804000	0.96469	0.557000	0.71058	.	.	.		0.388	SH3YL1-003	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322352.1	NM_015677	Intron	T	234273	C	T	234273	5	4	347	1	0	0	0	0	0	0	1	0	14278	695	24	3	761	3	SH3YL1	2	234273	Splice_Site	SNP	C	TCGA-UB-A7ME-01A-11D-A33K-10		234273	242965100	8	48961										
SMYD1	150572	hgsc.bcm.edu	37	chr2	88396229	88396229	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	agctgaagaagcagtactacTttgactgcacatgtgaacac	9	9	0	4			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr2:88396229T>A	ENST00000419482.2	+	6	899	c.814T>A	c.(814-816)Ttt>Att	p.F272I	SMYD1_ENST00000444564.2_Missense_Mutation_p.F259I|SMYD1_ENST00000438570.1_Intron	NM_198274.3	NP_938015.1	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	272	S-adenosyl-L-methionine binding. {ECO:0000250}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of myotube differentiation (GO:0010831)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			NS(1)|breast(4)|central_nervous_system(1)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	41						GCAGTACTACTTTGACTGCAC	0.498																																					p.F272I		Atlas-SNP	.											.	SMYD1	95	.	0			c.T814A						.						107	98	101					2																	88396229		2203	4300	6503	SO:0001583	missense	150572	exon6			TACTACTTTGACT	AF086123	CCDS33240.1	2p11.1	2011-07-01			ENSG00000115593	ENSG00000115593		"Zinc fingers, MYND-type", "Chromatin-modifying enzymes / K-methyltransferases"	20986	protein-coding gene	gene with protein product		606846				11923873	Standard	NM_198274		Approved	BOP, ZMYND22, KMT3D	uc002ssr.3	Q8NB12	OTTHUMG00000155045	ENST00000419482.2:c.814T>A	chr2.hg19:g.88396229T>A	ENSP00000393453:p.Phe272Ile	132.0	0.0		119.0	20.0	NM_198274	A0AV30|A6NE13	Missense_Mutation	SNP	ENST00000419482.2	hg19	CCDS33240.1	.	.	.	.	.	.	.	.	.	.	T	17.64	3.439165	0.63067	.	.	ENSG00000115593	ENST00000419482;ENST00000444564;ENST00000295833	T;T	0.81247	-1.47;-0.07	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	D	0.87366	0.6159	M	0.79475	2.455	0.80722	D	1	D	0.62365	0.991	P	0.56398	0.797	D	0.89151	0.3523	10	0.87932	D	0	-9.7348	15.002	0.71479	0.0:0.0:0.0:1.0	.	272	Q8NB12	SMYD1_HUMAN	I	272;259;93	ENSP00000393453:F272I;ENSP00000407888:F259I	ENSP00000295833:F93I	F	+	1	0	SMYD1	88177344	1.000000	0.71417	1.000000	0.80357	0.032000	0.12392	7.639000	0.83342	2.126000	0.65437	0.533000	0.62120	TTT	.	.		0.498	SMYD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338229.2	XM_097915		A	88396229	T	A	88396229	3	1	347	1	0	0	0	0	1	0	0	0	14836	1609	56	4	836	4	SMYD1	2	88396229	Missense_Mutation	SNP	T	TCGA-UB-A7ME-01A-11D-A33K-10	88161956	88396229	154803144	9	48962										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168103964	168103964	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	tgaggttaatcttccaaaagCccccaaaggcactgtaaaga	8	10	1	2			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr2:168103964C>A	ENST00000409195.1	+	9	6151	c.6062C>A	c.(6061-6063)gCc>gAc	p.A2021D	XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.A2021D|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.A1799D	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1846					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						CTTCCAAAAGCCCCCAAAGGC	0.408																																					p.A2021D		Atlas-SNP	.											.	XIRP2	914	.	0			c.C6062A						.						52	49	50					2																	168103964		1843	4084	5927	SO:0001583	missense	129446	exon9			CAAAAGCCCCCAA	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.6062C>A	chr2.hg19:g.168103964C>A	ENSP00000386840:p.Ala2021Asp	204.0	0.0		287.0	48.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	hg19	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	C	12.31	1.899282	0.33535	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.22539	1.95;1.95;1.95	5.64	2.8	0.32819	.	0.570193	0.18600	N	0.136500	T	0.39937	0.1097	M	0.67953	2.075	0.39365	D	0.965991	D;D;P	0.89917	1.0;1.0;0.928	D;D;P	0.91635	0.973;0.999;0.79	T	0.08659	-1.0711	10	0.29301	T	0.29	-0.7164	10.0376	0.42137	0.0:0.6677:0.2603:0.072	.	1846;1846;1799	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	D	2021;2021;1799	ENSP00000386840:A2021D;ENSP00000295237:A2021D;ENSP00000387255:A1799D	ENSP00000295237:A2021D	A	+	2	0	XIRP2	167812210	.	.	0.907000	0.35723	0.552000	0.35366	.	.	0.305000	0.22832	-0.283000	0.09986	GCC	.	.		0.408	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		A	168103964	C	A	168103964	3	1	347	1	0	0	0	0	1	0	0	0	17445	739	26	3	6092	3	XIRP2	2	168103964	Missense_Mutation	SNP	C	TCGA-UB-A7ME-01A-11D-A33K-10	79707735	168103964	75095409	10	48963										
FASTKD2	22868	hgsc.bcm.edu	37	chr2	207655393	207655393	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	tgcggcatttgaatgcaatgGgttttcatgtgatcttggtg	13	5	2	2			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr2:207655393G>T	ENST00000236980.6	+	11	2344	c.1996G>T	c.(1996-1998)Ggt>Tgt	p.G666C	FASTKD2_ENST00000403094.3_Missense_Mutation_p.G666C|FASTKD2_ENST00000402774.3_Missense_Mutation_p.G666C	NM_014929.3	NP_055744.2	Q9NYY8	FAKD2_HUMAN	FAST kinase domains 2	666	RAP. {ECO:0000255|PROSITE- ProRule:PRU00619}.				cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(2)	21				LUSC - Lung squamous cell carcinoma(261;0.0718)|Epithelial(149;0.119)|Lung(261;0.138)		GAATGCAATGGGTTTTCATGT	0.403																																					p.G666C		Atlas-SNP	.											.	FASTKD2	49	.	0			c.G1996T						.						148	150	149					2																	207655393		2203	4300	6503	SO:0001583	missense	22868	exon11			GCAATGGGTTTTC	BC001544	CCDS2371.1	2q33.3	2008-02-05	2006-07-07	2006-07-07	ENSG00000118246	ENSG00000118246			29160	protein-coding gene	gene with protein product		612322	"KIAA0971"	KIAA0971			Standard	NM_014929		Approved		uc002vbx.3	Q9NYY8	OTTHUMG00000132917	ENST00000236980.6:c.1996G>T	chr2.hg19:g.207655393G>T	ENSP00000236980:p.Gly666Cys	53.0	0.0		65.0	13.0	NM_001136193	Q9NVX6|Q9Y2H7	Missense_Mutation	SNP	ENST00000236980.6	hg19	CCDS2371.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.179008	0.78564	.	.	ENSG00000118246	ENST00000236980;ENST00000402774;ENST00000403094	D;D;D	0.88277	-2.36;-2.36;-2.36	5.96	5.96	0.96718	RAP domain (3);	0.000000	0.85682	D	0.000000	D	0.94896	0.8350	M	0.83118	2.625	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95008	0.8149	10	0.87932	D	0	-7.0316	17.3387	0.87289	0.0:0.0:1.0:0.0	.	666	Q9NYY8	FAKD2_HUMAN	C	666	ENSP00000236980:G666C;ENSP00000385990:G666C;ENSP00000384929:G666C	ENSP00000236980:G666C	G	+	1	0	FASTKD2	207363638	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.598000	0.67585	2.832000	0.97577	0.655000	0.94253	GGT	.	.		0.403	FASTKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256428.2	NM_014929		T	207655393	G	T	207655393	3	4	347	1	0	0	0	0	1	0	0	0	5694	1232	43	3	2034	3	FASTKD2	2	207655393	Missense_Mutation	SNP	G	TCGA-UB-A7ME-01A-11D-A33K-10	39551429	207655393	35543980	11	48964										
CXCR2	3579	hgsc.bcm.edu	37	chr2	218999787	218999787	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	cgtcactgatgtctacctgcTgaacctagccttggccgacc	9	15	2	2			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr2:218999787T>A	ENST00000318507.2	+	3	690	c.263T>A	c.(262-264)cTg>cAg	p.L88Q		NM_001557.3	NP_001548.1	P25025	CXCR2_HUMAN	chemokine (C-X-C motif) receptor 2	88					cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|inflammatory response (GO:0006954)|interleukin-8-mediated signaling pathway (GO:0038112)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	C-X-C chemokine receptor activity (GO:0016494)|interleukin-8 binding (GO:0019959)|interleukin-8 receptor activity (GO:0004918)|signal transducer activity (GO:0004871)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(11)|skin(1)|stomach(1)	22						GTCTACCTGCTGAACCTAGCC	0.567																																					p.L88Q		Atlas-SNP	.											.	CXCR2	54	.	0			c.T263A						.						145	137	139					2																	218999787		2203	4300	6503	SO:0001583	missense	3579	exon4			ACCTGCTGAACCT	U11869	CCDS2408.1	2q35	2012-08-08	2009-11-25	2009-11-25	ENSG00000180871	ENSG00000180871		"CD molecules", "GPCR / Class A : Chemokine receptors : C-X-C motif", "Interleukins and interleukin receptors"	6027	protein-coding gene	gene with protein product		146928	"interleukin 8 receptor, beta"	IL8RB		1427896	Standard	NM_001557		Approved	CMKAR2, CD182	uc002vha.2	P25025	OTTHUMG00000133107	ENST00000318507.2:c.263T>A	chr2.hg19:g.218999787T>A	ENSP00000319635:p.Leu88Gln	188.0	0.0		190.0	76.0	NM_001168298	Q8IUZ1|Q9P2T6|Q9P2T7	Missense_Mutation	SNP	ENST00000318507.2	hg19	CCDS2408.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.451960	0.84209	.	.	ENSG00000180871	ENST00000453237;ENST00000415392;ENST00000318507;ENST00000454148;ENST00000428565	T;T;T;T;T	0.74632	-0.86;-0.86;-0.86;-0.86;-0.86	5.19	5.19	0.71726	GPCR, rhodopsin-like superfamily (1);	0.341780	0.28209	N	0.016190	D	0.91358	0.7274	H	0.98646	4.29	0.45867	D	0.998725	D	0.76494	0.999	D	0.79108	0.992	D	0.94399	0.7621	10	0.87932	D	0	.	14.368	0.66820	0.0:0.0:0.0:1.0	.	88	P25025	CXCR2_HUMAN	Q	88	ENSP00000413686:L88Q;ENSP00000392348:L88Q;ENSP00000319635:L88Q;ENSP00000415148:L88Q;ENSP00000392698:L88Q	ENSP00000319635:L88Q	L	+	2	0	CXCR2	218708032	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	7.862000	0.87013	2.099000	0.63709	0.454000	0.30748	CTG	.	.		0.567	CXCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256772.2	NM_001557		A	218999787	T	A	218999787	3	1	347	1	0	0	0	0	1	0	0	0	4093	1580	55	4	265	4	CXCR2	2	218999787	Missense_Mutation	SNP	T	TCGA-UB-A7ME-01A-11D-A33K-10	11344394	218999787	24199586	12	48965										
ARPC2	10109	hgsc.bcm.edu	37	chr2	219110174	219110174	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	aggacgcagagccagccacaCagccccacaggtcctcttta	9	16	1	1			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr2:219110174C>T	ENST00000295685.10	+	7	842	c.581C>T	c.(580-582)aCa>aTa	p.T194I	ARPC2_ENST00000315717.5_Missense_Mutation_p.T194I|ARPC2_ENST00000477992.1_3'UTR	NM_005731.2	NP_005722.1	O15144	ARPC2_HUMAN	actin related protein 2/3 complex, subunit 2, 34kDa	194					Arp2/3 complex-mediated actin nucleation (GO:0034314)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural constituent of cytoskeleton (GO:0005200)			cervix(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)	6		Renal(207;0.0474)		Epithelial(149;1.21e-06)|all cancers(144;0.000212)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0103)		GCCAGCCACACAGCCCCACAG	0.522																																					p.T194I		Atlas-SNP	.											ARPC2,NS,carcinoma,0,1	ARPC2	25	.	0			c.C581T						.						95	99	98					2																	219110174		2203	4300	6503	SO:0001583	missense	10109	exon7			GCCACACAGCCCC	AF006085	CCDS2410.1	2q36.1	2011-07-06	2002-08-29		ENSG00000163466	ENSG00000163466		"Actin related protein 2/3 complex subunits"	705	protein-coding gene	gene with protein product		604224	"actin related protein 2/3 complex, subunit 2 (34 kD)"			9359840, 9230079	Standard	NM_005731		Approved	p34-Arc, ARC34	uc002vhd.4	O15144	OTTHUMG00000133618	ENST00000295685.10:c.581C>T	chr2.hg19:g.219110174C>T	ENSP00000295685:p.Thr194Ile	74.0	0.0		83.0	4.0	NM_005731	Q92801|Q9P1D4	Missense_Mutation	SNP	ENST00000295685.10	hg19	CCDS2410.1	.	.	.	.	.	.	.	.	.	.	C	33	5.264254	0.95399	.	.	ENSG00000163466	ENST00000315717;ENST00000295685;ENST00000456575	.	.	.	5.65	5.65	0.86999	.	0.091853	0.85682	D	0.000000	D	0.82912	0.5140	M	0.90542	3.125	0.80722	D	1	P	0.47762	0.9	P	0.54060	0.741	D	0.85537	0.1213	9	0.87932	D	0	.	19.9142	0.97043	0.0:1.0:0.0:0.0	.	194	O15144	ARPC2_HUMAN	I	194;194;9	.	ENSP00000295685:T194I	T	+	2	0	ARPC2	218818419	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.651000	0.83577	2.941000	0.99782	0.655000	0.94253	ACA	.	.		0.522	ARPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256777.2	NM_005731		T	219110174	C	T	219110174	3	4	347	1	0	0	0	0	1	0	0	0	971	478	17	3	607	3	ARPC2	2	219110174	Missense_Mutation	SNP	C	TCGA-UB-A7ME-01A-11D-A33K-10	110387	219110174	24089199	13	48966										
CYP8B1	1582	hgsc.bcm.edu	37	chr3	42916188	42916188	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	tgtctccatggcggaacagaTactcctgcccactggacatc	9	14	1	1			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr3:42916188T>C	ENST00000316161.4	-	1	1445	c.1121A>G	c.(1120-1122)tAt>tGt	p.Y374C	RP11-141M3.5_ENST00000471537.1_RNA|CYP8B1_ENST00000437102.1_Missense_Mutation_p.Y374C|KRBOX1_ENST00000426937.1_Intron	NM_004391.2	NP_004382.2	Q9UNU6	CP8B1_HUMAN	cytochrome P450, family 8, subfamily B, polypeptide 1	374					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	7alpha-hydroxycholest-4-en-3-one 12alpha-hydroxylase activity (GO:0033778)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|sterol 12-alpha-hydroxylase activity (GO:0008397)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(2)|prostate(2)|skin(5)	23				KIRC - Kidney renal clear cell carcinoma(284;0.213)|Kidney(284;0.249)		GCGGAACAGATACTCCTGCCC	0.587																																					p.Y374C		Atlas-SNP	.											.	CYP8B1	59	.	0			c.A1121G						.						90	88	89					3																	42916188		2203	4300	6503	SO:0001583	missense	1582	exon1			AACAGATACTCCT	AF090318	CCDS2707.1	3p22.1	2004-02-27	2003-01-14		ENSG00000180432	ENSG00000180432		"Cytochrome P450s"	2653	protein-coding gene	gene with protein product		602172	"cytochrome P450, subfamily VIIIB (sterol 12-alpha-hydroxylase), polypeptide 1"			10051404	Standard	NM_004391		Approved	CYP12	uc003cmh.3	Q9UNU6	OTTHUMG00000133047	ENST00000316161.4:c.1121A>G	chr3.hg19:g.42916188T>C	ENSP00000318867:p.Tyr374Cys	127.0	0.0		144.0	16.0	NM_004391	B2RCY3|O75958|Q6NWT2|Q6NWT3	Missense_Mutation	SNP	ENST00000316161.4	hg19	CCDS2707.1	.	.	.	.	.	.	.	.	.	.	T	9.804	1.181220	0.21787	.	.	ENSG00000180432	ENST00000437102;ENST00000316161	T;T	0.73469	-0.75;-0.75	4.5	0.549	0.17213	.	0.081309	0.51477	N	0.000089	T	0.73644	0.3613	L	0.59967	1.855	0.37161	D	0.902615	P;P	0.48089	0.905;0.905	P;P	0.53861	0.736;0.736	T	0.71866	-0.4463	10	0.59425	D	0.04	-8.3428	4.4697	0.11706	0.4442:0.086:0.0:0.4698	.	374;374	C9JFR9;Q9UNU6	.;CP8B1_HUMAN	C	374	ENSP00000404499:Y374C;ENSP00000318867:Y374C	ENSP00000318867:Y374C	Y	-	2	0	CYP8B1	42891192	0.989000	0.36119	0.010000	0.14722	0.063000	0.16089	1.971000	0.40530	-0.059000	0.13154	0.459000	0.35465	TAT	.	.		0.587	CYP8B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256653.1	NM_004391		C	42916188	T	C	42916188	3	2	347	1	0	0	0	0	1	0	0	0	4200	1406	49	2	388	2	CYP8B1	3	42916188	Missense_Mutation	SNP	T	TCGA-UB-A7ME-01A-11D-A33K-10		42916188	155106242	14	48967										
CCDC80	151887	hgsc.bcm.edu	37	chr3	112357309	112357309	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	tgctggcttgggaggacctgGcaccacatttgggtctcggt	15	10	1	0			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr3:112357309G>A	ENST00000206423.3	-	2	2397	c.1444C>T	c.(1444-1446)Cca>Tca	p.P482S	CCDC80_ENST00000439685.2_Missense_Mutation_p.P482S|CCDC80_ENST00000475181.1_5'Flank	NM_199511.1|NM_199512.1	NP_955805.1|NP_955806.1	Q76M96	CCD80_HUMAN	coiled-coil domain containing 80	482					extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(21)|ovary(3)|pancreas(2)|prostate(4)	51						GGAGGACCTGGCACCACATTT	0.567																																					p.P482S		Atlas-SNP	.											.	CCDC80	100	.	0			c.C1444T						.						67	69	68					3																	112357309		2203	4300	6503	SO:0001583	missense	151887	exon2			GACCTGGCACCAC	AY333429	CCDS2968.1	3q13.2	2010-12-24			ENSG00000091986	ENSG00000091986			30649	protein-coding gene	gene with protein product	"steroid sensitive gene 1"	608298				15325258, 18178152	Standard	XM_005247135		Approved	URB, SSG1, DRO1	uc003dzf.3	Q76M96	OTTHUMG00000159265	ENST00000206423.3:c.1444C>T	chr3.hg19:g.112357309G>A	ENSP00000206423:p.Pro482Ser	67.0	0.0		66.0	22.0	NM_199511	D3DN67|Q5PR20|Q6GPG9|Q8IVT6|Q8NBV1|Q8NHY8	Missense_Mutation	SNP	ENST00000206423.3	hg19	CCDS2968.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.193645	0.78902	.	.	ENSG00000091986	ENST00000206423;ENST00000439685;ENST00000444594	T;T	0.44482	0.92;0.92	5.68	5.68	0.88126	.	0.109608	0.64402	D	0.000005	T	0.35653	0.0939	L	0.34521	1.04	0.58432	D	0.999999	P;P;B	0.43169	0.728;0.8;0.352	B;B;B	0.41271	0.324;0.352;0.173	T	0.13522	-1.0506	10	0.49607	T	0.09	-8.7126	14.0057	0.64461	0.0723:0.0:0.9277:0.0	.	493;482;482	Q76M96-2;A3KC71;Q76M96	.;.;CCD80_HUMAN	S	482;482;110	ENSP00000206423:P482S;ENSP00000411814:P482S	ENSP00000206423:P482S	P	-	1	0	CCDC80	113839999	1.000000	0.71417	0.973000	0.42090	0.995000	0.86356	3.261000	0.51530	2.684000	0.91462	0.555000	0.69702	CCA	.	.		0.567	CCDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354219.1	NM_199511		A	112357309	G	A	112357309	3	1	347	1	0	0	0	0	1	0	0	0	2856	1203	42	3	1436	3	CCDC80	3	112357309	Missense_Mutation	SNP	G	TCGA-UB-A7ME-01A-11D-A33K-10	69441121	112357309	85665121	15	48968										
GRK7	131890	hgsc.bcm.edu	37	chr3	141535712	141535712	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	gatttctctgaggttcggggGgtggaatttgatgacaaaga	15	4	1	4			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr3:141535712G>T	ENST00000264952.2	+	4	1619	c.1482G>T	c.(1480-1482)ggG>ggT	p.G494G		NM_139209.2	NP_631948.1	Q8WTQ7	GRK7_HUMAN	G protein-coupled receptor kinase 7	494	AGC-kinase C-terminal.				protein autophosphorylation (GO:0046777)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual perception (GO:0007601)	membrane (GO:0016020)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|rhodopsin kinase activity (GO:0050254)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	26						AGGTTCGGGGGGTGGAATTTG	0.453																																					p.G494G		Atlas-SNP	.											.	GRK7	65	.	0			c.G1482T						.						150	148	148					3																	141535712		2203	4300	6503	SO:0001819	synonymous_variant	131890	exon4			TCGGGGGGTGGAA		CCDS3120.1	3q24	2004-02-04	2004-02-04	2004-02-04	ENSG00000114124	ENSG00000114124			17031	protein-coding gene	gene with protein product		606987		GPRK7		11717351, 11754336	Standard	NM_139209		Approved		uc011bnd.2	Q8WTQ7	OTTHUMG00000159068	ENST00000264952.2:c.1482G>T	chr3.hg19:g.141535712G>T		98.0	0.0		101.0	22.0	NM_139209		Silent	SNP	ENST00000264952.2	hg19	CCDS3120.1																																																																																			.	.		0.453	GRK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353168.1	NM_139209		T	141535712	G	T	141535712	2	4	347	1	0	0	0	0	0	0	0	1	6803	1219	43	3		3	GRK7	3	141535712	Silent	SNP	G	TCGA-UB-A7ME-01A-11D-A33K-10	29178403	141535712	56486718	16	48969										
MED28	80306	hgsc.bcm.edu	37	chr4	17625401	17625401	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	aggcatctgccaacatccctGcacctctgaagccaacgtga	8	15	2	2			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr4:17625401G>T	ENST00000237380.7	+	4	541	c.517G>T	c.(517-519)Gca>Tca	p.A173S		NM_025205.3	NP_079481.2	Q9H204	MED28_HUMAN	mediator complex subunit 28	173					negative regulation of smooth muscle cell differentiation (GO:0051151)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	cortical actin cytoskeleton (GO:0030864)|mediator complex (GO:0016592)|membrane (GO:0016020)				lung(6)|skin(2)	8						CAACATCCCTGCACCTCTGAA	0.582																																					p.A173S		Atlas-SNP	.											.	MED28	16	.	0			c.G517T						.						37	28	31					4																	17625401		2203	4300	6503	SO:0001583	missense	80306	exon4			ATCCCTGCACCTC	AF317678	CCDS33963.1	4p16	2007-07-30	2007-07-30		ENSG00000118579	ENSG00000118579			24628	protein-coding gene	gene with protein product		610311	"mediator of RNA polymerase II transcription, subunit 28 homolog (S. cerevisiae)"			11779215, 15467741	Standard	NM_025205		Approved	EG1, DKFZP434N185, magicin	uc003gpi.1	Q9H204	OTTHUMG00000161980	ENST00000237380.7:c.517G>T	chr4.hg19:g.17625401G>T	ENSP00000237380:p.Ala173Ser	265.0	0.0		171.0	57.0	NM_025205	Q9BZJ5	Missense_Mutation	SNP	ENST00000237380.7	hg19	CCDS33963.1	.	.	.	.	.	.	.	.	.	.	G	28.6	4.933400	0.92458	.	.	ENSG00000118579	ENST00000237380;ENST00000503945	.	.	.	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.74966	0.3786	L	0.44542	1.39	0.80722	D	1	D	0.69078	0.997	D	0.80764	0.994	T	0.76085	-0.3088	9	0.72032	D	0.01	-0.7114	19.7742	0.96385	0.0:0.0:1.0:0.0	.	173	Q9H204	MED28_HUMAN	S	173;170	.	ENSP00000237380:A173S	A	+	1	0	MED28	17234499	1.000000	0.71417	0.987000	0.45799	0.859000	0.49053	9.472000	0.97709	2.663000	0.90544	0.558000	0.71614	GCA	.	.		0.582	MED28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360055.3	NM_025205		T	17625401	G	T	17625401	3	4	347	1	0	0	0	0	1	0	0	0	9455	1319	46	3	531	3	MED28	4	17625401	Missense_Mutation	SNP	G	TCGA-UB-A7ME-01A-11D-A33K-10		17625401	173528875	17	48970										
KIAA1211	57482	hgsc.bcm.edu	37	chr4	57179476	57179476	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	gctcgcctggacaacagtgcCgccaagcacaagctggctgt	12	14	0	0	rs372203605		TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr4:57179476C>A	ENST00000504228.1	+	5	573	c.468C>A	c.(466-468)gcC>gcA	p.A156A	KIAA1211_ENST00000264229.6_Silent_p.A156A|KIAA1211_ENST00000541073.1_Silent_p.A149A			Q6ZU35	K1211_HUMAN	KIAA1211	156										endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					ACAACAGTGCCGCCAAGCACA	0.567													C|||	1	0.000199681	8e-04	0	5008	,	,		19920	0		0	False		,,,				2504	0				p.A156A		Atlas-SNP	.											.	KIAA1211	178	.	0			c.C468A						.	C		1,4093		0,1,2046	111	120	117		468	-5.1	0.9	4		117	0,8378		0,0,4189	no	coding-synonymous	KIAA1211	NM_020722.1		0,1,6235	AA,AC,CC		0.0,0.0244,0.0080		156/1234	57179476	1,12471	2047	4189	6236	SO:0001819	synonymous_variant	57482	exon7			CAGTGCCGCCAAG	AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.468C>A	chr4.hg19:g.57179476C>A		84.0	0.0		71.0	15.0	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Silent	SNP	ENST00000504228.1	hg19	CCDS43230.1																																																																																			.	.		0.567	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722		A	57179476	C	A	57179476	2	1	347	1	0	0	0	0	0	0	0	1	8224	639	23	1		1	KIAA1211	4	57179476	Silent	SNP	C	TCGA-UB-A7ME-01A-11D-A33K-10	39554075	57179476	133974800	18	48971										
AASDH	132949	hgsc.bcm.edu	37	chr4	57219583	57219583	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	actttaccgtgggatgtaaaTggtagagagtcgatcaatac	11	6	1	1			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr4:57219583T>C	ENST00000205214.6	-	9	1743	c.1563A>G	c.(1561-1563)ccA>ccG	p.P521P	AASDH_ENST00000502617.1_Silent_p.P521P|AASDH_ENST00000451613.1_Silent_p.P521P|AASDH_ENST00000513376.1_Silent_p.P421P|AASDH_ENST00000434343.2_Silent_p.P36P|AASDH_ENST00000510762.1_5'Flank|AASDH_ENST00000602986.1_Silent_p.P368P	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	521					fatty acid metabolic process (GO:0006631)		acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)			endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	40	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)				GGGATGTAAATGGTAGAGAGT	0.323																																					p.P521P		Atlas-SNP	.											.	AASDH	101	.	0			c.A1563G						.						73	72	72					4																	57219583		2203	4300	6503	SO:0001819	synonymous_variant	132949	exon9			TGTAAATGGTAGA	AF516672	CCDS3504.1, CCDS68705.1, CCDS68706.1, CCDS75126.1, CCDS75127.1	4q12	2010-12-14			ENSG00000157426	ENSG00000157426	1.2.1.31	"Acyl-CoA synthetase family"	23993	protein-coding gene	gene with protein product	"acyl-CoA synthetase family member 4"	614365				15865210, 12712191, 17762044	Standard	XM_005265721		Approved	NRPS998, LYS2, ACSF4	uc003hbn.3	Q4L235	OTTHUMG00000128841	ENST00000205214.6:c.1563A>G	chr4.hg19:g.57219583T>C		104.0	0.0		66.0	16.0	NM_181806	A5D8V3|A5PL22|Q63HK2|Q63HR7|Q6IPP8|Q6TFZ6|Q7Z5Y3|Q96BW4|Q9P064	Silent	SNP	ENST00000205214.6	hg19	CCDS3504.1																																																																																			.	.		0.323	AASDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250780.1	NM_181806		C	57219583	T	C	57219583	2	2	347	1	0	0	0	0	0	0	0	1	22	1451	51	2		2	AASDH	4	57219583	Silent	SNP	T	TCGA-UB-A7ME-01A-11D-A33K-10	40107	57219583	133934693	19	48972										
RUFY3	22902	hgsc.bcm.edu	37	chr4	71656987	71656987	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	aagaccttaaatagtgcagcAaataaactgatcccaaaaca	5	9	0	2			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr4:71656987A>T	ENST00000226328.4	+	13	1946	c.1383A>T	c.(1381-1383)gcA>gcT	p.A461A	RUFY3_ENST00000536664.1_Silent_p.A445A|RUFY3_ENST00000502653.1_Intron|RUFY3_ENST00000381006.3_Intron	NM_014961.3	NP_055776.1	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3	461					negative regulation of axonogenesis (GO:0050771)	filopodium (GO:0030175)|growth cone (GO:0030426)				endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	16		all_hematologic(202;0.248)	Lung(101;0.235)			ATAGTGCAGCAAATAAACTGA	0.328																																					p.A461A		Atlas-SNP	.											.	RUFY3	61	.	0			c.A1383T						.						123	115	118					4																	71656987		2203	4300	6503	SO:0001819	synonymous_variant	22902	exon13			TGCAGCAAATAAA	AF112221	CCDS3547.1, CCDS34001.1, CCDS47068.1, CCDS75138.1	4q13.3	2009-05-29			ENSG00000018189	ENSG00000018189		"Zinc fingers, FYVE domain containing"	30285	protein-coding gene	gene with protein product	"single axon-related 1"	611194				17439943	Standard	NM_001130709		Approved	RIPx, KIAA0871, Singar1	uc003hfr.3	Q7L099	OTTHUMG00000129910	ENST00000226328.4:c.1383A>T	chr4.hg19:g.71656987A>T		580.0	1.0		501.0	108.0	NM_014961	B3KM25|B4DYW7|D9N163|O94948|Q9UI00	Silent	SNP	ENST00000226328.4	hg19	CCDS3547.1																																																																																			.	.		0.328	RUFY3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252161.2	NM_014961		T	71656987	A	T	71656987	2	4	347	1	0	0	0	0	0	0	0	1	13755	117	5	4		4	RUFY3	4	71656987	Silent	SNP	A	TCGA-UB-A7ME-01A-11D-A33K-10	14437404	71656987	119497289	20	48973										
CENPE	1062	hgsc.bcm.edu	37	chr4	104084644	104084644	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	atgaatgctcacctcaagatCttgattatatacttctgcat	5	9	4	3			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr4:104084644C>A	ENST00000265148.3	-	17	1803	c.1714G>T	c.(1714-1716)Gat>Tat	p.D572Y	CENPE_ENST00000380026.3_Intron	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	572					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)			NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		ACCTCAAGATCTTGATTATAT	0.323																																					p.D572Y		Atlas-SNP	.											.	CENPE	253	.	0			c.G1714T						.						73	67	69					4																	104084644		2202	4296	6498	SO:0001583	missense	1062	exon17			CAAGATCTTGATT	Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"Kinesins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1856	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 61"	117143	"centromere protein E (312kD)"			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.1714G>T	chr4.hg19:g.104084644C>A	ENSP00000265148:p.Asp572Tyr	319.0	0.0		327.0	78.0	NM_001813	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	hg19	CCDS34042.1	.	.	.	.	.	.	.	.	.	.	C	16.49	3.137966	0.56936	.	.	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000503705	T;T	0.56103	0.48;0.48	4.98	4.98	0.66077	.	.	.	.	.	T	0.60090	0.2242	L	0.29908	0.895	0.33721	D	0.616939	D	0.89917	1.0	D	0.78314	0.991	T	0.68561	-0.5376	9	0.72032	D	0.01	.	12.1827	0.54221	0.0:0.9221:0.0:0.0779	.	572	Q02224	CENPE_HUMAN	Y	572	ENSP00000265148:D572Y;ENSP00000423981:D572Y	ENSP00000265148:D572Y	D	-	1	0	CENPE	104304093	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.157000	0.50716	2.755000	0.94549	0.555000	0.69702	GAT	.	.		0.323	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	104084644	C	A	104084644	3	1	347	1	0	0	0	0	1	0	0	0	3232	913	32	3	6523	3	CENPE	4	104084644	Missense_Mutation	SNP	C	TCGA-UB-A7ME-01A-11D-A33K-10	32427657	104084644	87069632	21	48974										
BBS12	166379	hgsc.bcm.edu	37	chr4	123664496	123664496	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	agccctttggatgttgtagaTaggaacaacagaatcgcaat	10	7	0	2			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr4:123664496T>C	ENST00000314218.3	+	2	1642	c.1449T>C	c.(1447-1449)gaT>gaC	p.D483D	BBS12_ENST00000542236.1_Silent_p.D483D	NM_152618.2	NP_689831.2	Q6ZW61	BBS12_HUMAN	Bardet-Biedl syndrome 12	483					cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|eating behavior (GO:0042755)|intraciliary transport (GO:0042073)|negative regulation of fat cell differentiation (GO:0045599)|photoreceptor cell maintenance (GO:0045494)	cilium (GO:0005929)	ATP binding (GO:0005524)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|prostate(4)	21						ATGTTGTAGATAGGAACAACA	0.453									Bardet-Biedl syndrome																												p.D483D		Atlas-SNP	.											.	BBS12	63	.	0			c.T1449C						.						79	77	77					4																	123664496		2203	4300	6503	SO:0001819	synonymous_variant	166379	exon3	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	TGTAGATAGGAAC	AK123553	CCDS3728.1	4q27	2014-06-17	2006-12-13	2006-12-13	ENSG00000181004	ENSG00000181004		"Heat Shock Proteins / Chaperonins"	26648	protein-coding gene	gene with protein product		610683	"chromosome 4 open reading frame 24"	C4orf24		17160889	Standard	NM_001178007		Approved	FLJ35630, FLJ41559	uc003ieu.3	Q6ZW61	OTTHUMG00000133070	ENST00000314218.3:c.1449T>C	chr4.hg19:g.123664496T>C		108.0	0.0		54.0	15.0	NM_001178007	D3DNX5|Q7Z342|Q7Z482|Q8NAB8	Silent	SNP	ENST00000314218.3	hg19	CCDS3728.1																																																																																			.	.		0.453	BBS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256710.1	NM_152618		C	123664496	T	C	123664496	2	2	347	1	0	0	0	0	0	0	0	1	1337	1403	49	2		2	BBS12	4	123664496	Silent	SNP	T	TCGA-UB-A7ME-01A-11D-A33K-10	19579852	123664496	67489780	22	48975										
SLC6A19	340024	hgsc.bcm.edu	37	chr5	1201802	1201802	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	tgcccaaccccggcctagacGcccggatcccgtccctggct	10	20	0	1	rs200291939		TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr5:1201802G>T	ENST00000304460.10	+	1	93	c.37G>T	c.(37-39)Gcc>Tcc	p.A13S		NM_001003841.2	NP_001003841.1	Q695T7	S6A19_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 19	13					amino acid transport (GO:0006865)|ion transport (GO:0006811)|response to nutrient (GO:0007584)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)|neutral amino acid transmembrane transporter activity (GO:0015175)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(25)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10)		Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			CGGCCTAGACGCCCGGATCCC	0.682																																					p.A13S		Atlas-SNP	.											.	SLC6A19	99	.	0			c.G37T						.						31	31	31					5																	1201802		2194	4299	6493	SO:0001583	missense	340024	exon1			CTAGACGCCCGGA	AK096054	CCDS34130.1	5p15	2013-07-19			ENSG00000174358	ENSG00000174358		"Solute carriers"	27960	protein-coding gene	gene with protein product	"Hartnup disease"	608893					Standard	NM_001003841		Approved		uc003jbw.4	Q695T7	OTTHUMG00000161636	ENST00000304460.10:c.37G>T	chr5.hg19:g.1201802G>T	ENSP00000305302:p.Ala13Ser	62.0	0.0		71.0	4.0	NM_001003841	A8K446	Missense_Mutation	SNP	ENST00000304460.10	hg19	CCDS34130.1	.	.	.	.	.	.	.	.	.	.	G	0.011	-1.697312	0.00725	.	.	ENSG00000174358	ENST00000304460	T	0.73681	-0.77	4.03	0.967	0.19674	.	0.600804	0.17869	N	0.159232	T	0.46328	0.1387	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.14587	-1.0467	10	0.10377	T	0.69	.	1.8582	0.03183	0.2512:0.1449:0.4561:0.1477	.	13	Q695T7	S6A19_HUMAN	S	13	ENSP00000305302:A13S	ENSP00000305302:A13S	A	+	1	0	SLC6A19	1254802	0.354000	0.24912	0.580000	0.28601	0.004000	0.04260	0.364000	0.20325	0.377000	0.24735	-1.446000	0.01064	GCC	.	G|0.999;A|0.001		0.682	SLC6A19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365557.1	XM_291120		T	1201802	G	T	1201802	3	4	347	1	0	0	0	0	1	0	0	0	14697	1087	38	1	39	1	SLC6A19	5	1201802	Missense_Mutation	SNP	G	TCGA-UB-A7ME-01A-11D-A33K-10		1201802	179713458	23	48976										
RIOK2	55781	hgsc.bcm.edu	37	chr5	96503531	96503531	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	cattttctgacccgtaaaccTctgctttttctgccacttct	4	14	4	1			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr5:96503531T>C	ENST00000283109.3	-	8	1105	c.1037A>G	c.(1036-1038)gAg>gGg	p.E346G	CTD-2215E18.1_ENST00000509481.1_Intron|RIOK2_ENST00000508447.1_Missense_Mutation_p.E346G	NM_018343.2	NP_060813.2	Q9BVS4	RIOK2_HUMAN	RIO kinase 2	346	Protein kinase.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|urinary_tract(2)	23		all_cancers(142;0.000125)|all_epithelial(76;8.48e-07)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0676)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0657)		CCCGTAAACCTCTGCTTTTTC	0.403																																					p.E346G		Atlas-SNP	.											.	RIOK2	82	.	0			c.A1037G						.						157	160	159					5																	96503531		2203	4300	6503	SO:0001583	missense	55781	exon8			TAAACCTCTGCTT	AK002021	CCDS4089.1, CCDS54884.1	5q14	2012-12-10	2012-12-10		ENSG00000058729	ENSG00000058729			18999	protein-coding gene	gene with protein product			"RIO kinase 2 (yeast)"				Standard	NM_018343		Approved	FLJ11159	uc003kmz.3	Q9BVS4	OTTHUMG00000128723	ENST00000283109.3:c.1037A>G	chr5.hg19:g.96503531T>C	ENSP00000283109:p.Glu346Gly	108.0	0.0		89.0	14.0	NM_001159749	D6RDI3|Q9NUT0	Missense_Mutation	SNP	ENST00000283109.3	hg19	CCDS4089.1	.	.	.	.	.	.	.	.	.	.	T	11.94	1.788397	0.31685	.	.	ENSG00000058729	ENST00000283109;ENST00000508447	T;T	0.19250	2.16;2.16	5.55	0.0328	0.14177	.	1.007380	0.07962	N	0.982614	T	0.10723	0.0262	N	0.08118	0	0.09310	N	1	B;B	0.17038	0.02;0.018	B;B	0.18263	0.016;0.021	T	0.38693	-0.9649	10	0.28530	T	0.3	-24.9149	8.4858	0.33071	0.0:0.0666:0.3751:0.5583	.	346;346	D6RDI3;Q9BVS4	.;RIOK2_HUMAN	G	346	ENSP00000283109:E346G;ENSP00000420932:E346G	ENSP00000283109:E346G	E	-	2	0	RIOK2	96529287	0.001000	0.12720	0.000000	0.03702	0.054000	0.15201	0.959000	0.29240	-0.210000	0.10140	0.477000	0.44152	GAG	.	.		0.403	RIOK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250628.1	NM_018343		C	96503531	T	C	96503531	3	2	347	1	0	0	0	0	1	0	0	0	13393	1551	54	2	661	2	RIOK2	5	96503531	Missense_Mutation	SNP	T	TCGA-UB-A7ME-01A-11D-A33K-10	95301729	96503531	84411729	24	48977										
PCDHB16	57717	hgsc.bcm.edu	37	chr5	140562737	140562737	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	gtgttggataaagagctggaTcgggaggaggagcctcaact	16	6	1	1			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr5:140562737T>A	ENST00000361016.2	+	1	1758	c.603T>A	c.(601-603)gaT>gaA	p.D201E		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	201	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AAGAGCTGGATCGGGAGGAGG	0.493																																					p.D201E		Atlas-SNP	.											.	PCDHB16	159	.	0			c.T603A						.						61	63	62					5																	140562737		2203	4300	6503	SO:0001583	missense	57717	exon1			GCTGGATCGGGAG	AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"Cadherins / Protocadherins : Clustered"	14546	other	protocadherin	"cadherin ME1", "protocadherin-3x", "PCDHbeta 16"	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325	ENST00000361016.2:c.603T>A	chr5.hg19:g.140562737T>A	ENSP00000354293:p.Asp201Glu	78.0	0.0		80.0	25.0	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	hg19	CCDS4251.1	.	.	.	.	.	.	.	.	.	.	T	19.16	3.774578	0.70107	.	.	ENSG00000196963	ENST00000361016	T	0.63255	-0.03	4.69	0.893	0.19236	Cadherin (4);Cadherin-like (1);	0.000000	0.35378	N	0.003248	D	0.85999	0.5828	H	0.99770	4.765	0.29178	N	0.876675	D	0.89917	1.0	D	0.97110	1.0	T	0.79650	-0.1715	10	0.87932	D	0	.	8.727	0.34476	0.0:0.3938:0.0:0.6062	.	201	Q9NRJ7	PCDBG_HUMAN	E	201	ENSP00000354293:D201E	ENSP00000354293:D201E	D	+	3	2	PCDHB16	140542921	0.000000	0.05858	0.996000	0.52242	0.775000	0.43874	-0.885000	0.04161	0.195000	0.20347	0.533000	0.62120	GAT	.	.		0.493	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957		A	140562737	T	A	140562737	3	1	347	1	0	0	0	0	1	0	0	0	11550	1432	50	4	605	4	PCDHB16	5	140562737	Missense_Mutation	SNP	T	TCGA-UB-A7ME-01A-11D-A33K-10	44059206	140562737	40352523	25	48978										
SH3TC2	79628	hgsc.bcm.edu	37	chr5	148388485	148388485	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	catagccttcgaggctaatcTgcagctctgtcagcttattg	9	11	3	0			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr5:148388485T>A	ENST00000515425.1	-	15	3508	c.3407A>T	c.(3406-3408)cAg>cTg	p.Q1136L	SH3TC2_ENST00000512049.1_Missense_Mutation_p.Q1129L|SH3TC2_ENST00000502274.1_5'Flank|SH3TC2_ENST00000538184.1_Missense_Mutation_p.Q683L	NM_024577.3	NP_078853.2	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	1136					cell death (GO:0008219)|peripheral nervous system myelin maintenance (GO:0032287)|regulation of ERBB signaling pathway (GO:1901184)|regulation of intracellular protein transport (GO:0033157)	cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAGGCTAATCTGCAGCTCTGT	0.532																																					p.Q1136L		Atlas-SNP	.											.	SH3TC2	178	.	0			c.A3407T						.						134	133	133					5																	148388485		2203	4300	6503	SO:0001583	missense	79628	exon15			CTAATCTGCAGCT	AK127248	CCDS4293.1	5q32	2014-09-17			ENSG00000169247	ENSG00000169247		"Tetratricopeptide (TTC) repeat domain containing"	29427	protein-coding gene	gene with protein product		608206				14574644	Standard	NM_024577		Approved	KIAA1985, CMT4C	uc003lpu.3	Q8TF17	OTTHUMG00000129930	ENST00000515425.1:c.3407A>T	chr5.hg19:g.148388485T>A	ENSP00000423660:p.Gln1136Leu	131.0	0.0		153.0	61.0	NM_024577	B3KWE5|Q14CC0|Q14CF5|Q9H8I5	Missense_Mutation	SNP	ENST00000515425.1	hg19	CCDS4293.1	.	.	.	.	.	.	.	.	.	.	T	6.423	0.446095	0.12164	.	.	ENSG00000169247	ENST00000538184;ENST00000515425;ENST00000512049	T;T;T	0.73681	-0.77;-0.73;-0.72	6.03	6.03	0.97812	Tetratricopeptide-like helical (1);	0.086978	0.48286	D	0.000193	T	0.53270	0.1786	N	0.16066	0.365	0.80722	D	1	B;B;B	0.18013	0.025;0.025;0.025	B;B;B	0.16722	0.016;0.01;0.016	T	0.51585	-0.8687	10	0.02654	T	1	-17.2873	11.6211	0.51119	0.1327:0.0:0.0:0.8673	.	1129;1136;1136	Q14CC0;E9PDF1;Q8TF17	.;.;S3TC2_HUMAN	L	683;1136;1129	ENSP00000441427:Q683L;ENSP00000423660:Q1136L;ENSP00000421860:Q1129L	ENSP00000425627:Q1136L	Q	-	2	0	SH3TC2	148368678	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	4.674000	0.61612	2.302000	0.77476	0.533000	0.62120	CAG	.	.		0.532	SH3TC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252186.2	NM_024577		A	148388485	T	A	148388485	3	1	347	1	0	0	0	0	1	0	0	0	14277	1580	55	4	471	4	SH3TC2	5	148388485	Missense_Mutation	SNP	T	TCGA-UB-A7ME-01A-11D-A33K-10	7825748	148388485	32526775	26	48979										
C1QTNF2	114898	hgsc.bcm.edu	37	chr5	159776435	159776435	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	cttgttggccagcgtgatgtCgtaggtgaagtagtagatcc	14	7	0	3			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr5:159776435C>T	ENST00000393975.3	-	3	736	c.733G>A	c.(733-735)Gac>Aac	p.D245N		NM_031908.4	NP_114114.2	Q9BXJ5	C1QT2_HUMAN	C1q and tumor necrosis factor related protein 2	200	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				activation of MAPK activity (GO:0000187)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|protein heterotrimerization (GO:0070208)|protein homooligomerization (GO:0051260)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)				breast(2)|endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|skin(3)	13	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			AGCGTGATGTCGTAGGTGAAG	0.572																																					p.D245N		Atlas-SNP	.											.	C1QTNF2	33	.	0			c.G733A						.						88	89	88					5																	159776435		2203	4300	6503	SO:0001583	missense	114898	exon3			TGATGTCGTAGGT	AF329836	CCDS4351.2	5q33.3	2008-05-15			ENSG00000145861	ENSG00000145861			14325	protein-coding gene	gene with protein product							Standard	XM_005265815		Approved	CTRP2	uc003lyd.3	Q9BXJ5	OTTHUMG00000130323	ENST00000393975.3:c.733G>A	chr5.hg19:g.159776435C>T	ENSP00000377545:p.Asp245Asn	67.0	0.0		77.0	19.0	NM_031908		Missense_Mutation	SNP	ENST00000393975.3	hg19	CCDS4351.2	.	.	.	.	.	.	.	.	.	.	C	20.8	4.056875	0.76074	.	.	ENSG00000145861	ENST00000393975	T	0.74842	-0.88	5.35	5.35	0.76521	Tumour necrosis factor-like (2);Complement C1q protein (4);	0.000000	0.85682	D	0.000000	T	0.76962	0.4061	N	0.16833	0.445	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.76389	-0.2977	10	0.31617	T	0.26	.	18.6668	0.91493	0.0:1.0:0.0:0.0	.	200	Q9BXJ5	C1QT2_HUMAN	N	245	ENSP00000377545:D245N	ENSP00000377545:D245N	D	-	1	0	C1QTNF2	159709013	1.000000	0.71417	0.996000	0.52242	0.973000	0.67179	7.818000	0.86416	2.513000	0.84729	0.591000	0.81541	GAC	.	.		0.572	C1QTNF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252672.2			T	159776435	C	T	159776435	3	4	347	1	0	0	0	0	1	0	0	0	1965	884	31	1	263	1	C1QTNF2	5	159776435	Missense_Mutation	SNP	C	TCGA-UB-A7ME-01A-11D-A33K-10	11387950	159776435	21138825	27	48980										
FGF18	8817	hgsc.bcm.edu	37	chr5	170876191	170876191	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	gacaccttcggtagtcaagtCcggatcaagggcaaggagac	13	10	2	1			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr5:170876191C>T	ENST00000274625.5	+	4	835	c.291C>T	c.(289-291)gtC>gtT	p.V97V		NM_003862.2	NP_003853.1	O76093	FGF18_HUMAN	fibroblast growth factor 18	97					anatomical structure morphogenesis (GO:0009653)|angiogenesis (GO:0001525)|cell-cell signaling (GO:0007267)|chondrocyte development (GO:0002063)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intramembranous ossification (GO:0001957)|lung development (GO:0030324)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleolus (GO:0005730)	growth factor activity (GO:0008083)|type 1 fibroblast growth factor receptor binding (GO:0005105)|type 2 fibroblast growth factor receptor binding (GO:0005111)			endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	9	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			GTAGTCAAGTCCGGATCAAGG	0.527																																					p.V97V		Atlas-SNP	.											.	FGF18	33	.	0			c.C291T						.						118	97	104					5																	170876191		2203	4300	6503	SO:0001819	synonymous_variant	8817	exon4			TCAAGTCCGGATC	AB007422	CCDS4378.1	5q34	2008-02-05			ENSG00000156427	ENSG00000156427			3674	protein-coding gene	gene with protein product		603726				9660775, 9742123	Standard	NM_003862		Approved	FGF-18, ZFGF5	uc003mbk.3	O76093	OTTHUMG00000130464	ENST00000274625.5:c.291C>T	chr5.hg19:g.170876191C>T		147.0	0.0		136.0	24.0	NM_003862	D3DQL7|Q6UWF1	Silent	SNP	ENST00000274625.5	hg19	CCDS4378.1																																																																																			.	.		0.527	FGF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252857.2	NM_033649, NM_003862		T	170876191	C	T	170876191	2	4	347	1	0	0	0	0	0	0	0	1	5854	842	30	3		3	FGF18	5	170876191	Silent	SNP	C	TCGA-UB-A7ME-01A-11D-A33K-10	11099756	170876191	10039069	28	48981										
CAGE1	285782	hgsc.bcm.edu	37	chr6	7334305	7334305	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	ctaattaaatcctctaaatgTttatttctctcttccaaact	1	10	3	0			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr6:7334305T>A	ENST00000512086.1	-	10	2404	c.2202A>T	c.(2200-2202)aaA>aaT	p.K734N	CAGE1_ENST00000502583.1_Missense_Mutation_p.K796N|CAGE1_ENST00000338150.4_Missense_Mutation_p.K761N|CAGE1_ENST00000296742.7_Missense_Mutation_p.K598N|CAGE1_ENST00000379918.4_Missense_Mutation_p.K774N|SSR1_ENST00000488834.1_5'UTR			Q8TC20	CAGE1_HUMAN	cancer antigen 1	734										breast(1)|cervix(1)|endometrium(3)|kidney(2)|lung(11)|urinary_tract(1)	19	Ovarian(93;0.0418)					CCTCTAAATGTTTATTTCTCT	0.274																																					p.K796N		Atlas-SNP	.											.	CAGE1	165	.	0			c.A2388T						.						35	32	33					6																	7334305		1762	3984	5746	SO:0001583	missense	285782	exon12			TAAATGTTTATTT	BC026194	CCDS47367.1, CCDS54964.1, CCDS54965.1	6p24.3	2009-08-06	2005-01-26	2005-01-27	ENSG00000164304	ENSG00000164304			21622	protein-coding gene	gene with protein product	"cancer/testis antigen 95"	608304	"cancer/testis antigen 3"	CTAG3		12531476	Standard	NM_205864		Approved	bA69L16.7, CT95	uc003mxl.2	Q8TC20	OTTHUMG00000014200	ENST00000512086.1:c.2202A>T	chr6.hg19:g.7334305T>A	ENSP00000427583:p.Lys734Asn	49.0	0.0		76.0	32.0	NM_001170692	D6RCT9|Q5TAM0|Q86TM4|Q8N7R5	Missense_Mutation	SNP	ENST00000512086.1	hg19		.	.	.	.	.	.	.	.	.	.	T	16.78	3.217091	0.58560	.	.	ENSG00000164304	ENST00000541116;ENST00000379918;ENST00000502583;ENST00000296742;ENST00000512086;ENST00000338150	T;T;T;T;T	0.37411	1.27;1.2;1.25;1.25;1.24	4.62	3.46	0.39613	.	0.131360	0.35349	N	0.003272	T	0.30572	0.0769	L	0.47716	1.5	0.22378	N	0.999155	D;D;D	0.67145	0.996;0.996;0.996	P;P;D	0.65573	0.907;0.876;0.936	T	0.06844	-1.0804	10	0.52906	T	0.07	-18.6693	6.8651	0.24088	0.0:0.104:0.0:0.896	.	761;796;734	Q8TC20-3;D6RCT9;Q8TC20	.;.;CAGE1_HUMAN	N	734;774;796;598;734;761	ENSP00000369250:K774N;ENSP00000425493:K796N;ENSP00000296742:K598N;ENSP00000427583:K734N;ENSP00000338107:K761N	ENSP00000296742:K598N	K	-	3	2	CAGE1	7279304	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	0.685000	0.25378	0.922000	0.37019	0.477000	0.44152	AAA	.	.		0.274	CAGE1-008	PUTATIVE	non_canonical_conserved|basic	protein_coding	protein_coding	OTTHUMT00000367136.1	NM_175745		A	7334305	T	A	7334305	3	1	347	1	0	0	0	0	1	0	0	0	2574	1722	60	4	249	4	CAGE1	6	7334305	Missense_Mutation	SNP	T	TCGA-UB-A7ME-01A-11D-A33K-10		7334305	163780762	29	48982										
BMP5	653	hgsc.bcm.edu	37	chr6	55620351	55620351	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	ttagtggcagccacatgagcGtactaccatatttctatatt	7	9	1	1			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr6:55620351G>A	ENST00000370830.3	-	7	2043	c.1345C>T	c.(1345-1347)Cgc>Tgc	p.R449C	BMP5_ENST00000446683.2_Missense_Mutation_p.R412C	NM_021073.2	NP_066551.1	P22003	BMP5_HUMAN	bone morphogenetic protein 5	449					cartilage development (GO:0051216)|growth (GO:0040007)|male genitalia development (GO:0030539)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of steroid biosynthetic process (GO:0010894)|ossification (GO:0001503)|pattern specification process (GO:0007389)|positive regulation of dendrite development (GO:1900006)|positive regulation of DNA-dependent DNA replication (GO:2000105)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system development (GO:0001501)|type B pancreatic cell development (GO:0003323)	extracellular space (GO:0005615)|membrane-bounded vesicle (GO:0031988)	BMP receptor binding (GO:0070700)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	45	Lung NSC(77;0.0462)		LUSC - Lung squamous cell carcinoma(124;0.181)			CCACATGAGCGTACTACCATA	0.328																																					p.R449C		Atlas-SNP	.											BMP5,colon,carcinoma,+1,1	BMP5	94	.	0			c.C1345T						.						55	58	57					6																	55620351		2203	4299	6502	SO:0001583	missense	653	exon7			ATGAGCGTACTAC		CCDS4958.1	6p12.1	2014-01-30			ENSG00000112175	ENSG00000112175		"Bone morphogenetic proteins", "Endogenous ligands"	1072	protein-coding gene	gene with protein product		112265				1427904, 11580864	Standard	NM_021073		Approved		uc003pcq.3	P22003	OTTHUMG00000014903	ENST00000370830.3:c.1345C>T	chr6.hg19:g.55620351G>A	ENSP00000359866:p.Arg449Cys	327.0	2.0		430.0	142.0	NM_021073	B4E0Y4|Q9H547|Q9NTM5	Missense_Mutation	SNP	ENST00000370830.3	hg19	CCDS4958.1	.	.	.	.	.	.	.	.	.	.	G	17.51	3.408449	0.62399	.	.	ENSG00000112175	ENST00000370830;ENST00000446683	D;D	0.89415	-2.51;-2.51	5.73	5.73	0.89815	Transforming growth factor-beta, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.93501	0.7926	M	0.76838	2.35	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.973;0.996	D	0.93716	0.7028	10	0.87932	D	0	.	15.0392	0.71774	0.0:0.0:0.8579:0.1421	.	412;449	B4E0Y4;P22003	.;BMP5_HUMAN	C	449;412	ENSP00000359866:R449C;ENSP00000391818:R412C	ENSP00000359866:R449C	R	-	1	0	BMP5	55728310	1.000000	0.71417	0.975000	0.42487	0.994000	0.84299	5.038000	0.64177	2.854000	0.98071	0.655000	0.94253	CGC	.	.		0.328	BMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041000.1			A	55620351	G	A	55620351	3	1	347	1	0	0	0	0	1	0	0	0	1463	1145	40	1	23	1	BMP5	6	55620351	Missense_Mutation	SNP	G	TCGA-UB-A7ME-01A-11D-A33K-10	48286046	55620351	115494716	30	48983										
EYS	346007	hgsc.bcm.edu	37	chr6	65707540	65707540	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	gatgcagtcatcaatgtcctGttcacatcttatcccaacat	5	12	4	0			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr6:65707540G>A	ENST00000370621.3	-	14	2720	c.2194C>T	c.(2194-2196)Cag>Tag	p.Q732*	EYS_ENST00000503581.1_Nonsense_Mutation_p.Q732*|EYS_ENST00000370616.2_Nonsense_Mutation_p.Q732*			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	732					detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						TCAATGTCCTGTTCACATCTT	0.408																																					p.Q732X		Atlas-SNP	.											.	EYS	527	.	0			c.C2194T						.						145	121	128					6																	65707540		692	1591	2283	SO:0001587	stop_gained	346007	exon14			TGTCCTGTTCACA		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.2194C>T	chr6.hg19:g.65707540G>A	ENSP00000359655:p.Gln732*	244.0	0.0		557.0	54.0	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Nonsense_Mutation	SNP	ENST00000370621.3	hg19		.	.	.	.	.	.	.	.	.	.	G	39	7.641406	0.98406	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	.	.	.	5.5	0.265	0.15612	.	0.596206	0.12821	N	0.436434	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	.	3.3294	0.07079	0.1402:0.2513:0.4787:0.1298	.	.	.	.	X	732	.	ENSP00000359650:Q732X	Q	-	1	0	EYS	65764261	1.000000	0.71417	0.109000	0.21407	0.955000	0.61496	1.652000	0.37313	-0.256000	0.09473	0.655000	0.94253	CAG	.	.		0.408	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		A	65707540	G	A	65707540	4	1	347	1	0	0	0	0	0	1	0	0	5334	1386	48	3	7205	3	EYS	6	65707540	Nonsense_Mutation	SNP	G	TCGA-UB-A7ME-01A-11D-A33K-10	10087189	65707540	105407527	31	48984										
CASP8AP2	9994	hgsc.bcm.edu	37	chr6	90573432	90573432	+	RNA	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	aggtctgttgacaatactatGcattgtgaagagcccatttg	10	7	1	3			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr6:90573432G>T	ENST00000551025.1	+	0	3441									caspase 8 associated protein 2											NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2)	51		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		ACAATACTATGCATTGTGAAG	0.413																																					p.M668I	Colon(187;1656 2025 17045 31481 39901)	Atlas-SNP	.											.	CASP8AP2	108	.	0			c.G2004T						.						57	54	55					6																	90573432		1913	4131	6044			9994	exon7			TACTATGCATTGT	AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"FLICE-associated huge protein"	606880	"CASP8 associated protein 2"			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		chr6.hg19:g.90573432G>T		93.0	0.0		89.0	30.0	NM_001137667		Missense_Mutation	SNP	ENST00000551025.1	hg19																																																																																				.	.		0.413	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667		T	90573432	G	T	90573432	1	4	347	0	1	0	0	0	0	0	0	0	2680	1319	46	3		3	CASP8AP2	6	90573432	RNA	SNP	G	TCGA-UB-A7ME-01A-11D-A33K-10	24865892	90573432	80541635	32	48985										
NCOA7	135112	hgsc.bcm.edu	37	chr6	126196071	126196071	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	aacacatgataaaaaagagaAgaagatggtggttcagaagc	11	4	1	5			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr6:126196071A>C	ENST00000368357.3	+	5	660	c.308A>C	c.(307-309)aAg>aCg	p.K103T	NCOA7_ENST00000229634.9_5'UTR|NCOA7_ENST00000392477.2_Missense_Mutation_p.K103T|RN7SKP56_ENST00000410513.1_RNA	NM_001199619.1|NM_001199620.1	NP_001186548.1|NP_001186549.1	Q8NI08	NCOA7_HUMAN	nuclear receptor coactivator 7	103					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(2)	39				UCEC - Uterine corpus endometrioid carcinoma (4;0.0803)|GBM - Glioblastoma multiforme(226;0.0193)|all cancers(137;0.237)		AAAAAAGAGAAGAAGATGGTG	0.333																																					p.K103T		Atlas-SNP	.											.	NCOA7	92	.	0			c.A308C						.						109	113	112					6																	126196071		2203	4300	6503	SO:0001583	missense	135112	exon5			AAGAGAAGAAGAT	AJ420542	CCDS5132.1, CCDS56448.1	6q22.33	2013-03-14			ENSG00000111912	ENSG00000111912			21081	protein-coding gene	gene with protein product	"TBC/LysM-associated domain containing 4"	609752				11971969	Standard	NM_001199619		Approved	ERAP140, dJ187J11.3, TLDC4	uc003qai.3	Q8NI08	OTTHUMG00000015513	ENST00000368357.3:c.308A>C	chr6.hg19:g.126196071A>C	ENSP00000357341:p.Lys103Thr	128.0	0.0		118.0	29.0	NM_001199619	B2RNS2|B7Z2C4|B9EH71|G8JL91|Q3LID6|Q4G0V1|Q5TF95|Q6IPQ4|Q6NE83|Q86T89|Q8N1W4	Missense_Mutation	SNP	ENST00000368357.3	hg19	CCDS5132.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.196721	0.79015	.	.	ENSG00000111912	ENST00000368357;ENST00000392477;ENST00000417494;ENST00000419660	T;T;T;T	0.56103	2.48;2.48;0.66;0.48	5.35	5.35	0.76521	.	0.168242	0.52532	D	0.000075	T	0.53417	0.1795	L	0.29908	0.895	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.78314	0.983;0.983;0.991	T	0.60551	-0.7241	10	0.87932	D	0	-23.875	14.958	0.71131	1.0:0.0:0.0:0.0	.	103;103;103	Q8NI08-2;Q8NI08-4;Q8NI08	.;.;NCOA7_HUMAN	T	103	ENSP00000357341:K103T;ENSP00000376269:K103T;ENSP00000406363:K103T;ENSP00000408211:K103T	ENSP00000357341:K103T	K	+	2	0	NCOA7	126237764	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.569000	0.60865	2.371000	0.80710	0.533000	0.62120	AAG	.	.		0.333	NCOA7-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042083.4	XM_059748		C	126196071	A	C	126196071	3	2	347	1	0	0	0	0	1	0	0	0	10243	72	3	5	318	5	NCOA7	6	126196071	Missense_Mutation	SNP	A	TCGA-UB-A7ME-01A-11D-A33K-10	35622639	126196071	44918996	33	48986										
THEMIS	387357	hgsc.bcm.edu	37	chr6	128134892	128134892	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	ttcccaggctgtaaaatgctTtggggcaggtggtttccttc	12	9	0	0			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr6:128134892T>A	ENST00000368248.2	-	4	1042	c.894A>T	c.(892-894)caA>caT	p.Q298H	THEMIS_ENST00000543064.1_Missense_Mutation_p.Q298H|THEMIS_ENST00000368250.1_Missense_Mutation_p.Q219H|THEMIS_ENST00000537166.1_Missense_Mutation_p.Q263H	NM_001010923.2	NP_001010923.1	Q8N1K5	THMS1_HUMAN	thymocyte selection associated	298	CABIT 2.				negative T cell selection (GO:0043383)|positive T cell selection (GO:0043368)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(3)	60						GTAAAATGCTTTGGGGCAGGT	0.393																																					p.Q298H		Atlas-SNP	.											.	THEMIS	168	.	0			c.A894T						.						114	120	118					6																	128134892		2203	4300	6503	SO:0001583	missense	387357	exon4			AATGCTTTGGGGC	AK094863	CCDS34534.1, CCDS55055.1	6q22.33	2012-02-08	2009-06-25	2009-06-25	ENSG00000172673	ENSG00000172673			21569	protein-coding gene	gene with protein product	"thymocyte expressed molecule involved in selection"	613607	"chromosome 6 open reading frame 207", "chromosome 6 open reading frame 190", "thymocyte selection pathway associated"	C6orf207, C6orf190, TSEPA		19597499, 19597498, 19597497	Standard	NM_001010923		Approved	bA325O24.4, FLJ40584, bA325O24.3	uc011ebt.2	Q8N1K5	OTTHUMG00000015534	ENST00000368248.2:c.894A>T	chr6.hg19:g.128134892T>A	ENSP00000357231:p.Gln298His	120.0	0.0		103.0	24.0	NM_001010923	A1L4F0|A8K7N1|B3KT31|B3KW32|B3KY07|F5H1J9|Q5T3C4|Q5T3C5|Q6MZT7	Missense_Mutation	SNP	ENST00000368248.2	hg19	CCDS34534.1	.	.	.	.	.	.	.	.	.	.	T	0.010	-1.776639	0.00640	.	.	ENSG00000172673	ENST00000368250;ENST00000543064;ENST00000368248;ENST00000537166;ENST00000434358	T;T;T;T;T	0.14766	2.48;2.48;2.48;2.48;2.48	5.59	2.99	0.34606	.	1.081190	0.06909	N	0.807252	T	0.03178	0.0093	L	0.36672	1.1	0.09310	N	1	P;B	0.37573	0.6;0.342	B;B	0.35607	0.206;0.141	T	0.40831	-0.9542	10	0.16420	T	0.52	0.8118	5.3567	0.16065	0.2843:0.0:0.3463:0.3695	.	298;298	F5H1J9;Q8N1K5	.;THMS1_HUMAN	H	219;298;298;263;66	ENSP00000357233:Q219H;ENSP00000439594:Q298H;ENSP00000357231:Q298H;ENSP00000439863:Q263H;ENSP00000387740:Q66H	ENSP00000357231:Q298H	Q	-	3	2	THEMIS	128176585	0.111000	0.22076	0.140000	0.22221	0.053000	0.15095	0.516000	0.22817	0.910000	0.36722	0.374000	0.22700	CAA	.	.		0.393	THEMIS-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_001010923		A	128134892	T	A	128134892	3	1	347	1	0	0	0	0	1	0	0	0	15875	1838	64	4	1164	4	THEMIS	6	128134892	Missense_Mutation	SNP	T	TCGA-UB-A7ME-01A-11D-A33K-10	1938821	128134892	42980175	34	48987										
SRCRB4D	136853	hgsc.bcm.edu	37	chr7	76023205	76023205	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	gctgtctcccgggaaggctgGgggccaactcctgtagctgt	15	12	1	0			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr7:76023205G>C	ENST00000275560.3	-	8	1310	c.963C>G	c.(961-963)ccC>ccG	p.P321P	SRCRB4D_ENST00000492979.2_5'Flank	NM_080744.1	NP_542782.1														autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(9)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	21						GGGAAGGCTGGGGGCCAACTC	0.662																																					p.P321P		Atlas-SNP	.											.	SRCRB4D	47	.	0			c.C963G						.						35	34	35					7																	76023205		2203	4298	6501	SO:0001819	synonymous_variant	136853	exon8			AGGCTGGGGGCCA																												ENST00000275560.3:c.963C>G	chr7.hg19:g.76023205G>C		117.0	0.0		205.0	37.0	NM_080744		Silent	SNP	ENST00000275560.3	hg19	CCDS5585.1																																																																																			.	.		0.662	SRCRB4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253001.3			C	76023205	G	C	76023205	2	2	347	1	0	0	0	0	0	0	0	1	15152	1219	43	4		4	SRCRB4D	7	76023205	Silent	SNP	G	TCGA-UB-A7ME-01A-11D-A33K-10		76023205	83115458	35	48988										
TCEA1	6917	hgsc.bcm.edu	37	chr8	54882968	54882968	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	ataccttccatcgatttccaCattcattacagacaacaaat	2	12	1	1			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr8:54882968C>T	ENST00000521604.2	-	9	1284	c.881G>A	c.(880-882)tGt>tAt	p.C294Y	TCEA1_ENST00000521086.2_5'UTR|TCEA1_ENST00000522635.1_Missense_Mutation_p.C110Y|TCEA1_ENST00000396401.3_Missense_Mutation_p.C273Y	NM_006756.2	NP_006747.1	P23193	TCEA1_HUMAN	transcription elongation factor A (SII), 1	294					DNA repair (GO:0006281)|erythrocyte differentiation (GO:0030218)|gene expression (GO:0010467)|nucleotide-excision repair (GO:0006289)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|regulation of DNA-templated transcription, elongation (GO:0032784)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(1)|lung(1)|skin(1)	4		Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;9.1e-07)|Epithelial(17;9.44e-05)|all cancers(17;0.000699)			TCGATTTCCACATTCATTACA	0.333			T	PLAG1	salivary adenoma																																p.C294Y		Atlas-SNP	.		Dom	yes		8	8q11.2	6917	"transcription elongation factor A (SII), 1"		E	.	TCEA1	30	.	0			c.G881A						.						87	80	82					8																	54882968		1850	4083	5933	SO:0001583	missense	6917	exon9			TTTCCACATTCAT	X62585	CCDS47857.1, CCDS47858.1	8q11.2	2011-01-25			ENSG00000187735	ENSG00000187735		"General transcription factors"	11612	protein-coding gene	gene with protein product		601425		TCEA, GTF2S		8812434, 8112616	Standard	NM_006756		Approved	SII, TF2S, TFIIS	uc003xru.3	P23193	OTTHUMG00000164262	ENST00000521604.2:c.881G>A	chr8.hg19:g.54882968C>T	ENSP00000428426:p.Cys294Tyr	236.0	0.0		397.0	56.0	NM_006756	A6NF25|A8K339|Q15563|Q6FG87	Missense_Mutation	SNP	ENST00000521604.2	hg19	CCDS47858.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.511255	0.85389	.	.	ENSG00000187735	ENST00000396401;ENST00000521604;ENST00000522635	.	.	.	4.9	4.9	0.64082	Zinc finger, TFIIS-type (4);	0.000000	0.85682	D	0.000000	D	0.92159	0.7514	H	0.99842	4.835	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.96044	0.9026	9	0.87932	D	0	-13.4066	18.4641	0.90749	0.0:1.0:0.0:0.0	.	110;273;294	B7Z4S1;P23193-2;P23193	.;.;TCEA1_HUMAN	Y	273;294;110	.	ENSP00000395483:C273Y	C	-	2	0	TCEA1	55045521	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.776000	0.85560	2.442000	0.82660	0.591000	0.81541	TGT	.	.		0.333	TCEA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377975.2	NM_006756		T	54882968	C	T	54882968	3	4	347	1	0	0	0	0	1	0	0	0	15682	478	17	3	32	3	TCEA1	8	54882968	Missense_Mutation	SNP	C	TCGA-UB-A7ME-01A-11D-A33K-10		54882968	91481054	36	48989										
SLC26A7	115111	hgsc.bcm.edu	37	chr8	92330525	92330525	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	gcgcaatgacaactggggctGccacccatgtggtgacttca	12	12	1	2			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr8:92330525G>T	ENST00000276609.3	+	5	798	c.559G>T	c.(559-561)Gcc>Tcc	p.A187S	SLC26A7_ENST00000523719.1_Missense_Mutation_p.A187S|SLC26A7_ENST00000309536.2_Missense_Mutation_p.A187S	NM_001282356.1|NM_052832.2	NP_001269285.1|NP_439897.1			solute carrier family 26 (anion exchanger), member 7											breast(1)|cervix(1)|endometrium(4)|large_intestine(10)|lung(26)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	50			BRCA - Breast invasive adenocarcinoma(11;0.00802)			AACTGGGGCTGCCACCCATGT	0.473																																					p.A187S		Atlas-SNP	.											.	SLC26A7	207	.	0			c.G559T						.						127	122	123					8																	92330525		2203	4300	6503	SO:0001583	missense	115111	exon5			GGGGCTGCCACCC	AF331521	CCDS6254.1, CCDS6255.1, CCDS75765.1	8q23	2013-07-18	2013-07-18		ENSG00000147606	ENSG00000147606		"Solute carriers"	14467	protein-coding gene	gene with protein product		608479	"solute carrier family 26, member 7"			11834742, 11829495, 16524946	Standard	NM_134266		Approved	SUT2	uc003yez.3	Q8TE54	OTTHUMG00000164062	ENST00000276609.3:c.559G>T	chr8.hg19:g.92330525G>T	ENSP00000276609:p.Ala187Ser	74.0	0.0		176.0	22.0	NM_134266		Missense_Mutation	SNP	ENST00000276609.3	hg19	CCDS6254.1	.	.	.	.	.	.	.	.	.	.	G	18.12	3.553871	0.65425	.	.	ENSG00000147606	ENST00000522862;ENST00000523719;ENST00000276609;ENST00000309536	D;D;D;D	0.96365	-3.99;-3.99;-3.99;-3.99	5.95	5.95	0.96441	Sulphate transporter (1);	0.000000	0.64402	D	0.000001	D	0.97353	0.9134	L	0.47716	1.5	0.47407	D	0.99941	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	D	0.96391	0.9289	10	0.35671	T	0.21	.	20.3921	0.98947	0.0:0.0:1.0:0.0	.	187;187	Q8TE54-2;Q8TE54	.;S26A7_HUMAN	S	187	ENSP00000428881:A187S;ENSP00000428849:A187S;ENSP00000276609:A187S;ENSP00000309504:A187S	ENSP00000276609:A187S	A	+	1	0	SLC26A7	92399701	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.408000	0.73285	2.822000	0.97130	0.650000	0.86243	GCC	.	.		0.473	SLC26A7-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377011.1			T	92330525	G	T	92330525	3	4	347	1	0	0	0	0	1	0	0	0	14537	1319	46	3	573	3	SLC26A7	8	92330525	Missense_Mutation	SNP	G	TCGA-UB-A7ME-01A-11D-A33K-10	37447557	92330525	54033497	37	48990										
RMI1	80010	hgsc.bcm.edu	37	chr9	86616085	86616085	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	agtggctccttactgatctgAgggatttggagcatcctctt	11	9	2	2			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr9:86616085A>T	ENST00000325875.3	+	3	516	c.184A>T	c.(184-186)Agg>Tgg	p.R62W		NM_024945.2	NP_079221.2	Q9H9A7	RMI1_HUMAN	RecQ mediated genome instability 1	62					DNA replication (GO:0006260)|glucose homeostasis (GO:0042593)|multicellular organism growth (GO:0035264)|reduction of food intake in response to dietary excess (GO:0002023)|response to glucose (GO:0009749)	nucleus (GO:0005634)				biliary_tract(1)|central_nervous_system(1)|kidney(2)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18						TACTGATCTGAGGGATTTGGA	0.363																																					p.R62W		Atlas-SNP	.											.	RMI1	50	.	0			c.A184T						.						97	101	100					9																	86616085		2203	4300	6503	SO:0001583	missense	80010	exon3			GATCTGAGGGATT	AK022950	CCDS6669.1	9q22.1	2013-06-10	2013-06-10	2006-06-12	ENSG00000178966	ENSG00000178966			25764	protein-coding gene	gene with protein product	"BLM-Associated Polypeptide, 75 kDa"	610404	"chromosome 9 open reading frame 76", "RMI1, RecQ mediated genome instability 1, homolog (S. cerevisiae)"	C9orf76		15775963, 20826341	Standard	NM_024945		Approved	FLJ12888, BLAP75	uc004anq.4	Q9H9A7	OTTHUMG00000020113	ENST00000325875.3:c.184A>T	chr9.hg19:g.86616085A>T	ENSP00000317039:p.Arg62Trp	146.0	0.0		123.0	37.0	NM_024945	Q05BX1|Q05CW3|Q5SQG8|Q5SQG9|Q6P1Q4|Q6PI89|Q7Z6L6	Missense_Mutation	SNP	ENST00000325875.3	hg19	CCDS6669.1	.	.	.	.	.	.	.	.	.	.	A	16.96	3.267373	0.59540	.	.	ENSG00000178966	ENST00000445877;ENST00000325875	T;T	0.53640	0.61;0.61	5.76	4.55	0.56014	Domain of unknown function DUF1767 (1);	0.000000	0.85682	D	0.000000	T	0.66626	0.2808	M	0.78916	2.43	0.50039	D	0.999849	D	0.71674	0.998	D	0.67900	0.954	T	0.71467	-0.4584	10	0.87932	D	0	0.6268	12.8735	0.57978	0.8644:0.1356:0.0:0.0	.	62	Q9H9A7	RMI1_HUMAN	W	62	ENSP00000402433:R62W;ENSP00000317039:R62W	ENSP00000317039:R62W	R	+	1	2	RMI1	85805905	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.765000	0.55272	2.322000	0.78497	0.528000	0.53228	AGG	.	.		0.363	RMI1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052870.1	NM_024945		T	86616085	A	T	86616085	3	4	347	1	0	0	0	0	1	0	0	0	13410	295	11	4	186	4	RMI1	9	86616085	Missense_Mutation	SNP	A	TCGA-UB-A7ME-01A-11D-A33K-10		86616085	54597346	38	48991										
PTGS1	5742	hgsc.bcm.edu	37	chr9	125141054	125141054	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	gttatttttgctctctgcagTgcgctccaaccttatcccca	6	14	1	0			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr9:125141054T>G	ENST00000362012.2	+	5	358	c.353T>G	c.(352-354)gTg>gGg	p.V118G	PTGS1_ENST00000223423.4_Splice_Site_p.V118G|PTGS1_ENST00000373698.5_Splice_Site_p.V9G|PTGS1_ENST00000540753.1_Splice_Site_p.V93G	NM_000962.3|NM_001271164.1|NM_001271367.1|NM_080591.2	NP_000953.2|NP_001258093.1|NP_001258296.1|NP_542158.1	P23219	PGH1_HUMAN	prostaglandin-endoperoxide synthase 1 (prostaglandin G/H synthase and cyclooxygenase)	118					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|prostaglandin biosynthetic process (GO:0001516)|regulation of blood pressure (GO:0008217)|regulation of cell proliferation (GO:0042127)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|photoreceptor outer segment (GO:0001750)	dioxygenase activity (GO:0051213)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)|prostaglandin-endoperoxide synthase activity (GO:0004666)			large_intestine(3)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	8					Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Antipyrine(DB01435)|Antrafenine(DB01419)|Balsalazide(DB01014)|Bortezomib(DB00188)|Bromfenac(DB00963)|Candesartan(DB00796)|Carprofen(DB00821)|Carvedilol(DB01136)|Chlorpropamide(DB00672)|Dapsone(DB00250)|Desmopressin(DB00035)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylcarbamazine(DB00711)|Diflunisal(DB00861)|Dihomo-gamma-linolenic acid(DB00154)|Diphenhydramine(DB01075)|Dronabinol(DB00470)|Eletriptan(DB00216)|Eszopiclone(DB00402)|Etodolac(DB00749)|Etoposide(DB00773)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|Hexobarbital(DB01355)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Icosapent(DB00159)|Ifosfamide(DB01181)|Imatinib(DB00619)|Indomethacin(DB00328)|Irbesartan(DB01029)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lornoxicam(DB06725)|Lumiracoxib(DB01283)|Magnesium salicylate(DB01397)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mesalazine(DB00244)|Minoxidil(DB00350)|Montelukast(DB00471)|Nabumetone(DB00461)|Naproxen(DB00788)|Nateglinide(DB00731)|Nepafenac(DB06802)|Niflumic Acid(DB04552)|Nortriptyline(DB00540)|Oxaprozin(DB00991)|Phenylbutazone(DB00812)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Rosiglitazone(DB00412)|Salicylate-sodium(DB01398)|Salicylic acid(DB00936)|Salsalate(DB01399)|Sulfamethoxazole(DB01015)|Sulfasalazine(DB00795)|Sulindac(DB00605)|Suprofen(DB00870)|Tenoxicam(DB00469)|Terbinafine(DB00857)|Thalidomide(DB01041)|Tiaprofenic acid(DB01600)|Tolmetin(DB00500)|Torasemide(DB00214)|Trabectedin(DB05109)|Triflusal(DB08814)|Trisalicylate-choline(DB01401)|Valproic Acid(DB00313)|Voriconazole(DB00582)|Zafirlukast(DB00549)|Zileuton(DB00744)|Zolpidem(DB00425)|Zopiclone(DB01198)	CTCTCTGCAGTGCGCTCCAAC	0.517																																					p.V118G		Atlas-SNP	.											.	PTGS1	84	.	0			c.T353G						.						152	133	139					9																	125141054		2203	4300	6503	SO:0001630	splice_region_variant	5742	exon5			CTGCAGTGCGCTC	M59979	CCDS6842.1, CCDS6843.1, CCDS59520.1, CCDS59521.1, CCDS75895.1	9q32-q33.3	2008-02-05			ENSG00000095303	ENSG00000095303	1.14.99.1		9604	protein-coding gene	gene with protein product		176805				2512924, 1907252	Standard	NM_000962		Approved	COX1, PGHS-1, PTGHS	uc004bmg.2	P23219	OTTHUMG00000020605	ENST00000362012.2:c.353-1T>G	chr9.hg19:g.125141054T>G		116.0	0.0		107.0	15.0	NM_000962	A8K1V7|B4DHQ2|B4E2S5|Q15122|Q3HY28|Q3HY29|Q5T7T6|Q5T7T7|Q5T7T8	Missense_Mutation	SNP	ENST00000362012.2	hg19	CCDS6842.1	.	.	.	.	.	.	.	.	.	.	T	3.558	-0.090208	0.07053	.	.	ENSG00000095303	ENST00000540753;ENST00000362012;ENST00000223423;ENST00000426608;ENST00000373698	T;T;T;T;T	0.10382	2.88;2.88;2.88;2.88;2.88	5.68	-0.726	0.11170	.	0.222920	0.45867	D	0.000325	T	0.04998	0.0134	N	0.11698	0.16	0.80722	D	1	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.10450	0.005;0.002;0.005	T	0.45440	-0.9261	9	.	.	.	.	9.9071	0.41384	0.0:0.3363:0.0:0.6637	.	93;118;118	B4DHQ2;P23219;P23219-2	.;PGH1_HUMAN;.	G	93;118;118;76;9	ENSP00000437709:V93G;ENSP00000354612:V118G;ENSP00000223423:V118G;ENSP00000411606:V76G;ENSP00000362802:V9G	.	V	+	2	0	PTGS1	124180875	0.504000	0.26123	0.884000	0.34674	0.084000	0.17831	0.784000	0.26816	-0.370000	0.08016	0.460000	0.39030	GTG	.	.		0.517	PTGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053933.1		Missense_Mutation	G	125141054	T	G	125141054	5	3	347	1	0	0	0	0	0	0	1	0	12768	1710	59	5	371	5	PTGS1	9	125141054	Splice_Site	SNP	T	TCGA-UB-A7ME-01A-11D-A33K-10	38524969	125141054	16072377	39	48992										
GLE1	2733	hgsc.bcm.edu	37	chr9	131296078	131296078	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	gtggcctctcaccatgaagcAgcattccccattgcagttgt	9	13	1	1	rs369775688		TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr9:131296078A>T	ENST00000309971.4	+	11	1600	c.1494A>T	c.(1492-1494)gcA>gcT	p.A498A	RP11-216B9.6_ENST00000434999.1_RNA|GLE1_ENST00000372770.4_Silent_p.A498A|GLE1_ENST00000539582.1_Silent_p.A244A	NM_001003722.1	NP_001003722.1	Q53GS7	GLE1_HUMAN	GLE1 RNA export mediator	498					mRNA export from nucleus (GO:0006406)|poly(A)+ mRNA export from nucleus (GO:0016973)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)|nuclear pore (GO:0005643)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	16						ACCATGAAGCAGCATTCCCCA	0.483																																					p.A498A		Atlas-SNP	.											.	GLE1	42	.	0			c.A1494T						.						121	119	120					9																	131296078		2203	4300	6503	SO:0001819	synonymous_variant	2733	exon11			TGAAGCAGCATTC	AF058922	CCDS6904.1, CCDS35154.1	9q34.13	2014-09-17	2013-06-18	2007-10-04	ENSG00000119392	ENSG00000119392			4315	protein-coding gene	gene with protein product		603371	"GLE1 (yeast homolog)-like, RNA export mediator", "GLE1 RNA export mediator-like (yeast)", "GLE1 RNA export mediator (yeast)", "lethal congenital contracture syndrome 1", "GLE1 RNA export mediator homolog (yeast)"	GLE1L, LCCS1		9618489, 18204449	Standard	NM_001499		Approved	hGLE1	uc004bvj.3	Q53GS7	OTTHUMG00000020749	ENST00000309971.4:c.1494A>T	chr9.hg19:g.131296078A>T		131.0	0.0		120.0	49.0	NM_001499	O75458|Q53GT9|Q5VVU1|Q8NCP6|Q9UFL6	Silent	SNP	ENST00000309971.4	hg19	CCDS35154.1																																																																																			.	.		0.483	GLE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054456.1	NM_001003722		T	131296078	A	T	131296078	2	4	347	1	0	0	0	0	0	0	0	1	6443	175	7	4		4	GLE1	9	131296078	Silent	SNP	A	TCGA-UB-A7ME-01A-11D-A33K-10	6155024	131296078	9917353	40	48993										
TPRN	286262	hgsc.bcm.edu	37	chr9	140086995	140086995	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	gtgcaaagggcttctcctctGagccggatccctcttcctcc	9	16	3	1			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr9:140086995G>A	ENST00000409012.4	-	2	1960	c.1874C>T	c.(1873-1875)tCa>tTa	p.S625L	TPRN_ENST00000321773.2_Missense_Mutation_p.S564L|TPRN_ENST00000541945.1_5'Flank	NM_001128228.2	NP_001121700.2	Q4KMQ1	TPRN_HUMAN	taperin	625	Glu-rich.				sensory perception of sound (GO:0007605)	stereocilium (GO:0032420)				breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)	8						CTTCTCCTCTGAGCCGGATCc	0.627																																					p.S625L		Atlas-SNP	.											.	TPRN	28	.	0			c.C1874T						.						46	36	39					9																	140086995		2200	4299	6499	SO:0001583	missense	286262	exon2			TCCTCTGAGCCGG	AK074735	CCDS56594.1	9q34.3	2011-01-06	2010-03-24	2010-03-24	ENSG00000176058	ENSG00000176058			26894	protein-coding gene	gene with protein product		613354	"chromosome 9 open reading frame 75", "deafness, autosomal recessive 79"	C9orf75, DFNB79		20170898, 20170899	Standard	NM_001128228		Approved	FLJ90254	uc004clu.3	Q4KMQ1	OTTHUMG00000020984	ENST00000409012.4:c.1874C>T	chr9.hg19:g.140086995G>A	ENSP00000387100:p.Ser625Leu	65.0	0.0		59.0	6.0	NM_001128228	B7ZKU5|Q5VSG5|Q5VSG6|Q6IPP2|Q8NCH2	Missense_Mutation	SNP	ENST00000409012.4	hg19	CCDS56594.1	.	.	.	.	.	.	.	.	.	.	G	7.993	0.753724	0.15778	.	.	ENSG00000176058	ENST00000333046;ENST00000409012;ENST00000321773	.	.	.	4.41	1.34	0.21922	.	3.145700	0.01400	N	0.013548	T	0.20700	0.0498	N	0.08118	0	0.09310	N	1	B	0.17038	0.02	B	0.09377	0.004	T	0.14504	-1.0470	9	0.30854	T	0.27	1.9806	5.6391	0.17554	0.3917:0.0:0.6083:0.0	.	625	Q4KMQ1	TPRN_HUMAN	L	423;625;564	.	ENSP00000313704:S564L	S	-	2	0	TPRN	139206816	0.001000	0.12720	0.003000	0.11579	0.438000	0.31896	1.093000	0.30939	0.081000	0.16988	0.561000	0.74099	TCA	.	.		0.627	TPRN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055323.3	NM_173691		A	140086995	G	A	140086995	3	1	347	1	0	0	0	0	1	0	0	0	16436	1294	45	3	353	3	TPRN	9	140086995	Missense_Mutation	SNP	G	TCGA-UB-A7ME-01A-11D-A33K-10	8790917	140086995	1126436	41	48994										
FBXO18	84893	hgsc.bcm.edu	37	chr10	5945116	5945116	+	Silent	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	catggtctctatcctaaaccGagaacaaaaagagggagtag	10	8	1	2			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr10:5945116G>C	ENST00000362091.4	+	2	250	c.135G>C	c.(133-135)ccG>ccC	p.P45P	FBXO18_ENST00000379999.5_Silent_p.P96P|FBXO18_ENST00000397269.3_5'UTR|FBXO18_ENST00000470089.1_Intron	NM_001258453.1|NM_178150.2	NP_001245382.1|NP_835363.1	Q8NFZ0	FBX18_HUMAN	F-box protein, helicase, 18	45					DNA catabolic process, endonucleolytic (GO:0000737)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|positive regulation of protein phosphorylation (GO:0001934)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)			NS(2)|breast(2)|kidney(2)|large_intestine(16)|lung(9)|ovary(2)|prostate(3)|skin(3)|stomach(1)	40						ATCCTAAACCGAGAACAAAAA	0.458																																					p.P96P		Atlas-SNP	.											.	FBXO18	108	.	0			c.G288C						.						74	71	72					10																	5945116		2203	4300	6503	SO:0001819	synonymous_variant	84893	exon3			TAAACCGAGAACA	AK095343	CCDS7072.1, CCDS7073.1, CCDS73064.1	10p15.1	2004-08-24	2004-06-15		ENSG00000134452	ENSG00000134452		"F-boxes /  "other""	13620	protein-coding gene	gene with protein product		607222	"F-box only protein 18"			10531037, 11956208	Standard	NM_032807		Approved	FBH1, FLJ14590, Fbx18	uc001iit.4	Q8NFZ0	OTTHUMG00000017609	ENST00000362091.4:c.135G>C	chr10.hg19:g.5945116G>C		76.0	0.0		114.0	37.0	NM_032807	Q5JVB0|Q5JVB1|Q7Z4Q6|Q7Z4R0|Q8N1P5|Q8N586|Q96E82|Q96K67|Q96SW7|Q9UFB2	Silent	SNP	ENST00000362091.4	hg19	CCDS7072.1																																																																																			.	.		0.458	FBXO18-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046596.1	NM_032807		C	5945116	G	C	5945116	2	2	347	1	0	0	0	0	0	0	0	1	5739	1045	37	4		4	FBXO18	10	5945116	Silent	SNP	G	TCGA-UB-A7ME-01A-11D-A33K-10		5945116	129589631	42	48995										
COL13A1	1305	hgsc.bcm.edu	37	chr10	71692351	71692351	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	gccggggagaagggcaatccAggagcagaggtacatgagag	18	7	0	3			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr10:71692351A>T	ENST00000398978.3	+	30	2178	c.1686A>T	c.(1684-1686)ccA>ccT	p.P562P	COL13A1_ENST00000517713.1_Intron|COL13A1_ENST00000398974.3_Silent_p.P550P|COL13A1_ENST00000398964.3_Silent_p.P533P|COL13A1_ENST00000522165.1_Silent_p.P543P|COL13A1_ENST00000398973.3_Silent_p.P562P|COL13A1_ENST00000357811.3_Silent_p.P540P|COL13A1_ENST00000354547.3_Silent_p.P540P|COL13A1_ENST00000398972.3_Silent_p.P562P|COL13A1_ENST00000398968.3_Silent_p.P543P|COL13A1_ENST00000520133.1_Intron|COL13A1_ENST00000520267.1_Intron|COL13A1_ENST00000398966.3_Silent_p.P540P|COL13A1_ENST00000398971.3_Intron|COL13A1_ENST00000356340.3_Silent_p.P562P|COL13A1_ENST00000398969.3_Intron	NM_001130103.1	NP_001123575.1			collagen, type XIII, alpha 1											endometrium(5)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	28						AGGGCAATCCAGGAGCAGAGG	0.507																																					p.P562P		Atlas-SNP	.											.	COL13A1	133	.	0			c.A1686T						.						100	119	113					10																	71692351		2018	4181	6199	SO:0001819	synonymous_variant	1305	exon30			CAATCCAGGAGCA	AJ293624	CCDS44419.1, CCDS44423.1, CCDS44424.1, CCDS44425.1, CCDS44427.1, CCDS44428.1, CCDS44423.2, CCDS44424.2, CCDS44425.2, CCDS44427.2, CCDS44428.2	10q22	2013-01-16			ENSG00000197467	ENSG00000197467		"Collagens"	2190	protein-coding gene	gene with protein product		120350					Standard	NM_001130103		Approved		uc001jql.3	Q5TAT6	OTTHUMG00000018394	ENST00000398978.3:c.1686A>T	chr10.hg19:g.71692351A>T		86.0	0.0		91.0	20.0	NM_001130103		Silent	SNP	ENST00000398978.3	hg19	CCDS44419.1																																																																																			.	.		0.507	COL13A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048468.1	NM_005203		T	71692351	A	T	71692351	2	4	347	1	0	0	0	0	0	0	0	1	3672	175	7	4		4	COL13A1	10	71692351	Silent	SNP	A	TCGA-UB-A7ME-01A-11D-A33K-10	65747235	71692351	63842396	43	48996										
PNLIPRP3	119548	hgsc.bcm.edu	37	chr10	118202641	118202641	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	aagatcacccgtatcaacatAgctggatggaaaacagatgg	10	8	2	2			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr10:118202641A>T	ENST00000369230.3	+	3	425	c.279A>T	c.(277-279)atA>atT	p.I93I		NM_001011709.2	NP_001011709.2	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3	93					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	triglyceride lipase activity (GO:0004806)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(29)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50				all cancers(201;0.0131)		GTATCAACATAGCTGGATGGA	0.398																																					p.I93I		Atlas-SNP	.											.	PNLIPRP3	101	.	0			c.A279T						.						119	107	111					10																	118202641		2203	4300	6503	SO:0001819	synonymous_variant	119548	exon3			CAACATAGCTGGA	BC015840	CCDS31292.1	10q26.12	2014-03-14			ENSG00000203837	ENSG00000203837	3.1.1.3		23492	protein-coding gene	gene with protein product							Standard	NM_001011709		Approved		uc001lcl.4	Q17RR3	OTTHUMG00000019100	ENST00000369230.3:c.279A>T	chr10.hg19:g.118202641A>T		90.0	0.0		88.0	15.0	NM_001011709		Silent	SNP	ENST00000369230.3	hg19	CCDS31292.1																																																																																			.	.		0.398	PNLIPRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050520.1	XM_058404		T	118202641	A	T	118202641	2	4	347	1	0	0	0	0	0	0	0	1	12161	410	15	4		4	PNLIPRP3	10	118202641	Silent	SNP	A	TCGA-UB-A7ME-01A-11D-A33K-10	46510290	118202641	17332106	44	48997										
ART5	116969	hgsc.bcm.edu	37	chr11	3661593	3661593	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	cccaggggcaggatgggaacAgcctgggcctgtggagcaaa	17	10	0	0			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr11:3661593A>T	ENST00000397068.3	-	2	458	c.66T>A	c.(64-66)gcT>gcA	p.A22A	ART5_ENST00000359918.4_Silent_p.A22A|TRPC2_ENST00000526541.1_RNA|ART5_ENST00000397067.3_Silent_p.A22A	NM_053017.3	NP_443750.2	Q96L15	NAR5_HUMAN	ADP-ribosyltransferase 5	22					protein ADP-ribosylation (GO:0006471)	extracellular region (GO:0005576)|membrane (GO:0016020)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|NAD+ nucleosidase activity (GO:0003953)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(6)|ovary(1)	11		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0336)|LUSC - Lung squamous cell carcinoma(625;0.19)		GGATGGGAACAGCCTGGGCCT	0.572																																					p.A22A		Atlas-SNP	.											.	ART5	38	.	0			c.T66A						.						22	23	22					11																	3661593		2095	4073	6168	SO:0001819	synonymous_variant	116969	exon2			GGGAACAGCCTGG	Y16835	CCDS7743.1, CCDS73242.1	11p15.4	2008-02-05			ENSG00000167311	ENSG00000167311			24049	protein-coding gene	gene with protein product		610625				11587854, 10448534	Standard	NM_001079536		Approved		uc001lyb.1	Q96L15	OTTHUMG00000011842	ENST00000397068.3:c.66T>A	chr11.hg19:g.3661593A>T		33.0	0.0		52.0	27.0	NM_053017	C9IYG7|Q6UX84|Q86W02	Silent	SNP	ENST00000397068.3	hg19	CCDS7743.1																																																																																			.	.		0.572	ART5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032760.2	NM_053017		T	3661593	A	T	3661593	2	4	347	1	0	0	0	0	0	0	0	1	1000	175	7	4		4	ART5	11	3661593	Silent	SNP	A	TCGA-UB-A7ME-01A-11D-A33K-10		3661593	131344923	45	48998										
VWCE	220001	hgsc.bcm.edu	37	chr11	61026465	61026465	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	agagtgggggctcctggaggGgtcgaaggccctggtgagag	21	7	0	2			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr11:61026465G>C	ENST00000335613.5	-	20	2936	c.2550C>G	c.(2548-2550)acC>acG	p.T850T	VWCE_ENST00000535710.1_Silent_p.T315T	NM_152718.2	NP_689931.2	Q96DN2	VWCE_HUMAN	von Willebrand factor C and EGF domains	850	Pro-rich.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37						CTCCTGGAGGGGTCGAAGGCC	0.657																																					p.T850T		Atlas-SNP	.											.	VWCE	84	.	0			c.C2550G						.						31	36	34					11																	61026465		2203	4299	6502	SO:0001819	synonymous_variant	220001	exon20			TGGAGGGGTCGAA	AK056571	CCDS8002.1	11q12.2	2006-08-04			ENSG00000167992	ENSG00000167992			26487	protein-coding gene	gene with protein product		611115				12869306	Standard	NM_152718		Approved	URG11, FLJ32009, VWC1	uc001nra.3	Q96DN2	OTTHUMG00000168208	ENST00000335613.5:c.2550C>G	chr11.hg19:g.61026465G>C		49.0	0.0		50.0	18.0	NM_152718	A5PKV0|Q7Z7L6|Q86WK8	Silent	SNP	ENST00000335613.5	hg19	CCDS8002.1																																																																																			.	.		0.657	VWCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398811.1	NM_152718		C	61026465	G	C	61026465	2	2	347	1	0	0	0	0	0	0	0	1	17260	1219	43	4		4	VWCE	11	61026465	Silent	SNP	G	TCGA-UB-A7ME-01A-11D-A33K-10	57364872	61026465	73980051	46	48999										
RPS3	6188	hgsc.bcm.edu	37	chr11	75115172	75115172	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	gctaaatccatgaagtttgtGgatggcctgatgatccacag	11	8	0	3			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr11:75115172G>A	ENST00000531188.1	+	5	521	c.459G>A	c.(457-459)gtG>gtA	p.V153V	SNORD15B_ENST00000384714.1_RNA|RPS3_ENST00000524851.1_Silent_p.V153V|RPS3_ENST00000278572.6_Silent_p.V169V|RPS3_ENST00000534440.1_Intron|RPS3_ENST00000526608.1_Silent_p.V141V|RPS3_ENST00000529285.1_Intron|RPS3_ENST00000527446.1_Silent_p.V153V	NM_001005.4|NM_001260506.1|NM_001260507.1	NP_000996.2|NP_001247435.1|NP_001247436.1	P23396	RS3_HUMAN	ribosomal protein S3	153					cellular protein metabolic process (GO:0044267)|cellular response to DNA damage stimulus (GO:0006974)|cytoplasmic translation (GO:0002181)|DNA catabolic process, endonucleolytic (GO:0000737)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|negative regulation of DNA repair (GO:0045738)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of DNA N-glycosylase activity (GO:1902546)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|ruffle membrane (GO:0032587)	damaged DNA binding (GO:0003684)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|enzyme binding (GO:0019899)|iron-sulfur cluster binding (GO:0051536)|mRNA binding (GO:0003729)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase A binding (GO:0051018)|protein kinase binding (GO:0019901)|structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)	6						TGAAGTTTGTGGATGGCCTGA	0.552																																					p.V169V		Atlas-SNP	.											.	RPS3	20	.	0			c.G507A						.						112	96	102					11																	75115172		2200	4293	6493	SO:0001819	synonymous_variant	6188	exon5			GTTTGTGGATGGC		CCDS8236.1, CCDS58161.1	11q13.3-q13.5	2011-04-05				ENSG00000149273		"S ribosomal proteins"	10420	protein-coding gene	gene with protein product	"IMR-90 ribosomal protein S3", "40S ribosomal protein S3"	600454				1712897, 7789996	Standard	NM_001005		Approved	FLJ26283, FLJ27450, MGC87870, S3	uc031qcs.1	P23396		ENST00000531188.1:c.459G>A	chr11.hg19:g.75115172G>A		98.0	0.0		177.0	19.0	NM_001260506	B2R7N5|J3KN86|Q498B5|Q8NI95	Silent	SNP	ENST00000531188.1	hg19	CCDS8236.1	.	.	.	.	.	.	.	.	.	.	g	10.24	1.296922	0.23650	.	.	ENSG00000149273	ENST00000525933	.	.	.	5.21	2.34	0.29019	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-18.6916	2.0172	0.03500	0.1703:0.159:0.5061:0.1647	.	.	.	.	X	81	.	.	W	+	2	0	RPS3	74792820	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.255000	0.43222	0.358000	0.24211	0.645000	0.84053	TGG	.	.		0.552	RPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384158.2	NM_001005		A	75115172	G	A	75115172	2	1	347	1	0	0	0	0	0	0	0	1	13658	1335	47	3		3	RPS3	11	75115172	Silent	SNP	G	TCGA-UB-A7ME-01A-11D-A33K-10	14088707	75115172	59891344	47	49000										
MFAP5	8076	hgsc.bcm.edu	37	chr12	8807070	8807070	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	ggtgcaatatcagccaaaacAgccaaaactgaaaaggcaca	8	10	1	1			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr12:8807070A>T	ENST00000359478.2	-	6	367	c.180T>A	c.(178-180)gcT>gcA	p.A60A	MFAP5_ENST00000540087.1_Silent_p.A60A|MFAP5_ENST00000535336.1_Silent_p.A60A|MFAP5_ENST00000396549.2_Silent_p.A60A|MFAP5_ENST00000543369.1_Silent_p.A48A|MFAP5_ENST00000433590.2_Intron|MFAP5_ENST00000538107.1_5'UTR	NM_003480.2	NP_003471.1	Q13361	MFAP5_HUMAN	microfibrillar associated protein 5	60					extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|microfibril (GO:0001527)	extracellular matrix structural constituent (GO:0005201)			breast(1)|endometrium(2)|large_intestine(4)|lung(5)|skin(1)	13	Lung SC(5;0.184)					CAGCCAAAACAGCCAAAACTG	0.498																																					p.A60A		Atlas-SNP	.											.	MFAP5	34	.	0			c.T180A						.						84	68	73					12																	8807070		2203	4300	6503	SO:0001819	synonymous_variant	8076	exon6			CAAAACAGCCAAA	AK124368	CCDS8595.1, CCDS73437.1	12p13.1-p12.3	2004-04-05				ENSG00000197614			29673	protein-coding gene	gene with protein product		601103				9792630, 8557636	Standard	XM_005253485		Approved	MAGP2, MP25	uc001qut.1	Q13361		ENST00000359478.2:c.180T>A	chr12.hg19:g.8807070A>T		168.0	0.0		197.0	63.0	NM_003480	B0AZL6|D3DUV1|Q7Z490	Silent	SNP	ENST00000359478.2	hg19	CCDS8595.1	.	.	.	.	.	.	.	.	.	.	A	11.13	1.548320	0.27652	.	.	ENSG00000197614	ENST00000535411	.	.	.	4.87	-3.33	0.04958	.	.	.	.	.	T	0.50939	0.1645	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46569	-0.9182	4	.	.	.	.	7.8546	0.29474	0.7577:0.1251:0.1171:0.0	.	.	.	.	Q	50	.	.	L	-	2	0	MFAP5	8698337	0.920000	0.31207	0.942000	0.38095	0.930000	0.56654	-0.288000	0.08377	-0.697000	0.05092	0.533000	0.62120	CTG	.	.		0.498	MFAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400656.2	NM_003480		T	8807070	A	T	8807070	2	4	347	1	0	0	0	0	0	0	0	1	9527	175	7	4		4	MFAP5	12	8807070	Silent	SNP	A	TCGA-UB-A7ME-01A-11D-A33K-10		8807070	125044825	48	49001										
PDE3A	5139	hgsc.bcm.edu	37	chr12	20792858	20792858	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	gggaatttatgaattattttCatgctttggagattggatat	10	2	1	2			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr12:20792858C>A	ENST00000359062.3	+	10	2258	c.2218C>A	c.(2218-2220)Cat>Aat	p.H740N	PDE3A_ENST00000544307.1_3'UTR	NM_000921.4|NM_001244683.1	NP_000912.3|NP_001231612.1	Q14432	PDE3A_HUMAN	phosphodiesterase 3A, cGMP-inhibited	740	Catalytic. {ECO:0000250}.				blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP-mediated signaling (GO:0019934)|diterpenoid metabolic process (GO:0016101)|lipid metabolic process (GO:0006629)|negative regulation of apoptotic process (GO:0043066)|negative regulation of vascular permeability (GO:0043116)|oocyte maturation (GO:0001556)|positive regulation of oocyte development (GO:0060282)|positive regulation of vascular permeability (GO:0043117)|regulation of meiosis (GO:0040020)|response to cAMP (GO:0051591)|response to drug (GO:0042493)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(7)|lung(29)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	58	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Caffeine(DB00201)|Cilostazol(DB01166)|Enoximone(DB04880)|Ibudilast(DB05266)|Levosimendan(DB00922)|Milrinone(DB00235)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Tofisopam(DB08811)	GAATTATTTTCATGCTTTGGA	0.313																																					p.H740N		Atlas-SNP	.											.	PDE3A	184	.	0			c.C2218A						.						85	85	85					12																	20792858		2202	4300	6502	SO:0001583	missense	5139	exon10			TATTTTCATGCTT		CCDS31754.1	12p12.2	2011-04-15			ENSG00000172572	ENSG00000172572	3.1.4.17	"Phosphodiesterases"	8778	protein-coding gene	gene with protein product		123805				1315035, 10679291	Standard	NM_000921		Approved	CGI-PDE	uc001reh.2	Q14432	OTTHUMG00000168962	ENST00000359062.3:c.2218C>A	chr12.hg19:g.20792858C>A	ENSP00000351957:p.His740Asn	64.0	0.0		91.0	17.0	NM_000921	O60865|Q13348|Q17RD1	Missense_Mutation	SNP	ENST00000359062.3	hg19	CCDS31754.1	.	.	.	.	.	.	.	.	.	.	C	19.50	3.838440	0.71373	.	.	ENSG00000172572	ENST00000359062	T	0.76448	-1.02	5.03	5.03	0.67393	5&apos (1);-cyclic nucleotide phosphodiesterase, catalytic domain (1);3&apos (1);	0.000000	0.85682	D	0.000000	T	0.80592	0.4652	L	0.31476	0.935	0.80722	D	1	D	0.65815	0.995	P	0.61477	0.889	T	0.79806	-0.1648	10	0.38643	T	0.18	.	18.1402	0.89637	0.0:1.0:0.0:0.0	.	740	Q14432	PDE3A_HUMAN	N	740	ENSP00000351957:H740N	ENSP00000351957:H740N	H	+	1	0	PDE3A	20684125	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.225000	0.65294	2.614000	0.88457	0.491000	0.48974	CAT	.	.		0.313	PDE3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401756.2			A	20792858	C	A	20792858	3	1	347	1	0	0	0	0	1	0	0	0	11646	826	29	3	2256	3	PDE3A	12	20792858	Missense_Mutation	SNP	C	TCGA-UB-A7ME-01A-11D-A33K-10	11985788	20792858	113059037	49	49002										
SLC38A1	81539	hgsc.bcm.edu	37	chr12	46633498	46633498	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	tttctacttcggtgaaatcaTtggagtcattgctaatgtta	8	6	3	1	rs375543520		TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr12:46633498T>C	ENST00000398637.5	-	3	780	c.86A>G	c.(85-87)aAt>aGt	p.N29S	SLC38A1_ENST00000546893.1_Missense_Mutation_p.N29S|SLC38A1_ENST00000549633.1_Intron|SLC38A1_ENST00000549049.1_Missense_Mutation_p.N29S|SLC38A1_ENST00000439706.1_Missense_Mutation_p.N29S|SLC38A1_ENST00000552197.1_Missense_Mutation_p.N29S	NM_001077484.1|NM_001278387.1|NM_001278388.1|NM_001278389.1|NM_030674.3	NP_001070952.1|NP_001265316.1|NP_001265317.1|NP_001265318.1|NP_109599.3	Q9H2H9	S38A1_HUMAN	solute carrier family 38, member 1	29					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|ion transport (GO:0006811)|neurotransmitter uptake (GO:0001504)|neutral amino acid transport (GO:0015804)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neutral amino acid transmembrane transporter activity (GO:0015175)|sodium:amino acid symporter activity (GO:0005283)			NS(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(2)	23	Lung SC(27;0.137)|Renal(347;0.236)		all cancers(1;0.00805)|OV - Ovarian serous cystadenocarcinoma(5;0.0106)|Epithelial(2;0.0344)			GGTGAAATCATTGGAGTCATT	0.383																																					p.N29S		Atlas-SNP	.											.	SLC38A1	58	.	0			c.A86G						.	T	SER/ASN,SER/ASN	1,3765		0,1,1882	168	156	160		86,86	4.9	1	12		160	0,8254		0,0,4127	no	missense,missense	SLC38A1	NM_001077484.1,NM_030674.3	46,46	0,1,6009	CC,CT,TT		0.0,0.0266,0.0083	possibly-damaging,possibly-damaging	29/488,29/488	46633498	1,12019	1883	4127	6010	SO:0001583	missense	81539	exon3			AAATCATTGGAGT	AF271070	CCDS41774.1, CCDS61106.1	12q13.11	2013-05-22				ENSG00000111371		"Solute carriers"	13447	protein-coding gene	gene with protein product		608490				10891391	Standard	NM_030674		Approved	ATA1, NAT2, SAT1	uc001rpc.3	Q9H2H9		ENST00000398637.5:c.86A>G	chr12.hg19:g.46633498T>C	ENSP00000381634:p.Asn29Ser	96.0	0.0		108.0	20.0	NM_030674	Q8NC61|Q8NCF8|Q96JX2|Q9H2Q2	Missense_Mutation	SNP	ENST00000398637.5	hg19	CCDS41774.1	.	.	.	.	.	.	.	.	.	.	T	14.59	2.579486	0.46006	2.66E-4	0.0	ENSG00000111371	ENST00000549049;ENST00000439706;ENST00000398637;ENST00000546893;ENST00000552197;ENST00000550173	T;T;T;T;T	0.07327	3.38;3.38;3.38;3.38;3.2	4.93	4.93	0.64822	.	0.000000	0.56097	D	0.000035	T	0.08179	0.0204	N	0.08118	0	0.39643	D	0.970346	D;P	0.58268	0.982;0.882	P;B	0.54889	0.763;0.332	T	0.44034	-0.9354	10	0.09084	T	0.74	-23.5277	14.896	0.70644	0.0:0.0:0.0:1.0	.	29;29	F8VX04;Q9H2H9	.;S38A1_HUMAN	S	29	ENSP00000449607:N29S;ENSP00000398142:N29S;ENSP00000381634:N29S;ENSP00000447853:N29S;ENSP00000449756:N29S	ENSP00000381634:N29S	N	-	2	0	SLC38A1	44919765	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	4.839000	0.62810	1.975000	0.57531	0.477000	0.44152	AAT	.	.		0.383	SLC38A1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404218.2			C	46633498	T	C	46633498	3	2	347	1	0	0	0	0	1	0	0	0	14616	1493	52	2	1437	2	SLC38A1	12	46633498	Missense_Mutation	SNP	T	TCGA-UB-A7ME-01A-11D-A33K-10	25840640	46633498	87218397	50	49003										
MAP3K12	7786	hgsc.bcm.edu	37	chr12	53879187	53879187	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	cctgcaaaggacatcttggtGctcttgtcactcagctcctt	8	13	4	0			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr12:53879187G>T	ENST00000267079.2	-	6	1020	c.795C>A	c.(793-795)agC>agA	p.S265R	MAP3K12_ENST00000547151.1_5'Flank|MAP3K12_ENST00000547035.1_Missense_Mutation_p.S298R|MAP3K12_ENST00000547488.1_Missense_Mutation_p.S298R	NM_001193511.1|NM_006301.3	NP_001180440.1|NP_006292.3	Q12852	M3K12_HUMAN	mitogen-activated protein kinase kinase kinase 12	265	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				histone phosphorylation (GO:0016572)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	37						ACATCTTGGTGCTCTTGTCAC	0.517																																					p.S298R		Atlas-SNP	.											.	MAP3K12	160	.	0			c.C894A						.						220	211	214					12																	53879187		2203	4300	6503	SO:0001583	missense	7786	exon5			CTTGGTGCTCTTG	U07358	CCDS8860.1, CCDS55831.1	12q13.13	2013-10-30			ENSG00000139625	ENSG00000139625		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6851	protein-coding gene	gene with protein product	"dual leucine zipper kinase DLK"	600447		ZPK		8037767	Standard	NM_006301		Approved	MUK, DLK, ZPKP1, MEKK12	uc001sdn.2	Q12852	OTTHUMG00000169854	ENST00000267079.2:c.795C>A	chr12.hg19:g.53879187G>T	ENSP00000267079:p.Ser265Arg	74.0	0.0		97.0	39.0	NM_001193511	B3KSS9|G3V1Y2|Q86VQ5|Q8WY25	Missense_Mutation	SNP	ENST00000267079.2	hg19	CCDS8860.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.309912	0.81247	.	.	ENSG00000139625	ENST00000267079;ENST00000547488;ENST00000547035	D;D;D	0.82255	-1.59;-1.59;-1.59	4.84	4.84	0.62591	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.52532	D	0.000062	D	0.85678	0.5752	N	0.25031	0.7	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	D	0.87713	0.2568	10	0.87932	D	0	.	17.24	0.87010	0.0:0.0:1.0:0.0	.	298;265	G3V1Y2;Q12852	.;M3K12_HUMAN	R	265;298;298	ENSP00000267079:S265R;ENSP00000449038:S298R;ENSP00000448689:S298R	ENSP00000267079:S265R	S	-	3	2	MAP3K12	52165454	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.724000	0.38064	2.688000	0.91661	0.561000	0.74099	AGC	.	.		0.517	MAP3K12-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406267.1	NM_006301		T	53879187	G	T	53879187	3	4	347	1	0	0	0	0	1	0	0	0	9255	1310	46	3	1824	3	MAP3K12	12	53879187	Missense_Mutation	SNP	G	TCGA-UB-A7ME-01A-11D-A33K-10	7245689	53879187	79972708	51	49004										
G2E3	55632	hgsc.bcm.edu	37	chr14	31077159	31077159	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	tttctttagttcacggtggtCcttcacctggtttcttttct	7	10	5	0			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr14:31077159C>T	ENST00000206595.6	+	12	1538	c.1384C>T	c.(1384-1386)Cct>Tct	p.P462S	G2E3_ENST00000553504.1_Missense_Mutation_p.P492S|G2E3_ENST00000438909.2_Missense_Mutation_p.P416S	NM_017769.3	NP_060239.2	Q7L622	G2E3_HUMAN	G2/M-phase specific E3 ubiquitin protein ligase	462	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				apoptotic process (GO:0006915)|blastocyst development (GO:0001824)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	23						TCACGGTGGTCCTTCACCTGG	0.363																																					p.P462S		Atlas-SNP	.											.	G2E3	82	.	0			c.C1384T						.						97	90	92					14																	31077159		2203	4300	6503	SO:0001583	missense	55632	exon12			GGTGGTCCTTCAC	AK000340	CCDS9638.1	14q12	2013-01-28	2010-09-17	2009-02-03	ENSG00000092140	ENSG00000092140		"Zinc fingers, PHD-type"	20338	protein-coding gene	gene with protein product	"PHD finger protein 7B"	611299	"KIAA1333"	KIAA1333		18511420, 17239372	Standard	NM_017769		Approved	FLJ20333, PHF7B	uc001wqk.2	Q7L622	OTTHUMG00000140204	ENST00000206595.6:c.1384C>T	chr14.hg19:g.31077159C>T	ENSP00000206595:p.Pro462Ser	89.0	0.0		178.0	19.0	NM_017769	Q9BVR2|Q9H9E9|Q9NXC0|Q9P2L3	Missense_Mutation	SNP	ENST00000206595.6	hg19	CCDS9638.1	.	.	.	.	.	.	.	.	.	.	C	33	5.265007	0.95399	.	.	ENSG00000092140	ENST00000206595;ENST00000438909;ENST00000553504	T;T;T	0.57595	0.39;0.39;0.39	5.43	5.43	0.79202	HECT (2);	0.000000	0.85682	D	0.000000	T	0.74215	0.3687	M	0.74258	2.255	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.77078	-0.2721	10	0.87932	D	0	-13.7913	19.2391	0.93875	0.0:1.0:0.0:0.0	.	462	Q7L622	G2E3_HUMAN	S	462;416;492	ENSP00000206595:P462S;ENSP00000391068:P416S;ENSP00000451653:P492S	ENSP00000206595:P462S	P	+	1	0	G2E3	30146910	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.692000	0.47018	2.510000	0.84645	0.591000	0.81541	CCT	.	.		0.363	G2E3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276613.2	NM_017769		T	31077159	C	T	31077159	3	4	347	1	0	0	0	0	1	0	0	0	6148	855	30	3	1426	3	G2E3	14	31077159	Missense_Mutation	SNP	C	TCGA-UB-A7ME-01A-11D-A33K-10		31077159	76272381	52	49005										
KIAA1409	57578	hgsc.bcm.edu	37	chr14	94088446	94088446	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	cggggcctgaaaaacactctAtactctcaacctccgacagc	7	15	2	1	rs375712940		TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr14:94088446A>G	ENST00000393151.2	+	30	4867	c.4867A>G	c.(4867-4869)Ata>Gta	p.I1623V	UNC79_ENST00000256339.4_Missense_Mutation_p.I1446V|UNC79_ENST00000553484.1_Missense_Mutation_p.I1645V|UNC79_ENST00000555664.1_Missense_Mutation_p.I1623V			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	1623					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						AAAACACTCTATACTCTCAAC	0.488																																					p.I1446V		Atlas-SNP	.											.	UNC79	366	.	0			c.A4336G						.						82	84	84					14																	94088446		2203	4300	6503	SO:0001583	missense	57578	exon30			CACTCTATACTCT	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"KIAA1409"	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.4867A>G	chr14.hg19:g.94088446A>G	ENSP00000376858:p.Ile1623Val	85.0	0.0		103.0	24.0	NM_020818	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	hg19		.	.	.	.	.	.	.	.	.	.	A	1.422	-0.572497	0.03882	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.18338	2.23;2.22;2.22;2.23	5.65	0.156	0.14910	.	0.478254	0.24339	N	0.039391	T	0.08133	0.0203	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.40905	-0.9538	10	0.09590	T	0.72	-1.9916	6.7468	0.23466	0.4307:0.1454:0.4239:0.0	.	1645	C9JQL1	.	V	1446;1623;1645;1623;1645	ENSP00000256339:I1446V;ENSP00000450868:I1623V;ENSP00000451360:I1645V;ENSP00000376858:I1623V	ENSP00000256339:I1446V	I	+	1	0	KIAA1409	93158199	0.168000	0.22989	0.000000	0.03702	0.947000	0.59692	0.772000	0.26647	-0.136000	0.11475	0.402000	0.26972	ATA	.	.		0.488	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		G	94088446	A	G	94088446	3	3	347	1	0	0	0	0	1	0	0	0	8239	449	16	2	4442	2	KIAA1409	14	94088446	Missense_Mutation	SNP	A	TCGA-UB-A7ME-01A-11D-A33K-10	63011287	94088446	13261094	53	49006										
DICER1	23405	hgsc.bcm.edu	37	chr14	95557445	95557445	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	ggtacatttgcagaaaacttTtctgcaatcaaaatgaaaga	7	6	2	3			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr14:95557445T>A	ENST00000526495.1	-	28	5820	c.5529A>T	c.(5527-5529)gaA>gaT	p.E1843D	DICER1_ENST00000527414.1_Splice_Site_p.E1843D|DICER1_ENST00000556045.1_Splice_Site_p.E741D|DICER1_ENST00000393063.1_Splice_Site_p.E1843D|DICER1_ENST00000541352.1_Splice_Site_p.K1789I|DICER1_ENST00000343455.3_Splice_Site_p.E1843D|DICER1_ENST00000527416.2_5'UTR			Q9UPY3	DICER_HUMAN	dicer 1, ribonuclease type III	1843					angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac muscle cell development (GO:0055013)|cerebral cortex development (GO:0021987)|defense response to virus (GO:0051607)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|hair follicle cell proliferation (GO:0071335)|hair follicle morphogenesis (GO:0031069)|inner ear receptor cell development (GO:0060119)|intestinal epithelial cell development (GO:0060576)|lung development (GO:0030324)|mRNA stabilization (GO:0048255)|multicellular organism growth (GO:0035264)|negative regulation of Schwann cell proliferation (GO:0010626)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nerve development (GO:0021675)|neuron projection morphogenesis (GO:0048812)|olfactory bulb interneuron differentiation (GO:0021889)|peripheral nervous system myelin formation (GO:0032290)|positive regulation of gene expression (GO:0010628)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of myelination (GO:0031643)|positive regulation of Schwann cell differentiation (GO:0014040)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|production of siRNA involved in RNA interference (GO:0030422)|regulation of cell cycle (GO:0051726)|regulation of enamel mineralization (GO:0070173)|regulation of neuron differentiation (GO:0045664)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of viral genome replication (GO:0045069)|reproductive structure development (GO:0048608)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|spinal cord motor neuron differentiation (GO:0021522)|spindle assembly (GO:0051225)|spleen development (GO:0048536)|stem cell maintenance (GO:0019827)|targeting of mRNA for destruction involved in RNA interference (GO:0030423)|zygote asymmetric cell division (GO:0010070)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|growth cone (GO:0030426)|RISC complex (GO:0016442)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|ribonuclease III activity (GO:0004525)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(13)|kidney(3)|large_intestine(10)|lung(33)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	75		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)		CAGAAAACTTTTCTGCAATCA	0.328			"Mis F, N"		"sex cord-stromal tumour, TGCT, embryonal rhadomyosarcoma"	pleuropulmonary blastoma			Familial Multinodular Goiter ;DICER 1 syndrome																												p.E1843D		Atlas-SNP	.	yes	Rec	yes	Familial Pleuropulmonary Blastoma	14	14q32.13	23405	"dicer 1, ribonuclease type III "		"E, M, O"	.	DICER1	181	.	0			c.A5529T						.						49	50	50					14																	95557445		2201	4300	6501	SO:0001630	splice_region_variant	23405	exon27	Familial Cancer Database	Adolescent Multinodular Goiter, incl. Multinodular Euthyroid Goiter & Non-Medullary Thyroid Cancer;incl. Pleuropulmonary Blastoma, Familial ; Cystic Nephroma, Familial	AAACTTTTCTGCA	AB028449	CCDS9931.1, CCDS55941.1	14q32.13	2014-09-17	2008-02-20		ENSG00000100697	ENSG00000100697			17098	protein-coding gene	gene with protein product	"dicer 1, double-stranded RNA-specific endoribonuclease"	606241	"Dicer1, Dcr-1 homolog (Drosophila)", "multinodular goitre 1"	MNG1		10051563, 10786632, 21205968	Standard	NM_177438		Approved	Dicer, KIAA0928, K12H4.8-LIKE, HERNA	uc001ydw.2	Q9UPY3	OTTHUMG00000166134	ENST00000526495.1:c.5528-1A>T	chr14.hg19:g.95557445T>A		103.0	0.0		124.0	27.0	NM_030621	A7E2D3|B3KRG4|E0AD28|O95943|Q9UQ02	Missense_Mutation	SNP	ENST00000526495.1	hg19	CCDS9931.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.79|13.79	2.343024|2.343024	0.41498|0.41498	.|.	.|.	ENSG00000100697|ENSG00000100697	ENST00000343455;ENST00000526495;ENST00000393063;ENST00000527414;ENST00000556045|ENST00000541352	D;D;D;D;D|T	0.85629|0.53423	-2.01;-2.01;-2.01;-2.01;-2.01|0.62	5.93|5.93	2.32|2.32	0.28847|0.28847	Ribonuclease III (3);|.	0.097745|.	0.64402|.	D|.	0.000001|.	T|T	0.42359|0.42359	0.1199|0.1199	.|.	.|.	.|.	0.25177|0.25177	N|N	0.990233|0.990233	B;P|.	0.35328|.	0.016;0.495|.	B;B|.	0.26517|.	0.011;0.07|.	T|T	0.27673|0.27673	-1.0067|-1.0067	9|6	0.19590|0.33940	T|T	0.45|0.23	.|.	9.4257|9.4257	0.38578|0.38578	0.0:0.2002:0.0:0.7998|0.0:0.2002:0.0:0.7998	.|.	741;1843|.	B3KRG4;Q9UPY3|.	.;DICER_HUMAN|.	D|I	1843;1843;1843;1843;741|1789	ENSP00000343745:E1843D;ENSP00000437256:E1843D;ENSP00000376783:E1843D;ENSP00000435681:E1843D;ENSP00000451041:E741D|ENSP00000444719:K1789I	ENSP00000343745:E1843D|ENSP00000444719:K1789I	E|K	-|-	3|2	2|0	DICER1|DICER1	94627198|94627198	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.658000|0.658000	0.38924|0.38924	2.338000|2.338000	0.43957|0.43957	0.158000|0.158000	0.19367|0.19367	-0.250000|-0.250000	0.11733|0.11733	GAA|AAA	.	.		0.328	DICER1-004	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387997.1		Missense_Mutation	A	95557445	T	A	95557445	5	1	347	1	0	0	0	0	0	0	1	0	4523	1855	64	4	247	4	DICER1	14	95557445	Splice_Site	SNP	T	TCGA-UB-A7ME-01A-11D-A33K-10	1468999	95557445	11792095	54	49007										
BCL11B	64919	hgsc.bcm.edu	37	chr14	99641808	99641808	+	Nonsense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	tggtcgcacagctggcacttGtagggcttctcgcccgtgtg	14	12	1	0			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr14:99641808G>C	ENST00000357195.3	-	4	1374	c.1365C>G	c.(1363-1365)taC>taG	p.Y455*	BCL11B_ENST00000443726.2_Nonsense_Mutation_p.Y261*|BCL11B_ENST00000345514.2_Nonsense_Mutation_p.Y384*	NM_001282237.1|NM_138576.2	NP_001269166.1|NP_612808.1	Q9C0K0	BC11B_HUMAN	B-cell CLL/lymphoma 11B (zinc finger protein)	455					alpha-beta T cell differentiation (GO:0046632)|epithelial cell morphogenesis (GO:0003382)|keratinocyte development (GO:0003334)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|odontogenesis of dentin-containing tooth (GO:0042475)|olfactory bulb axon guidance (GO:0071678)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive T cell selection (GO:0043368)|post-embryonic camera-type eye development (GO:0031077)|regulation of keratinocyte proliferation (GO:0010837)|regulation of lipid metabolic process (GO:0019216)|regulation of neuron differentiation (GO:0045664)|striatal medium spiny neuron differentiation (GO:0021773)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|thymus development (GO:0048538)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(3)|breast(1)|central_nervous_system(9)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(9)|prostate(2)|skin(2)	34		Melanoma(154;0.0866)|all_epithelial(191;0.241)		COAD - Colon adenocarcinoma(157;0.103)		GCTGGCACTTGTAGGGCTTCT	0.642			T	TLX3	T-ALL																																p.Y455X		Atlas-SNP	.		Dom	yes		14	14q32.1	64919	B-cell CLL/lymphoma 11B  (CTIP2)		L	.	BCL11B	108	.	0			c.C1365G						.						28	28	28					14																	99641808		2202	4300	6502	SO:0001587	stop_gained	64919	exon4			GCACTTGTAGGGC	AJ404614	CCDS9949.1, CCDS9950.1	14q32	2013-01-08			ENSG00000127152	ENSG00000127152		"Zinc fingers, C2H2-type"	13222	protein-coding gene	gene with protein product		606558		ZNF856B		11719382, 16950772	Standard	NM_138576		Approved	CTIP-2, CTIP2, hRIT1-alpha	uc001yga.3	Q9C0K0	OTTHUMG00000028967	ENST00000357195.3:c.1365C>G	chr14.hg19:g.99641808G>C	ENSP00000349723:p.Tyr455*	47.0	0.0		44.0	5.0	NM_138576	Q9H162	Nonsense_Mutation	SNP	ENST00000357195.3	hg19	CCDS9950.1	.	.	.	.	.	.	.	.	.	.	G	36	5.813304	0.96975	.	.	ENSG00000127152	ENST00000357195;ENST00000345514;ENST00000443726	.	.	.	3.72	3.72	0.42706	.	0.000000	0.64402	D	0.000011	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.4387	7.5413	0.27740	0.1963:0.0:0.8037:0.0	.	.	.	.	X	455;384;261	.	ENSP00000280435:Y384X	Y	-	3	2	BCL11B	98711561	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.468000	0.73551	1.794000	0.52575	0.462000	0.41574	TAC	.	.		0.642	BCL11B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000072332.2	NM_138576		C	99641808	G	C	99641808	4	2	347	1	0	0	0	0	0	1	0	0	1364	1372	48	4	1323	4	BCL11B	14	99641808	Nonsense_Mutation	SNP	G	TCGA-UB-A7ME-01A-11D-A33K-10	4084363	99641808	7707732	55	49008										
AQR	9716	hgsc.bcm.edu	37	chr15	35149307	35149307	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	aggtggtagttgtaataaagTctaattaaaaaaaaaaaaac	7	2	1	0			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr15:35149307T>A	ENST00000156471.5	-	35	4369	c.4144A>T	c.(4144-4146)Act>Tct	p.T1382S		NM_014691.2	NP_055506.1	O60306	AQR_HUMAN	aquarius intron-binding spliceosomal factor	1382					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(10)|lung(18)|ovary(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	57		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		TGTAATAAAGTCTAATTAAAA	0.353																																					p.T1382S		Atlas-SNP	.											.	AQR	139	.	0			c.A4144T						.						90	79	82					15																	35149307		1837	4078	5915	SO:0001630	splice_region_variant	9716	exon35			ATAAAGTCTAATT	AB011132	CCDS42013.1	15q13	2013-09-12	2013-09-12			ENSG00000021776			29513	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 164"	610548	"aquarius homolog (mouse)"			9626505, 16949364	Standard	NM_014691		Approved	KIAA0560, fSAP164, IBP160	uc001ziv.3	O60306		ENST00000156471.5:c.4144-1A>T	chr15.hg19:g.35149307T>A		47.0	0.0		44.0	15.0	NM_014691	A0JP17|A5YKK3|Q2YDX9|Q6IRU8|Q6PIC8	Missense_Mutation	SNP	ENST00000156471.5	hg19	CCDS42013.1	.	.	.	.	.	.	.	.	.	.	T	6.724	0.502394	0.12822	.	.	ENSG00000021776	ENST00000543879	.	.	.	5.5	3.18	0.36537	.	0.464126	0.25442	N	0.030646	T	0.24928	0.0605	L	0.29908	0.895	0.26649	N	0.97215	B	0.15473	0.013	B	0.11329	0.006	T	0.19679	-1.0298	9	0.08599	T	0.76	-15.6472	7.9422	0.29965	0.0:0.1791:0.0:0.8209	.	1382	O60306	AQR_HUMAN	S	1382	.	ENSP00000445700:T1382S	T	-	1	0	AQR	32936599	1.000000	0.71417	1.000000	0.80357	0.838000	0.47535	0.893000	0.28336	1.112000	0.41740	0.533000	0.62120	ACT	.	.		0.353	AQR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417526.2	NM_014691	Missense_Mutation	A	35149307	T	A	35149307	5	1	347	1	0	0	0	0	0	0	1	0	835	1681	58	4	317	4	AQR	15	35149307	Splice_Site	SNP	T	TCGA-UB-A7ME-01A-11D-A33K-10		35149307	67382085	56	49009										
LBXCOR1	390598	hgsc.bcm.edu	37	chr15	68126112	68126112	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	ccctgcaccatttctcctgcAagatgctgacgccccgccac	7	19	1	2			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr15:68126112A>C	ENST00000380035.2	+	9	2894	c.2836A>C	c.(2836-2838)Aag>Cag	p.K946Q	RP11-34F13.3_ENST00000558889.1_RNA|SKOR1_ENST00000554240.1_Missense_Mutation_p.K907Q|RP11-34F13.2_ENST00000502156.1_lincRNA|SKOR1_ENST00000389002.1_Missense_Mutation_p.K902Q|SKOR1_ENST00000554054.1_Missense_Mutation_p.K918Q|SKOR1_ENST00000341418.5_Missense_Mutation_p.K849Q			P84550	SKOR1_HUMAN	SKI family transcriptional corepressor 1	946					negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)			endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(7)|urinary_tract(1)	23						TTTCTCCTGCAAGATGCTGAC	0.677											OREG0023216	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K849Q		Atlas-SNP	.											.	SKOR1	144	.	0			c.A2545C						.						90	84	86					15																	68126112		2200	4298	6498	SO:0001583	missense	390598	exon15			TCCTGCAAGATGC		CCDS58374.1	15q23	2011-08-04	2010-06-23	2010-06-23	ENSG00000188779	ENSG00000188779		"SKI transcriptional corepressors"	21326	protein-coding gene	gene with protein product	"transcriptional corepressor CORL1", "functional smad suppressing element 15", "corepressor for LBX1"	611273	"Lbxcor1 homolog (mouse)"	LBXCOR1		15528197	Standard	NM_001258024		Approved	CORL1, FUSSEL15	uc031qsn.1	P84550		ENST00000380035.2:c.2836A>C	chr15.hg19:g.68126112A>C	ENSP00000369374:p.Lys946Gln	57.0	0.0	1104	69.0	17.0	NM_001258024	A6NIP4|A6NJY0|Q2VWA5	Missense_Mutation	SNP	ENST00000380035.2	hg19		.	.	.	.	.	.	.	.	.	.	A	31	5.080584	0.94050	.	.	ENSG00000188779	ENST00000341418;ENST00000554240;ENST00000554054;ENST00000380035;ENST00000389002	T;T;T;T;T	0.57907	0.37;0.37;0.37;0.37;0.37	5.32	5.32	0.75619	.	0.057165	0.64402	D	0.000002	T	0.59998	0.2235	N	0.24115	0.695	0.45194	D	0.998206	D	0.69078	0.997	D	0.80764	0.994	T	0.65162	-0.6235	10	0.72032	D	0.01	-24.1734	15.2538	0.73568	1.0:0.0:0.0:0.0	.	902	P84550-3	.	Q	849;907;918;946;902	ENSP00000343200:K849Q;ENSP00000451193:K907Q;ENSP00000452361:K918Q;ENSP00000369374:K946Q;ENSP00000373654:K902Q	ENSP00000343200:K849Q	K	+	1	0	SKOR1	65913166	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.696000	0.91302	2.137000	0.66172	0.459000	0.35465	AAG	.	.		0.677	SKOR1-003	KNOWN	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000410832.1	NM_001031807		C	68126112	A	C	68126112	3	2	347	1	0	0	0	0	1	0	0	0	8664	131	5	5	2742	5	LBXCOR1	15	68126112	Missense_Mutation	SNP	A	TCGA-UB-A7ME-01A-11D-A33K-10	32976805	68126112	34405280	57	49010										
FAM169B	283777	hgsc.bcm.edu	37	chr15	99023922	99023922	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	gtgaggtagaaaaaacatgtCatcatcatccaaatttctct	6	8	4	2			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr15:99023922C>T	ENST00000558256.1	-	4	340	c.91G>A	c.(91-93)Gac>Aac	p.D31N	FAM169B_ENST00000332908.4_Missense_Mutation_p.D31N	NM_182562.2	NP_872368.2	Q8N8A8	F169B_HUMAN	family with sequence similarity 169, member B	31										large_intestine(3)|lung(3)|urinary_tract(1)	7						AAAAACATGTCATCATCATCC	0.413																																					p.D31N		Atlas-SNP	.											.	FAM169B	23	.	0			c.G91A						.						103	102	102					15																	99023922		1900	4121	6021	SO:0001583	missense	283777	exon4			ACATGTCATCATC		CCDS45360.1	15q26.3	2008-08-08			ENSG00000185087	ENSG00000185087			26835	protein-coding gene	gene with protein product							Standard	NM_182562		Approved	FLJ39743, KIAA0888L	uc002buk.1	Q8N8A8		ENST00000558256.1:c.91G>A	chr15.hg19:g.99023922C>T	ENSP00000453554:p.Asp31Asn	116.0	0.0		137.0	24.0	NM_182562	B5MDL8	Missense_Mutation	SNP	ENST00000558256.1	hg19	CCDS45360.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.062678	0.76187	.	.	ENSG00000185087	ENST00000332908	T	0.68624	-0.34	5.07	4.16	0.48862	.	0.439493	0.24328	N	0.039496	T	0.70666	0.3250	L	0.29908	0.895	0.23056	N	0.998366	D	0.76494	0.999	D	0.68943	0.961	T	0.63668	-0.6585	10	0.72032	D	0.01	-3.5146	12.3111	0.54929	0.0:0.917:0.0:0.0829	.	31	Q8N8A8	F169B_HUMAN	N	31	ENSP00000332615:D31N	ENSP00000332615:D31N	D	-	1	0	FAM169B	96841445	0.989000	0.36119	0.572000	0.28498	0.994000	0.84299	1.182000	0.32029	1.127000	0.42034	0.655000	0.94253	GAC	.	.		0.413	FAM169B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415488.1	NM_182562		T	99023922	C	T	99023922	3	4	347	1	0	0	0	0	1	0	0	0	5493	826	29	3	503	3	FAM169B	15	99023922	Missense_Mutation	SNP	C	TCGA-UB-A7ME-01A-11D-A33K-10	30897810	99023922	3507470	58	49011										
SRRM2	23524	hgsc.bcm.edu	37	chr16	2812757	2812757	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	atctcaaagaagaagcaggtCcaattcaagcccagaaatga	8	9	2	4			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr16:2812757C>T	ENST00000301740.8	+	11	2777	c.2228C>T	c.(2227-2229)tCc>tTc	p.S743F		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	743	Arg-rich.|Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						AGAAGCAGGTCCAATTCAAGC	0.463																																					p.S743F		Atlas-SNP	.											.	SRRM2	263	.	0			c.C2228T						.						90	94	92					16																	2812757		2198	4300	6498	SO:0001583	missense	23524	exon11			GCAGGTCCAATTC	AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.2228C>T	chr16.hg19:g.2812757C>T	ENSP00000301740:p.Ser743Phe	92.0	0.0		103.0	25.0	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	hg19	CCDS32373.1	.	.	.	.	.	.	.	.	.	.	C	6.676	0.493295	0.12702	.	.	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000426305	T	0.29655	1.56	5.8	5.8	0.92144	.	0.000000	0.64402	D	0.000015	T	0.38983	0.1061	L	0.27053	0.805	0.39252	D	0.964056	D	0.65815	0.995	P	0.62014	0.897	T	0.30446	-0.9978	10	0.87932	D	0	-8.1768	12.4919	0.55905	0.1669:0.8331:0.0:0.0	.	743	Q9UQ35	SRRM2_HUMAN	F	743;743;708	ENSP00000301740:S743F	ENSP00000301740:S743F	S	+	2	0	SRRM2	2752758	0.994000	0.37717	1.000000	0.80357	0.728000	0.41692	3.406000	0.52637	2.746000	0.94184	0.563000	0.77884	TCC	.	.		0.463	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			T	2812757	C	T	2812757	3	4	347	1	0	0	0	0	1	0	0	0	15184	855	30	3	2266	3	SRRM2	16	2812757	Missense_Mutation	SNP	C	TCGA-UB-A7ME-01A-11D-A33K-10		2812757	87541996	59	49012										
PMFBP1	83449	hgsc.bcm.edu	37	chr16	72198720	72198720	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	ttgtcctgcaaggtcttcctCtgtctcttgcagacatcgtg	9	12	3	1			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr16:72198720C>A	ENST00000237353.10	-	3	369	c.108G>T	c.(106-108)caG>caT	p.Q36H	PMFBP1_ENST00000355636.6_5'UTR|PMFBP1_ENST00000537465.1_Missense_Mutation_p.Q36H|PMFBP1_ENST00000543746.1_5'UTR	NM_031293.2	NP_112583.2	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	36						cytoplasm (GO:0005737)				NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	45		Ovarian(137;0.179)				AGGTCTTCCTCTGTCTCTTGC	0.547																																					p.Q36H		Atlas-SNP	.											.	PMFBP1	101	.	0			c.G108T						.						121	101	108					16																	72198720		2198	4300	6498	SO:0001583	missense	83449	exon3			CTTCCTCTGTCTC	AF239683	CCDS32483.1	16q23.1	2008-08-04			ENSG00000118557	ENSG00000118557			17728	protein-coding gene	gene with protein product						11468771	Standard	NM_031293		Approved		uc002fcd.3	Q8TBY8	OTTHUMG00000167827	ENST00000237353.10:c.108G>T	chr16.hg19:g.72198720C>A	ENSP00000237353:p.Gln36His	50.0	0.0		62.0	8.0	NM_031293	B3KVI9|H7BY07|Q8NA09|Q9BY16|Q9H0H4	Missense_Mutation	SNP	ENST00000237353.10	hg19	CCDS32483.1	.	.	.	.	.	.	.	.	.	.	C	17.39	3.377496	0.61735	.	.	ENSG00000118557	ENST00000537465;ENST00000237353;ENST00000535461;ENST00000539172;ENST00000536211;ENST00000540440	T;T	0.21031	2.03;2.05	5.85	-1.37	0.09056	.	0.142984	0.32970	N	0.005423	T	0.10465	0.0256	N	0.19112	0.55	0.80722	D	1	B;B	0.32800	0.385;0.385	B;B	0.33295	0.161;0.161	T	0.12604	-1.0541	10	0.40728	T	0.16	-16.5788	6.1373	0.20241	0.0:0.4655:0.1295:0.4051	.	36;36	Q8TBY8-2;G3V1Q7	.;.	H	36	ENSP00000443817:Q36H;ENSP00000237353:Q36H	ENSP00000237353:Q36H	Q	-	3	2	PMFBP1	70756221	0.946000	0.32159	0.996000	0.52242	0.861000	0.49209	-0.376000	0.07465	-0.083000	0.12618	-0.794000	0.03295	CAG	.	.		0.547	PMFBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396473.2	NM_031293		A	72198720	C	A	72198720	3	1	347	1	0	0	0	0	1	0	0	0	12143	912	32	3	3051	3	PMFBP1	16	72198720	Missense_Mutation	SNP	C	TCGA-UB-A7ME-01A-11D-A33K-10	69385963	72198720	18156033	60	49013										
ARHGEF15	22899	hgsc.bcm.edu	37	chr17	8216406	8216417	+	In_Frame_Del	DEL	CGGTCACCCTGC	CGGTCACCCTGC	-													0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	cgcccccaccctccaagcatCggtcaccctgccgttgtcct							TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	CGGTCACCCTGC	CGGTCACCCTGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr17:8216406_8216417delCGGTCACCCTGC	ENST00000361926.3	+	3	878_889	c.768_779delCGGTCACCCTGC	c.(766-780)atcggtcaccctgcc>atc	p.GHPA257del	ARHGEF15_ENST00000421050.1_In_Frame_Del_p.GHPA257del	NM_173728.3	NP_776089.2	O94989	ARHGF_HUMAN	Rho guanine nucleotide exchange factor (GEF) 15	257					negative regulation of synapse maturation (GO:2000297)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|regulation of catalytic activity (GO:0050790)|retina vasculature morphogenesis in camera-type eye (GO:0061299)	cytoplasm (GO:0005737)|dendrite (GO:0030425)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(9)|large_intestine(5)|lung(11)|ovary(5)|prostate(3)|skin(2)|urinary_tract(1)	37						CTCCAAGCATCGGTCACCCTGCCGTTGTCCTC	0.651																																					p.256_260del		Atlas-Indel,Pindel	.											.	ARHGEF15	97	.	0			c.767_778del						.																																			SO:0001651	inframe_deletion	22899	exon3			.	AB020722	CCDS11139.1	17p13.1	2011-11-16			ENSG00000198844	ENSG00000198844		"Rho guanine nucleotide exchange factors"	15590	protein-coding gene	gene with protein product	"Rho guanine exchange factor (GEF) 15"	608504				10048485	Standard	NM_173728		Approved	KIAA0915, Vsm-RhoGEF, ARGEF15, FLJ13791, MGC44868	uc002glc.3	O94989	OTTHUMG00000108187	ENST00000361926.3:c.768_779delCGGTCACCCTGC	chr17.hg19:g.8216406_8216417delCGGTCACCCTGC	ENSP00000355026:p.Gly257_Ala260del	57.0	0.0		33.0	11.0	NM_025014	A8K6G1|Q8N449|Q9H8B4	In_Frame_Del	DEL	ENST00000361926.3	hg19	CCDS11139.1																																																																																			.	.		0.651	ARHGEF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226993.2	NM_173728		-	8216417	CGGTCACCCTGC	-	8216406	7	5	347	1	0	1	0	1	0	0	0	0	898	874	31	0	774	0	ARHGEF15	17	8216406	In_Frame_Del	DEL	CGGTCACCCTGC	TCGA-UB-A7ME-01A-11D-A33K-10		8216406	72978804	61	49014										
CSHL1	1444	hgsc.bcm.edu	37	chr17	61987890	61987890	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	cttctgttcctttgtgatatAggcttcttcctaggggaagg	11	8	2	1			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr17:61987890A>T	ENST00000309894.5	-	3	195	c.196T>A	c.(196-198)Tat>Aat	p.Y66N	CSHL1_ENST00000561003.1_Intron|CSHL1_ENST00000346606.6_5'UTR|CSHL1_ENST00000392824.4_Silent_p.P135P|CSHL1_ENST00000450719.3_5'UTR|CSHL1_ENST00000438387.2_Intron|CSHL1_ENST00000558099.1_5'UTR|CSHL1_ENST00000259003.10_Intron	NM_022579.1	NP_072101.1	Q14406	CSHL_HUMAN	chorionic somatomammotropin hormone-like 1	66						extracellular region (GO:0005576)	hormone activity (GO:0005179)|metal ion binding (GO:0046872)			endometrium(3)|lung(6)	9						TTTGTGATATAGGCTTCTTCC	0.517																																					p.Y66N		Atlas-SNP	.											.	CSHL1	42	.	0			c.T196A						.						143	138	140					17																	61987890		2203	4300	6503	SO:0001583	missense	1444	exon3			TGATATAGGCTTC	BC029365	CCDS11652.1, CCDS42370.1, CCDS45759.1	17q22-q24	2012-10-02							2442	protein-coding gene	gene with protein product	"chorionic somatomammotropin CS-5"	603515		CSHP1		8083227	Standard	NM_001318		Approved	hCS-L, CSL, CS-5, MGC149868	uc002jda.1	Q14406		ENST00000309894.5:c.196T>A	chr17.hg19:g.61987890A>T	ENSP00000309524:p.Tyr66Asn	94.0	0.0		97.0	44.0	NM_022579	D3DU26|D3DU27|Q0VDB2	Missense_Mutation	SNP	ENST00000309894.5	hg19	CCDS11652.1	.	.	.	.	.	.	.	.	.	.	a	8.783	0.928739	0.18131	.	.	ENSG00000204414	ENST00000309894;ENST00000259003;ENST00000450719	D	0.90197	-2.63	2.39	1.3	0.21679	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.213239	0.41938	D	0.000783	D	0.91553	0.7332	M	0.86420	2.815	0.20307	N	0.999916	P	0.37708	0.606	P	0.46510	0.519	D	0.85529	0.1208	10	0.72032	D	0.01	.	4.3681	0.11233	0.833:0.0:0.167:0.0	.	66	Q14406	CSHL_HUMAN	N	66;61;61	ENSP00000309524:Y66N	ENSP00000259003:Y61N	Y	-	1	0	GH1	59341622	1.000000	0.71417	0.179000	0.23059	0.003000	0.03518	2.996000	0.49449	0.348000	0.23949	-0.756000	0.03474	TAT	.	.		0.517	CSHL1-009	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444557.1	NM_022579		T	61987890	A	T	61987890	3	4	347	1	0	0	0	0	1	0	0	0	3944	420	15	4	484	4	CSHL1	17	61987890	Missense_Mutation	SNP	A	TCGA-UB-A7ME-01A-11D-A33K-10	53771484	61987890	19207320	62	49015										
SLC25A19	60386	hgsc.bcm.edu	37	chr17	73273550	73273550	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	agctccactgccacaaagcaGgttttggaggttctctgaac	10	11	1	1			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr17:73273550G>C	ENST00000402418.3	-	5	1567	c.658C>G	c.(658-660)Ctg>Gtg	p.L220V	SLC25A19_ENST00000416858.2_Missense_Mutation_p.L220V|SLC25A19_ENST00000375261.4_Missense_Mutation_p.L163V|SLC25A19_ENST00000442286.2_Missense_Mutation_p.L220V|SLC25A19_ENST00000320362.3_Missense_Mutation_p.L220V|SLC25A19_ENST00000580994.1_Missense_Mutation_p.L220V			Q9HC21	TPC_HUMAN	solute carrier family 25 (mitochondrial thiamine pyrophosphate carrier), member 19	220					deoxynucleotide transport (GO:0030302)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	deoxynucleotide transmembrane transporter activity (GO:0030233)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	9	all_cancers(13;5.98e-08)|all_epithelial(9;1.16e-08)|Breast(9;3.1e-08)		all cancers(21;6.82e-07)|Epithelial(20;6.86e-06)			CCACAAAGCAGGTTTTGGAGG	0.512																																					p.L220V		Atlas-SNP	.											.	SLC25A19	25	.	0			c.C658G						.						83	75	78					17																	73273550		2203	4300	6503	SO:0001583	missense	60386	exon6			AAAGCAGGTTTTG		CCDS11720.1	17q25.1	2013-05-22	2007-03-08		ENSG00000125454	ENSG00000125454		"Solute carriers"	14409	protein-coding gene	gene with protein product		606521	"solute carrier family 25 (mitochondrial deoxynucleotide carrier), member 19", "microcephaly, Amish"	MCPHA		11474176, 11226231, 19798730	Standard	NM_021734		Approved	DNC, MUP1, TPC	uc002jnw.4	Q9HC21		ENST00000402418.3:c.658C>G	chr17.hg19:g.73273550G>C	ENSP00000385312:p.Leu220Val	66.0	0.0		59.0	20.0	NM_001126122	E9PF74|Q6V9R7	Missense_Mutation	SNP	ENST00000402418.3	hg19	CCDS11720.1	.	.	.	.	.	.	.	.	.	.	G	16.12	3.031943	0.54790	.	.	ENSG00000125454	ENST00000416858;ENST00000442286;ENST00000320362;ENST00000402418;ENST00000375261	D;D;D;D;D	0.81499	-1.5;-1.5;-1.5;-1.5;-1.5	5.35	2.3	0.28687	Mitochondrial carrier domain (2);	0.067029	0.64402	D	0.000011	D	0.82435	0.5036	L	0.45581	1.43	0.45930	D	0.998765	D;P	0.61697	0.99;0.935	P;P	0.62014	0.897;0.513	T	0.81187	-0.1047	10	0.62326	D	0.03	-13.3282	9.0336	0.36273	0.3003:0.0:0.6997:0.0	.	163;220	E9PF74;Q9HC21	.;TPC_HUMAN	V	220;220;220;220;163	ENSP00000397818:L220V;ENSP00000402202:L220V;ENSP00000319574:L220V;ENSP00000385312:L220V;ENSP00000364410:L163V	ENSP00000319574:L220V	L	-	1	2	SLC25A19	70785145	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	4.657000	0.61490	0.648000	0.30732	-0.157000	0.13467	CTG	.	.		0.512	SLC25A19-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447282.1	NM_021734		C	73273550	G	C	73273550	3	2	347	1	0	0	0	0	1	0	0	0	14496	991	35	4	312	4	SLC25A19	17	73273550	Missense_Mutation	SNP	G	TCGA-UB-A7ME-01A-11D-A33K-10	11285660	73273550	7921660	63	49016										
SEC14L1	6397	hgsc.bcm.edu	37	chr17	75186883	75186883	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	ttcttggtttttaaatttatAggcctatgaaaggaggttcc	9	5	1	1			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr17:75186883A>T	ENST00000413679.2	+	4	366		c.e4-1		SEC14L1_ENST00000591437.1_Splice_Site|SEC14L1_ENST00000430767.4_Splice_Site|SEC14L1_ENST00000436233.4_Splice_Site|SEC14L1_ENST00000443798.4_Splice_Site|SEC14L1_ENST00000585618.1_Splice_Site|SEC14L1_ENST00000431431.2_Splice_Site|SEC14L1_ENST00000392476.2_Splice_Site	NM_001143998.1|NM_001143999.1|NM_003003.3	NP_001137470|NP_001137471|NP_002994	Q92503	S14L1_HUMAN	SEC14-like 1 (S. cerevisiae)						transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(2)	31						TTAAATTTATAGGCCTATGAA	0.483																																					.		Atlas-SNP	.											.	SEC14L1	81	.	0			c.64-2A>T						.						76	71	73					17																	75186883		2203	4300	6503	SO:0001630	splice_region_variant	6397	exon6			ATTTATAGGCCTA	D67029	CCDS11752.1, CCDS42385.1, CCDS45789.1	17q25.2	2008-02-01	2001-11-28			ENSG00000129657			10698	protein-coding gene	gene with protein product		601504	"SEC14 (S. cerevisiae)-like 1"	SEC14L		8697811	Standard	NM_001143998		Approved	PRELID4A	uc002jto.3	Q92503		ENST00000413679.2:c.64-1A>T	chr17.hg19:g.75186883A>T		41.0	0.0		39.0	12.0	NM_001204408	A8K4E8|B4DDI5|D5G3K1|Q99780	Splice_Site	SNP	ENST00000413679.2	hg19	CCDS11752.1	.	.	.	.	.	.	.	.	.	.	A	18.69	3.678316	0.68042	.	.	ENSG00000129657	ENST00000392476;ENST00000443798;ENST00000436233;ENST00000430767;ENST00000413679	.	.	.	5.07	5.07	0.68467	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3091	0.66403	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SEC14L1	72698478	1.000000	0.71417	0.995000	0.50966	0.757000	0.42996	8.834000	0.92094	2.035000	0.60131	0.482000	0.46254	.	.	.		0.483	SEC14L1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000436240.1	NM_003003	Intron	T	75186883	A	T	75186883	5	4	347	1	0	0	0	0	0	0	1	0	13996	434	15	4	68	4	SEC14L1	17	75186883	Splice_Site	SNP	A	TCGA-UB-A7ME-01A-11D-A33K-10	1913333	75186883	6008327	64	49017										
PCYT2	5833	hgsc.bcm.edu	37	chr17	79865686	79865686	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	ctttggttaccagcagcatgCggcccacgaggtctgtggtg	14	11	1	0			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr17:79865686C>A	ENST00000538936.2	-	5	563	c.455G>T	c.(454-456)cGc>cTc	p.R152L	PCYT2_ENST00000570388.1_Missense_Mutation_p.R74L|PCYT2_ENST00000538721.2_Missense_Mutation_p.R152L|PCYT2_ENST00000331285.3_Missense_Mutation_p.R74L|PCYT2_ENST00000571105.1_Missense_Mutation_p.R152L|PCYT2_ENST00000570391.1_Missense_Mutation_p.R120L	NM_001256435.1|NM_002861.3	NP_001243364.1|NP_002852.1	Q99447	PCY2_HUMAN	phosphate cytidylyltransferase 2, ethanolamine	152					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)	ethanolamine-phosphate cytidylyltransferase activity (GO:0004306)			breast(2)|endometrium(1)|lung(4)|ovary(1)	8	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)		Lamivudine(DB00709)	CAGCAGCATGCGGCCCACGAG	0.652																																					p.R152L		Atlas-SNP	.											.	PCYT2	23	.	0			c.G455T						.						77	59	65					17																	79865686		2203	4300	6503	SO:0001583	missense	5833	exon5			AGCATGCGGCCCA	D84307	CCDS11791.1, CCDS54178.1, CCDS58610.1, CCDS62364.1	17q25.3	2008-07-18				ENSG00000185813			8756	protein-coding gene	gene with protein product		602679				9083101	Standard	XM_005256386		Approved	ET	uc002kch.2	Q99447		ENST00000538936.2:c.455G>T	chr17.hg19:g.79865686C>A	ENSP00000439245:p.Arg152Leu	55.0	0.0		54.0	8.0	NM_002861	B7Z7A5|B7ZAS0|F5H8B1|Q6IBM3|Q96G08	Missense_Mutation	SNP	ENST00000538936.2	hg19	CCDS11791.1	.	.	.	.	.	.	.	.	.	.	C	35	5.432140	0.96150	.	.	ENSG00000185813	ENST00000538721;ENST00000538936;ENST00000331285	.	.	.	4.48	4.48	0.54585	Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.85682	D	0.000000	D	0.90164	0.6926	H	0.98068	4.14	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	D	0.94125	0.7383	9	0.87932	D	0	-28.9973	17.3427	0.87301	0.0:1.0:0.0:0.0	.	120;120;152;74;152	B7Z4W6;B7ZAS0;F5H8B1;B7Z7A5;Q99447	.;.;.;.;PCY2_HUMAN	L	152;152;74	.	ENSP00000331719:R74L	R	-	2	0	PCYT2	77458978	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	5.463000	0.66712	2.303000	0.77524	0.655000	0.94253	CGC	.	.		0.652	PCYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439939.1	NM_002861		A	79865686	C	A	79865686	3	1	347	1	0	0	0	0	1	0	0	0	11621	768	27	1	808	1	PCYT2	17	79865686	Missense_Mutation	SNP	C	TCGA-UB-A7ME-01A-11D-A33K-10	4678803	79865686	1329524	65	49018										
FASN	2194	hgsc.bcm.edu	37	chr17	80039126	80039126	+	Frame_Shift_Del	DEL	A	A	-													0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	gcacggacagcaccaggttgAgctcacgctccagcgtctgg							TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr17:80039126delA	ENST00000306749.2	-	38	6727	c.6509delT	c.(6508-6510)ctcfs	p.L2170fs	FASN_ENST00000579758.1_Intron	NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	2170	Acyl carrier. {ECO:0000255|PROSITE- ProRule:PRU00258}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	CACCAGGTTGAGCTCACGCTC	0.657																																					p.L2170fs	Colon(59;314 1043 11189 28578 32273)	Atlas-Indel,Pindel	.											.	FASN	154	.	0			c.6510delC						.						29	25	26					17																	80039126		2184	4284	6468	SO:0001589	frameshift_variant	2194	exon38			.	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.6509delT	chr17.hg19:g.80039126delA	ENSP00000304592:p.Leu2170fs	46.0	0.0		48.0	15.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Frame_Shift_Del	DEL	ENST00000306749.2	hg19	CCDS11801.1																																																																																			.	.		0.657	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		-	80039126	A	-	80039126	7	5	347	1	0	1	0	1	0	0	0	0	5691	304	11	0	1050	0	FASN	17	80039126	Frame_Shift_Del	DEL	A	TCGA-UB-A7ME-01A-11D-A33K-10	173440	80039126	1156084	66	49019										
SERPINB3	6317	hgsc.bcm.edu	37	chr18	61323009	61323009	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	ttgaagtaggtgatgatccgAatcctactacagcggtggca	12	8	0	3			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr18:61323009A>T	ENST00000283752.5	-	8	1198	c.1055T>A	c.(1054-1056)tTc>tAc	p.F352Y	SERPINB11_ENST00000489748.1_RNA|SERPINB3_ENST00000332821.8_Missense_Mutation_p.F300Y	NM_006919.2	NP_008850.1	P29508	SPB3_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 3	352					negative regulation of catalytic activity (GO:0043086)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)|virus receptor activity (GO:0001618)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	36						TGATGATCCGAATCCTACTAC	0.493																																					p.F352Y		Atlas-SNP	.											.	SERPINB3	90	.	0			c.T1055A						.						124	131	129					18																	61323009		2203	4300	6503	SO:0001583	missense	6317	exon8			GATCCGAATCCTA	U19568	CCDS11987.1	18q21.3	2014-02-18	2005-08-18		ENSG00000057149	ENSG00000057149		"Serine (or cysteine) peptidase inhibitors"	10569	protein-coding gene	gene with protein product		600517	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3"	SCC, SCCA1		7724531, 24172014	Standard	NM_006919		Approved	T4-A, HsT1196	uc002lji.3	P29508	OTTHUMG00000060403	ENST00000283752.5:c.1055T>A	chr18.hg19:g.61323009A>T	ENSP00000283752:p.Phe352Tyr	137.0	0.0		128.0	58.0	NM_006919	A6NDM2|B2RBT5|B3W5Y6|Q53H28|Q53YB5|Q86VF3|Q86W04|Q8IWL4|Q8IXI3|Q96J21|Q9BYF8	Missense_Mutation	SNP	ENST00000283752.5	hg19	CCDS11987.1	.	.	.	.	.	.	.	.	.	.	A	1.388	-0.581531	0.03854	.	.	ENSG00000057149	ENST00000283752;ENST00000332821	D;D	0.82255	-1.59;-1.59	2.99	-5.64	0.02466	Serpin domain (3);	450.141000	0.00166	N	0.000000	T	0.64000	0.2559	N	0.16166	0.38	0.09310	N	1	B;B	0.21688	0.059;0.022	B;B	0.17098	0.017;0.015	T	0.52373	-0.8584	10	0.24483	T	0.36	.	1.9358	0.03337	0.5159:0.1235:0.2404:0.1202	.	300;352	P29508-2;P29508	.;SPB3_HUMAN	Y	352;300	ENSP00000283752:F352Y;ENSP00000329498:F300Y	ENSP00000283752:F352Y	F	-	2	0	SERPINB3	59473989	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.452000	0.06787	-1.297000	0.02351	-3.778000	0.00021	TTC	.	.		0.493	SERPINB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133791.1	NM_006919		T	61323009	A	T	61323009	3	4	347	1	0	0	0	0	1	0	0	0	14117	246	9	4	121	4	SERPINB3	18	61323009	Missense_Mutation	SNP	A	TCGA-UB-A7ME-01A-11D-A33K-10		61323009	16754239	67	49020										
SERPINB3	6317	hgsc.bcm.edu	37	chr18	61323101	61323101	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	actccagatagcacgagaccGcggctcccggtcatgcctga	11	15	1	3			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr18:61323101G>A	ENST00000283752.5	-	8	1106	c.963C>T	c.(961-963)cgC>cgT	p.R321R	SERPINB11_ENST00000489748.1_RNA|SERPINB3_ENST00000332821.8_Silent_p.R269R	NM_006919.2	NP_008850.1	P29508	SPB3_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 3	321					negative regulation of catalytic activity (GO:0043086)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)|virus receptor activity (GO:0001618)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	36						GCACGAGACCGCGGCTCCCGG	0.542																																					p.R321R		Atlas-SNP	.											.	SERPINB3	90	.	0			c.C963T						.						138	124	129					18																	61323101		2203	4300	6503	SO:0001819	synonymous_variant	6317	exon8			GAGACCGCGGCTC	U19568	CCDS11987.1	18q21.3	2014-02-18	2005-08-18		ENSG00000057149	ENSG00000057149		"Serine (or cysteine) peptidase inhibitors"	10569	protein-coding gene	gene with protein product		600517	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3"	SCC, SCCA1		7724531, 24172014	Standard	NM_006919		Approved	T4-A, HsT1196	uc002lji.3	P29508	OTTHUMG00000060403	ENST00000283752.5:c.963C>T	chr18.hg19:g.61323101G>A		109.0	0.0		133.0	32.0	NM_006919	A6NDM2|B2RBT5|B3W5Y6|Q53H28|Q53YB5|Q86VF3|Q86W04|Q8IWL4|Q8IXI3|Q96J21|Q9BYF8	Silent	SNP	ENST00000283752.5	hg19	CCDS11987.1																																																																																			.	.		0.542	SERPINB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133791.1	NM_006919		A	61323101	G	A	61323101	2	1	347	1	0	0	0	0	0	0	0	1	14117	1074	38	1		1	SERPINB3	18	61323101	Silent	SNP	G	TCGA-UB-A7ME-01A-11D-A33K-10	92	61323101	16754147	68	49021										
SERPINB10	5273	hgsc.bcm.edu	37	chr18	61584734	61584734	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	ggagtcaaatgtgaccctgaAagtgaaaaaaaaaggaaaat	10	4	1	3			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr18:61584734A>C	ENST00000238508.3	+	3	272	c.213A>C	c.(211-213)gaA>gaC	p.E71D		NM_005024.1	NP_005015.1	P48595	SPB10_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 10	71					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)|skin(3)|stomach(2)	24		Esophageal squamous(42;0.131)				GTGACCCTGAAAGTGAAAAAA	0.274																																					p.E71D		Atlas-SNP	.											.	SERPINB10	53	.	0			c.A213C						.						29	29	29					18																	61584734		2178	4259	6437	SO:0001583	missense	5273	exon2			CCCTGAAAGTGAA	U35459	CCDS11990.1	18q21.3	2014-02-18	2005-08-18		ENSG00000242550	ENSG00000242550		"Serine (or cysteine) peptidase inhibitors"	8942	protein-coding gene	gene with protein product	"protease inhibitor 10 (ovalbumin type, bomapin)"	602058	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10"	PI10		9268635, 10871600, 24172014	Standard	NM_005024		Approved	bomapin		P48595	OTTHUMG00000060594	ENST00000238508.3:c.213A>C	chr18.hg19:g.61584734A>C	ENSP00000238508:p.Glu71Asp	238.0	0.0		304.0	107.0	NM_005024	Q4VAX4|Q4VAX7	Missense_Mutation	SNP	ENST00000238508.3	hg19	CCDS11990.1	.	.	.	.	.	.	.	.	.	.	A	5.785	0.329242	0.10956	.	.	ENSG00000242550	ENST00000238508	D	0.84944	-1.92	5.51	0.214	0.15249	Serpin domain (3);	0.621181	0.15380	N	0.265354	T	0.69931	0.3166	L	0.31420	0.93	0.09310	N	1	B;B	0.12630	0.006;0.002	B;B	0.15484	0.013;0.011	T	0.51919	-0.8644	9	.	.	.	.	2.094	0.03663	0.4:0.3572:0.0913:0.1515	.	71;71	P48595;B2RC45	SPB10_HUMAN;.	D	71	ENSP00000238508:E71D	.	E	+	3	2	SERPINB10	59735714	0.102000	0.21896	0.991000	0.47740	0.144000	0.21451	-0.108000	0.10857	0.147000	0.19030	0.528000	0.53228	GAA	.	.		0.274	SERPINB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134012.3	NM_005024		C	61584734	A	C	61584734	3	2	347	1	0	0	0	0	1	0	0	0	14112	11	1	5	219	5	SERPINB10	18	61584734	Missense_Mutation	SNP	A	TCGA-UB-A7ME-01A-11D-A33K-10	261633	61584734	16492514	69	49022										
ARID3A	1820	hgsc.bcm.edu	37	chr19	968403	968403	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	taatttgttcttcttcccacAgcctccgaaagccgccagga	7	14	2	0			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr19:968403A>T	ENST00000263620.3	+	8	1822		c.e8-1			NM_005224.2	NP_005215.1	Q99856	ARI3A_HUMAN	AT rich interactive domain 3A (BRIGHT-like)							cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)	p.?(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	10		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TTCTTCCCACAGCCTCCGAAA	0.512																																					.	Pancreas(29;54 1022 32760 50921)	Atlas-SNP	.											ARID3A,NS,carcinoma,0,1	ARID3A	35	.	1	Unknown(1)	endometrium(1)	c.1496-2A>T						.						72	68	69					19																	968403		2203	4300	6503	SO:0001630	splice_region_variant	1820	exon8			TCCCACAGCCTCC	U88047	CCDS12050.1	19p13.3	2013-02-07	2006-11-08	2004-01-30		ENSG00000116017		"-"	3031	protein-coding gene	gene with protein product		603265	"dead ringer-like 1 (Drosophila)", "AT rich interactive domain 3A (BRIGHT- like)"	DRIL1		9722953	Standard	NM_005224		Approved	BRIGHT	uc002lql.3	Q99856		ENST00000263620.3:c.1496-1A>T	chr19.hg19:g.968403A>T		153.0	0.0		151.0	55.0	NM_005224	Q5I858|Q6P9C6|Q8IZA7|Q8N4Z3	Splice_Site	SNP	ENST00000263620.3	hg19	CCDS12050.1	.	.	.	.	.	.	.	.	.	.	A	10.08	1.251681	0.22880	.	.	ENSG00000116017	ENST00000263620	.	.	.	4.41	4.41	0.53225	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.0247	0.30430	0.7931:0.2069:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ARID3A	919403	0.497000	0.26067	0.971000	0.41717	0.125000	0.20455	2.074000	0.41529	1.852000	0.53769	0.374000	0.22700	.	.	.		0.512	ARID3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458219.1	NM_005224	Intron	T	968403	A	T	968403	5	4	347	1	0	0	0	0	0	0	1	0	916	202	7	4	1520	4	ARID3A	19	968403	Splice_Site	SNP	A	TCGA-UB-A7ME-01A-11D-A33K-10		968403	58160580	70	49023										
LMNB2	84823	hgsc.bcm.edu	37	chr19	2435009	2435009	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	ccggccacaccttggcctggTaggtctgctccagctccagc	11	17	1	0			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr19:2435009T>A	ENST00000582871.1	-	5	871	c.785A>T	c.(784-786)tAc>tTc	p.Y262F	LMNB2_ENST00000325327.3_Missense_Mutation_p.Y282F	NM_032737.3	NP_116126.3	Q03252	LMNB2_HUMAN	lamin B2	262	Coil 2.|Rod.					lamin filament (GO:0005638)|nuclear inner membrane (GO:0005637)	structural molecule activity (GO:0005198)			NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTTGGCCTGGTAGGTCTGCTC	0.716																																					p.Y282F		Atlas-SNP	.											.	LMNB2	40	.	0			c.A845T						.						24	26	25					19																	2435009		2198	4299	6497	SO:0001583	missense	84823	exon5			GCCTGGTAGGTCT	M94362	CCDS12090.1, CCDS12090.2	19p13.3	2013-01-16			ENSG00000176619	ENSG00000176619		"Intermediate filaments type V, lamins"	6638	protein-coding gene	gene with protein product		150341		LMN2		1630457	Standard	NM_032737		Approved		uc002lvy.4	Q03252	OTTHUMG00000150626	ENST00000582871.1:c.785A>T	chr19.hg19:g.2435009T>A	ENSP00000462730:p.Tyr262Phe	17.0	0.0		15.0	5.0	NM_032737	O75292|Q14734|Q96DF6	Missense_Mutation	SNP	ENST00000582871.1	hg19		.	.	.	.	.	.	.	.	.	.	T	14.34	2.505047	0.44558	.	.	ENSG00000176619	ENST00000325327	.	.	.	4.83	4.83	0.62350	Filament (1);	0.123853	0.56097	D	0.000030	T	0.49795	0.1578	L	0.28400	0.85	0.48040	D	0.999571	P	0.38223	0.623	B	0.42959	0.403	T	0.46735	-0.9170	9	0.30078	T	0.28	.	13.2379	0.59979	0.0:0.0:0.0:1.0	.	262	Q03252	LMNB2_HUMAN	F	262	.	ENSP00000327054:Y262F	Y	-	2	0	LMNB2	2386009	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.974000	0.40559	1.807000	0.52817	0.459000	0.35465	TAC	.	.		0.716	LMNB2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_032737		A	2435009	T	A	2435009	3	1	347	1	0	0	0	0	1	0	0	0	8859	1638	57	4	1049	4	LMNB2	19	2435009	Missense_Mutation	SNP	T	TCGA-UB-A7ME-01A-11D-A33K-10	1466606	2435009	56693974	71	49024										
MUC16	94025	hgsc.bcm.edu	37	chr19	9085994	9085994	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	aatgacttcttccactggaaTggatgaaaaaggcaatgtta	9	6	1	2			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr19:9085994T>A	ENST00000397910.4	-	1	6024	c.5821A>T	c.(5821-5823)Att>Ttt	p.I1941F		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1941	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TCCACTGGAATGGATGAAAAA	0.488																																					p.I1941F		Atlas-SNP	.											.	MUC16	4315	.	0			c.A5821T						.						176	171	172					19																	9085994		2047	4187	6234	SO:0001583	missense	94025	exon1			CTGGAATGGATGA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.5821A>T	chr19.hg19:g.9085994T>A	ENSP00000381008:p.Ile1941Phe	60.0	0.0		69.0	35.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	7.373	0.627289	0.14257	.	.	ENSG00000181143	ENST00000397910	T	0.02709	4.19	0.235	0.235	0.15431	.	.	.	.	.	T	0.02970	0.0088	N	0.08118	0	.	.	.	P	0.47106	0.89	P	0.52554	0.702	T	0.45789	-0.9237	7	0.87932	D	0	.	.	.	.	.	1941	B5ME49	.	F	1941	ENSP00000381008:I1941F	ENSP00000381008:I1941F	I	-	1	0	MUC16	8946994	0.000000	0.05858	0.534000	0.28014	0.535000	0.34838	-1.631000	0.02026	0.263000	0.21812	0.260000	0.18958	ATT	.	.		0.488	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9085994	T	A	9085994	3	1	347	1	0	0	0	0	1	0	0	0	9982	1464	51	4	38038	4	MUC16	19	9085994	Missense_Mutation	SNP	T	TCGA-UB-A7ME-01A-11D-A33K-10	6650985	9085994	50042989	72	49025										
ZNF14	7561	hgsc.bcm.edu	37	chr19	19823308	19823308	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	ttcgaaagtatgtgggacaaCtgaaagccttaccacattgc	9	9	0	1			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr19:19823308C>T	ENST00000344099.3	-	4	920	c.782G>A	c.(781-783)aGt>aAt	p.S261N		NM_021030.2	NP_066358.2	P17017	ZNF14_HUMAN	zinc finger protein 14	261					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(2)|endometrium(1)|large_intestine(9)|lung(8)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	32		Renal(1328;0.0474)				TGTGGGACAACTGAAAGCCTT	0.383																																					p.S261N		Atlas-SNP	.											.	ZNF14	89	.	0			c.G782A						.						55	53	54					19																	19823308		2203	4300	6503	SO:0001583	missense	7561	exon4			GGACAACTGAAAG	AA286756	CCDS12409.1	19p13.11	2013-01-08	2006-05-10					"Zinc fingers, C2H2-type", "-"	12924	protein-coding gene	gene with protein product		194556	"zinc finger protein 14 (KOX 6)"				Standard	NM_021030		Approved	KOX6, GIOT-4	uc002nnk.1	P17017		ENST00000344099.3:c.782G>A	chr19.hg19:g.19823308C>T	ENSP00000340514:p.Ser261Asn	66.0	0.0		109.0	26.0	NM_021030	B9EGA4|Q9ULZ5	Missense_Mutation	SNP	ENST00000344099.3	hg19	CCDS12409.1	.	.	.	.	.	.	.	.	.	.	C	14.66	2.601996	0.46423	.	.	ENSG00000105708	ENST00000344099	T	0.07567	3.18	1.8	-0.656	0.11436	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05686	0.0149	L	0.39397	1.21	0.09310	N	1	B	0.12630	0.006	B	0.12837	0.008	T	0.43147	-0.9409	9	0.32370	T	0.25	.	0.5821	0.00714	0.2476:0.3311:0.2439:0.1774	.	261	P17017	ZNF14_HUMAN	N	261	ENSP00000340514:S261N	ENSP00000340514:S261N	S	-	2	0	ZNF14	19684308	0.000000	0.05858	0.003000	0.11579	0.942000	0.58702	-4.765000	0.00188	0.068000	0.16574	0.467000	0.42956	AGT	.	.		0.383	ZNF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460775.1	NM_021030		T	19823308	C	T	19823308	3	4	347	1	0	0	0	0	1	0	0	0	17743	565	20	3	1150	3	ZNF14	19	19823308	Missense_Mutation	SNP	C	TCGA-UB-A7ME-01A-11D-A33K-10	10737314	19823308	39305675	73	49026										
ZNF536	9745	hgsc.bcm.edu	37	chr19	31039817	31039817	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	cagaagagcggtgcatggacCggccacgtggaccctgcatt	14	12	0	2	rs202189721		TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr19:31039817C>T	ENST00000355537.3	+	4	3438	c.3291C>T	c.(3289-3291)acC>acT	p.T1097T		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	1097					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					GTGCATGGACCGGCCACGTGG	0.547																																					p.T1097T		Atlas-SNP	.											.	ZNF536	424	.	0			c.C3291T						.						81	93	89					19																	31039817		2203	4300	6503	SO:0001819	synonymous_variant	9745	exon4			ATGGACCGGCCAC		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"Zinc fingers, C2H2-type"	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.3291C>T	chr19.hg19:g.31039817C>T		77.0	0.0		108.0	18.0	NM_014717	A2RU18	Silent	SNP	ENST00000355537.3	hg19	CCDS32984.1																																																																																			.	C|0.999;T|0.001		0.547	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		T	31039817	C	T	31039817	2	4	347	1	0	0	0	0	0	0	0	1	17989	639	23	1		1	ZNF536	19	31039817	Silent	SNP	C	TCGA-UB-A7ME-01A-11D-A33K-10	11216509	31039817	28089166	74	49027										
CCDC123	84902	hgsc.bcm.edu	37	chr19	33378692	33378692	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	ctaactttcccaggcgaatgTtgctttttatgactttatta	6	8	0	1			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr19:33378692T>A	ENST00000305768.5	-	17	2019	c.1931A>T	c.(1930-1932)aAc>aTc	p.N644I		NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	644					cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	35						CAGGCGAATGTTGCTTTTTAT	0.398																																					p.N644I		Atlas-SNP	.											.	CEP89	82	.	0			c.A1931T						.						130	105	114					19																	33378692		2203	4299	6502	SO:0001583	missense	84902	exon17			CGAATGTTGCTTT	AL832158	CCDS32987.1	19q13.11	2014-02-20	2011-05-06	2011-05-06		ENSG00000121289			25907	protein-coding gene	gene with protein product		615470	"coiled-coil domain containing 123"	CCDC123		16395595	Standard	NM_032816		Approved	FLJ14640	uc002nty.3	Q96ST8		ENST00000305768.5:c.1931A>T	chr19.hg19:g.33378692T>A	ENSP00000306105:p.Asn644Ile	76.0	0.0		86.0	31.0	NM_032816	B9EGA6|Q8N5J8	Missense_Mutation	SNP	ENST00000305768.5	hg19	CCDS32987.1	.	.	.	.	.	.	.	.	.	.	T	11.71	1.720061	0.30503	.	.	ENSG00000121289	ENST00000305768	D	0.88277	-2.36	5.15	3.06	0.35304	.	0.332317	0.32884	N	0.005529	D	0.88265	0.6390	L	0.53249	1.67	0.80722	D	1	P	0.45212	0.853	P	0.49999	0.628	D	0.85478	0.1177	10	0.52906	T	0.07	-11.9859	8.2518	0.31730	0.0:0.2414:0.0:0.7586	.	644	Q96ST8	CEP89_HUMAN	I	644	ENSP00000306105:N644I	ENSP00000306105:N644I	N	-	2	0	CEP89	38070532	0.980000	0.34600	0.700000	0.30305	0.009000	0.06853	0.812000	0.27211	0.492000	0.27815	0.528000	0.53228	AAC	.	.		0.398	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816		A	33378692	T	A	33378692	3	1	347	1	0	0	0	0	1	0	0	0	2761	1725	60	4	432	4	CCDC123	19	33378692	Missense_Mutation	SNP	T	TCGA-UB-A7ME-01A-11D-A33K-10	2338875	33378692	25750291	75	49028										
ZNF383	163087	hgsc.bcm.edu	37	chr19	37734528	37734528	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	aggcttttagtagtggctcgGatctcattcgtcatcaggga	12	8	3	0			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr19:37734528G>C	ENST00000589413.1	+	8	1973	c.1390G>C	c.(1390-1392)Gat>Cat	p.D464H	ZNF383_ENST00000590503.1_Missense_Mutation_p.D464H|ZNF383_ENST00000352998.3_Missense_Mutation_p.D464H			Q8NA42	ZN383_HUMAN	zinc finger protein 383	464					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(8)|ovary(1)|skin(1)	15			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TAGTGGCTCGGATCTCATTCG	0.353																																					p.D464H		Atlas-SNP	.											.	ZNF383	42	.	0			c.G1390C						.						64	68	66					19																	37734528		2203	4300	6503	SO:0001583	missense	163087	exon5			GGCTCGGATCTCA	AY438646	CCDS12501.1	19q13.13	2013-01-08				ENSG00000188283		"Zinc fingers, C2H2-type", "-"	18609	protein-coding gene	gene with protein product							Standard	NM_152604		Approved	FLJ35863	uc002ofu.1	Q8NA42		ENST00000589413.1:c.1390G>C	chr19.hg19:g.37734528G>C	ENSP00000464871:p.Asp464His	104.0	0.0		127.0	18.0	NM_152604	Q6X2C7	Missense_Mutation	SNP	ENST00000589413.1	hg19	CCDS12501.1	.	.	.	.	.	.	.	.	.	.	G	11.78	1.741496	0.30865	.	.	ENSG00000188283	ENST00000352998	T	0.60299	0.2	3.8	2.77	0.32553	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.35008	0.0917	N	0.12831	0.26	0.24216	N	0.995456	B	0.02656	0.0	B	0.04013	0.001	T	0.10965	-1.0607	9	0.17832	T	0.49	.	9.0234	0.36213	0.114:0.0:0.886:0.0	.	464	Q8NA42	ZN383_HUMAN	H	464	ENSP00000340132:D464H	ENSP00000340132:D464H	D	+	1	0	ZNF383	42426368	0.000000	0.05858	1.000000	0.80357	0.976000	0.68499	0.512000	0.22755	2.118000	0.64928	0.563000	0.77884	GAT	.	.		0.353	ZNF383-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458141.1	NM_152604		C	37734528	G	C	37734528	3	2	347	1	0	0	0	0	1	0	0	0	17889	1174	41	4	1404	4	ZNF383	19	37734528	Missense_Mutation	SNP	G	TCGA-UB-A7ME-01A-11D-A33K-10	4355836	37734528	21394455	76	49029										
RYR1	6261	hgsc.bcm.edu	37	chr19	38945876	38945876	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	cttattttcctcatcctaggGgatgctctccatggtcctga	8	12	2	1			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr19:38945876G>C	ENST00000359596.3	+	14	1442	c.1442G>C	c.(1441-1443)gGg>gCg	p.G481A	RYR1_ENST00000355481.4_Splice_Site_p.G481A|RYR1_ENST00000360985.3_Splice_Site_p.G481A			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	481					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	TCATCCTAGGGGATGCTCTCC	0.502											OREG0005269	type=TRANSCRIPTION FACTOR BINDING SITE|Gene=RYR1|TFbs=REST|Dataset=NRSF/REST ChIPSeq sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.G481A		Atlas-SNP	.											.	RYR1	708	.	0			c.G1442C						.						156	136	143					19																	38945876		2203	4300	6503	SO:0001630	splice_region_variant	6261	exon14			CCTAGGGGATGCT	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.1441-1G>C	chr19.hg19:g.38945876G>C		91.0	0.0	882	67.0	25.0	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	G	14.93	2.682636	0.47991	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.90004	-2.6;-2.6;-2.6	3.97	3.97	0.46021	Intracellular calcium-release channel (1);	0.000000	0.64402	U	0.000002	D	0.95050	0.8397	M	0.88775	2.98	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.96142	0.9101	10	0.87932	D	0	.	15.8324	0.78764	0.0:0.0:1.0:0.0	.	481;481	P21817-2;P21817	.;RYR1_HUMAN	A	481	ENSP00000352608:G481A;ENSP00000347667:G481A;ENSP00000354254:G481A	ENSP00000347667:G481A	G	+	2	0	RYR1	43637716	1.000000	0.71417	1.000000	0.80357	0.769000	0.43574	9.568000	0.98166	2.044000	0.60594	0.407000	0.27541	GGG	.	.		0.502	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		Missense_Mutation	C	38945876	G	C	38945876	5	2	347	1	0	0	0	0	0	0	1	0	13783	1246	43	4	1496	4	RYR1	19	38945876	Splice_Site	SNP	G	TCGA-UB-A7ME-01A-11D-A33K-10	1211348	38945876	20183107	77	49030										
SPTBN4	57731	hgsc.bcm.edu	37	chr19	41021261	41021261	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	tgaacagcctgatgggccgcGttctggacgtgaaccacaca	12	12	1	3			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr19:41021261G>A	ENST00000352632.3	+	15	2895	c.2809G>A	c.(2809-2811)Gtt>Att	p.V937I	SPTBN4_ENST00000598249.1_Missense_Mutation_p.V937I|SPTBN4_ENST00000344104.3_Missense_Mutation_p.V937I|SPTBN4_ENST00000338932.3_Missense_Mutation_p.V937I|SPTBN4_ENST00000595535.1_Missense_Mutation_p.V937I			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	937					actin filament capping (GO:0051693)|adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cardiac conduction (GO:0061337)|central nervous system projection neuron axonogenesis (GO:0021952)|clustering of voltage-gated sodium channels (GO:0045162)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization to plasma membrane (GO:0090002)|fertilization (GO:0009566)|negative regulation of heart rate (GO:0010459)|positive regulation of multicellular organism growth (GO:0040018)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of sodium ion transport (GO:0002028)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|axon hillock (GO:0043203)|axon initial segment (GO:0043194)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|nuclear matrix (GO:0016363)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|PML body (GO:0016605)|spectrin (GO:0008091)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phosphatase binding (GO:0019902)|phospholipid binding (GO:0005543)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.V937I(1)		breast(4)|central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	73			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GATGGGCCGCGTTCTGGACGT	0.577																																					p.V937I		Atlas-SNP	.											SPTBN4,NS,carcinoma,0,2	SPTBN4	213	.	1	Substitution - Missense(1)	endometrium(1)	c.G2809A						.						55	41	46					19																	41021261		2203	4300	6503	SO:0001583	missense	57731	exon15			GGCCGCGTTCTGG	AF082075	CCDS12559.1, CCDS42569.1	19q13.13	2013-01-10				ENSG00000160460		"Pleckstrin homology (PH) domain containing"	14896	protein-coding gene	gene with protein product		606214				11086001	Standard	NM_020971		Approved	SPTBN3, KIAA1642	uc002onz.3	Q9H254		ENST00000352632.3:c.2809G>A	chr19.hg19:g.41021261G>A	ENSP00000263373:p.Val937Ile	64.0	0.0		105.0	20.0	NM_020971	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Missense_Mutation	SNP	ENST00000352632.3	hg19	CCDS12559.1	.	.	.	.	.	.	.	.	.	.	G	11.35	1.613249	0.28712	.	.	ENSG00000160460	ENST00000428507;ENST00000352632;ENST00000338932;ENST00000344104	T;T;T	0.54675	0.56;0.56;0.56	4.34	4.34	0.51931	.	0.204155	0.31257	N	0.007974	T	0.40094	0.1103	L	0.31157	0.91	0.80722	D	1	B;P	0.50528	0.268;0.936	B;P	0.44860	0.015;0.462	T	0.10543	-1.0625	10	0.20046	T	0.44	.	10.1124	0.42570	0.0969:0.0:0.9031:0.0	.	937;937	Q9H254;Q71S06	SPTN4_HUMAN;.	I	937	ENSP00000263373:V937I;ENSP00000340345:V937I;ENSP00000340741:V937I	ENSP00000340345:V937I	V	+	1	0	SPTBN4	45713101	0.726000	0.28059	0.978000	0.43139	0.951000	0.60555	2.116000	0.41930	2.256000	0.74724	0.491000	0.48974	GTT	.	.		0.577	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2			A	41021261	G	A	41021261	3	1	347	1	0	0	0	0	1	0	0	0	15136	1145	40	1	2863	1	SPTBN4	19	41021261	Missense_Mutation	SNP	G	TCGA-UB-A7ME-01A-11D-A33K-10	2075385	41021261	18107722	78	49031										
ZNF576	79177	hgsc.bcm.edu	37	chr19	44103150	44103150	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	gctccttcccctcctccaaaGccctaatcacccaccagcgc	4	22	1	0			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr19:44103150G>A	ENST00000336564.4	+	3	407	c.253G>A	c.(253-255)Gcc>Acc	p.A85T	ZNF576_ENST00000528387.1_Missense_Mutation_p.A85T|ZNF576_ENST00000533118.1_Missense_Mutation_p.A85T|ZNF576_ENST00000391965.2_Missense_Mutation_p.A85T|ZNF576_ENST00000525771.1_Missense_Mutation_p.A85T|SRRM5_ENST00000526798.1_Intron|IRGQ_ENST00000422989.1_5'Flank|SRRM5_ENST00000607544.1_Intron|ZNF576_ENST00000529930.1_Missense_Mutation_p.A85T	NM_001145347.1	NP_001138819.1	Q9H609	ZN576_HUMAN	zinc finger protein 576	85					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			endometrium(1)|prostate(1)	2		Prostate(69;0.0199)				CTCCTCCAAAGCCCTAATCAC	0.647																																					p.A85T		Atlas-SNP	.											.	ZNF576	11	.	0			c.G253A						.						96	104	102					19																	44103150		2203	4300	6503	SO:0001583	missense	79177	exon3			TCCAAAGCCCTAA	AK026353	CCDS12625.1	19q13.31	2013-09-20			ENSG00000124444	ENSG00000124444		"Zinc fingers, C2H2-type"	28357	protein-coding gene	gene with protein product						12477932	Standard	NM_024327		Approved	MGC2508	uc002owz.2	Q9H609	OTTHUMG00000165479	ENST00000336564.4:c.253G>A	chr19.hg19:g.44103150G>A	ENSP00000337852:p.Ala85Thr	73.0	0.0		128.0	36.0	NM_001145347	Q9BU03	Missense_Mutation	SNP	ENST00000336564.4	hg19	CCDS12625.1	.	.	.	.	.	.	.	.	.	.	G	15.55	2.865404	0.51588	.	.	ENSG00000124444	ENST00000391965;ENST00000525771;ENST00000533118;ENST00000528387;ENST00000529930;ENST00000336564	T;T;T;T;T;T	0.40476	1.03;1.03;1.03;1.03;1.03;1.03	3.7	2.67	0.31697	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.089718	0.46145	D	0.000306	T	0.18800	0.0451	N	0.10945	0.07	0.80722	D	1	B	0.15473	0.013	B	0.17979	0.02	T	0.05582	-1.0876	10	0.09843	T	0.71	-7.8118	7.1531	0.25622	0.1222:0.0:0.8778:0.0	.	85	Q9H609	ZN576_HUMAN	T	85	ENSP00000375827:A85T;ENSP00000436182:A85T;ENSP00000435899:A85T;ENSP00000435934:A85T;ENSP00000435463:A85T;ENSP00000337852:A85T	ENSP00000337852:A85T	A	+	1	0	ZNF576	48794990	1.000000	0.71417	1.000000	0.80357	0.553000	0.35397	4.096000	0.57734	1.142000	0.42291	0.591000	0.81541	GCC	.	.		0.647	ZNF576-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384397.1	NM_024327		A	44103150	G	A	44103150	3	1	347	1	0	0	0	0	1	0	0	0	18023	971	34	3	259	3	ZNF576	19	44103150	Missense_Mutation	SNP	G	TCGA-UB-A7ME-01A-11D-A33K-10	3081889	44103150	15025833	79	49032										
MYH14	79784	hgsc.bcm.edu	37	chr19	50789947	50789947	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	cagcaaggatgacgtcggcaAgagcgtgagcagggcccccg	16	12	0	3			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr19:50789947A>T	ENST00000596571.1	+	31	4625	c.4625A>T	c.(4624-4626)aAg>aTg	p.K1542M	MYH14_ENST00000440075.2_Missense_Mutation_p.K1583M|MYH14_ENST00000262269.8_Missense_Mutation_p.K1583M|MYH14_ENST00000425460.1_Missense_Mutation_p.K1550M|MYH14_ENST00000376970.2_Missense_Mutation_p.K1575M|MYH14_ENST00000601313.1_Missense_Mutation_p.K1583M|MYH14_ENST00000598205.1_Missense_Mutation_p.K1550M			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	1542					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		GACGTCGGCAAGAGCGTGAGC	0.622																																					p.K1583M		Atlas-SNP	.											.	MYH14	261	.	0			c.A4748T						.						11	16	14					19																	50789947		2080	4192	6272	SO:0001583	missense	79784	exon34			TCGGCAAGAGCGT	AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"Myosins / Myosin superfamily : Class II"	23212	protein-coding gene	gene with protein product		608568	"myosin, heavy polypeptide 14", "myosin, heavy chain 14"	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.4625A>T	chr19.hg19:g.50789947A>T	ENSP00000472819:p.Lys1542Met	94.0	0.0		95.0	29.0	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Missense_Mutation	SNP	ENST00000596571.1	hg19	CCDS59411.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.103194	0.76983	.	.	ENSG00000105357	ENST00000440075;ENST00000376970;ENST00000425460;ENST00000376965;ENST00000262269	D;D;D;D	0.81821	-1.54;-1.54;-1.54;-1.54	4.7	3.65	0.41850	Myosin tail (1);	.	.	.	.	D	0.88901	0.6563	M	0.86268	2.805	0.48452	D	0.999652	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.88617	0.3160	9	0.87932	D	0	.	8.9602	0.35842	0.8337:0.0:0.0:0.1663	.	1583;1542;1550	Q7Z406-2;Q7Z406;Q7Z406-6	.;MYH14_HUMAN;.	M	1583;1575;1550;1326;1583	ENSP00000406273:K1583M;ENSP00000366169:K1575M;ENSP00000407879:K1550M;ENSP00000262269:K1583M	ENSP00000262269:K1583M	K	+	2	0	MYH14	55481759	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.736000	0.91554	0.895000	0.36342	0.528000	0.53228	AAG	.	.		0.622	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729		T	50789947	A	T	50789947	3	4	347	1	0	0	0	0	1	0	0	0	10042	72	3	4	4878	4	MYH14	19	50789947	Missense_Mutation	SNP	A	TCGA-UB-A7ME-01A-11D-A33K-10	6686797	50789947	8339036	80	49033										
TMC4	147798	hgsc.bcm.edu	37	chr19	54672012	54672012	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	gaagagaggggaccattccaGgtaaccctgtggggggaagg	18	7	0	1			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr19:54672012G>A	ENST00000376591.4	-	5	831	c.700C>T	c.(700-702)Ctg>Ttg	p.L234L	TMC4_ENST00000301187.4_Silent_p.L228L|TMC4_ENST00000476013.2_5'UTR	NM_001145303.1|NM_144686.2	NP_001138775|NP_653287.2	Q7Z404	TMC4_HUMAN	transmembrane channel-like 4	234					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(7)|large_intestine(4)|lung(6)|pancreas(1)|skin(1)|urinary_tract(1)	22	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					GACCATTCCAGGTAACCCTGT	0.662											OREG0025670	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L234L		Atlas-SNP	.											.	TMC4	89	.	0			c.C700T						.						13	12	12					19																	54672012		2144	4204	6348	SO:0001819	synonymous_variant	147798	exon5			ATTCCAGGTAACC	AY236492	CCDS12882.1, CCDS46174.1	19q13.42	2008-02-05			ENSG00000167608	ENSG00000167608			22998	protein-coding gene	gene with protein product						12812529, 12906855	Standard	XM_005277069		Approved		uc010erf.3	Q7Z404	OTTHUMG00000066485	ENST00000376591.4:c.700C>T	chr19.hg19:g.54672012G>A		136.0	0.0	1002	130.0	38.0	NM_001145303	Q7Z5M3|Q8N5E4|Q8TBS7	Silent	SNP	ENST00000376591.4	hg19	CCDS46174.1																																																																																			.	.		0.662	TMC4-011	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000156164.2			A	54672012	G	A	54672012	2	1	347	1	0	0	0	0	0	0	0	1	16002	991	35	3		3	TMC4	19	54672012	Silent	SNP	G	TCGA-UB-A7ME-01A-11D-A33K-10	3882065	54672012	4456971	81	49034										
C20orf26	26074	hgsc.bcm.edu	37	chr20	20257971	20257971	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	tggagagcgccgtggcggacGcgctaggagccgccggagtc	19	12	0	1			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr20:20257971G>A	ENST00000245957.5	+	22	2741	c.2665G>A	c.(2665-2667)Gcg>Acg	p.A889T	C20orf26_ENST00000377309.2_Missense_Mutation_p.A245T	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN		889										NS(2)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(42)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	77				READ - Rectum adenocarcinoma(2;0.171)		CGTGGCGGACGCGCTAGGAGC	0.667																																					p.A889T		Atlas-SNP	.											.	C20orf26	188	.	0			c.G2665A						.						66	63	64					20																	20257971		2203	4300	6503	SO:0001583	missense	26074	exon22			GCGGACGCGCTAG																												ENST00000245957.5:c.2665G>A	chr20.hg19:g.20257971G>A	ENSP00000245957:p.Ala889Thr	101.0	0.0		105.0	21.0	NM_015585	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Missense_Mutation	SNP	ENST00000245957.5	hg19	CCDS33447.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.750304	0.89753	.	.	ENSG00000089101	ENST00000343997;ENST00000377309;ENST00000389655;ENST00000245957	T;T	0.20881	2.04;2.04	5.03	4.07	0.47477	.	0.000000	0.85682	D	0.000000	T	0.33990	0.0882	L	0.61387	1.9	0.80722	D	1	D;P	0.76494	0.999;0.868	P;B	0.56648	0.803;0.229	T	0.02925	-1.1093	10	0.28530	T	0.3	.	12.8135	0.57652	0.0791:0.0:0.9209:0.0	.	855;889	F8W6K4;Q8NHU2	.;CT026_HUMAN	T	829;245;855;889	ENSP00000366524:A245T;ENSP00000245957:A889T	ENSP00000245957:A889T	A	+	1	0	C20orf26	20205971	1.000000	0.71417	0.061000	0.19648	0.012000	0.07955	6.259000	0.72494	2.344000	0.79699	0.460000	0.39030	GCG	.	.		0.667	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3			A	20257971	G	A	20257971	3	1	347	1	0	0	0	0	1	0	0	0	2108	1087	38	1	2779	1	C20orf26	20	20257971	Missense_Mutation	SNP	G	TCGA-UB-A7ME-01A-11D-A33K-10		20257971	42767549	82	49035										
NAPB	63908	hgsc.bcm.edu	37	chr20	23360527	23360527	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	caataatttacattctcttgAatcagtaaatgctggaaaca	5	7	2	1			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr20:23360527A>C	ENST00000377026.4	-	9	797	c.712T>G	c.(712-714)Tca>Gca	p.S238A	RNA5SP479_ENST00000364858.1_RNA|NAPB_ENST00000472855.1_5'UTR|NAPB_ENST00000398425.3_Missense_Mutation_p.S144A|NAPB_ENST00000432543.2_Missense_Mutation_p.S199A	NM_001283018.1|NM_001283020.1|NM_022080.2	NP_001269947.1|NP_001269949.1|NP_071363.1	Q9H115	SNAB_HUMAN	N-ethylmaleimide-sensitive factor attachment protein, beta	238					intracellular protein transport (GO:0006886)|regulation of synaptic vesicle priming (GO:0010807)|SNARE complex disassembly (GO:0035494)|synaptic transmission, glutamatergic (GO:0035249)	extracellular vesicular exosome (GO:0070062)|synaptobrevin 2-SNAP-25-syntaxin-1a complex (GO:0070044)				endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	12	Lung NSC(19;0.0646)|Colorectal(13;0.0993)|all_lung(19;0.143)					CATTCTCTTGAATCAGTAAAT	0.328																																					p.S238A		Atlas-SNP	.											.	NAPB	22	.	0			c.T712G						.						49	52	51					20																	23360527		2202	4297	6499	SO:0001583	missense	63908	exon9			CTCTTGAATCAGT	AK022817	CCDS13152.1, CCDS63241.1, CCDS63242.1, CCDS74710.1	20p12.3-p11.21	2008-08-01			ENSG00000125814	ENSG00000125814			15751	protein-coding gene	gene with protein product		611270				8455721	Standard	NM_022080		Approved	SNAP-BETA, SNAPB	uc002wta.3	Q9H115	OTTHUMG00000032062	ENST00000377026.4:c.712T>G	chr20.hg19:g.23360527A>C	ENSP00000366225:p.Ser238Ala	350.0	0.0		447.0	108.0	NM_022080	B4DK44|Q4G0M0|Q4G187|Q5JXF9|Q8N3C4	Missense_Mutation	SNP	ENST00000377026.4	hg19	CCDS13152.1	.	.	.	.	.	.	.	.	.	.	A	18.55	3.648980	0.67358	.	.	ENSG00000125814	ENST00000377026;ENST00000398425;ENST00000432543;ENST00000431864	T;T;T	0.33438	1.41;1.41;1.41	5.76	5.76	0.90799	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.33498	0.0865	L	0.53249	1.67	0.80722	D	1	B;B;B;B	0.22746	0.041;0.074;0.033;0.018	B;B;B;B	0.25291	0.059;0.059;0.041;0.041	T	0.07083	-1.0791	10	0.49607	T	0.09	-9.0832	15.5474	0.76118	1.0:0.0:0.0:0.0	.	199;144;242;238	B4DK44;Q4G0M0;B4DIV0;Q9H115	.;.;.;SNAB_HUMAN	A	238;144;199;195	ENSP00000366225:S238A;ENSP00000381459:S144A;ENSP00000413600:S199A	ENSP00000366225:S238A	S	-	1	0	NAPB	23308527	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	9.238000	0.95380	2.322000	0.78497	0.528000	0.53228	TCA	.	.		0.328	NAPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078317.2	NM_022080		C	23360527	A	C	23360527	3	2	347	1	0	0	0	0	1	0	0	0	10171	246	9	5	196	5	NAPB	20	23360527	Missense_Mutation	SNP	A	TCGA-UB-A7ME-01A-11D-A33K-10	3102556	23360527	39664993	83	49036										
CST5	1473	hgsc.bcm.edu	37	chr20	23856826	23856826	+	Nonstop_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	acaggccttgcacagaccccTagactttccggcacttgtag	9	14	0	2			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr20:23856826T>A	ENST00000304710.4	-	3	501	c.428A>T	c.(427-429)tAg>tTg	p.*143L		NM_001900.4	NP_001891.2	P28325	CYTD_HUMAN	cystatin D	0					negative regulation of endopeptidase activity (GO:0010951)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|kidney(1)|large_intestine(1)|lung(6)|skin(1)|stomach(1)	11						CACAGACCCCTAGACTTTCCG	0.542																																					p.X143L		Atlas-SNP	.											.	CST5	24	.	0			c.A428T						.						84	90	88					20																	23856826		2203	4300	6503	SO:0001578	stop_lost	1473	exon3			GACCCCTAGACTT		CCDS13162.1	20p11.21	2008-04-15			ENSG00000170367	ENSG00000170367			2477	protein-coding gene	gene with protein product		123858				1939105	Standard	NM_001900		Approved		uc002wtr.1	P28325	OTTHUMG00000032089	ENST00000304710.4:c.428A>T	chr20.hg19:g.23856826T>A		97.0	0.0		142.0	56.0	NM_001900	Q5JRF5|Q9UCA0	Missense_Mutation	SNP	ENST00000304710.4	hg19	CCDS13162.1	.	.	.	.	.	.	.	.	.	.	T	1.773	-0.483848	0.04383	.	.	ENSG00000170367	ENST00000304710	.	.	.	2.01	0.887	0.19200	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.6683	0.08264	0.0:0.2028:0.0:0.7972	.	.	.	.	L	143	.	.	X	-	2	0	CST5	23804826	0.001000	0.12720	0.001000	0.08648	0.040000	0.13550	-0.115000	0.10741	0.228000	0.21019	0.368000	0.22195	TAG	.	.		0.542	CST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078355.2	NM_001900		A	23856826	T	A	23856826	4	1	347	1	0	0	0	0	0	0	0	0	3977	1535	53	4	4	4	CST5	20	23856826	Nonstop_Mutation	SNP	T	TCGA-UB-A7ME-01A-11D-A33K-10	496299	23856826	39168694	84	49037										
KIAA0406	9675	hgsc.bcm.edu	37	chr20	36642105	36642105	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	agggcactgtcactcacagcTtgtagtcgtgtctgcagatg	12	10	3	1			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr20:36642105T>A	ENST00000373448.2	-	3	352	c.114A>T	c.(112-114)caA>caT	p.Q38H	TTI1_ENST00000449821.1_Missense_Mutation_p.Q38H|TTI1_ENST00000487362.1_5'UTR|TTI1_ENST00000373447.3_Missense_Mutation_p.Q38H	NM_014657.1	NP_055472.1	O43156	TTI1_HUMAN	TELO2 interacting protein 1	38					regulation of TOR signaling (GO:0032006)	cytoplasm (GO:0005737)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)				breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(6)|liver(1)|lung(18)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	47						CACTCACAGCTTGTAGTCGTG	0.517																																					p.Q38H		Atlas-SNP	.											.	TTI1	104	.	0			c.A114T						.						142	117	126					20																	36642105		2203	4300	6503	SO:0001583	missense	9675	exon3			CACAGCTTGTAGT	BC013121	CCDS13300.1	20q11.23	2011-11-10	2011-11-10	2010-06-22	ENSG00000101407	ENSG00000101407			29029	protein-coding gene	gene with protein product	"smg-10 homolog, nonsense mediated mRNA decay factor (C. elegans)"	614425	"KIAA0406", "Tel2 interacting protein 1 homolog (S. pombe)"	KIAA0406		9455477, 20427287, 20371770	Standard	NM_014657		Approved	smg-10	uc002xhl.3	O43156	OTTHUMG00000032433	ENST00000373448.2:c.114A>T	chr20.hg19:g.36642105T>A	ENSP00000362547:p.Gln38His	109.0	0.0		188.0	55.0	NM_014657	D6W4K3|Q5JX67|Q96A38|Q9BR47|Q9H4K0	Missense_Mutation	SNP	ENST00000373448.2	hg19	CCDS13300.1	.	.	.	.	.	.	.	.	.	.	T	10.39	1.336970	0.24253	.	.	ENSG00000101407	ENST00000373448;ENST00000373447;ENST00000449821	T;T;T	0.65732	-0.17;-0.17;-0.17	5.33	-2.22	0.06952	Armadillo-type fold (1);	0.726659	0.14318	N	0.327231	T	0.41166	0.1147	L	0.36672	1.1	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.22661	-1.0210	10	0.45353	T	0.12	-17.3632	1.0147	0.01505	0.1797:0.286:0.1671:0.3671	.	38	O43156	TTI1_HUMAN	H	38	ENSP00000362547:Q38H;ENSP00000362546:Q38H;ENSP00000407270:Q38H	ENSP00000362546:Q38H	Q	-	3	2	TTI1	36075519	0.000000	0.05858	0.001000	0.08648	0.825000	0.46686	-1.608000	0.02068	-0.060000	0.13132	0.533000	0.62120	CAA	.	.		0.517	TTI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079138.2	NM_014657		A	36642105	T	A	36642105	3	1	347	1	0	0	0	0	1	0	0	0	8182	1606	56	4	3183	4	KIAA0406	20	36642105	Missense_Mutation	SNP	T	TCGA-UB-A7ME-01A-11D-A33K-10	12785279	36642105	26383415	85	49038										
RALGAPB	57148	hgsc.bcm.edu	37	chr20	37117219	37117219	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	gggcaggtgttaggtaccccTtcagtggctggtagtgagaa	16	7	1	1			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr20:37117219T>G	ENST00000262879.6	+	2	428	c.144T>G	c.(142-144)ccT>ccG	p.P48P	RALGAPB_ENST00000397038.1_5'UTR|RALGAPB_ENST00000397042.3_Silent_p.P48P|RALGAPB_ENST00000537204.1_Silent_p.P48P|RALGAPB_ENST00000397040.1_Silent_p.P48P			Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit (non-catalytic)	48					activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)|Ral protein signal transduction (GO:0032484)|regulation of exocyst localization (GO:0060178)		protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(29)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						TAGGTACCCCTTCAGTGGCTG	0.423																																					p.P48P		Atlas-SNP	.											.	RALGAPB	134	.	0			c.T144G						.						172	154	160					20																	37117219		2203	4300	6503	SO:0001819	synonymous_variant	57148	exon2			TACCCCTTCAGTG	AB033045	CCDS13305.1, CCDS63272.1	20q11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000170471	ENSG00000170471			29221	protein-coding gene	gene with protein product			"KIAA1219"	KIAA1219		19520869	Standard	XM_005260462		Approved	DKFZp781M2411, RalGAPbeta	uc002xiw.3	Q86X10	OTTHUMG00000140270	ENST00000262879.6:c.144T>G	chr20.hg19:g.37117219T>G		92.0	0.0		179.0	41.0	NM_020336	A2A2E8|A2A2E9|Q5TG31|Q8N3D1|Q8WWC0|Q9H3X8|Q9UJR1|Q9ULK1|Q9Y3G9	Silent	SNP	ENST00000262879.6	hg19	CCDS13305.1																																																																																			.	.		0.423	RALGAPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079191.1	NM_020336		G	37117219	T	G	37117219	2	3	347	1	0	0	0	0	0	0	0	1	13030	1596	56	5		5	RALGAPB	20	37117219	Silent	SNP	T	TCGA-UB-A7ME-01A-11D-A33K-10	475114	37117219	25908301	86	49039										
MATN4	8785	hgsc.bcm.edu	37	chr20	43929960	43929960	+	Splice_Site	DEL	C	C	-													0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	gagggtgggggtgttgctcaCccctgcagctcctctggtcc							TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr20:43929960delC	ENST00000372754.1	-	4	898		c.e4+1		MATN4_ENST00000353917.5_Intron|MATN4_ENST00000372756.1_Splice_Site|MATN4_ENST00000360607.6_Intron|MATN4_ENST00000342716.4_Splice_Site|MATN4_ENST00000372751.4_Splice_Site|MATN4_ENST00000537548.1_Splice_Site			O95460	MATN4_HUMAN	matrilin 4						extracellular matrix organization (GO:0030198)|response to axon injury (GO:0048678)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	27		Myeloproliferative disorder(115;0.0122)				GTGTTGCTCACCCCTGCAGCT	0.582											OREG0025977	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.		Atlas-Indel,Pindel	.											.	MATN4	57	.	0			c.766+2G>-						.						97	103	101					20																	43929960		2203	4300	6503	SO:0001630	splice_region_variant	8785	exon5			.	AJ007581	CCDS13348.1, CCDS46607.1	20q13.1-q13.2	2008-07-07			ENSG00000124159	ENSG00000124159			6910	protein-coding gene	gene with protein product		603897				9827539, 9027493	Standard	NM_003833		Approved		uc002xnn.2	O95460	OTTHUMG00000033043	ENST00000372754.1:c.889+1G>-	chr20.hg19:g.43929960delC		48.0	0.0	920	112.0	26.0	NM_003833	A6NH94|A6NKN5|Q5QPU2|Q5QPU3|Q5QPU4|Q8N2M5|Q8N2M7|Q9H1F8|Q9H1F9	Splice_Site	DEL	ENST00000372754.1	hg19																																																																																				.	.		0.582	MATN4-002	KNOWN	non_canonical_conserved|non_canonical_U12|not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000080335.1		Intron	-	43929960	C	-	43929960	8	5	347	1	0	1	0	1	0	0	1	0	9345	521	18	0	1006	0	MATN4	20	43929960	Splice_Site	DEL	C	TCGA-UB-A7ME-01A-11D-A33K-10	6812741	43929960	19095560	87	49040										
ZNF334	55713	hgsc.bcm.edu	37	chr20	45129982	45129982	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	aagaaagtttgatttgtggcGaaatgttttctcacatttgt	9	4	1	2			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr20:45129982G>A	ENST00000347606.4	-	5	2178	c.1996C>T	c.(1996-1998)Cgc>Tgc	p.R666C	ZNF334_ENST00000457685.2_Missense_Mutation_p.R628C|ZNF334_ENST00000593880.1_Missense_Mutation_p.R689C	NM_018102.4	NP_060572.3	Q9HCZ1	ZN334_HUMAN	zinc finger protein 334	666					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0122)				GATTTGTGGCGAAATGTTTTC	0.358																																					p.R666C		Atlas-SNP	.											ZNF334,colon,carcinoma,0,2	ZNF334	101	.	0			c.C1996T						.						146	142	143					20																	45129982		2203	4300	6503	SO:0001583	missense	55713	exon5			TGTGGCGAAATGT	AK001331	CCDS33480.1, CCDS74736.1	20q13.12	2013-09-20			ENSG00000198185	ENSG00000198185		"Zinc fingers, C2H2-type", "-"	15806	protein-coding gene	gene with protein product							Standard	NM_018102		Approved	bA179N14.1	uc002xsc.4	Q9HCZ1	OTTHUMG00000032654	ENST00000347606.4:c.1996C>T	chr20.hg19:g.45129982G>A	ENSP00000255129:p.Arg666Cys	116.0	0.0		221.0	20.0	NM_018102	Q5T6U2|Q9NVW4	Missense_Mutation	SNP	ENST00000347606.4	hg19	CCDS33480.1	.	.	.	.	.	.	.	.	.	.	G	11.97	1.797906	0.31777	.	.	ENSG00000198185	ENST00000457685;ENST00000347606	T;T	0.18502	2.21;2.21	3.23	-4.55	0.03441	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.11750	0.0286	L	0.48642	1.525	0.19300	N	0.99997	B;B;B	0.13145	0.007;0.007;0.007	B;B;B	0.06405	0.002;0.002;0.002	T	0.34279	-0.9835	9	0.42905	T	0.14	.	4.0552	0.09813	0.5027:0.0:0.2103:0.287	.	628;666;689	B3KQ93;Q9HCZ1;Q8N3P8	.;ZN334_HUMAN;.	C	628;666	ENSP00000402582:R628C;ENSP00000255129:R666C	ENSP00000255129:R666C	R	-	1	0	ZNF334	44563389	0.000000	0.05858	0.316000	0.25252	0.730000	0.41778	-1.703000	0.01900	-0.745000	0.04772	-0.229000	0.12294	CGC	.	.		0.358	ZNF334-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079575.1			A	45129982	G	A	45129982	3	1	347	1	0	0	0	0	1	0	0	0	17866	1058	37	1	50	1	ZNF334	20	45129982	Missense_Mutation	SNP	G	TCGA-UB-A7ME-01A-11D-A33K-10	1200022	45129982	17895538	88	49041										
OGFR	11054	hgsc.bcm.edu	37	chr20	61443964	61443964	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	agggtcggacctgtgggccaGagcatagcaagggtgggggc	20	8	0	1			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr20:61443964G>C	ENST00000290291.6	+	7	1022	c.997G>C	c.(997-999)Gag>Cag	p.E333Q	OGFR_ENST00000370461.1_Missense_Mutation_p.E281Q	NM_007346.2	NP_031372.2	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor	333					opioid receptor signaling pathway (GO:0038003)|regulation of cell growth (GO:0001558)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	opioid receptor activity (GO:0004985)			endometrium(2)|kidney(1)|lung(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	17	Breast(26;3.65e-08)					CTGTGGGCCAGAGCATAGCAA	0.716																																					p.E333Q		Atlas-SNP	.											.	OGFR	63	.	0			c.G997C						.																																			SO:0001583	missense	11054	exon7			GGGCCAGAGCATA	AF109134	CCDS13504.1	20q13.3	2008-05-02			ENSG00000060491	ENSG00000060491			15768	protein-coding gene	gene with protein product		606459				10677613	Standard	NM_007346		Approved	7-60	uc002ydj.3	Q9NZT2	OTTHUMG00000032937	ENST00000290291.6:c.997G>C	chr20.hg19:g.61443964G>C	ENSP00000290291:p.Glu333Gln	70.0	0.0		113.0	45.0	NM_007346	O96029|Q4VXW5|Q96CM2|Q9BQW1|Q9H4H0|Q9H7J5|Q9NZT3|Q9NZT4	Missense_Mutation	SNP	ENST00000290291.6	hg19	CCDS13504.1	.	.	.	.	.	.	.	.	.	.	G	7.545	0.661516	0.14645	.	.	ENSG00000060491	ENST00000290291;ENST00000370468;ENST00000357163;ENST00000370469;ENST00000370461	T;T;T	0.51325	1.69;0.71;1.24	4.11	1.6	0.23607	.	1.044460	0.07493	N	0.905908	T	0.29817	0.0745	L	0.34521	1.04	0.09310	N	1	P;P;P	0.44521	0.596;0.627;0.837	B;B;B	0.34722	0.188;0.139;0.139	T	0.16512	-1.0400	10	0.31617	T	0.26	-18.0957	4.5315	0.12008	0.1879:0.2316:0.5805:0.0	.	333;316;333	B3KMQ6;Q05BV5;Q9NZT2	.;.;OGFR_HUMAN	Q	333;333;333;188;281	ENSP00000290291:E333Q;ENSP00000359499:E333Q;ENSP00000359491:E281Q	ENSP00000290291:E333Q	E	+	1	0	OGFR	60914409	0.030000	0.19436	0.001000	0.08648	0.129000	0.20672	1.492000	0.35594	0.685000	0.31468	0.561000	0.74099	GAG	.	.		0.716	OGFR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080067.1			C	61443964	G	C	61443964	3	2	347	1	0	0	0	0	1	0	0	0	10852	943	33	4	1023	4	OGFR	20	61443964	Missense_Mutation	SNP	G	TCGA-UB-A7ME-01A-11D-A33K-10	16313982	61443964	1581556	89	49042										
SIK1	150094	hgsc.bcm.edu	37	chr21	44837443	44837443	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	ctctgctgctctagcacctcCtccagcaggctccagccctc	7	20	2	0			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr21:44837443C>A	ENST00000270162.6	-	13	2088	c.1956G>T	c.(1954-1956)gaG>gaT	p.E652D		NM_173354.3	NP_775490.2	P57059	SIK1_HUMAN	salt-inducible kinase 1	652					cardiac muscle cell differentiation (GO:0055007)|cell cycle (GO:0007049)|entrainment of circadian clock by photoperiod (GO:0043153)|intracellular signal transduction (GO:0035556)|negative regulation of CREB transcription factor activity (GO:0032792)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of triglyceride biosynthetic process (GO:0010868)|positive regulation of anoikis (GO:2000210)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell differentiation (GO:0045595)|regulation of mitotic cell cycle (GO:0007346)|regulation of myotube differentiation (GO:0010830)|regulation of sodium ion transport (GO:0002028)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|cAMP response element binding protein binding (GO:0008140)|magnesium ion binding (GO:0000287)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|testis(2)|urinary_tract(1)	21					Dabrafenib(DB08912)	CTAGCACCTCCTCCAGCAGGC	0.716																																					p.E652D		Atlas-SNP	.											.	SIK1	65	.	0			c.G1956T						.						8	10	9					21																	44837443		2068	4045	6113	SO:0001583	missense	150094	exon13			CACCTCCTCCAGC	BC038504	CCDS33575.1	21q22.3	2008-12-23	2008-12-23	2008-12-23	ENSG00000142178	ENSG00000142178			11142	protein-coding gene	gene with protein product	"myocardial SNF1-like kinase"	605705	"SNF1-like kinase"	SNF1LK		7893599	Standard	NM_173354		Approved	msk	uc002zdf.2	P57059	OTTHUMG00000086874	ENST00000270162.6:c.1956G>T	chr21.hg19:g.44837443C>A	ENSP00000270162:p.Glu652Asp	65.0	0.0		80.0	20.0	NM_173354	A6NC84|Q5R2V5|Q6ZNL8|Q86YJ2	Missense_Mutation	SNP	ENST00000270162.6	hg19	CCDS33575.1	.	.	.	.	.	.	.	.	.	.	C	14.92	2.679536	0.47886	.	.	ENSG00000142178	ENST00000270162	T	0.75477	-0.94	4.22	-2.68	0.06041	.	0.000000	0.85682	D	0.000000	T	0.75744	0.3891	L	0.36672	1.1	0.36851	D	0.887874	D	0.76494	0.999	D	0.76071	0.987	T	0.75263	-0.3379	10	0.59425	D	0.04	.	11.7196	0.51675	0.0:0.3652:0.0:0.6348	.	652	P57059	SIK1_HUMAN	D	652	ENSP00000270162:E652D	ENSP00000270162:E652D	E	-	3	2	SIK1	43661871	0.956000	0.32656	0.936000	0.37596	0.660000	0.38997	0.033000	0.13754	-0.724000	0.04908	-0.793000	0.03317	GAG	.	.		0.716	SIK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195654.1	NM_173354		A	44837443	C	A	44837443	3	1	347	1	0	0	0	0	1	0	0	0	14332	680	24	3	403	3	SIK1	21	44837443	Missense_Mutation	SNP	C	TCGA-UB-A7ME-01A-11D-A33K-10		44837443	3292452	90	49043										
KRTAP10-12	386685	hgsc.bcm.edu	37	chr21	46117560	46117561	+	Frame_Shift_Ins	INS	-	-	TT													0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	gcatctcctccccgtgtcaaINScagtcctgctgtgtgcccgt							TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr21:46117560_46117561insTT	ENST00000400365.3	+	1	474_475	c.444_445insTT	c.(445-447)cagfs	p.Q149fs	TSPEAR_ENST00000323084.4_Intron	NM_198699.1	NP_941972.1	P60413	KR10C_HUMAN	keratin associated protein 10-12	149	19 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(8)	9						CCCCGTGTCAACAGTCCTGCTG	0.619																																					p.Q148fs		Atlas-INDEL	.											.	KRTAP10-12	21	.	0			c.444_445insTT						.																																			SO:0001589	frameshift_variant	386685	exon1			.	AB076364	CCDS42967.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000189169	ENSG00000189169		"Keratin associated proteins"	20533	protein-coding gene	gene with protein product			"keratin associated protein 18-12"	KRTAP18-12			Standard	NM_198699		Approved	KRTAP18.12, KAP10.12	uc002zfw.1	P60413	OTTHUMG00000057629	Exception_encountered	chr21.hg19:g.46117560_46117561insTT	ENSP00000383216:p.Gln149fs	27.0	0.0		28.0	13.0	NM_198699	B2RPA3	Frame_Shift_Ins	INS	ENST00000400365.3	hg19	CCDS42967.1																																																																																			.	.		0.619	KRTAP10-12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128032.1	NM_198699		TT	46117561	-	TT	46117560	7	5	347	1	0	1	1	0	0	0	0	0	8517	40	2	0	446	0	KRTAP10-12	21	46117560	Frame_Shift_Ins	INS	-	TCGA-UB-A7ME-01A-11D-A33K-10	1280117	46117560	2012335	91	49044										
SMTN	6525	hgsc.bcm.edu	37	chr22	31484509	31484509	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	gtctctgcagctctcagcagCgggaagctgagcagcgggct	15	12	2	1			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr22:31484509C>T	ENST00000347557.2	+	4	429	c.211C>T	c.(211-213)Cgg>Tgg	p.R71W	SMTN_ENST00000475548.1_3'UTR|SMTN_ENST00000358743.1_Missense_Mutation_p.R71W|SMTN_ENST00000333137.7_Missense_Mutation_p.R71W	NM_001207017.1|NM_006932.4	NP_001193946.1|NP_008863.3	P53814	SMTN_HUMAN	smoothelin	71					muscle organ development (GO:0007517)|smooth muscle contraction (GO:0006939)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|structural constituent of muscle (GO:0008307)			breast(2)|endometrium(2)|large_intestine(5)|lung(9)|ovary(3)|pancreas(1)|prostate(3)	25						CTCTCAGCAGCGGGAAGCTGA	0.617																																					p.R127W		Atlas-SNP	.											.	SMTN	219	.	0			c.C379T						.						68	74	72					22																	31484509		2203	4300	6503	SO:0001583	missense	6525	exon3			CAGCAGCGGGAAG	AY061972	CCDS13886.1, CCDS13887.1, CCDS13888.1, CCDS74845.1, CCDS74846.1	22q12	2006-01-27			ENSG00000183963	ENSG00000183963			11126	protein-coding gene	gene with protein product		602127				9244445, 8707825	Standard	NM_006932		Approved		uc011ale.2	P53814	OTTHUMG00000151203	ENST00000347557.2:c.211C>T	chr22.hg19:g.31484509C>T	ENSP00000328635:p.Arg71Trp	73.0	0.0		103.0	19.0	NM_001207018	O00569|O95769|O95937|Q8N4H8|Q8WWW1|Q8WWW2|Q9P1S8|Q9UIT1|Q9UIT2	Missense_Mutation	SNP	ENST00000347557.2	hg19	CCDS13886.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.85|17.85	3.491066|3.491066	0.64074|0.64074	.|.	.|.	ENSG00000183963|ENSG00000183963	ENST00000438223|ENST00000426927;ENST00000440425;ENST00000358743;ENST00000347557;ENST00000333137;ENST00000329852;ENST00000404496;ENST00000431481	.|T;T;T;T;T;T	.|0.49139	.|0.79;0.84;0.88;0.88;0.88;0.88	4.79|4.79	2.61|2.61	0.31194|0.31194	.|.	.|0.249386	.|0.20992	.|N	.|0.082011	T|T	0.43612|0.43612	0.1255|0.1255	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D	.|0.71674	.|0.998;0.998;0.998;0.995;0.998;0.994	.|P;P;P;P;P;P	.|0.60886	.|0.88;0.745;0.817;0.817;0.745;0.629	T|T	0.50558|0.50558	-0.8814|-0.8814	5|10	.|0.87932	.|D	.|0	-9.7473|-9.7473	12.6639|12.6639	0.56830|0.56830	0.435:0.565:0.0:0.0|0.435:0.565:0.0:0.0	.|.	.|127;125;63;71;71;71	.|E7ETT8;B4E229;B5MC56;E7EWD0;P53814;P53814-5	.|.;.;.;.;SMTN_HUMAN;.	V|W	125|125;125;71;71;71;71;63;63	.|ENSP00000399432:R125W;ENSP00000401341:R125W;ENSP00000351593:R71W;ENSP00000328635:R71W;ENSP00000329532:R71W;ENSP00000394637:R63W	.|ENSP00000329393:R71W	A|R	+|+	2|1	0|2	SMTN|SMTN	29814509|29814509	0.974000|0.974000	0.33945|0.33945	0.994000|0.994000	0.49952|0.49952	0.961000|0.961000	0.63080|0.63080	0.254000|0.254000	0.18314|0.18314	0.516000|0.516000	0.28340|0.28340	-0.182000|-0.182000	0.12963|0.12963	GCG|CGG	.	.		0.617	SMTN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321766.1	NM_134270		T	31484509	C	T	31484509	3	4	347	1	0	0	0	0	1	0	0	0	14829	759	27	1	221	1	SMTN	22	31484509	Missense_Mutation	SNP	C	TCGA-UB-A7ME-01A-11D-A33K-10		31484509	19820057	92	49045										
FBXO7	25793	hgsc.bcm.edu	37	chr22	32881139	32881139	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	agtacatgcatcctctctgcGagggcagctccgctactctc	9	15	2	0	rs533307944		TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chr22:32881139G>C	ENST00000266087.7	+	4	1057	c.730G>C	c.(730-732)Gag>Cag	p.E244Q	FBXO7_ENST00000397426.1_Missense_Mutation_p.E130Q|FBXO7_ENST00000382058.3_Missense_Mutation_p.E165Q	NM_012179.3	NP_036311.3	Q9Y3I1	FBX7_HUMAN	F-box protein 7	244	Important for dimerization and interaction with PSMF1.				cell death (GO:0008219)|mitochondrion degradation (GO:0000422)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of lymphocyte differentiation (GO:0045620)|protein targeting to mitochondrion (GO:0006626)|protein ubiquitination (GO:0016567)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						TCCTCTCTGCGAGGGCAGCTC	0.502													G|||	1	0.000199681	0	0	5008	,	,		17541	0		0	False		,,,				2504	0.001				p.E244Q		Atlas-SNP	.											FBXO7_ENST00000382058,NS,carcinoma,0,3	FBXO7	131	.	0			c.G730C						.						149	126	134					22																	32881139		2203	4300	6503	SO:0001583	missense	25793	exon4			CTCTGCGAGGGCA	AF129537	CCDS13907.1, CCDS58806.1	22q12.3	2013-09-19	2004-06-15		ENSG00000100225	ENSG00000100225		"F-boxes /  "other"", "Parkinson disease"	13586	protein-coding gene	gene with protein product		605648	"F-box only protein 7"			10531035, 10531037, 19038853	Standard	NM_001257990		Approved	FBX7, Fbx, PARK15	uc003amq.3	Q9Y3I1	OTTHUMG00000030674	ENST00000266087.7:c.730G>C	chr22.hg19:g.32881139G>C	ENSP00000266087:p.Glu244Gln	112.0	0.0		151.0	25.0	NM_012179	B4DNB3|B4DWX5|Q5TGC4|Q5TI86|Q96HM6|Q9UF21|Q9UKT2	Missense_Mutation	SNP	ENST00000266087.7	hg19	CCDS13907.1	.	.	.	.	.	.	.	.	.	.	G	19.77	3.889329	0.72524	.	.	ENSG00000100225	ENST00000266087;ENST00000382058;ENST00000397426	T;T;T	0.75050	-0.9;-0.33;-0.31	5.42	4.38	0.52667	.	0.289081	0.39341	N	0.001393	D	0.83949	0.5365	M	0.78916	2.43	0.40423	D	0.979865	D;D;D	0.61697	0.99;0.985;0.982	P;D;P	0.63957	0.842;0.92;0.87	D	0.85884	0.1424	10	0.59425	D	0.04	-4.6036	12.504	0.55972	0.0858:0.0:0.9142:0.0	.	165;244;130	Q9Y3I1-2;Q9Y3I1;Q5TI86	.;FBX7_HUMAN;.	Q	244;165;130	ENSP00000266087:E244Q;ENSP00000371490:E165Q;ENSP00000380571:E130Q	ENSP00000266087:E244Q	E	+	1	0	FBXO7	31211139	1.000000	0.71417	0.905000	0.35620	0.845000	0.48019	5.826000	0.69293	1.315000	0.45114	0.655000	0.94253	GAG	.	.		0.502	FBXO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129001.1			C	32881139	G	C	32881139	3	2	347	1	0	0	0	0	1	0	0	0	5768	1059	37	4	785	4	FBXO7	22	32881139	Missense_Mutation	SNP	G	TCGA-UB-A7ME-01A-11D-A33K-10	1396630	32881139	18423427	93	49046										
USP9X	8239	hgsc.bcm.edu	37	chrX	41069765	41069765	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	tttcattcatttcttaggctTtggggtgagcctgttaatct	9	7	4	1			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chrX:41069765T>A	ENST00000324545.8	+	33	5652	c.5019T>A	c.(5017-5019)ctT>ctA	p.L1673L	USP9X_ENST00000378308.2_Silent_p.L1673L	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	1673	USP.				axon extension (GO:0048675)|BMP signaling pathway (GO:0030509)|cerebellar cortex structural organization (GO:0021698)|chromosome segregation (GO:0007059)|female gamete generation (GO:0007292)|gene expression (GO:0010467)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|protein deubiquitination (GO:0016579)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)	co-SMAD binding (GO:0070410)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						TTCTTAGGCTTTGGGGTGAGC	0.333																																					p.L1673L	Ovarian(172;1807 2695 35459 49286)	Atlas-SNP	.											.	USP9X	385	.	0			c.T5019A						.						111	105	107					X																	41069765		2162	4275	6437	SO:0001819	synonymous_variant	8239	exon33			TAGGCTTTGGGGT	X98296	CCDS43930.1, CCDS55403.1	Xp11.4	2010-08-03	2006-02-14		ENSG00000124486	ENSG00000124486		"Ubiquitin-specific peptidases"	12632	protein-coding gene	gene with protein product		300072	"ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila)", "ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila)", "ubiquitin specific peptidase 9, X-linked (fat facets-like, Drosophila)"			8922996	Standard	NM_001039590		Approved	DFFRX, FAF	uc004dfb.3	Q93008	OTTHUMG00000021367	ENST00000324545.8:c.5019T>A	chrX.hg19:g.41069765T>A		108.0	0.0		178.0	55.0	NM_001039591	O75550|Q8WWT3|Q8WX12	Silent	SNP	ENST00000324545.8	hg19	CCDS43930.1																																																																																			.	.		0.333	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652		A	41069765	T	A	41069765	2	1	347	1	0	0	0	0	0	0	0	1	17105	1828	64	4		4	USP9X	23	41069765	Silent	SNP	T	TCGA-UB-A7ME-01A-11D-A33K-10		41069765	114200795	94	49047										
PABPC5	140886	hgsc.bcm.edu	37	chrX	90691012	90691012	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0421052631578947	4	1	0.843290441176471	1.43359375	0.597330729166667	1	1	0	gcgatgacaacggctctaagGgttatgcctatgttcacttt	10	9	2	1			TCGA-UB-A7ME-01A-11D-A33K-10	TCGA-UB-A7ME-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	346d5148-fd4f-46cc-b15c-c87013dce4fb	a6a194d9-7740-4c01-b154-677cb12daba0	g.chrX:90691012G>T	ENST00000312600.3	+	2	650	c.436G>T	c.(436-438)Ggt>Tgt	p.G146C	PABPC5-AS1_ENST00000456187.1_RNA|PABPC5_ENST00000373105.1_Intron	NM_080832.2	NP_543022.1	Q96DU9	PABP5_HUMAN	poly(A) binding protein, cytoplasmic 5	146	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.					mitochondrion (GO:0005739)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(20)|ovary(1)|pancreas(1)	42						CGGCTCTAAGGGTTATGCCTA	0.493																																					p.G146C		Atlas-SNP	.											.	PABPC5	92	.	0			c.G436T						.						81	71	74					X																	90691012		2203	4300	6503	SO:0001583	missense	140886	exon2			TCTAAGGGTTATG	AJ278963	CCDS14460.1	Xq21.3	2013-02-12	2001-11-28		ENSG00000174740	ENSG00000174740		"RNA binding motif (RRM) containing"	13629	protein-coding gene	gene with protein product		300407	"poly(A)-binding protein, cytoplasmic 5"			11374897	Standard	NM_080832		Approved	PABP5	uc004efg.3	Q96DU9	OTTHUMG00000021959	ENST00000312600.3:c.436G>T	chrX.hg19:g.90691012G>T	ENSP00000308012:p.Gly146Cys	76.0	0.0		110.0	75.0	NM_080832	A8K240|Q5JQF4|Q6P529|Q9UFE5	Missense_Mutation	SNP	ENST00000312600.3	hg19	CCDS14460.1	.	.	.	.	.	.	.	.	.	.	G	17.94	3.511708	0.64522	.	.	ENSG00000174740	ENST00000312600;ENST00000402906	T	0.27557	1.66	4.43	4.43	0.53597	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.60702	0.2289	M	0.89163	3.01	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.68236	-0.5462	10	0.66056	D	0.02	.	13.8905	0.63736	0.0:0.0:1.0:0.0	.	146	Q96DU9	PABP5_HUMAN	C	146;114	ENSP00000308012:G146C	ENSP00000308012:G146C	G	+	1	0	PABPC5	90577668	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.211000	0.72182	2.450000	0.82876	0.600000	0.82982	GGT	.	.		0.493	PABPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057429.1	NM_080832		T	90691012	G	T	90691012	3	4	347	1	0	0	0	0	1	0	0	0	11376	1232	43	3	438	3	PABPC5	23	90691012	Missense_Mutation	SNP	G	TCGA-UB-A7ME-01A-11D-A33K-10	49621247	90691012	64579548	95	49048										
ANXA9	8416	hgsc.bcm.edu	37	chr1	150960818	150960818	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	aacttcatcaagccctccagGtgagaggggcactcctttcc	9	14	2	1			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr1:150960818G>A	ENST00000368947.4	+	12	1328		c.e12+1			NM_003568.2	NP_003559.2	O76027	ANXA9_HUMAN	annexin A9						single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	acetylcholine receptor activity (GO:0015464)|calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylserine binding (GO:0001786)|phospholipid binding (GO:0005543)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(1)|lung(4)|skin(2)	8	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			AGCCCTCCAGGTGAGAGGGGC	0.493																																					.		Atlas-SNP	.											.	ANXA9	28	.	0			c.852+1G>A						.						104	96	99					1																	150960818		2203	4300	6503	SO:0001630	splice_region_variant	8416	exon12			CTCCAGGTGAGAG	AJ009985	CCDS975.2	1q21.2	2008-02-05			ENSG00000143412	ENSG00000143412		"Annexins"	547	protein-coding gene	gene with protein product		603319		ANX31		9742942, 9931420	Standard	NM_003568		Approved		uc001ewa.2	O76027	OTTHUMG00000035063	ENST00000368947.4:c.852+1G>A	chr1.hg19:g.150960818G>A		80.0	0.0		119.0	43.0	NM_003568	Q5SZF1|Q6FI55|Q9BS00|Q9HBJ6	Splice_Site	SNP	ENST00000368947.4	hg19	CCDS975.2	.	.	.	.	.	.	.	.	.	.	G	22.6	4.316799	0.81469	.	.	ENSG00000143412	ENST00000368947	.	.	.	5.29	5.29	0.74685	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.4183	0.83750	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ANXA9	149227442	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.088000	0.64486	2.493000	0.84123	0.655000	0.94253	.	.	.		0.493	ANXA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084895.2	NM_003568	Intron	A	150960818	G	A	150960818	5	1	348	1	0	0	0	0	0	0	1	0	725	1275	44	3	891	3	ANXA9	1	150960818	Splice_Site	SNP	G	TCGA-UB-A7MF-01A-11D-A33K-10		150960818	98289803	1	49049										
KCNN3	3782	hgsc.bcm.edu	37	chr1	154842252	154842253	+	Missense_Mutation	DNP	AG	AG	CT													0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	tgctgctgctgaagctgcggAggctgaggctgcagcgaggg							TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	A|G	A|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr1:154842252_154842253AG>CT	ENST00000271915.4	-	1	503_504	c.188_189CT>AG	c.(187-189)cCT>cAG	p.P63Q	KCNN3_ENST00000358505.2_5'Flank	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	63	Gln-rich.|Pro-rich.				potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	gaagctgcggaggctgaggctg	0.698																																					p.P63P|p.P63H		Atlas-SNP	.											.	KCNN3	141	.	0			c.T189G|c.C188A						.																																			SO:0001583	missense	3782	exon1			CTGCGGAGGCTGA|TGCGGAGGCTGAG	AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.188_189delinsCT	chr1.hg19:g.154842252_154842253delinsCT	ENSP00000271915:p.Pro63Gln	65.0|66.0	0.0		93.0	9.0|10.0	NM_001204087	B1ANX0|O43517|Q86VF9|Q8WXG7	Silent|Missense_Mutation	SNP	ENST00000271915.4	hg19	CCDS30880.1																																																																																			.	.		0.698	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249		CT	154842253	AG	CT	154842252	3	2	348	1	0	0	0	0	1	0	0	0	8089	291	11	5	2060	5	KCNN3	1	154842252	Missense_Mutation	DNP	AG	TCGA-UB-A7MF-01A-11D-A33K-10	3881434	154842252	94408369	2	49050										
TNR	7143	hgsc.bcm.edu	37	chr1	175335172	175335172	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	tcccagaggatggggtaaagGtaattcggtagtggtcaatg	15	5	1	1			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr1:175335172G>C	ENST00000367674.2	-	11	2864	c.2156C>G	c.(2155-2157)aCc>aGc	p.T719S	TNR_ENST00000263525.2_Missense_Mutation_p.T719S			Q92752	TENR_HUMAN	tenascin R	719	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					TGGGGTAAAGGTAATTCGGTA	0.547																																					p.T719S		Atlas-SNP	.											.	TNR	399	.	0			c.C2156G						.						159	148	152					1																	175335172		2203	4300	6503	SO:0001583	missense	7143	exon11			GTAAAGGTAATTC	X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11953	protein-coding gene	gene with protein product	"restrictin", "janusin"	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.2156C>G	chr1.hg19:g.175335172G>C	ENSP00000356646:p.Thr719Ser	131.0	0.0		172.0	91.0	NM_003285	C9J563|Q15568|Q5R3G0	Missense_Mutation	SNP	ENST00000367674.2	hg19	CCDS1318.1	.	.	.	.	.	.	.	.	.	.	G	13.72	2.321118	0.41096	.	.	ENSG00000116147	ENST00000367674;ENST00000263525;ENST00000367673	T;T	0.58060	0.36;0.36	5.92	3.95	0.45737	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.052752	0.85682	D	0.000000	T	0.39517	0.1081	N	0.20357	0.565	0.45791	D	0.998675	B	0.28512	0.214	B	0.36289	0.221	T	0.15983	-1.0418	10	0.32370	T	0.25	.	9.9484	0.41623	0.0747:0.0:0.7886:0.1367	.	719	Q92752	TENR_HUMAN	S	719	ENSP00000356646:T719S;ENSP00000263525:T719S	ENSP00000263525:T719S	T	-	2	0	TNR	173601795	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	6.055000	0.71103	0.734000	0.32515	0.555000	0.69702	ACC	.	.		0.547	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285		C	175335172	G	C	175335172	3	2	348	1	0	0	0	0	1	0	0	0	16353	1261	44	4	1972	4	TNR	1	175335172	Missense_Mutation	SNP	G	TCGA-UB-A7MF-01A-11D-A33K-10	20492920	175335172	73915449	3	49051										
FAM5B	57795	hgsc.bcm.edu	37	chr1	177226365	177226365	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	agaaactgggaagaaagacaGagacaacaggaggtgcctct	13	7	1	4			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr1:177226365G>A	ENST00000361539.4	+	4	826	c.514G>A	c.(514-516)Gag>Aag	p.E172K	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	172	MACPF.				cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	extracellular region (GO:0005576)											AAGAAAGACAGAGACAACAGG	0.537																																					p.E172K		Atlas-SNP	.											.	FAM5B	191	.	0			c.G514A						.						83	80	81					1																	177226365		2203	4300	6503	SO:0001583	missense	57795	exon4			AAGACAGAGACAA		CCDS1320.1	1q24	2013-08-06	2013-08-06	2013-07-31	ENSG00000198797	ENSG00000198797			13746	protein-coding gene	gene with protein product			"family with sequence similarity 5, member B"	FAM5B		15193423	Standard	NM_021165		Approved	DBCCR1L2	uc001glf.3	Q9C0B6	OTTHUMG00000034953	ENST00000361539.4:c.514G>A	chr1.hg19:g.177226365G>A	ENSP00000354481:p.Glu172Lys	251.0	0.0		282.0	80.0	NM_021165	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Missense_Mutation	SNP	ENST00000361539.4	hg19	CCDS1320.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.135863	0.77662	.	.	ENSG00000198797	ENST00000361539	T	0.15256	2.44	5.05	5.05	0.67936	Membrane attack complex component/perforin (MACPF) domain (1);	0.000000	0.85682	D	0.000000	T	0.38401	0.1039	M	0.64997	1.995	0.80722	D	1	D;D	0.59767	0.981;0.986	P;P	0.61800	0.848;0.894	T	0.15665	-1.0429	10	0.72032	D	0.01	-22.3638	18.3758	0.90435	0.0:0.0:1.0:0.0	.	67;172	Q9C0B6-2;Q9C0B6	.;FAM5B_HUMAN	K	172	ENSP00000354481:E172K	ENSP00000354481:E172K	E	+	1	0	FAM5B	175492988	1.000000	0.71417	0.808000	0.32385	0.094000	0.18550	7.070000	0.76763	2.496000	0.84212	0.655000	0.94253	GAG	.	.		0.537	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1	NM_021165		A	177226365	G	A	177226365	3	1	348	1	0	0	0	0	1	0	0	0	5601	943	33	3	524	3	FAM5B	1	177226365	Missense_Mutation	SNP	G	TCGA-UB-A7MF-01A-11D-A33K-10	1891193	177226365	72024256	4	49052										
FAM72A	729533	hgsc.bcm.edu	37	chr1	206145524	206145525	+	Frame_Shift_Ins	INS	-	-	TC													0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	ttcctgcaacaacggacactINStctggatgtttcacagccag							TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr1:206145524_206145525insTC	ENST00000367128.3	+	3	1149_1150	c.301_302insTC	c.(301-303)ttcfs	p.F101fs	FAM72A_ENST00000470041.1_3'UTR|FAM72A_ENST00000341209.5_Frame_Shift_Ins_p.F61fs|FAM72A_ENST00000367129.2_Frame_Shift_Ins_p.F101fs			Q5TYM5	FA72A_HUMAN	family with sequence similarity 72, member A	101						mitochondrion (GO:0005739)				endometrium(2)	2						CAACGGACACTTCTGGATGTTT	0.376																																					p.F101fs		Atlas-INDEL	.											.	FAM72A	9	.	0			c.301_302insTC						.																																			SO:0001589	frameshift_variant	729533	exon3			.	CR407567	CCDS73016.1	1q32.1	2008-03-26			ENSG00000196550	ENSG00000196550			24044	protein-coding gene	gene with protein product		614710				12477932	Standard	NM_001123168		Approved	MGC57827, RP11-312O7.1	uc001hdr.4	Q5TYM5	OTTHUMG00000042552	ENST00000367128.3:c.302_303dupTC	chr1.hg19:g.206145525_206145526dupTC	ENSP00000356096:p.Phe101fs	481.0	0.0		596.0	92.0	NM_001123168	B2RV15|Q5TYM4	Frame_Shift_Ins	INS	ENST00000367128.3	hg19	CCDS41458.1																																																																																			.	.		0.376	FAM72A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100825.1			TC	206145525	-	TC	206145524	7	5	348	1	0	1	1	0	0	0	0	0	5622	1609	56	0	311	0	FAM72A	1	206145524	Frame_Shift_Ins	INS	-	TCGA-UB-A7MF-01A-11D-A33K-10	28919159	206145524	43105097	5	49053										
INTS7	25896	hgsc.bcm.edu	37	chr1	212190324	212190324	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	gacgaatactatgatgagcaTtcttcctctcaggaattatt	7	8	2	2			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr1:212190324T>C	ENST00000366994.3	-	4	517	c.413A>G	c.(412-414)aAt>aGt	p.N138S	INTS7_ENST00000469606.1_5'UTR|INTS7_ENST00000366993.3_Missense_Mutation_p.N138S|INTS7_ENST00000440600.2_Missense_Mutation_p.N89S|INTS7_ENST00000366992.3_Missense_Mutation_p.N138S	NM_001199811.1|NM_001199812.1|NM_015434.3	NP_001186740.1|NP_001186741.1|NP_056249.1	Q9NVH2	INT7_HUMAN	integrator complex subunit 7	138					cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|snRNA processing (GO:0016180)	chromosome (GO:0005694)|integrator complex (GO:0032039)				NS(1)|breast(1)|kidney(1)|large_intestine(8)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20				OV - Ovarian serous cystadenocarcinoma(81;0.00584)|all cancers(67;0.0318)|Epithelial(68;0.0852)		ATGATGAGCATTCTTCCTCTC	0.393																																					p.N138S		Atlas-SNP	.											.	INTS7	68	.	0			c.A413G						.						177	177	177					1																	212190324		2203	4300	6503	SO:0001583	missense	25896	exon4			TGAGCATTCTTCC	AK022509	CCDS1501.1, CCDS55684.1, CCDS55683.1, CCDS55685.1	1q32.3	2008-02-05	2006-03-15	2006-03-15	ENSG00000143493	ENSG00000143493			24484	protein-coding gene	gene with protein product		611350	"chromosome 1 open reading frame 73"	C1orf73		16239144	Standard	NM_015434		Approved	DKFZP434B168, INT7	uc001hiw.2	Q9NVH2	OTTHUMG00000037119	ENST00000366994.3:c.413A>G	chr1.hg19:g.212190324T>C	ENSP00000355961:p.Asn138Ser	183.0	0.0		223.0	76.0	NM_015434	B4DLZ6|B7WNP6|B7WPB6|Q8N4K7|Q8WUH5|Q9H9V3|Q9NVU5|Q9UFC6|Q9UFM3	Missense_Mutation	SNP	ENST00000366994.3	hg19	CCDS1501.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.428315	0.83667	.	.	ENSG00000143493	ENST00000366994;ENST00000366993;ENST00000366992;ENST00000440600	T;T;T;T	0.26223	1.75;1.75;1.75;1.75	5.88	5.88	0.94601	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.45895	0.1365	L	0.55834	1.745	0.80722	D	1	D;D;D;D	0.67145	0.996;0.996;0.996;0.994	D;D;D;D	0.73380	0.98;0.98;0.98;0.934	T	0.18713	-1.0328	10	0.30078	T	0.28	-32.3397	16.2879	0.82732	0.0:0.0:0.0:1.0	.	89;138;138;138	B4DLZ6;Q9NVH2-3;Q9NVH2-2;Q9NVH2	.;.;.;INT7_HUMAN	S	138;138;138;89	ENSP00000355961:N138S;ENSP00000355960:N138S;ENSP00000355959:N138S;ENSP00000388908:N89S	ENSP00000355959:N138S	N	-	2	0	INTS7	210256947	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.622000	0.83099	2.242000	0.73789	0.533000	0.62120	AAT	.	.		0.393	INTS7-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090142.1	NM_015434		C	212190324	T	C	212190324	3	2	348	1	0	0	0	0	1	0	0	0	7792	1493	52	2	2543	2	INTS7	1	212190324	Missense_Mutation	SNP	T	TCGA-UB-A7MF-01A-11D-A33K-10	6044800	212190324	37060297	6	49054										
DISC1	27185	hgsc.bcm.edu	37	chr1	231931028	231931028	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	ccctcaacttgtcacttaaaGaaatcactactaaggtaagt	5	10	3	1			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr1:231931028G>T	ENST00000602281.1	+	7	1728	c.1675G>T	c.(1675-1677)Gaa>Taa	p.E559*	TSNAX-DISC1_ENST00000602962.1_3'UTR|DISC1_ENST00000535983.1_Nonsense_Mutation_p.E559*|DISC1_ENST00000537876.1_Intron|DISC1_ENST00000602873.1_Intron|DISC1_ENST00000366633.3_Nonsense_Mutation_p.E559*|DISC1_ENST00000539444.1_Nonsense_Mutation_p.E559*|DISC1_ENST00000439617.2_Nonsense_Mutation_p.E559*|DISC1_ENST00000366636.4_Nonsense_Mutation_p.E559*|DISC1_ENST00000366637.3_5'UTR	NM_001164542.1|NM_001164544.1	NP_001158014.1|NP_001158016.1	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1	559	Interaction with TRAF3IP1.|Necessary and sufficient for interaction with PCNT and localization at the centrosome.|Required for localization to punctate cytoplasmic foci.				canonical Wnt signaling pathway (GO:0060070)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cerebral cortex radially oriented cell migration (GO:0021799)|microtubule cytoskeleton organization (GO:0000226)|mitochondrial calcium ion homeostasis (GO:0051560)|neuron migration (GO:0001764)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neuron projection development (GO:0010975)|regulation of synapse maturation (GO:0090128)|TOR signaling (GO:0031929)	cell junction (GO:0030054)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|postsynaptic membrane (GO:0045211)				breast(1)|cervix(1)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	15		all_cancers(173;0.0208)|Prostate(94;0.0975)				GTCACTTAAAGAAATCACTAC	0.353																																					p.E591X		Atlas-SNP	.											DISC1_ENST00000366638,caecum,carcinoma,0,6	DISC1	207	.	0			c.G1771T						.						80	81	81					1																	231931028		2203	4300	6503	SO:0001587	stop_gained	27185	exon8			CTTAAAGAAATCA	AF222980	CCDS31055.1, CCDS31056.1, CCDS53482.1, CCDS53483.1, CCDS53484.1, CCDS59205.1, CCDS59206.1, CCDS59207.1	1q42.1	2008-02-05			ENSG00000162946	ENSG00000162946			2888	protein-coding gene	gene with protein product		605210				10814723	Standard	NM_001164550		Approved		uc010pxh.2	Q9NRI5	OTTHUMG00000037835	ENST00000602281.1:c.1675G>T	chr1.hg19:g.231931028G>T	ENSP00000473425:p.Glu559*	71.0	0.0		85.0	5.0	NM_001164537	A6NLH2|C4P091|C4P095|C4P0A1|C4P0A3|C4P0B3|C4P0B6|C4P0C1|C9J6D0|O75045|Q5VT44|Q5VT45|Q8IXJ0|Q8IXJ1|Q9BX19|Q9NRI3|Q9NRI4	Nonsense_Mutation	SNP	ENST00000602281.1	hg19	CCDS59205.1	.	.	.	.	.	.	.	.	.	.	G	38	6.665954	0.97747	.	.	ENSG00000162946	ENST00000439617;ENST00000366637;ENST00000366636;ENST00000366638;ENST00000532576;ENST00000535983;ENST00000366633;ENST00000539444	.	.	.	4.72	2.84	0.33178	.	0.058100	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-14.0953	9.2333	0.37450	0.1675:0.0:0.8325:0.0	.	.	.	.	X	559;559;559;591;437;559;559;559	.	ENSP00000355593:E559X	E	+	1	0	DISC1	229997651	1.000000	0.71417	0.626000	0.29213	0.986000	0.74619	5.159000	0.64923	0.688000	0.31529	0.557000	0.71058	GAA	.	.		0.353	DISC1-019	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467451.1	NM_018662		T	231931028	G	T	231931028	4	4	348	1	0	0	0	0	0	1	0	0	4540	943	33	3	2074	3	DISC1	1	231931028	Nonsense_Mutation	SNP	G	TCGA-UB-A7MF-01A-11D-A33K-10	19740704	231931028	17319593	7	49055										
OR2L3	391192	hgsc.bcm.edu	37	chr1	248224001	248224001	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	cccatggaaaattacaatcaAacatcaactgatttcatctt	3	10	4	1			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr1:248224001A>T	ENST00000359959.3	+	1	18	c.18A>T	c.(16-18)caA>caT	p.Q6H	OR2L13_ENST00000366478.2_Intron	NM_001004687.1	NP_001004687.1	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L, member 3	6						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|large_intestine(7)|lung(28)|prostate(1)|skin(1)|urinary_tract(1)	41	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)			ATTACAATCAAACATCAACTG	0.393																																					p.Q6H		Atlas-SNP	.											.	OR2L3	97	.	0			c.A18T						.						181	180	180					1																	248224001		2203	4300	6503	SO:0001583	missense	391192	exon1			CAATCAAACATCA	AB065950	CCDS31104.1	1q44	2012-08-09			ENSG00000198128	ENSG00000198128		"GPCR / Class A : Olfactory receptors"	15009	protein-coding gene	gene with protein product							Standard	NM_001004687		Approved		uc001idx.1	Q8NG85	OTTHUMG00000040195	ENST00000359959.3:c.18A>T	chr1.hg19:g.248224001A>T	ENSP00000353044:p.Gln6His	160.0	0.0		180.0	80.0	NM_001004687	B9EH44	Missense_Mutation	SNP	ENST00000359959.3	hg19	CCDS31104.1	.	.	.	.	.	.	.	.	.	.	.	8.919	0.960659	0.18583	.	.	ENSG00000198128	ENST00000359959	T	0.00572	6.49	2.05	0.915	0.19366	.	.	.	.	.	T	0.00412	0.0013	N	0.16903	0.455	0.25872	N	0.983693	B	0.13594	0.008	B	0.18263	0.021	T	0.40251	-0.9573	9	0.25106	T	0.35	.	4.71	0.12868	0.6785:0.0:0.3215:0.0	.	6	Q8NG85	OR2L3_HUMAN	H	6	ENSP00000353044:Q6H	ENSP00000353044:Q6H	Q	+	3	2	OR2L3	246290624	0.095000	0.21747	0.051000	0.19133	0.366000	0.29705	0.389000	0.20751	0.928000	0.37168	0.379000	0.24179	CAA	.	.		0.393	OR2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096852.1	NM_001004687		T	248224001	A	T	248224001	3	4	348	1	0	0	0	0	1	0	0	0	11017	11	1	4	20	4	OR2L3	1	248224001	Missense_Mutation	SNP	A	TCGA-UB-A7MF-01A-11D-A33K-10	16292973	248224001	1026620	8	49056										
MYT1L	23040	hgsc.bcm.edu	37	chr2	1926072	1926072	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	tattacctttaccatagtatGgctttttgacatggctgtca	7	8	1	1			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr2:1926072G>T	ENST00000399161.2	-	10	2216	c.1469C>A	c.(1468-1470)cCa>cAa	p.P490Q	MYT1L_ENST00000428368.2_Missense_Mutation_p.P490Q	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	490					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.P490K(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		ACCATAGTATGGCTTTTTGAC	0.448																																					p.P490Q		Atlas-SNP	.											.,1	MYT1L	241	.	1	Substitution - Missense(1)	lung(1)	c.C1469A						.						117	110	112					2																	1926072		1919	4131	6050	SO:0001583	missense	23040	exon10			TAGTATGGCTTTT	AF036943	CCDS46222.1	2p25.3	2013-01-10			ENSG00000186487	ENSG00000186487		"Zinc fingers, C2HC-type containing"	7623	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 1"	613084				9373037	Standard	XM_006711862		Approved	KIAA1106, NZF1, ZC2HC4B	uc002qxd.3	Q9UL68	OTTHUMG00000151407	ENST00000399161.2:c.1469C>A	chr2.hg19:g.1926072G>T	ENSP00000382114:p.Pro490Gln	100.0	0.0		122.0	26.0	NM_015025	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Missense_Mutation	SNP	ENST00000399161.2	hg19		.	.	.	.	.	.	.	.	.	.	G	23.1	4.376907	0.82682	.	.	ENSG00000186487	ENST00000399161;ENST00000295067;ENST00000428368	T;T	0.43294	0.95;0.95	5.91	5.91	0.95273	.	0.165892	0.53938	D	0.000046	T	0.49490	0.1560	N	0.24115	0.695	0.80722	D	1	D;P	0.63880	0.993;0.846	P;B	0.60541	0.876;0.358	T	0.32052	-0.9921	10	0.29301	T	0.29	-14.9637	20.2936	0.98544	0.0:0.0:1.0:0.0	.	490;490	Q9UL68;Q9UL68-4	MYT1L_HUMAN;.	Q	490;438;490	ENSP00000382114:P490Q;ENSP00000396103:P490Q	ENSP00000295067:P438Q	P	-	2	0	MYT1L	1905079	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.787000	0.99055	2.801000	0.96364	0.655000	0.94253	CCA	.	.		0.448	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025		T	1926072	G	T	1926072	3	4	348	1	0	0	0	0	1	0	0	0	10116	1348	47	3	2149	3	MYT1L	2	1926072	Missense_Mutation	SNP	G	TCGA-UB-A7MF-01A-11D-A33K-10		1926072	241273301	9	49057										
NR4A2	4929	hgsc.bcm.edu	37	chr2	157186301	157186301	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	tgtgctgcacctggaagcccGgggtggtgggcgtcgggggc	21	10	0	0			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr2:157186301G>A	ENST00000339562.4	-	3	760	c.398C>T	c.(397-399)cCg>cTg	p.P133L	NR4A2_ENST00000429376.1_Missense_Mutation_p.P70L|NR4A2_ENST00000409108.2_Missense_Mutation_p.P133L|NR4A2_ENST00000409572.1_Missense_Mutation_p.P133L|NR4A2_ENST00000539077.1_Missense_Mutation_p.P144L|NR4A2_ENST00000426264.1_Missense_Mutation_p.P70L	NM_006186.3	NP_006177.1	P43354	NR4A2_HUMAN	nuclear receptor subfamily 4, group A, member 2	133	Gln-rich.|Pro-rich.				adult locomotory behavior (GO:0008344)|cellular response to extracellular stimulus (GO:0031668)|cellular response to oxidative stress (GO:0034599)|central nervous system projection neuron axonogenesis (GO:0021952)|death (GO:0016265)|dopamine biosynthetic process (GO:0042416)|dopaminergic neuron differentiation (GO:0071542)|gene expression (GO:0010467)|general adaptation syndrome (GO:0051866)|habenula development (GO:0021986)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of neuron apoptotic process (GO:0043524)|neuron maturation (GO:0042551)|neuron migration (GO:0001764)|positive regulation of catalytic activity (GO:0043085)|post-embryonic development (GO:0009791)|regulation of dopamine metabolic process (GO:0042053)|regulation of respiratory gaseous exchange (GO:0043576)|response to amphetamine (GO:0001975)|response to hypoxia (GO:0001666)|response to inorganic substance (GO:0010035)|response to insecticide (GO:0017085)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(1)	40						CTGGAAGCCCGGGGTGGTGGG	0.637																																					p.P133L		Atlas-SNP	.											.	NR4A2	82	.	0			c.C398T						.						57	69	65					2																	157186301		2203	4300	6503	SO:0001583	missense	4929	exon3			AAGCCCGGGGTGG	X75918	CCDS2201.1	2q22-q23	2013-01-16			ENSG00000153234	ENSG00000153234		"Nuclear hormone receptors"	7981	protein-coding gene	gene with protein product		601828		NURR1		7706727	Standard	NM_006186		Approved	TINUR, NOT, RNR1, HZF-3	uc002tyz.4	P43354	OTTHUMG00000131950	ENST00000339562.4:c.398C>T	chr2.hg19:g.157186301G>A	ENSP00000344479:p.Pro133Leu	70.0	0.0		66.0	9.0	NM_006186	Q16311|Q53RZ2|Q6NXU0	Missense_Mutation	SNP	ENST00000339562.4	hg19	CCDS2201.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.354232	0.82243	.	.	ENSG00000153234	ENST00000339562;ENST00000426264;ENST00000409572;ENST00000539077;ENST00000409108;ENST00000429376;ENST00000424077;ENST00000421709	D;D;D;D;D;D;D;D	0.95069	-3.07;-3.36;-3.07;-3.09;-3.38;-3.6;-1.87;-2.64	5.95	5.95	0.96441	.	0.483808	0.24678	N	0.036500	D	0.96259	0.8780	L	0.57536	1.79	0.80722	D	1	D	0.71674	0.998	P	0.59288	0.855	D	0.96147	0.9105	10	0.87932	D	0	.	20.3854	0.98941	0.0:0.0:1.0:0.0	.	133	P43354	NR4A2_HUMAN	L	133;70;133;144;133;70;133;70	ENSP00000344479:P133L;ENSP00000389986:P70L;ENSP00000386747:P133L;ENSP00000444925:P144L;ENSP00000386993:P133L;ENSP00000410952:P70L;ENSP00000406808:P133L;ENSP00000388120:P70L	ENSP00000344479:P133L	P	-	2	0	NR4A2	156894547	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	9.869000	0.99810	2.825000	0.97269	0.655000	0.94253	CCG	.	.		0.637	NR4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254909.2			A	157186301	G	A	157186301	3	1	348	1	0	0	0	0	1	0	0	0	10642	1116	39	1	1422	1	NR4A2	2	157186301	Missense_Mutation	SNP	G	TCGA-UB-A7MF-01A-11D-A33K-10	155260229	157186301	86013072	10	49058										
CWC22	57703	hgsc.bcm.edu	37	chr2	180853328	180853332	+	Frame_Shift_Del	DEL	TGATA	TGATA	-													0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	cttctggagaggagttcctcTgatatgaattaaggttttcc							TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	TGATA	TGATA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr2:180853328_180853332delTGATA	ENST00000410053.3	-	3	366_370	c.67_71delTATCA	c.(67-72)tatcagfs	p.YQ23fs	CWC22_ENST00000295749.6_Frame_Shift_Del_p.YQ23fs	NM_020943.2	NP_065994.1	Q9HCG8	CWC22_HUMAN	CWC22 spliceosome-associated protein	23	Arg-rich.				mRNA splicing, via spliceosome (GO:0000398)|regulation of mRNA splicing, via spliceosome (GO:0048024)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(8)|stomach(1)	30						GGAGTTCCTCTGATATGAATTAAGG	0.307																																					p.23_24del		Atlas-Indel,Pindel	.											.	CWC22	62	.	0			c.68_72del						.																																			SO:0001589	frameshift_variant	57703	exon3			.		CCDS46465.1	2q31.3	2014-07-03	2014-07-03		ENSG00000163510	ENSG00000163510			29322	protein-coding gene	gene with protein product	"functional spliceosome-associated protein b"	615186	"CWC22 spliceosome-associated protein homolog (S. cerevisiae)"			9136012, 23236153	Standard	NM_020943		Approved	KIAA1604, EIF4GL, fSAPb, NCM	uc010frh.1	Q9HCG8	OTTHUMG00000154244	ENST00000410053.3:c.67_71delTATCA	chr2.hg19:g.180853328_180853332delTGATA	ENSP00000387006:p.Tyr23fs	183.0	0.0		162.0	14.0	NM_020943	Q05DC2|Q4G135|Q52LF0|Q6PEX2|Q7Z6I0|Q9H5L3|Q9H6Q6	Frame_Shift_Del	DEL	ENST00000410053.3	hg19	CCDS46465.1																																																																																			.	.		0.307	CWC22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334537.1	NM_020943		-	180853332	TGATA	-	180853328	7	5	348	1	0	1	0	1	0	0	0	0	4070	1580	55	0	2727	0	CWC22	2	180853328	Frame_Shift_Del	DEL	TGATA	TCGA-UB-A7MF-01A-11D-A33K-10	23667027	180853328	62346045	11	49059										
STAT1	6772	hgsc.bcm.edu	37	chr2	191841668	191841668	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	aatattctcagcagccatgaCtttgtaattgcgaatgatgt	8	7	1	2			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr2:191841668C>G	ENST00000361099.3	-	22	2344	c.1957G>C	c.(1957-1959)Gtc>Ctc	p.V653L	STAT1_ENST00000392322.3_Missense_Mutation_p.V653L|STAT1_ENST00000540176.1_3'UTR|STAT1_ENST00000409465.1_Missense_Mutation_p.V653L|STAT1_ENST00000392323.2_Missense_Mutation_p.V655L	NM_007315.3	NP_009330.1	P42224	STAT1_HUMAN	signal transducer and activator of transcription 1, 91kDa	653	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				apoptotic process (GO:0006915)|blood circulation (GO:0008015)|cellular response to insulin stimulus (GO:0032869)|cellular response to interferon-beta (GO:0035458)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchymal cell proliferation involved in metanephros development (GO:0072136)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of macrophage fusion (GO:0034240)|negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003340)|negative regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072308)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|renal tubule development (GO:0061326)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|transcription from RNA polymerase II promoter (GO:0006366)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|tumor necrosis factor receptor binding (GO:0005164)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			OV - Ovarian serous cystadenocarcinoma(117;0.00434)|Epithelial(96;0.0555)|all cancers(119;0.141)			GCAGCCATGACTTTGTAATTG	0.418																																					p.V653L		Atlas-SNP	.											.	STAT1	93	.	0			c.G1957C						.						118	110	113					2																	191841668		2203	4300	6503	SO:0001583	missense	6772	exon22			CCATGACTTTGTA		CCDS2309.1, CCDS42793.1	2q32.2-q32.3	2014-09-17	2002-08-29		ENSG00000115415	ENSG00000115415		"SH2 domain containing"	11362	protein-coding gene	gene with protein product	"transcription factor ISGF-3 components p91/p84"	600555	"signal transducer and activator of transcription 1, 91kD"			7885841	Standard	NM_139266		Approved	STAT91, ISGF-3	uc002usj.2	P42224	OTTHUMG00000132699	ENST00000361099.3:c.1957G>C	chr2.hg19:g.191841668C>G	ENSP00000354394:p.Val653Leu	131.0	0.0		106.0	59.0	NM_007315	A8K989|B2RCA0|D2KFR8|D3DPI7|Q53S88|Q53XW4|Q68D00|Q9UDL5	Missense_Mutation	SNP	ENST00000361099.3	hg19	CCDS2309.1	.	.	.	.	.	.	.	.	.	.	C	13.27	2.186456	0.38609	.	.	ENSG00000115415	ENST00000361099;ENST00000409465;ENST00000392322;ENST00000392323	D;D;D;D	0.96427	-4.01;-4.01;-4.01;-4.01	5.53	5.53	0.82687	SH2 motif (3);	0.051635	0.85682	D	0.000000	D	0.92731	0.7689	N	0.25245	0.725	0.80722	D	1	B;B	0.26318	0.146;0.023	B;B	0.25140	0.058;0.05	D	0.88936	0.3376	10	0.25106	T	0.35	-31.2802	19.6556	0.95837	0.0:1.0:0.0:0.0	.	653;653	P42224-2;P42224	.;STAT1_HUMAN	L	653;653;653;655	ENSP00000354394:V653L;ENSP00000386244:V653L;ENSP00000376136:V653L;ENSP00000376137:V655L	ENSP00000354394:V653L	V	-	1	0	STAT1	191549913	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.798000	0.55522	2.882000	0.98803	0.655000	0.94253	GTC	.	.		0.418	STAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255997.3	NM_007315		G	191841668	C	G	191841668	3	3	348	1	0	0	0	0	1	0	0	0	15279	565	20	4	315	4	STAT1	2	191841668	Missense_Mutation	SNP	C	TCGA-UB-A7MF-01A-11D-A33K-10	10988340	191841668	51357705	12	49060										
C2orf62	375307	hgsc.bcm.edu	37	chr2	219225307	219225307	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	ggccctcagttcctcatcctCcccatggaacggaagatgag	10	14	2	2			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr2:219225307C>T	ENST00000289388.3	+	5	416	c.387C>T	c.(385-387)ctC>ctT	p.L129L	C2orf62_ENST00000481940.1_3'UTR|AC021016.8_ENST00000411433.1_RNA	NM_198559.1	NP_940961.1	Q7Z7H3	CATIP_HUMAN		129					actin filament polymerization (GO:0030041)|cilium organization (GO:0044782)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	16		Renal(207;0.0915)		Epithelial(149;8.08e-07)|all cancers(144;0.000146)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCCTCATCCTCCCCATGGAAC	0.552																																					p.L129L		Atlas-SNP	.											.	C2orf62	28	.	0			c.C387T						.						97	82	87					2																	219225307		2203	4300	6503	SO:0001819	synonymous_variant	375307	exon5			CATCCTCCCCATG																												ENST00000289388.3:c.387C>T	chr2.hg19:g.219225307C>T		41.0	0.0		39.0	10.0	NM_198559		Silent	SNP	ENST00000289388.3	hg19	CCDS2414.1																																																																																			.	.		0.552	C2orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256771.1			T	219225307	C	T	219225307	2	4	348	1	0	0	0	0	0	0	0	1	2183	842	30	3		3	C2orf62	2	219225307	Silent	SNP	C	TCGA-UB-A7MF-01A-11D-A33K-10	27383639	219225307	23974066	13	49061										
NDUFA10	4705	hgsc.bcm.edu	37	chr2	240946749	240946749	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	ttaccttttttgaatcttgaGcttcccttgcagaatattgt	6	8	1	3			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr2:240946749G>T	ENST00000252711.2	-	7	888	c.788C>A	c.(787-789)gCt>gAt	p.A263D	NDUFA10_ENST00000404554.1_Missense_Mutation_p.A263D|NDUFA10_ENST00000307300.4_Missense_Mutation_p.A293D	NM_004544.3	NP_004535.1	O95299	NDUAA_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 10, 42kDa	263					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	ATP binding (GO:0005524)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|nucleoside kinase activity (GO:0019206)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)	16		all_epithelial(40;4.26e-15)|Breast(86;4.4e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0396)|Lung NSC(271;0.128)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(121;7.82e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.5e-13)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;2.39e-05)|Lung(119;0.00519)|LUSC - Lung squamous cell carcinoma(224;0.0202)		TGAATCTTGAGCTTCCCTTGC	0.313																																					p.A263D		Atlas-SNP	.											.	NDUFA10	40	.	0			c.C788A						.						110	106	107					2																	240946749		2202	4298	6500	SO:0001583	missense	4705	exon7			TCTTGAGCTTCCC	AF087661	CCDS2531.1	2q37.3	2011-07-04	2002-08-29		ENSG00000130414	ENSG00000130414		"Mitochondrial respiratory chain complex / Complex I"	7684	protein-coding gene	gene with protein product	"complex I 42kDa subunit"	603835	"NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 10 (42kD)"			9878551	Standard	NM_004544		Approved	CI-42k	uc002vyn.3	O95299	OTTHUMG00000133350	ENST00000252711.2:c.788C>A	chr2.hg19:g.240946749G>T	ENSP00000252711:p.Ala263Asp	76.0	0.0		61.0	6.0	NM_004544	Q8WXC9	Missense_Mutation	SNP	ENST00000252711.2	hg19	CCDS2531.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	6.632|6.632|6.632	0.485114|0.485114|0.485114	0.12641|0.12641|0.12641	.|.|.	.|.|.	ENSG00000130414|ENSG00000130414|ENSG00000130414	ENST00000419408;ENST00000252711;ENST00000404554;ENST00000422018;ENST00000448880;ENST00000307300|ENST00000443626|ENST00000444548	D;D;D|D|.	0.94537|0.94758|.	-3.45;-3.45;-3.45|-3.51|.	4.34|4.34|4.34	2.51|2.51|2.51	0.30379|0.30379|0.30379	.|.|.	0.220526|.|.	0.46442|.|.	D|.|.	0.000297|.|.	T|T|T	0.44932|0.44932|0.44932	0.1317|0.1317|0.1317	M|M|M	0.65320|0.65320|0.65320	2|2|2	0.19775|0.19775|0.19775	N|N|N	0.999957|0.999957|0.999957	D;D|.|.	0.58268|.|.	0.982;0.979|.|.	P;P|.|.	0.61533|.|.	0.843;0.89|.|.	T|T|T	0.31971|0.31971|0.31971	-0.9924|-0.9924|-0.9924	10|7|5	0.34782|0.33940|.	T|T|.	0.22|0.23|.	-5.7217|-5.7217|-5.7217	7.0912|7.0912|7.0912	0.25285|0.25285|0.25285	0.2165:0.0:0.7835:0.0|0.2165:0.0:0.7835:0.0|0.2165:0.0:0.7835:0.0	.|.|.	293;263|.|.	Q8WXC9;O95299|.|.	.;NDUAA_HUMAN|.|.	D|I|R	28;263;263;263;26;293|196|33	ENSP00000252711:A263D;ENSP00000385697:A263D;ENSP00000302321:A293D|ENSP00000411527:L196I|.	ENSP00000252711:A263D|ENSP00000411527:L196I|.	A|L|S	-|-|-	2|1|3	0|0|2	NDUFA10|NDUFA10|NDUFA10	240595422|240595422|240595422	0.445000|0.445000|0.445000	0.25657|0.25657|0.25657	0.007000|0.007000|0.007000	0.13788|0.13788|0.13788	0.000000|0.000000|0.000000	0.00434|0.00434|0.00434	3.327000|3.327000|3.327000	0.52045|0.52045|0.52045	0.405000|0.405000|0.405000	0.25532|0.25532|0.25532	-0.291000|-0.291000|-0.291000	0.09656|0.09656|0.09656	GCT|CTC|AGC	.	.		0.313	NDUFA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257180.2	NM_004544		T	240946749	G	T	240946749	3	4	348	1	0	0	0	0	1	0	0	0	10269	971	34	3	295	3	NDUFA10	2	240946749	Missense_Mutation	SNP	G	TCGA-UB-A7MF-01A-11D-A33K-10	21721442	240946749	2252624	14	49062										
NKTR	4820	hgsc.bcm.edu	37	chr3	42672063	42672063	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	caaagcctgctccacacctgGatgggtaagagttacattct	9	11	1	1			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr3:42672063G>C	ENST00000232978.8	+	7	588	c.400G>C	c.(400-402)Gat>Cat	p.D134H	RP4-613B23.1_ENST00000445452.1_RNA|RP4-613B23.1_ENST00000434363.1_RNA|RP4-613B23.1_ENST00000438017.1_RNA	NM_005385.3	NP_005376.2	P30414	NKTR_HUMAN	natural killer cell triggering receptor	134	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				protein folding (GO:0006457)	membrane (GO:0016020)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	41				KIRC - Kidney renal clear cell carcinoma(284;0.24)		TCCACACCTGGATGGGTAAGA	0.453																																					p.D134H		Atlas-SNP	.											.	NKTR	116	.	0			c.G400C						.						160	138	145					3																	42672063		2203	4300	6503	SO:0001583	missense	4820	exon7			CACCTGGATGGGT		CCDS2702.1	3p22.1	2014-01-20	2014-01-20		ENSG00000114857	ENSG00000114857			7833	protein-coding gene	gene with protein product	"NK-tumor recognition protein", "natural-killer cells cyclophilin-related protein", "NK-TR protein"	161565	"natural killer-tumor recognition sequence"			8314596, 8144875	Standard	XM_005265173		Approved	p104	uc003clo.3	P30414	OTTHUMG00000133037	ENST00000232978.8:c.400G>C	chr3.hg19:g.42672063G>C	ENSP00000232978:p.Asp134His	141.0	0.0		89.0	12.0	NM_005385		Missense_Mutation	SNP	ENST00000232978.8	hg19	CCDS2702.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.673695	0.88445	.	.	ENSG00000114857	ENST00000232978	T	0.42900	0.96	5.37	5.37	0.77165	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (4);Cyclophilin-like (1);	0.048956	0.85682	D	0.000000	T	0.76378	0.3979	H	0.95780	3.72	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.84100	0.0395	10	0.87932	D	0	-16.2521	19.0902	0.93224	0.0:0.0:1.0:0.0	.	14;134	Q59EC3;P30414	.;NKTR_HUMAN	H	134	ENSP00000232978:D134H	ENSP00000232978:D134H	D	+	1	0	NKTR	42647067	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	8.914000	0.92735	2.519000	0.84933	0.455000	0.32223	GAT	.	.		0.453	NKTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256642.2	NM_005385		C	42672063	G	C	42672063	3	2	348	1	0	0	0	0	1	0	0	0	10457	1174	41	4	422	4	NKTR	3	42672063	Missense_Mutation	SNP	G	TCGA-UB-A7MF-01A-11D-A33K-10		42672063	155350367	15	49063										
APEH	327	hgsc.bcm.edu	37	chr3	49720485	49720485	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	acacccaggtgaagacaccaCtgttactgatgttgggccag	11	11	0	3			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr3:49720485C>T	ENST00000296456.5	+	21	2399	c.1999C>T	c.(1999-2001)Ctg>Ttg	p.L667L	APEH_ENST00000438011.1_Silent_p.L672L|AC099668.5_ENST00000563780.1_RNA	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase	667					beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GAAGACACCACTGTTACTGAT	0.597																																					p.L667L		Atlas-SNP	.											.	APEH	45	.	0			c.C1999T						.						88	73	78					3																	49720485		2203	4300	6503	SO:0001819	synonymous_variant	327	exon21			ACACCACTGTTAC	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"acylaminoacyl-peptidase"	102645	"N-acylaminoacyl-peptide hydrolase"	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882	ENST00000296456.5:c.1999C>T	chr3.hg19:g.49720485C>T		96.0	0.0		58.0	26.0	NM_001640	Q9BQ33|Q9P0Y2	Silent	SNP	ENST00000296456.5	hg19	CCDS2801.1																																																																																			.	.		0.597	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2			T	49720485	C	T	49720485	2	4	348	1	0	0	0	0	0	0	0	1	768	564	20	3		3	APEH	3	49720485	Silent	SNP	C	TCGA-UB-A7MF-01A-11D-A33K-10	7048422	49720485	148301945	16	49064										
P2RY1	5028	hgsc.bcm.edu	37	chr3	152554423	152554423	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	gtgatgaaaacgatgaacttGagggcccggcttgattttca	12	7	1	5			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr3:152554423G>C	ENST00000305097.3	+	1	1688	c.852G>C	c.(850-852)ttG>ttC	p.L284F	RP11-38P22.2_ENST00000460407.1_lincRNA	NM_002563.3	NP_002554.1	P47900	P2RY1_HUMAN	purinergic receptor P2Y, G-protein coupled, 1	284					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|aging (GO:0007568)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cell surface receptor signaling pathway (GO:0007166)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of binding (GO:0051100)|negative regulation of norepinephrine secretion (GO:0010700)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of hormone secretion (GO:0046887)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of ion transport (GO:0043270)|positive regulation of penile erection (GO:0060406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to plasma membrane (GO:0072659)|regulation of receptor activity (GO:0010469)|regulation of vasodilation (GO:0042312)|relaxation of muscle (GO:0090075)|response to growth factor (GO:0070848)|response to mechanical stimulus (GO:0009612)|sensory perception of pain (GO:0019233)|signal transduction involved in regulation of gene expression (GO:0023019)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell body (GO:0044297)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ADP binding (GO:0043531)|ADP-activated nucleotide receptor activity (GO:0045032)|ATP binding (GO:0005524)|ATP-activated nucleotide receptor activity (GO:0045031)|G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|receptor activity (GO:0004872)|scaffold protein binding (GO:0097110)			breast(1)|endometrium(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)	23			LUSC - Lung squamous cell carcinoma(72;0.0628)|Lung(72;0.11)			CGATGAACTTGAGGGCCCGGC	0.443																																					p.L284F		Atlas-SNP	.											.	P2RY1	49	.	0			c.G852C						.						109	111	111					3																	152554423		2203	4300	6503	SO:0001583	missense	5028	exon1			GAACTTGAGGGCC	U42029	CCDS3169.1	3q25.2	2012-08-08			ENSG00000169860	ENSG00000169860		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	8539	protein-coding gene	gene with protein product		601167				8579591	Standard	NM_002563		Approved	P2Y1	uc003ezq.3	P47900	OTTHUMG00000159694	ENST00000305097.3:c.852G>C	chr3.hg19:g.152554423G>C	ENSP00000304767:p.Leu284Phe	117.0	0.0		88.0	42.0	NM_002563		Missense_Mutation	SNP	ENST00000305097.3	hg19	CCDS3169.1	.	.	.	.	.	.	.	.	.	.	G	17.77	3.472105	0.63737	.	.	ENSG00000169860	ENST00000305097	T	0.38077	1.16	5.58	5.58	0.84498	GPCR, rhodopsin-like superfamily (1);	0.069347	0.64402	D	0.000019	T	0.38348	0.1037	L	0.49571	1.57	0.53005	D	0.999968	P	0.44946	0.846	P	0.47528	0.549	T	0.07404	-1.0774	10	0.32370	T	0.25	.	10.1406	0.42734	0.1519:0.0:0.8481:0.0	.	284	P47900	P2RY1_HUMAN	F	284	ENSP00000304767:L284F	ENSP00000304767:L284F	L	+	3	2	P2RY1	154037113	1.000000	0.71417	0.871000	0.34182	0.987000	0.75469	3.434000	0.52841	2.618000	0.88619	0.563000	0.77884	TTG	.	.		0.443	P2RY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356943.1	NM_002563		C	152554423	G	C	152554423	3	2	348	1	0	0	0	0	1	0	0	0	11355	1281	45	4	854	4	P2RY1	3	152554423	Missense_Mutation	SNP	G	TCGA-UB-A7MF-01A-11D-A33K-10	102833938	152554423	45468007	17	49065										
UGT2B4	7363	hgsc.bcm.edu	37	chr4	70359471	70359471	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	acgaactcaacatttggtaaGagtgggtgaggaaattgaaa	12	4	1	3			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr4:70359471G>C	ENST00000305107.6	-	2	856	c.810C>G	c.(808-810)ctC>ctG	p.L270L	UGT2B4_ENST00000381096.3_Silent_p.L134L|UGT2B4_ENST00000506580.1_5'UTR|UGT2B4_ENST00000512583.1_Silent_p.L270L	NM_021139.2	NP_066962.2	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B4	270					cellular glucuronidation (GO:0052695)|estrogen catabolic process (GO:0006711)|metabolic process (GO:0008152)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(29)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	47					Canagliflozin(DB08907)|Codeine(DB00318)|Dapagliflozin(DB06292)|Flurbiprofen(DB00712)|Ibuprofen(DB01050)|Morphine(DB00295)	CATTTGGTAAGAGTGGGTGAG	0.433																																					p.L270L		Atlas-SNP	.											.	UGT2B4	105	.	0			c.C810G						.						120	127	125					4																	70359471		2195	4299	6494	SO:0001819	synonymous_variant	7363	exon2			TGGTAAGAGTGGG	BC026264	CCDS43234.1, CCDS75137.1	4q13	2008-02-05	2005-07-20			ENSG00000156096		"UDP glucuronosyltransferases"	12553	protein-coding gene	gene with protein product		600067	"UDP glycosyltransferase 2 family, polypeptide B4"			3109396, 7835904	Standard	NM_021139		Approved	UGT2B11	uc003hek.4	P06133		ENST00000305107.6:c.810C>G	chr4.hg19:g.70359471G>C		87.0	0.0		111.0	60.0	NM_021139	A6NCP7|B4DT75|G5E9X8|O60731|O60867|O75614|P36538|Q1HBF9|Q6QQX7	Silent	SNP	ENST00000305107.6	hg19	CCDS43234.1																																																																																			.	.		0.433	UGT2B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365526.1	NM_021139		C	70359471	G	C	70359471	2	2	348	1	0	0	0	0	0	0	0	1	16976	929	33	4		4	UGT2B4	4	70359471	Silent	SNP	G	TCGA-UB-A7MF-01A-11D-A33K-10		70359471	120794805	18	49066										
SYNPO2	171024	hgsc.bcm.edu	37	chr4	119951206	119951206	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	gagaggcggacgaggaggaaGaaggtgacaaggaggataca	19	4	0	3			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr4:119951206G>C	ENST00000429713.2	+	4	1458	c.1276G>C	c.(1276-1278)Gaa>Caa	p.E426Q	SYNPO2_ENST00000448416.2_Intron|SYNPO2_ENST00000434046.2_Missense_Mutation_p.E426Q|SYNPO2_ENST00000307142.4_Missense_Mutation_p.E426Q	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	426	Poly-Glu.					actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|Z disc (GO:0030018)	14-3-3 protein binding (GO:0071889)|muscle alpha-actinin binding (GO:0051371)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						CGAGGAGGAAGAAGGTGACAA	0.507																																					p.E426Q		Atlas-SNP	.											.	SYNPO2	353	.	0			c.G1276C						.						183	172	176					4																	119951206		2203	4300	6503	SO:0001583	missense	171024	exon4			GAGGAAGAAGGTG	AJ010482	CCDS34054.1, CCDS47128.1, CCDS47129.1, CCDS75185.1, CCDS75186.1	4q26	2008-08-29			ENSG00000172403	ENSG00000172403			17732	protein-coding gene	gene with protein product						11673475, 17828378	Standard	NM_133477		Approved	MYOPODIN	uc010inb.3	Q9UMS6	OTTHUMG00000161165	ENST00000429713.2:c.1276G>C	chr4.hg19:g.119951206G>C	ENSP00000395143:p.Glu426Gln	138.0	0.0		125.0	93.0	NM_001128934	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Missense_Mutation	SNP	ENST00000429713.2	hg19	CCDS47129.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.6|20.6	4.018909|4.018909	0.75275|0.75275	.|.	.|.	ENSG00000172403|ENSG00000172403	ENST00000307142;ENST00000429713;ENST00000434046|ENST00000504178	T;T;T|.	0.10960|.	2.82;2.85;2.84|.	5.69|5.69	5.69|5.69	0.88448|0.88448	.|.	0.396576|.	0.23738|.	N|.	0.045058|.	T|T	0.74520|0.74520	0.3727|0.3727	M|M	0.64404|0.64404	1.975|1.975	0.80722|0.80722	D|D	1|1	B;P;P;B|.	0.43477|.	0.437;0.741;0.808;0.437|.	B;P;B;B|.	0.44394|.	0.203;0.448;0.261;0.143|.	T|T	0.71563|0.71563	-0.4555|-0.4555	10|5	0.51188|.	T|.	0.08|.	-3.0698|-3.0698	19.8006|19.8006	0.96506|0.96506	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	426;426;426;426|.	B9EG60;Q9UMS6-2;E9PEM2;Q9UMS6|.	.;.;.;SYNP2_HUMAN|.	Q|T	426|377	ENSP00000306015:E426Q;ENSP00000395143:E426Q;ENSP00000390965:E426Q|.	ENSP00000306015:E426Q|.	E|R	+|+	1|2	0|0	SYNPO2|SYNPO2	120170654|120170654	0.956000|0.956000	0.32656|0.32656	0.483000|0.483000	0.27378|0.27378	0.043000|0.043000	0.13939|0.13939	5.671000|5.671000	0.68095|0.68095	2.683000|2.683000	0.91414|0.91414	0.563000|0.563000	0.77884|0.77884	GAA|AGA	.	.		0.507	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1			C	119951206	G	C	119951206	3	2	348	1	0	0	0	0	1	0	0	0	15472	943	33	4	1290	4	SYNPO2	4	119951206	Missense_Mutation	SNP	G	TCGA-UB-A7MF-01A-11D-A33K-10	49591735	119951206	71203070	19	49067										
UCP1	7350	hgsc.bcm.edu	37	chr4	141489132	141489132	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	gtcgggcattcaccttggacCtggaaataagaaaggtgcag	13	8	1	1			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr4:141489132C>T	ENST00000262999.3	-	2	202		c.e2-1			NM_021833.4	NP_068605.1	P25874	UCP1_HUMAN	uncoupling protein 1 (mitochondrial, proton carrier)						brown fat cell differentiation (GO:0050873)|cellular metabolic process (GO:0044237)|mitochondrial transport (GO:0006839)|proton transport (GO:0015992)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	oxidative phosphorylation uncoupler activity (GO:0017077)			NS(1)|breast(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(1)|stomach(1)	16	all_hematologic(180;0.162)					CACCTTGGACCTGGAAATAAG	0.453																																					.		Atlas-SNP	.											.	UCP1	33	.	0			c.127-1G>A						.						69	69	69					4																	141489132		2203	4300	6503	SO:0001630	splice_region_variant	7350	exon3			TTGGACCTGGAAA	X51955	CCDS3753.1	4q28-q31	2013-05-22			ENSG00000109424	ENSG00000109424		"Solute carriers"	12517	protein-coding gene	gene with protein product		113730		UCP		2380264	Standard	NM_021833		Approved	SLC25A7	uc011chj.2	P25874	OTTHUMG00000133415	ENST00000262999.3:c.127-1G>A	chr4.hg19:g.141489132C>T		50.0	0.0		43.0	32.0	NM_021833	Q13218|Q4KMZ3|Q68G66	Splice_Site	SNP	ENST00000262999.3	hg19	CCDS3753.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.972372	0.74246	.	.	ENSG00000109424	ENST00000262999	.	.	.	5.51	5.51	0.81932	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.9102	0.86139	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	UCP1	141708582	1.000000	0.71417	0.997000	0.53966	0.747000	0.42532	7.090000	0.76916	2.597000	0.87782	0.655000	0.94253	.	.	.		0.453	UCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257273.1		Intron	T	141489132	C	T	141489132	5	4	348	1	0	0	0	0	0	0	1	0	16945	695	24	3	815	3	UCP1	4	141489132	Splice_Site	SNP	C	TCGA-UB-A7MF-01A-11D-A33K-10	21537926	141489132	49665144	20	49068										
DNAH5	1767	hgsc.bcm.edu	37	chr5	13788992	13788992	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	aacggtcagctataacacgtTtacactcatgcttccacagc	6	13	2	0			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr5:13788992T>C	ENST00000265104.4	-	51	8584	c.8480A>G	c.(8479-8481)aAa>aGa	p.K2827R		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2827					cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TATAACACGTTTACACTCATG	0.388									Kartagener syndrome																												p.K2827R		Atlas-SNP	.											.	DNAH5	868	.	0			c.A8480G						.						115	107	110					5																	13788992		2203	4300	6503	SO:0001583	missense	1767	exon51	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	ACACGTTTACACT	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.8480A>G	chr5.hg19:g.13788992T>C	ENSP00000265104:p.Lys2827Arg	141.0	0.0		183.0	116.0	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	hg19	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	T	12.68	2.009432	0.35415	.	.	ENSG00000039139	ENST00000265104	T	0.39997	1.05	6.06	6.06	0.98353	.	0.093306	0.64402	D	0.000001	T	0.39172	0.1068	L	0.52126	1.63	0.58432	D	0.999996	B	0.06786	0.001	B	0.08055	0.003	T	0.18808	-1.0325	10	0.18710	T	0.47	.	16.6093	0.84858	0.0:0.0:0.0:1.0	.	2827	Q8TE73	DYH5_HUMAN	R	2827	ENSP00000265104:K2827R	ENSP00000265104:K2827R	K	-	2	0	DNAH5	13841992	1.000000	0.71417	1.000000	0.80357	0.611000	0.37282	5.069000	0.64370	2.324000	0.78689	0.533000	0.62120	AAA	.	.		0.388	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		C	13788992	T	C	13788992	3	2	348	1	0	0	0	0	1	0	0	0	4606	1841	64	2	5510	2	DNAH5	5	13788992	Missense_Mutation	SNP	T	TCGA-UB-A7MF-01A-11D-A33K-10		13788992	167126268	21	49069										
TSLP	85480	hgsc.bcm.edu	37	chr5	110409224	110409224	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	agcagccacattgccttactGaaatccagagcctaaccttc	6	14	0	2			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr5:110409224G>T	ENST00000344895.3	+	3	431	c.232G>T	c.(232-234)Gaa>Taa	p.E78*	TSLP_ENST00000379706.4_5'UTR|TSLP_ENST00000420978.2_Nonsense_Mutation_p.E78*	NM_033035.4	NP_149024.1	Q969D9	TSLP_HUMAN	thymic stromal lymphopoietin	78						extracellular space (GO:0005615)				breast(1)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|stomach(1)	11		all_cancers(142;2.72e-05)|all_epithelial(76;4.39e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0417)|Ovarian(225;0.0443)|Colorectal(57;0.0464)|all_lung(232;0.0507)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.24e-08)|Epithelial(69;1.54e-07)|all cancers(49;1.73e-05)|COAD - Colon adenocarcinoma(37;0.109)		TTGCCTTACTGAAATCCAGAG	0.512																																					p.E78X		Atlas-SNP	.											.	TSLP	22	.	0			c.G232T						.						151	158	156					5																	110409224		2202	4300	6502	SO:0001587	stop_gained	85480	exon3			CTTACTGAAATCC	BC040592	CCDS4101.1	5q22.1	2007-08-24			ENSG00000145777	ENSG00000145777			30743	protein-coding gene	gene with protein product		607003				11418668, 11480573	Standard	NM_033035		Approved		uc003kpb.2	Q969D9	OTTHUMG00000128791	ENST00000344895.3:c.232G>T	chr5.hg19:g.110409224G>T	ENSP00000339804:p.Glu78*	311.0	0.0		251.0	42.0	NM_033035	Q8IW99	Nonsense_Mutation	SNP	ENST00000344895.3	hg19	CCDS4101.1	.	.	.	.	.	.	.	.	.	.	G	47	13.427668	0.99741	.	.	ENSG00000145777	ENST00000420978;ENST00000344895	.	.	.	4.93	-3.95	0.04118	.	1.790240	0.03195	N	0.173956	.	.	.	.	.	.	0.19775	N	0.999957	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.873	0.951	0.01376	0.1982:0.1532:0.3464:0.3022	.	.	.	.	X	78	.	ENSP00000339804:E78X	E	+	1	0	TSLP	110437123	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	-0.090000	0.11163	-0.403000	0.07622	0.655000	0.94253	GAA	.	.		0.512	TSLP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250717.1	NM_033035		T	110409224	G	T	110409224	4	4	348	1	0	0	0	0	0	1	0	0	16643	1291	45	3	242	3	TSLP	5	110409224	Nonsense_Mutation	SNP	G	TCGA-UB-A7MF-01A-11D-A33K-10	96620232	110409224	70506036	22	49070										
FBN2	2201	hgsc.bcm.edu	37	chr5	127680141	127680141	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	caacggcatttgaagcttccGattgtatttctgcacttccc	7	12	1	1	rs142809999		TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr5:127680141G>T	ENST00000508053.1	-	31	4253	c.3279C>A	c.(3277-3279)atC>atA	p.I1093I	FBN2_ENST00000262464.4_Silent_p.I1093I|FBN2_ENST00000508989.1_Silent_p.I1060I			P35556	FBN2_HUMAN	fibrillin 2	1093	EGF-like 15; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		I -> T (in DA9). {ECO:0000269|PubMed:11754102, ECO:0000269|PubMed:9714438}.		anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		TGAAGCTTCCGATTGTATTTC	0.423																																					p.I1093I		Atlas-SNP	.											.	FBN2	858	.	0			c.C3279A						.						137	131	133					5																	127680141		2203	4300	6503	SO:0001819	synonymous_variant	2201	exon25			GCTTCCGATTGTA	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.3279C>A	chr5.hg19:g.127680141G>T		122.0	0.0		74.0	17.0	NM_001999	B4DU01|Q59ES6	Silent	SNP	ENST00000508053.1	hg19	CCDS34222.1																																																																																			.	G|1.000;A|0.000		0.423	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		T	127680141	G	T	127680141	2	4	348	1	0	0	0	0	0	0	0	1	5711	1048	37	1		1	FBN2	5	127680141	Silent	SNP	G	TCGA-UB-A7MF-01A-11D-A33K-10	17270917	127680141	53235119	23	49071										
RIPK1	8737	hgsc.bcm.edu	37	chr6	3106166	3106166	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	ggatccaggaacagcaggtcCcagagtttggtacaggccaa	13	10	0	1			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr6:3106166C>T	ENST00000259808.4	+	9	1755	c.1457C>T	c.(1456-1458)cCc>cTc	p.P486L	RIPK1_ENST00000479389.1_3'UTR|RIPK1_ENST00000380409.2_Missense_Mutation_p.P486L|RIPK1_ENST00000541791.1_Missense_Mutation_p.P440L			Q13546	RIPK1_HUMAN	receptor (TNFRSF)-interacting serine-threonine kinase 1	486	Interaction with SQSTM1.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|amyloid fibril formation (GO:1990000)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular protein catabolic process (GO:0044257)|cellular response to growth factor stimulus (GO:0071363)|cellular response to tumor necrosis factor (GO:0071356)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|necroptotic signaling pathway (GO:0097527)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|peptidyl-serine autophosphorylation (GO:0036289)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of ATP:ADP antiporter activity (GO:0070926)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to tumor necrosis factor (GO:0034612)|ripoptosome assembly (GO:0097343)|ripoptosome assembly involved in necroptotic process (GO:1901026)|T cell apoptotic process (GO:0070231)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|death domain binding (GO:0070513)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	23	Ovarian(93;0.0386)	all_hematologic(90;0.0895)				ACAGCAGGTCCCAGAGTTTGG	0.473																																					p.P486L		Atlas-SNP	.											.	RIPK1	56	.	0			c.C1457T						.						97	76	83					6																	3106166		2203	4300	6503	SO:0001583	missense	8737	exon8			CAGGTCCCAGAGT	U25994	CCDS4482.1	6p25.2	2008-02-05			ENSG00000137275	ENSG00000137275			10019	protein-coding gene	gene with protein product		603453				7538908, 8612133	Standard	XM_005249458		Approved	RIP	uc003mux.3	Q13546	OTTHUMG00000014134	ENST00000259808.4:c.1457C>T	chr6.hg19:g.3106166C>T	ENSP00000259808:p.Pro486Leu	204.0	0.0		254.0	109.0	NM_003804	A0AV89|B2RAG1|B4E3F9|Q13180|Q59H33	Missense_Mutation	SNP	ENST00000259808.4	hg19	CCDS4482.1	.	.	.	.	.	.	.	.	.	.	C	12.32	1.902407	0.33628	.	.	ENSG00000137275	ENST00000259808;ENST00000541791;ENST00000380409;ENST00000453483	T;T;T	0.75704	-0.96;-0.45;-0.96	5.55	3.71	0.42584	.	0.726894	0.13977	N	0.349794	T	0.46776	0.1410	L	0.50333	1.59	0.09310	N	1	P;P	0.37276	0.589;0.544	B;B	0.30855	0.121;0.107	T	0.31081	-0.9956	10	0.42905	T	0.14	0.4965	8.4232	0.32714	0.1513:0.7674:0.0:0.0813	.	440;486	Q13546-2;Q13546	.;RIPK1_HUMAN	L	486;440;486;88	ENSP00000259808:P486L;ENSP00000442294:P440L;ENSP00000369773:P486L	ENSP00000259808:P486L	P	+	2	0	RIPK1	3051165	0.000000	0.05858	0.002000	0.10522	0.159000	0.22180	0.675000	0.25232	1.307000	0.44944	0.655000	0.94253	CCC	.	.		0.473	RIPK1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039659.2	NM_003804		T	3106166	C	T	3106166	3	4	348	1	0	0	0	0	1	0	0	0	13395	623	22	3	1487	3	RIPK1	6	3106166	Missense_Mutation	SNP	C	TCGA-UB-A7MF-01A-11D-A33K-10		3106166	168008901	24	49072										
LGSN	51557	hgsc.bcm.edu	37	chr6	64004842	64004842	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	tgaattggacatatccgtttCtcccacttcagttgaacaaa	6	10	2	2			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr6:64004842C>T	ENST00000370657.4	-	2	172	c.139G>A	c.(139-141)Gaa>Aaa	p.E47K	LGSN_ENST00000370658.5_Missense_Mutation_p.E47K			Q5TDP6	LGSN_HUMAN	lengsin, lens protein with glutamine synthetase domain	47					glutamine biosynthetic process (GO:0006542)	plasma membrane (GO:0005886)	glutamate-ammonia ligase activity (GO:0004356)			NS(1)|endometrium(2)|large_intestine(5)|lung(16)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						ATATCCGTTTCTCCCACTTCA	0.388																																					p.E47K		Atlas-SNP	.											.	LGSN	82	.	0			c.G139A						.						255	227	237					6																	64004842		2203	4300	6503	SO:0001583	missense	51557	exon2			CCGTTTCTCCCAC	AF242388	CCDS4964.1, CCDS55027.1	6q12	2013-09-19	2008-09-19	2008-09-19	ENSG00000146166	ENSG00000146166			21016	protein-coding gene	gene with protein product		611470	"glutamate-ammonia ligase (glutamine synthetase) domain containing 1"	GLULD1		12107412	Standard	NM_016571		Approved	LGS	uc003peh.3	Q5TDP6	OTTHUMG00000014946	ENST00000370657.4:c.139G>A	chr6.hg19:g.64004842C>T	ENSP00000359691:p.Glu47Lys	128.0	0.0		129.0	49.0	NM_016571	A1L421|Q0PVN9|Q0PVP0|Q9NYJ0	Missense_Mutation	SNP	ENST00000370657.4	hg19	CCDS4964.1	.	.	.	.	.	.	.	.	.	.	C	14.29	2.492673	0.44352	.	.	ENSG00000146166	ENST00000370658;ENST00000370657	T;T	0.31510	1.49;1.56	4.71	3.83	0.44106	.	0.373619	0.29900	N	0.010917	T	0.34716	0.0907	M	0.61703	1.905	0.34360	D	0.690862	P;P;D	0.63880	0.873;0.939;0.993	P;P;D	0.72625	0.543;0.584;0.978	T	0.18085	-1.0348	10	0.42905	T	0.14	-18.9088	6.6755	0.23092	0.0:0.8171:0.0:0.1829	.	47;47;47	Q5TDP6-3;Q5TDP6-2;Q5TDP6	.;.;LGSN_HUMAN	K	47	ENSP00000359692:E47K;ENSP00000359691:E47K	ENSP00000359691:E47K	E	-	1	0	LGSN	64062801	0.855000	0.29742	0.893000	0.35052	0.225000	0.24961	1.226000	0.32563	2.325000	0.78763	0.591000	0.81541	GAA	.	.		0.388	LGSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041076.2	NM_016571		T	64004842	C	T	64004842	3	4	348	1	0	0	0	0	1	0	0	0	8768	922	32	3	1402	3	LGSN	6	64004842	Missense_Mutation	SNP	C	TCGA-UB-A7MF-01A-11D-A33K-10	60898676	64004842	107110225	25	49073										
GPR63	81491	hgsc.bcm.edu	37	chr6	97246394	97246394	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	acacatagacagcactaggaCgtatccgtcgctttgtgtga	10	10	0	2			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr6:97246394C>T	ENST00000229955.3	-	2	1559	c.1214G>A	c.(1213-1215)cGt>cAt	p.R405H	GPR63_ENST00000417980.1_Missense_Mutation_p.R405H|RP3-417O22.3_ENST00000442184.1_RNA	NM_001143957.2|NM_030784.3	NP_001137429.1|NP_110411.1	Q9BZJ6	GPR63_HUMAN	G protein-coupled receptor 63	405						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			kidney(1)|large_intestine(5)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(76;6.89e-05)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.0618)|Colorectal(196;0.0721)		BRCA - Breast invasive adenocarcinoma(108;0.0912)		AGCACTAGGACGTATCCGTCG	0.463																																					p.R405H		Atlas-SNP	.											.	GPR63	60	.	0			c.G1214A						.						145	119	128					6																	97246394		2203	4300	6503	SO:0001583	missense	81491	exon2			CTAGGACGTATCC	AF317654	CCDS5036.1	6q16.1-q16.3	2012-08-21			ENSG00000112218	ENSG00000112218		"GPCR / Class A : Orphans"	13302	protein-coding gene	gene with protein product		606915					Standard	NM_030784		Approved	PSP24(beta), PSP24B	uc003pou.3	Q9BZJ6	OTTHUMG00000015245	ENST00000229955.3:c.1214G>A	chr6.hg19:g.97246394C>T	ENSP00000229955:p.Arg405His	159.0	0.0		163.0	69.0	NM_030784	Q9UJH3	Missense_Mutation	SNP	ENST00000229955.3	hg19	CCDS5036.1	.	.	.	.	.	.	.	.	.	.	C	14.77	2.633995	0.47049	.	.	ENSG00000112218	ENST00000536583;ENST00000417980;ENST00000229955;ENST00000369268	T;T;T	0.61510	0.1;0.1;0.1	5.35	5.35	0.76521	.	0.071658	0.64402	D	0.000016	T	0.36138	0.0956	L	0.42245	1.32	0.58432	D	0.999999	D	0.53151	0.958	B	0.36845	0.234	T	0.25916	-1.0118	10	0.27082	T	0.32	-9.8128	19.4213	0.94723	0.0:1.0:0.0:0.0	.	405	Q9BZJ6	GPR63_HUMAN	H	429;405;405;405	ENSP00000393170:R405H;ENSP00000229955:R405H;ENSP00000358273:R405H	ENSP00000229955:R405H	R	-	2	0	GPR63	97353115	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	4.502000	0.60400	2.675000	0.91044	0.650000	0.86243	CGT	.	.		0.463	GPR63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041566.2			T	97246394	C	T	97246394	3	4	348	1	0	0	0	0	1	0	0	0	6712	536	19	1	49	1	GPR63	6	97246394	Missense_Mutation	SNP	C	TCGA-UB-A7MF-01A-11D-A33K-10	33241552	97246394	73868673	26	49074										
GRIK2	2898	hgsc.bcm.edu	37	chr6	102134211	102134211	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	cgaaacccgattcaggtttgCtggatggatttatgacggta	12	7	1	1			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr6:102134211C>A	ENST00000421544.1	+	6	1424	c.934C>A	c.(934-936)Ctg>Atg	p.L312M	GRIK2_ENST00000318991.6_Missense_Mutation_p.L312M|GRIK2_ENST00000413795.1_Missense_Mutation_p.L312M|GRIK2_ENST00000369134.4_Missense_Mutation_p.L263M|GRIK2_ENST00000358361.3_Missense_Mutation_p.L312M|GRIK2_ENST00000369138.1_Missense_Mutation_p.L312M|GRIK2_ENST00000369137.3_Missense_Mutation_p.L312M	NM_021956.4	NP_068775.1	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	312					behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|glutamate receptor signaling pathway (GO:0007215)|intracellular protein transport (GO:0006886)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuronal action potential (GO:0019228)|positive regulation of synaptic transmission (GO:0050806)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission (GO:0050804)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	TTCAGGTTTGCTGGATGGATT	0.383																																					p.L312M		Atlas-SNP	.											.	GRIK2	487	.	0			c.C934A						.						90	91	91					6																	102134211		2203	4300	6503	SO:0001583	missense	2898	exon6			GGTTTGCTGGATG		CCDS5048.1, CCDS5049.1, CCDS55045.1	6q16.3	2012-08-29			ENSG00000164418	ENSG00000164418		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4580	protein-coding gene	gene with protein product		138244		GLUR6		8034316	Standard	NM_021956		Approved	GluK2, MRT6	uc003pqp.4	Q13002	OTTHUMG00000016328	ENST00000421544.1:c.934C>A	chr6.hg19:g.102134211C>A	ENSP00000397026:p.Leu312Met	124.0	0.0		117.0	15.0	NM_021956	A6NMY9|B5MCV0|D7RWZ3|D7RWZ4|D7RWZ5|D7RWZ6|D7RWZ7|Q8WWS1|Q96KS6|Q96KS7|Q96KS8	Missense_Mutation	SNP	ENST00000421544.1	hg19	CCDS5048.1	.	.	.	.	.	.	.	.	.	.	C	15.68	2.905806	0.52333	.	.	ENSG00000164418	ENST00000421544;ENST00000413795;ENST00000369138;ENST00000358361;ENST00000369137;ENST00000318991;ENST00000403289;ENST00000369134;ENST00000540076	D;D;D;T;D;D;D	0.83755	-1.76;-1.76;-1.76;2.0;-1.76;-1.76;-1.76	5.84	5.84	0.93424	Extracellular ligand-binding receptor (1);	0.000000	0.64402	D	0.000003	T	0.74612	0.3739	L	0.45352	1.415	0.44261	D	0.997119	B;B;B	0.21753	0.049;0.06;0.049	B;B;B	0.27380	0.047;0.079;0.047	T	0.69899	-0.5020	10	0.45353	T	0.12	.	20.1551	0.98106	0.0:1.0:0.0:0.0	.	312;312;312	Q13002-5;Q13002;Q13002-2	.;GRIK2_HUMAN;.	M	312;312;312;312;312;312;312;263;274	ENSP00000397026:L312M;ENSP00000405596:L312M;ENSP00000358134:L312M;ENSP00000351128:L312M;ENSP00000358133:L312M;ENSP00000313276:L312M;ENSP00000358130:L263M	ENSP00000313276:L312M	L	+	1	2	GRIK2	102240904	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.762000	0.55250	2.760000	0.94817	0.655000	0.94253	CTG	.	.		0.383	GRIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043718.1			A	102134211	C	A	102134211	3	1	348	1	0	0	0	0	1	0	0	0	6783	796	28	3	956	3	GRIK2	6	102134211	Missense_Mutation	SNP	C	TCGA-UB-A7MF-01A-11D-A33K-10	4887817	102134211	68980856	27	49075										
ARID1B	57492	hgsc.bcm.edu	37	chr6	157522371	157522371	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	gacgccaccgtcactgccaaAtcacatctccagggcgccca	8	18	3	0			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr6:157522371A>G	ENST00000350026.5	+	17	4605	c.4604A>G	c.(4603-4605)aAt>aGt	p.N1535S	ARID1B_ENST00000346085.5_Missense_Mutation_p.N1548S|ARID1B_ENST00000275248.4_Missense_Mutation_p.N1530S|ARID1B_ENST00000367148.1_Missense_Mutation_p.N1588S	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1535	Pro-rich.				chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		TCACTGCCAAATCACATCTCC	0.602																																					p.N1548S		Atlas-SNP	.											.	ARID1B	320	.	0			c.A4643G						.						135	131	133					6																	157522371		2203	4296	6499	SO:0001583	missense	57492	exon18			TGCCAAATCACAT	AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"-"	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.4604A>G	chr6.hg19:g.157522371A>G	ENSP00000055163:p.Asn1535Ser	45.0	0.0		50.0	20.0	NM_020732	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Missense_Mutation	SNP	ENST00000350026.5	hg19	CCDS5251.2	.	.	.	.	.	.	.	.	.	.	A	17.12	3.309092	0.60414	.	.	ENSG00000049618	ENST00000346085;ENST00000350026;ENST00000367148;ENST00000275248;ENST00000414678	T;T;T;T;T	0.02395	4.67;4.65;4.67;4.66;4.31	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	T	0.07638	0.0192	L	0.61218	1.895	0.58432	D	0.999998	D;D;D	0.71674	0.997;0.998;0.998	D;D;D	0.80764	0.985;0.994;0.994	T	0.07290	-1.0780	10	0.56958	D	0.05	.	14.9157	0.70795	1.0:0.0:0.0:0.0	.	1535;1548;1530	Q8NFD5;Q8NFD5-2;G3XAA0	ARI1B_HUMAN;.;.	S	1548;1535;1588;1530;1057	ENSP00000344546:N1548S;ENSP00000055163:N1535S;ENSP00000356116:N1588S;ENSP00000275248:N1530S;ENSP00000412835:N1057S	ENSP00000275248:N1530S	N	+	2	0	ARID1B	157564063	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.798000	0.91888	1.992000	0.58205	0.533000	0.62120	AAT	.	.		0.602	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732		G	157522371	A	G	157522371	3	3	348	1	0	0	0	0	1	0	0	0	914	101	4	2	4713	2	ARID1B	6	157522371	Missense_Mutation	SNP	A	TCGA-UB-A7MF-01A-11D-A33K-10	55388160	157522371	13592696	28	49076										
GPC2	221914	hgsc.bcm.edu	37	chr7	99769820	99769820	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	aaaggggccctggagcttatCagccaggatcaggagaccat	13	10	2	1			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr7:99769820C>T	ENST00000292377.2	-	6	1080	c.913G>A	c.(913-915)Gat>Aat	p.D305N	GPC2_ENST00000471050.1_5'UTR	NM_152742.1	NP_689955.1	Q8N158	GPC2_HUMAN	glypican 2	305					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|neuron differentiation (GO:0030182)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|smoothened signaling pathway (GO:0007224)	anchored component of membrane (GO:0031225)|endoplasmic reticulum (GO:0005783)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|pancreas(1)|skin(3)	18	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TGGAGCTTATCAGCCAGGATC	0.517																																					p.D305N		Atlas-SNP	.											.	GPC2	49	.	0			c.G913A						.						54	50	51					7																	99769820		2203	4300	6503	SO:0001583	missense	221914	exon6			GCTTATCAGCCAG	BX375153	CCDS5689.1	7q22.1	2007-02-16	2007-02-15		ENSG00000213420	ENSG00000213420		"Proteoglycans / Cell Surface : Glypicans"	4450	protein-coding gene	gene with protein product	"glypican proteoglycan 2, cerebroglycan proteoglycan"		"glypican 2 (cerebroglycan)"			8294498	Standard	NM_152742		Approved	cerebroglycan, FLJ38962, DKFZp547M109	uc003utv.3	Q8N158	OTTHUMG00000154894	ENST00000292377.2:c.913G>A	chr7.hg19:g.99769820C>T	ENSP00000292377:p.Asp305Asn	50.0	0.0		51.0	5.0	NM_152742	A4D2A7	Missense_Mutation	SNP	ENST00000292377.2	hg19	CCDS5689.1	.	.	.	.	.	.	.	.	.	.	C	19.30	3.801609	0.70682	.	.	ENSG00000213420	ENST00000292377	T	0.50813	0.73	5.1	4.22	0.49857	.	0.434050	0.25789	N	0.028290	T	0.37732	0.1014	L	0.49778	1.585	0.32594	N	0.526853	P	0.43231	0.801	B	0.37780	0.258	T	0.47381	-0.9122	10	0.16896	T	0.51	-18.9488	11.2782	0.49178	0.0:0.9096:0.0:0.0904	.	305	Q8N158	GPC2_HUMAN	N	305	ENSP00000292377:D305N	ENSP00000292377:D305N	D	-	1	0	GPC2	99607756	1.000000	0.71417	0.743000	0.31040	0.797000	0.45037	4.760000	0.62235	1.138000	0.42230	-0.350000	0.07774	GAT	.	.		0.517	GPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337556.1	NM_152742		T	99769820	C	T	99769820	3	4	348	1	0	0	0	0	1	0	0	0	6606	826	29	3	846	3	GPC2	7	99769820	Missense_Mutation	SNP	C	TCGA-UB-A7MF-01A-11D-A33K-10		99769820	59368843	29	49077										
ATP6V0A4	50617	hgsc.bcm.edu	37	chr7	138394421	138394421	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	gaggccctccatgatcagaaGgatggctactgtcaggacag	13	10	2	2			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr7:138394421G>C	ENST00000310018.2	-	21	2659	c.2377C>G	c.(2377-2379)Ctt>Gtt	p.L793V	ATP6V0A4_ENST00000393054.1_Missense_Mutation_p.L793V|ATP6V0A4_ENST00000353492.4_Missense_Mutation_p.L793V	NM_020632.2|NM_130840.2	NP_065683.2|NP_570855.2	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a4	793					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|excretion (GO:0007588)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|regulation of pH (GO:0006885)|sensory perception of sound (GO:0007605)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	ATPase binding (GO:0051117)|hydrogen ion transmembrane transporter activity (GO:0015078)			NS(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36						ATGATCAGAAGGATGGCTACT	0.537																																					p.L793V		Atlas-SNP	.											.	ATP6V0A4	93	.	0			c.C2377G						.						178	174	175					7																	138394421		2203	4300	6503	SO:0001583	missense	50617	exon20			TCAGAAGGATGGC	AF245517	CCDS5849.1	7q34	2011-06-09	2006-01-20	2002-05-10	ENSG00000105929	ENSG00000105929		"ATPases / V-type"	866	protein-coding gene	gene with protein product		605239	"ATPase, H+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1B", "ATPase, H+ transporting, lysosomal V0 subunit a isoform 4", "ATPase, H+ transporting, lysosomal V0 subunit A4"	ATP6N1B, ATP6N2, RTA1C		10577919, 10973252	Standard	XM_005250393		Approved	RDRTA2, VPP2, RTADR, a4, Vph1, Stv1	uc003vuf.3	Q9HBG4	OTTHUMG00000157122	ENST00000310018.2:c.2377C>G	chr7.hg19:g.138394421G>C	ENSP00000308122:p.Leu793Val	209.0	0.0		155.0	72.0	NM_130841	A4D1R4|A8KA80|Q32M47	Missense_Mutation	SNP	ENST00000310018.2	hg19	CCDS5849.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.158834	0.78226	.	.	ENSG00000105929	ENST00000310018;ENST00000393054;ENST00000353492	D;D;D	0.88741	-2.42;-2.42;-2.42	5.71	3.89	0.44902	.	0.000000	0.64402	D	0.000012	D	0.95987	0.8693	H	0.97291	3.975	0.58432	D	0.999996	D	0.89917	1.0	D	0.91635	0.999	D	0.95299	0.8402	10	0.87932	D	0	-24.0661	9.7684	0.40574	0.2128:0.0:0.7872:0.0	.	793	Q9HBG4	VPP4_HUMAN	V	793	ENSP00000308122:L793V;ENSP00000376774:L793V;ENSP00000253856:L793V	ENSP00000308122:L793V	L	-	1	0	ATP6V0A4	138044961	1.000000	0.71417	0.970000	0.41538	0.992000	0.81027	3.436000	0.52856	0.740000	0.32651	0.655000	0.94253	CTT	.	.		0.537	ATP6V0A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347514.1	NM_020632		C	138394421	G	C	138394421	3	2	348	1	0	0	0	0	1	0	0	0	1170	1000	35	4	153	4	ATP6V0A4	7	138394421	Missense_Mutation	SNP	G	TCGA-UB-A7MF-01A-11D-A33K-10	38624601	138394421	20744242	30	49078										
OR9A2	135924	hgsc.bcm.edu	37	chr7	142723964	142723964	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	atactgtctgcatcccaggaAgagcaatccccaaagcatca	7	13	2	1			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr7:142723964A>G	ENST00000350513.2	-	1	318	c.256T>C	c.(256-258)Ttc>Ctc	p.F86L		NM_001001658.1	NP_001001658.1	Q8NGT5	OR9A2_HUMAN	olfactory receptor, family 9, subfamily A, member 2	86						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(3)|endometrium(4)|large_intestine(1)|lung(14)|skin(3)	25	Melanoma(164;0.059)					CATCCCAGGAAGAGCAATCCC	0.493																																					p.F86L		Atlas-SNP	.											.	OR9A2	52	.	0			c.T256C						.						101	95	97					7																	142723964		2203	4300	6503	SO:0001583	missense	135924	exon1			CCAGGAAGAGCAA		CCDS34767.1	7q34	2014-07-10			ENSG00000179468	ENSG00000179468		"GPCR / Class A : Olfactory receptors"	15093	protein-coding gene	gene with protein product							Standard	NM_001001658		Approved		uc003wcc.1	Q8NGT5	OTTHUMG00000158386	ENST00000350513.2:c.256T>C	chr7.hg19:g.142723964A>G	ENSP00000316518:p.Phe86Leu	160.0	0.0		101.0	24.0	NM_001001658	B9EH51|Q6IF71|Q8NGD9	Missense_Mutation	SNP	ENST00000350513.2	hg19	CCDS34767.1	.	.	.	.	.	.	.	.	.	.	A	0.904	-0.721380	0.03182	.	.	ENSG00000179468	ENST00000350513	T	0.01388	4.95	4.62	3.45	0.39498	GPCR, rhodopsin-like superfamily (1);	3.169520	0.01368	N	0.012462	T	0.01730	0.0055	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.44862	-0.9300	10	0.33940	T	0.23	-8.7938	7.4943	0.27479	0.6535:0.0:0.0:0.3465	.	86	Q8NGT5	OR9A2_HUMAN	L	86	ENSP00000316518:F86L	ENSP00000316518:F86L	F	-	1	0	OR9A2	142434086	0.004000	0.15560	0.615000	0.29064	0.199000	0.23934	0.952000	0.29149	0.877000	0.35895	0.459000	0.35465	TTC	.	.		0.493	OR9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350862.1			G	142723964	A	G	142723964	3	3	348	1	0	0	0	0	1	0	0	0	11257	72	3	2	680	2	OR9A2	7	142723964	Missense_Mutation	SNP	A	TCGA-UB-A7MF-01A-11D-A33K-10	4329543	142723964	16414699	31	49079										
XPO7	23039	hgsc.bcm.edu	37	chr8	21827677	21827677	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	aactatgtgctcaactacctTgccactcggccgaagttggc	9	13	1	0			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr8:21827677T>C	ENST00000252512.9	+	4	382	c.282T>C	c.(280-282)ctT>ctC	p.L94L	XPO7_ENST00000434536.1_Silent_p.L94L|XPO7_ENST00000433566.4_Silent_p.L95L|XPO7_ENST00000518017.1_3'UTR	NM_015024.4	NP_055839.3	Q9UIA9	XPO7_HUMAN	exportin 7	94	Importin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00115}.				mRNA transport (GO:0051028)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	nuclear export signal receptor activity (GO:0005049)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				Colorectal(74;0.0187)|COAD - Colon adenocarcinoma(73;0.0724)		TCAACTACCTTGCCACTCGGC	0.408																																					p.L94L		Atlas-SNP	.											.	XPO7	79	.	0			c.T282C						.						198	192	194					8																	21827677		1865	4105	5970	SO:0001819	synonymous_variant	23039	exon4			CTACCTTGCCACT	AF064729	CCDS47818.1	8p21	2011-04-13	2003-03-11	2003-03-14	ENSG00000130227	ENSG00000130227		"Exportins"	14108	protein-coding gene	gene with protein product		606140	"RAN binding protein 16"	RANBP16		11024021, 9872452	Standard	NM_015024		Approved	KIAA0745	uc003xaa.4	Q9UIA9	OTTHUMG00000163789	ENST00000252512.9:c.282T>C	chr8.hg19:g.21827677T>C		86.0	0.0		52.0	12.0	NM_015024	O94846|Q6PJK9|Q8NEK7	Silent	SNP	ENST00000252512.9	hg19	CCDS47818.1	.	.	.	.	.	.	.	.	.	.	T	10.51	1.369361	0.24771	.	.	ENSG00000130227	ENST00000521303	T	0.76186	-1.0	5.55	4.32	0.51571	.	0.068550	0.64402	D	0.000011	T	0.78104	0.4231	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.79790	-0.1655	7	0.87932	D	0	-12.214	7.401	0.26965	0.1269:0.0:0.2475:0.6256	.	.	.	.	S	99	ENSP00000429290:L99S	ENSP00000429290:L99S	L	+	2	0	XPO7	21883623	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.272000	0.43373	2.239000	0.73571	0.482000	0.46254	TTG	.	.		0.408	XPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375494.1	NM_015024		C	21827677	T	C	21827677	2	2	348	1	0	0	0	0	0	0	0	1	17464	1799	63	2		2	XPO7	8	21827677	Silent	SNP	T	TCGA-UB-A7MF-01A-11D-A33K-10		21827677	124536345	32	49080										
KCNU1	157855	hgsc.bcm.edu	37	chr8	36675256	36675256	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	acaagtcaggagagatcaacActgaaattgttttcctggga	10	7	2	2			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr8:36675256A>G	ENST00000399881.3	+	10	1121	c.1084A>G	c.(1084-1086)Act>Gct	p.T362A		NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	362	RCK N-terminal.				multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		AGAGATCAACACTGAAATTGT	0.388																																					p.T362A		Atlas-SNP	.											.	KCNU1	359	.	0			c.A1084G						.						150	137	141					8																	36675256		1876	4096	5972	SO:0001583	missense	157855	exon10			ATCAACACTGAAA	BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.1084A>G	chr8.hg19:g.36675256A>G	ENSP00000382770:p.Thr362Ala	115.0	0.0		59.0	25.0	NM_001031836		Missense_Mutation	SNP	ENST00000399881.3	hg19	CCDS55220.1	.	.	.	.	.	.	.	.	.	.	A	9.583	1.124099	0.20959	.	.	ENSG00000215262	ENST00000399881	T	0.31247	1.5	5.31	2.72	0.32119	.	0.460878	0.15185	U	0.275862	T	0.22166	0.0534	L	0.47716	1.5	0.27653	N	0.947325	P	0.39282	0.666	B	0.31869	0.137	T	0.16660	-1.0395	10	0.87932	D	0	-2.0603	6.6891	0.23161	0.6897:0.1584:0.0:0.1519	.	362	A8MYU2	KCNU1_HUMAN	A	362	ENSP00000382770:T362A	ENSP00000382770:T362A	T	+	1	0	KCNU1	36794414	0.996000	0.38824	0.010000	0.14722	0.154000	0.21943	3.854000	0.55949	0.931000	0.37242	0.533000	0.62120	ACT	.	.		0.388	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836		G	36675256	A	G	36675256	3	3	348	1	0	0	0	0	1	0	0	0	8102	159	6	2	1122	2	KCNU1	8	36675256	Missense_Mutation	SNP	A	TCGA-UB-A7MF-01A-11D-A33K-10	14847579	36675256	109688766	33	49081										
CRISPLD1	83690	hgsc.bcm.edu	37	chr8	75929298	75929298	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	ttaggtacgaatgtcctgctGgctgtttggatagtaaagct	12	6	0	0			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr8:75929298G>T	ENST00000262207.4	+	9	1414	c.946G>T	c.(946-948)Ggc>Tgc	p.G316C	CRISPLD1_ENST00000517786.1_Missense_Mutation_p.G130C|CRISPLD1_ENST00000523524.1_Missense_Mutation_p.G128C	NM_031461.5	NP_113649.1	Q9H336	CRLD1_HUMAN	cysteine-rich secretory protein LCCL domain containing 1	316	LCCL 1. {ECO:0000255|PROSITE- ProRule:PRU00123}.				face morphogenesis (GO:0060325)	extracellular vesicular exosome (GO:0070062)				biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(10)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(64;0.0799)		Epithelial(68;0.155)|BRCA - Breast invasive adenocarcinoma(89;0.161)			ATGTCCTGCTGGCTGTTTGGA	0.274																																					p.G316C		Atlas-SNP	.											CRISPLD1,NS,carcinoma,0,1	CRISPLD1	94	.	0			c.G946T						.						88	92	91					8																	75929298		2203	4297	6500	SO:0001583	missense	83690	exon9			CCTGCTGGCTGTT	AL834301	CCDS6219.1, CCDS69497.1, CCDS75754.1	8q21.13	2005-09-23	2005-02-16	2005-02-16	ENSG00000121005	ENSG00000121005			18206	protein-coding gene	gene with protein product			"LCCL domain containing cysteine-rich secretory protein 1"	LCRISP1			Standard	NM_031461		Approved	Cocoacrisp, DKFZp762F133	uc003yan.3	Q9H336	OTTHUMG00000164529	ENST00000262207.4:c.946G>T	chr8.hg19:g.75929298G>T	ENSP00000262207:p.Gly316Cys	214.0	0.0		158.0	23.0	NM_031461	B2RA60|B7Z929	Missense_Mutation	SNP	ENST00000262207.4	hg19	CCDS6219.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.497223	0.85069	.	.	ENSG00000121005	ENST00000262207;ENST00000523524;ENST00000517786	D;D;D	0.90197	-2.63;-2.63;-2.63	5.12	5.12	0.69794	LCCL (5);	0.000000	0.85682	D	0.000000	D	0.96852	0.8972	H	0.94306	3.52	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97512	1.0067	10	0.87932	D	0	.	19.116	0.93340	0.0:0.0:1.0:0.0	.	130;316	B7Z929;Q9H336	.;CRLD1_HUMAN	C	316;128;130	ENSP00000262207:G316C;ENSP00000430105:G128C;ENSP00000429746:G130C	ENSP00000262207:G316C	G	+	1	0	CRISPLD1	76091853	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.237000	0.78164	2.821000	0.97095	0.650000	0.86243	GGC	.	.		0.274	CRISPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379117.1	NM_031461		T	75929298	G	T	75929298	3	4	348	1	0	0	0	0	1	0	0	0	3884	1348	47	3	976	3	CRISPLD1	8	75929298	Missense_Mutation	SNP	G	TCGA-UB-A7MF-01A-11D-A33K-10	39254042	75929298	70434724	34	49082										
RUNX1T1	862	hgsc.bcm.edu	37	chr8	93023242	93023242	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	tgcaataccttcaaaaatggGatgacaaaaggtctcagtgg	10	7	2	1			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr8:93023242G>T	ENST00000523629.1	-	5	1000	c.546C>A	c.(544-546)atC>atA	p.I182I	RUNX1T1_ENST00000520724.1_Silent_p.I145I|RUNX1T1_ENST00000521553.1_Silent_p.I145I|RUNX1T1_ENST00000518844.1_Silent_p.I155I|RUNX1T1_ENST00000360348.2_Silent_p.I145I|RUNX1T1_ENST00000436581.2_Silent_p.I193I|RUNX1T1_ENST00000422361.2_Silent_p.I145I|RUNX1T1_ENST00000396218.1_Silent_p.I155I|RUNX1T1_ENST00000265814.3_Silent_p.I182I	NM_001198626.1|NM_001198630.1|NM_001198633.1|NM_175634.2	NP_001185555.1|NP_001185559.1|NP_001185562.1|NP_783552.1	Q06455	MTG8_HUMAN	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	182	TAFH. {ECO:0000255|PROSITE- ProRule:PRU00440}.				fat cell differentiation (GO:0045444)|generation of precursor metabolites and energy (GO:0006091)|regulation of DNA binding (GO:0051101)|transcription, DNA-templated (GO:0006351)	nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(54)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	86			BRCA - Breast invasive adenocarcinoma(11;0.0141)			TCAAAAATGGGATGACAAAAG	0.358																																					p.I241I		Atlas-SNP	.											.	RUNX1T1	516	.	0			c.C723A						.						142	136	138					8																	93023242		2203	4300	6503	SO:0001819	synonymous_variant	862	exon5			AAATGGGATGACA	D43638	CCDS6256.1, CCDS6257.1, CCDS47891.1, CCDS56544.1, CCDS75766.1, CCDS75767.1	8q22	2007-01-29	2005-01-20	2005-01-22	ENSG00000079102	ENSG00000079102		"Zinc fingers, MYND-type"	1535	protein-coding gene	gene with protein product		133435	"core-binding factor, runt domain, alpha subunit 2; translocated to, 1; cyclin D-related"	AML1T1, CBFA2T1		1391946, 9790752	Standard	NM_004349		Approved	CDR, ETO, MTG8, ZMYND2	uc011lgi.2	Q06455	OTTHUMG00000164066	ENST00000523629.1:c.546C>A	chr8.hg19:g.93023242G>T		102.0	0.0		76.0	35.0	NM_001198679	B7Z4P4|E7EPN4|O14784|Q06456|Q14873|Q16239|Q16346|Q16347|Q6IBL1|Q6NXH1|Q7Z4J5|Q92479|Q9BRZ0	Silent	SNP	ENST00000523629.1	hg19	CCDS6256.1																																																																																			.	.		0.358	RUNX1T1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377045.3	NM_004349, NM_175635		T	93023242	G	T	93023242	2	4	348	1	0	0	0	0	0	0	0	1	13762	1164	41	3		3	RUNX1T1	8	93023242	Silent	SNP	G	TCGA-UB-A7MF-01A-11D-A33K-10	17093944	93023242	53340780	35	49083										
TRAPPC9	83696	hgsc.bcm.edu	37	chr8	141294100	141294100	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	caaacagtcactgaacacacCgaagaccgtggtatggtaac	9	11	1	2	rs147687394		TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr8:141294100C>T	ENST00000438773.2	-	14	2135	c.2002G>A	c.(2002-2004)Ggt>Agt	p.G668S	TRAPPC9_ENST00000389327.3_Missense_Mutation_p.G659S|TRAPPC9_ENST00000389328.4_Missense_Mutation_p.G766S	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	668					cell differentiation (GO:0030154)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	47						CTGAACACACCGAAGACCGTG	0.522																																					p.G766S		Atlas-SNP	.											.	TRAPPC9	114	.	0			c.G2296A						.	C	SER/GLY,SER/GLY	0,4406		0,0,2203	126	115	119		2002,2296	4.8	0.2	8	dbSNP_134	119	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	TRAPPC9	NM_001160372.1,NM_031466.5	56,56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	668/1149,766/1247	141294100	1,13005	2203	4300	6503	SO:0001583	missense	83696	exon14			ACACACCGAAGAC	BC006206	CCDS34946.1, CCDS55278.1	8q24.3	2010-10-22			ENSG00000167632	ENSG00000167632		"Trafficking protein particle complex"	30832	protein-coding gene	gene with protein product	"TRAPP 120 kDa subunit", "tularik gene 1"	611966				11572484	Standard	NM_031466		Approved	IKBKBBP, NIBP, KIAA1882, T1, TRS120, MRT13	uc003yvh.2	Q96Q05	OTTHUMG00000164187	ENST00000438773.2:c.2002G>A	chr8.hg19:g.141294100C>T	ENSP00000405060:p.Gly668Ser	102.0	0.0		73.0	10.0	NM_031466	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Missense_Mutation	SNP	ENST00000438773.2	hg19	CCDS55278.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.82|18.82	3.704744|3.704744	0.68615|0.68615	0.0|0.0	1.16E-4|1.16E-4	ENSG00000167632|ENSG00000167632	ENST00000389328;ENST00000389327;ENST00000438773|ENST00000520857	.|.	.|.	.|.	5.64|5.64	4.77|4.77	0.60923|0.60923	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.68137|0.68137	0.2968|0.2968	L|L	0.56199|0.56199	1.76|1.76	0.58432|0.58432	D|D	0.999999|0.999999	D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0|.	D;D;D;D|.	0.97110|.	1.0;1.0;1.0;1.0|.	T|T	0.66536|0.66536	-0.5899|-0.5899	9|5	0.42905|.	T|.	0.14|.	.|.	14.6364|14.6364	0.68692|0.68692	0.0:0.9302:0.0:0.0698|0.0:0.9302:0.0:0.0698	.|.	766;668;659;766|.	A6NIF0;Q96Q05;Q96Q05-3;Q96Q05-2|.	.;TPPC9_HUMAN;.;.|.	S|Q	766;659;668|511	.|.	ENSP00000373978:G659S|.	G|R	-|-	1|2	0|0	TRAPPC9|TRAPPC9	141363282|141363282	1.000000|1.000000	0.71417|0.71417	0.156000|0.156000	0.22583|0.22583	0.107000|0.107000	0.19398|0.19398	6.960000|6.960000	0.76036|0.76036	1.390000|1.390000	0.46547|0.46547	0.655000|0.655000	0.94253|0.94253	GGT|CGG	.	C|1.000;T|0.000		0.522	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466		T	141294100	C	T	141294100	3	4	348	1	0	0	0	0	1	0	0	0	16480	652	23	1	1484	1	TRAPPC9	8	141294100	Missense_Mutation	SNP	C	TCGA-UB-A7MF-01A-11D-A33K-10	48270858	141294100	5069922	36	49084										
TOPORS	10210	hgsc.bcm.edu	37	chr9	32550784	32550784	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	tcactcacctcggaggatgcCggcgcaggcctggctggggc	16	14	2	0			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr9:32550784C>T	ENST00000360538.2	-	2	302	c.186G>A	c.(184-186)ccG>ccA	p.P62P	TOPORS-AS1_ENST00000450093.1_RNA|TOPORS_ENST00000379858.1_Intron|TOPORS-AS1_ENST00000540066.1_RNA|TOPORS-AS1_ENST00000453396.1_RNA|TOPORS-AS1_ENST00000458036.1_RNA|TOPORS-AS1_ENST00000425533.1_RNA	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	62	E3 ubiquitin-protein ligase activity.|Required for DNA-binding.				cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of apoptotic process (GO:0043066)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein localization to nucleus (GO:0034504)|protein monoubiquitination (GO:0006513)|protein sumoylation (GO:0016925)|regulation of cell proliferation (GO:0042127)|retina layer formation (GO:0010842)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|gamma-tubulin complex (GO:0000930)|midbody (GO:0030496)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|PML body (GO:0016605)|spindle pole (GO:0000922)|ubiquitin ligase complex (GO:0000151)	antigen binding (GO:0003823)|DNA binding (GO:0003677)|DNA topoisomerase binding (GO:0044547)|SUMO ligase activity (GO:0019789)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		CGGAGGATGCCGGCGCAGGCC	0.716																																					p.P62P		Atlas-SNP	.											.	TOPORS	127	.	0			c.G186A						.						22	27	25					9																	32550784		2188	4264	6452	SO:0001819	synonymous_variant	10210	exon2			GGATGCCGGCGCA	AF098300	CCDS6527.1, CCDS56566.1	9p21	2013-01-09	2010-09-17		ENSG00000197579	ENSG00000197579		"RING-type (C3HC4) zinc fingers"	21653	protein-coding gene	gene with protein product		609507	"retinitis pigmentosa 31 (autosomal dominant)", "topoisomerase I binding, arginine/serine-rich"	RP31		10352183, 12083797, 17924349	Standard	NM_005802		Approved	TP53BPL, LUN	uc003zrb.3	Q9NS56	OTTHUMG00000019743	ENST00000360538.2:c.186G>A	chr9.hg19:g.32550784C>T		195.0	0.0		245.0	95.0	NM_005802	O43273|Q6P987|Q9NS55|Q9UNR9	Silent	SNP	ENST00000360538.2	hg19	CCDS6527.1																																																																																			.	.		0.716	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802		T	32550784	C	T	32550784	2	4	348	1	0	0	0	0	0	0	0	1	16385	639	23	1		1	TOPORS	9	32550784	Silent	SNP	C	TCGA-UB-A7MF-01A-11D-A33K-10		32550784	108662647	37	49085										
FAM69B	138311	hgsc.bcm.edu	37	chr9	139617859	139617859	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	gggctacacagccacctacgActtcaagatggccgacctgc	10	15	1	1			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr9:139617859A>G	ENST00000371692.4	+	5	1025	c.929A>G	c.(928-930)gAc>gGc	p.D310G	FAM69B_ENST00000371691.1_Missense_Mutation_p.D223G|SNHG7_ENST00000362567.2_RNA|SNHG7_ENST00000414282.1_RNA|SNHG7_ENST00000416970.1_RNA|SNHG7_ENST00000436596.1_RNA|SNHG7_ENST00000447221.1_RNA	NM_152421.3	NP_689634.2	Q5VUD6	FA69B_HUMAN	family with sequence similarity 69, member B	310						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				NS(1)|endometrium(3)|large_intestine(2)|lung(1)|prostate(1)	8	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;1.03e-05)|Epithelial(140;0.00013)		GCCACCTACGACTTCAAGATG	0.647																																					p.D310G		Atlas-SNP	.											.	FAM69B	22	.	0			c.A929G						.						39	39	39					9																	139617859		2203	4300	6503	SO:0001583	missense	138311	exon5			CCTACGACTTCAA		CCDS7004.1	9q34.3	2012-08-03			ENSG00000165716	ENSG00000165716			28290	protein-coding gene	gene with protein product		614543				21334309	Standard	NM_152421		Approved	MGC20262, C9orf136	uc004cik.3	Q5VUD6	OTTHUMG00000020940	ENST00000371692.4:c.929A>G	chr9.hg19:g.139617859A>G	ENSP00000360757:p.Asp310Gly	131.0	0.0		91.0	22.0	NM_152421	Q5VUD7|Q8N5N0|Q8WYU5	Missense_Mutation	SNP	ENST00000371692.4	hg19	CCDS7004.1	.	.	.	.	.	.	.	.	.	.	A	28.5	4.926912	0.92319	.	.	ENSG00000165716	ENST00000371692;ENST00000371691	T;T	0.47177	0.86;0.85	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.67411	0.2890	M	0.75615	2.305	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.67511	-0.5652	10	0.36615	T	0.2	-53.2084	14.3785	0.66895	1.0:0.0:0.0:0.0	.	310	Q5VUD6	FA69B_HUMAN	G	310;223	ENSP00000360757:D310G;ENSP00000360756:D223G	ENSP00000360756:D223G	D	+	2	0	FAM69B	138737680	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.480000	0.73604	1.992000	0.58205	0.459000	0.35465	GAC	.	.		0.647	FAM69B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055102.1	NM_152421		G	139617859	A	G	139617859	3	3	348	1	0	0	0	0	1	0	0	0	5611	275	10	2	947	2	FAM69B	9	139617859	Missense_Mutation	SNP	A	TCGA-UB-A7MF-01A-11D-A33K-10	107067075	139617859	1595572	38	49086										
KIAA1217	56243	hgsc.bcm.edu	37	chr10	24832181	24832187	+	Frame_Shift_Del	DEL	TCAAGCG	TCAAGCG	-													0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	ctcacactagactaacagaaTcaagcgtgcatgattttaaa					rs373416621		TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	TCAAGCG	TCAAGCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr10:24832181_24832187delTCAAGCG	ENST00000376454.3	+	19	4012_4018	c.3982_3988delTCAAGCG	c.(3982-3990)tcaagcgtgfs	p.SSV1328fs	KIAA1217_ENST00000458595.1_Intron|KIAA1217_ENST00000307544.6_Intron|KIAA1217_ENST00000376452.3_Intron|KIAA1217_ENST00000396446.1_Intron|KIAA1217_ENST00000396445.1_Intron|KIAA1217_ENST00000376451.2_Frame_Shift_Del_p.SSV1011fs|KIAA1217_ENST00000376462.1_Intron	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	1328					embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)		p.S1328T(1)		breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						ACTAACAGAATCAAGCGTGCATGATTT	0.43																																					p.1327_1329del		Atlas-Indel,Pindel	.											.	KIAA1217	235	.	1	Substitution - Missense(1)	endometrium(1)	c.3981_3987del						.																																			SO:0001589	frameshift_variant	56243	exon19			.	BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"sickle tail"					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.3982_3988delTCAAGCG	chr10.hg19:g.24832181_24832187delTCAAGCG	ENSP00000365637:p.Ser1328fs	118.0	0.0		117.0	32.0	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Frame_Shift_Del	DEL	ENST00000376454.3	hg19	CCDS31165.1																																																																																			.	.		0.43	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590		-	24832187	TCAAGCG	-	24832181	7	5	348	1	0	1	0	1	0	0	0	0	8225	1435	50	0	4056	0	KIAA1217	10	24832181	Frame_Shift_Del	DEL	TCAAGCG	TCGA-UB-A7MF-01A-11D-A33K-10		24832181	110702566	39	49087										
RASSF4	83937	hgsc.bcm.edu	37	chr10	45478109	45478109	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	cccagacggcctagctgcccTctgtgagtacccggtggctt	12	15	1	2			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr10:45478109T>A	ENST00000340258.5	+	4	392	c.279T>A	c.(277-279)ccT>ccA	p.P93P	RASSF4_ENST00000374417.2_Silent_p.P93P|RASSF4_ENST00000334940.6_Silent_p.P75P|RASSF4_ENST00000472561.1_3'UTR	NM_032023.3	NP_114412.2	Q8WYP3	RIN2_HUMAN	Ras association (RalGDS/AF-6) domain family member 4	629					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of catalytic activity (GO:0050790)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|small GTPase regulator activity (GO:0005083)			NS(1)|endometrium(2)|large_intestine(6)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16						CTAGCTGCCCTCTGTGAGTAC	0.662																																					p.P93P		Atlas-SNP	.											.	RASSF4	33	.	0			c.T279A						.						65	61	63					10																	45478109		2203	4300	6503	SO:0001819	synonymous_variant	83937	exon4			CTGCCCTCTGTGA	BC032593	CCDS7208.1	10q11.1	2008-02-22	2008-02-22		ENSG00000107551	ENSG00000107551			20793	protein-coding gene	gene with protein product		610559					Standard	NM_032023		Approved	AD037, MGC44914	uc001jbo.3	Q9H2L5	OTTHUMG00000018060	ENST00000340258.5:c.279T>A	chr10.hg19:g.45478109T>A		99.0	0.0		81.0	31.0	NM_032023	Q00425|Q5TFT8|Q9BQL3|Q9H071	Silent	SNP	ENST00000340258.5	hg19	CCDS7208.1																																																																																			.	.		0.662	RASSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047745.2	NM_032023		A	45478109	T	A	45478109	2	1	348	1	0	0	0	0	0	0	0	1	13103	1538	54	4		4	RASSF4	10	45478109	Silent	SNP	T	TCGA-UB-A7MF-01A-11D-A33K-10	20645928	45478109	90056638	40	49088										
ZNF488	118738	hgsc.bcm.edu	37	chr10	48371553	48371554	+	Stop_Codon_Del	DEL	TA	TA	-													0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	ggcacatgacttctcacagcTagcaggtgaccgcagaatga							TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	TA	TA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr10:48371553_48371554delTA	ENST00000395702.2	+	0	1248_1249				ZNF488_ENST00000494156.1_3'UTR|ZNF488_ENST00000586537.1_Stop_Codon_Del			Q96MN9	ZN488_HUMAN	zinc finger protein 488						negative regulation of transcription, DNA-templated (GO:0045892)|oligodendrocyte development (GO:0014003)|positive regulation of oligodendrocyte differentiation (GO:0048714)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|ovary(2)	14						TTCTCACAGCTAGCAGGTGACC	0.634																																					p.340_341del		Atlas-Indel,Pindel	.											.	ZNF488	38	.	0			c.1020_1021del						.																																			SO:0001567	stop_retained_variant	118738	exon2			.	AK056666	CCDS73120.1	10q11.22	2014-04-10			ENSG00000165388	ENSG00000265763		"Zinc fingers, C2H2-type"	23535	protein-coding gene	gene with protein product							Standard	NM_153034		Approved	FLJ32104	uc001jex.3	Q96MN9	OTTHUMG00000188322	Exception_encountered	chr10.hg19:g.48371553_48371554delTA		38.0	0.0		48.0	15.0	NM_153034	Q05CE0	Frame_Shift_Del	DEL	ENST00000395702.2	hg19	CCDS7217.1																																																																																			.	.		0.634	ZNF488-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314632.1	NM_153034		-	48371554	TA	-	48371553	7	5	348	1	0	1	0	1	0	0	0	0	17955	1535	53	0	1023	0	ZNF488	10	48371553	Stop_Codon_Del	DEL	TA	TCGA-UB-A7MF-01A-11D-A33K-10	2893444	48371553	87163194	41	49089										
ANK3	288	hgsc.bcm.edu	37	chr10	61833020	61833020	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	tgccagaatagtgcaacactGtcactttatcaaaatgctca	6	10	3	1			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr10:61833020G>A	ENST00000280772.2	-	37	7810	c.7619C>T	c.(7618-7620)aCa>aTa	p.T2540I	ANK3_ENST00000373827.2_Intron|ANK3_ENST00000355288.2_Intron|ANK3_ENST00000503366.1_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	2540					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						GTGCAACACTGTCACTTTATC	0.383																																					p.T2540I		Atlas-SNP	.											.	ANK3	703	.	0			c.C7619T						.						151	145	147					10																	61833020		2203	4300	6503	SO:0001583	missense	288	exon37			AACACTGTCACTT	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.7619C>T	chr10.hg19:g.61833020G>A	ENSP00000280772:p.Thr2540Ile	127.0	0.0		111.0	46.0	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	hg19	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	G	11.99	1.803204	0.31869	.	.	ENSG00000151150	ENST00000280772	T	0.70282	-0.47	5.47	5.47	0.80525	.	0.000000	0.43416	D	0.000573	T	0.74275	0.3695	L	0.58101	1.795	0.80722	D	1	D	0.53619	0.961	P	0.47206	0.541	T	0.76737	-0.2849	10	0.54805	T	0.06	.	19.3349	0.94312	0.0:0.0:1.0:0.0	.	2540	Q12955	ANK3_HUMAN	I	2540	ENSP00000280772:T2540I	ENSP00000280772:T2540I	T	-	2	0	ANK3	61503026	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.852000	0.86927	2.564000	0.86499	0.462000	0.41574	ACA	.	.		0.383	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		A	61833020	G	A	61833020	3	1	348	1	0	0	0	0	1	0	0	0	622	1377	48	3	5855	3	ANK3	10	61833020	Missense_Mutation	SNP	G	TCGA-UB-A7MF-01A-11D-A33K-10	13461467	61833020	73701727	42	49090										
TET1	80312	hgsc.bcm.edu	37	chr10	70450720	70450720	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	gcttctcctggtccccgaagActgcttcagccacaccagct	8	17	2	1			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr10:70450720A>G	ENST00000373644.4	+	12	5769	c.5560A>G	c.(5560-5562)Act>Gct	p.T1854A		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	1854					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						GTCCCCGAAGACTGCTTCAGC	0.512																																					p.T1854A		Atlas-SNP	.											TET1_ENST00000373644,NS,carcinoma,0,1	TET1	255	.	0			c.A5560G						.						83	79	80					10																	70450720		2203	4300	6503	SO:0001583	missense	80312	exon12			CCGAAGACTGCTT	AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"leukemia-associated protein with a CXXC domain", "ten-eleven translocation-1"	607790	"CXXC zinc finger 6", "tet oncogene 1"	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.5560A>G	chr10.hg19:g.70450720A>G	ENSP00000362748:p.Thr1854Ala	88.0	1.0		82.0	31.0	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	hg19	CCDS7281.1	.	.	.	.	.	.	.	.	.	.	A	4.708	0.131658	0.08981	.	.	ENSG00000138336	ENST00000373644	T	0.06142	3.34	5.48	0.382	0.16234	Methylcytosine dioxygenase TET, double-stranded beta helix fold domain (1);	17.798000	0.00166	N	0.000003	T	0.05135	0.0137	L	0.32530	0.975	0.09310	N	1	B	0.14805	0.011	B	0.10450	0.005	T	0.38457	-0.9660	10	0.19590	T	0.45	.	0.3069	0.00282	0.2961:0.2297:0.2566:0.2175	.	1854	Q8NFU7	TET1_HUMAN	A	1854	ENSP00000362748:T1854A	ENSP00000362748:T1854A	T	+	1	0	TET1	70120726	0.000000	0.05858	0.001000	0.08648	0.205000	0.24178	-0.170000	0.09897	0.393000	0.25203	0.533000	0.62120	ACT	.	.		0.512	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		G	70450720	A	G	70450720	3	3	348	1	0	0	0	0	1	0	0	0	15784	275	10	2	5602	2	TET1	10	70450720	Missense_Mutation	SNP	A	TCGA-UB-A7MF-01A-11D-A33K-10	8617700	70450720	65084027	43	49091										
TCERG1L	256536	hgsc.bcm.edu	37	chr10	133058601	133058601	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	ggctgcacgctggagggggaCgggccccggaggttctcagg	20	11	1	0			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr10:133058601C>T	ENST00000368642.4	-	4	862	c.777G>A	c.(775-777)ccG>ccA	p.P259P		NM_174937.3	NP_777597.2	Q5VWI1	TCRGL_HUMAN	transcription elongation regulator 1-like	259										cervix(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	31		all_cancers(35;1.22e-10)|all_epithelial(44;2.65e-09)|Lung NSC(174;0.00188)|all_lung(145;0.00307)|Melanoma(40;0.0179)|all_neural(114;0.0424)|Breast(234;0.0743)|Colorectal(57;0.09)		all cancers(32;0.000899)|OV - Ovarian serous cystadenocarcinoma(35;0.0021)|Epithelial(32;0.00276)		TGGAGGGGGACGGGCCCCGGA	0.687																																					p.P259P		Atlas-SNP	.											TCERG1L,caecum,carcinoma,0,1	TCERG1L	91	.	0			c.G777A						.						21	25	24					10																	133058601		2203	4299	6502	SO:0001819	synonymous_variant	256536	exon4			GGGGGACGGGCCC	AK096269	CCDS7662.2	10q26.3	2006-04-12			ENSG00000176769	ENSG00000176769			23533	protein-coding gene	gene with protein product							Standard	NM_174937		Approved	FLJ38950	uc001lkp.3	Q5VWI1	OTTHUMG00000019276	ENST00000368642.4:c.777G>A	chr10.hg19:g.133058601C>T		29.0	0.0		37.0	13.0	NM_174937	Q5VWI2|Q86XM8	Silent	SNP	ENST00000368642.4	hg19	CCDS7662.2																																																																																			.	.		0.687	TCERG1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091619.2	NM_174937		T	133058601	C	T	133058601	2	4	348	1	0	0	0	0	0	0	0	1	15701	523	19	1		1	TCERG1L	10	133058601	Silent	SNP	C	TCGA-UB-A7MF-01A-11D-A33K-10	62607881	133058601	2476146	44	49092										
KNDC1	85442	hgsc.bcm.edu	37	chr10	134999499	134999499	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	tgtcagcgagagcagctggcGggagagacctgccccaggaa	16	11	1	2			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr10:134999499G>A	ENST00000304613.3	+	6	668	c.647G>A	c.(646-648)cGg>cAg	p.R216Q	KNDC1_ENST00000368572.2_Missense_Mutation_p.R216Q|KNDC1_ENST00000368571.2_Missense_Mutation_p.R151Q			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	216	KIND 1. {ECO:0000255|PROSITE- ProRule:PRU00709}.				cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		AGCAGCTGGCGGGAGAGACCT	0.716																																					p.R216Q		Atlas-SNP	.											.	KNDC1	155	.	0			c.G647A						.						8	10	9					10																	134999499		2141	4216	6357	SO:0001583	missense	85442	exon6			GCTGGCGGGAGAG	AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"RasGEF domain family, member 2"	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.647G>A	chr10.hg19:g.134999499G>A	ENSP00000304437:p.Arg216Gln	37.0	0.0		67.0	15.0	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	hg19	CCDS7674.1	.	.	.	.	.	.	.	.	.	.	G	17.25	3.341647	0.61073	.	.	ENSG00000171798	ENST00000304613;ENST00000368572;ENST00000368571	T;T;T	0.20069	2.61;2.61;2.1	4.05	1.06	0.20224	KIND (2);	0.464800	0.20582	U	0.089515	T	0.18173	0.0436	L	0.51422	1.61	0.09310	N	1	D;P	0.57899	0.981;0.804	B;B	0.43103	0.408;0.085	T	0.12400	-1.0549	10	0.66056	D	0.02	.	6.8841	0.24189	0.3198:0.0:0.6802:0.0	.	151;216	Q76NI1-2;Q76NI1	.;VKIND_HUMAN	Q	216;216;151	ENSP00000304437:R216Q;ENSP00000357561:R216Q;ENSP00000357560:R151Q	ENSP00000304437:R216Q	R	+	2	0	KNDC1	134849489	0.838000	0.29461	0.003000	0.11579	0.016000	0.09150	0.295000	0.19065	0.111000	0.17947	0.538000	0.68166	CGG	.	.		0.716	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643		A	134999499	G	A	134999499	3	1	348	1	0	0	0	0	1	0	0	0	8435	1116	39	1	669	1	KNDC1	10	134999499	Missense_Mutation	SNP	G	TCGA-UB-A7MF-01A-11D-A33K-10	1940898	134999499	535248	45	49093										
VENTX	27287	hgsc.bcm.edu	37	chr10	135053718	135053718	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	ggcagcctctggcgtcccacCcccctaccccaggccggcct	10	22	1	0			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr10:135053718C>G	ENST00000325980.9	+	3	1196	c.685C>G	c.(685-687)Ccc>Gcc	p.P229A		NM_014468.3	NP_055283.1	O95231	VENTX_HUMAN	VENT homeobox	229					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			NS(1)|endometrium(1)|large_intestine(1)|lung(9)|soft_tissue(1)|upper_aerodigestive_tract(1)	14		all_cancers(35;4.15e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;7.8e-06)|Epithelial(32;9.31e-06)|all cancers(32;1.19e-05)		GGCGTCCCACCCCCCTACCCC	0.692																																					p.P229A		Atlas-SNP	.											.	VENTX	24	.	0			c.C685G						.						10	12	11					10																	135053718		2165	4240	6405	SO:0001583	missense	27287	exon3			TCCCACCCCCCTA	AF068006	CCDS7675.1	10q26.3	2011-06-20	2011-06-01	2005-09-27	ENSG00000151650	ENSG00000151650		"Homeoboxes / ANTP class : NKL subclass"	13639	protein-coding gene	gene with protein product		607158	"VENT-like homeobox 2", "VENT homeobox homolog (Xenopus laevis)"	VENTX2		10790436	Standard	NM_014468		Approved	HPX42B	uc010quy.1	O95231	OTTHUMG00000019307	ENST00000325980.9:c.685C>G	chr10.hg19:g.135053718C>G	ENSP00000357556:p.Pro229Ala	37.0	0.0		40.0	18.0	NM_014468	Q32MZ3	Missense_Mutation	SNP	ENST00000325980.9	hg19	CCDS7675.1	.	.	.	.	.	.	.	.	.	.	C	4.490	0.090850	0.08632	.	.	ENSG00000151650	ENST00000325980	D	0.91521	-2.86	2.12	0.0629	0.14346	.	0.876510	0.09573	U	0.783967	T	0.76004	0.3927	N	0.14661	0.345	0.09310	N	1	B	0.21225	0.053	B	0.17722	0.019	T	0.61148	-0.7121	10	0.07482	T	0.82	.	2.8706	0.05616	0.0:0.4989:0.3017:0.1994	.	229	O95231	VENTX_HUMAN	A	229	ENSP00000357556:P229A	ENSP00000357556:P229A	P	+	1	0	VENTX	134903708	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.720000	0.25896	0.013000	0.14918	-0.556000	0.04195	CCC	.	.		0.692	VENTX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051116.4	NM_014468		G	135053718	C	G	135053718	3	3	348	1	0	0	0	0	1	0	0	0	17168	623	22	4	695	4	VENTX	10	135053718	Missense_Mutation	SNP	C	TCGA-UB-A7MF-01A-11D-A33K-10	54219	135053718	481029	46	49094										
PIK3C2A	5286	hgsc.bcm.edu	37	chr11	17153463	17153463	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	aagccagaaatttcacttacAgttcatcccatttaataaga	4	9	2	2			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr11:17153463A>G	ENST00000265970.7	-	11	2230	c.2231T>C	c.(2230-2232)cTa>cCa	p.L744P	PIK3C2A_ENST00000531428.1_Intron|PIK3C2A_ENST00000540361.1_Splice_Site_p.L364P	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	744	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00041, ECO:0000255|PROSITE- ProRule:PRU00880}.				clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|exocytosis (GO:0006887)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|small molecule metabolic process (GO:0044281)|vascular smooth muscle contraction (GO:0014829)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol binding (GO:0035091)			central_nervous_system(4)|endometrium(5)|kidney(5)|large_intestine(7)|lung(24)|ovary(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	58						TTTCACTTACAGTTCATCCCA	0.313																																					p.L744P		Atlas-SNP	.											.	PIK3C2A	148	.	0			c.T2231C						.						105	116	112					11																	17153463		2200	4288	6488	SO:0001630	splice_region_variant	5286	exon11			ACTTACAGTTCAT	Y13367	CCDS7824.1	11p15.5-p14	2012-07-13	2012-07-13			ENSG00000011405	2.7.1.154		8971	protein-coding gene	gene with protein product		603601	"phosphoinositide-3-kinase, class 2, alpha polypeptide"			9337861	Standard	NM_002645		Approved	PI3K-C2alpha	uc001mmq.4	O00443		ENST00000265970.7:c.2231+1T>C	chr11.hg19:g.17153463A>G		174.0	0.0		215.0	41.0	NM_002645	B0LPH2|B4E2G4|Q14CQ9	Missense_Mutation	SNP	ENST00000265970.7	hg19	CCDS7824.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.091985	0.76756	.	.	ENSG00000011405	ENST00000265970;ENST00000540361	T;T	0.78003	-1.14;-1.14	5.81	5.81	0.92471	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);Phosphoinositide 3-kinase, C2 (2);	0.000000	0.85682	D	0.000000	D	0.85864	0.5796	L	0.57536	1.79	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85282	0.1062	9	.	.	.	-8.7055	16.1652	0.81750	1.0:0.0:0.0:0.0	.	744	O00443	P3C2A_HUMAN	P	744;364	ENSP00000265970:L744P;ENSP00000438687:L364P	.	L	-	2	0	PIK3C2A	17110039	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	8.962000	0.93254	2.230000	0.72887	0.528000	0.53228	CTA	.	.		0.313	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645	Missense_Mutation	G	17153463	A	G	17153463	5	3	348	1	0	0	0	0	0	0	1	0	11918	202	7	2	2917	2	PIK3C2A	11	17153463	Splice_Site	SNP	A	TCGA-UB-A7MF-01A-11D-A33K-10		17153463	117853053	47	49095										
NAV2	89797	hgsc.bcm.edu	37	chr11	20057523	20057523	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	agctgggacgacagcagctcCgtcagcagcggcatcagcga	14	13	2	0	rs199691877		TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr11:20057523C>A	ENST00000396087.3	+	13	2955	c.2856C>A	c.(2854-2856)tcC>tcA	p.S952S	NAV2_ENST00000533917.1_Silent_p.S15S|NAV2_ENST00000396085.1_Silent_p.S929S|NAV2_ENST00000540292.1_Silent_p.S883S|NAV2_ENST00000349880.4_Silent_p.S929S|NAV2_ENST00000360655.4_Silent_p.S865S|NAV2_ENST00000527559.2_Silent_p.S881S|NAV2_ENST00000311043.8_Silent_p.S15S	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	952					glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						ACAGCAGCTCCGTCAGCAGCG	0.547																																					p.S952S		Atlas-SNP	.											.	NAV2	255	.	0			c.C2856A						.						212	133	160					11																	20057523		2203	4300	6503	SO:0001819	synonymous_variant	89797	exon13			CAGCTCCGTCAGC	AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 2", "retinoic acid inducible gene in neuroblastoma 1", "helicase, APC down-regulated 1"	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.2856C>A	chr11.hg19:g.20057523C>A		113.0	0.0		97.0	36.0	NM_001244963	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Silent	SNP	ENST00000396087.3	hg19	CCDS58126.1																																																																																			.	C|1.000;T|0.000		0.547	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117		A	20057523	C	A	20057523	2	1	348	1	0	0	0	0	0	0	0	1	10193	639	23	1		1	NAV2	11	20057523	Silent	SNP	C	TCGA-UB-A7MF-01A-11D-A33K-10	2904060	20057523	114948993	48	49096										
C11orf49	79096	hgsc.bcm.edu	37	chr11	47182742	47182743	+	Splice_Site	INS	-	-	T													0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	atgaagagctggaacggctgINStaagtgtcaagtgggaggat					rs34737621|rs78089169|rs200603540		TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr11:47182742_47182743insT	ENST00000278460.7	+	8	880		c.e8+1		C11orf49_ENST00000543718.1_Splice_Site|C11orf49_ENST00000378618.2_Splice_Site|C11orf49_ENST00000395460.2_Frame_Shift_Ins_p.*275fs|C11orf49_ENST00000536126.1_Splice_Site|C11orf49_ENST00000378615.3_Splice_Site	NM_001003677.1|NM_024113.3	NP_001003677.1|NP_077018.1	Q9H6J7	CK049_HUMAN	chromosome 11 open reading frame 49							nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|skin(1)	11						TGGAACGGCTGTAAGTGTCAAG	0.569											OREG0020950	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L274fs		Atlas-Indel,Pindel	.											.	C11orf49	41	.	0			c.822_823insT						.		,,,	0,4264		0,0,2132					,,,	5.5	1		dbSNP_126	79	1,8253		0,1,4126	no	splice-5,splice-5,splice-5,frameshift	C11orf49	NM_024113.3,NM_001003678.1,NM_001003677.1,NM_001003676.1	,,,	0,1,6258	A1A1,A1R,RR		0.0121,0.0,0.0080	,,,	,,,		1,12517				SO:0001630	splice_region_variant	79096	exon8			.	AL136575	CCDS7925.1, CCDS31479.1, CCDS31480.1, CCDS41641.1	11p11.2	2006-02-02			ENSG00000149179	ENSG00000149179			28720	protein-coding gene	gene with protein product							Standard	NM_001003677		Approved	FLJ22210, MGC4707	uc001ndr.4	Q9H6J7	OTTHUMG00000166725	ENST00000278460.7:c.821+1->T	chr11.hg19:g.47182743_47182743dupT		101.0	0.0	944	79.0	17.0	NM_001003676	D3DQQ8|E9PAX7|Q7L077|Q96CS8|Q9BQH4|Q9BUW5	Frame_Shift_Ins	INS	ENST00000278460.7	hg19	CCDS7925.1																																																																																			.	.		0.569	C11orf49-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391218.1	NM_024113	Intron	T	47182743	-	T	47182742	8	5	348	1	0	1	1	0	0	0	1	0	1647	1391	48	0	852	0	C11orf49	11	47182742	Splice_Site	INS	-	TCGA-UB-A7MF-01A-11D-A33K-10	27125219	47182742	87823774	49	49097										
PIWIL4	143689	hgsc.bcm.edu	37	chr11	94354053	94354053	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	tctcctcagggcatagtcagTgtcccagcaccatgtcagta	9	13	4	0			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr11:94354053T>G	ENST00000299001.6	+	20	2665	c.2454T>G	c.(2452-2454)agT>agG	p.S818R	PIWIL4_ENST00000537419.1_Missense_Mutation_p.S169R|RP11-867G2.8_ENST00000537874.1_RNA|RP11-867G2.8_ENST00000536540.1_RNA	NM_152431.2	NP_689644.2	Q7Z3Z4	PIWL4_HUMAN	piwi-like RNA-mediated gene silencing 4	818	Piwi. {ECO:0000255|PROSITE- ProRule:PRU00150}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|piP-body (GO:0071547)	piRNA binding (GO:0034584)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|urinary_tract(2)	30		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				GCATAGTCAGTGTCCCAGCAC	0.393																																					p.S818R		Atlas-SNP	.											.	PIWIL4	70	.	0			c.T2454G						.						66	60	62					11																	94354053		2201	4298	6499	SO:0001583	missense	143689	exon20			AGTCAGTGTCCCA	AB079366	CCDS31656.1	11q12	2013-02-15	2013-02-15			ENSG00000134627		"Argonaute/PIWI family"	18444	protein-coding gene	gene with protein product		610315	"piwi-like 4 (Drosophila)"			12906857	Standard	NM_152431		Approved	FLJ36156, HIWI2, Miwi2	uc001pfa.3	Q7Z3Z4		ENST00000299001.6:c.2454T>G	chr11.hg19:g.94354053T>G	ENSP00000299001:p.Ser818Arg	90.0	0.0		76.0	17.0	NM_152431	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Missense_Mutation	SNP	ENST00000299001.6	hg19	CCDS31656.1	.	.	.	.	.	.	.	.	.	.	T	3.613	-0.079140	0.07141	.	.	ENSG00000134627	ENST00000299001;ENST00000537419	T;T	0.33438	1.41;1.41	5.41	-4.71	0.03279	Stem cell self-renewal protein Piwi (3);Ribonuclease H-like (1);	0.358550	0.26525	N	0.023890	T	0.05960	0.0155	N	0.02412	-0.56	0.29576	N	0.849507	B	0.06786	0.001	B	0.06405	0.002	T	0.30149	-0.9988	10	0.02654	T	1	-9.3505	1.0149	0.01505	0.2406:0.3289:0.2224:0.2081	.	818	Q7Z3Z4	PIWL4_HUMAN	R	818;169	ENSP00000299001:S818R;ENSP00000439710:S169R	ENSP00000299001:S818R	S	+	3	2	PIWIL4	93993701	0.829000	0.29322	0.399000	0.26333	0.955000	0.61496	-0.094000	0.11094	-0.480000	0.06803	0.454000	0.30748	AGT	.	.		0.393	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396388.1	NM_152431		G	94354053	T	G	94354053	3	3	348	1	0	0	0	0	1	0	0	0	11969	1693	59	5	2532	5	PIWIL4	11	94354053	Missense_Mutation	SNP	T	TCGA-UB-A7MF-01A-11D-A33K-10	47171311	94354053	40652463	50	49098										
GRIA4	2893	hgsc.bcm.edu	37	chr11	105795190	105795190	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	gaggaggtcattgacttttcTaagcccttcatgagtttggg	12	7	3	2			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr11:105795190T>A	ENST00000530497.1	+	11	1542	c.1542T>A	c.(1540-1542)tcT>tcA	p.S514S	GRIA4_ENST00000393127.2_Silent_p.S514S|GRIA4_ENST00000282499.5_Silent_p.S514S|GRIA4_ENST00000525187.1_Silent_p.S514S			P48058	GRIA4_HUMAN	glutamate receptor, ionotropic, AMPA 4	514					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(24)|liver(2)|lung(25)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	82		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)		TTGACTTTTCTAAGCCCTTCA	0.413																																					p.S514S		Atlas-SNP	.											.	GRIA4	380	.	0			c.T1542A						.						139	137	137					11																	105795190		2202	4299	6501	SO:0001819	synonymous_variant	2893	exon12			CTTTTCTAAGCCC	U16129	CCDS8333.1, CCDS41706.1, CCDS41707.1	11q22	2012-08-29	2012-02-03		ENSG00000152578	ENSG00000152578		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4574	protein-coding gene	gene with protein product		138246	"glutamate receptor, ionotrophic, AMPA 4"	GLUR4			Standard	NM_001077244		Approved	GluA4, GLURD	uc001pix.2	P48058	OTTHUMG00000166236	ENST00000530497.1:c.1542T>A	chr11.hg19:g.105795190T>A		104.0	0.0		100.0	20.0	NM_001077243	Q86XE8	Silent	SNP	ENST00000530497.1	hg19	CCDS8333.1																																																																																			.	.		0.413	GRIA4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388593.1			A	105795190	T	A	105795190	2	1	348	1	0	0	0	0	0	0	0	1	6779	1509	53	4		4	GRIA4	11	105795190	Silent	SNP	T	TCGA-UB-A7MF-01A-11D-A33K-10	11441137	105795190	29211326	51	49099										
PCSK7	9159	hgsc.bcm.edu	37	chr11	117096683	117096683	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	cattgatctgatagtgcttgTtgaacgccactgcctccatg	9	11	1	3			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr11:117096683T>C	ENST00000320934.3	-	6	1454	c.824A>G	c.(823-825)aAc>aGc	p.N275S	PCSK7_ENST00000540028.1_5'Flank	NM_004716.2	NP_004707.2	Q16549	PCSK7_HUMAN	proprotein convertase subtilisin/kexin type 7	275	Peptidase S8.				peptide hormone processing (GO:0016486)|protein processing (GO:0016485)	integral component of Golgi membrane (GO:0030173)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|skin(1)	16	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|Epithelial(105;6.71e-05)|all cancers(92;0.000537)		ATAGTGCTTGTTGAACGCCAC	0.542			T	IGH@	MLCLS						OREG0021371	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N275S		Atlas-SNP	.		Dom	yes		11	11q23.3	9159	proprotein convertase subtilisin/kexin type 7		L	.	PCSK7	59	.	0			c.A824G						.						149	108	122					11																	117096683		2201	4296	6497	SO:0001583	missense	9159	exon6			TGCTTGTTGAACG	U40623	CCDS8382.1	11q23-q24	2008-02-01			ENSG00000160613	ENSG00000160613			8748	protein-coding gene	gene with protein product		604872				8615762, 9820811	Standard	XM_006718938		Approved	PC7, PC8, LPC, SPC7	uc001pqr.3	Q16549	OTTHUMG00000165640	ENST00000320934.3:c.824A>G	chr11.hg19:g.117096683T>C	ENSP00000325917:p.Asn275Ser	54.0	0.0	1478	42.0	22.0	NM_004716	B0YJ60|Q3C1X1|Q53GM4|Q96FK8|Q9UL57	Missense_Mutation	SNP	ENST00000320934.3	hg19	CCDS8382.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.099839	0.76983	.	.	ENSG00000160613	ENST00000320934;ENST00000543900;ENST00000525027	T;D	0.87887	-1.37;-2.31	5.83	5.83	0.93111	Peptidase S8/S53, subtilisin/kexin/sedolisin (3);	0.000000	0.85682	D	0.000000	D	0.83608	0.5291	N	0.12663	0.25	0.80722	D	1	D	0.54397	0.966	P	0.57502	0.822	T	0.80616	-0.1303	10	0.10902	T	0.67	-39.2626	15.3821	0.74664	0.0:0.0:0.0:1.0	.	275	Q16549	PCSK7_HUMAN	S	275	ENSP00000325917:N275S;ENSP00000431181:N275S	ENSP00000325917:N275S	N	-	2	0	PCSK7	116601893	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.235000	0.73313	0.533000	0.62120	AAC	.	.		0.542	PCSK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385529.2	NM_004716		C	117096683	T	C	117096683	3	2	348	1	0	0	0	0	1	0	0	0	11614	1725	60	2	1581	2	PCSK7	11	117096683	Missense_Mutation	SNP	T	TCGA-UB-A7MF-01A-11D-A33K-10	11301493	117096683	17909833	52	49100										
CBL	867	hgsc.bcm.edu	37	chr11	119103248	119103248	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	cagatacctaccagcatctcCgtactatcttgtcaagatat	5	12	3	2	rs147438359		TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr11:119103248C>T	ENST00000264033.4	+	2	662	c.286C>T	c.(286-288)Cgt>Tgt	p.R96C		NM_005188.3	NP_005179.2	P22681	CBL_HUMAN	Cbl proto-oncogene, E3 ubiquitin protein ligase	96	4H.|Cbl-PTB. {ECO:0000255|PROSITE- ProRule:PRU00839}.|Sufficient for interaction with EPHB1.				cell surface receptor signaling pathway (GO:0007166)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|flotillin complex (GO:0016600)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ephrin receptor binding (GO:0046875)|ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R96S(1)		breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(194)|kidney(3)|large_intestine(9)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	251		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)		CCAGCATCTCCGTACTATCTT	0.428			"T, Mis S, O"	MLL	"AML, JMML, MDS"				Noonan syndrome;CBL gene-associated Juvenile Myelomonocytic Leukemia and Developmental Anomalies																												p.R96C		Atlas-SNP	.		"Dom, Rec"	yes		11	11q23.3	867	Cas-Br-M (murine) ecotropic retroviral transforming		L	.	CBL	408	.	1	Substitution - Missense(1)	lung(1)	c.C286T						.	C	CYS/ARG	0,4398		0,0,2199	96	92	93		286	5.9	1	11	dbSNP_134	93	1,8589	1.2+/-3.3	0,1,4294	no	missense	CBL	NM_005188.2	180	0,1,6493	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	96/907	119103248	1,12987	2199	4295	6494	SO:0001583	missense	867	exon2	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CBL-associated JMML	CATCTCCGTACTA	X57110	CCDS8418.1	11q23.3	2014-09-17	2012-02-23		ENSG00000110395	ENSG00000110395		"RING-type (C3HC4) zinc fingers"	1541	protein-coding gene	gene with protein product	"oncogene CBL2"	165360	"Cas-Br-M (murine) ecotropic retroviral transforming sequence"	CBL2		2013228	Standard	NM_005188		Approved	RNF55, c-Cbl	uc001pwe.4	P22681	OTTHUMG00000166170	ENST00000264033.4:c.286C>T	chr11.hg19:g.119103248C>T	ENSP00000264033:p.Arg96Cys	81.0	0.0		63.0	19.0	NM_005188	A3KMP8	Missense_Mutation	SNP	ENST00000264033.4	hg19	CCDS8418.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.154905	0.78114	0.0	1.16E-4	ENSG00000110395	ENST00000264033	T	0.79141	-1.24	5.91	5.91	0.95273	Adaptor protein Cbl, N-terminal helical (3);Adaptor protein Cbl, PTB domain (1);	0.094469	0.85682	D	0.000000	D	0.89238	0.6658	M	0.81497	2.545	0.80722	D	1	D	0.89917	1.0	D	0.74348	0.983	D	0.89541	0.3792	10	0.87932	D	0	-14.7254	20.2959	0.98551	0.0:1.0:0.0:0.0	.	96	P22681	CBL_HUMAN	C	96	ENSP00000264033:R96C	ENSP00000264033:R96C	R	+	1	0	CBL	118608458	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.893000	0.69798	2.793000	0.96121	0.655000	0.94253	CGT	.	C|1.000;T|0.000		0.428	CBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388219.4	NM_005188		T	119103248	C	T	119103248	3	4	348	1	0	0	0	0	1	0	0	0	2702	652	23	1	292	1	CBL	11	119103248	Missense_Mutation	SNP	C	TCGA-UB-A7MF-01A-11D-A33K-10	2006565	119103248	15903268	53	49101										
OR8G2	0	hgsc.bcm.edu	37	chr11	124095563	124095563	+	IGR	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	tggtcacagtggtgggcaacTtgagcatgatcacactgatt	12	8	2	3			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr11:124095563T>G								OR10D3 (38611 upstream) : OR8G1 (24859 downstream)																							GGTGGGCAACTTGAGCATGAT	0.502																																					p.L56V		Atlas-SNP	.											.	.	.	.	0			c.T166G						.						167	166	166					11																	124095563		2139	4282	6421	SO:0001628	intergenic_variant	26492	exon1			GGCAACTTGAGCA																													chr11.hg19:g.124095563T>G		96.0	0.0		85.0	15.0	NM_001007249		Missense_Mutation	SNP		hg19																																																																																				.	.	0	0.502									G	124095563	T	G	124095563	1	3	348	0	1	0	0	0	0	0	0	0	11244	1606	56	5		5	OR8G2	11	124095563	IGR	SNP	T	TCGA-UB-A7MF-01A-11D-A33K-10	4992315	124095563	10910953	54	49102										
CLEC6A	93978	hgsc.bcm.edu	37	chr12	8612254	8612254	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	tctgaactacactcatatcaTtcaagtctcacctgcttcag	4	13	6	1	rs142509792	byFrequency	TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr12:8612254T>C	ENST00000382073.3	+	3	369	c.183T>C	c.(181-183)caT>caC	p.H61H		NM_001007033.1	NP_001007034.1	Q6EIG7	CLC6A_HUMAN	C-type lectin domain family 6, member A	61					defense response to fungus (GO:0050832)|innate immune response (GO:0045087)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|large_intestine(2)|lung(7)	10	Lung SC(5;0.184)					ACTCATATCATTCAAGTCTCA	0.378																																					p.H61H		Atlas-SNP	.											.	CLEC6A	19	.	0			c.T183C						.						164	158	160					12																	8612254		2203	4300	6503	SO:0001819	synonymous_variant	93978	exon3			ATATCATTCAAGT	AY321309	CCDS31739.1	12p13	2005-09-21	2005-02-09	2005-02-11	ENSG00000205846	ENSG00000205846		"C-type lectin domain containing"	14556	protein-coding gene	gene with protein product		613579	"C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 10"	CLECSF10			Standard	NM_001007033		Approved	dectin-2	uc001qum.1	Q6EIG7	OTTHUMG00000168672	ENST00000382073.3:c.183T>C	chr12.hg19:g.8612254T>C		81.0	0.0		101.0	37.0	NM_001007033	A2RUK3	Silent	SNP	ENST00000382073.3	hg19	CCDS31739.1																																																																																			.	T|0.999;A|0.001		0.378	CLEC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400562.1	NM_001007033		C	8612254	T	C	8612254	2	2	348	1	0	0	0	0	0	0	0	1	3522	1490	52	2		2	CLEC6A	12	8612254	Silent	SNP	T	TCGA-UB-A7MF-01A-11D-A33K-10		8612254	125239641	55	49103										
CLEC4D	338339	hgsc.bcm.edu	37	chr12	8672896	8672896	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	gatgagaatgccaaaggtcaGtggcgttgggtggaccagac	16	7	1	2			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr12:8672896G>T	ENST00000299665.2	+	5	652	c.459G>T	c.(457-459)caG>caT	p.Q153H		NM_080387.4	NP_525126.2	Q8WXI8	CLC4D_HUMAN	C-type lectin domain family 4, member D	153	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				innate immune response (GO:0045087)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			large_intestine(4)|lung(6)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Lung SC(5;0.184)					CCAAAGGTCAGTGGCGTTGGG	0.398																																					p.Q153H		Atlas-SNP	.											.	CLEC4D	46	.	0			c.G459T						.						99	101	100					12																	8672896		2203	4300	6503	SO:0001583	missense	338339	exon5			AGGTCAGTGGCGT	AF411850	CCDS8593.1	12p13.31	2005-09-21	2005-02-09	2005-02-11		ENSG00000166527		"C-type lectin domain containing"	14554	protein-coding gene	gene with protein product		609964	"C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 8"	CLECSF8			Standard	NM_080387		Approved	Mpcl	uc001qun.3	Q8WXI8		ENST00000299665.2:c.459G>T	chr12.hg19:g.8672896G>T	ENSP00000299665:p.Gln153His	111.0	0.0		102.0	14.0	NM_080387	Q8N5J5	Missense_Mutation	SNP	ENST00000299665.2	hg19	CCDS8593.1	.	.	.	.	.	.	.	.	.	.	G	14.22	2.471819	0.43942	.	.	ENSG00000166527	ENST00000299665	T	0.19669	2.13	4.67	0.623	0.17654	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	.	.	.	.	T	0.32315	0.0825	L	0.54965	1.715	0.32729	N	0.509203	D	0.76494	0.999	D	0.69824	0.966	T	0.39396	-0.9616	8	.	.	.	.	4.1055	0.10035	0.246:0.0:0.5879:0.1661	.	153	Q8WXI8	CLC4D_HUMAN	H	153	ENSP00000299665:Q153H	.	Q	+	3	2	CLEC4D	8564163	0.975000	0.34042	0.959000	0.39883	0.694000	0.40290	0.328000	0.19681	-0.005000	0.14395	-0.195000	0.12781	CAG	.	.		0.398	CLEC4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400565.1	NM_080387		T	8672896	G	T	8672896	3	4	348	1	0	0	0	0	1	0	0	0	3516	1020	36	3	477	3	CLEC4D	12	8672896	Missense_Mutation	SNP	G	TCGA-UB-A7MF-01A-11D-A33K-10	60642	8672896	125178999	56	49104										
ADAMTS20	80070	hgsc.bcm.edu	37	chr12	43846137	43846137	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	ccacaaggagtaccatcttcAaccatatccttcaataggta	5	12	3	0			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr12:43846137A>T	ENST00000389420.3	-	14	2018	c.2019T>A	c.(2017-2019)gtT>gtA	p.V673V	ADAMTS20_ENST00000553158.1_Silent_p.V673V	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	673	Cys-rich.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		TACCATCTTCAACCATATCCT	0.353																																					p.V673V		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.T2019A						.						90	85	87					12																	43846137		2203	4300	6503	SO:0001819	synonymous_variant	80070	exon14			ATCTTCAACCATA	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.2019T>A	chr12.hg19:g.43846137A>T		85.0	0.0		75.0	14.0	NM_025003	A6NNC9|J3QT00	Silent	SNP	ENST00000389420.3	hg19	CCDS31778.2																																																																																			.	.		0.353	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		T	43846137	A	T	43846137	2	4	348	1	0	0	0	0	0	0	0	1	266	117	5	4		4	ADAMTS20	12	43846137	Silent	SNP	A	TCGA-UB-A7MF-01A-11D-A33K-10	35173241	43846137	90005758	57	49105										
HOXC11	3227	hgsc.bcm.edu	37	chr12	54367576	54367576	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	caagggggagcccgaggcacCcccggcctcgggactggcgt	17	15	0	0			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr12:54367576C>T	ENST00000546378.1	+	1	667	c.551C>T	c.(550-552)cCc>cTc	p.P184L	HOTAIR_ENST00000424518.1_RNA|HOTAIR_ENST00000455246.1_RNA|HOXC11_ENST00000243082.4_Missense_Mutation_p.P184L			O43248	HXC11_HUMAN	homeobox C11	184					anterior/posterior pattern specification (GO:0009952)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal joint morphogenesis (GO:0060272)|endoderm development (GO:0007492)|metanephros development (GO:0001656)|organ induction (GO:0001759)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			large_intestine(1)|ovary(1)	2						CCCGAGGCACCCCCGGCCTCG	0.721			T	NUP98	AML																																p.P184L		Atlas-SNP	.		Dom	yes		12	12q13.3	3227	homeo box C11		L	.	HOXC11	32	.	0			c.C551T						.						7	10	9					12																	54367576		2088	4003	6091	SO:0001583	missense	3227	exon1			AGGCACCCCCGGC		CCDS8867.1	12q13.13	2011-06-20	2005-12-22		ENSG00000123388	ENSG00000123388		"Homeoboxes / ANTP class : HOXL subclass"	5123	protein-coding gene	gene with protein product		605559	"homeo box C11"	HOX3H		1973146, 1358459	Standard	NM_014212		Approved		uc001sem.3	O43248	OTTHUMG00000160011	ENST00000546378.1:c.551C>T	chr12.hg19:g.54367576C>T	ENSP00000446680:p.Pro184Leu	70.0	0.0		74.0	13.0	NM_014212	A8K7D1|Q96DH2	Missense_Mutation	SNP	ENST00000546378.1	hg19	CCDS8867.1	.	.	.	.	.	.	.	.	.	.	C	11.33	1.607536	0.28623	.	.	ENSG00000123388	ENST00000546378;ENST00000243082	D;T	0.91686	-2.89;1.92	4.21	4.21	0.49690	.	0.300114	0.36200	N	0.002732	D	0.83248	0.5213	N	0.08118	0	0.47123	D	0.999327	B	0.19935	0.04	B	0.22152	0.038	T	0.81274	-0.1007	10	0.72032	D	0.01	.	12.3754	0.55277	0.0:0.8284:0.1716:0.0	.	184	O43248	HXC11_HUMAN	L	184	ENSP00000446680:P184L;ENSP00000243082:P184L	ENSP00000243082:P184L	P	+	2	0	HOXC11	52653843	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	3.005000	0.49521	2.338000	0.79540	0.555000	0.69702	CCC	.	.		0.721	HOXC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358869.2			T	54367576	C	T	54367576	3	4	348	1	0	0	0	0	1	0	0	0	7319	623	22	3	553	3	HOXC11	12	54367576	Missense_Mutation	SNP	C	TCGA-UB-A7MF-01A-11D-A33K-10	10521439	54367576	79484319	58	49106										
SLC6A15	55117	hgsc.bcm.edu	37	chr12	85279232	85279232	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	acaagtgtgtgaagcattttTcaccaaaggacactgatccc	8	10	1	2			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr12:85279232T>C	ENST00000266682.5	-	4	1097	c.556A>G	c.(556-558)Aaa>Gaa	p.K186E	SLC6A15_ENST00000552192.1_Missense_Mutation_p.K79E|SLC6A15_ENST00000450363.3_Missense_Mutation_p.K186E|SLC6A15_ENST00000551388.1_Intron	NM_182767.5	NP_877499.1	Q9H2J7	S6A15_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 15	186					amino acid transport (GO:0006865)|ion transport (GO:0006811)|leucine transport (GO:0015820)|neurotransmitter transport (GO:0006836)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)|proline:sodium symporter activity (GO:0005298)			kidney(1)|large_intestine(18)|lung(15)|ovary(1)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	44						GAAGCATTTTTCACCAAAGGA	0.358																																					p.K186E		Atlas-SNP	.											.	SLC6A15	159	.	0			c.A556G						.						79	79	79					12																	85279232		2203	4300	6503	SO:0001583	missense	55117	exon4			CATTTTTCACCAA	AF265577	CCDS9026.1, CCDS9027.1, CCDS53816.1	12q21.31	2013-07-15	2008-09-02		ENSG00000072041	ENSG00000072041		"Solute carriers"	13621	protein-coding gene	gene with protein product	"homolog of rat orphan transporter v7-3", "sodium/chloride dependent neurotransmitter transporter Homo sapiens orphan neurotransmitter transporter NTT7"	607971	"solute carrier family 6 (neurotransmitter transporter), member 15"			10471414, 11112352, 16185194	Standard	NM_182767		Approved	hv7-3, NTT73, FLJ10316, V7-3, SBAT1	uc001szv.4	Q9H2J7	OTTHUMG00000169742	ENST00000266682.5:c.556A>G	chr12.hg19:g.85279232T>C	ENSP00000266682:p.Lys186Glu	234.0	0.0		214.0	86.0	NM_018057	A8K592|B7Z2P7|E7ESJ5|Q9H9F5	Missense_Mutation	SNP	ENST00000266682.5	hg19	CCDS9026.1	.	.	.	.	.	.	.	.	.	.	T	14.99	2.700914	0.48307	.	.	ENSG00000072041	ENST00000266682;ENST00000552192;ENST00000450363	T;T;T	0.74106	-0.81;-0.81;-0.81	5.02	5.02	0.67125	.	0.340418	0.28865	N	0.013897	T	0.70605	0.3243	L	0.36672	1.1	0.58432	D	0.999994	B;P	0.41188	0.051;0.741	B;P	0.45712	0.063;0.491	T	0.68424	-0.5412	10	0.27785	T	0.31	.	15.0856	0.72148	0.0:0.0:0.0:1.0	.	186;186	Q9H9F5;Q9H2J7	.;S6A15_HUMAN	E	186;79;186	ENSP00000266682:K186E;ENSP00000450145:K79E;ENSP00000390706:K186E	ENSP00000266682:K186E	K	-	1	0	SLC6A15	83803363	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.649000	0.83500	2.036000	0.60181	0.477000	0.44152	AAA	.	.		0.358	SLC6A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405678.1	NM_018057, NM_182767		C	85279232	T	C	85279232	3	2	348	1	0	0	0	0	1	0	0	0	14693	1792	62	2	1786	2	SLC6A15	12	85279232	Missense_Mutation	SNP	T	TCGA-UB-A7MF-01A-11D-A33K-10	30911656	85279232	48572663	59	49107										
TBX3	6926	hgsc.bcm.edu	37	chr12	115109981	115109981	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	gcgcagccgcgggcgcatggTgttcagattgaggaaggggt	19	8	1	2			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr12:115109981T>A	ENST00000257566.3	-	8	2286	c.1897A>T	c.(1897-1899)Acc>Tcc	p.T633S	TBX3_ENST00000349155.2_Missense_Mutation_p.T613S	NM_016569.3	NP_057653.3	O15119	TBX3_HUMAN	T-box 3	633	Transcription repression.				anterior/posterior axis specification, embryo (GO:0008595)|atrioventricular bundle cell differentiation (GO:0003167)|blood vessel development (GO:0001568)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cardiac muscle cell fate commitment (GO:0060923)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|female genitalia development (GO:0030540)|follicle-stimulating hormone secretion (GO:0046884)|forelimb morphogenesis (GO:0035136)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|limbic system development (GO:0021761)|luteinizing hormone secretion (GO:0032275)|male genitalia development (GO:0030539)|mammary gland development (GO:0030879)|mammary placode formation (GO:0060596)|mesoderm morphogenesis (GO:0048332)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sinoatrial node cell development (GO:0060931)|skeletal system development (GO:0001501)|specification of organ position (GO:0010159)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum morphogenesis (GO:0060412)	nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			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)		GGGCGCATGGTGTTCAGATTG	0.706																																					p.T633S		Atlas-SNP	.											.	TBX3	106	.	0			c.A1897T						.						10	9	9					12																	115109981		2162	4243	6405	SO:0001583	missense	6926	exon8			GCATGGTGTTCAG	BC025258	CCDS9175.1, CCDS9176.1	12q24.21	2013-09-05	2008-07-31		ENSG00000135111	ENSG00000135111		"T-boxes"	11602	protein-coding gene	gene with protein product		601621	"ulnar mammary syndrome"	UMS		8988164	Standard	NM_005996		Approved	TBX3-ISO, XHL	uc001tvt.1	O15119	OTTHUMG00000169586	ENST00000257566.3:c.1897A>T	chr12.hg19:g.115109981T>A	ENSP00000257566:p.Thr633Ser	49.0	0.0		46.0	26.0	NM_016569	Q8TB20|Q9UKF8	Missense_Mutation	SNP	ENST00000257566.3	hg19	CCDS9176.1	.	.	.	.	.	.	.	.	.	.	T	2.019	-0.425280	0.04701	.	.	ENSG00000135111	ENST00000349155;ENST00000257566;ENST00000361100	D;D	0.83591	-1.74;-1.7	3.08	1.86	0.25419	.	3.810000	0.00397	N	0.000046	T	0.56659	0.2000	N	0.01352	-0.895	0.20563	N	0.999882	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.62756	-0.6787	10	0.02654	T	1	.	5.2988	0.15766	0.2551:0.0:0.0:0.7449	.	613;633	O15119-2;O15119	.;TBX3_HUMAN	S	613;633;507	ENSP00000257567:T613S;ENSP00000257566:T633S	ENSP00000257566:T633S	T	-	1	0	TBX3	113594364	0.995000	0.38212	0.940000	0.37924	0.998000	0.95712	0.445000	0.21677	0.530000	0.28619	0.533000	0.62120	ACC	.	.		0.706	TBX3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404947.2	NM_016569, NM_005996		A	115109981	T	A	115109981	3	1	348	1	0	0	0	0	1	0	0	0	15674	1696	59	4	338	4	TBX3	12	115109981	Missense_Mutation	SNP	T	TCGA-UB-A7MF-01A-11D-A33K-10	29830749	115109981	18741914	60	49108										
EFHA1	221154	hgsc.bcm.edu	37	chr13	22077105	22077105	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	ctctcacatttttccaataaAtatctttattttcagtgtta	2	8	3	0			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr13:22077105A>G	ENST00000382374.4	-	9	958	c.893T>C	c.(892-894)aTt>aCt	p.I298T	MICU2_ENST00000479790.1_5'UTR	NM_152726.2	NP_689939.1	Q8IYU8	MICU2_HUMAN	mitochondrial calcium uptake 2	298	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				mitochondrial calcium ion transport (GO:0006851)|negative regulation of mitochondrial calcium ion concentration (GO:0051562)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)	calcium channel complex (GO:0034704)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|uniplex complex (GO:1990246)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)										TTTCCAATAAATATCTTTATT	0.318																																					p.I298T		Atlas-SNP	.											.	EFHA1	33	.	0			c.T893C						.						52	55	54					13																	22077105		2203	4294	6497	SO:0001583	missense	221154	exon9			CAATAAATATCTT	AK091907	CCDS9297.1	13q12.11	2013-03-13	2013-03-13	2013-03-13	ENSG00000165487	ENSG00000165487		"EF-hand domain containing"	31830	protein-coding gene	gene with protein product		610632	"EF hand domain family A1", "EF-hand domain family, member A1"	EFHA1		23409044	Standard	NM_152726		Approved		uc001uof.3	Q8IYU8	OTTHUMG00000067414	ENST00000382374.4:c.893T>C	chr13.hg19:g.22077105A>G	ENSP00000371811:p.Ile298Thr	84.0	0.0		62.0	40.0	NM_152726	Q8N0T6|Q8NAX8	Missense_Mutation	SNP	ENST00000382374.4	hg19	CCDS9297.1	.	.	.	.	.	.	.	.	.	.	A	8.365	0.834027	0.16820	.	.	ENSG00000165487	ENST00000382374	T	0.59772	0.24	5.88	5.88	0.94601	.	0.422460	0.28198	N	0.016227	T	0.47097	0.1427	L	0.47716	1.5	0.39831	D	0.972978	B	0.31125	0.309	B	0.19666	0.026	T	0.47636	-0.9102	10	0.09084	T	0.74	-25.923	16.2744	0.82636	1.0:0.0:0.0:0.0	.	298	Q8IYU8	EFHA1_HUMAN	T	298	ENSP00000371811:I298T	ENSP00000371811:I298T	I	-	2	0	EFHA1	20975105	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	3.166000	0.50785	2.237000	0.73441	0.482000	0.46254	ATT	.	.		0.318	MICU2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144355.1	NM_152726		G	22077105	A	G	22077105	3	3	348	1	0	0	0	0	1	0	0	0	4945	101	4	2	427	2	EFHA1	13	22077105	Missense_Mutation	SNP	A	TCGA-UB-A7MF-01A-11D-A33K-10		22077105	93092773	61	49109										
NBEA	26960	hgsc.bcm.edu	37	chr13	36202217	36202217	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	ttctttcttgactcatttcaGgccctagaaagtgaatttgt	7	8	4	3			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr13:36202217G>T	ENST00000400445.3	+	49	7983		c.e49-1		NBEA_ENST00000310336.4_Splice_Site|NBEA_ENST00000379922.3_Splice_Site|NBEA_ENST00000540320.1_Splice_Site|NBEA_ENST00000379939.2_Splice_Site|NBEA_ENST00000537702.1_Splice_Site	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin						protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		ACTCATTTCAGGCCCTAGAAA	0.353																																					.		Atlas-SNP	.											.	NBEA	340	.	0			c.7450-1G>T						.						78	71	73					13																	36202217		1871	4114	5985	SO:0001630	splice_region_variant	26960	exon49			ATTTCAGGCCCTA	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.7450-1G>T	chr13.hg19:g.36202217G>T		113.0	0.0		57.0	18.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Splice_Site	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	G	16.66	3.185898	0.57909	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336;ENST00000422518;ENST00000402346;ENST00000543274;ENST00000537702;ENST00000379922	.	.	.	5.6	5.6	0.85130	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.6287	0.95691	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NBEA	35100217	1.000000	0.71417	1.000000	0.80357	0.476000	0.33039	9.722000	0.98770	2.652000	0.90054	0.563000	0.77884	.	.	.		0.353	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678	Intron	T	36202217	G	T	36202217	5	4	348	1	0	0	0	0	0	0	1	0	10196	1014	35	3	7643	3	NBEA	13	36202217	Splice_Site	SNP	G	TCGA-UB-A7MF-01A-11D-A33K-10	14125112	36202217	78967661	62	49110										
GPC6	10082	hgsc.bcm.edu	37	chr13	94680117	94680117	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	ggctgcttggcaaatcaggcTgacctcgacacagagtggaa	13	10	1	2			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr13:94680117T>C	ENST00000377047.4	+	4	1461	c.846T>C	c.(844-846)gcT>gcC	p.A282A	RNA5SP35_ENST00000391257.1_RNA	NM_005708.3	NP_005699.1	Q9Y625	GPC6_HUMAN	glypican 6	282					carbohydrate metabolic process (GO:0005975)|cell migration (GO:0016477)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	38	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				CAAATCAGGCTGACCTCGACA	0.502																																					p.A282A		Atlas-SNP	.											.	GPC6	102	.	0			c.T846C						.						137	124	129					13																	94680117		2203	4300	6503	SO:0001819	synonymous_variant	10082	exon4			TCAGGCTGACCTC	AF111178	CCDS9469.1	13q32	2008-02-05			ENSG00000183098	ENSG00000183098		"Proteoglycans / Cell Surface : Glypicans"	4454	protein-coding gene	gene with protein product	"glypican proteoglycan 6"	604404				10329016	Standard	NM_005708		Approved		uc001vlt.3	Q9Y625	OTTHUMG00000017205	ENST00000377047.4:c.846T>C	chr13.hg19:g.94680117T>C		85.0	0.0		178.0	12.0	NM_005708	A8K279|Q96SG5|Q96SG8|Q9H1P4	Silent	SNP	ENST00000377047.4	hg19	CCDS9469.1																																																																																			.	.		0.502	GPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045460.4	NM_005708		C	94680117	T	C	94680117	2	2	348	1	0	0	0	0	0	0	0	1	6610	1567	55	2		2	GPC6	13	94680117	Silent	SNP	T	TCGA-UB-A7MF-01A-11D-A33K-10	58477900	94680117	20489761	63	49111										
TPP2	7174	hgsc.bcm.edu	37	chr13	103328668	103328668	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	tttgacatttgcatataaacAtgcattagtaaataaaatgt	5	4	0	1			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr13:103328668A>T	ENST00000376065.4	+	28	3599	c.3563A>T	c.(3562-3564)cAt>cTt	p.H1188L	TPP2_ENST00000376052.3_Missense_Mutation_p.H1201L|TPP2_ENST00000466153.1_3'UTR	NM_003291.2	NP_003282.2	P29144	TPP2_HUMAN	tripeptidyl peptidase II	1188					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)|tripeptidyl-peptidase activity (GO:0008240)			breast(2)|endometrium(5)|kidney(2)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	52	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					GCATATAAACATGCATTAGTA	0.264																																					p.H1188L		Atlas-SNP	.											.	TPP2	124	.	0			c.A3563T						.						53	51	52					13																	103328668		2197	4290	6487	SO:0001583	missense	7174	exon28			ATAAACATGCATT	M55169	CCDS9502.1	13q32-q33	2008-02-05			ENSG00000134900	ENSG00000134900	3.4.14.10		12016	protein-coding gene	gene with protein product		190470				1670990	Standard	NM_003291		Approved		uc001vpi.4	P29144	OTTHUMG00000017305	ENST00000376065.4:c.3563A>T	chr13.hg19:g.103328668A>T	ENSP00000365233:p.His1188Leu	312.0	0.0		673.0	451.0	NM_003291	Q5VZU8	Missense_Mutation	SNP	ENST00000376065.4	hg19	CCDS9502.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.577770	0.86645	.	.	ENSG00000134900	ENST00000376065;ENST00000376052	.	.	.	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.74245	0.3691	L	0.46157	1.445	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.75311	-0.3362	9	0.54805	T	0.06	.	16.146	0.81569	1.0:0.0:0.0:0.0	.	1188	P29144	TPP2_HUMAN	L	1188;1201	.	ENSP00000365220:H1201L	H	+	2	0	TPP2	102126669	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	8.572000	0.90756	2.216000	0.71823	0.460000	0.39030	CAT	.	.		0.264	TPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045683.2			T	103328668	A	T	103328668	3	4	348	1	0	0	0	0	1	0	0	0	16427	217	8	4	3673	4	TPP2	13	103328668	Missense_Mutation	SNP	A	TCGA-UB-A7MF-01A-11D-A33K-10	8648551	103328668	11841210	64	49112										
MCF2L	23263	hgsc.bcm.edu	37	chr13	113750685	113750685	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	ccctgcccgtctcccaccagGttccaggtaaatacacggtc	8	17	1	0			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr13:113750685G>A	ENST00000375608.3	+	29	3224	c.3166G>A	c.(3166-3168)Gtt>Att	p.V1056I	MCF2L_ENST00000397030.1_Splice_Site_p.V1059I|MCF2L_ENST00000535094.2_Splice_Site_p.V1026I|MCF2L_ENST00000375604.2_Splice_Site_p.V1083I|MCF2L_ENST00000434480.2_Splice_Site_p.V1032I|MCF2L_ENST00000442652.2_Splice_Site_p.V1056I|MCF2L_ENST00000421756.1_Splice_Site_p.V1030I|MCF2L_ENST00000423482.2_Splice_Site_p.V1024I|MCF2L_ENST00000375601.3_Splice_Site_p.V1030I			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	1056	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular space (GO:0005615)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			kidney(1)|large_intestine(5)|ovary(1)|stomach(1)	8	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)				CTCCCACCAGGTTCCAGGTAA	0.716																																					p.V1026I		Atlas-SNP	.											.	MCF2L	182	.	0			c.G3076A						.						19	24	23					13																	113750685		1551	3557	5108	SO:0001630	splice_region_variant	23263	exon28			CACCAGGTTCCAG	AB002360	CCDS9527.2, CCDS45070.1, CCDS9527.3, CCDS45070.2	13q34	2013-01-10			ENSG00000126217	ENSG00000126217		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	14576	protein-coding gene	gene with protein product		609499				9205841	Standard	NM_001112732		Approved	KIAA0362, DBS, OST, ARHGEF14	uc010tjr.2	O15068	OTTHUMG00000017377	ENST00000375608.3:c.3166-1G>A	chr13.hg19:g.113750685G>A		107.0	0.0		190.0	18.0	NM_001112732	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Missense_Mutation	SNP	ENST00000375608.3	hg19		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	15.87|15.87|15.87	2.959717|2.959717|2.959717	0.53400|0.53400|0.53400	.|.|.	.|.|.	ENSG00000126217|ENSG00000126217|ENSG00000126217	ENST00000397017;ENST00000453297|ENST00000375608;ENST00000442652;ENST00000375604;ENST00000397030;ENST00000535094;ENST00000421756;ENST00000375601;ENST00000434480;ENST00000423482;ENST00000440749|ENST00000413354;ENST00000261963;ENST00000420013	.|T;T;T;T;T;T;T;T;T|.	.|0.37915|.	.|1.24;1.24;1.17;1.29;1.19;1.29;1.18;1.24;1.19|.	5.01|5.01|5.01	5.01|5.01|5.01	0.66863|0.66863|0.66863	.|Src homology-3 domain (1);|.	.|0.403683|.	.|0.26812|.	.|N|.	.|0.022378|.	T|T|.	0.55816|0.55816|.	0.1944|0.1944|.	M|M|M	0.75264|0.75264|0.75264	2.295|2.295|2.295	0.28288|0.28288|0.28288	N|N|N	0.923699|0.923699|0.923699	.|B;B;B;B|.	.|0.31705|.	.|0.336;0.336;0.336;0.227|.	.|B;B;B;B|.	.|0.38225|.	.|0.205;0.138;0.268;0.065|.	T|T|.	0.56195|0.56195|.	-0.8019|-0.8019|.	5|10|.	.|0.31617|.	.|T|.	.|0.26|.	.|.|.	7.3465|7.3465|7.3465	0.26666|0.26666|0.26666	0.1886:0.0:0.8114:0.0|0.1886:0.0:0.8114:0.0|0.1886:0.0:0.8114:0.0	.|.|.	.|1024;1026;1083;1056|.	.|E9PDN8;O15068-9;G5E9A1;O15068|.	.|.;.;.;MCF2L_HUMAN|.	D|I|X	711;236|1056;1056;1083;1059;1026;1030;1030;1032;1024;867|308;196;97	.|ENSP00000364758:V1056I;ENSP00000401422:V1056I;ENSP00000364754:V1083I;ENSP00000380225:V1059I;ENSP00000440374:V1026I;ENSP00000397285:V1030I;ENSP00000364751:V1030I;ENSP00000407722:V1032I;ENSP00000405639:V1024I|.	.|ENSP00000364751:V1030I|.	G|V|W	+|+|+	2|1|3	0|0|0	MCF2L|MCF2L|MCF2L	112798686|112798686|112798686	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.552000|0.552000|0.552000	0.28243|0.28243|0.28243	0.045000|0.045000|0.045000	0.14185|0.14185|0.14185	1.564000|1.564000|1.564000	0.36375|0.36375|0.36375	2.330000|2.330000|2.330000	0.79161|0.79161|0.79161	0.563000|0.563000|0.563000	0.77884|0.77884|0.77884	GGT|GTT|TGG	.	.		0.716	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4		Missense_Mutation	A	113750685	G	A	113750685	5	1	348	1	0	0	0	0	0	0	1	0	9388	1275	44	3	3452	3	MCF2L	13	113750685	Splice_Site	SNP	G	TCGA-UB-A7MF-01A-11D-A33K-10	10422017	113750685	1419193	65	49113										
MYH7	4625	hgsc.bcm.edu	37	chr14	23894029	23894029	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	tcctgcagcagggacaccatCttctcctccagctccttgcg	8	17	2	0			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr14:23894029C>G	ENST00000355349.3	-	22	2790	c.2628G>C	c.(2626-2628)aaG>aaC	p.K876N		NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	876					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		GGGACACCATCTTCTCCTCCA	0.587																																					p.K876N		Atlas-SNP	.											.	MYH7	349	.	0			c.G2628C						.						89	76	80					14																	23894029		2203	4300	6503	SO:0001583	missense	4625	exon22			CACCATCTTCTCC	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.2628G>C	chr14.hg19:g.23894029C>G	ENSP00000347507:p.Lys876Asn	73.0	0.0		79.0	19.0	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Missense_Mutation	SNP	ENST00000355349.3	hg19	CCDS9601.1	.	.	.	.	.	.	.	.	.	.	C	19.10	3.762397	0.69763	.	.	ENSG00000092054	ENST00000355349;ENST00000544444	D	0.94576	-3.46	4.73	4.73	0.59995	.	.	.	.	.	D	0.97362	0.9137	M	0.89414	3.03	0.58432	D	0.999991	D	0.76494	0.999	D	0.87578	0.998	D	0.97504	1.0062	9	0.62326	D	0.03	.	13.6731	0.62438	0.0:0.9226:0.0:0.0774	.	876	P12883	MYH7_HUMAN	N	876	ENSP00000347507:K876N	ENSP00000347507:K876N	K	-	3	2	MYH7	22963869	0.999000	0.42202	1.000000	0.80357	0.986000	0.74619	0.609000	0.24238	2.612000	0.88384	0.655000	0.94253	AAG	.	.		0.587	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257		G	23894029	C	G	23894029	3	3	348	1	0	0	0	0	1	0	0	0	10048	912	32	4	3255	4	MYH7	14	23894029	Missense_Mutation	SNP	C	TCGA-UB-A7MF-01A-11D-A33K-10		23894029	83455511	66	49114										
SH3GL3	6457	hgsc.bcm.edu	37	chr15	84241337	84241337	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	gcaatgcattgatagaagttGgtgaatccatgaagctaatg	11	5	0	4			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr15:84241337G>C	ENST00000427482.2	+	5	658	c.352G>C	c.(352-354)Ggt>Cgt	p.G118R	SH3GL3_ENST00000535412.1_Missense_Mutation_p.G118R|SH3GL3_ENST00000324537.5_Missense_Mutation_p.G126R|SH3GL3_ENST00000434347.1_Missense_Mutation_p.G126R	NM_003027.3	NP_003018.3	Q99963	SH3G3_HUMAN	SH3-domain GRB2-like 3	118	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				central nervous system development (GO:0007417)|endocytosis (GO:0006897)|signal transduction (GO:0007165)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)			central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	30						GATAGAAGTTGGTGAATCCAT	0.328																																					p.G118R		Atlas-SNP	.											.	SH3GL3	91	.	0			c.G352C						.						116	104	108					15																	84241337		2203	4300	6503	SO:0001583	missense	6457	exon5			GAAGTTGGTGAAT	AF036271	CCDS10325.2, CCDS73772.1	15q24	2006-11-24			ENSG00000140600	ENSG00000140600			10832	protein-coding gene	gene with protein product		603362				9169142	Standard	NR_026799		Approved	SH3D2C, SH3P13, CNSA3, EEN-B2, HsT19371	uc002bjw.3	Q99963	OTTHUMG00000147361	ENST00000427482.2:c.352G>C	chr15.hg19:g.84241337G>C	ENSP00000391372:p.Gly118Arg	74.0	0.0		77.0	24.0	NM_003027	O43553|O43554	Missense_Mutation	SNP	ENST00000427482.2	hg19	CCDS10325.2	.	.	.	.	.	.	.	.	.	.	G	35	5.542607	0.96474	.	.	ENSG00000140600	ENST00000427482;ENST00000535412;ENST00000324537;ENST00000434347	T;T;T;T	0.49720	0.77;0.77;0.77;0.77	5.13	5.13	0.70059	BAR (3);	0.051959	0.85682	D	0.000000	T	0.75309	0.3832	M	0.90595	3.13	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.997	T	0.81172	-0.1054	10	0.87932	D	0	-9.1028	17.9227	0.88972	0.0:0.0:1.0:0.0	.	118;118;126	Q8IVP1;Q99963;Q99963-3	.;SH3G3_HUMAN;.	R	118;118;126;126	ENSP00000391372:G118R;ENSP00000439239:G118R;ENSP00000320092:G126R;ENSP00000397871:G126R	ENSP00000320092:G126R	G	+	1	0	SH3GL3	82032341	1.000000	0.71417	0.755000	0.31263	0.991000	0.79684	7.374000	0.79633	2.550000	0.86006	0.585000	0.79938	GGT	.	.		0.328	SH3GL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347797.1	NM_003027		C	84241337	G	C	84241337	3	2	348	1	0	0	0	0	1	0	0	0	14267	1348	47	4	370	4	SH3GL3	15	84241337	Missense_Mutation	SNP	G	TCGA-UB-A7MF-01A-11D-A33K-10		84241337	18290055	67	49115										
CACNA1H	8912	hgsc.bcm.edu	37	chr16	1260417	1260417	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	cacacacaagatgtttgatcAcgtggtcctcgtcttcatct	7	12	4	2			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr16:1260417A>G	ENST00000348261.5	+	19	4141	c.3893A>G	c.(3892-3894)cAc>cGc	p.H1298R	CACNA1H_ENST00000565831.1_Missense_Mutation_p.H1298R|CACNA1H_ENST00000358590.4_Missense_Mutation_p.H1298R	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	1298					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	ATGTTTGATCACGTGGTCCTC	0.632																																					p.H1298R		Atlas-SNP	.											.	CACNA1H	317	.	0			c.A3893G						.						39	39	39					16																	1260417		2169	4250	6419	SO:0001583	missense	8912	exon19			TTGATCACGTGGT	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.3893A>G	chr16.hg19:g.1260417A>G	ENSP00000334198:p.His1298Arg	90.0	0.0		54.0	23.0	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	hg19	CCDS45375.1	.	.	.	.	.	.	.	.	.	.	A	16.67	3.186414	0.57909	.	.	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.97232	-4.3;-4.3	3.77	3.77	0.43336	.	0.000000	0.85682	D	0.000000	D	0.97216	0.9090	L	0.60455	1.87	0.42043	D	0.991084	P;P;P;B;D	0.62365	0.932;0.653;0.677;0.338;0.991	P;B;B;B;P	0.61397	0.888;0.414;0.097;0.132;0.874	D	0.97145	0.9827	10	0.54805	T	0.06	.	12.0946	0.53747	1.0:0.0:0.0:0.0	.	39;39;39;1298;1298	A2SX38;A2SX35;A2SX37;O95180-2;O95180	.;.;.;.;CAC1H_HUMAN	R	1298	ENSP00000334198:H1298R;ENSP00000351401:H1298R	ENSP00000334198:H1298R	H	+	2	0	CACNA1H	1200418	1.000000	0.71417	0.998000	0.56505	0.952000	0.60782	7.101000	0.76997	1.704000	0.51252	0.443000	0.29094	CAC	.	.		0.632	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407		G	1260417	A	G	1260417	3	3	348	1	0	0	0	0	1	0	0	0	2547	159	6	2	3963	2	CACNA1H	16	1260417	Missense_Mutation	SNP	A	TCGA-UB-A7MF-01A-11D-A33K-10		1260417	89094336	68	49116										
MLST8	64223	hgsc.bcm.edu	37	chr16	2257035	2257035	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	gtgccccggcccggcccgcaGgtcccggaacctgcagtgcc	14	19	0	0			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr16:2257035G>C	ENST00000569417.1	+	5	698		c.e5-1		MLST8_ENST00000561651.1_Splice_Site|MLST8_ENST00000382450.4_Splice_Site|AC009065.3_ENST00000517149.1_RNA|MLST8_ENST00000301725.7_Splice_Site|MLST8_ENST00000397124.1_Splice_Site|MLST8_ENST00000565250.1_Splice_Site|MLST8_ENST00000301724.10_Splice_Site|MLST8_ENST00000564088.1_Splice_Site	NM_022372.4	NP_071767.3	Q9BVC4	LST8_HUMAN	MTOR associated protein, LST8 homolog (S. cerevisiae)						epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of TOR signaling (GO:0032008)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of Rac GTPase activity (GO:0032314)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|cytosol (GO:0005829)				large_intestine(3)|lung(2)|skin(1)	6						CCGGCCCGCAGGTCCCGGAAC	0.662																																					.		Atlas-SNP	.											.	MLST8	60	.	0			c.345-1G>C						.						43	48	46					16																	2257035		1948	4130	6078	SO:0001630	splice_region_variant	64223	exon5			CCCGCAGGTCCCG		CCDS10462.2, CCDS58409.1	16p13.3	2013-01-09			ENSG00000167965	ENSG00000167965		"WD repeat domain containing"	24825	protein-coding gene	gene with protein product	"G protein beta subunit like"	612190				12477932	Standard	NM_022372		Approved	Lst8, Pop3, GBL, GbetaL	uc002cpc.3	Q9BVC4	OTTHUMG00000128827	ENST00000569417.1:c.345-1G>C	chr16.hg19:g.2257035G>C		189.0	0.0		152.0	34.0	NM_022372	B3KMM4|B4DY00|D3DU88|Q5M800|Q86Y18|Q8WUI5|Q9HA66|Q9UJV6	Splice_Site	SNP	ENST00000569417.1	hg19	CCDS10462.2	.	.	.	.	.	.	.	.	.	.	G	17.34	3.365872	0.61513	.	.	ENSG00000167965	ENST00000382450;ENST00000301724;ENST00000397124;ENST00000301725	.	.	.	4.81	4.81	0.61882	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.4217	0.83760	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MLST8	2197036	1.000000	0.71417	0.994000	0.49952	0.577000	0.36160	9.774000	0.98992	2.205000	0.71048	0.462000	0.41574	.	.	.		0.662	MLST8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250763.2	NM_022372	Intron	C	2257035	G	C	2257035	5	2	348	1	0	0	0	0	0	0	1	0	9643	1014	35	4	358	4	MLST8	16	2257035	Splice_Site	SNP	G	TCGA-UB-A7MF-01A-11D-A33K-10	996618	2257035	88097718	69	49117										
CES3	23491	hgsc.bcm.edu	37	chr16	67006828	67006828	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	acaatatctggagatcaaccCagtgccacgggccggacaga	11	12	2	2			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr16:67006828C>A	ENST00000303334.4	+	13	1663	c.1592C>A	c.(1591-1593)cCa>cAa	p.P531Q	CES3_ENST00000543856.1_Missense_Mutation_p.P170Q|CES3_ENST00000394037.1_Missense_Mutation_p.P528Q	NM_024922.5	NP_079198.2	Q6UWW8	EST3_HUMAN	carboxylesterase 3	531						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	carboxylic ester hydrolase activity (GO:0052689)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|ovary(3)|skin(1)	24		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0488)|Epithelial(162;0.127)		GAGATCAACCCAGTGCCACGG	0.567																																					p.P531Q		Atlas-SNP	.											.	CES3	56	.	0			c.C1592A						.						92	93	93					16																	67006828		2200	4300	6500	SO:0001583	missense	23491	exon13			TCAACCCAGTGCC	AK025389	CCDS10826.1, CCDS54022.1, CCDS54023.1	16q22.1	2014-05-13	2008-07-25		ENSG00000172828	ENSG00000172828		"Carboxylesterases"	1865	protein-coding gene	gene with protein product	"esterase 31", "brain carboxylesterase BR3"	605279	"carboxylesterase 3 (brain)"			10518925, 14581373, 15100172, 20931200	Standard	NM_001185176		Approved	FLJ21736, ES31	uc002eqt.3	Q6UWW8	OTTHUMG00000137525	ENST00000303334.4:c.1592C>A	chr16.hg19:g.67006828C>A	ENSP00000304782:p.Pro531Gln	109.0	0.0		83.0	38.0	NM_024922	B2Z3W9|F5H242|Q7Z6J1|Q9H6X7	Missense_Mutation	SNP	ENST00000303334.4	hg19	CCDS10826.1	.	.	.	.	.	.	.	.	.	.	C	15.27	2.783561	0.49891	.	.	ENSG00000172828	ENST00000303334;ENST00000394037;ENST00000543856	T;T;T	0.66099	-0.19;-0.19;-0.19	5.03	1.58	0.23477	Carboxylesterase, type B (1);	1.045480	0.07705	N	0.941121	T	0.50394	0.1613	N	0.17838	0.53	0.09310	N	1	P;B	0.47106	0.89;0.014	P;B	0.45712	0.491;0.063	T	0.41556	-0.9502	10	0.62326	D	0.03	.	6.7176	0.23312	0.0:0.2981:0.0:0.7019	.	170;531	F5H242;Q6UWW8	.;EST3_HUMAN	Q	531;528;170	ENSP00000304782:P531Q;ENSP00000377602:P528Q;ENSP00000445559:P170Q	ENSP00000304782:P531Q	P	+	2	0	CES3	65564329	0.000000	0.05858	0.013000	0.15412	0.017000	0.09413	-0.831000	0.04405	0.275000	0.22094	-0.516000	0.04426	CCA	.	.		0.567	CES3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268848.1	NM_024922		A	67006828	C	A	67006828	3	1	348	1	0	0	0	0	1	0	0	0	3273	594	21	3	1642	3	CES3	16	67006828	Missense_Mutation	SNP	C	TCGA-UB-A7MF-01A-11D-A33K-10	64749793	67006828	23347925	70	49118										
ATP6V0D1	9114	hgsc.bcm.edu	37	chr16	67472440	67472440	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	gggccaggacgctagaagatAgggatgtagttgtcgatttt	15	5	0	2			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr16:67472440A>T	ENST00000290949.3	-	8	1197	c.1047T>A	c.(1045-1047)ccT>ccA	p.P349P	ATP6V0D1_ENST00000602876.1_Silent_p.P272P|ATP6V0D1_ENST00000567694.1_5'Flank|ATP6V0D1_ENST00000540149.1_Silent_p.P390P	NM_004691.4	NP_004682.2	P61421	VA0D1_HUMAN	ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d1	349					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP hydrolysis coupled proton transport (GO:0015991)|brain development (GO:0007420)|cellular iron ion homeostasis (GO:0006879)|cellular protein metabolic process (GO:0044267)|cilium assembly (GO:0042384)|endoplasmic reticulum unfolded protein response (GO:0030968)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|axon terminus (GO:0043679)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|proton-transporting V-type ATPase, V0 domain (GO:0033179)|synaptic vesicle (GO:0008021)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	hydrogen-exporting ATPase activity, phosphorylative mechanism (GO:0008553)			large_intestine(3)|lung(3)|urinary_tract(2)	8		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0439)|Epithelial(162;0.101)		GCTAGAAGATAGGGATGTAGT	0.542																																					p.P349P		Atlas-SNP	.											.	ATP6V0D1	25	.	0			c.T1047A						.						90	80	83					16																	67472440		2198	4300	6498	SO:0001819	synonymous_variant	9114	exon8			GAAGATAGGGATG	X71490	CCDS10838.1	16q22	2010-04-21	2006-01-20	2002-05-10	ENSG00000159720	ENSG00000159720		"ATPases / V-type"	13724	protein-coding gene	gene with protein product		607028	"ATPase, H+ transporting, lysosomal (vacuolar proton pump), member D", "ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d isoform 1", "ATPase, H+ transporting, lysosomal 38kDa, V0 subunit D1"	ATP6D		8250920	Standard	NM_004691		Approved	ATP6DV, VATX, VPATPD, P39, Vma6	uc002ete.1	P61421	OTTHUMG00000137515	ENST00000290949.3:c.1047T>A	chr16.hg19:g.67472440A>T		132.0	0.0		98.0	26.0	NM_004691	P12953|Q02547	Silent	SNP	ENST00000290949.3	hg19	CCDS10838.1																																																																																			.	.		0.542	ATP6V0D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268835.1	NM_004691		T	67472440	A	T	67472440	2	4	348	1	0	0	0	0	0	0	0	1	1173	407	15	4		4	ATP6V0D1	16	67472440	Silent	SNP	A	TCGA-UB-A7MF-01A-11D-A33K-10	465612	67472440	22882313	71	49119										
DPEP2	64174	hgsc.bcm.edu	37	chr16	68026979	68026979	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	tgtgggctctgggggcgcccAgcgtggtgagggctctgggg	22	9	2	1			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr16:68026979A>T	ENST00000572888.1	-	1	787	c.137T>A	c.(136-138)cTg>cAg	p.L46Q	DPEP2_ENST00000393847.1_Missense_Mutation_p.L46Q|DPEP2_ENST00000412757.2_Missense_Mutation_p.L46Q			Q9H4A9	DPEP2_HUMAN	dipeptidase 2	46					arachidonic acid metabolic process (GO:0019369)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	dipeptidase activity (GO:0016805)|dipeptidyl-peptidase activity (GO:0008239)|metal ion binding (GO:0046872)|metalloexopeptidase activity (GO:0008235)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)|skin(2)|upper_aerodigestive_tract(1)	17		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0489)|all cancers(182;0.239)		GGGGGCGCCCAGCGTGGTGAG	0.692																																					p.L46Q		Atlas-SNP	.											.	DPEP2	43	.	0			c.T137A						.						16	18	18					16																	68026979		2181	4287	6468	SO:0001583	missense	64174	exon2			GCGCCCAGCGTGG	AJ295149	CCDS10857.1	16q22.1	2011-07-22			ENSG00000167261	ENSG00000167261	3.4.13.19		23028	protein-coding gene	gene with protein product		609925					Standard	NM_022355		Approved		uc002eve.4	Q9H4A9	OTTHUMG00000137542	ENST00000572888.1:c.137T>A	chr16.hg19:g.68026979A>T	ENSP00000458977:p.Leu46Gln	65.0	0.0		59.0	22.0	NM_022355	B2RCF8|Q6UX92|Q8TC95	Missense_Mutation	SNP	ENST00000572888.1	hg19	CCDS10857.1	.	.	.	.	.	.	.	.	.	.	A	8.991	0.977816	0.18812	.	.	ENSG00000167261	ENST00000393847;ENST00000412757;ENST00000268795	T;T	0.18502	2.21;2.21	3.29	-6.58	0.01836	.	1.769450	0.03395	N	0.202482	T	0.09774	0.0240	L	0.34521	1.04	0.09310	N	0.999999	B;B	0.29432	0.048;0.244	B;B	0.21546	0.01;0.035	T	0.13495	-1.0507	10	0.34782	T	0.22	0.0754	2.5432	0.04730	0.5502:0.1335:0.1819:0.1344	.	46;46	B4DNP7;Q9H4A9	.;DPEP2_HUMAN	Q	46	ENSP00000377430:L46Q;ENSP00000412549:L46Q	ENSP00000268795:L46Q	L	-	2	0	DPEP2	66584480	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.447000	0.06828	-1.645000	0.01515	-0.451000	0.05528	CTG	.	.		0.692	DPEP2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437026.1	NM_022355		T	68026979	A	T	68026979	3	4	348	1	0	0	0	0	1	0	0	0	4716	188	7	4	1363	4	DPEP2	16	68026979	Missense_Mutation	SNP	A	TCGA-UB-A7MF-01A-11D-A33K-10	554539	68026979	22327774	72	49120										
NFAT5	10725	hgsc.bcm.edu	37	chr16	69726159	69726159	+	Frame_Shift_Del	DEL	G	G	-													0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	gtactgctagtggcagcagtGgaagtgttgacttggtccaa							TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr16:69726159delG	ENST00000354436.2	+	12	2695	c.2377delG	c.(2377-2379)ggafs	p.G793fs	NFAT5_ENST00000432919.1_Frame_Shift_Del_p.G811fs|NFAT5_ENST00000566899.1_Frame_Shift_Del_p.G717fs|NFAT5_ENST00000567239.1_Frame_Shift_Del_p.G810fs|NFAT5_ENST00000393742.2_Frame_Shift_Del_p.G717fs|NFAT5_ENST00000349945.1_Frame_Shift_Del_p.G717fs	NM_006599.3	NP_006590.1	O94916	NFAT5_HUMAN	nuclear factor of activated T-cells 5, tonicity-responsive	793					cytokine production (GO:0001816)|excretion (GO:0007588)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of calcineurin-NFAT signaling cascade (GO:0070884)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						TGGCAGCAGTGGAAGTGTTGA	0.428																																					p.S810fs		Atlas-Indel,Pindel	.											.	NFAT5	184	.	0			c.2430delT						.						89	86	87					16																	69726159		2198	4300	6498	SO:0001589	frameshift_variant	10725	exon13			.	AF134870	CCDS10881.1, CCDS10882.1, CCDS45519.1	16q22.1	2009-11-24			ENSG00000102908	ENSG00000102908		"Nuclear factor of activated T-cells"	7774	protein-coding gene	gene with protein product		604708				10377394	Standard	NM_173214		Approved	TONEBP, KIAA0827, NFATL1, OREBP, NFATZ, NF-AT5	uc002exl.2	O94916	OTTHUMG00000137572	ENST00000354436.2:c.2377delG	chr16.hg19:g.69726159delG	ENSP00000346420:p.Gly793fs	65.0	0.0		68.0	17.0	NM_138713	A2RRB4|A6H8V5|E9PHR7|O95693|Q7LA65|Q969Q8|Q96QH3|Q9UN18	Frame_Shift_Del	DEL	ENST00000354436.2	hg19	CCDS10881.1																																																																																			.	.		0.428	NFAT5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268952.2	NM_138714		-	69726159	G	-	69726159	7	5	348	1	0	1	0	1	0	0	0	0	10369	1349	47	0	2481	0	NFAT5	16	69726159	Frame_Shift_Del	DEL	G	TCGA-UB-A7MF-01A-11D-A33K-10	1699180	69726159	20628594	73	49121										
VAC14	55697	hgsc.bcm.edu	37	chr16	70820268	70820268	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	gccacgaactcccggaccagCctggagagagaggagagagg	16	11	0	3			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr16:70820268C>A	ENST00000261776.5	-	2	365	c.105G>T	c.(103-105)aaG>aaT	p.K35N		NM_018052.3	NP_060522.3	Q08AM6	VAC14_HUMAN	Vac14 homolog (S. cerevisiae)	35					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of lipid kinase activity (GO:0043550)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|PAS complex (GO:0070772)	receptor activity (GO:0004872)			breast(2)|endometrium(2)|kidney(10)|large_intestine(1)|lung(10)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	33		Ovarian(137;0.0699)				CCCGGACCAGCCTGGAGAGAG	0.602																																					p.K35N		Atlas-SNP	.											.	VAC14	65	.	0			c.G105T						.						66	66	66					16																	70820268		2198	4300	6498	SO:0001630	splice_region_variant	55697	exon2			GACCAGCCTGGAG	AK056433	CCDS10896.1	16q22.1	2010-03-23	2005-02-09		ENSG00000103043	ENSG00000103043			25507	protein-coding gene	gene with protein product		604632	"Tax1 (human T-cell leukemia virus type I) binding protein 2"	TAX1BP2		15542851, 12719380	Standard	NM_018052		Approved	FLJ10305, ArPIKfyve	uc002ezm.3	Q08AM6	OTTHUMG00000137583	ENST00000261776.5:c.105-1G>T	chr16.hg19:g.70820268C>A		66.0	0.0		58.0	31.0	NM_018052	B3KPJ5|B3KSM8|Q13174|Q6IA12|Q7L4Y1|Q9BW96|Q9H6V6	Missense_Mutation	SNP	ENST00000261776.5	hg19	CCDS10896.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.531711	0.85706	.	.	ENSG00000103043	ENST00000261776	T	0.68025	-0.3	5.49	5.49	0.81192	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.80287	0.4595	M	0.70595	2.14	0.80722	D	1	D	0.58620	0.983	P	0.61275	0.886	T	0.80464	-0.1371	10	0.51188	T	0.08	.	19.3733	0.94498	0.0:1.0:0.0:0.0	.	35	Q08AM6	VAC14_HUMAN	N	35	ENSP00000261776:K35N	ENSP00000261776:K35N	K	-	3	2	VAC14	69377769	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	5.338000	0.65947	2.579000	0.87056	0.650000	0.86243	AAG	.	.		0.602	VAC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268973.3	NM_018052	Missense_Mutation	A	70820268	C	A	70820268	5	1	348	1	0	0	0	0	0	0	1	0	17126	753	26	3	2315	3	VAC14	16	70820268	Splice_Site	SNP	C	TCGA-UB-A7MF-01A-11D-A33K-10	1094109	70820268	19534485	74	49122										
PLCG2	5336	hgsc.bcm.edu	37	chr16	81922840	81922840	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	caaagttcattgatgacaccAtgcgtgaaactgctgagcct	9	10	1	4	rs372494175		TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr16:81922840A>T	ENST00000359376.3	+	10	1043	c.829A>T	c.(829-831)Atg>Ttg	p.M277L		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	277					B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						TGATGACACCATGCGTGAAAC	0.468																																					p.M277L		Atlas-SNP	.											.	PLCG2	276	.	0			c.A829T						.						190	182	185					16																	81922840		2037	4194	6231	SO:0001583	missense	5336	exon10			GACACCATGCGTG		CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"SH2 domain containing"	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.829A>T	chr16.hg19:g.81922840A>T	ENSP00000352336:p.Met277Leu	105.0	0.0		107.0	23.0	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Missense_Mutation	SNP	ENST00000359376.3	hg19	CCDS42204.1	.	.	.	.	.	.	.	.	.	.	A	9.795	1.179074	0.21787	.	.	ENSG00000197943	ENST00000359376	T	0.27256	1.68	5.09	3.98	0.46160	Phospholipase C, phosphoinositol-specific, EF-hand-like (1);	0.035665	0.85682	N	0.000000	T	0.25717	0.0626	N	0.15975	0.35	0.52501	D	0.999953	B;D	0.58268	0.009;0.982	B;P	0.59288	0.03;0.855	T	0.02512	-1.1148	10	0.18710	T	0.47	.	12.0579	0.53546	0.8557:0.1443:0.0:0.0	.	144;277	B4E3H3;P16885	.;PLCG2_HUMAN	L	277	ENSP00000352336:M277L	ENSP00000352336:M277L	M	+	1	0	PLCG2	80480341	1.000000	0.71417	0.731000	0.30826	0.521000	0.34408	4.616000	0.61197	0.867000	0.35654	0.460000	0.39030	ATG	.	.		0.468	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1			T	81922840	A	T	81922840	3	4	348	1	0	0	0	0	1	0	0	0	12045	217	8	4	863	4	PLCG2	16	81922840	Missense_Mutation	SNP	A	TCGA-UB-A7MF-01A-11D-A33K-10	11102572	81922840	8431913	75	49123										
TP53	7157	hgsc.bcm.edu	37	chr17	7578205	7578205	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	gctcatagggcaccaccacaCtatgtcgaaaagtgtttctg	9	11	2	0	rs587782177		TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr17:7578205C>A	ENST00000269305.4	-	6	833	c.644G>T	c.(643-645)aGt>aTt	p.S215I	TP53_ENST00000420246.2_Missense_Mutation_p.S215I|TP53_ENST00000445888.2_Missense_Mutation_p.S215I|TP53_ENST00000359597.4_Missense_Mutation_p.S215I|TP53_ENST00000455263.2_Missense_Mutation_p.S215I|TP53_ENST00000413465.2_Missense_Mutation_p.S215I|TP53_ENST00000574684.1_Intron	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	215	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		S -> C (in sporadic cancers; somatic mutation).|S -> G (in sporadic cancers; somatic mutation).|S -> I (in sporadic cancers; somatic mutation).|S -> K (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|S -> N (in sporadic cancers; somatic mutation).|S -> R (in sporadic cancers; somatic mutation).|S -> T (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.S215I(18)|p.S215N(9)|p.0?(8)|p.?(5)|p.S215T(3)|p.S215fs*32(3)|p.H214fs*5(2)|p.S122N(1)|p.S215fs*27(1)|p.S215del(1)|p.S215fs*29(1)|p.D208_V216delDRNTFRHSV(1)|p.S83I(1)|p.S83N(1)|p.T211_S215delTFRHS(1)|p.D208fs*1(1)|p.S215fs*31(1)|p.T211fs*28(1)|p.R213_S215>X(1)|p.S122I(1)|p.D207_V216del10(1)|p.S215_V218>M(1)|p.R209fs*6(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CACCACCACACTATGTCGAAA	0.537		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.S215I	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,lymphoid_neoplasm,+1,1	TP53	33396	.	64	Substitution - Missense(34)|Deletion - Frameshift(10)|Whole gene deletion(8)|Unknown(5)|Deletion - In frame(4)|Complex - deletion inframe(2)|Complex - frameshift(1)	biliary_tract(10)|oesophagus(10)|lung(9)|large_intestine(6)|ovary(6)|bone(5)|upper_aerodigestive_tract(4)|haematopoietic_and_lymphoid_tissue(4)|central_nervous_system(3)|liver(2)|breast(2)|stomach(1)|kidney(1)|skin(1)	c.G644T						.						125	112	116					17																	7578205		2203	4300	6503	SO:0001583	missense	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	ACCACACTATGTC	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.644G>T	chr17.hg19:g.7578205C>A	ENSP00000269305:p.Ser215Ile	144.0	0.0		121.0	57.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.898786	0.91962	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99856	-7.21;-7.21;-7.21;-7.21;-7.21;-7.21;-7.21;-7.21	5.28	5.28	0.74379	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99878	0.9942	M	0.90705	3.14	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;0.999;1.0;1.0;1.0;1.0	D	0.96464	0.9343	10	0.87932	D	0	-18.3023	16.7921	0.85592	0.0:1.0:0.0:0.0	.	176;215;215;122;215;215;215	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	I	215;215;215;215;215;215;204;122;83;122;83	ENSP00000410739:S215I;ENSP00000352610:S215I;ENSP00000269305:S215I;ENSP00000398846:S215I;ENSP00000391127:S215I;ENSP00000391478:S215I;ENSP00000425104:S83I;ENSP00000423862:S122I	ENSP00000269305:S215I	S	-	2	0	TP53	7518930	1.000000	0.71417	0.567000	0.28434	0.964000	0.63967	6.042000	0.70996	2.634000	0.89283	0.563000	0.77884	AGT	.	.		0.537	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7578205	C	A	7578205	3	1	348	1	0	0	0	0	1	0	0	0	16396	565	20	3	650	3	TP53	17	7578205	Missense_Mutation	SNP	C	TCGA-UB-A7MF-01A-11D-A33K-10		7578205	73617005	76	49124										
MYH8	4626	hgsc.bcm.edu	37	chr17	10307686	10307686	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	aggtcatttttctcttttaaGagagtgaccattttttcctc	6	8	2	2			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr17:10307686G>T	ENST00000403437.2	-	22	2743	c.2649C>A	c.(2647-2649)ctC>ctA	p.L883L	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	883					ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)			NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						TCTCTTTTAAGAGAGTGACCA	0.408									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling																												p.L883L		Atlas-SNP	.											.	MYH8	346	.	0			c.C2649A						.						135	122	126					17																	10307686		2203	4300	6503	SO:0001819	synonymous_variant	4626	exon22	Familial Cancer Database	Carney Complex Variant	TTTTAAGAGAGTG		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020		"Myosins / Myosin superfamily : Class II"	7578	protein-coding gene	gene with protein product		160741	"myosin, heavy polypeptide 8, skeletal muscle, perinatal"			2373371	Standard	NM_002472		Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.2649C>A	chr17.hg19:g.10307686G>T		133.0	0.0		93.0	29.0	NM_002472	Q14910	Silent	SNP	ENST00000403437.2	hg19	CCDS11153.1																																																																																			.	.		0.408	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472		T	10307686	G	T	10307686	2	4	348	1	0	0	0	0	0	0	0	1	10050	929	33	3		3	MYH8	17	10307686	Silent	SNP	G	TCGA-UB-A7MF-01A-11D-A33K-10	2729481	10307686	70887524	77	49125										
RAI1	10743	hgsc.bcm.edu	37	chr17	17696772	17696772	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	gtgccctttcggactcactcCctgcacgtccagcagccacc	8	19	1	0			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr17:17696772C>T	ENST00000353383.1	+	3	979	c.510C>T	c.(508-510)tcC>tcT	p.S170S	RAI1_ENST00000261641.6_Silent_p.S170S	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	170	Gln-rich.				circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		GGACTCACTCCCTGCACGTCC	0.622																																					p.S170S		Atlas-SNP	.											.	RAI1	121	.	0			c.C510T						.						63	62	62					17																	17696772		2203	4300	6503	SO:0001819	synonymous_variant	10743	exon3			TCACTCCCTGCAC	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"Smith-Magenis syndrome chromosome region"	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.510C>T	chr17.hg19:g.17696772C>T		149.0	0.0		81.0	14.0	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Silent	SNP	ENST00000353383.1	hg19	CCDS11188.1																																																																																			.	.		0.622	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665		T	17696772	C	T	17696772	2	4	348	1	0	0	0	0	0	0	0	1	13022	610	22	3		3	RAI1	17	17696772	Silent	SNP	C	TCGA-UB-A7MF-01A-11D-A33K-10	7389086	17696772	63498438	78	49126										
KIAA1267	284058	hgsc.bcm.edu	37	chr17	44110522	44110526	+	Frame_Shift_Del	DEL	GCAGG	GCAGG	-													0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	catctcctcacatttggcatGcagggcggcgaaggctgcgt							TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	GCAGG	GCAGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr17:44110522_44110526delGCAGG	ENST00000262419.6	-	13	3227_3231	c.2757_2761delCCTGC	c.(2755-2763)gccctgcatfs	p.LH920fs	KANSL1_ENST00000574590.1_Frame_Shift_Del_p.LH920fs|KANSL1_ENST00000572904.1_Frame_Shift_Del_p.LH920fs|KANSL1_ENST00000432791.1_Frame_Shift_Del_p.LH920fs|RP11-669E14.6_ENST00000570454.1_RNA|KANSL1_ENST00000393476.3_Frame_Shift_Del_p.LH214fs|KANSL1_ENST00000575318.1_Frame_Shift_Del_p.LH856fs	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	920	Sufficient for interaction with KAT8.				chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											CATTTGGCATGCAGGGCGGCGAAGG	0.61																																					p.920_921del		Atlas-Indel,Pindel	.											.	.	.	.	0			c.2758_2762del						.																																			SO:0001589	frameshift_variant	284058	exon13			.	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"centromere protein 36"	612452	"KIAA1267"	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.2757_2761delCCTGC	chr17.hg19:g.44110522_44110526delGCAGG	ENSP00000262419:p.Leu920fs	82.0	0.0		65.0	14.0	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Frame_Shift_Del	DEL	ENST00000262419.6	hg19	CCDS11503.1																																																																																			.	.		0.61	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443		-	44110526	GCAGG	-	44110522	7	5	348	1	0	1	0	1	0	0	0	0	8228	1319	46	0	568	0	KIAA1267	17	44110522	Frame_Shift_Del	DEL	GCAGG	TCGA-UB-A7MF-01A-11D-A33K-10	26413750	44110522	37084688	79	49127										
EFCAB3	146779	hgsc.bcm.edu	37	chr17	60493662	60493662	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	ctcaggaagaaaaagaaaacGgaaaggtttaaagggatttc	11	4	1	2			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr17:60493662G>A	ENST00000305286.3	+	10	1367	c.1289G>A	c.(1288-1290)cGg>cAg	p.R430Q	EFCAB3_ENST00000450662.2_Missense_Mutation_p.R482Q	NM_173503.3	NP_775774.1	Q8N7B9	EFCB3_HUMAN	EF-hand calcium binding domain 3	430							calcium ion binding (GO:0005509)			cervix(1)|endometrium(2)|large_intestine(5)|lung(6)|skin(3)	17			BRCA - Breast invasive adenocarcinoma(2;2.27e-11)			AAAAGAAAACGGAAAGGTTTA	0.333																																					p.R482Q		Atlas-SNP	.											.	EFCAB3	71	.	0			c.G1445A						.						74	81	79					17																	60493662		2202	4298	6500	SO:0001583	missense	146779	exon12			GAAAACGGAAAGG	AK098684	CCDS11632.1, CCDS45751.1	17q23.3	2013-01-10			ENSG00000172421	ENSG00000172421		"EF-hand domain containing"	26379	protein-coding gene	gene with protein product						12477932	Standard	NM_173503		Approved	FLJ25818	uc010wpc.2	Q8N7B9	OTTHUMG00000179175	ENST00000305286.3:c.1289G>A	chr17.hg19:g.60493662G>A	ENSP00000302649:p.Arg430Gln	75.0	0.0		50.0	15.0	NM_001144933	J3KQM8	Missense_Mutation	SNP	ENST00000305286.3	hg19	CCDS11632.1	.	.	.	.	.	.	.	.	.	.	G	6.933	0.541929	0.13250	.	.	ENSG00000172421	ENST00000450662;ENST00000305286	T;T	0.62498	0.02;0.08	5.04	4.08	0.47627	.	0.403035	0.21131	N	0.079658	T	0.48554	0.1506	L	0.40543	1.245	0.32193	N	0.578761	B	0.11235	0.004	B	0.09377	0.004	T	0.50857	-0.8778	10	0.17369	T	0.5	.	9.5007	0.39015	0.0961:0.0:0.9039:0.0	.	430	Q8N7B9	EFCB3_HUMAN	Q	482;430	ENSP00000403932:R482Q;ENSP00000302649:R430Q	ENSP00000302649:R430Q	R	+	2	0	EFCAB3	57847394	0.999000	0.42202	0.998000	0.56505	0.144000	0.21451	1.528000	0.35985	1.360000	0.45960	-0.263000	0.10527	CGG	.	.		0.333	EFCAB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379114.1	NM_173503		A	60493662	G	A	60493662	3	1	348	1	0	0	0	0	1	0	0	0	4937	1116	39	1	1491	1	EFCAB3	17	60493662	Missense_Mutation	SNP	G	TCGA-UB-A7MF-01A-11D-A33K-10	16383140	60493662	20701548	80	49128										
B3GNTL1	146712	hgsc.bcm.edu	37	chr17	80915065	80915065	+	Frame_Shift_Del	DEL	C	C	-													0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	ggccctgcacacctgagagtCctcgtggcaatagaagcctt							TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr17:80915065delC	ENST00000320865.3	-	10	935	c.922delG	c.(922-924)gacfs	p.D308fs	B3GNTL1_ENST00000576599.1_Frame_Shift_Del_p.D197fs	NM_001009905.1	NP_001009905.1	Q67FW5	B3GNL_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase-like 1	308							transferase activity, transferring glycosyl groups (GO:0016757)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	8	Breast(20;0.000443)|all_neural(118;0.0779)	all_cancers(8;0.0396)|all_epithelial(8;0.0556)	BRCA - Breast invasive adenocarcinoma(99;0.0517)|OV - Ovarian serous cystadenocarcinoma(97;0.0868)			ACCTGAGAGTCCTCGTGGCAA	0.622																																					p.D308fs		Atlas-Indel,Pindel	.											.	B3GNTL1	40	.	0			c.923delA						.						169	155	160					17																	80915065		2203	4300	6503	SO:0001589	frameshift_variant	146712	exon10			.	AY634364	CCDS32778.1	17q25.3	2013-02-22	2004-01-13	2004-01-14	ENSG00000175711	ENSG00000175711		"Glycosyltransferase family 2 domain containing"	21727	protein-coding gene	gene with protein product		615337					Standard	NM_001009905		Approved	B3GNT8	uc002kgg.1	Q67FW5	OTTHUMG00000177788	ENST00000320865.3:c.922delG	chr17.hg19:g.80915065delC	ENSP00000319979:p.Asp308fs	153.0	0.0		116.0	24.0	NM_001009905	Q6GV30|Q8WUT3	Frame_Shift_Del	DEL	ENST00000320865.3	hg19	CCDS32778.1																																																																																			.	.		0.622	B3GNTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438949.1	NM_001009905		-	80915065	C	-	80915065	7	5	348	1	0	1	0	1	0	0	0	0	1265	855	30	0	175	0	B3GNTL1	17	80915065	Frame_Shift_Del	DEL	C	TCGA-UB-A7MF-01A-11D-A33K-10	20421403	80915065	280145	81	49129										
TMEM200C	645369	hgsc.bcm.edu	37	chr18	5890394	5890394	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	cacagcagagtctcgcgtttGaccagctactgcgtccaaga	10	13	1	3			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr18:5890394G>C	ENST00000581347.2	-	3	2314	c.1669C>G	c.(1669-1671)Caa>Gaa	p.Q557E	RP11-945C19.4_ENST00000582939.1_RNA|TMEM200C_ENST00000383490.2_Missense_Mutation_p.Q557E|RP11-945C19.4_ENST00000580845.1_RNA|RP11-945C19.4_ENST00000577694.1_RNA			A6NKL6	T200C_HUMAN	transmembrane protein 200C	557						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(1)|large_intestine(4)|lung(5)|stomach(1)	12						TCTCGCGTTTGACCAGCTACT	0.677																																					p.Q557E		Atlas-SNP	.											.	TMEM200C	30	.	0			c.C1669G						.						24	28	27					18																	5890394		1924	4109	6033	SO:0001583	missense	645369	exon1			GCGTTTGACCAGC		CCDS45825.1	18p11.31	2009-09-08			ENSG00000206432	ENSG00000206432			37208	protein-coding gene	gene with protein product						15722956	Standard	NM_001080209		Approved	TTMA	uc002kmx.1	A6NKL6		ENST00000581347.2:c.1669C>G	chr18.hg19:g.5890394G>C	ENSP00000463375:p.Gln557Glu	50.0	0.0		49.0	8.0	NM_001080209		Missense_Mutation	SNP	ENST00000581347.2	hg19	CCDS45825.1	.	.	.	.	.	.	.	.	.	.	G	11.29	1.593891	0.28445	.	.	ENSG00000206432	ENST00000383490	.	.	.	4.62	-9.25	0.00666	.	.	.	.	.	T	0.11793	0.0287	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16158	-1.0412	8	0.11794	T	0.64	.	4.5462	0.12081	0.0835:0.0988:0.3352:0.4825	.	557	A6NKL6	T200C_HUMAN	E	557	.	ENSP00000372982:Q557E	Q	-	1	0	TMEM200C	5880394	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.798000	0.01747	-2.610000	0.00446	-0.305000	0.09177	CAA	.	.		0.677	TMEM200C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441917.4	NM_001080209		C	5890394	G	C	5890394	3	2	348	1	0	0	0	0	1	0	0	0	16140	1299	45	4	200	4	TMEM200C	18	5890394	Missense_Mutation	SNP	G	TCGA-UB-A7MF-01A-11D-A33K-10		5890394	72186854	82	49130										
GNAL	2774	hgsc.bcm.edu	37	chr18	11753928	11753928	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	gagcatagcccctatcactgActttgaatattcccaggtaa	7	11	1	2			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr18:11753928A>G	ENST00000423027.3	+	4	698	c.377A>G	c.(376-378)gAc>gGc	p.D126G	GNAL_ENST00000590972.1_3'UTR|GNAL_ENST00000535121.1_Missense_Mutation_p.D126G|GNAL_ENST00000334049.6_Missense_Mutation_p.D203G|GNAL_ENST00000269162.5_Missense_Mutation_p.D126G			P38405	GNAL_HUMAN	guanine nucleotide binding protein (G protein), alpha activating activity polypeptide, olfactory type	126					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|response to amphetamine (GO:0001975)|response to caffeine (GO:0031000)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(4)|ovary(1)	12						CCTATCACTGACTTTGAATAT	0.358																																					p.D203G		Atlas-SNP	.											.	GNAL	59	.	0			c.A608G						.						81	82	82					18																	11753928		2203	4300	6503	SO:0001583	missense	2774	exon4			TCACTGACTTTGA	AF493893	CCDS11851.1, CCDS11852.1, CCDS58614.1	18p11.22-p11.21	2003-12-17			ENSG00000141404	ENSG00000141404			4388	protein-coding gene	gene with protein product		139312				1302014	Standard	NM_182978		Approved		uc002kqc.3	P38405	OTTHUMG00000131660	ENST00000423027.3:c.377A>G	chr18.hg19:g.11753928A>G	ENSP00000408489:p.Asp126Gly	184.0	0.0		207.0	91.0	NM_182978	B7ZA26|Q86XU3	Missense_Mutation	SNP	ENST00000423027.3	hg19	CCDS11852.1	.	.	.	.	.	.	.	.	.	.	A	18.15	3.558818	0.65538	.	.	ENSG00000141404	ENST00000540217;ENST00000334049;ENST00000535121;ENST00000269162;ENST00000423027	T;T;T;T	0.44881	0.91;0.91;0.91;0.91	5.58	5.58	0.84498	G protein alpha subunit, helical insertion (2);	0.082890	0.85682	D	0.000000	T	0.54870	0.1885	M	0.76727	2.345	0.80722	D	1	P;B	0.35433	0.501;0.32	P;B	0.45071	0.468;0.247	T	0.56123	-0.8031	10	0.45353	T	0.12	.	15.7482	0.77962	1.0:0.0:0.0:0.0	.	126;203	P38405;Q86XU3	GNAL_HUMAN;.	G	65;203;126;126;126	ENSP00000334051:D203G;ENSP00000439023:D126G;ENSP00000269162:D126G;ENSP00000408489:D126G	ENSP00000269162:D126G	D	+	2	0	GNAL	11743928	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.957000	0.93082	2.125000	0.65367	0.459000	0.35465	GAC	.	.		0.358	GNAL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254561.2	NM_182978, NM_002071		G	11753928	A	G	11753928	3	3	348	1	0	0	0	0	1	0	0	0	6515	275	10	2	771	2	GNAL	18	11753928	Missense_Mutation	SNP	A	TCGA-UB-A7MF-01A-11D-A33K-10	5863534	11753928	66323320	83	49131										
NEDD4L	23327	hgsc.bcm.edu	37	chr18	56033299	56033299	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	tttgaagagtcctatcggagAattatgtccgtgaaaagacc	10	7	0	5			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr18:56033299A>G	ENST00000400345.3	+	21	2185	c.1902A>G	c.(1900-1902)agA>agG	p.R634R	NEDD4L_ENST00000589054.1_Intron|NEDD4L_ENST00000357895.5_Silent_p.R626R|NEDD4L_ENST00000456173.2_Silent_p.R493R|NEDD4L_ENST00000256832.7_Silent_p.R494R|NEDD4L_ENST00000435432.2_Silent_p.R493R|NEDD4L_ENST00000456986.1_Silent_p.R513R|NEDD4L_ENST00000382850.4_Silent_p.R614R|NEDD4L_ENST00000256830.9_Silent_p.R530R|NEDD4L_ENST00000586263.1_Silent_p.R606R|NEDD4L_ENST00000356462.6_Silent_p.R570R|NEDD4L_ENST00000431212.2_Silent_p.R513R	NM_001144967.2	NP_001138439.1	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase	634					cellular sodium ion homeostasis (GO:0006883)|excretion (GO:0007588)|gene expression (GO:0010467)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of sodium ion transmembrane transport (GO:1902306)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of cation channel activity (GO:2001259)|positive regulation of caveolin-mediated endocytosis (GO:2001288)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of sodium ion transport (GO:0010765)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane depolarization (GO:0003254)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of protein catabolic process (GO:0042176)|regulation of tight junction assembly (GO:2000810)|response to metal ion (GO:0010038)|response to salt stress (GO:0009651)|sodium ion transport (GO:0006814)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|ventricular cardiac muscle cell action potential (GO:0086005)|viral life cycle (GO:0019058)|viral process (GO:0016032)|water homeostasis (GO:0030104)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ion channel binding (GO:0044325)|ligase activity (GO:0016874)|potassium channel inhibitor activity (GO:0019870)|potassium channel regulator activity (GO:0015459)|sodium channel inhibitor activity (GO:0019871)|sodium channel regulator activity (GO:0017080)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(11)|ovary(1)|prostate(4)	37						CCTATCGGAGAATTATGTCCG	0.388																																					p.R634R		Atlas-SNP	.											.	NEDD4L	126	.	0			c.A1902G						.						113	106	108					18																	56033299		1846	4090	5936	SO:0001819	synonymous_variant	23327	exon21			TCGGAGAATTATG	AF210730	CCDS45872.1, CCDS45873.1, CCDS45874.1, CCDS45875.1, CCDS45876.1, CCDS58632.1, CCDS59323.1	18q21.31	2014-08-12	2012-02-23		ENSG00000049759				7728	protein-coding gene	gene with protein product		606384	"neural precursor cell expressed, developmentally down-regulated 4-like"			10594025, 11244092, 18322022	Standard	NM_001144965		Approved	KIAA0439, RSP5, NEDD4-2	uc002lgy.3	Q96PU5	OTTHUMG00000179875	ENST00000400345.3:c.1902A>G	chr18.hg19:g.56033299A>G		67.0	0.0		68.0	26.0	NM_001144967	O43165|Q3LSM7|Q7Z5F1|Q7Z5F2|Q7Z5N3|Q8N5A7|Q8WUU9|Q9BW58|Q9H2W4|Q9NT88	Silent	SNP	ENST00000400345.3	hg19	CCDS45872.1																																																																																			.	.		0.388	NEDD4L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448749.1			G	56033299	A	G	56033299	2	3	348	1	0	0	0	0	0	0	0	1	10320	243	9	2		2	NEDD4L	18	56033299	Silent	SNP	A	TCGA-UB-A7MF-01A-11D-A33K-10	44279371	56033299	22043949	84	49132										
ELANE	1991	hgsc.bcm.edu	37	chr19	855638	855638	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	cagggacgccgcctgggcaaCggggtgcagtgcctggccat	17	13	0	0	rs146878885	byFrequency	TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr19:855638C>T	ENST00000590230.1	+	5	582	c.441C>T	c.(439-441)aaC>aaT	p.N147N	ELANE_ENST00000263621.1_Silent_p.N147N			P08246	ELNE_HUMAN	elastase, neutrophil expressed	147	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				acute inflammatory response to antigenic stimulus (GO:0002438)|cellular calcium ion homeostasis (GO:0006874)|collagen catabolic process (GO:0030574)|defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|negative regulation of chemokine biosynthetic process (GO:0045079)|negative regulation of chemotaxis (GO:0050922)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-8 biosynthetic process (GO:0045415)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neutrophil mediated killing of fungus (GO:0070947)|phagocytosis (GO:0006909)|positive regulation of immune response (GO:0050778)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein catabolic process (GO:0030163)|proteolysis (GO:0006508)|response to lipopolysaccharide (GO:0032496)|response to UV (GO:0009411)|response to yeast (GO:0001878)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|secretory granule (GO:0030141)|transcriptional repressor complex (GO:0017053)	cytokine binding (GO:0019955)|endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|peptidase activity (GO:0008233)|protease binding (GO:0002020)|RNA polymerase II transcription corepressor activity (GO:0001106)|serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(1)|lung(4)|pancreas(1)	13					Alpha-1-proteinase inhibitor(DB00058)|Filgrastim(DB00099)|Pegfilgrastim(DB00019)	GCCTGGGCAACGGGGTGCAGT	0.687													C|||	5	0.000998403	0.003	0	5008	,	,		15709	0.001		0	False		,,,				2504	0				p.N147N		Atlas-SNP	.											.	ELANE	27	.	0			c.C441T						.	C		1,4405	2.1+/-5.4	0,1,2202	51	48	49		441	-8.6	0	19	dbSNP_134	49	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous	ELANE	NM_001972.2		0,2,6498	TT,TC,CC		0.0116,0.0227,0.0154		147/268	855638	2,12998	2203	4297	6500	SO:0001819	synonymous_variant	1991	exon4			GGGCAACGGGGTG		CCDS12045.1	19p13.3	2014-09-17	2009-05-05	2009-05-05	ENSG00000197561	ENSG00000197561	3.4.21.37		3309	protein-coding gene	gene with protein product	"neutrophil elastase", "leukocyte elastase", "medullasin"	130130	"elastase 2, neutrophil"	ELA2		2902087	Standard	XM_005259517		Approved	NE, HNE, HLE	uc002lqb.3	P08246		ENST00000590230.1:c.441C>T	chr19.hg19:g.855638C>T		25.0	0.0		31.0	5.0	NM_001972	P09649|Q6B0D9|Q6LDP5	Silent	SNP	ENST00000590230.1	hg19	CCDS12045.1																																																																																			.	C|1.000;T|0.000		0.687	ELANE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457890.2	NM_001972		T	855638	C	T	855638	2	4	348	1	0	0	0	0	0	0	0	1	5050	535	19	1		1	ELANE	19	855638	Silent	SNP	C	TCGA-UB-A7MF-01A-11D-A33K-10		855638	58273345	85	49133										
OR2Z1	284383	hgsc.bcm.edu	37	chr19	8842153	8842153	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	tggggctcttttatggtgccGccgtgttcatgtacatggtg	14	8	2	0	rs200115143		TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr19:8842153G>A	ENST00000324060.2	+	1	838	c.763G>A	c.(763-765)Gcc>Acc	p.A255T		NM_001004699.1	NP_001004699.1	Q8NG97	OR2Z1_HUMAN	olfactory receptor, family 2, subfamily Z, member 1	255						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A255T(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TTATGGTGCCGCCGTGTTCAT	0.562																																					p.A255T		Atlas-SNP	.											OR2Z1,NS,carcinoma,0,2	OR2Z1	53	.	1	Substitution - Missense(1)	stomach(1)	c.G763A						.						162	129	140					19																	8842153		2203	4300	6503	SO:0001583	missense	284383	exon1			GGTGCCGCCGTGT	AC008753	CCDS32895.1	19p13.2	2013-09-20	2002-11-13		ENSG00000181733	ENSG00000181733		"GPCR / Class A : Olfactory receptors"	15391	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily Z, member 2"	OR2Z2			Standard	NM_001004699		Approved		uc010xkg.2	Q8NG97	OTTHUMG00000182195	ENST00000324060.2:c.763G>A	chr19.hg19:g.8842153G>A	ENSP00000316284:p.Ala255Thr	103.0	0.0		89.0	4.0	NM_001004699	B9EH50|Q6IFK0|Q96R25	Missense_Mutation	SNP	ENST00000324060.2	hg19	CCDS32895.1	.	.	.	.	.	.	.	.	.	.	G	12.62	1.992148	0.35131	.	.	ENSG00000181733	ENST00000324060	T	0.00169	8.63	4.67	2.42	0.29668	GPCR, rhodopsin-like superfamily (1);	1.410570	0.04115	N	0.315375	T	0.00300	0.0009	L	0.52206	1.635	0.09310	N	1	D	0.61080	0.989	P	0.54210	0.745	T	0.54636	-0.8264	10	0.59425	D	0.04	.	4.0346	0.09724	0.196:0.2092:0.5948:0.0	.	255	Q8NG97	OR2Z1_HUMAN	T	255	ENSP00000316284:A255T	ENSP00000316284:A255T	A	+	1	0	OR2Z1	8703153	0.000000	0.05858	0.240000	0.24138	0.048000	0.14542	0.336000	0.19823	2.356000	0.79943	0.543000	0.68304	GCC	.	G|0.999;A|0.001		0.562	OR2Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459954.1			A	8842153	G	A	8842153	3	1	348	1	0	0	0	0	1	0	0	0	11045	1087	38	1	765	1	OR2Z1	19	8842153	Missense_Mutation	SNP	G	TCGA-UB-A7MF-01A-11D-A33K-10	7986515	8842153	50286830	86	49134										
MUC16	94025	hgsc.bcm.edu	37	chr19	8996440	8996440	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	gcctagggcttttggggtcaGggtggtgggtgcagatggca	20	6	1	1			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr19:8996440G>C	ENST00000397910.4	-	61	41335	c.41132C>G	c.(41131-41133)cCt>cGt	p.P13711R	MUC16_ENST00000380951.5_Missense_Mutation_p.P352R	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13713	SEA 11. {ECO:0000255|PROSITE- ProRule:PRU00188}.			Missing (in Ref. 3; AAK74120). {ECO:0000305}.	cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TTTGGGGTCAGGGTGGTGGGT	0.557																																					p.P13711R		Atlas-SNP	.											.	MUC16	4315	.	0			c.C41132G						.						81	76	78					19																	8996440		1936	4142	6078	SO:0001583	missense	94025	exon61			GGGTCAGGGTGGT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.41132C>G	chr19.hg19:g.8996440G>C	ENSP00000381008:p.Pro13711Arg	120.0	0.0		90.0	12.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	6.929|6.929	0.541051|0.541051	0.13250|0.13250	.|.	.|.	ENSG00000181143|ENSG00000181143	ENST00000542240|ENST00000397910;ENST00000380951	.|T;T	.|0.43294	.|0.95;0.95	3.36|3.36	-1.75|-1.75	0.08031|0.08031	.|SEA (1);	.|0.518513	.|0.14520	.|U	.|0.314548	T|T	0.26666|0.26666	0.0652|0.0652	N|N	0.01874|0.01874	-0.695|-0.695	.|.	.|.	.|.	.|P;D	.|0.71674	.|0.624;0.998	.|B;D	.|0.78314	.|0.329;0.991	T|T	0.30736|0.30736	-0.9968|-0.9968	4|9	.|0.32370	.|T	.|0.25	-0.2631|-0.2631	2.7492|2.7492	0.05275|0.05275	0.3706:0.0:0.4239:0.2056|0.3706:0.0:0.4239:0.2056	.|.	.|21356;13711	.|Q8WXI7;B5ME49	.|MUC16_HUMAN;.	V|R	551|13711;352	.|ENSP00000381008:P13711R;ENSP00000370338:P352R	.|ENSP00000370338:P352R	L|P	-|-	1|2	2|0	MUC16|MUC16	8857440|8857440	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.009000|0.009000	0.06853|0.06853	0.101000|0.101000	0.15251|0.15251	-0.009000|-0.009000	0.14296|0.14296	-0.397000|-0.397000	0.06425|0.06425	CTG|CCT	.	.		0.557	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	8996440	G	C	8996440	3	2	348	1	0	0	0	0	1	0	0	0	9982	1000	35	4	2487	4	MUC16	19	8996440	Missense_Mutation	SNP	G	TCGA-UB-A7MF-01A-11D-A33K-10	154287	8996440	50132543	87	49135										
GLT25D1	79709	hgsc.bcm.edu	37	chr19	17692114	17692114	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	caccgagacctcagtcgtatGgaacaatgagcacgtcaaga	10	11	2	3			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr19:17692114G>A	ENST00000252599.4	+	12	1850	c.1730G>A	c.(1729-1731)tGg>tAg	p.W577*		NM_024656.2	NP_078932.2	Q8NBJ5	GT251_HUMAN	collagen beta(1-O)galactosyltransferase 1	577					extracellular matrix organization (GO:0030198)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum lumen (GO:0005788)|membrane (GO:0016020)	procollagen galactosyltransferase activity (GO:0050211)										TCAGTCGTATGGAACAATGAG	0.592																																					p.W577X		Atlas-SNP	.											.	.	.	.	0			c.G1730A						.						173	137	149					19																	17692114		2203	4300	6503	SO:0001587	stop_gained	79709	exon12			TCGTATGGAACAA	AK075541	CCDS12363.1	19p13.11	2013-02-27	2013-02-27	2013-02-27	ENSG00000130309	ENSG00000130309			26182	protein-coding gene	gene with protein product			"glycosyltransferase 25 domain containing 1"	GLT25D1		19075007	Standard	NM_024656		Approved	FLJ22329	uc002nhc.1	Q8NBJ5		ENST00000252599.4:c.1730G>A	chr19.hg19:g.17692114G>A	ENSP00000252599:p.Trp577*	169.0	0.0		155.0	27.0	NM_024656	Q8NC64	Nonsense_Mutation	SNP	ENST00000252599.4	hg19	CCDS12363.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.926788	0.92319	.	.	ENSG00000130309	ENST00000252599	.	.	.	4.96	4.96	0.65561	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.13108	T	0.6	-7.8185	15.6857	0.77409	0.0:0.0:1.0:0.0	.	.	.	.	X	577	.	ENSP00000252599:W577X	W	+	2	0	GLT25D1	17553114	1.000000	0.71417	1.000000	0.80357	0.236000	0.25371	9.507000	0.97996	2.298000	0.77334	0.313000	0.20887	TGG	.	.		0.592	COLGALT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464216.1	NM_024656		A	17692114	G	A	17692114	4	1	348	1	0	0	0	0	0	1	0	0	6474	1357	47	3	1776	3	GLT25D1	19	17692114	Nonsense_Mutation	SNP	G	TCGA-UB-A7MF-01A-11D-A33K-10	8695674	17692114	41436869	88	49136										
ZNF98	148198	hgsc.bcm.edu	37	chr19	22575687	22575687	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	ttcttaactgtaaattttcaCgtccacattttttatatgtt	3	7	2	0	rs140301665	byFrequency	TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr19:22575687C>A	ENST00000357774.5	-	4	471	c.350G>T	c.(349-351)cGt>cTt	p.R117L		NM_001098626.1	NP_001092096.1	A6NK75	ZNF98_HUMAN	zinc finger protein 98	117					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)				TAAATTTTCACGTCCACATTT	0.343																																					p.R117L		Atlas-SNP	.											.	ZNF98	230	.	0			c.G350T						.						66	55	58					19																	22575687		1969	4170	6139	SO:0001583	missense	148198	exon4			TTTTCACGTCCAC		CCDS46031.1	19p12	2014-02-14	2010-04-20	2008-06-12	ENSG00000197360	ENSG00000197360		"Zinc fingers, C2H2-type", "-"	13174	protein-coding gene	gene with protein product	"zinc finger protein 739"	603980					Standard	NM_001098626		Approved	ZNF739, F7175	uc002nqt.2	A6NK75	OTTHUMG00000182940	ENST00000357774.5:c.350G>T	chr19.hg19:g.22575687C>A	ENSP00000350418:p.Arg117Leu	235.0	0.0		244.0	86.0	NM_001098626		Missense_Mutation	SNP	ENST00000357774.5	hg19	CCDS46031.1	.	.	.	.	.	.	.	.	.	.	.	0.316	-0.964637	0.02249	.	.	ENSG00000197360	ENST00000357774	T	0.06294	3.32	0.916	-1.83	0.07833	.	.	.	.	.	T	0.01353	0.0044	N	0.00254	-1.765	0.09310	N	1	B	0.11235	0.004	B	0.09377	0.004	T	0.44757	-0.9307	9	0.33141	T	0.24	.	3.7588	0.08596	0.0:0.2691:0.0:0.7309	.	117	A6NK75	ZNF98_HUMAN	L	117	ENSP00000350418:R117L	ENSP00000350418:R117L	R	-	2	0	ZNF98	22367527	0.000000	0.05858	0.033000	0.17914	0.033000	0.12548	-0.805000	0.04530	-0.779000	0.04560	-0.786000	0.03341	CGT	.	C|0.998;T|0.002		0.343	ZNF98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464398.1	NM_001098626		A	22575687	C	A	22575687	3	1	348	1	0	0	0	0	1	0	0	0	18218	536	19	1	1372	1	ZNF98	19	22575687	Missense_Mutation	SNP	C	TCGA-UB-A7MF-01A-11D-A33K-10	4883573	22575687	36553296	89	49137										
NOVA2	4858	hgsc.bcm.edu	37	chr19	46457193	46457193	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	gccctgtactaggcatacccGctctgtggttcctgttgagc	11	13	1	1			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr19:46457193G>A	ENST00000263257.5	-	3	435	c.241C>T	c.(241-243)Cgg>Tgg	p.R81W		NM_002516.2	NP_002507.1	Q9UNW9	NOVA2_HUMAN	neuro-oncological ventral antigen 2	81	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.				regulation of RNA metabolic process (GO:0051252)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(3)|large_intestine(5)|lung(13)	21		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00245)|GBM - Glioblastoma multiforme(486;0.0782)|Epithelial(262;0.179)		AGGCATACCCGCTCTGTGGTT	0.537																																					p.R81W		Atlas-SNP	.											NOVA2,NS,carcinoma,0,1	NOVA2	38	.	0			c.C241T						.						166	140	149					19																	46457193		2203	4300	6503	SO:0001583	missense	4858	exon3			ATACCCGCTCTGT	U70477	CCDS12679.1	19q13.3	2008-07-17				ENSG00000104967			7887	protein-coding gene	gene with protein product	"neuro-oncological ventral antigen 3"	601991		NOVA3		9344654, 10368286	Standard	NM_002516		Approved	ANOVA	uc002pdv.2	Q9UNW9		ENST00000263257.5:c.241C>T	chr19.hg19:g.46457193G>A	ENSP00000263257:p.Arg81Trp	100.0	0.0		77.0	23.0	NM_002516	O43267|Q9UEA1	Missense_Mutation	SNP	ENST00000263257.5	hg19	CCDS12679.1	.	.	.	.	.	.	.	.	.	.	G	14.24	2.476224	0.44044	.	.	ENSG00000104967	ENST00000263257	T	0.36340	1.26	5.17	1.67	0.24075	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.000000	0.85682	D	0.000000	T	0.71204	0.3312	H	0.99104	4.43	0.58432	D	0.999994	D	0.89917	1.0	D	0.87578	0.998	T	0.74680	-0.3584	10	0.87932	D	0	-11.7429	7.5401	0.27733	0.0845:0.0:0.6127:0.3027	.	81	Q9UNW9	NOVA2_HUMAN	W	81	ENSP00000263257:R81W	ENSP00000263257:R81W	R	-	1	2	NOVA2	51149033	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.067000	0.57527	0.763000	0.33175	0.591000	0.81541	CGG	.	.		0.537	NOVA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437210.2	NM_002516		A	46457193	G	A	46457193	3	1	348	1	0	0	0	0	1	0	0	0	10564	1086	38	1	1245	1	NOVA2	19	46457193	Missense_Mutation	SNP	G	TCGA-UB-A7MF-01A-11D-A33K-10	23881506	46457193	12671790	90	49138										
DBP	1628	hgsc.bcm.edu	37	chr19	49136708	49136708	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	cagctctgctcaccttctgcTcctccggcacctggattttt	7	16	3	0			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr19:49136708T>C	ENST00000222122.5	-	3	1198	c.755A>G	c.(754-756)gAg>gGg	p.E252G	DBP_ENST00000599385.1_Missense_Mutation_p.E50G|DBP_ENST00000593500.1_Missense_Mutation_p.E50G|DBP_ENST00000601104.1_Missense_Mutation_p.E252G	NM_001352.3	NP_001343.2	Q10586	DBP_HUMAN	D site of albumin promoter (albumin D-box) binding protein	252					liver development (GO:0001889)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|rhythmic process (GO:0048511)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	5		all_lung(116;0.000125)|Lung NSC(112;0.000202)|all_epithelial(76;0.000283)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;9.98e-05)|all cancers(93;0.000112)|GBM - Glioblastoma multiforme(486;0.00615)|Epithelial(262;0.0155)		CACCTTCTGCTCCTCCGGCAC	0.557																																					p.E252G		Atlas-SNP	.											.	DBP	16	.	0			c.A755G						.						230	236	234					19																	49136708		2203	4300	6503	SO:0001583	missense	1628	exon3			TTCTGCTCCTCCG	U06936	CCDS12728.1	19q13.33	2013-09-20			ENSG00000105516	ENSG00000105516			2697	protein-coding gene	gene with protein product		124097				1535333, 7835883	Standard	XR_243907		Approved	DABP	uc002pjx.4	Q10586	OTTHUMG00000183319	ENST00000222122.5:c.755A>G	chr19.hg19:g.49136708T>C	ENSP00000222122:p.Glu252Gly	75.0	0.0		69.0	18.0	NM_001352	A2I2P4	Missense_Mutation	SNP	ENST00000222122.5	hg19	CCDS12728.1	.	.	.	.	.	.	.	.	.	.	T	16.19	3.052345	0.55218	.	.	ENSG00000105516	ENST00000222122	T	0.45668	0.89	4.9	4.9	0.64082	.	0.202954	0.39687	U	0.001289	T	0.40932	0.1137	L	0.55990	1.75	0.80722	D	1	B	0.20671	0.047	B	0.25506	0.061	T	0.36720	-0.9736	10	0.59425	D	0.04	-16.2153	12.7938	0.57549	0.0:0.0:0.0:1.0	.	252	Q10586	DBP_HUMAN	G	252	ENSP00000222122:E252G	ENSP00000222122:E252G	E	-	2	0	DBP	53828520	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.244000	0.72391	1.977000	0.57605	0.533000	0.62120	GAG	.	.		0.557	DBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466167.1	NM_001352		C	49136708	T	C	49136708	3	2	348	1	0	0	0	0	1	0	0	0	4258	1551	54	2	230	2	DBP	19	49136708	Missense_Mutation	SNP	T	TCGA-UB-A7MF-01A-11D-A33K-10	2679515	49136708	9992275	91	49139										
SIGLEC12	89858	hgsc.bcm.edu	37	chr19	52001422	52001422	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	ggactgtgaggggctcagggTcaggctcccccaggtccagc	16	13	2	1			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr19:52001422T>C	ENST00000291707.3	-	5	1310	c.1255A>G	c.(1255-1257)Acc>Gcc	p.T419A	SIGLEC12_ENST00000598614.1_Missense_Mutation_p.T301A	NM_053003.2	NP_443729.1	Q96PQ1	SIG12_HUMAN	sialic acid binding Ig-like lectin 12 (gene/pseudogene)	419	Ig-like C2-type 2.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(2)|biliary_tract(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(1)|lung(23)|ovary(4)|prostate(2)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)	61		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.0102)		GGGCTCAGGGTCAGGCTCCCC	0.627																																					p.T419A		Atlas-SNP	.											.	SIGLEC12	243	.	0			c.A1255G						.						49	47	48					19																	52001422		2203	4300	6503	SO:0001583	missense	89858	exon5			TCAGGGTCAGGCT	AF282256	CCDS12833.1, CCDS59416.1	19q13.41	2013-01-29	2011-06-29	2004-10-20	ENSG00000254521	ENSG00000254521		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15482	protein-coding gene	gene with protein product		606094	"SIGLEC-like 1", "sialic acid binding Ig-like lectin 12"	SIGLECL1		11409877, 11328818, 21555517	Standard	NM_053003		Approved	SLG, S2V, Siglec-XII, Siglec-12, Siglec-L1	uc002pwx.1	Q96PQ1	OTTHUMG00000165524	ENST00000291707.3:c.1255A>G	chr19.hg19:g.52001422T>C	ENSP00000291707:p.Thr419Ala	63.0	0.0		36.0	19.0	NM_053003	Q8IYH7	Missense_Mutation	SNP	ENST00000291707.3	hg19	CCDS12833.1	.	.	.	.	.	.	.	.	.	.	.	2.382	-0.341845	0.05243	.	.	ENSG00000254521	ENST00000291707	T	0.11495	2.77	1.39	1.39	0.22231	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.665043	0.12424	U	0.470130	T	0.08537	0.0212	L	0.41356	1.27	0.09310	N	1	B;B	0.33379	0.41;0.285	B;B	0.37091	0.241;0.155	T	0.35649	-0.9780	10	0.16896	T	0.51	.	4.9309	0.13917	0.0:0.0:0.0:1.0	.	419;301	Q96PQ1;Q96PQ1-2	SIG12_HUMAN;.	A	419	ENSP00000291707:T419A	ENSP00000291707:T419A	T	-	1	0	SIGLEC12	56693234	0.000000	0.05858	0.041000	0.18516	0.130000	0.20726	-1.037000	0.03557	0.889000	0.36185	0.324000	0.21423	ACC	.	.		0.627	SIGLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384641.2	NM_053003		C	52001422	T	C	52001422	3	2	348	1	0	0	0	0	1	0	0	0	14323	1667	58	2	548	2	SIGLEC12	19	52001422	Missense_Mutation	SNP	T	TCGA-UB-A7MF-01A-11D-A33K-10	2864714	52001422	7127561	92	49140										
ZNF175	7728	hgsc.bcm.edu	37	chr19	52091277	52091277	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	cttacaaatgcagtgaatgtGggaaagccttcacttctaag	9	8	2	1			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr19:52091277G>A	ENST00000262259.2	+	5	2051	c.1693G>A	c.(1693-1695)Ggg>Agg	p.G565R	ZNF175_ENST00000436511.2_Intron	NM_007147.2	NP_009078.1	Q9Y473	ZN175_HUMAN	zinc finger protein 175	565					defense response to virus (GO:0051607)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24		all_neural(266;0.0299)		GBM - Glioblastoma multiforme(134;0.000426)|OV - Ovarian serous cystadenocarcinoma(262;0.0257)		CAGTGAATGTGGGAAAGCCTT	0.468																																					p.G565R		Atlas-SNP	.											.	ZNF175	65	.	0			c.G1693A						.						80	77	78					19																	52091277		2203	4300	6503	SO:0001583	missense	7728	exon5			GAATGTGGGAAAG	D50419	CCDS12837.1	19q13.4	2013-01-08			ENSG00000105497	ENSG00000105497		"Zinc fingers, C2H2-type", "-"	12964	protein-coding gene	gene with protein product		601139				8838321	Standard	NM_007147		Approved	OTK18	uc002pxb.3	Q9Y473	OTTHUMG00000167771	ENST00000262259.2:c.1693G>A	chr19.hg19:g.52091277G>A	ENSP00000262259:p.Gly565Arg	82.0	0.0		63.0	6.0	NM_007147	A8K9H2	Missense_Mutation	SNP	ENST00000262259.2	hg19	CCDS12837.1	.	.	.	.	.	.	.	.	.	.	G	19.68	3.872811	0.72180	.	.	ENSG00000105497	ENST00000262259	T	0.21361	2.01	2.37	2.37	0.29283	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.39708	0.1088	M	0.64170	1.965	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.30909	-0.9962	9	0.62326	D	0.03	.	10.8646	0.46847	0.0:0.0:1.0:0.0	.	565	Q9Y473	ZN175_HUMAN	R	565	ENSP00000262259:G565R	ENSP00000262259:G565R	G	+	1	0	ZNF175	56783089	1.000000	0.71417	0.986000	0.45419	0.977000	0.68977	3.547000	0.53663	1.650000	0.50662	0.655000	0.94253	GGG	.	.		0.468	ZNF175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396205.1	NM_007147		A	52091277	G	A	52091277	3	1	348	1	0	0	0	0	1	0	0	0	17760	1348	47	3	1707	3	ZNF175	19	52091277	Missense_Mutation	SNP	G	TCGA-UB-A7MF-01A-11D-A33K-10	89855	52091277	7037706	93	49141										
PAK7	57144	hgsc.bcm.edu	37	chr20	9520141	9520141	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	gtattgtctcatgagggggaCgatgcaagacggtggacctg	16	7	1	2	rs560752200		TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr20:9520141C>A	ENST00000378429.3	-	11	2674	c.2128G>T	c.(2128-2130)Gtc>Ttc	p.V710F	PAK7_ENST00000378423.1_Missense_Mutation_p.V710F|PAK7_ENST00000353224.5_Missense_Mutation_p.V710F	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	710					apoptotic process (GO:0006915)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|learning (GO:0007612)|locomotory behavior (GO:0007626)|memory (GO:0007613)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(44)|ovary(2)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)	81			COAD - Colon adenocarcinoma(9;0.194)			ATGAGGGGGACGATGCAAGAC	0.493																																					p.V710F		Atlas-SNP	.											.	PAK7	194	.	0			c.G2128T						.						237	218	225					20																	9520141		2203	4300	6503	SO:0001583	missense	57144	exon10			GGGGGACGATGCA	AB033090	CCDS13107.1	20p12	2008-06-17	2008-06-17		ENSG00000101349	ENSG00000101349			15916	protein-coding gene	gene with protein product		608038	"p21(CDKN1A)-activated kinase 7"			11756552, 10574462	Standard	NM_020341		Approved	KIAA1264, PAK5	uc002wnk.2	Q9P286	OTTHUMG00000031857	ENST00000378429.3:c.2128G>T	chr20.hg19:g.9520141C>A	ENSP00000367686:p.Val710Phe	112.0	0.0		116.0	57.0	NM_177990	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Missense_Mutation	SNP	ENST00000378429.3	hg19	CCDS13107.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.636534	0.87760	.	.	ENSG00000101349	ENST00000378429;ENST00000353224;ENST00000378423;ENST00000439520	T;T;T	0.75050	-0.9;-0.9;-0.9	5.48	5.48	0.80851	.	0.054780	0.64402	D	0.000001	T	0.76821	0.4041	L	0.57536	1.79	0.80722	D	1	P;P	0.52061	0.95;0.95	P;P	0.51079	0.658;0.658	T	0.76266	-0.3022	9	.	.	.	.	12.6695	0.56860	0.0:0.9245:0.0:0.0755	.	710;710	B0AZM9;Q9P286	.;PAK7_HUMAN	F	710;710;710;571	ENSP00000367686:V710F;ENSP00000322957:V710F;ENSP00000367679:V710F	.	V	-	1	0	PAK7	9468141	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	6.091000	0.71406	2.597000	0.87782	0.655000	0.94253	GTC	.	.		0.493	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1			A	9520141	C	A	9520141	3	1	348	1	0	0	0	0	1	0	0	0	11414	536	19	1	35	1	PAK7	20	9520141	Missense_Mutation	SNP	C	TCGA-UB-A7MF-01A-11D-A33K-10		9520141	53505379	94	49142										
C20orf186	149954	hgsc.bcm.edu	37	chr20	31672750	31672750	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	tgtccgtgcggctcctgcccGgcgtgggtgtctacctgagc	15	14	1	1			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr20:31672750G>T	ENST00000375483.3	+	4	730	c.730G>T	c.(730-732)Ggc>Tgc	p.G244C		NM_182519.2	NP_872325.2	P59827	BPIB4_HUMAN	BPI fold containing family B, member 4	244						cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)	p.G205C(1)									GCTCCTGCCCGGCGTGGGTGT	0.667																																					p.G244C		Atlas-SNP	.											C20orf186,NS,carcinoma,0,1	.	.	.	1	Substitution - Missense(1)	lung(1)	c.G730T						.						54	43	46					20																	31672750		2203	4300	6503	SO:0001583	missense	149954	exon4			CTGCCCGGCGTGG	AF549190	CCDS13213.2	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186191	ENSG00000186191		"BPI fold containing"	16179	protein-coding gene	gene with protein product		615718	"chromosome 20 open reading frame 186"	C20orf186		11971875, 21787333	Standard	NM_182519		Approved	dJ726C3.5, LPLUNC4	uc010zue.2	P59827	OTTHUMG00000032235	ENST00000375483.3:c.730G>T	chr20.hg19:g.31672750G>T	ENSP00000364632:p.Gly244Cys	20.0	0.0		16.0	5.0	NM_182519	Q5TDX6	Missense_Mutation	SNP	ENST00000375483.3	hg19	CCDS13213.2	.	.	.	.	.	.	.	.	.	.	G	17.80	3.478373	0.63849	.	.	ENSG00000186191	ENST00000375483	T	0.06142	3.34	3.39	3.39	0.38822	.	0.196114	0.34507	N	0.003914	T	0.20820	0.0501	M	0.71206	2.165	0.46678	D	0.999158	D	0.89917	1.0	D	0.97110	1.0	T	0.00521	-1.1691	10	0.87932	D	0	-17.045	10.14	0.42730	0.0:0.0:1.0:0.0	.	244	P59827	BPIB4_HUMAN	C	244	ENSP00000364632:G244C	ENSP00000364632:G244C	G	+	1	0	BPIFB4	31136411	0.998000	0.40836	0.994000	0.49952	0.910000	0.53928	4.873000	0.63057	1.749000	0.51849	0.484000	0.47621	GGC	.	.		0.667	BPIFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078655.5	NM_182519		T	31672750	G	T	31672750	3	4	348	1	0	0	0	0	1	0	0	0	2100	1116	39	1	744	1	C20orf186	20	31672750	Missense_Mutation	SNP	G	TCGA-UB-A7MF-01A-11D-A33K-10	22152609	31672750	31352770	95	49143										
PLCG1	5335	hgsc.bcm.edu	37	chr20	39802162	39802162	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	atgacagcaccaagcagaagAcagagtttgtgggtcagtct	12	8	2	4			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr20:39802162A>G	ENST00000373271.1	+	28	3787	c.3382A>G	c.(3382-3384)Aca>Gca	p.T1128A	PLCG1_ENST00000608689.1_3'UTR|PLCG1_ENST00000244007.3_Missense_Mutation_p.T1128A|PLCG1_ENST00000373272.2_Missense_Mutation_p.T1128A	NM_182811.1	NP_877963.1	P19174	PLCG1_HUMAN	phospholipase C, gamma 1	1128	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|cell migration (GO:0016477)|cellular response to epidermal growth factor stimulus (GO:0071364)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phospholipid catabolic process (GO:0009395)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cell projection (GO:0042995)|cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|protein kinase binding (GO:0019901)|receptor signaling protein activity (GO:0005057)			breast(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(16)|skin(6)|urinary_tract(2)	46		Myeloproliferative disorder(115;0.00878)				CAAGCAGAAGACAGAGTTTGT	0.572											OREG0025953	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T1128A		Atlas-SNP	.											.	PLCG1	111	.	0			c.A3382G						.						127	104	112					20																	39802162		2203	4300	6503	SO:0001583	missense	5335	exon28			CAGAAGACAGAGT	M34667	CCDS13313.1, CCDS13314.1	20q12-q13.1	2013-02-14	2004-01-29		ENSG00000124181	ENSG00000124181	3.1.4.11	"Pleckstrin homology (PH) domain containing", "EF-hand domain containing", "SH2 domain containing"	9065	protein-coding gene	gene with protein product		172420	"phospholipase C, gamma 1 (formerly subtype 148)"	PLC1		2167438, 3254788	Standard	NM_182811		Approved	PLC148, PLC-II, PLCgamma1, NCKAP3	uc002xjo.1	P19174	OTTHUMG00000033082	ENST00000373271.1:c.3382A>G	chr20.hg19:g.39802162A>G	ENSP00000362368:p.Thr1128Ala	49.0	0.0	888	45.0	4.0	NM_182811	B7ZLY7|B9EGH4|E1P5W4|Q2V575	Missense_Mutation	SNP	ENST00000373271.1	hg19	CCDS13314.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.133710	0.77662	.	.	ENSG00000124181	ENST00000244007;ENST00000373271;ENST00000373272	T;T;T	0.48522	0.81;0.81;0.81	5.2	5.2	0.72013	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.78735	0.4330	H	0.97077	3.935	0.80722	D	1	D;D;D	0.76494	0.998;0.998;0.999	D;D;D	0.74674	0.973;0.974;0.984	D	0.86422	0.1755	10	0.87932	D	0	.	15.0623	0.71964	1.0:0.0:0.0:0.0	.	1128;1128;1128	P19174-2;P19174;A2A284	.;PLCG1_HUMAN;.	A	1128	ENSP00000244007:T1128A;ENSP00000362368:T1128A;ENSP00000362369:T1128A	ENSP00000244007:T1128A	T	+	1	0	PLCG1	39235576	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.339000	0.96797	1.967000	0.57214	0.374000	0.22700	ACA	.	.		0.572	PLCG1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080514.3	NM_182811		G	39802162	A	G	39802162	3	3	348	1	0	0	0	0	1	0	0	0	12044	275	10	2	3492	2	PLCG1	20	39802162	Missense_Mutation	SNP	A	TCGA-UB-A7MF-01A-11D-A33K-10	8129412	39802162	23223358	96	49144										
POTEH	23784	hgsc.bcm.edu	37	chr22	16287459	16287459	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	gctccccctgcagcaggggaAgcagtggcagcaccacttgc	13	15	0	0			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr22:16287459A>T	ENST00000343518.6	-	1	478	c.427T>A	c.(427-429)Ttc>Atc	p.F143I		NM_001136213.1	NP_001129685.1	Q6S545	POTEH_HUMAN	POTE ankyrin domain family, member H	143										NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(20)|ovary(1)|skin(7)|urinary_tract(2)	37						CAGCAGGGGAAGCAGTGGCAG	0.607																																					p.F143I		Atlas-SNP	.											.	POTEH	114	.	0			c.T427A						.						101	114	109					22																	16287459		2010	3844	5854	SO:0001583	missense	23784	exon1			AGGGGAAGCAGTG	AY462874	CCDS74808.1	22q11.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000198062	ENSG00000198062		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	133	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 7"	608913	"actin, beta-like 1", "ANKRD26-like family C, member 3"	ACTBL1, A26C3		10591208, 15276201, 21439273	Standard	NM_001136213		Approved	POTE22, CT104.7	uc010gqp.2	Q6S545	OTTHUMG00000140314	ENST00000343518.6:c.427T>A	chr22.hg19:g.16287459A>T	ENSP00000340610:p.Phe143Ile	743.0	0.0		607.0	108.0	NM_001136213	A2CEK4|A6NCI1|A9Z1W0	Missense_Mutation	SNP	ENST00000343518.6	hg19	CCDS46658.1	.	.	.	.	.	.	.	.	.	.	.	8.190	0.795719	0.16327	.	.	ENSG00000198062	ENST00000359587;ENST00000343518;ENST00000355872	T	0.25250	1.81	.	.	.	.	.	.	.	.	T	0.22360	0.0539	L	0.53249	1.67	0.09310	N	1	B	0.34181	0.44	B	0.33750	0.169	T	0.18147	-1.0346	7	0.54805	T	0.06	.	.	.	.	.	143	Q6S545	POTEH_HUMAN	I	106;143;143	ENSP00000340610:F143I	ENSP00000340610:F143I	F	-	1	0	POTEH	14667459	0.000000	0.05858	0.003000	0.11579	0.137000	0.21094	-0.060000	0.11712	0.355000	0.24131	0.000000	0.15137	TTC	.	.		0.607	POTEH-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276918.4	NM_001136213		T	16287459	A	T	16287459	3	4	348	1	0	0	0	0	1	0	0	0	12276	72	3	4	1250	4	POTEH	22	16287459	Missense_Mutation	SNP	A	TCGA-UB-A7MF-01A-11D-A33K-10		16287459	35017107	97	49145										
SF3A1	10291	hgsc.bcm.edu	37	chr22	30733037	30733037	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	tgtttctgcgcaggaactccTcctctggcatgaggctgtcc	11	13	2	1			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr22:30733037T>A	ENST00000215793.8	-	13	2238	c.2084A>T	c.(2083-2085)gAg>gTg	p.E695V	SF3A1_ENST00000439242.1_Missense_Mutation_p.E630V	NM_005877.4	NP_005868.1	Q15459	SF3A1_HUMAN	splicing factor 3a, subunit 1, 120kDa	695					gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U2-type spliceosomal complex (GO:0005684)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|urinary_tract(1)	29						CAGGAACTCCTCCTCTGGCAT	0.557																																					p.E695V		Atlas-SNP	.											.	SF3A1	61	.	0			c.A2084T						.						112	102	106					22																	30733037		2203	4300	6503	SO:0001583	missense	10291	exon13			AACTCCTCCTCTG	X85237	CCDS13875.1	22q12.2	2014-09-17	2002-08-29		ENSG00000099995	ENSG00000099995			10765	protein-coding gene	gene with protein product		605595	"splicing factor 3a, subunit 1, 120kD"			7489498	Standard	NM_005877		Approved	SF3a120, SAP114, PRPF21, Prp21	uc003ahl.3	Q15459	OTTHUMG00000151005	ENST00000215793.8:c.2084A>T	chr22.hg19:g.30733037T>A	ENSP00000215793:p.Glu695Val	109.0	0.0		106.0	41.0	NM_005877	E9PAW1	Missense_Mutation	SNP	ENST00000215793.8	hg19	CCDS13875.1	.	.	.	.	.	.	.	.	.	.	T	19.65	3.867266	0.72065	.	.	ENSG00000099995	ENST00000439242;ENST00000215793;ENST00000536049	T;T	0.39787	1.06;1.06	5.17	5.17	0.71159	.	0.050977	0.85682	D	0.000000	T	0.60932	0.2307	M	0.73217	2.22	0.80722	D	1	D	0.53312	0.959	P	0.62089	0.898	T	0.62053	-0.6935	10	0.45353	T	0.12	-19.4209	15.1839	0.72982	0.0:0.0:0.0:1.0	.	695	Q15459	SF3A1_HUMAN	V	630;695;592	ENSP00000390336:E630V;ENSP00000215793:E695V	ENSP00000215793:E695V	E	-	2	0	SF3A1	29063037	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.479000	0.81095	2.170000	0.68504	0.533000	0.62120	GAG	.	.		0.557	SF3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320916.2	NM_005877		A	30733037	T	A	30733037	3	1	348	1	0	0	0	0	1	0	0	0	14161	1551	54	4	313	4	SF3A1	22	30733037	Missense_Mutation	SNP	T	TCGA-UB-A7MF-01A-11D-A33K-10	14445578	30733037	20571529	98	49146										
DNAJB7	150353	hgsc.bcm.edu	37	chr22	41257117	41257117	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	tgcacctctttacgcttcttTtttttcctcttaccaccctc	2	16	3	0			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chr22:41257117T>G	ENST00000307221.4	-	1	1013	c.882A>C	c.(880-882)aaA>aaC	p.K294N	XPNPEP3_ENST00000482652.1_Intron|XPNPEP3_ENST00000357137.4_Intron|XPNPEP3_ENST00000414396.1_Intron|XPNPEP3_ENST00000544094.1_5'Flank|XPNPEP3_ENST00000541156.1_Intron	NM_145174.1	NP_660157.1	Q7Z6W7	DNJB7_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 7	294	Poly-Lys.						chaperone binding (GO:0051087)			breast(2)|endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	10						TACGCTTCTTTTTTTTCCTCT	0.383																																					p.K294N		Atlas-SNP	.											.	DNAJB7	29	.	0			c.A882C						.						105	100	101					22																	41257117		2203	4300	6503	SO:0001583	missense	150353	exon1			CTTCTTTTTTTTC	AF085232	CCDS14008.1	22q13.2	2011-09-02			ENSG00000172404	ENSG00000172404		"Heat shock proteins / DNAJ (HSP40)"	24986	protein-coding gene	gene with protein product		611336				12477932	Standard	NM_145174		Approved	HSC3	uc003azj.3	Q7Z6W7	OTTHUMG00000151202	ENST00000307221.4:c.882A>C	chr22.hg19:g.41257117T>G	ENSP00000307197:p.Lys294Asn	149.0	0.0		159.0	62.0	NM_145174	Q2M220|Q5H904|Q8WYJ7	Missense_Mutation	SNP	ENST00000307221.4	hg19	CCDS14008.1	.	.	.	.	.	.	.	.	.	.	T	11.59	1.683980	0.29872	.	.	ENSG00000172404	ENST00000307221	T	0.69926	-0.44	4.58	-1.07	0.09968	.	0.634564	0.13633	N	0.373555	T	0.77928	0.4204	M	0.78049	2.395	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.75255	-0.3382	10	0.59425	D	0.04	.	8.7574	0.34654	0.0:0.516:0.0:0.484	.	294	Q7Z6W7	DNJB7_HUMAN	N	294	ENSP00000307197:K294N	ENSP00000307197:K294N	K	-	3	2	DNAJB7	39587063	0.998000	0.40836	0.985000	0.45067	0.013000	0.08279	0.311000	0.19380	-0.267000	0.09325	-0.326000	0.08463	AAA	.	.		0.383	DNAJB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321765.1	NM_145174		G	41257117	T	G	41257117	3	3	348	1	0	0	0	0	1	0	0	0	4627	1838	64	5	51	5	DNAJB7	22	41257117	Missense_Mutation	SNP	T	TCGA-UB-A7MF-01A-11D-A33K-10	10524080	41257117	10047449	99	49147										
MOSPD2	158747	hgsc.bcm.edu	37	chrX	14915353	14915353	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	cctgtcagaaactggaataaAtagcattgtaagcatttttt	7	6	1	1			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chrX:14915353A>G	ENST00000380492.3	+	5	558	c.470A>G	c.(469-471)aAt>aGt	p.N157S	MOSPD2_ENST00000482354.1_Missense_Mutation_p.N157S|MOSPD2_ENST00000495110.1_3'UTR	NM_001177475.1|NM_152581.3	NP_001170946.1|NP_689794.1	Q8NHP6	MSPD2_HUMAN	motile sperm domain containing 2	157	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.					integral component of membrane (GO:0016021)|membrane (GO:0016020)	structural molecule activity (GO:0005198)			breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20	Hepatocellular(33;0.183)					ACTGGAATAAATAGCATTGTA	0.388																																					p.N157S		Atlas-SNP	.											.	MOSPD2	46	.	0			c.A470G						.						150	145	146					X																	14915353		2203	4300	6503	SO:0001583	missense	158747	exon5			GAATAAATAGCAT	AL834345	CCDS14162.1	Xp22.31	2006-03-16			ENSG00000130150	ENSG00000130150			28381	protein-coding gene	gene with protein product						15533722	Standard	NM_152581		Approved	MGC26706	uc004cwi.3	Q8NHP6	OTTHUMG00000021170	ENST00000380492.3:c.470A>G	chrX.hg19:g.14915353A>G	ENSP00000369860:p.Asn157Ser	94.0	0.0		93.0	82.0	NM_152581	Q8N3H2|Q8NA83	Missense_Mutation	SNP	ENST00000380492.3	hg19	CCDS14162.1	.	.	.	.	.	.	.	.	.	.	A	3.749	-0.052072	0.07362	.	.	ENSG00000130150	ENST00000380492	T	0.73897	-0.79	5.23	2.6	0.31112	Cellular retinaldehyde-binding/triple function, C-terminal (5);	0.119539	0.85682	N	0.000000	T	0.24198	0.0586	N	0.00045	-2.445	0.36913	D	0.891003	B	0.14012	0.009	B	0.17098	0.017	T	0.44283	-0.9338	10	0.02654	T	1	-17.9392	5.4354	0.16478	0.4155:0.0:0.5845:0.0	.	157	Q8NHP6	MSPD2_HUMAN	S	157	ENSP00000369860:N157S	ENSP00000369860:N157S	N	+	2	0	MOSPD2	14825274	1.000000	0.71417	0.988000	0.46212	0.951000	0.60555	6.085000	0.71343	0.714000	0.32081	0.430000	0.28490	AAT	.	.		0.388	MOSPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055837.1	NM_152581		G	14915353	A	G	14915353	3	3	348	1	0	0	0	0	1	0	0	0	9725	101	4	2	488	2	MOSPD2	23	14915353	Missense_Mutation	SNP	A	TCGA-UB-A7MF-01A-11D-A33K-10		14915353	140355207	100	49148										
SSX5	6758	hgsc.bcm.edu	37	chrX	48054255	48054255	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0792079207920792	8	1	1.48751440645409	2.71757439640651	0.847883211678832	0.659442724458204	1	0	gctttcatcttttcccactcTttctcagagaagtatttggc	6	11	4	1			TCGA-UB-A7MF-01A-11D-A33K-10	TCGA-UB-A7MF-10A-01D-A33K-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	681bd4c8-baed-4557-911b-588c343ee8cd	ebf05fa8-848e-4a45-85ad-42311dac4923	g.chrX:48054255T>A	ENST00000376923.1	-	2	104	c.105A>T	c.(103-105)aaA>aaT	p.K35N	SSX5_ENST00000311798.1_Missense_Mutation_p.K76N|SSX5_ENST00000347757.1_Missense_Mutation_p.K35N			O60225	SSX5_HUMAN	synovial sarcoma, X breakpoint 5	35	KRAB-related. {ECO:0000255|PROSITE- ProRule:PRU00120}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			endometrium(3)|kidney(1)|large_intestine(6)|lung(7)|skin(1)	18						TTTCCCACTCTTTCTCAGAGA	0.403																																					p.K76N		Atlas-SNP	.											.	SSX5	41	.	0			c.A228T						.						125	108	114					X																	48054255		2203	4299	6502	SO:0001583	missense	6758	exon4			CCACTCTTTCTCA	BC016640	CCDS14288.1, CCDS14289.1	Xp11.23	2008-02-05			ENSG00000165583	ENSG00000165583			11339	protein-coding gene	gene with protein product		300327					Standard	NM_021015		Approved		uc004diz.1	O60225	OTTHUMG00000021471	ENST00000376923.1:c.105A>T	chrX.hg19:g.48054255T>A	ENSP00000366122:p.Lys35Asn	178.0	0.0		145.0	105.0	NM_021015	Q5JQ59|Q5JQ60|Q96AW3	Missense_Mutation	SNP	ENST00000376923.1	hg19	CCDS14289.1	.	.	.	.	.	.	.	.	.	.	N	5.887	0.347704	0.11126	.	.	ENSG00000165583	ENST00000311798;ENST00000376923;ENST00000347757	T;T;T	0.00840	5.63;5.63;5.63	1.51	-1.69	0.08186	Krueppel-associated box (2);Krueppel-associated box-related (1);	1.119480	0.06749	N	0.779719	T	0.01661	0.0053	M	0.77313	2.365	0.09310	N	1	B;B	0.15473	0.007;0.013	B;B	0.23419	0.016;0.046	T	0.47262	-0.9131	10	0.72032	D	0.01	.	2.2119	0.03950	0.0:0.2324:0.3169:0.4506	.	35;76	O60225;O60225-2	SSX5_HUMAN;.	N	76;35;35	ENSP00000312415:K76N;ENSP00000366122:K35N;ENSP00000290558:K35N	ENSP00000312415:K76N	K	-	3	2	SSX5	47939199	0.000000	0.05858	0.002000	0.10522	0.024000	0.10985	-0.673000	0.05239	-0.508000	0.06540	0.143000	0.16000	AAA	.	.		0.403	SSX5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056466.1	NM_021015		A	48054255	T	A	48054255	3	1	348	1	0	0	0	0	1	0	0	0	15223	1606	56	4	481	4	SSX5	23	48054255	Missense_Mutation	SNP	T	TCGA-UB-A7MF-01A-11D-A33K-10	33138902	48054255	107216305	101	49149										
CD1A	909	hgsc.bcm.edu	37	chr1	158225111	158225111	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	tcggtcatttgagggaattcGtagatacgcccatgaattgc	11	8	1	3	rs139349958		TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr1:158225111G>A	ENST00000289429.5	+	2	829	c.296G>A	c.(295-297)cGt>cAt	p.R99H		NM_001763.2	NP_001754.2	P06126	CD1A_HUMAN	CD1a molecule	99					antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)				NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(14)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(1)	32	all_hematologic(112;0.0378)				Antithymocyte globulin(DB00098)	GAGGGAATTCGTAGATACGCC	0.468																																					p.R99H		Atlas-SNP	.											.	CD1A	88	.	0			c.G296A						.	G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	86	83	84		296	0.1	0	1	dbSNP_134	84	0,8600		0,0,4300	no	missense	CD1A	NM_001763.2	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	99/328	158225111	1,13005	2203	4300	6503	SO:0001583	missense	909	exon2			GAATTCGTAGATA	M28825	CCDS1174.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158477	ENSG00000158477		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	1634	protein-coding gene	gene with protein product		188370	"CD1A antigen, a polypeptide", "CD1a antigen"	CD1		2447586, 2784820	Standard	NM_001763		Approved		uc001frt.3	P06126	OTTHUMG00000017512	ENST00000289429.5:c.296G>A	chr1.hg19:g.158225111G>A	ENSP00000289429:p.Arg99His	98.0	0.0		131.0	35.0	NM_001763	D3DVD7|Q13962|Q5TDJ8|Q9UMM4|Q9Y5M5	Missense_Mutation	SNP	ENST00000289429.5	hg19	CCDS1174.1	.	.	.	.	.	.	.	.	.	.	G	6.021	0.372180	0.11409	2.27E-4	0.0	ENSG00000158477	ENST00000289429	T	0.06687	3.27	4.07	0.103	0.14526	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	1.769060	0.03408	N	0.204308	T	0.00906	0.0030	N	0.02721	-0.515	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.44742	-0.9308	10	0.25106	T	0.35	0.0237	3.4602	0.07529	0.5867:0.0:0.1039:0.3094	.	99	P06126	CD1A_HUMAN	H	99	ENSP00000289429:R99H	ENSP00000289429:R99H	R	+	2	0	CD1A	156491735	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.021000	0.13489	-0.083000	0.12618	-0.397000	0.06425	CGT	.	G|1.000;A|0.000		0.468	CD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046349.2	NM_001763		A	158225111	G	A	158225111	3	1	349	1	0	0	0	0	1	0	0	0	2976	1145	40	1	302	1	CD1A	1	158225111	Missense_Mutation	SNP	G	TCGA-UB-AA0U-01A-11D-A382-10		158225111	91025510	1	49150										
C1orf35	79169	hgsc.bcm.edu	37	chr1	228289844	228289844	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	aggctgccgaggtcccgggcCcgccgctctctacgcggtga	15	16	1	1			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr1:228289844C>T	ENST00000272139.4	-	6	704	c.470G>A	c.(469-471)gGg>gAg	p.G157E	C1orf35_ENST00000472617.1_5'UTR	NM_024319.2	NP_077295.1	Q9BU76	MMTA2_HUMAN	chromosome 1 open reading frame 35	157							poly(A) RNA binding (GO:0044822)			large_intestine(1)|lung(1)|skin(1)	3		Prostate(94;0.0488)				GGTCCCGGGCCCGCCGCTCTC	0.746																																					p.G157E		Atlas-SNP	.											.	C1orf35	17	.	0			c.G470A						.						5	10	8					1																	228289844		1927	4019	5946	SO:0001583	missense	79169	exon6			CCGGGCCCGCCGC	AY137773	CCDS1566.1	1q42.13	2012-06-25			ENSG00000143793	ENSG00000143793			19032	protein-coding gene	gene with protein product	"multiple myeloma tumor-associated protein 2"					12545221	Standard	NM_024319		Approved	MGC4174, MMTAG2	uc001hrx.3	Q9BU76	OTTHUMG00000037793	ENST00000272139.4:c.470G>A	chr1.hg19:g.228289844C>T	ENSP00000272139:p.Gly157Glu	50.0	0.0		72.0	14.0	NM_024319	Q6P5Y0|Q6ZTZ6|Q6ZWA6|Q8IZH3	Missense_Mutation	SNP	ENST00000272139.4	hg19	CCDS1566.1	.	.	.	.	.	.	.	.	.	.	C	9.361	1.067920	0.20067	.	.	ENSG00000143793	ENST00000272139	.	.	.	4.13	2.03	0.26663	.	0.785067	0.11877	N	0.520881	T	0.26991	0.0661	L	0.40543	1.245	0.09310	N	1	B	0.33694	0.421	B	0.27500	0.08	T	0.12682	-1.0538	9	0.02654	T	1	-19.3943	11.6334	0.51189	0.0:0.6618:0.3382:0.0	.	157	Q9BU76	MMTA2_HUMAN	E	157	.	ENSP00000272139:G157E	G	-	2	0	C1orf35	226356467	0.000000	0.05858	0.001000	0.08648	0.711000	0.40976	0.575000	0.23729	1.057000	0.40506	0.491000	0.48974	GGG	.	.		0.746	C1orf35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092245.1	NM_024319		T	228289844	C	T	228289844	3	4	349	1	0	0	0	0	1	0	0	0	2040	623	22	3	333	3	C1orf35	1	228289844	Missense_Mutation	SNP	C	TCGA-UB-AA0U-01A-11D-A382-10	70064733	228289844	20960777	2	49151										
NLRP3	114548	hgsc.bcm.edu	37	chr1	247607349	247607349	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	agcactaatcagaatctcacGcacctttacctgcgaggcaa	7	13	2	1	rs201764635		TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr1:247607349G>A	ENST00000336119.3	+	7	3491	c.2745G>A	c.(2743-2745)acG>acA	p.T915T	NLRP3_ENST00000366497.2_Silent_p.T858T|NLRP3_ENST00000391828.3_Silent_p.T915T|NLRP3_ENST00000391827.2_Silent_p.T858T|NLRP3_ENST00000366496.2_Silent_p.T858T|NLRP3_ENST00000348069.2_Silent_p.T801T	NM_001127462.2|NM_001243133.1|NM_004895.4	NP_001120934.1|NP_001230062.1|NP_004886.3	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3	915					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|defense response (GO:0006952)|defense response to virus (GO:0051607)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|interleukin-1 secretion (GO:0050701)|interleukin-18 production (GO:0032621)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|NLRP3 inflammasome complex assembly (GO:0044546)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|NLRP3 inflammasome complex (GO:0072559)	ATP binding (GO:0005524)|peptidoglycan binding (GO:0042834)			NS(1)|breast(3)|endometrium(6)|kidney(1)|large_intestine(19)|lung(85)|ovary(9)|pancreas(2)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	142	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			AGAATCTCACGCACCTTTACC	0.512																																					p.T915T		Atlas-SNP	.											.	NLRP3	286	.	0			c.G2745A						.						197	157	171					1																	247607349		2203	4300	6503	SO:0001819	synonymous_variant	114548	exon7			TCTCACGCACCTT	AF054176	CCDS1632.1, CCDS1633.1, CCDS44346.1, CCDS44347.1	1q44	2014-09-17	2006-12-08	2006-12-08	ENSG00000162711	ENSG00000162711		"Nucleotide-binding domain and leucine rich repeat containing"	16400	protein-coding gene	gene with protein product	"Cryopyrin", "nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 3"	606416	"cold autoinflammatory syndrome 1"	C1orf7, CIAS1		10741953	Standard	NM_183395		Approved	AGTAVPRL, AII, AVP, FCAS, FCU, NALP3, PYPAF1, MWS, CLR1.1	uc001icr.3	Q96P20	OTTHUMG00000040647	ENST00000336119.3:c.2745G>A	chr1.hg19:g.247607349G>A		102.0	0.0		147.0	33.0	NM_004895	B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Silent	SNP	ENST00000336119.3	hg19	CCDS1632.1																																																																																			.	.		0.512	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	NM_004895		A	247607349	G	A	247607349	2	1	349	1	0	0	0	0	0	0	0	1	10487	1074	38	1		1	NLRP3	1	247607349	Silent	SNP	G	TCGA-UB-AA0U-01A-11D-A382-10	19317505	247607349	1643272	3	49152										
MYT1L	23040	hgsc.bcm.edu	37	chr2	1926738	1926738	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	caacaccgtgtccttgggctAatagtttaagggagtccact	10	10	0	0			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr2:1926738A>G	ENST00000399161.2	-	10	1550	c.803T>C	c.(802-804)tTa>tCa	p.L268S	MYT1L_ENST00000428368.2_Missense_Mutation_p.L268S	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	268					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		TCCTTGGGCTAATAGTTTAAG	0.413																																					p.L268S		Atlas-SNP	.											.	MYT1L	241	.	0			c.T803C						.						189	183	185					2																	1926738		1958	4150	6108	SO:0001583	missense	23040	exon10			TGGGCTAATAGTT	AF036943	CCDS46222.1	2p25.3	2013-01-10			ENSG00000186487	ENSG00000186487		"Zinc fingers, C2HC-type containing"	7623	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 1"	613084				9373037	Standard	XM_006711862		Approved	KIAA1106, NZF1, ZC2HC4B	uc002qxd.3	Q9UL68	OTTHUMG00000151407	ENST00000399161.2:c.803T>C	chr2.hg19:g.1926738A>G	ENSP00000382114:p.Leu268Ser	124.0	0.0		124.0	25.0	NM_015025	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Missense_Mutation	SNP	ENST00000399161.2	hg19		.	.	.	.	.	.	.	.	.	.	A	13.39	2.221583	0.39300	.	.	ENSG00000186487	ENST00000399161;ENST00000295067;ENST00000428368	T;T	0.59772	0.24;0.24	6.07	6.07	0.98685	.	0.082418	0.49305	D	0.000150	T	0.64757	0.2627	L	0.34521	1.04	0.33530	D	0.593518	D;D	0.89917	0.981;1.0	P;D	0.91635	0.69;0.999	T	0.64002	-0.6509	10	0.10636	T	0.68	-12.8367	16.6288	0.85011	1.0:0.0:0.0:0.0	.	268;268	Q9UL68;Q9UL68-4	MYT1L_HUMAN;.	S	268;216;268	ENSP00000382114:L268S;ENSP00000396103:L268S	ENSP00000295067:L216S	L	-	2	0	MYT1L	1905745	1.000000	0.71417	0.003000	0.11579	0.024000	0.10985	9.248000	0.95456	2.326000	0.78906	0.533000	0.62120	TTA	.	.		0.413	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025		G	1926738	A	G	1926738	3	3	349	1	0	0	0	0	1	0	0	0	10116	372	13	2	2815	2	MYT1L	2	1926738	Missense_Mutation	SNP	A	TCGA-UB-AA0U-01A-11D-A382-10		1926738	241272635	4	49153										
ASXL2	55252	hgsc.bcm.edu	37	chr2	25966699	25966699	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	ctgagattagagcaggacctGttggagaaggtgctttctcc	13	8	1	3			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr2:25966699G>A	ENST00000435504.4	-	13	2800	c.2507C>T	c.(2506-2508)aCa>aTa	p.T836I	ASXL2_ENST00000404843.1_Missense_Mutation_p.T576I|ASXL2_ENST00000336112.4_Missense_Mutation_p.T808I|ASXL2_ENST00000272341.4_Missense_Mutation_p.T576I			Q76L83	ASXL2_HUMAN	additional sex combs like transcriptional regulator 2	836					adult heart development (GO:0007512)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of histone H3-K27 trimethylation (GO:1902466)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(7)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(3)	33	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGCAGGACCTGTTGGAGAAGG	0.507																																					p.T836I		Atlas-SNP	.											.	ASXL2	217	.	0			c.C2507T						.						178	177	177					2																	25966699		2038	4180	6218	SO:0001583	missense	55252	exon12			GGACCTGTTGGAG			2p24.1	2014-06-17	2014-06-17		ENSG00000143970	ENSG00000143970			23805	protein-coding gene	gene with protein product		612991	"additional sex combs like 2 (Drosophila)"			12888926	Standard	NM_018263		Approved	ASXH2, FLJ10898, KIAA1685	uc002rgs.2	Q76L83	OTTHUMG00000152176	ENST00000435504.4:c.2507C>T	chr2.hg19:g.25966699G>A	ENSP00000391447:p.Thr836Ile	88.0	0.0		83.0	37.0	NM_018263	Q53TC9|Q5H9U4|Q76L81|Q86XM1|Q9C0H8|Q9NV67	Missense_Mutation	SNP	ENST00000435504.4	hg19		.	.	.	.	.	.	.	.	.	.	G	12.16	1.853462	0.32791	.	.	ENSG00000143970	ENST00000435504;ENST00000336112;ENST00000404843;ENST00000272341	T;T;T;T	0.22539	1.95;1.95;2.26;2.26	5.57	1.7	0.24286	.	1.494570	0.03580	N	0.230053	T	0.19604	0.0471	L	0.43152	1.355	0.09310	N	1	P;B	0.40398	0.716;0.201	B;B	0.36666	0.23;0.075	T	0.22591	-1.0212	10	0.54805	T	0.06	5.8076	6.2669	0.20932	0.142:0.0:0.5956:0.2624	.	576;836	Q76L83-2;Q76L83	.;ASXL2_HUMAN	I	836;808;576;576	ENSP00000391447:T836I;ENSP00000337250:T808I;ENSP00000383920:T576I;ENSP00000272341:T576I	ENSP00000272341:T576I	T	-	2	0	ASXL2	25820203	0.013000	0.17824	0.004000	0.12327	0.978000	0.69477	1.392000	0.34486	0.033000	0.15463	-0.253000	0.11424	ACA	.	.		0.507	ASXL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000325593.3	NM_018263		A	25966699	G	A	25966699	3	1	349	1	0	0	0	0	1	0	0	0	1067	1377	48	3	1804	3	ASXL2	2	25966699	Missense_Mutation	SNP	G	TCGA-UB-AA0U-01A-11D-A382-10	24039961	25966699	217232674	5	49154										
FOSL2	2355	hgsc.bcm.edu	37	chr2	28635208	28635208	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	ctagcgtcctggagcaggagTcacccgcatctccctccgaa	10	16	2	0			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr2:28635208T>C	ENST00000264716.4	+	4	1737	c.874T>C	c.(874-876)Tca>Cca	p.S292P	FOSL2_ENST00000379619.1_Missense_Mutation_p.S284P|FOSL2_ENST00000545753.1_Missense_Mutation_p.S253P	NM_005253.3	NP_005244.1	P15408	FOSL2_HUMAN	FOS-like antigen 2	292					cell death (GO:0008219)|cellular response to hormone stimulus (GO:0032870)|female pregnancy (GO:0007565)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to mechanical stimulus (GO:0009612)|response to morphine (GO:0043278)|response to progesterone (GO:0032570)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(1)|large_intestine(3)|lung(1)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	14	Acute lymphoblastic leukemia(172;0.155)					GGAGCAGGAGTCACCCGCATC	0.622																																					p.S292P		Atlas-SNP	.											.	FOSL2	39	.	0			c.T874C						.						78	63	68					2																	28635208		2203	4300	6503	SO:0001583	missense	2355	exon4			CAGGAGTCACCCG		CCDS1766.1	2p23.3	2013-01-10			ENSG00000075426	ENSG00000075426		"basic leucine zipper proteins"	3798	protein-coding gene	gene with protein product		601575					Standard	NM_005253		Approved	FRA2, FLJ23306	uc002rma.3	P15408	OTTHUMG00000097832	ENST00000264716.4:c.874T>C	chr2.hg19:g.28635208T>C	ENSP00000264716:p.Ser292Pro	50.0	0.0		42.0	12.0	NM_005253	B2RD58|B3KP27|B4DYV4|Q6FG46	Missense_Mutation	SNP	ENST00000264716.4	hg19	CCDS1766.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.003503	0.74932	.	.	ENSG00000075426	ENST00000379619;ENST00000264716;ENST00000545753	T;T;T	0.78481	-1.18;-0.17;-1.16	5.71	5.71	0.89125	.	0.574568	0.18921	N	0.127495	T	0.81470	0.4829	L	0.49350	1.555	0.54753	D	0.999988	D	0.65815	0.995	P	0.53185	0.72	T	0.83150	-0.0104	10	0.72032	D	0.01	-14.0961	15.9725	0.80031	0.0:0.0:0.0:1.0	.	292	P15408	FOSL2_HUMAN	P	284;292;253	ENSP00000368939:S284P;ENSP00000264716:S292P;ENSP00000439303:S253P	ENSP00000264716:S292P	S	+	1	0	FOSL2	28488712	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	2.605000	0.46283	2.174000	0.68829	0.533000	0.62120	TCA	.	.		0.622	FOSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215116.2	NM_005253		C	28635208	T	C	28635208	3	2	349	1	0	0	0	0	1	0	0	0	5996	1667	58	2	888	2	FOSL2	2	28635208	Missense_Mutation	SNP	T	TCGA-UB-AA0U-01A-11D-A382-10	2668509	28635208	214564165	6	49155										
IL1RL2	8808	hgsc.bcm.edu	37	chr2	102808479	102808479	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	gtggtttaccaaatttatcaGatgagtacaagcaaatatta	7	5	1	2			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr2:102808479G>A	ENST00000264257.2	+	4	514	c.388G>A	c.(388-390)Gat>Aat	p.D130N	IL1RL2_ENST00000481806.1_Intron|IL1RL2_ENST00000539491.1_Missense_Mutation_p.D130N|IL1RL2_ENST00000441515.2_Intron	NM_003854.2	NP_003845.2	Q9HB29	ILRL2_HUMAN	interleukin 1 receptor-like 2	130	Ig-like C2-type 2.				cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of T cell differentiation (GO:0045582)|regulation of inflammatory response (GO:0050727)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type I, activating receptor activity (GO:0004909)			breast(1)|cervix(1)|endometrium(5)|large_intestine(6)|liver(2)|lung(8)|ovary(2)|prostate(1)	26						AAATTTATCAGATGAGTACAA	0.368																																					p.D130N		Atlas-SNP	.											.	IL1RL2	118	.	0			c.G388A						.						106	103	104					2																	102808479		2203	4300	6503	SO:0001583	missense	8808	exon4			TTATCAGATGAGT	U49065	CCDS2056.1	2q12	2013-01-14			ENSG00000115598	ENSG00000115598		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5999	protein-coding gene	gene with protein product		604512				8898719, 10191101, 11466363	Standard	NM_003854		Approved	IL1R-rp2, IL1RRP2	uc002tbs.3	Q9HB29	OTTHUMG00000130776	ENST00000264257.2:c.388G>A	chr2.hg19:g.102808479G>A	ENSP00000264257:p.Asp130Asn	351.0	0.0		318.0	59.0	NM_003854	A4FU63|Q13525|Q45H74|Q53TU8|Q587I8	Missense_Mutation	SNP	ENST00000264257.2	hg19	CCDS2056.1	.	.	.	.	.	.	.	.	.	.	G	13.68	2.308224	0.40895	.	.	ENSG00000115598	ENST00000264257;ENST00000421464;ENST00000539491	T;T;T	0.12361	2.69;2.69;2.69	4.87	-1.8	0.07907	Immunoglobulin-like (1);	1.386070	0.04654	N	0.407677	T	0.09686	0.0238	L	0.41079	1.255	0.09310	N	1	B	0.17268	0.021	B	0.21360	0.034	T	0.35943	-0.9768	10	0.23891	T	0.37	.	0.2421	0.00193	0.2704:0.1474:0.281:0.3012	.	130	Q9HB29	ILRL2_HUMAN	N	130	ENSP00000264257:D130N;ENSP00000387611:D130N;ENSP00000442184:D130N	ENSP00000264257:D130N	D	+	1	0	IL1RL2	102174911	0.000000	0.05858	0.001000	0.08648	0.728000	0.41692	-0.256000	0.08757	-0.144000	0.11314	0.655000	0.94253	GAT	.	.		0.368	IL1RL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253290.1	NM_003854		A	102808479	G	A	102808479	3	1	349	1	0	0	0	0	1	0	0	0	7673	942	33	3	398	3	IL1RL2	2	102808479	Missense_Mutation	SNP	G	TCGA-UB-AA0U-01A-11D-A382-10	74173271	102808479	140390894	7	49156										
MAP3K2	10746	hgsc.bcm.edu	37	chr2	128084382	128084382	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	gggaggagaacttctatctcTactagtaggacctcaaggaa	11	8	3	1			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr2:128084382T>C	ENST00000409947.1	-	8	760	c.478A>G	c.(478-480)Aga>Gga	p.R160G	MAP3K2_ENST00000344908.5_Missense_Mutation_p.R160G			Q9Y2U5	M3K2_HUMAN	mitogen-activated protein kinase kinase kinase 2	160					activation of JUN kinase activity (GO:0007257)|activation of MAPK activity (GO:0000187)|cellular response to mechanical stimulus (GO:0071260)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|large_intestine(1)|lung(3)|ovary(2)	7	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0706)	Bosutinib(DB06616)	CTTCTATCTCTACTAGTAGGA	0.358																																					p.R160G		Atlas-SNP	.											.	MAP3K2	78	.	0			c.A478G						.						79	79	79					2																	128084382		1808	4076	5884	SO:0001583	missense	10746	exon7			TATCTCTACTAGT	AF111105	CCDS46404.1	2q21.1	2011-06-09			ENSG00000169967	ENSG00000169967		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6854	protein-coding gene	gene with protein product	"MAP/ERK kinase kinase 2"	609487		MEKK2		8621389, 10085062	Standard	NM_006609		Approved	MEKK2B	uc002toj.2	Q9Y2U5	OTTHUMG00000153397	ENST00000409947.1:c.478A>G	chr2.hg19:g.128084382T>C	ENSP00000387246:p.Arg160Gly	67.0	0.0		83.0	25.0	NM_006609	B9EG87|Q53QL9|Q53S75|Q59GZ6|Q8NC32|Q9NYK3	Missense_Mutation	SNP	ENST00000409947.1	hg19	CCDS46404.1	.	.	.	.	.	.	.	.	.	.	T	12.92	2.083803	0.36758	.	.	ENSG00000169967	ENST00000409947;ENST00000344908	T;T	0.67171	-0.25;-0.25	5.73	5.73	0.89815	.	0.046997	0.85682	D	0.000000	T	0.45397	0.1340	N	0.08118	0	0.45914	D	0.998756	B	0.23128	0.08	B	0.23275	0.045	T	0.42275	-0.9461	10	0.22109	T	0.4	.	12.2793	0.54755	0.0:0.0:0.1809:0.8191	.	160	Q9Y2U5	M3K2_HUMAN	G	160	ENSP00000387246:R160G;ENSP00000343463:R160G	ENSP00000343463:R160G	R	-	1	2	MAP3K2	127800852	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	5.646000	0.67916	2.187000	0.69744	0.402000	0.26972	AGA	.	.		0.358	MAP3K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331014.1	NM_006609		C	128084382	T	C	128084382	3	2	349	1	0	0	0	0	1	0	0	0	9259	1530	53	2	1421	2	MAP3K2	2	128084382	Missense_Mutation	SNP	T	TCGA-UB-AA0U-01A-11D-A382-10	25275903	128084382	115114991	8	49157										
ZRANB3	84083	hgsc.bcm.edu	37	chr2	136026637	136026637	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	attctgtgagctcggtcttcTgcttgttttatatgtccagg	10	8	3	1			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr2:136026637T>C	ENST00000264159.6	-	11	1397	c.1281A>G	c.(1279-1281)gcA>gcG	p.A427A	ZRANB3_ENST00000401392.1_Silent_p.A427A|ZRANB3_ENST00000536680.1_Silent_p.A427A	NM_032143.2	NP_115519.2	Q5FWF4	ZRAB3_HUMAN	zinc finger, RAN-binding domain containing 3	427	DNA annealing helicase activity.|Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|DNA rewinding (GO:0036292)|DNA strand renaturation (GO:0000733)|negative regulation of DNA recombination (GO:0045910)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to UV (GO:0009411)	nuclear replication fork (GO:0043596)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|endodeoxyribonuclease activity (GO:0004520)|helicase activity (GO:0004386)|K63-linked polyubiquitin binding (GO:0070530)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|upper_aerodigestive_tract(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.135)		CTCGGTCTTCTGCTTGTTTTA	0.403																																					p.A427A		Atlas-SNP	.											.	ZRANB3	109	.	0			c.A1281G						.						144	136	139					2																	136026637		1841	4092	5933	SO:0001819	synonymous_variant	84083	exon11			GTCTTCTGCTTGT	AL136824	CCDS46419.1, CCDS67963.1, CCDS74580.1	2q21.3	2013-05-13			ENSG00000121988	ENSG00000121988		"Zinc fingers, RAN-binding domain containing"	25249	protein-coding gene	gene with protein product						11230166	Standard	XM_005263809		Approved	DKFZP434B1727	uc002tum.3	Q5FWF4	OTTHUMG00000150475	ENST00000264159.6:c.1281A>G	chr2.hg19:g.136026637T>C		70.0	0.0		82.0	40.0	NM_032143	B3KYA1|B4E375|B5MDI3|D3DP76|E9PBP0|Q53SM1|Q6P2C4|Q8N1P4|Q9H0E8	Silent	SNP	ENST00000264159.6	hg19	CCDS46419.1																																																																																			.	.		0.403	ZRANB3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318254.1	NM_032143		C	136026637	T	C	136026637	2	2	349	1	0	0	0	0	0	0	0	1	18239	1567	55	2		2	ZRANB3	2	136026637	Silent	SNP	T	TCGA-UB-AA0U-01A-11D-A382-10	7942255	136026637	107172736	9	49158										
WDR12	55759	hgsc.bcm.edu	37	chr2	203765765	203765765	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	tactgatgagatgttctccaTttccatgtgtttgtccaagg	9	8	1	2			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr2:203765765T>C	ENST00000261015.4	-	3	963	c.214A>G	c.(214-216)Atg>Gtg	p.M72V	WDR12_ENST00000477723.1_5'UTR	NM_018256.3	NP_060726.3			WD repeat domain 12											endometrium(3)|large_intestine(1)|liver(1)|lung(6)|prostate(1)|skin(1)	13						ATGTTCTCCATTTCCATGTGT	0.368																																					p.M72V		Atlas-SNP	.											.	WDR12	35	.	0			c.A214G						.						120	98	105					2																	203765765		2203	4300	6503	SO:0001583	missense	55759	exon3			TCTCCATTTCCAT	AF242546	CCDS2356.1	2q33.1	2013-01-09			ENSG00000138442	ENSG00000138442		"WD repeat domain containing"	14098	protein-coding gene	gene with protein product						16043514, 17353269	Standard	NM_018256		Approved	YTM1, FLJ10881	uc002uzl.3	Q9GZL7	OTTHUMG00000132855	ENST00000261015.4:c.214A>G	chr2.hg19:g.203765765T>C	ENSP00000261015:p.Met72Val	74.0	0.0		67.0	13.0	NM_018256		Missense_Mutation	SNP	ENST00000261015.4	hg19	CCDS2356.1	.	.	.	.	.	.	.	.	.	.	T	8.634	0.894445	0.17613	.	.	ENSG00000138442	ENST00000261015	T	0.54866	0.55	5.83	1.84	0.25277	WD40 repeat-like-containing domain (1);	0.437153	0.25101	N	0.033138	T	0.29783	0.0744	N	0.22421	0.69	0.23809	N	0.996785	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.10894	-1.0610	10	0.30078	T	0.28	-0.6813	1.9179	0.03301	0.1492:0.3162:0.2896:0.245	.	72;72	Q53T99;Q9GZL7	.;WDR12_HUMAN	V	72	ENSP00000261015:M72V	ENSP00000261015:M72V	M	-	1	0	WDR12	203474010	0.963000	0.33076	0.998000	0.56505	0.933000	0.57130	0.250000	0.18235	0.047000	0.15862	-0.223000	0.12442	ATG	.	.		0.368	WDR12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256329.4	NM_018256		C	203765765	T	C	203765765	3	2	349	1	0	0	0	0	1	0	0	0	17289	1493	52	2	1101	2	WDR12	2	203765765	Missense_Mutation	SNP	T	TCGA-UB-AA0U-01A-11D-A382-10	67739128	203765765	39433608	10	49159										
IDH1	3417	hgsc.bcm.edu	37	chr2	209104688	209104688	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	ctactgtcttgccatctggaCaaaccagcacgctggtcatc	8	14	3	0			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr2:209104688C>G	ENST00000415913.1	-	8	1271	c.890G>C	c.(889-891)tGt>tCt	p.C297S	IDH1_ENST00000345146.2_Missense_Mutation_p.C297S|IDH1_ENST00000446179.1_Missense_Mutation_p.C297S	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	297					2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		GCCATCTGGACAAACCAGCAC	0.542			Mis		gliobastoma																																p.C297S	Pancreas(158;264 1958 3300 35450 36047)	Atlas-SNP	.		Dom	yes		2	2q33.3	3417	"isocitrate dehydrogenase 1 (NADP+), soluble"		O	.	IDH1	6310	.	0			c.G890C						.						137	106	117					2																	209104688		2203	4300	6503	SO:0001583	missense	3417	exon8			TCTGGACAAACCA		CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.890G>C	chr2.hg19:g.209104688C>G	ENSP00000390265:p.Cys297Ser	80.0	0.0		50.0	18.0	NM_005896	Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	hg19	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	C	19.27	3.795048	0.70452	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913	T;T;T	0.74737	-0.87;-0.87;-0.87	6.08	6.08	0.98989	Isopropylmalate dehydrogenase-like domain (2);	0.039026	0.85682	N	0.000000	T	0.81522	0.4840	L	0.31926	0.97	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.78800	-0.2062	10	0.38643	T	0.18	-8.9644	20.2672	0.98462	0.0:1.0:0.0:0.0	.	297	O75874	IDHC_HUMAN	S	297	ENSP00000260985:C297S;ENSP00000410513:C297S;ENSP00000390265:C297S	ENSP00000260985:C297S	C	-	2	0	IDH1	208812933	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.794000	0.85869	2.894000	0.99253	0.591000	0.81541	TGT	.	.		0.542	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			G	209104688	C	G	209104688	3	3	349	1	0	0	0	0	1	0	0	0	7503	478	17	4	366	4	IDH1	2	209104688	Missense_Mutation	SNP	C	TCGA-UB-AA0U-01A-11D-A382-10	5338923	209104688	34094685	11	49160										
ERBB4	2066	hgsc.bcm.edu	37	chr2	212251640	212251640	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	catccagctctcctcgtgggCtccgttctggggcaaacacg	11	15	2	0			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr2:212251640C>A	ENST00000342788.4	-	27	3729	c.3419G>T	c.(3418-3420)aGc>aTc	p.S1140I	ERBB4_ENST00000402597.1_Missense_Mutation_p.S1130I|ERBB4_ENST00000436443.1_Missense_Mutation_p.S1124I	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	1140					cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	TCCTCGTGGGCTCCGTTCTGG	0.532										TSP Lung(8;0.080)																											p.S1140I		Atlas-SNP	.											.	ERBB4	480	.	0			c.G3419T						.						157	143	148					2																	212251640		2203	4300	6503	SO:0001583	missense	2066	exon27			CGTGGGCTCCGTT	L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.3419G>T	chr2.hg19:g.212251640C>A	ENSP00000342235:p.Ser1140Ile	136.0	0.0		121.0	24.0	NM_005235	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	hg19	CCDS2394.1	.	.	.	.	.	.	.	.	.	.	C	13.38	2.219040	0.39201	.	.	ENSG00000178568	ENST00000342788;ENST00000436443;ENST00000402597	T;T;T	0.76186	-0.97;-1.0;-0.97	5.6	1.55	0.23275	.	0.705369	0.15165	N	0.276955	T	0.51176	0.1659	N	0.14661	0.345	0.21878	N	0.999492	B;B;B;B	0.15473	0.012;0.013;0.012;0.002	B;B;B;B	0.17098	0.004;0.017;0.004;0.002	T	0.40059	-0.9583	10	0.51188	T	0.08	.	1.7125	0.02895	0.1384:0.4338:0.1208:0.307	.	1114;1130;1124;1140	Q15303-4;Q15303-2;Q15303-3;Q15303	.;.;.;ERBB4_HUMAN	I	1140;1124;1130	ENSP00000342235:S1140I;ENSP00000403204:S1124I;ENSP00000385565:S1130I	ENSP00000342235:S1140I	S	-	2	0	ERBB4	211959885	0.301000	0.24444	1.000000	0.80357	0.996000	0.88848	0.957000	0.29215	0.306000	0.22856	0.462000	0.41574	AGC	.	.		0.532	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		A	212251640	C	A	212251640	3	1	349	1	0	0	0	0	1	0	0	0	5211	797	28	3	515	3	ERBB4	2	212251640	Missense_Mutation	SNP	C	TCGA-UB-AA0U-01A-11D-A382-10	3146952	212251640	30947733	12	49161										
XRCC5	7520	hgsc.bcm.edu	37	chr2	216977745	216977745	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	aactttgtttccaggcagctGttgtgctgtgtatggacgtg	13	7	0	0			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr2:216977745G>A	ENST00000392133.3	+	4	489	c.28G>A	c.(28-30)Gtt>Att	p.V10I	XRCC5_ENST00000392132.2_Missense_Mutation_p.V10I			P13010	XRCC5_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining)	10					brain development (GO:0007420)|cell proliferation (GO:0008283)|cellular hyperosmotic salinity response (GO:0071475)|cellular response to fatty acid (GO:0071398)|cellular response to X-ray (GO:0071481)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|hematopoietic stem cell differentiation (GO:0060218)|innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neurogenesis (GO:0050769)|positive regulation of type I interferon production (GO:0032481)|response to drug (GO:0042493)|telomere maintenance (GO:0000723)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|Ku70:Ku80 complex (GO:0043564)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nuclear chromosome, telomeric region (GO:0000784)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|telomeric DNA binding (GO:0042162)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			endometrium(1)|kidney(3)|large_intestine(8)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24		Renal(323;0.0328)		Epithelial(149;9.78e-06)|all cancers(144;0.000632)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.0117)		CCAGGCAGCTGTTGTGCTGTG	0.398								Non-homologous end-joining																													p.V10I		Atlas-SNP	.											.	XRCC5	64	.	0			c.G28A						.						161	155	157					2																	216977745		2203	4300	6503	SO:0001583	missense	7520	exon2			GCAGCTGTTGTGC	AF039597	CCDS2402.1	2q35	2008-07-31	2008-07-31		ENSG00000079246	ENSG00000079246			12833	protein-coding gene	gene with protein product	"Ku autoantigen, 80kDa"	194364	"X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining; Ku autoantigen, 80kD)"			9636207, 9214634	Standard	NM_021141		Approved	KU80, KARP-1, Ku86, KUB2	uc002vfy.3	P13010	OTTHUMG00000133059	ENST00000392133.3:c.28G>A	chr2.hg19:g.216977745G>A	ENSP00000375978:p.Val10Ile	97.0	0.0		89.0	19.0	NM_021141	A8K3X5|Q0Z7V0|Q4VBQ5|Q53HH7|Q7M4N0|Q9UCQ0|Q9UCQ1	Missense_Mutation	SNP	ENST00000392133.3	hg19	CCDS2402.1	.	.	.	.	.	.	.	.	.	.	G	9.363	1.068448	0.20067	.	.	ENSG00000079246	ENST00000392133;ENST00000392132	T;T	0.30182	1.54;1.54	5.12	4.24	0.50183	Ku70/Ku80, N-terminal alpha/beta (1);von Willebrand factor, type A (1);	0.167952	0.41500	D	0.000877	T	0.21962	0.0529	L	0.38838	1.175	0.36287	D	0.856165	B	0.17667	0.023	B	0.15870	0.014	T	0.14980	-1.0453	10	0.22109	T	0.4	.	9.2892	0.37775	0.1802:0.0:0.8198:0.0	.	10	P13010	XRCC5_HUMAN	I	10	ENSP00000375978:V10I;ENSP00000375977:V10I	ENSP00000375977:V10I	V	+	1	0	XRCC5	216685990	0.859000	0.29813	1.000000	0.80357	0.463000	0.32649	0.768000	0.26590	1.387000	0.46486	0.655000	0.94253	GTT	.	.		0.398	XRCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256675.3	NM_021141		A	216977745	G	A	216977745	3	1	349	1	0	0	0	0	1	0	0	0	17471	1377	48	3	34	3	XRCC5	2	216977745	Missense_Mutation	SNP	G	TCGA-UB-AA0U-01A-11D-A382-10	4726105	216977745	26221628	13	49162										
IGFBP5	3488	hgsc.bcm.edu	37	chr2	217559447	217559447	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	gaaggagcccaggctctgggCcggccccgcataggcggcca	16	15	1	0			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr2:217559447C>T	ENST00000233813.4	-	1	801	c.52G>A	c.(52-54)Gcc>Acc	p.A18T	AC007563.5_ENST00000447289.1_RNA	NM_000599.3	NP_000590.1	P24593	IBP5_HUMAN	insulin-like growth factor binding protein 5	18					cellular protein metabolic process (GO:0044267)|cellular response to cAMP (GO:0071320)|cellular response to organic cyclic compound (GO:0071407)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|hair follicle morphogenesis (GO:0031069)|intracellular signal transduction (GO:0035556)|mammary gland involution (GO:0060056)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of translation (GO:0017148)|osteoblast differentiation (GO:0001649)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell growth (GO:0001558)|regulation of glucose metabolic process (GO:0010906)|signal transduction (GO:0007165)|skeletal muscle tissue growth (GO:0048630)|striated muscle cell differentiation (GO:0051146)|type B pancreatic cell proliferation (GO:0044342)	extracellular region (GO:0005576)|insulin-like growth factor binding protein complex (GO:0016942)	insulin-like growth factor I binding (GO:0031994)			endometrium(1)|large_intestine(3)|lung(1)	5		Renal(323;0.0822)		Epithelial(149;2.1e-06)|all cancers(144;0.000165)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGGCTCTGGGCCGGCCCCGCA	0.687																																					p.A18T		Atlas-SNP	.											.	IGFBP5	13	.	0			c.G52A						.						4	6	5					2																	217559447		1887	3937	5824	SO:0001583	missense	3488	exon1			TCTGGGCCGGCCC		CCDS2405.1	2q35	2014-09-16			ENSG00000115461	ENSG00000115461			5474	protein-coding gene	gene with protein product		146734				7511611	Standard	NM_000599		Approved		uc002vgj.4	P24593	OTTHUMG00000133058	ENST00000233813.4:c.52G>A	chr2.hg19:g.217559447C>T	ENSP00000233813:p.Ala18Thr	93.0	0.0		83.0	27.0	NM_000599	Q5U0A3	Missense_Mutation	SNP	ENST00000233813.4	hg19	CCDS2405.1	.	.	.	.	.	.	.	.	.	.	C	13.96	2.393844	0.42410	.	.	ENSG00000115461	ENST00000233813;ENST00000449583	T;T	0.29397	1.57;2.09	4.32	2.27	0.28462	.	0.277575	0.35013	N	0.003513	T	0.14098	0.0341	N	0.16368	0.405	0.26804	N	0.969136	B	0.02656	0.0	B	0.01281	0.0	T	0.11767	-1.0574	10	0.19590	T	0.45	-23.989	4.9375	0.13948	0.3288:0.5621:0.0:0.1091	.	18	P24593	IBP5_HUMAN	T	18	ENSP00000233813:A18T;ENSP00000413474:A18T	ENSP00000233813:A18T	A	-	1	0	IGFBP5	217267692	0.986000	0.35501	0.981000	0.43875	0.950000	0.60333	1.234000	0.32660	1.938000	0.56188	0.455000	0.32223	GCC	.	.		0.687	IGFBP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256674.2	NM_000599		T	217559447	C	T	217559447	3	4	349	1	0	0	0	0	1	0	0	0	7591	739	26	3	782	3	IGFBP5	2	217559447	Missense_Mutation	SNP	C	TCGA-UB-AA0U-01A-11D-A382-10	581702	217559447	25639926	14	49163										
SLC4A3	6508	hgsc.bcm.edu	37	chr2	220502908	220502908	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	tcgtcgcatcatcggggactTtggcatccccatctccatcc	8	16	2	0			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr2:220502908T>A	ENST00000358055.3	+	18	3301	c.2789T>A	c.(2788-2790)tTt>tAt	p.F930Y	SLC4A3_ENST00000273063.6_Missense_Mutation_p.F957Y|SLC4A3_ENST00000373762.3_Missense_Mutation_p.F957Y|SLC4A3_ENST00000373760.2_Missense_Mutation_p.F930Y|SLC4A3_ENST00000317151.3_Missense_Mutation_p.F930Y			P48751	B3A3_HUMAN	solute carrier family 4 (anion exchanger), member 3	930	Membrane (anion exchange).				bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	51		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		ATCGGGGACTTTGGCATCCCC	0.597																																					p.F957Y		Atlas-SNP	.											.	SLC4A3	144	.	0			c.T2870A						.						83	56	66					2																	220502908		2203	4300	6503	SO:0001583	missense	6508	exon18			GGGACTTTGGCAT		CCDS2445.1, CCDS2446.1	2q35	2013-07-19	2013-07-19		ENSG00000114923	ENSG00000114923		"Solute carriers"	11029	protein-coding gene	gene with protein product	"Anion exchanger 3, neuronal"	106195	"solute carrier family 4, anion exchanger, member 3"			8001971	Standard	NM_005070		Approved	AE3, SLC2C	uc002vmo.4	P48751	OTTHUMG00000059238	ENST00000358055.3:c.2789T>A	chr2.hg19:g.220502908T>A	ENSP00000350756:p.Phe930Tyr	68.0	0.0		36.0	7.0	NM_201574	A6H8L2|A8K1Q9|B7ZVX6|B9EGD1|Q6YIQ9	Missense_Mutation	SNP	ENST00000358055.3	hg19	CCDS2445.1	.	.	.	.	.	.	.	.	.	.	T	33	5.272296	0.95429	.	.	ENSG00000114923	ENST00000358055;ENST00000373760;ENST00000273063;ENST00000373762;ENST00000356251;ENST00000317151	D;D;D;D;D	0.85629	-2.01;-2.01;-2.01;-2.01;-2.01	4.84	4.84	0.62591	Bicarbonate transporter, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.91945	0.7449	M	0.77486	2.375	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.93041	0.6457	10	0.87932	D	0	.	14.928	0.70893	0.0:0.0:0.0:1.0	.	634;930;957	P48751-2;P48751;P48751-3	.;B3A3_HUMAN;.	Y	930;930;957;957;190;930	ENSP00000350756:F930Y;ENSP00000362865:F930Y;ENSP00000273063:F957Y;ENSP00000362867:F957Y;ENSP00000314006:F930Y	ENSP00000273063:F957Y	F	+	2	0	SLC4A3	220211152	1.000000	0.71417	0.878000	0.34440	0.987000	0.75469	7.752000	0.85141	2.168000	0.68352	0.529000	0.55759	TTT	.	.		0.597	SLC4A3-009	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316472.1	NM_005070		A	220502908	T	A	220502908	3	1	349	1	0	0	0	0	1	0	0	0	14670	1841	64	4	2936	4	SLC4A3	2	220502908	Missense_Mutation	SNP	T	TCGA-UB-AA0U-01A-11D-A382-10	2943461	220502908	22696465	15	49164										
ADCY5	111	hgsc.bcm.edu	37	chr3	123166784	123166784	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	aggcagcaggcgcccagggaCagcaccgcgccgggccccgc	16	18	0	0			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr3:123166784C>T	ENST00000462833.1	-	1	1821	c.609G>A	c.(607-609)ctG>ctA	p.L203L		NM_183357.2	NP_899200.1	O95622	ADCY5_HUMAN	adenylate cyclase 5	203					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenosine receptor signaling pathway (GO:0001973)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			breast(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(22)|ovary(5)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(114;0.0342)		CGCCCAGGGACAGCAccgcgc	0.726																																					p.L203L		Atlas-SNP	.											.	ADCY5	169	.	0			c.G609A						.						7	8	8					3																	123166784		2143	4202	6345	SO:0001819	synonymous_variant	111	exon1			CAGGGACAGCACC	U65473	CCDS3022.1, CCDS56274.1	3q21.1	2013-02-04			ENSG00000173175	ENSG00000173175	4.6.1.1	"Adenylate cyclases"	236	protein-coding gene	gene with protein product		600293				10481931	Standard	NM_183357		Approved	AC5	uc003egh.2	O95622	OTTHUMG00000159517	ENST00000462833.1:c.609G>A	chr3.hg19:g.123166784C>T		43.0	0.0		43.0	13.0	NM_183357	B7Z8A6|Q7RTV7|Q8NFM3	Silent	SNP	ENST00000462833.1	hg19	CCDS3022.1																																																																																			.	.		0.726	ADCY5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355889.4	XM_171048		T	123166784	C	T	123166784	2	4	349	1	0	0	0	0	0	0	0	1	297	465	17	3		3	ADCY5	3	123166784	Silent	SNP	C	TCGA-UB-AA0U-01A-11D-A382-10		123166784	74855646	16	49165										
TRIM42	287015	hgsc.bcm.edu	37	chr3	140406640	140406640	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	aaagctgacaaggaggcaaaGcgaaaagagatcagaaatgg	13	5	1	3			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr3:140406640G>A	ENST00000286349.3	+	3	1307	c.1116G>A	c.(1114-1116)aaG>aaA	p.K372K		NM_152616.4	NP_689829.3	Q8IWZ5	TRI42_HUMAN	tripartite motif containing 42	372						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(11)|lung(33)|ovary(2)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						AGGAGGCAAAGCGAAAAGAGA	0.393																																					p.K372K		Atlas-SNP	.											.	TRIM42	143	.	0			c.G1116A						.						62	62	62					3																	140406640		2203	4300	6503	SO:0001819	synonymous_variant	287015	exon3			GGCAAAGCGAAAA	AF521868	CCDS3113.1	3q23	2014-02-17	2011-01-25		ENSG00000155890	ENSG00000155890		"Tripartite motif containing / Tripartite motif containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Fibronectin type III domain containing", "RING-type (C3HC4) zinc fingers"	19014	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 40"		"tripartite motif-containing 42"				Standard	NM_152616		Approved	FLJ40097, PPP1R40	uc003eto.2	Q8IWZ5	OTTHUMG00000160170	ENST00000286349.3:c.1116G>A	chr3.hg19:g.140406640G>A		200.0	0.0		137.0	47.0	NM_152616	A1L4B4|Q8N832|Q8NDL3	Silent	SNP	ENST00000286349.3	hg19	CCDS3113.1																																																																																			.	.		0.393	TRIM42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359531.2	NM_152616		A	140406640	G	A	140406640	2	1	349	1	0	0	0	0	0	0	0	1	16532	962	34	3		3	TRIM42	3	140406640	Silent	SNP	G	TCGA-UB-AA0U-01A-11D-A382-10	17239856	140406640	57615790	17	49166										
MECOM	2122	hgsc.bcm.edu	37	chr3	168840444	168840444	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	gaattaaattggacttccagTtaaatgccttgggacactga	9	7	0	1			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr3:168840444T>A	ENST00000464456.1	-	5	1538	c.338A>T	c.(337-339)aAc>aTc	p.N113I	MECOM_ENST00000392736.3_Missense_Mutation_p.N113I|MECOM_ENST00000264674.3_Missense_Mutation_p.N177I|MECOM_ENST00000472280.1_Missense_Mutation_p.N113I|MECOM_ENST00000468789.1_Missense_Mutation_p.N113I|MECOM_ENST00000494292.1_Missense_Mutation_p.N301I|MECOM_ENST00000433243.2_Missense_Mutation_p.N113I|MECOM_ENST00000460814.1_Missense_Mutation_p.N113I	NM_001164000.1	NP_001157472.1	Q13465	MDS1_HUMAN	MDS1 and EVI1 complex locus	0					regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	85						GGACTTCCAGTTAAATGCCTT	0.403																																					p.N301I		Atlas-SNP	.											.	MECOM	216	.	0			c.A902T						.						238	199	212					3																	168840444		2203	4300	6503	SO:0001583	missense	2122	exon6			TTCCAGTTAAATG	S82592, AF164154	CCDS3205.1, CCDS54669.1, CCDS54670.1	3q26.2	2013-01-08	2009-08-07	2009-08-07	ENSG00000085276	ENSG00000085276		"Zinc fingers, C2H2-type"	3498	protein-coding gene	gene with protein product		165215	"myelodysplasia syndrome 1", "ecotropic viral integration site 1"	MDS1, EVI1		2115646, 8171026, 8643684	Standard	NM_001105077		Approved	MDS1-EVI1, PRDM3	uc011bpj.1	Q03112	OTTHUMG00000158596	ENST00000464456.1:c.338A>T	chr3.hg19:g.168840444T>A	ENSP00000419770:p.Asn113Ile	130.0	0.0		95.0	32.0	NM_004991	Q13466|Q6FH90	Missense_Mutation	SNP	ENST00000464456.1	hg19	CCDS54669.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.125075	0.77436	.	.	ENSG00000085276	ENST00000264674;ENST00000392736;ENST00000464456;ENST00000472280;ENST00000494292;ENST00000468789;ENST00000460814;ENST00000433243;ENST00000492586;ENST00000484519	T;T;T;T;T;T;T;T;T;T	0.27557	2.49;2.5;2.5;2.49;2.5;2.5;2.5;2.49;2.5;1.66	5.68	4.51	0.55191	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.266003	0.32372	N	0.006197	T	0.37128	0.0992	N	0.13140	0.3	0.54753	D	0.999989	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.999	T	0.31251	-0.9950	10	0.62326	D	0.03	-16.2494	12.1338	0.53959	0.1285:0.0:0.0:0.8715	.	301;113;301;177;113	Q03112-3;Q03112-6;E7EQ57;Q03112-4;Q03112	.;.;.;.;EVI1_HUMAN	I	177;113;113;113;301;113;113;113;88;113	ENSP00000264674:N177I;ENSP00000376493:N113I;ENSP00000419770:N113I;ENSP00000420048:N113I;ENSP00000417899:N301I;ENSP00000419995:N113I;ENSP00000420466:N113I;ENSP00000394302:N113I;ENSP00000417506:N88I;ENSP00000417299:N113I	ENSP00000264674:N177I	N	-	2	0	MECOM	170323138	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.698000	0.84413	0.965000	0.38133	0.533000	0.62120	AAC	.	.		0.403	MECOM-020	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351519.1	NM_005241, NM_004991		A	168840444	T	A	168840444	3	1	349	1	0	0	0	0	1	0	0	0	9431	1725	60	4	2868	4	MECOM	3	168840444	Missense_Mutation	SNP	T	TCGA-UB-AA0U-01A-11D-A382-10	28433804	168840444	29181986	18	49167										
KIT	3815	hgsc.bcm.edu	37	chr4	55595596	55595596	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	ttatttgttcaaagcaggaaGatcatgcagaagctgcactt	9	7	2	2			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr4:55595596G>T	ENST00000288135.5	+	14	2183	c.2086G>T	c.(2086-2088)Gat>Tat	p.D696Y		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	696	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	AAAGCAGGAAGATCATGCAGA	0.368		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																												p.D696Y		Atlas-SNP	.	yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	.	KIT	7396	.	0			c.G2086T						.						109	113	111					4																	55595596		2203	4300	6503	SO:0001583	missense	3815	exon14	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	CAGGAAGATCATG	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.2086G>T	chr4.hg19:g.55595596G>T	ENSP00000288135:p.Asp696Tyr	74.0	0.0		66.0	16.0	NM_000222	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	hg19	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.970424	0.74246	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	D;D	0.88975	-2.45;-2.45	5.93	5.93	0.95920	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.380730	0.25178	N	0.032559	D	0.93354	0.7881	L	0.50333	1.59	0.58432	D	0.999993	D;D;D	0.89917	0.992;0.999;1.0	P;D;D	0.78314	0.843;0.977;0.991	D	0.93259	0.6641	10	0.87932	D	0	.	20.3363	0.98740	0.0:0.0:1.0:0.0	.	203;692;696	D5MAV8;P10721-2;P10721	.;.;KIT_HUMAN	Y	696;692	ENSP00000288135:D696Y;ENSP00000390987:D692Y	ENSP00000288135:D696Y	D	+	1	0	KIT	55290353	1.000000	0.71417	0.998000	0.56505	0.737000	0.42083	8.844000	0.92147	2.814000	0.96858	0.563000	0.77884	GAT	.	.		0.368	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			T	55595596	G	T	55595596	3	4	349	1	0	0	0	0	1	0	0	0	8338	942	33	3	2140	3	KIT	4	55595596	Missense_Mutation	SNP	G	TCGA-UB-AA0U-01A-11D-A382-10		55595596	135558680	19	49168										
C4orf26	152816	hgsc.bcm.edu	37	chr4	76489344	76489344	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	gacaagaagaggtatttacgCctcctggagattcacaaaat	9	8	1	3			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr4:76489344C>A	ENST00000311623.4	+	2	123	c.88C>A	c.(88-90)Cct>Act	p.P30T	C4orf26_ENST00000435974.2_Silent_p.R44R	NM_001257072.1|NM_178497.3	NP_001244001.1|NP_848592.2	Q17RF5	CD026_HUMAN	chromosome 4 open reading frame 26	30			P -> L (in dbSNP:rs2306175). {ECO:0000269|PubMed:14702039}.			extracellular region (GO:0005576)				kidney(1)|large_intestine(4)|stomach(1)	6			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			GGTATTTACGCCTCCTGGAGA	0.537																																					p.P30T		Atlas-SNP	.											.	C4orf26	24	.	0			c.C88A						.						69	72	71					4																	76489344		2203	4300	6503	SO:0001583	missense	152816	exon2			TTTACGCCTCCTG	AK074237	CCDS3569.1, CCDS56334.1, CCDS75142.1	4q21.1	2012-10-31			ENSG00000174792	ENSG00000174792			26300	protein-coding gene	gene with protein product		614829				22901946	Standard	NM_001206981		Approved	FLJ23657	uc011cbo.2	Q17RF5	OTTHUMG00000130104	ENST00000311623.4:c.88C>A	chr4.hg19:g.76489344C>A	ENSP00000311307:p.Pro30Thr	87.0	0.0		79.0	12.0	NM_001257072	B4DTI3|E7ETQ0|Q8TEC3	Missense_Mutation	SNP	ENST00000311623.4	hg19	CCDS3569.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.967942	0.74131	.	.	ENSG00000174792	ENST00000311623	T	0.64803	-0.12	4.6	4.6	0.57074	.	0.145749	0.32120	N	0.006545	T	0.65407	0.2688	L	0.29908	0.895	0.80722	D	1	D	0.61080	0.989	P	0.61658	0.892	T	0.67507	-0.5653	10	0.59425	D	0.04	.	13.1663	0.59573	0.0:1.0:0.0:0.0	.	30	Q17RF5	CD026_HUMAN	T	30	ENSP00000311307:P30T	ENSP00000311307:P30T	P	+	1	0	C4orf26	76708368	0.188000	0.23250	0.294000	0.24946	0.207000	0.24258	3.303000	0.51858	2.569000	0.86673	0.551000	0.68910	CCT	.	.		0.537	C4orf26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252410.1	NM_178497		A	76489344	C	A	76489344	3	1	349	1	0	0	0	0	1	0	0	0	2259	739	26	3	94	3	C4orf26	4	76489344	Missense_Mutation	SNP	C	TCGA-UB-AA0U-01A-11D-A382-10	20893748	76489344	114664932	20	49169										
THAP9	79725	hgsc.bcm.edu	37	chr4	83827764	83827764	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	gaagaaacagagtgtctgctAcgagctcaattttcaggtac	10	8	3	2			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr4:83827764A>T	ENST00000302236.5	+	3	615	c.564A>T	c.(562-564)ctA>ctT	p.L188L		NM_024672.4	NP_078948.3	Q9H5L6	THAP9_HUMAN	THAP domain containing 9	188					DNA integration (GO:0015074)|DNA recombination (GO:0006310)|transposition, DNA-mediated (GO:0006313)		metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transferase activity (GO:0016740)|transposase activity (GO:0004803)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(13)|lung(5)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(3)	33		Hepatocellular(203;0.114)				AGTGTCTGCTACGAGCTCAAT	0.358																																					p.L188L		Atlas-SNP	.											.	THAP9	65	.	0			c.A564T						.						54	56	55					4																	83827764		2203	4300	6503	SO:0001819	synonymous_variant	79725	exon3			TCTGCTACGAGCT	AK091412	CCDS3598.1	4q21.3	2013-01-25			ENSG00000168152	ENSG00000168152		"THAP (C2CH-type zinc finger) domain containing"	23192	protein-coding gene	gene with protein product		612537				12575992	Standard	NM_024672		Approved	FLJ34093	uc003hnt.2	Q9H5L6	OTTHUMG00000130291	ENST00000302236.5:c.564A>T	chr4.hg19:g.83827764A>T		191.0	0.0		236.0	52.0	NM_024672	B3KRE2|Q59AC9	Silent	SNP	ENST00000302236.5	hg19	CCDS3598.1																																																																																			.	.		0.358	THAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252633.1	NM_024672		T	83827764	A	T	83827764	2	4	349	1	0	0	0	0	0	0	0	1	15866	378	14	4		4	THAP9	4	83827764	Silent	SNP	A	TCGA-UB-AA0U-01A-11D-A382-10	7338420	83827764	107326512	21	49170										
DAB2	1601	hgsc.bcm.edu	37	chr5	39383019	39383019	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	agtccggttagagatctggtCaaattgctgaccaaagtagt	11	7	2	2			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr5:39383019C>A	ENST00000320816.6	-	10	1509	c.1042G>T	c.(1042-1044)Gac>Tac	p.D348Y	DAB2_ENST00000545653.1_Missense_Mutation_p.D327Y|DAB2_ENST00000512525.1_5'Flank|DAB2_ENST00000339788.6_Intron|DAB2_ENST00000509337.1_Missense_Mutation_p.D327Y	NM_001343.3	NP_001334.2	P98082	DAB2_HUMAN	Dab, mitogen-responsive phosphoprotein, homolog 2 (Drosophila)	348	Required for localization to clathrin- coated pits. {ECO:0000250}.				activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cell morphogenesis involved in differentiation (GO:0000904)|cell proliferation (GO:0008283)|cellular response to transforming growth factor beta stimulus (GO:0071560)|clathrin coat assembly (GO:0048268)|endoderm development (GO:0007492)|excretion (GO:0007588)|in utero embryonic development (GO:0001701)|leading edge cell differentiation (GO:0035026)|membrane organization (GO:0061024)|myeloid cell differentiation (GO:0030099)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of protein binding (GO:0032091)|negative regulation of protein localization to plasma membrane (GO:1903077)|negative regulation of transcription, DNA-templated (GO:0045892)|pinocytosis (GO:0006907)|positive regulation of cell migration (GO:0030335)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of endocytosis (GO:0045807)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of receptor recycling (GO:0001921)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|clathrin coat of coated pit (GO:0030132)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	cargo receptor activity (GO:0038024)|clathrin adaptor activity (GO:0035615)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein C-terminus binding (GO:0008022)|SMAD binding (GO:0046332)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(9)|lung(19)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	47	all_lung(31;0.000197)		Epithelial(62;0.137)			GAGATCTGGTCAAATTGCTGA	0.498																																					p.D348Y		Atlas-SNP	.											.	DAB2	124	.	0			c.G1042T						.						83	86	85					5																	39383019		2203	4300	6503	SO:0001583	missense	1601	exon10			TCTGGTCAAATTG	U53446	CCDS34149.1, CCDS58946.1	5p13.1	2013-10-03	2013-03-08		ENSG00000153071	ENSG00000153071			2662	protein-coding gene	gene with protein product		601236	"disabled (Drosophila) homolog 2 (mitogen-responsive phosphoprotein)", "disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)"			8660969, 9620555	Standard	NM_001343		Approved	DOC-2	uc003jlx.3	P98082	OTTHUMG00000162043	ENST00000320816.6:c.1042G>T	chr5.hg19:g.39383019C>A	ENSP00000313391:p.Asp348Tyr	53.0	0.0		41.0	9.0	NM_001343	A6NES5|Q13598|Q9BTY0|Q9UK04	Missense_Mutation	SNP	ENST00000320816.6	hg19	CCDS34149.1	.	.	.	.	.	.	.	.	.	.	C	18.00	3.525989	0.64860	.	.	ENSG00000153071	ENST00000320816;ENST00000545653;ENST00000509337	T;T;T	0.41758	1.0;0.99;0.99	5.73	5.73	0.89815	.	0.102151	0.64402	D	0.000003	T	0.64951	0.2645	M	0.62723	1.935	0.46901	D	0.999242	D;D	0.89917	1.0;1.0	D;D	0.75484	0.968;0.986	T	0.64947	-0.6287	10	0.87932	D	0	-15.0468	20.2602	0.98440	0.0:1.0:0.0:0.0	.	348;327	P98082;P98082-3	DAB2_HUMAN;.	Y	348;327;327	ENSP00000313391:D348Y;ENSP00000439919:D327Y;ENSP00000426245:D327Y	ENSP00000313391:D348Y	D	-	1	0	DAB2	39418776	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.577000	0.67444	2.861000	0.98227	0.655000	0.94253	GAC	.	.		0.498	DAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367014.1	NM_001343		A	39383019	C	A	39383019	3	1	349	1	0	0	0	0	1	0	0	0	4220	826	29	3	1290	3	DAB2	5	39383019	Missense_Mutation	SNP	C	TCGA-UB-AA0U-01A-11D-A382-10		39383019	141532241	22	49171										
RASA1	5921	hgsc.bcm.edu	37	chr5	86629119	86629119	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	aggcgtgtacgagctattctAccttacacaaaagtaccaga	8	10	1	1			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr5:86629119A>G	ENST00000274376.6	+	4	1428	c.864A>G	c.(862-864)ctA>ctG	p.L288L	RASA1_ENST00000506290.1_Silent_p.L122L|RASA1_ENST00000456692.2_Silent_p.L111L|RASA1_ENST00000512763.1_Silent_p.L121L	NM_002890.2	NP_002881.1	P20936	RASA1_HUMAN	RAS p21 protein activator (GTPase activating protein) 1	288	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				blood vessel morphogenesis (GO:0048514)|embryo development (GO:0009790)|intracellular signal transduction (GO:0035556)|mitotic cytokinesis (GO:0000281)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|regulation of RNA metabolic process (GO:0051252)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|ruffle (GO:0001726)	glycoprotein binding (GO:0001948)|GTPase binding (GO:0051020)|potassium channel inhibitor activity (GO:0019870)|Ras GTPase activator activity (GO:0005099)|receptor binding (GO:0005102)			NS(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(12)|lung(13)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	48		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		GAGCTATTCTACCTTACACAA	0.308																																					p.L288L		Atlas-SNP	.											.	RASA1	213	.	0			c.A864G						.						71	76	75					5																	86629119		2203	4300	6503	SO:0001819	synonymous_variant	5921	exon4			TATTCTACCTTAC		CCDS34200.1, CCDS47243.1	5q13	2013-02-14			ENSG00000145715	ENSG00000145715		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	9871	protein-coding gene	gene with protein product	"capillary malformation-arteriovenous malformation"	139150		RASA		15917201	Standard	NM_022650		Approved	GAP, CM-AVM, p120GAP, p120RASGAP	uc003kiw.3	P20936	OTTHUMG00000162605	ENST00000274376.6:c.864A>G	chr5.hg19:g.86629119A>G		358.0	0.0		296.0	95.0	NM_002890	B2R6W3|Q9UDI1	Silent	SNP	ENST00000274376.6	hg19	CCDS34200.1																																																																																			.	.		0.308	RASA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369729.1	NM_002890		G	86629119	A	G	86629119	2	3	349	1	0	0	0	0	0	0	0	1	13075	378	14	2		2	RASA1	5	86629119	Silent	SNP	A	TCGA-UB-AA0U-01A-11D-A382-10	47246100	86629119	94286141	23	49172										
BRD8	10902	hgsc.bcm.edu	37	chr5	137475827	137475827	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	cttccagactacttgagcctTttcttttgtctaaccagata	5	11	2	3			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr5:137475827T>C	ENST00000254900.5	-	27	4015	c.3644A>G	c.(3643-3645)aAa>aGa	p.K1215R	NME5_ENST00000265191.2_5'Flank	NM_139199.1	NP_631938	Q9H0E9	BRD8_HUMAN	bromodomain containing 8	1215					cell surface receptor signaling pathway (GO:0007166)|chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|intracellular receptor signaling pathway (GO:0030522)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Swr1 complex (GO:0000812)	sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid hormone receptor activity (GO:0004887)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(3)|urinary_tract(1)	35			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			ACTTGAGCCTTTTCTTTTGTC	0.373																																					p.K1215R		Atlas-SNP	.											.	BRD8	192	.	0			c.A3644G						.						155	150	152					5																	137475827		2203	4300	6503	SO:0001583	missense	10902	exon27			GAGCCTTTTCTTT	AF016270	CCDS4198.1, CCDS34241.1, CCDS54907.1	5q31	2008-02-05			ENSG00000112983	ENSG00000112983			19874	protein-coding gene	gene with protein product		602848				8611617, 9368056	Standard	NM_001164326		Approved	SMAP, p120	uc003lcf.1	Q9H0E9	OTTHUMG00000129204	ENST00000254900.5:c.3644A>G	chr5.hg19:g.137475827T>C	ENSP00000254900:p.Lys1215Arg	110.0	0.0		105.0	13.0	NM_139199	O43178|Q15355|Q58AB0|Q59GN0|Q969M9	Missense_Mutation	SNP	ENST00000254900.5	hg19	CCDS4198.1	.	.	.	.	.	.	.	.	.	.	T	0.012	-1.657231	0.00779	.	.	ENSG00000112983	ENST00000254900	T	0.22336	1.96	5.54	3.55	0.40652	.	0.251040	0.28544	N	0.014965	T	0.06508	0.0167	N	0.02916	-0.46	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.27773	-1.0064	10	0.02654	T	1	-0.8037	6.7984	0.23738	0.0:0.7567:0.0:0.2433	.	1215	Q9H0E9	BRD8_HUMAN	R	1215	ENSP00000254900:K1215R	ENSP00000254900:K1215R	K	-	2	0	BRD8	137503726	1.000000	0.71417	0.998000	0.56505	0.023000	0.10783	1.326000	0.33735	0.544000	0.28883	-0.408000	0.06270	AAA	.	.		0.373	BRD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251282.3	NM_006696		C	137475827	T	C	137475827	3	2	349	1	0	0	0	0	1	0	0	0	1508	1841	64	2	67	2	BRD8	5	137475827	Missense_Mutation	SNP	T	TCGA-UB-AA0U-01A-11D-A382-10	50846708	137475827	43439433	24	49173										
OR5V1	81696	hgsc.bcm.edu	37	chr6	29323776	29323776	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	agcagatgtcaataaaggccAagttccctagaaaataatac	7	8	1	2			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr6:29323776A>C	ENST00000377154.1	-	4	496	c.197T>G	c.(196-198)tTg>tGg	p.L66W	OR5V1_ENST00000543825.1_Missense_Mutation_p.L66W			Q9UGF6	OR5V1_HUMAN	olfactory receptor, family 5, subfamily V, member 1	66						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(3)|large_intestine(3)|liver(1)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						AATAAAGGCCAAGTTCCCTAG	0.413																																					p.L66W	Ovarian(32;43 883 21137 32120 42650)	Atlas-SNP	.											.	OR5V1	63	.	0			c.T197G						.						146	142	143					6																	29323776		2203	4300	6503	SO:0001583	missense	81696	exon1			AAGGCCAAGTTCC		CCDS4657.1	6p22.1	2013-09-23				ENSG00000243729		"GPCR / Class A : Olfactory receptors"	13972	protein-coding gene	gene with protein product							Standard	NM_030876		Approved	hs6M1-21	uc011dlo.2	Q9UGF6		ENST00000377154.1:c.197T>G	chr6.hg19:g.29323776A>C	ENSP00000366359:p.Leu66Trp	107.0	0.0		150.0	34.0	NM_030876	A2BDZ0|B0S860|Q5SQI9|Q6NTB5|Q8IVL3	Missense_Mutation	SNP	ENST00000377154.1	hg19	CCDS4657.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.114220	0.77210	.	.	ENSG00000243729	ENST00000377154;ENST00000377151;ENST00000543825	T;T	0.00590	6.36;6.36	4.36	4.36	0.52297	GPCR, rhodopsin-like superfamily (1);	0.000000	0.25352	N	0.031290	T	0.03095	0.0091	H	0.98542	4.26	0.29097	N	0.881741	D	0.89917	1.0	D	0.91635	0.999	T	0.16808	-1.0390	10	0.87932	D	0	-22.889	13.6517	0.62314	1.0:0.0:0.0:0.0	.	66	Q9UGF6	OR5V1_HUMAN	W	66	ENSP00000366359:L66W;ENSP00000443309:L66W	ENSP00000366356:L66W	L	-	2	0	OR5V1	29431755	0.676000	0.27567	0.840000	0.33206	0.991000	0.79684	6.204000	0.72143	1.956000	0.56807	0.438000	0.28831	TTG	.	.		0.413	OR5V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076398.3			C	29323776	A	C	29323776	3	2	349	1	0	0	0	0	1	0	0	0	11193	131	5	5	771	5	OR5V1	6	29323776	Missense_Mutation	SNP	A	TCGA-UB-AA0U-01A-11D-A382-10		29323776	141791291	25	49174										
TRERF1	55809	hgsc.bcm.edu	37	chr6	42204142	42204142	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	cctctaactcttcttcttctTcacttgtctagtgttaaggt	5	11	7	0			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr6:42204142T>A	ENST00000372922.4	-	16	3429	c.2867A>T	c.(2866-2868)gAa>gTa	p.E956V	TRERF1_ENST00000372917.4_Missense_Mutation_p.E873V|TRERF1_ENST00000340840.2_Missense_Mutation_p.E873V|TRERF1_ENST00000541110.1_Missense_Mutation_p.E976V|TRERF1_ENST00000354325.2_Missense_Mutation_p.E873V	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	956	Glu-rich.|Interacts with CREBBP.				cholesterol catabolic process (GO:0006707)|homeostatic process (GO:0042592)|multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone biosynthetic process (GO:0046885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|steroid biosynthetic process (GO:0006694)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			TTCTTCTTCTTCACTTGTCTA	0.473																																					p.E956V		Atlas-SNP	.											.	TRERF1	124	.	0			c.A2867T						.						53	51	52					6																	42204142		2162	4242	6404	SO:0001583	missense	55809	exon16			TCTTCTTCACTTG	AF297872	CCDS4867.1, CCDS75455.1	6p21.1-p12.1	2012-09-25			ENSG00000124496	ENSG00000124496			18273	protein-coding gene	gene with protein product		610322	"breast cancer anti-estrogen resistance 2"	BCAR2		11349124	Standard	XM_005249223		Approved	TReP-132, HSA277276, RAPA, dJ139D8.5	uc003osd.2	Q96PN7	OTTHUMG00000014698	ENST00000372922.4:c.2867A>T	chr6.hg19:g.42204142T>A	ENSP00000362013:p.Glu956Val	44.0	0.0		63.0	16.0	NM_033502	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Missense_Mutation	SNP	ENST00000372922.4	hg19	CCDS4867.1	.	.	.	.	.	.	.	.	.	.	T	17.45	3.391959	0.62066	.	.	ENSG00000124496	ENST00000541110;ENST00000372917;ENST00000372922;ENST00000340840;ENST00000354325	T;T;T;T;T	0.29397	1.57;1.57;1.57;1.57;1.57	5.61	4.46	0.54185	.	0.123452	0.39909	N	0.001235	T	0.09512	0.0234	N	0.19112	0.55	0.33433	D	0.58142	P;P;P;P;P	0.48640	0.763;0.651;0.651;0.763;0.913	B;B;B;B;P	0.45753	0.387;0.216;0.216;0.387;0.492	T	0.09885	-1.0654	10	0.33141	T	0.24	-16.0837	3.8988	0.09150	0.0:0.1468:0.2034:0.6498	.	873;976;956;712;712	Q96PN7-4;Q05GC8;Q96PN7;Q96PN7-2;Q96PN7-3	.;.;TREF1_HUMAN;.;.	V	976;873;956;873;873	ENSP00000439689:E976V;ENSP00000362008:E873V;ENSP00000362013:E956V;ENSP00000339438:E873V;ENSP00000346285:E873V	ENSP00000339438:E873V	E	-	2	0	TRERF1	42312120	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.589000	0.36644	2.131000	0.65755	0.533000	0.62120	GAA	.	.		0.473	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2	NM_033502		A	42204142	T	A	42204142	3	1	349	1	0	0	0	0	1	0	0	0	16490	1783	62	4	747	4	TRERF1	6	42204142	Missense_Mutation	SNP	T	TCGA-UB-AA0U-01A-11D-A382-10	12880366	42204142	128910925	26	49175										
MDN1	23195	hgsc.bcm.edu	37	chr6	90390402	90390402	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	atgcgtttcctgagctttggCaagcgacgcagaagctcccc	11	13	0	2			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr6:90390402C>T	ENST00000369393.3	-	74	12286	c.12171G>A	c.(12169-12171)ttG>ttA	p.L4057L	MDN1_ENST00000428876.1_Silent_p.L4057L			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	4057					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		TGAGCTTTGGCAAGCGACGCA	0.577																																					p.L4057L		Atlas-SNP	.											.	MDN1	478	.	0			c.G12171A						.						79	70	73					6																	90390402		2203	4300	6503	SO:0001819	synonymous_variant	23195	exon74			CTTTGGCAAGCGA	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.12171G>A	chr6.hg19:g.90390402C>T		76.0	0.0		55.0	23.0	NM_014611	O15019|Q5T794	Silent	SNP	ENST00000369393.3	hg19	CCDS5024.1																																																																																			.	.		0.577	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			T	90390402	C	T	90390402	2	4	349	1	0	0	0	0	0	0	0	1	9424	709	25	3		3	MDN1	6	90390402	Silent	SNP	C	TCGA-UB-AA0U-01A-11D-A382-10	48186260	90390402	80724665	27	49176										
REV3L	5980	hgsc.bcm.edu	37	chr6	111694493	111694493	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	ctcatttttttctatagcttGtcctggaaaaagatcctgaa	6	8	2	2			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr6:111694493G>T	ENST00000358835.3	-	14	5519	c.5065C>A	c.(5065-5067)Caa>Aaa	p.Q1689K	REV3L_ENST00000368805.1_Missense_Mutation_p.Q1689K|REV3L_ENST00000368802.3_Missense_Mutation_p.Q1689K|REV3L_ENST00000435970.1_Missense_Mutation_p.Q1611K			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	1689					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		TCTATAGCTTGTCCTGGAAAA	0.393								DNA polymerases (catalytic subunits)																													p.Q1689K		Atlas-SNP	.											.	REV3L	386	.	0			c.C5065A						.						61	61	61					6																	111694493		2203	4299	6502	SO:0001583	missense	5980	exon13			TAGCTTGTCCTGG	AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"DNA polymerases"	9968	protein-coding gene	gene with protein product	"polymerase, DNA, zeta"	602776	"REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta", "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.5065C>A	chr6.hg19:g.111694493G>T	ENSP00000351697:p.Gln1689Lys	90.0	0.0		77.0	38.0	NM_002912	O43214|Q5TC33	Missense_Mutation	SNP	ENST00000358835.3	hg19	CCDS5091.2	.	.	.	.	.	.	.	.	.	.	G	15.98	2.991219	0.54041	.	.	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970	T;T;T;T	0.01647	4.8;4.8;4.8;4.71	5.84	5.84	0.93424	Ribonuclease H-like (1);	0.153798	0.44483	D	0.000442	T	0.03178	0.0093	L	0.56769	1.78	0.45541	D	0.998492	D	0.67145	0.996	P	0.57620	0.824	T	0.65981	-0.6036	10	0.17369	T	0.5	.	18.3357	0.90287	0.0:0.0:1.0:0.0	.	1689	O60673	DPOLZ_HUMAN	K	1689;1689;1689;1611	ENSP00000357792:Q1689K;ENSP00000357795:Q1689K;ENSP00000351697:Q1689K;ENSP00000402003:Q1611K	ENSP00000351697:Q1689K	Q	-	1	0	REV3L	111801186	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.413000	0.90235	2.760000	0.94817	0.655000	0.94253	CAA	.	.		0.393	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		T	111694493	G	T	111694493	3	4	349	1	0	0	0	0	1	0	0	0	13255	1386	48	3	4407	3	REV3L	6	111694493	Missense_Mutation	SNP	G	TCGA-UB-AA0U-01A-11D-A382-10	21304091	111694493	59420574	28	49177										
DLL1	28514	hgsc.bcm.edu	37	chr6	170592454	170592454	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	gcacgaggttatagtccaccGctgggtagcgggccttgaag	15	10	0	1			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr6:170592454G>A	ENST00000366756.3	-	9	2246	c.1913C>T	c.(1912-1914)gCg>gTg	p.A638V		NM_005618.3	NP_005609.3	O00548	DLL1_HUMAN	delta-like 1 (Drosophila)	638					cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|cell-cell signaling (GO:0007267)|compartment pattern specification (GO:0007386)|determination of left/right symmetry (GO:0007368)|heart looping (GO:0001947)|hemopoiesis (GO:0030097)|inner ear development (GO:0048839)|left/right axis specification (GO:0070986)|loop of Henle development (GO:0072070)|negative regulation of auditory receptor cell differentiation (GO:0045608)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of myeloid cell differentiation (GO:0045638)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal tubule development (GO:0072014)|regulation of cell adhesion (GO:0030155)|somite specification (GO:0001757)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|Notch binding (GO:0005112)			NS(2)|breast(1)|endometrium(1)|large_intestine(7)|lung(17)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	33		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;6.71e-23)|BRCA - Breast invasive adenocarcinoma(81;4.81e-06)|GBM - Glioblastoma multiforme(31;0.0584)		ATAGTCCACCGCTGGGTAGCG	0.622																																					p.A638V		Atlas-SNP	.											.	DLL1	72	.	0			c.C1913T						.						180	150	160					6																	170592454		2203	4300	6503	SO:0001583	missense	28514	exon9			TCCACCGCTGGGT	AF003522	CCDS5313.1	6q13-q22.33	2008-07-28	2001-12-03		ENSG00000198719	ENSG00000198719			2908	protein-coding gene	gene with protein product		606582	"delta (Drosophila)-like 1"				Standard	NM_005618		Approved		uc003qxm.3	O00548	OTTHUMG00000016078	ENST00000366756.3:c.1913C>T	chr6.hg19:g.170592454G>A	ENSP00000355718:p.Ala638Val	45.0	0.0		21.0	11.0	NM_005618	B2RAK7|B5M0B3|Q9NU41|Q9UJV2	Missense_Mutation	SNP	ENST00000366756.3	hg19	CCDS5313.1	.	.	.	.	.	.	.	.	.	.	G	2.363	-0.346115	0.05208	.	.	ENSG00000198719	ENST00000366756	D	0.85861	-2.04	5.53	4.65	0.58169	.	0.792684	0.12374	N	0.474489	T	0.71048	0.3294	L	0.51422	1.61	0.09310	N	1	B	0.29341	0.242	B	0.21708	0.036	T	0.63193	-0.6692	10	0.31617	T	0.26	.	16.4331	0.83860	0.0:0.1446:0.8554:0.0	.	638	O00548	DLL1_HUMAN	V	638	ENSP00000355718:A638V	ENSP00000355718:A638V	A	-	2	0	DLL1	170434379	0.004000	0.15560	0.004000	0.12327	0.027000	0.11550	1.497000	0.35649	1.441000	0.47550	0.655000	0.94253	GCG	.	.		0.622	DLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043254.1			A	170592454	G	A	170592454	3	1	349	1	0	0	0	0	1	0	0	0	4568	1087	38	1	270	1	DLL1	6	170592454	Missense_Mutation	SNP	G	TCGA-UB-AA0U-01A-11D-A382-10	58897961	170592454	522613	29	49178										
SPAM1	6677	hgsc.bcm.edu	37	chr7	123599859	123599859	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	taaaagacactgatgctgttGatgtgtgtattgctgatggt	12	4	0	4			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr7:123599859G>A	ENST00000439500.1	+	6	1979	c.1366G>A	c.(1366-1368)Gat>Aat	p.D456N	SPAM1_ENST00000223028.7_Missense_Mutation_p.D456N|SPAM1_ENST00000340011.5_Missense_Mutation_p.D456N|SPAM1_ENST00000402183.2_Missense_Mutation_p.D456N|SPAM1_ENST00000460182.1_Missense_Mutation_p.D456N	NM_001174045.1|NM_001174046.1	NP_001167516.1|NP_001167517.1	P38567	HYALP_HUMAN	sperm adhesion molecule 1 (PH-20 hyaluronidase, zona pellucida binding)	456					binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	hyalurononglucosaminidase activity (GO:0004415)			breast(1)|cervix(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(23)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						TGATGCTGTTGATGTGTGTAT	0.393																																					p.D456N		Atlas-SNP	.											.	SPAM1	195	.	0			c.G1366A						.						168	156	160					7																	123599859		2203	4300	6503	SO:0001583	missense	6677	exon5			GCTGTTGATGTGT	L13781	CCDS5790.1, CCDS5791.1	7q31	2008-05-02			ENSG00000106304	ENSG00000106304			11217	protein-coding gene	gene with protein product		600930				8282124, 8575780	Standard	NM_153189		Approved	HYAL5, PH-20, SPAG15	uc003vle.3	P38567	OTTHUMG00000157284	ENST00000439500.1:c.1366G>A	chr7.hg19:g.123599859G>A	ENSP00000402123:p.Asp456Asn	81.0	0.0		111.0	25.0	NM_153189	Q8TC30	Missense_Mutation	SNP	ENST00000439500.1	hg19	CCDS5791.1	.	.	.	.	.	.	.	.	.	.	G	2.814	-0.246425	0.05867	.	.	ENSG00000106304	ENST00000402183;ENST00000460182;ENST00000340011;ENST00000439500;ENST00000223028	T;T;T;T;T	0.13778	2.57;2.57;2.56;2.57;2.57	5.8	-7.08	0.01558	.	1.576540	0.03004	N	0.148595	T	0.02230	0.0069	N	0.00483	-1.445	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.35748	-0.9776	10	0.02654	T	1	-14.9812	1.107	0.01696	0.2907:0.3059:0.2275:0.1759	.	456;456	Q8TC30;P38567	.;HYALP_HUMAN	N	456	ENSP00000386028:D456N;ENSP00000417934:D456N;ENSP00000345849:D456N;ENSP00000402123:D456N;ENSP00000223028:D456N	ENSP00000223028:D456N	D	+	1	0	SPAM1	123387095	0.008000	0.16893	0.000000	0.03702	0.005000	0.04900	0.078000	0.14761	-0.883000	0.03982	-0.355000	0.07637	GAT	.	.		0.393	SPAM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000348309.1			A	123599859	G	A	123599859	3	1	349	1	0	0	0	0	1	0	0	0	15001	1290	45	3	1376	3	SPAM1	7	123599859	Missense_Mutation	SNP	G	TCGA-UB-AA0U-01A-11D-A382-10		123599859	35538804	30	49179										
FLNC	2318	hgsc.bcm.edu	37	chr7	128478085	128478085	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	aaggatcgcacctatgctgtCtcctatgtgcccaaggtcgc	10	13	1	0			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr7:128478085C>A	ENST00000325888.8	+	6	1275	c.1014C>A	c.(1012-1014)gtC>gtA	p.V338V	FLNC_ENST00000346177.6_Silent_p.V338V	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	338					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						CCTATGCTGTCTCCTATGTGC	0.552																																					p.V338V		Atlas-SNP	.											.	FLNC	339	.	0			c.C1014A						.						146	155	152					7																	128478085		2105	4224	6329	SO:0001819	synonymous_variant	2318	exon6			TGCTGTCTCCTAT	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"actin binding protein 280"	102565	"filamin C, gamma (actin binding protein 280)"	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.1014C>A	chr7.hg19:g.128478085C>A		71.0	0.0		82.0	22.0	NM_001127487	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Silent	SNP	ENST00000325888.8	hg19	CCDS43644.1																																																																																			.	.		0.552	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3			A	128478085	C	A	128478085	2	1	349	1	0	0	0	0	0	0	0	1	5943	900	32	3		3	FLNC	7	128478085	Silent	SNP	C	TCGA-UB-AA0U-01A-11D-A382-10	4878226	128478085	30660578	31	49180										
PGCP	10404	hgsc.bcm.edu	37	chr8	97978226	97978226	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	agggtgccatggatgatggcGgtggagcctttatatcatgg	16	6	1	1	rs373415893		TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr8:97978226G>T	ENST00000220763.5	+	5	1123	c.913G>T	c.(913-915)Ggt>Tgt	p.G305C		NM_016134.2	NP_057218.1	Q9Y646	CBPQ_HUMAN	carboxypeptidase Q	305					peptide catabolic process (GO:0043171)|proteolysis (GO:0006508)|thyroid hormone generation (GO:0006590)|tissue regeneration (GO:0042246)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)	carboxypeptidase activity (GO:0004180)|metal ion binding (GO:0046872)|metallodipeptidase activity (GO:0070573)|protein homodimerization activity (GO:0042803)										GGATGATGGCGGTGGAGCCTT	0.378																																					p.G305C		Atlas-SNP	.											.	.	.	.	0			c.G913T						.						98	97	98					8																	97978226		2203	4300	6503	SO:0001583	missense	10404	exon5			GATGGCGGTGGAG	AF107834	CCDS6273.1	8q22.2	2012-02-17			ENSG00000104324	ENSG00000104324			16910	protein-coding gene	gene with protein product	"lysosomal dipeptidase", "Ser-Met dipeptidase", "plasma glutamate carboxypeptidase"					10206990	Standard	NM_016134		Approved	LDP, PGCP	uc003yhw.3	Q9Y646	OTTHUMG00000164690	ENST00000220763.5:c.913G>T	chr8.hg19:g.97978226G>T	ENSP00000220763:p.Gly305Cys	80.0	0.0		117.0	6.0	NM_016134	B2RD88|Q8NBZ1|Q9UNM8|Q9Y5X6	Missense_Mutation	SNP	ENST00000220763.5	hg19	CCDS6273.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.203969	0.79127	.	.	ENSG00000104324	ENST00000220763	T	0.49139	0.79	5.94	4.14	0.48551	Peptidase M28 (1);	0.191964	0.46442	D	0.000298	T	0.66416	0.2787	M	0.83953	2.67	0.48135	D	0.999599	D;P	0.58268	0.982;0.944	D;P	0.64410	0.925;0.893	T	0.69789	-0.5050	10	0.54805	T	0.06	-2.2955	10.4502	0.44518	0.1514:0.0:0.8486:0.0	.	305;305	B5MDX4;Q9Y646	.;PGCP_HUMAN	C	305	ENSP00000220763:G305C	ENSP00000220763:G305C	G	+	1	0	AC010859.1	98047402	1.000000	0.71417	0.951000	0.38953	0.990000	0.78478	5.541000	0.67212	1.524000	0.49035	0.561000	0.74099	GGT	.	.		0.378	CPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379757.2	NM_016134		T	97978226	G	T	97978226	3	4	349	1	0	0	0	0	1	0	0	0	11795	1116	39	1	927	1	PGCP	8	97978226	Missense_Mutation	SNP	G	TCGA-UB-AA0U-01A-11D-A382-10		97978226	48385796	32	49181										
NIPAL2	79815	hgsc.bcm.edu	37	chr8	99264768	99264768	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	ctgcaaagttccccgtctctCccacggccatcagcaggaca	8	17	2	0			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr8:99264768C>T	ENST00000341166.3	-	3	554	c.299G>A	c.(298-300)gGa>gAa	p.G100E	NIPAL2_ENST00000430223.2_Missense_Mutation_p.G100E|NIPAL2_ENST00000520545.1_5'Flank	NM_024759.1	NP_079035.1	Q9H841	NPAL2_HUMAN	NIPA-like domain containing 2	100						integral component of membrane (GO:0016021)	magnesium ion transmembrane transporter activity (GO:0015095)			cervix(3)|kidney(1)|large_intestine(2)|lung(5)|stomach(1)	12						CCCCGTCTCTCCCACGGCCAT	0.502																																					p.G100E		Atlas-SNP	.											.	NIPAL2	23	.	0			c.G299A						.						111	89	96					8																	99264768		2203	4300	6503	SO:0001583	missense	79815	exon3			GTCTCTCCCACGG	AK024017	CCDS6278.1	8q22.2	2009-03-24		2009-03-24	ENSG00000104361	ENSG00000104361			25854	protein-coding gene	gene with protein product				NPAL2		14702039	Standard	NM_024759		Approved	FLJ13955	uc003yil.1	Q9H841	OTTHUMG00000164668	ENST00000341166.3:c.299G>A	chr8.hg19:g.99264768C>T	ENSP00000339256:p.Gly100Glu	153.0	0.0		187.0	29.0	NM_024759	A2RTY8	Missense_Mutation	SNP	ENST00000341166.3	hg19	CCDS6278.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.906415	0.92107	.	.	ENSG00000104361	ENST00000430223;ENST00000341166	D;D	0.96587	-4.06;-4.06	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	D	0.98585	0.9527	M	0.92833	3.35	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99331	1.0909	10	0.87932	D	0	-13.2313	17.3107	0.87208	0.0:1.0:0.0:0.0	.	100;100	A2RTY8;Q9H841	.;NPAL2_HUMAN	E	100	ENSP00000407087:G100E;ENSP00000339256:G100E	ENSP00000339256:G100E	G	-	2	0	NIPAL2	99333944	1.000000	0.71417	0.962000	0.40283	0.817000	0.46193	7.208000	0.77907	2.830000	0.97506	0.585000	0.79938	GGA	.	.		0.502	NIPAL2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000379677.1	NM_024759		T	99264768	C	T	99264768	3	4	349	1	0	0	0	0	1	0	0	0	10434	855	30	3	847	3	NIPAL2	8	99264768	Missense_Mutation	SNP	C	TCGA-UB-AA0U-01A-11D-A382-10	1286542	99264768	47099254	33	49182										
COL22A1	169044	hgsc.bcm.edu	37	chr8	139890313	139890314	+	Missense_Mutation	DNP	CC	CC	AA													0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	cgtctcccgtgttggtgttgCccccgtggtaggcgagacgc					rs375895986		TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr8:139890313_139890314CC>AA	ENST00000303045.6	-	3	783_784	c.337_338GG>TT	c.(337-339)GGc>TTc	p.G113F	COL22A1_ENST00000435777.1_Missense_Mutation_p.G113F	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	113	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			GTTGGTGTTGCCCCCGTGGTAG	0.713										HNSCC(7;0.00092)																											p.G113V|p.G113C		Atlas-SNP	.											.	COL22A1	390	.	0			c.G338T|c.G337T						.																																			SO:0001583	missense	169044	exon3			GTGTTGCCCCCGT|TGTTGCCCCCGTG	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"Collagens"	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.337_338delinsAA	chr8.hg19:g.139890313_139890314delinsAA	ENSP00000303153:p.Gly113Phe	78.0|79.0	0.0		110.0	25.0	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Missense_Mutation	SNP	ENST00000303045.6	hg19	CCDS6376.1																																																																																			.	.		0.713	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257		AA	139890314	CC	AA	139890313	3	1	349	1	0	0	0	0	1	0	0	0	3683	739	26	3	4794	3	COL22A1	8	139890313	Missense_Mutation	DNP	CC	TCGA-UB-AA0U-01A-11D-A382-10	40625545	139890313	6473709	34	49183										
GPAA1	8733	hgsc.bcm.edu	37	chr8	145140996	145140996	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	tgggcctctacccctgctggCtgcttttctggaatgtgctc	11	13	2	0			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr8:145140996C>A	ENST00000355091.4	+	12	1955	c.1834C>A	c.(1834-1836)Ctg>Atg	p.L612M	GPAA1_ENST00000361036.6_Missense_Mutation_p.L552M	NM_003801.3	NP_003792.1	O43292	GPAA1_HUMAN	glycosylphosphatidylinositol anchor attachment 1	612					attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein complex assembly (GO:0006461)|protein retention in ER lumen (GO:0006621)	endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|membrane (GO:0016020)	tubulin binding (GO:0015631)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|upper_aerodigestive_tract(2)	19	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.02e-40)|all cancers(56;2.11e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CCCCTGCTGGCTGCTTTTCTG	0.612																																					p.L612M		Atlas-SNP	.											.	GPAA1	40	.	0			c.C1834A						.						60	64	63					8																	145140996		1992	4161	6153	SO:0001583	missense	8733	exon12			TGCTGGCTGCTTT	AB006969	CCDS43776.1	8q24.3	2012-12-10	2012-12-10		ENSG00000197858	ENSG00000197858			4446	protein-coding gene	gene with protein product	"GPI transamidase subunit"	603048	"anchor attachment protein 1 (Gaa1p, yeast) homolog", "GPAA1P anchor attachment protein 1 homolog (yeast)", "glycosylphosphatidylinositol anchor attachment protein 1 homolog (yeast)"			9828142	Standard	NM_003801		Approved	GAA1, hGAA1	uc003zax.3	O43292	OTTHUMG00000165438	ENST00000355091.4:c.1834C>A	chr8.hg19:g.145140996C>A	ENSP00000347206:p.Leu612Met	41.0	0.0		36.0	5.0	NM_003801	Q9NSS0|Q9UQ31	Missense_Mutation	SNP	ENST00000355091.4	hg19	CCDS43776.1	.	.	.	.	.	.	.	.	.	.	C	19.69	3.875526	0.72180	.	.	ENSG00000197858	ENST00000355091;ENST00000361036	.	.	.	5.13	4.25	0.50352	.	0.000000	0.64402	D	0.000003	T	0.69655	0.3135	L	0.58810	1.83	0.58432	D	0.999992	D	0.89917	1.0	D	0.91635	0.999	T	0.68996	-0.5262	9	0.44086	T	0.13	-15.6631	11.7676	0.51939	0.0:0.9116:0.0:0.0883	.	612	O43292	GPAA1_HUMAN	M	612;552	.	ENSP00000347206:L612M	L	+	1	2	GPAA1	145212984	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.439000	0.66556	2.404000	0.81709	0.655000	0.94253	CTG	.	.		0.612	GPAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384070.1	NM_003801		A	145140996	C	A	145140996	3	1	349	1	0	0	0	0	1	0	0	0	6595	796	28	3	1880	3	GPAA1	8	145140996	Missense_Mutation	SNP	C	TCGA-UB-AA0U-01A-11D-A382-10	5250683	145140996	1223026	35	49184										
ALDH1B1	219	hgsc.bcm.edu	37	chr9	38396813	38396813	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	aacccctttgagctggacacCcagcaggggcctcaggtgga	13	13	1	1			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr9:38396813C>T	ENST00000377698.3	+	2	1221	c.1068C>T	c.(1066-1068)acC>acT	p.T356T		NM_000692.4	NP_000683.3	P30837	AL1B1_HUMAN	aldehyde dehydrogenase 1 family, member B1	356					carbohydrate metabolic process (GO:0005975)|ethanol catabolic process (GO:0006068)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	aldehyde dehydrogenase (NAD) activity (GO:0004029)			NS(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(1)|stomach(2)|urinary_tract(2)	32				GBM - Glioblastoma multiforme(29;0.043)|Lung(182;0.115)		AGCTGGACACCCAGCAGGGGC	0.562																																					p.T356T		Atlas-SNP	.											.	ALDH1B1	50	.	0			c.C1068T						.						53	57	55					9																	38396813		2203	4300	6503	SO:0001819	synonymous_variant	219	exon2			GGACACCCAGCAG	M63967	CCDS6615.1	9p13	2008-02-05			ENSG00000137124	ENSG00000137124	1.2.1.3	"Aldehyde dehydrogenases"	407	protein-coding gene	gene with protein product		100670		ALDH5		2061311	Standard	NM_000692		Approved	ALDHX	uc004aay.3	P30837	OTTHUMG00000019938	ENST00000377698.3:c.1068C>T	chr9.hg19:g.38396813C>T		184.0	0.0		148.0	26.0	NM_000692	B2R8F0|Q8WX76|Q9BV45	Silent	SNP	ENST00000377698.3	hg19	CCDS6615.1																																																																																			.	.		0.562	ALDH1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052492.1			T	38396813	C	T	38396813	2	4	349	1	0	0	0	0	0	0	0	1	493	610	22	3		3	ALDH1B1	9	38396813	Silent	SNP	C	TCGA-UB-AA0U-01A-11D-A382-10		38396813	102816618	36	49185										
TNFSF15	9966	hgsc.bcm.edu	37	chr9	117552930	117552930	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	tgggttggctcagggtagctGtctgttaccttggtgatgac	15	7	2	2			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr9:117552930G>C	ENST00000374045.4	-	4	671	c.558C>G	c.(556-558)gaC>gaG	p.D186E	AL390240.1_ENST00000408807.1_RNA|TNFSF15_ENST00000374044.1_Missense_Mutation_p.D109E	NM_001204344.1|NM_005118.3	NP_001191273.1|NP_005109.2	O95150	TNF15_HUMAN	tumor necrosis factor (ligand) superfamily, member 15	186					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|cytokine metabolic process (GO:0042107)|immune response (GO:0006955)|positive regulation of cytokine secretion (GO:0050715)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|skin(1)	11						CAGGGTAGCTGTCTGTTACCT	0.537																																					p.D186E		Atlas-SNP	.											.	TNFSF15	23	.	0			c.C558G						.						228	177	195					9																	117552930		2203	4300	6503	SO:0001583	missense	9966	exon4			GTAGCTGTCTGTT	AF039390	CCDS6809.1	9q32	2008-07-21			ENSG00000181634	ENSG00000181634		"Tumor necrosis factor (ligand) superfamily"	11931	protein-coding gene	gene with protein product	"vascular endothelial cell growth inhibitor", "TNF superfamily ligand TL1A", "TNF ligand-related molecule 1", "vascular endothelial growth inhibitor-192A"	604052				9434163	Standard	NM_005118		Approved	TL1, VEGI, TL1A, VEGI192A, MGC129934, MGC129935	uc004bjh.3	O95150	OTTHUMG00000021011	ENST00000374045.4:c.558C>G	chr9.hg19:g.117552930G>C	ENSP00000363157:p.Asp186Glu	160.0	0.0		120.0	33.0	NM_005118	Q3SX69|Q5VJK8|Q5VWH1|Q8NFE9	Missense_Mutation	SNP	ENST00000374045.4	hg19	CCDS6809.1	.	.	.	.	.	.	.	.	.	.	G	14.44	2.535869	0.45176	.	.	ENSG00000181634	ENST00000374045;ENST00000374044	D;D	0.94457	-3.43;-3.43	6.03	0.978	0.19740	Tumour necrosis factor (3);Tumour necrosis factor-like (2);	0.428447	0.26262	N	0.025387	D	0.87819	0.6273	L	0.41710	1.295	0.34345	D	0.689213	B;B	0.13145	0.007;0.002	B;B	0.12156	0.007;0.004	T	0.77054	-0.2730	10	0.09338	T	0.73	-21.6492	7.2563	0.26179	0.1865:0.2267:0.5867:0.0	.	186;127	O95150;O95150-2	TNF15_HUMAN;.	E	186;109	ENSP00000363157:D186E;ENSP00000363156:D109E	ENSP00000363156:D109E	D	-	3	2	TNFSF15	116592751	0.998000	0.40836	0.955000	0.39395	0.905000	0.53344	1.078000	0.30754	-0.075000	0.12798	-0.140000	0.14226	GAC	.	.		0.537	TNFSF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055424.2	NM_005118		C	117552930	G	C	117552930	3	2	349	1	0	0	0	0	1	0	0	0	16323	1368	48	4	201	4	TNFSF15	9	117552930	Missense_Mutation	SNP	G	TCGA-UB-AA0U-01A-11D-A382-10	79156117	117552930	23660501	37	49186										
SPTAN1	6709	hgsc.bcm.edu	37	chr9	131353846	131353846	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	ccgcccagtcagcctcccggGagaatctcctggaggagcaa	12	15	2	1			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr9:131353846G>T	ENST00000372731.4	+	22	3207	c.3097G>T	c.(3097-3099)Gag>Tag	p.E1033*	SPTAN1_ENST00000358161.5_Nonsense_Mutation_p.E1033*|SPTAN1_ENST00000372739.3_Nonsense_Mutation_p.E1033*	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1033					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						AGCCTCCCGGGAGAATCTCCT	0.562																																					p.E1033X	NSCLC(120;833 1744 2558 35612 37579)	Atlas-SNP	.											.	SPTAN1	266	.	0			c.G3097T						.						83	86	85					9																	131353846		2203	4300	6503	SO:0001587	stop_gained	6709	exon22			TCCCGGGAGAATC	M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"EF-hand domain containing"	11273	protein-coding gene	gene with protein product	"alpha-fodrin"	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.3097G>T	chr9.hg19:g.131353846G>T	ENSP00000361816:p.Glu1033*	108.0	0.0		81.0	13.0	NM_003127	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Nonsense_Mutation	SNP	ENST00000372731.4	hg19	CCDS6905.1	.	.	.	.	.	.	.	.	.	.	G	43	10.271077	0.99372	.	.	ENSG00000197694	ENST00000358161;ENST00000372731;ENST00000372739;ENST00000372719	.	.	.	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	.	19.0596	0.93081	0.0:0.0:1.0:0.0	.	.	.	.	X	1033	.	ENSP00000350882:E1033X	E	+	1	0	SPTAN1	130393667	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	9.238000	0.95380	2.750000	0.94351	0.585000	0.79938	GAG	.	.		0.562	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127		T	131353846	G	T	131353846	4	4	349	1	0	0	0	0	0	1	0	0	15132	1175	41	3	3179	3	SPTAN1	9	131353846	Nonsense_Mutation	SNP	G	TCGA-UB-AA0U-01A-11D-A382-10	13800916	131353846	9859585	38	49187										
USP6NL	9712	hgsc.bcm.edu	37	chr10	11505654	11505655	+	In_Frame_Ins	INS	-	-	CGT													0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	ggcggctgtgctctctcgggINScgtcccggtcctgctctggg							TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr10:11505654_11505655insCGT	ENST00000609104.1	-	15	1666_1667	c.1272_1273insACG	c.(1270-1275)acgccc>acgACGccc	p.424_425insT	USP6NL_ENST00000277575.5_In_Frame_Ins_p.441_442insT|USP6NL_ENST00000379237.2_In_Frame_Ins_p.447_448insT	NM_014688.2	NP_055503.1	Q92738	US6NL_HUMAN	USP6 N-terminal like	424					Golgi organization (GO:0007030)|plasma membrane to endosome transport (GO:0048227)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of Golgi organization (GO:1903358)|retrograde transport, plasma membrane to Golgi (GO:0035526)|virion assembly (GO:0019068)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			endometrium(3)|kidney(2)|large_intestine(6)|lung(18)|prostate(1)|skin(1)|urinary_tract(1)	32						GCTCTCTCGGGCGTCCCGGTCC	0.653																																					p.P442delinsTP		Atlas-INDEL	.											.	USP6NL	57	.	0			c.1324_1325insACG						.																																			SO:0001652	inframe_insertion	9712	exon14			.	BC010351	CCDS44357.1, CCDS53492.1	10p13	2013-07-09			ENSG00000148429	ENSG00000148429			16858	protein-coding gene	gene with protein product	"related to the N terminus of tre"	605405	"USP6NL intronic transcript 1 (non-protein coding)"	USP6NL-IT1		8700515, 8700527, 12399475	Standard	XR_247492		Approved	RNTRE, KIAA0019, TRE2NL, RN-tre	uc001iks.1	Q92738	OTTHUMG00000017672	ENST00000609104.1:c.1270_1272dupACG	chr10.hg19:g.11505655_11505657dupCGT	ENSP00000476462:p.Thr424_Thr424dup	106.0	0.0		83.0	19.0	NM_001080491	A8KA79|Q15400|Q5VV10|Q7L0K9	In_Frame_Ins	INS	ENST00000609104.1	hg19	CCDS53492.1																																																																																			.	.		0.653	USP6NL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000046764.3	NM_014688		CGT	11505655	-	CGT	11505654	7	5	349	1	0	1	1	0	0	0	0	0	17102	1203	42	0	1217	0	USP6NL	10	11505654	In_Frame_Ins	INS	-	TCGA-UB-AA0U-01A-11D-A382-10		11505654	124029093	39	49188										
KIAA1217	56243	hgsc.bcm.edu	37	chr10	24508698	24508698	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	ggagacacaccctaggggggCcccgaagttccaaggaaata	13	11	0	1			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr10:24508698C>G	ENST00000376454.3	+	2	244	c.214C>G	c.(214-216)Ccc>Gcc	p.P72A	KIAA1217_ENST00000376452.3_Missense_Mutation_p.P72A|KIAA1217_ENST00000458595.1_Missense_Mutation_p.P72A|KIAA1217_ENST00000376462.1_5'UTR	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	72					embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						CCTAGGGGGGCCCCGAAGTTC	0.512																																					p.P72A		Atlas-SNP	.											.	KIAA1217	235	.	0			c.C214G						.																																			SO:0001583	missense	56243	exon2			GGGGGGCCCCGAA	BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"sickle tail"					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.214C>G	chr10.hg19:g.24508698C>G	ENSP00000365637:p.Pro72Ala	186.0	0.0		153.0	38.0	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Missense_Mutation	SNP	ENST00000376454.3	hg19	CCDS31165.1	.	.	.	.	.	.	.	.	.	.	C	0.013	-1.607175	0.00842	.	.	ENSG00000120549	ENST00000376456;ENST00000458595;ENST00000376454;ENST00000376452	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	5.77	2.87	0.33458	.	0.212895	0.29884	N	0.010944	T	0.21881	0.0527	N	0.08118	0	0.35714	D	0.816594	B;B;B;B	0.16166	0.016;0.009;0.001;0.016	B;B;B;B	0.16722	0.016;0.011;0.01;0.016	T	0.29027	-1.0025	10	0.02654	T	1	.	17.1008	0.86649	0.0:0.628:0.372:0.0	.	72;72;72;72	Q5T5P2-7;A6NLF3;Q5T5P2;Q5T5P2-2	.;.;SKT_HUMAN;.	A	72	ENSP00000365639:P72A;ENSP00000392625:P72A;ENSP00000365637:P72A;ENSP00000365635:P72A	ENSP00000365635:P72A	P	+	1	0	KIAA1217	24548704	1.000000	0.71417	0.995000	0.50966	0.236000	0.25371	2.556000	0.45862	0.346000	0.23899	-0.913000	0.02753	CCC	.	.		0.512	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590		G	24508698	C	G	24508698	3	3	349	1	0	0	0	0	1	0	0	0	8225	739	26	4	220	4	KIAA1217	10	24508698	Missense_Mutation	SNP	C	TCGA-UB-AA0U-01A-11D-A382-10	13003044	24508698	111026049	40	49189										
ARMC4	55130	hgsc.bcm.edu	37	chr10	28224053	28224053	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	gttgaatgccaccacatttcCggacaatgactcggttttca	8	11	1	2			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr10:28224053C>A	ENST00000305242.5	-	16	2473	c.2381G>T	c.(2380-2382)cGg>cTg	p.R794L	ARMC4_ENST00000537576.1_Missense_Mutation_p.R486L|ARMC4_ENST00000545014.1_Missense_Mutation_p.R319L	NM_018076.2	NP_060546.2	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	794					cell projection organization (GO:0030030)|cilium movement (GO:0003341)|left/right axis specification (GO:0070986)|outer dynein arm assembly (GO:0036158)|ventricular system development (GO:0021591)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(17)|liver(1)|lung(17)|ovary(5)|prostate(3)|skin(8)|stomach(2)|urinary_tract(3)	75						ACCACATTTCCGGACAATGAC	0.458																																					p.R794L		Atlas-SNP	.											.	ARMC4	177	.	0			c.G2381T						.						179	170	173					10																	28224053		2203	4300	6503	SO:0001583	missense	55130	exon16			CATTTCCGGACAA	AL136859	CCDS7157.1	10p12.1-p11.23	2014-02-03			ENSG00000169126	ENSG00000169126		"Armadillo repeat containing"	25583	protein-coding gene	gene with protein product		615408				11230166	Standard	XM_005252485		Approved	FLJ10817, FLJ10376, DKFZP434P1735, CILD23	uc001itz.3	Q5T2S8	OTTHUMG00000017867	ENST00000305242.5:c.2381G>T	chr10.hg19:g.28224053C>A	ENSP00000306410:p.Arg794Leu	171.0	0.0		155.0	43.0	NM_018076	A8K906|B7Z7I1|Q9H0C0	Missense_Mutation	SNP	ENST00000305242.5	hg19	CCDS7157.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.902699	0.92035	.	.	ENSG00000169126	ENST00000537576;ENST00000305242;ENST00000545014	T;T;T	0.61510	0.1;0.1;0.1	5.78	5.78	0.91487	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.76877	0.4049	M	0.79693	2.465	0.80722	D	1	B;D	0.60160	0.378;0.987	B;D	0.65323	0.35;0.934	T	0.73895	-0.3838	10	0.32370	T	0.25	-23.4861	20.0079	0.97439	0.0:1.0:0.0:0.0	.	319;794	B7Z7I1;Q5T2S8	.;ARMC4_HUMAN	L	486;794;319	ENSP00000443208:R486L;ENSP00000306410:R794L;ENSP00000441076:R319L	ENSP00000306410:R794L	R	-	2	0	ARMC4	28264059	1.000000	0.71417	0.995000	0.50966	0.994000	0.84299	7.762000	0.85270	2.722000	0.93159	0.655000	0.94253	CGG	.	.		0.458	ARMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047339.1	NM_018076		A	28224053	C	A	28224053	3	1	349	1	0	0	0	0	1	0	0	0	953	652	23	1	773	1	ARMC4	10	28224053	Missense_Mutation	SNP	C	TCGA-UB-AA0U-01A-11D-A382-10	3715355	28224053	107310694	41	49190										
ARHGAP22	58504	hgsc.bcm.edu	37	chr10	49654442	49654442	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	ctgccattccttttactttgGggccctggcaccttttgccc	8	15	0	0			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr10:49654442G>A	ENST00000249601.4	-	10	2385	c.2089C>T	c.(2089-2091)Cca>Tca	p.P697S	ARHGAP22_ENST00000477708.2_Missense_Mutation_p.P530S|ARHGAP22_ENST00000374170.1_Missense_Mutation_p.P538S|ARHGAP22_ENST00000417912.2_Missense_Mutation_p.P713S|ARHGAP22_ENST00000374172.1_Missense_Mutation_p.P588S|ARHGAP22_ENST00000417247.2_Missense_Mutation_p.P607S|ARHGAP22_ENST00000435790.2_Missense_Mutation_p.P703S	NM_001256024.1|NM_021226.3	NP_001242953.1|NP_067049.2	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 22	697					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)	p.P697T(1)		endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TTTTACTTTGGGGCCCTGGCA	0.542																																					p.P713S		Atlas-SNP	.											ARHGAP22,NS,carcinoma,0,1	ARHGAP22	94	.	1	Substitution - Missense(1)	prostate(1)	c.C2137T						.						108	99	102					10																	49654442		2203	4300	6503	SO:0001583	missense	58504	exon10			ACTTTGGGGCCCT	AY324801	CCDS7227.1, CCDS58079.1, CCDS58080.1, CCDS58081.1	10q11.23	2013-01-10			ENSG00000128805	ENSG00000128805		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	30320	protein-coding gene	gene with protein product		610585				8619474	Standard	NM_021226		Approved	RhoGAP2	uc010qgm.3	Q7Z5H3	OTTHUMG00000018176	ENST00000249601.4:c.2089C>T	chr10.hg19:g.49654442G>A	ENSP00000249601:p.Pro697Ser	106.0	0.0		105.0	33.0	NM_001256024	A0AVP7|A5YM75|B4DED8|B9EGA0|C9JDM2|O00152|Q6ZSB0	Missense_Mutation	SNP	ENST00000249601.4	hg19	CCDS7227.1	.	.	.	.	.	.	.	.	.	.	G	16.14	3.038571	0.55003	.	.	ENSG00000128805	ENST00000249601;ENST00000374172;ENST00000374170;ENST00000477708;ENST00000417247;ENST00000435790;ENST00000417912	T;T;T;T;T;T;T	0.47528	2.13;1.88;0.84;1.05;1.75;2.07;2.2	4.16	4.16	0.48862	.	0.614826	0.14995	N	0.286489	T	0.52757	0.1754	M	0.65975	2.015	0.09310	N	1	P;B;B;B;B;P	0.52316	0.952;0.1;0.161;0.1;0.161;0.908	P;B;B;B;B;B	0.49140	0.601;0.033;0.116;0.033;0.116;0.436	T	0.49679	-0.8914	10	0.66056	D	0.02	.	9.493	0.38971	0.1046:0.0:0.8954:0.0	.	703;697;713;697;607;530	B4DED8;A6NDI7;Q7Z5H3-2;Q7Z5H3;Q7Z5H3-3;D6R9V6	.;.;.;RHG22_HUMAN;.;.	S	697;588;538;530;607;703;713	ENSP00000249601:P697S;ENSP00000363287:P588S;ENSP00000363285:P538S;ENSP00000422868:P530S;ENSP00000410054:P607S;ENSP00000416701:P703S;ENSP00000412461:P713S	ENSP00000249601:P697S	P	-	1	0	ARHGAP22	49324448	0.003000	0.15002	0.003000	0.11579	0.386000	0.30323	0.419000	0.21247	1.869000	0.54173	0.491000	0.48974	CCA	.	.		0.542	ARHGAP22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358767.1	NM_021226		A	49654442	G	A	49654442	3	1	349	1	0	0	0	0	1	0	0	0	872	1232	43	3	11	3	ARHGAP22	10	49654442	Missense_Mutation	SNP	G	TCGA-UB-AA0U-01A-11D-A382-10	21430389	49654442	85880305	42	49191										
MBL2	4153	hgsc.bcm.edu	37	chr10	54528080	54528115	+	In_Frame_Del	DEL	ATCAGTGATGCCCAGGAAGGCTTCCTCCTTGATGAG	ATCAGTGATGCCCAGGAAGGCTTCCTCCTTGATGAG	-													0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	aactgcccttctgtcttctcAtcagtgatgcccaggaaggc					rs139637221|rs267602523		TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	ATCAGTGATGCCCAGGAAGGCTTCCTCCTTGATGAG	ATCAGTGATGCCCAGGAAGGCTTCCTCCTTGATGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr10:54528080_54528115delATCAGTGATGCCCAGGAAGGCTTCCTCCTTGATGAG	ENST00000373968.3	-	4	593_628	c.529_564delCTCATCAAGGAGGAAGCCTTCCTGGGCATCACTGAT	c.(529-564)ctcatcaaggaggaagccttcctgggcatcactgatdel	p.LIKEEAFLGITD177del		NM_000242.2	NP_000233.1	P11226	MBL2_HUMAN	mannose-binding lectin (protein C) 2, soluble	177	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				acute-phase response (GO:0006953)|complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|complement activation, lectin pathway (GO:0001867)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response (GO:0045087)|killing by host of symbiont cells (GO:0051873)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of viral process (GO:0048525)|opsonization (GO:0008228)|positive regulation of phagocytosis (GO:0050766)|response to oxidative stress (GO:0006979)	cell surface (GO:0009986)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium-dependent protein binding (GO:0048306)|mannose binding (GO:0005537)|receptor binding (GO:0005102)	p.E180E(1)		breast(1)|endometrium(2)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21						CTGTCTTCTCATCAGTGATGCCCAGGAAGGCTTCCTCCTTGATGAGATTCTGAATG	0.479																																					p.177_189del		Atlas-INDEL	.											.	MBL2	55	.	1	Substitution - coding silent(1)	lung(1)	c.530_565del						.																																			SO:0001651	inframe_deletion	4153	exon4			.	AF360991	CCDS7247.1	10q11.2	2014-09-17	2011-02-02		ENSG00000165471	ENSG00000165471		"Collectins"	6922	protein-coding gene	gene with protein product		154545	"mannose-binding lectin (protein C) 2, soluble (opsonic defect)"	MBL		1675710, 1672848	Standard	NM_000242		Approved	COLEC1	uc001jjt.3	P11226	OTTHUMG00000150270	ENST00000373968.3:c.529_564delCTCATCAAGGAGGAAGCCTTCCTGGGCATCACTGAT	chr10.hg19:g.54528080_54528115delATCAGTGATGCCCAGGAAGGCTTCCTCCTTGATGAG	ENSP00000363079:p.Leu177_Asp188del	104.0	0.0		114.0	10.0	NM_000242	Q4VB12|Q4VB13|Q4VB14|Q5SQS3|Q86SI4|Q96KE4|Q96TF7|Q96TF8|Q96TF9	In_Frame_Del	DEL	ENST00000373968.3	hg19	CCDS7247.1																																																																																			.	.		0.479	MBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048115.1	NM_000242		-	54528115	ATCAGTGATGCCCAGGAAGGCTTCCTCCTTGATGAG	-	54528080	7	5	349	1	0	1	0	1	0	0	0	0	9359	214	8	0	186	0	MBL2	10	54528080	In_Frame_Del	DEL	ATCAGTGATGCCCAGGAAGGCTTCCTCCTTGATGAG	TCGA-UB-AA0U-01A-11D-A382-10	4873638	54528080	81006667	43	49192										
TDRD1	56165	hgsc.bcm.edu	37	chr10	115977409	115977419	+	Splice_Site	DEL	TTGCAGGTAAG	TTGCAGGTAAG	-													0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	acaaccttgttgtgctttttTtgcaggtaagttgcaattga							TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	TTGCAGGTAAG	TTGCAGGTAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr10:115977409_115977419delTTGCAGGTAAG	ENST00000369280.1	+	17	2778_2783	c.2318_2323delTTGCAGGTAAG	c.(2317-2325)tttgcaggt>tgt	p.FAG773fs	TDRD1_ENST00000422662.1_Splice_Site_p.FAG377fs|TDRD1_ENST00000369281.2_Splice_Site_p.FAG716fs|TDRD1_ENST00000369282.1_Splice_Site_p.FAG773fs|TDRD1_ENST00000251864.2_Splice_Site_p.FAG773fs			Q9BXT4	TDRD1_HUMAN	tudor domain containing 1	773	Tudor 3. {ECO:0000255|PROSITE- ProRule:PRU00211}.				DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|germ cell development (GO:0007281)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|P granule (GO:0043186)|pi-body (GO:0071546)	metal ion binding (GO:0046872)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(5)	48		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0343)|all cancers(201;0.0754)		TGTGCTTTTTTTGCAGGTAAGTTGCAATTGA	0.336																																					p.773_775del		Atlas-INDEL	.											.	TDRD1	126	.	0			c.2317_2323del						.																																			SO:0001630	splice_region_variant	56165	exon17			.	AF285606	CCDS7588.1	10q26.11	2013-01-23			ENSG00000095627	ENSG00000095627		"Tudor domain containing"	11712	protein-coding gene	gene with protein product	"cancer/testis antigen 41.1"	605796				11279525	Standard	NM_198795		Approved	CT41.1	uc001lbg.1	Q9BXT4	OTTHUMG00000019083	ENST00000369280.1:c.2323+1TTGCAGGTAAG>-	chr10.hg19:g.115977409_115977419delTTGCAGGTAAG		184.0	0.0		184.0	18.0	NM_198795	A6NEN3|A6NMN2|B3KVI4|B4E2L5|D3DRC2|Q4G0Y8|Q6P518|Q9H7B3	Frame_Shift_Del	DEL	ENST00000369280.1	hg19																																																																																				.	.		0.336	TDRD1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050457.2		Frame_Shift_Del	-	115977419	TTGCAGGTAAG	-	115977409	8	5	349	1	0	1	0	1	0	0	1	0	15745	1841	64	0	2380	0	TDRD1	10	115977409	Splice_Site	DEL	TTGCAGGTAAG	TCGA-UB-AA0U-01A-11D-A382-10	61449329	115977409	19557338	44	49193										
NLRP6	171389	hgsc.bcm.edu	37	chr11	280376	280376	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	aagaccatggcggccaaaaaGatcctgtacgactgggcggc	13	11	0	2			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr11:280376G>A	ENST00000312165.5	+	4	642	c.642G>A	c.(640-642)aaG>aaA	p.K214K	NLRP6_ENST00000534750.1_Silent_p.K214K	NM_138329.1	NP_612202.2	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	214	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|regulation of inflammatory response (GO:0050727)|response to bacterium (GO:0009617)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|vasopressin receptor activity (GO:0005000)			breast(1)|skin(1)|upper_aerodigestive_tract(2)	4		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122)		CGGCCAAAAAGATCCTGTACG	0.697																																					p.K214K		Atlas-SNP	.											.	NLRP6	4	.	0			c.G642A						.						21	21	21					11																	280376		2171	4260	6431	SO:0001819	synonymous_variant	171389	exon4			CAAAAAGATCCTG	AF479748	CCDS7693.1, CCDS60680.1	11p15	2006-12-08	2006-12-08	2006-12-08	ENSG00000174885	ENSG00000174885		"Nucleotide-binding domain and leucine rich repeat containing"	22944	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 6"	609650	"NACHT, leucine rich repeat and PYD containing 6"	NALP6		12563287, 12019269	Standard	NM_138329		Approved	PYPAF5, PAN3, CLR11.4	uc010qvs.3	P59044	OTTHUMG00000119070	ENST00000312165.5:c.642G>A	chr11.hg19:g.280376G>A		31.0	0.0		34.0	13.0	NM_138329	A8K9F3|E9PJZ8	Silent	SNP	ENST00000312165.5	hg19	CCDS7693.1																																																																																			.	.		0.697	NLRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239283.1	NM_138329		A	280376	G	A	280376	2	1	349	1	0	0	0	0	0	0	0	1	10490	933	33	3		3	NLRP6	11	280376	Silent	SNP	G	TCGA-UB-AA0U-01A-11D-A382-10		280376	134726140	45	49194										
KRTAP5-5	439915	hgsc.bcm.edu	37	chr11	1651253	1651253	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	tgtgggggatgtggctccggCtgctgtgtgcctgtctgctg	18	9	1	0			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr11:1651253C>G	ENST00000399676.2	+	1	221	c.183C>G	c.(181-183)ggC>ggG	p.G61G		NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	61						keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|urinary_tract(1)	33		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		gtggctccggctgCTGTGTGC	0.682																																					p.G61G		Atlas-SNP	.											.	KRTAP5-5	86	.	0			c.C183G						.						59	72	67					11																	1651253		2199	4293	6492	SO:0001819	synonymous_variant	439915	exon1			CTCCGGCTGCTGT	AB125074	CCDS41592.1	11p15.5	2008-10-30			ENSG00000185940	ENSG00000185940		"Keratin associated proteins"	23601	protein-coding gene	gene with protein product						15144888	Standard	NM_001001480		Approved	KRTAP5.5, KRTAP5-11	uc001lty.3	Q701N2	OTTHUMG00000057554	ENST00000399676.2:c.183C>G	chr11.hg19:g.1651253C>G		144.0	0.0		161.0	23.0	NM_001001480	A8MWN2	Silent	SNP	ENST00000399676.2	hg19	CCDS41592.1																																																																																			.	.		0.682	KRTAP5-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127919.1			G	1651253	C	G	1651253	2	3	349	1	0	0	0	0	0	0	0	1	8573	784	28	4		4	KRTAP5-5	11	1651253	Silent	SNP	C	TCGA-UB-AA0U-01A-11D-A382-10	1370877	1651253	133355263	46	49195										
RRM1	6240	hgsc.bcm.edu	37	chr11	4127292	4127292	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	gtaggctcagatcaccatgaAagtaatccaaggcttgtaca	9	9	2	2			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr11:4127292A>G	ENST00000300738.5	+	3	329	c.125A>G	c.(124-126)aAa>aGa	p.K42R	RRM1_ENST00000423050.2_Intron	NM_001033.3	NP_001024.1	P23921	RIR1_HUMAN	ribonucleotide reductase M1	42	ATP-cone. {ECO:0000255|PROSITE- ProRule:PRU00492}.				cell proliferation in forebrain (GO:0021846)|deoxyribonucleotide biosynthetic process (GO:0009263)|DNA replication (GO:0006260)|male gonad development (GO:0008584)|mitotic cell cycle (GO:0000278)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein heterotetramerization (GO:0051290)|pyrimidine nucleobase metabolic process (GO:0006206)|response to ionizing radiation (GO:0010212)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor (GO:0004748)			breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|skin(2)	14		Medulloblastoma(188;0.0025)|Breast(177;0.00502)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0848)|LUSC - Lung squamous cell carcinoma(625;0.205)	Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Hydroxyurea(DB01005)	ATCACCATGAAAGTAATCCAA	0.408																																					p.K42R	NSCLC(45;1345 1376 6258 22925)|Ovarian(34;894 1053 6175 12768)	Atlas-SNP	.											.	RRM1	31	.	0			c.A125G						.						88	80	83					11																	4127292		2201	4298	6499	SO:0001583	missense	6240	exon3			CCATGAAAGTAAT	X59543	CCDS7750.1	11p15.5	2009-07-10	2008-03-11		ENSG00000167325	ENSG00000167325	1.17.14.1		10451	protein-coding gene	gene with protein product		180410	"ribonucleotide reductase M1 polypeptide"			7557993	Standard	NM_001033		Approved		uc001lyw.4	P23921	OTTHUMG00000133361	ENST00000300738.5:c.125A>G	chr11.hg19:g.4127292A>G	ENSP00000300738:p.Lys42Arg	82.0	0.0		104.0	19.0	NM_001033	Q9UNN2	Missense_Mutation	SNP	ENST00000300738.5	hg19	CCDS7750.1	.	.	.	.	.	.	.	.	.	.	A	16.14	3.037836	0.54896	.	.	ENSG00000167325	ENST00000300738;ENST00000536894	T	0.33216	1.42	5.77	5.77	0.91146	Ribonucleotide reductase R1 subunit, N-terminal (1);ATP-cone (2);	0.000000	0.85682	D	0.000000	T	0.28797	0.0714	L	0.42008	1.315	0.80722	D	1	B	0.12630	0.006	B	0.17098	0.017	T	0.03619	-1.1019	10	0.29301	T	0.29	-17.3309	15.2176	0.73281	1.0:0.0:0.0:0.0	.	42	P23921	RIR1_HUMAN	R	42;36	ENSP00000300738:K42R	ENSP00000300738:K42R	K	+	2	0	RRM1	4083868	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.836000	0.92105	2.326000	0.78906	0.533000	0.62120	AAA	.	.		0.408	RRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257197.1	NM_001033		G	4127292	A	G	4127292	3	3	349	1	0	0	0	0	1	0	0	0	13696	14	1	2	135	2	RRM1	11	4127292	Missense_Mutation	SNP	A	TCGA-UB-AA0U-01A-11D-A382-10	2476039	4127292	130879224	47	49196										
CHRM4	1132	hgsc.bcm.edu	37	chr11	46407264	46407264	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	agccacggggcgcggtggcgGtggcagcgctggcggggggg	25	10	0	0			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr11:46407264G>A	ENST00000433765.2	-	1	843	c.844C>T	c.(844-846)Ccg>Tcg	p.P282S		NM_000741.2	NP_000732.2	P08173	ACM4_HUMAN	cholinergic receptor, muscarinic 4	282					adenylate cyclase-inhibiting G-protein coupled acetylcholine receptor signaling pathway (GO:0007197)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|regulation of locomotion (GO:0040012)|signal transduction (GO:0007165)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)			breast(1)|endometrium(7)|kidney(1)|large_intestine(1)|lung(6)|prostate(3)|skin(1)	20				GBM - Glioblastoma multiforme(35;0.0254)|Lung(87;0.14)	Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Darifenacin(DB00496)|Desipramine(DB01151)|Doxepin(DB01142)|Fesoterodine(DB06702)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Isopropamide(DB01625)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paroxetine(DB00715)|Pethidine(DB00454)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Tolterodine(DB01036)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	CGCGGTGGCGGTGGCAGCGCT	0.672																																					p.P282S	Esophageal Squamous(171;1020 1936 4566 30205 42542)	Atlas-SNP	.											.	CHRM4	47	.	0			c.C844T						.						18	23	21					11																	46407264		2031	4155	6186	SO:0001583	missense	1132	exon1			GTGGCGGTGGCAG	M16405	CCDS44581.1	11p12-p11.2	2012-08-08			ENSG00000180720	ENSG00000180720		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1953	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 4"	118495				1577490	Standard	NM_000741		Approved		uc001nct.1	P08173	OTTHUMG00000154371	ENST00000433765.2:c.844C>T	chr11.hg19:g.46407264G>A	ENSP00000409378:p.Pro282Ser	59.0	0.0		41.0	15.0	NM_000741	B2RPP4|Q0VD60|Q4VBK7	Missense_Mutation	SNP	ENST00000433765.2	hg19	CCDS44581.1	.	.	.	.	.	.	.	.	.	.	g	0	-2.732138	0.00089	.	.	ENSG00000180720	ENST00000433765	T	0.57752	0.38	3.24	3.24	0.37175	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.26304	0.0642	N	0.02802	-0.49	0.09310	N	1	B	0.06786	0.001	B	0.15052	0.012	T	0.10154	-1.0642	9	0.17369	T	0.5	-7.3883	10.2254	0.43222	0.0:0.0:1.0:0.0	.	282	P08173	ACM4_HUMAN	S	282	ENSP00000409378:P282S	ENSP00000409378:P282S	P	-	1	0	CHRM4	46363840	0.992000	0.36948	0.678000	0.29963	0.011000	0.07611	3.454000	0.52986	2.117000	0.64856	0.457000	0.33378	CCG	.	.		0.672	CHRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334985.1	NM_000741		A	46407264	G	A	46407264	3	1	349	1	0	0	0	0	1	0	0	0	3381	1261	44	3	599	3	CHRM4	11	46407264	Missense_Mutation	SNP	G	TCGA-UB-AA0U-01A-11D-A382-10	42279972	46407264	88599252	48	49197										
C11orf9	745	hgsc.bcm.edu	37	chr11	61533636	61533637	+	Frame_Shift_Ins	INS	-	-	C													0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	ggcgctgcccccaagcccttINScccggggggcaccgggcccc							TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr11:61533636_61533637insC	ENST00000278836.5	+	3	437_438	c.341_342insC	c.(340-345)ttcccgfs	p.FP114fs	MYRF_ENST00000265460.5_Frame_Shift_Ins_p.FP105fs|TMEM258_ENST00000535042.1_5'Flank	NM_001127392.1	NP_001120864.1	Q9Y2G1	MRF_HUMAN	myelin regulatory factor	114	Pro-rich.				central nervous system myelin maintenance (GO:0032286)|central nervous system myelination (GO:0022010)|oligodendrocyte development (GO:0014003)|oligodendrocyte differentiation (GO:0048709)|positive regulation of myelination (GO:0031643)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)										CCCAAGCCCTTCCCGGGGGGCA	0.703																																					p.F114fs		Atlas-INDEL	.											.	.	.	.	0			c.341_342insC						.																																			SO:0001589	frameshift_variant	745	exon3			.		CCDS31579.1, CCDS44622.1	11q12-q13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000124920	ENSG00000124920			1181	protein-coding gene	gene with protein product	"myelin gene regulatory factor"	608329	"chromosome 11 open reading frame 9"	C11orf9		10828591, 12384578	Standard	NM_001127392		Approved	Ndt80, pqn-47, MRF	uc001nsc.1	Q9Y2G1	OTTHUMG00000168161	ENST00000278836.5:c.344dupC	chr11.hg19:g.61533639_61533639dupC	ENSP00000278836:p.Phe114fs	75.0	0.0		66.0	10.0	NM_001127392	O43582|Q9P1Q6	Frame_Shift_Ins	INS	ENST00000278836.5	hg19	CCDS44622.1																																																																																			.	.		0.703	MYRF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398519.2	NM_013279		C	61533637	-	C	61533636	7	5	349	1	0	1	1	0	0	0	0	0	1673	1783	62	0	374	0	C11orf9	11	61533636	Frame_Shift_Ins	INS	-	TCGA-UB-AA0U-01A-11D-A382-10	15126372	61533636	73472880	49	49198										
CATSPER1	117144	hgsc.bcm.edu	37	chr11	65787820	65787820	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	tttctcaaggcctttgaacaGcgccgtctggaagctatcca	9	12	2	1			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr11:65787820G>A	ENST00000312106.5	-	8	2169	c.2032C>T	c.(2032-2034)Ctg>Ttg	p.L678L		NM_053054.3	NP_444282.3	Q8NEC5	CTSR1_HUMAN	cation channel, sperm associated 1	678					calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|fusion of sperm to egg plasma membrane (GO:0007342)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|regulation of calcium ion transport (GO:0051924)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|central_nervous_system(1)|endometrium(9)|kidney(3)|large_intestine(6)|liver(3)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44						CCTTTGAACAGCGCCGTCTGG	0.637																																					p.L678L		Atlas-SNP	.											.	CATSPER1	101	.	0			c.C2032T						.						121	116	118					11																	65787820		2201	4296	6497	SO:0001819	synonymous_variant	117144	exon8			TGAACAGCGCCGT	AF407333	CCDS8127.1	11q12.1	2011-07-05			ENSG00000175294	ENSG00000175294		"Voltage-gated ion channels / Cation channels, sperm associated"	17116	protein-coding gene	gene with protein product		606389				11675491, 11595941, 16382101	Standard	NM_053054		Approved	CATSPER	uc001ogt.3	Q8NEC5	OTTHUMG00000166668	ENST00000312106.5:c.2032C>T	chr11.hg19:g.65787820G>A		77.0	0.0		71.0	15.0	NM_053054	Q96P76	Silent	SNP	ENST00000312106.5	hg19	CCDS8127.1																																																																																			.	.		0.637	CATSPER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391055.1	NM_053054		A	65787820	G	A	65787820	2	1	349	1	0	0	0	0	0	0	0	1	2689	962	34	3		3	CATSPER1	11	65787820	Silent	SNP	G	TCGA-UB-AA0U-01A-11D-A382-10	4254184	65787820	69218696	50	49199										
RNF121	55298	hgsc.bcm.edu	37	chr11	71640151	71640151	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	ggttggaggtggtgctgctgGggaacgggagctggatgagg	23	4	0	1			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr11:71640151G>A	ENST00000361756.3	+	1	405	c.44G>A	c.(43-45)gGg>gAg	p.G15E	RP11-849H4.2_ENST00000531488.1_5'Flank|RP11-849H4.2_ENST00000529844.1_5'Flank|RP11-849H4.2_ENST00000528511.2_5'Flank|RNF121_ENST00000530137.1_5'UTR|RP11-849H4.2_ENST00000529513.1_5'Flank|RNF121_ENST00000545854.1_5'UTR|RNF121_ENST00000490867.1_3'UTR|RNF121_ENST00000533380.1_5'UTR|RNF121_ENST00000393713.3_5'UTR	NM_018320.4	NP_060790.2	Q9H920	RN121_HUMAN	ring finger protein 121	15						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(1)|lung(6)|urinary_tract(1)	13						GGTGCTGCTGGGGAACGGGAG	0.652																																					p.G15E		Atlas-SNP	.											.	RNF121	19	.	0			c.G44A						.						104	67	80					11																	71640151		2112	4128	6240	SO:0001583	missense	55298	exon1			CTGCTGGGGAACG	AK001961	CCDS8203.1, CCDS73343.1	11q13.3	2008-02-05			ENSG00000137522	ENSG00000137522		"RING-type (C3HC4) zinc fingers"	21070	protein-coding gene	gene with protein product							Standard	NM_018320		Approved	FLJ11099	uc001ora.3	Q9H920	OTTHUMG00000157023	ENST00000361756.3:c.44G>A	chr11.hg19:g.71640151G>A	ENSP00000354571:p.Gly15Glu	80.0	0.0		99.0	13.0	NM_018320	B3KSW8|Q6IA57|Q6P449|Q96DB4	Missense_Mutation	SNP	ENST00000361756.3	hg19	CCDS8203.1	.	.	.	.	.	.	.	.	.	.	G	11.90	1.775954	0.31411	.	.	ENSG00000137522	ENST00000361756	T	0.15952	2.38	5.22	0.927	0.19437	.	0.385818	0.28700	N	0.014428	T	0.04543	0.0124	N	0.04508	-0.205	0.80722	D	1	P	0.37233	0.588	B	0.21708	0.036	T	0.48151	-0.9060	10	0.12430	T	0.62	.	7.6028	0.28085	0.0:0.3537:0.3892:0.2572	.	15	Q9H920	RN121_HUMAN	E	15	ENSP00000354571:G15E	ENSP00000354571:G15E	G	+	2	0	RNF121	71317799	1.000000	0.71417	0.995000	0.50966	0.995000	0.86356	0.633000	0.24598	0.088000	0.17205	0.563000	0.77884	GGG	.	.		0.652	RNF121-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347132.1	NM_018320		A	71640151	G	A	71640151	3	1	349	1	0	0	0	0	1	0	0	0	13446	1232	43	3	46	3	RNF121	11	71640151	Missense_Mutation	SNP	G	TCGA-UB-AA0U-01A-11D-A382-10	5852331	71640151	63366365	51	49200										
GRIA4	2893	hgsc.bcm.edu	37	chr11	105795410	105795410	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	gaaaggaaggacccagcgacCagcctcccaatgagtttggc	12	12	0	1			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr11:105795410C>T	ENST00000530497.1	+	11	1762	c.1762C>T	c.(1762-1764)Cag>Tag	p.Q588*	GRIA4_ENST00000282499.5_Nonsense_Mutation_p.Q588*|GRIA4_ENST00000525187.1_Nonsense_Mutation_p.Q588*|GRIA4_ENST00000393127.2_Nonsense_Mutation_p.Q588*			P48058	GRIA4_HUMAN	glutamate receptor, ionotropic, AMPA 4	588					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(24)|liver(2)|lung(25)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	82		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)		ACCCAGCGACCAGCCTCCCAA	0.473																																					p.Q588X		Atlas-SNP	.											.	GRIA4	380	.	0			c.C1762T						.						119	98	105					11																	105795410		2202	4299	6501	SO:0001587	stop_gained	2893	exon12			AGCGACCAGCCTC	U16129	CCDS8333.1, CCDS41706.1, CCDS41707.1	11q22	2012-08-29	2012-02-03		ENSG00000152578	ENSG00000152578		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4574	protein-coding gene	gene with protein product		138246	"glutamate receptor, ionotrophic, AMPA 4"	GLUR4			Standard	NM_001077244		Approved	GluA4, GLURD	uc001pix.2	P48058	OTTHUMG00000166236	ENST00000530497.1:c.1762C>T	chr11.hg19:g.105795410C>T	ENSP00000435775:p.Gln588*	215.0	0.0		174.0	30.0	NM_001077243	Q86XE8	Nonsense_Mutation	SNP	ENST00000530497.1	hg19	CCDS8333.1	.	.	.	.	.	.	.	.	.	.	C	42	9.547899	0.99201	.	.	ENSG00000152578	ENST00000282499;ENST00000393127;ENST00000530497;ENST00000525187	.	.	.	6.05	6.05	0.98169	.	0.000000	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	.	20.6013	0.99457	0.0:1.0:0.0:0.0	.	.	.	.	X	588	.	ENSP00000282499:Q588X	Q	+	1	0	GRIA4	105300620	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.948000	0.56660	2.878000	0.98634	0.650000	0.86243	CAG	.	.		0.473	GRIA4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388593.1			T	105795410	C	T	105795410	4	4	349	1	0	0	0	0	0	1	0	0	6779	595	21	3	1841	3	GRIA4	11	105795410	Nonsense_Mutation	SNP	C	TCGA-UB-AA0U-01A-11D-A382-10	34155259	105795410	29211106	52	49201										
ALG9	79796	hgsc.bcm.edu	37	chr11	111706981	111706981	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	gcaaaaggttttggtaactgAcctctgaactctgatggaat	10	7	2	3			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr11:111706981A>T	ENST00000531154.1	-	13	1468	c.996T>A	c.(994-996)ggT>ggA	p.G332G	ALG9_ENST00000524880.1_3'UTR|ALG9_ENST00000527228.1_5'UTR|ALG9_ENST00000398006.2_Silent_p.G325G	NM_024740.2	NP_079016.2	Q9H6U8	ALG9_HUMAN	ALG9, alpha-1,2-mannosyltransferase	496					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	dol-P-Man:Man(6)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase activity (GO:0052926)|dol-P-Man:Man(8)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase activity (GO:0052918)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;6.81e-07)|BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|all cancers(92;1.3e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0587)		TTGGTAACTGACCTCTGAACT	0.428																																					p.G503G		Atlas-SNP	.											.	ALG9	77	.	0			c.T1509A						.						82	79	80					11																	111706981		1864	4086	5950	SO:0001819	synonymous_variant	79796	exon14			TAACTGACCTCTG		CCDS41714.1, CCDS53709.1, CCDS73379.1, CCDS73380.1	11q23	2013-02-26	2013-02-26	2004-08-26	ENSG00000086848	ENSG00000086848	2.4.1.259, 2.4.1.261	"Dolichyl D-mannosyl phosphate dependent mannosyltransferases"	15672	protein-coding gene	gene with protein product	"dolichyl-P-Man:Man(6)GlcNAc(2)-PP-dolichol alpha-1,2-mannosyltransferase", "dolichyl-P-Man:Man(8)GlcNAc(2)-PP-dolichol alpha-1,2-mannosyltransferase", "dol-P-Man dependent alpha-1,2-mannosyltransferase"	606941	"disrupted in bipolar affective disorder 1", "asparagine-linked glycosylation 9 homolog (yeast, alpha 1,2 mannosyltransferase)", "asparagine-linked glycosylation 9, alpha- 1,2-mannosyltransferase homolog (S. cerevisiae, alpha- 1,2-mannosyltransferase)", "asparagine-linked glycosylation 9, alpha-1,2-mannosyltransferase homolog (S. cerevisiae)"	DIBD1		12030331, 15148656	Standard	NM_024740		Approved		uc021qql.1	Q9H6U8	OTTHUMG00000166819	ENST00000531154.1:c.996T>A	chr11.hg19:g.111706981A>T		101.0	0.0		62.0	21.0	NM_024740	Q6ZMD5|Q7Z4R4|Q96GS7|Q96PB9|Q9H068	Silent	SNP	ENST00000531154.1	hg19	CCDS41714.1	.	.	.	.	.	.	.	.	.	.	A	10.38	1.334845	0.24253	.	.	ENSG00000086848	ENST00000532425	.	.	.	5.2	-0.692	0.11301	.	.	.	.	.	T	0.43986	0.1272	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.26292	-1.0107	4	.	.	.	-13.6198	4.2235	0.10570	0.2664:0.0:0.4957:0.2379	.	.	.	.	D	81	.	.	V	-	2	0	ALG9	111212191	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	0.702000	0.25631	0.003000	0.14656	-0.376000	0.06991	GTC	.	.		0.428	ALG9-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000391485.1	NM_024740		T	111706981	A	T	111706981	2	4	349	1	0	0	0	0	0	0	0	1	524	262	10	4		4	ALG9	11	111706981	Silent	SNP	A	TCGA-UB-AA0U-01A-11D-A382-10	5911571	111706981	23299535	53	49202										
USP5	8078	hgsc.bcm.edu	37	chr12	6972521	6972521	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	cgaagactccttctgctcccCtcacttctcctctccgacat	4	19	4	1			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr12:6972521C>T	ENST00000229268.8	+	15	1986	c.1934C>T	c.(1933-1935)cCt>cTt	p.P645L	USP5_ENST00000389231.5_Intron|USP5_ENST00000541969.1_3'UTR	NM_001098536.1	NP_001092006.1	P45974	UBP5_HUMAN	ubiquitin specific peptidase 5 (isopeptidase T)	645	USP.				positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)	lysosome (GO:0005764)	cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin thiolesterase activity (GO:0004221)|zinc ion binding (GO:0008270)			breast(6)|endometrium(4)|kidney(2)|large_intestine(6)|lung(14)|skin(2)|urinary_tract(2)	36						TTCTGCTCCCCTCACTTCTCC	0.582																																					p.P645L		Atlas-SNP	.											.	USP5	124	.	0			c.C1934T						.						141	148	145					12																	6972521		2203	4300	6503	SO:0001583	missense	8078	exon15			GCTCCCCTCACTT	U35116	CCDS31733.1, CCDS41743.1	12p13	2007-03-02	2005-08-08		ENSG00000111667	ENSG00000111667		"Ubiquitin-specific peptidases"	12628	protein-coding gene	gene with protein product		601447	"ubiquitin specific protease 5 (isopeptidase T)"			12838346, 8723724	Standard	NM_003481		Approved	IsoT	uc001qri.4	P45974	OTTHUMG00000169233	ENST00000229268.8:c.1934C>T	chr12.hg19:g.6972521C>T	ENSP00000229268:p.Pro645Leu	111.0	0.0		77.0	40.0	NM_001098536	D3DUS7|D3DUS8|Q96J22	Missense_Mutation	SNP	ENST00000229268.8	hg19	CCDS41743.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.938615	0.73557	.	.	ENSG00000111667	ENST00000229268	T	0.22336	1.96	4.96	4.96	0.65561	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.07683	0.0193	N	0.00926	-1.1	0.80722	D	1	P	0.41345	0.746	B	0.38225	0.268	T	0.37174	-0.9717	10	0.08179	T	0.78	-2.5474	18.756	0.91833	0.0:1.0:0.0:0.0	.	645	P45974	UBP5_HUMAN	L	645	ENSP00000229268:P645L	ENSP00000229268:P645L	P	+	2	0	USP5	6842782	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.147000	0.64851	2.735000	0.93741	0.561000	0.74099	CCT	.	.		0.582	USP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402982.1			T	6972521	C	T	6972521	3	4	349	1	0	0	0	0	1	0	0	0	17096	681	24	3	1992	3	USP5	12	6972521	Missense_Mutation	SNP	C	TCGA-UB-AA0U-01A-11D-A382-10		6972521	126879374	54	49203										
ARID2	196528	hgsc.bcm.edu	37	chr12	46246680	46246680	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	tacagaatgtggtcccgcagGtaagttattccatgatcaca	9	9	1	2			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr12:46246680G>T	ENST00000334344.6	+	15	4945		c.e15+1		ARID2_ENST00000422737.1_Splice_Site|ARID2_ENST00000457135.1_Splice_Site|ARID2_ENST00000479608.1_Splice_Site|ARID2_ENST00000444670.1_Splice_Site	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)						chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		GGTCCCGCAGGTAAGTTATTC	0.383			"N, S, F"		hepatocellular carcinoma																																.		Atlas-SNP	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	311	.	0			c.4773+1G>T						.						29	23	25					12																	46246680		2200	4295	6495	SO:0001630	splice_region_variant	196528	exon15			CCGCAGGTAAGTT		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.4773+1G>T	chr12.hg19:g.46246680G>T		53.0	0.0		37.0	18.0	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Splice_Site	SNP	ENST00000334344.6	hg19	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.481141	0.84747	.	.	ENSG00000189079	ENST00000334344;ENST00000549153;ENST00000338636;ENST00000422737;ENST00000444670;ENST00000457135	.	.	.	6.02	6.02	0.97574	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.5407	0.99260	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ARID2	44532947	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	8.115000	0.89572	2.865000	0.98341	0.655000	0.94253	.	.	.		0.383	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875	Intron	T	46246680	G	T	46246680	5	4	349	1	0	0	0	0	0	0	1	0	915	1275	44	3	4832	3	ARID2	12	46246680	Splice_Site	SNP	G	TCGA-UB-AA0U-01A-11D-A382-10	39274159	46246680	87605215	55	49204										
LMBR1L	55716	hgsc.bcm.edu	37	chr12	49498238	49498238	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	atcccctacttacctttctgGagccagcaaagccctcagac	6	16	2	1			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr12:49498238G>A	ENST00000267102.8	-	5	770	c.428C>T	c.(427-429)tCc>tTc	p.S143F	LMBR1L_ENST00000553204.1_Intron|LMBR1L_ENST00000547382.1_Missense_Mutation_p.S143F|LMBR1L_ENST00000395141.4_Missense_Mutation_p.S138F	NM_018113.2	NP_060583.2	Q6UX01	LMBRL_HUMAN	limb development membrane protein 1-like	143					endocytosis (GO:0006897)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						TACCTTTCTGGAGCCAGCAAA	0.458																																					p.S143F		Atlas-SNP	.											LMBR1L_ENST00000267102,bladder,carcinoma,0,2	LMBR1L	61	.	0			c.C428T						.						131	134	133					12																	49498238		2203	4300	6503	SO:0001583	missense	55716	exon5			TTTCTGGAGCCAG	AB033000	CCDS8780.2, CCDS73466.1	12q13.12	2013-08-05	2013-08-05		ENSG00000139636	ENSG00000139636			18268	protein-coding gene	gene with protein product		610007	"limb region 1 homolog (mouse)-like"			10574461, 11287427	Standard	XM_005269022		Approved	FLJ10494, KIAA1174	uc001rth.4	Q6UX01	OTTHUMG00000150511	ENST00000267102.8:c.428C>T	chr12.hg19:g.49498238G>A	ENSP00000267102:p.Ser143Phe	118.0	0.0		103.0	18.0	NM_018113	Q969J4|Q96BY8|Q96HN8|Q9NT09|Q9NVE1|Q9NVU9|Q9ULP6	Missense_Mutation	SNP	ENST00000267102.8	hg19	CCDS8780.2	.	.	.	.	.	.	.	.	.	.	G	24.6	4.546393	0.86022	.	.	ENSG00000139636	ENST00000267102;ENST00000547382;ENST00000395141	T;T;T	0.34667	1.35;1.35;1.35	6.07	6.07	0.98685	LMBR1-like membrane protein (1);	0.000000	0.85682	D	0.000000	T	0.56529	0.1991	L	0.61387	1.9	0.80722	D	1	D;D;D;D	0.89917	0.997;0.997;0.999;1.0	D;D;D;D	0.87578	0.991;0.994;0.998;0.998	T	0.42548	-0.9445	10	0.09590	T	0.72	.	19.4154	0.94694	0.0:0.0:1.0:0.0	.	141;143;143;138	Q6UX01-2;Q6UX01-3;Q6UX01;Q6UX01-4	.;.;LMBRL_HUMAN;.	F	143;143;138	ENSP00000267102:S143F;ENSP00000447329:S143F;ENSP00000378573:S138F	ENSP00000267102:S143F	S	-	2	0	LMBR1L	47784505	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.824000	0.99380	2.884000	0.98904	0.655000	0.94253	TCC	.	.		0.458	LMBR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318696.1	NM_018113		A	49498238	G	A	49498238	3	1	349	1	0	0	0	0	1	0	0	0	8850	1174	41	3	1093	3	LMBR1L	12	49498238	Missense_Mutation	SNP	G	TCGA-UB-AA0U-01A-11D-A382-10	3251558	49498238	84353657	56	49205										
LGR5	8549	hgsc.bcm.edu	37	chr12	71977548	71977548	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	tcaacagttttcagatccccTctgtacatttcccccattaa	3	14	3	1			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr12:71977548T>G	ENST00000266674.5	+	18	2069	c.1758T>G	c.(1756-1758)ccT>ccG	p.P586P	RP11-186F10.2_ENST00000546601.1_RNA|LGR5_ENST00000540815.2_Silent_p.P562P|LGR5_ENST00000536515.1_Silent_p.P514P			O75473	LGR5_HUMAN	leucine-rich repeat containing G protein-coupled receptor 5	586					G-protein coupled receptor signaling pathway (GO:0007186)|inner ear development (GO:0048839)|positive regulation of canonical Wnt signaling pathway (GO:0090263)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)		NUP107/LGR5(2)	endometrium(2)|kidney(3)|large_intestine(2)|lung(24)|ovary(1)|pancreas(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(3)	48						TCAGATCCCCTCTGTACATTT	0.498																																					p.P586P		Atlas-SNP	.											.	LGR5	103	.	0			c.T1758G						.						180	156	164					12																	71977548		2203	4300	6503	SO:0001819	synonymous_variant	8549	exon18			ATCCCCTCTGTAC	AF062006	CCDS9000.1, CCDS61194.1, CCDS61195.1	12q22-q23	2012-08-21	2011-01-25	2004-11-12				"GPCR / Class A : Orphans"	4504	protein-coding gene	gene with protein product		606667	"G protein-coupled receptor 49", "leucine-rich repeat-containing G protein-coupled receptor 5"	GPR67, GPR49		9642114	Standard	NM_003667		Approved	HG38, FEX	uc001swl.4	O75473	OTTHUMG00000169543	ENST00000266674.5:c.1758T>G	chr12.hg19:g.71977548T>G		144.0	0.0		122.0	41.0	NM_003667	D8MCT0|Q4VAM0|Q4VAM2|Q9UP75	Silent	SNP	ENST00000266674.5	hg19	CCDS9000.1																																																																																			.	.		0.498	LGR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404744.1	NM_003667		G	71977548	T	G	71977548	2	3	349	1	0	0	0	0	0	0	0	1	8766	1538	54	5		5	LGR5	12	71977548	Silent	SNP	T	TCGA-UB-AA0U-01A-11D-A382-10	22479310	71977548	61874347	57	49206										
C12orf51	283450	hgsc.bcm.edu	37	chr12	112673514	112673514	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	ggactagctttggagacgggCgttggtcaagcagcagggag	18	7	1	1			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr12:112673514C>T	ENST00000430131.2	-	35	5398	c.4253G>A	c.(4252-4254)cGc>cAc	p.R1418H	HECTD4_ENST00000550722.1_Missense_Mutation_p.R1694H|HECTD4_ENST00000377560.5_Missense_Mutation_p.R1668H			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	1418					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										TGGAGACGGGCGTTGGTCAAG	0.557																																					p.R1706H		Atlas-SNP	.											.	.	.	.	0			c.G5117A						.						39	41	40					12																	112673514		2019	4178	6197	SO:0001583	missense	283450	exon36			GACGGGCGTTGGT	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 51"	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.4253G>A	chr12.hg19:g.112673514C>T	ENSP00000404379:p.Arg1418His	99.0	0.0		94.0	12.0	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Missense_Mutation	SNP	ENST00000430131.2	hg19		.	.	.	.	.	.	.	.	.	.	C	36	5.928818	0.97116	.	.	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722	T;T;T	0.51817	0.69;0.7;0.69	6.03	6.03	0.97812	.	.	.	.	.	T	0.54447	0.1859	N	0.12182	0.205	0.80722	D	1	D	0.71674	0.998	D	0.72075	0.976	T	0.59742	-0.7397	9	0.54805	T	0.06	.	20.5666	0.99351	0.0:1.0:0.0:0.0	.	1418	Q9Y4D8	K0614_HUMAN	H	1668;1418;1694	ENSP00000366783:R1668H;ENSP00000404379:R1418H;ENSP00000449784:R1694H	ENSP00000366783:R1668H	R	-	2	0	C12orf51	111157897	1.000000	0.71417	0.997000	0.53966	0.987000	0.75469	7.400000	0.79949	2.854000	0.98071	0.655000	0.94253	CGC	.	.		0.557	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		T	112673514	C	T	112673514	3	4	349	1	0	0	0	0	1	0	0	0	1698	768	27	1	7901	1	C12orf51	12	112673514	Missense_Mutation	SNP	C	TCGA-UB-AA0U-01A-11D-A382-10	40695966	112673514	21178381	58	49207										
C13orf23	80209	hgsc.bcm.edu	37	chr13	39587872	39587872	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	aagcagaagagtcagagttcTgaagagtaagagaagatagt	13	3	2	7			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr13:39587872T>C	ENST00000352251.3	-	11	2350	c.1517A>G	c.(1516-1518)cAg>cGg	p.Q506R	PROSER1_ENST00000350125.3_Missense_Mutation_p.Q484R|PROSER1_ENST00000484434.3_Intron	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	506	Ser-rich.																GTCAGAGTTCTGAAGAGTAAG	0.493																																					p.Q506R		Atlas-SNP	.											.	.	.	.	0			c.A1517G						.						79	77	78					13																	39587872		2203	4300	6503	SO:0001583	missense	80209	exon11			GAGTTCTGAAGAG	AK022723	CCDS9368.2	13q13.2	2011-08-09	2011-08-09	2011-08-09	ENSG00000120685	ENSG00000120685			20291	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 23"	C13orf23			Standard	NM_025138		Approved	bA50D16.2, FLJ12661	uc001uwy.4	Q86XN7	OTTHUMG00000016764	ENST00000352251.3:c.1517A>G	chr13.hg19:g.39587872T>C	ENSP00000332034:p.Gln506Arg	111.0	0.0		61.0	16.0	NM_025138	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	Missense_Mutation	SNP	ENST00000352251.3	hg19	CCDS9368.2	.	.	.	.	.	.	.	.	.	.	T	10.09	1.254041	0.22965	.	.	ENSG00000120685	ENST00000352251;ENST00000350125	T;T	0.32023	1.47;1.47	5.37	-3.55	0.04639	.	.	.	.	.	T	0.14356	0.0347	N	0.20986	0.625	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.08055	0.001;0.003	T	0.27054	-1.0085	8	.	.	.	4.993	2.6752	0.05079	0.114:0.1423:0.3893:0.3544	.	484;506	A6NJ97;Q86XN7	.;PRSR1_HUMAN	R	506;484	ENSP00000332034:Q506R;ENSP00000339123:Q484R	.	Q	-	2	0	PROSER1	38485872	0.802000	0.28943	0.000000	0.03702	0.402000	0.30811	1.137000	0.31479	-0.946000	0.03677	0.459000	0.35465	CAG	.	.		0.493	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5	NM_025138		C	39587872	T	C	39587872	3	2	349	1	0	0	0	0	1	0	0	0	1723	1580	55	2	1329	2	C13orf23	13	39587872	Missense_Mutation	SNP	T	TCGA-UB-AA0U-01A-11D-A382-10		39587872	75582006	59	49208										
DCT	1638	hgsc.bcm.edu	37	chr13	95112447	95112447	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	atcacttgagaatccagagtCccatctgctttatcaaaccc	5	13	3	2			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr13:95112447C>T	ENST00000377028.5	-	6	1490	c.1077G>A	c.(1075-1077)ggG>ggA	p.G359G	DCT_ENST00000446125.1_Silent_p.G359G|DCT_ENST00000490854.1_5'Flank	NM_001922.3	NP_001913.2	P40126	TYRP2_HUMAN	dopachrome tautomerase	359					cell development (GO:0048468)|developmental pigmentation (GO:0048066)|epidermis development (GO:0008544)|melanin biosynthetic process from tyrosine (GO:0006583)|positive regulation of neuroblast proliferation (GO:0002052)|ventricular zone neuroblast division (GO:0021847)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)	copper ion binding (GO:0005507)|dopachrome isomerase activity (GO:0004167)|oxidoreductase activity (GO:0016491)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	50	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;3.71e-42)|all_epithelial(2;3.76e-31)|all_lung(2;5.16e-14)|Lung NSC(4;1.33e-13)|Breast(118;0.0013)|Hepatocellular(115;0.00886)|Renal(2;0.00988)		COAD - Colon adenocarcinoma(199;7.07e-05)|GBM - Glioblastoma multiforme(99;0.000472)		AATCCAGAGTCCCATCTGCTT	0.413																																					p.G359G		Atlas-SNP	.											.	DCT	186	.	0			c.G1077A						.						85	80	82					13																	95112447		2203	4300	6503	SO:0001819	synonymous_variant	1638	exon6			CAGAGTCCCATCT	D17547	CCDS9470.1, CCDS45060.1	13q32	2012-09-28	2012-09-28		ENSG00000080166	ENSG00000080166	5.3.3.12		2709	protein-coding gene	gene with protein product	"dopachrome delta-isomerase"	191275	"tyrosine-related protein 2"	TYRP2		8306979	Standard	NM_001922		Approved		uc010afh.3	P40126	OTTHUMG00000017206	ENST00000377028.5:c.1077G>A	chr13.hg19:g.95112447C>T		228.0	0.0		272.0	41.0	NM_001129889	Q09GT4	Silent	SNP	ENST00000377028.5	hg19	CCDS9470.1																																																																																			.	.		0.413	DCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045461.3			T	95112447	C	T	95112447	2	4	349	1	0	0	0	0	0	0	0	1	4306	842	30	3		3	DCT	13	95112447	Silent	SNP	C	TCGA-UB-AA0U-01A-11D-A382-10	55524575	95112447	20057431	60	49209										
MCF2L	23263	hgsc.bcm.edu	37	chr13	113741578	113741578	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	ggcgacctgggcaagctgctGatgcagggctcgttcagcgt	16	11	1	1			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr13:113741578G>A	ENST00000375608.3	+	23	2551	c.2493G>A	c.(2491-2493)ctG>ctA	p.L831L	MCF2L_ENST00000375604.2_Silent_p.L858L|MCF2L_ENST00000442652.2_Silent_p.L831L|MCF2L_ENST00000535094.2_Silent_p.L801L|MCF2L_ENST00000423482.2_Silent_p.L799L|MCF2L_ENST00000434480.2_Silent_p.L807L|MCF2L_ENST00000375601.3_Silent_p.L805L|MCF2L_ENST00000375597.4_Silent_p.L799L|MCF2L_ENST00000421756.1_Silent_p.L805L|MCF2L_ENST00000397030.1_Silent_p.L834L			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	831	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular space (GO:0005615)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			kidney(1)|large_intestine(5)|ovary(1)|stomach(1)	8	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)				GCAAGCTGCTGATGCAGGGCT	0.637																																					p.L801L		Atlas-SNP	.											.	MCF2L	182	.	0			c.G2403A						.						61	55	57					13																	113741578		2203	4299	6502	SO:0001819	synonymous_variant	23263	exon22			GCTGCTGATGCAG	AB002360	CCDS9527.2, CCDS45070.1, CCDS9527.3, CCDS45070.2	13q34	2013-01-10			ENSG00000126217	ENSG00000126217		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	14576	protein-coding gene	gene with protein product		609499				9205841	Standard	NM_001112732		Approved	KIAA0362, DBS, OST, ARHGEF14	uc010tjr.2	O15068	OTTHUMG00000017377	ENST00000375608.3:c.2493G>A	chr13.hg19:g.113741578G>A		124.0	0.0		113.0	13.0	NM_001112732	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Silent	SNP	ENST00000375608.3	hg19		.	.	.	.	.	.	.	.	.	.	G	7.902	0.734581	0.15574	.	.	ENSG00000126217	ENST00000397017	.	.	.	4.34	-0.343	0.12632	.	.	.	.	.	T	0.50769	0.1635	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.38735	-0.9647	4	.	.	.	.	5.6299	0.17504	0.2053:0.6068:0.1879:0.0	.	.	.	.	N	462	.	.	D	+	1	0	MCF2L	112789579	1.000000	0.71417	0.999000	0.59377	0.773000	0.43773	1.088000	0.30877	0.044000	0.15775	-0.300000	0.09419	GAT	.	.		0.637	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4			A	113741578	G	A	113741578	2	1	349	1	0	0	0	0	0	0	0	1	9388	1277	45	3		3	MCF2L	13	113741578	Silent	SNP	G	TCGA-UB-AA0U-01A-11D-A382-10	18629131	113741578	1428300	61	49210										
TECPR2	9895	hgsc.bcm.edu	37	chr14	102881064	102881064	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	gctgctggtctctactctgcAaagaagtctgctcttttaca	8	11	4	1			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr14:102881064A>G	ENST00000359520.7	+	5	798	c.572A>G	c.(571-573)cAa>cGa	p.Q191R	TECPR2_ENST00000561228.1_3'UTR|TECPR2_ENST00000558678.1_Missense_Mutation_p.Q191R	NM_014844.3	NP_055659.2	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2	191					autophagy (GO:0006914)|cell death (GO:0008219)					breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(21)|ovary(2)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	50						TCTACTCTGCAAAGAAGTCTG	0.463																																					p.Q191R		Atlas-SNP	.											.	TECPR2	114	.	0			c.A572G						.						150	141	144					14																	102881064		2203	4300	6503	SO:0001583	missense	9895	exon5			CTCTGCAAAGAAG	AB019441	CCDS32162.1, CCDS58337.1	14q32.33	2009-02-27	2009-02-27	2009-02-27		ENSG00000196663			19957	protein-coding gene	gene with protein product		615000	"KIAA0329"	KIAA0329		9205841	Standard	NM_014844		Approved		uc001ylw.2	O15040		ENST00000359520.7:c.572A>G	chr14.hg19:g.102881064A>G	ENSP00000352510:p.Gln191Arg	105.0	0.0		116.0	38.0	NM_001172631	A5PKY3|A6NFY9|A7E2X3|H0YMM9|Q9UEG6	Missense_Mutation	SNP	ENST00000359520.7	hg19	CCDS32162.1	.	.	.	.	.	.	.	.	.	.	A	14.38	2.518822	0.44763	.	.	ENSG00000196663	ENST00000359520;ENST00000380088	T	0.01295	5.04	4.89	4.89	0.63831	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.057659	0.64402	D	0.000001	T	0.03390	0.0098	M	0.70595	2.14	0.42066	D	0.991188	B;P;P	0.48503	0.278;0.483;0.911	B;B;B	0.43680	0.057;0.065;0.427	T	0.50398	-0.8833	10	0.52906	T	0.07	.	14.5137	0.67804	1.0:0.0:0.0:0.0	.	191;191;191	B4DK51;A5PKY3;O15040	.;.;TCPR2_HUMAN	R	191	ENSP00000352510:Q191R	ENSP00000352510:Q191R	Q	+	2	0	TECPR2	101950817	1.000000	0.71417	0.030000	0.17652	0.596000	0.36781	8.847000	0.92166	1.825000	0.53177	0.459000	0.35465	CAA	.	.		0.463	TECPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415056.2	NM_014844		G	102881064	A	G	102881064	3	3	349	1	0	0	0	0	1	0	0	0	15759	130	5	2	586	2	TECPR2	14	102881064	Missense_Mutation	SNP	A	TCGA-UB-AA0U-01A-11D-A382-10		102881064	4468476	62	49211										
TMEM62	80021	hgsc.bcm.edu	37	chr15	43473452	43473452	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	tttgggatatttgttaatggAcatttcctacaaggcagcat	9	6	0	0			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr15:43473452A>G	ENST00000260403.2	+	13	1839	c.1560A>G	c.(1558-1560)ggA>ggG	p.G520G	TMEM62_ENST00000569369.1_3'UTR|RP11-473C18.3_ENST00000565685.1_RNA|EPB42_ENST00000563128.1_Intron	NM_024956.3	NP_079232.3	Q0P6H9	TMM62_HUMAN	transmembrane protein 62	520						integral component of membrane (GO:0016021)				breast(1)|cervix(1)|endometrium(3)|large_intestine(3)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	18		all_cancers(109;1.16e-10)|all_epithelial(112;2.01e-09)|Lung NSC(122;8.91e-07)|all_lung(180;8.8e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;4.23e-07)		TTGTTAATGGACATTTCCTAC	0.358																																					p.G520G		Atlas-SNP	.											.	TMEM62	47	.	0			c.A1560G						.						193	189	190					15																	43473452		2203	4299	6502	SO:0001819	synonymous_variant	80021	exon13			TAATGGACATTTC	BC009981	CCDS32210.1	15q15.2	2014-09-11			ENSG00000137842	ENSG00000137842			26269	protein-coding gene	gene with protein product							Standard	NM_024956		Approved	FLJ23375	uc001zqr.3	Q0P6H9	OTTHUMG00000176485	ENST00000260403.2:c.1560A>G	chr15.hg19:g.43473452A>G		72.0	0.0		59.0	7.0	NM_024956	Q6I9Y5|Q9H5J6	Silent	SNP	ENST00000260403.2	hg19	CCDS32210.1																																																																																			.	.		0.358	TMEM62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432227.1	NM_024956		G	43473452	A	G	43473452	2	3	349	1	0	0	0	0	0	0	0	1	16204	262	10	2		2	TMEM62	15	43473452	Silent	SNP	A	TCGA-UB-AA0U-01A-11D-A382-10		43473452	59057940	63	49212										
MNS1	55329	hgsc.bcm.edu	37	chr15	56736725	56736725	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	tgctcataagcttcctgcttTtttttttcttgttcttcaag	5	9	4	0			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr15:56736725T>C	ENST00000260453.3	-	5	767	c.603A>G	c.(601-603)aaA>aaG	p.K201K	TEX9_ENST00000352903.2_Intron|TEX9_ENST00000537232.1_Intron	NM_018365.2	NP_060835.1	Q8NEH6	MNS1_HUMAN	meiosis-specific nuclear structural 1	201	Glu-rich.				cilium organization (GO:0044782)|left/right axis specification (GO:0070986)|meiotic nuclear division (GO:0007126)	axoneme (GO:0005930)|intermediate filament (GO:0005882)|nuclear envelope (GO:0005635)|sperm flagellum (GO:0036126)	identical protein binding (GO:0042802)	p.?(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(4)|ovary(2)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	20				all cancers(107;0.0196)|GBM - Glioblastoma multiforme(80;0.101)		CTTCCTGCTTTTTTTTTTCTT	0.343																																					p.K201K		Atlas-SNP	.											.	MNS1	39	.	1	Unknown(1)	skin(1)	c.A603G						.						154	148	150					15																	56736725		2192	4292	6484	SO:0001819	synonymous_variant	55329	exon5			CTGCTTTTTTTTT	AK002084	CCDS10158.1	15q21.3	2013-01-16			ENSG00000138587	ENSG00000138587			29636	protein-coding gene	gene with protein product	"spermatogenesis associated 40"	610766				7625268, 8032679	Standard	NM_018365		Approved	FLJ11222, SPATA40	uc002adr.2	Q8NEH6	OTTHUMG00000132034	ENST00000260453.3:c.603A>G	chr15.hg19:g.56736725T>C		52.0	0.0		46.0	6.0	NM_018365	Q8IYT6|Q9NUP4	Silent	SNP	ENST00000260453.3	hg19	CCDS10158.1																																																																																			.	.		0.343	MNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255047.2	NM_018365		C	56736725	T	C	56736725	2	2	349	1	0	0	0	0	0	0	0	1	9686	1838	64	2		2	MNS1	15	56736725	Silent	SNP	T	TCGA-UB-AA0U-01A-11D-A382-10	13263273	56736725	45794667	64	49213										
DPP8	54878	hgsc.bcm.edu	37	chr15	65799617	65799617	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	agaggcttccaagagagcatTaagactgctgctctattgat	10	8	1	4	rs377607090		TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr15:65799617T>C	ENST00000341861.5	-	3	1964	c.384A>G	c.(382-384)ttA>ttG	p.L128L	DPP8_ENST00000339244.5_Silent_p.L128L|DPP8_ENST00000358939.4_Silent_p.L112L|DPP8_ENST00000321118.7_Silent_p.L128L|DPP8_ENST00000559233.1_Silent_p.L128L|DPP8_ENST00000321147.6_Silent_p.L128L|DPP8_ENST00000300141.6_Silent_p.L112L	NM_197960.2	NP_932064.1	Q6V1X1	DPP8_HUMAN	dipeptidyl-peptidase 8	128					immune response (GO:0006955)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(2)|endometrium(3)|large_intestine(11)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						AAGAGAGCATTAAGACTGCTG	0.338																																					p.L128L		Atlas-SNP	.											.	DPP8	78	.	0			c.A384G						.						107	106	107					15																	65799617		2201	4299	6500	SO:0001819	synonymous_variant	54878	exon4			GAGCATTAAGACT	AF221634	CCDS10207.1, CCDS10208.1, CCDS10209.1, CCDS10210.1	15q22	2008-07-18	2006-01-12		ENSG00000074603	ENSG00000074603			16490	protein-coding gene	gene with protein product	"dipeptidyl peptidase VIII", "dipeptidyl peptidase IV-related protein-1", "prolyl dipeptidase DPP8"	606819	"dipeptidylpeptidase 8"			11012666	Standard	XM_005254500		Approved	DP8, DPRP1, MSTP141, FLJ14920, FLJ20283, MGC26191	uc002aox.3	Q6V1X1	OTTHUMG00000133150	ENST00000341861.5:c.384A>G	chr15.hg19:g.65799617T>C		76.0	0.0		89.0	12.0	NM_197960	Q7Z4C8|Q7Z4D3|Q7Z4E1|Q8IWG7|Q8NEM5|Q96JX1|Q9HBM2|Q9HBM3|Q9HBM4|Q9HBM5|Q9NXF4	Silent	SNP	ENST00000341861.5	hg19	CCDS10207.1																																																																																			.	.		0.338	DPP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256847.1	NM_017743		C	65799617	T	C	65799617	2	2	349	1	0	0	0	0	0	0	0	1	4734	1751	61	2		2	DPP8	15	65799617	Silent	SNP	T	TCGA-UB-AA0U-01A-11D-A382-10	9062892	65799617	36731775	65	49214										
SMG1	23049	hgsc.bcm.edu	37	chr16	18937327	18937327	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	ggtgccgccgccgccgccgcCgctgctcagccgagaccccg	14	21	1	1			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr16:18937327C>T	ENST00000446231.2	-	1	449	c.37G>A	c.(37-39)Ggc>Agc	p.G13S	CTD-2288F12.1_ENST00000565782.1_RNA|SMG1_ENST00000567737.1_5'UTR|SMG1_ENST00000389467.3_Missense_Mutation_p.G13S			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	13	Interaction with SMG8 and SMG9.				DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						ccgccgccgccgctgcTCAGC	0.736																																					p.G13S		Atlas-SNP	.											.	SMG1	401	.	0			c.G37A						.						2	3	3					16																	18937327		1046	2801	3847	SO:0001583	missense	23049	exon1			CGCCGCCGCTGCT	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase-related kinase"	607032	"smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.37G>A	chr16.hg19:g.18937327C>T	ENSP00000402515:p.Gly13Ser	88.0	0.0		86.0	5.0	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	ENST00000446231.2	hg19	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	c	16.19	3.051895	0.55218	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	T;T	0.01240	5.12;5.12	4.27	3.31	0.37934	.	0.832224	0.10596	N	0.656220	T	0.00998	0.0033	N	0.14661	0.345	0.31512	N	0.663496	B	0.22346	0.068	B	0.08055	0.003	T	0.29912	-0.9996	10	0.12766	T	0.61	.	6.0417	0.19738	0.0:0.7231:0.0:0.2769	.	13	Q96Q15	SMG1_HUMAN	S	13	ENSP00000402515:G13S;ENSP00000374118:G13S	ENSP00000374118:G13S	G	-	1	0	SMG1	18844828	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.149000	0.42244	0.999000	0.39023	0.455000	0.32223	GGC	.	.		0.736	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		T	18937327	C	T	18937327	3	4	349	1	0	0	0	0	1	0	0	0	14810	652	23	1	11200	1	SMG1	16	18937327	Missense_Mutation	SNP	C	TCGA-UB-AA0U-01A-11D-A382-10		18937327	71417426	66	49215										
TRIM72	260434	hgsc.bcm.edu	37	chr16	31226434	31226434	+	IGR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	ctcctgcctgccgccgaggcCcacgcacgcctcaaggtgcg	12	19	1	0	rs553041719		TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr16:31226434C>T	ENST00000302964.3	-	0	813				TRIM72_ENST00000322122.3_Silent_p.A125A|PYDC1_ENST00000568383.1_5'Flank	NM_152901.2	NP_690865.1	Q8WXC3	PYDC1_HUMAN	PYD (pyrin domain) containing 1						innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of interleukin-1 beta secretion (GO:0050718)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(2)|lung(1)	5						CCGCCGAGGCCCACGCACGCC	0.697													C|||	1	0.000199681	0	0.0014	5008	,	,		13533	0		0	False		,,,				2504	0				p.A125A		Atlas-SNP	.											.	TRIM72	32	.	0			c.C375T						.						9	9	9					16																	31226434		1796	3450	5246	SO:0001628	intergenic_variant	493829	exon2			CGAGGCCCACGCA		CCDS10710.1	16p11.2	2008-02-05	2005-12-02		ENSG00000169900	ENSG00000169900			30261	protein-coding gene	gene with protein product		615700	"pyrin domain containing 1"			11786556, 16905547	Standard	NM_152901		Approved	ASC2, POP1	uc002ebo.3	Q8WXC3	OTTHUMG00000132407		chr16.hg19:g.31226434C>T		20.0	0.0		25.0	8.0	NM_001008274	B2R8L4|Q8NFP8	Silent	SNP	ENST00000302964.3	hg19	CCDS10710.1																																																																																			.	.		0.697	PYDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255543.2	NM_152901		T	31226434	C	T	31226434	1	4	349	0	1	0	0	0	0	0	0	0	16560	610	22	3		3	TRIM72	16	31226434	IGR	SNP	C	TCGA-UB-AA0U-01A-11D-A382-10	12289107	31226434	59128319	67	49216										
RBL2	5934	hgsc.bcm.edu	37	chr16	53499478	53499479	+	Frame_Shift_Ins	INS	-	-	A													0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	ctccactctgggaaaaaattINSagagacaatgaaaacagagt							TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr16:53499478_53499479insA	ENST00000262133.6	+	13	1964_1965	c.1827_1828insA	c.(1828-1830)agafs	p.R610fs	RBL2_ENST00000544545.1_Frame_Shift_Ins_p.R394fs|RBL2_ENST00000379935.4_3'UTR	NM_005611.3	NP_005602.3	Q08999	RBL2_HUMAN	retinoblastoma-like 2	610	Domain A.|Pocket; binds E1A.				chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						GGGAAAAAATTAGAGACAATGA	0.332																																					p.I609fs		Atlas-INDEL	.											.	RBL2	115	.	0			c.1827_1828insA						.																																			SO:0001589	frameshift_variant	5934	exon13			.	X74594	CCDS10748.1	16q12.2	2014-03-11	2014-03-11		ENSG00000103479	ENSG00000103479			9894	protein-coding gene	gene with protein product		180203				8361765, 8643454	Standard	NM_005611		Approved	Rb2, p130	uc002ehi.4	Q08999	OTTHUMG00000133198	ENST00000262133.6:c.1828dupA	chr16.hg19:g.53499479_53499479dupA	ENSP00000262133:p.Arg610fs	189.0	0.0		178.0	96.0	NM_005611	B7Z913|Q15073|Q16084|Q8NE70|Q92812	Frame_Shift_Ins	INS	ENST00000262133.6	hg19	CCDS10748.1																																																																																			.	.		0.332	RBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256908.3	NM_005611		A	53499479	-	A	53499478	7	5	349	1	0	1	1	0	0	0	0	0	13125	1742	61	0	1877	0	RBL2	16	53499478	Frame_Shift_Ins	INS	-	TCGA-UB-AA0U-01A-11D-A382-10	22273044	53499478	36855275	68	49217										
KIAA0182	23199	hgsc.bcm.edu	37	chr16	85690011	85690011	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	gcgcgagcgcgagcgtgagcGtgaggctgaccgcgagcggg	21	11	0	3	rs374600357		TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr16:85690011G>A	ENST00000253458.7	+	7	1228	c.1052G>A	c.(1051-1053)cGt>cAt	p.R351H	GSE1_ENST00000405402.2_Missense_Mutation_p.R247H|RN7SL381P_ENST00000577658.1_RNA|GSE1_ENST00000393243.1_Missense_Mutation_p.R278H	NM_014615.2	NP_055430.1	Q14687	GSE1_HUMAN	Gse1 coiled-coil protein	351																	gagcgtgagcgtgaggctgac	0.667																																					p.R351H		Atlas-SNP	.											.	.	.	.	0			c.G1052A						.	-	HIS/ARG,HIS/ARG	0,4276		0,0,2138	12	13	13		740,1052	4.6	1	16		13	4,8348		0,4,4172	no	missense,missense	KIAA0182	NM_001134473.1,NM_014615.2	29,29	0,4,6310	AA,AG,GG		0.0479,0.0,0.0317	probably-damaging,probably-damaging	247/1114,351/1218	85690011	4,12624	2138	4176	6314	SO:0001583	missense	23199	exon7			GTGAGCGTGAGGC	D80004	CCDS10952.1, CCDS45539.1, CCDS62007.1	16q24.1	2012-12-07	2012-12-07	2012-10-02	ENSG00000131149	ENSG00000131149			28979	protein-coding gene	gene with protein product	"genetic suppressor element 1"		"KIAA0182", "Gse1 coiled-coil protein homolog (mouse)"	KIAA0182		8724849, 8786132	Standard	NM_014615		Approved		uc002fix.4	Q14687	OTTHUMG00000137650	ENST00000253458.7:c.1052G>A	chr16.hg19:g.85690011G>A	ENSP00000253458:p.Arg351His	196.0	0.0		143.0	27.0	NM_014615	D3DUM4|Q8IY61|Q96GA4|Q9BW09	Missense_Mutation	SNP	ENST00000253458.7	hg19	CCDS10952.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	18.37|18.37	3.610108|3.610108	0.66558|0.66558	0.0|0.0	4.79E-4|4.79E-4	ENSG00000131149|ENSG00000131149	ENST00000405402;ENST00000253458;ENST00000393243|ENST00000412692	D;T;D|.	0.81579|.	-1.51;-0.04;-1.51|.	4.6|4.6	4.6|4.6	0.57074|0.57074	.|.	0.279493|.	0.35262|.	N|.	0.003324|.	T|T	0.69895|0.69895	0.3162|0.3162	L|L	0.60067|0.60067	1.865|1.865	0.48087|0.48087	D|D	0.999583|0.999583	D;D|.	0.89917|.	1.0;0.999|.	D;P|.	0.74023|.	0.982;0.902|.	T|T	0.69213|0.69213	-0.5204|-0.5204	10|5	0.52906|.	T|.	0.07|.	-17.7057|-17.7057	15.5565|15.5565	0.76200|0.76200	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	278;351|.	Q14687-3;Q14687|.	.;GSE1_HUMAN|.	H|M	247;351;278|158	ENSP00000384839:R247H;ENSP00000253458:R351H;ENSP00000376934:R278H|.	ENSP00000253458:R351H|.	R|V	+|+	2|1	0|0	KIAA0182|KIAA0182	84247512|84247512	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.778000|0.778000	0.44026|0.44026	8.163000|8.163000	0.89659|0.89659	2.271000|2.271000	0.75665|0.75665	0.556000|0.556000	0.70494|0.70494	CGT|GTG	.	.		0.667	GSE1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325527.1	NM_014615		A	85690011	G	A	85690011	3	1	349	1	0	0	0	0	1	0	0	0	8168	1145	40	1	1078	1	KIAA0182	16	85690011	Missense_Mutation	SNP	G	TCGA-UB-AA0U-01A-11D-A382-10	32190533	85690011	4664742	69	49218										
SCARF1	8578	hgsc.bcm.edu	37	chr17	1543920	1543920	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	gcaggactcacagctgcctgTgtctggagagcacggctcat	13	12	3	1			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr17:1543920T>C	ENST00000263071.4	-	5	881	c.832A>G	c.(832-834)Aca>Gca	p.T278A	SCARF1_ENST00000574545.1_5'UTR|SCARF1_ENST00000571272.1_Missense_Mutation_p.T278A|SCARF1_ENST00000348987.3_Missense_Mutation_p.T278A	NM_003693.2|NM_145350.1	NP_003684.2|NP_663325.1	Q14162	SREC_HUMAN	scavenger receptor class F, member 1	278					cell adhesion (GO:0007155)|cholesterol catabolic process (GO:0006707)|dendrite development (GO:0016358)|neuron remodeling (GO:0016322)|positive regulation of axon regeneration (GO:0048680)|positive regulation of neuron projection development (GO:0010976)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	endocytic vesicle membrane (GO:0030666)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	low-density lipoprotein particle binding (GO:0030169)|scavenger receptor activity (GO:0005044)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(3)|kidney(2)|lung(9)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		CAGCTGCCTGTGTCTGGAGAG	0.657																																					p.T278A		Atlas-SNP	.											.	SCARF1	46	.	0			c.A832G						.						31	26	28					17																	1543920		2201	4300	6501	SO:0001583	missense	8578	exon5			TGCCTGTGTCTGG	D63483	CCDS11007.1, CCDS45564.1	17p13.3	2008-07-18			ENSG00000074660	ENSG00000074660			16820	protein-coding gene	gene with protein product	"scavenger receptor expressed by endothelial cells", "acetyl LDL receptor"	607873				9395444, 8590280	Standard	NM_003693		Approved	SREC, KIAA0149	uc002fsz.2	Q14162	OTTHUMG00000090555	ENST00000263071.4:c.832A>G	chr17.hg19:g.1543920T>C	ENSP00000263071:p.Thr278Ala	204.0	0.0		131.0	57.0	NM_145350	A8MQ05|O43701|Q8NHD2|Q8NHD3|Q8NHD4|Q8NHD5	Missense_Mutation	SNP	ENST00000263071.4	hg19	CCDS11007.1	.	.	.	.	.	.	.	.	.	.	T	14.03	2.412905	0.42817	.	.	ENSG00000074660	ENST00000263071;ENST00000348987;ENST00000434376	T;T;T	0.32988	1.43;1.43;1.43	5.24	5.24	0.73138	Growth factor, receptor (1);	0.000000	0.47852	D	0.000201	T	0.46464	0.1394	M	0.75884	2.315	0.43467	D	0.995672	D;P;P	0.53745	0.962;0.86;0.938	P;B;P	0.61003	0.578;0.4;0.882	T	0.49466	-0.8937	10	0.48119	T	0.1	-10.1822	5.176	0.15135	0.0:0.2118:0.0:0.7882	.	278;278;278	Q14162-2;Q14162;Q14162-3	.;SREC_HUMAN;.	A	278	ENSP00000263071:T278A;ENSP00000323964:T278A;ENSP00000411167:T278A	ENSP00000263071:T278A	T	-	1	0	SCARF1	1490670	1.000000	0.71417	1.000000	0.80357	0.497000	0.33675	4.539000	0.60657	2.199000	0.70637	0.533000	0.62120	ACA	.	.		0.657	SCARF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207081.4	NM_003693		C	1543920	T	C	1543920	3	2	349	1	0	0	0	0	1	0	0	0	13898	1696	59	2	1688	2	SCARF1	17	1543920	Missense_Mutation	SNP	T	TCGA-UB-AA0U-01A-11D-A382-10		1543920	79651290	70	49219										
KRTAP4-1	85285	hgsc.bcm.edu	37	chr17	39340971	39340971	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	agtctgagagcaggatgggcGgcagcagctggatacaacac	15	9	1	1	rs375189286	byFrequency	TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr17:39340971G>T	ENST00000398472.1	-	1	623	c.136C>A	c.(136-138)Cgc>Agc	p.R46S				Q9BYQ7	KRA41_HUMAN	keratin associated protein 4-1	46	18 X 5 AA repeats of C-C-[GRQC]-[SPT]- [VSTL].					keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	5		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			CAGGATGGGCGGCAGCAGCTG	0.647																																					p.R46S		Atlas-SNP	.											.	KRTAP4-1	58	.	0			c.C136A						.						28	32	31					17																	39340971		2174	4287	6461	SO:0001583	missense	85285	exon1			ATGGGCGGCAGCA	AC006070		17q21.2	2013-06-25			ENSG00000198443	ENSG00000198443		"Keratin associated proteins"	18907	protein-coding gene	gene with protein product			"keratin associated protein 4-10"	KRTAP4-10		11279113	Standard	NM_033060		Approved	KAP4.1, KAP4.10	uc002hwe.4	Q9BYQ7	OTTHUMG00000132081	ENST00000398472.1:c.136C>A	chr17.hg19:g.39340971G>T	ENSP00000381489:p.Arg46Ser	114.0	0.0		124.0	38.0	NM_033060	A8MWS7|Q3SYF2	Missense_Mutation	SNP	ENST00000398472.1	hg19		.	.	.	.	.	.	.	.	.	.	G	11.91	1.781048	0.31502	.	.	ENSG00000244537;ENSG00000198443;ENSG00000198443	ENST00000458321;ENST00000398472;ENST00000334190	T	0.01455	4.87	4.81	3.8	0.43715	.	.	.	.	.	T	0.04137	0.0115	.	.	.	0.24121	N	0.995808	P	0.39665	0.682	P	0.47981	0.563	T	0.36089	-0.9762	8	0.39692	T	0.17	.	12.5323	0.56122	0.0:0.1696:0.8304:0.0	.	46	Q9BYQ7	KRA41_HUMAN	S	42;46;46	ENSP00000381489:R46S	ENSP00000335483:R46S	R	-	1	0	KRTAP4-2;KRTAP4-1	36594497	0.000000	0.05858	0.052000	0.19188	0.006000	0.05464	-0.517000	0.06275	0.927000	0.37143	0.655000	0.94253	CGC	.	.		0.647	KRTAP4-1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255108.1	NM_033060		T	39340971	G	T	39340971	3	4	349	1	0	0	0	0	1	0	0	0	8557	1116	39	1	255	1	KRTAP4-1	17	39340971	Missense_Mutation	SNP	G	TCGA-UB-AA0U-01A-11D-A382-10	37797051	39340971	41854239	71	49220										
ACLY	47	hgsc.bcm.edu	37	chr17	40030078	40030078	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	gctcaccttttctggaaccaGaggaggccgaggaccccgcc	12	15	2	1			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr17:40030078G>A	ENST00000352035.2	-	23	2758	c.2628C>T	c.(2626-2628)ctC>ctT	p.L876L	ACLY_ENST00000537919.1_Silent_p.L605L|ACLY_ENST00000393896.2_Silent_p.L866L|ACLY_ENST00000590151.1_Silent_p.L876L|ACLY_ENST00000353196.1_Silent_p.L866L	NM_001096.2	NP_001087.2	P53396	ACLY_HUMAN	ATP citrate lyase	876					ATP catabolic process (GO:0006200)|cellular carbohydrate metabolic process (GO:0044262)|cellular lipid metabolic process (GO:0044255)|citrate metabolic process (GO:0006101)|coenzyme A metabolic process (GO:0015936)|energy reserve metabolic process (GO:0006112)|lipid biosynthetic process (GO:0008610)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	citrate lyase complex (GO:0009346)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP citrate synthase activity (GO:0003878)|cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)		NTN1/ACLY(2)	breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(4)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	28		Breast(137;0.000143)				TCTGGAACCAGAGGAGGCCGA	0.577																																					p.L876L	Colon(64;807 1396 15971 30971)	Atlas-SNP	.											.	ACLY	85	.	0			c.C2628T						.						68	72	71					17																	40030078		2203	4300	6503	SO:0001819	synonymous_variant	47	exon23			GAACCAGAGGAGG	X64330	CCDS11412.1, CCDS11413.1	17q21.2	2010-04-27			ENSG00000131473	ENSG00000131473	2.3.3.8		115	protein-coding gene	gene with protein product	"ATP citrate synthase"	108728				1371749, 8088842	Standard	NM_001096		Approved	ATPCL, CLATP, ACL	uc002hyg.3	P53396	OTTHUMG00000133507	ENST00000352035.2:c.2628C>T	chr17.hg19:g.40030078G>A		44.0	0.0		51.0	9.0	NM_001096	B4DIM0|B4E3P0|Q13037|Q9BRL0	Silent	SNP	ENST00000352035.2	hg19	CCDS11412.1																																																																																			.	.		0.577	ACLY-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257465.1	NM_001096		A	40030078	G	A	40030078	2	1	349	1	0	0	0	0	0	0	0	1	143	929	33	3		3	ACLY	17	40030078	Silent	SNP	G	TCGA-UB-AA0U-01A-11D-A382-10	689107	40030078	41165132	72	49221										
MYST2	11143	hgsc.bcm.edu	37	chr17	47875714	47875714	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	agctgatcatgatgagtcacCgcctcgaactccaactggaa	9	12	2	3			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr17:47875714C>T	ENST00000259021.4	+	4	654	c.374C>T	c.(373-375)cCg>cTg	p.P125L	KAT7_ENST00000509773.1_Intron|KAT7_ENST00000510819.1_Intron|KAT7_ENST00000454930.2_Intron|KAT7_ENST00000424009.2_Missense_Mutation_p.P125L|KAT7_ENST00000503935.2_5'UTR|KAT7_ENST00000435742.2_5'UTR	NM_007067.4	NP_008998.1	O95251	KAT7_HUMAN	K(lysine) acetyltransferase 7	125					chromatin organization (GO:0006325)|DNA replication (GO:0006260)|histone H3 acetylation (GO:0043966)|histone H4-K12 acetylation (GO:0043983)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										GATGAGTCACCGCCTCGAACT	0.418																																					p.P125L		Atlas-SNP	.											.	.	.	.	0			c.C374T						.						82	73	76					17																	47875714		2203	4300	6503	SO:0001583	missense	11143	exon4			AGTCACCGCCTCG	AF074606	CCDS11554.1, CCDS56035.1, CCDS56036.1, CCDS56037.1, CCDS56038.1	17q21.32	2013-01-10	2011-07-21	2011-07-21	ENSG00000136504	ENSG00000136504	2.3.1.48	"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing"	17016	protein-coding gene	gene with protein product	"histone acetyltransferase binding to ORC1"	609880	"MYST histone acetyltransferase 2"	MYST2		10438470, 10930412	Standard	NM_001199155		Approved	HBOA, HBO1, ZC2HC7	uc002ipm.3	O95251	OTTHUMG00000161770	ENST00000259021.4:c.374C>T	chr17.hg19:g.47875714C>T	ENSP00000259021:p.Pro125Leu	80.0	0.0		111.0	5.0	NM_007067	B3KN74|B4DF85|B4DFB4|B4DFE0|B4DGY4|E7ER15|G5E9K7	Missense_Mutation	SNP	ENST00000259021.4	hg19	CCDS11554.1	.	.	.	.	.	.	.	.	.	.	C	36	5.681181	0.96774	.	.	ENSG00000136504	ENST00000259021;ENST00000424009	.	.	.	6.14	6.14	0.99180	.	0.000000	0.85682	D	0.000000	T	0.77177	0.4092	L	0.53249	1.67	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	T	0.72443	-0.4292	9	0.39692	T	0.17	-13.3576	20.4548	0.99139	0.0:1.0:0.0:0.0	.	125;125	O95251;G5E9K7	KAT7_HUMAN;.	L	125	.	ENSP00000259021:P125L	P	+	2	0	KAT7	45230713	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.796000	0.85898	2.937000	0.99478	0.650000	0.86243	CCG	.	.		0.418	KAT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366032.1	NM_007067		T	47875714	C	T	47875714	3	4	349	1	0	0	0	0	1	0	0	0	10112	652	23	1	388	1	MYST2	17	47875714	Missense_Mutation	SNP	C	TCGA-UB-AA0U-01A-11D-A382-10	7845636	47875714	33319496	73	49222										
C17orf64	124773	hgsc.bcm.edu	37	chr17	58506757	58506757	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	ctcggatgcgccggagaggtCcttgctggccgaccgggaag	17	12	0	1			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr17:58506757C>A	ENST00000269127.4	+	5	548	c.464C>A	c.(463-465)tCc>tAc	p.S155Y		NM_181707.2	NP_859058.2	Q86WR6	CQ064_HUMAN	chromosome 17 open reading frame 64	155								p.S45Y(1)		breast(2)|large_intestine(1)|lung(3)	6	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;5.81e-13)|all cancers(12;2.17e-11)|Colorectal(3;0.01)			CCGGAGAGGTCCTTGCTGGCC	0.602																																					p.S155Y		Atlas-SNP	.											C17orf64,NS,carcinoma,0,1	C17orf64	19	.	1	Substitution - Missense(1)	lung(1)	c.C464A						.						39	40	40					17																	58506757		2203	4300	6503	SO:0001583	missense	124773	exon5			AGAGGTCCTTGCT	BC048806	CCDS32698.2	17q23.2	2005-12-16			ENSG00000141371	ENSG00000141371			26990	protein-coding gene	gene with protein product						12477932	Standard	NM_181707		Approved		uc002iyq.3	Q86WR6	OTTHUMG00000157171	ENST00000269127.4:c.464C>A	chr17.hg19:g.58506757C>A	ENSP00000269127:p.Ser155Tyr	139.0	1.0		171.0	53.0	NM_181707	Q8IY87	Missense_Mutation	SNP	ENST00000269127.4	hg19	CCDS32698.2	.	.	.	.	.	.	.	.	.	.	C	11.67	1.709148	0.30322	.	.	ENSG00000141371	ENST00000269127	.	.	.	4.3	1.07	0.20283	.	0.717069	0.12126	N	0.497239	T	0.39989	0.1099	M	0.65975	2.015	0.09310	N	1	P	0.34462	0.454	B	0.37833	0.259	T	0.41520	-0.9504	9	0.87932	D	0	-5.0308	4.6136	0.12415	0.0:0.6097:0.1825:0.2078	.	155	Q86WR6	CQ064_HUMAN	Y	155	.	ENSP00000269127:S155Y	S	+	2	0	C17orf64	55861539	0.000000	0.05858	0.006000	0.13384	0.004000	0.04260	0.335000	0.19806	0.436000	0.26393	0.561000	0.74099	TCC	.	.		0.602	C17orf64-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000347743.1	NM_181707		A	58506757	C	A	58506757	3	1	349	1	0	0	0	0	1	0	0	0	1874	855	30	3	482	3	C17orf64	17	58506757	Missense_Mutation	SNP	C	TCGA-UB-AA0U-01A-11D-A382-10	10631043	58506757	22688453	74	49223										
GAA	2548	hgsc.bcm.edu	37	chr17	78092487	78092487	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	gagctggtacgtgtgaccagTgagggagctggcctgcagct	17	9	0	2			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr17:78092487T>C	ENST00000302262.3	+	19	2901	c.2682T>C	c.(2680-2682)agT>agC	p.S894S	GAA_ENST00000390015.3_Silent_p.S894S	NM_000152.3	NP_000143.2	P10253	LYAG_HUMAN	glucosidase, alpha; acid	894					cardiac muscle contraction (GO:0060048)|diaphragm contraction (GO:0002086)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|heart morphogenesis (GO:0003007)|locomotory behavior (GO:0007626)|lysosome organization (GO:0007040)|maltose metabolic process (GO:0000023)|muscle cell cellular homeostasis (GO:0046716)|neuromuscular process controlling balance (GO:0050885)|neuromuscular process controlling posture (GO:0050884)|regulation of the force of heart contraction (GO:0002026)|sucrose metabolic process (GO:0005985)|tissue development (GO:0009888)|vacuolar sequestering (GO:0043181)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|maltose alpha-glucosidase activity (GO:0032450)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|lung(6)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	21	all_neural(118;0.117)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.139)		Acarbose(DB00284)|Miglitol(DB00491)	GTGTGACCAGTGAGGGAGCTG	0.607																																					p.S894S		Atlas-SNP	.											.	GAA	66	.	0			c.T2682C						.						155	144	147					17																	78092487		2203	4300	6503	SO:0001819	synonymous_variant	2548	exon20			GACCAGTGAGGGA		CCDS32760.1	17q25.2-q25.3	2014-09-17	2008-08-01				3.2.1.20		4065	protein-coding gene	gene with protein product	"Pompe disease", "glycogen storage disease type II"	606800					Standard	NM_000152		Approved		uc002jxq.3	P10253		ENST00000302262.3:c.2682T>C	chr17.hg19:g.78092487T>C		60.0	0.0		56.0	11.0	NM_001079803	Q09GN4|Q14351|Q16302|Q8IWE7	Silent	SNP	ENST00000302262.3	hg19	CCDS32760.1																																																																																			.	.		0.607	GAA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437441.1			C	78092487	T	C	78092487	2	2	349	1	0	0	0	0	0	0	0	1	6155	1693	59	2		2	GAA	17	78092487	Silent	SNP	T	TCGA-UB-AA0U-01A-11D-A382-10	19585730	78092487	3102723	75	49224										
FBXO15	201456	hgsc.bcm.edu	37	chr18	71791775	71791775	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	caaggtgatgaaaatgaagaTttgccataacaaaagccagt	9	6	0	4			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr18:71791775T>C	ENST00000419743.2	-	7	1023	c.944A>G	c.(943-945)aAt>aGt	p.N315S	FBXO15_ENST00000269500.5_Missense_Mutation_p.N239S	NM_001142958.1	NP_001136430.1	Q8NCQ5	FBX15_HUMAN	F-box protein 15	315						SCF ubiquitin ligase complex (GO:0019005)				autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)	27		Esophageal squamous(42;0.103)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.143)		AAAATGAAGATTTGCCATAAC	0.333																																					p.N315S		Atlas-SNP	.											.	FBXO15	97	.	0			c.A944G						.						165	160	162					18																	71791775		2203	4300	6503	SO:0001583	missense	201456	exon7			TGAAGATTTGCCA	AK094215	CCDS45884.1	18q22.3	2006-03-09	2004-06-15		ENSG00000141665	ENSG00000141665		"F-boxes /  "other""	13617	protein-coding gene	gene with protein product		609093	"F-box only protein 15"			12665572	Standard	NM_152676		Approved	MGC39671, FBX15	uc002llf.2	Q8NCQ5	OTTHUMG00000132842	ENST00000419743.2:c.944A>G	chr18.hg19:g.71791775T>C	ENSP00000393154:p.Asn315Ser	157.0	0.0		116.0	48.0	NM_001142958	B3KST3	Missense_Mutation	SNP	ENST00000419743.2	hg19	CCDS45884.1	.	.	.	.	.	.	.	.	.	.	T	11.13	1.546799	0.27652	.	.	ENSG00000141665	ENST00000269500;ENST00000419743	T;T	0.47177	0.88;0.85	5.31	2.88	0.33553	.	0.256263	0.43747	N	0.000525	T	0.29389	0.0732	L	0.44542	1.39	0.28125	N	0.930441	P;P	0.38020	0.473;0.615	B;B	0.29267	0.056;0.1	T	0.14227	-1.0480	10	0.20519	T	0.43	-17.1188	5.7565	0.18176	0.0:0.0865:0.3281:0.5854	.	315;239	B3KST3;Q8NCQ5	.;FBX15_HUMAN	S	239;315	ENSP00000269500:N239S;ENSP00000393154:N315S	ENSP00000269500:N239S	N	-	2	0	FBXO15	69942755	0.995000	0.38212	0.999000	0.59377	0.993000	0.82548	0.447000	0.21710	0.320000	0.23234	0.460000	0.39030	AAT	.	.		0.333	FBXO15-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000444223.1	NM_152676		C	71791775	T	C	71791775	3	2	349	1	0	0	0	0	1	0	0	0	5736	1493	52	2	604	2	FBXO15	18	71791775	Missense_Mutation	SNP	T	TCGA-UB-AA0U-01A-11D-A382-10		71791775	6285473	76	49225										
RDH8	50700	hgsc.bcm.edu	37	chr19	10129559	10129559	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	ggcggcagggccacatcgtgGtgatcagcagtgtcatgggc	17	10	2	1			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr19:10129559G>A	ENST00000171214.1	+	3	664	c.415G>A	c.(415-417)Gtg>Atg	p.V139M	RDH8_ENST00000591589.1_Missense_Mutation_p.V159M	NM_015725.2	NP_056540.2	Q9NYR8	RDH8_HUMAN	retinol dehydrogenase 8 (all-trans)	139					estrogen biosynthetic process (GO:0006703)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|steroid biosynthetic process (GO:0006694)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|NADP-retinol dehydrogenase activity (GO:0052650)|retinol dehydrogenase activity (GO:0004745)			endometrium(3)|large_intestine(3)|lung(10)|ovary(3)|pancreas(1)|prostate(1)	21			Epithelial(33;4.24e-05)		Vitamin A(DB00162)	CCACATCGTGGTGATCAGCAG	0.577																																					p.V159M		Atlas-SNP	.											.	RDH8	51	.	0			c.G475A						.						77	75	75					19																	10129559		2203	4300	6503	SO:0001583	missense	50700	exon3			ATCGTGGTGATCA	AF229845	CCDS12223.1, CCDS12223.2	19p13.2	2011-09-14				ENSG00000080511	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	14423	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 28C, member 2"	608575				10753906, 19027726	Standard	NM_015725		Approved	PRRDH, SDR28C2	uc002mmr.4	Q9NYR8		ENST00000171214.1:c.415G>A	chr19.hg19:g.10129559G>A	ENSP00000171214:p.Val139Met	93.0	0.0		88.0	34.0	NM_015725	Q9H838	Missense_Mutation	SNP	ENST00000171214.1	hg19		.	.	.	.	.	.	.	.	.	.	G	23.4	4.414753	0.83449	.	.	ENSG00000080511	ENST00000171214	D	0.93307	-3.2	5.34	5.34	0.76211	NAD(P)-binding domain (1);	0.062472	0.64402	D	0.000006	D	0.93423	0.7902	N	0.17082	0.46	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	D	0.94101	0.7362	10	0.49607	T	0.09	.	16.5222	0.84320	0.0:0.0:1.0:0.0	.	139	Q9NYR8	RDH8_HUMAN	M	139	ENSP00000171214:V139M	ENSP00000171214:V139M	V	+	1	0	RDH8	9990559	1.000000	0.71417	1.000000	0.80357	0.732000	0.41865	7.596000	0.82721	2.492000	0.84095	0.491000	0.48974	GTG	.	.		0.577	RDH8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				A	10129559	G	A	10129559	3	1	349	1	0	0	0	0	1	0	0	0	13211	1261	44	3	425	3	RDH8	19	10129559	Missense_Mutation	SNP	G	TCGA-UB-AA0U-01A-11D-A382-10		10129559	48999424	77	49226										
SMARCA4	6597	hgsc.bcm.edu	37	chr19	11138584	11138584	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	ccctcatgaccatcatggaaGattactttgcgtatcgcggc	9	12	2	2			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr19:11138584G>A	ENST00000429416.3	+	25	3621	c.3340G>A	c.(3340-3342)Gat>Aat	p.D1114N	SMARCA4_ENST00000450717.3_Missense_Mutation_p.D1114N|SMARCA4_ENST00000358026.2_Missense_Mutation_p.D1114N|SMARCA4_ENST00000541122.2_Missense_Mutation_p.D1114N|SMARCA4_ENST00000444061.3_Missense_Mutation_p.D1114N|SMARCA4_ENST00000590574.1_Missense_Mutation_p.D1114N|SMARCA4_ENST00000589677.1_Missense_Mutation_p.D1114N|SMARCA4_ENST00000413806.3_Missense_Mutation_p.D1114N|SMARCA4_ENST00000344626.4_Missense_Mutation_p.D1114N	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	1114	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(2)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				CATCATGGAAGATTACTTTGC	0.458			"F, N, Mis"		NSCLC																																p.D1114N		Atlas-SNP	.		Rec	yes		19	19p13.2	6597	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"		E	.	SMARCA4	502	.	2	Unknown(2)	lung(2)	c.G3340A						.						180	175	177					19																	11138584		2203	4300	6503	SO:0001583	missense	6597	exon24			ATGGAAGATTACT	D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"SNF2-like 4", "global transcription activator homologous sequence", "sucrose nonfermenting-like 4", "mitotic growth and transcription activator", "BRM/SWI2-related gene 1", "homeotic gene regulator", "nuclear protein GRB1", "brahma protein-like 1", "ATP-dependent helicase SMARCA4"	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.3340G>A	chr19.hg19:g.11138584G>A	ENSP00000395654:p.Asp1114Asn	115.0	0.0		131.0	24.0	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	hg19	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	G	35	5.426567	0.96131	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	T;T;T;T;T;T;T	0.75938	-0.98;-0.98;-0.98;-0.98;-0.98;-0.98;-0.98	5.04	5.04	0.67666	Helicase, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.87297	0.6142	M	0.83312	2.635	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;0.999;1.0;1.0	D;D;D;D;D;D;D;D	0.97110	1.0;0.999;0.999;1.0;1.0;0.994;1.0;1.0	D	0.89009	0.3427	10	0.87932	D	0	-31.0813	17.3259	0.87246	0.0:0.0:1.0:0.0	.	1114;1114;1114;1114;1114;334;1114;1114	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;A7E2E1;P51532	.;.;.;.;.;.;.;SMCA4_HUMAN	N	1114;1114;1178;1114;1114;1114;1114;1114	ENSP00000395654:D1114N;ENSP00000350720:D1114N;ENSP00000343896:D1114N;ENSP00000445036:D1114N;ENSP00000392837:D1114N;ENSP00000397783:D1114N;ENSP00000414727:D1114N	ENSP00000343896:D1114N	D	+	1	0	SMARCA4	10999584	1.000000	0.71417	0.983000	0.44433	0.990000	0.78478	9.293000	0.96082	2.617000	0.88574	0.655000	0.94253	GAT	.	.		0.458	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		A	11138584	G	A	11138584	3	1	349	1	0	0	0	0	1	0	0	0	14785	942	33	3	3430	3	SMARCA4	19	11138584	Missense_Mutation	SNP	G	TCGA-UB-AA0U-01A-11D-A382-10	1009025	11138584	47990399	78	49227										
ZNF701	55762	hgsc.bcm.edu	37	chr19	53086589	53086589	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	taatcacaaatcaaaccttgCatgtcatcgtagacttcata	4	10	4	1			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr19:53086589C>A	ENST00000540331.1	+	5	1700	c.1475C>A	c.(1474-1476)gCa>gAa	p.A492E	ZNF701_ENST00000301093.2_Missense_Mutation_p.A492E|ZNF701_ENST00000391785.3_Missense_Mutation_p.A426E|CTD-3099C6.7_ENST00000599222.1_RNA	NM_001172655.1	NP_001166126.1	Q9NV72	ZN701_HUMAN	zinc finger protein 701	492					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(1)|large_intestine(2)|lung(6)	14				OV - Ovarian serous cystadenocarcinoma(262;0.0105)|GBM - Glioblastoma multiforme(134;0.0402)		TCAAACCTTGCATGTCATCGT	0.353																																					p.A492E	NSCLC(89;451 1475 9611 20673 52284)	Atlas-SNP	.											.	ZNF701	44	.	0			c.C1475A						.						50	42	44					19																	53086589		2203	4298	6501	SO:0001583	missense	55762	exon5			ACCTTGCATGTCA	AK001753	CCDS33092.1, CCDS54311.1	19q13.41	2013-01-08				ENSG00000167562		"Zinc fingers, C2H2-type", "-"	25597	protein-coding gene	gene with protein product							Standard	NM_018260		Approved	FLJ10891	uc021uyw.1	Q9NV72		ENST00000540331.1:c.1475C>A	chr19.hg19:g.53086589C>A	ENSP00000444339:p.Ala492Glu	245.0	0.0		188.0	8.0	NM_001172655	A2RRM8|B9EGF2|F5GZM6|Q66K42	Missense_Mutation	SNP	ENST00000540331.1	hg19	CCDS54311.1	.	.	.	.	.	.	.	.	.	.	c	0.275	-0.990405	0.02162	.	.	ENSG00000167562	ENST00000391785;ENST00000301093;ENST00000540331	T;T;T	0.17054	2.3;2.3;2.3	1.98	-3.96	0.04106	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06280	0.0162	N	0.11313	0.125	0.09310	N	1	B;B	0.11235	0.003;0.004	B;B	0.20577	0.03;0.004	T	0.26985	-1.0087	9	0.22706	T	0.39	.	0.4102	0.00440	0.2682:0.2962:0.1329:0.3027	.	492;426	F5GZM6;Q9NV72	.;ZN701_HUMAN	E	426;492;492	ENSP00000375662:A426E;ENSP00000301093:A492E;ENSP00000444339:A492E	ENSP00000301093:A492E	A	+	2	0	ZNF701	57778401	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-10.911000	0.00005	-3.031000	0.00266	-2.043000	0.00416	GCA	.	.		0.353	ZNF701-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463467.1	NM_018260		A	53086589	C	A	53086589	3	1	349	1	0	0	0	0	1	0	0	0	18120	710	25	3	1489	3	ZNF701	19	53086589	Missense_Mutation	SNP	C	TCGA-UB-AA0U-01A-11D-A382-10	41948005	53086589	6042394	79	49228			1	64		3	3	70	N	GA_C	1.895513e-08
ZNF701	55762	hgsc.bcm.edu	37	chr19	53086622	53086622	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	acttcatactggagagaaacCttacaagtgtaatgaatgtg	9	6	1	2	rs142390931		TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr19:53086622C>G	ENST00000540331.1	+	5	1733	c.1508C>G	c.(1507-1509)cCt>cGt	p.P503R	ZNF701_ENST00000301093.2_Missense_Mutation_p.P503R|ZNF701_ENST00000391785.3_Missense_Mutation_p.P437R|CTD-3099C6.7_ENST00000599222.1_RNA	NM_001172655.1	NP_001166126.1	Q9NV72	ZN701_HUMAN	zinc finger protein 701	503					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(1)|large_intestine(2)|lung(6)	14				OV - Ovarian serous cystadenocarcinoma(262;0.0105)|GBM - Glioblastoma multiforme(134;0.0402)		GGAGAGAAACCTTACAAGTGT	0.348																																					p.P503R	NSCLC(89;451 1475 9611 20673 52284)	Atlas-SNP	.											.	ZNF701	44	.	0			c.C1508G						.						44	40	41					19																	53086622		2200	4292	6492	SO:0001583	missense	55762	exon5			AGAAACCTTACAA	AK001753	CCDS33092.1, CCDS54311.1	19q13.41	2013-01-08				ENSG00000167562		"Zinc fingers, C2H2-type", "-"	25597	protein-coding gene	gene with protein product							Standard	NM_018260		Approved	FLJ10891	uc021uyw.1	Q9NV72		ENST00000540331.1:c.1508C>G	chr19.hg19:g.53086622C>G	ENSP00000444339:p.Pro503Arg	274.0	0.0		227.0	11.0	NM_001172655	A2RRM8|B9EGF2|F5GZM6|Q66K42	Missense_Mutation	SNP	ENST00000540331.1	hg19	CCDS54311.1	.	.	.	.	.	.	.	.	.	.	C	13.24	2.178537	0.38511	.	.	ENSG00000167562	ENST00000391785;ENST00000301093;ENST00000540331	T;T;T	0.27890	1.64;1.64;1.64	1.98	0.858	0.19030	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.48589	0.1508	M	0.68728	2.09	0.23524	N	0.997498	D;D	0.89917	1.0;1.0	D;D	0.91635	0.983;0.999	T	0.27606	-1.0069	9	0.87932	D	0	.	7.4095	0.27009	0.0:0.8493:0.0:0.1507	.	503;437	F5GZM6;Q9NV72	.;ZN701_HUMAN	R	437;503;503	ENSP00000375662:P437R;ENSP00000301093:P503R;ENSP00000444339:P503R	ENSP00000301093:P503R	P	+	2	0	ZNF701	57778434	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	0.201000	0.17276	0.156000	0.19299	0.462000	0.41574	CCT	.	C|1.000;T|0.000		0.348	ZNF701-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463467.1	NM_018260		G	53086622	C	G	53086622	3	3	349	1	0	0	0	0	1	0	0	0	18120	681	24	4	1522	4	ZNF701	19	53086622	Missense_Mutation	SNP	C	TCGA-UB-AA0U-01A-11D-A382-10	33	53086622	6042361	80	49229			1	64		3	3	70	N	GA_C	1.895513e-08
ZNF701	55762	hgsc.bcm.edu	37	chr19	53086658	53086659	+	Missense_Mutation	DNP	GA	GA	AC													0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	atgtggcaaggtttttaatcGaaaatcaaaccttgaacgtc							TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr19:53086658_53086659GA>AC	ENST00000540331.1	+	5	1769_1770	c.1544_1545GA>AC	c.(1543-1545)cGA>cAC	p.R515H	ZNF701_ENST00000301093.2_Missense_Mutation_p.R515H|ZNF701_ENST00000391785.3_Missense_Mutation_p.R449H|CTD-3099C6.7_ENST00000599222.1_RNA	NM_001172655.1	NP_001166126.1	Q9NV72	ZN701_HUMAN	zinc finger protein 701	515					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(1)|large_intestine(2)|lung(6)	14				OV - Ovarian serous cystadenocarcinoma(262;0.0105)|GBM - Glioblastoma multiforme(134;0.0402)		GTTTTTAATCGAAAATCAAACC	0.361																																					p.R515Q|p.R515R	NSCLC(89;451 1475 9611 20673 52284)	Atlas-SNP	.											ZNF701,NS,carcinoma,0,1|.	ZNF701	44	.	0			c.G1544A|c.A1545C						.																																			SO:0001583	missense	55762	exon5			TTAATCGAAAATC|TAATCGAAAATCA	AK001753	CCDS33092.1, CCDS54311.1	19q13.41	2013-01-08				ENSG00000167562		"Zinc fingers, C2H2-type", "-"	25597	protein-coding gene	gene with protein product							Standard	NM_018260		Approved	FLJ10891	uc021uyw.1	Q9NV72		Exception_encountered	chr19.hg19:g.53086658_53086659delinsAC	ENSP00000444339:p.Arg515His	315.0|314.0	0.0		242.0	28.0	NM_001172655	A2RRM8|B9EGF2|F5GZM6|Q66K42	Missense_Mutation|Silent	SNP	ENST00000540331.1	hg19	CCDS54311.1																																																																																			.	.		0.361	ZNF701-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463467.1	NM_018260		AC	53086659	GA	AC	53086658	3	1	349	1	0	0	0	0	1	0	0	0	18120	1058	37	1	1558	1	ZNF701	19	53086658	Missense_Mutation	DNP	GA	TCGA-UB-AA0U-01A-11D-A382-10	36	53086658	6042325	81	49230			1	64		3	3	70	N	GA_C	1.895513e-08
HSPBP1	23640	hgsc.bcm.edu	37	chr19	55790902	55790902	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	gaggagccgccgccgccgccCcctgaagagcaaccctggga	14	17	0	2			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr19:55790902C>G	ENST00000255631.5	-	3	385	c.75G>C	c.(73-75)ggG>ggC	p.G25G	HSPBP1_ENST00000376343.3_Silent_p.G25G|HSPBP1_ENST00000433386.2_Silent_p.G25G|HSPBP1_ENST00000587922.1_Silent_p.G25G|BRSK1_ENST00000590333.1_5'Flank	NM_001130106.1|NM_012267.4	NP_001123578.1|NP_036399.3	Q9NZL4	HPBP1_HUMAN	HSPA (heat shock 70kDa) binding protein, cytoplasmic cochaperone 1	25	Gly-rich.		Missing. {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9830037, ECO:0000269|Ref.3, ECO:0000269|Ref.6}.		negative regulation of catalytic activity (GO:0043086)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein folding (GO:0006457)		enzyme inhibitor activity (GO:0004857)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)|urinary_tract(1)	8			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0452)		CGCCGCCGCCCCCTGAAGAGC	0.692																																					p.G25G		Atlas-SNP	.											.	HSPBP1	24	.	0			c.G75C						.						7	10	9					19																	55790902		1738	3706	5444	SO:0001819	synonymous_variant	23640	exon2			GCCGCCCCCTGAA		CCDS33111.1	19q13.42	2008-12-16			ENSG00000133265	ENSG00000133265			24989	protein-coding gene	gene with protein product	"hsp70 interacting protein", "Hsp70 binding protein 1"	612939				10786638, 9830037	Standard	NM_001130106		Approved	HspBP1, FES1	uc002qkd.3	Q9NZL4		ENST00000255631.5:c.75G>C	chr19.hg19:g.55790902C>G		64.0	0.0		75.0	5.0	NM_012267	B3KQP0|B4DG11|O95351|Q6ZNU5	Silent	SNP	ENST00000255631.5	hg19	CCDS33111.1																																																																																			.	.		0.692	HSPBP1-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452670.1	NM_012267		G	55790902	C	G	55790902	2	3	349	1	0	0	0	0	0	0	0	1	7435	610	22	4		4	HSPBP1	19	55790902	Silent	SNP	C	TCGA-UB-AA0U-01A-11D-A382-10	2704244	55790902	3338081	82	49231										
MATN4	8785	hgsc.bcm.edu	37	chr20	43934157	43934157	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	ggccccagttcacctgtcaaCtggagctgggtttcccaggg	13	13	2	0			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr20:43934157C>G	ENST00000372754.1	-	1	74	c.66G>C	c.(64-66)caG>caC	p.Q22H	MATN4_ENST00000342716.4_Missense_Mutation_p.Q22H|RBPJL_ENST00000343694.3_5'Flank|MATN4_ENST00000372751.4_Missense_Mutation_p.Q22H|MATN4_ENST00000360607.6_Missense_Mutation_p.Q22H|MATN4_ENST00000353917.5_Missense_Mutation_p.Q22H|MATN4_ENST00000372756.1_Missense_Mutation_p.Q22H|MATN4_ENST00000537548.1_Missense_Mutation_p.Q22H|RBPJL_ENST00000372743.1_5'Flank|RBPJL_ENST00000372741.3_5'Flank			O95460	MATN4_HUMAN	matrilin 4	22					extracellular matrix organization (GO:0030198)|response to axon injury (GO:0048678)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	27		Myeloproliferative disorder(115;0.0122)				CACCTGTCAACTGGAGCTGGG	0.637																																					p.Q22H		Atlas-SNP	.											.	MATN4	57	.	0			c.G66C						.						31	23	26					20																	43934157		2183	4246	6429	SO:0001583	missense	8785	exon2			TGTCAACTGGAGC	AJ007581	CCDS13348.1, CCDS46607.1	20q13.1-q13.2	2008-07-07			ENSG00000124159	ENSG00000124159			6910	protein-coding gene	gene with protein product		603897				9827539, 9027493	Standard	NM_003833		Approved		uc002xnn.2	O95460	OTTHUMG00000033043	ENST00000372754.1:c.66G>C	chr20.hg19:g.43934157C>G	ENSP00000361840:p.Gln22His	35.0	0.0		48.0	16.0	NM_030592	A6NH94|A6NKN5|Q5QPU2|Q5QPU3|Q5QPU4|Q8N2M5|Q8N2M7|Q9H1F8|Q9H1F9	Missense_Mutation	SNP	ENST00000372754.1	hg19		.	.	.	.	.	.	.	.	.	.	C	11.28	1.593129	0.28357	.	.	ENSG00000124159	ENST00000372753;ENST00000372754;ENST00000372756;ENST00000353917;ENST00000360607;ENST00000342716;ENST00000537548;ENST00000255132;ENST00000372751	T;T;T;T;T;T;T;T	0.78003	-1.04;-1.14;-1.14;-1.14;-1.14;-1.14;-1.14;-1.04	3.89	3.89	0.44902	.	0.191348	0.25587	N	0.029654	D	0.85353	0.5677	M	0.70275	2.135	0.09310	N	1	P;D;D	0.71674	0.952;0.998;0.972	B;D;P	0.72982	0.395;0.979;0.599	T	0.76242	-0.3031	10	0.72032	D	0.01	.	11.6801	0.51453	0.0:1.0:0.0:0.0	.	22;22;22	A6NNA4;O95460-4;O95460-2	.;.;.	H	22	ENSP00000361839:Q22H;ENSP00000361840:Q22H;ENSP00000361842:Q22H;ENSP00000243983:Q22H;ENSP00000353819:Q22H;ENSP00000343164:Q22H;ENSP00000440328:Q22H;ENSP00000361837:Q22H	ENSP00000255132:Q22H	Q	-	3	2	MATN4	43367571	0.729000	0.28090	0.033000	0.17914	0.027000	0.11550	0.946000	0.29069	2.479000	0.83701	0.557000	0.71058	CAG	.	.		0.637	MATN4-002	KNOWN	non_canonical_conserved|non_canonical_U12|not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000080335.1			G	43934157	C	G	43934157	3	3	349	1	0	0	0	0	1	0	0	0	9345	564	20	4	1715	4	MATN4	20	43934157	Missense_Mutation	SNP	C	TCGA-UB-AA0U-01A-11D-A382-10		43934157	19091363	83	49232										
DSCAM	1826	hgsc.bcm.edu	37	chr21	41725589	41725589	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	cagggtgcccgagcgctttgCaaggcagctccacacgctgc	13	15	0	0			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr21:41725589C>A	ENST00000400454.1	-	5	1214	c.737G>T	c.(736-738)tGc>tTc	p.C246F		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	246	Ig-like C2-type 3.				cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				GAGCGCTTTGCAAGGCAGCTC	0.572																																					p.C246F	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.	DSCAM	347	.	0			c.G737T						.						32	32	32					21																	41725589		1924	4135	6059	SO:0001583	missense	1826	exon5			GCTTTGCAAGGCA	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.737G>T	chr21.hg19:g.41725589C>A	ENSP00000383303:p.Cys246Phe	51.0	0.0		52.0	9.0	NM_001271534	O60468	Missense_Mutation	SNP	ENST00000400454.1	hg19	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.529045	0.85706	.	.	ENSG00000171587	ENST00000400454	T	0.65178	-0.14	5.31	5.31	0.75309	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.86285	0.5896	H	0.96547	3.84	0.80722	D	1	D	0.65815	0.995	D	0.72982	0.979	D	0.90431	0.4424	10	0.87932	D	0	.	19.3181	0.94224	0.0:1.0:0.0:0.0	.	246	O60469	DSCAM_HUMAN	F	246	ENSP00000383303:C246F	ENSP00000383303:C246F	C	-	2	0	DSCAM	40647459	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.354000	0.79424	2.629000	0.89072	0.650000	0.86243	TGC	.	.		0.572	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		A	41725589	C	A	41725589	3	1	349	1	0	0	0	0	1	0	0	0	4770	710	25	3	5417	3	DSCAM	21	41725589	Missense_Mutation	SNP	C	TCGA-UB-AA0U-01A-11D-A382-10		41725589	6404306	84	49233										
GNAZ	2781	hgsc.bcm.edu	37	chr22	23438485	23438485	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	ctcaccttcaagatggtggaCgtgggggggcagaggtcaga	17	8	3	3	rs375941406		TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr22:23438485C>T	ENST00000248996.4	+	2	1269	c.603C>T	c.(601-603)gaC>gaT	p.D201D	RTDR1_ENST00000216036.4_Intron	NM_002073.2	NP_002064.1	P19086	GNAZ_HUMAN	guanine nucleotide binding protein (G protein), alpha z polypeptide	201					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|receptor signaling protein activity (GO:0005057)|signal transducer activity (GO:0004871)	p.D201D(1)		endometrium(3)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(5)|urinary_tract(1)	19	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.166)		AGATGGTGGACGTGGGGGGGC	0.572													C|||	1	0.000199681	0	0	5008	,	,		19093	0		0.001	False		,,,				2504	0				p.D201D		Atlas-SNP	.											GNAZ,NS,carcinoma,0,1	GNAZ	45	.	1	Substitution - coding silent(1)	lung(1)	c.C603T						.	C	,	0,4406		0,0,2203	131	137	135		603,	-8.9	0.4	22		135	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,intron	GNAZ,RTDR1	NM_002073.2,NM_014433.2	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	201/356,	23438485	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	2781	exon2			GGTGGACGTGGGG		CCDS13804.1	22q11.1-q11.2	2008-06-10			ENSG00000128266	ENSG00000128266			4395	protein-coding gene	gene with protein product		139160				2115889	Standard	NM_002073		Approved		uc002zwu.1	P19086	OTTHUMG00000150611	ENST00000248996.4:c.603C>T	chr22.hg19:g.23438485C>T		44.0	0.0		36.0	14.0	NM_002073	B2R6C1|Q4QRJ6	Silent	SNP	ENST00000248996.4	hg19	CCDS13804.1																																																																																			.	.		0.572	GNAZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319073.1	NM_002073		T	23438485	C	T	23438485	2	4	349	1	0	0	0	0	0	0	0	1	6522	535	19	1		1	GNAZ	22	23438485	Silent	SNP	C	TCGA-UB-AA0U-01A-11D-A382-10		23438485	27866081	85	49234										
GATSL3	652968	hgsc.bcm.edu	37	chr22	30683518	30683518	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	agcaccagccatgtggcctcAgctacttgcaggaactcaga	10	13	2	1			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chr22:30683518A>C	ENST00000407689.3	-	3	345	c.216T>G	c.(214-216)gcT>gcG	p.A72A	RP1-130H16.18_ENST00000447976.1_3'UTR|GATSL3_ENST00000404953.3_Silent_p.A72A|GATSL3_ENST00000459785.1_5'Flank	NM_001037666.2	NP_001032755.1	Q8WTX7	GATL3_HUMAN	GATS protein-like 3	72										breast(1)|endometrium(1)|lung(1)	3						ATGTGGCCTCAGCTACTTGCA	0.632											OREG0026457	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A72A		Atlas-SNP	.											.	GATSL3	14	.	0			c.T216G						.						24	27	26					22																	30683518		2185	4267	6452	SO:0001819	synonymous_variant	652968	exon3			GGCCTCAGCTACT		CCDS43001.1	22q12	2010-06-23			ENSG00000239282	ENSG00000239282			34423	protein-coding gene	gene with protein product							Standard	NM_001037666		Approved			Q8WTX7	OTTHUMG00000150929	ENST00000407689.3:c.216T>G	chr22.hg19:g.30683518A>C		49.0	0.0	819	42.0	17.0	NM_001037666	O76052|Q96ND9|Q9UIE8	Silent	SNP	ENST00000407689.3	hg19	CCDS43001.1																																																																																			.	.		0.632	GATSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320581.2	NM_001037666		C	30683518	A	C	30683518	2	2	349	1	0	0	0	0	0	0	0	1	6273	175	7	5		5	GATSL3	22	30683518	Silent	SNP	A	TCGA-UB-AA0U-01A-11D-A382-10	7245033	30683518	20621048	86	49235										
SHROOM4	57477	hgsc.bcm.edu	37	chrX	50350752	50350752	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	tcctcctcctcctcctcctgTtgcttctgctgctgctgttg	7	17	1	0	rs534812379		TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chrX:50350752T>C	ENST00000289292.7	-	6	3673	c.3390A>G	c.(3388-3390)caA>caG	p.Q1130Q	SHROOM4_ENST00000460112.3_Silent_p.Q1014Q|SHROOM4_ENST00000376020.2_Silent_p.Q1130Q			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1130	Gln-rich.			KQQ -> QQQQKQQE (in Ref. 1; BAA86516 and 3; AAI51241). {ECO:0000305}.	actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					cctcctcctgttgcttctgct	0.582																																					p.Q1130Q		Atlas-SNP	.											.	SHROOM4	171	.	0			c.A3390G						.						15	15	15					X																	50350752		2198	4291	6489	SO:0001819	synonymous_variant	57477	exon6			CTCCTGTTGCTTC	AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.3390A>G	chrX.hg19:g.50350752T>C		39.0	0.0		24.0	5.0	NM_020717	A7E2X9|D6RFW0|Q96LA0	Silent	SNP	ENST00000289292.7	hg19	CCDS35277.1																																																																																			.	.		0.582	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717		C	50350752	T	C	50350752	2	2	349	1	0	0	0	0	0	0	0	1	14311	1722	60	2		2	SHROOM4	23	50350752	Silent	SNP	T	TCGA-UB-AA0U-01A-11D-A382-10		50350752	104919808	87	49236										
MAGEC3	139081	hgsc.bcm.edu	37	chrX	140969562	140969562	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0681818181818182	6	1	1.15538793103448	0	1.40047021943574	0.0090497737556561	0.234306995109257	0	catctgaggaggtcatctggGaagtgctgaatgcaataggg	15	6	3	2			TCGA-UB-AA0U-01A-11D-A382-10	TCGA-UB-AA0U-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	86952660-bb3d-44f2-b8c2-842213a5fb20	d47d2cb3-bc69-4675-826a-152e65b30482	g.chrX:140969562G>T	ENST00000298296.1	+	4	889	c.889G>T	c.(889-891)Gaa>Taa	p.E297*	MAGEC3_ENST00000536088.1_Intron|MAGEC3_ENST00000448920.1_Intron|MAGEC3_ENST00000443323.2_Intron	NM_138702.1	NP_619647.1	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3	297	MAGE 1. {ECO:0000255|PROSITE- ProRule:PRU00127}.									NS(2)|breast(3)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|liver(1)|lung(32)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(2)	69	Acute lymphoblastic leukemia(192;6.56e-05)					GGTCATCTGGGAAGTGCTGAA	0.512																																					p.E297X		Atlas-SNP	.											.	MAGEC3	228	.	0			c.G889T						.						126	122	124					X																	140969562		2203	4300	6503	SO:0001587	stop_gained	139081	exon4			ATCTGGGAAGTGC	AF490508	CCDS14676.1, CCDS14677.1	Xq27.2	2009-03-25			ENSG00000165509	ENSG00000165509			23798	protein-coding gene	gene with protein product	"cancer/testis antigen family 7, member 2"	300469				10861452	Standard	NM_138702		Approved	HCA2, MAGE-C3, CT7.2	uc011mwp.2	Q8TD91	OTTHUMG00000022570	ENST00000298296.1:c.889G>T	chrX.hg19:g.140969562G>T	ENSP00000298296:p.Glu297*	66.0	0.0		58.0	27.0	NM_138702	Q3SYA7|Q5JZ43|Q9BZ80	Nonsense_Mutation	SNP	ENST00000298296.1	hg19	CCDS14676.1	.	.	.	.	.	.	.	.	.	.	G	15.41	2.826192	0.50739	.	.	ENSG00000165509	ENST00000298296	.	.	.	2.26	0.324	0.15898	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	.	2.2627	0.04071	0.1932:0.0:0.5038:0.303	.	.	.	.	X	297	.	ENSP00000298296:E297X	E	+	1	0	MAGEC3	140797228	0.584000	0.26766	0.001000	0.08648	0.008000	0.06430	1.367000	0.34204	-0.019000	0.14055	0.525000	0.51046	GAA	.	.		0.512	MAGEC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058606.1	NM_138702		T	140969562	G	T	140969562	4	4	349	1	0	0	0	0	0	1	0	0	9191	1175	41	3	903	3	MAGEC3	23	140969562	Nonsense_Mutation	SNP	G	TCGA-UB-AA0U-01A-11D-A382-10	90618810	140969562	14300998	88	49237										
PSME4	23198	hgsc.bcm.edu	37	chr2	54135494	54135494	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	tctttactaagttgaagcttTtccatcgggagtcaaattca	7	8	3	1			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr2:54135494T>G	ENST00000404125.1	-	24	2802	c.2747A>C	c.(2746-2748)aAa>aCa	p.K916T	PSME4_ENST00000421748.2_Missense_Mutation_p.K60T	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	916					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|spermatoproteasome complex (GO:1990111)	lysine-acetylated histone binding (GO:0070577)|peptidase activator activity (GO:0016504)			breast(5)|endometrium(8)|kidney(1)|large_intestine(11)|lung(26)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(2)	60			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			GTTGAAGCTTTTCCATCGGGA	0.333																																					p.K916T		Atlas-SNP	.											.	PSME4	247	.	0			c.A2747C						.						57	57	57					2																	54135494		2203	4298	6501	SO:0001583	missense	23198	exon24			AAGCTTTTCCATC	D38521	CCDS33197.2	2p16.1	2003-04-14			ENSG00000068878	ENSG00000068878		"Proteasome (prosome, macropain) subunits"	20635	protein-coding gene	gene with protein product		607705				7584044, 12093752	Standard	NM_014614		Approved	PA200, KIAA0077	uc002rxp.2	Q14997	OTTHUMG00000151852	ENST00000404125.1:c.2747A>C	chr2.hg19:g.54135494T>G	ENSP00000384211:p.Lys916Thr	112.0	0.0		89.0	14.0	NM_014614	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Missense_Mutation	SNP	ENST00000404125.1	hg19	CCDS33197.2	.	.	.	.	.	.	.	.	.	.	T	24.2	4.504778	0.85176	.	.	ENSG00000068878	ENST00000421748;ENST00000404125	T;T	0.12465	2.68;2.68	5.36	5.36	0.76844	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.37919	0.1021	M	0.77820	2.39	0.80722	D	1	D;D;D	0.76494	0.982;0.999;0.985	P;D;P	0.73708	0.819;0.981;0.729	T	0.13098	-1.0522	10	0.36615	T	0.2	.	15.3474	0.74350	0.0:0.0:0.0:1.0	.	291;60;916	Q14997-2;Q14997-3;Q14997	.;.;PSME4_HUMAN	T	60;916	ENSP00000410830:K60T;ENSP00000384211:K916T	ENSP00000384211:K916T	K	-	2	0	PSME4	53988998	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.040000	0.89188	2.012000	0.59069	0.533000	0.62120	AAA	.	.		0.333	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158		G	54135494	T	G	54135494	3	3	350	1	0	0	0	0	1	0	0	0	12721	1841	64	5	2876	5	PSME4	2	54135494	Missense_Mutation	SNP	T	TCGA-UB-AA0V-01A-11D-A382-10		54135494	189063879	1	49238										
ALMS1	7840	hgsc.bcm.edu	37	chr2	73613036	73613037	+	Missense_Mutation	DNP	GA	GA	CT													0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	catggccgggcgagctggagGaggaggaggaggaggaggag					rs61156725|rs72319667|rs3074417	byFrequency	TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr2:73613036_73613037GA>CT	ENST00000264448.6	+	1	151_152	c.40_41GA>CT	c.(40-42)GAg>CTg	p.E14L	ALMS1_ENST00000377715.1_Missense_Mutation_p.E14L|ALMS1_ENST00000409009.1_Missense_Mutation_p.E14L	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	14	Glu-rich.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.E27_E28delEE(1)		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						CGAGCTggaggaggaggaggag	0.693																																					p.E14Q|p.E14V		Atlas-SNP	.											.	ALMS1	384	.	1	Deletion - In frame(1)	ovary(1)	c.G40C|c.A41T						.																																			SO:0001583	missense	7840	exon1			CTGGAGGAGGAGG|TGGAGGAGGAGGA	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	Exception_encountered	chr2.hg19:g.73613036_73613037delinsCT	ENSP00000264448:p.Glu14Leu	172.0|169.0	0.0		175.0|179.0	9.0|13.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1																																																																																			.	.		0.693	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		CT	73613037	GA	CT	73613036	3	2	350	1	0	0	0	0	1	0	0	0	535	1175	41	4	42	4	ALMS1	2	73613036	Missense_Mutation	DNP	GA	TCGA-UB-AA0V-01A-11D-A382-10	19477542	73613036	169586337	2	49239										
ICA1L	130026	hgsc.bcm.edu	37	chr2	203693673	203693673	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	ttagttttccagtatttcttTtgcattcttctgactactga	5	8	3	2			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr2:203693673T>C	ENST00000392237.2	-	3	217	c.60A>G	c.(58-60)caA>caG	p.Q20Q	ICA1L_ENST00000418208.1_Silent_p.Q20Q|ICA1L_ENST00000425178.1_Silent_p.Q20Q|ICA1L_ENST00000358299.2_Silent_p.Q20Q	NM_138468.4	NP_612477.3	Q8NDH6	ICA1L_HUMAN	islet cell autoantigen 1,69kDa-like	20										breast(1)|endometrium(1)|large_intestine(7)|lung(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						AGTATTTCTTTTGCATTCTTC	0.388																																					p.Q20Q		Atlas-SNP	.											.	ICA1L	33	.	0			c.A60G						.						171	153	159					2																	203693673		2203	4300	6503	SO:0001819	synonymous_variant	130026	exon4			TTTCTTTTGCATT	AB053317	CCDS2354.1, CCDS74632.1	2q33	2008-02-05	2006-05-26	2006-05-26	ENSG00000163596	ENSG00000163596			14442	protein-coding gene	gene with protein product			"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 15", "amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 14"	ALS2CR15, ALS2CR14		11586298	Standard	NM_138468		Approved		uc002uzh.1	Q8NDH6	OTTHUMG00000132856	ENST00000392237.2:c.60A>G	chr2.hg19:g.203693673T>C		129.0	0.0		124.0	8.0	NM_178231	B3KRW6|Q53P45|Q53QZ4|Q53T97|Q96N47|Q96Q32|Q9BVQ2	Silent	SNP	ENST00000392237.2	hg19	CCDS2354.1																																																																																			.	.		0.388	ICA1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256330.1	NM_138468		C	203693673	T	C	203693673	2	2	350	1	0	0	0	0	0	0	0	1	7487	1838	64	2		2	ICA1L	2	203693673	Silent	SNP	T	TCGA-UB-AA0V-01A-11D-A382-10	130080637	203693673	39505700	3	49240										
CACNA1D	776	hgsc.bcm.edu	37	chr3	53835443	53835443	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	ggagcctcagagaaggtccaGtgtgaaaaggtaaccttgac	13	8	1	3			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr3:53835443G>T	ENST00000350061.5	+	42	5910	c.5399G>T	c.(5398-5400)aGt>aTt	p.S1800I	CACNA1D_ENST00000422281.2_Missense_Mutation_p.S1785I|CACNA1D_ENST00000288139.4_Missense_Mutation_p.S1820I|CACNA1D_ENST00000544977.1_Missense_Mutation_p.S179I	NM_001128840.1	NP_001122312.1	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type, alpha 1D subunit	1800					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|energy reserve metabolic process (GO:0006112)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during SA node cell action potential (GO:0086052)|positive regulation of calcium ion transport (GO:0051928)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|ankyrin binding (GO:0030506)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)|voltage-gated calcium channel activity involved in cardiac muscle cell action potential (GO:0086007)|voltage-gated calcium channel activity involved SA node cell action potential (GO:0086059)			breast(3)|central_nervous_system(9)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(13)|liver(1)|lung(29)|ovary(6)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	90				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	AGAAGGTCCAGTGTGAAAAGG	0.542																																					p.S1820I		Atlas-SNP	.											.	CACNA1D	324	.	0			c.G5459T						.						88	85	86					3																	53835443		2203	4300	6503	SO:0001583	missense	776	exon43			GGTCCAGTGTGAA	AB209171	CCDS2872.1, CCDS46848.1, CCDS46849.1	3p14.3	2012-03-07			ENSG00000157388	ENSG00000157388		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1391	protein-coding gene	gene with protein product		114206		CCHL1A2, CACNL1A2		1664412	Standard	NM_000720		Approved	Cav1.3, CACH3, CACN4	uc003dgu.5	Q01668	OTTHUMG00000158278	ENST00000350061.5:c.5399G>T	chr3.hg19:g.53835443G>T	ENSP00000288133:p.Ser1800Ile	52.0	0.0		54.0	9.0	NM_000720	B0FYA3|Q13916|Q13931|Q71UT1|Q9UDC3	Missense_Mutation	SNP	ENST00000350061.5	hg19	CCDS46848.1	.	.	.	.	.	.	.	.	.	.	G	3.603	-0.081132	0.07141	.	.	ENSG00000157388	ENST00000350061;ENST00000288139;ENST00000422281;ENST00000481478;ENST00000544977	D;D;D;D	0.96041	-3.87;-3.89;-3.88;-3.88	4.26	3.38	0.38709	.	8.018100	0.00166	N	0.000000	D	0.93396	0.7894	L	0.44542	1.39	0.42929	D	0.99431	B;B;B;B	0.17038	0.02;0.0;0.0;0.0	B;B;B;B	0.11329	0.006;0.001;0.0;0.001	T	0.77838	-0.2439	10	0.37606	T	0.19	.	9.3501	0.38133	0.0821:0.1451:0.7728:0.0	.	1785;1493;1800;1820	B0FYA3;Q59GD8;Q01668;Q01668-2	.;.;CAC1D_HUMAN;.	I	1800;1820;1785;1493;179	ENSP00000288133:S1800I;ENSP00000288139:S1820I;ENSP00000409174:S1785I;ENSP00000418014:S1493I	ENSP00000288139:S1820I	S	+	2	0	CACNA1D	53810483	1.000000	0.71417	0.998000	0.56505	0.313000	0.28021	3.473000	0.53122	1.104000	0.41587	-0.379000	0.06801	AGT	.	.		0.542	CACNA1D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350557.1	NM_000720		T	53835443	G	T	53835443	3	4	350	1	0	0	0	0	1	0	0	0	2543	1029	36	3	5737	3	CACNA1D	3	53835443	Missense_Mutation	SNP	G	TCGA-UB-AA0V-01A-11D-A382-10		53835443	144186987	4	49241										
CHRD	8646	hgsc.bcm.edu	37	chr3	184103890	184103890	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	ctgcggcacctggcaaaaggCatggcctccctgatgatcac	11	14	1	2			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr3:184103890C>T	ENST00000204604.1	+	15	2121	c.1875C>T	c.(1873-1875)ggC>ggT	p.G625G	CHRD_ENST00000348986.3_Silent_p.G585G|EIF2B5_ENST00000444495.1_Intron|CHRD_ENST00000450923.1_Silent_p.G625G|CHRD_ENST00000545352.1_Silent_p.G255G	NM_003741.2	NP_003732.2	Q9H2X0	CHRD_HUMAN	chordin	625	CHRD 4. {ECO:0000255|PROSITE- ProRule:PRU00230}.				BMP signaling pathway involved in spinal cord dorsal/ventral patterning (GO:0021919)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|gastrulation with mouth forming second (GO:0001702)|mesoderm formation (GO:0001707)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell migration (GO:0030336)|negative regulation of osteoblast differentiation (GO:0045668)|osteoblast differentiation (GO:0001649)|positive regulation of cell adhesion (GO:0045785)|positive regulation of mesenchymal cell proliferation (GO:0002053)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)	cytokine binding (GO:0019955)|heparin binding (GO:0008201)			NS(1)|biliary_tract(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(23)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48	all_cancers(143;6.33e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TGGCAAAAGGCATGGCCTCCC	0.622																																					p.G625G		Atlas-SNP	.											.	CHRD	149	.	0			c.C1875T						.						91	92	92					3																	184103890		2203	4300	6503	SO:0001819	synonymous_variant	8646	exon15			AAAAGGCATGGCC	AF076612	CCDS3266.1	3q27	2008-07-18			ENSG00000090539	ENSG00000090539			1949	protein-coding gene	gene with protein product		603475				9782094, 11472837	Standard	NM_003741		Approved		uc003fov.3	Q9H2X0	OTTHUMG00000141267	ENST00000204604.1:c.1875C>T	chr3.hg19:g.184103890C>T		257.0	0.0		216.0	9.0	NM_003741	O95254|Q2M1I8|Q6UW83|Q9H2D3|Q9H2W8|Q9H2W9|Q9P0Z2|Q9P0Z3|Q9P0Z4|Q9P0Z5	Silent	SNP	ENST00000204604.1	hg19	CCDS3266.1																																																																																			.	.		0.622	CHRD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280432.1	NM_003741		T	184103890	C	T	184103890	2	4	350	1	0	0	0	0	0	0	0	1	3374	697	25	3		3	CHRD	3	184103890	Silent	SNP	C	TCGA-UB-AA0V-01A-11D-A382-10	130268447	184103890	13918540	5	49242										
RXFP1	59350	hgsc.bcm.edu	37	chr4	159566234	159566234	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	catttttgtcatttgcatgcGaccttatatcaggtctgaga	8	8	3	1			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr4:159566234G>T	ENST00000307765.5	+	15	1540	c.1289G>T	c.(1288-1290)cGa>cTa	p.R430L	RXFP1_ENST00000460056.2_Missense_Mutation_p.R349L|RXFP1_ENST00000448688.2_Missense_Mutation_p.R325L|RXFP1_ENST00000343542.5_Missense_Mutation_p.R382L|RXFP1_ENST00000470033.1_Missense_Mutation_p.R397L	NM_001253727.1|NM_001253728.1|NM_001253730.1|NM_001253732.1|NM_001253733.1|NM_021634.3	NP_001240656.1|NP_001240657.1|NP_001240659.1|NP_001240661.1|NP_001240662.1|NP_067647.2	Q9HBX9	RXFP1_HUMAN	relaxin/insulin-like family peptide receptor 1	430					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|lung connective tissue development (GO:0060427)|nipple morphogenesis (GO:0060658)|parturition (GO:0007567)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|hormone binding (GO:0042562)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|liver(2)|lung(22)|prostate(1)|skin(10)	49	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0219)		ATTTGCATGCGACCTTATATC	0.378																																					p.R457L		Atlas-SNP	.											.	RXFP1	98	.	0			c.G1370T						.						126	118	120					4																	159566234		1882	4120	6002	SO:0001583	missense	59350	exon15			GCATGCGACCTTA	AF190500	CCDS43276.1, CCDS58929.1, CCDS58930.1, CCDS75204.1, CCDS75205.1, CCDS75206.1	4q31.3	2012-08-08	2006-05-09	2006-05-09	ENSG00000171509	ENSG00000171509		"GPCR / Class A : Relaxin family peptide receptors"	19718	protein-coding gene	gene with protein product		606654	"leucine-rich repeat-containing G protein-coupled receptor 7"	LGR7		15956688, 16507880	Standard	NM_021634		Approved	RXFPR1	uc003ipz.3	Q9HBX9	OTTHUMG00000149973	ENST00000307765.5:c.1289G>T	chr4.hg19:g.159566234G>T	ENSP00000303248:p.Arg430Leu	130.0	0.0		93.0	15.0	NM_001253727	B4DHD1|B4DTV2|Q2M215|Q3KU24|Q3KU25|Q3KU26	Missense_Mutation	SNP	ENST00000307765.5	hg19	CCDS43276.1	.	.	.	.	.	.	.	.	.	.	G	35	5.544072	0.96488	.	.	ENSG00000171509	ENST00000460056;ENST00000307765;ENST00000448688;ENST00000343542;ENST00000470033;ENST00000440678	T;T;T;T;T	0.30448	1.53;1.53;1.53;1.53;1.53	5.76	5.76	0.90799	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.48589	0.1508	L	0.55103	1.725	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;0.998;1.0;1.0	T	0.31194	-0.9952	10	0.02654	T	1	.	19.9731	0.97292	0.0:0.0:1.0:0.0	.	441;457;325;382;397;349;300;430	B3KV27;B4DGP2;B4DHD1;Q9HBX9-4;Q9HBX9-2;E9PCA3;Q59H16;Q9HBX9	.;.;.;.;.;.;.;RXFP1_HUMAN	L	349;430;325;382;397;300	ENSP00000423306:R349L;ENSP00000303248:R430L;ENSP00000414885:R325L;ENSP00000345889:R382L;ENSP00000420712:R397L	ENSP00000303248:R430L	R	+	2	0	RXFP1	159785684	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.661000	0.98601	2.715000	0.92844	0.563000	0.77884	CGA	.	.		0.378	RXFP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314865.1	NM_021634		T	159566234	G	T	159566234	3	4	350	1	0	0	0	0	1	0	0	0	13774	1058	37	1	1347	1	RXFP1	4	159566234	Missense_Mutation	SNP	G	TCGA-UB-AA0V-01A-11D-A382-10		159566234	31588042	6	49243										
DDX60L	91351	hgsc.bcm.edu	37	chr4	169336626	169336626	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	catcatcatgttttactgaaCatatatgcttctctaaatca	3	9	4	1			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr4:169336626C>A	ENST00000511577.1	-	22	3159	c.2912G>T	c.(2911-2913)tGt>tTt	p.C971F	DDX60L_ENST00000260184.7_Missense_Mutation_p.C971F|DDX60L_ENST00000505890.1_Missense_Mutation_p.C971F			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	971							ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		TTTTACTGAACATATATGCTT	0.333																																					p.C971F		Atlas-SNP	.											.	DDX60L	116	.	0			c.G2912T						.						106	102	103					4																	169336626		1903	4113	6016	SO:0001583	missense	91351	exon22			ACTGAACATATAT	AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.2912G>T	chr4.hg19:g.169336626C>A	ENSP00000422423:p.Cys971Phe	289.0	0.0		198.0	8.0	NM_001012967	Q96ND6	Missense_Mutation	SNP	ENST00000511577.1	hg19		.	.	.	.	.	.	.	.	.	.	C	14.52	2.560079	0.45590	.	.	ENSG00000181381	ENST00000260184;ENST00000511577;ENST00000505890;ENST00000505863	T;T;T;T	0.18960	2.19;2.19;2.18;2.91	3.23	3.23	0.37069	.	0.000000	0.41712	U	0.000825	T	0.39835	0.1093	M	0.62723	1.935	0.32137	N	0.586006	D;P;D	0.89917	1.0;0.881;1.0	D;P;D	0.91635	0.999;0.569;0.999	T	0.45948	-0.9226	10	0.18710	T	0.47	.	14.3534	0.66719	0.0:1.0:0.0:0.0	.	971;971;971	E9PAP8;D6R906;Q5H9U9	.;.;DDX6L_HUMAN	F	971;971;971;667	ENSP00000260184:C971F;ENSP00000422423:C971F;ENSP00000422202:C971F;ENSP00000421026:C667F	ENSP00000260184:C971F	C	-	2	0	DDX60L	169573201	0.989000	0.36119	0.065000	0.19835	0.858000	0.48976	3.216000	0.51176	1.481000	0.48307	0.313000	0.20887	TGT	.	.		0.333	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967		A	169336626	C	A	169336626	3	1	350	1	0	0	0	0	1	0	0	0	4381	478	17	3	2276	3	DDX60L	4	169336626	Missense_Mutation	SNP	C	TCGA-UB-AA0V-01A-11D-A382-10	9770392	169336626	21817650	7	49244										
SCRG1	11341	hgsc.bcm.edu	37	chr4	174312527	174312527	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	gcttgaactcctagcagcaaAgttagcccaatggtgaaaac	9	10	0	2			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr4:174312527A>T	ENST00000296506.3	-	2	521	c.39T>A	c.(37-39)acT>acA	p.T13T		NM_007281.2	NP_009212.1	O75711	SCRG1_HUMAN	stimulator of chondrogenesis 1	13					nervous system development (GO:0007399)	extracellular space (GO:0005615)				large_intestine(1)|lung(4)|skin(1)	6		Prostate(90;0.00601)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_neural(102;0.0837)|all_hematologic(60;0.107)		all cancers(43;1.15e-17)|Epithelial(43;4.33e-16)|OV - Ovarian serous cystadenocarcinoma(60;6.62e-09)|STAD - Stomach adenocarcinoma(60;0.00278)|GBM - Glioblastoma multiforme(59;0.00659)|LUSC - Lung squamous cell carcinoma(193;0.0919)		CTAGCAGCAAAGTTAGCCCAA	0.408																																					p.T13T		Atlas-SNP	.											.	SCRG1	9	.	0			c.T39A						.						167	154	158					4																	174312527		2203	4300	6503	SO:0001819	synonymous_variant	11341	exon2			CAGCAAAGTTAGC	AJ224677	CCDS3818.1	4q34.1	2009-07-09				ENSG00000164106			17036	protein-coding gene	gene with protein product	"scrapie responsive gene 1"	603163				9660755, 9516475	Standard	NM_007281		Approved	SCRG-1	uc003ite.3	O75711		ENST00000296506.3:c.39T>A	chr4.hg19:g.174312527A>T		110.0	0.0		101.0	8.0	NM_007281		Silent	SNP	ENST00000296506.3	hg19	CCDS3818.1																																																																																			.	.		0.408	SCRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364304.2	NM_007281		T	174312527	A	T	174312527	2	4	350	1	0	0	0	0	0	0	0	1	13951	59	3	4		4	SCRG1	4	174312527	Silent	SNP	A	TCGA-UB-AA0V-01A-11D-A382-10	4975901	174312527	16841749	8	49245										
MYO10	4651	hgsc.bcm.edu	37	chr5	16794770	16794770	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	gttacctgatgaggatgcacTggttgtcgtggcgcttccac	13	10	0	2			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr5:16794770T>C	ENST00000513610.1	-	4	906	c.452A>G	c.(451-453)cAg>cGg	p.Q151R		NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	151	Myosin motor.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						GAGGATGCACTGGTTGTCGTG	0.647																																					p.Q151R		Atlas-SNP	.											.	MYO10	198	.	0			c.A452G						.						30	35	33					5																	16794770		2144	4242	6386	SO:0001583	missense	4651	exon4			ATGCACTGGTTGT	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"Myosins / Myosin superfamily : Class X", "Pleckstrin homology (PH) domain containing"	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.452A>G	chr5.hg19:g.16794770T>C	ENSP00000421280:p.Gln151Arg	74.0	0.0		76.0	14.0	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Missense_Mutation	SNP	ENST00000513610.1	hg19	CCDS54834.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.580132	0.86645	.	.	ENSG00000145555	ENST00000513610;ENST00000513882;ENST00000502436	D;D;D	0.92495	-3.05;-3.05;-3.05	4.76	4.76	0.60689	Myosin head, motor domain (3);	.	.	.	.	D	0.97670	0.9236	H	0.98426	4.23	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.99126	1.0851	9	0.87932	D	0	.	14.5927	0.68378	0.0:0.0:0.0:1.0	.	118;151	E9PCN3;Q9HD67	.;MYO10_HUMAN	R	151;162;118	ENSP00000421280:Q151R;ENSP00000421309:Q162R;ENSP00000426783:Q118R	ENSP00000426783:Q118R	Q	-	2	0	MYO10	16847770	1.000000	0.71417	1.000000	0.80357	0.839000	0.47603	7.990000	0.88215	1.899000	0.54978	0.459000	0.35465	CAG	.	.		0.647	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		C	16794770	T	C	16794770	3	2	350	1	0	0	0	0	1	0	0	0	10071	1580	55	2	5876	2	MYO10	5	16794770	Missense_Mutation	SNP	T	TCGA-UB-AA0V-01A-11D-A382-10		16794770	164120490	9	49246										
RHOBTB3	22836	hgsc.bcm.edu	37	chr5	95067705	95067705	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	tgttgctgaacgcggccagcAcggtcgcgcgtccggtgttc	15	13	0	1			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr5:95067705A>G	ENST00000379982.3	+	2	653	c.145A>G	c.(145-147)Acg>Gcg	p.T49A	CTD-2154I11.2_ENST00000512486.1_RNA|RHOBTB3_ENST00000515852.1_3'UTR|RHOBTB3_ENST00000506817.1_Missense_Mutation_p.T49A|CTD-2154I11.2_ENST00000513235.1_RNA	NM_014899.3	NP_055714.3	O94955	RHBT3_HUMAN	Rho-related BTB domain containing 3	49	Rho-like.				ATP catabolic process (GO:0006200)|retrograde transport, endosome to Golgi (GO:0042147)|small GTPase mediated signal transduction (GO:0007264)	Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|GTP binding (GO:0005525)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|skin(1)	16		all_cancers(142;2.58e-06)|all_epithelial(76;4.19e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0164)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.79e-16)		CGCGGCCAGCACGGTCGCGCG	0.632																																					p.T49A		Atlas-SNP	.											.	RHOBTB3	43	.	0			c.A145G						.						69	59	63					5																	95067705		2203	4300	6503	SO:0001583	missense	22836	exon2			GCCAGCACGGTCG	AB020685	CCDS4077.1	5q15	2014-05-09			ENSG00000164292	ENSG00000164292		"BTB/POZ domain containing"	18757	protein-coding gene	gene with protein product		607353				11222756, 17035353	Standard	NM_014899		Approved	KIAA0878	uc003klm.3	O94955	OTTHUMG00000121171	ENST00000379982.3:c.145A>G	chr5.hg19:g.95067705A>G	ENSP00000369318:p.Thr49Ala	194.0	0.0		178.0	8.0	NM_014899	A0PJA4|A8K1W9|Q8IW06	Missense_Mutation	SNP	ENST00000379982.3	hg19	CCDS4077.1	.	.	.	.	.	.	.	.	.	.	A	16.93	3.256781	0.59321	.	.	ENSG00000164292	ENST00000506959;ENST00000506817;ENST00000379982	T;T;T	0.63417	1.56;1.51;-0.04	4.86	2.01	0.26516	.	0.419325	0.24289	N	0.039839	T	0.31827	0.0809	N	0.08118	0	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.002	T	0.04320	-1.0960	10	0.14252	T	0.57	-4.2856	3.5973	0.08010	0.6012:0.0:0.1084:0.2904	.	49;49	O94955;D6RG10	RHBT3_HUMAN;.	A	55;49;49	ENSP00000423688:T55A;ENSP00000426479:T49A;ENSP00000369318:T49A	ENSP00000369318:T49A	T	+	1	0	RHOBTB3	95093461	0.012000	0.17670	1.000000	0.80357	0.986000	0.74619	0.346000	0.19997	0.808000	0.34231	-0.379000	0.06801	ACG	.	.		0.632	RHOBTB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241658.1	NM_014899		G	95067705	A	G	95067705	3	3	350	1	0	0	0	0	1	0	0	0	13350	159	6	2	151	2	RHOBTB3	5	95067705	Missense_Mutation	SNP	A	TCGA-UB-AA0V-01A-11D-A382-10	78272935	95067705	85847555	10	49247										
GABRG2	2566	hgsc.bcm.edu	37	chr5	161580308	161580308	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	aaaatggactcctatgctcgGatcttcttccccactgcctt	6	14	2	0			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr5:161580308G>T	ENST00000361925.4	+	9	1558	c.1338G>T	c.(1336-1338)cgG>cgT	p.R446R	GABRG2_ENST00000414552.2_Silent_p.R494R|GABRG2_ENST00000356592.3_Silent_p.R454R|GABRG2_ENST00000393933.4_Silent_p.R351R			P18507	GBRG2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 2	446					adult behavior (GO:0030534)|cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|post-embryonic development (GO:0009791)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|GABA-A receptor complex (GO:1902711)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(15)|lung(24)|ovary(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	62	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CCTATGCTCGGATCTTCTTCC	0.458																																					p.R494R		Atlas-SNP	.											.	GABRG2	142	.	0			c.G1482T						.						277	278	278					5																	161580308		2203	4300	6503	SO:0001819	synonymous_variant	2566	exon11			TGCTCGGATCTTC		CCDS4358.1, CCDS4359.1, CCDS47333.1	5q34	2012-06-22			ENSG00000113327	ENSG00000113327		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4087	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma 2"	137164					Standard	NM_198904		Approved		uc010jjc.3	P18507	OTTHUMG00000130350	ENST00000361925.4:c.1338G>T	chr5.hg19:g.161580308G>T		118.0	0.0		127.0	7.0	NM_198903	F5HB82|Q6GRL6|Q6PCC3|Q9UDB3|Q9UN15	Silent	SNP	ENST00000361925.4	hg19	CCDS4358.1																																																																																			.	.		0.458	GABRG2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252706.1			T	161580308	G	T	161580308	2	4	350	1	0	0	0	0	0	0	0	1	6180	1161	41	3		3	GABRG2	5	161580308	Silent	SNP	G	TCGA-UB-AA0V-01A-11D-A382-10	66512603	161580308	19334952	11	49248										
AGXT2L2	85007	hgsc.bcm.edu	37	chr5	177652372	177652372	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	ttactgatctaataccaccaCgtcctggtgtcccgtgtagt	8	12	1	1			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr5:177652372C>T	ENST00000308158.5	-	4	631	c.397G>A	c.(397-399)Gtg>Atg	p.V133M	PHYKPL_ENST00000481811.1_Intron	NM_153373.2	NP_699204.1	Q8IUZ5	AT2L2_HUMAN	5-phosphohydroxy-L-lysine phospho-lyase	133						mitochondrion (GO:0005739)	lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)									L-Alanine(DB00160)	AATACCACCACGTCCTGGTGT	0.562																																					p.V133M		Atlas-SNP	.											.	AGXT2L2	51	.	0			c.G397A						.						99	81	87					5																	177652372		2203	4300	6503	SO:0001583	missense	85007	exon4			CCACCACGTCCTG	BC037567	CCDS4434.1	5q35.3	2013-06-12	2013-06-12	2013-06-12	ENSG00000175309	ENSG00000175309	4.2.3.134		28249	protein-coding gene	gene with protein product	"5-phosphonooxy-L-lysine phospho-lyase"	614683	"alanine-glyoxylate aminotransferase 2-like 2"	AGXT2L2		22241472	Standard	NM_153373		Approved	MGC15875	uc003miz.3	Q8IUZ5	OTTHUMG00000130892	ENST00000308158.5:c.397G>A	chr5.hg19:g.177652372C>T	ENSP00000310978:p.Val133Met	105.0	0.0		85.0	15.0	NM_153373	A8K7P6|B3KN36|D3DWP9|Q8WYS6|Q96HW8	Missense_Mutation	SNP	ENST00000308158.5	hg19	CCDS4434.1	.	.	.	.	.	.	.	.	.	.	C	16.09	3.025058	0.54683	.	.	ENSG00000175309	ENST00000308158;ENST00000323594	D;T	0.86627	-2.15;0.62	5.05	5.05	0.67936	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.91563	0.7335	M	0.82923	2.615	0.80722	D	1	D	0.59767	0.986	P	0.57057	0.812	D	0.89596	0.3831	10	0.16896	T	0.51	-10.0767	16.2489	0.82472	0.0:1.0:0.0:0.0	.	133	Q8IUZ5	AT2L2_HUMAN	M	133;147	ENSP00000310978:V133M;ENSP00000321290:V147M	ENSP00000310978:V133M	V	-	1	0	AGXT2L2	177584978	0.841000	0.29509	1.000000	0.80357	0.814000	0.46013	1.696000	0.37773	2.510000	0.84645	0.462000	0.41574	GTG	.	.		0.562	PHYKPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253477.1	NM_032921		T	177652372	C	T	177652372	3	4	350	1	0	0	0	0	1	0	0	0	407	536	19	1	991	1	AGXT2L2	5	177652372	Missense_Mutation	SNP	C	TCGA-UB-AA0V-01A-11D-A382-10	16072064	177652372	3262888	12	49249										
TRIM26	7726	hgsc.bcm.edu	37	chr6	30166750	30166750	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	ggcggctccctgagatggggCggacgtctgtggtgcagctg	19	10	1	1	rs371459188		TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr6:30166750C>T	ENST00000454678.2	-	4	567	c.131G>A	c.(130-132)cGc>cAc	p.R44H	TRIM26_ENST00000487829.1_5'UTR|TRIM26_ENST00000453195.1_Missense_Mutation_p.R44H|TRIM26_ENST00000437089.1_Missense_Mutation_p.R44H	NM_003449.4	NP_003440.1	Q12899	TRI26_HUMAN	tripartite motif containing 26	44					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)	cytoplasm (GO:0005737)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			lung(1)|ovary(2)	3						TGAGATGGGGCGGACGTCTGT	0.602																																					p.R44H		Atlas-SNP	.											.	TRIM26	74	.	0			c.G131A						.	C	HIS/ARG,HIS/ARG	0,3020		0,0,1510	48	45	46		131,131	5.6	0.9	6		46	1,5417		0,1,2708	no	missense,missense	TRIM26	NM_003449.4,NM_001242783.1	29,29	0,1,4218	TT,TC,CC		0.0185,0.0,0.0119	benign,benign	44/540,44/540	30166750	1,8437	1510	2709	4219	SO:0001583	missense	7726	exon3			ATGGGGCGGACGT	AB088090	CCDS4678.1	6p21.3	2013-01-09	2011-01-25	2001-11-23	ENSG00000234127	ENSG00000234127		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	12962	protein-coding gene	gene with protein product		600830	"tripartite motif-containing 26"	ZNF173		8530076	Standard	NM_003449		Approved	RNF95	uc003npt.3	Q12899	OTTHUMG00000031041	ENST00000454678.2:c.131G>A	chr6.hg19:g.30166750C>T	ENSP00000410446:p.Arg44His	83.0	0.0		73.0	11.0	NM_001242783	A6NG96|Q5SRL2	Missense_Mutation	SNP	ENST00000454678.2	hg19	CCDS4678.1	.	.	.	.	.	.	.	.	.	.	C	13.03	2.116427	0.37339	0.0	1.85E-4	ENSG00000234127	ENST00000453195;ENST00000454678;ENST00000437089;ENST00000416596;ENST00000420345;ENST00000418026;ENST00000434785	T;T;T;T;T;T	0.08282	3.11;3.11;3.11;3.11;3.11;3.11	5.59	5.59	0.84812	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.265447	0.27302	N	0.019995	T	0.04634	0.0126	L	0.58354	1.805	0.38578	D	0.950108	B	0.32245	0.361	B	0.22753	0.041	T	0.32587	-0.9901	10	0.22109	T	0.4	.	17.0723	0.86578	0.0:1.0:0.0:0.0	.	44	Q12899	TRI26_HUMAN	H	44	ENSP00000391879:R44H;ENSP00000410446:R44H;ENSP00000395491:R44H;ENSP00000413673:R44H;ENSP00000387530:R44H;ENSP00000400920:R44H	ENSP00000413673:R44H	R	-	2	0	TRIM26	30274729	0.002000	0.14202	0.911000	0.35937	0.044000	0.14063	-0.183000	0.09712	2.631000	0.89168	0.643000	0.83706	CGC	.	.		0.602	TRIM26-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253442.1	NM_003449		T	30166750	C	T	30166750	3	4	350	1	0	0	0	0	1	0	0	0	16515	768	27	1	1516	1	TRIM26	6	30166750	Missense_Mutation	SNP	C	TCGA-UB-AA0V-01A-11D-A382-10		30166750	140948317	13	49250										
GNMT	27232	hgsc.bcm.edu	37	chr6	42931160	42931160	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	tacggtgcaggtgccgggggCtggccaggatggctctcctg	18	11	1	0			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr6:42931160C>A	ENST00000372808.3	+	5	699	c.689C>A	c.(688-690)gCt>gAt	p.A230D		NM_018960.4	NP_061833.1	Q14749	GNMT_HUMAN	glycine N-methyltransferase	230					cellular protein modification process (GO:0006464)|glycogen metabolic process (GO:0005977)|methionine metabolic process (GO:0006555)|one-carbon metabolic process (GO:0006730)|protein homotetramerization (GO:0051289)|regulation of gluconeogenesis (GO:0006111)|S-adenosylmethionine metabolic process (GO:0046500)	cytoplasm (GO:0005737)	folic acid binding (GO:0005542)|glycine binding (GO:0016594)|glycine N-methyltransferase activity (GO:0017174)			kidney(2)|large_intestine(1)|lung(1)	4	Colorectal(47;0.196)		all cancers(41;0.00196)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0461)		Glycine(DB00145)|S-Adenosylmethionine(DB00118)	GTGCCGGGGGCTGGCCAGGAT	0.587																																					p.A230D		Atlas-SNP	.											.	GNMT	13	.	0			c.C689A						.						44	41	42					6																	42931160		2203	4300	6503	SO:0001583	missense	27232	exon5			CGGGGGCTGGCCA	AF101475	CCDS4876.1	6p12	2008-02-05			ENSG00000124713	ENSG00000124713			4415	protein-coding gene	gene with protein product		606628				10843803, 9495250	Standard	NM_018960		Approved		uc003otd.3	Q14749	OTTHUMG00000014712	ENST00000372808.3:c.689C>A	chr6.hg19:g.42931160C>A	ENSP00000361894:p.Ala230Asp	105.0	0.0		97.0	13.0	NM_018960	Q5T8W2|Q9NNZ1|Q9NS24	Missense_Mutation	SNP	ENST00000372808.3	hg19	CCDS4876.1	.	.	.	.	.	.	.	.	.	.	C	9.897	1.205836	0.22205	.	.	ENSG00000124713	ENST00000372808	T	0.69306	-0.39	5.74	5.74	0.90152	.	0.227351	0.45867	D	0.000335	T	0.45438	0.1342	L	0.59436	1.845	0.09310	N	1	B	0.13594	0.008	B	0.10450	0.005	T	0.19224	-1.0312	10	0.17369	T	0.5	-11.7295	15.1868	0.73009	0.1416:0.8584:0.0:0.0	.	230	Q14749	GNMT_HUMAN	D	230	ENSP00000361894:A230D	ENSP00000361894:A230D	A	+	2	0	GNMT	43039138	0.007000	0.16637	0.029000	0.17559	0.912000	0.54170	2.302000	0.43637	2.715000	0.92844	0.549000	0.68633	GCT	.	.		0.587	GNMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040568.1	NM_018960		A	42931160	C	A	42931160	3	1	350	1	0	0	0	0	1	0	0	0	6548	797	28	3	707	3	GNMT	6	42931160	Missense_Mutation	SNP	C	TCGA-UB-AA0V-01A-11D-A382-10	12764410	42931160	128183907	14	49251										
PEX7	5191	hgsc.bcm.edu	37	chr6	137191048	137191048	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	aatttgctggtgaccggggcGgttgactgtagtttgagagg	17	5	0	3			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr6:137191048G>T	ENST00000318471.4	+	7	735	c.654G>T	c.(652-654)gcG>gcT	p.A218A	PEX7_ENST00000541292.1_Silent_p.A218A	NM_000288.3	NP_000279.1	O00628	PEX7_HUMAN	peroxisomal biogenesis factor 7	218			A -> V (in RCDP1). {ECO:0000269|PubMed:9090381}.		endochondral ossification (GO:0001958)|ether lipid biosynthetic process (GO:0008611)|fatty acid beta-oxidation (GO:0006635)|neuron migration (GO:0001764)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)	cytosol (GO:0005829)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	enzyme binding (GO:0019899)|peroxisome matrix targeting signal-2 binding (GO:0005053)|protein homodimerization activity (GO:0042803)	p.A218A(1)		lung(7)|prostate(1)	8	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000257)|OV - Ovarian serous cystadenocarcinoma(155;0.00492)		TGACCGGGGCGGTTGACTGTA	0.403																																					p.A218A		Atlas-SNP	.											.	PEX7	24	.	1	Substitution - coding silent(1)	lung(1)	c.G654T						.						234	238	237					6																	137191048		2203	4300	6503	SO:0001819	synonymous_variant	5191	exon7			CGGGGCGGTTGAC	AF180814	CCDS5180.1	6q21-q22.2	2013-01-10			ENSG00000112357	ENSG00000112357		"WD repeat domain containing"	8860	protein-coding gene	gene with protein product	"Refsum disease"	601757				9090381, 10673331	Standard	NM_000288		Approved	PTS2R, RD	uc003qhd.3	O00628	OTTHUMG00000015650	ENST00000318471.4:c.654G>T	chr6.hg19:g.137191048G>T		97.0	0.0		68.0	13.0	NM_000288	C0H5X6	Silent	SNP	ENST00000318471.4	hg19	CCDS5180.1																																																																																			.	.		0.403	PEX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042387.2	NM_000288		T	137191048	G	T	137191048	2	4	350	1	0	0	0	0	0	0	0	1	11760	1103	39	1		1	PEX7	6	137191048	Silent	SNP	G	TCGA-UB-AA0V-01A-11D-A382-10	94259888	137191048	33924019	15	49252										
TFB1M	51106	hgsc.bcm.edu	37	chr6	155618121	155618121	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	tttgaaaagtcaaagtcatcTgagttctgccataaacaaaa	6	7	4	2			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr6:155618121T>C	ENST00000367166.4	-	4	567	c.512A>G	c.(511-513)cAg>cGg	p.Q171R		NM_016020.3	NP_057104.2	Q8WVM0	TFB1M_HUMAN	transcription factor B1, mitochondrial	171					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	mitochondrial nucleoid (GO:0042645)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|rRNA (adenine-N6,N6-)-dimethyltransferase activity (GO:0000179)			lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;1.48e-12)|BRCA - Breast invasive adenocarcinoma(81;0.0131)		CAAAGTCATCTGAGTTCTGCC	0.328																																					p.Q171R		Atlas-SNP	.											.	TFB1M	30	.	0			c.A512G						.						82	82	82					6																	155618121		2203	4300	6503	SO:0001583	missense	51106	exon4			GTCATCTGAGTTC	AF151833	CCDS5248.1	6q25.1-q25.3	2011-01-28			ENSG00000029639	ENSG00000029639			17037	protein-coding gene	gene with protein product	"dimethyladenosine transferase 1, mitochondrial"	607033				10810093, 11809803	Standard	NM_016020		Approved	mtTFB, CGI-75	uc003qqj.4	Q8WVM0	OTTHUMG00000015881	ENST00000367166.4:c.512A>G	chr6.hg19:g.155618121T>C	ENSP00000356134:p.Gln171Arg	63.0	0.0		72.0	9.0	NM_016020	Q05DR0|Q9Y384	Missense_Mutation	SNP	ENST00000367166.4	hg19	CCDS5248.1	.	.	.	.	.	.	.	.	.	.	T	8.239	0.806507	0.16467	.	.	ENSG00000029639	ENST00000367166	T	0.26373	1.74	6.08	0.845	0.18950	Ribosomal RNA adenine methylase transferase, N-terminal (1);	0.433285	0.27016	N	0.021360	T	0.02767	0.0083	N	0.04508	-0.205	0.33269	D	0.560762	B	0.02656	0.0	B	0.09377	0.004	T	0.44651	-0.9314	10	0.16896	T	0.51	-4.0831	6.8761	0.24147	0.0:0.1265:0.2543:0.6192	.	171	Q8WVM0	TFB1M_HUMAN	R	171	ENSP00000356134:Q171R	ENSP00000356134:Q171R	Q	-	2	0	TFB1M	155659813	1.000000	0.71417	0.996000	0.52242	0.885000	0.51271	1.722000	0.38042	-0.069000	0.12931	0.482000	0.46254	CAG	.	.		0.328	TFB1M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042809.1			C	155618121	T	C	155618121	3	2	350	1	0	0	0	0	1	0	0	0	15808	1580	55	2	544	2	TFB1M	6	155618121	Missense_Mutation	SNP	T	TCGA-UB-AA0V-01A-11D-A382-10	18427073	155618121	15496946	16	49253										
DTX2	113878	hgsc.bcm.edu	37	chr7	76132782	76132782	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	cctcctgcaaaaccatctatGgagagaagacggggacccag	11	12	1	2			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr7:76132782G>T	ENST00000324432.5	+	10	1939	c.1429G>T	c.(1429-1431)Gga>Tga	p.G477*	DTX2_ENST00000446820.2_Nonsense_Mutation_p.G430*|DTX2_ENST00000307569.8_Nonsense_Mutation_p.G430*|DTX2_ENST00000430490.2_Nonsense_Mutation_p.G477*|DTX2_ENST00000413936.2_Nonsense_Mutation_p.G477*|DTX2_ENST00000446600.1_Nonsense_Mutation_p.G386*	NM_020892.2	NP_065943.2	Q86UW9	DTX2_HUMAN	deltex 2, E3 ubiquitin ligase	477					Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(1)|skin(1)|stomach(2)	27						AACCATCTATGGAGAGAAGAC	0.572																																					p.G477X		Atlas-SNP	.											.	DTX2	64	.	0			c.G1429T						.						72	68	69					7																	76132782		2202	4297	6499	SO:0001587	stop_gained	113878	exon9			ATCTATGGAGAGA		CCDS5587.1, CCDS43605.1	7q11.23	2014-01-28	2014-01-28		ENSG00000091073	ENSG00000091073		"RING-type (C3HC4) zinc fingers"	15973	protein-coding gene	gene with protein product		613141	"deltex (Drosophila) homolog 2", "deltex homolog 2 (Drosophila)"			12670957	Standard	NM_020892		Approved	RNF58, KIAA1528	uc003ufh.4	Q86UW9	OTTHUMG00000162594	ENST00000324432.5:c.1429G>T	chr7.hg19:g.76132782G>T	ENSP00000322885:p.Gly477*	158.0	0.0		202.0	22.0	NM_001102594	Q6XM87|Q6XM88|Q96H69|Q9H890|Q9P200	Nonsense_Mutation	SNP	ENST00000324432.5	hg19	CCDS5587.1	.	.	.	.	.	.	.	.	.	.	.	41	8.707606	0.98922	.	.	ENSG00000091073	ENST00000324432;ENST00000307569;ENST00000541989;ENST00000446600;ENST00000413936;ENST00000430490;ENST00000446820	.	.	.	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-16.9077	18.9568	0.92661	0.0:0.0:1.0:0.0	.	.	.	.	X	477;430;386;386;477;477;430	.	ENSP00000305242:G430X	G	+	1	0	AC005522.1	75970718	1.000000	0.71417	0.995000	0.50966	0.707000	0.40811	9.823000	0.99369	2.725000	0.93324	0.655000	0.94253	GGA	.	.		0.572	DTX2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253104.2			T	76132782	G	T	76132782	4	4	350	1	0	0	0	0	0	1	0	0	4796	1349	47	3	1455	3	DTX2	7	76132782	Nonsense_Mutation	SNP	G	TCGA-UB-AA0V-01A-11D-A382-10		76132782	83005881	17	49254										
BSPRY	54836	hgsc.bcm.edu	37	chr9	116122865	116122865	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	tttgcgagagcgaggagcagCggttactggaacaggtgcat	16	7	0	1			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr9:116122865C>T	ENST00000374183.4	+	3	418	c.379C>T	c.(379-381)Cgg>Tgg	p.R127W	BSPRY_ENST00000462085.1_3'UTR	NM_017688.2	NP_060158.2	Q5W0U4	BSPRY_HUMAN	B-box and SPRY domain containing	127					calcium ion transport (GO:0006816)	cell leading edge (GO:0031252)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(1)|lung(4)|urinary_tract(1)	8						CGAGGAGCAGCGGTTACTGGA	0.582																																					p.R127W		Atlas-SNP	.											.	BSPRY	21	.	0			c.C379T						.						55	64	61					9																	116122865		2173	4281	6454	SO:0001583	missense	54836	exon3			GAGCAGCGGTTAC	AJ276691	CCDS43868.1	9q33.1	2008-02-05			ENSG00000119411	ENSG00000119411			18232	protein-coding gene	gene with protein product						10978534, 11099500	Standard	NM_017688		Approved	FLJ20150	uc004bhg.4	Q5W0U4	OTTHUMG00000021006	ENST00000374183.4:c.379C>T	chr9.hg19:g.116122865C>T	ENSP00000363298:p.Arg127Trp	91.0	0.0		66.0	7.0	NM_017688	B3KS19|Q96DJ2|Q9H4E4|Q9NXN0	Missense_Mutation	SNP	ENST00000374183.4	hg19	CCDS43868.1	.	.	.	.	.	.	.	.	.	.	C	19.28	3.797842	0.70567	.	.	ENSG00000119411	ENST00000374183	T	0.06371	3.31	5.84	0.296	0.15757	.	0.000000	0.85682	D	0.000000	T	0.15609	0.0376	L	0.36672	1.1	0.52099	D	0.999944	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.996	T	0.00293	-1.1841	10	0.72032	D	0.01	-9.6949	16.0697	0.80914	0.6051:0.3948:0.0:0.0	.	127;127	Q5W0U4-2;Q5W0U4	.;BSPRY_HUMAN	W	127	ENSP00000363298:R127W	ENSP00000363298:R127W	R	+	1	2	BSPRY	115162686	1.000000	0.71417	0.877000	0.34402	0.657000	0.38888	1.183000	0.32041	0.048000	0.15891	-0.188000	0.12872	CGG	.	.		0.582	BSPRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055399.1	NM_017688		T	116122865	C	T	116122865	3	4	350	1	0	0	0	0	1	0	0	0	1534	759	27	1	389	1	BSPRY	9	116122865	Missense_Mutation	SNP	C	TCGA-UB-AA0V-01A-11D-A382-10		116122865	25090566	18	49255										
CTNNA3	29119	hgsc.bcm.edu	37	chr10	69281647	69281647	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	caaattttccagctccttccCaagcttctggtaggttttct	6	12	2	0			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr10:69281647C>T	ENST00000433211.2	-	5	706	c.532G>A	c.(532-534)Ggg>Agg	p.G178R	CTNNA3_ENST00000373744.4_Missense_Mutation_p.G178R|CTNNA3_ENST00000545309.1_Missense_Mutation_p.G178R	NM_013266.2	NP_037398.2			catenin (cadherin-associated protein), alpha 3											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(1)|lung(50)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|stomach(1)|urinary_tract(1)	95						AGCTCCTTCCCAAGCTTCTGG	0.418																																					p.G178R		Atlas-SNP	.											.	CTNNA3	401	.	0			c.G532A						.						111	109	110					10																	69281647		2203	4300	6503	SO:0001583	missense	29119	exon5			CCTTCCCAAGCTT	AF091606	CCDS7269.1	10q21	2006-11-24			ENSG00000183230	ENSG00000183230			2511	protein-coding gene	gene with protein product		607667				12596047, 11590244	Standard	XM_005269717		Approved	VR22, MGC26194	uc001jmw.2	Q9UI47	OTTHUMG00000018334	ENST00000433211.2:c.532G>A	chr10.hg19:g.69281647C>T	ENSP00000389714:p.Gly178Arg	97.0	0.0		68.0	12.0	NM_013266		Missense_Mutation	SNP	ENST00000433211.2	hg19	CCDS7269.1	.	.	.	.	.	.	.	.	.	.	C	12.55	1.972476	0.34848	.	.	ENSG00000183230	ENST00000433211;ENST00000373744;ENST00000545309;ENST00000330298;ENST00000540598	T;T;T;T	0.39406	1.08;1.08;1.08;1.08	5.19	5.19	0.71726	.	0.255475	0.27640	N	0.018470	T	0.57344	0.2047	L	0.46819	1.47	0.42570	D	0.993174	D;D;B;D	0.89917	1.0;1.0;0.071;1.0	D;D;B;D	0.97110	1.0;1.0;0.073;0.999	T	0.58405	-0.7642	10	0.56958	D	0.05	-12.085	14.2164	0.65795	0.0:1.0:0.0:0.0	.	178;178;178;178	A8K141;F2Z2R0;Q9UI47-2;Q9UI47	.;.;.;CTNA3_HUMAN	R	178	ENSP00000389714:G178R;ENSP00000362849:G178R;ENSP00000441444:G178R;ENSP00000330570:G178R	ENSP00000330570:G178R	G	-	1	0	CTNNA3	68951653	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.261000	0.43276	2.430000	0.82344	0.467000	0.42956	GGG	.	.		0.418	CTNNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048282.2	NM_013266		T	69281647	C	T	69281647	3	4	350	1	0	0	0	0	1	0	0	0	4016	594	21	3	2211	3	CTNNA3	10	69281647	Missense_Mutation	SNP	C	TCGA-UB-AA0V-01A-11D-A382-10		69281647	66253100	19	49256										
MUC2	4583	hgsc.bcm.edu	37	chr11	1092613	1092618	+	In_Frame_Del	DEL	AGCCCT	AGCCCT	-													0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	gccctccaaccaccactcccAgccctccaaccaccactccc					rs201595190|rs201608750		TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	AGCCCT	AGCCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr11:1092613_1092618delAGCCCT	ENST00000441003.2	+	30	4459_4464	c.4432_4437delAGCCCT	c.(4432-4437)agccctdel	p.SP1478del	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_In_Frame_Del_p.SP1479del	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4213	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	caccactcccagccctccaaccacca	0.636																																					p.1477_1479del		Atlas-INDEL	.											.	MUC2	614	.	0			c.4431_4436del						.																																			SO:0001651	inframe_deletion	4583	exon30			.	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4432_4437delAGCCCT	chr11.hg19:g.1092613_1092618delAGCCCT	ENSP00000415183:p.Ser1478_Pro1479del	83.0	0.0		86.0	10.0	NM_002457	Q14878	In_Frame_Del	DEL	ENST00000441003.2	hg19																																																																																				.	.		0.636	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		-	1092618	AGCCCT	-	1092613	7	5	350	1	0	1	0	1	0	0	0	0	9984	188	7	0	4550	0	MUC2	11	1092613	In_Frame_Del	DEL	AGCCCT	TCGA-UB-AA0V-01A-11D-A382-10		1092613	133913903	20	49257										
MUC2	4583	hgsc.bcm.edu	37	chr11	1104063	1104063	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	ggtactcggccaaggcccagGccctggaccacagctgctcc	12	17	0	0			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr11:1104063G>A	ENST00000441003.2	+	49	8281	c.8254G>A	c.(8254-8256)Gcc>Acc	p.A2752T		NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	5114					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.A2752S(1)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	CAAGGCCCAGGCCCTGGACCA	0.682																																					p.A2748T		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	.	1	Substitution - Missense(1)	lung(1)	c.G8242A						.						16	20	19					11																	1104063		2031	4186	6217	SO:0001583	missense	4583	exon50			GCCCAGGCCCTGG	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.8254G>A	chr11.hg19:g.1104063G>A	ENSP00000415183:p.Ala2752Thr	122.0	0.0		99.0	21.0	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	hg19		.	.	.	.	.	.	.	.	.	.	G	0.676	-0.800040	0.02841	.	.	ENSG00000198788	ENST00000441003	T	0.11277	2.79	3.73	-5.78	0.02362	.	.	.	.	.	T	0.06188	0.0160	L	0.38953	1.18	0.09310	N	1	B	0.15930	0.015	B	0.09377	0.004	T	0.43893	-0.9363	9	0.12103	T	0.63	.	6.1504	0.20308	0.2051:0.0:0.4581:0.3368	.	2752	E7EUV1	.	T	2752	ENSP00000415183:A2752T	ENSP00000415183:A2752T	A	+	1	0	MUC2	1094063	0.000000	0.05858	0.004000	0.12327	0.026000	0.11368	-0.633000	0.05483	-1.827000	0.01204	-2.023000	0.00429	GCC	.	.		0.682	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		A	1104063	G	A	1104063	3	1	350	1	0	0	0	0	1	0	0	0	9984	1203	42	3	8440	3	MUC2	11	1104063	Missense_Mutation	SNP	G	TCGA-UB-AA0V-01A-11D-A382-10	11450	1104063	133902453	21	49258										
LUM	4060	hgsc.bcm.edu	37	chr12	91502234	91502234	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	tttaaaagcagctgaaacagCatcctctttcagccgattgt	7	10	2	1			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr12:91502234C>A	ENST00000266718.4	-	2	977	c.523G>T	c.(523-525)Gct>Tct	p.A175S	LUM_ENST00000548071.1_Intron	NM_002345.3	NP_002336.1	P51884	LUM_HUMAN	lumican	175					carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to growth factor (GO:0070848)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrillar collagen trimer (GO:0005583)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	24						GCTGAAACAGCATCCTCTTTC	0.448																																					p.A175S		Atlas-SNP	.											.	LUM	65	.	0			c.G523T						.						104	104	104					12																	91502234		2203	4300	6503	SO:0001583	missense	4060	exon2			AAACAGCATCCTC	BT006707	CCDS9038.1	12q21.33	2014-06-13			ENSG00000139329			"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	6724	protein-coding gene	gene with protein product	"lumican proteoglycan"	600616		LDC		7558030	Standard	NM_002345		Approved	SLRR2D	uc001tbm.3	P51884	OTTHUMG00000170074	ENST00000266718.4:c.523G>T	chr12.hg19:g.91502234C>A	ENSP00000266718:p.Ala175Ser	110.0	0.0		98.0	7.0	NM_002345	B2R6R5|Q96QM7	Missense_Mutation	SNP	ENST00000266718.4	hg19	CCDS9038.1	.	.	.	.	.	.	.	.	.	.	C	4.671	0.124668	0.08931	.	.	ENSG00000139329	ENST00000266718	T	0.58506	0.33	5.45	0.574	0.17368	.	0.468197	0.23836	N	0.044090	T	0.25457	0.0619	N	0.02973	-0.45	0.09310	N	1	B	0.12630	0.006	B	0.16722	0.016	T	0.13953	-1.0490	10	0.23891	T	0.37	-10.0698	4.7996	0.13290	0.2155:0.3543:0.0:0.4303	.	175	P51884	LUM_HUMAN	S	175	ENSP00000266718:A175S	ENSP00000266718:A175S	A	-	1	0	LUM	90026365	0.001000	0.12720	0.000000	0.03702	0.446000	0.32137	0.038000	0.13862	-0.166000	0.10890	-0.259000	0.10710	GCT	.	.		0.448	LUM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407150.2	NM_002345		A	91502234	C	A	91502234	3	1	350	1	0	0	0	0	1	0	0	0	9094	710	25	3	501	3	LUM	12	91502234	Missense_Mutation	SNP	C	TCGA-UB-AA0V-01A-11D-A382-10		91502234	42349661	22	49259										
DAOA	267012	hgsc.bcm.edu	37	chr13	106142224	106142224	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	ttacctttcacaagacctggCcaactgagaccggatctcct	7	14	2	2			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr13:106142224C>T	ENST00000375936.3	+	4	327				DAOA_ENST00000329625.5_Intron|DAOA-AS1_ENST00000448407.1_RNA	NM_001161812.1|NM_172370.3	NP_001155284.1|NP_758958.3	P59103	DAOA_HUMAN	D-amino acid oxidase activator						negative regulation of D-amino-acid oxidase activity (GO:1900758)|positive regulation of catalytic activity (GO:0043085)	Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)	enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|skin(1)	13	Lung NSC(43;0.01)|all_neural(89;0.0741)|Lung SC(71;0.14)|Medulloblastoma(90;0.169)					caagacctggccaactgagac	0.493																																					p.P58S		Atlas-SNP	.											.	DAOA	26	.	0			c.C172T						.						81	87	85					13																	106142224		2192	4295	6487	SO:0001627	intron_variant	267012	exon4			ACCTGGCCAACTG	AY138547	CCDS41905.1, CCDS53880.1, CCDS59242.1	13q33.2	2011-08-01			ENSG00000182346	ENSG00000182346			21191	protein-coding gene	gene with protein product	"G72 transcript"	607408				12364586, 15057823	Standard	NM_001161814		Approved	G72	uc010tjg.2	P59103	OTTHUMG00000041333	ENST00000375936.3:c.282-26C>T	chr13.hg19:g.106142224C>T		117.0	0.0		68.0	12.0	NM_001161812	A6NKG7|Q0VAE6|Q5VX59|Q86Y17|Q8IWM4	Missense_Mutation	SNP	ENST00000375936.3	hg19	CCDS41905.1																																																																																			.	.		0.493	DAOA-005	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000099040.2	NM_172370		T	106142224	C	T	106142224	1	4	350	0	1	0	0	0	0	0	0	0	4234	739	26	3		3	DAOA	13	106142224	Intron	SNP	C	TCGA-UB-AA0V-01A-11D-A382-10		106142224	9027654	23	49260										
C15orf2	23742	hgsc.bcm.edu	37	chr15	24923717	24923717	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	tccatctctcattccacactTggggccactgatgggcagca	9	14	2	1			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr15:24923717T>C	ENST00000329468.2	+	1	3177	c.2703T>C	c.(2701-2703)ctT>ctC	p.L901L		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	901					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											ATTCCACACTTGGGGCCACTG	0.502																																					p.L901L		Atlas-SNP	.											.	.	.	.	0			c.T2703C						.						126	134	131					15																	24923717		2203	4300	6503	SO:0001819	synonymous_variant	23742	exon1			CACACTTGGGGCC	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"chromosome 15 open reading frame 2"	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.2703T>C	chr15.hg19:g.24923717T>C		59.0	0.0		51.0	9.0	NM_018958		Silent	SNP	ENST00000329468.2	hg19	CCDS10015.1																																																																																			.	.		0.502	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		C	24923717	T	C	24923717	2	2	350	1	0	0	0	0	0	0	0	1	1786	1799	63	2		2	C15orf2	15	24923717	Silent	SNP	T	TCGA-UB-AA0V-01A-11D-A382-10		24923717	77607675	24	49261										
EPB42	2038	hgsc.bcm.edu	37	chr15	43507436	43507436	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	tccaggactgggcatctctcTcctccaccactgcactccac	6	19	2	0			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr15:43507436T>A	ENST00000441366.2	-	3	512	c.287A>T	c.(286-288)gAg>gTg	p.E96V	EPB42_ENST00000540029.1_Intron|EPB42_ENST00000300215.3_Missense_Mutation_p.E126V	NM_000119.2|NM_001114134.1	NP_000110.2|NP_001107606.1	P16452	EPB42_HUMAN	erythrocyte membrane protein band 4.2	96					cell morphogenesis (GO:0000902)|erythrocyte maturation (GO:0043249)|hemoglobin metabolic process (GO:0020027)|iron ion homeostasis (GO:0055072)|peptide cross-linking (GO:0018149)|regulation of cell shape (GO:0008360)|spleen development (GO:0048536)	cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)|structural constituent of cytoskeleton (GO:0005200)			endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.7e-07)		GGCATCTCTCTCCTCCACCAC	0.572																																					p.E126V		Atlas-SNP	.											.	EPB42	53	.	0			c.A377T						.						163	126	138					15																	43507436		2203	4299	6502	SO:0001583	missense	2038	exon3			TCTCTCTCCTCCA	M60298	CCDS10093.1, CCDS45249.1	15q15-q21	2013-05-02			ENSG00000166947	ENSG00000166947		"Transglutaminases"	3381	protein-coding gene	gene with protein product	"Erythrocyte surface protein band 4.2"	177070				1284644	Standard	NM_000119		Approved	PA, MGC116735, MGC116737	uc001zrb.4	P16452	OTTHUMG00000130701	ENST00000441366.2:c.287A>T	chr15.hg19:g.43507436T>A	ENSP00000396616:p.Glu96Val	98.0	0.0		100.0	6.0	NM_000119	Q4KKX0|Q4VB97	Missense_Mutation	SNP	ENST00000441366.2	hg19	CCDS45249.1	.	.	.	.	.	.	.	.	.	.	T	14.32	2.499570	0.44455	.	.	ENSG00000166947	ENST00000300215;ENST00000441366;ENST00000397027	D;D	0.85629	-2.01;-2.01	5.29	5.29	0.74685	Immunoglobulin E-set (1);Transglutaminase, N-terminal (1);Immunoglobulin-like fold (1);	0.411934	0.29594	N	0.011709	T	0.81187	0.4770	L	0.49640	1.575	0.38806	D	0.955304	B;B	0.34290	0.447;0.316	B;B	0.34385	0.153;0.181	T	0.82669	-0.0343	10	0.54805	T	0.06	-11.2564	11.5398	0.50659	0.0:0.0:0.0:1.0	.	126;96	P16452-2;P16452	.;EPB42_HUMAN	V	126;96;96	ENSP00000300215:E126V;ENSP00000396616:E96V	ENSP00000300215:E126V	E	-	2	0	EPB42	41294728	0.069000	0.21087	1.000000	0.80357	0.560000	0.35617	2.135000	0.42112	2.228000	0.72767	0.533000	0.62120	GAG	.	.		0.572	EPB42-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432219.1	NM_000119		A	43507436	T	A	43507436	3	1	350	1	0	0	0	0	1	0	0	0	5160	1551	54	4	1832	4	EPB42	15	43507436	Missense_Mutation	SNP	T	TCGA-UB-AA0V-01A-11D-A382-10	18583719	43507436	59023956	25	49262										
TRAF7	84231	hgsc.bcm.edu	37	chr16	2221291	2221291	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	ctggtgtttgcggagcagccCtcggtgaagctgtgctgtca	15	10	1	1			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr16:2221291C>G	ENST00000326181.6	+	6	507	c.375C>G	c.(373-375)ccC>ccG	p.P125P		NM_032271.2	NP_115647.2	Q6Q0C0	TRAF7_HUMAN	TNF receptor-associated factor 7, E3 ubiquitin protein ligase	125					activation of MAPKKK activity (GO:0000185)|apoptotic process (GO:0006915)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of MAPK cascade (GO:0043410)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic vesicle (GO:0031410)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	23						CGGAGCAGCCCTCGGTGAAGC	0.687																																					p.P125P		Atlas-SNP	.											.	TRAF7	158	.	0			c.C375G						.						24	19	21					16																	2221291		2164	4249	6413	SO:0001819	synonymous_variant	84231	exon6			GCAGCCCTCGGTG	AL136921	CCDS10461.1	16p13.3	2013-01-10	2012-02-23	2004-06-04	ENSG00000131653	ENSG00000131653		"RING-type (C3HC4) zinc fingers", "WD repeat domain containing"	20456	protein-coding gene	gene with protein product		606692	"ring finger and WD repeat domain 1", "TNF receptor-associated factor 7"	RFWD1		11230166, 15001576	Standard	NM_032271		Approved	RNF119, DKFZp586I021, MGC7807	uc002cow.3	Q6Q0C0	OTTHUMG00000128826	ENST00000326181.6:c.375C>G	chr16.hg19:g.2221291C>G		45.0	0.0		32.0	6.0	NM_032271	Q9H073	Silent	SNP	ENST00000326181.6	hg19	CCDS10461.1																																																																																			.	.		0.687	TRAF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250762.1	NM_032271		G	2221291	C	G	2221291	2	3	350	1	0	0	0	0	0	0	0	1	16461	668	24	4		4	TRAF7	16	2221291	Silent	SNP	C	TCGA-UB-AA0V-01A-11D-A382-10		2221291	88133462	26	49263										
ERCC4	2072	hgsc.bcm.edu	37	chr16	14016042	14016042	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	tgtggttgacttcttgactgAtagaataccttcagatttaa	8	6	2	5			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr16:14016042A>G	ENST00000311895.7	+	2	371	c.362A>G	c.(361-363)gAt>gGt	p.D121G	ERCC4_ENST00000575156.1_Missense_Mutation_p.D121G	NM_005236.2	NP_005227.1	Q92889	XPF_HUMAN	excision repair cross-complementation group 4	121	Helicase-like.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|negative regulation of telomere maintenance (GO:0032205)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair involved in interstrand cross-link repair (GO:1901255)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|nucleotide-excision repair, DNA incision, 5'-to lesion (GO:0006296)|resolution of meiotic recombination intermediates (GO:0000712)|response to UV (GO:0009411)|telomere maintenance (GO:0000723)|telomere maintenance via telomere shortening (GO:0010834)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	chromosome, telomeric region (GO:0000781)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleotide-excision repair factor 1 complex (GO:0000110)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	damaged DNA binding (GO:0003684)|endodeoxyribonuclease activity (GO:0004520)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(5)|lung(12)|ovary(4)|pancreas(1)|prostate(1)|skin(3)	38						TTCTTGACTGATAGAATACCT	0.289			"Mis, N, F"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.D121G		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (F)	16	16p13.3-p13.13	2072	"excision repair cross-complementing rodent repair deficiency, complementation group 4"		E	.	ERCC4	100	.	0			c.A362G						.						58	48	51					16																	14016042		2197	4300	6497	SO:0001583	missense	2072	exon2	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	TGACTGATAGAAT	L76568	CCDS32390.1	16p13.3	2014-09-17	2014-03-07		ENSG00000175595	ENSG00000175595			3436	protein-coding gene	gene with protein product	"xeroderma pigmentosum, complementation group F"	133520	"excision repair cross-complementing rodent repair deficiency, complementation group 4"	XPF		9579555, 8887684	Standard	NM_005236		Approved	RAD1, FANCQ	uc002dce.2	Q92889	OTTHUMG00000048194	ENST00000311895.7:c.362A>G	chr16.hg19:g.14016042A>G	ENSP00000310520:p.Asp121Gly	90.0	0.0		79.0	12.0	NM_005236	A5PKV6|A8K111|O00140|Q8TD83	Missense_Mutation	SNP	ENST00000311895.7	hg19	CCDS32390.1	.	.	.	.	.	.	.	.	.	.	A	13.50	2.255417	0.39896	.	.	ENSG00000175595	ENST00000311895;ENST00000439007;ENST00000389138	T	0.57595	0.39	5.33	4.24	0.50183	.	0.187561	0.56097	N	0.000038	T	0.32346	0.0826	N	0.13352	0.335	0.46241	D	0.998949	B;B	0.12630	0.006;0.002	B;B	0.13407	0.009;0.003	T	0.06661	-1.0814	10	0.21540	T	0.41	-18.006	9.6103	0.39659	0.9164:0.0:0.0835:0.0	.	121;121	A5PKV6;Q92889	.;XPF_HUMAN	G	121;110;110	ENSP00000310520:D121G	ENSP00000310520:D121G	D	+	2	0	ERCC4	13923543	1.000000	0.71417	0.093000	0.20910	0.813000	0.45954	7.073000	0.76784	0.864000	0.35578	0.533000	0.62120	GAT	.	.		0.289	ERCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109634.2	NM_005236		G	14016042	A	G	14016042	3	3	350	1	0	0	0	0	1	0	0	0	5217	333	12	2	368	2	ERCC4	16	14016042	Missense_Mutation	SNP	A	TCGA-UB-AA0V-01A-11D-A382-10	11794751	14016042	76338711	27	49264										
EIF4A1	1973	hgsc.bcm.edu	37	chr17	7477593	7477593	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	aacagatccagagacaatggCcccgatgggatggagcccga	13	11	0	2			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr17:7477593C>G	ENST00000293831.8	+	2	55	c.39C>G	c.(37-39)ggC>ggG	p.G13G	EIF4A1_ENST00000577269.1_Silent_p.G13G|SENP3-EIF4A1_ENST00000579777.1_RNA|EIF4A1_ENST00000380512.5_5'UTR|SNORA48_ENST00000386847.1_RNA|EIF4A1_ENST00000582746.1_Silent_p.G13G|SNORD10_ENST00000459579.1_RNA	NM_001416.3	NP_001407.1	P60842	IF4A1_HUMAN	eukaryotic translation initiation factor 4A1	13					cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|organ regeneration (GO:0031100)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			NS(1)|breast(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(8)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	22						GAGACAATGGCCCCGATGGGA	0.532																																					p.G13G	Melanoma(120;278 1668 15796 27423 46368)	Atlas-SNP	.											.	EIF4A1	38	.	0			c.C39G						.						71	68	69					17																	7477593		2203	4300	6503	SO:0001819	synonymous_variant	1973	exon2			CAATGGCCCCGAT	D13748	CCDS11113.1, CCDS58511.1	17p13	2012-02-23	2010-02-10		ENSG00000161960	ENSG00000161960		"DEAD-boxes"	3282	protein-coding gene	gene with protein product		602641	"eukaryotic translation initiation factor 4A, isoform 1"	EIF4A		8493113, 9790779	Standard	NM_001416		Approved	DDX2A, EIF-4A		P60842	OTTHUMG00000108149	ENST00000293831.8:c.39C>G	chr17.hg19:g.7477593C>G		106.0	0.0		72.0	11.0	NM_001416	B2R6L8|D3DTP9|J3QLC4|P04765|Q5U018|Q61516	Silent	SNP	ENST00000293831.8	hg19	CCDS11113.1																																																																																			.	.		0.532	EIF4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226952.6	NM_001416		G	7477593	C	G	7477593	2	3	350	1	0	0	0	0	0	0	0	1	5026	726	26	4		4	EIF4A1	17	7477593	Silent	SNP	C	TCGA-UB-AA0V-01A-11D-A382-10		7477593	73717617	28	49265										
GAS2L2	246176	hgsc.bcm.edu	37	chr17	34073120	34073120	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	cagcctgaggcccaggcactCggctgggccaaaggaacgag	15	13	0	1	rs139624793	byFrequency	TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr17:34073120C>A	ENST00000254466.6	-	6	1423	c.1396G>T	c.(1396-1398)Gag>Tag	p.E466*	GAS2L2_ENST00000587565.1_Nonsense_Mutation_p.E450*	NM_139285.3	NP_644814.1	Q8NHY3	GA2L2_HUMAN	growth arrest-specific 2 like 2	466					cell cycle arrest (GO:0007050)|microtubule bundle formation (GO:0001578)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	actin filament binding (GO:0051015)|cytoskeletal adaptor activity (GO:0008093)|microtubule binding (GO:0008017)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CCCAGGCACTCGGCTGGGCCA	0.622																																					p.E466X		Atlas-SNP	.											.	GAS2L2	94	.	0			c.G1396T						.						94	107	103					17																	34073120		2203	4300	6503	SO:0001587	stop_gained	246176	exon6			GGCACTCGGCTGG	AF508784	CCDS11298.1	17q21	2014-05-06			ENSG00000132139	ENSG00000270765			24846	protein-coding gene	gene with protein product		611398				12584248	Standard	NM_139285		Approved	GAR17	uc002hjv.2	Q8NHY3	OTTHUMG00000188386	ENST00000254466.6:c.1396G>T	chr17.hg19:g.34073120C>A	ENSP00000254466:p.Glu466*	100.0	0.0		100.0	16.0	NM_139285	Q8NHY4	Nonsense_Mutation	SNP	ENST00000254466.6	hg19	CCDS11298.1	.	.	.	.	.	.	.	.	.	.	C	15.46	2.839368	0.51057	.	.	ENSG00000132139	ENST00000254466	.	.	.	4.92	1.16	0.20824	.	4.932270	0.00166	N	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.9581	4.4245	0.11497	0.0:0.1775:0.3302:0.4923	.	.	.	.	X	466	.	ENSP00000254466:E466X	E	-	1	0	GAS2L2	31097233	0.000000	0.05858	0.047000	0.18901	0.062000	0.15995	-0.099000	0.11007	0.026000	0.15269	-0.290000	0.09829	GAG	.	C|0.997;T|0.003		0.622	GAS2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256497.1	NM_139285		A	34073120	C	A	34073120	4	1	350	1	0	0	0	0	0	1	0	0	6255	893	31	1	1250	1	GAS2L2	17	34073120	Nonsense_Mutation	SNP	C	TCGA-UB-AA0V-01A-11D-A382-10	26595527	34073120	47122090	29	49266										
PIP4K2B	8396	hgsc.bcm.edu	37	chr17	36935649	36935649	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	cctttaccttgaggtcatacTtgcgatgcacagtgagccga	10	11	1	2			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr17:36935649T>G	ENST00000269554.3	-	5	1121	c.641A>C	c.(640-642)aAg>aCg	p.K214T	PIP4K2B_ENST00000311500.6_5'UTR	NM_003559.4	NP_003550.1	P78356	PI42B_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, beta	214	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				cell surface receptor signaling pathway (GO:0007166)|intracellular signal transduction (GO:0035556)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|1-phosphatidylinositol-5-phosphate 4-kinase activity (GO:0016309)|ATP binding (GO:0005524)|receptor signaling protein activity (GO:0005057)			endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(8)|ovary(1)	19						GAGGTCATACTTGCGATGCAC	0.557																																					p.K214T		Atlas-SNP	.											.	PIP4K2B	35	.	0			c.A641C						.						174	143	154					17																	36935649		2203	4300	6503	SO:0001583	missense	8396	exon5			TCATACTTGCGAT	U85245	CCDS11329.1	17q21.2	2007-08-14	2007-08-14	2007-08-14		ENSG00000276293	2.7.1.149		8998	protein-coding gene	gene with protein product		603261	"phosphatidylinositol-4-phosphate 5-kinase, type II, beta"	PIP5K2B		9038203, 14691457, 9367159	Standard	NM_003559		Approved	PIP5KIIB, PIP5KIIbeta	uc002hqs.3	P78356		ENST00000269554.3:c.641A>C	chr17.hg19:g.36935649T>G	ENSP00000269554:p.Lys214Thr	98.0	0.0		74.0	13.0	NM_003559	Q5U0E8|Q8TBP2	Missense_Mutation	SNP	ENST00000269554.3	hg19	CCDS11329.1	.	.	.	.	.	.	.	.	.	.	T	28.8	4.952131	0.92660	.	.	ENSG00000141720	ENST00000269554;ENST00000311500	T	0.32023	1.47	5.1	5.1	0.69264	Phosphatidylinositol-4-phosphate 5-kinase, core (2);Phosphatidylinositol-4-phosphate 5-kinase, core, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.50309	0.1608	M	0.65320	2	0.80722	D	1	D;D;D	0.76494	0.997;0.999;0.998	D;D;D	0.78314	0.988;0.98;0.991	T	0.41752	-0.9491	10	0.28530	T	0.3	-22.5609	13.8398	0.63432	0.0:0.0:0.0:1.0	.	214;214;214	C9JMM2;P78356-2;P78356	.;.;PI42B_HUMAN	T	214	ENSP00000269554:K214T	ENSP00000269554:K214T	K	-	2	0	PIP4K2B	34189175	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.522000	0.81844	2.139000	0.66308	0.533000	0.62120	AAG	.	.		0.557	PIP4K2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256791.1	NM_003559		G	36935649	T	G	36935649	3	3	350	1	0	0	0	0	1	0	0	0	11946	1609	56	5	633	5	PIP4K2B	17	36935649	Missense_Mutation	SNP	T	TCGA-UB-AA0V-01A-11D-A382-10	2862529	36935649	44259561	30	49267										
KAT2A	2648	hgsc.bcm.edu	37	chr17	40269500	40269500	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	cacgagccacagcaacacccGccggttggccttgggcgtca	12	16	1	0			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr17:40269500G>A	ENST00000225916.5	-	10	1596	c.1543C>T	c.(1543-1545)Cgg>Tgg	p.R515W		NM_021078.2	NP_066564.2	Q92830	KAT2A_HUMAN	K(lysine) acetyltransferase 2A	515	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				cell proliferation (GO:0008283)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|histone deubiquitination (GO:0016578)|histone H3 acetylation (GO:0043966)|histone H3-K14 acetylation (GO:0044154)|in utero embryonic development (GO:0001701)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|positive regulation of gluconeogenesis (GO:0045722)|regulation of protein stability (GO:0031647)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|somitogenesis (GO:0001756)|telencephalon development (GO:0021537)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|extracellular space (GO:0005615)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|STAGA complex (GO:0030914)|transcription factor TFTC complex (GO:0033276)	chromatin binding (GO:0003682)|H3 histone acetyltransferase activity (GO:0010484)|histone acetyltransferase activity (GO:0004402)|histone acetyltransferase activity (H4-K12 specific) (GO:0043997)|histone deacetylase binding (GO:0042826)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						AGCAACACCCGCCGGTTGGCC	0.642																																					p.R515W		Atlas-SNP	.											.	KAT2A	54	.	0			c.C1543T						.						26	25	25					17																	40269500		2182	4276	6458	SO:0001583	missense	2648	exon10			ACACCCGCCGGTT	AF029777	CCDS11417.1	17q12-q21	2011-07-01	2008-07-04	2008-07-04	ENSG00000108773	ENSG00000108773		"Chromatin-modifying enzymes / K-acetyltransferases"	4201	protein-coding gene	gene with protein product		602301	"GCN5 general control of amino-acid synthesis 5-like 2 (yeast)"	GCN5L2		8552087	Standard	NM_021078		Approved	GCN5, PCAF-b	uc002hyx.2	Q92830	OTTHUMG00000133504	ENST00000225916.5:c.1543C>T	chr17.hg19:g.40269500G>A	ENSP00000225916:p.Arg515Trp	174.0	0.0		134.0	8.0	NM_021078	Q8N1A2|Q9UCW1	Missense_Mutation	SNP	ENST00000225916.5	hg19	CCDS11417.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.257103	0.80246	.	.	ENSG00000108773	ENST00000225916	T	0.05258	3.47	4.8	3.81	0.43845	GCN5-related N-acetyltransferase (GNAT) domain (1);Acyl-CoA N-acyltransferase (2);	0.132557	0.51477	D	0.000095	T	0.11965	0.0291	L	0.50333	1.59	0.47214	D	0.999354	D	0.76494	0.999	P	0.51355	0.667	T	0.01334	-1.1382	10	0.87932	D	0	-19.9842	11.7634	0.51916	0.0:0.0:0.5065:0.4935	.	515	Q92830	KAT2A_HUMAN	W	515	ENSP00000225916:R515W	ENSP00000225916:R515W	R	-	1	2	KAT2A	37523026	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.053000	0.57427	0.997000	0.38969	0.561000	0.74099	CGG	.	.		0.642	KAT2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257458.1	NM_021078		A	40269500	G	A	40269500	3	1	350	1	0	0	0	0	1	0	0	0	7990	1086	38	1	1006	1	KAT2A	17	40269500	Missense_Mutation	SNP	G	TCGA-UB-AA0V-01A-11D-A382-10	3333851	40269500	40925710	31	49268										
KDM4B	23030	hgsc.bcm.edu	37	chr19	5047661	5047661	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	acagcatcaactacctgcacTttggggagcctaagtcctgg	10	12	1	0			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr19:5047661T>G	ENST00000159111.4	+	6	825	c.607T>G	c.(607-609)Ttt>Gtt	p.F203V	KDM4B_ENST00000536461.1_Missense_Mutation_p.F203V|KDM4B_ENST00000592175.1_3'UTR|KDM4B_ENST00000381759.4_Missense_Mutation_p.F203V	NM_015015.2	NP_055830	O94953	KDM4B_HUMAN	lysine (K)-specific demethylase 4B	203	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(1)|liver(1)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32						CTACCTGCACTTTGGGGAGCC	0.642																																					p.F203V		Atlas-SNP	.											.	KDM4B	120	.	0			c.T607G						.						232	158	183					19																	5047661		2203	4300	6503	SO:0001583	missense	23030	exon6			CTGCACTTTGGGG	AB020683	CCDS12138.1	19p13.3	2013-01-23	2009-04-06	2009-04-06		ENSG00000127663		"Chromatin-modifying enzymes / K-demethylases", "Tudor domain containing"	29136	protein-coding gene	gene with protein product	"tudor domain containing 14B"	609765	"jumonji domain containing 2B"	JMJD2B		10048485, 15138608	Standard	NM_015015		Approved	KIAA0876, TDRD14B	uc002mbq.4	O94953		ENST00000159111.4:c.607T>G	chr19.hg19:g.5047661T>G	ENSP00000159111:p.Phe203Val	68.0	0.0		72.0	5.0	NM_015015	B9EGN8|D6W631|O75274|Q6P3R5|Q9P1V1|Q9UF40	Missense_Mutation	SNP	ENST00000159111.4	hg19	CCDS12138.1	.	.	.	.	.	.	.	.	.	.	T	25.1	4.606350	0.87157	.	.	ENSG00000127663	ENST00000159111;ENST00000381759;ENST00000536461	T;T;T	0.72394	-0.65;-0.65;-0.65	4.32	4.32	0.51571	Transcription factor jumonji/aspartyl beta-hydroxylase (2);Transcription factor jumonji (1);	0.000000	0.85682	D	0.000000	D	0.83653	0.5301	M	0.83118	2.625	0.80722	D	1	B;D;P	0.62365	0.376;0.991;0.753	B;D;P	0.68943	0.328;0.961;0.696	D	0.86435	0.1763	10	0.72032	D	0.01	-26.1242	13.6209	0.62136	0.0:0.0:0.0:1.0	.	203;203;203	F5GX28;O94953-2;O94953	.;.;KDM4B_HUMAN	V	203	ENSP00000159111:F203V;ENSP00000371178:F203V;ENSP00000440495:F203V	ENSP00000159111:F203V	F	+	1	0	KDM4B	4998661	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	7.779000	0.85648	1.803000	0.52742	0.533000	0.62120	TTT	.	.		0.642	KDM4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450558.1	NM_015015		G	5047661	T	G	5047661	3	3	350	1	0	0	0	0	1	0	0	0	8138	1609	56	5	621	5	KDM4B	19	5047661	Missense_Mutation	SNP	T	TCGA-UB-AA0V-01A-11D-A382-10		5047661	54081322	32	49269										
LONP1	257062	hgsc.bcm.edu	37	chr19	5719823	5719823	+	5'Flank	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	ggcgtgagcgccgttatgacCgggccttccccggcgcccgc	15	17	0	2			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr19:5719823C>T	ENST00000381624.3	+	0	0				LONP1_ENST00000360614.3_Silent_p.P107P|CATSPERD_ENST00000381614.2_5'Flank|LONP1_ENST00000590729.1_5'UTR|LONP1_ENST00000593119.1_Silent_p.P43P|LONP1_ENST00000585374.1_5'UTR|LONP1_ENST00000540670.2_Intron|LONP1_ENST00000590511.1_5'UTR	NM_152784.3	NP_689997.3	Q86XM0	CTSRD_HUMAN	catsper channel auxiliary subunit delta						multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)											CCGTTATGACCGGGCCTTccc	0.726																																					p.F107L		Atlas-SNP	.											.	LONP1	66	.	0			c.T321A						.						24	28	26					19																	5719823		2203	4299	6502	SO:0001631	upstream_gene_variant	9361	exon1			TATGACCGGGCCT	BC043005	CCDS12149.2	19p13.3	2013-10-11	2012-02-22	2012-02-22	ENSG00000174898	ENSG00000174898			28598	protein-coding gene	gene with protein product			"transmembrane protein 146"	TMEM146		21224844	Standard	NM_152784		Approved	MGC39581	uc002mda.3	Q86XM0	OTTHUMG00000143036		chr19.hg19:g.5719823C>T	Exception_encountered	116.0	0.0		90.0	11.0	NM_004793	Q6ZRP1	Missense_Mutation	SNP	ENST00000381624.3	hg19	CCDS12149.2																																																																																			.	.		0.726	CATSPERD-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286953.2	NM_152784		T	5719823	C	T	5719823	1	4	350	0	1	0	0	0	0	0	0	0	8901	639	23	1		1	LONP1	19	5719823	5'Flank	SNP	C	TCGA-UB-AA0V-01A-11D-A382-10	672162	5719823	53409160	33	49270										
UPF1	5976	hgsc.bcm.edu	37	chr19	18965500	18965500	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	ccaggtggattttgtgtggaAgtcgacctcctttgacaggt	13	8	0	1			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr19:18965500A>G	ENST00000599848.1	+	9	1489	c.1280A>G	c.(1279-1281)aAg>aGg	p.K427R	UPF1_ENST00000262803.5_Missense_Mutation_p.K416R			Q92900	RENT1_HUMAN	UPF1 regulator of nonsense transcripts homolog (yeast)	427					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|dosage compensation by inactivation of X chromosome (GO:0009048)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translational termination (GO:0006449)|RNA metabolic process (GO:0016070)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	40						TTTGTGTGGAAGTCGACCTCC	0.562																																					p.K416R		Atlas-SNP	.											.	UPF1	88	.	0			c.A1247G						.						171	154	160					19																	18965500		2203	4300	6503	SO:0001583	missense	5976	exon9			TGTGGAAGTCGAC	AF074016	CCDS12386.1, CCDS74315.1	19p13.2-p13.11	2012-02-29	2006-02-07	2006-02-07	ENSG00000005007	ENSG00000005007			9962	protein-coding gene	gene with protein product	"UP Frameshift 1", "smg-2 homolog, nonsense mediated mRNA decay factor (C. elegans)"	601430	"regulator of nonsense transcripts 1"	RENT1		8855285, 9064659	Standard	XM_005260015		Approved	HUPF1, KIAA0221, NORF1, pNORF1, smg-2	uc002nkf.3	Q92900		ENST00000599848.1:c.1280A>G	chr19.hg19:g.18965500A>G	ENSP00000470142:p.Lys427Arg	90.0	0.0		92.0	10.0	NM_002911	O00239|O43343|Q86Z25|Q92842	Missense_Mutation	SNP	ENST00000599848.1	hg19		.	.	.	.	.	.	.	.	.	.	A	17.54	3.415892	0.62511	.	.	ENSG00000005007	ENST00000262803	D	0.90955	-2.76	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	D	0.89674	0.6783	M	0.69248	2.105	0.80722	D	1	B;B	0.24317	0.061;0.101	B;B	0.27887	0.084;0.083	D	0.88140	0.2844	10	0.62326	D	0.03	-41.0483	13.8928	0.63750	1.0:0.0:0.0:0.0	.	427;416	Q92900;Q92900-2	RENT1_HUMAN;.	R	416	ENSP00000262803:K416R	ENSP00000262803:K416R	K	+	2	0	UPF1	18826500	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	8.925000	0.92832	1.896000	0.54893	0.533000	0.62120	AAG	.	.		0.562	UPF1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000464684.1	NM_002911		G	18965500	A	G	18965500	3	3	350	1	0	0	0	0	1	0	0	0	17018	72	3	2	1281	2	UPF1	19	18965500	Missense_Mutation	SNP	A	TCGA-UB-AA0V-01A-11D-A382-10	13245677	18965500	40163483	34	49271										
ZNF611	81856	hgsc.bcm.edu	37	chr19	53209500	53209500	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	gcatgcaaggtattgctcgtGattaaagagcttgccacata	10	8	0	2			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chr19:53209500G>A	ENST00000319783.1	-	7	1124	c.808C>T	c.(808-810)Cac>Tac	p.H270Y	ZNF611_ENST00000602162.1_Missense_Mutation_p.H201Y|ZNF611_ENST00000595798.1_Missense_Mutation_p.H201Y|ZNF611_ENST00000540744.1_Missense_Mutation_p.H270Y|ZNF611_ENST00000602046.1_5'Flank|ZNF611_ENST00000453741.2_Missense_Mutation_p.H201Y|ZNF611_ENST00000543227.1_Missense_Mutation_p.H270Y	NM_030972.3	NP_112234.3	Q8N823	ZN611_HUMAN	zinc finger protein 611	270					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.H270Y(1)		breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(262;0.0233)|GBM - Glioblastoma multiforme(134;0.04)		TATTGCTCGTGATTAAAGAGC	0.413																																					p.H270Y		Atlas-SNP	.											ZNF611,NS,carcinoma,0,1	ZNF611	72	.	1	Substitution - Missense(1)	kidney(1)	c.C808T						.						182	178	179					19																	53209500		2203	4300	6503	SO:0001583	missense	81856	exon7			GCTCGTGATTAAA	AK091389	CCDS12855.1, CCDS54312.1	19q13.42	2013-01-08			ENSG00000213020	ENSG00000213020		"Zinc fingers, C2H2-type", "-"	28766	protein-coding gene	gene with protein product						12477932	Standard	NM_030972		Approved	MGC5384	uc010ydq.2	Q8N823	OTTHUMG00000154908	ENST00000319783.1:c.808C>T	chr19.hg19:g.53209500G>A	ENSP00000322427:p.His270Tyr	133.0	0.0		134.0	19.0	NM_030972	B3KRD5|Q69YG9	Missense_Mutation	SNP	ENST00000319783.1	hg19	CCDS12855.1	.	.	.	.	.	.	.	.	.	.	.	1.672	-0.508772	0.04231	.	.	ENSG00000213020	ENST00000543227;ENST00000540744;ENST00000453741;ENST00000319783	T;T;T;T	0.06528	3.29;3.29;3.29;3.29	1.2	-2.4	0.06583	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04407	0.0121	N	0.25380	0.74	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.38156	-0.9674	9	0.41790	T	0.15	.	6.1684	0.20404	0.6045:0.0:0.3955:0.0	.	270	Q8N823	ZN611_HUMAN	Y	270;270;201;270	ENSP00000437616:H270Y;ENSP00000439211:H270Y;ENSP00000443505:H201Y;ENSP00000322427:H270Y	ENSP00000322427:H270Y	H	-	1	0	ZNF611	57901312	.	.	0.000000	0.03702	0.000000	0.00434	.	.	-1.461000	0.01909	-2.696000	0.00138	CAC	.	.		0.413	ZNF611-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337612.1	NM_030972		A	53209500	G	A	53209500	3	1	350	1	0	0	0	0	1	0	0	0	18052	1290	45	3	1313	3	ZNF611	19	53209500	Missense_Mutation	SNP	G	TCGA-UB-AA0V-01A-11D-A382-10	34244000	53209500	5919483	35	49272										
MXRA5	25878	hgsc.bcm.edu	37	chrX	3235500	3235500	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	cagcgcacgctgggcaggggCgcagccttggcagtgcagtg	18	12	0	0			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chrX:3235500C>A	ENST00000217939.6	-	6	6376	c.6222G>T	c.(6220-6222)gcG>gcT	p.A2074A		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	2074	Ig-like C2-type 5.					extracellular vesicular exosome (GO:0070062)		p.A2074A(2)		NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				TGGGCAGGGGCGCAGCCTTGG	0.647																																					p.A2074A		Atlas-SNP	.											.	MXRA5	815	.	2	Substitution - coding silent(2)	lung(2)	c.G6222T						.						27	23	24					X																	3235500		2181	4278	6459	SO:0001819	synonymous_variant	25878	exon6			CAGGGGCGCAGCC	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7539	protein-coding gene	gene with protein product	"adlican"					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.6222G>T	chrX.hg19:g.3235500C>A		152.0	0.0		97.0	8.0	NM_015419	Q6P1M7|Q9Y3Y8	Silent	SNP	ENST00000217939.6	hg19	CCDS14124.1																																																																																			.	.		0.647	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		A	3235500	C	A	3235500	2	1	350	1	0	0	0	0	0	0	0	1	10012	755	27	1		1	MXRA5	23	3235500	Silent	SNP	C	TCGA-UB-AA0V-01A-11D-A382-10		3235500	152035060	36	49273										
CDKL5	6792	hgsc.bcm.edu	37	chrX	18627641	18627641	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	acagcccccaaagaaaatagAcacctatacaatgatcctgt	5	12	0	3			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chrX:18627641A>G	ENST00000379989.3	+	15	2388	c.2103A>G	c.(2101-2103)agA>agG	p.R701R	CDKL5_ENST00000379996.3_Silent_p.R701R|CDKL5_ENST00000463994.1_3'UTR	NM_001037343.1	NP_001032420.1	O76039	CDKL5_HUMAN	cyclin-dependent kinase-like 5	701					neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of Rac GTPase activity (GO:0032855)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite development (GO:0050773)	cytoplasm (GO:0005737)|dendrite cytoplasm (GO:0032839)|dendritic growth cone (GO:0044294)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rac GTPase binding (GO:0048365)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(4)|skin(5)|stomach(1)	44	Hepatocellular(33;0.183)					AAGAAAATAGACACCTATACA	0.478																																					p.R701R		Atlas-SNP	.											.	CDKL5	124	.	0			c.A2103G						.						142	124	130					X																	18627641		2203	4300	6503	SO:0001819	synonymous_variant	6792	exon14			AAATAGACACCTA	Y15057	CCDS14186.1	Xp22	2011-11-04	2002-11-26	2002-11-29	ENSG00000008086	ENSG00000008086		"Cyclin-dependent kinases"	11411	protein-coding gene	gene with protein product		300203	"serine/threonine kinase 9"	STK9		9721213, 16935860	Standard	XM_005274584		Approved	EIEE2	uc004cym.3	O76039	OTTHUMG00000021214	ENST00000379989.3:c.2103A>G	chrX.hg19:g.18627641A>G		212.0	0.0		180.0	9.0	NM_003159	G9B9X4|Q14198|Q5H985|Q8IYC7|Q9UJL6	Silent	SNP	ENST00000379989.3	hg19	CCDS14186.1																																																																																			.	.		0.478	CDKL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055945.2	NM_003159		G	18627641	A	G	18627641	2	3	350	1	0	0	0	0	0	0	0	1	3159	272	10	2		2	CDKL5	23	18627641	Silent	SNP	A	TCGA-UB-AA0V-01A-11D-A382-10	15392141	18627641	136642919	37	49274										
EDA2R	60401	hgsc.bcm.edu	37	chrX	65822603	65822603	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	cctcctgagggggcactgtgGgtgtatctgcctccactaag	13	12	1	1			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chrX:65822603G>T	ENST00000374719.3	-	5	445	c.389C>A	c.(388-390)cCc>cAc	p.P130H	EDA2R_ENST00000253392.5_Missense_Mutation_p.P130H|EDA2R_ENST00000451436.2_Silent_p.T36T|EDA2R_ENST00000450752.1_Missense_Mutation_p.P130H|EDA2R_ENST00000396050.1_Missense_Mutation_p.P130H|EDA2R_ENST00000456230.2_Missense_Mutation_p.P130H	NM_021783.3	NP_068555	Q9HAV5	TNR27_HUMAN	ectodysplasin A2 receptor	130					cell differentiation (GO:0030154)|embryo development (GO:0009790)|epidermis development (GO:0008544)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|tumor necrosis factor-activated receptor activity (GO:0005031)			breast(1)|endometrium(2)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	13						GGGCACTGTGGGTGTATCTGC	0.557																																					p.P130H		Atlas-SNP	.											.	EDA2R	30	.	0			c.C389A						.						49	33	39					X																	65822603		2203	4298	6501	SO:0001583	missense	60401	exon4			ACTGTGGGTGTAT	AF298812	CCDS14386.1, CCDS56603.1	Xq11.1	2013-05-22			ENSG00000131080	ENSG00000131080		"Tumor necrosis factor receptor superfamily"	17756	protein-coding gene	gene with protein product		300276				11039935	Standard	NM_021783		Approved	XEDAR, EDA-A2R, EDAA2R, TNFRSF27	uc004dwt.2	Q9HAV5	OTTHUMG00000021736	ENST00000374719.3:c.389C>A	chrX.hg19:g.65822603G>T	ENSP00000363851:p.Pro130His	353.0	0.0		301.0	50.0	NM_001242310	Q5VYX9|Q5VYY0|Q6UWM2|Q8IZA6	Missense_Mutation	SNP	ENST00000374719.3	hg19	CCDS14386.1	.	.	.	.	.	.	.	.	.	.	G	8.677	0.904193	0.17760	.	.	ENSG00000131080	ENST00000374719;ENST00000396050;ENST00000253392;ENST00000456230;ENST00000450752	D;D;D;D;D	0.85013	-1.91;-1.91;-1.93;-1.91;-1.93	4.37	0.177	0.15054	.	0.379278	0.21973	N	0.066424	T	0.70029	0.3177	L	0.27053	0.805	0.09310	N	0.999997	B;B;B	0.20671	0.047;0.006;0.001	B;B;B	0.20955	0.032;0.007;0.002	T	0.56420	-0.7982	10	0.46703	T	0.11	0.0451	2.1098	0.03700	0.1057:0.1612:0.3809:0.3523	.	130;130;130	Q9HAV5-2;B2RBZ9;Q9HAV5	.;.;TNR27_HUMAN	H	130	ENSP00000363851:P130H;ENSP00000379365:P130H;ENSP00000253392:P130H;ENSP00000393935:P130H;ENSP00000402929:P130H	ENSP00000253392:P130H	P	-	2	0	EDA2R	65739328	0.948000	0.32251	0.030000	0.17652	0.890000	0.51754	0.763000	0.26517	-0.514000	0.06488	0.600000	0.82982	CCC	.	.		0.557	EDA2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057002.1	NM_021783		T	65822603	G	T	65822603	3	4	350	1	0	0	0	0	1	0	0	0	4906	1232	43	3	512	3	EDA2R	23	65822603	Missense_Mutation	SNP	G	TCGA-UB-AA0V-01A-11D-A382-10	47194962	65822603	89447957	38	49275										
DRP2	1821	hgsc.bcm.edu	37	chrX	100496711	100496711	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	ccgctttgtatggaagcaggCgacggtggccagtgaactgt	15	9	0	1			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chrX:100496711C>G	ENST00000395209.3	+	7	1141	c.614C>G	c.(613-615)gCg>gGg	p.A205G	DRP2_ENST00000538510.1_Missense_Mutation_p.A205G|DRP2_ENST00000541709.1_Missense_Mutation_p.A127G|DRP2_ENST00000402866.1_Missense_Mutation_p.A205G	NM_001939.2	NP_001930.2	Q13474	DRP2_HUMAN	dystrophin related protein 2	205					central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(3)|prostate(1)|skin(2)|urinary_tract(2)	31						TGGAAGCAGGCGACGGTGGCC	0.587																																					p.A205G		Atlas-SNP	.											.	DRP2	98	.	0			c.C614G						.						67	57	60					X																	100496711		2203	4300	6503	SO:0001583	missense	1821	exon7			AGCAGGCGACGGT	U43519	CCDS14480.2, CCDS55465.1	Xq22	2008-02-05			ENSG00000102385	ENSG00000102385			3032	protein-coding gene	gene with protein product		300052				8640231	Standard	NM_001939		Approved		uc004egz.2	Q13474	OTTHUMG00000022020	ENST00000395209.3:c.614C>G	chrX.hg19:g.100496711C>G	ENSP00000378635:p.Ala205Gly	99.0	0.0		66.0	12.0	NM_001939	A6ZKI5|A8K1B0|B1B1F3|B4DIZ0	Missense_Mutation	SNP	ENST00000395209.3	hg19	CCDS14480.2	.	.	.	.	.	.	.	.	.	.	C	19.31	3.803446	0.70682	.	.	ENSG00000102385	ENST00000402866;ENST00000395209;ENST00000541709;ENST00000538510	T;T;T;T	0.06608	3.38;3.38;3.28;3.38	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.20820	0.0501	M	0.64997	1.995	0.58432	D	0.999996	D	0.67145	0.996	P	0.59288	0.855	T	0.00175	-1.1955	10	0.72032	D	0.01	-10.1184	18.5061	0.90898	0.0:1.0:0.0:0.0	.	205	Q13474	DRP2_HUMAN	G	205;205;127;205	ENSP00000385038:A205G;ENSP00000378635:A205G;ENSP00000444752:A127G;ENSP00000441051:A205G	ENSP00000362007:A205G	A	+	2	0	DRP2	100383367	1.000000	0.71417	0.966000	0.40874	0.445000	0.32107	7.449000	0.80643	2.313000	0.78055	0.529000	0.55759	GCG	.	.		0.587	DRP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057522.3	NM_001939		G	100496711	C	G	100496711	3	3	350	1	0	0	0	0	1	0	0	0	4766	768	27	4	632	4	DRP2	23	100496711	Missense_Mutation	SNP	C	TCGA-UB-AA0V-01A-11D-A382-10	34674108	100496711	54773849	39	49276										
FATE1	89885	hgsc.bcm.edu	37	chrX	150889930	150889930	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	atggggatgcccatctccagGagtacgctggcaatttccaa	11	11	1	0	rs150252397	byFrequency	TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chrX:150889930G>T	ENST00000370350.3	+	3	383	c.298G>T	c.(298-300)Gag>Tag	p.E100*		NM_033085.2	NP_149076.1	Q969F0	FATE1_HUMAN	fetal and adult testis expressed 1	100						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(2)|lung(6)|ovary(1)	15	Acute lymphoblastic leukemia(192;6.56e-05)					CCATCTCCAGGAGTACGCTGG	0.567																																					p.E100X		Atlas-SNP	.											.	FATE1	30	.	0			c.G298T						.						107	86	93					X																	150889930		2203	4300	6503	SO:0001587	stop_gained	89885	exon3			CTCCAGGAGTACG	AF249872	CCDS14700.1	Xq28	2009-03-25			ENSG00000147378	ENSG00000147378			24683	protein-coding gene	gene with protein product	"cancer/testis antigen 43"	300450				11694338	Standard	NM_033085		Approved	FATE, CT43	uc004fex.3	Q969F0	OTTHUMG00000024172	ENST00000370350.3:c.298G>T	chrX.hg19:g.150889930G>T	ENSP00000359375:p.Glu100*	248.0	0.0		224.0	37.0	NM_033085		Nonsense_Mutation	SNP	ENST00000370350.3	hg19	CCDS14700.1	.	.	.	.	.	.	.	.	.	.	G	15.65	2.895857	0.52121	.	.	ENSG00000147378	ENST00000370350	.	.	.	3.8	3.8	0.43715	.	0.510762	0.16569	N	0.208726	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	-4.6367	10.2153	0.43164	0.0:0.0:1.0:0.0	.	.	.	.	X	100	.	ENSP00000359375:E100X	E	+	1	0	FATE1	150640586	0.974000	0.33945	0.024000	0.17045	0.053000	0.15095	3.539000	0.53604	2.166000	0.68216	0.436000	0.28706	GAG	.	G|1.000;C|0.000		0.567	FATE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060885.1	NM_033085		T	150889930	G	T	150889930	4	4	350	1	0	0	0	0	0	1	0	0	5701	1175	41	3	308	3	FATE1	23	150889930	Nonsense_Mutation	SNP	G	TCGA-UB-AA0V-01A-11D-A382-10	50393219	150889930	4380630	40	49277										
GABRQ	55879	hgsc.bcm.edu	37	chrX	151817747	151817747	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.024390243902439	1	1	0.648936170212766	0	0.825918762088975	1	1	0	gcagcttgttccctggatctGcataaattccctatggacaa	8	11	1	0			TCGA-UB-AA0V-01A-11D-A382-10	TCGA-UB-AA0V-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	68f1e904-8781-4297-b29d-d1307a32cccd	57fd105f-1165-48c1-bbee-848f6cd31d51	g.chrX:151817747G>A	ENST00000370306.2	+	5	581	c.561G>A	c.(559-561)ctG>ctA	p.L187L		NM_018558.2	NP_061028.3	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) A receptor, theta	187					neurotransmitter transport (GO:0006836)|signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|neurotransmitter transporter activity (GO:0005326)|transmembrane signaling receptor activity (GO:0004888)	p.L187L(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(9)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	52	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CCCTGGATCTGCATAAATTCC	0.502																																					p.L187L		Atlas-SNP	.											.	GABRQ	131	.	1	Substitution - coding silent(1)	lung(1)	c.G561A						.						191	147	162					X																	151817747		2203	4300	6503	SO:0001819	synonymous_variant	55879	exon5			GGATCTGCATAAA	U47334	CCDS14707.1	Xq28	2012-06-22	2012-02-03		ENSG00000147402	ENSG00000268089		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	14454	protein-coding gene	gene with protein product	"GABA(A) receptor, theta"	300349	"gamma-aminobutyric acid (GABA) receptor, theta"			10804200, 10449790	Standard	NM_018558		Approved	THETA	uc004ffp.1	Q9UN88	OTTHUMG00000022649	ENST00000370306.2:c.561G>A	chrX.hg19:g.151817747G>A		134.0	0.0		108.0	18.0	NM_018558	A6NFN1|Q32MB4|Q9NZK8	Silent	SNP	ENST00000370306.2	hg19	CCDS14707.1																																																																																			.	.		0.502	GABRQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058763.2	NM_018558		A	151817747	G	A	151817747	2	1	350	1	0	0	0	0	0	0	0	1	6183	1306	46	3		3	GABRQ	23	151817747	Silent	SNP	G	TCGA-UB-AA0V-01A-11D-A382-10	927817	151817747	3452813	41	49278										
KIAA2013	90231	hgsc.bcm.edu	37	chr1	11985677	11985677	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	tccgtggggttgttgagctgGatgcgctgcaggtagacgtg	18	7	0	2			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr1:11985677G>T	ENST00000376572.3	-	1	803	c.618C>A	c.(616-618)atC>atA	p.I206I	KIAA2013_ENST00000376576.3_Silent_p.I206I	NM_138346.2	NP_612355.1	Q8IYS2	K2013_HUMAN	KIAA2013	206						integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	7	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00149)|all_lung(284;0.00189)|Breast(348;0.00586)|Colorectal(325;0.0062)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0556)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.88e-06)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TGTTGAGCTGGATGCGCTGCA	0.701																																					p.I206I		Atlas-SNP	.											.	KIAA2013	25	.	0			c.C618A						.						9	12	11					1																	11985677		2083	4103	6186	SO:0001819	synonymous_variant	90231	exon1			GAGCTGGATGCGC	AB095933	CCDS141.1	1p36.22	2011-02-09			ENSG00000116685	ENSG00000116685			28513	protein-coding gene	gene with protein product						12477932	Standard	NM_138346		Approved	MGC33867, RP5-1077B9.1	uc001atk.3	Q8IYS2	OTTHUMG00000002391	ENST00000376572.3:c.618C>A	chr1.hg19:g.11985677G>T		73.0	0.0		85.0	26.0	NM_138346	Q5JXC1|Q8IVF8|Q8NDI7|Q9BSY1	Silent	SNP	ENST00000376572.3	hg19	CCDS141.1																																																																																			.	.		0.701	KIAA2013-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006858.1	NM_138346		T	11985677	G	T	11985677	2	4	351	1	0	0	0	0	0	0	0	1	8276	1164	41	3		3	KIAA2013	1	11985677	Silent	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10		11985677	237264944	1	49279										
SLC9A1	6548	hgsc.bcm.edu	37	chr1	27429729	27429732	+	Frame_Shift_Del	DEL	TTCG	TTCG	-													0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	agtacctgtgtgtggatctcTtcgttgatggagcgcttcgt							TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	TTCG	TTCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr1:27429729_27429732delTTCG	ENST00000263980.3	-	6	2132_2135	c.1557_1560delCGAA	c.(1555-1560)aacgaafs	p.NE519fs	SLC9A1_ENST00000545949.1_Frame_Shift_Del_p.NE180fs	NM_003047.4	NP_003038.2	P19634	SL9A1_HUMAN	solute carrier family 9, subfamily A (NHE1, cation proton antiporter 1), member 1	519	Interaction with CHP2.				carbohydrate metabolic process (GO:0005975)|cardiac muscle cell differentiation (GO:0055007)|cell growth (GO:0016049)|cellular response to acidic pH (GO:0071468)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|hydrogen ion transmembrane transport (GO:1902600)|ion transport (GO:0006811)|negative regulation of apoptotic process (GO:0043066)|neuron death (GO:0070997)|positive regulation of action potential (GO:0045760)|positive regulation of cell growth (GO:0030307)|positive regulation of mitochondrial membrane permeability (GO:0035794)|protein oligomerization (GO:0051259)|regulation of intracellular pH (GO:0051453)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|regulation of the force of heart contraction (GO:0002026)|response to acidic pH (GO:0010447)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|sodium ion export (GO:0071436)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium-dependent protein binding (GO:0048306)|sodium:proton antiporter activity (GO:0015385)|solute:proton antiporter activity (GO:0015299)			central_nervous_system(1)|cervix(3)|endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	27				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;2.19e-50)|OV - Ovarian serous cystadenocarcinoma(117;1.8e-29)|Colorectal(126;7.61e-09)|COAD - Colon adenocarcinoma(152;9.32e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000521)|KIRC - Kidney renal clear cell carcinoma(1967;0.00079)|STAD - Stomach adenocarcinoma(196;0.00125)|READ - Rectum adenocarcinoma(331;0.046)	Amiloride(DB00594)	TGTGGATCTCTTCGTTGATGGAGC	0.603											OREG0013277	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.520_521del		Atlas-INDEL	.											.	SLC9A1	68	.	0			c.1558_1561del						.																																			SO:0001589	frameshift_variant	6548	exon6			.	M81768	CCDS295.1	1p36.1-p35	2014-06-13	2012-03-22		ENSG00000090020	ENSG00000090020		"Solute carriers"	11071	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 143"	107310	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 1 (antiporter, Na+/H+, amiloride sensitive)", "solute carrier family 9 (sodium/hydrogen exchanger), member 1"	APNH, NHE1		8283968	Standard	NM_003047		Approved	PPP1R143	uc001bnm.4	P19634	OTTHUMG00000004271	ENST00000263980.3:c.1557_1560delCGAA	chr1.hg19:g.27429729_27429732delTTCG	ENSP00000263980:p.Asn519fs	74.0	0.0	794	61.0	20.0	NM_003047	B1ALD6|D3DPL4|Q96EM2	Frame_Shift_Del	DEL	ENST00000263980.3	hg19	CCDS295.1																																																																																			.	.		0.603	SLC9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012336.2	NM_003047		-	27429732	TTCG	-	27429729	7	5	351	1	0	1	0	1	0	0	0	0	14724	1606	56	0	915	0	SLC9A1	1	27429729	Frame_Shift_Del	DEL	TTCG	TCGA-WJ-A86L-01A-12D-A45V-10	15444052	27429729	221820892	2	49280										
TIE1	7075	hgsc.bcm.edu	37	chr1	43774664	43774664	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	cctttctccccagaccggatCccccagatcctcaacatggc	6	19	2	2			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr1:43774664C>T	ENST00000372476.3	+	8	1129	c.1050C>T	c.(1048-1050)atC>atT	p.I350I	TIE1_ENST00000441333.2_Intron|TIE1_ENST00000433781.2_5'UTR	NM_001253357.1|NM_005424.4	NP_001240286.1|NP_005415.1	P35590	TIE1_HUMAN	tyrosine kinase with immunoglobulin-like and EGF-like domains 1	350					angiogenesis (GO:0001525)|in utero embryonic development (GO:0001701)|mesoderm development (GO:0007498)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|peptidyl-tyrosine phosphorylation (GO:0018108)|plasma membrane fusion (GO:0045026)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(8)|lung(28)|ovary(3)|prostate(2)|salivary_gland(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	70	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				CAGACCGGATCCCCCAGATCC	0.597																																					p.I350I		Atlas-SNP	.											.	TIE1	132	.	0			c.C1050T						.						75	64	68					1																	43774664		2203	4300	6503	SO:0001819	synonymous_variant	7075	exon8			CCGGATCCCCCAG	BC038239	CCDS482.1	1p34-p33	2013-02-11	2004-12-13	2004-12-14	ENSG00000066056	ENSG00000066056	2.7.10.1	"Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	11809	protein-coding gene	gene with protein product		600222	"tyrosine kinase with immunoglobulin and epidermal growth factor homology domains 1"	TIE		1312667	Standard	NM_005424		Approved	JTK14	uc001ciu.3	P35590	OTTHUMG00000007282	ENST00000372476.3:c.1050C>T	chr1.hg19:g.43774664C>T		203.0	0.0		320.0	15.0	NM_005424	B5A949|B5A950	Silent	SNP	ENST00000372476.3	hg19	CCDS482.1																																																																																			.	.		0.597	TIE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019011.1	NM_005424		T	43774664	C	T	43774664	2	4	351	1	0	0	0	0	0	0	0	1	15908	845	30	3		3	TIE1	1	43774664	Silent	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	16344935	43774664	205475957	3	49281										
CYP4A11	1579	hgsc.bcm.edu	37	chr1	47401258	47401258	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	tgatggtgtccagggtcatcAaggagacgtgctgaaagacc	14	8	2	4			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr1:47401258A>G	ENST00000310638.4	-	5	603	c.572T>C	c.(571-573)tTg>tCg	p.L191S	CYP4A11_ENST00000457840.2_Missense_Mutation_p.L87S|CYP4A11_ENST00000462347.1_Missense_Mutation_p.L191S|CYP4A11_ENST00000496519.1_5'Flank|CYP4A11_ENST00000371905.1_Missense_Mutation_p.L191S|CYP4A11_ENST00000371904.4_Missense_Mutation_p.L191S	NM_000778.3	NP_000769.2	Q02928	CP4AB_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 11	191					arachidonic acid metabolic process (GO:0019369)|cellular lipid metabolic process (GO:0044255)|epoxygenase P450 pathway (GO:0019373)|fatty acid metabolic process (GO:0006631)|leukotriene B4 catabolic process (GO:0036101)|leukotriene metabolic process (GO:0006691)|long-chain fatty acid metabolic process (GO:0001676)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|positive regulation of icosanoid secretion (GO:0032305)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)			endometrium(2)|kidney(5)|large_intestine(6)|lung(6)|ovary(5)|prostate(3)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	36					Cisplatin(DB00515)|Clofibrate(DB00636)|Dexamethasone(DB01234)|Estrone(DB00655)|Ethanol(DB00898)|Lansoprazole(DB00448)|Pegvisomant(DB00082)|Pentamidine(DB00738)|Phenobarbital(DB01174)|Rifampicin(DB01045)|Tretinoin(DB00755)	CAGGGTCATCAAGGAGACGTG	0.567																																					p.L191S		Atlas-SNP	.											.	CYP4A11	77	.	0			c.T572C						.						109	91	97					1																	47401258		2203	4300	6503	SO:0001583	missense	1579	exon5			GTCATCAAGGAGA	L04751	CCDS543.1	1p33	2008-02-05	2003-01-14		ENSG00000187048	ENSG00000187048		"Cytochrome P450s"	2642	protein-coding gene	gene with protein product		601310	"cytochrome P450, subfamily IVA, polypeptide 11"	CYP4A2		7679927	Standard	NM_000778		Approved	CYP4AII	uc001cqp.4	Q02928	OTTHUMG00000008020	ENST00000310638.4:c.572T>C	chr1.hg19:g.47401258A>G	ENSP00000311095:p.Leu191Ser	409.0	1.0		388.0	158.0	NM_000778	Q06766|Q16865|Q16866|Q5VSP8|Q86SU6|Q8IWY5	Missense_Mutation	SNP	ENST00000310638.4	hg19	CCDS543.1	.	.	.	.	.	.	.	.	.	.	N	19.75	3.885441	0.72410	.	.	ENSG00000187048	ENST00000310638;ENST00000371904;ENST00000371905;ENST00000457840	T;T;T;T	0.68903	-0.36;-0.36;-0.36;-0.36	5.14	3.99	0.46301	.	0.225843	0.37577	N	0.002028	T	0.72220	0.3433	M	0.74647	2.275	0.44728	D	0.997729	P	0.45011	0.848	P	0.48524	0.58	T	0.74318	-0.3704	10	0.59425	D	0.04	.	12.36	0.55197	0.8587:0.1413:0.0:0.0	.	191	Q02928	CP4AB_HUMAN	S	191;191;191;87	ENSP00000311095:L191S;ENSP00000360971:L191S;ENSP00000360972:L191S;ENSP00000406272:L87S	ENSP00000311095:L191S	L	-	2	0	CYP4A11	47173845	1.000000	0.71417	0.993000	0.49108	0.954000	0.61252	7.088000	0.76901	0.885000	0.36088	0.528000	0.53228	TTG	.	.		0.567	CYP4A11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022022.1	NM_000778		G	47401258	A	G	47401258	3	3	351	1	0	0	0	0	1	0	0	0	4185	131	5	2	1019	2	CYP4A11	1	47401258	Missense_Mutation	SNP	A	TCGA-WJ-A86L-01A-12D-A45V-10	3626594	47401258	201849363	4	49282										
LMO4	8543	hgsc.bcm.edu	37	chr1	87797781	87797781	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	gcggtgcgcaggctgcggggGcaagattgcggaccgctttc	18	11	0	1			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr1:87797781G>T	ENST00000370544.5	+	2	863	c.83G>T	c.(82-84)gGc>gTc	p.G28V	LMO4_ENST00000489303.1_3'UTR|LMO4_ENST00000370542.1_Missense_Mutation_p.G28V	NM_006769.3	NP_006760.1	P61968	LMO4_HUMAN	LIM domain only 4	28	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				negative regulation of protein complex assembly (GO:0031333)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell activation (GO:0050865)|regulation of cell fate specification (GO:0042659)|spinal cord association neuron differentiation (GO:0021527)|spinal cord motor neuron differentiation (GO:0021522)|thymus development (GO:0048538)|transcription from RNA polymerase II promoter (GO:0006366)|ventral spinal cord interneuron differentiation (GO:0021514)|ventricular septum development (GO:0003281)	transcription factor complex (GO:0005667)	enhancer sequence-specific DNA binding (GO:0001158)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(1)	9		Lung NSC(277;0.179)		all cancers(265;0.00456)|Epithelial(280;0.0148)|BRCA - Breast invasive adenocarcinoma(282;0.153)		GGCTGCGGGGGCAAGATTGCG	0.682																																					p.G28V		Atlas-SNP	.											.	LMO4	21	.	0			c.G83T						.						35	38	37					1																	87797781		2202	4300	6502	SO:0001583	missense	8543	exon2			GCGGGGGCAAGAT	U24576	CCDS713.1	1p22.3	2008-02-05			ENSG00000143013	ENSG00000143013			6644	protein-coding gene	gene with protein product		603129					Standard	NM_006769		Approved		uc001dmi.3	P61968	OTTHUMG00000010248	ENST00000370544.5:c.83G>T	chr1.hg19:g.87797781G>T	ENSP00000359575:p.Gly28Val	110.0	0.0		87.0	43.0	NM_006769	D3DT23|O00158|O88894	Missense_Mutation	SNP	ENST00000370544.5	hg19	CCDS713.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.389354	0.82902	.	.	ENSG00000143013	ENST00000370544;ENST00000370542	D;D	0.87491	-2.26;-2.26	5.57	5.57	0.84162	Zinc finger, LIM-type (5);	0.000000	0.85682	D	0.000000	D	0.89206	0.6649	M	0.70903	2.155	0.80722	D	1	D	0.54047	0.964	P	0.52386	0.697	D	0.88314	0.2958	10	0.44086	T	0.13	.	19.5493	0.95311	0.0:0.0:1.0:0.0	.	28	P61968	LMO4_HUMAN	V	28	ENSP00000359575:G28V;ENSP00000359573:G28V	ENSP00000359573:G28V	G	+	2	0	LMO4	87570369	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.750000	0.85110	2.621000	0.88768	0.650000	0.86243	GGC	.	.		0.682	LMO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028264.2	NM_006769		T	87797781	G	T	87797781	3	4	351	1	0	0	0	0	1	0	0	0	8863	1203	42	3	85	3	LMO4	1	87797781	Missense_Mutation	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	40396523	87797781	161452840	5	49283										
PHGDH	26227	hgsc.bcm.edu	37	chr1	120286648	120286648	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	cagcatgtgactgaagccttCcagttccacttctaaccttg	7	13	1	2			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr1:120286648C>G	ENST00000369409.4	+	12	1723	c.1587C>G	c.(1585-1587)ttC>ttG	p.F529L	PHGDH_ENST00000482968.1_3'UTR|PHGDH_ENST00000369407.3_Missense_Mutation_p.F495L	NM_006623.3	NP_006614.2	O43175	SERA_HUMAN	phosphoglycerate dehydrogenase	529					brain development (GO:0007420)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|G1 to G0 transition (GO:0070314)|gamma-aminobutyric acid metabolic process (GO:0009448)|glial cell development (GO:0021782)|glutamine metabolic process (GO:0006541)|glycine metabolic process (GO:0006544)|L-serine biosynthetic process (GO:0006564)|neural tube development (GO:0021915)|neuron projection development (GO:0031175)|regulation of gene expression (GO:0010468)|small molecule metabolic process (GO:0044281)|spinal cord development (GO:0021510)|taurine metabolic process (GO:0019530)|threonine metabolic process (GO:0006566)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	electron carrier activity (GO:0009055)|NAD binding (GO:0051287)|phosphoglycerate dehydrogenase activity (GO:0004617)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)	18	all_cancers(5;1.18e-09)|all_epithelial(5;2.16e-10)|Melanoma(3;1.93e-05)|all_neural(166;0.219)	all_lung(203;3.66e-05)|Lung NSC(69;0.000202)|all_epithelial(167;0.0347)		Lung(183;0.0111)|LUSC - Lung squamous cell carcinoma(189;0.0593)		CTGAAGCCTTCCAGTTCCACT	0.542											OREG0013728	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F529L		Atlas-SNP	.											.	PHGDH	51	.	0			c.C1587G						.						122	109	113					1																	120286648		2203	4300	6503	SO:0001583	missense	26227	exon12			AGCCTTCCAGTTC	BC011262	CCDS904.1	1p12	2008-02-05			ENSG00000092621	ENSG00000092621	1.1.1.95		8923	protein-coding gene	gene with protein product		606879					Standard	NM_006623		Approved	SERA, PGDH, PDG	uc001ehz.3	O43175	OTTHUMG00000012100	ENST00000369409.4:c.1587C>G	chr1.hg19:g.120286648C>G	ENSP00000358417:p.Phe529Leu	94.0	0.0	1502	94.0	40.0	NM_006623	B2RD08|Q5SZU3|Q9BQ01	Missense_Mutation	SNP	ENST00000369409.4	hg19	CCDS904.1	.	.	.	.	.	.	.	.	.	.	C	15.11	2.735718	0.49045	.	.	ENSG00000092621	ENST00000369409;ENST00000537497;ENST00000369407	D;D	0.90444	-2.66;-2.67	5.94	5.03	0.67393	.	0.145791	0.64402	D	0.000006	T	0.75671	0.3881	L	0.29908	0.895	0.35803	D	0.823254	B;B;P;P	0.42692	0.07;0.07;0.655;0.787	B;B;B;B	0.41236	0.021;0.021;0.231;0.351	T	0.74325	-0.3702	10	0.14656	T	0.56	-10.1735	11.1037	0.48190	0.0:0.9153:0.0:0.0847	.	495;495;402;529	B3KSC3;Q5SZU1;F5H634;O43175	.;.;.;SERA_HUMAN	L	529;402;495	ENSP00000358417:F529L;ENSP00000358415:F495L	ENSP00000358415:F495L	F	+	3	2	PHGDH	120088171	1.000000	0.71417	1.000000	0.80357	0.728000	0.41692	1.254000	0.32897	1.523000	0.49018	0.650000	0.86243	TTC	.	.		0.542	PHGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033464.1	NM_006623		G	120286648	C	G	120286648	3	3	351	1	0	0	0	0	1	0	0	0	11850	854	30	4	1633	4	PHGDH	1	120286648	Missense_Mutation	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	32488867	120286648	128963973	6	49284										
NBPF10	100132406	hgsc.bcm.edu	37	chr1	145304611	145304611	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	ctcaactctcattggctcatCctctcatgttgaatgggagg	9	11	4	1			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr1:145304611C>T	ENST00000369339.3	+	7	984	c.731C>T	c.(730-732)tCc>tTc	p.S244F	RP11-458D21.5_ENST00000468030.1_3'UTR|NBPF10_ENST00000369338.1_Missense_Mutation_p.S244F|NBPF10_ENST00000342960.5_Missense_Mutation_p.S515F			Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	515	NBPF 1. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			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)		ATTGGCTCATCCTCTCATGTT	0.428																																					p.S515F		Atlas-SNP	.											.	NBPF10	221	.	0			c.C1544T						.																																			SO:0001583	missense	100132406	exon10			GCTCATCCTCTCA	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"neuroblastoma breakpoint family"	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000369339.3:c.731C>T	chr1.hg19:g.145304611C>T	ENSP00000358345:p.Ser244Phe	194.0	0.0		462.0	75.0	NM_001039703	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000369339.3	hg19		.	.	.	.	.	.	.	.	.	.	.	9.728	1.161525	0.21538	.	.	ENSG00000163386	ENST00000448873;ENST00000369338;ENST00000369334;ENST00000342960;ENST00000449032	T;T	0.04406	3.68;3.63	0.745	0.745	0.18359	.	.	.	.	.	T	0.05502	0.0145	L	0.58810	1.83	0.09310	N	1	P;D;D;P	0.61080	0.676;0.969;0.989;0.952	P;P;D;P	0.64042	0.485;0.805;0.921;0.583	T	0.30679	-0.9970	9	0.62326	D	0.03	.	4.8431	0.13500	0.0:1.0:0.0:0.0	.	190;480;446;244	Q4VC10;Q3BBV7;Q5U227;A8MQ30	.;.;.;.	F	440;244;244;515;4	ENSP00000358344:S244F;ENSP00000345684:S515F	ENSP00000345684:S515F	S	+	2	0	NBPF10	144015968	0.000000	0.05858	0.007000	0.13788	0.035000	0.12851	-0.959000	0.03853	0.682000	0.31407	0.162000	0.16502	TCC	.	.		0.428	NBPF10-001	KNOWN	not_best_in_genome_evidence|basic	protein_coding	protein_coding	OTTHUMT00000038550.3	NM_001039703		T	145304611	C	T	145304611	3	4	351	1	0	0	0	0	1	0	0	0	10202	855	30	3	1582	3	NBPF10	1	145304611	Missense_Mutation	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	25017963	145304611	103946010	7	49285										
CD1A	909	hgsc.bcm.edu	37	chr1	158225110	158225110	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	ttcggtcatttgagggaattCgtagatacgcccatgaattg	11	7	1	3			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr1:158225110C>G	ENST00000289429.5	+	2	828	c.295C>G	c.(295-297)Cgt>Ggt	p.R99G		NM_001763.2	NP_001754.2	P06126	CD1A_HUMAN	CD1a molecule	99					antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)				NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(14)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(1)	32	all_hematologic(112;0.0378)				Antithymocyte globulin(DB00098)	TGAGGGAATTCGTAGATACGC	0.468																																					p.R99G		Atlas-SNP	.											CD1A,right_lower_lobe,carcinoma,0,1	CD1A	88	.	0			c.C295G						.						88	84	85					1																	158225110		2203	4300	6503	SO:0001583	missense	909	exon2			GGAATTCGTAGAT	M28825	CCDS1174.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158477	ENSG00000158477		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	1634	protein-coding gene	gene with protein product		188370	"CD1A antigen, a polypeptide", "CD1a antigen"	CD1		2447586, 2784820	Standard	NM_001763		Approved		uc001frt.3	P06126	OTTHUMG00000017512	ENST00000289429.5:c.295C>G	chr1.hg19:g.158225110C>G	ENSP00000289429:p.Arg99Gly	77.0	0.0		141.0	34.0	NM_001763	D3DVD7|Q13962|Q5TDJ8|Q9UMM4|Q9Y5M5	Missense_Mutation	SNP	ENST00000289429.5	hg19	CCDS1174.1	.	.	.	.	.	.	.	.	.	.	C	10.31	1.314224	0.23908	.	.	ENSG00000158477	ENST00000289429	T	0.06528	3.29	4.07	-0.567	0.11763	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	1.769060	0.03408	N	0.204308	T	0.02727	0.0082	L	0.42245	1.32	0.09310	N	1	B	0.30455	0.28	B	0.35278	0.199	T	0.46992	-0.9151	10	0.66056	D	0.02	0.0237	6.903	0.24293	0.4838:0.3544:0.1618:0.0	.	99	P06126	CD1A_HUMAN	G	99	ENSP00000289429:R99G	ENSP00000289429:R99G	R	+	1	0	CD1A	156491734	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.176000	0.09811	0.106000	0.17784	-0.203000	0.12734	CGT	.	.		0.468	CD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046349.2	NM_001763		G	158225110	C	G	158225110	3	3	351	1	0	0	0	0	1	0	0	0	2976	884	31	4	301	4	CD1A	1	158225110	Missense_Mutation	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	12920499	158225110	91025511	8	49286										
OR10Z1	128368	hgsc.bcm.edu	37	chr1	158576910	158576910	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	tcttggcagcaatactgaggAtcccctctgctgaggggcag	13	11	2	2			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr1:158576910A>G	ENST00000361284.1	+	1	682	c.682A>G	c.(682-684)Atc>Gtc	p.I228V		NM_001004478.1	NP_001004478.1	Q8NGY1	O10Z1_HUMAN	olfactory receptor, family 10, subfamily Z, member 1	228						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(6)|lung(21)|pancreas(1)|prostate(3)|skin(4)	37	all_hematologic(112;0.0378)					AATACTGAGGATCCCCTCTGC	0.502																																					p.I228V		Atlas-SNP	.											.	OR10Z1	99	.	0			c.A682G						.						157	154	155					1																	158576910		2203	4300	6503	SO:0001583	missense	128368	exon1			CTGAGGATCCCCT	AB065635	CCDS30901.1	1q23.1	2012-08-23			ENSG00000198967	ENSG00000198967		"GPCR / Class A : Olfactory receptors"	14996	protein-coding gene	gene with protein product							Standard	NM_001004478		Approved		uc010pio.2	Q8NGY1	OTTHUMG00000019637	ENST00000361284.1:c.682A>G	chr1.hg19:g.158576910A>G	ENSP00000354707:p.Ile228Val	56.0	0.0		112.0	36.0	NM_001004478	Q5VYL0|Q6IFR7	Missense_Mutation	SNP	ENST00000361284.1	hg19	CCDS30901.1	.	.	.	.	.	.	.	.	.	.	A	12.26	1.885767	0.33255	.	.	ENSG00000198967	ENST00000361284	T	0.00267	8.38	5.25	5.25	0.73442	GPCR, rhodopsin-like superfamily (1);	0.167587	0.28600	N	0.014761	T	0.00210	0.0006	L	0.58428	1.81	0.24946	N	0.991823	D	0.60575	0.988	P	0.61722	0.893	T	0.53865	-0.8378	10	0.51188	T	0.08	.	14.274	0.66167	1.0:0.0:0.0:0.0	.	228	Q8NGY1	O10Z1_HUMAN	V	228	ENSP00000354707:I228V	ENSP00000354707:I228V	I	+	1	0	OR10Z1	156843534	0.956000	0.32656	0.772000	0.31596	0.173000	0.22820	3.915000	0.56409	2.197000	0.70478	0.528000	0.53228	ATC	.	.		0.502	OR10Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051853.1	NM_001004478		G	158576910	A	G	158576910	3	3	351	1	0	0	0	0	1	0	0	0	10932	333	12	2	684	2	OR10Z1	1	158576910	Missense_Mutation	SNP	A	TCGA-WJ-A86L-01A-12D-A45V-10	351800	158576910	90673711	9	49287										
CACNA1E	777	hgsc.bcm.edu	37	chr1	181724436	181724436	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	acatactcattgtgtacaagCtcttcatgttcatctttgct	5	10	5	0			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr1:181724436C>G	ENST00000367573.2	+	28	3892	c.3892C>G	c.(3892-3894)Ctc>Gtc	p.L1298V	CACNA1E_ENST00000357570.5_Missense_Mutation_p.L1249V|CACNA1E_ENST00000358338.5_Missense_Mutation_p.L1230V|CACNA1E_ENST00000367570.1_Missense_Mutation_p.L1298V|CACNA1E_ENST00000360108.3_Missense_Mutation_p.L1279V|CACNA1E_ENST00000526775.1_Missense_Mutation_p.L1279V|CACNA1E_ENST00000367567.4_Missense_Mutation_p.L905V	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1298					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						TGTGTACAAGCTCTTCATGTT	0.473																																					p.L1298V		Atlas-SNP	.											.	CACNA1E	778	.	0			c.C3892G						.						219	210	213					1																	181724436		2039	4212	6251	SO:0001583	missense	777	exon28			TACAAGCTCTTCA	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.3892C>G	chr1.hg19:g.181724436C>G	ENSP00000356545:p.Leu1298Val	54.0	0.0		111.0	33.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.549492	0.86127	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.98701	-5.08;-5.08;-5.08;-5.08;-5.08;-5.08;-5.08	5.29	4.38	0.52667	Ion transport (1);	0.060200	0.64402	D	0.000002	D	0.98957	0.9645	M	0.81802	2.56	0.80722	D	1	P;D;P	0.69078	0.939;0.997;0.827	P;D;B	0.72338	0.901;0.977;0.269	D	0.99593	1.0976	10	0.87932	D	0	.	13.1804	0.59651	0.0:0.9224:0.0:0.0776	.	1279;1298;1298	Q15878-2;Q15878;Q15878-3	.;CAC1E_HUMAN;.	V	1298;1279;1249;1230;905;1279;1298	ENSP00000356542:L1298V;ENSP00000434814:L1279V;ENSP00000350183:L1249V;ENSP00000351101:L1230V;ENSP00000356539:L905V;ENSP00000353222:L1279V;ENSP00000356545:L1298V	ENSP00000350183:L1249V	L	+	1	0	CACNA1E	179991059	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.676000	0.84012	1.227000	0.43598	0.650000	0.86243	CTC	.	.		0.473	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		G	181724436	C	G	181724436	3	3	351	1	0	0	0	0	1	0	0	0	2544	797	28	4	4002	4	CACNA1E	1	181724436	Missense_Mutation	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	23147526	181724436	67526185	10	49288										
ELK4	2005	hgsc.bcm.edu	37	chr1	205589082	205589082	+	Intron	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	aatggtgacaccataaagagCgagcaagctacctgtgaaaa	10	8	0	3			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr1:205589082C>A	ENST00000357992.4	-	3	1420				ELK4_ENST00000289703.4_Silent_p.S364S|ELK4_ENST00000468523.1_5'Flank	NM_001973.3	NP_001964.2	P28324	ELK4_HUMAN	ELK4, ETS-domain protein (SRF accessory protein 1)						cell differentiation (GO:0030154)|histone H3 deacetylation (GO:0070932)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)	p.S364S(1)	SLC45A3/ELK4(18)	breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|skin(1)	12	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0908)			CCATAAAGAGCGAGCAAGCTA	0.418			T	SLC45A3	prostate																																p.S364S		Atlas-SNP	.		Dom	yes		1	1q32	2005	"ELK4, ETS-domain protein (SRF accessory protein 1)"		E	ELK4_ENST00000289703,colon,carcinoma,0,1	ELK4	45	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1092T						.						77	79	78					1																	205589082		2203	4300	6503	SO:0001627	intron_variant	2005	exon3			AAAGAGCGAGCAA	M85165	CCDS1456.1, CCDS1457.1	1q32	2008-02-05			ENSG00000158711	ENSG00000158711			3326	protein-coding gene	gene with protein product		600246				7851904, 8575773	Standard	NM_001973		Approved	SAP1		P28324	OTTHUMG00000037221	ENST00000357992.4:c.1080+11G>T	chr1.hg19:g.205589082C>A		93.0	0.0		143.0	42.0	NM_021795	P28323|Q6GSJ2	Silent	SNP	ENST00000357992.4	hg19	CCDS1456.1																																																																																			.	.		0.418	ELK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090615.1	NM_021795		A	205589082	C	A	205589082	1	1	351	0	1	0	0	0	0	0	0	0	5063	755	27	1		1	ELK4	1	205589082	Intron	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	23864646	205589082	43661539	11	49289										
SLC26A9	115019	hgsc.bcm.edu	37	chr1	205886474	205886474	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	tacaaggagagctcagcatcCcctggagcctggaagggagg	15	10	1	1			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr1:205886474C>A	ENST00000367135.3	-	20	2378	c.2265G>T	c.(2263-2265)ggG>ggT	p.G755G	SLC26A9_ENST00000367134.2_Silent_p.G755G|SLC26A9_ENST00000340781.4_Silent_p.G755G	NM_052934.3	NP_443166.1	Q7LBE3	S26A9_HUMAN	solute carrier family 26 (anion exchanger), member 9	755					anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|positive regulation of gene expression (GO:0010628)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|ATPase binding (GO:0051117)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride channel activity (GO:0005254)|secondary active sulfate transmembrane transporter activity (GO:0008271)			NS(1)|breast(3)|endometrium(11)|kidney(1)|large_intestine(6)|lung(17)|ovary(1)|skin(7)|urinary_tract(5)	52	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0458)			GCTCAGCATCCCCTGGAGCCT	0.587																																					p.G755G		Atlas-SNP	.											.	SLC26A9	176	.	0			c.G2265T						.						178	163	168					1																	205886474		2203	4300	6503	SO:0001819	synonymous_variant	115019	exon20			AGCATCCCCTGGA	AF331525	CCDS30989.1, CCDS30990.1	1q32.1	2013-07-18	2013-07-18		ENSG00000174502	ENSG00000174502		"Solute carriers"	14469	protein-coding gene	gene with protein product	"anion transporter/exchanger-9"	608481	"solute carrier family 26, member 9"			11834742	Standard	NM_134325		Approved		uc001hdp.3	Q7LBE3	OTTHUMG00000036001	ENST00000367135.3:c.2265G>T	chr1.hg19:g.205886474C>A		70.0	0.0		74.0	23.0	NM_134325	A7E2V6|B1AVM8|B1AVM9|B7ZKK2|Q96PK9|Q96RN0	Silent	SNP	ENST00000367135.3	hg19	CCDS30990.1																																																																																			.	.		0.587	SLC26A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087742.1	NM_052934		A	205886474	C	A	205886474	2	1	351	1	0	0	0	0	0	0	0	1	14539	610	22	3		3	SLC26A9	1	205886474	Silent	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	297392	205886474	43364147	12	49290										
PLXNA2	5362	hgsc.bcm.edu	37	chr1	208257756	208257756	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	gacactgaacgctggagctgTtgaagcgcagagcggggacc	16	10	0	3			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr1:208257756T>C	ENST00000367033.3	-	10	3024	c.2267A>G	c.(2266-2268)aAc>aGc	p.N756S		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	756					axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		GCTGGAGCTGTTGAAGCGCAG	0.617																																					p.N756S		Atlas-SNP	.											.	PLXNA2	178	.	0			c.A2267G						.						62	67	65					1																	208257756		2203	4300	6503	SO:0001583	missense	5362	exon10			GAGCTGTTGAAGC	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"Plexins"	9100	protein-coding gene	gene with protein product	"plexin 2", "plexin-A2", "semaphorin receptor OCT", "transmembrane protein OCT"	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.2267A>G	chr1.hg19:g.208257756T>C	ENSP00000356000:p.Asn756Ser	90.0	0.0		103.0	59.0	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	hg19	CCDS31013.1	.	.	.	.	.	.	.	.	.	.	T	17.34	3.363753	0.61513	.	.	ENSG00000076356	ENST00000367033	T	0.00949	5.51	5.7	4.55	0.56014	.	0.041334	0.85682	D	0.000000	T	0.01905	0.0060	M	0.71206	2.165	0.80722	D	1	P	0.51057	0.941	P	0.45343	0.477	T	0.67757	-0.5588	10	0.16896	T	0.51	.	12.036	0.53425	0.1295:0.0:0.0:0.8705	.	756	O75051	PLXA2_HUMAN	S	756	ENSP00000356000:N756S	ENSP00000356000:N756S	N	-	2	0	PLXNA2	206324379	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.751000	0.85126	0.946000	0.37632	0.528000	0.53228	AAC	.	.		0.617	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179		C	208257756	T	C	208257756	3	2	351	1	0	0	0	0	1	0	0	0	12129	1725	60	2	3509	2	PLXNA2	1	208257756	Missense_Mutation	SNP	T	TCGA-WJ-A86L-01A-12D-A45V-10	2371282	208257756	40992865	13	49291										
RPS6KC1	26750	hgsc.bcm.edu	37	chr1	213403855	213403855	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	tgtaggttttacttgtaatgGacacaaggacagaacagact	10	6	0	2			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr1:213403855G>A	ENST00000366960.3	+	9	1210	c.1060G>A	c.(1060-1062)Gac>Aac	p.D354N	RPS6KC1_ENST00000543470.1_Missense_Mutation_p.D142N|RPS6KC1_ENST00000366959.3_Missense_Mutation_p.D342N|RPS6KC1_ENST00000490299.1_3'UTR|RPS6KC1_ENST00000543354.1_Missense_Mutation_p.D57N	NM_012424.3	NP_036556.2	Q96S38	KS6C1_HUMAN	ribosomal protein S6 kinase, 52kDa, polypeptide 1	354	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(6)|kidney(4)|large_intestine(8)|liver(2)|lung(15)|ovary(3)|prostate(1)|urinary_tract(3)	43				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)		ACTTGTAATGGACACAAGGAC	0.353																																					p.D354N		Atlas-SNP	.											.	RPS6KC1	114	.	0			c.G1060A						.						63	65	65					1																	213403855		2202	4300	6502	SO:0001583	missense	26750	exon9			GTAATGGACACAA	AF037447	CCDS1513.1, CCDS44317.1, CCDS73028.1, CCDS73029.1, CCDS73030.1	1q41	2011-04-05	2002-08-29		ENSG00000136643	ENSG00000136643			10439	protein-coding gene	gene with protein product			"ribosomal protein S6 kinase, 52kD, polypeptide 1"			10552933	Standard	XM_005273095		Approved	humS6PKh1	uc010ptr.2	Q96S38	OTTHUMG00000036926	ENST00000366960.3:c.1060G>A	chr1.hg19:g.213403855G>A	ENSP00000355927:p.Asp354Asn	82.0	0.0		122.0	29.0	NM_012424	B1APS8|B3KVM4|D3DTA4|Q8TDD3|Q9NSF4|Q9UL66	Missense_Mutation	SNP	ENST00000366960.3	hg19	CCDS1513.1	.	.	.	.	.	.	.	.	.	.	G	32	5.140250	0.94560	.	.	ENSG00000136643	ENST00000543470;ENST00000366960;ENST00000366959;ENST00000543354	T;T;T;T	0.26223	1.75;1.75;1.75;1.75	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.50616	0.1626	L	0.56769	1.78	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.987;0.987	T	0.48864	-0.8997	10	0.87932	D	0	-27.0026	19.6558	0.95837	0.0:0.0:1.0:0.0	.	142;354;342	F5H7T0;Q96S38;B1APS8	.;KS6C1_HUMAN;.	N	142;354;342;57	ENSP00000442306:D142N;ENSP00000355927:D354N;ENSP00000355926:D342N;ENSP00000439282:D57N	ENSP00000355926:D342N	D	+	1	0	RPS6KC1	211470478	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.409000	0.90223	2.719000	0.93026	0.655000	0.94253	GAC	.	.		0.353	RPS6KC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089690.3	NM_012424		A	213403855	G	A	213403855	3	1	351	1	0	0	0	0	1	0	0	0	13673	1174	41	3	1094	3	RPS6KC1	1	213403855	Missense_Mutation	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	5146099	213403855	35846766	14	49292										
USH2A	7399	hgsc.bcm.edu	37	chr1	216420308	216420308	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	gatgcactgccctgtcttagCattacagacagtcccaggga	10	12	1	1			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr1:216420308C>A	ENST00000307340.3	-	13	2814	c.2428G>T	c.(2428-2430)Gct>Tct	p.A810S	USH2A_ENST00000366942.3_Missense_Mutation_p.A810S|USH2A_ENST00000366943.2_Missense_Mutation_p.A810S	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	810	Laminin EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00460}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			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)		CCTGTCTTAGCATTACAGACA	0.463										HNSCC(13;0.011)																											p.A810S		Atlas-SNP	.											.	USH2A	1168	.	0			c.G2428T						.						116	110	112					1																	216420308		2203	4300	6503	SO:0001583	missense	7399	exon13			TCTTAGCATTACA	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.2428G>T	chr1.hg19:g.216420308C>A	ENSP00000305941:p.Ala810Ser	127.0	0.0		224.0	73.0	NM_007123	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	9.229	1.035302	0.19590	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	T;T;T	0.60424	0.19;0.19;0.19	5.65	0.136	0.14780	EGF-like, laminin (2);	0.327586	0.21579	N	0.072262	T	0.36690	0.0976	L	0.28400	0.85	0.09310	N	1	B;B	0.17038	0.011;0.02	B;B	0.17098	0.017;0.017	T	0.12915	-1.0529	10	0.27082	T	0.32	.	4.3236	0.11029	0.1225:0.4311:0.3186:0.1278	.	810;810	O75445-2;O75445	.;USH2A_HUMAN	S	810	ENSP00000305941:A810S;ENSP00000355910:A810S;ENSP00000355909:A810S	ENSP00000305941:A810S	A	-	1	0	USH2A	214486931	0.000000	0.05858	0.000000	0.03702	0.696000	0.40369	-0.836000	0.04382	-0.239000	0.09710	-0.165000	0.13383	GCT	.	.		0.463	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		A	216420308	C	A	216420308	3	1	351	1	0	0	0	0	1	0	0	0	17051	710	25	3	13434	3	USH2A	1	216420308	Missense_Mutation	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	3016453	216420308	32830313	15	49293										
OR2T4	127074	hgsc.bcm.edu	37	chr1	248524962	248524962	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	actcttcagacaatccaaacAtccaatggccaatatcacct	3	14	3	1			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr1:248524962A>C	ENST00000366475.1	+	1	80	c.80A>C	c.(79-81)cAt>cCt	p.H27P		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	27						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CAATCCAAACATCCAATGGCC	0.493																																					p.H27P		Atlas-SNP	.											.	OR2T4	126	.	0			c.A80C						.						108	92	97					1																	248524962		2203	4299	6502	SO:0001583	missense	127074	exon1			CCAAACATCCAAT	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"GPCR / Class A : Olfactory receptors"	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.80A>C	chr1.hg19:g.248524962A>C	ENSP00000355431:p.His27Pro	253.0	0.0		361.0	91.0	NM_001004696	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	hg19	CCDS31113.1	.	.	.	.	.	.	.	.	.	.	A	9.295	1.051596	0.19827	.	.	ENSG00000196944	ENST00000366475	T	0.01629	4.72	1.28	1.28	0.21552	.	.	.	.	.	T	0.01156	0.0038	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.47636	-0.9102	9	0.40728	T	0.16	.	6.2492	0.20835	1.0:0.0:0.0:0.0	.	27	Q8NH00	OR2T4_HUMAN	P	27	ENSP00000355431:H27P	ENSP00000355431:H27P	H	+	2	0	OR2T4	246591585	0.518000	0.26234	0.516000	0.27786	0.274000	0.26718	0.000000	0.12993	0.505000	0.28104	0.352000	0.21897	CAT	.	.		0.493	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696		C	248524962	A	C	248524962	3	2	351	1	0	0	0	0	1	0	0	0	11036	217	8	5	82	5	OR2T4	1	248524962	Missense_Mutation	SNP	A	TCGA-WJ-A86L-01A-12D-A45V-10	32104654	248524962	725659	16	49294										
KIAA1841	84542	hgsc.bcm.edu	37	chr2	61297534	61297534	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	atttcctgaacaataataacCaaatggtattggacatgatc	6	7	0	2			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr2:61297534C>G	ENST00000402291.1	+	3	290	c.49C>G	c.(49-51)Caa>Gaa	p.Q17E	KIAA1841_ENST00000356719.2_Missense_Mutation_p.Q17E|KIAA1841_ENST00000295031.5_Missense_Mutation_p.Q17E|KIAA1841_ENST00000453873.1_Missense_Mutation_p.Q17E|KIAA1841_ENST00000482513.1_3'UTR	NM_001129993.1	NP_001123465.1	Q6NSI8	K1841_HUMAN	KIAA1841	17										breast(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	25			Epithelial(17;0.193)			CAATAATAACCAAATGGTATT	0.373																																					p.Q17E		Atlas-SNP	.											.	KIAA1841	95	.	0			c.C49G						.						115	113	113					2																	61297534		2203	4300	6503	SO:0001583	missense	84542	exon3			AATAACCAAATGG	BC070104	CCDS1867.1, CCDS46296.1	2p15	2010-06-22			ENSG00000162929	ENSG00000162929			29387	protein-coding gene	gene with protein product						11347906	Standard	NM_032506		Approved		uc002saw.4	Q6NSI8	OTTHUMG00000129421	ENST00000402291.1:c.49C>G	chr2.hg19:g.61297534C>G	ENSP00000385579:p.Gln17Glu	93.0	0.0		98.0	40.0	NM_032506	Q49AF0|Q6ZND0|Q96JI6	Missense_Mutation	SNP	ENST00000402291.1	hg19	CCDS46296.1	.	.	.	.	.	.	.	.	.	.	C	12.04	1.818084	0.32145	.	.	ENSG00000162929	ENST00000402291;ENST00000295031;ENST00000356719;ENST00000453873	.	.	.	5.95	5.95	0.96441	.	0.268713	0.39274	N	0.001401	T	0.44138	0.1279	L	0.29908	0.895	0.34599	D	0.716367	P;B;P	0.46859	0.729;0.435;0.885	B;B;B	0.40066	0.21;0.104;0.318	T	0.49224	-0.8962	9	0.22109	T	0.4	-16.1475	20.3932	0.98965	0.0:1.0:0.0:0.0	.	17;17;17	Q6NSI8-2;Q6NSI8;Q6NSI8-4	.;K1841_HUMAN;.	E	17	.	ENSP00000295031:Q17E	Q	+	1	0	KIAA1841	61151038	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.417000	0.44653	2.824000	0.97209	0.655000	0.94253	CAA	.	.		0.373	KIAA1841-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325477.1	NM_032506		G	61297534	C	G	61297534	3	3	351	1	0	0	0	0	1	0	0	0	8270	595	21	4	51	4	KIAA1841	2	61297534	Missense_Mutation	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10		61297534	181901839	17	49295										
APLF	200558	hgsc.bcm.edu	37	chr2	68753315	68753315	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	cagaaaatacatcagcagaaCaagacacaggagaagagtgc	10	8	1	5			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr2:68753315C>A	ENST00000303795.4	+	6	916	c.745C>A	c.(745-747)Caa>Aaa	p.Q249K		NM_173545.2	NP_775816.1	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor	249					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of DNA ligation (GO:0051106)|regulation of isotype switching (GO:0045191)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|endodeoxyribonuclease activity (GO:0004520)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	25						ATCAGCAGAACAAGACACAGG	0.338																																					p.Q249K		Atlas-SNP	.											.	APLF	69	.	0			c.C745A						.						107	111	110					2																	68753315		2203	4300	6503	SO:0001583	missense	200558	exon6			GCAGAACAAGACA	BC030711	CCDS1888.1	2p14	2014-02-20	2008-10-01	2008-10-01	ENSG00000169621	ENSG00000169621			28724	protein-coding gene	gene with protein product	"XRCC1-interacting protein 1", "zinc finger, CX5CX6HX5H motif containing 1"	611035	"chromosome 2 open reading frame 13"	C2orf13		18474613, 18077224, 17353262	Standard	NM_173545		Approved	MGC47799, Xip1, ZCCHH1	uc002sep.3	Q8IW19	OTTHUMG00000129566	ENST00000303795.4:c.745C>A	chr2.hg19:g.68753315C>A	ENSP00000307004:p.Gln249Lys	250.0	0.0		273.0	137.0	NM_173545	A8K476|Q53P47|Q53PB9|Q53QU0	Missense_Mutation	SNP	ENST00000303795.4	hg19	CCDS1888.1	.	.	.	.	.	.	.	.	.	.	c	10.75	1.439547	0.25900	.	.	ENSG00000169621	ENST00000303795	T	0.23147	1.92	4.71	0.44	0.16572	.	1.022680	0.07738	N	0.946347	T	0.24699	0.0599	M	0.62723	1.935	0.09310	N	1	B;B	0.31318	0.037;0.319	B;B	0.27608	0.018;0.081	T	0.25641	-1.0126	10	0.27082	T	0.32	.	9.035	0.36282	0.1587:0.3777:0.4636:0.0	.	249;249	F8WET0;Q8IW19	.;APLF_HUMAN	K	249	ENSP00000307004:Q249K	ENSP00000307004:Q249K	Q	+	1	0	APLF	68606819	0.982000	0.34865	0.002000	0.10522	0.475000	0.33008	0.242000	0.18087	-0.019000	0.14055	0.585000	0.79938	CAA	.	.		0.338	APLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251759.1	NM_173545		A	68753315	C	A	68753315	3	1	351	1	0	0	0	0	1	0	0	0	776	479	17	3	767	3	APLF	2	68753315	Missense_Mutation	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	7455781	68753315	174446058	18	49296										
ITGA4	3676	hgsc.bcm.edu	37	chr2	182388920	182388920	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	agatattagctttctcctggAtgtgagctcactcagcagag	10	9	3	3			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr2:182388920A>T	ENST00000397033.2	+	20	2622	c.2192A>T	c.(2191-2193)gAt>gTt	p.D731V		NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	731					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|chorio-allantoic fusion (GO:0060710)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|face development (GO:0060324)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|negative regulation of protein homodimerization activity (GO:0090074)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha4-beta7 complex (GO:0034669)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)|Tinzaparin(DB06822)	TTTCTCCTGGATGTGAGCTCA	0.338																																					p.D731V		Atlas-SNP	.											.	ITGA4	142	.	0			c.A2192T						.						71	66	67					2																	182388920		1831	4076	5907	SO:0001583	missense	3676	exon20			TCCTGGATGTGAG		CCDS42788.1	2q31-q32	2010-03-23			ENSG00000115232	ENSG00000115232		"CD molecules", "Integrins"	6140	protein-coding gene	gene with protein product		192975		CD49D		1537388	Standard	NM_000885		Approved	CD49d	uc002unu.3	P13612	OTTHUMG00000154212	ENST00000397033.2:c.2192A>T	chr2.hg19:g.182388920A>T	ENSP00000380227:p.Asp731Val	165.0	0.0		141.0	54.0	NM_000885	D3DPG4|Q7Z4L6	Missense_Mutation	SNP	ENST00000397033.2	hg19	CCDS42788.1	.	.	.	.	.	.	.	.	.	.	A	19.05	3.751738	0.69533	.	.	ENSG00000115232	ENST00000397033	T	0.52057	0.68	5.91	5.91	0.95273	Integrin alpha-2 (1);	0.000000	0.85682	D	0.000000	T	0.67988	0.2952	M	0.72118	2.19	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.66960	-0.5791	10	0.38643	T	0.18	.	16.3436	0.83110	1.0:0.0:0.0:0.0	.	553;731	Q59H74;P13612	.;ITA4_HUMAN	V	731	ENSP00000380227:D731V	ENSP00000380227:D731V	D	+	2	0	ITGA4	182097165	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	6.778000	0.75043	2.269000	0.75478	0.533000	0.62120	GAT	.	.		0.338	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1			T	182388920	A	T	182388920	3	4	351	1	0	0	0	0	1	0	0	0	7887	333	12	4	2270	4	ITGA4	2	182388920	Missense_Mutation	SNP	A	TCGA-WJ-A86L-01A-12D-A45V-10	113635605	182388920	60810453	19	49297										
FAM171B	165215	hgsc.bcm.edu	37	chr2	187626928	187626928	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	gccatcccaggcttcagattGgagccgatactcaagcagct	10	13	2	1			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr2:187626928G>A	ENST00000304698.5	+	8	2062	c.1859G>A	c.(1858-1860)tGg>tAg	p.W620*		NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	620						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)			NS(1)|breast(6)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(22)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						GCTTCAGATTGGAGCCGATAC	0.473																																					p.W620X		Atlas-SNP	.											.	FAM171B	146	.	0			c.G1859A						.						79	85	83					2																	187626928		2203	4300	6503	SO:0001587	stop_gained	165215	exon8			CAGATTGGAGCCG	AF361495	CCDS33347.1	2q32.2	2008-06-16	2008-06-16	2008-06-16	ENSG00000144369	ENSG00000144369			29412	protein-coding gene	gene with protein product			"KIAA1946"	KIAA1946		11853319	Standard	NM_177454		Approved	FLJ34104	uc002ups.3	Q6P995	OTTHUMG00000154278	ENST00000304698.5:c.1859G>A	chr2.hg19:g.187626928G>A	ENSP00000304108:p.Trp620*	86.0	0.0		93.0	35.0	NM_177454	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	Nonsense_Mutation	SNP	ENST00000304698.5	hg19	CCDS33347.1	.	.	.	.	.	.	.	.	.	.	G	39	7.364543	0.98238	.	.	ENSG00000144369	ENST00000304698	.	.	.	6.03	6.03	0.97812	.	0.056641	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.6	20.5666	0.99351	0.0:0.0:1.0:0.0	.	.	.	.	X	620	.	ENSP00000304108:W620X	W	+	2	0	FAM171B	187335173	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.194000	0.94962	2.854000	0.98071	0.655000	0.94253	TGG	.	.		0.473	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1	NM_177454		A	187626928	G	A	187626928	4	1	351	1	0	0	0	0	0	1	0	0	5496	1357	47	3	1889	3	FAM171B	2	187626928	Nonsense_Mutation	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	5238008	187626928	55572445	20	49298										
RAPH1	65059	hgsc.bcm.edu	37	chr2	204354655	204354655	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	cctttcaaggtgccatgtttCaatgtatgtcggctaacagg	10	9	2	0			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr2:204354655C>A	ENST00000319170.5	-	4	683	c.384G>T	c.(382-384)ttG>ttT	p.L128F	RAPH1_ENST00000308091.4_Missense_Mutation_p.L128F|RAPH1_ENST00000419464.1_Missense_Mutation_p.L128F|RAPH1_ENST00000418114.1_Missense_Mutation_p.L128F|RAPH1_ENST00000374489.2_Missense_Mutation_p.L128F|RAPH1_ENST00000439222.1_Missense_Mutation_p.L128F|RAPH1_ENST00000374488.2_Missense_Mutation_p.L128F|RAPH1_ENST00000453034.1_Missense_Mutation_p.L128F|RAPH1_ENST00000374493.3_Missense_Mutation_p.L128F|RAPH1_ENST00000457812.1_Missense_Mutation_p.L128F|RAPH1_ENST00000423104.1_Missense_Mutation_p.L128F	NM_213589.1	NP_998754.1	Q70E73	RAPH1_HUMAN	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	128					axon extension (GO:0048675)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				breast(5)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TGCCATGTTTCAATGTATGTC	0.443																																					p.L128F		Atlas-SNP	.											.	RAPH1	118	.	0			c.G384T						.						235	225	228					2																	204354655		2203	4300	6503	SO:0001583	missense	65059	exon4			ATGTTTCAATGTA	AJ584699	CCDS2359.1, CCDS2360.1	2q33	2013-01-10	2003-11-25	2003-11-26	ENSG00000173166	ENSG00000173166		"Pleckstrin homology (PH) domain containing"	14436	protein-coding gene	gene with protein product	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 18"	609035	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 9"	ALS2CR9, ALS2CR18			Standard	NM_203365		Approved	KIAA1681	uc002vad.3	Q70E73	OTTHUMG00000132876	ENST00000319170.5:c.384G>T	chr2.hg19:g.204354655C>A	ENSP00000316543:p.Leu128Phe	119.0	0.0		118.0	49.0	NM_213589	Q96Q37|Q9C0I2	Missense_Mutation	SNP	ENST00000319170.5	hg19	CCDS2359.1	.	.	.	.	.	.	.	.	.	.	C	8.392	0.839969	0.16891	.	.	ENSG00000173166	ENST00000457812;ENST00000319170;ENST00000374493;ENST00000374489;ENST00000374488;ENST00000308091;ENST00000439222;ENST00000419464;ENST00000423104;ENST00000453034;ENST00000432342;ENST00000418114;ENST00000413201;ENST00000428637	T;T;T;T;T;T;T;T;T;T;T	0.44881	0.94;0.94;0.93;0.91;0.91;0.93;0.91;0.94;0.91;0.93;0.94	5.51	1.78	0.24846	.	0.423925	0.17554	N	0.170057	T	0.23649	0.0572	N	0.22421	0.69	0.09310	N	0.999991	B;B;B	0.24882	0.113;0.006;0.031	B;B;B	0.25140	0.058;0.016;0.024	T	0.18555	-1.0333	10	0.59425	D	0.04	-8.5221	1.6917	0.02853	0.151:0.2113:0.4018:0.2358	.	128;128;128	Q70E73-6;C9K0J5;Q70E73	.;.;RAPH1_HUMAN	F	128	ENSP00000392854:L128F;ENSP00000316543:L128F;ENSP00000363617:L128F;ENSP00000363613:L128F;ENSP00000363612:L128F;ENSP00000311293:L128F;ENSP00000411138:L128F;ENSP00000390578:L128F;ENSP00000397751:L128F;ENSP00000406662:L128F;ENSP00000396711:L128F	ENSP00000311293:L128F	L	-	3	2	RAPH1	204062900	0.989000	0.36119	0.984000	0.44739	0.258000	0.26162	0.522000	0.22909	0.356000	0.24157	-0.312000	0.09012	TTG	.	.		0.443	RAPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256363.2	NM_025252		A	204354655	C	A	204354655	3	1	351	1	0	0	0	0	1	0	0	0	13065	825	29	3	3583	3	RAPH1	2	204354655	Missense_Mutation	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	16727727	204354655	38844718	21	49299										
UGT1A9	54600	hgsc.bcm.edu	37	chr2	234580748	234580748	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	ctcagggggcatgaggtggtTgtagtcatgccagaggtgag	18	6	2	3			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr2:234580748T>C	ENST00000354728.4	+	1	250	c.168T>C	c.(166-168)gtT>gtC	p.V56V	UGT1A1_ENST00000609637.1_Silent_p.V56V|UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A10_ENST00000373445.1_Intron			O60656	UD19_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A9	56					cellular glucuronidation (GO:0052695)|cellular lipid metabolic process (GO:0044255)|drug metabolic process (GO:0017144)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|metabolic process (GO:0008152)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of fatty acid metabolic process (GO:0045922)|retinoic acid metabolic process (GO:0042573)|small molecule metabolic process (GO:0044281)|xenobiotic glucuronidation (GO:0052697)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)	p.V56V(1)		breast(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	37		Breast(86;0.000766)|all_lung(227;0.00269)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0331)|Lung NSC(271;0.0459)|Lung SC(224;0.128)		Epithelial(121;1.26e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000436)|Lung(119;0.00347)|LUSC - Lung squamous cell carcinoma(224;0.00757)	Acetaminophen(DB00316)|Buprenorphine(DB00921)|Canagliflozin(DB08907)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Entacapone(DB00494)|Etodolac(DB00749)|Ezogabine(DB04953)|Flurbiprofen(DB00712)|Haloperidol(DB00502)|Human Serum Albumin(DB00062)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ketobemidone(DB06738)|Lumiracoxib(DB01283)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Nateglinide(DB00731)|Niflumic Acid(DB04552)|Oxazepam(DB00842)|Propofol(DB00818)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sulfamethoxazole(DB01015)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zileuton(DB00744)	ATGAGGTGGTTGTAGTCATGC	0.532																																					p.V56V		Atlas-SNP	.											UGT1A9,NS,carcinoma,0,1	UGT1A9	79	.	1	Substitution - coding silent(1)	kidney(1)	c.T168C						.						100	85	90					2																	234580748		2203	4300	6503	SO:0001819	synonymous_variant	54600	exon1			GGTGGTTGTAGTC	AF056188	CCDS2505.1	2q37	2010-03-05	2005-07-20		ENSG00000241119	ENSG00000241119		"UDP glucuronosyltransferases"	12541	other	complex locus constituent		606434	"UDP glycosyltransferase 1 family, polypeptide A9"			9295054, 1910331	Standard	NM_021027		Approved	HLUGP4, LUGP4, UGT1AI		O60656	OTTHUMG00000059124	ENST00000354728.4:c.168T>C	chr2.hg19:g.234580748T>C		79.0	0.0		73.0	29.0	NM_021027	B8K285|P36509|Q9HAX0	Silent	SNP	ENST00000354728.4	hg19	CCDS2505.1																																																																																			.	.		0.532	UGT1A9-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130995.1	NM_021027		C	234580748	T	C	234580748	2	2	351	1	0	0	0	0	0	0	0	1	16967	1799	63	2		2	UGT1A9	2	234580748	Silent	SNP	T	TCGA-WJ-A86L-01A-12D-A45V-10	30226093	234580748	8618625	22	49300										
OXTR	5021	hgsc.bcm.edu	37	chr3	8794828	8794828	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	tgcacgagttcgtggaagagGtggcccgtgaacagcatgta	15	8	0	2			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr3:8794828G>A	ENST00000316793.3	-	4	1629	c.1005C>T	c.(1003-1005)caC>caT	p.H335H	CAV3_ENST00000472766.1_Intron	NM_000916.3	NP_000907.2	P30559	OXYR_HUMAN	oxytocin receptor	335					cell surface receptor signaling pathway (GO:0007166)|digestive tract development (GO:0048565)|eating behavior (GO:0042755)|ERK1 and ERK2 cascade (GO:0070371)|estrous cycle phase (GO:0060206)|female pregnancy (GO:0007565)|heart development (GO:0007507)|lactation (GO:0007595)|maternal behavior (GO:0042711)|maternal process involved in parturition (GO:0060137)|memory (GO:0007613)|muscle contraction (GO:0006936)|negative regulation of gastric acid secretion (GO:0060455)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of norepinephrine secretion (GO:0010701)|positive regulation of penile erection (GO:0060406)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of uterine smooth muscle contraction (GO:0070474)|response to amphetamine (GO:0001975)|response to anoxia (GO:0034059)|response to cocaine (GO:0042220)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to peptide hormone (GO:0043434)|response to progesterone (GO:0032570)|sleep (GO:0030431)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|suckling behavior (GO:0001967)|telencephalon development (GO:0021537)	apical plasma membrane (GO:0016324)|cell-cell adherens junction (GO:0005913)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	oxytocin receptor activity (GO:0004990)|peptide hormone binding (GO:0017046)|vasopressin receptor activity (GO:0005000)			NS(1)|endometrium(2)|large_intestine(4)|lung(5)|urinary_tract(1)	13				OV - Ovarian serous cystadenocarcinoma(96;0.15)	Carbetocin(DB01282)|Oxytocin(DB00107)	CGTGGAAGAGGTGGCCCGTGA	0.617																																					p.H335H		Atlas-SNP	.											.	OXTR	31	.	0			c.C1005T						.						73	65	67					3																	8794828		2203	4300	6503	SO:0001819	synonymous_variant	5021	exon4			GAAGAGGTGGCCC		CCDS2570.1	3p25	2012-08-08			ENSG00000180914	ENSG00000180914		"GPCR / Class A : Vasopressin and oxytocin receptors"	8529	protein-coding gene	gene with protein product		167055				1313946	Standard	NM_000916		Approved		uc003brc.3	P30559	OTTHUMG00000090537	ENST00000316793.3:c.1005C>T	chr3.hg19:g.8794828G>A		126.0	0.0		117.0	45.0	NM_000916	Q15071	Silent	SNP	ENST00000316793.3	hg19	CCDS2570.1																																																																																			.	.		0.617	OXTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207061.2			A	8794828	G	A	8794828	2	1	351	1	0	0	0	0	0	0	0	1	11347	1252	44	3		3	OXTR	3	8794828	Silent	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10		8794828	189227602	23	49301										
DLEC1	9940	hgsc.bcm.edu	37	chr3	38080872	38080872	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	tattcctccctcgcctactcTgaggccttccactacagctt	5	17	1	1			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr3:38080872T>A	ENST00000308059.6	+	1	177	c.156T>A	c.(154-156)tcT>tcA	p.S52S	DLEC1_ENST00000346219.3_Silent_p.S52S|DLEC1_ENST00000452631.2_Silent_p.S52S					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		TCGCCTACTCTGAGGCCTTCC	0.687																																					p.S52S		Atlas-SNP	.											.	DLEC1	278	.	0			c.T156A						.						52	62	59					3																	38080872		2023	4195	6218	SO:0001819	synonymous_variant	9940	exon1			CTACTCTGAGGCC	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"cilia and flagella associated protein 81"	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.156T>A	chr3.hg19:g.38080872T>A		157.0	0.0		130.0	53.0	NM_007337		Silent	SNP	ENST00000308059.6	hg19	CCDS2672.2																																																																																			.	.		0.687	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337		A	38080872	T	A	38080872	2	1	351	1	0	0	0	0	0	0	0	1	4554	1567	55	4		4	DLEC1	3	38080872	Silent	SNP	T	TCGA-WJ-A86L-01A-12D-A45V-10	29286044	38080872	159941558	24	49302										
MST1	63891	hgsc.bcm.edu	37	chr3	49725184	49725184	+	5'Flank	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	aggcccagtggccactcaccGgcagtccattaagggcccac	11	16	1	0	rs191996618		TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr3:49725184G>A	ENST00000327697.6	+	0	0				MST1_ENST00000449682.2_Splice_Site_p.R81W|MST1_ENST00000494828.2_Intron|MST1_ENST00000545762.1_Splice_Site_p.R67W|AC099668.5_ENST00000563780.1_RNA|RNF123_ENST00000432042.1_5'Flank|MST1_ENST00000383728.3_Intron	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123						protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.R67W(1)		NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		GCCACTCACCGGCAGTCCATT	0.617																																					p.R81W		Atlas-SNP	.											MST1,trunk,malignant_melanoma,0,1	MST1	84	.	1	Substitution - Missense(1)	skin(1)	c.C241T						.																																			SO:0001631	upstream_gene_variant	4485	exon2			CTCACCGGCAGTC	AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"RING-type (C3HC4) zinc fingers"	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891		chr3.hg19:g.49725184G>A	Exception_encountered	93.0	2.0		73.0	5.0	NM_020998	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Missense_Mutation	SNP	ENST00000327697.6	hg19	CCDS33758.1	.	.	.	.	.	.	.	.	.	.	G	11.82	1.753661	0.31046	.	.	ENSG00000173531	ENST00000449682;ENST00000545762	T;T	0.71222	-0.55;-0.55	4.22	2.22	0.28083	.	0.177772	0.26836	N	0.022260	T	0.63908	0.2551	M	0.65498	2.005	0.39552	D	0.968993	B;P	0.35208	0.169;0.49	B;B	0.28784	0.049;0.094	T	0.65973	-0.6038	10	0.54805	T	0.06	.	11.5769	0.50866	0.0:0.0:0.4124:0.5876	.	67;81	B7Z538;G3XAK1	.;.	W	81;67	ENSP00000414287:R81W;ENSP00000437535:R67W	ENSP00000411117:R81W	R	-	1	2	MST1	49700188	1.000000	0.71417	0.998000	0.56505	0.537000	0.34900	1.595000	0.36708	0.595000	0.29777	-0.293000	0.09583	CGG	.	.		0.617	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064		A	49725184	G	A	49725184	1	1	351	0	1	0	0	0	0	0	0	0	9899	1130	39	1		1	MST1	3	49725184	5'Flank	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	11644312	49725184	148297246	25	49303										
EPHA3	2042	hgsc.bcm.edu	37	chr3	89480381	89480381	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	gcatgaagtacctgtcagacAtgggctatgttcaccgagac	11	10	2	3			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr3:89480381A>T	ENST00000336596.2	+	13	2443	c.2218A>T	c.(2218-2220)Atg>Ttg	p.M740L	EPHA3_ENST00000494014.1_Missense_Mutation_p.M740L	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	740	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		CCTGTCAGACATGGGCTATGT	0.488										TSP Lung(6;0.00050)																											p.M740L		Atlas-SNP	.											.	EPHA3	501	.	0			c.A2218T						.						168	144	152					3																	89480381		2203	4300	6503	SO:0001583	missense	2042	exon13			TCAGACATGGGCT	M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3387	protein-coding gene	gene with protein product		179611	"EphA3"	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.2218A>T	chr3.hg19:g.89480381A>T	ENSP00000337451:p.Met740Leu	91.0	0.0		106.0	43.0	NM_005233	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	hg19	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.186290	0.78789	.	.	ENSG00000044524	ENST00000336596;ENST00000494014	D;D	0.82344	-1.6;-1.6	5.33	5.33	0.75918	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.74076	0.3669	N	0.01668	-0.77	0.80722	D	1	P	0.44139	0.827	P	0.56278	0.795	T	0.76769	-0.2837	9	.	.	.	.	15.5821	0.76452	1.0:0.0:0.0:0.0	.	740	P29320	EPHA3_HUMAN	L	740	ENSP00000337451:M740L;ENSP00000419190:M740L	.	M	+	1	0	EPHA3	89563071	1.000000	0.71417	0.976000	0.42696	0.878000	0.50629	9.287000	0.95975	2.139000	0.66308	0.477000	0.44152	ATG	.	.		0.488	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		T	89480381	A	T	89480381	3	4	351	1	0	0	0	0	1	0	0	0	5170	217	8	4	2294	4	EPHA3	3	89480381	Missense_Mutation	SNP	A	TCGA-WJ-A86L-01A-12D-A45V-10	39755197	89480381	108542049	26	49304										
FAM162A	26355	hgsc.bcm.edu	37	chr3	122126169	122126169	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	aaagaacaagatgcgagtgaAgatcagctatctaatgattg	10	5	2	5			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr3:122126169A>C	ENST00000477892.1	+	4	389	c.305A>C	c.(304-306)aAg>aCg	p.K102T	FAM162A_ENST00000469967.1_Missense_Mutation_p.K102T|FAM162A_ENST00000232125.5_Missense_Mutation_p.K92T	NM_014367.3	NP_055182.3	Q96A26	F162A_HUMAN	family with sequence similarity 162, member A	102	Required for proapoptotic activity.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to hypoxia (GO:0071456)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|transformed cell apoptotic process (GO:0006927)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)	6						ATGCGAGTGAAGATCAGCTAT	0.413																																					p.K102T		Atlas-SNP	.											.	FAM162A	18	.	0			c.A305C						.						176	171	173					3																	122126169		1963	4169	6132	SO:0001583	missense	26355	exon4			GAGTGAAGATCAG	AF191020	CCDS43139.1	3q21.1	2008-06-05	2008-06-05	2008-06-05	ENSG00000114023	ENSG00000114023			17865	protein-coding gene	gene with protein product		608017	"chromosome 3 open reading frame 28"	C3orf28		11085516	Standard	NM_014367		Approved	E2IG5	uc003eez.3	Q96A26	OTTHUMG00000159494	ENST00000477892.1:c.305A>C	chr3.hg19:g.122126169A>C	ENSP00000419088:p.Lys102Thr	68.0	0.0		66.0	27.0	NM_014367	Q9NRN6|Q9UJX8	Missense_Mutation	SNP	ENST00000477892.1	hg19	CCDS43139.1	.	.	.	.	.	.	.	.	.	.	A	14.08	2.429549	0.43122	.	.	ENSG00000114023	ENST00000232125;ENST00000477892;ENST00000469967;ENST00000440333	T;T;T	0.40225	1.04;1.04;1.04	5.54	4.36	0.52297	.	0.087798	0.85682	D	0.000000	T	0.61173	0.2326	M	0.80847	2.515	0.36610	D	0.875176	D;D	0.76494	0.999;0.999	D;D	0.71656	0.974;0.934	T	0.69957	-0.5004	10	0.66056	D	0.02	.	8.2745	0.31864	0.9107:0.0:0.0893:0.0	.	102;102	E9PH05;Q96A26	.;F162A_HUMAN	T	92;102;102;101	ENSP00000232125:K92T;ENSP00000419088:K102T;ENSP00000419491:K102T	ENSP00000232125:K92T	K	+	2	0	FAM162A	123608859	1.000000	0.71417	0.998000	0.56505	0.009000	0.06853	4.484000	0.60271	2.323000	0.78572	0.528000	0.53228	AAG	.	.		0.413	FAM162A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355766.1	NM_014367		C	122126169	A	C	122126169	3	2	351	1	0	0	0	0	1	0	0	0	5479	72	3	5	319	5	FAM162A	3	122126169	Missense_Mutation	SNP	A	TCGA-WJ-A86L-01A-12D-A45V-10	32645788	122126169	75896261	27	49305										
PLXNA1	5361	hgsc.bcm.edu	37	chr3	126726661	126726661	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	gctgcctgtcctgtgtcaacGgctcctttccctgccactgg	10	16	1	0			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr3:126726661G>T	ENST00000393409.2	+	8	2017	c.2017G>T	c.(2017-2019)Ggc>Tgc	p.G673C	PLXNA1_ENST00000251772.4_Missense_Mutation_p.G650C	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	673					axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)			breast(3)|central_nervous_system(5)|endometrium(10)|kidney(5)|large_intestine(4)|lung(32)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	67				GBM - Glioblastoma multiforme(114;0.155)		CTGTGTCAACGGCTCCTTTCC	0.617																																					p.G673C		Atlas-SNP	.											.	PLXNA1	185	.	0			c.G2017T						.						80	68	72					3																	126726661		2203	4300	6503	SO:0001583	missense	5361	exon8			GTCAACGGCTCCT	X87832	CCDS33847.1, CCDS33847.2	3q21.2	2006-12-19				ENSG00000114554		"Plexins"	9099	protein-coding gene	gene with protein product		601055		PLXN1		8570614	Standard	NM_032242		Approved	NOV	uc003ejg.3	Q9UIW2		ENST00000393409.2:c.2017G>T	chr3.hg19:g.126726661G>T	ENSP00000377061:p.Gly673Cys	42.0	0.0		27.0	20.0	NM_032242		Missense_Mutation	SNP	ENST00000393409.2	hg19	CCDS33847.2	.	.	.	.	.	.	.	.	.	.	G	18.33	3.600044	0.66332	.	.	ENSG00000114554	ENST00000393409;ENST00000251772	T;T	0.17213	2.29;2.29	3.63	3.63	0.41609	.	0.000000	0.64402	D	0.000016	T	0.33089	0.0851	L	0.41236	1.265	0.58432	D	0.99999	D	0.89917	1.0	D	0.85130	0.997	T	0.18493	-1.0335	10	0.87932	D	0	.	15.8357	0.78796	0.0:0.0:1.0:0.0	.	673	Q9UIW2	PLXA1_HUMAN	C	673;650	ENSP00000377061:G673C;ENSP00000251772:G650C	ENSP00000251772:G650C	G	+	1	0	PLXNA1	128209351	1.000000	0.71417	0.994000	0.49952	0.967000	0.64934	3.957000	0.56730	2.025000	0.59659	0.467000	0.42956	GGC	.	.		0.617	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356451.1	NM_032242		T	126726661	G	T	126726661	3	4	351	1	0	0	0	0	1	0	0	0	12128	1116	39	1	2047	1	PLXNA1	3	126726661	Missense_Mutation	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	4600492	126726661	71295769	28	49306										
TBC1D1	23216	hgsc.bcm.edu	37	chr4	38138875	38138875	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	cggtcggccctgctgcagacGgtggaggagctgcggcggcg	20	12	0	1	rs375379532		TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr4:38138875G>A	ENST00000261439.4	+	20	3781	c.3426G>A	c.(3424-3426)acG>acA	p.T1142T	TBC1D1_ENST00000407365.1_3'UTR|TBC1D1_ENST00000508802.1_Silent_p.T1133T	NM_001253914.1|NM_001253915.1|NM_015173.3	NP_001240843.1|NP_001240844.1|NP_055988.2	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1	1142					membrane organization (GO:0061024)|regulation of protein localization (GO:0032880)	cytosol (GO:0005829)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)			NS(1)|breast(3)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	36						TGCTGCAGACGGTGGAGGAGC	0.642													G|||	1	0.000199681	8e-04	0	5008	,	,		15446	0		0	False		,,,				2504	0				p.T1142T		Atlas-SNP	.											.	TBC1D1	94	.	0			c.G3426A						.	G		1,4403	2.1+/-5.4	0,1,2201	31	36	34		3426	-2.6	0	4		34	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TBC1D1	NM_015173.2		0,2,6500	AA,AG,GG		0.0116,0.0227,0.0154		1142/1169	38138875	2,13002	2202	4300	6502	SO:0001819	synonymous_variant	23216	exon20			GCAGACGGTGGAG	AB029031	CCDS33972.1, CCDS58897.1	4p14	2013-07-09			ENSG00000065882	ENSG00000065882			11578	protein-coding gene	gene with protein product		609850				10965142, 18258599	Standard	NM_015173		Approved	TBC, TBC1, KIAA1108	uc003gtb.3	Q86TI0	OTTHUMG00000150302	ENST00000261439.4:c.3426G>A	chr4.hg19:g.38138875G>A		109.0	0.0		138.0	44.0	NM_015173	B7Z3D9|E9PGH8|Q96K82|Q9UPP4	Silent	SNP	ENST00000261439.4	hg19	CCDS33972.1	.	.	.	.	.	.	.	.	.	.	G	0.992	-0.693597	0.03303	2.27E-4	1.16E-4	ENSG00000065882	ENST00000510573	.	.	.	5.16	-2.62	0.06152	.	.	.	.	.	T	0.20577	0.0495	.	.	.	0.26265	N	0.978517	.	.	.	.	.	.	T	0.28332	-1.0047	4	.	.	.	-0.0394	3.4262	0.07412	0.2121:0.4531:0.1507:0.1841	.	.	.	.	S	830	.	.	G	+	1	0	TBC1D1	37815270	0.566000	0.26618	0.002000	0.10522	0.122000	0.20287	0.029000	0.13666	-0.434000	0.07275	-0.156000	0.13503	GGT	.	.		0.642	TBC1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317443.2	NM_015173		A	38138875	G	A	38138875	2	1	351	1	0	0	0	0	0	0	0	1	15612	1103	39	1		1	TBC1D1	4	38138875	Silent	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10		38138875	153015401	29	49307										
PHOX2B	8929	hgsc.bcm.edu	37	chr4	41748004	41748004	+	Silent	SNP	C	C	T													0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	cctccagctgccgccgctgcCgctgccgccgccgccgctgc					rs543135182|rs17879189	byFrequency	TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr4:41748004C>T	ENST00000226382.2	-	3	1124	c.765G>A	c.(763-765)gcG>gcA	p.A255A	RP11-227F19.1_ENST00000508038.1_RNA	NM_003924.3	NP_003915.2	Q99453	PHX2B_HUMAN	paired-like homeobox 2b	255	Poly-Ala.		Missing. {ECO:0000269|PubMed:14566559}.		autonomic nervous system development (GO:0048483)|brainstem development (GO:0003360)|cell differentiation in hindbrain (GO:0021533)|cellular response to BMP stimulus (GO:0071773)|dopaminergic neuron differentiation (GO:0071542)|efferent axon development in a lateral line nerve (GO:0048894)|enteric nervous system development (GO:0048484)|glial cell differentiation (GO:0010001)|hindbrain tangential cell migration (GO:0021934)|inner ear development (GO:0048839)|medullary reticular formation development (GO:0021723)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neuron migration (GO:0001764)|noradrenergic neuron development (GO:0003358)|noradrenergic neuron differentiation (GO:0003357)|parasympathetic nervous system development (GO:0048486)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression (GO:0010468)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|respiratory system development (GO:0060541)|retrotrapezoid nucleus neuron differentiation (GO:0061452)|skeletal muscle cell differentiation (GO:0035914)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)			autonomic_ganglia(7)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	30						ccgccgctgccgctgccgccg	0.821			"Mis, F"		neuroblastoma	neuroblastoma	congenital central hypoventilation syndrome		Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome				C|||	2	0.000399361	0	0	5008	,	,		3548	0		0.001	False		,,,				2504	0.001				p.A255A		Atlas-SNP	.	yes	Rec	yes	familial neuroblastoma	4	4p12	8929	paired-like homeobox 2b	yes	O	.	PHOX2B	53	.	0			c.G765A						.						2	4	3					4																	41748004		698	1850	2548	SO:0001819	synonymous_variant	8929	exon3	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	CGCTGCCGCTGCC	D82344	CCDS3463.1	4p13	2014-09-17	2003-02-10	2003-02-14	ENSG00000109132	ENSG00000109132		"Homeoboxes / PRD class"	9143	protein-coding gene	gene with protein product		603851	"paired mesoderm homeobox 2b"	PMX2B		9039501, 10395798	Standard	NM_003924		Approved	Phox2b, NBPhox	uc003gwf.4	Q99453	OTTHUMG00000099379	ENST00000226382.2:c.765G>A	chr4.hg19:g.41748004C>T		99.0	0.0		141.0	69.0	NM_003924	Q6PJD9	Silent	SNP	ENST00000226382.2	hg19	CCDS3463.1																																																																																			.	.		0.821	PHOX2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216832.2			T	41748004	C	T	41748004	2	4	351	1	0	0	0	0	0	0	0	1	11868	639	23	1		1	PHOX2B	4	41748004	Silent	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	3609129	41748004	149406272	30	49308	258	2								
PHOX2B	8929	hgsc.bcm.edu	37	chr4	41748009	41748009	+	Frame_Shift_Del	DEL	C	C	-													0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	agctgccgccgctgccgctgCcgccgccgccgctgccgcgg					rs17879189		TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr4:41748009delC	ENST00000226382.2	-	3	1119	c.760delG	c.(760-762)gcafs	p.A260fs	RP11-227F19.1_ENST00000508038.1_RNA	NM_003924.3	NP_003915.2	Q99453	PHX2B_HUMAN	paired-like homeobox 2b	260	Poly-Ala.				autonomic nervous system development (GO:0048483)|brainstem development (GO:0003360)|cell differentiation in hindbrain (GO:0021533)|cellular response to BMP stimulus (GO:0071773)|dopaminergic neuron differentiation (GO:0071542)|efferent axon development in a lateral line nerve (GO:0048894)|enteric nervous system development (GO:0048484)|glial cell differentiation (GO:0010001)|hindbrain tangential cell migration (GO:0021934)|inner ear development (GO:0048839)|medullary reticular formation development (GO:0021723)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neuron migration (GO:0001764)|noradrenergic neuron development (GO:0003358)|noradrenergic neuron differentiation (GO:0003357)|parasympathetic nervous system development (GO:0048486)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression (GO:0010468)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|respiratory system development (GO:0060541)|retrotrapezoid nucleus neuron differentiation (GO:0061452)|skeletal muscle cell differentiation (GO:0035914)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)			autonomic_ganglia(7)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	30						gctgccgctgccgccgccgcc	0.821			"Mis, F"		neuroblastoma	neuroblastoma	congenital central hypoventilation syndrome		Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																												p.A254fs		Atlas-INDEL	.	yes	Rec	yes	familial neuroblastoma	4	4p12	8929	paired-like homeobox 2b	yes	O	.	PHOX2B	53	.	0			c.761delC						.						2	3	3					4																	41748009		528	1561	2089	SO:0001589	frameshift_variant	8929	exon3	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	.	D82344	CCDS3463.1	4p13	2014-09-17	2003-02-10	2003-02-14	ENSG00000109132	ENSG00000109132		"Homeoboxes / PRD class"	9143	protein-coding gene	gene with protein product		603851	"paired mesoderm homeobox 2b"	PMX2B		9039501, 10395798	Standard	NM_003924		Approved	Phox2b, NBPhox	uc003gwf.4	Q99453	OTTHUMG00000099379	ENST00000226382.2:c.760delG	chr4.hg19:g.41748009delC	ENSP00000226382:p.Ala260fs	78.0	0.0		128.0	49.0	NM_003924	Q6PJD9	Frame_Shift_Del	DEL	ENST00000226382.2	hg19	CCDS3463.1																																																																																			.	.		0.821	PHOX2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216832.2			-	41748009	C	-	41748009	7	5	351	1	0	1	0	1	0	0	0	0	11868	739	26	0	188	0	PHOX2B	4	41748009	Frame_Shift_Del	DEL	C	TCGA-WJ-A86L-01A-12D-A45V-10	5	41748009	149406267	31	49309	258	2								
FRAS1	80144	hgsc.bcm.edu	37	chr4	79350344	79350344	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	tgttccaggtcacagctccaCggctggcggtcagcccagga	13	14	2	0			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr4:79350344C>A	ENST00000325942.6	+	36	5247	c.4807C>A	c.(4807-4809)Cgg>Agg	p.R1603R	FRAS1_ENST00000264895.6_Silent_p.R1603R	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	1603					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						CACAGCTCCACGGCTGGCGGT	0.517																																					p.R1603R		Atlas-SNP	.											.	FRAS1	779	.	0			c.C4807A						.						46	49	48					4																	79350344		2054	4193	6247	SO:0001819	synonymous_variant	80144	exon36			GCTCCACGGCTGG	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.4807C>A	chr4.hg19:g.79350344C>A		50.0	0.0		53.0	22.0	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000325942.6	hg19	CCDS54772.1	.	.	.	.	.	.	.	.	.	.	C	0.033	-1.319831	0.01320	.	.	ENSG00000138759	ENST00000510944	.	.	.	5.61	-1.1	0.09872	.	.	.	.	.	T	0.19127	0.0459	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.24190	-1.0167	4	.	.	.	.	1.4515	0.02376	0.2465:0.1524:0.3944:0.2067	.	.	.	.	K	52	.	.	T	+	2	0	FRAS1	79569368	0.001000	0.12720	0.002000	0.10522	0.000000	0.00434	-0.289000	0.08365	0.044000	0.15775	-0.122000	0.15005	ACG	.	.		0.517	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2			A	79350344	C	A	79350344	2	1	351	1	0	0	0	0	0	0	0	1	6050	527	19	1		1	FRAS1	4	79350344	Silent	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	37602335	79350344	111803932	32	49310										
FRAS1	80144	hgsc.bcm.edu	37	chr4	79432632	79432632	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	tcgcaaccttgaaatacctgGatgtcaaacataaggagcat	8	9	1	1			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr4:79432632G>A	ENST00000264895.6	+	64	10425	c.9985G>A	c.(9985-9987)Gat>Aat	p.D3329N		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3325					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)	p.D3330Y(1)|p.D3329Y(1)		breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						GAAATACCTGGATGTCAAACA	0.512																																					p.D3329N		Atlas-SNP	.											FRAS1_ENST00000264895,NS,carcinoma,0,2	FRAS1	779	.	2	Substitution - Missense(2)	lung(2)	c.G9985A						.						49	48	48					4																	79432632		1969	4156	6125	SO:0001583	missense	80144	exon64			TACCTGGATGTCA	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"Fraser syndrome 1"			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.9985G>A	chr4.hg19:g.79432632G>A	ENSP00000264895:p.Asp3329Asn	107.0	0.0		118.0	51.0	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000264895.6	hg19	CCDS54771.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	32|32	5.175004|5.175004	0.94807|0.94807	.|.	.|.	ENSG00000138759|ENSG00000138759	ENST00000264895|ENST00000512123	T|.	0.12672|.	2.66|.	5.86|5.86	5.86|5.86	0.93980|0.93980	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.70185|0.70185	0.3195|0.3195	L|L	0.46741|0.46741	1.465|1.465	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	0.994;1.0|.	D;D|.	0.74023|.	0.911;0.982|.	T|T	0.64149|0.64149	-0.6475|-0.6475	10|5	0.44086|.	T|.	0.13|.	.|.	20.1882|20.1882	0.98224|0.98224	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	3328;3329|.	Q86XX4-2;E9PHH6|.	.;.|.	N|E	3329|1557	ENSP00000264895:D3329N|.	ENSP00000264895:D3329N|.	D|G	+|+	1|2	0|0	FRAS1|FRAS1	79651656|79651656	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.893000|0.893000	0.52053|0.52053	9.657000|9.657000	0.98554|0.98554	2.783000|2.783000	0.95769|0.95769	0.591000|0.591000	0.81541|0.81541	GAT|GGA	.	.		0.512	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	79432632	G	A	79432632	3	1	351	1	0	0	0	0	1	0	0	0	6050	1174	41	3	10314	3	FRAS1	4	79432632	Missense_Mutation	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	82288	79432632	111721644	33	49311										
QRFPR	84109	hgsc.bcm.edu	37	chr4	122250606	122250606	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	atcactgaatgcttctccttTggtttcctccactggattct	6	12	3	1			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr4:122250606T>C	ENST00000394427.2	-	6	1570	c.1159A>G	c.(1159-1161)Aaa>Gaa	p.K387E	Y_RNA_ENST00000384419.1_RNA|QRFPR_ENST00000334383.5_3'UTR	NM_198179.2	NP_937822.2	Q96P65	QRFPR_HUMAN	pyroglutamylated RFamide peptide receptor	387					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide Y receptor activity (GO:0004983)			endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(2)|skin(3)|stomach(1)	28						GCTTCTCCTTTGGTTTCCTCC	0.418																																					p.K387E		Atlas-SNP	.											.	QRFPR	65	.	0			c.A1159G						.						238	235	236					4																	122250606		2203	4300	6503	SO:0001583	missense	84109	exon6			CTCCTTTGGTTTC	AF411117	CCDS3719.1	4q27	2012-08-10	2008-12-18	2008-12-18	ENSG00000186867	ENSG00000186867		"GPCR / Class A : RF amide peptide receptors"	15565	protein-coding gene	gene with protein product		606925	"G protein-coupled receptor 103"	GPR103		11574155	Standard	NM_198179		Approved		uc010inj.1	Q96P65	OTTHUMG00000133036	ENST00000394427.2:c.1159A>G	chr4.hg19:g.122250606T>C	ENSP00000377948:p.Lys387Glu	107.0	0.0		123.0	55.0	NM_198179		Missense_Mutation	SNP	ENST00000394427.2	hg19	CCDS3719.1	.	.	.	.	.	.	.	.	.	.	T	10.00	1.233287	0.22626	.	.	ENSG00000186867	ENST00000394427	T	0.72394	-0.65	5.16	2.74	0.32292	.	0.290888	0.36703	N	0.002447	T	0.49677	0.1571	L	0.27053	0.805	0.46028	D	0.998822	B	0.14805	0.011	B	0.10450	0.005	T	0.34650	-0.9820	10	0.06099	T	0.92	.	8.9893	0.36014	0.0:0.1523:0.0:0.8477	.	387	Q96P65	QRFPR_HUMAN	E	387	ENSP00000377948:K387E	ENSP00000377948:K387E	K	-	1	0	QRFPR	122470056	0.626000	0.27120	0.900000	0.35374	0.099000	0.18886	2.414000	0.44627	0.805000	0.34159	0.260000	0.18958	AAA	.	.		0.418	QRFPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256641.2	NM_198179		C	122250606	T	C	122250606	3	2	351	1	0	0	0	0	1	0	0	0	12893	1821	63	2	140	2	QRFPR	4	122250606	Missense_Mutation	SNP	T	TCGA-WJ-A86L-01A-12D-A45V-10	42817974	122250606	68903670	34	49312										
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123179983	123179983	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	actcatacccatagtgactcTgcattaaaaataaaggtata	5	8	2	1			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr4:123179983T>C	ENST00000264501.4	+	42	7120	c.6747T>C	c.(6745-6747)tcT>tcC	p.S2249S	KIAA1109_ENST00000388738.3_Silent_p.S2249S|KIAA1109_ENST00000455637.1_Silent_p.S2249S			Q2LD37	K1109_HUMAN	KIAA1109	2249					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						ATAGTGACTCTGCATTAAAAA	0.368																																					p.S2249S		Atlas-SNP	.											.	KIAA1109	424	.	0			c.T6747C						.						78	73	74					4																	123179983		1831	4087	5918	SO:0001819	synonymous_variant	84162	exon40			TGACTCTGCATTA	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.6747T>C	chr4.hg19:g.123179983T>C		81.0	0.0		75.0	26.0	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Silent	SNP	ENST00000264501.4	hg19	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.156|9.156	1.017492|1.017492	0.19355|0.19355	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000419325|ENST00000446180	.|.	.|.	.|.	5.96|5.96	3.39|3.39	0.38822|0.38822	.|.	.|.	.|.	.|.	.|.	T|T	0.59046|0.59046	0.2165|0.2165	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.55392|0.55392	-0.8148|-0.8148	4|4	.|.	.|.	.|.	.|.	9.4181|9.4181	0.38534|0.38534	0.1206:0.0:0.1267:0.7527|0.1206:0.0:0.1267:0.7527	.|.	.|.	.|.	.|.	R|P	207|822	.|.	.|.	C|L	+|+	1|2	0|0	KIAA1109|KIAA1109	123399433|123399433	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	2.559000|2.559000	0.45888|0.45888	1.060000|1.060000	0.40578|0.40578	0.477000|0.477000	0.44152|0.44152	TGC|CTG	.	.		0.368	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		C	123179983	T	C	123179983	2	2	351	1	0	0	0	0	0	0	0	1	8217	1567	55	2		2	KIAA1109	4	123179983	Silent	SNP	T	TCGA-WJ-A86L-01A-12D-A45V-10	929377	123179983	67974293	35	49313										
SCOC	60592	hgsc.bcm.edu	37	chr4	141294733	141294742	+	Frame_Shift_Del	DEL	GGCTGGGACG	GGCTGGGACG	-													0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	gtcaggattggcgggcgagcGgctgggacgggatgggattc							TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	GGCTGGGACG	GGCTGGGACG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr4:141294733_141294742delGGCTGGGACG	ENST00000608372.1	+	1	70_79	c.43_52delGGCTGGGACG	c.(43-54)ggctgggacgggfs	p.GWDG15fs	SCOC_ENST00000394203.3_Intron|SCOC_ENST00000506597.1_Frame_Shift_Del_p.GWDG15fs|SCOC_ENST00000512749.1_Intron|SCOC_ENST00000510586.1_5'Flank|RP11-425I13.3_ENST00000512692.2_RNA|RP11-425I13.3_ENST00000609616.1_RNA|RP11-425I13.3_ENST00000608178.1_RNA|SCOC_ENST00000506322.1_Intron|SCOC_ENST00000394201.4_5'Flank|SCOC_ENST00000338517.4_Intron|SCOC_ENST00000394205.3_Intron|SCOC_ENST00000502535.1_5'Flank			Q9UIL1	SCOC_HUMAN	short coiled-coil protein	15					positive regulation of macroautophagy (GO:0016239)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)				kidney(1)|large_intestine(1)|lung(2)|skin(1)	5	all_hematologic(180;0.162)					GCGGGCGAGCGGCTGGGACGGGATGGGATT	0.648																																					p.14_17del		Atlas-INDEL	.											.	SCOC	11	.	0			c.42_51del						.																																			SO:0001589	frameshift_variant	60592	exon1			.	AK027797	CCDS3750.1, CCDS54806.1, CCDS54807.1	4q28.3	2014-05-22	2003-03-19		ENSG00000153130	ENSG00000153130			20335	protein-coding gene	gene with protein product			"short coiled coil protein"			11303027	Standard	NM_032547		Approved	HRIHFB2072, SCOCO	uc011che.1	Q9UIL1	OTTHUMG00000133416	ENST00000608372.1:c.43_52delGGCTGGGACG	chr4.hg19:g.141294733_141294742delGGCTGGGACG	ENSP00000477352:p.Gly15fs	82.0	0.0		51.0	17.0	NM_001153552	B7WPH7|D3DNY7|E9PB65|Q6P5T9|Q7L2Y0|Q7Z4P2|Q96JY9|Q9BZB2	Frame_Shift_Del	DEL	ENST00000608372.1	hg19	CCDS54806.1																																																																																			.	.		0.648	SCOC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257274.2			-	141294742	GGCTGGGACG	-	141294733	7	5	351	1	0	1	0	1	0	0	0	0	13948	1116	39	0	119	0	SCOC	4	141294733	Frame_Shift_Del	DEL	GGCTGGGACG	TCGA-WJ-A86L-01A-12D-A45V-10	18114750	141294733	49859543	36	49314										
DDX60L	91351	hgsc.bcm.edu	37	chr4	169327112	169327112	+	Frame_Shift_Del	DEL	G	G	-													0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	gaaaattaccttcttcacttGgccatttttaatccaatttg							TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr4:169327112delG	ENST00000511577.1	-	24	3449	c.3202delC	c.(3202-3204)caafs	p.Q1068fs	DDX60L_ENST00000505890.1_Frame_Shift_Del_p.Q1068fs|DDX60L_ENST00000260184.7_Frame_Shift_Del_p.Q1068fs			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	1068							ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		TTCTTCACTTGGCCATTTTTA	0.274																																					p.Q1068fs		Atlas-INDEL	.											.	DDX60L	116	.	0			c.3203delA						.						110	98	101					4																	169327112		1837	4119	5956	SO:0001589	frameshift_variant	91351	exon24			.	AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.3202delC	chr4.hg19:g.169327112delG	ENSP00000422423:p.Gln1068fs	99.0	0.0		81.0	32.0	NM_001012967	Q96ND6	Frame_Shift_Del	DEL	ENST00000511577.1	hg19																																																																																				.	.		0.274	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967		-	169327112	G	-	169327112	7	5	351	1	0	1	0	1	0	0	0	0	4381	1357	47	0	1978	0	DDX60L	4	169327112	Frame_Shift_Del	DEL	G	TCGA-WJ-A86L-01A-12D-A45V-10	28032379	169327112	21827164	37	49315										
ADAMTS16	170690	hgsc.bcm.edu	37	chr5	5235288	5235288	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	ctacaagtggaagccttacaCtcaagtagaaggtaaatctc	8	9	2	1			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr5:5235288C>G	ENST00000274181.7	+	13	2150	c.2012C>G	c.(2011-2013)aCt>aGt	p.T671S	ADAMTS16_ENST00000513709.1_3'UTR	NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16	671	Cys-rich.				branching involved in ureteric bud morphogenesis (GO:0001658)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(72)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	107						AAGCCTTACACTCAAGTAGAA	0.468																																					p.T671S		Atlas-SNP	.											.	ADAMTS16	543	.	0			c.C2012G						.						63	66	65					5																	5235288		1940	4138	6078	SO:0001583	missense	170690	exon13			CTTACACTCAAGT	AJ315734	CCDS43299.1	5p15	2008-07-18	2005-08-19		ENSG00000145536	ENSG00000145536		"ADAM metallopeptidases with thrombospondin type 1 motif"	17108	protein-coding gene	gene with protein product		607510	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 16"			11867212	Standard	NM_139056		Approved	ADAMTS16s	uc003jdl.3	Q8TE57	OTTHUMG00000161663	ENST00000274181.7:c.2012C>G	chr5.hg19:g.5235288C>G	ENSP00000274181:p.Thr671Ser	111.0	0.0		108.0	52.0	NM_139056	C6G490|Q8IVE2	Missense_Mutation	SNP	ENST00000274181.7	hg19	CCDS43299.1	.	.	.	.	.	.	.	.	.	.	C	14.41	2.526794	0.44969	.	.	ENSG00000145536	ENST00000274181;ENST00000536857	T	0.03468	3.92	4.57	3.69	0.42338	.	0.058374	0.64402	D	0.000003	T	0.10551	0.0258	L	0.51853	1.615	0.53688	D	0.999979	D;D	0.89917	0.999;1.0	D;D	0.80764	0.991;0.994	T	0.28235	-1.0050	10	0.09084	T	0.74	.	13.1971	0.59745	0.1609:0.8391:0.0:0.0	.	671;671	Q8TE57;Q8TE57-2	ATS16_HUMAN;.	S	671	ENSP00000274181:T671S	ENSP00000274181:T671S	T	+	2	0	ADAMTS16	5288288	1.000000	0.71417	0.781000	0.31783	0.204000	0.24138	7.400000	0.79949	1.050000	0.40346	-0.169000	0.13324	ACT	.	.		0.468	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365657.1	NM_139056		G	5235288	C	G	5235288	3	3	351	1	0	0	0	0	1	0	0	0	261	565	20	4	2062	4	ADAMTS16	5	5235288	Missense_Mutation	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10		5235288	175679972	38	49316										
CDH10	1008	hgsc.bcm.edu	37	chr5	24537662	24537662	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	aaaaggccttttcctccctaTcaattcgccttgtggcatga	7	12	1	1			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr5:24537662T>A	ENST00000264463.4	-	3	860	c.353A>T	c.(352-354)gAt>gTt	p.D118V		NM_006727.3	NP_006718.2	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 (T2-cadherin)	118	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(29)|lung(111)|ovary(6)|pancreas(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)	185				STAD - Stomach adenocarcinoma(35;0.0556)		TTCCTCCCTATCAATTCGCCT	0.398										HNSCC(23;0.051)																											p.D118V		Atlas-SNP	.											.	CDH10	391	.	0			c.A353T						.						153	141	145					5																	24537662		2203	4300	6503	SO:0001583	missense	1008	exon3			TCCCTATCAATTC	AF039747	CCDS3892.1	5p14.2	2010-01-26			ENSG00000040731	ENSG00000040731		"Cadherins / Major cadherins"	1749	protein-coding gene	gene with protein product		604555				2059658	Standard	NM_006727		Approved		uc003jgr.2	Q9Y6N8	OTTHUMG00000090667	ENST00000264463.4:c.353A>T	chr5.hg19:g.24537662T>A	ENSP00000264463:p.Asp118Val	92.0	0.0		84.0	46.0	NM_006727	Q9ULB3	Missense_Mutation	SNP	ENST00000264463.4	hg19	CCDS3892.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.450592	0.84101	.	.	ENSG00000040731	ENST00000264463	T	0.65364	-0.15	5.82	5.82	0.92795	Cadherin (5);Cadherin-like (1);	0.000000	0.85682	D	0.000000	D	0.87354	0.6156	H	0.98295	4.195	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92124	0.5706	10	0.87932	D	0	.	15.3558	0.74425	0.0:0.0:0.0:1.0	.	118	Q9Y6N8	CAD10_HUMAN	V	118	ENSP00000264463:D118V	ENSP00000264463:D118V	D	-	2	0	CDH10	24573419	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	7.698000	0.84413	2.225000	0.72522	0.455000	0.32223	GAT	.	.		0.398	CDH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207345.2	NM_006727		A	24537662	T	A	24537662	3	1	351	1	0	0	0	0	1	0	0	0	3098	1435	50	4	2053	4	CDH10	5	24537662	Missense_Mutation	SNP	T	TCGA-WJ-A86L-01A-12D-A45V-10	19302374	24537662	156377598	39	49317										
CMYA5	202333	hgsc.bcm.edu	37	chr5	79032250	79032250	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	ctttcagaaggaaagaagcaGcaggaacatcagccttattc	9	9	2	2			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr5:79032250G>T	ENST00000446378.2	+	2	7693	c.7662G>T	c.(7660-7662)caG>caT	p.Q2554H		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2554					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		GAAAGAAGCAGCAGGAACATC	0.368																																					p.Q2554H		Atlas-SNP	.											.	CMYA5	643	.	0			c.G7662T						.						69	66	67					5																	79032250		1893	4115	6008	SO:0001583	missense	202333	exon2			GAAGCAGCAGGAA	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.7662G>T	chr5.hg19:g.79032250G>T	ENSP00000394770:p.Gln2554His	86.0	0.0		98.0	35.0	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	hg19	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	G	9.557	1.117480	0.20877	.	.	ENSG00000164309	ENST00000446378	T	0.21361	2.01	5.16	0.983	0.19767	.	1.661270	0.03317	N	0.191328	T	0.24736	0.0600	L	0.57536	1.79	0.09310	N	1	B	0.32693	0.38	B	0.37198	0.243	T	0.26985	-1.0087	10	0.51188	T	0.08	.	3.7823	0.08686	0.186:0.0:0.4559:0.3581	.	2554	Q8N3K9	CMYA5_HUMAN	H	2554	ENSP00000394770:Q2554H	ENSP00000394770:Q2554H	Q	+	3	2	CMYA5	79068006	0.851000	0.29673	0.457000	0.27056	0.331000	0.28603	0.180000	0.16860	0.331000	0.23511	0.462000	0.41574	CAG	.	.		0.368	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		T	79032250	G	T	79032250	3	4	351	1	0	0	0	0	1	0	0	0	3592	962	34	3	7668	3	CMYA5	5	79032250	Missense_Mutation	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	54494588	79032250	101883010	40	49318										
CTNNA1	1495	hgsc.bcm.edu	37	chr5	138260300	138260300	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	gtgcaattcgaggccgggcaGcccgggtcattcacgtagtc	14	12	2	0			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr5:138260300G>T	ENST00000302763.7	+	12	1738	c.1648G>T	c.(1648-1650)Gcc>Tcc	p.A550S	CTNNA1_ENST00000540387.1_Missense_Mutation_p.A180S|CTNNA1_ENST00000355078.5_Missense_Mutation_p.A447S|CTNNA1_ENST00000518825.1_Missense_Mutation_p.A550S	NM_001903.2	NP_001894.2	P35221	CTNA1_HUMAN	catenin (cadherin-associated protein), alpha 1, 102kDa	550					adherens junction organization (GO:0034332)|aging (GO:0007568)|apical junction assembly (GO:0043297)|axon regeneration (GO:0031103)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular protein localization (GO:0034613)|cellular response to indole-3-methanol (GO:0071681)|epithelial cell-cell adhesion (GO:0090136)|establishment or maintenance of cell polarity (GO:0007163)|gap junction assembly (GO:0016264)|male gonad development (GO:0008584)|muscle cell differentiation (GO:0042692)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell motility (GO:2000146)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|negative regulation of neuroblast proliferation (GO:0007406)|odontogenesis of dentin-containing tooth (GO:0042475)|ovarian follicle development (GO:0001541)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of smoothened signaling pathway (GO:0045880)|protein heterooligomerization (GO:0051291)|response to estrogen (GO:0043627)	acrosomal vesicle (GO:0001669)|actin cytoskeleton (GO:0015629)|catenin complex (GO:0016342)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|gamma-catenin binding (GO:0045295)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)|vinculin binding (GO:0017166)			NS(1)|breast(7)|cervix(2)|endometrium(4)|kidney(6)|large_intestine(16)|lung(9)|oesophagus(2)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	52			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			AGGCCGGGCAGCCCGGGTCAT	0.522																																					p.A550S		Atlas-SNP	.											.	CTNNA1	114	.	0			c.G1648T						.						54	49	50					5																	138260300		2203	4300	6503	SO:0001583	missense	1495	exon12			CGGGCAGCCCGGG	D13866	CCDS34243.1, CCDS75315.1	5q31.2	2008-02-05	2002-08-29			ENSG00000044115			2509	protein-coding gene	gene with protein product		116805	"catenin (cadherin-associated protein), alpha 1 (102kD)"			1924379	Standard	XM_005271898		Approved	CAP102	uc003ldh.3	P35221		ENST00000302763.7:c.1648G>T	chr5.hg19:g.138260300G>T	ENSP00000304669:p.Ala550Ser	153.0	0.0		113.0	55.0	NM_001903	Q12795|Q8N1C0	Missense_Mutation	SNP	ENST00000302763.7	hg19	CCDS34243.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.934068	0.73442	.	.	ENSG00000044115	ENST00000355078;ENST00000302763;ENST00000537034;ENST00000541863;ENST00000518825;ENST00000540387	T;T;T;T	0.37411	1.2;1.2;1.2;1.2	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.33147	0.0853	L	0.41415	1.275	0.80722	D	1	B;B;B	0.14012	0.009;0.002;0.001	B;B;B	0.26770	0.073;0.027;0.054	T	0.13683	-1.0500	10	0.09338	T	0.73	-14.4517	19.3816	0.94540	0.0:0.0:1.0:0.0	.	550;427;550	G3XAM7;B4DKT9;P35221	.;.;CTNA1_HUMAN	S	447;550;550;535;550;180	ENSP00000347190:A447S;ENSP00000304669:A550S;ENSP00000427821:A550S;ENSP00000438476:A180S	ENSP00000304669:A550S	A	+	1	0	CTNNA1	138288199	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.756000	0.94617	0.655000	0.94253	GCC	.	.		0.522	CTNNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373868.1	NM_001903		T	138260300	G	T	138260300	3	4	351	1	0	0	0	0	1	0	0	0	4014	971	34	3	1690	3	CTNNA1	5	138260300	Missense_Mutation	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	59228050	138260300	42654960	41	49319										
PCDHA6	56142	hgsc.bcm.edu	37	chr5	140208117	140208117	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	ctgatttacgaatctaggctGccagattctgtgtttccact	8	10	2	2			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr5:140208117G>A	ENST00000529310.1	+	1	555	c.441G>A	c.(439-441)ctG>ctA	p.L147L	PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000527624.1_Silent_p.L147L|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018909.2|NM_031848.2|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6	147					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(42)|prostate(8)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	89			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AATCTAGGCTGCCAGATTCTG	0.498																																					p.L147L		Atlas-SNP	.											.	PCDHA6	442	.	0			c.G441A						.						88	93	91					5																	140208117		2203	4300	6503	SO:0001819	synonymous_variant	56142	exon1			TAGGCTGCCAGAT	AF152484	CCDS47281.1, CCDS47282.1	5q31	2010-11-26			ENSG00000081842	ENSG00000081842		"Cadherins / Protocadherins : Clustered"	8672	other	complex locus constituent	"KIAA0345-like 8"	606312		CNRS2		10380929, 10662547	Standard	NM_018909		Approved	CNR2, CRNR2, PCDH-ALPHA6		Q9UN73	OTTHUMG00000163353	ENST00000529310.1:c.441G>A	chr5.hg19:g.140208117G>A		148.0	0.0		129.0	63.0	NM_018909	O75283|Q9NRT8	Silent	SNP	ENST00000529310.1	hg19	CCDS47281.1																																																																																			.	.		0.498	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372829.3	NM_018909		A	140208117	G	A	140208117	2	1	351	1	0	0	0	0	0	0	0	1	11537	1306	46	3		3	PCDHA6	5	140208117	Silent	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	1947817	140208117	40707143	42	49320										
GABRG2	2566	hgsc.bcm.edu	37	chr5	161576316	161576316	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	aaagataaaaagaagaaaaaCcctgtatgtatcattttcca	5	6	1	3			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr5:161576316C>G	ENST00000361925.4	+	8	1345	c.1125C>G	c.(1123-1125)aaC>aaG	p.N375K	GABRG2_ENST00000393933.4_Missense_Mutation_p.N280K|GABRG2_ENST00000414552.2_Missense_Mutation_p.N415K|GABRG2_ENST00000356592.3_Missense_Mutation_p.N375K			P18507	GBRG2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 2	375					adult behavior (GO:0030534)|cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|post-embryonic development (GO:0009791)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|GABA-A receptor complex (GO:1902711)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(15)|lung(24)|ovary(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	62	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	AGAAGAAAAACCCTGTATGTA	0.393																																					p.N415K		Atlas-SNP	.											.	GABRG2	142	.	0			c.C1245G						.						93	80	84					5																	161576316		2203	4300	6503	SO:0001583	missense	2566	exon9			GAAAAACCCTGTA		CCDS4358.1, CCDS4359.1, CCDS47333.1	5q34	2012-06-22			ENSG00000113327	ENSG00000113327		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4087	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma 2"	137164					Standard	NM_198904		Approved		uc010jjc.3	P18507	OTTHUMG00000130350	ENST00000361925.4:c.1125C>G	chr5.hg19:g.161576316C>G	ENSP00000354651:p.Asn375Lys	52.0	0.0		72.0	28.0	NM_198903	F5HB82|Q6GRL6|Q6PCC3|Q9UDB3|Q9UN15	Missense_Mutation	SNP	ENST00000361925.4	hg19	CCDS4358.1	.	.	.	.	.	.	.	.	.	.	C	0.880	-0.729058	0.03135	.	.	ENSG00000113327	ENST00000356592;ENST00000414552;ENST00000361925;ENST00000393933	D;D;D;D	0.85088	-1.85;-1.85;-1.94;-1.94	5.61	-0.367	0.12541	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.873625	0.09863	N	0.745948	T	0.72622	0.3483	N	0.25647	0.755	0.80722	D	1	B;B;B	0.16603	0.01;0.005;0.018	B;B;B	0.18263	0.008;0.021;0.012	T	0.57957	-0.7721	10	0.02654	T	1	.	12.4207	0.55518	0.0:0.5703:0.0:0.4297	.	415;375;375	F5HB82;P18507;P18507-2	.;GBRG2_HUMAN;.	K	375;415;375;280	ENSP00000349000:N375K;ENSP00000410732:N415K;ENSP00000354651:N375K;ENSP00000377510:N280K	ENSP00000349000:N375K	N	+	3	2	GABRG2	161508894	0.336000	0.24757	0.993000	0.49108	0.726000	0.41606	-0.392000	0.07314	-0.160000	0.11002	-0.961000	0.02630	AAC	.	.		0.393	GABRG2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252706.1			G	161576316	C	G	161576316	3	3	351	1	0	0	0	0	1	0	0	0	6180	506	18	4	1279	4	GABRG2	5	161576316	Missense_Mutation	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	21368199	161576316	19338944	43	49321										
RANBP17	64901	hgsc.bcm.edu	37	chr5	170319441	170319441	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	agcccaagctggctccctttGtcatccaagctcttattcaa	6	14	3	0			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr5:170319441G>T	ENST00000523189.1	+	4	471	c.307G>T	c.(307-309)Gtc>Ttc	p.V103F		NM_022897.3	NP_075048.1	Q9H2T7	RBP17_HUMAN	RAN binding protein 17	103					mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)	GTP binding (GO:0005525)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	50	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			GGCTCCCTTTGTCATCCAAGC	0.403			T	TRD@	ALL																																p.V103F		Atlas-SNP	.		Dom	yes		5	5q34	64901	RAN binding protein 17		L	.	RANBP17	108	.	0			c.G307T						.						171	167	168					5																	170319441		2203	4300	6503	SO:0001583	missense	64901	exon4			CCCTTTGTCATCC	AF222747	CCDS34287.1	5q34	2009-01-12			ENSG00000204764	ENSG00000204764			14428	protein-coding gene	gene with protein product		606141				11024021	Standard	NM_022897		Approved		uc003mba.3	Q9H2T7	OTTHUMG00000163203	ENST00000523189.1:c.307G>T	chr5.hg19:g.170319441G>T	ENSP00000427975:p.Val103Phe	124.0	0.0		110.0	51.0	NM_022897	Q8IU74	Missense_Mutation	SNP	ENST00000523189.1	hg19	CCDS34287.1	.	.	.	.	.	.	.	.	.	.	G	33	5.270013	0.95429	.	.	ENSG00000204764	ENST00000523189;ENST00000545246;ENST00000519944	T	0.73152	-0.72	5.92	5.92	0.95590	Armadillo-type fold (1);	0.000000	0.56097	D	0.000024	D	0.88559	0.6469	M	0.92122	3.275	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.80764	0.994;0.994	D	0.90012	0.4122	10	0.66056	D	0.02	-14.9791	19.9157	0.97061	0.0:0.0:1.0:0.0	.	103;153	Q9H2T7;B4DQG2	RBP17_HUMAN;.	F	103;21;21	ENSP00000427975:V103F	ENSP00000373770:V103F	V	+	1	0	RANBP17	170252019	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.386000	0.97228	2.813000	0.96785	0.561000	0.74099	GTC	.	.		0.403	RANBP17-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372036.1	NM_022897		T	170319441	G	T	170319441	3	4	351	1	0	0	0	0	1	0	0	0	13042	1377	48	3	321	3	RANBP17	5	170319441	Missense_Mutation	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	8743125	170319441	10595819	44	49322										
SCUBE3	222663	hgsc.bcm.edu	37	chr6	35211877	35211877	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	tcaccaccaagcatgaagggGccatttccttccaagactgt	8	13	1	2			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr6:35211877G>A	ENST00000274938.7	+	17	2209	c.2209G>A	c.(2209-2211)Gcc>Acc	p.A737T	SCUBE3_ENST00000394681.1_Missense_Mutation_p.A753T	NM_152753.2	NP_689966.2			signal peptide, CUB domain, EGF-like 3											breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(12)|lung(11)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	37						GCATGAAGGGGCCATTTCCTT	0.567																																					p.A737T		Atlas-SNP	.											.	SCUBE3	99	.	0			c.G2209A						.						90	79	82					6																	35211877		2203	4299	6502	SO:0001583	missense	222663	exon17			GAAGGGGCCATTT	AF452494.1	CCDS4800.1	6p21.3	2008-02-05	2004-05-19	2004-05-21		ENSG00000146197			13655	protein-coding gene	gene with protein product		614708	"CUB domain and EGF-like repeat containing 3"	CEGF3		12270931	Standard	NM_152753		Approved	FLJ34743	uc003okf.1	Q8IX30		ENST00000274938.7:c.2209G>A	chr6.hg19:g.35211877G>A	ENSP00000274938:p.Ala737Thr	79.0	0.0		69.0	31.0	NM_152753		Missense_Mutation	SNP	ENST00000274938.7	hg19	CCDS4800.1	.	.	.	.	.	.	.	.	.	.	G	17.97	3.519592	0.64634	.	.	ENSG00000146197	ENST00000394681;ENST00000274938	T;T	0.21031	2.03;2.03	5.75	5.75	0.90469	Tyrosine-protein kinase ephrin type A/B receptor-like (1);Growth factor, receptor (1);	0.000000	0.85682	D	0.000000	T	0.30479	0.0766	L	0.42744	1.35	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.85130	0.995;0.997	T	0.00692	-1.1607	10	0.23891	T	0.37	.	19.9447	0.97177	0.0:0.0:1.0:0.0	.	753;737	Q8IX30-2;Q8IX30	.;SCUB3_HUMAN	T	753;737	ENSP00000378174:A753T;ENSP00000274938:A737T	ENSP00000274938:A737T	A	+	1	0	SCUBE3	35319855	1.000000	0.71417	0.999000	0.59377	0.983000	0.72400	3.594000	0.54008	2.719000	0.93026	0.655000	0.94253	GCC	.	.		0.567	SCUBE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040275.1	NM_152753		A	35211877	G	A	35211877	3	1	351	1	0	0	0	0	1	0	0	0	13961	1203	42	3	2275	3	SCUBE3	6	35211877	Missense_Mutation	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10		35211877	135903190	45	49323										
MOCS1	4337	hgsc.bcm.edu	37	chr6	39876849	39876849	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	accgatgaggatcatgggccGgttcttcatctgggaaatac	12	9	4	1	rs149586823		TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr6:39876849G>A	ENST00000340692.5	-	10	1135	c.1132C>T	c.(1132-1134)Cgg>Tgg	p.R378W	MOCS1_ENST00000373186.4_Missense_Mutation_p.R378W|MOCS1_ENST00000308559.7_Intron|MOCS1_ENST00000373188.2_Missense_Mutation_p.R378W|MOCS1_ENST00000373175.4_Missense_Mutation_p.R349W|MOCS1_ENST00000432280.2_Missense_Mutation_p.R349W|MOCS1_ENST00000373195.3_Intron|MOCS1_ENST00000425303.2_Missense_Mutation_p.R378W			Q9NZB8	MOCS1_HUMAN	molybdenum cofactor synthesis 1	378	Molybdenum cofactor biosynthesis protein A.				Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|molybdopterin synthase complex (GO:0019008)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|cyclic pyranopterin monophosphate synthase activity (GO:0061597)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)	p.R378W(2)		central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	21	Ovarian(28;0.0355)|Colorectal(47;0.196)					ATCATGGGCCGGTTCTTCATC	0.597																																					p.R378W	NSCLC(84;861 1413 23785 24908 42279)|Melanoma(182;611 2047 9114 11847 26639)	Atlas-SNP	.											MOCS1_ENST00000340692,NS,carcinoma,0,2	MOCS1	87	.	2	Substitution - Missense(2)	endometrium(2)	c.C1132T						.						113	96	102					6																	39876849		2203	4300	6503	SO:0001583	missense	4337	exon9			TGGGCCGGTTCTT	AJ224328	CCDS4846.1, CCDS43460.1	6p21.2	2012-05-08			ENSG00000124615	ENSG00000124615			7190	protein-coding gene	gene with protein product		603707				9731530, 10053004	Standard	NM_001075098		Approved	MOCOD	uc003opb.3	Q9NZB8	OTTHUMG00000014656	ENST00000340692.5:c.1132C>T	chr6.hg19:g.39876849G>A	ENSP00000344794:p.Arg378Trp	74.0	0.0		63.0	36.0	NM_005943	B3KPT7|B4DTP1|O14940|O14941|O75710|Q5J7W0|Q5TCE1|Q5TCE2|Q5TCE6|Q5TCE9|Q5TCF0|Q5TCF1|Q8N418|Q9NZB7|Q9UEM1	Missense_Mutation	SNP	ENST00000340692.5	hg19		.	.	.	.	.	.	.	.	.	.	g	18.84	3.709600	0.68730	.	.	ENSG00000124615	ENST00000373186;ENST00000373175;ENST00000373188;ENST00000340692;ENST00000425303;ENST00000432280	T;T	0.48201	0.83;0.82	5.2	4.3	0.51218	.	0.062741	0.64402	D	0.000008	T	0.48677	0.1513	L	0.39898	1.24	0.45867	D	0.998724	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.997;1.0	T	0.40403	-0.9565	9	.	.	.	-26.4702	13.4252	0.61022	0.0:0.0:0.7233:0.2767	.	378;378;378	Q9NZB8-5;Q9NZB8-8;Q9NZB8-6	.;.;.	W	378;349;378;378;378;349	ENSP00000344794:R378W;ENSP00000416478:R378W	.	R	-	1	2	MOCS1	39984827	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.041000	0.41213	2.409000	0.81822	0.645000	0.84053	CGG	.	G|1.000;C|0.000		0.597	MOCS1-005	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000040476.2	NM_005943		A	39876849	G	A	39876849	3	1	351	1	0	0	0	0	1	0	0	0	9699	1115	39	1	29	1	MOCS1	6	39876849	Missense_Mutation	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	4664972	39876849	131238218	46	49324										
PHIP	55023	hgsc.bcm.edu	37	chr6	79692616	79692616	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	accaaaccttttgttttcttTctttgggcttctttttcttt	4	9	4	0			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr6:79692616T>A	ENST00000275034.4	-	23	2923	c.2756A>T	c.(2755-2757)gAa>gTa	p.E919V	PHIP_ENST00000479165.1_5'UTR	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	919	Lys-rich.				cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		ttgttttctttctttgggctt	0.294																																					p.E919V		Atlas-SNP	.											.	PHIP	177	.	0			c.A2756T						.						45	42	43					6																	79692616		2199	4293	6492	SO:0001583	missense	55023	exon23			TTTCTTTCTTTGG	AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	15673	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 14"	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.2756A>T	chr6.hg19:g.79692616T>A	ENSP00000275034:p.Glu919Val	19.0	0.0		18.0	10.0	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000275034.4	hg19	CCDS4987.1	.	.	.	.	.	.	.	.	.	.	T	15.94	2.982290	0.53827	.	.	ENSG00000146247	ENST00000275034	T	0.43688	0.94	4.95	4.95	0.65309	.	0.000000	0.85682	D	0.000000	T	0.18593	0.0446	L	0.34521	1.04	0.52099	D	0.999948	P;P	0.38978	0.652;0.652	B;B	0.36464	0.225;0.225	T	0.03750	-1.1007	9	.	.	.	-6.8477	13.7982	0.63184	0.0:0.0:0.0:1.0	.	919;919	A7J992;Q8WWQ0	.;PHIP_HUMAN	V	919	ENSP00000275034:E919V	.	E	-	2	0	PHIP	79749335	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.662000	0.83803	1.856000	0.53863	0.377000	0.23210	GAA	.	.		0.294	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2			A	79692616	T	A	79692616	3	1	351	1	0	0	0	0	1	0	0	0	11851	1783	62	4	2781	4	PHIP	6	79692616	Missense_Mutation	SNP	T	TCGA-WJ-A86L-01A-12D-A45V-10	39815767	79692616	91422451	47	49325										
PHIP	55023	hgsc.bcm.edu	37	chr6	79727210	79727210	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	caatacttacagtatgaaacTccaattctgatattttctct	3	9	2	2			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr6:79727210T>A	ENST00000275034.4	-	11	1252	c.1085A>T	c.(1084-1086)gAg>gTg	p.E362V		NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	362					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		AGTATGAAACTCCAATTCTGA	0.338																																					p.E362V		Atlas-SNP	.											.	PHIP	177	.	0			c.A1085T						.						41	42	42					6																	79727210		2203	4296	6499	SO:0001583	missense	55023	exon11			TGAAACTCCAATT	AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	15673	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 14"	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.1085A>T	chr6.hg19:g.79727210T>A	ENSP00000275034:p.Glu362Val	218.0	0.0		236.0	96.0	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000275034.4	hg19	CCDS4987.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.385424	0.82792	.	.	ENSG00000146247	ENST00000275034	T	0.60920	0.15	5.28	5.28	0.74379	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);	0.000000	0.64402	D	0.000001	T	0.57577	0.2063	L	0.37750	1.13	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.85130	0.997;0.997	T	0.58538	-0.7619	9	.	.	.	-14.2641	14.3848	0.66938	0.0:0.0:0.0:1.0	.	362;362	A7J992;Q8WWQ0	.;PHIP_HUMAN	V	362	ENSP00000275034:E362V	.	E	-	2	0	PHIP	79783929	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	1.987000	0.57996	0.454000	0.30748	GAG	.	.		0.338	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2			A	79727210	T	A	79727210	3	1	351	1	0	0	0	0	1	0	0	0	11851	1551	54	4	4500	4	PHIP	6	79727210	Missense_Mutation	SNP	T	TCGA-WJ-A86L-01A-12D-A45V-10	34594	79727210	91387857	48	49326										
TWISTNB	221830	hgsc.bcm.edu	37	chr7	19748398	19748398	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	atcggtacctctcagaatagCgaaggagctccgcatcaagc	10	12	2	1			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr7:19748398C>T	ENST00000222567.5	-	1	312	c.242G>A	c.(241-243)cGc>cAc	p.R81H		NM_001002926.1	NP_001002926.1	Q3B726	RPA43_HUMAN	TWIST neighbor	81					transcription from RNA polymerase I promoter (GO:0006360)	DNA-directed RNA polymerase I complex (GO:0005736)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed RNA polymerase activity (GO:0003899)			kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(2)	20						CTCAGAATAGCGAAGGAGCTC	0.572											OREG0017879	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R81H		Atlas-SNP	.											.	TWISTNB	63	.	0			c.G242A						.						116	104	108					7																	19748398		2203	4300	6503	SO:0001583	missense	221830	exon1			GAATAGCGAAGGA	AK090846	CCDS34606.1	7p21.1	2010-08-05			ENSG00000105849	ENSG00000105849			18027	protein-coding gene	gene with protein product		608312				12438708	Standard	NM_001002926		Approved		uc003sup.1	Q3B726	OTTHUMG00000152497	ENST00000222567.5:c.242G>A	chr7.hg19:g.19748398C>T	ENSP00000222567:p.Arg81His	48.0	0.0	735	56.0	31.0	NM_001002926	A0PJ45|B7Z724	Missense_Mutation	SNP	ENST00000222567.5	hg19	CCDS34606.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.968558	0.74131	.	.	ENSG00000105849	ENST00000222567	.	.	.	4.06	4.06	0.47325	RNA polymerase Rpb7, N-terminal (1);	0.351936	0.26753	N	0.022674	T	0.69142	0.3078	M	0.63843	1.955	0.37807	D	0.927926	D	0.89917	1.0	D	0.70716	0.97	T	0.72297	-0.4335	9	0.46703	T	0.11	-11.8811	10.4566	0.44555	0.0:0.9085:0.0:0.0915	.	81	Q3B726	RPA43_HUMAN	H	81	.	ENSP00000222567:R81H	R	-	2	0	TWISTNB	19714923	1.000000	0.71417	1.000000	0.80357	0.854000	0.48673	3.602000	0.54066	2.246000	0.74042	0.655000	0.94253	CGC	.	.		0.572	TWISTNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326463.1			T	19748398	C	T	19748398	3	4	351	1	0	0	0	0	1	0	0	0	16799	768	27	1	790	1	TWISTNB	7	19748398	Missense_Mutation	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10		19748398	139390265	49	49327										
ABCB5	340273	hgsc.bcm.edu	37	chr7	20698196	20698196	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	gcagaaacagaggatcgcaaTtgctcgtgccttagttcgaa	11	9	0	2			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr7:20698196T>G	ENST00000404938.2	+	14	2256	c.1604T>G	c.(1603-1605)aTt>aGt	p.I535S	ABCB5_ENST00000258738.6_Missense_Mutation_p.I90S|ABCB5_ENST00000443026.2_Missense_Mutation_p.I90S|ABCB5_ENST00000406935.1_Missense_Mutation_p.I90S	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	535	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (GO:0002485)|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO:0002489)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|cell differentiation (GO:0030154)|compound eye corneal lens development (GO:0048058)|positive regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002591)|regulation of membrane potential (GO:0042391)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|efflux transmembrane transporter activity (GO:0015562)	p.I90N(2)|p.I535N(1)		breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(1)|pancreas(1)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)	77						AGGATCGCAATTGCTCGTGCC	0.438																																					p.I535S		Atlas-SNP	.											ABCB5_ENST00000443026,NS,carcinoma,0,3	ABCB5	357	.	3	Substitution - Missense(3)	lung(3)	c.T1604G						.						133	117	122					7																	20698196		2203	4300	6503	SO:0001583	missense	340273	exon14			TCGCAATTGCTCG	U66692	CCDS5371.1, CCDS55090.1, CCDS55091.1, CCDS55092.1	7p14	2012-03-14			ENSG00000004846	ENSG00000004846		"ATP binding cassette transporters / subfamily B"	46	protein-coding gene	gene with protein product	"P-glycoprotein ABCB5", "ATP-binding cassette protein"	611785				8894702, 12960149	Standard	NM_001163942		Approved	EST422562, ABCB5beta, ABCB5alpha	uc010kuh.3	Q2M3G0	OTTHUMG00000094789	ENST00000404938.2:c.1604T>G	chr7.hg19:g.20698196T>G	ENSP00000384881:p.Ile535Ser	66.0	0.0		67.0	30.0	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Missense_Mutation	SNP	ENST00000404938.2	hg19	CCDS55090.1	.	.	.	.	.	.	.	.	.	.	T	18.87	3.715060	0.68844	.	.	ENSG00000004846	ENST00000404938;ENST00000443026;ENST00000406935;ENST00000258738	D;D;D;D	0.96136	-3.92;-3.92;-3.92;-3.92	5.77	4.61	0.57282	ABC transporter, conserved site (1);ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.086851	0.46442	D	0.000297	D	0.98563	0.9520	H	0.98883	4.36	0.51767	D	0.999934	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;0.998;1.0	D	0.98552	1.0637	10	0.87932	D	0	.	10.7801	0.46374	0.0:0.074:0.0:0.926	.	90;535;90;90	B5MD19;A7BKA4;Q2M3G0;Q2M3G0-2	.;.;ABCB5_HUMAN;.	S	535;90;90;90	ENSP00000384881:I535S;ENSP00000406730:I90S;ENSP00000383899:I90S;ENSP00000258738:I90S	ENSP00000258738:I90S	I	+	2	0	ABCB5	20664721	1.000000	0.71417	0.983000	0.44433	0.492000	0.33523	6.102000	0.71486	2.330000	0.79161	0.528000	0.53228	ATT	.	.		0.438	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559		G	20698196	T	G	20698196	3	3	351	1	0	0	0	0	1	0	0	0	44	1493	52	5	1654	5	ABCB5	7	20698196	Missense_Mutation	SNP	T	TCGA-WJ-A86L-01A-12D-A45V-10	949798	20698196	138440467	50	49328										
TBX20	57057	hgsc.bcm.edu	37	chr7	35242082	35242082	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	cagcagaggaatggcgtagtCcttgaatggcagcatagggc	15	8	0	2			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr7:35242082C>T	ENST00000408931.3	-	8	1830	c.1304G>A	c.(1303-1305)gGa>gAa	p.G435E		NM_001077653.2|NM_001166220.1	NP_001071121.1|NP_001159692.1	Q9UMR3	TBX20_HUMAN	T-box 20	435					aortic valve morphogenesis (GO:0003180)|atrial septum morphogenesis (GO:0060413)|blood circulation (GO:0008015)|cardiac chamber formation (GO:0003207)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|dorsal/ventral pattern formation (GO:0009953)|embryonic heart tube elongation (GO:0036306)|embryonic heart tube morphogenesis (GO:0003143)|endocardial cushion formation (GO:0003272)|endocardial cushion morphogenesis (GO:0003203)|endoderm formation (GO:0001706)|foramen ovale closure (GO:0035922)|heart looping (GO:0001947)|lateral mesoderm formation (GO:0048370)|muscle contraction (GO:0006936)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron migration (GO:0001764)|outflow tract septum morphogenesis (GO:0003148)|patterning of blood vessels (GO:0001569)|pericardium morphogenesis (GO:0003344)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary valve formation (GO:0003193)|pulmonary vein morphogenesis (GO:0060577)|tricuspid valve development (GO:0003175)|visceral motor neuron differentiation (GO:0021524)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(1)|lung(9)|prostate(1)|skin(1)|stomach(1)	18						ATGGCGTAGTCCTTGAATGGC	0.488																																					p.G435E		Atlas-SNP	.											TBX20_ENST00000408931,colon,carcinoma,0,1	TBX20	96	.	0			c.G1304A						.						32	31	31					7																	35242082		1922	4129	6051	SO:0001583	missense	57057	exon8			CGTAGTCCTTGAA	AJ237589	CCDS43568.1	7p14.3	2014-09-17			ENSG00000164532	ENSG00000164532		"T-boxes"	11598	protein-coding gene	gene with protein product		606061				10936053	Standard	NM_001077653		Approved		uc011kas.2	Q9UMR3	OTTHUMG00000099411	ENST00000408931.3:c.1304G>A	chr7.hg19:g.35242082C>T	ENSP00000386170:p.Gly435Glu	123.0	1.0		160.0	53.0	NM_001077653	A4D1Y6|Q000T4|Q0IJ70|Q0VAS1|Q9Y2N5	Missense_Mutation	SNP	ENST00000408931.3	hg19	CCDS43568.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.805639	0.90623	.	.	ENSG00000164532	ENST00000408931	D	0.88509	-2.39	5.66	5.66	0.87406	.	0.696409	0.13852	N	0.358302	D	0.91033	0.7179	N	0.19112	0.55	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.90044	0.4144	10	0.39692	T	0.17	.	19.7407	0.96230	0.0:1.0:0.0:0.0	.	435	Q9UMR3	TBX20_HUMAN	E	435	ENSP00000386170:G435E	ENSP00000386170:G435E	G	-	2	0	TBX20	35208607	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.487000	0.81328	2.654000	0.90174	0.609000	0.83330	GGA	.	.		0.488	TBX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216870.2	NM_020417		T	35242082	C	T	35242082	3	4	351	1	0	0	0	0	1	0	0	0	15671	855	30	3	42	3	TBX20	7	35242082	Missense_Mutation	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	14543886	35242082	123896581	51	49329										
ASL	435	hgsc.bcm.edu	37	chr7	65557597	65557597	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	aaagctgtgttcatggccgaGaccaagggggtcgccctcaa	13	11	2	1			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr7:65557597G>T	ENST00000304874.9	+	16	1299	c.1197G>T	c.(1195-1197)gaG>gaT	p.E399D	ASL_ENST00000380839.4_Missense_Mutation_p.E373D|ASL_ENST00000395331.3_Missense_Mutation_p.E379D|AC068533.7_ENST00000450043.1_Missense_Mutation_p.D168Y|ASL_ENST00000464970.1_3'UTR|ASL_ENST00000395332.3_Missense_Mutation_p.E399D	NM_000048.3	NP_000039.2	P04424	ARLY_HUMAN	argininosuccinate lyase	399					arginine biosynthetic process via ornithine (GO:0042450)|arginine catabolic process (GO:0006527)|cellular nitrogen compound metabolic process (GO:0034641)|internal protein amino acid acetylation (GO:0006475)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	argininosuccinate lyase activity (GO:0004056)			breast(3)|endometrium(3)|large_intestine(2)|lung(9)|upper_aerodigestive_tract(1)	18					L-Arginine(DB00125)	TCATGGCCGAGACCAAGGGGG	0.637																																					p.E399D		Atlas-SNP	.											.	ASL	39	.	0			c.G1197T						.						69	69	69					7																	65557597		2203	4300	6503	SO:0001583	missense	435	exon16			GGCCGAGACCAAG		CCDS5531.1, CCDS47597.1, CCDS47598.1	7q11.21	2012-10-02			ENSG00000126522	ENSG00000126522	4.3.2.1		746	protein-coding gene	gene with protein product		608310					Standard	NM_001024943		Approved		uc003tuo.3	P04424	OTTHUMG00000022876	ENST00000304874.9:c.1197G>T	chr7.hg19:g.65557597G>T	ENSP00000307188:p.Glu399Asp	59.0	0.0		54.0	25.0	NM_000048	E7EMI0|E9PE48|Q6LDS5|Q96HS2	Missense_Mutation	SNP	ENST00000304874.9	hg19	CCDS5531.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	19.99|19.99	3.928957|3.928957	0.73327|0.73327	.|.	.|.	ENSG00000249319|ENSG00000126522	ENST00000450043|ENST00000304874;ENST00000380839;ENST00000395332;ENST00000395331	.|D;D;D;D	.|0.91407	.|-2.84;-2.84;-2.84;-2.84	5.28|5.28	4.4|4.4	0.53042|0.53042	.|L-Aspartase-like (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.94699|0.94699	0.8290|0.8290	M|M	0.85099|0.85099	2.735|2.735	0.58432|0.58432	D|D	0.999998|0.999998	.|D;D;D	.|0.89917	.|1.0;0.995;0.991	.|D;D;D	.|0.91635	.|0.999;0.994;0.994	D|D	0.93749|0.93749	0.7057|0.7057	5|10	.|0.41790	.|T	.|0.15	.|.	9.4249|9.4249	0.38574|0.38574	0.1618:0.0:0.8382:0.0|0.1618:0.0:0.8382:0.0	.|.	.|373;379;399	.|E9PE48;E7EMI0;P04424	.|.;.;ARLY_HUMAN	Y|D	168|399;373;399;379	.|ENSP00000307188:E399D;ENSP00000370219:E373D;ENSP00000378741:E399D;ENSP00000378740:E379D	.|ENSP00000307188:E399D	D|E	+|+	1|3	0|2	AC068533.7|ASL	65195032|65195032	1.000000|1.000000	0.71417|0.71417	0.985000|0.985000	0.45067|0.45067	0.871000|0.871000	0.50021|0.50021	2.509000|2.509000	0.45459|0.45459	1.357000|1.357000	0.45904|0.45904	0.491000|0.491000	0.48974|0.48974	GAC|GAG	.	.		0.637	ASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251695.2	NM_000048		T	65557597	G	T	65557597	3	4	351	1	0	0	0	0	1	0	0	0	1044	933	33	3	1255	3	ASL	7	65557597	Missense_Mutation	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	30315515	65557597	93581066	52	49330										
DLX5	1749	hgsc.bcm.edu	37	chr7	96653687	96653687	+	Frame_Shift_Del	DEL	G	G	-													0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	ttggctgggtagctcccggcGgagccgttcacgccgtgata							TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr7:96653687delG	ENST00000222598.4	-	1	722	c.249delC	c.(247-249)tccfs	p.S83fs	DLX5_ENST00000486603.2_Frame_Shift_Del_p.S83fs|DLX5_ENST00000493764.1_5'UTR	NM_005221.5	NP_005212.1	P56178	DLX5_HUMAN	distal-less homeobox 5	83					anatomical structure formation involved in morphogenesis (GO:0048646)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|cell proliferation (GO:0008283)|cellular response to BMP stimulus (GO:0071773)|embryonic limb morphogenesis (GO:0030326)|endochondral ossification (GO:0001958)|epithelial cell differentiation (GO:0030855)|face morphogenesis (GO:0060325)|inner ear morphogenesis (GO:0042472)|nervous system development (GO:0007399)|olfactory pit development (GO:0060166)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)	20	all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858)					AGCTCCCGGCGGAGCCGTTCA	0.622																																					p.A84fs		Atlas-INDEL	.											.	DLX5	52	.	0			c.250delG						.						52	53	52					7																	96653687		2203	4300	6503	SO:0001589	frameshift_variant	1749	exon1			.		CCDS5647.1	7q21.3	2011-06-20	2005-12-22		ENSG00000105880	ENSG00000105880		"Homeoboxes / ANTP class : NKL subclass"	2918	protein-coding gene	gene with protein product		600028	"distal-less homeo box 5"			7907794	Standard	XM_005250185		Approved		uc003uon.3	P56178	OTTHUMG00000154200	ENST00000222598.4:c.249delC	chr7.hg19:g.96653687delG	ENSP00000222598:p.Ser83fs	95.0	0.0		112.0	50.0	NM_005221	B7Z4P3|Q9UPL1	Frame_Shift_Del	DEL	ENST00000222598.4	hg19	CCDS5647.1																																																																																			.	.		0.622	DLX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334371.2			-	96653687	G	-	96653687	7	5	351	1	0	1	0	1	0	0	0	0	4576	1103	39	0	632	0	DLX5	7	96653687	Frame_Shift_Del	DEL	G	TCGA-WJ-A86L-01A-12D-A45V-10	31096090	96653687	62484976	53	49331										
PUS7	54517	hgsc.bcm.edu	37	chr7	105098324	105098326	+	In_Frame_Del	DEL	AGT	AGT	-													0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	cgaatggccatggtggcgtaAgtagaagggggtagagaaaa							TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	AGT	AGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr7:105098324_105098326delAGT	ENST00000356362.2	-	16	2111_2113	c.1897_1899delACT	c.(1897-1899)actdel	p.T633del	PUS7_ENST00000469408.1_In_Frame_Del_p.T633del	NM_019042.3	NP_061915.2	Q96PZ0	PUS7_HUMAN	pseudouridylate synthase 7 (putative)	633					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)			breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(8)|pancreas(1)|skin(1)	23						TGGTGGCGTAAGTAGAAGGGGGT	0.468																																					p.633_634del	Colon(138;2387 3051 17860)	Atlas-INDEL	.											.	PUS7	59	.	0			c.1898_1900del						.																																			SO:0001651	inframe_deletion	54517	exon16			.	AK128629	CCDS34725.1	7q22.3	2014-02-14	2014-02-14		ENSG00000091127	ENSG00000091127			26033	protein-coding gene	gene with protein product			"pseudouridylate synthase 7 homolog (S. cerevisiae)"			11572484	Standard	NM_019042		Approved	FLJ20485	uc003vcx.3	Q96PZ0	OTTHUMG00000157399	ENST00000356362.2:c.1897_1899delACT	chr7.hg19:g.105098324_105098326delAGT	ENSP00000348722:p.Thr633del	78.0	0.0		89.0	34.0	NM_019042	Q75MG4|Q9NX19	In_Frame_Del	DEL	ENST00000356362.2	hg19	CCDS34725.1																																																																																			.	.		0.468	PUS7-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348681.1	NM_019042		-	105098326	AGT	-	105098324	7	5	351	1	0	1	0	1	0	0	0	0	12848	59	3	0	90	0	PUS7	7	105098324	In_Frame_Del	DEL	AGT	TCGA-WJ-A86L-01A-12D-A45V-10	8444637	105098324	54040339	54	49332										
PODXL	5420	hgsc.bcm.edu	37	chr7	131241029	131241029	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	ggccactcaccattctgggaGggcgacggcgacggcgacgg	17	13	2	0	rs11277659|rs547816245|rs532078953|rs79759078|rs571821675	byFrequency	TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr7:131241029G>C	ENST00000378555.3	-	1	337	c.90C>G	c.(88-90)ccC>ccG	p.P30P	PODXL_ENST00000537928.1_Silent_p.P30P|PODXL_ENST00000322985.9_Silent_p.P30P|PODXL_ENST00000465001.1_Intron|PODXL_ENST00000541194.1_Silent_p.P30P			O00592	PODXL_HUMAN	podocalyxin-like	30					cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					CATTCTGGGAGggcgacggcg	0.751																																					p.P30P		Atlas-SNP	.											.	PODXL	53	.	0			c.C90G						.						5	7	6					7																	131241029		1981	3946	5927	SO:0001819	synonymous_variant	5420	exon1			CTGGGAGGGCGAC		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.90C>G	chr7.hg19:g.131241029G>C		78.0	0.0		76.0	7.0	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Silent	SNP	ENST00000378555.3	hg19	CCDS34755.1																																																																																			.	.		0.751	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111		C	131241029	G	C	131241029	2	2	351	1	0	0	0	0	0	0	0	1	12189	987	35	4		4	PODXL	7	131241029	Silent	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	26142705	131241029	27897634	55	49333										
KIAA1549	57670	hgsc.bcm.edu	37	chr7	138552730	138552730	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	gtggcacgcactgggcatccGatgtaggctgagttgtggac	16	9	0	1			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr7:138552730G>A	ENST00000422774.1	-	15	4968	c.4920C>T	c.(4918-4920)atC>atT	p.I1640I	KIAA1549_ENST00000242365.4_Silent_p.I1590I|KIAA1549_ENST00000440172.1_Silent_p.I1640I			Q9HCM3	K1549_HUMAN	KIAA1549	1640						integral component of membrane (GO:0016021)			KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						CTGGGCATCCGATGTAGGCTG	0.627			O	BRAF	pilocytic astrocytoma																																p.I1640I	NSCLC(119;1534 1718 44213 46230 50068)	Atlas-SNP	.		Dom	yes		7	7q34	57670	KIAA1549		O	.	KIAA1549	314	.	0			c.C4920T						.						50	57	55					7																	138552730		2028	4162	6190	SO:0001819	synonymous_variant	57670	exon15			GCATCCGATGTAG		CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.4920C>T	chr7.hg19:g.138552730G>A		44.0	0.0		41.0	21.0	NM_020910	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Silent	SNP	ENST00000422774.1	hg19	CCDS56513.1																																																																																			.	.		0.627	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1			A	138552730	G	A	138552730	2	1	351	1	0	0	0	0	0	0	0	1	8253	1048	37	1		1	KIAA1549	7	138552730	Silent	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	7311701	138552730	20585933	56	49334										
C7orf33	202865	hgsc.bcm.edu	37	chr7	148288121	148288121	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	gcccagtggggcaaggcgccGgattgaccttcgcctgagtg	16	12	0	2	rs142396932		TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr7:148288121G>A	ENST00000307003.2	+	1	465	c.104G>A	c.(103-105)cGg>cAg	p.R35Q		NM_145304.2	NP_660347.1	Q8WU49	CG033_HUMAN	chromosome 7 open reading frame 33	35										central_nervous_system(1)|large_intestine(4)|lung(7)|prostate(2)	14	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)			GCAAGGCGCCGGATTGACCTT	0.567																																					p.R35Q		Atlas-SNP	.											.	C7orf33	28	.	0			c.G104A						.	G	GLN/ARG	0,4406		0,0,2203	83	71	75		104	-1.6	0	7	dbSNP_134	75	1,8599	1.2+/-3.3	0,1,4299	no	missense	C7orf33	NM_145304.2	43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	35/178	148288121	1,13005	2203	4300	6503	SO:0001583	missense	202865	exon1			GGCGCCGGATTGA	BC021251	CCDS5890.1	7q36.1	2011-11-24			ENSG00000170279	ENSG00000170279			21724	protein-coding gene	gene with protein product							Standard	NM_145304		Approved		uc003wew.3	Q8WU49	OTTHUMG00000152756	ENST00000307003.2:c.104G>A	chr7.hg19:g.148288121G>A	ENSP00000304071:p.Arg35Gln	114.0	0.0		91.0	35.0	NM_145304		Missense_Mutation	SNP	ENST00000307003.2	hg19	CCDS5890.1	.	.	.	.	.	.	.	.	.	.	G	9.336	1.061899	0.19987	0.0	1.16E-4	ENSG00000170279	ENST00000307003	.	.	.	2.59	-1.64	0.08318	.	.	.	.	.	T	0.15998	0.0385	N	0.08118	0	0.09310	N	1	B	0.14012	0.009	B	0.09377	0.004	T	0.18808	-1.0325	8	0.87932	D	0	.	3.8741	0.09048	0.2632:0.3981:0.3387:0.0	.	35	Q8WU49	CG033_HUMAN	Q	35	.	ENSP00000304071:R35Q	R	+	2	0	C7orf33	147919054	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.266000	0.08631	-0.427000	0.07350	-1.154000	0.01816	CGG	.	G|1.000;A|0.000		0.567	C7orf33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327684.1	NM_145304		A	148288121	G	A	148288121	3	1	351	1	0	0	0	0	1	0	0	0	2390	1116	39	1	106	1	C7orf33	7	148288121	Missense_Mutation	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	9735391	148288121	10850542	57	49335										
PREX2	80243	hgsc.bcm.edu	37	chr8	69032459	69032459	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	aattaccaatctcctaaaagGgcaggctgttgtgagggcct	11	9	1	1			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr8:69032459G>C	ENST00000288368.4	+	29	3810	c.3533G>C	c.(3532-3534)gGg>gCg	p.G1178A		NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	1178					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						CTCCTAAAAGGGCAGGCTGTT	0.383																																					p.G1178A		Atlas-SNP	.											PREX2,NS,neuroblastoma,0,1	PREX2	614	.	0			c.G3533C						.						117	117	117					8																	69032459		2203	4300	6503	SO:0001583	missense	80243	exon29			TAAAAGGGCAGGC	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.3533G>C	chr8.hg19:g.69032459G>C	ENSP00000288368:p.Gly1178Ala	96.0	0.0		75.0	37.0	NM_024870	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	hg19	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	G	32	5.176183	0.94846	.	.	ENSG00000046889	ENST00000288368	T	0.38560	1.13	5.29	5.29	0.74685	.	0.058678	0.64402	D	0.000002	T	0.60741	0.2292	M	0.68593	2.085	0.80722	D	1	D	0.57571	0.98	P	0.58721	0.844	T	0.61907	-0.6966	10	0.54805	T	0.06	.	19.3067	0.94165	0.0:0.0:1.0:0.0	.	1178	Q70Z35	PREX2_HUMAN	A	1178	ENSP00000288368:G1178A	ENSP00000288368:G1178A	G	+	2	0	PREX2	69195013	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.174000	0.94824	2.623000	0.88846	0.650000	0.86243	GGG	.	.		0.383	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		C	69032459	G	C	69032459	3	2	351	1	0	0	0	0	1	0	0	0	12489	1232	43	4	3876	4	PREX2	8	69032459	Missense_Mutation	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10		69032459	77331563	58	49336										
CNGB3	54714	hgsc.bcm.edu	37	chr8	87616352	87616352	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	aaacaccgacccagctttcaGagtaaccagaactttagtac	6	12	1	2			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr8:87616352G>T	ENST00000320005.5	-	15	1797	c.1750C>A	c.(1750-1752)Ctg>Atg	p.L584M		NM_019098.4	NP_061971.3	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	584					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(15)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	80						CCAGCTTTCAGAGTAACCAGA	0.368																																					p.L584M		Atlas-SNP	.											.	CNGB3	176	.	0			c.C1750A						.						79	78	79					8																	87616352		2203	4300	6503	SO:0001583	missense	54714	exon15			CTTTCAGAGTAAC	AF228520	CCDS6244.1	8q21.3	2013-01-23	2003-06-25		ENSG00000170289	ENSG00000170289		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2153	protein-coding gene	gene with protein product		605080	"achromatopsia (rod monochromacy) 3", "achromatopsia (rod monochromacy) 1"	ACHM3, ACHM1, RMCH		10888875, 10958649, 16382102	Standard	NM_019098		Approved		uc003ydx.3	Q9NQW8	OTTHUMG00000163738	ENST00000320005.5:c.1750C>A	chr8.hg19:g.87616352G>T	ENSP00000316605:p.Leu584Met	86.0	0.0		75.0	33.0	NM_019098	C9JA51|Q9NRE9	Missense_Mutation	SNP	ENST00000320005.5	hg19	CCDS6244.1	.	.	.	.	.	.	.	.	.	.	G	18.89	3.720129	0.68844	.	.	ENSG00000170289	ENST00000320005	D	0.97994	-4.65	5.97	5.09	0.68999	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.087662	0.47455	D	0.000222	D	0.98548	0.9515	M	0.82193	2.58	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.98537	1.0630	10	0.87932	D	0	.	12.6571	0.56793	0.13:0.0:0.87:0.0	.	584;584	Q9NQW8-2;Q9NQW8	.;CNGB3_HUMAN	M	584	ENSP00000316605:L584M	ENSP00000316605:L584M	L	-	1	2	CNGB3	87685468	0.997000	0.39634	1.000000	0.80357	0.929000	0.56500	2.207000	0.42788	2.837000	0.97791	0.655000	0.94253	CTG	.	.		0.368	CNGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375107.1	NM_019098		T	87616352	G	T	87616352	3	4	351	1	0	0	0	0	1	0	0	0	3603	933	33	3	695	3	CNGB3	8	87616352	Missense_Mutation	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	18583893	87616352	58747670	59	49337										
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110417293	110417294	+	Missense_Mutation	DNP	CC	CC	AA													0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	agaagatcaaggtaaccagcCcatgtgtggaagctaattca							TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr8:110417293_110417294CC>AA	ENST00000378402.5	+	16	1707_1708	c.1603_1604CC>AA	c.(1603-1605)CCa>AAa	p.P535K		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	535					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			GGTAACCAGCCCATGTGTGGAA	0.297										HNSCC(38;0.096)																											p.P535T|p.P535Q		Atlas-SNP	.											.|PKHD1L1,NS,carcinoma,0,1	PKHD1L1	522	.	0			c.C1603A|c.C1604A						.																																			SO:0001583	missense	93035	exon16			ACCAGCCCATGTG|CCAGCCCATGTGT	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	Exception_encountered	chr8.hg19:g.110417293_110417294delinsAA	ENSP00000367655:p.Pro535Lys	203.0|204.0	0.0		134.0	37.0|38.0	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	hg19	CCDS47911.1																																																																																			.	.		0.297	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		AA	110417294	CC	AA	110417293	3	1	351	1	0	0	0	0	1	0	0	0	11981	623	22	3	1665	3	PKHD1L1	8	110417293	Missense_Mutation	DNP	CC	TCGA-WJ-A86L-01A-12D-A45V-10	22800941	110417293	35946729	60	49338										
C8orf85	441376	hgsc.bcm.edu	37	chr8	117954838	117954838	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	caccagctggctagaactttActggacctaaacatgaaagt	8	10	0	2			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr8:117954838A>C	ENST00000378279.3	+	2	411	c.366A>C	c.(364-366)ttA>ttC	p.L122F	AARD_ENST00000523536.1_3'UTR	NM_001025357.2	NP_001020528.1	Q4LEZ3	AARD_HUMAN	alanine and arginine rich domain containing protein	122					lung development (GO:0030324)												CTAGAACTTTACTGGACCTAA	0.373																																					p.L122F		Atlas-SNP	.											.	.	.	.	0			c.A366C						.						61	58	59					8																	117954838		2203	4300	6503	SO:0001583	missense	441376	exon2			AACTTTACTGGAC	AB181519, BC140924	CCDS34935.1	8q24.11	2012-04-19	2012-04-19	2012-04-19	ENSG00000205002	ENSG00000205002			33842	protein-coding gene	gene with protein product	"Alanine and arginine-rich domain-containing protein"		"chromosome 8 open reading frame 85"	C8orf85			Standard	NM_001025357		Approved	LOC441376	uc003yof.3	Q4LEZ3	OTTHUMG00000164961	ENST00000378279.3:c.366A>C	chr8.hg19:g.117954838A>C	ENSP00000367528:p.Leu122Phe	95.0	0.0		54.0	33.0	NM_001025357	A5PKU8	Missense_Mutation	SNP	ENST00000378279.3	hg19	CCDS34935.1	.	.	.	.	.	.	.	.	.	.	A	14.80	2.643868	0.47258	.	.	ENSG00000205002	ENST00000378279	T	0.62639	0.01	5.38	-1.26	0.09376	.	0.276132	0.19444	N	0.114103	T	0.48840	0.1522	L	0.29908	0.895	0.24012	N	0.996175	P	0.50272	0.933	P	0.47786	0.557	T	0.46442	-0.9191	10	0.87932	D	0	-0.8538	5.4565	0.16594	0.3226:0.3046:0.3728:0.0	.	122	Q4LEZ3	AARD_HUMAN	F	122	ENSP00000367528:L122F	ENSP00000367528:L122F	L	+	3	2	C8orf85	118024019	0.018000	0.18449	0.871000	0.34182	0.649000	0.38597	-0.512000	0.06313	-0.095000	0.12351	-0.290000	0.09829	TTA	.	.		0.373	AARD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381195.1	NM_001025357		C	117954838	A	C	117954838	3	2	351	1	0	0	0	0	1	0	0	0	2443	388	14	5	372	5	C8orf85	8	117954838	Missense_Mutation	SNP	A	TCGA-WJ-A86L-01A-12D-A45V-10	7537545	117954838	28409184	61	49339										
DENND3	22898	hgsc.bcm.edu	37	chr8	142166010	142166010	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	atcacctactccaagtccacGgacgataacgtggacattcc	7	14	1	0			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr8:142166010G>T	ENST00000262585.2	+	8	1175	c.897G>T	c.(895-897)acG>acT	p.T299T	DENND3_ENST00000424248.1_Silent_p.T299T|DENND3_ENST00000519811.1_Silent_p.T379T	NM_014957.2	NP_055772.2	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	299					cellular protein catabolic process (GO:0044257)|endosome to lysosome transport (GO:0008333)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(4)|stomach(2)|urinary_tract(1)	55	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)			CCAAGTCCACGGACGATAACG	0.433																																					p.T299T		Atlas-SNP	.											.	DENND3	127	.	0			c.G897T						.						115	111	113					8																	142166010		2203	4300	6503	SO:0001819	synonymous_variant	22898	exon8			GTCCACGGACGAT	AB020677	CCDS34947.1	8q24.3	2013-01-10				ENSG00000105339		"DENN/MADD domain containing", "WD repeat domain containing"	29134	protein-coding gene	gene with protein product						10048485	Standard	NM_014957		Approved	KIAA0870	uc003yvy.3	A2RUS2		ENST00000262585.2:c.897G>T	chr8.hg19:g.142166010G>T		65.0	0.0		60.0	32.0	NM_014957	B7ZM28|O94947|Q2TAM7|Q6ZMS6|Q96DK3	Silent	SNP	ENST00000262585.2	hg19	CCDS34947.1	.	.	.	.	.	.	.	.	.	.	G	5.284	0.237884	0.10023	.	.	ENSG00000105339	ENST00000518668	.	.	.	5.06	-10.1	0.00402	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-0.7352	2.1436	0.03781	0.24:0.2567:0.0798:0.4236	.	.	.	.	X	356	.	.	G	+	1	0	DENND3	142235192	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.117000	0.03283	-2.854000	0.00330	-0.136000	0.14681	GGA	.	.		0.433	DENND3-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_014957		T	142166010	G	T	142166010	2	4	351	1	0	0	0	0	0	0	0	1	4434	1103	39	1		1	DENND3	8	142166010	Silent	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	24211172	142166010	4198012	62	49340										
PTCH1	5727	hgsc.bcm.edu	37	chr9	98232184	98232184	+	Frame_Shift_Del	DEL	G	G	-													0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	ggaaaaatgagcagaaccatGgcaaaattgaacaccactac							TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr9:98232184delG	ENST00000331920.6	-	13	2057	c.1758delC	c.(1756-1758)gccfs	p.A586fs	PTCH1_ENST00000430669.2_Frame_Shift_Del_p.A520fs|PTCH1_ENST00000429896.2_Frame_Shift_Del_p.A435fs|PTCH1_ENST00000437951.1_Frame_Shift_Del_p.A520fs|PTCH1_ENST00000421141.1_Frame_Shift_Del_p.A435fs|PTCH1_ENST00000375274.2_Frame_Shift_Del_p.A585fs|PTCH1_ENST00000418258.1_Frame_Shift_Del_p.A435fs	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	586	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)			NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				GCAGAACCATGGCAAAATTGA	0.438																																					p.M587fs		Atlas-INDEL	.											.	PTCH1	1850	.	0			c.1759delA						.						102	99	100					9																	98232184		2203	4300	6503	SO:0001589	frameshift_variant	5727	exon13			.	AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"patched (Drosophila) homolog", "patched homolog (Drosophila)", "patched homolog 1 (Drosophila)"	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.1758delC	chr9.hg19:g.98232184delG	ENSP00000332353:p.Ala586fs	90.0	0.0		79.0	32.0	NM_000264	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Frame_Shift_Del	DEL	ENST00000331920.6	hg19	CCDS6714.1																																																																																			.	.		0.438	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264		-	98232184	G	-	98232184	7	5	351	1	0	1	0	1	0	0	0	0	12742	1335	47	0	2629	0	PTCH1	9	98232184	Frame_Shift_Del	DEL	G	TCGA-WJ-A86L-01A-12D-A45V-10		98232184	42981247	63	49341										
GRIN3A	116443	hgsc.bcm.edu	37	chr9	104449360	104449360	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	aggaggaagtcggtgatgttCcagtcttcctggcacagcaa	13	9	1	1			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr9:104449360C>T	ENST00000361820.3	-	2	1422	c.822G>A	c.(820-822)tgG>tgA	p.W274*		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	274					calcium ion transport (GO:0006816)|dendrite development (GO:0016358)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|response to ethanol (GO:0045471)|rhythmic process (GO:0048511)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|identical protein binding (GO:0042802)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|protein phosphatase 2A binding (GO:0051721)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(44)|ovary(4)|pancreas(1)|skin(7)|upper_aerodigestive_tract(1)	80		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Acetylcysteine(DB06151)|Amantadine(DB00915)|Atomoxetine(DB00289)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Gabapentin(DB00996)|Halothane(DB01159)|Ketamine(DB01221)|Ketobemidone(DB06738)|Memantine(DB01043)|Methadone(DB00333)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Procaine(DB00721)|Secobarbital(DB00418)|Tramadol(DB00193)	CGGTGATGTTCCAGTCTTCCT	0.453																																					p.W274X		Atlas-SNP	.											.	GRIN3A	186	.	0			c.G822A						.						138	125	129					9																	104449360		2203	4300	6503	SO:0001587	stop_gained	116443	exon2			GATGTTCCAGTCT		CCDS6758.1	9q31.1	2012-08-29			ENSG00000198785	ENSG00000198785		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	16767	protein-coding gene	gene with protein product		606650					Standard	NM_133445		Approved	GluN3A	uc004bbp.2	Q8TCU5	OTTHUMG00000020387	ENST00000361820.3:c.822G>A	chr9.hg19:g.104449360C>T	ENSP00000355155:p.Trp274*	135.0	0.0		149.0	7.0	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Nonsense_Mutation	SNP	ENST00000361820.3	hg19	CCDS6758.1	.	.	.	.	.	.	.	.	.	.	C	43	10.470887	0.99411	.	.	ENSG00000198785	ENST00000361820	.	.	.	5.82	5.82	0.92795	.	0.257045	0.39020	N	0.001492	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	.	20.1178	0.97943	0.0:1.0:0.0:0.0	.	.	.	.	X	274	.	ENSP00000355155:W274X	W	-	3	0	GRIN3A	103489181	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.664000	0.83830	2.759000	0.94783	0.557000	0.71058	TGG	.	.		0.453	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1			T	104449360	C	T	104449360	4	4	351	1	0	0	0	0	0	1	0	0	6792	856	30	3	2557	3	GRIN3A	9	104449360	Nonsense_Mutation	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	6217176	104449360	36764071	64	49342										
CYLC2	1539	hgsc.bcm.edu	37	chr9	105767953	105767953	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	gaaggatgcaaagaagaaggGcaagtaggccttggataaga	15	4	0	3	rs373184793		TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr9:105767953G>A	ENST00000374798.3	+	5	1110	c.1040G>A	c.(1039-1041)gGc>gAc	p.G347D	CYLC2_ENST00000487798.1_Missense_Mutation_p.G347D	NM_001340.3	NP_001331.1	Q14093	CYLC2_HUMAN	cylicin, basic protein of sperm head cytoskeleton 2	347	31 X 3 AA repeats of K-K-X.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(14)|ovary(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)	41		all_hematologic(171;0.125)				aagaagaagggcaagtaggCC	0.358													G|||	1	0.000199681	0	0.0014	5008	,	,		17707	0		0	False		,,,				2504	0				p.G347D		Atlas-SNP	.											.	CYLC2	109	.	0			c.G1040A						.	G	ASP/GLY	0,4404		0,0,2202	53	57	55		1040	-2.8	0	9		55	1,8595	1.2+/-3.3	0,1,4297	no	missense	CYLC2	NM_001340.3	94	0,1,6499	AA,AG,GG		0.0116,0.0,0.0077	benign	347/349	105767953	1,12999	2202	4298	6500	SO:0001583	missense	1539	exon5			AGAAGGGCAAGTA	Z46788	CCDS35085.1	9q31.2	2008-07-21			ENSG00000155833	ENSG00000155833			2583	protein-coding gene	gene with protein product		604035				7737358	Standard	NM_001340		Approved		uc004bbs.2	Q14093	OTTHUMG00000020396	ENST00000374798.3:c.1040G>A	chr9.hg19:g.105767953G>A	ENSP00000420256:p.Gly347Asp	251.0	0.0		220.0	96.0	NM_001340	B2R8F4|Q5VVJ9	Missense_Mutation	SNP	ENST00000374798.3	hg19	CCDS35085.1	.	.	.	.	.	.	.	.	.	.	G	11.28	1.592247	0.28357	0.0	1.16E-4	ENSG00000155833	ENST00000374798;ENST00000487798	T;T	0.17528	2.27;2.27	4.39	-2.82	0.05787	.	.	.	.	.	T	0.07369	0.0186	N	0.08118	0	0.09310	N	1	B	0.30851	0.297	B	0.30179	0.112	T	0.37454	-0.9705	9	0.30078	T	0.28	4.4222	8.044	0.30538	0.1769:0.5598:0.2633:0.0	.	347	Q14093	CYLC2_HUMAN	D	347	ENSP00000420256:G347D;ENSP00000417674:G347D	ENSP00000420256:G347D	G	+	2	0	CYLC2	104807774	0.002000	0.14202	0.004000	0.12327	0.064000	0.16182	-0.386000	0.07370	-0.695000	0.05105	-0.291000	0.09656	GGC	.	.		0.358	CYLC2-001	KNOWN	alternative_3_UTR|NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053463.3	NM_001340		A	105767953	G	A	105767953	3	1	351	1	0	0	0	0	1	0	0	0	4144	1203	42	3	1058	3	CYLC2	9	105767953	Missense_Mutation	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	1318593	105767953	35445478	65	49343										
DDX31	64794	hgsc.bcm.edu	37	chr9	135505734	135505734	+	Frame_Shift_Del	DEL	C	C	-													0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	ctgctcccatggcagccaatCcgggcggttcttccaatccg							TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr9:135505734delC	ENST00000372159.3	-	16	2014	c.1863delG	c.(1861-1863)cggfs	p.R621fs	DDX31_ENST00000438527.3_Frame_Shift_Del_p.R492fs|DDX31_ENST00000372153.1_Frame_Shift_Del_p.G613fs	NM_022779.7	NP_073616.6	Q9H8H2	DDX31_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 31	621	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(1)	27				OV - Ovarian serous cystadenocarcinoma(145;2.67e-06)|Epithelial(140;7.61e-05)		GGCAGCCAATCCGGGCGGTTC	0.478																																					p.I622fs		Atlas-INDEL	.											.	DDX31	76	.	0			c.1864delA						.						103	109	107					9																	135505734		2203	4300	6503	SO:0001589	frameshift_variant	64794	exon16			.	AF427339	CCDS6951.1, CCDS6952.1	9q34.2	2012-04-17	2003-06-13		ENSG00000125485	ENSG00000125485		"DEAD-boxes", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	16715	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 25"		"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 31"				Standard	NM_022779		Approved	FLJ13633, FLJ23349, FLJ14578, PPP1R25	uc004cbq.1	Q9H8H2	OTTHUMG00000020843	ENST00000372159.3:c.1863delG	chr9.hg19:g.135505734delC	ENSP00000361232:p.Arg621fs	81.0	0.0		76.0	37.0	NM_022779	Q5K6N2|Q5K6N3|Q5K6N4|Q5VZJ4|Q5VZJ9|Q96E91|Q96NY2|Q96SX5|Q9H5K6	Frame_Shift_Del	DEL	ENST00000372159.3	hg19	CCDS6951.1																																																																																			.	.		0.478	DDX31-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054794.1	NM_138620		-	135505734	C	-	135505734	7	5	351	1	0	1	0	1	0	0	0	0	4358	842	30	0	712	0	DDX31	9	135505734	Frame_Shift_Del	DEL	C	TCGA-WJ-A86L-01A-12D-A45V-10	29737781	135505734	5707697	66	49344										
GATA3	2625	hgsc.bcm.edu	37	chr10	8106075	8106075	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	aaatgaacggacagaaccggCccctcattaagcccaagcga	9	13	1	2			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr10:8106075C>A	ENST00000346208.3	+	4	1350	c.895C>A	c.(895-897)Ccc>Acc	p.P299T	GATA3_ENST00000379328.3_Missense_Mutation_p.P300T|GATA3_ENST00000461472.1_Intron			P23771	GATA3_HUMAN	GATA binding protein 3	299	Flexible linker.				anatomical structure formation involved in morphogenesis (GO:0048646)|anatomical structure morphogenesis (GO:0009653)|aortic valve morphogenesis (GO:0003180)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cardiac right ventricle morphogenesis (GO:0003215)|cell fate determination (GO:0001709)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|cellular response to interferon-alpha (GO:0035457)|cellular response to interleukin-4 (GO:0071353)|cellular response to tumor necrosis factor (GO:0071356)|defense response (GO:0006952)|developmental growth (GO:0048589)|ear development (GO:0043583)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|interferon-gamma secretion (GO:0072643)|interleukin-4 secretion (GO:0072602)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|lymphocyte migration (GO:0072676)|male gonad development (GO:0008584)|mast cell differentiation (GO:0060374)|mesenchymal to epithelial transition (GO:0060231)|mesonephros development (GO:0001823)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell motility (GO:2000146)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell proliferation involved in mesonephros development (GO:2000607)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway involved in ureteric bud formation (GO:2000703)|negative regulation of glial cell-derived neurotrophic factor receptor signaling pathway involved in ureteric bud formation (GO:2000734)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct formation (GO:0072179)|nephric duct morphogenesis (GO:0072178)|neuron migration (GO:0001764)|norepinephrine biosynthetic process (GO:0042421)|otic vesicle development (GO:0071599)|parathyroid gland development (GO:0060017)|parathyroid hormone secretion (GO:0035898)|pharyngeal system development (GO:0060037)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-13 secretion (GO:2000667)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of interleukin-5 secretion (GO:2000664)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of signal transduction (GO:0009967)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of thyroid hormone generation (GO:2000611)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ureteric bud formation (GO:0072107)|post-embryonic development (GO:0009791)|pro-T cell differentiation (GO:0002572)|regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043370)|regulation of cellular response to X-ray (GO:2000683)|regulation of cytokine biosynthetic process (GO:0042035)|regulation of establishment of cell polarity (GO:2000114)|regulation of histone H3-K27 methylation (GO:0061085)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to gamma radiation (GO:0010332)|response to virus (GO:0009615)|signal transduction (GO:0007165)|sympathetic nervous system development (GO:0048485)|T cell receptor signaling pathway (GO:0050852)|T-helper 2 cell differentiation (GO:0045064)|thymic T cell selection (GO:0045061)|thymus development (GO:0048538)|TOR signaling (GO:0031929)|transcription from RNA polymerase II promoter (GO:0006366)|type IV hypersensitivity (GO:0001806)|ureter maturation (GO:0035799)|ureteric bud formation (GO:0060676)|uterus development (GO:0060065)|ventricular septum development (GO:0003281)	nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|enhancer sequence-specific DNA binding (GO:0001158)|HMG box domain binding (GO:0071837)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)			NS(1)|breast(44)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(24)|ovary(3)|skin(2)	87						ACAGAACCGGCCCCTCATTAA	0.572			"F, N, S"		breast		"HDR syndrome (HYPOPARATHYROIDISM, SENSORINEURAL DEAFNESS, AND RENAL DISEASE)"																														p.P300T		Atlas-SNP	.		Rec	yes		10	10p15	2625	GATA binding protein 3	yes	E	.	GATA3	182	.	0			c.C898A						.						108	100	103					10																	8106075		2203	4300	6503	SO:0001583	missense	2625	exon4			AACCGGCCCCTCA	X55122	CCDS7083.1, CCDS31143.1	10p15	2013-01-25	2001-11-28		ENSG00000107485	ENSG00000107485		"GATA zinc finger domain containing"	4172	protein-coding gene	gene with protein product		131320	"GATA-binding protein 3"			2050118, 15087456	Standard	NM_002051		Approved	HDR	uc001ijz.3	P23771	OTTHUMG00000017640	ENST00000346208.3:c.895C>A	chr10.hg19:g.8106075C>A	ENSP00000341619:p.Pro299Thr	139.0	0.0		103.0	43.0	NM_001002295	Q5VWG7|Q5VWG8|Q96J16	Missense_Mutation	SNP	ENST00000346208.3	hg19	CCDS7083.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.953624	0.92660	.	.	ENSG00000107485	ENST00000379328;ENST00000346208	D;D	0.99745	-6.61;-6.61	5.29	5.29	0.74685	Zinc finger, NHR/GATA-type (1);Zinc finger, GATA-type (2);	0.000000	0.85682	D	0.000000	D	0.99851	0.9931	H	0.97516	4.02	0.80722	D	1	D;D	0.89917	1.0;0.989	D;D	0.97110	1.0;0.976	D	0.96664	0.9491	10	0.87932	D	0	-9.3523	18.9039	0.92453	0.0:1.0:0.0:0.0	.	299;300	P23771;P23771-2	GATA3_HUMAN;.	T	300;299	ENSP00000368632:P300T;ENSP00000341619:P299T	ENSP00000341619:P299T	P	+	1	0	GATA3	8146081	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.752000	0.85141	2.625000	0.88918	0.655000	0.94253	CCC	.	.		0.572	GATA3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046719.1	NM_001002295		A	8106075	C	A	8106075	3	1	351	1	0	0	0	0	1	0	0	0	6263	739	26	3	908	3	GATA3	10	8106075	Missense_Mutation	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10		8106075	127428672	67	49345										
CHST3	9469	hgsc.bcm.edu	37	chr10	73767585	73767585	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	tggccgcagaggcctgccgcCgcaaggagcacatggccctc	14	16	0	1			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr10:73767585C>G	ENST00000373115.4	+	3	1233	c.796C>G	c.(796-798)Cgc>Ggc	p.R266G		NM_004273.4	NP_004264.2	Q7LGC8	CHST3_HUMAN	carbohydrate (chondroitin 6) sulfotransferase 3	266					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)|T cell homeostasis (GO:0043029)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin 6-sulfotransferase activity (GO:0008459)|proteoglycan sulfotransferase activity (GO:0050698)|sulfotransferase activity (GO:0008146)			endometrium(1)|lung(5)	6						GGCCTGCCGCCGCAAGGAGCA	0.677																																					p.R266G		Atlas-SNP	.											.	CHST3	36	.	0			c.C796G						.						11	12	11					10																	73767585		2000	3968	5968	SO:0001583	missense	9469	exon3			TGCCGCCGCAAGG	AB017915	CCDS7312.1	10q22.1	2007-03-14			ENSG00000122863	ENSG00000122863		"Sulfotransferases, membrane-bound"	1971	protein-coding gene	gene with protein product		603799				9883891, 9714738	Standard	NM_004273		Approved	C6ST, C6ST1	uc001jsn.3	Q7LGC8	OTTHUMG00000018431	ENST00000373115.4:c.796C>G	chr10.hg19:g.73767585C>G	ENSP00000362207:p.Arg266Gly	38.0	0.0		43.0	28.0	NM_004273	O75099|Q52M30	Missense_Mutation	SNP	ENST00000373115.4	hg19	CCDS7312.1	.	.	.	.	.	.	.	.	.	.	C	14.78	2.637042	0.47049	.	.	ENSG00000122863	ENST00000373115	D	0.82711	-1.64	5.8	5.8	0.92144	Sulfotransferase domain (1);	0.183504	0.50627	D	0.000114	T	0.78052	0.4223	L	0.39898	1.24	0.40911	D	0.984231	P	0.38992	0.653	B	0.39185	0.293	T	0.78718	-0.2095	10	0.44086	T	0.13	-29.025	13.9427	0.64066	0.1516:0.8484:0.0:0.0	.	266	Q7LGC8	CHST3_HUMAN	G	266	ENSP00000362207:R266G	ENSP00000362207:R266G	R	+	1	0	CHST3	73437591	0.906000	0.30813	1.000000	0.80357	0.997000	0.91878	1.100000	0.31025	2.758000	0.94735	0.561000	0.74099	CGC	.	.		0.677	CHST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048563.1	NM_004273		G	73767585	C	G	73767585	3	3	351	1	0	0	0	0	1	0	0	0	3407	652	23	4	802	4	CHST3	10	73767585	Missense_Mutation	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	65661510	73767585	61767162	68	49346										
OPN4	94233	hgsc.bcm.edu	37	chr10	88417835	88417835	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	acatgttcattatcaacctcGcggtcagcgacttcctcatg	7	13	4	0			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr10:88417835G>A	ENST00000241891.5	+	3	504	c.337G>A	c.(337-339)Gcg>Acg	p.A113T	OPN4_ENST00000372071.2_Missense_Mutation_p.A124T	NM_033282.3	NP_150598.1	Q9UHM6	OPN4_HUMAN	opsin 4	113					phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|rhodopsin mediated signaling pathway (GO:0016056)|rhythmic process (GO:0048511)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	11-cis retinal binding (GO:0005502)|G-protein coupled photoreceptor activity (GO:0008020)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(5)|ovary(3)	18						TATCAACCTCGCGGTCAGCGA	0.562																																					p.A124T		Atlas-SNP	.											.	OPN4	61	.	0			c.G370A						.						117	113	114					10																	88417835		2203	4300	6503	SO:0001583	missense	94233	exon4			AACCTCGCGGTCA	AF147788	CCDS7376.1, CCDS31237.1	10q22	2012-08-08	2008-04-16		ENSG00000122375	ENSG00000122375		"GPCR / Class A : Opsin receptors"	14449	protein-coding gene	gene with protein product	"melanopsin"	606665	"opsin 4 (melanopsin)"			10632589	Standard	NM_001030015		Approved	MOP, melanopsin	uc001kdp.3	Q9UHM6	OTTHUMG00000018654	ENST00000241891.5:c.337G>A	chr10.hg19:g.88417835G>A	ENSP00000241891:p.Ala113Thr	63.0	0.0		70.0	33.0	NM_001030015	B7ZLB3|Q14D01|Q2PP22|Q8NGQ9	Missense_Mutation	SNP	ENST00000241891.5	hg19	CCDS7376.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.211457	0.79240	.	.	ENSG00000122375	ENST00000372071;ENST00000241891;ENST00000443292	T;T;T	0.56103	0.48;0.48;0.48	5.29	4.33	0.51752	GPCR, rhodopsin-like superfamily (1);	0.063064	0.64402	D	0.000011	T	0.76990	0.4065	M	0.91459	3.21	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.996;0.984	T	0.82481	-0.0436	10	0.87932	D	0	.	13.7968	0.63175	0.0:0.0:0.8462:0.1537	.	124;113;124	C9JWU6;Q9UHM6;Q9UHM6-2	.;OPN4_HUMAN;.	T	124;113;124	ENSP00000361141:A124T;ENSP00000241891:A113T;ENSP00000393132:A124T	ENSP00000241891:A113T	A	+	1	0	OPN4	88407815	1.000000	0.71417	0.142000	0.22268	0.623000	0.37688	7.903000	0.87398	2.469000	0.83416	0.491000	0.48974	GCG	.	.		0.562	OPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049158.2	NM_033282		A	88417835	G	A	88417835	3	1	351	1	0	0	0	0	1	0	0	0	10891	1087	38	1	384	1	OPN4	10	88417835	Missense_Mutation	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	14650250	88417835	47116912	69	49347										
JAKMIP3	282973	hgsc.bcm.edu	37	chr10	133930963	133930963	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	gcaggtggaggaggcgctgaCgctggtgatccaagcggaca	18	9	0	2	rs371280434		TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr10:133930963C>T	ENST00000298622.4	+	2	656	c.518C>T	c.(517-519)aCg>aTg	p.T173M		NM_001105521.2	NP_001098991.1	Q5VZ66	JKIP3_HUMAN	Janus kinase and microtubule interacting protein 3	173						Golgi apparatus (GO:0005794)				breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	31		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)		GAGGCGCTGACGCTGGTGATC	0.607																																					p.T173M		Atlas-SNP	.											.	JAKMIP3	69	.	0			c.C518T						.	C	MET/THR	0,4328		0,0,2164	51	61	58		518	4.7	0.9	10		58	1,8533		0,1,4266	no	missense	JAKMIP3	NM_001105521.2	81	0,1,6430	TT,TC,CC		0.0117,0.0,0.0078	probably-damaging	173/845	133930963	1,12861	2164	4267	6431	SO:0001583	missense	282973	exon2			CGCTGACGCTGGT	AL832756	CCDS44494.1	10q26.3	2009-04-23	2009-04-23	2008-01-28	ENSG00000188385	ENSG00000188385			23523	protein-coding gene	gene with protein product	"neuroendocrine long coiled-coil 2"	611198	"chromosome 10 open reading frame 39", "chromosome 10 open reading frame 14"	C10orf39, C10orf14		15277531, 17572408	Standard	NM_001105521		Approved	FLJ37857, NECC2, KIAA4091, bA140A10.5	uc001lkx.4	Q5VZ66	OTTHUMG00000150167	ENST00000298622.4:c.518C>T	chr10.hg19:g.133930963C>T	ENSP00000298622:p.Thr173Met	88.0	0.0		101.0	53.0	NM_001105521	A6PW00|Q69YM6|Q6ZT29	Missense_Mutation	SNP	ENST00000298622.4	hg19	CCDS44494.1	.	.	.	.	.	.	.	.	.	.	C	17.15	3.315954	0.60524	0.0	1.17E-4	ENSG00000188385	ENST00000298622	T	0.08720	3.06	4.66	4.66	0.58398	.	0.054130	0.64402	D	0.000001	T	0.15652	0.0377	L	0.43152	1.355	0.28758	N	0.901076	D	0.76494	0.999	P	0.55667	0.781	T	0.01033	-1.1474	10	0.66056	D	0.02	-31.4226	12.8191	0.57683	0.1632:0.8368:0.0:0.0	.	173	Q5VZ66	JKIP3_HUMAN	M	173	ENSP00000298622:T173M	ENSP00000298622:T173M	T	+	2	0	JAKMIP3	133780953	0.855000	0.29742	0.941000	0.38009	0.963000	0.63663	1.395000	0.34520	2.419000	0.82065	0.591000	0.81541	ACG	.	.		0.607	JAKMIP3-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051049.3	NM_194303		T	133930963	C	T	133930963	3	4	351	1	0	0	0	0	1	0	0	0	7951	536	19	1	524	1	JAKMIP3	10	133930963	Missense_Mutation	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	45513128	133930963	1603784	70	49348										
INSC	387755	hgsc.bcm.edu	37	chr11	15243031	15243031	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	ctccatctgcaggtggatggCgttctgtgcttggccgacat	13	11	2	0			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr11:15243031C>T	ENST00000379554.3	+	8	1015	c.969C>T	c.(967-969)ggC>ggT	p.G323G	INSC_ENST00000447214.2_3'UTR|INSC_ENST00000528567.1_Silent_p.G276G|INSC_ENST00000530161.1_Silent_p.G276G|INSC_ENST00000379556.3_Silent_p.G276G|INSC_ENST00000525218.1_Silent_p.G234G|INSC_ENST00000424273.1_Silent_p.G234G	NM_001031853.3	NP_001027024.3	Q1MX18	INSC_HUMAN	inscuteable homolog (Drosophila)	323					establishment of mitotic spindle orientation (GO:0000132)|lung epithelial cell differentiation (GO:0060487)|nervous system development (GO:0007399)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)				NS(2)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(3)|lung(24)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49						AGGTGGATGGCGTTCTGTGCT	0.612																																					p.G323G		Atlas-SNP	.											.	INSC	104	.	0			c.C969T						.						63	71	68					11																	15243031		2136	4244	6380	SO:0001819	synonymous_variant	387755	exon8			GGATGGCGTTCTG	AB231744	CCDS41621.1, CCDS41622.1, CCDS60735.1, CCDS60736.1	11p15.2	2014-02-05			ENSG00000188487	ENSG00000188487			33116	protein-coding gene	gene with protein product	"inscuteable spindle orientation adaptor protein"	610668				16458856	Standard	NM_001031853		Approved		uc001mly.4	Q1MX18	OTTHUMG00000165838	ENST00000379554.3:c.969C>T	chr11.hg19:g.15243031C>T		135.0	0.0		165.0	65.0	NM_001031853	A0PJX5|Q1MX19|Q3C1V6|Q4AC95|Q4AC96|Q4AC97|Q4AC98	Silent	SNP	ENST00000379554.3	hg19	CCDS41621.1																																																																																			.	.		0.612	INSC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386590.1	NM_001031853		T	15243031	C	T	15243031	2	4	351	1	0	0	0	0	0	0	0	1	7773	755	27	1		1	INSC	11	15243031	Silent	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10		15243031	119763485	71	49349										
MS4A15	219995	hgsc.bcm.edu	37	chr11	60541328	60541328	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	aggatgtggacaggggctatCtggccgtgcttactatcttc	13	9	2	0			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr11:60541328C>A	ENST00000405633.3	+	6	596	c.517C>A	c.(517-519)Ctg>Atg	p.L173M	MS4A15_ENST00000337911.4_Missense_Mutation_p.L80M|MS4A15_ENST00000528170.1_Missense_Mutation_p.L132M	NM_001098835.1	NP_001092305.1	Q8N5U1	M4A15_HUMAN	membrane-spanning 4-domains, subfamily A, member 15	173						integral component of membrane (GO:0016021)				breast(1)|large_intestine(2)|lung(3)	6						CAGGGGCTATCTGGCCGTGCT	0.572																																					p.L173M		Atlas-SNP	.											.	MS4A15	37	.	0			c.C517A						.						245	190	209					11																	60541328		2203	4300	6503	SO:0001583	missense	219995	exon6			GGCTATCTGGCCG	AY584608	CCDS7991.1, CCDS44617.1, CCDS60802.1	11q12.2	2008-03-25							28573	protein-coding gene	gene with protein product							Standard	NM_001098835		Approved		uc009ynf.1	Q8N5U1		ENST00000405633.3:c.517C>A	chr11.hg19:g.60541328C>A	ENSP00000386022:p.Leu173Met	45.0	0.0		69.0	30.0	NM_001098835	A9UJY6|A9UJY7|F2Z2J5	Missense_Mutation	SNP	ENST00000405633.3	hg19	CCDS44617.1	.	.	.	.	.	.	.	.	.	.	C	8.805	0.933861	0.18206	.	.	ENSG00000166961	ENST00000528170;ENST00000337911;ENST00000405633	T;T;T	0.15017	2.46;2.46;2.82	4.83	1.93	0.25924	.	1.432310	0.04687	N	0.413446	T	0.36963	0.0986	M	0.63428	1.95	0.25018	N	0.991359	D;D	0.76494	0.979;0.999	P;D	0.83275	0.725;0.996	T	0.07986	-1.0744	10	0.34782	T	0.22	-15.1267	5.9902	0.19456	0.0:0.6787:0.0:0.3213	.	132;173	F2Z2J5;Q8N5U1	.;M4A15_HUMAN	M	132;80;173	ENSP00000434165:L132M;ENSP00000338692:L80M;ENSP00000386022:L173M	ENSP00000338692:L80M	L	+	1	2	MS4A15	60297904	0.396000	0.25262	0.924000	0.36721	0.062000	0.15995	0.521000	0.22893	0.474000	0.27392	0.555000	0.69702	CTG	.	.		0.572	MS4A15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395618.1			A	60541328	C	A	60541328	3	1	351	1	0	0	0	0	1	0	0	0	9868	912	32	3	535	3	MS4A15	11	60541328	Missense_Mutation	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	45298297	60541328	74465188	72	49350										
CD6	923	hgsc.bcm.edu	37	chr11	60785356	60785356	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	agtcgagcacctcttcagggGaggattactgcaatagtccc	11	11	2	0			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr11:60785356G>T	ENST00000313421.7	+	11	1894	c.1708G>T	c.(1708-1710)Gag>Tag	p.E570*	CD6_ENST00000352009.5_Nonsense_Mutation_p.E538*|CD6_ENST00000452451.2_Nonsense_Mutation_p.E529*|CD6_ENST00000346437.4_Nonsense_Mutation_p.E497*|CD6_ENST00000344028.5_Nonsense_Mutation_p.E538*	NM_006725.4	NP_006716.3	P30203	CD6_HUMAN	CD6 molecule	570					cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	scavenger receptor activity (GO:0005044)			endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)	18						CTCTTCAGGGGAGGATTACTG	0.562																																					p.E570X	Pancreas(169;904 2017 4767 38890 42505)	Atlas-SNP	.											.	CD6	122	.	0			c.G1708T						.						79	80	79					11																	60785356		2203	4299	6502	SO:0001587	stop_gained	923	exon11			TCAGGGGAGGATT		CCDS7999.1, CCDS58137.1, CCDS58138.1	11q12.2	2006-03-28	2006-03-28		ENSG00000013725	ENSG00000013725		"CD molecules"	1691	protein-coding gene	gene with protein product		186720	"CD6 antigen"			9013954	Standard	NM_006725		Approved	Tp120	uc001nqq.3	P30203	OTTHUMG00000167823	ENST00000313421.7:c.1708G>T	chr11.hg19:g.60785356G>T	ENSP00000323280:p.Glu570*	113.0	0.0		112.0	57.0	NM_006725	A4KAD4|A4KAD5|Q9UMF2|Q9Y4K7|Q9Y4K8|Q9Y4K9|Q9Y4L0	Nonsense_Mutation	SNP	ENST00000313421.7	hg19	CCDS7999.1	.	.	.	.	.	.	.	.	.	.	G	34	5.365653	0.95900	.	.	ENSG00000013725	ENST00000344028;ENST00000346437;ENST00000313421;ENST00000452451;ENST00000352009	.	.	.	5.31	5.31	0.75309	.	1.075250	0.07326	N	0.878367	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	14.4929	0.67665	0.0:0.0:1.0:0.0	.	.	.	.	X	538;497;570;529;538	.	ENSP00000323280:E570X	E	+	1	0	CD6	60541932	1.000000	0.71417	0.986000	0.45419	0.206000	0.24218	4.746000	0.62133	2.497000	0.84241	0.467000	0.42956	GAG	.	.		0.562	CD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396449.1	NM_006725		T	60785356	G	T	60785356	4	4	351	1	0	0	0	0	0	1	0	0	3030	1175	41	3	1750	3	CD6	11	60785356	Nonsense_Mutation	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	244028	60785356	74221160	73	49351										
HEPHL1	341208	hgsc.bcm.edu	37	chr11	93839186	93839186	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	gaaagatttttgggaatctcCatggcctcataatgaacgaa	9	7	2	2			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr11:93839186C>G	ENST00000315765.9	+	17	2943	c.2935C>G	c.(2935-2937)Cat>Gat	p.H979D		NM_001098672.1	NP_001092142.1	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	979	Plastocyanin-like 6.				copper ion transport (GO:0006825)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	61		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				TGGGAATCTCCATGGCCTCAT	0.338																																					p.H979D		Atlas-SNP	.											.	HEPHL1	144	.	0			c.C2935G						.						97	93	94					11																	93839186		1854	4090	5944	SO:0001583	missense	341208	exon17			AATCTCCATGGCC	BX641008	CCDS44710.1	11q21	2008-02-05			ENSG00000181333	ENSG00000181333			30477	protein-coding gene	gene with protein product							Standard	NM_001098672		Approved	DKFZp686F22190	uc001pep.2	Q6MZM0	OTTHUMG00000167751	ENST00000315765.9:c.2935C>G	chr11.hg19:g.93839186C>G	ENSP00000313699:p.His979Asp	135.0	0.0		152.0	57.0	NM_001098672	Q3C1W7	Missense_Mutation	SNP	ENST00000315765.9	hg19	CCDS44710.1	.	.	.	.	.	.	.	.	.	.	C	12.47	1.947578	0.34377	.	.	ENSG00000181333	ENST00000315765	D	0.99737	-6.59	5.95	5.04	0.67666	Cupredoxin (2);Multicopper oxidase, type 2 (1);	0.387744	0.31601	N	0.007377	D	0.98229	0.9414	L	0.33753	1.03	0.27523	N	0.951331	B	0.10296	0.003	B	0.16289	0.015	D	0.94491	0.7701	10	0.13108	T	0.6	.	12.28	0.54759	0.0:0.8142:0.1204:0.0654	.	979	Q6MZM0	HPHL1_HUMAN	D	979	ENSP00000313699:H979D	ENSP00000313699:H979D	H	+	1	0	HEPHL1	93478834	0.740000	0.28207	0.964000	0.40570	0.991000	0.79684	2.877000	0.48506	1.511000	0.48818	0.655000	0.94253	CAT	.	.		0.338	HEPHL1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396103.2	XM_291947		G	93839186	C	G	93839186	3	3	351	1	0	0	0	0	1	0	0	0	7064	594	21	4	3001	4	HEPHL1	11	93839186	Missense_Mutation	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	33053830	93839186	41167330	74	49352										
OR8B8	26493	hgsc.bcm.edu	37	chr11	124310418	124310418	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	ttcacataggtgctggtgcaAgcacactcaagaaggggaag	13	8	2	1			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr11:124310418A>G	ENST00000328064.2	-	1	636	c.564T>C	c.(562-564)gcT>gcC	p.A188A		NM_012378.1	NP_036510.1	Q15620	OR8B8_HUMAN	olfactory receptor, family 8, subfamily B, member 8	188					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		TGCTGGTGCAAGCACACTCAA	0.493																																					p.A188A		Atlas-SNP	.											.	OR8B8	76	.	0			c.T564C						.						169	134	146					11																	124310418		2201	4299	6500	SO:0001819	synonymous_variant	26493	exon1			GGTGCAAGCACAC	AF238488	CCDS8446.1	11q24.2	2012-08-09			ENSG00000197125	ENSG00000197125		"GPCR / Class A : Olfactory receptors"	8477	protein-coding gene	gene with protein product						9119360	Standard	NM_012378		Approved	TPCR85	uc010sal.2	Q15620	OTTHUMG00000165917	ENST00000328064.2:c.564T>C	chr11.hg19:g.124310418A>G		134.0	0.0		137.0	66.0	NM_012378	A1L446|Q96RC8	Silent	SNP	ENST00000328064.2	hg19	CCDS8446.1																																																																																			.	.		0.493	OR8B8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387056.1	NM_012378		G	124310418	A	G	124310418	2	3	351	1	0	0	0	0	0	0	0	1	11239	59	3	2		2	OR8B8	11	124310418	Silent	SNP	A	TCGA-WJ-A86L-01A-12D-A45V-10	30471232	124310418	10696098	75	49353										
IGSF9B	22997	hgsc.bcm.edu	37	chr11	133801020	133801020	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	actgtgcttgcttctgctggGcttccctaccttggtgaaca	10	12	1	1			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr11:133801020G>T	ENST00000321016.8	-	11	1608	c.1378C>A	c.(1378-1380)Ccc>Acc	p.P460T	IGSF9B_ENST00000533871.2_Missense_Mutation_p.P460T			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	460	Ig-like 5.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		CTTCTGCTGGGCTTCCCTACC	0.617																																					p.P460T		Atlas-SNP	.											.	IGSF9B	290	.	0			c.C1378A						.						71	81	77					11																	133801020		2159	4262	6421	SO:0001583	missense	22997	exon11			TGCTGGGCTTCCC	AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.1378C>A	chr11.hg19:g.133801020G>T	ENSP00000317980:p.Pro460Thr	64.0	0.0		66.0	4.0	NM_014987	G5EA26	Missense_Mutation	SNP	ENST00000321016.8	hg19		.	.	.	.	.	.	.	.	.	.	G	15.00	2.704614	0.48412	.	.	ENSG00000080854	ENST00000321016;ENST00000533871;ENST00000527648	T;T;T	0.68025	-0.3;-0.3;-0.3	3.95	3.95	0.45737	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.65037	0.2653	L	0.52823	1.66	0.49213	D	0.999764	B	0.32968	0.392	B	0.37304	0.246	T	0.65352	-0.6189	9	0.33141	T	0.24	.	16.1704	0.81808	0.0:0.0:1.0:0.0	.	460	Q9UPX0	TUTLB_HUMAN	T	460;302;460	ENSP00000317980:P460T;ENSP00000436552:P302T;ENSP00000436576:P460T	ENSP00000317980:P460T	P	-	1	0	IGSF9B	133306230	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.247000	0.72411	2.029000	0.59856	0.549000	0.68633	CCC	.	.		0.617	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502		T	133801020	G	T	133801020	3	4	351	1	0	0	0	0	1	0	0	0	7615	1203	42	3	2707	3	IGSF9B	11	133801020	Missense_Mutation	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	9490602	133801020	1205496	76	49354										
SLCO1C1	53919	hgsc.bcm.edu	37	chr12	20903660	20903660	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	tttgattgatacttcatgccTcaaatggggatttaaaagat	8	5	2	3			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr12:20903660T>C	ENST00000266509.2	+	14	2218	c.1850T>C	c.(1849-1851)cTc>cCc	p.L617P	SLCO1C1_ENST00000545102.1_Missense_Mutation_p.L499P|SLCO1C1_ENST00000381552.1_Missense_Mutation_p.L617P|SLCO1C1_ENST00000545604.1_Missense_Mutation_p.L617P|SLCO1C1_ENST00000540354.1_Missense_Mutation_p.L568P	NM_017435.4	NP_059131.1	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family, member 1C1	617					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			NS(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	60	Esophageal squamous(101;0.149)				Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Meclofenamic acid(DB00939)|Methotrexate(DB00563)|Ouabain(DB01092)|Phenytoin(DB00252)|Probenecid(DB01032)	ACTTCATGCCTCAAATGGGGA	0.363																																					p.L617P		Atlas-SNP	.											.	SLCO1C1	216	.	0			c.T1850C						.						118	112	114					12																	20903660		2203	4300	6503	SO:0001583	missense	53919	exon14			CATGCCTCAAATG	AF260704	CCDS8683.1, CCDS53757.1, CCDS53758.1, CCDS53759.1	12p12.2	2013-05-22	2003-11-25	2003-11-26	ENSG00000139155	ENSG00000139155		"Solute carriers"	13819	protein-coding gene	gene with protein product		613389	"solute carrier family 21 (organic anion transporter), member 14"	SLC21A14			Standard	NM_017435		Approved	OATP-F, OATP1C1, OATP1	uc010sii.2	Q9NYB5	OTTHUMG00000168966	ENST00000266509.2:c.1850T>C	chr12.hg19:g.20903660T>C	ENSP00000266509:p.Leu617Pro	149.0	0.0		144.0	72.0	NM_017435	B7Z251|B7Z3Q3|B7Z8P1|F5GZD6|Q5JPA4	Missense_Mutation	SNP	ENST00000266509.2	hg19	CCDS8683.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.207992	0.79240	.	.	ENSG00000139155	ENST00000545604;ENST00000540354;ENST00000266509;ENST00000381552;ENST00000545102	T;T;T;T;T	0.55930	0.49;0.49;0.49;0.49;0.49	5.32	5.32	0.75619	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.78861	0.4350	M	0.93720	3.45	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;0.998;0.998	D	0.84469	0.0598	10	0.87932	D	0	.	13.6737	0.62440	0.0:0.0:0.0:1.0	.	499;568;617;617	F5GZD6;B7Z3Q3;Q5JPA4;Q9NYB5	.;.;.;SO1C1_HUMAN	P	617;568;617;617;499	ENSP00000444149:L617P;ENSP00000438665:L568P;ENSP00000266509:L617P;ENSP00000370964:L617P;ENSP00000444527:L499P	ENSP00000266509:L617P	L	+	2	0	SLCO1C1	20794927	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.638000	0.74309	2.229000	0.72834	0.533000	0.62120	CTC	.	.		0.363	SLCO1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401765.1	NM_017435		C	20903660	T	C	20903660	3	2	351	1	0	0	0	0	1	0	0	0	14740	1551	54	2	1900	2	SLCO1C1	12	20903660	Missense_Mutation	SNP	T	TCGA-WJ-A86L-01A-12D-A45V-10		20903660	112948235	77	49355										
KIAA0528	9847	hgsc.bcm.edu	37	chr12	22697019	22697019	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	acgaaggcatcagtcaggtcActagcacggtccatcactgg	11	12	4	0			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr12:22697019A>C	ENST00000333957.4	-	2	321	c.66T>G	c.(64-66)agT>agG	p.S22R	C2CD5_ENST00000396028.2_Missense_Mutation_p.S22R|C2CD5_ENST00000545552.1_Missense_Mutation_p.S22R|C2CD5_ENST00000544930.1_5'UTR|C2CD5_ENST00000542676.1_Missense_Mutation_p.S22R|C2CD5_ENST00000446597.1_Missense_Mutation_p.S22R|C2CD5_ENST00000536386.1_Missense_Mutation_p.S22R	NM_014802.1	NP_055617.1	Q86YS7	C2CD5_HUMAN	C2 calcium-dependent domain containing 5	22	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				cellular response to insulin stimulus (GO:0032869)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|intracellular protein transmembrane transport (GO:0065002)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)										CAGTCAGGTCACTAGCACGGT	0.612																																					p.S22R		Atlas-SNP	.											.	.	.	.	0			c.T66G						.						175	130	145					12																	22697019		2203	4300	6503	SO:0001583	missense	9847	exon2			CAGGTCACTAGCA	AB011100	CCDS31758.1, CCDS66337.1, CCDS66338.1, CCDS66339.1, CCDS66340.1	12p12.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000111731	ENSG00000111731			29062	protein-coding gene	gene with protein product	"138 kDa C2 domain-containing phosphoprotein"		"KIAA0528"	KIAA0528		21907143	Standard	XM_005253538		Approved	CDP138	uc001rfq.3	Q86YS7	OTTHUMG00000169100	ENST00000333957.4:c.66T>G	chr12.hg19:g.22697019A>C	ENSP00000334229:p.Ser22Arg	65.0	0.0		76.0	34.0	NM_014802	B4DJ03|B4DRN7|B7ZLL0|F5H2A1|F5H5R1|O60280|Q17RY7|Q7Z619|Q86SU3	Missense_Mutation	SNP	ENST00000333957.4	hg19	CCDS31758.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.946608	0.73672	.	.	ENSG00000111731	ENST00000333957;ENST00000446597;ENST00000536386;ENST00000396028;ENST00000542676;ENST00000545552	T;T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95;0.95	4.28	1.93	0.25924	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.56171	0.1967	M	0.68728	2.09	0.80722	D	1	P;P;D;D;D	0.89917	0.925;0.939;0.999;1.0;0.999	P;P;D;D;D	0.85130	0.644;0.758;0.99;0.997;0.968	T	0.51942	-0.8641	10	0.51188	T	0.08	-18.0284	7.4334	0.27141	0.6409:0.0:0.3591:0.0	.	22;22;22;22;22	F5H2A1;B4DRN7;B7ZLL0;Q86YS7-2;Q86YS7	.;.;.;.;K0528_HUMAN	R	22	ENSP00000334229:S22R;ENSP00000388756:S22R;ENSP00000439392:S22R;ENSP00000379345:S22R;ENSP00000441951:S22R;ENSP00000443204:S22R	ENSP00000334229:S22R	S	-	3	2	KIAA0528	22588286	0.999000	0.42202	1.000000	0.80357	0.989000	0.77384	0.832000	0.27490	0.303000	0.22785	0.482000	0.46254	AGT	.	.		0.612	C2CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402257.1	NM_014802		C	22697019	A	C	22697019	3	2	351	1	0	0	0	0	1	0	0	0	8191	156	6	5	3032	5	KIAA0528	12	22697019	Missense_Mutation	SNP	A	TCGA-WJ-A86L-01A-12D-A45V-10	1793359	22697019	111154876	78	49356										
KRT6A	3853	hgsc.bcm.edu	37	chr12	52884732	52884732	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	ttgttcatgtaggcagcatcCacatcctggggaaagagcca	11	10	1	1	rs368725695		TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr12:52884732C>T	ENST00000330722.6	-	4	890	c.822G>A	c.(820-822)gtG>gtA	p.V274V		NM_005554.3	NP_005545.1	P02538	K2C6A_HUMAN	keratin 6A	274	Coil 1B.|Rod.				cell differentiation (GO:0030154)|positive regulation of cell proliferation (GO:0008284)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	39				BRCA - Breast invasive adenocarcinoma(357;0.189)		AGGCAGCATCCACATCCTGGG	0.502																																					p.V274V		Atlas-SNP	.											.	KRT6A	89	.	0			c.G822A						.						69	65	67					12																	52884732		2203	4297	6500	SO:0001819	synonymous_variant	3853	exon4			AGCATCCACATCC	BC014152, L42593, L42610	CCDS41786.1	12q13.13	2013-01-16			ENSG00000205420	ENSG00000205420		"-", "Intermediate filaments type II, keratins (basic)"	6443	protein-coding gene	gene with protein product		148041	"keratin 6C", "keratin 6D"	KRT6C, KRT6D		1713141, 16831889	Standard	NM_005554		Approved	CK6C, K6C, CK6D, K6D	uc001sam.3	P02538	OTTHUMG00000169597	ENST00000330722.6:c.822G>A	chr12.hg19:g.52884732C>T		129.0	0.0		147.0	55.0	NM_005554	A4QPC1|P48667|Q08AR4|Q6NT67|Q96CL4	Silent	SNP	ENST00000330722.6	hg19	CCDS41786.1																																																																																			.	.		0.502	KRT6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404978.2	NM_005554		T	52884732	C	T	52884732	2	4	351	1	0	0	0	0	0	0	0	1	8489	581	21	3		3	KRT6A	12	52884732	Silent	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	30187713	52884732	80967163	79	49357										
KRT78	196374	hgsc.bcm.edu	37	chr12	53238491	53238491	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	acgtgtcgctggcctgggtcTggagctggcccagctcctgc	15	14	1	0			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr12:53238491T>G	ENST00000304620.4	-	5	836	c.773A>C	c.(772-774)cAg>cCg	p.Q258P	KRT78_ENST00000359499.4_Missense_Mutation_p.Q148P	NM_173352.2	NP_775487.2	Q8N1N4	K2C78_HUMAN	keratin 78	258	Coil 1B.|Rod.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	18						GGCCTGGGTCTGGAGCTGGCC	0.597																																					p.Q258P		Atlas-SNP	.											.	KRT78	41	.	0			c.A773C						.						69	58	61					12																	53238491		2203	4300	6503	SO:0001583	missense	196374	exon5			TGGGTCTGGAGCT	AK096419	CCDS8840.1, CCDS73473.1	12q13.13	2013-06-25			ENSG00000170423	ENSG00000170423		"-", "Intermediate filaments type II, keratins (basic)"	28926	protein-coding gene	gene with protein product		611159				16831889	Standard	XM_005268695		Approved	K5B	uc001sbc.1	Q8N1N4	OTTHUMG00000169880	ENST00000304620.4:c.773A>C	chr12.hg19:g.53238491T>G	ENSP00000306261:p.Gln258Pro	30.0	0.0		29.0	16.0	NM_173352	A8K4D6|Q5HYM7|Q7RTT2	Missense_Mutation	SNP	ENST00000304620.4	hg19	CCDS8840.1	.	.	.	.	.	.	.	.	.	.	T	16.88	3.243818	0.58995	.	.	ENSG00000170423	ENST00000359499;ENST00000304620;ENST00000539860;ENST00000547110	D;D;D	0.90069	-2.61;-2.61;-2.61	5.28	1.42	0.22433	Filament (1);	0.297821	0.18436	N	0.141294	D	0.95046	0.8396	H	0.96777	3.88	0.27207	N	0.960013	D	0.71674	0.998	D	0.65684	0.937	D	0.88319	0.2961	10	0.87932	D	0	.	7.0869	0.25261	0.0:0.0749:0.2797:0.6454	.	258	Q8N1N4	K2C78_HUMAN	P	148;258;29;29	ENSP00000352479:Q148P;ENSP00000306261:Q258P;ENSP00000447817:Q29P	ENSP00000306261:Q258P	Q	-	2	0	KRT78	51524758	1.000000	0.71417	0.005000	0.12908	0.009000	0.06853	5.074000	0.64401	0.052000	0.16007	0.460000	0.39030	CAG	.	.		0.597	KRT78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406380.1	NM_173352		G	53238491	T	G	53238491	3	3	351	1	0	0	0	0	1	0	0	0	8500	1580	55	5	809	5	KRT78	12	53238491	Missense_Mutation	SNP	T	TCGA-WJ-A86L-01A-12D-A45V-10	353759	53238491	80613404	80	49358										
APAF1	317	hgsc.bcm.edu	37	chr12	99121087	99121087	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	gcttatctctgctggaggatAtattaaggtaagagttcccc	10	8	1	1			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr12:99121087A>G	ENST00000551964.1	+	26	4329	c.3593A>G	c.(3592-3594)tAt>tGt	p.Y1198C	APAF1_ENST00000552268.1_Intron|APAF1_ENST00000357310.1_Missense_Mutation_p.Y1155C|APAF1_ENST00000333991.1_Intron|APAF1_ENST00000549007.1_Missense_Mutation_p.Y1113C|APAF1_ENST00000339433.3_Missense_Mutation_p.Y1113C|APAF1_ENST00000547045.1_Missense_Mutation_p.Y1155C|APAF1_ENST00000359972.2_Missense_Mutation_p.Y1144C|APAF1_ENST00000550527.1_Missense_Mutation_p.Y1187C	NM_181861.1	NP_863651.1	O14727	APAF_HUMAN	apoptotic peptidase activating factor 1	1198					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|forebrain development (GO:0030900)|intrinsic apoptotic signaling pathway (GO:0097193)|nervous system development (GO:0007399)|neural tube closure (GO:0001843)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|regulation of apoptotic DNA fragmentation (GO:1902510)|regulation of apoptotic process (GO:0042981)|response to G1 DNA damage checkpoint signaling (GO:0072432)	apoptosome (GO:0043293)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(1)	42					Adenosine triphosphate(DB00171)	GCTGGAGGATATATTAAGGTA	0.428																																					p.Y1198C		Atlas-SNP	.											.	APAF1	111	.	0			c.A3593G						.						65	67	66					12																	99121087		2203	4300	6503	SO:0001583	missense	317	exon26			GAGGATATATTAA	AF013263	CCDS9069.1, CCDS9070.1, CCDS9071.1, CCDS55862.1, CCDS55863.1	12q23	2013-01-10	2006-10-23			ENSG00000120868		"WD repeat domain containing"	576	protein-coding gene	gene with protein product		602233	"apoptotic protease activating factor", "apoptotic peptidase activating factor"			9267021, 10702682	Standard	NM_181861		Approved	CED4, APAF-1	uc001tfz.3	O14727	OTTHUMG00000170214	ENST00000551964.1:c.3593A>G	chr12.hg19:g.99121087A>G	ENSP00000448165:p.Tyr1198Cys	46.0	0.0		31.0	14.0	NM_181861	B2RMX8|O43297|Q7Z438|Q9BXZ6|Q9UBZ5|Q9UGN8|Q9UGN9|Q9UGP0|Q9UJ58|Q9UJ59|Q9UJ60|Q9UJ61|Q9UJ62|Q9UJ63|Q9UJ64|Q9UJ65|Q9UJ66|Q9UJ67|Q9UNC9	Missense_Mutation	SNP	ENST00000551964.1	hg19	CCDS9069.1	.	.	.	.	.	.	.	.	.	.	A	13.35	2.210136	0.39003	.	.	ENSG00000120868	ENST00000551964;ENST00000359972;ENST00000357310;ENST00000339433;ENST00000550527;ENST00000547045;ENST00000549007	T;T;T;T;T;T;T	0.81163	-1.46;-1.46;2.23;1.06;-1.46;2.23;1.06	5.79	1.81	0.25067	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.255939	0.40554	N	0.001071	T	0.78698	0.4324	L	0.29908	0.895	0.34824	D	0.739014	P;P;P;D;D	0.71674	0.916;0.949;0.879;0.987;0.998	P;P;P;P;P	0.62298	0.841;0.866;0.669;0.9;0.896	T	0.79857	-0.1626	10	0.46703	T	0.11	-8.9857	7.613	0.28142	0.6265:0.1282:0.0:0.2453	.	1113;1155;1144;1198;1187	C9JLV4;O14727-4;O14727-3;O14727;O14727-2	.;.;.;APAF_HUMAN;.	C	1198;1144;1155;1113;1187;1155;1113	ENSP00000448165:Y1198C;ENSP00000353059:Y1144C;ENSP00000349862:Y1155C;ENSP00000341830:Y1113C;ENSP00000448449:Y1187C;ENSP00000449791:Y1155C;ENSP00000448161:Y1113C	ENSP00000341830:Y1113C	Y	+	2	0	APAF1	97645218	1.000000	0.71417	0.604000	0.28916	0.402000	0.30811	3.113000	0.50376	0.418000	0.25898	0.528000	0.53228	TAT	.	.		0.428	APAF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408006.1	NM_181861.1		G	99121087	A	G	99121087	3	3	351	1	0	0	0	0	1	0	0	0	755	449	16	2	3691	2	APAF1	12	99121087	Missense_Mutation	SNP	A	TCGA-WJ-A86L-01A-12D-A45V-10	45882596	99121087	34730808	81	49359										
HNF1A	6927	hgsc.bcm.edu	37	chr12	121437070	121437070	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	ccctctctcccctgcggccaGccctctacagccacaagccc	6	23	2	0			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr12:121437070G>A	ENST00000257555.6	+	8	1727		c.e8-1		HNF1A_ENST00000541395.1_Splice_Site|RP11-216P16.2_ENST00000606238.1_RNA|HNF1A_ENST00000544413.1_Splice_Site			P20823	HNF1A_HUMAN	HNF1 homeobox A						glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CCTGCGGCCAGCCCTCTACAG	0.667									Hepatic Adenoma, Familial Clustering of																												.		Atlas-SNP	.											.	HNF1A	302	.	0			c.1502-1G>A						.						47	51	49					12																	121437070		2203	4300	6503	SO:0001630	splice_region_variant	6927	exon8	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	CGGCCAGCCCTCT	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100		"Homeoboxes / HNF class"	11621	protein-coding gene	gene with protein product		142410	"transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor"	MODY3, TCF1		1535333, 7795649	Standard	NM_000545		Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	ENST00000257555.6:c.1502-1G>A	chr12.hg19:g.121437070G>A		118.0	0.0		103.0	43.0	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Splice_Site	SNP	ENST00000257555.6	hg19	CCDS9209.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.752217	0.89753	.	.	ENSG00000135100	ENST00000257555;ENST00000535125;ENST00000537424;ENST00000543027;ENST00000541395;ENST00000544413	.	.	.	5.52	5.52	0.82312	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.4622	0.90743	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	HNF1A	119921453	0.818000	0.29161	1.000000	0.80357	0.933000	0.57130	0.923000	0.28757	2.601000	0.87937	0.650000	0.86243	.	.	.		0.667	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545	Intron	A	121437070	G	A	121437070	5	1	351	1	0	0	0	0	0	0	1	0	7260	985	34	3	1531	3	HNF1A	12	121437070	Splice_Site	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	22315983	121437070	12414825	82	49360										
TRPC4	7223	hgsc.bcm.edu	37	chr13	38320590	38320590	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	ttatcaaggagtataggaggCacctaaaaaaaaaaaaggca	9	5	1	0			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr13:38320590C>T	ENST00000379705.3	-	3	1238	c.381G>A	c.(379-381)gtG>gtA	p.V127V	TRPC4_ENST00000338947.5_Intron|TRPC4_ENST00000379679.1_Intron|TRPC4_ENST00000379673.2_Silent_p.V127V|TRPC4_ENST00000379681.3_Silent_p.V127V|TRPC4_ENST00000358477.2_Silent_p.V127V|TRPC4_ENST00000355779.2_Silent_p.V127V|TRPC4_ENST00000426868.2_Silent_p.V127V|TRPC4_ENST00000447043.1_Silent_p.V127V			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	127	Multimerization domain. {ECO:0000250}.				axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|gamma-aminobutyric acid secretion (GO:0014051)|ion transmembrane transport (GO:0034220)|oligodendrocyte differentiation (GO:0048709)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|calcium channel complex (GO:0034704)|caveola (GO:0005901)|cell surface (GO:0009986)|cortical cytoskeleton (GO:0030863)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			NS(2)|breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(26)|lung(30)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	83				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		GTATAGGAGGCACCTAAAAAA	0.338																																					p.V127V		Atlas-SNP	.											.	TRPC4	389	.	0			c.G381A						.						56	68	64					13																	38320590		2159	4246	6405	SO:0001819	synonymous_variant	7223	exon3			AGGAGGCACCTAA	U40983	CCDS9365.1, CCDS45035.1, CCDS45036.1, CCDS45038.1, CCDS45039.1	13q13.3	2013-01-10			ENSG00000133107	ENSG00000133107		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	12336	protein-coding gene	gene with protein product		603651				8646775, 16382100	Standard	NM_016179		Approved	HTRP4, TRP4	uc010abx.3	Q9UBN4	OTTHUMG00000016752	ENST00000379705.3:c.381G>A	chr13.hg19:g.38320590C>T		49.0	0.0		37.0	26.0	NM_003306	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Silent	SNP	ENST00000379705.3	hg19	CCDS9365.1																																																																																			.	.		0.338	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306		T	38320590	C	T	38320590	2	4	351	1	0	0	0	0	0	0	0	1	16595	697	25	3		3	TRPC4	13	38320590	Silent	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10		38320590	76849288	83	49361										
TBC1D4	9882	hgsc.bcm.edu	37	chr13	76055872	76055872	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	gctccagggggtgcgggaacGgctcatcctgaatgcagctg	16	11	1	1			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr13:76055872G>C	ENST00000377636.3	-	1	378	c.32C>G	c.(31-33)cCg>cGg	p.P11R	TBC1D4_ENST00000431480.2_Missense_Mutation_p.P11R|TBC1D4_ENST00000377625.2_Missense_Mutation_p.P11R|TBC1D4_ENST00000425511.1_5'UTR	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	11					cellular response to insulin stimulus (GO:0032869)|membrane organization (GO:0061024)|negative regulation of vesicle fusion (GO:0031339)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		GTGCGGGAACGGCTCATCCTG	0.726																																					p.P11R		Atlas-SNP	.											.	TBC1D4	142	.	0			c.C32G						.						9	11	11					13																	76055872		1797	3987	5784	SO:0001583	missense	9882	exon1			GGGAACGGCTCAT	AB011175	CCDS41901.1, CCDS66563.1, CCDS66564.1	13q22.2	2013-07-09			ENSG00000136111	ENSG00000136111			19165	protein-coding gene	gene with protein product	"Akt substrate of 160 kDa"	612465				11829485, 11994271, 15304337	Standard	XM_005266603		Approved	KIAA0603, AS160, DKFZp779C0666	uc001vjl.1	O60343	OTTHUMG00000017088	ENST00000377636.3:c.32C>G	chr13.hg19:g.76055872G>C	ENSP00000366863:p.Pro11Arg	96.0	0.0		58.0	49.0	NM_014832	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Missense_Mutation	SNP	ENST00000377636.3	hg19	CCDS41901.1	.	.	.	.	.	.	.	.	.	.	G	17.58	3.425262	0.62733	.	.	ENSG00000136111	ENST00000377636;ENST00000431480;ENST00000377625	T;T;T	0.03951	3.8;3.78;3.75	3.87	3.02	0.34903	.	0.739627	0.11772	N	0.530988	T	0.13243	0.0321	L	0.40543	1.245	0.80722	D	1	D;D;D	0.76494	0.989;0.989;0.999	P;P;D	0.79784	0.865;0.865;0.993	T	0.03840	-1.0999	10	0.72032	D	0.01	-9.3355	9.7031	0.40198	0.0983:0.0:0.9017:0.0	.	11;11;11	O60343-2;O60343-3;O60343	.;.;TBCD4_HUMAN	R	11	ENSP00000366863:P11R;ENSP00000395986:P11R;ENSP00000366852:P11R	ENSP00000366852:P11R	P	-	2	0	TBC1D4	74953873	1.000000	0.71417	0.995000	0.50966	0.982000	0.71751	3.836000	0.55813	0.950000	0.37743	0.462000	0.41574	CCG	.	.		0.726	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832		C	76055872	G	C	76055872	3	2	351	1	0	0	0	0	1	0	0	0	15637	1116	39	4	3948	4	TBC1D4	13	76055872	Missense_Mutation	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	37735282	76055872	39114006	84	49362										
GPC6	10082	hgsc.bcm.edu	37	chr13	95055461	95055461	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	tgtcctggcactgcagagacTgtgcagataatcttgggttt	12	8	1	2			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr13:95055461T>A	ENST00000377047.4	+	9	2273	c.1658T>A	c.(1657-1659)cTg>cAg	p.L553Q		NM_005708.3	NP_005699.1	Q9Y625	GPC6_HUMAN	glypican 6	553					carbohydrate metabolic process (GO:0005975)|cell migration (GO:0016477)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	38	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				CTGCAGAGACTGTGCAGATAA	0.517																																					p.L553Q		Atlas-SNP	.											.	GPC6	102	.	0			c.T1658A						.						55	47	49					13																	95055461		2203	4300	6503	SO:0001583	missense	10082	exon9			AGAGACTGTGCAG	AF111178	CCDS9469.1	13q32	2008-02-05			ENSG00000183098	ENSG00000183098		"Proteoglycans / Cell Surface : Glypicans"	4454	protein-coding gene	gene with protein product	"glypican proteoglycan 6"	604404				10329016	Standard	NM_005708		Approved		uc001vlt.3	Q9Y625	OTTHUMG00000017205	ENST00000377047.4:c.1658T>A	chr13.hg19:g.95055461T>A	ENSP00000366246:p.Leu553Gln	31.0	0.0		34.0	31.0	NM_005708	A8K279|Q96SG5|Q96SG8|Q9H1P4	Missense_Mutation	SNP	ENST00000377047.4	hg19	CCDS9469.1	.	.	.	.	.	.	.	.	.	.	T	6.784	0.513575	0.12944	.	.	ENSG00000183098	ENST00000377047	T	0.52057	0.68	5.77	4.54	0.55810	.	0.192672	0.34314	N	0.004079	T	0.35307	0.0927	L	0.47716	1.5	0.37437	D	0.914276	B	0.02656	0.0	B	0.04013	0.001	T	0.24404	-1.0161	10	0.11794	T	0.64	.	8.564	0.33527	0.3863:0.0:0.0:0.6137	.	553	Q9Y625	GPC6_HUMAN	Q	553	ENSP00000366246:L553Q	ENSP00000366246:L553Q	L	+	2	0	GPC6	93853462	1.000000	0.71417	1.000000	0.80357	0.433000	0.31745	4.347000	0.59373	2.203000	0.70933	0.454000	0.30748	CTG	.	.		0.517	GPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045460.4	NM_005708		A	95055461	T	A	95055461	3	1	351	1	0	0	0	0	1	0	0	0	6610	1580	55	4	1692	4	GPC6	13	95055461	Missense_Mutation	SNP	T	TCGA-WJ-A86L-01A-12D-A45V-10	18999589	95055461	20114417	85	49363										
FLJ10357	55701	hgsc.bcm.edu	37	chr14	21555482	21555482	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	ctccccactctctgcagccgCccgcacccgggcctccgtgg	10	22	1	0			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr14:21555482C>T	ENST00000298694.4	+	21	4374	c.4247C>T	c.(4246-4248)gCc>gTc	p.A1416V	ARHGEF40_ENST00000298693.3_Intron			Q8TER5	ARH40_HUMAN	Rho guanine nucleotide exchange factor (GEF) 40	1416						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(4)|ovary(3)|upper_aerodigestive_tract(2)	9						TCTGCAGCCGCCCGCACCCGG	0.701																																					p.A1416V		Atlas-SNP	.											.	ARHGEF40	84	.	0			c.C4247T						.						31	41	38					14																	21555482		2193	4288	6481	SO:0001583	missense	55701	exon21			CAGCCGCCCGCAC		CCDS32041.1	14q11.2	2012-07-24			ENSG00000165801	ENSG00000165801		"Rho guanine nucleotide exchange factors"	25516	protein-coding gene	gene with protein product		610018				16143467	Standard	NM_001278529		Approved	solo, FLJ10357	uc001vzp.3	Q8TER5		ENST00000298694.4:c.4247C>T	chr14.hg19:g.21555482C>T	ENSP00000298694:p.Ala1416Val	44.0	0.0		72.0	26.0	NM_018071	A5PL07|Q9BWP5|Q9H7L6|Q9NTF9|Q9NW24	Missense_Mutation	SNP	ENST00000298694.4	hg19	CCDS32041.1	.	.	.	.	.	.	.	.	.	.	C	15.33	2.801172	0.50315	.	.	ENSG00000165801	ENST00000298694	T	0.02606	4.23	5.32	4.4	0.53042	.	0.000000	0.47093	D	0.000248	T	0.05135	0.0137	N	0.11427	0.14	0.80722	D	1	D	0.65815	0.995	D	0.68353	0.957	T	0.59156	-0.7507	10	0.37606	T	0.19	.	11.7417	0.51796	0.0:0.8219:0.1781:0.0	.	1416	Q8TER5	ARH40_HUMAN	V	1416	ENSP00000298694:A1416V	ENSP00000298694:A1416V	A	+	2	0	ARHGEF40	20625322	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.127000	0.57944	1.181000	0.42912	0.563000	0.77884	GCC	.	.		0.701	ARHGEF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413122.1			T	21555482	C	T	21555482	3	4	351	1	0	0	0	0	1	0	0	0	5934	739	26	3	4329	3	FLJ10357	14	21555482	Missense_Mutation	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10		21555482	85794058	86	49364										
PRMT5	10419	hgsc.bcm.edu	37	chr14	23398484	23398484	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	tgcttggccacagcccctagTgtgtcagctatttcggggac	12	12	1	0			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr14:23398484T>A	ENST00000324366.8	-	1	310	c.87A>T	c.(85-87)acA>acT	p.T29T	PRMT5_ENST00000553897.1_Silent_p.T29T|PRMT5_ENST00000553641.1_5'UTR|PRMT5_ENST00000397440.4_5'UTR|PRMT5_ENST00000216350.8_5'UTR|PRMT5-AS1_ENST00000590290.1_RNA|PRMT5-AS1_ENST00000587245.2_RNA|RP11-298I3.1_ENST00000548819.1_RNA|PRMT5-AS1_ENST00000595662.1_RNA|PRMT5-AS1_ENST00000599580.2_RNA|PRMT5_ENST00000538452.1_5'UTR|RP11-298I3.1_ENST00000548322.1_RNA|PRMT5_ENST00000397441.2_5'UTR	NM_006109.3	NP_006100.2	O14744	ANM5_HUMAN	protein arginine methyltransferase 5	29	TIM barrel. {ECO:0000269|PubMed:23071334}.				cell proliferation (GO:0008283)|circadian regulation of gene expression (GO:0032922)|endothelial cell activation (GO:0042118)|gene expression (GO:0010467)|histone H4-R3 methylation (GO:0043985)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to symmetrical-dimethyl arginine (GO:0019918)|peptidyl-arginine N-methylation (GO:0035246)|regulation of mitosis (GO:0007088)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|methylosome (GO:0034709)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|histone-arginine N-methyltransferase activity (GO:0008469)|methyltransferase activity (GO:0008168)|protein-arginine omega-N symmetric methyltransferase activity (GO:0035243)|ribonucleoprotein complex binding (GO:0043021)|transcription corepressor activity (GO:0003714)			endometrium(4)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	25	all_cancers(95;2.76e-05)			GBM - Glioblastoma multiforme(265;0.0126)		CAGCCCCTAGTGTGTCAGCTA	0.672																																					p.T29T		Atlas-SNP	.											.	PRMT5	101	.	0			c.A87T						.						59	55	56					14																	23398484		2203	4300	6503	SO:0001819	synonymous_variant	10419	exon1			CCCTAGTGTGTCA	AF015913	CCDS9579.1, CCDS41922.1, CCDS61394.1, CCDS61395.1, CCDS61396.1	14q11.2	2014-06-12	2006-02-16	2006-02-16	ENSG00000100462	ENSG00000100462	2.1.1.125	"Protein arginine methyltransferases"	10894	protein-coding gene	gene with protein product		604045	"skb1 (S. pombe) homolog", "SKB1 homolog (S. pombe)"	HRMT1L5, SKB1		9843966	Standard	NM_001282955		Approved	SKB1Hs	uc001whm.1	O14744	OTTHUMG00000028709	ENST00000324366.8:c.87A>T	chr14.hg19:g.23398484T>A		36.0	0.0		45.0	19.0	NM_006109	A8MTP3|A8MZ91|B4DX49|B4DY30|B5BU10|D3DS33|E2QRE7|Q6IBR1|Q9UKH1	Silent	SNP	ENST00000324366.8	hg19	CCDS9579.1																																																																																			.	.		0.672	PRMT5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071674.3			A	23398484	T	A	23398484	2	1	351	1	0	0	0	0	0	0	0	1	12551	1683	59	4		4	PRMT5	14	23398484	Silent	SNP	T	TCGA-WJ-A86L-01A-12D-A45V-10	1843002	23398484	83951056	87	49365										
DCAF11	80344	hgsc.bcm.edu	37	chr14	24590150	24590150	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	catggaagcttcacgccaggCtgccacacagcaaaactggg	11	13	1	0			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr14:24590150C>A	ENST00000446197.3	+	12	1923	c.1196C>A	c.(1195-1197)gCt>gAt	p.A399D	DCAF11_ENST00000559115.1_Missense_Mutation_p.A399D|DCAF11_ENST00000396936.1_Missense_Mutation_p.A299D|DCAF11_ENST00000396941.4_Missense_Mutation_p.A373D|RP11-468E2.6_ENST00000558325.1_5'Flank	NM_025230.4	NP_079506.3	Q8TEB1	DCA11_HUMAN	DDB1 and CUL4 associated factor 11	399					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)											TCACGCCAGGCTGCCACACAG	0.542																																					p.A399D		Atlas-SNP	.											.	.	.	.	0			c.C1196A						.						75	74	74					14																	24590150		2203	4300	6503	SO:0001583	missense	80344	exon12			GCCAGGCTGCCAC	AF130070	CCDS9610.1, CCDS41929.1	14q11.2	2013-01-09	2009-07-17	2009-07-17	ENSG00000100897	ENSG00000100897		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	20258	protein-coding gene	gene with protein product		613317	"WD repeat domain 23"	WDR23			Standard	NM_025230		Approved	PRO2389, GL014	uc001wlv.3	Q8TEB1	OTTHUMG00000028793	ENST00000446197.3:c.1196C>A	chr14.hg19:g.24590150C>A	ENSP00000415556:p.Ala399Asp	113.0	0.0		164.0	88.0	NM_025230	B3KQ83|D3DS56|Q5D039|Q86U00|Q86U39|Q8NDN2|Q9H2J0|Q9H3A3|Q9H5C9	Missense_Mutation	SNP	ENST00000446197.3	hg19	CCDS9610.1	.	.	.	.	.	.	.	.	.	.	c	26.7	4.762284	0.89932	.	.	ENSG00000100897	ENST00000326009;ENST00000446197;ENST00000396936;ENST00000396941	T;T	0.63255	0.64;-0.03	6.17	6.17	0.99709	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.74658	0.3745	L	0.53249	1.67	0.80722	D	1	D;D;D;D;D	0.67145	0.995;0.996;0.981;0.992;0.994	P;D;P;P;P	0.66497	0.858;0.944;0.901;0.901;0.88	T	0.69405	-0.5154	10	0.33940	T	0.23	-14.5028	18.3732	0.90420	0.0:1.0:0.0:0.0	.	322;373;299;399;399	Q59GN6;Q8TEB1-2;Q8TEB1-3;A8K9T2;Q8TEB1	.;.;.;.;DCA11_HUMAN	D	399;373;299;373	ENSP00000380142:A299D;ENSP00000380146:A373D	ENSP00000323680:A399D	A	+	2	0	DCAF11	23659990	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.837000	0.75354	2.941000	0.99782	0.655000	0.94253	GCT	.	.		0.542	DCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071907.4			A	24590150	C	A	24590150	3	1	351	1	0	0	0	0	1	0	0	0	4264	797	28	3	1238	3	DCAF11	14	24590150	Missense_Mutation	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	1191666	24590150	82759390	88	49366										
GNPNAT1	64841	hgsc.bcm.edu	37	chr14	53251349	53251349	+	Frame_Shift_Del	DEL	G	G	-													0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	gtagacttgggtcaaacataGgagtttcatcaggtttcatt							TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr14:53251349delG	ENST00000216410.3	-	2	207	c.20delC	c.(19-21)cctfs	p.P7fs	RN7SL588P_ENST00000583393.1_RNA|GNPNAT1_ENST00000554230.1_Intron	NM_198066.3	NP_932332.1	Q96EK6	GNA1_HUMAN	glucosamine-phosphate N-acetyltransferase 1	7					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|glucosamine metabolic process (GO:0006041)|liver development (GO:0001889)|N-acetylglucosamine metabolic process (GO:0006044)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine biosynthetic process (GO:0006048)	cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|membrane (GO:0016020)	glucosamine 6-phosphate N-acetyltransferase activity (GO:0004343)|monosaccharide binding (GO:0048029)			liver(1)|lung(1)|prostate(1)|skin(1)	4	Breast(41;0.176)					GTCAAACATAGGAGTTTCATC	0.348																																					p.P7fs		Atlas-INDEL	.											.	GNPNAT1	14	.	0			c.21delT						.						47	45	46					14																	53251349		2203	4300	6503	SO:0001589	frameshift_variant	64841	exon2			.	AK001469	CCDS9712.1	14q22.1	2011-11-16			ENSG00000100522	ENSG00000100522	2.3.1.4		19980	protein-coding gene	gene with protein product							Standard	NM_198066		Approved	Gpnat1, FLJ10607	uc001xab.3	Q96EK6	OTTHUMG00000152334	ENST00000216410.3:c.20delC	chr14.hg19:g.53251349delG	ENSP00000216410:p.Pro7fs	85.0	0.0		80.0	34.0	NM_198066		Frame_Shift_Del	DEL	ENST00000216410.3	hg19	CCDS9712.1																																																																																			.	.		0.348	GNPNAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276898.1			-	53251349	G	-	53251349	7	5	351	1	0	1	0	1	0	0	0	0	6552	1000	35	0	554	0	GNPNAT1	14	53251349	Frame_Shift_Del	DEL	G	TCGA-WJ-A86L-01A-12D-A45V-10	28661199	53251349	54098191	89	49367										
RTN1	6252	hgsc.bcm.edu	37	chr14	60212828	60212828	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	atgttgttcttggtgcttcaCctcctcgggtctggttatgt	11	9	3	0			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr14:60212828C>A	ENST00000267484.5	-	2	948	c.613G>T	c.(613-615)Gtg>Ttg	p.V205L		NM_021136.2	NP_066959.1	Q16799	RTN1_HUMAN	reticulon 1	205					neuron differentiation (GO:0030182)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)				central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(30)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(108;0.0968)		TGGTGCTTCACCTCCTCGGGT	0.458																																					p.V205L		Atlas-SNP	.											.	RTN1	139	.	0			c.G613T						.						261	254	257					14																	60212828		2203	4300	6503	SO:0001583	missense	6252	exon2			GCTTCACCTCCTC	L10333	CCDS9740.1, CCDS9741.1	14q21-q22	2008-08-29			ENSG00000139970	ENSG00000139970			10467	protein-coding gene	gene with protein product		600865	"neuroendocrine-specific protein"	NSP		8275708	Standard	NM_206852		Approved		uc001xen.1	Q16799	OTTHUMG00000028947	ENST00000267484.5:c.613G>T	chr14.hg19:g.60212828C>A	ENSP00000267484:p.Val205Leu	106.0	0.0		92.0	13.0	NM_021136	Q16800|Q16801|Q5BKZ4|Q9BQ59	Missense_Mutation	SNP	ENST00000267484.5	hg19	CCDS9740.1	.	.	.	.	.	.	.	.	.	.	C	5.891	0.348424	0.11126	.	.	ENSG00000139970	ENST00000267484;ENST00000433623	T	0.22336	1.96	5.7	-0.0625	0.13780	.	1.487350	0.03984	N	0.293816	T	0.19366	0.0465	L	0.51422	1.61	0.09310	N	1	B	0.17667	0.023	B	0.09377	0.004	T	0.25745	-1.0123	10	0.28530	T	0.3	.	5.839	0.18623	0.0:0.1995:0.5321:0.2684	.	205	Q16799	RTN1_HUMAN	L	205;131	ENSP00000267484:V205L	ENSP00000267484:V205L	V	-	1	0	RTN1	59282581	0.000000	0.05858	0.020000	0.16555	0.145000	0.21501	0.156000	0.16382	0.309000	0.22966	0.557000	0.71058	GTG	.	.		0.458	RTN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000072278.2			A	60212828	C	A	60212828	3	1	351	1	0	0	0	0	1	0	0	0	13740	507	18	3	1814	3	RTN1	14	60212828	Missense_Mutation	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	6961479	60212828	47136712	90	49368										
PCNX	22990	hgsc.bcm.edu	37	chr14	71524347	71524347	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	tacagtacaggggactgtttCatccttgcctctgactatct	8	11	3	1			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr14:71524347C>T	ENST00000304743.2	+	26	5204	c.4758C>T	c.(4756-4758)ttC>ttT	p.F1586F	PCNX_ENST00000238570.5_Intron|PCNX_ENST00000439984.3_Silent_p.F1475F	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	1586						integral component of membrane (GO:0016021)				NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		GGGACTGTTTCATCCTTGCCT	0.448																																					p.F1586F		Atlas-SNP	.											.	PCNX	198	.	0			c.C4758T						.						339	342	341					14																	71524347		2203	4300	6503	SO:0001819	synonymous_variant	22990	exon26			CTGTTTCATCCTT	AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"pecanex-like 1 (Drosophila)"	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.4758C>T	chr14.hg19:g.71524347C>T		91.0	0.0		73.0	28.0	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Silent	SNP	ENST00000304743.2	hg19	CCDS9806.1																																																																																			.	.		0.448	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982		T	71524347	C	T	71524347	2	4	351	1	0	0	0	0	0	0	0	1	11600	825	29	3		3	PCNX	14	71524347	Silent	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	11311519	71524347	35825193	91	49369										
NEK9	91754	hgsc.bcm.edu	37	chr14	75593444	75593444	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	cgtggcttccccgaaggcgcCgcggcccaggacgcggatgg	17	15	0	0			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr14:75593444C>A	ENST00000238616.5	-	1	339	c.181G>T	c.(181-183)Ggc>Tgc	p.G61C	RP11-950C14.7_ENST00000556236.1_RNA	NM_033116.4	NP_149107.4	Q8TD19	NEK9_HUMAN	NIMA-related kinase 9	61	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			endometrium(4)|kidney(2)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	31				BRCA - Breast invasive adenocarcinoma(234;0.00718)		CCGAAGGCGCCGCGGCCCAGG	0.761																																					p.G61C		Atlas-SNP	.											.	NEK9	64	.	0			c.G181T						.						7	10	9					14																	75593444		2001	3888	5889	SO:0001583	missense	91754	exon1			AGGCGCCGCGGCC	AY048580	CCDS9839.1	14q24.2	2012-11-15	2012-11-15		ENSG00000119638	ENSG00000119638			18591	protein-coding gene	gene with protein product		609798	"NIMA (never in mitosis gene a)- related kinase 9"			11864968	Standard	NM_033116		Approved	Nek8, NERCC, DKFZp434D0935, MGC16714	uc001xrl.3	Q8TD19	OTTHUMG00000171768	ENST00000238616.5:c.181G>T	chr14.hg19:g.75593444C>A	ENSP00000238616:p.Gly61Cys	160.0	0.0		180.0	83.0	NM_033116	Q52LK6|Q8NCN0|Q8TCY4|Q9UPI4|Q9Y6S4|Q9Y6S5|Q9Y6S6	Missense_Mutation	SNP	ENST00000238616.5	hg19	CCDS9839.1	.	.	.	.	.	.	.	.	.	.	C	31	5.084849	0.94100	.	.	ENSG00000119638	ENST00000238616;ENST00000540227	D	0.85339	-1.97	4.01	3.12	0.35913	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.059310	0.64402	D	0.000002	D	0.95626	0.8578	H	0.99758	4.755	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95902	0.8916	10	0.87932	D	0	.	11.8808	0.52574	0.0:0.9138:0.0:0.0862	.	61	Q8TD19	NEK9_HUMAN	C	61;43	ENSP00000238616:G61C	ENSP00000238616:G61C	G	-	1	0	NEK9	74663197	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.713000	0.74686	1.016000	0.39470	0.561000	0.74099	GGC	.	.		0.761	NEK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415021.1	NM_033116		A	75593444	C	A	75593444	3	1	351	1	0	0	0	0	1	0	0	0	10340	652	23	1	2846	1	NEK9	14	75593444	Missense_Mutation	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	4069097	75593444	31756096	92	49370										
HSP90AA1	3320	hgsc.bcm.edu	37	chr14	102552710	102552710	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	tcttgggtctgggtttcctcAggcatctggaacgacaccgc	12	12	4	0			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr14:102552710A>T	ENST00000216281.8	-	2	211	c.6T>A	c.(4-6)ccT>ccA	p.P2P	HSP90AA1_ENST00000441629.2_5'Flank|HSP90AA1_ENST00000334701.7_Silent_p.P124P	NM_005348.3	NP_005339.3	P07900	HS90A_HUMAN	heat shock protein 90kDa alpha (cytosolic), class A member 1	2					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone-mediated protein complex assembly (GO:0051131)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|mitochondrial transport (GO:0006839)|mitotic cell cycle (GO:0000278)|nitric oxide metabolic process (GO:0046209)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|protein import into mitochondrial outer membrane (GO:0045040)|protein refolding (GO:0042026)|regulation of nitric-oxide synthase activity (GO:0050999)|response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|identical protein binding (GO:0042802)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|TPR domain binding (GO:0030911)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(6)|large_intestine(3)|liver(1)|lung(10)|ovary(2)|prostate(1)	28					Nedocromil(DB00716)|Rifabutin(DB00615)	GGGTTTCCTCAGGCATCTGGA	0.488																																					p.P124P		Atlas-SNP	.											.	HSP90AA1	65	.	0			c.T372A						.						88	90	90					14																	102552710		2203	4300	6503	SO:0001819	synonymous_variant	3320	exon3			TTCCTCAGGCATC	M27024	CCDS9967.1, CCDS32160.1	14q32.33	2011-09-02	2006-02-24	2006-02-24	ENSG00000080824	ENSG00000080824		"Heat shock proteins / HSPC"	5253	protein-coding gene	gene with protein product		140571	"heat shock 90kD protein 1, alpha", "heat shock 90kDa protein 1, alpha"	HSPC1, HSPCA		2527334, 16269234	Standard	NM_001017963		Approved	Hsp89, Hsp90, FLJ31884, HSP90N	uc001ykv.4	P07900		ENST00000216281.8:c.6T>A	chr14.hg19:g.102552710A>T		124.0	0.0		95.0	32.0	NM_001017963	A8K500|B3KPJ9|Q2PP14|Q5CAQ6|Q5CAQ7|Q9BVQ5	Silent	SNP	ENST00000216281.8	hg19	CCDS9967.1																																																																																			.	.		0.488	HSP90AA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414952.2	NM_005348		T	102552710	A	T	102552710	2	4	351	1	0	0	0	0	0	0	0	1	7410	175	7	4		4	HSP90AA1	14	102552710	Silent	SNP	A	TCGA-WJ-A86L-01A-12D-A45V-10	26959266	102552710	4796830	93	49371										
INF2	64423	hgsc.bcm.edu	37	chr14	105180840	105180840	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	tgctcaggccctgaagccccTcaagttctccagcaaccagc	8	17	3	1			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr14:105180840T>A	ENST00000392634.4	+	21	3453	c.3341T>A	c.(3340-3342)cTc>cAc	p.L1114H	INF2_ENST00000330634.7_Missense_Mutation_p.L1114H	NM_022489.3	NP_071934.3	Q27J81	INF2_HUMAN	inverted formin, FH2 and WH2 domain containing	1114					actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|regulation of cellular component size (GO:0032535)|regulation of mitochondrial fission (GO:0090140)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.176)		CTGAAGCCCCTCAAGTTCTCC	0.652																																					p.L1114H		Atlas-SNP	.											.	INF2	148	.	0			c.T3341A						.						34	41	39					14																	105180840		2020	4172	6192	SO:0001583	missense	64423	exon21			AGCCCCTCAAGTT	AK025709	CCDS9989.2, CCDS45173.1	14q32.33	2009-09-07	2007-11-29	2007-11-29	ENSG00000203485	ENSG00000203485			23791	protein-coding gene	gene with protein product	"inverted formin 2"	610982	"chromosome 14 open reading frame 151", "chromosome 14 open reading frame 173"	C14orf151, C14orf173		16818491	Standard	NM_001031714		Approved	MGC13251	uc001ypb.2	Q27J81	OTTHUMG00000029811	ENST00000392634.4:c.3341T>A	chr14.hg19:g.105180840T>A	ENSP00000376410:p.Leu1114His	50.0	0.0		75.0	32.0	NM_022489	Q27J83|Q69YL8|Q6P1X7|Q6PK22|Q86TR7|Q9BRM1|Q9H6N1	Missense_Mutation	SNP	ENST00000392634.4	hg19	CCDS9989.2	.	.	.	.	.	.	.	.	.	.	T	14.51	2.555781	0.45487	.	.	ENSG00000203485	ENST00000330634;ENST00000392634	D;D	0.82167	-1.57;-1.58	5.0	5.0	0.66597	.	0.599365	0.12676	U	0.448421	D	0.83427	0.5252	L	0.32530	0.975	0.24797	N	0.992729	D;D	0.61697	0.99;0.983	P;P	0.56474	0.799;0.635	T	0.74836	-0.3529	10	0.72032	D	0.01	.	11.0831	0.48072	0.0:0.0:0.0:1.0	.	1114;1114	Q27J81-2;Q27J81	.;INF2_HUMAN	H	1114	ENSP00000376406:L1114H;ENSP00000376410:L1114H	ENSP00000252527:L582H	L	+	2	0	INF2	104251885	0.577000	0.26708	0.066000	0.19879	0.948000	0.59901	2.211000	0.42825	1.871000	0.54225	0.482000	0.46254	CTC	.	.		0.652	INF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074371.4	NM_022489		A	105180840	T	A	105180840	3	1	351	1	0	0	0	0	1	0	0	0	7743	1551	54	4	3423	4	INF2	14	105180840	Missense_Mutation	SNP	T	TCGA-WJ-A86L-01A-12D-A45V-10	2628130	105180840	2168700	94	49372										
NIPA1	123606	hgsc.bcm.edu	37	chr15	23049159	23049159	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	agggctctctgactggacggGttgttatgcaagatgtcttg	14	7	2	2			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr15:23049159G>A	ENST00000337435.4	-	5	684	c.660C>T	c.(658-660)aaC>aaT	p.N220N	NIPA1_ENST00000437912.2_Silent_p.N145N|NIPA1_ENST00000538684.1_Silent_p.N50N|NIPA1_ENST00000561183.1_Silent_p.N145N	NM_001142275.1|NM_144599.4	NP_001135747.1|NP_653200.2	Q7RTP0	NIPA1_HUMAN	non imprinted in Prader-Willi/Angelman syndrome 1	220					cell death (GO:0008219)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	magnesium ion transmembrane transporter activity (GO:0015095)			endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|skin(1)	15		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;4.18e-06)|Epithelial(43;3.97e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00165)		GACTGGACGGGTTGTTATGCA	0.582																																					p.N220N		Atlas-SNP	.											.	NIPA1	26	.	0			c.C660T						.						115	98	104					15																	23049159		2203	4300	6503	SO:0001819	synonymous_variant	123606	exon5			GGACGGGTTGTTA	BK001020	CCDS73691.1, CCDS73692.1	15q11.2	2006-10-06			ENSG00000170113	ENSG00000170113			17043	protein-coding gene	gene with protein product		608145	"spastic paraplegia 6 (autosomal dominant)"	SPG6		14508710	Standard	NM_144599		Approved	MGC35570	uc001yvc.3	Q7RTP0	OTTHUMG00000129099	ENST00000337435.4:c.660C>T	chr15.hg19:g.23049159G>A		95.0	0.0		73.0	30.0	NM_144599	B2RA76|Q5HYA9|Q7KZB0|Q86XW4	Silent	SNP	ENST00000337435.4	hg19	CCDS10011.1																																																																																			.	.		0.582	NIPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251135.2	NM_144599		A	23049159	G	A	23049159	2	1	351	1	0	0	0	0	0	0	0	1	10431	1252	44	3		3	NIPA1	15	23049159	Silent	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10		23049159	79482233	95	49373										
AQR	9716	hgsc.bcm.edu	37	chr15	35196558	35196558	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	ttaaagttattttcctttggTtttctcctcattattatatt	3	6	2	0			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr15:35196558T>C	ENST00000156471.5	-	19	2205	c.1980A>G	c.(1978-1980)aaA>aaG	p.K660K		NM_014691.2	NP_055506.1	O60306	AQR_HUMAN	aquarius intron-binding spliceosomal factor	660					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(10)|lung(18)|ovary(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	57		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		TTTCCTTTGGTTTTCTCCTCA	0.289																																					p.K660K		Atlas-SNP	.											.	AQR	139	.	0			c.A1980G						.						82	76	78					15																	35196558		1788	4057	5845	SO:0001819	synonymous_variant	9716	exon19			CTTTGGTTTTCTC	AB011132	CCDS42013.1	15q13	2013-09-12	2013-09-12			ENSG00000021776			29513	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 164"	610548	"aquarius homolog (mouse)"			9626505, 16949364	Standard	NM_014691		Approved	KIAA0560, fSAP164, IBP160	uc001ziv.3	O60306		ENST00000156471.5:c.1980A>G	chr15.hg19:g.35196558T>C		65.0	0.0		96.0	41.0	NM_014691	A0JP17|A5YKK3|Q2YDX9|Q6IRU8|Q6PIC8	Silent	SNP	ENST00000156471.5	hg19	CCDS42013.1																																																																																			.	.		0.289	AQR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417526.2	NM_014691		C	35196558	T	C	35196558	2	2	351	1	0	0	0	0	0	0	0	1	835	1722	60	2		2	AQR	15	35196558	Silent	SNP	T	TCGA-WJ-A86L-01A-12D-A45V-10	12147399	35196558	67334834	96	49374										
MYO1E	4643	hgsc.bcm.edu	37	chr15	59480390	59480390	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	tcgaatgttctctttcagacCcaaatattcgacttgatgct	6	10	2	2			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr15:59480390C>T	ENST00000288235.4	-	18	2230	c.1831G>A	c.(1831-1833)Ggt>Agt	p.G611S		NM_004998.3	NP_004989.2	Q12965	MYO1E_HUMAN	myosin IE	611	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(6)|lung(10)|pancreas(2)|prostate(1)|urinary_tract(1)	33				all cancers(107;0.207)		TCTTTCAGACCCAAATATTCG	0.458																																					p.G611S		Atlas-SNP	.											.	MYO1E	99	.	0			c.G1831A						.						153	145	148					15																	59480390		2191	4291	6482	SO:0001583	missense	4643	exon18			TCAGACCCAAATA	U14391	CCDS32254.1	15q21-q22	2011-09-27				ENSG00000157483		"Myosins / Myosin superfamily : Class I"	7599	protein-coding gene	gene with protein product	"myosin-IC"	601479				8884266	Standard	NM_004998		Approved	MYO1C, HuncM-IC, MGC104638	uc002aga.4	Q12965		ENST00000288235.4:c.1831G>A	chr15.hg19:g.59480390C>T	ENSP00000288235:p.Gly611Ser	46.0	0.0		46.0	25.0	NM_004998	Q14778	Missense_Mutation	SNP	ENST00000288235.4	hg19	CCDS32254.1	.	.	.	.	.	.	.	.	.	.	C	35	5.418885	0.96092	.	.	ENSG00000157483	ENST00000288235	D	0.98666	-5.06	4.82	4.82	0.62117	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.99296	0.9754	M	0.91510	3.215	0.80722	D	1	D	0.76494	0.999	D	0.77004	0.989	D	0.98977	1.0803	10	0.87932	D	0	.	17.7194	0.88347	0.0:1.0:0.0:0.0	.	611	Q12965	MYO1E_HUMAN	S	611	ENSP00000288235:G611S	ENSP00000288235:G611S	G	-	1	0	MYO1E	57267682	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	7.556000	0.82233	2.503000	0.84419	0.655000	0.94253	GGT	.	.		0.458	MYO1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416024.1	NM_004998		T	59480390	C	T	59480390	3	4	351	1	0	0	0	0	1	0	0	0	10081	623	22	3	1539	3	MYO1E	15	59480390	Missense_Mutation	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	24283832	59480390	43051002	97	49375										
SEMA7A	8482	hgsc.bcm.edu	37	chr15	74704300	74704300	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	gatctccatgatgttgaaggCgaagctgtgctcctgctccc	11	12	1	2			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr15:74704300C>T	ENST00000261918.4	-	11	1896	c.1348G>A	c.(1348-1350)Gcc>Acc	p.A450T	SEMA7A_ENST00000543145.2_Missense_Mutation_p.A436T|SEMA7A_ENST00000542748.1_Missense_Mutation_p.A285T	NM_003612.3	NP_003603.1	O75326	SEM7A_HUMAN	semaphorin 7A, GPI membrane anchor (John Milton Hagen blood group)	450	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon extension (GO:0048675)|axon guidance (GO:0007411)|immune response (GO:0006955)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|olfactory lobe development (GO:0021988)|osteoblast differentiation (GO:0001649)|positive regulation of axon extension (GO:0045773)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of protein phosphorylation (GO:0001934)|regulation of inflammatory response (GO:0050727)	anchored component of membrane (GO:0031225)|external side of plasma membrane (GO:0009897)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(3)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(3)|lung(12)|upper_aerodigestive_tract(1)	30						ATGTTGAAGGCGAAGCTGTGC	0.637																																					p.A450T		Atlas-SNP	.											.	SEMA7A	58	.	0			c.G1348A						.						120	83	95					15																	74704300		2197	4296	6493	SO:0001583	missense	8482	exon11			TGAAGGCGAAGCT	AF069493	CCDS10262.1, CCDS53958.1, CCDS53959.1	15q22.3-q23	2014-07-18	2006-02-23		ENSG00000138623	ENSG00000138623		"Semaphorins", "CD molecules", "Blood group antigens", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10741	protein-coding gene	gene with protein product	"John Milton Hagen blood group", "H-Sema K1"	607961	"sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A", "sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A (JMH blood group)"	SEMAL		9721204	Standard	NM_003612		Approved	H-Sema-L, CD108	uc002axv.3	O75326	OTTHUMG00000139000	ENST00000261918.4:c.1348G>A	chr15.hg19:g.74704300C>T	ENSP00000261918:p.Ala450Thr	56.0	0.0		77.0	15.0	NM_003612	B4DDP7|F5H1S0|Q1XE81|Q1XE82|Q1XE83|Q1XE84|Q3MIY5	Missense_Mutation	SNP	ENST00000261918.4	hg19	CCDS10262.1	.	.	.	.	.	.	.	.	.	.	C	3.830	-0.036002	0.07497	.	.	ENSG00000138623	ENST00000261918;ENST00000543145;ENST00000542748	T;T;T	0.10860	2.83;2.83;2.83	4.5	0.41	0.16387	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.632817	0.15519	N	0.258152	T	0.07908	0.0198	L	0.38175	1.15	0.09310	N	1	B;B	0.33755	0.371;0.424	B;B	0.30782	0.073;0.12	T	0.29336	-1.0015	10	0.31617	T	0.26	-8.3131	9.3934	0.38388	0.0:0.6481:0.0:0.3519	.	436;450	F5H1S0;O75326	.;SEM7A_HUMAN	T	450;436;285	ENSP00000261918:A450T;ENSP00000438966:A436T;ENSP00000441493:A285T	ENSP00000261918:A450T	A	-	1	0	SEMA7A	72491353	0.016000	0.18221	0.002000	0.10522	0.000000	0.00434	0.818000	0.27295	-0.192000	0.10432	-1.579000	0.00862	GCC	.	.		0.637	SEMA7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272904.3	NM_003612		T	74704300	C	T	74704300	3	4	351	1	0	0	0	0	1	0	0	0	14058	768	27	1	668	1	SEMA7A	15	74704300	Missense_Mutation	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	15223910	74704300	27827092	98	49376										
ZNF774	342132	hgsc.bcm.edu	37	chr15	90903908	90903908	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	ctcaaatttcatcactcaccAgaggacccacacaggggtga	8	13	4	2			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr15:90903908A>G	ENST00000354377.3	+	4	1031	c.845A>G	c.(844-846)cAg>cGg	p.Q282R	ZNF774_ENST00000379090.5_Intron	NM_001004309.2	NP_001004309.2	Q6NX45	ZN774_HUMAN	zinc finger protein 774	282					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|stomach(1)	14	Melanoma(11;0.00551)|Lung NSC(78;0.0158)|all_lung(78;0.0331)		BRCA - Breast invasive adenocarcinoma(143;0.0224)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			ATCACTCACCAGAGGACCCAC	0.512																																					p.Q282R		Atlas-SNP	.											.	ZNF774	35	.	0			c.A845G						.						57	60	59					15																	90903908		2199	4298	6497	SO:0001583	missense	342132	exon4			CTCACCAGAGGAC	BC067279	CCDS32330.1	15q26.1	2013-01-08				ENSG00000196391		"Zinc fingers, C2H2-type"	33108	protein-coding gene	gene with protein product							Standard	NM_001004309		Approved	MGC75360	uc002bpk.4	Q6NX45		ENST00000354377.3:c.845A>G	chr15.hg19:g.90903908A>G	ENSP00000346348:p.Gln282Arg	84.0	0.0		61.0	19.0	NM_001004309	A8K020	Missense_Mutation	SNP	ENST00000354377.3	hg19	CCDS32330.1	.	.	.	.	.	.	.	.	.	.	A	13.41	2.228331	0.39399	.	.	ENSG00000196391	ENST00000354377	T	0.21543	2.0	5.52	5.52	0.82312	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.33834	N	0.004513	T	0.23133	0.0559	L	0.54908	1.71	0.80722	D	1	B	0.18013	0.025	B	0.20384	0.029	T	0.02220	-1.1193	10	0.40728	T	0.16	.	13.571	0.61847	1.0:0.0:0.0:0.0	.	282	Q6NX45	ZN774_HUMAN	R	282	ENSP00000346348:Q282R	ENSP00000346348:Q282R	Q	+	2	0	ZNF774	88704912	0.966000	0.33281	1.000000	0.80357	0.990000	0.78478	0.936000	0.28938	2.103000	0.63969	0.459000	0.35465	CAG	.	.		0.512	ZNF774-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418048.1	NM_001004309		G	90903908	A	G	90903908	3	3	351	1	0	0	0	0	1	0	0	0	18162	188	7	2	855	2	ZNF774	15	90903908	Missense_Mutation	SNP	A	TCGA-WJ-A86L-01A-12D-A45V-10	16199608	90903908	11627484	99	49377										
ABCC11	85320	hgsc.bcm.edu	37	chr16	48232119	48232119	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	cctttttctgcattaactcaCtgtgagttccattttcacag	5	11	3	1			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr16:48232119C>T	ENST00000394747.1	-	15	2499	c.2150G>A	c.(2149-2151)aGt>aAt	p.S717N	ABCC11_ENST00000356608.2_Missense_Mutation_p.S717N|ABCC11_ENST00000394748.1_Missense_Mutation_p.S717N|ABCC11_ENST00000537808.1_Missense_Mutation_p.S717N|ABCC11_ENST00000353782.5_Missense_Mutation_p.S717N	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	717	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				organic anion transport (GO:0015711)|purine nucleotide transport (GO:0015865)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)|purine nucleotide transmembrane transporter activity (GO:0015216)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(3)|prostate(2)|skin(5)|urinary_tract(2)	83		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)			Conjugated Estrogens(DB00286)|Folic Acid(DB00158)|Indomethacin(DB00328)|Methotrexate(DB00563)|Probenecid(DB01032)	CATTAACTCACTGTGAGTTCC	0.438																																					p.S717N		Atlas-SNP	.											.	ABCC11	177	.	0			c.G2150A						.						180	168	172					16																	48232119		2201	4300	6501	SO:0001583	missense	85320	exon15			AACTCACTGTGAG	AF367202	CCDS10732.1, CCDS10733.1	16q12	2012-03-14			ENSG00000121270	ENSG00000121270		"ATP binding cassette transporters / subfamily C"	14639	protein-coding gene	gene with protein product		607040				11483364, 11435397	Standard	NM_033151		Approved	MRP8	uc002efg.1	Q96J66	OTTHUMG00000133146	ENST00000394747.1:c.2150G>A	chr16.hg19:g.48232119C>T	ENSP00000378230:p.Ser717Asn	138.0	0.0		126.0	57.0	NM_033151	Q8TDJ0|Q96JA6|Q9BX80	Missense_Mutation	SNP	ENST00000394747.1	hg19	CCDS10732.1	.	.	.	.	.	.	.	.	.	.	C	6.018	0.371661	0.11409	.	.	ENSG00000121270	ENST00000353782;ENST00000356608;ENST00000394748;ENST00000394747;ENST00000537808	T;T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15;-0.15	5.69	-2.73	0.05950	ABC transporter-like (1);	0.707775	0.14400	N	0.321945	T	0.36303	0.0962	N	0.13168	0.305	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.003	T	0.12760	-1.0535	10	0.31617	T	0.26	-0.2843	6.5429	0.22390	0.126:0.2515:0.0:0.6225	.	717;717	Q96J66-2;Q96J66	.;ABCCB_HUMAN	N	717	ENSP00000311326:S717N;ENSP00000349017:S717N;ENSP00000378231:S717N;ENSP00000378230:S717N;ENSP00000438530:S717N	ENSP00000311326:S717N	S	-	2	0	ABCC11	46789620	0.000000	0.05858	0.182000	0.23118	0.193000	0.23685	-0.222000	0.09190	-0.464000	0.06963	0.561000	0.74099	AGT	.	.		0.438	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583		T	48232119	C	T	48232119	3	4	351	1	0	0	0	0	1	0	0	0	51	565	20	3	2058	3	ABCC11	16	48232119	Missense_Mutation	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10		48232119	42122634	100	49378										
NFAT5	10725	hgsc.bcm.edu	37	chr16	69727754	69727754	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	atgaatcaagagcaacagccCatgcaatttcagagtcagtc	8	10	3	3			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr16:69727754C>T	ENST00000354436.2	+	12	4290	c.3972C>T	c.(3970-3972)ccC>ccT	p.P1324P	NFAT5_ENST00000432919.1_Silent_p.P1342P|NFAT5_ENST00000349945.1_Silent_p.P1248P|NFAT5_ENST00000566899.1_Silent_p.P1248P|NFAT5_ENST00000567239.1_Silent_p.P1341P|NFAT5_ENST00000393742.2_Silent_p.P1248P	NM_006599.3	NP_006590.1	O94916	NFAT5_HUMAN	nuclear factor of activated T-cells 5, tonicity-responsive	1324					cytokine production (GO:0001816)|excretion (GO:0007588)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of calcineurin-NFAT signaling cascade (GO:0070884)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P1342P(1)|p.P1248P(1)		NS(1)|breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						AGCAACAGCCCATGCAATTTC	0.463																																					p.P1342P		Atlas-SNP	.											NFAT5_ENST00000432919,NS,carcinoma,0,2	NFAT5	184	.	2	Substitution - coding silent(2)	cervix(2)	c.C4026T						.						94	89	91					16																	69727754		2198	4300	6498	SO:0001819	synonymous_variant	10725	exon13			ACAGCCCATGCAA	AF134870	CCDS10881.1, CCDS10882.1, CCDS45519.1	16q22.1	2009-11-24			ENSG00000102908	ENSG00000102908		"Nuclear factor of activated T-cells"	7774	protein-coding gene	gene with protein product		604708				10377394	Standard	NM_173214		Approved	TONEBP, KIAA0827, NFATL1, OREBP, NFATZ, NF-AT5	uc002exl.2	O94916	OTTHUMG00000137572	ENST00000354436.2:c.3972C>T	chr16.hg19:g.69727754C>T		127.0	0.0		71.0	57.0	NM_138713	A2RRB4|A6H8V5|E9PHR7|O95693|Q7LA65|Q969Q8|Q96QH3|Q9UN18	Silent	SNP	ENST00000354436.2	hg19	CCDS10881.1																																																																																			.	.		0.463	NFAT5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268952.2	NM_138714		T	69727754	C	T	69727754	2	4	351	1	0	0	0	0	0	0	0	1	10369	581	21	3		3	NFAT5	16	69727754	Silent	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	21495635	69727754	20626999	101	49379										
ZCCHC14	23174	hgsc.bcm.edu	37	chr16	87451264	87451264	+	Frame_Shift_Del	DEL	G	G	-													0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	gcatgggagcagtgaggcaaGggggcggcggagccggccgg							TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr16:87451264delG	ENST00000268616.4	-	8	991	c.774delC	c.(772-774)cccfs	p.P258fs		NM_015144.2	NP_055959.1	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14	258							nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	36				BRCA - Breast invasive adenocarcinoma(80;0.0285)		AGTGAGGCAAGGGGGCGGCGG	0.692																																					p.L259fs		Atlas-INDEL	.											.	ZCCHC14	87	.	0			c.775delT						.						55	66	62					16																	87451264		2198	4300	6498	SO:0001589	frameshift_variant	23174	exon8			.	AB011151	CCDS10961.1	16q24.2	2013-01-10			ENSG00000140948	ENSG00000140948		"Zinc fingers, CCHC domain containing", "Sterile alpha motif (SAM) domain containing"	24134	protein-coding gene	gene with protein product						9628581	Standard	XM_005255858		Approved	BDG29, MGC14139	uc002fjz.1	Q8WYQ9	OTTHUMG00000137655	ENST00000268616.4:c.774delC	chr16.hg19:g.87451264delG	ENSP00000268616:p.Pro258fs	68.0	0.0		75.0	26.0	NM_015144	D3DUN1|O60324|Q3MJD8|Q9UFP0	Frame_Shift_Del	DEL	ENST00000268616.4	hg19	CCDS10961.1																																																																																			.	.		0.692	ZCCHC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269107.1	NM_015144		-	87451264	G	-	87451264	7	5	351	1	0	1	0	1	0	0	0	0	17598	987	35	0	2099	0	ZCCHC14	16	87451264	Frame_Shift_Del	DEL	G	TCGA-WJ-A86L-01A-12D-A45V-10	17723510	87451264	2903489	102	49380										
CDH15	1013	hgsc.bcm.edu	37	chr16	89260206	89260206	+	Frame_Shift_Del	DEL	G	G	-													0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	gcgtcacccgacagcgctgaGcctgcctctgggaccgccgc							TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr16:89260206delG	ENST00000289746.2	+	13	2101	c.2036delG	c.(2035-2037)agcfs	p.S679fs		NM_004933.2	NP_004924.1	P55291	CAD15_HUMAN	cadherin 15, type 1, M-cadherin (myotubule)	679					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)	caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(80;0.0261)		ACAGCGCTGAGCCTGCCTCTG	0.711																																					p.S679fs		Atlas-INDEL	.											.	CDH15	54	.	0			c.2035delA						.						13	14	14					16																	89260206		2121	4242	6363	SO:0001589	frameshift_variant	1013	exon13			.	D83542	CCDS10976.1	16q24.3	2010-01-26	2008-10-30		ENSG00000129910	ENSG00000129910		"Cadherins / Major cadherins"	1754	protein-coding gene	gene with protein product		114019	"cadherin 15, M-cadherin (myotubule)"	CDH3, CDH14		1427864	Standard	NM_004933		Approved		uc002fmt.3	P55291	OTTHUMG00000138045	ENST00000289746.2:c.2036delG	chr16.hg19:g.89260206delG	ENSP00000289746:p.Ser679fs	56.0	0.0		41.0	30.0	NM_004933		Frame_Shift_Del	DEL	ENST00000289746.2	hg19	CCDS10976.1																																																																																			.	.		0.711	CDH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269920.1	NM_004933		-	89260206	G	-	89260206	7	5	351	1	0	1	0	1	0	0	0	0	3102	971	34	0	2086	0	CDH15	16	89260206	Frame_Shift_Del	DEL	G	TCGA-WJ-A86L-01A-12D-A45V-10	1808942	89260206	1094547	103	49381										
ZNF232	7775	hgsc.bcm.edu	37	chr17	5013065	5013065	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	tctcttgtccctgtgtacccTgaagggccagagtttcagct	10	12	2	2			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr17:5013065T>C	ENST00000250076.3	-	3	776	c.122A>G	c.(121-123)cAg>cGg	p.Q41R	ZNF232_ENST00000575538.1_5'UTR|ZNF232_ENST00000416429.2_Missense_Mutation_p.Q14R|ZNF232_ENST00000575898.1_Missense_Mutation_p.Q41R|AC012146.7_ENST00000413077.1_RNA|AC012146.7_ENST00000571138.1_RNA	NM_014519.2	NP_055334.2	Q9UNY5	ZN232_HUMAN	zinc finger protein 232	14					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(2)|liver(1)|lung(4)|ovary(1)|prostate(2)	11						CTGTGTACCCTGAAGGGCCAG	0.517																																					p.Q41R		Atlas-SNP	.											.	ZNF232	42	.	0			c.A122G						.						151	142	145					17																	5013065		2203	4300	6503	SO:0001583	missense	7775	exon3			GTACCCTGAAGGG	AF080169	CCDS11068.1	17p13.2	2013-01-09			ENSG00000167840	ENSG00000167840		"-", "Zinc fingers, C2H2-type"	13026	protein-coding gene	gene with protein product						11311944	Standard	NM_014519		Approved	ZSCAN11	uc002gat.3	Q9UNY5	OTTHUMG00000099450	ENST00000250076.3:c.122A>G	chr17.hg19:g.5013065T>C	ENSP00000250076:p.Gln41Arg	73.0	0.0		42.0	31.0	NM_014519		Missense_Mutation	SNP	ENST00000250076.3	hg19	CCDS11068.1	.	.	.	.	.	.	.	.	.	.	T	0.825	-0.747437	0.03065	.	.	ENSG00000167840	ENST00000250076;ENST00000416429	T;T	0.08458	3.09;3.41	3.68	1.39	0.22231	.	0.000000	0.31031	N	0.008395	T	0.03651	0.0104	N	0.08118	0	0.09310	N	1	P;P;P;P	0.40476	0.596;0.596;0.596;0.718	B;B;B;B	0.41174	0.189;0.189;0.189;0.349	T	0.34775	-0.9815	10	0.30078	T	0.28	.	3.0022	0.06017	0.2124:0.1191:0.0:0.6685	.	41;14;14;14	B4DNA7;B4DP49;Q9UNY5;Q9UNY5-2	.;.;ZN232_HUMAN;.	R	41;14	ENSP00000250076:Q41R;ENSP00000416430:Q14R	ENSP00000250076:Q41R	Q	-	2	0	ZNF232	4953789	0.000000	0.05858	0.146000	0.22360	0.141000	0.21300	-0.031000	0.12287	0.138000	0.18790	0.459000	0.35465	CAG	.	.		0.517	ZNF232-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216915.1	NM_014519		C	5013065	T	C	5013065	3	2	351	1	0	0	0	0	1	0	0	0	17800	1580	55	2	1224	2	ZNF232	17	5013065	Missense_Mutation	SNP	T	TCGA-WJ-A86L-01A-12D-A45V-10		5013065	76182145	104	49382										
TP53	7157	hgsc.bcm.edu	37	chr17	7578239	7578239	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	gtttctgtcatccaaatactCcacacgcaaatttccttcca	3	14	2	0			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr17:7578239C>A	ENST00000269305.4	-	6	799	c.610G>T	c.(610-612)Gag>Tag	p.E204*	TP53_ENST00000455263.2_Nonsense_Mutation_p.E204*|TP53_ENST00000574684.1_Intron|TP53_ENST00000420246.2_Nonsense_Mutation_p.E204*|TP53_ENST00000445888.2_Nonsense_Mutation_p.E204*|TP53_ENST00000413465.2_Nonsense_Mutation_p.E204*|TP53_ENST00000359597.4_Nonsense_Mutation_p.E204*	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	204	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		E -> A (in sporadic cancers; somatic mutation).|E -> D (in sporadic cancers; somatic mutation).|E -> G (in sporadic cancers; somatic mutation).|E -> K (in sporadic cancers; somatic mutation).|E -> Q (in a sporadic cancer; somatic mutation).|E -> V (in a sporadic cancer; somatic mutation).|VE -> LV (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.E204*(33)|p.0?(8)|p.?(5)|p.E72*(3)|p.E111*(3)|p.E204K(2)|p.E204fs*43(2)|p.E204Q(1)|p.E204fs*4(1)|p.V203_E204>V*(1)|p.V203_E204>LV(1)|p.E204fs*39(1)|p.G199fs*42(1)|p.E204_N210delEYLDDRN(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TCCAAATACTCCACACGCAAA	0.542		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.E204X	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,carcinoma,+2,65	TP53	33396	.	63	Substitution - Nonsense(39)|Whole gene deletion(8)|Deletion - Frameshift(5)|Unknown(5)|Substitution - Missense(3)|Complex - compound substitution(2)|Deletion - In frame(1)	lung(15)|haematopoietic_and_lymphoid_tissue(7)|large_intestine(6)|upper_aerodigestive_tract(5)|biliary_tract(5)|NS(5)|breast(4)|bone(4)|oesophagus(3)|ovary(3)|central_nervous_system(2)|stomach(1)|liver(1)|urinary_tract(1)|pancreas(1)	c.G610T						.						133	118	123					17																	7578239		2203	4300	6503	SO:0001587	stop_gained	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AATACTCCACACG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.610G>T	chr17.hg19:g.7578239C>A	ENSP00000269305:p.Glu204*	147.0	0.0		61.0	50.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	14.28	2.489037	0.44249	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	.	.	.	5.41	-0.604	0.11626	.	0.445020	0.26082	N	0.026458	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	-5.2849	1.4244	0.02320	0.133:0.2829:0.3261:0.258	.	.	.	.	X	204;204;204;204;204;204;193;111;72;111;72	.	ENSP00000269305:E204X	E	-	1	0	TP53	7518964	0.600000	0.26899	0.018000	0.16275	0.030000	0.12068	0.945000	0.29056	-0.004000	0.14419	0.655000	0.94253	GAG	.	.		0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7578239	C	A	7578239	4	1	351	1	0	0	0	0	0	1	0	0	16396	864	30	3	684	3	TP53	17	7578239	Nonsense_Mutation	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	2565174	7578239	73616971	105	49383										
C17orf66	256957	hgsc.bcm.edu	37	chr17	34183788	34183788	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	cttgagctcttccacagtttGagccacagcctgcctcacag	8	15	2	2			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr17:34183788G>A	ENST00000311880.2	-	12	1322	c.1174C>T	c.(1174-1176)Caa>Taa	p.Q392*	C17orf66_ENST00000592980.1_Nonsense_Mutation_p.Q352*	NM_152781.2	NP_689994.2	A2RTY3	HEAT9_HUMAN		392					hematopoietic progenitor cell differentiation (GO:0002244)					breast(3)|central_nervous_system(1)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(6)|lung(11)|skin(2)|stomach(4)	38		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0184)		TCCACAGTTTGAGCCACAGCC	0.527																																					p.Q392X		Atlas-SNP	.											.	C17orf66	57	.	0			c.C1174T						.						51	44	47					17																	34183788		2203	4300	6503	SO:0001587	stop_gained	256957	exon12			CAGTTTGAGCCAC																												ENST00000311880.2:c.1174C>T	chr17.hg19:g.34183788G>A	ENSP00000309560:p.Gln392*	30.0	0.0		40.0	15.0	NM_152781	B4DX21|B4DXA4|B4DXF0|Q8N4R4|Q96M46	Nonsense_Mutation	SNP	ENST00000311880.2	hg19	CCDS11299.1	.	.	.	.	.	.	.	.	.	.	G	16.99	3.274961	0.59649	.	.	ENSG00000172653	ENST00000311880	.	.	.	4.05	0.934	0.19477	.	0.552277	0.15382	N	0.265292	.	.	.	.	.	.	0.53005	D	0.999968	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	.	4.2399	0.10643	0.0:0.5865:0.1962:0.2174	.	.	.	.	X	392	.	ENSP00000309560:Q392X	Q	-	1	0	C17orf66	31207901	0.985000	0.35326	0.728000	0.30774	0.386000	0.30323	0.131000	0.15870	0.133000	0.18654	-0.841000	0.03054	CAA	.	.		0.527	C17orf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256487.1			A	34183788	G	A	34183788	4	1	351	1	0	0	0	0	0	1	0	0	1876	1299	45	3	554	3	C17orf66	17	34183788	Nonsense_Mutation	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	26605549	34183788	47011422	106	49384										
PIGW	284098	hgsc.bcm.edu	37	chr17	34893593	34893593	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	cattagtcttcctaggaatcGgacgattagccattataaaa	7	8	1	0			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr17:34893593G>A	ENST00000592983.1	+	2	1223	c.643G>A	c.(643-645)Gga>Aga	p.G215R	MYO19_ENST00000586007.1_5'Flank|MYO19_ENST00000590081.1_Intron|MYO19_ENST00000268852.9_5'Flank|PIGW_ENST00000328396.2_Missense_Mutation_p.G215R|MYO19_ENST00000544606.1_5'Flank|MYO19_ENST00000431794.3_5'Flank			Q7Z7B1	PIGW_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class W	215					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transferase activity, transferring acyl groups (GO:0016746)			breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CCTAGGAATCGGACGATTAGC	0.358																																					p.G215R		Atlas-SNP	.											.	PIGW	50	.	0			c.G643A						.						100	104	103					17																	34893593		2203	4300	6503	SO:0001583	missense	284098	exon2			GGAATCGGACGAT	AB097818	CCDS11313.1	17q21.1	2014-05-06	2006-06-28		ENSG00000184886	ENSG00000277161		"Phosphatidylinositol glycan anchor biosynthesis"	23213	protein-coding gene	gene with protein product		610275	"phosphatidylinositol glycan, class W"			14517336, 12714589	Standard	XM_005257238		Approved	Gwt1, FLJ37433	uc002hmz.1	Q7Z7B1	OTTHUMG00000188438	ENST00000592983.1:c.643G>A	chr17.hg19:g.34893593G>A	ENSP00000468778:p.Gly215Arg	132.0	0.0		187.0	53.0	NM_178517	Q8N9G3	Missense_Mutation	SNP	ENST00000592983.1	hg19	CCDS11313.1	.	.	.	.	.	.	.	.	.	.	G	17.06	3.293729	0.60086	.	.	ENSG00000184886	ENST00000328396	.	.	.	5.59	5.59	0.84812	.	0.193818	0.43260	D	0.000596	D	0.83857	0.5345	M	0.84846	2.72	0.54753	D	0.999981	D	0.89917	1.0	D	0.73708	0.981	D	0.85025	0.0914	8	.	.	.	-9.1117	18.5841	0.91182	0.0:0.0:1.0:0.0	.	215	Q7Z7B1	PIGW_HUMAN	R	215	.	.	G	+	1	0	PIGW	31967706	1.000000	0.71417	0.952000	0.39060	0.920000	0.55202	6.034000	0.70933	2.631000	0.89168	0.561000	0.74099	GGA	.	.		0.358	PIGW-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451318.1	NM_178517		A	34893593	G	A	34893593	3	1	351	1	0	0	0	0	1	0	0	0	11911	1117	39	1	645	1	PIGW	17	34893593	Missense_Mutation	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	709805	34893593	46301617	107	49385										
SYNRG	11276	hgsc.bcm.edu	37	chr17	35945538	35945538	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	tgctgctgttcaaatcgtttCctgaaggaaaaatgatctaa	8	7	2	2			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr17:35945538C>T	ENST00000339208.6	-	5	512	c.372G>A	c.(370-372)caG>caA	p.Q124Q	SYNRG_ENST00000394378.2_Splice_Site_p.Q124Q|SYNRG_ENST00000345615.4_Splice_Site_p.Q124Q|SYNRG_ENST00000502449.2_Splice_Site_p.Q124Q|SYNRG_ENST00000346661.4_Splice_Site_p.Q124Q|SYNRG_ENST00000585472.1_Splice_Site_p.Q123Q|SYNRG_ENST00000591288.1_Splice_Site_p.Q124Q	NM_001163544.1|NM_001163545.1|NM_007247.4	NP_001157016.1|NP_001157017.1|NP_009178.3	Q9UMZ2	SYNRG_HUMAN	synergin, gamma	124					endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)	AP-1 adaptor complex (GO:0030121)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						CAAATCGTTTCCTGAAGGAAA	0.373																																					p.Q124Q		Atlas-SNP	.											.	SYNRG	101	.	0			c.G372A						.						97	100	99					17																	35945538		2203	4300	6503	SO:0001630	splice_region_variant	11276	exon5			TCGTTTCCTGAAG	AF169548	CCDS11321.1, CCDS11322.1, CCDS11322.2, CCDS54113.1, CCDS54114.1, CCDS59284.1, CCDS59285.1	17q12	2014-04-16	2009-07-20	2009-07-20	ENSG00000006114	ENSG00000275066			557	protein-coding gene	gene with protein product	"gamma-synergin", "adaptor-related protein complex 1 gamma subunit-binding protein 1"	607291	"AP1 gamma subunit binding protein 1"	AP1GBP1		10477754	Standard	XM_005256980		Approved	SYNG, MGC104959	uc010wdf.2	Q9UMZ2	OTTHUMG00000188473	ENST00000339208.6:c.372-1G>A	chr17.hg19:g.35945538C>T		31.0	0.0		42.0	14.0	NM_001163544	A8MWU4|B7ZKZ2|B7ZKZ3|Q17RI2|Q5BKU5|Q6ZT17	Silent	SNP	ENST00000339208.6	hg19	CCDS11321.1																																																																																			.	.		0.373	SYNRG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256811.2	NM_007247	Silent	T	35945538	C	T	35945538	5	4	351	1	0	0	0	0	0	0	1	0	15475	869	30	3	3717	3	SYNRG	17	35945538	Splice_Site	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	1051945	35945538	45249672	108	49386										
ATP6V0A1	535	hgsc.bcm.edu	37	chr17	40620123	40620123	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	cccgggacatgattgacttaGaggtaaacacttctgggaaa	11	8	1	3	rs370052932		TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr17:40620123G>A	ENST00000343619.4	+	4	415	c.292G>A	c.(292-294)Gag>Aag	p.E98K	ATP6V0A1_ENST00000546249.1_Missense_Mutation_p.E98K|ATP6V0A1_ENST00000544137.1_Intron|ATP6V0A1_ENST00000585525.1_Missense_Mutation_p.E98K|ATP6V0A1_ENST00000264649.6_Missense_Mutation_p.E98K|ATP6V0A1_ENST00000537728.1_Missense_Mutation_p.E98K|ATP6V0A1_ENST00000393829.2_Missense_Mutation_p.E98K	NM_001130021.1	NP_001123493.1	Q93050	VPP1_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a1	98					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	ATPase binding (GO:0051117)|hydrogen ion transmembrane transporter activity (GO:0015078)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|urinary_tract(3)	26		all_cancers(22;1.18e-05)|Breast(137;0.000105)|all_epithelial(22;0.000254)		BRCA - Breast invasive adenocarcinoma(366;0.137)		GATTGACTTAGAGGTAAACAC	0.393													G|||	1	0.000199681	0	0	5008	,	,		14047	0.001		0	False		,,,				2504	0				p.E98K		Atlas-SNP	.											.	ATP6V0A1	67	.	0			c.G292A						.						59	58	58					17																	40620123		2203	4300	6503	SO:0001583	missense	535	exon4			GACTTAGAGGTAA	U73006	CCDS11426.1, CCDS45683.1, CCDS45684.1	17q21	2010-04-21	2006-01-20	2002-05-10	ENSG00000033627	ENSG00000033627		"ATPases / V-type"	865	protein-coding gene	gene with protein product		192130	"ATPase, H+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1A (110/116kD)", "ATPase, H+ transporting, lysosomal V0 subunit a isoform 1", "ATPase, H+ transporting, lysosomal V0 subunit A1"	VPP1, ATP6N1, ATP6N1A		7774924	Standard	NM_001130020		Approved	a1, Vph1, Stv1	uc002hzs.3	Q93050		ENST00000343619.4:c.292G>A	chr17.hg19:g.40620123G>A	ENSP00000342951:p.Glu98Lys	241.0	0.0		313.0	203.0	NM_001130020	B7Z3B7|Q8N5G7|Q9NSX0	Missense_Mutation	SNP	ENST00000343619.4	hg19	CCDS45684.1	.	.	.	.	.	.	.	.	.	.	G	37	6.103178	0.97286	.	.	ENSG00000033627	ENST00000343619;ENST00000546249;ENST00000393829;ENST00000264649;ENST00000537728	D;D;D;D;D	0.85702	-2.02;-2.02;-2.02;-2.02;-2.02	5.99	5.99	0.97316	.	0.092594	0.64402	N	0.000001	D	0.93151	0.7819	M	0.87758	2.905	0.80722	D	1	P;P;P;P;D;D	0.62365	0.811;0.934;0.871;0.933;0.991;0.982	P;P;P;P;P;P	0.61800	0.838;0.861;0.861;0.559;0.894;0.894	D	0.93373	0.6737	10	0.87932	D	0	-24.4696	20.4777	0.99188	0.0:0.0:1.0:0.0	.	98;98;98;98;98;98	B7Z641;B7Z2A9;B7Z3B7;Q93050;Q93050-1;F5H569	.;.;.;VPP1_HUMAN;.;.	K	98	ENSP00000342951:E98K;ENSP00000444676:E98K;ENSP00000377415:E98K;ENSP00000264649:E98K;ENSP00000443991:E98K	ENSP00000264649:E98K	E	+	1	0	ATP6V0A1	37873649	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.643000	0.98464	2.840000	0.97914	0.655000	0.94253	GAG	.	.		0.393	ATP6V0A1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450364.1	NM_001130020		A	40620123	G	A	40620123	3	1	351	1	0	0	0	0	1	0	0	0	1168	943	33	3	302	3	ATP6V0A1	17	40620123	Missense_Mutation	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	4674585	40620123	40575087	109	49387										
EFTUD2	9343	hgsc.bcm.edu	37	chr17	42937333	42937333	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	aggccatcaagcatcttgggCagctctgaggggttgactgg	15	9	3	2			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr17:42937333C>T	ENST00000426333.2	-	18	2097	c.1800G>A	c.(1798-1800)ctG>ctA	p.L600L	EFTUD2_ENST00000591382.1_Silent_p.L600L|EFTUD2_ENST00000592576.1_Silent_p.L590L|EFTUD2_ENST00000402521.3_Silent_p.L565L	NM_001142605.1|NM_001258354.1|NM_004247.3	NP_001136077.1|NP_001245283.1|NP_004238.3	Q15029	U5S1_HUMAN	elongation factor Tu GTP binding domain containing 2	600					gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	32		Prostate(33;0.109)				GCATCTTGGGCAGCTCTGAGG	0.532																																					p.L600L	Ovarian(10;65 485 10258 29980 30707)	Atlas-SNP	.											.	EFTUD2	85	.	0			c.G1800A						.						142	125	130					17																	42937333		2203	4300	6503	SO:0001819	synonymous_variant	9343	exon18			CTTGGGCAGCTCT	D21163	CCDS11489.1, CCDS45707.1, CCDS59295.1	17q21.31	2014-08-12			ENSG00000108883	ENSG00000108883			30858	protein-coding gene	gene with protein product	"U5 snRNP specific protein, 116 kD"	603892				9233818	Standard	NM_004247		Approved	U5-116KD, Snrp116, Snu114, SNRNP116	uc002ihn.2	Q15029	OTTHUMG00000179865	ENST00000426333.2:c.1800G>A	chr17.hg19:g.42937333C>T		132.0	0.0		173.0	56.0	NM_004247	B4DK30|B4DMC0|D3DX58|K7EJ81|Q9BUR0	Silent	SNP	ENST00000426333.2	hg19	CCDS11489.1																																																																																			.	.		0.532	EFTUD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448672.1	NM_004247		T	42937333	C	T	42937333	2	4	351	1	0	0	0	0	0	0	0	1	4963	697	25	3		3	EFTUD2	17	42937333	Silent	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	2317210	42937333	38257877	110	49388										
PNPO	55163	hgsc.bcm.edu	37	chr17	46023698	46023698	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	cccctggacagtatctgagaAagaaaaatgaggaactggaa	11	7	1	3			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr17:46023698A>C	ENST00000225573.4	+	6	661	c.556A>C	c.(556-558)Aag>Cag	p.K186Q	PNPO_ENST00000434554.2_Missense_Mutation_p.K143Q|PNPO_ENST00000534893.1_Missense_Mutation_p.K91Q|RP11-6N17.6_ENST00000582142.1_RNA|RP11-6N17.6_ENST00000580372.1_RNA|RP11-6N17.9_ENST00000582262.1_RNA|PNPO_ENST00000544840.1_Missense_Mutation_p.K168Q	NM_018129.3	NP_060599.1	Q9NVS9	PNPO_HUMAN	pyridoxamine 5'-phosphate oxidase	186					pyridoxine biosynthetic process (GO:0008615)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	FMN binding (GO:0010181)|pyridoxamine-phosphate oxidase activity (GO:0004733)			endometrium(2)|large_intestine(1)|lung(1)|urinary_tract(1)	5						GTATCTGAGAAAGAAAAATGA	0.498																																					p.K186Q		Atlas-SNP	.											.	PNPO	18	.	0			c.A556C						.						78	81	80					17																	46023698		2203	4300	6503	SO:0001583	missense	55163	exon6			CTGAGAAAGAAAA	AF468030	CCDS11522.1	17q21.32	2008-11-27	2006-07-12			ENSG00000108439	1.4.3.5		30260	protein-coding gene	gene with protein product		603287	"pyridoxine 5'-phosphate oxidase"			9601034, 15182361	Standard	NM_018129		Approved	PDXPO	uc002imo.3	Q9NVS9		ENST00000225573.4:c.556A>C	chr17.hg19:g.46023698A>C	ENSP00000225573:p.Lys186Gln	90.0	0.0		111.0	37.0	NM_018129	B4E0V0|B4E152|B4E1D7|D3DTT9	Missense_Mutation	SNP	ENST00000225573.4	hg19	CCDS11522.1	.	.	.	.	.	.	.	.	.	.	A	16.04	3.011247	0.54361	.	.	ENSG00000108439	ENST00000225573;ENST00000434554;ENST00000544840;ENST00000534893	T;T;T;T	0.76316	-1.01;-1.01;-1.01;-1.01	5.43	4.36	0.52297	FMN-binding split barrel-related (1);FMN-binding split barrel (1);	0.341357	0.35495	N	0.003174	T	0.48447	0.1500	N	0.05608	-0.01	0.33004	D	0.526586	P;B;B	0.36483	0.555;0.007;0.036	B;B;B	0.30316	0.114;0.001;0.006	T	0.57213	-0.7850	10	0.09338	T	0.73	-3.6318	6.1252	0.20176	0.7508:0.1648:0.0844:0.0	.	143;168;186	B4E152;B4E1D7;Q9NVS9	.;.;PNPO_HUMAN	Q	186;143;168;91	ENSP00000225573:K186Q;ENSP00000399960:K143Q;ENSP00000446182:K168Q;ENSP00000437480:K91Q	ENSP00000225573:K186Q	K	+	1	0	PNPO	43378697	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.794000	0.47853	2.064000	0.61679	0.459000	0.35465	AAG	.	.		0.498	PNPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441407.1	NM_018129		C	46023698	A	C	46023698	3	2	351	1	0	0	0	0	1	0	0	0	12181	15	1	5	578	5	PNPO	17	46023698	Missense_Mutation	SNP	A	TCGA-WJ-A86L-01A-12D-A45V-10	3086365	46023698	35171512	111	49389										
HOXB5	3215	hgsc.bcm.edu	37	chr17	46670490	46670490	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	gagagagaattaccatggctGatgtgaagcttcctcatcca	10	9	1	4			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr17:46670490G>A	ENST00000239151.5	-	1	833	c.555C>T	c.(553-555)atC>atT	p.I185I	HOXB-AS3_ENST00000492897.3_RNA|HOXB-AS3_ENST00000480872.1_RNA|HOXB-AS3_ENST00000467155.2_RNA|HOXB3_ENST00000472863.1_5'Flank|HOXB-AS3_ENST00000487849.3_RNA|HOXB3_ENST00000552000.2_Intron|HOXB3_ENST00000498678.1_5'Flank|HOXB-AS3_ENST00000474040.1_RNA|HOXB-AS3_ENST00000474324.1_RNA|HOXB-AS3_ENST00000477144.1_RNA|HOXB-AS3_ENST00000429755.4_RNA|HOXB-AS3_ENST00000460041.1_RNA|HOXB3_ENST00000460160.1_5'Flank|HOXB-AS3_ENST00000481995.1_RNA|HOXB3_ENST00000476342.1_5'Flank|HOXB-AS3_ENST00000465846.2_RNA|HOXB-AS3_ENST00000476204.1_RNA	NM_002147.3	NP_002138.1	P09067	HXB5_HUMAN	homeobox B5	185					anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|endothelial cell differentiation (GO:0045446)	nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)			large_intestine(1)|lung(2)	3						TACCATGGCTGATGTGAAGCT	0.577																																					p.I185I		Atlas-SNP	.											.	HOXB5	20	.	0			c.C555T						.						40	44	42					17																	46670490		2202	4300	6502	SO:0001819	synonymous_variant	3215	exon1			ATGGCTGATGTGA		CCDS11530.1	17q21.32	2011-06-20	2005-12-22		ENSG00000120075	ENSG00000120075		"Homeoboxes / ANTP class : HOXL subclass"	5116	protein-coding gene	gene with protein product		142960	"homeo box B5"	HOX2, HOX2A		1973146, 1358459	Standard	NM_002147		Approved		uc002inr.3	P09067	OTTHUMG00000159913	ENST00000239151.5:c.555C>T	chr17.hg19:g.46670490G>A		45.0	0.0		117.0	74.0	NM_002147	B2RC69|P09069|Q17RP4	Silent	SNP	ENST00000239151.5	hg19	CCDS11530.1																																																																																			.	.		0.577	HOXB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358148.2			A	46670490	G	A	46670490	2	1	351	1	0	0	0	0	0	0	0	1	7313	1280	45	3		3	HOXB5	17	46670490	Silent	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	646792	46670490	34524720	112	49390										
ITGA3	3675	hgsc.bcm.edu	37	chr17	48148229	48148229	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	aaacagctacatgattcagcGcaaggagtgggacttatctg	11	8	2	1	rs140829923		TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr17:48148229G>A	ENST00000320031.8	+	5	1016	c.686G>A	c.(685-687)cGc>cAc	p.R229H	ITGA3_ENST00000544892.1_Missense_Mutation_p.R4H|ITGA3_ENST00000007722.7_Missense_Mutation_p.R229H	NM_002204.2|NM_005501.2	NP_002195.1|NP_005492.1	P26006	ITA3_HUMAN	integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3 receptor)	229					blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|lung development (GO:0030324)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|negative regulation of cell projection organization (GO:0031345)|nephron development (GO:0072006)|neuron migration (GO:0001764)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|regulation of BMP signaling pathway (GO:0030510)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of Wnt signaling pathway (GO:0030111)|renal filtration (GO:0097205)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|skin development (GO:0043588)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integrin alpha3-beta1 complex (GO:0034667)|integrin complex (GO:0008305)|invadopodium membrane (GO:0071438)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	glycoprotein binding (GO:0001948)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)	p.R229H(1)		endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)	31						ATGATTCAGCGCAAGGAGTGG	0.488																																					p.R229H		Atlas-SNP	.											ITGA3,colon,carcinoma,0,1	ITGA3	128	.	1	Substitution - Missense(1)	large_intestine(1)	c.G686A						.	G	HIS/ARG,HIS/ARG	0,4406		0,0,2203	193	200	197		686,686	5.7	1	17	dbSNP_134	197	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ITGA3	NM_002204.2,NM_005501.2	29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	229/1052,229/1067	48148229	1,13005	2203	4300	6503	SO:0001583	missense	3675	exon5			TTCAGCGCAAGGA	M59911	CCDS11557.1, CCDS11558.1	17q21.33	2010-03-23	2003-10-13		ENSG00000005884	ENSG00000005884		"CD molecules", "Integrins"	6139	protein-coding gene	gene with protein product		605025	"antigen identified by monoclonal antibody J143"	MSK18		1655803, 9704023	Standard	NM_005501		Approved	CD49c, VLA3a, VCA-2, GAP-B3	uc010dbm.3	P26006	OTTHUMG00000161890	ENST00000320031.8:c.686G>A	chr17.hg19:g.48148229G>A	ENSP00000315190:p.Arg229His	125.0	0.0		217.0	60.0	NM_005501	A7E246|B7ZM80|B9EGQ1|D3DTX4|D3DTX5	Missense_Mutation	SNP	ENST00000320031.8	hg19	CCDS11558.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.643051	0.87859	0.0	1.16E-4	ENSG00000005884	ENST00000544892;ENST00000007722;ENST00000538917;ENST00000320031	T;T;T	0.60040	0.22;0.22;0.22	5.69	5.69	0.88448	.	0.254993	0.34386	N	0.004011	T	0.68604	0.3019	L	0.52126	1.63	0.36301	D	0.857007	D;P	0.89917	1.0;0.476	D;B	0.64237	0.923;0.07	T	0.72478	-0.4281	10	0.42905	T	0.14	.	15.3058	0.73990	0.0:0.0:1.0:0.0	.	229;229	P26006-1;P26006	.;ITA3_HUMAN	H	4;229;215;229	ENSP00000446133:R4H;ENSP00000007722:R229H;ENSP00000315190:R229H	ENSP00000007722:R229H	R	+	2	0	ITGA3	45503228	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	5.342000	0.65970	2.682000	0.91365	0.655000	0.94253	CGC	.	G|1.000;A|0.000		0.488	ITGA3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000366298.1	NM_005501		A	48148229	G	A	48148229	3	1	351	1	0	0	0	0	1	0	0	0	7886	1087	38	1	704	1	ITGA3	17	48148229	Missense_Mutation	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	1477739	48148229	33046981	113	49391										
CD300LB	124599	hgsc.bcm.edu	37	chr17	72518959	72518959	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	gctcctcagggaccctctgaGaccccttcaaccagaggatg	10	15	3	2			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr17:72518959G>A	ENST00000392621.1	-	4	639	c.635C>T	c.(634-636)tCt>tTt	p.S212F		NM_174892.2	NP_777552	A8K4G0	CLM7_HUMAN	CD300 molecule-like family member b	175					cellular response to lipopolysaccharide (GO:0071222)|innate immune response (GO:0045087)|neutrophil mediated immunity (GO:0002446)|positive regulation of mast cell activation (GO:0033005)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|skin(1)	21						GACCCTCTGAGACCCCTTCAA	0.532																																					p.S212F		Atlas-SNP	.											.	CD300LB	38	.	0			c.C635T						.						129	112	118					17																	72518959		2203	4300	6503	SO:0001583	missense	124599	exon4			CTCTGAGACCCCT	AF427618	CCDS11700.1, CCDS11700.2	17q25.1	2013-01-11	2006-03-29		ENSG00000178789	ENSG00000178789		"Immunoglobulin superfamily / V-set domain containing"	30811	protein-coding gene	gene with protein product	"triggering receptor expressed on myeloid cells 5"	610705	"CD300 antigen like family member B"			12975309	Standard	NM_174892		Approved	TREM5, CLM7	uc002jkx.2	A8K4G0	OTTHUMG00000067606	ENST00000392621.1:c.635C>T	chr17.hg19:g.72518959G>A	ENSP00000376397:p.Ser212Phe	97.0	0.0		107.0	47.0	NM_174892	Q1EG73|Q8IX40|Q8N6D1	Missense_Mutation	SNP	ENST00000392621.1	hg19	CCDS11700.1	.	.	.	.	.	.	.	.	.	.	G	11.94	1.789374	0.31685	.	.	ENSG00000178789	ENST00000392621;ENST00000314401	.	.	.	4.39	-0.662	0.11413	.	1.430260	0.04706	N	0.416838	T	0.31104	0.0786	L	0.38175	1.15	0.09310	N	1	B	0.23058	0.079	B	0.18871	0.023	T	0.31998	-0.9923	9	0.62326	D	0.03	-8.2911	3.7213	0.08457	0.3843:0.1847:0.431:0.0	.	175	A8K4G0	CLM7_HUMAN	F	175;212	.	ENSP00000317337:S212F	S	-	2	0	CD300LB	70030554	0.000000	0.05858	0.000000	0.03702	0.430000	0.31655	0.213000	0.17521	0.038000	0.15604	-0.362000	0.07510	TCT	.	.		0.532	CD300LB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145082.2	NM_174892		A	72518959	G	A	72518959	3	1	351	1	0	0	0	0	1	0	0	0	3001	942	33	3	85	3	CD300LB	17	72518959	Missense_Mutation	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	24370730	72518959	8676251	114	49392										
SLC25A10	1468	hgsc.bcm.edu	37	chr17	79682599	79682599	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	gcctctccccttccacgagaAggtgttgctgggctccgtca	11	15	2	1			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr17:79682599A>T	ENST00000350690.5	+	3	391	c.305A>T	c.(304-306)aAg>aTg	p.K102M	SLC25A10_ENST00000541223.1_Missense_Mutation_p.K257M|SLC25A10_ENST00000571730.1_Missense_Mutation_p.K257M|SLC25A10_ENST00000545862.1_Missense_Mutation_p.K59M|SLC25A10_ENST00000331531.5_Missense_Mutation_p.K102M	NM_001270953.1|NM_012140.4	NP_001257882.1|NP_036272.2	Q9UBX3	DIC_HUMAN	solute carrier family 25 (mitochondrial carrier; dicarboxylate transporter), member 10	102					carbohydrate metabolic process (GO:0005975)|cellular nitrogen compound metabolic process (GO:0034641)|dicarboxylic acid transport (GO:0006835)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|ion transport (GO:0006811)|mitochondrial transport (GO:0006839)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	dicarboxylic acid transmembrane transporter activity (GO:0005310)			endometrium(1)|lung(9)|ovary(1)|prostate(1)|skin(2)	14	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0117)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)		Succinic acid(DB00139)	TTCCACGAGAAGGTGTTGCTG	0.692																																					p.K102M		Atlas-SNP	.											.	SLC25A10	24	.	0			c.A305T						.						100	105	103					17																	79682599		2203	4300	6503	SO:0001583	missense	1468	exon3			ACGAGAAGGTGTT		CCDS11786.1, CCDS59301.1, CCDS74176.1	17q25.3	2013-07-15			ENSG00000183048	ENSG00000183048		"Solute carriers"	10980	protein-coding gene	gene with protein product		606794		DIC		9733776, 10072589	Standard	NM_001270953		Approved		uc031rew.1	Q9UBX3	OTTHUMG00000178173	ENST00000350690.5:c.305A>T	chr17.hg19:g.79682599A>T	ENSP00000345580:p.Lys102Met	77.0	0.0		83.0	32.0	NM_001270888	Q542Z3|Q96BA1|Q96IP1	Missense_Mutation	SNP	ENST00000350690.5	hg19	CCDS11786.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.102274	0.76983	.	.	ENSG00000183048	ENST00000541223;ENST00000331531;ENST00000350690;ENST00000545862	T;T;T;T	0.79940	-1.32;-1.32;-1.32;-1.32	3.88	3.88	0.44766	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.89798	0.6819	M	0.87547	2.89	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.77004	0.989;0.972;0.983	D	0.91115	0.4925	10	0.72032	D	0.01	-8.1945	12.3824	0.55313	1.0:0.0:0.0:0.0	.	257;102;102	B4DLN1;Q9UBX3-2;Q9UBX3	.;.;DIC_HUMAN	M	257;102;102;59	ENSP00000439565:K257M;ENSP00000328403:K102M;ENSP00000345580:K102M;ENSP00000446242:K59M	ENSP00000328403:K102M	K	+	2	0	SLC25A10	77293004	1.000000	0.71417	1.000000	0.80357	0.716000	0.41182	8.251000	0.89838	1.414000	0.47017	0.260000	0.18958	AAG	.	.		0.692	SLC25A10-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000440816.1			T	79682599	A	T	79682599	3	4	351	1	0	0	0	0	1	0	0	0	14487	72	3	4	315	4	SLC25A10	17	79682599	Missense_Mutation	SNP	A	TCGA-WJ-A86L-01A-12D-A45V-10	7163640	79682599	1512611	115	49393										
DCXR	51181	hgsc.bcm.edu	37	chr17	79993869	79993869	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	aagcccccttccaccggcaaAgtggaacccgtggtcatgcc	10	16	1	0	rs552483270	byFrequency	TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr17:79993869A>C	ENST00000306869.2	-	8	751	c.702T>G	c.(700-702)acT>acG	p.T234T	RP13-650J16.1_ENST00000584705.1_RNA|RP13-650J16.1_ENST00000582558.1_RNA|DCXR_ENST00000584318.1_5'Flank	NM_001195218.1|NM_016286.3	NP_001182147.1|NP_057370.1	Q7Z4W1	DCXR_HUMAN	dicarbonyl/L-xylulose reductase	234					D-xylose metabolic process (GO:0042732)|glucose metabolic process (GO:0006006)|NADP metabolic process (GO:0006739)|oxidation-reduction process (GO:0055114)|protein homotetramerization (GO:0051289)|xylulose metabolic process (GO:0005997)	brush border (GO:0005903)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)	L-xylulose reductase (NADP+) activity (GO:0050038)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)			kidney(1)|lung(3)	4	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)			CCACCGGCAAAGTGGAACCCG	0.612																																					p.T234T		Atlas-SNP	.											.	DCXR	10	.	0			c.T702G						.						63	54	57					17																	79993869		2203	4300	6503	SO:0001819	synonymous_variant	51181	exon8			CGGCAAAGTGGAA	AB013846	CCDS11799.1	17q25.3	2011-09-14				ENSG00000169738	1.1.1.10	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	18985	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 20C, member 1"	608347				11882650, 19027726	Standard	NM_016286		Approved	KIDCR, DCR, SDR20C1	uc002kdg.3	Q7Z4W1		ENST00000306869.2:c.702T>G	chr17.hg19:g.79993869A>C		59.0	0.0		64.0	34.0	NM_016286	Q9BTZ3|Q9UHY9	Silent	SNP	ENST00000306869.2	hg19	CCDS11799.1																																																																																			.	.		0.612	DCXR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442153.2			C	79993869	A	C	79993869	2	2	351	1	0	0	0	0	0	0	0	1	4321	59	3	5		5	DCXR	17	79993869	Silent	SNP	A	TCGA-WJ-A86L-01A-12D-A45V-10	311270	79993869	1201341	116	49394										
ZNF521	25925	hgsc.bcm.edu	37	chr18	22807356	22807356	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	cgcagcatcacattcactgcAgtggtacttcttgtccccgg	9	14	3	0			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr18:22807356A>G	ENST00000361524.3	-	4	674	c.526T>C	c.(526-528)Tgc>Cgc	p.C176R	ZNF521_ENST00000584787.1_5'UTR|ZNF521_ENST00000579111.1_5'Flank|ZNF521_ENST00000538137.2_Missense_Mutation_p.C176R	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	176					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					CATTCACTGCAGTGGTACTTC	0.478			T	PAX5	ALL																																p.C176R		Atlas-SNP	.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	.	ZNF521	269	.	0			c.T526C						.						136	126	130					18																	22807356		2203	4300	6503	SO:0001583	missense	25925	exon4			CACTGCAGTGGTA	AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"Zinc fingers, C2H2-type"	24605	protein-coding gene	gene with protein product	"early hematopoietic zinc finger"	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.526T>C	chr18.hg19:g.22807356A>G	ENSP00000354794:p.Cys176Arg	128.0	0.0		123.0	57.0	NM_015461	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Missense_Mutation	SNP	ENST00000361524.3	hg19	CCDS32806.1	.	.	.	.	.	.	.	.	.	.	A	10.53	1.376616	0.24857	.	.	ENSG00000198795	ENST00000361524;ENST00000538137;ENST00000399425	D;D	0.85258	-1.96;-1.96	5.98	5.98	0.97165	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.95217	0.8449	H	0.96604	3.85	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96705	0.9521	10	0.87932	D	0	-23.0284	16.4622	0.84064	1.0:0.0:0.0:0.0	.	176	Q96K83	ZN521_HUMAN	R	176;210;176	ENSP00000354794:C176R;ENSP00000382352:C176R	ENSP00000354794:C176R	C	-	1	0	ZNF521	21061354	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.289000	0.77006	0.533000	0.62120	TGC	.	.		0.478	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461		G	22807356	A	G	22807356	3	3	351	1	0	0	0	0	1	0	0	0	17980	188	7	2	3429	2	ZNF521	18	22807356	Missense_Mutation	SNP	A	TCGA-WJ-A86L-01A-12D-A45V-10		22807356	55269892	117	49395										
TAF4B	6875	hgsc.bcm.edu	37	chr18	23866000	23866000	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	tacagtgtcctcaagccagtCtgaaaagtcaattattgttt	7	8	3	1			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr18:23866000C>A	ENST00000269142.5	+	7	2125	c.1127C>A	c.(1126-1128)tCt>tAt	p.S376Y	TAF4B_ENST00000578121.1_Missense_Mutation_p.S376Y|TAF4B_ENST00000400466.2_Missense_Mutation_p.S376Y	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	376					gene expression (GO:0010467)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|NF-kappaB binding (GO:0051059)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|prostate(1)|skin(1)	29	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			TCAAGCCAGTCTGAAAAGTCA	0.458																																					p.S376Y		Atlas-SNP	.											.	TAF4B	71	.	0			c.C1127A						.						102	98	100					18																	23866000		1924	4150	6074	SO:0001583	missense	6875	exon7			GCCAGTCTGAAAA	Y09321	CCDS42421.1	18q11.1	2008-08-01	2002-08-29	2001-12-07		ENSG00000141384			11538	protein-coding gene	gene with protein product	"TATA box binding protein (TBP)-associated factor 4B"	601689	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, C2, 105kD"	TAF2C2		8858156, 10849440	Standard	XM_005258339		Approved	TAFII105	uc002kvu.4	Q92750		ENST00000269142.5:c.1127C>A	chr18.hg19:g.23866000C>A	ENSP00000269142:p.Ser376Tyr	91.0	0.0		79.0	33.0	NM_005640	Q29YA4|Q29YA5	Missense_Mutation	SNP	ENST00000269142.5	hg19	CCDS42421.1	.	.	.	.	.	.	.	.	.	.	c	3.205	-0.162789	0.06502	.	.	ENSG00000141384	ENST00000418698;ENST00000269142;ENST00000400466	T;T;T	0.24908	1.83;1.85;1.83	5.35	4.44	0.53790	.	2.069230	0.01903	N	0.039345	T	0.25382	0.0617	L	0.27053	0.805	0.09310	N	0.999993	B;B	0.10296	0.003;0.003	B;B	0.06405	0.002;0.002	T	0.30327	-0.9982	10	0.87932	D	0	0.9424	11.3256	0.49446	0.1421:0.7206:0.1372:0.0	.	376;376	Q92750;A4PBF7	TAF4B_HUMAN;.	Y	376	ENSP00000389365:S376Y;ENSP00000269142:S376Y;ENSP00000383314:S376Y	ENSP00000269142:S376Y	S	+	2	0	TAF4B	22119998	0.720000	0.27996	0.645000	0.29479	0.162000	0.22319	1.527000	0.35975	1.190000	0.43042	0.558000	0.71614	TCT	.	.		0.458	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000446260.3	NM_005640		A	23866000	C	A	23866000	3	1	351	1	0	0	0	0	1	0	0	0	15542	913	32	3	1153	3	TAF4B	18	23866000	Missense_Mutation	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	1058644	23866000	54211248	118	49396										
ZNF407	55628	hgsc.bcm.edu	37	chr18	72346892	72346892	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	agatcccgttctggggaataAggaaattctgatgaattcac	10	7	3	3			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr18:72346892A>T	ENST00000299687.5	+	1	3917	c.3917A>T	c.(3916-3918)aAg>aTg	p.K1306M	ZNF407_ENST00000309902.6_Missense_Mutation_p.K1306M|ZNF407_ENST00000582337.1_Missense_Mutation_p.K1306M|ZNF407_ENST00000577538.1_Missense_Mutation_p.K1306M	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	1306					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		CTGGGGAATAAGGAAATTCTG	0.448																																					p.K1306M		Atlas-SNP	.											.	ZNF407	231	.	0			c.A3917T						.						31	32	32					18																	72346892		1865	4106	5971	SO:0001583	missense	55628	exon1			GGAATAAGGAAAT	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"Zinc fingers, C2H2-type"	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.3917A>T	chr18.hg19:g.72346892A>T	ENSP00000299687:p.Lys1306Met	85.0	0.0		100.0	4.0	NM_001146190	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Missense_Mutation	SNP	ENST00000299687.5	hg19	CCDS45885.1	.	.	.	.	.	.	.	.	.	.	A	11.21	1.571474	0.28003	.	.	ENSG00000215421	ENST00000299687;ENST00000309902	T;T	0.12465	2.68;3.09	5.67	4.51	0.55191	.	0.202274	0.39985	N	0.001217	T	0.22820	0.0551	L	0.34521	1.04	0.22811	N	0.9987	D;D;D	0.89917	1.0;1.0;0.999	D;D;P	0.73380	0.98;0.964;0.862	T	0.02966	-1.1088	10	0.54805	T	0.06	.	8.5994	0.33736	0.8535:0.0:0.1465:0.0	.	1306;1306;1306	Q9C0G0-3;Q9C0G0-2;Q9C0G0	.;.;ZN407_HUMAN	M	1306	ENSP00000299687:K1306M;ENSP00000310359:K1306M	ENSP00000299687:K1306M	K	+	2	0	ZNF407	70475880	1.000000	0.71417	0.961000	0.40146	0.021000	0.10359	2.414000	0.44627	1.378000	0.46305	0.655000	0.94253	AAG	.	.		0.448	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757		T	72346892	A	T	72346892	3	4	351	1	0	0	0	0	1	0	0	0	17902	72	3	4	3919	4	ZNF407	18	72346892	Missense_Mutation	SNP	A	TCGA-WJ-A86L-01A-12D-A45V-10	48480892	72346892	5730356	119	49397										
AP3D1	8943	hgsc.bcm.edu	37	chr19	2137788	2137788	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	gaaggcggcccagctgatgtCgtatcccaacatctgtaact	10	12	1	1			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr19:2137788C>T	ENST00000345016.5	-	3	442	c.211G>A	c.(211-213)Gac>Aac	p.D71N	AP3D1_ENST00000356926.4_Missense_Mutation_p.D71N|AP3D1_ENST00000350812.6_Missense_Mutation_p.D71N|AP3D1_ENST00000355272.6_Missense_Mutation_p.D71N	NM_003938.6	NP_003929.4	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1 subunit	71					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|endosome to melanosome transport (GO:0035646)|eye pigment biosynthetic process (GO:0006726)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein localization to membrane (GO:0072657)|protein localization to organelle (GO:0033365)|regulation of sequestering of zinc ion (GO:0061088)|synaptic vesicle membrane organization (GO:0048499)	endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane coat (GO:0030117)|terminal bouton (GO:0043195)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(23)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGCTGATGTCGTATCCCAAC	0.542																																					p.D71N		Atlas-SNP	.											.	AP3D1	81	.	0			c.G211A						.						153	152	152					19																	2137788		1995	4181	6176	SO:0001583	missense	8943	exon3			TGATGTCGTATCC	U91930	CCDS42459.1, CCDS58638.1	19p13.3	2014-09-04			ENSG00000065000	ENSG00000065000			568	protein-coding gene	gene with protein product		607246				9151686, 9303295	Standard	NM_003938		Approved	ADTD	uc002lva.4	O14617	OTTHUMG00000180354	ENST00000345016.5:c.211G>A	chr19.hg19:g.2137788C>T	ENSP00000344055:p.Asp71Asn	86.0	0.0		136.0	37.0	NM_001261826	O00202|O75262|Q59HF5|Q96G11|Q9H3C6	Missense_Mutation	SNP	ENST00000345016.5	hg19	CCDS42459.1	.	.	.	.	.	.	.	.	.	.	C	19.69	3.874782	0.72180	.	.	ENSG00000065000	ENST00000356926;ENST00000345016;ENST00000355272;ENST00000343722;ENST00000350812	T;T;T;T	0.16073	2.37;2.37;2.37;2.37	5.24	5.24	0.73138	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.54447	0.1859	M	0.93150	3.385	0.37522	D	0.917579	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.87578	0.998;0.957;0.996	T	0.71321	-0.4628	10	0.87932	D	0	-54.9574	17.7918	0.88554	0.0:1.0:0.0:0.0	.	71;71;71	O14617-5;O14617;G5E988	.;AP3D1_HUMAN;.	N	71	ENSP00000349398:D71N;ENSP00000344055:D71N;ENSP00000347416:D71N;ENSP00000342321:D71N	ENSP00000341579:D71N	D	-	1	0	AP3D1	2088788	1.000000	0.71417	0.954000	0.39281	0.529000	0.34654	7.468000	0.80943	2.447000	0.82792	0.563000	0.77884	GAC	.	.		0.542	AP3D1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450912.1			T	2137788	C	T	2137788	3	4	351	1	0	0	0	0	1	0	0	0	746	884	31	1	3520	1	AP3D1	19	2137788	Missense_Mutation	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10		2137788	56991195	120	49398										
DPP9	91039	hgsc.bcm.edu	37	chr19	4704012	4704012	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	ggcagggcagattttggggtCcatccggggccctgagcact	16	11	0	2			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr19:4704012C>G	ENST00000598800.1	-	8	1073	c.568G>C	c.(568-570)Gac>Cac	p.D190H	DPP9_ENST00000597849.1_Missense_Mutation_p.D219H|DPP9_ENST00000262960.9_Missense_Mutation_p.D219H|DPP9_ENST00000594671.1_Missense_Mutation_p.D190H			Q86TI2	DPP9_HUMAN	dipeptidyl-peptidase 9	190						cytoplasm (GO:0005737)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|identical protein binding (GO:0042802)|serine-type peptidase activity (GO:0008236)			cervix(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00884)		ATTTTGGGGTCCATCCGGGGC	0.627																																					p.D219H		Atlas-SNP	.											.	DPP9	59	.	0			c.G655C						.						50	55	53					19																	4704012		1943	4146	6089	SO:0001583	missense	91039	exon7			TGGGGTCCATCCG	AF452102	CCDS45928.1	19p13.3	2014-06-11	2006-01-12		ENSG00000142002	ENSG00000142002			18648	protein-coding gene	gene with protein product		608258	"dipeptidylpeptidase 9"				Standard	NM_139159		Approved		uc002mba.3	Q86TI2	OTTHUMG00000182040	ENST00000598800.1:c.568G>C	chr19.hg19:g.4704012C>G	ENSP00000469603:p.Asp190His	71.0	0.0		69.0	23.0	NM_139159	O75273|O75868|Q1ZZB8|Q6AI37|Q6UAL0|Q6ZMT2|Q6ZNJ5|Q8N2J7|Q8N3F5|Q8WXD8|Q96NT8|Q9BVR3	Missense_Mutation	SNP	ENST00000598800.1	hg19		.	.	.	.	.	.	.	.	.	.	C	24.3	4.516656	0.85495	.	.	ENSG00000142002	ENST00000357909;ENST00000381797;ENST00000262960	T	0.32515	1.45	4.64	4.64	0.57946	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.60366	0.2263	M	0.85041	2.73	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	T	0.66368	-0.5941	10	0.54805	T	0.06	-45.6084	16.6576	0.85232	0.0:1.0:0.0:0.0	.	190;219	Q86TI2;Q1ZZB8	DPP9_HUMAN;.	H	298;160;219	ENSP00000262960:D219H	ENSP00000262960:D219H	D	-	1	0	DPP9	4655012	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	7.559000	0.82265	2.424000	0.82194	0.561000	0.74099	GAC	.	.		0.627	DPP9-026	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000459343.2			G	4704012	C	G	4704012	3	3	351	1	0	0	0	0	1	0	0	0	4735	855	30	4	2087	4	DPP9	19	4704012	Missense_Mutation	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	2566224	4704012	54424971	121	49399										
MUC16	94025	hgsc.bcm.edu	37	chr19	9064481	9064481	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	atctctgggtgtggaaatccCtgaattactatagagtgggt	12	6	1	2	rs546210055		TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr19:9064481C>A	ENST00000397910.4	-	3	23168	c.22965G>T	c.(22963-22965)caG>caT	p.Q7655H		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	7657	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTGGAAATCCCTGAATTACTA	0.507																																					p.Q7655H		Atlas-SNP	.											.	MUC16	4315	.	0			c.G22965T						.						82	82	82					19																	9064481		1902	4103	6005	SO:0001583	missense	94025	exon3			AAATCCCTGAATT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.22965G>T	chr19.hg19:g.9064481C>A	ENSP00000381008:p.Gln7655His	97.0	0.0		112.0	33.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	N	3.578	-0.086191	0.07097	.	.	ENSG00000181143	ENST00000397910	T	0.27104	1.69	2.19	-3.85	0.04243	.	.	.	.	.	T	0.12944	0.0314	N	0.24115	0.695	.	.	.	B	0.23540	0.087	B	0.26517	0.07	T	0.34527	-0.9825	8	0.87932	D	0	.	0.3705	0.00378	0.1994:0.3237:0.1967:0.2802	.	7655	B5ME49	.	H	7655	ENSP00000381008:Q7655H	ENSP00000381008:Q7655H	Q	-	3	2	MUC16	8925481	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.464000	0.02359	-0.752000	0.04728	0.400000	0.26472	CAG	.	.		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9064481	C	A	9064481	3	1	351	1	0	0	0	0	1	0	0	0	9982	680	24	3	20886	3	MUC16	19	9064481	Missense_Mutation	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	4360469	9064481	50064502	122	49400										
NOTCH3	4854	hgsc.bcm.edu	37	chr19	15302777	15302777	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	tagggctcactcaccaggaaGacaggcacagtcgtaagtga	12	10	2	2			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr19:15302777G>A	ENST00000263388.2	-	4	748	c.673C>T	c.(673-675)Ctt>Ttt	p.L225F		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	225	EGF-like 5. {ECO:0000255|PROSITE- ProRule:PRU00076}.				forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			TCACCAGGAAGACAGGCACAG	0.657																																					p.L225F		Atlas-SNP	.											.	NOTCH3	340	.	0			c.C673T						.						59	51	54					19																	15302777		2203	4300	6503	SO:0001583	missense	4854	exon4			CAGGAAGACAGGC	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"Ankyrin repeat domain containing"	7883	protein-coding gene	gene with protein product		600276	"Notch (Drosophila) homolog 3", "Notch homolog 3 (Drosophila)"	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.673C>T	chr19.hg19:g.15302777G>A	ENSP00000263388:p.Leu225Phe	43.0	0.0		54.0	27.0	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Missense_Mutation	SNP	ENST00000263388.2	hg19	CCDS12326.1	.	.	.	.	.	.	.	.	.	.	g	16.47	3.133634	0.56828	.	.	ENSG00000074181	ENST00000263388;ENST00000539383	D	0.99548	-6.14	5.35	4.31	0.51392	Epidermal growth factor-like (1);EGF-like region, conserved site (2);Epidermal growth factor-like, type 3 (1);	.	.	.	.	D	0.99223	0.9730	L	0.49126	1.545	0.49130	D	0.999756	D;D	0.89917	0.998;1.0	D;D	0.87578	0.985;0.998	D	0.98705	1.0702	9	0.38643	T	0.18	.	8.9869	0.35999	0.1706:0.0:0.8294:0.0	.	228;225	Q59FL3;Q9UM47	.;NOTC3_HUMAN	F	225;227	ENSP00000263388:L225F	ENSP00000263388:L225F	L	-	1	0	NOTCH3	15163777	1.000000	0.71417	1.000000	0.80357	0.709000	0.40893	2.410000	0.44592	1.258000	0.44101	0.558000	0.71614	CTT	.	.		0.657	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435		A	15302777	G	A	15302777	3	1	351	1	0	0	0	0	1	0	0	0	10559	942	33	3	6412	3	NOTCH3	19	15302777	Missense_Mutation	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	6238296	15302777	43826206	123	49401										
DMKN	93099	hgsc.bcm.edu	37	chr19	36003635	36003635	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	cagacctccaggattgccctGgccctggcctccaaggccac	10	18	0	1	rs561680729		TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr19:36003635G>A	ENST00000339686.3	-	2	660	c.484C>T	c.(484-486)Cag>Tag	p.Q162*	DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000451297.2_Nonsense_Mutation_p.Q162*|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000424570.2_Nonsense_Mutation_p.Q162*|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000429837.1_Nonsense_Mutation_p.Q162*|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000418261.1_Nonsense_Mutation_p.Q162*|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000447113.2_Nonsense_Mutation_p.Q162*|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000419602.1_Nonsense_Mutation_p.Q162*|DMKN_ENST00000440396.1_Nonsense_Mutation_p.Q162*	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	162	Gly-rich.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			GGATTGCCCTGGCCCTGGCCT	0.582													G|||	1	0.000199681	0	0	5008	,	,		18230	0.001		0	False		,,,				2504	0				p.Q162X		Atlas-SNP	.											.	DMKN	116	.	0			c.C484T						.						42	44	43					19																	36003635		2203	4300	6503	SO:0001587	stop_gained	93099	exon2			TGCCCTGGCCCTG	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.484C>T	chr19.hg19:g.36003635G>A	ENSP00000342012:p.Gln162*	42.0	0.0		41.0	19.0	NM_001190347	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Nonsense_Mutation	SNP	ENST00000339686.3	hg19	CCDS12463.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.357609	0.82243	.	.	ENSG00000161249	ENST00000339686;ENST00000392207;ENST00000429837;ENST00000419602;ENST00000447113;ENST00000440396;ENST00000418261;ENST00000424570;ENST00000451297	.	.	.	4.66	3.6	0.41247	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	0.0835	10.7739	0.46338	0.0:0.1912:0.8088:0.0	.	.	.	.	X	162	.	ENSP00000342012:Q162X	Q	-	1	0	DMKN	40695475	0.079000	0.21365	0.008000	0.14137	0.313000	0.28021	2.540000	0.45727	1.140000	0.42260	0.467000	0.42956	CAG	.	.		0.582	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317		A	36003635	G	A	36003635	4	1	351	1	0	0	0	0	0	1	0	0	4584	1357	47	3	1323	3	DMKN	19	36003635	Nonsense_Mutation	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	20700858	36003635	23125348	124	49402										
RBM42	79171	hgsc.bcm.edu	37	chr19	36120568	36120568	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	aattatcgcgaccaacacatAccagcaggtacggctgagct	9	12	0	1			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr19:36120568A>G	ENST00000262633.4	+	2	380	c.275A>G	c.(274-276)tAc>tGc	p.Y92C	RBM42_ENST00000588161.1_Missense_Mutation_p.Y92C|RBM42_ENST00000586618.1_Missense_Mutation_p.Y92C|RBM42_ENST00000592202.1_Missense_Mutation_p.Y92C|RBM42_ENST00000589871.1_Missense_Mutation_p.Y92C|RBM42_ENST00000360475.4_Missense_Mutation_p.Y92C|RBM42_ENST00000589559.1_Missense_Mutation_p.Y92C	NM_024321.3	NP_077297.2	Q9BTD8	RBM42_HUMAN	RNA binding motif protein 42	92						cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|large_intestine(7)|lung(9)|prostate(1)	21	all_lung(56;1.58e-07)|Lung NSC(56;2.43e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			ACCAACACATACCAGCAGGTA	0.562																																					p.Y92C		Atlas-SNP	.											.	RBM42	40	.	0			c.A275G						.						72	65	67					19																	36120568		2203	4300	6503	SO:0001583	missense	79171	exon2			ACACATACCAGCA	BC004204	CCDS12468.1	19q13.12	2013-02-12				ENSG00000126254		"RNA binding motif (RRM) containing"	28117	protein-coding gene	gene with protein product		613232				12477932	Standard	NM_024321		Approved	MGC10433	uc002oan.3	Q9BTD8		ENST00000262633.4:c.275A>G	chr19.hg19:g.36120568A>G	ENSP00000262633:p.Tyr92Cys	61.0	0.0		51.0	25.0	NM_024321	O00320|Q8N5R7|Q9BU66	Missense_Mutation	SNP	ENST00000262633.4	hg19	CCDS12468.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.522841	0.85600	.	.	ENSG00000126254	ENST00000262633;ENST00000360475	T;T	0.32753	1.71;1.44	4.34	4.34	0.51931	.	0.000000	0.85682	D	0.000000	T	0.49558	0.1564	L	0.57536	1.79	0.58432	D	0.999996	D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;0.999	D;D;D;D;D	0.87578	0.998;0.996;0.993;0.996;0.99	T	0.51949	-0.8640	10	0.87932	D	0	-4.6272	11.5485	0.50706	1.0:0.0:0.0:0.0	.	92;92;92;92;92	B4DWT0;Q9BTD8-4;Q9BTD8-3;Q9BTD8-2;Q9BTD8	.;.;.;.;RBM42_HUMAN	C	92	ENSP00000262633:Y92C;ENSP00000353663:Y92C	ENSP00000262633:Y92C	Y	+	2	0	RBM42	40812408	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	8.269000	0.89878	1.827000	0.53221	0.459000	0.35465	TAC	.	.		0.562	RBM42-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459057.2	NM_024321		G	36120568	A	G	36120568	3	3	351	1	0	0	0	0	1	0	0	0	13151	391	14	2	281	2	RBM42	19	36120568	Missense_Mutation	SNP	A	TCGA-WJ-A86L-01A-12D-A45V-10	116933	36120568	23008415	125	49403										
PLD3	23646	hgsc.bcm.edu	37	chr19	40882529	40882529	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	tcctcaggttctggcctgccAttgacgatgggctgcggcgg	15	12	2	1			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr19:40882529A>G	ENST00000409587.1	+	11	1430	c.1033A>G	c.(1033-1035)Att>Gtt	p.I345V	PLD3_ENST00000356508.5_Missense_Mutation_p.I345V|PLD3_ENST00000409419.1_Missense_Mutation_p.I345V|PLD3_ENST00000409281.1_Missense_Mutation_p.I345V|PLD3_ENST00000409735.4_Missense_Mutation_p.I345V			Q8IV08	PLD3_HUMAN	phospholipase D family, member 3	345					cell death (GO:0008219)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phospholipase D activity (GO:0004630)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	20			Lung(22;0.000636)|LUSC - Lung squamous cell carcinoma(20;0.00248)			CTGGCCTGCCATTGACGATGG	0.647																																					p.I345V		Atlas-SNP	.											.	PLD3	71	.	0			c.A1033G						.						76	77	77					19																	40882529		2203	4300	6503	SO:0001583	missense	23646	exon11			CCTGCCATTGACG	BC000553	CCDS33027.1	19q13.2	2014-03-14	2005-05-20		ENSG00000105223	ENSG00000105223			17158	protein-coding gene	gene with protein product		615698	"phospholipase D3"			9140189, 15794758	Standard	XM_005258704		Approved	HU-K4	uc002onj.4	Q8IV08	OTTHUMG00000152736	ENST00000409587.1:c.1033A>G	chr19.hg19:g.40882529A>G	ENSP00000387050:p.Ile345Val	24.0	0.0		26.0	9.0	NM_012268	Q92853|Q9BW87	Missense_Mutation	SNP	ENST00000409587.1	hg19	CCDS33027.1	.	.	.	.	.	.	.	.	.	.	A	12.81	2.048867	0.36181	.	.	ENSG00000105223	ENST00000409419;ENST00000409587;ENST00000356508;ENST00000536031;ENST00000409735;ENST00000409281	T;T;T;T;T	0.56611	0.45;0.45;0.45;0.45;0.45	4.29	3.25	0.37280	Phospholipase D/viral envelope (1);	0.107102	0.64402	D	0.000008	T	0.55545	0.1927	M	0.81682	2.555	0.52099	D	0.999945	B	0.18310	0.027	B	0.29785	0.107	T	0.56238	-0.8012	10	0.66056	D	0.02	-10.9258	9.0962	0.36640	0.9086:0.0:0.0914:0.0	.	345	Q8IV08	PLD3_HUMAN	V	345;345;345;326;345;345	ENSP00000386293:I345V;ENSP00000387050:I345V;ENSP00000348901:I345V;ENSP00000386938:I345V;ENSP00000387022:I345V	ENSP00000348901:I345V	I	+	1	0	PLD3	45574369	1.000000	0.71417	0.997000	0.53966	0.449000	0.32228	4.095000	0.57728	0.668000	0.31126	0.260000	0.18958	ATT	.	.		0.647	PLD3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327721.1	NM_012268		G	40882529	A	G	40882529	3	3	351	1	0	0	0	0	1	0	0	0	12056	217	8	2	1067	2	PLD3	19	40882529	Missense_Mutation	SNP	A	TCGA-WJ-A86L-01A-12D-A45V-10	4761961	40882529	18246454	126	49404										
NPAS1	4861	hgsc.bcm.edu	37	chr19	47548495	47548495	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	caggctgccccagcggagaaCgaggccccccagacccaggg	14	17	0	2	rs147026903		TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr19:47548495C>A	ENST00000602212.1	+	12	1579	c.1359C>A	c.(1357-1359)aaC>aaA	p.N453K	NPAS1_ENST00000602189.1_Missense_Mutation_p.N278K|NPAS1_ENST00000449844.2_Missense_Mutation_p.N453K|NPAS1_ENST00000439365.2_3'UTR			Q99742	NPAS1_HUMAN	neuronal PAS domain protein 1	453					central nervous system development (GO:0007417)|maternal behavior (GO:0042711)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|startle response (GO:0001964)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			endometrium(2)|kidney(1)|large_intestine(2)|lung(1)	6		all_cancers(25;4.31e-08)|all_epithelial(76;2.96e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.102)		all cancers(93;6.02e-05)|OV - Ovarian serous cystadenocarcinoma(262;7.35e-05)|Epithelial(262;0.00389)|GBM - Glioblastoma multiforme(486;0.0252)		CAGCGGAGAACGAGGCCCCCC	0.662																																					p.N453K		Atlas-SNP	.											.	NPAS1	32	.	0			c.C1359A						.						38	43	41					19																	47548495		2199	4300	6499	SO:0001583	missense	4861	exon11			GGAGAACGAGGCC	U77968	CCDS12694.1	19q13.2-q13.3	2013-05-21				ENSG00000130751		"Basic helix-loop-helix proteins"	7894	protein-coding gene	gene with protein product	"neuronal PAS1", "member of PAS superfamily 5"	603346				9012850, 9079689	Standard	NM_002517		Approved	MOP5, PASD5, bHLHe11	uc002pfy.3	Q99742		ENST00000602212.1:c.1359C>A	chr19.hg19:g.47548495C>A	ENSP00000469142:p.Asn453Lys	131.0	0.0		150.0	32.0	NM_002517	B4DR69|Q99632|Q9BY83	Missense_Mutation	SNP	ENST00000602212.1	hg19	CCDS12694.1	.	.	.	.	.	.	.	.	.	.	C	0.338	-0.952149	0.02285	.	.	ENSG00000130751	ENST00000449844	T	0.40756	1.02	4.11	-3.78	0.04333	.	1.463600	0.04399	N	0.363777	T	0.14830	0.0358	N	0.02539	-0.55	0.19945	N	0.999947	B	0.15141	0.012	B	0.12837	0.008	T	0.16630	-1.0396	10	0.10111	T	0.7	.	4.8982	0.13760	0.0:0.3158:0.2757:0.4085	.	453	Q99742	NPAS1_HUMAN	K	453	ENSP00000405290:N453K	ENSP00000405290:N453K	N	+	3	2	NPAS1	52240335	0.000000	0.05858	0.049000	0.19019	0.167000	0.22549	-2.202000	0.01235	-0.608000	0.05731	-0.802000	0.03209	AAC	.	C|1.000;G|0.000		0.662	NPAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466658.1	NM_002517		A	47548495	C	A	47548495	3	1	351	1	0	0	0	0	1	0	0	0	10571	535	19	1	1401	1	NPAS1	19	47548495	Missense_Mutation	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	6665966	47548495	11580488	127	49405										
DHX34	9704	hgsc.bcm.edu	37	chr19	47865878	47865878	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	ttccgcctctatgccgaatcGgactatgatgccttcgcccc	8	16	1	1			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr19:47865878G>T	ENST00000328771.4	+	6	1870	c.1521G>T	c.(1519-1521)tcG>tcT	p.S507S	DHX34_ENST00000471451.1_Intron	NM_014681.5	NP_055496.2	Q14147	DHX34_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 34	507	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	membrane (GO:0016020)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(5)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;7.16e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000489)|GBM - Glioblastoma multiforme(486;0.00413)|Epithelial(262;0.0132)		ATGCCGAATCGGACTATGATG	0.647																																					p.S507S		Atlas-SNP	.											.	DHX34	98	.	0			c.G1521T						.						26	27	27					19																	47865878		2203	4300	6503	SO:0001819	synonymous_variant	9704	exon6			CGAATCGGACTAT	D50924	CCDS12700.1	19q13.3	2003-06-13	2003-06-13	2003-06-13	ENSG00000134815	ENSG00000134815		"DEAH-boxes"	16719	protein-coding gene	gene with protein product		615475	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 34"	DDX34		10708517, 8590280	Standard	NM_014681		Approved	KIAA0134	uc010xyn.2	Q14147	OTTHUMG00000149959	ENST00000328771.4:c.1521G>T	chr19.hg19:g.47865878G>T		108.0	0.0		110.0	53.0	NM_014681	B4DMY8	Silent	SNP	ENST00000328771.4	hg19	CCDS12700.1																																																																																			.	.		0.647	DHX34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314313.3	NM_014681		T	47865878	G	T	47865878	2	4	351	1	0	0	0	0	0	0	0	1	4509	1103	39	1		1	DHX34	19	47865878	Silent	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	317383	47865878	11263105	128	49406										
ZIM3	114026	hgsc.bcm.edu	37	chr19	57646441	57646441	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	gaaggtttttccacattcacTacatctataggtcctctctc	5	12	3	0			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr19:57646441T>C	ENST00000269834.1	-	5	1649	c.1264A>G	c.(1264-1266)Agt>Ggt	p.S422G	U3_ENST00000516874.1_RNA	NM_052882.1	NP_443114.1	Q96PE6	ZIM3_HUMAN	zinc finger, imprinted 3	422					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(27)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	52		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.243)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		CCACATTCACTACATCTATAG	0.388																																					p.S422G		Atlas-SNP	.											.	ZIM3	107	.	0			c.A1264G						.						163	165	165					19																	57646441		2203	4300	6503	SO:0001583	missense	114026	exon5			ATTCACTACATCT	AF365931	CCDS33125.1	19q13.4	2013-01-08				ENSG00000141946		"Zinc fingers, C2H2-type", "-"	16366	protein-coding gene	gene with protein product							Standard	NM_052882		Approved	ZNF657	uc002qnz.1	Q96PE6		ENST00000269834.1:c.1264A>G	chr19.hg19:g.57646441T>C	ENSP00000269834:p.Ser422Gly	89.0	0.0		78.0	40.0	NM_052882	Q14CA6	Missense_Mutation	SNP	ENST00000269834.1	hg19	CCDS33125.1	.	.	.	.	.	.	.	.	.	.	T	11.38	1.621654	0.28889	.	.	ENSG00000141946	ENST00000269834	T	0.07688	3.17	2.71	1.63	0.23807	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07188	0.0182	L	0.43152	1.355	0.09310	N	1	P	0.36183	0.542	B	0.35971	0.215	T	0.32666	-0.9898	9	0.51188	T	0.08	.	3.3939	0.07299	0.2322:0.0:0.2387:0.5291	.	422	Q96PE6	ZIM3_HUMAN	G	422	ENSP00000269834:S422G	ENSP00000269834:S422G	S	-	1	0	ZIM3	62338253	0.000000	0.05858	0.004000	0.12327	0.028000	0.11728	-3.834000	0.00354	0.245000	0.21373	0.260000	0.18958	AGT	.	.		0.388	ZIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465078.1			C	57646441	T	C	57646441	3	2	351	1	0	0	0	0	1	0	0	0	17700	1522	53	2	158	2	ZIM3	19	57646441	Missense_Mutation	SNP	T	TCGA-WJ-A86L-01A-12D-A45V-10	9780563	57646441	1482542	129	49407										
SEL1L2	80343	hgsc.bcm.edu	37	chr20	13894546	13894546	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	cagccattttctccatagctTtcaagtttcccatgtcagct	5	13	3	0			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr20:13894546T>G	ENST00000284951.5	-	5	505	c.431A>C	c.(430-432)aAa>aCa	p.K144T	SEL1L2_ENST00000378072.5_Missense_Mutation_p.K144T|SEL1L2_ENST00000486903.1_5'UTR			Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2 (C. elegans)	144						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	51						CTCCATAGCTTTCAAGTTTCC	0.363																																					p.K144T		Atlas-SNP	.											.	SEL1L2	103	.	0			c.A431C						.						74	68	70					20																	13894546		1813	4081	5894	SO:0001583	missense	80343	exon5			ATAGCTTTCAAGT	AL137678	CCDS59443.1	20p12.1	2011-03-31	2006-11-24	2006-11-24	ENSG00000101251	ENSG00000101251			15897	protein-coding gene	gene with protein product		614289	"chromosome 20 open reading frame 50"	C20orf50			Standard	NM_001271539		Approved	DKFZp434C1826	uc010zrl.3	Q5TEA6	OTTHUMG00000031910	ENST00000284951.5:c.431A>C	chr20.hg19:g.13894546T>G	ENSP00000284951:p.Lys144Thr	106.0	0.0		91.0	32.0	NM_001271539	B4DXX5	Missense_Mutation	SNP	ENST00000284951.5	hg19		.	.	.	.	.	.	.	.	.	.	T	20.5	4.005641	0.74932	.	.	ENSG00000101251	ENST00000378072;ENST00000284951;ENST00000473203	T;T;T	0.55234	0.72;0.72;0.53	5.87	5.87	0.94306	Tetratricopeptide-like helical (1);	0.108090	0.40640	N	0.001058	T	0.56031	0.1958	L	0.46157	1.445	0.43381	D	0.995488	D;P	0.57257	0.979;0.546	P;B	0.52957	0.714;0.115	T	0.52373	-0.8584	10	0.30078	T	0.28	-10.0748	12.9575	0.58438	0.0:0.0:0.0:1.0	.	144;144	B4DXX5;Q5TEA6	.;SE1L2_HUMAN	T	144;144;32	ENSP00000367312:K144T;ENSP00000284951:K144T;ENSP00000420372:K32T	ENSP00000284951:K144T	K	-	2	0	SEL1L2	13842546	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.875000	0.39578	2.371000	0.80710	0.533000	0.62120	AAA	.	.		0.363	SEL1L2-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078067.3	NM_025229		G	13894546	T	G	13894546	3	3	351	1	0	0	0	0	1	0	0	0	14026	1841	64	5	1699	5	SEL1L2	20	13894546	Missense_Mutation	SNP	T	TCGA-WJ-A86L-01A-12D-A45V-10		13894546	49130974	130	49408										
TRPM2	7226	hgsc.bcm.edu	37	chr21	45819301	45819301	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	tggaggccaaggacatgaagTttgtgtctcacgggggcatc	15	8	1	1			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr21:45819301T>C	ENST00000397928.1	+	14	2630	c.2185T>C	c.(2185-2187)Ttt>Ctt	p.F729L	TRPM2_ENST00000300481.9_Missense_Mutation_p.F709L|TRPM2_ENST00000498430.1_3'UTR|TRPM2_ENST00000397932.2_Missense_Mutation_p.F729L|TRPM2_ENST00000300482.5_Missense_Mutation_p.F729L	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	729					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)			breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						GGACATGAAGTTTGTGTCTCA	0.632																																					p.F729L		Atlas-SNP	.											.	TRPM2	196	.	0			c.T2185C						.						62	55	57					21																	45819301		2203	4296	6499	SO:0001583	missense	7226	exon14			ATGAAGTTTGTGT	AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"Voltage-gated ion channels / Transient receptor potential cation channels", "Nudix motif containing"	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.2185T>C	chr21.hg19:g.45819301T>C	ENSP00000381023:p.Phe729Leu	80.0	0.0		89.0	35.0	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Missense_Mutation	SNP	ENST00000397928.1	hg19	CCDS13710.1	.	.	.	.	.	.	.	.	.	.	T	33	5.230953	0.95207	.	.	ENSG00000142185	ENST00000300482;ENST00000397928;ENST00000300481;ENST00000397932	T;T;T;T	0.75938	-0.98;-0.98;-0.98;-0.98	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	D	0.85500	0.5711	M	0.76574	2.34	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.997	D	0.87504	0.2435	10	0.87932	D	0	-22.3412	14.8441	0.70246	0.0:0.0:0.0:1.0	.	729;515;729	E9PGK7;Q5KTC1;O94759	.;.;TRPM2_HUMAN	L	729;729;709;729	ENSP00000300482:F729L;ENSP00000381023:F729L;ENSP00000300481:F709L;ENSP00000381026:F729L	ENSP00000300481:F709L	F	+	1	0	TRPM2	44643729	1.000000	0.71417	0.988000	0.46212	0.961000	0.63080	5.784000	0.68990	1.911000	0.55334	0.454000	0.30748	TTT	.	.		0.632	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307		C	45819301	T	C	45819301	3	2	351	1	0	0	0	0	1	0	0	0	16601	1725	60	2	2239	2	TRPM2	21	45819301	Missense_Mutation	SNP	T	TCGA-WJ-A86L-01A-12D-A45V-10		45819301	2310594	131	49409										
THOC5	8563	hgsc.bcm.edu	37	chr22	29913322	29913322	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	ccttggcagggaagaggtacTggcaatcactggtaactggc	14	9	1	1			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr22:29913322T>C	ENST00000490103.1	-	16	1645	c.1523A>G	c.(1522-1524)cAg>cGg	p.Q508R	THOC5_ENST00000397871.1_Missense_Mutation_p.Q508R|CTA-256D12.11_ENST00000411969.1_RNA|THOC5_ENST00000397872.1_Missense_Mutation_p.Q508R|THOC5_ENST00000397873.2_Missense_Mutation_p.Q508R	NM_003678.4	NP_003669.4	Q13769	THOC5_HUMAN	THO complex 5	508					blastocyst development (GO:0001824)|cell morphogenesis (GO:0000902)|monocyte differentiation (GO:0030224)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|negative regulation of DNA damage checkpoint (GO:2000002)|negative regulation of macrophage differentiation (GO:0045650)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|primitive hemopoiesis (GO:0060215)|regulation of mRNA export from nucleus (GO:0010793)|regulation of stem cell division (GO:2000035)|RNA splicing (GO:0008380)|stem cell division (GO:0017145)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	mRNA binding (GO:0003729)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(4)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GAAGAGGTACTGGCAATCACT	0.483																																					p.Q508R		Atlas-SNP	.											.	THOC5	58	.	0			c.A1523G						.						126	101	110					22																	29913322		2203	4300	6503	SO:0001583	missense	8563	exon17			AGGTACTGGCAAT	AB023200	CCDS13859.1	22q12	2013-02-11			ENSG00000100296	ENSG00000100296		"THO complex subunits"	19074	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 79"	612733	"chromosome 22 open reading frame 19"	C22orf19		11979277, 8242058, 10231032, 19015024, 18373705	Standard	NM_003678		Approved	PK1.3, KIAA0983, Fmip, fSAP79	uc003afs.3	Q13769	OTTHUMG00000151291	ENST00000490103.1:c.1523A>G	chr22.hg19:g.29913322T>C	ENSP00000420306:p.Gln508Arg	125.0	0.0		102.0	49.0	NM_001002878	O60839|Q9UPZ5	Missense_Mutation	SNP	ENST00000490103.1	hg19	CCDS13859.1	.	.	.	.	.	.	.	.	.	.	T	17.57	3.421666	0.62622	.	.	ENSG00000100296	ENST00000490103;ENST00000397872;ENST00000397871;ENST00000397873	T;T;T;T	0.23552	1.9;1.9;1.9;1.9	5.81	5.81	0.92471	.	0.152728	0.64402	D	0.000015	T	0.26702	0.0653	M	0.62723	1.935	0.53688	D	0.999979	P	0.42827	0.791	B	0.37650	0.255	T	0.06807	-1.0806	10	0.15066	T	0.55	-26.8255	15.8194	0.78628	0.0:0.0:0.0:1.0	.	508	Q13769	THOC5_HUMAN	R	508	ENSP00000420306:Q508R;ENSP00000380970:Q508R;ENSP00000380969:Q508R;ENSP00000380971:Q508R	ENSP00000380969:Q508R	Q	-	2	0	THOC5	28243322	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.020000	0.70826	2.206000	0.71126	0.533000	0.62120	CAG	.	.		0.483	THOC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322097.1	NM_003678		C	29913322	T	C	29913322	3	2	351	1	0	0	0	0	1	0	0	0	15883	1580	55	2	548	2	THOC5	22	29913322	Missense_Mutation	SNP	T	TCGA-WJ-A86L-01A-12D-A45V-10		29913322	21391244	132	49410										
TTC38	55020	hgsc.bcm.edu	37	chr22	46685390	46685390	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	aggctgaggacgggaaccctGaccgcgtcctggagctgctc	15	13	0	2			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr22:46685390G>T	ENST00000381031.3	+	12	1250	c.1174G>T	c.(1174-1176)Gac>Tac	p.D392Y	TTC38_ENST00000445282.2_Missense_Mutation_p.D334Y	NM_017931.2	NP_060401	Q5R3I4	TTC38_HUMAN	tetratricopeptide repeat domain 38	392						extracellular vesicular exosome (GO:0070062)				endometrium(4)|large_intestine(3)|lung(4)|ovary(1)	12						CGGGAACCCTGACCGCGTCCT	0.697																																					p.D392Y		Atlas-SNP	.											.	TTC38	40	.	0			c.G1174T						.						26	33	31					22																	46685390		2079	4198	6277	SO:0001583	missense	55020	exon12			AACCCTGACCGCG		CCDS43030.1	22q13	2013-01-11			ENSG00000075234	ENSG00000075234		"Tetratricopeptide (TTC) repeat domain containing"	26082	protein-coding gene	gene with protein product							Standard	NM_017931		Approved	FLJ20699	uc003bhi.3	Q5R3I4	OTTHUMG00000150494	ENST00000381031.3:c.1174G>T	chr22.hg19:g.46685390G>T	ENSP00000370419:p.Asp392Tyr	72.0	0.0		59.0	29.0	NM_017931	Q8WV27|Q9NWP8	Missense_Mutation	SNP	ENST00000381031.3	hg19	CCDS43030.1	.	.	.	.	.	.	.	.	.	.	G	14.89	2.670675	0.47781	.	.	ENSG00000075234	ENST00000381031;ENST00000445282	T;T	0.47869	0.83;0.85	4.77	4.77	0.60923	.	0.230464	0.47455	D	0.000225	T	0.70544	0.3236	M	0.83953	2.67	0.52099	D	0.99994	D;D	0.89917	1.0;0.998	D;D	0.78314	0.991;0.969	T	0.75886	-0.3159	10	0.66056	D	0.02	-14.916	15.2969	0.73916	0.0:0.0:1.0:0.0	.	334;392	E7ES35;Q5R3I4	.;TTC38_HUMAN	Y	392;334	ENSP00000370419:D392Y;ENSP00000393960:D334Y	ENSP00000370419:D392Y	D	+	1	0	TTC38	45064054	1.000000	0.71417	0.872000	0.34217	0.064000	0.16182	5.079000	0.64431	2.212000	0.71576	0.655000	0.94253	GAC	.	.		0.697	TTC38-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000318469.1	NM_017931		T	46685390	G	T	46685390	3	4	351	1	0	0	0	0	1	0	0	0	16721	1290	45	3	1220	3	TTC38	22	46685390	Missense_Mutation	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	16772068	46685390	4619176	133	49411										
DCAF8L2	347442	hgsc.bcm.edu	37	chrX	27765410	27765410	+	Frame_Shift_Del	DEL	A	A	-													0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	ggaggaggaagaggaggaggAggaggaggaggaggaggagg							TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chrX:27765410delA	ENST00000451261.2	+	5	797	c.398delA	c.(397-399)gagfs	p.E147fs		NM_001136533.1	NP_001130005.1	P0C7V8	DC8L2_HUMAN	DDB1 and CUL4 associated factor 8-like 2	147	Glu-rich.			Missing (in Ref. 1; AAI57860). {ECO:0000305}.						central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						gaggaggaggaggaggaggag	0.567																																					p.E133fs		Atlas-INDEL	.											.	DCAF8L2	79	.	0			c.397delG						.			40,2596		12,12,4,1144,296	17	15	16				0	X	dbSNP_126	16	48,4641		10,13,15,1764,1100	no	frameshift	DCAF8L2	NM_001136533.1		22,25,19,2908,1396	A1A1,A1R,A1,RR,R		1.0237,1.5175,1.2014			27765410	88,7237	692	1585	2277	SO:0001589	frameshift_variant	347442	exon1			.		CCDS59162.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17		ENSG00000189186		"WD repeat domain containing"	31811	protein-coding gene	gene with protein product			"WD repeat domain 42C"	WDR42C			Standard	NM_001136533		Approved		uc011mjy.2	P0C7V8		ENST00000451261.2:c.398delA	chrX.hg19:g.27765410delA	ENSP00000462745:p.Glu147fs	60.0	0.0		52.0	10.0	NM_001136533	B2RXH9|J3KT06	Frame_Shift_Del	DEL	ENST00000451261.2	hg19	CCDS59162.1																																																																																			.	.		0.567	DCAF8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056143.4	XM_293354		-	27765410	A	-	27765410	7	5	351	1	0	1	0	1	0	0	0	0	4280	304	11	0	400	0	DCAF8L2	23	27765410	Frame_Shift_Del	DEL	A	TCGA-WJ-A86L-01A-12D-A45V-10		27765410	127505150	134	49412			1	65		2	2	14	N	G_A	5.753031e-05
DCAF8L2	347442	hgsc.bcm.edu	37	chrX	27765423	27765423	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	gaggaggaggaggaggaggaGgaggaggaggaggaggagga	27	0	0	0			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chrX:27765423G>A	ENST00000451261.2	+	5	810	c.411G>A	c.(409-411)gaG>gaA	p.E137E		NM_001136533.1	NP_001130005.1	P0C7V8	DC8L2_HUMAN	DDB1 and CUL4 associated factor 8-like 2	137	Glu-rich.									central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						aggaggaggaggaggaggagg	0.592																																					p.E137E		Atlas-SNP	.											.	DCAF8L2	79	.	0			c.G411A						.						13	13	13					X																	27765423		692	1584	2276	SO:0001819	synonymous_variant	347442	exon1			GGAGGAGGAGGAG		CCDS59162.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17		ENSG00000189186		"WD repeat domain containing"	31811	protein-coding gene	gene with protein product			"WD repeat domain 42C"	WDR42C			Standard	NM_001136533		Approved		uc011mjy.2	P0C7V8		ENST00000451261.2:c.411G>A	chrX.hg19:g.27765423G>A		11.0	0.0		47.0	33.0	NM_001136533	B2RXH9|J3KT06	Silent	SNP	ENST00000451261.2	hg19	CCDS59162.1																																																																																			.	.		0.592	DCAF8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056143.4	XM_293354		A	27765423	G	A	27765423	2	1	351	1	0	0	0	0	0	0	0	1	4280	991	35	3		3	DCAF8L2	23	27765423	Silent	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	13	27765423	127505137	135	49413			1	65		2	2	14	N	G_A	5.753031e-05
BMP15	9210	hgsc.bcm.edu	37	chrX	50658936	50658936	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	acttcccttcctcagaaggaGattcctcaaaaccttccctg	5	15	2	2			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chrX:50658936G>T	ENST00000252677.3	+	2	508	c.508G>T	c.(508-510)Gat>Tat	p.D170Y		NM_005448.2	NP_005439.2	O95972	BMP15_HUMAN	bone morphogenetic protein 15	170					female gamete generation (GO:0007292)|granulosa cell development (GO:0060016)|ovarian follicle development (GO:0001541)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)				NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|skin(1)	26	Ovarian(276;0.236)					CTCAGAAGGAGATTCCTCAAA	0.478																																					p.D170Y		Atlas-SNP	.											.	BMP15	62	.	0			c.G508T						.						110	86	94					X																	50658936		2203	4299	6502	SO:0001583	missense	9210	exon2			GAAGGAGATTCCT	AF082349	CCDS14334.1	Xp11.2	2013-02-06			ENSG00000130385	ENSG00000130385		"Bone morphogenetic proteins"	1068	protein-coding gene	gene with protein product		300247				9849956	Standard	NM_005448		Approved	GDF9B	uc011mnw.2	O95972	OTTHUMG00000021525	ENST00000252677.3:c.508G>T	chrX.hg19:g.50658936G>T	ENSP00000252677:p.Asp170Tyr	298.0	0.0		254.0	118.0	NM_005448	Q17RM6|Q5JST1|Q9UMS1	Missense_Mutation	SNP	ENST00000252677.3	hg19	CCDS14334.1	.	.	.	.	.	.	.	.	.	.	g	0.001	-2.882156	0.00061	.	.	ENSG00000130385	ENST00000252677	T	0.79454	-1.27	5.42	1.53	0.23141	.	1.054580	0.07219	N	0.860493	T	0.48978	0.1530	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32824	-0.9892	10	0.15952	T	0.53	.	4.858	0.13570	0.2699:0.0:0.5831:0.147	.	170	O95972	BMP15_HUMAN	Y	170	ENSP00000252677:D170Y	ENSP00000252677:D170Y	D	+	1	0	BMP15	50675676	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.213000	0.17521	-0.134000	0.11516	0.556000	0.70494	GAT	.	.		0.478	BMP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056572.1	NM_005448		T	50658936	G	T	50658936	3	4	351	1	0	0	0	0	1	0	0	0	1458	942	33	3	514	3	BMP15	23	50658936	Missense_Mutation	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	22893513	50658936	104611624	136	49414										
FOXR2	139628	hgsc.bcm.edu	37	chrX	55650548	55650548	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	agagtctctgccatcttcctCcagtgagcagtctcctttac	7	14	3	2			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chrX:55650548C>T	ENST00000339140.3	+	1	716	c.404C>T	c.(403-405)tCc>tTc	p.S135F		NM_198451.3	NP_940853.1	Q6PJQ5	FOXR2_HUMAN	forkhead box R2	135					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|liver(1)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	19						CCATCTTCCTCCAGTGAGCAG	0.517																																					p.S135F		Atlas-SNP	.											.	FOXR2	42	.	0			c.C404T						.						77	69	72					X																	55650548		2203	4300	6503	SO:0001583	missense	139628	exon1			CTTCCTCCAGTGA	BC012934	CCDS35308.1	Xp11	2006-12-15			ENSG00000189299	ENSG00000189299		"Forkhead boxes"	30469	protein-coding gene	gene with protein product						15202009, 15202027	Standard	NM_198451		Approved	MGC21658, FOXN6	uc004duo.3	Q6PJQ5	OTTHUMG00000021661	ENST00000339140.3:c.404C>T	chrX.hg19:g.55650548C>T	ENSP00000427329:p.Ser135Phe	134.0	0.0		134.0	72.0	NM_198451		Missense_Mutation	SNP	ENST00000339140.3	hg19	CCDS35308.1	.	.	.	.	.	.	.	.	.	.	C	1.498	-0.552799	0.03996	.	.	ENSG00000189299	ENST00000339140	D	0.94457	-3.43	3.63	1.55	0.23275	.	1.787790	0.03253	N	0.182135	D	0.91019	0.7175	L	0.58101	1.795	0.09310	N	1	B	0.31485	0.325	B	0.29267	0.1	T	0.76252	-0.3027	10	0.13470	T	0.59	.	3.4904	0.07636	0.3258:0.5363:0.0:0.1379	.	135	Q6PJQ5	FOXR2_HUMAN	F	135	ENSP00000427329:S135F	ENSP00000427329:S135F	S	+	2	0	FOXR2	55667273	0.004000	0.15560	0.000000	0.03702	0.071000	0.16799	0.350000	0.20079	0.231000	0.21079	0.600000	0.82982	TCC	.	.		0.517	FOXR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056877.2	NM_198451		T	55650548	C	T	55650548	3	4	351	1	0	0	0	0	1	0	0	0	6040	855	30	3	406	3	FOXR2	23	55650548	Missense_Mutation	SNP	C	TCGA-WJ-A86L-01A-12D-A45V-10	4991612	55650548	99620012	137	49415										
DACH2	117154	hgsc.bcm.edu	37	chrX	86069740	86069740	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0437956204379562	6	1	0.789937733499377	0	1.0103854730806	0.0149068322981366	0.256887052341599	0	aaaaaaaccaagagaaaattGcaggaagccttggaatttga	9	5	0	2			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chrX:86069740G>T	ENST00000373125.4	+	10	1587	c.1587G>T	c.(1585-1587)ttG>ttT	p.L529F	DACH2_ENST00000508860.1_Missense_Mutation_p.L362F|DACH2_ENST00000373131.1_Missense_Mutation_p.L516F|DACH2_ENST00000510272.1_Missense_Mutation_p.L310F	NM_053281.3	NP_444511.1	Q96NX9	DACH2_HUMAN	dachshund family transcription factor 2	529	DACHbox-C.				development of primary female sexual characteristics (GO:0046545)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(14)|lung(28)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	71						AGAGAAAATTGCAGGAAGCCT	0.443																																					p.L529F		Atlas-SNP	.											.	DACH2	263	.	0			c.G1587T						.						62	57	59					X																	86069740		2203	4300	6503	SO:0001583	missense	117154	exon10			AAAATTGCAGGAA	AF428101	CCDS14455.1, CCDS48140.1, CCDS55457.1	Xq21.3	2014-02-03	2014-02-03		ENSG00000126733	ENSG00000126733			16814	protein-coding gene	gene with protein product		300608	"dachshund homolog 2 (Drosophila)"				Standard	NM_053281		Approved		uc004eew.2	Q96NX9	OTTHUMG00000021944	ENST00000373125.4:c.1587G>T	chrX.hg19:g.86069740G>T	ENSP00000362217:p.Leu529Phe	115.0	0.0		136.0	17.0	NM_053281	B1AJV3|B4DQG3|Q8NAY3|Q8ND17|Q96N55	Missense_Mutation	SNP	ENST00000373125.4	hg19	CCDS14455.1	.	.	.	.	.	.	.	.	.	.	G	15.21	2.766361	0.49574	.	.	ENSG00000126733	ENST00000344497;ENST00000373131;ENST00000373125;ENST00000508860;ENST00000510272;ENST00000400297;ENST00000484479	D;D	0.90788	-2.7;-2.73	4.76	2.86	0.33363	.	0.000000	0.51477	D	0.000098	D	0.93436	0.7906	M	0.72894	2.215	0.50467	D	0.999872	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.87578	0.996;0.998;0.997;0.998	D	0.91433	0.5167	10	0.72032	D	0.01	.	7.7703	0.29004	0.0913:0.0:0.7436:0.165	.	395;529;516;529	Q1RMF5;A8K3I1;Q96NX9-2;Q96NX9	.;.;.;DACH2_HUMAN	F	529;516;529;362;310;362;194	ENSP00000362223:L516F;ENSP00000362217:L529F	ENSP00000345134:L529F	L	+	3	2	DACH2	85956396	1.000000	0.71417	0.999000	0.59377	0.622000	0.37654	0.726000	0.25984	0.212000	0.20703	0.415000	0.27848	TTG	.	.		0.443	DACH2-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359266.1	NM_053281		T	86069740	G	T	86069740	3	4	351	1	0	0	0	0	1	0	0	0	4223	1310	46	3	1625	3	DACH2	23	86069740	Missense_Mutation	SNP	G	TCGA-WJ-A86L-01A-12D-A45V-10	30419192	86069740	69200820	138	49416										
PER3	8863	hgsc.bcm.edu	37	chr1	7887311	7887311	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cgcaggggagcgcatcagaaCgcacagccctgctgcccctc	12	17	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:7887311C>T	ENST00000361923.2	+	17	2473	c.2298C>T	c.(2296-2298)aaC>aaT	p.N766N	RP3-467L1.4_ENST00000451646.1_RNA|PER3_ENST00000377532.3_Silent_p.N774N	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	766					circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		CGCATCAGAACGCACAGCCCT	0.692																																					p.N766N		Atlas-SNP	.											.	PER3	95	.	0			c.C2298T						.						37	43	41					1																	7887311		2203	4299	6502	SO:0001819	synonymous_variant	8863	exon17			TCAGAACGCACAG	BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"period (Drosophila) homolog 3", "period homolog 3 (Drosophila)"			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.2298C>T	chr1.hg19:g.7887311C>T		158.0	0.0		115.0	23.0	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Silent	SNP	ENST00000361923.2	hg19	CCDS89.1																																																																																			.	.		0.692	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831		T	7887311	C	T	7887311	2	4	352	1	0	0	0	0	0	0	0	1	11740	535	19	1		1	PER3	1	7887311	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10		7887311	241363310	1	49417										
TMEM51	55092	hgsc.bcm.edu	37	chr1	15541785	15541785	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agaccttctctgtggcctacGtgctggtcggggccggggtg	17	11	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:15541785G>A	ENST00000428417.1	+	2	648	c.202G>A	c.(202-204)Gtg>Atg	p.V68M	TMEM51_ENST00000434578.2_Missense_Mutation_p.V68M|TMEM51_ENST00000376014.3_Missense_Mutation_p.V68M|TMEM51_ENST00000376008.2_Missense_Mutation_p.V68M|TMEM51_ENST00000400796.3_Missense_Mutation_p.V68M	NM_001136217.1	NP_001129689.1	Q9NW97	TMM51_HUMAN	transmembrane protein 51	68						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(3)|large_intestine(2)|lung(5)|prostate(2)	14		Renal(390;0.00145)|Breast(348;0.00186)|Colorectal(325;0.00215)|all_lung(284;0.00459)|Lung NSC(340;0.0104)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;2.07e-06)|COAD - Colon adenocarcinoma(227;7.14e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000175)|KIRC - Kidney renal clear cell carcinoma(229;0.00141)|STAD - Stomach adenocarcinoma(313;0.00644)|READ - Rectum adenocarcinoma(331;0.0751)		TGTGGCCTACGTGCTGGTCGG	0.627																																					p.V68M		Atlas-SNP	.											.	TMEM51	28	.	0			c.G202A						.						123	115	117					1																	15541785		2203	4300	6503	SO:0001583	missense	55092	exon2			GCCTACGTGCTGG	AK098467	CCDS154.1	1p36.21	2008-02-05	2005-05-22	2005-05-22	ENSG00000171729	ENSG00000171729			25488	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 72"	C1orf72		12477932	Standard	NM_018022		Approved	FLJ10199	uc001avx.3	Q9NW97	OTTHUMG00000002046	ENST00000428417.1:c.202G>A	chr1.hg19:g.15541785G>A	ENSP00000394899:p.Val68Met	64.0	0.0		50.0	6.0	NM_018022	A8K819	Missense_Mutation	SNP	ENST00000428417.1	hg19	CCDS154.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.863707	0.91511	.	.	ENSG00000171729	ENST00000428417;ENST00000376014;ENST00000451326;ENST00000434578;ENST00000400796;ENST00000376008;ENST00000303840	T;T;T;T;T;T	0.55234	0.53;0.53;0.53;0.53;0.53;0.53	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.72969	0.3527	M	0.71581	2.175	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.75673	-0.3236	10	0.87932	D	0	-1.7495	18.2265	0.89918	0.0:0.0:1.0:0.0	.	68;68	Q9BSA0;Q9NW97	.;TMM51_HUMAN	M	68	ENSP00000394899:V68M;ENSP00000365182:V68M;ENSP00000412298:V68M;ENSP00000409665:V68M;ENSP00000383600:V68M;ENSP00000365176:V68M	ENSP00000303666:V68M	V	+	1	0	TMEM51	15414372	1.000000	0.71417	0.997000	0.53966	0.961000	0.63080	8.744000	0.91596	2.564000	0.86499	0.655000	0.94253	GTG	.	.		0.627	TMEM51-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005699.3	NM_018022		A	15541785	G	A	15541785	3	1	352	1	0	0	0	0	1	0	0	0	16192	1145	40	1	204	1	TMEM51	1	15541785	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	7654474	15541785	233708836	2	49418										
C1orf63	57035	hgsc.bcm.edu	37	chr1	25571731	25571731	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agactagctggcaagtcaatGttggttgttcctagagcttt	11	7	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:25571731G>A	ENST00000243189.7	-	3	858	c.582C>T	c.(580-582)aaC>aaT	p.N194N	C1orf63_ENST00000417642.2_Silent_p.N187N|RP3-465N24.6_ENST00000607698.1_lincRNA|C1orf63_ENST00000431849.2_Silent_p.N194N	NM_020317.3	NP_064713.3	Q9BUV0	RSRP1_HUMAN		194										breast(1)|large_intestine(1)|lung(4)|pancreas(1)	7		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;7.9e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;6.43e-07)|STAD - Stomach adenocarcinoma(196;0.000333)|BRCA - Breast invasive adenocarcinoma(304;0.000443)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.000932)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GCAAGTCAATGTTGGTTGTTC	0.378																																					p.N194N		Atlas-SNP	.											.	C1orf63	17	.	0			c.C582T						.						150	135	140					1																	25571731		2203	4300	6503	SO:0001819	synonymous_variant	57035	exon3			GTCAATGTTGGTT																												ENST00000243189.7:c.582C>T	chr1.hg19:g.25571731G>A		67.0	0.0		55.0	7.0	NM_020317	A8K917|Q49AA4|Q5TH71|Q9GZP6	Silent	SNP	ENST00000243189.7	hg19	CCDS260.1																																																																																			.	.		0.378	C1orf63-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000101966.2			A	25571731	G	A	25571731	2	1	352	1	0	0	0	0	0	0	0	1	2055	1368	48	3		3	C1orf63	1	25571731	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	10029946	25571731	223678890	3	49419										
SLC9A1	6548	hgsc.bcm.edu	37	chr1	27440501	27440501	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	caccgcccaccaggcacacgGcgtacatgaggccgcccagg	12	18	0	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:27440501G>A	ENST00000263980.3	-	2	1204	c.629C>T	c.(628-630)gCc>gTc	p.A210V	SLC9A1_ENST00000545949.1_Intron|SLC9A1_ENST00000374086.3_Missense_Mutation_p.A210V	NM_003047.4	NP_003038.2	P19634	SL9A1_HUMAN	solute carrier family 9, subfamily A (NHE1, cation proton antiporter 1), member 1	210					carbohydrate metabolic process (GO:0005975)|cardiac muscle cell differentiation (GO:0055007)|cell growth (GO:0016049)|cellular response to acidic pH (GO:0071468)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|hydrogen ion transmembrane transport (GO:1902600)|ion transport (GO:0006811)|negative regulation of apoptotic process (GO:0043066)|neuron death (GO:0070997)|positive regulation of action potential (GO:0045760)|positive regulation of cell growth (GO:0030307)|positive regulation of mitochondrial membrane permeability (GO:0035794)|protein oligomerization (GO:0051259)|regulation of intracellular pH (GO:0051453)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|regulation of the force of heart contraction (GO:0002026)|response to acidic pH (GO:0010447)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|sodium ion export (GO:0071436)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium-dependent protein binding (GO:0048306)|sodium:proton antiporter activity (GO:0015385)|solute:proton antiporter activity (GO:0015299)			central_nervous_system(1)|cervix(3)|endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	27				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;2.19e-50)|OV - Ovarian serous cystadenocarcinoma(117;1.8e-29)|Colorectal(126;7.61e-09)|COAD - Colon adenocarcinoma(152;9.32e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000521)|KIRC - Kidney renal clear cell carcinoma(1967;0.00079)|STAD - Stomach adenocarcinoma(196;0.00125)|READ - Rectum adenocarcinoma(331;0.046)	Amiloride(DB00594)	CAGGCACACGGCGTACATGAG	0.627																																					p.A210V		Atlas-SNP	.											.	SLC9A1	68	.	0			c.C629T						.						94	77	83					1																	27440501		2203	4300	6503	SO:0001583	missense	6548	exon2			CACACGGCGTACA	M81768	CCDS295.1	1p36.1-p35	2014-06-13	2012-03-22		ENSG00000090020	ENSG00000090020		"Solute carriers"	11071	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 143"	107310	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 1 (antiporter, Na+/H+, amiloride sensitive)", "solute carrier family 9 (sodium/hydrogen exchanger), member 1"	APNH, NHE1		8283968	Standard	NM_003047		Approved	PPP1R143	uc001bnm.4	P19634	OTTHUMG00000004271	ENST00000263980.3:c.629C>T	chr1.hg19:g.27440501G>A	ENSP00000263980:p.Ala210Val	87.0	0.0		93.0	25.0	NM_003047	B1ALD6|D3DPL4|Q96EM2	Missense_Mutation	SNP	ENST00000263980.3	hg19	CCDS295.1	.	.	.	.	.	.	.	.	.	.	G	32	5.150636	0.94645	.	.	ENSG00000090020	ENST00000263980;ENST00000374086	T;T	0.15139	2.45;2.45	5.8	5.8	0.92144	Cation/H+ exchanger (1);	0.045679	0.85682	D	0.000000	T	0.36690	0.0976	M	0.65498	2.005	0.80722	D	1	P;P	0.48764	0.915;0.784	P;B	0.54889	0.763;0.213	T	0.01349	-1.1378	10	0.51188	T	0.08	.	19.0453	0.93018	0.0:0.0:1.0:0.0	.	210;210	P19634-2;P19634	.;SL9A1_HUMAN	V	210	ENSP00000263980:A210V;ENSP00000363199:A210V	ENSP00000263980:A210V	A	-	2	0	SLC9A1	27313088	0.998000	0.40836	0.999000	0.59377	0.883000	0.51084	2.429000	0.44758	2.751000	0.94390	0.655000	0.94253	GCC	.	.		0.627	SLC9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012336.2	NM_003047		A	27440501	G	A	27440501	3	1	352	1	0	0	0	0	1	0	0	0	14724	1203	42	3	1862	3	SLC9A1	1	27440501	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	1868770	27440501	221810120	4	49420										
BAI2	576	hgsc.bcm.edu	37	chr1	32202242	32202242	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gcccaatgacagccaggtagGactgccaggcctcggtaagc	13	13	0	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:32202242G>A	ENST00000373658.3	-	21	3403	c.3062C>T	c.(3061-3063)tCc>tTc	p.S1021F	BAI2_ENST00000373655.2_Missense_Mutation_p.S1021F|BAI2_ENST00000398556.3_Missense_Mutation_p.S969F|BAI2_ENST00000465256.1_5'UTR|BAI2_ENST00000398538.1_Missense_Mutation_p.S1009F|BAI2_ENST00000527361.1_Missense_Mutation_p.S1021F|BAI2_ENST00000398547.1_Missense_Mutation_p.S954F|BAI2_ENST00000398542.1_Missense_Mutation_p.S954F|BAI2_ENST00000257070.4_Missense_Mutation_p.S1021F|BAI2_ENST00000440175.2_Missense_Mutation_p.S663F	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	1021					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(2)|endometrium(1)|large_intestine(7)|liver(2)|lung(24)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	55		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)		AGCCAGGTAGGACTGCCAGGC	0.632																																					p.S1021F		Atlas-SNP	.											.	BAI2	128	.	0			c.C3062T						.						80	66	71					1																	32202242		2203	4300	6503	SO:0001583	missense	576	exon21			AGGTAGGACTGCC	AB005298	CCDS72746.1, CCDS72747.1	1p35	2014-08-08			ENSG00000121753	ENSG00000121753		"-", "GPCR / Class B : Orphans"	944	protein-coding gene	gene with protein product		602683				9533023	Standard	XM_006710783		Approved		uc001btn.3	O60241	OTTHUMG00000003885	ENST00000373658.3:c.3062C>T	chr1.hg19:g.32202242G>A	ENSP00000362762:p.Ser1021Phe	168.0	0.0		133.0	10.0	NM_001703	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Missense_Mutation	SNP	ENST00000373658.3	hg19	CCDS346.2	.	.	.	.	.	.	.	.	.	.	G	22.3	4.265003	0.80358	.	.	ENSG00000121753	ENST00000398556;ENST00000398547;ENST00000373658;ENST00000373655;ENST00000398542;ENST00000257070;ENST00000527361;ENST00000440175;ENST00000398538	T;T;T;T;T;T;T;T;T	0.37058	1.22;1.22;1.22;1.22;1.22;1.22;1.22;1.22;1.22	4.66	4.66	0.58398	GPCR, family 2-like (1);	0.000000	0.40385	N	0.001110	T	0.52901	0.1763	L	0.43923	1.385	0.80722	D	1	D;D;D;D;D	0.89917	0.999;1.0;1.0;0.999;1.0	D;D;D;D;D	0.97110	0.999;0.999;0.997;1.0;0.999	T	0.51276	-0.8726	10	0.42905	T	0.14	.	17.5532	0.87882	0.0:0.0:1.0:0.0	.	1021;1009;663;1021;1021	O60241-4;O60241-3;B4DKC3;O60241-2;O60241	.;.;.;.;BAI2_HUMAN	F	969;954;1021;1021;954;1021;1021;663;1009	ENSP00000381564:S969F;ENSP00000381555:S954F;ENSP00000362762:S1021F;ENSP00000362759:S1021F;ENSP00000381550:S954F;ENSP00000257070:S1021F;ENSP00000435397:S1021F;ENSP00000391071:S663F;ENSP00000381548:S1009F	ENSP00000257070:S1021F	S	-	2	0	BAI2	31974829	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.864000	0.99589	2.312000	0.78011	0.462000	0.41574	TCC	.	.		0.632	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703		A	32202242	G	A	32202242	3	1	352	1	0	0	0	0	1	0	0	0	1299	1174	41	3	1747	3	BAI2	1	32202242	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	4761741	32202242	217048379	5	49421										
TMEM48	55706	hgsc.bcm.edu	37	chr1	54269665	54269665	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tattgagaaagcaacatcagGtcctgcaaggctaaatacta	8	8	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:54269665G>T	ENST00000371429.3	-	10	1600	c.1002C>A	c.(1000-1002)gaC>gaA	p.D334E	NDC1_ENST00000537333.1_5'UTR|NDC1_ENST00000234725.8_Missense_Mutation_p.D219E|NDC1_ENST00000540001.1_Missense_Mutation_p.D334E	NM_001168551.1|NM_018087.4	NP_001162023.1|NP_060557.3	Q9BTX1	NDC1_HUMAN	NDC1 transmembrane nucleoporin	334					mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore distribution (GO:0031081)|protein transport (GO:0015031)|spermatogenesis (GO:0007283)|synapsis (GO:0007129)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)										GCAACATCAGGTCCTGCAAGG	0.338																																					p.D334E		Atlas-SNP	.											.	TMEM48	47	.	0			c.C1002A						.						150	153	152					1																	54269665		2203	4300	6503	SO:0001583	missense	55706	exon10			CATCAGGTCCTGC	AL354613	CCDS583.1	1p32.3	2014-01-28	2013-05-23	2013-05-23	ENSG00000058804	ENSG00000058804			25525	protein-coding gene	gene with protein product	"nuclear division cycle 1 homolog (S. cerevisiae)"	610115	"transmembrane protein 48"	TMEM48		16779818, 12958361	Standard	NR_033142		Approved	FLJ10407, NET3		Q9BTX1	OTTHUMG00000008073	ENST00000371429.3:c.1002C>A	chr1.hg19:g.54269665G>T	ENSP00000360483:p.Asp334Glu	216.0	0.0		163.0	54.0	NM_018087	B4DHA3|B4DQQ5|G3XA81|Q8NB76|Q9H9T6|Q9NSG3|Q9NSG4|Q9NVZ7	Missense_Mutation	SNP	ENST00000371429.3	hg19	CCDS583.1	.	.	.	.	.	.	.	.	.	.	G	19.58	3.854563	0.71719	.	.	ENSG00000058804	ENST00000371429;ENST00000360494;ENST00000540001;ENST00000234725	T;T;T	0.28895	1.59;1.59;1.59	5.62	3.73	0.42828	.	0.044992	0.85682	D	0.000000	T	0.45657	0.1353	M	0.73962	2.25	0.52099	D	0.999945	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.56456	-0.7976	10	0.02654	T	1	.	8.8221	0.35032	0.2294:0.0:0.7706:0.0	.	294;334	B4DHA3;Q9BTX1	.;NDC1_HUMAN	E	334;334;334;219	ENSP00000360483:D334E;ENSP00000440873:D334E;ENSP00000234725:D219E	ENSP00000234725:D219E	D	-	3	2	TMEM48	54042253	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.577000	0.46042	1.381000	0.46364	0.543000	0.68304	GAC	.	.		0.338	NDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022101.1	NM_018087		T	54269665	G	T	54269665	3	4	352	1	0	0	0	0	1	0	0	0	16187	1252	44	3	1058	3	TMEM48	1	54269665	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	22067423	54269665	194980956	6	49422										
JUN	3725	hgsc.bcm.edu	37	chr1	59247776	59247776	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ttgcaactgctgcgttagcaTgagttggcacccactgttaa	10	10	0	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:59247776T>C	ENST00000371222.2	-	1	2009	c.967A>G	c.(967-969)Atg>Gtg	p.M323V		NM_002228.3	NP_002219.1	P05412	JUN_HUMAN	jun proto-oncogene	323					aging (GO:0007568)|angiogenesis (GO:0001525)|axon regeneration (GO:0031103)|cellular response to calcium ion (GO:0071277)|cellular response to potassium ion starvation (GO:0051365)|circadian rhythm (GO:0007623)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|leading edge cell differentiation (GO:0035026)|learning (GO:0007612)|liver development (GO:0001889)|membrane depolarization (GO:0051899)|microglial cell activation (GO:0001774)|monocyte differentiation (GO:0030224)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA binding (GO:0043392)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress (GO:1990441)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA replication (GO:0045740)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of monocyte differentiation (GO:0045657)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle (GO:0051726)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|release of cytochrome c from mitochondria (GO:0001836)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|SMAD protein import into nucleus (GO:0007184)|SMAD protein signal transduction (GO:0060395)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nuclear chromosome (GO:0000228)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	cAMP response element binding (GO:0035497)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|R-SMAD binding (GO:0070412)|Rho GTPase activator activity (GO:0005100)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|kidney(2)|lung(5)|skin(1)	10	all_cancers(7;8.55e-07)				Arsenic trioxide(DB01169)|Irbesartan(DB01029)|Pseudoephedrine(DB00852)|Vinblastine(DB00570)	TGCGTTAGCATGAGTTGGCAC	0.498			A		sarcoma						OREG0013518	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.M323V		Atlas-SNP	.		Dom	yes		1	1p32-p31	3725	jun oncogene		M	.	JUN	26	.	0			c.A967G						.						114	111	112					1																	59247776		2203	4300	6503	SO:0001583	missense	3725	exon1			TTAGCATGAGTTG	AY217548	CCDS610.1	1p32-p31	2013-01-10	2010-08-27		ENSG00000177606	ENSG00000177606		"basic leucine zipper proteins"	6204	protein-coding gene	gene with protein product		165160	"v-jun avian sarcoma virus 17 oncogene homolog", "v-jun sarcoma virus 17 oncogene homolog (avian)", "jun oncogene"			3194415	Standard	NM_002228		Approved	c-Jun, AP-1	uc001cze.3	P05412	OTTHUMG00000008376	ENST00000371222.2:c.967A>G	chr1.hg19:g.59247776T>C	ENSP00000360266:p.Met323Val	131.0	0.0	1037	87.0	33.0	NM_002228	Q6FHM7|Q96G93	Missense_Mutation	SNP	ENST00000371222.2	hg19	CCDS610.1	.	.	.	.	.	.	.	.	.	.	T	14.20	2.463108	0.43736	.	.	ENSG00000177606	ENST00000371222	T	0.22945	1.93	4.09	4.09	0.47781	.	0.045766	0.85682	D	0.000000	T	0.30039	0.0752	L	0.54323	1.7	0.58432	D	0.999993	P	0.37985	0.613	B	0.41466	0.358	T	0.16276	-1.0408	10	0.72032	D	0.01	-20.9304	13.2541	0.60068	0.0:0.0:0.0:1.0	.	323	P05412	JUN_HUMAN	V	323	ENSP00000360266:M323V	ENSP00000360266:M323V	M	-	1	0	JUN	59020364	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.044000	0.71012	1.713000	0.51359	0.459000	0.35465	ATG	.	.		0.498	JUN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023042.1	NM_002228		C	59247776	T	C	59247776	3	2	352	1	0	0	0	0	1	0	0	0	7978	1464	51	2	32	2	JUN	1	59247776	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	4978111	59247776	190002845	7	49423										
C1orf87	127795	hgsc.bcm.edu	37	chr1	60506733	60506733	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	taagctttctcctgggaatgCcatgcacataggataaggac	10	9	1	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:60506733C>A	ENST00000371201.3	-	4	520	c.413G>T	c.(412-414)gGc>gTc	p.G138V	C1orf87_ENST00000450089.2_Intron	NM_152377.2	NP_689590.1	Q8N0U7	CA087_HUMAN	chromosome 1 open reading frame 87	138							calcium ion binding (GO:0005509)			breast(2)|endometrium(2)|large_intestine(6)|lung(19)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33						CCTGGGAATGCCATGCACATA	0.483																																					p.G138V	NSCLC(75;811 1386 4923 13371 51772)	Atlas-SNP	.											.	C1orf87	55	.	0			c.G413T						.						141	121	128					1																	60506733		2203	4300	6503	SO:0001583	missense	127795	exon4			GGAATGCCATGCA	AK124828	CCDS614.1	1p32.1	2014-04-03			ENSG00000162598	ENSG00000162598			28547	protein-coding gene	gene with protein product	"carcinoma-related EF-hand protein"					12477932	Standard	NM_152377		Approved	MGC34837, CREF	uc001czs.2	Q8N0U7	OTTHUMG00000008992	ENST00000371201.3:c.413G>T	chr1.hg19:g.60506733C>A	ENSP00000360244:p.Gly138Val	205.0	0.0		177.0	79.0	NM_152377	Q6ZU07|Q8IVS0	Missense_Mutation	SNP	ENST00000371201.3	hg19	CCDS614.1	.	.	.	.	.	.	.	.	.	.	C	14.43	2.534068	0.45073	.	.	ENSG00000162598	ENST00000371201	T	0.22743	1.94	5.25	4.33	0.51752	.	0.215706	0.33040	N	0.005349	T	0.34803	0.0910	L	0.56769	1.78	0.80722	D	1	D	0.57257	0.979	P	0.61658	0.892	T	0.09796	-1.0658	10	0.72032	D	0.01	-7.3235	7.2841	0.26328	0.0:0.7404:0.1704:0.0892	.	138	Q8N0U7	CA087_HUMAN	V	138	ENSP00000360244:G138V	ENSP00000360244:G138V	G	-	2	0	C1orf87	60279321	0.959000	0.32827	0.915000	0.36163	0.292000	0.27327	0.389000	0.20751	1.445000	0.47624	0.305000	0.20034	GGC	.	.		0.483	C1orf87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024943.1	NM_152377		A	60506733	C	A	60506733	3	1	352	1	0	0	0	0	1	0	0	0	2066	739	26	3	1263	3	C1orf87	1	60506733	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	1258957	60506733	188743888	8	49424										
IL12RB2	3595	hgsc.bcm.edu	37	chr1	67852322	67852322	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cattgctatcatcatggtggGcattttctcaacgcattact	7	10	3	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:67852322G>A	ENST00000262345.1	+	14	2556	c.1916G>A	c.(1915-1917)gGc>gAc	p.G639D	IL12RB2_ENST00000371000.1_Missense_Mutation_p.G639D|IL12RB2_ENST00000544434.1_Missense_Mutation_p.G553D|IL12RB2_ENST00000541374.1_Missense_Mutation_p.G639D|IL12RB2_ENST00000465396.1_3'UTR	NM_001559.2	NP_001550.1	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2	639					cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma production (GO:0032609)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interferon-gamma production (GO:0032729)|response to lipopolysaccharide (GO:0032496)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(21)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	45						ATCATGGTGGGCATTTTCTCA	0.418																																					p.G639D		Atlas-SNP	.											.	IL12RB2	94	.	0			c.G1916A						.						227	192	204					1																	67852322		2203	4300	6503	SO:0001583	missense	3595	exon14			TGGTGGGCATTTT	U64198	CCDS638.1, CCDS58006.1, CCDS58007.1, CCDS72805.1	1p31.3-p31.2	2014-07-15			ENSG00000081985	ENSG00000081985		"Interleukins and interleukin receptors", "Fibronectin type III domain containing"	5972	protein-coding gene	gene with protein product		601642				9284929, 8943050	Standard	NM_001559		Approved		uc001ddu.3	Q99665	OTTHUMG00000009094	ENST00000262345.1:c.1916G>A	chr1.hg19:g.67852322G>A	ENSP00000262345:p.Gly639Asp	172.0	0.0		123.0	54.0	NM_001559	B1AN98|B7ZKL9|F5H7L6|Q2M3V3	Missense_Mutation	SNP	ENST00000262345.1	hg19	CCDS638.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.095174	0.76870	.	.	ENSG00000081985	ENST00000262345;ENST00000371000;ENST00000541374;ENST00000544434	T;T;T;T	0.46063	0.88;1.01;1.01;1.55	4.96	4.96	0.65561	.	0.348277	0.34291	N	0.004086	T	0.52158	0.1717	M	0.67953	2.075	0.40844	D	0.983698	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.993;0.982;0.995	T	0.48811	-0.9002	10	0.35671	T	0.21	-21.2028	14.0762	0.64891	0.0:0.0:1.0:0.0	.	553;639;639	F5H7L6;Q99665-2;Q99665	.;.;I12R2_HUMAN	D	639;639;639;553	ENSP00000262345:G639D;ENSP00000360039:G639D;ENSP00000445276:G639D;ENSP00000442443:G553D	ENSP00000262345:G639D	G	+	2	0	IL12RB2	67624910	0.989000	0.36119	0.987000	0.45799	0.983000	0.72400	1.871000	0.39539	2.469000	0.83416	0.551000	0.68910	GGC	.	.		0.418	IL12RB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025202.2	NM_001559		A	67852322	G	A	67852322	3	1	352	1	0	0	0	0	1	0	0	0	7636	1203	42	3	1966	3	IL12RB2	1	67852322	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	7345589	67852322	181398299	9	49425										
DEPDC1	55635	hgsc.bcm.edu	37	chr1	68948426	68948427	+	Frame_Shift_Ins	INS	-	-	T													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tagaatctgattcttctttgINStttttttctctatgaagcag							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:68948426_68948427insT	ENST00000456315.2	-	8	1178_1179	c.1064_1065insA	c.(1063-1065)aacfs	p.N355fs	RP4-694A7.2_ENST00000425820.1_RNA|DEPDC1_ENST00000370966.5_Intron	NM_001114120.1	NP_001107592.1	Q5TB30	DEP1A_HUMAN	DEP domain containing 1	355					intracellular signal transduction (GO:0035556)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	GTPase activator activity (GO:0005096)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13				OV - Ovarian serous cystadenocarcinoma(397;7.21e-36)		ATTCTTCTTTGTTTTTTTCTCT	0.342																																					p.N355fs		Atlas-INDEL	.											.	DEPDC1	102	.	0			c.1065_1066insA						.																																			SO:0001589	frameshift_variant	55635	exon8			.	AK000361	CCDS644.1, CCDS44159.1	1p31.2	2008-08-19			ENSG00000024526	ENSG00000024526			22949	protein-coding gene	gene with protein product		612002					Standard	NM_001114120		Approved	DEP.8, FLJ20354, SDP35, DEPDC1A	uc001dem.4	Q5TB30	OTTHUMG00000009212	ENST00000456315.2:c.1065dupA	chr1.hg19:g.68948433_68948433dupT	ENSP00000412292:p.Asn355fs	148.0	0.0		77.0	21.0	NM_001114120	A8QXE0|A8QXE1|Q05DU3|Q5TB28|Q9H9I3|Q9NX21|Q9NXZ0	Frame_Shift_Ins	INS	ENST00000456315.2	hg19	CCDS44159.1																																																																																			.	.		0.342	DEPDC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025514.2	NM_017779		T	68948427	-	T	68948426	7	5	352	1	0	1	1	0	0	0	0	0	4441	1368	48	0	1390	0	DEPDC1	1	68948426	Frame_Shift_Ins	INS	-	TCGA-WQ-A9G7-01A-11D-A36X-10	1096104	68948426	180302195	10	49426										
HS2ST1	9653	hgsc.bcm.edu	37	chr1	87563588	87563588	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gaagctctggcttcaaatccCgttcttctgtggccatagct	9	12	4	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:87563588C>A	ENST00000370550.5	+	5	1019	c.656C>A	c.(655-657)cCg>cAg	p.P219Q	RP5-1052I5.2_ENST00000370548.2_Missense_Mutation_p.P193Q|HS2ST1_ENST00000370551.4_Missense_Mutation_p.P219Q|HS2ST1_ENST00000356813.4_Missense_Mutation_p.P193Q	NM_012262.3	NP_036394.1	Q7LGA3	HS2ST_HUMAN	heparan sulfate 2-O-sulfotransferase 1	219					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	sulfotransferase activity (GO:0008146)	p.P219L(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)	9		Lung NSC(277;0.153)		all cancers(265;0.00699)|Epithelial(280;0.0261)		CTTCAAATCCCGTTCTTCTGT	0.453																																					p.P219Q		Atlas-SNP	.											HS2ST1_ENST00000370548,NS,malignant_melanoma,+1,1	HS2ST1	43	.	1	Substitution - Missense(1)	large_intestine(1)	c.C656A						.						152	144	147					1																	87563588		2203	4300	6503	SO:0001583	missense	9653	exon5			AAATCCCGTTCTT	AB007917	CCDS711.1, CCDS44171.1	1p22.3	2008-02-05			ENSG00000153936	ENSG00000153936		"Sulfotransferases, membrane-bound"	5193	protein-coding gene	gene with protein product		604844				9455484	Standard	NM_012262		Approved	KIAA0448	uc010osk.2	Q7LGA3	OTTHUMG00000010255	ENST00000370550.5:c.656C>A	chr1.hg19:g.87563588C>A	ENSP00000359581:p.Pro219Gln	103.0	0.0		166.0	33.0	NM_012262	D3DT22|O75036|Q32NB5|Q8TAC5|Q9H441|Q9NUJ9	Missense_Mutation	SNP	ENST00000370550.5	hg19	CCDS711.1	.	.	.	.	.	.	.	.	.	.	C	34	5.342786	0.95783	.	.	ENSG00000153936	ENST00000370551;ENST00000370550;ENST00000370548;ENST00000356813	D;D;D	0.81739	-1.53;-1.53;-1.53	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	D	0.87819	0.6273	M	0.76170	2.325	0.80722	D	1	D;D	0.89917	1.0;0.987	D;P	0.78314	0.991;0.891	D	0.85234	0.1034	10	0.35671	T	0.21	-34.4699	19.6092	0.95599	0.0:1.0:0.0:0.0	.	219;193	Q7LGA3;Q7LGA3-2	HS2ST_HUMAN;.	Q	219;219;193;193	ENSP00000359581:P219Q;ENSP00000359579:P193Q;ENSP00000349268:P193Q	ENSP00000349268:P193Q	P	+	2	0	HS2ST1	87336176	1.000000	0.71417	0.983000	0.44433	0.964000	0.63967	7.776000	0.85560	2.693000	0.91896	0.655000	0.94253	CCG	.	.		0.453	HS2ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028279.2	NM_012262		A	87563588	C	A	87563588	3	1	352	1	0	0	0	0	1	0	0	0	7371	652	23	1	674	1	HS2ST1	1	87563588	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	18615162	87563588	161687033	11	49427										
GBP3	2635	hgsc.bcm.edu	37	chr1	89476691	89476693	+	In_Frame_Del	DEL	CTT	CTT	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cgaataaattcccgccttcaCttcttcttctagaggactga							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:89476691_89476693delCTT	ENST00000370481.4	-	8	1476_1478	c.1256_1258delAAG	c.(1255-1260)gaagtg>gtg	p.E419del		NM_018284.2	NP_060754.2	Q8WXF7	ATLA1_HUMAN	guanylate binding protein 3	0					axonogenesis (GO:0007409)|cell death (GO:0008219)|endoplasmic reticulum organization (GO:0007029)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi cis cisterna (GO:0000137)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	26		Lung NSC(277;0.123)		all cancers(265;0.0103)|Epithelial(280;0.0293)		CCCGCCTTCACTTCTTCTTCTAG	0.419																																					p.419_420del		Atlas-INDEL	.											.	GBP3	53	.	0			c.1257_1259del						.																																			SO:0001651	inframe_deletion	2635	exon8			.	BC063819	CCDS717.2	1p22.2	2008-02-05			ENSG00000117226	ENSG00000117226			4184	protein-coding gene	gene with protein product		600413				7518790	Standard	NM_018284		Approved	FLJ10961	uc001dmt.3	Q9H0R5	OTTHUMG00000010616	ENST00000370481.4:c.1256_1258delAAG	chr1.hg19:g.89476697_89476699delCTT	ENSP00000359512:p.Glu419del	89.0	0.0		145.0	69.0	NM_018284	A6NND5|A8K2C0|G5E9T1|O95890|Q69YH7|Q96FK0	In_Frame_Del	DEL	ENST00000370481.4	hg19	CCDS717.2																																																																																			.	.		0.419	GBP3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313541.3	NM_018284		-	89476693	CTT	-	89476691	7	5	352	1	0	1	0	1	0	0	0	0	6283	565	20	0	545	0	GBP3	1	89476691	In_Frame_Del	DEL	CTT	TCGA-WQ-A9G7-01A-11D-A36X-10	1913103	89476691	159773930	12	49428										
GBP7	388646	hgsc.bcm.edu	37	chr1	89615112	89615112	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggggaatctcacttgctgggCcatctgctggctgtagtggt	15	9	2	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:89615112C>T	ENST00000294671.2	-	7	1153	c.1015G>A	c.(1015-1017)Gcc>Acc	p.A339T		NM_207398.2	NP_997281.2	Q8N8V2	GBP7_HUMAN	guanylate binding protein 7	339						membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Lung NSC(277;0.0908)		all cancers(265;0.00835)|Epithelial(280;0.0322)		ACTTGCTGGGCCATCTGCTGG	0.562																																					p.A339T		Atlas-SNP	.											.	GBP7	57	.	0			c.G1015A						.						122	109	113					1																	89615112		2203	4300	6503	SO:0001583	missense	388646	exon7			GCTGGGCCATCTG	AK096141	CCDS720.1	1p22.2	2008-02-05			ENSG00000213512	ENSG00000213512			29606	protein-coding gene	gene with protein product		612468					Standard	NM_207398		Approved	FLJ38822, GBP4L	uc001dna.2	Q8N8V2	OTTHUMG00000010659	ENST00000294671.2:c.1015G>A	chr1.hg19:g.89615112C>T	ENSP00000294671:p.Ala339Thr	113.0	0.0		151.0	11.0	NM_207398		Missense_Mutation	SNP	ENST00000294671.2	hg19	CCDS720.1	.	.	.	.	.	.	.	.	.	.	C	7.777	0.708730	0.15239	.	.	ENSG00000213512	ENST00000294671	T	0.02140	4.43	3.37	1.38	0.22167	Guanylate-binding protein, C-terminal (3);	0.444655	0.24647	N	0.036752	T	0.00724	0.0024	L	0.38733	1.17	0.27072	N	0.963298	B	0.26672	0.156	B	0.29267	0.1	T	0.48163	-0.9059	10	0.38643	T	0.18	.	5.773	0.18263	0.0:0.6276:0.0:0.3724	.	339	Q8N8V2	GBP7_HUMAN	T	339	ENSP00000294671:A339T	ENSP00000294671:A339T	A	-	1	0	GBP7	89387700	0.022000	0.18835	0.997000	0.53966	0.056000	0.15407	0.010000	0.13242	0.629000	0.30376	0.390000	0.25778	GCC	.	.		0.562	GBP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029401.1	NM_207398		T	89615112	C	T	89615112	3	4	352	1	0	0	0	0	1	0	0	0	6287	739	26	3	921	3	GBP7	1	89615112	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	138421	89615112	159635509	13	49429										
LRRC8D	55144	hgsc.bcm.edu	37	chr1	90400489	90400498	+	Frame_Shift_Del	DEL	ACGGCACTAA	ACGGCACTAA	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aaagttagtcattcataatgAcggcactaaactcttggtac					rs372637181		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	ACGGCACTAA	ACGGCACTAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:90400489_90400498delACGGCACTAA	ENST00000337338.5	+	3	2269_2278	c.1862_1871delACGGCACTAA	c.(1861-1872)gacggcactaaafs	p.DGTK621fs	LRRC8D_ENST00000394593.3_Frame_Shift_Del_p.DGTK621fs	NM_001134479.1	NP_001127951.1	Q7L1W4	LRC8D_HUMAN	leucine rich repeat containing 8 family, member D	621					ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(2)|skin(1)	29		all_lung(203;0.0894)|Lung NSC(277;0.227)		all cancers(265;0.0109)|Epithelial(280;0.0427)		ATTCATAATGACGGCACTAAACTCTTGGTA	0.438																																					p.621_624del		Atlas-INDEL	.											.	LRRC8D	78	.	0			c.1861_1870del						.																																			SO:0001589	frameshift_variant	55144	exon3			.	AK001332	CCDS726.1	1p22.2	2008-02-05	2005-06-29	2005-06-29	ENSG00000171492	ENSG00000171492			16992	protein-coding gene	gene with protein product		612890	"leucine rich repeat containing 5"	LRRC5			Standard	NM_018103		Approved	FLJ10470	uc001dnn.3	Q7L1W4	OTTHUMG00000010583	ENST00000337338.5:c.1862_1871delACGGCACTAA	chr1.hg19:g.90400489_90400498delACGGCACTAA	ENSP00000338887:p.Asp621fs	107.0	0.0		152.0	16.0	NM_018103	D3DT29|Q6UWB2|Q9NVW3	Frame_Shift_Del	DEL	ENST00000337338.5	hg19	CCDS726.1																																																																																			.	.		0.438	LRRC8D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029203.2	NM_018103		-	90400498	ACGGCACTAA	-	90400489	7	5	352	1	0	1	0	1	0	0	0	0	9033	275	10	0	1864	0	LRRC8D	1	90400489	Frame_Shift_Del	DEL	ACGGCACTAA	TCGA-WQ-A9G7-01A-11D-A36X-10	785377	90400489	158850132	14	49430										
BARHL2	343472	hgsc.bcm.edu	37	chr1	91182580	91182580	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gagaagaaggcgccgtccctAcggtatcaatctccgaacag	11	12	2	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:91182580A>G	ENST00000370445.4	-	1	214	c.173T>C	c.(172-174)gTa>gCa	p.V58A		NM_020063.1	NP_064447.1	Q9NY43	BARH2_HUMAN	BarH-like homeobox 2	58					cell fate determination (GO:0001709)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|positive regulation of translation (GO:0045727)|regulation of axon extension (GO:0030516)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)			cervix(2)|endometrium(1)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24		all_lung(203;0.0263)|Lung SC(238;0.128)		all cancers(265;0.000897)|Epithelial(280;0.00516)|OV - Ovarian serous cystadenocarcinoma(397;0.211)		CGCCGTCCCTACGGTATCAAT	0.607																																					p.V58A	GBM(199;3561 4100 22440)	Atlas-SNP	.											.	BARHL2	62	.	0			c.T173C						.						69	77	74					1																	91182580		2203	4300	6503	SO:0001583	missense	343472	exon1			GTCCCTACGGTAT	AJ251753	CCDS730.1	1p22.2	2011-07-08	2007-07-09		ENSG00000143032	ENSG00000143032		"Homeoboxes / ANTP class : NKL subclass"	954	protein-coding gene	gene with protein product		605212	"BarH (Drosophila)-like 2"				Standard	NM_020063		Approved		uc001dns.3	Q9NY43	OTTHUMG00000010020	ENST00000370445.4:c.173T>C	chr1.hg19:g.91182580A>G	ENSP00000359474:p.Val58Ala	137.0	0.0		253.0	23.0	NM_020063	A0AVP2|Q7Z4N7	Missense_Mutation	SNP	ENST00000370445.4	hg19	CCDS730.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.728580	0.89390	.	.	ENSG00000143032	ENST00000370445	D	0.94000	-3.33	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	D	0.89908	0.6851	N	0.24115	0.695	0.58432	D	0.999997	D	0.58970	0.984	D	0.68192	0.956	D	0.87867	0.2668	10	0.08837	T	0.75	.	14.3156	0.66450	1.0:0.0:0.0:0.0	.	58	Q9NY43	BARH2_HUMAN	A	58	ENSP00000359474:V58A	ENSP00000359474:V58A	V	-	2	0	BARHL2	90955168	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	8.097000	0.89539	2.267000	0.75376	0.528000	0.53228	GTA	.	.		0.607	BARHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027728.2			G	91182580	A	G	91182580	3	3	352	1	0	0	0	0	1	0	0	0	1314	391	14	2	1002	2	BARHL2	1	91182580	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	782091	91182580	158068041	15	49431										
CDC7	8317	hgsc.bcm.edu	37	chr1	91985737	91985737	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ttctttctttgcttagtggaCgatatccattttataaagca	6	7	2	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:91985737C>T	ENST00000428239.1	+	11	1490	c.1231C>T	c.(1231-1233)Cga>Tga	p.R411*	CDC7_ENST00000234626.6_Nonsense_Mutation_p.R411*|CDC7_ENST00000430031.2_Nonsense_Mutation_p.R383*	NM_001134420.1	NP_001127892.1	O00311	CDC7_HUMAN	cell division cycle 7	411	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle phase transition (GO:0044770)|cell division (GO:0051301)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|stomach(2)	23		all_lung(203;0.0165)|Lung NSC(277;0.0562)		all cancers(265;0.00108)|Epithelial(280;0.0184)|KIRC - Kidney renal clear cell carcinoma(1967;0.124)		GCTTAGTGGACGATATCCATT	0.328																																					p.R411X		Atlas-SNP	.											.	CDC7	74	.	0			c.C1231T						.						120	121	121					1																	91985737		2203	4300	6503	SO:0001587	stop_gained	8317	exon11			AGTGGACGATATC	AF015592	CCDS734.1	1p22	2013-01-17	2013-01-17	2003-07-23	ENSG00000097046	ENSG00000097046			1745	protein-coding gene	gene with protein product		603311	"CDC7 (cell division cycle 7, S. cerevisiae, homolog)-like 1", "CDC7 cell division cycle 7 (S. cerevisiae)", "cell division cycle 7 (S. cerevisiae)", "cell division cycle 7 homolog (S. cerevisiae)"	CDC7L1		9405610, 9250678	Standard	NM_003503		Approved	Hsk1, huCdc7, HsCdc7	uc001dof.3	O00311	OTTHUMG00000047810	ENST00000428239.1:c.1231C>T	chr1.hg19:g.91985737C>T	ENSP00000393139:p.Arg411*	104.0	0.0		167.0	33.0	NM_001134419	D3DT31|O00558|Q5T5U5	Nonsense_Mutation	SNP	ENST00000428239.1	hg19	CCDS734.1	.	.	.	.	.	.	.	.	.	.	C	37	6.097844	0.97281	.	.	ENSG00000097046	ENST00000430031;ENST00000234626;ENST00000428239	.	.	.	5.69	3.82	0.43975	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-26.5105	8.5322	0.33342	0.2741:0.6567:0.0:0.0693	.	.	.	.	X	383;411;411	.	ENSP00000234626:R411X	R	+	1	2	CDC7	91758325	1.000000	0.71417	0.999000	0.59377	0.984000	0.73092	2.718000	0.47236	0.758000	0.33059	0.455000	0.32223	CGA	.	.		0.328	CDC7-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027928.1	NM_003503		T	91985737	C	T	91985737	4	4	352	1	0	0	0	0	0	1	0	0	3086	528	19	1	1269	1	CDC7	1	91985737	Nonsense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	803157	91985737	157264884	16	49432										
CDC14A	8556	hgsc.bcm.edu	37	chr1	100889837	100889837	+	Frame_Shift_Del	DEL	C	C	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gcactcctgtctggctcaaaCcccccctatcttccattcag							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:100889837delC	ENST00000336454.3	+	5	724	c.369delC	c.(367-369)aacfs	p.N123fs	CDC14A_ENST00000370125.2_Frame_Shift_Del_p.N123fs|CDC14A_ENST00000542213.1_Frame_Shift_Del_p.N65fs|CDC14A_ENST00000544534.1_Frame_Shift_Del_p.N123fs|CDC14A_ENST00000370124.3_Frame_Shift_Del_p.N123fs|CDC14A_ENST00000469387.1_3'UTR|CDC14A_ENST00000361544.6_Frame_Shift_Del_p.N123fs	NM_003672.3	NP_003663.2	Q9UNH5	CC14A_HUMAN	cell division cycle 14A	123	A.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|endometrium(5)|kidney(6)|large_intestine(6)|lung(10)|skin(2)|urinary_tract(1)	31		all_epithelial(167;3.71e-06)|all_lung(203;0.00097)|Lung NSC(277;0.001)		Epithelial(280;0.0676)|all cancers(265;0.127)|COAD - Colon adenocarcinoma(174;0.201)|Lung(183;0.227)|Colorectal(144;0.241)		CTGGCTCAAACCCCCCCTATC	0.403																																					p.N123fs		Atlas-INDEL	.											.,1	CDC14A	65	.	0			c.368delA						.						95	99	98					1																	100889837		2203	4300	6503	SO:0001589	frameshift_variant	8556	exon5			.	AF000367	CCDS769.1, CCDS770.1, CCDS771.1	1p21	2013-01-17	2013-01-17		ENSG00000079335	ENSG00000079335		"Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"	1718	protein-coding gene	gene with protein product		603504	"CDC10 (cell division cycle 10, S. cerevisiae, homolog)", "CDC14 cell division cycle 14 homolog A (S. cerevisiae)"			9367992, 10409437	Standard	NM_033312		Approved	Cdc14A1, Cdc14A2, cdc14	uc001dtf.2	Q9UNH5	OTTHUMG00000010987	ENST00000336454.3:c.369delC	chr1.hg19:g.100889837delC	ENSP00000336739:p.Asn123fs	119.0	0.0		105.0	40.0	NM_033313	A6MA65|B1AQ14|B1AQ15|O43171|O60727|O60728|Q52LH9|Q8IXX0	Frame_Shift_Del	DEL	ENST00000336454.3	hg19	CCDS769.1																																																																																			.	.		0.403	CDC14A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000030220.1	NM_033312		-	100889837	C	-	100889837	7	5	352	1	0	1	0	1	0	0	0	0	3058	506	18	0	387	0	CDC14A	1	100889837	Frame_Shift_Del	DEL	C	TCGA-WQ-A9G7-01A-11D-A36X-10	8904100	100889837	148360784	17	49433										
CHI3L2	1117	hgsc.bcm.edu	37	chr1	111773538	111773538	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	caagagtgaagtgatgctctAccagaccatcaacagtctca	8	11	3	4			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:111773538A>G	ENST00000445067.2	+	5	1016	c.245A>G	c.(244-246)tAc>tGc	p.Y82C	CHI3L2_ENST00000369744.2_Missense_Mutation_p.Y72C|CHI3L2_ENST00000369748.4_Missense_Mutation_p.Y82C|CHI3L2_ENST00000466741.1_Missense_Mutation_p.Y3C|CHI3L2_ENST00000524472.1_Missense_Mutation_p.Y3C			Q15782	CH3L2_HUMAN	chitinase 3-like 2	82					carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)	extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(8)|prostate(1)	19		all_cancers(81;1.89e-05)|all_epithelial(167;7.36e-06)|all_lung(203;0.00018)|Lung NSC(277;0.000359)		Lung(183;0.0171)|Colorectal(144;0.0387)|all cancers(265;0.0464)|LUSC - Lung squamous cell carcinoma(189;0.0872)|Epithelial(280;0.0994)|COAD - Colon adenocarcinoma(174;0.141)		GTGATGCTCTACCAGACCATC	0.448																																					p.Y82C		Atlas-SNP	.											.	CHI3L2	38	.	0			c.A245G						.						72	59	63					1																	111773538		2203	4300	6503	SO:0001583	missense	1117	exon3			TGCTCTACCAGAC	U49835	CCDS30802.1, CCDS30803.1, CCDS41367.1	1p13.3	2008-02-05			ENSG00000064886	ENSG00000064886			1933	protein-coding gene	gene with protein product		601526				8702629	Standard	NM_001025197		Approved	YKL-39, YKL39	uc001eam.3	Q15782	OTTHUMG00000012174	ENST00000445067.2:c.245A>G	chr1.hg19:g.111773538A>G	ENSP00000437082:p.Tyr82Cys	100.0	0.0		100.0	18.0	NM_004000	A6NNY3|B4DPR7|Q15749|Q15783|Q5VUV7|Q96F97	Missense_Mutation	SNP	ENST00000445067.2	hg19	CCDS30802.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.71|14.71	2.616037|2.616037	0.46631|0.46631	.|.	.|.	ENSG00000064886|ENSG00000064886	ENST00000533831|ENST00000445067;ENST00000528451;ENST00000486561;ENST00000369744;ENST00000369748;ENST00000474304;ENST00000466741;ENST00000477185;ENST00000467038;ENST00000497587;ENST00000524472	.|T;T;T;T;T;T;T;T;T;T	.|0.15487	.|3.33;3.33;3.33;3.33;3.33;3.33;3.33;2.42;3.33;3.33	3.77|3.77	1.37|1.37	0.22104|0.22104	.|Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	.|0.874363	.|0.09496	.|N	.|0.794310	T|T	0.36496|0.36496	0.0969|0.0969	H|H	0.96833|0.96833	3.89|3.89	0.20821|0.20821	N|N	0.999849|0.999849	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.81914	.|0.995;0.995;0.995	T|T	0.09037|0.09037	-1.0693|-1.0693	5|10	.|0.87932	.|D	.|0	0.5251|0.5251	5.0021|5.0021	0.14269|0.14269	0.711:0.1847:0.1043:0.0|0.711:0.1847:0.1043:0.0	.|.	.|3;72;82	.|B4DPR7;A6NNY3;Q15782	.|.;.;CH3L2_HUMAN	A|C	51|82;82;82;72;82;82;3;3;3;3;3	.|ENSP00000437082:Y82C;ENSP00000436077:Y82C;ENSP00000431968:Y82C;ENSP00000358759:Y72C;ENSP00000358763:Y82C;ENSP00000437086:Y3C;ENSP00000436272:Y3C;ENSP00000431978:Y3C;ENSP00000436006:Y3C;ENSP00000432049:Y3C	.|ENSP00000358759:Y72C	T|Y	+|+	1|2	0|0	CHI3L2|CHI3L2	111575061|111575061	0.992000|0.992000	0.36948|0.36948	0.003000|0.003000	0.11579|0.11579	0.054000|0.054000	0.15201|0.15201	4.154000|4.154000	0.58125|0.58125	0.068000|0.068000	0.16574|0.16574	0.533000|0.533000	0.62120|0.62120	ACC|TAC	.	.		0.448	CHI3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033669.4	NM_004000		G	111773538	A	G	111773538	3	3	352	1	0	0	0	0	1	0	0	0	3343	391	14	2	255	2	CHI3L2	1	111773538	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	10883701	111773538	137477083	18	49434										
SPAG17	200162	hgsc.bcm.edu	37	chr1	118539117	118539117	+	Frame_Shift_Del	DEL	A	A	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gatccatcagcatacataacAaaaaacctatttgaagaaat							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:118539117delA	ENST00000336338.5	-	34	4994	c.4929delT	c.(4927-4929)tttfs	p.F1643fs		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1643						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		CATACATAACAAAAAACCTAT	0.284																																					p.V1644fs		Atlas-INDEL	.											.	SPAG17	263	.	0			c.4930delG						.						55	60	59					1																	118539117		2203	4299	6502	SO:0001589	frameshift_variant	200162	exon34			.		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.4929delT	chr1.hg19:g.118539117delA	ENSP00000337804:p.Phe1643fs	175.0	0.0		299.0	42.0	NM_206996	Q8NAZ1|Q9NT21	Frame_Shift_Del	DEL	ENST00000336338.5	hg19	CCDS899.1																																																																																			.	.		0.284	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		-	118539117	A	-	118539117	7	5	352	1	0	1	0	1	0	0	0	0	14994	127	5	0	1802	0	SPAG17	1	118539117	Frame_Shift_Del	DEL	A	TCGA-WQ-A9G7-01A-11D-A36X-10	6765579	118539117	130711504	19	49435										
HSD3B1	3283	hgsc.bcm.edu	37	chr1	120057162	120057162	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gaaggctcagcgagatctggCgtataagccactctacagct	11	11	3	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:120057162C>T	ENST00000369413.3	+	4	1161	c.1016C>T	c.(1015-1017)gCg>gTg	p.A339V	HSD3B1_ENST00000235547.6_Missense_Mutation_p.A341V|HSD3B1_ENST00000528909.1_Missense_Mutation_p.A339V			P14060	3BHS1_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	339					androgen biosynthetic process (GO:0006702)|estrogen biosynthetic process (GO:0006703)|glucocorticoid biosynthetic process (GO:0006704)|mineralocorticoid biosynthetic process (GO:0006705)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|smooth endoplasmic reticulum membrane (GO:0030868)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|steroid delta-isomerase activity (GO:0004769)	p.A339V(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(18)|ovary(2)|prostate(1)|skin(1)	32	all_neural(166;0.219)	all_lung(203;3.16e-06)|Lung NSC(69;2.19e-05)|all_epithelial(167;0.000624)		Lung(183;0.0106)|LUSC - Lung squamous cell carcinoma(189;0.0554)	Trilostane(DB01108)	CGAGATCTGGCGTATAAGCCA	0.512																																					p.A339V		Atlas-SNP	.											HSD3B1,caecum,carcinoma,0,1	HSD3B1	53	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1016T						.						84	74	77					1																	120057162		2203	4300	6503	SO:0001583	missense	3283	exon4			ATCTGGCGTATAA	S45679	CCDS903.1	1p12	2014-06-03			ENSG00000203857	ENSG00000203857	1.1.1.145, 5.3.3.1	"Short chain dehydrogenase/reductase superfamily / Extended SDR fold"	5217	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 11E, member 1"	109715		HSDB3, HSD3B		2779585, 19027726	Standard	NM_000862		Approved	SDR11E1	uc001ehv.1	P14060	OTTHUMG00000012525	ENST00000369413.3:c.1016C>T	chr1.hg19:g.120057162C>T	ENSP00000358421:p.Ala339Val	260.0	0.0		194.0	100.0	NM_000862	A8K691|Q14545|Q8IV65	Missense_Mutation	SNP	ENST00000369413.3	hg19	CCDS903.1	.	.	.	.	.	.	.	.	.	.	C	9.829	1.187937	0.21954	.	.	ENSG00000203857	ENST00000369413;ENST00000235547;ENST00000528909	D;D;D	0.88201	-2.35;-2.35;-2.35	3.26	2.32	0.28847	.	0.049786	0.85682	D	0.000000	T	0.80391	0.4614	L	0.50333	1.59	0.28587	N	0.909855	B;D	0.56287	0.135;0.975	B;P	0.46825	0.019;0.528	T	0.74247	-0.3727	10	0.66056	D	0.02	-8.2779	10.0193	0.42033	0.0:0.2225:0.7774:0.0	.	341;339	Q5TDG2;P14060	.;3BHS1_HUMAN	V	339;341;339	ENSP00000358421:A339V;ENSP00000235547:A341V;ENSP00000432268:A339V	ENSP00000235547:A341V	A	+	2	0	HSD3B1	119858685	1.000000	0.71417	0.548000	0.28192	0.070000	0.16714	7.202000	0.77856	0.673000	0.31224	0.313000	0.20887	GCG	.	.		0.512	HSD3B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034993.3	NM_000862		T	120057162	C	T	120057162	3	4	352	1	0	0	0	0	1	0	0	0	7399	768	27	1	1026	1	HSD3B1	1	120057162	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	1518045	120057162	129193459	20	49436										
HMGCS2	3158	hgsc.bcm.edu	37	chr1	120298061	120298061	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agtactcactgggacagaagCgaggccaggcacccgtacag	13	12	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:120298061C>T	ENST00000369406.3	-	6	1225	c.1176G>A	c.(1174-1176)tcG>tcA	p.S392S	HMGCS2_ENST00000476640.1_5'Flank|HMGCS2_ENST00000544913.2_Silent_p.S350S	NM_005518.3	NP_005509.1	P54868	HMCS2_HUMAN	3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial)	392					cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|isoprenoid biosynthetic process (GO:0008299)|ketone body biosynthetic process (GO:0046951)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	hydroxymethylglutaryl-CoA synthase activity (GO:0004421)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(13)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	28	all_cancers(5;6.38e-10)|all_epithelial(5;1.1e-10)|Melanoma(3;1.93e-05)|Breast(55;0.218)|all_neural(166;0.219)	all_lung(203;1.29e-06)|Lung NSC(69;9.35e-06)|all_epithelial(167;0.00124)		Lung(183;0.0112)|LUSC - Lung squamous cell carcinoma(189;0.0595)		GGGACAGAAGCGAGGCCAGGC	0.562																																					p.S392S		Atlas-SNP	.											.	HMGCS2	58	.	0			c.G1176A						.						275	258	264					1																	120298061		2203	4300	6503	SO:0001819	synonymous_variant	3158	exon6			CAGAAGCGAGGCC	BC044217	CCDS905.1, CCDS53353.1	1p13-p12	2014-09-17	2010-04-30		ENSG00000134240	ENSG00000134240			5008	protein-coding gene	gene with protein product		600234	"3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 (mitochondrial)"			7851882, 7893153	Standard	NM_005518		Approved		uc001eid.3	P54868	OTTHUMG00000012101	ENST00000369406.3:c.1176G>A	chr1.hg19:g.120298061C>T		132.0	0.0		126.0	22.0	NM_005518	B7Z8R3|D3Y5K6|Q5SZU2|Q6IBF4	Silent	SNP	ENST00000369406.3	hg19	CCDS905.1																																																																																			.	.		0.562	HMGCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033469.2	NM_005518		T	120298061	C	T	120298061	2	4	352	1	0	0	0	0	0	0	0	1	7242	755	27	1		1	HMGCS2	1	120298061	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	240899	120298061	128952560	21	49437										
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144882534	144882534	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tcacattcccctcctcttggTgttggtgcttcccaggggaa	10	13	2	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:144882534T>C	ENST00000369354.3	-	24	3674	c.3485A>G	c.(3484-3486)cAc>cGc	p.H1162R	PDE4DIP_ENST00000530740.1_Missense_Mutation_p.H1299R|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.H1299R|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.H1162R|PDE4DIP_ENST00000313382.9_Intron			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1162					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		CTCCTCTTGGTGTTGGTGCTT	0.527			T	PDGFRB	MPD																																p.H1162R		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.A3485G						.						131	123	125					1																	144882534		2203	4296	6499	SO:0001583	missense	9659	exon24			TCTTGGTGTTGGT	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"myomegalin"	608117	"cardiomyopathy associated 2"	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.3485A>G	chr1.hg19:g.144882534T>C	ENSP00000358360:p.His1162Arg	165.0	0.0		199.0	17.0	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	hg19	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	T	9.618	1.132980	0.21041	.	.	ENSG00000178104	ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	T;T;T;T	0.01359	4.98;4.98;4.98;4.98	5.14	-9.43	0.00607	.	.	.	.	.	T	0.00271	0.0008	L	0.36672	1.1	0.09310	N	1	B	0.31730	0.337	B	0.19666	0.026	T	0.49899	-0.8890	9	0.06757	T	0.87	.	5.7034	0.17895	0.1023:0.5721:0.1031:0.2225	.	1162	Q5VU43	MYOME_HUMAN	R	1162;1162;1299;1299	ENSP00000358360:H1162R;ENSP00000358363:H1162R;ENSP00000435654:H1299R;ENSP00000358366:H1299R	ENSP00000358360:H1162R	H	-	2	0	PDE4DIP	143593891	0.000000	0.05858	0.000000	0.03702	0.067000	0.16453	-1.438000	0.02416	-1.600000	0.01603	-0.250000	0.11733	CAC	.	.		0.527	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		C	144882534	T	C	144882534	3	2	352	1	0	0	0	0	1	0	0	0	11652	1696	59	2	3639	2	PDE4DIP	1	144882534	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	24584473	144882534	104368087	22	49438										
PLEKHO1	51177	hgsc.bcm.edu	37	chr1	150131092	150131092	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cttcccctgaggaaccaaccTcttgtgctgagagctttcgg	10	13	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:150131092T>G	ENST00000369124.4	+	6	882	c.604T>G	c.(604-606)Tct>Gct	p.S202A	PLEKHO1_ENST00000025469.6_Missense_Mutation_p.S168A|PLEKHO1_ENST00000479194.1_3'UTR|PLEKHO1_ENST00000369126.1_Missense_Mutation_p.S19A	NM_016274.4	NP_057358.2	Q53GL0	PKHO1_HUMAN	pleckstrin homology domain containing, family O member 1	202	Interaction with ATM, CKIP, IFP35 and NMI.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|skin(2)	22	Lung NSC(24;7.78e-28)|Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			GGAACCAACCTCTTGTGCTGA	0.607																																					p.S202A		Atlas-SNP	.											.	PLEKHO1	37	.	0			c.T604G						.						85	83	84					1																	150131092		2203	4300	6503	SO:0001583	missense	51177	exon6			CCAACCTCTTGTG	AF073836	CCDS945.1	1q21.2	2013-01-10			ENSG00000023902	ENSG00000023902		"Pleckstrin homology (PH) domain containing"	24310	protein-coding gene	gene with protein product		608335				10799509	Standard	NM_016274		Approved	CKIP-1, OC120	uc001ett.3	Q53GL0	OTTHUMG00000012510	ENST00000369124.4:c.604T>G	chr1.hg19:g.150131092T>G	ENSP00000358120:p.Ser202Ala	122.0	0.0		157.0	28.0	NM_016274	Q336K5|Q8IZ51|Q9NRV3|Q9UL48	Missense_Mutation	SNP	ENST00000369124.4	hg19	CCDS945.1	.	.	.	.	.	.	.	.	.	.	T	18.58	3.653815	0.67472	.	.	ENSG00000023902	ENST00000369126;ENST00000025469;ENST00000369124;ENST00000441340	T;T;T	0.46063	0.88;1.86;1.86	4.97	4.97	0.65823	.	0.504521	0.21728	N	0.070020	T	0.17450	0.0419	L	0.54323	1.7	0.32880	D	0.510442	B	0.30406	0.278	B	0.27887	0.084	T	0.08006	-1.0743	10	0.18710	T	0.47	-16.4123	8.1287	0.31014	0.2811:0.0:0.0:0.7189	.	202	Q53GL0	PKHO1_HUMAN	A	19;168;202;82	ENSP00000025469:S168A;ENSP00000358120:S202A;ENSP00000409060:S82A	ENSP00000025469:S168A	S	+	1	0	PLEKHO1	148397716	0.793000	0.28825	0.888000	0.34837	0.973000	0.67179	2.704000	0.47118	2.083000	0.62718	0.533000	0.62120	TCT	.	.		0.607	PLEKHO1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034962.1	NM_016274		G	150131092	T	G	150131092	3	3	352	1	0	0	0	0	1	0	0	0	12093	1551	54	5	626	5	PLEKHO1	1	150131092	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	5248558	150131092	99119529	23	49439										
CA14	23632	hgsc.bcm.edu	37	chr1	150234003	150234003	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggatatgaccagcctggcacCgagcctttggacctgcacaa	11	13	0	1	rs373006346		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:150234003C>A	ENST00000369111.4	+	3	1192	c.222C>A	c.(220-222)acC>acA	p.T74T	snoU13_ENST00000458929.1_RNA	NM_012113.1	NP_036245.1	Q9ULX7	CAH14_HUMAN	carbonic anhydrase XIV	74					bicarbonate transport (GO:0015701)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbonate dehydratase activity (GO:0004089)|metal ion binding (GO:0046872)			central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(2)|prostate(2)	18	Lung NSC(24;7.29e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)		Acetazolamide(DB00819)|Zonisamide(DB00909)	AGCCTGGCACCGAGCCTTTGG	0.522																																					p.T74T		Atlas-SNP	.											.	CA14	37	.	0			c.C222A						.						98	76	84					1																	150234003		2203	4300	6503	SO:0001819	synonymous_variant	23632	exon3			TGGCACCGAGCCT	AB025904	CCDS947.1	1q21	2008-02-05			ENSG00000118298	ENSG00000118298		"Carbonic anhydrases"	1372	protein-coding gene	gene with protein product		604832				10512682	Standard	XM_005245059		Approved		uc001etx.3	Q9ULX7	OTTHUMG00000012549	ENST00000369111.4:c.222C>A	chr1.hg19:g.150234003C>A		76.0	0.0		102.0	6.0	NM_012113	Q5TB24|Q8NCF4	Silent	SNP	ENST00000369111.4	hg19	CCDS947.1																																																																																			.	.		0.522	CA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035064.2	NM_012113		A	150234003	C	A	150234003	2	1	352	1	0	0	0	0	0	0	0	1	2517	639	23	1		1	CA14	1	150234003	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	102911	150234003	99016618	24	49440										
RPRD2	23248	hgsc.bcm.edu	37	chr1	150444476	150444476	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	atatgcttaaaaacgcctcaCgtaagccctcagatgataag	7	10	2	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:150444476C>T	ENST00000369068.4	+	11	3056	c.3052C>T	c.(3052-3054)Cgt>Tgt	p.R1018C	RPRD2_ENST00000539519.1_3'UTR|RPRD2_ENST00000401000.4_Missense_Mutation_p.R992C|RPRD2_ENST00000492220.1_3'UTR	NM_015203.3	NP_056018.2	Q5VT52	RPRD2_HUMAN	regulation of nuclear pre-mRNA domain containing 2	1018						DNA-directed RNA polymerase II, holoenzyme (GO:0016591)				central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						AAACGCCTCACGTAAGCCCTC	0.537																																					p.R1018C		Atlas-SNP	.											.	RPRD2	189	.	0			c.C3052T						.						200	201	201					1																	150444476		1983	4166	6149	SO:0001583	missense	23248	exon11			GCCTCACGTAAGC	BX641025	CCDS44216.1, CCDS72907.1	1q21.2	2012-02-09	2008-08-15	2008-07-28	ENSG00000163125	ENSG00000163125			29039	protein-coding gene	gene with protein product		614695	"KIAA0460"	KIAA0460		22231121	Standard	XM_005245033		Approved	FLJ32145, HSPC099	uc009wlr.3	Q5VT52	OTTHUMG00000012808	ENST00000369068.4:c.3052C>T	chr1.hg19:g.150444476C>T	ENSP00000358064:p.Arg1018Cys	204.0	0.0		286.0	33.0	NM_015203	A8K6N8|B3KPT1|B4E2Q6|O75048|Q5VT51|Q5VT53|Q6MZL4|Q86XD2|Q9P0D7	Missense_Mutation	SNP	ENST00000369068.4	hg19	CCDS44216.1	.	.	.	.	.	.	.	.	.	.	C	15.94	2.979642	0.53827	.	.	ENSG00000163125	ENST00000401000;ENST00000369068	T;T	0.61742	0.08;0.09	5.21	5.21	0.72293	.	0.000000	0.64402	D	0.000002	T	0.56746	0.2006	N	0.24115	0.695	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.72338	0.948;0.977	T	0.63368	-0.6653	10	0.87932	D	0	-6.6907	16.0135	0.80420	0.0:0.8659:0.1341:0.0	.	1018;992	Q5VT52;Q5VT52-3	RPRD2_HUMAN;.	C	992;1018	ENSP00000383785:R992C;ENSP00000358064:R1018C	ENSP00000358064:R1018C	R	+	1	0	RPRD2	148711100	0.992000	0.36948	0.957000	0.39632	0.991000	0.79684	3.558000	0.53749	2.702000	0.92279	0.655000	0.94253	CGT	.	.		0.537	RPRD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000035844.1	NM_015203		T	150444476	C	T	150444476	3	4	352	1	0	0	0	0	1	0	0	0	13632	536	19	1	3094	1	RPRD2	1	150444476	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	210473	150444476	98806145	25	49441										
KPRP	448834	hgsc.bcm.edu	37	chr1	152732288	152732288	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gaccacacaggtgaagtgccAgtctaagaccaagcaggtga	12	10	1	3			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:152732288A>G	ENST00000606109.1	+	1	252	c.224A>G	c.(223-225)cAg>cGg	p.Q75R	KPRP_ENST00000368773.1_Missense_Mutation_p.Q75R			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	75	Gln-rich.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|breast(1)|endometrium(9)|kidney(1)|large_intestine(10)|lung(21)|ovary(6)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			GTGAAGTGCCAGTCTAAGACC	0.537																																					p.Q75R		Atlas-SNP	.											.	KPRP	152	.	0			c.A224G						.						185	159	168					1																	152732288		2203	4300	6503	SO:0001583	missense	448834	exon2			AGTGCCAGTCTAA	AY960854	CCDS30862.1	1q21.3	2008-02-05	2007-02-02	2006-12-07	ENSG00000203786	ENSG00000203786			31823	protein-coding gene	gene with protein product		613260	"chromosome 1 open reading frame 45"	C1orf45		16297201	Standard	NM_001025231		Approved		uc001fal.1	Q5T749	OTTHUMG00000012402	ENST00000606109.1:c.224A>G	chr1.hg19:g.152732288A>G	ENSP00000475216:p.Gln75Arg	150.0	0.0		229.0	44.0	NM_001025231		Missense_Mutation	SNP	ENST00000606109.1	hg19	CCDS30862.1	.	.	.	.	.	.	.	.	.	.	A	10.04	1.241963	0.22796	.	.	ENSG00000203786	ENST00000368773	T	0.19105	2.17	4.71	2.11	0.27256	.	0.000000	0.37393	N	0.002117	T	0.13200	0.0320	L	0.55481	1.735	0.09310	N	1	D	0.58268	0.982	P	0.52481	0.7	T	0.04737	-1.0930	10	0.72032	D	0.01	-0.3361	4.9542	0.14031	0.6222:0.1925:0.0:0.1853	.	75	Q5T749	KPRP_HUMAN	R	75	ENSP00000357762:Q75R	ENSP00000357762:Q75R	Q	+	2	0	KPRP	150998912	0.021000	0.18746	0.018000	0.16275	0.388000	0.30384	1.492000	0.35594	0.869000	0.35703	0.533000	0.62120	CAG	.	.		0.537	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231		G	152732288	A	G	152732288	3	3	352	1	0	0	0	0	1	0	0	0	8445	188	7	2	226	2	KPRP	1	152732288	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	2287812	152732288	96518333	26	49442										
IVL	3713	hgsc.bcm.edu	37	chr1	152882316	152882316	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cagtgaccctctcccctgccCtcagtcaggagctcctcaag	8	18	4	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:152882316C>A	ENST00000368764.3	+	2	107	c.43C>A	c.(43-45)Ctc>Atc	p.L15I	IVL_ENST00000392667.2_5'UTR			P07476	INVO_HUMAN	involucrin	15					isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CTCCCCTGCCCTCAGTCAGGA	0.547																																					p.L15I		Atlas-SNP	.											.	IVL	100	.	0			c.C43A						.						86	73	78					1																	152882316		2203	4300	6503	SO:0001583	missense	3713	exon2			CCTGCCCTCAGTC	BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.43C>A	chr1.hg19:g.152882316C>A	ENSP00000357753:p.Leu15Ile	77.0	0.0		131.0	27.0	NM_005547	Q5T7P4	Missense_Mutation	SNP	ENST00000368764.3	hg19	CCDS1030.1	.	.	.	.	.	.	.	.	.	.	C	12.59	1.984475	0.35036	.	.	ENSG00000163207	ENST00000368764	T	0.13307	2.6	4.5	-0.0113	0.13993	Involucrin, N-terminal (1);	.	.	.	.	T	0.08846	0.0219	M	0.65498	2.005	0.09310	N	0.999998	P	0.41624	0.757	P	0.50934	0.654	T	0.24119	-1.0169	9	0.44086	T	0.13	-0.0874	2.2448	0.04029	0.2302:0.3287:0.3349:0.1062	.	15	P07476	INVO_HUMAN	I	15	ENSP00000357753:L15I	ENSP00000357753:L15I	L	+	1	0	IVL	151148940	0.000000	0.05858	0.001000	0.08648	0.840000	0.47671	-0.452000	0.06787	0.123000	0.18342	0.561000	0.74099	CTC	.	.		0.547	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547		A	152882316	C	A	152882316	3	1	352	1	0	0	0	0	1	0	0	0	7938	681	24	3	45	3	IVL	1	152882316	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	150028	152882316	96368305	27	49443										
INTS3	65123	hgsc.bcm.edu	37	chr1	153744418	153744418	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cctgctcatcaagaacaacaGcctgcctcgcaagagacaga	8	14	2	3			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:153744418G>A	ENST00000318967.2	+	26	3267	c.2699G>A	c.(2698-2700)aGc>aAc	p.S900N	INTS3_ENST00000512605.1_Missense_Mutation_p.S694N|INTS3_ENST00000435409.2_Missense_Mutation_p.S900N|SLC27A3_ENST00000271857.2_5'Flank|INTS3_ENST00000456435.1_Missense_Mutation_p.S694N|INTS3_ENST00000476843.1_3'UTR	NM_023015.3	NP_075391.3	Q68E01	INT3_HUMAN	integrator complex subunit 3	901					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|mitotic cell cycle checkpoint (GO:0007093)|response to ionizing radiation (GO:0010212)|snRNA processing (GO:0016180)	integrator complex (GO:0032039)|nucleus (GO:0005634)|SOSS complex (GO:0070876)				breast(1)|cervix(4)|endometrium(10)|kidney(1)|large_intestine(6)|lung(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	38	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			AAGAACAACAGCCTGCCTCGC	0.602											OREG0013827	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S900N		Atlas-SNP	.											.	INTS3	83	.	0			c.G2699A						.						79	59	66					1																	153744418		2203	4300	6503	SO:0001583	missense	65123	exon26			ACAACAGCCTGCC	BX640950	CCDS1052.1	1q21.3	2012-03-16	2006-03-15	2006-03-15	ENSG00000143624	ENSG00000143624			26153	protein-coding gene	gene with protein product	"sensor of single-strand DNA complex subunit A"	611347	"chromosome 1 open reading frame 60"	C1orf60		16239144	Standard	NM_023015		Approved	FLJ21919, INT3, SOSS-A	uc001fct.3	Q68E01	OTTHUMG00000037089	ENST00000318967.2:c.2699G>A	chr1.hg19:g.153744418G>A	ENSP00000318641:p.Ser900Asn	75.0	0.0	1757	109.0	11.0	NM_023015	A8K1W0|B4DQC8|B4E3U9|D3DV57|Q4G0E5|Q5VUQ5|Q5VUQ6|Q5VUR0|Q5VUR1|Q68DJ1|Q69YR5|Q6AI57|Q6DKG7|Q6MZQ4|Q6MZZ9|Q8NC46|Q8TB23|Q9H6S9	Missense_Mutation	SNP	ENST00000318967.2	hg19	CCDS1052.1	.	.	.	.	.	.	.	.	.	.	G	13.62	2.290761	0.40494	.	.	ENSG00000143624	ENST00000318967;ENST00000456435;ENST00000435409;ENST00000512605	.	.	.	4.52	4.52	0.55395	.	0.101407	0.64402	D	0.000002	T	0.24736	0.0600	N	0.12182	0.205	0.39135	D	0.961937	B;B;B	0.09022	0.002;0.0;0.001	B;B;B	0.06405	0.002;0.0;0.001	T	0.06935	-1.0799	9	0.35671	T	0.21	.	14.7903	0.69837	0.0:0.0:1.0:0.0	.	694;901;900	Q68E01-3;Q68E01;Q68E01-2	.;INT3_HUMAN;.	N	900;694;900;694	.	ENSP00000318641:S900N	S	+	2	0	INTS3	152011042	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.391000	0.59652	2.341000	0.79615	0.563000	0.77884	AGC	.	.		0.602	INTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090045.2	NM_023015		A	153744418	G	A	153744418	3	1	352	1	0	0	0	0	1	0	0	0	7788	971	34	3	2801	3	INTS3	1	153744418	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	862102	153744418	95506203	28	49444										
SLC27A3	11000	hgsc.bcm.edu	37	chr1	153747867	153747869	+	In_Frame_Del	DEL	AGG	AGG	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gcgcacgcgcgctccctggaAggagaagtctcagctagaac							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:153747867_153747869delAGG	ENST00000368661.3	+	1	100_102	c.35_37delAGG	c.(34-39)aaggag>aag	p.E13del	SLC27A3_ENST00000271857.2_In_Frame_Del_p.E94del|SLC27A3_ENST00000484014.1_3'UTR	NM_024330.1	NP_077306.1	Q5K4L6	S27A3_HUMAN	solute carrier family 27 (fatty acid transporter), member 3	13					fatty acid metabolic process (GO:0006631)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)	fatty-acyl-CoA synthase activity (GO:0004321)|ligase activity (GO:0016874)|nucleotide binding (GO:0000166)			NS(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	14	all_lung(78;6.47e-32)|Lung NSC(65;2.52e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			GCTCCCTGGAAGGAGAAGTCTCA	0.655																																					p.12_12del		Atlas-INDEL	.											.	SLC27A3	42	.	0			c.34_36del						.																																			SO:0001651	inframe_deletion	11000	exon1			.	BC009916	CCDS1053.1	1q21.1	2013-05-22			ENSG00000143554	ENSG00000143554		"Acyl-CoA synthetase family", "Solute carriers"	10997	protein-coding gene	gene with protein product		604193				9671728	Standard	NM_024330		Approved	FATP3, MGC4365, ACSVL3	uc001fcz.3	Q5K4L6	OTTHUMG00000037155	ENST00000368661.3:c.35_37delAGG	chr1.hg19:g.153747867_153747869delAGG	ENSP00000357650:p.Glu13del	60.0	0.0		75.0	11.0	NM_024330	Q5VUQ7|Q5VUQ8|Q5VUR3|Q6ZV16|Q8N2X7|Q8TEJ0|Q96SW5|Q9BTJ5|Q9BTY5	In_Frame_Del	DEL	ENST00000368661.3	hg19	CCDS1053.1																																																																																			.	.		0.655	SLC27A3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_024330		-	153747869	AGG	-	153747867	7	5	352	1	0	1	0	1	0	0	0	0	14542	72	3	0	37	0	SLC27A3	1	153747867	In_Frame_Del	DEL	AGG	TCGA-WQ-A9G7-01A-11D-A36X-10	3449	153747867	95502754	29	49445										
DENND4B	9909	hgsc.bcm.edu	37	chr1	153916546	153916547	+	Frame_Shift_Ins	INS	-	-	G													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cacacaccccagctcaacgaINSgggggggcttgtcacggccc							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:153916546_153916547insG	ENST00000361217.4	-	2	722_723	c.304_305insC	c.(304-306)ctcfs	p.L102fs		NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	102	MABP. {ECO:0000255|PROSITE- ProRule:PRU00831}.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab protein signal transduction (GO:0032483)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	36	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			CAGCTCAACGAGGGGGGGCTTG	0.634																																					p.L102fs		Atlas-INDEL	.											.	DENND4B	210	.	0			c.305_306insC						.																																			SO:0001589	frameshift_variant	9909	exon2			.	AB007945	CCDS44228.1	1q21.3	2012-10-03	2006-01-27	2006-01-27	ENSG00000198837	ENSG00000198837		"DENN/MADD domain containing"	29044	protein-coding gene	gene with protein product			"KIAA0476"	KIAA0476		9455484, 12906859	Standard	NM_014856		Approved		uc001fdd.1	O75064	OTTHUMG00000037157	ENST00000361217.4:c.305dupC	chr1.hg19:g.153916553_153916553dupG	ENSP00000354597:p.Leu102fs	132.0	0.0		167.0	24.0	NM_014856	Q5T4K0	Frame_Shift_Ins	INS	ENST00000361217.4	hg19	CCDS44228.1																																																																																			.	.		0.634	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806		G	153916547	-	G	153916546	7	5	352	1	0	1	1	0	0	0	0	0	4436	304	11	0	4293	0	DENND4B	1	153916546	Frame_Shift_Ins	INS	-	TCGA-WQ-A9G7-01A-11D-A36X-10	168679	153916546	95334075	30	49446										
SHC1	6464	hgsc.bcm.edu	37	chr1	154942720	154942720	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gtctggcatggctgcccctaCgatcccctccccatcatcag	8	18	3	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:154942720C>T	ENST00000368445.5	-	1	497	c.283G>A	c.(283-285)Gta>Ata	p.V95I	SHC1_ENST00000368450.1_Intron|SHC1_ENST00000606391.1_Intron|SHC1_ENST00000448116.2_Missense_Mutation_p.V95I|SHC1_ENST00000368449.4_Intron|SHC1_ENST00000368453.4_Intron	NM_183001.4	NP_892113.4	P29353	SHC1_HUMAN	SHC (Src homology 2 domain containing) transforming protein 1	95				V -> D (in Ref. 2; AAB49972). {ECO:0000305}.	actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|Ras protein signal transduction (GO:0007265)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of growth (GO:0040008)|single organismal cell-cell adhesion (GO:0016337)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|Shc-EGFR complex (GO:0070435)	ephrin receptor binding (GO:0046875)|epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phospholipid binding (GO:0005543)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)			breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	20	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			GCTGCCCCTACGATCCCCTCC	0.687																																					p.V95I	NSCLC(4;32 234 1864 2492 3259 13747 17376)	Atlas-SNP	.											SHC1_ENST00000448116,NS,carcinoma,0,1	SHC1	91	.	0			c.G283A						.						27	33	31					1																	154942720		2203	4299	6502	SO:0001583	missense	6464	exon1			CCCCTACGATCCC	U73377	CCDS1076.1, CCDS30881.1, CCDS44233.1, CCDS44234.1	1q21	2013-02-14	2002-01-14		ENSG00000160691	ENSG00000160691		"SH2 domain containing"	10840	protein-coding gene	gene with protein product		600560	"SHC (Src homology 2 domain-containing) transforming protein 1"	SHC		1623525	Standard	NM_003029		Approved	p66	uc001ffw.3	P29353	OTTHUMG00000037295	ENST00000368445.5:c.283G>A	chr1.hg19:g.154942720C>T	ENSP00000357430:p.Val95Ile	209.0	0.0		294.0	33.0	NM_183001	B5BU19|D3DV78|O15290|Q5T180|Q5T183|Q5T184|Q5T185|Q5T186|Q8N4K5|Q96CL1	Missense_Mutation	SNP	ENST00000368445.5	hg19	CCDS30881.1	.	.	.	.	.	.	.	.	.	.	C	11.39	1.625547	0.28889	.	.	ENSG00000160691	ENST00000368445;ENST00000448116;ENST00000368443	T;T	0.63417	-0.04;-0.04	4.06	-3.1	0.05315	.	2.000660	0.02576	N	0.098336	T	0.12603	0.0306	N	0.03608	-0.345	0.09310	N	1	B;B	0.26318	0.011;0.146	B;B	0.14578	0.001;0.011	T	0.03335	-1.1047	10	0.30854	T	0.27	.	3.8341	0.08886	0.262:0.337:0.0:0.4011	.	95;95	P29353-6;P29353	.;SHC1_HUMAN	I	95;95;31	ENSP00000357430:V95I;ENSP00000401303:V95I	ENSP00000357428:V31I	V	-	1	0	SHC1	153209344	0.000000	0.05858	0.001000	0.08648	0.981000	0.71138	-0.336000	0.07863	-0.785000	0.04522	0.555000	0.69702	GTA	.	.		0.687	SHC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090781.2	NM_183001		T	154942720	C	T	154942720	3	4	352	1	0	0	0	0	1	0	0	0	14285	536	19	1	1519	1	SHC1	1	154942720	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	1026174	154942720	94307901	31	49447										
ARHGEF2	9181	hgsc.bcm.edu	37	chr1	155922509	155922509	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cctgggcagggtgggcagggCcatcccactgccaccatcct	13	16	0	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:155922509C>T	ENST00000361247.4	-	15	1993	c.1894G>A	c.(1894-1896)Gcc>Acc	p.A632T	ARHGEF2_ENST00000313695.7_Missense_Mutation_p.A604T|ARHGEF2_ENST00000462460.2_Missense_Mutation_p.A677T|ARHGEF2_ENST00000313667.4_Missense_Mutation_p.A631T|ARHGEF2_ENST00000368316.1_Missense_Mutation_p.A604T|ARHGEF2_ENST00000368315.4_Missense_Mutation_p.A633T|ARHGEF2_ENST00000477754.2_Intron	NM_001162383.1|NM_001162384.1	NP_001155855.1|NP_001155856.1	Q92974	ARHG2_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 2	632					actin filament organization (GO:0007015)|apoptotic signaling pathway (GO:0097190)|cell morphogenesis (GO:0000902)|cellular hyperosmotic response (GO:0071474)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to tumor necrosis factor (GO:0071356)|establishment of mitotic spindle orientation (GO:0000132)|innate immune response (GO:0045087)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress (GO:1902219)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of necroptotic process (GO:0060546)|negative regulation of neurogenesis (GO:0050768)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cell proliferation (GO:0042127)|regulation of Rho protein signal transduction (GO:0035023)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)|vesicle (GO:0031982)	microtubule binding (GO:0008017)|Rac GTPase binding (GO:0048365)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho GTPase binding (GO:0017048)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(4)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|skin(2)	40	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					GTGGGCAGGGCCATCCCACTG	0.652																																					p.A632T	Melanoma(178;35 2768 6610 28839)	Atlas-SNP	.											ARHGEF2,NS,carcinoma,0,1	ARHGEF2	81	.	0			c.G1894A						.						91	84	86					1																	155922509		2203	4300	6503	SO:0001583	missense	9181	exon15			GCAGGGCCATCCC	AB014551	CCDS1125.1, CCDS53375.1, CCDS53376.1	1q21-q22	2013-01-10	2009-06-12		ENSG00000116584	ENSG00000116584		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	682	protein-coding gene	gene with protein product		607560	"rho/rac guanine nucleotide exchange factor (GEF) 2"			9857026, 9734811	Standard	NM_004723		Approved	LFP40, GEF-H1, KIAA0651, P40	uc001fmt.2	Q92974	OTTHUMG00000017464	ENST00000361247.4:c.1894G>A	chr1.hg19:g.155922509C>T	ENSP00000354837:p.Ala632Thr	184.0	0.0		226.0	43.0	NM_001162383	D3DVA6|O75142|Q15079|Q5VY92|Q8TDA3|Q8WUG4|Q9H023	Missense_Mutation	SNP	ENST00000361247.4	hg19	CCDS53376.1	.	.	.	.	.	.	.	.	.	.	C	9.381	1.072961	0.20147	.	.	ENSG00000116584	ENST00000313695;ENST00000361247;ENST00000368315;ENST00000368316;ENST00000313667	T;T;T;T;T	0.63580	-0.05;0.08;0.07;-0.05;-0.05	5.14	-3.25	0.05079	.	0.855362	0.09933	N	0.736904	T	0.08802	0.0218	N	0.02539	-0.55	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.21861	-1.0233	10	0.15952	T	0.53	-7.9738	1.977	0.03418	0.3165:0.3538:0.2132:0.1165	.	676;632;631	D3DVA5;Q92974;Q92974-2	.;ARHG2_HUMAN;.	T	604;632;633;604;631	ENSP00000315325:A604T;ENSP00000354837:A632T;ENSP00000357298:A633T;ENSP00000357299:A604T;ENSP00000314787:A631T	ENSP00000314787:A631T	A	-	1	0	ARHGEF2	154189133	0.016000	0.18221	0.226000	0.23910	0.870000	0.49936	0.042000	0.13949	-0.704000	0.05042	-1.289000	0.01358	GCC	.	.		0.652	ARHGEF2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046204.2	NM_004723		T	155922509	C	T	155922509	3	4	352	1	0	0	0	0	1	0	0	0	903	739	26	3	1098	3	ARHGEF2	1	155922509	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	979789	155922509	93328112	32	49448										
NES	10763	hgsc.bcm.edu	37	chr1	156640020	156640020	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gtctccccttgagggggtggCctctgctctccagtggggtc	15	13	3	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:156640020C>T	ENST00000368223.3	-	4	4092	c.3960G>A	c.(3958-3960)agG>agA	p.R1320R		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin	1320	Tail.			DPTGEQRPPPQG -> TPLESRGHPLK (in Ref. 1; CAA46780). {ECO:0000305}.	brain development (GO:0007420)|cell projection morphogenesis (GO:0048858)|central nervous system development (GO:0007417)|embryonic camera-type eye development (GO:0031076)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of catalytic activity (GO:0043086)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein binding (GO:0032091)|positive regulation of intermediate filament depolymerization (GO:0030844)|positive regulation of neural precursor cell proliferation (GO:2000179)|stem cell proliferation (GO:0072089)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	intermediate filament binding (GO:0019215)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(30)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(4)	64	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GAGGGGGTGGCCTCTGCTCTC	0.662																																					p.R1320R		Atlas-SNP	.											.	NES	196	.	0			c.G3960A						.						53	64	60					1																	156640020		2203	4299	6502	SO:0001819	synonymous_variant	10763	exon4			GGGTGGCCTCTGC	X65964	CCDS1151.1	1q23	2013-01-16			ENSG00000132688	ENSG00000132688		"Intermediate filaments type IV"	7756	protein-coding gene	gene with protein product		600915				1478958, 9104587	Standard	NM_006617		Approved	FLJ21841	uc001fpq.3	P48681	OTTHUMG00000034299	ENST00000368223.3:c.3960G>A	chr1.hg19:g.156640020C>T		46.0	0.0		97.0	6.0	NM_006617	O00552|Q3LIF5|Q5SYZ6	Silent	SNP	ENST00000368223.3	hg19	CCDS1151.1																																																																																			.	.		0.662	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	NM_006617		T	156640020	C	T	156640020	2	4	352	1	0	0	0	0	0	0	0	1	10346	738	26	3		3	NES	1	156640020	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	717511	156640020	92610601	33	49449										
AIM2	9447	hgsc.bcm.edu	37	chr1	159033322	159033322	+	Frame_Shift_Del	DEL	T	T	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tcagctgtagtttttctccaTtttttgacagtgtgaagaat							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:159033322delT	ENST00000368130.4	-	5	1247	c.959delA	c.(958-960)aatfs	p.N320fs	AIM2_ENST00000411768.1_5'Flank	NM_004833.1	NP_004824.1	O14862	AIM2_HUMAN	absent in melanoma 2	320	HIN-200. {ECO:0000255|PROSITE- ProRule:PRU00106}.				activation of innate immune response (GO:0002218)|apoptotic process (GO:0006915)|cellular response to drug (GO:0035690)|cellular response to interferon-beta (GO:0035458)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta secretion (GO:0050702)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein oligomerization (GO:0032461)|pyroptosis (GO:0070269)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	AIM2 inflammasome complex (GO:0097169)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)			breast(1)|large_intestine(1)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(1)	16	all_hematologic(112;0.0429)					TTTTTCTCCATTTTTTGACAG	0.408																																					p.N320fs		Atlas-INDEL	.											.	AIM2	70	.	0			c.960delT						.						242	228	233					1																	159033322		2203	4300	6503	SO:0001589	frameshift_variant	9447	exon5			.	AF024714	CCDS1181.1	1q22	2008-07-18			ENSG00000163568	ENSG00000163568			357	protein-coding gene	gene with protein product		604578				9242382	Standard	NM_004833		Approved	PYHIN4	uc001ftj.1	O14862	OTTHUMG00000037183	ENST00000368130.4:c.959delA	chr1.hg19:g.159033322delT	ENSP00000357112:p.Asn320fs	92.0	0.0		115.0	37.0	NM_004833	A8K7M7|Q5T3V9|Q96FG9	Frame_Shift_Del	DEL	ENST00000368130.4	hg19	CCDS1181.1																																																																																			.	.		0.408	AIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090341.1	NM_004833		-	159033322	T	-	159033322	7	5	352	1	0	1	0	1	0	0	0	0	432	1493	52	0	80	0	AIM2	1	159033322	Frame_Shift_Del	DEL	T	TCGA-WQ-A9G7-01A-11D-A36X-10	2393302	159033322	90217299	34	49450										
IGSF9	57549	hgsc.bcm.edu	37	chr1	159901663	159901663	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agcaggggatgagcagctccCgccctacttcttggaaatat	11	11	1	1	rs376059608		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:159901663C>T	ENST00000368094.1	-	11	1498	c.1301G>A	c.(1300-1302)cGg>cAg	p.R434Q	IGSF9_ENST00000493195.1_5'UTR|IGSF9_ENST00000361509.3_Missense_Mutation_p.R418Q	NM_001135050.1	NP_001128522.1	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9	434	Ig-like 5.				dendrite development (GO:0016358)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)				central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(13)|lung(17)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_hematologic(112;0.0597)	Breast(1374;0.000126)	BRCA - Breast invasive adenocarcinoma(70;0.111)			GAGCAGCTCCCGCCCTACTTC	0.592																																					p.R434Q		Atlas-SNP	.											.	IGSF9	123	.	0			c.G1301A						.	C	GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	56	65	62		1301,1253	4.4	1	1		62	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	IGSF9	NM_001135050.1,NM_020789.3	43,43	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging,probably-damaging	434/1180,418/1164	159901663	2,13004	2203	4300	6503	SO:0001583	missense	57549	exon11			AGCTCCCGCCCTA	AB037776	CCDS1190.1, CCDS44254.1	1q22-q23	2013-02-11			ENSG00000085552	ENSG00000085552		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	18132	protein-coding gene	gene with protein product		609738				11991715	Standard	NM_020789		Approved	KIAA1355, Nrt1, IGSF9A	uc001fur.2	Q9P2J2	OTTHUMG00000022794	ENST00000368094.1:c.1301G>A	chr1.hg19:g.159901663C>T	ENSP00000357073:p.Arg434Gln	54.0	0.0		68.0	17.0	NM_001135050		Missense_Mutation	SNP	ENST00000368094.1	hg19	CCDS44254.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.401258	0.83120	2.27E-4	1.16E-4	ENSG00000085552	ENST00000361509;ENST00000368094;ENST00000198587	T;T	0.77229	-1.08;-1.08	4.41	4.41	0.53225	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.35677	N	0.003043	T	0.69584	0.3127	N	0.25060	0.705	0.40030	D	0.975525	D;P	0.63046	0.992;0.898	P;B	0.59889	0.865;0.432	T	0.70626	-0.4820	9	.	.	.	-16.1096	14.5219	0.67856	0.0:1.0:0.0:0.0	.	434;434	Q9P2J2;C9JI81	TUTLA_HUMAN;.	Q	418;434;434	ENSP00000355049:R418Q;ENSP00000357073:R434Q	.	R	-	2	0	IGSF9	158168287	1.000000	0.71417	0.999000	0.59377	0.549000	0.35272	7.083000	0.76859	2.003000	0.58678	0.561000	0.74099	CGG	.	.		0.592	IGSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059115.1	NM_020789		T	159901663	C	T	159901663	3	4	352	1	0	0	0	0	1	0	0	0	7614	652	23	1	2282	1	IGSF9	1	159901663	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	868341	159901663	89348958	35	49451										
IGSF8	93185	hgsc.bcm.edu	37	chr1	160062224	160062224	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gtagtctcagccgatggcttCggggccccaccagctctacg	12	15	2	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:160062224C>T	ENST00000368086.1	-	5	1790	c.1574G>A	c.(1573-1575)cGa>cAa	p.R525Q	IGSF8_ENST00000460351.1_5'Flank|IGSF8_ENST00000314485.7_Missense_Mutation_p.R525Q			Q969P0	IGSF8_HUMAN	immunoglobulin superfamily, member 8	525	Ig-like C2-type 4.				cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|nervous system development (GO:0007399)|single fertilization (GO:0007338)|skeletal muscle tissue development (GO:0007519)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(19)|pancreas(1)|prostate(1)|skin(1)	33	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			CCGATGGCTTCGGGGCCCCAC	0.672																																					p.R525Q		Atlas-SNP	.											.	IGSF8	59	.	0			c.G1574A						.						37	40	39					1																	160062224		2203	4299	6502	SO:0001583	missense	93185	exon5			TGGCTTCGGGGCC	AF407274	CCDS1195.1	1q23.1	2013-01-11			ENSG00000162729	ENSG00000162729		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	17813	protein-coding gene	gene with protein product		606644				11504738, 11673522	Standard	NM_001206665		Approved	CD81P3, EWI2, PGRL, CD316	uc009wtf.3	Q969P0	OTTHUMG00000024075	ENST00000368086.1:c.1574G>A	chr1.hg19:g.160062224C>T	ENSP00000357065:p.Arg525Gln	103.0	0.0		147.0	42.0	NM_052868	Q8NG09|Q96DP4|Q9BTG9	Missense_Mutation	SNP	ENST00000368086.1	hg19	CCDS1195.1	.	.	.	.	.	.	.	.	.	.	C	6.973	0.549573	0.13374	.	.	ENSG00000162729	ENST00000314485;ENST00000368086	T;T	0.22336	1.96;1.96	3.06	2.13	0.27403	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	1.233450	0.06182	U	0.679576	T	0.03095	0.0091	N	0.19112	0.55	0.22684	N	0.998852	B	0.15473	0.013	B	0.06405	0.002	T	0.41680	-0.9495	10	0.13470	T	0.59	0.5119	2.6959	0.05135	0.2261:0.5172:0.0:0.2567	.	525	Q969P0	IGSF8_HUMAN	Q	525	ENSP00000316664:R525Q;ENSP00000357065:R525Q	ENSP00000316664:R525Q	R	-	2	0	IGSF8	158328848	0.030000	0.19436	0.999000	0.59377	0.993000	0.82548	-0.243000	0.08915	0.477000	0.27464	0.400000	0.26472	CGA	.	.		0.672	IGSF8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060636.1	NM_052868		T	160062224	C	T	160062224	3	4	352	1	0	0	0	0	1	0	0	0	7613	884	31	1	275	1	IGSF8	1	160062224	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	160561	160062224	89188397	36	49452										
FCER1G	2207	hgsc.bcm.edu	37	chr1	161188700	161188700	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	accaggaaccaggagacttaCgagactctgaagcatgagaa	11	9	1	4			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:161188700C>T	ENST00000289902.1	+	5	253	c.228C>T	c.(226-228)taC>taT	p.Y76Y	AL590714.1_ENST00000594609.1_5'Flank|FCER1G_ENST00000490414.1_3'UTR|FCER1G_ENST00000367992.3_Intron	NM_004106.1	NP_004097.1	P30273	FCERG_HUMAN	Fc fragment of IgE, high affinity I, receptor for; gamma polypeptide	76	ITAM. {ECO:0000255|PROSITE- ProRule:PRU00379}.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|Fc receptor mediated stimulatory signaling pathway (GO:0002431)|Fc-epsilon receptor signaling pathway (GO:0038095)|immunoglobulin mediated immune response (GO:0016064)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|mast cell activation (GO:0045576)|negative regulation of mast cell apoptotic process (GO:0033026)|neutrophil activation involved in immune response (GO:0002283)|neutrophil chemotaxis (GO:0030593)|phagocytosis, engulfment (GO:0006911)|platelet activation (GO:0030168)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of mast cell cytokine production (GO:0032765)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of phagocytosis (GO:0050766)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I hypersensitivity (GO:0001812)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation of type III hypersensitivity (GO:0001805)|protein localization to plasma membrane (GO:0072659)|regulation of platelet activation (GO:0010543)|serotonin secretion by platelet (GO:0002554)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|Fc-epsilon receptor I complex (GO:0032998)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	IgE receptor activity (GO:0019767)			endometrium(1)|lung(5)	6	all_cancers(52;1.35e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Benzylpenicilloyl Polylysine(DB00895)	AGGAGACTTACGAGACTCTGA	0.542																																					p.Y76Y		Atlas-SNP	.											.	FCER1G	11	.	0			c.C228T						.						113	114	114					1																	161188700		2203	4300	6503	SO:0001819	synonymous_variant	2207	exon5			GACTTACGAGACT		CCDS1225.1	1q23	2008-02-05			ENSG00000158869	ENSG00000158869			3611	protein-coding gene	gene with protein product		147139				2138619	Standard	NM_004106		Approved		uc001fyz.1	P30273	OTTHUMG00000034343	ENST00000289902.1:c.228C>T	chr1.hg19:g.161188700C>T		113.0	0.0		157.0	21.0	NM_004106	Q5VTW4	Silent	SNP	ENST00000289902.1	hg19	CCDS1225.1																																																																																			.	.		0.542	FCER1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083012.1	NM_004106		T	161188700	C	T	161188700	2	4	352	1	0	0	0	0	0	0	0	1	5783	547	19	1		1	FCER1G	1	161188700	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	1126476	161188700	88061921	37	49453										
ILDR2	387597	hgsc.bcm.edu	37	chr1	166890453	166890453	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gtgcgcccgcgactccgagcGctcgaagcggctcccgcccc	13	20	0	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:166890453G>A	ENST00000271417.3	-	9	1430	c.1375C>T	c.(1375-1377)Cgc>Tgc	p.R459C	ILDR2_ENST00000469934.2_Intron|ILDR2_ENST00000526687.1_Missense_Mutation_p.R351C|ILDR2_ENST00000529387.1_Intron|ILDR2_ENST00000528703.1_Missense_Mutation_p.R400C|ILDR2_ENST00000525740.1_Missense_Mutation_p.R332C|ILDR2_ENST00000529071.1_Missense_Mutation_p.R440C	NM_199351.2	NP_955383.1	Q71H61	ILDR2_HUMAN	immunoglobulin-like domain containing receptor 2	459					cell differentiation (GO:0030154)|homeostasis of number of cells within a tissue (GO:0048873)|insulin secretion (GO:0030073)|pancreas development (GO:0031016)|response to glucose (GO:0009749)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				NS(3)|breast(1)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	22						GACTCCGAGCGCTCGAAGCGG	0.706																																					p.R459C		Atlas-SNP	.											.	ILDR2	79	.	0			c.C1375T						.						5	7	6					1																	166890453		1724	3545	5269	SO:0001583	missense	387597	exon9			CCGAGCGCTCGAA	AF503509	CCDS1256.1	1q24.1	2008-12-18	2008-12-18	2008-12-18	ENSG00000143195	ENSG00000143195			18131	protein-coding gene	gene with protein product	"LISCH-like"		"chromosome 1 open reading frame 32"	C1orf32			Standard	NM_199351		Approved		uc001gdx.2	Q71H61	OTTHUMG00000034320	ENST00000271417.3:c.1375C>T	chr1.hg19:g.166890453G>A	ENSP00000271417:p.Arg459Cys	37.0	0.0		76.0	28.0	NM_199351		Missense_Mutation	SNP	ENST00000271417.3	hg19	CCDS1256.1	.	.	.	.	.	.	.	.	.	.	G	12.83	2.056137	0.36277	.	.	ENSG00000143195	ENST00000271417;ENST00000525740;ENST00000529071;ENST00000526687;ENST00000528703	T;T;T;T;T	0.79554	0.37;-1.28;0.37;-1.27;-0.26	4.28	3.24	0.37175	.	0.652062	0.14351	N	0.325100	T	0.72423	0.3458	L	0.58101	1.795	0.35681	D	0.814095	D	0.59767	0.986	P	0.46339	0.513	T	0.73388	-0.3998	10	0.44086	T	0.13	.	13.2225	0.59896	0.0:0.0:0.7277:0.2723	.	459	Q71H61	ILDR2_HUMAN	C	459;332;440;351;400	ENSP00000271417:R459C;ENSP00000436120:R332C;ENSP00000436882:R440C;ENSP00000434273:R351C;ENSP00000432750:R400C	ENSP00000271417:R459C	R	-	1	0	ILDR2	165157077	0.998000	0.40836	0.972000	0.41901	0.034000	0.12701	1.073000	0.30691	1.922000	0.55676	0.558000	0.71614	CGC	.	.		0.706	ILDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082880.2	NM_199351		A	166890453	G	A	166890453	3	1	352	1	0	0	0	0	1	0	0	0	7719	1087	38	1	552	1	ILDR2	1	166890453	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	5701753	166890453	82360168	38	49454										
ASTN1	460	hgsc.bcm.edu	37	chr1	176926868	176926868	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	atacagcggaaattcttactGcagcccccgttatctttgct	7	12	2	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:176926868G>A	ENST00000367654.3	-	11	2068	c.1857C>T	c.(1855-1857)tgC>tgT	p.C619C	ASTN1_ENST00000424564.2_Silent_p.C611C|ASTN1_ENST00000361833.2_Silent_p.C611C|ASTN1_ENST00000281881.3_5'UTR|ASTN1_ENST00000367657.3_Silent_p.C611C	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	619	EGF-like 2.				locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						AATTCTTACTGCAGCCCCCGT	0.532																																					p.C611C		Atlas-SNP	.											.	ASTN1	314	.	0			c.C1833T						.						81	77	78					1																	176926868		2203	4300	6503	SO:0001819	synonymous_variant	460	exon11			CTTACTGCAGCCC	AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"astrotactin"	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.1857C>T	chr1.hg19:g.176926868G>A		186.0	0.0		262.0	32.0	NM_004319	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Silent	SNP	ENST00000367654.3	hg19																																																																																				.	.		0.532	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319		A	176926868	G	A	176926868	2	1	352	1	0	0	0	0	0	0	0	1	1064	1311	46	3		3	ASTN1	1	176926868	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	10036415	176926868	72323753	39	49455										
SEC16B	89866	hgsc.bcm.edu	37	chr1	177902746	177902746	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tggcggaactctcagaaataCttcgtggtctagcagccaat	10	10	2	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:177902746C>T	ENST00000308284.6	-	21	2686	c.2597G>A	c.(2596-2598)aGt>aAt	p.S866N	RP4-798P15.3_ENST00000354921.3_RNA|SEC16B_ENST00000495165.1_5'UTR	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	866					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|peroxisome fission (GO:0016559)|peroxisome organization (GO:0007031)|positive regulation of gene expression (GO:0010628)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endoplasmic reticulum (GO:0070972)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)				central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)|stomach(1)	35						CTCAGAAATACTTCGTGGTCT	0.468																																					p.S866N		Atlas-SNP	.											.	SEC16B	92	.	0			c.G2597A						.						61	61	61					1																	177902746		1910	4129	6039	SO:0001583	missense	89866	exon21			GAAATACTTCGTG	AK090411	CCDS44281.1	1q25.2	2012-10-08	2007-06-20	2007-06-20	ENSG00000120341	ENSG00000120341			30301	protein-coding gene	gene with protein product	"regucalcin gene promotor region related protein"	612855	"leucine zipper transcription regulator 2"	LZTR2		11572484, 11605020	Standard	NM_033127		Approved	RGPR, PGPR-p117	uc001gli.1	Q96JE7	OTTHUMG00000167206	ENST00000308284.6:c.2597G>A	chr1.hg19:g.177902746C>T	ENSP00000308339:p.Ser866Asn	83.0	0.0		90.0	15.0	NM_033127	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Missense_Mutation	SNP	ENST00000308284.6	hg19	CCDS44281.1	.	.	.	.	.	.	.	.	.	.	C	8.850	0.944302	0.18356	.	.	ENSG00000120341	ENST00000308284;ENST00000414025;ENST00000239472	T	0.15256	2.44	5.65	-11.3	0.00108	.	1.426080	0.03897	N	0.279737	T	0.06690	0.0171	N	0.04768	-0.165	0.09310	N	1	B;B;B;B	0.06786	0.001;0.001;0.001;0.0	B;B;B;B	0.06405	0.002;0.001;0.001;0.001	T	0.25710	-1.0124	10	0.34782	T	0.22	0.3745	8.471	0.32986	0.0:0.2047:0.3889:0.4063	.	421;867;866;563	B1AM07;B1AM08;Q96JE7;Q96PW0	.;.;SC16B_HUMAN;.	N	866;550;581	ENSP00000308339:S866N	ENSP00000239472:S581N	S	-	2	0	AL359075.1	176169369	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.568000	0.05909	-2.888000	0.00316	-0.137000	0.14449	AGT	.	.		0.468	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127		T	177902746	C	T	177902746	3	4	352	1	0	0	0	0	1	0	0	0	14002	565	20	3	609	3	SEC16B	1	177902746	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	975878	177902746	71347875	40	49456										
TOR3A	64222	hgsc.bcm.edu	37	chr1	179054904	179054904	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ccacggctggtctggcacagGcaagaacttcgtggcacgga	14	12	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:179054904G>A	ENST00000367627.3	+	3	1267	c.515G>A	c.(514-516)gGc>gAc	p.G172D	TOR3A_ENST00000352445.6_Missense_Mutation_p.G172D	NM_022371.3	NP_071766.2	Q9H497	TOR3A_HUMAN	torsin family 3, member A	172					ATP catabolic process (GO:0006200)|chaperone mediated protein folding requiring cofactor (GO:0051085)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|pancreas(1)|urinary_tract(1)	13						TCTGGCACAGGCAAGAACTTC	0.572																																					p.G172D		Atlas-SNP	.											.	TOR3A	28	.	0			c.G515A						.						94	74	80					1																	179054904		2203	4300	6503	SO:0001583	missense	64222	exon3			GCACAGGCAAGAA	BC001085	CCDS1329.1	1q25.2	2008-02-05	2003-04-02		ENSG00000186283	ENSG00000186283			11997	protein-coding gene	gene with protein product		607555	"ATP-dependant interferon responsive"	ADIR		10644435	Standard	NM_022371		Approved	FLJ22345, ADIR2	uc001gmd.3	Q9H497	OTTHUMG00000035077	ENST00000367627.3:c.515G>A	chr1.hg19:g.179054904G>A	ENSP00000356599:p.Gly172Asp	89.0	0.0		93.0	32.0	NM_022371	B4DSY0|B7ZB65|Q5M7Y7|Q8WVA7|Q8WWM2|Q9H495|Q9H6E7	Missense_Mutation	SNP	ENST00000367627.3	hg19	CCDS1329.1	.	.	.	.	.	.	.	.	.	.	G	34	5.388732	0.95988	.	.	ENSG00000186283	ENST00000367627;ENST00000367625;ENST00000352445;ENST00000447595	D;T;D;D	0.92048	-2.96;-0.32;-2.96;-2.96	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	D	0.97451	0.9166	H	0.95365	3.66	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98406	1.0570	10	0.87932	D	0	-31.3179	18.4682	0.90763	0.0:0.0:1.0:0.0	.	172	Q9H497	TOR3A_HUMAN	D	172;125;172;64	ENSP00000356599:G172D;ENSP00000356597:G125D;ENSP00000335351:G172D;ENSP00000410195:G64D	ENSP00000335351:G172D	G	+	2	0	TOR3A	177321527	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.476000	0.97823	2.606000	0.88127	0.655000	0.94253	GGC	.	.		0.572	TOR3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084927.1	NM_022371		A	179054904	G	A	179054904	3	1	352	1	0	0	0	0	1	0	0	0	16391	1203	42	3	525	3	TOR3A	1	179054904	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	1152158	179054904	70195717	41	49457										
TDRD5	163589	hgsc.bcm.edu	37	chr1	179609580	179609580	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gcttgggtgagaccagtagaGgtatgtttgcttgtctccca	13	8	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:179609580G>T	ENST00000367614.1	+	11	2159	c.1800G>T	c.(1798-1800)gaG>gaT	p.E600D	TDRD5_ENST00000294848.8_Splice_Site_p.E600D|TDRD5_ENST00000444136.1_Splice_Site_p.E600D	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	600					DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)				NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						GACCAGTAGAGGTATGTTTGC	0.403																																					p.E600D		Atlas-SNP	.											.	TDRD5	149	.	0			c.G1800T						.						185	150	162					1																	179609580		2203	4300	6503	SO:0001630	splice_region_variant	163589	exon11			AGTAGAGGTATGT	AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"Tudor domain containing"	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.1800+1G>T	chr1.hg19:g.179609580G>T		79.0	0.0		126.0	15.0	NM_173533	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Missense_Mutation	SNP	ENST00000367614.1	hg19	CCDS1332.1	.	.	.	.	.	.	.	.	.	.	G	17.24	3.339404	0.60963	.	.	ENSG00000162782	ENST00000367614;ENST00000294848;ENST00000444136;ENST00000417329	T;T;T;T	0.32753	2.67;2.67;2.83;1.44	5.82	5.82	0.92795	.	0.434585	0.24889	N	0.034781	T	0.30759	0.0775	L	0.59436	1.845	0.54753	D	0.999986	P;B	0.39903	0.694;0.376	B;B	0.34779	0.189;0.067	T	0.04495	-1.0947	10	0.26408	T	0.33	-10.4851	16.8044	0.85622	0.0:0.0:1.0:0.0	.	600;600	Q8NAT2-1;Q8NAT2	.;TDRD5_HUMAN	D	600;600;600;56	ENSP00000356586:E600D;ENSP00000294848:E600D;ENSP00000406052:E600D;ENSP00000410744:E56D	ENSP00000294848:E600D	E	+	3	2	TDRD5	177876203	1.000000	0.71417	0.998000	0.56505	0.975000	0.68041	6.688000	0.74557	2.752000	0.94435	0.655000	0.94253	GAG	.	.		0.403	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533	Missense_Mutation	T	179609580	G	T	179609580	5	4	352	1	0	0	0	0	0	0	1	0	15748	1014	35	3	1838	3	TDRD5	1	179609580	Splice_Site	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	554676	179609580	69641041	42	49458										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186076037	186076037	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tggaggatacaggaagatatAcatgtctggcatccagtcct	11	8	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:186076037A>G	ENST00000271588.4	+	70	11021	c.10792A>G	c.(10792-10794)Aca>Gca	p.T3598A	HMCN1_ENST00000367492.2_Missense_Mutation_p.T3598A	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	3598	Ig-like C2-type 34.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.T3598S(1)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						AGGAAGATATACATGTCTGGC	0.333																																					p.T3598A		Atlas-SNP	.											HMCN1,colon,carcinoma,-2,1	HMCN1	797	.	1	Substitution - Missense(1)	ovary(1)	c.A10792G						.						188	188	188					1																	186076037		2203	4300	6503	SO:0001583	missense	83872	exon70			AGATATACATGTC	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.10792A>G	chr1.hg19:g.186076037A>G	ENSP00000271588:p.Thr3598Ala	87.0	0.0		123.0	19.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	A	19.41	3.822714	0.71028	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.80033	-1.33;-1.33	5.38	5.38	0.77491	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.142752	0.64402	D	0.000007	D	0.85682	0.5753	M	0.64567	1.98	0.40244	D	0.977999	D	0.69078	0.997	D	0.69142	0.962	D	0.84838	0.0806	10	0.33940	T	0.23	.	9.8489	0.41043	0.9233:0.0:0.0767:0.0	.	3598	Q96RW7	HMCN1_HUMAN	A	3598	ENSP00000271588:T3598A;ENSP00000356462:T3598A	ENSP00000271588:T3598A	T	+	1	0	HMCN1	184342660	0.994000	0.37717	0.241000	0.24154	0.865000	0.49528	5.594000	0.67557	2.042000	0.60477	0.397000	0.26171	ACA	.	.		0.333	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		G	186076037	A	G	186076037	3	3	352	1	0	0	0	0	1	0	0	0	7229	391	14	2	11070	2	HMCN1	1	186076037	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	6466457	186076037	63174584	43	49459										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186135392	186135392	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gggacttactactgctcctgCcctaaaggcctcaccatagc	8	15	1	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:186135392C>A	ENST00000271588.4	+	99	15625	c.15396C>A	c.(15394-15396)tgC>tgA	p.C5132*	HMCN1_ENST00000367492.2_Nonsense_Mutation_p.C5132*	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	5132	EGF-like 1; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						ACTGCTCCTGCCCTAAAGGCC	0.453																																					p.C5132X		Atlas-SNP	.											.	HMCN1	797	.	0			c.C15396A						.						98	82	87					1																	186135392		2203	4300	6503	SO:0001587	stop_gained	83872	exon99			CTCCTGCCCTAAA	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.15396C>A	chr1.hg19:g.186135392C>A	ENSP00000271588:p.Cys5132*	82.0	0.0		100.0	7.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Nonsense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	C	56	26.144844	0.99967	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	.	.	.	5.44	-1.17	0.09648	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.1066	0.25366	0.0:0.4605:0.1095:0.43	.	.	.	.	X	5132	.	ENSP00000271588:C5132X	C	+	3	2	HMCN1	184402015	0.910000	0.30920	0.244000	0.24202	0.660000	0.38997	0.026000	0.13599	-0.539000	0.06273	0.650000	0.86243	TGC	.	.		0.453	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		A	186135392	C	A	186135392	4	1	352	1	0	0	0	0	0	1	0	0	7229	747	26	3	15790	3	HMCN1	1	186135392	Nonsense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	59355	186135392	63115229	44	49460										
KCNT2	343450	hgsc.bcm.edu	37	chr1	196274397	196274397	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gaaagagcaagagagtaacaGtctttggctctgaattgcat	11	6	2	3			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:196274397G>T	ENST00000294725.9	-	22	3477	c.2562C>A	c.(2560-2562)gaC>gaA	p.D854E	KCNT2_ENST00000498426.1_5'UTR|KCNT2_ENST00000451324.2_Intron|KCNT2_ENST00000609185.1_Missense_Mutation_p.D780E|KCNT2_ENST00000367433.5_Missense_Mutation_p.D830E|KCNT2_ENST00000367431.4_Missense_Mutation_p.D780E			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	854					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(16)|lung(43)|ovary(5)|pancreas(1)|prostate(1)|skin(11)|stomach(2)|upper_aerodigestive_tract(1)	97						GAGAGTAACAGTCTTTGGCTC	0.353																																					p.D854E		Atlas-SNP	.											.	KCNT2	243	.	0			c.C2562A						.						136	126	129					1																	196274397		2203	4300	6503	SO:0001583	missense	343450	exon22			GTAACAGTCTTTG	BX647852, AY359444, AK127807	CCDS1384.1, CCDS72994.1, CCDS72995.1	1q31.3	2012-07-05			ENSG00000162687	ENSG00000162687		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18866	protein-coding gene	gene with protein product	"sodium and chloride activated ATP sensitive potassium channel"	610044				16382103	Standard	NM_198503		Approved	KCa4.2, SLICK, SLO2.1	uc001gtd.1	Q6UVM3	OTTHUMG00000035611	ENST00000294725.9:c.2562C>A	chr1.hg19:g.196274397G>T	ENSP00000294725:p.Asp854Glu	85.0	0.0		137.0	8.0	NM_198503	Q3SY59|Q5VTN1|Q6ZMT3	Missense_Mutation	SNP	ENST00000294725.9	hg19	CCDS1384.1	.	.	.	.	.	.	.	.	.	.	G	19.99	3.929055	0.73327	.	.	ENSG00000162687	ENST00000367433;ENST00000367431;ENST00000294725	T;T;T	0.80653	-1.4;-1.4;-1.4	4.56	3.63	0.41609	.	0.192749	0.36234	N	0.002716	D	0.86322	0.5905	M	0.62154	1.92	0.80722	D	1	D;D;D;D;D	0.71674	0.985;0.996;0.998;0.991;0.985	P;D;D;P;P	0.72982	0.826;0.954;0.979;0.885;0.826	D	0.86851	0.2023	10	0.87932	D	0	-9.8673	10.7182	0.46026	0.1584:0.0:0.8416:0.0	.	854;812;830;780;854	A9LNM6;Q6UVM3-4;Q6UVM3-2;Q6UVM3-3;Q6UVM3	.;.;.;.;KCNT2_HUMAN	E	830;780;854	ENSP00000356403:D830E;ENSP00000356401:D780E;ENSP00000294725:D854E	ENSP00000294725:D854E	D	-	3	2	KCNT2	194541020	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.675000	0.61619	1.241000	0.43820	0.650000	0.86243	GAC	.	.		0.353	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503		T	196274397	G	T	196274397	3	4	352	1	0	0	0	0	1	0	0	0	8101	1020	36	3	873	3	KCNT2	1	196274397	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	10139005	196274397	52976224	45	49461										
ELF3	1999	hgsc.bcm.edu	37	chr1	201982384	201982385	+	Frame_Shift_Del	DEL	AA	AA	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gccggccccgaaagctgagcAaagagtactgggactgtctc							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:201982384_201982385delAA	ENST00000359651.3	+	6	3955_3956	c.763_764delAA	c.(763-765)aaafs	p.K255fs	RP11-465N4.4_ENST00000419190.1_RNA|RP11-510N19.5_ENST00000504773.1_RNA|ELF3_ENST00000367283.3_Frame_Shift_Del_p.K255fs|ELF3_ENST00000367284.5_Frame_Shift_Del_p.K255fs					E74-like factor 3 (ets domain transcription factor, epithelial-specific )											breast(2)|endometrium(2)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	20						AAAGCTGAGCAAAGAGTACTGG	0.639																																					p.254_255del		Atlas-INDEL	.											.	ELF3	92	.	0			c.762_763del						.																																			SO:0001589	frameshift_variant	1999	exon7			.	AF016295	CCDS1419.1	1q32.2	2008-02-05			ENSG00000163435	ENSG00000163435			3318	protein-coding gene	gene with protein product		602191		ESX		9395241, 9129154	Standard	NM_001114309		Approved	EPR-1, ESE-1, ERT	uc001gxh.4	P78545	OTTHUMG00000035867	ENST00000359651.3:c.763_764delAA	chr1.hg19:g.201982384_201982385delAA	ENSP00000352673:p.Lys255fs	231.0	0.0		302.0	30.0	NM_001114309		Frame_Shift_Del	DEL	ENST00000359651.3	hg19	CCDS1419.1																																																																																			.	.		0.639	ELF3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087360.1	NM_004433		-	201982385	AA	-	201982384	7	5	352	1	0	1	0	1	0	0	0	0	5057	131	5	0	785	0	ELF3	1	201982384	Frame_Shift_Del	DEL	AA	TCGA-WQ-A9G7-01A-11D-A36X-10	5707987	201982384	47268237	46	49462										
NFASC	23114	hgsc.bcm.edu	37	chr1	204924033	204924033	+	Frame_Shift_Del	DEL	C	C	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cctttgacgctccagtgcaaCcccccgcctggacttccatc							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:204924033delC	ENST00000401399.1	+	6	688	c.489delC	c.(487-489)aacfs	p.N163fs	NFASC_ENST00000338515.6_Frame_Shift_Del_p.N163fs|NFASC_ENST00000367171.4_Frame_Shift_Del_p.N163fs|NFASC_ENST00000367169.4_Frame_Shift_Del_p.N163fs|NFASC_ENST00000338586.6_Frame_Shift_Del_p.N163fs|NFASC_ENST00000339876.6_Frame_Shift_Del_p.N163fs|NFASC_ENST00000367172.4_Frame_Shift_Del_p.N163fs|NFASC_ENST00000513543.1_Frame_Shift_Del_p.N157fs|NFASC_ENST00000404907.1_Frame_Shift_Del_p.N157fs|NFASC_ENST00000404076.1_Frame_Shift_Del_p.N157fs|NFASC_ENST00000403080.1_Frame_Shift_Del_p.N163fs|NFASC_ENST00000360049.4_Frame_Shift_Del_p.N157fs|NFASC_ENST00000539706.1_Frame_Shift_Del_p.N157fs|NFASC_ENST00000367170.4_Frame_Shift_Del_p.N163fs			O94856	NFASC_HUMAN	neurofascin	163	Ig-like C2-type 2.				axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)		p.P159fs*12(1)|p.P165fs*12(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			TCCAGTGCAACCCCCCGCCTG	0.562																																					p.N163fs		Atlas-INDEL	.											.	NFASC	396	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.488delA						.						144	145	145					1																	204924033		2203	4300	6503	SO:0001589	frameshift_variant	23114	exon7			.	AK027553	CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1	1q32.1	2013-02-11	2010-06-24		ENSG00000163531	ENSG00000163531		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	29866	protein-coding gene	gene with protein product		609145	"neurofascin homolog (chicken)"			1377696, 8672144	Standard	NM_015090		Approved	NRCAML, KIAA0756, FLJ46866, NF	uc001hbj.3	O94856	OTTHUMG00000151697	ENST00000401399.1:c.489delC	chr1.hg19:g.204924033delC	ENSP00000385637:p.Asn163fs	110.0	0.0		134.0	30.0	NM_001005388	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Frame_Shift_Del	DEL	ENST00000401399.1	hg19	CCDS53460.1																																																																																			.	.		0.562	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388		-	204924033	C	-	204924033	7	5	352	1	0	1	0	1	0	0	0	0	10368	506	18	0	507	0	NFASC	1	204924033	Frame_Shift_Del	DEL	C	TCGA-WQ-A9G7-01A-11D-A36X-10	2941649	204924033	44326588	47	49463										
CD55	1604	hgsc.bcm.edu	37	chr1	207495135	207495135	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ccgtcgcgcggccgagcgtgCccgcggcgctgcccctcctc	14	21	0	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:207495135C>T	ENST00000367064.3	+	1	283	c.25C>T	c.(25-27)Ccc>Tcc	p.P9S	CD55_ENST00000367063.2_Missense_Mutation_p.P9S|CD55_ENST00000367062.4_Missense_Mutation_p.P9S|CD55_ENST00000367065.5_Missense_Mutation_p.P9S|CD55_ENST00000391920.4_Missense_Mutation_p.P9S|CD55_ENST00000391921.4_Missense_Mutation_p.P9S|CD55_ENST00000367067.4_Missense_Mutation_p.P9S|CD55_ENST00000314754.8_Missense_Mutation_p.P9S	NM_000574.3	NP_000565.1	P08174	DAF_HUMAN	CD55 molecule, decay accelerating factor for complement (Cromer blood group)	9					CD4-positive, alpha-beta T cell cytokine production (GO:0035743)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|maternal process involved in parturition (GO:0060137)|negative regulation of complement activation (GO:0045916)|positive regulation of CD4-positive, alpha-beta T cell activation (GO:2000516)|positive regulation of CD4-positive, alpha-beta T cell proliferation (GO:2000563)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of complement activation (GO:0030449)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|respiratory burst (GO:0045730)|response to peptide hormone (GO:0043434)|response to virus (GO:0009615)|spermatogenesis (GO:0007283)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	enzyme inhibitor activity (GO:0004857)|lipid binding (GO:0008289)|virus receptor activity (GO:0001618)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	16					Chloramphenicol(DB00446)	GCCGAGCGTGCCCGCGGCGCT	0.771											OREG0031708	type=REGULATORY REGION|TFbs=RELA|Dataset=RELA (p65) ChIP-PET Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with paired-end diTag sequencing (ChIP-PET)																									p.P9S		Atlas-SNP	.											.	CD55	55	.	0			c.C25T						.						2	2	2					1																	207495135		1155	2320	3475	SO:0001583	missense	1604	exon1			AGCGTGCCCGCGG	BC001288	CCDS31006.1, CCDS44307.1, CCDS73022.1	1q32	2014-09-17	2006-03-28	2006-02-23	ENSG00000196352	ENSG00000196352		"CD molecules", "Blood group antigens"	2665	protein-coding gene	gene with protein product		125240	"decay accelerating factor for complement (CD55, Cromer blood group system)"	DAF			Standard	XM_005273077		Approved	CR, TC, CROM	uc001hfr.4	P08174	OTTHUMG00000036255	ENST00000367064.3:c.25C>T	chr1.hg19:g.207495135C>T	ENSP00000356031:p.Pro9Ser	41.0	0.0	2168	86.0	14.0	NM_001114752	B1AP14|D3DT83|D3DT84|E7ER69|P09679|P78361|Q14UF2|Q14UF3|Q14UF4|Q14UF5|Q14UF6	Missense_Mutation	SNP	ENST00000367064.3	hg19	CCDS31006.1	.	.	.	.	.	.	.	.	.	.	C	16.78	3.217896	0.58560	.	.	ENSG00000196352	ENST00000367064;ENST00000367063;ENST00000391921;ENST00000367067;ENST00000536840;ENST00000314754;ENST00000367065;ENST00000391920;ENST00000367062	T;T;T;T;T;T;T;T	0.37411	1.25;1.46;1.6;3.66;1.33;1.32;1.2;1.24	3.38	1.39	0.22231	.	0.517672	0.17471	N	0.173092	T	0.34803	0.0910	N	0.24115	0.695	0.09310	N	1	D;P;P;P;B	0.54601	0.967;0.799;0.518;0.663;0.384	D;B;B;B;B	0.65140	0.932;0.169;0.162;0.098;0.078	T	0.10590	-1.0623	10	0.33940	T	0.23	.	3.6887	0.08338	0.2419:0.6247:0.0:0.1334	.	9;9;9;9;9	B1AP15;Q14UF4;P08174-2;P08174;B1AP13	.;.;.;DAF_HUMAN;.	S	9	ENSP00000356031:P9S;ENSP00000356030:P9S;ENSP00000375788:P9S;ENSP00000356034:P9S;ENSP00000316333:P9S;ENSP00000356032:P9S;ENSP00000375787:P9S;ENSP00000356029:P9S	ENSP00000316333:P9S	P	+	1	0	CD55	205561758	0.006000	0.16342	0.000000	0.03702	0.001000	0.01503	1.129000	0.31381	0.133000	0.18654	-0.258000	0.10820	CCC	.	.		0.771	CD55-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000088208.2	NM_000574		T	207495135	C	T	207495135	3	4	352	1	0	0	0	0	1	0	0	0	3026	739	26	3	27	3	CD55	1	207495135	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	2571102	207495135	41755486	48	49464										
USH2A	7399	hgsc.bcm.edu	37	chr1	216062118	216062118	+	Frame_Shift_Del	DEL	C	C	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ctctggacttgggatcccttCcggtgcccctgggagtgtcc							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:216062118delC	ENST00000307340.3	-	41	8259	c.7873delG	c.(7873-7875)gaafs	p.E2625fs	RP5-1111A8.3_ENST00000414995.1_RNA|USH2A_ENST00000366943.2_Frame_Shift_Del_p.E2625fs	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	2625	Fibronectin type-III 13. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			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)		GGGATCCCTTCCGGTGCCCCT	0.507										HNSCC(13;0.011)																											p.E2625fs		Atlas-INDEL	.											.	USH2A	1168	.	0			c.7874delA						.						76	79	78					1																	216062118		2203	4300	6503	SO:0001589	frameshift_variant	7399	exon41			.	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.7873delG	chr1.hg19:g.216062118delC	ENSP00000305941:p.Glu2625fs	114.0	0.0		170.0	27.0	NM_206933	Q5VVM9|Q6S362|Q9NS27	Frame_Shift_Del	DEL	ENST00000307340.3	hg19	CCDS31025.1																																																																																			.	.		0.507	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		-	216062118	C	-	216062118	7	5	352	1	0	1	0	1	0	0	0	0	17051	864	30	0	7863	0	USH2A	1	216062118	Frame_Shift_Del	DEL	C	TCGA-WQ-A9G7-01A-11D-A36X-10	8566983	216062118	33188503	49	49465										
GPATCH2	55105	hgsc.bcm.edu	37	chr1	217784290	217784290	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ttaagatactttcaaagacaGgatctggtacatttttgtct	7	6	3	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:217784290G>T	ENST00000366935.3	-	4	1069	c.959C>A	c.(958-960)cCt>cAt	p.P320H	GPATCH2_ENST00000366934.3_Missense_Mutation_p.P320H	NM_018040.2	NP_060510.1	Q9NW75	GPTC2_HUMAN	G patch domain containing 2	320					negative regulation of phosphatase activity (GO:0010923)		nucleic acid binding (GO:0003676)			NS(1)|breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)	35				OV - Ovarian serous cystadenocarcinoma(81;0.0397)|all cancers(67;0.0744)|GBM - Glioblastoma multiforme(131;0.0872)		TTCAAAGACAGGATCTGGTAC	0.448																																					p.P320H		Atlas-SNP	.											.	GPATCH2	53	.	0			c.C959A						.						160	143	149					1																	217784290		2203	4300	6503	SO:0001583	missense	55105	exon4			AAGACAGGATCTG	AK001114	CCDS1518.1, CCDS73031.1	1q41	2013-01-28		2006-12-13	ENSG00000092978	ENSG00000092978		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "G patch domain containing"	25499	protein-coding gene	gene with protein product	"cancer/testis antigen 110", "protein phosphatase 1, regulatory subunit 30"			GPATC2		19432882, 15375528	Standard	XM_005273174		Approved	FLJ10252, CT110, PPP1R30	uc001hlf.1	Q9NW75	OTTHUMG00000000527	ENST00000366935.3:c.959C>A	chr1.hg19:g.217784290G>T	ENSP00000355902:p.Pro320His	112.0	0.0		140.0	17.0	NM_018040	Q5VYK7|Q5VYK8|Q86YE7	Missense_Mutation	SNP	ENST00000366935.3	hg19	CCDS1518.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.856738	0.91433	.	.	ENSG00000092978	ENST00000366935;ENST00000366934	T;T	0.57907	0.37;0.37	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.74543	0.3730	M	0.75447	2.3	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.76564	-0.2913	10	0.87932	D	0	-15.1347	19.7375	0.96212	0.0:0.0:1.0:0.0	.	320;320	Q9NW75-2;Q9NW75	.;GPTC2_HUMAN	H	320	ENSP00000355902:P320H;ENSP00000355901:P320H	ENSP00000355901:P320H	P	-	2	0	GPATCH2	215850913	1.000000	0.71417	0.971000	0.41717	0.998000	0.95712	9.458000	0.97634	2.649000	0.89929	0.591000	0.81541	CCT	.	.		0.448	GPATCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001272.1	NM_018040		T	217784290	G	T	217784290	3	4	352	1	0	0	0	0	1	0	0	0	6599	1000	35	3	655	3	GPATCH2	1	217784290	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	1722172	217784290	31466331	50	49466										
IARS2	55699	hgsc.bcm.edu	37	chr1	220273982	220273985	+	Frame_Shift_Del	DEL	AGAA	AGAA	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	atctttcagctatggaaattAgaaagaaaggtaaataatct							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	AGAA	AGAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:220273982_220273985delAGAA	ENST00000302637.5	+	3	645_648	c.541_544delAGAA	c.(541-546)agaaagfs	p.RK181fs	IARS2_ENST00000366922.1_Frame_Shift_Del_p.RK109fs	NM_018060.3	NP_060530.3	Q9NSE4	SYIM_HUMAN	isoleucyl-tRNA synthetase 2, mitochondrial	181					gene expression (GO:0010467)|isoleucyl-tRNA aminoacylation (GO:0006428)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|isoleucine-tRNA ligase activity (GO:0004822)			NS(1)|breast(1)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(7)|lung(17)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	51				GBM - Glioblastoma multiforme(131;0.0554)	L-Isoleucine(DB00167)	TATGGAAATTAGAAAGAAAGGTAA	0.353																																					p.180_181del		Atlas-INDEL	.											.	IARS2	106	.	0			c.540_543del						.																																			SO:0001589	frameshift_variant	55699	exon3			.	AK022665	CCDS1523.1	1q41	2011-07-01	2007-02-26		ENSG00000067704	ENSG00000067704	6.1.1.5	"Aminoacyl tRNA synthetases / Class I"	29685	protein-coding gene	gene with protein product	"isoleucine tRNA ligase 2, mitochondrial"	612801					Standard	NM_018060		Approved	FLJ10326	uc001hmc.3	Q9NSE4	OTTHUMG00000037287	ENST00000302637.5:c.541_544delAGAA	chr1.hg19:g.220273986_220273989delAGAA	ENSP00000303279:p.Arg181fs	224.0	0.0		329.0	24.0	NM_018060	B2RPG8|Q1M2P9|Q6PI85|Q7L439|Q86WU9|Q96D91|Q9H9Q8|Q9NW42	Frame_Shift_Del	DEL	ENST00000302637.5	hg19	CCDS1523.1																																																																																			.	.		0.353	IARS2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018060		-	220273985	AGAA	-	220273982	7	5	352	1	0	1	0	1	0	0	0	0	7483	412	15	0	551	0	IARS2	1	220273982	Frame_Shift_Del	DEL	AGAA	TCGA-WQ-A9G7-01A-11D-A36X-10	2489692	220273982	28976639	51	49467										
RAB3GAP2	25782	hgsc.bcm.edu	37	chr1	220330778	220330778	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gtccttccacggagagccacGcatcctcagtatccagcaca	8	16	1	1	rs369410531		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:220330778G>A	ENST00000358951.2	-	31	3505	c.3389C>T	c.(3388-3390)gCg>gTg	p.A1130V		NM_012414.3	NP_036546.2	Q9H2M9	RBGPR_HUMAN	RAB3 GTPase activating protein subunit 2 (non-catalytic)	1130					establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|intracellular protein transport (GO:0006886)|positive regulation of catalytic activity (GO:0043085)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of GTPase activity (GO:0043087)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	enzyme activator activity (GO:0008047)|enzyme regulator activity (GO:0030234)|GTPase activator activity (GO:0005096)|protein heterodimerization activity (GO:0046982)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(1)	39				GBM - Glioblastoma multiforme(131;0.0443)		GGAGAGCCACGCATCCTCAGT	0.502																																					p.A1130V		Atlas-SNP	.											RAB3GAP2,NS,carcinoma,+1,1	RAB3GAP2	120	.	0			c.C3389T						.	G	VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	111	99	103		3389	3.6	0.1	1		103	0,8600		0,0,4300	no	missense	RAB3GAP2	NM_012414.3	64	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	1130/1394	220330778	1,13005	2203	4300	6503	SO:0001583	missense	25782	exon31			AGCCACGCATCCT	AB020646	CCDS31028.1	1q41	2014-03-03			ENSG00000118873	ENSG00000118873			17168	protein-coding gene	gene with protein product		609275				15696165, 16532399, 24482476	Standard	NM_012414		Approved	RAB3-GAP150, KIAA0839, DKFZP434D245, SPG69	uc010puk.1	Q9H2M9	OTTHUMG00000037139	ENST00000358951.2:c.3389C>T	chr1.hg19:g.220330778G>A	ENSP00000351832:p.Ala1130Val	144.0	0.0		189.0	28.0	NM_012414	A6H8V0|O75872|Q9HAB0|Q9UFJ7|Q9UQ15	Missense_Mutation	SNP	ENST00000358951.2	hg19	CCDS31028.1	.	.	.	.	.	.	.	.	.	.	G	7.358	0.624306	0.14193	2.27E-4	0.0	ENSG00000118873	ENST00000358951	T	0.33438	1.41	5.47	3.6	0.41247	.	0.278782	0.39834	N	0.001253	T	0.18800	0.0451	L	0.29908	0.895	0.49299	D	0.999779	B;B	0.34372	0.451;0.451	B;B	0.34242	0.178;0.178	T	0.03840	-1.0999	10	0.02654	T	1	.	11.9408	0.52899	0.1413:0.0:0.8587:0.0	.	1130;1130	Q9H2M9;A6H8V0	RBGPR_HUMAN;.	V	1130	ENSP00000351832:A1130V	ENSP00000351832:A1130V	A	-	2	0	RAB3GAP2	218397401	0.997000	0.39634	0.071000	0.20095	0.988000	0.76386	3.624000	0.54231	0.678000	0.31325	0.655000	0.94253	GCG	.	.		0.502	RAB3GAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090205.2	NM_012414		A	220330778	G	A	220330778	3	1	352	1	0	0	0	0	1	0	0	0	12951	1087	38	1	812	1	RAB3GAP2	1	220330778	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	56796	220330778	28919843	52	49468										
HHIPL2	79802	hgsc.bcm.edu	37	chr1	222721145	222721145	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	attccatgatgtcccagtacCgggcagcgatgcggcggtcc	13	13	0	1	rs377410734		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:222721145C>T	ENST00000343410.6	-	1	300	c.242G>A	c.(241-243)cGg>cAg	p.R81Q		NM_024746.3	NP_079022.2	Q6UWX4	HIPL2_HUMAN	HHIP-like 2	81					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)			NS(2)|endometrium(8)|kidney(4)|large_intestine(7)|lung(28)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59				GBM - Glioblastoma multiforme(131;0.0185)		GTCCCAGTACCGGGCAGCGAT	0.517																																					p.R81Q		Atlas-SNP	.											.	HHIPL2	122	.	0			c.G242A						.						61	62	61					1																	222721145		1975	4142	6117	SO:0001583	missense	79802	exon1			CAGTACCGGGCAG	BC007638	CCDS1530.2	1q41	2008-02-05	2008-01-16	2008-01-16	ENSG00000143512	ENSG00000143512			25842	protein-coding gene	gene with protein product			"KIAA1822-like"	KIAA1822L		12975309	Standard	NM_024746		Approved	FLJ13840	uc001hnh.1	Q6UWX4	OTTHUMG00000037545	ENST00000343410.6:c.242G>A	chr1.hg19:g.222721145C>T	ENSP00000342118:p.Arg81Gln	137.0	0.0		180.0	16.0	NM_024746	Q6GU65|Q96BT4|Q96BU5|Q9H8A0	Missense_Mutation	SNP	ENST00000343410.6	hg19	CCDS1530.2	.	.	.	.	.	.	.	.	.	.	C	9.510	1.105474	0.20632	.	.	ENSG00000143512	ENST00000343410	T	0.55760	0.5	4.93	3.06	0.35304	Folate receptor-like (1);	0.255249	0.33364	N	0.004981	T	0.46983	0.1421	L	0.51853	1.615	0.09310	N	1	P	0.42757	0.789	P	0.45449	0.481	T	0.28964	-1.0027	10	0.32370	T	0.25	-8.9264	6.5416	0.22382	0.0:0.5772:0.0:0.4228	.	81	Q6UWX4	HIPL2_HUMAN	Q	81	ENSP00000342118:R81Q	ENSP00000342118:R81Q	R	-	2	0	HHIPL2	220787768	0.002000	0.14202	0.443000	0.26883	0.008000	0.06430	0.864000	0.27926	0.482000	0.27582	-0.140000	0.14226	CGG	.	.		0.517	HHIPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091499.2	NM_024746		T	222721145	C	T	222721145	3	4	352	1	0	0	0	0	1	0	0	0	7103	652	23	1	1968	1	HHIPL2	1	222721145	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	2390367	222721145	26529476	53	49469										
PARP1	142	hgsc.bcm.edu	37	chr1	226570848	226570848	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tatacggtcctgttttttaaCcttcaatttcttgaggtaag	7	7	2	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:226570848C>T	ENST00000366794.5	-	8	1191	c.1048G>A	c.(1048-1050)Gtt>Att	p.V350I		NM_001618.3	NP_001609.2	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase 1	350					base-excision repair (GO:0006284)|cellular response to insulin stimulus (GO:0032869)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|gene expression (GO:0010467)|macrophage differentiation (GO:0030225)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|protein ADP-ribosylation (GO:0006471)|protein autoprocessing (GO:0016540)|protein poly-ADP-ribosylation (GO:0070212)|regulation of growth rate (GO:0040009)|signal transduction involved in regulation of gene expression (GO:0023019)|telomere maintenance (GO:0000723)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NAD binding (GO:0051287)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(4)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	44	Breast(184;0.133)			GBM - Glioblastoma multiforme(131;0.0531)		TGTTTTTTAACCTTCAATTTC	0.502								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA																													p.V350I		Atlas-SNP	.											.	PARP1	100	.	0			c.G1048A						.						110	137	128					1																	226570848		2203	4300	6503	SO:0001583	missense	142	exon8			TTTTAACCTTCAA	BC037545	CCDS1554.1	1q41-q42	2010-02-16	2008-07-28	2004-08-26	ENSG00000143799	ENSG00000143799	2.4.2.30	"Poly (ADP-ribose) polymerases"	270	protein-coding gene	gene with protein product		173870	"ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)", "poly (ADP-ribose) polymerase family, member 1"	PPOL, ADPRT		10964595	Standard	NM_001618		Approved	PARP	uc001hqd.4	P09874	OTTHUMG00000037556	ENST00000366794.5:c.1048G>A	chr1.hg19:g.226570848C>T	ENSP00000355759:p.Val350Ile	105.0	0.0		140.0	18.0	NM_001618	B1ANJ4|Q8IUZ9	Missense_Mutation	SNP	ENST00000366794.5	hg19	CCDS1554.1	.	.	.	.	.	.	.	.	.	.	C	13.28	2.189165	0.38707	.	.	ENSG00000143799	ENST00000366794	T	0.08984	3.03	5.27	-9.98	0.00438	.	0.427152	0.29515	N	0.011930	T	0.02119	0.0066	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40590	-0.9555	10	0.22706	T	0.39	-14.2178	2.8665	0.05603	0.1672:0.4042:0.078:0.3506	.	350	P09874	PARP1_HUMAN	I	350	ENSP00000355759:V350I	ENSP00000355759:V350I	V	-	1	0	PARP1	224637471	1.000000	0.71417	0.736000	0.30914	0.770000	0.43624	1.122000	0.31295	-1.426000	0.01994	-0.258000	0.10820	GTT	.	.		0.502	PARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091519.1	NM_001618		T	226570848	C	T	226570848	3	4	352	1	0	0	0	0	1	0	0	0	11463	507	18	3	2060	3	PARP1	1	226570848	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	3849703	226570848	22679773	54	49470										
OBSCN	84033	hgsc.bcm.edu	37	chr1	228547615	228547615	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ccgggtgaagaagatgggccCgcagggtgtgtctcccacca	15	12	1	3			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:228547615C>T	ENST00000422127.1	+	80	18705				OBSCN_ENST00000366709.4_Missense_Mutation_p.P3460L|OBSCN_ENST00000284548.11_Missense_Mutation_p.P6341L|OBSCN_ENST00000366707.4_Intron|OBSCN_ENST00000570156.2_Intron	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF						apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				AAGATGGGCCCGCAGGGTGTG	0.662																																					p.P6341L		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C19022T						.						19	23	22					1																	228547615		1928	4121	6049	SO:0001627	intron_variant	84033	exon81			TGGGCCCGCAGGG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.18662-2662C>T	chr1.hg19:g.228547615C>T		313.0	0.0		441.0	52.0	NM_052843	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	C	12.54	1.969036	0.34754	.	.	ENSG00000154358	ENST00000284548;ENST00000366709	T;T	0.56776	0.44;0.58	4.71	0.316	0.15857	.	.	.	.	.	T	0.27900	0.0687	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.16808	-1.0390	9	0.35671	T	0.21	.	6.1206	0.20151	0.2851:0.493:0.0:0.2219	.	6341	Q5VST9-3	.	L	6341;3460	ENSP00000284548:P6341L;ENSP00000355670:P3460L	ENSP00000284548:P6341L	P	+	2	0	OBSCN	226614238	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-0.089000	0.11180	0.211000	0.20683	-0.254000	0.11334	CCG	.	.		0.662	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228547615	C	T	228547615	1	4	352	0	1	0	0	0	0	0	0	0	10821	652	23	1		1	OBSCN	1	228547615	Intron	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	1976767	228547615	20703006	55	49471										
ABCB10	23456	hgsc.bcm.edu	37	chr1	229666151	229666151	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cttttctcatttaagatgacCccctctgaaacataaaatgg	5	10	2	3			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:229666151C>A	ENST00000344517.4	-	8	1482	c.1440G>T	c.(1438-1440)ggG>ggT	p.G480G		NM_012089.2	NP_036221.2	Q9NRK6	ABCBA_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 10	480					transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of mitochondrial membrane (GO:0032592)|mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)	31	Breast(184;0.143)|Ovarian(103;0.249)	Prostate(94;0.167)				TTAAGATGACCCCCTCTGAAA	0.413																																					p.G480G		Atlas-SNP	.											.	ABCB10	71	.	0			c.G1440T						.						78	86	83					1																	229666151		2203	4300	6503	SO:0001819	synonymous_variant	23456	exon8			GATGACCCCCTCT	U18237	CCDS1580.1	1q32	2012-03-14			ENSG00000135776	ENSG00000135776		"ATP binding cassette transporters / subfamily B"	41	protein-coding gene	gene with protein product	"ATP-binding cassette sub-family B member 10, mitochondrial", "ATP-binding cassette transporter 10", "ABC transporter 10 protein", "mitochondrial ATP-binding cassette 2"	605454				7766993	Standard	NM_012089		Approved	EST20237, M-ABC2, MTABC2	uc001htp.4	Q9NRK6	OTTHUMG00000039471	ENST00000344517.4:c.1440G>T	chr1.hg19:g.229666151C>A		73.0	0.0		82.0	14.0	NM_012089	Q13040|Q6P1Q8|Q9H3V0	Silent	SNP	ENST00000344517.4	hg19	CCDS1580.1																																																																																			.	.		0.413	ABCB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095240.1	NM_012089		A	229666151	C	A	229666151	2	1	352	1	0	0	0	0	0	0	0	1	41	610	22	3		3	ABCB10	1	229666151	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	1118536	229666151	19584470	56	49472										
FMN2	56776	hgsc.bcm.edu	37	chr1	240492397	240492397	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gagcacagtcagacgaactcGaaaaaatagaaaagcatggc	10	8	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:240492397G>A	ENST00000319653.9	+	9	4467	c.4237G>A	c.(4237-4239)Gaa>Aaa	p.E1413K	FMN2_ENST00000545751.1_Missense_Mutation_p.E9K	NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1413	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			AGACGAACTCGAAAAAATAGA	0.378																																					p.E1413K		Atlas-SNP	.											.	FMN2	451	.	0			c.G4237A						.						91	90	91					1																	240492397		2203	4300	6503	SO:0001583	missense	56776	exon9			GAACTCGAAAAAA	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.4237G>A	chr1.hg19:g.240492397G>A	ENSP00000318884:p.Glu1413Lys	237.0	0.0		341.0	34.0	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	hg19	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	G	14.63	2.591412	0.46214	.	.	ENSG00000155816	ENST00000319653;ENST00000441342;ENST00000545751;ENST00000537355	T;T;T	0.16324	2.35;2.35;2.35	5.41	5.41	0.78517	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.000000	0.64402	D	0.000009	T	0.41190	0.1148	M	0.66506	2.035	0.80722	D	1	P;B;D;D	0.89917	0.512;0.085;1.0;0.975	B;B;D;P	0.75020	0.243;0.062;0.985;0.766	T	0.05241	-1.0897	10	0.28530	T	0.3	.	19.2064	0.93732	0.0:0.0:1.0:0.0	.	9;59;42;1413	B4DP05;F5H2C1;B4DN09;Q9NZ56	.;.;.;FMN2_HUMAN	K	1413;59;9;40	ENSP00000318884:E1413K;ENSP00000388922:E59K;ENSP00000437918:E9K	ENSP00000318884:E1413K	E	+	1	0	FMN2	238559020	1.000000	0.71417	1.000000	0.80357	0.396000	0.30629	9.814000	0.99346	2.523000	0.85059	0.655000	0.94253	GAA	.	.		0.378	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		A	240492397	G	A	240492397	3	1	352	1	0	0	0	0	1	0	0	0	5958	1059	37	1	4271	1	FMN2	1	240492397	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	10826246	240492397	8758224	57	49473										
AHCTF1	25909	hgsc.bcm.edu	37	chr1	247024553	247024553	+	Frame_Shift_Del	DEL	T	T	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gtttccactggaactgcacaTtttttaggtgtagtaaatac							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:247024553delT	ENST00000391829.2	-	29	3903	c.3780delA	c.(3778-3780)aaafs	p.K1260fs	AHCTF1_ENST00000470300.1_5'UTR|AHCTF1_ENST00000326225.3_Frame_Shift_Del_p.K1269fs|AHCTF1_ENST00000366508.1_Frame_Shift_Del_p.K1295fs			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	1260	Disordered. {ECO:0000250}.|Necessary for nuclear localization. {ECO:0000250}.				cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(6)|cervix(3)|endometrium(8)|kidney(6)|large_intestine(12)|liver(2)|lung(21)|ovary(5)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	74	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			GAACTGCACATTTTTTAGGTG	0.358																																					p.C1270fs	Colon(145;197 1800 4745 15099 26333)	Atlas-INDEL	.											.	AHCTF1	187	.	0			c.3808delT						.						30	29	29					1																	247024553		2203	4293	6496	SO:0001589	frameshift_variant	25909	exon29			.		CCDS1629.1, CCDS1629.2	1q44	2008-09-09			ENSG00000153207	ENSG00000153207			24618	protein-coding gene	gene with protein product	"ELYS transcription factor like protein TMBS62"	610853				11952839	Standard	NM_015446		Approved	ELYS	uc001ibv.2	Q8WYP5	OTTHUMG00000040706	ENST00000391829.2:c.3780delA	chr1.hg19:g.247024553delT	ENSP00000375705:p.Lys1260fs	211.0	0.0		287.0	30.0	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Frame_Shift_Del	DEL	ENST00000391829.2	hg19																																																																																				.	.		0.358	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446		-	247024553	T	-	247024553	7	5	352	1	0	1	0	1	0	0	0	0	408	1490	52	0	3052	0	AHCTF1	1	247024553	Frame_Shift_Del	DEL	T	TCGA-WQ-A9G7-01A-11D-A36X-10	6532156	247024553	2226068	58	49474										
OR1C1	26188	hgsc.bcm.edu	37	chr1	247921056	247921056	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cagtggagaagataagtccaTaagatacgaggatacagaca	11	6	0	4	rs546878207		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:247921056T>C	ENST00000408896.2	-	1	926	c.653A>G	c.(652-654)tAt>tGt	p.Y218C		NM_012353.2	NP_036485.2	Q15619	OR1C1_HUMAN	olfactory receptor, family 1, subfamily C, member 1	218					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(32)|skin(2)|upper_aerodigestive_tract(1)	46	all_cancers(71;4.34e-05)|all_epithelial(71;1.13e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0786)|Lung NSC(105;0.0858)	all_cancers(173;0.0247)	OV - Ovarian serous cystadenocarcinoma(106;0.0168)			GATAAGTCCATAAGATACGAG	0.488																																					p.Y218C		Atlas-SNP	.											.	OR1C1	86	.	0			c.A653G						.						55	54	54					1																	247921056		2025	4192	6217	SO:0001583	missense	26188	exon1			AGTCCATAAGATA	X89674	CCDS41481.1	1q44	2012-08-09			ENSG00000221888	ENSG00000221888		"GPCR / Class A : Olfactory receptors"	8182	protein-coding gene	gene with protein product						9119360	Standard	NM_012353		Approved	TPCR27, HSTPCR27	uc010pza.2	Q15619	OTTHUMG00000040198	ENST00000408896.2:c.653A>G	chr1.hg19:g.247921056T>C	ENSP00000386138:p.Tyr218Cys	128.0	0.0		160.0	40.0	NM_012353	B9EIR9|Q5VVD2|Q6IF97|Q8NGZ1|Q96R83	Missense_Mutation	SNP	ENST00000408896.2	hg19	CCDS41481.1	.	.	.	.	.	.	.	.	.	.	T	9.224	1.034033	0.19590	.	.	ENSG00000221888	ENST00000408896	T	0.00520	6.85	3.22	3.22	0.36961	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.03871	0.0109	H	0.98721	4.31	0.09310	N	0.999997	D	0.89917	1.0	D	0.97110	1.0	T	0.15350	-1.0440	9	0.87932	D	0	.	11.6139	0.51078	0.0:0.0:0.0:1.0	.	218	Q15619	OR1C1_HUMAN	C	218	ENSP00000386138:Y218C	ENSP00000386138:Y218C	Y	-	2	0	OR1C1	245987679	0.957000	0.32711	0.274000	0.24659	0.110000	0.19582	1.681000	0.37618	1.466000	0.48025	0.482000	0.46254	TAT	.	.		0.488	OR1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096855.1			C	247921056	T	C	247921056	3	2	352	1	0	0	0	0	1	0	0	0	10961	1406	49	2	293	2	OR1C1	1	247921056	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	896503	247921056	1329565	59	49475										
OR2T4	127074	hgsc.bcm.edu	37	chr1	248525091	248525091	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ttttgtggttttcctgatggCgttgtctggaaatgctgtcc	12	7	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr1:248525091C>T	ENST00000366475.1	+	1	209	c.209C>T	c.(208-210)gCg>gTg	p.A70V		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	70						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TTCCTGATGGCGTTGTCTGGA	0.468																																					p.A70V		Atlas-SNP	.											.	OR2T4	126	.	0			c.C209T						.						316	255	276					1																	248525091		2203	4300	6503	SO:0001583	missense	127074	exon1			TGATGGCGTTGTC	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"GPCR / Class A : Olfactory receptors"	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.209C>T	chr1.hg19:g.248525091C>T	ENSP00000355431:p.Ala70Val	459.0	0.0		643.0	74.0	NM_001004696	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	hg19	CCDS31113.1	.	.	.	.	.	.	.	.	.	.	C	13.73	2.324466	0.41197	.	.	ENSG00000196944	ENST00000366475	T	0.00281	8.32	3.48	1.5	0.22942	.	0.151835	0.30611	N	0.009244	T	0.00241	0.0007	L	0.41961	1.31	0.09310	N	1	P	0.35551	0.509	B	0.40677	0.337	T	0.38067	-0.9678	10	0.72032	D	0.01	.	8.9727	0.35917	0.0:0.805:0.0:0.195	.	70	Q8NH00	OR2T4_HUMAN	V	70	ENSP00000355431:A70V	ENSP00000355431:A70V	A	+	2	0	OR2T4	246591714	0.000000	0.05858	0.719000	0.30619	0.041000	0.13682	0.002000	0.13061	0.435000	0.26365	0.485000	0.47835	GCG	.	.		0.468	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696		T	248525091	C	T	248525091	3	4	352	1	0	0	0	0	1	0	0	0	11036	768	27	1	211	1	OR2T4	1	248525091	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	604035	248525091	725530	60	49476										
TTC15	51112	hgsc.bcm.edu	37	chr2	3392013	3392013	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tgcagcccagccccagcctcAgcacgttcttcggagacacg	10	17	2	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:3392013A>G	ENST00000324266.5	+	2	814	c.619A>G	c.(619-621)Agc>Ggc	p.S207G	TRAPPC12_ENST00000382110.2_Missense_Mutation_p.S207G	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	207					vesicle-mediated transport (GO:0016192)												CCCCAGCCTCAGCACGTTCTT	0.667																																					p.S207G		Atlas-SNP	.											.	.	.	.	0			c.A619G						.						32	39	37					2																	3392013		2203	4300	6503	SO:0001583	missense	51112	exon2			AGCCTCAGCACGT	BC017475	CCDS1652.1	2p25.3	2013-01-10	2011-12-12	2011-12-12	ENSG00000171853	ENSG00000171853		"Trafficking protein particle complex", "Tetratricopeptide (TTC) repeat domain containing"	24284	protein-coding gene	gene with protein product		614139	"tetratricopeptide repeat domain 15"	TTC15		10810093, 21525244, 20562859	Standard	NM_016030		Approved	CGI-87, TTC-15	uc002qxm.1	Q8WVT3	OTTHUMG00000090328	ENST00000324266.5:c.619A>G	chr2.hg19:g.3392013A>G	ENSP00000324318:p.Ser207Gly	102.0	0.0		87.0	5.0	NM_016030	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Missense_Mutation	SNP	ENST00000324266.5	hg19	CCDS1652.1	.	.	.	.	.	.	.	.	.	.	A	18.49	3.635691	0.67130	.	.	ENSG00000171853	ENST00000382110;ENST00000304601;ENST00000324266	T;T	0.58506	0.33;0.33	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.73666	0.3616	M	0.71581	2.175	0.58432	D	0.999999	D;D;D	0.89917	0.997;0.997;1.0	D;D;D	0.85130	0.985;0.97;0.997	T	0.76688	-0.2867	10	0.72032	D	0.01	.	12.9248	0.58254	1.0:0.0:0.0:0.0	.	190;207;207	E7ENL7;Q8WVT3;Q53S18	.;TPC12_HUMAN;.	G	207;190;207	ENSP00000371544:S207G;ENSP00000324318:S207G	ENSP00000303612:S190G	S	+	1	0	TTC15	3371020	1.000000	0.71417	0.956000	0.39512	0.234000	0.25298	8.571000	0.90752	2.232000	0.73038	0.533000	0.62120	AGC	.	.		0.667	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206693.2	NM_016030		G	3392013	A	G	3392013	3	3	352	1	0	0	0	0	1	0	0	0	16697	188	7	2	621	2	TTC15	2	3392013	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10		3392013	239807360	61	49477										
CAD	790	hgsc.bcm.edu	37	chr2	27454347	27454347	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ttcttccaggtgaagtcatgGgcattgggcgttcatttgag	13	7	3	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:27454347G>A	ENST00000403525.1	+	15	2254	c.2110G>A	c.(2110-2112)Ggc>Agc	p.G704S	CAD_ENST00000464159.1_3'UTR|CAD_ENST00000264705.4_Missense_Mutation_p.G767S			O76075	DFFB_HUMAN	carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	0					apoptotic chromosome condensation (GO:0030263)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			NS(1)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(40)|ovary(6)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	92	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGAAGTCATGGGCATTGGGCG	0.502																																					p.G767S		Atlas-SNP	.											.	CAD	199	.	0			c.G2299A						.						143	121	129					2																	27454347		2203	4300	6503	SO:0001583	missense	790	exon16			GTCATGGGCATTG	D78586	CCDS1742.1	2p22-p21	2012-10-02			ENSG00000084774	ENSG00000084774	2.1.3.2, 3.5.2.-		1424	protein-coding gene	gene with protein product		114010				8619816, 2565865	Standard	NM_004341		Approved		uc002rji.3	P27708	OTTHUMG00000097070	ENST00000403525.1:c.2110G>A	chr2.hg19:g.27454347G>A	ENSP00000384510:p.Gly704Ser	55.0	0.0		63.0	23.0	NM_004341	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Missense_Mutation	SNP	ENST00000403525.1	hg19		.	.	.	.	.	.	.	.	.	.	G	11.27	1.588724	0.28357	.	.	ENSG00000084774	ENST00000264705;ENST00000403525	D;D	0.97352	-4.35;-4.35	5.46	5.46	0.80206	ATP-grasp fold, subdomain 2 (1);Carbamoyl-phosphate synthase, large subunit, CPS-domain (1);	0.214234	0.48286	D	0.000183	D	0.90521	0.7030	N	0.05608	-0.01	0.49483	D	0.999796	B;B	0.06786	0.0;0.001	B;B	0.06405	0.002;0.002	D	0.86395	0.1738	10	0.08599	T	0.76	-0.4809	13.2374	0.59976	0.0:0.0:0.8411:0.1589	.	704;767	F8VPD4;P27708	.;PYR1_HUMAN	S	767;704	ENSP00000264705:G767S;ENSP00000384510:G704S	ENSP00000264705:G767S	G	+	1	0	CAD	27307851	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.222000	0.78025	2.733000	0.93635	0.655000	0.94253	GGC	.	.		0.502	CAD-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000324970.1			A	27454347	G	A	27454347	3	1	352	1	0	0	0	0	1	0	0	0	2567	1232	43	3	2361	3	CAD	2	27454347	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	24062334	27454347	215745026	62	49478										
CEBPZ	10153	hgsc.bcm.edu	37	chr2	37449694	37449694	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tgcatcaataaaattttcttCatcatcagactcctaacaaa	2	10	5	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:37449694C>T	ENST00000234170.5	-	4	2039	c.1894G>A	c.(1894-1896)Gaa>Aaa	p.E632K		NM_005760.2	NP_005751.2	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein (C/EBP), zeta	632					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|endometrium(2)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28		all_hematologic(82;0.21)				AAATTTTCTTCATCATCAGAC	0.328																																					p.E632K		Atlas-SNP	.											.	CEBPZ	68	.	0			c.G1894A						.						84	79	81					2																	37449694		2202	4300	6502	SO:0001583	missense	10153	exon4			TTTCTTCATCATC	M37197	CCDS1787.1	2p22.3	2008-09-03	2008-09-03		ENSG00000115816	ENSG00000115816			24218	protein-coding gene	gene with protein product		612828				2247079, 12534345	Standard	NM_005760		Approved	CBF2, CTF2	uc002rpz.3	Q03701	OTTHUMG00000100960	ENST00000234170.5:c.1894G>A	chr2.hg19:g.37449694C>T	ENSP00000234170:p.Glu632Lys	54.0	0.0		54.0	8.0	NM_005760	Q8NE75	Missense_Mutation	SNP	ENST00000234170.5	hg19	CCDS1787.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.345188	0.82022	.	.	ENSG00000115816	ENST00000234170;ENST00000545744	T	0.15834	2.39	5.2	5.2	0.72013	Armadillo-type fold (1);CCAAT-binding factor (1);	0.045272	0.85682	D	0.000000	T	0.40015	0.1100	L	0.61387	1.9	0.52099	D	0.999942	D	0.76494	0.999	D	0.71870	0.975	T	0.16453	-1.0402	10	0.87932	D	0	.	16.8847	0.86072	0.0:1.0:0.0:0.0	.	632	Q03701	CEBPZ_HUMAN	K	632	ENSP00000234170:E632K	ENSP00000234170:E632K	E	-	1	0	CEBPZ	37303198	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	4.633000	0.61318	2.573000	0.86826	0.650000	0.86243	GAA	.	.		0.328	CEBPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218569.2	NM_005760		T	37449694	C	T	37449694	3	4	352	1	0	0	0	0	1	0	0	0	3206	835	29	3	1322	3	CEBPZ	2	37449694	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	9995347	37449694	205749679	63	49479										
SLC8A1	6546	hgsc.bcm.edu	37	chr2	40656189	40656191	+	In_Frame_Del	DEL	AAG	AAG	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	actgatatgtcccttgttcaAagaagatcttactaacaggg							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:40656189_40656191delAAG	ENST00000403092.1	-	2	1263_1265	c.1230_1232delCTT	c.(1228-1233)ttcttt>ttt	p.410_411FF>F	SLC8A1_ENST00000406785.2_In_Frame_Del_p.410_411FF>F|SLC8A1_ENST00000542756.1_In_Frame_Del_p.410_411FF>F|SLC8A1_ENST00000402441.1_In_Frame_Del_p.410_411FF>F|SLC8A1_ENST00000542024.1_In_Frame_Del_p.410_411FF>F|SLC8A1_ENST00000408028.2_In_Frame_Del_p.410_411FF>F|SLC8A1_ENST00000405901.3_In_Frame_Del_p.410_411FF>F|SLC8A1_ENST00000405269.1_In_Frame_Del_p.410_411FF>F|SLC8A1_ENST00000332839.4_In_Frame_Del_p.410_411FF>F|SLC8A1_ENST00000406391.2_In_Frame_Del_p.410_411FF>F			P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 1	410	Calx-beta 1.				blood coagulation (GO:0007596)|calcium ion export (GO:1901660)|calcium ion homeostasis (GO:0055074)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|cardiac muscle cell development (GO:0055013)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular response to caffeine (GO:0071313)|cellular response to reactive oxygen species (GO:0034614)|cellular sodium ion homeostasis (GO:0006883)|cytosolic calcium ion transport (GO:0060401)|embryonic heart tube development (GO:0035050)|embryonic placenta development (GO:0001892)|heart morphogenesis (GO:0003007)|ion transport (GO:0006811)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|muscle contraction (GO:0006936)|muscle fiber development (GO:0048747)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|post-embryonic development (GO:0009791)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|relaxation of smooth muscle (GO:0044557)|sodium ion export (GO:0071436)|sodium ion import (GO:0097369)|transmembrane transport (GO:0055085)|vascular smooth muscle contraction (GO:0014829)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|calcium:sodium antiporter activity (GO:0005432)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|liver(1)|lung(57)|ovary(2)|pancreas(1)|skin(7)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)	100					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)	CCCTTGTTCAAAGAAGATCTTAC	0.453																																					p.411_411del		Atlas-INDEL	.											.	SLC8A1	221	.	0			c.1231_1233del						.																																			SO:0001651	inframe_deletion	6546	exon2			.		CCDS1806.1, CCDS46264.1, CCDS46265.1, CCDS59430.1	2p22.1	2013-07-15			ENSG00000183023	ENSG00000183023		"Solute carriers"	11068	protein-coding gene	gene with protein product	"Na+/Ca++ exchanger"	182305		NCX1		1559714	Standard	NM_021097		Approved		uc002rrx.3	P32418	OTTHUMG00000102183	ENST00000403092.1:c.1230_1232delCTT	chr2.hg19:g.40656192_40656194delAAG	ENSP00000384763:p.Phe411del	95.0	0.0		101.0	12.0	NM_001112802	A8K6N1|D6W595|O95849|Q4QQG6|Q587I6|Q59GN4|Q9UBL8|Q9UD55|Q9UDN1|Q9UDN2|Q9UKX6	In_Frame_Del	DEL	ENST00000403092.1	hg19	CCDS1806.1																																																																																			.	.		0.453	SLC8A1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326065.1	NM_021097		-	40656191	AAG	-	40656189	7	5	352	1	0	1	0	1	0	0	0	0	14721	14	1	0	1837	0	SLC8A1	2	40656189	In_Frame_Del	DEL	AAG	TCGA-WQ-A9G7-01A-11D-A36X-10	3206495	40656189	202543184	64	49480										
SRBD1	55133	hgsc.bcm.edu	37	chr2	45829136	45829136	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tctttggtttggattccttgGgagggggctgtttacggctt	15	6	1	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:45829136G>T	ENST00000263736.4	-	3	229	c.167C>A	c.(166-168)cCc>cAc	p.P56H		NM_018079.4	NP_060549.4	Q8N5C6	SRBD1_HUMAN	S1 RNA binding domain 1	56					nucleobase-containing compound metabolic process (GO:0006139)		hydrolase activity, acting on ester bonds (GO:0016788)|RNA binding (GO:0003723)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(13)|large_intestine(8)|lung(15)|skin(2)|stomach(1)|urinary_tract(1)	49		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	LUSC - Lung squamous cell carcinoma(58;0.0917)|Lung(47;0.154)			GGATTCCTTGGGAGGGGGCTG	0.493																																					p.P56H		Atlas-SNP	.											.	SRBD1	107	.	0			c.C167A						.						159	161	160					2																	45829136		2203	4300	6503	SO:0001583	missense	55133	exon3			TCCTTGGGAGGGG	AK056536	CCDS1823.1	2p21	2008-02-05			ENSG00000068784	ENSG00000068784			25521	protein-coding gene	gene with protein product						12477932	Standard	NM_018079		Approved	FLJ10379	uc002rus.3	Q8N5C6	OTTHUMG00000128814	ENST00000263736.4:c.167C>A	chr2.hg19:g.45829136G>T	ENSP00000263736:p.Pro56His	95.0	0.0		112.0	21.0	NM_018079	Q53T56|Q96TA4|Q9NW11	Missense_Mutation	SNP	ENST00000263736.4	hg19	CCDS1823.1	.	.	.	.	.	.	.	.	.	.	G	14.85	2.658543	0.47467	.	.	ENSG00000068784	ENST00000263736	T	0.24350	1.86	5.7	3.82	0.43975	.	1.121610	0.06649	N	0.762340	T	0.20251	0.0487	N	0.14661	0.345	0.80722	D	1	B	0.32918	0.39	B	0.33196	0.159	T	0.03750	-1.1007	10	0.87932	D	0	.	12.8924	0.58080	0.0:0.3098:0.6902:0.0	.	56	Q8N5C6	SRBD1_HUMAN	H	56	ENSP00000263736:P56H	ENSP00000263736:P56H	P	-	2	0	SRBD1	45682640	0.965000	0.33210	0.929000	0.37066	0.854000	0.48673	1.578000	0.36525	1.384000	0.46424	0.557000	0.71058	CCC	.	.		0.493	SRBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250747.3	NM_018079		T	45829136	G	T	45829136	3	4	352	1	0	0	0	0	1	0	0	0	15148	1232	43	3	2896	3	SRBD1	2	45829136	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	5172947	45829136	197370237	65	49481										
CNRIP1	25927	hgsc.bcm.edu	37	chr2	68521038	68521038	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ccacatcagactgcgtgtctCgttgggcttgcattcatact	9	12	3	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:68521038C>T	ENST00000263655.3	-	3	1056	c.451G>A	c.(451-453)Gag>Aag	p.E151K	CNRIP1_ENST00000409559.3_Intron|CNRIP1_ENST00000481714.1_5'UTR	NM_015463.2	NP_056278.1	Q96F85	CNRP1_HUMAN	cannabinoid receptor interacting protein 1	151										kidney(1)|large_intestine(5)|liver(1)|lung(1)|skin(1)	9						CTGCGTGTCTCGTTGGGCTTG	0.468																																					p.E151K		Atlas-SNP	.											.	CNRIP1	45	.	0			c.G451A						.						147	117	127					2																	68521038		2203	4300	6503	SO:0001583	missense	25927	exon3			GTGTCTCGTTGGG	AL110235	CCDS1886.1, CCDS46311.1	2p13	2008-02-05	2007-11-29	2007-11-29	ENSG00000119865	ENSG00000119865			24546	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 32"	C2orf32		12477932	Standard	NM_015463		Approved	DKFZP566K1924, CRIP1, CRIP1a, CRIP1b	uc002sek.4	Q96F85	OTTHUMG00000129565	ENST00000263655.3:c.451G>A	chr2.hg19:g.68521038C>T	ENSP00000263655:p.Glu151Lys	110.0	0.0		108.0	14.0	NM_015463	B2R4D0|Q49AN4|Q9UFZ0	Missense_Mutation	SNP	ENST00000263655.3	hg19	CCDS1886.1	.	.	.	.	.	.	.	.	.	.	C	36	5.650642	0.96714	.	.	ENSG00000119865	ENST00000263655	.	.	.	5.68	5.68	0.88126	.	0.240456	0.48286	D	0.000186	T	0.63558	0.2521	L	0.55990	1.75	0.80722	D	1	D	0.60160	0.987	P	0.48304	0.573	T	0.67225	-0.5724	9	0.72032	D	0.01	-8.2808	19.8015	0.96509	0.0:1.0:0.0:0.0	.	151	Q96F85	CNRP1_HUMAN	K	151	.	ENSP00000263655:E151K	E	-	1	0	CNRIP1	68374542	1.000000	0.71417	0.963000	0.40424	0.935000	0.57460	7.818000	0.86416	2.678000	0.91216	0.650000	0.86243	GAG	.	.		0.468	CNRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251758.1	NM_015463		T	68521038	C	T	68521038	3	4	352	1	0	0	0	0	1	0	0	0	3635	893	31	1	108	1	CNRIP1	2	68521038	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	22691902	68521038	174678335	66	49482										
ASPRV1	151516	hgsc.bcm.edu	37	chr2	70188363	70188363	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ctccctggtcctggggactgAgcctattgtagacacccagg	12	13	0	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:70188363A>G	ENST00000320256.4	-	1	1034	c.458T>C	c.(457-459)cTc>cCc	p.L153P	PCBP1-AS1_ENST00000457076.1_RNA|PCBP1-AS1_ENST00000435880.2_RNA|PCBP1-AS1_ENST00000418564.1_RNA|PCBP1-AS1_ENST00000413436.1_RNA|PCBP1-AS1_ENST00000596259.1_RNA|PCBP1-AS1_ENST00000419542.1_RNA	NM_152792.2	NP_690005.2			aspartic peptidase, retroviral-like 1											endometrium(3)|large_intestine(4)|lung(6)|ovary(1)	14						CTGGGGACTGAGCCTATTGTA	0.562																																					p.L153P		Atlas-SNP	.											.	ASPRV1	41	.	0			c.T458C						.						42	44	43					2																	70188363		2203	4300	6503	SO:0001583	missense	151516	exon1			GGACTGAGCCTAT	AK055994	CCDS1897.1	2p13.3	2008-02-20			ENSG00000244617	ENSG00000244617			26321	protein-coding gene	gene with protein product	"Skin ASpartic Protease"	611765				16098038, 16565508	Standard	NM_152792		Approved	Taps, SASPase, FLJ25084	uc002sfz.4	Q53RT3	OTTHUMG00000129647	ENST00000320256.4:c.458T>C	chr2.hg19:g.70188363A>G	ENSP00000315383:p.Leu153Pro	67.0	0.0		69.0	11.0	NM_152792		Missense_Mutation	SNP	ENST00000320256.4	hg19	CCDS1897.1	.	.	.	.	.	.	.	.	.	.	A	12.30	1.895339	0.33442	.	.	ENSG00000244617	ENST00000320256	T	0.61627	0.09	5.99	5.99	0.97316	.	0.155181	0.28760	N	0.014238	T	0.65481	0.2695	L	0.29908	0.895	0.46678	D	0.999159	D	0.89917	1.0	D	0.85130	0.997	T	0.68739	-0.5329	10	0.87932	D	0	-15.2793	12.8861	0.58045	1.0:0.0:0.0:0.0	.	153	Q53RT3	APRV1_HUMAN	P	153	ENSP00000315383:L153P	ENSP00000315383:L153P	L	-	2	0	ASPRV1	70041867	0.975000	0.34042	0.104000	0.21259	0.018000	0.09664	4.811000	0.62606	2.291000	0.77112	0.533000	0.62120	CTC	.	.		0.562	ASPRV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334161.1	NM_152792		G	70188363	A	G	70188363	3	3	352	1	0	0	0	0	1	0	0	0	1058	304	11	2	577	2	ASPRV1	2	70188363	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	1667325	70188363	173011010	67	49483										
MPHOSPH10	10199	hgsc.bcm.edu	37	chr2	71377061	71377061	+	Frame_Shift_Del	DEL	A	A	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tctaaattacaagatcaagtAaaaatgcaaatcaatgatgc							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:71377061delA	ENST00000244230.2	+	11	2314	c.1962delA	c.(1960-1962)gtafs	p.V654fs		NM_005791.2	NP_005782.1	O00566	MPP10_HUMAN	M-phase phosphoprotein 10 (U3 small nucleolar ribonucleoprotein)	654					negative regulation of phosphatase activity (GO:0010923)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|rRNA processing (GO:0006364)	chromosome (GO:0005694)|nucleolus (GO:0005730)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|pancreas(2)|skin(2)|stomach(1)	26						AAGATCAAGTAAAAATGCAAA	0.289																																					p.V654fs		Atlas-INDEL	.											.	MPHOSPH10	81	.	0			c.1961delT						.						85	87	87					2																	71377061		2203	4298	6501	SO:0001589	frameshift_variant	10199	exon11			.	X98494	CCDS1916.1	2p13.3	2014-06-12			ENSG00000124383	ENSG00000124383			7213	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 106"	605503				8885239, 9450966	Standard	NM_005791		Approved	MPP10, MPP10P, CT90, PPP1R106	uc002sht.2	O00566	OTTHUMG00000129715	ENST00000244230.2:c.1962delA	chr2.hg19:g.71377061delA	ENSP00000244230:p.Val654fs	458.0	0.0		381.0	119.0	NM_005791	A0AVJ8	Frame_Shift_Del	DEL	ENST00000244230.2	hg19	CCDS1916.1																																																																																			.	.		0.289	MPHOSPH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251924.2	NM_005791		-	71377061	A	-	71377061	7	5	352	1	0	1	0	1	0	0	0	0	9734	349	13	0	2004	0	MPHOSPH10	2	71377061	Frame_Shift_Del	DEL	A	TCGA-WQ-A9G7-01A-11D-A36X-10	1188698	71377061	171822312	68	49484										
SEMA4F	10505	hgsc.bcm.edu	37	chr2	74902504	74902504	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gagtatgatgtgctctacctGgggacaggtatatttaatgg	13	5	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:74902504G>A	ENST00000357877.2	+	10	1514	c.1365G>A	c.(1363-1365)ctG>ctA	p.L455L	SEMA4F_ENST00000339773.5_Silent_p.L300L|SEMA4F_ENST00000473350.1_Intron	NM_004263.3	NP_004254.2	O95754	SEM4F_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4F	455	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell-cell signaling (GO:0007267)|negative regulation of axon extension (GO:0030517)|nervous system development (GO:0007399)|retinal ganglion cell axon guidance (GO:0031290)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor activity (GO:0004872)			biliary_tract(1)|breast(2)|endometrium(8)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	45						TGCTCTACCTGGGGACAGGTA	0.517											OREG0014721	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L455L		Atlas-SNP	.											.	SEMA4F	89	.	0			c.G1365A						.						36	37	37					2																	74902504		2203	4300	6503	SO:0001819	synonymous_variant	10505	exon10			CTACCTGGGGACA	AF038652	CCDS1955.1, CCDS62942.1, CCDS74529.1	2p13.1	2008-05-21			ENSG00000135622	ENSG00000135622		"Semaphorins"	10734	protein-coding gene	gene with protein product	"m-Sema M"	603706		SEMAM		10051670	Standard	NM_004263		Approved	SEMAW	uc002sna.2	O95754	OTTHUMG00000129952	ENST00000357877.2:c.1365G>A	chr2.hg19:g.74902504G>A		93.0	0.0	1156	88.0	14.0	NM_004263	Q542Y7|Q9NS35	Silent	SNP	ENST00000357877.2	hg19	CCDS1955.1																																																																																			.	.		0.517	SEMA4F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252214.2	NM_004263		A	74902504	G	A	74902504	2	1	352	1	0	0	0	0	0	0	0	1	14050	1335	47	3		3	SEMA4F	2	74902504	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	3525443	74902504	168296869	69	49485										
DNAH6	1768	hgsc.bcm.edu	37	chr2	84806683	84806684	+	Frame_Shift_Ins	INS	-	-	A													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tgcttcctcgtcaaagcaagINSaaaaaagtggatgccattat							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:84806683_84806684insA	ENST00000237449.6	+	13	2117_2118	c.2109_2110insA	c.(2110-2112)aaafs	p.K704fs	DNAH6_ENST00000389394.3_Frame_Shift_Ins_p.K704fs|DNAH6_ENST00000398278.2_Frame_Shift_Ins_p.K704fs			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	704	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						GTCAAAGCAAGAAAAAAGTGGA	0.322																																					p.K703fs		Atlas-INDEL	.											.	DNAH6	194	.	0			c.2109_2110insA						.																																			SO:0001589	frameshift_variant	1768	exon14			.	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.2115dupA	chr2.hg19:g.84806689_84806689dupA	ENSP00000237449:p.Lys704fs	75.0	0.0		82.0	20.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Frame_Shift_Ins	INS	ENST00000237449.6	hg19	CCDS46348.1																																																																																			.	.		0.322	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		A	84806684	-	A	84806683	7	5	352	1	0	1	1	0	0	0	0	0	4607	933	33	0	2159	0	DNAH6	2	84806683	Frame_Shift_Ins	INS	-	TCGA-WQ-A9G7-01A-11D-A36X-10	9904179	84806683	158392690	70	49486										
ADRA2B	151	hgsc.bcm.edu	37	chr2	96781723	96781723	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggccaccaggatgtcggcggCggccagcgacaccaggaaca	15	14	0	0	rs370956755		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:96781723C>T	ENST00000409345.3	-	1	261	c.166G>A	c.(166-168)Gcc>Acc	p.A56T		NM_000682.5	NP_000673	P18089	ADA2B_HUMAN	adrenoceptor alpha 2B	56					activation of MAPK activity by adrenergic receptor signaling pathway (GO:0071883)|activation of protein kinase B activity (GO:0032148)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|female pregnancy (GO:0007565)|G-protein coupled receptor signaling pathway (GO:0007186)|MAPK cascade (GO:0000165)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of norepinephrine secretion (GO:0010700)|platelet activation (GO:0030168)|positive regulation of blood pressure (GO:0045777)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of uterine smooth muscle contraction (GO:0070474)|regulation of vascular smooth muscle contraction (GO:0003056)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha2-adrenergic receptor activity (GO:0004938)|epinephrine binding (GO:0051379)			endometrium(2)|large_intestine(2)|lung(9)|ovary(3)	16					Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Apraclonidine(DB00964)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bethanidine(DB00217)|Brimonidine(DB00484)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Clozapine(DB00363)|Desipramine(DB01151)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Etomidate(DB00292)|Fenoldopam(DB00800)|Guanabenz(DB00629)|Guanfacine(DB01018)|Lisuride(DB00589)|Loxapine(DB00408)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methamphetamine(DB01577)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxymetazoline(DB00935)|Paliperidone(DB01267)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Pramipexole(DB00413)|Prazosin(DB00457)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Tizanidine(DB00697)|Tolazoline(DB00797)|Trimipramine(DB00726)|Xylometazoline(DB06694)|Yohimbine(DB01392)|Ziprasidone(DB00246)	ATGTCGGCGGCGGCCAGCGAC	0.627																																					p.A56T		Atlas-SNP	.											.	ADRA2B	115	.	0			c.G166A						.	A	THR/ALA	0,4404		0,0,2202	37	45	42		166	4.5	1	2		42	1,8597		0,1,4298	no	missense	ADRA2B	NM_000682.5	58	0,1,6500	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	56/448	96781723	1,13001	2202	4299	6501	SO:0001583	missense	151	exon1			CGGCGGCGGCCAG	M34041	CCDS56129.1	2q11.1	2014-05-06	2012-05-09		ENSG00000222040	ENSG00000274286		"GPCR / Class A : Adrenoceptors : alpha"	282	protein-coding gene	gene with protein product		104260	"adrenergic, alpha-2B-, receptor"	ADRA2L1, ADRA2RL1		2164221	Standard	NM_000682		Approved	ADRARL1	uc021vlh.1	P18089	OTTHUMG00000188276	ENST00000409345.3:c.166G>A	chr2.hg19:g.96781723C>T	ENSP00000387281:p.Ala56Thr	236.0	0.0		213.0	33.0	NM_000682	Q4TUH9|Q53RF2|Q9BZK0	Missense_Mutation	SNP	ENST00000409345.3	hg19	CCDS56129.1	.	.	.	.	.	.	.	.	.	.	c	22.1	4.250248	0.80024	0.0	1.16E-4	ENSG00000222040	ENST00000409345	T	0.19669	2.13	4.48	4.48	0.54585	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.32645	0.0836	M	0.70903	2.155	0.54753	D	0.999986	D	0.56746	0.977	P	0.48552	0.581	T	0.17868	-1.0355	9	0.54805	T	0.06	.	14.755	0.69557	0.0:1.0:0.0:0.0	.	56	P18089	ADA2B_HUMAN	T	56	ENSP00000387281:A56T	ENSP00000387281:A56T	A	-	1	0	ADRA2B	96145450	0.978000	0.34361	0.994000	0.49952	0.990000	0.78478	2.592000	0.46171	2.334000	0.79466	0.450000	0.29827	GCC	.	.		0.627	ADRA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334990.1			T	96781723	C	T	96781723	3	4	352	1	0	0	0	0	1	0	0	0	338	768	27	1	1181	1	ADRA2B	2	96781723	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	11975040	96781723	146417650	71	49487										
AFF3	3899	hgsc.bcm.edu	37	chr2	100289003	100289003	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ataaaagagaatcttacctgTtcattctcctcttcatcact	3	11	6	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:100289003T>A	ENST00000409236.2	-	10	1252	c.1140A>T	c.(1138-1140)gaA>gaT	p.E380D	AFF3_ENST00000356421.2_Missense_Mutation_p.E405D|AFF3_ENST00000409579.1_Missense_Mutation_p.E405D|AFF3_ENST00000317233.4_Missense_Mutation_p.E380D			P51826	AFF3_HUMAN	AF4/FMR2 family, member 3	380					embryonic hindlimb morphogenesis (GO:0035116)|regulation of transcription, DNA-templated (GO:0006355)|response to tumor necrosis factor (GO:0034612)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)			NS(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(9)|kidney(4)|large_intestine(20)|liver(1)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(3)	86						ATCTTACCTGTTCATTCTCCT	0.438																																					p.E405D		Atlas-SNP	.											.	AFF3	164	.	0			c.A1215T						.						215	190	199					2																	100289003		2203	4300	6503	SO:0001583	missense	3899	exon11			TACCTGTTCATTC	U34360	CCDS33258.1, CCDS42723.1	2q11.2-q12	2008-02-05	2005-06-27	2005-06-27	ENSG00000144218	ENSG00000144218			6473	protein-coding gene	gene with protein product		601464	"lymphoid nuclear protein related to AF4"	LAF4		8662235, 8555498	Standard	XM_005263945		Approved	MLLT2-like	uc002taf.3	P51826	OTTHUMG00000153011	ENST00000409236.2:c.1140A>T	chr2.hg19:g.100289003T>A	ENSP00000387207:p.Glu380Asp	100.0	0.0		69.0	8.0	NM_001025108	B7ZM46|B9EGL9|D3DVI6|Q53RD6|Q53S47|Q53SI6|Q53TB9|Q59F27|Q8IWJ5	Missense_Mutation	SNP	ENST00000409236.2	hg19	CCDS42723.1	.	.	.	.	.	.	.	.	.	.	T	11.28	1.592804	0.28357	.	.	ENSG00000144218	ENST00000317233;ENST00000356421;ENST00000409579;ENST00000409236;ENST00000433370;ENST00000444786;ENST00000432288	T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18	5.35	-2.21	0.06973	.	0.275556	0.27185	N	0.020528	T	0.32436	0.0829	N	0.05124	-0.11	0.29734	N	0.837622	B;B;B	0.33964	0.434;0.018;0.041	B;B;B	0.34418	0.182;0.028;0.016	T	0.37126	-0.9719	10	0.22109	T	0.4	.	8.655	0.34058	0.0:0.5008:0.1342:0.365	.	534;380;405	B7Z4I6;P51826;P51826-2	.;AFF3_HUMAN;.	D	380;405;405;380;380;534;405	ENSP00000317421:E380D;ENSP00000348793:E405D;ENSP00000386834:E405D;ENSP00000387207:E380D	ENSP00000317421:E380D	E	-	3	2	AFF3	99655435	0.332000	0.24722	0.997000	0.53966	0.994000	0.84299	-0.854000	0.04299	-0.165000	0.10908	0.533000	0.62120	GAA	.	.		0.438	AFF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328982.3	NM_002285		A	100289003	T	A	100289003	3	1	352	1	0	0	0	0	1	0	0	0	358	1722	60	4	2596	4	AFF3	2	100289003	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	3507280	100289003	142910370	72	49488										
TGFBRAP1	9392	hgsc.bcm.edu	37	chr2	105924248	105924248	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gccgtccacagccacagcgaGgggctgctcggcagtcgaca	14	15	0	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:105924248G>C	ENST00000393359.2	-	2	937	c.511C>G	c.(511-513)Ctc>Gtc	p.L171V	TGFBRAP1_ENST00000258449.1_Missense_Mutation_p.L171V			Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor associated protein 1	171	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				intracellular protein transport (GO:0006886)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|membrane (GO:0016020)	SMAD binding (GO:0046332)|small GTPase regulator activity (GO:0005083)|transforming growth factor beta receptor binding (GO:0005160)			central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	31						GCCACAGCGAGGGGCTGCTCG	0.557																																					p.L171V	Esophageal Squamous(183;794 2019 9730 21801 48859)	Atlas-SNP	.											.	TGFBRAP1	70	.	0			c.C511G						.						119	119	119					2																	105924248		2203	4300	6503	SO:0001583	missense	9392	exon2			CAGCGAGGGGCTG	AF022795	CCDS2067.1	2q12.1	2008-02-05			ENSG00000135966	ENSG00000135966			16836	protein-coding gene	gene with protein product		606237				9545258, 11278302	Standard	NM_001142621		Approved	TRAP-1, TRAP1	uc002tcr.4	Q8WUH2	OTTHUMG00000130809	ENST00000393359.2:c.511C>G	chr2.hg19:g.105924248G>C	ENSP00000377027:p.Leu171Val	85.0	0.0		89.0	24.0	NM_004257	A8K5R7|D3DVJ8|O60466	Missense_Mutation	SNP	ENST00000393359.2	hg19	CCDS2067.1	.	.	.	.	.	.	.	.	.	.	G	4.431	0.079691	0.08533	.	.	ENSG00000135966	ENST00000393359;ENST00000258449	T;T	0.04758	3.56;3.56	5.32	3.28	0.37604	Citron-like (2);	0.231473	0.44285	N	0.000463	T	0.02230	0.0069	N	0.11560	0.145	0.32097	N	0.591051	B	0.09022	0.002	B	0.20384	0.029	T	0.33163	-0.9879	10	0.16420	T	0.52	-10.6698	2.2192	0.03968	0.3909:0.3106:0.2985:0.0	.	171	Q8WUH2	TGFA1_HUMAN	V	171	ENSP00000377027:L171V;ENSP00000258449:L171V	ENSP00000258449:L171V	L	-	1	0	TGFBRAP1	105290680	1.000000	0.71417	0.348000	0.25681	0.853000	0.48598	3.881000	0.56152	0.684000	0.31448	0.655000	0.94253	CTC	.	.		0.557	TGFBRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253354.2	NM_004257		C	105924248	G	C	105924248	3	2	352	1	0	0	0	0	1	0	0	0	15839	1000	35	4	2115	4	TGFBRAP1	2	105924248	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	5635245	105924248	137275125	73	49489										
SULT1C3	442038	hgsc.bcm.edu	37	chr2	108881280	108881280	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gtgtgactgttccacatacaGgacccaaagcgggaaattga	11	9	0	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:108881280G>T	ENST00000329106.2	+	6	621		c.e6-1			NM_001008743.1	NP_001008743.1	Q6IMI6	ST1C3_HUMAN	sulfotransferase family, cytosolic, 1C, member 3						sulfur compound metabolic process (GO:0006790)	cytoplasm (GO:0005737)	alcohol sulfotransferase activity (GO:0004027)|aryl sulfotransferase activity (GO:0004062)			breast(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(1)|skin(4)	16						TCCACATACAGGACCCAAAGC	0.393																																					.		Atlas-SNP	.											.	SULT1C3	53	.	0			c.622-1G>T						.						57	56	56					2																	108881280		2203	4300	6503	SO:0001630	splice_region_variant	442038	exon6			CATACAGGACCCA	BC146362	CCDS33267.1	2q12.3	2007-07-26			ENSG00000196228	ENSG00000196228		"Sulfotransferases, cytosolic"	33543	protein-coding gene	gene with protein product						14676822, 17425406	Standard	NM_001008743		Approved		uc010ywo.2	Q6IMI6	OTTHUMG00000153227	ENST00000329106.2:c.622-1G>T	chr2.hg19:g.108881280G>T		159.0	0.0		150.0	13.0	NM_001008743	Q6IMI5	Splice_Site	SNP	ENST00000329106.2	hg19	CCDS33267.1	.	.	.	.	.	.	.	.	.	.	g	21.4	4.144370	0.77888	.	.	ENSG00000196228	ENST00000329106	.	.	.	4.9	4.9	0.64082	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.2242	0.86965	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SULT1C3	108247712	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.905000	0.69893	2.534000	0.85438	0.655000	0.94253	.	.	.		0.393	SULT1C3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330255.1	NM_001008743	Intron	T	108881280	G	T	108881280	5	4	352	1	0	0	0	0	0	0	1	0	15393	1014	35	3	643	3	SULT1C3	2	108881280	Splice_Site	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	2957032	108881280	134318093	74	49490										
SH3RF3	344558	hgsc.bcm.edu	37	chr2	110049067	110049067	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggatggctggttcaagggggCgtctctgaggaccggggtct	19	8	3	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:110049067C>T	ENST00000309415.6	+	6	1514	c.1514C>T	c.(1513-1515)gCg>gTg	p.A505V		NM_001099289.1	NP_001092759.1	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3	505	SH3 3. {ECO:0000255|PROSITE- ProRule:PRU00192}.						zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(5)|ovary(2)	18						TTCAAGGGGGCGTCTCTGAGG	0.617																																					p.A505V		Atlas-SNP	.											.	SH3RF3	62	.	0			c.C1514T						.						36	42	40					2																	110049067		1999	4174	6173	SO:0001583	missense	344558	exon6			AGGGGGCGTCTCT	AK074131	CCDS74557.1	2q13	2013-01-11	2008-05-14	2008-05-14	ENSG00000172985	ENSG00000172985		"RING-type (C3HC4) zinc fingers"	24699	protein-coding gene	gene with protein product			"SH3 multiple domains 4"	SH3MD4		16374509	Standard	XM_006712493		Approved	FLJ00204, POSH2	uc010ywt.1	Q8TEJ3	OTTHUMG00000153439	ENST00000309415.6:c.1514C>T	chr2.hg19:g.110049067C>T	ENSP00000309186:p.Ala505Val	126.0	0.0		84.0	8.0	NM_001099289	A0SDZ7|A8MPR1|Q8NDU1	Missense_Mutation	SNP	ENST00000309415.6	hg19		.	.	.	.	.	.	.	.	.	.	C	20.5	3.993756	0.74703	.	.	ENSG00000172985	ENST00000418513;ENST00000309415	T;T	0.28255	1.62;1.62	4.9	4.01	0.46588	Src homology-3 domain (4);	0.101080	0.64402	D	0.000002	T	0.21718	0.0523	.	.	.	0.35910	D	0.83105	B	0.15473	0.013	B	0.18263	0.021	T	0.15009	-1.0452	9	0.21014	T	0.42	-6.2418	13.4773	0.61316	0.0:0.924:0.0:0.076	.	505	Q8TEJ3	SH3R3_HUMAN	V	505	ENSP00000414997:A505V;ENSP00000309186:A505V	ENSP00000309186:A505V	A	+	2	0	SH3RF3	109415499	0.998000	0.40836	0.043000	0.18650	0.952000	0.60782	4.566000	0.60843	1.399000	0.46721	0.561000	0.74099	GCG	.	.		0.617	SH3RF3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001099289		T	110049067	C	T	110049067	3	4	352	1	0	0	0	0	1	0	0	0	14275	768	27	1	1536	1	SH3RF3	2	110049067	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	1167787	110049067	133150306	75	49491										
SLC20A1	6574	hgsc.bcm.edu	37	chr2	113418726	113418726	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tttgtgtctgtagtggcttcAgtattgaactggcatctgcc	11	8	3	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:113418726A>G	ENST00000272542.3	+	10	2340	c.1801A>G	c.(1801-1803)Agt>Ggt	p.S601G		NM_005415.4	NP_005406.3	Q8WUM9	S20A1_HUMAN	solute carrier family 20 (phosphate transporter), member 1	601					ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	high-affinity inorganic phosphate:sodium symporter activity (GO:0005316)|inorganic phosphate transmembrane transporter activity (GO:0005315)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|sodium:phosphate symporter activity (GO:0005436)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(2)|lung(8)|ovary(3)|skin(1)|urinary_tract(3)	28						TAGTGGCTTCAGTATTGAACT	0.413																																					p.S601G		Atlas-SNP	.											.	SLC20A1	59	.	0			c.A1801G						.						121	109	113					2																	113418726		2203	4300	6503	SO:0001583	missense	6574	exon10			GGCTTCAGTATTG		CCDS2099.1	2q13	2013-05-22			ENSG00000144136	ENSG00000144136		"Solute carriers"	10946	protein-coding gene	gene with protein product	"gibbon ape leukemia virus receptor 1"	137570		GLVR1		8041748	Standard	NM_005415		Approved	PiT-1, Glvr-1	uc002tib.3	Q8WUM9	OTTHUMG00000131317	ENST00000272542.3:c.1801A>G	chr2.hg19:g.113418726A>G	ENSP00000272542:p.Ser601Gly	73.0	0.0		77.0	9.0	NM_005415	Q08344|Q6DHX8|Q9UQ82	Missense_Mutation	SNP	ENST00000272542.3	hg19	CCDS2099.1	.	.	.	.	.	.	.	.	.	.	A	31	5.066537	0.93898	.	.	ENSG00000144136	ENST00000272542	D	0.91295	-2.82	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	D	0.95401	0.8507	M	0.90595	3.13	0.80722	D	1	D	0.60575	0.988	P	0.60886	0.88	D	0.96110	0.9076	10	0.87932	D	0	-12.8881	13.8691	0.63608	1.0:0.0:0.0:0.0	.	601	Q8WUM9	S20A1_HUMAN	G	601	ENSP00000272542:S601G	ENSP00000272542:S601G	S	+	1	0	SLC20A1	113135197	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.207000	0.95064	2.168000	0.68352	0.528000	0.53228	AGT	.	.		0.413	SLC20A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254086.2	NM_005415		G	113418726	A	G	113418726	3	3	352	1	0	0	0	0	1	0	0	0	14453	188	7	2	1835	2	SLC20A1	2	113418726	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	3369659	113418726	129780647	76	49492										
SCTR	6344	hgsc.bcm.edu	37	chr2	120199162	120199162	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tgaggaagcagtagaggacgGccaccaccagtccctgccag	13	13	0	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:120199162G>A	ENST00000019103.5	-	12	1421	c.1154C>T	c.(1153-1155)gCc>gTc	p.A385V		NM_002980.2	NP_002971.2	P47872	SCTR_HUMAN	secretin receptor	385					digestion (GO:0007586)|excretion (GO:0007588)|G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasmic microtubule (GO:0005881)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	secretin receptor activity (GO:0015055)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)	19					Secretin(DB00021)	GTAGAGGACGGCCACCACCAG	0.602																																					p.A385V		Atlas-SNP	.											.	SCTR	45	.	0			c.C1154T						.						82	68	73					2																	120199162		2203	4300	6503	SO:0001583	missense	6344	exon12			AGGACGGCCACCA		CCDS2127.1	2q14.1	2012-08-10			ENSG00000080293	ENSG00000080293		"GPCR / Class B : Glucagon receptors"	10608	protein-coding gene	gene with protein product		182098				1646711	Standard	NM_002980		Approved		uc002tma.3	P47872	OTTHUMG00000131407	ENST00000019103.5:c.1154C>T	chr2.hg19:g.120199162G>A	ENSP00000019103:p.Ala385Val	87.0	0.0		81.0	28.0	NM_002980	Q12961|Q13213|Q53T00	Missense_Mutation	SNP	ENST00000019103.5	hg19	CCDS2127.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.866985	0.91511	.	.	ENSG00000080293	ENST00000019103	T	0.37235	1.21	4.78	4.78	0.61160	GPCR, family 2-like (1);GPCR, family 2, secretin-like, conserved site (1);	0.000000	0.56097	D	0.000031	T	0.64080	0.2566	M	0.84585	2.705	0.58432	D	0.999999	D	0.63046	0.992	D	0.70716	0.97	T	0.70414	-0.4878	10	0.66056	D	0.02	.	16.5385	0.84378	0.0:0.0:1.0:0.0	.	385	P47872	SCTR_HUMAN	V	385	ENSP00000019103:A385V	ENSP00000019103:A385V	A	-	2	0	SCTR	119915632	1.000000	0.71417	0.983000	0.44433	0.928000	0.56348	9.216000	0.95154	2.467000	0.83353	0.655000	0.94253	GCC	.	.		0.602	SCTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254198.2			A	120199162	G	A	120199162	3	1	352	1	0	0	0	0	1	0	0	0	13958	1203	42	3	176	3	SCTR	2	120199162	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	6780436	120199162	123000211	77	49493										
TMEM163	81615	hgsc.bcm.edu	37	chr2	135470783	135470783	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tactcactaaaggcagccacCgcgagggccagggtgacaat	12	12	1	1	rs543616754		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:135470783C>T	ENST00000281924.6	-	2	373	c.309G>A	c.(307-309)gcG>gcA	p.A103A		NM_030923.4	NP_112185.1	Q8TC26	TM163_HUMAN	transmembrane protein 163	103						cell junction (GO:0030054)|early endosome membrane (GO:0031901)|integral component of synaptic vesicle membrane (GO:0030285)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(5)|lung(8)|stomach(1)|urinary_tract(1)	16				BRCA - Breast invasive adenocarcinoma(221;0.154)		AGGCAGCCACCGCGAGGGCCA	0.517																																					p.A103A		Atlas-SNP	.											TMEM163,caecum,adenoma,0,1	TMEM163	34	.	0			c.G309A						.						170	142	151					2																	135470783		2203	4300	6503	SO:0001819	synonymous_variant	81615	exon2			AGCCACCGCGAGG		CCDS2172.1	2q21.3	2008-02-05			ENSG00000152128	ENSG00000152128			25380	protein-coding gene	gene with protein product						17623043	Standard	NM_030923		Approved	DKFZP566N034, SV31	uc002ttx.3	Q8TC26	OTTHUMG00000131713	ENST00000281924.6:c.309G>A	chr2.hg19:g.135470783C>T		100.0	0.0		93.0	15.0	NM_030923	Q53QM3|Q53SV7|Q69YH3|Q9UFG3	Silent	SNP	ENST00000281924.6	hg19	CCDS2172.1																																																																																			.	.		0.517	TMEM163-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254631.2	NM_030923		T	135470783	C	T	135470783	2	4	352	1	0	0	0	0	0	0	0	1	16093	639	23	1		1	TMEM163	2	135470783	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	15271621	135470783	107728590	78	49494										
ZRANB3	84083	hgsc.bcm.edu	37	chr2	135985392	135985392	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	caagacttaccattacctggCtgggatgtaagtccgtcttc	9	11	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:135985392C>G	ENST00000264159.6	-	14	2264	c.2148G>C	c.(2146-2148)caG>caC	p.Q716H	ZRANB3_ENST00000401392.1_Missense_Mutation_p.Q716H|ZRANB3_ENST00000536680.1_Missense_Mutation_p.Q716H|ZRANB3_ENST00000412849.1_5'UTR	NM_032143.2	NP_115519.2	Q5FWF4	ZRAB3_HUMAN	zinc finger, RAN-binding domain containing 3	716					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|DNA rewinding (GO:0036292)|DNA strand renaturation (GO:0000733)|negative regulation of DNA recombination (GO:0045910)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to UV (GO:0009411)	nuclear replication fork (GO:0043596)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|endodeoxyribonuclease activity (GO:0004520)|helicase activity (GO:0004386)|K63-linked polyubiquitin binding (GO:0070530)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|upper_aerodigestive_tract(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.135)		CATTACCTGGCTGGGATGTAA	0.388																																					p.Q716H		Atlas-SNP	.											.	ZRANB3	109	.	0			c.G2148C						.						128	110	116					2																	135985392		1857	4090	5947	SO:0001583	missense	84083	exon14			ACCTGGCTGGGAT	AL136824	CCDS46419.1, CCDS67963.1, CCDS74580.1	2q21.3	2013-05-13			ENSG00000121988	ENSG00000121988		"Zinc fingers, RAN-binding domain containing"	25249	protein-coding gene	gene with protein product						11230166	Standard	XM_005263809		Approved	DKFZP434B1727	uc002tum.3	Q5FWF4	OTTHUMG00000150475	ENST00000264159.6:c.2148G>C	chr2.hg19:g.135985392C>G	ENSP00000264159:p.Gln716His	95.0	0.0		88.0	13.0	NM_032143	B3KYA1|B4E375|B5MDI3|D3DP76|E9PBP0|Q53SM1|Q6P2C4|Q8N1P4|Q9H0E8	Missense_Mutation	SNP	ENST00000264159.6	hg19	CCDS46419.1	.	.	.	.	.	.	.	.	.	.	C	11.10	1.539003	0.27475	.	.	ENSG00000121988	ENST00000538542;ENST00000283060;ENST00000401392;ENST00000264159;ENST00000536680	D;D;D	0.91011	-2.76;-2.77;-2.74	4.84	2.08	0.27032	.	0.808984	0.11441	N	0.563767	D	0.88078	0.6340	L	0.57536	1.79	0.09310	N	1	P;P	0.44309	0.832;0.697	P;P	0.44477	0.45;0.451	T	0.77558	-0.2543	10	0.36615	T	0.2	-19.4711	6.3648	0.21449	0.0:0.7008:0.0:0.2992	.	716;716	Q5FWF4;Q5FWF4-3	ZRAB3_HUMAN;.	H	181;181;716;716;716	ENSP00000383979:Q716H;ENSP00000264159:Q716H;ENSP00000441320:Q716H	ENSP00000264159:Q716H	Q	-	3	2	ZRANB3	135701862	0.826000	0.29277	0.095000	0.20976	0.447000	0.32167	0.681000	0.25320	0.755000	0.32990	-0.300000	0.09419	CAG	.	.		0.388	ZRANB3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318254.1	NM_032143		G	135985392	C	G	135985392	3	3	352	1	0	0	0	0	1	0	0	0	18239	796	28	4	1123	4	ZRANB3	2	135985392	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	514609	135985392	107213981	79	49495										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141299487	141299487	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cagtccgaccagaatatataAttgtcataaacagccaaact	5	10	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:141299487A>T	ENST00000389484.3	-	44	8219	c.7248T>A	c.(7246-7248)aaT>aaA	p.N2416K		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2416					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		AGAATATATAATTGTCATAAA	0.373										TSP Lung(27;0.18)																											p.N2416K	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.T7248A						.						81	78	79					2																	141299487		2203	4299	6502	SO:0001583	missense	53353	exon44			TATATAATTGTCA	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.7248T>A	chr2.hg19:g.141299487A>T	ENSP00000374135:p.Asn2416Lys	140.0	0.0		117.0	22.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	A	16.57	3.161377	0.57368	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.91237	-2.81	5.46	3.12	0.35913	Six-bladed beta-propeller, TolB-like (1);	0.206592	0.40728	U	0.001025	D	0.83115	0.5184	L	0.42744	1.35	0.32782	N	0.502422	B	0.24258	0.1	B	0.15870	0.014	T	0.78768	-0.2075	10	0.35671	T	0.21	.	4.8781	0.13665	0.5622:0.1514:0.2864:0.0	.	2416	Q9NZR2	LRP1B_HUMAN	K	2416;2354	ENSP00000374135:N2416K	ENSP00000374135:N2416K	N	-	3	2	LRP1B	141015957	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	2.012000	0.40932	0.905000	0.36596	0.402000	0.26972	AAT	.	.		0.373	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		T	141299487	A	T	141299487	3	4	352	1	0	0	0	0	1	0	0	0	8964	98	4	4	6743	4	LRP1B	2	141299487	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	5314095	141299487	101899886	80	49496										
LRP1B	53353	hgsc.bcm.edu	37	chr2	141709436	141709436	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	atttggtacttgccagagtcGcagtgccatttgctgctaat	10	9	0	1	rs146639012		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:141709436G>A	ENST00000389484.3	-	19	3932	c.2961C>T	c.(2959-2961)tgC>tgT	p.C987C		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	987	LDL-receptor class A 6. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TGCCAGAGTCGCAGTGCCATT	0.453										TSP Lung(27;0.18)			G|||	1	0.000199681	8e-04	0	5008	,	,		18933	0		0	False		,,,				2504	0				p.C987C	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.C2961T						.	G		1,4405	2.1+/-5.4	0,1,2202	172	138	149		2961	-4.9	0.9	2	dbSNP_134	149	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	LRP1B	NM_018557.2		0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154		987/4600	141709436	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	53353	exon19			AGAGTCGCAGTGC	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.2961C>T	chr2.hg19:g.141709436G>A		107.0	0.0		86.0	11.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	hg19	CCDS2182.1																																																																																			.	G|1.000;A|0.000		0.453	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		A	141709436	G	A	141709436	2	1	352	1	0	0	0	0	0	0	0	1	8964	1079	38	1		1	LRP1B	2	141709436	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	409949	141709436	101489937	81	49497										
SCN3A	6328	hgsc.bcm.edu	37	chr2	166032889	166032889	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ttcaggtcctgggggtaccaAcagtgcctgtgccatctttt	11	11	2	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:166032889A>G	ENST00000360093.3	-	3	507	c.16T>C	c.(16-18)Ttg>Ctg	p.L6L	SCN3A_ENST00000283254.7_Silent_p.L6L|SCN3A_ENST00000409101.3_Silent_p.L6L	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	6					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GGGGGTACCAACAGTGCCTGT	0.423																																					p.L6L		Atlas-SNP	.											.	SCN3A	544	.	0			c.T16C						.						100	99	99					2																	166032889		2203	4299	6502	SO:0001819	synonymous_variant	6328	exon3			GTACCAACAGTGC	AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10590	protein-coding gene	gene with protein product		182391	"sodium channel, voltage-gated, type III, alpha polypeptide"			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.16T>C	chr2.hg19:g.166032889A>G		61.0	0.0		65.0	30.0	NM_001081676	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Silent	SNP	ENST00000360093.3	hg19																																																																																				.	.		0.423	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922		G	166032889	A	G	166032889	2	3	352	1	0	0	0	0	0	0	0	1	13933	40	2	2		2	SCN3A	2	166032889	Silent	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	24323453	166032889	77166484	82	49498										
LRP2	4036	hgsc.bcm.edu	37	chr2	170033019	170033019	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cggaagtcatctggacactcGcaagtgaacccttttcctcc	8	14	2	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:170033019G>A	ENST00000263816.3	-	54	10758	c.10473C>T	c.(10471-10473)tgC>tgT	p.C3491C	LRP2_ENST00000461418.1_5'Flank	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	3491	EGF-like 13. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	CTGGACACTCGCAAGTGAACC	0.512																																					p.C3491C		Atlas-SNP	.											LRP2,NS,carcinoma,0,1	LRP2	751	.	0			c.C10473T						.						174	134	148					2																	170033019		2203	4300	6503	SO:0001819	synonymous_variant	4036	exon54			ACACTCGCAAGTG		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.10473C>T	chr2.hg19:g.170033019G>A		97.0	0.0		107.0	5.0	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	hg19	CCDS2232.1																																																																																			.	.		0.512	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		A	170033019	G	A	170033019	2	1	352	1	0	0	0	0	0	0	0	1	8965	1079	38	1		1	LRP2	2	170033019	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	4000130	170033019	73166354	83	49499										
TTN	7273	hgsc.bcm.edu	37	chr2	179588283	179588283	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ttcaaaatagatgttgcaccGgtctcctttcactagttctc	6	11	4	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:179588283G>A	ENST00000591111.1	-	72	20817	c.20593C>T	c.(20593-20595)Cgg>Tgg	p.R6865W	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|RP11-171I2.1_ENST00000590024.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R7182W|TTN_ENST00000342175.6_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.R5938W|TTN_ENST00000460472.2_Intron			Q8WZ42	TITIN_HUMAN	titin	12456	Ig-like 50.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATGTTGCACCGGTCTCCTTTC	0.428																																					p.R7182W		Atlas-SNP	.											.	TTN	18412	.	0			c.C21544T						.						81	77	78					2																	179588283		1869	4097	5966	SO:0001583	missense	7273	exon74			TGCACCGGTCTCC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.20593C>T	chr2.hg19:g.179588283G>A	ENSP00000465570:p.Arg6865Trp	107.0	0.0		132.0	23.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	6.070	0.381286	0.11466	.	.	ENSG00000155657	ENST00000342992	T	0.53206	0.63	6.16	0.56	0.17279	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.54870	0.1885	M	0.88979	2.995	0.23515	N	0.997517	P	0.51057	0.941	B	0.43360	0.417	T	0.54036	-0.8353	9	0.87932	D	0	.	10.5719	0.45204	0.0961:0.0:0.245:0.6589	.	6865	Q8WZ42	TITIN_HUMAN	W	5938	ENSP00000343764:R5938W	ENSP00000343764:R5938W	R	-	1	2	TTN	179296528	0.000000	0.05858	0.512000	0.27736	0.723000	0.41478	0.901000	0.28445	0.207000	0.20607	-0.188000	0.12872	CGG	.	.		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179588283	G	A	179588283	3	1	352	1	0	0	0	0	1	0	0	0	16750	1115	39	1	83141	1	TTN	2	179588283	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	9555264	179588283	63611090	84	49500										
CLK1	1195	hgsc.bcm.edu	37	chr2	201722550	201722550	+	Frame_Shift_Del	DEL	A	A	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gtactaagtcccaatagttcAaaaacaatgcaaatgtgacc							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:201722550delA	ENST00000321356.4	-	7	858	c.723delT	c.(721-723)tttfs	p.F241fs	CLK1_ENST00000409769.2_Frame_Shift_Del_p.F64fs|CLK1_ENST00000434813.2_Frame_Shift_Del_p.F283fs	NM_004071.3	NP_004062.2	P49759	CLK1_HUMAN	CDC-like kinase 1	241	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|regulation of RNA splicing (GO:0043484)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			NS(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(12)|ovary(1)|pancreas(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33						CCAATAGTTCAAAAACAATGC	0.363																																					p.E284fs		Atlas-INDEL	.											.	CLK1	103	.	0			c.850delG						.						105	100	102					2																	201722550		2203	4300	6503	SO:0001589	frameshift_variant	1195	exon7			.	L29219	CCDS2331.1, CCDS54427.1	2q33	2008-05-02			ENSG00000013441	ENSG00000013441		"CDC-like kinases"	2068	protein-coding gene	gene with protein product		601951				9856501	Standard	NM_004071		Approved		uc002uwe.2	P49759	OTTHUMG00000132784	ENST00000321356.4:c.723delT	chr2.hg19:g.201722550delA	ENSP00000326830:p.Phe241fs	146.0	0.0		119.0	24.0	NM_001162407	B4DFW7|Q0P694|Q8N5V8	Frame_Shift_Del	DEL	ENST00000321356.4	hg19	CCDS2331.1																																																																																			.	.		0.363	CLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256192.2			-	201722550	A	-	201722550	7	5	352	1	0	1	0	1	0	0	0	0	3538	127	5	0	759	0	CLK1	2	201722550	Frame_Shift_Del	DEL	A	TCGA-WQ-A9G7-01A-11D-A36X-10	22134267	201722550	41476823	85	49501										
ALS2	57679	hgsc.bcm.edu	37	chr2	202622187	202622187	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cctctgtttcttcttctctgAtatccacaagacttgaactt	4	12	4	3			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:202622187A>G	ENST00000264276.6	-	5	1781	c.1409T>C	c.(1408-1410)aTc>aCc	p.I470T		NM_020919.3	NP_065970.2	Q96Q42	ALS2_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	470					behavioral fear response (GO:0001662)|cell death (GO:0008219)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|locomotory behavior (GO:0007626)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Rab GTPase activity (GO:0032851)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of Ran GTPase activity (GO:0032853)|protein localization (GO:0008104)|receptor recycling (GO:0001881)|regulation of endosome size (GO:0051036)|response to oxidative stress (GO:0006979)|synaptic transmission, glutamatergic (GO:0035249)|vesicle organization (GO:0016050)	centrosome (GO:0005813)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome (GO:0005769)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|ruffle (GO:0001726)|vesicle (GO:0031982)	protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(22)|ovary(1)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	72						TTCTTCTCTGATATCCACAAG	0.443																																					p.I470T		Atlas-SNP	.											.	ALS2	172	.	0			c.T1409C						.						207	193	197					2																	202622187		1874	4097	5971	SO:0001583	missense	57679	exon5			TCTCTGATATCCA	AB053305	CCDS42800.1, CCDS46492.1	2q33-q35	2014-09-17	2004-06-23		ENSG00000003393	ENSG00000003393		"Rho guanine nucleotide exchange factors"	443	protein-coding gene	gene with protein product	"alsin"	606352	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 6"	ALS2CR6		11586298	Standard	NM_020919		Approved		uc002uyo.3	Q96Q42	OTTHUMG00000154507	ENST00000264276.6:c.1409T>C	chr2.hg19:g.202622187A>G	ENSP00000264276:p.Ile470Thr	122.0	0.0		123.0	15.0	NM_020919	Q53TT1|Q53TV2|Q8N1E0|Q96PC4|Q96Q41|Q9H973|Q9HCK9	Missense_Mutation	SNP	ENST00000264276.6	hg19	CCDS42800.1	.	.	.	.	.	.	.	.	.	.	A	18.79	3.699875	0.68501	.	.	ENSG00000003393	ENST00000264276	T	0.58358	0.34	5.9	5.9	0.94986	.	0.107189	0.64402	D	0.000007	T	0.58119	0.2100	N	0.17082	0.46	0.80722	D	1	D;D;D	0.89917	1.0;0.997;0.984	D;D;P	0.83275	0.996;0.917;0.835	T	0.59273	-0.7485	10	0.34782	T	0.22	.	16.3318	0.83023	1.0:0.0:0.0:0.0	.	470;470;470	Q96Q42-3;Q6IQ41;Q96Q42	.;.;ALS2_HUMAN	T	470	ENSP00000264276:I470T	ENSP00000264276:I470T	I	-	2	0	ALS2	202330432	1.000000	0.71417	1.000000	0.80357	0.589000	0.36550	8.283000	0.89909	2.248000	0.74166	0.460000	0.39030	ATC	.	.		0.443	ALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335562.3	NM_020919		G	202622187	A	G	202622187	3	3	352	1	0	0	0	0	1	0	0	0	550	333	12	2	3684	2	ALS2	2	202622187	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	899637	202622187	40577186	86	49502										
ACADL	33	hgsc.bcm.edu	37	chr2	211081128	211081129	+	Frame_Shift_Ins	INS	-	-	G													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	acatttgcctgcagtcatctINSggggaataaagtgcttaatc							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:211081128_211081129insG	ENST00000233710.3	-	4	705_706	c.478_479insC	c.(478-480)cagfs	p.Q160fs	AC006994.2_ENST00000412065.1_RNA	NM_001608.3	NP_001599.1	P28330	ACADL_HUMAN	acyl-CoA dehydrogenase, long chain	160					carnitine catabolic process (GO:0042413)|carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid catabolic process (GO:0044242)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|long-chain fatty acid catabolic process (GO:0042758)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of fatty acid oxidation (GO:0046322)|oxidation-reduction process (GO:0055114)|protein homotetramerization (GO:0051289)|regulation of cholesterol metabolic process (GO:0090181)|small molecule metabolic process (GO:0044281)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)|palmitoyl-CoA oxidase activity (GO:0016401)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	14		Renal(323;0.202)		Epithelial(149;0.00631)|Lung(261;0.0438)|LUSC - Lung squamous cell carcinoma(261;0.0466)|all cancers(144;0.0621)		TGCAGTCATCTGGGGAATAAAG	0.406																																					p.Q160fs		Atlas-INDEL	.											.	ACADL	38	.	0			c.479_480insC						.																																			SO:0001589	frameshift_variant	33	exon4			.	M74096	CCDS2389.1	2q34	2012-07-13	2010-04-30		ENSG00000115361	ENSG00000115361	1.3.99.13		88	protein-coding gene	gene with protein product		609576	"acyl-Coenzyme A dehydrogenase, long chain"			1774065	Standard	NM_001608		Approved	LCAD, ACAD4	uc002vdz.4	P28330	OTTHUMG00000132989	ENST00000233710.3:c.479dupC	chr2.hg19:g.211081132_211081132dupG	ENSP00000233710:p.Gln160fs	95.0	0.0		93.0	12.0	NM_001608	B2R8T3|Q8IUN8	Frame_Shift_Ins	INS	ENST00000233710.3	hg19	CCDS2389.1																																																																																			.	.		0.406	ACADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256561.2	NM_001608		G	211081129	-	G	211081128	7	5	352	1	0	1	1	0	0	0	0	0	112	1580	55	0	845	0	ACADL	2	211081128	Frame_Shift_Ins	INS	-	TCGA-WQ-A9G7-01A-11D-A36X-10	8458941	211081128	32118245	87	49503										
ZNF142	7701	hgsc.bcm.edu	37	chr2	219508083	219508084	+	Frame_Shift_Ins	INS	-	-	C													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gttttcctcccccgccacgtINSccccccctgcagccttcagc							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:219508083_219508084insC	ENST00000449707.1	-	8	3576_3577	c.3155_3156insG	c.(3154-3156)ggafs	p.G1052fs	ZNF142_ENST00000411696.2_Frame_Shift_Ins_p.G1052fs	NM_001105537.1	NP_001099007.1	P52746	ZN142_HUMAN	zinc finger protein 142	1052					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G1052fs*20(1)|p.G889fs*20(1)		breast(7)|endometrium(7)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38		Renal(207;0.0474)		Epithelial(149;5.21e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		CCCCGCCACGTCCCCCCCTGCA	0.604																																					p.G1052fs	Colon(170;867 1942 8995 15834 18053)	Atlas-INDEL	.											.,2	ZNF142	190	.	2	Deletion - Frameshift(2)	lung(2)	c.3156_3157insG						.																																			SO:0001589	frameshift_variant	7701	exon8			.	U09849	CCDS42817.1	2q35	2013-01-08	2006-06-13		ENSG00000115568	ENSG00000115568		"Zinc fingers, C2H2-type"	12927	protein-coding gene	gene with protein product		604083	"zinc finger protein 142 (clone pHZ-49)"				Standard	NM_001105537		Approved	KIAA0236, pHZ-49	uc002vin.4	P52746	OTTHUMG00000154736	ENST00000449707.1:c.3156dupG	chr2.hg19:g.219508090_219508090dupC	ENSP00000408643:p.Gly1052fs	143.0	0.0		140.0	26.0	NM_001105537	Q92510	Frame_Shift_Ins	INS	ENST00000449707.1	hg19	CCDS42817.1																																																																																			.	.		0.604	ZNF142-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336833.1	NM_005081		C	219508084	-	C	219508083	7	5	352	1	0	1	1	0	0	0	0	0	17746	1654	58	0	1919	0	ZNF142	2	219508083	Frame_Shift_Ins	INS	-	TCGA-WQ-A9G7-01A-11D-A36X-10	8426955	219508083	23691290	88	49504										
SPEG	10290	hgsc.bcm.edu	37	chr2	220313610	220313610	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gcccaggagccgcgggccggCgggcaggacagagccggggg	22	13	0	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:220313610C>T	ENST00000312358.7	+	4	1862	c.1730C>T	c.(1729-1731)gCg>gTg	p.A577V	SPEG_ENST00000485813.1_3'UTR|SPEG_ENST00000396698.1_Missense_Mutation_p.A473V|SPEG_ENST00000396695.2_5'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	577	Pro-rich.				cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		CGCGGGCCGGCGGGCAGGACA	0.751																																					p.A577V		Atlas-SNP	.											.	SPEG	272	.	0			c.C1730T						.						2	3	3					2																	220313610		1369	3172	4541	SO:0001583	missense	10290	exon4			GGCCGGCGGGCAG	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"Immunoglobulin superfamily / I-set domain containing"	16901	protein-coding gene	gene with protein product		615950	"aortic preferentially expressed gene 1"	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.1730C>T	chr2.hg19:g.220313610C>T	ENSP00000311684:p.Ala577Val	39.0	0.0		29.0	9.0	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	hg19	CCDS42824.1	.	.	.	.	.	.	.	.	.	.	C	0.016	-1.536243	0.00942	.	.	ENSG00000072195	ENST00000312358;ENST00000265327;ENST00000396698	T;T	0.64085	-0.08;0.3	3.9	-1.25	0.09405	.	1.254290	0.06059	N	0.657967	T	0.39963	0.1098	N	0.14661	0.345	0.20307	N	0.999918	B	0.09022	0.002	B	0.04013	0.001	T	0.13335	-1.0513	10	0.26408	T	0.33	.	4.6178	0.12435	0.0:0.4452:0.3509:0.2039	.	577	Q15772	SPEG_HUMAN	V	577;577;473	ENSP00000311684:A577V;ENSP00000379926:A473V	ENSP00000265327:A577V	A	+	2	0	SPEG	220021854	0.002000	0.14202	0.035000	0.18076	0.055000	0.15305	-1.633000	0.02022	-0.485000	0.06754	-0.379000	0.06801	GCG	.	.		0.751	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		T	220313610	C	T	220313610	3	4	352	1	0	0	0	0	1	0	0	0	15051	768	27	1	1744	1	SPEG	2	220313610	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	805527	220313610	22885763	89	49505										
OBSL1	23363	hgsc.bcm.edu	37	chr2	220435528	220435528	+	Frame_Shift_Del	DEL	C	C	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gcacgtcagcaccacctccgCcccccgcagcacccactggg							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:220435528delC	ENST00000404537.1	-	1	483	c.427delG	c.(427-429)gcgfs	p.A143fs	INHA_ENST00000489456.1_Intron|OBSL1_ENST00000373873.4_Frame_Shift_Del_p.A143fs|OBSL1_ENST00000373876.1_Frame_Shift_Del_p.A143fs|OBSL1_ENST00000265318.4_Frame_Shift_Del_p.A143fs|OBSL1_ENST00000491370.1_Intron|OBSL1_ENST00000289656.3_Intron|INHA_ENST00000243786.2_5'Flank|OBSL1_ENST00000603926.1_Frame_Shift_Del_p.A143fs	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	143	Ig-like 2.				cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)						Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		ACCACCTCCGCCCCCCGCAGC	0.746																																					p.A143fs		Atlas-INDEL	.											.	OBSL1	120	.	0			c.428delC						.						3	4	4					2																	220435528		1598	3556	5154	SO:0001589	frameshift_variant	23363	exon1			.	BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.427delG	chr2.hg19:g.220435528delC	ENSP00000385636:p.Ala143fs	354.0	0.0		402.0	61.0	NM_001173431	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Frame_Shift_Del	DEL	ENST00000404537.1	hg19	CCDS46520.1																																																																																			.	.		0.746	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1			-	220435528	C	-	220435528	7	5	352	1	0	1	0	1	0	0	0	0	10822	739	26	0	5499	0	OBSL1	2	220435528	Frame_Shift_Del	DEL	C	TCGA-WQ-A9G7-01A-11D-A36X-10	121918	220435528	22763845	90	49506										
SP110	3431	hgsc.bcm.edu	37	chr2	231033882	231033882	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ccgtcattggcttcatgaaaAccgagcacgtctttgagatc	9	11	3	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:231033882A>G	ENST00000358662.4	-	18	2106	c.2028T>C	c.(2026-2028)ggT>ggC	p.G676G	AC009950.2_ENST00000454058.1_RNA|SP110_ENST00000258381.6_Silent_p.G700G|AC009950.2_ENST00000594622.1_RNA|AC009950.2_ENST00000595586.2_RNA|AC009950.2_ENST00000600787.1_RNA|AC009950.2_ENST00000445199.1_RNA|AC009950.2_ENST00000609120.1_RNA	NM_004509.3	NP_004500	Q9HB58	SP110_HUMAN	SP110 nuclear body protein	676	Bromo.				regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			breast(4)|endometrium(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Renal(207;0.0112)|all_lung(227;0.0223)|Lung NSC(271;0.0983)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.169)		Epithelial(121;2.61e-12)|all cancers(144;6.39e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.0097)		CTTCATGAAAACCGAGCACGT	0.468																																					p.G700G		Atlas-SNP	.											.	SP110	105	.	0			c.T2100C						.						185	191	189					2																	231033882		2203	4300	6503	SO:0001819	synonymous_variant	3431	exon19			ATGAAAACCGAGC	L22343	CCDS2474.1, CCDS2475.1, CCDS2476.1, CCDS54435.1	2q37.1	2014-09-17	2001-12-19	2001-12-20	ENSG00000135899	ENSG00000135899			5401	protein-coding gene	gene with protein product		604457	"interferon-induced protein 41, 30kD"	IFI41, IFI75		7693701, 10388521	Standard	NM_080424		Approved		uc002vqg.3	Q9HB58	OTTHUMG00000133204	ENST00000358662.4:c.2028T>C	chr2.hg19:g.231033882A>G		66.0	0.0		68.0	11.0	NM_080424	B4DVI4|F5H1M1|Q14976|Q14977|Q53TG2|Q8WUZ6|Q9HCT8	Silent	SNP	ENST00000358662.4	hg19	CCDS2474.1																																																																																			.	.		0.468	SP110-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000332414.1	NM_080424		G	231033882	A	G	231033882	2	3	352	1	0	0	0	0	0	0	0	1	14976	30	2	2		2	SP110	2	231033882	Silent	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	10598354	231033882	12165491	91	49507										
ESPNL	339768	hgsc.bcm.edu	37	chr2	239039675	239039675	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gagcccgccacgcggggttgCggggccaggaggccgccagg	20	14	0	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:239039675C>T	ENST00000343063.3	+	9	2583	c.2320C>T	c.(2320-2322)Cgg>Tgg	p.R774W	ESPNL_ENST00000409169.1_Missense_Mutation_p.R730W|ESPNL_ENST00000477241.1_3'UTR|ESPNL_ENST00000409506.1_Missense_Mutation_p.R406W	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	774										endometrium(1)|lung(8)|pancreas(2)|skin(2)	13		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		CGCGGGGTTGCGGGGCCAGGA	0.716																																					p.R774W		Atlas-SNP	.											.	ESPNL	63	.	0			c.C2320T						.						2	2	2					2																	239039675		1412	3156	4568	SO:0001583	missense	339768	exon9			GGGTTGCGGGGCC	AK124559	CCDS2525.1	2q37.3	2013-01-10			ENSG00000144488	ENSG00000144488		"Ankyrin repeat domain containing"	27937	protein-coding gene	gene with protein product						12975309	Standard	NM_194312		Approved	FLJ42568	uc002vxq.4	Q6ZVH7	OTTHUMG00000133335	ENST00000343063.3:c.2320C>T	chr2.hg19:g.239039675C>T	ENSP00000339115:p.Arg774Trp	67.0	0.0		76.0	17.0	NM_194312	Q66K27|Q6ZVG1|Q8IVU2	Missense_Mutation	SNP	ENST00000343063.3	hg19	CCDS2525.1	.	.	.	.	.	.	.	.	.	.	C	6.914	0.538302	0.13188	.	.	ENSG00000144488	ENST00000343063;ENST00000409169;ENST00000409506	T;T;T	0.63913	-0.07;1.04;0.62	4.08	-1.1	0.09872	.	0.695284	0.12220	N	0.488437	T	0.51381	0.1671	L	0.44542	1.39	0.09310	N	1	D;D	0.65815	0.995;0.992	P;B	0.46975	0.533;0.332	T	0.44667	-0.9313	10	0.44086	T	0.13	-11.6203	4.8088	0.13333	0.629:0.2175:0.0:0.1535	.	730;774	Q6ZVH7-2;Q6ZVH7	.;ESPNL_HUMAN	W	774;730;406	ENSP00000339115:R774W;ENSP00000386577:R730W;ENSP00000386579:R406W	ENSP00000339115:R774W	R	+	1	2	ESPNL	238704414	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-1.379000	0.02554	0.140000	0.18849	0.313000	0.20887	CGG	.	.		0.716	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312		T	239039675	C	T	239039675	3	4	352	1	0	0	0	0	1	0	0	0	5257	759	27	1	2354	1	ESPNL	2	239039675	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	8005793	239039675	4159698	92	49508										
HDAC4	9759	hgsc.bcm.edu	37	chr2	240056341	240056341	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gtctgtgcgccaaactcgtcTggggacagaacacacgatga	12	11	2	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:240056341T>C	ENST00000345617.3	-	10	1770		c.e10-2		HDAC4_ENST00000553145.1_Splice_Site|HDAC4_ENST00000543185.1_Splice_Site|HDAC4_ENST00000541256.1_Splice_Site	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4						B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		CAAACTCGTCTGGGGACAGAA	0.532																																					.		Atlas-SNP	.											.	HDAC4	127	.	0			c.979-2A>G						.						110	103	106					2																	240056341		2203	4300	6503	SO:0001630	splice_region_variant	9759	exon11			CTCGTCTGGGGAC	AB006626	CCDS2529.1	2q37.3	2014-02-12			ENSG00000068024	ENSG00000068024			14063	protein-coding gene	gene with protein product		605314	"brachydactyly-mental retardation syndrome"	BDMR		10206986, 10220385, 20691407	Standard	NM_006037		Approved	KIAA0288, HDAC-A, HDACA, HD4, HA6116, HDAC-4	uc002vyk.4	P56524	OTTHUMG00000133344	ENST00000345617.3:c.979-2A>G	chr2.hg19:g.240056341T>C		73.0	0.0		79.0	11.0	NM_006037	Q9UND6	Splice_Site	SNP	ENST00000345617.3	hg19	CCDS2529.1	.	.	.	.	.	.	.	.	.	.	T	16.64	3.178223	0.57692	.	.	ENSG00000068024	ENST00000345617;ENST00000456922;ENST00000541256;ENST00000393621;ENST00000445704	.	.	.	4.32	4.32	0.51571	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.2038	0.65721	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	HDAC4	239721278	1.000000	0.71417	0.984000	0.44739	0.602000	0.36980	7.571000	0.82399	1.896000	0.54893	0.459000	0.35465	.	.	.		0.532	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037	Intron	C	240056341	T	C	240056341	5	2	352	1	0	0	0	0	0	0	1	0	7018	1594	55	2	2349	2	HDAC4	2	240056341	Splice_Site	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	1016666	240056341	3143032	93	49509										
OR6B2	389090	hgsc.bcm.edu	37	chr2	240969782	240969782	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggaagagcaggtactgcagcCctggggccgtggggaggccc	19	11	0	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr2:240969782C>T	ENST00000402971.2	-	1	124	c.65G>A	c.(64-66)gGg>gAg	p.G22E		NM_001005853.1	NP_001005853.1	Q6IFH4	OR6B2_HUMAN	olfactory receptor, family 6, subfamily B, member 2	22						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(4)|lung(9)|prostate(1)	15		all_epithelial(40;1.64e-11)|Breast(86;0.000327)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.229)|Melanoma(123;0.238)		Epithelial(121;3.4e-29)|all cancers(36;2.08e-27)|OV - Ovarian serous cystadenocarcinoma(60;4.63e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.56e-05)|Lung(119;0.00344)|LUSC - Lung squamous cell carcinoma(224;0.0148)		GTACTGCAGCCCTGGGGCCGT	0.592																																					p.G22E		Atlas-SNP	.											.	OR6B2	30	.	0			c.G65A						.						42	46	45					2																	240969782		2016	4183	6199	SO:0001583	missense	389090	exon1			TGCAGCCCTGGGG		CCDS46559.1	2q37.3	2012-08-09	2004-10-07	2004-10-07	ENSG00000182083	ENSG00000182083		"GPCR / Class A : Olfactory receptors"	15041	protein-coding gene	gene with protein product			"olfactory receptor, family 6, subfamily B, member 2 pseudogene"	OR6B2P			Standard	XM_005247004		Approved		uc010zoc.2	Q6IFH4	OTTHUMG00000152400	ENST00000402971.2:c.65G>A	chr2.hg19:g.240969782C>T	ENSP00000384563:p.Gly22Glu	191.0	0.0		156.0	47.0	NM_001005853	B2RPR3|Q8NGW0	Missense_Mutation	SNP	ENST00000402971.2	hg19	CCDS46559.1	.	.	.	.	.	.	.	.	.	.	N	0.001	-2.963569	0.00049	.	.	ENSG00000182083	ENST00000402971	T	0.00421	7.46	4.28	0.271	0.15640	.	1.961550	0.02720	N	0.113895	T	0.00144	0.0004	N	0.01515	-0.825	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.35101	-0.9802	10	0.02654	T	1	.	4.1485	0.10227	0.1622:0.5469:0.0:0.2909	.	22	Q6IFH4	OR6B2_HUMAN	E	22	ENSP00000384563:G22E	ENSP00000384563:G22E	G	-	2	0	OR6B2	240618455	0.000000	0.05858	0.023000	0.16930	0.024000	0.10985	-0.703000	0.05063	-0.072000	0.12864	-0.225000	0.12378	GGG	.	.		0.592	OR6B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326079.1	NM_001005853		T	240969782	C	T	240969782	3	4	352	1	0	0	0	0	1	0	0	0	11197	623	22	3	875	3	OR6B2	2	240969782	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	913441	240969782	2229591	94	49510										
TATDN2	9797	hgsc.bcm.edu	37	chr3	10312434	10312434	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aaagttcagaaaaatttacaGcagctccttccctaaggaat	6	9	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr3:10312434G>A	ENST00000287652.4	+	4	2619	c.1568G>A	c.(1567-1569)aGc>aAc	p.S523N	RP11-438J1.1_ENST00000450534.1_3'UTR|TATDN2_ENST00000448281.2_Missense_Mutation_p.S523N	NM_014760.3	NP_055575.3	Q93075	TATD2_HUMAN	TatD DNase domain containing 2	523					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|DNA catabolic process (GO:0006308)|endoplasmic reticulum unfolded protein response (GO:0030968)	intracellular organelle (GO:0043229)|nucleoplasm (GO:0005654)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(9)|pancreas(2)|prostate(1)|stomach(2)	28						AAAATTTACAGCAGCTCCTTC	0.478																																					p.S523N		Atlas-SNP	.											.	TATDN2	59	.	0			c.G1568A						.						77	82	80					3																	10312434		2203	4300	6503	SO:0001583	missense	9797	exon4			TTTACAGCAGCTC	D86972	CCDS33698.1	3p25.3	2010-11-24			ENSG00000157014	ENSG00000157014			28988	protein-coding gene	gene with protein product						9039502	Standard	NM_014760		Approved	KIAA0218	uc003bvf.3	Q93075	OTTHUMG00000155361	ENST00000287652.4:c.1568G>A	chr3.hg19:g.10312434G>A	ENSP00000287652:p.Ser523Asn	100.0	0.0		122.0	30.0	NM_014760	Q3MIL9|Q5BKU0	Missense_Mutation	SNP	ENST00000287652.4	hg19	CCDS33698.1	.	.	.	.	.	.	.	.	.	.	G	12.83	2.056096	0.36277	.	.	ENSG00000157014	ENST00000287652;ENST00000448281	T;T	0.25085	1.82;1.82	5.0	4.11	0.48088	.	0.440605	0.22282	N	0.062102	T	0.15825	0.0381	N	0.13235	0.315	0.23669	N	0.997159	B	0.29212	0.237	B	0.35353	0.201	T	0.10800	-1.0614	10	0.59425	D	0.04	-12.6026	6.6027	0.22708	0.0956:0.1842:0.7202:0.0	.	523	Q93075	TATD2_HUMAN	N	523	ENSP00000287652:S523N;ENSP00000408736:S523N	ENSP00000287652:S523N	S	+	2	0	TATDN2	10287434	0.996000	0.38824	0.997000	0.53966	0.996000	0.88848	2.704000	0.47118	2.494000	0.84150	0.644000	0.83932	AGC	.	.		0.478	TATDN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339641.1	XM_376203		A	10312434	G	A	10312434	3	1	352	1	0	0	0	0	1	0	0	0	15607	971	34	3	1578	3	TATDN2	3	10312434	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10		10312434	187709996	95	49511										
CAPN7	23473	hgsc.bcm.edu	37	chr3	15282001	15282001	+	Frame_Shift_Del	DEL	A	A	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggctgcgatttatccagttgAaaaatccttggagtcattta							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr3:15282001delA	ENST00000253693.2	+	13	1682	c.1429delA	c.(1429-1431)aaafs	p.K477fs		NM_014296.2	NP_055111.1	Q9Y6W3	CAN7_HUMAN	calpain 7	477	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				positive regulation of epithelial cell migration (GO:0010634)|self proteolysis (GO:0097264)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|endopeptidase activity (GO:0004175)|MIT domain binding (GO:0090541)			breast(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|skin(2)	22						TATCCAGTTGAAAAATCCTTG	0.333																																					p.L476fs		Atlas-INDEL	.											.	CAPN7	63	.	0			c.1428delG						.						59	63	62					3																	15282001		2201	4299	6500	SO:0001589	frameshift_variant	23473	exon13			.	AB028639	CCDS2624.1	3p24	2008-07-18			ENSG00000131375	ENSG00000131375			1484	protein-coding gene	gene with protein product	"calpain like protease", "homolog of Aspergillus Nidulans PALB"	606400				8163008, 10051333	Standard	NM_014296		Approved	PalBH	uc003bzn.3	Q9Y6W3	OTTHUMG00000129863	ENST00000253693.2:c.1429delA	chr3.hg19:g.15282001delA	ENSP00000253693:p.Lys477fs	93.0	0.0		139.0	10.0	NM_014296		Frame_Shift_Del	DEL	ENST00000253693.2	hg19	CCDS2624.1																																																																																			.	.		0.333	CAPN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252105.2	NM_014296		-	15282001	A	-	15282001	7	5	352	1	0	1	0	1	0	0	0	0	2633	247	9	0	1479	0	CAPN7	3	15282001	Frame_Shift_Del	DEL	A	TCGA-WQ-A9G7-01A-11D-A36X-10	4969567	15282001	182740429	96	49512										
METTL6	131965	hgsc.bcm.edu	37	chr3	15455608	15455608	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tgctgctggctttaaacctaAgcatggcatgatcatacagt	9	9	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr3:15455608A>C	ENST00000443029.1	-	5	833	c.593T>G	c.(592-594)cTt>cGt	p.L198R	METTL6_ENST00000450816.2_Missense_Mutation_p.L153R|METTL6_ENST00000383790.3_Missense_Mutation_p.L198R			Q8TCB7	METL6_HUMAN	methyltransferase like 6	198							methyltransferase activity (GO:0008168)			endometrium(1)|kidney(1)|large_intestine(9)|lung(3)|prostate(1)	15						TTTAAACCTAAGCATGGCATG	0.388																																					p.L198R		Atlas-SNP	.											.	METTL6	27	.	0			c.T593G						.						127	117	120					3																	15455608		1868	4102	5970	SO:0001583	missense	131965	exon5			AACCTAAGCATGG	AK057791	CCDS43056.1	3p25.1	2005-11-02			ENSG00000206562	ENSG00000206562			28343	protein-coding gene	gene with protein product						12477932	Standard	NM_152396		Approved	MGC24132	uc003bzs.1	Q8TCB7	OTTHUMG00000156431	ENST00000443029.1:c.593T>G	chr3.hg19:g.15455608A>C	ENSP00000407613:p.Leu198Arg	109.0	0.0		140.0	23.0	NM_152396	Q96LU4	Missense_Mutation	SNP	ENST00000443029.1	hg19	CCDS43056.1	.	.	.	.	.	.	.	.	.	.	A	26.9	4.783999	0.90282	.	.	ENSG00000206562	ENST00000383790;ENST00000450816	T;T	0.38240	1.59;1.15	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.68284	0.2984	M	0.91196	3.185	0.80722	D	1	D;P	0.76494	0.999;0.85	D;B	0.76575	0.988;0.378	T	0.75665	-0.3239	10	0.62326	D	0.03	-17.4123	16.0504	0.80755	1.0:0.0:0.0:0.0	.	153;198	B4DDX3;Q8TCB7	.;METL6_HUMAN	R	198;153	ENSP00000373300:L198R;ENSP00000410726:L153R	ENSP00000373300:L198R	L	-	2	0	METTL6	15430612	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.303000	0.78871	2.330000	0.79161	0.477000	0.44152	CTT	.	.		0.388	METTL6-007	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346373.1	NM_152396		C	15455608	A	C	15455608	3	2	352	1	0	0	0	0	1	0	0	0	9513	72	3	5	269	5	METTL6	3	15455608	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	173607	15455608	182566822	97	49513										
CDHR4	389118	hgsc.bcm.edu	37	chr3	49833197	49833197	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gtgatattctgagcctgctcGctggaccaaaaggggggcac	14	10	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr3:49833197G>A	ENST00000412678.2	-	7	719	c.711C>T	c.(709-711)ctC>ctT	p.L237L	CDHR4_ENST00000462108.1_5'Flank	NM_001007540.2	NP_001007541.2	A6H8M9	CDHR4_HUMAN	cadherin-related family member 4	237	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(3)	11						GAGCCTGCTCGCTGGACCAAA	0.617																																					p.L237L		Atlas-SNP	.											.	CDHR4	37	.	0			c.C711T						.						46	52	50					3																	49833197		692	1591	2283	SO:0001630	splice_region_variant	389118	exon7			CTGCTCGCTGGAC		CCDS46829.1	3p21.31	2011-07-01	2010-01-25	2010-01-25	ENSG00000187492	ENSG00000187492		"Cadherins / Cadherin-related"	34527	protein-coding gene	gene with protein product			"cadherin-like 29"	CDH29			Standard	NM_001007540		Approved	VLLR9392	uc010hkz.3	A6H8M9	OTTHUMG00000158198	ENST00000412678.2:c.711-1C>T	chr3.hg19:g.49833197G>A		114.0	0.0		113.0	56.0	NM_001007540	Q6UXT0	Silent	SNP	ENST00000412678.2	hg19	CCDS46829.1																																																																																			.	.		0.617	CDHR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350387.1	NM_001007540	Silent	A	49833197	G	A	49833197	5	1	352	1	0	0	0	0	0	0	1	0	3123	1101	38	1	1707	1	CDHR4	3	49833197	Splice_Site	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	34377589	49833197	148189233	98	49514										
IFRD2	7866	hgsc.bcm.edu	37	chr3	50326695	50326695	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gtccctcgcacctcaaggtcCcgggcaagctcaaagagcag	11	15	2	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr3:50326695C>A	ENST00000429673.2	-	8	1067	c.1068G>T	c.(1066-1068)cgG>cgT	p.R356R	IFRD2_ENST00000336089.4_Silent_p.R458R|IFRD2_ENST00000417626.2_Silent_p.R292R|IFRD2_ENST00000436390.1_Silent_p.R292R|IFRD2_ENST00000484043.1_5'Flank			Q12894	IFRD2_HUMAN	interferon-related developmental regulator 2	356						nucleus (GO:0005634)				breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)	14				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		CCTCAAGGTCCCGGGCAAGCT	0.602																																					p.R356R		Atlas-SNP	.											.	IFRD2	34	.	0			c.G1068T						.						30	32	31					3																	50326695		1988	4162	6150	SO:0001819	synonymous_variant	7866	exon8			AAGGTCCCGGGCA	U09585		3p21.3	2008-07-18			ENSG00000214706	ENSG00000214706			5457	protein-coding gene	gene with protein product	"interferon-related protein"	602725				9050919	Standard	NM_006764		Approved	SKMc15, SM15, IFNRP	uc011bdp.2	Q12894	OTTHUMG00000156935	ENST00000429673.2:c.1068G>T	chr3.hg19:g.50326695C>A		217.0	1.0		180.0	99.0	NM_006764	Q9BVB4|Q9UJ88	Silent	SNP	ENST00000429673.2	hg19	CCDS46831.1																																																																																			.	.		0.602	IFRD2-202	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_006764		A	50326695	C	A	50326695	2	1	352	1	0	0	0	0	0	0	0	1	7563	610	22	3		3	IFRD2	3	50326695	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	493498	50326695	147695735	99	49515										
BAP1	8314	hgsc.bcm.edu	37	chr3	52437802	52437803	+	Frame_Shift_Del	DEL	TT	TT	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gagaggtccttctgggactcTttgagcttctcagccaagac							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr3:52437802_52437803delTT	ENST00000460680.1	-	13	1829_1830	c.1358_1359delAA	c.(1357-1359)aaafs	p.K453fs	BAP1_ENST00000296288.5_Frame_Shift_Del_p.K435fs	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.K453fs*15(1)		NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		TCTGGGACTCTTTGAGCTTCTC	0.594			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.453_454del	GBM(101;493 1458 7992 21037 25532)	Atlas-INDEL	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.	BAP1	371	.	1	Deletion - Frameshift(1)	kidney(1)	c.1359_1360del						.																																			SO:0001589	frameshift_variant	8314	exon13			.	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.1358_1359delAA	chr3.hg19:g.52437802_52437803delTT	ENSP00000417132:p.Lys453fs	52.0	0.0		52.0	25.0	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Frame_Shift_Del	DEL	ENST00000460680.1	hg19	CCDS2853.1																																																																																			.	.		0.594	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			-	52437803	TT	-	52437802	7	5	352	1	0	1	0	1	0	0	0	0	1311	1606	56	0	850	0	BAP1	3	52437802	Frame_Shift_Del	DEL	TT	TCGA-WQ-A9G7-01A-11D-A36X-10	2111107	52437802	145584628	100	49516										
ARL6	84100	hgsc.bcm.edu	37	chr3	97487017	97487017	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aaggaggttcatgttttgtgCcttgggctagataatagtgg	14	4	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr3:97487017C>T	ENST00000463745.1	+	2	543	c.66C>T	c.(64-66)tgC>tgT	p.C22C	ARL6_ENST00000496713.1_3'UTR|ARL6_ENST00000335979.2_Silent_p.C22C|ARL6_ENST00000394206.1_Silent_p.C22C	NM_001278293.1	NP_001265222.1	Q9H0F7	ARL6_HUMAN	ADP-ribosylation factor-like 6	22					cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|fat cell differentiation (GO:0045444)|melanosome transport (GO:0032402)|protein polymerization (GO:0051258)|protein targeting to membrane (GO:0006612)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)|Wnt signaling pathway (GO:0016055)	axonemal microtubule (GO:0005879)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane coat (GO:0030117)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|metal ion binding (GO:0046872)|phospholipid binding (GO:0005543)			large_intestine(1)|lung(4)	5		Lung NSC(201;0.0193)|Prostate(884;0.174)		LUSC - Lung squamous cell carcinoma(29;0.0118)|Lung(72;0.0189)		ATGTTTTGTGCCTTGGGCTAG	0.358																																					p.C22C		Atlas-SNP	.											.	ARL6	19	.	0			c.C66T						.						126	122	123					3																	97487017		2203	4300	6503	SO:0001819	synonymous_variant	84100	exon3			TTTGTGCCTTGGG	BC024239	CCDS2928.1	3q11.2	2014-05-09			ENSG00000113966	ENSG00000113966		"ADP-ribosylation factors-like", "ADP-ribosylation factors"	13210	protein-coding gene	gene with protein product		608845		BBS3		15258860, 15314642, 21282186	Standard	NM_032146		Approved	RP55	uc003drv.3	Q9H0F7	OTTHUMG00000159189	ENST00000463745.1:c.66C>T	chr3.hg19:g.97487017C>T		140.0	0.0		115.0	44.0	NM_177976	A8KA93|D3DN31	Silent	SNP	ENST00000463745.1	hg19	CCDS2928.1																																																																																			.	.		0.358	ARL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353756.1	NM_032146		T	97487017	C	T	97487017	2	4	352	1	0	0	0	0	0	0	0	1	941	747	26	3		3	ARL6	3	97487017	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	45049215	97487017	100535413	101	49517										
OR5H14	403273	hgsc.bcm.edu	37	chr3	97869067	97869067	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tggagtctctattttacactGtcatagttcctttattaaat	5	7	2	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr3:97869067G>T	ENST00000437310.1	+	1	898	c.838G>T	c.(838-840)Gtc>Ttc	p.V280F	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005514.1	NP_001005514.1	A6NHG9	O5H14_HUMAN	olfactory receptor, family 5, subfamily H, member 14	280						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	31						ATTTTACACTGTCATAGTTCC	0.383																																					p.V280F		Atlas-SNP	.											.	OR5H14	56	.	0			c.G838T						.						51	49	50					3																	97869067		2203	4297	6500	SO:0001583	missense	403273	exon1			TACACTGTCATAG		CCDS33798.1	3q11.2	2013-09-23			ENSG00000236032	ENSG00000236032		"GPCR / Class A : Olfactory receptors"	31286	protein-coding gene	gene with protein product							Standard	NM_001005514		Approved		uc003dsg.1	A6NHG9	OTTHUMG00000160079	ENST00000437310.1:c.838G>T	chr3.hg19:g.97869067G>T	ENSP00000401706:p.Val280Phe	130.0	0.0		156.0	17.0	NM_001005514	B9EH15	Missense_Mutation	SNP	ENST00000437310.1	hg19	CCDS33798.1	.	.	.	.	.	.	.	.	.	.	G	11.33	1.606806	0.28623	.	.	ENSG00000236032	ENST00000437310	T	0.00307	8.17	2.49	-1.94	0.07571	GPCR, rhodopsin-like superfamily (1);	0.747131	0.11450	N	0.562910	T	0.00496	0.0016	M	0.79011	2.435	0.09310	N	1	D	0.59767	0.986	D	0.65874	0.939	T	0.41378	-0.9512	10	0.54805	T	0.06	.	7.3162	0.26501	0.5215:0.0:0.4785:0.0	.	280	A6NHG9	O5H14_HUMAN	F	280	ENSP00000401706:V280F	ENSP00000401706:V280F	V	+	1	0	OR5H14	99351757	0.000000	0.05858	0.256000	0.24389	0.653000	0.38743	-2.644000	0.00862	-0.417000	0.07461	0.195000	0.17529	GTC	.	.		0.383	OR5H14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359112.1			T	97869067	G	T	97869067	3	4	352	1	0	0	0	0	1	0	0	0	11169	1377	48	3	840	3	OR5H14	3	97869067	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	382050	97869067	100153363	102	49518										
ZXDC	79364	hgsc.bcm.edu	37	chr3	126180881	126180881	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agaggagctcacagaagtgaCgtcaatagtcaggattccgg	13	8	3	3			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr3:126180881C>T	ENST00000389709.3	-	6	1677	c.1624G>A	c.(1624-1626)Gtc>Atc	p.V542I	ZXDC_ENST00000336332.5_Missense_Mutation_p.V542I	NM_025112.4	NP_079388.3	Q2QGD7	ZXDC_HUMAN	ZXD family zinc finger C	542					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|LRR domain binding (GO:0030275)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|ovary(1)	17				GBM - Glioblastoma multiforme(114;0.155)		ACAGAAGTGACGTCAATAGTC	0.552																																					p.V542I		Atlas-SNP	.											.	ZXDC	87	.	0			c.G1624A						.						57	64	61					3																	126180881		2055	4210	6265	SO:0001583	missense	79364	exon6			AAGTGACGTCAAT	AK023923	CCDS43145.1, CCDS43146.1	3q21.3	2014-02-12			ENSG00000070476	ENSG00000070476		"Zinc fingers, C2H2-type"	28160	protein-coding gene	gene with protein product		615746				8619474, 9110174	Standard	XM_005247757		Approved	MGC11349, FLJ13861	uc003eiv.3	Q2QGD7	OTTHUMG00000162754	ENST00000389709.3:c.1624G>A	chr3.hg19:g.126180881C>T	ENSP00000374359:p.Val542Ile	98.0	0.0		122.0	7.0	NM_025112	C5J0H9|Q6DKI8|Q7L3L1|Q8NAU2	Missense_Mutation	SNP	ENST00000389709.3	hg19	CCDS43145.1	.	.	.	.	.	.	.	.	.	.	C	17.66	3.444415	0.63178	.	.	ENSG00000070476	ENST00000389709;ENST00000336332	T;T	0.09817	2.94;2.94	5.15	5.15	0.70609	.	0.205390	0.41712	D	0.000824	T	0.14527	0.0351	M	0.68593	2.085	0.25411	N	0.988358	D;P	0.55800	0.973;0.954	B;B	0.39935	0.314;0.166	T	0.21109	-1.0255	10	0.39692	T	0.17	-17.6845	16.4671	0.84083	0.0:1.0:0.0:0.0	.	542;542	Q2QGD7-2;Q2QGD7	.;ZXDC_HUMAN	I	542	ENSP00000374359:V542I;ENSP00000337694:V542I	ENSP00000337694:V542I	V	-	1	0	ZXDC	127663571	1.000000	0.71417	0.141000	0.22245	0.987000	0.75469	4.504000	0.60414	2.548000	0.85928	0.591000	0.81541	GTC	.	.		0.552	ZXDC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370327.2	NM_025112		T	126180881	C	T	126180881	3	4	352	1	0	0	0	0	1	0	0	0	18267	536	19	1	978	1	ZXDC	3	126180881	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	28311814	126180881	71841549	103	49519										
CHST13	166012	hgsc.bcm.edu	37	chr3	126261099	126261099	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cctggcctacctgctggaccCgcgcacgcggcgtgaggagc	15	16	0	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr3:126261099C>T	ENST00000319340.2	+	3	754	c.704C>T	c.(703-705)cCg>cTg	p.P235L		NM_152889.2	NP_690849.1	Q8NET6	CHSTD_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 13	235					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin 4-sulfotransferase activity (GO:0047756)|N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)			central_nervous_system(1)|large_intestine(2)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(114;0.151)		CTGCTGGACCCGCGCACGCGG	0.741																																					p.P235L		Atlas-SNP	.											.	CHST13	21	.	0			c.C704T						.						4	5	5					3																	126261099		1938	3886	5824	SO:0001583	missense	166012	exon3			TGGACCCGCGCAC	AY120869	CCDS3039.1	3q21.3	2008-02-05			ENSG00000180767	ENSG00000180767	2.8.2.5	"Sulfotransferases, membrane-bound"	21755	protein-coding gene	gene with protein product		610124				12080076	Standard	NM_152889		Approved	C4ST3	uc003eja.3	Q8NET6	OTTHUMG00000162721	ENST00000319340.2:c.704C>T	chr3.hg19:g.126261099C>T	ENSP00000317404:p.Pro235Leu	29.0	0.0		24.0	5.0	NM_152889	Q3SYA3|Q3SYA5	Missense_Mutation	SNP	ENST00000319340.2	hg19	CCDS3039.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.951223	0.73787	.	.	ENSG00000180767	ENST00000319340	T	0.71934	-0.61	4.44	4.44	0.53790	.	0.000000	0.85682	U	0.000000	D	0.84955	0.5587	M	0.85373	2.75	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.87865	0.2667	10	0.87932	D	0	-34.7611	14.5206	0.67847	0.0:1.0:0.0:0.0	.	235	Q8NET6	CHSTD_HUMAN	L	235	ENSP00000317404:P235L	ENSP00000317404:P235L	P	+	2	0	CHST13	127743789	1.000000	0.71417	0.998000	0.56505	0.316000	0.28119	7.404000	0.79996	2.006000	0.58801	0.297000	0.19635	CCG	.	.		0.741	CHST13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370201.2	NM_152889		T	126261099	C	T	126261099	3	4	352	1	0	0	0	0	1	0	0	0	3403	652	23	1	714	1	CHST13	3	126261099	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	80218	126261099	71761331	104	49520										
ABTB1	80325	hgsc.bcm.edu	37	chr3	127395229	127395229	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tactttgccaacatgctggaCaccaaatggaagggcaagag	11	9	0	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr3:127395229C>G	ENST00000232744.8	+	5	521	c.435C>G	c.(433-435)gaC>gaG	p.D145E	ABTB1_ENST00000393363.3_Missense_Mutation_p.D3E|ABTB1_ENST00000468137.1_Missense_Mutation_p.D3E|ABTB1_ENST00000453791.2_Missense_Mutation_p.D3E					ankyrin repeat and BTB (POZ) domain containing 1											central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	10						ACATGCTGGACACCAAATGGA	0.572																																					p.D145E		Atlas-SNP	.											.	ABTB1	36	.	0			c.C435G						.						165	124	138					3																	127395229		2203	4300	6503	SO:0001583	missense	80325	exon5			GCTGGACACCAAA	AB053324	CCDS3045.1, CCDS46901.1	3q21	2013-01-10			ENSG00000114626	ENSG00000114626		"BTB/POZ domain containing", "Ankyrin repeat domain containing"	18275	protein-coding gene	gene with protein product		608308				10891360, 11494141	Standard	NM_172027		Approved	BPOZ, EF1ABP, Btb3, BTBD21	uc003ejt.3	Q969K4	OTTHUMG00000159636	ENST00000232744.8:c.435C>G	chr3.hg19:g.127395229C>G	ENSP00000232744:p.Asp145Glu	116.0	0.0		117.0	35.0	NM_172027		Missense_Mutation	SNP	ENST00000232744.8	hg19	CCDS3045.1	.	.	.	.	.	.	.	.	.	.	C	0.023	-1.400469	0.01165	.	.	ENSG00000114626	ENST00000393363;ENST00000232744;ENST00000453791;ENST00000468137	T;T;T;T	0.65549	0.28;-0.16;0.28;0.28	4.73	0.527	0.17084	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.055795	0.64402	D	0.000001	T	0.24967	0.0606	N	0.02357	-0.585	0.28472	N	0.915398	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.002	T	0.32613	-0.9900	10	0.02654	T	1	-16.0659	5.8792	0.18846	0.0:0.4144:0.3003:0.2853	.	145;120	Q969K4;Q969K4-3	ABTB1_HUMAN;.	E	3;145;3;3	ENSP00000377030:D3E;ENSP00000232744:D145E;ENSP00000412684:D3E;ENSP00000417366:D3E	ENSP00000232744:D145E	D	+	3	2	ABTB1	128877919	0.984000	0.35163	1.000000	0.80357	0.026000	0.11368	0.111000	0.15458	0.419000	0.25927	0.561000	0.74099	GAC	.	.		0.572	ABTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356595.1	NM_172027		G	127395229	C	G	127395229	3	3	352	1	0	0	0	0	1	0	0	0	102	477	17	4	453	4	ABTB1	3	127395229	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	1134130	127395229	70627201	105	49521										
STAG1	10274	hgsc.bcm.edu	37	chr3	136240141	136240143	+	In_Frame_Del	DEL	TCA	TCA	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ttactgtgtccatcatatacTcatcataaattatgctatac							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	TCA	TCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr3:136240141_136240143delTCA	ENST00000383202.2	-	7	844_846	c.588_590delTGA	c.(586-591)gatgag>gag	p.D196del	STAG1_ENST00000236698.5_In_Frame_Del_p.D196del|STAG1_ENST00000480733.1_In_Frame_Del_p.D196del|STAG1_ENST00000434713.2_De_novo_Start_InFrame	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	196					chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						CATCATATACTCATCATAAATTA	0.404																																					p.197_197del		Atlas-INDEL	.											.	STAG1	135	.	0			c.589_591del						.																																			SO:0001651	inframe_deletion	10274	exon7			.	Z75330	CCDS3090.1	3q22.2-q22.3	2011-08-12			ENSG00000118007	ENSG00000118007			11354	protein-coding gene	gene with protein product		604358				9305759	Standard	XM_006713471		Approved	SA-1, SCC3A	uc003era.1	Q8WVM7	OTTHUMG00000159798	ENST00000383202.2:c.588_590delTGA	chr3.hg19:g.136240144_136240146delTCA	ENSP00000372689:p.Asp196del	272.0	0.0		247.0	30.0	NM_005862	O00539|Q6P275	In_Frame_Del	DEL	ENST00000383202.2	hg19	CCDS3090.1																																																																																			.	.		0.404	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357366.1	NM_005862		-	136240143	TCA	-	136240141	7	5	352	1	0	1	0	1	0	0	0	0	15257	1551	54	0	3298	0	STAG1	3	136240141	In_Frame_Del	DEL	TCA	TCGA-WQ-A9G7-01A-11D-A36X-10	8844912	136240141	61782289	106	49522										
PAQR9	344838	hgsc.bcm.edu	37	chr3	142681759	142681759	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agcgacaggcagctgaacacGtgcgccgtgcagctcatggc	14	13	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr3:142681759G>A	ENST00000340634.3	-	1	419	c.420C>T	c.(418-420)caC>caT	p.H140H	RP11-372E1.6_ENST00000608686.1_RNA|RP11-372E1.6_ENST00000598139.1_RNA|RP11-372E1.6_ENST00000593321.1_RNA|RP11-372E1.6_ENST00000493825.1_RNA|RP11-372E1.6_ENST00000594095.1_RNA|RP11-372E1.6_ENST00000478823.1_RNA|RP11-372E1.6_ENST00000497652.1_RNA|RP11-372E1.6_ENST00000598787.1_RNA|RP11-372E1.6_ENST00000608349.1_RNA|RP11-372E1.6_ENST00000607937.1_RNA|RP11-372E1.6_ENST00000595248.1_RNA|RP11-372E1.6_ENST00000595774.1_RNA	NM_198504.2	NP_940906.1	Q6ZVX9	PAQR9_HUMAN	progestin and adipoQ receptor family member IX	140						integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			endometrium(2)|large_intestine(7)|lung(12)|prostate(1)	22						AGCTGAACACGTGCGCCGTGC	0.652																																					p.H140H		Atlas-SNP	.											.	PAQR9	57	.	0			c.C420T						.						48	47	47					3																	142681759		2203	4300	6503	SO:0001819	synonymous_variant	344838	exon1			GAACACGTGCGCC	AY424287	CCDS3128.1	3q23	2008-05-02			ENSG00000188582	ENSG00000188582			30131	protein-coding gene	gene with protein product		614580					Standard	NM_198504		Approved	FLJ41938	uc003evg.3	Q6ZVX9	OTTHUMG00000159313	ENST00000340634.3:c.420C>T	chr3.hg19:g.142681759G>A		89.0	0.0		96.0	19.0	NM_198504	Q147T6	Silent	SNP	ENST00000340634.3	hg19	CCDS3128.1																																																																																			.	.		0.652	PAQR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354538.1	NM_198504		A	142681759	G	A	142681759	2	1	352	1	0	0	0	0	0	0	0	1	11451	1136	40	1		1	PAQR9	3	142681759	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	6441618	142681759	55340671	107	49523										
CP	1356	hgsc.bcm.edu	37	chr3	148925301	148925301	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tgcccgtgaaagaaagctgcGtgcacatcaacttcattacc	8	12	2	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr3:148925301G>A	ENST00000264613.6	-	5	1147	c.885C>T	c.(883-885)caC>caT	p.H295H		NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	295	F5/8 type A 1.|Plastocyanin-like 2.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)	chaperone binding (GO:0051087)|copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	AGAAAGCTGCGTGCACATCAA	0.448																																					p.H295H		Atlas-SNP	.											.	CP	112	.	0			c.C885T						.						131	116	121					3																	148925301		2203	4300	6503	SO:0001819	synonymous_variant	1356	exon5			AGCTGCGTGCACA	M13536	CCDS3141.1	3q23-q25	2010-07-01			ENSG00000047457	ENSG00000047457	1.16.3.1		2295	protein-coding gene	gene with protein product		117700					Standard	NM_000096		Approved		uc003ewy.4	P00450	OTTHUMG00000159563	ENST00000264613.6:c.885C>T	chr3.hg19:g.148925301G>A		139.0	0.0		166.0	25.0	NM_000096	Q14063|Q2PP18|Q9UKS4	Silent	SNP	ENST00000264613.6	hg19	CCDS3141.1																																																																																			.	.		0.448	CP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317498.1	NM_000096		A	148925301	G	A	148925301	2	1	352	1	0	0	0	0	0	0	0	1	3789	1136	40	1		1	CP	3	148925301	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	6243542	148925301	49097129	108	49524										
MBNL1	4154	hgsc.bcm.edu	37	chr3	152164531	152164531	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tcactgaagcgacccctcgaGgcaacctttgacctggtact	9	14	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr3:152164531G>T	ENST00000463374.1	+	5	1357	c.846G>T	c.(844-846)gaG>gaT	p.E282D	MBNL1_ENST00000355460.2_Intron|MBNL1_ENST00000485910.1_Intron|MBNL1_ENST00000357472.3_Intron|MBNL1_ENST00000324196.5_Intron|MBNL1_ENST00000282488.7_Intron|MBNL1_ENST00000545754.1_Intron|MBNL1_ENST00000324210.5_Intron|MBNL1_ENST00000498502.1_Missense_Mutation_p.E282D|MBNL1_ENST00000282486.6_Missense_Mutation_p.E282D|MBNL1_ENST00000492948.1_Intron|MBNL1_ENST00000493459.1_Missense_Mutation_p.E225D|Y_RNA_ENST00000364347.1_RNA|MBNL1_ENST00000485509.1_Intron	NM_207293.1	NP_997176.1	Q9NR56	MBNL1_HUMAN	muscleblind-like splicing regulator 1	282					alternative mRNA splicing, via spliceosome (GO:0000380)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|mRNA splice site selection (GO:0006376)|myoblast differentiation (GO:0045445)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|skeletal muscle tissue development (GO:0007519)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			GACCCCTCGAGGCAACCTTTG	0.418																																					p.E282D		Atlas-SNP	.											.	MBNL1	100	.	0			c.G846T						.						116	100	106					3																	152164531		2203	4300	6503	SO:0001583	missense	4154	exon5			CCTCGAGGCAACC	Y13829	CCDS3163.1, CCDS3164.1, CCDS3165.1, CCDS3166.1, CCDS3167.1, CCDS3168.1, CCDS54656.1	3q25	2013-01-18	2012-02-23	2003-03-14	ENSG00000152601	ENSG00000152601		"Zinc fingers, CCCH-type domain containing"	6923	protein-coding gene	gene with protein product		606516	"muscleblind (Drosophila)-like", "muscleblind-like (Drosophila)"	MBNL			Standard	NM_021038		Approved	KIAA0428, EXP42, EXP40, EXP35, EXP	uc003ezm.3	Q9NR56	OTTHUMG00000159163	ENST00000463374.1:c.846G>T	chr3.hg19:g.152164531G>T	ENSP00000418108:p.Glu282Asp	81.0	0.0		81.0	19.0	NM_207293	E9PBW7|O43311|O43797|Q86UV8|Q86UV9|Q96P92|Q96RE3	Missense_Mutation	SNP	ENST00000463374.1	hg19	CCDS3165.1	.	.	.	.	.	.	.	.	.	.	G	9.076	0.998188	0.19043	.	.	ENSG00000152601	ENST00000282486;ENST00000493459;ENST00000498502;ENST00000463374	.	.	.	5.47	5.47	0.80525	.	0.138889	0.46145	D	0.000305	T	0.41488	0.1161	N	0.12182	0.205	0.80722	D	1	B;B	0.06786	0.0;0.001	B;B	0.15052	0.012;0.003	T	0.26326	-1.0106	9	0.15952	T	0.53	.	18.9468	0.92625	0.0:0.0:1.0:0.0	.	282;225	Q9NR56;Q86VM6	MBNL1_HUMAN;.	D	282;225;282;282	.	ENSP00000282486:E282D	E	+	3	2	MBNL1	153647221	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.384000	0.79751	2.558000	0.86282	0.563000	0.77884	GAG	.	.		0.418	MBNL1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353604.1	NM_021038		T	152164531	G	T	152164531	3	4	352	1	0	0	0	0	1	0	0	0	9362	991	35	3	864	3	MBNL1	3	152164531	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	3239230	152164531	45857899	109	49525										
PLCH1	23007	hgsc.bcm.edu	37	chr3	155198960	155198960	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggagccggtggagtggcgatTcactgcaggggtgggtgctg	21	7	1	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr3:155198960T>C	ENST00000340059.7	-	23	4878	c.4879A>G	c.(4879-4881)Aat>Gat	p.N1627D	PLCH1_ENST00000414191.1_Missense_Mutation_p.N1589D|PLCH1_ENST00000494598.1_Intron|PLCH1_ENST00000334686.6_Missense_Mutation_p.N1589D|PLCH1_ENST00000447496.2_3'UTR|PLCH1_ENST00000460012.1_Missense_Mutation_p.N1589D	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	1627					inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phosphatidylinositol-mediated signaling (GO:0048015)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase C activity (GO:0050429)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			NS(3)|breast(3)|endometrium(9)|kidney(4)|large_intestine(20)|lung(45)|ovary(2)|prostate(5)|skin(8)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	107			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			GAGTGGCGATTCACTGCAGGG	0.582																																					p.N1627D		Atlas-SNP	.											.	PLCH1	406	.	0			c.A4879G						.						97	99	98					3																	155198960		2203	4300	6503	SO:0001583	missense	23007	exon23			GGCGATTCACTGC	AB028992	CCDS33881.1, CCDS46939.1, CCDS46940.1	3q25	2013-01-10	2006-03-16	2006-03-16	ENSG00000114805	ENSG00000114805	3.1.4.11	"EF-hand domain containing"	29185	protein-coding gene	gene with protein product		612835	"phospholipase C-like 3"	PLCL3		15702972	Standard	NM_014996		Approved	KIAA1069, MGC117152, DKFZp434C1372, PLCeta1	uc021xge.1	Q4KWH8	OTTHUMG00000158477	ENST00000340059.7:c.4879A>G	chr3.hg19:g.155198960T>C	ENSP00000345988:p.Asn1627Asp	133.0	0.0		113.0	21.0	NM_001130960	Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	Missense_Mutation	SNP	ENST00000340059.7	hg19	CCDS46939.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.954627	0.73902	.	.	ENSG00000114805	ENST00000460012;ENST00000340059;ENST00000334686;ENST00000414191	T;T;T;T	0.39056	1.1;1.12;1.1;1.1	5.26	5.26	0.73747	.	0.660669	0.16452	N	0.213785	T	0.49253	0.1546	M	0.62723	1.935	0.53005	D	0.999968	P;P	0.49559	0.925;0.877	P;B	0.46585	0.521;0.321	T	0.54397	-0.8300	10	0.72032	D	0.01	.	14.8434	0.70243	0.0:0.0:0.0:1.0	.	1589;1627	Q4KWH8-2;Q4KWH8	.;PLCH1_HUMAN	D	1589;1627;1589;1589	ENSP00000417502:N1589D;ENSP00000345988:N1627D;ENSP00000335469:N1589D;ENSP00000412977:N1589D	ENSP00000335469:N1589D	N	-	1	0	PLCH1	156681654	1.000000	0.71417	0.631000	0.29282	0.707000	0.40811	5.738000	0.68613	1.979000	0.57680	0.533000	0.62120	AAT	.	.		0.582	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351125.1	NM_014996		C	155198960	T	C	155198960	3	2	352	1	0	0	0	0	1	0	0	0	12046	1783	62	2	206	2	PLCH1	3	155198960	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	3034429	155198960	42823470	110	49526										
ZBBX	79740	hgsc.bcm.edu	37	chr3	167000188	167000188	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tgattgagcagctgcacttcTtgatcgaggatgagaggatg	14	6	1	4			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr3:167000188T>C	ENST00000392766.2	-	19	2315	c.1975A>G	c.(1975-1977)Aga>Gga	p.R659G	ZBBX_ENST00000455345.2_Missense_Mutation_p.R698G|ZBBX_ENST00000307529.5_Missense_Mutation_p.R698G|ZBBX_ENST00000392764.1_Missense_Mutation_p.R630G|ZBBX_ENST00000392767.2_Missense_Mutation_p.R659G	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	659	Ser-rich.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(9)|liver(1)|lung(38)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	70						GCTGCACTTCTTGATCGAGGA	0.388																																					p.R698G		Atlas-SNP	.											.	ZBBX	299	.	0			c.A2092G						.						143	135	137					3																	167000188		1850	4086	5936	SO:0001583	missense	79740	exon20			CACTTCTTGATCG	AK026702	CCDS3199.2, CCDS56295.1, CCDS56296.1	3q26.1	2010-03-23			ENSG00000169064	ENSG00000169064			26245	protein-coding gene	gene with protein product						12477932	Standard	NM_024687		Approved	FLJ23049	uc011bpc.2	A8MT70	OTTHUMG00000133560	ENST00000392766.2:c.1975A>G	chr3.hg19:g.167000188T>C	ENSP00000376519:p.Arg659Gly	286.0	0.0		294.0	42.0	NM_001199201	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Missense_Mutation	SNP	ENST00000392766.2	hg19	CCDS3199.2	.	.	.	.	.	.	.	.	.	.	T	6.910	0.537550	0.13188	.	.	ENSG00000169064	ENST00000392766;ENST00000392767;ENST00000455345;ENST00000307529;ENST00000392764	T;T;T;T;T	0.14766	2.65;2.65;2.65;2.65;2.48	5.28	4.05	0.47172	.	0.250823	0.37623	N	0.002007	T	0.12987	0.0315	L	0.38175	1.15	0.19945	N	0.999942	B;B	0.30634	0.288;0.19	B;B	0.36244	0.22;0.07	T	0.15954	-1.0419	10	0.46703	T	0.11	-4.0714	10.0579	0.42257	0.0:0.0:0.1689:0.8311	.	698;659	A8MT70-2;A8MT70	.;ZBBX_HUMAN	G	659;659;698;698;630	ENSP00000376519:R659G;ENSP00000376520:R659G;ENSP00000390232:R698G;ENSP00000305065:R698G;ENSP00000376517:R630G	ENSP00000305065:R698G	R	-	1	2	ZBBX	168482882	1.000000	0.71417	0.039000	0.18376	0.019000	0.09904	2.284000	0.43478	1.995000	0.58328	0.528000	0.53228	AGA	.	.		0.388	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687		C	167000188	T	C	167000188	3	2	352	1	0	0	0	0	1	0	0	0	17531	1617	56	2	439	2	ZBBX	3	167000188	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	11801228	167000188	31022242	111	49527										
SAMD7	344658	hgsc.bcm.edu	37	chr3	169656232	169656233	+	Frame_Shift_Ins	INS	-	-	T													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ctggagtgatacaatgaacaINSttttttgtccccaggataca							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr3:169656232_169656233insT	ENST00000428432.2	+	9	1668_1669	c.1279_1280insT	c.(1279-1281)attfs	p.I427fs	RP11-379K17.4_ENST00000487580.1_RNA|SAMD7_ENST00000335556.3_Frame_Shift_Ins_p.I427fs	NM_182610.2	NP_872416.1	Q7Z3H4	SAMD7_HUMAN	sterile alpha motif domain containing 7	427								p.C429fs*6(1)		NS(1)|biliary_tract(1)|breast(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	31	all_cancers(22;1.55e-22)|all_epithelial(15;2.41e-27)|all_lung(20;3.52e-17)|Lung NSC(18;1.44e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0106)			TACAATGAACATTTTTTGTCCC	0.391																																					p.I427fs		Atlas-INDEL	.											.	SAMD7	69	.	1	Deletion - Frameshift(1)	lung(1)	c.1279_1280insT						.																																			SO:0001589	frameshift_variant	344658	exon9			.	BX537903	CCDS3209.1	3q26.31	2013-01-10			ENSG00000187033	ENSG00000187033		"Sterile alpha motif (SAM) domain containing"	25394	protein-coding gene	gene with protein product							Standard	NM_182610		Approved	DKFZp686E1583	uc003fgd.3	Q7Z3H4	OTTHUMG00000158730	ENST00000428432.2:c.1285dupT	chr3.hg19:g.169656238_169656238dupT	ENSP00000391299:p.Ile427fs	157.0	0.0		139.0	38.0	NM_182610		Frame_Shift_Ins	INS	ENST00000428432.2	hg19	CCDS3209.1																																																																																			.	.		0.391	SAMD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351959.1	NM_182610		T	169656233	-	T	169656232	7	5	352	1	0	1	1	0	0	0	0	0	13839	217	8	0	1305	0	SAMD7	3	169656232	Frame_Shift_Ins	INS	-	TCGA-WQ-A9G7-01A-11D-A36X-10	2656044	169656232	28366198	112	49528										
ACTL6A	86	hgsc.bcm.edu	37	chr3	179294051	179294051	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tgattttggacagtggagccActcataccactgcaattcca	8	11	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr3:179294051A>G	ENST00000429709.2	+	6	736	c.523A>G	c.(523-525)Act>Gct	p.T175A	ACTL6A_ENST00000450518.2_Missense_Mutation_p.T133A|ACTL6A_ENST00000392662.1_Missense_Mutation_p.T133A|ACTL6A_ENST00000467615.1_3'UTR	NM_004301.3	NP_004292.1	O96019	ACL6A_HUMAN	actin-like 6A	175					ATP-dependent chromatin remodeling (GO:0043044)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|nervous system development (GO:0007399)|neural retina development (GO:0003407)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	Ino80 complex (GO:0031011)|npBAF complex (GO:0071564)|NuA4 histone acetyltransferase complex (GO:0035267)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|urinary_tract(1)	21	all_cancers(143;3.94e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)			CAGTGGAGCCACTCATACCAC	0.388																																					p.T175A		Atlas-SNP	.											.	ACTL6A	43	.	0			c.A523G						.						167	165	166					3																	179294051		2203	4300	6503	SO:0001583	missense	86	exon6			GGAGCCACTCATA	AK098691	CCDS3231.1, CCDS43174.1	3q26.33	2011-07-06			ENSG00000136518	ENSG00000136518		"INO80 complex subunits"	24124	protein-coding gene	gene with protein product	"BAF complex 53 kDa subunit", "BRG1-associated factor", "actin-related protein 4", "INO80 complex subunit K"	604958				9845365, 10380635	Standard	NM_004301		Approved	Actl6, BAF53A, Arp4, Baf53a, INO80K	uc003fjw.3	O96019	OTTHUMG00000157782	ENST00000429709.2:c.523A>G	chr3.hg19:g.179294051A>G	ENSP00000397552:p.Thr175Ala	92.0	0.0		100.0	22.0	NM_004301	B3KMN1|D3DNR9|Q8TAE5|Q9BVS8|Q9H0W6	Missense_Mutation	SNP	ENST00000429709.2	hg19	CCDS3231.1	.	.	.	.	.	.	.	.	.	.	A	29.4	5.004762	0.93287	.	.	ENSG00000136518	ENST00000429709;ENST00000450518;ENST00000392662	D;D;D	0.97430	-4.38;-4.38;-4.38	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	D	0.96664	0.8911	L	0.39566	1.225	0.80722	D	1	D	0.54047	0.964	P	0.57846	0.828	D	0.95832	0.8859	10	0.29301	T	0.29	.	15.322	0.74129	1.0:0.0:0.0:0.0	.	175	O96019	ACL6A_HUMAN	A	175;133;133	ENSP00000397552:T175A;ENSP00000394014:T133A;ENSP00000376430:T133A	ENSP00000376430:T133A	T	+	1	0	ACTL6A	180776745	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.339000	0.96797	2.019000	0.59389	0.528000	0.53228	ACT	.	.		0.388	ACTL6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349599.1	NM_004301		G	179294051	A	G	179294051	3	3	352	1	0	0	0	0	1	0	0	0	198	159	6	2	545	2	ACTL6A	3	179294051	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	9637819	179294051	18728379	113	49529										
NDUFB5	4711	hgsc.bcm.edu	37	chr3	179336273	179336273	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gatatatgaaagaacaatggCcgtccttcagattgaagctg	10	7	1	4			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr3:179336273C>T	ENST00000259037.3	+	5	527	c.413C>T	c.(412-414)gCc>gTc	p.A138V	NDUFB5_ENST00000493866.1_Missense_Mutation_p.A86V|NDUFB5_ENST00000473500.1_3'UTR|NDUFB5_ENST00000472629.1_Missense_Mutation_p.A126V	NM_002492.3	NP_002483.1	O43674	NDUB5_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5, 16kDa	138					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			endometrium(1)|lung(6)|skin(1)	8	all_cancers(143;9.62e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.18)			AGAACAATGGCCGTCCTTCAG	0.388																																					p.A138V		Atlas-SNP	.											.	NDUFB5	22	.	0			c.C413T						.						77	77	77					3																	179336273		2203	4300	6503	SO:0001583	missense	4711	exon5			CAATGGCCGTCCT	AF047181	CCDS3234.1, CCDS56297.1, CCDS75054.1	3q27.1	2011-07-04	2002-08-29		ENSG00000136521	ENSG00000136521		"Mitochondrial respiratory chain complex / Complex I"	7700	protein-coding gene	gene with protein product	"complex I SGDH subunit"	603841	"NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5 (16kD, SGDH)"			9425316	Standard	NM_002492		Approved	SGDH, CI-SGDH, MGC12314	uc003fkc.3	O43674	OTTHUMG00000157480	ENST00000259037.3:c.413C>T	chr3.hg19:g.179336273C>T	ENSP00000259037:p.Ala138Val	117.0	0.0		130.0	20.0	NM_002492	Q561V6	Missense_Mutation	SNP	ENST00000259037.3	hg19	CCDS3234.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.83|17.83	3.484529|3.484529	0.63962|0.63962	.|.	.|.	ENSG00000136521|ENSG00000136521	ENST00000259037;ENST00000493866;ENST00000472629|ENST00000482604	T;T;T|.	0.50548|.	0.74;0.74;0.74|.	5.97|5.97	5.05|5.05	0.67936|0.67936	.|.	0.099668|.	0.64402|.	D|.	0.000002|.	T|T	0.78660|0.78660	0.4318|0.4318	M|M	0.85859|0.85859	2.78|2.78	0.58432|0.58432	D|D	0.999999|0.999999	D;D|.	0.69078|.	0.997;0.993|.	D;D|.	0.72625|.	0.978;0.942|.	T|T	0.80367|0.80367	-0.1412|-0.1412	10|5	0.46703|.	T|.	0.11|.	-21.1701|-21.1701	14.9473|14.9473	0.71042|0.71042	0.1436:0.8564:0.0:0.0|0.1436:0.8564:0.0:0.0	.|.	86;138|.	Q561V6;O43674|.	.;NDUB5_HUMAN|.	V|S	138;86;126|155	ENSP00000259037:A138V;ENSP00000419656:A86V;ENSP00000419248:A126V|.	ENSP00000259037:A138V|.	A|P	+|+	2|1	0|0	NDUFB5|NDUFB5	180818967|180818967	0.997000|0.997000	0.39634|0.39634	0.997000|0.997000	0.53966|0.53966	0.122000|0.122000	0.20287|0.20287	3.877000|3.877000	0.56123|0.56123	2.831000|2.831000	0.97527|0.97527	0.643000|0.643000	0.83706|0.83706	GCC|CCG	.	.		0.388	NDUFB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348937.2	NM_002492		T	179336273	C	T	179336273	3	4	352	1	0	0	0	0	1	0	0	0	10293	739	26	3	431	3	NDUFB5	3	179336273	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	42222	179336273	18686157	114	49530										
CHRD	8646	hgsc.bcm.edu	37	chr3	184105204	184105204	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gagctggcgggcagcgggtaCgcggtggcaccccgttgtgc	19	12	0	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr3:184105204C>T	ENST00000204604.1	+	19	2636	c.2390C>T	c.(2389-2391)aCg>aTg	p.T797M	EIF2B5_ENST00000444495.1_Intron|CHRD_ENST00000450923.1_Missense_Mutation_p.T797M|CHRD_ENST00000545352.1_Missense_Mutation_p.T339M|CHRD_ENST00000348986.3_Missense_Mutation_p.T757M	NM_003741.2	NP_003732.2	Q9H2X0	CHRD_HUMAN	chordin	797	VWFC 3. {ECO:0000255|PROSITE- ProRule:PRU00220}.				BMP signaling pathway involved in spinal cord dorsal/ventral patterning (GO:0021919)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|gastrulation with mouth forming second (GO:0001702)|mesoderm formation (GO:0001707)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell migration (GO:0030336)|negative regulation of osteoblast differentiation (GO:0045668)|osteoblast differentiation (GO:0001649)|positive regulation of cell adhesion (GO:0045785)|positive regulation of mesenchymal cell proliferation (GO:0002053)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)	cytokine binding (GO:0019955)|heparin binding (GO:0008201)			NS(1)|biliary_tract(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(23)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48	all_cancers(143;6.33e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GCAGCGGGTACGCGGTGGCAC	0.597																																					p.T797M		Atlas-SNP	.											CHRD,NS,carcinoma,0,1	CHRD	149	.	0			c.C2390T						.						43	39	40					3																	184105204		2203	4300	6503	SO:0001583	missense	8646	exon19			CGGGTACGCGGTG	AF076612	CCDS3266.1	3q27	2008-07-18			ENSG00000090539	ENSG00000090539			1949	protein-coding gene	gene with protein product		603475				9782094, 11472837	Standard	NM_003741		Approved		uc003fov.3	Q9H2X0	OTTHUMG00000141267	ENST00000204604.1:c.2390C>T	chr3.hg19:g.184105204C>T	ENSP00000204604:p.Thr797Met	76.0	0.0		61.0	18.0	NM_003741	O95254|Q2M1I8|Q6UW83|Q9H2D3|Q9H2W8|Q9H2W9|Q9P0Z2|Q9P0Z3|Q9P0Z4|Q9P0Z5	Missense_Mutation	SNP	ENST00000204604.1	hg19	CCDS3266.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.789368	0.90367	.	.	ENSG00000090539	ENST00000204604;ENST00000450923;ENST00000348986;ENST00000545352	T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18	5.15	5.15	0.70609	von Willebrand factor, type C (2);	0.000000	0.85682	D	0.000000	T	0.76659	0.4018	M	0.61703	1.905	0.36095	D	0.843706	D;D;D;D	0.89917	1.0;0.999;0.992;1.0	D;D;P;D	0.74023	0.982;0.941;0.746;0.976	T	0.81549	-0.0882	10	0.49607	T	0.09	-16.0676	17.1933	0.86886	0.0:1.0:0.0:0.0	.	339;757;797;797	B7Z6F4;Q9H2X0-5;E7ESX1;Q9H2X0	.;.;.;CHRD_HUMAN	M	797;797;757;339	ENSP00000204604:T797M;ENSP00000408972:T797M;ENSP00000334036:T757M;ENSP00000442948:T339M	ENSP00000204604:T797M	T	+	2	0	CHRD	185587898	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.089000	0.76909	2.402000	0.81655	0.563000	0.77884	ACG	.	.		0.597	CHRD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280432.1	NM_003741		T	184105204	C	T	184105204	3	4	352	1	0	0	0	0	1	0	0	0	3374	536	19	1	2464	1	CHRD	3	184105204	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	4768931	184105204	13917226	115	49531										
ETV5	2119	hgsc.bcm.edu	37	chr3	185797806	185797806	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agagttgcctgaggtgggggAaataggggattctgatgggt	19	3	1	3			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr3:185797806A>G	ENST00000306376.5	-	7	696	c.450T>C	c.(448-450)ttT>ttC	p.F150F	ETV5_ENST00000537818.1_Silent_p.F192F|ETV5_ENST00000434744.1_Silent_p.F150F|ETV5-AS1_ENST00000453370.1_RNA	NM_004454.2	NP_004445.1	P41161	ETV5_HUMAN	ets variant 5	150					cell differentiation (GO:0030154)|cellular response to oxidative stress (GO:0034599)|locomotory behavior (GO:0007626)|male germ-line stem cell asymmetric division (GO:0048133)|neuromuscular synaptic transmission (GO:0007274)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|regulation of synapse organization (GO:0050807)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|cervix(1)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	28	all_cancers(143;4.06e-12)|Ovarian(172;0.0386)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.62e-24)			GAGGTGGGGGAAATAGGGGAT	0.607			T	"TMPRSS2, SCL45A3"	Prostate																																p.F150F		Atlas-SNP	.		Dom	yes		3	3q28	2119	ets variant gene 5		E	.	ETV5	106	.	0			c.T450C						.						19	24	23					3																	185797806		2179	4288	6467	SO:0001819	synonymous_variant	2119	exon7			TGGGGGAAATAGG	BC007333	CCDS33906.1	3q28	2008-09-12	2008-09-12		ENSG00000244405	ENSG00000244405			3494	protein-coding gene	gene with protein product	"ets-related molecule"	601600	"ets variant gene 5 (ets-related molecule)"			8152800	Standard	NM_004454		Approved	ERM	uc003fpz.3	P41161	OTTHUMG00000156639	ENST00000306376.5:c.450T>C	chr3.hg19:g.185797806A>G		61.0	0.0		76.0	9.0	NM_004454	A6NH46|B7Z7D7|Q6IBN5	Silent	SNP	ENST00000306376.5	hg19	CCDS33906.1																																																																																			.	.		0.607	ETV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344947.1	NM_004454		G	185797806	A	G	185797806	2	3	352	1	0	0	0	0	0	0	0	1	5284	243	9	2		2	ETV5	3	185797806	Silent	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	1692602	185797806	12224624	116	49532										
SLC26A1	10861	hgsc.bcm.edu	37	chr4	985227	985227	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cccggccagcaatgagtaggCgatggcctgcggcaccagga	15	13	0	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr4:985227C>T	ENST00000361661.2	-	3	642	c.265G>A	c.(265-267)Gcc>Acc	p.A89T	SLC26A1_ENST00000398520.2_Missense_Mutation_p.A89T|SLC26A1_ENST00000398516.2_Missense_Mutation_p.A89T|SLC26A1_ENST00000513138.1_5'Flank|IDUA_ENST00000453894.1_Intron|IDUA_ENST00000247933.4_Intron	NM_213613.2	NP_998778.1	Q9H2B4	S26A1_HUMAN	solute carrier family 26 (anion exchanger), member 1	89					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|chloride transport (GO:0006821)|glycosaminoglycan metabolic process (GO:0030203)|ion transport (GO:0006811)|oxalate transport (GO:0019532)|small molecule metabolic process (GO:0044281)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|chloride transmembrane transporter activity (GO:0015108)|oxalate transmembrane transporter activity (GO:0019531)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			central_nervous_system(1)|endometrium(4)|pancreas(1)|prostate(1)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			AATGAGTAGGCGATGGCCTGC	0.632																																					p.A89T		Atlas-SNP	.											.	SLC26A1	44	.	0			c.G265A						.						99	93	95					4																	985227		2203	4300	6503	SO:0001583	missense	10861	exon2			AGTAGGCGATGGC	AF297659	CCDS33933.1, CCDS33934.1	4p16.3	2013-07-18	2013-07-18		ENSG00000145217	ENSG00000145217		"Solute carriers"	10993	protein-coding gene	gene with protein product		610130	"solute carrier family 26 (sulfate transporter), member 1"				Standard	NM_213613		Approved	SAT-1, EDM4	uc003gcc.3	Q9H2B4	OTTHUMG00000160003	ENST00000361661.2:c.265G>A	chr4.hg19:g.985227C>T	ENSP00000354721:p.Ala89Thr	164.0	0.0		203.0	21.0	NM_022042	A8K9N2|Q7Z5R3|Q96BK0	Missense_Mutation	SNP	ENST00000361661.2	hg19	CCDS33934.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.525832	0.85600	.	.	ENSG00000145217	ENST00000398520;ENST00000361661;ENST00000398516	D;D;D	0.95103	-3.61;-3.61;-3.61	4.99	4.99	0.66335	.	0.052718	0.85682	D	0.000000	D	0.98330	0.9446	H	0.97940	4.11	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.993	D	0.99482	1.0948	10	0.62326	D	0.03	.	15.7529	0.78001	0.0:1.0:0.0:0.0	.	89;89	Q9H2B4;Q96BK0	S26A1_HUMAN;.	T	89	ENSP00000381532:A89T;ENSP00000354721:A89T;ENSP00000381528:A89T	ENSP00000354721:A89T	A	-	1	0	SLC26A1	975227	1.000000	0.71417	1.000000	0.80357	0.350000	0.29205	5.955000	0.70306	2.299000	0.77371	0.313000	0.20887	GCC	.	.		0.632	SLC26A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358783.1	NM_022042, NM_134425		T	985227	C	T	985227	3	4	352	1	0	0	0	0	1	0	0	0	14529	768	27	1	1951	1	SLC26A1	4	985227	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10		985227	190169049	117	49533										
ADD1	118	hgsc.bcm.edu	37	chr4	2910332	2910332	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tggacaggagcctcgtccagGtgagagcccagagtgtctct	14	11	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr4:2910332G>A	ENST00000398129.1	+	11	1625		c.e11+1		ADD1_ENST00000398123.2_Splice_Site|ADD1_ENST00000503455.2_Splice_Site|ADD1_ENST00000264758.7_Splice_Site|ADD1_ENST00000513328.2_Splice_Site|ADD1_ENST00000355842.3_Splice_Site|ADD1_ENST00000446856.1_Splice_Site|ADD1_ENST00000398125.1_Splice_Site			P35611	ADDA_HUMAN	adducin 1 (alpha)						actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|barbed-end actin filament capping (GO:0051016)|cell morphogenesis (GO:0000902)|cell volume homeostasis (GO:0006884)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to retinoic acid (GO:0071300)|endoplasmic reticulum unfolded protein response (GO:0030968)|erythrocyte differentiation (GO:0030218)|hemoglobin metabolic process (GO:0020027)|homeostasis of number of cells within a tissue (GO:0048873)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein binding (GO:0032092)	cytosol (GO:0005829)|dendritic spine (GO:0043197)|F-actin capping protein complex (GO:0008290)|focal adhesion (GO:0005925)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|spectrin binding (GO:0030507)|structural molecule activity (GO:0005198)|transcription factor binding (GO:0008134)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		CCTCGTCCAGGTGAGAGCCCA	0.512																																					.	Esophageal Squamous(71;505 1201 20414 34538 37449)	Atlas-SNP	.											.	ADD1	56	.	0			c.1698+1G>A						.						142	110	121					4																	2910332		2203	4300	6503	SO:0001630	splice_region_variant	118	exon12			GTCCAGGTGAGAG	L07261	CCDS3363.1, CCDS3364.1, CCDS43205.1, CCDS75094.1	4p16.3	2009-04-22			ENSG00000087274	ENSG00000087274			243	protein-coding gene	gene with protein product		102680				1840603	Standard	NM_001119		Approved		uc003gfq.3	P35611	OTTHUMG00000122080	ENST00000398129.1:c.1605+1G>A	chr4.hg19:g.2910332G>A		103.0	0.0		101.0	26.0	NM_176801	A2A3N8|A2A3P0|B4DI79|D3DVR3|D3DVR4|D3DVR5|Q13734|Q14729|Q16156|Q86XM2|Q9UJB6	Splice_Site	SNP	ENST00000398129.1	hg19	CCDS43205.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.907462	0.92107	.	.	ENSG00000087274	ENST00000264758;ENST00000446856;ENST00000398125;ENST00000513328;ENST00000503455;ENST00000355842;ENST00000398123;ENST00000398129;ENST00000514940;ENST00000536424	.	.	.	5.91	5.91	0.95273	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.3052	0.98627	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ADD1	2880130	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.271000	0.95698	2.808000	0.96608	0.655000	0.94253	.	.	.		0.512	ADD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242840.1	NM_014189	Intron	A	2910332	G	A	2910332	5	1	352	1	0	0	0	0	0	0	1	0	304	1275	44	3	1741	3	ADD1	4	2910332	Splice_Site	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	1925105	2910332	188243944	118	49534										
HTT	3064	hgsc.bcm.edu	37	chr4	3162106	3162106	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	actagagctggccacactgcAggacattgggaaggtttgtg	14	8	0	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr4:3162106A>G	ENST00000355072.5	+	29	3996	c.3851A>G	c.(3850-3852)cAg>cGg	p.Q1284R		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	1284					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		GCCACACTGCAGGACATTGGG	0.507																																					p.Q1284R		Atlas-SNP	.											.	HTT	221	.	0			c.A3851G						.						210	202	204					4																	3162106		1983	4119	6102	SO:0001583	missense	3064	exon29			CACTGCAGGACAT	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.3851A>G	chr4.hg19:g.3162106A>G	ENSP00000347184:p.Gln1284Arg	104.0	0.0		110.0	26.0	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	hg19	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	A	11.64	1.699900	0.30142	.	.	ENSG00000197386	ENST00000355072	T	0.66280	-0.2	4.27	4.27	0.50696	.	0.248990	0.40908	D	0.000993	T	0.50548	0.1622	L	0.46157	1.445	0.29864	N	0.827429	P	0.35656	0.514	B	0.33521	0.165	T	0.50972	-0.8764	10	0.26408	T	0.33	.	9.6577	0.39936	0.8246:0.1754:0.0:0.0	.	1284	P42858	HD_HUMAN	R	1284	ENSP00000347184:Q1284R	ENSP00000347184:Q1284R	Q	+	2	0	HTT	3131904	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	6.402000	0.73260	1.681000	0.50988	0.460000	0.39030	CAG	.	.		0.507	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		G	3162106	A	G	3162106	3	3	352	1	0	0	0	0	1	0	0	0	7466	188	7	2	3965	2	HTT	4	3162106	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	251774	3162106	187992170	119	49535										
HGFAC	3083	hgsc.bcm.edu	37	chr4	3444865	3444865	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	acttcggagggcagtgcacaCaggaagtggtgggtccgggc	18	9	0	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr4:3444865C>T	ENST00000382774.3	+	3	502	c.387C>T	c.(385-387)caC>caT	p.H129H	HGFAC_ENST00000511533.1_Silent_p.H129H	NM_001528.2	NP_001519.1	Q04756	HGFA_HUMAN	HGF activator	129	Fibronectin type-II. {ECO:0000255|PROSITE-ProRule:PRU00478, ECO:0000255|PROSITE-ProRule:PRU00479}.				proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|rough endoplasmic reticulum (GO:0005791)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		GCAGTGCACACAGGAAGTGGT	0.697																																					p.H129H		Atlas-SNP	.											.	HGFAC	69	.	0			c.C387T						.						14	18	17					4																	3444865		2180	4272	6452	SO:0001819	synonymous_variant	3083	exon3			TGCACACAGGAAG	D14012	CCDS3369.1, CCDS75098.1	4p16	2008-02-07			ENSG00000109758	ENSG00000109758	3.4.21.-		4894	protein-coding gene	gene with protein product		604552				7683665, 8226803	Standard	XM_005247966		Approved	HGFAP, HGFA	uc003ghc.3	Q04756	OTTHUMG00000090281	ENST00000382774.3:c.387C>T	chr4.hg19:g.3444865C>T		80.0	0.0		110.0	27.0	NM_001528	Q14726|Q2M1W7|Q53X47	Silent	SNP	ENST00000382774.3	hg19	CCDS3369.1																																																																																			.	.		0.697	HGFAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206607.3			T	3444865	C	T	3444865	2	4	352	1	0	0	0	0	0	0	0	1	7095	477	17	3		3	HGFAC	4	3444865	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	282759	3444865	187709411	120	49536										
KIAA0232	9778	hgsc.bcm.edu	37	chr4	6865898	6865898	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gataatccagtttcttcgggAcagctggaagaggtatgtgt	13	6	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr4:6865898A>G	ENST00000307659.5	+	7	4244	c.3789A>G	c.(3787-3789)ggA>ggG	p.G1263G	KIAA0232_ENST00000425103.1_Silent_p.G1263G	NM_014743.2	NP_055558.2	Q92628	K0232_HUMAN	KIAA0232	1263							ATP binding (GO:0005524)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(12)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	41						TTTCTTCGGGACAGCTGGAAG	0.393																																					p.G1263G		Atlas-SNP	.											.	KIAA0232	102	.	0			c.A3789G						.						81	74	76					4																	6865898		1867	4112	5979	SO:0001819	synonymous_variant	9778	exon7			TTCGGGACAGCTG	D86985	CCDS43209.1	4p16.1	2012-11-29			ENSG00000170871	ENSG00000170871			28992	protein-coding gene	gene with protein product						9039502	Standard	NM_014743		Approved		uc003gjq.4	Q92628	OTTHUMG00000160072	ENST00000307659.5:c.3789A>G	chr4.hg19:g.6865898A>G		124.0	0.0		126.0	14.0	NM_014743	A7E2D2	Silent	SNP	ENST00000307659.5	hg19	CCDS43209.1																																																																																			.	.		0.393	KIAA0232-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359102.2	NM_014743		G	6865898	A	G	6865898	2	3	352	1	0	0	0	0	0	0	0	1	8172	262	10	2		2	KIAA0232	4	6865898	Silent	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	3421033	6865898	184288378	121	49537										
LCORL	254251	hgsc.bcm.edu	37	chr4	17910804	17910804	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aagggagttttctgcttgatTcatttggatacttttacata	8	5	2	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr4:17910804T>C	ENST00000382226.5	-	5	703	c.595A>G	c.(595-597)Aat>Gat	p.N199D	LCORL_ENST00000539056.1_Missense_Mutation_p.N112D|LCORL_ENST00000326877.4_Missense_Mutation_p.N199D|LCORL_ENST00000382224.1_Missense_Mutation_p.N115D	NM_001166139.1	NP_001159611.1	Q8N3X6	LCORL_HUMAN	ligand dependent nuclear receptor corepressor-like	199					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)			kidney(1)|large_intestine(1)|lung(1)|prostate(1)	4						TCTGCTTGATTCATTTGGATA	0.373																																					p.N199D		Atlas-SNP	.											.	LCORL	60	.	0			c.A595G						.						186	177	180					4																	17910804		2203	4300	6503	SO:0001583	missense	254251	exon5			CTTGATTCATTTG		CCDS3425.1, CCDS54749.1	4p15.32	2006-06-14			ENSG00000178177	ENSG00000178177			30776	protein-coding gene	gene with protein product		611799				12560079	Standard	NM_153686		Approved	MLR1, FLJ30696	uc021xmr.1	Q8N3X6	OTTHUMG00000128538	ENST00000382226.5:c.595A>G	chr4.hg19:g.17910804T>C	ENSP00000371661:p.Asn199Asp	159.0	0.0		181.0	47.0	NM_001166139	Q96NK1	Missense_Mutation	SNP	ENST00000382226.5	hg19	CCDS54749.1	.	.	.	.	.	.	.	.	.	.	T	18.03	3.533469	0.64972	.	.	ENSG00000178177	ENST00000326877;ENST00000539056;ENST00000382224;ENST00000382226	.	.	.	5.43	5.43	0.79202	.	0.257812	0.38381	N	0.001714	T	0.48892	0.1525	L	0.29908	0.895	0.31446	N	0.671323	D;P	0.55385	0.971;0.557	P;B	0.53062	0.717;0.297	T	0.55250	-0.8170	9	0.38643	T	0.18	.	15.4731	0.75456	0.0:0.0:0.0:1.0	.	112;199	B4DSW0;Q8N3X6-3	.;.	D	199;112;115;199	.	ENSP00000317566:N199D	N	-	1	0	LCORL	17519902	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.505000	0.66981	2.066000	0.61787	0.482000	0.46254	AAT	.	.		0.373	LCORL-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_153686		C	17910804	T	C	17910804	3	2	352	1	0	0	0	0	1	0	0	0	8699	1783	62	2	1410	2	LCORL	4	17910804	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	11044906	17910804	173243472	122	49538										
DHX15	1665	hgsc.bcm.edu	37	chr4	24578249	24578249	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	atctcctctatcacgttctcGgtctcgatctttagaccgat	6	13	6	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr4:24578249G>A	ENST00000336812.4	-	2	280	c.124C>T	c.(124-126)Cga>Tga	p.R42*		NM_001358.2	NP_001349.2	O43143	DHX15_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 15	42					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|U12-type spliceosomal complex (GO:0005689)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(5)|liver(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	30		Breast(46;0.0503)				TCACGTTCTCGGTCTCGATCT	0.423																																					p.R42X		Atlas-SNP	.											.	DHX15	69	.	0			c.C124T						.						142	123	130					4																	24578249		2203	4300	6503	SO:0001587	stop_gained	1665	exon2			GTTCTCGGTCTCG	AB001636	CCDS33966.1	4p15.3	2013-05-13	2013-05-13	2003-06-20	ENSG00000109606	ENSG00000109606		"DEAH-boxes"	2738	protein-coding gene	gene with protein product		603403	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 15", "DEAH (Asp-Glu-Ala-His) box polypeptide 15"	DDX15		9388478	Standard	NM_001358		Approved	HRH2, DBP1, PRP43, PrPp43p, PRPF43	uc003gqx.3	O43143	OTTHUMG00000160304	ENST00000336812.4:c.124C>T	chr4.hg19:g.24578249G>A	ENSP00000336741:p.Arg42*	92.0	0.0		102.0	29.0	NM_001358	Q9NQT7	Nonsense_Mutation	SNP	ENST00000336812.4	hg19	CCDS33966.1	.	.	.	.	.	.	.	.	.	.	G	31	5.079828	0.94050	.	.	ENSG00000109606	ENST00000336812;ENST00000535946	.	.	.	5.59	3.67	0.42095	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.5456	11.1918	0.48690	0.0:0.0:0.4959:0.5041	.	.	.	.	X	42;31	.	ENSP00000336741:R42X	R	-	1	2	DHX15	24187347	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.474000	0.60203	1.369000	0.46134	0.650000	0.86243	CGA	.	.		0.423	DHX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360143.1	NM_001358		A	24578249	G	A	24578249	4	1	352	1	0	0	0	0	0	1	0	0	4503	1124	39	1	2315	1	DHX15	4	24578249	Nonsense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	6667445	24578249	166576027	123	49539										
TLR6	10333	hgsc.bcm.edu	37	chr4	38829083	38829083	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agtttctctcatgaagacaaAtctgtatatcttctttttct	4	8	6	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr4:38829083A>G	ENST00000381950.1	-	1	2077	c.2012T>C	c.(2011-2013)aTt>aCt	p.I671T	TLR6_ENST00000436693.2_Missense_Mutation_p.I671T			Q9Y2C9	TLR6_HUMAN	toll-like receptor 6	671	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to diacyl bacterial lipopeptide (GO:0071726)|defense response to bacterium (GO:0042742)|detection of diacyl bacterial lipopeptide (GO:0042496)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|nitric oxide metabolic process (GO:0046209)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of JUN kinase activity (GO:0043507)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 6 signaling pathway (GO:0034150)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Toll-like receptor 2-Toll-like receptor 6 protein complex (GO:0035355)	diacyl lipopeptide binding (GO:0042498)|lipopeptide binding (GO:0071723)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						ATGAAGACAAATCTGTATATC	0.373																																					p.I671T		Atlas-SNP	.											.	TLR6	67	.	0			c.T2012C						.						107	111	109					4																	38829083		2203	4300	6503	SO:0001583	missense	10333	exon2			AGACAAATCTGTA		CCDS3446.1	4p16.1	2009-11-23			ENSG00000174130	ENSG00000174130		"CD molecules"	16711	protein-coding gene	gene with protein product		605403				10231569	Standard	NM_006068		Approved	CD286	uc010ifg.2	Q9Y2C9	OTTHUMG00000128579	ENST00000381950.1:c.2012T>C	chr4.hg19:g.38829083A>G	ENSP00000371376:p.Ile671Thr	107.0	0.0		116.0	16.0	NM_006068	B3Y640|B6CH35|B6RFS4|B6RFS5|Q2NKL3	Missense_Mutation	SNP	ENST00000381950.1	hg19	CCDS3446.1	.	.	.	.	.	.	.	.	.	.	A	11.63	1.695387	0.30052	.	.	ENSG00000174130	ENST00000436693;ENST00000381950	T;T	0.07216	3.21;3.21	4.55	4.55	0.56014	Toll/interleukin-1 receptor homology (TIR) domain (4);	0.489229	0.19928	N	0.102939	T	0.26085	0.0636	L	0.61387	1.9	0.36695	D	0.879788	D	0.63046	0.992	D	0.83275	0.996	T	0.12502	-1.0545	10	0.87932	D	0	.	13.7108	0.62667	1.0:0.0:0.0:0.0	.	671	Q9Y2C9	TLR6_HUMAN	T	671	ENSP00000389600:I671T;ENSP00000371376:I671T	ENSP00000371376:I671T	I	-	2	0	TLR6	38505478	1.000000	0.71417	0.773000	0.31616	0.047000	0.14425	9.073000	0.93992	1.913000	0.55393	0.459000	0.35465	ATT	.	.		0.373	TLR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250431.1			G	38829083	A	G	38829083	3	3	352	1	0	0	0	0	1	0	0	0	15970	101	4	2	382	2	TLR6	4	38829083	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	14250834	38829083	152325193	124	49540										
PPAT	5471	hgsc.bcm.edu	37	chr4	57269502	57269502	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tgttcctgaggaggggtataCgccagtaactgggtaatcat	13	7	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr4:57269502C>T	ENST00000264220.2	-	4	605	c.468G>A	c.(466-468)gcG>gcA	p.A156A	PPAT_ENST00000507648.1_5'UTR	NM_002703.4	NP_002694.3	Q06203	PUR1_HUMAN	phosphoribosyl pyrophosphate amidotransferase	156	Glutamine amidotransferase type-2. {ECO:0000255|PROSITE-ProRule:PRU00609}.				'de novo' IMP biosynthetic process (GO:0006189)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|G1/S transition of mitotic cell cycle (GO:0000082)|glutamine catabolic process (GO:0006543)|kidney development (GO:0001822)|lactation (GO:0007595)|maternal process involved in female pregnancy (GO:0060135)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|organ regeneration (GO:0031100)|protein homotetramerization (GO:0051289)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide biosynthetic process (GO:0006164)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|amidophosphoribosyltransferase activity (GO:0004044)|metal ion binding (GO:0046872)			cervix(1)|endometrium(2)|large_intestine(6)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	20	Glioma(25;0.08)|all_neural(26;0.101)				Fluorouracil(DB00544)|L-Glutamine(DB00130)|Mercaptopurine(DB01033)	GAGGGGTATACGCCAGTAACT	0.428																																					p.A156A		Atlas-SNP	.											.	PPAT	41	.	0			c.G468A						.						84	80	81					4																	57269502		2203	4300	6503	SO:0001819	synonymous_variant	5471	exon4			GGTATACGCCAGT		CCDS3505.1	4q12	2012-10-02			ENSG00000128059	ENSG00000128059	2.4.2.14		9238	protein-coding gene	gene with protein product		172450					Standard	NM_002703		Approved	GPAT, PRAT	uc003hbr.3	Q06203	OTTHUMG00000128842	ENST00000264220.2:c.468G>A	chr4.hg19:g.57269502C>T		80.0	0.0		59.0	11.0	NM_002703		Silent	SNP	ENST00000264220.2	hg19	CCDS3505.1																																																																																			.	.		0.428	PPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250781.2	NM_002703		T	57269502	C	T	57269502	2	4	352	1	0	0	0	0	0	0	0	1	12311	523	19	1		1	PPAT	4	57269502	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	18440419	57269502	133884774	125	49541										
GRSF1	2926	hgsc.bcm.edu	37	chr4	71702012	71702012	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggggtggtggaaggtcttccAggtaagtagttttggactcc	16	6	1	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr4:71702012A>G	ENST00000254799.6	-	2	494	c.377T>C	c.(376-378)cTg>cCg	p.L126P	GRSF1_ENST00000439371.1_5'UTR|GRSF1_ENST00000502323.1_5'UTR|GRSF1_ENST00000508091.1_5'UTR|GRSF1_ENST00000545193.1_Missense_Mutation_p.L8P	NM_002092.3	NP_002083	Q12849	GRSF1_HUMAN	G-rich RNA sequence binding factor 1	126	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				anterior/posterior pattern specification (GO:0009952)|morphogenesis of embryonic epithelium (GO:0016331)|mRNA polyadenylation (GO:0006378)|tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|upper_aerodigestive_tract(2)	17		all_hematologic(202;0.21)	Lung(101;0.235)			AAGGTCTTCCAGGTAAGTAGT	0.398																																					p.L126P		Atlas-SNP	.											.	GRSF1	35	.	0			c.T377C						.						80	81	81					4																	71702012		1838	4086	5924	SO:0001583	missense	2926	exon2			TCTTCCAGGTAAG	BC040485	CCDS47069.1, CCDS47070.1	4q13	2013-07-16				ENSG00000132463		"RNA binding motif (RRM) containing"	4610	protein-coding gene	gene with protein product		604851				8036161	Standard	NM_001098477		Approved		uc010iia.1	Q12849		ENST00000254799.6:c.377T>C	chr4.hg19:g.71702012A>G	ENSP00000254799:p.Leu126Pro	263.0	0.0		193.0	41.0	NM_002092	B3KPW0|Q4W5S5|Q6ZST3|Q8IWD6|Q8NBD2	Missense_Mutation	SNP	ENST00000254799.6	hg19	CCDS47069.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.46|14.46	2.542465|2.542465	0.45280|0.45280	.|.	.|.	ENSG00000132463|ENSG00000132463	ENST00000254799;ENST00000540657;ENST00000499044;ENST00000545193|ENST00000514161	T;T;T|.	0.19669|.	2.17;2.14;2.13|.	4.51|4.51	3.32|3.32	0.38043|0.38043	RNA recognition motif domain (1);|.	0.619363|.	0.13459|.	N|.	0.386308|.	T|T	0.42585|0.42585	0.1209|0.1209	L|L	0.36672|0.36672	1.1|1.1	0.80722|0.80722	D|D	1|1	B;B|.	0.09022|.	0.001;0.002|.	B;B|.	0.08055|.	0.001;0.003|.	T|T	0.20874|0.20874	-1.0262|-1.0262	10|5	0.72032|.	D|.	0.01|.	-4.6671|-4.6671	3.7749|3.7749	0.08656|0.08656	0.6121:0.0:0.0959:0.292|0.6121:0.0:0.0959:0.292	.|.	39;126|.	B7Z5F9;Q12849|.	.;GRSF1_HUMAN|.	P|R	126;58;99;8|63	ENSP00000254799:L126P;ENSP00000427354:L99P;ENSP00000443380:L8P|.	ENSP00000254799:L126P|.	L|W	-|-	2|1	0|0	GRSF1|GRSF1	71920876|71920876	1.000000|1.000000	0.71417|0.71417	0.990000|0.990000	0.47175|0.47175	0.710000|0.710000	0.40934|0.40934	3.033000|3.033000	0.49743|0.49743	0.754000|0.754000	0.32968|0.32968	0.533000|0.533000	0.62120|0.62120	CTG|TGG	.	.		0.398	GRSF1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362642.1	NM_002092		G	71702012	A	G	71702012	3	3	352	1	0	0	0	0	1	0	0	0	6818	188	7	2	1097	2	GRSF1	4	71702012	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	14432510	71702012	119452264	126	49542										
SPRY1	10252	hgsc.bcm.edu	37	chr4	124323492	124323492	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agataatccttgctcctgttCacaatcacactgctgctcta	5	13	3	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr4:124323492C>T	ENST00000394339.2	+	2	1086	c.746C>T	c.(745-747)tCa>tTa	p.S249L	SPRY1_ENST00000339241.1_Missense_Mutation_p.S249L	NM_001258039.1|NM_005841.2	NP_001244968.1|NP_005832.1	O43609	SPY1_HUMAN	sprouty homolog 1, antagonist of FGF signaling (Drosophila)	249	Cys-rich.|SPR. {ECO:0000255|PROSITE- ProRule:PRU00572}.				epidermal growth factor receptor signaling pathway (GO:0007173)|multicellular organismal development (GO:0007275)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)	cytosol (GO:0005829)|plasma membrane (GO:0005886)				NS(1)|large_intestine(4)|lung(2)|ovary(1)|skin(3)	11						TGCTCCTGTTCACAATCACAC	0.458																																					p.S249L		Atlas-SNP	.											.	SPRY1	28	.	0			c.C746T						.						279	236	251					4																	124323492		2203	4300	6503	SO:0001583	missense	10252	exon2			CCTGTTCACAATC	AF041037	CCDS3731.1	4q	2009-04-17	2001-11-28		ENSG00000164056	ENSG00000164056			11269	protein-coding gene	gene with protein product		602465	"sprouty (Drosophila) homolog 1 (antagonist of FGF signaling)"			9458049, 15962011	Standard	NM_001258038		Approved	hSPRY1	uc003ifa.4	O43609	OTTHUMG00000133071	ENST00000394339.2:c.746C>T	chr4.hg19:g.124323492C>T	ENSP00000377871:p.Ser249Leu	70.0	0.0		53.0	14.0	NM_001258039	D3DNX6|Q6PNE0	Missense_Mutation	SNP	ENST00000394339.2	hg19	CCDS3731.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.235710	0.79800	.	.	ENSG00000164056	ENST00000339241;ENST00000394339	T;T	0.64438	-0.1;-0.1	4.91	4.91	0.64330	.	0.176335	0.38897	N	0.001525	T	0.64527	0.2606	L	0.58101	1.795	0.58432	D	0.999996	P	0.38300	0.626	B	0.42625	0.393	T	0.63541	-0.6614	9	.	.	.	-7.9347	17.9168	0.88954	0.0:1.0:0.0:0.0	.	249	O43609	SPY1_HUMAN	L	249	ENSP00000343785:S249L;ENSP00000377871:S249L	.	S	+	2	0	SPRY1	124542942	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	5.245000	0.65405	2.541000	0.85698	0.561000	0.74099	TCA	.	.		0.458	SPRY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256711.1			T	124323492	C	T	124323492	3	4	352	1	0	0	0	0	1	0	0	0	15120	838	29	3	748	3	SPRY1	4	124323492	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	52621480	124323492	66830784	127	49543										
ABCE1	6059	hgsc.bcm.edu	37	chr4	146030397	146030397	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aaagccaaaccttggaaagtAcgatgtatgtattatcacct	7	8	1	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr4:146030397A>G	ENST00000296577.4	+	5	916	c.401A>G	c.(400-402)tAc>tGc	p.Y134C	OTUD4_ENST00000455611.2_5'Flank|ABCE1_ENST00000502803.1_Intron	NM_001040876.1|NM_002940.2	NP_001035809.1|NP_002931.2	P61221	ABCE1_HUMAN	ATP-binding cassette, sub-family E (OABP), member 1	134	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				negative regulation of catalytic activity (GO:0043086)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|iron-sulfur cluster binding (GO:0051536)|ribonuclease inhibitor activity (GO:0008428)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|lung(5)|prostate(2)|skin(3)	18	all_hematologic(180;0.151)					CTTGGAAAGTACGATGTATGT	0.308																																					p.Y134C		Atlas-SNP	.											.	ABCE1	47	.	0			c.A401G						.						65	65	65					4																	146030397		2203	4300	6503	SO:0001583	missense	6059	exon5			GAAAGTACGATGT	X74987	CCDS34071.1	4q31	2012-03-14			ENSG00000164163	ENSG00000164163		"ATP binding cassette transporters / subfamily E"	69	protein-coding gene	gene with protein product		601213		RNASEL1, RNASELI, RNS4I		7539425	Standard	NM_002940		Approved	RLI, OABP	uc003ijy.3	P61221	OTTHUMG00000161478	ENST00000296577.4:c.401A>G	chr4.hg19:g.146030397A>G	ENSP00000296577:p.Tyr134Cys	50.0	0.0		45.0	24.0	NM_002940	O88793|Q13181|Q13864|Q6NR76|Q96AL0|Q96B10|Q99K66	Missense_Mutation	SNP	ENST00000296577.4	hg19	CCDS34071.1	.	.	.	.	.	.	.	.	.	.	A	17.05	3.289314	0.59976	.	.	ENSG00000164163	ENST00000296577;ENST00000502586	D;D	0.93712	-3.27;-3.27	5.86	5.86	0.93980	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.155822	0.64402	D	0.000016	D	0.96178	0.8754	M	0.77486	2.375	0.58432	D	0.999997	D	0.58970	0.984	P	0.61275	0.886	D	0.96416	0.9308	10	0.66056	D	0.02	-30.1932	16.5602	0.84551	1.0:0.0:0.0:0.0	.	134	P61221	ABCE1_HUMAN	C	134	ENSP00000296577:Y134C;ENSP00000421250:Y134C	ENSP00000296577:Y134C	Y	+	2	0	ABCE1	146249847	1.000000	0.71417	0.996000	0.52242	0.857000	0.48899	4.586000	0.60984	2.367000	0.80283	0.528000	0.53228	TAC	.	.		0.308	ABCE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365104.1	NM_002940		G	146030397	A	G	146030397	3	3	352	1	0	0	0	0	1	0	0	0	64	391	14	2	415	2	ABCE1	4	146030397	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	21706905	146030397	45123879	128	49544										
ODZ3	55714	hgsc.bcm.edu	37	chr4	183609359	183609359	+	Frame_Shift_Del	DEL	G	G	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggctcacacggcgtttgcatGggggggacgtgtcgctgtga							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr4:183609359delG	ENST00000511685.1	+	12	2199	c.2076delG	c.(2074-2076)atgfs	p.M692fs	TENM3_ENST00000406950.2_Frame_Shift_Del_p.M692fs|TENM3_ENST00000502950.1_3'UTR			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	692	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										GCGTTTGCATGGGGGGGACGT	0.592																																					p.M692fs		Atlas-INDEL	.											.	.	.	.	0			c.2075delT						.						109	116	113					4																	183609359		1969	4158	6127	SO:0001589	frameshift_variant	55714	exon11			.	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.2076delG	chr4.hg19:g.183609359delG	ENSP00000424226:p.Met692fs	62.0	0.0		49.0	16.0	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Frame_Shift_Del	DEL	ENST00000511685.1	hg19	CCDS47165.1																																																																																			.	.		0.592	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			-	183609359	G	-	183609359	7	5	352	1	0	1	0	1	0	0	0	0	10845	1348	47	0	2118	0	ODZ3	4	183609359	Frame_Shift_Del	DEL	G	TCGA-WQ-A9G7-01A-11D-A36X-10	37578962	183609359	7544917	129	49545										
NR2F1	7025	hgsc.bcm.edu	37	chr5	92923806	92923806	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gcccaacaacattatgggcaTcgagaacatctgcgagctgg	11	11	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr5:92923806T>C	ENST00000327111.3	+	2	2334	c.647T>C	c.(646-648)aTc>aCc	p.I216T	NR2F1-AS1_ENST00000513055.1_RNA	NM_005654.4	NP_005645.1	P10589	COT1_HUMAN	nuclear receptor subfamily 2, group F, member 1	216					cerebral cortex regionalization (GO:0021796)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|retinoic acid-responsive element binding (GO:0044323)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(4)|large_intestine(6)|lung(2)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	21		all_cancers(142;1.62e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0126)|Lung NSC(167;0.0155)|Ovarian(174;0.0218)|Prostate(281;0.173)|Colorectal(57;0.19)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0416)|all cancers(79;9.57e-18)		ATTATGGGCATCGAGAACATC	0.647																																					p.I216T		Atlas-SNP	.											.	NR2F1	56	.	0			c.T647C						.						79	77	78					5																	92923806		2203	4300	6503	SO:0001583	missense	7025	exon2			TGGGCATCGAGAA	BC004154	CCDS4068.1	5q14	2013-01-16			ENSG00000175745	ENSG00000175745		"Nuclear hormone receptors"	7975	protein-coding gene	gene with protein product		132890		ERBAL3, TFCOUP1		8530078	Standard	NM_005654		Approved	EAR-3, COUP-TFI, TCFCOUP1, SVP44	uc003kkj.3	P10589	OTTHUMG00000119079	ENST00000327111.3:c.647T>C	chr5.hg19:g.92923806T>C	ENSP00000325819:p.Ile216Thr	133.0	0.0		118.0	17.0	NM_005654		Missense_Mutation	SNP	ENST00000327111.3	hg19	CCDS4068.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.130539	0.77549	.	.	ENSG00000175745	ENST00000327111	T	0.52295	0.67	4.47	4.47	0.54385	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (1);	0.056958	0.64402	D	0.000002	T	0.62672	0.2447	L	0.56769	1.78	0.80722	D	1	D	0.59767	0.986	D	0.65573	0.936	T	0.67019	-0.5776	10	0.87932	D	0	.	13.8968	0.63778	0.0:0.0:0.0:1.0	.	216	P10589	COT1_HUMAN	T	216	ENSP00000325819:I216T	ENSP00000325819:I216T	I	+	2	0	NR2F1	92949562	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.780000	0.85658	1.857000	0.53885	0.334000	0.21626	ATC	.	.		0.647	NR2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239293.2	NM_005654		C	92923806	T	C	92923806	3	2	352	1	0	0	0	0	1	0	0	0	10636	1435	50	2	653	2	NR2F1	5	92923806	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10		92923806	87991454	130	49546										
WDR36	134430	hgsc.bcm.edu	37	chr5	110456746	110456746	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agtgatgaattgatagaataTgattcgccagaacagttgaa	10	4	0	7			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr5:110456746T>C	ENST00000513710.2	+	19	2227	c.2223T>C	c.(2221-2223)taT>taC	p.Y741Y	WDR36_ENST00000506538.2_Silent_p.Y741Y			Q8NI36	WDR36_HUMAN	WD repeat domain 36	741					regulation of axon extension (GO:0030516)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|rRNA processing (GO:0006364)|visual perception (GO:0007601)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(9)|kidney(4)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(142;2.72e-05)|all_epithelial(76;4.4e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0418)|Ovarian(225;0.0443)|Colorectal(57;0.0465)|all_lung(232;0.0508)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.39e-08)|Epithelial(69;1.82e-07)|all cancers(49;2.04e-05)|COAD - Colon adenocarcinoma(37;0.111)		TGATAGAATATGATTCGCCAG	0.303																																					p.Y741Y		Atlas-SNP	.											.	WDR36	111	.	0			c.T2223C						.						131	146	141					5																	110456746		2202	4299	6501	SO:0001819	synonymous_variant	134430	exon19			AGAATATGATTCG	AF385437	CCDS4102.1	5q22.2	2013-01-09			ENSG00000134987	ENSG00000134987		"WD repeat domain containing"	30696	protein-coding gene	gene with protein product		609669	"glaucoma 1, open angle, G"	GLC1G		15590835, 15677485	Standard	NM_139281		Approved	TA-WDRP, UTP21	uc003kpd.3	Q8NI36	OTTHUMG00000128790	ENST00000513710.2:c.2223T>C	chr5.hg19:g.110456746T>C		206.0	0.0		207.0	47.0	NM_139281	A2RUS4|Q68E02|Q8N1Q2	Silent	SNP	ENST00000513710.2	hg19	CCDS4102.1																																																																																			.	.		0.303	WDR36-008	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000373504.3	NM_139281		C	110456746	T	C	110456746	2	2	352	1	0	0	0	0	0	0	0	1	17305	1471	51	2		2	WDR36	5	110456746	Silent	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	17532940	110456746	70458514	131	49547										
FTMT	94033	hgsc.bcm.edu	37	chr5	121187928	121187928	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	atcaacctcgagctctatgcGtcctacgtgtacttgtccat	7	13	2	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr5:121187928G>A	ENST00000321339.1	+	1	279	c.270G>A	c.(268-270)gcG>gcA	p.A90A		NM_177478.1	NP_803431.1	Q8N4E7	FTMT_HUMAN	ferritin mitochondrial	90	Ferritin-like diiron. {ECO:0000255|PROSITE-ProRule:PRU00085}.				cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)|positive regulation of cell proliferation (GO:0008284)|positive regulation of lyase activity (GO:0051349)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of transferase activity (GO:0051347)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ferric iron binding (GO:0008199)|ferroxidase activity (GO:0004322)	p.A90A(2)		NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	33		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	Epithelial(69;0.000171)|OV - Ovarian serous cystadenocarcinoma(64;0.000188)|all cancers(49;0.0027)		AGCTCTATGCGTCCTACGTGT	0.617																																					p.A90A		Atlas-SNP	.											FTMT,NS,carcinoma,0,2	FTMT	71	.	2	Substitution - coding silent(2)	lung(1)|endometrium(1)	c.G270A						.						86	68	74					5																	121187928		2203	4300	6503	SO:0001819	synonymous_variant	94033	exon1			CTATGCGTCCTAC	BC034419	CCDS4128.1	5q23.1	2008-02-05			ENSG00000181867	ENSG00000181867			17345	protein-coding gene	gene with protein product		608847				11323407	Standard	NM_177478		Approved	MtF	uc003kss.3	Q8N4E7	OTTHUMG00000128912	ENST00000321339.1:c.270G>A	chr5.hg19:g.121187928G>A		113.0	1.0		150.0	43.0	NM_177478		Silent	SNP	ENST00000321339.1	hg19	CCDS4128.1																																																																																			.	.		0.617	FTMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250884.1	NM_177478		A	121187928	G	A	121187928	2	1	352	1	0	0	0	0	0	0	0	1	6093	1132	40	1		1	FTMT	5	121187928	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	10731182	121187928	59727332	132	49548										
ADAMTS19	171019	hgsc.bcm.edu	37	chr5	129039961	129039961	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aagtgtggcaaaggcatacgTcatcggaccgttagatgtac	12	8	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr5:129039961T>C	ENST00000274487.4	+	21	3316	c.3171T>C	c.(3169-3171)cgT>cgC	p.R1057R	CTC-575N7.1_ENST00000503616.1_RNA|ADAMTS19_ENST00000509467.1_3'UTR	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	1057	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		AAGGCATACGTCATCGGACCG	0.423																																					p.R1057R		Atlas-SNP	.											.	ADAMTS19	216	.	0			c.T3171C						.						240	216	224					5																	129039961		2203	4300	6503	SO:0001819	synonymous_variant	171019	exon21			CATACGTCATCGG	AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"ADAM metallopeptidases with thrombospondin type 1 motif"	17111	protein-coding gene	gene with protein product		607513	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.3171T>C	chr5.hg19:g.129039961T>C		141.0	0.0		149.0	16.0	NM_133638		Silent	SNP	ENST00000274487.4	hg19	CCDS4146.1																																																																																			.	.		0.423	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638		C	129039961	T	C	129039961	2	2	352	1	0	0	0	0	0	0	0	1	264	1654	58	2		2	ADAMTS19	5	129039961	Silent	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	7852033	129039961	51875299	133	49549										
VDAC1	7416	hgsc.bcm.edu	37	chr5	133311575	133311575	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tacccaccgagaagcaggcgTcagggtcaatctgatacttg	11	11	3	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr5:133311575T>C	ENST00000265333.3	-	7	933	c.689A>G	c.(688-690)gAc>gGc	p.D230G	VDAC1_ENST00000395044.3_Missense_Mutation_p.D230G|VDAC1_ENST00000395047.2_Missense_Mutation_p.D230G	NM_003374.2	NP_003365.1	P21796	VDAC1_HUMAN	voltage-dependent anion channel 1	230					anion transport (GO:0006820)|apoptotic process (GO:0006915)|behavioral fear response (GO:0001662)|epithelial cell differentiation (GO:0030855)|learning (GO:0007612)|neuron-neuron synaptic transmission (GO:0007270)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|pore complex (GO:0046930)	porin activity (GO:0015288)|protein kinase binding (GO:0019901)|voltage-gated anion channel activity (GO:0008308)			endometrium(1)|large_intestine(1)|lung(1)|skin(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00806)|Kidney(363;0.02)		Dihydroxyaluminium(DB01375)	GAAGCAGGCGTCAGGGTCAAT	0.512																																					p.D230G	NSCLC(127;1776 1806 35523 41489 48154)	Atlas-SNP	.											.	VDAC1	17	.	0			c.A689G						.						159	154	156					5																	133311575		2203	4300	6503	SO:0001583	missense	7416	exon7			CAGGCGTCAGGGT		CCDS4168.1	5q31	2011-11-15			ENSG00000213585	ENSG00000213585		"Voltage-dependent anion channels"	12669	protein-coding gene	gene with protein product		604492				7517385	Standard	NM_003374		Approved	MGC111064, PORIN	uc003kyr.2	P21796	OTTHUMG00000129118	ENST00000265333.3:c.689A>G	chr5.hg19:g.133311575T>C	ENSP00000265333:p.Asp230Gly	141.0	0.0		158.0	21.0	NM_003374	B3KVK4|D3DQ93|Q5FVE7|Q9UIQ5|Q9UPL0	Missense_Mutation	SNP	ENST00000265333.3	hg19	CCDS4168.1	.	.	.	.	.	.	.	.	.	.	T	18.99	3.739223	0.69304	.	.	ENSG00000213585	ENST00000265333;ENST00000395044;ENST00000395047	T;T;T	0.43294	0.95;0.95;0.95	5.54	5.54	0.83059	.	0.090614	0.64402	D	0.000001	T	0.50480	0.1618	M	0.62266	1.93	0.80722	D	1	B	0.24618	0.107	B	0.38264	0.269	T	0.50338	-0.8840	10	0.48119	T	0.1	.	15.9731	0.80036	0.0:0.0:0.0:1.0	.	230	P21796	VDAC1_HUMAN	G	230	ENSP00000265333:D230G;ENSP00000378484:D230G;ENSP00000378487:D230G	ENSP00000265333:D230G	D	-	2	0	VDAC1	133339474	1.000000	0.71417	0.920000	0.36463	0.980000	0.70556	7.959000	0.87885	2.234000	0.73211	0.472000	0.43445	GAC	.	.		0.512	VDAC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259208.1			C	133311575	T	C	133311575	3	2	352	1	0	0	0	0	1	0	0	0	17161	1667	58	2	174	2	VDAC1	5	133311575	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	4271614	133311575	47603685	134	49550										
WDR55	54853	hgsc.bcm.edu	37	chr5	140049100	140049100	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggtggatgactaccgtcggcGcaaaaaaaagggaggaccac	14	9	0	1	rs367668945		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr5:140049100G>A	ENST00000358337.5	+	7	1250	c.1013G>A	c.(1012-1014)cGc>cAc	p.R338H	WDR55_ENST00000520764.1_3'UTR	NM_017706.4	NP_060176	Q9H6Y2	WDR55_HUMAN	WD repeat domain 55	338					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)		p.R338H(1)		NS(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TACCGTCGGCGCAAAAAAAAG	0.592																																					p.R338H		Atlas-SNP	.											WDR55,NS,carcinoma,0,2	WDR55	27	.	1	Substitution - Missense(1)	prostate(1)	c.G1013A						.	G	HIS/ARG	0,4406		0,0,2203	43	45	45		1013	5.3	1	5		45	1,8599	1.2+/-3.3	0,1,4299	no	missense	WDR55	NM_017706.4	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	338/384	140049100	1,13005	2203	4300	6503	SO:0001583	missense	54853	exon7			GTCGGCGCAAAAA	AK000202	CCDS4235.1	5q31.3	2013-01-09			ENSG00000120314	ENSG00000120314		"WD repeat domain containing"	25971	protein-coding gene	gene with protein product						12477932	Standard	NM_017706		Approved	FLJ20195, FLJ21702	uc003lgr.4	Q9H6Y2	OTTHUMG00000129506	ENST00000358337.5:c.1013G>A	chr5.hg19:g.140049100G>A	ENSP00000351100:p.Arg338His	255.0	0.0		322.0	36.0	NM_017706	Q9NXK4	Missense_Mutation	SNP	ENST00000358337.5	hg19	CCDS4235.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.923002	0.92319	0.0	1.16E-4	ENSG00000120314	ENST00000358337	T	0.30714	1.52	5.28	5.28	0.74379	.	0.184033	0.35903	N	0.002909	T	0.36468	0.0968	L	0.34521	1.04	0.80722	D	1	D	0.69078	0.997	P	0.54140	0.743	T	0.02885	-1.1098	10	0.30854	T	0.27	-11.5367	16.4095	0.83703	0.0:0.0:1.0:0.0	.	338	Q9H6Y2	WDR55_HUMAN	H	338	ENSP00000351100:R338H	ENSP00000351100:R338H	R	+	2	0	WDR55	140029284	1.000000	0.71417	0.999000	0.59377	0.914000	0.54420	7.329000	0.79170	2.473000	0.83533	0.467000	0.42956	CGC	.	.		0.592	WDR55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251680.3	NM_017706		A	140049100	G	A	140049100	3	1	352	1	0	0	0	0	1	0	0	0	17322	1087	38	1	1039	1	WDR55	5	140049100	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	6737525	140049100	40866160	135	49551										
PCDHB15	56121	hgsc.bcm.edu	37	chr5	140625888	140625888	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agtttgtgcaggcgctctacGaggtgcaggtcccagagaac	14	10	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr5:140625888G>A	ENST00000231173.3	+	1	742	c.742G>A	c.(742-744)Gag>Aag	p.E248K		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	248	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(8)|kidney(3)|large_intestine(14)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	61			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGCGCTCTACGAGGTGCAGGT	0.562																																					p.E248K		Atlas-SNP	.											.	PCDHB15	138	.	0			c.G742A						.						35	37	36					5																	140625888		2203	4300	6503	SO:0001583	missense	56121	exon1			CTCTACGAGGTGC	AF152494	CCDS4257.1	5q31	2011-06-07			ENSG00000113248	ENSG00000113248		"Cadherins / Protocadherins : Clustered"	8686	other	protocadherin		606341				10380929	Standard	NM_018935		Approved	PCDH-BETA15	uc003lje.3	Q9Y5E8	OTTHUMG00000129609	ENST00000231173.3:c.742G>A	chr5.hg19:g.140625888G>A	ENSP00000231173:p.Glu248Lys	107.0	0.0		125.0	38.0	NM_018935	Q8IUX5	Missense_Mutation	SNP	ENST00000231173.3	hg19	CCDS4257.1	.	.	.	.	.	.	.	.	.	.	G	0.089	-1.169992	0.01660	.	.	ENSG00000113248	ENST00000231173	T	0.52295	0.67	5.13	-0.955	0.10356	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.27489	0.0675	N	0.16130	0.375	0.09310	N	1	B	0.16166	0.016	B	0.18263	0.021	T	0.20940	-1.0260	9	0.39692	T	0.17	.	7.9624	0.30079	0.3911:0.4786:0.1302:0.0	.	248	Q9Y5E8	PCDBF_HUMAN	K	248	ENSP00000231173:E248K	ENSP00000231173:E248K	E	+	1	0	PCDHB15	140606072	0.000000	0.05858	0.083000	0.20561	0.023000	0.10783	0.025000	0.13577	-0.030000	0.13804	-0.339000	0.08088	GAG	.	.		0.562	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935		A	140625888	G	A	140625888	3	1	352	1	0	0	0	0	1	0	0	0	11549	1059	37	1	744	1	PCDHB15	5	140625888	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	576788	140625888	40289372	136	49552										
CSNK1A1	1452	hgsc.bcm.edu	37	chr5	148929723	148929723	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gggatgcctggccttctgagAttctagcttcactgccactt	10	12	3	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr5:148929723A>G	ENST00000377843.2	-	2	624	c.145T>C	c.(145-147)Tct>Cct	p.S49P	CSNK1A1_ENST00000504676.1_5'UTR|CSNK1A1_ENST00000515435.1_5'UTR|CSNK1A1_ENST00000515748.2_Missense_Mutation_p.S49P|CSNK1A1_ENST00000261798.5_Missense_Mutation_p.S49P|CSNK1A1_ENST00000515768.1_Missense_Mutation_p.S49P	NM_001025105.1|NM_001892.4	NP_001020276.1|NP_001883.4	P48729	KC1A_HUMAN	casein kinase 1, alpha 1	49	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell surface receptor signaling pathway (GO:0007166)|mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear speck (GO:0016607)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|lung(4)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.0407)		GCCTTCTGAGATTCTAGCTTC	0.517																																					p.S49P	Colon(5;64 69 1309 10383)	Atlas-SNP	.											.	CSNK1A1	63	.	0			c.T145C						.						111	117	115					5																	148929723		2183	4300	6483	SO:0001583	missense	1452	exon2			TCTGAGATTCTAG	AF119911	CCDS47303.1, CCDS47304.1, CCDS64291.1	5q32	2013-01-17			ENSG00000113712	ENSG00000113712			2451	protein-coding gene	gene with protein product	"clock regulator kinase"	600505				8050587	Standard	NM_001025105		Approved	CK1, CK1a, CK1alpha, CKIa, CKIalpha	uc003lqw.2	P48729	OTTHUMG00000163463	ENST00000377843.2:c.145T>C	chr5.hg19:g.148929723A>G	ENSP00000367074:p.Ser49Pro	65.0	0.0		79.0	11.0	NM_001025105	D3DQG0|D3DQG1|Q4JJA0|Q5U046|Q5U047|Q6FGA2|Q71TU5|Q96HD2|Q9UDK3	Missense_Mutation	SNP	ENST00000377843.2	hg19	CCDS47303.1	.	.	.	.	.	.	.	.	.	.	A	17.53	3.411939	0.62511	.	.	ENSG00000113712	ENST00000261798;ENST00000377843;ENST00000322237;ENST00000515768;ENST00000515748	T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19	5.35	5.35	0.76521	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	U	0.000001	T	0.49270	0.1547	N	0.16602	0.42	0.80722	D	1	B;B;B	0.19445	0.001;0.013;0.036	B;B;B	0.26310	0.013;0.068;0.059	T	0.44651	-0.9314	10	0.39692	T	0.17	.	15.36	0.74464	1.0:0.0:0.0:0.0	.	49;49;49	Q71TU5;P48729;P48729-2	.;KC1A_HUMAN;.	P	49	ENSP00000261798:S49P;ENSP00000367074:S49P;ENSP00000421689:S49P;ENSP00000421268:S49P	ENSP00000261798:S49P	S	-	1	0	CSNK1A1	148909916	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	8.973000	0.93428	2.026000	0.59711	0.459000	0.35465	TCT	.	.		0.517	CSNK1A1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001892		G	148929723	A	G	148929723	3	3	352	1	0	0	0	0	1	0	0	0	3952	333	12	2	992	2	CSNK1A1	5	148929723	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	8303835	148929723	31985537	137	49553										
PPARGC1B	133522	hgsc.bcm.edu	37	chr5	149219652	149219652	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agaacgccaagcatccggcaCgccaggaagcggcgggaaaa	14	12	0	1	rs566927619		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr5:149219652C>T	ENST00000309241.5	+	9	2699	c.2667C>T	c.(2665-2667)caC>caT	p.H889H	PPARGC1B_ENST00000394320.3_Silent_p.H889H|PPARGC1B_ENST00000403750.1_Silent_p.H825H|PPARGC1B_ENST00000360453.4_Silent_p.H850H	NM_133263.3	NP_573570.3	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 beta	889					actin filament organization (GO:0007015)|bone trabecula formation (GO:0060346)|cellular lipid metabolic process (GO:0044255)|cellular response to reactive oxygen species (GO:0034614)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone resorption (GO:0045780)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of phosphorylation (GO:0042327)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)|transcription from mitochondrial promoter (GO:0006390)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AF-2 domain binding (GO:0050682)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|receptor activator activity (GO:0030546)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(2)|lung(15)|ovary(3)|prostate(2)|stomach(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			GCATCCGGCACGCCAGGAAGC	0.582													C|||	1	0.000199681	0	0	5008	,	,		19045	0		0	False		,,,				2504	0.001				p.H889H		Atlas-SNP	.											.	PPARGC1B	74	.	0			c.C2667T						.						61	56	58					5																	149219652		2203	4300	6503	SO:0001819	synonymous_variant	133522	exon9			CCGGCACGCCAGG	AF468496	CCDS4298.1, CCDS54933.1, CCDS54934.1	5q33.1	2013-02-12	2006-10-17		ENSG00000155846	ENSG00000155846		"RNA binding motif (RRM) containing"	30022	protein-coding gene	gene with protein product		608886	"peroxisome proliferative activated receptor, gamma, coactivator 1, beta"			11793024, 11854298	Standard	NM_133263		Approved	PERC, PGC1B	uc003lrc.3	Q86YN6	OTTHUMG00000130055	ENST00000309241.5:c.2667C>T	chr5.hg19:g.149219652C>T		68.0	0.0		89.0	23.0	NM_133263	A2RUM8|A2RUN0|B3KVW0|Q86YN3|Q86YN4|Q86YN5|Q8N1N9|Q8TDE4|Q8TDE5	Silent	SNP	ENST00000309241.5	hg19	CCDS4298.1	.	.	.	.	.	.	.	.	.	.	C	7.591	0.670805	0.14776	.	.	ENSG00000155846	ENST00000434684	.	.	.	5.05	-10.1	0.00402	.	.	.	.	.	T	0.35941	0.0949	.	.	.	0.28343	N	0.921242	.	.	.	.	.	.	T	0.42310	-0.9459	4	.	.	.	-4.1421	13.7315	0.62789	0.0:0.1706:0.1338:0.6957	.	.	.	.	C	576	.	.	R	+	1	0	PPARGC1B	149199845	0.000000	0.05858	0.136000	0.22124	0.973000	0.67179	-3.459000	0.00464	-2.092000	0.00857	-0.379000	0.06801	CGC	.	.		0.582	PPARGC1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252334.1	NM_133263		T	149219652	C	T	149219652	2	4	352	1	0	0	0	0	0	0	0	1	12310	535	19	1		1	PPARGC1B	5	149219652	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	289929	149219652	31695608	138	49554										
PDE6A	5145	hgsc.bcm.edu	37	chr5	149262997	149262997	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cccatcccaactcacataacGatttccttccgtgtctgctc	4	17	2	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr5:149262997G>A	ENST00000255266.5	-	17	2249	c.2130C>T	c.(2128-2130)atC>atT	p.I710I		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	710					cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	44			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Caffeine(DB00201)	CTCACATAACGATTTCCTTCC	0.488																																					p.I710I		Atlas-SNP	.											.	PDE6A	98	.	0			c.C2130T						.						238	166	191					5																	149262997		2203	4300	6503	SO:0001819	synonymous_variant	5145	exon17			CATAACGATTTCC		CCDS4299.1	5q31.2-q34	2013-02-14			ENSG00000132915	ENSG00000132915	3.1.4.17	"Phosphodiesterases"	8785	protein-coding gene	gene with protein product		180071		PDEA		2155175	Standard	NM_000440		Approved	RP43	uc003lrg.4	P16499	OTTHUMG00000130047	ENST00000255266.5:c.2130C>T	chr5.hg19:g.149262997G>A		99.0	0.0		104.0	34.0	NM_000440	Q0P638	Silent	SNP	ENST00000255266.5	hg19	CCDS4299.1																																																																																			.	.		0.488	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2			A	149262997	G	A	149262997	2	1	352	1	0	0	0	0	0	0	0	1	11654	1048	37	1		1	PDE6A	5	149262997	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	43345	149262997	31652263	139	49555										
CCNG1	900	hgsc.bcm.edu	37	chr5	162869465	162869465	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aaataagtgttccaaaccaaAtgttcagaagttgaaatgga	8	5	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr5:162869465A>C	ENST00000340828.2	+	6	1006	c.782A>C	c.(781-783)aAt>aCt	p.N261T	CCNG1_ENST00000510664.1_Missense_Mutation_p.N133T|CCNG1_ENST00000393929.1_Missense_Mutation_p.N261T|CCNG1_ENST00000504553.1_Intron|CCNG1_ENST00000512163.1_Missense_Mutation_p.N127T|CCNG1_ENST00000511683.2_Missense_Mutation_p.N127T|AC112205.1_ENST00000599797.1_Intron	NM_004060.3	NP_004051.1	P51959	CCNG1_HUMAN	cyclin G1	261					brain development (GO:0007420)|cell growth (GO:0016049)|mitotic G2 DNA damage checkpoint (GO:0007095)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|response to organonitrogen compound (GO:0010243)|syncytium formation (GO:0006949)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(2)	12	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0597)|OV - Ovarian serous cystadenocarcinoma(192;0.107)|Epithelial(171;0.164)		TCCAAACCAAATGTTCAGAAG	0.378																																					p.N261T		Atlas-SNP	.											.	CCNG1	28	.	0			c.A782C						.						117	116	116					5																	162869465		2203	4300	6503	SO:0001583	missense	900	exon7			AACCAAATGTTCA	D78341	CCDS4360.1	5q32-q34	2010-11-15			ENSG00000113328	ENSG00000113328			1592	protein-coding gene	gene with protein product		601578		CCNG		8954786, 8806701	Standard	NM_004060		Approved		uc003lzb.3	P51959	OTTHUMG00000130380	ENST00000340828.2:c.782A>C	chr5.hg19:g.162869465A>C	ENSP00000344635:p.Asn261Thr	131.0	0.0		148.0	35.0	NM_199246	B2R7B2|B4DLW7|D3DQK7|Q15757|Q96L32	Missense_Mutation	SNP	ENST00000340828.2	hg19	CCDS4360.1	.	.	.	.	.	.	.	.	.	.	A	19.04	3.750760	0.69533	.	.	ENSG00000113328	ENST00000512163;ENST00000393929;ENST00000340828;ENST00000511683;ENST00000510664	T;T;T;T;T	0.33654	1.4;1.4;1.4;1.4;1.4	5.79	5.79	0.91817	.	0.042274	0.85682	D	0.000000	T	0.35770	0.0943	L	0.46157	1.445	0.80722	D	1	P	0.48294	0.908	B	0.41374	0.355	T	0.20974	-1.0259	10	0.56958	D	0.05	6.1324	16.1376	0.81497	1.0:0.0:0.0:0.0	.	261	P51959	CCNG1_HUMAN	T	127;261;261;127;133	ENSP00000424315:N127T;ENSP00000377506:N261T;ENSP00000344635:N261T;ENSP00000424141:N127T;ENSP00000422379:N133T	ENSP00000344635:N261T	N	+	2	0	CCNG1	162802043	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.360000	0.66086	2.212000	0.71576	0.533000	0.62120	AAT	.	.		0.378	CCNG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252750.3	NM_004060		C	162869465	A	C	162869465	3	2	352	1	0	0	0	0	1	0	0	0	2925	101	4	5	800	5	CCNG1	5	162869465	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	13606468	162869465	18045795	140	49556										
ODZ2	57451	hgsc.bcm.edu	37	chr5	167626887	167626887	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aggttcttcatgaagaaatcGagctccctggttccaatgtg	10	9	2	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr5:167626887G>A	ENST00000518659.1	+	17	3220	c.3181G>A	c.(3181-3183)Gag>Aag	p.E1061K	TENM2_ENST00000519204.1_Missense_Mutation_p.E940K|TENM2_ENST00000520394.1_Missense_Mutation_p.E829K|TENM2_ENST00000403607.2_Missense_Mutation_p.E885K|TENM2_ENST00000545108.1_Missense_Mutation_p.E1061K	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	1061					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										TGAAGAAATCGAGCTCCCTGG	0.493																																					p.E1052K		Atlas-SNP	.											ODZ2_ENST00000519204,NS,carcinoma,-1,3	.	.	.	0			c.G3154A						.						165	159	161					5																	167626887		1934	4150	6084	SO:0001583	missense	57451	exon17			GAAATCGAGCTCC	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"odz, odd Oz/ten-m homolog 2 (Drosophila)"	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.3181G>A	chr5.hg19:g.167626887G>A	ENSP00000429430:p.Glu1061Lys	57.0	0.0		82.0	11.0	NM_001122679	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	hg19		.	.	.	.	.	.	.	.	.	.	G	10.77	1.444277	0.25987	.	.	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	D;D;D;D;D	0.89196	-2.01;-2.0;-2.11;-2.47;-2.48	5.05	5.05	0.67936	.	0.199119	0.52532	D	0.000078	D	0.91616	0.7351	L	0.40543	1.245	0.49483	D	0.999793	B;B;D	0.71674	0.331;0.223;0.998	B;B;D	0.73380	0.036;0.016;0.98	D	0.90017	0.4125	10	0.28530	T	0.3	.	18.4354	0.90643	0.0:0.0:1.0:0.0	.	1061;1061;829	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	K	1061;1061;940;829;885	ENSP00000429430:E1061K;ENSP00000438635:E1061K;ENSP00000428964:E940K;ENSP00000427874:E829K;ENSP00000384905:E885K	ENSP00000384905:E885K	E	+	1	0	ODZ2	167559465	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	8.031000	0.88826	2.338000	0.79540	0.561000	0.74099	GAG	.	.		0.493	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		A	167626887	G	A	167626887	3	1	352	1	0	0	0	0	1	0	0	0	10844	1059	37	1	3220	1	ODZ2	5	167626887	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	4757422	167626887	13288373	141	49557										
FGFR4	2264	hgsc.bcm.edu	37	chr5	176518089	176518089	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggcctttcatggggagaaccGcattggaggcattcgggtga	16	8	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr5:176518089G>A	ENST00000292408.4	+	5	832	c.587G>A	c.(586-588)cGc>cAc	p.R196H	FGFR4_ENST00000393637.1_Missense_Mutation_p.R196H|FGFR4_ENST00000502906.1_Missense_Mutation_p.R196H|FGFR4_ENST00000393648.2_Missense_Mutation_p.R196H|FGFR4_ENST00000292410.3_Missense_Mutation_p.R196H	NM_002011.3|NM_213647.1	NP_002002.3|NP_998812.1	P22455	FGFR4_HUMAN	fibroblast growth factor receptor 4	196	Ig-like C2-type 2.				alveolar secondary septum development (GO:0061144)|cell migration (GO:0016477)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphate ion homeostasis (GO:0055062)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of proteolysis (GO:0045862)|protein autophosphorylation (GO:0046777)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cholesterol homeostasis (GO:2000188)|regulation of extracellular matrix disassembly (GO:0010715)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	34	all_cancers(89;5.93e-05)|Renal(175;0.000269)|Lung NSC(126;0.0088)|all_lung(126;0.0142)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Palifermin(DB00039)|Ponatinib(DB08901)	GGGGAGAACCGCATTGGAGGC	0.562										TSP Lung(9;0.080)																											p.R196H		Atlas-SNP	.											.	FGFR4	174	.	0			c.G587A						.						68	63	64					5																	176518089		2203	4300	6503	SO:0001583	missense	2264	exon4			AGAACCGCATTGG	AF202063	CCDS4410.1, CCDS4411.1	5q35.2	2013-09-19			ENSG00000160867	ENSG00000160867		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3691	protein-coding gene	gene with protein product		134935					Standard	XM_005265837		Approved	JTK2, CD334	uc003mfm.3	P22455	OTTHUMG00000151523	ENST00000292408.4:c.587G>A	chr5.hg19:g.176518089G>A	ENSP00000292408:p.Arg196His	85.0	0.0		83.0	21.0	NM_022963	G3JVM2|G3JVM5|G3JVM7|G3JVM9|O43785|Q14309|Q71TW8|Q8TDA0|Q96KE5	Missense_Mutation	SNP	ENST00000292408.4	hg19	CCDS4410.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.699222	0.88830	.	.	ENSG00000160867	ENST00000292408;ENST00000503708;ENST00000393648;ENST00000502906;ENST00000292410;ENST00000393637;ENST00000377207	T;T;T;T;T;T	0.72051	1.19;-0.62;1.19;1.19;1.19;1.19	4.74	4.74	0.60224	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.84889	0.5572	M	0.79805	2.47	0.51233	D	0.999919	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.996;0.999	D	0.87125	0.2193	10	0.72032	D	0.01	.	17.5207	0.87786	0.0:0.0:1.0:0.0	.	196;196;196;196	B5A965;B4DVP5;P22455-2;P22455	.;.;.;FGFR4_HUMAN	H	196;196;196;196;196;196;308	ENSP00000292408:R196H;ENSP00000424905:R196H;ENSP00000377259:R196H;ENSP00000424960:R196H;ENSP00000292410:R196H;ENSP00000377254:R196H	ENSP00000292408:R196H	R	+	2	0	FGFR4	176450695	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.569000	0.98170	2.470000	0.83445	0.561000	0.74099	CGC	.	.		0.562	FGFR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253410.1			A	176518089	G	A	176518089	3	1	352	1	0	0	0	0	1	0	0	0	5876	1087	38	1	601	1	FGFR4	5	176518089	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	8891202	176518089	4397171	142	49558										
PDLIM7	9260	hgsc.bcm.edu	37	chr5	176916601	176916601	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggtccacagcccagggcgggCggctggtagggctgggggcg	22	11	0	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr5:176916601C>T	ENST00000355841.2	-	9	728	c.662G>A	c.(661-663)cGc>cAc	p.R221H	PDLIM7_ENST00000356618.4_Silent_p.P200P|PDLIM7_ENST00000393551.1_Silent_p.P200P|PDLIM7_ENST00000359895.2_Missense_Mutation_p.R187H	NM_005451.3	NP_005442.2	Q9NR12	PDLI7_HUMAN	PDZ and LIM domain 7 (enigma)	221					actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of osteoblast differentiation (GO:0045669)|receptor-mediated endocytosis (GO:0006898)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ruffle (GO:0001726)|stress fiber (GO:0001725)	zinc ion binding (GO:0008270)	p.R221H(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	10	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCAGGGCGGGCGGCTGGTAGG	0.711																																					p.R221H		Atlas-SNP	.											PDLIM7,NS,haematopoietic_neoplasm,0,1	PDLIM7	32	.	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G662A						.						10	14	13					5																	176916601		2188	4272	6460	SO:0001583	missense	9260	exon9			GGCGGGCGGCTGG	BC001093	CCDS4422.1, CCDS4423.1, CCDS4424.1	5q35.3	2008-02-05			ENSG00000196923	ENSG00000196923			22958	protein-coding gene	gene with protein product		605903				11874232	Standard	NM_005451		Approved	ENIGMA	uc003mhc.1	Q9NR12	OTTHUMG00000130853	ENST00000355841.2:c.662G>A	chr5.hg19:g.176916601C>T	ENSP00000348099:p.Arg221His	66.0	0.0		98.0	33.0	NM_005451	Q14250|Q5XG82|Q6NVZ5|Q96C91|Q9BXB8|Q9BXB9	Missense_Mutation	SNP	ENST00000355841.2	hg19	CCDS4422.1	.	.	.	.	.	.	.	.	.	.	C	17.02	3.282994	0.59867	.	.	ENSG00000196923	ENST00000359895;ENST00000355841	T;T	0.52526	0.76;0.66	5.23	5.23	0.72850	.	0.085883	0.44285	N	0.000467	T	0.45316	0.1336	M	0.68317	2.08	0.80722	D	1	B;P	0.35192	0.358;0.489	B;B	0.26094	0.04;0.066	T	0.49952	-0.8884	10	0.48119	T	0.1	.	15.9056	0.79427	0.0:0.8649:0.1351:0.0	.	221;187	Q9NR12;Q9NR12-2	PDLI7_HUMAN;.	H	187;221	ENSP00000352964:R187H;ENSP00000348099:R221H	ENSP00000348099:R221H	R	-	2	0	PDLIM7	176849207	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	7.660000	0.83776	2.431000	0.82371	0.555000	0.69702	CGC	.	.		0.711	PDLIM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253423.1	NM_005451		T	176916601	C	T	176916601	3	4	352	1	0	0	0	0	1	0	0	0	11693	768	27	1	731	1	PDLIM7	5	176916601	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	398512	176916601	3998659	143	49559										
N4BP3	23138	hgsc.bcm.edu	37	chr5	177548875	177548875	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gaaggagcgcgtgctgcgctAccagcgggagatccagggag	18	10	0	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr5:177548875A>G	ENST00000274605.5	+	5	1867	c.1508A>G	c.(1507-1509)tAc>tGc	p.Y503C		NM_015111.1	NP_055926.1	O15049	N4BP3_HUMAN	NEDD4 binding protein 3	503						cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)				breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(1)|skin(1)	9	all_cancers(89;0.00294)|Renal(175;0.000269)|Lung NSC(126;0.00858)|all_lung(126;0.0139)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GTGCTGCGCTACCAGCGGGAG	0.677																																					p.Y503C		Atlas-SNP	.											.	N4BP3	25	.	0			c.A1508G						.						15	20	18					5																	177548875		2200	4294	6494	SO:0001583	missense	23138	exon5			TGCGCTACCAGCG	AB002339	CCDS34307.1	5q35.3	2012-05-17				ENSG00000145911			29852	protein-coding gene	gene with protein product						9205841, 11717310	Standard	XM_006714834		Approved	LZTS4	uc003mik.1	O15049		ENST00000274605.5:c.1508A>G	chr5.hg19:g.177548875A>G	ENSP00000274605:p.Tyr503Cys	67.0	0.0		80.0	8.0	NM_015111	B4DIL3|D3DWP3|Q6ZSQ6|Q7Z6I3	Missense_Mutation	SNP	ENST00000274605.5	hg19	CCDS34307.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.386752	0.82902	.	.	ENSG00000145911	ENST00000274605	T	0.64618	-0.11	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.78898	0.4356	M	0.78916	2.43	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.81607	-0.0856	10	0.72032	D	0.01	-19.9832	13.6226	0.62146	1.0:0.0:0.0:0.0	.	503	O15049	N4BP3_HUMAN	C	503	ENSP00000274605:Y503C	ENSP00000274605:Y503C	Y	+	2	0	N4BP3	177481481	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.311000	0.96282	2.115000	0.64714	0.379000	0.24179	TAC	.	.		0.677	N4BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373552.2	NM_015111		G	177548875	A	G	177548875	3	3	352	1	0	0	0	0	1	0	0	0	10122	391	14	2	1522	2	N4BP3	5	177548875	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	632274	177548875	3366385	144	49560										
COL23A1	91522	hgsc.bcm.edu	37	chr5	177669109	177669109	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tggcccttcactcctttccgGccggggacccctcgttctcc	9	19	2	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr5:177669109G>C	ENST00000390654.3	-	27	1872	c.1515C>G	c.(1513-1515)ggC>ggG	p.G505G		NM_173465.3	NP_775736.2	Q86Y22	CONA1_HUMAN	collagen, type XXIII, alpha 1	505	Collagen-like 5.|Gly-rich.				collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	19	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)		CTCCTTTCCGGCCGGGGACCC	0.652																																					p.G505G		Atlas-SNP	.											.	COL23A1	47	.	0			c.C1515G						.						16	20	18					5																	177669109		1910	4073	5983	SO:0001819	synonymous_variant	91522	exon27			TTTCCGGCCGGGG	AL137461	CCDS4436.1	5q35.3	2013-01-16			ENSG00000050767	ENSG00000050767		"Collagens"	22990	protein-coding gene	gene with protein product		610043				12644459	Standard	NM_173465		Approved	DKFZp434K0621	uc021yiz.1	Q86Y22	OTTHUMG00000130890	ENST00000390654.3:c.1515C>G	chr5.hg19:g.177669109G>C		97.0	0.0		97.0	32.0	NM_173465	Q8IVR4|Q9NT93	Silent	SNP	ENST00000390654.3	hg19	CCDS4436.1																																																																																			.	.		0.652	COL23A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253475.1	NM_173465		C	177669109	G	C	177669109	2	2	352	1	0	0	0	0	0	0	0	1	3684	1190	42	4		4	COL23A1	5	177669109	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	120234	177669109	3246151	145	49561										
C6orf146	222826	hgsc.bcm.edu	37	chr6	4069257	4069259	+	In_Frame_Del	DEL	ATC	ATC	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	atagaacttttgggattcttAtcataagtttcaatcaattg							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	ATC	ATC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr6:4069257_4069259delATC	ENST00000274673.3	-	7	1601_1603	c.1198_1200delGAT	c.(1198-1200)gatdel	p.D400del	FAM217A_ENST00000380188.2_5'UTR	NM_173563.2	NP_775834.2	Q8IXS0	F217A_HUMAN	family with sequence similarity 217, member A	400																	TGGGATTCTTATCATAAGTTTCA	0.35																																					p.400_401del		Atlas-INDEL	.											.	.	.	.	0			c.1199_1201del						.																																			SO:0001651	inframe_deletion	222826	exon7			.	BC039349	CCDS4489.1	6p25.1	2012-02-07	2012-02-07	2012-02-07	ENSG00000145975	ENSG00000145975			21362	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 146"	C6orf146			Standard	NM_173563		Approved	MGC43581	uc003mvx.3	Q8IXS0	OTTHUMG00000014159	ENST00000274673.3:c.1198_1200delGAT	chr6.hg19:g.4069257_4069259delATC	ENSP00000274673:p.Asp400del	135.0	0.0		177.0	32.0	NM_173563	Q5JYK1	In_Frame_Del	DEL	ENST00000274673.3	hg19	CCDS4489.1																																																																																			.	.		0.35	FAM217A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352577.2	NM_173563		-	4069259	ATC	-	4069257	7	5	352	1	0	1	0	1	0	0	0	0	2337	446	16	0	330	0	C6orf146	6	4069257	In_Frame_Del	DEL	ATC	TCGA-WQ-A9G7-01A-11D-A36X-10		4069257	167045810	146	49562										
HIVEP1	3096	hgsc.bcm.edu	37	chr6	12124209	12124209	+	Frame_Shift_Del	DEL	C	C	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	attcgattgtggaagcatcaCcccaccccagacaacaccac							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr6:12124209delC	ENST00000379388.2	+	4	4513	c.4181delC	c.(4180-4182)accfs	p.T1394fs	HIVEP1_ENST00000541134.1_5'Flank	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	1394					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				GGAAGCATCACCCCACCCCAG	0.498																																					p.T1394fs		Atlas-INDEL	.											.	HIVEP1	242	.	0			c.4180delA						.						133	136	135					6																	12124209		2074	4205	6279	SO:0001589	frameshift_variant	3096	exon4			.	J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"Zinc fingers, C2H2-type"	4920	protein-coding gene	gene with protein product		194540	"human immunodeficiency virus type I enhancer-binding protein 1", "zinc finger protein 40"	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.4181delC	chr6.hg19:g.12124209delC	ENSP00000368698:p.Thr1394fs	119.0	0.0		141.0	25.0	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Frame_Shift_Del	DEL	ENST00000379388.2	hg19	CCDS43426.1																																																																																			.	.		0.498	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114		-	12124209	C	-	12124209	7	5	352	1	0	1	0	1	0	0	0	0	7195	507	18	0	4191	0	HIVEP1	6	12124209	Frame_Shift_Del	DEL	C	TCGA-WQ-A9G7-01A-11D-A36X-10	8054952	12124209	158990858	147	49563										
NUP153	9972	hgsc.bcm.edu	37	chr6	17629463	17629463	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gttaaagaaactgggttgctTaaaccagaagaaagtccaaa	9	6	0	3			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr6:17629463T>C	ENST00000262077.2	-	18	2966	c.2967A>G	c.(2965-2967)ttA>ttG	p.L989L	NUP153_ENST00000537253.1_Silent_p.L1020L	NM_005124.2	NP_005115.2	P49790	NU153_HUMAN	nucleoporin 153kDa	989					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of RNA export from nucleus (GO:0046832)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)|viral penetration into host nucleus (GO:0075732)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleocytoplasmic transporter activity (GO:0005487)|protein anchor (GO:0043495)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			NS(2)|breast(6)|endometrium(4)|kidney(3)|large_intestine(7)|lung(23)|ovary(3)|skin(3)|urinary_tract(2)	53	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.125)	all cancers(50;0.0981)|Epithelial(50;0.112)			CTGGGTTGCTTAAACCAGAAG	0.343																																					p.L989L		Atlas-SNP	.											.	NUP153	116	.	0			c.A2967G						.						46	49	48					6																	17629463		2199	4300	6499	SO:0001819	synonymous_variant	9972	exon18			GTTGCTTAAACCA	Z25535	CCDS4541.1, CCDS64359.1, CCDS75407.1	6p22.3	2008-07-29	2002-08-29		ENSG00000124789	ENSG00000124789			8062	protein-coding gene	gene with protein product		603948	"nucleoporin 153kD"			8110839	Standard	NM_001278209		Approved	HNUP153	uc003ncd.2	P49790	OTTHUMG00000014312	ENST00000262077.2:c.2967A>G	chr6.hg19:g.17629463T>C		175.0	0.0		196.0	63.0	NM_005124	B4DIK2|E7EPX5|F6QR24|Q4LE47|Q5T9I7|Q7Z743	Silent	SNP	ENST00000262077.2	hg19	CCDS4541.1																																																																																			.	.		0.343	NUP153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039953.1			C	17629463	T	C	17629463	2	2	352	1	0	0	0	0	0	0	0	1	10764	1751	61	2		2	NUP153	6	17629463	Silent	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	5505254	17629463	153485604	148	49564										
FAM65B	9750	hgsc.bcm.edu	37	chr6	24850823	24850823	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	acaggcaatgacaatactgtAccttgatggagatgaaccca	9	9	0	4			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr6:24850823A>G	ENST00000259698.4	-	10	974		c.e10+1		FAM65B_ENST00000378023.4_Splice_Site|FAM65B_ENST00000538035.1_Splice_Site|FAM65B_ENST00000540914.1_Splice_Site|FAM65B_ENST00000510784.2_Splice_Site	NM_014722.2	NP_055537.2	Q9Y4F9	FA65B_HUMAN	family with sequence similarity 65, member B						cell differentiation (GO:0030154)|muscle organ development (GO:0007517)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	25						ACAATACTGTACCTTGATGGA	0.507																																					.		Atlas-SNP	.											.	FAM65B	134	.	0			c.798+2T>C						.						121	129	126					6																	24850823		2040	4196	6236	SO:0001630	splice_region_variant	9750	exon11			TACTGTACCTTGA	U49187	CCDS47383.1, CCDS47384.1, CCDS69057.1, CCDS69058.1, CCDS75410.1	6p22.3-p21.32	2012-11-30	2008-06-13	2008-06-13	ENSG00000111913	ENSG00000111913			13872	protein-coding gene	gene with protein product	"myogenesis-related and NCAM-associated protein homolog (chicken)"	611410	"chromosome 6 open reading frame 32"	C6orf32		9205841, 17150207, 17825087	Standard	NM_001286447		Approved	KIAA0386, DIFF48, MYONAP	uc003neo.1	Q9Y4F9	OTTHUMG00000014375	ENST00000259698.4:c.798+1T>C	chr6.hg19:g.24850823A>G		59.0	0.0		66.0	8.0	NM_014722	A6NHP2|Q13529|Q5VV37|Q5VV38|Q9BQ28	Splice_Site	SNP	ENST00000259698.4	hg19	CCDS47383.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.523496	0.85600	.	.	ENSG00000111913	ENST00000259698;ENST00000538035;ENST00000378023;ENST00000540914;ENST00000510784	.	.	.	5.34	5.34	0.76211	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.5984	0.76606	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	FAM65B	24958802	1.000000	0.71417	0.963000	0.40424	0.965000	0.64279	8.962000	0.93254	2.139000	0.66308	0.454000	0.30748	.	.	.		0.507	FAM65B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040024.2		Intron	G	24850823	A	G	24850823	5	3	352	1	0	0	0	0	0	0	1	0	5608	405	14	2	2472	2	FAM65B	6	24850823	Splice_Site	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	7221360	24850823	146264244	149	49565										
HIST1H2BF	8343	hgsc.bcm.edu	37	chr6	26199792	26199792	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aagtgtttatttatcatgccTgaacctgctaagtccgctcc	7	11	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr6:26199792T>C	ENST00000359985.1	+	1	45	c.6T>C	c.(4-6)ccT>ccC	p.P2P	HIST1H3D_ENST00000377831.5_5'Flank|HIST1H2AD_ENST00000341023.1_5'Flank|HIST1H3D_ENST00000356476.2_5'Flank	NM_003522.3	NP_003513.1	P62807	H2B1C_HUMAN	histone cluster 1, H2bf	2					antibacterial humoral response (GO:0019731)|chromatin organization (GO:0006325)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|nucleosome assembly (GO:0006334)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|liver(2)|lung(7)|upper_aerodigestive_tract(3)	17		all_hematologic(11;0.196)				TTATCATGCCTGAACCTGCTA	0.488																																					p.P2P		Atlas-SNP	.											.	HIST1H2BF	25	.	0			c.T6C						.						85	83	84					6																	26199792		2203	4300	6503	SO:0001819	synonymous_variant	8343	exon1			CATGCCTGAACCT	Z80779	CCDS4592.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000197846	ENSG00000277224		"Histones / Replication-dependent"	4752	protein-coding gene	gene with protein product		602804	"H2B histone family, member G", "histone 1, H2bf"	H2BFG		9119399, 12408966	Standard	NM_003522		Approved	H2B/g	uc003ngx.3	P62807	OTTHUMG00000014445	ENST00000359985.1:c.6T>C	chr6.hg19:g.26199792T>C		106.0	0.0		121.0	15.0	NM_003522	P02278|Q3B872|Q4VB69|Q93078|Q93080	Silent	SNP	ENST00000359985.1	hg19	CCDS4592.1																																																																																			.	.		0.488	HIST1H2BF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040108.1	NM_003522		C	26199792	T	C	26199792	2	2	352	1	0	0	0	0	0	0	0	1	7154	1567	55	2		2	HIST1H2BF	6	26199792	Silent	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	1348969	26199792	144915275	150	49566										
ZSCAN16	80345	hgsc.bcm.edu	37	chr6	28097499	28097499	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tgatgagtgtggaaaagcctTcattcagcgctcacatctca	9	10	4	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr6:28097499T>C	ENST00000340487.4	+	4	967	c.818T>C	c.(817-819)tTc>tCc	p.F273S	ZSCAN16-AS1_ENST00000602810.1_RNA|ZSCAN16-AS1_ENST00000600652.1_RNA	NM_025231.1	NP_079507.1	Q9H4T2	ZSC16_HUMAN	zinc finger and SCAN domain containing 16	273					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(5)|liver(1)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10						GGAAAAGCCTTCATTCAGCGC	0.443																																					p.F273S		Atlas-SNP	.											.	ZSCAN16	24	.	0			c.T818C						.						85	83	84					6																	28097499		2203	4300	6503	SO:0001583	missense	80345	exon4			AAGCCTTCATTCA	AK025844	CCDS4644.1	6p21.33	2013-01-08	2007-02-20	2007-02-20	ENSG00000196812	ENSG00000196812		"-", "Zinc fingers, C2H2-type"	20813	protein-coding gene	gene with protein product			"zinc finger protein 392", "zinc finger protein 435"	ZNF392, ZNF435			Standard	NM_025231		Approved	FLJ22191, dJ265C24.3	uc003nkm.3	Q9H4T2	OTTHUMG00000014509	ENST00000340487.4:c.818T>C	chr6.hg19:g.28097499T>C	ENSP00000366527:p.Phe273Ser	92.0	0.0		111.0	10.0	NM_025231	Q9H6K2	Missense_Mutation	SNP	ENST00000340487.4	hg19	CCDS4644.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.707692	0.89018	.	.	ENSG00000196812	ENST00000340487	T	0.44482	0.92	5.08	5.08	0.68730	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.36338	N	0.002645	T	0.63022	0.2476	M	0.89353	3.025	0.45594	D	0.998535	D	0.89917	1.0	D	0.97110	1.0	T	0.72340	-0.4323	10	0.87932	D	0	.	13.8354	0.63406	0.0:0.0:0.0:1.0	.	273	Q9H4T2	ZSC16_HUMAN	S	273	ENSP00000366527:F273S	ENSP00000366527:F273S	F	+	2	0	ZSCAN16	28205478	1.000000	0.71417	0.971000	0.41717	0.999000	0.98932	5.718000	0.68455	1.922000	0.55676	0.533000	0.62120	TTC	.	.		0.443	ZSCAN16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040177.1	NM_025231		C	28097499	T	C	28097499	3	2	352	1	0	0	0	0	1	0	0	0	18244	1783	62	2	828	2	ZSCAN16	6	28097499	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	1897707	28097499	143017568	151	49567										
UBD	10537	hgsc.bcm.edu	37	chr6	29523920	29523920	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	atcactgggcttcaccacttTcagggtaaggtggatggtct	12	9	4	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr6:29523920T>A	ENST00000377050.4	-	2	458	c.235A>T	c.(235-237)Aaa>Taa	p.K79*	GABBR1_ENST00000355973.3_3'UTR	NM_006398.3	NP_006389.2	O15205	UBD_HUMAN	ubiquitin D	79	Ubiquitin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00214}.				aggresome assembly (GO:0070842)|myeloid dendritic cell differentiation (GO:0043011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein modification by small protein conjugation (GO:0032446)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|response to interferon-gamma (GO:0034341)|response to organonitrogen compound (GO:0010243)|response to tumor necrosis factor (GO:0034612)|ubiquitin-dependent protein catabolic process (GO:0006511)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	proteasome binding (GO:0070628)			kidney(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						TTCACCACTTTCAGGGTAAGG	0.527																																					p.K79X		Atlas-SNP	.											.	UBD	13	.	0			c.A235T						.						65	69	68					6																	29523920		1510	2709	4219	SO:0001587	stop_gained	10537	exon2			CCACTTTCAGGGT	Y12653	CCDS4662.1	6p21.3	2008-04-11			ENSG00000213886	ENSG00000213886			18795	protein-coding gene	gene with protein product		606050				9368598, 8662070	Standard	NM_006398		Approved	FAT10	uc003nmo.3	O15205	OTTHUMG00000031289	ENST00000377050.4:c.235A>T	chr6.hg19:g.29523920T>A	ENSP00000366249:p.Lys79*	193.0	0.0		218.0	52.0	NM_006398	B0UZT6|Q5STL2|Q5SUK2|Q96EC7	Nonsense_Mutation	SNP	ENST00000377050.4	hg19	CCDS4662.1	.	.	.	.	.	.	.	.	.	.	T	36	5.640803	0.96693	.	.	ENSG00000213886	ENST00000377050	.	.	.	5.16	3.97	0.46021	.	0.000000	0.38164	U	0.001782	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.22706	T	0.39	-19.6413	9.032	0.36264	0.0:0.0:0.1864:0.8136	.	.	.	.	X	79	.	ENSP00000366249:K79X	K	-	1	0	UBD	29631899	1.000000	0.71417	0.998000	0.56505	0.823000	0.46562	3.262000	0.51538	0.768000	0.33290	0.496000	0.49642	AAA	.	.		0.527	UBD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076628.3			A	29523920	T	A	29523920	4	1	352	1	0	0	0	0	0	1	0	0	16858	1792	62	4	266	4	UBD	6	29523920	Nonsense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	1426421	29523920	141591147	152	49568										
DDR1	780	hgsc.bcm.edu	37	chr6	30863232	30863232	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ccttctggccacttacgcccGtccccctcgaggcccgggcc	10	21	1	0	rs145280414		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr6:30863232G>A	ENST00000324771.8	+	14	2113	c.1565G>A	c.(1564-1566)cGt>cAt	p.R522H	DDR1_ENST00000452441.1_Missense_Mutation_p.R522H|DDR1_ENST00000508312.1_Intron|DDR1_ENST00000376575.3_Missense_Mutation_p.R522H|DDR1_ENST00000376567.2_Intron|DDR1_ENST00000376570.4_Intron|DDR1_ENST00000446312.1_Intron|DDR1_ENST00000361741.4_Missense_Mutation_p.V226I|DDR1_ENST00000376569.3_Intron|DDR1_ENST00000454612.2_Intron|DDR1_ENST00000418800.2_Intron|DDR1_ENST00000513240.1_Missense_Mutation_p.R522H|DDR1_ENST00000376568.3_Missense_Mutation_p.R522H			Q08345	DDR1_HUMAN	discoidin domain receptor tyrosine kinase 1	522	Gly/Pro-rich.				branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|ear development (GO:0043583)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine autophosphorylation (GO:0038083)|protein autophosphorylation (GO:0046777)|regulation of cell growth (GO:0001558)|regulation of cell-matrix adhesion (GO:0001952)|regulation of extracellular matrix disassembly (GO:0010715)|smooth muscle cell migration (GO:0014909)|smooth muscle cell-matrix adhesion (GO:0061302)|wound healing, spreading of cells (GO:0044319)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.R522H(2)		central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(1)|prostate(1)|skin(1)	29					Imatinib(DB00619)	ACTTACGCCCGTCCCCCTCGA	0.677																																					p.R522H		Atlas-SNP	.											DDR1_ENST00000376575,caecum,carcinoma,0,4	DDR1	213	.	2	Substitution - Missense(2)	ovary(2)	c.G1565A						.	G	,,,,HIS/ARG,HIS/ARG	0,4406		0,0,2203	113	123	120		,,,,1565,1565	4.9	1	6	dbSNP_134	120	1,8599	1.2+/-3.3	0,1,4299	no	intron,intron,intron,intron,missense,missense	DDR1	NM_001202521.1,NM_001202522.1,NM_001202523.1,NM_001954.4,NM_013993.2,NM_013994.2	,,,,29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,,probably-damaging,probably-damaging	,,,,522/914,522/920	30863232	1,13005	2203	4300	6503	SO:0001583	missense	780	exon11			ACGCCCGTCCCCC	X99031	CCDS4690.1, CCDS34385.1, CCDS47396.1, CCDS56411.1, CCDS75419.1	6p21.33	2010-02-17	2008-01-23		ENSG00000204580	ENSG00000204580	2.7.10.1	"CD molecules"	2730	protein-coding gene	gene with protein product		600408	"discoidin domain receptor family, member 1"	NTRK4, PTK3A, NEP, CAK, EDDR1		7789998	Standard	NM_001954		Approved	RTK6, CD167	uc003nrv.3	Q08345	OTTHUMG00000031236	ENST00000324771.8:c.1565G>A	chr6.hg19:g.30863232G>A	ENSP00000318217:p.Arg522His	46.0	0.0		51.0	9.0	NM_013994	B5A975|B5A976|B7Z2K0|Q14196|Q16562|Q2L6H3|Q4LE50|Q5ST11|Q5ST12|Q6NSK4|Q9UD35|Q9UD36|Q9UD37|Q9UD86|Q9UDL2	Missense_Mutation	SNP	ENST00000324771.8	hg19	CCDS34385.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.32|18.32	3.598772|3.598772	0.66332|0.66332	0.0|0.0	1.16E-4|1.16E-4	ENSG00000204580|ENSG00000204580	ENST00000324771;ENST00000376575;ENST00000376568;ENST00000452441;ENST00000513240|ENST00000417521;ENST00000361741	D;D;D;D;D|T;T	0.85629|0.79554	-1.86;-2.01;-1.86;-1.86;-2.01|-1.21;-1.28	4.95|4.95	4.95|4.95	0.65309|0.65309	.|.	0.000000|.	0.64402|.	D|.	0.000001|.	T|T	0.49541|0.49541	0.1563|0.1563	N|N	0.19112|0.19112	0.55|0.55	0.18873|0.18873	N|N	0.999988|0.999988	D;D|B	0.71674|0.17852	0.998;0.974|0.024	P;B|B	0.58660|0.10450	0.843;0.32|0.005	T|T	0.26052|0.26052	-1.0114|-1.0114	10|9	0.46703|0.22109	T|T	0.11|0.4	.|.	10.9028|10.9028	0.47062|0.47062	0.0:0.0:0.8123:0.1876|0.0:0.0:0.8123:0.1876	.|.	522;522|291	Q08345-5;Q08345|A2ABM8	.;DDR1_HUMAN|.	H|I	522|291;226	ENSP00000318217:R522H;ENSP00000365759:R522H;ENSP00000365752:R522H;ENSP00000405039:R522H;ENSP00000427552:R522H|ENSP00000398682:V291I;ENSP00000354844:V226I	ENSP00000318217:R522H|ENSP00000354844:V226I	R|V	+|+	2|1	0|0	DDR1|DDR1	30971211|30971211	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	3.137000|3.137000	0.50562|0.50562	2.303000|2.303000	0.77524|0.77524	0.460000|0.460000	0.39030|0.39030	CGT|GTC	.	G|1.000;A|0.000		0.677	DDR1-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076494.3	NM_013994		A	30863232	G	A	30863232	3	1	352	1	0	0	0	0	1	0	0	0	4338	1145	40	1	1607	1	DDR1	6	30863232	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	1339312	30863232	140251835	153	49569										
C6orf27	80737	hgsc.bcm.edu	37	chr6	31741028	31741028	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aggccactcacctggagaaaTccctgtctcccaggcggctt	10	15	2	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr6:31741028T>C	ENST00000375688.4	-	6	1108	c.908A>G	c.(907-909)gAt>gGt	p.D303G	VWA7_ENST00000447450.1_Missense_Mutation_p.D303G|VWA7_ENST00000467576.1_5'UTR|VWA7_ENST00000375686.3_Missense_Mutation_p.D303G			Q9Y334	VWA7_HUMAN	von Willebrand factor A domain containing 7	303						extracellular region (GO:0005576)											CCTGGAGAAATCCCTGTCTCC	0.632																																					p.D303G		Atlas-SNP	.											.	.	.	.	0			c.A908G						.						23	23	23					6																	31741028		2203	4299	6502	SO:0001583	missense	80737	exon6			GAGAAATCCCTGT		CCDS4721.2	6p21	2011-12-13	2011-12-13	2011-12-13	ENSG00000204396	ENSG00000204396			13939	protein-coding gene	gene with protein product		609693	"chromosome 6 open reading frame 27"	C6orf27			Standard	NM_025258		Approved	G7c, NG37	uc011dog.2	Q9Y334	OTTHUMG00000031132	ENST00000375688.4:c.908A>G	chr6.hg19:g.31741028T>C	ENSP00000364840:p.Asp303Gly	48.0	0.0		57.0	10.0	NM_025258	A2BEX8|A6NHR6|B0V041|Q5SSR5|Q96QC8|Q9UMP9	Missense_Mutation	SNP	ENST00000375688.4	hg19	CCDS4721.2	.	.	.	.	.	.	.	.	.	.	T	0.671	-0.801756	0.02841	.	.	ENSG00000204396	ENST00000375688;ENST00000375686;ENST00000447450	T;T;T	0.31769	2.75;2.5;1.48	5.92	-1.56	0.08532	.	0.797000	0.12050	N	0.504198	T	0.03477	0.0100	N	0.11560	0.145	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45116	-0.9283	10	0.13108	T	0.6	7.0E-4	5.7662	0.18227	0.0:0.2613:0.3738:0.3649	.	303	Q9Y334	G7C_HUMAN	G	303	ENSP00000364840:D303G;ENSP00000364838:D303G;ENSP00000390554:D303G	ENSP00000364838:D303G	D	-	2	0	C6orf27	31849007	0.000000	0.05858	0.001000	0.08648	0.362000	0.29581	-1.518000	0.02246	-0.379000	0.07906	-1.267000	0.01435	GAT	.	.		0.632	VWA7-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076233.2	NM_025258		C	31741028	T	C	31741028	3	2	352	1	0	0	0	0	1	0	0	0	2364	1435	50	2	1814	2	C6orf27	6	31741028	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	877796	31741028	139374039	154	49570										
VARS	7407	hgsc.bcm.edu	37	chr6	31749894	31749894	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggcaccgctgggtcactgacAgtgacaaagtaggctgggat	15	9	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr6:31749894A>C	ENST00000375663.3	-	18	2651	c.2211T>G	c.(2209-2211)acT>acG	p.T737T	VARS_ENST00000444930.2_3'UTR|VARS_ENST00000482996.1_5'UTR	NM_006295.2	NP_006286.1	P26640	SYVC_HUMAN	valyl-tRNA synthetase	737					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	30					L-Valine(DB00161)	GGTCACTGACAGTGACAAAGT	0.622																																					p.T737T		Atlas-SNP	.											.	VARS	76	.	0			c.T2211G						.						49	53	52					6																	31749894		2203	4300	6503	SO:0001819	synonymous_variant	7407	exon18			ACTGACAGTGACA	BC012808	CCDS34412.1	6p21.3	2011-07-01		2005-07-05	ENSG00000204394	ENSG00000204394	6.1.1.9	"Aminoacyl tRNA synthetases / Class I"	12651	protein-coding gene	gene with protein product	"valine tRNA ligase 1, cytoplasmic"	192150	"valyl-tRNA synthetase 2"	VARS2		15779907	Standard	XM_005249362		Approved		uc003nxe.3	P26640	OTTHUMG00000031286	ENST00000375663.3:c.2211T>G	chr6.hg19:g.31749894A>C		127.0	0.0		138.0	14.0	NM_006295	B0V1N1|B4DZ61|Q5JQ90|Q96E77|Q9UQM2	Silent	SNP	ENST00000375663.3	hg19	CCDS34412.1	.	.	.	.	.	.	.	.	.	.	A	0.678	-0.799216	0.02841	.	.	ENSG00000204394	ENST00000428445	.	.	.	5.24	-8.01	0.01122	.	.	.	.	.	T	0.35537	0.0935	.	.	.	0.58432	D	0.999998	.	.	.	.	.	.	T	0.55909	-0.8066	4	.	.	.	-21.1472	11.1581	0.48499	0.144:0.0:0.6465:0.2095	.	.	.	.	G	55	.	.	C	-	1	0	VARS	31857873	0.001000	0.12720	0.025000	0.17156	0.169000	0.22640	-1.935000	0.01550	-1.600000	0.01603	-0.376000	0.06991	TGT	.	.		0.622	VARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076619.2	NM_006295		C	31749894	A	C	31749894	2	2	352	1	0	0	0	0	0	0	0	1	17138	175	7	5		5	VARS	6	31749894	Silent	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	8866	31749894	139365173	155	49571										
RXRB	6257	hgsc.bcm.edu	37	chr6	33164232	33164233	+	Frame_Shift_Ins	INS	-	-	C													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tgctgccgctacccccggttINScccccaggaccctcaacgcc							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr6:33164232_33164233insC	ENST00000374680.3	-	5	1182_1183	c.971_972insG	c.(970-972)ggafs	p.G324fs	RXRB_ENST00000374685.4_Frame_Shift_Ins_p.G324fs|RXRB_ENST00000413614.2_Frame_Shift_Ins_p.G228fs|RXRB_ENST00000544186.1_Frame_Shift_Ins_p.G134fs	NM_001270401.1|NM_021976.4	NP_001257330.1|NP_068811.1	P28702	RXRB_HUMAN	retinoid X receptor, beta	324	Hinge.				cardiac muscle cell proliferation (GO:0060038)|cellular response to retinoic acid (GO:0071300)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|maternal placenta development (GO:0001893)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	9-cis retinoic acid receptor activity (GO:0004886)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(1)|skin(2)	15					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Tazarotene(DB00799)|Tretinoin(DB00755)	TACCCCCGGTTCCCCCAGGACC	0.639																																					p.G324fs		Atlas-INDEL	.											.	RXRB	34	.	0			c.972_973insG						.																																			SO:0001589	frameshift_variant	6257	exon5			.	M84820	CCDS4768.1, CCDS59007.1	6p21.3	2013-01-16			ENSG00000204231	ENSG00000204231		"Nuclear hormone receptors"	10478	protein-coding gene	gene with protein product	"nuclear receptor subfamily 2 group B member 2"	180246				8257090	Standard	NM_021976		Approved	NR2B2, H-2RIIBP, RCoR-1	uc003odc.4	P28702	OTTHUMG00000031298	ENST00000374680.3:c.972dupG	chr6.hg19:g.33164237_33164237dupC	ENSP00000363812:p.Gly324fs	85.0	0.0		113.0	10.0	NM_021976	P28703|Q59G65|Q5JP92|Q5STQ1	Frame_Shift_Ins	INS	ENST00000374680.3	hg19	CCDS4768.1																																																																																			.	.		0.639	RXRB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076642.2	NM_021976		C	33164233	-	C	33164232	7	5	352	1	0	1	1	0	0	0	0	0	13779	1770	62	0	653	0	RXRB	6	33164232	Frame_Shift_Ins	INS	-	TCGA-WQ-A9G7-01A-11D-A36X-10	1414338	33164232	137950835	156	49572										
VPS52	6293	hgsc.bcm.edu	37	chr6	33239413	33239413	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggtcccagcccgcaacaccaGttcccgggccgcagccgcca	11	20	0	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr6:33239413G>A	ENST00000445902.2	-	1	258	c.40C>T	c.(40-42)Ctg>Ttg	p.L14L	RPS18_ENST00000439602.2_5'Flank|VPS52_ENST00000478934.1_Intron|VPS52_ENST00000436044.2_Intron|VPS52_ENST00000482399.1_Silent_p.L14L|RPS18_ENST00000474973.1_5'Flank	NM_022553.4	NP_072047.4	Q8N1B4	VPS52_HUMAN	vacuolar protein sorting 52 homolog (S. cerevisiae)	14					ectodermal cell differentiation (GO:0010668)|embryonic ectodermal digestive tract development (GO:0048611)|protein transport (GO:0015031)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(8)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	28						CGCAACACCAGTTCCCGGGCC	0.672																																					p.L14L		Atlas-SNP	.											.	VPS52	56	.	0			c.C40T						.						18	20	19					6																	33239413		2201	4299	6500	SO:0001819	synonymous_variant	6293	exon1			ACACCAGTTCCCG	AJ223319	CCDS4770.2	6p21.3	2010-02-17	2006-12-19	2003-09-05	ENSG00000223501	ENSG00000223501			10518	protein-coding gene	gene with protein product		603443	"SAC2 suppressor of actin mutations 2-like (yeast)", "vacuolar protein sorting 52 (yeast)"	SACM2L		9790748	Standard	NM_022553		Approved	ARE1	uc003odm.1	Q8N1B4	OTTHUMG00000031276	ENST00000445902.2:c.40C>T	chr6.hg19:g.33239413G>A		139.0	0.0		149.0	17.0	NM_022553	A2BF38|B0UZZ4|B4DNI9|Q53GR4|Q5JPA0|Q5SQW1|Q8IUN6|Q9NPT5	Silent	SNP	ENST00000445902.2	hg19	CCDS4770.2																																																																																			.	.		0.672	VPS52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076598.2	NM_022553		A	33239413	G	A	33239413	2	1	352	1	0	0	0	0	0	0	0	1	17229	1020	36	3		3	VPS52	6	33239413	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	75181	33239413	137875654	157	49573										
TEAD3	7005	hgsc.bcm.edu	37	chr6	35443844	35443844	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aggcggggttcgtctggccgAtgtgcacaaacaggtgtttg	16	8	1	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr6:35443844A>T	ENST00000402886.3	-	8	725	c.572T>A	c.(571-573)aTc>aAc	p.I191N	TEAD3_ENST00000338863.7_Missense_Mutation_p.I251N			Q99594	TEAD3_HUMAN	TEA domain family member 3	251	Pro-rich.|Transcriptional activation. {ECO:0000255}.				female pregnancy (GO:0007565)|gene expression (GO:0010467)|hippo signaling (GO:0035329)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	10						CGTCTGGCCGATGTGCACAAA	0.597																																					p.I251N		Atlas-SNP	.											.	TEAD3	52	.	0			c.T752A						.						35	35	35					6																	35443844		1934	4158	6092	SO:0001583	missense	7005	exon10			TGGCCGATGTGCA	X94439	CCDS47414.1	6p21.2	2008-07-28			ENSG00000007866	ENSG00000007866			11716	protein-coding gene	gene with protein product		603170		TEAD5		9889009, 9148898	Standard	NM_003214		Approved	TEF-5, ETFR-1	uc003oku.4	Q99594	OTTHUMG00000014571	ENST00000402886.3:c.572T>A	chr6.hg19:g.35443844A>T	ENSP00000384577:p.Ile191Asn	62.0	0.0		93.0	10.0	NM_003214	O95910|Q5BJG7|Q8N6Y4	Missense_Mutation	SNP	ENST00000402886.3	hg19		.	.	.	.	.	.	.	.	.	.	A	22.0	4.226010	0.79576	.	.	ENSG00000007866	ENST00000338863;ENST00000402886;ENST00000373905;ENST00000433586	T;T;T	0.41065	1.01;1.01;1.01	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.67887	0.2941	M	0.93808	3.46	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.78157	-0.2313	10	0.87932	D	0	-29.7681	14.723	0.69323	1.0:0.0:0.0:0.0	.	191;267;251	B5MCM0;Q7Z6V0;Q99594	.;.;TEAD3_HUMAN	N	251;191;267;162	ENSP00000345772:I251N;ENSP00000384577:I191N;ENSP00000416400:I162N	ENSP00000345772:I251N	I	-	2	0	TEAD3	35551822	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	9.188000	0.94921	2.078000	0.62432	0.459000	0.35465	ATC	.	.		0.597	TEAD3-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316961.2			T	35443844	A	T	35443844	3	4	352	1	0	0	0	0	1	0	0	0	15755	333	12	4	571	4	TEAD3	6	35443844	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	2204431	35443844	135671223	158	49574										
DAAM2	23500	hgsc.bcm.edu	37	chr6	39867871	39867871	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aggagctggagtatcagaggCgccaggtacgggagcccagt	17	9	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr6:39867871C>T	ENST00000398904.2	+	23	2880	c.2698C>T	c.(2698-2700)Cgc>Tgc	p.R900C	DAAM2_ENST00000538976.1_Missense_Mutation_p.R899C|RP11-61I13.3_ENST00000437947.1_RNA|RP11-61I13.3_ENST00000430595.1_RNA|RP11-61I13.3_ENST00000420293.1_RNA|RP11-61I13.3_ENST00000606829.1_RNA|DAAM2_ENST00000274867.4_Missense_Mutation_p.R900C			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	900	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)|determination of left/right symmetry (GO:0007368)					NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(18)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)	49	Ovarian(28;0.0355)|Colorectal(47;0.196)					GTATCAGAGGCGCCAGGTACG	0.577																																					p.R900C		Atlas-SNP	.											.	DAAM2	101	.	0			c.C2698T						.						33	36	35					6																	39867871		2032	4181	6213	SO:0001583	missense	23500	exon23			CAGAGGCGCCAGG	AB002379	CCDS54999.1, CCDS56426.1	6p21.1	2008-07-30			ENSG00000146122	ENSG00000146122			18143	protein-coding gene	gene with protein product		606627				11779461, 12632087	Standard	NM_015345		Approved	KIAA0381	uc003oow.3	Q86T65	OTTHUMG00000014653	ENST00000398904.2:c.2698C>T	chr6.hg19:g.39867871C>T	ENSP00000381876:p.Arg900Cys	77.0	0.0		95.0	11.0	NM_001201427	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	Missense_Mutation	SNP	ENST00000398904.2	hg19	CCDS56426.1	.	.	.	.	.	.	.	.	.	.	C	15.31	2.795680	0.50208	.	.	ENSG00000146122	ENST00000274867;ENST00000398904;ENST00000538976	T;T;T	0.17854	2.25;2.25;2.26	5.13	5.13	0.70059	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.549954	0.19539	N	0.111855	T	0.07234	0.0183	L	0.34521	1.04	0.80722	D	1	B;B	0.10296	0.001;0.003	B;B	0.11329	0.005;0.006	T	0.05146	-1.0903	10	0.59425	D	0.04	.	11.4076	0.49906	0.2964:0.7036:0.0:0.0	.	899;900	G5EA45;Q86T65	.;DAAM2_HUMAN	C	900;900;899	ENSP00000274867:R900C;ENSP00000381876:R900C;ENSP00000437808:R899C	ENSP00000274867:R900C	R	+	1	0	DAAM2	39975849	0.552000	0.26505	0.982000	0.44146	0.961000	0.63080	2.459000	0.45023	2.667000	0.90743	0.561000	0.74099	CGC	.	.		0.577	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1			T	39867871	C	T	39867871	3	4	352	1	0	0	0	0	1	0	0	0	4218	768	27	1	2781	1	DAAM2	6	39867871	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	4424027	39867871	131247196	159	49575										
LRFN2	57497	hgsc.bcm.edu	37	chr6	40360329	40360329	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gccgttggtctgcgagtacaCattgctcacggccgctgcca	12	14	2	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr6:40360329C>T	ENST00000338305.6	-	3	2265	c.1723G>A	c.(1723-1725)Gtg>Atg	p.V575M		NM_020737.1	NP_065788.1	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III domain containing 2	575						cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	58	Ovarian(28;0.0418)|Colorectal(47;0.196)					TGCGAGTACACATTGCTCACG	0.677																																					p.V575M		Atlas-SNP	.											.	LRFN2	133	.	0			c.G1723A						.						37	34	35					6																	40360329		2203	4300	6503	SO:0001583	missense	57497	exon3			AGTACACATTGCT	AB033072	CCDS34443.1	6p21.2-p21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000156564	ENSG00000156564		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	21226	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 2"	612808	"KIAA1246"	KIAA1246, SALM1		16495444, 16828986	Standard	NM_020737		Approved	FIGLER2	uc003oph.1	Q9ULH4	OTTHUMG00000014662	ENST00000338305.6:c.1723G>A	chr6.hg19:g.40360329C>T	ENSP00000345985:p.Val575Met	71.0	0.0		57.0	19.0	NM_020737	A5PKU3|Q5SYP9	Missense_Mutation	SNP	ENST00000338305.6	hg19	CCDS34443.1	.	.	.	.	.	.	.	.	.	.	c	14.02	2.410940	0.42817	.	.	ENSG00000156564	ENST00000338305	T	0.60797	0.16	5.41	0.515	0.17013	.	0.291752	0.38272	N	0.001752	T	0.31888	0.0811	L	0.42245	1.32	0.31112	N	0.70984	P	0.37663	0.604	B	0.39840	0.311	T	0.15954	-1.0419	10	0.66056	D	0.02	.	10.9102	0.47103	0.0:0.727:0.0:0.273	.	575	Q9ULH4	LRFN2_HUMAN	M	575	ENSP00000345985:V575M	ENSP00000345985:V575M	V	-	1	0	LRFN2	40468307	0.724000	0.28038	0.973000	0.42090	0.841000	0.47740	0.607000	0.24209	-0.213000	0.10094	0.651000	0.88453	GTG	.	.		0.677	LRFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040488.1	XM_166372		T	40360329	C	T	40360329	3	4	352	1	0	0	0	0	1	0	0	0	8947	478	17	3	650	3	LRFN2	6	40360329	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	492458	40360329	130754738	160	49576										
GNMT	27232	hgsc.bcm.edu	37	chr6	42930828	42930828	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aggggaccagagtgagcaccGgctggcgctgaaaaacattg	15	9	0	3	rs563826316		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr6:42930828G>A	ENST00000372808.3	+	4	480	c.470G>A	c.(469-471)cGg>cAg	p.R157Q		NM_018960.4	NP_061833.1	Q14749	GNMT_HUMAN	glycine N-methyltransferase	157					cellular protein modification process (GO:0006464)|glycogen metabolic process (GO:0005977)|methionine metabolic process (GO:0006555)|one-carbon metabolic process (GO:0006730)|protein homotetramerization (GO:0051289)|regulation of gluconeogenesis (GO:0006111)|S-adenosylmethionine metabolic process (GO:0046500)	cytoplasm (GO:0005737)	folic acid binding (GO:0005542)|glycine binding (GO:0016594)|glycine N-methyltransferase activity (GO:0017174)			kidney(2)|large_intestine(1)|lung(1)	4	Colorectal(47;0.196)		all cancers(41;0.00196)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0461)		Glycine(DB00145)|S-Adenosylmethionine(DB00118)	AGTGAGCACCGGCTGGCGCTG	0.622													G|||	1	0.000199681	0	0	5008	,	,		12371	0		0	False		,,,				2504	0.001				p.R157Q		Atlas-SNP	.											.	GNMT	13	.	0			c.G470A						.						37	38	37					6																	42930828		2203	4300	6503	SO:0001583	missense	27232	exon4			AGCACCGGCTGGC	AF101475	CCDS4876.1	6p12	2008-02-05			ENSG00000124713	ENSG00000124713			4415	protein-coding gene	gene with protein product		606628				10843803, 9495250	Standard	NM_018960		Approved		uc003otd.3	Q14749	OTTHUMG00000014712	ENST00000372808.3:c.470G>A	chr6.hg19:g.42930828G>A	ENSP00000361894:p.Arg157Gln	27.0	0.0		54.0	5.0	NM_018960	Q5T8W2|Q9NNZ1|Q9NS24	Missense_Mutation	SNP	ENST00000372808.3	hg19	CCDS4876.1	.	.	.	.	.	.	.	.	.	.	G	15.02	2.710368	0.48517	.	.	ENSG00000124713	ENST00000372808	T	0.66638	-0.22	5.6	0.992	0.19819	.	0.175951	0.48767	N	0.000162	T	0.31358	0.0794	L	0.41124	1.26	0.37147	D	0.901973	B	0.18166	0.026	B	0.19666	0.026	T	0.07083	-1.0791	10	0.15952	T	0.53	-5.393	8.0625	0.30642	0.5244:0.0:0.4756:0.0	.	157	Q14749	GNMT_HUMAN	Q	157	ENSP00000361894:R157Q	ENSP00000361894:R157Q	R	+	2	0	GNMT	43038806	1.000000	0.71417	1.000000	0.80357	0.777000	0.43975	2.794000	0.47853	0.259000	0.21709	-0.367000	0.07326	CGG	.	.		0.622	GNMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040568.1	NM_018960		A	42930828	G	A	42930828	3	1	352	1	0	0	0	0	1	0	0	0	6548	1116	39	1	484	1	GNMT	6	42930828	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	2570499	42930828	128184239	161	49577										
CUL9	23113	hgsc.bcm.edu	37	chr6	43172484	43172484	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ccttctccctctgtctctacAgtcagcaagaacagcaaggg	8	14	4	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr6:43172484A>C	ENST00000252050.4	+	22	4423		c.e22-1		CUL9_ENST00000354495.3_Splice_Site|CUL9_ENST00000372647.2_Splice_Site	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9						microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						CTGTCTCTACAGTCAGCAAGA	0.597																																					.		Atlas-SNP	.											.	CUL9	248	.	0			c.4340-2A>C						.						70	77	75					6																	43172484		2203	4300	6503	SO:0001630	splice_region_variant	23113	exon22			CTCTACAGTCAGC	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"parkin-like cytoplasmic p53 binding protein", "p53-associated parkin-like cytoplasmic protein"	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.4340-1A>C	chr6.hg19:g.43172484A>C		85.0	0.0		100.0	28.0	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Splice_Site	SNP	ENST00000252050.4	hg19	CCDS4890.1	.	.	.	.	.	.	.	.	.	.	A	19.49	3.837526	0.71373	.	.	ENSG00000112659	ENST00000252050;ENST00000354495;ENST00000372647	.	.	.	4.94	4.94	0.65067	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.1747	0.59619	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CUL9	43280462	1.000000	0.71417	0.990000	0.47175	0.895000	0.52256	6.605000	0.74155	1.861000	0.53984	0.459000	0.35465	.	.	.		0.597	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089	Intron	C	43172484	A	C	43172484	5	2	352	1	0	0	0	0	0	0	1	0	4063	202	7	5	4420	5	CUL9	6	43172484	Splice_Site	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	241656	43172484	127942583	162	49578										
CUL9	23113	hgsc.bcm.edu	37	chr6	43192000	43192000	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ctccctaggccccaggcctcCtcagggccagaggcagaaga	12	16	1	3			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr6:43192000C>A	ENST00000252050.4	+	41	7455	c.7371C>A	c.(7369-7371)tcC>tcA	p.S2457S	CUL9_ENST00000354495.3_Silent_p.S2347S|CUL9_ENST00000372647.2_Silent_p.S2429S|RP3-330M21.5_ENST00000500590.1_RNA	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	2457					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						CCCAGGCCTCCTCAGGGCCAG	0.607																																					p.S2457S		Atlas-SNP	.											.	CUL9	248	.	0			c.C7371A						.						66	59	61					6																	43192000		2203	4300	6503	SO:0001819	synonymous_variant	23113	exon41			GGCCTCCTCAGGG	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"parkin-like cytoplasmic p53 binding protein", "p53-associated parkin-like cytoplasmic protein"	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.7371C>A	chr6.hg19:g.43192000C>A		105.0	0.0		123.0	14.0	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Silent	SNP	ENST00000252050.4	hg19	CCDS4890.1																																																																																			.	.		0.607	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		A	43192000	C	A	43192000	2	1	352	1	0	0	0	0	0	0	0	1	4063	668	24	3		3	CUL9	6	43192000	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	19516	43192000	127923067	163	49579										
GTPBP2	54676	hgsc.bcm.edu	37	chr6	43593198	43593198	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gaaaaggttgagccgagcccGgccccgcccattgtccagct	12	15	0	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr6:43593198G>A	ENST00000307126.5	-	5	606	c.607C>T	c.(607-609)Cgg>Tgg	p.R203W	GTPBP2_ENST00000307114.7_Missense_Mutation_p.R115W|GTPBP2_ENST00000476510.1_5'UTR	NM_019096.3	NP_061969.3			GTP binding protein 2											breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(3)|prostate(1)|skin(2)|urinary_tract(1)	18	all_cancers(18;9.36e-06)|Lung NSC(15;0.00161)|all_lung(25;0.004)		all cancers(41;0.000501)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167)			AGCCGAGCCCGGCCCCGCCCA	0.597																																					p.R203W	GBM(116;405 1620 28302 32150 44768)	Atlas-SNP	.											.	GTPBP2	39	.	0			c.C607T						.						86	88	87					6																	43593198		2203	4300	6503	SO:0001583	missense	54676	exon5			GAGCCCGGCCCCG	AB024574	CCDS4903.1, CCDS69124.1	6p21	2008-07-28			ENSG00000172432	ENSG00000172432			4670	protein-coding gene	gene with protein product		607434				10833435, 11054535	Standard	NM_019096		Approved		uc003ovs.3	Q9BX10	OTTHUMG00000014744	ENST00000307126.5:c.607C>T	chr6.hg19:g.43593198G>A	ENSP00000303997:p.Arg203Trp	104.0	0.0		147.0	25.0	NM_019096		Missense_Mutation	SNP	ENST00000307126.5	hg19	CCDS4903.1	.	.	.	.	.	.	.	.	.	.	G	15.67	2.902242	0.52227	.	.	ENSG00000172432	ENST00000307126;ENST00000307114;ENST00000452781	T;T;T	0.72051	-0.62;-0.62;0.77	4.38	2.34	0.29019	Protein synthesis factor, GTP-binding (1);	0.000000	0.85682	D	0.000000	T	0.80082	0.4558	M	0.86268	2.805	0.58432	D	0.999993	D;D	0.89917	1.0;1.0	D;D	0.77557	0.99;0.986	T	0.82615	-0.0370	10	0.49607	T	0.09	-14.4158	13.6858	0.62515	0.0:0.0:0.647:0.353	.	195;203	Q9BX10-4;Q9BX10	.;GTPB2_HUMAN	W	203;115;195	ENSP00000303997:R203W;ENSP00000304893:R115W;ENSP00000410676:R195W	ENSP00000304893:R115W	R	-	1	2	GTPBP2	43701176	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.434000	0.44802	1.009000	0.39289	0.462000	0.41574	CGG	.	.		0.597	GTPBP2-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040679.1			A	43593198	G	A	43593198	3	1	352	1	0	0	0	0	1	0	0	0	6889	1115	39	1	1233	1	GTPBP2	6	43593198	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	401198	43593198	127521869	164	49580										
TFAP2D	83741	hgsc.bcm.edu	37	chr6	50740417	50740417	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agctctaagcactttccaaaCagttctcagtgaaatgctga	7	10	2	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr6:50740417C>T	ENST00000008391.3	+	8	1427	c.1199C>T	c.(1198-1200)aCa>aTa	p.T400I		NM_172238.3	NP_758438.2			transcription factor AP-2 delta (activating enhancer binding protein 2 delta)									p.T400K(1)		NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(26)|ovary(6)|pancreas(1)|prostate(5)|stomach(1)	60	Lung NSC(77;0.0334)					ACTTTCCAAACAGTTCTCAGT	0.458																																					p.T400I		Atlas-SNP	.											TFAP2D,NS,carcinoma,0,2	TFAP2D	144	.	1	Substitution - Missense(1)	lung(1)	c.C1199T						.						66	64	65					6																	50740417		2203	4300	6503	SO:0001583	missense	83741	exon8			TCCAAACAGTTCT	AY028376	CCDS4933.1	6p12.3	2008-02-05	2004-10-26	2004-10-27		ENSG00000008197			15581	protein-coding gene	gene with protein product		610161	"transcription factor AP-2 beta (activating enhancer-binding protein 2 beta)-like 1"	TFAP2BL1		11733187	Standard	NM_172238		Approved		uc003paf.3	Q7Z6R9		ENST00000008391.3:c.1199C>T	chr6.hg19:g.50740417C>T	ENSP00000008391:p.Thr400Ile	129.0	1.0		126.0	24.0	NM_172238		Missense_Mutation	SNP	ENST00000008391.3	hg19	CCDS4933.1	.	.	.	.	.	.	.	.	.	.	C	17.67	3.446102	0.63178	.	.	ENSG00000008197	ENST00000008391	D	0.96885	-4.16	5.46	5.46	0.80206	Transcription factor AP-2, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.90858	0.7128	N	0.14661	0.345	0.80722	D	1	B	0.30146	0.27	B	0.34346	0.18	D	0.90275	0.4310	10	0.87932	D	0	-21.0128	19.3034	0.94151	0.0:1.0:0.0:0.0	.	400	Q7Z6R9	AP2D_HUMAN	I	400	ENSP00000008391:T400I	ENSP00000008391:T400I	T	+	2	0	TFAP2D	50848376	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.487000	0.81328	2.577000	0.86979	0.467000	0.42956	ACA	.	.		0.458	TFAP2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040881.1	NM_172238		T	50740417	C	T	50740417	3	4	352	1	0	0	0	0	1	0	0	0	15805	478	17	3	1229	3	TFAP2D	6	50740417	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	7147219	50740417	120374650	165	49581										
EYS	346007	hgsc.bcm.edu	37	chr6	65707487	65707487	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	atactaacgagatgcaggtcTttgcaggtagaattgtgctc	11	7	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr6:65707487T>G	ENST00000370621.3	-	14	2773	c.2247A>C	c.(2245-2247)aaA>aaC	p.K749N	EYS_ENST00000503581.1_Missense_Mutation_p.K749N|EYS_ENST00000370616.2_Missense_Mutation_p.K749N			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	749	EGF-like 9; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						GATGCAGGTCTTTGCAGGTAG	0.398																																					p.K749N		Atlas-SNP	.											.	EYS	527	.	0			c.A2247C						.						128	101	109					6																	65707487		692	1591	2283	SO:0001583	missense	346007	exon14			CAGGTCTTTGCAG		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.2247A>C	chr6.hg19:g.65707487T>G	ENSP00000359655:p.Lys749Asn	220.0	0.0		251.0	36.0	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	hg19		.	.	.	.	.	.	.	.	.	.	T	6.608	0.480623	0.12581	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	D;D;D	0.88431	-2.38;-2.38;-2.38	5.5	4.3	0.51218	.	0.769944	0.10661	N	0.648727	T	0.68851	0.3046	N	0.13352	0.335	0.54753	D	0.999987	P	0.49090	0.919	P	0.45506	0.483	T	0.64050	-0.6498	10	0.25751	T	0.34	.	4.6221	0.12460	0.3205:0.0814:0.0:0.5981	.	749	Q5T1H1-1	.	N	749	ENSP00000424243:K749N;ENSP00000359655:K749N;ENSP00000359650:K749N	ENSP00000359650:K749N	K	-	3	2	EYS	65764208	0.998000	0.40836	0.003000	0.11579	0.720000	0.41350	3.163000	0.50763	0.878000	0.35920	0.533000	0.62120	AAA	.	.		0.398	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		G	65707487	T	G	65707487	3	3	352	1	0	0	0	0	1	0	0	0	5334	1606	56	5	7152	5	EYS	6	65707487	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	14967070	65707487	105407580	166	49582										
SMAP1	60682	hgsc.bcm.edu	37	chr6	71546688	71546688	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gagcctaaaaaaagtaccagCcctaaaaaagctgcggagcc	9	11	0	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr6:71546688C>T	ENST00000370455.3	+	7	869	c.621C>T	c.(619-621)agC>agT	p.S207S	SMAP1_ENST00000370452.3_Silent_p.S180S|SMAP1_ENST00000316999.5_Silent_p.S180S	NM_001044305.1|NM_001281440.1	NP_001037770.1|NP_001268369.1	Q8IYB5	SMAP1_HUMAN	small ArfGAP 1	207					positive regulation of erythrocyte differentiation (GO:0045648)|regulation of ARF GTPase activity (GO:0032312)|regulation of clathrin-mediated endocytosis (GO:2000369)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(6)|prostate(1)|urinary_tract(1)	15						AAAGTACCAGCCCTAAAAAAG	0.323																																					p.S207S		Atlas-SNP	.											.	SMAP1	77	.	0			c.C621T						.						40	43	42					6																	71546688		2203	4300	6503	SO:0001819	synonymous_variant	60682	exon7			TACCAGCCCTAAA	AK023221	CCDS4973.1, CCDS43478.1, CCDS64459.1, CCDS75478.1	6q12-q13	2009-11-30	2008-09-05		ENSG00000112305	ENSG00000112305		"ADP-ribosylation factor GTPase activating proteins"	19651	protein-coding gene	gene with protein product		611372	"stromal membrane-associated protein 1", "stromal membrane-associated GTPase-activating protein 1"			9644265, 12119110	Standard	NM_001044305		Approved	FLJ13159, SMAP-1	uc003pfr.3	Q8IYB5	OTTHUMG00000014996	ENST00000370455.3:c.621C>T	chr6.hg19:g.71546688C>T		316.0	1.0		446.0	152.0	NM_001044305	Q53H70|Q5SYQ2|Q6PK24|Q8NDH4|Q96L38|Q96L39|Q9H8X4	Silent	SNP	ENST00000370455.3	hg19	CCDS43478.1	.	.	.	.	.	.	.	.	.	.	C	0.347	-0.946911	0.02304	.	.	ENSG00000112305	ENST00000439432	.	.	.	5.12	3.28	0.37604	.	.	.	.	.	T	0.39279	0.1072	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.34502	-0.9826	4	.	.	.	-25.5792	5.5114	0.16882	0.1832:0.6566:0.0:0.1602	.	.	.	.	S	82	.	.	P	+	1	0	SMAP1	71603409	1.000000	0.71417	1.000000	0.80357	0.008000	0.06430	2.741000	0.47426	1.257000	0.44085	0.655000	0.94253	CCC	.	.		0.323	SMAP1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041149.1	NM_001044305		T	71546688	C	T	71546688	2	4	352	1	0	0	0	0	0	0	0	1	14781	738	26	3		3	SMAP1	6	71546688	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	5839201	71546688	99568379	167	49583										
SYNCRIP	10492	hgsc.bcm.edu	37	chr6	86350164	86350164	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cacattgacattaacattacCtgaacatgagagagatcact	6	9	1	4			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr6:86350164C>T	ENST00000369622.3	-	3	767	c.267G>A	c.(265-267)caG>caA	p.Q89Q	SYNCRIP_ENST00000355238.6_Splice_Site_p.Q89Q	NM_001159675.1|NM_006372.4	NP_001153147.1|NP_006363.4	O60506	HNRPQ_HUMAN	synaptotagmin binding, cytoplasmic RNA interacting protein	89					cellular response to interferon-gamma (GO:0071346)|CRD-mediated mRNA stabilization (GO:0070934)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of translation (GO:0017148)|osteoblast differentiation (GO:0001649)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|CRD-mediated mRNA stability complex (GO:0070937)|endoplasmic reticulum (GO:0005783)|GAIT complex (GO:0097452)|histone pre-mRNA 3'end processing complex (GO:0071204)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(10)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	33		all_cancers(76;0.000137)|Acute lymphoblastic leukemia(125;3.66e-08)|Prostate(29;8.2e-07)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0297)		BRCA - Breast invasive adenocarcinoma(108;0.0389)		TTAACATTACCTGAACATGAG	0.289																																					p.Q89Q		Atlas-SNP	.											.	SYNCRIP	80	.	0			c.G267A						.						88	88	88					6																	86350164		2203	4298	6501	SO:0001630	splice_region_variant	10492	exon3			CATTACCTGAACA	AF037448	CCDS5005.1, CCDS55041.1, CCDS75491.1	6q14-q15	2013-05-23			ENSG00000135316	ENSG00000135316		"RNA binding motif (RRM) containing"	16918	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein Q"					9847309, 11352648	Standard	NM_006372		Approved	NSAP1, GRY-RBP, dJ3J17.2, HNRPQ1, hnRNP-Q, HNRNPQ	uc003pla.2	O60506	OTTHUMG00000015141	ENST00000369622.3:c.267+1G>A	chr6.hg19:g.86350164C>T		92.0	0.0		93.0	54.0	NM_006372	E1P501|E1P502|Q53H05|Q5TCG2|Q5TCG3|Q8IW78|Q8N599|Q96LC1|Q96LC2|Q9Y583	Silent	SNP	ENST00000369622.3	hg19	CCDS5005.1																																																																																			.	.		0.289	SYNCRIP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041396.1	NM_006372	Silent	T	86350164	C	T	86350164	5	4	352	1	0	0	0	0	0	0	1	0	15459	695	24	3	1686	3	SYNCRIP	6	86350164	Splice_Site	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	14803476	86350164	84764903	168	49584										
ZNF292	23036	hgsc.bcm.edu	37	chr6	87966812	87966812	+	Frame_Shift_Del	DEL	T	T	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aataatggaaagtttgtttaTtttttgccatcaccggtgaa							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr6:87966812delT	ENST00000369577.3	+	8	3508	c.3465delT	c.(3463-3465)tatfs	p.Y1155fs	ZNF292_ENST00000339907.4_Frame_Shift_Del_p.Y1150fs	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	1155						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		AGTTTGTTTATTTTTTGCCAT	0.408																																					p.Y1155fs		Atlas-INDEL	.											.	ZNF292	479	.	0			c.3464delA						.						54	51	52					6																	87966812		1912	4110	6022	SO:0001589	frameshift_variant	23036	exon8			.	AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"Zinc fingers, C2H2-type"	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.3465delT	chr6.hg19:g.87966812delT	ENSP00000358590:p.Tyr1155fs	59.0	0.0		68.0	34.0	NM_015021	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Frame_Shift_Del	DEL	ENST00000369577.3	hg19	CCDS47457.1																																																																																			.	.		0.408	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021		-	87966812	T	-	87966812	7	5	352	1	0	1	0	1	0	0	0	0	17841	1500	52	0	3495	0	ZNF292	6	87966812	Frame_Shift_Del	DEL	T	TCGA-WQ-A9G7-01A-11D-A36X-10	1616648	87966812	83148255	169	49585										
C6orf167	253714	hgsc.bcm.edu	37	chr6	97681837	97681837	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agtgaagatacattcgtaatTgttcttctagaatgacaccc	7	8	2	4			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr6:97681837T>C	ENST00000275053.4	-	12	1467	c.1202A>G	c.(1201-1203)cAa>cGa	p.Q401R	MMS22L_ENST00000369251.2_Intron	NM_198468.2	NP_940870.2	Q6ZRQ5	MMS22_HUMAN	MMS22-like, DNA repair protein	401					double-strand break repair via homologous recombination (GO:0000724)|replication fork processing (GO:0031297)	nuclear replication fork (GO:0043596)				breast(1)|endometrium(9)|kidney(2)|large_intestine(12)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	50						CATTCGTAATTGTTCTTCTAG	0.328																																					p.Q401R		Atlas-SNP	.											.	MMS22L	102	.	0			c.A1202G						.						93	96	95					6																	97681837		2203	4298	6501	SO:0001583	missense	253714	exon12			CGTAATTGTTCTT		CCDS5039.1	6q16.3	2010-11-11	2010-11-11	2010-11-11	ENSG00000146263	ENSG00000146263			21475	protein-coding gene	gene with protein product		615614	"chromosome 6 open reading frame 167"	C6orf167		21055983, 21055984	Standard	NM_198468		Approved	dJ39B17.2	uc003ppb.3	Q6ZRQ5	OTTHUMG00000015248	ENST00000275053.4:c.1202A>G	chr6.hg19:g.97681837T>C	ENSP00000275053:p.Gln401Arg	208.0	0.0		202.0	83.0	NM_198468	D6R9Y8|D6RBQ4|E1P529|Q5THT2|Q68CQ6|Q68D32	Missense_Mutation	SNP	ENST00000275053.4	hg19	CCDS5039.1	.	.	.	.	.	.	.	.	.	.	T	16.07	3.018412	0.54576	.	.	ENSG00000146263	ENST00000275053;ENST00000510018	T;T	0.35236	1.32;1.32	5.39	5.39	0.77823	.	0.130571	0.52532	D	0.000062	T	0.21590	0.0520	M	0.64997	1.995	0.80722	D	1	P	0.35656	0.514	B	0.30855	0.121	T	0.04427	-1.0952	10	0.27082	T	0.32	-6.1107	15.6977	0.77512	0.0:0.0:0.0:1.0	.	401	Q6ZRQ5	MMS22_HUMAN	R	401;289	ENSP00000275053:Q401R;ENSP00000427288:Q289R	ENSP00000275053:Q401R	Q	-	2	0	MMS22L	97788558	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.212000	0.65225	2.169000	0.68431	0.533000	0.62120	CAA	.	.		0.328	MMS22L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041573.3	NM_198468		C	97681837	T	C	97681837	3	2	352	1	0	0	0	0	1	0	0	0	2344	1812	63	2	2585	2	C6orf167	6	97681837	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	9715025	97681837	73433230	170	49586										
ASCC3	10973	hgsc.bcm.edu	37	chr6	101247376	101247376	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tcatacacatggggataatgTattttttcaacgtctgcatc	7	8	3	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr6:101247376T>C	ENST00000369162.2	-	7	1544	c.1200A>G	c.(1198-1200)atA>atG	p.I400M	ASCC3_ENST00000522650.1_Missense_Mutation_p.I400M	NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	400					cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		GGGGATAATGTATTTTTTCAA	0.383																																					p.I400M		Atlas-SNP	.											.	ASCC3	205	.	0			c.A1200G						.						131	130	130					6																	101247376		2202	4300	6502	SO:0001583	missense	10973	exon7			ATAATGTATTTTT	AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"RNA helicase family"	614217	"helicase, ATP binding 1"	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.1200A>G	chr6.hg19:g.101247376T>C	ENSP00000358159:p.Ile400Met	39.0	0.0		48.0	24.0	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Missense_Mutation	SNP	ENST00000369162.2	hg19	CCDS5046.1	.	.	.	.	.	.	.	.	.	.	T	10.87	1.473820	0.26423	.	.	ENSG00000112249	ENST00000369162;ENST00000522650	T;T	0.58506	0.45;0.33	5.32	-7.77	0.01227	.	0.258915	0.37669	N	0.001993	T	0.28863	0.0716	L	0.36672	1.1	0.80722	D	1	D;P	0.54047	0.964;0.855	P;B	0.53912	0.737;0.143	T	0.51309	-0.8722	10	0.45353	T	0.12	.	0.579	0.00709	0.3995:0.1501:0.1667:0.2837	.	400;400	E7EW23;Q8N3C0	.;HELC1_HUMAN	M	400	ENSP00000358159:I400M;ENSP00000430769:I400M	ENSP00000358159:I400M	I	-	3	3	ASCC3	101354097	1.000000	0.71417	0.592000	0.28758	0.221000	0.24807	0.661000	0.25023	-0.975000	0.03546	0.383000	0.25322	ATA	.	.		0.383	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828		C	101247376	T	C	101247376	3	2	352	1	0	0	0	0	1	0	0	0	1033	1628	57	2	5552	2	ASCC3	6	101247376	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	3565539	101247376	69867691	171	49587										
FBXO5	26271	hgsc.bcm.edu	37	chr6	153296638	153296638	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ccttccaaatatgcaggggtGtaggaaactagtcttccaat	9	9	1	0	rs143943044		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr6:153296638G>A	ENST00000229758.3	-	2	280	c.222C>T	c.(220-222)taC>taT	p.Y74Y	FBXO5_ENST00000477822.1_5'Flank|FBXO5_ENST00000367241.3_Silent_p.Y28Y	NM_012177.3	NP_036309.1	Q9UKT4	FBX5_HUMAN	F-box protein 5	74					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|G1/S transition of mitotic cell cycle (GO:0000082)|inhibition of mitotic anaphase-promoting complex activity (GO:0060565)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|microtubule polymerization (GO:0046785)|mitotic cell cycle (GO:0000278)|negative regulation of meiosis (GO:0045835)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|oocyte maturation (GO:0001556)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|spindle assembly involved in female meiosis I (GO:0007057)|vesicle organization (GO:0016050)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)	15		Ovarian(120;0.125)		OV - Ovarian serous cystadenocarcinoma(155;4.38e-10)|BRCA - Breast invasive adenocarcinoma(81;0.0893)		ATGCAGGGGTGTAGGAAACTA	0.403																																					p.Y74Y	NSCLC(121;372 1757 17721 17977 29669)	Atlas-SNP	.											.	FBXO5	40	.	0			c.C222T						.	G	,	2,4404	4.2+/-10.8	0,2,2201	113	117	115		84,222	-2.2	0	6	dbSNP_134	115	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	FBXO5	NM_001142522.1,NM_012177.3	,	0,3,6500	AA,AG,GG		0.0116,0.0454,0.0231	,	28/402,74/448	153296638	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	26271	exon2			AGGGGTGTAGGAA	AF129535	CCDS5242.1, CCDS47501.1	6q25-q26	2008-02-05	2004-06-15		ENSG00000112029	ENSG00000112029		"F-boxes /  "other""	13584	protein-coding gene	gene with protein product		606013	"F-box only protein 5"			10531035, 10531037	Standard	NM_012177		Approved	FBX5, Fbxo31, EMI1	uc003qpg.3	Q9UKT4	OTTHUMG00000015854	ENST00000229758.3:c.222C>T	chr6.hg19:g.153296638G>A		72.0	0.0		87.0	24.0	NM_012177	B3KNX5|Q5TF47|Q8WV29|Q9UGC8	Silent	SNP	ENST00000229758.3	hg19	CCDS5242.1																																																																																			.	G|1.000;A|0.000		0.403	FBXO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042757.1			A	153296638	G	A	153296638	2	1	352	1	0	0	0	0	0	0	0	1	5766	1372	48	3		3	FBXO5	6	153296638	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	52049262	153296638	17818429	172	49588										
ZDHHC14	79683	hgsc.bcm.edu	37	chr6	158014023	158014023	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tcttcttttctccacagataTcgcaaacggcaccagttcag	6	13	4	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr6:158014023T>A	ENST00000359775.5	+	3	1299	c.410T>A	c.(409-411)aTc>aAc	p.I137N	ZDHHC14_ENST00000341375.8_3'UTR|ZDHHC14_ENST00000414563.2_Missense_Mutation_p.I137N			Q8IZN3	ZDH14_HUMAN	zinc finger, DHHC-type containing 14	137					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|skin(1)	17		Breast(66;0.00586)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.9e-17)|BRCA - Breast invasive adenocarcinoma(81;5.8e-05)		TCCACAGATATCGCAAACGGC	0.572																																					p.I137N		Atlas-SNP	.											.	ZDHHC14	39	.	0			c.T410A						.						76	76	76					6																	158014023		2203	4296	6499	SO:0001583	missense	79683	exon3			CAGATATCGCAAA	AF542388	CCDS5252.1, CCDS47510.1	6q25.3	2008-05-02			ENSG00000175048	ENSG00000175048		"Zinc fingers, DHHC-type"	20341	protein-coding gene	gene with protein product							Standard	NM_024630		Approved	FLJ20984, NEW1CP	uc003qqt.3	Q8IZN3	OTTHUMG00000015896	ENST00000359775.5:c.410T>A	chr6.hg19:g.158014023T>A	ENSP00000352821:p.Ile137Asn	170.0	0.0		167.0	21.0	NM_024630	A6NDB7|Q5JS07|Q5JS08|Q6PHS4|Q8IZN2|Q9H7F1	Missense_Mutation	SNP	ENST00000359775.5	hg19	CCDS5252.1	.	.	.	.	.	.	.	.	.	.	T	13.30	2.197250	0.38806	.	.	ENSG00000175048	ENST00000359775;ENST00000414563;ENST00000538483	T;T	0.23552	1.9;1.9	5.71	5.71	0.89125	.	0.226100	0.31358	N	0.007799	T	0.06962	0.0177	N	0.05050	-0.12	0.25921	N	0.983111	B;P;B	0.38455	0.001;0.632;0.015	B;B;B	0.41764	0.012;0.366;0.026	T	0.42666	-0.9438	10	0.38643	T	0.18	-18.6663	15.9869	0.80160	0.0:0.0:0.0:1.0	.	141;137;137	A4FVA9;Q8IZN3;Q8IZN3-2	.;ZDH14_HUMAN;.	N	137;137;141	ENSP00000352821:I137N;ENSP00000410713:I137N	ENSP00000352821:I137N	I	+	2	0	ZDHHC14	157934011	1.000000	0.71417	0.293000	0.24932	0.726000	0.41606	3.821000	0.55700	-0.685000	0.05177	-0.140000	0.14226	ATC	.	.		0.572	ZDHHC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042841.2	NM_153746		A	158014023	T	A	158014023	3	1	352	1	0	0	0	0	1	0	0	0	17619	1435	50	4	420	4	ZDHHC14	6	158014023	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	4717385	158014023	13101044	173	49589										
FAM120B	84498	hgsc.bcm.edu	37	chr6	170697398	170697398	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gattacatcaaccccagagcCgtgcagctgggctcccttct	9	15	2	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr6:170697398C>A	ENST00000476287.1	+	7	2415	c.2307C>A	c.(2305-2307)gcC>gcA	p.A769A	FAM120B_ENST00000537664.1_Silent_p.A792A|FAM120B_ENST00000252510.9_Silent_p.A101A|FAM120B_ENST00000540480.1_Silent_p.A781A	NM_032448.1	NP_115824.1	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	769					cell differentiation (GO:0030154)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(2)	44		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)		ACCCCAGAGCCGTGCAGCTGG	0.537																																					p.A769A		Atlas-SNP	.											.	FAM120B	108	.	0			c.C2307A						.						65	56	59					6																	170697398		2203	4300	6503	SO:0001819	synonymous_variant	84498	exon7			CAGAGCCGTGCAG	AB058741	CCDS5314.1, CCDS75555.1	6q27	2011-04-13	2006-07-04	2006-07-04	ENSG00000112584	ENSG00000112584			21109	protein-coding gene	gene with protein product	"PPARgamma constitutive coactivator 1", "constitutive coactivator of PPAR-gamma"	612266	"KIAA1838"	KIAA1838		14585507	Standard	NM_032448		Approved	PGCC1, CCPG	uc003qxp.3	Q96EK7	OTTHUMG00000016080	ENST00000476287.1:c.2307C>A	chr6.hg19:g.170697398C>A		88.0	0.0		84.0	13.0	NM_032448	B4DL34|Q86V68|Q96JI9	Silent	SNP	ENST00000476287.1	hg19	CCDS5314.1																																																																																			.	.		0.537	FAM120B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000043259.2	NM_032448		A	170697398	C	A	170697398	2	1	352	1	0	0	0	0	0	0	0	1	5422	639	23	1		1	FAM120B	6	170697398	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	12683375	170697398	417669	174	49590										
MICALL2	79778	hgsc.bcm.edu	37	chr7	1487299	1487299	+	Frame_Shift_Del	DEL	G	G	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	atagtggaggcttccgggctGgggcgggcgagggcagcttg							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr7:1487299delG	ENST00000297508.7	-	4	612	c.437delC	c.(436-438)ccafs	p.P146fs	MICALL2_ENST00000405088.4_Intron	NM_182924.3	NP_891554.1	Q8IY33	MILK2_HUMAN	MICAL-like 2	146	Forms an intramolecular interaction with the C-terminal coiled coil domain keeping the protein in a closed conformation. {ECO:0000250}.				actin cytoskeleton reorganization (GO:0031532)|actin filament polymerization (GO:0030041)|endocytic recycling (GO:0032456)|neuron projection development (GO:0031175)|substrate adhesion-dependent cell spreading (GO:0034446)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|stress fiber (GO:0001725)|tight junction (GO:0005923)	actin filament binding (GO:0051015)|filamin binding (GO:0031005)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(8)|ovary(2)|skin(2)	19		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;6.01e-15)		CTTCCGGGCTGGGGCGGGCGA	0.677																																					p.P146fs		Atlas-INDEL	.											.	MICALL2	63	.	0			c.438delA						.						22	23	22					7																	1487299		2151	4264	6415	SO:0001589	frameshift_variant	79778	exon4			.	BC037988	CCDS5324.1	7p22.3	2006-11-24			ENSG00000164877	ENSG00000164877			29672	protein-coding gene	gene with protein product	"junctional Rab13-binding protein"					12110185, 16525024	Standard	NM_182924		Approved	MGC46023, FLJ23471, MICAL-L2, JRAB	uc003skj.4	Q8IY33	OTTHUMG00000119021	ENST00000297508.7:c.437delC	chr7.hg19:g.1487299delG	ENSP00000297508:p.Pro146fs	109.0	0.0		157.0	47.0	NM_182924	D3YTD2|Q7RTP4|Q7Z655|Q8TEQ4|Q9H5F9	Frame_Shift_Del	DEL	ENST00000297508.7	hg19	CCDS5324.1																																																																																			.	.		0.677	MICALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239223.2	NM_182924		-	1487299	G	-	1487299	7	5	352	1	0	1	0	1	0	0	0	0	9583	1348	47	0	2333	0	MICALL2	7	1487299	Frame_Shift_Del	DEL	G	TCGA-WQ-A9G7-01A-11D-A36X-10		1487299	157651364	175	49591										
TNRC18	84629	hgsc.bcm.edu	37	chr7	5427704	5427704	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	actttataaggctctgcatgGccgaggcctctccagacccg	10	14	2	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr7:5427704G>A	ENST00000430969.1	-	5	2099	c.1751C>T	c.(1750-1752)gCc>gTc	p.A584V	TNRC18_ENST00000399537.4_Missense_Mutation_p.A584V	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	584							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		GCTCTGCATGGCCGAGGCCTC	0.687																																					p.A584V		Atlas-SNP	.											.	TNRC18	311	.	0			c.C1751T						.						6	8	8					7																	5427704		1916	4044	5960	SO:0001583	missense	84629	exon5			TGCATGGCCGAGG	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"Trinucleotide (CAG) repeat containing"	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.1751C>T	chr7.hg19:g.5427704G>A	ENSP00000395538:p.Ala584Val	100.0	0.0		161.0	44.0	NM_001080495	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	hg19	CCDS47534.1	.	.	.	.	.	.	.	.	.	.	g	16.63	3.176940	0.57692	.	.	ENSG00000182095	ENST00000399537;ENST00000430969	T;T	0.45668	0.91;0.89	4.81	4.81	0.61882	.	.	.	.	.	T	0.61763	0.2373	M	0.63843	1.955	0.45822	D	0.998694	D	0.76494	0.999	D	0.66084	0.941	T	0.66658	-0.5868	9	0.87932	D	0	.	17.921	0.88966	0.0:0.0:1.0:0.0	.	584	O15417	TNC18_HUMAN	V	584	ENSP00000382452:A584V;ENSP00000395538:A584V	ENSP00000382452:A584V	A	-	2	0	TNRC18	5394230	1.000000	0.71417	0.998000	0.56505	0.906000	0.53458	8.654000	0.91092	2.217000	0.71921	0.550000	0.68814	GCC	.	.		0.687	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				A	5427704	G	A	5427704	3	1	352	1	0	0	0	0	1	0	0	0	16354	1203	42	3	7259	3	TNRC18	7	5427704	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	3940405	5427704	153710959	176	49592										
OSBPL3	26031	hgsc.bcm.edu	37	chr7	24859857	24859857	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gataggcggatggtggctgaCctgatggaaacaaaggacag	16	6	0	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr7:24859857C>T	ENST00000313367.2	-	17	2336	c.1885G>A	c.(1885-1887)Gtc>Atc	p.V629I	OSBPL3_ENST00000353930.1_Splice_Site_p.V593I|OSBPL3_ENST00000352860.1_Splice_Site_p.V598I|OSBPL3_ENST00000396431.1_Splice_Site_p.V598I|OSBPL3_ENST00000396429.1_Splice_Site_p.V593I|OSBPL3_ENST00000409069.1_Splice_Site_p.V562I|OSBPL3_ENST00000431825.2_Splice_Site_p.V562I	NM_015550.2	NP_056365.1	Q9H4L5	OSBL3_HUMAN	oxysterol binding protein-like 3	629					lipid transport (GO:0006869)	cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(19)|prostate(1)|skin(3)|urinary_tract(1)	43						TGGTGGCTGACCTGATGGAAA	0.398											OREG0017898	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V629I		Atlas-SNP	.											.	OSBPL3	100	.	0			c.G1885A						.						93	86	89					7																	24859857		2203	4300	6503	SO:0001630	splice_region_variant	26031	exon17			GGCTGACCTGATG	AB014604	CCDS5390.1, CCDS5391.1, CCDS5392.1, CCDS47564.1	7p15.3	2013-01-10			ENSG00000070882	ENSG00000070882		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16370	protein-coding gene	gene with protein product		606732		OSBP3		9734811	Standard	XM_005249698		Approved	ORP-3, ORP3, KIAA0704	uc003sxf.3	Q9H4L5	OTTHUMG00000023277	ENST00000313367.2:c.1885-1G>A	chr7.hg19:g.24859857C>T		417.0	1.0	774	524.0	159.0	NM_015550	A4D167|A4D168|A4D169|A4D170|A4D171|A4D172|B8ZZ79|B8ZZP0|O14591|O43357|O43358|Q8N702|Q8N703|Q8N704|Q8NFH0|Q8NFH1|Q8NI12|Q8NI13|Q9BZF4|Q9UED6	Missense_Mutation	SNP	ENST00000313367.2	hg19	CCDS5390.1	.	.	.	.	.	.	.	.	.	.	C	34	5.407932	0.96051	.	.	ENSG00000070882	ENST00000313367;ENST00000352860;ENST00000353930;ENST00000431825;ENST00000396431;ENST00000396429;ENST00000409069	T;T;T;T;T;T;T	0.57273	0.41;0.41;0.41;0.41;0.41;0.41;0.41	5.69	5.69	0.88448	Oxysterol-binding protein, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.78817	0.4343	M	0.88241	2.94	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.97110	0.998;0.999;1.0;0.999	T	0.82184	-0.0583	10	0.87932	D	0	-16.6111	19.8097	0.96542	0.0:1.0:0.0:0.0	.	562;598;593;629	Q9H4L5-4;Q9H4L5-2;Q9H4L5-3;Q9H4L5	.;.;.;OSBL3_HUMAN	I	629;598;593;562;598;593;562	ENSP00000315410:V629I;ENSP00000315331:V598I;ENSP00000315277:V593I;ENSP00000389779:V562I;ENSP00000379708:V598I;ENSP00000379706:V593I;ENSP00000386953:V562I	ENSP00000315410:V629I	V	-	1	0	OSBPL3	24826382	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	7.744000	0.85034	2.685000	0.91497	0.484000	0.47621	GTC	.	.		0.398	OSBPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214085.2		Missense_Mutation	T	24859857	C	T	24859857	5	4	352	1	0	0	0	0	0	0	1	0	11288	521	18	3	806	3	OSBPL3	7	24859857	Splice_Site	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	19432153	24859857	134278806	177	49593										
ADCYAP1R1	117	hgsc.bcm.edu	37	chr7	31123783	31123783	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agtggtgagccggaactgcaCggaggatggctggtcggaac	18	8	0	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr7:31123783C>T	ENST00000304166.4	+	7	645	c.356C>T	c.(355-357)aCg>aTg	p.T119M	ADCYAP1R1_ENST00000409489.1_Missense_Mutation_p.T119M|ADCYAP1R1_ENST00000409363.1_Missense_Mutation_p.T98M|ADCYAP1R1_ENST00000396211.2_Missense_Mutation_p.T119M	NM_001118.4|NM_001199635.1|NM_001199636.1	NP_001109.2|NP_001186564.1|NP_001186565.1	P41586	PACR_HUMAN	adenylate cyclase activating polypeptide 1 (pituitary) receptor type I	119					activation of adenylate cyclase activity (GO:0007190)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)|vasoactive intestinal polypeptide receptor activity (GO:0004999)			endometrium(1)|large_intestine(4)|liver(2)|lung(24)|ovary(1)|skin(2)|stomach(1)	35						CGGAACTGCACGGAGGATGGC	0.498																																					p.T119M	Ovarian(44;225 1186 2158 11092)	Atlas-SNP	.											.	ADCYAP1R1	78	.	0			c.C356T						.						168	162	164					7																	31123783		2203	4300	6503	SO:0001583	missense	117	exon7			ACTGCACGGAGGA		CCDS5433.1, CCDS56480.1, CCDS56481.1	7p14.3	2012-09-20			ENSG00000078549	ENSG00000078549		"GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"	242	protein-coding gene	gene with protein product	"PACAP receptor 1"	102981				7902709	Standard	NM_001199635		Approved	PAC1, PACAPR, PAC1R	uc003tcg.3	P41586	OTTHUMG00000023884	ENST00000304166.4:c.356C>T	chr7.hg19:g.31123783C>T	ENSP00000306620:p.Thr119Met	127.0	0.0		140.0	26.0	NM_001118	A8K1Y1|B7ZLA7|B8ZZK3|Q17S10	Missense_Mutation	SNP	ENST00000304166.4	hg19	CCDS5433.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.004655	0.74932	.	.	ENSG00000078549	ENST00000304166;ENST00000409363;ENST00000396211;ENST00000409489	T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28	5.66	5.66	0.87406	GPCR, family 2, extracellular hormone receptor domain (3);	0.000000	0.85682	D	0.000000	D	0.83492	0.5266	M	0.82716	2.605	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;0.997;0.998	D;D;D;D;D	0.97110	0.998;1.0;1.0;0.923;0.957	D	0.85565	0.1230	10	0.87932	D	0	.	17.2566	0.87059	0.0:1.0:0.0:0.0	.	119;119;119;98;119	B7ZLA7;Q17S10;E9PFU5;B8ZZK3;P41586	.;.;.;.;PACR_HUMAN	M	119;98;119;119	ENSP00000306620:T119M;ENSP00000387335:T98M;ENSP00000379514:T119M;ENSP00000386395:T119M	ENSP00000306620:T119M	T	+	2	0	ADCYAP1R1	31090308	1.000000	0.71417	0.961000	0.40146	0.428000	0.31595	7.429000	0.80309	2.653000	0.90120	0.563000	0.77884	ACG	.	.		0.498	ADCYAP1R1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000215041.3	NM_001118		T	31123783	C	T	31123783	3	4	352	1	0	0	0	0	1	0	0	0	303	536	19	1	378	1	ADCYAP1R1	7	31123783	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	6263926	31123783	128014880	178	49594										
GLI3	2737	hgsc.bcm.edu	37	chr7	42017310	42017310	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agtctcgagtaggcctttgtGcaaccttcaaactgaggaca	10	10	2	1	rs532041527	byFrequency	TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr7:42017310G>A	ENST00000395925.3	-	12	1743	c.1659C>T	c.(1657-1659)tgC>tgT	p.C553C	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	553					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						AGGCCTTTGTGCAACCTTCAA	0.448									Pallister-Hall syndrome;Greig Cephalopolysyndactyly		OREG0018015	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	2	0.000399361	0	0	5008	,	,		21019	0		0	False		,,,				2504	0.002				p.C553C		Atlas-SNP	.											.	GLI3	312	.	0			c.C1659T						.						202	170	181					7																	42017310		2203	4300	6503	SO:0001819	synonymous_variant	2737	exon12	Familial Cancer Database	;	CTTTGTGCAACCT		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"Zinc fingers, C2H2-type"	4319	protein-coding gene	gene with protein product	"zinc finger protein GLI3", "oncogene GLI3", "DNA-binding protein"	165240	"Greig cephalopolysyndactyly syndrome", "GLI-Kruppel family member GLI3", "glioma-associated oncogene family zinc finger 3"	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.1659C>T	chr7.hg19:g.42017310G>A		174.0	0.0	905	177.0	49.0	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Silent	SNP	ENST00000395925.3	hg19	CCDS5465.1																																																																																			.	.		0.448	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168		A	42017310	G	A	42017310	2	1	352	1	0	0	0	0	0	0	0	1	6447	1311	46	3		3	GLI3	7	42017310	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	10893527	42017310	117121353	179	49595										
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47925412	47925412	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ctggagcctcccccaggactGcagagtcccccgcaggagga	13	16	0	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr7:47925412G>A	ENST00000289672.2	-	18	3127	c.3077C>T	c.(3076-3078)gCa>gTa	p.A1026V		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	1026	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						CCCCAGGACTGCAGAGTCCCC	0.617																																					p.A1026V		Atlas-SNP	.											.	PKD1L1	328	.	0			c.C3077T						.						71	79	76					7																	47925412		2203	4300	6503	SO:0001583	missense	168507	exon18			AGGACTGCAGAGT	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"polycystin-1L1"	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.3077C>T	chr7.hg19:g.47925412G>A	ENSP00000289672:p.Ala1026Val	108.0	0.0		134.0	47.0	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	hg19	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	G	7.805	0.714549	0.15306	.	.	ENSG00000158683	ENST00000289672	T	0.21932	1.98	4.78	-1.15	0.09709	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	2586.730000	0.00166	N	0.000000	T	0.20941	0.0504	L	0.53249	1.67	0.09310	N	1	B	0.14805	0.011	B	0.22386	0.039	T	0.14671	-1.0464	10	0.29301	T	0.29	0.093	4.2287	0.10592	0.4096:0.0:0.436:0.1544	.	1026	Q8TDX9	PK1L1_HUMAN	V	1026	ENSP00000289672:A1026V	ENSP00000289672:A1026V	A	-	2	0	PKD1L1	47891937	0.001000	0.12720	0.000000	0.03702	0.005000	0.04900	0.794000	0.26958	-0.470000	0.06901	-0.931000	0.02705	GCA	.	.		0.617	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		A	47925412	G	A	47925412	3	1	352	1	0	0	0	0	1	0	0	0	11973	1319	46	3	5632	3	PKD1L1	7	47925412	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	5908102	47925412	111213251	180	49596										
CLDN4	1364	hgsc.bcm.edu	37	chr7	73245764	73245764	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggcactgccgcaggacctgcAggcggcccgcgccctcgtca	14	18	1	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr7:73245764A>G	ENST00000435050.1	+	2	2913	c.233A>G	c.(232-234)cAg>cGg	p.Q78R	CLDN4_ENST00000340958.2_Missense_Mutation_p.Q78R|CLDN4_ENST00000431918.1_Missense_Mutation_p.Q78R			O14493	CLD4_HUMAN	claudin 4	78	Interaction with EPHA2.				calcium-independent cell-cell adhesion (GO:0016338)|establishment of skin barrier (GO:0061436)|female pregnancy (GO:0007565)|response to progesterone (GO:0032570)|signal transduction (GO:0007165)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|basal plasma membrane (GO:0009925)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)|transmembrane signaling receptor activity (GO:0004888)			kidney(2)|lung(4)|urinary_tract(1)	7		Lung NSC(55;0.159)				CAGGACCTGCAGGCGGCCCGC	0.637																																					p.Q78R		Atlas-SNP	.											.	CLDN4	10	.	0			c.A233G						.						78	70	73					7																	73245764		2203	4300	6503	SO:0001583	missense	1364	exon1			ACCTGCAGGCGGC	AB000712	CCDS5560.1	7q11.23	2008-07-18			ENSG00000189143	ENSG00000189143		"Claudins"	2046	protein-coding gene	gene with protein product	"Clostridium perfringens enterotoxin receptor 1", "Williams-Beuren syndrome chromosomal region 8 protein"	602909		CPETR, CPETR1		9334247, 9892664	Standard	NM_001305		Approved	CPE-R, WBSCR8, hCPE-R	uc003tzi.4	O14493	OTTHUMG00000023425	ENST00000435050.1:c.233A>G	chr7.hg19:g.73245764A>G	ENSP00000409544:p.Gln78Arg	79.0	0.0		112.0	5.0	NM_001305		Missense_Mutation	SNP	ENST00000435050.1	hg19	CCDS5560.1	.	.	.	.	.	.	.	.	.	.	A	33	5.262208	0.95368	.	.	ENSG00000189143	ENST00000435050;ENST00000431918;ENST00000340958;ENST00000543176	D;D;D	0.89746	-2.56;-2.56;-2.56	5.37	5.37	0.77165	.	0.055575	0.64402	D	0.000001	D	0.94159	0.8126	M	0.86028	2.79	0.53688	D	0.999978	D	0.65815	0.995	D	0.64595	0.927	D	0.94904	0.8059	10	0.87932	D	0	.	13.3146	0.60399	1.0:0.0:0.0:0.0	.	78	O14493	CLD4_HUMAN	R	78;78;78;65	ENSP00000409544:Q78R;ENSP00000388639:Q78R;ENSP00000342445:Q78R	ENSP00000342445:Q78R	Q	+	2	0	CLDN4	72883700	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.339000	0.96797	2.045000	0.60652	0.459000	0.35465	CAG	.	.		0.637	CLDN4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348030.1	NM_001305		G	73245764	A	G	73245764	3	3	352	1	0	0	0	0	1	0	0	0	3489	188	7	2	235	2	CLDN4	7	73245764	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	25320352	73245764	85892899	181	49597										
TRRAP	8295	hgsc.bcm.edu	37	chr7	98528292	98528292	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tgttttcttacatcgtggagCgcctgtgtgcatgttgttat	11	7	1	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr7:98528292C>T	ENST00000359863.4	+	25	3639	c.3430C>T	c.(3430-3432)Cgc>Tgc	p.R1144C	TRRAP_ENST00000355540.3_Missense_Mutation_p.R1144C|TRRAP_ENST00000446306.3_Missense_Mutation_p.R1143C	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	1144					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			CATCGTGGAGCGCCTGTGTGC	0.488																																					p.R1144C		Atlas-SNP	.											.	TRRAP	863	.	0			c.C3430T						.						175	174	175					7																	98528292		2203	4300	6503	SO:0001583	missense	8295	exon25			GTGGAGCGCCTGT	AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.3430C>T	chr7.hg19:g.98528292C>T	ENSP00000352925:p.Arg1144Cys	81.0	0.0		89.0	32.0	NM_001244580	A4D265|O75218|Q9Y631|Q9Y6H4	Missense_Mutation	SNP	ENST00000359863.4	hg19	CCDS59066.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.043468	0.93685	.	.	ENSG00000196367	ENST00000359863;ENST00000355540;ENST00000446306	T;T	0.64618	3.56;-0.11	5.53	5.53	0.82687	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.78078	0.4227	M	0.62723	1.935	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.70716	0.966;0.91;0.97	T	0.79077	-0.1951	10	0.87932	D	0	.	19.8174	0.96576	0.0:1.0:0.0:0.0	.	1144;858;1144	Q9Y4A5-2;Q59FH1;Q9Y4A5	.;.;TRRAP_HUMAN	C	1144;1144;1142	ENSP00000352925:R1144C;ENSP00000347733:R1144C	ENSP00000347733:R1144C	R	+	1	0	TRRAP	98366228	1.000000	0.71417	1.000000	0.80357	0.725000	0.41563	7.772000	0.85439	2.757000	0.94681	0.591000	0.81541	CGC	.	.		0.488	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496		T	98528292	C	T	98528292	3	4	352	1	0	0	0	0	1	0	0	0	16616	768	27	1	3524	1	TRRAP	7	98528292	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	25282528	98528292	60610371	182	49598										
ZNF394	84124	hgsc.bcm.edu	37	chr7	99092121	99092121	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tgcttttccaccctgtcctcAtgggtactgccacacttaga	7	14	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr7:99092121A>G	ENST00000337673.6	-	3	920	c.717T>C	c.(715-717)caT>caC	p.H239H	ZNF789_ENST00000494186.1_Intron|ZNF789_ENST00000493485.1_Intron|ZNF394_ENST00000426306.2_3'UTR|ZNF394_ENST00000394177.3_5'Flank	NM_032164.2	NP_115540.2	Q53GI3	ZN394_HUMAN	zinc finger protein 394	239					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(5)|stomach(1)|urinary_tract(1)	16	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					CCCTGTCCTCATGGGTACTGC	0.498																																					p.H239H	Ovarian(24;589 697 9939 12704 40742)	Atlas-SNP	.											.	ZNF394	48	.	0			c.T717C						.						95	96	96					7																	99092121		2203	4300	6503	SO:0001819	synonymous_variant	84124	exon3			GTCCTCATGGGTA	BC025241	CCDS5666.1	7q22.1	2014-01-28			ENSG00000160908	ENSG00000160908		"Zinc fingers, C2H2-type", "-", "-", "-"	18832	protein-coding gene	gene with protein product							Standard	NM_032164		Approved	ZKSCAN14, FLJ12298, ZSCAN46	uc003uqs.3	Q53GI3	OTTHUMG00000154660	ENST00000337673.6:c.717T>C	chr7.hg19:g.99092121A>G		45.0	0.0		64.0	17.0	NM_032164	A4D281|Q05DA6|Q6P5X9|Q8TB27|Q9HA37|Q9UD51	Silent	SNP	ENST00000337673.6	hg19	CCDS5666.1																																																																																			.	.		0.498	ZNF394-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336498.1	NM_032164		G	99092121	A	G	99092121	2	3	352	1	0	0	0	0	0	0	0	1	17895	214	8	2		2	ZNF394	7	99092121	Silent	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	563829	99092121	60046542	183	49599										
PRKAR2B	5577	hgsc.bcm.edu	37	chr7	106685627	106685627	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cgaggacggggaggaggaggAggcggcgcccgcggacgcag	23	10	0	0	rs368313660		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr7:106685627A>C	ENST00000265717.4	+	1	534	c.275A>C	c.(274-276)gAg>gCg	p.E92A		NM_002736.2	NP_002727.2	P31323	KAP3_HUMAN	protein kinase, cAMP-dependent, regulatory, type II, beta	92	Dimerization and phosphorylation.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fatty acid metabolic process (GO:0006631)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|mitotic cell cycle (GO:0000278)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	14						GAGGAGGAGGAGGCGGCGCCC	0.756													A|||	1	0.000199681	8e-04	0	5008	,	,		8914	0		0	False		,,,				2504	0				p.E92A		Atlas-SNP	.											.	PRKAR2B	34	.	0			c.A275C						.	A	ALA/GLU	1,3291		0,1,1645	2	2	2		275	4.3	1	7		2	0,6650		0,0,3325	no	missense	PRKAR2B	NM_002736.2	107	0,1,4970	CC,CA,AA		0.0,0.0304,0.0101	benign	92/419	106685627	1,9941	1646	3325	4971	SO:0001583	missense	5577	exon1			AGGAGGAGGCGGC		CCDS5740.1	7q22.3	2010-04-22			ENSG00000005249	ENSG00000005249	2.7.11.1		9392	protein-coding gene	gene with protein product		176912		PRKAR2		1358799	Standard	NM_002736		Approved		uc003vdx.3	P31323	OTTHUMG00000137418	ENST00000265717.4:c.275A>C	chr7.hg19:g.106685627A>C	ENSP00000265717:p.Glu92Ala	85.0	0.0		111.0	40.0	NM_002736	A4D0R9	Missense_Mutation	SNP	ENST00000265717.4	hg19	CCDS5740.1	.	.	.	.	.	.	.	.	.	.	A	18.81	3.703735	0.68501	3.04E-4	0.0	ENSG00000005249	ENST00000265717;ENST00000543645;ENST00000539794	D	0.82167	-1.58	4.29	4.29	0.51040	.	0.372936	0.27797	N	0.017808	T	0.73737	0.3625	L	0.32530	0.975	0.51482	D	0.999921	P	0.46987	0.888	B	0.38985	0.287	T	0.75673	-0.3236	10	0.42905	T	0.14	-8.6524	13.2761	0.60188	1.0:0.0:0.0:0.0	.	92	P31323	KAP3_HUMAN	A	92;92;79	ENSP00000265717:E92A	ENSP00000265717:E92A	E	+	2	0	PRKAR2B	106472863	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	4.232000	0.58645	1.813000	0.52934	0.379000	0.24179	GAG	.	.		0.756	PRKAR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268386.1			C	106685627	A	C	106685627	3	2	352	1	0	0	0	0	1	0	0	0	12518	304	11	5	277	5	PRKAR2B	7	106685627	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	7593506	106685627	52453036	184	49600										
HBP1	26959	hgsc.bcm.edu	37	chr7	106840668	106840668	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aatgaagagagaagaatgtaCacattagaagcaaaggcttt	10	4	0	5	rs538604670		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr7:106840668C>T	ENST00000222574.4	+	10	1635	c.1449C>T	c.(1447-1449)taC>taT	p.Y483Y	HBP1_ENST00000461963.1_3'UTR|HBP1_ENST00000468410.1_Silent_p.Y483Y|HBP1_ENST00000485846.1_Silent_p.Y483Y	NM_012257.3	NP_036389.2	O60381	HBP1_HUMAN	HMG-box transcription factor 1	483					cell cycle arrest (GO:0007050)|positive regulation of potassium ion transport (GO:0043268)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA binding (GO:0003723)			large_intestine(4)|lung(3)|prostate(1)|skin(2)	10						GAAGAATGTACACATTAGAAG	0.358																																					p.Y493Y		Atlas-SNP	.											.	HBP1	31	.	0			c.C1479T						.						132	123	126					7																	106840668		2203	4300	6503	SO:0001819	synonymous_variant	26959	exon10			AATGTACACATTA	BC017069	CCDS5741.1	7q22-q31	2003-10-08			ENSG00000105856	ENSG00000105856			23200	protein-coding gene	gene with protein product						9030690, 11500377	Standard	NM_001244262		Approved		uc011klv.2	O60381	OTTHUMG00000157642	ENST00000222574.4:c.1449C>T	chr7.hg19:g.106840668C>T		137.0	0.0		202.0	47.0	NM_001244262	B3KVB7|Q8TBM1|Q8TE93|Q96AJ2	Silent	SNP	ENST00000222574.4	hg19	CCDS5741.1																																																																																			.	.		0.358	HBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349297.1	NM_012257		T	106840668	C	T	106840668	2	4	352	1	0	0	0	0	0	0	0	1	6994	489	17	3		3	HBP1	7	106840668	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	155041	106840668	52297995	185	49601										
HYAL4	23553	hgsc.bcm.edu	37	chr7	123509038	123509038	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ccaaactactctgggtcatgCccagaagacgaagtcttgag	10	11	3	3			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr7:123509038C>T	ENST00000223026.4	+	3	1349	c.711C>T	c.(709-711)tgC>tgT	p.C237C	HYAL4_ENST00000476325.1_Silent_p.C237C	NM_012269.2	NP_036401.2	Q2M3T9	HYAL4_HUMAN	hyaluronoglucosaminidase 4	237					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate catabolic process (GO:0030207)|glycosaminoglycan catabolic process (GO:0006027)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)	hyalurononglucosaminidase activity (GO:0004415)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	23						CTGGGTCATGCCCAGAAGACG	0.448																																					p.C237C		Atlas-SNP	.											.	HYAL4	65	.	0			c.C711T						.						79	83	81					7																	123509038		2203	4300	6503	SO:0001819	synonymous_variant	23553	exon3			GTCATGCCCAGAA	AF009010	CCDS5789.1	7q31.3	2010-01-14			ENSG00000106302	ENSG00000106302			5323	protein-coding gene	gene with protein product	"hyaluronidase 4"	604510				10493834	Standard	NM_012269		Approved		uc003vlc.3	Q2M3T9	OTTHUMG00000157349	ENST00000223026.4:c.711C>T	chr7.hg19:g.123509038C>T		125.0	0.0		123.0	14.0	NM_012269	D0VXG1|Q9UL99|Q9Y6T9	Silent	SNP	ENST00000223026.4	hg19	CCDS5789.1																																																																																			.	.		0.448	HYAL4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348545.1	NM_012269		T	123509038	C	T	123509038	2	4	352	1	0	0	0	0	0	0	0	1	7475	747	26	3		3	HYAL4	7	123509038	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	16668370	123509038	35629625	186	49602										
SLC35B4	84912	hgsc.bcm.edu	37	chr7	133979689	133979689	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gaagacaaacaaggtgcccaGccagtgccacagggtgaagg	14	10	0	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr7:133979689G>A	ENST00000378509.4	-	10	1191	c.892C>T	c.(892-894)Ctg>Ttg	p.L298L	SLC35B4_ENST00000466599.1_5'UTR	NM_032826.4	NP_116215.1	Q969S0	S35B4_HUMAN	solute carrier family 35 (UDP-xylose/UDP-N-acetylglucosamine transporter), member B4	298					carbohydrate transport (GO:0008643)|regulation of gluconeogenesis (GO:0006111)|transmembrane transport (GO:0055085)|UDP-N-acetylglucosamine transport (GO:0015788)|UDP-xylose transport (GO:0015790)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	UDP-N-acetylglucosamine transmembrane transporter activity (GO:0005462)|UDP-xylose transmembrane transporter activity (GO:0005464)			large_intestine(1)|lung(2)|skin(1)|stomach(1)	5						AAGGTGCCCAGCCAGTGCCAC	0.517																																					p.L298L		Atlas-SNP	.											.	SLC35B4	19	.	0			c.C892T						.						153	139	143					7																	133979689		2203	4300	6503	SO:0001819	synonymous_variant	84912	exon10			TGCCCAGCCAGTG	AB052892	CCDS34756.1	7q33	2013-07-17	2013-07-17		ENSG00000205060	ENSG00000205060		"Solute carriers"	20584	protein-coding gene	gene with protein product		610923	"solute carrier family 35, member B4"				Standard	NM_032826		Approved	FLJ14697, YEA4	uc003vrn.3	Q969S0	OTTHUMG00000155321	ENST00000378509.4:c.892C>T	chr7.hg19:g.133979689G>A		116.0	0.0		119.0	32.0	NM_032826	A4D1P3|A6NNS4|Q53GQ7|Q8TCU7|Q96K33	Silent	SNP	ENST00000378509.4	hg19	CCDS34756.1																																																																																			.	.		0.517	SLC35B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339444.2	NM_032826		A	133979689	G	A	133979689	2	1	352	1	0	0	0	0	0	0	0	1	14593	962	34	3		3	SLC35B4	7	133979689	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	10470651	133979689	25158974	187	49603										
DOK2	9046	hgsc.bcm.edu	37	chr8	21767272	21767272	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gggctatcaggccggggcagCgacgcggggattgtggctgg	21	9	1	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr8:21767272C>T	ENST00000276420.4	-	5	1047	c.789G>A	c.(787-789)tcG>tcA	p.S263S	DOK2_ENST00000544659.1_Silent_p.S109S	NM_003974.2	NP_003965.2	O60496	DOK2_HUMAN	docking protein 2, 56kDa	263	Pro-rich.				blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|leukocyte migration (GO:0050900)|Ras protein signal transduction (GO:0007265)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)	receptor signaling protein activity (GO:0005057)			NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(9)|ovary(2)|prostate(3)|skin(1)	26				Colorectal(74;0.0145)|COAD - Colon adenocarcinoma(73;0.0608)		GCCGGGGCAGCGACGCGGGGA	0.662																																					p.S263S		Atlas-SNP	.											.	DOK2	51	.	0			c.G789A						.						49	57	54					8																	21767272		2203	4299	6502	SO:0001819	synonymous_variant	9046	exon5			GGGCAGCGACGCG	AF034970	CCDS6016.1	8p21.3	2008-08-07	2002-08-29		ENSG00000147443	ENSG00000147443			2991	protein-coding gene	gene with protein product		604997	"docking protein 2, 56kD"			9478921, 14645010	Standard	NM_003974		Approved	p56dok-2, Dok-2	uc003wzy.1	O60496	OTTHUMG00000131075	ENST00000276420.4:c.789G>A	chr8.hg19:g.21767272C>T		55.0	0.0		30.0	10.0	NM_003974	Q8N5A4	Silent	SNP	ENST00000276420.4	hg19	CCDS6016.1																																																																																			.	.		0.662	DOK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253735.3	NM_003974		T	21767272	C	T	21767272	2	4	352	1	0	0	0	0	0	0	0	1	4699	755	27	1		1	DOK2	8	21767272	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10		21767272	124596750	188	49604										
HR	55806	hgsc.bcm.edu	37	chr8	21976493	21976493	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aagcggcggatgcgctgggcGtcctgtgcccggaacacgtg	17	12	0	0	rs371739727		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr8:21976493G>A	ENST00000381418.4	-	16	4663	c.3183C>T	c.(3181-3183)gaC>gaT	p.D1061D	HR_ENST00000312841.8_Silent_p.D1061D	NM_005144.4	NP_005135.2	O43593	HAIR_HUMAN	hair growth associated	1061	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	27		Breast(100;0.000162)|Acute lymphoblastic leukemia(644;0.0775)|Prostate(55;0.116)		KIRC - Kidney renal clear cell carcinoma(542;1.19e-05)|BRCA - Breast invasive adenocarcinoma(99;3.56e-05)|Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)		TGCGCTGGGCGTCCTGTGCCC	0.677																																					p.D1061D		Atlas-SNP	.											HR,NS,carcinoma,0,1	HR	71	.	0			c.C3183T						.	G	,	0,4406		0,0,2203	42	47	45		3183,3183	1	1	8		45	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	HR	NM_005144.4,NM_018411.4	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	1061/1190,1061/1135	21976493	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	55806	exon16			CTGGGCGTCCTGT	AF039196	CCDS6022.1, CCDS6023.1	8p12	2012-12-07	2012-12-07		ENSG00000168453	ENSG00000168453			5172	protein-coding gene	gene with protein product		602302	"hairless (mouse) homolog", "hairless homolog (mouse)"	ALUNC		10051399, 9463324	Standard	NM_018411		Approved	AU	uc003xas.3	O43593	OTTHUMG00000097089	ENST00000381418.4:c.3183C>T	chr8.hg19:g.21976493G>A		182.0	1.0		129.0	48.0	NM_018411	Q6GS30|Q96H33|Q9NPE1	Silent	SNP	ENST00000381418.4	hg19	CCDS6022.1																																																																																			.	.		0.677	HR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214213.1			A	21976493	G	A	21976493	2	1	352	1	0	0	0	0	0	0	0	1	7356	1136	40	1		1	HR	8	21976493	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	209221	21976493	124387529	189	49605										
PURG	29942	hgsc.bcm.edu	37	chr8	30889771	30889771	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tatttcctattgtccctctcGatatagtctgttttcaggac	6	10	3	0	rs11574152	byFrequency	TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr8:30889771G>A	ENST00000475541.1	-	1	1460	c.528C>T	c.(526-528)atC>atT	p.I176I	WRN_ENST00000298139.5_5'Flank|PURG_ENST00000339382.2_Silent_p.I176I	NM_013357.2	NP_037489.1	Q9UJV8	PURG_HUMAN	purine-rich element binding protein G	176						nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(3)|lung(5)|ovary(2)|urinary_tract(1)	12				KIRC - Kidney renal clear cell carcinoma(542;0.0895)|Kidney(114;0.108)		TGTCCCTCTCGATATAGTCTG	0.527																																					p.I176I		Atlas-SNP	.											.	PURG	79	.	0			c.C528T						.						73	76	75					8																	30889771		2203	4300	6503	SO:0001819	synonymous_variant	29942	exon1			CCTCTCGATATAG	AF195513	CCDS34878.1, CCDS6081.1	8p11	2004-02-09			ENSG00000172733	ENSG00000172733			17930	protein-coding gene	gene with protein product						12034829	Standard	NM_013357		Approved	PURG-A, PURG-B	uc003xin.3	Q9UJV8	OTTHUMG00000157357	ENST00000475541.1:c.528C>T	chr8.hg19:g.30889771G>A		70.0	0.0		58.0	16.0	NM_013357	Q8TE64	Silent	SNP	ENST00000475541.1	hg19	CCDS6081.1																																																																																			.	G|0.999;T|0.001		0.527	PURG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348565.1	NM_013357		A	30889771	G	A	30889771	2	1	352	1	0	0	0	0	0	0	0	1	12844	1048	37	1		1	PURG	8	30889771	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	8913278	30889771	115474251	190	49606										
C8orf41	80185	hgsc.bcm.edu	37	chr8	33357912	33357912	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gtggcctcctgtagcagggcGctcttaacagactcaggtgt	13	11	2	1	rs145192530		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr8:33357912G>A	ENST00000431156.2	-	7	1974	c.1356C>T	c.(1354-1356)agC>agT	p.S452S	MAK16_ENST00000360128.6_3'UTR|TTI2_ENST00000360742.5_Silent_p.S452S|TTI2_ENST00000520636.1_Silent_p.S421S|TTI2_ENST00000519356.1_5'UTR	NM_001102401.2	NP_001095871.1	Q6NXR4	TTI2_HUMAN	TELO2 interacting protein 2	452																	GTAGCAGGGCGCTCTTAACAG	0.512																																					p.S452S		Atlas-SNP	.											.	.	.	.	0			c.C1356T						.	G	,,	1,4405	2.1+/-5.4	0,1,2202	102	88	93		1356,1356,	-10.5	0	8	dbSNP_134	93	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,utr-3	TTI2,MAK16	NM_001102401.1,NM_025115.2,NM_032509.3	,,	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	,,	452/509,452/509,	33357912	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	80185	exon7			CAGGGCGCTCTTA	AK026916	CCDS6090.1	8p12	2011-11-10	2011-11-10	2011-09-22		ENSG00000129696			26262	protein-coding gene	gene with protein product		614426	"chromosome 8 open reading frame 41", "Tel2 interacting protein 2 homolog (S. pombe)"	C8orf41		20801936, 20810650	Standard	NM_025115		Approved	FLJ23263	uc003xjm.5	Q6NXR4		ENST00000431156.2:c.1356C>T	chr8.hg19:g.33357912G>A		87.0	0.0		86.0	42.0	NM_001265581	D3DSV7|Q96IM2|Q9H5N4	Silent	SNP	ENST00000431156.2	hg19	CCDS6090.1																																																																																			.	G|1.000;A|0.000		0.512	TTI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376555.1	NM_025115		A	33357912	G	A	33357912	2	1	352	1	0	0	0	0	0	0	0	1	2429	1078	38	1		1	C8orf41	8	33357912	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	2468141	33357912	113006110	191	49607										
IKBKB	3551	hgsc.bcm.edu	37	chr8	42178286	42178286	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aactcctggtagaacggatgAtggctctgcagaccgacatt	11	10	1	3			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr8:42178286A>G	ENST00000520810.1	+	16	1798	c.1612A>G	c.(1612-1614)Atg>Gtg	p.M538V	IKBKB_ENST00000522147.1_Intron|IKBKB_ENST00000416505.2_Missense_Mutation_p.M479V|IKBKB_ENST00000379708.3_Missense_Mutation_p.M315V|IKBKB_ENST00000520835.1_Missense_Mutation_p.M536V	NM_001556.2	NP_001547.1	O14920	IKKB_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta	538					B cell homeostasis (GO:0001782)|cellular response to tumor necrosis factor (GO:0071356)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of cation channel activity (GO:2001259)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|serine phosphorylation of STAT protein (GO:0042501)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|scaffold protein binding (GO:0097110)			breast(4)|lung(1)|ovary(2)|skin(1)	8	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;6.21e-12)|Lung NSC(13;1.04e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;1.37e-10)|Colorectal(10;0.00102)|OV - Ovarian serous cystadenocarcinoma(14;0.00168)|Lung(22;0.00467)|LUSC - Lung squamous cell carcinoma(45;0.024)|COAD - Colon adenocarcinoma(11;0.0264)		Acetylcysteine(DB06151)|Acetylsalicylic acid(DB00945)|Arsenic trioxide(DB01169)|Auranofin(DB00995)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	AGAACGGATGATGGCTCTGCA	0.567																																					p.M538V		Atlas-SNP	.											.	IKBKB	88	.	0			c.A1612G						.						92	94	93					8																	42178286		2203	4300	6503	SO:0001583	missense	3551	exon16			CGGATGATGGCTC	AF029684	CCDS6128.1, CCDS55228.1, CCDS56535.1	8p11.2	2008-08-18			ENSG00000104365	ENSG00000104365			5960	protein-coding gene	gene with protein product		603258				9878263, 9763654	Standard	NM_001556		Approved	IKK2, NFKBIKB, IKK-beta, IKKB	uc003xow.2	O14920	OTTHUMG00000164092	ENST00000520810.1:c.1612A>G	chr8.hg19:g.42178286A>G	ENSP00000430684:p.Met538Val	83.0	0.0		101.0	12.0	NM_001556	B4DZ30|B4E0U4|O75327	Missense_Mutation	SNP	ENST00000520810.1	hg19	CCDS6128.1	.	.	.	.	.	.	.	.	.	.	A	12.96	2.094800	0.36952	.	.	ENSG00000104365	ENST00000520810;ENST00000416505;ENST00000520835;ENST00000379708	T;T;T;T	0.26223	1.75;1.75;1.75;1.75	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.41026	0.1141	L	0.51422	1.61	0.49213	D	0.999766	D;P;D;B	0.54964	0.969;0.537;0.969;0.22	D;B;D;B	0.63381	0.914;0.219;0.914;0.074	T	0.09751	-1.0660	10	0.19147	T	0.46	.	15.1344	0.72552	1.0:0.0:0.0:0.0	.	479;536;315;538	B4E0U4;O14920-2;B3KRB7;O14920	.;.;.;IKKB_HUMAN	V	538;479;536;315	ENSP00000430684:M538V;ENSP00000404920:M479V;ENSP00000430868:M536V;ENSP00000369030:M315V	ENSP00000369030:M315V	M	+	1	0	IKBKB	42297443	1.000000	0.71417	1.000000	0.80357	0.160000	0.22226	4.907000	0.63300	2.059000	0.61396	0.379000	0.24179	ATG	.	.		0.567	IKBKB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377214.1			G	42178286	A	G	42178286	3	3	352	1	0	0	0	0	1	0	0	0	7620	333	12	2	1670	2	IKBKB	8	42178286	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	8820374	42178286	104185736	192	49608										
SNAI2	6591	hgsc.bcm.edu	37	chr8	49832741	49832741	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gggtctgaaagcttggactgTagtctttcctcttcatcact	9	10	5	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr8:49832741T>C	ENST00000396822.1	-	3	696	c.339A>G	c.(337-339)ctA>ctG	p.L113L	SNAI2_ENST00000020945.1_Silent_p.L113L			O43623	SNAI2_HUMAN	snail family zinc finger 2	113					canonical Wnt signaling pathway (GO:0060070)|cartilage morphogenesis (GO:0060536)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to ionizing radiation (GO:0071479)|desmosome disassembly (GO:0035921)|embryo development (GO:0009790)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|epithelium development (GO:0060429)|negative regulation of anoikis (GO:2000811)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell-cell adhesion by negative regulation of transcription from RNA polymerase II promoter (GO:1900387)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of stem cell proliferation (GO:2000647)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|negative regulation of vitamin D receptor signaling pathway (GO:0070563)|neural crest cell development (GO:0014032)|Notch signaling pathway (GO:0007219)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of histone acetylation (GO:0035066)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of chemokine production (GO:0032642)|regulation of osteoblast differentiation (GO:0045667)|regulation of tight junction assembly (GO:2000810)|sensory perception of sound (GO:0007605)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)			endometrium(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)	18		all_cancers(86;0.0368)|all_epithelial(80;0.000624)|Lung NSC(129;0.0019)|all_lung(136;0.00502)				GCTTGGACTGTAGTCTTTCCT	0.483																																					p.L113L		Atlas-SNP	.											.	SNAI2	53	.	0			c.A339G						.						164	158	160					8																	49832741		2203	4300	6503	SO:0001819	synonymous_variant	6591	exon2			GGACTGTAGTCTT	U97060	CCDS6146.1	8q11.21	2013-05-23	2013-05-23	2002-02-28	ENSG00000019549	ENSG00000019549		"Snail homologs", "Zinc fingers, C2H2-type"	11094	protein-coding gene	gene with protein product		602150	"slug homolog, zinc finger protein (chicken)", "snail homolog 2 (Drosophila)"	SLUG		9337409, 9721220	Standard	NM_003068		Approved	SLUGH1, SNAIL2	uc003xqp.3	O43623	OTTHUMG00000149912	ENST00000396822.1:c.339A>G	chr8.hg19:g.49832741T>C		160.0	0.0		190.0	43.0	NM_003068	B2R6P6|Q53FC1	Silent	SNP	ENST00000396822.1	hg19	CCDS6146.1																																																																																			.	.		0.483	SNAI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313873.2	NM_003068		C	49832741	T	C	49832741	2	2	352	1	0	0	0	0	0	0	0	1	14842	1625	57	2		2	SNAI2	8	49832741	Silent	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	7654455	49832741	96531281	193	49609										
C8orf45	157777	hgsc.bcm.edu	37	chr8	67796211	67796211	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tattttaattataacaagtgAtactctactcatagacaggt	5	6	2	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr8:67796211A>T	ENST00000422365.2	+	9	1226	c.1055A>T	c.(1054-1056)gAt>gTt	p.D352V	MCMDC2_ENST00000541540.1_Missense_Mutation_p.D289V|MCMDC2_ENST00000492775.1_Missense_Mutation_p.D352V|MCMDC2_ENST00000313616.5_Missense_Mutation_p.D352V|MCMDC2_ENST00000396592.3_Missense_Mutation_p.D352V	NM_173518.4	NP_775789.3	Q4G0Z9	MCMD2_HUMAN	minichromosome maintenance domain containing 2	352					DNA replication (GO:0006260)		ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(2)|kidney(2)|lung(5)	9						ATAACAAGTGATACTCTACTC	0.333																																					p.D352V		Atlas-SNP	.											.	MCMDC2	84	.	0			c.A1055T						.						48	49	49					8																	67796211		2203	4300	6503	SO:0001583	missense	157777	exon9			CAAGTGATACTCT	BC034576	CCDS6197.2, CCDS47868.1, CCDS47869.1	8q13.1	2012-04-13	2012-04-13	2012-04-13	ENSG00000178460	ENSG00000178460			26368	protein-coding gene	gene with protein product			"chromosome 8 open reading frame 45"	C8orf45			Standard	NM_173518		Approved	FLJ25692	uc003xwz.4	Q4G0Z9	OTTHUMG00000157068	ENST00000422365.2:c.1055A>T	chr8.hg19:g.67796211A>T	ENSP00000413632:p.Asp352Val	50.0	0.0		77.0	13.0	NM_173518	B4DYZ3|B4DZM4|B4E293|Q6P533|Q7Z3P4	Missense_Mutation	SNP	ENST00000422365.2	hg19	CCDS6197.2	.	.	.	.	.	.	.	.	.	.	A	21.2	4.109835	0.77096	.	.	ENSG00000178460	ENST00000379356;ENST00000396592;ENST00000422365;ENST00000492775;ENST00000313616;ENST00000541540	T;T;T;T;T	0.36520	1.25;1.25;1.25;1.25;1.25	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.59418	0.2192	M	0.65498	2.005	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.998;0.998;0.999	T	0.63152	-0.6701	10	0.87932	D	0	-14.3958	15.8218	0.78654	1.0:0.0:0.0:0.0	.	289;352;352;352	Q4G0Z9-4;Q4G0Z9;B4DXX4;G3XAN3	.;CH045_HUMAN;.;.	V	224;352;352;352;352;289	ENSP00000379837:D352V;ENSP00000413632:D352V;ENSP00000428037:D352V;ENSP00000317234:D352V;ENSP00000445629:D289V	ENSP00000317234:D352V	D	+	2	0	C8orf45	67958765	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	8.271000	0.89883	2.201000	0.70794	0.533000	0.62120	GAT	.	.		0.333	MCMDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347350.1	NM_173518		T	67796211	A	T	67796211	3	4	352	1	0	0	0	0	1	0	0	0	2432	333	12	4	1085	4	C8orf45	8	67796211	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	17963470	67796211	78567811	194	49610										
ARFGEF1	10565	hgsc.bcm.edu	37	chr8	68151115	68151115	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ttgctagtgcctggacatatGcatctctctccagctataaa	7	11	2	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr8:68151115G>A	ENST00000262215.3	-	21	3382	c.2993C>T	c.(2992-2994)gCa>gTa	p.A998V	ARFGEF1_ENST00000520381.1_Missense_Mutation_p.A452V|ARFGEF1_ENST00000518230.1_5'Flank	NM_006421.4	NP_006412.2	Q9Y6D6	BIG1_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)	998					endomembrane system organization (GO:0010256)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein glycosylation in Golgi (GO:0090284)|positive regulation of wound healing (GO:0090303)|protein transport (GO:0015031)|regulation of ARF protein signal transduction (GO:0032012)|regulation of establishment of cell polarity (GO:2000114)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|small nuclear ribonucleoprotein complex (GO:0030532)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|guanyl-nucleotide exchange factor activity (GO:0005085)|myosin binding (GO:0017022)|protein kinase A regulatory subunit binding (GO:0034237)			breast(1)|endometrium(14)|kidney(4)|large_intestine(17)|lung(20)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)			CTGGACATATGCATCTCTCTC	0.358																																					p.A998V		Atlas-SNP	.											.	ARFGEF1	196	.	0			c.C2993T						.						128	113	118					8																	68151115		2203	4300	6503	SO:0001583	missense	10565	exon21			ACATATGCATCTC	AF084520	CCDS6199.1	8q13	2011-08-18	2011-08-18		ENSG00000066777	ENSG00000066777			15772	protein-coding gene	gene with protein product		604141				10212200, 8917509	Standard	NM_006421		Approved	DKFZP434L057, BIG1, ARFGEP1, p200	uc003xxo.2	Q9Y6D6	OTTHUMG00000164626	ENST00000262215.3:c.2993C>T	chr8.hg19:g.68151115G>A	ENSP00000262215:p.Ala998Val	69.0	0.0		124.0	14.0	NM_006421	Q9NV46|Q9UFV2|Q9UNL0	Missense_Mutation	SNP	ENST00000262215.3	hg19	CCDS6199.1	.	.	.	.	.	.	.	.	.	.	G	32	5.170752	0.94807	.	.	ENSG00000066777	ENST00000520381;ENST00000262215	T;T	0.64618	-0.11;0.6	5.32	5.32	0.75619	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.83298	0.5224	M	0.88241	2.94	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.957	D	0.86269	0.1660	10	0.87932	D	0	.	19.3677	0.94471	0.0:0.0:1.0:0.0	.	998;452	Q9Y6D6;E5RIF2	BIG1_HUMAN;.	V	452;998	ENSP00000428429:A452V;ENSP00000262215:A998V	ENSP00000262215:A998V	A	-	2	0	ARFGEF1	68313669	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.800000	0.99124	2.628000	0.89032	0.650000	0.86243	GCA	.	.		0.358	ARFGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379441.4	NM_006421		A	68151115	G	A	68151115	3	1	352	1	0	0	0	0	1	0	0	0	852	1319	46	3	2632	3	ARFGEF1	8	68151115	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	354904	68151115	78212907	195	49611										
EYA1	2138	hgsc.bcm.edu	37	chr8	72267025	72267025	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gcagacactcaccttcggtgCcattgggagtcatggaatta	11	10	2	1	rs267601985		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr8:72267025C>T	ENST00000340726.3	-	3	755	c.116G>A	c.(115-117)gGc>gAc	p.G39D	EYA1_ENST00000388743.2_Missense_Mutation_p.G39D|EYA1_ENST00000303824.7_Missense_Mutation_p.G39D|EYA1_ENST00000388740.3_Intron|EYA1_ENST00000388742.4_Missense_Mutation_p.G39D|EYA1_ENST00000419131.1_Missense_Mutation_p.G39D|EYA1_ENST00000388741.2_Intron	NM_000503.4	NP_000494.2	Q99502	EYA1_HUMAN	EYA transcriptional coactivator and phosphatase 1	39					anatomical structure morphogenesis (GO:0009653)|aorta morphogenesis (GO:0035909)|branching involved in ureteric bud morphogenesis (GO:0001658)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|double-strand break repair (GO:0006302)|embryonic skeletal system morphogenesis (GO:0048704)|establishment of mitotic spindle orientation (GO:0000132)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|histone dephosphorylation (GO:0016576)|lung epithelial cell differentiation (GO:0060487)|metanephros development (GO:0001656)|middle ear morphogenesis (GO:0042474)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|neuron fate specification (GO:0048665)|otic vesicle morphogenesis (GO:0071600)|outer ear morphogenesis (GO:0042473)|outflow tract morphogenesis (GO:0003151)|pattern specification process (GO:0007389)|pharyngeal system development (GO:0060037)|positive regulation of DNA repair (GO:0045739)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of neuron differentiation (GO:0045664)|response to ionizing radiation (GO:0010212)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|striated muscle tissue development (GO:0014706)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)|RNA binding (GO:0003723)	p.G39D(1)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(15)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	44	Breast(64;0.046)		Epithelial(68;0.0837)|all cancers(69;0.247)			ACCTTCGGTGCCATTGGGAGT	0.438																																					p.G39D		Atlas-SNP	.											EYA1,NS,carcinoma,0,1	EYA1	108	.	1	Substitution - Missense(1)	ovary(1)	c.G116A						.						142	145	144					8																	72267025		2203	4300	6503	SO:0001583	missense	2138	exon2			TCGGTGCCATTGG	AJ000098	CCDS34906.1, CCDS34907.1, CCDS47873.1, CCDS75750.1	8q13.3	2014-06-19	2014-06-19		ENSG00000104313	ENSG00000104313		"Protein tyrosine phosphatases / Asp-based PTPs"	3519	protein-coding gene	gene with protein product		601653	"eyes absent (Drosophila) homolog 1", "eyes absent homolog 1 (Drosophila)"	BOR		9020840	Standard	XM_005251184		Approved		uc003xys.4	Q99502	OTTHUMG00000149894	ENST00000340726.3:c.116G>A	chr8.hg19:g.72267025C>T	ENSP00000342626:p.Gly39Asp	103.0	0.0		117.0	17.0	NM_172059	A6NHQ0|G5E9R4|Q0P516|Q8WX80	Missense_Mutation	SNP	ENST00000340726.3	hg19	CCDS34906.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.868080	0.91587	.	.	ENSG00000104313	ENST00000388742;ENST00000340726;ENST00000303824;ENST00000388743;ENST00000419131	T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.77363	0.4119	L	0.53249	1.67	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.97110	1.0;1.0;0.978	T	0.77699	-0.2490	10	0.66056	D	0.02	-15.8674	19.8144	0.96560	0.0:1.0:0.0:0.0	.	39;39;39	A6NCB9;Q99502;G5E9R4	.;EYA1_HUMAN;.	D	39	ENSP00000373394:G39D;ENSP00000342626:G39D;ENSP00000303221:G39D;ENSP00000373395:G39D;ENSP00000410176:G39D	ENSP00000303221:G39D	G	-	2	0	EYA1	72429579	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.814000	0.86154	2.676000	0.91093	0.650000	0.86243	GGC	.	.		0.438	EYA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313788.2	NM_000503, NM_172060		T	72267025	C	T	72267025	3	4	352	1	0	0	0	0	1	0	0	0	5330	739	26	3	1726	3	EYA1	8	72267025	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	4115910	72267025	74096997	196	49612										
GDAP1	54332	hgsc.bcm.edu	37	chr8	75276245	75276245	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggccagcaaccttggctctgCggtgaatccttcaccctggc	11	15	2	1	rs367790253		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr8:75276245C>T	ENST00000220822.7	+	6	800	c.720C>T	c.(718-720)tgC>tgT	p.C240C	GDAP1_ENST00000521096.1_3'UTR|GDAP1_ENST00000434412.2_Silent_p.C172C	NM_001040875.2|NM_018972.2	NP_001035808.1|NP_061845.2	Q8TB36	GDAP1_HUMAN	ganglioside induced differentiation associated protein 1	240	GST C-terminal.				cell death (GO:0008219)|mitochondrial fission (GO:0000266)|protein targeting to mitochondrion (GO:0006626)|response to retinoic acid (GO:0032526)	integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	Breast(64;0.00769)	Myeloproliferative disorder(644;0.0122)	BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.104)|all cancers(69;0.234)			CTTGGCTCTGCGGTGAATCCT	0.517																																					p.C240C		Atlas-SNP	.											.	GDAP1	36	.	0			c.C720T						.	C	,	0,4406		0,0,2203	54	53	53		516,720	-8.3	0.7	8		53	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	GDAP1	NM_001040875.1,NM_018972.2	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	172/291,240/359	75276245	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	54332	exon6			GCTCTGCGGTGAA		CCDS34911.1, CCDS47877.1	8q13.3	2014-09-17	2012-02-09						15968	protein-coding gene	gene with protein product		606598	"Charcot-Marie-Tooth neuropathy 4A"	CMT4A		8268915, 11743579	Standard	NM_018972		Approved	CMT4	uc003yah.3	Q8TB36		ENST00000220822.7:c.720C>T	chr8.hg19:g.75276245C>T		140.0	0.0		193.0	22.0	NM_018972	A8K957|E7FJF3|E7FJF4	Silent	SNP	ENST00000220822.7	hg19	CCDS34911.1																																																																																			.	.		0.517	GDAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379061.1	NM_018972		T	75276245	C	T	75276245	2	4	352	1	0	0	0	0	0	0	0	1	6315	776	27	1		1	GDAP1	8	75276245	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	3009220	75276245	71087777	197	49613										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77617094	77617094	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tgtgtgtccaaagatgtcccTaacaatgtggacttgtccaa	9	9	0	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr8:77617094T>C	ENST00000521891.2	+	2	1219	c.771T>C	c.(769-771)ccT>ccC	p.P257P	ZFHX4_ENST00000455469.2_Silent_p.P257P|ZFHX4_ENST00000518282.1_Silent_p.P257P|ZFHX4_ENST00000050961.6_Silent_p.P257P|ZFHX4_ENST00000517683.1_Intron	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	257					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			AAGATGTCCCTAACAATGTGG	0.418										HNSCC(33;0.089)																											p.P257P		Atlas-SNP	.											.	ZFHX4	878	.	0			c.T771C						.						182	178	180					8																	77617094		2120	4270	6390	SO:0001819	synonymous_variant	79776	exon2			TGTCCCTAACAAT		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.771T>C	chr8.hg19:g.77617094T>C		101.0	0.0		117.0	41.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Silent	SNP	ENST00000521891.2	hg19	CCDS47878.2																																																																																			.	.		0.418	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		C	77617094	T	C	77617094	2	2	352	1	0	0	0	0	0	0	0	1	17650	1509	53	2		2	ZFHX4	8	77617094	Silent	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	2340849	77617094	68746928	198	49614										
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77617133	77617133	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aaattcgatggttgtgttagCgatgggaaaaggaaacctgt	13	4	0	0	rs369214100	byFrequency	TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr8:77617133C>T	ENST00000521891.2	+	2	1258	c.810C>T	c.(808-810)agC>agT	p.S270S	ZFHX4_ENST00000455469.2_Silent_p.S270S|ZFHX4_ENST00000518282.1_Silent_p.S270S|ZFHX4_ENST00000050961.6_Silent_p.S270S|ZFHX4_ENST00000517683.1_Intron	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	270					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			GTTGTGTTAGCGATGGGAAAA	0.413										HNSCC(33;0.089)			C|||	3	0.000599042	0.0023	0	5008	,	,		21803	0		0	False		,,,				2504	0				p.S270S		Atlas-SNP	.											.	ZFHX4	878	.	0			c.C810T						.	C		3,4203		0,3,2100	244	237	239		810	2.5	1	8		239	0,8518		0,0,4259	no	coding-synonymous	ZFHX4	NM_024721.4		0,3,6359	TT,TC,CC		0.0,0.0713,0.0236		270/3617	77617133	3,12721	2103	4259	6362	SO:0001819	synonymous_variant	79776	exon2			TGTTAGCGATGGG		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.810C>T	chr8.hg19:g.77617133C>T		109.0	0.0		161.0	7.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Silent	SNP	ENST00000521891.2	hg19	CCDS47878.2																																																																																			.	.		0.413	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		T	77617133	C	T	77617133	2	4	352	1	0	0	0	0	0	0	0	1	17650	767	27	1		1	ZFHX4	8	77617133	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	39	77617133	68746889	199	49615										
PAG1	55824	hgsc.bcm.edu	37	chr8	81897456	81897456	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cacttctcgccgtgagcatgGtatccactgcgctctcggga	11	14	2	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr8:81897456G>A	ENST00000220597.4	-	7	1141	c.431C>T	c.(430-432)aCc>aTc	p.T144I		NM_018440.3	NP_060910.3	Q9NWQ8	PHAG1_HUMAN	phosphoprotein membrane anchor with glycosphingolipid microdomains 1	144					epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular signal transduction (GO:0035556)|negative regulation of T cell activation (GO:0050868)|positive regulation of signal transduction (GO:0009967)|regulation of T cell activation (GO:0050863)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	SH2 domain binding (GO:0042169)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(2)	11	Lung NSC(7;5.76e-06)|all_lung(9;2e-05)		BRCA - Breast invasive adenocarcinoma(6;0.0567)|Epithelial(68;0.0634)|all cancers(69;0.197)			CGTGAGCATGGTATCCACTGC	0.592																																					p.T144I		Atlas-SNP	.											.	PAG1	39	.	0			c.C431T						.						62	61	62					8																	81897456		2203	4300	6503	SO:0001583	missense	55824	exon7			AGCATGGTATCCA	AF240634	CCDS6227.1	8q21.13	2014-04-30	2014-04-30						30043	protein-coding gene	gene with protein product	"Csk-binding protein", "transmembrane adaptor protein PAG"	605767	"phosphoprotein associated with glycosphingolipid microdomains 1"			10790433	Standard	XM_006716461		Approved	PAG, CBP	uc003ybz.3	Q9NWQ8		ENST00000220597.4:c.431C>T	chr8.hg19:g.81897456G>A	ENSP00000220597:p.Thr144Ile	101.0	0.0		139.0	36.0	NM_018440	A8K1A3|Q2M1Z9|Q5BKU4|Q9NYK0	Missense_Mutation	SNP	ENST00000220597.4	hg19	CCDS6227.1	.	.	.	.	.	.	.	.	.	.	G	10.84	1.464855	0.26335	.	.	ENSG00000076641	ENST00000220597	.	.	.	5.23	2.36	0.29203	.	0.302345	0.32175	N	0.006466	T	0.32526	0.0832	M	0.62723	1.935	0.09310	N	1	P	0.45078	0.85	B	0.40534	0.332	T	0.21827	-1.0234	9	0.66056	D	0.02	-7.1764	7.2214	0.25990	0.0681:0.1242:0.6788:0.129	.	144	Q9NWQ8	PAG1_HUMAN	I	144	.	ENSP00000220597:T144I	T	-	2	0	PAG1	82060011	0.962000	0.33011	0.670000	0.29842	0.316000	0.28119	2.035000	0.41155	0.244000	0.21351	-0.150000	0.13652	ACC	.	.		0.592	PAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379352.3	NM_018440		A	81897456	G	A	81897456	3	1	352	1	0	0	0	0	1	0	0	0	11397	1261	44	3	879	3	PAG1	8	81897456	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	4280323	81897456	64466566	200	49616										
SDC2	6383	hgsc.bcm.edu	37	chr8	97621775	97621775	+	Stop_Codon_Del	DEL	A	A	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tactaaggagttttatgcgtAaaactccaacttagtgtctc							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr8:97621775delA	ENST00000302190.4	+	0	1526				SDC2_ENST00000518385.1_Stop_Codon_Del|SDC2_ENST00000519914.1_Stop_Codon_Del|SDC2_ENST00000522911.1_Stop_Codon_Del	NM_002998.3	NP_002989.2	P34741	SDC2_HUMAN	syndecan 2						carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dendrite morphogenesis (GO:0048813)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|regulation of dendrite morphogenesis (GO:0048814)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)			breast(1)|cervix(1)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|stomach(2)	16	Breast(36;3.41e-05)				Sargramostim(DB00020)	TTTTATGCGTAAAACTCCAAC	0.353																																					p.X202K		Atlas-INDEL	.											.	SDC2	33	.	0			c.604delT						.						76	69	71					8																	97621775		2203	4300	6503	SO:0001567	stop_retained_variant	6383	exon5			.	BC030133	CCDS6272.1	8q22-q23	2011-08-11	2007-02-15		ENSG00000169439	ENSG00000169439		"Proteoglycans / Cell Surface : Syndecans", "CD molecules"	10659	protein-coding gene	gene with protein product	"syndecan proteoglycan 2"	142460	"heparan sulfate proteoglycan 1, cell surface-associated"	HSPG, HSPG1		8187643	Standard	NM_002998		Approved	fibroglycan, SYND2, CD362	uc003yhv.1	P34741	OTTHUMG00000164689	Exception_encountered	chr8.hg19:g.97621775delA		69.0	0.0		86.0	14.0	NM_002998	B3KQA3|Q6PIS6|Q9H6V1	Frame_Shift_Del	DEL	ENST00000302190.4	hg19	CCDS6272.1																																																																																			.	.		0.353	SDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379750.1	NM_002998		-	97621775	A	-	97621775	7	5	352	1	0	1	0	1	0	0	0	0	13967	369	13	0	623	0	SDC2	8	97621775	Stop_Codon_Del	DEL	A	TCGA-WQ-A9G7-01A-11D-A36X-10	15724319	97621775	48742247	201	49617										
ZHX2	22882	hgsc.bcm.edu	37	chr8	123965549	123965549	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ttccatggggtctggcaaaaAaggccaagatgtgggagccc	14	9	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr8:123965549A>G	ENST00000314393.4	+	3	2634	c.1799A>G	c.(1798-1800)aAa>aGa	p.K600R		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	600					mRNA catabolic process (GO:0006402)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	45	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			TCTGGCAAAAAAGGCCAAGAT	0.562																																					p.K600R	Esophageal Squamous(94;1056 1388 11767 13799 49639)	Atlas-SNP	.											.	ZHX2	106	.	0			c.A1799G						.						63	63	63					8																	123965549		2203	4300	6503	SO:0001583	missense	22882	exon3			GCAAAAAAGGCCA	AB020661	CCDS6336.1	8q24.13	2012-03-09	2004-01-23		ENSG00000178764	ENSG00000178764		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	18513	protein-coding gene	gene with protein product		609185	"zinc-fingers and homeoboxes 2"			10048485, 12741956	Standard	XM_005250837		Approved	KIAA0854	uc003ypk.1	Q9Y6X8	OTTHUMG00000165077	ENST00000314393.4:c.1799A>G	chr8.hg19:g.123965549A>G	ENSP00000314709:p.Lys600Arg	108.0	0.0		162.0	17.0	NM_014943		Missense_Mutation	SNP	ENST00000314393.4	hg19	CCDS6336.1	.	.	.	.	.	.	.	.	.	.	A	5.747	0.322283	0.10900	.	.	ENSG00000178764	ENST00000314393	T	0.17691	2.26	5.41	5.41	0.78517	Homeodomain-like (1);	0.338364	0.31438	N	0.007658	T	0.20129	0.0484	N	0.08118	0	0.50632	D	0.99988	D	0.76494	0.999	D	0.80764	0.994	T	0.22906	-1.0203	10	0.15499	T	0.54	-18.8478	14.1764	0.65544	1.0:0.0:0.0:0.0	.	600	Q9Y6X8	ZHX2_HUMAN	R	600	ENSP00000314709:K600R	ENSP00000314709:K600R	K	+	2	0	ZHX2	124034730	0.998000	0.40836	0.992000	0.48379	0.202000	0.24057	4.212000	0.58514	2.279000	0.76181	0.459000	0.35465	AAA	.	.		0.562	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943		G	123965549	A	G	123965549	3	3	352	1	0	0	0	0	1	0	0	0	17691	14	1	2	1801	2	ZHX2	8	123965549	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	26343774	123965549	22398473	202	49618										
BAI1	575	hgsc.bcm.edu	37	chr8	143563066	143563066	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tacagccccacccctggggaCgtacaggtgggctccccgag	13	16	0	0	rs376677183		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr8:143563066C>T	ENST00000517894.1	+	11	3018	c.2124C>T	c.(2122-2124)gaC>gaT	p.D708D	BAI1_ENST00000323289.5_Silent_p.D708D			O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1	708					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)|signal transduction (GO:0007165)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(28)|ovary(4)|pancreas(1)|prostate(7)	57	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					CCCCTGGGGACGTACAGGTGG	0.612													C|||	1	0.000199681	0	0	5008	,	,		19424	0.001		0	False		,,,				2504	0				p.D708D		Atlas-SNP	.											.	BAI1	146	.	0			c.C2124T						.	C		0,3942		0,0,1971	34	39	37		2124	-7.6	0.7	8		37	1,8239		0,1,4119	no	coding-synonymous	BAI1	NM_001702.2		0,1,6090	TT,TC,CC		0.0121,0.0,0.0082		708/1585	143563066	1,12181	1971	4120	6091	SO:0001819	synonymous_variant	575	exon10			TGGGGACGTACAG	AB005297	CCDS64985.1	8q24.3	2014-08-08			ENSG00000181790	ENSG00000181790		"-", "GPCR / Class B : Orphans"	943	protein-coding gene	gene with protein product		602682				9533023	Standard	NM_001702		Approved		uc003ywm.3	O14514	OTTHUMG00000164732	ENST00000517894.1:c.2124C>T	chr8.hg19:g.143563066C>T		48.0	0.0		76.0	5.0	NM_001702		Silent	SNP	ENST00000517894.1	hg19																																																																																				.	.		0.612	BAI1-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379963.3	NM_001702		T	143563066	C	T	143563066	2	4	352	1	0	0	0	0	0	0	0	1	1298	535	19	1		1	BAI1	8	143563066	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	19597517	143563066	2800956	203	49619										
BAI1	575	hgsc.bcm.edu	37	chr8	143599549	143599549	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	acgctcatcgtgggctgtggCgtgtcctctctcaccctgct	11	15	3	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr8:143599549C>T	ENST00000517894.1	+	19	3762	c.2868C>T	c.(2866-2868)ggC>ggT	p.G956G	BAI1_ENST00000323289.5_Silent_p.G956G			O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1	956					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)|signal transduction (GO:0007165)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(28)|ovary(4)|pancreas(1)|prostate(7)	57	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					TGGGCTGTGGCGTGTCCTCTC	0.637																																					p.G956G		Atlas-SNP	.											BAI1,caecum,carcinoma,0,1	BAI1	146	.	0			c.C2868T						.																																			SO:0001819	synonymous_variant	575	exon18			CTGTGGCGTGTCC	AB005297	CCDS64985.1	8q24.3	2014-08-08			ENSG00000181790	ENSG00000181790		"-", "GPCR / Class B : Orphans"	943	protein-coding gene	gene with protein product		602682				9533023	Standard	NM_001702		Approved		uc003ywm.3	O14514	OTTHUMG00000164732	ENST00000517894.1:c.2868C>T	chr8.hg19:g.143599549C>T		62.0	0.0		100.0	12.0	NM_001702		Silent	SNP	ENST00000517894.1	hg19																																																																																				.	.		0.637	BAI1-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379963.3	NM_001702		T	143599549	C	T	143599549	2	4	352	1	0	0	0	0	0	0	0	1	1298	755	27	1		1	BAI1	8	143599549	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	36483	143599549	2764473	204	49620										
ZNF696	79943	hgsc.bcm.edu	37	chr8	144378780	144378780	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ctccttcctccgcgagcaccGccgcatccacaccggggaga	10	19	0	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr8:144378780G>A	ENST00000330143.3	+	3	1344	c.935G>A	c.(934-936)cGc>cAc	p.R312H		NM_030895.2	NP_112157.2	Q9H7X3	ZN696_HUMAN	zinc finger protein 696	312				R -> C (in Ref. 1; BAB14850). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	8	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)			CGCGAGCACCGCCGCATCCAC	0.736																																					p.R312H		Atlas-SNP	.											.	ZNF696	18	.	0			c.G935A						.						6	8	7					8																	144378780		1911	3821	5732	SO:0001583	missense	79943	exon3			AGCACCGCCGCAT	AK024191	CCDS6399.1	8q24.3	2013-01-08				ENSG00000185730		"Zinc fingers, C2H2-type"	25872	protein-coding gene	gene with protein product							Standard	NM_030895		Approved	FLJ14129	uc003yxy.4	Q9H7X3		ENST00000330143.3:c.935G>A	chr8.hg19:g.144378780G>A	ENSP00000328515:p.Arg312His	46.0	0.0		51.0	17.0	NM_030895	A0AVE2	Missense_Mutation	SNP	ENST00000330143.3	hg19	CCDS6399.1	.	.	.	.	.	.	.	.	.	.	G	14.75	2.628239	0.46944	.	.	ENSG00000185730	ENST00000330143	T	0.18502	2.21	2.65	1.75	0.24633	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09335	0.0230	L	0.39566	1.225	0.58432	D	0.999993	P	0.40250	0.709	B	0.30855	0.121	T	0.19095	-1.0316	8	.	.	.	.	3.9547	0.09385	0.3233:0.0:0.6767:0.0	.	312	Q9H7X3	ZN696_HUMAN	H	312	ENSP00000328515:R312H	.	R	+	2	0	ZNF696	144450155	0.000000	0.05858	0.998000	0.56505	0.819000	0.46315	-0.938000	0.03938	1.489000	0.48450	0.551000	0.68910	CGC	.	.		0.736	ZNF696-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381164.2	NM_030895		A	144378780	G	A	144378780	3	1	352	1	0	0	0	0	1	0	0	0	18114	1087	38	1	941	1	ZNF696	8	144378780	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	779231	144378780	1985242	205	49621										
NAPRT1	642475	hgsc.bcm.edu	37	chr8	144657636	144657636	+	5'Flank	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gcagccttgctcccaggcaaCgtctgcttctcggggtcctc	11	16	2	0	rs143442304		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr8:144657636C>T	ENST00000398882.3	-	0	0				RP11-661A12.9_ENST00000531730.1_RNA|NAPRT1_ENST00000449291.2_Silent_p.T416T|NAPRT1_ENST00000276844.7_Silent_p.T416T|NAPRT1_ENST00000435154.3_Silent_p.T416T|NAPRT1_ENST00000426292.3_Silent_p.T416T|NAPRT1_ENST00000460623.1_5'UTR	NM_001100878.1	NP_001094348.1	A6NGR9	MROH6_HUMAN	maestro heat-like repeat family member 6																		TCCCAGGCAACGTCTGCTTCT	0.662																																					p.T416T		Atlas-SNP	.											.	NAPRT1	47	.	0			c.G1248A						.	C		0,4404		0,0,2202	52	59	56		1248	-9.8	0	8	dbSNP_134	56	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	NAPRT1	NM_145201.4		0,1,6501	TT,TC,CC		0.0116,0.0,0.0077		416/539	144657636	1,13003	2202	4300	6502	SO:0001631	upstream_gene_variant	93100	exon10			AGGCAACGTCTGC	AF289596	CCDS47928.1	8q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000204839	ENSG00000204839		"maestro heat-like repeat containing"	27814	protein-coding gene	gene with protein product			"chromosome 8 open reading frame 73"	C8orf73		12477932	Standard	NM_001100878		Approved		uc010mff.3	A6NGR9	OTTHUMG00000165164		chr8.hg19:g.144657636C>T	Exception_encountered	196.0	0.0		301.0	62.0	NM_145201	A8MWB1	Silent	SNP	ENST00000398882.3	hg19	CCDS47928.1																																																																																			.	C|1.000;T|0.000		0.662	MROH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382330.3	NM_001100878		T	144657636	C	T	144657636	1	4	352	0	1	0	0	0	0	0	0	0	10174	523	19	1		1	NAPRT1	8	144657636	5'Flank	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	278856	144657636	1706386	206	49622										
SPATC1	375686	hgsc.bcm.edu	37	chr8	145095783	145095784	+	Frame_Shift_Ins	INS	-	-	C													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cacccacatcgcccagggtgINSccccccatcccccttcccga					rs576544596	byFrequency	TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr8:145095783_145095784insC	ENST00000377470.3	+	3	1183_1184	c.1081_1082insC	c.(1081-1083)gccfs	p.A361fs	SPATC1_ENST00000447830.2_Frame_Shift_Ins_p.A361fs	NM_198572.2	NP_940974.2	Q76KD6	SPERI_HUMAN	spermatogenesis and centriole associated 1	361						centrosome (GO:0005813)|cytoplasm (GO:0005737)				NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;3.67e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CGCCCAGGGTGCCCCCCATCCC	0.658																																					p.A361fs		Atlas-INDEL	.											SPATC1_ENST00000377470,NS,carcinoma,0,2	SPATC1	77	.	0			c.1081_1082insC						.																																			SO:0001589	frameshift_variant	375686	exon3			.	BC053547	CCDS6413.2, CCDS47937.1	8q24.3	2005-01-11			ENSG00000186583	ENSG00000186583			30510	protein-coding gene	gene with protein product		610874				15280373	Standard	NM_198572		Approved	MGC61633, SPATA15, SPERIOLIN	uc011lkw.2	Q76KD6	OTTHUMG00000156976	ENST00000377470.3:c.1087dupC	chr8.hg19:g.145095789_145095789dupC	ENSP00000366690:p.Ala361fs	81.0	0.0		114.0	24.0	NM_001134374	B4DWW9|Q5U5I8|Q7Z6L7	Frame_Shift_Ins	INS	ENST00000377470.3	hg19	CCDS6413.2																																																																																			.	.		0.658	SPATC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346926.1	NM_198572		C	145095784	-	C	145095783	7	5	352	1	0	1	1	0	0	0	0	0	15032	1319	46	0	1091	0	SPATC1	8	145095783	Frame_Shift_Ins	INS	-	TCGA-WQ-A9G7-01A-11D-A36X-10	438147	145095783	1268239	207	49623										
PPP1R16A	84988	hgsc.bcm.edu	37	chr8	145724317	145724317	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agtgctgcattgatgatttcCgagagatggtgcagcagctc	13	8	0	3			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr8:145724317C>T	ENST00000292539.4	+	4	1266	c.349C>T	c.(349-351)Cga>Tga	p.R117*	CTD-2517M14.5_ENST00000569326.1_RNA|PPP1R16A_ENST00000435887.1_Nonsense_Mutation_p.R117*|CTD-2517M22.14_ENST00000532766.1_RNA			Q96I34	PP16A_HUMAN	protein phosphatase 1, regulatory subunit 16A	117						plasma membrane (GO:0005886)				NS(1)|endometrium(1)|kidney(2)|lung(3)|prostate(1)	8	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			TGATGATTTCCGAGAGATGGT	0.647																																					p.R117X		Atlas-SNP	.											PPP1R16A,colon,carcinoma,0,1	PPP1R16A	25	.	0			c.C349T						.						66	54	58					8																	145724317		2203	4300	6503	SO:0001587	stop_gained	84988	exon3			GATTTCCGAGAGA		CCDS6429.1	8q24.3	2013-01-10	2011-10-04		ENSG00000160972	ENSG00000160972		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	14941	protein-coding gene	gene with protein product		609172	"protein phosphatase 1, regulatory (inhibitor) subunit 16A"			11948623	Standard	NM_032902		Approved	MGC14333, MYPT3	uc003zdf.3	Q96I34	OTTHUMG00000165173	ENST00000292539.4:c.349C>T	chr8.hg19:g.145724317C>T	ENSP00000292539:p.Arg117*	55.0	0.0		82.0	6.0	NM_032902	D3DWM5	Nonsense_Mutation	SNP	ENST00000292539.4	hg19	CCDS6429.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	40|40	8.082493|8.082493	0.98646|0.98646	.|.	.|.	ENSG00000255182|ENSG00000160972	ENST00000527086|ENST00000292539;ENST00000435887	.|.	.|.	.|.	5.0|5.0	3.09|3.09	0.35607|0.35607	.|.	0.386006|0.386006	0.25817|0.25817	N|N	0.028101|0.028101	T|.	0.46464|.	0.1394|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.53337|.	-0.8453|.	5|.	0.87932|0.17369	D|T	0|0.5	.|.	12.0623|12.0623	0.53568|0.53568	0.0:0.4491:0.5509:0.0|0.0:0.4491:0.5509:0.0	.|.	.|.	.|.	.|.	Q|X	41|117	.|.	ENSP00000437304:R41Q|ENSP00000292539:R117X	R|R	-|+	2|1	0|2	CTD-2517M22.14|PPP1R16A	145695125|145695125	0.981000|0.981000	0.34729|0.34729	0.998000|0.998000	0.56505|0.56505	0.885000|0.885000	0.51271|0.51271	2.581000|2.581000	0.46077|0.46077	1.061000|1.061000	0.40601|0.40601	0.462000|0.462000	0.41574|0.41574	CGG|CGA	.	.		0.647	PPP1R16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382459.1	NM_032902		T	145724317	C	T	145724317	4	4	352	1	0	0	0	0	0	1	0	0	12377	644	23	1	359	1	PPP1R16A	8	145724317	Nonsense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	628534	145724317	639705	208	49624										
PPP1R16A	84988	hgsc.bcm.edu	37	chr8	145727136	145727136	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cctgaggggcccgagagcccTgagacagctgagcctggcct	15	14	0	4			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr8:145727136T>C	ENST00000292539.4	+	11	2354	c.1437T>C	c.(1435-1437)ccT>ccC	p.P479P	CTD-2517M14.5_ENST00000569326.1_RNA|GPT_ENST00000528431.1_5'Flank|GPT_ENST00000394955.2_5'Flank|PPP1R16A_ENST00000435887.1_Silent_p.P479P|CTD-2517M22.14_ENST00000532766.1_RNA			Q96I34	PP16A_HUMAN	protein phosphatase 1, regulatory subunit 16A	479						plasma membrane (GO:0005886)				NS(1)|endometrium(1)|kidney(2)|lung(3)|prostate(1)	8	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			CCGAGAGCCCTGAGACAGCTG	0.697																																					p.P479P		Atlas-SNP	.											.	PPP1R16A	25	.	0			c.T1437C						.						25	24	24					8																	145727136		2162	4268	6430	SO:0001819	synonymous_variant	84988	exon10			GAGCCCTGAGACA		CCDS6429.1	8q24.3	2013-01-10	2011-10-04		ENSG00000160972	ENSG00000160972		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	14941	protein-coding gene	gene with protein product		609172	"protein phosphatase 1, regulatory (inhibitor) subunit 16A"			11948623	Standard	NM_032902		Approved	MGC14333, MYPT3	uc003zdf.3	Q96I34	OTTHUMG00000165173	ENST00000292539.4:c.1437T>C	chr8.hg19:g.145727136T>C		134.0	0.0		171.0	16.0	NM_032902	D3DWM5	Silent	SNP	ENST00000292539.4	hg19	CCDS6429.1	.	.	.	.	.	.	.	.	.	.	T	5.864	0.343643	0.11126	.	.	ENSG00000160972	ENST00000528430	.	.	.	4.13	-8.26	0.01021	.	.	.	.	.	T	0.13884	0.0336	.	.	.	0.09310	N	0.999992	.	.	.	.	.	.	T	0.22347	-1.0219	4	.	.	.	.	0.4524	0.00503	0.2289:0.2853:0.2134:0.2724	.	.	.	.	P	147	.	.	L	+	2	0	PPP1R16A	145697944	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-7.505000	0.00035	-1.318000	0.02289	-1.271000	0.01417	CTG	.	.		0.697	PPP1R16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382459.1	NM_032902		C	145727136	T	C	145727136	2	2	352	1	0	0	0	0	0	0	0	1	12377	1567	55	2		2	PPP1R16A	8	145727136	Silent	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	2819	145727136	636886	209	49625										
KCNV2	169522	hgsc.bcm.edu	37	chr9	2718843	2718843	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cgcggccagacggtgggcagCgtgggtaaggtgggtcaggt	21	8	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr9:2718843C>T	ENST00000382082.3	+	1	1342	c.1104C>T	c.(1102-1104)agC>agT	p.S368S		NM_133497.3	NP_598004.1	Q8TDN2	KCNV2_HUMAN	potassium channel, subfamily V, member 2	368					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(2)	35				GBM - Glioblastoma multiforme(50;0.0257)		CGGTGGGCAGCGTGGGTAAGG	0.662																																					p.S368S		Atlas-SNP	.											.	KCNV2	72	.	0			c.C1104T						.						94	80	84					9																	2718843		2203	4298	6501	SO:0001819	synonymous_variant	169522	exon1			GGGCAGCGTGGGT	AF348983	CCDS6447.1	9p24.2	2011-07-05			ENSG00000168263	ENSG00000168263		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	19698	protein-coding gene	gene with protein product		607604				12060745, 16382104	Standard	NM_133497		Approved	Kv8.2	uc003zho.2	Q8TDN2	OTTHUMG00000019449	ENST00000382082.3:c.1104C>T	chr9.hg19:g.2718843C>T		45.0	0.0		48.0	9.0	NM_133497	Q5T6X0	Silent	SNP	ENST00000382082.3	hg19	CCDS6447.1	.	.	.	.	.	.	.	.	.	.	C	5.598	0.295110	0.10622	.	.	ENSG00000168263	ENST00000423608	.	.	.	4.79	-2.35	0.06684	.	.	.	.	.	T	0.54303	0.1850	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57423	-0.7814	5	0.87932	D	0	.	2.9204	0.05767	0.1006:0.2427:0.4078:0.2489	.	.	.	.	C	319	.	ENSP00000409635:R319C	R	+	1	0	KCNV2	2708843	0.998000	0.40836	0.997000	0.53966	0.668000	0.39293	0.311000	0.19380	-0.160000	0.11002	-0.300000	0.09419	CGT	.	.		0.662	KCNV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051528.1	NM_133497		T	2718843	C	T	2718843	2	4	352	1	0	0	0	0	0	0	0	1	8104	767	27	1		1	KCNV2	9	2718843	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10		2718843	138494588	210	49626										
KDM4C	23081	hgsc.bcm.edu	37	chr9	7174674	7174674	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tgaatatgtggccgaccctgTataccgcacttttttgaaga	9	9	0	3			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr9:7174674T>C	ENST00000381309.3	+	22	3681	c.3116T>C	c.(3115-3117)gTa>gCa	p.V1039A	KDM4C_ENST00000442236.2_Missense_Mutation_p.V784A|KDM4C_ENST00000428870.2_Missense_Mutation_p.V726A	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	1039			V -> I (in dbSNP:rs913588). {ECO:0000269|PubMed:15489334}.		histone H3-K9 demethylation (GO:0033169)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	androgen receptor binding (GO:0050681)|dioxygenase activity (GO:0051213)|enzyme binding (GO:0019899)|histone demethylase activity (H3-K9 specific) (GO:0032454)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43						GCCGACCCTGTATACCGCACT	0.468																																					p.V1039A		Atlas-SNP	.											.	KDM4C	186	.	0			c.T3116C						.						165	170	168					9																	7174674		2203	4300	6503	SO:0001583	missense	23081	exon22			ACCCTGTATACCG	AB018323	CCDS6471.1, CCDS55285.1, CCDS55286.1, CCDS55287.1	9p24-p23	2013-01-23	2009-04-06	2009-04-06	ENSG00000107077	ENSG00000107077		"Chromatin-modifying enzymes / K-demethylases", "Tudor domain containing"	17071	protein-coding gene	gene with protein product	"tudor domain containing 14C"	605469	"jumonji domain containing 2C"	JMJD2C		9872452, 15138608	Standard	NM_015061		Approved	GASC1, KIAA0780, TDRD14C	uc003zkh.3	Q9H3R0	OTTHUMG00000019536	ENST00000381309.3:c.3116T>C	chr9.hg19:g.7174674T>C	ENSP00000370710:p.Val1039Ala	162.0	0.0		141.0	9.0	NM_015061	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Missense_Mutation	SNP	ENST00000381309.3	hg19	CCDS6471.1	.	.	.	.	.	.	.	.	.	.	T	6.736	0.504562	0.12822	.	.	ENSG00000107077	ENST00000381309;ENST00000442236;ENST00000428870	T;T;T	0.34667	1.35;1.35;1.35	5.69	3.16	0.36331	.	0.240620	0.33005	N	0.005393	T	0.14184	0.0343	N	0.08118	0	0.23341	N	0.99787	B;B	0.30406	0.278;0.07	B;B	0.24974	0.057;0.024	T	0.24977	-1.0145	10	0.08599	T	0.76	-13.4956	7.9865	0.30216	0.1135:0.0:0.3183:0.5682	.	784;1039	E7EV17;Q9H3R0	.;KDM4C_HUMAN	A	1039;784;726	ENSP00000370710:V1039A;ENSP00000409353:V784A;ENSP00000405739:V726A	ENSP00000370710:V1039A	V	+	2	0	KDM4C	7164674	0.430000	0.25538	0.997000	0.53966	0.872000	0.50106	1.312000	0.33574	0.942000	0.37525	0.482000	0.46254	GTA	.	.		0.468	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061		C	7174674	T	C	7174674	3	2	352	1	0	0	0	0	1	0	0	0	8139	1638	57	2	3440	2	KDM4C	9	7174674	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	4455831	7174674	134038757	211	49627										
ADAMTSL1	92949	hgsc.bcm.edu	37	chr9	18777687	18777687	+	Frame_Shift_Del	DEL	G	G	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cctcctccaccggggacgccGggggaggctctcgaaggcca							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr9:18777687delG	ENST00000380548.4	+	19	3799	c.3460delG	c.(3460-3462)gggfs	p.G1156fs		NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	1156						proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(2)|lung(17)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(50;1.29e-17)		CGGGGACGCCGGGGGAGGCTC	0.667																																					p.A1153fs		Atlas-INDEL	.											.	ADAMTSL1	306	.	0			c.3459delC						.						23	28	27					9																	18777687		2103	4205	6308	SO:0001589	frameshift_variant	92949	exon19			.	AF176313	CCDS6485.1, CCDS47954.1	9p21.3	2013-01-11			ENSG00000178031	ENSG00000178031		"Immunoglobulin superfamily / I-set domain containing"	14632	protein-coding gene	gene with protein product	"punctin"	609198	"chromosome 9 open reading frame 94"	C9orf94		9628581, 11805097	Standard	NM_001040272		Approved	ADAMTSR1, FLJ35283	uc003zne.4	Q8N6G6	OTTHUMG00000019604	ENST00000380548.4:c.3460delG	chr9.hg19:g.18777687delG	ENSP00000369921:p.Gly1156fs	89.0	0.0		69.0	18.0	NM_001040272	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Frame_Shift_Del	DEL	ENST00000380548.4	hg19	CCDS47954.1																																																																																			.	.		0.667	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1			-	18777687	G	-	18777687	7	5	352	1	0	1	0	1	0	0	0	0	274	1116	39	0	3538	0	ADAMTSL1	9	18777687	Frame_Shift_Del	DEL	G	TCGA-WQ-A9G7-01A-11D-A36X-10	11603013	18777687	122435744	212	49628										
TOPORS	10210	hgsc.bcm.edu	37	chr9	32544180	32544180	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	atgtaagcagcgatctaagtAagacacattatcaaatctat	6	7	3	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr9:32544180A>G	ENST00000360538.2	-	3	459	c.343T>C	c.(343-345)Tac>Cac	p.Y115H	TOPORS_ENST00000379858.1_Missense_Mutation_p.Y50H	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	115	E3 ubiquitin-protein ligase activity.|Required for DNA-binding.				cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of apoptotic process (GO:0043066)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein localization to nucleus (GO:0034504)|protein monoubiquitination (GO:0006513)|protein sumoylation (GO:0016925)|regulation of cell proliferation (GO:0042127)|retina layer formation (GO:0010842)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|gamma-tubulin complex (GO:0000930)|midbody (GO:0030496)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|PML body (GO:0016605)|spindle pole (GO:0000922)|ubiquitin ligase complex (GO:0000151)	antigen binding (GO:0003823)|DNA binding (GO:0003677)|DNA topoisomerase binding (GO:0044547)|SUMO ligase activity (GO:0019789)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		CGATCTAAGTAAGACACATTA	0.403																																					p.Y115H		Atlas-SNP	.											.	TOPORS	127	.	0			c.T343C						.						111	109	110					9																	32544180		2203	4300	6503	SO:0001583	missense	10210	exon3			CTAAGTAAGACAC	AF098300	CCDS6527.1, CCDS56566.1	9p21	2013-01-09	2010-09-17		ENSG00000197579	ENSG00000197579		"RING-type (C3HC4) zinc fingers"	21653	protein-coding gene	gene with protein product		609507	"retinitis pigmentosa 31 (autosomal dominant)", "topoisomerase I binding, arginine/serine-rich"	RP31		10352183, 12083797, 17924349	Standard	NM_005802		Approved	TP53BPL, LUN	uc003zrb.3	Q9NS56	OTTHUMG00000019743	ENST00000360538.2:c.343T>C	chr9.hg19:g.32544180A>G	ENSP00000353735:p.Tyr115His	1704.0	0.0		1442.0	140.0	NM_005802	O43273|Q6P987|Q9NS55|Q9UNR9	Missense_Mutation	SNP	ENST00000360538.2	hg19	CCDS6527.1	.	.	.	.	.	.	.	.	.	.	A	15.05	2.718341	0.48622	.	.	ENSG00000197579	ENST00000360538;ENST00000379858	T;T	0.67698	-0.28;-0.28	5.6	5.6	0.85130	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.000000	0.45606	D	0.000341	T	0.43033	0.1229	N	0.03903	-0.33	0.36841	D	0.887385	P	0.41475	0.751	B	0.40375	0.327	T	0.55140	-0.8187	10	0.39692	T	0.17	-12.7378	9.5859	0.39517	0.9205:0.0:0.0795:0.0	.	115	Q9NS56	TOPRS_HUMAN	H	115;50	ENSP00000353735:Y115H;ENSP00000369187:Y50H	ENSP00000353735:Y115H	Y	-	1	0	TOPORS	32534180	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	5.075000	0.64407	2.263000	0.75096	0.533000	0.62120	TAC	.	.		0.403	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802		G	32544180	A	G	32544180	3	3	352	1	0	0	0	0	1	0	0	0	16385	362	13	2	2798	2	TOPORS	9	32544180	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	13766493	32544180	108669251	213	49629										
C9orf23	138716	hgsc.bcm.edu	37	chr9	34611031	34611031	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tgtcctcagtctgaaggaaaCgtagcttggtgagctggtgc	14	8	2	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr9:34611031C>T	ENST00000297613.4	-	2	543	c.263G>A	c.(262-264)cGt>cAt	p.R88H	RPP25L_ENST00000378959.4_Missense_Mutation_p.R88H|DCTN3_ENST00000479399.1_5'Flank	NM_148179.2	NP_680545.1	Q8N5L8	RP25L_HUMAN	ribonuclease P/MRP 25kDa subunit-like	88						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)										CTGAAGGAAACGTAGCTTGGT	0.622																																					p.R88H		Atlas-SNP	.											.	.	.	.	0			c.G263A						.						64	55	58					9																	34611031		2203	4300	6503	SO:0001583	missense	138716	exon2			AGGAAACGTAGCT	BC032136	CCDS6559.1	9p11.2	2012-03-06	2012-03-06	2012-03-06	ENSG00000164967	ENSG00000164967			19909	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 23"	C9orf23		16998185	Standard	NM_148178		Approved	bA296L22.5, MGC29635	uc003zuv.3	Q8N5L8	OTTHUMG00000000443	ENST00000297613.4:c.263G>A	chr9.hg19:g.34611031C>T	ENSP00000297613:p.Arg88His	87.0	0.0		84.0	15.0	NM_148179	D3DRM5	Missense_Mutation	SNP	ENST00000297613.4	hg19	CCDS6559.1	.	.	.	.	.	.	.	.	.	.	C	9.879	1.201092	0.22121	.	.	ENSG00000164967	ENST00000378959;ENST00000297613	.	.	.	4.72	3.74	0.42951	.	0.657220	0.16033	N	0.232780	T	0.24812	0.0602	L	0.27053	0.805	0.21762	N	0.999557	B	0.20671	0.047	B	0.14023	0.01	T	0.09930	-1.0652	9	0.15066	T	0.55	-30.2489	6.9321	0.24447	0.19:0.7091:0.0:0.1009	.	88	Q8N5L8	CI023_HUMAN	H	88	.	ENSP00000297613:R88H	R	-	2	0	C9orf23	34601031	0.001000	0.12720	0.895000	0.35142	0.844000	0.47949	-0.669000	0.05262	2.448000	0.82819	0.643000	0.83706	CGT	.	.		0.622	RPP25L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001130.1	NM_148179		T	34611031	C	T	34611031	3	4	352	1	0	0	0	0	1	0	0	0	2476	536	19	1	232	1	C9orf23	9	34611031	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	2066851	34611031	106602400	214	49630										
SHB	6461	hgsc.bcm.edu	37	chr9	37919975	37919975	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tctctttggttttggccagtTtcatgtgcataaaaccctgg	9	9	2	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr9:37919975T>C	ENST00000377707.3	-	6	1938	c.1373A>G	c.(1372-1374)aAa>aGa	p.K458R	RP11-613M10.9_ENST00000540557.1_Intron	NM_003028.2	NP_003019.2	Q15464	SHB_HUMAN	Src homology 2 domain containing adaptor protein B	458	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(2)|endometrium(4)|lung(1)|prostate(1)|skin(1)|soft_tissue(1)|stomach(1)	11		all_epithelial(88;0.122)		GBM - Glioblastoma multiforme(29;3.27e-05)|Lung(182;0.0658)		TTTGGCCAGTTTCATGTGCAT	0.512																																					p.K458R		Atlas-SNP	.											.	SHB	31	.	0			c.A1373G						.						120	122	121					9																	37919975		1949	4154	6103	SO:0001583	missense	6461	exon6			GCCAGTTTCATGT		CCDS43806.1	9p13.2	2013-09-23	2005-05-24		ENSG00000107338	ENSG00000107338		"SH2 domain containing"	10838	protein-coding gene	gene with protein product		600314	"SHB adaptor protein (a Src homology 2 protein)", "SHB (Src homology 2 domain containing) adaptor protein B"			7713524	Standard	NM_003028		Approved		uc004aax.3	Q15464	OTTHUMG00000019936	ENST00000377707.3:c.1373A>G	chr9.hg19:g.37919975T>C	ENSP00000366936:p.Lys458Arg	99.0	0.0		117.0	25.0	NM_003028	B9EGM0|D3DRQ5|Q504U5|Q5VUM8	Missense_Mutation	SNP	ENST00000377707.3	hg19	CCDS43806.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.431847	0.83776	.	.	ENSG00000107338	ENST00000377707	T	0.57752	0.38	5.51	5.51	0.81932	SH2 motif (4);	0.000000	0.64402	D	0.000008	T	0.55986	0.1955	L	0.31065	0.9	0.80722	D	1	D	0.59767	0.986	P	0.61800	0.894	T	0.51309	-0.8722	10	0.23302	T	0.38	-8.4246	13.5872	0.61937	0.0:0.0:0.0:1.0	.	458	Q15464	SHB_HUMAN	R	458	ENSP00000366936:K458R	ENSP00000366936:K458R	K	-	2	0	SHB	37909975	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.686000	0.84128	2.080000	0.62538	0.533000	0.62120	AAA	.	.		0.512	SHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052490.1			C	37919975	T	C	37919975	3	2	352	1	0	0	0	0	1	0	0	0	14283	1841	64	2	160	2	SHB	9	37919975	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	3308944	37919975	103293456	215	49631										
PRKACG	5568	hgsc.bcm.edu	37	chr9	71628335	71628335	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tctcatagatgagcacccctAgggcccaccagtccacggcc	9	17	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr9:71628335A>G	ENST00000377276.2	-	1	704	c.674T>C	c.(673-675)cTa>cCa	p.L225P		NM_002732.3	NP_002723.2	P22612	KAPCG_HUMAN	protein kinase, cAMP-dependent, catalytic, gamma	225	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|carbohydrate metabolic process (GO:0005975)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|male gonad development (GO:0008584)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)|triglyceride catabolic process (GO:0019433)|water transport (GO:0006833)	cytosol (GO:0005829)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						GAGCACCCCTAGGGCCCACCA	0.612																																					p.L225P	Esophageal Squamous(110;2236 2623 32146)	Atlas-SNP	.											PRKACG,middle_lobe,carcinoma,0,1	PRKACG	65	.	0			c.T674C						.						66	64	65					9																	71628335		2203	4300	6503	SO:0001583	missense	5568	exon1			ACCCCTAGGGCCC	M34182	CCDS6625.1	9q13	2012-10-02			ENSG00000165059	ENSG00000165059	2.7.11.1		9382	protein-coding gene	gene with protein product		176893				2342480, 9598317	Standard	NM_002732		Approved	PKACg	uc004agy.3	P22612	OTTHUMG00000019974	ENST00000377276.2:c.674T>C	chr9.hg19:g.71628335A>G	ENSP00000366488:p.Leu225Pro	82.0	0.0		89.0	12.0	NM_002732	O60850|Q5VZ02|Q86YI1	Missense_Mutation	SNP	ENST00000377276.2	hg19	CCDS6625.1	.	.	.	.	.	.	.	.	.	.	A	14.25	2.479836	0.44044	.	.	ENSG00000165059	ENST00000377276	T	0.11930	2.73	1.16	1.16	0.20824	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.25881	U	0.027688	T	0.46541	0.1398	H	0.98155	4.16	0.52501	D	0.999956	D	0.89917	1.0	D	0.85130	0.997	T	0.48625	-0.9019	10	0.87932	D	0	.	6.0938	0.20008	1.0:0.0:0.0:0.0	.	225	P22612	KAPCG_HUMAN	P	225	ENSP00000366488:L225P	ENSP00000366488:L225P	L	-	2	0	PRKACG	70818155	0.018000	0.18449	0.004000	0.12327	0.004000	0.04260	2.762000	0.47597	0.470000	0.27294	0.460000	0.39030	CTA	.	.		0.612	PRKACG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052559.1			G	71628335	A	G	71628335	3	3	352	1	0	0	0	0	1	0	0	0	12511	420	15	2	385	2	PRKACG	9	71628335	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	33708360	71628335	69585096	216	49632										
SECISBP2	79048	hgsc.bcm.edu	37	chr9	91940370	91940370	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tatatactgaagacatggccTttggagcttcaacttttcca	7	9	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr9:91940370T>G	ENST00000375807.3	+	3	282	c.211T>G	c.(211-213)Ttt>Gtt	p.F71V	SECISBP2_ENST00000534113.2_Missense_Mutation_p.F3V|SECISBP2_ENST00000470305.1_3'UTR|SECISBP2_ENST00000339901.4_Intron	NM_001282688.1|NM_001282690.1|NM_024077.3	NP_001269617.1|NP_001269619.1|NP_076982.3	Q96T21	SEBP2_HUMAN	SECIS binding protein 2	71					translation (GO:0006412)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|ribonucleoprotein complex binding (GO:0043021)|selenocysteine insertion sequence binding (GO:0035368)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(3)|skin(2)	32						AGACATGGCCTTTGGAGCTTC	0.348																																					p.F71V		Atlas-SNP	.											.	SECISBP2	64	.	0			c.T211G						.						106	97	100					9																	91940370		2203	4300	6503	SO:0001583	missense	79048	exon3			ATGGCCTTTGGAG	AF380995	CCDS6683.1, CCDS65076.1, CCDS65077.1	9q22	2008-02-05			ENSG00000187742	ENSG00000187742			30972	protein-coding gene	gene with protein product		607693				11230166	Standard	XM_005252193		Approved		uc004aqj.1	Q96T21	OTTHUMG00000020182	ENST00000375807.3:c.211T>G	chr9.hg19:g.91940370T>G	ENSP00000364965:p.Phe71Val	82.0	0.0		91.0	5.0	NM_024077	F8W892|Q5HYY1|Q8IYC0|Q9H0A1	Missense_Mutation	SNP	ENST00000375807.3	hg19	CCDS6683.1	.	.	.	.	.	.	.	.	.	.	T	13.51	2.258034	0.39896	.	.	ENSG00000187742	ENST00000375807;ENST00000395669;ENST00000534113	T;T	0.78707	-0.68;-1.2	4.17	3.05	0.35203	.	0.319059	0.27700	N	0.018207	T	0.63034	0.2477	L	0.29908	0.895	0.24874	N	0.992264	P;P;P	0.48407	0.851;0.91;0.851	B;B;B	0.42462	0.253;0.388;0.253	T	0.59984	-0.7351	10	0.66056	D	0.02	-17.5344	4.4782	0.11753	0.0:0.1565:0.1854:0.6581	.	91;71;71	Q59H19;B4DZC7;Q96T21	.;.;SEBP2_HUMAN	V	71;91;3	ENSP00000364965:F71V;ENSP00000436650:F3V	ENSP00000364965:F71V	F	+	1	0	SECISBP2	91130190	0.076000	0.21285	0.970000	0.41538	0.972000	0.66771	0.169000	0.16641	1.879000	0.54435	0.379000	0.24179	TTT	.	.		0.348	SECISBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052990.3	NM_024077		G	91940370	T	G	91940370	3	3	352	1	0	0	0	0	1	0	0	0	14021	1609	56	5	221	5	SECISBP2	9	91940370	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	20312035	91940370	49273061	217	49633										
C9orf129	445577	hgsc.bcm.edu	37	chr9	96080811	96080812	+	Frame_Shift_Ins	INS	-	-	C													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	acgttaggtgagcagacatgINSccccccatgccagtgggctg							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr9:96080811_96080812insC	ENST00000375419.1	-	5	822_823	c.459_460insG	c.(457-462)gggcatfs	p.H154fs	WNK2_ENST00000471076.1_Intron|WNK2_ENST00000356055.3_Intron|WNK2_ENST00000349097.3_Intron|WNK2_ENST00000395477.2_Intron|WNK2_ENST00000395475.2_Intron	NM_001098808.1	NP_001092278.1	Q5T035	CI129_HUMAN	chromosome 9 open reading frame 129	154										endometrium(2)|large_intestine(1)|lung(1)|ovary(2)	6						GAGCAGACATGCCCCCCATGCC	0.599																																					p.H154fs		Atlas-INDEL	.											.	C9orf129	18	.	0			c.460_461insG						.																																			SO:0001589	frameshift_variant	445577	exon5			.		CCDS43850.1	9q22.31	2012-04-02			ENSG00000204352	ENSG00000204352			31116	protein-coding gene	gene with protein product							Standard	NM_001098808		Approved	bA165J3.3	uc010mre.3	Q5T035	OTTHUMG00000020248	ENST00000375419.1:c.460dupG	chr9.hg19:g.96080817_96080817dupC	ENSP00000364568:p.His154fs	88.0	0.0		124.0	20.0	NM_001098808		Frame_Shift_Ins	INS	ENST00000375419.1	hg19	CCDS43850.1																																																																																			.	.		0.599	C9orf129-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053147.1	NM_001098808		C	96080812	-	C	96080811	7	5	352	1	0	1	1	0	0	0	0	0	2458	1319	46	0	134	0	C9orf129	9	96080811	Frame_Shift_Ins	INS	-	TCGA-WQ-A9G7-01A-11D-A36X-10	4140441	96080811	45132620	218	49634										
HSD17B3	3293	hgsc.bcm.edu	37	chr9	99006674	99006674	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ttggaaaatgcgcacacaaaCgcctggagcaagaaggagag	13	8	0	2	rs560518006		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr9:99006674C>T	ENST00000375263.3	-	9	656	c.609G>A	c.(607-609)gcG>gcA	p.A203A	HSD17B3_ENST00000464104.1_5'UTR|HSD17B3_ENST00000375262.2_Silent_p.A203A|RP11-240L7.4_ENST00000448857.1_RNA	NM_000197.1	NP_000188.1	P37058	DHB3_HUMAN	hydroxysteroid (17-beta) dehydrogenase 3	203			A -> V (in MPH). {ECO:0000269|PubMed:8075637}.		androgen biosynthetic process (GO:0006702)|male genitalia development (GO:0030539)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)			breast(1)|endometrium(3)|large_intestine(2)|lung(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13		Acute lymphoblastic leukemia(62;0.0171)|all_hematologic(171;0.214)				CGCACACAAACGCCTGGAGCA	0.537																																					p.A203A		Atlas-SNP	.											.	HSD17B3	32	.	0			c.G609A						.						155	139	144					9																	99006674		2203	4300	6503	SO:0001819	synonymous_variant	3293	exon9			CACAAACGCCTGG		CCDS6716.1	9q22	2011-09-20			ENSG00000130948	ENSG00000130948	1.1.1.62	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	5212	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 12C, member 2"	605573				8075637, 19027726	Standard	NM_000197		Approved	SDR12C2	uc004awa.1	P37058	OTTHUMG00000020292	ENST00000375263.3:c.609G>A	chr9.hg19:g.99006674C>T		98.0	0.0		70.0	32.0	NM_000197	Q5U0Q6	Silent	SNP	ENST00000375263.3	hg19	CCDS6716.1																																																																																			.	.		0.537	HSD17B3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053259.1	NM_000197		T	99006674	C	T	99006674	2	4	352	1	0	0	0	0	0	0	0	1	7394	523	19	1		1	HSD17B3	9	99006674	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	2925863	99006674	42206757	219	49635										
TEX10	54881	hgsc.bcm.edu	37	chr9	103065915	103065915	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ccggtaccatgcttcttaccGtgatattcttgatgatctgc	8	11	3	3	rs371930194		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr9:103065915G>A	ENST00000374902.4	-	14	2851	c.2675C>T	c.(2674-2676)aCg>aTg	p.T892M	TEX10_ENST00000477648.1_5'UTR|TEX10_ENST00000535814.1_Splice_Site_p.T876M	NM_017746.3	NP_060216.2	Q9NXF1	TEX10_HUMAN	testis expressed 10	892						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|MLL1 complex (GO:0071339)				NS(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	38		Acute lymphoblastic leukemia(62;0.0527)		OV - Ovarian serous cystadenocarcinoma(323;0.157)		GCTTCTTACCGTGATATTCTT	0.498																																					p.T892M		Atlas-SNP	.											.	TEX10	99	.	0			c.C2675T						.	G	MET/THR,MET/THR	0,4406		0,0,2203	200	194	196		2627,2675	3.9	1	9		196	1,8599	1.2+/-3.3	0,1,4299	no	missense-near-splice,missense-near-splice	TEX10	NM_001161584.1,NM_017746.3	81,81	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	876/914,892/930	103065915	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	54881	exon14			CTTACCGTGATAT	AB060968	CCDS6748.1, CCDS55330.1	9q31.1	2012-05-02	2007-03-13		ENSG00000136891	ENSG00000136891			25988	protein-coding gene	gene with protein product			"testis expressed gene 10", "testis expressed sequence 10"			12477932	Standard	NM_017746		Approved	FLJ20287, bA208F1.2, Ipi1	uc004bas.3	Q9NXF1	OTTHUMG00000020366	ENST00000374902.4:c.2676+1C>T	chr9.hg19:g.103065915G>A		173.0	0.0		166.0	26.0	NM_017746	B4DYV2|Q5T722|Q5T723|Q8NCN8|Q8TDY0	Missense_Mutation	SNP	ENST00000374902.4	hg19	CCDS6748.1	.	.	.	.	.	.	.	.	.	.	G	10.53	1.375314	0.24857	0.0	1.16E-4	ENSG00000136891	ENST00000535814;ENST00000374902;ENST00000444730	.	.	.	6.02	3.89	0.44902	.	0.207319	0.52532	N	0.000077	T	0.26666	0.0652	N	0.11201	0.11	0.80722	D	1	B;B;B	0.22211	0.01;0.066;0.01	B;B;B	0.11329	0.003;0.006;0.003	T	0.07693	-1.0759	9	0.11794	T	0.64	-0.6483	7.3446	0.26656	0.2708:0.0:0.7292:0.0	.	876;760;892	B4DYV2;E7ERG2;Q9NXF1	.;.;TEX10_HUMAN	M	876;892;760	.	ENSP00000364037:T892M	T	-	2	0	TEX10	102105736	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.672000	0.46850	1.572000	0.49736	0.655000	0.94253	ACG	.	.		0.498	TEX10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053416.1	NM_017746	Missense_Mutation	A	103065915	G	A	103065915	5	1	352	1	0	0	0	0	0	0	1	0	15787	1159	40	1	122	1	TEX10	9	103065915	Splice_Site	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	4059241	103065915	38147516	220	49636										
DEC1	50514	hgsc.bcm.edu	37	chr9	118163488	118163488	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ttaggtttttactgatgcccTgcacagagagaggtctgtaa	11	7	1	3			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr9:118163488T>C	ENST00000374016.1	+	7	623	c.104T>C	c.(103-105)cTg>cCg	p.L35P		NM_017418.2	NP_059114.1	Q9P2X7	DEC1_HUMAN	deleted in esophageal cancer 1	35					negative regulation of cell proliferation (GO:0008285)					kidney(1)|large_intestine(1)|ovary(1)	3						ACTGATGCCCTGCACAGAGAG	0.473																																					p.L35P		Atlas-SNP	.											.	DEC1	8	.	0			c.T104C						.						121	122	122					9																	118163488		2203	4300	6503	SO:0001583	missense	50514	exon7			ATGCCCTGCACAG	AB022761	CCDS6812.1	9q32	2008-02-05			ENSG00000173077	ENSG00000173077			23658	protein-coding gene	gene with protein product		604767				8603412, 10612805	Standard	NM_017418		Approved	CTS9	uc004bjk.1	Q9P2X7	OTTHUMG00000020549	ENST00000374016.1:c.104T>C	chr9.hg19:g.118163488T>C	ENSP00000363128:p.Leu35Pro	34.0	0.0		61.0	11.0	NM_017418		Missense_Mutation	SNP	ENST00000374016.1	hg19	CCDS6812.1	.	.	.	.	.	.	.	.	.	.	T	7.210	0.595245	0.13875	.	.	ENSG00000173077	ENST00000374016	T	0.60171	0.21	3.57	2.41	0.29592	.	.	.	.	.	T	0.70159	0.3192	.	.	.	0.09310	N	1	D	0.89917	1.0	D	0.78314	0.991	T	0.56366	-0.7991	8	0.87932	D	0	.	6.2152	0.20651	0.2229:0.0:0.0:0.7771	.	35	Q9P2X7	DEC1_HUMAN	P	35	ENSP00000363128:L35P	ENSP00000363128:L35P	L	+	2	0	DEC1	117203309	0.000000	0.05858	0.001000	0.08648	0.253000	0.25986	-0.022000	0.12480	0.722000	0.32252	0.533000	0.62120	CTG	.	.		0.473	DEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053791.1	NM_017418		C	118163488	T	C	118163488	3	2	352	1	0	0	0	0	1	0	0	0	4383	1580	55	2	114	2	DEC1	9	118163488	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	15097573	118163488	23049943	221	49637										
PKN3	29941	hgsc.bcm.edu	37	chr9	131480648	131480650	+	In_Frame_Del	DEL	AGA	AGA	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggggctgcagttcttacacgAgaagaagatcatttacaggt							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr9:131480648_131480650delAGA	ENST00000291906.4	+	17	2423_2425	c.2030_2032delAGA	c.(2029-2034)gagaag>gag	p.K679del	ZDHHC12_ENST00000467312.1_5'Flank|PKN3_ENST00000485301.1_3'UTR	NM_013355.3	NP_037487.2	Q6P5Z2	PKN3_HUMAN	protein kinase N3	679	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				epithelial cell migration (GO:0010631)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24						TTCTTACACGAGAAGAAGATCAT	0.591																																					p.677_677del		Atlas-INDEL	.											.	PKN3	62	.	0			c.2029_2031del						.																																			SO:0001651	inframe_deletion	29941	exon17			.	AB019692	CCDS6908.1	9q34.13	2008-02-05			ENSG00000160447	ENSG00000160447			17999	protein-coding gene	gene with protein product		610714				10441506	Standard	NM_013355		Approved	PKNbeta	uc004bvw.3	Q6P5Z2	OTTHUMG00000020757	ENST00000291906.4:c.2030_2032delAGA	chr9.hg19:g.131480654_131480656delAGA	ENSP00000291906:p.Lys679del	100.0	0.0		71.0	11.0	NM_013355	Q9UM03	In_Frame_Del	DEL	ENST00000291906.4	hg19	CCDS6908.1																																																																																			.	.		0.591	PKN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054487.1	NM_013355		-	131480650	AGA	-	131480648	7	5	352	1	0	1	0	1	0	0	0	0	11990	304	11	0	2096	0	PKN3	9	131480648	In_Frame_Del	DEL	AGA	TCGA-WQ-A9G7-01A-11D-A36X-10	13317160	131480648	9732783	222	49638										
COL5A1	1289	hgsc.bcm.edu	37	chr9	137687112	137687112	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tctcccatctgtccagggtcCgaggggtgaaagaggccccc	13	14	2	2	rs375600865		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr9:137687112C>T	ENST00000371817.3	+	34	3164	c.2750C>T	c.(2749-2751)cCg>cTg	p.P917L		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	917	Triple-helical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)	p.P917L(2)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		GTCCAGGGTCCGAGGGGTGAA	0.632																																					p.P917L		Atlas-SNP	.											COL5A1,NS,carcinoma,0,2	COL5A1	323	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.C2750T						.	C	LEU/PRO	0,4406		0,0,2203	82	88	86		2750	4.2	0.9	9		86	1,8599	1.2+/-3.3	0,1,4299	no	missense	COL5A1	NM_000093.3	98	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	917/1839	137687112	1,13005	2203	4300	6503	SO:0001583	missense	1289	exon34			AGGGTCCGAGGGG	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"Collagens"	2209	protein-coding gene	gene with protein product	"alpha 1 type V collagen"	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.2750C>T	chr9.hg19:g.137687112C>T	ENSP00000360882:p.Pro917Leu	69.0	0.0		97.0	12.0	NM_000093	Q15094|Q5SUX4	Missense_Mutation	SNP	ENST00000371817.3	hg19	CCDS6982.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.000058	0.74818	0.0	1.16E-4	ENSG00000130635	ENST00000371817	D	0.96885	-4.16	4.22	4.22	0.49857	.	0.000000	0.64402	U	0.000001	D	0.95847	0.8648	N	0.21448	0.665	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94278	0.7517	10	0.19147	T	0.46	.	16.5867	0.84729	0.0:1.0:0.0:0.0	.	917	P20908	CO5A1_HUMAN	L	917	ENSP00000360882:P917L	ENSP00000360882:P917L	P	+	2	0	COL5A1	136826933	1.000000	0.71417	0.871000	0.34182	0.700000	0.40528	7.279000	0.78599	1.904000	0.55121	0.297000	0.19635	CCG	.	.		0.632	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093		T	137687112	C	T	137687112	3	4	352	1	0	0	0	0	1	0	0	0	3698	652	23	1	2884	1	COL5A1	9	137687112	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	6206464	137687112	3526319	223	49639										
KIAA0649	9858	hgsc.bcm.edu	37	chr9	138376419	138376419	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aaatgggaggcctttggcccGccagggagctgtaggttccc	15	11	0	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr9:138376419G>A	ENST00000356818.2	+	4	612	c.63G>A	c.(61-63)ccG>ccA	p.P21P	PPP1R26_ENST00000605660.1_Silent_p.P21P|PPP1R26_ENST00000605286.1_Silent_p.P21P|PPP1R26_ENST00000602993.1_Intron|PPP1R26_ENST00000604351.1_Silent_p.P21P|PPP1R26_ENST00000401470.3_Silent_p.P21P	NM_014811.3	NP_055626.3	Q5T8A7	PPR26_HUMAN	protein phosphatase 1, regulatory subunit 26	21					negative regulation of phosphatase activity (GO:0010923)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										CCTTTGGCCCGCCAGGGAGCT	0.632																																					p.P21P		Atlas-SNP	.											.	.	.	.	0			c.G63A						.						40	47	45					9																	138376419		2202	4299	6501	SO:0001819	synonymous_variant	9858	exon4			TGGCCCGCCAGGG	AB014549	CCDS6988.1	9q34.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000196422	ENSG00000196422		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	29089	protein-coding gene	gene with protein product	"DRIM/UTP20 interacting protein", "1A6/DRIM (down-regulated in metastasis) interacting protein"	614056	"KIAA0649"	KIAA0649		9734811, 16053918	Standard	NM_014811		Approved		uc004cfr.1	Q5T8A7	OTTHUMG00000020904	ENST00000356818.2:c.63G>A	chr9.hg19:g.138376419G>A		62.0	0.0		77.0	13.0	NM_014811	Q86WU0|Q8WVV0|Q9Y4D3	Silent	SNP	ENST00000356818.2	hg19	CCDS6988.1																																																																																			.	.		0.632	PPP1R26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054987.1	NM_014811		A	138376419	G	A	138376419	2	1	352	1	0	0	0	0	0	0	0	1	8196	1074	38	1		1	KIAA0649	9	138376419	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	689307	138376419	2837012	224	49640										
KIAA0649	9858	hgsc.bcm.edu	37	chr9	138376561	138376561	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gcaccagcgatgagcgcgccGcacagaggggccacagggca	16	14	0	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr9:138376561G>A	ENST00000356818.2	+	4	754	c.205G>A	c.(205-207)Gca>Aca	p.A69T	PPP1R26_ENST00000605660.1_Missense_Mutation_p.A69T|PPP1R26_ENST00000605286.1_Missense_Mutation_p.A69T|PPP1R26_ENST00000602993.1_Intron|PPP1R26_ENST00000604351.1_Missense_Mutation_p.A69T|PPP1R26_ENST00000401470.3_Missense_Mutation_p.A69T	NM_014811.3	NP_055626.3	Q5T8A7	PPR26_HUMAN	protein phosphatase 1, regulatory subunit 26	69					negative regulation of phosphatase activity (GO:0010923)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										TGAGCGCGCCGCACAGAGGGG	0.706																																					p.A69T		Atlas-SNP	.											.	.	.	.	0			c.G205A						.						23	28	26					9																	138376561		2201	4292	6493	SO:0001583	missense	9858	exon4			CGCGCCGCACAGA	AB014549	CCDS6988.1	9q34.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000196422	ENSG00000196422		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	29089	protein-coding gene	gene with protein product	"DRIM/UTP20 interacting protein", "1A6/DRIM (down-regulated in metastasis) interacting protein"	614056	"KIAA0649"	KIAA0649		9734811, 16053918	Standard	NM_014811		Approved		uc004cfr.1	Q5T8A7	OTTHUMG00000020904	ENST00000356818.2:c.205G>A	chr9.hg19:g.138376561G>A	ENSP00000349274:p.Ala69Thr	25.0	0.0		54.0	10.0	NM_014811	Q86WU0|Q8WVV0|Q9Y4D3	Missense_Mutation	SNP	ENST00000356818.2	hg19	CCDS6988.1	.	.	.	.	.	.	.	.	.	.	g	3.118	-0.181271	0.06380	.	.	ENSG00000196422	ENST00000356818;ENST00000401470	T;T	0.61510	0.1;0.1	5.22	-6.15	0.02105	.	0.818482	0.10476	N	0.670191	T	0.30070	0.0753	N	0.14661	0.345	0.09310	N	1	B	0.20261	0.043	B	0.09377	0.004	T	0.37753	-0.9692	10	0.08179	T	0.78	0.1834	10.7556	0.46234	0.6756:0.2272:0.0972:0.0	.	69	Q5T8A7	PPR26_HUMAN	T	69	ENSP00000349274:A69T;ENSP00000385826:A69T	ENSP00000349274:A69T	A	+	1	0	KIAA0649	137516382	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.739000	0.04866	-1.256000	0.02478	-1.865000	0.00557	GCA	.	.		0.706	PPP1R26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054987.1	NM_014811		A	138376561	G	A	138376561	3	1	352	1	0	0	0	0	1	0	0	0	8196	1087	38	1	207	1	KIAA0649	9	138376561	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	142	138376561	2836870	225	49641										
NOTCH1	4851	hgsc.bcm.edu	37	chr9	139405699	139405699	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aggggctgggggcacacgggGccagcaccacctcacacgtg	16	14	1	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr9:139405699G>A	ENST00000277541.6	-	16	2567	c.2492C>T	c.(2491-2493)gCc>gTc	p.A831V		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	831	EGF-like 22. {ECO:0000255|PROSITE- ProRule:PRU00076}.				anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		GGCACACGGGGCCAGCACCAC	0.667			"T, Mis, O"	TRB@	T-ALL					HNSCC(8;0.001)																											p.A831V		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"Notch homolog 1, translocation-associated (Drosophila) (TAN1)"		L	.	NOTCH1	1980	.	0			c.C2492T						.						23	30	27					9																	139405699		2100	4203	6303	SO:0001583	missense	4851	exon16			CACGGGGCCAGCA	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"Ankyrin repeat domain containing"	7881	protein-coding gene	gene with protein product		190198	"Notch (Drosophila) homolog 1 (translocation-associated)", "Notch homolog 1, translocation-associated (Drosophila)"	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.2492C>T	chr9.hg19:g.139405699G>A	ENSP00000277541:p.Ala831Val	57.0	0.0		63.0	20.0	NM_017617	Q59ED8|Q5SXM3	Missense_Mutation	SNP	ENST00000277541.6	hg19	CCDS43905.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.461636	0.84425	.	.	ENSG00000148400	ENST00000277541	D	0.87491	-2.26	4.63	4.63	0.57726	Epidermal growth factor-like, type 3 (1);	0.060554	0.64402	D	0.000004	D	0.89480	0.6727	L	0.31207	0.915	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.90107	0.4189	10	0.48119	T	0.1	.	16.4616	0.84056	0.0:0.0:1.0:0.0	.	831	P46531	NOTC1_HUMAN	V	831	ENSP00000277541:A831V	ENSP00000277541:A831V	A	-	2	0	NOTCH1	138525520	1.000000	0.71417	0.999000	0.59377	0.905000	0.53344	5.008000	0.63991	2.120000	0.65058	0.462000	0.41574	GCC	.	.		0.667	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		A	139405699	G	A	139405699	3	1	352	1	0	0	0	0	1	0	0	0	10556	1203	42	3	5251	3	NOTCH1	9	139405699	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	1029138	139405699	1807732	226	49642										
FBXW5	54461	hgsc.bcm.edu	37	chr9	139835867	139835867	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggtggcggctgcatggggtcGgccaccaccgcaccgttggg	18	13	0	0	rs372957829		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr9:139835867G>A	ENST00000325285.3	-	8	1372	c.1293C>T	c.(1291-1293)gcC>gcT	p.A431A	FBXW5_ENST00000483559.1_5'UTR	NM_018998.3	NP_061871.1	Q969U6	FBXW5_HUMAN	F-box and WD repeat domain containing 5	431					centrosome duplication (GO:0051298)|mitotic nuclear division (GO:0007067)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	protein kinase binding (GO:0019901)			breast(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	12	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.19)	OV - Ovarian serous cystadenocarcinoma(145;7.8e-06)|Epithelial(140;0.000106)		GCATGGGGTCGGCCACCACCG	0.701																																					p.A431A		Atlas-SNP	.											.	FBXW5	36	.	0			c.C1293T						.	G		0,4404		0,0,2202	30	32	32		1293	-6.3	0.9	9		32	1,8591		0,1,4295	no	coding-synonymous	FBXW5	NM_018998.2		0,1,6497	AA,AG,GG		0.0116,0.0,0.0077		431/567	139835867	1,12995	2202	4296	6498	SO:0001819	synonymous_variant	54461	exon8			GGGGTCGGCCACC	BC014130	CCDS7014.1	9q34.3	2013-01-09	2007-02-08		ENSG00000159069	ENSG00000159069		"F-boxes / WD-40 domains", "WD repeat domain containing"	13613	protein-coding gene	gene with protein product		609072	"F-box and WD-40 domain protein 5"				Standard	NM_018998		Approved	DKFZP434B205, MGC20962, Fbw5	uc004cjx.3	Q969U6	OTTHUMG00000020967	ENST00000325285.3:c.1293C>T	chr9.hg19:g.139835867G>A		42.0	0.0		56.0	10.0	NM_018998	B2RDZ6|Q59ET5|Q5SPZ8|Q5SPZ9|Q5SQ00|Q5SQ02|Q5SQ03|Q5SQ04|Q8WY79|Q96GJ6|Q9BSU8|Q9H6A8|Q9HBQ6|Q9NSZ3	Silent	SNP	ENST00000325285.3	hg19	CCDS7014.1																																																																																			.	.		0.701	FBXW5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055227.1	NM_018998		A	139835867	G	A	139835867	2	1	352	1	0	0	0	0	0	0	0	1	5776	1103	39	1		1	FBXW5	9	139835867	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	430168	139835867	1377564	227	49643										
FUT7	2529	hgsc.bcm.edu	37	chr9	139925470	139925470	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	caccagtgcgttgcgccagaAtttctccgtaatgtagtcgc	10	12	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr9:139925470A>T	ENST00000314412.6	-	2	1739	c.721T>A	c.(721-723)Ttc>Atc	p.F241I	ABCA2_ENST00000341511.6_5'Flank|ABCA2_ENST00000265662.5_5'Flank|C9orf139_ENST00000314330.2_Intron|ABCA2_ENST00000492260.1_5'Flank|ABCA2_ENST00000371605.3_5'Flank	NM_004479.3	NP_004470.1	Q11130	FUT7_HUMAN	fucosyltransferase 7 (alpha (1,3) fucosyltransferase)	241					CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|leukocyte migration involved in immune response (GO:0002522)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			NS(1)|endometrium(1)|lung(4)|ovary(1)|skin(1)	8	all_cancers(76;0.0893)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.96e-05)|Epithelial(140;0.000486)		TTGCGCCAGAATTTCTCCGTA	0.637																																					p.F241I		Atlas-SNP	.											.	FUT7	24	.	0			c.T721A						.						96	113	107					9																	139925470		2202	4299	6501	SO:0001583	missense	2529	exon2			GCCAGAATTTCTC	X78031, AB012668	CCDS7022.1	9q34.3	2013-02-26			ENSG00000180549	ENSG00000180549		"Fucosyltransferases"	4018	protein-coding gene	gene with protein product		602030				8207002, 8182079	Standard	NM_004479		Approved		uc004ckq.2	Q11130	OTTHUMG00000020964	ENST00000314412.6:c.721T>A	chr9.hg19:g.139925470A>T	ENSP00000318142:p.Phe241Ile	138.0	0.0		152.0	13.0	NM_004479	B2R7U7|Q6DK54	Missense_Mutation	SNP	ENST00000314412.6	hg19	CCDS7022.1	.	.	.	.	.	.	.	.	.	.	a	12.87	2.066367	0.36470	.	.	ENSG00000180549	ENST00000314412	T	0.27402	1.67	4.68	-0.255	0.12988	.	0.146210	0.47093	U	0.000241	T	0.31482	0.0798	M	0.78223	2.4	0.34904	D	0.746755	B	0.17268	0.021	B	0.23018	0.043	T	0.35276	-0.9795	10	0.72032	D	0.01	-3.2918	8.0478	0.30559	0.4487:0.0:0.5513:0.0	.	241	Q11130	FUT7_HUMAN	I	241	ENSP00000318142:F241I	ENSP00000318142:F241I	F	-	1	0	FUT7	139045291	1.000000	0.71417	1.000000	0.80357	0.333000	0.28666	3.899000	0.56288	0.182000	0.20032	0.370000	0.22315	TTC	.	.		0.637	FUT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055220.1	NM_004479		T	139925470	A	T	139925470	3	4	352	1	0	0	0	0	1	0	0	0	6117	101	4	4	311	4	FUT7	9	139925470	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	89603	139925470	1287961	228	49644										
ITIH5	80760	hgsc.bcm.edu	37	chr10	7697622	7697622	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gcaacagtctgacttgcctcGggaccctgagtccatcctag	10	14	1	2	rs139355305	byFrequency	TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr10:7697622G>T	ENST00000256861.6	-	2	185	c.107C>A	c.(106-108)cCg>cAg	p.P36Q	ITIH5_ENST00000397146.2_Missense_Mutation_p.P36Q|ITIH5_ENST00000397145.2_Missense_Mutation_p.P36Q|ITIH5_ENST00000446830.2_5'UTR	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	36	VIT. {ECO:0000255|PROSITE- ProRule:PRU00801}.				hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						GACTTGCCTCGGGACCCTGAG	0.403																																					p.P36Q		Atlas-SNP	.											ITIH5_ENST00000397145,right_lower_lobe,carcinoma,0,2	ITIH5	343	.	0			c.C107A						.						81	84	83					10																	7697622		2203	4300	6503	SO:0001583	missense	80760	exon2			TGCCTCGGGACCC			10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"inter-alpha (globulin) inhibitor H5"			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.107C>A	chr10.hg19:g.7697622G>T	ENSP00000256861:p.Pro36Gln	67.0	0.0		53.0	9.0	NM_001001851	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Missense_Mutation	SNP	ENST00000256861.6	hg19		.	.	.	.	.	.	.	.	.	.	G	13.53	2.265276	0.40095	.	.	ENSG00000123243	ENST00000256861;ENST00000397146;ENST00000397145	T;T;T	0.03386	4.6;3.95;3.96	4.76	4.76	0.60689	Vault protein inter-alpha-trypsin (1);	0.473535	0.22228	N	0.062845	T	0.12433	0.0302	.	.	.	0.38942	D	0.958168	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.23940	-1.0174	9	0.19147	T	0.46	-25.5494	13.627	0.62170	0.0:0.0:1.0:0.0	.	36;36	G5E9D8;Q86UX2	.;ITIH5_HUMAN	Q	36	ENSP00000256861:P36Q;ENSP00000380333:P36Q;ENSP00000380332:P36Q	ENSP00000256861:P36Q	P	-	2	0	ITIH5	7737628	0.991000	0.36638	0.936000	0.37596	0.111000	0.19643	4.289000	0.59013	2.355000	0.79922	0.650000	0.86243	CCG	.	G|1.000;A|0.000		0.403	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569		T	7697622	G	T	7697622	3	4	352	1	0	0	0	0	1	0	0	0	7916	1116	39	1	2910	1	ITIH5	10	7697622	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10		7697622	127837125	229	49645										
CUBN	8029	hgsc.bcm.edu	37	chr10	17126368	17126368	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gggctgcttcatcatatagaCgcattgcctggtgtgagtga	13	8	2	3	rs370770104		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr10:17126368C>T	ENST00000377833.4	-	17	2268	c.2203G>A	c.(2203-2205)Gtc>Atc	p.V735I		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	735	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ATCATATAGACGCATTGCCTG	0.502																																					p.V735I		Atlas-SNP	.											.	CUBN	515	.	0			c.G2203A						.	C	ILE/VAL	0,4406		0,0,2203	130	112	118		2203	-6.4	0	10		118	1,8599	1.2+/-3.3	0,1,4299	no	missense	CUBN	NM_001081.3	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	735/3624	17126368	1,13005	2203	4300	6503	SO:0001583	missense	8029	exon17			TATAGACGCATTG	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.2203G>A	chr10.hg19:g.17126368C>T	ENSP00000367064:p.Val735Ile	134.0	0.0		128.0	18.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	C	0.014	-1.579104	0.00879	0.0	1.16E-4	ENSG00000107611	ENST00000377833	T	0.28895	1.59	5.69	-6.42	0.01932	CUB (5);	0.796683	0.10415	N	0.677428	T	0.13329	0.0323	N	0.11870	0.19	0.80722	D	1	B	0.10296	0.003	B	0.09377	0.004	T	0.47947	-0.9077	10	0.02654	T	1	.	15.8666	0.79069	0.0:0.5151:0.0:0.4849	.	735	O60494	CUBN_HUMAN	I	735	ENSP00000367064:V735I	ENSP00000367064:V735I	V	-	1	0	CUBN	17166374	0.001000	0.12720	0.007000	0.13788	0.009000	0.06853	-0.181000	0.09740	-1.199000	0.02666	-1.648000	0.00760	GTC	.	.		0.502	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		T	17126368	C	T	17126368	3	4	352	1	0	0	0	0	1	0	0	0	4053	536	19	1	8872	1	CUBN	10	17126368	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	9428746	17126368	118408379	230	49646										
HNRNPF	3185	hgsc.bcm.edu	37	chr10	43883054	43883054	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ctgtgcttcaacacccaatcCatctcggttctgtgggactt	8	13	3	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr10:43883054C>T	ENST00000544000.1	-	4	686	c.279G>A	c.(277-279)atG>atA	p.M93I	HNRNPF_ENST00000337970.3_Missense_Mutation_p.M93I|HNRNPF_ENST00000357065.4_Missense_Mutation_p.M93I|HNRNPF_ENST00000498176.1_5'Flank|HNRNPF_ENST00000443950.2_Missense_Mutation_p.M93I|HNRNPF_ENST00000356053.3_Missense_Mutation_p.M93I	NM_001098207.1	NP_001091677.1	P52597	HNRPF_HUMAN	heterogeneous nuclear ribonucleoprotein F	93					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA splicing (GO:0043484)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|urinary_tract(1)	19						ACACCCAATCCATCTCGGTTC	0.502																																					p.M93I		Atlas-SNP	.											.	HNRNPF	57	.	0			c.G279A						.						193	149	164					10																	43883054		2203	4300	6503	SO:0001583	missense	3185	exon4			CCAATCCATCTCG		CCDS7204.1	10q11.21	2013-02-12		2008-04-18	ENSG00000169813	ENSG00000169813		"RNA binding motif (RRM) containing"	5039	protein-coding gene	gene with protein product		601037		HNRPF		7499401	Standard	NM_001098208		Approved		uc001jas.2	P52597	OTTHUMG00000018029	ENST00000544000.1:c.279G>A	chr10.hg19:g.43883054C>T	ENSP00000438061:p.Met93Ile	72.0	0.0		72.0	29.0	NM_001098204	B3KM84|Q5T0N2|Q96AU2	Missense_Mutation	SNP	ENST00000544000.1	hg19	CCDS7204.1	.	.	.	.	.	.	.	.	.	.	C	13.21	2.167713	0.38315	.	.	ENSG00000169813	ENST00000544000;ENST00000443950;ENST00000356053;ENST00000357065;ENST00000337970;ENST00000540544	T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58	4.04	2.19	0.27852	.	0.076118	0.85682	N	0.000000	T	0.34948	0.0915	M	0.72576	2.205	0.58432	D	0.999993	B	0.19706	0.038	B	0.33690	0.168	T	0.23868	-1.0176	10	0.56958	D	0.05	-12.2548	8.5719	0.33574	0.0:0.8047:0.0:0.1953	.	93	P52597	HNRPF_HUMAN	I	93;93;93;93;93;16	ENSP00000438061:M93I;ENSP00000400433:M93I;ENSP00000348345:M93I;ENSP00000349573:M93I;ENSP00000338477:M93I	ENSP00000338477:M93I	M	-	3	0	HNRNPF	43203060	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.318000	0.65829	0.668000	0.31126	-0.136000	0.14681	ATG	.	.		0.502	HNRNPF-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047705.2			T	43883054	C	T	43883054	3	4	352	1	0	0	0	0	1	0	0	0	7274	594	21	3	972	3	HNRNPF	10	43883054	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	26756686	43883054	91651693	231	49647										
ARHGAP22	58504	hgsc.bcm.edu	37	chr10	49659075	49659075	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cggagccccaccccactgcgCattgcaggcccccgcgcggg	13	20	0	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr10:49659075C>A	ENST00000249601.4	-	9	1393	c.1097G>T	c.(1096-1098)tGc>tTc	p.C366F	ARHGAP22_ENST00000435790.2_Missense_Mutation_p.C372F|ARHGAP22_ENST00000477708.2_Missense_Mutation_p.C199F|ARHGAP22_ENST00000417912.2_Missense_Mutation_p.C382F|ARHGAP22_ENST00000374170.1_Missense_Mutation_p.C207F|ARHGAP22_ENST00000374172.1_Missense_Mutation_p.C257F|ARHGAP22_ENST00000417247.2_Missense_Mutation_p.C276F	NM_001256024.1|NM_021226.3	NP_001242953.1|NP_067049.2	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 22	366					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						CCCCACTGCGCATTGCAGGCC	0.721																																					p.C382F		Atlas-SNP	.											.	ARHGAP22	94	.	0			c.G1145T						.						8	10	9					10																	49659075		2012	4091	6103	SO:0001583	missense	58504	exon9			ACTGCGCATTGCA	AY324801	CCDS7227.1, CCDS58079.1, CCDS58080.1, CCDS58081.1	10q11.23	2013-01-10			ENSG00000128805	ENSG00000128805		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	30320	protein-coding gene	gene with protein product		610585				8619474	Standard	NM_021226		Approved	RhoGAP2	uc010qgm.3	Q7Z5H3	OTTHUMG00000018176	ENST00000249601.4:c.1097G>T	chr10.hg19:g.49659075C>A	ENSP00000249601:p.Cys366Phe	117.0	0.0		108.0	17.0	NM_001256024	A0AVP7|A5YM75|B4DED8|B9EGA0|C9JDM2|O00152|Q6ZSB0	Missense_Mutation	SNP	ENST00000249601.4	hg19	CCDS7227.1	.	.	.	.	.	.	.	.	.	.	C	8.408	0.843478	0.16963	.	.	ENSG00000128805	ENST00000249601;ENST00000374172;ENST00000374170;ENST00000477708;ENST00000417247;ENST00000435790;ENST00000417912	T;T;T;T;T;T;T	0.24350	2.93;2.61;1.86;2.26;2.6;2.89;2.94	4.95	4.95	0.65309	.	0.347798	0.27749	N	0.018020	T	0.39627	0.1085	M	0.61703	1.905	0.09310	N	1	P;P;P;P;P;D	0.71674	0.592;0.829;0.907;0.899;0.817;0.998	B;B;B;B;P;P	0.58820	0.285;0.332;0.346;0.332;0.477;0.846	T	0.21861	-1.0233	10	0.27785	T	0.31	.	10.9701	0.47434	0.0:0.9091:0.0:0.0909	.	372;366;382;366;276;199	B4DED8;A6NDI7;Q7Z5H3-2;Q7Z5H3;Q7Z5H3-3;D6R9V6	.;.;.;RHG22_HUMAN;.;.	F	366;257;207;199;276;372;382	ENSP00000249601:C366F;ENSP00000363287:C257F;ENSP00000363285:C207F;ENSP00000422868:C199F;ENSP00000410054:C276F;ENSP00000416701:C372F;ENSP00000412461:C382F	ENSP00000249601:C366F	C	-	2	0	ARHGAP22	49329081	0.928000	0.31464	0.064000	0.19789	0.032000	0.12392	1.901000	0.39838	2.306000	0.77630	0.313000	0.20887	TGC	.	.		0.721	ARHGAP22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358767.1	NM_021226		A	49659075	C	A	49659075	3	1	352	1	0	0	0	0	1	0	0	0	872	710	25	3	1007	3	ARHGAP22	10	49659075	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	5776021	49659075	85875672	232	49648										
OGDHL	55753	hgsc.bcm.edu	37	chr10	50947771	50947771	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gccgcacccacttggcctggCcggtgctgatgaactggtcg	14	14	0	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr10:50947771C>T	ENST00000374103.4	-	17	2340	c.2255G>A	c.(2254-2256)gGc>gAc	p.G752D	OGDHL_ENST00000419399.1_Missense_Mutation_p.G695D|OGDHL_ENST00000432695.1_Missense_Mutation_p.G543D|OGDHL_ENST00000490844.1_5'Flank	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	752					glycolytic process (GO:0006096)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	61						CTTGGCCTGGCCGGTGCTGAT	0.627																																					p.G752D		Atlas-SNP	.											.	OGDHL	149	.	0			c.G2255A						.						107	87	94					10																	50947771		2203	4300	6503	SO:0001583	missense	55753	exon17			GCCTGGCCGGTGC	AK001713	CCDS7234.1, CCDS44390.1, CCDS44391.1	10q11.23	2013-09-20			ENSG00000197444	ENSG00000197444			25590	protein-coding gene	gene with protein product						10574462	Standard	NM_018245		Approved	FLJ10851	uc001jie.3	Q9ULD0	OTTHUMG00000018200	ENST00000374103.4:c.2255G>A	chr10.hg19:g.50947771C>T	ENSP00000363216:p.Gly752Asp	69.0	0.0		65.0	13.0	NM_018245	A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	Missense_Mutation	SNP	ENST00000374103.4	hg19	CCDS7234.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.690156	0.88735	.	.	ENSG00000197444	ENST00000374103;ENST00000419399;ENST00000432695	D;D;D	0.93811	-3.29;-3.29;-3.29	4.48	4.48	0.54585	Transketolase-like, pyrimidine-binding domain (2);	0.056650	0.64402	D	0.000001	D	0.97917	0.9315	H	0.96805	3.885	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.99813	1.1042	10	0.87932	D	0	.	17.1694	0.86825	0.0:1.0:0.0:0.0	.	695;543;752	Q9ULD0-2;Q9ULD0-3;Q9ULD0	.;.;OGDHL_HUMAN	D	752;695;543	ENSP00000363216:G752D;ENSP00000401356:G695D;ENSP00000390240:G543D	ENSP00000363216:G752D	G	-	2	0	OGDHL	50617777	1.000000	0.71417	0.970000	0.41538	0.935000	0.57460	6.060000	0.71141	2.057000	0.61298	0.289000	0.19496	GGC	.	.		0.627	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1	NM_018245		T	50947771	C	T	50947771	3	4	352	1	0	0	0	0	1	0	0	0	10849	739	26	3	805	3	OGDHL	10	50947771	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	1288696	50947771	84586976	233	49649										
ANK3	288	hgsc.bcm.edu	37	chr10	61828444	61828444	+	Frame_Shift_Del	DEL	T	T	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ccggccttttcactctttgaTtttaaaggtgctgcctctgt							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr10:61828444delT	ENST00000280772.2	-	37	12386	c.12195delA	c.(12193-12195)aaafs	p.K4065fs	ANK3_ENST00000355288.2_Intron|ANK3_ENST00000373827.2_Intron|ANK3_ENST00000503366.1_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	4065					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						CACTCTTTGATTTTAAAGGTG	0.512																																					p.S4066fs		Atlas-INDEL	.											.	ANK3	703	.	0			c.12196delT						.						117	121	119					10																	61828444		2203	4300	6503	SO:0001589	frameshift_variant	288	exon37			.	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.12195delA	chr10.hg19:g.61828444delT	ENSP00000280772:p.Lys4065fs	70.0	0.0		76.0	17.0	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Frame_Shift_Del	DEL	ENST00000280772.2	hg19	CCDS7258.1																																																																																			.	.		0.512	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		-	61828444	T	-	61828444	7	5	352	1	0	1	0	1	0	0	0	0	622	1490	52	0	1279	0	ANK3	10	61828444	Frame_Shift_Del	DEL	T	TCGA-WQ-A9G7-01A-11D-A36X-10	10880673	61828444	73706303	234	49650										
SIRT1	23411	hgsc.bcm.edu	37	chr10	69648662	69648662	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ccatatacttttgttcagcaAcatcttatgattggcacaga	6	9	2	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr10:69648662A>G	ENST00000212015.6	+	3	623	c.570A>G	c.(568-570)caA>caG	p.Q190Q	SIRT1_ENST00000406900.1_5'Flank|SIRT1_ENST00000497639.1_3'UTR|SIRT1_ENST00000432464.1_Intron	NM_012238.4	NP_036370.2	Q96EB6	SIR1_HUMAN	sirtuin 1	190	Interaction with CCAR2.|Interaction with HIST1H1E.				angiogenesis (GO:0001525)|cell aging (GO:0007569)|cellular glucose homeostasis (GO:0001678)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to starvation (GO:0009267)|cellular response to tumor necrosis factor (GO:0071356)|cellular triglyceride homeostasis (GO:0035356)|cholesterol homeostasis (GO:0042632)|chromatin organization (GO:0006325)|chromatin silencing (GO:0006342)|chromatin silencing at rDNA (GO:0000183)|circadian regulation of gene expression (GO:0032922)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|establishment of chromatin silencing (GO:0006343)|fatty acid homeostasis (GO:0055089)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of chromatin silencing (GO:0006344)|methylation-dependent chromatin silencing (GO:0006346)|muscle organ development (GO:0007517)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|negative regulation of cell growth (GO:0030308)|negative regulation of cellular response to testosterone stimulus (GO:2000655)|negative regulation of cellular senescence (GO:2000773)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of helicase activity (GO:0051097)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of neuron death (GO:1901215)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of peptidyl-lysine acetylation (GO:2000757)|negative regulation of phosphorylation (GO:0042326)|negative regulation of prostaglandin biosynthetic process (GO:0031393)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|ovulation from ovarian follicle (GO:0001542)|peptidyl-lysine acetylation (GO:0018394)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular senescence (GO:2000774)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of chromatin silencing (GO:0031937)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of DNA repair (GO:0045739)|positive regulation of histone H3-K9 methylation (GO:0051574)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of macroautophagy (GO:0016239)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein deacetylation (GO:0006476)|protein destabilization (GO:0031648)|protein ubiquitination (GO:0016567)|pyrimidine dimer repair by nucleotide-excision repair (GO:0000720)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cell proliferation (GO:0042127)|regulation of endodeoxyribonuclease activity (GO:0032071)|regulation of glucose metabolic process (GO:0010906)|regulation of mitotic cell cycle (GO:0007346)|regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035358)|regulation of protein import into nucleus, translocation (GO:0033158)|regulation of smooth muscle cell apoptotic process (GO:0034391)|response to hydrogen peroxide (GO:0042542)|response to insulin (GO:0032868)|response to oxidative stress (GO:0006979)|rRNA processing (GO:0006364)|single strand break repair (GO:0000012)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)|triglyceride mobilization (GO:0006642)|viral process (GO:0016032)|white fat cell differentiation (GO:0050872)	chromatin silencing complex (GO:0005677)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear envelope (GO:0005635)|nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|rDNA heterochromatin (GO:0033553)	bHLH transcription factor binding (GO:0043425)|deacetylase activity (GO:0019213)|enzyme binding (GO:0019899)|histone binding (GO:0042393)|histone deacetylase activity (GO:0004407)|HLH domain binding (GO:0043398)|identical protein binding (GO:0042802)|keratin filament binding (GO:1990254)|metal ion binding (GO:0046872)|mitogen-activated protein kinase binding (GO:0051019)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (GO:0017136)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent protein deacetylase activity (GO:0034979)|p53 binding (GO:0002039)|protein C-terminus binding (GO:0008022)|protein deacetylase activity (GO:0033558)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(3)|skin(1)	14						TTGTTCAGCAACATCTTATGA	0.358																																					p.Q190Q		Atlas-SNP	.											.	SIRT1	38	.	0			c.A570G						.						138	137	137					10																	69648662		2203	4300	6503	SO:0001819	synonymous_variant	23411	exon3			TCAGCAACATCTT	AF083106	CCDS7273.1, CCDS44412.1	10q21	2010-06-25	2010-06-25		ENSG00000096717	ENSG00000096717			14929	protein-coding gene	gene with protein product		604479	"sirtuin (silent mating type information regulation 2, S. cerevisiae, homolog) 1", "sirtuin (silent mating type information regulation 2 homolog) 1 (S. cerevisiae)"			10381378	Standard	NM_012238		Approved	SIR2L1	uc001jnd.3	Q96EB6	OTTHUMG00000018340	ENST00000212015.6:c.570A>G	chr10.hg19:g.69648662A>G		59.0	0.0		44.0	12.0	NM_012238	Q2XNF6|Q5JVQ0|Q9GZR9|Q9Y6F0	Silent	SNP	ENST00000212015.6	hg19	CCDS7273.1																																																																																			.	.		0.358	SIRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048296.1			G	69648662	A	G	69648662	2	3	352	1	0	0	0	0	0	0	0	1	14352	40	2	2		2	SIRT1	10	69648662	Silent	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	7820218	69648662	65886085	235	49651										
LIPK	643414	hgsc.bcm.edu	37	chr10	90512278	90512278	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cttttattgtatttagcttaCacctcctttatacaacatta	2	9	0	0	rs200951684		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr10:90512278C>T	ENST00000404190.1	+	9	965	c.965C>T	c.(964-966)aCa>aTa	p.T322I		NM_001080518.1	NP_001073987.1	Q5VXJ0	LIPK_HUMAN	lipase, family member K	322					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	hydrolase activity, acting on ester bonds (GO:0016788)			endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)	12		Colorectal(252;0.0381)		Colorectal(12;7.03e-05)|COAD - Colon adenocarcinoma(12;8.33e-05)		ATTTAGCTTACACCTCCTTTA	0.338																																					p.T322I		Atlas-SNP	.											.	LIPK	50	.	0			c.C965T						.						28	25	26					10																	90512278		1835	4082	5917	SO:0001583	missense	643414	exon9			AGCTTACACCTCC		CCDS44455.1	10q23.31	2008-02-04	2007-02-27	2007-02-27	ENSG00000204021	ENSG00000204021			23444	protein-coding gene	gene with protein product		613922	"lipase-like, ab-hydrolase domain containing 2"	LIPL2			Standard	NM_001080518		Approved	bA186O14.2	uc010qmv.2	Q5VXJ0	OTTHUMG00000018693	ENST00000404190.1:c.965C>T	chr10.hg19:g.90512278C>T	ENSP00000383900:p.Thr322Ile	82.0	0.0		86.0	17.0	NM_001080518	A7KIH8	Missense_Mutation	SNP	ENST00000404190.1	hg19	CCDS44455.1	.	.	.	.	.	.	.	.	.	.	C	11.56	1.675558	0.29783	.	.	ENSG00000204021	ENST00000404190	T	0.61742	0.08	5.65	1.75	0.24633	Alpha/beta hydrolase fold-1 (1);	0.437153	0.21888	N	0.067627	T	0.60222	0.2252	M	0.81942	2.565	0.09310	N	1	P	0.36354	0.549	B	0.42214	0.38	T	0.52823	-0.8524	10	0.38643	T	0.18	-5.2805	8.9719	0.35912	0.0:0.6962:0.0:0.3038	.	322	Q5VXJ0	LIPK_HUMAN	I	322	ENSP00000383900:T322I	ENSP00000383900:T322I	T	+	2	0	LIPK	90502258	0.035000	0.19736	0.060000	0.19600	0.533000	0.34776	0.869000	0.27996	0.503000	0.28060	-0.140000	0.14226	ACA	.	.		0.338	LIPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049253.2	XM_061222		T	90512278	C	T	90512278	3	4	352	1	0	0	0	0	1	0	0	0	8836	478	17	3	999	3	LIPK	10	90512278	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	20863616	90512278	45022469	236	49652										
TCTN3	26123	hgsc.bcm.edu	37	chr10	97453178	97453178	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agatagcagtccctgtcgcaGcagcaatttatatcgcaggc	10	11	0	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr10:97453178G>A	ENST00000371217.5	-	2	335	c.312C>T	c.(310-312)tgC>tgT	p.C104C	TCTN3_ENST00000430368.2_Silent_p.C104C|TCTN3_ENST00000371209.5_Silent_p.C104C|TCTN3_ENST00000265993.9_Silent_p.C122C			Q6NUS6	TECT3_HUMAN	tectonic family member 3	104	Cys-rich.				apoptotic process (GO:0006915)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(3)|endometrium(1)|large_intestine(2)|lung(8)|urinary_tract(1)	15		Colorectal(252;0.0815)		Epithelial(162;1.69e-07)|all cancers(201;5.63e-06)		CCCTGTCGCAGCAGCAATTTA	0.498											OREG0020392	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C104C		Atlas-SNP	.											.	TCTN3	66	.	0			c.C312T						.						98	89	92					10																	97453178		692	1591	2283	SO:0001819	synonymous_variant	26123	exon2			GTCGCAGCAGCAA	AK098295	CCDS31258.2, CCDS44461.1	10q24.1	2014-01-28	2007-08-20	2007-08-20	ENSG00000119977	ENSG00000119977		"Tectonic proteins"	24519	protein-coding gene	gene with protein product		613847	"chromosome 10 open reading frame 61"	C10orf61		12975309	Standard	NM_015631		Approved	DKFZP564D116, TECT3, JBTS18	uc001klb.4	Q6NUS6	OTTHUMG00000018814	ENST00000371217.5:c.312C>T	chr10.hg19:g.97453178G>A		176.0	0.0	1328	168.0	21.0	NM_015631	A6NIC8|B0QZ90|B4DR81|Q6P7P3|Q6UW27|Q6ZQQ0|Q8N7K1|Q8NBQ0|Q96GF7|Q9Y3U1	Silent	SNP	ENST00000371217.5	hg19	CCDS31258.2	.	.	.	.	.	.	.	.	.	.	G	12.15	1.850868	0.32699	.	.	ENSG00000119977	ENST00000424175	.	.	.	5.92	4.06	0.47325	.	.	.	.	.	T	0.59770	0.2218	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57528	-0.7796	4	.	.	.	-17.8507	9.562	0.39376	0.1656:0.0:0.8344:0.0	.	.	.	.	V	84	.	.	A	-	2	0	TCTN3	97443168	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.732000	0.47352	1.520000	0.48965	0.655000	0.94253	GCT	.	.		0.498	TCTN3-009	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000471858.1	NM_015631		A	97453178	G	A	97453178	2	1	352	1	0	0	0	0	0	0	0	1	15739	963	34	3		3	TCTN3	10	97453178	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	6940900	97453178	38081569	237	49653										
CNNM1	26507	hgsc.bcm.edu	37	chr10	101089165	101089165	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	atggcggcggccgcggcggcGgcagcagcggtgggtgtcag	22	11	1	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr10:101089165G>A	ENST00000356713.4	+	1	310	c.21G>A	c.(19-21)gcG>gcA	p.A7A	CNNM1_ENST00000370534.4_5'Flank|CNNM1_ENST00000446890.1_Silent_p.A7A|CNNM1_ENST00000370528.3_Silent_p.A7A	NM_020348.2	NP_065081.2	Q9NRU3	CNNM1_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 1	7					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(5)|ovary(1)|prostate(1)|skin(1)	25		Colorectal(252;0.234)		Epithelial(162;6.82e-10)|all cancers(201;5.62e-08)		ccgcggcggcggcagcagcgg	0.721																																					p.A7A		Atlas-SNP	.											.	CNNM1	101	.	0			c.G21A						.						2	2	2					10																	101089165		1032	2150	3182	SO:0001819	synonymous_variant	26507	exon1			GGCGGCGGCAGCA	AF169226	CCDS7478.2	10q24.2	2014-08-08	2014-08-07		ENSG00000119946	ENSG00000119946			102	protein-coding gene	gene with protein product		607802	"cyclin M1"	ACDP1		21393841	Standard	NM_020348		Approved		uc001kpp.4	Q9NRU3	OTTHUMG00000018881	ENST00000356713.4:c.21G>A	chr10.hg19:g.101089165G>A		38.0	0.0		43.0	16.0	NM_020348	Q4QQG7|Q4QQH8|Q4QQP9|Q9NT45	Silent	SNP	ENST00000356713.4	hg19	CCDS7478.2																																																																																			.	.		0.721	CNNM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049792.2	NM_020348		A	101089165	G	A	101089165	2	1	352	1	0	0	0	0	0	0	0	1	3614	1103	39	1		1	CNNM1	10	101089165	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	3635987	101089165	34445582	238	49654										
FAM178A	55719	hgsc.bcm.edu	37	chr10	102684351	102684351	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aaagcaaagactaataaggcCgattctaatgtatcttcagg	8	7	3	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr10:102684351C>T	ENST00000238961.4	+	5	2135	c.1593C>T	c.(1591-1593)gcC>gcT	p.A531A	FAM178A_ENST00000370269.3_Silent_p.A531A|FAM178A_ENST00000370271.3_Silent_p.A531A	NM_018121.3	NP_060591.3	Q8IX21	F178A_HUMAN	family with sequence similarity 178, member A	531						chromatin (GO:0000785)|extracellular space (GO:0005615)|nucleus (GO:0005634)											CTAATAAGGCCGATTCTAATG	0.423																																					p.A531A		Atlas-SNP	.											.	FAM178A	9	.	0			c.C1593T						.						98	99	99					10																	102684351		2203	4300	6503	SO:0001819	synonymous_variant	55719	exon5			TAAGGCCGATTCT	AF460991	CCDS7500.1, CCDS44470.1, CCDS65918.1	10q24.31	2008-07-18	2008-07-18	2008-07-18	ENSG00000119906	ENSG00000119906			17814	protein-coding gene	gene with protein product		610348	"chromosome 10 open reading frame 6"	C10orf6		12459258	Standard	NM_018121		Approved	FLJ10512, FLJ25012	uc001krs.3	Q8IX21	OTTHUMG00000018919	ENST00000238961.4:c.1593C>T	chr10.hg19:g.102684351C>T		182.0	0.0		135.0	18.0	NM_001136123	A8K950|B1AL17|Q5W0L8|Q6GMU6|Q9NPE8	Silent	SNP	ENST00000238961.4	hg19	CCDS7500.1																																																																																			.	.		0.423	FAM178A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049897.3			T	102684351	C	T	102684351	2	4	352	1	0	0	0	0	0	0	0	1	5508	639	23	1		1	FAM178A	10	102684351	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	1595186	102684351	32850396	239	49655										
PSD	5662	hgsc.bcm.edu	37	chr10	104171962	104171962	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gaacttgaggtactccccagCcaccagtttgctgaagtcat	9	12	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr10:104171962C>T	ENST00000020673.5	-	7	2297	c.1771G>A	c.(1771-1773)Gct>Act	p.A591T	PSD_ENST00000406432.1_Missense_Mutation_p.A591T	NM_001270966.1|NM_002779.4	NP_001257895.1|NP_002770.3	A5PKW4	PSD1_HUMAN	pleckstrin and Sec7 domain containing	591	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)|signal transducer activity (GO:0004871)			breast(4)|endometrium(2)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				Epithelial(162;1.27e-08)|all cancers(201;2.85e-07)		TACTCCCCAGCCACCAGTTTG	0.592																																					p.A591T		Atlas-SNP	.											.	PSD	164	.	0			c.G1771A						.						135	155	148					10																	104171962		2203	4300	6503	SO:0001583	missense	5662	exon8			CCCCAGCCACCAG	X99688	CCDS31272.1, CCDS73187.1	10q24	2013-01-10	2004-04-28		ENSG00000059915	ENSG00000059915		"Pleckstrin homology (PH) domain containing"	9507	protein-coding gene	gene with protein product		602327	"pleckstrin and Sec7 domain protein"			9417912	Standard	NM_002779		Approved	KIAA2011, TYL, PSD1	uc009xxd.2	A5PKW4	OTTHUMG00000018954	ENST00000020673.5:c.1771G>A	chr10.hg19:g.104171962C>T	ENSP00000020673:p.Ala591Thr	94.0	0.0		99.0	35.0	NM_001270965	B1AKX7|D3DR87|Q15673|Q8IVG0	Missense_Mutation	SNP	ENST00000020673.5	hg19	CCDS31272.1	.	.	.	.	.	.	.	.	.	.	C	35	5.499076	0.96355	.	.	ENSG00000059915	ENST00000020673;ENST00000541902;ENST00000406432	T;T	0.54479	0.57;0.57	5.32	5.32	0.75619	SEC7-like (4);	0.059561	0.64402	D	0.000003	T	0.79435	0.4445	M	0.91510	3.215	0.54753	D	0.999985	D	0.71674	0.998	D	0.79108	0.992	D	0.84350	0.0532	10	0.87932	D	0	.	18.9992	0.92826	0.0:1.0:0.0:0.0	.	591	A5PKW4	PSD1_HUMAN	T	591;494;591	ENSP00000020673:A591T;ENSP00000384830:A591T	ENSP00000020673:A591T	A	-	1	0	PSD	104161952	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.434000	0.80377	2.500000	0.84329	0.561000	0.74099	GCT	.	.		0.592	PSD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050041.2			T	104171962	C	T	104171962	3	4	352	1	0	0	0	0	1	0	0	0	12658	739	26	3	1347	3	PSD	10	104171962	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	1487611	104171962	31362785	240	49656										
CYP17A1	1586	hgsc.bcm.edu	37	chr10	104595102	104595102	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tgccagtgtgcgccagagtcAgcgaaggcgatacccttacg	13	12	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr10:104595102A>G	ENST00000369887.3	-	2	516	c.345T>C	c.(343-345)gcT>gcC	p.A115A	CYP17A1-AS1_ENST00000369884.4_RNA|CYP17A1_ENST00000489268.1_5'UTR	NM_000102.3	NP_000093.1	P05093	CP17A_HUMAN	cytochrome P450, family 17, subfamily A, polypeptide 1	115					adrenal gland development (GO:0030325)|androgen biosynthetic process (GO:0006702)|biphenyl metabolic process (GO:0018879)|cellular response to antibiotic (GO:0071236)|cellular response to gonadotropin stimulus (GO:0071371)|cellular response to lipopolysaccharide (GO:0071222)|dibenzo-p-dioxin metabolic process (GO:0018894)|glucocorticoid biosynthetic process (GO:0006704)|hippocampus development (GO:0021766)|hormone biosynthetic process (GO:0042446)|Leydig cell differentiation (GO:0033327)|ovulation (GO:0030728)|phenol-containing compound metabolic process (GO:0018958)|phthalate metabolic process (GO:0018963)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|progesterone metabolic process (GO:0042448)|response to acetate (GO:0010034)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to fungicide (GO:0060992)|response to herbicide (GO:0009635)|response to insecticide (GO:0017085)|response to ionizing radiation (GO:0010212)|response to methylmercury (GO:0051597)|response to nutrient levels (GO:0031667)|response to retinoic acid (GO:0032526)|response to steroid hormone (GO:0048545)|sex differentiation (GO:0007548)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	axon (GO:0030424)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)	17-alpha-hydroxyprogesterone aldolase activity (GO:0047442)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|steroid 17-alpha-monooxygenase activity (GO:0004508)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.122)|all_hematologic(284;0.152)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)	Abiraterone(DB05812)|Aminophenazone(DB01424)|Dexamethasone(DB01234)|Metoclopramide(DB01233)|Progesterone(DB00396)	CGCCAGAGTCAGCGAAGGCGA	0.562											OREG0020487	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A115A		Atlas-SNP	.											.	CYP17A1	48	.	0			c.T345C						.						159	123	135					10																	104595102		2203	4300	6503	SO:0001819	synonymous_variant	1586	exon2			AGAGTCAGCGAAG	M19489	CCDS7541.1	10q24.3	2010-05-04	2003-02-14	2003-02-28	ENSG00000148795	ENSG00000148795	1.14.99.9	"Cytochrome P450s"	2593	protein-coding gene	gene with protein product	"Steroid 17-alpha-monooxygenase"	609300	"cytochrome P450, subfamily XVII (steroid 17-alpha-hydroxylase), adrenal hyperplasia"	CYP17		1347802	Standard	NM_000102		Approved	P450C17, CPT7, S17AH	uc001kwg.3	P05093	OTTHUMG00000018969	ENST00000369887.3:c.345T>C	chr10.hg19:g.104595102A>G		115.0	0.0	172	72.0	10.0	NM_000102	Q5TZV7	Silent	SNP	ENST00000369887.3	hg19	CCDS7541.1																																																																																			.	.		0.562	CYP17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050101.1	NM_000102		G	104595102	A	G	104595102	2	3	352	1	0	0	0	0	0	0	0	1	4149	175	7	2		2	CYP17A1	10	104595102	Silent	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	423140	104595102	30939645	241	49657										
NEURL	9148	hgsc.bcm.edu	37	chr10	105344832	105344832	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ccgggcccctgcacagcggcGacatcctgggcctggtggtc	15	16	0	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr10:105344832G>A	ENST00000369780.4	+	4	1598	c.1189G>A	c.(1189-1191)Gac>Aac	p.D397N	NEURL_ENST00000369777.2_Missense_Mutation_p.D380N	NM_004210.4	NP_004201.3	O76050	NEUL1_HUMAN		397	NHR 2. {ECO:0000255|PROSITE- ProRule:PRU00400}.				brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|lactation (GO:0007595)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Notch signaling pathway (GO:0045746)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse maturation (GO:0090129)|protein monoubiquitination (GO:0006513)|skeletal muscle tissue development (GO:0007519)|sperm axoneme assembly (GO:0007288)|sperm motility (GO:0030317)	apical dendrite (GO:0097440)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ligase activity (GO:0016874)|translation factor activity, non-nucleic acid binding (GO:0045183)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	17				Epithelial(162;2.12e-09)|all cancers(201;6.99e-08)|BRCA - Breast invasive adenocarcinoma(275;0.125)		GCACAGCGGCGACATCCTGGG	0.726																																					p.D397N		Atlas-SNP	.											.	NEURL	38	.	0			c.G1189A						.						8	8	8					10																	105344832		2092	4146	6238	SO:0001583	missense	9148	exon4			AGCGGCGACATCC																												ENST00000369780.4:c.1189G>A	chr10.hg19:g.105344832G>A	ENSP00000358795:p.Asp397Asn	18.0	0.0		17.0	6.0	NM_004210	Q5TDR2|Q5TDR3|Q8TAN0|Q9H463	Missense_Mutation	SNP	ENST00000369780.4	hg19	CCDS7551.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.972686	0.92919	.	.	ENSG00000107954	ENST00000369780;ENST00000369777	.	.	.	4.98	4.98	0.66077	NEUZ (2);	0.000000	0.85682	D	0.000000	T	0.77136	0.4086	L	0.59912	1.85	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.79619	-0.1728	9	0.72032	D	0.01	-38.4716	18.2474	0.89991	0.0:0.0:1.0:0.0	.	397	O76050	NEU1A_HUMAN	N	397;380	.	ENSP00000358792:D380N	D	+	1	0	NEURL	105334822	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.870000	0.87175	2.310000	0.77875	0.491000	0.48974	GAC	.	.		0.726	NEURL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050170.1			A	105344832	G	A	105344832	3	1	352	1	0	0	0	0	1	0	0	0	10354	1058	37	1	1203	1	NEURL	10	105344832	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	749730	105344832	30189915	242	49658										
NHLRC2	374354	hgsc.bcm.edu	37	chr10	115663496	115663499	+	Splice_Site	DEL	GTAA	GTAA	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aaactaaaatggtatctgtgGtaagtaattttaaaatataa							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	GTAA	GTAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr10:115663496_115663499delGTAA	ENST00000369301.3	+	9	1916		c.e9+1			NM_198514.3	NP_940916.2	Q8NBF2	NHLC2_HUMAN	NHL repeat containing 2											breast(1)|endometrium(2)|kidney(4)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	15				Epithelial(162;0.017)|all cancers(201;0.0187)		GGTATCTGTGGTAAGTAATTTTAA	0.328																																					p.568_568del		Atlas-INDEL	.											.	NHLRC2	56	.	0			c.1704_1704del						.																																			SO:0001630	splice_region_variant	374354	exon9			.	AK090631	CCDS7585.1	10q26.11	2006-03-31			ENSG00000196865	ENSG00000196865			24731	protein-coding gene	gene with protein product						12477932	Standard	NM_198514		Approved	FLJ25621, FLJ20147, FLJ33312, MGC45492, DKFZp779F115	uc001lax.2	Q8NBF2	OTTHUMG00000019078	ENST00000369301.3:c.1704+1GTAA>-	chr10.hg19:g.115663500_115663503delGTAA		334.0	0.0		288.0	34.0	NM_198514	Q8N1H1|Q8N5A6	Frame_Shift_Del	DEL	ENST00000369301.3	hg19	CCDS7585.1																																																																																			.	.		0.328	NHLRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050446.1	NM_198514	Intron	-	115663499	GTAA	-	115663496	8	5	352	1	0	1	0	1	0	0	1	0	10415	1275	44	0	1739	0	NHLRC2	10	115663496	Splice_Site	DEL	GTAA	TCGA-WQ-A9G7-01A-11D-A36X-10	10318664	115663496	19871251	243	49659										
FGFR2	2263	hgsc.bcm.edu	37	chr10	123310909	123310929	+	In_Frame_Del	DEL	GTTGGCCGCAGGCACAGCATG	GTTGGCCGCAGGCACAGCATG	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gggcagcgaaacttgacagtGttggccgcaggcacagcatg							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	GTTGGCCGCAGGCACAGCATG	GTTGGCCGCAGGCACAGCATG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr10:123310909_123310929delGTTGGCCGCAGGCACAGCATG	ENST00000358487.5	-	5	771_791	c.499_519delCATGCTGTGCCTGCGGCCAAC	c.(499-519)catgctgtgcctgcggccaacdel	p.HAVPAAN167del	FGFR2_ENST00000369056.1_In_Frame_Del_p.HAVPAAN167del|FGFR2_ENST00000457416.2_In_Frame_Del_p.HAVPAAN167del|FGFR2_ENST00000359354.2_In_Frame_Del_p.HAVPAAN167del|FGFR2_ENST00000357555.5_In_Frame_Del_p.HAVPAAN78del|FGFR2_ENST00000369059.1_In_Frame_Del_p.HAVPAAN52del|FGFR2_ENST00000346997.2_In_Frame_Del_p.HAVPAAN167del|FGFR2_ENST00000490349.1_5'UTR|FGFR2_ENST00000356226.4_In_Frame_Del_p.HAVPAAN52del|FGFR2_ENST00000351936.6_In_Frame_Del_p.HAVPAAN167del|FGFR2_ENST00000369060.4_In_Frame_Del_p.HAVPAAN167del|FGFR2_ENST00000360144.3_In_Frame_Del_p.HAVPAAN78del|FGFR2_ENST00000369061.4_In_Frame_Del_p.HAVPAAN167del	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2	167	Heparin-binding.|Ig-like C2-type 2.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)	p.A172A(1)|p.A83A(1)		breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	ACTTGACAGTGTTGGCCGCAGGCACAGCATGGAGCCGCTTT	0.525		5	Mis		"gastric. NSCLC, endometrial"		"Crouzon, Pfeiffer, and Apert syndromes"		Saethre-Chotzen syndrome;Apert syndrome																												p.167_174del		Atlas-INDEL	.		Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	.	FGFR2	758	.	2	Substitution - coding silent(2)	large_intestine(2)	c.500_520del	GRCh37	CP025146	FGFR2	X		.																																			SO:0001651	inframe_deletion	2263	exon5	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	.	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3689	protein-coding gene	gene with protein product	"Crouzon syndrome", "Pfeiffer syndrome"	176943	"bacteria-expressed kinase", "keratinocyte growth factor receptor", "craniofacial dysostosis 1", "Jackson-Weiss syndrome"	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.499_519delCATGCTGTGCCTGCGGCCAAC	chr10.hg19:g.123310909_123310929delGTTGGCCGCAGGCACAGCATG	ENSP00000351276:p.His167_Asn173del	98.0	0.0		57.0	12.0	NM_000141	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	In_Frame_Del	DEL	ENST00000358487.5	hg19	CCDS31298.1																																																																																			.	.		0.525	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141		-	123310929	GTTGGCCGCAGGCACAGCATG	-	123310909	7	5	352	1	0	1	0	1	0	0	0	0	5874	1368	48	0	2258	0	FGFR2	10	123310909	In_Frame_Del	DEL	GTTGGCCGCAGGCACAGCATG	TCGA-WQ-A9G7-01A-11D-A36X-10	7647413	123310909	12223838	244	49660										
ACADSB	36	hgsc.bcm.edu	37	chr10	124812642	124812642	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gtaggctacaccaaagattaCcctgtggagaaatacttccg	9	10	0	2	rs142095937	byFrequency	TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr10:124812642C>T	ENST00000358776.4	+	10	1208	c.1194C>T	c.(1192-1194)taC>taT	p.Y398Y	ACADSB_ENST00000368869.4_Silent_p.Y296Y	NM_001609.3	NP_001600.1	P45954	ACDSB_HUMAN	acyl-CoA dehydrogenase, short/branched chain	398					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|fatty acid metabolic process (GO:0006631)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	17		all_neural(114;0.0765)|Colorectal(57;0.102)|all_lung(145;0.11)|Lung NSC(174;0.163)		Colorectal(40;0.0811)|COAD - Colon adenocarcinoma(40;0.0835)	L-Isoleucine(DB00167)|Valproic Acid(DB00313)	CCAAAGATTACCCTGTGGAGA	0.373																																					p.Y398Y		Atlas-SNP	.											.	ACADSB	45	.	0			c.C1194T						.						116	111	113					10																	124812642		2203	4300	6503	SO:0001819	synonymous_variant	36	exon10			AGATTACCCTGTG	U12778	CCDS7634.1	10q25-q26	2014-09-17	2010-04-30		ENSG00000196177	ENSG00000196177	1.3.99.-		91	protein-coding gene	gene with protein product		600301	"acyl-Coenzyme A dehydrogenase, short/branched chain"			7698750, 7759115	Standard	NM_001609		Approved	SBCAD, ACAD7	uc001lhb.3	P45954	OTTHUMG00000019200	ENST00000358776.4:c.1194C>T	chr10.hg19:g.124812642C>T		107.0	0.0		113.0	22.0	NM_001609	B4DQ51|Q5SQN6|Q96CX7	Silent	SNP	ENST00000358776.4	hg19	CCDS7634.1																																																																																			.	C|0.999;G|0.001		0.373	ACADSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050843.1	NM_001609		T	124812642	C	T	124812642	2	4	352	1	0	0	0	0	0	0	0	1	115	518	18	3		3	ACADSB	10	124812642	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	1501733	124812642	10722105	245	49661										
DHX32	55760	hgsc.bcm.edu	37	chr10	127526922	127526922	+	Nonsense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cctgcttatgtgtcagcattAagtagttacctgatccatca	7	10	2	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr10:127526922A>C	ENST00000284690.3	-	10	2406	c.1916T>G	c.(1915-1917)tTa>tGa	p.L639*	DHX32_ENST00000368721.1_Nonsense_Mutation_p.L263*|BCCIP_ENST00000429863.2_Intron|DHX32_ENST00000284688.6_Nonsense_Mutation_p.L558*|BCCIP_ENST00000299130.3_Intron|BCCIP_ENST00000368759.5_Intron	NM_018180.2	NP_060650.2	Q7L7V1	DHX32_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 32	639						mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(2)|stomach(1)	29		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				TGTCAGCATTAAGTAGTTACC	0.388																																					p.L639X		Atlas-SNP	.											.	DHX32	67	.	0			c.T1916G						.						130	120	124					10																	127526922		2203	4300	6503	SO:0001587	stop_gained	55760	exon10			AGCATTAAGTAGT		CCDS7652.1	10q26.11-q26.2	2008-01-07	2004-01-29	2004-01-30	ENSG00000089876	ENSG00000089876		"DEAH-boxes"	16717	protein-coding gene	gene with protein product		607960	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32"	DDX32			Standard	NM_018180		Approved	FLJ10889, FLJ10694, DHLP1	uc001ljf.1	Q7L7V1	OTTHUMG00000019238	ENST00000284690.3:c.1916T>G	chr10.hg19:g.127526922A>C	ENSP00000284690:p.Leu639*	65.0	0.0		47.0	21.0	NM_018180	A8MSV2|D3DRF9|Q49AG5|Q5T3L0|Q5T3L5|Q96NY1|Q9BUN0|Q9H769|Q9NSL5|Q9NV74|Q9NVJ7	Nonsense_Mutation	SNP	ENST00000284690.3	hg19	CCDS7652.1	.	.	.	.	.	.	.	.	.	.	A	43	9.834421	0.99275	.	.	ENSG00000089876	ENST00000368721;ENST00000284690;ENST00000284688	.	.	.	4.94	4.94	0.65067	.	0.157768	0.43919	D	0.000508	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-16.9198	13.8068	0.63238	1.0:0.0:0.0:0.0	.	.	.	.	X	263;639;558	.	ENSP00000284688:L558X	L	-	2	0	DHX32	127516912	1.000000	0.71417	0.919000	0.36401	0.978000	0.69477	9.066000	0.93949	1.851000	0.53745	0.459000	0.35465	TTA	.	.		0.388	DHX32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050945.2	NM_018180		C	127526922	A	C	127526922	4	2	352	1	0	0	0	0	0	1	0	0	4507	372	13	5	323	5	DHX32	10	127526922	Nonsense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	2714280	127526922	8007825	246	49662										
DPYSL4	10570	hgsc.bcm.edu	37	chr10	134012411	134012411	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gccaagcaggcaaactgcccGctgtacgtcaccaaggtgat	11	13	1	1	rs377151543		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr10:134012411G>A	ENST00000338492.4	+	8	911	c.747G>A	c.(745-747)ccG>ccA	p.P249P	DPYSL4_ENST00000368627.1_Silent_p.P149P|DPYSL4_ENST00000368629.1_Silent_p.P149P	NM_006426.2	NP_006417.2	O14531	DPYL4_HUMAN	dihydropyrimidinase-like 4	249					axon guidance (GO:0007411)|nervous system development (GO:0007399)|pyrimidine nucleobase catabolic process (GO:0006208)	cytosol (GO:0005829)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		all_cancers(35;4.33e-08)|all_epithelial(44;6.75e-06)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)|Colorectal(31;0.19)		OV - Ovarian serous cystadenocarcinoma(35;7.21e-05)|Epithelial(32;8.01e-05)|all cancers(32;9.29e-05)|BRCA - Breast invasive adenocarcinoma(275;0.206)		CAAACTGCCCGCTGTACGTCA	0.677																																					p.P249P		Atlas-SNP	.											.	DPYSL4	91	.	0			c.G747A						.	G		0,4406		0,0,2203	86	71	76		747	-6.8	0.4	10		76	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	DPYSL4	NM_006426.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		249/573	134012411	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	10570	exon8			CTGCCCGCTGTAC	AB006713	CCDS7665.1	10q25.2-q26	2008-05-14			ENSG00000151640	ENSG00000151640			3016	protein-coding gene	gene with protein product		608407				8973361, 9652388	Standard	NM_006426		Approved	ULIP4, DRP-4	uc009ybb.3	O14531	OTTHUMG00000019283	ENST00000338492.4:c.747G>A	chr10.hg19:g.134012411G>A		158.0	0.0		134.0	28.0	NM_006426	B2RMQ1|D3DRG5|O00240|Q5T0Q7	Silent	SNP	ENST00000338492.4	hg19	CCDS7665.1																																																																																			.	.		0.677	DPYSL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051050.2			A	134012411	G	A	134012411	2	1	352	1	0	0	0	0	0	0	0	1	4751	1074	38	1		1	DPYSL4	10	134012411	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	6485489	134012411	1522336	247	49663										
C10orf125	282969	hgsc.bcm.edu	37	chr10	135168879	135168879	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tggtcttcaccaggcctacaGcagggggttgagggcaagca	15	10	2	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr10:135168879G>T	ENST00000368552.3	-	6	477	c.460C>A	c.(460-462)Ctg>Atg	p.L154M	FUOM_ENST00000465384.1_5'UTR|FUOM_ENST00000368551.1_Missense_Mutation_p.L109M|FUOM_ENST00000447176.1_Missense_Mutation_p.L110M|FUOM_ENST00000278025.4_3'UTR	NM_001098483.1	NP_001091953.1	A2VDF0	FUCM_HUMAN	fucose mutarotase	154					female mating behavior (GO:0060180)|fucose metabolic process (GO:0006004)|fucosylation (GO:0036065)|negative regulation of neuron differentiation (GO:0045665)		fucose binding (GO:0042806)|racemase and epimerase activity, acting on carbohydrates and derivatives (GO:0016857)										CAGGCCTACAGCAGGGGGTTG	0.647																																					p.L154M		Atlas-SNP	.											C10orf125_ENST00000368552,NS,carcinoma,0,1	.	.	.	0			c.C460A						.						20	24	23					10																	135168879		2194	4291	6485	SO:0001583	missense	282969	exon6			CCTACAGCAGGGG	AK129527	CCDS7680.1	10q26.3	2012-07-10	2012-07-10	2012-07-10	ENSG00000148803	ENSG00000148803	5.1.3.n2		24733	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 125"	C10orf125		17602138	Standard	NM_001098483		Approved	FLJ26016, FucU, FucM	uc001lmt.2	A2VDF0	OTTHUMG00000019315	ENST00000368552.3:c.460C>A	chr10.hg19:g.135168879G>T	ENSP00000357540:p.Leu154Met	66.0	0.0		44.0	17.0	NM_001098483	A1L300|Q5VWY2|Q5VWY3|Q6ZPD2	Missense_Mutation	SNP	ENST00000368552.3	hg19	CCDS44499.1	.	.	.	.	.	.	.	.	.	.	G	10.59	1.393844	0.25205	.	.	ENSG00000148803	ENST00000447176;ENST00000368551;ENST00000368552	.	.	.	3.1	-2.24	0.06909	.	.	.	.	.	T	0.16257	0.0391	N	0.08118	0	0.09310	N	1	B	0.27853	0.191	B	0.30029	0.11	T	0.22208	-1.0223	8	0.52906	T	0.07	.	3.7475	0.08554	0.3047:0.0:0.485:0.2103	.	154	A2VDF0	FUCM_HUMAN	M	110;109;154	.	ENSP00000357539:L109M	L	-	1	2	C10orf125	135018869	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.150000	0.16263	-0.471000	0.06891	-0.373000	0.07131	CTG	.	.		0.647	FUOM-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_198472		T	135168879	G	T	135168879	3	4	352	1	0	0	0	0	1	0	0	0	1593	962	34	3	8	3	C10orf125	10	135168879	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	1156468	135168879	365868	248	49664										
LRRC56	115399	hgsc.bcm.edu	37	chr11	551775	551775	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gggggccccctgcctgaaggCctgctttctgaggacctggc	15	14	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:551775C>A	ENST00000270115.7	+	10	1421	c.921C>A	c.(919-921)ggC>ggA	p.G307G		NM_198075.3	NP_932341.1	Q8IYG6	LRC56_HUMAN	leucine rich repeat containing 56	307										kidney(1)|lung(4)|skin(1)	6		all_cancers(49;2.16e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TGCCTGAAGGCCTGCTTTCTG	0.662																																					p.G307G		Atlas-SNP	.											.	LRRC56	23	.	0			c.C921A						.						34	41	39					11																	551775		2200	4299	6499	SO:0001819	synonymous_variant	115399	exon10			TGAAGGCCTGCTT		CCDS7700.1	11p15.5	2005-10-18			ENSG00000161328	ENSG00000161328			25430	protein-coding gene	gene with protein product						12477932	Standard	NM_198075		Approved	FLJ00101, DKFZp761L1518	uc010qvz.2	Q8IYG6	OTTHUMG00000132003	ENST00000270115.7:c.921C>A	chr11.hg19:g.551775C>A		76.0	0.0		97.0	37.0	NM_198075	Q8N3Q4	Silent	SNP	ENST00000270115.7	hg19	CCDS7700.1																																																																																			.	.		0.662	LRRC56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254969.1	NM_198075		A	551775	C	A	551775	2	1	352	1	0	0	0	0	0	0	0	1	9021	726	26	3		3	LRRC56	11	551775	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10		551775	134454741	249	49665										
OR51I2	390064	hgsc.bcm.edu	37	chr11	5475291	5475291	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	atgaggcttgcctgtgctgaTatcagtatcaacagcatcta	9	9	3	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:5475291T>C	ENST00000341449.2	+	1	654	c.573T>C	c.(571-573)gaT>gaC	p.D191D	HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_Intron	NM_001004754.2	NP_001004754.1	Q9H344	O51I2_HUMAN	olfactory receptor, family 51, subfamily I, member 2	191					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;1.09e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CCTGTGCTGATATCAGTATCA	0.453																																					p.D191D		Atlas-SNP	.											.	OR51I2	76	.	0			c.T573C						.						305	261	276					11																	5475291		2201	4297	6498	SO:0001819	synonymous_variant	390064	exon1			TGCTGATATCAGT	BK004381	CCDS31383.1	11p15.4	2012-08-09			ENSG00000187918	ENSG00000187918		"GPCR / Class A : Olfactory receptors"	15201	protein-coding gene	gene with protein product							Standard	NM_001004754		Approved		uc010qzf.2	Q9H344	OTTHUMG00000066902	ENST00000341449.2:c.573T>C	chr11.hg19:g.5475291T>C		64.0	0.0		71.0	10.0	NM_001004754	Q6IF81	Silent	SNP	ENST00000341449.2	hg19	CCDS31383.1																																																																																			.	.		0.453	OR51I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143385.1	NM_001004754		C	5475291	T	C	5475291	2	2	352	1	0	0	0	0	0	0	0	1	11110	1403	49	2		2	OR51I2	11	5475291	Silent	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	4923516	5475291	129531225	250	49666										
OR52E8	390079	hgsc.bcm.edu	37	chr11	5878052	5878052	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tcctgactccatagattacaGgattgagggctggtgggaca	13	8	0	3			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:5878052G>T	ENST00000537935.1	-	1	912	c.881C>A	c.(880-882)cCt>cAt	p.P294H	TRIM5_ENST00000380027.1_Intron	NM_001005168.1	NP_001005168.1	Q6IFG1	O52E8_HUMAN	olfactory receptor, family 52, subfamily E, member 8	294						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	20		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.114)		Epithelial(150;2.37e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATAGATTACAGGATTGAGGGC	0.418																																					p.P294H		Atlas-SNP	.											.	OR52E8	54	.	0			c.C881A						.						100	118	112					11																	5878052		2143	4296	6439	SO:0001583	missense	390079	exon1			ATTACAGGATTGA	BK004301	CCDS31400.1	11p15.4	2012-08-09	2003-12-15		ENSG00000183269	ENSG00000183269		"GPCR / Class A : Olfactory receptors"	15217	protein-coding gene	gene with protein product			"olfactory receptor, family 52, subfamily E, member 8 pseudogene"				Standard	NM_001005168		Approved		uc010qzr.2	Q6IFG1	OTTHUMG00000168803	ENST00000537935.1:c.881C>A	chr11.hg19:g.5878052G>T	ENSP00000444054:p.Pro294His	134.0	0.0		179.0	23.0	NM_001005168	B9EH38	Missense_Mutation	SNP	ENST00000537935.1	hg19	CCDS31400.1	.	.	.	.	.	.	.	.	.	.	G	14.64	2.595211	0.46318	.	.	ENSG00000183269	ENST00000537935	T	0.64260	-0.09	4.12	4.12	0.48240	GPCR, rhodopsin-like superfamily (1);	0.121233	0.37178	N	0.002206	T	0.80654	0.4664	H	0.97390	3.995	0.43971	D	0.996654	P	0.52842	0.956	P	0.49829	0.623	D	0.88570	0.3129	10	0.87932	D	0	.	15.4396	0.75173	0.0:0.0:1.0:0.0	.	294	Q6IFG1	O52E8_HUMAN	H	294	ENSP00000444054:P294H	ENSP00000444054:P294H	P	-	2	0	OR52E8	5834628	1.000000	0.71417	0.991000	0.47740	0.312000	0.27988	9.094000	0.94168	2.302000	0.77476	0.549000	0.68633	CCT	.	.		0.418	OR52E8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401145.1	NM_001005168		T	5878052	G	T	5878052	3	4	352	1	0	0	0	0	1	0	0	0	11127	1000	35	3	74	3	OR52E8	11	5878052	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	402761	5878052	129128464	251	49667										
OR52L1	338751	hgsc.bcm.edu	37	chr11	6007754	6007754	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ctacatagcaatccagagccAtggccacaagtacccctgac	7	15	0	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:6007754A>G	ENST00000332249.4	-	1	461	c.407T>C	c.(406-408)aTg>aCg	p.M136T		NM_001005173.2	NP_001005173.2	Q8NGH7	O52L1_HUMAN	olfactory receptor, family 52, subfamily L, member 1	136						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(11)|pancreas(1)|skin(3)|soft_tissue(1)	30		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.98e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATCCAGAGCCATGGCCACAAG	0.537																																					p.M136T	Melanoma(121;653 1666 10547 22796 51255)	Atlas-SNP	.											.	OR52L1	100	.	0			c.T407C						.						43	44	44					11																	6007754		2086	4226	6312	SO:0001583	missense	338751	exon1			AGAGCCATGGCCA	AB065819	CCDS44529.1	11p15.4	2012-08-09			ENSG00000183313	ENSG00000183313		"GPCR / Class A : Olfactory receptors"	14785	protein-coding gene	gene with protein product							Standard	NM_001005173		Approved		uc001mcd.2	Q8NGH7	OTTHUMG00000165374	ENST00000332249.4:c.407T>C	chr11.hg19:g.6007754A>G	ENSP00000330338:p.Met136Thr	93.0	0.0		132.0	13.0	NM_001005173	B2RPA6|Q6IFK9	Missense_Mutation	SNP	ENST00000332249.4	hg19	CCDS44529.1	.	.	.	.	.	.	.	.	.	.	A	14.72	2.620907	0.46736	.	.	ENSG00000183313	ENST00000332249	T	0.00462	7.26	2.97	2.97	0.34412	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49305	D	0.000141	T	0.02193	0.0068	H	0.98089	4.145	0.44207	D	0.997032	D	0.55800	0.973	P	0.61201	0.885	T	0.04041	-1.0982	10	0.87932	D	0	.	10.2936	0.43610	1.0:0.0:0.0:0.0	.	136	Q8NGH7	O52L1_HUMAN	T	136	ENSP00000330338:M136T	ENSP00000330338:M136T	M	-	2	0	OR52L1	5964330	1.000000	0.71417	1.000000	0.80357	0.808000	0.45660	8.550000	0.90675	1.357000	0.45904	0.260000	0.18958	ATG	.	.		0.537	OR52L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383754.1	NM_001005173		G	6007754	A	G	6007754	3	3	352	1	0	0	0	0	1	0	0	0	11134	217	8	2	586	2	OR52L1	11	6007754	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	129702	6007754	128998762	252	49668										
TEAD1	7003	hgsc.bcm.edu	37	chr11	12883850	12883850	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tcaggacaggcaagacgaggAccagaaaacaggtaaaataa	11	7	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:12883850A>G	ENST00000527575.1	+	3	369	c.256A>G	c.(256-258)Acc>Gcc	p.T86A	TEAD1_ENST00000527636.1_Missense_Mutation_p.T86A|TEAD1_ENST00000334310.6_Missense_Mutation_p.T71A|TEAD1_ENST00000361985.2_Missense_Mutation_p.T86A|TEAD1_ENST00000361905.4_Missense_Mutation_p.T71A			P28347	TEAD1_HUMAN	TEA domain family member 1 (SV40 transcriptional enhancer factor)	86					gene expression (GO:0010467)|hippo signaling (GO:0035329)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)	17				Epithelial(150;0.00223)|BRCA - Breast invasive adenocarcinoma(625;0.236)		CAAGACGAGGACCAGAAAACA	0.448																																					p.T86A		Atlas-SNP	.											.	TEAD1	40	.	0			c.A256G						.						120	106	111					11																	12883850		2200	4294	6494	SO:0001583	missense	7003	exon4			ACGAGGACCAGAA	X84839	CCDS7810.1, CCDS7810.2	11p15.4	2008-11-12				ENSG00000187079			11714	protein-coding gene	gene with protein product		189967	"atrophia areata, peripapillary chorioretinal degeneration"	TCF13, AA		1851669, 9889009, 15016762	Standard	NM_021961		Approved	TEF-1	uc021qdx.1	P28347		ENST00000527575.1:c.256A>G	chr11.hg19:g.12883850A>G	ENSP00000435977:p.Thr86Ala	119.0	0.0		139.0	35.0	NM_021961	A4FUP2|E7EV65	Missense_Mutation	SNP	ENST00000527575.1	hg19		.	.	.	.	.	.	.	.	.	.	A	29.7	5.024988	0.93518	.	.	ENSG00000187079	ENST00000361905;ENST00000527636;ENST00000527575;ENST00000334310;ENST00000361985	T;T;T;T;T	0.52754	0.65;0.65;0.65;0.65;0.65	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.69424	0.3109	M	0.93594	3.435	0.80722	D	1	P	0.36837	0.571	P	0.46208	0.507	T	0.76465	-0.2949	10	0.87932	D	0	.	15.7943	0.78398	1.0:0.0:0.0:0.0	.	86	P28347	TEAD1_HUMAN	A	71;86;86;71;86	ENSP00000355332:T71A;ENSP00000435233:T86A;ENSP00000435977:T86A;ENSP00000334754:T71A;ENSP00000354588:T86A	ENSP00000334754:T71A	T	+	1	0	TEAD1	12840426	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.208000	0.71279	0.533000	0.62120	ACC	.	.		0.448	TEAD1-002	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000386888.1	NM_021961		G	12883850	A	G	12883850	3	3	352	1	0	0	0	0	1	0	0	0	15753	275	10	2	262	2	TEAD1	11	12883850	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	6876096	12883850	122122666	253	49669										
MRGPRX4	117196	hgsc.bcm.edu	37	chr11	18195145	18195145	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	acaggcctgagtatgctgagCgccatcagcaccgagcgctg	13	13	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:18195145C>T	ENST00000314254.3	+	1	762	c.342C>T	c.(340-342)agC>agT	p.S114S	RP11-113D6.6_ENST00000527671.1_Intron	NM_054032.3	NP_473373.2	Q96LA9	MRGX4_HUMAN	MAS-related GPR, member X4	114						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32						GTATGCTGAGCGCCATCAGCA	0.567																																					p.S114S		Atlas-SNP	.											MRGPRX4,NS,carcinoma,0,1	MRGPRX4	68	.	0			c.C342T						.						129	114	119					11																	18195145		2199	4293	6492	SO:0001819	synonymous_variant	117196	exon1			GCTGAGCGCCATC	AY042216	CCDS7831.1	11p15.1	2013-10-10			ENSG00000179817	ENSG00000179817		"GPCR / Class A : Orphans"	17617	protein-coding gene	gene with protein product		607230				11551509	Standard	NM_054032		Approved	MRGX4	uc001mnv.1	Q96LA9	OTTHUMG00000166442	ENST00000314254.3:c.342C>T	chr11.hg19:g.18195145C>T		69.0	0.0		96.0	12.0	NM_054032	Q3KNU3|Q3KNU4|Q502W0|Q8TDD6|Q8TDD7	Silent	SNP	ENST00000314254.3	hg19	CCDS7831.1																																																																																			.	.		0.567	MRGPRX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389788.1	NM_054032		T	18195145	C	T	18195145	2	4	352	1	0	0	0	0	0	0	0	1	9778	767	27	1		1	MRGPRX4	11	18195145	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	5311295	18195145	116811371	254	49670										
KCNA4	3739	hgsc.bcm.edu	37	chr11	30034166	30034166	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gcccgggcctgggcagcataAccataaggcatgtgactgtt	13	11	0	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:30034166A>G	ENST00000328224.6	-	2	1293	c.60T>C	c.(58-60)ggT>ggC	p.G20G	KCNA4_ENST00000526518.1_5'Flank	NM_002233.3	NP_002224.1	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 4	20					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	potassium ion binding (GO:0030955)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(39)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	78					Dalfampridine(DB06637)	GGGCAGCATAACCATAAGGCA	0.597																																					p.G20G		Atlas-SNP	.											.	KCNA4	158	.	0			c.T60C						.						72	72	72					11																	30034166		1946	4136	6082	SO:0001819	synonymous_variant	3739	exon2			AGCATAACCATAA	M55514	CCDS41629.1	11p14	2012-07-05	2002-07-10			ENSG00000182255		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6222	protein-coding gene	gene with protein product		176266	"potassium voltage-gated channel, shaker-related subfamily, member 4-like"	KCNA4L		2263489, 16382104	Standard	NM_002233		Approved	Kv1.4, HK1, HPCN2	uc001msk.3	P22459		ENST00000328224.6:c.60T>C	chr11.hg19:g.30034166A>G		39.0	0.0		41.0	6.0	NM_002233		Silent	SNP	ENST00000328224.6	hg19	CCDS41629.1																																																																																			.	.		0.597	KCNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388074.2	NM_002233		G	30034166	A	G	30034166	2	3	352	1	0	0	0	0	0	0	0	1	8014	30	2	2		2	KCNA4	11	30034166	Silent	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	11839021	30034166	104972350	255	49671										
HIPK3	10114	hgsc.bcm.edu	37	chr11	33309022	33309022	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gccagtcatgtatcaaagacTgtttgttcaacatatctaca	6	9	4	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:33309022T>C	ENST00000303296.4	+	2	1367	c.1062T>C	c.(1060-1062)acT>acC	p.T354T	HIPK3_ENST00000456517.1_Silent_p.T354T|HIPK3_ENST00000525975.1_Silent_p.T354T|HIPK3_ENST00000379016.3_Silent_p.T354T	NM_005734.3	NP_005725.3	Q9H422	HIPK3_HUMAN	homeodomain interacting protein kinase 3	354	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|mRNA transcription (GO:0009299)|negative regulation of apoptotic process (GO:0043066)|negative regulation of JUN kinase activity (GO:0043508)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			endometrium(3)|kidney(3)|large_intestine(9)|liver(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	39						TATCAAAGACTGTTTGTTCAA	0.378																																					p.T354T		Atlas-SNP	.											.,1	HIPK3	92	.	0			c.T1062C						.						102	105	104					11																	33309022		2202	4298	6500	SO:0001819	synonymous_variant	10114	exon2			AAAGACTGTTTGT	AF004849	CCDS7884.1, CCDS41634.1	11p13	2008-07-18	2001-11-29		ENSG00000110422	ENSG00000110422			4915	protein-coding gene	gene with protein product		604424	"homeodomain-interacting protein kinase 3"			9373137, 9748262	Standard	NM_005734		Approved	PKY, DYRK6, YAK1, FIST3	uc031pzm.1	Q9H422	OTTHUMG00000132269	ENST00000303296.4:c.1062T>C	chr11.hg19:g.33309022T>C		149.0	0.0		162.0	20.0	NM_001048200	O14632|Q2PBG4|Q2PBG5|Q92632|Q9HAS2	Silent	SNP	ENST00000303296.4	hg19	CCDS7884.1																																																																																			.	.		0.378	HIPK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255358.1	NM_005734		C	33309022	T	C	33309022	2	2	352	1	0	0	0	0	0	0	0	1	7127	1567	55	2		2	HIPK3	11	33309022	Silent	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	3274856	33309022	101697494	256	49672										
C11orf41	25758	hgsc.bcm.edu	37	chr11	33566862	33566862	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tgcatcggctgcagtggtcaCgactggcaaaatggcatcca	12	11	1	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:33566862C>T	ENST00000321505.4	+	2	2612	c.2432C>T	c.(2431-2433)aCg>aTg	p.T811M	KIAA1549L_ENST00000389726.3_Missense_Mutation_p.T817M|KIAA1549L_ENST00000265654.5_Missense_Mutation_p.T817M			Q6ZVL6	K154L_HUMAN	KIAA1549-like	811						integral component of membrane (GO:0016021)											GCAGTGGTCACGACTGGCAAA	0.532																																					p.T811M		Atlas-SNP	.											.	.	.	.	0			c.C2432T						.						34	40	38					11																	33566862		2135	4255	6390	SO:0001583	missense	25758	exon2			TGGTCACGACTGG	U10991	CCDS44565.1, CCDS44565.2	11p13	2012-08-09	2012-08-09	2012-08-09	ENSG00000110427	ENSG00000110427			24836	protein-coding gene	gene with protein product		612297	"chromosome 11 open reading frame 69", "chromosome 11 open reading frame 41"	C11orf69, C11orf41			Standard	NM_012194		Approved	G2, MGC34830	uc021qfs.1	Q6ZVL6	OTTHUMG00000150410	ENST00000321505.4:c.2432C>T	chr11.hg19:g.33566862C>T	ENSP00000315295:p.Thr811Met	63.0	0.0		73.0	18.0	NM_012194	B0QYU0	Missense_Mutation	SNP	ENST00000321505.4	hg19	CCDS44565.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.41|11.41	1.630600|1.630600	0.28978|0.28978	.|.	.|.	ENSG00000110427|ENSG00000110427	ENST00000526400|ENST00000321505;ENST00000389726;ENST00000265654;ENST00000536568	.|.	.|.	.|.	5.81|5.81	4.9|4.9	0.64082|0.64082	.|.	.|0.256102	.|0.38058	.|N	.|0.001828	.|T	.|0.56934	.|0.2019	L|L	0.60455|0.60455	1.87|1.87	0.09310|0.09310	N|N	0.999999|0.999999	.|D;D	.|0.89917	.|0.998;1.0	.|P;D	.|0.69824	.|0.732;0.966	.|T	.|0.51068	.|-0.8752	.|9	.|0.56958	.|D	.|0.05	-4.9075|-4.9075	10.223|10.223	0.43209|0.43209	0.0:0.849:0.0:0.151|0.0:0.849:0.0:0.151	.|.	.|817;817	.|E9PAT2;Q6ZVL6-2	.|.;.	X|M	209|811;817;817;650	.|.	.|ENSP00000265654:T817M	R|T	+|+	1|2	2|0	C11orf41|C11orf41	33523438|33523438	0.901000|0.901000	0.30685|0.30685	0.770000|0.770000	0.31555|0.31555	0.006000|0.006000	0.05464|0.05464	1.813000|1.813000	0.38962|0.38962	1.470000|1.470000	0.48102|0.48102	0.561000|0.561000	0.74099|0.74099	CGA|ACG	.	.		0.532	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194		T	33566862	C	T	33566862	3	4	352	1	0	0	0	0	1	0	0	0	1642	536	19	1	2456	1	C11orf41	11	33566862	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	257840	33566862	101439654	257	49673										
PHF21A	51317	hgsc.bcm.edu	37	chr11	45955607	45955607	+	Frame_Shift_Del	DEL	G	G	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tggaggtggcggcattggcaGggggggtgcagtccgggcca							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:45955607delG	ENST00000418153.2	-	18	2154	c.1955delC	c.(1954-1956)cctfs	p.P652fs	PHF21A_ENST00000257821.4_Frame_Shift_Del_p.P653fs|PHF21A_ENST00000323180.6_Frame_Shift_Del_p.P606fs			Q96BD5	PF21A_HUMAN	PHD finger protein 21A	652	Required for transcriptional repression.				blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|suckling behavior (GO:0001967)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(10)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	29						GGCATTGGCAGGGGGGGTGCA	0.617																																					p.P652fs		Atlas-INDEL	.											.	PHF21A	107	.	0			c.1956delT						.						31	38	36					11																	45955607		2202	4299	6501	SO:0001589	frameshift_variant	51317	exon18			.	AL359593	CCDS31474.1, CCDS44578.1	11p11.2	2013-01-28			ENSG00000135365	ENSG00000135365		"Zinc fingers, PHD-type"	24156	protein-coding gene	gene with protein product		608325				11214970, 12032298	Standard	NM_001101802		Approved	BHC80, KIAA1696, BM-006	uc001ncc.4	Q96BD5	OTTHUMG00000167038	ENST00000418153.2:c.1955delC	chr11.hg19:g.45955607delG	ENSP00000398824:p.Pro652fs	72.0	0.0		83.0	25.0	NM_001101802	D3DQP5|Q6AWA2|Q9C0G7|Q9H8V9|Q9HAK6|Q9NZE9	Frame_Shift_Del	DEL	ENST00000418153.2	hg19	CCDS44578.1																																																																																			.	.		0.617	PHF21A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392583.1	NM_016621		-	45955607	G	-	45955607	7	5	352	1	0	1	0	1	0	0	0	0	11842	1000	35	0	91	0	PHF21A	11	45955607	Frame_Shift_Del	DEL	G	TCGA-WQ-A9G7-01A-11D-A36X-10	12388745	45955607	89050909	258	49674										
AMBRA1	55626	hgsc.bcm.edu	37	chr11	46456582	46456582	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gttctgcaccagcacattcaCggaagctgcatcagacaaag	9	12	3	1	rs377069728		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:46456582C>T	ENST00000458649.2	-	13	3056	c.2638G>A	c.(2638-2640)Gtg>Atg	p.V880M	AMBRA1_ENST00000314845.3_Missense_Mutation_p.V790M|AMBRA1_ENST00000528950.1_Missense_Mutation_p.V851M|AMBRA1_ENST00000298834.3_Missense_Mutation_p.V820M|AMBRA1_ENST00000533727.1_Missense_Mutation_p.V761M|AMBRA1_ENST00000426438.1_Missense_Mutation_p.V851M|AMBRA1_ENST00000534300.1_Missense_Mutation_p.V820M			Q9C0C7	AMRA1_HUMAN	autophagy/beclin-1 regulator 1	880					autophagy (GO:0006914)|cell differentiation (GO:0030154)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neural tube development (GO:0021915)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|phagocytic vesicle (GO:0045335)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	39				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)		AGCACATTCACGGAAGCTGCA	0.473																																					p.V883M		Atlas-SNP	.											.	AMBRA1	201	.	0			c.G2647A						.	C	MET/VAL	0,4402		0,0,2201	29	27	28		2368	4.1	1	11		28	1,8597	1.2+/-3.3	0,1,4298	no	missense	AMBRA1	NM_017749.2	21	0,1,6499	TT,TC,CC		0.0116,0.0,0.0077	benign	790/1209	46456582	1,12999	2201	4299	6500	SO:0001583	missense	55626	exon15			CATTCACGGAAGC	AB051523	CCDS31475.1, CCDS58132.1, CCDS73281.1	11p11.2	2013-01-09			ENSG00000110497	ENSG00000110497		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	25990	protein-coding gene	gene with protein product	"WD repeat domain 94", "DDB1 and CUL4 associated factor 3"	611359				17622796, 17603510, 17589504	Standard	NM_001267782		Approved	FLJ20294, KIAA1736, WDR94, DCAF3	uc001ncv.3	Q9C0C7	OTTHUMG00000166500	ENST00000458649.2:c.2638G>A	chr11.hg19:g.46456582C>T	ENSP00000415327:p.Val880Met	79.0	0.0		86.0	10.0	NM_001267782	A6XN33|D3DQP8|G3V193|Q86XD6|Q9H8Z0|Q9NXE7	Missense_Mutation	SNP	ENST00000458649.2	hg19		.	.	.	.	.	.	.	.	.	.	C	19.57	3.851865	0.71719	0.0	1.16E-4	ENSG00000110497	ENST00000314845;ENST00000533727;ENST00000534300;ENST00000426438;ENST00000298834;ENST00000458649;ENST00000528950	T;T;T;T;T;T;T	0.71817	-0.49;-0.6;-0.19;-0.32;-0.19;-0.34;-0.32	5.95	4.1	0.47936	WD40/YVTN repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.53254	0.1785	N	0.22421	0.69	0.43156	D	0.994933	B;B;B;B;B;B	0.32968	0.174;0.266;0.266;0.392;0.125;0.392	B;B;B;B;B;B	0.26517	0.032;0.07;0.07;0.07;0.027;0.07	T	0.54827	-0.8235	10	0.62326	D	0.03	.	10.3113	0.43710	0.0:0.7991:0.0:0.2009	.	880;851;820;761;883;790	Q9C0C7;Q9C0C7-3;Q9C0C7-2;G3V193;Q9C0C7-5;Q9C0C7-4	AMRA1_HUMAN;.;.;.;.;.	M	790;761;820;851;820;880;851	ENSP00000318313:V790M;ENSP00000433372:V761M;ENSP00000431926:V820M;ENSP00000410899:V851M;ENSP00000298834:V820M;ENSP00000415327:V880M;ENSP00000433945:V851M	ENSP00000298834:V820M	V	-	1	0	AMBRA1	46413158	0.985000	0.35326	1.000000	0.80357	0.994000	0.84299	2.622000	0.46427	0.868000	0.35678	-0.137000	0.14449	GTG	.	.		0.473	AMBRA1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000390103.1	NM_017749		T	46456582	C	T	46456582	3	4	352	1	0	0	0	0	1	0	0	0	565	536	19	1	1282	1	AMBRA1	11	46456582	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	500975	46456582	88549934	259	49675										
OR4C13	283092	hgsc.bcm.edu	37	chr11	49974682	49974682	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gcaaggcacgaagccctctcTacctgtgtctcccacatcac	7	17	3	0	rs145221317		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:49974682T>C	ENST00000555099.1	+	1	740	c.708T>C	c.(706-708)tcT>tcC	p.S236S		NM_001001955.2	NP_001001955.2	Q8NGP0	OR4CD_HUMAN	olfactory receptor, family 4, subfamily C, member 13	236						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(24)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	43						AAGCCCTCTCTACCTGTGTCT	0.463																																					p.S236S		Atlas-SNP	.											.	OR4C13	96	.	0			c.T708C						.						181	155	164					11																	49974682		2201	4296	6497	SO:0001819	synonymous_variant	283092	exon1			CCTCTCTACCTGT	AB065750	CCDS31495.1	11p11.12	2012-10-03			ENSG00000258817	ENSG00000258817		"GPCR / Class A : Olfactory receptors"	15169	protein-coding gene	gene with protein product							Standard	NM_001001955		Approved		uc010rhz.2	Q8NGP0	OTTHUMG00000166686	ENST00000555099.1:c.708T>C	chr11.hg19:g.49974682T>C		84.0	0.0		94.0	11.0	NM_001001955	A6NJJ3|B9EH30|Q6IF48|Q96R68	Silent	SNP	ENST00000555099.1	hg19	CCDS31495.1																																																																																			.	T|1.000;C|0.000		0.463	OR4C13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391103.1	NM_001001955		C	49974682	T	C	49974682	2	2	352	1	0	0	0	0	0	0	0	1	11056	1509	53	2		2	OR4C13	11	49974682	Silent	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	3518100	49974682	85031834	260	49676										
OR8J3	81168	hgsc.bcm.edu	37	chr11	55905120	55905120	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aggaagaccaggaagaggggAatctggagctctggacagct	16	7	2	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:55905120A>G	ENST00000301529.1	-	1	74	c.75T>C	c.(73-75)atT>atC	p.I25I		NM_001004064.1	NP_001004064.1	Q8NGG0	OR8J3_HUMAN	olfactory receptor, family 8, subfamily J, member 3	25						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(1)|lung(38)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	59	Esophageal squamous(21;0.00693)					GGAAGAGGGGAATCTGGAGCT	0.493																																					p.I25I		Atlas-SNP	.											.	OR8J3	112	.	0			c.T75C						.						118	118	118					11																	55905120		2201	4296	6497	SO:0001819	synonymous_variant	81168	exon1			GAGGGGAATCTGG		CCDS31520.1	11q12.2	2012-08-09			ENSG00000167822	ENSG00000167822		"GPCR / Class A : Olfactory receptors"	15312	protein-coding gene	gene with protein product							Standard	NM_001004064		Approved		uc010riz.2	Q8NGG0	OTTHUMG00000166834	ENST00000301529.1:c.75T>C	chr11.hg19:g.55905120A>G		127.0	0.0		133.0	22.0	NM_001004064	Q6IFB6|Q96RC2	Silent	SNP	ENST00000301529.1	hg19	CCDS31520.1																																																																																			.	.		0.493	OR8J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391542.1	NM_001004064		G	55905120	A	G	55905120	2	3	352	1	0	0	0	0	0	0	0	1	11251	242	9	2		2	OR8J3	11	55905120	Silent	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	5930438	55905120	79101396	261	49677										
OR5AR1	219493	hgsc.bcm.edu	37	chr11	56431409	56431409	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cattgcccccaggatgctggCtgacttcctaacaaatcaca	7	14	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:56431409C>T	ENST00000302969.2	+	1	272	c.248C>T	c.(247-249)gCt>gTt	p.A83V		NM_001004730.1	NP_001004730.1	Q8NGP9	O5AR1_HUMAN	olfactory receptor, family 5, subfamily AR, member 1 (gene/pseudogene)	83						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(12)|prostate(1)|skin(3)|stomach(1)	26						AGGATGCTGGCTGACTTCCTA	0.483																																					p.A83V		Atlas-SNP	.											.	OR5AR1	68	.	0			c.C248T						.						211	213	212					11																	56431409		2201	4296	6497	SO:0001583	missense	219493	exon1			TGCTGGCTGACTT	AB065740	CCDS31535.1	11q11	2013-10-10	2013-10-10		ENSG00000172459	ENSG00000172459		"GPCR / Class A : Olfactory receptors"	15260	protein-coding gene	gene with protein product			"olfactory receptor, family 5, subfamily AR, member 1"				Standard	NM_001004730		Approved		uc010rjm.2	Q8NGP9	OTTHUMG00000154213	ENST00000302969.2:c.248C>T	chr11.hg19:g.56431409C>T	ENSP00000302639:p.Ala83Val	109.0	0.0		115.0	30.0	NM_001004730	Q6IF61	Missense_Mutation	SNP	ENST00000302969.2	hg19	CCDS31535.1	.	.	.	.	.	.	.	.	.	.	C	1.182	-0.637902	0.03557	.	.	ENSG00000172459	ENST00000302969	T	0.02015	4.5	5.04	5.04	0.67666	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47455	D	0.000227	T	0.01387	0.0045	N	0.10916	0.065	0.09310	N	0.999992	P	0.52842	0.956	B	0.41764	0.366	T	0.49579	-0.8925	10	0.05436	T	0.98	.	12.6251	0.56626	0.1654:0.8346:0.0:0.0	.	83	Q8NGP9	O5AR1_HUMAN	V	83	ENSP00000302639:A83V	ENSP00000302639:A83V	A	+	2	0	OR5AR1	56187985	0.000000	0.05858	1.000000	0.80357	0.988000	0.76386	-0.699000	0.05087	2.632000	0.89209	0.573000	0.79308	GCT	.	.		0.483	OR5AR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334434.1	NM_001004730		T	56431409	C	T	56431409	3	4	352	1	0	0	0	0	1	0	0	0	11154	797	28	3	250	3	OR5AR1	11	56431409	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	526289	56431409	78575107	262	49678										
CTNND1	1500	hgsc.bcm.edu	37	chr11	57583392	57583392	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tgcatgtgttcacagcaggaCgaggggcaggaatctctgga	15	8	2	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:57583392C>T	ENST00000399050.4	+	20	3350	c.2814C>T	c.(2812-2814)gaC>gaT	p.D938D	CTNND1_ENST00000361796.4_Intron|CTNND1_ENST00000532245.1_Intron|CTNND1_ENST00000529919.1_Intron|CTNND1_ENST00000426142.2_Intron|CTNND1_ENST00000530748.1_Intron|CTNND1_ENST00000524630.1_Intron|CTNND1_ENST00000534579.1_Intron|CTNND1_ENST00000532787.1_Silent_p.D810D|CTNND1_ENST00000415361.2_Silent_p.D837D|CTNND1_ENST00000529873.1_Silent_p.D857D|CTNND1_ENST00000358694.6_Intron|CTNND1_ENST00000526772.1_Intron|CTNND1_ENST00000533667.1_Silent_p.D588D|CTNND1_ENST00000526357.1_Silent_p.D878D|CTNND1_ENST00000532844.1_Silent_p.D884D|CTNND1_ENST00000528232.1_Intron|CTNND1_ENST00000526938.1_Intron|CTNND1_ENST00000530094.1_Silent_p.D831D|CTNND1_ENST00000361332.4_Silent_p.D932D|CTNND1_ENST00000531014.1_Silent_p.D609D|CTNND1_ENST00000528621.1_Intron|CTNND1_ENST00000529526.1_Intron|CTNND1_ENST00000428599.2_Intron|CTNND1_ENST00000527467.1_Silent_p.D615D|CTNND1_ENST00000532649.1_Intron|CTNND1_ENST00000532463.1_Intron|CTNND1_ENST00000525902.1_Intron|CTNND1_ENST00000361391.6_Silent_p.D911D|CTNND1_ENST00000399039.4_Intron|CTNND1_ENST00000360682.6_Silent_p.D917D|CTNND1_ENST00000529986.1_Intron	NM_001085458.1	NP_001078927.1	O60716	CTND1_HUMAN	catenin (cadherin-associated protein), delta 1	938					adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|regulation of transcription, DNA-templated (GO:0006355)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)|zonula adherens (GO:0005915)	cadherin binding (GO:0045296)|receptor binding (GO:0005102)			breast(5)|endometrium(8)|kidney(4)|large_intestine(7)|liver(2)|lung(16)|ovary(1)|upper_aerodigestive_tract(2)	45		all_epithelial(135;0.155)				CACAGCAGGACGAGGGGCAGG	0.478																																					p.D938D		Atlas-SNP	.											.	CTNND1	203	.	0			c.C2814T						.						68	72	71					11																	57583392		1941	4118	6059	SO:0001819	synonymous_variant	1500	exon20			GCAGGACGAGGGG	AB002382	CCDS44604.1, CCDS44605.1, CCDS44606.1, CCDS44607.1, CCDS44608.1, CCDS44609.1, CCDS53632.1, CCDS53633.1, CCDS53634.1, CCDS55763.1, CCDS55764.1, CCDS55765.1, CCDS55766.1, CCDS55767.1, CCDS73290.1	11q12.1	2013-02-14				ENSG00000198561		"Armadillo repeat containing"	2515	protein-coding gene	gene with protein product		601045		CTNND		8808291	Standard	NM_001085460		Approved	KIAA0384, p120, p120cas, p120ctn	uc001nmc.4	O60716		ENST00000399050.4:c.2814C>T	chr11.hg19:g.57583392C>T		108.0	0.0		134.0	26.0	NM_001085458	A8K939|O15088|O60713|O60714|O60715|O60935|Q6DHZ7|Q6RBX8|Q9UP71|Q9UP72|Q9UP73	Silent	SNP	ENST00000399050.4	hg19	CCDS44604.1																																																																																			.	.		0.478	CTNND1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393944.1	NM_001331		T	57583392	C	T	57583392	2	4	352	1	0	0	0	0	0	0	0	1	4021	535	19	1		1	CTNND1	11	57583392	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	1151983	57583392	77423124	263	49679										
PLAC1L	219990	hgsc.bcm.edu	37	chr11	59814440	59814440	+	Frame_Shift_Del	DEL	T	T	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	atcagtgtggcttacaccagTttctactgagaatgaaataa							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:59814440delT	ENST00000278855.2	+	4	556	c.371delT	c.(370-372)gttfs	p.V124fs		NM_173801.3	NP_776162.2	Q86WS3	OOSP2_HUMAN		124						extracellular region (GO:0005576)				breast(1)|lung(9)|ovary(2)|prostate(2)|skin(1)	15						CTTACACCAGTTTCTACTGAG	0.368																																					p.V124fs		Atlas-INDEL	.											.	PLAC1L	36	.	0			c.370delG						.						166	160	162					11																	59814440		2201	4295	6496	SO:0001589	frameshift_variant	219990	exon4			.																												ENST00000278855.2:c.371delT	chr11.hg19:g.59814440delT	ENSP00000278855:p.Val124fs	110.0	0.0		138.0	37.0	NM_173801	E9PJA4|Q8N9U6	Frame_Shift_Del	DEL	ENST00000278855.2	hg19	CCDS7979.1																																																																																			.	.		0.368	PLAC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394411.1			-	59814440	T	-	59814440	7	5	352	1	0	1	0	1	0	0	0	0	12022	1725	60	0	385	0	PLAC1L	11	59814440	Frame_Shift_Del	DEL	T	TCGA-WQ-A9G7-01A-11D-A36X-10	2231048	59814440	75192076	264	49680										
AHNAK	79026	hgsc.bcm.edu	37	chr11	62289805	62289805	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	acttcaggggcctttagatcAccttccatcttaggcagaga	9	11	3	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:62289805A>G	ENST00000378024.4	-	5	12358	c.12084T>C	c.(12082-12084)ggT>ggC	p.G4028G	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	4028					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				CCTTTAGATCACCTTCCATCT	0.502																																					p.G4028G		Atlas-SNP	.											.	AHNAK	532	.	0			c.T12084C						.						173	181	179					11																	62289805		2202	4299	6501	SO:0001819	synonymous_variant	79026	exon5			TAGATCACCTTCC	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.12084T>C	chr11.hg19:g.62289805A>G		118.0	0.0		113.0	12.0	NM_001620	A1A586	Silent	SNP	ENST00000378024.4	hg19	CCDS31584.1																																																																																			.	.		0.502	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		G	62289805	A	G	62289805	2	3	352	1	0	0	0	0	0	0	0	1	414	146	6	2		2	AHNAK	11	62289805	Silent	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	2475365	62289805	72716711	265	49681										
MEN1	4221	hgsc.bcm.edu	37	chr11	64577275	64577275	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ttctcgaggatagagggacaGgtcgacggcgcctcggatct	15	10	2	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:64577275G>T	ENST00000337652.1	-	2	810	c.307C>A	c.(307-309)Ctg>Atg	p.L103M	MEN1_ENST00000377326.3_Missense_Mutation_p.L103M|MEN1_ENST00000394374.2_Missense_Mutation_p.L103M|MEN1_ENST00000312049.6_Missense_Mutation_p.L103M|MEN1_ENST00000443283.1_Missense_Mutation_p.L103M|MEN1_ENST00000377316.2_Missense_Mutation_p.L103M|MEN1_ENST00000315422.4_Missense_Mutation_p.L103M|MEN1_ENST00000377321.1_Missense_Mutation_p.L103M|MEN1_ENST00000394376.1_Missense_Mutation_p.L103M|MEN1_ENST00000377313.1_Missense_Mutation_p.L103M	NM_130803.2	NP_570715	O00255	MEN1_HUMAN	multiple endocrine neoplasia I	103					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)	p.D102fs*10(1)|p.I97_L103del(1)		NS(7)|adrenal_gland(5)|breast(2)|central_nervous_system(5)|endometrium(1)|gastrointestinal_tract_(site_indeterminate)(15)|large_intestine(2)|lung(21)|ovary(1)|pancreas(64)|parathyroid(181)|pituitary(7)|prostate(4)|retroperitoneum(1)|skin(1)|small_intestine(13)|soft_tissue(4)|stomach(1)|thymus(2)	337						TAGAGGGACAGGTCGACGGCG	0.627			"D, Mis, N, F, S"		"parathyroid tumors, Pancreatic neuroendocrine tumors"	"parathyroid adenoma, pituitary adenoma, pancreatic islet cell, carcinoid"			Multiple Endocrine Neoplasia, type 1;Hyperparathyroidism, Familial Isolated																												p.L103M	Esophageal Squamous(1;83 158 15500 18603 18803 29295)	Atlas-SNP	.	yes	Rec	yes	Multiple Endocrine Neoplasia Type 1	11	11q13	4221	multiple endocrine neoplasia type 1 gene		E	.	MEN1	442	.	2	Deletion - Frameshift(1)|Deletion - In frame(1)	parathyroid(2)	c.C307A	GRCh37	CD972306	MEN1	D		.						41	44	43					11																	64577275		2201	4297	6498	SO:0001583	missense	4221	exon2	Familial Cancer Database	MEN1, Wermer disease;FIHP, FIHPT, HRPT1, Familial Isolated Primary Hyperparathyroidism	GGGACAGGTCGAC	U93236	CCDS8083.1, CCDS31600.1	11q13	2014-09-17			ENSG00000133895	ENSG00000133895			7010	protein-coding gene	gene with protein product	"menin"	613733					Standard	NM_130799		Approved		uc001obn.3	O00255	OTTHUMG00000045366	ENST00000337652.1:c.307C>A	chr11.hg19:g.64577275G>T	ENSP00000337088:p.Leu103Met	119.0	0.0		134.0	24.0	NM_130800	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Missense_Mutation	SNP	ENST00000337652.1	hg19	CCDS8083.1	.	.	.	.	.	.	.	.	.	.	G	12.57	1.977103	0.34848	.	.	ENSG00000133895	ENST00000377316;ENST00000377321;ENST00000377326;ENST00000312049;ENST00000315422;ENST00000337652;ENST00000394376;ENST00000394374;ENST00000443283;ENST00000377313;ENST00000440873;ENST00000450708;ENST00000413626;ENST00000429702;ENST00000424912	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.99445	-5.91;-5.91;-5.91;-5.91;-5.91;-5.91;-5.91;-5.91;-5.91;-5.91;-5.91;-5.91;-5.91;-5.91;-5.91	5.02	2.16	0.27623	.	0.085427	0.49305	D	0.000156	D	0.98673	0.9555	L	0.35341	1.055	0.42496	D	0.992919	D;P;D	0.71674	0.998;0.886;0.998	P;B;D	0.66196	0.904;0.2;0.942	D	0.97439	1.0020	10	0.45353	T	0.12	-21.4809	8.8713	0.35318	0.2473:0.0:0.7527:0.0	.	103;103;103	O00255-2;O00255-3;O00255	.;.;MEN1_HUMAN	M	103	ENSP00000366533:L103M;ENSP00000366538:L103M;ENSP00000366543:L103M;ENSP00000308975:L103M;ENSP00000323747:L103M;ENSP00000337088:L103M;ENSP00000377901:L103M;ENSP00000377899:L103M;ENSP00000396940:L103M;ENSP00000366530:L103M;ENSP00000413944:L103M;ENSP00000394933:L103M;ENSP00000411218:L103M;ENSP00000402752:L103M;ENSP00000388016:L103M	ENSP00000308975:L103M	L	-	1	2	MEN1	64333851	1.000000	0.71417	0.999000	0.59377	0.121000	0.20230	2.763000	0.47605	0.263000	0.21812	-1.036000	0.02392	CTG	.	.		0.627	MEN1-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000143881.1			T	64577275	G	T	64577275	3	4	352	1	0	0	0	0	1	0	0	0	9481	991	35	3	1576	3	MEN1	11	64577275	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	2287470	64577275	70429241	266	49682										
TIGD3	220359	hgsc.bcm.edu	37	chr11	65123857	65123857	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cggcagctttggtgcatgtgAtcaagtacaggtgctgctgt	14	8	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:65123857A>C	ENST00000309880.5	+	2	785	c.578A>C	c.(577-579)gAt>gCt	p.D193A		NM_145719.2	NP_663771.1	Q6B0B8	TIGD3_HUMAN	tigger transposable element derived 3	193	DDE.					nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(3)|large_intestine(1)|lung(9)|prostate(2)|skin(2)	17						GGTGCATGTGATCAAGTACAG	0.587																																					p.D193A		Atlas-SNP	.											.	TIGD3	32	.	0			c.A578C						.						103	111	108					11																	65123857		2201	4297	6498	SO:0001583	missense	220359	exon2			CATGTGATCAAGT		CCDS8101.1	11q13.1	2008-07-21				ENSG00000173825			18334	protein-coding gene	gene with protein product							Standard	NM_145719		Approved		uc001odo.4	Q6B0B8		ENST00000309880.5:c.578A>C	chr11.hg19:g.65123857A>C	ENSP00000308354:p.Asp193Ala	36.0	0.0		75.0	22.0	NM_145719		Missense_Mutation	SNP	ENST00000309880.5	hg19	CCDS8101.1	.	.	.	.	.	.	.	.	.	.	A	11.92	1.782219	0.31502	.	.	ENSG00000173825	ENST00000309880	T	0.41400	1.0	4.05	2.92	0.33932	.	0.224065	0.22760	N	0.055971	T	0.38957	0.1060	L	0.59436	1.845	0.09310	N	1	B	0.29936	0.262	B	0.35727	0.209	T	0.36986	-0.9725	10	0.56958	D	0.05	-7.2567	6.3025	0.21121	0.8847:0.0:0.1153:0.0	.	193	Q6B0B8	TIGD3_HUMAN	A	193	ENSP00000308354:D193A	ENSP00000308354:D193A	D	+	2	0	TIGD3	64880433	0.970000	0.33590	0.016000	0.15963	0.950000	0.60333	2.756000	0.47549	0.733000	0.32492	0.374000	0.22700	GAT	.	.		0.587	TIGD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387310.1	NM_145719		C	65123857	A	C	65123857	3	2	352	1	0	0	0	0	1	0	0	0	15912	333	12	5	580	5	TIGD3	11	65123857	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	546582	65123857	69882659	267	49683										
FRMD8	83786	hgsc.bcm.edu	37	chr11	65156924	65156924	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gtgcccatgagctgcaccgcGctgtccgcgaggtcctgcag	14	15	0	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:65156924G>A	ENST00000317568.5	+	3	341	c.178G>A	c.(178-180)Gct>Act	p.A60T	FRMD8_ENST00000355991.5_Intron|FRMD8_ENST00000416776.2_Missense_Mutation_p.A60T	NM_031904.3	NP_114110.1	Q9BZ67	FRMD8_HUMAN	FERM domain containing 8	60	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoskeleton (GO:0005856)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|urinary_tract(1)	17						GCTGCACCGCGCTGTCCGCGA	0.642																																					p.A60T		Atlas-SNP	.											.	FRMD8	28	.	0			c.G178A						.						76	54	62					11																	65156924		2201	4297	6498	SO:0001583	missense	83786	exon3			CACCGCGCTGTCC	AK074850	CCDS8102.1, CCDS73320.1	11q13.1	2007-08-14			ENSG00000126391	ENSG00000126391			25462	protein-coding gene	gene with protein product						12477932	Standard	NM_031904		Approved	FLJ90369, FKSG44	uc001odu.4	Q9BZ67	OTTHUMG00000166275	ENST00000317568.5:c.178G>A	chr11.hg19:g.65156924G>A	ENSP00000319726:p.Ala60Thr	38.0	0.0		43.0	10.0	NM_031904	B4E2P1|Q86V56|Q8NCB5	Missense_Mutation	SNP	ENST00000317568.5	hg19	CCDS8102.1	.	.	.	.	.	.	.	.	.	.	G	10.95	1.496332	0.26861	.	.	ENSG00000126391	ENST00000317568;ENST00000416776;ENST00000526201;ENST00000525156	D;D	0.83075	-1.68;-1.65	5.11	2.09	0.27110	Band 4.1 domain (1);FERM domain (1);	0.498482	0.22461	N	0.059753	T	0.72503	0.3468	L	0.53249	1.67	0.09310	N	1	B;B	0.11235	0.001;0.004	B;B	0.04013	0.0;0.001	T	0.52571	-0.8558	10	0.15066	T	0.55	-8.6362	4.4981	0.11851	0.1712:0.0:0.5344:0.2944	.	60;60	B4E2P1;Q9BZ67	.;FRMD8_HUMAN	T	60;60;52;60	ENSP00000319726:A60T;ENSP00000392111:A60T	ENSP00000319726:A60T	A	+	1	0	FRMD8	64913500	0.000000	0.05858	0.001000	0.08648	0.897000	0.52465	0.535000	0.23114	0.558000	0.29135	0.561000	0.74099	GCT	.	.		0.642	FRMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388833.1	NM_031904		A	65156924	G	A	65156924	3	1	352	1	0	0	0	0	1	0	0	0	6064	1087	38	1	184	1	FRMD8	11	65156924	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	33067	65156924	69849592	268	49684										
PCNXL3	399909	hgsc.bcm.edu	37	chr11	65396885	65396885	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	acacagctggacaggaacccTggtgtgtacccagccatcca	10	14	0	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:65396885T>C	ENST00000355703.3	+	25	4538	c.3999T>C	c.(3997-3999)ccT>ccC	p.P1333P		NM_032223.2	NP_115599.2	Q9H6A9	PCX3_HUMAN	pecanex-like 3 (Drosophila)	1333						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)	13						ACAGGAACCCTGGTGTGTACC	0.572																																					p.P1333P		Atlas-SNP	.											.	PCNXL3	140	.	0			c.T3999C						.						54	53	53					11																	65396885		2013	4168	6181	SO:0001630	splice_region_variant	399909	exon25			GAACCCTGGTGTG	BX640978	CCDS44650.1	11q12.1	2008-07-21			ENSG00000197136	ENSG00000197136			18760	protein-coding gene	gene with protein product						15146197	Standard	NM_032223		Approved	FLJ22427	uc001oey.2	Q9H6A9	OTTHUMG00000166539	ENST00000355703.3:c.4000+1T>C	chr11.hg19:g.65396885T>C		122.0	0.0		121.0	14.0	NM_032223	Q6MZN8	Silent	SNP	ENST00000355703.3	hg19	CCDS44650.1																																																																																			.	.		0.572	PCNXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390321.1	NM_032223	Silent	C	65396885	T	C	65396885	5	2	352	1	0	0	0	0	0	0	1	0	11602	1594	55	2	4097	2	PCNXL3	11	65396885	Splice_Site	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	239961	65396885	69609631	269	49685										
CCDC87	55231	hgsc.bcm.edu	37	chr11	66359567	66359567	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agggcatggattggcctctcCggagctcagggcagaaaggc	16	10	2	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:66359567C>T	ENST00000333861.3	-	1	987	c.920G>A	c.(919-921)cGg>cAg	p.R307Q	CCS_ENST00000533244.1_5'Flank|CCS_ENST00000310190.4_5'Flank	NM_018219.2	NP_060689.2	Q9NVE4	CCD87_HUMAN	coiled-coil domain containing 87	307					cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)					central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28						TTGGCCTCTCCGGAGCTCAGG	0.627																																					p.R307Q		Atlas-SNP	.											.	CCDC87	83	.	0			c.G920A						.						37	42	40					11																	66359567		2199	4295	6494	SO:0001583	missense	55231	exon1			CCTCTCCGGAGCT	BC034469	CCDS8145.1	11q13.2	2006-03-15			ENSG00000182791	ENSG00000182791			25579	protein-coding gene	gene with protein product						12477932	Standard	NM_018219		Approved	FLJ10786	uc001oiq.4	Q9NVE4	OTTHUMG00000167237	ENST00000333861.3:c.920G>A	chr11.hg19:g.66359567C>T	ENSP00000328487:p.Arg307Gln	95.0	0.0		82.0	23.0	NM_018219	Q8NE76	Missense_Mutation	SNP	ENST00000333861.3	hg19	CCDS8145.1	.	.	.	.	.	.	.	.	.	.	C	5.973	0.363529	0.11296	.	.	ENSG00000182791	ENST00000333861	T	0.32753	1.44	4.27	-0.612	0.11597	.	1.173640	0.06510	N	0.737917	T	0.11153	0.0272	N	0.03016	-0.435	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.29518	-1.0009	10	0.16896	T	0.51	.	4.052	0.09800	0.0:0.3625:0.2122:0.4253	.	307	Q9NVE4	CCD87_HUMAN	Q	307	ENSP00000328487:R307Q	ENSP00000328487:R307Q	R	-	2	0	CCDC87	66116143	0.000000	0.05858	0.000000	0.03702	0.665000	0.39181	-0.720000	0.04969	-0.094000	0.12374	0.514000	0.50259	CGG	.	.		0.627	CCDC87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393825.1	NM_018219		T	66359567	C	T	66359567	3	4	352	1	0	0	0	0	1	0	0	0	2864	652	23	1	1633	1	CCDC87	11	66359567	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	962682	66359567	68646949	270	49686										
LRP5	4041	hgsc.bcm.edu	37	chr11	68192642	68192642	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gccctggacggcaccgagcgCgaggtcctcttcaccaccgg	13	17	2	0	rs141446007	byFrequency	TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:68192642C>T	ENST00000294304.7	+	15	3415	c.3309C>T	c.(3307-3309)cgC>cgT	p.R1103R		NM_002335.2	NP_002326.2	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein 5	1103	Beta-propeller 4.				adipose tissue development (GO:0060612)|anatomical structure regression (GO:0060033)|anterior/posterior pattern specification (GO:0009952)|apoptotic process involved in patterning of blood vessels (GO:1902262)|bone marrow development (GO:0048539)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|cell migration involved in gastrulation (GO:0042074)|cell-cell signaling involved in mammary gland development (GO:0060764)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic limb morphogenesis (GO:0030326)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocytosis (GO:0006897)|extracellular matrix-cell signaling (GO:0035426)|gastrulation with mouth forming second (GO:0001702)|glucose catabolic process (GO:0006007)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|osteoblast development (GO:0002076)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mitosis (GO:0045840)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of bone remodeling (GO:0046850)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to peptide hormone (GO:0043434)|retina morphogenesis in camera-type eye (GO:0060042)|retinal blood vessel morphogenesis (GO:0061304)|somatic stem cell maintenance (GO:0035019)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	coreceptor activity (GO:0015026)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(24)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						GCACCGAGCGCGAGGTCCTCT	0.657													C|||	2	0.000399361	8e-04	0	5008	,	,		17873	0.001		0	False		,,,				2504	0				p.R1103R		Atlas-SNP	.											.	LRP5	136	.	0			c.C3309T						.	C		4,4396	8.1+/-20.4	0,4,2196	107	73	84		3309	-8.2	0.9	11	dbSNP_134	84	0,8588		0,0,4294	no	coding-synonymous	LRP5	NM_002335.2		0,4,6490	TT,TC,CC		0.0,0.0909,0.0308		1103/1616	68192642	4,12984	2200	4294	6494	SO:0001819	synonymous_variant	4041	exon15			CGAGCGCGAGGTC	AF064548	CCDS8181.1	11q13.4	2014-01-28	2003-03-12		ENSG00000162337	ENSG00000162337		"Low density lipoprotein receptors"	6697	protein-coding gene	gene with protein product		603506	"osteoporosis pseudoglioma syndrome", "exudative vitreoretinopathy 1"	LRP7, OPPG, EVR1		9714764, 10049586	Standard	XM_005273994		Approved	LR3, BMND1, HBM, OPS, OPTA1, VBCH2, EVR4	uc001ont.3	O75197	OTTHUMG00000167570	ENST00000294304.7:c.3309C>T	chr11.hg19:g.68192642C>T		73.0	0.0		79.0	12.0	NM_002335	Q96TD6|Q9UES7|Q9UP66	Silent	SNP	ENST00000294304.7	hg19	CCDS8181.1																																																																																			.	C|1.000;T|0.000		0.657	LRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395088.1	NM_002335		T	68192642	C	T	68192642	2	4	352	1	0	0	0	0	0	0	0	1	8969	755	27	1		1	LRP5	11	68192642	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	1833075	68192642	66813874	271	49687										
LRP5	4041	hgsc.bcm.edu	37	chr11	68201261	68201261	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	acctgcgcctgcgctgcgacGgcgaggcagactgtcaggac	15	14	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:68201261G>A	ENST00000294304.7	+	18	4061	c.3955G>A	c.(3955-3957)Ggc>Agc	p.G1319S		NM_002335.2	NP_002326.2	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein 5	1319	LDL-receptor class A 2. {ECO:0000255|PROSITE-ProRule:PRU00124}.				adipose tissue development (GO:0060612)|anatomical structure regression (GO:0060033)|anterior/posterior pattern specification (GO:0009952)|apoptotic process involved in patterning of blood vessels (GO:1902262)|bone marrow development (GO:0048539)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|cell migration involved in gastrulation (GO:0042074)|cell-cell signaling involved in mammary gland development (GO:0060764)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic limb morphogenesis (GO:0030326)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocytosis (GO:0006897)|extracellular matrix-cell signaling (GO:0035426)|gastrulation with mouth forming second (GO:0001702)|glucose catabolic process (GO:0006007)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|osteoblast development (GO:0002076)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mitosis (GO:0045840)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of bone remodeling (GO:0046850)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to peptide hormone (GO:0043434)|retina morphogenesis in camera-type eye (GO:0060042)|retinal blood vessel morphogenesis (GO:0061304)|somatic stem cell maintenance (GO:0035019)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	coreceptor activity (GO:0015026)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(24)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						GCGCTGCGACGGCGAGGCAGA	0.706																																					p.G1319S		Atlas-SNP	.											.	LRP5	136	.	0			c.G3955A						.						38	37	38					11																	68201261		2199	4292	6491	SO:0001583	missense	4041	exon18			TGCGACGGCGAGG	AF064548	CCDS8181.1	11q13.4	2014-01-28	2003-03-12		ENSG00000162337	ENSG00000162337		"Low density lipoprotein receptors"	6697	protein-coding gene	gene with protein product		603506	"osteoporosis pseudoglioma syndrome", "exudative vitreoretinopathy 1"	LRP7, OPPG, EVR1		9714764, 10049586	Standard	XM_005273994		Approved	LR3, BMND1, HBM, OPS, OPTA1, VBCH2, EVR4	uc001ont.3	O75197	OTTHUMG00000167570	ENST00000294304.7:c.3955G>A	chr11.hg19:g.68201261G>A	ENSP00000294304:p.Gly1319Ser	210.0	0.0		194.0	59.0	NM_002335	Q96TD6|Q9UES7|Q9UP66	Missense_Mutation	SNP	ENST00000294304.7	hg19	CCDS8181.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.374237	0.82573	.	.	ENSG00000162337	ENST00000294304	D	0.96774	-4.12	4.39	4.39	0.52855	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.49305	U	0.000149	D	0.97879	0.9303	M	0.85710	2.77	0.80722	D	1	D;D	0.62365	0.991;0.991	P;P	0.60541	0.876;0.876	D	0.98614	1.0664	10	0.62326	D	0.03	.	17.2343	0.86994	0.0:0.0:1.0:0.0	.	1319;1319	Q9UES7;O75197	.;LRP5_HUMAN	S	1319	ENSP00000294304:G1319S	ENSP00000294304:G1319S	G	+	1	0	LRP5	67957837	1.000000	0.71417	0.997000	0.53966	0.552000	0.35366	9.523000	0.98034	2.298000	0.77334	0.456000	0.33151	GGC	.	.		0.706	LRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395088.1	NM_002335		A	68201261	G	A	68201261	3	1	352	1	0	0	0	0	1	0	0	0	8969	1116	39	1	4025	1	LRP5	11	68201261	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	8619	68201261	66805255	272	49688										
KRTAP5-11	440051	hgsc.bcm.edu	37	chr11	71293746	71293746	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gaacaggctggcacacagcaGcacacaggcttgcagcagca	12	13	0	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:71293746G>A	ENST00000398530.1	-	1	175	c.138C>T	c.(136-138)tgC>tgT	p.C46C	KRTAP5-11_ENST00000526239.1_Intron|AP000867.1_ENST00000343767.3_Intron	NM_001005405.2	NP_001005405.1	Q6L8G4	KR511_HUMAN	keratin associated protein 5-11	46	6 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						GCACACAGCAGCACACAGGCT	0.657																																					p.C46C		Atlas-SNP	.											.	KRTAP5-11	36	.	0			c.C138T						.						88	107	101					11																	71293746		2200	4293	6493	SO:0001819	synonymous_variant	440051	exon1			ACAGCAGCACACA	AB126080	CCDS41685.1	11q13.4	2008-11-06			ENSG00000204571	ENSG00000204571		"Keratin associated proteins"	23606	protein-coding gene	gene with protein product						15144888	Standard	NM_001005405		Approved	KRTAP5.11, KRTAP5-6	uc001oqu.3	Q6L8G4	OTTHUMG00000057586	ENST00000398530.1:c.138C>T	chr11.hg19:g.71293746G>A		145.0	0.0		153.0	33.0	NM_001005405		Silent	SNP	ENST00000398530.1	hg19	CCDS41685.1																																																																																			.	.		0.657	KRTAP5-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127969.1	NM_001005405		A	71293746	G	A	71293746	2	1	352	1	0	0	0	0	0	0	0	1	8569	963	34	3		3	KRTAP5-11	11	71293746	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	3092485	71293746	63712770	273	49689										
CHRDL2	25884	hgsc.bcm.edu	37	chr11	74414512	74414512	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggccgggtgccacacctcccCgtgggagtacgtcttcccgc	13	17	1	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:74414512C>T	ENST00000376332.3	-	8	1280	c.784G>A	c.(784-786)Ggg>Agg	p.G262R	CHRDL2_ENST00000263671.5_Missense_Mutation_p.G262R|CHRDL2_ENST00000534159.1_5'UTR	NM_001278473.1	NP_001265402.1	Q6WN34	CRDL2_HUMAN	chordin-like 2	262	VWFC 3. {ECO:0000255|PROSITE- ProRule:PRU00220}.				cartilage development (GO:0051216)|cell differentiation (GO:0030154)|ossification (GO:0001503)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)				endometrium(1)|kidney(1)|large_intestine(6)|lung(4)|prostate(1)|skin(2)	15	Hepatocellular(1;0.098)					CACACCTCCCCGTGGGAGTAC	0.647																																					p.G262R		Atlas-SNP	.											CHRDL2,NS,malignant_melanoma,0,1	CHRDL2	47	.	0			c.G784A						.						29	27	28					11																	74414512		2200	4293	6493	SO:0001583	missense	25884	exon8			CCTCCCCGTGGGA	AL110168	CCDS8234.1, CCDS60893.1	11q13.4	2013-09-20			ENSG00000054938	ENSG00000054938			24168	protein-coding gene	gene with protein product		613127				12853144, 12975309	Standard	NM_015424		Approved	BNF1	uc001ovh.3	Q6WN34	OTTHUMG00000165623	ENST00000376332.3:c.784G>A	chr11.hg19:g.74414512C>T	ENSP00000365510:p.Gly262Arg	122.0	0.0		110.0	23.0	NM_015424	A5PKU9|Q6WN30|Q6WN31|Q6WN32|Q7Z5J3	Missense_Mutation	SNP	ENST00000376332.3	hg19		.	.	.	.	.	.	.	.	.	.	C	31	5.081673	0.94050	.	.	ENSG00000054938	ENST00000263671;ENST00000376332;ENST00000376323;ENST00000393519	T;T	0.74002	-0.8;-0.8	5.62	5.62	0.85841	von Willebrand factor, type C (3);	0.000000	0.85682	D	0.000000	D	0.85305	0.5666	M	0.69358	2.11	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.86351	0.1711	10	0.87932	D	0	-23.1034	17.1513	0.86779	0.0:1.0:0.0:0.0	.	262;262	Q6WN34;Q6WN34-2	CRDL2_HUMAN;.	R	262;262;148;146	ENSP00000263671:G262R;ENSP00000365510:G262R	ENSP00000263671:G262R	G	-	1	0	CHRDL2	74092160	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.818000	0.86416	2.645000	0.89757	0.462000	0.41574	GGG	.	.		0.647	CHRDL2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000385391.1			T	74414512	C	T	74414512	3	4	352	1	0	0	0	0	1	0	0	0	3376	652	23	1	591	1	CHRDL2	11	74414512	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	3120766	74414512	60592004	274	49690										
KLHL35	283212	hgsc.bcm.edu	37	chr11	75140869	75140869	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gagcctcgagcagcagcgggCggcactcgccgcaggcctgc	16	16	0	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:75140869C>T	ENST00000539798.1	-	1	805	c.806G>A	c.(805-807)cGc>cAc	p.R269H	KLHL35_ENST00000376292.4_Missense_Mutation_p.R49H	NM_001039548.2	NP_001034637.2	Q6PF15	KLH35_HUMAN	kelch-like family member 35	269										lung(2)|stomach(1)	3						CAGCAGCGGGCGGCACTCGCC	0.736																																					p.R269H	Colon(77;683 1691 18820 23811)	Atlas-SNP	.											.	KLHL35	15	.	0			c.G806A						.						2	4	3					11																	75140869		1341	3145	4486	SO:0001583	missense	283212	exon1			AGCGGGCGGCACT		CCDS44685.1, CCDS44685.2	11q13.4	2013-02-22	2013-02-22		ENSG00000149243	ENSG00000149243		"Kelch-like", "BTB/POZ domain containing"	26597	protein-coding gene	gene with protein product			"kelch-like 35 (Drosophila)"				Standard	NM_001039548		Approved	FLJ33790	uc001owm.2	Q6PF15	OTTHUMG00000133573	ENST00000539798.1:c.806G>A	chr11.hg19:g.75140869C>T	ENSP00000438526:p.Arg269His	28.0	0.0		41.0	8.0	NM_001039548	A2RU06|F5H412|Q86XM7|Q8NBB1	Missense_Mutation	SNP	ENST00000539798.1	hg19	CCDS44685.2	.	.	.	.	.	.	.	.	.	.	C	13.13	2.145285	0.37825	.	.	ENSG00000149243	ENST00000376292;ENST00000539798	T;T	0.71698	-0.59;-0.49	4.89	3.95	0.45737	.	0.345798	0.27891	N	0.017428	T	0.60327	0.2260	L	0.54323	1.7	0.35809	D	0.823696	B	0.14438	0.01	B	0.09377	0.004	T	0.62364	-0.6870	10	0.34782	T	0.22	.	6.4375	0.21831	0.1802:0.7254:0.0:0.0944	.	49	Q6PF15	KLH35_HUMAN	H	49;269	ENSP00000365469:R49H;ENSP00000438526:R269H	ENSP00000365469:R49H	R	-	2	0	KLHL35	74818517	0.635000	0.27199	0.999000	0.59377	0.991000	0.79684	0.824000	0.27379	2.542000	0.85734	0.561000	0.74099	CGC	.	.		0.736	KLHL35-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_173583		T	75140869	C	T	75140869	3	4	352	1	0	0	0	0	1	0	0	0	8397	768	27	1	969	1	KLHL35	11	75140869	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	726357	75140869	59865647	275	49691										
GAB2	9846	hgsc.bcm.edu	37	chr11	77934490	77934490	+	Frame_Shift_Del	DEL	G	G	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gtttgaggttgcggttgacaGggggtggctgaatctcactt							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:77934490delG	ENST00000361507.4	-	6	1620	c.1535delC	c.(1534-1536)cctfs	p.P512fs	GAB2_ENST00000340149.2_Frame_Shift_Del_p.P474fs	NM_080491.2	NP_536739.1	Q9UQC2	GAB2_HUMAN	GRB2-associated binding protein 2	512					cell migration (GO:0016477)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of mast cell degranulation (GO:0043306)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)		INTS4/GAB2(2)	NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(8)|ovary(5)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(14;3.31e-18)|all_epithelial(13;5.3e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.58e-23)			GCGGTTGACAGGGGGTGGCTG	0.552																																					p.P512fs		Atlas-INDEL	.											.	GAB2	63	.	0			c.1536delT						.						155	144	148					11																	77934490		2200	4292	6492	SO:0001589	frameshift_variant	9846	exon6			.	AB011143	CCDS8259.1, CCDS8260.1	11q13.4-q13.5	2013-01-10			ENSG00000033327	ENSG00000033327		"Pleckstrin homology (PH) domain containing"	14458	protein-coding gene	gene with protein product	"Grb2-associated binder 2"	606203				10391903, 10068651	Standard	NM_080491		Approved	KIAA0571	uc001ozh.3	Q9UQC2	OTTHUMG00000166673	ENST00000361507.4:c.1535delC	chr11.hg19:g.77934490delG	ENSP00000354952:p.Pro512fs	154.0	0.0		169.0	22.0	NM_080491	A2RRM2|A6NEW9|A7MD36|O60317	Frame_Shift_Del	DEL	ENST00000361507.4	hg19	CCDS8259.1																																																																																			.	.		0.552	GAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391085.1	NM_080491		-	77934490	G	-	77934490	7	5	352	1	0	1	0	1	0	0	0	0	6157	1000	35	0	515	0	GAB2	11	77934490	Frame_Shift_Del	DEL	G	TCGA-WQ-A9G7-01A-11D-A36X-10	2793621	77934490	57072026	276	49692										
MTNR1B	4544	hgsc.bcm.edu	37	chr11	92714946	92714946	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gtccctggagtacgacccacGcatctattcctgcaccttca	7	16	2	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:92714946G>A	ENST00000257068.2	+	2	563	c.557G>A	c.(556-558)cGc>cAc	p.R186H		NM_005959.3	NP_005950.1	P49286	MTR1B_HUMAN	melatonin receptor 1B	186					G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose homeostasis (GO:0042593)|regulation of insulin secretion (GO:0050796)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|melatonin receptor activity (GO:0008502)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(19)|ovary(1)|prostate(2)|urinary_tract(1)	33		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)			Agomelatine(DB06594)|Melatonin(DB01065)|Ramelteon(DB00980)	TACGACCCACGCATCTATTCC	0.617																																					p.R186H		Atlas-SNP	.											MTNR1B,colon,carcinoma,+1,2	MTNR1B	75	.	0			c.G557A						.						91	87	88					11																	92714946		2201	4298	6499	SO:0001583	missense	4544	exon2			ACCCACGCATCTA	AB033598	CCDS8290.1	11q21-q22	2012-08-08			ENSG00000134640	ENSG00000134640		"GPCR / Class A : Melatonin receptors"	7464	protein-coding gene	gene with protein product		600804					Standard	NM_005959		Approved		uc001pdk.1	P49286	OTTHUMG00000167364	ENST00000257068.2:c.557G>A	chr11.hg19:g.92714946G>A	ENSP00000257068:p.Arg186His	88.0	0.0		109.0	14.0	NM_005959		Missense_Mutation	SNP	ENST00000257068.2	hg19	CCDS8290.1	.	.	.	.	.	.	.	.	.	.	G	17.96	3.515259	0.64634	.	.	ENSG00000134640	ENST00000257068	T	0.72394	-0.65	4.21	3.28	0.37604	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.79233	0.4411	M	0.87617	2.895	0.58432	D	0.999997	P	0.47409	0.895	P	0.50162	0.633	T	0.81061	-0.1103	10	0.39692	T	0.17	-21.8726	13.6018	0.62024	0.0:0.0:0.8434:0.1566	.	186	P49286	MTR1B_HUMAN	H	186	ENSP00000257068:R186H	ENSP00000257068:R186H	R	+	2	0	MTNR1B	92354594	1.000000	0.71417	0.691000	0.30163	0.603000	0.37013	7.031000	0.76491	1.097000	0.41459	0.491000	0.48974	CGC	.	.		0.617	MTNR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394323.1			A	92714946	G	A	92714946	3	1	352	1	0	0	0	0	1	0	0	0	9961	1087	38	1	563	1	MTNR1B	11	92714946	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	14780456	92714946	42291570	277	49693										
TAF1D	79101	hgsc.bcm.edu	37	chr11	93471438	93471438	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gtggtcttcctgttggctggTacctcctctttttctttttt	8	10	3	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:93471438T>C	ENST00000448108.2	-	3	946	c.296A>G	c.(295-297)tAc>tGc	p.Y99C	TAF1D_ENST00000546088.1_5'Flank	NM_024116.3	NP_077021.1	Q9H5J8	TAF1D_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, D, 41kDa	99					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	microtubule organizing center (GO:0005815)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			large_intestine(1)|lung(3)|prostate(1)|skin(2)	7						TGTTGGCTGGTACCTCCTCTT	0.363																																					p.Y99C		Atlas-SNP	.											.	TAF1D	18	.	0			c.A296G						.						143	150	147					11																	93471438		2201	4298	6499	SO:0001583	missense	79101	exon3			GGCTGGTACCTCC		CCDS8293.1	11q21	2012-05-30	2008-09-30	2008-09-30	ENSG00000166012	ENSG00000166012			28759	protein-coding gene	gene with protein product		612823	"Josephin domain containing 3"	JOSD3		15520167, 17318177	Standard	NM_024116		Approved	MGC5306, TAF(I)41	uc001pec.3	Q9H5J8	OTTHUMG00000167451	ENST00000448108.2:c.296A>G	chr11.hg19:g.93471438T>C	ENSP00000410409:p.Tyr99Cys	83.0	0.0		75.0	11.0	NM_024116	Q6I9Y6	Missense_Mutation	SNP	ENST00000448108.2	hg19	CCDS8293.1	.	.	.	.	.	.	.	.	.	.	T	12.17	1.857106	0.32791	.	.	ENSG00000166012	ENST00000448108	.	.	.	5.44	4.32	0.51571	.	0.000000	0.64402	D	0.000003	T	0.70404	0.3220	M	0.66939	2.045	0.42256	D	0.991992	D	0.89917	1.0	D	0.91635	0.999	T	0.71464	-0.4585	9	0.66056	D	0.02	-7.3068	8.0462	0.30551	0.0:0.0916:0.0:0.9084	.	99	Q9H5J8	TAF1D_HUMAN	C	99	.	ENSP00000314971:Y99C	Y	-	2	0	TAF1D	93111086	0.963000	0.33076	0.175000	0.22980	0.029000	0.11900	3.759000	0.55227	1.022000	0.39626	0.528000	0.53228	TAC	.	.		0.363	TAF1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394662.2	NM_024116		C	93471438	T	C	93471438	3	2	352	1	0	0	0	0	1	0	0	0	15537	1638	57	2	556	2	TAF1D	11	93471438	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	756492	93471438	41535078	278	49694										
C11orf54	28970	hgsc.bcm.edu	37	chr11	93486913	93486914	+	Frame_Shift_Ins	INS	-	-	A													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cttattgcctcttgtaaaccINSaaaaaaaagtaagtactttt							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:93486913_93486914insA	ENST00000331239.4	+	4	399_400	c.220_221insA	c.(220-222)caafs	p.Q74fs	C11orf54_ENST00000540113.1_Frame_Shift_Ins_p.Q55fs|C11orf54_ENST00000528099.1_Frame_Shift_Ins_p.Q74fs|C11orf54_ENST00000354421.3_Frame_Shift_Ins_p.Q74fs|C11orf54_ENST00000528288.1_Frame_Shift_Ins_p.Q74fs			Q9H0W9	CK054_HUMAN	chromosome 11 open reading frame 54	74					metabolic process (GO:0008152)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|large_intestine(1)|lung(5)	8		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				TCTTGTAAACCAAAAAAAAGTA	0.356																																					p.Q74fs		Atlas-INDEL	.											.	C11orf54	23	.	0			c.220_221insA						.																																			SO:0001589	frameshift_variant	28970	exon4			.	AF092133	CCDS8294.1, CCDS66204.1, CCDS73365.1, CCDS73366.1	11q21	2012-08-09			ENSG00000182919	ENSG00000182919			30204	protein-coding gene	gene with protein product		615810				16522806	Standard	NM_014039		Approved	PTD012	uc001pef.3	Q9H0W9	OTTHUMG00000167452	ENST00000331239.4:c.228dupA	chr11.hg19:g.93486921_93486921dupA	ENSP00000331209:p.Gln74fs	100.0	0.0		103.0	30.0	NM_014039	A8K850|Q6FI88|Q6XYB0|Q96EI3|Q96IX1|Q9Y6B4	Frame_Shift_Ins	INS	ENST00000331239.4	hg19																																																																																				.	.		0.356	C11orf54-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394671.1	NM_014039		A	93486914	-	A	93486913	7	5	352	1	0	1	1	0	0	0	0	0	1651	595	21	0	230	0	C11orf54	11	93486913	Frame_Shift_Ins	INS	-	TCGA-WQ-A9G7-01A-11D-A36X-10	15475	93486913	41519603	279	49695										
CNTN5	53942	hgsc.bcm.edu	37	chr11	100221535	100221535	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ctggagtctatattattgaaGttcgagcatatagtgaagga	11	4	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:100221535G>A	ENST00000524871.1	+	24	3423	c.3133G>A	c.(3133-3135)Gtt>Att	p.V1045I	CNTN5_ENST00000418526.2_Missense_Mutation_p.V971I|CNTN5_ENST00000524560.1_3'UTR|CNTN5_ENST00000279463.3_Missense_Mutation_p.V1045I|CNTN5_ENST00000528682.1_Missense_Mutation_p.V1045I	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	1045	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(12)|lung(38)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	81		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		TATTATTGAAGTTCGAGCATA	0.393																																					p.V1045I		Atlas-SNP	.											.	CNTN5	324	.	0			c.G3133A						.						129	126	127					11																	100221535		1879	4109	5988	SO:0001583	missense	53942	exon23			ATTGAAGTTCGAG	AB013802	CCDS53696.1, CCDS53697.1, CCDS58168.1	11q22.1	2013-02-11			ENSG00000149972	ENSG00000149972		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2175	protein-coding gene	gene with protein product		607219					Standard	NM_014361		Approved	NB-2, hNB-2	uc021qpb.1	O94779	OTTHUMG00000167579	ENST00000524871.1:c.3133G>A	chr11.hg19:g.100221535G>A	ENSP00000435637:p.Val1045Ile	127.0	0.0		178.0	35.0	NM_001243270	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Missense_Mutation	SNP	ENST00000524871.1	hg19	CCDS53696.1	.	.	.	.	.	.	.	.	.	.	G	3.766	-0.048681	0.07407	.	.	ENSG00000149972	ENST00000528682;ENST00000524871;ENST00000418526;ENST00000279463	T;T;T;T	0.70749	-0.51;-0.51;-0.51;-0.51	5.4	4.49	0.54785	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.056281	0.64402	N	0.000001	T	0.56411	0.1983	N	0.25485	0.75	0.54753	D	0.999987	B;B	0.20550	0.011;0.046	B;B	0.20184	0.016;0.028	T	0.49986	-0.8880	9	.	.	.	.	13.0124	0.58739	0.0777:0.0:0.9223:0.0	.	971;1045	O94779-2;O94779	.;CNTN5_HUMAN	I	1045;1045;971;1045	ENSP00000436185:V1045I;ENSP00000435637:V1045I;ENSP00000393229:V971I;ENSP00000279463:V1045I	.	V	+	1	0	CNTN5	99726745	1.000000	0.71417	0.990000	0.47175	0.852000	0.48524	4.260000	0.58835	1.266000	0.44231	0.555000	0.69702	GTT	.	.		0.393	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361		A	100221535	G	A	100221535	3	1	352	1	0	0	0	0	1	0	0	0	3646	1029	36	3	3219	3	CNTN5	11	100221535	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	6734622	100221535	34784981	280	49696										
CARD18	59082	hgsc.bcm.edu	37	chr11	105009586	105009586	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gttgagggtcttcttcacagAgatgcttgataaatttgcag	11	6	3	3			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:105009586A>T	ENST00000530950.1	-	2	226	c.227T>A	c.(226-228)cTc>cAc	p.L76H	CARD18_ENST00000532895.1_Missense_Mutation_p.L37H|CARD18_ENST00000526823.1_Missense_Mutation_p.L37H	NM_021571.3	NP_067546.1	P57730	CAR18_HUMAN	caspase recruitment domain family, member 18	76	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				inflammatory response (GO:0006954)|regulation of apoptotic process (GO:0042981)		cysteine-type endopeptidase inhibitor activity (GO:0004869)			central_nervous_system(1)|ovary(1)	2						TTCTTCACAGAGATGCTTGAT	0.423																																					p.L76H		Atlas-SNP	.											.	CARD18	18	.	0			c.T227A						.						236	218	224					11																	105009586		1902	4118	6020	SO:0001583	missense	59082	exon2			TCACAGAGATGCT	AY358231	CCDS53705.1	11q22.3	2008-09-02				ENSG00000255501			28861	protein-coding gene	gene with protein product		605354				11051551	Standard	NM_021571		Approved	UNQ5804, ICEBERG, pseudo-ICE	uc021qpy.1	P57730		ENST00000530950.1:c.227T>A	chr11.hg19:g.105009586A>T	ENSP00000436691:p.Leu76His	173.0	0.0		181.0	11.0	NM_021571	A2RRF8	Missense_Mutation	SNP	ENST00000530950.1	hg19	CCDS53705.1	.	.	.	.	.	.	.	.	.	.	.	12.01	1.809571	0.31961	.	.	ENSG00000255501	ENST00000530950;ENST00000526823;ENST00000532895	T;T;T	0.39056	1.1;1.1;1.1	2.69	1.54	0.23209	DEATH-like (2);Caspase Recruitment (3);	0.500084	0.19225	N	0.119580	T	0.55609	0.1931	.	.	.	0.09310	N	1	D	0.76494	0.999	D	0.75484	0.986	T	0.41233	-0.9520	9	0.87932	D	0	.	4.6446	0.12566	0.8456:0.0:0.1544:0.0	.	76	P57730	CAR18_HUMAN	H	76;37;37	ENSP00000436691:L76H;ENSP00000437035:L37H;ENSP00000437187:L37H	ENSP00000437035:L37H	L	-	2	0	CARD18	104514796	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	1.497000	0.35649	0.444000	0.26612	0.456000	0.33151	CTC	.	.		0.423	CARD18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388183.2	NM_021571		T	105009586	A	T	105009586	3	4	352	1	0	0	0	0	1	0	0	0	2651	304	11	4	49	4	CARD18	11	105009586	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	4788051	105009586	29996930	281	49697										
KIAA1826	84437	hgsc.bcm.edu	37	chr11	105880665	105880665	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gtcgtcgtttttccaactctAgtttctgtttctcaatattt	5	9	3	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:105880665A>G	ENST00000301919.4	-	3	2050	c.635T>C	c.(634-636)cTa>cCa	p.L212P	MSANTD4_ENST00000529805.1_5'Flank	NM_032424.1	NP_115800.1	Q8NCY6	MSD4_HUMAN	Myb/SANT-like DNA-binding domain containing 4 with coiled-coils	212						nucleus (GO:0005634)											TTCCAACTCTAGTTTCTGTTT	0.433																																					p.L212P		Atlas-SNP	.											.	.	.	.	0			c.T635C						.						88	91	90					11																	105880665		2201	4299	6500	SO:0001583	missense	84437	exon3			AACTCTAGTTTCT	AB058729	CCDS31663.1	11q22	2012-03-13	2012-03-13	2012-03-13	ENSG00000170903	ENSG00000170903			29383	protein-coding gene	gene with protein product			"KIAA1826"	KIAA1826			Standard	XM_005271697		Approved		uc001piz.3	Q8NCY6	OTTHUMG00000166240	ENST00000301919.4:c.635T>C	chr11.hg19:g.105880665A>G	ENSP00000304713:p.Leu212Pro	56.0	0.0		60.0	19.0	NM_032424	Q96JK1|Q96JZ3|Q9H2N4	Missense_Mutation	SNP	ENST00000301919.4	hg19	CCDS31663.1	.	.	.	.	.	.	.	.	.	.	A	13.78	2.338112	0.41398	.	.	ENSG00000170903	ENST00000301919	.	.	.	5.78	5.78	0.91487	.	0.073082	0.56097	D	0.000033	T	0.50565	0.1623	L	0.27053	0.805	0.49389	D	0.999782	P	0.52463	0.953	P	0.49140	0.601	T	0.55617	-0.8113	9	0.72032	D	0.01	-26.5451	16.1035	0.81203	1.0:0.0:0.0:0.0	.	212	Q8NCY6	K1826_HUMAN	P	212	.	ENSP00000304713:L212P	L	-	2	0	KIAA1826	105385875	0.968000	0.33430	0.094000	0.20943	0.320000	0.28249	8.199000	0.89731	2.207000	0.71202	0.402000	0.26972	CTA	.	.		0.433	MSANTD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388619.1	NM_032424		G	105880665	A	G	105880665	3	3	352	1	0	0	0	0	1	0	0	0	8269	420	15	2	406	2	KIAA1826	11	105880665	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	871079	105880665	29125851	282	49698										
CWF19L2	143884	hgsc.bcm.edu	37	chr11	107299544	107299544	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cccagcaaatgtagactttgTatcccgtagatgttcttttt	7	9	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:107299544T>A	ENST00000282251.5	-	8	1441	c.1414A>T	c.(1414-1416)Aca>Tca	p.T472S	CWF19L2_ENST00000433523.1_Missense_Mutation_p.T472S	NM_152434.2	NP_689647.2	Q2TBE0	C19L2_HUMAN	CWF19-like 2, cell cycle control (S. pombe)	472							catalytic activity (GO:0003824)			endometrium(4)|kidney(2)|large_intestine(13)|lung(21)	40		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)		GTAGACTTTGTATCCCGTAGA	0.348																																					p.T472S		Atlas-SNP	.											.	CWF19L2	135	.	0			c.A1414T						.						159	165	163					11																	107299544		2201	4298	6499	SO:0001583	missense	143884	exon8			ACTTTGTATCCCG	AK056905	CCDS8336.2	11q23.1	2005-09-22			ENSG00000152404	ENSG00000152404			26508	protein-coding gene	gene with protein product						14702039	Standard	NM_152434		Approved	FLJ32343	uc010rvp.2	Q2TBE0	OTTHUMG00000152975	ENST00000282251.5:c.1414A>T	chr11.hg19:g.107299544T>A	ENSP00000282251:p.Thr472Ser	104.0	0.0		99.0	31.0	NM_152434	A4FU66|A4FU67|A4FU68|Q6PHW1|Q96MI1	Missense_Mutation	SNP	ENST00000282251.5	hg19	CCDS8336.2	.	.	.	.	.	.	.	.	.	.	T	4.603	0.112113	0.08831	.	.	ENSG00000152404	ENST00000282251;ENST00000433523	T;T	0.26660	1.72;1.72	5.42	1.7	0.24286	.	1.046460	0.07405	N	0.891416	T	0.18257	0.0438	L	0.46157	1.445	0.09310	N	1	B	0.14805	0.011	B	0.10450	0.005	T	0.37957	-0.9683	10	0.02654	T	1	-1.3545	5.3414	0.15986	0.0:0.1526:0.1481:0.6993	.	472	Q2TBE0	C19L2_HUMAN	S	472	ENSP00000282251:T472S;ENSP00000387533:T472S	ENSP00000282251:T472S	T	-	1	0	CWF19L2	106804754	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.456000	0.21859	0.083000	0.17047	-0.969000	0.02612	ACA	.	.		0.348	CWF19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328825.2	NM_152434		A	107299544	T	A	107299544	3	1	352	1	0	0	0	0	1	0	0	0	4074	1638	57	4	1314	4	CWF19L2	11	107299544	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	1418879	107299544	27706972	283	49699										
PPP2R1B	5519	hgsc.bcm.edu	37	chr11	111613287	111613287	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aatcttttgtagagatttggCcacattgaagcgaacatttg	9	6	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:111613287C>T	ENST00000527614.1	-	13	1722	c.1657G>A	c.(1657-1659)Gcc>Acc	p.A553T	PPP2R1B_ENST00000427203.2_Missense_Mutation_p.A392T|PPP2R1B_ENST00000341980.6_Missense_Mutation_p.A508T|PPP2R1B_ENST00000311129.5_Missense_Mutation_p.A553T|PPP2R1B_ENST00000426998.2_Missense_Mutation_p.A489T|PPP2R1B_ENST00000393055.2_Missense_Mutation_p.A426T	NM_001177562.1|NM_002716.4	NP_001171033.1|NP_002707.3	P30154	2AAB_HUMAN	protein phosphatase 2, regulatory subunit A, beta	553					apoptotic process involved in morphogenesis (GO:0060561)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)	extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|liver(1)|lung(10)|prostate(1)|urinary_tract(2)	22		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|Epithelial(105;2.36e-06)|all cancers(92;3.78e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0761)		AGAGATTTGGCCACATTGAAG	0.368																																					p.A553T		Atlas-SNP	.											.	PPP2R1B	44	.	0			c.G1657A						.						100	93	96					11																	111613287		2201	4297	6498	SO:0001583	missense	5519	exon13			ATTTGGCCACATT	AF087438	CCDS8348.1, CCDS8349.1, CCDS53706.1, CCDS53707.1, CCDS53708.1	11q23.1	2010-06-18	2010-04-14		ENSG00000137713	ENSG00000137713	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9303	protein-coding gene	gene with protein product	"PP2A-A-beta", "protein phosphatase 2A, regulatory subunit A, beta isoform"	603113	"protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), beta isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit A, beta isoform"			2159327, 9795170	Standard	NM_181699		Approved	PR65B, PP2A-Abeta	uc001plw.1	P30154	OTTHUMG00000166741	ENST00000527614.1:c.1657G>A	chr11.hg19:g.111613287C>T	ENSP00000437193:p.Ala553Thr	46.0	0.0		61.0	7.0	NM_002716	A8MY67|B0YJ69|B4DGQ6|B4DK91|B4DWW5|F8W8G1|O75620|Q8NHV8	Missense_Mutation	SNP	ENST00000527614.1	hg19	CCDS8349.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	34|34	5.348282|5.348282	0.95807|0.95807	.|.	.|.	ENSG00000137713|ENSG00000137713	ENST00000311129;ENST00000426998;ENST00000527614;ENST00000427203;ENST00000341980;ENST00000393055|ENST00000412902;ENST00000531890	T;T;T;T;T;T|.	0.23348|.	1.91;1.91;1.91;1.91;1.91;1.91|.	5.47|5.47	5.47|5.47	0.80525|0.80525	Armadillo-like helical (1);Armadillo-type fold (1);|.	0.159080|.	0.56097|.	D|.	0.000040|.	D|D	0.86339|0.86339	0.5909|0.5909	M|M	0.93678|0.93678	3.445|3.445	0.80722|0.80722	D|D	1|1	D;D;D;P;P;P|.	0.63880|.	0.993;0.97;0.988;0.952;0.48;0.769|.	D;P;D;P;B;P|.	0.66497|.	0.944;0.887;0.94;0.774;0.354;0.554|.	D|D	0.89457|0.89457	0.3734|0.3734	10|6	0.87932|0.66056	D|D	0|0.02	-9.7494|-9.7494	16.8268|16.8268	0.85933|0.85933	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	426;508;392;489;553;553|.	A8MY67;F8W8G1;B7Z1G3;B4DWW5;P30154;P30154-2|.	.;.;.;.;2AAB_HUMAN;.|.	T|D	553;489;553;392;508;426|425;181	ENSP00000311344:A553T;ENSP00000410671:A489T;ENSP00000437193:A553T;ENSP00000415759:A392T;ENSP00000343317:A508T;ENSP00000376775:A426T|.	ENSP00000311344:A553T|ENSP00000403301:G425D	A|G	-|-	1|2	0|0	PPP2R1B|PPP2R1B	111118497|111118497	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	7.396000|7.396000	0.79891|0.79891	2.573000|2.573000	0.86826|0.86826	0.555000|0.555000	0.69702|0.69702	GCC|GGC	.	.		0.368	PPP2R1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391298.1	NM_002716		T	111613287	C	T	111613287	3	4	352	1	0	0	0	0	1	0	0	0	12395	739	26	3	383	3	PPP2R1B	11	111613287	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	4313743	111613287	23393229	284	49700										
C11orf57	55216	hgsc.bcm.edu	37	chr11	111953315	111953316	+	Frame_Shift_Ins	INS	-	-	A													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agcagaaaaaaaggtcacacINSaaaaaacagaagaaaagcaa							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:111953315_111953316insA	ENST00000280352.9	+	6	1134_1135	c.498_499insA	c.(499-501)aaafs	p.K167fs	C11orf57_ENST00000420986.2_Frame_Shift_Ins_p.K167fs|TIMM8B_ENST00000507614.1_5'Flank|C11orf57_ENST00000532163.1_Frame_Shift_Ins_p.K139fs|C11orf57_ENST00000393047.3_Frame_Shift_Ins_p.K168fs	NM_001082970.1|NM_018195.3	NP_001076439.1|NP_060665.3	Q6ZUT1	CK057_HUMAN	chromosome 11 open reading frame 57	167	Lys-rich.									autonomic_ganglia(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|prostate(1)	12		all_cancers(61;9.8e-15)|all_epithelial(67;6.57e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;3.6e-07)|BRCA - Breast invasive adenocarcinoma(274;6.17e-07)|all cancers(92;7.01e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0521)		AAAGGTCACACAAAAAACAGAA	0.411																																					p.H167fs		Atlas-INDEL	.											.,1	C11orf57	41	.	0			c.501_502insA						.																																			SO:0001589	frameshift_variant	55216	exon6			.	BX538107	CCDS8356.2, CCDS41715.1, CCDS73383.1	11q23.1	2006-03-09			ENSG00000150776	ENSG00000150776			25569	protein-coding gene	gene with protein product						12477932	Standard	NM_001082970		Approved	FLJ10726	uc001pmw.4	Q6ZUT1	OTTHUMG00000150213	ENST00000280352.9:c.504dupA	chr11.hg19:g.111953321_111953321dupA	ENSP00000339076:p.Lys167fs	309.0	0.0		361.0	86.0	NM_001082969	Q5RL41|Q6IN53|Q7Z357|Q8N2T3	Frame_Shift_Ins	INS	ENST00000280352.9	hg19	CCDS41715.1																																																																																			.	.		0.411	C11orf57-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000316852.1	NM_018195		A	111953316	-	A	111953315	7	5	352	1	0	1	1	0	0	0	0	0	1652	477	17	0	519	0	C11orf57	11	111953315	Frame_Shift_Ins	INS	-	TCGA-WQ-A9G7-01A-11D-A36X-10	340028	111953315	23053201	285	49701										
HYOU1	10525	hgsc.bcm.edu	37	chr11	118923017	118923017	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	actcgctcaccagactcattTcggcactctggagggcctgc	10	15	3	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:118923017T>C	ENST00000404233.3	-	10	1236	c.1112A>G	c.(1111-1113)gAa>gGa	p.E371G	HYOU1_ENST00000543287.1_Missense_Mutation_p.E284G|HYOU1_ENST00000529972.1_Missense_Mutation_p.E371G|HYOU1_ENST00000525859.1_Missense_Mutation_p.E371G	NM_001130991.1|NM_006389.3	NP_001124463.1|NP_006380.1	Q9Y4L1	HYOU1_HUMAN	hypoxia up-regulated 1	371					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|response to ischemia (GO:0002931)|response to stress (GO:0006950)	endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(10)|prostate(1)|skin(2)	33	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.78e-05)		CAGACTCATTTCGGCACTCTG	0.557																																					p.E371G		Atlas-SNP	.											.	HYOU1	88	.	0			c.A1112G						.						111	118	116					11																	118923017		2200	4295	6495	SO:0001583	missense	10525	exon10			CTCATTTCGGCAC	U65785	CCDS8408.1	11q23.1-q23.3	2011-09-02			ENSG00000149428	ENSG00000149428		"Heat shock proteins / HSP70"	16931	protein-coding gene	gene with protein product	"glucose-regulated protein 170"	601746				9020069, 10037731	Standard	XM_005271390		Approved	ORP150, HSP12A, Grp170	uc001pux.3	Q9Y4L1	OTTHUMG00000166354	ENST00000404233.3:c.1112A>G	chr11.hg19:g.118923017T>C	ENSP00000384144:p.Glu371Gly	52.0	0.0		70.0	23.0	NM_006389	A8C1Z0|B7Z909|Q2I204|Q53H25	Missense_Mutation	SNP	ENST00000404233.3	hg19	CCDS8408.1	.	.	.	.	.	.	.	.	.	.	T	7.284	0.609761	0.14066	.	.	ENSG00000149428	ENST00000404233;ENST00000353883;ENST00000529972;ENST00000536103;ENST00000535579;ENST00000525859;ENST00000544701;ENST00000543287;ENST00000530473	T;T;T;T;T	0.24538	1.85;1.85;1.85;1.85;1.85	5.26	4.14	0.48551	.	0.191701	0.53938	N	0.000048	T	0.13329	0.0323	N	0.05031	-0.125	0.58432	D	0.999996	P;B;B;B	0.36837	0.571;0.057;0.01;0.01	B;B;B;B	0.40410	0.328;0.047;0.009;0.009	T	0.12941	-1.0528	10	0.13853	T	0.58	-11.2552	10.7933	0.46445	0.0:0.0748:0.0:0.9252	.	362;415;371;371	B3KXH0;B7Z2N4;Q9Y4L1;A8C1Z0	.;.;HYOU1_HUMAN;.	G	371;362;371;371;220;371;414;284;371	ENSP00000384144:E371G;ENSP00000437313:E371G;ENSP00000433397:E371G;ENSP00000442727:E284G;ENSP00000431874:E371G	ENSP00000278752:E362G	E	-	2	0	HYOU1	118428227	0.951000	0.32395	0.023000	0.16930	0.283000	0.27025	2.540000	0.45727	1.022000	0.39626	-0.256000	0.11100	GAA	.	.		0.557	HYOU1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389353.1	NM_006389		C	118923017	T	C	118923017	3	2	352	1	0	0	0	0	1	0	0	0	7479	1783	62	2	1955	2	HYOU1	11	118923017	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	6969702	118923017	16083499	286	49702										
THY1	7070	hgsc.bcm.edu	37	chr11	119291593	119291593	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gggtacctgttagcaggagaGcgatgctgatggccaggttc	16	8	0	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:119291593G>A	ENST00000284240.5	-	2	1062	c.23C>T	c.(22-24)gCt>gTt	p.A8V	USP2-AS1_ENST00000498979.2_RNA|USP2-AS1_ENST00000578923.1_RNA|USP2-AS1_ENST00000530002.1_RNA|THY1_ENST00000580275.1_Missense_Mutation_p.A8V|THY1_ENST00000527590.1_Intron|THY1_ENST00000528522.1_Missense_Mutation_p.A8V|USP2-AS1_ENST00000500970.1_RNA|RP11-334E6.12_ENST00000578216.1_RNA	NM_006288.3	NP_006279.2	P04216	THY1_HUMAN	Thy-1 cell surface antigen	8					angiogenesis (GO:0001525)|cytoskeleton organization (GO:0007010)|focal adhesion assembly (GO:0048041)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell migration (GO:0030336)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell receptor signaling pathway (GO:0050860)|positive regulation of GTPase activity (GO:0043547)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of T cell activation (GO:0050870)|retinal cone cell development (GO:0046549)|single organismal cell-cell adhesion (GO:0016337)|T cell receptor signaling pathway (GO:0050852)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	GPI anchor binding (GO:0034235)|integrin binding (GO:0005178)|Rho GTPase activator activity (GO:0005100)			breast(1)|kidney(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12		Medulloblastoma(222;0.0523)|Breast(348;0.174)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.83e-05)		TAGCAGGAGAGCGATGCTGAT	0.597																																					p.A8V		Atlas-SNP	.											.	THY1	21	.	0			c.C23T						.						199	176	184					11																	119291593		2199	4295	6494	SO:0001583	missense	7070	exon2			AGGAGAGCGATGC	M11749	CCDS8424.1	11q23.3	2013-01-14				ENSG00000154096		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	11801	protein-coding gene	gene with protein product		188230				2864690	Standard	NM_006288		Approved	CD90	uc001pwr.3	P04216		ENST00000284240.5:c.23C>T	chr11.hg19:g.119291593G>A	ENSP00000284240:p.Ala8Val	88.0	0.0		102.0	27.0	NM_006288	Q16008|Q9NSP1	Missense_Mutation	SNP	ENST00000284240.5	hg19	CCDS8424.1	.	.	.	.	.	.	.	.	.	.	G	8.597	0.885933	0.17540	.	.	ENSG00000154096	ENST00000284240;ENST00000528522;ENST00000524970;ENST00000524659	.	.	.	4.79	2.93	0.34026	Immunoglobulin-like (1);	0.404958	0.26609	N	0.023424	T	0.38852	0.1056	L	0.38175	1.15	0.33419	D	0.579591	B	0.10296	0.003	B	0.08055	0.003	T	0.42241	-0.9463	9	0.38643	T	0.18	-4.7717	8.2006	0.31421	0.1805:0.0:0.8195:0.0	.	8	P04216	THY1_HUMAN	V	8	.	ENSP00000284240:A8V	A	-	2	0	THY1	118796803	1.000000	0.71417	0.260000	0.24451	0.253000	0.25986	2.184000	0.42575	0.639000	0.30564	0.655000	0.94253	GCT	.	.		0.597	THY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388370.2	NM_006288		A	119291593	G	A	119291593	3	1	352	1	0	0	0	0	1	0	0	0	15900	971	34	3	474	3	THY1	11	119291593	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	368576	119291593	15714923	287	49703										
ASAM	79827	hgsc.bcm.edu	37	chr11	122968527	122968527	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ttttggttcccttcattatcGgtgagcagccattcaatatc	7	10	2	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:122968527G>A	ENST00000448775.2	-	2	502	c.162C>T	c.(160-162)acC>acT	p.T54T		NM_024769.2	NP_079045.1	Q9H6B4	CLMP_HUMAN	CXADR-like membrane protein	54	Ig-like C2-type 1.				digestive tract development (GO:0048565)	cell surface (GO:0009986)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				endometrium(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	14						CTTCATTATCGGTGAGCAGCC	0.488																																					p.T54T		Atlas-SNP	.											.	CLMP	39	.	0			c.C162T						.						162	157	159					11																	122968527		2202	4299	6501	SO:0001819	synonymous_variant	79827	exon2			ATTATCGGTGAGC	BC009371	CCDS8441.1	11q24	2013-01-29			ENSG00000166250	ENSG00000166250		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	24039	protein-coding gene	gene with protein product	"adipocyte-specific adhesion molecule", "coxsackie- and adenovirus receptor-like membrane protein", "adipocyte adhesion molecule"	611693				12851705, 14573622	Standard	NM_024769		Approved	ASAM, FLJ22415, ACAM	uc001pyt.3	Q9H6B4		ENST00000448775.2:c.162C>T	chr11.hg19:g.122968527G>A		90.0	0.0		96.0	13.0	NM_024769		Silent	SNP	ENST00000448775.2	hg19	CCDS8441.1																																																																																			.	.		0.488	CLMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387542.1	NM_024769		A	122968527	G	A	122968527	2	1	352	1	0	0	0	0	0	0	0	1	1009	1103	39	1		1	ASAM	11	122968527	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	3676934	122968527	12037989	288	49704										
CDON	50937	hgsc.bcm.edu	37	chr11	125893349	125893349	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	taacatacagcagtgtacatAagggtccaagatccggatgc	10	9	0	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:125893349A>G	ENST00000392693.3	-	2	150	c.23T>C	c.(22-24)tTa>tCa	p.L8S	CDON_ENST00000263577.7_Missense_Mutation_p.L8S	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	8					anterior/posterior pattern specification (GO:0009952)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cerebral cortex development (GO:0021987)|embryonic body morphogenesis (GO:0010172)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|lens development in camera-type eye (GO:0002088)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein heterodimerization activity (GO:0043497)|skeletal muscle satellite cell differentiation (GO:0014816)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(9)|ovary(3)|prostate(2)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	61	all_hematologic(175;0.177)	Breast(109;0.00157)|Lung NSC(97;0.0127)|all_lung(97;0.0133)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.51e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0604)		CAGTGTACATAAGGGTCCAAG	0.448																																					p.L8S		Atlas-SNP	.											.	CDON	137	.	0			c.T23C						.						121	117	119					11																	125893349		2201	4299	6500	SO:0001583	missense	50937	exon2			GTACATAAGGGTC	AF004841	CCDS8468.1, CCDS58192.1	11q24.2	2013-02-11	2012-12-07		ENSG00000064309	ENSG00000064309		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	17104	protein-coding gene	gene with protein product	"cell adhesion molecule-related/down-regulated by oncogenes"	608707	"Cdon homolog (mouse)"			9214393	Standard	NM_016952		Approved	ORCAM, CDO, CDON1	uc009zbw.3	Q4KMG0	OTTHUMG00000165862	ENST00000392693.3:c.23T>C	chr11.hg19:g.125893349A>G	ENSP00000376458:p.Leu8Ser	72.0	0.0		88.0	20.0	NM_016952	O14631	Missense_Mutation	SNP	ENST00000392693.3	hg19	CCDS58192.1	.	.	.	.	.	.	.	.	.	.	A	5.805	0.332750	0.11013	.	.	ENSG00000064309	ENST00000392693;ENST00000263577;ENST00000531586;ENST00000527967;ENST00000534818	T;T;T;T;T	0.78707	-0.48;-0.5;0.08;-0.31;-1.2	5.44	1.87	0.25490	.	0.178360	0.26987	N	0.021499	D	0.82273	0.5001	M	0.72894	2.215	0.09310	N	1	D;P;P	0.76494	0.999;0.567;0.693	D;B;B	0.63488	0.915;0.159;0.302	T	0.72007	-0.4420	10	0.87932	D	0	-1.0854	5.1486	0.14998	0.6341:0.1414:0.2245:0.0	.	8;8;8	E9PRD8;Q4KMG0;Q4KMG0-2	.;CDON_HUMAN;.	S	8	ENSP00000376458:L8S;ENSP00000263577:L8S;ENSP00000434212:L8S;ENSP00000436940:L8S;ENSP00000437176:L8S	ENSP00000263577:L8S	L	-	2	0	CDON	125398559	0.985000	0.35326	0.203000	0.23512	0.005000	0.04900	1.502000	0.35704	0.068000	0.16574	-0.326000	0.08463	TTA	.	.		0.448	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952		G	125893349	A	G	125893349	3	3	352	1	0	0	0	0	1	0	0	0	3172	372	13	2	3847	2	CDON	11	125893349	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	2924822	125893349	9113167	289	49705										
GLB1L2	89944	hgsc.bcm.edu	37	chr11	134217281	134217281	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	caagggcttcaccgaagcagTggacctttattttgaccacc	9	12	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr11:134217281T>C	ENST00000535456.2	+	5	700	c.512T>C	c.(511-513)gTg>gCg	p.V171A	GLB1L2_ENST00000389881.3_Missense_Mutation_p.V171A|GLB1L2_ENST00000529077.1_3'UTR|GLB1L2_ENST00000339772.7_Missense_Mutation_p.V171A	NM_138342.3	NP_612351.2	Q8IW92	GLBL2_HUMAN	galactosidase, beta 1-like 2	171					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	beta-galactosidase activity (GO:0004565)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	41	all_hematologic(175;0.127)	all_cancers(12;2.85e-18)|all_epithelial(12;1.21e-12)|all_lung(97;0.000276)|Lung NSC(97;0.000518)|Breast(109;0.00122)|Medulloblastoma(222;0.0399)|all_neural(223;0.0412)|Esophageal squamous(93;0.0844)		Epithelial(10;1.37e-11)|all cancers(11;2.2e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000885)|Lung(977;0.223)		ACCGAAGCAGTGGACCTTTAT	0.512																																					p.V171A		Atlas-SNP	.											.	GLB1L2	79	.	0			c.T512C						.						268	262	264					11																	134217281		2201	4297	6498	SO:0001583	missense	89944	exon5			AAGCAGTGGACCT		CCDS31724.1	11q25	2008-01-29			ENSG00000149328	ENSG00000149328			25129	protein-coding gene	gene with protein product						12975309	Standard	NM_138342		Approved		uc001qhp.3	Q8IW92	OTTHUMG00000167179	ENST00000535456.2:c.512T>C	chr11.hg19:g.134217281T>C	ENSP00000444628:p.Val171Ala	102.0	0.0		106.0	19.0	NM_138342	A6NCE6|Q6UX60|Q8NC62|Q8NCB3|Q8NCJ1|Q96HP3	Missense_Mutation	SNP	ENST00000535456.2	hg19	CCDS31724.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.569730	0.86439	.	.	ENSG00000149328	ENST00000339772;ENST00000535456;ENST00000389881	D;D;D	0.98135	-4.74;-4.74;-4.74	5.93	4.81	0.61882	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.205952	0.41605	D	0.000860	D	0.97929	0.9319	M	0.76938	2.355	0.50467	D	0.999878	P	0.50156	0.932	P	0.55087	0.768	D	0.97510	1.0066	10	0.59425	D	0.04	-19.0472	11.7315	0.51739	0.0:0.0684:0.0:0.9316	.	171	Q8IW92	GLBL2_HUMAN	A	171	ENSP00000344659:V171A;ENSP00000444628:V171A;ENSP00000374531:V171A	ENSP00000344659:V171A	V	+	2	0	GLB1L2	133722491	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	3.891000	0.56227	1.071000	0.40834	0.533000	0.62120	GTG	.	.		0.512	GLB1L2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393629.2	NM_138342		C	134217281	T	C	134217281	3	2	352	1	0	0	0	0	1	0	0	0	6437	1696	59	2	530	2	GLB1L2	11	134217281	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	8323932	134217281	789235	290	49706										
B4GALNT3	283358	hgsc.bcm.edu	37	chr12	668587	668587	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agactgggagctgctggacaGgtgactgggaagaggagggc	20	6	0	3			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr12:668587G>A	ENST00000266383.5	+	19	2901	c.2888G>A	c.(2887-2889)aGg>aAg	p.R963K		NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	963					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			CTGCTGGACAGGTGACTGGGA	0.637																																					p.R963K		Atlas-SNP	.											.	B4GALNT3	64	.	0			c.G2888A						.						68	71	70					12																	668587		2203	4300	6503	SO:0001630	splice_region_variant	283358	exon19			TGGACAGGTGACT	AB089940	CCDS8504.1	12p13.33	2013-02-19			ENSG00000139044	ENSG00000139044	2.4.1.-	"Beta 4-glycosyltransferases"	24137	protein-coding gene	gene with protein product		612220				12966086	Standard	NM_173593		Approved	B4GalNac-T3, FLJ16224, FLJ40362	uc001qii.1	Q6L9W6	OTTHUMG00000129283	ENST00000266383.5:c.2888+1G>A	chr12.hg19:g.668587G>A		122.0	0.0		148.0	17.0	NM_173593	Q6ZNC1|Q8N7T6	Missense_Mutation	SNP	ENST00000266383.5	hg19	CCDS8504.1	.	.	.	.	.	.	.	.	.	.	G	36	5.748106	0.96882	.	.	ENSG00000139044	ENST00000266383	T	0.56103	0.48	4.83	4.83	0.62350	.	0.046006	0.85682	N	0.000000	T	0.70448	0.3225	M	0.62266	1.93	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.70461	-0.4865	10	0.42905	T	0.14	-23.5802	18.2881	0.90120	0.0:0.0:1.0:0.0	.	963	Q6L9W6	B4GN3_HUMAN	K	963	ENSP00000266383:R963K	ENSP00000266383:R963K	R	+	2	0	B4GALNT3	538848	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	9.745000	0.98856	2.383000	0.81215	0.462000	0.41574	AGG	.	.		0.637	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593	Missense_Mutation	A	668587	G	A	668587	5	1	352	1	0	0	0	0	0	0	1	0	1268	1014	35	3	2962	3	B4GALNT3	12	668587	Splice_Site	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10		668587	133183308	291	49707										
CACNA1C	775	hgsc.bcm.edu	37	chr12	2719737	2719737	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tggaatacgccctcaaggccCggcccctgcggaggtacatc	12	15	1	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr12:2719737C>T	ENST00000347598.4	+	29	3649	c.3649C>T	c.(3649-3651)Cgg>Tgg	p.R1217W	CACNA1C_ENST00000399621.1_Missense_Mutation_p.R1197W|CACNA1C_ENST00000399597.1_Missense_Mutation_p.R1197W|CACNA1C_ENST00000399638.1_Missense_Mutation_p.R1197W|CACNA1C_ENST00000399606.1_Missense_Mutation_p.R1217W|CACNA1C_ENST00000335762.5_Missense_Mutation_p.R1222W|CACNA1C_ENST00000399603.1_Missense_Mutation_p.R1197W|CACNA1C_ENST00000399649.1_Missense_Mutation_p.R1197W|CACNA1C_ENST00000327702.7_Missense_Mutation_p.R1197W|CACNA1C_ENST00000399637.1_Missense_Mutation_p.R1197W|CACNA1C_ENST00000399629.1_Missense_Mutation_p.R1197W|CACNA1C_ENST00000399595.1_Missense_Mutation_p.R1197W|CACNA1C_ENST00000399641.1_Missense_Mutation_p.R1197W|CACNA1C_ENST00000399591.1_Missense_Mutation_p.R1197W|CACNA1C_ENST00000406454.3_Missense_Mutation_p.R1197W|CACNA1C_ENST00000344100.3_Missense_Mutation_p.R1197W|CACNA1C_ENST00000399601.1_Missense_Mutation_p.R1197W|CACNA1C_ENST00000399644.1_Missense_Mutation_p.R1197W|CACNA1C_ENST00000402845.3_Missense_Mutation_p.R1197W|CACNA1C_ENST00000480911.1_Missense_Mutation_p.R1197W|CACNA1C_ENST00000399617.1_Missense_Mutation_p.R1197W|CACNA1C_ENST00000399655.1_Missense_Mutation_p.R1197W|CACNA1C_ENST00000399634.1_Missense_Mutation_p.R1197W	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	1217					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CCTCAAGGCCCGGCCCCTGCG	0.592																																					p.R1217W		Atlas-SNP	.											.	CACNA1C	1023	.	0			c.C3649T						.						90	98	95					12																	2719737		2125	4259	6384	SO:0001583	missense	775	exon29			AAGGCCCGGCCCC	AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.3649C>T	chr12.hg19:g.2719737C>T	ENSP00000266376:p.Arg1217Trp	106.0	0.0		151.0	61.0	NM_199460	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Missense_Mutation	SNP	ENST00000347598.4	hg19	CCDS44788.1	.	.	.	.	.	.	.	.	.	.	C	34	5.318408	0.95682	.	.	ENSG00000151067	ENST00000335762;ENST00000399655;ENST00000480911;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595;ENST00000322367	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.96716	-4.05;-4.05;-4.08;-4.05;-4.04;-4.04;-4.06;-3.97;-4.0;-4.05;-3.98;-3.98;-4.06;-4.1;-3.97;-3.89;-4.09;-4.06;-4.05;-4.08;-3.99;-4.06;-4.1	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	D	0.98375	0.9460	M	0.87682	2.9	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.91635	0.997;0.997;0.987;0.997;0.997;0.997;0.999;0.994;0.994;0.997;0.996;0.992;0.998;0.993;0.996;0.995;0.998;0.999;0.998;0.997;0.999;0.999;0.997;0.992;0.996	D	0.99274	1.0894	10	0.87932	D	0	.	19.1876	0.93649	0.0:1.0:0.0:0.0	.	1197;1194;1217;1197;1197;1197;1197;1197;1197;1217;1197;1168;1217;1197;1197;1197;1197;1197;1197;1197;1197;1197;1197;1197;1197	Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-23;Q13936-28;Q13936-11;E9PDJ1;E9PDJ0;F5GY28;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;F5H638;Q13936-12	.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	W	1222;1197;1197;1197;1197;1197;1197;1197;1197;1197;1217;1217;1197;1197;1197;1197;1197;1197;1197;1197;1197;1197;1197;1038	ENSP00000336982:R1222W;ENSP00000382563:R1197W;ENSP00000437936:R1197W;ENSP00000382552:R1197W;ENSP00000382547:R1197W;ENSP00000382506:R1197W;ENSP00000382530:R1197W;ENSP00000382546:R1197W;ENSP00000382500:R1197W;ENSP00000382549:R1197W;ENSP00000266376:R1217W;ENSP00000382515:R1217W;ENSP00000382510:R1197W;ENSP00000341092:R1197W;ENSP00000382537:R1197W;ENSP00000329877:R1197W;ENSP00000382557:R1197W;ENSP00000385724:R1197W;ENSP00000382512:R1197W;ENSP00000382542:R1197W;ENSP00000382526:R1197W;ENSP00000385896:R1197W;ENSP00000382504:R1197W	ENSP00000323129:R1038W	R	+	1	2	CACNA1C	2589998	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.995000	0.70631	2.610000	0.88304	0.655000	0.94253	CGG	.	.		0.592	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719		T	2719737	C	T	2719737	3	4	352	1	0	0	0	0	1	0	0	0	2542	643	23	1	3871	1	CACNA1C	12	2719737	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	2051150	2719737	131132158	292	49708										
PHC1	1911	hgsc.bcm.edu	37	chr12	9087824	9087824	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggccctttgggagtggacagCccatctgctggtgagcattt	14	10	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr12:9087824C>T	ENST00000543824.1	+	12	2690	c.2358C>T	c.(2356-2358)agC>agT	p.S786S	PHC1_ENST00000536844.1_Silent_p.S392S|PHC1_ENST00000433083.2_Silent_p.S741S|PHC1_ENST00000544916.1_Silent_p.S786S			P78364	PHC1_HUMAN	polyhomeotic homolog 1 (Drosophila)	786					cellular response to retinoic acid (GO:0071300)|histone ubiquitination (GO:0016574)|multicellular organismal development (GO:0007275)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|large_intestine(8)|liver(2)|lung(3)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	27						GAGTGGACAGCCCATCTGCTG	0.483																																					p.S786S		Atlas-SNP	.											.	PHC1	67	.	0			c.C2358T						.						38	36	37					12																	9087824		2203	4300	6503	SO:0001819	synonymous_variant	1911	exon11			GGACAGCCCATCT	U89277	CCDS8597.1	12p13	2013-01-10	2006-09-12	2002-11-15	ENSG00000111752	ENSG00000111752		"Sterile alpha motif (SAM) domain containing"	3182	protein-coding gene	gene with protein product		602978	"early development regulator 1 (homolog of polyhomeotic 1)", "polyhomeotic-like 1 (Drosophila)"	EDR1		9121482	Standard	XM_005253334		Approved	HPH1, RAE28	uc001qvd.3	P78364	OTTHUMG00000168275	ENST00000543824.1:c.2358C>T	chr12.hg19:g.9087824C>T		53.0	0.0		46.0	8.0	NM_004426	D3DUV4|Q8WVM3|Q9BU63	Silent	SNP	ENST00000543824.1	hg19	CCDS8597.1																																																																																			.	.		0.483	PHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399115.1	NM_004426		T	9087824	C	T	9087824	2	4	352	1	0	0	0	0	0	0	0	1	11825	738	26	3		3	PHC1	12	9087824	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	6368087	9087824	124764071	293	49709										
GYS2	2998	hgsc.bcm.edu	37	chr12	21693401	21693401	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ctctcagttctgttcctctgGataatcctttggcggcgtga	10	11	3	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr12:21693401G>T	ENST00000261195.2	-	14	2006	c.1752C>A	c.(1750-1752)atC>atA	p.I584I		NM_021957.3	NP_068776.2	P54840	GYS2_HUMAN	glycogen synthase 2 (liver)	584					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|ectoplasm (GO:0043265)	glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein homodimerization activity (GO:0042803)			NS(1)|breast(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(14)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						TGTTCCTCTGGATAATCCTTT	0.433																																					p.I584I	Colon(149;9 1820 3690 10544 50424)	Atlas-SNP	.											.	GYS2	110	.	0			c.C1752A						.						164	168	167					12																	21693401		2203	4300	6503	SO:0001819	synonymous_variant	2998	exon14			CCTCTGGATAATC		CCDS8690.1	12p12.2-p11.2	2013-02-22			ENSG00000111713	ENSG00000111713	2.4.1.11	"Glycosyltransferase group 1 domain containing"	4707	protein-coding gene	gene with protein product		138571					Standard	NM_021957		Approved		uc001rfb.3	P54840	OTTHUMG00000169135	ENST00000261195.2:c.1752C>A	chr12.hg19:g.21693401G>T		128.0	0.0		119.0	22.0	NM_021957	A0AVD8	Silent	SNP	ENST00000261195.2	hg19	CCDS8690.1																																																																																			.	.		0.433	GYS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402396.1	NM_021957		T	21693401	G	T	21693401	2	4	352	1	0	0	0	0	0	0	0	1	6922	1164	41	3		3	GYS2	12	21693401	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	12605577	21693401	112158494	294	49710										
ABCC9	10060	hgsc.bcm.edu	37	chr12	21960410	21960410	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ccccaccttcagtgacaaccGcatctaaatcagagaaagaa	6	13	3	3			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr12:21960410G>A	ENST00000261201.4	-	36	4318	c.4319C>T	c.(4318-4320)gCg>gTg	p.A1440V	ABCC9_ENST00000345162.2_Missense_Mutation_p.A1404V|ABCC9_ENST00000261200.4_Missense_Mutation_p.A1440V	NM_005691.2	NP_005682.2	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	1440	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				defense response to virus (GO:0051607)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	ATP-sensitive potassium channel complex (GO:0008282)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcomere (GO:0030017)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|sulfonylurea receptor activity (GO:0008281)|transporter activity (GO:0005215)	p.A1440G(2)		NS(2)|breast(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|lung(56)|ovary(4)|pancreas(1)|prostate(4)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(5)	118					Adenosine triphosphate(DB00171)|Glyburide(DB01016)	AGTGACAACCGCATCTAAATC	0.398																																					p.A1440V		Atlas-SNP	.											ABCC9_ENST00000261201,NS,carcinoma,0,4	ABCC9	411	.	2	Substitution - Missense(2)	lung(2)	c.C4319T						.						96	87	90					12																	21960410		2203	4300	6503	SO:0001583	missense	10060	exon36			ACAACCGCATCTA	AF061323	CCDS8693.1, CCDS8694.1	12p12.1	2014-09-17			ENSG00000069431	ENSG00000069431		"ATP binding cassette transporters / subfamily C"	60	protein-coding gene	gene with protein product	"sulfonylurea receptor 2"	601439				9457174, 15034580	Standard	NM_020297		Approved	SUR2, CMD1O	uc001rfh.3	O60706	OTTHUMG00000169094	ENST00000261201.4:c.4319C>T	chr12.hg19:g.21960410G>A	ENSP00000261201:p.Ala1440Val	77.0	0.0		101.0	47.0	NM_005691	O60707	Missense_Mutation	SNP	ENST00000261201.4	hg19	CCDS8694.1	.	.	.	.	.	.	.	.	.	.	G	19.75	3.886336	0.72410	.	.	ENSG00000069431	ENST00000261200;ENST00000544039;ENST00000261201;ENST00000345162	D;D;D;D	0.93859	-3.3;-3.3;-3.3;-3.3	5.02	5.02	0.67125	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.055041	0.64402	D	0.000001	D	0.92841	0.7723	N	0.21508	0.67	0.80722	D	1	D;D	0.69078	0.991;0.997	P;P	0.62184	0.77;0.899	D	0.90464	0.4448	10	0.17832	T	0.49	-15.5615	18.5246	0.90967	0.0:0.0:1.0:0.0	.	1440;1440	O60706;O60706-2	ABCC9_HUMAN;.	V	1440;1067;1440;1404	ENSP00000261200:A1440V;ENSP00000440521:A1067V;ENSP00000261201:A1440V;ENSP00000261202:A1404V	ENSP00000261200:A1440V	A	-	2	0	ABCC9	21851677	1.000000	0.71417	0.958000	0.39756	0.982000	0.71751	9.504000	0.97986	2.585000	0.87301	0.561000	0.74099	GCG	.	.		0.398	ABCC9-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402230.1	NM_005691		A	21960410	G	A	21960410	3	1	352	1	0	0	0	0	1	0	0	0	59	1087	38	1	484	1	ABCC9	12	21960410	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	267009	21960410	111891485	295	49711										
KLHDC5	57542	hgsc.bcm.edu	37	chr12	27933999	27933999	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	acctggtcaatgtcaggggcTatgggtctgccatcctggac	13	11	3	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr12:27933999T>C	ENST00000381271.2	+	1	1047	c.736T>C	c.(736-738)Tat>Cat	p.Y246H	RP11-860B13.1_ENST00000545904.1_RNA	NM_020782.1	NP_065833.1	Q9P2K6	KLH42_HUMAN	kelch-like family member 42	246					mitotic nuclear division (GO:0007067)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of microtubule-based process (GO:0032886)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											TGTCAGGGGCTATGGGTCTGC	0.597																																					p.Y246H		Atlas-SNP	.											.	.	.	.	0			c.T736C						.						73	56	62					12																	27933999		2203	4300	6503	SO:0001583	missense	57542	exon1			AGGGGCTATGGGT	AB037761	CCDS31763.1	12p11.22	2013-04-24	2013-02-22	2013-01-30	ENSG00000087448	ENSG00000087448		"Kelch-like"	29252	protein-coding gene	gene with protein product			"kelch domain containing 5"	KLHDC5		19261606	Standard	NM_020782		Approved	KIAA1340, Ctb9	uc001rij.3	Q9P2K6	OTTHUMG00000169217	ENST00000381271.2:c.736T>C	chr12.hg19:g.27933999T>C	ENSP00000370671:p.Tyr246His	90.0	0.0		93.0	17.0	NM_020782	Q2VPK1|Q8N334	Missense_Mutation	SNP	ENST00000381271.2	hg19	CCDS31763.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	22.0|22.0	4.228854|4.228854	0.79576|0.79576	.|.	.|.	ENSG00000087448|ENSG00000087448	ENST00000543254|ENST00000381271	.|T	.|0.61274	.|0.12	5.25|5.25	4.03|4.03	0.46877|0.46877	.|Kelch-type beta propeller (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.49133|0.49133	0.1539|0.1539	N|N	0.04090|0.04090	-0.28|-0.28	0.49687|0.49687	D|D	0.999813|0.999813	.|D	.|0.76494	.|0.999	.|D	.|0.75020	.|0.985	T|T	0.43750|0.43750	-0.9372|-0.9372	5|10	.|0.16420	.|T	.|0.52	.|.	10.3918|10.3918	0.44175|0.44175	0.1462:0.0:0.0:0.8538|0.1462:0.0:0.0:0.8538	.|.	.|246	.|Q9P2K6	.|KLDC5_HUMAN	P|H	67|246	.|ENSP00000370671:Y246H	.|ENSP00000370671:Y246H	L|Y	+|+	2|1	0|0	KLHDC5|KLHDC5	27825266|27825266	1.000000|1.000000	0.71417|0.71417	0.873000|0.873000	0.34254|0.34254	0.982000|0.982000	0.71751|0.71751	4.871000|4.871000	0.63042|0.63042	1.995000|1.995000	0.58328|0.58328	0.477000|0.477000	0.44152|0.44152	CTA|TAT	.	.		0.597	KLHL42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402904.1	NM_020782		C	27933999	T	C	27933999	3	2	352	1	0	0	0	0	1	0	0	0	8368	1522	53	2	738	2	KLHDC5	12	27933999	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	5973589	27933999	105917896	296	49712										
FMNL3	91010	hgsc.bcm.edu	37	chr12	50042064	50042064	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggacgctgttgtcatggatgCtgcactcacgccgaatcagc	12	12	3	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr12:50042064C>G	ENST00000293590.5	-	22	2821	c.2588G>C	c.(2587-2589)aGc>aCc	p.S863T	FMNL3_ENST00000352151.5_Missense_Mutation_p.S812T|FMNL3_ENST00000335154.5_Missense_Mutation_p.S863T|FMNL3_ENST00000550488.1_Missense_Mutation_p.S863T			Q8IVF7	FMNL3_HUMAN	formin-like 3	863	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)|cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)	GTPase activating protein binding (GO:0032794)			breast(4)|endometrium(7)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(2)|stomach(1)	39						GTCATGGATGCTGCACTCACG	0.597																																					p.S863T		Atlas-SNP	.											.	FMNL3	137	.	0			c.G2588C						.						97	102	101					12																	50042064		2156	4256	6412	SO:0001583	missense	91010	exon22			TGGATGCTGCACT	AK128195	CCDS41780.1, CCDS44874.1	12q13.12	2006-04-10							23698	protein-coding gene	gene with protein product						12684686	Standard	NM_198900		Approved	DKFZp762B245, MGC45819, WBP3	uc001ruv.1	Q8IVF7	OTTHUMG00000169651	ENST00000293590.5:c.2588G>C	chr12.hg19:g.50042064C>G	ENSP00000293590:p.Ser863Thr	70.0	0.0		87.0	12.0	NM_175736	B0JZA7|Q6ZRJ1	Missense_Mutation	SNP	ENST00000293590.5	hg19		.	.	.	.	.	.	.	.	.	.	C	10.57	1.386580	0.25031	.	.	ENSG00000161791	ENST00000335154;ENST00000550488;ENST00000352151;ENST00000293590	T;T;T;T	0.17054	2.3;2.3;2.3;2.3	4.79	4.79	0.61399	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.193529	0.52532	D	0.000067	T	0.12433	0.0302	N	0.20445	0.575	0.46167	D	0.998907	B;B;B	0.29085	0.041;0.232;0.157	B;B;B	0.33521	0.036;0.147;0.165	T	0.10497	-1.0627	10	0.37606	T	0.19	.	10.6975	0.45907	0.0:0.9109:0.0:0.0891	.	812;863;863	Q8IVF7-2;Q8IVF7-3;Q8IVF7	.;.;FMNL3_HUMAN	T	863;863;812;863	ENSP00000335655:S863T;ENSP00000447479:S863T;ENSP00000344311:S812T;ENSP00000293590:S863T	ENSP00000293590:S863T	S	-	2	0	FMNL3	48328331	0.844000	0.29557	0.980000	0.43619	0.921000	0.55340	0.941000	0.29005	2.655000	0.90218	0.655000	0.94253	AGC	.	.		0.597	FMNL3-201	KNOWN	basic	protein_coding	protein_coding		NM_175736		G	50042064	C	G	50042064	3	3	352	1	0	0	0	0	1	0	0	0	5961	797	28	4	515	4	FMNL3	12	50042064	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	22108065	50042064	83809831	297	49713										
KRT79	338785	hgsc.bcm.edu	37	chr12	53227586	53227586	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	accttgtcgatgaaggaggcGaacttgttgttgagggtctt	14	6	1	2	rs376301539		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr12:53227586G>A	ENST00000330553.5	-	1	493	c.459C>T	c.(457-459)ttC>ttT	p.F153F		NM_175834.2	NP_787028.1	Q5XKE5	K2C79_HUMAN	keratin 79	153	Coil 1A.|Rod.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	enzyme binding (GO:0019899)|structural molecule activity (GO:0005198)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						TGAAGGAGGCGAACTTGTTGT	0.607																																					p.F153F		Atlas-SNP	.											KRT79,bladder,carcinoma,0,1	KRT79	78	.	0			c.C459T						.	G		3,4403	6.2+/-15.9	0,3,2200	128	126	127		459	-8.5	0.4	12		127	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KRT79	NM_175834.2		0,4,6499	AA,AG,GG		0.0116,0.0681,0.0308		153/536	53227586	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	338785	exon1			GGAGGCGAACTTG	AJ564105	CCDS8839.1	12q13.13	2014-02-12	2007-07-03		ENSG00000185640	ENSG00000185640		"-", "Intermediate filaments type II, keratins (basic)"	28930	protein-coding gene	gene with protein product	"keratin 6-like"	611160				11683385	Standard	NM_175834		Approved	K6L, KRT6L	uc001sbb.3	Q5XKE5	OTTHUMG00000169878	ENST00000330553.5:c.459C>T	chr12.hg19:g.53227586G>A		95.0	0.0		91.0	22.0	NM_175834	Q6P465|Q7Z793	Silent	SNP	ENST00000330553.5	hg19	CCDS8839.1																																																																																			.	.		0.607	KRT79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406376.1	NM_175834		A	53227586	G	A	53227586	2	1	352	1	0	0	0	0	0	0	0	1	8501	1049	37	1		1	KRT79	12	53227586	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	3185522	53227586	80624309	298	49714										
LRP1	4035	hgsc.bcm.edu	37	chr12	57605934	57605934	+	Frame_Shift_Del	DEL	G	G	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agcaccaacggatgaccaacGgggccatgaacgtggagatt							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr12:57605934delG	ENST00000243077.3	+	88	13850	c.13384delG	c.(13384-13386)gggfs	p.G4462fs		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	4462	Interaction with MAFB. {ECO:0000250}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	GATGACCAACGGGGCCATGAA	0.547																																					p.N4461fs		Atlas-INDEL	.											.	LRP1	428	.	0			c.13383delC						.						87	86	86					12																	57605934		2203	4300	6503	SO:0001589	frameshift_variant	4035	exon88			.	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"CD molecules", "Low density lipoprotein receptors"	6692	protein-coding gene	gene with protein product		107770	"alpha-2-macroglobulin receptor"	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.13384delG	chr12.hg19:g.57605934delG	ENSP00000243077:p.Gly4462fs	181.0	0.0		152.0	17.0	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Frame_Shift_Del	DEL	ENST00000243077.3	hg19	CCDS8932.1																																																																																			.	.		0.547	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		-	57605934	G	-	57605934	7	5	352	1	0	1	0	1	0	0	0	0	8960	1116	39	0	13734	0	LRP1	12	57605934	Frame_Shift_Del	DEL	G	TCGA-WQ-A9G7-01A-11D-A36X-10	4378348	57605934	76245961	299	49715										
PTPRB	5787	hgsc.bcm.edu	37	chr12	70983909	70983909	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cacagaatcattgaagagtaGgatccgatactgctcccagt	9	10	1	3			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr12:70983909G>A	ENST00000261266.5	-	6	1260	c.1231C>T	c.(1231-1233)Cta>Tta	p.L411L	PTPRB_ENST00000451516.2_Intron|PTPRB_ENST00000550358.1_Silent_p.L629L|PTPRB_ENST00000538708.1_Silent_p.L411L|PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000334414.6_Silent_p.L629L|PTPRB_ENST00000550857.1_Intron|PTPRB_ENST00000551525.1_Silent_p.L628L	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	411	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			TTGAAGAGTAGGATCCGATAC	0.507											OREG0021990	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L629L		Atlas-SNP	.											.	PTPRB	676	.	0			c.C1885T						.						129	130	130					12																	70983909		2007	4194	6201	SO:0001819	synonymous_variant	5787	exon8			AGAGTAGGATCCG	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.1231C>T	chr12.hg19:g.70983909G>A		141.0	0.0	1126	146.0	14.0	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Silent	SNP	ENST00000261266.5	hg19	CCDS44944.1																																																																																			.	.		0.507	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1			A	70983909	G	A	70983909	2	1	352	1	0	0	0	0	0	0	0	1	12811	991	35	3		3	PTPRB	12	70983909	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	13377975	70983909	62867986	300	49716										
PTPRB	5787	hgsc.bcm.edu	37	chr12	70983921	70983921	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gaagagtaggatccgatactGctcccagtctccagcagggg	13	11	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr12:70983921G>A	ENST00000261266.5	-	6	1248	c.1219C>T	c.(1219-1221)Cag>Tag	p.Q407*	PTPRB_ENST00000451516.2_Intron|PTPRB_ENST00000550358.1_Nonsense_Mutation_p.Q625*|PTPRB_ENST00000538708.1_Nonsense_Mutation_p.Q407*|PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000334414.6_Nonsense_Mutation_p.Q625*|PTPRB_ENST00000550857.1_Intron|PTPRB_ENST00000551525.1_Nonsense_Mutation_p.Q624*	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	407	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			ATCCGATACTGCTCCCAGTCT	0.507											OREG0021990	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q625X		Atlas-SNP	.											.	PTPRB	676	.	0			c.C1873T						.						122	122	122					12																	70983921		1998	4193	6191	SO:0001587	stop_gained	5787	exon8			GATACTGCTCCCA	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.1219C>T	chr12.hg19:g.70983921G>A	ENSP00000261266:p.Gln407*	146.0	0.0	1126	148.0	13.0	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Nonsense_Mutation	SNP	ENST00000261266.5	hg19	CCDS44944.1	.	.	.	.	.	.	.	.	.	.	G	36	5.602099	0.96614	.	.	ENSG00000127329	ENST00000334414;ENST00000550358;ENST00000544694;ENST00000538708;ENST00000261266;ENST00000551525;ENST00000548122	.	.	.	5.63	2.76	0.32466	.	0.581795	0.18753	N	0.132136	.	.	.	.	.	.	0.30472	N	0.773229	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	.	7.2451	0.26117	0.1333:0.0:0.5032:0.3634	.	.	.	.	X	625;625;625;407;407;624;504	.	ENSP00000261266:Q407X	Q	-	1	0	PTPRB	69270188	0.439000	0.25610	0.976000	0.42696	0.976000	0.68499	1.263000	0.33004	0.709000	0.31976	0.655000	0.94253	CAG	.	.		0.507	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1			A	70983921	G	A	70983921	4	1	352	1	0	0	0	0	0	1	0	0	12811	1328	46	3	4882	3	PTPRB	12	70983921	Nonsense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	12	70983921	62867974	301	49717										
CAPS2	84698	hgsc.bcm.edu	37	chr12	75678791	75678791	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	catttcaccaataataccacGtttgaattctccataatcaa	2	11	3	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr12:75678791G>A	ENST00000409445.3	-	16	1718	c.1522C>T	c.(1522-1524)Cgt>Tgt	p.R508C	RP11-560G2.1_ENST00000549953.1_RNA|CAPS2_ENST00000442339.2_Missense_Mutation_p.R98C|CAPS2_ENST00000409004.1_5'UTR|CAPS2_ENST00000409799.1_Missense_Mutation_p.R426C|CAPS2_ENST00000393284.3_Missense_Mutation_p.R276C	NM_032606.3	NP_115995.2	Q9BXY5	CAYP2_HUMAN	calcyphosine 2	508	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)			endometrium(2)|large_intestine(1)|lung(4)|ovary(2)|skin(1)	10						ATAATACCACGTTTGAATTCT	0.313																																					p.R508C		Atlas-SNP	.											CAPS2_ENST00000409445,colon,carcinoma,0,2	CAPS2	96	.	0			c.C1522T						.						131	118	122					12																	75678791		2203	4300	6503	SO:0001583	missense	84698	exon16			TACCACGTTTGAA	AF251056	CCDS9008.2, CCDS66424.1, CCDS73497.1	12q14.1	2013-01-10	2005-05-09		ENSG00000180881	ENSG00000180881		"EF-hand domain containing"	16471	protein-coding gene	gene with protein product		607724	"calcyphosphine 2"			11846421	Standard	NM_032606		Approved		uc001sxk.4	Q9BXY5	OTTHUMG00000152787	ENST00000409445.3:c.1522C>T	chr12.hg19:g.75678791G>A	ENSP00000386959:p.Arg508Cys	53.0	0.0		79.0	16.0	NM_032606	Q6PH84|Q8N242|Q8NAY5	Missense_Mutation	SNP	ENST00000409445.3	hg19	CCDS9008.2	.	.	.	.	.	.	.	.	.	.	G	10.66	1.413460	0.25465	.	.	ENSG00000180881	ENST00000409799;ENST00000409445;ENST00000378703;ENST00000393284;ENST00000442339	T;T;T;T	0.71698	-0.59;-0.59;-0.59;-0.59	5.53	4.64	0.57946	EF-hand-like domain (1);	0.221670	0.38837	N	0.001548	T	0.66665	0.2812	M	0.71581	2.175	0.58432	D	0.999991	P;B;P;B;B	0.43412	0.456;0.084;0.806;0.394;0.211	B;B;B;B;B	0.34931	0.089;0.021;0.192;0.076;0.052	T	0.70292	-0.4912	10	0.44086	T	0.13	-6.2187	14.4315	0.67254	0.0707:0.0:0.9293:0.0	.	98;276;244;508;426	A2RRN2;Q9BXY5-2;Q9BXY5-3;Q9BXY5;B9A061	.;.;.;CAYP2_HUMAN;.	C	426;508;244;276;98	ENSP00000386977:R426C;ENSP00000386959:R508C;ENSP00000376963:R276C;ENSP00000389633:R98C	ENSP00000367975:R244C	R	-	1	0	CAPS2	73965058	0.987000	0.35691	0.958000	0.39756	0.027000	0.11550	3.983000	0.56916	1.471000	0.48121	0.650000	0.86243	CGT	.	.		0.313	CAPS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000327880.2			A	75678791	G	A	75678791	3	1	352	1	0	0	0	0	1	0	0	0	2640	1145	40	1	163	1	CAPS2	12	75678791	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	4694870	75678791	58173104	302	49718										
PLXNC1	10154	hgsc.bcm.edu	37	chr12	94543433	94543433	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cctcaagctgtgcgagggcgCgggcagcctgcacttcgtgg	16	13	1	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr12:94543433C>T	ENST00000258526.4	+	1	935	c.686C>T	c.(685-687)gCg>gTg	p.A229V		NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	229	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(12)|lung(30)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						TGCGAGGGCGCGGGCAGCCTG	0.692																																					p.A229V		Atlas-SNP	.											.	PLXNC1	135	.	0			c.C686T						.						25	30	28					12																	94543433		2160	4277	6437	SO:0001583	missense	10154	exon1			AGGGCGCGGGCAG	AF030339	CCDS9049.1	12q23	2009-04-17				ENSG00000136040		"CD molecules", "Plexins"	9106	protein-coding gene	gene with protein product		604259					Standard	NR_037687		Approved	VESPR, CD232	uc001tdc.3	O60486	OTTHUMG00000170235	ENST00000258526.4:c.686C>T	chr12.hg19:g.94543433C>T	ENSP00000258526:p.Ala229Val	86.0	0.0		109.0	16.0	NM_005761	Q59H25	Missense_Mutation	SNP	ENST00000258526.4	hg19	CCDS9049.1	.	.	.	.	.	.	.	.	.	.	C	11.70	1.717256	0.30413	.	.	ENSG00000136040	ENST00000258526	T	0.04454	3.62	5.04	0.625	0.17665	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (2);	1.228560	0.05696	N	0.593164	T	0.04724	0.0128	L	0.40543	1.245	0.31950	N	0.609752	B	0.14012	0.009	B	0.06405	0.002	T	0.38714	-0.9648	10	0.54805	T	0.06	.	1.6628	0.02796	0.2562:0.3207:0.2776:0.1455	.	229	O60486	PLXC1_HUMAN	V	229	ENSP00000258526:A229V	ENSP00000258526:A229V	A	+	2	0	PLXNC1	93067564	0.099000	0.21834	0.268000	0.24571	0.995000	0.86356	0.320000	0.19540	0.118000	0.18165	0.561000	0.74099	GCG	.	.		0.692	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2			T	94543433	C	T	94543433	3	4	352	1	0	0	0	0	1	0	0	0	12135	768	27	1	688	1	PLXNC1	12	94543433	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	18864642	94543433	39308462	303	49719										
USP44	84101	hgsc.bcm.edu	37	chr12	95927482	95927483	+	Frame_Shift_Ins	INS	-	-	T													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tacttctctttttactactaINSttttttcctgaaatggttct							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr12:95927482_95927483insT	ENST00000258499.3	-	2	838_839	c.550_551insA	c.(550-552)atafs	p.I184fs	USP44_ENST00000537435.2_Frame_Shift_Ins_p.I184fs|USP44_ENST00000552440.1_Frame_Shift_Ins_p.I184fs|USP44_ENST00000393091.2_Frame_Shift_Ins_p.I184fs	NM_001278393.1|NM_032147.2	NP_001265322.1|NP_115523.2	Q9H0E7	UBP44_HUMAN	ubiquitin specific peptidase 44	184					mitotic nuclear division (GO:0007067)|negative regulation of mitotic anaphase-promoting complex activity (GO:0060564)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein deubiquitination (GO:0016579)|regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266)|regulation of spindle checkpoint (GO:0090231)	nucleus (GO:0005634)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(5)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	36						TTTTACTACTATTTTTTCCTGA	0.356																																					p.I184fs		Atlas-INDEL	.											.	USP44	83	.	0			c.551_552insA						.																																			SO:0001589	frameshift_variant	84101	exon2			.	AK027434	CCDS9053.1	12q21.33	2005-08-08	2005-08-08			ENSG00000136014		"Ubiquitin-specific peptidases"	20064	protein-coding gene	gene with protein product		610993	"ubiquitin specific protease 44"			12838346	Standard	NM_001278393		Approved	FLJ14528	uc001teg.3	Q9H0E7		ENST00000258499.3:c.551dupA	chr12.hg19:g.95927488_95927488dupT	ENSP00000258499:p.Ile184fs	89.0	0.0		92.0	41.0	NM_032147	B2RDW3	Frame_Shift_Ins	INS	ENST00000258499.3	hg19	CCDS9053.1																																																																																			.	.		0.356	USP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408312.1	NM_032147		T	95927483	-	T	95927482	7	5	352	1	0	1	1	0	0	0	0	0	17090	449	16	0	1607	0	USP44	12	95927482	Frame_Shift_Ins	INS	-	TCGA-WQ-A9G7-01A-11D-A36X-10	1384049	95927482	37924413	304	49720										
MAPKAPK5	8550	hgsc.bcm.edu	37	chr12	112327908	112327908	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tggaagtataaccgggaatgCaaactcctaagagatactct	9	8	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr12:112327908C>T	ENST00000551404.2	+	13	1395	c.1287C>T	c.(1285-1287)tgC>tgT	p.C429C	MAPKAPK5_ENST00000550735.2_Silent_p.C427C			Q8IW41	MAPK5_HUMAN	mitogen-activated protein kinase-activated protein kinase 5	429					activation of MAPK activity (GO:0000187)|MAPK cascade (GO:0000165)|negative regulation of TOR signaling (GO:0032007)|protein autophosphorylation (GO:0046777)|Ras protein signal transduction (GO:0007265)|regulation of translation (GO:0006417)|signal transduction (GO:0007165)|stress-induced premature senescence (GO:0090400)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|lung(11)|ovary(1)	13						ACCGGGAATGCAAACTCCTAA	0.428																																					p.C429C		Atlas-SNP	.											.	MAPKAPK5	56	.	0			c.C1287T						.						66	64	65					12																	112327908		1896	4121	6017	SO:0001819	synonymous_variant	8550	exon13			GGAATGCAAACTC	AF032437	CCDS44975.1, CCDS44976.1	12q24.13	2012-05-30			ENSG00000089022	ENSG00000089022			6889	protein-coding gene	gene with protein product		606723				9628874	Standard	NM_003668		Approved	PRAK	uc001tta.4	Q8IW41	OTTHUMG00000169605	ENST00000551404.2:c.1287C>T	chr12.hg19:g.112327908C>T		105.0	0.0		102.0	22.0	NM_139078	B3KVA5|O60491|Q86X46|Q9BVX9|Q9UG86	Silent	SNP	ENST00000551404.2	hg19	CCDS44975.1																																																																																			.	.		0.428	MAPKAPK5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405019.2	NM_139078		T	112327908	C	T	112327908	2	4	352	1	0	0	0	0	0	0	0	1	9300	718	25	3		3	MAPKAPK5	12	112327908	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	16400426	112327908	21523987	305	49721										
C12orf51	283450	hgsc.bcm.edu	37	chr12	112613605	112613605	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	acgctacggatatcttgcctGgctcggtcaataacaaattt	8	10	2	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr12:112613605G>T	ENST00000430131.2	-	65	11408	c.10263C>A	c.(10261-10263)gcC>gcA	p.A3421A	HECTD4_ENST00000377560.5_Silent_p.A3671A|HECTD4_ENST00000550722.1_Silent_p.A3697A			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	3421					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										TATCTTGCCTGGCTCGGTCAA	0.502																																					p.A3709A		Atlas-SNP	.											.	.	.	.	0			c.C11127A						.						67	71	70					12																	112613605		1939	4134	6073	SO:0001819	synonymous_variant	283450	exon66			TTGCCTGGCTCGG	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 51"	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.10263C>A	chr12.hg19:g.112613605G>T		135.0	0.0		115.0	5.0	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Silent	SNP	ENST00000430131.2	hg19																																																																																				.	.		0.502	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		T	112613605	G	T	112613605	2	4	352	1	0	0	0	0	0	0	0	1	1698	1335	47	3		3	C12orf51	12	112613605	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	285697	112613605	21238290	306	49722										
DTX1	1840	hgsc.bcm.edu	37	chr12	113534661	113534661	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gatccaacctcacgggccacGgctacccggacgctagctac	10	17	1	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr12:113534661G>A	ENST00000257600.3	+	9	2283	c.1780G>A	c.(1780-1782)Ggc>Agc	p.G594S	DTX1_ENST00000547974.1_3'UTR	NM_004416.2	NP_004407.2	Q86Y01	DTX1_HUMAN	deltex 1, E3 ubiquitin ligase	594					cell surface receptor signaling pathway (GO:0007166)|glial cell differentiation (GO:0010001)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of T cell differentiation (GO:0045581)|Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)|regulation of Notch signaling pathway (GO:0008593)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Notch binding (GO:0005112)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	32						CACGGGCCACGGCTACCCGGA	0.627																																					p.G594S		Atlas-SNP	.											.	DTX1	83	.	0			c.G1780A						.						79	56	64					12																	113534661		2203	4300	6503	SO:0001583	missense	1840	exon9			GGCCACGGCTACC	AF053700	CCDS9164.1	12q24	2014-01-28	2014-01-28			ENSG00000135144			3060	protein-coding gene	gene with protein product		602582	"deltex homolog 1 (Drosophila)"			9590294, 12670957	Standard	NM_004416		Approved	hDx-1	uc001tuk.1	Q86Y01	OTTHUMG00000169610	ENST00000257600.3:c.1780G>A	chr12.hg19:g.113534661G>A	ENSP00000257600:p.Gly594Ser	66.0	0.0		48.0	10.0	NM_004416	O60630|Q9BS04	Missense_Mutation	SNP	ENST00000257600.3	hg19	CCDS9164.1	.	.	.	.	.	.	.	.	.	.	G	34	5.331477	0.95733	.	.	ENSG00000135144	ENST00000257600	T	0.49139	0.79	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	T	0.71392	0.3334	M	0.87097	2.86	0.80722	D	1	D	0.71674	0.998	D	0.64776	0.929	T	0.76372	-0.2983	10	0.51188	T	0.08	-0.4624	17.065	0.86556	0.0:0.0:1.0:0.0	.	594	Q86Y01	DTX1_HUMAN	S	594	ENSP00000257600:G594S	ENSP00000257600:G594S	G	+	1	0	DTX1	112019044	1.000000	0.71417	1.000000	0.80357	0.769000	0.43574	9.790000	0.99075	2.306000	0.77630	0.561000	0.74099	GGC	.	.		0.627	DTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405045.2			A	113534661	G	A	113534661	3	1	352	1	0	0	0	0	1	0	0	0	4795	1116	39	1	1814	1	DTX1	12	113534661	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	921056	113534661	20317234	307	49723										
RBM19	9904	hgsc.bcm.edu	37	chr12	114392958	114392958	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ctgtgacattgaacggggctCcccgcagcttcacggtgtgg	14	12	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr12:114392958C>A	ENST00000545145.2	-	7	977	c.899G>T	c.(898-900)gGa>gTa	p.G300V	RBM19_ENST00000392561.3_Missense_Mutation_p.G300V|RBM19_ENST00000261741.5_Missense_Mutation_p.G300V	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	300	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					GAACGGGGCTCCCCGCAGCTT	0.577																																					p.G300V		Atlas-SNP	.											.	RBM19	117	.	0			c.G899T						.						146	130	136					12																	114392958		2203	4300	6503	SO:0001583	missense	9904	exon7			GGGGCTCCCCGCA	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"RNA binding motif (RRM) containing"	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.899G>T	chr12.hg19:g.114392958C>A	ENSP00000442053:p.Gly300Val	93.0	0.0		72.0	9.0	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Missense_Mutation	SNP	ENST00000545145.2	hg19	CCDS9172.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.728349	0.89390	.	.	ENSG00000122965	ENST00000545145;ENST00000392561;ENST00000261741	T;T;T	0.12361	2.69;2.69;2.69	5.05	5.05	0.67936	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.000000	0.85682	D	0.000000	T	0.53318	0.1789	H	0.97186	3.955	0.80722	D	1	D	0.64830	0.994	D	0.73380	0.98	T	0.70995	-0.4720	10	0.62326	D	0.03	-12.6066	17.9972	0.89187	0.0:1.0:0.0:0.0	.	300	Q9Y4C8	RBM19_HUMAN	V	300	ENSP00000442053:G300V;ENSP00000376344:G300V;ENSP00000261741:G300V	ENSP00000261741:G300V	G	-	2	0	RBM19	112877341	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	7.141000	0.77330	2.353000	0.79882	0.655000	0.94253	GGA	.	.		0.577	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196		A	114392958	C	A	114392958	3	1	352	1	0	0	0	0	1	0	0	0	13136	855	30	3	2055	3	RBM19	12	114392958	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	858297	114392958	19458937	308	49724										
MLXIP	22877	hgsc.bcm.edu	37	chr12	122625584	122625584	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gaggagctgcaccggacggcGctctcctggctggaccagca	15	14	1	0	rs561027162	byFrequency	TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr12:122625584G>A	ENST00000319080.7	+	16	2724	c.2592G>A	c.(2590-2592)gcG>gcA	p.A864A	MLXIP_ENST00000538698.1_Silent_p.A471A					MLX interacting protein											NS(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)	20	all_neural(191;0.0837)|Medulloblastoma(191;0.163)	Lung NSC(355;0.0659)		OV - Ovarian serous cystadenocarcinoma(86;0.000599)|Epithelial(86;0.00102)|BRCA - Breast invasive adenocarcinoma(302;0.233)		ACCGGACGGCGCTCTCCTGGC	0.622													G|||	2	0.000399361	0	0	5008	,	,		18872	0.001		0.001	False		,,,				2504	0				p.A864A	Esophageal Squamous(105;787 1493 16200 18566 52466)	Atlas-SNP	.											.	MLXIP	46	.	0			c.G2592A						.						55	56	55					12																	122625584		2114	4222	6336	SO:0001819	synonymous_variant	22877	exon16			GACGGCGCTCTCC	AB020674	CCDS73540.1	12q21.31	2013-05-21				ENSG00000175727		"Basic helix-loop-helix proteins"	17055	protein-coding gene	gene with protein product		608090				10048485, 11073985	Standard	XM_006719290		Approved	MONDOA, KIAA0867, MIR, bHLHe36	uc001ubq.3	Q9HAP2		ENST00000319080.7:c.2592G>A	chr12.hg19:g.122625584G>A		47.0	0.0		41.0	20.0	NM_014938		Silent	SNP	ENST00000319080.7	hg19																																																																																				.	.		0.622	MLXIP-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401718.2	NM_014938		A	122625584	G	A	122625584	2	1	352	1	0	0	0	0	0	0	0	1	9645	1074	38	1		1	MLXIP	12	122625584	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	8232626	122625584	11226311	309	49725										
PITPNM2	57605	hgsc.bcm.edu	37	chr12	123481370	123481370	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gcctcctggtactggggggaGgaggtggccagcagggggag	22	8	0	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr12:123481370G>T	ENST00000542749.1	-	10	1623	c.1560C>A	c.(1558-1560)tcC>tcA	p.S520S	PITPNM2_ENST00000392428.1_Silent_p.S241S|PITPNM2_ENST00000280562.5_Silent_p.S520S|PITPNM2_ENST00000320201.4_Silent_p.S520S			Q9BZ72	PITM2_HUMAN	phosphatidylinositol transfer protein, membrane-associated 2	520					metabolic process (GO:0008152)|transport (GO:0006810)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)			NS(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	39	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.55e-05)|Epithelial(86;8.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.123)		ACTGGGGGGAGGAGGTGGCCA	0.627																																					p.S520S		Atlas-SNP	.											.	PITPNM2	105	.	0			c.C1560A						.						49	50	50					12																	123481370		2202	4300	6502	SO:0001819	synonymous_variant	57605	exon11			GGGGGAGGAGGTG	AF334585	CCDS9242.1, CCDS73543.1	12q24.31	2008-02-05				ENSG00000090975			21044	protein-coding gene	gene with protein product		608920				10022914	Standard	XM_005253582		Approved	RDGBA2, RDGB2, NIR3	uc001uej.1	Q9BZ72		ENST00000542749.1:c.1560C>A	chr12.hg19:g.123481370G>T		119.0	0.0		102.0	56.0	NM_020845	Q9P271	Silent	SNP	ENST00000542749.1	hg19	CCDS9242.1																																																																																			.	.		0.627	PITPNM2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401342.1	NM_020845		T	123481370	G	T	123481370	2	4	352	1	0	0	0	0	0	0	0	1	11960	987	35	3		3	PITPNM2	12	123481370	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	855786	123481370	10370525	310	49726										
TMEM132D	121256	hgsc.bcm.edu	37	chr12	130015679	130015679	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ttccagtataatccgtgcgcTccttgacatcccaaatggaa	7	12	0	1	rs540786652		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr12:130015679T>C	ENST00000422113.2	-	3	1366	c.1040A>G	c.(1039-1041)gAg>gGg	p.E347G		NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	347					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		ATCCGTGCGCTCCTTGACATC	0.532																																					p.E347G		Atlas-SNP	.											.	TMEM132D	299	.	0			c.A1040G						.						117	108	111					12																	130015679		2203	4300	6503	SO:0001583	missense	121256	exon3			GTGCGCTCCTTGA	AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 153"	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.1040A>G	chr12.hg19:g.130015679T>C	ENSP00000408581:p.Glu347Gly	84.0	0.0		103.0	5.0	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	hg19	CCDS9266.1	.	.	.	.	.	.	.	.	.	.	T	9.282	1.048383	0.19827	.	.	ENSG00000151952	ENST00000422113	T	0.13778	2.56	5.09	2.67	0.31697	.	0.244803	0.27682	N	0.018294	T	0.11665	0.0284	L	0.55481	1.735	0.09310	N	1	B	0.33238	0.403	B	0.30782	0.12	T	0.19582	-1.0301	9	.	.	.	-9.0924	6.6242	0.22820	0.0:0.079:0.1547:0.7663	.	347	Q14C87	T132D_HUMAN	G	347	ENSP00000408581:E347G	.	E	-	2	0	TMEM132D	128581632	0.095000	0.21747	0.003000	0.11579	0.092000	0.18411	1.729000	0.38115	0.263000	0.21812	0.533000	0.62120	GAG	.	.		0.532	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448		C	130015679	T	C	130015679	3	2	352	1	0	0	0	0	1	0	0	0	16062	1551	54	2	2287	2	TMEM132D	12	130015679	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	6534309	130015679	3836216	311	49727										
STX2	2054	hgsc.bcm.edu	37	chr12	131283121	131283121	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ttttttgtttcttctttagcGtgttctacatagtctgtggc	8	7	4	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr12:131283121G>A	ENST00000392373.2	-	9	829	c.735C>T	c.(733-735)caC>caT	p.H245H	STX2_ENST00000261653.6_Silent_p.H245H	NM_194356.2	NP_919337.1	P32856	STX2_HUMAN	syntaxin 2	245	t-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00202}.				acrosome reaction (GO:0007340)|cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|intracellular protein transport (GO:0006886)|organ morphogenesis (GO:0009887)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|signal transduction (GO:0007165)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)	calcium-dependent protein binding (GO:0048306)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)	16	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.79e-06)|all cancers(50;5.27e-05)|Epithelial(86;5.29e-05)		CTTCTTTAGCGTGTTCTACAT	0.333																																					p.H245H		Atlas-SNP	.											.	STX2	66	.	0			c.C735T						.						304	265	278					12																	131283121		2202	4299	6501	SO:0001819	synonymous_variant	2054	exon9			TTTAGCGTGTTCT	D14582	CCDS9269.1, CCDS9270.1	12q24	2008-02-05	2006-04-25	2006-04-25	ENSG00000111450	ENSG00000111450			3403	protein-coding gene	gene with protein product		132350	"epimorphin"	STX2B, STX2C, STX2A, EPIM		8938452, 15943887	Standard	NM_001980		Approved	EPM	uc001uio.4	P32856	OTTHUMG00000168365	ENST00000392373.2:c.735C>T	chr12.hg19:g.131283121G>A		67.0	0.0		75.0	7.0	NM_194356	Q86VW8	Silent	SNP	ENST00000392373.2	hg19	CCDS9270.1																																																																																			.	.		0.333	STX2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399455.2	NM_194356		A	131283121	G	A	131283121	2	1	352	1	0	0	0	0	0	0	0	1	15360	1136	40	1		1	STX2	12	131283121	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	1267442	131283121	2568774	312	49728										
ULK1	8408	hgsc.bcm.edu	37	chr12	132402065	132402066	+	Frame_Shift_Ins	INS	-	-	C													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ctcccccgagcgggagcacgINScccccccagggcccccgcac					rs376230231		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr12:132402065_132402066insC	ENST00000321867.4	+	22	2643_2644	c.2292_2293insC	c.(2293-2295)cccfs	p.P765fs	ULK1_ENST00000540647.1_5'Flank	NM_003565.2	NP_003556	O75385	ULK1_HUMAN	unc-51 like autophagy activating kinase 1	765					autophagic vacuole assembly (GO:0000045)|axon extension (GO:0048675)|cellular response to nutrient levels (GO:0031669)|cerebellar granule cell differentiation (GO:0021707)|negative regulation of collateral sprouting (GO:0048671)|neuron projection development (GO:0031175)|neuron projection regeneration (GO:0031102)|positive regulation of autophagy (GO:0010508)|positive regulation of macroautophagy (GO:0016239)|protein autophosphorylation (GO:0046777)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|radial glia guided migration of cerebellar granule cell (GO:0021933)|Ras protein signal transduction (GO:0007265)|receptor internalization (GO:0031623)|regulation of autophagy (GO:0010506)|regulation of neurotrophin TRK receptor signaling pathway (GO:0051386)|response to starvation (GO:0042594)	ATG1/UKL1 signaling complex (GO:0034273)|autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extrinsic component of autophagic vacuole membrane (GO:0097635)|extrinsic component of omegasome membrane (GO:0097629)|extrinsic component of pre-autophagosomal structure membrane (GO:0097632)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)	ATP binding (GO:0005524)|protein complex binding (GO:0032403)|protein serine/threonine kinase activity (GO:0004674)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	29	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07)		GCGGGAGCACGCCCCCCCAGGG	0.718																																					p.T764fs		Atlas-INDEL	.											.	ULK1	92	.	0			c.2292_2293insC						.																																			SO:0001589	frameshift_variant	8408	exon22			.	AF045458	CCDS9274.1	12q24.3	2014-02-12	2013-07-02		ENSG00000177169	ENSG00000177169			12558	protein-coding gene	gene with protein product	"ATG1 autophagy related 1 homolog (S. cerevisiae)"	603168	"unc-51 (C. elegans)-like kinase 1", "unc-51-like kinase 1 (C. elegans)"			9693035	Standard	NM_003565		Approved	ATG1, ATG1A	uc001uje.3	O75385	OTTHUMG00000168052	ENST00000321867.4:c.2299dupC	chr12.hg19:g.132402072_132402072dupC	ENSP00000324560:p.Pro765fs	215.0	0.0		222.0	40.0	NM_003565	Q9UQ28	Frame_Shift_Ins	INS	ENST00000321867.4	hg19	CCDS9274.1																																																																																			.	.		0.718	ULK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397769.3			C	132402066	-	C	132402065	7	5	352	1	0	1	1	0	0	0	0	0	16990	1074	38	0	2378	0	ULK1	12	132402065	Frame_Shift_Ins	INS	-	TCGA-WQ-A9G7-01A-11D-A36X-10	1118944	132402065	1449830	313	49729										
TPTE2	93492	hgsc.bcm.edu	37	chr13	20004677	20004677	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	actacttggacttttagatcAcatacatcacctgttccaac	4	12	2	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr13:20004677A>G	ENST00000400230.2	-	17	1277	c.1233T>C	c.(1231-1233)tgT>tgC	p.C411C	TPTE2_ENST00000255310.6_Silent_p.C334C|TPTE2_ENST00000457266.2_Silent_p.C300C|TPTE2_ENST00000390680.2_Silent_p.C334C|TPTE2_ENST00000400103.2_Silent_p.C300C|TPTE2_ENST00000382977.4_Silent_p.C411C|TPTE2_ENST00000382978.1_Silent_p.C371C|TPTE2_ENST00000382975.4_Silent_p.C371C			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	411	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		CTTTTAGATCACATACATCAC	0.318																																					p.C411C		Atlas-SNP	.											.	TPTE2	225	.	0			c.T1233C						.						64	57	60					13																	20004677		2202	4298	6500	SO:0001819	synonymous_variant	93492	exon18			TAGATCACATACA	AJ421032	CCDS9285.1, CCDS45013.1, CCDS45014.1	13q12.11	2012-12-10			ENSG00000132958	ENSG00000132958		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	17299	protein-coding gene	gene with protein product		606791				11716755, 12717346, 15057823	Standard	NM_130785		Approved	TPIP	uc001umd.3	Q6XPS3	OTTHUMG00000016493	ENST00000400230.2:c.1233T>C	chr13.hg19:g.20004677A>G		267.0	0.0		238.0	73.0	NM_199254	A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	Silent	SNP	ENST00000400230.2	hg19	CCDS45014.1																																																																																			.	.		0.318	TPTE2-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_199254		G	20004677	A	G	20004677	2	3	352	1	0	0	0	0	0	0	0	1	16446	157	6	2		2	TPTE2	13	20004677	Silent	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10		20004677	95165201	314	49730										
CENPJ	55835	hgsc.bcm.edu	37	chr13	25480425	25480425	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aaaatgatatttcatcagcaGcttgttctaaaaacaaaaat	4	6	3	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr13:25480425G>A	ENST00000381884.4	-	7	1936	c.1751C>T	c.(1750-1752)gCt>gTt	p.A584V	CENPJ_ENST00000545981.1_Missense_Mutation_p.A584V	NM_018451.4	NP_060921.3	Q9HC77	CENPJ_HUMAN	centromere protein J	584					cell division (GO:0051301)|centriole replication (GO:0007099)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|microtubule polymerization (GO:0046785)|mitotic cell cycle (GO:0000278)|regulation of centriole replication (GO:0046599)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|gamma-tubulin small complex (GO:0008275)|microtubule (GO:0005874)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|tubulin binding (GO:0015631)			endometrium(5)|kidney(4)|large_intestine(14)|lung(13)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.00793)|Epithelial(112;0.0411)|OV - Ovarian serous cystadenocarcinoma(117;0.139)		TTCATCAGCAGCTTGTTCTAA	0.358																																					p.A584V		Atlas-SNP	.											.	CENPJ	116	.	0			c.C1751T						.						49	55	53					13																	25480425		2203	4300	6503	SO:0001583	missense	55835	exon7			TCAGCAGCTTGTT	AF139625	CCDS9310.1	13q12.12	2013-11-05			ENSG00000151849	ENSG00000151849			17272	protein-coding gene	gene with protein product	"centrosomal P4.1-associated protein"	609279	"microcephaly, primary autosomal recessive 6"	MCPH6		11003675, 22699936	Standard	NM_018451		Approved	CPAP, BM032, LAP, LIP1, Sas-4, SASS4, SCKL4	uc001upt.5	Q9HC77	OTTHUMG00000016595	ENST00000381884.4:c.1751C>T	chr13.hg19:g.25480425G>A	ENSP00000371308:p.Ala584Val	95.0	0.0		86.0	28.0	NM_018451	Q2KHM6|Q5JPD5|Q5T6R5|Q96KS5|Q9C067	Missense_Mutation	SNP	ENST00000381884.4	hg19	CCDS9310.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.729922	0.89390	.	.	ENSG00000151849	ENST00000381884;ENST00000545981;ENST00000445729	T;T	0.70516	-0.49;0.04	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	D	0.85331	0.5672	M	0.78637	2.42	0.58432	D	0.999998	D	0.89917	1.0	D	0.87578	0.998	D	0.85703	0.1314	10	0.72032	D	0.01	.	19.3185	0.94226	0.0:0.0:1.0:0.0	.	584	Q9HC77	CENPJ_HUMAN	V	584	ENSP00000371308:A584V;ENSP00000441090:A584V	ENSP00000371308:A584V	A	-	2	0	CENPJ	24378425	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.983000	0.70540	2.850000	0.98022	0.650000	0.86243	GCT	.	.		0.358	CENPJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044209.1	NM_018451		A	25480425	G	A	25480425	3	1	352	1	0	0	0	0	1	0	0	0	3236	971	34	3	2309	3	CENPJ	13	25480425	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	5475748	25480425	89689453	315	49731										
DCLK1	9201	hgsc.bcm.edu	37	chr13	36700191	36700191	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tgcgtcgggctcggcaggccGttcacccgcgaccctcggct	14	17	1	0	rs373323934		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr13:36700191G>A	ENST00000360631.3	-	2	295	c.84C>T	c.(82-84)aaC>aaT	p.N28N	DCLK1_ENST00000379892.4_Silent_p.N28N|DCLK1_ENST00000255448.4_Silent_p.N28N			O15075	DCLK1_HUMAN	doublecortin-like kinase 1	28					axon extension (GO:0048675)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|forebrain development (GO:0030900)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)			breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(18)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(6)|urinary_tract(1)	64		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		TCGGCAGGCCGTTCACCCGCG	0.612																																					p.N28N		Atlas-SNP	.											DCLK1_ENST00000255448,colon,carcinoma,0,6	DCLK1	350	.	0			c.C84T						.	G		0,4406		0,0,2203	65	64	64		84	-3.9	1	13		64	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	DCLK1	NM_004734.4		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		28/730	36700191	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9201	exon2			CAGGCCGTTCACC	AB002367	CCDS9354.1, CCDS55895.1, CCDS73561.1	13q13.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000133083	ENSG00000133083			2700	protein-coding gene	gene with protein product		604742	"doublecortin and CaM kinase-like 1"	DCAMKL1		9747029, 10036192	Standard	NM_004734		Approved	KIAA0369, DCLK, DCDC3A	uc001uvf.3	O15075	OTTHUMG00000016729	ENST00000360631.3:c.84C>T	chr13.hg19:g.36700191G>A		48.0	0.0		63.0	18.0	NM_004734	B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1	Silent	SNP	ENST00000360631.3	hg19																																																																																				.	.		0.612	DCLK1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000044487.1	NM_004734		A	36700191	G	A	36700191	2	1	352	1	0	0	0	0	0	0	0	1	4293	1136	40	1		1	DCLK1	13	36700191	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	11219766	36700191	78469687	316	49732										
SOHLH2	54937	hgsc.bcm.edu	37	chr13	36765969	36765969	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aggaaaatatcccaggtgttCgctgtaggacctctgcaggg	13	9	1	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr13:36765969C>T	ENST00000379881.3	-	5	581	c.493G>A	c.(493-495)Gaa>Aaa	p.E165K	SOHLH2_ENST00000317764.6_Missense_Mutation_p.E165K|SOHLH2_ENST00000554962.1_Missense_Mutation_p.E242K|CCDC169-SOHLH2_ENST00000511166.1_Missense_Mutation_p.E242K	NM_017826.2	NP_060296.2	Q9NX45	SOLH2_HUMAN	spermatogenesis and oogenesis specific basic helix-loop-helix 2	165					multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;4.63e-08)|Epithelial(112;2.67e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00272)|BRCA - Breast invasive adenocarcinoma(63;0.00685)|GBM - Glioblastoma multiforme(144;0.0273)		CCCAGGTGTTCGCTGTAGGAC	0.378																																					p.E242K		Atlas-SNP	.											.	.	.	.	0			c.G724A						.						119	123	122					13																	36765969		2203	4300	6503	SO:0001583	missense	100526761	exon10			GGTGTTCGCTGTA	AK000456	CCDS9355.1, CCDS61309.1	13q13.3	2013-05-21			ENSG00000120669	ENSG00000120669		"Basic helix-loop-helix proteins"	26026	protein-coding gene	gene with protein product	"spermatogenesis associated 28"					12477932	Standard	NM_017826		Approved	FLJ20449, TEB1, bHLHe81, SPATA28		Q9NX45	OTTHUMG00000016728	ENST00000379881.3:c.493G>A	chr13.hg19:g.36765969C>T	ENSP00000369210:p.Glu165Lys	208.0	0.0		179.0	29.0	NM_001198910	B4DX90|Q5EGC3|Q8TC74|Q96QX4	Missense_Mutation	SNP	ENST00000379881.3	hg19	CCDS9355.1	.	.	.	.	.	.	.	.	.	.	c	16.25	3.070052	0.55539	.	.	ENSG00000120669;ENSG00000120669;ENSG00000120669;ENSG00000250709	ENST00000379881;ENST00000554962;ENST00000317764;ENST00000511166	T;T;T;T	0.50001	1.34;1.33;0.76;1.33	5.12	3.41	0.39046	.	0.329961	0.26345	N	0.024918	T	0.27384	0.0672	L	0.29908	0.895	0.09310	N	0.999997	P;P	0.43169	0.58;0.8	B;B	0.29077	0.098;0.098	T	0.18587	-1.0332	10	0.59425	D	0.04	0.7929	8.0186	0.30395	0.0:0.8168:0.0:0.1832	.	242;165	B4DX90;Q9NX45	.;SOLH2_HUMAN	K	165;242;165;242	ENSP00000369210:E165K;ENSP00000451542:E242K;ENSP00000326838:E165K;ENSP00000421868:E242K	ENSP00000421868:E242K	E	-	1	0	CCDC169-SOHLH2;SOHLH2	35663969	0.872000	0.30054	0.344000	0.25628	0.060000	0.15804	1.817000	0.39002	0.875000	0.35847	-0.213000	0.12676	GAA	.	.		0.378	SOHLH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044477.2	NM_017826		T	36765969	C	T	36765969	3	4	352	1	0	0	0	0	1	0	0	0	14939	893	31	1	812	1	SOHLH2	13	36765969	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	65778	36765969	78403909	317	49733										
TRIM13	10206	hgsc.bcm.edu	37	chr13	50586446	50586446	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gtgctactcgtggggagcacAccaaacatgtcttctgttct	10	11	3	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr13:50586446A>G	ENST00000378182.3	+	2	1108	c.370A>G	c.(370-372)Acc>Gcc	p.T124A	TRIM13_ENST00000478111.1_Intron|TRIM13_ENST00000420995.2_Missense_Mutation_p.T124A|KCNRG_ENST00000312942.1_5'Flank|KCNRG_ENST00000360473.4_5'Flank|TRIM13_ENST00000298772.5_Missense_Mutation_p.T127A|TRIM13_ENST00000356017.4_Missense_Mutation_p.T127A|TRIM13_ENST00000457662.2_Missense_Mutation_p.T124A	NM_001007278.1|NM_005798.3|NM_052811.2|NM_213590.1	NP_001007279.1|NP_005789.2|NP_434698.1|NP_998755.1	O60858	TRI13_HUMAN	tripartite motif containing 13	124					anatomical structure morphogenesis (GO:0009653)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|innate immune response (GO:0045087)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of cell death (GO:0010942)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of macroautophagy (GO:0016239)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|response to gamma radiation (GO:0010332)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|perinuclear endoplasmic reticulum (GO:0097038)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(5)|lung(2)|ovary(2)|upper_aerodigestive_tract(1)	10		Acute lymphoblastic leukemia(7;3.41e-06)|Lung NSC(96;3.08e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;1.53e-10)|COAD - Colon adenocarcinoma(199;0.205)		TGGGGAGCACACCAAACATGT	0.507																																					p.T127A		Atlas-SNP	.											.	TRIM13	30	.	0			c.A379G						.						141	128	132					13																	50586446		2203	4300	6503	SO:0001583	missense	10206	exon4			GAGCACACCAAAC	AF220127	CCDS9423.1, CCDS41888.1	13q14	2013-01-09	2011-01-25	2006-09-26	ENSG00000204977	ENSG00000204977		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	9976	protein-coding gene	gene with protein product		605661	"ret finger protein 2", "tripartite motif-containing 13"	RFP2		9599022	Standard	NM_213590		Approved	Leu5, RNF77, DLEU5	uc001vdp.1	O60858	OTTHUMG00000016926	ENST00000378182.3:c.370A>G	chr13.hg19:g.50586446A>G	ENSP00000367424:p.Thr124Ala	144.0	0.0		112.0	23.0	NM_001007278	B2RB49|Q5UBW0|Q5W0U8|Q5W0U9|Q9BQ47|Q9C021	Missense_Mutation	SNP	ENST00000378182.3	hg19	CCDS9423.1	.	.	.	.	.	.	.	.	.	.	A	11.44	1.640375	0.29157	.	.	ENSG00000204977	ENST00000442421;ENST00000378183;ENST00000420995;ENST00000378182;ENST00000356017;ENST00000457662;ENST00000298772	T;T;T;T;T;T;T	0.40225	1.04;1.04;1.04;1.04;1.04;1.04;1.04	5.4	4.22	0.49857	Zinc finger, B-box (3);	0.166402	0.51477	N	0.000081	T	0.28034	0.0691	N	0.19112	0.55	0.26035	N	0.981682	B;B	0.06786	0.001;0.001	B;B	0.09377	0.004;0.003	T	0.17623	-1.0363	10	0.48119	T	0.1	-1.196	10.9053	0.47076	0.9261:0.0:0.0739:0.0	.	124;127	O60858;O60858-3	TRI13_HUMAN;.	A	124;124;124;124;127;124;127	ENSP00000404586:T124A;ENSP00000367425:T124A;ENSP00000412943:T124A;ENSP00000367424:T124A;ENSP00000348299:T127A;ENSP00000399206:T124A;ENSP00000298772:T127A	ENSP00000298772:T127A	T	+	1	0	TRIM13	49484447	0.988000	0.35896	0.998000	0.56505	0.957000	0.61999	3.432000	0.52824	0.889000	0.36185	0.533000	0.62120	ACC	.	.		0.507	TRIM13-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354875.1	NM_001007278		G	50586446	A	G	50586446	3	3	352	1	0	0	0	0	1	0	0	0	16503	159	6	2	385	2	TRIM13	13	50586446	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	13820477	50586446	64583432	318	49734										
THSD1	55901	hgsc.bcm.edu	37	chr13	52952234	52952234	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ttgcctgtgacttgcggatcAgagtctggctggggcttatg	15	8	2	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr13:52952234A>G	ENST00000258613.4	-	5	2049	c.1871T>C	c.(1870-1872)cTg>cCg	p.L624P	THSD1_ENST00000544466.1_Missense_Mutation_p.L245P|THSD1_ENST00000349258.4_Missense_Mutation_p.L571P	NM_018676.3	NP_061146.1	Q9NS62	THSD1_HUMAN	thrombospondin, type I, domain containing 1	624					hematopoietic progenitor cell differentiation (GO:0002244)	cell periphery (GO:0071944)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Breast(56;0.000207)|Lung NSC(96;0.00145)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.8e-08)		CTTGCGGATCAGAGTCTGGCT	0.617																																					p.L624P		Atlas-SNP	.											.	THSD1	89	.	0			c.T1871C						.						49	48	49					13																	52952234		2203	4300	6503	SO:0001583	missense	55901	exon5			CGGATCAGAGTCT	AK096289	CCDS9432.1, CCDS9433.1	13q14.13	2010-04-20	2004-03-11		ENSG00000136114	ENSG00000136114			17754	protein-coding gene	gene with protein product			"thrombospondin, type I, domain 1"				Standard	NM_018676		Approved	TMTSP	uc001vgo.3	Q9NS62	OTTHUMG00000016963	ENST00000258613.4:c.1871T>C	chr13.hg19:g.52952234A>G	ENSP00000258613:p.Leu624Pro	68.0	0.0		43.0	18.0	NM_018676	A2A3J3|B2RCF5|Q6P3U1|Q6UXZ2	Missense_Mutation	SNP	ENST00000258613.4	hg19	CCDS9432.1	.	.	.	.	.	.	.	.	.	.	A	15.04	2.715188	0.48622	.	.	ENSG00000136114	ENST00000349258;ENST00000544466;ENST00000258613	T;T;T	0.36340	1.98;1.26;2.16	5.34	5.34	0.76211	.	0.294110	0.28262	N	0.015981	T	0.54398	0.1856	L	0.53249	1.67	0.40322	D	0.978834	D;D	0.76494	0.988;0.999	P;D	0.68192	0.885;0.956	T	0.59037	-0.7529	10	0.87932	D	0	-7.7746	14.5637	0.68159	1.0:0.0:0.0:0.0	.	571;624	Q9NS62-2;Q9NS62	.;THSD1_HUMAN	P	571;245;624	ENSP00000340650:L571P;ENSP00000438512:L245P;ENSP00000258613:L624P	ENSP00000258613:L624P	L	-	2	0	THSD1	51850235	0.907000	0.30839	0.075000	0.20258	0.554000	0.35429	3.938000	0.56583	2.030000	0.59900	0.451000	0.29950	CTG	.	.		0.617	THSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045058.3			G	52952234	A	G	52952234	3	3	352	1	0	0	0	0	1	0	0	0	15892	188	7	2	691	2	THSD1	13	52952234	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	2365788	52952234	62217644	319	49735										
KLF12	11278	hgsc.bcm.edu	37	chr13	74289619	74289619	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggagtctggggattcagaccGtctctggcgtcttgtgctct	14	10	5	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr13:74289619G>A	ENST00000377669.2	-	6	939	c.913C>T	c.(913-915)Cgg>Tgg	p.R305W	KLF12_ENST00000377666.4_Missense_Mutation_p.R305W	NM_007249.4	NP_009180.3	Q9Y4X4	KLF12_HUMAN	Kruppel-like factor 12	305					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	16		Prostate(6;0.00217)|Breast(118;0.0838)		GBM - Glioblastoma multiforme(99;0.00677)		GATTCAGACCGTCTCTGGCGT	0.463																																					p.R305W		Atlas-SNP	.											.	KLF12	42	.	0			c.C913T						.						142	127	132					13																	74289619		2203	4300	6503	SO:0001583	missense	11278	exon7			CAGACCGTCTCTG	AJ243274	CCDS9449.1	13q22	2013-01-08			ENSG00000118922	ENSG00000118922		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	6346	protein-coding gene	gene with protein product	"KLF12 zinc finger transcriptional repressor", "AP-2rep transcription factor", "AP-2 repressor"	607531				10704285	Standard	NM_007249		Approved	AP-2rep, HSPC122, AP2REP	uc001vjf.3	Q9Y4X4	OTTHUMG00000017078	ENST00000377669.2:c.913C>T	chr13.hg19:g.74289619G>A	ENSP00000366897:p.Arg305Trp	138.0	0.0		137.0	15.0	NM_007249	A8K5T2|L0R3J4|Q5VZM7|Q9UHZ0	Missense_Mutation	SNP	ENST00000377669.2	hg19	CCDS9449.1	.	.	.	.	.	.	.	.	.	.	G	18.31	3.595308	0.66219	.	.	ENSG00000118922	ENST00000377669;ENST00000342812;ENST00000377666	T;T	0.06849	3.25;3.25	5.81	4.01	0.46588	.	0.054133	0.64402	D	0.000001	T	0.21921	0.0528	M	0.75085	2.285	0.51482	D	0.999925	D	0.89917	1.0	P	0.56278	0.795	T	0.00964	-1.1498	10	0.37606	T	0.19	.	13.6405	0.62249	0.0:0.0:0.4399:0.5601	.	305	Q9Y4X4	KLF12_HUMAN	W	305	ENSP00000366897:R305W;ENSP00000366894:R305W	ENSP00000344057:R305W	R	-	1	2	KLF12	73187620	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	2.547000	0.45786	0.719000	0.32188	0.655000	0.94253	CGG	.	.		0.463	KLF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045271.2	NM_007249		A	74289619	G	A	74289619	3	1	352	1	0	0	0	0	1	0	0	0	8349	1144	40	1	303	1	KLF12	13	74289619	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	21337385	74289619	40880259	320	49736										
TUBGCP3	10426	hgsc.bcm.edu	37	chr13	113212590	113212590	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ctgatgccactgctgcccacGctgccggagctctgggctga	13	15	1	2	rs541731896	byFrequency	TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr13:113212590G>A	ENST00000261965.3	-	5	654	c.468C>T	c.(466-468)agC>agT	p.S156S	TUBGCP3_ENST00000375669.3_Silent_p.S156S	NM_006322.4	NP_006313.1	Q96CW5	GCP3_HUMAN	tubulin, gamma complex associated protein 3	156					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|single fertilization (GO:0007338)	centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|polar microtubule (GO:0005827)|spindle (GO:0005819)	gamma-tubulin binding (GO:0043015)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|prostate(3)|urinary_tract(1)	25	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)					TGCTGCCCACGCTGCCGGAGC	0.627													G|||	4	0.000798722	0	0	5008	,	,		17009	0.004		0	False		,,,				2504	0				p.S156S		Atlas-SNP	.											.	TUBGCP3	74	.	0			c.C468T						.						72	71	71					13																	113212590		2203	4300	6503	SO:0001819	synonymous_variant	10426	exon5			GCCCACGCTGCCG	AF042378	CCDS9525.1, CCDS66584.1, CCDS73599.1	13q34	2008-07-18			ENSG00000126216	ENSG00000126216			18598	protein-coding gene	gene with protein product	"spindle pole body protein"					9566967, 9566969	Standard	XM_005268293		Approved	GCP3, Spc98p, SPBC98	uc001vse.1	Q96CW5	OTTHUMG00000017367	ENST00000261965.3:c.468C>T	chr13.hg19:g.113212590G>A		108.0	0.0		103.0	16.0	NM_006322	O43631|O60852|O60853|Q5T8L2|Q7Z4K1|Q96I79	Silent	SNP	ENST00000261965.3	hg19	CCDS9525.1																																																																																			.	.		0.627	TUBGCP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045825.2	NM_006322		A	113212590	G	A	113212590	2	1	352	1	0	0	0	0	0	0	0	1	16782	1078	38	1		1	TUBGCP3	13	113212590	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	38922971	113212590	1957288	321	49737										
NYNRIN	57523	hgsc.bcm.edu	37	chr14	24877347	24877347	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ccccgggggatctgggaggcTgaggtgacccgggcctttgg	19	11	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr14:24877347T>C	ENST00000382554.3	+	3	789	c.471T>C	c.(469-471)gcT>gcC	p.A157A		NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	157					DNA integration (GO:0015074)	integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(8)|lung(21)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	56						TCTGGGAGGCTGAGGTGACCC	0.672																																					p.A157A		Atlas-SNP	.											.	NYNRIN	120	.	0			c.T471C						.						15	19	18					14																	24877347		1922	4105	6027	SO:0001819	synonymous_variant	57523	exon3			GGAGGCTGAGGTG	AB037726	CCDS45090.1	14q11.2	2009-10-14	2009-10-14	2009-10-14		ENSG00000205978			20165	protein-coding gene	gene with protein product	"Cousin of GIN1"		"KIAA1305"	KIAA1305		19561090, 17114934	Standard	NM_025081		Approved	FLJ11811, CGIN1	uc001wpf.4	Q9P2P1		ENST00000382554.3:c.471T>C	chr14.hg19:g.24877347T>C		38.0	0.0		21.0	6.0	NM_025081	Q6P153|Q86TR3|Q9HAC4	Silent	SNP	ENST00000382554.3	hg19	CCDS45090.1																																																																																			.	.		0.672	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412939.1			C	24877347	T	C	24877347	2	2	352	1	0	0	0	0	0	0	0	1	10805	1567	55	2		2	NYNRIN	14	24877347	Silent	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10		24877347	82472193	322	49738										
SIX4	51804	hgsc.bcm.edu	37	chr14	61190367	61190367	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agcaggctctcgttgccacgTagcaggtcgctctggggcag	15	12	2	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr14:61190367T>C	ENST00000216513.4	-	1	485	c.426A>G	c.(424-426)ctA>ctG	p.L142L		NM_017420.4	NP_059116.3	Q9UIU6	SIX4_HUMAN	SIX homeobox 4	142					anatomical structure morphogenesis (GO:0009653)|embryonic cranial skeleton morphogenesis (GO:0048701)|generation of neurons (GO:0048699)|inner ear morphogenesis (GO:0042472)|metanephric mesenchyme development (GO:0072075)|myoblast migration (GO:0051451)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of ureteric bud formation (GO:0072107)|regulation of branch elongation involved in ureteric bud branching (GO:0072095)|regulation of protein localization (GO:0032880)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|skeletal muscle tissue development (GO:0007519)|thymus development (GO:0048538)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(1)|large_intestine(11)|liver(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28				OV - Ovarian serous cystadenocarcinoma(108;0.0275)		CGTTGCCACGTAGCAGGTCGC	0.687																																					p.L142L		Atlas-SNP	.											.	SIX4	69	.	0			c.A426G						.						8	9	9					14																	61190367		2178	4268	6446	SO:0001819	synonymous_variant	51804	exon1			GCCACGTAGCAGG	AB024687	CCDS9749.2	14q23.1	2012-10-02	2007-07-13		ENSG00000100625	ENSG00000100625		"Homeoboxes / SINE class"	10890	protein-coding gene	gene with protein product		606342	"sine oculis homeobox (Drosophila) homolog 4", "sine oculis homeobox homolog 4 (Drosophila)"			10512683, 10640827	Standard	NM_017420		Approved	AREC3	uc001xfc.3	Q9UIU6	OTTHUMG00000028996	ENST00000216513.4:c.426A>G	chr14.hg19:g.61190367T>C		113.0	0.0		86.0	19.0	NM_017420	Q4QQH5|Q4V764	Silent	SNP	ENST00000216513.4	hg19	CCDS9749.2																																																																																			.	.		0.687	SIX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072397.2			C	61190367	T	C	61190367	2	2	352	1	0	0	0	0	0	0	0	1	14364	1625	57	2		2	SIX4	14	61190367	Silent	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	36313020	61190367	46159173	323	49739										
MPP5	64398	hgsc.bcm.edu	37	chr14	67768752	67768755	+	Frame_Shift_Del	DEL	GAGA	GAGA	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agctagagcccattacagatGagagagtttatgaaagtatt							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	GAGA	GAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr14:67768752_67768755delGAGA	ENST00000261681.4	+	6	1379_1382	c.718_721delGAGA	c.(718-723)gagagafs	p.ER240fs	MPP5_ENST00000555925.1_Frame_Shift_Del_p.ER206fs	NM_022474.3	NP_071919.2	Q8N3R9	MPP5_HUMAN	membrane protein, palmitoylated 5 (MAGUK p55 subfamily member 5)	240	Interaction with LIN7C. {ECO:0000250}.				cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|establishment of protein localization to plasma membrane (GO:0090002)|morphogenesis of an epithelial sheet (GO:0002011)|myelin assembly (GO:0032288)|peripheral nervous system myelin maintenance (GO:0032287)|protein localization to myelin sheath abaxonal region (GO:0035750)|tight junction assembly (GO:0070830)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lateral loop (GO:0043219)|myelin sheath adaxonal region (GO:0035749)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein domain specific binding (GO:0019904)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|skin(1)	18				all cancers(60;0.000388)|OV - Ovarian serous cystadenocarcinoma(108;0.00762)|BRCA - Breast invasive adenocarcinoma(234;0.0106)		CATTACAGATGAGAGAGTTTATGA	0.417																																					p.239_240del		Atlas-INDEL	.											.	MPP5	46	.	0			c.717_720del						.																																			SO:0001589	frameshift_variant	64398	exon6			.	AK022677	CCDS9779.1, CCDS58325.1	14q23.3	2008-08-11				ENSG00000072415			18669	protein-coding gene	gene with protein product	"stardust"	606958				11927608	Standard	NM_022474		Approved	PALS1, FLJ12615	uc001xjc.4	Q8N3R9		ENST00000261681.4:c.718_721delGAGA	chr14.hg19:g.67768752_67768755delGAGA	ENSP00000261681:p.Glu240fs	195.0	0.0		123.0	50.0	NM_022474	A1L380|Q7Z631|Q86T98|Q8N7I5|Q9H9Q0	Frame_Shift_Del	DEL	ENST00000261681.4	hg19	CCDS9779.1																																																																																			.	.		0.417	MPP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412498.1	NM_022474		-	67768755	GAGA	-	67768752	7	5	352	1	0	1	0	1	0	0	0	0	9746	1291	45	0	732	0	MPP5	14	67768752	Frame_Shift_Del	DEL	GAGA	TCGA-WQ-A9G7-01A-11D-A36X-10	6578385	67768752	39580788	324	49740										
HEATR4	399671	hgsc.bcm.edu	37	chr14	73945440	73945440	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cccacagcaatccttttctcGggggaggtgcgtagatcttt	11	11	2	1	rs78875724	byFrequency	TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr14:73945440G>A	ENST00000553558.1	-	18	3273	c.2952C>T	c.(2950-2952)ccC>ccT	p.P984P	HEATR4_ENST00000560393.1_Silent_p.P937P|HEATR4_ENST00000566478.1_5'UTR|RP1-240K6.3_ENST00000515412.2_RNA|HEATR4_ENST00000334988.2_Silent_p.P984P	NM_001220484.1	NP_001207413.1	Q86WZ0	HEAT4_HUMAN	HEAT repeat containing 4	984										breast(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00386)|OV - Ovarian serous cystadenocarcinoma(108;0.0719)		TCCTTTTCTCGGGGGAGGTGC	0.478																																					p.P984P		Atlas-SNP	.											.	HEATR4	126	.	0			c.C2952T						.						136	124	128					14																	73945440		2203	4300	6503	SO:0001819	synonymous_variant	399671	exon17			TTTCTCGGGGGAG	BC047590	CCDS9815.1, CCDS9815.2	14q24.3	2013-09-20			ENSG00000187105	ENSG00000187105			16761	protein-coding gene	gene with protein product						15489334	Standard	NM_203309		Approved	MGC48595	uc021rwf.2	Q86WZ0	OTTHUMG00000171602	ENST00000553558.1:c.2952C>T	chr14.hg19:g.73945440G>A		173.0	0.0		170.0	12.0	NM_203309	B7Z7V9|E9KL41	Silent	SNP	ENST00000553558.1	hg19	CCDS9815.2																																																																																			.	G|0.962;T|0.038		0.478	HEATR4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414422.2	NM_203309		A	73945440	G	A	73945440	2	1	352	1	0	0	0	0	0	0	0	1	7039	1103	39	1		1	HEATR4	14	73945440	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	6176688	73945440	33404100	325	49741										
C14orf43	91748	hgsc.bcm.edu	37	chr14	74205773	74205773	+	Frame_Shift_Del	DEL	G	G	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tctgggttcatatctgggttGggggggaaggggtagggtgc							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr14:74205773delG	ENST00000286523.5	-	2	1721	c.939delC	c.(937-939)cccfs	p.P313fs	ELMSAN1_ENST00000486739.1_5'Flank|ELMSAN1_ENST00000394071.2_Frame_Shift_Del_p.P313fs	NM_194278.3	NP_919254.2	Q6PJG2	EMSA1_HUMAN	ELM2 and Myb/SANT-like domain containing 1	313	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)										TATCTGGGTTGGGGGGGAAGG	0.662																																					p.N314fs		Atlas-INDEL	.											.	.	.	.	0			c.940delA						.						21	22	22					14																	74205773		2203	4299	6502	SO:0001589	frameshift_variant	91748	exon2			.	BF971739	CCDS9819.1	14q24.3	2012-09-25	2012-09-25	2012-09-25	ENSG00000156030	ENSG00000156030			19853	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 117", "chromosome 14 open reading frame 43"	C14orf117, C14orf43			Standard	NM_194278		Approved	LSR68	uc001xou.3	Q6PJG2	OTTHUMG00000150359	ENST00000286523.5:c.939delC	chr14.hg19:g.74205773delG	ENSP00000286523:p.Pro313fs	47.0	0.0		45.0	18.0	NM_194278	Q6PK13|Q6PK59|Q6ZS23	Frame_Shift_Del	DEL	ENST00000286523.5	hg19	CCDS9819.1																																																																																			.	.		0.662	ELMSAN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317793.1	NM_194278		-	74205773	G	-	74205773	7	5	352	1	0	1	0	1	0	0	0	0	1776	1335	47	0	2242	0	C14orf43	14	74205773	Frame_Shift_Del	DEL	G	TCGA-WQ-A9G7-01A-11D-A36X-10	260333	74205773	33143767	326	49742										
C14orf174	161394	hgsc.bcm.edu	37	chr14	77845085	77845085	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gaaacgatgagctagagcacCgtgagcctaaaagaggaaag	13	7	0	4			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr14:77845085C>T	ENST00000216471.4	+	1	1610	c.1324C>T	c.(1324-1326)Cgt>Tgt	p.R442C	SAMD15_ENST00000533095.2_Intron|TMED8_ENST00000216468.7_5'Flank	NM_001010860.1	NP_001010860.1	Q9P1V8	SAM15_HUMAN	sterile alpha motif domain containing 15	442										breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						GCTAGAGCACCGTGAGCCTAA	0.388																																					p.R442C		Atlas-SNP	.											.	SAMD15	60	.	0			c.C1324T						.						71	69	70					14																	77845085		2203	4300	6503	SO:0001583	missense	161394	exon1			GAGCACCGTGAGC	AK093282	CCDS32126.1	14q24.3	2013-01-10	2010-10-20	2010-10-20	ENSG00000100583	ENSG00000100583		"Sterile alpha motif (SAM) domain containing"	18631	protein-coding gene	gene with protein product			"family with sequence similarity 15, member A", "chromosome 14 open reading frame 174"	FAM15A, C14orf174			Standard	XM_006720069		Approved	FLJ35963	uc001xtq.1	Q9P1V8		ENST00000216471.4:c.1324C>T	chr14.hg19:g.77845085C>T	ENSP00000216471:p.Arg442Cys	178.0	0.0		143.0	41.0	NM_001010860	Q2M3P3	Missense_Mutation	SNP	ENST00000216471.4	hg19	CCDS32126.1	.	.	.	.	.	.	.	.	.	.	C	9.337	1.062073	0.19987	.	.	ENSG00000100583	ENST00000216471	T	0.18657	2.2	4.4	-0.0839	0.13692	.	.	.	.	.	T	0.11580	0.0282	L	0.34521	1.04	0.09310	N	1	P	0.40931	0.733	B	0.27796	0.083	T	0.12837	-1.0532	9	0.56958	D	0.05	1.411	7.7965	0.29150	0.0:0.6192:0.0:0.3808	.	442	Q9P1V8	SAM15_HUMAN	C	442	ENSP00000216471:R442C	ENSP00000216471:R442C	R	+	1	0	SAMD15	76914838	0.005000	0.15991	0.000000	0.03702	0.002000	0.02628	0.121000	0.15667	-0.124000	0.11724	0.555000	0.69702	CGT	.	.		0.388	SAMD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394587.2	NM_001010860		T	77845085	C	T	77845085	3	4	352	1	0	0	0	0	1	0	0	0	1761	652	23	1	1326	1	C14orf174	14	77845085	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	3639312	77845085	29504455	327	49743										
PTPN21	11099	hgsc.bcm.edu	37	chr14	88970793	88970793	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	atttctgatgtagtaaggccActttttgggttgcttcttcc	9	8	2	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr14:88970793A>G	ENST00000556564.1	-	6	847	c.563T>C	c.(562-564)gTg>gCg	p.V188A	PTPN21_ENST00000554628.1_5'UTR|RP11-507K2.2_ENST00000555444.1_RNA|PTPN21_ENST00000328736.3_Missense_Mutation_p.V188A	NM_007039.3	NP_008970.2	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type 21	188	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|liver(1)|lung(7)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						TAGTAAGGCCACTTTTTGGGT	0.333																																					p.V188A		Atlas-SNP	.											.	PTPN21	113	.	0			c.T563C						.						193	180	185					14																	88970793		2203	4299	6502	SO:0001583	missense	11099	exon6			AAGGCCACTTTTT	X79510	CCDS9884.1	14q31	2011-06-09				ENSG00000070778		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9651	protein-coding gene	gene with protein product		603271				7519780	Standard	NM_007039		Approved	PTPD1, PTPRL10	uc001xwv.4	Q16825		ENST00000556564.1:c.563T>C	chr14.hg19:g.88970793A>G	ENSP00000452414:p.Val188Ala	96.0	0.0		77.0	12.0	NM_007039		Missense_Mutation	SNP	ENST00000556564.1	hg19	CCDS9884.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.535202	0.85812	.	.	ENSG00000070778	ENST00000328736;ENST00000556564;ENST00000555243	T;T;T	0.81247	-1.47;-1.47;-1.47	5.3	5.3	0.74995	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.171358	0.40385	N	0.001106	D	0.88373	0.6419	M	0.70275	2.135	0.46823	D	0.999212	B;D	0.65815	0.448;0.995	P;D	0.66716	0.55;0.946	D	0.89778	0.3959	10	0.87932	D	0	.	15.5502	0.76145	1.0:0.0:0.0:0.0	.	188;188	G3V3S6;Q16825	.;PTN21_HUMAN	A	188	ENSP00000330276:V188A;ENSP00000452414:V188A;ENSP00000451401:V188A	ENSP00000330276:V188A	V	-	2	0	PTPN21	88040546	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.882000	0.92420	2.131000	0.65755	0.533000	0.62120	GTG	.	.		0.333	PTPN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410303.1			G	88970793	A	G	88970793	3	3	352	1	0	0	0	0	1	0	0	0	12801	159	6	2	3017	2	PTPN21	14	88970793	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	11125708	88970793	18378747	328	49744										
DLK1	8788	hgsc.bcm.edu	37	chr14	101200731	101200731	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	caactgcgccagcagcccgtGccagaacgggggcacctgcc	13	17	0	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr14:101200731G>A	ENST00000341267.4	+	5	892	c.650G>A	c.(649-651)tGc>tAc	p.C217Y	DLK1_ENST00000331224.6_Missense_Mutation_p.C217Y	NM_003836.5	NP_003827	P80370	DLK1_HUMAN	delta-like 1 homolog (Drosophila)	217	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell differentiation (GO:0030154)|embryonic skeletal system development (GO:0048706)|multicellular organismal development (GO:0007275)|negative regulation of Notch signaling pathway (GO:0045746)|Notch signaling pathway (GO:0007219)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)	external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(16)|ovary(2)|prostate(1)|skin(1)	29		Melanoma(154;0.155)				AGCAGCCCGTGCCAGAACGGG	0.657																																					p.C217Y		Atlas-SNP	.											.	DLK1	57	.	0			c.G650A						.						30	36	34					14																	101200731		2203	4300	6503	SO:0001583	missense	8788	exon5			GCCCGTGCCAGAA	U15979	CCDS9963.1	14q32	2011-12-05	2001-12-03			ENSG00000185559			2907	protein-coding gene	gene with protein product		176290	"delta-like homolog (Drosophila)"			8095043, 7925474	Standard	NM_003836		Approved	FA1, pG2, Pref-1, ZOG, Delta1	uc001yhs.4	P80370		ENST00000341267.4:c.650G>A	chr14.hg19:g.101200731G>A	ENSP00000340292:p.Cys217Tyr	111.0	0.0		95.0	33.0	NM_003836	P15803|Q96DW5	Missense_Mutation	SNP	ENST00000341267.4	hg19	CCDS9963.1	.	.	.	.	.	.	.	.	.	.	G	15.45	2.837962	0.50951	.	.	ENSG00000185559	ENST00000341267;ENST00000331224	D;T	0.99992	-12.4;-0.98	4.7	4.7	0.59300	EGF (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.99994	0.9999	H	0.99619	4.66	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.99996	1.5401	10	0.87932	D	0	.	16.6457	0.85176	0.0:0.0:1.0:0.0	.	217;217	P80370-2;P80370	.;DLK1_HUMAN	Y	217	ENSP00000340292:C217Y;ENSP00000331081:C217Y	ENSP00000331081:C217Y	C	+	2	0	DLK1	100270484	1.000000	0.71417	0.983000	0.44433	0.034000	0.12701	9.853000	0.99521	2.149000	0.67028	0.491000	0.48974	TGC	.	.		0.657	DLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414389.1			A	101200731	G	A	101200731	3	1	352	1	0	0	0	0	1	0	0	0	4566	1319	46	3	668	3	DLK1	14	101200731	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	12229938	101200731	6148809	329	49745										
TRAF3	7187	hgsc.bcm.edu	37	chr14	103371803	103371803	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agggtctacctgaacggggaCgggatggggaaggggacgca	20	7	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr14:103371803C>T	ENST00000560371.1	+	11	1606	c.1389C>T	c.(1387-1389)gaC>gaT	p.D463D	TRAF3_ENST00000347662.4_Silent_p.D438D|TRAF3_ENST00000392745.2_Silent_p.D463D|TRAF3_ENST00000351691.5_Silent_p.D438D|TRAF3_ENST00000539721.1_Silent_p.D380D	NM_003300.3|NM_145725.2	NP_003291.2|NP_663777.1	Q13114	TRAF3_HUMAN	TNF receptor-associated factor 3	463	MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.				apoptotic process (GO:0006915)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|regulation of apoptotic process (GO:0042981)|regulation of cytokine production (GO:0001817)|regulation of defense response to virus (GO:0050688)|regulation of interferon-beta production (GO:0032648)|regulation of proteolysis (GO:0030162)|signal transduction (GO:0007165)|Toll signaling pathway (GO:0008063)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endosome (GO:0005768)|mitochondrion (GO:0005739)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.D463D(1)		breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|liver(2)|lung(7)|ovary(1)|prostate(2)	30		all_cancers(154;7.87e-06)|all_epithelial(191;0.0024)		Epithelial(152;9.92e-24)|all cancers(159;2.23e-21)|OV - Ovarian serous cystadenocarcinoma(161;7.85e-12)|Colorectal(3;0.0971)		TGAACGGGGACGGGATGGGGA	0.527																																					p.D463D		Atlas-SNP	.											TRAF3,NS,carcinoma,+2,1	TRAF3	60	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1389T						.						208	183	192					14																	103371803		2203	4300	6503	SO:0001819	synonymous_variant	7187	exon12			CGGGGACGGGATG	U21092	CCDS9975.1, CCDS9976.1, CCDS55946.1	14q32.32	2014-09-17				ENSG00000131323			12033	protein-coding gene	gene with protein product		601896				7530216, 7859281	Standard	NM_145725		Approved	CAP-1, CD40bp, CRAF1, LAP1	uc001ymd.2	Q13114		ENST00000560371.1:c.1389C>T	chr14.hg19:g.103371803C>T		149.0	0.0		89.0	13.0	NM_145725	B7Z8C4|Q12990|Q13076|Q13947|Q6AZX1|Q9UNL1	Silent	SNP	ENST00000560371.1	hg19	CCDS9975.1																																																																																			.	.		0.527	TRAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415735.1	NM_145725		T	103371803	C	T	103371803	2	4	352	1	0	0	0	0	0	0	0	1	16454	535	19	1		1	TRAF3	14	103371803	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	2171072	103371803	3977737	330	49746										
OR4M2	390538	hgsc.bcm.edu	37	chr15	22369119	22369119	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	acagttacttctgtgacatcAcacaggttgtccggattgcc	9	11	2	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr15:22369119A>T	ENST00000332663.2	+	1	642	c.544A>T	c.(544-546)Aca>Tca	p.T182S	RP11-69H14.6_ENST00000558896.1_RNA	NM_001004719.2	NP_001004719.2	Q8NGB6	OR4M2_HUMAN	olfactory receptor, family 4, subfamily M, member 2	182						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|endometrium(2)|kidney(4)|large_intestine(6)|lung(38)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	63		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		CTGTGACATCACACAGGTTGT	0.483																																					p.T182S		Atlas-SNP	.											.	OR4M2	140	.	0			c.A544T						.						285	218	241					15																	22369119		2203	4297	6500	SO:0001583	missense	390538	exon1			GACATCACACAGG	AC060768	CCDS32172.1	15q11.2	2013-09-23			ENSG00000182974	ENSG00000182974		"GPCR / Class A : Olfactory receptors"	15373	protein-coding gene	gene with protein product							Standard	NM_001004719		Approved		uc010tzu.2	Q8NGB6	OTTHUMG00000171738	ENST00000332663.2:c.544A>T	chr15.hg19:g.22369119A>T	ENSP00000329467:p.Thr182Ser	312.0	0.0		245.0	23.0	NM_001004719	B9EH16|Q6IEY2	Missense_Mutation	SNP	ENST00000332663.2	hg19	CCDS32172.1	.	.	.	.	.	.	.	.	.	.	.	12.64	1.999847	0.35320	.	.	ENSG00000182974	ENST00000332663	T	0.00069	8.77	2.5	2.5	0.30297	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	D	0.000095	T	0.00109	0.0003	N	0.05230	-0.09	0.24325	N	0.995025	B	0.29955	0.263	B	0.39465	0.3	T	0.17501	-1.0367	10	0.46703	T	0.11	-4.0207	8.5824	0.33637	1.0:0.0:0.0:0.0	.	182	Q8NGB6	OR4M2_HUMAN	S	182	ENSP00000329467:T182S	ENSP00000329467:T182S	T	+	1	0	OR4M2	19870483	0.000000	0.05858	1.000000	0.80357	0.992000	0.81027	0.858000	0.27845	1.167000	0.42706	0.368000	0.22195	ACA	.	.		0.483	OR4M2-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414921.1			T	22369119	A	T	22369119	3	4	352	1	0	0	0	0	1	0	0	0	11085	159	6	4	546	4	OR4M2	15	22369119	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10		22369119	80162273	331	49747										
GPR176	11245	hgsc.bcm.edu	37	chr15	40093624	40093624	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ctcaggggtggggcagagggCgcaaactgtggcccctgctc	17	12	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr15:40093624C>T	ENST00000561100.1	-	3	2122	c.1257G>A	c.(1255-1257)gcG>gcA	p.A419A	RP11-37C7.1_ENST00000558616.1_RNA|GPR176_ENST00000560729.1_5'Flank|GPR176_ENST00000299092.3_Silent_p.A418A|GPR176_ENST00000543580.1_Silent_p.A374A	NM_007223.1	NP_009154.1	Q14439	GP176_HUMAN	G protein-coupled receptor 176	419					G-protein coupled receptor signaling pathway (GO:0007186)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(3)|liver(1)|lung(9)|ovary(2)|pancreas(1)|skin(2)	23		all_cancers(109;4.05e-15)|all_epithelial(112;2.96e-13)|Lung NSC(122;8.53e-11)|all_lung(180;2.71e-09)|Melanoma(134;0.091)|Colorectal(260;0.198)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;4.4e-06)|BRCA - Breast invasive adenocarcinoma(123;0.123)		GGGCAGAGGGCGCAAACTGTG	0.572																																					p.A419A		Atlas-SNP	.											.	GPR176	41	.	0			c.G1257A						.						139	136	137					15																	40093624		2203	4300	6503	SO:0001819	synonymous_variant	11245	exon3			AGAGGGCGCAAAC	BC067106	CCDS10051.1, CCDS61588.1, CCDS61589.1	15q14-q15.1	2012-08-21			ENSG00000166073	ENSG00000166073		"GPCR / Class A : Orphans"	32370	protein-coding gene	gene with protein product		612183				7893747	Standard	NM_007223		Approved	Gm1012	uc010uck.2	Q14439	OTTHUMG00000129873	ENST00000561100.1:c.1257G>A	chr15.hg19:g.40093624C>T		69.0	0.0		36.0	10.0	NM_007223	Q6NXF6	Silent	SNP	ENST00000561100.1	hg19	CCDS10051.1																																																																																			.	.		0.572	GPR176-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252117.2	NM_007223		T	40093624	C	T	40093624	2	4	352	1	0	0	0	0	0	0	0	1	6681	755	27	1		1	GPR176	15	40093624	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	17724505	40093624	62437768	332	49748										
RPAP1	26015	hgsc.bcm.edu	37	chr15	41810241	41810241	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gagagaagatgaagctattgAcatgagccacagccacagca	11	9	0	5			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr15:41810241A>G	ENST00000304330.4	-	23	4051	c.3935T>C	c.(3934-3936)gTc>gCc	p.V1312A	RPAP1_ENST00000561603.1_Missense_Mutation_p.S1060P	NM_015540.2	NP_056355.2	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	1312						nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	45		all_cancers(109;6.59e-20)|all_epithelial(112;7.67e-17)|Lung NSC(122;5.34e-11)|all_lung(180;4.17e-10)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		OV - Ovarian serous cystadenocarcinoma(18;2.84e-17)|GBM - Glioblastoma multiforme(113;1.68e-06)|Colorectal(105;0.0163)|BRCA - Breast invasive adenocarcinoma(123;0.117)		GAAGCTATTGACATGAGCCAC	0.562																																					p.V1312A		Atlas-SNP	.											.	RPAP1	111	.	0			c.T3935C						.						85	80	81					15																	41810241		2203	4300	6503	SO:0001583	missense	26015	exon23			CTATTGACATGAG	BC000246	CCDS10079.1	15q14	2004-03-16			ENSG00000103932	ENSG00000103932			24567	protein-coding gene	gene with protein product		611475				10718198	Standard	XM_005254297		Approved	DKFZP727M111, KIAA1403, MGC858, FLJ12732	uc001zod.3	Q9BWH6	OTTHUMG00000130342	ENST00000304330.4:c.3935T>C	chr15.hg19:g.41810241A>G	ENSP00000306123:p.Val1312Ala	86.0	0.0		79.0	5.0	NM_015540	Q9H9I2|Q9NSQ5|Q9P2E4|Q9UFS7	Missense_Mutation	SNP	ENST00000304330.4	hg19	CCDS10079.1	.	.	.	.	.	.	.	.	.	.	A	28.3	4.906068	0.92107	.	.	ENSG00000103932	ENST00000304330	T	0.15834	2.39	5.23	5.23	0.72850	.	0.061949	0.64402	D	0.000005	T	0.23926	0.0579	M	0.66939	2.045	0.44247	D	0.997092	B	0.17038	0.02	B	0.24155	0.051	T	0.03086	-1.1074	10	0.62326	D	0.03	-10.574	15.302	0.73958	1.0:0.0:0.0:0.0	.	1312	Q9BWH6	RPAP1_HUMAN	A	1312	ENSP00000306123:V1312A	ENSP00000306123:V1312A	V	-	2	0	RPAP1	39597533	1.000000	0.71417	0.996000	0.52242	0.992000	0.81027	9.139000	0.94554	2.191000	0.70037	0.533000	0.62120	GTC	.	.		0.562	RPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252694.2	NM_015540		G	41810241	A	G	41810241	3	3	352	1	0	0	0	0	1	0	0	0	13556	275	10	2	258	2	RPAP1	15	41810241	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	1716617	41810241	60721151	333	49749										
ZSCAN29	146050	hgsc.bcm.edu	37	chr15	43656143	43656143	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ttggaataacactggagcacGggttatgacagcccctgggg	14	9	0	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr15:43656143G>A	ENST00000396976.2	-	4	1794	c.1660C>T	c.(1660-1662)Cgt>Tgt	p.R554C	ZSCAN29_ENST00000562072.1_Intron|ZSCAN29_ENST00000568898.1_Intron|ZSCAN29_ENST00000396972.1_Intron	NM_152455.3	NP_689668.3	Q8IWY8	ZSC29_HUMAN	zinc finger and SCAN domain containing 29	554					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(7)|skin(2)	24		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.97e-07)		ACTGGAGCACGGGTTATGACA	0.443																																					p.R554C		Atlas-SNP	.											.	ZSCAN29	57	.	0			c.C1660T						.						79	70	73					15																	43656143		2201	4299	6500	SO:0001583	missense	146050	exon4			GAGCACGGGTTAT	AF525399	CCDS10095.2	15q15.3	2013-01-08	2007-03-08	2007-03-08	ENSG00000140265	ENSG00000140265		"-", "Zinc fingers, C2H2-type"	26673	protein-coding gene	gene with protein product			"zinc finger protein 690"	ZNF690		12434312	Standard	NM_152455		Approved	FLJ35867, Zfp690	uc001zrk.1	Q8IWY8	OTTHUMG00000130767	ENST00000396976.2:c.1660C>T	chr15.hg19:g.43656143G>A	ENSP00000380174:p.Arg554Cys	104.0	0.0		109.0	11.0	NM_152455	B3KVB9|Q32M75|Q32M76|Q8NA40	Missense_Mutation	SNP	ENST00000396976.2	hg19	CCDS10095.2	.	.	.	.	.	.	.	.	.	.	G	15.34	2.804248	0.50315	.	.	ENSG00000140265	ENST00000396976	T	0.08102	3.13	5.63	3.65	0.41850	.	0.536676	0.19852	N	0.104612	T	0.09512	0.0234	M	0.62723	1.935	0.80722	D	1	D	0.63880	0.993	B	0.41299	0.353	T	0.14924	-1.0455	10	0.37606	T	0.19	-1.332	8.3678	0.32397	0.0823:0.0:0.7635:0.1542	.	554	Q8IWY8	ZSC29_HUMAN	C	554	ENSP00000380174:R554C	ENSP00000380174:R554C	R	-	1	0	ZSCAN29	41443435	0.976000	0.34144	0.899000	0.35326	0.637000	0.38172	1.859000	0.39418	1.388000	0.46506	0.491000	0.48974	CGT	.	.		0.443	ZSCAN29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253278.1	NM_152455		A	43656143	G	A	43656143	3	1	352	1	0	0	0	0	1	0	0	0	18251	1116	39	1	906	1	ZSCAN29	15	43656143	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	1845902	43656143	58875249	334	49750										
TRPM7	54822	hgsc.bcm.edu	37	chr15	50884267	50884267	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tgacagatgtggtatgctagTagatgaactgcctaattttt	10	5	0	4			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr15:50884267T>C	ENST00000313478.7	-	26	4446	c.4165A>G	c.(4165-4167)Act>Gct	p.T1389A	TRPM7_ENST00000560955.1_Missense_Mutation_p.T1389A	NM_017672.4	NP_060142.3	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel, subfamily M, member 7	1389					actomyosin structure organization (GO:0031032)|calcium ion transmembrane transport (GO:0070588)|calcium-dependent cell-matrix adhesion (GO:0016340)|cellular magnesium ion homeostasis (GO:0010961)|ion transmembrane transport (GO:0034220)|necroptotic process (GO:0070266)|protein autophosphorylation (GO:0046777)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(17)|lung(13)|ovary(4)|pancreas(1)|skin(4)|stomach(3)	52				all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)		GGTATGCTAGTAGATGAACTG	0.398																																					p.T1389A		Atlas-SNP	.											.	TRPM7	145	.	0			c.A4165G						.						104	98	100					15																	50884267		1809	4082	5891	SO:0001583	missense	54822	exon26			TGCTAGTAGATGA	AF346629	CCDS42035.1, CCDS73725.1	15q21	2011-12-14				ENSG00000092439		"Voltage-gated ion channels / Transient receptor potential cation channels"	17994	protein-coding gene	gene with protein product		605692				11161216, 11385574, 16382100	Standard	XM_005254486		Approved	CHAK1, LTRPC7, TRP-PLIK	uc001zyt.4	Q96QT4		ENST00000313478.7:c.4165A>G	chr15.hg19:g.50884267T>C	ENSP00000320239:p.Thr1389Ala	71.0	0.0		66.0	8.0	NM_017672	Q6ZMF5|Q86VJ4|Q8NBW2|Q9BXB2|Q9NXQ2	Missense_Mutation	SNP	ENST00000313478.7	hg19	CCDS42035.1	.	.	.	.	.	.	.	.	.	.	T	13.65	2.301723	0.40694	.	.	ENSG00000092439	ENST00000313478	T	0.49720	0.77	6.04	4.92	0.64577	.	0.752659	0.13497	N	0.383521	T	0.28034	0.0691	N	0.08118	0	0.19575	N	0.999963	B	0.02656	0.0	B	0.01281	0.0	T	0.16541	-1.0399	10	0.20046	T	0.44	-9.5747	11.926	0.52819	0.0:0.0673:0.0:0.9327	.	1389	Q96QT4	TRPM7_HUMAN	A	1389	ENSP00000320239:T1389A	ENSP00000320239:T1389A	T	-	1	0	TRPM7	48671559	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	3.814000	0.55643	1.120000	0.41904	0.529000	0.55759	ACT	.	.		0.398	TRPM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418604.1	NM_017672		C	50884267	T	C	50884267	3	2	352	1	0	0	0	0	1	0	0	0	16606	1638	57	2	1488	2	TRPM7	15	50884267	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	7228124	50884267	51647125	335	49751										
SPG21	51324	hgsc.bcm.edu	37	chr15	65268816	65268816	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agtttcagggtactcactttAtccaattgtaaatggtctaa	7	7	3	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr15:65268816A>G	ENST00000204566.2	-	4	598	c.303T>C	c.(301-303)gaT>gaC	p.D101D	SPG21_ENST00000416889.2_Intron|SPG21_ENST00000560564.1_5'UTR|SPG21_ENST00000559199.1_5'UTR|SPG21_ENST00000433215.2_Silent_p.D101D	NM_016630.3	NP_057714.1	Q9NZD8	SPG21_HUMAN	spastic paraplegia 21 (autosomal recessive, Mast syndrome)	101					antigen receptor-mediated signaling pathway (GO:0050851)|cell death (GO:0008219)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network transport vesicle (GO:0030140)	CD4 receptor binding (GO:0042609)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|urinary_tract(1)	10						TACTCACTTTATCCAATTGTA	0.358																																					p.D101D		Atlas-SNP	.											.	SPG21	29	.	0			c.T303C						.						51	52	52					15																	65268816		2202	4299	6501	SO:0001819	synonymous_variant	51324	exon4			CACTTTATCCAAT	AF208861	CCDS10198.1, CCDS45279.1	15q21-q22	2008-02-05	2007-04-23		ENSG00000090487	ENSG00000090487			20373	protein-coding gene	gene with protein product	"maspardin"	608181				11113139, 14564668	Standard	XM_006720564		Approved	ACP33, GL010, BM-019, MAST	uc002aoe.3	Q9NZD8	OTTHUMG00000133098	ENST00000204566.2:c.303T>C	chr15.hg19:g.65268816A>G		252.0	0.0		218.0	45.0	NM_001127889	B4DW44|Q6ZMB6	Silent	SNP	ENST00000204566.2	hg19	CCDS10198.1																																																																																			.	.		0.358	SPG21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256758.3	NM_016630		G	65268816	A	G	65268816	2	3	352	1	0	0	0	0	0	0	0	1	15058	446	16	2		2	SPG21	15	65268816	Silent	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	14384549	65268816	37262576	336	49752										
ZWILCH	55055	hgsc.bcm.edu	37	chr15	66821892	66821892	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gatcatccagagtctacaacGtggtgatatacagccatggg	11	9	2	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr15:66821892G>A	ENST00000307897.5	+	12	1516	c.1136G>A	c.(1135-1137)cGt>cAt	p.R379H	ZWILCH_ENST00000565627.1_Missense_Mutation_p.R265H|ZWILCH_ENST00000535141.2_Missense_Mutation_p.R265H|ZWILCH_ENST00000446801.2_Missense_Mutation_p.R265H	NM_017975.3	NP_060445.3	Q9H900	ZWILC_HUMAN	zwilch kinetochore protein	379					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)	cytosol (GO:0005829)|kinetochore (GO:0000776)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|liver(1)|lung(6)|ovary(1)	18						AGTCTACAACGTGGTGATATA	0.413																																					p.R379H		Atlas-SNP	.											.	ZWILCH	46	.	0			c.G1136A						.						169	157	161					15																	66821892		2201	4299	6500	SO:0001583	missense	55055	exon12			TACAACGTGGTGA	AK023175	CCDS10219.1, CCDS73746.1	15q22.31	2013-01-17	2012-12-13		ENSG00000174442	ENSG00000174442			25468	protein-coding gene	gene with protein product		609984	"Zwilch, kinetochore associated, homolog (Drosophila)"			12686595	Standard	NM_017975		Approved	FLJ10036, KNTC1AP	uc002aqb.3	Q9H900	OTTHUMG00000133194	ENST00000307897.5:c.1136G>A	chr15.hg19:g.66821892G>A	ENSP00000311429:p.Arg379His	71.0	0.0		45.0	9.0	NM_017975	B3KVB8|Q6N049|Q8N404|Q96SY7|Q9NWG7	Missense_Mutation	SNP	ENST00000307897.5	hg19	CCDS10219.1	.	.	.	.	.	.	.	.	.	.	G	7.962	0.747174	0.15710	.	.	ENSG00000174442	ENST00000307897;ENST00000446801;ENST00000535141	T;T;T	0.49432	0.78;0.78;0.78	5.68	3.81	0.43845	.	0.510391	0.23380	N	0.048807	T	0.35799	0.0944	L	0.48362	1.52	0.23120	N	0.998268	B	0.11235	0.004	B	0.06405	0.002	T	0.24333	-1.0163	10	0.12103	T	0.63	-3.5573	9.1237	0.36801	0.2851:0.0:0.7149:0.0	.	379	Q9H900	ZWILC_HUMAN	H	379;265;265	ENSP00000311429:R379H;ENSP00000402217:R265H;ENSP00000437749:R265H	ENSP00000311429:R379H	R	+	2	0	ZWILCH	64608946	0.120000	0.22244	0.696000	0.30242	0.907000	0.53573	0.470000	0.22084	0.754000	0.32968	0.563000	0.77884	CGT	.	.		0.413	ZWILCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256904.4	NM_017975		A	66821892	G	A	66821892	3	1	352	1	0	0	0	0	1	0	0	0	18263	1145	40	1	1182	1	ZWILCH	15	66821892	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	1553076	66821892	35709500	337	49753										
THSD4	79875	hgsc.bcm.edu	37	chr15	72057470	72057470	+	Frame_Shift_Del	DEL	C	C	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aatgttctttcctggagaaaCcccccagccagcaatcctgc							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr15:72057470delC	ENST00000355327.3	+	16	2835	c.2701delC	c.(2701-2703)cccfs	p.P902fs	THSD4_ENST00000357769.4_Frame_Shift_Del_p.P542fs|THSD4_ENST00000567838.1_3'UTR|THSD4_ENST00000261862.6_Frame_Shift_Del_p.P902fs			Q6ZMP0	THSD4_HUMAN	thrombospondin, type I, domain containing 4	902	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.				elastic fiber assembly (GO:0048251)	extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)	metalloendopeptidase activity (GO:0004222)			breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(20)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						CCTGGAGAAACCCCCCAGCCA	0.522																																					p.K900fs		Atlas-INDEL	.											.	THSD4	75	.	0			c.2700delA						.						101	103	102					15																	72057470		1909	4133	6042	SO:0001589	frameshift_variant	79875	exon15			.	AK023772	CCDS10238.2, CCDS66817.1	15q23	2009-11-09			ENSG00000187720	ENSG00000187720			25835	protein-coding gene	gene with protein product		614476				19734141	Standard	NM_001286429		Approved	FVSY9334, PRO34005, FLJ13710, ADAMTSL6	uc002atb.1	Q6ZMP0	OTTHUMG00000133389	ENST00000355327.3:c.2701delC	chr15.hg19:g.72057470delC	ENSP00000347484:p.Pro902fs	136.0	0.0		113.0	20.0	NM_024817	B2RTY3|B4DR13|Q6MZI3|Q6UXZ8|Q9H8E4	Frame_Shift_Del	DEL	ENST00000355327.3	hg19	CCDS10238.2																																																																																			.	.		0.522	THSD4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257253.2	NM_024817		-	72057470	C	-	72057470	7	5	352	1	0	1	0	1	0	0	0	0	15893	507	18	0	2759	0	THSD4	15	72057470	Frame_Shift_Del	DEL	C	TCGA-WQ-A9G7-01A-11D-A36X-10	5235578	72057470	30473922	338	49754										
C15orf60	283677	hgsc.bcm.edu	37	chr15	73832844	73832844	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aggaagggttttcactcattGgtagcaaggactggttgaag	14	5	2	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr15:73832844G>T	ENST00000331090.6	+	3	296	c.268G>T	c.(268-270)Ggt>Tgt	p.G90C	C15orf60_ENST00000560581.1_Intron	NM_001042367.1	NP_001035826.1	Q7Z4M0	RE114_HUMAN		90					DNA recombination (GO:0006310)|meiotic nuclear division (GO:0007126)					endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|pancreas(1)|prostate(2)	17						TTCACTCATTGGTAGCAAGGA	0.378																																					p.G90C		Atlas-SNP	.											.	C15orf60	26	.	0			c.G268T						.						324	298	306					15																	73832844		1862	4088	5950	SO:0001583	missense	283677	exon3			CTCATTGGTAGCA																												ENST00000331090.6:c.268G>T	chr15.hg19:g.73832844G>T	ENSP00000328423:p.Gly90Cys	113.0	0.0		95.0	4.0	NM_001042367		Missense_Mutation	SNP	ENST00000331090.6	hg19	CCDS45296.1	.	.	.	.	.	.	.	.	.	.	G	15.81	2.943173	0.53079	.	.	ENSG00000183324	ENST00000331090	T	0.50277	0.75	4.97	3.98	0.46160	.	0.593958	0.17972	N	0.155808	T	0.58495	0.2126	L	0.48362	1.52	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.56111	-0.8033	10	0.46703	T	0.11	-9.4765	10.479	0.44682	0.0:0.197:0.803:0.0	.	90	Q7Z4M0	CO060_HUMAN	C	90	ENSP00000328423:G90C	ENSP00000328423:G90C	G	+	1	0	C15orf60	71619897	0.956000	0.32656	0.998000	0.56505	0.889000	0.51656	1.301000	0.33447	2.297000	0.77311	0.563000	0.77884	GGT	.	.		0.378	C15orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419069.1			T	73832844	G	T	73832844	3	4	352	1	0	0	0	0	1	0	0	0	1810	1348	47	3	278	3	C15orf60	15	73832844	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	1775374	73832844	28698548	339	49755										
C15orf59	388135	hgsc.bcm.edu	37	chr15	74043430	74043430	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tcaccaccactgctggggtcGtcactgggctgcccgaggtc	13	15	2	0	rs146110202		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr15:74043430G>A	ENST00000569673.1	-	2	1246	c.42C>T	c.(40-42)gaC>gaT	p.D14D	C15orf59_ENST00000379822.4_Silent_p.D14D			Q2T9L4	CO059_HUMAN	chromosome 15 open reading frame 59	14										breast(1)|endometrium(2)|large_intestine(2)|lung(6)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						TGCTGGGGTCGTCACTGGGCT	0.657																																					p.D14D		Atlas-SNP	.											.	C15orf59	38	.	0			c.C42T						.						65	58	60					15																	74043430		2198	4297	6495	SO:0001819	synonymous_variant	388135	exon1			GGGGTCGTCACTG		CCDS32289.1	15q24.1	2012-09-27			ENSG00000205363	ENSG00000205363			33753	protein-coding gene	gene with protein product							Standard	XM_005254369		Approved	MGC131524, LOC388135	uc002avy.3	Q2T9L4	OTTHUMG00000172556	ENST00000569673.1:c.42C>T	chr15.hg19:g.74043430G>A		46.0	0.0		41.0	6.0	NM_001039614		Silent	SNP	ENST00000569673.1	hg19	CCDS32289.1																																																																																			.	G|1.000;C|0.000		0.657	C15orf59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419077.2	NM_001039614		A	74043430	G	A	74043430	2	1	352	1	0	0	0	0	0	0	0	1	1809	1136	40	1		1	C15orf59	15	74043430	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	210586	74043430	28487962	340	49756										
AP3B2	8120	hgsc.bcm.edu	37	chr15	83357549	83357549	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggtcttgctgctcctcagcgTagcgtaccaggtacacatag	11	12	2	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr15:83357549T>C	ENST00000261722.3	-	4	506	c.299A>G	c.(298-300)tAc>tGc	p.Y100C	RP11-752G15.3_ENST00000560650.1_RNA|AP3B2_ENST00000535348.1_Intron|AP3B2_ENST00000535359.1_Missense_Mutation_p.Y100C|AP3B2_ENST00000561455.1_5'UTR|AP3B2_ENST00000542200.1_Missense_Mutation_p.Y100C	NM_004644.3	NP_004635.2	Q13367	AP3B2_HUMAN	adaptor-related protein complex 3, beta 2 subunit	100					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|intracellular protein transport (GO:0006886)|post-Golgi vesicle-mediated transport (GO:0006892)	AP-3 adaptor complex (GO:0030123)|COPI-coated vesicle (GO:0030137)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(4)|endometrium(1)|kidney(1)|large_intestine(4)|lung(21)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(2)	41			BRCA - Breast invasive adenocarcinoma(143;0.229)			CTCCTCAGCGTAGCGTACCAG	0.607																																					p.Y100C		Atlas-SNP	.											.	AP3B2	103	.	0			c.A299G						.						77	83	81					15																	83357549		2120	4237	6357	SO:0001583	missense	8120	exon4			TCAGCGTAGCGTA	U37673	CCDS45331.1, CCDS61736.1, CCDS61737.1	15q	2008-07-07			ENSG00000103723	ENSG00000103723			567	protein-coding gene	gene with protein product		602166				7671305, 1851215	Standard	NM_004644		Approved	NAPTB	uc010uoh.2	Q13367	OTTHUMG00000168009	ENST00000261722.3:c.299A>G	chr15.hg19:g.83357549T>C	ENSP00000261722:p.Tyr100Cys	102.0	0.0		81.0	11.0	NM_004644	A4Z4T7|B7ZKR7|B7ZKS0|O14808|Q52LY8	Missense_Mutation	SNP	ENST00000261722.3	hg19	CCDS45331.1	.	.	.	.	.	.	.	.	.	.	T	27.1	4.800788	0.90538	.	.	ENSG00000103723	ENST00000261722;ENST00000535359;ENST00000541693;ENST00000542200;ENST00000535513	T;T;T;T	0.13657	2.57;2.57;2.57;2.57	5.95	5.95	0.96441	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.53514	0.1801	H	0.97077	3.935	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.991;0.997;1.0	T	0.70339	-0.4899	10	0.87932	D	0	-10.8441	16.0639	0.80859	0.0:0.0:0.0:1.0	.	100;100;100	F5H0E6;B7ZKS0;Q13367	.;.;AP3B2_HUMAN	C	100;100;56;100;100	ENSP00000261722:Y100C;ENSP00000440984:Y100C;ENSP00000441961:Y56C;ENSP00000440719:Y100C	ENSP00000261722:Y100C	Y	-	2	0	AP3B2	81154603	1.000000	0.71417	0.879000	0.34478	0.971000	0.66376	7.911000	0.87458	2.268000	0.75426	0.533000	0.62120	TAC	.	.		0.607	AP3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397463.1			C	83357549	T	C	83357549	3	2	352	1	0	0	0	0	1	0	0	0	745	1638	57	2	2965	2	AP3B2	15	83357549	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	9314119	83357549	19173843	341	49757										
KIF7	374654	hgsc.bcm.edu	37	chr15	90192526	90192526	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tggctcccgtgtgccgcgccGcgttgcccatctccaggagg	14	16	1	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr15:90192526G>A	ENST00000394412.3	-	4	678	c.602C>T	c.(601-603)gCg>gTg	p.A201V		NM_198525.2	NP_940927.2	Q2M1P5	KIF7_HUMAN	kinesin family member 7	201	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of smoothened signaling pathway (GO:0045880)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|kinesin complex (GO:0005871)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|stomach(1)|urinary_tract(1)	25	Lung NSC(78;0.0237)|all_lung(78;0.0478)		BRCA - Breast invasive adenocarcinoma(143;0.128)			GTGCCGCGCCGCGTTGCCCAT	0.701																																					p.A201V		Atlas-SNP	.											.	KIF7	130	.	0			c.C602T						.						1	2	2					15																	90192526		483	1220	1703	SO:0001583	missense	374654	exon4			CGCGCCGCGTTGC	AY358384	CCDS32325.2	15q26.1	2011-06-02			ENSG00000166813	ENSG00000166813		"Kinesins"	30497	protein-coding gene	gene with protein product		611254				11416179, 15547730	Standard	NM_198525		Approved	JBTS12	uc002bof.2	Q2M1P5	OTTHUMG00000157177	ENST00000394412.3:c.602C>T	chr15.hg19:g.90192526G>A	ENSP00000377934:p.Ala201Val	81.0	0.0		64.0	8.0	NM_198525	Q3SXY0|Q6UXE9|Q8IW72	Missense_Mutation	SNP	ENST00000394412.3	hg19	CCDS32325.2	.	.	.	.	.	.	.	.	.	.	g	27.7	4.857665	0.91433	.	.	ENSG00000166813	ENST00000394412	T	0.75821	-0.97	4.03	4.03	0.46877	Kinesin, motor domain (4);	.	.	.	.	T	0.68403	0.2997	M	0.72576	2.205	0.40517	D	0.980792	P	0.48911	0.917	B	0.38106	0.265	T	0.70073	-0.4972	9	0.29301	T	0.29	.	11.1029	0.48186	0.0938:0.0:0.9062:0.0	.	201	Q2M1P5	KIF7_HUMAN	V	201	ENSP00000377934:A201V	ENSP00000377934:A201V	A	-	2	0	KIF7	87993530	1.000000	0.71417	0.803000	0.32268	0.981000	0.71138	6.325000	0.72901	2.244000	0.73946	0.645000	0.84053	GCG	.	.		0.701	KIF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347782.1	NM_198525		A	90192526	G	A	90192526	3	1	352	1	0	0	0	0	1	0	0	0	8318	1087	38	1	3493	1	KIF7	15	90192526	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	6834977	90192526	12338866	342	49758										
C15orf58	390637	hgsc.bcm.edu	37	chr15	90784264	90784264	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	atctcatggcagaagggattCagtggccaaggaatgcacct	12	9	2	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr15:90784264C>T	ENST00000558017.1	+	4	544	c.124C>T	c.(124-126)Cag>Tag	p.Q42*	GDPGP1_ENST00000329600.6_Nonsense_Mutation_p.Q42*	NM_001013657.2	NP_001013679.2	Q6ZNW5	GDPP1_HUMAN	GDP-D-glucose phosphorylase 1	42					glucose metabolic process (GO:0006006)	cytoplasm (GO:0005737)	GDP-D-glucose phosphorylase activity (GO:0080048)|guanyl-nucleotide exchange factor activity (GO:0005085)|hydrolase activity (GO:0016787)|nucleotide binding (GO:0000166)|nucleotidyltransferase activity (GO:0016779)										AGAAGGGATTCAGTGGCCAAG	0.547																																					p.Q42X		Atlas-SNP	.											.	.	.	.	0			c.C124T						.						170	171	171					15																	90784264		2199	4298	6497	SO:0001587	stop_gained	390637	exon4			GGGATTCAGTGGC		CCDS32327.1	15q26.1	2012-05-04	2012-05-04	2012-05-04	ENSG00000183208	ENSG00000183208	2.7.7.78		34360	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 58"	C15orf58		21507950	Standard	NM_001013657		Approved		uc002bpc.3	Q6ZNW5		ENST00000558017.1:c.124C>T	chr15.hg19:g.90784264C>T	ENSP00000452793:p.Gln42*	81.0	0.0		56.0	12.0	NM_001013657		Nonsense_Mutation	SNP	ENST00000558017.1	hg19	CCDS32327.1	.	.	.	.	.	.	.	.	.	.	C	16.66	3.185852	0.57909	.	.	ENSG00000183208	ENST00000329600	.	.	.	5.35	5.35	0.76521	.	0.370861	0.25648	N	0.029223	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07482	T	0.82	-19.6182	12.1766	0.54188	0.0:0.8286:0.1714:0.0	.	.	.	.	X	42	.	ENSP00000368405:Q42X	Q	+	1	0	C15orf58	88585268	0.996000	0.38824	0.994000	0.49952	0.532000	0.34746	3.731000	0.55013	2.792000	0.96026	0.557000	0.71058	CAG	.	.		0.547	GDPGP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416973.1	NM_001013657		T	90784264	C	T	90784264	4	4	352	1	0	0	0	0	0	1	0	0	1808	827	29	3	126	3	C15orf58	15	90784264	Nonsense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	591738	90784264	11747128	343	49759										
FURIN	5045	hgsc.bcm.edu	37	chr15	91424700	91424700	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gggccggccctgacagactgCctcagctgccccagccacgc	12	19	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr15:91424700C>T	ENST00000268171.3	+	16	2256	c.1977C>T	c.(1975-1977)tgC>tgT	p.C659C	FES_ENST00000328850.3_5'Flank|FES_ENST00000414248.2_5'Flank|FES_ENST00000394302.1_5'Flank	NM_002569.2	NP_002560.1	P09958	FURIN_HUMAN	furin (paired basic amino acid cleaving enzyme)	659					cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of low-density lipoprotein particle receptor catabolic process (GO:0032804)|negative regulation of transforming growth factor beta1 production (GO:0032911)|nerve growth factor processing (GO:0032455)|nerve growth factor production (GO:0032902)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|post-translational protein modification (GO:0043687)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)|regulation of protein catabolic process (GO:0042176)|secretion by cell (GO:0032940)|signal peptide processing (GO:0006465)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|nerve growth factor binding (GO:0048406)|peptidase activity (GO:0008233)|peptide binding (GO:0042277)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(4)|endometrium(4)|large_intestine(3)|liver(2)|lung(13)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	36	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			TGACAGACTGCCTCAGCTGCC	0.672																																					p.C659C		Atlas-SNP	.											.	FURIN	85	.	0			c.C1977T						.						29	32	31					15																	91424700		2197	4293	6490	SO:0001819	synonymous_variant	5045	exon16			AGACTGCCTCAGC	X17094	CCDS10364.1	15q26.1	2007-01-24	2002-12-04	2002-12-06	ENSG00000140564	ENSG00000140564			8568	protein-coding gene	gene with protein product		136950	"paired basic amino acid cleaving enzyme (furin, membrane associated receptor protein)"	PCSK3, FUR, PACE		2251280, 1741956	Standard	NM_002569		Approved	SPC1	uc002bpu.1	P09958	OTTHUMG00000149831	ENST00000268171.3:c.1977C>T	chr15.hg19:g.91424700C>T		81.0	0.0		75.0	11.0	NM_002569	Q14336|Q6LBS3|Q9UCZ5	Silent	SNP	ENST00000268171.3	hg19	CCDS10364.1																																																																																			.	.		0.672	FURIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313492.1	NM_002569		T	91424700	C	T	91424700	2	4	352	1	0	0	0	0	0	0	0	1	6107	747	26	3		3	FURIN	15	91424700	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	640436	91424700	11106692	344	49760										
MCTP2	55784	hgsc.bcm.edu	37	chr15	94943190	94943190	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ttttactccccgggaaaagcGctttgttgaagacagccgca	10	11	0	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr15:94943190G>A	ENST00000357742.4	+	15	1931	c.1931G>A	c.(1930-1932)cGc>cAc	p.R644H	MCTP2_ENST00000331706.4_Missense_Mutation_p.R232H|MCTP2_ENST00000557742.1_Missense_Mutation_p.R232H|MCTP2_ENST00000451018.3_Missense_Mutation_p.R644H	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2	644					calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|liver(1)|lung(12)|ovary(1)|pancreas(1)|skin(9)|stomach(2)	49	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)			CGGGAAAAGCGCTTTGTTGAA	0.458																																					p.R644H		Atlas-SNP	.											.	MCTP2	122	.	0			c.G1931A						.						93	93	93					15																	94943190		2197	4298	6495	SO:0001583	missense	55784	exon15			AAAAGCGCTTTGT	AK002037	CCDS32338.1, CCDS53975.1, CCDS53976.1	15q26.2	2006-02-08				ENSG00000140563			25636	protein-coding gene	gene with protein product						15528213	Standard	NM_018349		Approved	FLJ11175, FLJ33303	uc002btj.3	Q6DN12		ENST00000357742.4:c.1931G>A	chr15.hg19:g.94943190G>A	ENSP00000350377:p.Arg644His	129.0	0.0		108.0	20.0	NM_001159643	A2RRC2|C6G483|C6G484|Q49AB0|Q8TAX2|Q9NUS2|Q9NUW7	Missense_Mutation	SNP	ENST00000357742.4	hg19	CCDS32338.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.605122	0.87157	.	.	ENSG00000140563	ENST00000451018;ENST00000331706;ENST00000357742	T;T;T	0.68025	-0.3;-0.04;-0.14	5.22	4.31	0.51392	C2 calcium/lipid-binding domain, CaLB (1);	0.150976	0.64402	N	0.000019	T	0.73860	0.3641	L	0.50333	1.59	0.49582	D	0.999802	D;D;D	0.76494	0.969;0.998;0.999	P;P;P	0.60415	0.635;0.874;0.864	T	0.76664	-0.2876	10	0.87932	D	0	.	13.5101	0.61506	0.0757:0.0:0.9243:0.0	.	644;232;644	Q6DN12-2;Q6DN12-4;Q6DN12	.;.;MCTP2_HUMAN	H	644;232;644	ENSP00000395109:R644H;ENSP00000329646:R232H;ENSP00000350377:R644H	ENSP00000329646:R232H	R	+	2	0	MCTP2	92744194	1.000000	0.71417	0.999000	0.59377	0.974000	0.67602	4.154000	0.58125	1.190000	0.43042	0.563000	0.77884	CGC	.	.		0.458	MCTP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415060.3	NM_018349		A	94943190	G	A	94943190	3	1	352	1	0	0	0	0	1	0	0	0	9410	1087	38	1	1989	1	MCTP2	15	94943190	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	3518490	94943190	7588202	345	49761										
FBXL16	146330	hgsc.bcm.edu	37	chr16	744677	744677	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ctccccagggccaggaggtgCttcagcccgaagtcttgcac	12	15	2	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr16:744677C>T	ENST00000397621.1	-	5	1579	c.1248G>A	c.(1246-1248)aaG>aaA	p.K416K	FBXL16_ENST00000562585.1_5'UTR|FBXL16_ENST00000562563.1_Silent_p.K204K|FBXL16_ENST00000324361.5_Silent_p.K416K|LA16c-313D11.12_ENST00000566927.1_RNA	NM_153350.3	NP_699181.2	Q8N461	FXL16_HUMAN	F-box and leucine-rich repeat protein 16	416										endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|ovary(1)	10		Hepatocellular(780;0.0218)				CCAGGAGGTGCTTCAGCCCGA	0.647																																					p.K416K		Atlas-SNP	.											.	FBXL16	25	.	0			c.G1248A						.						49	45	46					16																	744677		2194	4295	6489	SO:0001819	synonymous_variant	146330	exon5			GAGGTGCTTCAGC	BC036680	CCDS10421.1	16p13.3	2011-06-09	2004-06-15	2004-06-16	ENSG00000127585	ENSG00000127585		"F-boxes / Leucine-rich repeats"	14150	protein-coding gene	gene with protein product		609082	"chromosome 16 open reading frame 22"	C16orf22		11157797	Standard	NM_153350		Approved	MGC33974, Fbl16	uc021taa.1	Q8N461	OTTHUMG00000090420	ENST00000397621.1:c.1248G>A	chr16.hg19:g.744677C>T		119.0	0.0		107.0	39.0	NM_153350	B3KR59|D3DU60|Q2MHR2|Q96S14|Q9UJI0	Silent	SNP	ENST00000397621.1	hg19	CCDS10421.1																																																																																			.	.		0.647	FBXL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206851.2	NM_153350		T	744677	C	T	744677	2	4	352	1	0	0	0	0	0	0	0	1	5720	796	28	3		3	FBXL16	16	744677	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10		744677	89610076	346	49762										
CHTF18	63922	hgsc.bcm.edu	37	chr16	844174	844174	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gtcctgcatgccgctgcctcTgcgggcgagcacgagaaggt	15	13	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr16:844174T>C	ENST00000262315.9	+	15	1986	c.1923T>C	c.(1921-1923)tcT>tcC	p.S641S	CHTF18_ENST00000317063.6_Silent_p.S850S|CHTF18_ENST00000455171.2_Silent_p.S669S	NM_022092.2	NP_071375.1	Q8WVB6	CTF18_HUMAN	CTF18, chromosome transmission fidelity factor 18 homolog (S. cerevisiae)	641					cell cycle (GO:0007049)|DNA replication (GO:0006260)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(1)|kidney(3)|liver(2)|lung(4)|prostate(1)	11		Hepatocellular(780;0.00335)				CCGCTGCCTCTGCGGGCGAGC	0.687																																					p.S641S		Atlas-SNP	.											.	CHTF18	52	.	0			c.T1923C						.						38	46	44					16																	844174		2174	4274	6448	SO:0001819	synonymous_variant	63922	exon15			TGCCTCTGCGGGC	BC018184	CCDS45371.1	16p13.3	2010-04-21	2003-12-09		ENSG00000127586	ENSG00000127586		"ATPases / AAA-type"	18435	protein-coding gene	gene with protein product		613201	"chromosome 16 open reading frame 41"	C16orf41		12171929	Standard	NM_022092		Approved	CHL12, C321D2.4, Ctf18	uc002cke.4	Q8WVB6	OTTHUMG00000047838	ENST00000262315.9:c.1923T>C	chr16.hg19:g.844174T>C		132.0	0.0		105.0	54.0	NM_022092	B7ZBA2|D3DU68|Q7Z6Y4|Q7Z6Y6|Q9BR83|Q9BRG5|Q9H7K3	Silent	SNP	ENST00000262315.9	hg19	CCDS45371.1																																																																																			.	.		0.687	CHTF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109061.3	NM_022092		C	844174	T	C	844174	2	2	352	1	0	0	0	0	0	0	0	1	3416	1567	55	2		2	CHTF18	16	844174	Silent	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	99497	844174	89510579	347	49763										
RPS2	6187	hgsc.bcm.edu	37	chr16	2012581	2012581	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tcatgagcagcttcttaggcAcaggtgcggagacgatgcca	13	10	2	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr16:2012581A>G	ENST00000343262.4	-	6	682	c.626T>C	c.(625-627)gTg>gCg	p.V209A	RPS2_ENST00000530225.1_Intron|SNORA64_ENST00000384674.1_RNA|RPS2_ENST00000526522.1_Missense_Mutation_p.V151A|SNHG9_ENST00000459373.1_lincRNA|SNORA10_ENST00000384084.1_RNA|RPS2_ENST00000529806.1_Missense_Mutation_p.V179A	NM_002952.3	NP_002943.2	P15880	RS2_HUMAN	ribosomal protein S2	209					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of transferase activity (GO:0051347)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|urinary_tract(2)	7						CTTCTTAGGCACAGGTGCGGA	0.622																																					p.V209A		Atlas-SNP	.											.	RPS2	18	.	0			c.T626C						.						22	24	24					16																	2012581		2190	4270	6460	SO:0001583	missense	6187	exon6			TTAGGCACAGGTG	AB007147	CCDS10452.1	16p13.3	2011-04-05			ENSG00000140988	ENSG00000140988		"S ribosomal proteins"	10404	protein-coding gene	gene with protein product		603624				9582194	Standard	NM_002952		Approved	LLREP3, S2	uc002cno.2	P15880	OTTHUMG00000128708	ENST00000343262.4:c.626T>C	chr16.hg19:g.2012581A>G	ENSP00000341885:p.Val209Ala	106.0	0.0		68.0	9.0	NM_002952	B2R5G0|D3DU82|Q3MIB1	Missense_Mutation	SNP	ENST00000343262.4	hg19	CCDS10452.1	.	.	.	.	.	.	.	.	.	.	a	20.9	4.074141	0.76415	.	.	ENSG00000140988	ENST00000526522;ENST00000533186;ENST00000343262;ENST00000529806;ENST00000527302	.	.	.	4.52	4.52	0.55395	Ribosomal protein S5 domain 2-type fold (1);Ribosomal protein S5, C-terminal (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);	0.000000	0.64402	U	0.000007	T	0.52773	0.1755	L	0.58583	1.82	0.80722	D	1	P;B	0.35507	0.506;0.182	B;B	0.34931	0.192;0.147	T	0.53927	-0.8369	9	0.34782	T	0.22	.	13.1915	0.59713	1.0:0.0:0.0:0.0	.	209;151	P15880;E9PQD7	RS2_HUMAN;.	A	151;111;209;179;209	.	ENSP00000341885:V209A	V	-	2	0	RPS2	1952582	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	7.388000	0.79795	1.716000	0.51395	0.524000	0.50904	GTG	.	.		0.622	RPS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250613.2	NM_002952		G	2012581	A	G	2012581	3	3	352	1	0	0	0	0	1	0	0	0	13646	159	6	2	263	2	RPS2	16	2012581	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	1168407	2012581	88342172	348	49764										
CREBBP	1387	hgsc.bcm.edu	37	chr16	3778436	3778436	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tgctgctgttgttgctgctgCtgttgctgctgctgctgcag	14	10	0	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr16:3778436C>T	ENST00000262367.5	-	31	7421	c.6612G>A	c.(6610-6612)caG>caA	p.Q2204Q	CREBBP_ENST00000382070.3_Silent_p.Q2166Q	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	2204	Poly-Gln.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		gttgctgctgctgttgctgct	0.597			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																														p.Q2204Q		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP	546	.	0			c.G6612A						.						33	31	31					16																	3778436		2192	4287	6479	SO:0001819	synonymous_variant	1387	exon31			CTGCTGCTGTTGC	U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.6612G>A	chr16.hg19:g.3778436C>T		68.0	0.0		46.0	18.0	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Silent	SNP	ENST00000262367.5	hg19	CCDS10509.1																																																																																			.	.		0.597	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		T	3778436	C	T	3778436	2	4	352	1	0	0	0	0	0	0	0	1	3863	796	28	3		3	CREBBP	16	3778436	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	1765855	3778436	86576317	349	49765										
VASN	114990	hgsc.bcm.edu	37	chr16	4432614	4432614	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	caacctgccgctcctcattgCgcccgccctggccgcggtgc	11	20	1	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr16:4432614C>T	ENST00000304735.3	+	2	1891	c.1736C>T	c.(1735-1737)gCg>gTg	p.A579V	CORO7_ENST00000537233.2_Intron|CORO7_ENST00000539968.1_Intron|CORO7-PAM16_ENST00000572467.1_Intron|CORO7_ENST00000574025.1_Intron|CORO7_ENST00000251166.4_Intron|CORO7_ENST00000423908.2_Intron	NM_138440.2	NP_612449.2	Q6EMK4	VASN_HUMAN	vasorin	579					cellular response to hypoxia (GO:0071456)|cellular response to redox state (GO:0071461)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	transforming growth factor beta binding (GO:0050431)			breast(1)|lung(3)|prostate(1)|skin(1)	6						CTCCTCATTGCGCCCGCCCTG	0.746																																					p.A579V		Atlas-SNP	.											.	VASN	21	.	0			c.C1736T						.						6	10	8					16																	4432614		2021	3964	5985	SO:0001583	missense	114990	exon2			TCATTGCGCCCGC	AY358299	CCDS10514.1	16p13.3	2008-02-05	2006-03-30	2006-03-30	ENSG00000168140	ENSG00000168140			18517	protein-coding gene	gene with protein product		608843	"slit-like 2 (Drosophila)"	SLITL2		15247411	Standard	NM_138440		Approved		uc002cwj.1	Q6EMK4	OTTHUMG00000129469	ENST00000304735.3:c.1736C>T	chr16.hg19:g.4432614C>T	ENSP00000306864:p.Ala579Val	135.0	0.0		111.0	24.0	NM_138440	Q6UXL4|Q6UXL5|Q96CX1	Missense_Mutation	SNP	ENST00000304735.3	hg19	CCDS10514.1	.	.	.	.	.	.	.	.	.	.	C	4.589	0.109486	0.08780	.	.	ENSG00000168140	ENST00000304735	T	0.53206	0.63	5.46	4.41	0.53225	.	0.278844	0.35739	N	0.003016	T	0.20941	0.0504	N	0.04880	-0.145	0.36322	D	0.858317	B	0.21452	0.056	B	0.08055	0.003	T	0.17319	-1.0373	10	0.28530	T	0.3	-15.4703	4.2941	0.10892	0.0:0.7068:0.0:0.2932	.	579	Q6EMK4	VASN_HUMAN	V	579	ENSP00000306864:A579V	ENSP00000306864:A579V	A	+	2	0	VASN	4372615	1.000000	0.71417	0.276000	0.24689	0.925000	0.55904	3.874000	0.56101	2.561000	0.86390	0.655000	0.94253	GCG	.	.		0.746	VASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251632.1	NM_138440		T	4432614	C	T	4432614	3	4	352	1	0	0	0	0	1	0	0	0	17142	768	27	1	1738	1	VASN	16	4432614	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	654178	4432614	85922139	350	49766										
ROGDI	79641	hgsc.bcm.edu	37	chr16	4851539	4851539	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	atgaagttctcttgcttggcGggcccctcagtgccggagcc	13	13	2	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr16:4851539G>A	ENST00000322048.7	-	3	543	c.165C>T	c.(163-165)ccC>ccT	p.P55P	ROGDI_ENST00000586336.1_5'UTR	NM_024589.2	NP_078865.1	Q9GZN7	ROGDI_HUMAN	rogdi homolog (Drosophila)	55					hemopoiesis (GO:0030097)|positive regulation of cell proliferation (GO:0008284)	intracellular (GO:0005622)|nucleus (GO:0005634)				endometrium(2)|lung(1)|ovary(1)|skin(1)	5						CTTGCTTGGCGGGCCCCTCAG	0.657																																					p.P55P		Atlas-SNP	.											.	ROGDI	11	.	0			c.C165T						.						28	31	30					16																	4851539		2196	4300	6496	SO:0001819	synonymous_variant	79641	exon3			CTTGGCGGGCCCC	AK026039	CCDS10523.1	16p13.3	2014-09-17			ENSG00000067836	ENSG00000067836			29478	protein-coding gene	gene with protein product		614574				11230166	Standard	NM_024589		Approved	FLJ22386	uc002cxv.4	Q9GZN7	OTTHUMG00000129479	ENST00000322048.7:c.165C>T	chr16.hg19:g.4851539G>A		81.0	0.0		61.0	22.0	NM_024589	Q6IA00	Silent	SNP	ENST00000322048.7	hg19	CCDS10523.1																																																																																			.	.		0.657	ROGDI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251643.3	NM_024589		A	4851539	G	A	4851539	2	1	352	1	0	0	0	0	0	0	0	1	13535	1103	39	1		1	ROGDI	16	4851539	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	418925	4851539	85503214	351	49767										
GRIN2A	2903	hgsc.bcm.edu	37	chr16	9858337	9858337	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ctgggatagtgaatcctggcGtatggaatccacggatttct	12	8	1	1	rs560057284	byFrequency	TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr16:9858337G>A	ENST00000396573.2	-	14	3373	c.3064C>T	c.(3064-3066)Cgc>Tgc	p.R1022C	GRIN2A_ENST00000535259.1_Missense_Mutation_p.R865C|GRIN2A_ENST00000330684.3_Missense_Mutation_p.R1022C|GRIN2A_ENST00000396575.2_Missense_Mutation_p.R1022C|GRIN2A_ENST00000562109.1_Missense_Mutation_p.R1022C|GRIN2A_ENST00000404927.2_Missense_Mutation_p.R1022C	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	1022					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)	p.R1022C(1)		NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GAATCCTGGCGTATGGAATCC	0.532													G|||	2	0.000399361	0	0	5008	,	,		16566	0.002		0	False		,,,				2504	0				p.R1022C		Atlas-SNP	.											GRIN2A,NS,carcinoma,0,1	GRIN2A	366	.	1	Substitution - Missense(1)	endometrium(1)	c.C3064T						.						107	113	111					16																	9858337		2197	4300	6497	SO:0001583	missense	2903	exon14			CCTGGCGTATGGA		CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.3064C>T	chr16.hg19:g.9858337G>A	ENSP00000379818:p.Arg1022Cys	78.0	0.0		54.0	17.0	NM_000833	O00669|Q17RZ6	Missense_Mutation	SNP	ENST00000396573.2	hg19	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	G	18.27	3.587603	0.66105	.	.	ENSG00000183454	ENST00000396573;ENST00000404927;ENST00000535259;ENST00000330684;ENST00000396575	T;T;T;T;T	0.13196	2.61;2.62;2.62;2.61;2.61	5.33	5.33	0.75918	Glutamate [NMDA] receptor, epsilon subunit, C-terminal (1);	0.050105	0.85682	D	0.000000	T	0.37404	0.1002	M	0.67953	2.075	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.996;0.964;0.998	T	0.03139	-1.1068	9	.	.	.	.	18.0262	0.89270	0.0:0.0:1.0:0.0	.	865;1022;1022	F5GZ52;Q17RZ6;Q12879	.;.;NMDE1_HUMAN	C	1022;1022;865;1022;1022	ENSP00000379818:R1022C;ENSP00000385872:R1022C;ENSP00000441572:R865C;ENSP00000332549:R1022C;ENSP00000379820:R1022C	.	R	-	1	0	GRIN2A	9765838	1.000000	0.71417	0.944000	0.38274	0.803000	0.45373	7.520000	0.81821	2.491000	0.84063	0.655000	0.94253	CGC	.	.		0.532	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			A	9858337	G	A	9858337	3	1	352	1	0	0	0	0	1	0	0	0	6788	1145	40	1	1334	1	GRIN2A	16	9858337	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	5006798	9858337	80496416	352	49768										
TMC5	79838	hgsc.bcm.edu	37	chr16	19471655	19471655	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tggaagagaaaaggaaccttAggtatggactaaaggctttt	12	4	0	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr16:19471655A>G	ENST00000396229.2	+	6	1896	c.1147A>G	c.(1147-1149)Agg>Ggg	p.R383G	TMC5_ENST00000564959.1_Splice_Site_p.S45G|TMC5_ENST00000219821.5_Splice_Site_p.R137G|TMC5_ENST00000561503.1_Splice_Site_p.R24G|TMC5_ENST00000542583.2_Splice_Site_p.R383G|TMC5_ENST00000541464.1_Splice_Site_p.R383G|TMC5_ENST00000381414.4_Splice_Site_p.R383G	NM_001105248.1	NP_001098718.1	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5	383					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|liver(2)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						AAGGAACCTTAGGTATGGACT	0.403																																					p.R383G		Atlas-SNP	.											.	TMC5	169	.	0			c.A1147G						.						76	67	70					16																	19471655		2197	4300	6497	SO:0001630	splice_region_variant	79838	exon6			AACCTTAGGTATG	AY263164	CCDS10577.1, CCDS42126.1, CCDS45431.1	16p13.11	2008-02-05			ENSG00000103534	ENSG00000103534			22999	protein-coding gene	gene with protein product						12812529, 12906855	Standard	NM_024780		Approved	FLJ13593	uc010var.2	Q6UXY8	OTTHUMG00000131458	ENST00000396229.2:c.1148+1A>G	chr16.hg19:g.19471655A>G		444.0	0.0		325.0	125.0	NM_001105249	Q68DK8|Q8IY20|Q8NHV6|Q9H8I7	Missense_Mutation	SNP	ENST00000396229.2	hg19	CCDS45431.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.59|16.59	3.165545|3.165545	0.57476|0.57476	.|.	.|.	ENSG00000103534|ENSG00000103534	ENST00000541464;ENST00000381414;ENST00000396229;ENST00000542583;ENST00000219821|ENST00000440743	T;T;T;T;T|.	0.60797|.	0.16;0.16;0.16;0.16;0.16|.	5.28|5.28	5.28|5.28	0.74379|0.74379	.|.	.|.	.|.	.|.	.|.	T|T	0.58652|0.58652	0.2137|0.2137	L|L	0.59436|0.59436	1.845|1.845	0.54753|0.54753	D|D	0.999988|0.999988	D;D;D;P;P|B	0.65815|0.17038	0.985;0.995;0.991;0.954;0.853|0.02	P;P;P;P;P|B	0.62560|0.22386	0.798;0.904;0.804;0.632;0.474|0.039	T|T	0.54622|0.54622	-0.8266|-0.8266	9|7	0.66056|.	D|.	0.02|.	-15.142|-15.142	13.9455|13.9455	0.64082|0.64082	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	383;137;137;383;383|45	F5GYU8;Q6UXY8-3;B3KUQ8;Q6UXY8;Q6UXY8-2|E7EU57	.;.;.;TMC5_HUMAN;.|.	G|G	383;383;383;383;137|45	ENSP00000441227:R383G;ENSP00000370822:R383G;ENSP00000379531:R383G;ENSP00000446274:R383G;ENSP00000219821:R137G|.	ENSP00000219821:R137G|.	R|S	+|+	1|1	2|0	TMC5|TMC5	19379156|19379156	1.000000|1.000000	0.71417|0.71417	0.937000|0.937000	0.37676|0.37676	0.885000|0.885000	0.51271|0.51271	4.615000|4.615000	0.61190|0.61190	2.210000|2.210000	0.71456|0.71456	0.533000|0.533000	0.62120|0.62120	AGG|AGC	.	.		0.403	TMC5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435888.1	NM_024780	Missense_Mutation	G	19471655	A	G	19471655	5	3	352	1	0	0	0	0	0	0	1	0	16003	434	15	2	1475	2	TMC5	16	19471655	Splice_Site	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	9613318	19471655	70883098	353	49769										
GSG1L	146395	hgsc.bcm.edu	37	chr16	27895830	27895830	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agagcaccgtgaagacagccGcgaaggcattgagcttgagc	14	10	0	5	rs141366433		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr16:27895830G>A	ENST00000447459.2	-	3	611	c.527C>T	c.(526-528)gCg>gTg	p.A176V	GSG1L_ENST00000380897.3_Missense_Mutation_p.A21V|GSG1L_ENST00000569166.1_Missense_Mutation_p.A21V|GSG1L_ENST00000395724.3_Intron|GSG1L_ENST00000380898.2_Missense_Mutation_p.A21V	NM_001109763.1	NP_001103233.1	Q6UXU4	GSG1L_HUMAN	GSG1-like	176					regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)	asymmetric synapse (GO:0032279)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A21V(1)|p.A176V(1)		endometrium(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(4)	17						GAAGACAGCCGCGAAGGCATT	0.577																																					p.A176V		Atlas-SNP	.											GSG1L_ENST00000447459,NS,carcinoma,0,2	GSG1L	82	.	2	Substitution - Missense(2)	endometrium(2)	c.C527T						.	G	VAL/ALA,VAL/ALA	1,4393	2.1+/-5.4	0,1,2196	89	80	83		527,62	5.2	0.8	16	dbSNP_134	83	0,8600		0,0,4300	no	missense,missense	GSG1L	NM_001109763.1,NM_144675.2	64,64	0,1,6496	AA,AG,GG		0.0,0.0228,0.0077	possibly-damaging,possibly-damaging	176/332,21/177	27895830	1,12993	2197	4300	6497	SO:0001583	missense	146395	exon3			ACAGCCGCGAAGG	AK128775	CCDS10631.1, CCDS45450.1	16p11.2	2014-01-20			ENSG00000169181	ENSG00000169181			28283	protein-coding gene	gene with protein product						22813734	Standard	NM_001109763		Approved	MGC18079, PRO19651, KTSR5831	uc002doz.2	Q6UXU4	OTTHUMG00000131676	ENST00000447459.2:c.527C>T	chr16.hg19:g.27895830G>A	ENSP00000394954:p.Ala176Val	102.0	0.0		78.0	19.0	NM_001109763	Q7Z6F8|Q8TB81	Missense_Mutation	SNP	ENST00000447459.2	hg19	CCDS45450.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.744264	0.89663	2.28E-4	0.0	ENSG00000169181	ENST00000447459;ENST00000380898;ENST00000380897	T;D;D	0.91068	0.9;-2.78;-2.78	5.16	5.16	0.70880	.	.	.	.	.	D	0.93374	0.7887	L	0.46157	1.445	0.80722	D	1	D;D	0.89917	0.996;1.0	P;D	0.75484	0.858;0.986	D	0.92447	0.5967	9	0.37606	T	0.19	.	17.7781	0.88515	0.0:0.0:1.0:0.0	.	21;176	Q6UXU4-4;Q6UXU4	.;GSG1L_HUMAN	V	176;21;21	ENSP00000394954:A176V;ENSP00000370283:A21V;ENSP00000370282:A21V	ENSP00000370282:A21V	A	-	2	0	GSG1L	27803331	1.000000	0.71417	0.816000	0.32577	0.916000	0.54674	9.805000	0.99149	2.551000	0.86045	0.655000	0.94253	GCG	.	G|1.000;A|0.000		0.577	GSG1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433832.2	NM_144675		A	27895830	G	A	27895830	3	1	352	1	0	0	0	0	1	0	0	0	6830	1087	38	1	488	1	GSG1L	16	27895830	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	8424175	27895830	62458923	354	49770										
CORO1A	11151	hgsc.bcm.edu	37	chr16	30198463	30198463	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	atctacagtgtggactggagCcgagatggaggcctcatttg	14	8	2	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr16:30198463C>T	ENST00000219150.5	+	5	860	c.555C>T	c.(553-555)agC>agT	p.S185S	RP11-455F5.5_ENST00000567153.1_RNA|CORO1A_ENST00000570045.1_Silent_p.S185S|RP11-455F5.5_ENST00000568506.1_RNA|RP11-455F5.5_ENST00000566144.1_RNA|CORO1A_ENST00000565497.1_Silent_p.S185S	NM_001193333.2|NM_007074.3	NP_001180262.1|NP_009005.1	P31146	COR1A_HUMAN	coronin, actin binding protein, 1A	185					actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|calcium ion transport (GO:0006816)|cell-substrate adhesion (GO:0031589)|cellular component movement (GO:0006928)|cellular response to interleukin-4 (GO:0071353)|homeostasis of number of cells within a tissue (GO:0048873)|innate immune response (GO:0045087)|leukocyte chemotaxis (GO:0030595)|negative regulation of actin nucleation (GO:0051126)|phagocytosis (GO:0006909)|phagolysosome assembly (GO:0001845)|positive chemotaxis (GO:0050918)|positive regulation of cell migration (GO:0030335)|positive regulation of T cell proliferation (GO:0042102)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|T cell homeostasis (GO:0043029)|uropod organization (GO:0032796)	actin filament (GO:0005884)|cell-cell junction (GO:0005911)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|lamellipodium (GO:0030027)|membrane (GO:0016020)|phagocytic cup (GO:0001891)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	actin filament binding (GO:0051015)|cytoskeletal protein binding (GO:0008092)|phosphatidylinositol 3-kinase binding (GO:0043548)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	9						TGGACTGGAGCCGAGATGGAG	0.612																																					p.S185S		Atlas-SNP	.											.	CORO1A	36	.	0			c.C555T						.						89	77	81					16																	30198463		2197	4300	6497	SO:0001819	synonymous_variant	11151	exon6			CTGGAGCCGAGAT	X89109	CCDS10673.1	16p11.2	2014-09-17	2001-11-28		ENSG00000102879	ENSG00000102879		"Coronins", "WD repeat domain containing"	2252	protein-coding gene	gene with protein product	"Clabp TACO"	605000	"coronin, actin-binding protein, 1A"			9778037	Standard	NM_007074		Approved	HCORO1, p57, coronin-1	uc002dww.3	P31146	OTTHUMG00000132148	ENST00000219150.5:c.555C>T	chr16.hg19:g.30198463C>T		59.0	0.0		39.0	13.0	NM_001193333	B2RBL1|Q2YD73	Silent	SNP	ENST00000219150.5	hg19	CCDS10673.1																																																																																			.	.		0.612	CORO1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255195.2	NM_007074		T	30198463	C	T	30198463	2	4	352	1	0	0	0	0	0	0	0	1	3755	738	26	3		3	CORO1A	16	30198463	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	2302633	30198463	60156290	355	49771										
C16orf70	80262	hgsc.bcm.edu	37	chr16	67181027	67181027	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ccacctgagaacagcggaacTcccctagggacaccaccacc	8	18	0	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr16:67181027T>C	ENST00000219139.3	+	16	1450	c.1262T>C	c.(1261-1263)cTc>cCc	p.L421P	C16orf70_ENST00000569600.1_Missense_Mutation_p.L421P	NM_025187.3	NP_079463.2	Q9BSU1	CP070_HUMAN	chromosome 16 open reading frame 70	421										cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(3)|skin(1)	17		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0017)|Epithelial(162;0.00655)|all cancers(182;0.0579)		ACAGCGGAACTCCCCTAGGGA	0.592																																					p.L421P		Atlas-SNP	.											.	C16orf70	38	.	0			c.T1262C						.						146	128	134					16																	67181027		2198	4300	6498	SO:0001583	missense	80262	exon16			CGGAACTCCCCTA	AK022138	CCDS10828.1	16q22.1	2011-01-25	2006-04-12	2006-04-12	ENSG00000125149	ENSG00000125149			29564	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 6"	C16orf6, LIN10		12477932	Standard	NM_025187		Approved	lin-10, FLJ12076	uc002erd.3	Q9BSU1	OTTHUMG00000137510	ENST00000219139.3:c.1262T>C	chr16.hg19:g.67181027T>C	ENSP00000219139:p.Leu421Pro	84.0	0.0		67.0	23.0	NM_025187	Q9HA86	Missense_Mutation	SNP	ENST00000219139.3	hg19	CCDS10828.1	.	.	.	.	.	.	.	.	.	.	T	13.97	2.395201	0.42512	.	.	ENSG00000125149	ENST00000219139	.	.	.	5.93	5.93	0.95920	.	0.136093	0.48286	D	0.000187	T	0.36276	0.0961	N	0.14661	0.345	0.80722	D	1	P	0.44090	0.826	B	0.37943	0.261	T	0.42224	-0.9464	9	0.87932	D	0	-3.1548	13.7675	0.63004	0.0:0.0:0.0:1.0	.	421	Q9BSU1	CP070_HUMAN	P	421	.	ENSP00000219139:L421P	L	+	2	0	C16orf70	65738528	1.000000	0.71417	0.998000	0.56505	0.780000	0.44128	3.892000	0.56235	2.281000	0.76405	0.533000	0.62120	CTC	.	.		0.592	C16orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268829.2	NM_025187		C	67181027	T	C	67181027	3	2	352	1	0	0	0	0	1	0	0	0	1831	1551	54	2	1324	2	C16orf70	16	67181027	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	36982564	67181027	23173726	356	49772										
KIAA0895L	653319	hgsc.bcm.edu	37	chr16	67214463	67214463	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agggatgggggactggtaggCgggctggggggtgcctgatc	23	6	0	1	rs564826051		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr16:67214463C>T	ENST00000290881.7	-	3	977	c.51G>A	c.(49-51)ccG>ccA	p.P17P	KIAA0895L_ENST00000563831.2_Intron|KIAA0895L_ENST00000563902.1_Silent_p.P17P|KIAA0895L_ENST00000561621.1_Silent_p.P17P			Q68EN5	K895L_HUMAN	KIAA0895-like	17	Pro-rich.									breast(2)|endometrium(5)|kidney(2)|large_intestine(3)|lung(2)|prostate(2)|skin(1)	17						GACTGGTAGGCGGGCTGGGGG	0.652													C|||	1	0.000199681	0	0	5008	,	,		16828	0		0	False		,,,				2504	0.001				p.P17P		Atlas-SNP	.											KIAA0895L,NS,carcinoma,0,1	KIAA0895L	32	.	0			c.G51A						.						27	32	30					16																	67214463		1838	3880	5718	SO:0001819	synonymous_variant	653319	exon2			GGTAGGCGGGCTG	AK092303	CCDS42177.1	16q22.1	2008-11-27				ENSG00000196123			34408	protein-coding gene	gene with protein product							Standard	NM_001040715		Approved	LOC653319	uc002ert.3	Q68EN5		ENST00000290881.7:c.51G>A	chr16.hg19:g.67214463C>T		102.0	1.0		62.0	11.0	NM_001040715	A2VCS8|Q8N3H9|Q8NAQ5|Q96IE5	Silent	SNP	ENST00000290881.7	hg19	CCDS42177.1																																																																																			.	.		0.652	KIAA0895L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421193.4	NM_001040715		T	67214463	C	T	67214463	2	4	352	1	0	0	0	0	0	0	0	1	8207	755	27	1		1	KIAA0895L	16	67214463	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	33436	67214463	23140290	357	49773										
RLTPR	146206	hgsc.bcm.edu	37	chr16	67683458	67683458	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ccgcgctggatatcagcggcAacgccatgggggacgcgggc	17	13	1	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr16:67683458A>G	ENST00000334583.6	+	20	2183	c.1855A>G	c.(1855-1857)Aac>Gac	p.N619D	RLTPR_ENST00000545661.1_Missense_Mutation_p.N583D	NM_001013838.1	NP_001013860.1	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing	619	Tropomodulin-like.				cell migration (GO:0016477)|establishment of protein localization (GO:0045184)|homeostasis of number of cells (GO:0048872)|maintenance of cell polarity (GO:0030011)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma secretion (GO:1902715)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|F-actin capping protein complex (GO:0008290)|immunological synapse (GO:0001772)|membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(4)|kidney(1)|lung(9)|urinary_tract(2)	18		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)		TATCAGCGGCAACGCCATGGG	0.687																																					p.N619D		Atlas-SNP	.											.	RLTPR	124	.	0			c.A1855G						.						25	29	28					16																	67683458		1977	4136	6113	SO:0001583	missense	146206	exon20			AGCGGCAACGCCA	AB113647	CCDS45513.1	16q22.1	2010-09-10				ENSG00000159753			27089	protein-coding gene	gene with protein product	"RGD, leucine-rich repeat, tropomodulin and proline-rich containing protein", "leucine rich repeat containing 16C"	610859				15588584, 19846667	Standard	XM_005255807		Approved	LRRC16C, CARMIL2	uc002etn.3	Q6F5E8		ENST00000334583.6:c.1855A>G	chr16.hg19:g.67683458A>G	ENSP00000334958:p.Asn619Asp	36.0	0.0		35.0	11.0	NM_001013838	B8X2Z3	Missense_Mutation	SNP	ENST00000334583.6	hg19	CCDS45513.1	.	.	.	.	.	.	.	.	.	.	A	28.5	4.926971	0.92319	.	.	ENSG00000159753	ENST00000334583;ENST00000545661	T;T	0.80393	-1.37;-1.37	5.09	3.96	0.45880	.	0.111326	0.64402	D	0.000016	D	0.93141	0.7816	H	0.98466	4.24	0.49483	D	0.999798	D;D	0.76494	0.999;0.999	D;D	0.83275	0.977;0.996	D	0.93755	0.7062	10	0.87932	D	0	-11.1006	11.5317	0.50614	0.8498:0.1502:0.0:0.0	.	583;619	B8X2Z3;Q6F5E8	.;LR16C_HUMAN	D	619;583	ENSP00000334958:N619D;ENSP00000441481:N583D	ENSP00000334958:N619D	N	+	1	0	RLTPR	66240959	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.467000	0.80930	0.749000	0.32854	0.459000	0.35465	AAC	.	.		0.687	RLTPR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467858.1	NM_001013838		G	67683458	A	G	67683458	3	3	352	1	0	0	0	0	1	0	0	0	13409	130	5	2	1933	2	RLTPR	16	67683458	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	468995	67683458	22671295	358	49774										
SF3B3	23450	hgsc.bcm.edu	37	chr16	70605061	70605061	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aacatccccctctctgtgggCgggaccacctcagctttcgc	9	17	2	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr16:70605061C>T	ENST00000302516.5	+	25	3683	c.3472C>T	c.(3472-3474)Cgg>Tgg	p.R1158W		NM_012426.4	NP_036558.3	Q15393	SF3B3_HUMAN	splicing factor 3b, subunit 3, 130kDa	1158					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|protein complex assembly (GO:0006461)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	nucleic acid binding (GO:0003676)			breast(2)|endometrium(8)|kidney(2)|large_intestine(8)|liver(3)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	53		Ovarian(137;0.0694)				TCTCTGTGGGCGGGACCACCT	0.522																																					p.R1158W		Atlas-SNP	.											SF3B3,NS,adenocarcinoma,0,1	SF3B3	99	.	0			c.C3472T						.						133	122	125					16																	70605061		2198	4300	6498	SO:0001583	missense	23450	exon25			TGTGGGCGGGACC	AJ001443	CCDS10894.1	16q22	2008-08-01	2002-08-29		ENSG00000189091	ENSG00000189091			10770	protein-coding gene	gene with protein product		605592	"splicing factor 3b, subunit 3, 130kD"			10490618	Standard	NM_012426		Approved	SAP130, SF3b130, RSE1, KIAA0017	uc002ezf.3	Q15393	OTTHUMG00000137582	ENST00000302516.5:c.3472C>T	chr16.hg19:g.70605061C>T	ENSP00000305790:p.Arg1158Trp	90.0	0.0		87.0	36.0	NM_012426	Q6NTI8|Q96GC0|Q9BPY2|Q9UFX7|Q9UJ29	Missense_Mutation	SNP	ENST00000302516.5	hg19	CCDS10894.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.960641	0.74016	.	.	ENSG00000189091	ENST00000302516	T	0.48522	0.81	5.78	3.61	0.41365	Cleavage/polyadenylation specificity factor, A subunit, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.75781	0.3896	M	0.93978	3.48	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.83820	0.0246	10	0.66056	D	0.02	.	15.5067	0.75745	0.3664:0.6336:0.0:0.0	.	1158	Q15393	SF3B3_HUMAN	W	1158	ENSP00000305790:R1158W	ENSP00000305790:R1158W	R	+	1	2	SF3B3	69162562	0.702000	0.27816	1.000000	0.80357	0.987000	0.75469	1.387000	0.34430	1.405000	0.46838	0.563000	0.77884	CGG	.	.		0.522	SF3B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268972.1	NM_012426		T	70605061	C	T	70605061	3	4	352	1	0	0	0	0	1	0	0	0	14167	759	27	1	3566	1	SF3B3	16	70605061	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	2921603	70605061	19749692	359	49775										
ABR	29	hgsc.bcm.edu	37	chr17	909329	909329	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cctgcctcgggctacacgtcGgtggagaagtacagtgtgtt	14	10	0	1	rs375629677		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr17:909329G>A	ENST00000302538.5	-	23	2717	c.2571C>T	c.(2569-2571)acC>acT	p.T857T	ABR_ENST00000536794.2_Silent_p.T639T|ABR_ENST00000544583.2_Silent_p.T811T|ABR_ENST00000543210.2_Silent_p.T308T|ABR_ENST00000572441.1_Intron|ABR_ENST00000574437.1_Silent_p.T811T|ABR_ENST00000291107.2_Silent_p.T820T	NM_001282149.1|NM_021962.3	NP_001269078.1|NP_068781.2	Q12979	ABR_HUMAN	active BCR-related	857					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|brain development (GO:0007420)|inner ear morphogenesis (GO:0042472)|negative regulation of cell migration (GO:0030336)|negative regulation of inflammatory response (GO:0050728)|negative regulation of neutrophil degranulation (GO:0043314)|neuromuscular process controlling balance (GO:0050885)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phagocytosis (GO:0050766)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to lipopolysaccharide (GO:0032496)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|Rac GTPase activator activity (GO:0030675)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)		GCTACACGTCGGTGGAGAAGT	0.602																																					p.T857T	Esophageal Squamous(197;2016 2115 4129 29033 46447)	Atlas-SNP	.											.	ABR	119	.	0			c.C2571T						.	G	,,	0,4392		0,0,2196	52	38	43		2460,2433,2571	-11.2	0.1	17		43	1,8571		0,1,4285	no	coding-synonymous,coding-synonymous,coding-synonymous	ABR	NM_001092.3,NM_001159746.1,NM_021962.2	,,	0,1,6481	AA,AG,GG		0.0117,0.0,0.0077	,,	820/823,811/814,857/860	909329	1,12963	2196	4286	6482	SO:0001819	synonymous_variant	29	exon23			CACGTCGGTGGAG	L19704	CCDS10999.1, CCDS11000.1, CCDS54060.1, CCDS58497.1, CCDS73936.1	17p13	2013-01-10	2012-02-27		ENSG00000159842	ENSG00000159842		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	81	protein-coding gene	gene with protein product		600365	"active BCR-related gene"			2587217, 7479768	Standard	NM_001092		Approved	MDB	uc002fsd.4	Q12979	OTTHUMG00000090313	ENST00000302538.5:c.2571C>T	chr17.hg19:g.909329G>A		68.0	0.0		57.0	7.0	NM_021962	B3KW89|B7Z6H7|D3DTH3|D3DTH4|F5H3S2|F5H8B3|Q13693|Q13694	Silent	SNP	ENST00000302538.5	hg19	CCDS10999.1																																																																																			.	.		0.602	ABR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206675.4			A	909329	G	A	909329	2	1	352	1	0	0	0	0	0	0	0	1	99	1103	39	1		1	ABR	17	909329	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10		909329	80285881	360	49776										
ATP2A3	489	hgsc.bcm.edu	37	chr17	3844585	3844585	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cagcatgcctacgcagcccaCgaaggtcaggtccgtctgta	11	14	2	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr17:3844585C>T	ENST00000352011.3	-	14	1834	c.1780G>A	c.(1780-1782)Gtg>Atg	p.V594M	ATP2A3_ENST00000309890.7_Missense_Mutation_p.V594M|ATP2A3_ENST00000359983.3_Missense_Mutation_p.V594M|ATP2A3_ENST00000397043.3_Missense_Mutation_p.V594M|ATP2A3_ENST00000397039.1_De_novo_Start_InFrame|ATP2A3_ENST00000397035.3_Missense_Mutation_p.V594M|ATP2A3_ENST00000397041.3_Missense_Mutation_p.V594M			Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous	594					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	36				LUAD - Lung adenocarcinoma(1115;0.000692)|Lung(3;0.0766)		ACGCAGCCCACGAAGGTCAGG	0.662																																					p.V594M	GBM(32;29 774 15719 37967)	Atlas-SNP	.											.	ATP2A3	148	.	0			c.G1780A						.						47	46	46					17																	3844585		2202	4300	6502	SO:0001583	missense	489	exon14			AGCCCACGAAGGT		CCDS11041.1, CCDS11042.1, CCDS42234.1, CCDS45579.1, CCDS45580.1	17p13.3	2012-10-22			ENSG00000074370	ENSG00000074370	3.6.3.8	"ATPases / P-type"	813	protein-coding gene	gene with protein product	"sarcoplasmic/endoplasmic reticulum calcium ATPase 3", "calcium pump 3"	601929				8809064	Standard	NM_005173		Approved	SERCA3	uc002fwy.2	Q93084		ENST00000352011.3:c.1780G>A	chr17.hg19:g.3844585C>T	ENSP00000301387:p.Val594Met	99.0	0.0		99.0	43.0	NM_174956	A8MZG0|D3DTJ8|O60900|O60901|O75501|O75502|Q16115|Q6JHX1|Q8TEX5|Q8TEX6	Missense_Mutation	SNP	ENST00000352011.3	hg19	CCDS11041.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.620014	0.87460	.	.	ENSG00000074370	ENST00000397043;ENST00000352011;ENST00000359983;ENST00000397041;ENST00000397045;ENST00000309890;ENST00000397035	D;D;D;D;D;D	0.99105	-5.43;-5.43;-5.43;-5.43;-5.43;-5.43	4.16	4.16	0.48862	ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.85682	D	0.000000	D	0.99251	0.9739	M	0.83384	2.64	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.91635	0.999;0.979;0.982;0.979;0.979;0.979	D	0.98797	1.0738	10	0.87932	D	0	.	16.725	0.85419	0.0:1.0:0.0:0.0	.	594;594;594;594;594;594	Q93084-4;Q93084-2;Q93084;Q93084-6;G3XAE1;Q93084-3	.;.;AT2A3_HUMAN;.;.;.	M	594	ENSP00000380236:V594M;ENSP00000301387:V594M;ENSP00000353072:V594M;ENSP00000380234:V594M;ENSP00000312577:V594M;ENSP00000380229:V594M	ENSP00000312577:V594M	V	-	1	0	ATP2A3	3791334	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.562000	0.82300	2.607000	0.88179	0.561000	0.74099	GTG	.	.		0.662	ATP2A3-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438401.1	NM_174953		T	3844585	C	T	3844585	3	4	352	1	0	0	0	0	1	0	0	0	1138	536	19	1	1462	1	ATP2A3	17	3844585	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	2935256	3844585	77350625	361	49777										
CHD3	1107	hgsc.bcm.edu	37	chr17	7798461	7798461	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tggtgaatggctgtgtccccGatgcacagtgagtggaaaca	14	8	0	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr17:7798461G>A	ENST00000330494.7	+	9	1646	c.1496G>A	c.(1495-1497)cGa>cAa	p.R499Q	CHD3_ENST00000358181.4_Missense_Mutation_p.R499Q|CHD3_ENST00000380358.4_Missense_Mutation_p.R558Q	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	499	Chromo 1. {ECO:0000255|PROSITE- ProRule:PRU00053}.				centrosome organization (GO:0051297)|chromatin assembly or disassembly (GO:0006333)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|spindle organization (GO:0007051)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(11)|kidney(6)|large_intestine(13)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	65		Prostate(122;0.202)				CTGTGTCCCCGATGCACAGTG	0.552																																					p.R558Q		Atlas-SNP	.											.	CHD3	169	.	0			c.G1673A						.						211	159	177					17																	7798461		2203	4300	6503	SO:0001583	missense	1107	exon9			GTCCCCGATGCAC	U08379	CCDS32553.2, CCDS32554.1, CCDS32555.1	17p13	2013-01-28			ENSG00000170004	ENSG00000170004		"Zinc fingers, PHD-type"	1918	protein-coding gene	gene with protein product		602120				9326634, 7560064	Standard	NM_001005271		Approved	Mi-2a, ZFH, Mi2-ALPHA	uc002gjd.2	Q12873	OTTHUMG00000150427	ENST00000330494.7:c.1496G>A	chr17.hg19:g.7798461G>A	ENSP00000332628:p.Arg499Gln	104.0	0.0		78.0	14.0	NM_001005271	D3DTQ9|E9PG89|Q9Y4I0	Missense_Mutation	SNP	ENST00000330494.7	hg19	CCDS32554.1	.	.	.	.	.	.	.	.	.	.	G	16.76	3.210991	0.58343	.	.	ENSG00000170004	ENST00000380358;ENST00000358181;ENST00000330494	T;T;T	0.21543	2.0;2.0;2.0	5.01	5.01	0.66863	Zinc finger, PHD-finger (2);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);Zinc finger, RING-type (1);Zinc finger, PHD-type (1);Chromo domain-like (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.33180	N	0.005184	T	0.47820	0.1466	M	0.70275	2.135	0.80722	D	1	D;D;D	0.76494	0.998;0.998;0.999	D;D;D	0.80764	0.986;0.992;0.994	T	0.47824	-0.9087	10	0.66056	D	0.02	-6.7131	18.5172	0.90939	0.0:0.0:1.0:0.0	.	499;499;558	Q12873-2;Q12873;E9PG89	.;CHD3_HUMAN;.	Q	558;499;499	ENSP00000369716:R558Q;ENSP00000350907:R499Q;ENSP00000332628:R499Q	ENSP00000332628:R499Q	R	+	2	0	CHD3	7739186	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.657000	0.98554	2.611000	0.88343	0.561000	0.74099	CGA	.	.		0.552	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1	NM_001005273		A	7798461	G	A	7798461	3	1	352	1	0	0	0	0	1	0	0	0	3328	1058	37	1	1811	1	CHD3	17	7798461	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	3953876	7798461	73396749	362	49778										
KCNAB3	9196	hgsc.bcm.edu	37	chr17	7832645	7832645	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aggattcccgtgccccccgcCggccggcccaccattaccgc	10	21	0	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr17:7832645C>T	ENST00000303790.2	-	1	108	c.109G>A	c.(109-111)Ggc>Agc	p.G37S	CNTROB_ENST00000563694.1_5'Flank|CNTROB_ENST00000380262.3_5'Flank|RP11-1099M24.7_ENST00000573621.1_Intron|CNTROB_ENST00000380255.3_5'Flank	NM_004732.3	NP_004723.2	O43448	KCAB3_HUMAN	potassium voltage-gated channel, shaker-related subfamily, beta member 3	37					potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|endometrium(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)	8		Prostate(122;0.157)				TGCCCCCCGCCGGCCGGCCCA	0.741																																					p.G37S		Atlas-SNP	.											.	KCNAB3	30	.	0			c.G109A						.						2	3	3					17																	7832645		1529	3234	4763	SO:0001583	missense	9196	exon1			CCCCGCCGGCCGG	AF016411	CCDS11124.1	17p13.1	2006-11-29			ENSG00000170049	ENSG00000170049		"Potassium channels", "Aldo-keto reductases"	6230	protein-coding gene	gene with protein product		604111				9857044	Standard	NM_004732		Approved	AKR6A9, KCNA3B	uc002gjm.2	O43448	OTTHUMG00000108170	ENST00000303790.2:c.109G>A	chr17.hg19:g.7832645C>T	ENSP00000302719:p.Gly37Ser	123.0	0.0		117.0	9.0	NM_004732	Q4VAW0	Missense_Mutation	SNP	ENST00000303790.2	hg19	CCDS11124.1	.	.	.	.	.	.	.	.	.	.	C	12.67	2.008717	0.35415	.	.	ENSG00000170049	ENST00000303790	T	0.04758	3.56	4.62	3.62	0.41486	.	0.201092	0.29791	N	0.011188	T	0.03178	0.0093	N	0.22421	0.69	0.31232	N	0.696248	B	0.19200	0.034	B	0.06405	0.002	T	0.17349	-1.0372	10	0.22706	T	0.39	.	7.238	0.26079	0.0:0.8039:0.0:0.1961	.	37	O43448	KCAB3_HUMAN	S	37	ENSP00000302719:G37S	ENSP00000302719:G37S	G	-	1	0	KCNAB3	7773370	0.000000	0.05858	0.985000	0.45067	0.439000	0.31926	0.194000	0.17135	2.404000	0.81709	0.655000	0.94253	GGC	.	.		0.741	KCNAB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226974.1	NM_004732		T	7832645	C	T	7832645	3	4	352	1	0	0	0	0	1	0	0	0	8020	652	23	1	1161	1	KCNAB3	17	7832645	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	34184	7832645	73362565	363	49779										
ELAC2	60528	hgsc.bcm.edu	37	chr17	12897811	12897811	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cttcatgtatcaggagggtgGcatctttccctggagaagca	12	9	3	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr17:12897811G>A	ENST00000338034.4	-	22	2278	c.2039C>T	c.(2038-2040)gCc>gTc	p.A680V	ELAC2_ENST00000426905.3_Missense_Mutation_p.A640V|ELAC2_ENST00000395962.2_Missense_Mutation_p.A661V	NM_018127.6|NM_173717.1	NP_060597.4|NP_776065.1	Q9BQ52	RNZ2_HUMAN	elaC ribonuclease Z 2	680					mitochondrial tRNA 3'-trailer cleavage, endonucleolytic (GO:0072684)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|skin(1)	23						CAGGAGGGTGGCATCTTTCCC	0.552																																					p.A680V		Atlas-SNP	.											.	ELAC2	48	.	0			c.C2039T						.						261	217	232					17																	12897811		2203	4300	6503	SO:0001583	missense	60528	exon22			AGGGTGGCATCTT	AF304370	CCDS11164.1, CCDS54093.1	17p11.2	2013-05-24	2013-05-24		ENSG00000006744	ENSG00000006744	3.1.26.11		14198	protein-coding gene	gene with protein product	"tRNase Z (long form)"	605367	"elaC (E. coli) homolog 2", "elaC homolog 2 (E. coli)"			10986046, 16636667, 21559454	Standard	NM_018127		Approved	FLJ10530, HPC2	uc010vvr.2	Q9BQ52	OTTHUMG00000058764	ENST00000338034.4:c.2039C>T	chr17.hg19:g.12897811G>A	ENSP00000337445:p.Ala680Val	142.0	0.0		98.0	12.0	NM_018127	B4DPL9|Q6IA94|Q9HAS8|Q9HAS9|Q9NVT1	Missense_Mutation	SNP	ENST00000338034.4	hg19	CCDS11164.1	.	.	.	.	.	.	.	.	.	.	G	16.51	3.143749	0.57044	.	.	ENSG00000006744	ENST00000426905;ENST00000338034;ENST00000395962	T;T;T	0.77750	-1.12;-1.12;-1.12	5.2	5.2	0.72013	Beta-lactamase-like (1);	0.000000	0.85682	D	0.000000	D	0.85974	0.5822	L	0.59436	1.845	0.80722	D	1	D;P;D;P;D;D;D;P	0.89917	1.0;0.924;1.0;0.875;1.0;1.0;1.0;0.733	D;P;D;P;D;D;D;P	0.97110	1.0;0.842;0.997;0.781;1.0;1.0;0.999;0.58	D	0.86768	0.1971	10	0.72032	D	0.01	-28.4324	16.2815	0.82692	0.0:0.0:1.0:0.0	.	640;663;661;478;680;440;665;308	B4DPL9;E9PGJ0;G5E9D5;E7ES68;Q9BQ52;B3KSU9;B4DT15;Q9BQ52-3	.;.;.;.;RNZ2_HUMAN;.;.;.	V	640;680;661	ENSP00000405223:A640V;ENSP00000337445:A680V;ENSP00000379291:A661V	ENSP00000337445:A680V	A	-	2	0	ELAC2	12838536	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.086000	0.94088	2.713000	0.92767	0.655000	0.94253	GCC	.	.		0.552	ELAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129934.5			A	12897811	G	A	12897811	3	1	352	1	0	0	0	0	1	0	0	0	5049	1203	42	3	453	3	ELAC2	17	12897811	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	5065166	12897811	68297399	364	49780										
CDRT1	374286	hgsc.bcm.edu	37	chr17	15492292	15492292	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ttcctgtatacctgctgctaCacaccactgaaaaggatcag	7	12	1	1	rs542008653		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr17:15492292C>T	ENST00000395906.3	-	12	2255	c.2256G>A	c.(2254-2256)gtG>gtA	p.V752V	CDRT1_ENST00000583965.1_3'UTR|CDRT1_ENST00000354433.3_Silent_p.V252V|RP11-385D13.1_ENST00000455584.2_Intron	NM_006382.3	NP_006373.2	O95170	CDRT1_HUMAN	CMT1A duplicated region transcript 1	752										endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	10				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(2;1.36e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0541)		CCTGCTGCTACACACCACTGA	0.577													.|||	1	0.000199681	0	0	5008	,	,		17122	0		0	False		,,,				2504	0.001				p.V752V		Atlas-SNP	.											.	CDRT1	83	.	0			c.G2256A						.						35	35	35					17																	15492292		2202	4278	6480	SO:0001819	synonymous_variant	374286	exon12			CTGCTACACACCA	U65652	CCDS45619.1, CCDS73996.1	17p11	2013-01-10			ENSG00000241322	ENSG00000241322		"F-boxes / WD-40 domains", "WD repeat domain containing"	14379	protein-coding gene	gene with protein product		604596	"F-box and WD repeat domain containing 10 pseudogene 1", "F-box and WD-40 domain protein 10 pseudogene 1"	FBXW10P1		9787083, 11381029	Standard	NM_006382		Approved	HREP, SM25H2, FBXW10B		O95170	OTTHUMG00000059074	ENST00000395906.3:c.2256G>A	chr17.hg19:g.15492292C>T		80.0	0.0		94.0	41.0	NM_006382	O43848|O95611	Silent	SNP	ENST00000395906.3	hg19	CCDS45619.1																																																																																			.	.		0.577	CDRT1-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448127.1	NM_006382		T	15492292	C	T	15492292	2	4	352	1	0	0	0	0	0	0	0	1	3176	465	17	3		3	CDRT1	17	15492292	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	2594481	15492292	65702918	365	49781										
TP53I13	90313	hgsc.bcm.edu	37	chr17	27899414	27899414	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cccactgtctccctgctgccGggggcgcctggaggcaatgc	14	16	1	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr17:27899414G>A	ENST00000301057.7	+	6	883	c.768G>A	c.(766-768)ccG>ccA	p.P256P	RP11-68I3.4_ENST00000579050.1_RNA|RP11-68I3.2_ENST00000581474.1_RNA	NM_138349.2	NP_612358.3	Q8NBR0	P5I13_HUMAN	tumor protein p53 inducible protein 13	256						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|kidney(1)|lung(1)|urinary_tract(1)	4				READ - Rectum adenocarcinoma(3;0.236)		CCCTGCTGCCGGGGGCGCCTG	0.652																																					p.P256P		Atlas-SNP	.											.	TP53I13	17	.	0			c.G768A						.						29	32	31					17																	27899414		1972	4114	6086	SO:0001819	synonymous_variant	90313	exon6			GCTGCCGGGGGCG	AK075341	CCDS42289.1	17q11.2	2006-01-16				ENSG00000167543			25102	protein-coding gene	gene with protein product						14767535	Standard	NM_138349		Approved	DSCP1	uc002hee.3	Q8NBR0		ENST00000301057.7:c.768G>A	chr17.hg19:g.27899414G>A		64.0	0.0		82.0	9.0	NM_138349	Q7L5U3	Silent	SNP	ENST00000301057.7	hg19	CCDS42289.1																																																																																			.	.		0.652	TP53I13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447804.2	NM_138349		A	27899414	G	A	27899414	2	1	352	1	0	0	0	0	0	0	0	1	16401	1103	39	1		1	TP53I13	17	27899414	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	12407122	27899414	53295796	366	49782										
RHOT1	55288	hgsc.bcm.edu	37	chr17	30530945	30530945	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gtgaagatcataaatcctacTatgcgattaacactgtttat	6	7	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr17:30530945T>C	ENST00000333942.6	+	16	1608	c.1369T>C	c.(1369-1371)Tat>Cat	p.Y457H	RHOT1_ENST00000394692.2_Missense_Mutation_p.Y457H|RHOT1_ENST00000583994.1_Missense_Mutation_p.Y330H|RHOT1_ENST00000354266.3_Missense_Mutation_p.Y436H|RHOT1_ENST00000581094.1_Missense_Mutation_p.Y457H|RHOT1_ENST00000545287.2_Missense_Mutation_p.Y457H|RHOT1_ENST00000358365.3_Missense_Mutation_p.Y457H	NM_018307.3	NP_060777.3	Q8IXI2	MIRO1_HUMAN	ras homolog family member T1	457	Miro 2.				cellular homeostasis (GO:0019725)|mitochondrial outer membrane permeabilization (GO:0097345)|mitochondrion transport along microtubule (GO:0047497)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(10)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28		Myeloproliferative disorder(56;0.0255)|Breast(31;0.116)|Ovarian(249;0.182)				TAAATCCTACTATGCGATTAA	0.303																																					p.Y457H		Atlas-SNP	.											.	RHOT1	69	.	0			c.T1369C						.						102	102	102					17																	30530945		2203	4297	6500	SO:0001583	missense	55288	exon16			TCCTACTATGCGA	AJ517412	CCDS32610.1, CCDS32611.1, CCDS32612.1, CCDS74030.1, CCDS74031.1	17q11.2-q12	2013-01-10	2012-02-27	2004-03-24		ENSG00000126858		"EF-hand domain containing"	21168	protein-coding gene	gene with protein product	"mitochondrial Rho (MIRO) GTPase 1"	613888	"ras homolog gene family, member T1"	ARHT1		12482879	Standard	NM_001033567		Approved	MIRO-1, FLJ11040	uc002hgw.3	Q8IXI2		ENST00000333942.6:c.1369T>C	chr17.hg19:g.30530945T>C	ENSP00000334724:p.Tyr457His	94.0	0.0		106.0	23.0	NM_001033568	A4FVB6|A6NFV0|B4DG48|J9JIH9|Q6NUR3|Q6P9F8|Q6PJG1|Q6YMW8|Q86UB0|Q8IW28|Q8IXJ7|Q9H067|Q9H9N8|Q9NUZ2	Missense_Mutation	SNP	ENST00000333942.6	hg19	CCDS32612.1	.	.	.	.	.	.	.	.	.	.	T	15.31	2.796507	0.50208	.	.	ENSG00000126858	ENST00000358365;ENST00000354266;ENST00000394692;ENST00000333942	T;T;T	0.68624	-0.34;-0.34;-0.34	5.7	5.7	0.88788	Mitochondrial Rho-like (1);MIRO (1);	0.000000	0.85682	D	0.000000	T	0.73377	0.3579	M	0.78285	2.405	0.80722	D	1	P;B;P;P	0.35944	0.529;0.234;0.482;0.48	B;B;B;B	0.42959	0.403;0.316;0.333;0.2	T	0.73588	-0.3935	10	0.39692	T	0.17	-13.4029	15.9589	0.79910	0.0:0.0:0.0:1.0	.	457;457;457;457	Q8IXI2-2;Q8IXI2;Q8IXI2-5;Q8IXI2-3	.;MIRO1_HUMAN;.;.	H	457	ENSP00000351132:Y457H;ENSP00000378184:Y457H;ENSP00000334724:Y457H	ENSP00000334724:Y457H	Y	+	1	0	RHOT1	27555058	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.040000	0.89188	2.178000	0.69098	0.477000	0.44152	TAT	.	.		0.303	RHOT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000447097.1	NM_018307		C	30530945	T	C	30530945	3	2	352	1	0	0	0	0	1	0	0	0	13358	1522	53	2	1431	2	RHOT1	17	30530945	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	2631531	30530945	50664265	367	49783										
MLLT6	4302	hgsc.bcm.edu	37	chr17	36876002	36876002	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ccaggttccctctggccgcaGgtcccccatcagcagcctcc	9	20	2	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr17:36876002G>T	ENST00000325718.7	+	14	2100		c.e14-1		CTB-58E17.9_ENST00000579499.1_RNA|MIR4726_ENST00000577947.1_RNA	NM_005937.3	NP_005928	P55198	AF17_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6						regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(3)|lung(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8	Breast(7;4.43e-21)					TCTGGCCGCAGGTCCCCCATC	0.682			T	MLL	AL																																.		Atlas-SNP	.		Dom	yes		17	17q21	4302	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6 (AF17)"		L	.	MLLT6	80	.	0			c.2010-1G>T						.						25	28	27					17																	36876002		2202	4300	6502	SO:0001630	splice_region_variant	4302	exon14			GCCGCAGGTCCCC		CCDS11327.1	17q21	2014-04-10	2001-11-28		ENSG00000108292	ENSG00000275023		"Zinc fingers, PHD-type"	7138	protein-coding gene	gene with protein product	"Myeloid/lymphoid or mixed-lineage leukemia, translocated to, 6", "trithorax homolog"	600328	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 6"			8058765	Standard	NM_005937		Approved	AF17, FLJ23480	uc002hqi.4	P55198	OTTHUMG00000188498	ENST00000325718.7:c.2010-1G>T	chr17.hg19:g.36876002G>T		153.0	0.0		164.0	52.0	NM_005937	Q59F28|Q96IU3|Q9H5F6|Q9UF49	Splice_Site	SNP	ENST00000325718.7	hg19	CCDS11327.1	.	.	.	.	.	.	.	.	.	.	G	12.90	2.077356	0.36662	.	.	ENSG00000108292	ENST00000325718	.	.	.	4.94	3.98	0.46160	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.3496	0.55141	0.0834:0.0:0.9166:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MLLT6	34129528	1.000000	0.71417	0.996000	0.52242	0.355000	0.29361	6.187000	0.72039	1.224000	0.43551	0.561000	0.74099	.	.	.		0.682	MLLT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256799.1	NM_005937	Intron	T	36876002	G	T	36876002	5	4	352	1	0	0	0	0	0	0	1	0	9639	1014	35	3	2063	3	MLLT6	17	36876002	Splice_Site	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	6345057	36876002	44319208	368	49784										
PSMB3	5691	hgsc.bcm.edu	37	chr17	36912245	36912245	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	acctcttgtatgagaaacggTgagtgcaagtgtagctagca	12	7	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr17:36912245T>C	ENST00000225426.4	+	3	387		c.e3+2		RNU6-866P_ENST00000516469.1_RNA	NM_002795.2	NP_002786.2	P49720	PSB3_HUMAN	proteasome (prosome, macropain) subunit, beta type, 3						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)			endometrium(2)|large_intestine(1)|lung(1)	4						TGAGAAACGGTGAGTGCAAGT	0.468																																					.		Atlas-SNP	.											.	PSMB3	9	.	0			c.296+2T>C						.						103	88	93					17																	36912245		2203	4300	6503	SO:0001630	splice_region_variant	5691	exon3			AAACGGTGAGTGC	BC013008	CCDS11328.1	17q12	2014-05-06			ENSG00000108294	ENSG00000277791		"Proteasome (prosome, macropain) subunits"	9540	protein-coding gene	gene with protein product		602176				7918633	Standard	NM_002795		Approved	HC10-II, MGC4147	uc002hqr.3	P49720	OTTHUMG00000188503	ENST00000225426.4:c.296+2T>C	chr17.hg19:g.36912245T>C		81.0	0.0		72.0	23.0	NM_002795	P31147|Q0P6J7|Q96E27	Splice_Site	SNP	ENST00000225426.4	hg19	CCDS11328.1	.	.	.	.	.	.	.	.	.	.	T	17.47	3.398092	0.62177	.	.	ENSG00000108294	ENST00000225426	.	.	.	5.04	5.04	0.67666	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.7633	0.62979	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	PSMB3	34165771	1.000000	0.71417	0.998000	0.56505	0.678000	0.39670	7.677000	0.84024	2.114000	0.64651	0.533000	0.62120	.	.	.		0.468	PSMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256810.2	NM_002795	Intron	C	36912245	T	C	36912245	5	2	352	1	0	0	0	0	0	0	1	0	12690	1710	59	2	308	2	PSMB3	17	36912245	Splice_Site	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	36243	36912245	44282965	369	49785										
TOP2A	7153	hgsc.bcm.edu	37	chr17	38564371	38564371	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cgtacactcagtggagtttcGgccccctaaaataaaaatat	7	10	1	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr17:38564371G>A	ENST00000423485.1	-	12	1506	c.1348C>T	c.(1348-1350)Cga>Tga	p.R450*		NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	450			R -> Q (in teniposide (VM-26) resistant cells). {ECO:0000269|PubMed:1652758}.		apoptotic chromosome condensation (GO:0030263)|ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA ligation (GO:0006266)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|embryonic cleavage (GO:0040016)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|positive regulation of apoptotic process (GO:0043065)|positive regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral genome replication (GO:0045070)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|DNA-dependent ATPase activity (GO:0008094)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(9)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	39		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	GTGGAGTTTCGGCCCCCtaaa	0.393																																					p.R450X		Atlas-SNP	.											.	TOP2A	124	.	0			c.C1348T						.						29	27	28					17																	38564371		1828	4077	5905	SO:0001587	stop_gained	7153	exon12			AGTTTCGGCCCCC		CCDS45672.1	17q21-q22	2008-08-06	2002-08-29		ENSG00000131747	ENSG00000131747	5.99.1.2		11989	protein-coding gene	gene with protein product		126430	"topoisomerase (DNA) II alpha (170kD)"	TOP2			Standard	NM_001067		Approved		uc002huq.3	P11388	OTTHUMG00000155008	ENST00000423485.1:c.1348C>T	chr17.hg19:g.38564371G>A	ENSP00000411532:p.Arg450*	200.0	0.0		227.0	43.0	NM_001067	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Nonsense_Mutation	SNP	ENST00000423485.1	hg19	CCDS45672.1	.	.	.	.	.	.	.	.	.	.	G	39	7.328321	0.98214	.	.	ENSG00000131747	ENST00000423485;ENST00000269577;ENST00000348049;ENST00000357601	.	.	.	5.36	4.34	0.51931	.	0.120978	0.53938	D	0.000042	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	.	10.8116	0.46551	0.0:0.0:0.5751:0.4249	.	.	.	.	X	450;530;473;486	.	ENSP00000269577:R530X	R	-	1	2	TOP2A	35817897	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	6.902000	0.75699	2.515000	0.84797	0.591000	0.81541	CGA	.	.		0.393	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1			A	38564371	G	A	38564371	4	1	352	1	0	0	0	0	0	1	0	0	16380	1124	39	1	3343	1	TOP2A	17	38564371	Nonsense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	1652126	38564371	42630839	370	49786										
KRT12	3859	hgsc.bcm.edu	37	chr17	39019563	39019563	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tgcgcgcagtaatcgccctcGgcttcggccaaggagtcctc	12	15	0	0	rs373922617		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr17:39019563G>A	ENST00000251643.4	-	6	1151	c.1128C>T	c.(1126-1128)gcC>gcT	p.A376A	RP5-1110E20.1_ENST00000579136.1_RNA	NM_000223.3	NP_000214.1	Q99456	K1C12_HUMAN	keratin 12	376	Coil 2.|Rod.				visual perception (GO:0007601)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(2)	15		Breast(137;0.000301)			Griseofulvin(DB00400)	AATCGCCCTCGGCTTCGGCCA	0.612																																					p.A376A		Atlas-SNP	.											.	KRT12	53	.	0			c.C1128T						.						20	18	19					17																	39019563		2199	4290	6489	SO:0001819	synonymous_variant	3859	exon6			GCCCTCGGCTTCG		CCDS11378.1	17q21.2	2013-06-20	2008-08-01		ENSG00000187242	ENSG00000187242		"-", "Intermediate filaments type I, keratins (acidic)"	6414	protein-coding gene	gene with protein product	"Meesmann corneal dystrophy"	601687				9171831, 16831889	Standard	NM_000223		Approved	K12	uc002hvk.2	Q99456	OTTHUMG00000133369	ENST00000251643.4:c.1128C>T	chr17.hg19:g.39019563G>A		140.0	0.0		150.0	55.0	NM_000223	B2R9E0	Silent	SNP	ENST00000251643.4	hg19	CCDS11378.1																																																																																			.	.		0.612	KRT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257214.2	NM_000223		A	39019563	G	A	39019563	2	1	352	1	0	0	0	0	0	0	0	1	8458	1103	39	1		1	KRT12	17	39019563	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	455192	39019563	42175647	371	49787										
KCNH4	23415	hgsc.bcm.edu	37	chr17	40315341	40315341	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tgctgccagagtcctcaatgCcatccactatcctgggaaca	8	14	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr17:40315341C>T	ENST00000264661.3	-	14	2821	c.2489G>A	c.(2488-2490)gGc>gAc	p.G830D	KCNH4_ENST00000607371.1_Missense_Mutation_p.G830D	NM_012285.2	NP_036417.1	Q9UQ05	KCNH4_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 4	830					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(15)|skin(2)|urinary_tract(1)	32		all_cancers(22;1.24e-06)|all_epithelial(22;4.33e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.126)		GTCCTCAATGCCATCCACTAT	0.632																																					p.G830D	NSCLC(117;707 1703 2300 21308 31858)	Atlas-SNP	.											.	KCNH4	105	.	0			c.G2489A						.						46	41	43					17																	40315341		2203	4300	6503	SO:0001583	missense	23415	exon14			TCAATGCCATCCA	AB022698	CCDS11420.1	17q21	2012-07-05				ENSG00000089558		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6253	protein-coding gene	gene with protein product		604528				10455180, 16382104	Standard	NM_012285		Approved	Kv12.3, elk1	uc002hzb.2	Q9UQ05		ENST00000264661.3:c.2489G>A	chr17.hg19:g.40315341C>T	ENSP00000264661:p.Gly830Asp	52.0	0.0		45.0	12.0	NM_012285		Missense_Mutation	SNP	ENST00000264661.3	hg19	CCDS11420.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.284845	0.80803	.	.	ENSG00000089558	ENST00000264661	D	0.99270	-5.66	4.27	4.27	0.50696	.	0.000000	0.38326	N	0.001739	D	0.99086	0.9686	M	0.67397	2.05	0.49213	D	0.999768	D	0.89917	1.0	D	0.69307	0.963	D	0.98722	1.0709	10	0.62326	D	0.03	.	12.1652	0.54125	0.0:1.0:0.0:0.0	.	830	Q9UQ05	KCNH4_HUMAN	D	830	ENSP00000264661:G830D	ENSP00000264661:G830D	G	-	2	0	KCNH4	37568867	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.321000	0.65846	2.242000	0.73789	0.552000	0.68991	GGC	.	.		0.632	KCNH4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449791.2	NM_012285		T	40315341	C	T	40315341	3	4	352	1	0	0	0	0	1	0	0	0	8043	739	26	3	576	3	KCNH4	17	40315341	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	1295778	40315341	40879869	372	49788										
AOC2	314	hgsc.bcm.edu	37	chr17	41001289	41001289	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggctagcaaccagactaatgCgtggggtcaccagcgcgggt	15	11	1	1	rs267604890		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr17:41001289C>T	ENST00000253799.3	+	2	1802	c.1775C>T	c.(1774-1776)gCg>gTg	p.A592V	AOC2_ENST00000452774.2_Missense_Mutation_p.A592V|AOC3_ENST00000308423.2_5'Flank	NM_009590.2	NP_033720.2	O75106	AOC2_HUMAN	amine oxidase, copper containing 2 (retina-specific)	592					amine metabolic process (GO:0009308)|catecholamine metabolic process (GO:0006584)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	aliphatic-amine oxidase activity (GO:0052595)|aminoacetone:oxygen oxidoreductase(deaminating) activity (GO:0052594)|copper ion binding (GO:0005507)|electron carrier activity (GO:0009055)|phenethylamine:oxygen oxidoreductase (deaminating) activity (GO:0052596)|primary amine oxidase activity (GO:0008131)|quinone binding (GO:0048038)|tryptamine:oxygen oxidoreductase (deaminating) activity (GO:0052593)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(14)|ovary(4)|skin(2)	30		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)		CAGACTAATGCGTGGGGTCAC	0.612													C|||	1	0.000199681	8e-04	0	5008	,	,		19136	0		0	False		,,,				2504	0				p.A592V		Atlas-SNP	.											AOC2,colon,carcinoma,0,1	AOC2	61	.	0			c.C1775T						.						80	88	85					17																	41001289		2203	4300	6503	SO:0001583	missense	314	exon2			CTAATGCGTGGGG	AF081363	CCDS11443.1, CCDS45690.1	17q21	2012-07-13				ENSG00000131480	1.4.3.21		549	protein-coding gene	gene with protein product		602268				9119395, 9722954	Standard	NM_001158		Approved	RAO, DAO2	uc002ibu.3	O75106		ENST00000253799.3:c.1775C>T	chr17.hg19:g.41001289C>T	ENSP00000253799:p.Ala592Val	83.0	0.0		100.0	24.0	NM_009590	A5PKW2|O00120|O75105|Q4TTW5|Q9UNY0	Missense_Mutation	SNP	ENST00000253799.3	hg19	CCDS11443.1	.	.	.	.	.	.	.	.	.	.	C	11.58	1.681062	0.29872	.	.	ENSG00000131480	ENST00000253799;ENST00000452774	T;T	0.04015	3.73;3.73	5.15	3.14	0.36123	Copper amine oxidase, C-terminal (3);	0.699813	0.14479	N	0.317073	T	0.05547	0.0146	L	0.47716	1.5	0.09310	N	0.999994	P;P	0.42039	0.769;0.727	B;B	0.40199	0.322;0.216	T	0.34625	-0.9821	10	0.34782	T	0.22	-40.0355	7.4503	0.27234	0.4413:0.4786:0.0:0.0801	.	592;592	O75106;O75106-2	AOC2_HUMAN;.	V	592	ENSP00000253799:A592V;ENSP00000406134:A592V	ENSP00000253799:A592V	A	+	2	0	AOC2	38254815	0.202000	0.23423	0.933000	0.37362	0.386000	0.30323	0.856000	0.27818	0.724000	0.32296	0.655000	0.94253	GCG	.	.		0.612	AOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452442.1	NM_009590, NM_001158		T	41001289	C	T	41001289	3	4	352	1	0	0	0	0	1	0	0	0	727	768	27	1	1781	1	AOC2	17	41001289	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	685948	41001289	40193921	373	49789										
TMUB2	79089	hgsc.bcm.edu	37	chr17	42266521	42266521	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggtcctagcttggctctctaCctacgtagcagacagcggta	11	12	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr17:42266521C>T	ENST00000587989.1	+	3	320	c.167C>T	c.(166-168)aCc>aTc	p.T56I	TMUB2_ENST00000589184.1_Intron|ASB16-AS1_ENST00000592897.1_RNA|TMUB2_ENST00000592825.1_Missense_Mutation_p.T36I|ASB16-AS1_ENST00000588785.1_RNA|ASB16-AS1_ENST00000591166.1_RNA|TMUB2_ENST00000538716.2_Missense_Mutation_p.T56I|TMUB2_ENST00000357984.3_Missense_Mutation_p.T36I|ASB16-AS1_ENST00000585457.1_RNA|TMUB2_ENST00000446571.3_Missense_Mutation_p.T36I|TMUB2_ENST00000587172.1_Missense_Mutation_p.T36I|TMUB2_ENST00000319511.6_Missense_Mutation_p.T36I|TMUB2_ENST00000589785.1_Missense_Mutation_p.T36I|TMUB2_ENST00000589856.1_Missense_Mutation_p.T36I|TMUB2_ENST00000590235.1_Missense_Mutation_p.T36I			Q71RG4	TMUB2_HUMAN	transmembrane and ubiquitin-like domain containing 2	56						integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(1)|lung(3)	8		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.113)		TGGCTCTCTACCTACGTAGCA	0.582																																					p.T56I		Atlas-SNP	.											.	TMUB2	29	.	0			c.C167T						.						130	113	119					17																	42266521		2203	4300	6503	SO:0001583	missense	79089	exon3			TCTCTACCTACGT		CCDS11479.1, CCDS54134.1	17q21	2006-06-27				ENSG00000168591			28459	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_177441		Approved	MGC3123	uc002ifo.3	Q71RG4		ENST00000587989.1:c.167C>T	chr17.hg19:g.42266521C>T	ENSP00000466971:p.Thr56Ile	80.0	0.0		75.0	11.0	NM_001076674	B3KU81|Q8NDI2|Q9BPZ5|Q9HAG3	Missense_Mutation	SNP	ENST00000587989.1	hg19	CCDS54134.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.633878	0.87660	.	.	ENSG00000168591	ENST00000446571;ENST00000357984;ENST00000538716;ENST00000319511	T;T;T;T	0.73047	-0.55;-0.63;-0.71;-0.63	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	D	0.83912	0.5357	M	0.73962	2.25	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.996;0.999;0.998;0.997	D	0.86293	0.1675	10	0.87932	D	0	.	16.9385	0.86209	0.0:1.0:0.0:0.0	.	36;36;36;56	E7ESS3;Q71RG4-3;Q71RG4-4;Q71RG4	.;.;.;TMUB2_HUMAN	I	36;36;56;36	ENSP00000413127:T36I;ENSP00000350672:T36I;ENSP00000444565:T56I;ENSP00000313214:T36I	ENSP00000313214:T36I	T	+	2	0	TMUB2	39622047	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.384000	0.79751	2.252000	0.74401	0.561000	0.74099	ACC	.	.		0.582	TMUB2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457711.1	NM_177441		T	42266521	C	T	42266521	3	4	352	1	0	0	0	0	1	0	0	0	16280	507	18	3	173	3	TMUB2	17	42266521	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	1265232	42266521	38928689	374	49790										
FMNL1	752	hgsc.bcm.edu	37	chr17	43322423	43322423	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gtcattgctgagaagtacccGcaactcacaggcttccacag	9	13	2	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr17:43322423G>A	ENST00000331495.3	+	21	3012	c.2676G>A	c.(2674-2676)ccG>ccA	p.P892P	MAP3K14-AS1_ENST00000592422.1_RNA|FMNL1_ENST00000328118.3_Silent_p.P892P|MAP3K14-AS1_ENST00000588504.1_RNA|CTD-2020K17.4_ENST00000589518.1_RNA|FMNL1_ENST00000587489.1_Silent_p.P470P|MAP3K14-AS1_ENST00000588698.1_RNA|MAP3K14-AS1_ENST00000590100.1_RNA|MAP3K14-AS1_ENST00000591263.1_RNA|CTD-2020K17.4_ENST00000420431.2_RNA|MAP3K14-AS1_ENST00000585346.1_RNA|CTD-2020K17.4_ENST00000591361.1_RNA	NM_005892.3	NP_005883	O95466	FMNL_HUMAN	formin-like 1	892	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin filament severing (GO:0051014)|cortical actin cytoskeleton organization (GO:0030866)|regulation of cell shape (GO:0008360)|substrate-dependent cell migration (GO:0006929)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|GTPase activating protein binding (GO:0032794)|Rac GTPase binding (GO:0048365)			biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(12)|pancreas(1)|skin(1)|urinary_tract(2)	33						AGAAGTACCCGCAACTCACAG	0.587																																					p.P892P	GBM(164;1247 1997 8702 11086 51972)	Atlas-SNP	.											.	FMNL1	78	.	0			c.G2676A						.						82	75	77					17																	43322423		2203	4300	6503	SO:0001819	synonymous_variant	752	exon21			GTACCCGCAACTC	AJ008112	CCDS11497.1	17q21.31	2008-05-14	2003-12-02	2003-12-03		ENSG00000184922			1212	protein-coding gene	gene with protein product		604656	"formin-like"	C17orf1B, FMNL		9799091	Standard	NM_005892		Approved	C17orf1	uc002iin.3	O95466		ENST00000331495.3:c.2676G>A	chr17.hg19:g.43322423G>A		107.0	0.0		107.0	18.0	NM_005892	D2DGW2|Q6DKG5|Q6IBP3|Q86UH1|Q8N671|Q8TDH1|Q96H10	Silent	SNP	ENST00000331495.3	hg19	CCDS11497.1																																																																																			.	.		0.587	FMNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450198.1	NM_005892		A	43322423	G	A	43322423	2	1	352	1	0	0	0	0	0	0	0	1	5959	1074	38	1		1	FMNL1	17	43322423	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	1055902	43322423	37872787	375	49791										
NSF	4905	hgsc.bcm.edu	37	chr17	44803929	44803929	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tttcagatctttgatgatgcGtacaaatcccagctcagttg	8	9	3	3			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr17:44803929G>A	ENST00000398238.4	+	16	1883	c.1776G>A	c.(1774-1776)gcG>gcA	p.A592A	NSF_ENST00000575068.1_Silent_p.A587A|NSF_ENST00000225282.8_Silent_p.A498A	NM_006178.3	NP_006169.2	P46459	NSF_HUMAN	N-ethylmaleimide-sensitive factor	592					exocytosis (GO:0006887)|plasma membrane fusion (GO:0045026)|positive regulation of receptor recycling (GO:0001921)|potassium ion transport (GO:0006813)|protein transport (GO:0015031)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|syntaxin-1 binding (GO:0017075)			kidney(2)|large_intestine(1)|liver(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)	14		Melanoma(429;0.203)	BRCA - Breast invasive adenocarcinoma(9;0.0257)	BRCA - Breast invasive adenocarcinoma(366;0.241)		TTGATGATGCGTACAAATCCC	0.383																																					p.A592A	Ovarian(25;472 742 1472 36813 50223)	Atlas-SNP	.											.	NSF	27	.	0			c.G1776A						.						269	265	266					17																	44803929		1975	4157	6132	SO:0001819	synonymous_variant	4905	exon16			TGATGCGTACAAA		CCDS42354.1	17q21	2010-04-21			ENSG00000073969	ENSG00000073969		"ATPases / AAA-type"	8016	protein-coding gene	gene with protein product	"N-ethylmaleimide-sensitive factor-like protein"	601633				1315316, 8875895	Standard	NM_006178		Approved	SKD2	uc002iku.3	P46459	OTTHUMG00000134315	ENST00000398238.4:c.1776G>A	chr17.hg19:g.44803929G>A		92.0	0.0		94.0	30.0	NM_006178	A8K2D9|B4DFA2|Q8N6D7|Q9UKZ2	Silent	SNP	ENST00000398238.4	hg19	CCDS42354.1																																																																																			.	.		0.383	NSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259348.2	NM_006178		A	44803929	G	A	44803929	2	1	352	1	0	0	0	0	0	0	0	1	10680	1132	40	1		1	NSF	17	44803929	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	1481506	44803929	36391281	376	49792										
TMEM92	162461	hgsc.bcm.edu	37	chr17	48356249	48356249	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tgtcgcaactgcagagagccGgagccagacagcccagtgga	14	12	0	2	rs563916883		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr17:48356249G>A	ENST00000300433.3	+	5	368	c.258G>A	c.(256-258)ccG>ccA	p.P86P	TMEM92_ENST00000507382.1_Silent_p.P86P|RP11-893F2.9_ENST00000508851.1_RNA|TMEM92_ENST00000511882.1_3'UTR	NM_001168215.1	NP_001161687.1	Q6UXU6	TMM92_HUMAN	transmembrane protein 92	86	Pro-rich.					integral component of membrane (GO:0016021)				NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|liver(1)|lung(1)	7						GCAGAGAGCCGGAGCCAGACA	0.617													G|||	1	0.000199681	8e-04	0	5008	,	,		17169	0		0	False		,,,				2504	0				p.P86P		Atlas-SNP	.											.	TMEM92	13	.	0			c.G258A						.						80	89	86					17																	48356249		2203	4300	6503	SO:0001819	synonymous_variant	162461	exon4			AGAGCCGGAGCCA		CCDS11562.1	17q21.33	2005-12-13							26579	protein-coding gene	gene with protein product						12975309	Standard	NM_153229		Approved	FLJ33318	uc002iqn.2	Q6UXU6		ENST00000300433.3:c.258G>A	chr17.hg19:g.48356249G>A		60.0	0.0		43.0	6.0	NM_153229	Q8NBF0	Silent	SNP	ENST00000300433.3	hg19	CCDS11562.1																																																																																			.	.		0.617	TMEM92-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367053.2	NM_153229		A	48356249	G	A	48356249	2	1	352	1	0	0	0	0	0	0	0	1	16236	1103	39	1		1	TMEM92	17	48356249	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	3552320	48356249	32838961	377	49793										
SPAG9	9043	hgsc.bcm.edu	37	chr17	49071264	49071266	+	In_Frame_Del	DEL	TTC	TTC	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	atccaaactagactggataaTtcttcttgattttttaactc							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr17:49071264_49071266delTTC	ENST00000262013.7	-	19	2465_2467	c.2257_2259delGAA	c.(2257-2259)gaadel	p.E753del	SPAG9_ENST00000505279.1_In_Frame_Del_p.E743del|SPAG9_ENST00000510283.1_In_Frame_Del_p.E596del|SPAG9_ENST00000357122.4_In_Frame_Del_p.E739del	NM_001130528.2	NP_001124000.1	O60271	JIP4_HUMAN	sperm associated antigen 9	753					activation of JUN kinase activity (GO:0007257)|muscle cell differentiation (GO:0042692)|negative regulation of protein homodimerization activity (GO:0090074)|positive regulation of cell migration (GO:0030335)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron differentiation (GO:0045666)|protein homooligomerization (GO:0051260)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|striated muscle cell differentiation (GO:0051146)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)				NS(1)|breast(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			GACTGGATAATTCTTCTTGATTT	0.365																																					p.753_754del		Atlas-INDEL	.											.	SPAG9	151	.	0			c.2258_2260del						.																																			SO:0001651	inframe_deletion	9043	exon19			.	AB011088	CCDS11577.1, CCDS45740.1, CCDS58577.1, CCDS58578.1	17q21.33	2013-09-23			ENSG00000008294	ENSG00000008294			14524	protein-coding gene	gene with protein product	"sperm surface protein", "JNK/SAPK-associated protein", "JNK interacting protein", "sperm specific protein", "c-Jun NH2-terminal kinase-associated leucine zipper protein", "Max-binding protein", "JNK-associated leucine-zipper protein", "HLC-4 protein", "lung cancer oncogene 4", "proliferation-inducing gene 6", "cancer/testis antigen 89"	605430				9480848, 11106729	Standard	NM_003971		Approved	HSS, SYD1, KIAA0516, MGC14967, MGC74461, MGC117291, JLP, PHET, HLC4, PIG6, FLJ13450, FLJ14006, FLJ26141, FLJ34602, CT89	uc002itc.3	O60271	OTTHUMG00000162316	ENST00000262013.7:c.2257_2259delGAA	chr17.hg19:g.49071267_49071269delTTC	ENSP00000262013:p.Glu753del	117.0	0.0		105.0	12.0	NM_001130528	A6H8U5|A8MSX0|B4DHH2|O60905|Q3KQU8|Q3MKM7|Q86WC7|Q86WC8|Q8IZX7|Q96II0|Q9H811	In_Frame_Del	DEL	ENST00000262013.7	hg19	CCDS45740.1																																																																																			.	.		0.365	SPAG9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368543.2	NM_003971		-	49071266	TTC	-	49071264	7	5	352	1	0	1	0	1	0	0	0	0	15000	1490	52	0	1754	0	SPAG9	17	49071264	In_Frame_Del	DEL	TTC	TCGA-WQ-A9G7-01A-11D-A36X-10	715015	49071264	32123946	378	49794										
ANKFN1	162282	hgsc.bcm.edu	37	chr17	54543932	54543932	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	attctactgataaccatccaGgtatgtagtttttttcttaa	5	7	2	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr17:54543932G>T	ENST00000318698.2	+	14	1817	c.1782G>T	c.(1780-1782)caG>caT	p.Q594H	ANKFN1_ENST00000566473.2_Splice_Site_p.Q594H	NM_153228.2	NP_694960.2	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain containing 1	594										NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(11)|lung(27)|ovary(1)|prostate(1)|skin(1)	53						TAACCATCCAGGTATGTAGTT	0.398																																					p.Q594H		Atlas-SNP	.											.	ANKFN1	115	.	0			c.G1782T						.						52	48	50					17																	54543932		2203	4300	6503	SO:0001630	splice_region_variant	162282	exon14			CATCCAGGTATGT	AK095654	CCDS32686.1	17q23.2	2014-02-12	2005-11-15		ENSG00000153930	ENSG00000153930		"Ankyrin repeat domain containing", "Fibronectin type III domain containing"	26766	protein-coding gene	gene with protein product							Standard	NM_153228		Approved	FLJ38335	uc002iun.1	Q8N957	OTTHUMG00000155010	ENST00000318698.2:c.1782+1G>T	chr17.hg19:g.54543932G>T		90.0	0.0		102.0	11.0	NM_153228		Missense_Mutation	SNP	ENST00000318698.2	hg19	CCDS32686.1	.	.	.	.	.	.	.	.	.	.	g	15.84	2.951644	0.53186	.	.	ENSG00000153930	ENST00000318698	T	0.25085	1.82	5.81	5.81	0.92471	.	0.052171	0.85682	D	0.000000	T	0.22044	0.0531	N	0.25094	0.71	0.80722	D	1	B	0.19073	0.033	B	0.16289	0.015	T	0.02519	-1.1147	10	0.37606	T	0.19	-9.2603	20.0804	0.97772	0.0:0.0:1.0:0.0	.	594	Q8N957	ANKF1_HUMAN	H	594	ENSP00000321627:Q594H	ENSP00000321627:Q594H	Q	+	3	2	ANKFN1	51898931	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	7.648000	0.83479	2.763000	0.94921	0.651000	0.88453	CAG	.	.		0.398	ANKFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338043.1	NM_153228	Missense_Mutation	T	54543932	G	T	54543932	5	4	352	1	0	0	0	0	0	0	1	0	625	1014	35	3	1836	3	ANKFN1	17	54543932	Splice_Site	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	5472668	54543932	26651278	379	49795										
BZRAP1	9256	hgsc.bcm.edu	37	chr17	56385233	56385233	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agtgcttggcctgaggactcGgacacctctcttctgggggc	14	12	2	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr17:56385233G>A	ENST00000343736.4	-	23	4964	c.4801C>T	c.(4801-4803)Cga>Tga	p.R1601*	BZRAP1_ENST00000268893.6_Nonsense_Mutation_p.R1541*|BZRAP1_ENST00000355701.3_Nonsense_Mutation_p.R1601*			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	1601						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	benzodiazepine receptor binding (GO:0030156)			cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CTGAGGACTCGGACACCTCTC	0.637																																					p.R1601X		Atlas-SNP	.											.	BZRAP1	287	.	0			c.C4801T						.						64	55	58					17																	56385233		2203	4300	6503	SO:0001587	stop_gained	9256	exon23			GGACTCGGACACC	AB014512	CCDS11605.1, CCDS45742.1	17q22-q23	2014-01-09	2014-01-09						16831	protein-coding gene	gene with protein product		610764				9734811, 9915832	Standard	NM_004758		Approved	PRAX-1, KIAA0612, RIM-BP1, RIMBP1	uc002ivx.5	O95153		ENST00000343736.4:c.4801C>T	chr17.hg19:g.56385233G>A	ENSP00000345824:p.Arg1601*	91.0	0.0		76.0	17.0	NM_004758	O75111|Q8N5W3	Nonsense_Mutation	SNP	ENST00000343736.4	hg19	CCDS11605.1	.	.	.	.	.	.	.	.	.	.	G	43	9.871398	0.99284	.	.	ENSG00000005379	ENST00000355701;ENST00000343736;ENST00000268893	.	.	.	5.76	3.79	0.43588	.	0.981110	0.08360	N	0.957834	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.5512	0.39310	0.1597:0.0:0.8403:0.0	.	.	.	.	X	1601;1601;1541	.	ENSP00000268893:R1541X	R	-	1	2	BZRAP1	53740232	0.064000	0.20934	0.042000	0.18584	0.396000	0.30629	2.398000	0.44486	1.448000	0.47680	0.563000	0.77884	CGA	.	.		0.637	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758		A	56385233	G	A	56385233	4	1	352	1	0	0	0	0	0	1	0	0	1579	1124	39	1	808	1	BZRAP1	17	56385233	Nonsense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	1841301	56385233	24809977	380	49796										
MTMR4	9110	hgsc.bcm.edu	37	chr17	56584581	56584581	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tccagggcacaggctttagcAatggacgtgaccaggtactc	12	11	0	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr17:56584581A>C	ENST00000323456.5	-	9	889	c.765T>G	c.(763-765)atT>atG	p.I255M	MTMR4_ENST00000579925.1_Missense_Mutation_p.I255M	NM_004687.4	NP_004678.3	Q9NYA4	MTMR4_HUMAN	myotubularin related protein 4	255	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|small molecule metabolic process (GO:0044281)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|early endosome membrane (GO:0031901)|extracellular space (GO:0005615)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(10)|endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|skin(5)	36	Medulloblastoma(34;0.127)|all_neural(34;0.237)					AGGCTTTAGCAATGGACGTGA	0.612																																					p.I255M		Atlas-SNP	.											.	MTMR4	91	.	0			c.T765G						.						60	57	58					17																	56584581		2203	4300	6503	SO:0001583	missense	9110	exon9			TTTAGCAATGGAC	AB014547	CCDS11608.1	17q22-q23	2011-06-09				ENSG00000108389		"Zinc fingers, FYVE domain containing", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7452	protein-coding gene	gene with protein product		603559				9736772	Standard	NM_004687		Approved	KIAA0647, ZFYVE11	uc002iwj.2	Q9NYA4		ENST00000323456.5:c.765T>G	chr17.hg19:g.56584581A>C	ENSP00000325285:p.Ile255Met	97.0	0.0		88.0	27.0	NM_004687	D3DTZ6|Q8IV27|Q9Y4D5	Missense_Mutation	SNP	ENST00000323456.5	hg19	CCDS11608.1	.	.	.	.	.	.	.	.	.	.	A	19.74	3.884753	0.72410	.	.	ENSG00000108389	ENST00000323456	D	0.94280	-3.39	5.39	-4.8	0.03190	Myotubularin phosphatase domain (1);Myotubularin-related (1);	0.062950	0.64402	D	0.000007	D	0.95674	0.8593	M	0.90425	3.115	0.49130	D	0.999751	D	0.89917	1.0	D	0.85130	0.997	D	0.92943	0.6374	10	0.87932	D	0	.	7.643	0.28305	0.5047:0.0:0.3929:0.1024	.	255	Q9NYA4	MTMR4_HUMAN	M	255	ENSP00000325285:I255M	ENSP00000325285:I255M	I	-	3	3	MTMR4	53939580	0.172000	0.23043	0.966000	0.40874	0.991000	0.79684	-0.283000	0.08433	-0.925000	0.03775	-0.462000	0.05337	ATT	.	.		0.612	MTMR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444721.1	NM_004687		C	56584581	A	C	56584581	3	2	352	1	0	0	0	0	1	0	0	0	9955	126	5	5	2866	5	MTMR4	17	56584581	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	199348	56584581	24610629	381	49797										
TEX2	55852	hgsc.bcm.edu	37	chr17	62272409	62272409	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agactgaatgtgtcaaagtcGcatggtaggtttctggatca	12	6	3	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr17:62272409G>A	ENST00000583097.1	-	3	1863	c.1691C>T	c.(1690-1692)gCg>gTg	p.A564V	TEX2_ENST00000258991.3_Missense_Mutation_p.A564V|TEX2_ENST00000584379.1_Missense_Mutation_p.A564V			Q8IWB9	TEX2_HUMAN	testis expressed 2	564					signal transduction (GO:0007165)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)				breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(8;1.33e-10)	READ - Rectum adenocarcinoma(1115;0.0689)		TGTCAAAGTCGCATGGTAGGT	0.383																																					p.A564V		Atlas-SNP	.											TEX2,NS,carcinoma,+1,1	TEX2	89	.	0			c.C1691T						.						101	90	93					17																	62272409		2203	4300	6503	SO:0001583	missense	55852	exon3			AAAGTCGCATGGT	AB051525	CCDS11658.1, CCDS74131.1	17q23.3	2007-03-13	2007-03-13			ENSG00000136478			30884	protein-coding gene	gene with protein product	"transmembrane protein 96"		"testis expressed sequence 2"			11214970	Standard	XM_005257507		Approved	HT008, TMEM96, KIAA1738	uc002jee.3	Q8IWB9		ENST00000583097.1:c.1691C>T	chr17.hg19:g.62272409G>A	ENSP00000462665:p.Ala564Val	98.0	0.0		87.0	8.0	NM_018469	Q6AHZ5|Q8N3L0|Q9C0C5	Missense_Mutation	SNP	ENST00000583097.1	hg19		.	.	.	.	.	.	.	.	.	.	G	16.69	3.192176	0.58017	.	.	ENSG00000136478	ENST00000258991	T	0.39997	1.05	6.07	5.11	0.69529	Pleckstrin homology domain (1);	0.102234	0.64402	D	0.000002	T	0.41511	0.1162	L	0.36672	1.1	0.80722	D	1	D;P	0.58970	0.984;0.802	P;B	0.50896	0.653;0.143	T	0.15350	-1.0440	10	0.11794	T	0.64	-16.78	15.5075	0.75753	0.0661:0.0:0.9339:0.0	.	564;564	Q8IWB9-2;Q8IWB9	.;TEX2_HUMAN	V	564	ENSP00000258991:A564V	ENSP00000258991:A564V	A	-	2	0	TEX2	59626141	1.000000	0.71417	0.940000	0.37924	0.989000	0.77384	9.338000	0.96553	1.581000	0.49865	0.655000	0.94253	GCG	.	.		0.383	TEX2-003	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000443745.1	NM_018469		A	62272409	G	A	62272409	3	1	352	1	0	0	0	0	1	0	0	0	15796	1087	38	1	1753	1	TEX2	17	62272409	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	5687828	62272409	18922801	382	49798										
BPTF	2186	hgsc.bcm.edu	37	chr17	65924473	65924473	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tctccttcacttttttagaaAcgactggagcagcagaagcc	8	11	2	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr17:65924473A>G	ENST00000321892.4	+	18	6193	c.6132A>G	c.(6130-6132)aaA>aaG	p.K2044K	BPTF_ENST00000335221.5_Silent_p.K2044K|BPTF_ENST00000306378.6_Silent_p.K1918K|BPTF_ENST00000424123.3_Silent_p.K1905K			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	2044					anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			TTTTTTAGAAACGACTGGAGC	0.418																																					p.K2044K		Atlas-SNP	.											.	BPTF	415	.	0			c.A6132G						.						45	42	43					17																	65924473		2203	4300	6503	SO:0001819	synonymous_variant	2186	exon18			TTAGAAACGACTG	AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"Zinc fingers, PHD-type"	3581	protein-coding gene	gene with protein product		601819	"fetal Alzheimer antigen"	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.6132A>G	chr17.hg19:g.65924473A>G		222.0	0.0		217.0	24.0	NM_004459	Q6NX67|Q7Z7D6|Q9UIG2	Silent	SNP	ENST00000321892.4	hg19																																																																																				.	.		0.418	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459		G	65924473	A	G	65924473	2	3	352	1	0	0	0	0	0	0	0	1	1497	40	2	2		2	BPTF	17	65924473	Silent	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	3652064	65924473	15270737	383	49799										
ABCA9	10350	hgsc.bcm.edu	37	chr17	67029868	67029868	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cagccatgttagtacttaccGggcaaaattttgtcaaaata	7	8	1	0	rs146940647		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr17:67029868G>A	ENST00000340001.4	-	9	1486	c.1275C>T	c.(1273-1275)ccC>ccT	p.P425P	ABCA9_ENST00000370732.2_Splice_Site_p.P425P|ABCA9_ENST00000453985.2_Splice_Site_p.P425P	NM_080283.3	NP_525022.2	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 9	425					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(21)|lung(35)|ovary(4)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	91	Breast(10;1.47e-12)					AGTACTTACCGGGCAAAATTT	0.299																																					p.P425P		Atlas-SNP	.											.	ABCA9	192	.	0			c.C1275T						.	G		2,4404	4.2+/-10.8	0,2,2201	90	100	96		1275	-0.1	1	17	dbSNP_134	96	0,8596		0,0,4298	yes	coding-synonymous-near-splice	ABCA9	NM_080283.3		0,2,6499	AA,AG,GG		0.0,0.0454,0.0154		425/1625	67029868	2,13000	2203	4298	6501	SO:0001630	splice_region_variant	10350	exon9			CTTACCGGGCAAA	AF423307	CCDS11681.1	17q24	2012-03-14			ENSG00000154258	ENSG00000154258		"ATP binding cassette transporters / subfamily A"	39	protein-coding gene	gene with protein product		612507					Standard	XM_005256934		Approved	EST640918	uc002jhu.3	Q8IUA7	OTTHUMG00000140371	ENST00000340001.4:c.1276+1C>T	chr17.hg19:g.67029868G>A		297.0	0.0		268.0	41.0	NM_080283	Q6P655|Q8N2S4|Q8WWZ5|Q96MD8	Silent	SNP	ENST00000340001.4	hg19	CCDS11681.1																																																																																			.	G|1.000;A|0.000		0.299	ABCA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277072.2	NM_172386	Silent	A	67029868	G	A	67029868	5	1	352	1	0	0	0	0	0	0	1	0	39	1130	39	1	3723	1	ABCA9	17	67029868	Splice_Site	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	1105395	67029868	14165342	384	49800										
GRIN2C	2905	hgsc.bcm.edu	37	chr17	72845978	72845978	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ccaccatcacactgatgcccGtctccacaaagggtacagag	8	15	2	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr17:72845978G>A	ENST00000293190.5	-	7	1732	c.1586C>T	c.(1585-1587)aCg>aTg	p.T529M	GRIN2C_ENST00000347612.4_Missense_Mutation_p.T529M|GRIN2C_ENST00000578159.1_5'Flank	NM_000835.3	NP_000826.2	Q14957	NMDE3_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2C	529					directional locomotion (GO:0033058)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of protein catabolic process (GO:0042177)|neuromuscular process controlling balance (GO:0050885)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|response to wounding (GO:0009611)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	33	all_lung(278;0.172)|Lung NSC(278;0.207)				Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	ACTGATGCCCGTCTCCACAAA	0.627																																					p.T529M		Atlas-SNP	.											.	GRIN2C	144	.	0			c.C1586T						.						106	96	99					17																	72845978		2203	4300	6503	SO:0001583	missense	2905	exon7			ATGCCCGTCTCCA		CCDS32724.1, CCDS62330.1	17q25.1	2012-08-29			ENSG00000161509	ENSG00000161509		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4587	protein-coding gene	gene with protein product		138254		NMDAR2C		9480759	Standard	NM_001278553		Approved	GluN2C	uc002jlt.1	Q14957	OTTHUMG00000044524	ENST00000293190.5:c.1586C>T	chr17.hg19:g.72845978G>A	ENSP00000293190:p.Thr529Met	81.0	0.0		88.0	9.0	NM_000835	B2RTT1	Missense_Mutation	SNP	ENST00000293190.5	hg19	CCDS32724.1	.	.	.	.	.	.	.	.	.	.	G	15.17	2.754016	0.49362	.	.	ENSG00000161509	ENST00000293190;ENST00000347612	T	0.30981	1.51	4.19	4.19	0.49359	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (1);	0.000000	0.85682	D	0.000000	T	0.62502	0.2433	M	0.89478	3.035	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.72337	-0.4324	10	0.72032	D	0.01	.	17.0587	0.86541	0.0:0.0:1.0:0.0	.	563;529	Q8IW23;Q14957	.;NMDE3_HUMAN	M	529;563	ENSP00000293190:T529M	ENSP00000293190:T529M	T	-	2	0	GRIN2C	70357573	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	9.468000	0.97676	2.313000	0.78055	0.491000	0.48974	ACG	.	.		0.627	GRIN2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103824.1			A	72845978	G	A	72845978	3	1	352	1	0	0	0	0	1	0	0	0	6790	1145	40	1	2143	1	GRIN2C	17	72845978	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	5816110	72845978	8349232	385	49801										
EVPL	2125	hgsc.bcm.edu	37	chr17	74005326	74005326	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tccagcaccgggtccttctcGtggcgcaccacctccttgct	9	18	1	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr17:74005326G>A	ENST00000301607.3	-	22	4213	c.3960C>T	c.(3958-3960)caC>caT	p.H1320H	EVPL_ENST00000586740.1_Silent_p.H1342H	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	1320	Central fibrous rod domain.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						GGTCCTTCTCGTGGCGCACCA	0.701																																					p.H1320H		Atlas-SNP	.											EVPL,NS,carcinoma,0,1	EVPL	155	.	0			c.C3960T						.						102	113	109					17																	74005326		2202	4300	6502	SO:0001819	synonymous_variant	2125	exon22			CTTCTCGTGGCGC	U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.3960C>T	chr17.hg19:g.74005326G>A		25.0	0.0		19.0	4.0	NM_001988	A0AUV5	Silent	SNP	ENST00000301607.3	hg19	CCDS11737.1																																																																																			.	.		0.701	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988		A	74005326	G	A	74005326	2	1	352	1	0	0	0	0	0	0	0	1	5294	1136	40	1		1	EVPL	17	74005326	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	1159348	74005326	7189884	386	49802										
DNAH17	8632	hgsc.bcm.edu	37	chr17	76535911	76535911	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gtcgtcaatgtagatgacatAatccttccagggcaggctca	10	10	2	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr17:76535911A>G	ENST00000585328.1	-	18	2708	c.2584T>C	c.(2584-2586)Tat>Cat	p.Y862H	DNAH17_ENST00000389840.5_Missense_Mutation_p.Y862H	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	862	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			TAGATGACATAATCCTTCCAG	0.453																																					p.Y862H		Atlas-SNP	.											.	DNAH17	347	.	0			c.T2584C						.						68	68	68					17																	76535911		2010	4172	6182	SO:0001583	missense	8632	exon18			TGACATAATCCTT	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"Axonemal dyneins"	2946	protein-coding gene	gene with protein product		610063	"dynein, axonemal, heavy polypeptide 17", "dynein, axonemal, heavy chain like 1", "dynein, axonemal, heavy like 1"	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.2584T>C	chr17.hg19:g.76535911A>G	ENSP00000465516:p.Tyr862His	309.0	0.0		310.0	118.0	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Missense_Mutation	SNP	ENST00000585328.1	hg19		.	.	.	.	.	.	.	.	.	.	A	17.98	3.520295	0.64747	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.36157	1.27	4.97	4.97	0.65823	.	.	.	.	.	T	0.59473	0.2196	M	0.83774	2.66	0.42318	D	0.992241	.	.	.	.	.	.	T	0.67620	-0.5624	7	0.87932	D	0	.	14.6508	0.68794	1.0:0.0:0.0:0.0	.	.	.	.	H	862	ENSP00000374490:Y862H	ENSP00000300671:Y862H	Y	-	1	0	DNAH17	74047506	1.000000	0.71417	0.218000	0.23776	0.396000	0.30629	8.121000	0.89582	1.861000	0.53984	0.533000	0.62120	TAT	.	.		0.453	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		G	76535911	A	G	76535911	3	3	352	1	0	0	0	0	1	0	0	0	4603	362	13	2	11060	2	DNAH17	17	76535911	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	2530585	76535911	4659299	387	49803										
CBX8	57332	hgsc.bcm.edu	37	chr17	77769341	77769341	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gaaactcgtaagttttggccTttgccttggcctgcgcctgc	11	12	0	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr17:77769341T>C	ENST00000269385.4	-	5	380	c.263A>G	c.(262-264)aAg>aGg	p.K88R	CBX8_ENST00000485449.1_5'UTR	NM_020649.2	NP_065700.1	Q9HC52	CBX8_HUMAN	chromobox homolog 8	88					histone ubiquitination (GO:0016574)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	heterochromatin (GO:0000792)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	methylated histone binding (GO:0035064)|single-stranded RNA binding (GO:0003727)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)	14			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			AGTTTTGGCCTTTGCCTTGGC	0.642																																					p.K88R		Atlas-SNP	.											.	CBX8	42	.	0			c.A263G						.						14	17	16					17																	77769341		2170	4263	6433	SO:0001583	missense	57332	exon5			TTGGCCTTTGCCT	AF174482	CCDS11765.1	17q25.3	2010-07-06	2010-06-24		ENSG00000141570	ENSG00000141570			15962	protein-coding gene	gene with protein product	"polycomb 3", "Pc class 3 homolog (Drosophila)"		"chromobox homolog 8 (Drosophila Pc class)"			10825164	Standard	NM_020649		Approved	RC1, HPC3, PC3	uc002jxd.2	Q9HC52	OTTHUMG00000150416	ENST00000269385.4:c.263A>G	chr17.hg19:g.77769341T>C	ENSP00000269385:p.Lys88Arg	37.0	0.0		38.0	5.0	NM_020649	Q96H39|Q9NR07	Missense_Mutation	SNP	ENST00000269385.4	hg19	CCDS11765.1	.	.	.	.	.	.	.	.	.	.	T	10.96	1.499783	0.26861	.	.	ENSG00000141570	ENST00000269385;ENST00000427800;ENST00000413392	T;T;T	0.48836	0.8;1.49;1.49	4.72	3.64	0.41730	.	0.221289	0.34460	N	0.003948	T	0.34513	0.0900	L	0.38838	1.175	0.46678	D	0.999154	B	0.21753	0.06	B	0.20577	0.03	T	0.07404	-1.0774	10	0.19590	T	0.45	-21.3299	10.0454	0.42184	0.0:0.0805:0.0:0.9195	.	88	Q9HC52	CBX8_HUMAN	R	88;63;78	ENSP00000269385:K88R;ENSP00000408753:K63R;ENSP00000405058:K78R	ENSP00000269385:K88R	K	-	2	0	CBX8	75383936	1.000000	0.71417	0.994000	0.49952	0.912000	0.54170	5.794000	0.69067	0.642000	0.30620	0.459000	0.35465	AAG	.	.		0.642	CBX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318011.1	NM_020649		C	77769341	T	C	77769341	3	2	352	1	0	0	0	0	1	0	0	0	2726	1606	56	2	885	2	CBX8	17	77769341	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	1233430	77769341	3425869	388	49804										
AATK	9625	hgsc.bcm.edu	37	chr17	79096552	79096552	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ccttggcacacaggtaggacAgcagcaggtgcacctcctcg	12	14	0	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr17:79096552A>G	ENST00000326724.4	-	11	1208	c.1184T>C	c.(1183-1185)cTg>cCg	p.L395P	MIR657_ENST00000385003.1_RNA|AATK_ENST00000572339.1_5'Flank|AATK_ENST00000417379.1_Missense_Mutation_p.L292P	NM_001080395.2	NP_001073864.2	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	395	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				brain development (GO:0007420)|negative regulation of axon extension (GO:0030517)|neuron apoptotic process (GO:0051402)|peptidyl-tyrosine autophosphorylation (GO:0038083)|Rab protein signal transduction (GO:0032482)	axonal growth cone (GO:0044295)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(2)|lung(8)|ovary(3)|prostate(1)|stomach(4)|upper_aerodigestive_tract(1)	21	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			CAGGTAGGACAGCAGCAGGTG	0.726																																					p.L395P		Atlas-SNP	.											.	AATK	102	.	0			c.T1184C						.						8	10	10					17																	79096552		2036	4151	6187	SO:0001583	missense	9625	exon11			TAGGACAGCAGCA	AB014541	CCDS45807.1, CCDS58607.1	17q25.3	2014-06-12			ENSG00000181409	ENSG00000181409			21	protein-coding gene	gene with protein product	"lemur tyrosine kinase 1", "protein phosphatase 1, regulatory subunit 77"	605276				9734811, 10083745	Standard	NM_001080395		Approved	AATYK, KIAA0641, LMTK1, LMR1, AATYK1, PPP1R77	uc010dia.3	Q6ZMQ8	OTTHUMG00000132717	ENST00000326724.4:c.1184T>C	chr17.hg19:g.79096552A>G	ENSP00000324196:p.Leu395Pro	84.0	0.0		83.0	36.0	NM_001080395	O75136|Q6ZN31|Q86X28	Missense_Mutation	SNP	ENST00000326724.4	hg19	CCDS45807.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	a|a	22.8|22.8	4.334837|4.334837	0.81801|0.81801	.|.	.|.	ENSG00000181409|ENSG00000181409	ENST00000417379|ENST00000326724;ENST00000374792	.|D;D	.|0.84442	.|-1.85;-1.68	4.61|4.61	3.53|3.53	0.40419|0.40419	.|Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.|0.257134	.|0.31450	.|N	.|0.007630	D|D	0.92107|0.92107	0.7498|0.7498	M|M	0.88181|0.88181	2.935|2.935	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.87578	.|0.998	D|D	0.92424|0.92424	0.5948|0.5948	5|10	.|0.87932	.|D	.|0	.|.	9.2376|9.2376	0.37475|0.37475	0.912:0.0:0.088:0.0|0.912:0.0:0.088:0.0	.|.	.|395	.|Q6ZMQ8	.|LMTK1_HUMAN	R|P	348|395	.|ENSP00000324196:L395P;ENSP00000363924:L395P	.|ENSP00000324196:L395P	C|L	-|-	1|2	0|0	AATK|AATK	76711147|76711147	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.983000|0.983000	0.72400|0.72400	5.766000|5.766000	0.68843|0.68843	1.701000|1.701000	0.51217|0.51217	0.375000|0.375000	0.23000|0.23000	TGT|CTG	.	.		0.726	AATK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256055.1	NM_004920		G	79096552	A	G	79096552	3	3	352	1	0	0	0	0	1	0	0	0	26	188	7	2	2956	2	AATK	17	79096552	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	1327211	79096552	2098658	389	49805										
HEXDC	284004	hgsc.bcm.edu	37	chr17	80400207	80400208	+	Frame_Shift_Ins	INS	-	-	C													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggacctcagcgaggtgtctgINScccccccgctgccacccacc							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr17:80400207_80400208insC	ENST00000327949.9	+	12	1419_1420	c.1408_1409insC	c.(1408-1410)gccfs	p.A470fs	HEXDC_ENST00000337014.6_Frame_Shift_Ins_p.P500fs|HEXDC_ENST00000577944.1_Frame_Shift_Ins_p.CP472fs			Q8WVB3	HEXDC_HUMAN	hexosaminidase (glycosyl hydrolase family 20, catalytic domain) containing	470					carbohydrate metabolic process (GO:0005975)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	beta-N-acetylhexosaminidase activity (GO:0004563)			breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	16	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)			CGAGGTGTCTGCCCCCCCGCTG	0.688																																					p.L499fs		Atlas-INDEL	.											.,1	HEXDC	43	.	0			c.1497_1498insC						.																																			SO:0001589	frameshift_variant	284004	exon12			.	AK074405	CCDS42402.1	17q25.3	2011-12-19			ENSG00000169660	ENSG00000169660			26307	protein-coding gene	gene with protein product						12477932	Standard	NM_173620		Approved	FLJ23825	uc002kev.4	Q8WVB3		ENST00000327949.9:c.1415dupC	chr17.hg19:g.80400214_80400214dupC	ENSP00000332634:p.Ala470fs	96.0	0.0		96.0	17.0	NM_173620	B7UUP6|Q8IYN4|Q8TE81	Frame_Shift_Ins	INS	ENST00000327949.9	hg19																																																																																				.	.		0.688	HEXDC-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000443513.1	NM_173620		C	80400208	-	C	80400207	7	5	352	1	0	1	1	0	0	0	0	0	7084	1306	46	0	1539	0	HEXDC	17	80400207	Frame_Shift_Ins	INS	-	TCGA-WQ-A9G7-01A-11D-A36X-10	1303655	80400207	795003	390	49806										
NDC80	10403	hgsc.bcm.edu	37	chr18	2599168	2599169	+	Splice_Site	DEL	TA	TA	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tcaaatacagggctcaagttTatgtaagtaatcatgactac							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	TA	TA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr18:2599168_2599169delTA	ENST00000261597.4	+	12	1554_1555	c.1372_1373delTA	c.(1372-1374)tat>t	p.Y458fs		NM_006101.2	NP_006092.1	O14777	NDC80_HUMAN	NDC80 kinetochore complex component	458	Interaction with NEK2 and ZWINT.|Interaction with PSMC2 and SMC1A.|Interaction with the C-terminus of CDCA1 and the SPBC24-SPBC25 subcomplex.				attachment of spindle microtubules to kinetochore (GO:0008608)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)				NS(1)|biliary_tract(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(2)|urinary_tract(2)	22						GGCTCAAGTTTATGTAAGTAAT	0.351																																					p.457_458del		Atlas-INDEL	.											.	NDC80	62	.	0			c.1371_1372del						.																																			SO:0001630	splice_region_variant	10403	exon12			.	AF017790	CCDS11827.1	18p11.31	2013-01-17	2013-01-17	2007-03-02	ENSG00000080986	ENSG00000080986			16909	protein-coding gene	gene with protein product		607272	"highly expressed in cancer, rich in leucine heptad repeats (yeast)", "kinetochore associated 2", "NDC80 kinetochore complex component homolog (S. cerevisiae)"	KNTC2		9315664, 12351790	Standard	NM_006101		Approved	HEC, HEC1, hsNDC80, TID3	uc002kli.3	O14777	OTTHUMG00000131483	ENST00000261597.4:c.1374+1TA>-	chr18.hg19:g.2599168_2599169delTA		59.0	0.0		63.0	13.0	NM_006101	Q6PJX2	Frame_Shift_Del	DEL	ENST00000261597.4	hg19	CCDS11827.1																																																																																			.	.		0.351	NDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254327.1	NM_006101	Frame_Shift_Del	-	2599169	TA	-	2599168	8	5	352	1	0	1	0	1	0	0	1	0	10251	1754	61	0	1414	0	NDC80	18	2599168	Splice_Site	DEL	TA	TCGA-WQ-A9G7-01A-11D-A36X-10		2599168	75478080	391	49807										
LAMA1	284217	hgsc.bcm.edu	37	chr18	6942222	6942222	+	Frame_Shift_Del	DEL	T	T	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gaggtctggctgcgcaggcaTttttgcttcacaccagctgt							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr18:6942222delT	ENST00000389658.3	-	63	9177	c.9084delA	c.(9082-9084)aaafs	p.K3028fs		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	3028	Laminin G-like 5. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				TGCGCAGGCATTTTTGCTTCA	0.468																																					p.C3029fs		Atlas-INDEL	.											.	LAMA1	458	.	0			c.9085delT						.						46	48	48					18																	6942222		2203	4300	6503	SO:0001589	frameshift_variant	284217	exon63			.	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.9084delA	chr18.hg19:g.6942222delT	ENSP00000374309:p.Lys3028fs	42.0	0.0		55.0	10.0	NM_005559		Frame_Shift_Del	DEL	ENST00000389658.3	hg19	CCDS32787.1																																																																																			.	.		0.468	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		-	6942222	T	-	6942222	7	5	352	1	0	1	0	1	0	0	0	0	8614	1490	52	0	147	0	LAMA1	18	6942222	Frame_Shift_Del	DEL	T	TCGA-WQ-A9G7-01A-11D-A36X-10	4343054	6942222	71135026	392	49808										
ANKRD12	23253	hgsc.bcm.edu	37	chr18	9255558	9255559	+	Frame_Shift_Ins	INS	-	-	A													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cgagaaatcttttagggaggINSaaaaaataaaagatctaaaa							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr18:9255558_9255559insA	ENST00000262126.4	+	9	2533_2534	c.2293_2294insA	c.(2293-2295)gaafs	p.E765fs	ANKRD12_ENST00000383440.2_Frame_Shift_Ins_p.E742fs|ANKRD12_ENST00000400020.3_Frame_Shift_Ins_p.E742fs	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	765						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						TTTTAGGGAGGAAAAAATAAAA	0.351																																					p.E765fs		Atlas-INDEL	.											.	ANKRD12	167	.	0			c.2293_2294insA						.																																			SO:0001589	frameshift_variant	23253	exon9			.	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.2299dupA	chr18.hg19:g.9255564_9255564dupA	ENSP00000262126:p.Glu765fs	103.0	0.0		123.0	49.0	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Frame_Shift_Ins	INS	ENST00000262126.4	hg19	CCDS11843.1																																																																																			.	.		0.351	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		A	9255559	-	A	9255558	7	5	352	1	0	1	1	0	0	0	0	0	640	1175	41	0	2323	0	ANKRD12	18	9255558	Frame_Shift_Ins	INS	-	TCGA-WQ-A9G7-01A-11D-A36X-10	2313336	9255558	68821690	393	49809										
FAM59A	64762	hgsc.bcm.edu	37	chr18	29850320	29850320	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cggggtggaacaggtggggcGttcaggagccggcattcttc	18	9	2	0	rs368693154		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr18:29850320G>A	ENST00000269209.6	-	5	1596	c.1593C>T	c.(1591-1593)aaC>aaT	p.N531N	GAREM_ENST00000399218.4_Silent_p.N531N			Q9H706	GAREM_HUMAN	GRB2 associated, regulator of MAPK1	531	Necessary for interaction with GRB2.|Pro-rich.				cellular response to epidermal growth factor stimulus (GO:0071364)|epidermal growth factor receptor signaling pathway (GO:0007173)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)										CAGGTGGGGCGTTCAGGAGCC	0.597													g|||	1	0.000199681	8e-04	0	5008	,	,		16312	0		0	False		,,,				2504	0				p.N531N		Atlas-SNP	.											.	.	.	.	0			c.C1593T						.	G	,	1,4405	2.1+/-5.4	0,1,2202	90	77	81		1593,1593	2	1	18		81	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	FAM59A	NM_001242409.1,NM_022751.2	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	531/877,531/876	29850320	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	64762	exon5			TGGGGCGTTCAGG	AK025263	CCDS11905.1, CCDS56057.1	18q12.1	2012-11-30	2012-11-30	2012-11-30	ENSG00000141441	ENSG00000141441			26136	protein-coding gene	gene with protein product	"Grb2-associated and regulator of Erk/MAPK"		"chromosome 18 open reading frame 11", "family with sequence similarity 59, member A"	C18orf11, FAM59A		19509291	Standard	NM_001242409		Approved	FLJ21610	uc002kxl.3	Q9H706	OTTHUMG00000132273	ENST00000269209.6:c.1593C>T	chr18.hg19:g.29850320G>A		131.0	0.0		112.0	22.0	NM_022751	Q0VAG3|Q0VAG4|Q8ND03|Q9BSF5	Silent	SNP	ENST00000269209.6	hg19	CCDS56057.1																																																																																			.	.		0.597	GAREM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255365.1	NM_022751		A	29850320	G	A	29850320	2	1	352	1	0	0	0	0	0	0	0	1	5600	1136	40	1		1	FAM59A	18	29850320	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	20594762	29850320	48226928	394	49810										
ZBTB7C	201501	hgsc.bcm.edu	37	chr18	45566490	45566490	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agttgagataggcaccgtagTcgttctccgccttgatgggt	13	9	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr18:45566490T>G	ENST00000588982.1	-	3	1490	c.989A>C	c.(988-990)gAc>gCc	p.D330A	ZBTB7C_ENST00000586438.1_Missense_Mutation_p.D330A|ZBTB7C_ENST00000332053.2_Missense_Mutation_p.D330A|ZBTB7C_ENST00000590800.1_Missense_Mutation_p.D330A|ZBTB7C_ENST00000535628.2_Missense_Mutation_p.D330A			A1YPR0	ZBT7C_HUMAN	zinc finger and BTB domain containing 7C	330							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(8)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23						GGCACCGTAGTCGTTCTCCGC	0.632																																					p.D330A		Atlas-SNP	.											.	ZBTB7C	73	.	0			c.A989C						.						73	73	73					18																	45566490		2203	4300	6503	SO:0001583	missense	201501	exon2			CCGTAGTCGTTCT	Y14591	CCDS32830.1	18q21.1	2013-01-08		2005-04-07	ENSG00000184828	ENSG00000184828		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	31700	protein-coding gene	gene with protein product			"zinc finger and BTB domain containing 36"	ZBTB36			Standard	NM_001039360		Approved	ZNF857C	uc002ldb.3	A1YPR0		ENST00000588982.1:c.989A>C	chr18.hg19:g.45566490T>G	ENSP00000468782:p.Asp330Ala	48.0	0.0		62.0	8.0	NM_001039360	O73453	Missense_Mutation	SNP	ENST00000588982.1	hg19	CCDS32830.1	.	.	.	.	.	.	.	.	.	.	T	19.84	3.901489	0.72754	.	.	ENSG00000184828	ENST00000535628;ENST00000332053	T;T	0.11495	2.77;2.77	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.17916	0.0430	L	0.27053	0.805	0.58432	D	0.999999	D;D	0.69078	0.997;0.997	D;D	0.67103	0.949;0.949	T	0.11767	-1.0574	10	0.12103	T	0.63	.	15.2867	0.73833	0.0:0.0:0.0:1.0	.	330;330	B2RG49;A1YPR0	.;ZBT7C_HUMAN	A	330	ENSP00000439781:D330A;ENSP00000328732:D330A	ENSP00000328732:D330A	D	-	2	0	ZBTB7C	43820488	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.259000	0.72494	2.013000	0.59113	0.459000	0.35465	GAC	.	.		0.632	ZBTB7C-025	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450731.1	NM_001039360		G	45566490	T	G	45566490	3	3	352	1	0	0	0	0	1	0	0	0	17570	1667	58	5	878	5	ZBTB7C	18	45566490	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	15716170	45566490	32510758	395	49811										
MEX3C	51320	hgsc.bcm.edu	37	chr18	48723154	48723154	+	Intron	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	acccccgccgccgccgccgcGgccgccgcctcccgggcatc	12	25	0	0	rs78074704|rs62092914|rs147438518		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr18:48723154G>C	ENST00000591040.1	-	2	43				MEX3C_ENST00000592416.1_5'Flank			Q5U5Q3	MEX3C_HUMAN	mex-3 RNA binding family member C						chondrocyte hypertrophy (GO:0003415)|energy homeostasis (GO:0097009)|regulation of fat cell differentiation (GO:0045598)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(11)|ovary(1)|skin(1)	17		Colorectal(6;0.003)|all_epithelial(6;0.0473)		Colorectal(16;0.0175)|READ - Rectum adenocarcinoma(32;0.15)		ccgccgccgcggccgccgccT	0.771																																					p.A179A		Atlas-SNP	.											MEX3C_ENST00000406189,NS,carcinoma,0,1	MEX3C	77	.	0			c.C537G						.						3	3	3					18																	48723154		1139	2266	3405	SO:0001627	intron_variant	51320	exon1			CGCCGCGGCCGCC	BC041122	CCDS11951.2	18q21.1	2013-08-21	2013-08-21	2007-07-18	ENSG00000176624	ENSG00000176624		"RING-type (C3HC4) zinc fingers", "Mex-3 homologs"	28040	protein-coding gene	gene with protein product		611005	"ring finger and KH domain containing 2", "mex-3 homolog C (C. elegans)"	RKHD2		17267406	Standard	NM_016626		Approved	FLJ38871, RNF194	uc002lfc.4	Q5U5Q3	OTTHUMG00000132693	ENST00000591040.1:c.757-19208C>G	chr18.hg19:g.48723154G>C		37.0	0.0		56.0	11.0	NM_016626	A1L022|Q9NZE3	Silent	SNP	ENST00000591040.1	hg19																																																																																				.	.		0.771	MEX3C-003	KNOWN	mRNA_end_NF|basic	processed_transcript	protein_coding	OTTHUMT00000449559.1	NM_016626		C	48723154	G	C	48723154	1	2	352	0	1	0	0	0	0	0	0	0	9520	1103	39	4		4	MEX3C	18	48723154	Intron	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	3156664	48723154	29354094	396	49812										
RTTN	25914	hgsc.bcm.edu	37	chr18	67753861	67753861	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tcacccacctgccaagtataAtcctttataatttctgtagg	5	11	2	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr18:67753861A>G	ENST00000255674.6	-	32	4648	c.4362T>C	c.(4360-4362)gaT>gaC	p.D1454D	RTTN_ENST00000437017.1_Silent_p.D1454D|RTTN_ENST00000454359.1_3'UTR	NM_173630.3	NP_775901.3	Q86VV8	RTTN_HUMAN	rotatin	1454					determination of left/right symmetry (GO:0007368)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(35)|ovary(4)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Esophageal squamous(42;0.129)				GCCAAGTATAATCCTTTATAA	0.249																																					p.D1454D		Atlas-SNP	.											.	RTTN	184	.	0			c.T4362C						.						85	93	90					18																	67753861		1787	4055	5842	SO:0001819	synonymous_variant	25914	exon32			AGTATAATCCTTT	AL117635	CCDS42443.1	18q22.1	2008-08-01				ENSG00000176225			18654	protein-coding gene	gene with protein product		610436				11900971	Standard	NM_173630		Approved	DKFZP434G145	uc002lkp.2	Q86VV8		ENST00000255674.6:c.4362T>C	chr18.hg19:g.67753861A>G		294.0	0.0		307.0	47.0	NM_173630	Q68CS9|Q6ZRL8|Q6ZTK3|Q86TG4|Q8N8N8|Q8TBQ4|Q96IN9|Q9UFJ4	Silent	SNP	ENST00000255674.6	hg19	CCDS42443.1																																																																																			.	.		0.249	RTTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442988.1	NM_173630		G	67753861	A	G	67753861	2	3	352	1	0	0	0	0	0	0	0	1	13752	98	4	2		2	RTTN	18	67753861	Silent	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	19030707	67753861	10323387	397	49813										
PPAP2C	8612	hgsc.bcm.edu	37	chr19	282794	282794	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	atcccaaaggaagagtgtccCgagtagaaagacaacctgag	11	9	0	4			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:282794C>T	ENST00000269812.3	-	4	547	c.498G>A	c.(496-498)tcG>tcA	p.S166S	PPAP2C_ENST00000327790.3_Silent_p.S187S|PPAP2C_ENST00000434325.2_Silent_p.S110S	NM_003712.2|NM_177526.1	NP_003703.1|NP_803545.1	O43688	LPP2_HUMAN	phosphatidic acid phosphatase type 2C	166					dephosphorylation (GO:0016311)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidate phosphatase activity (GO:0008195)|phosphoprotein phosphatase activity (GO:0004721)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(1)|skin(1)	5		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AAGAGTGTCCCGAGTAGAAAG	0.587																																					p.S187S		Atlas-SNP	.											.	PPAP2C	38	.	0			c.G561A						.						109	92	98					19																	282794		2203	4300	6503	SO:0001819	synonymous_variant	8612	exon4			GTGTCCCGAGTAG	AF035959	CCDS12023.1, CCDS12024.1, CCDS45889.1	19p13	2009-05-27				ENSG00000141934	3.1.3.4		9230	protein-coding gene	gene with protein product		607126				9570154, 9607309	Standard	NM_177543		Approved	PAP-2c, LPP2	uc002loh.3	O43688		ENST00000269812.3:c.498G>A	chr19.hg19:g.282794C>T		90.0	0.0		115.0	25.0	NM_177543	A6NLV0|E9PAY8	Silent	SNP	ENST00000269812.3	hg19	CCDS12023.1																																																																																			.	.		0.587	PPAP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451777.2			T	282794	C	T	282794	2	4	352	1	0	0	0	0	0	0	0	1	12301	639	23	1		1	PPAP2C	19	282794	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10		282794	58846189	398	49814										
ODF3L2	284451	hgsc.bcm.edu	37	chr19	464152	464152	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggggcgggcggggggggtgcGgcccaccaccgtgtagctgg	23	11	0	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:464152G>A	ENST00000315489.4	-	4	797	c.562C>T	c.(562-564)Cgc>Tgc	p.R188C	ODF3L2_ENST00000382696.3_Missense_Mutation_p.R152C	NM_182577.2	NP_872383.1	Q3SX64	OD3L2_HUMAN	outer dense fiber of sperm tails 3-like 2	188	Pro-rich.					cytoplasmic microtubule (GO:0005881)				large_intestine(1)|lung(2)	3						gggggggtgcggcccACCACC	0.697																																					p.R188C		Atlas-SNP	.											.	ODF3L2	18	.	0			c.C562T						.						3	3	3					19																	464152		1557	3170	4727	SO:0001583	missense	284451	exon4			GGGTGCGGCCCAC	AK097378	CCDS12027.1	19p13.3	2010-04-23	2008-07-04	2008-07-04		ENSG00000181781			26841	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 19"	C19orf19		14702039	Standard	NM_182577		Approved	FLJ40059	uc002lor.3	Q3SX64		ENST00000315489.4:c.562C>T	chr19.hg19:g.464152G>A	ENSP00000318029:p.Arg188Cys	69.0	0.0		64.0	19.0	NM_182577	Q3SX65|Q8N1L2	Missense_Mutation	SNP	ENST00000315489.4	hg19	CCDS12027.1	.	.	.	.	.	.	.	.	.	.	G	10.35	1.326900	0.24080	.	.	ENSG00000181781	ENST00000315489;ENST00000382696	T;T	0.55930	1.01;0.49	3.8	0.197	0.15164	.	0.283333	0.34555	N	0.003873	T	0.63534	0.2519	M	0.86502	2.82	0.34587	D	0.715127	P;D	0.64830	0.941;0.994	B;P	0.58873	0.244;0.847	T	0.66492	-0.5910	10	0.87932	D	0	-20.4769	2.293	0.04143	0.1011:0.1663:0.3923:0.3403	.	152;188	Q3SX64-2;Q3SX64	.;OD3L2_HUMAN	C	188;152	ENSP00000318029:R188C;ENSP00000372143:R152C	ENSP00000318029:R188C	R	-	1	0	ODF3L2	415152	0.917000	0.31117	0.025000	0.17156	0.002000	0.02628	1.872000	0.39549	-0.069000	0.12931	-0.325000	0.08501	CGC	.	.		0.697	ODF3L2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451849.2	NM_182577		A	464152	G	A	464152	3	1	352	1	0	0	0	0	1	0	0	0	10841	1116	39	1	311	1	ODF3L2	19	464152	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	181358	464152	58664831	399	49815										
REEP6	92840	hgsc.bcm.edu	37	chr19	1495386	1495386	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tgtgtaccccgcatatgcctCgtgagtgcacggctggctgc	13	13	0	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:1495386C>T	ENST00000233596.3	+	2	313	c.209C>T	c.(208-210)tCa>tTa	p.S70L		NM_138393.1	NP_612402.1	Q96HR9	REEP6_HUMAN	receptor accessory protein 6	70					regulation of intracellular transport (GO:0032386)	apical part of cell (GO:0045177)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				lung(1)|ovary(1)	2		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCATATGCCTCGTGAGTGCAC	0.627																																					p.S70L		Atlas-SNP	.											.	REEP6	21	.	0			c.C209T						.						100	88	92					19																	1495386		2201	4300	6501	SO:0001630	splice_region_variant	92840	exon2			ATGCCTCGTGAGT	BC008201	CCDS12070.1	19p13.3	2012-12-20	2006-02-08	2006-02-07	ENSG00000115255	ENSG00000115255		"Receptor accessory proteins"	30078	protein-coding gene	gene with protein product	"polyposis locus protein 1-like 1", "deleted in polyposis 1-like 1"	609346	"chromosome 19 open reading frame 32"	C19orf32		16271481, 15550249	Standard	NM_138393		Approved	DP1L1, FLJ25383	uc002ltc.3	Q96HR9	OTTHUMG00000180072	ENST00000233596.3:c.209+1C>T	chr19.hg19:g.1495386C>T		42.0	0.0		51.0	8.0	NM_138393	B2RE01|D6W5Z0|Q96LM0	Missense_Mutation	SNP	ENST00000233596.3	hg19	CCDS12070.1	.	.	.	.	.	.	.	.	.	.	C	18.85	3.711835	0.68730	.	.	ENSG00000115255	ENST00000233596;ENST00000395479	D	0.95447	-3.71	4.48	4.48	0.54585	.	.	.	.	.	D	0.98789	0.9592	H	0.99347	4.525	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.954	D	0.99395	1.0926	9	0.72032	D	0.01	-0.8094	15.7471	0.77955	0.0:1.0:0.0:0.0	.	70;70	B4DF39;Q96HR9	.;REEP6_HUMAN	L	70	ENSP00000233596:S70L	ENSP00000233596:S70L	S	+	2	0	REEP6	1446386	1.000000	0.71417	0.994000	0.49952	0.064000	0.16182	7.476000	0.81055	2.046000	0.60703	0.556000	0.70494	TCA	.	.		0.627	REEP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449623.1	NM_138393	Missense_Mutation	T	1495386	C	T	1495386	5	4	352	1	0	0	0	0	0	0	1	0	13224	898	31	1	215	1	REEP6	19	1495386	Splice_Site	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	1031234	1495386	57633597	400	49816										
TLE2	7089	hgsc.bcm.edu	37	chr19	3006585	3006585	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cagctgccgggcgtgccgcgGgatgcccgcgcctaccagtg	16	16	0	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:3006585G>T	ENST00000262953.6	-	15	1595	c.1333C>A	c.(1333-1335)Ccg>Acg	p.P445T	TLE2_ENST00000586422.1_Intron|TLE2_ENST00000447365.2_Missense_Mutation_p.P112T|TLE2_ENST00000443826.3_Missense_Mutation_p.P323T|TLE2_ENST00000455444.2_Missense_Mutation_p.P323T|TLE2_ENST00000591529.1_Missense_Mutation_p.P459T|TLE2_ENST00000590536.1_Missense_Mutation_p.P446T|TLE2_ENST00000426948.2_Missense_Mutation_p.P459T	NM_003260.4	NP_003251.2	Q04725	TLE2_HUMAN	transducin-like enhancer of split 2	445					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|prostate(1)	13				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCGTGCCGCGGGATGCCCGCG	0.692																																					p.P459T		Atlas-SNP	.											.	TLE2	35	.	0			c.C1375A						.						13	17	16					19																	3006585		2088	4208	6296	SO:0001583	missense	7089	exon16			GCCGCGGGATGCC	M99436	CCDS45911.1, CCDS45912.1, CCDS45913.1, CCDS74255.1	19p13.3	2014-03-07	2014-03-07					"WD repeat domain containing"	11838	protein-coding gene	gene with protein product	"enhancer of split groucho 2"	601041	"transducin-like enhancer of split 2, homolog of Drosophila E(sp1)", "transducin-like enhancer of split 2 (E(sp1) homolog, Drosophila)"			8808280	Standard	NM_003260		Approved	ESG2, GRG2, ESG, FLJ41188	uc002lww.3	Q04725		ENST00000262953.6:c.1333C>A	chr19.hg19:g.3006585G>T	ENSP00000262953:p.Pro445Thr	227.0	0.0		222.0	84.0	NM_001144761	B4DE03|E9PEV7|F8WCH2|Q8WVY0|Q9Y6S0	Missense_Mutation	SNP	ENST00000262953.6	hg19	CCDS45911.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.784479	0.90282	.	.	ENSG00000065717	ENST00000262953;ENST00000455444;ENST00000450017;ENST00000447365;ENST00000443826;ENST00000426948;ENST00000439015	T;T;T;T;T	0.12039	2.72;2.72;2.72;2.72;2.72	3.87	3.87	0.44632	WD40 repeat-like-containing domain (1);	0.111765	0.64402	D	0.000008	T	0.40448	0.1117	M	0.83603	2.65	0.58432	D	0.999995	D;D;D;D;D;D	0.89917	1.0;1.0;0.983;0.999;1.0;1.0	D;D;P;D;D;D	0.85130	0.997;0.996;0.609;0.961;0.997;0.997	T	0.48007	-0.9072	10	0.87932	D	0	-19.3704	15.0009	0.71469	0.0:0.0:1.0:0.0	.	353;323;112;459;323;445	B4DZU9;E9PEV7;B4DE62;F8WCH2;B4DE03;Q04725	.;.;.;.;.;TLE2_HUMAN	T	445;323;439;112;323;459;353	ENSP00000262953:P445T;ENSP00000413107:P323T;ENSP00000406523:P112T;ENSP00000392427:P323T;ENSP00000392869:P459T	ENSP00000262953:P445T	P	-	1	0	TLE2	2957585	1.000000	0.71417	0.997000	0.53966	0.937000	0.57800	7.716000	0.84723	2.183000	0.69458	0.456000	0.33151	CCG	.	.		0.692	TLE2-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000452194.2	NM_003260		T	3006585	G	T	3006585	3	4	352	1	0	0	0	0	1	0	0	0	15954	1232	43	3	922	3	TLE2	19	3006585	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	1511199	3006585	56122398	401	49817										
TMEM146	257062	hgsc.bcm.edu	37	chr19	5778650	5778650	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aggcacagagcccccgggacGccaccgcactcctcacggag	12	18	1	1	rs556362293		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:5778650G>A	ENST00000381624.3	+	22	2421	c.2360G>A	c.(2359-2361)cGc>cAc	p.R787H	CATSPERD_ENST00000309164.7_3'UTR	NM_152784.3	NP_689997.3	Q86XM0	CTSRD_HUMAN	catsper channel auxiliary subunit delta	787					multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)											CCCCCGGGACGCCACCGCACT	0.582													G|||	1	0.000199681	0	0	5008	,	,		17120	0		0	False		,,,				2504	0.001				p.R787H		Atlas-SNP	.											TMEM146,NS,lymphoid_neoplasm,0,2	.	.	.	0			c.G2360A						.						42	49	47					19																	5778650		2118	4226	6344	SO:0001583	missense	257062	exon22			CGGGACGCCACCG	BC043005	CCDS12149.2	19p13.3	2013-10-11	2012-02-22	2012-02-22	ENSG00000174898	ENSG00000174898			28598	protein-coding gene	gene with protein product			"transmembrane protein 146"	TMEM146		21224844	Standard	NM_152784		Approved	MGC39581	uc002mda.3	Q86XM0	OTTHUMG00000143036	ENST00000381624.3:c.2360G>A	chr19.hg19:g.5778650G>A	ENSP00000371037:p.Arg787His	161.0	0.0		174.0	31.0	NM_152784	Q6ZRP1	Missense_Mutation	SNP	ENST00000381624.3	hg19	CCDS12149.2	.	.	.	.	.	.	.	.	.	.	G	1.069	-0.670465	0.03403	.	.	ENSG00000174898	ENST00000381624;ENST00000381613	T	0.26067	1.76	1.09	-2.19	0.07015	.	.	.	.	.	T	0.12092	0.0294	N	0.12182	0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22347	-1.0219	9	0.72032	D	0.01	.	4.6743	0.12705	0.5611:0.0:0.4389:0.0	.	787	Q86XM0	TM146_HUMAN	H	787;456	ENSP00000371037:R787H	ENSP00000371026:R456H	R	+	2	0	TMEM146	5729650	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.309000	0.02728	-0.927000	0.03766	-1.056000	0.02311	CGC	.	.		0.582	CATSPERD-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286953.2	NM_152784		A	5778650	G	A	5778650	3	1	352	1	0	0	0	0	1	0	0	0	16075	1087	38	1	2446	1	TMEM146	19	5778650	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	2772065	5778650	53350333	402	49818										
PSPN	5623	hgsc.bcm.edu	37	chr19	6375770	6375770	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cgagaactctccatcggccaCgggaaccccacgggcatcgg	12	16	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:6375770C>T	ENST00000245810.1	-	1	90	c.91G>A	c.(91-93)Gtg>Atg	p.V31M	PSPN_ENST00000597721.1_Missense_Mutation_p.V31M	NM_004158.2	NP_004149.1	O60542	PSPN_HUMAN	persephin	31					axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|central nervous system development (GO:0007417)|nervous system development (GO:0007399)	extracellular space (GO:0005615)	receptor binding (GO:0005102)			lung(1)|ovary(1)|skin(1)	3						CCATCGGCCACGGGAACCCCA	0.647																																					p.V31M		Atlas-SNP	.											.	PSPN	5	.	0			c.G91A						.						48	43	45					19																	6375770		2203	4300	6503	SO:0001583	missense	5623	exon1			CGGCCACGGGAAC	AF040962	CCDS12164.1	19p13.3	2014-01-30				ENSG00000125650		"Endogenous ligands"	9579	protein-coding gene	gene with protein product		602921				10072588	Standard	NM_004158		Approved	PSP	uc010xja.2	O60542		ENST00000245810.1:c.91G>A	chr19.hg19:g.6375770C>T	ENSP00000245810:p.Val31Met	220.0	0.0		222.0	45.0	NM_004158		Missense_Mutation	SNP	ENST00000245810.1	hg19	CCDS12164.1	.	.	.	.	.	.	.	.	.	.	C	11.13	1.548062	0.27652	.	.	ENSG00000125650	ENST00000545374;ENST00000245810	D	0.89939	-2.59	3.45	0.948	0.19561	.	.	.	.	.	T	0.78509	0.4294	L	0.27053	0.805	0.09310	N	1	D	0.54772	0.968	B	0.39876	0.312	T	0.70212	-0.4934	9	0.62326	D	0.03	-9.747	5.3807	0.16189	0.2344:0.5371:0.2285:0.0	.	31	O60542	PSPN_HUMAN	M	31	ENSP00000245810:V31M	ENSP00000245810:V31M	V	-	1	0	PSPN	6326770	0.000000	0.05858	0.050000	0.19076	0.031000	0.12232	-0.596000	0.05720	0.732000	0.32470	0.313000	0.20887	GTG	.	.		0.647	PSPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398032.1	NM_004158		T	6375770	C	T	6375770	3	4	352	1	0	0	0	0	1	0	0	0	12730	536	19	1	386	1	PSPN	19	6375770	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	597120	6375770	52753213	403	49819										
XAB2	56949	hgsc.bcm.edu	37	chr19	7687478	7687478	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ccagaccttcagtgacttgtAcacgcggttctgcacgggct	11	13	2	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:7687478A>G	ENST00000358368.4	-	11	1478	c.1441T>C	c.(1441-1443)Tac>Cac	p.Y481H	XAB2_ENST00000534844.1_Missense_Mutation_p.Y478H	NM_020196.2	NP_064581.2	Q9HCS7	SYF1_HUMAN	XPA binding protein 2	481					blastocyst development (GO:0001824)|DNA repair (GO:0006281)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	26						AGTGACTTGTACACGCGGTTC	0.687								Direct reversal of damage;Nucleotide excision repair (NER)																													p.Y481H		Atlas-SNP	.											.	XAB2	69	.	0			c.T1441C						.						47	45	46					19																	7687478		2203	4300	6503	SO:0001583	missense	56949	exon11			ACTTGTACACGCG	AB026111	CCDS32892.1	19p13.3	2013-08-21				ENSG00000076924			14089	protein-coding gene	gene with protein product	"SYF1 homolog, RNA splicing factor (S. cerevisiae)", "SYF1 pre-mRNA-splicing factor"	610850				10944529	Standard	NM_020196		Approved	HCNP, HCRN, SYF1, NTC90	uc002mgx.3	Q9HCS7		ENST00000358368.4:c.1441T>C	chr19.hg19:g.7687478A>G	ENSP00000351137:p.Tyr481His	35.0	0.0		39.0	5.0	NM_020196	Q8TET6|Q96HB0|Q96IW0|Q9NRG6|Q9ULP3	Missense_Mutation	SNP	ENST00000358368.4	hg19	CCDS32892.1	.	.	.	.	.	.	.	.	.	.	A	3.964	-0.009680	0.07727	.	.	ENSG00000076924	ENST00000358368;ENST00000534844	T;T	0.12255	2.7;2.7	3.95	3.95	0.45737	.	0.073373	0.56097	D	0.000027	T	0.06917	0.0176	N	0.13327	0.33	0.58432	D	0.999994	B	0.11235	0.004	B	0.10450	0.005	T	0.12091	-1.0561	10	0.02654	T	1	-27.8417	11.9474	0.52936	1.0:0.0:0.0:0.0	.	481	Q9HCS7	SYF1_HUMAN	H	481;478	ENSP00000351137:Y481H;ENSP00000438225:Y478H	ENSP00000351137:Y481H	Y	-	1	0	XAB2	7593478	1.000000	0.71417	0.998000	0.56505	0.630000	0.37929	6.901000	0.75693	1.659000	0.50751	0.379000	0.24179	TAC	.	.		0.687	XAB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461021.1	NM_020196		G	7687478	A	G	7687478	3	3	352	1	0	0	0	0	1	0	0	0	17433	391	14	2	1162	2	XAB2	19	7687478	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	1311708	7687478	51441505	404	49820										
FBN3	84467	hgsc.bcm.edu	37	chr19	8145942	8145942	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggacagcggcaggtgaaggcGcccacagtgttgacacagag	16	10	0	3			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:8145942G>A	ENST00000600128.1	-	59	7812	c.7398C>T	c.(7396-7398)ggC>ggT	p.G2466G	FBN3_ENST00000270509.2_Silent_p.G2466G|FBN3_ENST00000601739.1_Silent_p.G2466G			Q75N90	FBN3_HUMAN	fibrillin 3	2466	EGF-like 40; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						AGGTGAAGGCGCCCACAGTGT	0.662																																					p.G2466G		Atlas-SNP	.											.	FBN3	300	.	0			c.C7398T						.						72	63	66					19																	8145942		2203	4300	6503	SO:0001819	synonymous_variant	84467	exon58			GAAGGCGCCCACA		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.7398C>T	chr19.hg19:g.8145942G>A		24.0	0.0		35.0	6.0	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	hg19	CCDS12196.1																																																																																			.	.		0.662	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447		A	8145942	G	A	8145942	2	1	352	1	0	0	0	0	0	0	0	1	5712	1074	38	1		1	FBN3	19	8145942	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	458464	8145942	50983041	405	49821										
OR7D4	125958	hgsc.bcm.edu	37	chr19	9324680	9324680	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agcatgggggtgaccatggcGtacatcactgaggcggtgga	17	8	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:9324680G>A	ENST00000308682.2	-	1	862	c.834C>T	c.(832-834)taC>taT	p.Y278Y		NM_001005191.2	NP_001005191.1	Q8NG98	OR7D4_HUMAN	olfactory receptor, family 7, subfamily D, member 4	278						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)|skin(3)|stomach(1)	26						TGACCATGGCGTACATCACTG	0.557																																					p.Y278Y		Atlas-SNP	.											OR7D4,NS,carcinoma,0,1	OR7D4	66	.	0			c.C834T						.						70	63	65					19																	9324680		2203	4300	6503	SO:0001819	synonymous_variant	125958	exon1			CATGGCGTACATC		CCDS32901.1	19p13.2	2013-12-17		2004-03-10	ENSG00000174667	ENSG00000174667		"GPCR / Class A : Olfactory receptors"	8380	protein-coding gene	gene with protein product		611538		OR7D4P			Standard	NM_001005191		Approved	hg105, OR19-B	uc002mla.2	Q8NG98	OTTHUMG00000179936	ENST00000308682.2:c.834C>T	chr19.hg19:g.9324680G>A		66.0	0.0		68.0	27.0	NM_001005191	A8CAH8|A8CAH9|A8CAI0|A8CAI1|B9EH79	Silent	SNP	ENST00000308682.2	hg19	CCDS32901.1																																																																																			.	.		0.557	OR7D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449004.1			A	9324680	G	A	9324680	2	1	352	1	0	0	0	0	0	0	0	1	11229	1140	40	1		1	OR7D4	19	9324680	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	1178738	9324680	49804303	406	49822										
DOCK6	57572	hgsc.bcm.edu	37	chr19	11322519	11322519	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	catcttcaccgtgtccgtcaGgatcatgtgcaggttgaaca	10	11	4	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:11322519G>A	ENST00000294618.7	-	37	4695	c.4684C>T	c.(4684-4686)Ctg>Ttg	p.L1562L	DOCK6_ENST00000319867.7_Silent_p.L901L|CTC-510F12.2_ENST00000588634.1_RNA	NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	1562					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(8)|liver(2)|lung(9)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	39						GTGTCCGTCAGGATCATGTGC	0.592																																					p.L1562L		Atlas-SNP	.											.	DOCK6	104	.	0			c.C4684T						.						55	55	55					19																	11322519		2048	4183	6231	SO:0001819	synonymous_variant	57572	exon37			CCGTCAGGATCAT		CCDS45975.1	19p13.2	2011-08-04			ENSG00000130158	ENSG00000130158			19189	protein-coding gene	gene with protein product		614194				12432077	Standard	NM_020812		Approved	KIAA1395, ZIR1	uc002mqs.5	Q96HP0		ENST00000294618.7:c.4684C>T	chr19.hg19:g.11322519G>A		88.0	0.0		69.0	11.0	NM_020812	A6H8X5|Q7Z7P4|Q9P2F2	Silent	SNP	ENST00000294618.7	hg19	CCDS45975.1																																																																																			.	.		0.592	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812		A	11322519	G	A	11322519	2	1	352	1	0	0	0	0	0	0	0	1	4693	991	35	3		3	DOCK6	19	11322519	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	1997839	11322519	47806464	407	49823										
RFX1	5989	hgsc.bcm.edu	37	chr19	14090352	14090352	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggagtggcctggaccacagaTctctgggaggggaaaggcaa	17	8	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:14090352T>A	ENST00000254325.4	-	7	975	c.741A>T	c.(739-741)agA>agT	p.R247S		NM_002918.4	NP_002909.4	P22670	RFX1_HUMAN	regulatory factor X, 1 (influences HLA class II expression)	247					immune response (GO:0006955)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(19;6.67e-23)			GGACCACAGATCTCTGGGAGG	0.612																																					p.R247S		Atlas-SNP	.											.	RFX1	63	.	0			c.A741T						.						47	51	50					19																	14090352		2203	4300	6503	SO:0001583	missense	5989	exon7			CACAGATCTCTGG		CCDS12301.1	19p13.1	2008-07-17				ENSG00000132005			9982	protein-coding gene	gene with protein product	"trans-acting regulatory factor 1", "enhancer factor C", "MHC class II regulatory factor RFX"	600006				1505960, 8289803	Standard	NM_002918		Approved	EF-C	uc002mxv.3	P22670		ENST00000254325.4:c.741A>T	chr19.hg19:g.14090352T>A	ENSP00000254325:p.Arg247Ser	76.0	0.0		89.0	11.0	NM_002918		Missense_Mutation	SNP	ENST00000254325.4	hg19	CCDS12301.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.024166	0.75390	.	.	ENSG00000132005	ENST00000254325	T	0.47528	0.84	4.7	2.37	0.29283	RFX1 transcription activation region (1);	0.089033	0.43579	D	0.000554	T	0.49098	0.1537	L	0.33485	1.01	0.41127	D	0.985851	D	0.62365	0.991	D	0.78314	0.991	T	0.46062	-0.9218	10	0.40728	T	0.16	-23.4529	4.2842	0.10846	0.0:0.5895:0.0:0.4105	.	247	P22670	RFX1_HUMAN	S	247	ENSP00000254325:R247S	ENSP00000254325:R247S	R	-	3	2	RFX1	13951352	1.000000	0.71417	0.998000	0.56505	0.751000	0.42716	1.458000	0.35223	0.974000	0.38366	-0.232000	0.12228	AGA	.	.		0.612	RFX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458510.1	NM_002918		A	14090352	T	A	14090352	3	1	352	1	0	0	0	0	1	0	0	0	13277	1432	50	4	2258	4	RFX1	19	14090352	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	2767833	14090352	45038631	408	49824										
JAK3	3718	hgsc.bcm.edu	37	chr19	17942173	17942173	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gtttcgggcggccaggtcgcGgtgcacgcagcggcgggagc	20	12	0	0	rs200202992		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:17942173G>A	ENST00000527670.1	-	20	2871	c.2842C>T	c.(2842-2844)Cgc>Tgc	p.R948C	JAK3_ENST00000534444.1_Missense_Mutation_p.R948C|JAK3_ENST00000458235.1_Missense_Mutation_p.R948C			P52333	JAK3_HUMAN	Janus kinase 3	948	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell differentiation (GO:0030183)|enzyme linked receptor protein signaling pathway (GO:0007167)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of dendritic cell cytokine production (GO:0002731)|negative regulation of FasL biosynthetic process (GO:0045221)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of T cell activation (GO:0050868)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|negative regulation of thymocyte apoptotic process (GO:0070244)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of T cell apoptotic process (GO:0070232)|response to interleukin-15 (GO:0070672)|response to interleukin-2 (GO:0070669)|response to interleukin-4 (GO:0070670)|response to interleukin-9 (GO:0071104)|STAT protein import into nucleus (GO:0007262)|T cell homeostasis (GO:0043029)|tyrosine phosphorylation of STAT protein (GO:0007260)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)	p.R948C(1)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(85)|kidney(4)|large_intestine(11)|lung(22)|ovary(3)|prostate(5)|skin(1)|stomach(2)|upper_aerodigestive_tract(5)	147					Tofacitinib(DB08895)	GCCAGGTCGCGGTGCACGCAG	0.642		2	Mis		"acute megakaryocytic leukemia, ETP ALL"																																p.R948C		Atlas-SNP	.		Dom	yes		19	19p13.1	3718	Janus kinase 3		L	JAK3_ENST00000458235,head_neck,carcinoma,0,3	JAK3	341	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.C2842T						.						100	90	93					19																	17942173		2203	4300	6503	SO:0001583	missense	3718	exon21			GGTCGCGGTGCAC	U31601	CCDS12366.1	19p13-p12	2014-09-17	2009-04-23		ENSG00000105639	ENSG00000105639	2.7.10.1		6193	protein-coding gene	gene with protein product	"tyrosine-protein kinase JAK3", "leukocyte Janus kinase"	600173				8921370, 9226382	Standard	NM_000215		Approved	L-JAK, JAKL, LJAK, JAK3_HUMAN, JAK-3	uc002nhn.4	P52333	OTTHUMG00000165648	ENST00000527670.1:c.2842C>T	chr19.hg19:g.17942173G>A	ENSP00000432511:p.Arg948Cys	66.0	1.0		55.0	4.0	NM_000215	Q13259|Q13260|Q13611|Q8N1E8|Q99699|Q9Y6S2	Missense_Mutation	SNP	ENST00000527670.1	hg19	CCDS12366.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.271589	0.80469	.	.	ENSG00000105639	ENST00000458235;ENST00000527670;ENST00000534444	T;T;D	0.88818	-0.88;-0.88;-2.43	3.43	2.25	0.28309	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.146397	0.44688	D	0.000439	D	0.93284	0.7860	M	0.85373	2.75	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92590	0.6082	10	0.87932	D	0	-22.2012	7.5508	0.27796	0.0:0.0:0.6005:0.3995	.	948;948	P52333-2;P52333	.;JAK3_HUMAN	C	948	ENSP00000391676:R948C;ENSP00000432511:R948C;ENSP00000436421:R948C	ENSP00000391676:R948C	R	-	1	0	JAK3	17803173	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	0.581000	0.23819	1.883000	0.54544	0.462000	0.41574	CGC	.	.		0.642	JAK3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385549.1	NM_000215		A	17942173	G	A	17942173	3	1	352	1	0	0	0	0	1	0	0	0	7948	1116	39	1	548	1	JAK3	19	17942173	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	3851821	17942173	41186810	409	49825										
MAST3	23031	hgsc.bcm.edu	37	chr19	18218416	18218416	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gaaggagctgagcctgccacGccgaggacgtgggtgagttc	17	10	0	2	rs368179436		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:18218416G>A	ENST00000262811.6	+	2	59	c.59G>A	c.(58-60)cGc>cAc	p.R20H		NM_015016.1	NP_055831.1	O60307	MAST3_HUMAN	microtubule associated serine/threonine kinase 3	20							ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(6)|ovary(4)|pancreas(1)|stomach(1)	31						AGCCTGCCACGCCGAGGACGT	0.567																																					p.R20H		Atlas-SNP	.											.	MAST3	83	.	0			c.G59A						.	G	HIS/ARG	0,3916		0,0,1958	105	113	111		59	4.3	1	19		111	1,8277		0,1,4138	no	missense	MAST3	NM_015016.1	29	0,1,6096	AA,AG,GG		0.0121,0.0,0.0082	possibly-damaging	20/1310	18218416	1,12193	1958	4139	6097	SO:0001583	missense	23031	exon2			TGCCACGCCGAGG	AB011133	CCDS46014.1	19p13	2008-02-05				ENSG00000099308			19036	protein-coding gene	gene with protein product		612258					Standard	NM_015016		Approved	KIAA0561	uc002nhz.4	O60307		ENST00000262811.6:c.59G>A	chr19.hg19:g.18218416G>A	ENSP00000262811:p.Arg20His	68.0	0.0		52.0	7.0	NM_015016	Q7LDZ8|Q9UPI0	Missense_Mutation	SNP	ENST00000262811.6	hg19	CCDS46014.1	.	.	.	.	.	.	.	.	.	.	G	17.25	3.343020	0.61073	0.0	1.21E-4	ENSG00000099308	ENST00000262811	T	0.72051	-0.62	4.29	4.29	0.51040	.	.	.	.	.	T	0.66557	0.2801	L	0.51422	1.61	0.30329	N	0.786876	P	0.34562	0.457	B	0.34590	0.186	T	0.69807	-0.5045	9	0.59425	D	0.04	-0.0014	13.8648	0.63581	0.0:0.0:1.0:0.0	.	20	O60307	MAST3_HUMAN	H	20	ENSP00000262811:R20H	ENSP00000262811:R20H	R	+	2	0	MAST3	18079416	1.000000	0.71417	0.992000	0.48379	0.965000	0.64279	5.024000	0.64090	2.103000	0.63969	0.561000	0.74099	CGC	.	.		0.567	MAST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466526.2	XM_038150		A	18218416	G	A	18218416	3	1	352	1	0	0	0	0	1	0	0	0	9335	1087	38	1	65	1	MAST3	19	18218416	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	276243	18218416	40910567	410	49826										
ZNF91	7644	hgsc.bcm.edu	37	chr19	23543832	23543832	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gtttctctccagtatgaattCtcttatgtttagcaagggct	8	8	2	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:23543832C>T	ENST00000300619.7	-	4	2154	c.1949G>A	c.(1948-1950)aGa>aAa	p.R650K	ZNF91_ENST00000596528.1_5'Flank|ZNF91_ENST00000397082.2_Missense_Mutation_p.R618K|ZNF91_ENST00000599743.1_Intron	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	650					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.R650I(1)					all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				AGTATGAATTCTCTTATGTTT	0.383																																					p.R650K		Atlas-SNP	.											ZNF91_ENST00000300619,NS,carcinoma,0,3	ZNF91	349	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1949A						.						57	60	59					19																	23543832		2098	4239	6337	SO:0001583	missense	7644	exon4			TGAATTCTCTTAT	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"Zinc fingers, C2H2-type", "-"	13166	protein-coding gene	gene with protein product		603971	"zinc finger protein 91 (HPF7, HTF10)"			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.1949G>A	chr19.hg19:g.23543832C>T	ENSP00000300619:p.Arg650Lys	162.0	0.0		179.0	27.0	NM_003430	A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	hg19	CCDS42541.1	.	.	.	.	.	.	.	.	.	.	C	8.797	0.931978	0.18131	.	.	ENSG00000167232	ENST00000300619;ENST00000397082	T;T	0.18338	2.22;2.22	1.71	0.586	0.17434	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13415	0.0325	L	0.48877	1.53	0.26529	N	0.974284	B;P	0.42409	0.41;0.779	B;B	0.36666	0.147;0.23	T	0.12811	-1.0533	9	0.44086	T	0.13	.	8.1214	0.30974	0.2433:0.7567:0.0:0.0	.	618;650	Q05481-2;Q05481	.;ZNF91_HUMAN	K	650;618	ENSP00000300619:R650K;ENSP00000380272:R618K	ENSP00000300619:R650K	R	-	2	0	ZNF91	23335672	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-2.082000	0.01365	0.055000	0.16094	-1.048000	0.02349	AGA	.	.		0.383	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430		T	23543832	C	T	23543832	3	4	352	1	0	0	0	0	1	0	0	0	18215	913	32	3	1630	3	ZNF91	19	23543832	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	5325416	23543832	35585151	411	49827										
ZNF536	9745	hgsc.bcm.edu	37	chr19	30935510	30935510	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tcggccaacgagttccgctgCgaggtgtgcggtcaggtgtt	16	10	1	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:30935510C>T	ENST00000355537.3	+	2	1188	c.1041C>T	c.(1039-1041)tgC>tgT	p.C347C		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	347					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					AGTTCCGCTGCGAGGTGTGCG	0.652																																					p.C347C		Atlas-SNP	.											.	ZNF536	424	.	0			c.C1041T						.						95	105	102					19																	30935510		2203	4300	6503	SO:0001819	synonymous_variant	9745	exon2			CCGCTGCGAGGTG		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"Zinc fingers, C2H2-type"	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.1041C>T	chr19.hg19:g.30935510C>T		54.0	0.0		66.0	14.0	NM_014717	A2RU18	Silent	SNP	ENST00000355537.3	hg19	CCDS32984.1																																																																																			.	.		0.652	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		T	30935510	C	T	30935510	2	4	352	1	0	0	0	0	0	0	0	1	17989	776	27	1		1	ZNF536	19	30935510	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	7391678	30935510	28193473	412	49828										
PEPD	5184	hgsc.bcm.edu	37	chr19	34003533	34003533	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ccccggtgtcggtgcagtagCgctgagtctcctccccgccc	12	18	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:34003533C>T	ENST00000244137.7	-	2	200	c.167G>A	c.(166-168)cGc>cAc	p.R56H	PEPD_ENST00000397032.4_Missense_Mutation_p.R56H|PEPD_ENST00000436370.3_Missense_Mutation_p.R56H	NM_000285.3	NP_000276.2	P12955	PEPD_HUMAN	peptidase D	56					cellular amino acid metabolic process (GO:0006520)|collagen catabolic process (GO:0030574)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)	aminopeptidase activity (GO:0004177)|dipeptidase activity (GO:0016805)|manganese ion binding (GO:0030145)|metallocarboxypeptidase activity (GO:0004181)			endometrium(3)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)	17	Esophageal squamous(110;0.137)					GGTGCAGTAGCGCTGAGTCTC	0.652																																					p.R56H		Atlas-SNP	.											.	PEPD	48	.	0			c.G167A						.						32	39	37					19																	34003533		2106	4223	6329	SO:0001583	missense	5184	exon2			CAGTAGCGCTGAG	BC015027	CCDS42544.1, CCDS54244.1, CCDS54245.1	19q13.11	2008-02-05				ENSG00000124299	3.4.13.9		8840	protein-coding gene	gene with protein product	"prolidase"	613230				2925654, 1972707	Standard	NM_000285		Approved		uc002nur.4	P12955		ENST00000244137.7:c.167G>A	chr19.hg19:g.34003533C>T	ENSP00000244137:p.Arg56His	59.0	0.0		76.0	12.0	NM_000285	A8K3Z1|A8K416|A8K696|A8MX47|B4DDB7|B4DGJ1|E9PCE8|Q8TBN9|Q9BT75	Missense_Mutation	SNP	ENST00000244137.7	hg19	CCDS42544.1	.	.	.	.	.	.	.	.	.	.	C	18.58	3.654629	0.67472	.	.	ENSG00000124299	ENST00000244137;ENST00000397032;ENST00000436370	T;T;T	0.79554	-1.28;-1.28;-1.28	4.83	4.83	0.62350	Peptidase M24B, X-Pro dipeptidase/aminopeptidase P N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.81221	0.4777	M	0.80982	2.52	0.80722	D	1	B;P;P	0.45474	0.169;0.632;0.859	B;B;B	0.39027	0.037;0.288;0.21	D	0.83948	0.0315	10	0.44086	T	0.13	-34.6234	16.8537	0.86000	0.0:1.0:0.0:0.0	.	56;56;56	E9PCE8;A8MX47;P12955	.;.;PEPD_HUMAN	H	56	ENSP00000244137:R56H;ENSP00000380226:R56H;ENSP00000391890:R56H	ENSP00000244137:R56H	R	-	2	0	PEPD	38695373	1.000000	0.71417	1.000000	0.80357	0.809000	0.45718	5.253000	0.65452	2.403000	0.81681	0.305000	0.20034	CGC	.	.		0.652	PEPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451432.3	NM_000285		T	34003533	C	T	34003533	3	4	352	1	0	0	0	0	1	0	0	0	11737	768	27	1	1370	1	PEPD	19	34003533	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	3068023	34003533	25125450	413	49829										
LSM14A	26065	hgsc.bcm.edu	37	chr19	34685491	34685491	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tgacattaaagaccttactgTttgtgagccaccaaaaccac	6	11	0	3			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:34685491T>A	ENST00000433627.5	+	2	305	c.230T>A	c.(229-231)gTt>gAt	p.V77D	LSM14A_ENST00000540746.2_Missense_Mutation_p.V77D|LSM14A_ENST00000544216.3_Missense_Mutation_p.V77D	NM_001114093.1	NP_001107565.1	Q8ND56	LS14A_HUMAN	LSM14A, SCD6 homolog A (S. cerevisiae)	77					cytoplasmic mRNA processing body assembly (GO:0033962)|multicellular organismal development (GO:0007275)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of translation (GO:0006417)|RIG-I signaling pathway (GO:0039529)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|intracellular membrane-bounded organelle (GO:0043231)	double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(7)|skin(1)	22	Esophageal squamous(110;0.162)					GACCTTACTGTTTGTGAGCCA	0.433																																					p.V77D		Atlas-SNP	.											.	LSM14A	44	.	0			c.T230A						.						219	187	198					19																	34685491		2203	4300	6503	SO:0001583	missense	26065	exon2			TTACTGTTTGTGA	AL834398	CCDS12435.1, CCDS46040.1	19q13.12	2010-01-27	2006-12-21	2006-01-24		ENSG00000257103			24489	protein-coding gene	gene with protein product		610677	"chromosome 19 open reading frame 13", "family with sequence similarity 61, member A", "LSM14 homolog A (SCD6, S. cerevisiae)"	C19orf13, FAM61A		12477932	Standard	NM_015578		Approved	DKFZP434D1335, RAP55A, RAP55	uc002nva.4	Q8ND56		ENST00000433627.5:c.230T>A	chr19.hg19:g.34685491T>A	ENSP00000413964:p.Val77Asp	126.0	0.0		127.0	40.0	NM_001114093	B4DTG6|Q76LX7|Q96AR3|Q96K73|Q96SN5|Q9UFR3	Missense_Mutation	SNP	ENST00000433627.5	hg19	CCDS46040.1	.	.	.	.	.	.	.	.	.	.	T	32	5.162407	0.94727	.	.	ENSG00000257103	ENST00000544216;ENST00000433627;ENST00000540746	T;T;T	0.56611	0.45;0.46;0.52	5.42	5.42	0.78866	Like-Sm ribonucleoprotein (LSM)-related domain (1);	0.000000	0.85682	D	0.000000	T	0.78916	0.4359	M	0.93106	3.38	0.80722	D	1	D;D;D	0.89917	1.0;0.984;0.997	D;P;D	0.81914	0.995;0.825;0.973	D	0.84620	0.0683	10	0.87932	D	0	-16.3008	15.7539	0.78009	0.0:0.0:0.0:1.0	.	77;77;77	B4DTG6;Q8ND56;Q8ND56-2	.;LS14A_HUMAN;.	D	77	ENSP00000446271:V77D;ENSP00000413964:V77D;ENSP00000446451:V77D	ENSP00000314768:V77D	V	+	2	0	LSM14A	39377331	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.985000	0.88162	2.189000	0.69895	0.533000	0.62120	GTT	.	.		0.433	LSM14A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451576.3	NM_015578		A	34685491	T	A	34685491	3	1	352	1	0	0	0	0	1	0	0	0	9063	1725	60	4	236	4	LSM14A	19	34685491	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	681958	34685491	24443492	414	49830										
ZNF568	374900	hgsc.bcm.edu	37	chr19	37440932	37440932	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ctttcattcagatgtcaaacCttattagacaccacagaatt	4	10	3	3			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:37440932C>T	ENST00000333987.7	+	7	1383	c.877C>T	c.(877-879)Ctt>Ttt	p.L293F	ZNF568_ENST00000427117.1_Intron|ZNF568_ENST00000415168.1_Missense_Mutation_p.L229F|ZNF568_ENST00000455427.2_Intron	NM_001204835.1|NM_198539.3	NP_001191764.1|NP_940941.2	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	293					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(9)|ovary(1)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GATGTCAAACCTTATTAGACA	0.368																																					p.L293F		Atlas-SNP	.											.	ZNF568	106	.	0			c.C877T						.						38	41	40					19																	37440932		2150	4267	6417	SO:0001583	missense	374900	exon7			TCAAACCTTATTA	BX640681	CCDS42558.1, CCDS56092.1, CCDS56093.1, CCDS74351.1	19q13.12	2013-09-20			ENSG00000198453	ENSG00000198453		"Zinc fingers, C2H2-type", "-"	25392	protein-coding gene	gene with protein product							Standard	NM_198539		Approved	DKFZp686B0797	uc002ofc.3	Q3ZCX4	OTTHUMG00000048160	ENST00000333987.7:c.877C>T	chr19.hg19:g.37440932C>T	ENSP00000334685:p.Leu293Phe	99.0	0.0		94.0	29.0	NM_198539	B4DS92|E7ER33|Q6N060|Q8NA64	Missense_Mutation	SNP	ENST00000333987.7	hg19	CCDS42558.1	.	.	.	.	.	.	.	.	.	.	C	13.33	2.205184	0.39003	.	.	ENSG00000198453	ENST00000333987;ENST00000415168	T;T	0.52057	0.68;0.68	3.95	1.74	0.24563	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.33382	N	0.004973	T	0.62950	0.2470	M	0.78344	2.41	0.21256	N	0.999741	D	0.89917	1.0	D	0.91635	0.999	T	0.51498	-0.8698	10	0.56958	D	0.05	.	6.7282	0.23369	0.1751:0.7258:0.0:0.099	.	293	Q3ZCX4	ZN568_HUMAN	F	293;229	ENSP00000334685:L293F;ENSP00000394514:L229F	ENSP00000334685:L293F	L	+	1	0	ZNF568	42132772	0.000000	0.05858	0.154000	0.22540	0.996000	0.88848	-0.187000	0.09656	0.414000	0.25790	0.655000	0.94253	CTT	.	.		0.368	ZNF568-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109572.2	NM_198539		T	37440932	C	T	37440932	3	4	352	1	0	0	0	0	1	0	0	0	18014	681	24	3	895	3	ZNF568	19	37440932	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	2755441	37440932	21688051	415	49831										
ZNF585A	199704	hgsc.bcm.edu	37	chr19	37643170	37643170	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	catactgtctctctccagtgTgaattttctgatgtatattg	7	8	3	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:37643170T>C	ENST00000356958.4	-	5	1889	c.1631A>G	c.(1630-1632)cAc>cGc	p.H544R	ZNF585A_ENST00000355533.2_Intron|ZNF585A_ENST00000392157.2_Missense_Mutation_p.H489R|ZNF585A_ENST00000588723.1_Intron|ZNF585A_ENST00000292841.5_Missense_Mutation_p.H489R			Q6P3V2	Z585A_HUMAN	zinc finger protein 585A	544					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(4)|central_nervous_system(1)|endometrium(2)|large_intestine(17)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CTCTCCAGTGTGAATTTTCTG	0.408																																					p.H489R		Atlas-SNP	.											.	ZNF585A	117	.	0			c.A1466G						.						91	90	90					19																	37643170		2203	4300	6503	SO:0001583	missense	199704	exon6			CCAGTGTGAATTT	AK074345	CCDS12499.1, CCDS74353.1	19q13.13	2013-01-08				ENSG00000196967		"Zinc fingers, C2H2-type", "-"	26305	protein-coding gene	gene with protein product						12477932	Standard	NM_199126		Approved	FLJ23765	uc002ofn.1	Q6P3V2		ENST00000356958.4:c.1631A>G	chr19.hg19:g.37643170T>C	ENSP00000349440:p.His544Arg	261.0	0.0		283.0	37.0	NM_199126	Q8TE95|Q96MV3	Missense_Mutation	SNP	ENST00000356958.4	hg19		.	.	.	.	.	.	.	.	.	.	T	17.78	3.474327	0.63737	.	.	ENSG00000196967	ENST00000356958;ENST00000292841;ENST00000392157	T;T;T	0.67523	-0.27;-0.27;-0.27	3.03	3.03	0.35002	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.38548	N	0.001655	T	0.79522	0.4460	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.81495	-0.0907	9	0.87932	D	0	.	10.64	0.45588	0.0:0.0:0.0:1.0	.	544	Q6P3V2	Z585A_HUMAN	R	544;489;489	ENSP00000349440:H544R;ENSP00000292841:H489R;ENSP00000375998:H489R	ENSP00000292841:H489R	H	-	2	0	ZNF585A	42335010	1.000000	0.71417	0.982000	0.44146	0.991000	0.79684	7.315000	0.78998	1.395000	0.46643	0.529000	0.55759	CAC	.	.		0.408	ZNF585A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000457980.2	NM_152655		C	37643170	T	C	37643170	3	2	352	1	0	0	0	0	1	0	0	0	18032	1696	59	2	682	2	ZNF585A	19	37643170	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	202238	37643170	21485813	416	49832										
ZNF793	390927	hgsc.bcm.edu	37	chr19	38028487	38028487	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agaacacacacaggagagagAccctttgtctgcagtgaatg	11	9	1	4			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:38028487A>G	ENST00000587143.1	+	6	1162	c.927A>G	c.(925-927)agA>agG	p.R309R	ZNF793_ENST00000589319.1_Intron|ZNF793_ENST00000588578.1_3'UTR|ZNF793_ENST00000445217.1_Silent_p.R309R|ZNF793_ENST00000542455.1_Silent_p.R309R			Q6ZN11	ZN793_HUMAN	zinc finger protein 793	309					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(2)|lung(1)	3			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CAGGAGAGAGACCCTTTGTCT	0.458																																					p.R309R	Melanoma(44;400 1431 1499 19093)	Atlas-SNP	.											.	ZNF793	50	.	0			c.A927G						.						80	90	87					19																	38028487		2178	4287	6465	SO:0001819	synonymous_variant	390927	exon8			AGAGAGACCCTTT	AK131417	CCDS46062.1	19q13.12	2013-01-08				ENSG00000188227		"Zinc fingers, C2H2-type", "-"	33115	protein-coding gene	gene with protein product							Standard	NM_001013659		Approved		uc010efm.3	Q6ZN11		ENST00000587143.1:c.927A>G	chr19.hg19:g.38028487A>G		114.0	0.0		93.0	18.0	NM_001013659	E9PGN4|Q7Z3Q9	Silent	SNP	ENST00000587143.1	hg19	CCDS46062.1																																																																																			.	.		0.458	ZNF793-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458621.1	NM_001013659		G	38028487	A	G	38028487	2	3	352	1	0	0	0	0	0	0	0	1	18180	272	10	2		2	ZNF793	19	38028487	Silent	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	385317	38028487	21100496	417	49833										
ECH1	1891	hgsc.bcm.edu	37	chr19	39307754	39307754	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agtaccggatgtcacaggcgGtgacaaggtccacacctagg	13	11	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:39307754G>A	ENST00000221418.4	-	6	771	c.539C>T	c.(538-540)aCc>aTc	p.T180I		NM_001398.2	NP_001389.2	Q13011	ECH1_HUMAN	enoyl CoA hydratase 1, peroxisomal	180					fatty acid beta-oxidation (GO:0006635)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)	isomerase activity (GO:0016853)|receptor binding (GO:0005102)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)	6	all_cancers(60;9.36e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)			GTCACAGGCGGTGACAAGGTC	0.602																																					p.T180I		Atlas-SNP	.											.	ECH1	14	.	0			c.C539T						.						51	43	45					19																	39307754		2199	4292	6491	SO:0001583	missense	1891	exon6			CAGGCGGTGACAA	U16660	CCDS33014.1	19q13.1	2010-04-30	2010-04-30			ENSG00000104823			3149	protein-coding gene	gene with protein product		600696	"enoyl Coenzyme A hydratase 1, peroxisomal"			7558027	Standard	XM_005258610		Approved	HPXEL		Q13011		ENST00000221418.4:c.539C>T	chr19.hg19:g.39307754G>A	ENSP00000221418:p.Thr180Ile	86.0	0.0		107.0	37.0	NM_001398	A8K745|Q8WVX0|Q96EZ9	Missense_Mutation	SNP	ENST00000221418.4	hg19	CCDS33014.1	.	.	.	.	.	.	.	.	.	.	g	16.98	3.270985	0.59540	.	.	ENSG00000104823	ENST00000221418	T	0.63417	-0.04	5.45	3.28	0.37604	Enoyl-CoA hydratase/isomerase, conserved site (1);Crotonase, core (1);	0.354167	0.27700	N	0.018212	T	0.73102	0.3544	M	0.62723	1.935	0.47341	D	0.99939	D	0.76494	0.999	D	0.85130	0.997	T	0.74328	-0.3701	10	0.72032	D	0.01	.	9.2486	0.37541	0.076:0.2707:0.6533:0.0	.	180	Q13011	ECH1_HUMAN	I	180	ENSP00000221418:T180I	ENSP00000221418:T180I	T	-	2	0	ECH1	43999594	1.000000	0.71417	0.756000	0.31282	0.525000	0.34531	4.654000	0.61469	1.301000	0.44836	0.579000	0.79373	ACC	.	.		0.602	ECH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462650.1			A	39307754	G	A	39307754	3	1	352	1	0	0	0	0	1	0	0	0	4894	1261	44	3	467	3	ECH1	19	39307754	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	1279267	39307754	19821229	418	49834										
FCGBP	8857	hgsc.bcm.edu	37	chr19	40392050	40392050	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	attgctggatgggcacgcagGcttggccgttgtagaggaag	17	7	0	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:40392050G>A	ENST00000221347.6	-	17	8343	c.8336C>T	c.(8335-8337)gCc>gTc	p.A2779V		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2779	Cys-rich.|TIL 6.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GGGCACGCAGGCTTGGCCGTT	0.607																																					p.A2779V		Atlas-SNP	.											.	FCGBP	416	.	0			c.C8336T						.						40	39	40					19																	40392050		2185	4297	6482	SO:0001583	missense	8857	exon17			ACGCAGGCTTGGC	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.8336C>T	chr19.hg19:g.40392050G>A	ENSP00000221347:p.Ala2779Val	212.0	0.0		207.0	40.0	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	hg19	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	G	0.693	-0.793780	0.02862	.	.	ENSG00000090920	ENST00000221347	D	0.90844	-2.74	2.66	1.55	0.23275	Protease inhibitor I8, cysteine-rich trypsin inhibitor-like (2);	1.572440	0.04474	U	0.376608	D	0.90147	0.6921	N	0.16903	0.455	0.09310	N	1	D	0.60160	0.987	D	0.65140	0.932	T	0.80946	-0.1155	10	0.27785	T	0.31	.	10.0626	0.42284	0.0:0.3955:0.6045:0.0	.	2779	Q9Y6R7	FCGBP_HUMAN	V	2779	ENSP00000221347:A2779V	ENSP00000221347:A2779V	A	-	2	0	FCGBP	45083890	0.000000	0.05858	0.246000	0.24233	0.021000	0.10359	-1.739000	0.01840	0.421000	0.25980	0.298000	0.19748	GCC	.	.		0.607	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		A	40392050	G	A	40392050	3	1	352	1	0	0	0	0	1	0	0	0	5786	1203	42	3	7961	3	FCGBP	19	40392050	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	1084296	40392050	18736933	419	49835										
DMRTC2	63946	hgsc.bcm.edu	37	chr19	42352585	42352585	+	Frame_Shift_Del	DEL	C	C	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cagtcctgctggcaccgacaCcccccgggaaggtaaggaga							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:42352585delC	ENST00000269945.3	+	4	487	c.436delC	c.(436-438)cccfs	p.P147fs	DMRTC2_ENST00000602098.1_3'UTR|DMRTC2_ENST00000596827.1_Frame_Shift_Del_p.P147fs	NM_001040283.1	NP_001035373.1	Q8IXT2	DMRTD_HUMAN	DMRT-like family C2	147	Pro-rich.				male meiosis I (GO:0007141)|positive regulation of histone H3-K9 dimethylation (GO:1900111)|positive regulation of histone H3-K9 trimethylation (GO:1900114)|sex differentiation (GO:0007548)|spermatid nucleus elongation (GO:0007290)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|XY body (GO:0001741)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)	10						GGCACCGACACCCCCCGGGAA	0.602																																					p.T145fs		Atlas-INDEL	.											.	DMRTC2	31	.	0			c.435delA						.																																			SO:0001589	frameshift_variant	63946	exon4			.	AJ291669	CCDS33034.1	19q13.2	2008-07-16				ENSG00000142025			13911	protein-coding gene	gene with protein product		614806				11863363	Standard	NM_001040283		Approved		uc002ors.3	Q8IXT2		ENST00000269945.3:c.436delC	chr19.hg19:g.42352585delC	ENSP00000269945:p.Pro147fs	254.0	0.0		257.0	45.0	NM_001040283	Q8N6Q2|Q96M39|Q96SD4	Frame_Shift_Del	DEL	ENST00000269945.3	hg19	CCDS33034.1																																																																																			.	.		0.602	DMRTC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463045.1	NM_001040283		-	42352585	C	-	42352585	7	5	352	1	0	1	0	1	0	0	0	0	4593	507	18	0	446	0	DMRTC2	19	42352585	Frame_Shift_Del	DEL	C	TCGA-WQ-A9G7-01A-11D-A36X-10	1960535	42352585	16776398	420	49836										
ZNF227	7770	hgsc.bcm.edu	37	chr19	44740750	44740750	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	atatatgtgaggagtgtggtAaggccttcagtctcccctca	11	9	3	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:44740750A>G	ENST00000313040.7	+	6	2372	c.2167A>G	c.(2167-2169)Aag>Gag	p.K723E	ZNF227_ENST00000391961.2_Missense_Mutation_p.K672E|ZNF227_ENST00000589005.1_Missense_Mutation_p.K672E|ZNF235_ENST00000589799.1_3'UTR	NM_182490.1	NP_872296.1	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	723					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(2)|stomach(1)|urinary_tract(1)	24		Prostate(69;0.0435)				GGAGTGTGGTAAGGCCTTCAG	0.488																																					p.K723E		Atlas-SNP	.											.	ZNF227	62	.	0			c.A2167G						.						101	103	103					19																	44740750		2203	4300	6503	SO:0001583	missense	7770	exon6			TGTGGTAAGGCCT	AK092253	CCDS12636.1, CCDS74388.1	19q13.32	2013-01-08						"Zinc fingers, C2H2-type", "-"	13020	protein-coding gene	gene with protein product							Standard	XM_005259232		Approved		uc002oyu.3	Q86WZ6		ENST00000313040.7:c.2167A>G	chr19.hg19:g.44740750A>G	ENSP00000321049:p.Lys723Glu	104.0	0.0		88.0	34.0	NM_182490	B3KRU7|B7Z5P9	Missense_Mutation	SNP	ENST00000313040.7	hg19	CCDS12636.1	.	.	.	.	.	.	.	.	.	.	A	17.10	3.303774	0.60305	.	.	ENSG00000131115	ENST00000313040;ENST00000328297;ENST00000391961;ENST00000418980;ENST00000377916	T;T	0.27104	1.69;1.69	3.92	2.9	0.33743	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.50171	0.1600	M	0.86097	2.795	0.80722	D	1	P;D;D;P	0.76494	0.942;0.999;0.999;0.942	P;D;D;P	0.80764	0.542;0.991;0.994;0.542	T	0.55179	-0.8181	9	0.87932	D	0	.	8.6523	0.34042	0.9004:0.0:0.0996:0.0	.	644;702;675;723	B7Z6M2;Q658S5;Q9NS43;Q86WZ6	.;.;.;ZN227_HUMAN	E	723;680;672;702;362	ENSP00000321049:K723E;ENSP00000375823:K672E	ENSP00000321049:K723E	K	+	1	0	ZNF227	49432590	0.999000	0.42202	0.969000	0.41365	0.987000	0.75469	4.331000	0.59273	1.780000	0.52325	0.460000	0.39030	AAG	.	.		0.488	ZNF227-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460720.1	NM_182490		G	44740750	A	G	44740750	3	3	352	1	0	0	0	0	1	0	0	0	17796	363	13	2	2181	2	ZNF227	19	44740750	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	2388165	44740750	14388233	421	49837										
SYMPK	8189	hgsc.bcm.edu	37	chr19	46318890	46318890	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggagtcttcatagcatcttcTccaacaggtgcgagggtctg	12	10	5	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:46318890T>A	ENST00000245934.7	-	27	3997	c.3753A>T	c.(3751-3753)ggA>ggT	p.G1251G	RSPH6A_ENST00000597055.1_5'Flank|SYMPK_ENST00000598155.1_5'UTR|RSPH6A_ENST00000221538.3_5'Flank	NM_004819.2	NP_004810.2	Q92797	SYMPK_HUMAN	symplekin	1251					cell adhesion (GO:0007155)|mRNA polyadenylation (GO:0006378)|positive regulation of protein dephosphorylation (GO:0035307)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(25)|ovary(1)|urinary_tract(1)	45		all_neural(266;0.0299)|Ovarian(192;0.0308)		OV - Ovarian serous cystadenocarcinoma(262;0.00509)|GBM - Glioblastoma multiforme(486;0.0593)		TAGCATCTTCTCCAACAGGTG	0.682																																					p.G1251G		Atlas-SNP	.											.	SYMPK	104	.	0			c.A3753T						.						19	20	20					19																	46318890		2202	4300	6502	SO:0001819	synonymous_variant	8189	exon27			ATCTTCTCCAACA	U49240	CCDS12676.2	19q13.3	2008-02-05			ENSG00000125755	ENSG00000125755			22935	protein-coding gene	gene with protein product		602388				9330635	Standard	NM_004819		Approved	SYM, SPK	uc002pdn.3	Q92797	OTTHUMG00000150151	ENST00000245934.7:c.3753A>T	chr19.hg19:g.46318890T>A		112.0	0.0		102.0	19.0	NM_004819	O00521|O00689|O00733|Q59GT5|Q8N2U5	Silent	SNP	ENST00000245934.7	hg19	CCDS12676.2																																																																																			.	.		0.682	SYMPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316581.1	NM_004819		A	46318890	T	A	46318890	2	1	352	1	0	0	0	0	0	0	0	1	15454	1538	54	4		4	SYMPK	19	46318890	Silent	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	1578140	46318890	12810093	422	49838										
IRF2BP1	26145	hgsc.bcm.edu	37	chr19	46387532	46387532	+	Frame_Shift_Del	DEL	G	G	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cctgcacagggtacagcacaGgggggccccaggggtcgccc							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:46387532delG	ENST00000302165.3	-	1	1844	c.1501delC	c.(1501-1503)ctgfs	p.L501fs		NM_015649.1	NP_056464.1	Q8IU81	I2BP1_HUMAN	interferon regulatory factor 2 binding protein 1	501					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)			cervix(1)|kidney(1)|lung(2)	4		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00442)|GBM - Glioblastoma multiforme(486;0.0402)|Epithelial(262;0.231)		GTACAGCACAGGGGGGCCCCA	0.682																																					p.L501fs		Atlas-INDEL	.											.	IRF2BP1	23	.	0			c.1502delT						.						12	14	13					19																	46387532		2174	4257	6431	SO:0001589	frameshift_variant	26145	exon1			.	AY278022	CCDS12678.1	19q13.32	2008-02-05							21728	protein-coding gene	gene with protein product		615331				12799427	Standard	NM_015649		Approved	DKFZP434M154, IRF-2BP1	uc002pds.1	Q8IU81		ENST00000302165.3:c.1501delC	chr19.hg19:g.46387532delG	ENSP00000307265:p.Leu501fs	81.0	0.0		87.0	16.0	NM_015649	Q53EL7|Q6DC95|Q9BRZ9|Q9Y4P4	Frame_Shift_Del	DEL	ENST00000302165.3	hg19	CCDS12678.1																																																																																			.	.		0.682	IRF2BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461683.1	NM_015649		-	46387532	G	-	46387532	7	5	352	1	0	1	0	1	0	0	0	0	7838	991	35	0	257	0	IRF2BP1	19	46387532	Frame_Shift_Del	DEL	G	TCGA-WQ-A9G7-01A-11D-A36X-10	68642	46387532	12741451	423	49839										
KDELR1	10945	hgsc.bcm.edu	37	chr19	48887541	48887541	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gaggactgtctggaccaggcCtgccacaatggcgatgaggt	15	10	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:48887541C>T	ENST00000330720.2	-	4	744	c.550G>A	c.(550-552)Ggc>Agc	p.G184S	KDELR1_ENST00000597017.1_Missense_Mutation_p.G122S	NM_006801.2	NP_006792.1	P24390	ERD21_HUMAN	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 1	184					intracellular protein transport (GO:0006886)|protein retention in ER lumen (GO:0006621)|vesicle-mediated transport (GO:0016192)	cis-Golgi network (GO:0005801)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	KDEL sequence binding (GO:0005046)			NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|pancreas(1)|urinary_tract(1)	11		all_epithelial(76;2.48e-06)|all_lung(116;5.76e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Prostate(7;0.122)|Breast(70;0.203)		all cancers(93;0.000114)|OV - Ovarian serous cystadenocarcinoma(262;0.000136)|Epithelial(262;0.01)|GBM - Glioblastoma multiforme(486;0.0145)		TGGACCAGGCCTGCCACAATG	0.522																																					p.G184S		Atlas-SNP	.											.	KDELR1	26	.	0			c.G550A						.						70	60	64					19																	48887541		2203	4300	6503	SO:0001583	missense	10945	exon4			CCAGGCCTGCCAC	X55885	CCDS12718.1	19q13.3	2008-05-02				ENSG00000105438			6304	protein-coding gene	gene with protein product		131235				2172835	Standard	NM_006801		Approved	ERD2.1, ERD2, HDEL	uc002pjb.1	P24390		ENST00000330720.2:c.550G>A	chr19.hg19:g.48887541C>T	ENSP00000329471:p.Gly184Ser	143.0	0.0		117.0	19.0	NM_006801	B2R6N4|Q54A39|Q8NBW7	Missense_Mutation	SNP	ENST00000330720.2	hg19	CCDS12718.1	.	.	.	.	.	.	.	.	.	.	C	36	5.718211	0.96839	.	.	ENSG00000105438	ENST00000330720	T	0.79141	-1.24	4.68	4.68	0.58851	.	0.000000	0.64402	D	0.000009	D	0.91543	0.7329	H	0.95260	3.645	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.93894	0.7182	10	0.87932	D	0	.	16.8929	0.86092	0.0:1.0:0.0:0.0	.	184	P24390	ERD21_HUMAN	S	184	ENSP00000329471:G184S	ENSP00000329471:G184S	G	-	1	0	KDELR1	53579353	1.000000	0.71417	0.966000	0.40874	0.993000	0.82548	7.549000	0.82163	2.607000	0.88179	0.655000	0.94253	GGC	.	.		0.522	KDELR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465708.1			T	48887541	C	T	48887541	3	4	352	1	0	0	0	0	1	0	0	0	8128	681	24	3	96	3	KDELR1	19	48887541	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	2500009	48887541	10241442	424	49840										
SPACA4	171169	hgsc.bcm.edu	37	chr19	49110275	49110275	+	Frame_Shift_Del	DEL	C	C	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tgcttctggtgatggctctgCccccaggcacgacgggcgtc							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:49110275delC	ENST00000321762.1	+	1	276	c.40delC	c.(40-42)cccfs	p.P15fs	FAM83E_ENST00000263266.3_Intron	NM_133498.2	NP_598005.1	Q8TDM5	SACA4_HUMAN	sperm acrosome associated 4	15					cell adhesion (GO:0007155)	anchored component of membrane (GO:0031225)|cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)				central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)	5		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;9.98e-05)|all cancers(93;0.000112)|GBM - Glioblastoma multiforme(486;0.00615)|Epithelial(262;0.0155)		GATGGCTCTGCCCCCAGGCAC	0.652																																					p.L13fs		Atlas-INDEL	.											.	SPACA4	9	.	0			c.39delG						.						59	53	55					19																	49110275		2203	4300	6503	SO:0001589	frameshift_variant	171169	exon1			.		CCDS12725.1	19q13.33	2013-10-24			ENSG00000177202	ENSG00000177202			16441	protein-coding gene	gene with protein product		609932					Standard	NM_133498		Approved	SAMP14	uc002pjo.3	Q8TDM5	OTTHUMG00000183316	ENST00000321762.1:c.40delC	chr19.hg19:g.49110275delC	ENSP00000312774:p.Pro15fs	38.0	0.0		41.0	15.0	NM_133498		Frame_Shift_Del	DEL	ENST00000321762.1	hg19	CCDS12725.1																																																																																			.	.		0.652	SPACA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466149.1	NM_133498		-	49110275	C	-	49110275	7	5	352	1	0	1	0	1	0	0	0	0	14989	739	26	0	42	0	SPACA4	19	49110275	Frame_Shift_Del	DEL	C	TCGA-WQ-A9G7-01A-11D-A36X-10	222734	49110275	10018708	425	49841										
PNKP	11284	hgsc.bcm.edu	37	chr19	50370458	50370458	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gcccggggcctccacctcgcCcatcctgggtgccggcctgg	14	19	0	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:50370458C>A	ENST00000322344.3	-	2	113	c.4G>T	c.(4-6)Ggc>Tgc	p.G2C	PNKP_ENST00000596014.1_Missense_Mutation_p.G2C|PNKP_ENST00000595792.1_5'UTR|PNKP_ENST00000600910.1_Missense_Mutation_p.G2C|PNKP_ENST00000600573.1_Missense_Mutation_p.G2C	NM_007254.3	NP_009185.2	Q96T60	PNKP_HUMAN	polynucleotide kinase 3'-phosphatase	2					dephosphorylation (GO:0016311)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide phosphorylation (GO:0046939)|nucleotide-excision repair, DNA damage removal (GO:0000718)|polynucleotide 3' dephosphorylation (GO:0098506)|response to oxidative stress (GO:0006979)|response to radiation (GO:0009314)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|damaged DNA binding (GO:0003684)|double-stranded DNA binding (GO:0003690)|endonuclease activity (GO:0004519)|nucleotide kinase activity (GO:0019201)|polynucleotide 3'-phosphatase activity (GO:0046403)|purine nucleotide binding (GO:0017076)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|urinary_tract(1)	19		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0118)|OV - Ovarian serous cystadenocarcinoma(262;0.0134)		TCCACCTCGCCCATCCTGGGT	0.697								Other BER factors																													p.G2C		Atlas-SNP	.											.	PNKP	71	.	0			c.G4T						.						8	10	9					19																	50370458		2066	4089	6155	SO:0001583	missense	11284	exon2			CCTCGCCCATCCT	AF126486	CCDS12783.1	19q13.3-q13.4	2008-02-05				ENSG00000039650			9154	protein-coding gene	gene with protein product		605610				10446192, 10446193	Standard	NM_007254		Approved	PNK	uc002pqj.3	Q96T60		ENST00000322344.3:c.4G>T	chr19.hg19:g.50370458C>A	ENSP00000323511:p.Gly2Cys	93.0	0.0		113.0	20.0	NM_007254	Q9BUL2|Q9P1V2|Q9UKU8|Q9UNF8|Q9UNI0	Missense_Mutation	SNP	ENST00000322344.3	hg19	CCDS12783.1	.	.	.	.	.	.	.	.	.	.	C	13.05	2.122739	0.37436	.	.	ENSG00000039650	ENST00000322344	T	0.44482	0.92	5.17	2.99	0.34606	.	0.646359	0.12800	N	0.438122	T	0.21718	0.0523	N	0.08118	0	0.24408	N	0.994671	B	0.33379	0.41	B	0.31751	0.135	T	0.13656	-1.0501	10	0.66056	D	0.02	-7.3769	6.2095	0.20621	0.1903:0.713:0.0:0.0966	.	2	Q96T60	PNKP_HUMAN	C	2	ENSP00000323511:G2C	ENSP00000323511:G2C	G	-	1	0	PNKP	55062270	0.643000	0.27269	0.865000	0.33974	0.157000	0.22087	0.125000	0.15749	0.530000	0.28619	0.655000	0.94253	GGC	.	.		0.697	PNKP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465830.1	NM_007254		A	50370458	C	A	50370458	3	1	352	1	0	0	0	0	1	0	0	0	12156	623	22	3	1625	3	PNKP	19	50370458	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	1260183	50370458	8758525	426	49842										
KLK6	5653	hgsc.bcm.edu	37	chr19	51462437	51462437	+	Frame_Shift_Del	DEL	T	T	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gggtcacttggcctgaatggTtttttggatccagttcgtgt							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:51462437delT	ENST00000376851.3	-	6	1157	c.718delA	c.(718-720)accfs	p.T240fs	KLK6_ENST00000376853.4_Frame_Shift_Del_p.K111fs|KLK6_ENST00000310157.2_Frame_Shift_Del_p.T240fs|KLK6_ENST00000456750.2_Frame_Shift_Del_p.T133fs|CTB-147C22.8_ENST00000601506.1_RNA|CTB-147C22.8_ENST00000594939.1_RNA|KLK6_ENST00000391808.1_Frame_Shift_Del_p.T133fs|KLK6_ENST00000594641.1_Frame_Shift_Del_p.T240fs	NM_001012964.1	NP_001012982.1	Q92876	KLK6_HUMAN	kallikrein-related peptidase 6	240	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				amyloid precursor protein metabolic process (GO:0042982)|central nervous system development (GO:0007417)|collagen catabolic process (GO:0030574)|hormone metabolic process (GO:0042445)|myelination (GO:0042552)|neuron death (GO:0070997)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|protein autoprocessing (GO:0016540)|regulation of cell differentiation (GO:0045595)|regulation of neuron projection development (GO:0010975)|response to wounding (GO:0009611)|tissue regeneration (GO:0042246)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|skin(4)	13		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00372)|GBM - Glioblastoma multiforme(134;0.00871)		GCCTGAATGGTTTTTTGGATC	0.547																																					p.T240fs		Atlas-INDEL	.											.	KLK6	35	.	0			c.719delC						.						485	454	465					19																	51462437		2203	4300	6503	SO:0001589	frameshift_variant	5653	exon6			.	U62801	CCDS12811.1, CCDS42599.1	19q13.3	2011-09-07	2006-10-27			ENSG00000167755		"Kallikreins", "Serine peptidases / Serine peptidases"	6367	protein-coding gene	gene with protein product		602652	"protease, serine, 18", "kallikrein 6 (neurosin, zyme)"	PRSS9, PRSS18		9003450, 16800724, 16800723	Standard	NM_002774		Approved	Bssp, Klk7, neurosin	uc002pui.3	Q92876		ENST00000376851.3:c.718delA	chr19.hg19:g.51462437delT	ENSP00000366047:p.Thr240fs	155.0	0.0		145.0	30.0	NM_001012964	A6NJA1|A8MW09|Q6H301	Frame_Shift_Del	DEL	ENST00000376851.3	hg19	CCDS12811.1																																																																																			.	.		0.547	KLK6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465060.1	NM_002774		-	51462437	T	-	51462437	7	5	352	1	0	1	0	1	0	0	0	0	8417	1725	60	0	20	0	KLK6	19	51462437	Frame_Shift_Del	DEL	T	TCGA-WQ-A9G7-01A-11D-A36X-10	1091979	51462437	7666546	427	49843										
ZNF480	147657	hgsc.bcm.edu	37	chr19	52825303	52825303	+	Frame_Shift_Del	DEL	T	T	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	atgtaatgtctgtggcaaggTttttagttacaattcaaact					rs375581081		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:52825303delT	ENST00000595962.1	+	5	866	c.800delT	c.(799-801)gttfs	p.V267fs	ZNF480_ENST00000335090.6_Frame_Shift_Del_p.V190fs|CTD-2525I3.6_ENST00000594379.1_RNA|ZNF480_ENST00000334564.7_Frame_Shift_Del_p.V224fs|ZNF480_ENST00000490272.1_3'UTR	NM_144684.2	NP_653285.2	Q8WV37	ZN480_HUMAN	zinc finger protein 480	267					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	12				GBM - Glioblastoma multiforme(134;0.00212)|OV - Ovarian serous cystadenocarcinoma(262;0.00369)		TGTGGCAAGGTTTTTAGTTAC	0.363																																					p.V267fs		Atlas-INDEL	.											.	ZNF480	123	.	0			c.799delG						.						34	36	35					19																	52825303		2200	4299	6499	SO:0001589	frameshift_variant	147657	exon5			.	AY512662	CCDS12850.2, CCDS74437.1	19q13.41	2013-01-08			ENSG00000198464	ENSG00000198464		"Zinc fingers, C2H2-type", "-"	23305	protein-coding gene	gene with protein product		613910				15219843	Standard	XM_005258525		Approved	MGC32104	uc010ydl.2	Q8WV37	OTTHUMG00000157507	ENST00000595962.1:c.800delT	chr19.hg19:g.52825303delT	ENSP00000471754:p.Val267fs	114.0	0.0		114.0	11.0	NM_144684	Q5JPG9|Q6P0Q4|Q8N1M5	Frame_Shift_Del	DEL	ENST00000595962.1	hg19	CCDS12850.2																																																																																			.	.		0.363	ZNF480-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349001.3	NM_144684		-	52825303	T	-	52825303	7	5	352	1	0	1	0	1	0	0	0	0	17950	1725	60	0	814	0	ZNF480	19	52825303	Frame_Shift_Del	DEL	T	TCGA-WQ-A9G7-01A-11D-A36X-10	1362866	52825303	6303680	428	49844										
ZNF528	84436	hgsc.bcm.edu	37	chr19	52919436	52919436	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	caaatgtaataaatgtggcaCagcgtttagagagttttcag	10	5	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:52919436C>T	ENST00000360465.3	+	7	1757	c.1331C>T	c.(1330-1332)aCa>aTa	p.T444I	ZNF528_ENST00000391788.2_3'UTR	NM_032423.2	NP_115799.2	Q3MIS6	ZN528_HUMAN	zinc finger protein 528	444					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(6)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	39				GBM - Glioblastoma multiforme(134;0.00249)|OV - Ovarian serous cystadenocarcinoma(262;0.00817)		AAATGTGGCACAGCGTTTAGA	0.388																																					p.T444I		Atlas-SNP	.											.	ZNF528	95	.	0			c.C1331T						.						77	79	78					19																	52919436		2203	4300	6503	SO:0001583	missense	84436	exon7			GTGGCACAGCGTT	AB058730	CCDS33091.1	19q13	2013-01-08			ENSG00000167555	ENSG00000167555		"Zinc fingers, C2H2-type", "-"	29384	protein-coding gene	gene with protein product		615580				11347906	Standard	NM_032423		Approved	KIAA1827	uc002pzh.3	Q3MIS6	OTTHUMG00000156494	ENST00000360465.3:c.1331C>T	chr19.hg19:g.52919436C>T	ENSP00000353652:p.Thr444Ile	128.0	0.0		126.0	15.0	NM_032423	B3KPN4|Q86T88|Q96JK0	Missense_Mutation	SNP	ENST00000360465.3	hg19	CCDS33091.1	.	.	.	.	.	.	.	.	.	.	C	8.089	0.774151	0.16051	.	.	ENSG00000167555	ENST00000360465	T	0.35789	1.29	1.71	-0.766	0.11020	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.20414	0.0491	N	0.25890	0.77	0.09310	N	0.999999	P	0.45474	0.859	B	0.38880	0.284	T	0.14282	-1.0478	9	0.87932	D	0	.	4.0916	0.09972	0.6205:0.2247:0.1548:0.0	.	444	Q3MIS6	ZN528_HUMAN	I	444	ENSP00000353652:T444I	ENSP00000353652:T444I	T	+	2	0	ZNF528	57611248	0.001000	0.12720	0.040000	0.18447	0.060000	0.15804	0.609000	0.24238	-0.054000	0.13266	-0.535000	0.04281	ACA	.	.		0.388	ZNF528-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344336.1	NM_032423		T	52919436	C	T	52919436	3	4	352	1	0	0	0	0	1	0	0	0	17984	478	17	3	1345	3	ZNF528	19	52919436	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	94133	52919436	6209547	429	49845										
ZNF534	147658	hgsc.bcm.edu	37	chr19	52941014	52941014	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ctaaattgggaagcagtgcaGgaaacaagtcacttaaaaat	9	6	1	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:52941014G>A	ENST00000332323.6	+	4	401	c.340G>A	c.(340-342)Gga>Aga	p.G114R	ZNF534_ENST00000432303.2_Intron|ZNF534_ENST00000301085.4_Intron|ZNF534_ENST00000433050.1_Missense_Mutation_p.G101R	NM_001143939.1	NP_001137411.1	Q76KX8	ZN534_HUMAN	zinc finger protein 534	114					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|lung(1)|prostate(1)|skin(1)	4						AAGCAGTGCAGGAAACAAGTC	0.353																																					p.G114R		Atlas-SNP	.											.	ZNF534	105	.	0			c.G340A						.						54	46	49					19																	52941014		1568	3582	5150	SO:0001583	missense	147658	exon4			AGTGCAGGAAACA	AK058073	CCDS46165.1, CCDS46166.1	19q13.41	2013-01-08	2004-02-06	2004-02-11	ENSG00000198633	ENSG00000198633		"Zinc fingers, C2H2-type", "-"	26337	protein-coding gene	gene with protein product			"KRAB domain only 3"	KRBO3			Standard	NM_001143938		Approved	FLJ25344	uc002pzk.3	Q76KX8	OTTHUMG00000156493	ENST00000332323.6:c.340G>A	chr19.hg19:g.52941014G>A	ENSP00000327538:p.Gly114Arg	306.0	0.0		274.0	88.0	NM_001143939	Q76KX9	Missense_Mutation	SNP	ENST00000332323.6	hg19	CCDS46165.1	.	.	.	.	.	.	.	.	.	.	G	9.084	1.000152	0.19121	.	.	ENSG00000198633	ENST00000332323;ENST00000433050;ENST00000391790	T;T	0.06768	3.26;3.32	1.69	1.69	0.24217	.	.	.	.	.	T	0.09423	0.0232	L	0.58302	1.8	0.09310	N	0.999997	P;B	0.44734	0.842;0.128	B;B	0.43809	0.432;0.045	T	0.22068	-1.0227	9	0.26408	T	0.33	.	4.1353	0.10167	0.2258:0.0:0.7742:0.0	.	101;114	Q76KX8-2;Q76KX8	.;ZN534_HUMAN	R	114;101;113	ENSP00000327538:G114R;ENSP00000391358:G101R	ENSP00000327538:G114R	G	+	1	0	ZNF534	57632826	0.430000	0.25538	0.115000	0.21578	0.028000	0.11728	3.246000	0.51414	0.903000	0.36546	0.205000	0.17691	GGA	.	.		0.353	ZNF534-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460877.1	NM_182512		A	52941014	G	A	52941014	3	1	352	1	0	0	0	0	1	0	0	0	17988	1001	35	3	354	3	ZNF534	19	52941014	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	21578	52941014	6187969	430	49846										
MYADM	91663	hgsc.bcm.edu	37	chr19	54377623	54377623	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tcgagagatgtaagctgcagCcgcagccatgcctactacgt	11	12	0	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:54377623C>T	ENST00000391769.2	+	3	1120	c.840C>T	c.(838-840)agC>agT	p.S280S	MYADM_ENST00000336967.3_Silent_p.S280S|AC008440.5_ENST00000413496.2_RNA|MYADM_ENST00000391768.2_Silent_p.S280S|MYADM_ENST00000391771.1_Silent_p.S280S|MYADM_ENST00000391770.4_Silent_p.S280S	NM_001020821.1	NP_001018657.1	Q96S97	MYADM_HUMAN	myeloid-associated differentiation marker	280	MARVEL 2. {ECO:0000255|PROSITE- ProRule:PRU00581}.				establishment of endothelial barrier (GO:0061028)|membrane raft organization (GO:0031579)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of gene expression (GO:0010629)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of protein kinase C signaling (GO:0090038)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of cell migration (GO:0030335)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|protein targeting to plasma membrane (GO:0072661)	cell-cell junction (GO:0005911)|cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|ruffle (GO:0001726)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	12	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.0488)		TAAGCTGCAGCCGCAGCCATG	0.617																																					p.S280S		Atlas-SNP	.											.	MYADM	39	.	0			c.C840T						.						53	47	49					19																	54377623		2203	4300	6503	SO:0001819	synonymous_variant	91663	exon3			CTGCAGCCGCAGC	AF087882	CCDS12866.1	19q13.33-q13.4	2004-07-23			ENSG00000179820	ENSG00000179820			7544	protein-coding gene	gene with protein product		609959				10733104, 12075932	Standard	NM_001020818		Approved		uc002qcl.3	Q96S97	OTTHUMG00000060775	ENST00000391769.2:c.840C>T	chr19.hg19:g.54377623C>T		73.0	0.0		86.0	13.0	NM_138373	B2RE58|Q542Z1|Q7Z507|Q8N9R4|Q96CS6|Q96SK9	Silent	SNP	ENST00000391769.2	hg19	CCDS12866.1																																																																																			.	.		0.617	MYADM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134337.1	NM_138373		T	54377623	C	T	54377623	2	4	352	1	0	0	0	0	0	0	0	1	10015	738	26	3		3	MYADM	19	54377623	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	1436609	54377623	4751360	431	49847										
PRKCG	5582	hgsc.bcm.edu	37	chr19	54406355	54406355	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ctaccagccctatgggaagtCtgtcgattggtggtcctttg	12	10	1	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:54406355C>T	ENST00000263431.3	+	15	1886	c.1604C>T	c.(1603-1605)tCt>tTt	p.S535F	PRKCG_ENST00000542049.1_Missense_Mutation_p.S422F|PRKCG_ENST00000540413.1_Missense_Mutation_p.S535F	NM_002739.3	NP_002730.1	P05129	KPCG_HUMAN	protein kinase C, gamma	535	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cell death (GO:0008219)|chemosensory behavior (GO:0007635)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein ubiquitination (GO:0031397)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of mismatch repair (GO:0032425)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to morphine (GO:0043278)|response to pain (GO:0048265)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic membrane (GO:0097060)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(4)|ovary(2)|pancreas(2)|skin(1)	10	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)	Tamoxifen(DB00675)	TATGGGAAGTCTGTCGATTGG	0.547																																					p.S535F		Atlas-SNP	.											.	PRKCG	246	.	0			c.C1604T						.						358	323	335					19																	54406355		2203	4300	6503	SO:0001583	missense	5582	exon15			GGAAGTCTGTCGA	M13977	CCDS12867.1	19q13.4	2014-09-17			ENSG00000126583	ENSG00000126583	2.7.11.1		9402	protein-coding gene	gene with protein product	"PKC-gamma"	176980		PKCG, SCA14		8432525, 3755548	Standard	NM_002739		Approved	PKCC, MGC57564	uc002qcq.1	P05129	OTTHUMG00000064846	ENST00000263431.3:c.1604C>T	chr19.hg19:g.54406355C>T	ENSP00000263431:p.Ser535Phe	113.0	0.0		144.0	44.0	NM_002739	B7Z8Q0	Missense_Mutation	SNP	ENST00000263431.3	hg19	CCDS12867.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.667345	0.88348	.	.	ENSG00000126583	ENST00000540413;ENST00000263431;ENST00000542049	T;T;T	0.66995	-0.24;-0.24;-0.24	5.43	5.43	0.79202	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	D	0.83686	0.5308	M	0.85099	2.735	0.80722	D	1	D;D;D	0.89917	0.995;0.999;1.0	D;D;D	0.79108	0.925;0.986;0.992	D	0.85973	0.1478	9	0.87932	D	0	.	17.1095	0.86672	0.0:1.0:0.0:0.0	.	422;535;535	B7Z8Q0;F5H5C4;P05129	.;.;KPCG_HUMAN	F	535;535;422	ENSP00000443493:S535F;ENSP00000263431:S535F;ENSP00000438090:S422F	ENSP00000263431:S535F	S	+	2	0	PRKCG	59098167	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.586000	0.82596	2.719000	0.93026	0.655000	0.94253	TCT	.	.		0.547	PRKCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139233.3	NM_002739		T	54406355	C	T	54406355	3	4	352	1	0	0	0	0	1	0	0	0	12524	913	32	3	1662	3	PRKCG	19	54406355	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	28732	54406355	4722628	432	49848										
LENG8	114823	hgsc.bcm.edu	37	chr19	54965734	54965734	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	acgctgaacagtggccctcaGcctgggacagctccagccac	11	16	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:54965734G>A	ENST00000326764.5	+	6	1031	c.552G>A	c.(550-552)caG>caA	p.Q184Q	LENG8_ENST00000376514.2_Intron	NM_052925.2	NP_443157.1	Q96PV6	LENG8_HUMAN	leukocyte receptor cluster (LRC) member 8	147										breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.139)		GTGGCCCTCAGCCTGGGACAG	0.677																																					p.Q184Q		Atlas-SNP	.											LENG8,NS,carcinoma,0,1	LENG8	73	.	0			c.G552A						.						19	20	20					19																	54965734		2200	4298	6498	SO:0001819	synonymous_variant	114823	exon6			CCCTCAGCCTGGG	AF211975	CCDS12894.1	19q13.4	2008-02-05			ENSG00000167615	ENSG00000167615			15500	protein-coding gene	gene with protein product						10941842	Standard	XM_005278248		Approved	KIAA1932, MGC40108, pp13842	uc002qfw.2	Q96PV6	OTTHUMG00000065548	ENST00000326764.5:c.552G>A	chr19.hg19:g.54965734G>A		136.0	0.0		123.0	26.0	NM_052925	B0VJY9|Q8IZ27|Q8NCX6	Silent	SNP	ENST00000326764.5	hg19	CCDS12894.1																																																																																			.	.		0.677	LENG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140523.2	NM_052925		A	54965734	G	A	54965734	2	1	352	1	0	0	0	0	0	0	0	1	8733	962	34	3		3	LENG8	19	54965734	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	559379	54965734	4163249	433	49849										
C19orf51	352909	hgsc.bcm.edu	37	chr19	55676758	55676758	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cttgcagccccatcttctccGgttcctccagggctaggctg	10	16	2	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr19:55676758G>A	ENST00000524407.2	-	4	335	c.302C>T	c.(301-303)cCg>cTg	p.P101L	DNAAF3_ENST00000455045.1_Missense_Mutation_p.P47L|snoU13_ENST00000459370.1_RNA|DNAAF3_ENST00000527223.2_Missense_Mutation_p.P169L|CTD-2587H24.5_ENST00000591665.1_RNA|DNAAF3_ENST00000391720.4_Missense_Mutation_p.P148L			Q8N9W5	DAAF3_HUMAN	dynein, axonemal, assembly factor 3	101					axonemal dynein complex assembly (GO:0070286)|motile cilium assembly (GO:0044458)	cytoplasm (GO:0005737)											CATCTTCTCCGGTTCCTCCAG	0.532																																					p.P169L		Atlas-SNP	.											.	.	.	.	0			c.C506T						.						66	71	69					19																	55676758		1960	4158	6118	SO:0001583	missense	352909	exon4			TTCTCCGGTTCCT	AK097388	CCDS12918.2, CCDS58679.1, CCDS58680.1, CCDS59422.1	19q13.42	2012-10-05	2012-03-09	2012-03-09	ENSG00000167646	ENSG00000167646			30492	protein-coding gene	gene with protein product		614566	"chromosome 19 open reading frame 51", "ciliary dyskinesia, primary 2"	C19orf51, CILD2		22387996	Standard	NM_001256714		Approved	FLJ40069, FLJ36139, PF22, PCD	uc002qjl.2	Q8N9W5	OTTHUMG00000128547	ENST00000524407.2:c.302C>T	chr19.hg19:g.55676758G>A	ENSP00000432046:p.Pro101Leu	73.0	0.0		95.0	11.0	NM_001256714	A8MUY0|E3W9A1|E9PAX5|Q6P4F6|Q8N9W0|Q96AR2	Missense_Mutation	SNP	ENST00000524407.2	hg19	CCDS59422.1	.	.	.	.	.	.	.	.	.	.	G	10.38	1.334702	0.24253	.	.	ENSG00000167646	ENST00000301249;ENST00000455045;ENST00000391720	T;T	0.18657	2.2;2.2	4.64	3.6	0.41247	.	0.196427	0.42294	D	0.000736	T	0.37237	0.0996	L	0.49455	1.56	0.28535	N	0.912415	D;D;B;D	0.89917	1.0;1.0;0.163;1.0	D;D;B;D	0.87578	0.998;0.976;0.042;0.99	T	0.11941	-1.0567	10	0.37606	T	0.19	-8.062	11.8649	0.52488	0.0881:0.0:0.9119:0.0	.	169;47;122;101	E9PAX5;E3W9A1;Q8N9W5-3;Q8N9W5	.;.;.;CS051_HUMAN	L	169;47;148	ENSP00000394343:P47L;ENSP00000375600:P148L	ENSP00000301249:P169L	P	-	2	0	C19orf51	60368570	0.954000	0.32549	0.101000	0.21167	0.169000	0.22640	2.857000	0.48349	1.094000	0.41399	0.650000	0.86243	CCG	.	.		0.532	DNAAF3-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250388.5	NM_178837		A	55676758	G	A	55676758	3	1	352	1	0	0	0	0	1	0	0	0	1935	1116	39	1	1359	1	C19orf51	19	55676758	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	711024	55676758	3452225	434	49850										
C20orf96	140680	hgsc.bcm.edu	37	chr20	256674	256674	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tcccgggtctgggcttggagCtcttccacctcggcccttaa	11	15	2	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr20:256674C>T	ENST00000360321.2	-	10	1104	c.966G>A	c.(964-966)gaG>gaA	p.E322E	C20orf96_ENST00000382369.5_Silent_p.E287E	NM_080571.1|NM_153269.2	NP_542138.1|NP_695001.2	Q9NUD7	CT096_HUMAN	chromosome 20 open reading frame 96	322										endometrium(3)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	12		all_cancers(10;0.00959)|Lung NSC(37;0.227)	OV - Ovarian serous cystadenocarcinoma(29;0.149)			GGGCTTGGAGCTCTTCCACCT	0.527																																					p.E322E		Atlas-SNP	.											.	C20orf96	28	.	0			c.G966A						.						89	89	89					20																	256674		2203	4300	6503	SO:0001819	synonymous_variant	140680	exon10			TTGGAGCTCTTCC	AL034548	CCDS12994.1, CCDS74685.1	20p13	2012-10-30			ENSG00000196476	ENSG00000196476			16227	protein-coding gene	gene with protein product							Standard	NM_153269		Approved	dJ1103G7.2	uc002wde.2	Q9NUD7	OTTHUMG00000031626	ENST00000360321.2:c.966G>A	chr20.hg19:g.256674C>T		126.0	0.0		86.0	38.0	NM_153269	A3KPE0|B2RPH9|Q8N840|Q8NAX5	Silent	SNP	ENST00000360321.2	hg19	CCDS12994.1																																																																																			.	.		0.527	C20orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077439.2	NM_153269		T	256674	C	T	256674	2	4	352	1	0	0	0	0	0	0	0	1	2124	796	28	3		3	C20orf96	20	256674	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10		256674	62768846	435	49851										
CENPB	1059	hgsc.bcm.edu	37	chr20	3766272	3766272	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	caggacccggcgagactctgCagccattcgggtgtccaagg	14	13	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr20:3766272C>T	ENST00000379751.4	-	1	1065	c.859G>A	c.(859-861)Gca>Aca	p.A287T	CDC25B_ENST00000379598.5_5'Flank|CDC25B_ENST00000344256.6_5'Flank	NM_001810.5	NP_001801.1	P07199	CENPB_HUMAN	centromere protein B, 80kDa	287					regulation of transcription, DNA-templated (GO:0006355)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|nucleus (GO:0005634)	centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|satellite DNA binding (GO:0003696)|sequence-specific DNA binding (GO:0043565)			kidney(1)|large_intestine(2)|lung(4)|skin(1)	8						CGAGACTCTGCAGCCATTCGG	0.672																																					p.A287T		Atlas-SNP	.											.	CENPB	24	.	0			c.G859A						.						20	21	20					20																	3766272		2195	4299	6494	SO:0001583	missense	1059	exon1			ACTCTGCAGCCAT	X05299	CCDS13064.1	20p13	2013-11-05	2002-08-29		ENSG00000125817	ENSG00000125817			1852	protein-coding gene	gene with protein product		117140	"centromere protein B (80kD)"			8406460, 11884609	Standard	NM_001810		Approved		uc002wjk.3	P07199	OTTHUMG00000031761	ENST00000379751.4:c.859G>A	chr20.hg19:g.3766272C>T	ENSP00000369075:p.Ala287Thr	198.0	0.0		233.0	16.0	NM_001810	Q96EI4	Missense_Mutation	SNP	ENST00000379751.4	hg19	CCDS13064.1	.	.	.	.	.	.	.	.	.	.	c	12.66	2.005136	0.35415	.	.	ENSG00000125817	ENST00000379751	T	0.44482	0.92	4.24	-2.27	0.06846	.	0.574921	0.12892	U	0.430469	T	0.32734	0.0839	L	0.36672	1.1	0.23386	N	0.997789	D	0.54397	0.966	P	0.49953	0.627	T	0.33752	-0.9856	10	0.15066	T	0.55	-1.3942	7.0224	0.24922	0.5645:0.3466:0.0:0.0889	.	287	P07199	CENPB_HUMAN	T	287	ENSP00000369075:A287T	ENSP00000369075:A287T	A	-	1	0	CENPB	3714272	0.000000	0.05858	0.937000	0.37676	0.834000	0.47266	-0.928000	0.03980	-0.379000	0.07906	0.457000	0.33378	GCA	.	.		0.672	CENPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077772.2	NM_001810		T	3766272	C	T	3766272	3	4	352	1	0	0	0	0	1	0	0	0	3229	710	25	3	944	3	CENPB	20	3766272	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	3509598	3766272	59259248	436	49852										
PROKR2	128674	hgsc.bcm.edu	37	chr20	5294612	5294612	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agacgtagagggagacggtgCgcaggtagttgacggaggca	19	6	0	4			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr20:5294612C>T	ENST00000217270.3	-	1	403	c.404G>A	c.(403-405)cGc>cAc	p.R135H	PROKR2_ENST00000546004.1_Missense_Mutation_p.R135H	NM_144773.2	NP_658986.1	Q8NFJ6	PKR2_HUMAN	prokineticin receptor 2	135					circadian rhythm (GO:0007623)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(3)|lung(22)|ovary(5)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	53						GGAGACGGTGCGCAGGTAGTT	0.622										HNSCC(71;0.22)																											p.R135H		Atlas-SNP	.											PROKR2,NS,carcinoma,0,1	PROKR2	90	.	0			c.G404A						.						104	79	87					20																	5294612		2203	4300	6503	SO:0001583	missense	128674	exon1			ACGGTGCGCAGGT	AL121755	CCDS13089.1	20p12.3	2012-08-08	2006-02-15	2006-02-15	ENSG00000101292	ENSG00000101292		"GPCR / Class A : Prokineticin receptors"	15836	protein-coding gene	gene with protein product		607123	"G protein-coupled receptor 73-like 1", "Kallmann syndrome 3 (autosomal dominant)"	GPR73L1, KAL3		11886876, 17054399	Standard	NM_144773		Approved	GPR73b, PKR2, GPRg2, dJ680N4.3	uc010zqw.2	Q8NFJ6	OTTHUMG00000031800	ENST00000217270.3:c.404G>A	chr20.hg19:g.5294612C>T	ENSP00000217270:p.Arg135His	121.0	1.0		173.0	23.0	NM_144773	A5JUU1|Q2M3C0|Q5TDY1|Q9NTT0	Missense_Mutation	SNP	ENST00000217270.3	hg19	CCDS13089.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.278795	0.80692	.	.	ENSG00000101292	ENST00000546004;ENST00000217270	T;T	0.37235	1.21;1.21	5.12	5.12	0.69794	GPCR, rhodopsin-like superfamily (1);	0.112601	0.64402	D	0.000011	T	0.54727	0.1876	L	0.50919	1.6	0.54753	D	0.999985	D	0.89917	1.0	D	0.78314	0.991	T	0.54589	-0.8271	10	0.56958	D	0.05	.	16.398	0.83630	0.0:1.0:0.0:0.0	.	135	Q8NFJ6	PKR2_HUMAN	H	135	ENSP00000440790:R135H;ENSP00000217270:R135H	ENSP00000217270:R135H	R	-	2	0	PROKR2	5242612	0.994000	0.37717	0.993000	0.49108	0.989000	0.77384	3.910000	0.56371	2.525000	0.85131	0.643000	0.83706	CGC	.	.		0.622	PROKR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077854.1	NM_144773		T	5294612	C	T	5294612	3	4	352	1	0	0	0	0	1	0	0	0	12565	768	27	1	757	1	PROKR2	20	5294612	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	1528340	5294612	57730908	437	49853										
SSTR4	6754	hgsc.bcm.edu	37	chr20	23017003	23017003	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ttgatgccaccgtcaaccacGtgtcccttatccttagctat	6	14	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr20:23017003G>A	ENST00000255008.3	+	1	947	c.883G>A	c.(883-885)Gtg>Atg	p.V295M	RP4-753D10.3_ENST00000440921.1_RNA	NM_001052.2	NP_001043.2	P31391	SSR4_HUMAN	somatostatin receptor 4	295					arachidonic acid metabolic process (GO:0019369)|cell migration (GO:0016477)|cellular response to glucocorticoid stimulus (GO:0071385)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP metabolic process (GO:0030815)|negative regulation of cell proliferation (GO:0008285)|positive regulation of MAPK cascade (GO:0043410)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)	p.V295L(2)		breast(1)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)	32	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)					CGTCAACCACGTGTCCCTTAT	0.562																																					p.V295M	Esophageal Squamous(15;850 1104 16640)	Atlas-SNP	.											SSTR4,NS,carcinoma,0,2	SSTR4	83	.	2	Substitution - Missense(2)	upper_aerodigestive_tract(1)|lung(1)	c.G883A						.						205	205	205					20																	23017003		2203	4300	6503	SO:0001583	missense	6754	exon1			AACCACGTGTCCC		CCDS42856.1	20p11.21	2014-07-11			ENSG00000132671	ENSG00000132671		"GPCR / Class A : Somatostatin receptors"	11333	protein-coding gene	gene with protein product		182454				8483934	Standard	NM_001052		Approved		uc002wsr.2	P31391	OTTHUMG00000032054	ENST00000255008.3:c.883G>A	chr20.hg19:g.23017003G>A	ENSP00000255008:p.Val295Met	80.0	0.0		86.0	17.0	NM_001052	Q17RM1|Q17RM3|Q9UIY1	Missense_Mutation	SNP	ENST00000255008.3	hg19	CCDS42856.1	.	.	.	.	.	.	.	.	.	.	G	15.54	2.863182	0.51482	.	.	ENSG00000132671	ENST00000255008	T	0.40756	1.02	3.36	2.4	0.29515	GPCR, rhodopsin-like superfamily (1);	0.228496	0.21195	U	0.078570	T	0.32704	0.0838	L	0.45422	1.42	0.27023	N	0.964426	B	0.30686	0.29	B	0.32805	0.153	T	0.28808	-1.0032	10	0.72032	D	0.01	.	6.3952	0.21609	0.2355:0.0:0.7645:0.0	.	295	P31391	SSR4_HUMAN	M	295	ENSP00000255008:V295M	ENSP00000255008:V295M	V	+	1	0	SSTR4	22965003	0.212000	0.23540	0.991000	0.47740	0.975000	0.68041	1.530000	0.36007	0.608000	0.30000	0.655000	0.94253	GTG	.	.		0.562	SSTR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078308.1			A	23017003	G	A	23017003	3	1	352	1	0	0	0	0	1	0	0	0	15215	1145	40	1	885	1	SSTR4	20	23017003	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	17722391	23017003	40008517	438	49854										
CD93	22918	hgsc.bcm.edu	37	chr20	23065156	23065156	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tccccacctgcaggctcctgGgggccagaggcagctgtggc	15	15	0	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr20:23065156G>T	ENST00000246006.4	-	1	1821	c.1674C>A	c.(1672-1674)ccC>ccA	p.P558P		NM_012072.3	NP_036204.2	Q9NPY3	C1QR1_HUMAN	CD93 molecule	558					macrophage activation (GO:0042116)|phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|complement component C1q binding (GO:0001849)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(10)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	39	Colorectal(13;0.0352)|Lung NSC(19;0.0542)|all_lung(19;0.118)					CAGGCTCCTGGGGGCCAGAGG	0.627																																					p.P558P		Atlas-SNP	.											.	CD93	84	.	0			c.C1674A						.						62	66	64					20																	23065156		2203	4300	6503	SO:0001819	synonymous_variant	22918	exon1			CTCCTGGGGGCCA	U94333	CCDS13149.1	20p11.21	2009-01-29	2006-03-28	2006-02-22	ENSG00000125810	ENSG00000125810		"CD molecules"	15855	protein-coding gene	gene with protein product		120577	"matrix-remodelling associated 4", "complement component 1, q subcomponent, receptor 1", "CD93 antigen"	MXRA4, C1QR1		9047234, 10648005	Standard	NM_012072		Approved	C1qRP, C1qR(P), dJ737E23.1, CDw93, ECSM3	uc002wsv.3	Q9NPY3	OTTHUMG00000032058	ENST00000246006.4:c.1674C>A	chr20.hg19:g.23065156G>T		48.0	0.0		52.0	9.0	NM_012072	O00274	Silent	SNP	ENST00000246006.4	hg19	CCDS13149.1																																																																																			.	.		0.627	CD93-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078312.2	NM_012072		T	23065156	G	T	23065156	2	4	352	1	0	0	0	0	0	0	0	1	3049	1219	43	3		3	CD93	20	23065156	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	48153	23065156	39960364	439	49855										
GSS	2937	hgsc.bcm.edu	37	chr20	33519901	33519901	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	atgtctgggcacttggcagcAtgtgacctctccagcagtag	12	11	2	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr20:33519901A>G	ENST00000216951.2	-	10	968	c.870T>C	c.(868-870)caT>caC	p.H290H	GSS_ENST00000451957.2_Silent_p.H179H|GSS_ENST00000541098.1_Silent_p.H162H	NM_000178.2	NP_000169.1	P48637	GSHB_HUMAN	glutathione synthetase	290					aging (GO:0007568)|cellular amino acid metabolic process (GO:0006520)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|nervous system development (GO:0007399)|response to amino acid (GO:0043200)|response to cadmium ion (GO:0046686)|response to nutrient levels (GO:0031667)|response to oxidative stress (GO:0006979)|response to tumor necrosis factor (GO:0034612)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|glutathione binding (GO:0043295)|glutathione synthase activity (GO:0004363)|glycine binding (GO:0016594)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(18;0.035)		Acetylcysteine(DB06151)|Glutathione(DB00143)|Glycine(DB00145)|L-Cysteine(DB00151)	ACTTGGCAGCATGTGACCTCT	0.527																																					p.H290H		Atlas-SNP	.											.	GSS	33	.	0			c.T870C						.						98	90	93					20																	33519901		2203	4300	6503	SO:0001819	synonymous_variant	2937	exon10			GGCAGCATGTGAC		CCDS13245.1	20q11.2	1996-06-18			ENSG00000100983	ENSG00000100983	6.3.2.3		4624	protein-coding gene	gene with protein product		601002				8825653	Standard	NM_000178		Approved		uc002xbg.3	P48637	OTTHUMG00000032315	ENST00000216951.2:c.870T>C	chr20.hg19:g.33519901A>G		248.0	0.0		271.0	37.0	NM_000178	B2R697|B6F210|E1P5P9|Q4TTD9	Silent	SNP	ENST00000216951.2	hg19	CCDS13245.1																																																																																			.	.		0.527	GSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078821.2			G	33519901	A	G	33519901	2	3	352	1	0	0	0	0	0	0	0	1	6838	214	8	2		2	GSS	20	33519901	Silent	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	10454745	33519901	29505619	440	49856										
FAM65C	140876	hgsc.bcm.edu	37	chr20	49225478	49225478	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gtctccgggacagaggcgtgCgtagcccaccaagcctggaa	14	13	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr20:49225478C>T	ENST00000327979.2	-	9	1054	c.643G>A	c.(643-645)Gca>Aca	p.A215T	FAM65C_ENST00000045083.2_Missense_Mutation_p.A215T|FAM65C_ENST00000535356.1_Missense_Mutation_p.A219T			Q96MK2	FA65C_HUMAN	family with sequence similarity 65, member C	215										endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|liver(1)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CAGAGGCGTGCGTAGCCCACC	0.652																																					p.A215T		Atlas-SNP	.											.	FAM65C	87	.	0			c.G643A						.						44	34	38					20																	49225478		2198	4299	6497	SO:0001583	missense	140876	exon9			GGCGTGCGTAGCC	AL133230	CCDS13431.2	20q13.13	2011-11-24	2008-06-13	2008-06-13	ENSG00000042062	ENSG00000042062			16168	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 175", "chromosome 20 open reading frame 176"	C20orf175, C20orf176			Standard	XM_005260294		Approved	dJ530I15.2, dJ530I15.3	uc002xvm.3	Q96MK2	OTTHUMG00000032724	ENST00000327979.2:c.643G>A	chr20.hg19:g.49225478C>T	ENSP00000332663:p.Ala215Thr	98.0	0.0		91.0	18.0	NM_080829	Q5QPB6|Q9NQQ2	Missense_Mutation	SNP	ENST00000327979.2	hg19	CCDS13431.2	.	.	.	.	.	.	.	.	.	.	C	34	5.398429	0.96030	.	.	ENSG00000042062	ENST00000327979;ENST00000045083;ENST00000535356	T;T;T	0.02737	4.18;4.18;4.18	4.75	4.75	0.60458	.	0.000000	0.85682	D	0.000000	T	0.16685	0.0401	M	0.80183	2.485	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.00563	-1.1669	10	0.87932	D	0	-13.9061	16.5474	0.84450	0.0:1.0:0.0:0.0	.	219;215	F5H0X2;Q96MK2	.;FA65C_HUMAN	T	215;215;219	ENSP00000332663:A215T;ENSP00000045083:A215T;ENSP00000439802:A219T	ENSP00000045083:A215T	A	-	1	0	FAM65C	48658885	1.000000	0.71417	0.996000	0.52242	0.995000	0.86356	5.824000	0.69279	2.182000	0.69389	0.561000	0.74099	GCA	.	.		0.652	FAM65C-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257962.1			T	49225478	C	T	49225478	3	4	352	1	0	0	0	0	1	0	0	0	5609	768	27	1	2253	1	FAM65C	20	49225478	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	15705577	49225478	13800042	441	49857										
ZNF217	7764	hgsc.bcm.edu	37	chr20	52193651	52193651	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tcaaatttttggtttgcgcaCtgtcagcggttaatagtgca	10	7	2	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr20:52193651C>T	ENST00000371471.2	-	4	2077	c.1652G>A	c.(1651-1653)aGt>aAt	p.S551N	ZNF217_ENST00000302342.3_Missense_Mutation_p.S551N|RP4-724E16.2_ENST00000424252.1_RNA			O75362	ZN217_HUMAN	zinc finger protein 217	551					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			GGTTTGCGCACTGTCAGCGGT	0.418																																					p.S551N		Atlas-SNP	.											.	ZNF217	227	.	0			c.G1652A						.						138	133	135					20																	52193651		2203	4300	6503	SO:0001583	missense	7764	exon3			TGCGCACTGTCAG	AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"Zinc fingers, C2H2-type"	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.1652G>A	chr20.hg19:g.52193651C>T	ENSP00000360526:p.Ser551Asn	74.0	0.0		89.0	28.0	NM_006526	E1P5Y6|Q14DB8	Missense_Mutation	SNP	ENST00000371471.2	hg19	CCDS13443.1	.	.	.	.	.	.	.	.	.	.	C	14.89	2.668981	0.47677	.	.	ENSG00000171940	ENST00000371471;ENST00000302342	T;T	0.09350	2.99;2.99	5.69	5.69	0.88448	.	0.682298	0.15015	N	0.285313	T	0.13200	0.0320	L	0.57536	1.79	0.27702	N	0.94576	P	0.34462	0.454	B	0.32677	0.15	T	0.10154	-1.0642	10	0.31617	T	0.26	-7.7665	12.7297	0.57191	0.0:0.9246:0.0:0.0754	.	551	O75362	ZN217_HUMAN	N	551	ENSP00000360526:S551N;ENSP00000304308:S551N	ENSP00000304308:S551N	S	-	2	0	ZNF217	51627058	0.001000	0.12720	0.407000	0.26434	0.852000	0.48524	1.005000	0.29834	2.679000	0.91253	0.650000	0.86243	AGT	.	.		0.418	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526		T	52193651	C	T	52193651	3	4	352	1	0	0	0	0	1	0	0	0	17787	565	20	3	1502	3	ZNF217	20	52193651	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	2968173	52193651	10831869	442	49858										
LAMA5	3911	hgsc.bcm.edu	37	chr20	60888755	60888755	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gaagacgaagtcgtctggccGcaggttgagcagcccctctg	14	12	2	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr20:60888755G>A	ENST00000252999.3	-	63	8674	c.8608C>T	c.(8608-8610)Cgg>Tgg	p.R2870W		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2870	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			TCGTCTGGCCGCAGGTTGAGC	0.662																																					p.R2870W		Atlas-SNP	.											.	LAMA5	268	.	0			c.C8608T						.						94	76	82					20																	60888755		2203	4296	6499	SO:0001583	missense	3911	exon63			CTGGCCGCAGGTT	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"Laminins"	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.8608C>T	chr20.hg19:g.60888755G>A	ENSP00000252999:p.Arg2870Trp	41.0	0.0		70.0	7.0	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	hg19	CCDS33502.1	.	.	.	.	.	.	.	.	.	.	g	15.02	2.710200	0.48517	.	.	ENSG00000130702	ENST00000252999	T	0.78246	-1.16	4.2	0.14	0.14804	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	1.215770	0.05785	U	0.609342	T	0.69593	0.3128	L	0.29908	0.895	0.19575	N	0.999967	D	0.52996	0.957	P	0.44394	0.448	T	0.61451	-0.7060	10	0.72032	D	0.01	.	8.7331	0.34512	0.0:0.1069:0.3587:0.5344	.	2870	O15230	LAMA5_HUMAN	W	2870	ENSP00000252999:R2870W	ENSP00000252999:R2870W	R	-	1	2	LAMA5	60322150	0.000000	0.05858	0.008000	0.14137	0.662000	0.39071	0.183000	0.16919	0.186000	0.20125	0.457000	0.33378	CGG	.	.		0.662	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		A	60888755	G	A	60888755	3	1	352	1	0	0	0	0	1	0	0	0	8618	1086	38	1	2551	1	LAMA5	20	60888755	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	8695104	60888755	2136765	443	49859										
ARFGAP1	55738	hgsc.bcm.edu	37	chr20	61917759	61917760	+	Frame_Shift_Ins	INS	-	-	T													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gatggcgggacgtcaccaccINStttttttcggggaaagcaga							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr20:61917759_61917760insT	ENST00000370283.4	+	12	1016_1017	c.876_877insT	c.(877-879)tttfs	p.F293fs	ARFGAP1_ENST00000519273.2_Frame_Shift_Ins_p.F180fs|ARFGAP1_ENST00000547204.1_Frame_Shift_Ins_p.F227fs|ARFGAP1_ENST00000519604.1_Frame_Shift_Ins_p.F248fs|ARFGAP1_ENST00000370275.4_Frame_Shift_Ins_p.PF372fs|ARFGAP1_ENST00000518794.2_3'UTR|MIR4326_ENST00000582203.1_RNA|ARFGAP1_ENST00000353546.3_Frame_Shift_Ins_p.F301fs	NM_018209.2	NP_060679.1	Q8N6T3	ARFG1_HUMAN	ADP-ribosylation factor GTPase activating protein 1	293					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|COPI coating of Golgi vesicle (GO:0048205)|endoplasmic reticulum unfolded protein response (GO:0030968)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	cytosol (GO:0005829)|Golgi-associated vesicle membrane (GO:0030660)|synapse (GO:0045202)	ARF GTPase activator activity (GO:0008060)|GTPase activator activity (GO:0005096)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)|pancreas(1)	13	all_cancers(38;1.59e-09)					ACGTCACCACCTTTTTTTCGGG	0.624																																					p.T300fs		Atlas-INDEL	.											.,1	ARFGAP1	38	.	0			c.900_901insT						.																																			SO:0001589	frameshift_variant	55738	exon13			.	AK001629	CCDS13515.1, CCDS13516.1, CCDS63326.1, CCDS63327.1, CCDS63328.1	20q13.33	2009-11-30	2002-08-20	2002-08-23	ENSG00000101199	ENSG00000101199		"ADP-ribosylation factor GTPase activating proteins"	15852	protein-coding gene	gene with protein product		608377	"ADP-ribosylation factor 1 GTPase activating protein"	ARF1GAP		11210549	Standard	NM_018209		Approved	FLJ10767, bA261N11.3	uc002yel.3	Q8N6T3	OTTHUMG00000032965	ENST00000370283.4:c.883dupT	chr20.hg19:g.61917766_61917766dupT	ENSP00000359306:p.Phe293fs	105.0	0.0		113.0	24.0	NM_175609	B7Z3U0|B7Z8H8|B7ZBI3|E1P5I9|E7EV62|Q6PK71|Q96KC4|Q96T02|Q9NSU3|Q9NVF6|Q9UIL0	Frame_Shift_Ins	INS	ENST00000370283.4	hg19	CCDS13515.1																																																																																			.	.		0.624	ARFGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080134.3	NM_018209		T	61917760	-	T	61917759	7	5	352	1	0	1	1	0	0	0	0	0	849	668	24	0	952	0	ARFGAP1	20	61917759	Frame_Shift_Ins	INS	-	TCGA-WQ-A9G7-01A-11D-A36X-10	1029004	61917759	1107761	444	49860										
SRMS	6725	hgsc.bcm.edu	37	chr20	62172859	62172859	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cgtcgtccacgagcacgttcCgggcggccaagtcccggtgc	14	16	0	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr20:62172859C>T	ENST00000217188.1	-	6	1101	c.1061G>A	c.(1060-1062)cGg>cAg	p.R354Q		NM_080823.2	NP_543013.1	Q9H3Y6	SRMS_HUMAN	src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristylation sites	354	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				peptidyl-tyrosine autophosphorylation (GO:0038083)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(9)|prostate(2)|stomach(1)	19	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06)			GAGCACGTTCCGGGCGGCCAA	0.701																																					p.R354Q		Atlas-SNP	.											.	SRMS	48	.	0			c.G1061A						.						19	19	19					20																	62172859		2187	4291	6478	SO:0001583	missense	6725	exon6			ACGTTCCGGGCGG		CCDS13525.1	20q13.33	2013-02-14	2003-08-22		ENSG00000125508	ENSG00000125508		"SH2 domain containing"	11298	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 148"	C20orf148		7935409	Standard	NM_080823		Approved	SRM, dJ697K14.1	uc002yfi.1	Q9H3Y6	OTTHUMG00000032977	ENST00000217188.1:c.1061G>A	chr20.hg19:g.62172859C>T	ENSP00000217188:p.Arg354Gln	123.0	0.0		124.0	26.0	NM_080823		Missense_Mutation	SNP	ENST00000217188.1	hg19	CCDS13525.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.947896	0.73787	.	.	ENSG00000125508	ENST00000217188	D	0.87334	-2.24	4.16	4.16	0.48862	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000014	D	0.92980	0.7766	M	0.79343	2.45	0.47308	D	0.99938	D	0.76494	0.999	D	0.75020	0.985	D	0.93926	0.7210	10	0.62326	D	0.03	.	16.4298	0.83837	0.0:1.0:0.0:0.0	.	354	Q9H3Y6	SRMS_HUMAN	Q	354	ENSP00000217188:R354Q	ENSP00000217188:R354Q	R	-	2	0	SRMS	61643303	1.000000	0.71417	0.959000	0.39883	0.022000	0.10575	4.160000	0.58164	2.039000	0.60335	0.561000	0.74099	CGG	.	.		0.701	SRMS-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080148.1	NM_080823		T	62172859	C	T	62172859	3	4	352	1	0	0	0	0	1	0	0	0	15167	652	23	1	417	1	SRMS	20	62172859	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	255100	62172859	852661	445	49861										
TNFRSF6B	8771	hgsc.bcm.edu	37	chr20	62328389	62328389	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ctacctagagcgctgccgctActgcaacgtcctctgcgggg	12	15	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr20:62328389A>G	ENST00000369996.1	+	1	369	c.269A>G	c.(268-270)tAc>tGc	p.Y90C	RTEL1_ENST00000318100.4_Silent_p.L1392L|ARFRP1_ENST00000485858.1_5'Flank|RTEL1-TNFRSF6B_ENST00000482936.1_Silent_p.L1392L	NM_003823.3	NP_003814.1	O95407	TNF6B_HUMAN	tumor necrosis factor receptor superfamily, member 6b, decoy	90					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)	extracellular space (GO:0005615)	receptor activity (GO:0004872)			central_nervous_system(1)|lung(2)|skin(1)	4	all_cancers(38;4.66e-12)|all_epithelial(29;2.56e-13)|Lung NSC(23;1.06e-08)|all_lung(23;3.34e-08)		Epithelial(9;1.78e-08)|all cancers(9;7.89e-08)|OV - Ovarian serous cystadenocarcinoma(5;0.00504)			CGCTGCCGCTACTGCAACGTC	0.687																																					p.Y90C		Atlas-SNP	.											.	TNFRSF6B	22	.	0			c.A269G						.						21	23	22					20																	62328389		2186	4280	6466	SO:0001583	missense	8771	exon1			GCCGCTACTGCAA	AF104419	CCDS13532.1	20q13.33	2012-06-27						"Tumor necrosis factor receptor superfamily"	11921	protein-coding gene	gene with protein product		603361				9872321, 10318773	Standard	NM_003823		Approved	DcR3, DCR3, TR6, M68	uc002yfz.3	O95407	OTTHUMG00000143724	ENST00000369996.1:c.269A>G	chr20.hg19:g.62328389A>G	ENSP00000359013:p.Tyr90Cys	102.0	0.0		115.0	16.0	NM_003823		Missense_Mutation	SNP	ENST00000369996.1	hg19	CCDS13532.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.683001	0.88542	.	.	ENSG00000243509	ENST00000370006;ENST00000369996;ENST00000342852	D	0.91068	-2.78	4.0	4.0	0.46444	TNFR/CD27/30/40/95 cysteine-rich region (3);	.	.	.	.	D	0.94807	0.8323	M	0.81341	2.54	0.36702	D	0.880189	D	0.89917	1.0	D	0.91635	0.999	D	0.96489	0.9362	9	0.59425	D	0.04	-51.921	12.9181	0.58216	1.0:0.0:0.0:0.0	.	90	O95407	TNF6B_HUMAN	C	90	ENSP00000359013:Y90C	ENSP00000342328:Y90C	Y	+	2	0	TNFRSF6B	61798833	1.000000	0.71417	1.000000	0.80357	0.599000	0.36880	6.743000	0.74848	1.457000	0.47850	0.459000	0.35465	TAC	.	.		0.687	TNFRSF6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080182.1			G	62328389	A	G	62328389	3	3	352	1	0	0	0	0	1	0	0	0	16313	391	14	2	271	2	TNFRSF6B	20	62328389	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	155530	62328389	697131	446	49862										
C20orf135	140701	hgsc.bcm.edu	37	chr20	62493729	62493729	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cgacgaccttgtgccgctggCgctgaaggtcatgccccaca	12	15	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr20:62493729C>T	ENST00000369916.3	+	1	1164	c.836C>T	c.(835-837)gCg>gTg	p.A279V	TPD52L2_ENST00000351424.4_5'Flank|TPD52L2_ENST00000346249.4_5'Flank|C20ORF135_ENST00000601296.1_5'Flank|TPD52L2_ENST00000217121.5_5'Flank|TPD52L2_ENST00000352482.4_5'Flank|TPD52L2_ENST00000348257.5_5'Flank|TPD52L2_ENST00000369927.4_5'Flank|TPD52L2_ENST00000358548.4_5'Flank	NM_080622.3	NP_542189.1	Q9H3Z7	ABHGB_HUMAN	abhydrolase domain containing 16B	279							hydrolase activity (GO:0016787)			endometrium(2)|kidney(1)|lung(3)	6						GTGCCGCTGGCGCTGAAGGTC	0.667																																					p.A279V		Atlas-SNP	.											.	ABHD16B	22	.	0			c.C836T						.						30	22	25					20																	62493729		2201	4295	6496	SO:0001583	missense	140701	exon1			CGCTGGCGCTGAA		CCDS13539.1	20q13.33	2013-01-17	2010-12-09	2010-12-09	ENSG00000183260	ENSG00000183260		"Abhydrolase domain containing"	16128	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 135"	C20orf135			Standard	NM_080622		Approved	dJ591C20.1	uc002ygx.1	Q9H3Z7	OTTHUMG00000033010	ENST00000369916.3:c.836C>T	chr20.hg19:g.62493729C>T	ENSP00000358932:p.Ala279Val	51.0	0.0		57.0	9.0	NM_080622		Missense_Mutation	SNP	ENST00000369916.3	hg19	CCDS13539.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.093455	0.76756	.	.	ENSG00000183260	ENST00000369916	T	0.38240	1.15	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	T	0.61874	0.2382	M	0.81112	2.525	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.64786	-0.6325	10	0.45353	T	0.12	0.2397	15.4277	0.75065	0.0:1.0:0.0:0.0	.	279	Q9H3Z7	ABHGB_HUMAN	V	279	ENSP00000358932:A279V	ENSP00000358932:A279V	A	+	2	0	ABHD16B	61964173	1.000000	0.71417	0.969000	0.41365	0.848000	0.48234	5.025000	0.64097	2.235000	0.73313	0.491000	0.48974	GCG	.	.		0.667	ABHD16B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080254.1			T	62493729	C	T	62493729	3	4	352	1	0	0	0	0	1	0	0	0	2090	768	27	1	838	1	C20orf135	20	62493729	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	165340	62493729	531791	447	49863										
KRTAP13-2	337959	hgsc.bcm.edu	37	chr21	31744329	31744329	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggctggactccacataggacGtctggcagctggtgggctcc	15	12	1	0	rs202124632		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr21:31744329G>A	ENST00000399889.2	-	1	228	c.203C>T	c.(202-204)aCg>aTg	p.T68M		NM_181621.3	NP_853652.1	Q52LG2	KR132_HUMAN	keratin associated protein 13-2	68	5 X 10 AA approximate repeats.					intermediate filament (GO:0005882)				endometrium(1)|kidney(1)|lung(14)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	21						CACATAGGACGTCTGGCAGCT	0.607																																					p.T68M		Atlas-SNP	.											.	KRTAP13-2	29	.	0			c.C203T						.	G	MET/THR	0,4406		0,0,2203	56	56	56		203	-2.7	0	21		56	1,8599	1.2+/-3.3	0,1,4299	no	missense	KRTAP13-2	NM_181621.3	81	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	68/176	31744329	1,13005	2203	4300	6503	SO:0001583	missense	337959	exon1			TAGGACGTCTGGC	AP001708	CCDS13589.1	21q22.1	2011-02-10			ENSG00000182816	ENSG00000182816		"Keratin associated proteins"	18923	protein-coding gene	gene with protein product						12359730	Standard	NM_181621		Approved	KAP13-2	uc002ynz.4	Q52LG2	OTTHUMG00000057793	ENST00000399889.2:c.203C>T	chr21.hg19:g.31744329G>A	ENSP00000382777:p.Thr68Met	145.0	0.0		116.0	23.0	NM_181621		Missense_Mutation	SNP	ENST00000399889.2	hg19	CCDS13589.1	.	.	.	.	.	.	.	.	.	.	G	7.820	0.717638	0.15372	0.0	1.16E-4	ENSG00000182816	ENST00000399889	T	0.03242	4.0	4.39	-2.74	0.05932	.	0.658638	0.12375	N	0.474447	T	0.06735	0.0172	M	0.80508	2.5	0.09310	N	1	D	0.54207	0.965	P	0.47891	0.56	T	0.08597	-1.0714	10	0.45353	T	0.12	.	2.8407	0.05528	0.168:0.3592:0.3445:0.1283	.	68	Q52LG2	KR132_HUMAN	M	68	ENSP00000382777:T68M	ENSP00000382777:T68M	T	-	2	0	KRTAP13-2	30666200	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-0.125000	0.10579	-0.716000	0.04962	-0.140000	0.14226	ACG	.	G|0.999;A|0.001		0.607	KRTAP13-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128245.1			A	31744329	G	A	31744329	3	1	352	1	0	0	0	0	1	0	0	0	8532	1145	40	1	328	1	KRTAP13-2	21	31744329	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10		31744329	16385566	448	49864										
HLCS	3141	hgsc.bcm.edu	37	chr21	38128905	38128906	+	Frame_Shift_Del	DEL	TT	TT	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggccctttgtcctgaaactcTttgatcagtttctccagcac							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr21:38128905_38128906delTT	ENST00000399120.1	-	11	3176_3177	c.1946_1947delAA	c.(1945-1947)aaafs	p.K649fs	HLCS_ENST00000336648.4_Frame_Shift_Del_p.K649fs	NM_001242784.1	NP_001229713.1	P50747	BPL1_HUMAN	holocarboxylase synthetase (biotin-(proprionyl-CoA-carboxylase (ATP-hydrolysing)) ligase)	649	BPL/LPL catalytic. {ECO:0000255|PROSITE- ProRule:PRU01067}.				biotin metabolic process (GO:0006768)|cell proliferation (GO:0008283)|histone biotinylation (GO:0071110)|histone modification (GO:0016570)|protein biotinylation (GO:0009305)|response to biotin (GO:0070781)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nuclear lamina (GO:0005652)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin-[acetyl-CoA-carboxylase] ligase activity (GO:0004077)|biotin-[methylcrotonoyl-CoA-carboxylase] ligase activity (GO:0004078)|biotin-[methylmalonyl-CoA-carboxytransferase] ligase activity (GO:0004079)|biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activity (GO:0004080)|biotin-protein ligase activity (GO:0018271)|enzyme binding (GO:0019899)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(46;0.0422)			Biotin(DB00121)	CCTGAAACTCTTTGATCAGTTT	0.465																																					p.649_650del		Atlas-INDEL	.											.	HLCS	64	.	0			c.1947_1948del						.																																			SO:0001589	frameshift_variant	3141	exon11			.		CCDS13647.1	21q22.1	2012-07-13	2010-04-30		ENSG00000159267	ENSG00000159267	6.3.4.9, 6.3.4.10, 6.3.4.11, 6.3.4.15		4976	protein-coding gene	gene with protein product		609018	"holocarboxylase synthetase (biotin-[proprionyl-Coenzyme A-carboxylase (ATP-hydrolysing)] ligase)", "holocarboxylase synthetase (biotin-(proprionyl-Coenzyme A-carboxylase (ATP-hydrolysing)) ligase)"			7842009	Standard	NM_000411		Approved	HCS	uc021wjb.1	P50747	OTTHUMG00000086636	ENST00000399120.1:c.1946_1947delAA	chr21.hg19:g.38128905_38128906delTT	ENSP00000382071:p.Lys649fs	196.0	0.0		173.0	59.0	NM_000411	B2RAH1|D3DSG6|Q99451	Frame_Shift_Del	DEL	ENST00000399120.1	hg19	CCDS13647.1																																																																																			.	.		0.465	HLCS-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194687.2			-	38128906	TT	-	38128905	7	5	352	1	0	1	0	1	0	0	0	0	7222	1606	56	0	241	0	HLCS	21	38128905	Frame_Shift_Del	DEL	TT	TCGA-WQ-A9G7-01A-11D-A36X-10	6384576	38128905	10000990	449	49865										
SLC19A1	6573	hgsc.bcm.edu	37	chr21	46951806	46951806	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agtagccggccacacgctggTagcgcgcgggccgcacgaga	16	14	0	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr21:46951806T>C	ENST00000311124.4	-	3	598	c.446A>G	c.(445-447)tAc>tGc	p.Y149C	SLC19A1_ENST00000380010.4_Missense_Mutation_p.Y149C|SLC19A1_ENST00000567670.1_Missense_Mutation_p.Y149C|SLC19A1_ENST00000485649.2_Missense_Mutation_p.Y109C	NM_194255.2	NP_919231.1	P41440	S19A1_HUMAN	solute carrier family 19 (folate transporter), member 1	149					folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|methotrexate transporter activity (GO:0015350)			endometrium(4)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	10				Colorectal(79;0.0569)|READ - Rectum adenocarcinoma(84;0.172)	Methotrexate(DB00563)|Pralatrexate(DB06813)	CACACGCTGGTAGCGCGCGGG	0.662																																					p.Y149C		Atlas-SNP	.											.	SLC19A1	53	.	0			c.A446G						.						26	23	24					21																	46951806		2179	4281	6460	SO:0001583	missense	6573	exon3			CGCTGGTAGCGCG	U15939	CCDS13725.1, CCDS56217.1, CCDS56218.1	21q22.3	2013-05-22			ENSG00000173638	ENSG00000173638		"Solute carriers"	10937	protein-coding gene	gene with protein product		600424				9570943	Standard	NM_194255		Approved	FOLT	uc002zhl.2	P41440	OTTHUMG00000090397	ENST00000311124.4:c.446A>G	chr21.hg19:g.46951806T>C	ENSP00000308895:p.Tyr149Cys	67.0	0.0		48.0	5.0	NM_001205206	B2R7U8|B7Z8C3|E9PFY4|O00553|O60227|Q13026|Q9BTX8	Missense_Mutation	SNP	ENST00000311124.4	hg19	CCDS13725.1	.	.	.	.	.	.	.	.	.	.	T	14.95	2.688652	0.48097	.	.	ENSG00000173638	ENST00000311124;ENST00000380010;ENST00000485649;ENST00000427839;ENST00000443742	D;D;D;D;D	0.93488	-3.23;-3.23;-3.23;-3.23;-3.23	4.95	3.78	0.43462	Major facilitator superfamily domain, general substrate transporter (1);	0.061993	0.64402	D	0.000002	D	0.97182	0.9079	H	0.94964	3.605	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.77557	0.99;0.99;0.989;0.99	D	0.96828	0.9609	10	0.87932	D	0	-27.4956	10.3217	0.43769	0.1475:0.0:0.0:0.8525	.	109;171;149;149	B7Z8C3;D3DSM6;E9PFY4;P41440	.;.;.;S19A1_HUMAN	C	149;149;109;149;149	ENSP00000308895:Y149C;ENSP00000369347:Y149C;ENSP00000441772:Y109C;ENSP00000401850:Y149C;ENSP00000411345:Y149C	ENSP00000308895:Y149C	Y	-	2	0	SLC19A1	45776234	1.000000	0.71417	0.985000	0.45067	0.011000	0.07611	4.627000	0.61276	0.821000	0.34540	0.379000	0.24179	TAC	.	.		0.662	SLC19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206796.1			C	46951806	T	C	46951806	3	2	352	1	0	0	0	0	1	0	0	0	14443	1638	57	2	1345	2	SLC19A1	21	46951806	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	8822901	46951806	1178089	450	49866										
DIP2A	23181	hgsc.bcm.edu	37	chr21	47959885	47959885	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gtgcaagttctcctgaggcgCtgactgtcgccatccgcagg	13	13	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr21:47959885C>G	ENST00000417564.2	+	17	2038	c.2017C>G	c.(2017-2019)Ctg>Gtg	p.L673V	DIP2A_ENST00000400274.1_Missense_Mutation_p.L669V|DIP2A_ENST00000435722.3_Missense_Mutation_p.L673V|DIP2A_ENST00000457905.3_Missense_Mutation_p.L673V|DIP2A_ENST00000427143.2_Missense_Mutation_p.L609V|DIP2A_ENST00000466639.1_Missense_Mutation_p.L630V|DIP2A_ENST00000318711.7_Missense_Mutation_p.L674V			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	673					multicellular organismal development (GO:0007275)|negative regulation of gene expression (GO:0010629)|regulation of apoptotic process (GO:0042981)	cell surface (GO:0009986)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(22)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		TCCTGAGGCGCTGACTGTCGC	0.532																																					p.L673V		Atlas-SNP	.											.	DIP2A	332	.	0			c.C2017G						.						133	139	137					21																	47959885		2131	4242	6373	SO:0001583	missense	23181	exon17			GAGGCGCTGACTG	AF490768	CCDS46655.1, CCDS46656.1, CCDS46657.1, CCDS54490.1, CCDS54491.1	21q22.3	2010-08-20	2006-01-13	2006-01-13	ENSG00000160305	ENSG00000160305			17217	protein-coding gene	gene with protein product		607711	"chromosome 21 open reading frame 106"	C21orf106			Standard	NM_015151		Approved	Dip2, KIAA0184	uc002zjo.2	Q14689	OTTHUMG00000090717	ENST00000417564.2:c.2017C>G	chr21.hg19:g.47959885C>G	ENSP00000392066:p.Leu673Val	49.0	0.0		58.0	4.0	NM_206891	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Missense_Mutation	SNP	ENST00000417564.2	hg19	CCDS46655.1	.	.	.	.	.	.	.	.	.	.	C	11.16	1.558272	0.27827	.	.	ENSG00000160305	ENST00000400274;ENST00000427143;ENST00000318711;ENST00000358985;ENST00000457905;ENST00000466639;ENST00000435722;ENST00000417564	T;T;T;T;T;T;T	0.41065	1.01;1.01;1.01;1.01;1.01;1.01;1.01	4.7	3.81	0.43845	AMP-dependent synthetase/ligase (1);	0.077515	0.52532	D	0.000078	T	0.54127	0.1839	M	0.73372	2.23	0.46241	D	0.998941	B;P;D;P;P;P;B	0.58268	0.287;0.594;0.982;0.897;0.499;0.843;0.031	B;P;P;P;P;P;B	0.57244	0.314;0.493;0.768;0.816;0.648;0.628;0.05	T	0.53085	-0.8488	10	0.33940	T	0.23	-13.2254	11.3259	0.49448	0.0:0.9116:0.0:0.0884	.	674;609;630;609;673;673;673	E9PER1;E7EMA5;Q14689-3;B4E0F0;Q14689;Q14689-4;Q14689-2	.;.;.;.;DIP2A_HUMAN;.;.	V	669;609;674;630;673;630;673;673	ENSP00000383133:L669V;ENSP00000400528:L609V;ENSP00000323633:L674V;ENSP00000393434:L673V;ENSP00000430249:L630V;ENSP00000415089:L673V;ENSP00000392066:L673V	ENSP00000323633:L674V	L	+	1	2	DIP2A	46784313	0.018000	0.18449	0.023000	0.16930	0.536000	0.34869	0.307000	0.19296	2.158000	0.67659	0.655000	0.94253	CTG	.	.		0.532	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151		G	47959885	C	G	47959885	3	3	352	1	0	0	0	0	1	0	0	0	4529	796	28	4	2083	4	DIP2A	21	47959885	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	1008079	47959885	170010	451	49867										
PEX26	55670	hgsc.bcm.edu	37	chr22	18561184	18561184	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tctgcagcccccctcaggggGctcgggggacccctgcgcag	15	17	2	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr22:18561184G>A	ENST00000329627.7	+	2	248	c.42G>A	c.(40-42)ggG>ggA	p.G14G	XXbac-B476C20.9_ENST00000426483.1_RNA|XXbac-B476C20.9_ENST00000607927.1_RNA|PEX26_ENST00000428061.2_Silent_p.G14G|PEX26_ENST00000399744.3_Silent_p.G14G	NM_017929.5	NP_060399.1	Q7Z412	PEX26_HUMAN	peroxisomal biogenesis factor 26	14					protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome membrane (GO:0045046)	integral component of peroxisomal membrane (GO:0005779)|peroxisome (GO:0005777)	ATPase binding (GO:0051117)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)			breast(1)|kidney(2)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						CCCTCAGGGGGCTCGGGGGAC	0.726																																					p.G14G		Atlas-SNP	.											.	PEX26	27	.	0			c.G42A						.						4	5	5					22																	18561184		1910	3798	5708	SO:0001819	synonymous_variant	55670	exon1			CAGGGGGCTCGGG	AB089678	CCDS13750.1, CCDS56221.1	22q11.21	2008-08-26	2008-08-26		ENSG00000215193	ENSG00000215193			22965	protein-coding gene	gene with protein product		608666	"peroxisome biogenesis factor 26"			12717447, 12851857	Standard	NM_017929		Approved	FLJ20695	uc002znp.4	Q7Z412	OTTHUMG00000149970	ENST00000329627.7:c.42G>A	chr22.hg19:g.18561184G>A		57.0	0.0		83.0	32.0	NM_001127649	F6UBB5|Q7Z413|Q7Z414|Q7Z415|Q7Z416|Q96B12|Q9NWQ0|Q9NXU0	Silent	SNP	ENST00000329627.7	hg19	CCDS13750.1																																																																																			.	.		0.726	PEX26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314644.3	NM_017929		A	18561184	G	A	18561184	2	1	352	1	0	0	0	0	0	0	0	1	11755	1190	42	3		3	PEX26	22	18561184	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10		18561184	32743382	452	49868										
HIRA	7290	hgsc.bcm.edu	37	chr22	19344473	19344473	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aggagcctgtgcaatgcaaaGtagagatcggggatggcagg	17	6	0	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr22:19344473G>A	ENST00000263208.5	-	19	2592	c.2336C>T	c.(2335-2337)aCt>aTt	p.T779I	HIRA_ENST00000340170.4_Intron|HIRA_ENST00000546308.1_Missense_Mutation_p.T735I|HIRA_ENST00000541063.1_Missense_Mutation_p.T735I	NM_003325.3	NP_003316.3	P54198	HIRA_HUMAN	histone cell cycle regulator	779	Interaction with PAX3. {ECO:0000250}.|Interaction with histone H2B.|Interaction with histone H4.				anatomical structure morphogenesis (GO:0009653)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|gastrulation (GO:0007369)|muscle cell differentiation (GO:0042692)|osteoblast differentiation (GO:0001649)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(2)|prostate(1)|skin(1)	37	Colorectal(54;0.0993)					GCAATGCAAAGTAGAGATCGG	0.602																																					p.T779I		Atlas-SNP	.											.	HIRA	100	.	0			c.C2336T						.						253	194	214					22																	19344473		2203	4300	6503	SO:0001583	missense	7290	exon19			TGCAAAGTAGAGA	X75296	CCDS13759.1	22q11.2	2013-05-03	2013-05-03		ENSG00000100084	ENSG00000100084		"WD repeat domain containing"	4916	protein-coding gene	gene with protein product	"DiGeorge critical region gene 1"	600237	"HIR (histone cell cycle regulation defective) homolog A (S. cerevisiae)", "HIR histone cell cycle regulation defective homolog A (S. cerevisiae)"	TUPLE1		8111380, 7633437, 9731536	Standard	NM_003325		Approved	DGCR1, TUP1	uc002zpf.1	P54198	OTTHUMG00000150134	ENST00000263208.5:c.2336C>T	chr22.hg19:g.19344473G>A	ENSP00000263208:p.Thr779Ile	78.0	0.0		110.0	9.0	NM_003325	Q05BU9|Q8IXN2	Missense_Mutation	SNP	ENST00000263208.5	hg19	CCDS13759.1	.	.	.	.	.	.	.	.	.	.	G	15.94	2.980184	0.53827	.	.	ENSG00000100084	ENST00000263208;ENST00000541063;ENST00000539600;ENST00000546308	T;T;T	0.68624	-0.34;-0.19;-0.22	5.55	4.52	0.55395	TUP1-like enhancer of split (1);	0.115737	0.64402	D	0.000014	T	0.54532	0.1864	N	0.25647	0.755	0.80722	D	1	P;B	0.38078	0.617;0.379	B;B	0.39738	0.308;0.129	T	0.51419	-0.8708	10	0.21540	T	0.41	-14.6448	14.6662	0.68910	0.0711:0.0:0.9289:0.0	.	735;779	F5H4M2;P54198	.;HIRA_HUMAN	I	779;735;288;735	ENSP00000263208:T779I;ENSP00000446073:T735I;ENSP00000441870:T735I	ENSP00000263208:T779I	T	-	2	0	HIRA	17724473	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.378000	0.79679	2.592000	0.87571	0.655000	0.94253	ACT	.	.		0.602	HIRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316488.2	NM_003325		A	19344473	G	A	19344473	3	1	352	1	0	0	0	0	1	0	0	0	7129	1029	36	3	745	3	HIRA	22	19344473	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	783289	19344473	31960093	453	49869										
RTDR1	27156	hgsc.bcm.edu	37	chr22	23406095	23406095	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ctcacctgacattaaggagcGcacgggcggccttgctgcgg	14	13	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr22:23406095G>A	ENST00000216036.4	-	5	834	c.638C>T	c.(637-639)gCg>gTg	p.A213V		NM_014433.2	NP_055248.1	Q9UHP6	RTDR1_HUMAN		213										breast(1)|endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	18	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.175)		ATTAAGGAGCGCACGGGCGGC	0.632																																					p.A213V		Atlas-SNP	.											.	RTDR1	39	.	0			c.C638T						.						68	61	64					22																	23406095		2203	4300	6503	SO:0001583	missense	27156	exon5			AGGAGCGCACGGG																												ENST00000216036.4:c.638C>T	chr22.hg19:g.23406095G>A	ENSP00000216036:p.Ala213Val	77.0	0.0		88.0	31.0	NM_014433		Missense_Mutation	SNP	ENST00000216036.4	hg19	CCDS13803.1	.	.	.	.	.	.	.	.	.	.	G	5.511	0.279316	0.10458	.	.	ENSG00000100218	ENST00000216036	T	0.54279	0.58	4.71	1.43	0.22495	Armadillo-like helical (1);Armadillo-type fold (1);	1.325690	0.04962	N	0.462276	T	0.46521	0.1397	L	0.56769	1.78	0.09310	N	0.999997	B	0.29115	0.233	B	0.20384	0.029	T	0.22765	-1.0207	10	0.28530	T	0.3	-5.5588	6.8903	0.24226	0.3029:0.0:0.6971:0.0	.	213	Q9UHP6	RTDR1_HUMAN	V	213	ENSP00000216036:A213V	ENSP00000216036:A213V	A	-	2	0	RTDR1	21736095	0.002000	0.14202	0.000000	0.03702	0.002000	0.02628	1.081000	0.30791	0.169000	0.19679	0.555000	0.69702	GCG	.	.		0.632	RTDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319049.1			A	23406095	G	A	23406095	3	1	352	1	0	0	0	0	1	0	0	0	13734	1087	38	1	420	1	RTDR1	22	23406095	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	4061622	23406095	27898471	454	49870										
MYO18B	84700	hgsc.bcm.edu	37	chr22	26159258	26159258	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ctcctcttttctctgtcatcCcagggggcttcattaagcaa	7	13	4	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr22:26159258C>A	ENST00000407587.2	+	3	269	c.100C>A	c.(100-102)Cca>Aca	p.P34T	MYO18B_ENST00000335473.7_Missense_Mutation_p.P34T|MYO18B_ENST00000536101.1_Missense_Mutation_p.P34T			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	34						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						CTCTGTCATCCCAGGGGGCTT	0.547																																					p.P34T		Atlas-SNP	.											MYO18B,NS,carcinoma,0,1	MYO18B	322	.	0			c.C100A						.						33	35	35					22																	26159258		1876	4109	5985	SO:0001583	missense	84700	exon3			GTCATCCCAGGGG	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.100C>A	chr22.hg19:g.26159258C>A	ENSP00000386096:p.Pro34Thr	118.0	0.0		118.0	21.0	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	hg19		.	.	.	.	.	.	.	.	.	.	C	20.7	4.026083	0.75390	.	.	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.97575	-4.41;-4.41;-4.44	5.09	5.09	0.68999	.	0.000000	0.39615	N	0.001313	D	0.98090	0.9370	M	0.69823	2.125	0.36602	D	0.87471	D	0.89917	1.0	D	0.87578	0.998	D	0.99962	1.1748	10	0.87932	D	0	.	15.5718	0.76345	0.0:1.0:0.0:0.0	.	34	F5GYU7	.	T	34	ENSP00000441229:P34T;ENSP00000334563:P34T;ENSP00000386096:P34T	ENSP00000334563:P34T	P	+	1	0	MYO18B	24489258	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.291000	0.59025	2.531000	0.85337	0.467000	0.42956	CCA	.	.		0.547	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		A	26159258	C	A	26159258	3	1	352	1	0	0	0	0	1	0	0	0	10075	623	22	3	106	3	MYO18B	22	26159258	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	2753163	26159258	25145308	455	49871										
NF2	4771	hgsc.bcm.edu	37	chr22	30069387	30069387	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gcatcaaggccacagcgattCgcacggaggaggagaagcgc	15	11	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr22:30069387C>T	ENST00000338641.4	+	12	1693	c.1252C>T	c.(1252-1254)Cgc>Tgc	p.R418C	NF2_ENST00000413209.2_Intron|NF2_ENST00000403435.1_Missense_Mutation_p.R389C|NF2_ENST00000353887.4_Missense_Mutation_p.R335C|NF2_ENST00000334961.7_Missense_Mutation_p.R335C|NF2_ENST00000403999.3_Missense_Mutation_p.R418C|NF2_ENST00000347330.5_Intron|NF2_ENST00000361676.4_Missense_Mutation_p.R376C|NF2_ENST00000361452.4_Missense_Mutation_p.R377C|NF2_ENST00000361166.4_Missense_Mutation_p.R418C|NF2_ENST00000397789.3_Missense_Mutation_p.R418C	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)	418	Glu-rich.		R -> C (in vestibular schwannoma). {ECO:0000269|PubMed:8012353}.		actin cytoskeleton organization (GO:0030036)|cell-cell junction organization (GO:0045216)|ectoderm development (GO:0007398)|hippocampus development (GO:0021766)|lens fiber cell differentiation (GO:0070306)|mesoderm formation (GO:0001707)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of DNA replication (GO:0008156)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell differentiation (GO:0045597)|positive regulation of stress fiber assembly (GO:0051496)|regulation of hippo signaling (GO:0035330)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of protein localization to nucleus (GO:1900180)|regulation of protein stability (GO:0031647)|Schwann cell proliferation (GO:0014010)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|cleavage furrow (GO:0032154)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome (GO:0005769)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.?(3)|p.M375fs*20(1)		NS(1)|bone(2)|breast(5)|central_nervous_system(21)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(17)|large_intestine(9)|liver(1)|lung(9)|meninges(372)|ovary(2)|pituitary(1)|pleura(9)|prostate(1)|skin(7)|soft_tissue(303)|stomach(2)|thyroid(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	776						CACAGCGATTCGCACGGAGGA	0.612			"D, Mis, N, F, S, O"		"meningioma, acoustic neuroma, renal "	"meningioma, acoustic neuroma"			Neurofibromatosis, type 2																												p.R418C		Atlas-SNP	.	yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	NF2_ENST00000403999,NS,carcinoma,0,4	NF2	1312	.	4	Unknown(3)|Deletion - Frameshift(1)	large_intestine(1)|stomach(1)|central_nervous_system(1)|skin(1)	c.C1252T	GRCh37	CM942127	NF2	M		.						58	50	52					22																	30069387		2203	4300	6503	SO:0001583	missense	4771	exon12	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	GCGATTCGCACGG	L11353	CCDS13861.1, CCDS13862.1, CCDS13863.1, CCDS13864.1, CCDS13865.1, CCDS54516.1	22q12.2	2014-09-17	2007-12-17		ENSG00000186575	ENSG00000186575		"A-kinase anchor proteins"	7773	protein-coding gene	gene with protein product	"moesin-ezrin-radixin like", "schwannomin"	607379	"neurofibromin 2 (bilateral acoustic neuroma)"			10591208	Standard	NM_000268		Approved	merlin	uc003age.4	P35240	OTTHUMG00000030727	ENST00000338641.4:c.1252C>T	chr22.hg19:g.30069387C>T	ENSP00000344666:p.Arg418Cys	136.0	0.0		155.0	20.0	NM_000268	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Missense_Mutation	SNP	ENST00000338641.4	hg19	CCDS13861.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.097507	0.76870	.	.	ENSG00000186575	ENST00000338641;ENST00000403435;ENST00000361452;ENST00000397822;ENST00000403999;ENST00000334961;ENST00000353887;ENST00000397789;ENST00000361676;ENST00000361166	D;D;D;D;D;D;D;D;D	0.83250	-1.7;-1.7;-1.7;-1.7;-1.7;-1.7;-1.7;-1.7;-1.7	6.06	2.59	0.31030	Ezrin/radixin/moesin, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.88074	0.6339	L	0.58101	1.795	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;0.999;0.998;0.999;0.998;0.999;1.0;0.999	D;P;D;D;D;P;P;P	0.67725	0.953;0.886;0.921;0.953;0.921;0.899;0.899;0.854	D	0.87468	0.2412	9	.	.	.	.	16.1807	0.81895	0.3826:0.6174:0.0:0.0	.	393;389;377;418;418;376;335;418	B7Z4B6;P35240-8;P35240-5;P35240;P35240-2;P35240-6;P35240-4;P35240-3	.;.;.;MERL_HUMAN;.;.;.;.	C	418;389;377;393;418;335;335;418;376;418	ENSP00000344666:R418C;ENSP00000384029:R389C;ENSP00000354897:R377C;ENSP00000384797:R418C;ENSP00000335652:R335C;ENSP00000340626:R335C;ENSP00000380891:R418C;ENSP00000355183:R376C;ENSP00000354529:R418C	.	R	+	1	0	NF2	28399387	0.220000	0.23631	0.990000	0.47175	0.915000	0.54546	0.907000	0.28531	0.838000	0.34948	0.655000	0.94253	CGC	.	.		0.612	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268		T	30069387	C	T	30069387	3	4	352	1	0	0	0	0	1	0	0	0	10366	884	31	1	1298	1	NF2	22	30069387	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	3910129	30069387	21235179	456	49872										
SEC14L3	266629	hgsc.bcm.edu	37	chr22	30857443	30857443	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aaactccgaagccgatgtccGcaccatcagatgagaactgc	9	13	1	2	rs144684185		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr22:30857443G>A	ENST00000215812.4	-	11	1025	c.935C>T	c.(934-936)gCg>gTg	p.A312V	SEC14L3_ENST00000402286.1_Missense_Mutation_p.A235V|SEC14L3_ENST00000403066.1_Missense_Mutation_p.A253V|SEC14L3_ENST00000539629.1_Missense_Mutation_p.A253V|SEC14L3_ENST00000401751.1_Missense_Mutation_p.A253V|SEC14L3_ENST00000540910.1_Missense_Mutation_p.A235V|SEC14L3_ENST00000415957.2_Missense_Mutation_p.A253V	NM_174975.4	NP_777635.1	Q9UDX4	S14L3_HUMAN	SEC14-like 3 (S. cerevisiae)	312	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.					extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			NS(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(3)|pancreas(1)|skin(2)|urinary_tract(1)	19					Vitamin E(DB00163)	GCCGATGTCCGCACCATCAGA	0.607																																					p.A312V	Esophageal Squamous(108;290 1516 3584 23771 37333)	Atlas-SNP	.											.	SEC14L3	46	.	0			c.C935T						.	G	VAL/ALA	0,4406		0,0,2203	56	51	53		935	-2.5	0	22	dbSNP_134	53	1,8599	1.2+/-3.3	0,1,4299	no	missense	SEC14L3	NM_174975.4	64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	312/401	30857443	1,13005	2203	4300	6503	SO:0001583	missense	266629	exon11			ATGTCCGCACCAT	AY158086	CCDS13877.1, CCDS58800.1, CCDS58801.1	22q12.2	2013-09-23			ENSG00000100012	ENSG00000100012			18655	protein-coding gene	gene with protein product		612824					Standard	NM_174975		Approved	TAP2	uc003ahy.3	Q9UDX4	OTTHUMG00000151259	ENST00000215812.4:c.935C>T	chr22.hg19:g.30857443G>A	ENSP00000215812:p.Ala312Val	65.0	0.0		78.0	16.0	NM_174975	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Missense_Mutation	SNP	ENST00000215812.4	hg19	CCDS13877.1	.	.	.	.	.	.	.	.	.	.	G	11.05	1.526214	0.27299	0.0	1.16E-4	ENSG00000100012	ENST00000403066;ENST00000415957;ENST00000215812;ENST00000402286;ENST00000401751;ENST00000539629;ENST00000540910	T;T;T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96;0.96;0.96	5.52	-2.46	0.06461	GOLD (2);	0.286036	0.38663	N	0.001608	T	0.34337	0.0894	M	0.75447	2.3	0.23331	N	0.997895	P;P	0.42584	0.784;0.635	B;B	0.25987	0.065;0.049	T	0.41610	-0.9499	10	0.51188	T	0.08	0.0087	15.6975	0.77512	0.0:0.5808:0.3161:0.1031	.	235;312	E9PE57;Q9UDX4	.;S14L3_HUMAN	V	253;253;312;235;253;253;235	ENSP00000385941:A253V;ENSP00000401864:A253V;ENSP00000215812:A312V;ENSP00000385004:A235V;ENSP00000383896:A253V;ENSP00000444691:A253V;ENSP00000439752:A235V	ENSP00000215812:A312V	A	-	2	0	SEC14L3	29187443	0.100000	0.21855	0.000000	0.03702	0.178000	0.23041	0.888000	0.28268	-0.553000	0.06158	-0.211000	0.12701	GCG	.	G|1.000;A|0.000		0.607	SEC14L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321950.4	NM_174975		A	30857443	G	A	30857443	3	1	352	1	0	0	0	0	1	0	0	0	13998	1087	38	1	275	1	SEC14L3	22	30857443	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	788056	30857443	20447123	457	49873										
TIMP3	7078	hgsc.bcm.edu	37	chr22	33255323	33255323	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gcagctggtaccgaggatggGcccccccggataaaagcatc	13	13	0	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr22:33255323G>C	ENST00000266085.6	+	5	896	c.595G>C	c.(595-597)Gcc>Ccc	p.A199P	SYN3_ENST00000332840.5_Intron|SYN3_ENST00000358763.2_Intron	NM_000362.4	NP_000353.1	P35625	TIMP3_HUMAN	TIMP metallopeptidase inhibitor 3	199					cellular response to organic substance (GO:0071310)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|metalloendopeptidase inhibitor activity (GO:0008191)			endometrium(2)|large_intestine(3)|lung(1)|urinary_tract(1)	7						CCGAGGATGGGCCCCCCCGGA	0.607																																					p.A199P		Atlas-SNP	.											TIMP3,NS,adenoma,0,1	TIMP3	31	.	0			c.G595C						.						58	49	52					22																	33255323		2203	4300	6503	SO:0001583	missense	7078	exon5			GGATGGGCCCCCC		CCDS13911.1	22q12.3	2013-01-08	2008-07-31		ENSG00000100234	ENSG00000100234			11822	protein-coding gene	gene with protein product		188826	"tissue inhibitor of metalloproteinase 3 (Sorsby fundus dystrophy, pseudoinflammatory)"	SFD		8188246, 12652295	Standard	NM_000362		Approved		uc003anb.3	P35625	OTTHUMG00000030784	ENST00000266085.6:c.595G>C	chr22.hg19:g.33255323G>C	ENSP00000266085:p.Ala199Pro	27.0	0.0		49.0	18.0	NM_000362	B2RBY9|Q5THV4|Q9UC74|Q9UGS2	Missense_Mutation	SNP	ENST00000266085.6	hg19	CCDS13911.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.10|12.10	1.835667|1.835667	0.32421|0.32421	.|.	.|.	ENSG00000100234|ENSG00000100234	ENST00000266085;ENST00000538671|ENST00000382049	D|.	0.95137|.	-3.62|.	3.91|3.91	3.91|3.91	0.45181|0.45181	Tissue inhibitor of metalloproteinases-like, OB-fold (1);|.	0.316966|.	0.33670|.	N|.	0.004663|.	T|T	0.47930|0.47930	0.1472|0.1472	L|L	0.31120|0.31120	0.905|0.905	0.27786|0.27786	N|N	0.94299|0.94299	B|.	0.22800|.	0.075|.	B|.	0.14578|.	0.011|.	T|T	0.51474|0.51474	-0.8701|-0.8701	10|6	0.42905|0.87932	T|D	0.14|0	-14.9435|-14.9435	16.1096|16.1096	0.81250|0.81250	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	199|.	P35625|.	TIMP3_HUMAN|.	P|A	199;133|201	ENSP00000266085:A199P|.	ENSP00000266085:A199P|ENSP00000371481:G201A	A|G	+|+	1|2	0|0	TIMP3|TIMP3	31585323|31585323	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	2.715000|2.715000	0.47210|0.47210	2.019000|2.019000	0.59389|0.59389	0.561000|0.561000	0.74099|0.74099	GCC|GGC	.	.		0.607	TIMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075672.2	NM_000362		C	33255323	G	C	33255323	3	2	352	1	0	0	0	0	1	0	0	0	15934	1203	42	4	613	4	TIMP3	22	33255323	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	2397880	33255323	18049243	458	49874										
CACNG2	10369	hgsc.bcm.edu	37	chr22	36960548	36960548	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gcggccttcagggggtccctGctgagcgtgtacatggagat	16	10	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr22:36960548G>A	ENST00000300105.6	-	4	1803	c.822C>T	c.(820-822)agC>agT	p.S274S	RP5-1119A7.17_ENST00000562756.1_RNA	NM_006078.3	NP_006069.1	Q9Y698	CCG2_HUMAN	calcium channel, voltage-dependent, gamma subunit 2	274					membrane depolarization (GO:0051899)|membrane hyperpolarization (GO:0060081)|neuromuscular junction development (GO:0007528)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	18						GGGGGTCCCTGCTGAGCGTGT	0.627																																					p.S274S		Atlas-SNP	.											.	CACNG2	43	.	0			c.C822T						.						68	69	68					22																	36960548		2203	4300	6503	SO:0001819	synonymous_variant	10369	exon4			GTCCCTGCTGAGC	AF096322	CCDS13931.1	22q13.1	2006-08-01			ENSG00000166862	ENSG00000166862		"Calcium channel subunits"	1406	protein-coding gene	gene with protein product		602911					Standard	NM_006078		Approved	stargazin, MGC138502, MGC138504	uc003aps.2	Q9Y698	OTTHUMG00000030612	ENST00000300105.6:c.822C>T	chr22.hg19:g.36960548G>A		119.0	0.0		143.0	22.0	NM_006078	Q2M1M1|Q5TGT3|Q9UGZ7	Silent	SNP	ENST00000300105.6	hg19	CCDS13931.1																																																																																			.	.		0.627	CACNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075500.2			A	36960548	G	A	36960548	2	1	352	1	0	0	0	0	0	0	0	1	2559	1310	46	3		3	CACNG2	22	36960548	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	3705225	36960548	14344018	459	49875										
CARD10	29775	hgsc.bcm.edu	37	chr22	37904630	37904630	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tcctgcgcctcccgccagtcAtgctctaggatgtccagcag	10	16	2	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr22:37904630A>G	ENST00000403299.1	-	6	1185	c.969T>C	c.(967-969)caT>caC	p.H323H	CARD10_ENST00000406271.3_Silent_p.H37H|CARD10_ENST00000251973.5_Silent_p.H323H|CARD10_ENST00000494166.1_5'UTR			Q9BWT7	CAR10_HUMAN	caspase recruitment domain family, member 10	323					activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein complex assembly (GO:0006461)|regulation of apoptotic process (GO:0042981)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)	receptor signaling complex scaffold activity (GO:0030159)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	Melanoma(58;0.0574)					CCCGCCAGTCATGCTCTAGGA	0.711																																					p.H323H		Atlas-SNP	.											.	CARD10	55	.	0			c.T969C						.						11	12	12					22																	37904630		2193	4289	6482	SO:0001819	synonymous_variant	29775	exon5			CCAGTCATGCTCT	AF086324	CCDS13948.1	22q13.1	2008-05-22			ENSG00000100065	ENSG00000100065			16422	protein-coding gene	gene with protein product		607209				11259443, 11356195	Standard	NM_014550		Approved	CARMA3, BIMP1	uc003asu.1	Q9BWT7	OTTHUMG00000150592	ENST00000403299.1:c.969T>C	chr22.hg19:g.37904630A>G		46.0	0.0		61.0	21.0	NM_014550	Q14CQ8|Q5TFG6|Q8NC81|Q9UGR5|Q9UGR6|Q9Y3H0	Silent	SNP	ENST00000403299.1	hg19	CCDS13948.1																																																																																			.	.		0.711	CARD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318997.1	NM_014550		G	37904630	A	G	37904630	2	3	352	1	0	0	0	0	0	0	0	1	2646	214	8	2		2	CARD10	22	37904630	Silent	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	944082	37904630	13399936	460	49876										
CDC42EP1	11135	hgsc.bcm.edu	37	chr22	37962638	37962639	+	Frame_Shift_Ins	INS	-	-	C													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tggtgcggagggtgggggcgINScccccccggaggatggcatc					rs150186371		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr22:37962638_37962639insC	ENST00000249014.4	+	2	702_703	c.282_283insC	c.(283-285)cccfs	p.P95fs		NM_152243.2	NP_689449.1	Q00587	BORG5_HUMAN	CDC42 effector protein (Rho GTPase binding) 1	95					positive regulation of pseudopodium assembly (GO:0031274)|regulation of cell shape (GO:0008360)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(4)|prostate(5)	15	Melanoma(58;0.0574)					GGGTGGGGGCGCCCCCCCGGAG	0.693																																					p.A94fs		Atlas-INDEL	.											.,1	CDC42EP1	53	.	0			c.282_283insC						.			16,4230		0,16,2107						-9.9	0			29	14,8214		0,14,4100	no	frameshift	CDC42EP1	NM_152243.2		0,30,6207	A1A1,A1R,RR		0.1702,0.3768,0.2405				30,12444				SO:0001589	frameshift_variant	11135	exon2			.	M88338	CCDS13949.1	22q13.1	2008-06-11			ENSG00000128283	ENSG00000128283			17014	protein-coding gene	gene with protein product	"55 kDa bone marrow stromal/endothelial cell protein", "serum constituent protein"	606084				1629197, 10430899	Standard	NM_152243		Approved	MSE55, CEP1, Borg5	uc003asz.4	Q00587	OTTHUMG00000150591	ENST00000249014.4:c.289dupC	chr22.hg19:g.37962645_37962645dupC	ENSP00000249014:p.Pro95fs	194.0	0.0		166.0	42.0	NM_152243	A8K825|Q96GN1	Frame_Shift_Ins	INS	ENST00000249014.4	hg19	CCDS13949.1																																																																																			.	.		0.693	CDC42EP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318993.1	NM_152243		C	37962639	-	C	37962638	7	5	352	1	0	1	1	0	0	0	0	0	3077	1074	38	0	284	0	CDC42EP1	22	37962638	Frame_Shift_Ins	INS	-	TCGA-WQ-A9G7-01A-11D-A36X-10	58008	37962638	13341928	461	49877										
CDC42EP1	11135	hgsc.bcm.edu	37	chr22	37964226	37964226	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cgggcttcgccgctctgactCtctcttgtccttccgcctgg	10	17	3	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr22:37964226C>T	ENST00000249014.4	+	3	995	c.575C>T	c.(574-576)tCt>tTt	p.S192F		NM_152243.2	NP_689449.1	Q00587	BORG5_HUMAN	CDC42 effector protein (Rho GTPase binding) 1	192					positive regulation of pseudopodium assembly (GO:0031274)|regulation of cell shape (GO:0008360)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(4)|prostate(5)	15	Melanoma(58;0.0574)					CGCTCTGACTCTCTCTTGTCC	0.652																																					p.S192F		Atlas-SNP	.											.	CDC42EP1	53	.	0			c.C575T						.						69	75	73					22																	37964226		2203	4300	6503	SO:0001583	missense	11135	exon3			CTGACTCTCTCTT	M88338	CCDS13949.1	22q13.1	2008-06-11			ENSG00000128283	ENSG00000128283			17014	protein-coding gene	gene with protein product	"55 kDa bone marrow stromal/endothelial cell protein", "serum constituent protein"	606084				1629197, 10430899	Standard	NM_152243		Approved	MSE55, CEP1, Borg5	uc003asz.4	Q00587	OTTHUMG00000150591	ENST00000249014.4:c.575C>T	chr22.hg19:g.37964226C>T	ENSP00000249014:p.Ser192Phe	67.0	0.0		70.0	19.0	NM_152243	A8K825|Q96GN1	Missense_Mutation	SNP	ENST00000249014.4	hg19	CCDS13949.1	.	.	.	.	.	.	.	.	.	.	C	15.62	2.887172	0.52014	.	.	ENSG00000128283	ENST00000249014	T	0.61627	0.09	5.15	5.15	0.70609	.	0.000000	0.64402	D	0.000001	T	0.76601	0.4010	M	0.79123	2.44	0.53005	D	0.999963	D	0.89917	1.0	D	0.76071	0.987	T	0.80072	-0.1535	10	0.87932	D	0	-22.987	16.4323	0.83853	0.0:1.0:0.0:0.0	.	192	Q00587	BORG5_HUMAN	F	192	ENSP00000249014:S192F	ENSP00000249014:S192F	S	+	2	0	CDC42EP1	36294172	1.000000	0.71417	1.000000	0.80357	0.437000	0.31866	6.374000	0.73132	2.397000	0.81536	0.491000	0.48974	TCT	.	.		0.652	CDC42EP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318993.1	NM_152243		T	37964226	C	T	37964226	3	4	352	1	0	0	0	0	1	0	0	0	3077	913	32	3	581	3	CDC42EP1	22	37964226	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	1588	37964226	13340340	462	49878										
TRIOBP	11078	hgsc.bcm.edu	37	chr22	38121789	38121789	+	Frame_Shift_Del	DEL	C	C	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	atgccccccgggcgtcctcgCccccccgccacacccaattt							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr22:38121789delC	ENST00000406386.3	+	7	3481	c.3226delC	c.(3226-3228)cccfs	p.P1077fs		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	1077					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					GGCGTCCTCGCCCCCCCGCCA	0.652																																					p.S1075fs		Atlas-INDEL	.											TRIOBP_ENST00000344404,NS,carcinoma,0,3	TRIOBP	262	.	0			c.3225delG						.						43	47	46					22																	38121789		1882	4079	5961	SO:0001589	frameshift_variant	11078	exon7			.	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"Pleckstrin homology (PH) domain containing"	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.3226delC	chr22.hg19:g.38121789delC	ENSP00000384312:p.Pro1077fs	95.0	0.0		87.0	14.0	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Frame_Shift_Del	DEL	ENST00000406386.3	hg19	CCDS43015.1																																																																																			.	.		0.652	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2			-	38121789	C	-	38121789	7	5	352	1	0	1	0	1	0	0	0	0	16568	739	26	0	3244	0	TRIOBP	22	38121789	Frame_Shift_Del	DEL	C	TCGA-WQ-A9G7-01A-11D-A36X-10	157563	38121789	13182777	463	49879										
APOBEC3G	60489	hgsc.bcm.edu	37	chr22	39482298	39482298	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ttctaggctccacataaacaCggtttccttgaaggccgcca	8	13	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr22:39482298C>T	ENST00000407997.3	+	6	1107	c.750C>T	c.(748-750)caC>caT	p.H250H	APOBEC3G_ENST00000452957.2_Silent_p.H250H	NM_021822.3	NP_068594.1	Q9HC16	ABC3G_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3G	250	Necessary for homooligomerization.				base conversion or substitution editing (GO:0016553)|cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)|negative regulation of viral genome replication (GO:0045071)|negative regulation of viral process (GO:0048525)|positive regulation of defense response to virus by host (GO:0002230)|viral process (GO:0016032)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|ribonucleoprotein complex (GO:0030529)	cytidine deaminase activity (GO:0004126)|deoxycytidine deaminase activity (GO:0047844)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			central_nervous_system(1)|large_intestine(4)|lung(5)|skin(1)|stomach(1)	12	Melanoma(58;0.04)					CACATAAACACGGTTTCCTTG	0.483																																					p.H250H		Atlas-SNP	.											.	APOBEC3G	69	.	0			c.C750T						.						69	72	71					22																	39482298		2203	4300	6503	SO:0001819	synonymous_variant	60489	exon6			TAAACACGGTTTC	AF182420	CCDS13984.1	22q13.1-q13.2	2008-05-15			ENSG00000239713	ENSG00000239713		"Apolipoprotein B mRNA editing enzymes"	17357	protein-coding gene	gene with protein product		607113				11863358	Standard	NM_021822		Approved	CEM15, MDS019, dJ494G10.1, FLJ12740, bK150C2.7		Q9HC16	OTTHUMG00000151081	ENST00000407997.3:c.750C>T	chr22.hg19:g.39482298C>T		126.0	0.0		131.0	22.0	NM_021822	B2RDR9|Q45F02|Q5TF77|Q7Z2N1|Q7Z2N4|Q9H9H8	Silent	SNP	ENST00000407997.3	hg19	CCDS13984.1																																																																																			.	.		0.483	APOBEC3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321219.1	NM_021822		T	39482298	C	T	39482298	2	4	352	1	0	0	0	0	0	0	0	1	794	535	19	1		1	APOBEC3G	22	39482298	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	1360509	39482298	11822268	464	49880										
EFCAB6	64800	hgsc.bcm.edu	37	chr22	44168976	44168976	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gacagtgttggatttgcaacAgctgtggctataaaagagat	12	5	0	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr22:44168976A>G	ENST00000262726.7	-	4	400	c.147T>C	c.(145-147)gcT>gcC	p.A49A	EFCAB6_ENST00000396231.2_Intron|EFCAB6_ENST00000358439.4_Intron|EFCAB6_ENST00000356087.4_Intron	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	49					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				GATTTGCAACAGCTGTGGCTA	0.373																																					p.A49A		Atlas-SNP	.											.	EFCAB6	177	.	0			c.T147C						.						53	54	53					22																	44168976		2203	4300	6503	SO:0001819	synonymous_variant	64800	exon4			TGCAACAGCTGTG	Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"EF-hand domain containing"	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.147T>C	chr22.hg19:g.44168976A>G		99.0	0.0		113.0	14.0	NM_022785	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Silent	SNP	ENST00000262726.7	hg19	CCDS14049.1																																																																																			.	.		0.373	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785		G	44168976	A	G	44168976	2	3	352	1	0	0	0	0	0	0	0	1	4941	175	7	2		2	EFCAB6	22	44168976	Silent	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	4686678	44168976	7135590	465	49881										
SAPS2	9701	hgsc.bcm.edu	37	chr22	50879410	50879410	+	Frame_Shift_Del	DEL	C	C	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	caggggtcccggccgggaggCccccccgctgcccacagtgg							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chr22:50879410delC	ENST00000216061.5	+	23	2925	c.2555delC	c.(2554-2556)gccfs	p.A852fs	PPP6R2_ENST00000359139.3_Frame_Shift_Del_p.A819fs|PPP6R2_ENST00000395741.3_Frame_Shift_Del_p.A819fs|PPP6R2_ENST00000395744.3_Frame_Shift_Del_p.A818fs			O75170	PP6R2_HUMAN	protein phosphatase 6, regulatory subunit 2	852						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	22						GGCCGGGAGGCCCCCCCGCTG	0.721																																					p.A845fs		Atlas-INDEL	.											.	PPP6R2	71	.	0			c.2533delG						.						16	19	18					22																	50879410		2198	4294	6492	SO:0001589	frameshift_variant	9701	exon22			.	AB014585	CCDS33681.1, CCDS56235.1, CCDS56236.1, CCDS74881.1	22q13.33	2012-04-17	2010-06-28	2010-06-28	ENSG00000100239	ENSG00000100239		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"	19253	protein-coding gene	gene with protein product		610877	"KIAA0685", "SAPS domain family, member 2"	KIAA0685, SAPS2		16769727	Standard	NM_014678		Approved	dJ579N16.1, SAP190	uc003blc.3	O75170	OTTHUMG00000150199	ENST00000216061.5:c.2555delC	chr22.hg19:g.50879410delC	ENSP00000216061:p.Ala852fs	84.0	0.0		87.0	18.0	NM_001242898	A6PVG3|B7Z7T3|Q5U5P3|Q7Z2L2|Q7Z5G5|Q7Z731|Q9UGB9	Frame_Shift_Del	DEL	ENST00000216061.5	hg19																																																																																				.	.		0.721	PPP6R2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316809.1	NM_014678		-	50879410	C	-	50879410	7	5	352	1	0	1	0	1	0	0	0	0	13852	739	26	0	2527	0	SAPS2	22	50879410	Frame_Shift_Del	DEL	C	TCGA-WQ-A9G7-01A-11D-A36X-10	6710434	50879410	425156	466	49882										
IL3RA	3563	hgsc.bcm.edu	37	chrX	1484120	1484120	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agagtgtatgaattcttgagCgcctggagcaccccccagcg	12	12	1	3			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chrX:1484120C>T	ENST00000331035.4	+	9	1198	c.849C>T	c.(847-849)agC>agT	p.S283S	IL3RA_ENST00000381469.2_Silent_p.S205S	NM_001267713.1|NM_002183.3	NP_001254642.1|NP_002174.1	P26951	IL3RA_HUMAN	interleukin 3 receptor, alpha (low affinity)	283					cellular response to interleukin-3 (GO:0036016)|interleukin-3-mediated signaling pathway (GO:0038156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-3 receptor activity (GO:0004912)			lung(1)|skin(2)	3		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Sargramostim(DB00020)	AATTCTTGAGCGCCTGGAGCA	0.627																																					p.S283S		Atlas-SNP	.											.	IL3RA	49	.	0			c.C849T						.						62	72	68					X																	1484120		2199	4288	6487	SO:0001819	synonymous_variant	3563	exon9			CTTGAGCGCCTGG	M74782	CCDS14113.1, CCDS59158.1	Xp22.3 and Yp13.3	2008-07-21			ENSG00000185291	ENSG00000185291		"Pseudoautosomal regions / PAR1", "Interleukins and interleukin receptors", "CD molecules"	6012	protein-coding gene	gene with protein product		308385, 430000				1833064	Standard	NM_002183		Approved	CD123	uc004cps.3	P26951	OTTHUMG00000021059	ENST00000331035.4:c.849C>T	chrX.hg19:g.1484120C>T		260.0	0.0		292.0	16.0	NM_002183	A8K3F3|B9VI81|Q5HYQ7|Q5HYQ8|Q9UEH7	Silent	SNP	ENST00000331035.4	hg19	CCDS14113.1																																																																																			.	.		0.627	IL3RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055600.3			T	1484120	C	T	1484120	2	4	352	1	0	0	0	0	0	0	0	1	7704	767	27	1		1	IL3RA	23	1484120	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10		1484120	153786440	467	49883										
SFRS17A	8227	hgsc.bcm.edu	37	chrX	1712781	1712781	+	Frame_Shift_Del	DEL	G	G	-													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gacatgaacgagaccctgccGggggagcggccggacaccat							TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chrX:1712781delG	ENST00000313871.3	+	2	622	c.426delG	c.(424-426)ccgfs	p.P142fs	AKAP17A_ENST00000381261.3_Frame_Shift_Del_p.P142fs	NM_005088.2	NP_005079.2	Q02040	AK17A_HUMAN	A kinase (PRKA) anchor protein 17A	142					B cell activation (GO:0042113)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein kinase A binding (GO:0051018)			breast(2)|endometrium(5)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)	26						AGACCCTGCCGGGGGAGCGGC	0.667																																					p.P142fs		Atlas-INDEL	.											.	AKAP17A	46	.	0			c.425delC						.						113	128	123					X																	1712781		2203	4296	6499	SO:0001589	frameshift_variant	8227	exon2			.	L03426	CCDS14116.1	Xp22.33 and Yp11.32	2010-09-08	2010-09-08	2010-09-08	ENSG00000197976	ENSG00000197976		"Pseudoautosomal regions / PAR1", "A-kinase anchor proteins"	18783	protein-coding gene	gene with protein product		312095, 465000	"chromosome X and Y open reading frame 3", "splicing factor, arginine/serine-rich 17A"	CXYorf3, SFRS17A		9736779, 1438229, 19840947	Standard	NR_027383		Approved	XE7, XE7Y, DXYS155E, MGC39904, 721P, CCDC133	uc004cqa.3	Q02040	OTTHUMG00000021063	ENST00000313871.3:c.426delG	chrX.hg19:g.1712781delG	ENSP00000324827:p.Pro142fs	161.0	0.0		167.0	26.0	NM_005088	Q02832|Q2TB98|Q5JQ74|Q5JQ76|Q8N6U9	Frame_Shift_Del	DEL	ENST00000313871.3	hg19	CCDS14116.1																																																																																			.	.		0.667	AKAP17A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055609.2	NM_005088		-	1712781	G	-	1712781	7	5	352	1	0	1	0	1	0	0	0	0	14188	1103	39	0	428	0	SFRS17A	23	1712781	Frame_Shift_Del	DEL	G	TCGA-WQ-A9G7-01A-11D-A36X-10	228661	1712781	153557779	468	49884										
FAM9A	171482	hgsc.bcm.edu	37	chrX	8763403	8763403	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	atcatctttctgcttctctgCgatgtattctttaaggacat	6	9	5	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chrX:8763403C>T	ENST00000543214.1	-	7	682	c.547G>A	c.(547-549)Gca>Aca	p.A183T	FAM9A_ENST00000381003.3_Missense_Mutation_p.A183T	NM_001171186.1	NP_001164657.1	Q8IZU1	FAM9A_HUMAN	family with sequence similarity 9, member A	183	Glu-rich.					nucleus (GO:0005634)				endometrium(11)|kidney(2)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	18		Hepatocellular(5;0.219)				TGCTTCTCTGCGATGTATTCT	0.468																																					p.A183T		Atlas-SNP	.											.	FAM9A	57	.	0			c.G547A						.						132	110	118					X																	8763403		2203	4300	6503	SO:0001583	missense	171482	exon7			TCTCTGCGATGTA		CCDS14131.1	Xp22.32	2012-11-29			ENSG00000183304	ENSG00000183304			18403	protein-coding gene	gene with protein product	"testis expressed 39A"	300477					Standard	NM_174951		Approved	TEX39A	uc004csg.3	Q8IZU1	OTTHUMG00000021110	ENST00000543214.1:c.547G>A	chrX.hg19:g.8763403C>T	ENSP00000440163:p.Ala183Thr	91.0	0.0		84.0	28.0	NM_174951	B7ZLH5|Q2M2D1	Missense_Mutation	SNP	ENST00000543214.1	hg19	CCDS14131.1	.	.	.	.	.	.	.	.	.	.	c	1.178	-0.638873	0.03557	.	.	ENSG00000183304	ENST00000381003;ENST00000543214	.	.	.	0.611	-1.19	0.09585	.	.	.	.	.	T	0.06325	0.0163	N	0.02247	-0.625	0.09310	N	1	P	0.50943	0.94	B	0.35240	0.198	T	0.24835	-1.0149	7	0.20519	T	0.43	.	.	.	.	.	183	Q8IZU1	FAM9A_HUMAN	T	183	.	ENSP00000370391:A183T	A	-	1	0	FAM9A	8723403	0.048000	0.20356	0.000000	0.03702	0.000000	0.00434	0.947000	0.29082	-0.480000	0.06803	-0.497000	0.04613	GCA	.	.		0.468	FAM9A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055697.1	NM_174951		T	8763403	C	T	8763403	3	4	352	1	0	0	0	0	1	0	0	0	5667	768	27	1	463	1	FAM9A	23	8763403	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	7050622	8763403	146507157	469	49885										
DCAF8L2	347442	hgsc.bcm.edu	37	chrX	27765399	27765399	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gagggaggggaggaggaggaAgaggaggaggaggaggagga	27	0	0	1	rs371896121		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chrX:27765399A>G	ENST00000451261.2	+	5	786	c.387A>G	c.(385-387)gaA>gaG	p.E129E		NM_001136533.1	NP_001130005.1	P0C7V8	DC8L2_HUMAN	DDB1 and CUL4 associated factor 8-like 2	129	Glu-rich.									central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						aggaggaggaagaggaggagg	0.572																																					p.E129E		Atlas-SNP	.											.	DCAF8L2	79	.	0			c.A387G						.						24	21	22					X																	27765399		692	1589	2281	SO:0001819	synonymous_variant	347442	exon1			GGAGGAAGAGGAG		CCDS59162.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17		ENSG00000189186		"WD repeat domain containing"	31811	protein-coding gene	gene with protein product			"WD repeat domain 42C"	WDR42C			Standard	NM_001136533		Approved		uc011mjy.2	P0C7V8		ENST00000451261.2:c.387A>G	chrX.hg19:g.27765399A>G		33.0	0.0		34.0	5.0	NM_001136533	B2RXH9|J3KT06	Silent	SNP	ENST00000451261.2	hg19	CCDS59162.1																																																																																			.	.		0.572	DCAF8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056143.4	XM_293354		G	27765399	A	G	27765399	2	3	352	1	0	0	0	0	0	0	0	1	4280	69	3	2		2	DCAF8L2	23	27765399	Silent	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	19001996	27765399	127505161	470	49886										
FAM47A	158724	hgsc.bcm.edu	37	chrX	34149344	34149344	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cagtctcggaaggctccgagCggagactggacccccgacga	14	14	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chrX:34149344C>T	ENST00000346193.3	-	1	1103	c.1052G>A	c.(1051-1053)cGc>cAc	p.R351H		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	351										NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	97						AGGCTCCGAGCGGAGACTGGA	0.657																																					p.R351H		Atlas-SNP	.											.	FAM47A	249	.	0			c.G1052A						.						23	25	24					X																	34149344		2190	4294	6484	SO:0001583	missense	158724	exon1			TCCGAGCGGAGAC	BC026171	CCDS43926.1	Xp21.1	2004-08-09			ENSG00000185448	ENSG00000185448			29962	protein-coding gene	gene with protein product	"similar to hypothetical protein FLJ35782"					12477932	Standard	NM_203408		Approved	MGC27003	uc004ddg.3	Q5JRC9	OTTHUMG00000021339	ENST00000346193.3:c.1052G>A	chrX.hg19:g.34149344C>T	ENSP00000345029:p.Arg351His	130.0	0.0		157.0	26.0	NM_203408	A8K8I9|Q8TAA0	Missense_Mutation	SNP	ENST00000346193.3	hg19	CCDS43926.1	.	.	.	.	.	.	.	.	.	.	N	1.759	-0.487340	0.04352	.	.	ENSG00000185448	ENST00000346193	T	0.09538	2.97	0.226	-0.452	0.12205	.	.	.	.	.	T	0.04048	0.0113	N	0.04508	-0.205	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.40021	-0.9585	8	0.39692	T	0.17	.	.	.	.	.	351	Q5JRC9	FA47A_HUMAN	H	351	ENSP00000345029:R351H	ENSP00000345029:R351H	R	-	2	0	FAM47A	34059265	0.772000	0.28567	0.001000	0.08648	0.001000	0.01503	-1.078000	0.03413	-0.826000	0.04284	-0.832000	0.03076	CGC	.	.		0.657	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408		T	34149344	C	T	34149344	3	4	352	1	0	0	0	0	1	0	0	0	5577	768	27	1	1327	1	FAM47A	23	34149344	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	6383945	34149344	121121216	471	49887										
RP2	6102	hgsc.bcm.edu	37	chrX	46713333	46713333	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aatacatggagtaacattcaTgactttacacctgtgtcagg	8	8	2	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chrX:46713333T>C	ENST00000218340.3	+	2	686	c.525T>C	c.(523-525)caT>caC	p.H175H		NM_006915.2	NP_008846.2	O75695	XRP2_HUMAN	retinitis pigmentosa 2 (X-linked recessive)	175	C-CAP/cofactor C-like. {ECO:0000255|PROSITE-ProRule:PRU00659}.				cell morphogenesis (GO:0000902)|CTP biosynthetic process (GO:0006241)|cytoskeleton organization (GO:0007010)|GTP biosynthetic process (GO:0006183)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|protein transport (GO:0015031)|UTP biosynthetic process (GO:0006228)|visual perception (GO:0007601)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|periciliary membrane compartment (GO:1990075)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|GTPase activator activity (GO:0005096)|nucleoside diphosphate kinase activity (GO:0004550)|unfolded protein binding (GO:0051082)			NS(1)|large_intestine(4)|lung(5)|stomach(1)	11						GTAACATTCATGACTTTACAC	0.403																																					p.H175H		Atlas-SNP	.											.	RP2	37	.	0			c.T525C						.						102	87	92					X																	46713333		2203	4300	6503	SO:0001819	synonymous_variant	6102	exon2			CATTCATGACTTT	AJ007590	CCDS14270.1	Xp11.3	2013-01-08			ENSG00000102218	ENSG00000102218			10274	protein-coding gene	gene with protein product		300757				6325945, 9697692, 19852809	Standard	NM_006915		Approved	TBCCD2, NME10, NM23-H10	uc004dgw.4	O75695	OTTHUMG00000021430	ENST00000218340.3:c.525T>C	chrX.hg19:g.46713333T>C		201.0	0.0		225.0	9.0	NM_006915	Q86XJ7|Q9NU67	Silent	SNP	ENST00000218340.3	hg19	CCDS14270.1																																																																																			.	.		0.403	RP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056375.1	NM_006915		C	46713333	T	C	46713333	2	2	352	1	0	0	0	0	0	0	0	1	13549	1461	51	2		2	RP2	23	46713333	Silent	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	12563989	46713333	108557227	472	49888										
TIMP1	7076	hgsc.bcm.edu	37	chrX	47444965	47444965	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	aactgcaggatggactcttgCacatcactacctgcagtttt	8	11	2	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chrX:47444965C>T	ENST00000218388.4	+	5	522	c.352C>T	c.(352-354)Cac>Tac	p.H118Y	TIMP1_ENST00000377017.1_Missense_Mutation_p.H54Y|SYN1_ENST00000340666.4_Intron|MIR4769_ENST00000584126.1_RNA|SYN1_ENST00000295987.7_Intron|TIMP1_ENST00000456754.2_3'UTR|TIMP1_ENST00000377018.2_Missense_Mutation_p.H112Y	NM_003254.2	NP_003245.1	P01033	TIMP1_HUMAN	TIMP metallopeptidase inhibitor 1	118	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				aging (GO:0007568)|blood coagulation (GO:0007596)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|negative regulation of metalloenzyme activity (GO:0048553)|negative regulation of trophoblast cell migration (GO:1901164)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cell proliferation (GO:0008284)|regulation of integrin-mediated signaling pathway (GO:2001044)|response to cytokine (GO:0034097)|response to peptide hormone (GO:0043434)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	cytokine activity (GO:0005125)|metal ion binding (GO:0046872)|metalloendopeptidase inhibitor activity (GO:0008191)			endometrium(1)|large_intestine(2)	3						TGGACTCTTGCACATCACTAC	0.582																																					p.H118Y		Atlas-SNP	.											.	TIMP1	12	.	0			c.C352T						.						46	38	41					X																	47444965		2203	4300	6503	SO:0001583	missense	7076	exon5			CTCTTGCACATCA		CCDS14281.1	Xp11.3-p11.23	2008-07-29	2005-08-08		ENSG00000102265	ENSG00000102265			11820	protein-coding gene	gene with protein product		305370	"tissue inhibitor of metalloproteinase 1 (erythroid potentiating activity, collagenase inhibitor)"	TIMP, CLGI			Standard	XM_005272645		Approved	EPO	uc004dif.3	P01033	OTTHUMG00000021447	ENST00000218388.4:c.352C>T	chrX.hg19:g.47444965C>T	ENSP00000218388:p.His118Tyr	233.0	0.0		240.0	48.0	NM_003254	Q14252|Q9UCU1	Missense_Mutation	SNP	ENST00000218388.4	hg19	CCDS14281.1	.	.	.	.	.	.	.	.	.	.	c	0.033	-1.323223	0.01309	.	.	ENSG00000102265	ENST00000218388;ENST00000377018;ENST00000377017	D;D;D	0.94330	-3.4;-3.4;-3.4	5.29	-0.22	0.13130	Tissue inhibitor of metalloproteinases-like, OB-fold (1);Netrin domain (1);	0.412581	0.23197	N	0.050824	D	0.85771	0.5774	N	0.25647	0.755	0.22266	N	0.99925	B;B	0.21071	0.051;0.01	B;B	0.31337	0.128;0.004	T	0.70270	-0.4918	10	0.10377	T	0.69	.	8.7409	0.34556	0.0:0.4903:0.0:0.5097	.	112;118	B4DJK3;P01033	.;TIMP1_HUMAN	Y	118;112;54	ENSP00000218388:H118Y;ENSP00000366217:H112Y;ENSP00000366216:H54Y	ENSP00000218388:H118Y	H	+	1	0	TIMP1	47329909	0.998000	0.40836	0.620000	0.29132	0.539000	0.34962	0.333000	0.19768	-0.099000	0.12263	0.519000	0.50382	CAC	.	.		0.582	TIMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056423.1	NM_003254		T	47444965	C	T	47444965	3	4	352	1	0	0	0	0	1	0	0	0	15932	710	25	3	366	3	TIMP1	23	47444965	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	731632	47444965	107825595	473	49889										
GRIPAP1	56850	hgsc.bcm.edu	37	chrX	48847397	48847397	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ctctttctccatttcccattTcagctccacctctgccaacg	3	18	4	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chrX:48847397T>C	ENST00000376441.1	-	7	617	c.583A>G	c.(583-585)Aaa>Gaa	p.K195E	GRIPAP1_ENST00000376425.3_Missense_Mutation_p.K195E|GRIPAP1_ENST00000376444.3_Missense_Mutation_p.K150E|GRIPAP1_ENST00000376423.4_Missense_Mutation_p.K142E|GRIPAP1_ENST00000473581.1_5'UTR	NM_020137.3	NP_064522.3	Q4V328	GRAP1_HUMAN	GRIP1 associated protein 1	195						blood microparticle (GO:0072562)|endosome (GO:0005768)				breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(2)	10						ATTTCCCATTTCAGCTCCACC	0.607																																					p.K195E		Atlas-SNP	.											.	GRIPAP1	128	.	0			c.A583G						.						95	85	88					X																	48847397		2203	4300	6503	SO:0001583	missense	56850	exon7			CCCATTTCAGCTC	AB032993	CCDS35248.1	Xp11.23	2008-02-05			ENSG00000068400	ENSG00000068400			18706	protein-coding gene	gene with protein product		300408				10896157	Standard	NM_020137		Approved	GRASP-1, GRASP1, KIAA1167, MPMGp800B12492Q3, DKFZp434P0630	uc004dly.1	Q4V328	OTTHUMG00000033192	ENST00000376441.1:c.583A>G	chrX.hg19:g.48847397T>C	ENSP00000365624:p.Lys195Glu	169.0	0.0		176.0	47.0	NM_020137	A6NL78|Q3MJ75|Q4V327|Q4V330|Q5HYG1|Q6N046|Q96DH8|Q9NQ43|Q9ULQ3	Missense_Mutation	SNP	ENST00000376441.1	hg19	CCDS35248.1	.	.	.	.	.	.	.	.	.	.	T	18.69	3.678208	0.68042	.	.	ENSG00000068400	ENST00000376425;ENST00000376444;ENST00000376441;ENST00000537291;ENST00000376423	T;T;T;T	0.29397	1.57;1.57;1.57;1.57	5.05	5.05	0.67936	.	0.280477	0.33401	N	0.004950	T	0.38480	0.1042	L	0.34521	1.04	0.32150	N	0.584303	D;D;D	0.71674	0.986;0.982;0.998	P;P;D	0.80764	0.795;0.831;0.994	T	0.28650	-1.0037	10	0.10111	T	0.7	-16.9781	11.4077	0.49908	0.0:0.0:0.0:1.0	.	142;85;195	Q4V328-2;Q4V328-3;Q4V328	.;.;GRAP1_HUMAN	E	195;150;195;195;142	ENSP00000365608:K195E;ENSP00000365627:K150E;ENSP00000365624:K195E;ENSP00000365606:K142E	ENSP00000365606:K142E	K	-	1	0	GRIPAP1	48732341	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.253000	0.51469	1.675000	0.50919	0.451000	0.29950	AAA	.	.		0.607	GRIPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080970.2	NM_207672		C	48847397	T	C	48847397	3	2	352	1	0	0	0	0	1	0	0	0	6798	1792	62	2	2076	2	GRIPAP1	23	48847397	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	1402432	48847397	106423163	474	49890										
PRICKLE3	4007	hgsc.bcm.edu	37	chrX	49032590	49032590	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggggagcccctctcagaaagCgggagggctcctcagggcct	16	13	2	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chrX:49032590C>T	ENST00000376317.3	-	9	1374	c.1280G>A	c.(1279-1281)cGc>cAc	p.R427H	PRICKLE3_ENST00000540849.1_Missense_Mutation_p.R359H|PRICKLE3_ENST00000538114.1_Missense_Mutation_p.R263H|PRICKLE3_ENST00000536904.1_Missense_Mutation_p.R346H	NM_006150.3	NP_006141.2	O43900	PRIC3_HUMAN	prickle homolog 3 (Drosophila)	427				Missing (in Ref. 7; AAB92357). {ECO:0000305}.			zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|skin(2)	22						TCTCAGAAAGCGGGAGGGCTC	0.677																																					p.R427H		Atlas-SNP	.											.	PRICKLE3	59	.	0			c.G1280A						.						5	6	6					X																	49032590		1836	3777	5613	SO:0001583	missense	4007	exon9			AGAAAGCGGGAGG	BC016856	CCDS14320.1	Xp11.23	2008-02-05	2007-09-18	2007-09-18	ENSG00000012211	ENSG00000012211			6645	protein-coding gene	gene with protein product		300111	"LIM domain only 6"	LMO6		9344658	Standard	XM_005272605		Approved		uc004dmy.1	O43900	OTTHUMG00000024134	ENST00000376317.3:c.1280G>A	chrX.hg19:g.49032590C>T	ENSP00000365494:p.Arg427His	98.0	0.0		92.0	19.0	NM_006150	B7Z8F2|O76007|Q53XR5	Missense_Mutation	SNP	ENST00000376317.3	hg19	CCDS14320.1	.	.	.	.	.	.	.	.	.	.	-	2.314	-0.357254	0.05138	.	.	ENSG00000012211	ENST00000376317;ENST00000536904;ENST00000540849;ENST00000538114	T;T;T;T	0.69435	-0.39;-0.4;-0.39;-0.39	4.09	-3.27	0.05048	.	0.906261	0.09107	N	0.847581	T	0.35189	0.0923	N	0.04508	-0.205	0.09310	N	1	B;B;B	0.09022	0.001;0.002;0.002	B;B;B	0.04013	0.0;0.001;0.001	T	0.21348	-1.0248	10	0.13108	T	0.6	-3.0129	6.1358	0.20233	0.0:0.2317:0.1532:0.615	.	389;346;427	B7Z6S4;B7Z8F2;O43900	.;.;PRIC3_HUMAN	H	427;346;359;263	ENSP00000365494:R427H;ENSP00000441385:R346H;ENSP00000446051:R359H;ENSP00000441743:R263H	ENSP00000365494:R427H	R	-	2	0	PRICKLE3	48919534	0.000000	0.05858	0.059000	0.19551	0.725000	0.41563	-1.870000	0.01641	-0.788000	0.04504	-0.322000	0.08575	CGC	.	.		0.677	PRICKLE3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060811.1	NM_006150		T	49032590	C	T	49032590	3	4	352	1	0	0	0	0	1	0	0	0	12500	768	27	1	571	1	PRICKLE3	23	49032590	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	185193	49032590	106237970	475	49891										
CACNA1F	778	hgsc.bcm.edu	37	chrX	49082873	49082873	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggggctgggggccctcacagGcagcgtgtacagctggccag	18	12	1	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chrX:49082873G>A	ENST00000376265.2	-	11	1555	c.1494C>T	c.(1492-1494)tgC>tgT	p.C498C	CACNA1F_ENST00000376251.1_Silent_p.C433C|CACNA1F_ENST00000323022.5_Silent_p.C487C	NM_005183.2	NP_005174.2	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type, alpha 1F subunit	498					axonogenesis (GO:0007409)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|dendrite morphogenesis (GO:0048813)|detection of light stimulus involved in visual perception (GO:0050908)|membrane depolarization during action potential (GO:0086010)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|perikaryon (GO:0043204)|photoreceptor outer segment (GO:0001750)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			autonomic_ganglia(1)|breast(8)|central_nervous_system(3)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(4)|urinary_tract(1)	85					Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	GCCCTCACAGGCAGCGTGTAC	0.612																																					p.C498C		Atlas-SNP	.											.	CACNA1F	218	.	0			c.C1494T						.						38	34	36					X																	49082873		2200	4280	6480	SO:0001819	synonymous_variant	778	exon11			TCACAGGCAGCGT	AA019975	CCDS35253.1, CCDS59166.1, CCDS59167.1	Xp11.23	2013-01-23	2007-02-16		ENSG00000102001	ENSG00000102001		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1393	protein-coding gene	gene with protein product		300110	"Aland island eye disease (Forsius-Eriksson ocular albinism, ocular albinism type 2)"	CSNB2, AIED		9344658, 9662400, 16382099, 12111638, 17525176	Standard	NM_005183		Approved	Cav1.4, JM8, JMC8, CSNBX2, CORDX3, CSNB2A, OA2	uc010nip.3	O60840	OTTHUMG00000022703	ENST00000376265.2:c.1494C>T	chrX.hg19:g.49082873G>A		74.0	0.0		85.0	5.0	NM_005183	A6NI29|F5CIQ9|O43901|O95226|Q9UHB1	Silent	SNP	ENST00000376265.2	hg19	CCDS35253.1																																																																																			.	.		0.612	CACNA1F-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358157.1	NM_005183		A	49082873	G	A	49082873	2	1	352	1	0	0	0	0	0	0	0	1	2545	1195	42	3		3	CACNA1F	23	49082873	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	50283	49082873	106187687	476	49892										
HEPH	9843	hgsc.bcm.edu	37	chrX	65483530	65483530	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tcaccaaagagactgaaaaaGgtacgtaaaatgatgcacag	9	7	1	3			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chrX:65483530G>A	ENST00000343002.2	+	19	3908	c.3244G>A	c.(3244-3246)Gca>Aca	p.A1082T	HEPH_ENST00000419594.1_Splice_Site_p.A893T|HEPH_ENST00000374727.3_Splice_Site_p.A1085T|HEPH_ENST00000441993.2_Splice_Site_p.V1085M|HEPH_ENST00000519389.1_Splice_Site_p.A1136T|HEPH_ENST00000336279.5_Splice_Site_p.A815T			Q9BQS7	HEPH_HUMAN	hephaestin	1082	Plastocyanin-like 6.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|iron ion transport (GO:0006826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	copper ion binding (GO:0005507)|ferrous iron binding (GO:0008198)|ferroxidase activity (GO:0004322)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(56)|ovary(5)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	89						GACTGAAAAAGGTACGTAAAA	0.438																																					p.A1136T		Atlas-SNP	.											.	HEPH	224	.	0			c.G3406A						.						221	153	176					X																	65483530		2203	4300	6503	SO:0001630	splice_region_variant	9843	exon20			GAAAAAGGTACGT	AB014598	CCDS14384.2, CCDS14385.1, CCDS48133.1, CCDS14384.3, CCDS65277.1	Xq11-q12	2008-02-05			ENSG00000089472	ENSG00000089472			4866	protein-coding gene	gene with protein product		300167				9988272, 9734811	Standard	NM_014799		Approved	KIAA0698, CPL	uc011moz.2	Q9BQS7	OTTHUMG00000021732	ENST00000343002.2:c.3244+1G>A	chrX.hg19:g.65483530G>A		238.0	0.0		286.0	81.0	NM_138737	B1AJX8|D3DVT7|E9PHN8|O75180|Q6UW45|Q9C058	Missense_Mutation	SNP	ENST00000343002.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.81|12.81	2.048543|2.048543	0.36181|0.36181	.|.	.|.	ENSG00000089472|ENSG00000089472	ENST00000519389;ENST00000374727;ENST00000336279;ENST00000419594;ENST00000343002|ENST00000441993	D;D;D;D;D|D	0.99287|0.99264	-5.69;-5.67;-5.68;-5.69;-5.67|-5.65	3.95|3.95	3.95|3.95	0.45737|0.45737	.|.	0.257731|.	0.26967|.	N|.	0.021584|.	D|D	0.97704|0.97704	0.9247|0.9247	L|L	0.51422|0.51422	1.61|1.61	0.33550|0.33550	D|D	0.59603|0.59603	B;P|B	0.35551|0.23490	0.094;0.509|0.086	B;B|B	0.30495|0.25884	0.026;0.116|0.064	D|D	0.99979|0.99979	1.2422|1.2422	10|9	0.22706|0.44086	T|T	0.39|0.13	.|.	10.4386|10.4386	0.44450|0.44450	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1136;893|1083	E9PHN8;E7ES21|Q9BQS7	.;.|HEPH_HUMAN	T|M	1136;1085;815;893;1082|1085	ENSP00000430620:A1136T;ENSP00000363859:A1085T;ENSP00000337418:A815T;ENSP00000413211:A893T;ENSP00000343939:A1082T|ENSP00000411687:V1085M	ENSP00000337418:A815T|ENSP00000411687:V1085M	A|V	+|+	1|1	0|0	HEPH|HEPH	65400255|65400255	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.331000|0.331000	0.28603|0.28603	3.394000|3.394000	0.52551|0.52551	2.221000|2.221000	0.72209|0.72209	0.600000|0.600000	0.82982|0.82982	GCA|GTG	.	.		0.438	HEPH-002	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000056995.1	NM_138737	Missense_Mutation	A	65483530	G	A	65483530	5	1	352	1	0	0	0	0	0	0	1	0	7063	1014	35	3	3484	3	HEPH	23	65483530	Splice_Site	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	16400657	65483530	89787030	477	49893										
HDX	139324	hgsc.bcm.edu	37	chrX	83723918	83723918	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agaattctctgggggtaatcGctaactgccaatgaaaacac	9	9	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chrX:83723918G>A	ENST00000297977.5	-	3	924	c.813C>T	c.(811-813)agC>agT	p.S271S	HDX_ENST00000373177.2_Silent_p.S271S|HDX_ENST00000506585.2_Silent_p.S213S	NM_001177479.1|NM_144657.4	NP_001170950.1|NP_653258.2	Q7Z353	HDX_HUMAN	highly divergent homeobox	271						nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(6)|kidney(2)|large_intestine(12)|liver(1)|lung(19)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						GGGGGTAATCGCTAACTGCCA	0.448																																					p.S271S	Pancreas(53;231 1169 36156 43751 51139)	Atlas-SNP	.											.	HDX	124	.	0			c.C813T						.						91	87	89					X																	83723918		2203	4300	6503	SO:0001819	synonymous_variant	139324	exon3			GTAATCGCTAACT	BX538112	CCDS35342.1, CCDS55456.1	Xq21.1	2012-03-09	2007-07-13	2007-07-13	ENSG00000165259	ENSG00000165259		"Homeoboxes / POU class"	26411	protein-coding gene	gene with protein product			"chromosome X open reading frame 43"	CXorf43			Standard	NM_144657		Approved	FLJ30678	uc004eek.2	Q7Z353	OTTHUMG00000021926	ENST00000297977.5:c.813C>T	chrX.hg19:g.83723918G>A		166.0	0.0		159.0	35.0	NM_144657	A8K1Y5|B7ZL18|Q5JZB4|Q96NK7	Silent	SNP	ENST00000297977.5	hg19	CCDS35342.1																																																																																			.	.		0.448	HDX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057379.2	NM_144657		A	83723918	G	A	83723918	2	1	352	1	0	0	0	0	0	0	0	1	7035	1078	38	1		1	HDX	23	83723918	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	18240388	83723918	71546642	478	49894										
BEX4	56271	hgsc.bcm.edu	37	chrX	102471235	102471236	+	Frame_Shift_Ins	INS	-	-	G													0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gcctggaggaaatatcaggcINSgggggcgagttaggcgactt					rs62623366		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chrX:102471235_102471236insG	ENST00000372695.5	+	3	389_390	c.154_155insG	c.(154-156)cggfs	p.R52fs	BEX4_ENST00000372691.3_Frame_Shift_Ins_p.R52fs	NM_001080425.3	NP_001073894.1	Q9NWD9	BEX4_HUMAN	brain expressed, X-linked 4	52						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(2)	9						AAATATCAGGCGGGGGCGAGTT	0.52																																					p.R52fs		Atlas-INDEL	.											.	BEX4	15	.	0			c.154_155insG						.																																			SO:0001589	frameshift_variant	56271	exon3			.	AL035494	CCDS35355.1	Xq22.1-q22.3	2014-03-21	2008-11-04	2007-08-24	ENSG00000102409	ENSG00000102409			25475	protein-coding gene	gene with protein product		300692	"brain expressed X-linked-like 1", "BEX family member 4"	BEXL1		15958283, 16221301	Standard	NM_001080425		Approved	FLJ10097	uc004ejw.4	Q9NWD9	OTTHUMG00000022091	ENST00000372695.5:c.159dupG	chrX.hg19:g.102471240_102471240dupG	ENSP00000361780:p.Arg52fs	349.0	0.0		396.0	52.0	NM_001080425		Frame_Shift_Ins	INS	ENST00000372695.5	hg19	CCDS35355.1																																																																																			.	.		0.52	BEX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057694.1	XM_043653		G	102471236	-	G	102471235	7	5	352	1	0	1	1	0	0	0	0	0	1412	759	27	0	156	0	BEX4	23	102471235	Frame_Shift_Ins	INS	-	TCGA-WQ-A9G7-01A-11D-A36X-10	18747317	102471235	52799325	479	49895										
ESX1	80712	hgsc.bcm.edu	37	chrX	103498837	103498837	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ccggggcaagccacttaccgCgccacaacgtcgggatattg	12	14	0	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chrX:103498837C>T	ENST00000372588.4	-	2	587	c.504G>A	c.(502-504)gcG>gcA	p.A168A		NM_153448.3	NP_703149.1	Q8N693	ESX1_HUMAN	ESX homeobox 1	168					labyrinthine layer blood vessel development (GO:0060716)|labyrinthine layer morphogenesis (GO:0060713)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding (GO:0043565)			endometrium(2)|large_intestine(10)|lung(12)|ovary(1)|skin(2)	27						CCACTTACCGCGCCACAACGT	0.627																																					p.A168A	Pancreas(200;1705 2227 25194 28471 45274)	Atlas-SNP	.											.	ESX1	57	.	0			c.G504A						.						48	50	50					X																	103498837		2202	4298	6500	SO:0001819	synonymous_variant	80712	exon2			TTACCGCGCCACA	AL049631	CCDS14516.1	Xq22.2	2011-06-20	2007-07-11	2006-02-08	ENSG00000123576	ENSG00000123576		"Homeoboxes / PRD class"	14865	protein-coding gene	gene with protein product		300154	"extraembryonic, spermatogenesis, homeobox 1 homolog (mouse)"	ESX1L		11374906, 17242862	Standard	NM_153448		Approved	ESXR1	uc004ely.3	Q8N693	OTTHUMG00000022125	ENST00000372588.4:c.504G>A	chrX.hg19:g.103498837C>T		152.0	0.0		165.0	50.0	NM_153448	B0QYU3|Q7Z6K7	Silent	SNP	ENST00000372588.4	hg19	CCDS14516.1																																																																																			.	.		0.627	ESX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057763.2	NM_153448		T	103498837	C	T	103498837	2	4	352	1	0	0	0	0	0	0	0	1	5265	755	27	1		1	ESX1	23	103498837	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	1027602	103498837	51771723	480	49896										
TEX13A	56157	hgsc.bcm.edu	37	chrX	104464092	104464092	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ccggagatctccctccttctGcccccaataggtgtactttt	7	15	2	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chrX:104464092G>A	ENST00000413579.1	-	5	895	c.784C>T	c.(784-786)Cag>Tag	p.Q262*	IL1RAPL2_ENST00000344799.4_Intron|IL1RAPL2_ENST00000372582.1_Intron|TEX13A_ENST00000372578.3_Silent_p.G262G|TEX13A_ENST00000372575.1_Silent_p.G262G			Q9BXU3	TX13A_HUMAN	testis expressed 13A	262							zinc ion binding (GO:0008270)			large_intestine(5)|ovary(2)|upper_aerodigestive_tract(1)	8						CCCTCCTTCTGCCCCCAATAG	0.557																																					p.Q262X		Atlas-SNP	.											.	TEX13A	55	.	0			c.C784T						.						67	66	66					X																	104464092		2007	4165	6172	SO:0001587	stop_gained	56157	exon5			CCTTCTGCCCCCA	AF285597	CCDS76005.1	Xq28	2012-04-20	2007-03-13		ENSG00000133149	ENSG00000268629			11735	protein-coding gene	gene with protein product		300312	"testis expressed sequence 13A"			11279525	Standard	NM_031274		Approved		uc004ema.3	Q9BXU3	OTTHUMG00000022133	ENST00000413579.1:c.784C>T	chrX.hg19:g.104464092G>A	ENSP00000399753:p.Gln262*	160.0	0.0		169.0	45.0	NM_031274	B1B1G8|Q32NB6	Nonsense_Mutation	SNP	ENST00000413579.1	hg19		.	.	.	.	.	.	.	.	.	.	G	14.65	2.600065	0.46318	.	.	ENSG00000133149	ENST00000413579	.	.	.	3.45	0.451	0.16629	.	0.485125	0.15503	N	0.258925	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	.	8.4708	0.32984	0.0:0.0:0.4039:0.5961	.	.	.	.	X	262	.	ENSP00000399753:Q262X	Q	-	1	0	TEX13A	104350748	0.077000	0.21312	0.004000	0.12327	0.002000	0.02628	0.749000	0.26320	-0.027000	0.13873	-1.496000	0.00964	CAG	.	.		0.557	TEX13A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_031274		A	104464092	G	A	104464092	4	1	352	1	0	0	0	0	0	1	0	0	15791	1306	46	3	449	3	TEX13A	23	104464092	Nonsense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	965255	104464092	50806468	481	49897										
CAPN6	827	hgsc.bcm.edu	37	chrX	110491972	110491972	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ctcctggatgtagaggtggtGgaggcggaatttgcggttca	17	6	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chrX:110491972G>A	ENST00000324068.1	-	10	1476	c.1309C>T	c.(1309-1311)Cac>Tac	p.H437Y	CAPN6_ENST00000541758.1_Missense_Mutation_p.H182Y	NM_014289.3	NP_055104.2	Q9Y6Q1	CAN6_HUMAN	calpain 6	437	Domain III.				microtubule bundle formation (GO:0001578)|proteolysis (GO:0006508)|regulation of cytoskeleton organization (GO:0051493)	perinuclear region of cytoplasm (GO:0048471)|spindle microtubule (GO:0005876)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|microtubule binding (GO:0008017)			cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(25)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	47						TAGAGGTGGTGGAGGCGGAAT	0.448																																					p.H437Y		Atlas-SNP	.											.	CAPN6	120	.	0			c.C1309T						.						102	91	94					X																	110491972		2203	4300	6503	SO:0001583	missense	827	exon10			GGTGGTGGAGGCG	AF029232	CCDS14555.1	Xq23	2008-07-29			ENSG00000077274	ENSG00000077274			1483	protein-coding gene	gene with protein product		300146				9503024, 9339374	Standard	NM_014289		Approved	CAPNX, CalpM, CANPX	uc004epc.2	Q9Y6Q1	OTTHUMG00000022203	ENST00000324068.1:c.1309C>T	chrX.hg19:g.110491972G>A	ENSP00000317214:p.His437Tyr	140.0	0.0		157.0	55.0	NM_014289	D3DUY7|Q9UEQ1|Q9UJA8	Missense_Mutation	SNP	ENST00000324068.1	hg19	CCDS14555.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.480561	0.84747	.	.	ENSG00000077274	ENST00000324068;ENST00000541758	D;D	0.88431	-2.38;-2.38	4.94	4.94	0.65067	Peptidase C2, calpain, large subunit, domain III (2);Peptidase C2, calpain, domain III (1);	0.317386	0.38778	N	0.001576	D	0.92348	0.7572	L	0.55990	1.75	0.80722	D	1	D	0.65815	0.995	D	0.67382	0.951	D	0.92229	0.5791	10	0.46703	T	0.11	.	16.0038	0.80344	0.0:0.0:1.0:0.0	.	437	Q9Y6Q1	CAN6_HUMAN	Y	437;182	ENSP00000317214:H437Y;ENSP00000441736:H182Y	ENSP00000317214:H437Y	H	-	1	0	CAPN6	110378628	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.980000	0.93460	2.294000	0.77228	0.529000	0.55759	CAC	.	.		0.448	CAPN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057922.1			A	110491972	G	A	110491972	3	1	352	1	0	0	0	0	1	0	0	0	2632	1348	47	3	632	3	CAPN6	23	110491972	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	6027880	110491972	44778588	482	49898										
MCTS1	28985	hgsc.bcm.edu	37	chrX	119739358	119739358	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	atagagcaatttccaggtatTgaaccatggcttaatcaaat	7	7	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chrX:119739358T>C	ENST00000371317.5	+	2	365	c.108T>C	c.(106-108)atT>atC	p.I36I	MCTS1_ENST00000487133.1_3'UTR|MCTS1_ENST00000371315.3_Silent_p.I37I	NM_014060.2	NP_054779.1	Q9ULC4	MCTS1_HUMAN	malignant T cell amplified sequence 1	36					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|formation of translation preinitiation complex (GO:0001731)|IRES-dependent translational initiation (GO:0002192)|positive regulation of cell proliferation (GO:0008284)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|ribosome disassembly (GO:0032790)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	translation initiation factor activity (GO:0003743)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|stomach(1)|urinary_tract(1)	10						TTCCAGGTATTGAACCATGGC	0.353																																					p.I37I		Atlas-SNP	.											.	MCTS1	40	.	0			c.T111C						.						96	96	96					X																	119739358		2203	4295	6498	SO:0001819	synonymous_variant	28985	exon2			AGGTATTGAACCA	AB034206	CCDS14601.1, CCDS48160.1	Xq24	2008-05-14			ENSG00000232119	ENSG00000232119			23357	protein-coding gene	gene with protein product		300587				9766643	Standard	NM_014060		Approved	MCT-1	uc011mub.2	Q9ULC4	OTTHUMG00000022303	ENST00000371317.5:c.108T>C	chrX.hg19:g.119739358T>C		399.0	1.0		479.0	121.0	NM_001137554	B4DGY2|Q502X6	Silent	SNP	ENST00000371317.5	hg19	CCDS14601.1																																																																																			.	.		0.353	MCTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058110.1	NM_014060		C	119739358	T	C	119739358	2	2	352	1	0	0	0	0	0	0	0	1	9411	1800	63	2		2	MCTS1	23	119739358	Silent	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	9247386	119739358	35531202	483	49899										
C1GALT1C1	29071	hgsc.bcm.edu	37	chrX	119760167	119760167	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ccatacatcatcacatgcatCtgatttggagtcagtccatt	6	11	4	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chrX:119760167C>G	ENST00000304661.5	-	2	1093	c.855G>C	c.(853-855)caG>caC	p.Q285H	C1GALT1C1_ENST00000371313.2_Missense_Mutation_p.Q285H	NM_001011551.2	NP_001011551.1	Q96EU7	C1GLC_HUMAN	C1GALT1-specific chaperone 1	285					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	11						TCACATGCATCTGATTTGGAG	0.413																																					p.Q285H		Atlas-SNP	.											.	C1GALT1C1	22	.	0			c.G855C						.						170	141	151					X																	119760167		2203	4300	6503	SO:0001583	missense	29071	exon3			ATGCATCTGATTT	AJ238398	CCDS14602.1	Xq24	2008-02-05			ENSG00000171155	ENSG00000171155			24338	protein-coding gene	gene with protein product		300611				11042152, 12361956	Standard	NM_152692		Approved	COSMC, C1GALT2	uc004esz.3	Q96EU7	OTTHUMG00000022305	ENST00000304661.5:c.855G>C	chrX.hg19:g.119760167C>G	ENSP00000304364:p.Gln285His	271.0	0.0		344.0	111.0	NM_152692	A8K246|Q8WWS3|Q9NZX1	Missense_Mutation	SNP	ENST00000304661.5	hg19	CCDS14602.1	.	.	.	.	.	.	.	.	.	.	C	8.110	0.778585	0.16120	.	.	ENSG00000171155	ENST00000304661;ENST00000371313	T;T	0.46819	0.86;0.86	5.46	0.37	0.16160	.	0.315127	0.35320	N	0.003300	T	0.33147	0.0853	L	0.46157	1.445	0.46376	D	0.999012	B	0.16166	0.016	B	0.18561	0.022	T	0.05971	-1.0853	9	.	.	.	-12.5479	5.6306	0.17508	0.0:0.3883:0.2535:0.3581	.	285	Q96EU7	C1GLC_HUMAN	H	285	ENSP00000304364:Q285H;ENSP00000360363:Q285H	.	Q	-	3	2	C1GALT1C1	119644195	0.961000	0.32948	0.998000	0.56505	0.957000	0.61999	0.086000	0.14935	-0.015000	0.14150	-0.498000	0.04607	CAG	.	.		0.413	C1GALT1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058117.1	NM_152692		G	119760167	C	G	119760167	3	3	352	1	0	0	0	0	1	0	0	0	1955	912	32	4	105	4	C1GALT1C1	23	119760167	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	20809	119760167	35510393	484	49900										
GLUD2	2747	hgsc.bcm.edu	37	chrX	120181885	120181885	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	caagccctgcaaccatgtgcTgagtctctccttccccatcc	6	18	1	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chrX:120181885T>C	ENST00000328078.1	+	1	424	c.347T>C	c.(346-348)cTg>cCg	p.L116P		NM_012084.3	NP_036216.2	P49448	DHE4_HUMAN	glutamate dehydrogenase 2	116					glutamate biosynthetic process (GO:0006537)|glutamate catabolic process (GO:0006538)|glutamate metabolic process (GO:0006536)|oxidation-reduction process (GO:0055114)	mitochondrion (GO:0005739)	ADP binding (GO:0043531)|glutamate dehydrogenase (NAD+) activity (GO:0004352)|glutamate dehydrogenase [NAD(P)+] activity (GO:0004353)|GTP binding (GO:0005525)|leucine binding (GO:0070728)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|urinary_tract(1)	38						AACCATGTGCTGAGTCTCTCC	0.647																																					p.L116P		Atlas-SNP	.											.	GLUD2	89	.	0			c.T347C						.						77	56	63					X																	120181885		2203	4296	6499	SO:0001583	missense	2747	exon1			ATGTGCTGAGTCT	U08997	CCDS14603.1	Xq24-q25	2008-02-05	2003-02-24	2003-02-28	ENSG00000182890	ENSG00000182890			4336	protein-coding gene	gene with protein product		300144	"glutamate dehydrogenase pseudogene 1"	GLUDP1		8207021, 9109504	Standard	NM_012084		Approved		uc004eto.3	P49448	OTTHUMG00000022320	ENST00000328078.1:c.347T>C	chrX.hg19:g.120181885T>C	ENSP00000327589:p.Leu116Pro	484.0	0.0		533.0	92.0	NM_012084	B2R8G0|Q9UDQ4	Missense_Mutation	SNP	ENST00000328078.1	hg19	CCDS14603.1	.	.	.	.	.	.	.	.	.	.	T	19.94	3.919106	0.73098	.	.	ENSG00000182890	ENST00000328078	D	0.97352	-4.35	1.61	1.61	0.23674	Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain (1);	0.000000	0.64402	D	0.000005	D	0.98585	0.9527	H	0.96604	3.85	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.97569	1.0103	10	0.87932	D	0	-3.1044	6.8732	0.24133	0.0:0.0:0.0:1.0	.	116	P49448	DHE4_HUMAN	P	116	ENSP00000327589:L116P	ENSP00000327589:L116P	L	+	2	0	GLUD2	120009566	1.000000	0.71417	0.099000	0.21106	0.459000	0.32528	5.137000	0.64789	0.925000	0.37094	0.384000	0.25694	CTG	.	.		0.647	GLUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058133.1	NM_012084		C	120181885	T	C	120181885	3	2	352	1	0	0	0	0	1	0	0	0	6485	1580	55	2	349	2	GLUD2	23	120181885	Missense_Mutation	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	421718	120181885	35088675	485	49901										
STAG2	10735	hgsc.bcm.edu	37	chrX	123191803	123191803	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gccaaccttgttaagacattGgtttttttctttctagaaag	7	7	2	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chrX:123191803G>A	ENST00000371160.1	+	15	1682	c.1392G>A	c.(1390-1392)ttG>ttA	p.L464L	STAG2_ENST00000371157.3_Silent_p.L464L|STAG2_ENST00000371144.3_Silent_p.L464L|STAG2_ENST00000371145.3_Silent_p.L464L|STAG2_ENST00000354548.5_Silent_p.L395L|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Silent_p.L464L	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	464					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						TTAAGACATTGGTTTTTTTCT	0.348																																					p.L464L		Atlas-SNP	.											.	STAG2	309	.	0			c.G1392A						.						133	120	125					X																	123191803		2203	4300	6503	SO:0001819	synonymous_variant	10735	exon15			GACATTGGTTTTT	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.1392G>A	chrX.hg19:g.123191803G>A		126.0	0.0		132.0	14.0	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Silent	SNP	ENST00000371160.1	hg19	CCDS14607.1																																																																																			.	.		0.348	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		A	123191803	G	A	123191803	2	1	352	1	0	0	0	0	0	0	0	1	15258	1339	47	3		3	STAG2	23	123191803	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	3009918	123191803	32078757	486	49902										
ODZ1	10178	hgsc.bcm.edu	37	chrX	123517731	123517731	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	taagtgtcatgatagatatcGccataaggtgtgtatagtat	10	4	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chrX:123517731G>A	ENST00000371130.3	-	29	7092	c.7029C>T	c.(7027-7029)ggC>ggT	p.G2343G	STAG2_ENST00000469481.1_Intron|TENM1_ENST00000422452.2_Silent_p.G2350G	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	2343					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										GATAGATATCGCCATAAGGTG	0.428																																					p.G2350G		Atlas-SNP	.											.	.	.	.	0			c.C7050T						.						110	100	103					X																	123517731		2203	4300	6503	SO:0001819	synonymous_variant	10178	exon30			GATATCGCCATAA	AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.7029C>T	chrX.hg19:g.123517731G>A		179.0	0.0		210.0	25.0	NM_001163278	B2RTR5|Q5JZ17	Silent	SNP	ENST00000371130.3	hg19	CCDS14609.1																																																																																			.	.		0.428	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		A	123517731	G	A	123517731	2	1	352	1	0	0	0	0	0	0	0	1	10843	1074	38	1		1	ODZ1	23	123517731	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	325928	123517731	31752829	487	49903										
OCRL	4952	hgsc.bcm.edu	37	chrX	128701327	128701327	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	agtatgactctaaaacagacCggtgggattccaggtaaagt	11	7	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chrX:128701327C>T	ENST00000371113.4	+	14	1618	c.1453C>T	c.(1453-1455)Cgg>Tgg	p.R485W	OCRL_ENST00000357121.5_Missense_Mutation_p.R485W	NM_000276.3	NP_000267.2	Q01968	OCRL_HUMAN	oculocerebrorenal syndrome of Lowe	485	5-phosphatase.				cilium assembly (GO:0042384)|in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|lipid metabolic process (GO:0006629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|Golgi-associated vesicle (GO:0005798)|nucleus (GO:0005634)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	inositol phosphate phosphatase activity (GO:0052745)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)			breast(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(24)|ovary(2)|upper_aerodigestive_tract(3)	48						TAAAACAGACCGGTGGGATTC	0.393																																					p.R485W		Atlas-SNP	.											.	OCRL	117	.	0			c.C1453T						.						70	58	62					X																	128701327		2203	4300	6503	SO:0001583	missense	4952	exon14			ACAGACCGGTGGG	U57627	CCDS35393.1, CCDS35394.1	Xq25	2014-06-18			ENSG00000122126	ENSG00000122126			8108	protein-coding gene	gene with protein product		300535					Standard	NM_001587		Approved	OCRL1	uc004euq.3	Q01968	OTTHUMG00000022706	ENST00000371113.4:c.1453C>T	chrX.hg19:g.128701327C>T	ENSP00000360154:p.Arg485Trp	469.0	0.0		518.0	161.0	NM_000276	A6NKI1|A8KAP2|B7ZLX2|O60800|Q15684|Q15774|Q4VY09|Q4VY10|Q5JQF1|Q5JQF2|Q9UJG5|Q9UMA5	Missense_Mutation	SNP	ENST00000371113.4	hg19	CCDS35393.1	.	.	.	.	.	.	.	.	.	.	C	18.44	3.623662	0.66901	.	.	ENSG00000122126	ENST00000371113;ENST00000357121	T;T	0.80738	-1.41;-1.41	5.86	3.86	0.44501	Endonuclease/exonuclease/phosphatase (2);Inositol polyphosphate-related phosphatase (1);	0.193093	0.46145	D	0.000312	D	0.89887	0.6845	M	0.89414	3.03	0.58432	D	0.999996	D;D	0.89917	1.0;0.998	D;P	0.63703	0.917;0.849	D	0.91769	0.5426	10	0.72032	D	0.01	.	14.5239	0.67873	0.2837:0.7162:0.0:0.0	.	485;485	Q01968-2;Q01968	.;OCRL_HUMAN	W	485	ENSP00000360154:R485W;ENSP00000349635:R485W	ENSP00000349635:R485W	R	+	1	2	OCRL	128529008	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.301000	0.43628	1.179000	0.42884	0.600000	0.82982	CGG	.	.		0.393	OCRL-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058917.1	NM_000276		T	128701327	C	T	128701327	3	4	352	1	0	0	0	0	1	0	0	0	10832	643	23	1	1507	1	OCRL	23	128701327	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	5183596	128701327	26569233	488	49904										
BCORL1	63035	hgsc.bcm.edu	37	chrX	129185869	129185869	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tttgcctgtgacctcctacaTaatcctcctgggagctcaga	8	13	1	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chrX:129185869T>C	ENST00000218147.7	+	12	4928	c.4731T>C	c.(4729-4731)caT>caC	p.H1577H	BCORL1_ENST00000303743.5_Silent_p.H1651H|BCORL1_ENST00000359304.2_Silent_p.H1447H|BCORL1_ENST00000540052.1_Silent_p.H1577H			Q5H9F3	BCORL_HUMAN	BCL6 corepressor-like 1	1577					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|liver(3)|lung(30)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	75						ACCTCCTACATAATCCTCCTG	0.468																																					p.H1577H		Atlas-SNP	.											.	BCORL1	213	.	0			c.T4731C						.						195	171	179					X																	129185869		2203	4300	6503	SO:0001819	synonymous_variant	63035	exon11			CCTACATAATCCT	AL136450	CCDS14616.1	Xq25-q26.1	2014-09-17	2010-06-10		ENSG00000085185	ENSG00000085185		"Ankyrin repeat domain containing"	25657	protein-coding gene	gene with protein product		300688	"chromosome X open reading frame 10", "BCL6 co-repressor-like 1"	CXorf10			Standard	NM_021946		Approved	FLJ11362	uc022cdu.1	Q5H9F3	OTTHUMG00000022379	ENST00000218147.7:c.4731T>C	chrX.hg19:g.129185869T>C		195.0	0.0		207.0	9.0	NM_021946	B5MDQ8|Q5H9F2|Q5H9F4|Q6ZVE0|Q8TEN3|Q9Y528	Silent	SNP	ENST00000218147.7	hg19	CCDS14616.1																																																																																			.	.		0.468	BCORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058223.1	NM_021946		C	129185869	T	C	129185869	2	2	352	1	0	0	0	0	0	0	0	1	1387	1403	49	2		2	BCORL1	23	129185869	Silent	SNP	T	TCGA-WQ-A9G7-01A-11D-A36X-10	484542	129185869	26084691	489	49905										
ENOX2	10495	hgsc.bcm.edu	37	chrX	129759306	129759306	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	atttaggtcagcttcaagccCtcgaagccacagaatttcca	7	12	2	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chrX:129759306C>A	ENST00000370927.1	-	13	1836	c.1815G>T	c.(1813-1815)gaG>gaT	p.E605D	ENOX2_ENST00000370935.1_Missense_Mutation_p.E576D|ENOX2_ENST00000394363.1_Missense_Mutation_p.E576D|ENOX2_ENST00000338144.3_Missense_Mutation_p.E605D			Q16206	ENOX2_HUMAN	ecto-NOX disulfide-thiol exchanger 2	605					cell growth (GO:0016049)|oxidation-reduction process (GO:0055114)|regulation of growth (GO:0040008)|ultradian rhythm (GO:0007624)	cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)	nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|protein disulfide oxidoreductase activity (GO:0015035)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(3)	33						GCTTCAAGCCCTCGAAGCCAC	0.423																																					p.E605D	Ovarian(101;828 1506 2951 9500 35258)	Atlas-SNP	.											.	ENOX2	70	.	0			c.G1815T						.						118	95	103					X																	129759306		2203	4300	6503	SO:0001583	missense	10495	exon16			CAAGCCCTCGAAG	AF207881	CCDS14626.1, CCDS14627.1	Xq25	2013-02-12	2007-03-23	2007-03-23	ENSG00000165675	ENSG00000165675		"RNA binding motif (RRM) containing"	2259	protein-coding gene	gene with protein product		300282	"cytosolic ovarian carcinoma antigen 1"	COVA1		8150545, 11888291	Standard	NM_006375		Approved	APK1, tNOX	uc004evw.3	Q16206	OTTHUMG00000022401	ENST00000370927.1:c.1815G>T	chrX.hg19:g.129759306C>A	ENSP00000359965:p.Glu605Asp	308.0	0.0		314.0	13.0	NM_182314	A8K197|A8K1C2|Q5VTJ1|Q5VTJ2|Q8WUX0|Q9NTP6|Q9UH82	Missense_Mutation	SNP	ENST00000370927.1	hg19	CCDS14626.1	.	.	.	.	.	.	.	.	.	.	C	10.63	1.404322	0.25378	.	.	ENSG00000165675	ENST00000370935;ENST00000338144;ENST00000394363;ENST00000350369;ENST00000370927	.	.	.	4.98	2.04	0.26737	.	0.199430	0.44902	D	0.000419	T	0.22898	0.0553	N	0.11427	0.14	0.34614	D	0.717876	B;B	0.10296	0.003;0.003	B;B	0.11329	0.006;0.006	T	0.08066	-1.0740	9	0.40728	T	0.16	-13.2107	3.6445	0.08180	0.1933:0.596:0.0:0.2107	.	605;633	Q16206;A4QPE1	ENOX2_HUMAN;.	D	576;605;576;633;605	.	ENSP00000337146:E605D	E	-	3	2	ENOX2	129586987	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	1.472000	0.35376	0.594000	0.29761	0.538000	0.68166	GAG	.	.		0.423	ENOX2-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058277.1	NM_182314		A	129759306	C	A	129759306	3	1	352	1	0	0	0	0	1	0	0	0	5129	680	24	3	21	3	ENOX2	23	129759306	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	573437	129759306	25511254	490	49906										
TFDP3	51270	hgsc.bcm.edu	37	chrX	132352255	132352255	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	attaagaccttgagttcttcGttagcttcagtgagactgac	9	8	2	4			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chrX:132352255G>A	ENST00000310125.4	-	1	121	c.33C>T	c.(31-33)aaC>aaT	p.N11N		NM_016521.2	NP_057605.3	Q5H9I0	TFDP3_HUMAN	transcription factor Dp family, member 3	11					cellular response to DNA damage stimulus (GO:0006974)|G1/S transition of mitotic cell cycle (GO:0000082)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(4)|large_intestine(1)|lung(8)|ovary(1)|prostate(2)	19	Acute lymphoblastic leukemia(192;0.000127)					TGAGTTCTTCGTTAGCTTCAG	0.468																																					p.N11N		Atlas-SNP	.											.	TFDP3	92	.	0			c.C33T						.						58	43	47					X																	132352255		692	1591	2283	SO:0001819	synonymous_variant	51270	exon1			TTCTTCGTTAGCT	AF219119	CCDS14636.2	Xq26.2	2009-03-25			ENSG00000183434	ENSG00000183434			24603	protein-coding gene	gene with protein product	"E2F-like protein", "cancer/testis antigen 30"	300772				12097419	Standard	NM_016521		Approved	HCA661, E2F-like, CT30	uc004exb.1	Q5H9I0	OTTHUMG00000022433	ENST00000310125.4:c.33C>T	chrX.hg19:g.132352255G>A		259.0	0.0		268.0	85.0	NM_016521	Q6DK49|Q9NZ54	Silent	SNP	ENST00000310125.4	hg19	CCDS14636.2																																																																																			.	.		0.468	TFDP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058337.1	NM_016521		A	132352255	G	A	132352255	2	1	352	1	0	0	0	0	0	0	0	1	15814	1136	40	1		1	TFDP3	23	132352255	Silent	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	2592949	132352255	22918305	491	49907										
SAGE1	55511	hgsc.bcm.edu	37	chrX	134987456	134987456	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	tgaagagaggatggaaaatgGccaatctcgaactgacaaag	12	6	1	3			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chrX:134987456G>A	ENST00000370709.3	+	4	359	c.359G>A	c.(358-360)gGc>gAc	p.G120D	SAGE1_ENST00000535938.1_Missense_Mutation_p.G120D|SAGE1_ENST00000537770.1_Missense_Mutation_p.G120D|SAGE1_ENST00000324447.3_Missense_Mutation_p.G120D			Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	120						nucleus (GO:0005634)				breast(5)|endometrium(5)|large_intestine(10)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	55	Acute lymphoblastic leukemia(192;0.000127)					ATGGAAAATGGCCAATCTCGA	0.463																																					p.G120D		Atlas-SNP	.											.	SAGE1	160	.	0			c.G359A						.						207	133	158					X																	134987456		2203	4300	6503	SO:0001583	missense	55511	exon5			AAAATGGCCAATC	AJ278111	CCDS14652.1	Xq26	2009-03-25			ENSG00000181433	ENSG00000181433			30369	protein-coding gene	gene with protein product	"cancer/testis antigen 14"	300359				10919659	Standard	NM_018666		Approved	SAGE, CT14	uc004ezh.3	Q9NXZ1	OTTHUMG00000022496	ENST00000370709.3:c.359G>A	chrX.hg19:g.134987456G>A	ENSP00000359743:p.Gly120Asp	108.0	0.0		107.0	13.0	NM_018666	Q5JNW0	Missense_Mutation	SNP	ENST00000370709.3	hg19	CCDS14652.1	.	.	.	.	.	.	.	.	.	.	G	6.879	0.531693	0.13127	.	.	ENSG00000181433	ENST00000324447;ENST00000535938;ENST00000537770;ENST00000370709	T;T;T;T	0.52295	0.67;0.67;1.5;0.67	1.32	1.32	0.21799	.	0.219686	0.28927	U	0.013700	T	0.44159	0.1280	N	0.19112	0.55	0.18873	N	0.999987	B;D	0.76494	0.002;0.999	B;D	0.74023	0.017;0.982	T	0.15838	-1.0423	10	0.31617	T	0.26	.	5.5445	0.17055	0.0:0.0:1.0:0.0	.	120;120	F5H2Z8;Q9NXZ1	.;SAGE1_HUMAN	D	120	ENSP00000323191:G120D;ENSP00000445959:G120D;ENSP00000438276:G120D;ENSP00000359743:G120D	ENSP00000323191:G120D	G	+	2	0	SAGE1	134815122	0.648000	0.27313	0.522000	0.27862	0.066000	0.16364	0.286000	0.18902	0.932000	0.37266	0.284000	0.19432	GGC	.	.		0.463	SAGE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058448.1	NM_018666		A	134987456	G	A	134987456	3	1	352	1	0	0	0	0	1	0	0	0	13824	1203	42	3	373	3	SAGE1	23	134987456	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	2635201	134987456	20283104	492	49908										
GPR112	139378	hgsc.bcm.edu	37	chrX	135431189	135431189	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	cccatctctgactagctttaAgagtgcttctggacccacaa	7	13	2	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chrX:135431189A>G	ENST00000394143.1	+	6	5615	c.5324A>G	c.(5323-5325)aAg>aGg	p.K1775R	GPR112_ENST00000412101.1_Missense_Mutation_p.K1570R|GPR112_ENST00000370652.1_Missense_Mutation_p.K1775R|GPR112_ENST00000394141.1_Missense_Mutation_p.K1570R|GPR112_ENST00000287534.4_Missense_Mutation_p.K1712R	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	1775					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					ACTAGCTTTAAGAGTGCTTCT	0.373																																					p.K1775R		Atlas-SNP	.											.	GPR112	459	.	0			c.A5324G						.						156	148	151					X																	135431189		2203	4300	6503	SO:0001583	missense	139378	exon6			GCTTTAAGAGTGC	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"-", "GPCR / Class B : Orphans"	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.5324A>G	chrX.hg19:g.135431189A>G	ENSP00000377699:p.Lys1775Arg	293.0	0.0		339.0	94.0	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	hg19	CCDS35409.1	.	.	.	.	.	.	.	.	.	.	a	16.58	3.163536	0.57476	.	.	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.32272	1.5;1.5;1.46;1.59;1.46	3.57	-2.58	0.06228	.	.	.	.	.	T	0.18173	0.0436	L	0.34521	1.04	0.09310	N	1	P;P;P	0.50819	0.939;0.879;0.849	P;B;B	0.48063	0.565;0.308;0.239	T	0.17501	-1.0367	9	0.07175	T	0.84	.	1.1328	0.01749	0.2965:0.385:0.1281:0.1904	.	1712;1570;1775	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	R	1775;1775;1570;1712;1570	ENSP00000377699:K1775R;ENSP00000359686:K1775R;ENSP00000416526:K1570R;ENSP00000287534:K1712R;ENSP00000377697:K1570R	ENSP00000287534:K1712R	K	+	2	0	GPR112	135258855	0.000000	0.05858	0.001000	0.08648	0.375000	0.29983	0.064000	0.14437	-0.112000	0.11979	0.372000	0.22366	AAG	.	.		0.373	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1			G	135431189	A	G	135431189	3	3	352	1	0	0	0	0	1	0	0	0	6637	72	3	2	5334	2	GPR112	23	135431189	Missense_Mutation	SNP	A	TCGA-WQ-A9G7-01A-11D-A36X-10	443733	135431189	19839371	493	49909										
ZIC3	7547	hgsc.bcm.edu	37	chrX	136648912	136648912	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	gggagtgggcagcttcggcgCgccgcgccaccacgagatgc	17	14	0	1			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chrX:136648912C>T	ENST00000287538.5	+	1	612	c.62C>T	c.(61-63)gCg>gTg	p.A21V	RP1-137H15.2_ENST00000442841.1_RNA|RP1-137H15.2_ENST00000456631.1_RNA|ZIC3_ENST00000370606.3_Missense_Mutation_p.A21V	NM_003413.3	NP_003404.1	O60481	ZIC3_HUMAN	Zic family member 3	21					anterior/posterior pattern specification (GO:0009952)|cell differentiation (GO:0030154)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of left/right asymmetry in nervous system (GO:0035545)|determination of left/right symmetry (GO:0007368)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|heart looping (GO:0001947)|lung development (GO:0030324)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|large_intestine(3)|liver(1)|lung(18)|ovary(3)|soft_tissue(2)|urinary_tract(1)	37	Acute lymphoblastic leukemia(192;0.000127)					AGCTTCGGCGCGCCGCGCCAC	0.726																																					p.A21V		Atlas-SNP	.											.	ZIC3	93	.	0			c.C62T						.						11	10	10					X																	136648912		2175	4270	6445	SO:0001583	missense	7547	exon1			TCGGCGCGCCGCG	AF028706	CCDS14663.1	Xq24-q27.1	2013-01-08	2011-05-19		ENSG00000156925	ENSG00000156925		"Zinc fingers, C2H2-type"	12874	protein-coding gene	gene with protein product		300265	"heterotaxy 1", "Zic family member 3 (odd-paired homolog, Drosophila)"	HTX1		8298651, 7747776	Standard	NM_003413		Approved	HTX, ZNF203	uc004fak.3	O60481	OTTHUMG00000022525	ENST00000287538.5:c.62C>T	chrX.hg19:g.136648912C>T	ENSP00000287538:p.Ala21Val	126.0	0.0		151.0	16.0	NM_003413	B2CNW4|Q14DE5|Q5JY75	Missense_Mutation	SNP	ENST00000287538.5	hg19	CCDS14663.1	.	.	.	.	.	.	.	.	.	.	c	14.71	2.616537	0.46736	.	.	ENSG00000156925	ENST00000287538;ENST00000370606	T;T	0.11930	2.73;2.78	3.97	3.97	0.46021	.	0.060777	0.64402	D	0.000004	T	0.06735	0.0172	N	0.14661	0.345	0.32859	D	0.507747	P	0.35226	0.491	B	0.25405	0.06	T	0.23547	-1.0185	10	0.18710	T	0.47	.	12.7167	0.57119	0.0:1.0:0.0:0.0	.	21	O60481	ZIC3_HUMAN	V	21	ENSP00000287538:A21V;ENSP00000359638:A21V	ENSP00000287538:A21V	A	+	2	0	ZIC3	136476578	0.871000	0.30034	1.000000	0.80357	0.981000	0.71138	5.664000	0.68045	1.847000	0.53656	0.525000	0.51046	GCG	.	.		0.726	ZIC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058526.1			T	136648912	C	T	136648912	3	4	352	1	0	0	0	0	1	0	0	0	17695	768	27	1	64	1	ZIC3	23	136648912	Missense_Mutation	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	1217723	136648912	18621648	494	49910										
SOX3	6658	hgsc.bcm.edu	37	chrX	139586440	139586440	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ttggcccagccgttcacgtgCgtgtacgtgtccaggcgctg	14	13	1	0			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chrX:139586440C>T	ENST00000370536.2	-	1	785	c.786G>A	c.(784-786)acG>acA	p.T262T		NM_005634.2	NP_005625.2	P41225	SOX3_HUMAN	SRY (sex determining region Y)-box 3	262					central nervous system development (GO:0007417)|face development (GO:0060324)|hypothalamus development (GO:0021854)|negative regulation of neuron differentiation (GO:0045665)|neuron development (GO:0048666)|organ morphogenesis (GO:0009887)|pituitary gland development (GO:0021983)|sensory organ development (GO:0007423)|Sertoli cell development (GO:0060009)|sex determination (GO:0007530)|spermatid differentiation (GO:0048515)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|pancreas(1)|skin(1)	10	Acute lymphoblastic leukemia(192;7.65e-05)					CGTTCACGTGCGTGTACGTGT	0.786																																					p.T262T		Atlas-SNP	.											.	SOX3	44	.	0			c.G786A						.						4	4	4					X																	139586440		1398	2852	4250	SO:0001819	synonymous_variant	6658	exon1			CACGTGCGTGTAC		CCDS14669.1	Xq27.1	2013-10-17			ENSG00000134595	ENSG00000134595		"SRY (sex determining region Y)-boxes"	11199	protein-coding gene	gene with protein product		313430	"panhypopituitarism"	PHP		15800844	Standard	NM_005634		Approved		uc004fbd.1	P41225	OTTHUMG00000022544	ENST00000370536.2:c.786G>A	chrX.hg19:g.139586440C>T		160.0	0.0		168.0	21.0	NM_005634	P35714|Q5JWI3|Q9NP49	Silent	SNP	ENST00000370536.2	hg19	CCDS14669.1																																																																																			.	.		0.786	SOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058577.1			T	139586440	C	T	139586440	2	4	352	1	0	0	0	0	0	0	0	1	14966	755	27	1		1	SOX3	23	139586440	Silent	SNP	C	TCGA-WQ-A9G7-01A-11D-A36X-10	2937528	139586440	15684120	495	49911										
SLITRK4	139065	hgsc.bcm.edu	37	chrX	142717165	142717165	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	ggcttgtgaatggtgcagacGgcttatttaaaagtttggga	14	4	0	2			TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chrX:142717165G>A	ENST00000381779.4	-	2	1985	c.1760C>T	c.(1759-1761)cCg>cTg	p.P587L	SLITRK4_ENST00000338017.4_Missense_Mutation_p.P587L|SLITRK4_ENST00000356928.1_Missense_Mutation_p.P587L	NM_001184749.2|NM_001184750.1|NM_173078.4	NP_001171678.1|NP_001171679.1|NP_775101.1	Q8IW52	SLIK4_HUMAN	SLIT and NTRK-like family, member 4	587						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(27)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	60	Acute lymphoblastic leukemia(192;6.56e-05)					TGGTGCAGACGGCTTATTTAA	0.453																																					p.P587L		Atlas-SNP	.											.	SLITRK4	162	.	0			c.C1760T						.						109	110	109					X																	142717165		2203	4300	6503	SO:0001583	missense	139065	exon2			GCAGACGGCTTAT	BC040986	CCDS14679.1	Xq27.3	2004-06-23			ENSG00000179542	ENSG00000179542			23502	protein-coding gene	gene with protein product		300562				14557068	Standard	NM_001184749		Approved	DKFZp547M2010	uc004fby.3	Q8IW52	OTTHUMG00000022580	ENST00000381779.4:c.1760C>T	chrX.hg19:g.142717165G>A	ENSP00000371198:p.Pro587Leu	145.0	0.0		180.0	20.0	NM_001184750	Q5JXG3|Q8TCM8|Q96DL3	Missense_Mutation	SNP	ENST00000381779.4	hg19	CCDS14679.1	.	.	.	.	.	.	.	.	.	.	G	10.44	1.350036	0.24426	.	.	ENSG00000179542	ENST00000381779;ENST00000356928;ENST00000338017	T;T;T	0.56611	0.45;0.45;0.45	5.71	4.85	0.62838	.	0.060395	0.64402	U	0.000002	T	0.42359	0.1199	L	0.36672	1.1	0.80722	D	1	B	0.17852	0.024	B	0.14578	0.011	T	0.20075	-1.0286	10	0.28530	T	0.3	-5.1881	12.7043	0.57051	0.0818:0.0:0.9182:0.0	.	587	Q8IW52	SLIK4_HUMAN	L	587	ENSP00000371198:P587L;ENSP00000349400:P587L;ENSP00000336627:P587L	ENSP00000336627:P587L	P	-	2	0	SLITRK4	142544831	1.000000	0.71417	0.996000	0.52242	0.889000	0.51656	5.513000	0.67037	1.179000	0.42884	-0.190000	0.12839	CCG	.	.		0.453	SLITRK4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058617.1	NM_173078		A	142717165	G	A	142717165	3	1	352	1	0	0	0	0	1	0	0	0	14760	1116	39	1	757	1	SLITRK4	23	142717165	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	3130725	142717165	12553395	496	49912										
MTMR1	8776	hgsc.bcm.edu	37	chrX	149931129	149931129	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0140845070422535	7	1	0.234133831847378	0.98856506780004	0.20771406093853	0.0291375291375292	0.304738562091504	0	acagcgggaggtggccacgcGcgccgtctcatcctcatctg	13	15	3	0	rs200100741		TCGA-WQ-A9G7-01A-11D-A36X-10	TCGA-WQ-A9G7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b21e6c1-c220-41e9-b999-323e7bd7079a	60cdfad5-5cd4-4b7e-964b-b6e042e046da	g.chrX:149931129G>A	ENST00000370390.3	+	15	2082	c.1925G>A	c.(1924-1926)cGc>cAc	p.R642H	MTMR1_ENST00000544228.1_Missense_Mutation_p.R642H|MTMR1_ENST00000445323.2_Missense_Mutation_p.R650H|MTMR1_ENST00000541925.1_Missense_Mutation_p.R548H|MTMR1_ENST00000538506.1_Intron	NM_003828.2	NP_003819.1	Q13613	MTMR1_HUMAN	myotubularin related protein 1	642					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(5)|ovary(2)|prostate(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					GTGGCCACGCGCGCCGTCTCA	0.667																																					p.R642H		Atlas-SNP	.											.	MTMR1	82	.	0			c.G1925A						.						62	56	58					X																	149931129		2203	4300	6503	SO:0001583	missense	8776	exon15			CCACGCGCGCCGT	U58032	CCDS14695.1	Xq28	2011-06-09			ENSG00000063601	ENSG00000063601		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7449	protein-coding gene	gene with protein product		300171				9828128	Standard	XM_005274765		Approved		uc004fei.3	Q13613	OTTHUMG00000024159	ENST00000370390.3:c.1925G>A	chrX.hg19:g.149931129G>A	ENSP00000359417:p.Arg642His	151.0	0.0		175.0	53.0	NM_003828	A0A024RC07|Q9UBX6|Q9UEM0|Q9UQD5	Missense_Mutation	SNP	ENST00000370390.3	hg19	CCDS14695.1	.	.	.	.	.	.	.	.	.	.	G	13.86	2.364218	0.41902	.	.	ENSG00000063601	ENST00000541925;ENST00000370390;ENST00000445323;ENST00000544228	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	5.14	5.14	0.70334	.	0.186575	0.44902	D	0.000420	T	0.44074	0.1276	L	0.60455	1.87	0.80722	D	1	B;B	0.32543	0.109;0.375	B;B	0.32583	0.041;0.148	T	0.46289	-0.9202	10	0.56958	D	0.05	.	17.8016	0.88589	0.0:0.0:1.0:0.0	.	642;650	Q13613;F8WA39	MTMR1_HUMAN;.	H	548;642;650;642	ENSP00000441879:R548H;ENSP00000359417:R642H;ENSP00000414178:R650H;ENSP00000440534:R642H	ENSP00000359417:R642H	R	+	2	0	MTMR1	149681787	1.000000	0.71417	0.110000	0.21437	0.015000	0.08874	4.791000	0.62460	2.134000	0.65973	0.529000	0.55759	CGC	.	.		0.667	MTMR1-013	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060863.2	NM_003828, NM_176789		A	149931129	G	A	149931129	3	1	352	1	0	0	0	0	1	0	0	0	9947	1087	38	1	1983	1	MTMR1	23	149931129	Missense_Mutation	SNP	G	TCGA-WQ-A9G7-01A-11D-A36X-10	7213964	149931129	5339431	497	49913										
PHF13	148479	hgsc.bcm.edu	37	chr1	6681657	6681657	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	gtttgacatccgccgttccaAccgctcgcggacgggctccc	11	17	0	1			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr1:6681657A>G	ENST00000377648.4	+	4	1245	c.863A>G	c.(862-864)aAc>aGc	p.N288S	PHF13_ENST00000495385.1_Intron	NM_153812.2	NP_722519.2	Q86YI8	PHF13_HUMAN	PHD finger protein 13	288					chromatin modification (GO:0016568)|chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(1)|lung(3)	7	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;1.46e-33)|all_epithelial(116;9.26e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Breast(487;0.000353)|Renal(390;0.0007)|Colorectal(325;0.00104)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443)		Colorectal(212;1.19e-07)|COAD - Colon adenocarcinoma(227;1.3e-05)|Kidney(185;4.88e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000501)|KIRC - Kidney renal clear cell carcinoma(229;0.000871)|STAD - Stomach adenocarcinoma(132;0.0165)|READ - Rectum adenocarcinoma(331;0.0642)		CGCCGTTCCAACCGCTCGCGG	0.587																																					p.N288S		Atlas-SNP	.											.	PHF13	24	.	0			c.A863G						.						49	47	47					1																	6681657		2203	4300	6503	SO:0001583	missense	148479	exon4			GTTCCAACCGCTC	AK027492	CCDS85.1	1p36.23	2013-01-28			ENSG00000116273	ENSG00000116273		"Zinc fingers, PHD-type"	22983	protein-coding gene	gene with protein product							Standard	NM_153812		Approved	MGC43399	uc001aob.4	Q86YI8	OTTHUMG00000001439	ENST00000377648.4:c.863A>G	chr1.hg19:g.6681657A>G	ENSP00000366876:p.Asn288Ser	156.0	0.0		110.0	6.0	NM_153812	B3KUQ7|Q59FB6|Q5TH65|Q8N551|Q9UJP2	Missense_Mutation	SNP	ENST00000377648.4	hg19	CCDS85.1	.	.	.	.	.	.	.	.	.	.	A	15.31	2.794796	0.50102	.	.	ENSG00000116273	ENST00000377648	T	0.46819	0.86	5.66	3.33	0.38152	Zinc finger, FYVE/PHD-type (1);	0.251869	0.45606	N	0.000345	T	0.30135	0.0755	N	0.24115	0.695	0.51482	D	0.999924	B	0.02656	0.0	B	0.04013	0.001	T	0.05099	-1.0906	10	0.27082	T	0.32	31.1691	8.5183	0.33259	0.8345:0.0:0.1655:0.0	.	288	Q86YI8	PHF13_HUMAN	S	288	ENSP00000366876:N288S	ENSP00000366876:N288S	N	+	2	0	PHF13	6604244	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.168000	0.58216	0.419000	0.25927	0.533000	0.62120	AAC	.	.		0.587	PHF13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004201.1	NM_153812		G	6681657	A	G	6681657	3	3	353	1	0	0	0	0	1	0	0	0	11833	43	2	2	877	2	PHF13	1	6681657	Missense_Mutation	SNP	A	TCGA-WQ-AB4B-01A-11D-A40P-10		6681657	242568964	1	49914										
FBXO2	26232	hgsc.bcm.edu	37	chr1	11710798	11710798	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	acgcggcggcggccgccgccTcctcctcctgctggtcctcc	12	21	0	0			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr1:11710798T>G	ENST00000354287.4	-	2	457	c.116A>C	c.(115-117)gAg>gCg	p.E39A	FBXO2_ENST00000475961.1_5'UTR	NM_012168.5	NP_036300.2	Q9UK22	FBX2_HUMAN	F-box protein 2	39					cellular protein modification process (GO:0006464)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glycoprotein catabolic process (GO:0006516)|negative regulation of cell proliferation (GO:0008285)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of protein ubiquitination (GO:0031396)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	cytosol (GO:0005829)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|SCF ubiquitin ligase complex (GO:0019005)	beta-amyloid binding (GO:0001540)|carbohydrate binding (GO:0030246)|ubiquitin-protein transferase activity (GO:0004842)			kidney(1)|large_intestine(1)|lung(4)	6	Ovarian(185;0.249)	Lung NSC(185;9.37e-06)|all_lung(284;1.39e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|BRCA - Breast invasive adenocarcinoma(304;1.88e-06)|Colorectal(212;4.88e-06)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|Lung(427;0.0146)|LUSC - Lung squamous cell carcinoma(448;0.0228)|READ - Rectum adenocarcinoma(331;0.0649)		GGccgccgcctcctcctcctg	0.761																																					p.E39A		Atlas-SNP	.											FBXO2,NS,carcinoma,0,1	FBXO2	25	.	0			c.A116C						.						2	2	2					1																	11710798		1686	3300	4986	SO:0001583	missense	26232	exon2			GCCGCCTCCTCCT	AF174594	CCDS130.1	1p36.21	2010-04-21	2004-06-15		ENSG00000116661	ENSG00000116661		"F-boxes /  "other""	13581	protein-coding gene	gene with protein product		607112	"F-box only protein 2", "organ of Corti protein 1"	OCP1		10531035, 10531037	Standard	NM_012168		Approved	FBX2, Nfb42, Fbs1, Fbg1	uc001asj.3	Q9UK22	OTTHUMG00000002072	ENST00000354287.4:c.116A>C	chr1.hg19:g.11710798T>G	ENSP00000346240:p.Glu39Ala	25.0	0.0		16.0	2.0	NM_012168	B2R7K7|Q5TGY0|Q6FGJ7|Q8TB29|Q9UKC6	Missense_Mutation	SNP	ENST00000354287.4	hg19	CCDS130.1	.	.	.	.	.	.	.	.	.	.	T	7.272	0.607315	0.14002	.	.	ENSG00000116661	ENST00000354287;ENST00000452872	T	0.25579	1.79	4.36	-8.72	0.00845	F-box domain, Skp2-like (1);	0.961229	0.08522	N	0.933284	T	0.08670	0.0215	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.35450	-0.9788	10	0.14252	T	0.57	-18.8732	7.4313	0.27128	0.1044:0.0755:0.6098:0.2103	.	39;39	A6NNP0;Q9UK22	.;FBX2_HUMAN	A	39	ENSP00000346240:E39A	ENSP00000346240:E39A	E	-	2	0	FBXO2	11633385	0.000000	0.05858	0.000000	0.03702	0.077000	0.17291	-0.403000	0.07214	-1.473000	0.01881	0.454000	0.30748	GAG	.	.		0.761	FBXO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005764.1	NM_012168		G	11710798	T	G	11710798	3	3	353	1	0	0	0	0	1	0	0	0	5740	1551	54	5	794	5	FBXO2	1	11710798	Missense_Mutation	SNP	T	TCGA-WQ-AB4B-01A-11D-A40P-10	5029141	11710798	237539823	2	49915										
TNFRSF8	943	hgsc.bcm.edu	37	chr1	12169683	12169683	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	aggggtcagccctgcctgtgCcagcccagagaactgcaagg	14	13	1	1			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr1:12169683C>T	ENST00000263932.2	+	5	704	c.482C>T	c.(481-483)gCc>gTc	p.A161V	TNFRSF8_ENST00000417814.2_Missense_Mutation_p.A50V	NM_001243.3|NM_001281430.1	NP_001234.2|NP_001268359.1	P28908	TNR8_HUMAN	tumor necrosis factor receptor superfamily, member 8	161					cellular response to mechanical stimulus (GO:0071260)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of TRAIL biosynthetic process (GO:0045556)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	27	Ovarian(185;0.249)	Lung NSC(185;8.71e-05)|all_lung(284;9.89e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Brentuximab vedotin(DB08870)	CCTGCCTGTGCCAGCCCAGAG	0.637																																					p.A161V		Atlas-SNP	.											.	TNFRSF8	70	.	0			c.C482T						.						48	50	49					1																	12169683		2203	4300	6503	SO:0001583	missense	943	exon5			CCTGTGCCAGCCC	M83554	CCDS144.1, CCDS59989.1	1p36	2008-02-05			ENSG00000120949	ENSG00000120949		"Tumor necrosis factor receptor superfamily", "CD molecules"	11923	protein-coding gene	gene with protein product		153243		CD30, D1S166E		1330892, 1310894	Standard	XM_006711049		Approved	KI-1	uc001atq.3	P28908	OTTHUMG00000001827	ENST00000263932.2:c.482C>T	chr1.hg19:g.12169683C>T	ENSP00000263932:p.Ala161Val	85.0	0.0		68.0	4.0	NM_001243	B1AN79|B9EGD9|D3YTD8|Q6P4D9	Missense_Mutation	SNP	ENST00000263932.2	hg19	CCDS144.1	.	.	.	.	.	.	.	.	.	.	.	14.55	2.568433	0.45798	.	.	ENSG00000120949	ENST00000263932;ENST00000417814	T;T	0.08282	3.11;3.11	3.86	2.93	0.34026	.	1.566950	0.03490	N	0.216408	T	0.11537	0.0281	L	0.36672	1.1	0.21184	N	0.999767	P;B	0.38300	0.626;0.437	B;B	0.40782	0.34;0.115	T	0.36016	-0.9765	10	0.54805	T	0.06	-2.817	9.6714	0.40015	0.0:0.7892:0.2108:0.0	.	50;161	D3YTD8;P28908	.;TNR8_HUMAN	V	161;50	ENSP00000263932:A161V;ENSP00000390650:A50V	ENSP00000263932:A161V	A	+	2	0	TNFRSF8	12092270	0.006000	0.16342	0.473000	0.27253	0.159000	0.22180	0.332000	0.19751	1.158000	0.42547	0.563000	0.77884	GCC	.	.		0.637	TNFRSF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005130.1			T	12169683	C	T	12169683	3	4	353	1	0	0	0	0	1	0	0	0	16314	739	26	3	500	3	TNFRSF8	1	12169683	Missense_Mutation	SNP	C	TCGA-WQ-AB4B-01A-11D-A40P-10	458885	12169683	237080938	3	49916										
PADI2	11240	hgsc.bcm.edu	37	chr1	17410314	17410314	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	ttcttcacctctttcaggaaCaggtaattatccttcatgct	5	11	5	0	rs141844952		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr1:17410314C>T	ENST00000375486.4	-	9	1020	c.957G>A	c.(955-957)ctG>ctA	p.L319L	PADI2_ENST00000466151.1_5'Flank|PADI2_ENST00000375481.1_Silent_p.L319L|PADI2_ENST00000444885.2_Silent_p.L203L	NM_007365.2	NP_031391.2	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II	319					chromatin-mediated maintenance of transcription (GO:0048096)|histone H3-R26 citrullination (GO:0036413)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of lymphocyte chemotaxis (GO:1901624)|protein citrullination (GO:0018101)|regulation of chromatin disassembly (GO:0010848)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptionally active chromatin (GO:0035327)	calcium ion binding (GO:0005509)|estrogen receptor binding (GO:0030331)|protein-arginine deiminase activity (GO:0004668)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(12)|ovary(4)|pancreas(1)|skin(5)|urinary_tract(3)	29		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)	L-Citrulline(DB00155)	CTTTCAGGAACAGGTAATTAT	0.522																																					p.L319L		Atlas-SNP	.											.	PADI2	72	.	0			c.G957A						.	C		1,4405	2.1+/-5.4	0,1,2202	116	112	114		957	3.8	1	1	dbSNP_134	114	0,8600		0,0,4300	no	coding-synonymous	PADI2	NM_007365.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		319/666	17410314	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	11240	exon9			CAGGAACAGGTAA	AB030176	CCDS177.1	1p35.2-p35.1	2008-02-05			ENSG00000117115	ENSG00000117115	3.5.3.15	"Peptidyl arginine deiminases"	18341	protein-coding gene	gene with protein product		607935				2768262	Standard	NM_007365		Approved	KIAA0994, PDI2	uc001baf.3	Q9Y2J8	OTTHUMG00000002295	ENST00000375486.4:c.957G>A	chr1.hg19:g.17410314C>T		93.0	0.0		67.0	30.0	NM_007365	Q96DA7|Q9UPN2	Silent	SNP	ENST00000375486.4	hg19	CCDS177.1																																																																																			.	C|1.000;T|0.000		0.522	PADI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006624.1			T	17410314	C	T	17410314	2	4	353	1	0	0	0	0	0	0	0	1	11387	465	17	3		3	PADI2	1	17410314	Silent	SNP	C	TCGA-WQ-AB4B-01A-11D-A40P-10	5240631	17410314	231840307	4	49917										
IPP	3652	hgsc.bcm.edu	37	chr1	46195357	46195357	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	tctgcagaaaactacaaaacTtgttctctttgggagatttg	8	7	2	2			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr1:46195357T>G	ENST00000396478.3	-	4	911	c.809A>C	c.(808-810)aAg>aCg	p.K270T		NM_005897.2	NP_005888.1	Q9Y573	IPP_HUMAN	intracisternal A particle-promoted polypeptide	270						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	actin binding (GO:0003779)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|stomach(2)	20	Acute lymphoblastic leukemia(166;0.155)					ACTACAAAACTTGTTCTCTTT	0.368																																					p.K270T		Atlas-SNP	.											.	IPP	66	.	0			c.A809C						.						115	118	117					1																	46195357		2203	4300	6503	SO:0001583	missense	3652	exon4			CAAAACTTGTTCT	BC032544	CCDS30702.1, CCDS44132.1	1p34-p32	2013-01-30			ENSG00000197429	ENSG00000197429		"Kelch-like", "BTB/POZ domain containing"	6108	protein-coding gene	gene with protein product	"kelch-like family member 27"	147485				1905535, 8432546	Standard	NM_005897		Approved	KLHL27	uc001cou.3	Q9Y573	OTTHUMG00000008004	ENST00000396478.3:c.809A>C	chr1.hg19:g.46195357T>G	ENSP00000379739:p.Lys270Thr	294.0	0.0		247.0	52.0	NM_001145349	A2A6V4|D3DQ11|Q8N5C3	Missense_Mutation	SNP	ENST00000396478.3	hg19	CCDS30702.1	.	.	.	.	.	.	.	.	.	.	T	13.72	2.322093	0.41096	.	.	ENSG00000197429	ENST00000359942;ENST00000396478	T;T	0.74526	-0.67;-0.85	5.67	2.99	0.34606	.	0.193743	0.52532	D	0.000068	T	0.53706	0.1813	N	0.08118	0	0.50467	D	0.999871	B;B	0.28713	0.04;0.22	B;B	0.30495	0.066;0.116	T	0.55347	-0.8155	10	0.72032	D	0.01	.	9.1481	0.36946	0.0:0.0737:0.1264:0.7998	.	270;270	Q9Y573;A2A6V3	IPP_HUMAN;.	T	270	ENSP00000353024:K270T;ENSP00000379739:K270T	ENSP00000353024:K270T	K	-	2	0	IPP	45967944	1.000000	0.71417	0.995000	0.50966	0.669000	0.39330	4.668000	0.61568	0.965000	0.38133	0.459000	0.35465	AAG	.	.		0.368	IPP-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021974.3	NM_005897		G	46195357	T	G	46195357	3	3	353	1	0	0	0	0	1	0	0	0	7809	1609	56	5	1071	5	IPP	1	46195357	Missense_Mutation	SNP	T	TCGA-WQ-AB4B-01A-11D-A40P-10	28785043	46195357	203055264	5	49918										
CA14	23632	hgsc.bcm.edu	37	chr1	150235583	150235583	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	gttttttatagaaggtcccaGatttcaatggaacaggtaag	10	5	1	2			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr1:150235583G>T	ENST00000369111.4	+	7	1675	c.705G>T	c.(703-705)caG>caT	p.Q235H	snoU13_ENST00000458929.1_RNA	NM_012113.1	NP_036245.1	Q9ULX7	CAH14_HUMAN	carbonic anhydrase XIV	235					bicarbonate transport (GO:0015701)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbonate dehydratase activity (GO:0004089)|metal ion binding (GO:0046872)			central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(2)|prostate(2)	18	Lung NSC(24;7.29e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)		Acetazolamide(DB00819)|Zonisamide(DB00909)	GAAGGTCCCAGATTTCAATGG	0.517																																					p.Q235H		Atlas-SNP	.											.	CA14	37	.	0			c.G705T						.						85	89	88					1																	150235583		2203	4300	6503	SO:0001583	missense	23632	exon7			GTCCCAGATTTCA	AB025904	CCDS947.1	1q21	2008-02-05			ENSG00000118298	ENSG00000118298		"Carbonic anhydrases"	1372	protein-coding gene	gene with protein product		604832				10512682	Standard	XM_005245059		Approved		uc001etx.3	Q9ULX7	OTTHUMG00000012549	ENST00000369111.4:c.705G>T	chr1.hg19:g.150235583G>T	ENSP00000358107:p.Gln235His	165.0	0.0		211.0	11.0	NM_012113	Q5TB24|Q8NCF4	Missense_Mutation	SNP	ENST00000369111.4	hg19	CCDS947.1	.	.	.	.	.	.	.	.	.	.	G	11.64	1.699784	0.30142	.	.	ENSG00000118298	ENST00000369111	T	0.67865	-0.29	5.65	3.73	0.42828	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.181255	0.50627	D	0.000107	T	0.64114	0.2569	L	0.46885	1.475	0.42869	D	0.994131	D	0.69078	0.997	P	0.61874	0.895	T	0.67515	-0.5651	10	0.62326	D	0.03	.	12.0904	0.53722	0.0724:0.1231:0.8045:0.0	.	235	Q9ULX7	CAH14_HUMAN	H	235	ENSP00000358107:Q235H	ENSP00000358107:Q235H	Q	+	3	2	CA14	148502207	1.000000	0.71417	1.000000	0.80357	0.099000	0.18886	0.766000	0.26560	0.459000	0.27016	-0.797000	0.03246	CAG	.	.		0.517	CA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035064.2	NM_012113		T	150235583	G	T	150235583	3	4	353	1	0	0	0	0	1	0	0	0	2517	933	33	3	731	3	CA14	1	150235583	Missense_Mutation	SNP	G	TCGA-WQ-AB4B-01A-11D-A40P-10	104040226	150235583	99015038	6	49919										
TADA1	117143	hgsc.bcm.edu	37	chr1	166826920	166826920	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	gatcctttcaatgttaagagCatagacagtatgtgtaggga	11	5	1	2			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr1:166826920C>G	ENST00000367874.4	-	8	985	c.892G>C	c.(892-894)Gct>Cct	p.A298P	TADA1_ENST00000467021.1_5'UTR	NM_053053.3	NP_444281.1	Q96BN2	TADA1_HUMAN	transcriptional adaptor 1	298					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|STAGA complex (GO:0030914)	transcription coactivator activity (GO:0003713)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	11						ATGTTAAGAGCATAGACAGTA	0.428																																					p.A298P		Atlas-SNP	.											.	TADA1	32	.	0			c.G892C						.						144	142	142					1																	166826920		2203	4300	6503	SO:0001583	missense	117143	exon8			TAAGAGCATAGAC	BC015401	CCDS1255.1	1q24.1	2009-10-02	2009-10-02	2009-10-02	ENSG00000152382	ENSG00000152382			30631	protein-coding gene	gene with protein product		612763	"transcriptional adaptor 1 (HFI1 homolog, yeast)-like", "transcriptional adaptor 1 (HFI1 homolog, yeast)"	TADA1L		11564863	Standard	NM_053053		Approved	STAF42, ADA1, hADA1, HFI1	uc001gdw.3	Q96BN2	OTTHUMG00000034321	ENST00000367874.4:c.892G>C	chr1.hg19:g.166826920C>G	ENSP00000356848:p.Ala298Pro	152.0	0.0		172.0	59.0	NM_053053	A8K4J9	Missense_Mutation	SNP	ENST00000367874.4	hg19	CCDS1255.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.803470	0.90623	.	.	ENSG00000152382	ENST00000367874	T	0.51817	0.69	4.53	4.53	0.55603	.	0.000000	0.85682	D	0.000000	T	0.56906	0.2017	M	0.65498	2.005	0.48087	D	0.999580	D	0.69078	0.997	D	0.63597	0.916	T	0.62525	-0.6836	9	0.66056	D	0.02	-8.9363	15.1518	0.72706	0.0:1.0:0.0:0.0	.	298	Q96BN2	TADA1_HUMAN	P	298	ENSP00000356848:A298P	ENSP00000356848:A298P	A	-	1	0	TADA1	165093544	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	7.182000	0.77689	2.486000	0.83907	0.655000	0.94253	GCT	.	.		0.428	TADA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082881.1	NM_053053		G	166826920	C	G	166826920	3	3	353	1	0	0	0	0	1	0	0	0	15524	710	25	4	119	4	TADA1	1	166826920	Missense_Mutation	SNP	C	TCGA-WQ-AB4B-01A-11D-A40P-10	16591337	166826920	82423701	7	49920										
HMCN1	83872	hgsc.bcm.edu	37	chr1	186047303	186047303	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	gggagatacacatgtgtggcTgtgaatgaggctggagaaga	17	4	0	5			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr1:186047303T>A	ENST00000271588.4	+	55	8779	c.8550T>A	c.(8548-8550)gcT>gcA	p.A2850A	HMCN1_ENST00000367492.2_Silent_p.A2850A	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2850	Ig-like C2-type 26.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						CATGTGTGGCTGTGAATGAGG	0.398																																					p.A2850A		Atlas-SNP	.											.	HMCN1	797	.	0			c.T8550A						.						225	210	215					1																	186047303		2203	4300	6503	SO:0001819	synonymous_variant	83872	exon55			TGTGGCTGTGAAT	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.8550T>A	chr1.hg19:g.186047303T>A		179.0	0.0		214.0	32.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	hg19	CCDS30956.1																																																																																			.	.		0.398	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		A	186047303	T	A	186047303	2	1	353	1	0	0	0	0	0	0	0	1	7229	1567	55	4		4	HMCN1	1	186047303	Silent	SNP	T	TCGA-WQ-AB4B-01A-11D-A40P-10	19220383	186047303	63203318	8	49921										
PGBD5	79605	hgsc.bcm.edu	37	chr1	230492809	230492809	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	tcatgacgagggcgaggctgCggttgctgtagaagcctccg	16	10	1	2			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr1:230492809C>T	ENST00000525115.1	-	2	406	c.383G>A	c.(382-384)cGc>cAc	p.R128H	PGBD5_ENST00000321327.2_Missense_Mutation_p.R227H|PGBD5_ENST00000391860.1_Missense_Mutation_p.R82H			Q8N414	PGBD5_HUMAN	piggyBac transposable element derived 5	128						integral component of membrane (GO:0016021)				biliary_tract(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(2)|skin(1)	33	Breast(184;0.0397)	Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;0.201)		GGCGAGGCTGCGGTTGCTGTA	0.617																																					p.R197H		Atlas-SNP	.											PGBD5,rectum,carcinoma,-1,1	PGBD5	73	.	0			c.G590A						.						97	79	85					1																	230492809		2203	4300	6503	SO:0001583	missense	79605	exon2			AGGCTGCGGTTGC	AK021475		1q42.13	2008-02-05			ENSG00000177614	ENSG00000177614			19405	protein-coding gene	gene with protein product							Standard	NM_001258311		Approved	DKFZp761A0620, FLJ11413	uc031psq.1	Q8N414	OTTHUMG00000037759	ENST00000525115.1:c.383G>A	chr1.hg19:g.230492809C>T	ENSP00000431404:p.Arg128His	134.0	0.0		134.0	6.0	NM_001258311	A0PJF3|B9EK58|Q5SR37|Q6PJN2	Missense_Mutation	SNP	ENST00000525115.1	hg19		.	.	.	.	.	.	.	.	.	.	C	13.52	2.261577	0.39995	.	.	ENSG00000177614	ENST00000391860;ENST00000321327;ENST00000525115	T;T;T	0.17213	2.29;2.29;2.29	6.03	-0.976	0.10286	.	0.230823	0.43110	D	0.000606	T	0.06735	0.0172	N	0.11560	0.145	0.21897	N	0.999483	B	0.19706	0.038	B	0.12837	0.008	T	0.30238	-0.9985	10	0.29301	T	0.29	-24.9672	6.1131	0.20112	0.0:0.3787:0.1334:0.4879	.	128	Q8N414	PGBD5_HUMAN	H	82;227;128	ENSP00000375733:R82H;ENSP00000322530:R227H;ENSP00000431404:R128H	ENSP00000322530:R227H	R	-	2	0	PGBD5	228559432	0.020000	0.18652	0.181000	0.23098	0.929000	0.56500	0.340000	0.19892	-0.053000	0.13289	-0.880000	0.02959	CGC	.	.		0.617	PGBD5-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000382617.1	NM_024554		T	230492809	C	T	230492809	3	4	353	1	0	0	0	0	1	0	0	0	11793	768	27	1	1008	1	PGBD5	1	230492809	Missense_Mutation	SNP	C	TCGA-WQ-AB4B-01A-11D-A40P-10	44445506	230492809	18757812	9	49922										
LRPPRC	10128	hgsc.bcm.edu	37	chr2	44152227	44152227	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	atacagttttagcagattgtAgtacatctggtctctatcac	7	8	3	1			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr2:44152227A>G	ENST00000260665.7	-	27	2932	c.2875T>C	c.(2875-2877)Tac>Cac	p.Y959H		NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	959					mitochondrion transport along microtubule (GO:0047497)|mRNA transport (GO:0051028)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of mitochondrial translation (GO:0070129)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(3)|endometrium(3)|kidney(5)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|skin(2)	41		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				AGCAGATTGTAGTACATCTGG	0.358																																					p.Y959H		Atlas-SNP	.											.	LRPPRC	105	.	0			c.T2875C						.						164	171	169					2																	44152227		2203	4300	6503	SO:0001583	missense	10128	exon27			GATTGTAGTACAT	M92439	CCDS33189.1	2p21	2012-02-24	2012-02-24		ENSG00000138095	ENSG00000138095			15714	protein-coding gene	gene with protein product		607544	"Leigh syndrome, French-Canadian type (cytochrome oxidase deficiency)"	LSFC		8012652, 8619474, 22045337	Standard	NM_133259		Approved	GP130, LRP130	uc002rtr.2	P42704	OTTHUMG00000152782	ENST00000260665.7:c.2875T>C	chr2.hg19:g.44152227A>G	ENSP00000260665:p.Tyr959His	95.0	0.0		63.0	13.0	NM_133259	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Missense_Mutation	SNP	ENST00000260665.7	hg19	CCDS33189.1	.	.	.	.	.	.	.	.	.	.	A	14.33	2.503770	0.44558	.	.	ENSG00000138095	ENST00000465633;ENST00000260665	T	0.13089	2.62	5.72	5.72	0.89469	Tetratricopeptide-like helical (1);	0.244318	0.43110	D	0.000603	T	0.12987	0.0315	L	0.41824	1.3	0.80722	D	1	P;B	0.39443	0.674;0.221	B;B	0.36959	0.237;0.086	T	0.12268	-1.0554	10	0.17369	T	0.5	-3.5427	16.2988	0.82793	1.0:0.0:0.0:0.0	.	859;959	F5H4J6;P42704	.;LPPRC_HUMAN	H	859;959	ENSP00000260665:Y959H	ENSP00000260665:Y959H	Y	-	1	0	LRPPRC	44005731	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	5.259000	0.65485	2.311000	0.77944	0.533000	0.62120	TAC	.	.		0.358	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259		G	44152227	A	G	44152227	3	3	353	1	0	0	0	0	1	0	0	0	8974	420	15	2	1357	2	LRPPRC	2	44152227	Missense_Mutation	SNP	A	TCGA-WQ-AB4B-01A-11D-A40P-10		44152227	199047146	10	49923										
ANTXR1	84168	hgsc.bcm.edu	37	chr2	69408989	69408989	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	tcttattatggtgggagaggCgttggaggcattaaaagaat	14	3	1	2			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr2:69408989C>T	ENST00000303714.4	+	15	1483	c.1161C>T	c.(1159-1161)ggC>ggT	p.G387G	RNU6-1216P_ENST00000362590.2_RNA|RNA5SP96_ENST00000516041.1_RNA	NM_032208.2	NP_115584.1	Q9H6X2	ANTR1_HUMAN	anthrax toxin receptor 1	387					actin cytoskeleton reorganization (GO:0031532)|reproductive process (GO:0022414)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|integral component of membrane (GO:0016021)|lamellipodium membrane (GO:0031258)	actin filament binding (GO:0051015)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|transmembrane signaling receptor activity (GO:0004888)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(16)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	29						GTGGGAGAGGCGTTGGAGGCA	0.488									Familial Infantile Hemangioma																												p.G387G		Atlas-SNP	.											.	ANTXR1	128	.	0			c.C1161T						.						118	110	113					2																	69408989		2203	4300	6503	SO:0001819	synonymous_variant	84168	exon15	Familial Cancer Database	Infantile Capillary Hemangioma, HCI, Hereditary Capillary Hemangioma	GAGAGGCGTTGGA	AF421380	CCDS1892.1, CCDS46313.1, CCDS46314.1	2p13.1	2006-04-12			ENSG00000169604	ENSG00000169604			21014	protein-coding gene	gene with protein product	"anthrax toxin receptor", "tumor endothelial marker 8 precursor"	606410				10947988, 11559528	Standard	NM_032208		Approved	TEM8, FLJ21776, FLJ10601, ATR	uc002sfg.3	Q9H6X2	OTTHUMG00000129575	ENST00000303714.4:c.1161C>T	chr2.hg19:g.69408989C>T		154.0	0.0		96.0	23.0	NM_032208	A8K7U8|J7K7G4|J7KF88|Q4ZFV6|Q53QD8|Q96P02|Q9NVP3	Silent	SNP	ENST00000303714.4	hg19	CCDS1892.1																																																																																			.	.		0.488	ANTXR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251770.2	NM_032208		T	69408989	C	T	69408989	2	4	353	1	0	0	0	0	0	0	0	1	711	755	27	1		1	ANTXR1	2	69408989	Silent	SNP	C	TCGA-WQ-AB4B-01A-11D-A40P-10	25256762	69408989	173790384	11	49924										
DPP4	1803	hgsc.bcm.edu	37	chr2	162894911	162894911	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	tggttcaattttaacataaaTgtcattgttccaaacatatg	5	6	2	0			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr2:162894911T>C	ENST00000360534.3	-	8	1074	c.514A>G	c.(514-516)Att>Gtt	p.I172V		NM_001935.3	NP_001926.2	P27487	DPP4_HUMAN	dipeptidyl-peptidase 4	172					cell adhesion (GO:0007155)|endothelial cell migration (GO:0043542)|negative regulation of extracellular matrix disassembly (GO:0010716)|positive regulation of cell proliferation (GO:0008284)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|response to hypoxia (GO:0001666)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intercellular canaliculus (GO:0046581)|invadopodium membrane (GO:0071438)|lamellipodium (GO:0030027)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dipeptidyl-peptidase activity (GO:0008239)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	48					Alogliptin(DB06203)|Atorvastatin(DB01076)|Linagliptin(DB08882)|Liraglutide(DB06655)|Saxagliptin(DB06335)|Sitagliptin(DB01261)|Vildagliptin(DB04876)	TTAACATAAATGTCATTGTTC	0.303																																					p.I172V		Atlas-SNP	.											.	DPP4	90	.	0			c.A514G						.						61	60	60					2																	162894911		2201	4285	6486	SO:0001583	missense	1803	exon8			CATAAATGTCATT	M74777	CCDS2216.1	2q24.2	2013-09-19	2008-08-01		ENSG00000197635	ENSG00000197635	3.4.14.5	"CD molecules"	3009	protein-coding gene	gene with protein product		102720	"dipeptidylpeptidase IV (CD26, adenosine deaminase complexing protein 2)", "adenosine deaminase complexing protein 2"	CD26, ADCP2		8101391	Standard	NM_001935		Approved	DPPIV	uc002ubz.3	P27487	OTTHUMG00000132056	ENST00000360534.3:c.514A>G	chr2.hg19:g.162894911T>C	ENSP00000353731:p.Ile172Val	271.0	0.0		186.0	19.0	NM_001935	Q53TN1	Missense_Mutation	SNP	ENST00000360534.3	hg19	CCDS2216.1	.	.	.	.	.	.	.	.	.	.	T	13.54	2.267346	0.40095	.	.	ENSG00000197635	ENST00000360534	T	0.35421	1.31	6.03	-3.32	0.04973	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.613796	0.17661	N	0.166325	T	0.24084	0.0583	N	0.25992	0.78	0.47584	D	0.999464	B	0.09022	0.002	B	0.20577	0.03	T	0.06752	-1.0809	10	0.42905	T	0.14	-6.6896	14.2923	0.66286	0.0:0.4933:0.0:0.5067	.	172	P27487	DPP4_HUMAN	V	172	ENSP00000353731:I172V	ENSP00000353731:I172V	I	-	1	0	DPP4	162603157	0.147000	0.22687	0.985000	0.45067	0.992000	0.81027	-0.527000	0.06200	-0.374000	0.07967	0.455000	0.32223	ATT	.	.		0.303	DPP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255079.2			C	162894911	T	C	162894911	3	2	353	1	0	0	0	0	1	0	0	0	4731	1464	51	2	1862	2	DPP4	2	162894911	Missense_Mutation	SNP	T	TCGA-WQ-AB4B-01A-11D-A40P-10	93485922	162894911	80304462	12	49925										
ANKRD44	91526	hgsc.bcm.edu	37	chr2	197948233	197948233	+	Splice_Site	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	gctgcatagtgcaaaggggtCctgaaaaacaaacagcaatt	10	8	0	1			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr2:197948233C>T	ENST00000328737.2	-	14	1318	c.1242G>A	c.(1240-1242)agG>agA	p.R414R	ANKRD44_ENST00000337207.5_Splice_Site_p.R414R|ANKRD44_ENST00000282272.8_Splice_Site_p.R431R|ANKRD44_ENST00000477852.1_5'UTR|ANKRD44_ENST00000450567.1_Splice_Site_p.R414R|ANKRD44_ENST00000409153.1_Splice_Site_p.R439R|ANKRD44_ENST00000539527.1_Splice_Site_p.R367R			Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	439										NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(20)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.246)			GCAAAGGGGTCCTGAAAAACA	0.468																																					p.R439R		Atlas-SNP	.											.	ANKRD44	281	.	0			c.G1317A						.						98	86	90					2																	197948233		2203	4300	6503	SO:0001630	splice_region_variant	91526	exon14			AGGGGTCCTGAAA	AK097086	CCDS33355.1, CCDS33355.2, CCDS74619.1	2q33.1	2013-01-10			ENSG00000065413	ENSG00000065413		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits", "Ankyrin repeat domain containing"	25259	protein-coding gene	gene with protein product	"protein phosphatase 6 ankyrin repeat subunit B"						Standard	NM_153697		Approved	PP6-ARS-B	uc021vuj.1	Q8N8A2	OTTHUMG00000154411	ENST00000328737.2:c.1242-1G>A	chr2.hg19:g.197948233C>T		88.0	0.0		74.0	11.0	NM_001195144	Q53SL9|Q6P480|Q86VL5|Q8IZ72|Q9UFA4	Silent	SNP	ENST00000328737.2	hg19																																																																																				.	.		0.468	ANKRD44-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335113.1	NM_153697	Silent	T	197948233	C	T	197948233	5	4	353	1	0	0	0	0	0	0	1	0	672	869	30	3	1569	3	ANKRD44	2	197948233	Splice_Site	SNP	C	TCGA-WQ-AB4B-01A-11D-A40P-10	35053322	197948233	45251140	13	49926										
SIAH2	6478	hgsc.bcm.edu	37	chr3	150480232	150480232	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	gggcttaccttacagggaaaCaggactgccgaggccacctt	12	12	0	0			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr3:150480232C>T	ENST00000312960.3	-	1	932	c.405G>A	c.(403-405)ctG>ctA	p.L135L	SIAH2_ENST00000472885.1_5'Flank|SIAH2-AS1_ENST00000461943.1_RNA	NM_005067.5	NP_005058.3	O43255	SIAH2_HUMAN	siah E3 ubiquitin protein ligase 2	135	SBD.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|cellular protein catabolic process (GO:0044257)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|regulation of protein ubiquitination (GO:0031396)|regulation of RNA biosynthetic process (GO:2001141)|small GTPase mediated signal transduction (GO:0007264)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	ligase activity (GO:0016874)|transcription corepressor activity (GO:0003714)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|pancreas(1)	16			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			TACAGGGAAACAGGACTGCCG	0.667																																					p.L135L		Atlas-SNP	.											.	SIAH2	33	.	0			c.G405A						.						24	23	23					3																	150480232		2203	4300	6503	SO:0001819	synonymous_variant	6478	exon1			GGGAAACAGGACT	U76248	CCDS3152.1	3q25	2012-02-23	2012-02-23		ENSG00000181788	ENSG00000181788	6.3.2.1		10858	protein-coding gene	gene with protein product		602213	"seven in absentia (Drosophila) homolog 2", "seven in absentia homolog 2 (Drosophila)"			9334332	Standard	NM_005067		Approved		uc003eyi.3	O43255	OTTHUMG00000159847	ENST00000312960.3:c.405G>A	chr3.hg19:g.150480232C>T		94.0	0.0		52.0	23.0	NM_005067	O43270	Silent	SNP	ENST00000312960.3	hg19	CCDS3152.1																																																																																			.	.		0.667	SIAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357697.1	NM_005067		T	150480232	C	T	150480232	2	4	353	1	0	0	0	0	0	0	0	1	14315	465	17	3		3	SIAH2	3	150480232	Silent	SNP	C	TCGA-WQ-AB4B-01A-11D-A40P-10		150480232	47542198	14	49927										
ATP13A3	79572	hgsc.bcm.edu	37	chr3	194140666	194140666	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	tgatgaataatataaaaataTataaaaaaatcacagaaaaa	3	2	1	3			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr3:194140666T>C	ENST00000439040.1	-	31	4135	c.3344A>G	c.(3343-3345)tAt>tGt	p.Y1115C	ATP13A3_ENST00000256031.4_Missense_Mutation_p.Y1115C			Q9H7F0	AT133_HUMAN	ATPase type 13A3	1115						integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			NS(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	24	all_cancers(143;6.01e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	OV - Ovarian serous cystadenocarcinoma(49;3.83e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;5.98e-05)		tataaaaatatataaaaaaat	0.294																																					p.Y1115C		Atlas-SNP	.											.	ATP13A3	94	.	0			c.A3344G						.						24	24	24					3																	194140666		1775	4045	5820	SO:0001583	missense	79572	exon30			AAAATATATAAAA	AJ306929	CCDS43187.1	3q29	2010-04-20			ENSG00000133657	ENSG00000133657		"ATPases / P-type"	24113	protein-coding gene	gene with protein product	"ATPase family homolog up regulated in senescence cells"	610232				11867234	Standard	NM_024524		Approved	AFURS1	uc003fty.4	Q9H7F0	OTTHUMG00000156034	ENST00000439040.1:c.3344A>G	chr3.hg19:g.194140666T>C	ENSP00000416508:p.Tyr1115Cys	717.0	0.0		620.0	30.0	NM_024524	Q8NC11|Q96KS1	Missense_Mutation	SNP	ENST00000439040.1	hg19	CCDS43187.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	10.34|10.34	1.321999|1.321999	0.23994|0.23994	.|.	.|.	ENSG00000133657|ENSG00000133657	ENST00000429136|ENST00000439040;ENST00000256031	.|D;D	.|0.88896	.|-2.44;-2.44	5.63|5.63	3.16|3.16	0.36331|0.36331	.|.	.|0.062472	.|0.64402	.|D	.|0.000003	D|D	0.84817|0.84817	0.5556|0.5556	L|L	0.44542|0.44542	1.39|1.39	0.46774|0.46774	D|D	0.999192|0.999192	.|B	.|0.33073	.|0.396	.|B	.|0.39068	.|0.289	T|T	0.79293|0.79293	-0.1863|-0.1863	5|10	.|0.48119	.|T	.|0.1	-0.8404|-0.8404	8.1453|8.1453	0.31108|0.31108	0.1333:0.0:0.1397:0.7269|0.1333:0.0:0.1397:0.7269	.|.	.|1115	.|Q9H7F0	.|AT133_HUMAN	M|C	20|1115	.|ENSP00000416508:Y1115C;ENSP00000256031:Y1115C	.|ENSP00000256031:Y1115C	I|Y	-|-	3|2	3|0	ATP13A3|ATP13A3	195621955|195621955	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.312000|0.312000	0.27988|0.27988	3.153000|3.153000	0.50685|0.50685	0.374000|0.374000	0.24650|0.24650	0.528000|0.528000	0.53228|0.53228	ATA|TAT	.	.		0.294	ATP13A3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342799.2	NM_024524		C	194140666	T	C	194140666	3	2	353	1	0	0	0	0	1	0	0	0	1125	1406	49	2	348	2	ATP13A3	3	194140666	Missense_Mutation	SNP	T	TCGA-WQ-AB4B-01A-11D-A40P-10	43660434	194140666	3881764	15	49928										
ALB	213	hgsc.bcm.edu	37	chr4	74272459	74272459	+	Frame_Shift_Del	DEL	A	A	-													0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	tgttgctgatgagtcagctgAaaattgtgacaaatcacttg							TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr4:74272459delA	ENST00000503124.1	+	2	220	c.13delA	c.(13-15)aaafs	p.K5fs	ALB_ENST00000295897.4_Frame_Shift_Del_p.E84fs|ALB_ENST00000509063.1_Frame_Shift_Del_p.E84fs|ALB_ENST00000415165.2_Intron|ALB_ENST00000401494.3_Intron			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GAGTCAGCTGAAAATTGTGAC	0.318																																					p.E84fs		Atlas-INDEL	.											.,1	ALB	132	.	0			c.250delG						.						98	91	93					4																	74272459		2203	4300	6503	SO:0001589	frameshift_variant	213	exon3			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.13delA	chr4.hg19:g.74272459delA	ENSP00000421027:p.Lys5fs	92.0	0.0		75.0	12.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Frame_Shift_Del	DEL	ENST00000503124.1	hg19																																																																																				.	.		0.318	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		-	74272459	A	-	74272459	7	5	353	1	0	1	0	1	0	0	0	0	486	246	9	0	261	0	ALB	4	74272459	Frame_Shift_Del	DEL	A	TCGA-WQ-AB4B-01A-11D-A40P-10		74272459	116881817	16	49929										
ALB	213	hgsc.bcm.edu	37	chr4	74280793	74280793	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	aaggcatcctgattactctgTcgtgctgctgctgagacttg	11	10	1	2			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr4:74280793T>C	ENST00000503124.1	+	7	857	c.650T>C	c.(649-651)gTc>gCc	p.V217A	ALB_ENST00000295897.4_Missense_Mutation_p.V367A|ALB_ENST00000509063.1_Missense_Mutation_p.V367A|ALB_ENST00000415165.2_Missense_Mutation_p.V175A|ALB_ENST00000505649.1_3'UTR|ALB_ENST00000401494.3_Missense_Mutation_p.V252A			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GATTACTCTGTCGTGCTGCTG	0.393																																					p.V367A		Atlas-SNP	.											.	ALB	132	.	0			c.T1100C						.						152	150	150					4																	74280793		2203	4300	6503	SO:0001583	missense	213	exon9			ACTCTGTCGTGCT	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.650T>C	chr4.hg19:g.74280793T>C	ENSP00000421027:p.Val217Ala	132.0	0.0		80.0	34.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000503124.1	hg19		.	.	.	.	.	.	.	.	.	.	T	3.922	-0.017930	0.07681	.	.	ENSG00000163631	ENST00000295897;ENST00000415165;ENST00000503124;ENST00000509063;ENST00000401494;ENST00000430202	T;T;T;T;T	0.72167	-0.63;-0.63;-0.63;-0.63;-0.63	5.84	-3.86	0.04230	Serum albumin-like (1);Serum albumin, N-terminal (3);	1.621470	0.03192	N	0.173403	T	0.64438	0.2598	L	0.39326	1.205	0.09310	N	1	B;B;B;B;B	0.20887	0.049;0.005;0.005;0.001;0.0	B;B;B;B;B	0.33521	0.165;0.017;0.025;0.017;0.01	T	0.57613	-0.7781	10	0.52906	T	0.07	-3.9051	7.6293	0.28230	0.1091:0.4242:0.0:0.4667	.	252;175;217;367;367	B7WNR0;C9JKR2;D6RHD5;A6NBZ8;P02768	.;.;.;.;ALBU_HUMAN	A	367;175;217;367;252;376	ENSP00000295897:V367A;ENSP00000401820:V175A;ENSP00000421027:V217A;ENSP00000422784:V367A;ENSP00000384695:V252A	ENSP00000295897:V367A	V	+	2	0	ALB	74499657	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.891000	0.04135	-0.563000	0.06078	-0.959000	0.02639	GTC	.	.		0.393	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		C	74280793	T	C	74280793	3	2	353	1	0	0	0	0	1	0	0	0	486	1667	58	2	1134	2	ALB	4	74280793	Missense_Mutation	SNP	T	TCGA-WQ-AB4B-01A-11D-A40P-10	8334	74280793	116873483	17	49930										
PDHA2	5161	hgsc.bcm.edu	37	chr4	96761441	96761441	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	tctttatctgttggaagaggGtccccctgtcactacagtgc	10	11	3	1			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr4:96761441G>T	ENST00000295266.4	+	1	203	c.140G>T	c.(139-141)gGt>gTt	p.G47V		NM_005390.4	NP_005381.1	P29803	ODPAT_HUMAN	pyruvate dehydrogenase (lipoamide) alpha 2	47					glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|pyruvate metabolic process (GO:0006090)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	pyruvate dehydrogenase (acetyl-transferring) activity (GO:0004739)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(23)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	46		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.23e-06)		TTGGAAGAGGGTCCCCCTGTC	0.493																																					p.G47V		Atlas-SNP	.											.	PDHA2	118	.	0			c.G140T						.						61	60	60					4																	96761441		2203	4300	6503	SO:0001583	missense	5161	exon1			AAGAGGGTCCCCC		CCDS3644.1	4q22-q23	2009-11-09			ENSG00000163114	ENSG00000163114	1.2.4.1		8807	protein-coding gene	gene with protein product		179061		PDHAL			Standard	NM_005390		Approved		uc003htr.4	P29803	OTTHUMG00000130990	ENST00000295266.4:c.140G>T	chr4.hg19:g.96761441G>T	ENSP00000295266:p.Gly47Val	183.0	0.0		137.0	25.0	NM_005390	B2R9Q3|Q0VDI5|Q4VC02|Q6NXQ1	Missense_Mutation	SNP	ENST00000295266.4	hg19	CCDS3644.1	.	.	.	.	.	.	.	.	.	.	G	17.31	3.357804	0.61403	.	.	ENSG00000163114	ENST00000295266	D	0.97455	-4.39	4.64	3.79	0.43588	.	0.114328	0.64402	D	0.000019	D	0.97040	0.9033	M	0.86178	2.8	0.80722	D	1	D	0.56968	0.978	P	0.49252	0.604	D	0.96691	0.9511	10	0.87932	D	0	-7.6399	10.5765	0.45229	0.0974:0.0:0.9026:0.0	.	47	P29803	ODPAT_HUMAN	V	47	ENSP00000295266:G47V	ENSP00000295266:G47V	G	+	2	0	PDHA2	96980464	1.000000	0.71417	0.708000	0.30435	0.114000	0.19823	3.147000	0.50639	2.581000	0.87130	0.467000	0.42956	GGT	.	.		0.493	PDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253608.1			T	96761441	G	T	96761441	3	4	353	1	0	0	0	0	1	0	0	0	11674	1261	44	3	142	3	PDHA2	4	96761441	Missense_Mutation	SNP	G	TCGA-WQ-AB4B-01A-11D-A40P-10	22480648	96761441	94392835	18	49931										
CDKN2AIP	55602	hgsc.bcm.edu	37	chr4	184367702	184367702	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	ctcaaagcagctcagagatcGaggtgcccttgttgggctcc	12	12	2	1			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr4:184367702G>T	ENST00000504169.1	+	3	1072	c.865G>T	c.(865-867)Gag>Tag	p.E289*	CDKN2AIP_ENST00000506835.1_3'UTR|CDKN2AIP_ENST00000302350.4_3'UTR	NM_017632.2	NP_060102.1	Q9NXV6	CARF_HUMAN	CDKN2A interacting protein	289	Ser-rich.				negative regulation of cell growth (GO:0030308)|positive regulation of signal transduction (GO:0009967)|regulation of protein stability (GO:0031647)	cytoplasm (GO:0005737)|granular component (GO:0001652)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	p53 binding (GO:0002039)|RNA binding (GO:0003723)			endometrium(1)|kidney(2)|large_intestine(2)|lung(1)	6		all_lung(41;6.9e-12)|Lung NSC(41;1.28e-11)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;1.15e-26)|Epithelial(43;2.98e-22)|OV - Ovarian serous cystadenocarcinoma(60;7.64e-10)|GBM - Glioblastoma multiforme(59;4.22e-06)|Colorectal(24;5.87e-06)|STAD - Stomach adenocarcinoma(60;2.09e-05)|COAD - Colon adenocarcinoma(29;5.15e-05)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.155)		CTCAGAGATCGAGGTGCCCTT	0.473																																					p.E289X		Atlas-SNP	.											.	CDKN2AIP	31	.	0			c.G865T						.						61	60	60					4																	184367702		2203	4300	6503	SO:0001587	stop_gained	55602	exon3			GAGATCGAGGTGC	AK000043	CCDS34110.1	4q35.1	2008-02-05			ENSG00000168564	ENSG00000168564			24325	protein-coding gene	gene with protein product	"collaborates/cooperates with ARF (alternate reading frame) protein"	615914				12154087, 16803988	Standard	NM_017632		Approved	FLJ20036, CARF	uc003ivp.1	Q9NXV6	OTTHUMG00000160626	ENST00000504169.1:c.865G>T	chr4.hg19:g.184367702G>T	ENSP00000427108:p.Glu289*	172.0	0.0		159.0	39.0	NM_017632	Q8TBM5|Q9NYH0	Nonsense_Mutation	SNP	ENST00000504169.1	hg19	CCDS34110.1	.	.	.	.	.	.	.	.	.	.	G	32	5.173377	0.94807	.	.	ENSG00000168564	ENST00000504169	.	.	.	5.55	4.69	0.59074	.	0.224065	0.31472	N	0.007594	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	-3.1462	13.9202	0.63926	0.0:0.1825:0.8175:0.0	.	.	.	.	X	289	.	ENSP00000427108:E289X	E	+	1	0	CDKN2AIP	184604696	0.244000	0.23889	0.907000	0.35723	0.748000	0.42578	1.034000	0.30204	1.582000	0.49881	0.655000	0.94253	GAG	.	.		0.473	CDKN2AIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361488.1	NM_017632		T	184367702	G	T	184367702	4	4	353	1	0	0	0	0	0	1	0	0	3164	1059	37	1	875	1	CDKN2AIP	4	184367702	Nonsense_Mutation	SNP	G	TCGA-WQ-AB4B-01A-11D-A40P-10	87606261	184367702	6786574	19	49932										
ANKRD55	79722	hgsc.bcm.edu	37	chr5	55422893	55422893	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	tgattatggacggcccctggTgatggctcagaatgatggag	15	7	1	4			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr5:55422893T>G	ENST00000341048.4	-	8	804	c.653A>C	c.(652-654)cAc>cCc	p.H218P	RNU6-299P_ENST00000517223.1_RNA|ANKRD55_ENST00000504958.2_Missense_Mutation_p.H175P|ANKRD55_ENST00000505970.2_Intron	NM_024669.2	NP_078945.2	Q3KP44	ANR55_HUMAN	ankyrin repeat domain 55	218										breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(1)	34		Lung NSC(810;8.69e-05)|Prostate(74;0.00634)|Breast(144;0.0334)|Ovarian(174;0.223)				CGGCCCCTGGTGATGGCTCAG	0.468																																					p.H218P		Atlas-SNP	.											.	ANKRD55	70	.	0			c.A653C						.						104	101	102					5																	55422893		2203	4300	6503	SO:0001583	missense	79722	exon8			CCCTGGTGATGGC	AK021857	CCDS34161.1	5q11.2	2013-01-10			ENSG00000164512	ENSG00000164512		"Ankyrin repeat domain containing"	25681	protein-coding gene	gene with protein product		615189					Standard	XM_005248599		Approved	FLJ11795	uc003jqu.3	Q3KP44	OTTHUMG00000162305	ENST00000341048.4:c.653A>C	chr5.hg19:g.55422893T>G	ENSP00000342295:p.His218Pro	150.0	0.0		187.0	57.0	NM_024669	B3KVT8|Q3KP45|Q9HAD3	Missense_Mutation	SNP	ENST00000341048.4	hg19	CCDS34161.1	.	.	.	.	.	.	.	.	.	.	T	11.35	1.613934	0.28712	.	.	ENSG00000164512	ENST00000507283;ENST00000341048;ENST00000504958	T;T	0.52526	2.44;0.66	5.62	1.76	0.24704	.	0.565396	0.18369	N	0.143301	T	0.30417	0.0764	L	0.29908	0.895	0.09310	N	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.15009	-1.0452	10	0.39692	T	0.17	.	5.6323	0.17518	0.0:0.2:0.2783:0.5217	.	218	B3KVT8	.	P	218;218;175	ENSP00000342295:H218P;ENSP00000424230:H175P	ENSP00000342295:H218P	H	-	2	0	ANKRD55	55458650	1.000000	0.71417	0.909000	0.35828	0.799000	0.45148	1.024000	0.30077	0.428000	0.26173	0.460000	0.39030	CAC	.	.		0.468	ANKRD55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368510.4	NM_024669		G	55422893	T	G	55422893	3	3	353	1	0	0	0	0	1	0	0	0	681	1696	59	5	1211	5	ANKRD55	5	55422893	Missense_Mutation	SNP	T	TCGA-WQ-AB4B-01A-11D-A40P-10		55422893	125492367	20	49933										
DOCK2	1794	hgsc.bcm.edu	37	chr5	169507279	169507280	+	Missense_Mutation	DNP	CC	CC	AA													0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	tgccagccagtccatgcctaCcatcccaggtatgccccctg							TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr5:169507279_169507280CC>AA	ENST00000256935.8	+	50	5359_5360	c.5279_5280CC>AA	c.(5278-5280)aCC>aAA	p.T1760K	DOCK2_ENST00000523351.1_3'UTR|DOCK2_ENST00000520908.1_Missense_Mutation_p.T1252K|DOCK2_ENST00000540750.1_Missense_Mutation_p.T821K	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1760					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TCCATGCCTACCATCCCAGGTA	0.574																																					p.T1760N|p.T1760T		Atlas-SNP	.											.	DOCK2	389	.	0			c.C5279A|c.C5280A						.																																			SO:0001583	missense	1794	exon50			TGCCTACCATCCC|GCCTACCATCCCA	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	Exception_encountered	chr5.hg19:g.169507279_169507280delinsAA	ENSP00000256935:p.Thr1760Lys	78.0|77.0	0.0		91.0|90.0	26.0|27.0	NM_004946	Q2M3I0|Q96AK7	Missense_Mutation|Silent	SNP	ENST00000256935.8	hg19	CCDS4371.1																																																																																			.	.		0.574	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		AA	169507280	CC	AA	169507279	3	1	353	1	0	0	0	0	1	0	0	0	4689	507	18	3	5477	3	DOCK2	5	169507279	Missense_Mutation	DNP	CC	TCGA-WQ-AB4B-01A-11D-A40P-10	114084386	169507279	11407981	21	49934										
PKHD1	5314	hgsc.bcm.edu	37	chr6	51910977	51910977	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	ggtgatgagcagaaatttgtAcagggacatctgtgagagaa	14	4	1	5			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr6:51910977A>G	ENST00000371117.3	-	24	2692	c.2417T>C	c.(2416-2418)gTa>gCa	p.V806A	PKHD1_ENST00000340994.4_Missense_Mutation_p.V806A	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	806					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					AGAAATTTGTACAGGGACATC	0.418																																					p.V806A		Atlas-SNP	.											.	PKHD1	927	.	0			c.T2417C						.						175	160	165					6																	51910977		2203	4300	6503	SO:0001583	missense	5314	exon24			ATTTGTACAGGGA	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.2417T>C	chr6.hg19:g.51910977A>G	ENSP00000360158:p.Val806Ala	151.0	0.0		105.0	11.0	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	hg19	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	A	12.46	1.945864	0.34377	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.87029	-2.01;-2.2	5.74	4.58	0.56647	.	0.079049	0.52532	N	0.000068	D	0.82508	0.5052	L	0.50333	1.59	0.30216	N	0.797228	D;D	0.67145	0.986;0.996	P;P	0.61070	0.775;0.883	T	0.75513	-0.3291	10	0.18710	T	0.47	.	9.6843	0.40089	0.9182:0.0:0.0818:0.0	.	806;806	P08F94-2;P08F94	.;PKHD1_HUMAN	A	806	ENSP00000360158:V806A;ENSP00000341097:V806A	ENSP00000341097:V806A	V	-	2	0	PKHD1	52018936	0.998000	0.40836	0.728000	0.30774	0.083000	0.17756	3.868000	0.56055	1.014000	0.39417	0.459000	0.35465	GTA	.	.		0.418	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		G	51910977	A	G	51910977	3	3	353	1	0	0	0	0	1	0	0	0	11980	391	14	2	10022	2	PKHD1	6	51910977	Missense_Mutation	SNP	A	TCGA-WQ-AB4B-01A-11D-A40P-10		51910977	119204090	22	49935										
COL12A1	1303	hgsc.bcm.edu	37	chr6	75847218	75847218	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	atatttctgcacacgaccacTagcaggatcccacttaacag	6	13	1	0			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr6:75847218T>C	ENST00000322507.8	-	31	5638	c.5329A>G	c.(5329-5331)Agt>Ggt	p.S1777G	COL12A1_ENST00000345356.6_Missense_Mutation_p.S613G|COL12A1_ENST00000483888.2_Missense_Mutation_p.S1777G|COL12A1_ENST00000416123.2_Missense_Mutation_p.S1777G	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	1777	Fibronectin type-III 13. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						ACACGACCACTAGCAGGATCC	0.398																																					p.S1777G		Atlas-SNP	.											.	COL12A1	385	.	0			c.A5329G						.						82	78	79					6																	75847218		1889	4108	5997	SO:0001583	missense	1303	exon31			GACCACTAGCAGG	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.5329A>G	chr6.hg19:g.75847218T>C	ENSP00000325146:p.Ser1777Gly	125.0	0.0		99.0	33.0	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	hg19	CCDS43482.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.404|9.404	1.078749|1.078749	0.20227|0.20227	.|.	.|.	ENSG00000111799|ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000345356;ENST00000416123;ENST00000483888|ENST00000419671	T;T;T;T|.	0.55760|.	0.5;0.5;0.5;0.5|.	5.31|5.31	4.15|4.15	0.48705|0.48705	Fibronectin, type III (4);Immunoglobulin-like fold (1);|.	0.133460|.	0.52532|.	D|.	0.000062|.	T|.	0.40222|.	0.1108|.	M|M	0.69358|0.69358	2.11|2.11	0.30327|0.30327	N|N	0.786996|0.786996	B;P|.	0.43431|.	0.003;0.807|.	B;B|.	0.41510|.	0.002;0.359|.	T|.	0.31475|.	-0.9942|.	10|.	0.32370|.	T|.	0.25|.	.|.	11.2307|11.2307	0.48910|0.48910	0.0:0.0723:0.0:0.9277|0.0:0.0723:0.0:0.9277	.|.	613;1777|.	Q99715-2;Q99715|.	.;COCA1_HUMAN|.	G|W	1777;1777;613;1777;1777|511	ENSP00000325146:S1777G;ENSP00000305147:S613G;ENSP00000412864:S1777G;ENSP00000421216:S1777G|.	ENSP00000325146:S1777G|.	S|X	-|-	1|2	0|0	COL12A1|COL12A1	75903938|75903938	0.998000|0.998000	0.40836|0.40836	1.000000|1.000000	0.80357|0.80357	0.424000|0.424000	0.31475|0.31475	4.008000|4.008000	0.57103|0.57103	0.960000|0.960000	0.38005|0.38005	-0.353000|-0.353000	0.07706|0.07706	AGT|TAG	.	.		0.398	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		C	75847218	T	C	75847218	3	2	353	1	0	0	0	0	1	0	0	0	3671	1522	53	2	4006	2	COL12A1	6	75847218	Missense_Mutation	SNP	T	TCGA-WQ-AB4B-01A-11D-A40P-10	23936241	75847218	95267849	23	49936										
TBX18	9096	hgsc.bcm.edu	37	chr6	85446692	85446699	+	Frame_Shift_Del	DEL	TGGTTAGT	TGGTTAGT	-													0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	tataggaaccctgatgggtcTggttagtggcgaaggcattg							TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	TGGTTAGT	TGGTTAGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr6:85446692_85446699delTGGTTAGT	ENST00000369663.5	-	8	1865_1872	c.1528_1535delACTAACCA	c.(1528-1536)actaaccagfs	p.TNQ510fs	TBX18_ENST00000606784.1_Intron	NM_001080508.1	NP_001073977.1	O95935	TBX18_HUMAN	T-box 18	510					anterior/posterior axis specification (GO:0009948)|cochlea morphogenesis (GO:0090103)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060829)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation involved in ureter development (GO:2000729)|sensory perception of sound (GO:0007605)|sinoatrial node development (GO:0003163)|smooth muscle cell differentiation (GO:0051145)|somitogenesis (GO:0001756)|ureter development (GO:0072189)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(9)|liver(1)|lung(31)|ovary(2)|pancreas(3)|prostate(6)|skin(3)	61		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)		CTGATGGGTCTGGTTAGTGGCGAAGGCA	0.51																																					p.510_512del		Atlas-INDEL	.											.	TBX18	131	.	0			c.1529_1536del						.																																			SO:0001589	frameshift_variant	9096	exon8			.	AJ010278	CCDS34495.1	6q14.1-q15	2012-12-19			ENSG00000112837	ENSG00000112837		"T-boxes"	11595	protein-coding gene	gene with protein product		604613				9888994, 16688725, 23242162	Standard	NM_001080508		Approved		uc003pkl.2	O95935	OTTHUMG00000015129	ENST00000369663.5:c.1528_1535delACTAACCA	chr6.hg19:g.85446692_85446699delTGGTTAGT	ENSP00000358677:p.Thr510fs	174.0	0.0		129.0	28.0	NM_001080508	A2RU13|Q7Z6U4|Q9UJI6	Frame_Shift_Del	DEL	ENST00000369663.5	hg19	CCDS34495.1																																																																																			.	.		0.51	TBX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041378.2	NM_001080508		-	85446699	TGGTTAGT	-	85446692	7	5	353	1	0	1	0	1	0	0	0	0	15668	1580	55	0	292	0	TBX18	6	85446692	Frame_Shift_Del	DEL	TGGTTAGT	TCGA-WQ-AB4B-01A-11D-A40P-10	9599474	85446692	85668375	24	49937										
PRDM13	59336	hgsc.bcm.edu	37	chr6	100057092	100057092	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	cgagcattgcgagacgtccaGccaggggaggagctgacagt	16	10	0	2			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr6:100057092G>T	ENST00000369215.4	+	3	611	c.306G>T	c.(304-306)caG>caT	p.Q102H		NM_021620.3	NP_067633.2	Q9H4Q3	PRD13_HUMAN	PR domain containing 13	102	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurogenesis (GO:0022008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(9)|prostate(1)	17		all_cancers(76;1.64e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0128)|Colorectal(196;0.069)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0598)		GAGACGTCCAGCCAGGGGAGG	0.507																																					p.Q102H		Atlas-SNP	.											.	PRDM13	65	.	0			c.G306T						.						58	64	62					6																	100057092		2101	4232	6333	SO:0001583	missense	59336	exon3			CGTCCAGCCAGGG	AY004253	CCDS43487.1	6q16.2	2012-03-28			ENSG00000112238	ENSG00000112238			13998	protein-coding gene	gene with protein product							Standard	NM_021620		Approved		uc003pqg.1	Q9H4Q3	OTTHUMG00000015269	ENST00000369215.4:c.306G>T	chr6.hg19:g.100057092G>T	ENSP00000358217:p.Gln102His	114.0	0.0		99.0	37.0	NM_021620	Q5TGC1|Q5TGC2	Missense_Mutation	SNP	ENST00000369215.4	hg19	CCDS43487.1	.	.	.	.	.	.	.	.	.	.	G	15.43	2.831009	0.50845	.	.	ENSG00000112238	ENST00000369215;ENST00000369214	D;D	0.86030	-2.06;-2.06	5.51	4.64	0.57946	SET domain (2);	0.000000	0.37095	N	0.002247	D	0.85344	0.5675	L	0.43152	1.355	0.36210	D	0.851305	D	0.67145	0.996	P	0.61800	0.894	D	0.87446	0.2398	10	0.87932	D	0	-28.6127	14.3412	0.66627	0.0736:0.0:0.9264:0.0	.	102	Q9H4Q3	PRD13_HUMAN	H	102;112	ENSP00000358217:Q102H;ENSP00000358216:Q112H	ENSP00000358216:Q112H	Q	+	3	2	PRDM13	100163813	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.650000	0.46665	2.620000	0.88729	0.456000	0.33151	CAG	.	.		0.507	PRDM13-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041619.2			T	100057092	G	T	100057092	3	4	353	1	0	0	0	0	1	0	0	0	12466	962	34	3	316	3	PRDM13	6	100057092	Missense_Mutation	SNP	G	TCGA-WQ-AB4B-01A-11D-A40P-10	14610400	100057092	71057975	25	49938										
PCLO	27445	hgsc.bcm.edu	37	chr7	82545902	82545902	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	ctgttaattcccatttccagGtatcgtagcttagcatcaat	6	10	1	0			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr7:82545902G>A	ENST00000333891.9	-	7	11737	c.11400C>T	c.(11398-11400)taC>taT	p.Y3800Y	PCLO_ENST00000423517.2_Silent_p.Y3800Y|PCLO_ENST00000437081.1_Silent_p.Y520Y	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						CCATTTCCAGGTATCGTAGCT	0.443																																					p.Y3800Y		Atlas-SNP	.											PCLO_ENST00000333891,right_upper_lobe,carcinoma,0,2	PCLO	1506	.	0			c.C11400T						.						175	155	162					7																	82545902		1896	4127	6023	SO:0001819	synonymous_variant	27445	exon7			TTCCAGGTATCGT	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.11400C>T	chr7.hg19:g.82545902G>A		144.0	0.0		129.0	9.0	NM_014510		Silent	SNP	ENST00000333891.9	hg19	CCDS47630.1																																																																																			.	.		0.443	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82545902	G	A	82545902	2	1	353	1	0	0	0	0	0	0	0	1	11592	1256	44	3		3	PCLO	7	82545902	Silent	SNP	G	TCGA-WQ-AB4B-01A-11D-A40P-10		82545902	76592761	26	49939										
ZNF800	168850	hgsc.bcm.edu	37	chr7	127014205	127014205	+	Frame_Shift_Del	DEL	T	T	-													0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	ttggcagtattattagggccTttttctcttttagagtttgt							TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr7:127014205delT	ENST00000393313.1	-	5	1776	c.1185delA	c.(1183-1185)aaafs	p.K395fs	ZNF800_ENST00000485577.1_5'Flank|ZNF800_ENST00000265827.3_Frame_Shift_Del_p.K395fs|ZNF800_ENST00000393312.1_Frame_Shift_Del_p.K395fs			Q2TB10	ZN800_HUMAN	zinc finger protein 800	395					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(8)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	32						TATTAGGGCCTTTTTCTCTTT	0.358																																					p.G396fs		Atlas-INDEL	.											.	ZNF800	78	.	0			c.1186delG						.						94	102	99					7																	127014205		2202	4297	6499	SO:0001589	frameshift_variant	168850	exon5			.	AF218032	CCDS5795.1	7q31.33	2008-05-02			ENSG00000048405	ENSG00000048405		"Zinc fingers, C2H2-type"	27267	protein-coding gene	gene with protein product						12477932	Standard	NM_176814		Approved		uc003vly.1	Q2TB10	OTTHUMG00000023456	ENST00000393313.1:c.1185delA	chr7.hg19:g.127014205delT	ENSP00000376989:p.Lys395fs	135.0	0.0		155.0	24.0	NM_176814	Q9HBN0	Frame_Shift_Del	DEL	ENST00000393313.1	hg19	CCDS5795.1																																																																																			.	.		0.358	ZNF800-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141823.1	NM_176814		-	127014205	T	-	127014205	7	5	353	1	0	1	0	1	0	0	0	0	18184	1606	56	0	817	0	ZNF800	7	127014205	Frame_Shift_Del	DEL	T	TCGA-WQ-AB4B-01A-11D-A40P-10	44468303	127014205	32124458	27	49940										
DPP6	1804	hgsc.bcm.edu	37	chr7	154667719	154667719	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	tggtggtaaagtgtgacggcCgtggcagcggcttccaaggg	18	8	0	1			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr7:154667719C>T	ENST00000377770.3	+	20	2128	c.1987C>T	c.(1987-1989)Cgt>Tgt	p.R663C	DPP6_ENST00000427557.1_Missense_Mutation_p.R556C|DPP6_ENST00000332007.3_Missense_Mutation_p.R601C|DPP6_ENST00000404039.1_Missense_Mutation_p.R599C			P42658	DPP6_HUMAN	dipeptidyl-peptidase 6	663					cell death (GO:0008219)|neuronal action potential (GO:0019228)|positive regulation of potassium ion transmembrane transport (GO:1901381)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(3)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(35)|pancreas(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	71	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			GTGTGACGGCCGTGGCAGCGG	0.657																																					p.R663C	NSCLC(125;1384 1783 2490 7422 34254)	Atlas-SNP	.											.	DPP6	383	.	0			c.C1987T						.						26	33	30					7																	154667719		2046	4179	6225	SO:0001583	missense	1804	exon20			GACGGCCGTGGCA	M96859	CCDS75682.1, CCDS75683.1, CCDS75684.1	7q36.2	2006-08-07	2006-01-12		ENSG00000130226	ENSG00000130226			3010	protein-coding gene	gene with protein product		126141	"dipeptidylpeptidase VI", "dipeptidylpeptidase 6"			1729689	Standard	XM_006715871		Approved	DPPX	uc003wlk.3	P42658	OTTHUMG00000151511	ENST00000377770.3:c.1987C>T	chr7.hg19:g.154667719C>T	ENSP00000367001:p.Arg663Cys	106.0	0.0		94.0	16.0	NM_130797		Missense_Mutation	SNP	ENST00000377770.3	hg19		.	.	.	.	.	.	.	.	.	.	C	20.7	4.035684	0.75617	.	.	ENSG00000130226	ENST00000404039;ENST00000377770;ENST00000332007;ENST00000427557	T;T;T;T	0.61040	0.14;0.14;0.14;0.14	4.92	4.92	0.64577	Peptidase S9, prolyl oligopeptidase, catalytic domain (1);	0.057468	0.64402	D	0.000001	D	0.82609	0.5074	M	0.94101	3.495	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.995;0.997;0.997	D	0.87920	0.2703	10	0.87932	D	0	-10.5253	18.0911	0.89476	0.0:1.0:0.0:0.0	.	556;601;663;599	E9PDL2;P42658-2;P42658;E9PF59	.;.;DPP6_HUMAN;.	C	599;663;601;556	ENSP00000385578:R599C;ENSP00000367001:R663C;ENSP00000328226:R601C;ENSP00000397303:R556C	ENSP00000328226:R601C	R	+	1	0	DPP6	154298652	1.000000	0.71417	0.996000	0.52242	0.622000	0.37654	3.714000	0.54889	2.246000	0.74042	0.430000	0.28490	CGT	.	.		0.657	DPP6-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322932.1	NM_130797		T	154667719	C	T	154667719	3	4	353	1	0	0	0	0	1	0	0	0	4732	652	23	1	2181	1	DPP6	7	154667719	Missense_Mutation	SNP	C	TCGA-WQ-AB4B-01A-11D-A40P-10	27653514	154667719	4470944	28	49941										
ANGPT1	284	hgsc.bcm.edu	37	chr8	108315574	108315574	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	taaatggtttctcttcctctCtttttcctccctttagtaaa	3	11	2	0			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr8:108315574C>A	ENST00000520734.1	-	4	515	c.230G>T	c.(229-231)aGa>aTa	p.R77I	ANGPT1_ENST00000520052.1_Missense_Mutation_p.R76I|ANGPT1_ENST00000518386.1_Intron			Q15389	ANGP1_HUMAN	angiopoietin 1	277					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell-substrate adhesion (GO:0031589)|glomerulus vasculature development (GO:0072012)|hemopoiesis (GO:0030097)|heparin biosynthetic process (GO:0030210)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of vascular permeability (GO:0043116)|positive chemotaxis (GO:0050918)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of receptor internalization (GO:0002092)|protein localization to cell surface (GO:0034394)|regulation of satellite cell proliferation (GO:0014842)|sprouting angiogenesis (GO:0002040)|Tie signaling pathway (GO:0048014)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(13)|ovary(4)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	43	Breast(1;5.06e-08)		OV - Ovarian serous cystadenocarcinoma(57;5.53e-09)			CTCTTCCTCTCTTTTTCCTCC	0.318																																					p.R277I		Atlas-SNP	.											.	ANGPT1	111	.	0			c.G830T						.						87	97	94					8																	108315574		2202	4300	6502	SO:0001583	missense	284	exon5			TCCTCTCTTTTTC	D13628	CCDS6306.1, CCDS56551.1	8q23.1	2013-02-06			ENSG00000154188	ENSG00000154188		"Fibrinogen C domain containing"	484	protein-coding gene	gene with protein product		601667				9545648	Standard	NM_001146		Approved	KIAA0003, Ang1	uc003ymn.3	Q15389	OTTHUMG00000164812	ENST00000520734.1:c.230G>T	chr8.hg19:g.108315574C>A	ENSP00000430750:p.Arg77Ile	99.0	0.0		141.0	8.0	NM_001146	Q5HYA0	Missense_Mutation	SNP	ENST00000520734.1	hg19		.	.	.	.	.	.	.	.	.	.	C	12.91	2.080763	0.36758	.	.	ENSG00000154188	ENST00000517746;ENST00000297450;ENST00000395820;ENST00000520734;ENST00000520052	T;T;T;T	0.55413	0.52;0.93;0.56;0.55	4.45	1.55	0.23275	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (1);	0.547716	0.21379	N	0.075514	T	0.40067	0.1102	L	0.44542	1.39	0.39218	D	0.963449	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.18366	-1.0339	10	0.40728	T	0.16	.	7.5852	0.27989	0.0:0.4198:0.0:0.5802	.	76;277;277	E7ERK4;Q5HYA0;Q15389	.;.;ANGP1_HUMAN	I	277;276;89;77;76	ENSP00000428340:R277I;ENSP00000297450:R276I;ENSP00000430750:R77I;ENSP00000429349:R76I	ENSP00000297450:R276I	R	-	2	0	ANGPT1	108384750	0.954000	0.32549	1.000000	0.80357	0.999000	0.98932	0.007000	0.13174	0.107000	0.17824	0.650000	0.86243	AGA	.	.		0.318	ANGPT1-002	PUTATIVE	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000380428.2	NM_001146, NM_139290		A	108315574	C	A	108315574	3	1	353	1	0	0	0	0	1	0	0	0	610	913	32	3	686	3	ANGPT1	8	108315574	Missense_Mutation	SNP	C	TCGA-WQ-AB4B-01A-11D-A40P-10		108315574	38048448	29	49942										
COL22A1	169044	hgsc.bcm.edu	37	chr8	139601631	139601631	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	ggtcctgtctccccttgaggGccagggatcccaggaagtcc	13	14	1	1			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr8:139601631G>A	ENST00000303045.6	-	65	5192	c.4746C>T	c.(4744-4746)ggC>ggT	p.G1582G	COL22A1_ENST00000341807.4_5'UTR|COL22A1_ENST00000435777.1_Silent_p.G1562G	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	1582	Collagen-like 16.|Gly-rich.|Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			CCCCTTGAGGGCCAGGGATCC	0.602										HNSCC(7;0.00092)																											p.G1582G		Atlas-SNP	.											.	COL22A1	390	.	0			c.C4746T						.						53	46	48					8																	139601631		2203	4300	6503	SO:0001819	synonymous_variant	169044	exon65			TTGAGGGCCAGGG	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"Collagens"	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.4746C>T	chr8.hg19:g.139601631G>A		233.0	0.0		338.0	33.0	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Silent	SNP	ENST00000303045.6	hg19	CCDS6376.1																																																																																			.	.		0.602	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257		A	139601631	G	A	139601631	2	1	353	1	0	0	0	0	0	0	0	1	3683	1190	42	3		3	COL22A1	8	139601631	Silent	SNP	G	TCGA-WQ-AB4B-01A-11D-A40P-10	31286057	139601631	6762391	30	49943										
TOPORS	10210	hgsc.bcm.edu	37	chr9	32543499	32543499	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	agttcgattaagtaaaaatgGtcttaaatcagacacaaatg	7	5	2	1			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr9:32543499G>A	ENST00000360538.2	-	3	1140	c.1024C>T	c.(1024-1026)Cca>Tca	p.P342S	TOPORS_ENST00000379858.1_Missense_Mutation_p.P277S	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	342	Required for DNA-binding.				cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of apoptotic process (GO:0043066)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein localization to nucleus (GO:0034504)|protein monoubiquitination (GO:0006513)|protein sumoylation (GO:0016925)|regulation of cell proliferation (GO:0042127)|retina layer formation (GO:0010842)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|gamma-tubulin complex (GO:0000930)|midbody (GO:0030496)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|PML body (GO:0016605)|spindle pole (GO:0000922)|ubiquitin ligase complex (GO:0000151)	antigen binding (GO:0003823)|DNA binding (GO:0003677)|DNA topoisomerase binding (GO:0044547)|SUMO ligase activity (GO:0019789)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		AGTAAAAATGGTCTTAAATCA	0.373																																					p.P342S		Atlas-SNP	.											.	TOPORS	127	.	0			c.C1024T						.						55	55	55					9																	32543499		2202	4300	6502	SO:0001583	missense	10210	exon3			AAAATGGTCTTAA	AF098300	CCDS6527.1, CCDS56566.1	9p21	2013-01-09	2010-09-17		ENSG00000197579	ENSG00000197579		"RING-type (C3HC4) zinc fingers"	21653	protein-coding gene	gene with protein product		609507	"retinitis pigmentosa 31 (autosomal dominant)", "topoisomerase I binding, arginine/serine-rich"	RP31		10352183, 12083797, 17924349	Standard	NM_005802		Approved	TP53BPL, LUN	uc003zrb.3	Q9NS56	OTTHUMG00000019743	ENST00000360538.2:c.1024C>T	chr9.hg19:g.32543499G>A	ENSP00000353735:p.Pro342Ser	68.0	0.0		69.0	15.0	NM_005802	O43273|Q6P987|Q9NS55|Q9UNR9	Missense_Mutation	SNP	ENST00000360538.2	hg19	CCDS6527.1	.	.	.	.	.	.	.	.	.	.	G	10.46	1.355316	0.24512	.	.	ENSG00000197579	ENST00000360538;ENST00000379858	T;T	0.18810	2.19;2.21	5.93	5.93	0.95920	.	0.000000	0.49916	D	0.000125	T	0.29524	0.0736	L	0.54323	1.7	0.58432	D	0.999993	D	0.62365	0.991	P	0.50192	0.634	T	0.00577	-1.1662	10	0.41790	T	0.15	-32.9389	13.1153	0.59297	0.0766:0.0:0.9234:0.0	.	342	Q9NS56	TOPRS_HUMAN	S	342;277	ENSP00000353735:P342S;ENSP00000369187:P277S	ENSP00000353735:P342S	P	-	1	0	TOPORS	32533499	1.000000	0.71417	1.000000	0.80357	0.417000	0.31264	7.623000	0.83113	2.805000	0.96524	0.655000	0.94253	CCA	.	.		0.373	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802		A	32543499	G	A	32543499	3	1	353	1	0	0	0	0	1	0	0	0	16385	1261	44	3	2117	3	TOPORS	9	32543499	Missense_Mutation	SNP	G	TCGA-WQ-AB4B-01A-11D-A40P-10		32543499	108669932	31	49944										
TRPM3	80036	hgsc.bcm.edu	37	chr9	73213415	73213415	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	gagacggatataccagtaaaTgatgttcacgcagtagatga	11	6	1	4			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr9:73213415T>A	ENST00000377111.2	-	20	3175	c.2932A>T	c.(2932-2934)Att>Ttt	p.I978F	TRPM3_ENST00000408909.2_Missense_Mutation_p.I837F|TRPM3_ENST00000377110.3_Missense_Mutation_p.I978F|TRPM3_ENST00000377105.1_Missense_Mutation_p.I837F|TRPM3_ENST00000357533.2_Missense_Mutation_p.I982F|TRPM3_ENST00000377106.1_Missense_Mutation_p.I850F|TRPM3_ENST00000396285.1_Missense_Mutation_p.I825F|TRPM3_ENST00000423814.3_Missense_Mutation_p.I1005F|TRPM3_ENST00000360823.2_Missense_Mutation_p.I840F|TRPM3_ENST00000396292.4_Missense_Mutation_p.I850F|TRPM3_ENST00000358082.3_Missense_Mutation_p.I840F|TRPM3_ENST00000396280.5_Missense_Mutation_p.I827F	NM_001007471.2	NP_001007472.2	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	1003					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						TACCAGTAAATGATGTTCACG	0.478																																					p.I978F		Atlas-SNP	.											.	TRPM3	700	.	0			c.A2932T						.						137	129	132					9																	73213415		2203	4300	6503	SO:0001583	missense	80036	exon20			AGTAAATGATGTT	AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"Voltage-gated ion channels / Transient receptor potential cation channels"	17992	protein-coding gene	gene with protein product	"melastatin 2"	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377111.2:c.2932A>T	chr9.hg19:g.73213415T>A	ENSP00000366315:p.Ile978Phe	179.0	0.0		183.0	29.0	NM_001007471	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Missense_Mutation	SNP	ENST00000377111.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.33|17.33	3.361424|3.361424	0.61403|0.61403	.|.	.|.	ENSG00000083067|ENSG00000083067	ENST00000396280|ENST00000377111;ENST00000377110;ENST00000377106;ENST00000360823;ENST00000377105;ENST00000357533;ENST00000408909;ENST00000396285;ENST00000396292;ENST00000358082;ENST00000423814	.|T;T;T;T;T;T;T;T;T;T;T	.|0.74737	.|-0.87;-0.87;-0.87;-0.87;-0.87;-0.87;-0.87;-0.87;-0.87;-0.87;-0.87	4.87|4.87	3.7|3.7	0.42460|0.42460	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.85026|0.85026	0.5603|0.5603	M|M	0.80422|0.80422	2.495|2.495	0.46927|0.46927	D|D	0.999253|0.999253	.|D;B;D;D;B;P;P;B	.|0.76494	.|0.963;0.169;0.999;0.97;0.027;0.884;0.95;0.001	.|P;B;D;P;B;P;P;B	.|0.87578	.|0.723;0.227;0.998;0.819;0.174;0.8;0.712;0.018	D|D	0.85462|0.85462	0.1167|0.1167	5|10	.|0.72032	.|D	.|0.01	-13.6893|-13.6893	11.0597|11.0597	0.47940|0.47940	0.1393:0.0:0.0:0.8607|0.1393:0.0:0.0:0.8607	.|.	.|978;978;968;982;840;837;950;825	.|Q9HCF6-2;Q9HCF6-10;Q9HCF6-4;A2A3F7;A2A3F4;G5E9G1;Q9HCF6-8;A2A3F3	.|.;.;.;.;.;.;.;.	L|F	826|978;978;850;840;837;982;837;825;850;840;1005	.|ENSP00000366315:I978F;ENSP00000366314:I978F;ENSP00000366310:I850F;ENSP00000354066:I840F;ENSP00000366309:I837F;ENSP00000350140:I982F;ENSP00000386127:I837F;ENSP00000379581:I825F;ENSP00000379587:I850F;ENSP00000350791:I840F;ENSP00000389542:I1005F	.|ENSP00000350140:I982F	H|I	-|-	2|1	0|0	TRPM3|TRPM3	72403235|72403235	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.984000|0.984000	0.73092|0.73092	8.031000|8.031000	0.88826|0.88826	0.780000|0.780000	0.33566|0.33566	0.467000|0.467000	0.42956|0.42956	CAT|ATT	.	.		0.478	TRPM3-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000214157.5	NM_206945		A	73213415	T	A	73213415	3	1	353	1	0	0	0	0	1	0	0	0	16602	1464	51	4	2215	4	TRPM3	9	73213415	Missense_Mutation	SNP	T	TCGA-WQ-AB4B-01A-11D-A40P-10	40669916	73213415	68000016	32	49945										
TRIM32	22954	hgsc.bcm.edu	37	chr9	119460448	119460448	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	tccctgtcaaagaagcagctGaggagcggcgtcgggacttt	14	10	1	2			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr9:119460448G>A	ENST00000450136.1	+	2	588	c.427G>A	c.(427-429)Gag>Aag	p.E143K	ASTN2_ENST00000361209.2_Intron|ASTN2_ENST00000361477.3_Intron|ASTN2_ENST00000313400.4_Intron|ASTN2_ENST00000373996.3_Intron|TRIM32_ENST00000373983.2_Missense_Mutation_p.E143K	NM_001099679.1|NM_012210.3	NP_001093149.1|NP_036342.2	Q13049	TRI32_HUMAN	tripartite motif containing 32	143					fat cell differentiation (GO:0045444)|innate immune response (GO:0045087)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell motility (GO:2000147)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neurogenesis (GO:0050769)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of proteolysis (GO:0045862)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of type I interferon production (GO:0032481)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of type I interferon production (GO:0032479)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|striated muscle myosin thick filament (GO:0005863)	ligase activity (GO:0016874)|myosin binding (GO:0017022)|protein self-association (GO:0043621)|RNA binding (GO:0003723)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|translation initiation factor binding (GO:0031369)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(5)|liver(1)|lung(6)|prostate(1)|skin(2)|urinary_tract(1)	26						AGAAGCAGCTGAGGAGCGGCG	0.592																																					p.E143K	Esophageal Squamous(92;212 1916 19711 26951)	Atlas-SNP	.											.	TRIM32	67	.	0			c.G427A						.						49	56	53					9																	119460448		2202	4299	6501	SO:0001583	missense	22954	exon2			GCAGCTGAGGAGC	U18543	CCDS6817.1	9q33.1	2014-09-17	2011-01-25		ENSG00000119401	ENSG00000119401		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16380	protein-coding gene	gene with protein product		602290	"limb girdle muscular dystrophy 2H (autosomal recessive)", "tripartite motif-containing 32"	LGMD2H		11331580, 7778269, 16606853	Standard	NM_001099679		Approved	HT2A, TATIP, BBS11	uc004bjx.2	Q13049	OTTHUMG00000021026	ENST00000450136.1:c.427G>A	chr9.hg19:g.119460448G>A	ENSP00000408292:p.Glu143Lys	110.0	0.0		106.0	50.0	NM_012210	Q9NQP8	Missense_Mutation	SNP	ENST00000450136.1	hg19	CCDS6817.1	.	.	.	.	.	.	.	.	.	.	G	15.06	2.719889	0.48728	.	.	ENSG00000119401	ENST00000450136;ENST00000373983;ENST00000411410	T;T;T	0.65178	-0.14;-0.14;0.4	5.36	5.36	0.76844	.	0.140662	0.45867	D	0.000331	T	0.45597	0.1350	L	0.27053	0.805	0.47994	D	0.999568	B	0.31318	0.319	B	0.24701	0.055	T	0.40040	-0.9584	9	.	.	.	-20.3697	12.4378	0.55608	0.0767:0.0:0.9233:0.0	.	143	Q13049	TRI32_HUMAN	K	143	ENSP00000408292:E143K;ENSP00000363095:E143K;ENSP00000412603:E143K	.	E	+	1	0	TRIM32	118500269	1.000000	0.71417	0.981000	0.43875	0.952000	0.60782	7.630000	0.83225	2.486000	0.83907	0.655000	0.94253	GAG	.	.		0.592	TRIM32-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055466.2	NM_012210		A	119460448	G	A	119460448	3	1	353	1	0	0	0	0	1	0	0	0	16521	1291	45	3	429	3	TRIM32	9	119460448	Missense_Mutation	SNP	G	TCGA-WQ-AB4B-01A-11D-A40P-10	46247033	119460448	21752983	33	49946										
ATRNL1	26033	hgsc.bcm.edu	37	chr10	117278802	117278802	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	tcacaacacaatacaatcatGgaccttgtgcagttttttgt	6	9	2	0			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr10:117278802G>A	ENST00000355044.3	+	25	3810	c.3684G>A	c.(3682-3684)atG>atA	p.M1228I	ATRNL1_ENST00000423111.2_Missense_Mutation_p.M279I|ATRNL1_ENST00000303745.7_Missense_Mutation_p.M21I	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	1228					G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(11)|liver(2)|lung(44)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		ATACAATCATGGACCTTGTGC	0.328																																					p.M1228I		Atlas-SNP	.											.	ATRNL1	219	.	0			c.G3684A						.						140	133	135					10																	117278802		2202	4300	6502	SO:0001583	missense	26033	exon25			AATCATGGACCTT	AB011106	CCDS7592.1, CCDS73204.1	10q26	2004-03-04			ENSG00000107518	ENSG00000107518			29063	protein-coding gene	gene with protein product		612869				9628581	Standard	NM_001276282		Approved	KIAA0534, FLJ45344, ALP	uc001lcg.3	Q5VV63	OTTHUMG00000019096	ENST00000355044.3:c.3684G>A	chr10.hg19:g.117278802G>A	ENSP00000347152:p.Met1228Ile	102.0	0.0		96.0	42.0	NM_207303	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Missense_Mutation	SNP	ENST00000355044.3	hg19	CCDS7592.1	.	.	.	.	.	.	.	.	.	.	G	16.69	3.192783	0.58017	.	.	ENSG00000107518	ENST00000355044;ENST00000423111;ENST00000303745	T;T;T	0.44881	0.91;0.91;0.91	5.98	5.98	0.97165	.	0.034093	0.85682	D	0.000000	T	0.25901	0.0631	N	0.05306	-0.075	0.41861	D	0.990225	B;B	0.12013	0.005;0.001	B;B	0.11329	0.006;0.002	T	0.07751	-1.0756	10	0.28530	T	0.3	-15.5861	17.3533	0.87329	0.0:0.0:1.0:0.0	.	279;1228	B4DH41;Q5VV63	.;ATRN1_HUMAN	I	1228;279;21	ENSP00000347152:M1228I;ENSP00000409624:M279I;ENSP00000307660:M21I	ENSP00000307660:M21I	M	+	3	0	ATRNL1	117268792	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.537000	0.82033	2.843000	0.97960	0.585000	0.79938	ATG	.	.		0.328	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349		A	117278802	G	A	117278802	3	1	353	1	0	0	0	0	1	0	0	0	1207	1348	47	3	3782	3	ATRNL1	10	117278802	Missense_Mutation	SNP	G	TCGA-WQ-AB4B-01A-11D-A40P-10		117278802	18255945	34	49947										
FOXI2	399823	hgsc.bcm.edu	37	chr10	129537185	129537185	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	agaccgcggccgccggcttcCgcctcagtcacctcctctac	9	20	3	1			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr10:129537185C>T	ENST00000388920.4	+	2	952	c.913C>T	c.(913-915)Cgc>Tgc	p.R305C		NM_207426.2	NP_997309.2	Q6ZQN5	FOXI2_HUMAN	forkhead box I2	305					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R305G(1)|p.R121G(1)		large_intestine(1)|lung(3)	4		all_epithelial(44;0.0021)|all_lung(145;0.0586)|Lung NSC(174;0.0765)|all_neural(114;0.201)|Glioma(114;0.222)				CGCCGGCTTCCGCCTCAGTCA	0.697																																					p.R305C	Esophageal Squamous(54;1038 1280 2528 31583)	Atlas-SNP	.											FOXI2_ENST00000388920,NS,carcinoma,0,2	FOXI2	35	.	2	Substitution - Missense(2)	lung(2)	c.C913T						.						9	13	12					10																	129537185		2153	4242	6395	SO:0001583	missense	399823	exon2			GGCTTCCGCCTCA	AK128865	CCDS7655.2	10q26.2	2008-04-10			ENSG00000186766	ENSG00000186766		"Forkhead boxes"	32448	protein-coding gene	gene with protein product							Standard	NM_207426		Approved	FLJ46831	uc009yas.2	Q6ZQN5	OTTHUMG00000019250	ENST00000388920.4:c.913C>T	chr10.hg19:g.129537185C>T	ENSP00000373572:p.Arg305Cys	63.0	0.0		72.0	6.0	NM_207426		Missense_Mutation	SNP	ENST00000388920.4	hg19	CCDS7655.2	.	.	.	.	.	.	.	.	.	.	C	11.67	1.707772	0.30322	.	.	ENSG00000186766	ENST00000388920	D	0.93133	-3.17	4.14	2.06	0.26882	.	0.117488	0.52532	D	0.000074	D	0.86506	0.5949	L	0.32530	0.975	0.31787	N	0.630135	D	0.61697	0.99	B	0.43809	0.432	D	0.85324	0.1086	10	0.87932	D	0	.	2.4968	0.04623	0.2033:0.5074:0.1818:0.1075	.	305	Q6ZQN5	FOXI2_HUMAN	C	305	ENSP00000373572:R305C	ENSP00000373572:R305C	R	+	1	0	FOXI2	129427175	0.658000	0.27402	0.951000	0.38953	0.499000	0.33736	0.440000	0.21592	0.883000	0.36040	0.555000	0.69702	CGC	.	.		0.697	FOXI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050984.2	NM_207426		T	129537185	C	T	129537185	3	4	353	1	0	0	0	0	1	0	0	0	6018	652	23	1	919	1	FOXI2	10	129537185	Missense_Mutation	SNP	C	TCGA-WQ-AB4B-01A-11D-A40P-10	12258383	129537185	5997562	35	49948										
MUC6	4588	hgsc.bcm.edu	37	chr11	1031883	1031883	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	ccccagctccacgatgatccGcgagatgctcccgtctgggc	11	17	1	2			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr11:1031883G>A	ENST00000421673.2	-	3	336	c.286C>T	c.(286-288)Cgg>Tgg	p.R96W		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	96	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		ACGATGATCCGCGAGATGCTC	0.657																																					p.R96W		Atlas-SNP	.											.	MUC6	408	.	0			c.C286T						.						53	59	57					11																	1031883		2132	4223	6355	SO:0001583	missense	4588	exon3			TGATCCGCGAGAT	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"Mucins"	7517	protein-coding gene	gene with protein product		158374	"mucin 6, gastric"			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.286C>T	chr11.hg19:g.1031883G>A	ENSP00000406861:p.Arg96Trp	63.0	0.0		73.0	9.0	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	hg19	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	G	9.224	1.034049	0.19590	.	.	ENSG00000184956	ENST00000421673;ENST00000525923	T;T	0.59772	0.24;0.24	4.03	0.176	0.15049	von Willebrand factor, type D domain (3);	0.000000	0.28555	U	0.014939	T	0.72463	0.3463	M	0.78344	2.41	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.65344	-0.6191	10	0.62326	D	0.03	.	12.1996	0.54317	0.0:0.0:0.4457:0.5543	.	96	Q6W4X9	MUC6_HUMAN	W	96;120	ENSP00000406861:R96W;ENSP00000433790:R120W	ENSP00000406861:R96W	R	-	1	2	MUC6	1021883	0.024000	0.19004	0.043000	0.18650	0.036000	0.12997	1.104000	0.31074	0.282000	0.22254	-0.360000	0.07572	CGG	.	.		0.657	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540		A	1031883	G	A	1031883	3	1	353	1	0	0	0	0	1	0	0	0	9989	1086	38	1	7157	1	MUC6	11	1031883	Missense_Mutation	SNP	G	TCGA-WQ-AB4B-01A-11D-A40P-10		1031883	133974633	36	49949										
MUC5B	727897	hgsc.bcm.edu	37	chr11	1251007	1251007	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	cggccgcacctacagcccggGcacctccttcaacaccacct	7	21	1	0			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr11:1251007G>A	ENST00000529681.1	+	10	1248	c.1190G>A	c.(1189-1191)gGc>gAc	p.G397D	MUC5B_ENST00000447027.1_Missense_Mutation_p.G400D	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	397					cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		TACAGCCCGGGCACCTCCTTC	0.677																																					p.G397D		Atlas-SNP	.											.	MUC5B	473	.	0			c.G1190A						.						17	21	20					11																	1251007		2113	4204	6317	SO:0001583	missense	727897	exon10			GCCCGGGCACCTC	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.1190G>A	chr11.hg19:g.1251007G>A	ENSP00000436812:p.Gly397Asp	41.0	0.0		45.0	14.0	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	hg19	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	G	11.87	1.767852	0.31320	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.27890	1.64;1.89	3.82	3.82	0.43975	VWC out (1);	.	.	.	.	T	0.64538	0.2607	M	0.92507	3.315	0.49915	D	0.999837	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.999	T	0.76597	-0.2901	9	0.87932	D	0	.	15.9105	0.79470	0.0:0.0:1.0:0.0	.	397;1056;400	Q9HC84;A7Y9J9;E9PBJ0	MUC5B_HUMAN;.;.	D	397;400;398;433	ENSP00000436812:G397D;ENSP00000415793:G400D	ENSP00000343037:G398D	G	+	2	0	MUC5B	1207583	1.000000	0.71417	0.147000	0.22382	0.293000	0.27360	6.443000	0.73447	1.972000	0.57404	0.313000	0.20887	GGC	.	.		0.677	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		A	1251007	G	A	1251007	3	1	353	1	0	0	0	0	1	0	0	0	9988	1203	42	3	1237	3	MUC5B	11	1251007	Missense_Mutation	SNP	G	TCGA-WQ-AB4B-01A-11D-A40P-10	219124	1251007	133755509	37	49950										
TCIRG1	10312	hgsc.bcm.edu	37	chr11	67815394	67815394	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	atgcttaccctggatcccaaCgtcaccggtgtcttcctggg	10	14	2	0			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr11:67815394C>T	ENST00000265686.3	+	13	1617	c.1509C>T	c.(1507-1509)aaC>aaT	p.N503N	TCIRG1_ENST00000532635.1_Silent_p.N287N|RP11-802E16.3_ENST00000529934.1_RNA	NM_006019.3	NP_006010.2	Q13488	VPP3_HUMAN	T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 subunit A3	503					ATP hydrolysis coupled proton transport (GO:0015991)|cellular defense response (GO:0006968)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of cell proliferation (GO:0008284)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	hydrogen ion transmembrane transporter activity (GO:0015078)|transporter activity (GO:0005215)			breast(1)|endometrium(4)|large_intestine(3)|lung(4)|ovary(3)|prostate(1)	16						TGGATCCCAACGTCACCGGTG	0.662																																					p.N503N		Atlas-SNP	.											.	TCIRG1	40	.	0			c.C1509T						.						123	101	109					11																	67815394		2200	4294	6494	SO:0001819	synonymous_variant	10312	exon13			TCCCAACGTCACC	AF025374	CCDS8177.1, CCDS53670.1	11q13.2	2014-09-17	2006-01-20		ENSG00000110719	ENSG00000110719		"ATPases / V-type"	11647	protein-coding gene	gene with protein product	"T-cell immune response cDNA 7"	604592	"T-cell, immune regulator 1", "T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein a isoform 3", "T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3"			8579597, 9806637	Standard	NM_006019		Approved	TIRC7, OC-116, OC116, ATP6N1C, Atp6i, a3, ATP6V0A3	uc001one.3	Q13488	OTTHUMG00000167358	ENST00000265686.3:c.1509C>T	chr11.hg19:g.67815394C>T		140.0	0.0		118.0	36.0	NM_006019	O75877|Q8WVC5	Silent	SNP	ENST00000265686.3	hg19	CCDS8177.1																																																																																			.	.		0.662	TCIRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394305.1	NM_006019		T	67815394	C	T	67815394	2	4	353	1	0	0	0	0	0	0	0	1	15718	535	19	1		1	TCIRG1	11	67815394	Silent	SNP	C	TCGA-WQ-AB4B-01A-11D-A40P-10	66564387	67815394	67191122	38	49951										
CCDC60	160777	hgsc.bcm.edu	37	chr12	119978493	119978493	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	cagagccggatcaacataccCattgggccctacagcgccct	9	16	1	1			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr12:119978493C>T	ENST00000327554.2	+	14	2091	c.1626C>T	c.(1624-1626)ccC>ccT	p.P542P	RP11-768F21.1_ENST00000509470.2_lincRNA	NM_178499.3	NP_848594.2	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60	542										endometrium(4)|kidney(3)|large_intestine(8)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)		TCAACATACCCATTGGGCCCT	0.532																																					p.P542P		Atlas-SNP	.											.	CCDC60	84	.	0			c.C1626T						.						112	104	106					12																	119978493		2203	4300	6503	SO:0001819	synonymous_variant	160777	exon14			CATACCCATTGGG	BC040553	CCDS9190.1	12q24.23	2006-02-03			ENSG00000183273	ENSG00000183273			28610	protein-coding gene	gene with protein product						12477932	Standard	NM_178499		Approved	MGC39827	uc001txe.3	Q8IWA6	OTTHUMG00000168943	ENST00000327554.2:c.1626C>T	chr12.hg19:g.119978493C>T		72.0	0.0		57.0	18.0	NM_178499		Silent	SNP	ENST00000327554.2	hg19	CCDS9190.1																																																																																			.	.		0.532	CCDC60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401680.1	NM_178499		T	119978493	C	T	119978493	2	4	353	1	0	0	0	0	0	0	0	1	2833	581	21	3		3	CCDC60	12	119978493	Silent	SNP	C	TCGA-WQ-AB4B-01A-11D-A40P-10		119978493	13873402	39	49952										
COG3	83548	hgsc.bcm.edu	37	chr13	46085912	46085912	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	tccaccagagggcagtgttcCaaggattatcacaggaagca	11	10	1	1			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr13:46085912C>A	ENST00000349995.5	+	16	1844	c.1732C>A	c.(1732-1734)Caa>Aaa	p.Q578K	COG3_ENST00000465942.1_3'UTR	NM_031431.3	NP_113619	Q96JB2	COG3_HUMAN	component of oligomeric golgi complex 3	578					ER to Golgi vesicle-mediated transport (GO:0006888)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|stomach(1)	24		Lung NSC(96;0.000145)|Breast(56;0.000596)|Prostate(109;0.00438)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000124)		GGCAGTGTTCCAAGGATTATC	0.398																																					p.Q578K	Ovarian(150;1048 1859 18083 21577 42700)	Atlas-SNP	.											.	COG3	52	.	0			c.C1732A						.						118	106	110					13																	46085912		2203	4300	6503	SO:0001583	missense	83548	exon16			GTGTTCCAAGGAT	AF131829	CCDS9398.1	13q14.11	2008-02-05			ENSG00000136152	ENSG00000136152		"Components of oligomeric golgi complex"	18619	protein-coding gene	gene with protein product		606975				11980916	Standard	NM_031431		Approved	SEC34	uc001vak.3	Q96JB2	OTTHUMG00000016855	ENST00000349995.5:c.1732C>A	chr13.hg19:g.46085912C>A	ENSP00000258654:p.Gln578Lys	82.0	0.0		83.0	9.0	NM_031431	B2RAW5|Q5VT70|Q8IXX4|Q9BZ92	Missense_Mutation	SNP	ENST00000349995.5	hg19	CCDS9398.1	.	.	.	.	.	.	.	.	.	.	C	19.92	3.916668	0.73098	.	.	ENSG00000136152	ENST00000349995	T	0.41065	1.01	5.41	5.41	0.78517	.	0.059460	0.64402	D	0.000001	T	0.49029	0.1533	M	0.77820	2.39	0.80722	D	1	B;B	0.22909	0.077;0.045	B;B	0.25614	0.062;0.042	T	0.44097	-0.9350	10	0.35671	T	0.21	-11.8392	18.3612	0.90375	0.0:1.0:0.0:0.0	.	415;578	B4E2F3;Q96JB2	.;COG3_HUMAN	K	578	ENSP00000258654:Q578K	ENSP00000258654:Q578K	Q	+	1	0	COG3	44983913	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.601000	0.67606	2.814000	0.96858	0.591000	0.81541	CAA	.	.		0.398	COG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044777.2			A	46085912	C	A	46085912	3	1	353	1	0	0	0	0	1	0	0	0	3661	595	21	3	1794	3	COG3	13	46085912	Missense_Mutation	SNP	C	TCGA-WQ-AB4B-01A-11D-A40P-10		46085912	69083966	40	49953										
FAM179B	23116	hgsc.bcm.edu	37	chr14	45496671	45496671	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	tatcttgatgttgagaatgaAaaagatgtaaggttatttgc	10	2	1	4			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr14:45496671A>G	ENST00000361577.3	+	9	3712	c.3498A>G	c.(3496-3498)gaA>gaG	p.E1166E	FAM179B_ENST00000382233.2_3'UTR|KLHL28_ENST00000553817.1_Intron|FAM179B_ENST00000361462.2_Silent_p.E1166E	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	1166										endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						TTGAGAATGAAAAAGATGTAA	0.303																																					p.E1166E		Atlas-SNP	.											.	FAM179B	115	.	0			c.A3498G						.						42	43	43					14																	45496671		2203	4300	6503	SO:0001819	synonymous_variant	23116	exon9			GAATGAAAAAGAT	AB007883	CCDS9681.1	14q21.3	2008-07-21	2008-07-21	2008-07-21	ENSG00000198718	ENSG00000198718			19959	protein-coding gene	gene with protein product			"KIAA0423"	KIAA0423			Standard	XM_005267451		Approved		uc001wvv.3	Q9Y4F4	OTTHUMG00000140264	ENST00000361577.3:c.3498A>G	chr14.hg19:g.45496671A>G		210.0	0.0		167.0	39.0	NM_015091	Q68D66|Q6PG27	Silent	SNP	ENST00000361577.3	hg19	CCDS9681.1																																																																																			.	.		0.303	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781		G	45496671	A	G	45496671	2	3	353	1	0	0	0	0	0	0	0	1	5511	11	1	2		2	FAM179B	14	45496671	Silent	SNP	A	TCGA-WQ-AB4B-01A-11D-A40P-10		45496671	61852869	41	49954										
ZFP36L1	677	hgsc.bcm.edu	37	chr14	69256295	69256295	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	ctgaagatgggcaggcgtctTgagttgtccaaggtcgggga	17	7	1	3			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr14:69256295T>G	ENST00000439696.2	-	2	1273	c.972A>C	c.(970-972)tcA>tcC	p.S324S	ZFP36L1_ENST00000336440.3_Silent_p.S324S|ZFP36L1_ENST00000555997.1_3'UTR	NM_001244701.1|NM_004926.3	NP_001231630.1|NP_004917.2	Q07352	TISB_HUMAN	ZFP36 ring finger protein-like 1	324					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|T cell differentiation in thymus (GO:0033077)|vasculogenesis (GO:0001570)	cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(4)|kidney(1)|large_intestine(1)|liver(2)|lung(9)|ovary(1)|prostate(2)|urinary_tract(1)	21				all cancers(60;0.00203)|BRCA - Breast invasive adenocarcinoma(234;0.00205)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		GCAGGCGTCTTGAGTTGTCCA	0.612											OREG0022753	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S393S		Atlas-SNP	.											.	ZFP36L1	47	.	0			c.A1179C						.						93	95	95					14																	69256295		2203	4300	6503	SO:0001819	synonymous_variant	677	exon3			GCGTCTTGAGTTG	X79066	CCDS9791.1	14q22-q24	2012-11-27	2012-11-27	2001-11-23		ENSG00000185650		"RING-type (C3HC4) zinc fingers"	1107	protein-coding gene	gene with protein product		601064	"zinc finger protein, C3H type, 36-like 1", "zinc finger protein 36, C3H type-like 1"	BRF1		8024689	Standard	NM_004926		Approved	RNF162B, Berg36, ERF1, TIS11B, cMG1	uc021rve.1	Q07352		ENST00000439696.2:c.972A>C	chr14.hg19:g.69256295T>G		105.0	0.0	1113	73.0	11.0	NM_001244701	Q13851	Silent	SNP	ENST00000439696.2	hg19	CCDS9791.1																																																																																			.	.		0.612	ZFP36L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413227.1			G	69256295	T	G	69256295	2	3	353	1	0	0	0	0	0	0	0	1	17661	1799	63	5		5	ZFP36L1	14	69256295	Silent	SNP	T	TCGA-WQ-AB4B-01A-11D-A40P-10	23759624	69256295	38093245	42	49955										
GABRA5	2558	hgsc.bcm.edu	37	chr15	27193200	27193200	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	acgtcgaatacaacctcagtCtcagtaaaaccctctgaaga	6	12	3	2			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr15:27193200C>A	ENST00000335625.5	+	11	2097	c.1209C>A	c.(1207-1209)gtC>gtA	p.V403V	GABRA5_ENST00000400081.3_Silent_p.V403V|GABRA5_ENST00000355395.5_Silent_p.V403V	NM_000810.3	NP_000801.1	P31644	GBRA5_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 5	403					associative learning (GO:0008306)|behavioral fear response (GO:0001662)|brain development (GO:0007420)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(1)|upper_aerodigestive_tract(1)	49		all_lung(180;4.59e-13)|Breast(32;0.000563)|Colorectal(260;0.227)		all cancers(64;1.45e-08)|Epithelial(43;4.96e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0232)|Lung(196;0.182)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zopiclone(DB01198)	CAACCTCAGTCTCAGTAAAAC	0.428																																					p.V403V		Atlas-SNP	.											.	GABRA5	127	.	0			c.C1209A						.						48	46	46					15																	27193200		1853	4099	5952	SO:0001819	synonymous_variant	2558	exon11			CTCAGTCTCAGTA		CCDS45194.1	15q12	2012-06-22			ENSG00000186297	ENSG00000186297		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4079	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 5"	137142				1321750	Standard	NM_000810		Approved		uc021sgi.1	P31644	OTTHUMG00000171824	ENST00000335625.5:c.1209C>A	chr15.hg19:g.27193200C>A		395.0	0.0		427.0	180.0	NM_001165037	A8K338|Q14DC2|Q53XL6|Q9NYT3|Q9NYT4|Q9NYT5	Silent	SNP	ENST00000335625.5	hg19	CCDS45194.1																																																																																			.	.		0.428	GABRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415234.1			A	27193200	C	A	27193200	2	1	353	1	0	0	0	0	0	0	0	1	6172	900	32	3		3	GABRA5	15	27193200	Silent	SNP	C	TCGA-WQ-AB4B-01A-11D-A40P-10		27193200	75338192	43	49956										
PARP6	56965	hgsc.bcm.edu	37	chr15	72541642	72541642	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	ggtagatgcctttgccatagGctgctccatgcagcttgcag	12	11	0	1			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr15:72541642G>A	ENST00000569795.1	-	20	2192	c.1505C>T	c.(1504-1506)gCc>gTc	p.A502V	PARP6_ENST00000260376.7_Intron|PARP6_ENST00000413097.2_Intron|PARP6_ENST00000287196.9_Missense_Mutation_p.A502V			Q2NL67	PARP6_HUMAN	poly (ADP-ribose) polymerase family, member 6	502	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.						NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(8)|skin(1)|urinary_tract(1)	18						TTTGCCATAGGCTGCTCCATG	0.493																																					p.A502V		Atlas-SNP	.											.	PARP6	44	.	0			c.C1505T						.						85	86	86					15																	72541642		1939	4130	6069	SO:0001583	missense	56965	exon19			CCATAGGCTGCTC	AL390093	CCDS10241.2	15q22	2010-02-16			ENSG00000137817	ENSG00000137817		"Poly (ADP-ribose) polymerases"	26921	protein-coding gene	gene with protein product						15273990	Standard	XM_005254557		Approved	pART17	uc002auc.3	Q2NL67	OTTHUMG00000133443	ENST00000569795.1:c.1505C>T	chr15.hg19:g.72541642G>A	ENSP00000456348:p.Ala502Val	58.0	0.0		70.0	31.0	NM_020214	Q9H7C5|Q9H9X6|Q9HAF3|Q9NPS6|Q9UFG4	Missense_Mutation	SNP	ENST00000569795.1	hg19	CCDS10241.2	.	.	.	.	.	.	.	.	.	.	G	26.1	4.704153	0.88924	.	.	ENSG00000137817	ENST00000419739;ENST00000287196	T;T	0.13089	2.62;2.62	4.93	4.93	0.64822	Poly(ADP-ribose) polymerase, catalytic domain (2);	0.000000	0.64402	U	0.000002	T	0.28200	0.0696	L	0.39514	1.22	0.80722	D	1	P;D;D	0.69078	0.94;0.997;0.995	P;D;P	0.74348	0.842;0.983;0.893	T	0.00662	-1.1621	10	0.26408	T	0.33	-31.6893	17.6582	0.88184	0.0:0.0:1.0:0.0	.	503;502;435	Q0VDG0;Q2NL67;A0PJ50	.;PARP6_HUMAN;.	V	503;502	ENSP00000403265:A503V;ENSP00000287196:A502V	ENSP00000287196:A502V	A	-	2	0	PARP6	70328696	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.645000	0.83430	2.719000	0.93026	0.655000	0.94253	GCC	.	.		0.493	PARP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257315.2	NM_020214		A	72541642	G	A	72541642	3	1	353	1	0	0	0	0	1	0	0	0	11473	1203	42	3	407	3	PARP6	15	72541642	Missense_Mutation	SNP	G	TCGA-WQ-AB4B-01A-11D-A40P-10	45348442	72541642	29989750	44	49957										
BAIAP3	8938	hgsc.bcm.edu	37	chr16	1396324	1396324	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	ccctggacgatgatctgcaaCgggaggcccacacggtgaca	13	13	1	2			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr16:1396324C>T	ENST00000324385.5	+	25	2718	c.2560C>T	c.(2560-2562)Cgg>Tgg	p.R854W	BAIAP3_ENST00000397488.2_Missense_Mutation_p.R836W|BAIAP3_ENST00000564213.1_3'UTR|BAIAP3_ENST00000426824.3_Missense_Mutation_p.R819W|BAIAP3_ENST00000562208.1_Missense_Mutation_p.R796W|BAIAP3_ENST00000421665.2_Missense_Mutation_p.R783W|BAIAP3_ENST00000397489.1_Missense_Mutation_p.R836W|BAIAP3_ENST00000568887.1_Missense_Mutation_p.R791W	NM_003933.4	NP_003924.2	O94812	BAIP3_HUMAN	BAI1-associated protein 3	854					G-protein coupled receptor signaling pathway (GO:0007186)|neurotransmitter secretion (GO:0007269)		protein C-terminus binding (GO:0008022)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(25)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42		Hepatocellular(780;0.0893)				TGATCTGCAACGGGAGGCCCA	0.701																																					p.R854W		Atlas-SNP	.											.	BAIAP3	88	.	0			c.C2560T						.						37	39	38					16																	1396324		2195	4297	6492	SO:0001583	missense	8938	exon25			CTGCAACGGGAGG	AB017111	CCDS10434.1, CCDS55978.1, CCDS55979.1, CCDS58402.1, CCDS58403.1, CCDS66894.1	16p13.3	2008-07-04			ENSG00000007516	ENSG00000007516			948	protein-coding gene	gene with protein product		604009				9790924	Standard	NM_003933		Approved	BAP3, KIAA0734	uc002clk.2	O94812	OTTHUMG00000047833	ENST00000324385.5:c.2560C>T	chr16.hg19:g.1396324C>T	ENSP00000324510:p.Arg854Trp	171.0	0.0		153.0	50.0	NM_003933	A2A2B2|B2RCD7|B4DGS5|B4DIK3|B4DRK9|B4DRP1|E7EUB9|H3BUH8|H3BVI3|H7C2Q1|O94839|Q2M226|Q658J2|Q76N05|Q96RZ3|Q9UJK1	Missense_Mutation	SNP	ENST00000324385.5	hg19	CCDS10434.1	.	.	.	.	.	.	.	.	.	.	C	16.24	3.067661	0.55539	.	.	ENSG00000007516	ENST00000426824;ENST00000397488;ENST00000324385;ENST00000397489;ENST00000421665	T;T;T;T;T	0.72394	-0.65;-0.65;-0.65;-0.65;-0.62	3.98	2.94	0.34122	.	0.187167	0.43416	D	0.000562	T	0.76011	0.3928	L	0.59436	1.845	0.54753	D	0.999984	D;D;D;D	0.89917	0.999;0.999;0.999;1.0	P;P;P;D	0.63192	0.614;0.684;0.781;0.912	T	0.76926	-0.2778	10	0.66056	D	0.02	-20.9903	8.256	0.31756	0.3634:0.6366:0.0:0.0	.	783;796;854;836	E7EUB9;B4DIK3;O94812;A2A2B2	.;.;BAIP3_HUMAN;.	W	819;836;854;836;783	ENSP00000407242:R819W;ENSP00000380625:R836W;ENSP00000324510:R854W;ENSP00000380626:R836W;ENSP00000409533:R783W	ENSP00000324510:R854W	R	+	1	2	BAIAP3	1336325	0.724000	0.28038	0.996000	0.52242	0.221000	0.24807	0.919000	0.28692	2.046000	0.60703	0.491000	0.48974	CGG	.	.		0.701	BAIAP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109056.3			T	1396324	C	T	1396324	3	4	353	1	0	0	0	0	1	0	0	0	1304	527	19	1	2658	1	BAIAP3	16	1396324	Missense_Mutation	SNP	C	TCGA-WQ-AB4B-01A-11D-A40P-10		1396324	88958429	45	49958										
TP53	7157	hgsc.bcm.edu	37	chr17	7577538	7577538	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	tgatggtgaggatgggcctcCggttcatgccgcccatgcag	15	11	1	2	rs11540652		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr17:7577538C>T	ENST00000269305.4	-	7	932	c.743G>A	c.(742-744)cGg>cAg	p.R248Q	TP53_ENST00000445888.2_Missense_Mutation_p.R248Q|TP53_ENST00000413465.2_Missense_Mutation_p.R248Q|TP53_ENST00000359597.4_Missense_Mutation_p.R248Q|TP53_ENST00000455263.2_Missense_Mutation_p.R248Q|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Missense_Mutation_p.R248Q	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	248	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.		NR -> IP (in a sporadic cancer; somatic mutation).|NR -> KW (in sporadic cancers; somatic mutation).|R -> C (in a sporadic cancer; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:7682763}.|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs11540652). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:2263646, ECO:0000269|PubMed:7682763, ECO:0000269|PubMed:7887414}.|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:8829627}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R248Q(580)|p.R248L(75)|p.R248P(19)|p.R155Q(18)|p.0?(8)|p.?(5)|p.R155L(3)|p.R155P(2)|p.N247_R248delNR(2)|p.R248fs*16(2)|p.M246_P250delMNRRP(2)|p.R248_P250delRRP(1)|p.unknown(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*96(1)|p.R248fs*>39(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GATGGGCCTCCGGTTCATGCC	0.572	R248Q(BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(HCC1143_BREAST)|R248Q(HCC70_BREAST)|R248Q(HEC1A_ENDOMETRIUM)|R248Q(HS683_CENTRAL_NERVOUS_SYSTEM)|R248Q(HSC4_UPPER_AERODIGESTIVE_TRACT)|R248Q(KASUMI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KYSE150_OESOPHAGUS)|R248Q(MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NAMALWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NCIH211_LUNG)|R248Q(NCIN87_STOMACH)|R248Q(NIHOVCAR3_OVARY)|R248Q(NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(P12ICHIKAWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(PANC0203_PANCREAS)|R248Q(PC14_LUNG)|R248Q(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(RT112_URINARY_TRACT)|R248Q(SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SF295_CENTRAL_NERVOUS_SYSTEM)|R248Q(SKUT1_SOFT_TISSUE)|R248Q(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SW1463_LARGE_INTESTINE)|R248Q(WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.R248Q	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,adenocarcinoma,0,4	TP53	33396	.	725	Substitution - Missense(698)|Whole gene deletion(8)|Deletion - In frame(7)|Unknown(6)|Insertion - Frameshift(3)|Deletion - Frameshift(2)|Complex - compound substitution(1)	large_intestine(138)|breast(83)|haematopoietic_and_lymphoid_tissue(74)|lung(71)|upper_aerodigestive_tract(63)|central_nervous_system(46)|oesophagus(37)|urinary_tract(37)|ovary(36)|stomach(35)|endometrium(23)|skin(18)|prostate(11)|bone(10)|biliary_tract(9)|liver(9)|pancreas(7)|vulva(3)|kidney(3)|cervix(3)|peritoneum(2)|thyroid(2)|soft_tissue(1)|pituitary(1)|adrenal_gland(1)|small_intestine(1)|thymus(1)	c.G743A	GRCh37	CM920675	TP53	M	rs11540652	.	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	152	112	126	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	743,743,743,743,347,347,347	3.7	1	17	dbSNP_120	126	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense,missense	TP53	NM_000546.4,NM_001126112.1,NM_001126113.1,NM_001126114.1,NM_001126115.1,NM_001126116.1,NM_001126117.1	43,43,43,43,43,43,43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	248/394,248/394,248/347,248/342,116/262,116/210,116/215	7577538	1,13005	2203	4300	6503	SO:0001583	missense	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GGCCTCCGGTTCA	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.743G>A	chr17.hg19:g.7577538C>T	ENSP00000269305:p.Arg248Gln	98.0	0.0		86.0	18.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.822907	0.90873	0.0	1.16E-4	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99864	-7.28;-7.28;-7.28;-7.28;-7.28;-7.28;-7.28;-7.28	4.62	3.65	0.41850	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99840	0.9927	M	0.88640	2.97	0.58432	A	0.999994	D;D;D;D;D;D	0.89917	1.0;0.994;1.0;1.0;1.0;1.0	D;P;D;D;D;D	0.91635	0.996;0.882;0.999;0.995;0.996;0.995	D	0.96819	0.9602	9	0.72032	D	0.01	-9.5643	10.6687	0.45745	0.0:0.9059:0.0:0.0941	rs11540652;rs11540652	248;248;155;248;248;248	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	Q	248;248;248;248;248;248;237;155;116;155	ENSP00000410739:R248Q;ENSP00000352610:R248Q;ENSP00000269305:R248Q;ENSP00000398846:R248Q;ENSP00000391127:R248Q;ENSP00000391478:R248Q;ENSP00000425104:R116Q;ENSP00000423862:R155Q	ENSP00000269305:R248Q	R	-	2	0	TP53	7518263	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	5.884000	0.69729	1.305000	0.44909	0.462000	0.41574	CGG	.	.		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7577538	C	T	7577538	3	4	353	1	0	0	0	0	1	0	0	0	16396	652	23	1	547	1	TP53	17	7577538	Missense_Mutation	SNP	C	TCGA-WQ-AB4B-01A-11D-A40P-10		7577538	73617672	46	49959										
SOX9	6662	hgsc.bcm.edu	37	chr17	70120053	70120053	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	cccgcagcagcccccacaggCcccgccggccccgcaggcgc	12	24	0	0			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr17:70120053C>T	ENST00000245479.2	+	3	1427	c.1055C>T	c.(1054-1056)gCc>gTc	p.A352V		NM_000346.3	NP_000337.1	P48436	SOX9_HUMAN	SRY (sex determining region Y)-box 9	352	Gln/Pro-rich.				astrocyte fate commitment (GO:0060018)|branching involved in ureteric bud morphogenesis (GO:0001658)|cAMP-mediated signaling (GO:0019933)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cell fate specification (GO:0001708)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to heparin (GO:0071504)|cellular response to interleukin-1 (GO:0071347)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|chondrocyte hypertrophy (GO:0003415)|chromatin remodeling (GO:0006338)|cochlea morphogenesis (GO:0090103)|cytoskeleton organization (GO:0007010)|endocardial cushion morphogenesis (GO:0003203)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation involved in prostatic bud elongation (GO:0060517)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|ERK1 and ERK2 cascade (GO:0070371)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|heart valve development (GO:0003170)|heart valve formation (GO:0003188)|heart valve morphogenesis (GO:0003179)|intestinal epithelial structure maintenance (GO:0060729)|intrahepatic bile duct development (GO:0035622)|limb bud formation (GO:0060174)|lung epithelial cell differentiation (GO:0060487)|male germ-line sex determination (GO:0019100)|male gonad development (GO:0008584)|mammary gland development (GO:0030879)|metanephric nephron tubule formation (GO:0072289)|morphogenesis of a branching epithelium (GO:0061138)|negative regulation of apoptotic process (GO:0043066)|negative regulation of biomineral tissue development (GO:0070168)|negative regulation of bone mineralization (GO:0030502)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of immune system process (GO:0002683)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of ossification (GO:0030279)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell development (GO:0014032)|notochord development (GO:0030903)|nucleosome assembly (GO:0006334)|oligodendrocyte differentiation (GO:0048709)|ossification (GO:0001503)|otic vesicle formation (GO:0030916)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of extracellular matrix assembly (GO:1901203)|positive regulation of kidney development (GO:0090184)|positive regulation of male gonad development (GO:2000020)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein complex assembly (GO:0006461)|protein kinase B signaling (GO:0043491)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in lung morphogenesis (GO:0061046)|regulation of cell adhesion (GO:0030155)|regulation of cell cycle process (GO:0010564)|regulation of cell proliferation (GO:0042127)|regulation of cell proliferation involved in tissue homeostasis (GO:0060784)|regulation of epithelial cell proliferation involved in lung morphogenesis (GO:2000794)|renal vesicle induction (GO:0072034)|retina development in camera-type eye (GO:0060041)|retinal rod cell differentiation (GO:0060221)|Sertoli cell development (GO:0060009)|Sertoli cell differentiation (GO:0060008)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|spermatogenesis (GO:0007283)|tissue homeostasis (GO:0001894)|transcription from RNA polymerase II promoter (GO:0006366)|ureter morphogenesis (GO:0072197)|ureter smooth muscle cell differentiation (GO:0072193)|ureter urothelium development (GO:0072190)	nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enhancer binding (GO:0035326)|enhancer sequence-specific DNA binding (GO:0001158)|pre-mRNA intronic binding (GO:0097157)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase activity (GO:0004672)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(4)|large_intestine(11)|lung(5)|pancreas(1)|upper_aerodigestive_tract(2)	26		Colorectal(1115;0.245)	STAD - Stomach adenocarcinoma(260;0.119)			cccccacaggccccgccggcc	0.796																																					p.A352V	Pancreas(42;83 1041 2320 35205 39456)	Atlas-SNP	.											.	SOX9	91	.	0			c.C1055T						.						1	1	1					17																	70120053		522	1250	1772	SO:0001583	missense	6662	exon3			CACAGGCCCCGCC	S74506	CCDS11689.1	17q24.3	2013-10-17	2008-07-31		ENSG00000125398	ENSG00000125398		"SRY (sex determining region Y)-boxes"	11204	protein-coding gene	gene with protein product		608160	"campomelic dysplasia, autosomal sex-reversal"	CMD1, CMPD1		8348155	Standard	NM_000346		Approved	SRA1	uc002jiw.3	P48436	OTTHUMG00000166300	ENST00000245479.2:c.1055C>T	chr17.hg19:g.70120053C>T	ENSP00000245479:p.Ala352Val	135.0	0.0		61.0	23.0	NM_000346	Q53Y80	Missense_Mutation	SNP	ENST00000245479.2	hg19	CCDS11689.1	.	.	.	.	.	.	.	.	.	.	C	12.70	2.017390	0.35606	.	.	ENSG00000125398	ENST00000245479	T	0.77877	-1.13	3.95	1.68	0.24146	.	0.708385	0.11410	U	0.566885	T	0.61261	0.2333	N	0.19112	0.55	0.09310	N	1	B	0.12013	0.005	B	0.11329	0.006	T	0.45145	-0.9281	10	0.22109	T	0.4	.	9.3668	0.38230	0.3819:0.6181:0.0:0.0	.	352	P48436	SOX9_HUMAN	V	352	ENSP00000245479:A352V	ENSP00000245479:A352V	A	+	2	0	SOX9	67631648	.	.	0.953000	0.39169	0.700000	0.40528	.	.	0.607000	0.29982	0.313000	0.20887	GCC	.	.		0.796	SOX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389032.1	NM_000346		T	70120053	C	T	70120053	3	4	353	1	0	0	0	0	1	0	0	0	14973	739	26	3	1065	3	SOX9	17	70120053	Missense_Mutation	SNP	C	TCGA-WQ-AB4B-01A-11D-A40P-10	62542515	70120053	11075157	47	49960										
UNK	85451	hgsc.bcm.edu	37	chr17	73805893	73805893	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	cactctttgtgcaacacaaaTgcacgcagcatcggccctac	7	15	1	0			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr17:73805893T>C	ENST00000589666.1	+	2	267	c.157T>C	c.(157-159)Tgc>Cgc	p.C53R	UNK_ENST00000293218.3_Missense_Mutation_p.C129R	NM_001080419.2	NP_001073888.2	Q9C0B0	UNK_HUMAN	unkempt family zinc finger	53							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			cervix(3)|endometrium(8)|kidney(2)|large_intestine(5)|lung(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	25			all cancers(21;2.61e-06)|Epithelial(20;7.39e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|LUSC - Lung squamous cell carcinoma(166;0.154)			GCAACACAAATGCACGCAGCA	0.617																																					p.C53R		Atlas-SNP	.											.	UNK	87	.	0			c.T157C						.						28	33	32					17																	73805893		2168	4287	6455	SO:0001583	missense	85451	exon2			CACAAATGCACGC	AB051540	CCDS45778.1, CCDS45778.2	17q25.3	2013-10-17	2013-10-17	2007-02-06		ENSG00000132478		"Zinc fingers, CCCH-type domain containing"	29369	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 5", "zinc finger CCCH-type containing 5", "unkempt homolog (Drosophila)"	ZC3HDC5, ZC3H5		11214970	Standard	NM_001080419		Approved	KIAA1753	uc021udd.2	Q9C0B0		ENST00000589666.1:c.157T>C	chr17.hg19:g.73805893T>C	ENSP00000464893:p.Cys53Arg	154.0	0.0		124.0	29.0	NM_001080419		Missense_Mutation	SNP	ENST00000589666.1	hg19	CCDS45778.2	.	.	.	.	.	.	.	.	.	.	T	25.5	4.649439	0.87958	.	.	ENSG00000132478	ENST00000293218	.	.	.	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.77903	0.4200	M	0.73319	2.225	0.80722	D	1	D	0.71674	0.998	D	0.80764	0.994	T	0.80928	-0.1163	9	0.87932	D	0	-2.283	15.1024	0.72292	0.0:0.0:0.0:1.0	.	53	Q9C0B0	UNK_HUMAN	R	129	.	ENSP00000293218:C129R	C	+	1	0	UNK	71317488	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.040000	0.89188	1.971000	0.57363	0.459000	0.35465	TGC	.	.		0.617	UNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448835.1	NM_001080419		C	73805893	T	C	73805893	3	2	353	1	0	0	0	0	1	0	0	0	17015	1464	51	2	395	2	UNK	17	73805893	Missense_Mutation	SNP	T	TCGA-WQ-AB4B-01A-11D-A40P-10	3685840	73805893	7389317	48	49961										
ZNF91	7644	hgsc.bcm.edu	37	chr19	23542679	23542679	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	ttatgtgtagtaagctttgaGgatcgattaaaagctttgcc	10	5	0	1			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr19:23542679G>A	ENST00000300619.7	-	4	3307	c.3102C>T	c.(3100-3102)tcC>tcT	p.S1034S	ZNF91_ENST00000397082.2_Silent_p.S1002S|ZNF91_ENST00000599743.1_Intron|ZNF91_ENST00000596528.1_5'Flank	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	1034					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				TAAGCTTTGAGGATCGATTAA	0.388																																					p.S1034S		Atlas-SNP	.											.	ZNF91	349	.	0			c.C3102T						.						76	79	78					19																	23542679		2193	4290	6483	SO:0001819	synonymous_variant	7644	exon4			CTTTGAGGATCGA	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"Zinc fingers, C2H2-type", "-"	13166	protein-coding gene	gene with protein product		603971	"zinc finger protein 91 (HPF7, HTF10)"			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.3102C>T	chr19.hg19:g.23542679G>A		38.0	0.0		50.0	4.0	NM_003430	A8K5E1|B7Z6G6	Silent	SNP	ENST00000300619.7	hg19	CCDS42541.1																																																																																			.	.		0.388	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430		A	23542679	G	A	23542679	2	1	353	1	0	0	0	0	0	0	0	1	18215	987	35	3		3	ZNF91	19	23542679	Silent	SNP	G	TCGA-WQ-AB4B-01A-11D-A40P-10		23542679	35586304	49	49962										
RYR1	6261	hgsc.bcm.edu	37	chr19	38964339	38964340	+	In_Frame_Ins	INS	-	-	GGG													0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	cccgggggcaccccgcaggcINSggggggagaggcgcagcccg							TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr19:38964339_38964340insGGG	ENST00000359596.3	+	28	4088_4089	c.4088_4089insGGG	c.(4087-4092)gcgggg>gcGGGgggg	p.1365_1366insG	RYR1_ENST00000355481.4_In_Frame_Ins_p.1365_1366insG|RYR1_ENST00000360985.3_In_Frame_Ins_p.1365_1366insG			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1365	6 X approximate repeats.|B30.2/SPRY 3. {ECO:0000255|PROSITE- ProRule:PRU00548}.			GEAQ -> RGA (in Ref. 1; AA sequence). {ECO:0000305}.	calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	ACCCCGCAGGCGGGGGGAGAGG	0.678																																					p.A1363delinsAG		Atlas-INDEL	.											.	RYR1	708	.	0			c.4088_4089insGGG						.																																			SO:0001652	inframe_insertion	6261	exon28			.	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.4092_4094dupGGG	chr19.hg19:g.38964343_38964345dupGGG	ENSP00000352608:p.Gly1365_Gly1365dup	367.0	0.0		357.0	32.0	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	In_Frame_Ins	INS	ENST00000359596.3	hg19	CCDS33011.1																																																																																			.	.		0.678	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			GGG	38964340	-	GGG	38964339	7	5	353	1	0	1	1	0	0	0	0	0	13783	768	27	0	4198	0	RYR1	19	38964339	In_Frame_Ins	INS	-	TCGA-WQ-AB4B-01A-11D-A40P-10	15421660	38964339	20164644	50	49963										
KLK10	5655	hgsc.bcm.edu	37	chr19	51520439	51520439	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	cgcgcagtggaacgagaggcCgttgaagagcgagacctgcc	16	11	0	4			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr19:51520439C>A	ENST00000309958.3	-	3	414	c.196G>T	c.(196-198)Ggc>Tgc	p.G66C	CTC-518B2.12_ENST00000596286.1_RNA|KLK10_ENST00000358789.3_Missense_Mutation_p.G66C|KLK10_ENST00000391805.1_Missense_Mutation_p.G66C	NM_002776.4	NP_002767.2	O43240	KLK10_HUMAN	kallikrein-related peptidase 10	66	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cell cycle (GO:0007049)	extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	13		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00885)		AACGAGAGGCCGTTGAAGAGC	0.682											OREG0025646	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G66C		Atlas-SNP	.											.	KLK10	32	.	0			c.G196T						.						19	20	20					19																	51520439		2201	4298	6499	SO:0001583	missense	5655	exon3			AGAGGCCGTTGAA	AF024605	CCDS12817.1	19q13	2011-03-07	2006-10-27			ENSG00000129451		"Kallikreins"	6358	protein-coding gene	gene with protein product		602673	"kallikrein 10"	PRSSL1		8764136, 9533035, 16800724, 16800723, 10675891	Standard	NM_145888		Approved	NES1	uc002pva.3	O43240		ENST00000309958.3:c.196G>T	chr19.hg19:g.51520439C>A	ENSP00000311746:p.Gly66Cys	125.0	0.0	978	120.0	7.0	NM_145888	A6NC12|Q53YL3|Q99920|Q9GZW9	Missense_Mutation	SNP	ENST00000309958.3	hg19	CCDS12817.1	.	.	.	.	.	.	.	.	.	.	c	19.88	3.909627	0.72868	.	.	ENSG00000129451	ENST00000391805;ENST00000309958;ENST00000358789	D;D;D	0.93712	-3.27;-3.27;-3.27	4.21	2.02	0.26589	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.460059	0.16140	N	0.227786	D	0.96719	0.8929	H	0.94771	3.58	0.25555	N	0.98704	D	0.76494	0.999	D	0.72982	0.979	D	0.89774	0.3956	10	0.72032	D	0.01	.	5.5442	0.17055	0.0:0.7345:0.0:0.2655	.	66	O43240	KLK10_HUMAN	C	66	ENSP00000375681:G66C;ENSP00000311746:G66C;ENSP00000351640:G66C	ENSP00000311746:G66C	G	-	1	0	KLK10	56212251	0.000000	0.05858	0.964000	0.40570	0.967000	0.64934	0.744000	0.26245	0.854000	0.35336	0.491000	0.48974	GGC	.	.		0.682	KLK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464337.2	NM_002776		A	51520439	C	A	51520439	3	1	353	1	0	0	0	0	1	0	0	0	8407	652	23	1	650	1	KLK10	19	51520439	Missense_Mutation	SNP	C	TCGA-WQ-AB4B-01A-11D-A40P-10	12556100	51520439	7608544	51	49964										
ZNF665	79788	hgsc.bcm.edu	37	chr19	53668097	53668097	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	acgaattgtgtctgaagaccTtgccgcaatcattacatttg	8	9	2	2			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr19:53668097T>C	ENST00000600412.1	-	2	1566	c.1451A>G	c.(1450-1452)aAg>aGg	p.K484R	CTD-2245F17.2_ENST00000600257.1_RNA|ZNF665_ENST00000396424.3_Missense_Mutation_p.K549R			Q9H7R5	ZN665_HUMAN	zinc finger protein 665	484					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	35				GBM - Glioblastoma multiforme(134;0.0196)		TCTGAAGACCTTGCCGCAATC	0.383																																					p.K549R		Atlas-SNP	.											.	ZNF665	136	.	0			c.A1646G						.						147	157	154					19																	53668097		2200	4300	6500	SO:0001583	missense	79788	exon4			AAGACCTTGCCGC		CCDS46169.1	19q13.42	2013-01-08				ENSG00000197497		"Zinc fingers, C2H2-type", "-"	25885	protein-coding gene	gene with protein product							Standard	NM_024733		Approved	FLJ14345	uc010eqm.1	Q9H7R5		ENST00000600412.1:c.1451A>G	chr19.hg19:g.53668097T>C	ENSP00000469154:p.Lys484Arg	121.0	0.0		96.0	22.0	NM_024733	A8K5T8	Missense_Mutation	SNP	ENST00000600412.1	hg19		.	.	.	.	.	.	.	.	.	.	T	14.94	2.686521	0.47991	.	.	ENSG00000197497	ENST00000396424	T	0.26223	1.75	2.44	1.35	0.21983	.	.	.	.	.	T	0.42539	0.1207	M	0.64080	1.96	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.14896	-1.0456	9	0.49607	T	0.09	.	6.7458	0.23460	0.2103:0.0:0.0:0.7897	.	549	Q9H7R5-2	.	R	549	ENSP00000379702:K549R	ENSP00000379702:K549R	K	-	2	0	ZNF665	58359909	0.042000	0.20092	0.001000	0.08648	0.032000	0.12392	1.624000	0.37018	0.158000	0.19367	0.443000	0.29094	AAG	.	.		0.383	ZNF665-002	PUTATIVE	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000464179.1	NM_024733		C	53668097	T	C	53668097	3	2	353	1	0	0	0	0	1	0	0	0	18088	1609	56	2	394	2	ZNF665	19	53668097	Missense_Mutation	SNP	T	TCGA-WQ-AB4B-01A-11D-A40P-10	2147658	53668097	5460886	52	49965										
VSTM1	284415	hgsc.bcm.edu	37	chr19	54545432	54545432	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	caagcatctacctcttggtgGattcctcagatgatgaacct	8	11	3	3			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr19:54545432G>C	ENST00000338372.2	-	6	681	c.506C>G	c.(505-507)tCc>tGc	p.S169C	VSTM1_ENST00000366170.2_Missense_Mutation_p.S81C|VSTM1_ENST00000376626.1_Missense_Mutation_p.S138C|VSTM1_ENST00000425006.2_3'UTR	NM_198481.3	NP_940883.2	Q6UX27	VSTM1_HUMAN	V-set and transmembrane domain containing 1	169					immune system process (GO:0002376)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)		p.S169Y(1)		breast(1)|large_intestine(3)|lung(11)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.165)		CCTCTTGGTGGATTCCTCAGA	0.502																																					p.S169C		Atlas-SNP	.											VSTM1,NS,carcinoma,0,1	VSTM1	30	.	1	Substitution - Missense(1)	lung(1)	c.C506G						.						151	154	153					19																	54545432		2203	4300	6503	SO:0001583	missense	284415	exon6			TTGGTGGATTCCT	AY358542	CCDS12872.1, CCDS74441.1, CCDS74442.1	19q13.42	2013-01-11			ENSG00000189068	ENSG00000189068		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29455	protein-coding gene	gene with protein product						12975309	Standard	NM_198481		Approved	UNQ3033	uc002qcw.4	Q6UX27	OTTHUMG00000064906	ENST00000338372.2:c.506C>G	chr19.hg19:g.54545432G>C	ENSP00000343366:p.Ser169Cys	147.0	0.0		101.0	36.0	NM_198481	B6A8C6|D2DJS3|D2DJS4|Q496B6|Q496B7	Missense_Mutation	SNP	ENST00000338372.2	hg19	CCDS12872.1	.	.	.	.	.	.	.	.	.	.	G	13.70	2.315608	0.40996	.	.	ENSG00000189068	ENST00000419106;ENST00000338372;ENST00000376626;ENST00000366170	T;T;T;T	0.53640	2.22;6.65;6.42;0.61	3.24	3.24	0.37175	.	0.864640	0.09428	U	0.803465	T	0.45478	0.1344	N	0.19112	0.55	0.31378	N	0.679365	D;D	0.71674	0.996;0.998	P;P	0.54372	0.75;0.75	T	0.48043	-0.9069	10	0.56958	D	0.05	-12.1574	10.3077	0.43691	0.0:0.0:1.0:0.0	.	138;169	D2DJS4;Q6UX27	.;VSTM1_HUMAN	C	59;169;138;81	ENSP00000409412:S59C;ENSP00000343366:S169C;ENSP00000365813:S138C;ENSP00000444153:S81C	ENSP00000343366:S169C	S	-	2	0	VSTM1	59237244	0.009000	0.17119	0.003000	0.11579	0.006000	0.05464	2.618000	0.46393	2.151000	0.67156	0.543000	0.68304	TCC	.	.		0.502	VSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139358.3	NM_198481		C	54545432	G	C	54545432	3	2	353	1	0	0	0	0	1	0	0	0	17243	1174	41	4	220	4	VSTM1	19	54545432	Missense_Mutation	SNP	G	TCGA-WQ-AB4B-01A-11D-A40P-10	877335	54545432	4583551	53	49966										
LILRA3	11026	hgsc.bcm.edu	37	chr19	54802132	54802132	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	ttggtcaaaaggaaagtgtgCatccctccctgtgactgaca	10	10	1	2			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr19:54802132C>G	ENST00000251390.3	-	6	1147	c.1056G>C	c.(1054-1056)atG>atC	p.M352I	LILRA3_ENST00000391745.1_Missense_Mutation_p.M369I|LILRA3_ENST00000391744.3_Missense_Mutation_p.M288I	NM_006865.3	NP_006856.3	Q8N6C8	LIRA3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (without TM domain), member 3	352	Ig-like C2-type 4.				defense response (GO:0006952)|immune system process (GO:0002376)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			NS(3)|breast(1)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GGAAAGTGTGCATCCCTCCCT	0.582																																					p.M352I		Atlas-SNP	.											.	LILRA3	65	.	0			c.G1056C						.						94	81	86					19																	54802132		2194	4154	6348	SO:0001583	missense	11026	exon6			AGTGTGCATCCCT	U91926		19q13.4	2013-01-11						"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6604	protein-coding gene	gene with protein product		604818				9278324, 9548455	Standard	XM_006710242		Approved	LIR-4, HM43, ILT6, HM31, LIR4, CD85e		Q8N6C8		ENST00000251390.3:c.1056G>C	chr19.hg19:g.54802132C>G	ENSP00000251390:p.Met352Ile	93.0	0.0		88.0	34.0	NM_006865	J3KPM2|O15469|O15470|O75016|Q8N151|Q8N154|Q8NHJ1|Q8NHJ2|Q8NHJ3|Q8NHJ4	Missense_Mutation	SNP	ENST00000251390.3	hg19	CCDS12887.1	.	.	.	.	.	.	.	.	.	.	C	5.534	0.283521	0.10458	.	.	ENSG00000170866	ENST00000251390;ENST00000391744;ENST00000391745	T;T;T	0.02863	4.13;4.13;4.13	2.4	-0.0432	0.13860	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	4.906520	0.00589	N	0.000348	T	0.03608	0.0103	L	0.40543	1.245	0.09310	N	1	B;B	0.16603	0.018;0.006	B;B	0.23574	0.047;0.023	T	0.44081	-0.9351	10	0.30078	T	0.28	.	4.5605	0.12158	0.2569:0.4922:0.2509:0.0	.	352;352	E7EU74;Q8N6C8	.;LIRA3_HUMAN	I	352;288;369	ENSP00000251390:M352I;ENSP00000375624:M288I;ENSP00000375625:M369I	ENSP00000251390:M352I	M	-	3	0	LILRA3	59493944	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.083000	0.03397	0.093000	0.17368	0.586000	0.80456	ATG	.	.		0.582	LILRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140236.1			G	54802132	C	G	54802132	3	3	353	1	0	0	0	0	1	0	0	0	8795	710	25	4	271	4	LILRA3	19	54802132	Missense_Mutation	SNP	C	TCGA-WQ-AB4B-01A-11D-A40P-10	256700	54802132	4326851	54	49967										
LENG8	114823	hgsc.bcm.edu	37	chr19	54967900	54967900	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	agcgagagctgaagaagcagAagcgggcagcccgcttccag	15	11	0	4			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr19:54967900A>T	ENST00000326764.5	+	11	2010	c.1531A>T	c.(1531-1533)Aag>Tag	p.K511*	LENG8_ENST00000376514.2_Intron	NM_052925.2	NP_443157.1	Q96PV6	LENG8_HUMAN	leukocyte receptor cluster (LRC) member 8	474										breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.139)		GAAGAAGCAGAAGCGGGCAGC	0.662																																					p.K511X		Atlas-SNP	.											.	LENG8	73	.	0			c.A1531T						.						25	30	28					19																	54967900		2199	4299	6498	SO:0001587	stop_gained	114823	exon11			AAGCAGAAGCGGG	AF211975	CCDS12894.1	19q13.4	2008-02-05			ENSG00000167615	ENSG00000167615			15500	protein-coding gene	gene with protein product						10941842	Standard	XM_005278248		Approved	KIAA1932, MGC40108, pp13842	uc002qfw.2	Q96PV6	OTTHUMG00000065548	ENST00000326764.5:c.1531A>T	chr19.hg19:g.54967900A>T	ENSP00000318374:p.Lys511*	127.0	0.0		123.0	5.0	NM_052925	B0VJY9|Q8IZ27|Q8NCX6	Nonsense_Mutation	SNP	ENST00000326764.5	hg19	CCDS12894.1	.	.	.	.	.	.	.	.	.	.	A	42	9.764237	0.99257	.	.	ENSG00000167615	ENST00000326764;ENST00000301196;ENST00000376526;ENST00000431846	.	.	.	4.11	4.11	0.48088	.	0.356790	0.28241	N	0.016067	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-30.1172	11.6829	0.51468	1.0:0.0:0.0:0.0	.	.	.	.	X	511;474;474;511	.	ENSP00000301196:K474X	K	+	1	0	LENG8	59659712	1.000000	0.71417	0.998000	0.56505	0.795000	0.44927	5.760000	0.68793	1.816000	0.52996	0.379000	0.24179	AAG	.	.		0.662	LENG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140523.2	NM_052925		T	54967900	A	T	54967900	4	4	353	1	0	0	0	0	0	1	0	0	8733	247	9	4	1569	4	LENG8	19	54967900	Nonsense_Mutation	SNP	A	TCGA-WQ-AB4B-01A-11D-A40P-10	165768	54967900	4161083	55	49968										
U2AF2	11338	hgsc.bcm.edu	37	chr19	56180129	56180129	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	ccaagggctacgccttctgtGagtacgtggacatcaacgtc	11	12	2	1			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr19:56180129G>C	ENST00000308924.4	+	9	956	c.916G>C	c.(916-918)Gag>Cag	p.E306Q	CTD-2537I9.13_ENST00000592252.1_RNA|U2AF2_ENST00000590551.1_Missense_Mutation_p.E142Q|U2AF2_ENST00000450554.2_Missense_Mutation_p.E306Q|CTD-2537I9.12_ENST00000589456.1_RNA|CTD-2537I9.12_ENST00000585940.1_RNA			P26368	U2AF2_HUMAN	U2 small nuclear RNA auxiliary factor 2	306	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	enzyme binding (GO:0019899)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(2)	21		Colorectal(82;0.00244)|Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)		CGCCTTCTGTGAGTACGTGGA	0.617																																					p.E306Q		Atlas-SNP	.											.	U2AF2	62	.	0			c.G916C						.						70	68	69					19																	56180129		2203	4300	6503	SO:0001583	missense	11338	exon9			TTCTGTGAGTACG	BC008740	CCDS12933.1, CCDS46197.1	19q13.43	2014-09-17	2006-04-11			ENSG00000063244		"RNA binding motif (RRM) containing"	23156	protein-coding gene	gene with protein product	"U2 small nuclear ribonucleoprotein auxiliary factor (65kD)", "splicing factor U2AF 65 kD subunit", "U2 snRNP auxiliary factor large subunit"	191318	"U2 (RNU2) small nuclear RNA auxiliary factor 2"			1538748	Standard	XM_006722994		Approved	U2AF65	uc002qlu.3	P26368		ENST00000308924.4:c.916G>C	chr19.hg19:g.56180129G>C	ENSP00000307863:p.Glu306Gln	72.0	0.0		73.0	19.0	NM_001012478	Q96HC5	Missense_Mutation	SNP	ENST00000308924.4	hg19	CCDS12933.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.974313	0.92919	.	.	ENSG00000063244	ENST00000308924;ENST00000450554	T;T	0.20069	2.1;2.1	4.4	4.4	0.53042	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.51381	0.1671	M	0.87269	2.87	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.992	T	0.58999	-0.7536	10	0.46703	T	0.11	-24.3302	16.1527	0.81634	0.0:0.0:1.0:0.0	.	306;306	P26368;P26368-2	U2AF2_HUMAN;.	Q	306	ENSP00000307863:E306Q;ENSP00000388475:E306Q	ENSP00000307863:E306Q	E	+	1	0	U2AF2	60871941	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.145000	0.94634	2.184000	0.69523	0.655000	0.94253	GAG	.	.		0.617	U2AF2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453599.1	NM_007279		C	56180129	G	C	56180129	3	2	353	1	0	0	0	0	1	0	0	0	16838	1291	45	4	950	4	U2AF2	19	56180129	Missense_Mutation	SNP	G	TCGA-WQ-AB4B-01A-11D-A40P-10	1212229	56180129	2948854	56	49969										
NKX2-2	4821	hgsc.bcm.edu	37	chr20	21493051	21493065	+	In_Frame_Del	DEL	GACTCGTCGGCCGAG	GACTCGTCGGCCGAG	-													0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	tctccttgtcattgtccggtGactcgtcggccgagggctcc					rs375040957		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	GACTCGTCGGCCGAG	GACTCGTCGGCCGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr20:21493051_21493065delGACTCGTCGGCCGAG	ENST00000377142.4	-	2	674_688	c.318_332delCTCGGCCGACGAGTC	c.(316-333)ccctcggccgacgagtca>cca	p.SADES107del	NKX2-2-AS1_ENST00000549659.1_RNA	NM_002509.3	NP_002500.1	O95096	NKX22_HUMAN	NK2 homeobox 2	107					astrocyte differentiation (GO:0048708)|brain development (GO:0007420)|digestive tract development (GO:0048565)|endocrine pancreas development (GO:0031018)|negative regulation of neuron differentiation (GO:0045665)|neuron fate specification (GO:0048665)|oligodendrocyte development (GO:0014003)|optic nerve development (GO:0021554)|pancreatic A cell fate commitment (GO:0003326)|pancreatic PP cell fate commitment (GO:0003329)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to glucose (GO:0009749)|response to progesterone (GO:0032570)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)|spinal cord oligodendrocyte cell fate specification (GO:0021530)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell development (GO:0003323)|type B pancreatic cell fate commitment (GO:0003327)|ventral spinal cord interneuron fate determination (GO:0060580)	nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|core promoter proximal region DNA binding (GO:0001159)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	21						ATTGTCCGGTGACTCGTCGGCCGAGGGCTCCGGGG	0.693																																					p.107_111del		Atlas-INDEL	.											.	NKX2-2	49	.	0			c.319_333del						.																																			SO:0001651	inframe_deletion	4821	exon2			.	AF019415	CCDS13145.1	20p11.22	2012-03-09	2007-07-09	2002-10-04	ENSG00000125820	ENSG00000125820		"Homeoboxes / ANTP class : NKL subclass"	7835	protein-coding gene	gene with protein product		604612	"NK-2 (Drosophila) homolog B", "NK2 transcription factor related, locus 2 (Drosophila)"	NKX2B		9703340, 1346742	Standard	NM_002509		Approved	NKX2.2	uc002wsi.3	O95096	OTTHUMG00000170524	ENST00000377142.4:c.318_332delCTCGGCCGACGAGTC	chr20.hg19:g.21493051_21493065delGACTCGTCGGCCGAG	ENSP00000366347:p.Ser107_Ser111del	54.0	0.0		55.0	25.0	NM_002509		In_Frame_Del	DEL	ENST00000377142.4	hg19	CCDS13145.1																																																																																			.	.		0.693	NKX2-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078278.9			-	21493065	GACTCGTCGGCCGAG	-	21493051	7	5	353	1	0	1	0	1	0	0	0	0	10459	1294	45	0	493	0	NKX2-2	20	21493051	In_Frame_Del	DEL	GACTCGTCGGCCGAG	TCGA-WQ-AB4B-01A-11D-A40P-10		21493051	41532469	57	49970										
PREX1	57580	hgsc.bcm.edu	37	chr20	47267479	47267479	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	aatgctctccagcttggtgtCacagatgttgcggaactcaa	10	10	3	1			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr20:47267479C>A	ENST00000371941.3	-	23	2792	c.2770G>T	c.(2770-2772)Gac>Tac	p.D924Y	PREX1_ENST00000396220.1_Missense_Mutation_p.D924Y	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	924					actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			AGCTTGGTGTCACAGATGTTG	0.602																																					p.D924Y		Atlas-SNP	.											.	PREX1	441	.	0			c.G2770T						.						104	80	88					20																	47267479		2203	4300	6503	SO:0001583	missense	57580	exon23			TGGTGTCACAGAT	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.2770G>T	chr20.hg19:g.47267479C>A	ENSP00000361009:p.Asp924Tyr	63.0	0.0		77.0	16.0	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	hg19	CCDS13410.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.325429	0.81580	.	.	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.49139	0.79;0.79	5.11	5.11	0.69529	.	0.099066	0.41294	U	0.000919	T	0.65863	0.2732	L	0.54323	1.7	0.58432	D	0.999999	D;D	0.89917	0.972;1.0	P;D	0.76575	0.707;0.988	T	0.68667	-0.5348	10	0.72032	D	0.01	.	18.5354	0.91009	0.0:1.0:0.0:0.0	.	924;221	Q8TCU6;Q8TCU6-2	PREX1_HUMAN;.	Y	924	ENSP00000361009:D924Y;ENSP00000379522:D924Y	ENSP00000361009:D924Y	D	-	1	0	PREX1	46700886	1.000000	0.71417	0.982000	0.44146	0.882000	0.50991	4.292000	0.59031	2.365000	0.80145	0.462000	0.41574	GAC	.	.		0.602	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		A	47267479	C	A	47267479	3	1	353	1	0	0	0	0	1	0	0	0	12488	826	29	3	2281	3	PREX1	20	47267479	Missense_Mutation	SNP	C	TCGA-WQ-AB4B-01A-11D-A40P-10	25774428	47267479	15758041	58	49971			1	66		3	3	498	C		5.430283e-07
PREX1	57580	hgsc.bcm.edu	37	chr20	47267528	47267528	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	atggtcacgatggcgctgctCagggccatgagccgcctgca	14	13	2	1			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr20:47267528C>T	ENST00000371941.3	-	23	2743	c.2721G>A	c.(2719-2721)ctG>ctA	p.L907L	PREX1_ENST00000396220.1_Silent_p.L907L	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	907					actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			TGGCGCTGCTCAGGGCCATGA	0.572																																					p.L907L		Atlas-SNP	.											.	PREX1	441	.	0			c.G2721A						.						90	73	79					20																	47267528		2203	4300	6503	SO:0001819	synonymous_variant	57580	exon23			GCTGCTCAGGGCC	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.2721G>A	chr20.hg19:g.47267528C>T		74.0	0.0		92.0	17.0	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Silent	SNP	ENST00000371941.3	hg19	CCDS13410.1																																																																																			.	.		0.572	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		T	47267528	C	T	47267528	2	4	353	1	0	0	0	0	0	0	0	1	12488	813	29	3		3	PREX1	20	47267528	Silent	SNP	C	TCGA-WQ-AB4B-01A-11D-A40P-10	49	47267528	15757992	59	49972			1	66		3	3	498	C		5.430283e-07
PREX1	57580	hgsc.bcm.edu	37	chr20	47267976	47267976	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	ccgcggggctccacgatcttCtccagcacatggcacctgac	10	17	2	1			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr20:47267976C>T	ENST00000371941.3	-	22	2635	c.2613G>A	c.(2611-2613)gaG>gaA	p.E871E	PREX1_ENST00000396220.1_Silent_p.E871E	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	871					actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			CCACGATCTTCTCCAGCACAT	0.627																																					p.E871E		Atlas-SNP	.											.	PREX1	441	.	0			c.G2613A						.						60	50	54					20																	47267976		2203	4300	6503	SO:0001819	synonymous_variant	57580	exon22			GATCTTCTCCAGC	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.2613G>A	chr20.hg19:g.47267976C>T		85.0	0.0		112.0	14.0	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Silent	SNP	ENST00000371941.3	hg19	CCDS13410.1																																																																																			.	.		0.627	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		T	47267976	C	T	47267976	2	4	353	1	0	0	0	0	0	0	0	1	12488	912	32	3		3	PREX1	20	47267976	Silent	SNP	C	TCGA-WQ-AB4B-01A-11D-A40P-10	448	47267976	15757544	60	49973			1	66		3	3	498	C		5.430283e-07
TSHZ2	128553	hgsc.bcm.edu	37	chr20	51870809	51870809	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	ggatatggacaaagaggatgCtcaaaaggttctgaaatgta	12	4	2	2			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr20:51870809C>A	ENST00000371497.5	+	2	1699	c.812C>A	c.(811-813)gCt>gAt	p.A271D	RP4-678D15.1_ENST00000606932.1_RNA|TSHZ2_ENST00000603338.2_Missense_Mutation_p.A268D|TSHZ2_ENST00000329613.6_Missense_Mutation_p.A268D	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	271					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A271D(1)		NS(2)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(16)|lung(38)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	84			STAD - Stomach adenocarcinoma(23;0.1)			AAAGAGGATGCTCAAAAGGTT	0.438																																					p.A271D		Atlas-SNP	.											TSHZ2,NS,carcinoma,0,1	TSHZ2	209	.	1	Substitution - Missense(1)	lung(1)	c.C812A						.						74	57	63					20																	51870809		2203	4300	6503	SO:0001583	missense	128553	exon2			AGGATGCTCAAAA	AF230201	CCDS33490.1, CCDS54474.1	20q13.2	2013-11-20	2007-07-16	2006-03-14	ENSG00000182463	ENSG00000182463		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	13010	protein-coding gene	gene with protein product		614118	"chromosome 20 open reading frame 17", "zinc finger protein 218", "teashirt family zinc finger 2"	C20orf17, ZNF218		9671742	Standard	NM_173485		Approved	ZABC2, OVC10-2, TSH2	uc021wex.1	Q9NRE2	OTTHUMG00000033058	ENST00000371497.5:c.812C>A	chr20.hg19:g.51870809C>A	ENSP00000360552:p.Ala271Asp	207.0	1.0		281.0	12.0	NM_173485	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	Missense_Mutation	SNP	ENST00000371497.5	hg19	CCDS33490.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.599344	0.87055	.	.	ENSG00000182463	ENST00000371497;ENST00000329613	T;T	0.43294	0.95;0.95	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.64832	0.2634	M	0.61703	1.905	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.66011	-0.6029	10	0.87932	D	0	-1.2317	19.7465	0.96253	0.0:1.0:0.0:0.0	.	271	Q9NRE2	TSH2_HUMAN	D	271;268	ENSP00000360552:A271D;ENSP00000333114:A268D	ENSP00000333114:A268D	A	+	2	0	TSHZ2	51304216	1.000000	0.71417	0.992000	0.48379	0.935000	0.57460	7.440000	0.80464	2.732000	0.93576	0.643000	0.83706	GCT	.	.		0.438	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	NM_173485		A	51870809	C	A	51870809	3	1	353	1	0	0	0	0	1	0	0	0	16639	797	28	3	818	3	TSHZ2	20	51870809	Missense_Mutation	SNP	C	TCGA-WQ-AB4B-01A-11D-A40P-10	4602833	51870809	11154711	61	49974										
CCT8L2	150160	hgsc.bcm.edu	37	chr22	17071949	17071949	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	aaatccttgggctttgactaTtagggtgtcccacacccctt	8	12	0	1			TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chr22:17071949T>C	ENST00000359963.3	-	1	1751	c.1492A>G	c.(1492-1494)Ata>Gta	p.I498V		NM_014406.4	NP_055221.1	Q96SF2	TCPQM_HUMAN	chaperonin containing TCP1, subunit 8 (theta)-like 2	498					anion transport (GO:0006820)|cellular protein metabolic process (GO:0044267)|potassium ion transmembrane transport (GO:0071805)|transport (GO:0006810)	cytoplasm (GO:0005737)	anion channel activity (GO:0005253)|ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)			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)				GCTTTGACTATTAGGGTGTCC	0.517																																					p.I498V		Atlas-SNP	.											.	CCT8L2	150	.	0			c.A1492G						.						120	115	116					22																	17071949		2203	4298	6501	SO:0001583	missense	150160	exon1			TGACTATTAGGGT	AP003553	CCDS13738.1	22q11.1	2011-09-01			ENSG00000198445	ENSG00000198445			15553	protein-coding gene	gene with protein product							Standard	NM_014406		Approved	CESK1	uc002zlp.1	Q96SF2	OTTHUMG00000141302	ENST00000359963.3:c.1492A>G	chr22.hg19:g.17071949T>C	ENSP00000353048:p.Ile498Val	165.0	0.0		156.0	68.0	NM_014406	A4QPH3|Q9UJS3	Missense_Mutation	SNP	ENST00000359963.3	hg19	CCDS13738.1	.	.	.	.	.	.	.	.	.	.	t	0.014	-1.584846	0.00872	.	.	ENSG00000198445	ENST00000359963	T	0.78595	-1.19	1.98	0.89	0.19218	.	1.691540	0.03909	N	0.281555	T	0.53706	0.1813	N	0.04203	-0.255	0.09310	N	1	B	0.06786	0.001	B	0.14023	0.01	T	0.42548	-0.9445	10	0.12766	T	0.61	-0.1711	3.786	0.08700	0.0:0.208:0.0:0.792	.	498	Q96SF2	TCPQM_HUMAN	V	498	ENSP00000353048:I498V	ENSP00000353048:I498V	I	-	1	0	CCT8L2	15451949	0.000000	0.05858	0.077000	0.20336	0.207000	0.24258	-0.124000	0.10595	0.063000	0.16370	0.312000	0.20444	ATA	.	.		0.517	CCT8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280580.1			C	17071949	T	C	17071949	3	2	353	1	0	0	0	0	1	0	0	0	2963	1493	52	2	185	2	CCT8L2	22	17071949	Missense_Mutation	SNP	T	TCGA-WQ-AB4B-01A-11D-A40P-10		17071949	34232617	62	49975										
UPF3B	65109	hgsc.bcm.edu	37	chrX	118975107	118975108	+	Frame_Shift_Ins	INS	-	-	A													0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	atcttctttagcttttctatINSatctttcctttttcgtttct							TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chrX:118975107_118975108insA	ENST00000276201.2	-	7	807_808	c.738_739insT	c.(736-741)gatatafs	p.I247fs	UPF3B_ENST00000345865.2_Frame_Shift_Ins_p.I247fs|UPF3B_ENST00000478840.1_5'UTR	NM_080632.2	NP_542199.1	Q9BZI7	REN3B_HUMAN	UPF3 regulator of nonsense transcripts homolog B (yeast)	247	Necessary for interaction with UPF2.|Sufficient for association with EJC core.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(12)|ovary(2)|prostate(1)	30						AGcttttctatatctttccttt	0.347																																					p.I247fs		Atlas-INDEL	.											.	UPF3B	74	.	0			c.739_740insT						.																																			SO:0001589	frameshift_variant	65109	exon7			.	AF318576	CCDS14587.1, CCDS14588.1	Xq25-q26	2014-01-31			ENSG00000125351	ENSG00000125351			20439	protein-coding gene	gene with protein product		300298	"mental retardation, X-linked 62"	MRX62		11113196, 11163187, 19238151	Standard	NM_023010		Approved	RENT3B, UPF3X, HUPF3B	uc004erz.2	Q9BZI7	OTTHUMG00000022282	ENST00000276201.2:c.739dupT	chrX.hg19:g.118975108_118975108dupA	ENSP00000276201:p.Ile247fs	40.0	0.0		53.0	33.0	NM_023010	D3DWI3|D3DWI4|Q0VAK8|Q9H1J0	Frame_Shift_Ins	INS	ENST00000276201.2	hg19	CCDS14588.1																																																																																			.	.		0.347	UPF3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058068.1			A	118975108	-	A	118975107	7	5	353	1	0	1	1	0	0	0	0	0	17021	1406	49	0	732	0	UPF3B	23	118975107	Frame_Shift_Ins	INS	-	TCGA-WQ-AB4B-01A-11D-A40P-10		118975107	36295453	63	49976										
NLGN4Y	22829	hgsc.bcm.edu	37	chrY	16941993	16942000	+	3'UTR	DEL	GTGTCCAA	GTGTCCAA	-													0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	ccaacgactttgacttctccGtgtccaacttcgtggacaac							TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	GTGTCCAA	GTGTCCAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chrY:16941993_16942000delGTGTCCAA	ENST00000476359.1	+	0	1740_1747							Q8NFZ3	NLGNY_HUMAN	neuroligin 4, Y-linked						learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)			large_intestine(3)|lung(7)|prostate(2)|skin(2)	14						TGACTTCTCCGTGTCCAACTTCGTGGAC	0.543																																					p.398_401del		Atlas-INDEL	.											.	NLGN4Y	44	.	0			c.1194_1201del						.																																			SO:0001624	3_prime_UTR_variant	22829	exon5			.		CCDS14788.1, CCDS55553.1, CCDS56619.1	Yq11.221	2013-09-20	2004-05-21		ENSG00000165246	ENSG00000165246			15529	protein-coding gene	gene with protein product		400028	"neuroligin 4, Y linked"			10231032	Standard	NM_014893		Approved	KIAA0951	uc004ftg.2	Q8NFZ3	OTTHUMG00000036618	ENST00000476359.1:c.*1744GTGTCCAA>-	chrY.hg19:g.16941993_16942000delGTGTCCAA		290.0	0.0		223.0	36.0	NM_014893	F5H6W0|Q14D08|Q7Z3T5|Q8N5B6|Q9Y2F8	Frame_Shift_Del	DEL	ENST00000476359.1	hg19																																																																																				.	.		0.543	NLGN4Y-004	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000089064.2	NM_014893		-	16942000	GTGTCCAA	-	16941993	6	5	353	0	1	1	0	1	0	0	0	0	10474	1145	40	0		0	NLGN4Y	24	16941993	3'UTR	DEL	GTGTCCAA	TCGA-WQ-AB4B-01A-11D-A40P-10		16941993	42431573	64	49977			2	67		2	2	13	N	GTGTCCAA_GTGGACAACCTTT	2.519613e-05
NLGN4Y	22829	hgsc.bcm.edu	37	chrY	16942005	16942017	+	3'UTR	DEL	GTGGACAACCTTT	GTGGACAACCTTT	-													0.0615384615384615	4	1	1.06738544474394	1.86792452830189	0.933962264150943	0.569230769230769	1	0	acttctccgtgtccaacttcGtggacaacctttacggctac							TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	GTGGACAACCTTT	GTGGACAACCTTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	g.chrY:16942005_16942017delGTGGACAACCTTT	ENST00000476359.1	+	0	1752_1764							Q8NFZ3	NLGNY_HUMAN	neuroligin 4, Y-linked						learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)			large_intestine(3)|lung(7)|prostate(2)|skin(2)	14						GTCCAACTTCGTGGACAACCTTTACGGCTACCC	0.554																																					p.402_406del		Atlas-INDEL	.											.	NLGN4Y	44	.	0			c.1206_1218del						.																																			SO:0001624	3_prime_UTR_variant	22829	exon5			.		CCDS14788.1, CCDS55553.1, CCDS56619.1	Yq11.221	2013-09-20	2004-05-21		ENSG00000165246	ENSG00000165246			15529	protein-coding gene	gene with protein product		400028	"neuroligin 4, Y linked"			10231032	Standard	NM_014893		Approved	KIAA0951	uc004ftg.2	Q8NFZ3	OTTHUMG00000036618	ENST00000476359.1:c.*1761GTGGACAACCTTT>-	chrY.hg19:g.16942005_16942017delGTGGACAACCTTT		270.0	0.0		225.0	36.0	NM_014893	F5H6W0|Q14D08|Q7Z3T5|Q8N5B6|Q9Y2F8	Frame_Shift_Del	DEL	ENST00000476359.1	hg19																																																																																				.	.		0.554	NLGN4Y-004	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000089064.2	NM_014893		-	16942017	GTGGACAACCTTT	-	16942005	6	5	353	0	1	1	0	1	0	0	0	0	10474	1145	40	0		0	NLGN4Y	24	16942005	3'UTR	DEL	GTGGACAACCTTT	TCGA-WQ-AB4B-01A-11D-A40P-10	12	16942005	42431561	65	49978			2	67		2	2	13	N	GTGTCCAA_GTGGACAACCTTT	2.519613e-05
NADK	65220	hgsc.bcm.edu	37	chr1	1684446	1684446	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	tctcaaaccagtcgctcacgGggtcccgcacacagatggag	11	14	2	1			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr1:1684446G>T	ENST00000341426.5	-	12	1459	c.1238C>A	c.(1237-1239)cCc>cAc	p.P413H	NADK_ENST00000378625.1_Missense_Mutation_p.P558H|NADK_ENST00000342348.5_Missense_Mutation_p.P381H|NADK_ENST00000344463.4_Missense_Mutation_p.P558H|NADK_ENST00000341991.3_Missense_Mutation_p.P413H	NM_023018.4	NP_075394.3	O95544	NADK_HUMAN	NAD kinase	413					ATP metabolic process (GO:0046034)|NAD metabolic process (GO:0019674)|NADP biosynthetic process (GO:0006741)|phosphorylation (GO:0016310)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			NS(1)|autonomic_ganglia(1)|endometrium(4)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)|stomach(1)|urinary_tract(1)	17	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.61e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;8.75e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.33e-23)|GBM - Glioblastoma multiforme(42;1.35e-07)|Colorectal(212;0.000203)|COAD - Colon adenocarcinoma(227;0.000225)|Kidney(185;0.00265)|STAD - Stomach adenocarcinoma(132;0.00655)|BRCA - Breast invasive adenocarcinoma(365;0.00855)|KIRC - Kidney renal clear cell carcinoma(229;0.0382)|Lung(427;0.207)		GTCGCTCACGGGGTCCCGCAC	0.637																																					p.P558H		Atlas-SNP	.											.	NADK	79	.	0			c.C1673A						.						45	32	36					1																	1684446		2200	4299	6499	SO:0001583	missense	65220	exon14			CTCACGGGGTCCC	BC001709	CCDS30565.1, CCDS55561.1, CCDS55562.1	1p36.33	2013-04-29			ENSG00000008130	ENSG00000008130	2.7.1.23		29831	protein-coding gene	gene with protein product		611616				11594753	Standard	NM_023018		Approved	FLJ13052	uc001aie.3	O95544	OTTHUMG00000000942	ENST00000341426.5:c.1238C>A	chr1.hg19:g.1684446G>T	ENSP00000341679:p.Pro413His	197.0	0.0		128.0	43.0	NM_001198994	A6NNN3|A8K296|B7Z434|F5GXR5|Q5QPS4|Q9H2P2|Q9H931	Missense_Mutation	SNP	ENST00000341426.5	hg19	CCDS30565.1	.	.	.	.	.	.	.	.	.	.	G	19.98	3.926685	0.73327	.	.	ENSG00000008130	ENST00000341426;ENST00000341991;ENST00000378625;ENST00000344463;ENST00000342348	T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02	5.22	4.29	0.51040	ATP-NAD kinase, PpnK-type (1);	0.000000	0.85682	D	0.000000	T	0.44705	0.1306	M	0.72118	2.19	0.52501	D	0.999958	B;B;B	0.27192	0.171;0.049;0.157	B;B;B	0.28011	0.085;0.027;0.04	T	0.43940	-0.9360	10	0.51188	T	0.08	-16.1012	13.7765	0.63057	0.0:0.0:0.8449:0.1551	.	381;558;413	F5GXR5;Q5QPS4;O95544	.;.;NADK_HUMAN	H	413;413;558;558;381	ENSP00000341679:P413H;ENSP00000344340:P413H;ENSP00000367890:P558H;ENSP00000340925:P558H;ENSP00000339727:P381H	ENSP00000341679:P413H	P	-	2	0	NADK	1674306	1.000000	0.71417	0.620000	0.29132	0.978000	0.69477	5.978000	0.70501	1.181000	0.42912	0.561000	0.74099	CCC	.	.		0.637	NADK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002769.1	NM_023018		T	1684446	G	T	1684446	3	4	354	1	0	0	0	0	1	0	0	0	10146	1232	43	3	106	3	NADK	1	1684446	Missense_Mutation	SNP	G	TCGA-WX-AA44-01A-11D-A38X-10		1684446	247566175	1	49979										
PLCH2	9651	hgsc.bcm.edu	37	chr1	2430060	2430060	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	agcagcttcccaagccgcgcGactccatgctgggggaccgt	13	15	0	0			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr1:2430060G>A	ENST00000419816.2	+	17	2597	c.2323G>A	c.(2323-2325)Gac>Aac	p.D775N	PLCH2_ENST00000378488.3_Missense_Mutation_p.D739N|PLCH2_ENST00000378486.3_Missense_Mutation_p.D775N|PLCH2_ENST00000449969.1_Missense_Mutation_p.D748N|PLCH2_ENST00000288766.5_Intron			O75038	PLCH2_HUMAN	phospholipase C, eta 2	775	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phosphatidylinositol metabolic process (GO:0046488)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(8)|ovary(1)|prostate(3)|skin(1)	20	all_cancers(77;0.000161)|all_epithelial(69;5.98e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;7.32e-16)|all_lung(118;1.15e-06)|Lung NSC(185;6.26e-05)|Renal(390;0.00571)|Breast(487;0.00832)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;1.44e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.78e-23)|GBM - Glioblastoma multiforme(42;2.8e-08)|Colorectal(212;4.19e-05)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00034)|BRCA - Breast invasive adenocarcinoma(365;0.00443)|KIRC - Kidney renal clear cell carcinoma(229;0.00548)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.2)		CAAGCCGCGCGACTCCATGCT	0.706																																					p.D775N		Atlas-SNP	.											.	PLCH2	131	.	0			c.G2323A						.						9	10	10					1																	2430060		1884	4063	5947	SO:0001583	missense	9651	exon17			CCGCGCGACTCCA	AB007919	CCDS59959.1	1p36.32	2013-01-10	2006-03-16	2006-03-16	ENSG00000149527	ENSG00000149527	3.1.4.11	"EF-hand domain containing"	29037	protein-coding gene	gene with protein product		612836	"phospholipase C-like 4"	PLCL4		15899900	Standard	XM_006711054		Approved	KIAA0450, PLCeta2, RP3-395M20.1, PLC-eta2	uc001aji.1	O75038	OTTHUMG00000000719	ENST00000419816.2:c.2323G>A	chr1.hg19:g.2430060G>A	ENSP00000389803:p.Asp775Asn	237.0	0.0		128.0	31.0	NM_014638	A2VCM3|B9DI80|Q3LUA8|Q86XJ2|Q86XU1|Q86YU7|Q8TEH5|Q8WUS6	Missense_Mutation	SNP	ENST00000419816.2	hg19		.	.	.	.	.	.	.	.	.	.	G	29.9	5.044346	0.93685	.	.	ENSG00000149527	ENST00000449969;ENST00000378486;ENST00000378488;ENST00000343889;ENST00000278878	T;T;T	0.26660	1.91;1.87;1.72	4.84	4.84	0.62591	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	2.401790	0.01812	N	0.033481	T	0.41743	0.1172	N	0.17278	0.47	0.80722	D	1	D;D;D;D	0.76494	0.996;0.999;0.995;0.996	P;D;P;D	0.68039	0.905;0.955;0.808;0.929	T	0.19614	-1.0300	10	0.38643	T	0.18	.	16.9045	0.86123	0.0:0.0:1.0:0.0	.	622;527;748;775	B9DI81;B9DI82;O75038-2;O75038	.;.;.;PLCH2_HUMAN	N	748;775;739;622;527	ENSP00000397289:D748N;ENSP00000367747:D775N;ENSP00000367749:D739N	ENSP00000278878:D527N	D	+	1	0	PLCH2	2419920	1.000000	0.71417	0.936000	0.37596	0.701000	0.40568	9.076000	0.94009	2.224000	0.72417	0.561000	0.74099	GAC	.	.		0.706	PLCH2-009	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467514.1	NM_014638		A	2430060	G	A	2430060	3	1	354	1	0	0	0	0	1	0	0	0	12047	1058	37	1	2389	1	PLCH2	1	2430060	Missense_Mutation	SNP	G	TCGA-WX-AA44-01A-11D-A38X-10	745614	2430060	246820561	2	49980										
UBXN11	91544	hgsc.bcm.edu	37	chr1	26608874	26608879	+	In_Frame_Del	DEL	GGGGCC	GGGGCC	-													0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	ccgggaccgggaccgggactGgggccgggaccgggaccggg					rs1134582|rs1134581|rs140364749	byFrequency	TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	GGGGCC	GGGGCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr1:26608874_26608879delGGGGCC	ENST00000374222.1	-	16	1938_1943	c.1474_1479delGGCCCC	c.(1474-1479)ggccccdel	p.GP492del	UBXN11_ENST00000374223.1_In_Frame_Del_p.GP249del|UBXN11_ENST00000374221.3_In_Frame_Del_p.GP492del|UBXN11_ENST00000314675.7_In_Frame_Del_p.GP372del|UBXN11_ENST00000357089.4_In_Frame_Del_p.GP459del|UBXN11_ENST00000374217.2_In_Frame_Del_p.GP459del			Q5T124	UBX11_HUMAN	UBX domain protein 11	492	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.		Missing.|Missing. {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.2}.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G490_P515delGPGPSPGPGPGPSPGPGPGPSPCPGP(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						gaccgggactggggccgggaccggga	0.714																																					p.492_494del		Atlas-INDEL	.											UBXN11,NS,carcinoma,0,1	UBXN11	54	.	1	Deletion - In frame(1)	ovary(1)	c.1475_1480del						.																																			SO:0001651	inframe_deletion	91544	exon16			.	AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"UBX domain containing"	30600	protein-coding gene	gene with protein product	"socius"	609151	"UBX domain containing 5"	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.1474_1479delGGCCCC	chr1.hg19:g.26608874_26608879delGGGGCC	ENSP00000363339:p.Gly492_Pro493del	33.0	0.0		27.0	10.0	NM_183008	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	In_Frame_Del	DEL	ENST00000374222.1	hg19	CCDS41288.1																																																																																			.	.		0.714	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345		-	26608879	GGGGCC	-	26608874	7	5	354	1	0	1	0	1	0	0	0	0	16928	1335	47	0	87	0	UBXN11	1	26608874	In_Frame_Del	DEL	GGGGCC	TCGA-WX-AA44-01A-11D-A38X-10	24178814	26608874	222641747	3	49981										
AK2	204	hgsc.bcm.edu	37	chr1	33478935	33478935	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	ggggtggtttgagtgtggtaGgcttgcaggcggattttcaa	18	4	1	1			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr1:33478935G>T	ENST00000373449.2	-	6	608	c.567C>A	c.(565-567)gcC>gcA	p.A189A	AK2_ENST00000548033.1_Silent_p.A147A|AK2_ENST00000491241.1_5'Flank|AK2_ENST00000467905.1_Silent_p.A189A|AK2_ENST00000480134.1_3'UTR|AK2_ENST00000354858.6_Silent_p.A189A|RP1-117O3.2_ENST00000427524.1_RNA	NM_001199199.1|NM_013411.4	NP_001186128.1|NP_037543.1			adenylate kinase 2											kidney(1)|large_intestine(2)|lung(4)|skin(1)	8		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)				GAGTGTGGTAGGCTTGCAGGC	0.532																																					p.A189A		Atlas-SNP	.											.	AK2	27	.	0			c.C567A						.						112	103	106					1																	33478935		2203	4300	6503	SO:0001819	synonymous_variant	204	exon6			GTGGTAGGCTTGC	U84371	CCDS373.1, CCDS374.1	1p35.1	2014-09-17			ENSG00000004455	ENSG00000004455	2.7.4.3	"Adenylate kinases"	362	protein-coding gene	gene with protein product		103020				8843353, 6961883	Standard	NM_013411		Approved		uc001bwp.2	P54819	OTTHUMG00000004131	ENST00000373449.2:c.567C>A	chr1.hg19:g.33478935G>T		106.0	0.0		82.0	4.0	NM_013411		Silent	SNP	ENST00000373449.2	hg19	CCDS373.1																																																																																			.	.		0.532	AK2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011884.1	NM_001625		T	33478935	G	T	33478935	2	4	354	1	0	0	0	0	0	0	0	1	440	987	35	3		3	AK2	1	33478935	Silent	SNP	G	TCGA-WX-AA44-01A-11D-A38X-10	6870061	33478935	215771686	4	49982										
KIAA0319L	79932	hgsc.bcm.edu	37	chr1	35972470	35972470	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	tagaaagcccaaatcatctgCagtttggaatttttttaaaa	6	6	2	1			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr1:35972470C>T	ENST00000325722.3	-	3	643	c.409G>A	c.(409-411)Gca>Aca	p.A137T		NM_024874.4	NP_079150.3	Q8IZA0	K319L_HUMAN	KIAA0319-like	137						cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(12)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	34		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				AAATCATCTGCAGTTTGGAAT	0.512																																					p.A137T		Atlas-SNP	.											.	KIAA0319L	156	.	0			c.G409A						.						80	88	86					1																	35972470		2203	4300	6503	SO:0001583	missense	79932	exon3			CATCTGCAGTTTG	AY163234	CCDS390.1	1p34.3	2008-10-24			ENSG00000142687	ENSG00000142687			30071	protein-coding gene	gene with protein product		613535				11347906	Standard	NM_024874		Approved	KIAA1837	uc001byx.3	Q8IZA0	OTTHUMG00000004370	ENST00000325722.3:c.409G>A	chr1.hg19:g.35972470C>T	ENSP00000318406:p.Ala137Thr	137.0	0.0		140.0	45.0	NM_024874	B1AN13|D3DPR8|O95010|Q6PJJ7|Q7L1C9|Q8N2B3|Q8NDA0|Q8WY39|Q8WYZ5|Q96IC3|Q96JJ0|Q9BUW6|Q9H7V0	Missense_Mutation	SNP	ENST00000325722.3	hg19	CCDS390.1	.	.	.	.	.	.	.	.	.	.	C	5.576	0.291067	0.10567	.	.	ENSG00000142687	ENST00000325722;ENST00000426982;ENST00000440579;ENST00000373258;ENST00000469892;ENST00000494948	T;T;T;T;T	0.44881	3.24;3.24;2.75;1.54;0.91	5.78	2.86	0.33363	.	0.960190	0.08638	N	0.915916	T	0.23289	0.0563	N	0.12746	0.255	0.09310	N	1	B;B;B	0.23185	0.081;0.028;0.0	B;B;B	0.20184	0.028;0.007;0.001	T	0.29027	-1.0025	10	0.13108	T	0.6	0.6907	7.8738	0.29582	0.0:0.6577:0.0:0.3423	.	137;137;137	B4DYG9;B1AN14;Q8IZA0	.;.;K319L_HUMAN	T	137	ENSP00000318406:A137T;ENSP00000395883:A137T;ENSP00000407576:A137T;ENSP00000362355:A137T;ENSP00000419396:A137T	ENSP00000318406:A137T	A	-	1	0	KIAA0319L	35745057	0.124000	0.22315	0.000000	0.03702	0.506000	0.33950	0.197000	0.17197	0.338000	0.23692	0.655000	0.94253	GCA	.	.		0.512	KIAA0319L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012684.2	NM_024874		T	35972470	C	T	35972470	3	4	354	1	0	0	0	0	1	0	0	0	8178	710	25	3	2816	3	KIAA0319L	1	35972470	Missense_Mutation	SNP	C	TCGA-WX-AA44-01A-11D-A38X-10	2493535	35972470	213278151	5	49983										
SCP2	6342	hgsc.bcm.edu	37	chr1	53443897	53443897	+	Frame_Shift_Del	DEL	C	C	-													0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	acttcctcttagtcccacttCagatggtgctgcagcagcaa							TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr1:53443897delC	ENST00000528311.1	+	8	736	c.440delC	c.(439-441)tcafs	p.S147fs	SCP2_ENST00000371513.5_Frame_Shift_Del_p.S184fs|SCP2_ENST00000473584.1_3'UTR|SCP2_ENST00000407246.2_Frame_Shift_Del_p.S204fs|SCP2_ENST00000371509.4_Frame_Shift_Del_p.S184fs|SCP2_ENST00000371514.3_Frame_Shift_Del_p.S228fs	NM_001193617.1	NP_001180546.1	Q9BX26	SYCP2_HUMAN	sterol carrier protein 2	868					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	15						AGTCCCACTTCAGATGGTGCT	0.438																																					p.S228fs		Atlas-INDEL	.											.	SCP2	44	.	0			c.682delT						.						75	71	73					1																	53443897		2203	4300	6503	SO:0001589	frameshift_variant	6342	exon9			.	M75884	CCDS572.1, CCDS30719.1, CCDS41338.1, CCDS44149.1, CCDS44150.1, CCDS53317.1, CCDS53318.1, CCDS53319.1	1p32	2010-08-20			ENSG00000116171	ENSG00000116171			10606	protein-coding gene	gene with protein product		184755				1703300, 1718316	Standard	NM_001007098		Approved		uc001cur.2	P22307	OTTHUMG00000008936	ENST00000528311.1:c.440delC	chr1.hg19:g.53443897delC	ENSP00000434132:p.Ser147fs	58.0	0.0		57.0	22.0	NM_002979	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Frame_Shift_Del	DEL	ENST00000528311.1	hg19	CCDS53319.1																																																																																			.	.		0.438	SCP2-010	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387558.1	NM_002979		-	53443897	C	-	53443897	7	5	354	1	0	1	0	1	0	0	0	0	13949	838	29	0	717	0	SCP2	1	53443897	Frame_Shift_Del	DEL	C	TCGA-WX-AA44-01A-11D-A38X-10	17471427	53443897	195806724	6	49984										
AMPD2	271	hgsc.bcm.edu	37	chr1	110173592	110173592	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	gccactggctgggacccaacTataccaaggaaggccctgag	12	13	0	1			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr1:110173592T>A	ENST00000256578.3	+	18	2818	c.2458T>A	c.(2458-2460)Tat>Aat	p.Y820N	AMPD2_ENST00000528667.1_Missense_Mutation_p.Y820N|AMPD2_ENST00000528454.1_Missense_Mutation_p.Y702N|AMPD2_ENST00000393688.3_Missense_Mutation_p.Y701N|RP5-1160K1.6_ENST00000369843.3_RNA|AMPD2_ENST00000342115.4_Missense_Mutation_p.Y739N|AMPD2_ENST00000358729.4_Missense_Mutation_p.Y745N	NM_004037.7	NP_004028.3	Q01433	AMPD2_HUMAN	adenosine monophosphate deaminase 2	820					cell death (GO:0008219)|cyclic purine nucleotide metabolic process (GO:0052652)|energy homeostasis (GO:0097009)|IMP biosynthetic process (GO:0006188)|IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			breast(1)|large_intestine(3)|ovary(2)|skin(1)	7		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Lung(183;0.0425)|all cancers(265;0.0884)|Colorectal(144;0.109)|Epithelial(280;0.111)|LUSC - Lung squamous cell carcinoma(189;0.228)		GGGACCCAACTATACCAAGGA	0.637																																					p.Y820N		Atlas-SNP	.											.	AMPD2	75	.	0			c.T2458A						.						45	49	48					1																	110173592		2203	4300	6503	SO:0001583	missense	271	exon18			CCCAACTATACCA	S47833	CCDS804.1, CCDS805.1, CCDS30796.1, CCDS58016.1	1p13.3	2014-03-03	2010-02-10		ENSG00000116337	ENSG00000116337	3.5.4.6		469	protein-coding gene	gene with protein product	"AMPD isoform L"	102771	"adenosine monophosphate deaminase 2 (isoform L)"			1400401, 24482476	Standard	NM_004037		Approved	SPG63	uc009wfh.2	Q01433	OTTHUMG00000011649	ENST00000256578.3:c.2458T>A	chr1.hg19:g.110173592T>A	ENSP00000256578:p.Tyr820Asn	304.0	0.0		238.0	60.0	NM_004037	B4DK50|B4DZI5|E9PNG0|Q14856|Q14857|Q16686|Q16687|Q16688|Q16729|Q5T693|Q5T695|Q96IA1|Q9UDX8|Q9UDX9|Q9UMU4	Missense_Mutation	SNP	ENST00000256578.3	hg19	CCDS805.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	28.6|28.6	4.933508|4.933508	0.92458|0.92458	.|.	.|.	ENSG00000116337|ENSG00000116337	ENST00000369840|ENST00000342115;ENST00000528667;ENST00000256578;ENST00000358729;ENST00000528454;ENST00000393688	.|D;D;D;D;D;D	.|0.83075	.|-1.68;-1.68;-1.68;-1.68;-1.68;-1.68	4.89|4.89	4.89|4.89	0.63831|0.63831	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.90359|0.90359	0.6983|0.6983	M|M	0.89601|0.89601	3.045|3.045	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;1.0;0.997;1.0	.|D;D;P;D	.|0.66847	.|0.944;0.947;0.862;0.947	D|D	0.92145|0.92145	0.5723|0.5723	5|10	.|0.66056	.|D	.|0.02	-20.7374|-20.7374	13.6159|13.6159	0.62108|0.62108	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|745;701;820;739	.|Q01433-4;Q01433-3;Q01433;Q01433-2	.|.;.;AMPD2_HUMAN;.	Q|N	801|739;820;820;745;702;701	.|ENSP00000345498:Y739N;ENSP00000436541:Y820N;ENSP00000256578:Y820N;ENSP00000351573:Y745N;ENSP00000437164:Y702N;ENSP00000377292:Y701N	.|ENSP00000256578:Y820N	L|Y	+|+	2|1	0|0	AMPD2|AMPD2	109975115|109975115	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.959000|0.959000	0.62525|0.62525	4.888000|4.888000	0.63164|0.63164	2.064000|2.064000	0.61679|0.61679	0.459000|0.459000	0.35465|0.35465	CTA|TAT	.	.		0.637	AMPD2-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390615.1			A	110173592	T	A	110173592	3	1	354	1	0	0	0	0	1	0	0	0	586	1522	53	4	2569	4	AMPD2	1	110173592	Missense_Mutation	SNP	T	TCGA-WX-AA44-01A-11D-A38X-10	56729695	110173592	139077029	7	49985										
PGLYRP4	57115	hgsc.bcm.edu	37	chr1	153317739	153317739	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	tgtctggtcgtgacactccaGtccagggacatggtgtataa	12	9	1	1			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr1:153317739G>T	ENST00000359650.5	-	4	323	c.259C>A	c.(259-261)Ctg>Atg	p.L87M	PGLYRP4_ENST00000490266.1_5'UTR|PGLYRP4_ENST00000368739.3_Missense_Mutation_p.L83M	NM_020393.2	NP_065126.2	Q96LB8	PGRP4_HUMAN	peptidoglycan recognition protein 4	87					defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|skin(1)|stomach(1)	23	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.171)			TGACACTCCAGTCCAGGGACA	0.557																																					p.L87M		Atlas-SNP	.											.	PGLYRP4	45	.	0			c.C259A						.						125	105	112					1																	153317739		2203	4300	6503	SO:0001583	missense	57115	exon4			ACTCCAGTCCAGG	AF242518	CCDS30871.1	1q21	2008-02-05			ENSG00000163218	ENSG00000163218			30015	protein-coding gene	gene with protein product	"peptidoglycan recognition protein I beta precursor"	608198				11461926	Standard	XR_241090		Approved	SBBI67, PGRPIB, PGLYRPIbeta, PGRP-Ibeta	uc001fbo.3	Q96LB8	OTTHUMG00000037057	ENST00000359650.5:c.259C>A	chr1.hg19:g.153317739G>T	ENSP00000352672:p.Leu87Met	27.0	0.0		57.0	36.0	NM_020393	A8K838|Q3B822|Q3B823|Q5SY63|Q5SY64|Q9HD75	Missense_Mutation	SNP	ENST00000359650.5	hg19	CCDS30871.1	.	.	.	.	.	.	.	.	.	.	G	4.518	0.096149	0.08681	.	.	ENSG00000163218	ENST00000368739;ENST00000359650	T;T	0.13778	2.56;2.56	3.2	1.2	0.21068	Peptidoglycan recognition protein family domain, metazoa/bacteria (1);N-acetylmuramoyl-L-alanine amidase domain (4);	.	.	.	.	T	0.02012	0.0063	N	0.10733	0.035	0.09310	N	0.999995	B;B	0.33826	0.427;0.344	B;B	0.33392	0.101;0.163	T	0.42258	-0.9462	9	0.54805	T	0.06	-10.9919	5.8315	0.18582	0.2582:0.0:0.7418:0.0	.	83;87	Q96LB8-2;Q96LB8	.;PGRP4_HUMAN	M	83;87	ENSP00000357728:L83M;ENSP00000352672:L87M	ENSP00000352672:L87M	L	-	1	2	PGLYRP4	151584363	0.031000	0.19500	0.400000	0.26346	0.156000	0.22039	-0.096000	0.11059	0.180000	0.19960	0.313000	0.20887	CTG	.	.		0.557	PGLYRP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000089978.1	NM_020393		T	153317739	G	T	153317739	3	4	354	1	0	0	0	0	1	0	0	0	11805	1020	36	3	886	3	PGLYRP4	1	153317739	Missense_Mutation	SNP	G	TCGA-WX-AA44-01A-11D-A38X-10	43144147	153317739	95932882	8	49986										
LYST	1130	hgsc.bcm.edu	37	chr1	235892901	235892901	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	caaaatttgacttacctagtAacaattcaccagctgtctct	4	11	2	1			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr1:235892901A>G	ENST00000389794.3	-	37	9275	c.9101T>C	c.(9100-9102)tTa>tCa	p.L3034S	LYST_ENST00000389793.2_Missense_Mutation_p.L3034S|LYST_ENST00000473037.1_5'UTR			Q99698	LYST_HUMAN	lysosomal trafficking regulator	3034					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			CTTACCTAGTAACAATTCACC	0.328																																					p.L3034S		Atlas-SNP	.											.	LYST	370	.	0			c.T9101C						.						93	88	90					1																	235892901		2202	4299	6501	SO:0001583	missense	1130	exon37			CCTAGTAACAATT	U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"WD repeat domain containing"	1968	protein-coding gene	gene with protein product		606897	"Chediak-Higashi syndrome 1"	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.9101T>C	chr1.hg19:g.235892901A>G	ENSP00000374444:p.Leu3034Ser	51.0	0.0		95.0	17.0	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Missense_Mutation	SNP	ENST00000389794.3	hg19	CCDS31062.1	.	.	.	.	.	.	.	.	.	.	A	25.6	4.651337	0.88056	.	.	ENSG00000143669	ENST00000389794;ENST00000389793	T;T	0.64085	-0.08;-0.08	5.78	5.78	0.91487	PH-BEACH domain (1);	0.000000	0.85682	D	0.000000	T	0.78432	0.4282	M	0.69823	2.125	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.79359	-0.1836	10	0.51188	T	0.08	.	16.1167	0.81309	1.0:0.0:0.0:0.0	.	3034	Q99698	LYST_HUMAN	S	3034	ENSP00000374444:L3034S;ENSP00000374443:L3034S	ENSP00000374443:L3034S	L	-	2	0	LYST	233959524	1.000000	0.71417	0.997000	0.53966	0.979000	0.70002	8.862000	0.92283	2.204000	0.70986	0.528000	0.53228	TTA	.	.		0.328	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			G	235892901	A	G	235892901	3	3	354	1	0	0	0	0	1	0	0	0	9137	372	13	2	2372	2	LYST	1	235892901	Missense_Mutation	SNP	A	TCGA-WX-AA44-01A-11D-A38X-10	82575162	235892901	13357720	9	49987										
FMN2	56776	hgsc.bcm.edu	37	chr1	240493999	240493999	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	ataagactcgaggacaggcaGatggctttggattagacatt	12	6	0	3			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr1:240493999G>T	ENST00000319653.9	+	11	4764	c.4534G>T	c.(4534-4536)Gat>Tat	p.D1512Y	FMN2_ENST00000545751.1_Missense_Mutation_p.D108Y	NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1512	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			AGGACAGGCAGATGGCTTTGG	0.423																																					p.D1512Y		Atlas-SNP	.											.	FMN2	451	.	0			c.G4534T						.						144	134	137					1																	240493999		2203	4300	6503	SO:0001583	missense	56776	exon11			CAGGCAGATGGCT	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.4534G>T	chr1.hg19:g.240493999G>T	ENSP00000318884:p.Asp1512Tyr	74.0	0.0		141.0	60.0	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	hg19	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	G	34	5.292763	0.95546	.	.	ENSG00000155816	ENST00000319653;ENST00000545751;ENST00000537355	T;T	0.17528	2.27;2.27	5.67	5.67	0.87782	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.000000	0.64402	D	0.000006	T	0.42539	0.1207	M	0.64630	1.985	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	T	0.07770	-1.0755	10	0.49607	T	0.09	.	19.7714	0.96367	0.0:0.0:1.0:0.0	.	108;158;141;1512	B4DP05;F5H2C1;B4DN09;Q9NZ56	.;.;.;FMN2_HUMAN	Y	1512;108;139	ENSP00000318884:D1512Y;ENSP00000437918:D108Y	ENSP00000318884:D1512Y	D	+	1	0	FMN2	238560622	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	9.814000	0.99346	2.666000	0.90696	0.655000	0.94253	GAT	.	.		0.423	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		T	240493999	G	T	240493999	3	4	354	1	0	0	0	0	1	0	0	0	5958	942	33	3	4576	3	FMN2	1	240493999	Missense_Mutation	SNP	G	TCGA-WX-AA44-01A-11D-A38X-10	4601098	240493999	8756622	10	49988										
KLF11	8462	hgsc.bcm.edu	37	chr2	10188153	10188153	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	actcagcactaacttggtgtCctgtcagccctgcttgcaca	8	14	2	0	rs370039403		TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr2:10188153C>G	ENST00000305883.1	+	3	851	c.689C>G	c.(688-690)tCc>tGc	p.S230C	KLF11_ENST00000540845.1_Missense_Mutation_p.S213C|KLF11_ENST00000535335.1_Missense_Mutation_p.S213C	NM_003597.4	NP_003588.1	O14901	KLF11_HUMAN	Kruppel-like factor 11	230					apoptotic process (GO:0006915)|cellular response to peptide (GO:1901653)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.133)|OV - Ovarian serous cystadenocarcinoma(76;0.228)		AACTTGGTGTCCTGTCAGCCC	0.532																																					p.S230C	Melanoma(56;431 1507 23687 50789)	Atlas-SNP	.											.	KLF11	45	.	0			c.C689G						.						101	95	97					2																	10188153		2203	4300	6503	SO:0001583	missense	8462	exon3			TGGTGTCCTGTCA	AF028008	CCDS1668.1, CCDS54333.1	2p25	2013-01-08	2004-11-29	2004-12-01	ENSG00000172059	ENSG00000172059		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	11811	protein-coding gene	gene with protein product		603301	"TGFB inducible early growth response 2"	TIEG2		9748269, 11087666	Standard	NM_001177716		Approved	Tieg3, MODY7	uc002raf.1	O14901	OTTHUMG00000119004	ENST00000305883.1:c.689C>G	chr2.hg19:g.10188153C>G	ENSP00000307023:p.Ser230Cys	102.0	0.0		64.0	17.0	NM_003597	B4DZE7|Q9EPF4	Missense_Mutation	SNP	ENST00000305883.1	hg19	CCDS1668.1	.	.	.	.	.	.	.	.	.	.	C	14.51	2.557236	0.45590	.	.	ENSG00000172059	ENST00000305883;ENST00000540845;ENST00000535335	T;T;T	0.15372	2.45;2.43;2.43	5.26	4.36	0.52297	.	0.610386	0.15778	N	0.245094	T	0.28433	0.0703	M	0.67953	2.075	0.09310	N	1	D	0.71674	0.998	P	0.54270	0.747	T	0.13229	-1.0517	9	.	.	.	.	6.7518	0.23491	0.1727:0.7118:0.0:0.1155	.	230	O14901	KLF11_HUMAN	C	230;213;213	ENSP00000307023:S230C;ENSP00000444690:S213C;ENSP00000442722:S213C	.	S	+	2	0	KLF11	10105604	0.018000	0.18449	0.116000	0.21606	0.710000	0.40934	1.819000	0.39022	1.154000	0.42482	0.407000	0.27541	TCC	.	.		0.532	KLF11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000239202.3	NM_003597		G	10188153	C	G	10188153	3	3	354	1	0	0	0	0	1	0	0	0	8348	855	30	4	699	4	KLF11	2	10188153	Missense_Mutation	SNP	C	TCGA-WX-AA44-01A-11D-A38X-10		10188153	233011220	11	49989										
ABCG5	64240	hgsc.bcm.edu	37	chr2	44041621	44041621	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	aaatagaatacttaccacaaGtgaaattcagtccgtagaac	6	8	1	3			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr2:44041621G>C	ENST00000260645.1	-	12	1896	c.1757C>G	c.(1756-1758)aCt>aGt	p.T586S	ABCG5_ENST00000543989.1_Missense_Mutation_p.T191S|ABCG5_ENST00000405322.1_Missense_Mutation_p.T415S	NM_022436.2	NP_071881.1	Q9H222	ABCG5_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 5	586	ABC transmembrane type-2.				ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|excretion (GO:0007588)|intestinal cholesterol absorption (GO:0030299)|negative regulation of intestinal cholesterol absorption (GO:0045796)|negative regulation of intestinal phytosterol absorption (GO:0010949)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cholesterol transporter activity (GO:0017127)|protein heterodimerization activity (GO:0046982)			breast(1)|kidney(2)|large_intestine(4)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	33		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)			Ezetimibe(DB00973)	CTTACCACAAGTGAAATTCAG	0.308																																					p.T586S		Atlas-SNP	.											.	ABCG5	72	.	0			c.C1757G						.						71	71	71					2																	44041621		2202	4294	6496	SO:0001583	missense	64240	exon12			CCACAAGTGAAAT	T93792	CCDS1814.1	2p21	2012-03-14	2008-07-31		ENSG00000138075	ENSG00000138075		"ATP binding cassette transporters / subfamily G"	13886	protein-coding gene	gene with protein product	"sterolin 1"	605459				11099417, 11452359	Standard	NM_022436		Approved	STSL	uc002rtn.3	Q9H222	OTTHUMG00000128758	ENST00000260645.1:c.1757C>G	chr2.hg19:g.44041621G>C	ENSP00000260645:p.Thr586Ser	240.0	0.0		199.0	53.0	NM_022436	Q2T9G2|Q96QZ2|Q96QZ3	Missense_Mutation	SNP	ENST00000260645.1	hg19	CCDS1814.1	.	.	.	.	.	.	.	.	.	.	G	19.40	3.819732	0.71028	.	.	ENSG00000138075	ENST00000260645;ENST00000405322;ENST00000543989	D;T;T	0.90004	-2.6;-1.21;1.1	5.09	4.22	0.49857	.	0.923410	0.09161	N	0.840237	D	0.92519	0.7624	M	0.61703	1.905	0.52099	D	0.999949	P;D	0.76494	0.695;0.999	B;D	0.80764	0.383;0.994	D	0.86197	0.1616	10	0.08599	T	0.76	.	13.493	0.61407	0.0759:0.0:0.9241:0.0	.	415;586	E7EX35;Q9H222	.;ABCG5_HUMAN	S	586;415;191	ENSP00000260645:T586S;ENSP00000384513:T415S;ENSP00000445107:T191S	ENSP00000260645:T586S	T	-	2	0	ABCG5	43895125	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.419000	0.66435	1.369000	0.46134	0.557000	0.71058	ACT	.	.		0.308	ABCG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250675.1	NM_022436		C	44041621	G	C	44041621	3	2	354	1	0	0	0	0	1	0	0	0	71	1029	36	4	206	4	ABCG5	2	44041621	Missense_Mutation	SNP	G	TCGA-WX-AA44-01A-11D-A38X-10	33853468	44041621	199157752	12	49990										
GALNT5	11227	hgsc.bcm.edu	37	chr2	158140942	158140942	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	tcaaggagattctgctggtaGatgacttcagcaccaaaggt	11	8	3	3			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr2:158140942G>C	ENST00000259056.4	+	2	2088	c.1603G>C	c.(1603-1605)Gat>Cat	p.D535H		NM_014568.1	NP_055383.1	Q7Z7M9	GALT5_HUMAN	polypeptide N-acetylgalactosaminyltransferase 5	535	Catalytic subdomain A.				cellular protein metabolic process (GO:0044267)|glycosaminoglycan biosynthetic process (GO:0006024)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(4)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	56						TCTGCTGGTAGATGACTTCAG	0.438																																					p.D535H		Atlas-SNP	.											.	GALNT5	112	.	0			c.G1603C						.						150	125	133					2																	158140942		2203	4300	6503	SO:0001583	missense	11227	exon2			CTGGTAGATGACT	AJ245539	CCDS2203.1	2q24.1	2014-03-13	2014-03-13		ENSG00000136542	ENSG00000136542	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4127	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 5"	615129	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 5 (GalNAc-T5)"			10545594	Standard	NM_014568		Approved	GalNAc-T5	uc002tzg.3	Q7Z7M9	OTTHUMG00000131965	ENST00000259056.4:c.1603G>C	chr2.hg19:g.158140942G>C	ENSP00000259056:p.Asp535His	47.0	0.0		88.0	26.0	NM_014568	A5PKZ1|Q9UGK7|Q9UHL6	Missense_Mutation	SNP	ENST00000259056.4	hg19	CCDS2203.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.686456	0.88639	.	.	ENSG00000136542	ENST00000259056	T	0.75704	-0.96	5.3	5.3	0.74995	Glycosyl transferase, family 2 (1);	0.047140	0.85682	D	0.000000	D	0.90738	0.7093	H	0.95745	3.715	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.92849	0.6295	10	0.87932	D	0	.	19.4456	0.94845	0.0:0.0:1.0:0.0	.	535	Q7Z7M9	GALT5_HUMAN	H	535	ENSP00000259056:D535H	ENSP00000259056:D535H	D	+	1	0	GALNT5	157849188	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	9.785000	0.99042	2.861000	0.98227	0.655000	0.94253	GAT	.	.		0.438	GALNT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254925.2	NM_014568		C	158140942	G	C	158140942	3	2	354	1	0	0	0	0	1	0	0	0	6224	942	33	4	1609	4	GALNT5	2	158140942	Missense_Mutation	SNP	G	TCGA-WX-AA44-01A-11D-A38X-10	114099321	158140942	85058431	13	49991										
FRZB	2487	hgsc.bcm.edu	37	chr2	183703315	183703315	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	cacatcatggcacttagtctTtatctctttaactttagccc	4	12	3	0			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr2:183703315T>A	ENST00000295113.4	-	4	1228	c.619A>T	c.(619-621)Aag>Tag	p.K207*		NM_001463.3	NP_001454.2	Q92765	SFRP3_HUMAN	frizzled-related protein	207	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				brain development (GO:0007420)|cochlea morphogenesis (GO:0090103)|convergent extension involved in organogenesis (GO:0060029)|epithelium development (GO:0060429)|gonad development (GO:0008406)|mammary gland involution (GO:0060056)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell development (GO:0010721)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of hepatocyte differentiation (GO:0070367)|negative regulation of Wnt signaling pathway (GO:0030178)|neural crest cell differentiation (GO:0014033)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fat cell differentiation (GO:0045600)|skeletal system development (GO:0001501)|somite development (GO:0061053)|vasculature development (GO:0001944)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)	PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)	21			OV - Ovarian serous cystadenocarcinoma(117;0.109)|Epithelial(96;0.231)			CACTTAGTCTTTATCTCTTTA	0.398																																					p.K207X		Atlas-SNP	.											.	FRZB	42	.	0			c.A619T						.						116	111	113					2																	183703315		2203	4300	6503	SO:0001587	stop_gained	2487	exon4			TAGTCTTTATCTC	U24163	CCDS2286.1	2q32.1	2013-09-19			ENSG00000162998	ENSG00000162998		"Secreted frizzled-related proteins"	3959	protein-coding gene	gene with protein product		605083				8824257, 9118218	Standard	NM_001463		Approved	FRZB-PEN, FRZB1, SRFP3, FRP-3, SFRP3, FRE, FRITZ, FRZB-1, FZRB, hFIZ	uc002upa.2	Q92765	OTTHUMG00000132597	ENST00000295113.4:c.619A>T	chr2.hg19:g.183703315T>A	ENSP00000295113:p.Lys207*	71.0	0.0		106.0	33.0	NM_001463	O00181|Q99686	Nonsense_Mutation	SNP	ENST00000295113.4	hg19	CCDS2286.1	.	.	.	.	.	.	.	.	.	.	T	42	9.698131	0.99241	.	.	ENSG00000162998	ENST00000295113	.	.	.	5.15	4.0	0.46444	.	0.045057	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.8213	0.46606	0.0:0.0742:0.0:0.9258	.	.	.	.	X	207	.	ENSP00000295113:K207X	K	-	1	0	FRZB	183411560	1.000000	0.71417	0.470000	0.27216	0.973000	0.67179	7.975000	0.88055	0.817000	0.34445	0.455000	0.32223	AAG	.	.		0.398	FRZB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255808.1	NM_001463		A	183703315	T	A	183703315	4	1	354	1	0	0	0	0	0	1	0	0	6073	1850	64	4	370	4	FRZB	2	183703315	Nonsense_Mutation	SNP	T	TCGA-WX-AA44-01A-11D-A38X-10	25562373	183703315	59496058	14	49992										
STK17B	9262	hgsc.bcm.edu	37	chr2	197010770	197010770	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	cacaggctgaaaatttctccAcctgcagcactaaaataaaa	5	11	1	1			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr2:197010770A>C	ENST00000263955.4	-	4	631	c.345T>G	c.(343-345)ggT>ggG	p.G115G	STK17B_ENST00000409228.1_Silent_p.G115G	NM_004226.3	NP_004217.1	O94768	ST17B_HUMAN	serine/threonine kinase 17b	115	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of fibroblast apoptotic process (GO:2000271)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|kidney(2)|large_intestine(1)|lung(10)	15			OV - Ovarian serous cystadenocarcinoma(117;0.141)			AAATTTCTCCACCTGCAGCAC	0.318																																					p.G115G		Atlas-SNP	.											.	STK17B	28	.	0			c.T345G						.						51	49	50					2																	197010770		2203	4300	6503	SO:0001819	synonymous_variant	9262	exon4			TTCTCCACCTGCA	AB011421	CCDS2315.1	2q33.1	2008-02-05	2007-02-12		ENSG00000081320	ENSG00000081320			11396	protein-coding gene	gene with protein product	"death-associated protein kinase-related 2"	604727	"serine/threonine kinase 17b (apoptosis-inducing)"			9786912	Standard	NM_004226		Approved	DRAK2	uc002utk.3	O94768	OTTHUMG00000132735	ENST00000263955.4:c.345T>G	chr2.hg19:g.197010770A>C		55.0	0.0		89.0	28.0	NM_004226		Silent	SNP	ENST00000263955.4	hg19	CCDS2315.1																																																																																			.	.		0.318	STK17B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256092.2			C	197010770	A	C	197010770	2	2	354	1	0	0	0	0	0	0	0	1	15306	146	6	5		5	STK17B	2	197010770	Silent	SNP	A	TCGA-WX-AA44-01A-11D-A38X-10	13307455	197010770	46188603	15	49993										
EPHA4	2043	hgsc.bcm.edu	37	chr2	222290755	222290755	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	attcagtactggctcagacgGgaaccattctgccgtgcatc	10	12	3	1			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr2:222290755G>T	ENST00000281821.2	-	17	2995	c.2954C>A	c.(2953-2955)cCc>cAc	p.P985H	EPHA4_ENST00000469354.1_5'Flank|EPHA4_ENST00000392071.4_Missense_Mutation_p.P934H|EPHA4_ENST00000409854.1_3'UTR|EPHA4_ENST00000409938.1_Missense_Mutation_p.P985H	NM_004438.3	NP_004429.1	P54764	EPHA4_HUMAN	EPH receptor A4	985					adult walking behavior (GO:0007628)|cell adhesion (GO:0007155)|corticospinal tract morphogenesis (GO:0021957)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|glial cell migration (GO:0008347)|motor neuron axon guidance (GO:0008045)|negative regulation of axon regeneration (GO:0048681)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001108)|protein autophosphorylation (GO:0046777)|regulation of astrocyte differentiation (GO:0048710)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rap GTPase activity (GO:0032317)	axon (GO:0030424)|axon terminus (GO:0043679)|axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|DH domain binding (GO:0097161)|GPI-linked ephrin receptor activity (GO:0005004)|PH domain binding (GO:0042731)|protein kinase activity (GO:0004672)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		GGCTCAGACGGGAACCATTCT	0.433																																					p.P985H		Atlas-SNP	.											.	EPHA4	263	.	0			c.C2954A						.						231	214	220					2																	222290755		2203	4300	6503	SO:0001583	missense	2043	exon17			CAGACGGGAACCA	L36645	CCDS2447.1	2q36.3	2013-02-11	2004-10-28		ENSG00000116106	ENSG00000116106	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3388	protein-coding gene	gene with protein product		602188	"EphA4"	TYRO1		9267020	Standard	NM_004438		Approved	Hek8	uc002vmq.3	P54764	OTTHUMG00000133142	ENST00000281821.2:c.2954C>A	chr2.hg19:g.222290755G>T	ENSP00000281821:p.Pro985His	91.0	0.0		94.0	24.0	NM_004438	A8K2P1|B2R601|B7Z6Q8|Q2M380	Missense_Mutation	SNP	ENST00000281821.2	hg19	CCDS2447.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.171916	0.78452	.	.	ENSG00000116106	ENST00000281821;ENST00000409938;ENST00000392071	T;T;T	0.71817	-0.6;-0.6;-0.6	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.75221	0.3820	L	0.35288	1.05	0.80722	D	1	D	0.71674	0.998	P	0.61397	0.888	T	0.66276	-0.5964	10	0.13108	T	0.6	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	985	P54764	EPHA4_HUMAN	H	985;985;934	ENSP00000281821:P985H;ENSP00000386829:P985H;ENSP00000375923:P934H	ENSP00000281821:P985H	P	-	2	0	EPHA4	221998999	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.476000	0.97823	2.941000	0.99782	0.655000	0.94253	CCC	.	.		0.433	EPHA4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256836.3			T	222290755	G	T	222290755	3	4	354	1	0	0	0	0	1	0	0	0	5171	1232	43	3	10	3	EPHA4	2	222290755	Missense_Mutation	SNP	G	TCGA-WX-AA44-01A-11D-A38X-10	25279985	222290755	20908618	16	49994										
NCL	4691	hgsc.bcm.edu	37	chr2	232325441	232325441	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	tcatcatcttcatcatcttcGtcgtcgtcgtcatcctcgtc	5	15	7	0	rs66781921|rs534320031	byFrequency	TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr2:232325441G>T	ENST00000322723.4	-	4	990	c.750C>A	c.(748-750)gaC>gaA	p.D250E	SNORD82_ENST00000365530.1_RNA	NM_005381.2	NP_005372.2	P19338	NUCL_HUMAN	nucleolin	250	Asp/Glu-rich (acidic).				angiogenesis (GO:0001525)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)	cell cortex (GO:0005938)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)|telomeric DNA binding (GO:0042162)	p.D250E(1)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(3)	35		Ovarian(221;1.34e-05)|Renal(207;0.0112)|Lung NSC(271;0.0339)|all_lung(227;0.0616)|all_hematologic(139;0.0748)|Hepatocellular(293;0.137)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.65e-111)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)|COAD - Colon adenocarcinoma(134;0.141)|STAD - Stomach adenocarcinoma(1183;0.18)		catcatcttcgtcgtcgtcgt	0.433																																					p.D250E		Atlas-SNP	.											NCL,NS,carcinoma,0,1	NCL	80	.	1	Substitution - Missense(1)	endometrium(1)	c.C750A						.						249	205	220					2																	232325441		2203	4300	6503	SO:0001583	missense	4691	exon4			ATCTTCGTCGTCG		CCDS33397.1	2q37.1	2013-09-19			ENSG00000115053	ENSG00000115053		"RNA binding motif (RRM) containing"	7667	protein-coding gene	gene with protein product		164035				2394707, 3409881	Standard	NM_005381		Approved	C23	uc002vru.3	P19338	OTTHUMG00000153866	ENST00000322723.4:c.750C>A	chr2.hg19:g.232325441G>T	ENSP00000318195:p.Asp250Glu	78.0	1.0		46.0	2.0	NM_005381	Q53SK1|Q8NB06|Q9UCF0|Q9UDG1	Missense_Mutation	SNP	ENST00000322723.4	hg19	CCDS33397.1	.	.	.	.	.	.	.	.	.	.	G	0.938	-0.710431	0.03230	.	.	ENSG00000115053	ENST00000322723	T	0.19938	2.11	5.46	-10.9	0.00192	.	0.806964	0.11391	N	0.568775	T	0.06826	0.0174	N	0.22421	0.69	0.26746	N	0.970293	B	0.02656	0.0	B	0.04013	0.001	T	0.27226	-1.0080	10	0.07030	T	0.85	-2.921	3.1311	0.06424	0.3801:0.1164:0.3434:0.1601	.	250	P19338	NUCL_HUMAN	E	250	ENSP00000318195:D250E	ENSP00000318195:D250E	D	-	3	2	NCL	232033685	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-10.346000	0.00006	-3.764000	0.00110	-0.259000	0.10710	GAC	.	.		0.433	NCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332731.1	NM_005381		T	232325441	G	T	232325441	3	4	354	1	0	0	0	0	1	0	0	0	10235	1136	40	1	1426	1	NCL	2	232325441	Missense_Mutation	SNP	G	TCGA-WX-AA44-01A-11D-A38X-10	10034686	232325441	10873932	17	49995										
C3orf20	84077	hgsc.bcm.edu	37	chr3	14755616	14755616	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	cctggattctccttgctggcCctattcaatactgaaggcca	8	13	2	1			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr3:14755616C>T	ENST00000253697.3	+	8	1715	c.1263C>T	c.(1261-1263)gcC>gcT	p.A421A	C3orf20_ENST00000495387.1_3'UTR|C3orf20_ENST00000412910.1_Silent_p.A299A|C3orf20_ENST00000435614.1_Silent_p.A299A	NM_032137.4	NP_115513.4	Q8ND61	CC020_HUMAN	chromosome 3 open reading frame 20	421						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(13)|lung(11)|ovary(4)|skin(2)	40						CCTTGCTGGCCCTATTCAATA	0.502																																					p.A421A		Atlas-SNP	.											.	C3orf20	109	.	0			c.C1263T						.						94	86	89					3																	14755616		2203	4300	6503	SO:0001819	synonymous_variant	84077	exon8			GCTGGCCCTATTC	AL136781	CCDS33706.1, CCDS54555.1	3p25.1	2011-01-25			ENSG00000131379	ENSG00000131379			25320	protein-coding gene	gene with protein product						11230166	Standard	NM_032137		Approved	DKFZP434N1817	uc003byy.3	Q8ND61	OTTHUMG00000155545	ENST00000253697.3:c.1263C>T	chr3.hg19:g.14755616C>T		44.0	0.0		40.0	11.0	NM_032137	Q7L0U6|Q8NCP2|Q9H0I7	Silent	SNP	ENST00000253697.3	hg19	CCDS33706.1																																																																																			.	.		0.502	C3orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340586.1	NM_032137		T	14755616	C	T	14755616	2	4	354	1	0	0	0	0	0	0	0	1	2215	610	22	3		3	C3orf20	3	14755616	Silent	SNP	C	TCGA-WX-AA44-01A-11D-A38X-10		14755616	183266814	18	49996										
UBP1	7342	hgsc.bcm.edu	37	chr3	33481287	33481287	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	cccgagaggctggcgtcgaaGtcgtgcaccagcccggactc	14	15	0	1			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr3:33481287G>C	ENST00000283629.3	-	1	583	c.54C>G	c.(52-54)gaC>gaG	p.D18E	UBP1_ENST00000447368.2_Missense_Mutation_p.D18E|UBP1_ENST00000283628.5_Missense_Mutation_p.D18E	NM_001128161.1|NM_014517.4	NP_001121633.1|NP_055332.3	Q9NZI7	UBIP1_HUMAN	upstream binding protein 1 (LBP-1a)	18					angiogenesis (GO:0001525)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|urinary_tract(2)	23						TGGCGTCGAAGTCGTGCACCA	0.692																																					p.D18E		Atlas-SNP	.											.	UBP1	42	.	0			c.C54G						.						52	55	54					3																	33481287		2203	4299	6502	SO:0001583	missense	7342	exon1			GTCGAAGTCGTGC	AF198487	CCDS2659.1, CCDS46788.1	3p22.3	2004-03-02			ENSG00000153560	ENSG00000153560			12507	protein-coding gene	gene with protein product		609784				8114710	Standard	NM_014517		Approved	LBP-1a	uc010hga.3	Q9NZI7	OTTHUMG00000130749	ENST00000283629.3:c.54C>G	chr3.hg19:g.33481287G>C	ENSP00000283629:p.Asp18Glu	190.0	0.0		214.0	72.0	NM_001128160	Q68CT0|Q86Y57|Q9H8V0|Q9UD76|Q9UD78	Missense_Mutation	SNP	ENST00000283629.3	hg19	CCDS2659.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.610799	0.87258	.	.	ENSG00000153560	ENST00000283629;ENST00000447368;ENST00000283628;ENST00000456378	T;T;T;T	0.51817	1.97;1.91;1.97;0.69	3.93	2.54	0.30619	.	0.000000	0.85682	D	0.000000	T	0.50650	0.1628	L	0.27053	0.805	0.51012	D	0.999906	P;D	0.65815	0.799;0.995	B;D	0.67548	0.199;0.952	T	0.50980	-0.8763	10	0.66056	D	0.02	-10.7836	10.2933	0.43610	0.1247:0.0:0.8753:0.0	.	18;18	Q9NZI7-4;Q9NZI7	.;UBIP1_HUMAN	E	18	ENSP00000283629:D18E;ENSP00000395558:D18E;ENSP00000283628:D18E;ENSP00000401614:D18E	ENSP00000283628:D18E	D	-	3	2	UBP1	33456291	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.044000	0.64214	0.688000	0.31529	0.555000	0.69702	GAC	.	.		0.692	UBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253249.2	NM_014517		C	33481287	G	C	33481287	3	2	354	1	0	0	0	0	1	0	0	0	16910	1020	36	4	1632	4	UBP1	3	33481287	Missense_Mutation	SNP	G	TCGA-WX-AA44-01A-11D-A38X-10	18725671	33481287	164541143	19	49997										
NBEAL2	23218	hgsc.bcm.edu	37	chr3	47049823	47049823	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	cgcggacagtttgtagcggcActacggcctctgggtgccac	14	13	1	0			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr3:47049823A>G	ENST00000450053.3	+	51	7949	c.7770A>G	c.(7768-7770)gcA>gcG	p.A2590A	NBEAL2_ENST00000383740.2_Silent_p.A839A|NBEAL2_ENST00000292309.5_Silent_p.A2406A	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	2590					blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		TTGTAGCGGCACTACGGCCTC	0.592																																					p.A2590A		Atlas-SNP	.											.	NBEAL2	267	.	0			c.A7770G						.						55	53	54					3																	47049823		2034	4175	6209	SO:0001819	synonymous_variant	23218	exon51			AGCGGCACTACGG	AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"WD repeat domain containing"	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.7770A>G	chr3.hg19:g.47049823A>G		113.0	0.0		63.0	18.0	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Silent	SNP	ENST00000450053.3	hg19	CCDS46817.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	3.108|3.108	-0.183326|-0.183326	0.06340|0.06340	.|.	.|.	ENSG00000160796|ENSG00000160796	ENST00000416683|ENST00000443829	.|.	.|.	.|.	5.16|5.16	1.23|1.23	0.21249|0.21249	.|.	.|.	.|.	.|.	.|.	T|T	0.51346|0.51346	0.1669|0.1669	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.38628|0.38628	-0.9652|-0.9652	4|4	.|.	.|.	.|.	.|.	5.0993|5.0993	0.14751|0.14751	0.6681:0.1534:0.1785:0.0|0.6681:0.1534:0.1785:0.0	.|.	.|.	.|.	.|.	R|A	1878|929	.|.	.|.	H|T	+|+	2|1	0|0	NBEAL2|NBEAL2	47024827|47024827	0.000000|0.000000	0.05858|0.05858	0.868000|0.868000	0.34077|0.34077	0.320000|0.320000	0.28249|0.28249	-1.412000|-1.412000	0.02476|0.02476	0.376000|0.376000	0.24707|0.24707	0.459000|0.459000	0.35465|0.35465	CAC|ACT	.	.		0.592	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064		G	47049823	A	G	47049823	2	3	354	1	0	0	0	0	0	0	0	1	10198	146	6	2		2	NBEAL2	3	47049823	Silent	SNP	A	TCGA-WX-AA44-01A-11D-A38X-10	13568536	47049823	150972607	20	49998										
COL7A1	1294	hgsc.bcm.edu	37	chr3	48626421	48626421	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	ctcgacacacgacccacaggCtcaggggctggggacagagg	15	13	1	1	rs146407483		TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr3:48626421C>A	ENST00000328333.8	-	18	2429	c.2322G>T	c.(2320-2322)gaG>gaT	p.E774D	COL7A1_ENST00000454817.1_Missense_Mutation_p.E774D	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	774	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.|Nonhelical region (NC1).				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		GACCCACAGGCTCAGGGGCTG	0.582																																					p.E774D		Atlas-SNP	.											.	COL7A1	320	.	0			c.G2322T						.						69	69	69					3																	48626421		2203	4300	6503	SO:0001583	missense	1294	exon18			CACAGGCTCAGGG	L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"Collagens", "Fibronectin type III domain containing"	2214	protein-coding gene	gene with protein product	"collagen VII, alpha-1 polypeptide", "LC collagen"	120120	"epidermolysis bullosa, dystrophic, dominant and recessive"	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.2322G>T	chr3.hg19:g.48626421C>A	ENSP00000332371:p.Glu774Asp	463.0	0.0		305.0	76.0	NM_000094	Q14054|Q16507	Missense_Mutation	SNP	ENST00000328333.8	hg19	CCDS2773.1	.	.	.	.	.	.	.	.	.	.	C	11.56	1.675701	0.29783	.	.	ENSG00000114270	ENST00000328333;ENST00000454817	T;T	0.56103	0.48;0.48	5.08	-0.0304	0.13914	Immunoglobulin-like fold (1);	0.664905	0.12803	N	0.437782	T	0.31482	0.0798	N	0.20766	0.605	0.23555	N	0.997425	B	0.06786	0.001	B	0.04013	0.001	T	0.16689	-1.0394	10	0.52906	T	0.07	.	4.0515	0.09798	0.1535:0.4965:0.0:0.3499	.	774	Q02388	CO7A1_HUMAN	D	774	ENSP00000332371:E774D;ENSP00000412569:E774D	ENSP00000332371:E774D	E	-	3	2	COL7A1	48601425	1.000000	0.71417	0.475000	0.27278	0.916000	0.54674	1.335000	0.33839	-0.235000	0.09767	0.462000	0.41574	GAG	.	C|1.000;T|0.000		0.582	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094		A	48626421	C	A	48626421	3	1	354	1	0	0	0	0	1	0	0	0	3706	796	28	3	6916	3	COL7A1	3	48626421	Missense_Mutation	SNP	C	TCGA-WX-AA44-01A-11D-A38X-10	1576598	48626421	149396009	21	49999										
CISH	1154	hgsc.bcm.edu	37	chr3	50645277	50645277	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	cataggcagggccggggtggGagcaggatcggggctgtcgc	21	9	0	0			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr3:50645277G>A	ENST00000348721.3	-	3	718	c.538C>T	c.(538-540)Ccc>Tcc	p.P180S	CISH_ENST00000443053.2_Missense_Mutation_p.P197S	NM_145071.2	NP_659508.1	Q9NSE2	CISH_HUMAN	cytokine inducible SH2-containing protein	180					intracellular signal transduction (GO:0035556)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of signal transduction (GO:0009968)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein ubiquitination (GO:0016567)|regulation of cell growth (GO:0001558)	cytosol (GO:0005829)|plasma membrane (GO:0005886)				breast(2)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)		GCCGGGGTGGGAGCAGGATCG	0.627																																					p.P197S		Atlas-SNP	.											.	CISH	27	.	0			c.C589T						.						53	56	55					3																	50645277		2203	4300	6503	SO:0001583	missense	1154	exon4			GGGTGGGAGCAGG	Z77852	CCDS2831.1, CCDS46834.1	3p21.3	2013-02-14			ENSG00000114737	ENSG00000114737		"Suppressors of cytokine signaling", "SH2 domain containing"	1984	protein-coding gene	gene with protein product		602441				9465889, 7796808	Standard	NM_013324		Approved	CIS, G18, CIS-1, SOCS	uc003dax.3	Q9NSE2	OTTHUMG00000156853	ENST00000348721.3:c.538C>T	chr3.hg19:g.50645277G>A	ENSP00000294173:p.Pro180Ser	81.0	0.0		78.0	23.0	NM_013324	B2R9N1|G5E9R1|Q9NS38|Q9Y5R1	Missense_Mutation	SNP	ENST00000348721.3	hg19	CCDS2831.1	.	.	.	.	.	.	.	.	.	.	G	7.554	0.663378	0.14710	.	.	ENSG00000114737	ENST00000443053;ENST00000348721	T;T	0.42900	0.96;1.0	5.9	4.09	0.47781	SH2 motif (1);	0.732533	0.13829	N	0.359889	T	0.36936	0.0985	L	0.58101	1.795	0.42300	D	0.992179	B;B	0.21452	0.056;0.008	B;B	0.32022	0.139;0.041	T	0.07424	-1.0773	10	0.10111	T	0.7	-0.2431	5.7517	0.18150	0.159:0.0:0.6742:0.1668	.	197;180	G5E9R1;Q9NSE2	.;CISH_HUMAN	S	197;180	ENSP00000409346:P197S;ENSP00000294173:P180S	ENSP00000294173:P180S	P	-	1	0	CISH	50620281	0.984000	0.35163	0.029000	0.17559	0.268000	0.26511	2.522000	0.45572	0.796000	0.33947	0.563000	0.77884	CCC	.	.		0.627	CISH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346245.1	NM_145071		A	50645277	G	A	50645277	3	1	354	1	0	0	0	0	1	0	0	0	3439	1174	41	3	242	3	CISH	3	50645277	Missense_Mutation	SNP	G	TCGA-WX-AA44-01A-11D-A38X-10	2018856	50645277	147377153	22	50000										
EPHA3	2042	hgsc.bcm.edu	37	chr3	89390994	89390994	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	ggcccctggacacaggaggcCggaaagatgttaccttcaac	12	12	1	1			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr3:89390994C>A	ENST00000336596.2	+	5	1285	c.1060C>A	c.(1060-1062)Cgg>Agg	p.R354R	EPHA3_ENST00000494014.1_Silent_p.R354R|EPHA3_ENST00000452448.2_Silent_p.R354R	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	354	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		CACAGGAGGCCGGAAAGATGT	0.458										TSP Lung(6;0.00050)																											p.R354R		Atlas-SNP	.											.	EPHA3	501	.	0			c.C1060A						.						95	94	94					3																	89390994		2203	4300	6503	SO:0001819	synonymous_variant	2042	exon5			GGAGGCCGGAAAG	M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3387	protein-coding gene	gene with protein product		179611	"EphA3"	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.1060C>A	chr3.hg19:g.89390994C>A		129.0	0.0		182.0	56.0	NM_005233	Q9H2V3|Q9H2V4	Silent	SNP	ENST00000336596.2	hg19	CCDS2922.1																																																																																			.	.		0.458	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		A	89390994	C	A	89390994	2	1	354	1	0	0	0	0	0	0	0	1	5170	643	23	1		1	EPHA3	3	89390994	Silent	SNP	C	TCGA-WX-AA44-01A-11D-A38X-10	38745717	89390994	108631436	23	50001										
PHC3	80012	hgsc.bcm.edu	37	chr3	169840463	169840463	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	agtgggtggtggtggggttcTatccatccggacacattcat	14	8	2	0			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr3:169840463T>G	ENST00000494943.1	-	9	1890	c.1822A>C	c.(1822-1824)Aga>Cga	p.R608R	PHC3_ENST00000495893.2_Silent_p.R620R|PHC3_ENST00000467570.1_Silent_p.R567R			Q8NDX5	PHC3_HUMAN	polyhomeotic homolog 3 (Drosophila)	608	Pro-rich.				multicellular organismal development (GO:0007275)	actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(1)|upper_aerodigestive_tract(2)	26	all_cancers(22;2.67e-22)|all_epithelial(15;4.73e-27)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)			GGTGGGGTTCTATCCATCCGG	0.433																																					p.R620R		Atlas-SNP	.											.	PHC3	113	.	0			c.A1858C						.						138	135	136					3																	169840463		1921	4135	6056	SO:0001819	synonymous_variant	80012	exon9			GGGTTCTATCCAT		CCDS46952.1	3q26.32	2014-01-28	2006-09-12		ENSG00000173889	ENSG00000173889		"Sterile alpha motif (SAM) domain containing"	15682	protein-coding gene	gene with protein product	"early development regulator 3", "polyhomeotic like 3"		"polyhomeotic like 3 (Drosophila)"			12167701, 12384788	Standard	NM_024947		Approved	EDR3, FLJ12967, FLJ12729, HPH3	uc003fgl.2	Q8NDX5	OTTHUMG00000158777	ENST00000494943.1:c.1822A>C	chr3.hg19:g.169840463T>G		93.0	0.0		135.0	26.0	NM_024947	A2RRP9|Q5HYF0|Q6NSG2|Q8NFT7|Q8NFZ1|Q8TBM2|Q9H971|Q9H9I4	Silent	SNP	ENST00000494943.1	hg19		.	.	.	.	.	.	.	.	.	.	T	3.909	-0.020481	0.07634	.	.	ENSG00000173889	ENST00000486042	.	.	.	6.16	3.72	0.42706	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-12.5244	13.4437	0.61127	0.0:0.0:0.2459:0.7541	.	.	.	.	S	81	.	.	X	-	2	0	PHC3	171323157	0.998000	0.40836	0.958000	0.39756	0.270000	0.26580	4.007000	0.57093	0.519000	0.28406	-0.321000	0.08615	TAG	.	.		0.433	PHC3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000352182.3	NM_024947		G	169840463	T	G	169840463	2	3	354	1	0	0	0	0	0	0	0	1	11827	1530	53	5		5	PHC3	3	169840463	Silent	SNP	T	TCGA-WX-AA44-01A-11D-A38X-10	80449469	169840463	28181967	24	50002										
SLIT2	9353	hgsc.bcm.edu	37	chr4	20598095	20598095	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	cctcgtaccagcccctgtgaTaattttgattgtcagaatgg	9	10	1	3			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr4:20598095T>C	ENST00000504154.1	+	32	3630	c.3378T>C	c.(3376-3378)gaT>gaC	p.D1126D	SLIT2_ENST00000503823.1_Silent_p.D1118D|SLIT2_ENST00000273739.5_Silent_p.D1139D|SLIT2_ENST00000503837.1_Silent_p.D1122D	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	1126	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)			NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						GCCCCTGTGATAATTTTGATT	0.403																																					p.D1126D		Atlas-SNP	.											.	SLIT2	290	.	0			c.T3378C						.						109	110	110					4																	20598095		2203	4300	6503	SO:0001819	synonymous_variant	9353	exon32			CTGTGATAATTTT	AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"slit (Drosophila) homolog 2"	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.3378T>C	chr4.hg19:g.20598095T>C		101.0	0.0		106.0	10.0	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Silent	SNP	ENST00000504154.1	hg19	CCDS3426.1																																																																																			.	.		0.403	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2			C	20598095	T	C	20598095	2	2	354	1	0	0	0	0	0	0	0	1	14755	1403	49	2		2	SLIT2	4	20598095	Silent	SNP	T	TCGA-WX-AA44-01A-11D-A38X-10		20598095	170556181	25	50003										
PTPN13	5783	hgsc.bcm.edu	37	chr4	87692453	87692453	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	aaagcaaaaaacagtgcaagTccccatccagaagagacagt	8	10	0	2			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr4:87692453T>C	ENST00000411767.2	+	31	4996	c.4933T>C	c.(4933-4935)Tcc>Ccc	p.S1645P	PTPN13_ENST00000316707.6_Missense_Mutation_p.S1454P|PTPN13_ENST00000436978.1_Missense_Mutation_p.S1650P|PTPN13_ENST00000427191.2_Missense_Mutation_p.S1626P|PTPN13_ENST00000511467.1_Missense_Mutation_p.S1650P			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	1645					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		ACAGTGCAAGTCCCCATCCAG	0.453																																					p.S1650P		Atlas-SNP	.											.	PTPN13	203	.	0			c.T4948C						.						51	51	51					4																	87692453		2057	4211	6268	SO:0001583	missense	5783	exon31			TGCAAGTCCCCAT		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.4933T>C	chr4.hg19:g.87692453T>C	ENSP00000407249:p.Ser1645Pro	239.0	0.0		264.0	75.0	NM_080685	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	hg19	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	T	12.96	2.093373	0.36952	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T;T	0.55234	0.53;0.57;0.68;0.54;0.57	5.22	2.75	0.32379	.	0.280939	0.25523	N	0.030090	T	0.39708	0.1088	L	0.48642	1.525	0.31921	N	0.613487	B;B;B;B	0.13594	0.005;0.002;0.005;0.008	B;B;B;B	0.16289	0.007;0.009;0.007;0.015	T	0.40059	-0.9583	10	0.51188	T	0.08	.	3.382	0.07257	0.1363:0.073:0.1426:0.6482	.	1454;1626;1645;1650	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	P	1626;1650;1454;1645;1650;1594	ENSP00000408368:S1626P;ENSP00000394794:S1650P;ENSP00000322675:S1454P;ENSP00000407249:S1645P;ENSP00000426626:S1650P	ENSP00000322675:S1454P	S	+	1	0	PTPN13	87911477	0.948000	0.32251	0.443000	0.26883	0.957000	0.61999	2.336000	0.43938	0.389000	0.25086	0.533000	0.62120	TCC	.	.		0.453	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			C	87692453	T	C	87692453	3	2	354	1	0	0	0	0	1	0	0	0	12795	1667	58	2	5066	2	PTPN13	4	87692453	Missense_Mutation	SNP	T	TCGA-WX-AA44-01A-11D-A38X-10	67094358	87692453	103461823	26	50004										
RPS3A	6189	hgsc.bcm.edu	37	chr4	152021639	152021639	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	catcttcttaaaatccagggTtgatccattttctaagaaag	6	8	3	2			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr4:152021639T>C	ENST00000274065.4	+	2	145	c.65T>C	c.(64-66)gTt>gCt	p.V22A	RPS3A_ENST00000509736.1_Intron|SNORD73_ENST00000364394.1_RNA|RPS3A_ENST00000514682.1_5'UTR|RPS3A_ENST00000512690.1_Missense_Mutation_p.V22A|RPS3A_ENST00000322686.6_Missense_Mutation_p.V9A|RPS3A_ENST00000506126.1_5'UTR	NM_001006.4	NP_000997.1			ribosomal protein S3A											endometrium(1)|lung(1)|ovary(1)|pancreas(1)	4	all_hematologic(180;0.093)					AAATCCAGGGTTGATCCATTT	0.348																																					p.V22A		Atlas-SNP	.											.	RPS3A	11	.	0			c.T65C						.						72	80	78					4																	152021639		2203	4300	6503	SO:0001583	missense	6189	exon2			CCAGGGTTGATCC	X87373	CCDS3775.1	4q31.2-q31.3	2011-04-05			ENSG00000145425	ENSG00000145425		"S ribosomal proteins"	10421	protein-coding gene	gene with protein product		180478		MFTL		8647443, 1398113	Standard	NM_001006		Approved	S3A	uc003ilz.4	P61247	OTTHUMG00000161445	ENST00000274065.4:c.65T>C	chr4.hg19:g.152021639T>C	ENSP00000346050:p.Val22Ala	41.0	0.0		43.0	7.0	NM_001006		Missense_Mutation	SNP	ENST00000274065.4	hg19	CCDS3775.1	.	.	.	.	.	.	.	.	.	.	T	18.14	3.557485	0.65425	.	.	ENSG00000145425	ENST00000274065;ENST00000322686;ENST00000515792;ENST00000510993	.	.	.	5.08	5.08	0.68730	.	.	.	.	.	T	0.75488	0.3856	M	0.79693	2.465	0.80722	D	1	P	0.43578	0.811	P	0.53649	0.731	T	0.78084	-0.2342	8	0.51188	T	0.08	.	14.8989	0.70664	0.0:0.0:0.0:1.0	.	22	P61247	RS3A_HUMAN	A	22;9;16;2	.	ENSP00000346050:V22A	V	+	2	0	RPS3A	152241089	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	7.860000	0.86993	1.914000	0.55421	0.374000	0.22700	GTT	.	.		0.348	RPS3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364957.1			C	152021639	T	C	152021639	3	2	354	1	0	0	0	0	1	0	0	0	13659	1725	60	2	71	2	RPS3A	4	152021639	Missense_Mutation	SNP	T	TCGA-WX-AA44-01A-11D-A38X-10	64329186	152021639	39132637	27	50005										
FGA	2243	hgsc.bcm.edu	37	chr4	155507395	155507395	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	gttcccagagcctgggctatCtggcctaaaacttccagatt	9	12	1	2			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr4:155507395C>T	ENST00000302053.3	-	5	1264	c.1186G>A	c.(1186-1188)Gat>Aat	p.D396N	FGA_ENST00000403106.3_Missense_Mutation_p.D396N	NM_000508.3	NP_000499.1	P02671	FIBA_HUMAN	fibrinogen alpha chain	396					blood coagulation (GO:0007596)|blood coagulation, common pathway (GO:0072377)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|extracellular matrix organization (GO:0030198)|negative regulation of blood coagulation, common pathway (GO:2000261)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	structural molecule activity (GO:0005198)			NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	73	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)	CCTGGGCTATCTGGCCTAAAA	0.537																																					p.D396N	NSCLC(143;340 1922 20892 22370 48145)	Atlas-SNP	.											.	FGA	179	.	0			c.G1186A						.						84	89	88					4																	155507395		2203	4300	6503	SO:0001583	missense	2243	exon5			GGCTATCTGGCCT		CCDS3787.1, CCDS47152.1	4q28	2014-09-17			ENSG00000171560	ENSG00000171560		"Fibrinogen C domain containing", "Endogenous ligands"	3661	protein-coding gene	gene with protein product		134820	"fibrinogen, A alpha polypeptide"				Standard	NM_000508		Approved		uc003iod.1	P02671	OTTHUMG00000150330	ENST00000302053.3:c.1186G>A	chr4.hg19:g.155507395C>T	ENSP00000306361:p.Asp396Asn	70.0	0.0		73.0	22.0	NM_000508	A8K3E4|D3DP14|D3DP15|Q4QQH7|Q9BX62|Q9UCH2	Missense_Mutation	SNP	ENST00000302053.3	hg19	CCDS3787.1	.	.	.	.	.	.	.	.	.	.	C	17.29	3.352952	0.61293	.	.	ENSG00000171560	ENST00000302053;ENST00000403106	T;T	0.58940	0.3;2.67	5.37	4.49	0.54785	.	20.628700	0.00166	N	0.000000	T	0.72890	0.3517	M	0.72479	2.2	0.27544	N	0.950705	D;P	0.53462	0.96;0.933	P;P	0.52856	0.711;0.518	T	0.60068	-0.7335	10	0.72032	D	0.01	.	13.2259	0.59914	0.1592:0.8408:0.0:0.0	.	396;396	P02671-2;P02671	.;FIBA_HUMAN	N	396	ENSP00000306361:D396N;ENSP00000385981:D396N	ENSP00000306361:D396N	D	-	1	0	FGA	155726845	0.969000	0.33509	0.759000	0.31340	0.952000	0.60782	1.655000	0.37345	2.511000	0.84671	0.650000	0.86243	GAT	.	.		0.537	FGA-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317593.1	NM_000508		T	155507395	C	T	155507395	3	4	354	1	0	0	0	0	1	0	0	0	5838	913	32	3	1466	3	FGA	4	155507395	Missense_Mutation	SNP	C	TCGA-WX-AA44-01A-11D-A38X-10	3485756	155507395	35646881	28	50006										
RAPGEF2	9693	hgsc.bcm.edu	37	chr4	160259466	160259467	+	Frame_Shift_Ins	INS	-	-	ATTG													0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	tttcctctttgttcagtgatINSattgggattggtcagtctca					rs574693523		TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr4:160259466_160259467insATTG	ENST00000264431.4	+	12	2075_2076	c.1656_1657insATTG	c.(1657-1659)attfs	p.-553fs		NM_014247.2	NP_055062.1	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor (GEF) 2						adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|blood vessel development (GO:0001568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|forebrain neuron development (GO:0021884)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of cell proliferation (GO:0008285)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of melanin biosynthetic process (GO:0048022)|nerve growth factor signaling pathway (GO:0038180)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of vasculogenesis (GO:2001214)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|regulation of synaptic plasticity (GO:0048167)|small GTPase mediated signal transduction (GO:0007264)|ventricular system development (GO:0021591)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	beta-1 adrenergic receptor binding (GO:0031697)|calcium ion binding (GO:0005509)|cAMP binding (GO:0030552)|diacylglycerol binding (GO:0019992)|PDZ domain binding (GO:0030165)|Rap GTPase activator activity (GO:0046582)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	70	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		TGTTCAGTGATATTGGGATTGG	0.351																																					p.D552fs		Atlas-INDEL	.											.	RAPGEF2	171	.	0			c.1656_1657insATTG						.																																			SO:0001589	frameshift_variant	9693	exon12			.	AB002311	CCDS43277.1	4q32.1	2004-03-01	2004-03-01	2004-03-01					16854	protein-coding gene	gene with protein product	"Rap GEP"	609530	"PDZ domain containing guanine nucleotide exchange factor (GEF) 1"	PDZGEF1		9205841, 10934204	Standard	NM_014247		Approved	PDZ-GEF1, RA-GEF, DKFZP586O1422, KIAA0313	uc003iqg.4	Q9Y4G8		ENST00000264431.4:c.1657_1660dupATTG	chr4.hg19:g.160259467_160259470dupATTG	ENSP00000264431:p.Ile553fs	107.0	0.0		137.0	31.0	NM_014247	D3DP27	Frame_Shift_Ins	INS	ENST00000264431.4	hg19	CCDS43277.1																																																																																			.	.		0.351	RAPGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364980.2	NM_014247		ATTG	160259467	-	ATTG	160259466	7	5	354	1	0	1	1	0	0	0	0	0	13059	1403	49	0	1702	0	RAPGEF2	4	160259466	Frame_Shift_Ins	INS	-	TCGA-WX-AA44-01A-11D-A38X-10	4752071	160259466	30894810	29	50007										
IRX4	50805	hgsc.bcm.edu	37	chr5	1878257	1878257	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	ggcccggggtccaggagggcGcccttggcggtggcccaggc	20	14	0	0			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr5:1878257G>A	ENST00000505790.1	-	6	1842	c.1386C>T	c.(1384-1386)ggC>ggT	p.G462G	IRX4_ENST00000231357.2_Silent_p.G462G|IRX4_ENST00000505938.1_5'Flank|IRX4_ENST00000513692.1_Silent_p.G462G	NM_001278634.1	NP_001265563.1	P78413	IRX4_HUMAN	iroquois homeobox 4	462					establishment of organ orientation (GO:0048561)|heart development (GO:0007507)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|lung(7)|ovary(1)|prostate(1)	10				GBM - Glioblastoma multiforme(108;0.242)		CCAGGAGGGCGCCCTTGGCGG	0.706																																					p.G462G		Atlas-SNP	.											.	IRX4	45	.	0			c.C1386T						.						4	5	5					5																	1878257		2047	4066	6113	SO:0001819	synonymous_variant	50805	exon5			GAGGGCGCCCTTG	AF124733	CCDS3867.1, CCDS75225.1	5p15.33	2011-06-20	2007-07-13		ENSG00000113430	ENSG00000113430		"Homeoboxes / TALE class"	6129	protein-coding gene	gene with protein product		606199	"iroquois homeobox protein 4"			10625552	Standard	NM_016358		Approved		uc003jcz.2	P78413	OTTHUMG00000090411	ENST00000505790.1:c.1386C>T	chr5.hg19:g.1878257G>A		73.0	0.0		57.0	16.0	NM_016358	B2RMW5|D3DTC5|H1AFL0|H1AFL1|Q2NL64|Q9UHR2	Silent	SNP	ENST00000505790.1	hg19	CCDS3867.1																																																																																			.	.		0.706	IRX4-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365500.1	NM_016358		A	1878257	G	A	1878257	2	1	354	1	0	0	0	0	0	0	0	1	7855	1074	38	1		1	IRX4	5	1878257	Silent	SNP	G	TCGA-WX-AA44-01A-11D-A38X-10		1878257	179037003	30	50008										
C5orf22	55322	hgsc.bcm.edu	37	chr5	31538643	31538643	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	gaccagacttgcctagaaccAtcatgttcatgttcttctga	7	11	4	3			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr5:31538643A>G	ENST00000325366.9	+	4	781	c.654A>G	c.(652-654)ccA>ccG	p.P218P	C5orf22_ENST00000355907.3_5'UTR	NM_018356.2	NP_060826.2	Q49AR2	CE022_HUMAN	chromosome 5 open reading frame 22	218										kidney(3)|large_intestine(2)|lung(10)|ovary(2)|skin(1)	18						GCCTAGAACCATCATGTTCAT	0.428																																					p.P218P		Atlas-SNP	.											.	C5orf22	48	.	0			c.A654G						.						64	61	62					5																	31538643		2203	4300	6503	SO:0001819	synonymous_variant	55322	exon4			AGAACCATCATGT	AK002055	CCDS3895.1	5p13.3	2012-02-22			ENSG00000082213	ENSG00000082213			25639	protein-coding gene	gene with protein product							Standard	NM_018356		Approved	FLJ11193	uc003jhj.4	Q49AR2	OTTHUMG00000131067	ENST00000325366.9:c.654A>G	chr5.hg19:g.31538643A>G		202.0	0.0		225.0	90.0	NM_018356	Q8ND28|Q8WU61|Q9NUR1	Silent	SNP	ENST00000325366.9	hg19	CCDS3895.1																																																																																			.	.		0.428	C5orf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253726.2	NM_018356		G	31538643	A	G	31538643	2	3	354	1	0	0	0	0	0	0	0	1	2287	204	8	2		2	C5orf22	5	31538643	Silent	SNP	A	TCGA-WX-AA44-01A-11D-A38X-10	29660386	31538643	149376617	31	50009										
NNT	23530	hgsc.bcm.edu	37	chr5	43644303	43644303	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	gattttattaggtaaaaaagCtccagttttatttaataaag	6	3	0	0			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr5:43644303C>T	ENST00000264663.5	+	8	1195	c.974C>T	c.(973-975)gCt>gTt	p.A325V	NNT_ENST00000512996.2_Missense_Mutation_p.A194V|NNT_ENST00000344920.4_Missense_Mutation_p.A325V	NM_012343.3	NP_036475.3	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	325					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)|proton transport (GO:0015992)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	NAD binding (GO:0051287)|NAD(P)+ transhydrogenase (AB-specific) activity (GO:0008750)|NAD(P)+ transhydrogenase (B-specific) activity (GO:0003957)|NAD(P)+ transhydrogenase activity (GO:0008746)|NADP binding (GO:0050661)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(7)|large_intestine(6)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(6;2.58e-06)					GGTAAAAAAGCTCCAGTTTTA	0.338																																					p.A325V		Atlas-SNP	.											.	NNT	92	.	0			c.C974T						.						59	65	63					5																	43644303		2203	4300	6503	SO:0001583	missense	23530	exon8			AAAAAGCTCCAGT	U40490	CCDS3949.1	5p12	2008-02-05			ENSG00000112992	ENSG00000112992	1.6.1.1		7863	protein-coding gene	gene with protein product		607878				9271681, 9524818	Standard	NM_182977		Approved		uc003jof.3	Q13423	OTTHUMG00000096961	ENST00000264663.5:c.974C>T	chr5.hg19:g.43644303C>T	ENSP00000264663:p.Ala325Val	183.0	0.0		211.0	69.0	NM_182977	Q16796|Q2TB60|Q8N3V4	Missense_Mutation	SNP	ENST00000264663.5	hg19	CCDS3949.1	.	.	.	.	.	.	.	.	.	.	C	33	5.261755	0.95368	.	.	ENSG00000112992	ENST00000264663;ENST00000344920;ENST00000512996	D;D;D	0.83837	-1.77;-1.77;-1.77	5.62	5.62	0.85841	Alanine dehydrogenase/PNT, C-terminal (1);	0.150606	0.64402	D	0.000012	D	0.95714	0.8606	H	0.99820	4.81	0.80722	D	1	D	0.71674	0.998	D	0.64410	0.925	D	0.97817	1.0254	10	0.87932	D	0	-6.5698	19.6476	0.95789	0.0:1.0:0.0:0.0	.	325	Q13423	NNTM_HUMAN	V	325;325;194	ENSP00000264663:A325V;ENSP00000343873:A325V;ENSP00000426343:A194V	ENSP00000264663:A325V	A	+	2	0	NNT	43680060	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.210000	0.77924	2.655000	0.90218	0.650000	0.86243	GCT	.	.		0.338	NNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214026.1	NM_182977		T	43644303	C	T	43644303	3	4	354	1	0	0	0	0	1	0	0	0	10519	797	28	3	1000	3	NNT	5	43644303	Missense_Mutation	SNP	C	TCGA-WX-AA44-01A-11D-A38X-10	12105660	43644303	137270957	32	50010										
ANKRD43	134548	hgsc.bcm.edu	37	chr5	132149934	132149934	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	gcggagcccgggcccggggcAgcgaaagggccgccgcagca	19	15	0	0			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr5:132149934A>T	ENST00000378693.2	+	1	902	c.621A>T	c.(619-621)gcA>gcT	p.A207A		NM_175873.4	NP_787069.3	Q2M3V2	SWAHA_HUMAN	sosondowah ankyrin repeat domain family member A	207	Pro-rich.																GGCCCGGGGCAGCGAAAGGGC	0.776																																					p.A207A		Atlas-SNP	.											.	.	.	.	0			c.A621T						.						2	3	3					5																	132149934		977	2531	3508	SO:0001819	synonymous_variant	134548	exon1			CGGGGCAGCGAAA	AK090823	CCDS43361.1	5q23.3	2013-01-10	2012-01-12	2012-01-12	ENSG00000198944	ENSG00000198944		"Ankyrin repeat domain containing"	27033	protein-coding gene	gene with protein product			"ankyrin repeat domain 43"	ANKRD43		22234889	Standard	NM_175873		Approved		uc003kxw.3	Q2M3V2	OTTHUMG00000059844	ENST00000378693.2:c.621A>T	chr5.hg19:g.132149934A>T		47.0	0.0		35.0	14.0	NM_175873	Q8NAE7	Silent	SNP	ENST00000378693.2	hg19	CCDS43361.1																																																																																			.	.		0.776	SOWAHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133062.1	NM_175873		T	132149934	A	T	132149934	2	4	354	1	0	0	0	0	0	0	0	1	671	175	7	4		4	ANKRD43	5	132149934	Silent	SNP	A	TCGA-WX-AA44-01A-11D-A38X-10	88505631	132149934	48765326	33	50011										
DIAPH1	1729	hgsc.bcm.edu	37	chr5	140915624	140915624	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	cacctgtaatcccagcacttTggaaggctgaggtgggcaga	13	10	0	2			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr5:140915624T>C	ENST00000398557.4	-	19	2623				DIAPH1_ENST00000253811.6_Intron|DIAPH1_ENST00000518047.1_Intron|DIAPH1_ENST00000494967.1_5'Flank|DIAPH1_ENST00000398566.3_Intron|DIAPH1_ENST00000389054.3_Intron|DIAPH1_ENST00000398562.2_Intron|DIAPH1_ENST00000389057.5_Intron|DIAPH1_ENST00000520569.1_Intron	NM_005219.4	NP_005210.3	O60610	DIAP1_HUMAN	diaphanous-related formin 1						actin filament polymerization (GO:0030041)|cellular response to histamine (GO:0071420)|cytoskeleton organization (GO:0007010)|positive regulation of cell migration (GO:0030335)|protein localization to microtubule (GO:0035372)|regulation of cell shape (GO:0008360)|regulation of microtubule-based process (GO:0032886)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|mitotic spindle (GO:0072686)|ruffle membrane (GO:0032587)	ion channel binding (GO:0044325)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(12)|pancreas(1)|skin(2)|stomach(2)	23			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			cccagcactttggaaggctga	0.413																																					p.K827E		Atlas-SNP	.											.	DIAPH1	64	.	0			c.A2479G						.						87	72	77					5																	140915624		692	1591	2283	SO:0001627	intron_variant	1729	exon18			GCACTTTGGAAGG	BC007411		5q31	2013-05-24	2013-05-24		ENSG00000131504	ENSG00000131504			2876	protein-coding gene	gene with protein product		602121	"diaphanous (Drosophila, homolog) 1", "diaphanous homolog 1 (Drosophila)"	DFNA1		9360932, 1350680	Standard	NM_005219		Approved	hDIA1, LFHL1	uc003llb.4	O60610	OTTHUMG00000149893	ENST00000398557.4:c.2483-1624A>G	chr5.hg19:g.140915624T>C		506.0	1.0		376.0	131.0	NM_005219	A6NF18|B7ZKW2|E9PEZ2|Q17RN4|Q59FH8|Q9UC76	Missense_Mutation	SNP	ENST00000398557.4	hg19	CCDS43374.1																																																																																			.	.		0.413	DIAPH1-203	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_005219		C	140915624	T	C	140915624	1	2	354	0	1	0	0	0	0	0	0	0	4520	1821	63	2		2	DIAPH1	5	140915624	Intron	SNP	T	TCGA-WX-AA44-01A-11D-A38X-10	8765690	140915624	39999636	34	50012										
UBLCP1	134510	hgsc.bcm.edu	37	chr5	158697408	158697408	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	ccctgacaatgatgatgttgTtaatgactttgatattgaag	9	5	0	6			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr5:158697408T>G	ENST00000296786.6	+	4	613	c.287T>G	c.(286-288)gTt>gGt	p.V96G		NM_145049.3	NP_659486.2	Q8WVY7	UBCP1_HUMAN	ubiquitin-like domain containing CTD phosphatase 1	96						nucleolus (GO:0005730)|nucleus (GO:0005634)	phosphoprotein phosphatase activity (GO:0004721)			endometrium(1)|kidney(3)|large_intestine(4)|ovary(1)	9	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GATGATGTTGTTAATGACTTT	0.323																																					p.V96G		Atlas-SNP	.											.	UBLCP1	27	.	0			c.T287G						.						154	157	156					5																	158697408		2203	4300	6503	SO:0001583	missense	134510	exon4			ATGTTGTTAATGA	AK057996	CCDS4345.1	5q33.3	2010-06-21			ENSG00000164332	ENSG00000164332	3.1.3.16	"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	28110	protein-coding gene	gene with protein product	"CTD phosphatase-like with ubiquitin domain 1"	609867				15883030	Standard	NM_145049		Approved	MGC10067, CPUB1	uc003lxq.2	Q8WVY7	OTTHUMG00000130305	ENST00000296786.6:c.287T>G	chr5.hg19:g.158697408T>G	ENSP00000296786:p.Val96Gly	82.0	0.0		93.0	43.0	NM_145049	D3DQJ7|Q96DK5	Missense_Mutation	SNP	ENST00000296786.6	hg19	CCDS4345.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.142989	0.77888	.	.	ENSG00000164332	ENST00000296786	.	.	.	5.92	5.92	0.95590	.	0.212531	0.48767	D	0.000179	T	0.61438	0.2347	M	0.70595	2.14	0.80722	D	1	D	0.53312	0.959	B	0.43575	0.424	T	0.67337	-0.5696	9	0.56958	D	0.05	-1.2641	16.3631	0.83280	0.0:0.0:0.0:1.0	.	96	Q8WVY7	UBCP1_HUMAN	G	96	.	ENSP00000296786:V96G	V	+	2	0	UBLCP1	158629986	1.000000	0.71417	0.986000	0.45419	0.915000	0.54546	7.698000	0.84413	2.266000	0.75297	0.533000	0.62120	GTT	.	.		0.323	UBLCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252650.2	NM_145049		G	158697408	T	G	158697408	3	3	354	1	0	0	0	0	1	0	0	0	16906	1725	60	5	297	5	UBLCP1	5	158697408	Missense_Mutation	SNP	T	TCGA-WX-AA44-01A-11D-A38X-10	17781784	158697408	22217852	35	50013										
HLA-DMA	3108	hgsc.bcm.edu	37	chr6	32917403	32917403	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	ctcaccccaataggcaattgCtgtgtagcggtcaatttcgt	9	11	2	0			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr6:32917403C>T	ENST00000374843.4	-	3	722	c.637G>A	c.(637-639)Gca>Aca	p.A213T	HLA-DMA_ENST00000395305.3_Missense_Mutation_p.A118T|XXbac-BPG181M17.5_ENST00000429234.1_Intron|HLA-DMA_ENST00000395303.3_Missense_Mutation_p.A179T|HLA-DMA_ENST00000464392.1_5'UTR	NM_006120.3	NP_006111.2	P28067	DMA_HUMAN	major histocompatibility complex, class II, DM alpha	213	Alpha-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|chaperone mediated protein folding requiring cofactor (GO:0051085)|immunoglobulin mediated immune response (GO:0016064)|inner ear development (GO:0048839)|peptide antigen assembly with MHC class II protein complex (GO:0002503)|positive regulation of immune response (GO:0050778)|positive regulation of T cell differentiation (GO:0045582)|positive thymic T cell selection (GO:0045059)|protein transport (GO:0015031)	cell surface (GO:0009986)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|multivesicular body (GO:0005771)	MHC class II protein complex binding (GO:0023026)			kidney(1)|large_intestine(2)|lung(8)	11						TAGGCAATTGCTGTGTAGCGG	0.483																																					p.A213T		Atlas-SNP	.											.	HLA-DMA	20	.	0			c.G637A						.						101	99	99					6																	32917403		1511	2709	4220	SO:0001583	missense	3108	exon3			CAATTGCTGTGTA		CCDS4761.1	6p21.3	2013-01-11			ENSG00000204257	ENSG00000204257		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4934	protein-coding gene	gene with protein product		142855				1922385	Standard	NM_006120		Approved	D6S222E, RING6	uc003ocm.2	P28067	OTTHUMG00000031173	ENST00000374843.4:c.637G>A	chr6.hg19:g.32917403C>T	ENSP00000363976:p.Ala213Thr	138.0	0.0		218.0	43.0	NM_006120	Q29639|Q29640	Missense_Mutation	SNP	ENST00000374843.4	hg19	CCDS4761.1	.	.	.	.	.	.	.	.	.	.	C	12.43	1.934760	0.34189	.	.	ENSG00000204257	ENST00000395305;ENST00000395303;ENST00000374843;ENST00000456800	T;T;T;T	0.08193	3.12;4.92;3.12;3.12	5.13	3.35	0.38373	.	0.543879	0.21095	N	0.080254	T	0.02012	0.0063	L	0.29908	0.895	0.09310	N	0.999999	B	0.32245	0.361	B	0.26969	0.075	T	0.38757	-0.9646	10	0.66056	D	0.02	.	7.1458	0.25583	0.0:0.8052:0.0:0.1948	.	213	Q31604	.	T	118;179;213;243	ENSP00000378716:A118T;ENSP00000378714:A179T;ENSP00000363976:A213T;ENSP00000409668:A243T	ENSP00000363976:A213T	A	-	1	0	HLA-DMA	33025381	0.082000	0.21442	0.239000	0.24122	0.936000	0.57629	0.552000	0.23376	1.537000	0.49254	0.643000	0.83706	GCA	.	.		0.483	HLA-DMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076325.2	NM_006120		T	32917403	C	T	32917403	3	4	354	1	0	0	0	0	1	0	0	0	7207	797	28	3	160	3	HLA-DMA	6	32917403	Missense_Mutation	SNP	C	TCGA-WX-AA44-01A-11D-A38X-10		32917403	138197664	36	50014										
COL11A2	1302	hgsc.bcm.edu	37	chr6	33136316	33136316	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	tcgctttccaagtggccctgGgggtccattctccccggtgg	13	14	1	0			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr6:33136316G>T	ENST00000374708.4	-	52	3940	c.3682C>A	c.(3682-3684)Cca>Aca	p.P1228T	COL11A2_ENST00000361917.1_Missense_Mutation_p.P1207T|COL11A2_ENST00000374714.1_Missense_Mutation_p.P1288T|COL11A2_ENST00000341947.2_Missense_Mutation_p.P1314T|COL11A2_ENST00000395197.1_Missense_Mutation_p.P1254T|COL11A2_ENST00000357486.1_Missense_Mutation_p.P1293T|COL11A2_ENST00000374712.1_Missense_Mutation_p.P1233T|COL11A2_ENST00000477772.1_Intron|COL11A2_ENST00000374713.1_Missense_Mutation_p.P1267T	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	1314	Triple-helical region.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						AGTGGCCCTGGGGGTCCATTC	0.632																																					p.P1314T	Melanoma(1;90 116 3946 5341 17093)	Atlas-SNP	.											.	COL11A2	124	.	0			c.C3940A						.						52	47	49					6																	33136316		1511	2709	4220	SO:0001583	missense	1302	exon54			GCCCTGGGGGTCC	U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"Collagens"	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000374708.4:c.3682C>A	chr6.hg19:g.33136316G>T	ENSP00000363840:p.Pro1228Thr	103.0	0.0		128.0	22.0	NM_080680	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Missense_Mutation	SNP	ENST00000374708.4	hg19	CCDS43452.1	.	.	.	.	.	.	.	.	.	.	G	15.63	2.891734	0.52014	.	.	ENSG00000204248	ENST00000374708;ENST00000341947;ENST00000357486;ENST00000374714;ENST00000374713;ENST00000395197;ENST00000374712;ENST00000361917	D;D;D;D;D;D;D;D	0.98666	-2.87;-5.06;-5.06;-5.06;-3.33;-2.84;-3.33;-3.33	4.25	4.25	0.50352	.	0.000000	0.85682	D	0.000000	D	0.96012	0.8701	L	0.41961	1.31	0.58432	D	0.999998	P;P;P	0.40180	0.705;0.705;0.58	B;B;B	0.40864	0.342;0.342;0.185	D	0.96418	0.9309	10	0.45353	T	0.12	.	14.2085	0.65750	0.0:0.0:1.0:0.0	.	1207;1228;1314	P13942-8;P13942-6;P13942	.;.;COBA2_HUMAN	T	1228;1314;1293;1288;1267;1254;1233;1207	ENSP00000363840:P1228T;ENSP00000339915:P1314T;ENSP00000350079:P1293T;ENSP00000363846:P1288T;ENSP00000363845:P1267T;ENSP00000378623:P1254T;ENSP00000363844:P1233T;ENSP00000355123:P1207T	ENSP00000339915:P1314T	P	-	1	0	COL11A2	33244294	0.907000	0.30839	0.999000	0.59377	0.994000	0.84299	1.847000	0.39299	2.205000	0.71048	0.551000	0.68910	CCA	.	.		0.632	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2			T	33136316	G	T	33136316	3	4	354	1	0	0	0	0	1	0	0	0	3670	1232	43	3	1322	3	COL11A2	6	33136316	Missense_Mutation	SNP	G	TCGA-WX-AA44-01A-11D-A38X-10	218913	33136316	137978751	37	50015										
RUNX2	860	hgsc.bcm.edu	37	chr6	45390520	45390520	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	gctgcggcggcggcggcggcTgcggcggcggcagctgcagt	22	13	0	0			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr6:45390520T>G	ENST00000371438.1	+	2	607	c.249T>G	c.(247-249)gcT>gcG	p.A83A	RUNX2_ENST00000541979.1_Silent_p.A151A|RUNX2_ENST00000352853.5_Silent_p.A151A|RP1-244F24.1_ENST00000606796.1_RNA|RUNX2_ENST00000576263.1_Silent_p.A83A|RUNX2_ENST00000465038.2_Silent_p.A83A|RUNX2_ENST00000371436.6_Silent_p.A83A|RUNX2_ENST00000371432.3_Silent_p.A69A|RUNX2_ENST00000359524.5_Silent_p.A69A	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN	runt-related transcription factor 2	83	Poly-Ala.		Missing. {ECO:0000269|PubMed:9182765}.		BMP signaling pathway (GO:0030509)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|chondrocyte development (GO:0002063)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|endochondral ossification (GO:0001958)|gene expression (GO:0010467)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|osteoblast fate commitment (GO:0002051)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|stem cell differentiation (GO:0048863)|T cell differentiation (GO:0030217)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(18)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						cggcggcggctgcggcggcgg	0.731																																					p.A83A		Atlas-SNP	.											.	RUNX2	128	.	0			c.T249G						.						3	5	5					6																	45390520		1080	2501	3581	SO:0001819	synonymous_variant	860	exon3			GGCGGCTGCGGCG	AF001450	CCDS43467.1, CCDS43468.1, CCDS43467.2, CCDS43468.2	6p21	2010-08-20			ENSG00000124813	ENSG00000124813			10472	protein-coding gene	gene with protein product		600211		CCD, CBFA1, CCD1		7835892	Standard	NM_001024630		Approved	AML3, PEBP2A1, PEBP2aA1	uc011dvx.2	Q13950	OTTHUMG00000014774	ENST00000371438.1:c.249T>G	chr6.hg19:g.45390520T>G		35.0	0.0		125.0	5.0	NM_001024630	O14614|O14615|O95181	Silent	SNP	ENST00000371438.1	hg19	CCDS43467.2																																																																																			.	.		0.731	RUNX2-003	KNOWN	not_organism_supported|upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040755.2	NM_004348		G	45390520	T	G	45390520	2	3	354	1	0	0	0	0	0	0	0	1	13763	1567	55	5		5	RUNX2	6	45390520	Silent	SNP	T	TCGA-WX-AA44-01A-11D-A38X-10	12254204	45390520	125724547	38	50016										
KIAA1586	57691	hgsc.bcm.edu	37	chr6	56917588	56917588	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	aatgaagtgagcaaaaatcaCtgcagattgtctaaggcaaa	9	6	2	3			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr6:56917588C>A	ENST00000370733.4	+	4	498	c.291C>A	c.(289-291)caC>caA	p.H97Q	KIAA1586_ENST00000488682.1_3'UTR|KIAA1586_ENST00000545356.1_Missense_Mutation_p.H70Q	NM_020931.2	NP_065982.1	Q9HCI6	K1586_HUMAN	KIAA1586	97							nucleic acid binding (GO:0003676)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|skin(1)	18	Lung NSC(77;0.0969)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			GCAAAAATCACTGCAGATTGT	0.333																																					p.H97Q		Atlas-SNP	.											.	KIAA1586	59	.	0			c.C291A						.						74	73	73					6																	56917588		2203	4300	6503	SO:0001583	missense	57691	exon4			AAATCACTGCAGA	AB046806	CCDS34480.1, CCDS69138.1	6p12.1	2014-03-27			ENSG00000168116	ENSG00000168116			21360	protein-coding gene	gene with protein product						10997877	Standard	NM_001286274		Approved		uc003pdj.3	Q9HCI6	OTTHUMG00000014915	ENST00000370733.4:c.291C>A	chr6.hg19:g.56917588C>A	ENSP00000359768:p.His97Gln	164.0	0.0		264.0	53.0	NM_020931	A8K4M3|Q8IW25	Missense_Mutation	SNP	ENST00000370733.4	hg19	CCDS34480.1	.	.	.	.	.	.	.	.	.	.	c	15.04	2.714653	0.48622	.	.	ENSG00000168116	ENST00000370733;ENST00000545356	T;T	0.35605	1.31;1.3	3.87	-7.23	0.01480	.	.	.	.	.	T	0.08714	0.0216	N	0.08118	0	0.09310	N	1	D;D	0.58620	0.983;0.983	P;P	0.49276	0.605;0.605	T	0.18967	-1.0320	9	0.72032	D	0.01	.	7.7501	0.28892	0.1469:0.5755:0.0:0.2776	.	70;97	F5H2N6;Q9HCI6	.;K1586_HUMAN	Q	97;70	ENSP00000359768:H97Q;ENSP00000445507:H70Q	ENSP00000359768:H97Q	H	+	3	2	KIAA1586	57025547	0.000000	0.05858	0.005000	0.12908	0.012000	0.07955	-1.280000	0.02804	-1.715000	0.01389	-0.600000	0.04104	CAC	.	.		0.333	KIAA1586-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041033.1	NM_020931		A	56917588	C	A	56917588	3	1	354	1	0	0	0	0	1	0	0	0	8254	564	20	3	305	3	KIAA1586	6	56917588	Missense_Mutation	SNP	C	TCGA-WX-AA44-01A-11D-A38X-10	11527068	56917588	114197479	39	50017										
SDK1	221935	hgsc.bcm.edu	37	chr7	3998631	3998631	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	tagaagaaactgtggacatcGgatgtcaagccatgggtgag	14	6	1	3			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr7:3998631G>A	ENST00000404826.2	+	8	1358	c.1219G>A	c.(1219-1221)Gga>Aga	p.G407R	SDK1_ENST00000389531.3_Missense_Mutation_p.G407R	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	407	Ig-like C2-type 4.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.G407R(1)		NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		TGTGGACATCGGATGTCAAGC	0.463																																					p.G407R		Atlas-SNP	.											SDK1,NS,carcinoma,0,1	SDK1	361	.	1	Substitution - Missense(1)	endometrium(1)	c.G1219A						.						109	106	107					7																	3998631		2203	4300	6503	SO:0001583	missense	221935	exon8			GACATCGGATGTC	AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19307	protein-coding gene	gene with protein product		607216	"sidekick homolog 1 (chicken)", "sidekick homolog 1, cell adhesion molecule (chicken)"			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.1219G>A	chr7.hg19:g.3998631G>A	ENSP00000385899:p.Gly407Arg	88.0	0.0		81.0	30.0	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	hg19	CCDS34590.1	.	.	.	.	.	.	.	.	.	.	G	2.682	-0.275082	0.05679	.	.	ENSG00000146555	ENST00000404826;ENST00000389531	T;T	0.65916	-0.18;-0.18	5.35	-2.58	0.06228	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.646500	0.03537	N	0.223269	T	0.23688	0.0573	N	0.00661	-1.28	0.09310	N	1	P	0.35507	0.506	B	0.27887	0.084	T	0.08534	-1.0717	10	0.38643	T	0.18	.	3.2049	0.06662	0.3475:0.2714:0.299:0.0821	.	407	Q7Z5N4	SDK1_HUMAN	R	407	ENSP00000385899:G407R;ENSP00000374182:G407R	ENSP00000374182:G407R	G	+	1	0	SDK1	3965157	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	0.278000	0.18753	-0.401000	0.07644	-1.814000	0.00607	GGA	.	.		0.463	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744		A	3998631	G	A	3998631	3	1	354	1	0	0	0	0	1	0	0	0	13983	1117	39	1	1249	1	SDK1	7	3998631	Missense_Mutation	SNP	G	TCGA-WX-AA44-01A-11D-A38X-10		3998631	155140032	40	50018										
TNS3	64759	hgsc.bcm.edu	37	chr7	47343131	47343131	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	cggccgctccccagcagggaAaccatgggcttggggctgct	15	14	0	0			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr7:47343131A>T	ENST00000398879.1	-	22	3240	c.2874T>A	c.(2872-2874)gtT>gtA	p.V958V	TNS3_ENST00000311160.9_Silent_p.V958V|TNS3_ENST00000355730.3_Silent_p.V718V			Q68CZ2	TENS3_HUMAN	tensin 3	958					cell migration (GO:0016477)|lung alveolus development (GO:0048286)|positive regulation of cell proliferation (GO:0008284)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(17)|endometrium(5)|kidney(4)|large_intestine(7)|liver(1)|lung(16)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	64						CCAGCAGGGAAACCATGGGCT	0.612																																					p.V958V		Atlas-SNP	.											.	TNS3	140	.	0			c.T2874A						.						14	17	16					7																	47343131		2012	4183	6195	SO:0001819	synonymous_variant	64759	exon22			CAGGGAAACCATG	AF378756	CCDS5506.2	7p12.3	2013-02-14	2005-05-13	2005-05-13	ENSG00000136205	ENSG00000136205		"SH2 domain containing"	21616	protein-coding gene	gene with protein product	"tumor endothelial marker 6"	606825	"tensin-like SH2 domain-containing 1"	TENS1		11559528	Standard	NM_022748		Approved	TEM6, H_NH0549I23.2, FLJ13732	uc003tnw.3	Q68CZ2	OTTHUMG00000074075	ENST00000398879.1:c.2874T>A	chr7.hg19:g.47343131A>T		60.0	0.0		56.0	7.0	NM_022748	B2RNV1|Q6IPQ2|Q8IZW7|Q8NAD0|Q96PE0|Q96S48	Silent	SNP	ENST00000398879.1	hg19	CCDS5506.2																																																																																			.	.		0.612	TNS3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157253.1	NM_022748		T	47343131	A	T	47343131	2	4	354	1	0	0	0	0	0	0	0	1	16359	1	1	4		4	TNS3	7	47343131	Silent	SNP	A	TCGA-WX-AA44-01A-11D-A38X-10	43344500	47343131	111795532	41	50019										
ABCA13	154664	hgsc.bcm.edu	37	chr7	48412063	48412063	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	agttctattggttctacataAccaattaagttttgttaatc	5	6	2	0			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr7:48412063A>G	ENST00000435803.1	+	33	11126	c.11102A>G	c.(11101-11103)aAc>aGc	p.N3701S		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	3701					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						GTTCTACATAACCAATTAAGT	0.333																																					p.N3701S		Atlas-SNP	.											.	ABCA13	1192	.	0			c.A11102G						.						100	93	95					7																	48412063		1860	4093	5953	SO:0001583	missense	154664	exon33			TACATAACCAATT	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.11102A>G	chr7.hg19:g.48412063A>G	ENSP00000411096:p.Asn3701Ser	68.0	0.0		58.0	12.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	A	12.70	2.017932	0.35606	.	.	ENSG00000179869	ENST00000435803	D	0.86865	-2.18	5.61	4.45	0.53987	.	0.222991	0.31102	N	0.008243	D	0.86826	0.6026	L	0.46741	1.465	0.44175	D	0.996981	B;P	0.50819	0.138;0.939	B;P	0.51453	0.027;0.67	D	0.86162	0.1594	10	0.54805	T	0.06	.	10.9893	0.47541	0.9266:0.0:0.0734:0.0	.	1403;3701	Q86UQ4-3;Q86UQ4	.;ABCAD_HUMAN	S	3701	ENSP00000411096:N3701S	ENSP00000411096:N3701S	N	+	2	0	ABCA13	48382609	0.977000	0.34250	0.277000	0.24703	0.050000	0.14768	1.899000	0.39818	1.062000	0.40625	0.533000	0.62120	AAC	.	.		0.333	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		G	48412063	A	G	48412063	3	3	354	1	0	0	0	0	1	0	0	0	31	43	2	2	11061	2	ABCA13	7	48412063	Missense_Mutation	SNP	A	TCGA-WX-AA44-01A-11D-A38X-10	1068932	48412063	110726600	42	50020										
MAGI2	9863	hgsc.bcm.edu	37	chr7	77807384	77807384	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	gccaaatccagactccatccTccgaagatgaacatccaatt	5	14	0	3			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr7:77807384T>G	ENST00000354212.4	-	14	2600	c.2347A>C	c.(2347-2349)Agg>Cgg	p.R783R	MAGI2_ENST00000522391.1_Silent_p.R783R|MAGI2_ENST00000419488.1_Silent_p.R769R	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	783	PDZ 4. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|glomerular visceral epithelial cell development (GO:0072015)|mitotic cell cycle arrest (GO:0071850)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase B signaling (GO:0051898)|nerve growth factor signaling pathway (GO:0038180)|planar cell polarity pathway involved in axis elongation (GO:0003402)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of receptor internalization (GO:0002092)|protein heterooligomerization (GO:0051291)|receptor clustering (GO:0043113)|SMAD protein signal transduction (GO:0060395)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|late endosome (GO:0005770)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)|synapse (GO:0045202)|tight junction (GO:0005923)	beta-1 adrenergic receptor binding (GO:0031697)|phosphatase binding (GO:0019902)|receptor signaling complex scaffold activity (GO:0030159)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|type II activin receptor binding (GO:0070699)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(37)|ovary(5)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(3)	84		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				GACTCCATCCTCCGAAGATGA	0.468																																					p.R783R		Atlas-SNP	.											.	MAGI2	246	.	0			c.A2347C						.						95	90	92					7																	77807384		2203	4300	6503	SO:0001819	synonymous_variant	9863	exon14			CCATCCTCCGAAG	AB014605	CCDS5594.1, CCDS75623.1	7q21	2005-08-09			ENSG00000187391	ENSG00000187391			18957	protein-coding gene	gene with protein product		606382				10681527, 9734811	Standard	XM_005250725		Approved	AIP1, ARIP1, KIAA0705, ACVRIP1, MAGI-2	uc003ugx.3	Q86UL8	OTTHUMG00000130697	ENST00000354212.4:c.2347A>C	chr7.hg19:g.77807384T>G		65.0	0.0		95.0	22.0	NM_012301	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Silent	SNP	ENST00000354212.4	hg19	CCDS5594.1																																																																																			.	.		0.468	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301		G	77807384	T	G	77807384	2	3	354	1	0	0	0	0	0	0	0	1	9200	1550	54	5		5	MAGI2	7	77807384	Silent	SNP	T	TCGA-WX-AA44-01A-11D-A38X-10	29395321	77807384	81331279	43	50021										
ACHE	43	hgsc.bcm.edu	37	chr7	100488791	100488791	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	cccgctggcccctgcataccGgtggcgctgagcaatttggg	14	14	0	1			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr7:100488791G>A	ENST00000412389.1	-	3	1877	c.1722C>T	c.(1720-1722)acC>acT	p.T574T	ACHE_ENST00000419336.2_Splice_Site_p.T486T|ACHE_ENST00000302913.4_Splice_Site_p.T574T|ACHE_ENST00000411582.1_Splice_Site_p.T574T|UFSP1_ENST00000388761.2_5'Flank|ACHE_ENST00000241069.5_Splice_Site_p.T574T|ACHE_ENST00000428317.1_Splice_Site_p.T574T			P22303	ACES_HUMAN	acetylcholinesterase (Yt blood group)	574					acetylcholine catabolic process (GO:0006581)|acetylcholine catabolic process in synaptic cleft (GO:0001507)|amyloid precursor protein metabolic process (GO:0042982)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|choline metabolic process (GO:0019695)|DNA replication (GO:0006260)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|negative regulation of synaptic transmission, cholinergic (GO:0032223)|nervous system development (GO:0007399)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter receptor biosynthetic process (GO:0045212)|osteoblast development (GO:0002076)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of protein secretion (GO:0050714)|protein tetramerization (GO:0051262)|receptor internalization (GO:0031623)|regulation of axonogenesis (GO:0050770)|regulation of dendrite morphogenesis (GO:0048814)|regulation of receptor recycling (GO:0001919)|response to wounding (GO:0009611)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	acetylcholine binding (GO:0042166)|acetylcholinesterase activity (GO:0003990)|beta-amyloid binding (GO:0001540)|cholinesterase activity (GO:0004104)|collagen binding (GO:0005518)|hydrolase activity (GO:0016787)|laminin binding (GO:0043236)|protein homodimerization activity (GO:0042803)|serine hydrolase activity (GO:0017171)			large_intestine(3)|lung(7)|skin(3)|urinary_tract(3)	16	Lung NSC(181;0.041)|all_lung(186;0.0581)				Ambenonium(DB01122)|Choline(DB00122)|Decamethonium(DB01245)|Demecarium(DB00944)|Dipivefrin(DB00449)|Donepezil(DB00843)|Edrophonium(DB01010)|Ephedrine(DB01364)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Isoflurophate(DB00677)|Mefloquine(DB00358)|Minaprine(DB00805)|Neostigmine(DB01400)|Physostigmine(DB00981)|Pralidoxime(DB00733)|Pyridostigmine(DB00545)|Rivastigmine(DB00989)|Tubocurarine(DB01199)	CCTGCATACCGGTGGCGCTGA	0.706																																					p.T574T		Atlas-SNP	.											.	ACHE	80	.	0			c.C1722T						.						6	7	6					7																	100488791		2056	4095	6151	SO:0001630	splice_region_variant	43	exon4			CATACCGGTGGCG		CCDS5709.1, CCDS5710.1, CCDS64736.1	7q22	2014-07-19	2014-01-02		ENSG00000087085	ENSG00000087085	3.1.1.7	"Blood group antigens"	108	protein-coding gene	gene with protein product	"Yt blood group"	100740	"acetylcholinesterase (YT blood group)", "acetylcholinesterase (Yt blood group)", "acetylcholinesterase"	YT		1380483	Standard	XM_005250357		Approved		uc003uxe.3	P22303	OTTHUMG00000157033	ENST00000412389.1:c.1723+1C>T	chr7.hg19:g.100488791G>A		184.0	0.0		146.0	6.0	NM_000665	A4D2E2|B7ZKZ0|D6W5X7|Q16169|Q29S23|Q2M324|Q504V3|Q53F46|Q86TM9|Q86YX9|Q9BXP7	Silent	SNP	ENST00000412389.1	hg19	CCDS5709.1																																																																																			.	.		0.706	ACHE-013	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347201.1	NM_015831	Silent	A	100488791	G	A	100488791	5	1	354	1	0	0	0	0	0	0	1	0	141	1130	39	1	265	1	ACHE	7	100488791	Splice_Site	SNP	G	TCGA-WX-AA44-01A-11D-A38X-10	22681407	100488791	58649872	44	50022										
CTTNBP2	83992	hgsc.bcm.edu	37	chr7	117364621	117364621	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	cttcagtgcttaggtctggcTtattccaggtgggtaaagag	13	7	2	1			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr7:117364621T>C	ENST00000160373.3	-	19	4518	c.4427A>G	c.(4426-4428)aAg>aGg	p.K1476R		NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	1476					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)				breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		TAGGTCTGGCTTATTCCAGGT	0.502																																					p.K1476R		Atlas-SNP	.											.	CTTNBP2	200	.	0			c.A4427G						.						89	74	79					7																	117364621		2203	4300	6503	SO:0001583	missense	83992	exon19			TCTGGCTTATTCC		CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"Ankyrin repeat domain containing"	15679	protein-coding gene	gene with protein product		609772	"cortactin binding protein 2"	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.4427A>G	chr7.hg19:g.117364621T>C	ENSP00000160373:p.Lys1476Arg	44.0	0.0		46.0	14.0	NM_033427	O43389|Q7LG11|Q9C0A5	Missense_Mutation	SNP	ENST00000160373.3	hg19	CCDS5774.1	.	.	.	.	.	.	.	.	.	.	T	14.21	2.467354	0.43839	.	.	ENSG00000077063	ENST00000160373	T	0.67698	-0.28	5.24	2.88	0.33553	.	0.561590	0.21322	N	0.076456	T	0.59918	0.2229	M	0.62723	1.935	0.27795	N	0.942677	B	0.20052	0.041	B	0.16722	0.016	T	0.51458	-0.8703	10	0.32370	T	0.25	-26.758	9.3473	0.38115	0.0:0.1479:0.0:0.8521	.	1476	Q8WZ74	CTTB2_HUMAN	R	1476	ENSP00000160373:K1476R	ENSP00000160373:K1476R	K	-	2	0	CTTNBP2	117151857	1.000000	0.71417	0.794000	0.32065	0.150000	0.21749	3.872000	0.56085	0.407000	0.25591	-0.250000	0.11733	AAG	.	.		0.502	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		C	117364621	T	C	117364621	3	2	354	1	0	0	0	0	1	0	0	0	4047	1609	56	2	584	2	CTTNBP2	7	117364621	Missense_Mutation	SNP	T	TCGA-WX-AA44-01A-11D-A38X-10	16875830	117364621	41774042	45	50023										
LMOD2	442721	hgsc.bcm.edu	37	chr7	123302963	123302963	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	tcccaaaggctgccaccaccTcctcctcctccccctcctcc	3	25	0	0			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr7:123302963T>A	ENST00000458573.2	+	2	1480	c.1323T>A	c.(1321-1323)ccT>ccA	p.P441P	LMOD2_ENST00000456238.2_Intron	NM_207163.1	NP_997046.1	Q6P5Q4	LMOD2_HUMAN	leiomodin 2 (cardiac)	441	Pro-rich.					cytoskeleton (GO:0005856)		p.P441P(1)									tgccaccacctcctcctcctc	0.572																																					p.P441P		Atlas-SNP	.											LMOD2_ENST00000458573,NS,carcinoma,0,1	LMOD2	62	.	1	Substitution - coding silent(1)	endometrium(1)	c.T1323A						.						19	18	19					7																	123302963		1881	4064	5945	SO:0001819	synonymous_variant	442721	exon2			ACCACCTCCTCCT	AC006333	CCDS47693.1	7q31.32	2008-08-08			ENSG00000170807	ENSG00000170807			6648	protein-coding gene	gene with protein product		608006					Standard	NM_207163		Approved		uc003vky.2	Q6P5Q4	OTTHUMG00000157149	ENST00000458573.2:c.1323T>A	chr7.hg19:g.123302963T>A		75.0	1.0		95.0	4.0	NM_207163	A4D0W9|A4D0Y2|Q8WVJ8	Silent	SNP	ENST00000458573.2	hg19	CCDS47693.1																																																																																			.	.		0.572	LMOD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348525.1			A	123302963	T	A	123302963	2	1	354	1	0	0	0	0	0	0	0	1	8866	1538	54	4		4	LMOD2	7	123302963	Silent	SNP	T	TCGA-WX-AA44-01A-11D-A38X-10	5938342	123302963	35835700	46	50024										
PODXL	5420	hgsc.bcm.edu	37	chr7	131241029	131241029	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	ggccactcaccattctgggaGggcgacggcgacggcgacgg	17	13	2	0	rs11277659|rs547816245|rs532078953|rs79759078|rs571821675	byFrequency	TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr7:131241029G>C	ENST00000378555.3	-	1	337	c.90C>G	c.(88-90)ccC>ccG	p.P30P	PODXL_ENST00000541194.1_Silent_p.P30P|PODXL_ENST00000322985.9_Silent_p.P30P|PODXL_ENST00000465001.1_Intron|PODXL_ENST00000537928.1_Silent_p.P30P			O00592	PODXL_HUMAN	podocalyxin-like	30					cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					CATTCTGGGAGggcgacggcg	0.751																																					p.P30P		Atlas-SNP	.											.	PODXL	53	.	0			c.C90G						.						5	7	6					7																	131241029		1981	3946	5927	SO:0001819	synonymous_variant	5420	exon1			CTGGGAGGGCGAC		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.90C>G	chr7.hg19:g.131241029G>C		102.0	0.0		84.0	5.0	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Silent	SNP	ENST00000378555.3	hg19	CCDS34755.1																																																																																			.	.		0.751	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111		C	131241029	G	C	131241029	2	2	354	1	0	0	0	0	0	0	0	1	12189	987	35	4		4	PODXL	7	131241029	Silent	SNP	G	TCGA-WX-AA44-01A-11D-A38X-10	7938066	131241029	27897634	47	50025										
TUSC3	7991	hgsc.bcm.edu	37	chr8	15601113	15601113	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	ttcgaaaggcgatgttggaaAaagacggagtaagtctctgt	13	5	1	1			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr8:15601113A>G	ENST00000503731.1	+	8	1077	c.929A>G	c.(928-930)aAa>aGa	p.K310R	TUSC3_ENST00000506802.1_Missense_Mutation_p.K310R|TUSC3_ENST00000382020.4_Missense_Mutation_p.K310R	NM_006765.3	NP_006756.2	Q13454	TUSC3_HUMAN	tumor suppressor candidate 3	310					cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cognition (GO:0050890)|magnesium ion transport (GO:0015693)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|oligosaccharyltransferase complex (GO:0008250)	magnesium ion transmembrane transporter activity (GO:0015095)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(10)|ovary(2)	28				Colorectal(111;0.113)		GATGTTGGAAAAAGACGGAGT	0.393																																					p.K310R		Atlas-SNP	.											.	TUSC3	98	.	0			c.A929G						.						193	212	206					8																	15601113		2203	4300	6503	SO:0001583	missense	7991	exon8			TTGGAAAAAGACG	AK026149	CCDS5993.1, CCDS5994.1	8p22	2010-10-22			ENSG00000104723	ENSG00000104723			30242	protein-coding gene	gene with protein product	"oligosaccharyltransferase 3 homolog A (S. cerevisiae)"	601385				8661104, 10097140	Standard	NM_178234		Approved	MGC13453, N33, OST3A, MRT7	uc003wwt.3	Q13454	OTTHUMG00000094803	ENST00000503731.1:c.929A>G	chr8.hg19:g.15601113A>G	ENSP00000424544:p.Lys310Arg	69.0	0.0		45.0	4.0	NM_178234	A8MSM0|D3DSP2|Q14911|Q14912|Q96FW0	Missense_Mutation	SNP	ENST00000503731.1	hg19	CCDS5994.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.607140	0.87157	.	.	ENSG00000104723	ENST00000382020;ENST00000506802;ENST00000503731	T;T;T	0.79554	-1.28;-1.28;-1.28	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.86719	0.6000	L	0.56769	1.78	0.80722	D	1	D;D;P	0.56035	0.967;0.974;0.815	D;D;P	0.70487	0.928;0.969;0.534	D	0.84431	0.0577	10	0.26408	T	0.33	-19.3015	15.1798	0.72947	1.0:0.0:0.0:0.0	.	310;310;310	D6RIY7;Q13454-2;Q13454	.;.;TUSC3_HUMAN	R	310	ENSP00000371450:K310R;ENSP00000425777:K310R;ENSP00000424544:K310R	ENSP00000221167:K310R	K	+	2	0	TUSC3	15645484	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	8.894000	0.92506	2.247000	0.74100	0.477000	0.44152	AAA	.	.		0.393	TUSC3-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365367.1	NM_006765		G	15601113	A	G	15601113	3	3	354	1	0	0	0	0	1	0	0	0	16793	14	1	2	959	2	TUSC3	8	15601113	Missense_Mutation	SNP	A	TCGA-WX-AA44-01A-11D-A38X-10		15601113	130762909	48	50026										
ZCCHC6	79670	hgsc.bcm.edu	37	chr9	88938154	88938154	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	gagggaatcatttctgatgtCtggccctgtactgagtgggt	14	7	3	2			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr9:88938154C>A	ENST00000375963.3	-	13	2683	c.2511G>T	c.(2509-2511)caG>caT	p.Q837H	ZCCHC6_ENST00000375961.2_Missense_Mutation_p.Q837H|ZCCHC6_ENST00000469004.1_5'Flank|ZCCHC6_ENST00000277141.6_Missense_Mutation_p.Q126H|ZCCHC6_ENST00000375960.2_Missense_Mutation_p.Q714H	NM_001185059.1|NM_024617.3	NP_001171988.1|NP_078893.2	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6	837	Glu-rich.				RNA 3'-end processing (GO:0031123)		poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	46						TTTCTGATGTCTGGCCCTGTA	0.458																																					p.Q837H		Atlas-SNP	.											.	ZCCHC6	105	.	0			c.G2511T						.						86	76	79					9																	88938154		2203	4300	6503	SO:0001583	missense	79670	exon13			TGATGTCTGGCCC	AL832026	CCDS35057.1, CCDS55323.1	9q21	2014-03-05			ENSG00000083223	ENSG00000083223		"Zinc fingers, CCHC domain containing"	25817	protein-coding gene	gene with protein product	"TUTase7"					11214970	Standard	NM_001185059		Approved	KIAA1711, FLJ13409, PAPD6, TUT7	uc004aoq.3	Q5VYS8	OTTHUMG00000020137	ENST00000375963.3:c.2511G>T	chr9.hg19:g.88938154C>A	ENSP00000365130:p.Gln837His	83.0	0.0		99.0	32.0	NM_024617	Q5H9T0|Q5VYS5|Q5VYS7|Q658Z9|Q659A2|Q6MZJ3|Q8N5F0|Q96N57|Q96NE8|Q9C0F2|Q9H8M6	Missense_Mutation	SNP	ENST00000375963.3	hg19	CCDS35057.1	.	.	.	.	.	.	.	.	.	.	C	11.12	1.545372	0.27652	.	.	ENSG00000083223	ENST00000277141;ENST00000375960;ENST00000375961;ENST00000375963	T;T;T;T	0.58797	0.31;0.74;0.78;0.79	5.39	-1.24	0.09435	.	0.763186	0.12704	N	0.446123	T	0.36220	0.0959	N	0.24115	0.695	0.09310	N	1	B;B	0.10296	0.003;0.0	B;B	0.09377	0.004;0.001	T	0.15809	-1.0424	10	0.46703	T	0.11	-11.2467	4.7547	0.13077	0.0982:0.3362:0.4017:0.1639	.	714;837	Q5VYS8-4;Q5VYS8	.;TUT7_HUMAN	H	126;714;837;837	ENSP00000277141:Q126H;ENSP00000365127:Q714H;ENSP00000365128:Q837H;ENSP00000365130:Q837H	ENSP00000277141:Q126H	Q	-	3	2	ZCCHC6	88127974	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-1.533000	0.02215	-0.392000	0.07751	0.585000	0.79938	CAG	.	.		0.458	ZCCHC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052918.1	NM_024617		A	88938154	C	A	88938154	3	1	354	1	0	0	0	0	1	0	0	0	17607	912	32	3	2036	3	ZCCHC6	9	88938154	Missense_Mutation	SNP	C	TCGA-WX-AA44-01A-11D-A38X-10		88938154	52275277	49	50027										
BICD2	23299	hgsc.bcm.edu	37	chr9	95491346	95491346	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	cagaggccaggcgctcattcTccgactgcgtgttggtgagg	15	11	2	2			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr9:95491346T>C	ENST00000375512.3	-	2	480	c.413A>G	c.(412-414)gAg>gGg	p.E138G	BICD2_ENST00000356884.6_Missense_Mutation_p.E138G	NM_015250.3	NP_056065.1	Q8TD16	BICD2_HUMAN	bicaudal D homolog 2 (Drosophila)	138					cell death (GO:0008219)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	Rab GTPase binding (GO:0017137)			cervix(3)|endometrium(4)|kidney(1)|large_intestine(6)|lung(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23						GCGCTCATTCTCCGACTGCGT	0.617																																					p.E138G		Atlas-SNP	.											.	BICD2	68	.	0			c.A413G						.						120	85	97					9																	95491346		2203	4300	6503	SO:0001583	missense	23299	exon2			TCATTCTCCGACT	AB014599	CCDS6700.1, CCDS35064.1	9q22.32	2008-02-05			ENSG00000185963	ENSG00000185963			17208	protein-coding gene	gene with protein product		609797				9734811	Standard	NM_001003800		Approved	KIAA0699	uc004asp.1	Q8TD16	OTTHUMG00000021036	ENST00000375512.3:c.413A>G	chr9.hg19:g.95491346T>C	ENSP00000364662:p.Glu138Gly	47.0	0.0		48.0	11.0	NM_001003800	O75181|Q5TBQ2|Q5TBQ3|Q96LH2|Q9BT84|Q9H561	Missense_Mutation	SNP	ENST00000375512.3	hg19	CCDS6700.1	.	.	.	.	.	.	.	.	.	.	T	30	5.055155	0.93793	.	.	ENSG00000185963	ENST00000356884;ENST00000375512	T;T	0.58358	0.34;0.34	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.68016	0.2955	M	0.84948	2.725	0.80722	D	1	D;P	0.56521	0.976;0.801	P;P	0.53360	0.724;0.516	T	0.74383	-0.3683	10	0.62326	D	0.03	-31.4664	13.6329	0.62206	0.0:0.0:0.0:1.0	.	138;138	Q8TD16-2;Q8TD16	.;BICD2_HUMAN	G	138	ENSP00000349351:E138G;ENSP00000364662:E138G	ENSP00000349351:E138G	E	-	2	0	BICD2	94531167	1.000000	0.71417	0.920000	0.36463	0.883000	0.51084	7.819000	0.86621	2.168000	0.68352	0.533000	0.62120	GAG	.	.		0.617	BICD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055508.1	NM_015250		C	95491346	T	C	95491346	3	2	354	1	0	0	0	0	1	0	0	0	1429	1551	54	2	2188	2	BICD2	9	95491346	Missense_Mutation	SNP	T	TCGA-WX-AA44-01A-11D-A38X-10	6553192	95491346	45722085	50	50028										
LRRC8A	56262	hgsc.bcm.edu	37	chr9	131670444	131670444	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	cctagtcatcttctacggccTcatctgcatgtatacactgt	6	13	5	0			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr9:131670444T>A	ENST00000259324.5	+	3	1524	c.1001T>A	c.(1000-1002)cTc>cAc	p.L334H	LRRC8A_ENST00000372599.3_Missense_Mutation_p.L334H|LRRC8A_ENST00000372600.4_Missense_Mutation_p.L334H	NM_001127244.1	NP_001120716.1	Q8IWT6	LRC8A_HUMAN	leucine rich repeat containing 8 family, member A	334					anion transport (GO:0006820)|cell volume homeostasis (GO:0006884)|pre-B cell differentiation (GO:0002329)|response to osmotic stress (GO:0006970)	cell surface (GO:0009986)|ion channel complex (GO:0034702)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|skin(3)	28						TTCTACGGCCTCATCTGCATG	0.577																																					p.L334H		Atlas-SNP	.											.	LRRC8A	69	.	0			c.T1001A						.						221	159	180					9																	131670444		2203	4300	6503	SO:0001583	missense	56262	exon3			ACGGCCTCATCTG	AB037858	CCDS35155.1	9q34.2	2014-09-17	2005-06-29	2005-06-29	ENSG00000136802	ENSG00000136802			19027	protein-coding gene	gene with protein product		608360	"leucine rich repeat containing 8"	LRRC8			Standard	NM_001127244		Approved	KIAA1437, FLJ10337	uc010myp.3	Q8IWT6	OTTHUMG00000020766	ENST00000259324.5:c.1001T>A	chr9.hg19:g.131670444T>A	ENSP00000259324:p.Leu334His	76.0	0.0		56.0	5.0	NM_001127244	Q6UXM2|Q8NCI0|Q9P2B1	Missense_Mutation	SNP	ENST00000259324.5	hg19	CCDS35155.1	.	.	.	.	.	.	.	.	.	.	T	17.40	3.379878	0.61845	.	.	ENSG00000136802	ENST00000372600;ENST00000372599;ENST00000259324	T;T;T	0.55930	0.49;0.49;0.49	5.27	5.27	0.74061	.	0.062950	0.64402	D	0.000004	T	0.65396	0.2687	M	0.73217	2.22	0.58432	D	0.999999	D	0.56968	0.978	P	0.54815	0.761	T	0.70666	-0.4809	10	0.87932	D	0	.	14.3778	0.66889	0.0:0.0:0.0:1.0	.	334	Q8IWT6	LRC8A_HUMAN	H	334	ENSP00000361682:L334H;ENSP00000361680:L334H;ENSP00000259324:L334H	ENSP00000259324:L334H	L	+	2	0	LRRC8A	130710265	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	8.040000	0.89188	1.997000	0.58415	0.379000	0.24179	CTC	.	.		0.577	LRRC8A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054516.2	NM_019594		A	131670444	T	A	131670444	3	1	354	1	0	0	0	0	1	0	0	0	9030	1551	54	4	1003	4	LRRC8A	9	131670444	Missense_Mutation	SNP	T	TCGA-WX-AA44-01A-11D-A38X-10	36179098	131670444	9542987	51	50029										
CRAT	1384	hgsc.bcm.edu	37	chr9	131866547	131866547	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	tagatgaccacaggctggcgGtactggaggtaggcggtctt	16	8	1	2			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr9:131866547G>A	ENST00000318080.2	-	3	624	c.330C>T	c.(328-330)taC>taT	p.Y110Y	AL158151.2_ENST00000408594.1_RNA|CRAT_ENST00000464290.1_Intron	NM_000755.3|NM_001257363.1	NP_000746|NP_001244292.1	P43155	CACP_HUMAN	carnitine O-acetyltransferase	110					carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carnitine O-acetyltransferase activity (GO:0004092)|receptor binding (GO:0005102)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(2)	13				UCEC - Uterine corpus endometrioid carcinoma (4;0.0178)	L-Carnitine(DB00583)	CAGGCTGGCGGTACTGGAGGT	0.637																																					p.Y110Y		Atlas-SNP	.											.	CRAT	43	.	0			c.C330T						.						48	37	41					9																	131866547		2202	4300	6502	SO:0001819	synonymous_variant	1384	exon3			CTGGCGGTACTGG	X78706	CCDS6919.1	9q34.1	2010-04-27	2010-04-27		ENSG00000095321	ENSG00000095321	2.3.1.7		2342	protein-coding gene	gene with protein product		600184	"carnitine acetyltransferase"			7829107	Standard	NM_000755		Approved	CAT1	uc004bxh.3	P43155	OTTHUMG00000147343	ENST00000318080.2:c.330C>T	chr9.hg19:g.131866547G>A		262.0	0.0		198.0	54.0	NM_000755	Q5T952|Q9BW16	Silent	SNP	ENST00000318080.2	hg19	CCDS6919.1																																																																																			.	.		0.637	CRAT-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253700.1			A	131866547	G	A	131866547	2	1	354	1	0	0	0	0	0	0	0	1	3849	1256	44	3		3	CRAT	9	131866547	Silent	SNP	G	TCGA-WX-AA44-01A-11D-A38X-10	196103	131866547	9346884	52	50030										
LHX3	8022	hgsc.bcm.edu	37	chr9	139089248	139089248	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	ggggtaacccccgctgctccCcgtggataggtcagaactgg	14	13	1	1			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr9:139089248C>A	ENST00000371748.5	-	6	1213	c.1117G>T	c.(1117-1119)Ggg>Tgg	p.G373W	LHX3_ENST00000371746.3_Missense_Mutation_p.G378W	NM_178138.4	NP_835258.1	Q9UBR4	LHX3_HUMAN	LIM homeobox 3	373					inner ear development (GO:0048839)|lung development (GO:0030324)|medial motor column neuron differentiation (GO:0021526)|motor neuron axon guidance (GO:0008045)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|pituitary gland development (GO:0021983)|placenta development (GO:0001890)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|spinal cord association neuron differentiation (GO:0021527)|spinal cord motor neuron cell fate specification (GO:0021520)|ventral spinal cord interneuron specification (GO:0021521)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			large_intestine(2)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	8		Myeloproliferative disorder(178;0.0511)		Epithelial(140;8.43e-08)|OV - Ovarian serous cystadenocarcinoma(145;1.26e-07)		CCGCTGCTCCCCGTGGATAGG	0.697																																					p.G378W		Atlas-SNP	.											.	LHX3	23	.	0			c.G1132T						.						12	16	14					9																	139089248		2165	4258	6423	SO:0001583	missense	8022	exon6			TGCTCCCCGTGGA	AF096169	CCDS6994.1, CCDS6995.1	9q34.3	2011-06-20			ENSG00000107187	ENSG00000107187		"Homeoboxes / LIM class"	6595	protein-coding gene	gene with protein product		600577				10598593, 10717474	Standard	NM_178138		Approved		uc004cgz.3	Q9UBR4	OTTHUMG00000020924	ENST00000371748.5:c.1117G>T	chr9.hg19:g.139089248C>A	ENSP00000360813:p.Gly373Trp	251.0	0.0		178.0	54.0	NM_014564	Q5TB39|Q5TB40|Q9NZB5|Q9P0I8|Q9P0I9	Missense_Mutation	SNP	ENST00000371748.5	hg19	CCDS6994.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.405285	0.83230	.	.	ENSG00000107187	ENST00000371748;ENST00000371746;ENST00000325195	D;D	0.90676	-2.56;-2.71	4.27	4.27	0.50696	.	0.063354	0.64402	D	0.000007	D	0.93828	0.8026	L	0.57536	1.79	0.80722	D	1	D;D	0.76494	0.999;0.988	D;P	0.72625	0.978;0.908	D	0.94529	0.7734	10	0.72032	D	0.01	.	15.846	0.78890	0.0:1.0:0.0:0.0	.	373;378	Q9UBR4;F1T0D9	LHX3_HUMAN;.	W	373;378;373	ENSP00000360813:G373W;ENSP00000360811:G378W	ENSP00000319224:G373W	G	-	1	0	LHX3	138229069	1.000000	0.71417	0.936000	0.37596	0.870000	0.49936	7.127000	0.77210	2.190000	0.69967	0.591000	0.81541	GGG	.	.		0.697	LHX3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055048.3			A	139089248	C	A	139089248	3	1	354	1	0	0	0	0	1	0	0	0	8781	623	22	3	80	3	LHX3	9	139089248	Missense_Mutation	SNP	C	TCGA-WX-AA44-01A-11D-A38X-10	7222701	139089248	2124183	53	50031										
SLC34A3	142680	hgsc.bcm.edu	37	chr9	140127035	140127035	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	ctgtgtcctcagagctccgcGtggccggcaggctgcgccgc	15	16	1	1	rs532224704	byFrequency	TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr9:140127035G>A	ENST00000538474.1	+	4	408	c.184G>A	c.(184-186)Gtg>Atg	p.V62M	SLC34A3_ENST00000361134.2_Missense_Mutation_p.V62M	NM_001177316.1|NM_001177317.1	NP_001170787|NP_001170788	Q8N130	NPT2C_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 3	62					cellular phosphate ion homeostasis (GO:0030643)|ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|sodium:phosphate symporter activity (GO:0005436)			kidney(3)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		AGAGCTCCGCGTGGCCGGCAG	0.687																																					p.V62M		Atlas-SNP	.											.	SLC34A3	32	.	0			c.G184A						.						24	27	26					9																	140127035		2188	4267	6455	SO:0001583	missense	142680	exon4			CTCCGCGTGGCCG	AB055000	CCDS7038.1	9q34.3	2013-07-17	2013-07-17		ENSG00000198569	ENSG00000198569		"Solute carriers"	20305	protein-coding gene	gene with protein product		609826	"solute carrier family 34 (sodium phosphate), member 3"			11880379, 16358215, 16358214	Standard	NM_080877		Approved	NPTIIc, FLJ38680	uc004cmf.1	Q8N130	OTTHUMG00000131780	ENST00000538474.1:c.184G>A	chr9.hg19:g.140127035G>A	ENSP00000442397:p.Val62Met	62.0	0.0		48.0	5.0	NM_001177317	A2BFA1	Missense_Mutation	SNP	ENST00000538474.1	hg19	CCDS7038.1	.	.	.	.	.	.	.	.	.	.	g	9.266	1.044518	0.19748	.	.	ENSG00000198569	ENST00000538474;ENST00000361134	T;T	0.29917	1.55;1.55	3.74	-7.47	0.01365	.	1.172260	0.06411	N	0.720637	T	0.14442	0.0349	N	0.22421	0.69	0.09310	N	1	B	0.19583	0.037	B	0.06405	0.002	T	0.20405	-1.0276	10	0.41790	T	0.15	-5.0215	2.4859	0.04598	0.1622:0.2386:0.4809:0.1184	.	62	Q8N130	NPT2C_HUMAN	M	62	ENSP00000442397:V62M;ENSP00000355353:V62M	ENSP00000355353:V62M	V	+	1	0	SLC34A3	139246856	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.444000	0.02403	-1.584000	0.01636	-0.696000	0.03686	GTG	.	.		0.687	SLC34A3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254712.1	NM_080877		A	140127035	G	A	140127035	3	1	354	1	0	0	0	0	1	0	0	0	14584	1145	40	1	194	1	SLC34A3	9	140127035	Missense_Mutation	SNP	G	TCGA-WX-AA44-01A-11D-A38X-10	1037787	140127035	1086396	54	50032										
PRTFDC1	56952	hgsc.bcm.edu	37	chr10	25140374	25140374	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	tatcccaccacaaataagttTggaatctcaaatccagcatc	4	12	1	0			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr10:25140374T>C	ENST00000320152.6	-	8	601	c.573A>G	c.(571-573)ccA>ccG	p.P191P	PRTFDC1_ENST00000376378.1_Intron	NM_020200.5	NP_064585.1	Q9NRG1	PRDC1_HUMAN	phosphoribosyl transferase domain containing 1	191					nucleoside metabolic process (GO:0009116)	cytosol (GO:0005829)	magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9						CAAATAAGTTTGGAATCTCAA	0.353																																					p.P191P		Atlas-SNP	.											.	PRTFDC1	29	.	0			c.A573G						.						83	84	84					10																	25140374		2203	4300	6503	SO:0001819	synonymous_variant	56952	exon8			TAAGTTTGGAATC	AF226056	CCDS7145.1, CCDS60506.1	10p12.31	2003-11-10			ENSG00000099256	ENSG00000099256			23333	protein-coding gene	gene with protein product		610751					Standard	XM_005252537		Approved	HHGP	uc001ise.1	Q9NRG1	OTTHUMG00000017829	ENST00000320152.6:c.573A>G	chr10.hg19:g.25140374T>C		43.0	0.0		40.0	9.0	NM_020200	B7Z1Z3|Q53HA7|Q59EL9|Q5VV18|Q5VV20	Silent	SNP	ENST00000320152.6	hg19	CCDS7145.1																																																																																			.	.		0.353	PRTFDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047243.2	NM_020200		C	25140374	T	C	25140374	2	2	354	1	0	0	0	0	0	0	0	1	12649	1799	63	2		2	PRTFDC1	10	25140374	Silent	SNP	T	TCGA-WX-AA44-01A-11D-A38X-10		25140374	110394373	55	50033										
HIPK3	10114	hgsc.bcm.edu	37	chr11	33350093	33350093	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	tggggttgccattttgtgaaGccatagacatgtggtcattg	13	6	1	2			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr11:33350093G>A	ENST00000303296.4	+	3	1440	c.1135G>A	c.(1135-1137)Gcc>Acc	p.A379T	HIPK3_ENST00000379016.3_Missense_Mutation_p.A379T|HIPK3_ENST00000525975.1_Missense_Mutation_p.A379T|HIPK3_ENST00000456517.1_Missense_Mutation_p.A379T	NM_005734.3	NP_005725.3	Q9H422	HIPK3_HUMAN	homeodomain interacting protein kinase 3	379	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|mRNA transcription (GO:0009299)|negative regulation of apoptotic process (GO:0043066)|negative regulation of JUN kinase activity (GO:0043508)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			endometrium(3)|kidney(3)|large_intestine(9)|liver(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	39						ATTTTGTGAAGCCATAGACAT	0.373																																					p.A379T		Atlas-SNP	.											.	HIPK3	92	.	0			c.G1135A						.						113	112	113					11																	33350093		2202	4298	6500	SO:0001583	missense	10114	exon3			TGTGAAGCCATAG	AF004849	CCDS7884.1, CCDS41634.1	11p13	2008-07-18	2001-11-29		ENSG00000110422	ENSG00000110422			4915	protein-coding gene	gene with protein product		604424	"homeodomain-interacting protein kinase 3"			9373137, 9748262	Standard	NM_005734		Approved	PKY, DYRK6, YAK1, FIST3	uc031pzm.1	Q9H422	OTTHUMG00000132269	ENST00000303296.4:c.1135G>A	chr11.hg19:g.33350093G>A	ENSP00000304226:p.Ala379Thr	64.0	0.0		52.0	18.0	NM_001048200	O14632|Q2PBG4|Q2PBG5|Q92632|Q9HAS2	Missense_Mutation	SNP	ENST00000303296.4	hg19	CCDS7884.1	.	.	.	.	.	.	.	.	.	.	G	29.4	4.999085	0.93227	.	.	ENSG00000110422	ENST00000525975;ENST00000303296;ENST00000379016;ENST00000456517	T;T;T;T	0.22743	1.94;1.94;1.94;1.94	5.46	4.54	0.55810	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.100422	0.43747	D	0.000536	T	0.45216	0.1331	L	0.61036	1.89	0.80722	D	1	D;D	0.76494	0.995;0.999	D;D	0.83275	0.948;0.996	T	0.48714	-0.9011	10	0.87932	D	0	.	16.6049	0.84826	0.0:0.1303:0.8697:0.0	.	379;379	Q9H422-2;Q9H422	.;HIPK3_HUMAN	T	379	ENSP00000431710:A379T;ENSP00000304226:A379T;ENSP00000368301:A379T;ENSP00000398241:A379T	ENSP00000304226:A379T	A	+	1	0	HIPK3	33306669	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.781000	0.99029	1.410000	0.46936	0.563000	0.77884	GCC	.	.		0.373	HIPK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255358.1	NM_005734		A	33350093	G	A	33350093	3	1	354	1	0	0	0	0	1	0	0	0	7127	971	34	3	1141	3	HIPK3	11	33350093	Missense_Mutation	SNP	G	TCGA-WX-AA44-01A-11D-A38X-10		33350093	101656423	56	50034										
OR5D14	219436	hgsc.bcm.edu	37	chr11	55563748	55563748	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	gttagtgggcgccacaaagcCttctccacctgggcctccca	10	16	1	0			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr11:55563748C>T	ENST00000335605.1	+	1	717	c.717C>T	c.(715-717)gcC>gcT	p.A239A		NM_001004735.1	NP_001004735.1	Q8NGL3	OR5DE_HUMAN	olfactory receptor, family 5, subfamily D, member 14	239						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(30)|ovary(2)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	48		all_epithelial(135;0.196)				GCCACAAAGCCTTCTCCACCT	0.458																																					p.A239A		Atlas-SNP	.											.	OR5D14	116	.	0			c.C717T						.						125	117	120					11																	55563748		2200	4296	6496	SO:0001819	synonymous_variant	219436	exon1			CAAAGCCTTCTCC	AB065779	CCDS31508.1	11q11	2012-08-09			ENSG00000186113	ENSG00000186113		"GPCR / Class A : Olfactory receptors"	15281	protein-coding gene	gene with protein product							Standard	NM_001004735		Approved		uc010rim.2	Q8NGL3	OTTHUMG00000166809	ENST00000335605.1:c.717C>T	chr11.hg19:g.55563748C>T		102.0	0.0		100.0	35.0	NM_001004735	Q6IF69|Q6IFD4|Q96RB5	Silent	SNP	ENST00000335605.1	hg19	CCDS31508.1																																																																																			.	.		0.458	OR5D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391513.1	NM_001004735		T	55563748	C	T	55563748	2	4	354	1	0	0	0	0	0	0	0	1	11164	668	24	3		3	OR5D14	11	55563748	Silent	SNP	C	TCGA-WX-AA44-01A-11D-A38X-10	22213655	55563748	79442768	57	50035										
OR5M10	390167	hgsc.bcm.edu	37	chr11	56344387	56344387	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	aaagactgcaattattttggActcctctacagacttctctg	6	10	2	2			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr11:56344387A>T	ENST00000526812.2	-	1	876	c.811T>A	c.(811-813)Tcc>Acc	p.S271T		NM_001004741.1	NP_001004741.1	Q6IEU7	OR5MA_HUMAN	olfactory receptor, family 5, subfamily M, member 10	271						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(15)|upper_aerodigestive_tract(2)|urinary_tract(2)	25						ATTATTTTGGACTCCTCTACA	0.413																																					p.S271T		Atlas-SNP	.											.	OR5M10	56	.	0			c.T811A						.						188	182	183					11																	56344387		1829	4084	5913	SO:0001583	missense	390167	exon1			TTTTGGACTCCTC	BK004515	CCDS53630.1	11q11	2012-08-09				ENSG00000254834		"GPCR / Class A : Olfactory receptors"	15290	protein-coding gene	gene with protein product							Standard	NM_001004741		Approved		uc001niz.1	Q6IEU7		ENST00000526812.2:c.811T>A	chr11.hg19:g.56344387A>T	ENSP00000436004:p.Ser271Thr	210.0	0.0		238.0	68.0	NM_001004741	B9EIL9	Missense_Mutation	SNP	ENST00000526812.2	hg19	CCDS53630.1	.	.	.	.	.	.	.	.	.	.	A	11.69	1.714139	0.30413	.	.	ENSG00000254834	ENST00000526812	T	0.00107	8.72	4.2	0.171	0.15026	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00109	0.0003	N	0.10837	0.055	0.09310	N	1	B	0.33919	0.432	B	0.40940	0.344	T	0.10753	-1.0616	9	0.72032	D	0.01	.	1.7829	0.03035	0.4346:0.3124:0.094:0.1591	.	271	Q6IEU7	OR5MA_HUMAN	T	271	ENSP00000436004:S271T	ENSP00000436004:S271T	S	-	1	0	OR5M10	56100963	0.000000	0.05858	0.001000	0.08648	0.307000	0.27823	-0.609000	0.05635	-0.075000	0.12798	0.514000	0.50259	TCC	.	.		0.413	OR5M10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391609.1	NM_001004741		T	56344387	A	T	56344387	3	4	354	1	0	0	0	0	1	0	0	0	11182	275	10	4	140	4	OR5M10	11	56344387	Missense_Mutation	SNP	A	TCGA-WX-AA44-01A-11D-A38X-10	780639	56344387	78662129	58	50036										
NPAS4	266743	hgsc.bcm.edu	37	chr11	66188745	66188745	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	gctgctgccgctggccgaagCggacaaggtccggctgtcct	15	14	0	0			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr11:66188745C>T	ENST00000311034.2	+	1	271	c.95C>T	c.(94-96)gCg>gTg	p.A32V		NM_178864.3	NP_849195.2	Q8IUM7	NPAS4_HUMAN	neuronal PAS domain protein 4	32	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(4)|endometrium(2)|kidney(3)|large_intestine(11)|liver(2)|lung(20)|ovary(1)|prostate(3)|skin(3)	49						CTGGCCGAAGCGGACAAGGTC	0.647																																					p.A32V		Atlas-SNP	.											.	NPAS4	133	.	0			c.C95T						.						66	53	57					11																	66188745		2200	4295	6495	SO:0001583	missense	266743	exon1			CCGAAGCGGACAA	AB049469	CCDS8138.1	11q13.2	2013-05-21			ENSG00000174576	ENSG00000174576		"Basic helix-loop-helix proteins"	18983	protein-coding gene	gene with protein product		608554				14701734	Standard	NM_178864		Approved	PASD10, NXF, Le-PAS, bHLHe79	uc001ohx.1	Q8IUM7	OTTHUMG00000167045	ENST00000311034.2:c.95C>T	chr11.hg19:g.66188745C>T	ENSP00000311196:p.Ala32Val	245.0	0.0		191.0	69.0	NM_178864	B7ZL81|Q8N8S5|Q8N9Q9	Missense_Mutation	SNP	ENST00000311034.2	hg19	CCDS8138.1	.	.	.	.	.	.	.	.	.	.	C	34	5.313768	0.95655	.	.	ENSG00000174576	ENST00000311034	T	0.51071	0.72	5.19	5.19	0.71726	Helix-loop-helix DNA-binding (1);	0.228511	0.31102	N	0.008255	T	0.42314	0.1197	N	0.14661	0.345	0.54753	D	0.99998	D	0.63880	0.993	P	0.53490	0.727	T	0.41016	-0.9532	10	0.62326	D	0.03	-4.3398	11.8591	0.52454	0.0:0.8243:0.1757:0.0	.	32	Q8IUM7	NPAS4_HUMAN	V	32	ENSP00000311196:A32V	ENSP00000311196:A32V	A	+	2	0	NPAS4	65945321	0.998000	0.40836	0.999000	0.59377	0.948000	0.59901	1.746000	0.38288	2.691000	0.91804	0.563000	0.77884	GCG	.	.		0.647	NPAS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392634.1	NM_178864		T	66188745	C	T	66188745	3	4	354	1	0	0	0	0	1	0	0	0	10574	768	27	1	97	1	NPAS4	11	66188745	Missense_Mutation	SNP	C	TCGA-WX-AA44-01A-11D-A38X-10	9844358	66188745	68817771	59	50037										
UBE4A	9354	hgsc.bcm.edu	37	chr11	118242363	118242363	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	tgttacctttactcctgcttCcagagagccaaggaagaggt	10	10	0	2			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr11:118242363C>T	ENST00000431736.2	+	5	615	c.543C>T	c.(541-543)ttC>ttT	p.F181F	UBE4A_ENST00000252108.3_Silent_p.F181F					ubiquitination factor E4A											autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(7)|liver(2)|lung(14)|ovary(3)|prostate(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	56	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)		ACTCCTGCTTCCAGAGAGCCA	0.433																																					p.F181F		Atlas-SNP	.											.	UBE4A	97	.	0			c.C543T						.						98	93	95					11																	118242363		2200	4296	6496	SO:0001819	synonymous_variant	9354	exon5			CTGCTTCCAGAGA	D50916	CCDS8396.1, CCDS55790.1	11q23.3	2013-01-28	2011-05-19					"U-box domain containing"	12499	protein-coding gene	gene with protein product		603753	"ubiquitination factor E4A (homologous to yeast UFD2)", "ubiquitination factor E4A (UFD2 homolog, yeast)"			10089879	Standard	NM_004788		Approved	UBOX2, UFD2, KIAA0126, E4	uc001psv.3	Q14139	OTTHUMG00000168100	ENST00000431736.2:c.543C>T	chr11.hg19:g.118242363C>T		52.0	0.0		35.0	9.0	NM_004788		Silent	SNP	ENST00000431736.2	hg19	CCDS8396.1																																																																																			.	.		0.433	UBE4A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398143.1	NM_004788		T	118242363	C	T	118242363	2	4	354	1	0	0	0	0	0	0	0	1	16897	854	30	3		3	UBE4A	11	118242363	Silent	SNP	C	TCGA-WX-AA44-01A-11D-A38X-10	52053618	118242363	16764153	60	50038										
PZP	5858	hgsc.bcm.edu	37	chr12	9345225	9345240	+	Frame_Shift_Del	DEL	AATGTAACTTCCACTT	AATGTAACTTCCACTT	-													0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	ccagccacaggctccaggtgAatgtaacttccacttaagga					rs140140094|rs376566013	byFrequency	TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	AATGTAACTTCCACTT	AATGTAACTTCCACTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr12:9345225_9345240delAATGTAACTTCCACTT	ENST00000261336.2	-	12	1378_1393	c.1350_1365delAAGTGGAAGTTACATT	c.(1348-1365)ttaagtggaagttacattfs	p.LSGSYI450fs	PZP_ENST00000381997.2_Frame_Shift_Del_p.LSGSYI319fs	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	450					female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						GCTCCAGGTGAATGTAACTTCCACTTAAGGAGAAAA	0.509																																					p.451_456del	Melanoma(125;1402 1695 4685 34487 38571)	Atlas-INDEL	.											.	PZP	422	.	0			c.1351_1366del						.																																			SO:0001589	frameshift_variant	5858	exon12			.	X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.1350_1365delAAGTGGAAGTTACATT	chr12.hg19:g.9345225_9345240delAATGTAACTTCCACTT	ENSP00000261336:p.Leu450fs	76.0	0.0		85.0	20.0	NM_002864	A6ND27|Q15273|Q2NKL2|Q7M4N7	Frame_Shift_Del	DEL	ENST00000261336.2	hg19	CCDS8600.1																																																																																			.	.		0.509	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864		-	9345240	AATGTAACTTCCACTT	-	9345225	7	5	354	1	0	1	0	1	0	0	0	0	12884	242	9	0	3183	0	PZP	12	9345225	Frame_Shift_Del	DEL	AATGTAACTTCCACTT	TCGA-WX-AA44-01A-11D-A38X-10		9345225	124506670	61	50039										
TIMELESS	8914	hgsc.bcm.edu	37	chr12	56817448	56817448	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	tcctcttcctcctcctcctcCtcttcttcttcctctgcccc	1	23	5	0			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr12:56817448C>T	ENST00000553532.1	-	17	2160	c.2010G>A	c.(2008-2010)gaG>gaA	p.E670E	TIMELESS_ENST00000229201.4_Silent_p.E669E|TIMELESS_ENST00000554616.1_Intron					timeless circadian clock									p.E670E(1)		NS(1)|breast(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(8)|lung(14)|ovary(7)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	49						cctcctcctcctcttcttctt	0.527																																					p.E670E		Atlas-SNP	.											TIMELESS,NS,carcinoma,0,1	TIMELESS	107	.	1	Substitution - coding silent(1)	kidney(1)	c.G2010A						.						51	49	50					12																	56817448		2203	4300	6503	SO:0001819	synonymous_variant	8914	exon17			CTCCTCCTCTTCT	AF098162	CCDS8918.1	12q13.3	2012-12-14	2012-12-14		ENSG00000111602	ENSG00000111602			11813	protein-coding gene	gene with protein product	"Tof1 homolog (S. cerevisiae)", "timeless circadian clock 1"	603887	"timeless (Drosophila) homolog", "timeless homolog (Drosophila)"			9856465	Standard	NM_003920		Approved	hTIM, TIM, TIM1	uc001slf.2	Q9UNS1	OTTHUMG00000170600	ENST00000553532.1:c.2010G>A	chr12.hg19:g.56817448C>T		56.0	0.0		56.0	3.0	NM_003920		Silent	SNP	ENST00000553532.1	hg19	CCDS8918.1																																																																																			.	.		0.527	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920		T	56817448	C	T	56817448	2	4	354	1	0	0	0	0	0	0	0	1	15919	680	24	3		3	TIMELESS	12	56817448	Silent	SNP	C	TCGA-WX-AA44-01A-11D-A38X-10	47472223	56817448	77034447	62	50040										
ZMYM2	7750	hgsc.bcm.edu	37	chr13	20567236	20567236	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	gacacaagttcagtgggaggAttagaattgactgatcagac	12	6	2	4			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr13:20567236A>G	ENST00000382874.2	+	4	214	c.24A>G	c.(22-24)ggA>ggG	p.G8G	ZMYM2_ENST00000382881.3_Silent_p.G8G|ZMYM2_ENST00000382869.3_Silent_p.G8G|ZMYM2_ENST00000382871.2_Silent_p.G8G	NM_001190964.1	NP_001177893.1	Q9UBW7	ZMYM2_HUMAN	zinc finger, MYM-type 2	8					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|PML body (GO:0016605)	ubiquitin conjugating enzyme binding (GO:0031624)|zinc ion binding (GO:0008270)			large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	10		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)		CAGTGGGAGGATTAGAATTGA	0.388																																					p.G8G		Atlas-SNP	.											.	ZMYM2	191	.	0			c.A24G						.						130	127	128					13																	20567236		2051	4253	6304	SO:0001819	synonymous_variant	7750	exon4			GGGAGGATTAGAA	AF012126	CCDS45016.1	13q11-q12	2013-01-08	2006-07-13	2006-07-13	ENSG00000121741	ENSG00000121741		"Zinc fingers, MYM type"	12989	protein-coding gene	gene with protein product		602221	"zinc finger protein 198"	ZNF198		9499416, 9425908	Standard	XM_005266517		Approved	RAMP, FIM, MYM	uc001ums.3	Q9UBW7	OTTHUMG00000016507	ENST00000382874.2:c.24A>G	chr13.hg19:g.20567236A>G		116.0	0.0		161.0	38.0	NM_001190964	A6NDG0|A6NI02|O43212|O43434|O60898|Q5W0Q4|Q5W0T3|Q63HP0|Q8NE39|Q9H0V5|Q9H538|Q9UEU2	Silent	SNP	ENST00000382874.2	hg19	CCDS45016.1																																																																																			.	.		0.388	ZMYM2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044051.2	NM_003453		G	20567236	A	G	20567236	2	3	354	1	0	0	0	0	0	0	0	1	17715	320	12	2		2	ZMYM2	13	20567236	Silent	SNP	A	TCGA-WX-AA44-01A-11D-A38X-10		20567236	94602642	63	50041										
RB1	5925	hgsc.bcm.edu	37	chr13	48923090	48923090	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	ctgctttctatttgtttaatAggatatctactgaaataaat	5	5	2	1			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr13:48923090A>T	ENST00000267163.4	+	6	677		c.e6-1			NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1						androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(6)		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(DB00071)|Insulin Regular(DB00030)"	TTTGTTTAATAGGATATCTAC	0.259		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)																											.		Atlas-SNP	.	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	.,2	RB1	1068	.	21	Whole gene deletion(15)|Unknown(6)	bone(11)|breast(6)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	c.540-2A>T	GRCh37	CS030548	RB1	S		.						54	58	57					13																	48923090		2194	4275	6469	SO:0001630	splice_region_variant	5925	exon6	Familial Cancer Database		TTTAATAGGATAT	M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"Endogenous ligands"	9884	protein-coding gene	gene with protein product	"prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130"	614041	"osteosarcoma"	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.540-1A>T	chr13.hg19:g.48923090A>T		40.0	0.0		33.0	19.0	NM_000321	A8K5E3|P78499|Q5VW46|Q8IZL4	Splice_Site	SNP	ENST00000267163.4	hg19	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	A	19.66	3.870042	0.72065	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	.	.	.	5.23	5.23	0.72850	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.792	0.52075	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	RB1	47821091	0.998000	0.40836	1.000000	0.80357	0.994000	0.84299	5.041000	0.64196	2.111000	0.64477	0.528000	0.53228	.	.	.		0.259	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1		Intron	T	48923090	A	T	48923090	5	4	354	1	0	0	0	0	0	0	1	0	13113	434	15	4	560	4	RB1	13	48923090	Splice_Site	SNP	A	TCGA-WX-AA44-01A-11D-A38X-10	28355854	48923090	66246788	64	50042										
PCDH17	27253	hgsc.bcm.edu	37	chr13	58208511	58208511	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	gctatctggtgagcactgtgCgcgccctagacagcgacttc	12	13	1	2			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr13:58208511C>A	ENST00000377918.3	+	1	1857	c.1831C>A	c.(1831-1833)Cgc>Agc	p.R611S		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	611	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(30)|liver(2)|lung(54)|ovary(4)|pancreas(2)|prostate(5)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		GAGCACTGTGCGCGCCCTAGA	0.657																																					p.R611S	Melanoma(72;952 1291 1619 12849 33676)	Atlas-SNP	.											PCDH17,caecum,carcinoma,0,1	PCDH17	304	.	0			c.C1831A						.						34	33	34					13																	58208511		2202	4296	6498	SO:0001583	missense	27253	exon1			ACTGTGCGCGCCC	AF029343	CCDS31986.1	13q21.1	2010-01-26			ENSG00000118946	ENSG00000118946		"Cadherins / Protocadherins : Non-clustered"	14267	protein-coding gene	gene with protein product		611760				10835267	Standard	NM_001040429		Approved	PCDH68, PCH68	uc001vhq.1	O14917	OTTHUMG00000016992	ENST00000377918.3:c.1831C>A	chr13.hg19:g.58208511C>A	ENSP00000367151:p.Arg611Ser	45.0	0.0		50.0	2.0	NM_001040429	A8K1R5|Q5VVW9|Q5VVX0	Missense_Mutation	SNP	ENST00000377918.3	hg19	CCDS31986.1	.	.	.	.	.	.	.	.	.	.	C	8.436	0.849830	0.17034	.	.	ENSG00000118946	ENST00000377918	T	0.51071	0.72	5.36	4.46	0.54185	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.45518	0.1346	N	0.16066	0.365	0.48341	D	0.999635	P;D	0.57257	0.929;0.979	P;P	0.60789	0.705;0.879	T	0.31392	-0.9945	9	.	.	.	.	12.7714	0.57423	0.2873:0.7127:0.0:0.0	.	611;611	O14917-2;O14917	.;PCD17_HUMAN	S	611	ENSP00000367151:R611S	.	R	+	1	0	PCDH17	57106512	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	4.027000	0.57239	2.500000	0.84329	0.561000	0.74099	CGC	.	.		0.657	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429		A	58208511	C	A	58208511	3	1	354	1	0	0	0	0	1	0	0	0	11521	768	27	1	1833	1	PCDH17	13	58208511	Missense_Mutation	SNP	C	TCGA-WX-AA44-01A-11D-A38X-10	9285421	58208511	56961367	65	50043										
NFATC4	4776	hgsc.bcm.edu	37	chr14	24845640	24845640	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	cccatgaagaccctgcttgcGaaactccttacctatcagaa	6	14	1	3			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr14:24845640G>A	ENST00000250373.4	+	9	2338	c.2197G>A	c.(2197-2199)Gaa>Aaa	p.E733K	NFATC4_ENST00000554591.1_Missense_Mutation_p.E796K|NFATC4_ENST00000556279.1_Missense_Mutation_p.E765K|NFATC4_ENST00000554966.1_Missense_Mutation_p.E746K|NFATC4_ENST00000553879.1_Missense_Mutation_p.E663K|NFATC4_ENST00000413692.2_Missense_Mutation_p.E796K|NFATC4_ENST00000556169.1_Missense_Mutation_p.E721K|NFATC4_ENST00000539237.2_Missense_Mutation_p.E765K|NFATC4_ENST00000424781.2_Missense_Mutation_p.E746K|NFATC4_ENST00000555393.1_Missense_Mutation_p.E21K|NFATC4_ENST00000556759.1_Missense_Mutation_p.E268K|NFATC4_ENST00000555590.1_Missense_Mutation_p.E746K|NFATC4_ENST00000555167.1_Missense_Mutation_p.E268K|NFATC4_ENST00000557767.1_Missense_Mutation_p.E21K|NFATC4_ENST00000554473.1_Missense_Mutation_p.E268K|NFATC4_ENST00000557451.1_Missense_Mutation_p.E663K|NFATC4_ENST00000554344.1_Missense_Mutation_p.E663K|NFATC4_ENST00000422617.3_Missense_Mutation_p.E721K|NFATC4_ENST00000553708.1_Missense_Mutation_p.E733K|NFATC4_ENST00000554661.1_Missense_Mutation_p.E663K|NFATC4_ENST00000554050.1_Missense_Mutation_p.E733K|NFATC4_ENST00000553469.1_Missense_Mutation_p.E765K|NFATC4_ENST00000555802.1_Missense_Mutation_p.E21K|NFATC4_ENST00000555453.1_Missense_Mutation_p.E721K	NM_004554.4	NP_004545.2	Q14934	NFAC4_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4	733	Pro-rich.				cellular respiration (GO:0045333)|cellular response to lithium ion (GO:0071285)|cellular response to UV (GO:0034644)|heart development (GO:0007507)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of synaptic plasticity (GO:0048167)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription coactivator activity (GO:0003713)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(7)|liver(4)|lung(12)|ovary(1)|skin(2)	34				GBM - Glioblastoma multiforme(265;0.018)		CCCTGCTTGCGAAACTCCTTA	0.617																																					p.E796K		Atlas-SNP	.											.	NFATC4	115	.	0			c.G2386A						.						59	63	62					14																	24845640		2203	4300	6503	SO:0001583	missense	4776	exon10			GCTTGCGAAACTC	BC053855	CCDS9629.1, CCDS45089.1, CCDS55909.1, CCDS55910.1, CCDS55911.1, CCDS73625.1	14q11.2	2009-11-24			ENSG00000100968	ENSG00000100968		"Nuclear factor of activated T-cells"	7778	protein-coding gene	gene with protein product		602699				7749981	Standard	NM_004554		Approved	NFAT3	uc010tok.2	Q14934	OTTHUMG00000029351	ENST00000250373.4:c.2197G>A	chr14.hg19:g.24845640G>A	ENSP00000250373:p.Glu733Lys	86.0	0.0		67.0	20.0	NM_001198967	B4DDG5|B4DY55|B5B2U7|B5B2U8|B5B2U9|B5B2V0|B5B2V1|B5B2V2|B5B2V3|B5B2V4|B5B2V5|B5B2V7|B5B2V8|B5B2V9|B5B2W0|B5B2W1|B5B2W2|B5B2W3|B5B2W4|B5B2W5|B5B2W6|B5B2W7|B5B2W8|B5B2W9|B5B2X0|Q7Z598|Q96H68	Missense_Mutation	SNP	ENST00000250373.4	hg19	CCDS9629.1	.	.	.	.	.	.	.	.	.	.	G	12.72	2.021647	0.35701	.	.	ENSG00000100968	ENST00000413692;ENST00000554591;ENST00000555590;ENST00000554966;ENST00000424781;ENST00000539237;ENST00000556279;ENST00000553469;ENST00000554050;ENST00000250373;ENST00000553708;ENST00000553879;ENST00000554344;ENST00000554661;ENST00000556169;ENST00000557451;ENST00000422617;ENST00000555453;ENST00000554473;ENST00000556759;ENST00000555167;ENST00000557767;ENST00000555393;ENST00000555802	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.56776	3.26;3.26;3.28;3.27;3.27;3.27;3.28;3.27;3.28;3.29;3.27;2.96;2.96;2.96;2.95;2.95;2.95;2.96;1.55;1.53;1.52;0.44;0.47	5.13	5.13	0.70059	.	0.000000	0.64402	D	0.000017	T	0.32406	0.0828	N	0.19112	0.55	0.27737	N	0.944606	B;B;B;B;B;B;B;B;B;B;B;B;B	0.33198	0.401;0.401;0.401;0.401;0.401;0.401;0.401;0.401;0.401;0.401;0.401;0.401;0.279	B;B;B;B;B;B;B;B;B;B;B;B;B	0.26770	0.03;0.044;0.044;0.044;0.044;0.044;0.044;0.044;0.073;0.073;0.073;0.044;0.02	T	0.13335	-1.0513	10	0.09590	T	0.72	-5.1132	13.9397	0.64048	0.0:0.0:1.0:0.0	.	721;721;765;765;746;746;746;796;796;721;765;796;733	Q14934-17;Q14934-9;Q14934-14;Q14934-4;Q14934-15;Q14934-6;Q14934-7;Q14934-2;Q14934-3;Q14934-10;Q14934-5;Q14934-11;Q14934	.;.;.;.;.;.;.;.;.;.;.;.;NFAC4_HUMAN	K	796;796;746;746;746;765;765;765;733;733;733;663;663;663;721;663;721;721;268;268;268;21;21;21	ENSP00000388910:E796K;ENSP00000452039:E796K;ENSP00000451224:E746K;ENSP00000450644:E746K;ENSP00000388668:E746K;ENSP00000439350:E765K;ENSP00000452270:E765K;ENSP00000451502:E765K;ENSP00000451151:E733K;ENSP00000250373:E733K;ENSP00000450590:E733K;ENSP00000452349:E663K;ENSP00000450469:E663K;ENSP00000450733:E663K;ENSP00000451454:E721K;ENSP00000451284:E663K;ENSP00000396788:E721K;ENSP00000450686:E721K;ENSP00000450810:E268K;ENSP00000451183:E268K;ENSP00000451395:E268K;ENSP00000451801:E21K;ENSP00000451590:E21K	ENSP00000250373:E733K	E	+	1	0	NFATC4	23915480	0.813000	0.29090	0.997000	0.53966	0.918000	0.54935	2.738000	0.47401	2.667000	0.90743	0.561000	0.74099	GAA	.	.		0.617	NFATC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073206.6	NM_004554		A	24845640	G	A	24845640	3	1	354	1	0	0	0	0	1	0	0	0	10374	1059	37	1	2424	1	NFATC4	14	24845640	Missense_Mutation	SNP	G	TCGA-WX-AA44-01A-11D-A38X-10		24845640	82503900	66	50044										
SEL1L	6400	hgsc.bcm.edu	37	chr14	82000074	82000074	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	cacagcagcagcgtcagcccTatccggacccgcatcctcct	8	19	1	0			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr14:82000074T>C	ENST00000336735.4	-	1	131	c.15A>G	c.(13-15)atA>atG	p.I5M	SEL1L_ENST00000555824.1_Missense_Mutation_p.I5M	NM_005065.5	NP_005056.3	Q9UBV2	SE1L1_HUMAN	sel-1 suppressor of lin-12-like (C. elegans)	5					Notch signaling pathway (GO:0007219)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	28				BRCA - Breast invasive adenocarcinoma(234;0.0299)		GCGTCAGCCCTATCCGGACCC	0.716																																					p.I5M		Atlas-SNP	.											.	SEL1L	67	.	0			c.A15G						.						43	35	38					14																	82000074		2202	4298	6500	SO:0001583	missense	6400	exon1			CAGCCCTATCCGG		CCDS9876.1, CCDS58333.1	14q31	2011-03-31	2001-11-28		ENSG00000071537	ENSG00000071537			10717	protein-coding gene	gene with protein product	"sel-1 suppressor of lin-12-like 1 (C. elegans)"	602329	"sel-1 (suppressor of lin-12, C.elegans)-like"			9417916, 10051412, 16331677	Standard	NM_005065		Approved	IBD2, SEL1L1	uc010tvv.2	Q9UBV2		ENST00000336735.4:c.15A>G	chr14.hg19:g.82000074T>C	ENSP00000337053:p.Ile5Met	104.0	0.0		106.0	36.0	NM_001244984	Q6UWT6|Q9P1T9|Q9UHK7	Missense_Mutation	SNP	ENST00000336735.4	hg19	CCDS9876.1	.	.	.	.	.	.	.	.	.	.	T	14.11	2.437859	0.43326	.	.	ENSG00000071537	ENST00000336735;ENST00000555824;ENST00000557372	T;T;T	0.38887	1.62;1.35;1.11	5.58	-5.48	0.02592	.	0.734945	0.12917	N	0.428472	T	0.15132	0.0365	N	0.08118	0	0.09310	N	1	B;B	0.14805	0.006;0.011	B;B	0.17722	0.006;0.019	T	0.10917	-1.0609	10	0.59425	D	0.04	-19.228	0.2545	0.00210	0.3384:0.2346:0.1985:0.2285	.	5;5	Q9UBV2;Q9UBV2-2	SE1L1_HUMAN;.	M	5	ENSP00000337053:I5M;ENSP00000450709:I5M;ENSP00000451144:I5M	ENSP00000337053:I5M	I	-	3	3	SEL1L	81069827	0.357000	0.24938	0.031000	0.17742	0.950000	0.60333	-0.201000	0.09464	-0.874000	0.04027	-1.142000	0.01873	ATA	.	.		0.716	SEL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413325.1	NM_005065		C	82000074	T	C	82000074	3	2	354	1	0	0	0	0	1	0	0	0	14025	1512	53	2	2453	2	SEL1L	14	82000074	Missense_Mutation	SNP	T	TCGA-WX-AA44-01A-11D-A38X-10	57154434	82000074	25349466	67	50045										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105406860	105406860	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	tcctccacgctgcattctggGtccacctttggccctgtttc	8	16	1	0			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr14:105406860G>A	ENST00000333244.5	-	7	15047	c.14928C>T	c.(14926-14928)gaC>gaT	p.D4976D	AHNAK2_ENST00000557457.1_5'UTR	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4976						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				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)			TGCATTCTGGGTCCACCTTTG	0.527																																					p.D4976D		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C14928T						.						49	48	49					14																	105406860		2003	4169	6172	SO:0001819	synonymous_variant	113146	exon7			TTCTGGGTCCACC	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.14928C>T	chr14.hg19:g.105406860G>A		144.0	0.0		97.0	27.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	hg19	CCDS45177.1																																																																																			.	.		0.527	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105406860	G	A	105406860	2	1	354	1	0	0	0	0	0	0	0	1	415	1252	44	3		3	AHNAK2	14	105406860	Silent	SNP	G	TCGA-WX-AA44-01A-11D-A38X-10	23406786	105406860	1942680	68	50046										
CHD9	80205	hgsc.bcm.edu	37	chr16	53338133	53338133	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	ttctgtggaaaccaggacacTaataaaatctgagcctgtaa	8	8	2	1			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr16:53338133T>C	ENST00000398510.3	+	30	6302	c.6215T>C	c.(6214-6216)cTa>cCa	p.L2072P	CHD9_ENST00000447540.1_Missense_Mutation_p.L2072P|CHD9_ENST00000564845.1_Missense_Mutation_p.L2072P|CHD9_ENST00000566029.1_Missense_Mutation_p.L2072P			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	2072					cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				ACCAGGACACTAATAAAATCT	0.403																																					p.L2072P		Atlas-SNP	.											.	CHD9	203	.	0			c.T6215C						.						36	34	35					16																	53338133		1846	4080	5926	SO:0001583	missense	80205	exon31			GGACACTAATAAA	AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.6215T>C	chr16.hg19:g.53338133T>C	ENSP00000381522:p.Leu2072Pro	30.0	0.0		45.0	17.0	NM_025134	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Missense_Mutation	SNP	ENST00000398510.3	hg19		.	.	.	.	.	.	.	.	.	.	T	10.14	1.268789	0.23136	.	.	ENSG00000177200	ENST00000447540;ENST00000398510	T;T	0.70516	-0.49;-0.49	6.16	3.74	0.42951	.	0.300668	0.23256	N	0.050190	T	0.46737	0.1408	N	0.03608	-0.345	0.43338	D	0.995381	B;P;B;P	0.36315	0.412;0.547;0.412;0.547	B;B;B;B	0.33960	0.133;0.173;0.084;0.173	T	0.48525	-0.9028	10	0.30854	T	0.27	-3.5851	14.6633	0.68888	0.0:0.0:0.3663:0.6337	.	2072;2072;2072;2072	B7ZML1;Q3L8U1-3;Q3L8U1;Q3L8U1-2	.;.;CHD9_HUMAN;.	P	2072	ENSP00000396345:L2072P;ENSP00000381522:L2072P	ENSP00000381522:L2072P	L	+	2	0	CHD9	51895634	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.913000	0.28611	1.131000	0.42111	0.528000	0.53228	CTA	.	.		0.403	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134		C	53338133	T	C	53338133	3	2	354	1	0	0	0	0	1	0	0	0	3334	1522	53	2	6333	2	CHD9	16	53338133	Missense_Mutation	SNP	T	TCGA-WX-AA44-01A-11D-A38X-10		53338133	37016620	69	50047										
TMCO7	79613	hgsc.bcm.edu	37	chr16	69056820	69056820	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	gtgctcacagggccagcagcTtggccaaccttggggagctg	15	12	1	0			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr16:69056820T>G	ENST00000261778.1	+	16	2944	c.2932T>G	c.(2932-2934)Ttg>Gtg	p.L978V		NM_024562.1	NP_078838.1	Q9C0B7	TNG6_HUMAN	transport and golgi organization 6 homolog (Drosophila)	978						integral component of membrane (GO:0016021)											GGCCAGCAGCTTGGCCAACCT	0.512																																					p.L978V		Atlas-SNP	.											.	.	.	.	0			c.T2932G						.						42	43	43					16																	69056820		1941	4150	6091	SO:0001583	missense	79613	exon16			AGCAGCTTGGCCA		CCDS45516.1	16q22.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000103047	ENSG00000103047			25749	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 7"	TMCO7		11214970	Standard	NM_024562		Approved	FLJ12688, KIAA1746	uc002ewi.4	Q9C0B7	OTTHUMG00000176743	ENST00000261778.1:c.2932T>G	chr16.hg19:g.69056820T>G	ENSP00000261778:p.Leu978Val	90.0	0.0		47.0	17.0	NM_024562	Q569F9|Q9H9K1	Missense_Mutation	SNP	ENST00000261778.1	hg19	CCDS45516.1	.	.	.	.	.	.	.	.	.	.	T	16.49	3.137422	0.56936	.	.	ENSG00000103047	ENST00000261778	T	0.68903	-0.36	4.31	-0.476	0.12100	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.64402	D	0.000003	T	0.78566	0.4303	M	0.83774	2.66	0.44275	D	0.997134	D	0.69078	0.997	D	0.78314	0.991	T	0.76528	-0.2926	10	0.59425	D	0.04	-4.1844	9.2696	0.37664	0.0:0.5982:0.0:0.4018	.	978	Q9C0B7	TMCO7_HUMAN	V	978	ENSP00000261778:L978V	ENSP00000261778:L978V	L	+	1	2	TMCO7	67614321	1.000000	0.71417	0.945000	0.38365	0.747000	0.42532	1.820000	0.39032	-0.152000	0.11156	0.363000	0.22086	TTG	.	.		0.512	TANGO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433471.2	XM_928235.2		G	69056820	T	G	69056820	3	3	354	1	0	0	0	0	1	0	0	0	16016	1606	56	5	2994	5	TMCO7	16	69056820	Missense_Mutation	SNP	T	TCGA-WX-AA44-01A-11D-A38X-10	15718687	69056820	21297933	70	50048										
TP53	7157	hgsc.bcm.edu	37	chr17	7576928	7576928	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	ctggtgttgttgggcagtgcTaggaaagaggcaaggaaagg	18	4	0	1	rs397516439		TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr17:7576928T>C	ENST00000269305.4	-	9	1109		c.e9-2		TP53_ENST00000413465.2_Intron|TP53_ENST00000455263.2_Splice_Site|TP53_ENST00000420246.2_Splice_Site|TP53_ENST00000359597.4_Splice_Site|TP53_ENST00000445888.2_Splice_Site|TP53_ENST00000574684.1_5'Flank	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53						apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.?(28)|p.0?(8)|p.A307fs*34(1)|p.L308fs*31(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TGGGCAGTGCTAGGAAAGAGG	0.493		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											.	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,NS,carcinoma,0,37	TP53	33396	.	38	Unknown(28)|Whole gene deletion(8)|Deletion - Frameshift(2)	lung(11)|upper_aerodigestive_tract(6)|breast(5)|bone(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|urinary_tract(2)|liver(2)|large_intestine(1)|stomach(1)|gastrointestinal_tract_(site_indeterminate)(1)|ovary(1)	c.920-2A>G						.						137	124	129					17																	7576928		2203	4300	6503	SO:0001630	splice_region_variant	7157	exon10	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	CAGTGCTAGGAAA	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.920-2A>G	chr17.hg19:g.7576928T>C		195.0	0.0		81.0	40.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Splice_Site	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	8.085	0.773141	0.16051	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	.	.	.	4.71	3.58	0.41010	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.665	0.28426	0.187:0.0:0.0:0.813	.	.	.	.	.	-1	.	.	.	-	.	.	TP53	7517653	0.089000	0.21612	0.933000	0.37362	0.236000	0.25371	0.838000	0.27572	1.993000	0.58246	0.459000	0.35465	.	.	.		0.493	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	Intron	C	7576928	T	C	7576928	5	2	354	1	0	0	0	0	0	0	1	0	16396	1536	53	2	364	2	TP53	17	7576928	Splice_Site	SNP	T	TCGA-WX-AA44-01A-11D-A38X-10		7576928	73618282	71	50049										
KRT34	3885	hgsc.bcm.edu	37	chr17	39535325	39535325	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	gctccaggtcacagcggatcTctgccagctgagactccacg	11	15	2	1			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr17:39535325T>A	ENST00000394001.1	-	6	1136	c.1106A>T	c.(1105-1107)gAg>gTg	p.E369V		NM_021013.3	NP_066293.2	O76011	KRT34_HUMAN	keratin 34	369	Coil 2.|Rod.				epidermis development (GO:0008544)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Breast(137;0.000496)				ACAGCGGATCTCTGCCAGCTG	0.622																																					p.E369V		Atlas-SNP	.											.	KRT34	71	.	0			c.A1106T						.						134	113	120					17																	39535325		2203	4300	6503	SO:0001583	missense	3885	exon6			CGGATCTCTGCCA	Y16790	CCDS11390.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000131737	ENSG00000131737		"-", "Intermediate filaments type I, keratins (acidic)"	6452	protein-coding gene	gene with protein product	"hard keratin type I 4"	602763	"keratin, hair, acidic, 4"	KRTHA4		2431943, 9756910, 16831889	Standard	NM_021013		Approved	Ha-4	uc002hwm.3	O76011	OTTHUMG00000133436	ENST00000394001.1:c.1106A>T	chr17.hg19:g.39535325T>A	ENSP00000377570:p.Glu369Val	75.0	0.0		92.0	27.0	NM_021013	Q8IUT8|Q8N4W2	Missense_Mutation	SNP	ENST00000394001.1	hg19	CCDS11390.1	.	.	.	.	.	.	.	.	.	.	N	13.09	2.134600	0.37630	.	.	ENSG00000131737	ENST00000394001;ENST00000251648	D	0.92348	-3.02	5.05	5.05	0.67936	Filament (1);	0.000000	0.64402	D	0.000004	D	0.96321	0.8800	M	0.91717	3.235	0.27353	N	0.956199	D	0.76494	0.999	D	0.78314	0.991	D	0.91692	0.5367	10	0.87932	D	0	.	10.3761	0.44083	0.0:0.0803:0.0:0.9197	.	369	O76011	KRT34_HUMAN	V	327;369	ENSP00000377570:E327V	ENSP00000251648:E369V	E	-	2	0	KRT34	36788851	0.005000	0.15991	0.970000	0.41538	0.067000	0.16453	0.881000	0.28173	2.031000	0.59945	0.528000	0.53228	GAG	.	.		0.622	KRT34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257304.3	NM_021013		A	39535325	T	A	39535325	3	1	354	1	0	0	0	0	1	0	0	0	8480	1551	54	4	212	4	KRT34	17	39535325	Missense_Mutation	SNP	T	TCGA-WX-AA44-01A-11D-A38X-10	31958397	39535325	41659885	72	50050										
HOXB2	3212	hgsc.bcm.edu	37	chr17	46620596	46620596	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	agttgaggtcgggaaggaaaGgtgaatcctggcgccccgag	17	8	0	2			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr17:46620596G>T	ENST00000330070.4	-	2	2072	c.905C>A	c.(904-906)cCt>cAt	p.P302H	HOXB2_ENST00000504772.3_5'Flank|HOXB-AS1_ENST00000504972.3_RNA|HOXB-AS1_ENST00000435312.1_RNA|HOXB-AS1_ENST00000508688.1_RNA	NM_002145.3	NP_002136.1	P14652	HXB2_HUMAN	homeobox B2	302					anterior/posterior pattern specification (GO:0009952)|blood circulation (GO:0008015)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|facial nerve structural organization (GO:0021612)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|neural nucleus development (GO:0048857)|rhombomere 3 development (GO:0021569)|rhombomere 4 development (GO:0021570)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)	11						GGGAAGGAAAGGTGAATCCTG	0.692																																					p.P302H		Atlas-SNP	.											.	HOXB2	23	.	0			c.C905A						.						39	45	43					17																	46620596		2203	4300	6503	SO:0001583	missense	3212	exon2			AGGAAAGGTGAAT		CCDS11527.1	17q21.32	2012-02-22	2005-12-22		ENSG00000173917	ENSG00000173917		"Homeoboxes / ANTP class : HOXL subclass"	5113	protein-coding gene	gene with protein product		142967	"homeo box B2"	HOX2, HOX2H		1973146, 1358459	Standard	XM_005257276		Approved		uc002inm.3	P14652	OTTHUMG00000159930	ENST00000330070.4:c.905C>A	chr17.hg19:g.46620596G>T	ENSP00000331741:p.Pro302His	66.0	0.0		66.0	24.0	NM_002145	P10913|P17485	Missense_Mutation	SNP	ENST00000330070.4	hg19	CCDS11527.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.846010	0.91277	.	.	ENSG00000173917	ENST00000330070	T	0.09723	2.95	5.57	4.57	0.56435	.	0.256303	0.40064	N	0.001185	T	0.10294	0.0252	L	0.32530	0.975	0.40052	D	0.975782	B	0.28760	0.221	B	0.22386	0.039	T	0.06862	-1.0803	10	0.87932	D	0	.	15.3464	0.74340	0.0:0.0:0.8592:0.1408	.	302	P14652	HXB2_HUMAN	H	302	ENSP00000331741:P302H	ENSP00000331741:P302H	P	-	2	0	HOXB2	43975595	0.998000	0.40836	0.212000	0.23672	0.843000	0.47879	4.899000	0.63245	1.324000	0.45282	0.650000	0.86243	CCT	.	.		0.692	HOXB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358384.2			T	46620596	G	T	46620596	3	4	354	1	0	0	0	0	1	0	0	0	7310	1000	35	3	169	3	HOXB2	17	46620596	Missense_Mutation	SNP	G	TCGA-WX-AA44-01A-11D-A38X-10	7085271	46620596	34574614	73	50051										
GPR142	350383	hgsc.bcm.edu	37	chr17	72367914	72367914	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	gcgcgccttgccaccaggacCaggaggccctcctactacta	10	17	0	0			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr17:72367914C>T	ENST00000335666.4	+	4	612	c.564C>T	c.(562-564)acC>acT	p.T188T		NM_181790.1	NP_861455.1	Q7Z601	GP142_HUMAN	G protein-coupled receptor 142	188						cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(21)|ovary(2)|prostate(1)|skin(4)	35						CCACCAGGACCAGGAGGCCCT	0.637																																					p.T188T		Atlas-SNP	.											.	GPR142	74	.	0			c.C564T						.						52	46	48					17																	72367914		2203	4300	6503	SO:0001819	synonymous_variant	350383	exon4			CAGGACCAGGAGG	AY255622	CCDS11698.1	17q25.2	2012-08-21				ENSG00000257008		"GPCR / Class A : Orphans"	20088	protein-coding gene	gene with protein product		609046				14623098	Standard	NM_181790		Approved	PGR2	uc010wqy.2	Q7Z601		ENST00000335666.4:c.564C>T	chr17.hg19:g.72367914C>T		62.0	0.0		37.0	14.0	NM_181790	A4CYJ8|Q86SL3	Silent	SNP	ENST00000335666.4	hg19	CCDS11698.1																																																																																			.	.		0.637	GPR142-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442545.1	NM_181790		T	72367914	C	T	72367914	2	4	354	1	0	0	0	0	0	0	0	1	6658	581	21	3		3	GPR142	17	72367914	Silent	SNP	C	TCGA-WX-AA44-01A-11D-A38X-10	25747318	72367914	8827296	74	50052										
MEX3C	51320	hgsc.bcm.edu	37	chr18	48723154	48723154	+	Intron	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	acccccgccgccgccgccgcGgccgccgcctcccgggcatc	12	25	0	0	rs78074704|rs62092914|rs147438518		TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr18:48723154G>C	ENST00000591040.1	-	2	43				MEX3C_ENST00000592416.1_5'Flank			Q5U5Q3	MEX3C_HUMAN	mex-3 RNA binding family member C						chondrocyte hypertrophy (GO:0003415)|energy homeostasis (GO:0097009)|regulation of fat cell differentiation (GO:0045598)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(11)|ovary(1)|skin(1)	17		Colorectal(6;0.003)|all_epithelial(6;0.0473)		Colorectal(16;0.0175)|READ - Rectum adenocarcinoma(32;0.15)		ccgccgccgcggccgccgccT	0.771																																					p.A179A		Atlas-SNP	.											MEX3C_ENST00000406189,NS,carcinoma,0,1	MEX3C	77	.	0			c.C537G						.						3	3	3					18																	48723154		1139	2266	3405	SO:0001627	intron_variant	51320	exon1			CGCCGCGGCCGCC	BC041122	CCDS11951.2	18q21.1	2013-08-21	2013-08-21	2007-07-18	ENSG00000176624	ENSG00000176624		"RING-type (C3HC4) zinc fingers", "Mex-3 homologs"	28040	protein-coding gene	gene with protein product		611005	"ring finger and KH domain containing 2", "mex-3 homolog C (C. elegans)"	RKHD2		17267406	Standard	NM_016626		Approved	FLJ38871, RNF194	uc002lfc.4	Q5U5Q3	OTTHUMG00000132693	ENST00000591040.1:c.757-19208C>G	chr18.hg19:g.48723154G>C		39.0	2.0		47.0	6.0	NM_016626	A1L022|Q9NZE3	Silent	SNP	ENST00000591040.1	hg19																																																																																				.	.		0.771	MEX3C-003	KNOWN	mRNA_end_NF|basic	processed_transcript	protein_coding	OTTHUMT00000449559.1	NM_016626		C	48723154	G	C	48723154	1	2	354	0	1	0	0	0	0	0	0	0	9520	1103	39	4		4	MEX3C	18	48723154	Intron	SNP	G	TCGA-WX-AA44-01A-11D-A38X-10		48723154	29354094	75	50053										
CCDC151	115948	hgsc.bcm.edu	37	chr19	11532471	11532471	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	tagttatctgcctggggatcCagctcctttcccgcgaagcg	11	13	1	0			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr19:11532471C>G	ENST00000356392.4	-	11	1551	c.1464G>C	c.(1462-1464)ctG>ctC	p.L488L	CCDC151_ENST00000545100.1_Silent_p.L434L|CCDC151_ENST00000586836.1_Silent_p.L297L|CCDC151_ENST00000591179.1_Silent_p.L428L|RGL3_ENST00000393423.3_5'Flank|RGL3_ENST00000380456.3_5'Flank	NM_145045.4	NP_659482.3	A5D8V7	CC151_HUMAN	coiled-coil domain containing 151	488										endometrium(2)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	12						CCTGGGGATCCAGCTCCTTTC	0.667																																					p.L488L		Atlas-SNP	.											.	CCDC151	44	.	0			c.G1464C						.						54	58	56					19																	11532471		1905	4095	6000	SO:0001819	synonymous_variant	115948	exon11			GGGATCCAGCTCC		CCDS42501.1	19p13.2	2014-02-20				ENSG00000198003			28303	protein-coding gene	gene with protein product		615956				24067530	Standard	NM_145045		Approved	MGC20983	uc002mrs.3	A5D8V7		ENST00000356392.4:c.1464G>C	chr19.hg19:g.11532471C>G		104.0	0.0		77.0	34.0	NM_145045	B4DXT0|Q96CG5	Silent	SNP	ENST00000356392.4	hg19	CCDS42501.1																																																																																			.	.		0.667	CCDC151-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458800.1	NM_145045		G	11532471	C	G	11532471	2	3	354	1	0	0	0	0	0	0	0	1	2788	581	21	4		4	CCDC151	19	11532471	Silent	SNP	C	TCGA-WX-AA44-01A-11D-A38X-10		11532471	47596512	76	50054										
FAM32A	26017	hgsc.bcm.edu	37	chr19	16296481	16296481	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	aagcgaaactcctggaagcaAtgggaacgagcaaaaagaac	11	8	0	1			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr19:16296481A>G	ENST00000263384.7	+	2	146	c.121A>G	c.(121-123)Atg>Gtg	p.M41V	CTD-2562J15.4_ENST00000591038.1_RNA|FAM32A_ENST00000588367.1_Missense_Mutation_p.M41V|FAM32A_ENST00000589852.1_Missense_Mutation_p.M21V	NM_014077.2	NP_054796.1	Q9Y421	FA32A_HUMAN	family with sequence similarity 32, member A	41	Lys-rich.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			lung(1)	1						CCTGGAAGCAATGGGAACGAG	0.592											OREG0025331	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.M41V		Atlas-SNP	.											.	FAM32A	6	.	0			c.A121G						.						36	38	37					19																	16296481		2196	4279	6475	SO:0001583	missense	26017	exon2			GAAGCAATGGGAA	BC000639	CCDS12341.1	19p13.12-p13.11	2013-09-19			ENSG00000105058	ENSG00000105058			24563	protein-coding gene	gene with protein product		614554				11230166, 10810093	Standard	NM_014077		Approved	DKFZP586O0120	uc002ndt.3	Q9Y421	OTTHUMG00000182279	ENST00000263384.7:c.121A>G	chr19.hg19:g.16296481A>G	ENSP00000263384:p.Met41Val	231.0	0.0	709	159.0	43.0	NM_014077	Q9BT02	Missense_Mutation	SNP	ENST00000263384.7	hg19	CCDS12341.1	.	.	.	.	.	.	.	.	.	.	A	6.820	0.520384	0.13005	.	.	ENSG00000105058	ENST00000263384	.	.	.	3.54	3.54	0.40534	.	0.322184	0.34314	N	0.004075	T	0.24431	0.0592	N	0.16066	0.365	0.25261	N	0.989597	B	0.19445	0.036	B	0.20184	0.028	T	0.13602	-1.0503	9	0.28530	T	0.3	-41.5663	10.2853	0.43564	1.0:0.0:0.0:0.0	.	41	Q9Y421	FA32A_HUMAN	V	41	.	ENSP00000263384:M41V	M	+	1	0	FAM32A	16157481	1.000000	0.71417	0.998000	0.56505	0.914000	0.54420	4.574000	0.60900	1.620000	0.50308	0.456000	0.33151	ATG	.	.		0.592	FAM32A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460346.1	NM_014077		G	16296481	A	G	16296481	3	3	354	1	0	0	0	0	1	0	0	0	5560	101	4	2	127	2	FAM32A	19	16296481	Missense_Mutation	SNP	A	TCGA-WX-AA44-01A-11D-A38X-10	4764010	16296481	42832502	77	50055										
DPY19L3	147991	hgsc.bcm.edu	37	chr19	32968508	32968508	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	gctgtgcacgggaaggacccTaaccaaccacccgcactatg	10	15	0	0			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr19:32968508T>A	ENST00000342179.5	+	17	1993	c.1778T>A	c.(1777-1779)cTa>cAa	p.L593Q	DPY19L3_ENST00000586987.1_Missense_Mutation_p.L593Q|DPY19L3_ENST00000392250.2_Missense_Mutation_p.L593Q	NM_207325.2	NP_997208.2	Q6ZPD9	D19L3_HUMAN	dpy-19-like 3 (C. elegans)	593						integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(17)|ovary(4)|pancreas(1)	32	Esophageal squamous(110;0.162)					GGAAGGACCCTAACCAACCAC	0.577																																					p.L593Q		Atlas-SNP	.											.	DPY19L3	70	.	0			c.T1778A						.						129	109	116					19																	32968508		2203	4300	6503	SO:0001583	missense	147991	exon17			GGACCCTAACCAA		CCDS12422.1	19q13.11	2008-02-05				ENSG00000178904			27120	protein-coding gene	gene with protein product		613894					Standard	NM_207325		Approved		uc002ntg.3	Q6ZPD9		ENST00000342179.5:c.1778T>A	chr19.hg19:g.32968508T>A	ENSP00000344937:p.Leu593Gln	88.0	0.0		113.0	36.0	NM_001172774	Q68DC7|Q6ZTB7|Q6ZTS2	Missense_Mutation	SNP	ENST00000342179.5	hg19	CCDS12422.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.848505	0.91277	.	.	ENSG00000178904	ENST00000392250;ENST00000342179	T;T	0.58060	0.36;0.36	5.4	5.4	0.78164	.	0.000000	0.64402	D	0.000008	T	0.72526	0.3471	M	0.74258	2.255	0.49798	D	0.999823	D	0.89917	1.0	D	0.91635	0.999	T	0.76537	-0.2923	10	0.87932	D	0	-2.0715	15.4079	0.74893	0.0:0.0:0.0:1.0	.	593	Q6ZPD9	D19L3_HUMAN	Q	593	ENSP00000376081:L593Q;ENSP00000344937:L593Q	ENSP00000344937:L593Q	L	+	2	0	DPY19L3	37660348	0.999000	0.42202	0.598000	0.28837	0.945000	0.59286	8.040000	0.89188	2.046000	0.60703	0.460000	0.39030	CTA	.	.		0.577	DPY19L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450311.1	NM_207325		A	32968508	T	A	32968508	3	1	354	1	0	0	0	0	1	0	0	0	4744	1522	53	4	1840	4	DPY19L3	19	32968508	Missense_Mutation	SNP	T	TCGA-WX-AA44-01A-11D-A38X-10	16672027	32968508	26160475	78	50056										
LRFN1	57622	hgsc.bcm.edu	37	chr19	39805160	39805160	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	ttcgggcgtggcgcaggtctCtaagtcgtcctcgcgggtca	15	12	2	0			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr19:39805160C>A	ENST00000248668.4	-	1	816	c.817G>T	c.(817-819)Gag>Tag	p.E273*	CTC-246B18.8_ENST00000601911.1_RNA	NM_020862.1	NP_065913.1	Q9P244	LRFN1_HUMAN	leucine rich repeat and fibronectin type III domain containing 1	273	LRRCT.					cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				central_nervous_system(2)|cervix(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	18	all_cancers(60;1.85e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;1.96e-27)|all cancers(26;2.05e-24)|Lung(45;0.000278)|LUSC - Lung squamous cell carcinoma(53;0.000335)			GCGCAGGTCTCTAAGTCGTCC	0.687																																					p.E273X		Atlas-SNP	.											.	LRFN1	59	.	0			c.G817T						.						22	29	26					19																	39805160		2192	4290	6482	SO:0001587	stop_gained	57622	exon1			AGGTCTCTAAGTC	BC014678	CCDS46071.1	19q13.2	2013-02-11				ENSG00000128011		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	29290	protein-coding gene	gene with protein product		612807				10819331, 16828986	Standard	NM_020862		Approved	KIAA1484, SALM2	uc002okw.2	Q9P244		ENST00000248668.4:c.817G>T	chr19.hg19:g.39805160C>A	ENSP00000248668:p.Glu273*	105.0	0.0		52.0	11.0	NM_020862	Q8TBS9	Nonsense_Mutation	SNP	ENST00000248668.4	hg19	CCDS46071.1	.	.	.	.	.	.	.	.	.	.	C	34	5.351134	0.95830	.	.	ENSG00000128011	ENST00000248668	.	.	.	4.3	4.3	0.51218	.	0.000000	0.44097	D	0.000499	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	.	14.2826	0.66224	0.0:1.0:0.0:0.0	.	.	.	.	X	273	.	ENSP00000248668:E273X	E	-	1	0	LRFN1	44497000	1.000000	0.71417	1.000000	0.80357	0.699000	0.40488	7.610000	0.82949	2.234000	0.73211	0.491000	0.48974	GAG	.	.		0.687	LRFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463835.1	NM_020862		A	39805160	C	A	39805160	4	1	354	1	0	0	0	0	0	1	0	0	8946	922	32	3	1506	3	LRFN1	19	39805160	Nonsense_Mutation	SNP	C	TCGA-WX-AA44-01A-11D-A38X-10	6836652	39805160	19323823	79	50057										
CLC	1178	hgsc.bcm.edu	37	chr19	40225044	40225044	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	cacggctgttcatgaccacaCgacgaccaaagcacacttgg	9	14	1	1	rs140514392	byFrequency	TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr19:40225044C>T	ENST00000221804.4	-	3	257	c.182G>A	c.(181-183)cGt>cAt	p.R61H		NM_001828.5	NP_001819.2	Q05315	LEG10_HUMAN	Charcot-Leyden crystal galectin	61	Galectin. {ECO:0000255|PROSITE- ProRule:PRU00639}.				multicellular organismal development (GO:0007275)|regulation of activated T cell proliferation (GO:0046006)|regulation of T cell anergy (GO:0002667)|regulation of T cell cytokine production (GO:0002724)|T cell apoptotic process (GO:0070231)	cytosol (GO:0005829)	carbohydrate binding (GO:0030246)|cysteine-type endopeptidase activity involved in apoptotic process (GO:0097153)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(2)|stomach(1)	12	all_cancers(60;2.99e-06)|all_lung(34;4.7e-08)|Lung NSC(34;5.46e-08)|Ovarian(47;0.06)	Renal(1328;0.000147)|Hepatocellular(1079;0.0202)|Myeloproliferative disorder(2;0.0255)	Epithelial(26;6.43e-25)|OV - Ovarian serous cystadenocarcinoma(5;1.07e-24)|all cancers(26;8.38e-23)	GBM - Glioblastoma multiforme(1328;4.97e-06)|STAD - Stomach adenocarcinoma(1328;0.00655)		CATGACCACACGACGACCAAA	0.488																																					p.R61H		Atlas-SNP	.											.	CLC	20	.	0			c.G182A						.						234	195	208					19																	40225044		2203	4300	6503	SO:0001583	missense	1178	exon3			ACCACACGACGAC	L01664	CCDS33025.1	19q13.1	2013-06-12	2013-06-12		ENSG00000105205	ENSG00000105205		"Lectins, galactoside-binding"	2014	protein-coding gene	gene with protein product	"eosinophil lysophospholipase", "lysolecithin acylhydrolase", "galectin 10", "lectin, galactoside-binding, soluble, 10"	153310	"Charcot-Leyden crystal protein"			1577491, 11834744	Standard	NM_001828		Approved	LGALS10, MGC149659, Gal-10	uc002omh.3	Q05315		ENST00000221804.4:c.182G>A	chr19.hg19:g.40225044C>T	ENSP00000221804:p.Arg61His	74.0	0.0		78.0	31.0	NM_001828	C5HZ13|C5HZ14|Q0VDE3	Missense_Mutation	SNP	ENST00000221804.4	hg19	CCDS33025.1	.	.	.	.	.	.	.	.	.	.	.	0.064	-1.217737	0.01542	.	.	ENSG00000105205	ENST00000221804	T	0.05513	3.43	1.3	-2.6	0.06190	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	.	.	.	.	T	0.03434	0.0099	N	0.25647	0.755	0.09310	N	1	B	0.06786	0.001	B	0.13407	0.009	T	0.47522	-0.9111	9	0.15499	T	0.54	.	2.7047	0.05159	0.0:0.3035:0.2606:0.4359	.	61	Q05315	LPPL_HUMAN	H	61	ENSP00000221804:R61H	ENSP00000221804:R61H	R	-	2	0	CLC	44916884	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.490000	0.00453	-1.016000	0.03371	-0.704000	0.03662	CGT	.	C|0.999;A|0.001		0.488	CLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465225.1	NM_001828		T	40225044	C	T	40225044	3	4	354	1	0	0	0	0	1	0	0	0	3458	536	19	1	254	1	CLC	19	40225044	Missense_Mutation	SNP	C	TCGA-WX-AA44-01A-11D-A38X-10	419884	40225044	18903939	80	50058										
ZNF229	7772	hgsc.bcm.edu	37	chr19	44934548	44934548	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	cacccttgatggggagcagcAtcttctgagaactggaagtc	12	10	2	2			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr19:44934548A>G	ENST00000588931.1	-	6	841	c.408T>C	c.(406-408)gaT>gaC	p.D136D	CTC-512J12.4_ENST00000588655.1_RNA|ZNF229_ENST00000591289.1_Intron|ZNF229_ENST00000291187.4_Silent_p.D130D	NM_014518.2	NP_055333.2	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	136					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|central_nervous_system(2)|endometrium(6)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	45		Prostate(69;0.0352)				GGGGAGCAGCATCTTCTGAGA	0.488																																					p.D136D		Atlas-SNP	.											.	ZNF229	123	.	0			c.T408C						.						110	105	107					19																	44934548		1885	4105	5990	SO:0001819	synonymous_variant	7772	exon6			AGCAGCATCTTCT	AF192979	CCDS42574.1, CCDS62706.1	19q13.2	2013-01-08				ENSG00000278318		"Zinc fingers, C2H2-type", "-"	13022	protein-coding gene	gene with protein product							Standard	XM_006723372		Approved		uc002oze.1	Q9UJW7		ENST00000588931.1:c.408T>C	chr19.hg19:g.44934548A>G		66.0	0.0		80.0	24.0	NM_014518	B2RWN3|Q59FV2|Q86WL9	Silent	SNP	ENST00000588931.1	hg19	CCDS42574.1																																																																																			.	.		0.488	ZNF229-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460833.1	NM_014518		G	44934548	A	G	44934548	2	3	354	1	0	0	0	0	0	0	0	1	17797	214	8	2		2	ZNF229	19	44934548	Silent	SNP	A	TCGA-WX-AA44-01A-11D-A38X-10	4709504	44934548	14194435	81	50059										
ZNF766	90321	hgsc.bcm.edu	37	chr19	52794386	52794386	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	gccatgtgtgtggtaaggtcTttaggcacagttcatggttt	13	6	2	0			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr19:52794386T>G	ENST00000439461.1	+	4	1385	c.1342T>G	c.(1342-1344)Ttt>Gtt	p.F448V	ZNF766_ENST00000593612.1_Intron|ZNF766_ENST00000599581.1_3'UTR|CTD-2525I3.5_ENST00000594865.1_RNA|ZNF766_ENST00000359102.4_Intron	NM_001010851.2	NP_001010851.1	Q5HY98	ZN766_HUMAN	zinc finger protein 766	448					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	17				GBM - Glioblastoma multiforme(134;0.00236)|OV - Ovarian serous cystadenocarcinoma(262;0.00871)		TGGTAAGGTCTTTAGGCACAG	0.413																																					p.F448V		Atlas-SNP	.											.	ZNF766	45	.	0			c.T1342G						.						142	149	147					19																	52794386		2202	4299	6501	SO:0001583	missense	90321	exon4			AAGGTCTTTAGGC	AK024074	CCDS46163.1	19q13.33	2013-01-08				ENSG00000196214		"Zinc fingers, C2H2-type", "-"	28063	protein-coding gene	gene with protein product							Standard	XM_006723458		Approved		uc002pyr.1	Q5HY98		ENST00000439461.1:c.1342T>G	chr19.hg19:g.52794386T>G	ENSP00000409652:p.Phe448Val	118.0	0.0		125.0	39.0	NM_001010851	B2RNE0|Q7Z326	Missense_Mutation	SNP	ENST00000439461.1	hg19	CCDS46163.1	.	.	.	.	.	.	.	.	.	.	T	15.00	2.702212	0.48307	.	.	ENSG00000196214	ENST00000439461	T	0.46063	0.88	2.17	2.17	0.27698	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.67748	0.2926	M	0.91561	3.22	0.80722	D	1	P	0.39940	0.696	P	0.62885	0.908	T	0.70525	-0.4848	9	0.87932	D	0	.	9.0249	0.36222	0.0:0.0:0.0:1.0	.	448	Q5HY98	ZN766_HUMAN	V	448	ENSP00000409652:F448V	ENSP00000409652:F448V	F	+	1	0	ZNF766	57486198	0.936000	0.31750	0.003000	0.11579	0.003000	0.03518	4.085000	0.57657	0.981000	0.38548	0.491000	0.48974	TTT	.	.		0.413	ZNF766-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462764.1	NM_001010851		G	52794386	T	G	52794386	3	3	354	1	0	0	0	0	1	0	0	0	18155	1609	56	5	1356	5	ZNF766	19	52794386	Missense_Mutation	SNP	T	TCGA-WX-AA44-01A-11D-A38X-10	7859838	52794386	6334597	82	50060										
NLRP13	126204	hgsc.bcm.edu	37	chr19	56424387	56424387	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	tttatggcagctgagatagaAaacataggagaacctttgct	10	6	0	3			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr19:56424387A>C	ENST00000342929.3	-	5	795	c.796T>G	c.(796-798)Ttc>Gtc	p.F266V	NLRP13_ENST00000588751.1_Missense_Mutation_p.F266V	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	266	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.						ATP binding (GO:0005524)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(58)|ovary(4)|pancreas(2)|prostate(2)|skin(13)|stomach(2)|urinary_tract(1)	109		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)		CTGAGATAGAAAACATAGGAG	0.468																																					p.F266V		Atlas-SNP	.											.	NLRP13	220	.	0			c.T796G						.						64	68	67					19																	56424387		2203	4300	6503	SO:0001583	missense	126204	exon5			GATAGAAAACATA	AY154468	CCDS33119.1	19q13.43	2008-02-05	2006-12-08	2006-12-08	ENSG00000173572	ENSG00000173572		"Nucleotide-binding domain and leucine rich repeat containing"	22937	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 13"	609660	"NACHT, leucine rich repeat and PYD containing 13"	NALP13		12563287	Standard	NM_176810		Approved	NOD14, PAN13, CLR19.7	uc010ygg.2	Q86W25	OTTHUMG00000167839	ENST00000342929.3:c.796T>G	chr19.hg19:g.56424387A>C	ENSP00000343891:p.Phe266Val	112.0	0.0		102.0	28.0	NM_176810	Q7RTR5	Missense_Mutation	SNP	ENST00000342929.3	hg19	CCDS33119.1	.	.	.	.	.	.	.	.	.	.	A	13.03	2.114372	0.37339	.	.	ENSG00000173572	ENST00000342929	D	0.87334	-2.24	2.81	2.81	0.32909	NACHT nucleoside triphosphatase (1);	.	.	.	.	D	0.91147	0.7212	M	0.69248	2.105	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80830	-0.1207	9	0.87932	D	0	.	7.7212	0.28733	1.0:0.0:0.0:0.0	.	266	Q86W25	NAL13_HUMAN	V	266	ENSP00000343891:F266V	ENSP00000343891:F266V	F	-	1	0	NLRP13	61116199	0.997000	0.39634	0.026000	0.17262	0.003000	0.03518	4.794000	0.62482	1.271000	0.44313	0.482000	0.46254	TTC	.	.		0.468	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810		C	56424387	A	C	56424387	3	2	354	1	0	0	0	0	1	0	0	0	10484	14	1	5	2361	5	NLRP13	19	56424387	Missense_Mutation	SNP	A	TCGA-WX-AA44-01A-11D-A38X-10	3630001	56424387	2704596	83	50061										
ZNF582	147948	hgsc.bcm.edu	37	chr19	56895920	56895920	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	agatccgattgaaggccttgCcacattccttacactgatag	8	11	0	3			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr19:56895920C>A	ENST00000301310.4	-	5	1024	c.866G>T	c.(865-867)gGc>gTc	p.G289V	AC006116.12_ENST00000589671.1_RNA|ZNF582_ENST00000586929.1_Missense_Mutation_p.G289V	NM_144690.1	NP_653291.1	Q96NG8	ZN582_HUMAN	zinc finger protein 582	289					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0547)		GAAGGCCTTGCCACATTCCTT	0.413																																					p.G289V	Ovarian(183;1887 2032 4349 30507 51343)	Atlas-SNP	.											.	ZNF582	56	.	0			c.G866T						.						72	62	65					19																	56895920		2203	4300	6503	SO:0001583	missense	147948	exon5			GCCTTGCCACATT	AK055489	CCDS33121.1	19q13.43	2013-07-15			ENSG00000018869	ENSG00000018869		"Zinc fingers, C2H2-type", "-"	26421	protein-coding gene	gene with protein product		615600				12477932	Standard	NM_144690		Approved	FLJ30927	uc002qmz.1	Q96NG8	OTTHUMG00000181939	ENST00000301310.4:c.866G>T	chr19.hg19:g.56895920C>A	ENSP00000301310:p.Gly289Val	55.0	0.0		74.0	25.0	NM_144690	B4DQZ9|B7Z9R3|Q6PJT6	Missense_Mutation	SNP	ENST00000301310.4	hg19	CCDS33121.1	.	.	.	.	.	.	.	.	.	.	C	16.80	3.222858	0.58668	.	.	ENSG00000018869	ENST00000301310	T	0.01495	4.83	4.88	0.258	0.15578	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.431973	0.17275	N	0.180205	T	0.11537	0.0281	H	0.95187	3.635	0.44780	D	0.997788	D;D	0.76494	0.999;0.998	D;D	0.68483	0.958;0.914	T	0.00792	-1.1564	10	0.87932	D	0	.	5.9047	0.18986	0.0:0.6153:0.1392:0.2454	.	289;320	Q96NG8;B4DQZ9	ZN582_HUMAN;.	V	289	ENSP00000301310:G289V	ENSP00000301310:G289V	G	-	2	0	ZNF582	61587732	0.969000	0.33509	0.009000	0.14445	0.022000	0.10575	2.395000	0.44459	0.053000	0.16036	-0.140000	0.14226	GGC	.	.		0.413	ZNF582-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458387.2	NM_144690		A	56895920	C	A	56895920	3	1	354	1	0	0	0	0	1	0	0	0	18029	739	26	3	691	3	ZNF582	19	56895920	Missense_Mutation	SNP	C	TCGA-WX-AA44-01A-11D-A38X-10	471533	56895920	2233063	84	50062										
SNX5	27131	hgsc.bcm.edu	37	chr20	17934754	17934754	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	agtcgggcttcgtaggagcaGgtggaatctgcagcagaggc	17	8	1	1	rs6045116		TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr20:17934754G>C	ENST00000377768.3	-	5	587	c.275C>G	c.(274-276)cCt>cGt	p.P92R	SNX5_ENST00000377759.4_Missense_Mutation_p.P92R|SNX5_ENST00000483485.1_5'UTR	NM_152227.1	NP_689413.1	Q9Y5X3	SNX5_HUMAN	sorting nexin 5	92	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				intracellular protein transport (GO:0006886)|pinocytosis (GO:0006907)	cytoplasmic vesicle (GO:0031410)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|extrinsic component of endosome membrane (GO:0031313)|macropinocytic cup (GO:0070685)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	11						CGTAGGAGCAGGTGGAATCTG	0.502																																					p.P92R		Atlas-SNP	.											.	SNX5	38	.	0			c.C275G						.						105	101	102					20																	17934754		2203	4300	6503	SO:0001583	missense	27131	exon4			GGAGCAGGTGGAA	AF121855	CCDS13130.1	20p11	2008-05-22			ENSG00000089006	ENSG00000089006		"Sorting nexins"	14969	protein-coding gene	gene with protein product		605937				10600472, 17148574	Standard	NM_152227		Approved		uc002wqc.3	Q9Y5X3	OTTHUMG00000031953	ENST00000377768.3:c.275C>G	chr20.hg19:g.17934754G>C	ENSP00000366998:p.Pro92Arg	54.0	0.0		52.0	18.0	NM_014426	B7ZKN3|D3DW26|Q52LC4|Q7KZN0|Q9BWP0	Missense_Mutation	SNP	ENST00000377768.3	hg19	CCDS13130.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.920699	0.92249	.	.	ENSG00000089006	ENST00000377768;ENST00000377759;ENST00000431277;ENST00000419004	T;T;T;T	0.44083	0.93;0.93;0.93;0.93	5.6	5.6	0.85130	Phox homologous domain (5);	0.000000	0.85682	D	0.000000	T	0.80082	0.4558	H	0.98594	4.275	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.87407	0.2373	10	0.87932	D	0	-2.9516	19.9784	0.97317	0.0:0.0:1.0:0.0	.	113;92	B7Z476;Q9Y5X3	.;SNX5_HUMAN	R	92;92;55;57	ENSP00000366998:P92R;ENSP00000366988:P92R;ENSP00000404448:P55R;ENSP00000406731:P57R	ENSP00000366988:P92R	P	-	2	0	SNX5	17882754	1.000000	0.71417	0.968000	0.41197	0.923000	0.55619	9.787000	0.99055	2.800000	0.96347	0.455000	0.32223	CCT	.	.		0.502	SNX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078137.4			C	17934754	G	C	17934754	3	2	354	1	0	0	0	0	1	0	0	0	14920	1000	35	4	979	4	SNX5	20	17934754	Missense_Mutation	SNP	G	TCGA-WX-AA44-01A-11D-A38X-10		17934754	45090766	85	50063										
CDH26	60437	hgsc.bcm.edu	37	chr20	58564168	58564168	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	aaagaggagggcgccaggccTgggaccctgttgggaacttt	16	9	0	1			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chr20:58564168T>C	ENST00000244047.5	+	9	1544	c.1233T>C	c.(1231-1233)ccT>ccC	p.P411P	CDH26_ENST00000348616.4_Silent_p.P411P			Q8IXH8	CAD26_HUMAN	cadherin 26	411	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(11)|lung(14)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	44	all_lung(29;0.00963)		BRCA - Breast invasive adenocarcinoma(7;5.58e-09)			GCGCCAGGCCTGGGACCCTGT	0.552																																					p.P411P		Atlas-SNP	.											.	CDH26	229	.	0			c.T1233C						.						149	178	168					20																	58564168		2203	4300	6503	SO:0001819	synonymous_variant	60437	exon9			CAGGCCTGGGACC	AF169690, AK055202	CCDS13485.1, CCDS13486.1	20q13.33	2010-01-26	2009-11-20		ENSG00000124215	ENSG00000124215		"Cadherins / Major cadherins"	15902	protein-coding gene	gene with protein product			"cadherin-like 26"				Standard	NM_177980		Approved	VR20	uc002ybe.3	Q8IXH8	OTTHUMG00000032874	ENST00000244047.5:c.1233T>C	chr20.hg19:g.58564168T>C		89.0	0.0		104.0	36.0	NM_177980	A2A2M5|B3KNX3|Q6P5Y6|Q8TCH3|Q9BQN4|Q9NRU1	Silent	SNP	ENST00000244047.5	hg19		.	.	.	.	.	.	.	.	.	.	T	7.768	0.706872	0.15239	.	.	ENSG00000124215	ENST00000370991	.	.	.	5.06	-9.48	0.00591	.	.	.	.	.	T	0.31295	0.0792	.	.	.	0.48901	D	0.999721	.	.	.	.	.	.	T	0.39396	-0.9616	4	.	.	.	.	0.5394	0.00642	0.2141:0.2734:0.2199:0.2926	.	.	.	.	P	3	.	.	L	+	2	0	CDH26	57997563	0.012000	0.17670	0.001000	0.08648	0.055000	0.15305	-1.518000	0.02246	-2.180000	0.00766	0.533000	0.62120	CTG	.	.		0.552	CDH26-201	KNOWN	basic	protein_coding	protein_coding		NM_177980		C	58564168	T	C	58564168	2	2	354	1	0	0	0	0	0	0	0	1	3112	1567	55	2		2	CDH26	20	58564168	Silent	SNP	T	TCGA-WX-AA44-01A-11D-A38X-10	40629414	58564168	4461352	86	50064										
ITGB1BP2	26548	hgsc.bcm.edu	37	chrX	70524435	70524435	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	tggtaaccgtgtgttccaagCacagatgaagctctgggggg	15	8	1	2			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chrX:70524435C>A	ENST00000373829.3	+	10	870	c.797C>A	c.(796-798)gCa>gAa	p.A266E	ITGB1BP2_ENST00000465388.1_3'UTR|ITGB1BP2_ENST00000538820.1_Missense_Mutation_p.A248E	NM_012278.1	NP_036410.1	Q9UKP3	ITBP2_HUMAN	integrin beta 1 binding protein (melusin) 2	266	CS. {ECO:0000255|PROSITE- ProRule:PRU00547}.				muscle organ development (GO:0007517)|signal transduction (GO:0007165)	Z disc (GO:0030018)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			breast(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)	14	Renal(35;0.156)					GTGTTCCAAGCACAGATGAAG	0.488																																					p.A266E		Atlas-SNP	.											.	ITGB1BP2	35	.	0			c.C797A						.						122	97	106					X																	70524435		2203	4300	6503	SO:0001583	missense	26548	exon10			TCCAAGCACAGAT	AF140690	CCDS14411.1	Xq12.1-q13	2008-02-05			ENSG00000147166	ENSG00000147166			6154	protein-coding gene	gene with protein product		300332				10506186	Standard	XM_005262255		Approved	CHORDC3	uc004dzr.1	Q9UKP3	OTTHUMG00000021793	ENST00000373829.3:c.797C>A	chrX.hg19:g.70524435C>A	ENSP00000362935:p.Ala266Glu	41.0	0.0		37.0	11.0	NM_012278	Q32N04|Q549J7	Missense_Mutation	SNP	ENST00000373829.3	hg19	CCDS14411.1	.	.	.	.	.	.	.	.	.	.	C	0.578	-0.838456	0.02692	.	.	ENSG00000147166	ENST00000373829;ENST00000538820	T;T	0.14266	2.52;2.52	5.11	3.13	0.36017	CS-like domain (1);CS domain (1);HSP20-like chaperone (1);	0.399250	0.28414	N	0.015437	T	0.06096	0.0158	N	0.08118	0	0.32429	N	0.548342	B;B	0.18013	0.025;0.025	B;B	0.18561	0.022;0.022	T	0.24728	-1.0152	10	0.15499	T	0.54	-0.6733	8.6763	0.34181	0.4465:0.5535:0.0:0.0	.	248;266	Q32N04;Q9UKP3	.;ITBP2_HUMAN	E	266;248	ENSP00000362935:A266E;ENSP00000440289:A248E	ENSP00000362935:A266E	A	+	2	0	ITGB1BP2	70441160	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.088000	0.30877	1.088000	0.41272	0.513000	0.50165	GCA	.	.		0.488	ITGB1BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057126.1	NM_012278		A	70524435	C	A	70524435	3	1	354	1	0	0	0	0	1	0	0	0	7901	710	25	3	835	3	ITGB1BP2	23	70524435	Missense_Mutation	SNP	C	TCGA-WX-AA44-01A-11D-A38X-10		70524435	84746125	87	50065										
CDX4	1046	hgsc.bcm.edu	37	chrX	72667261	72667261	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	cgcactatatggggtatcctCatatgcccagcatggatcct	9	12	1	0	rs373883804		TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chrX:72667261C>A	ENST00000373514.2	+	1	172	c.172C>A	c.(172-174)Cat>Aat	p.H58N		NM_005193.1	NP_005184.1	O14627	CDX4_HUMAN	caudal type homeobox 4	58					anterior/posterior pattern specification (GO:0009952)|blood vessel development (GO:0001568)|labyrinthine layer development (GO:0060711)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			endometrium(4)|kidney(1)|large_intestine(1)|lung(11)|skin(1)	18	Renal(35;0.156)					GGGGTATCCTCATATGCCCAG	0.637																																					p.H58N		Atlas-SNP	.											.	CDX4	52	.	0			c.C172A						.						50	43	45					X																	72667261		2203	4300	6503	SO:0001583	missense	1046	exon1			TATCCTCATATGC	AF029879	CCDS14424.1	Xq13.2	2012-03-09	2007-07-09		ENSG00000131264	ENSG00000131264		"Homeoboxes / ANTP class : HOXL subclass"	1808	protein-coding gene	gene with protein product		300025	"caudal type homeo box transcription factor 4"			7655457	Standard	NM_005193		Approved		uc011mqk.2	O14627	OTTHUMG00000021831	ENST00000373514.2:c.172C>A	chrX.hg19:g.72667261C>A	ENSP00000362613:p.His58Asn	117.0	0.0		123.0	34.0	NM_005193	A1A513|Q5JS20	Missense_Mutation	SNP	ENST00000373514.2	hg19	CCDS14424.1	.	.	.	.	.	.	.	.	.	.	.	12.92	2.083806	0.36758	.	.	ENSG00000131264	ENST00000373514	T	0.50548	0.74	2.57	2.57	0.30868	Caudal-like activation domain (1);	0.000000	0.85682	D	0.000000	T	0.66177	0.2763	M	0.83118	2.625	0.58432	D	0.999993	D	0.69078	0.997	D	0.77004	0.989	T	0.67677	-0.5609	10	0.40728	T	0.16	-10.0391	10.3983	0.44214	0.0:1.0:0.0:0.0	.	58	O14627	CDX4_HUMAN	N	58	ENSP00000362613:H58N	ENSP00000362613:H58N	H	+	1	0	CDX4	72583986	1.000000	0.71417	0.522000	0.27862	0.074000	0.17049	5.939000	0.70179	1.561000	0.49584	0.436000	0.28706	CAT	.	.		0.637	CDX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057229.2	NM_005193		A	72667261	C	A	72667261	3	1	354	1	0	0	0	0	1	0	0	0	3186	826	29	3	174	3	CDX4	23	72667261	Missense_Mutation	SNP	C	TCGA-WX-AA44-01A-11D-A38X-10	2142826	72667261	82603299	88	50066										
USP26	83844	hgsc.bcm.edu	37	chrX	132160217	132160217	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	gagaggtgtgcctgggctgcTggcaggtttacctccagctt	15	10	0	1			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chrX:132160217T>A	ENST00000511190.1	-	6	2501	c.2032A>T	c.(2032-2034)Agc>Tgc	p.S678C	USP26_ENST00000370832.1_Missense_Mutation_p.S678C|USP26_ENST00000406273.1_Missense_Mutation_p.S678C	NM_031907.1	NP_114113.1	Q9BXU7	UBP26_HUMAN	ubiquitin specific peptidase 26	678	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(3)	60	Acute lymphoblastic leukemia(192;0.000127)					CCTGGGCTGCTGGCAGGTTTA	0.418																																					p.S678C	NSCLC(104;342 1621 36940 47097 52632)	Atlas-SNP	.											.	USP26	135	.	0			c.A2032T						.						83	79	80					X																	132160217		2203	4299	6502	SO:0001583	missense	83844	exon1			GGCTGCTGGCAGG	AF285593	CCDS14635.1	Xq26.2	2012-07-13	2005-08-08		ENSG00000134588	ENSG00000134588	3.4.19.12	"Ubiquitin-specific peptidases"	13485	protein-coding gene	gene with protein product		300309	"ubiquitin specific protease 26"			12838346	Standard	NM_031907		Approved		uc011mvf.2	Q9BXU7	OTTHUMG00000022429	ENST00000511190.1:c.2032A>T	chrX.hg19:g.132160217T>A	ENSP00000423390:p.Ser678Cys	77.0	0.0		91.0	30.0	NM_031907	B9WRT6|Q5H9H4	Missense_Mutation	SNP	ENST00000511190.1	hg19	CCDS14635.1	.	.	.	.	.	.	.	.	.	.	T	13.73	2.324474	0.41197	.	.	ENSG00000134588	ENST00000370832;ENST00000511190;ENST00000406273	T;T;T	0.61859	0.07;0.07;0.07	3.76	-0.233	0.13078	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.190917	0.25792	N	0.028280	T	0.63651	0.2529	M	0.62723	1.935	0.09310	N	1	D	0.89917	1.0	D	0.85130	0.997	T	0.54214	-0.8327	10	0.87932	D	0	-3.6931	1.5307	0.02535	0.1716:0.1053:0.1742:0.5488	.	678	Q9BXU7	UBP26_HUMAN	C	678	ENSP00000359869:S678C;ENSP00000423390:S678C;ENSP00000384360:S678C	ENSP00000359869:S678C	S	-	1	0	USP26	131987883	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.101000	0.15251	-0.125000	0.11703	-0.314000	0.08810	AGC	.	.		0.418	USP26-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359441.1	NM_031907		A	132160217	T	A	132160217	3	1	354	1	0	0	0	0	1	0	0	0	17072	1580	55	4	712	4	USP26	23	132160217	Missense_Mutation	SNP	T	TCGA-WX-AA44-01A-11D-A38X-10	59492956	132160217	23110343	89	50067										
SLITRK4	139065	hgsc.bcm.edu	37	chrX	142717487	142717487	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	ctttaggagattattgtttaAgtacagtaactgcaaatttg	8	4	0	1			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chrX:142717487A>C	ENST00000381779.4	-	2	1663	c.1438T>G	c.(1438-1440)Tta>Gta	p.L480V	SLITRK4_ENST00000338017.4_Missense_Mutation_p.L480V|SLITRK4_ENST00000356928.1_Missense_Mutation_p.L480V	NM_001184749.2|NM_001184750.1|NM_173078.4	NP_001171678.1|NP_001171679.1|NP_775101.1	Q8IW52	SLIK4_HUMAN	SLIT and NTRK-like family, member 4	480						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(27)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	60	Acute lymphoblastic leukemia(192;6.56e-05)					TTATTGTTTAAGTACAGTAAC	0.408																																					p.L480V		Atlas-SNP	.											.	SLITRK4	162	.	0			c.T1438G						.						71	77	75					X																	142717487		2203	4300	6503	SO:0001583	missense	139065	exon2			TGTTTAAGTACAG	BC040986	CCDS14679.1	Xq27.3	2004-06-23			ENSG00000179542	ENSG00000179542			23502	protein-coding gene	gene with protein product		300562				14557068	Standard	NM_001184749		Approved	DKFZp547M2010	uc004fby.3	Q8IW52	OTTHUMG00000022580	ENST00000381779.4:c.1438T>G	chrX.hg19:g.142717487A>C	ENSP00000371198:p.Leu480Val	175.0	0.0		226.0	59.0	NM_001184750	Q5JXG3|Q8TCM8|Q96DL3	Missense_Mutation	SNP	ENST00000381779.4	hg19	CCDS14679.1	.	.	.	.	.	.	.	.	.	.	A	14.41	2.528030	0.44969	.	.	ENSG00000179542	ENST00000381779;ENST00000356928;ENST00000338017	T;T;T	0.74842	-0.88;-0.88;-0.88	5.49	1.5	0.22942	.	0.000000	0.64402	D	0.000001	T	0.81460	0.4827	M	0.70903	2.155	0.58432	D	0.999997	D	0.89917	1.0	D	0.97110	1.0	T	0.78553	-0.2160	10	0.62326	D	0.03	-5.0587	6.6644	0.23032	0.4439:0.0:0.5561:0.0	.	480	Q8IW52	SLIK4_HUMAN	V	480	ENSP00000371198:L480V;ENSP00000349400:L480V;ENSP00000336627:L480V	ENSP00000336627:L480V	L	-	1	2	SLITRK4	142545153	1.000000	0.71417	0.978000	0.43139	0.928000	0.56348	1.098000	0.31000	0.321000	0.23259	0.486000	0.48141	TTA	.	.		0.408	SLITRK4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058617.1	NM_173078		C	142717487	A	C	142717487	3	2	354	1	0	0	0	0	1	0	0	0	14760	69	3	5	1079	5	SLITRK4	23	142717487	Missense_Mutation	SNP	A	TCGA-WX-AA44-01A-11D-A38X-10	10557270	142717487	12553073	90	50068										
AVPR2	554	hgsc.bcm.edu	37	chrX	153171245	153171245	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.021978021978022	2	1	0.635139573070608	1.19088669950739	0.433049708911778	1	1	0	gctctgttccaagtgctgccCcagctggcctggaaggccac	12	15	1	0			TCGA-WX-AA44-01A-11D-A38X-10	TCGA-WX-AA44-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	398106b4-bf09-4e9f-aeb5-3a8a1abdf3a0	126b3540-5f43-46f5-b374-f13a3d006e05	g.chrX:153171245C>T	ENST00000358927.2	+	3	494	c.285C>T	c.(283-285)ccC>ccT	p.P95P	AVPR2_ENST00000337474.5_Silent_p.P95P|AVPR2_ENST00000370049.1_Silent_p.P95P			P30518	V2R_HUMAN	arginine vasopressin receptor 2	95			P -> L (in XNDI).		activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|excretion (GO:0007588)|hemostasis (GO:0007599)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|interferon-gamma production (GO:0032609)|negative regulation of renal sodium excretion (GO:0035814)|negative regulation of urine volume (GO:0035811)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of systemic arterial blood pressure (GO:0003084)|response to cytokine (GO:0034097)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	vasopressin receptor activity (GO:0005000)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	26	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)				Conivaptan(DB00872)|Desmopressin(DB00035)|Terlipressin(DB02638)|Tolvaptan(DB06212)|Vasopressin(DB00067)	AAGTGCTGCCCCAGCTGGCCT	0.657																																					p.P95P		Atlas-SNP	.											.	AVPR2	43	.	0			c.C285T						.						40	43	42					X																	153171245		2203	4300	6503	SO:0001819	synonymous_variant	554	exon2			GCTGCCCCAGCTG	Z11687	CCDS14735.1, CCDS55539.1	Xq28	2014-09-17	2008-08-01		ENSG00000126895	ENSG00000126895		"GPCR / Class A : Vasopressin and oxytocin receptors"	897	protein-coding gene	gene with protein product	"nephrogenic diabetes insipidus"	300538		DIR3, DIR		1324225	Standard	NM_000054		Approved	V2R	uc004fjh.4	P30518	OTTHUMG00000024227	ENST00000358927.2:c.285C>T	chrX.hg19:g.153171245C>T		127.0	0.0		96.0	37.0	NM_001146151	C5HF20|O43192|Q3MJD3|Q9UCV9	Silent	SNP	ENST00000358927.2	hg19	CCDS14735.1																																																																																			.	.		0.657	AVPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061127.2			T	153171245	C	T	153171245	2	4	354	1	0	0	0	0	0	0	0	1	1233	610	22	3		3	AVPR2	23	153171245	Silent	SNP	C	TCGA-WX-AA44-01A-11D-A38X-10	10453758	153171245	2099315	91	50069										
COL16A1	1307	hgsc.bcm.edu	37	chr1	32157042	32157042	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	gtcccaggcagtcctatcccAgggggtccagggaggccggg	17	13	0	0			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr1:32157042A>G	ENST00000373672.3	-	19	1890	c.1374T>C	c.(1372-1374)ccT>ccC	p.P458P	COL16A1_ENST00000373668.3_Silent_p.P458P|COL16A1_ENST00000271069.6_Silent_p.P458P	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	458	Triple-helical region 9 (COL9) with 3 imperfections.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female pregnancy (GO:0007565)|integrin-mediated signaling pathway (GO:0007229)	collagen type XVI trimer (GO:0005597)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(15)|ovary(8)|prostate(4)	48		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		GTCCTATCCCAGGGGGTCCAG	0.657																																					p.P458P	Colon(143;498 1786 21362 25193 36625)	Atlas-SNP	.											.	COL16A1	137	.	0			c.T1374C						.						35	43	40					1																	32157042		1877	4093	5970	SO:0001819	synonymous_variant	1307	exon19			TATCCCAGGGGGT	M92642	CCDS41297.1	1p35-p34	2013-01-16			ENSG00000084636	ENSG00000084636		"Collagens"	2193	protein-coding gene	gene with protein product		120326				1631157	Standard	NM_001856		Approved		uc001btk.1	Q07092	OTTHUMG00000003883	ENST00000373672.3:c.1374T>C	chr1.hg19:g.32157042A>G		191.0	0.0		138.0	48.0	NM_001856	Q16593|Q59F89|Q71RG9	Silent	SNP	ENST00000373672.3	hg19	CCDS41297.1																																																																																			.	.		0.657	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856		G	32157042	A	G	32157042	2	3	355	1	0	0	0	0	0	0	0	1	3675	175	7	2		2	COL16A1	1	32157042	Silent	SNP	A	TCGA-WX-AA46-01A-11D-A38X-10		32157042	217093579	1	50070										
IFI44L	10964	hgsc.bcm.edu	37	chr1	79107135	79107135	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	cacaggtcatgaatgtccatAaaatgctaggcattcctatt	7	9	1	1			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr1:79107135A>G	ENST00000370751.5	+	8	1344	c.1165A>G	c.(1165-1167)Aaa>Gaa	p.K389E	IFI44L_ENST00000476521.1_3'UTR|IFI44L_ENST00000342282.3_Missense_Mutation_p.K131E	NM_006820.2	NP_006811.2	Q53G44	IF44L_HUMAN	interferon-induced protein 44-like	389					defense response to virus (GO:0051607)|immune response (GO:0006955)	cytoplasm (GO:0005737)				endometrium(4)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	22						GAATGTCCATAAAATGCTAGG	0.318																																					p.K389E		Atlas-SNP	.											.	IFI44L	93	.	0			c.A1165G						.																																			SO:0001583	missense	10964	exon8			GTCCATAAAATGC	AB000115	CCDS687.2	1p22.3	2008-07-18	2004-11-12	2004-11-12	ENSG00000137959	ENSG00000137959			17817	protein-coding gene	gene with protein product		613975	"chromosome 1 open reading frame 29"	C1orf29			Standard	NM_006820		Approved	GS3686	uc010oro.2	Q53G44	OTTHUMG00000009724	ENST00000370751.5:c.1165A>G	chr1.hg19:g.79107135A>G	ENSP00000359787:p.Lys389Glu	98.0	0.0		111.0	6.0	NM_006820	Q86TE1|Q96B64|Q99984	Missense_Mutation	SNP	ENST00000370751.5	hg19	CCDS687.2	.	.	.	.	.	.	.	.	.	.	A	6.120	0.390370	0.11581	.	.	ENSG00000137959	ENST00000370751;ENST00000342282	T;T	0.28895	3.16;1.59	4.11	-3.89	0.04193	.	2.356070	0.01429	N	0.014659	T	0.07369	0.0186	L	0.60455	1.87	0.09310	N	1	B	0.20550	0.046	B	0.15870	0.014	T	0.13791	-1.0496	10	0.11182	T	0.66	-0.0955	0.8403	0.01149	0.3049:0.3283:0.2061:0.1606	.	389	Q53G44	IF44L_HUMAN	E	389;131	ENSP00000359787:K389E;ENSP00000342833:K131E	ENSP00000342833:K131E	K	+	1	0	IFI44L	78879723	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-0.338000	0.07842	-0.408000	0.07565	0.456000	0.33151	AAA	.	.		0.318	IFI44L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026834.3	NM_006820		G	79107135	A	G	79107135	3	3	355	1	0	0	0	0	1	0	0	0	7527	363	13	2	1191	2	IFI44L	1	79107135	Missense_Mutation	SNP	A	TCGA-WX-AA46-01A-11D-A38X-10	46950093	79107135	170143486	2	50071										
COL11A1	1301	hgsc.bcm.edu	37	chr1	103455118	103455118	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	acctttgaatcctggaaaacCatcttcaccctaaaacatta	3	12	2	1	rs387906611		TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr1:103455118C>A	ENST00000370096.3	-	29	2662	c.2350G>T	c.(2350-2352)Ggt>Tgt	p.G784C	COL11A1_ENST00000358392.2_Missense_Mutation_p.G796C|COL11A1_ENST00000353414.4_Missense_Mutation_p.G745C|COL11A1_ENST00000512756.1_Missense_Mutation_p.G668C	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	784	Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		CCTGGAAAACCATCTTCACCC	0.294																																					p.G796C		Atlas-SNP	.											.	COL11A1	972	.	0			c.G2386T						.						59	63	62					1																	103455118		2203	4295	6498	SO:0001583	missense	1301	exon29			GAAAACCATCTTC	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.2350G>T	chr1.hg19:g.103455118C>A	ENSP00000359114:p.Gly784Cys	576.0	1.0		596.0	176.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	hg19	CCDS778.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.638621	0.87760	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000512756	D;D;D;D	0.99637	-6.29;-6.29;-5.89;-5.89	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	D	0.99862	0.9935	H	0.98370	4.215	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.96794	0.9584	10	0.87932	D	0	.	19.2483	0.93912	0.0:1.0:0.0:0.0	.	668;745;796;784	E9PCU0;P12107-3;P12107-2;P12107	.;.;.;COBA1_HUMAN	C	784;796;745;668	ENSP00000359114:G784C;ENSP00000351163:G796C;ENSP00000302551:G745C;ENSP00000426533:G668C	ENSP00000302551:G745C	G	-	1	0	COL11A1	103227706	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.695000	0.74593	2.882000	0.98803	0.655000	0.94253	GGT	.	.		0.294	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		A	103455118	C	A	103455118	3	1	355	1	0	0	0	0	1	0	0	0	3669	594	21	3	3226	3	COL11A1	1	103455118	Missense_Mutation	SNP	C	TCGA-WX-AA46-01A-11D-A38X-10	24347983	103455118	145795503	3	50072										
VAV3	10451	hgsc.bcm.edu	37	chr1	108138911	108138911	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	gaaactgcagagttgtatctAaggttctgaacccttccttg	9	9	2	2			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr1:108138911A>G	ENST00000370056.4	-	25	2547	c.2273T>C	c.(2272-2274)tTa>tCa	p.L758S	VAV3_ENST00000343258.4_5'UTR|VAV3_ENST00000544443.1_Missense_Mutation_p.L162S|VAV3_ENST00000527011.1_Missense_Mutation_p.L758S|VAV3_ENST00000415432.2_Missense_Mutation_p.L198S	NM_006113.4	NP_006104.4	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor	758	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.|Sufficient for interaction with ROS1.				angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of signal transduction (GO:0009967)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|vesicle fusion (GO:0006906)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|SH3/SH2 adaptor activity (GO:0005070)	p.L758*(1)		NS(2)|breast(5)|endometrium(4)|kidney(2)|large_intestine(14)|lung(20)|ovary(6)|prostate(3)|stomach(1)|urinary_tract(1)	58		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)		AGTTGTATCTAAGGTTCTGAA	0.393																																					p.L758S		Atlas-SNP	.											VAV3,NS,carcinoma,0,1	VAV3	176	.	1	Substitution - Nonsense(1)	breast(1)	c.T2273C						.						161	152	155					1																	108138911		2203	4300	6503	SO:0001583	missense	10451	exon25			GTATCTAAGGTTC	AF118886	CCDS785.1, CCDS44181.1	1p13.3	2013-02-14	2007-07-25		ENSG00000134215	ENSG00000134215		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "SH2 domain containing"	12659	protein-coding gene	gene with protein product		605541	"vav 3 oncogene"				Standard	NM_001079874		Approved		uc001dvk.1	Q9UKW4	OTTHUMG00000010995	ENST00000370056.4:c.2273T>C	chr1.hg19:g.108138911A>G	ENSP00000359073:p.Leu758Ser	103.0	0.0		109.0	42.0	NM_006113	B1AMM0|B1APV5|B4E232|B7ZLR1|E9PQ97|O60498|O95230|Q9Y5X8	Missense_Mutation	SNP	ENST00000370056.4	hg19	CCDS785.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.534895	0.85812	.	.	ENSG00000134215	ENST00000370056;ENST00000527011;ENST00000544443;ENST00000415432	T;D;T;T	0.94687	1.43;-3.49;1.43;1.43	5.22	5.22	0.72569	SH2 motif (2);	0.000000	0.64402	D	0.000001	D	0.97717	0.9251	M	0.93328	3.405	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.97110	1.0;0.992;0.997;1.0	D	0.98977	1.0803	10	0.87932	D	0	.	15.1068	0.72326	1.0:0.0:0.0:0.0	.	758;162;758;198	E9PQ97;B7Z3Z5;Q9UKW4;Q9UKW4-3	.;.;VAV3_HUMAN;.	S	758;758;162;198	ENSP00000359073:L758S;ENSP00000432540:L758S;ENSP00000446404:L162S;ENSP00000394897:L198S	ENSP00000359073:L758S	L	-	2	0	VAV3	107940434	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.914000	0.75764	1.980000	0.57719	0.477000	0.44152	TTA	.	.		0.393	VAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030242.2	NM_006113		G	108138911	A	G	108138911	3	3	355	1	0	0	0	0	1	0	0	0	17148	372	13	2	282	2	VAV3	1	108138911	Missense_Mutation	SNP	A	TCGA-WX-AA46-01A-11D-A38X-10	4683793	108138911	141111710	4	50073										
BCAN	63827	hgsc.bcm.edu	37	chr1	156616814	156616814	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	tcaaggtgaacgaggcctacCggttccgcgtggcactgcct	13	13	1	1	rs115373136	byFrequency	TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr1:156616814C>T	ENST00000329117.5	+	3	649	c.313C>T	c.(313-315)Cgg>Tgg	p.R105W	RP11-284F21.10_ENST00000605886.1_RNA|RP11-284F21.7_ENST00000448869.1_RNA|BCAN_ENST00000361588.5_Missense_Mutation_p.R105W	NM_021948.4	NP_068767.3	Q96GW7	PGCB_HUMAN	brevican	105	Ig-like V-type.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hippocampus development (GO:0021766)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	55	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CGAGGCCTACCGGTTCCGCGT	0.682																																					p.R105W		Atlas-SNP	.											.	BCAN	174	.	0			c.C313T						.						47	35	39					1																	156616814		2203	4298	6501	SO:0001583	missense	63827	exon3			GCCTACCGGTTCC	BC027971	CCDS1149.1, CCDS1150.1	1q31	2013-05-07			ENSG00000132692	ENSG00000132692		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	23059	protein-coding gene	gene with protein product	"chondroitin sulfate proteoglycan 7", "brevican proteoglycan"	600347				11054543, 11873941	Standard	NM_021948		Approved	BEHAB, MGC13038, CSPG7	uc001fpp.3	Q96GW7	OTTHUMG00000033322	ENST00000329117.5:c.313C>T	chr1.hg19:g.156616814C>T	ENSP00000331210:p.Arg105Trp	192.0	0.0		153.0	45.0	NM_198427	D3DVC2|Q5SZ10|Q5T3I5|Q8TBB9|Q9HBK1|Q9HBK4	Missense_Mutation	SNP	ENST00000329117.5	hg19	CCDS1149.1	.	.	.	.	.	.	.	.	.	.	C	16.51	3.143221	0.57044	.	.	ENSG00000132692	ENST00000441358;ENST00000255029;ENST00000329117;ENST00000457777;ENST00000361588	T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22	4.61	2.47	0.30058	Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin V-set, subgroup (1);Immunoglobulin-like fold (1);	0.000000	0.52532	D	0.000061	T	0.75042	0.3796	M	0.77616	2.38	0.38665	D	0.952163	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.972	T	0.79876	-0.1618	10	0.87932	D	0	-20.2388	12.8011	0.57586	0.3062:0.6938:0.0:0.0	.	105;105	Q96GW7;Q96GW7-2	PGCB_HUMAN;.	W	105	ENSP00000392731:R105W;ENSP00000331210:R105W;ENSP00000389898:R105W;ENSP00000354925:R105W	ENSP00000255029:R105W	R	+	1	2	BCAN	154883438	0.000000	0.05858	1.000000	0.80357	0.530000	0.34684	-0.350000	0.07721	1.088000	0.41272	0.455000	0.32223	CGG	.	C|0.989;G|0.011		0.682	BCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081844.2	NM_021948		T	156616814	C	T	156616814	3	4	355	1	0	0	0	0	1	0	0	0	1345	643	23	1	319	1	BCAN	1	156616814	Missense_Mutation	SNP	C	TCGA-WX-AA46-01A-11D-A38X-10	48477903	156616814	92633807	5	50074										
CNTN2	6900	hgsc.bcm.edu	37	chr1	205036323	205036323	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	cgggtcatagccagcaacatTctgggcactggggagcctag	14	11	2	0			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr1:205036323T>G	ENST00000331830.4	+	16	2354	c.2070T>G	c.(2068-2070)atT>atG	p.I690M		NM_005076.3	NP_005067.1	Q02246	CNTN2_HUMAN	contactin 2 (axonal)	690	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|central nervous system myelination (GO:0022010)|cerebral cortex GABAergic interneuron migration (GO:0021853)|clustering of voltage-gated potassium channels (GO:0045163)|establishment of protein localization to juxtaparanode region of axon (GO:0071206)|learning (GO:0007612)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|positive regulation of protein processing (GO:0010954)|presynaptic membrane organization (GO:0097090)|receptor internalization (GO:0031623)|regulation of astrocyte differentiation (GO:0048710)|regulation of axon diameter (GO:0031133)|regulation of neuronal synaptic plasticity (GO:0048168)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|juxtaparanode region of axon (GO:0044224)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated potassium channel complex (GO:0008076)	carbohydrate binding (GO:0030246)|identical protein binding (GO:0042802)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(11)|lung(23)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	54	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			CCAGCAACATTCTGGGCACTG	0.577																																					p.I690M	Melanoma(183;2548 2817 37099 41192)	Atlas-SNP	.											.	CNTN2	116	.	0			c.T2070G						.						84	85	85					1																	205036323		2203	4300	6503	SO:0001583	missense	6900	exon16			CAACATTCTGGGC	X67734	CCDS1449.1	1q32.1	2013-02-11			ENSG00000184144	ENSG00000184144		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2172	protein-coding gene	gene with protein product		190197		TAX, AXT		8307567, 8586965	Standard	NM_005076		Approved	TAG-1, TAX1	uc001hbr.3	Q02246	OTTHUMG00000037105	ENST00000331830.4:c.2070T>G	chr1.hg19:g.205036323T>G	ENSP00000330633:p.Ile690Met	231.0	0.0		234.0	17.0	NM_005076	P78432|Q5T054	Missense_Mutation	SNP	ENST00000331830.4	hg19	CCDS1449.1	.	.	.	.	.	.	.	.	.	.	T	17.46	3.395047	0.62066	.	.	ENSG00000184144	ENST00000331830	T	0.56941	0.43	5.61	3.72	0.42706	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.51477	D	0.000088	T	0.64294	0.2585	L	0.58669	1.825	0.44352	D	0.997242	D;D	0.76494	0.999;0.999	D;D	0.74674	0.984;0.984	T	0.62586	-0.6823	10	0.52906	T	0.07	.	8.6501	0.34029	0.0:0.7603:0.0:0.2397	.	690;581	Q02246;Q68DA2	CNTN2_HUMAN;.	M	690	ENSP00000330633:I690M	ENSP00000330633:I690M	I	+	3	3	CNTN2	203302946	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.021000	0.30040	0.704000	0.31869	-0.456000	0.05471	ATT	.	.		0.577	CNTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090080.3	NM_005076		G	205036323	T	G	205036323	3	3	355	1	0	0	0	0	1	0	0	0	3643	1771	62	5	2128	5	CNTN2	1	205036323	Missense_Mutation	SNP	T	TCGA-WX-AA46-01A-11D-A38X-10	48419509	205036323	44214298	6	50075										
TTN	7273	hgsc.bcm.edu	37	chr2	179433556	179433556	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	ttacagcaacaactctaaaaAgatattcttccccttgagtt	4	10	2	2	rs572569285		TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr2:179433556A>C	ENST00000591111.1	-	276	72604	c.72380T>G	c.(72379-72381)cTt>cGt	p.L24127R	TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.L16828R|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.L23200R|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.L16895R|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.L16703R|TTN_ENST00000589042.1_Missense_Mutation_p.L25768R|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000586707.1_RNA			Q8WZ42	TITIN_HUMAN	titin	24127	Fibronectin type-III 75. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AACTCTAAAAAGATATTCTTC	0.418																																					p.L25768R		Atlas-SNP	.											.	TTN	18412	.	0			c.T77303G						.						94	93	93					2																	179433556		1881	4109	5990	SO:0001583	missense	7273	exon326			CTAAAAAGATATT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.72380T>G	chr2.hg19:g.179433556A>C	ENSP00000465570:p.Leu24127Arg	71.0	0.0		98.0	10.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	9.978	1.227375	0.22542	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.55930	0.49;0.49;0.49;0.49	5.83	5.83	0.93111	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.46249	0.1383	N	0.05608	-0.01	0.47698	D	0.999491	D;D;D;D	0.56521	0.976;0.976;0.976;0.976	P;P;P;P	0.52109	0.69;0.69;0.69;0.69	T	0.57423	-0.7814	9	0.87932	D	0	.	16.1893	0.81975	1.0:0.0:0.0:0.0	.	16703;16828;16895;24127	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	R	23200;16703;16895;16828;16701	ENSP00000343764:L23200R;ENSP00000434586:L16703R;ENSP00000340554:L16895R;ENSP00000352154:L16828R	ENSP00000340554:L16895R	L	-	2	0	TTN	179141802	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	3.887000	0.56197	2.217000	0.71921	0.528000	0.53228	CTT	.	.		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179433556	A	C	179433556	3	2	355	1	0	0	0	0	1	0	0	0	16750	72	3	5	30824	5	TTN	2	179433556	Missense_Mutation	SNP	A	TCGA-WX-AA46-01A-11D-A38X-10		179433556	63765817	7	50076										
ALPPL2	251	hgsc.bcm.edu	37	chr2	233274402	233274402	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	ctggttcacggcgtgcaggaGcagaccttcatagcgcacgt	13	12	2	1			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr2:233274402G>T	ENST00000295453.3	+	11	1471	c.1419G>T	c.(1417-1419)gaG>gaT	p.E473D		NM_031313.2	NP_112603.2	P10696	PPBN_HUMAN	alkaline phosphatase, placental-like 2	473					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|metal ion binding (GO:0046872)			breast(2)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(1)	13		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)	Amifostine(DB01143)	GCGTGCAGGAGCAGACCTTCA	0.731																																					p.E473D		Atlas-SNP	.											.	ALPPL2	36	.	0			c.G1419T						.						16	19	18					2																	233274402		2186	4261	6447	SO:0001583	missense	251	exon11			GCAGGAGCAGACC	J04948	CCDS2491.1	2q37	2008-05-20			ENSG00000163286	ENSG00000163286			441	protein-coding gene	gene with protein product		171810					Standard	NM_031313		Approved		uc002vss.4	P10696	OTTHUMG00000133257	ENST00000295453.3:c.1419G>T	chr2.hg19:g.233274402G>T	ENSP00000295453:p.Glu473Asp	184.0	0.0		146.0	8.0	NM_031313	A8KAF2|Q16727|Q53S81|Q96CM1	Missense_Mutation	SNP	ENST00000295453.3	hg19	CCDS2491.1	.	.	.	.	.	.	.	.	.	.	g	15.73	2.921168	0.52653	.	.	ENSG00000163286	ENST00000295453	D	0.96913	-4.17	2.54	1.61	0.23674	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	D	0.95918	0.8671	M	0.62209	1.925	0.48087	D	0.999588	P	0.47762	0.9	P	0.53649	0.731	D	0.94222	0.7468	10	0.87932	D	0	.	8.8221	0.35032	0.1214:0.0:0.8786:0.0	.	473	P10696	PPBN_HUMAN	D	473	ENSP00000295453:E473D	ENSP00000295453:E473D	E	+	3	2	ALPPL2	232982646	1.000000	0.71417	0.996000	0.52242	0.166000	0.22503	1.512000	0.35812	0.352000	0.24053	0.205000	0.17691	GAG	.	.		0.731	ALPPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257034.2	NM_031313		T	233274402	G	T	233274402	3	4	355	1	0	0	0	0	1	0	0	0	549	962	34	3	1461	3	ALPPL2	2	233274402	Missense_Mutation	SNP	G	TCGA-WX-AA46-01A-11D-A38X-10	53840846	233274402	9924971	8	50077										
BRPF1	7862	hgsc.bcm.edu	37	chr3	9781391	9781391	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	ggcgccaacggcacctctttCagtgtccgcaagacagccta	10	15	2	1			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr3:9781391C>G	ENST00000457855.1	+	2	1319	c.1308C>G	c.(1306-1308)ttC>ttG	p.F436L	BRPF1_ENST00000424362.1_Missense_Mutation_p.F436L|BRPF1_ENST00000302054.3_Missense_Mutation_p.F436L|BRPF1_ENST00000433861.2_Missense_Mutation_p.F436L|BRPF1_ENST00000383829.2_Missense_Mutation_p.F436L			P55201	BRPF1_HUMAN	bromodomain and PHD finger containing, 1	436					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	49	Medulloblastoma(99;0.227)					GCACCTCTTTCAGTGTCCGCA	0.597																																					p.F436L		Atlas-SNP	.											.	BRPF1	104	.	0			c.C1308G						.						51	48	49					3																	9781391		2203	4300	6503	SO:0001583	missense	7862	exon3			CTCTTTCAGTGTC	M91585	CCDS2575.1, CCDS33692.1	3p26-p25	2008-07-18			ENSG00000156983	ENSG00000156983			14255	protein-coding gene	gene with protein product	"peregrin", "bromodomain-containing protein, 140kD"	602410				8946209, 7906940	Standard	NM_001003694		Approved	BR140	uc003bsf.3	P55201	OTTHUMG00000097033	ENST00000457855.1:c.1308C>G	chr3.hg19:g.9781391C>G	ENSP00000410210:p.Phe436Leu	173.0	0.0		173.0	10.0	NM_001003694	B4DEZ6|Q7Z6E0|Q8TCM6|Q9UHI0	Missense_Mutation	SNP	ENST00000457855.1	hg19	CCDS2575.1	.	.	.	.	.	.	.	.	.	.	C	16.86	3.240670	0.58995	.	.	ENSG00000156983	ENST00000433861;ENST00000424362;ENST00000383829;ENST00000302054;ENST00000457855	T;T;T;T;T	0.16897	2.32;2.31;3.7;2.31;2.31	6.04	5.16	0.70880	Zinc finger, PHD-type (1);	0.000000	0.85682	D	0.000000	T	0.19005	0.0456	L	0.32530	0.975	0.80722	D	1	P;B;B;P	0.44260	0.83;0.198;0.198;0.597	P;B;B;P	0.51582	0.674;0.155;0.108;0.656	T	0.06320	-1.0833	10	0.11794	T	0.64	.	10.5988	0.45354	0.0:0.853:0.0:0.147	.	436;436;436;436	P55201-4;P55201-3;P55201-2;P55201	.;.;.;BRPF1_HUMAN	L	436	ENSP00000402485:F436L;ENSP00000398863:F436L;ENSP00000373340:F436L;ENSP00000306297:F436L;ENSP00000410210:F436L	ENSP00000306297:F436L	F	+	3	2	BRPF1	9756391	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.811000	0.55620	1.539000	0.49286	0.561000	0.74099	TTC	.	.		0.597	BRPF1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338485.1	NM_001003694		G	9781391	C	G	9781391	3	3	355	1	0	0	0	0	1	0	0	0	1522	825	29	4	1314	4	BRPF1	3	9781391	Missense_Mutation	SNP	C	TCGA-WX-AA46-01A-11D-A38X-10		9781391	188241039	9	50078										
TRA2B	6434	hgsc.bcm.edu	37	chr3	185644397	185644397	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	agtctttcttacctagattcAgatcgggacctggactttga	9	9	3	3			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr3:185644397A>T	ENST00000453386.2	-	2	437	c.162T>A	c.(160-162)tcT>tcA	p.S54S	TRA2B_ENST00000382191.4_Intron|TRA2B_ENST00000471134.1_5'Flank	NM_004593.2	NP_004584.1	P62995	TRA2B_HUMAN	transformer 2 beta homolog (Drosophila)	54	Arg/Ser-rich (RS1 domain).				mRNA splicing, via spliceosome (GO:0000398)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing, via transesterification reactions (GO:0000375)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|kidney(1)|large_intestine(6)|lung(4)|ovary(3)|prostate(1)|urinary_tract(1)	18						ACCTAGATTCAGATCGGGACC	0.478																																					p.S54S		Atlas-SNP	.											.	TRA2B	36	.	0			c.T162A						.						119	117	118					3																	185644397		2203	4300	6503	SO:0001819	synonymous_variant	6434	exon2			AGATTCAGATCGG	AF057159	CCDS33905.1, CCDS58872.1	3q26.2-q27	2014-06-13	2009-02-27	2009-02-27	ENSG00000136527	ENSG00000136527		"RNA binding motif (RRM) containing"	10781	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 156"	602719	"splicing factor, arginine/serine-rich 10 (transformer 2 homolog, Drosophila)"	SFRS10		9790768	Standard	NM_004593		Approved	Htra2-beta, PPP1R156	uc003fpv.3	P62995	OTTHUMG00000156641	ENST00000453386.2:c.162T>A	chr3.hg19:g.185644397A>T		91.0	0.0		92.0	9.0	NM_004593	B4DVK2|D3DNU3|O15449|Q15815|Q64283	Silent	SNP	ENST00000453386.2	hg19	CCDS33905.1																																																																																			.	.		0.478	TRA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344984.1	NM_004593		T	185644397	A	T	185644397	2	4	355	1	0	0	0	0	0	0	0	1	16449	175	7	4		4	TRA2B	3	185644397	Silent	SNP	A	TCGA-WX-AA46-01A-11D-A38X-10	175863006	185644397	12378033	10	50079										
KIAA1211	57482	hgsc.bcm.edu	37	chr4	57180592	57180592	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	gacgcggagcggagggagcgTgaggagcgcgagcgcctgga	22	9	0	1	rs386674634		TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr4:57180592T>G	ENST00000504228.1	+	6	1029	c.924T>G	c.(922-924)cgT>cgG	p.R308R	KIAA1211_ENST00000264229.6_Silent_p.R308R|KIAA1211_ENST00000541073.1_Silent_p.R301R			Q6ZU35	K1211_HUMAN	KIAA1211	308	Glu-rich.									endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					GGAGGGAGCGTGAGGAGCGCG	0.736																																					p.R308R		Atlas-SNP	.											KIAA1211,NS,carcinoma,+2,2	KIAA1211	178	.	0			c.T924G						.						5	7	6					4																	57180592		1903	3760	5663	SO:0001819	synonymous_variant	57482	exon8			GGAGCGTGAGGAG	AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.924T>G	chr4.hg19:g.57180592T>G		136.0	0.0		130.0	31.0	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Silent	SNP	ENST00000504228.1	hg19	CCDS43230.1																																																																																			.	.		0.736	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722		G	57180592	T	G	57180592	2	3	355	1	0	0	0	0	0	0	0	1	8224	1683	59	5		5	KIAA1211	4	57180592	Silent	SNP	T	TCGA-WX-AA46-01A-11D-A38X-10		57180592	133973684	11	50080										
AMBN	258	hgsc.bcm.edu	37	chr4	71467282	71467282	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	aagaagcacttcagcctccaAttcacctgggacatctgccc	7	15	3	1			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr4:71467282A>G	ENST00000322937.6	+	6	545	c.442A>G	c.(442-444)Att>Gtt	p.I148V	AMBN_ENST00000449493.2_Missense_Mutation_p.I133V	NM_016519.5	NP_057603.1	Q9NP70	AMBN_HUMAN	ameloblastin (enamel matrix protein)	148					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|odontogenesis of dentin-containing tooth (GO:0042475)	proteinaceous extracellular matrix (GO:0005578)	growth factor activity (GO:0008083)|structural constituent of tooth enamel (GO:0030345)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(1)	29			Lung(101;0.235)			TCAGCCTCCAATTCACCTGGG	0.532											OREG0016218	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I148V		Atlas-SNP	.											.	AMBN	73	.	0			c.A442G						.						129	123	125					4																	71467282		2203	4300	6503	SO:0001583	missense	258	exon6			CCTCCAATTCACC	AF209780	CCDS3543.1	4q21	2006-11-28	2006-04-27		ENSG00000178522	ENSG00000178522			452	protein-coding gene	gene with protein product		601259	"ameloblastin, enamel matrix protein"			9126491	Standard	NM_016519		Approved		uc003hfl.3	Q9NP70	OTTHUMG00000129913	ENST00000322937.6:c.442A>G	chr4.hg19:g.71467282A>G	ENSP00000313809:p.Ile148Val	111.0	0.0	1130	104.0	6.0	NM_016519	Q3B862|Q9H2X1|Q9H4L1	Missense_Mutation	SNP	ENST00000322937.6	hg19	CCDS3543.1	.	.	.	.	.	.	.	.	.	.	A	0.008	-1.905229	0.00512	.	.	ENSG00000178522	ENST00000322937;ENST00000538728;ENST00000449493	T;T	0.32753	1.44;1.44	5.95	-3.55	0.04639	.	0.916713	0.09309	N	0.819802	T	0.09512	0.0234	N	0.04508	-0.205	0.09310	N	1	B	0.06786	0.001	B	0.12837	0.008	T	0.33954	-0.9848	10	0.12103	T	0.63	-0.0492	1.8736	0.03214	0.4452:0.2415:0.2025:0.1107	.	148	Q9NP70	AMBN_HUMAN	V	148;148;133	ENSP00000313809:I148V;ENSP00000391234:I133V	ENSP00000313809:I148V	I	+	1	0	AMBN	71501871	0.000000	0.05858	0.057000	0.19452	0.040000	0.13550	-0.059000	0.11731	-0.325000	0.08577	-0.376000	0.06991	ATT	.	.		0.532	AMBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252165.1	NM_016519		G	71467282	A	G	71467282	3	3	355	1	0	0	0	0	1	0	0	0	563	101	4	2	464	2	AMBN	4	71467282	Missense_Mutation	SNP	A	TCGA-WX-AA46-01A-11D-A38X-10	14286690	71467282	119686994	12	50081										
ABLIM3	22885	hgsc.bcm.edu	37	chr5	148617156	148617156	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	cgagatgctggagagatgtgGctatggagaggtatcgcatc	16	6	0	3			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr5:148617156G>A	ENST00000506113.1	+	10	1516	c.1034G>A	c.(1033-1035)gGc>gAc	p.G345D	RP11-331K21.1_ENST00000522685.1_RNA|ABLIM3_ENST00000356541.3_Intron|RP11-331K21.1_ENST00000512647.2_RNA|ABLIM3_ENST00000508983.1_Missense_Mutation_p.G345D|ABLIM3_ENST00000519549.1_3'UTR|ABLIM3_ENST00000504238.1_Intron|ABLIM3_ENST00000309868.7_Missense_Mutation_p.G345D|ABLIM3_ENST00000326685.7_Intron|AC012613.2_ENST00000523176.1_RNA			O94929	ABLM3_HUMAN	actin binding LIM protein family, member 3	345					actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|cilium assembly (GO:0042384)|lamellipodium assembly (GO:0030032)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAGAGATGTGGCTATGGAGAG	0.532																																					p.G345D		Atlas-SNP	.											.	ABLIM3	91	.	0			c.G1034A						.						134	133	134					5																	148617156		2203	4300	6503	SO:0001583	missense	22885	exon11			GATGTGGCTATGG	AB020650	CCDS4294.1	5q33.1	2008-02-05			ENSG00000173210	ENSG00000173210			29132	protein-coding gene	gene with protein product		611305					Standard	XM_005268392		Approved	KIAA0843	uc003lpy.2	O94929	OTTHUMG00000129932	ENST00000506113.1:c.1034G>A	chr5.hg19:g.148617156G>A	ENSP00000425394:p.Gly345Asp	113.0	0.0		105.0	11.0	NM_014945	A8K121|Q19VH3|Q658S1|Q68CI5|Q9BV32	Missense_Mutation	SNP	ENST00000506113.1	hg19	CCDS4294.1	.	.	.	.	.	.	.	.	.	.	G	16.89	3.247128	0.59103	.	.	ENSG00000173210	ENST00000309868;ENST00000506113;ENST00000508983	T;T;T	0.52754	0.65;0.65;0.67	5.79	5.79	0.91817	.	0.153166	0.53938	D	0.000042	T	0.33876	0.0878	N	0.08118	0	0.80722	D	1	B	0.15930	0.015	B	0.15484	0.013	T	0.12243	-1.0555	10	0.54805	T	0.06	.	20.0313	0.97540	0.0:0.0:1.0:0.0	.	345	O94929	ABLM3_HUMAN	D	345	ENSP00000310309:G345D;ENSP00000425394:G345D;ENSP00000420855:G345D	ENSP00000310309:G345D	G	+	2	0	ABLIM3	148597349	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.889000	0.56212	2.746000	0.94184	0.655000	0.94253	GGC	.	.		0.532	ABLIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373435.1	NM_014945		A	148617156	G	A	148617156	3	1	355	1	0	0	0	0	1	0	0	0	96	1203	42	3	1072	3	ABLIM3	5	148617156	Missense_Mutation	SNP	G	TCGA-WX-AA46-01A-11D-A38X-10		148617156	32298104	13	50082										
TXNDC5	81567	hgsc.bcm.edu	37	chr6	7899894	7899894	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	ggtacttcacagcttcttggCctggcttgaaaagctttaag	10	9	2	1			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr6:7899894C>A	ENST00000379757.4	-	3	471	c.434G>T	c.(433-435)gGc>gTc	p.G145V	TXNDC5_ENST00000473453.1_Missense_Mutation_p.G37V|TXNDC5_ENST00000539054.1_Missense_Mutation_p.G73V|BLOC1S5-TXNDC5_ENST00000439343.2_3'UTR	NM_030810.3	NP_110437.2	Q8NBS9	TXND5_HUMAN	thioredoxin domain containing 5 (endoplasmic reticulum)	145	Thioredoxin 1. {ECO:0000255|PROSITE- ProRule:PRU00691}.				apoptotic cell clearance (GO:0043277)|cell redox homeostasis (GO:0045454)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	protein disulfide isomerase activity (GO:0003756)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|skin(2)	22	Ovarian(93;0.0398)					AGCTTCTTGGCCTGGCTTGAA	0.448																																					p.G145V	Ovarian(119;1430 1625 3928 26125 34589)	Atlas-SNP	.											.	TXNDC5	33	.	0			c.G434T						.						87	84	85					6																	7899894		2203	4300	6503	SO:0001583	missense	81567	exon3			TCTTGGCCTGGCT	AK025006	CCDS4505.1, CCDS47369.1	6p24.3	2011-10-19	2009-02-23		ENSG00000239264	ENSG00000239264		"Protein disulfide isomerases"	21073	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 15"		"thioredoxin domain containing 5"				Standard	NM_001145549		Approved	MGC3178, FLJ21353, FLJ90810, EndoPDI, Hcc-2, ERp46, PDIA15	uc003mxv.3	Q8NBS9	OTTHUMG00000014216	ENST00000379757.4:c.434G>T	chr6.hg19:g.7899894C>A	ENSP00000369081:p.Gly145Val	68.0	0.0		78.0	17.0	NM_030810	B2RDM2|Q5TCQ0|Q8ND33|Q8TCT2|Q9BVH9	Missense_Mutation	SNP	ENST00000379757.4	hg19	CCDS4505.1	.	.	.	.	.	.	.	.	.	.	.	17.58	3.424782	0.62733	.	.	ENSG00000239264	ENST00000539054;ENST00000379757;ENST00000473453	T;T;T	0.56611	0.45;0.45;0.45	5.5	5.5	0.81552	Thioredoxin domain (1);Thioredoxin-like fold (3);	0.144069	0.64402	D	0.000007	T	0.74854	0.3771	H	0.94183	3.505	0.80722	D	1	B;D	0.69078	0.218;0.997	B;D	0.70716	0.196;0.97	T	0.79897	-0.1609	10	0.51188	T	0.08	.	13.9999	0.64427	0.0:0.9276:0.0:0.0724	.	73;145	Q86UY0;Q8NBS9	.;TXND5_HUMAN	V	73;145;37	ENSP00000442453:G73V;ENSP00000369081:G145V;ENSP00000420784:G37V	ENSP00000442453:G73V	G	-	2	0	TXNDC5	7844893	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.763000	0.55257	2.735000	0.93741	0.655000	0.94253	GGC	.	.		0.448	TXNDC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039792.1	NM_030810		A	7899894	C	A	7899894	3	1	355	1	0	0	0	0	1	0	0	0	16814	739	26	3	896	3	TXNDC5	6	7899894	Missense_Mutation	SNP	C	TCGA-WX-AA46-01A-11D-A38X-10		7899894	163215173	14	50083										
ZNF318	24149	hgsc.bcm.edu	37	chr6	43305119	43305119	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	atatttctagctgtaatggcCccaactccagggaactacat	7	11	1	0			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr6:43305119C>T	ENST00000361428.2	-	10	6694	c.6617G>A	c.(6616-6618)gGg>gAg	p.G2206E	ZNF318_ENST00000318149.3_Intron	NM_014345.2	NP_055160.2	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	2206					meiotic nuclear division (GO:0007126)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(21)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	61			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)			CTGTAATGGCCCCAACTCCAG	0.468																																					p.G2206E		Atlas-SNP	.											.	ZNF318	175	.	0			c.G6617A						.						83	73	76					6																	43305119		2203	4300	6503	SO:0001583	missense	24149	exon10			AATGGCCCCAACT	AF090114	CCDS4895.2	6p21.1	2013-09-19			ENSG00000171467	ENSG00000171467		"Zinc fingers, C2H2-type"	13578	protein-coding gene	gene with protein product						10873617	Standard	NM_014345		Approved	HRIHFB2436, ZFP318	uc003oux.3	Q5VUA4	OTTHUMG00000014732	ENST00000361428.2:c.6617G>A	chr6.hg19:g.43305119C>T	ENSP00000354964:p.Gly2206Glu	100.0	0.0		91.0	8.0	NM_014345	O94796|Q4G0E4|Q8NEM6|Q9UNU8|Q9Y2W9	Missense_Mutation	SNP	ENST00000361428.2	hg19	CCDS4895.2	.	.	.	.	.	.	.	.	.	.	C	11.80	1.745686	0.30955	.	.	ENSG00000171467	ENST00000361428	T	0.13901	2.55	5.66	3.89	0.44902	.	0.253773	0.28971	N	0.013545	T	0.10937	0.0267	L	0.32530	0.975	0.09310	N	0.999999	D	0.76494	0.999	D	0.72075	0.976	T	0.11518	-1.0584	10	0.37606	T	0.19	-7.2305	8.9849	0.35988	0.0:0.7649:0.0:0.2351	.	2206	Q5VUA4	ZN318_HUMAN	E	2206	ENSP00000354964:G2206E	ENSP00000354964:G2206E	G	-	2	0	ZNF318	43413097	0.036000	0.19791	0.891000	0.34965	0.511000	0.34104	0.340000	0.19892	0.750000	0.32877	0.655000	0.94253	GGG	.	.		0.468	ZNF318-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040601.2	NM_014345		T	43305119	C	T	43305119	3	4	355	1	0	0	0	0	1	0	0	0	17851	623	22	3	226	3	ZNF318	6	43305119	Missense_Mutation	SNP	C	TCGA-WX-AA46-01A-11D-A38X-10	35405225	43305119	127809948	15	50084										
AMD1	262	hgsc.bcm.edu	37	chr6	111196314	111196314	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	gctagtctcacggtgatggaAgctgcacattttttcgaagg	12	8	1	1			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr6:111196314A>G	ENST00000368885.3	+	1	342	c.6A>G	c.(4-6)gaA>gaG	p.E2E	AMD1_ENST00000451850.2_Silent_p.E2E|AMD1_ENST00000368882.3_5'UTR|AMD1_ENST00000368877.5_Silent_p.E2E|AMD1_ENST00000368876.1_5'Flank	NM_001634.4	NP_001625.2	P17707	DCAM_HUMAN	adenosylmethionine decarboxylase 1	2					cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|S-adenosylmethioninamine biosynthetic process (GO:0006557)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)|spermine biosynthetic process (GO:0006597)	cytosol (GO:0005829)	adenosylmethionine decarboxylase activity (GO:0004014)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(2)	8		all_cancers(87;3.83e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00225)|Colorectal(196;0.0209)		OV - Ovarian serous cystadenocarcinoma(136;0.0522)|Epithelial(106;0.111)|all cancers(137;0.143)	S-Adenosylmethionine(DB00118)	CGGTGATGGAAGCTGCACATT	0.547																																					p.E2E		Atlas-SNP	.											.	AMD1	23	.	0			c.A6G						.						58	52	54					6																	111196314		2202	4300	6502	SO:0001819	synonymous_variant	262	exon1			GATGGAAGCTGCA	M88006	CCDS5086.1, CCDS75504.1, CCDS75505.1	6q21	2014-05-13			ENSG00000123505	ENSG00000123505	4.1.1.50		457	protein-coding gene	gene with protein product		180980	"S-adenosylmethionine decarboxylase 1"				Standard	NM_001634		Approved	SAMDC	uc003puk.1	P17707	OTTHUMG00000015369	ENST00000368885.3:c.6A>G	chr6.hg19:g.111196314A>G		47.0	0.0		63.0	9.0	NM_001634	E1P5F7|Q5VXN4|Q5VXN6|Q9BWK4	Silent	SNP	ENST00000368885.3	hg19	CCDS5086.1																																																																																			.	.		0.547	AMD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041816.1			G	111196314	A	G	111196314	2	3	355	1	0	0	0	0	0	0	0	1	566	69	3	2		2	AMD1	6	111196314	Silent	SNP	A	TCGA-WX-AA46-01A-11D-A38X-10	67891195	111196314	59918753	16	50085										
MED23	9439	hgsc.bcm.edu	37	chr6	131941772	131941772	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	gaaatataaaatttacccagTgtggaagtttgccttcagga	9	6	1	0			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr6:131941772T>C	ENST00000368068.3	-	7	772	c.593A>G	c.(592-594)cAc>cGc	p.H198R	MED23_ENST00000354577.4_Missense_Mutation_p.H198R|MED23_ENST00000368060.3_Missense_Mutation_p.H198R|MED23_ENST00000403834.3_Missense_Mutation_p.H198R|MED23_ENST00000539158.1_Missense_Mutation_p.H198R|MED23_ENST00000368053.4_Missense_Mutation_p.H198R|MED23_ENST00000540546.1_Missense_Mutation_p.H198R|MED23_ENST00000368058.1_Missense_Mutation_p.H198R	NM_004830.3	NP_004821.2	Q9ULK4	MED23_HUMAN	mediator complex subunit 23	198					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(12)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	44	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608)		ATTTACCCAGTGTGGAAGTTT	0.398																																					p.H198R		Atlas-SNP	.											.	MED23	112	.	0			c.A593G						.						50	51	51					6																	131941772		2203	4300	6503	SO:0001583	missense	9439	exon7			ACCCAGTGTGGAA	AF104255	CCDS5146.1, CCDS5147.1, CCDS59039.1	6q22.33-q24.1	2008-02-05	2007-08-08	2007-07-30	ENSG00000112282	ENSG00000112282			2372	protein-coding gene	gene with protein product		605042	"cofactor required for Sp1 transcriptional activation, subunit 3, 130kDa"	CRSP3		9989412	Standard	NM_004830		Approved	CRSP130, DRIP130, Sur2	uc003qcs.2	Q9ULK4	OTTHUMG00000015565	ENST00000368068.3:c.593A>G	chr6.hg19:g.131941772T>C	ENSP00000357047:p.His198Arg	252.0	0.0		252.0	32.0	NM_015979	B9TX55|O95403|Q5JWT3|Q5JWT4|Q6P9H6|Q9H0J2|Q9NTT9|Q9NTU0|Q9Y5P7|Q9Y667	Missense_Mutation	SNP	ENST00000368068.3	hg19	CCDS5147.1	.	.	.	.	.	.	.	.	.	.	T	17.94	3.510387	0.64522	.	.	ENSG00000112282	ENST00000354577;ENST00000368068;ENST00000403834;ENST00000368060;ENST00000368058;ENST00000368053;ENST00000540546;ENST00000539158	T;T;T;T;T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16;-1.16;-1.16;-1.16;-1.16	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.82171	0.4979	L	0.57536	1.79	0.80722	D	1	B;D;D	0.89917	0.435;1.0;0.999	B;D;D	0.77557	0.07;0.99;0.983	T	0.81986	-0.0681	10	0.39692	T	0.17	-5.9422	15.6489	0.77076	0.0:0.0:0.0:1.0	.	198;198;198	Q9ULK4-2;Q9ULK4;Q9ULK4-3	.;MED23_HUMAN;.	R	198	ENSP00000346588:H198R;ENSP00000357047:H198R;ENSP00000384536:H198R;ENSP00000357039:H198R;ENSP00000357037:H198R;ENSP00000357032:H198R;ENSP00000437818:H198R;ENSP00000445072:H198R	ENSP00000346588:H198R	H	-	2	0	MED23	131983465	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.698000	0.84413	2.117000	0.64856	0.402000	0.26972	CAC	.	.		0.398	MED23-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042215.1			C	131941772	T	C	131941772	3	2	355	1	0	0	0	0	1	0	0	0	9450	1696	59	2	3634	2	MED23	6	131941772	Missense_Mutation	SNP	T	TCGA-WX-AA46-01A-11D-A38X-10	20745458	131941772	39173295	17	50086										
CREB5	9586	hgsc.bcm.edu	37	chr7	28547252	28547252	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	agatcaaactccgaccccaaCgagattcctgaagaactgcg	8	13	1	4			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr7:28547252C>T	ENST00000357727.2	+	4	578	c.188C>T	c.(187-189)aCg>aTg	p.T63M	CREB5_ENST00000396300.2_Missense_Mutation_p.T56M|CREB5_ENST00000409603.1_Missense_Mutation_p.T30M|CREB5_ENST00000396299.2_Missense_Mutation_p.T30M	NM_182898.2	NP_878901.2	Q02930	CREB5_HUMAN	cAMP responsive element binding protein 5	63					adipose tissue development (GO:0060612)|fat cell differentiation (GO:0045444)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(13)|prostate(1)|skin(3)	32						CCGACCCCAACGAGATTCCTG	0.517																																					p.T63M		Atlas-SNP	.											.	CREB5	115	.	0			c.C188T						.						112	120	117					7																	28547252		2203	4300	6503	SO:0001583	missense	9586	exon4			CCCCAACGAGATT	L05515	CCDS5417.1, CCDS5418.1, CCDS43562.1, CCDS43563.1	7p15	2013-01-10			ENSG00000146592	ENSG00000146592		"basic leucine zipper proteins"	16844	protein-coding gene	gene with protein product	"cAMP response element binding protein CRE-Bpa"					8378084, 8440710	Standard	XM_005249906		Approved	H_GS165L15.1, CRE-BPA	uc003szr.3	Q02930	OTTHUMG00000097081	ENST00000357727.2:c.188C>T	chr7.hg19:g.28547252C>T	ENSP00000350359:p.Thr63Met	106.0	0.0		151.0	11.0	NM_182898	A8KA51|B4DU13|B5BUH3|C9JK47|Q05886|Q06246|Q75N02|Q86UJ9	Missense_Mutation	SNP	ENST00000357727.2	hg19	CCDS5417.1	.	.	.	.	.	.	.	.	.	.	C	19.73	3.881284	0.72294	.	.	ENSG00000146592	ENST00000396299;ENST00000424599;ENST00000357727;ENST00000396300;ENST00000409603	T;T;T;T;T	0.34275	1.37;1.37;1.37;1.37;1.37	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.66117	0.2757	M	0.84948	2.725	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.71087	-0.4694	10	0.87932	D	0	-18.3352	18.3806	0.90449	0.0:1.0:0.0:0.0	.	63	Q02930	CREB5_HUMAN	M	30;56;63;56;30	ENSP00000379593:T30M;ENSP00000394088:T56M;ENSP00000350359:T63M;ENSP00000379594:T56M;ENSP00000387197:T30M	ENSP00000350359:T63M	T	+	2	0	CREB5	28513777	1.000000	0.71417	0.998000	0.56505	0.984000	0.73092	7.450000	0.80656	2.650000	0.89964	0.655000	0.94253	ACG	.	.		0.517	CREB5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214204.4	NM_004904		T	28547252	C	T	28547252	3	4	355	1	0	0	0	0	1	0	0	0	3862	536	19	1	202	1	CREB5	7	28547252	Missense_Mutation	SNP	C	TCGA-WX-AA46-01A-11D-A38X-10		28547252	130591411	18	50087										
AKR1B1	231	hgsc.bcm.edu	37	chr7	134136358	134136358	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	cttgctgacgatgaagagctCctcacgcttcaccacctgct	8	15	2	3			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr7:134136358C>A	ENST00000285930.4	-	2	293	c.214G>T	c.(214-216)Gag>Tag	p.E72*	AKR1B1_ENST00000489022.1_5'UTR	NM_001628.2	NP_001619.1	P15121	ALDR_HUMAN	aldo-keto reductase family 1, member B1 (aldose reductase)	72					C21-steroid hormone biosynthetic process (GO:0006700)|carbohydrate metabolic process (GO:0005975)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|response to stress (GO:0006950)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|electron carrier activity (GO:0009055)|glyceraldehyde oxidoreductase activity (GO:0043795)			kidney(1)|large_intestine(5)|lung(2)|ovary(3)|prostate(1)|skin(2)	14					Sulindac(DB00605)	ATGAAGAGCTCCTCACGCTTC	0.587																																					p.E72X		Atlas-SNP	.											AKR1B1,NS,carcinoma,0,1	AKR1B1	32	.	0			c.G214T						.						118	97	104					7																	134136358		2203	4300	6503	SO:0001587	stop_gained	231	exon2			AGAGCTCCTCACG	J04795	CCDS5831.1	7q35	2010-04-08			ENSG00000085662	ENSG00000085662	1.1.1.21	"Aldo-keto reductases"	381	protein-coding gene	gene with protein product		103880		ALDR1		1901827	Standard	NM_001628		Approved	AR	uc003vrp.1	P15121	OTTHUMG00000155322	ENST00000285930.4:c.214G>T	chr7.hg19:g.134136358C>A	ENSP00000285930:p.Glu72*	51.0	0.0		111.0	44.0	NM_001628	B2R8N3|Q5U031|Q6FGA4|Q6ICP2|Q9BS21|Q9UCI9	Nonsense_Mutation	SNP	ENST00000285930.4	hg19	CCDS5831.1	.	.	.	.	.	.	.	.	.	.	C	37	6.060052	0.97246	.	.	ENSG00000085662	ENST00000285930	.	.	.	5.23	5.23	0.72850	.	0.193737	0.53938	D	0.000051	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.1639	0.89718	0.0:1.0:0.0:0.0	.	.	.	.	X	72	.	ENSP00000285930:E72X	E	-	1	0	AKR1B1	133786898	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	5.959000	0.70339	2.608000	0.88229	0.561000	0.74099	GAG	.	.		0.587	AKR1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339448.2	NM_001628		A	134136358	C	A	134136358	4	1	355	1	0	0	0	0	0	1	0	0	466	864	30	3	772	3	AKR1B1	7	134136358	Nonsense_Mutation	SNP	C	TCGA-WX-AA46-01A-11D-A38X-10	105589106	134136358	25002305	19	50088										
WRN	7486	hgsc.bcm.edu	37	chr8	30974005	30974005	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	ggcatgagttttagcacaagGaaagacattcatcataggtt	10	6	2	2			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr8:30974005G>T	ENST00000298139.5	+	20	2658	c.2409G>T	c.(2407-2409)agG>agT	p.R803S		NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN	Werner syndrome, RecQ helicase-like	803	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				aging (GO:0007568)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to starvation (GO:0009267)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|double-strand break repair (GO:0006302)|multicellular organismal aging (GO:0010259)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleolus to nucleoplasm transport (GO:0032066)|positive regulation of hydrolase activity (GO:0051345)|regulation of apoptotic process (GO:0042981)|regulation of growth rate (GO:0040009)|replication fork processing (GO:0031297)|replicative cell aging (GO:0001302)|response to oxidative stress (GO:0006979)|response to UV-C (GO:0010225)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	3'-5' DNA helicase activity (GO:0043138)|3'-5' exonuclease activity (GO:0008408)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|exonuclease activity (GO:0004527)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|Y-form DNA binding (GO:0000403)			central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(13)|lung(28)|ovary(3)|skin(3)|upper_aerodigestive_tract(3)	60		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		TTAGCACAAGGAAAGACATTC	0.388			"Mis, N, F, S"			"osteosarcoma, meningioma, others"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome																												p.R803S	Ovarian(18;161 598 2706 14834 27543)	Atlas-SNP	.	yes	Rec		Werner Syndrome	8	8p12-p11.2	7486	Werner syndrome (RECQL2)		"L, E, M, O"	.	WRN	116	.	0			c.G2409T						.						120	114	116					8																	30974005		2203	4300	6503	SO:0001583	missense	7486	exon20	Familial Cancer Database	WS, Adult Progeria	CACAAGGAAAGAC		CCDS6082.1	8p12	2014-09-17	2009-03-19		ENSG00000165392	ENSG00000165392			12791	protein-coding gene	gene with protein product		604611	"Werner syndrome"			9288107	Standard	NM_000553		Approved	RECQL2, RECQ3	uc003xio.4	Q14191	OTTHUMG00000163894	ENST00000298139.5:c.2409G>T	chr8.hg19:g.30974005G>T	ENSP00000298139:p.Arg803Ser	63.0	0.0		79.0	14.0	NM_000553	A1KYY9	Missense_Mutation	SNP	ENST00000298139.5	hg19	CCDS6082.1	.	.	.	.	.	.	.	.	.	.	G	13.75	2.330462	0.41297	.	.	ENSG00000165392	ENST00000298139	D	0.82433	-1.61	5.66	3.86	0.44501	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.94735	0.8301	H	0.99777	4.77	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.94247	0.7490	10	0.87932	D	0	-19.7967	8.7149	0.34405	0.2295:0.0:0.7705:0.0	.	213;803	Q59F09;Q14191	.;WRN_HUMAN	S	803	ENSP00000298139:R803S	ENSP00000298139:R803S	R	+	3	2	WRN	31093547	1.000000	0.71417	0.596000	0.28811	0.013000	0.08279	2.176000	0.42500	1.392000	0.46585	0.557000	0.71058	AGG	.	.		0.388	WRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376248.1			T	30974005	G	T	30974005	3	4	355	1	0	0	0	0	1	0	0	0	17417	1165	41	3	2483	3	WRN	8	30974005	Missense_Mutation	SNP	G	TCGA-WX-AA46-01A-11D-A38X-10		30974005	115390017	20	50089										
MYST3	7994	hgsc.bcm.edu	37	chr8	41812897	41812897	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	atgacagagggacagcggacTtgtggatcagggggaccagt	17	7	1	2			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr8:41812897T>C	ENST00000396930.3	-	10	2058	c.1515A>G	c.(1513-1515)caA>caG	p.Q505Q	KAT6A_ENST00000406337.1_Silent_p.Q505Q|KAT6A_ENST00000265713.2_Silent_p.Q505Q|KAT6A_ENST00000485568.1_Silent_p.Q505Q	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	505	Catalytic.|Interaction with PML.|Interaction with RUNX1-1.|MYST-type HAT.				aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										GACAGCGGACTTGTGGATCAG	0.423																																					p.Q505Q		Atlas-SNP	.											.	.	.	.	0			c.A1515G						.						93	84	87					8																	41812897		2203	4300	6503	SO:0001819	synonymous_variant	7994	exon10			GCGGACTTGTGGA	U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	13013	protein-coding gene	gene with protein product	"Monocytic leukemia zinc finger protein"	601408	"runt-related transcription factor binding protein 2", "MYST histone acetyltransferase (monocytic leukemia) 3"	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.1515A>G	chr8.hg19:g.41812897T>C		94.0	0.0		108.0	13.0	NM_001099412	Q76L81	Silent	SNP	ENST00000396930.3	hg19	CCDS6124.1																																																																																			.	.		0.423	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766		C	41812897	T	C	41812897	2	2	355	1	0	0	0	0	0	0	0	1	10113	1606	56	2		2	MYST3	8	41812897	Silent	SNP	T	TCGA-WX-AA46-01A-11D-A38X-10	10838892	41812897	104551125	21	50090										
DBH	1621	hgsc.bcm.edu	37	chr9	136501520	136501520	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	gccctcagtcgctgggccagCctgcccggccccagcatgcg	13	19	1	0			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr9:136501520C>T	ENST00000393056.2	+	1	39	c.27C>T	c.(25-27)agC>agT	p.S9S		NM_000787.3	NP_000778.3	P09172	DOPO_HUMAN	dopamine beta-hydroxylase (dopamine beta-monooxygenase)	9					behavioral response to ethanol (GO:0048149)|blood vessel remodeling (GO:0001974)|catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|cytokine production (GO:0001816)|dopamine catabolic process (GO:0042420)|fear response (GO:0042596)|glucose homeostasis (GO:0042593)|homoiothermy (GO:0042309)|leukocyte mediated immunity (GO:0002443)|leukocyte migration (GO:0050900)|locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|memory (GO:0007613)|norepinephrine biosynthetic process (GO:0042421)|positive regulation of vasoconstriction (GO:0045907)|regulation of cell proliferation (GO:0042127)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)|response to amphetamine (GO:0001975)|response to pain (GO:0048265)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|secretory granule lumen (GO:0034774)	catalytic activity (GO:0003824)|copper ion binding (GO:0005507)|dopamine beta-monooxygenase activity (GO:0004500)|L-ascorbic acid binding (GO:0031418)			central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	36				OV - Ovarian serous cystadenocarcinoma(145;2.33e-07)|Epithelial(140;1.5e-06)|all cancers(34;1.66e-05)	Disulfiram(DB00822)|Dopamine(DB00988)|Propylthiouracil(DB00550)|Vitamin C(DB00126)	GCTGGGCCAGCCTGCCCGGCC	0.677																																					p.S9S		Atlas-SNP	.											DBH,NS,carcinoma,0,1	DBH	86	.	0			c.C27T						.						32	34	33					9																	136501520		2203	4298	6501	SO:0001819	synonymous_variant	1621	exon1			GGCCAGCCTGCCC	X13256	CCDS6977.2	9q34	2013-06-03			ENSG00000123454	ENSG00000123454	1.14.17.1		2689	protein-coding gene	gene with protein product		609312					Standard	NM_000787		Approved	DBM	uc004cel.3	P09172	OTTHUMG00000020878	ENST00000393056.2:c.27C>T	chr9.hg19:g.136501520C>T		281.0	0.0		229.0	16.0	NM_000787	Q5T381|Q96AG2	Silent	SNP	ENST00000393056.2	hg19	CCDS6977.2																																																																																			.	.		0.677	DBH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054929.2	NM_000787		T	136501520	C	T	136501520	2	4	355	1	0	0	0	0	0	0	0	1	4252	738	26	3		3	DBH	9	136501520	Silent	SNP	C	TCGA-WX-AA46-01A-11D-A38X-10		136501520	4711911	22	50091										
WDR37	22884	hgsc.bcm.edu	37	chr10	1118109	1118109	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	agaagtaatgcccacagaaaGcgcaagttgttcgactgctc	10	10	0	2			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr10:1118109G>C	ENST00000358220.1	+	2	158	c.14G>C	c.(13-15)aGc>aCc	p.S5T	WDR37_ENST00000263150.4_Missense_Mutation_p.S5T|WDR37_ENST00000381329.1_Missense_Mutation_p.S5T			Q9Y2I8	WDR37_HUMAN	WD repeat domain 37	5										breast(2)|endometrium(2)|kidney(1)|lung(9)|prostate(2)|skin(1)	17		all_epithelial(10;0.0449)|Colorectal(49;0.142)		Epithelial(11;0.134)		CCCACAGAAAGCGCAAGTTGT	0.463																																					p.S5T		Atlas-SNP	.											.	WDR37	52	.	0			c.G14C						.						90	85	87					10																	1118109		2203	4300	6503	SO:0001583	missense	22884	exon2			CAGAAAGCGCAAG	AB023199	CCDS7057.1	10p15.3	2013-01-09			ENSG00000047056	ENSG00000047056		"WD repeat domain containing"	31406	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_014023		Approved	KIAA0982	uc001igf.1	Q9Y2I8	OTTHUMG00000017540	ENST00000358220.1:c.14G>C	chr10.hg19:g.1118109G>C	ENSP00000350954:p.Ser5Thr	112.0	0.0		107.0	8.0	NM_014023	A8K976|D3DRQ7|Q5SW03|Q8WVG2|Q9NTJ6	Missense_Mutation	SNP	ENST00000358220.1	hg19	CCDS7057.1	.	.	.	.	.	.	.	.	.	.	G	15.53	2.860172	0.51482	.	.	ENSG00000047056	ENST00000358220;ENST00000381329;ENST00000263150	T;T;T	0.73575	-0.07;-0.76;-0.07	5.58	5.58	0.84498	.	0.041495	0.85682	D	0.000000	T	0.67002	0.2847	L	0.31294	0.92	0.53005	D	0.999965	B;B;B	0.15141	0.001;0.001;0.012	B;B;B	0.12156	0.002;0.002;0.007	T	0.60214	-0.7307	10	0.38643	T	0.18	.	19.573	0.95428	0.0:0.0:1.0:0.0	.	5;5;5	A8K976;Q9Y2I8;E7EQ49	.;WDR37_HUMAN;.	T	5	ENSP00000350954:S5T;ENSP00000370730:S5T;ENSP00000263150:S5T	ENSP00000263150:S5T	S	+	2	0	WDR37	1108109	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.394000	0.79862	2.628000	0.89032	0.563000	0.77884	AGC	.	.		0.463	WDR37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046418.1	NM_014023		C	1118109	G	C	1118109	3	2	355	1	0	0	0	0	1	0	0	0	17306	971	34	4	16	4	WDR37	10	1118109	Missense_Mutation	SNP	G	TCGA-WX-AA46-01A-11D-A38X-10		1118109	134416638	23	50092										
GPR158	57512	hgsc.bcm.edu	37	chr10	25888075	25888075	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	cacgagcagaggtttgtcctTgggagtttgagaccccagct	13	10	0	2			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr10:25888075T>A	ENST00000376351.3	+	11	3879	c.3520T>A	c.(3520-3522)Tgg>Agg	p.W1174R	GPR158_ENST00000490549.1_3'UTR	NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	1174					protein localization to plasma membrane (GO:0072659)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|cervix(1)|endometrium(9)|kidney(10)|large_intestine(20)|lung(56)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	119						GGTTTGTCCTTGGGAGTTTGA	0.448																																					p.W1174R		Atlas-SNP	.											.	GPR158	255	.	0			c.T3520A						.						47	51	50					10																	25888075		2203	4300	6503	SO:0001583	missense	57512	exon11			TGTCCTTGGGAGT	AB032962	CCDS31166.1	10p12.31	2012-08-21			ENSG00000151025	ENSG00000151025		"GPCR / Class C : Orphans"	23689	protein-coding gene	gene with protein product		614573					Standard	NM_020752		Approved	KIAA1136	uc001isj.3	Q5T848	OTTHUMG00000017832	ENST00000376351.3:c.3520T>A	chr10.hg19:g.25888075T>A	ENSP00000365529:p.Trp1174Arg	31.0	0.0		36.0	16.0	NM_020752	Q6QR81|Q9ULT3	Missense_Mutation	SNP	ENST00000376351.3	hg19	CCDS31166.1	.	.	.	.	.	.	.	.	.	.	T	16.40	3.113571	0.56398	.	.	ENSG00000151025	ENST00000376351	T	0.80393	-1.37	5.74	5.74	0.90152	.	0.000000	0.64402	D	0.000002	D	0.85084	0.5616	L	0.34521	1.04	0.58432	D	0.999997	D	0.89917	1.0	D	0.87578	0.998	D	0.86915	0.2063	10	0.87932	D	0	.	16.0368	0.80635	0.0:0.0:0.0:1.0	.	1174	Q5T848	GP158_HUMAN	R	1174	ENSP00000365529:W1174R	ENSP00000365529:W1174R	W	+	1	0	GPR158	25928081	1.000000	0.71417	1.000000	0.80357	0.474000	0.32979	5.599000	0.67592	2.183000	0.69458	0.533000	0.62120	TGG	.	.		0.448	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	XM_166110		A	25888075	T	A	25888075	3	1	355	1	0	0	0	0	1	0	0	0	6671	1812	63	4	3562	4	GPR158	10	25888075	Missense_Mutation	SNP	T	TCGA-WX-AA46-01A-11D-A38X-10	24769966	25888075	109646672	24	50093										
C10orf72	196740	hgsc.bcm.edu	37	chr10	50285295	50285295	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	cgcttgttaaacacagactgCcagacgatgaccagcatgaa	9	11	0	4			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr10:50285295C>T	ENST00000332853.4	-	4	626	c.603G>A	c.(601-603)tgG>tgA	p.W201*		NM_001031746.3	NP_001026916.2	Q8IW00	VSTM4_HUMAN	V-set and transmembrane domain containing 4	201						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(14)|skin(2)	31						ACACAGACTGCCAGACGATGA	0.522																																					p.W201X		Atlas-SNP	.											.	VSTM4	83	.	0			c.G603A						.						136	107	117					10																	50285295		2203	4300	6503	SO:0001587	stop_gained	196740	exon4			AGACTGCCAGACG	BC041414	CCDS7228.1, CCDS31198.1	10q11.23	2013-01-11	2011-07-01	2011-07-01	ENSG00000165633	ENSG00000165633		"Immunoglobulin superfamily / V-set domain containing"	26470	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 72"	C10orf72			Standard	XR_246075		Approved	FLJ31737	uc001jhf.2	Q8IW00	OTTHUMG00000018184	ENST00000332853.4:c.603G>A	chr10.hg19:g.50285295C>T	ENSP00000331062:p.Trp201*	74.0	0.0		75.0	4.0	NM_001031746	B4DNI6|Q96MX7	Nonsense_Mutation	SNP	ENST00000332853.4	hg19	CCDS31198.1	.	.	.	.	.	.	.	.	.	.	C	37	6.212578	0.97380	.	.	ENSG00000165633	ENST00000332853	.	.	.	5.4	2.2	0.27929	.	0.238309	0.43416	D	0.000562	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.10902	T	0.67	-3.5597	14.7508	0.69525	0.0:0.4146:0.5854:0.0	.	.	.	.	X	201	.	ENSP00000331062:W201X	W	-	3	0	VSTM4	49955301	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	0.766000	0.26560	0.700000	0.31782	0.655000	0.94253	TGG	.	.		0.522	VSTM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047966.2	NM_144984		T	50285295	C	T	50285295	4	4	355	1	0	0	0	0	0	1	0	0	1617	740	26	3	379	3	C10orf72	10	50285295	Nonsense_Mutation	SNP	C	TCGA-WX-AA46-01A-11D-A38X-10	24397220	50285295	85249452	25	50094										
KIAA1279	26128	hgsc.bcm.edu	37	chr10	70775761	70775761	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	catgcttactatgatatgatGgatttgaaggttgccattgc	10	6	0	3			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr10:70775761G>C	ENST00000361983.4	+	7	1557	c.1455G>C	c.(1453-1455)atG>atC	p.M485I		NM_015634.3	NP_056449.1	Q96EK5	KBP_HUMAN	KIAA1279	485					cell differentiation (GO:0030154)|mitochondrial transport (GO:0006839)|nervous system development (GO:0007399)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)	kinesin binding (GO:0019894)			breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	14						ATGATATGATGGATTTGAAGG	0.393																																					p.M485I		Atlas-SNP	.											.	KIAA1279	35	.	0			c.G1455C						.						69	65	66					10																	70775761		2203	4300	6503	SO:0001583	missense	26128	exon7			TATGATGGATTTG	BC012180	CCDS7284.1	10q22.1	2008-02-05			ENSG00000198954	ENSG00000198954			23419	protein-coding gene	gene with protein product		609367					Standard	NM_015634		Approved	DKFZP586B0923, TTC20	uc001joy.3	Q96EK5	OTTHUMG00000018363	ENST00000361983.4:c.1455G>C	chr10.hg19:g.70775761G>C	ENSP00000354848:p.Met485Ile	139.0	0.0		116.0	6.0	NM_015634	A8K5M8|Q9BR89|Q9ULE1|Q9Y428	Missense_Mutation	SNP	ENST00000361983.4	hg19	CCDS7284.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.414728	0.83449	.	.	ENSG00000198954	ENST00000361983	T	0.47528	0.84	5.63	5.63	0.86233	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.56992	0.2023	M	0.68952	2.095	0.80722	D	1	P	0.49253	0.921	P	0.47251	0.542	T	0.56353	-0.7993	10	0.42905	T	0.14	-3.0587	20.0572	0.97657	0.0:0.0:1.0:0.0	.	485	Q96EK5	KBP_HUMAN	I	485	ENSP00000354848:M485I	ENSP00000354848:M485I	M	+	3	0	KIAA1279	70445767	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.777000	0.99008	2.826000	0.97356	0.655000	0.94253	ATG	.	.		0.393	KIAA1279-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048370.1	NM_015634		C	70775761	G	C	70775761	3	2	355	1	0	0	0	0	1	0	0	0	8230	1348	47	4	1481	4	KIAA1279	10	70775761	Missense_Mutation	SNP	G	TCGA-WX-AA46-01A-11D-A38X-10	20490466	70775761	64758986	26	50095										
C10orf12	26148	hgsc.bcm.edu	37	chr10	98741959	98741959	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	tcacgaggaaggaggtggagAcgtttcacctcgaaaagaac	13	8	2	2			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr10:98741959A>G	ENST00000286067.2	+	1	919	c.812A>G	c.(811-813)gAc>gGc	p.D271G		NM_015652.2	NP_056467.2	Q8N655	CJ012_HUMAN	chromosome 10 open reading frame 12	271										NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(3)|prostate(2)|skin(2)|stomach(4)	45		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		GGAGGTGGAGACGTTTCACCT	0.522																																					p.D271G		Atlas-SNP	.											.	C10orf12	94	.	0			c.A812G						.						86	88	87					10																	98741959		2203	4300	6503	SO:0001583	missense	26148	exon1			GTGGAGACGTTTC	BC024315	CCDS7452.1	10q24.2	2014-03-11			ENSG00000155640	ENSG00000155640			23420	protein-coding gene	gene with protein product						24550272	Standard	NM_015652		Approved	DKFZP564P1916, FLJ13022	uc001kmv.3	Q8N655	OTTHUMG00000018840	ENST00000286067.2:c.812A>G	chr10.hg19:g.98741959A>G	ENSP00000286067:p.Asp271Gly	130.0	0.0		125.0	7.0	NM_015652	Q9H945|Q9Y457	Missense_Mutation	SNP	ENST00000286067.2	hg19	CCDS7452.1	.	.	.	.	.	.	.	.	.	.	A	0.177	-1.065558	0.01934	.	.	ENSG00000155640	ENST00000286067;ENST00000539886	T	0.08282	3.11	6.05	2.36	0.29203	.	0.554792	0.15939	N	0.237297	T	0.04952	0.0133	L	0.27053	0.805	0.09310	N	1	B;B	0.12013	0.005;0.005	B;B	0.09377	0.004;0.004	T	0.38628	-0.9652	10	0.33940	T	0.23	-5.3828	1.9858	0.03436	0.482:0.2682:0.1206:0.1292	.	105;271	A0PJI9;Q8N655	.;CJ012_HUMAN	G	271;105	ENSP00000286067:D271G	ENSP00000286067:D271G	D	+	2	0	C10orf12	98731949	.	.	0.004000	0.12327	0.077000	0.17291	.	.	0.477000	0.27464	0.533000	0.62120	GAC	.	.		0.522	C10orf12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049627.1	NM_015652		G	98741959	A	G	98741959	3	3	355	1	0	0	0	0	1	0	0	0	1591	275	10	2	814	2	C10orf12	10	98741959	Missense_Mutation	SNP	A	TCGA-WX-AA46-01A-11D-A38X-10	27966198	98741959	36792788	27	50096										
PNLIPRP1	5407	hgsc.bcm.edu	37	chr10	118351992	118351992	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	tcaaatggacagaaagacccGgttcatcatccatggcttca	8	11	4	2	rs141478509		TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr10:118351992G>T	ENST00000528052.1	+	4	340	c.269G>T	c.(268-270)cGg>cTg	p.R90L	PNLIPRP1_ENST00000442761.1_Missense_Mutation_p.R90L|PNLIPRP1_ENST00000358834.4_Missense_Mutation_p.R90L|PNLIPRP1_ENST00000534537.1_Missense_Mutation_p.R90L|PNLIPRP1_ENST00000480870.2_3'UTR			P54315	LIPR1_HUMAN	pancreatic lipase-related protein 1	90					lipid metabolic process (GO:0006629)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|triglyceride lipase activity (GO:0004806)			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)		AGAAAGACCCGGTTCATCATC	0.493																																					p.R90L		Atlas-SNP	.											.	PNLIPRP1	82	.	0			c.G269T						.						128	126	127					10																	118351992		2203	4300	6503	SO:0001583	missense	5407	exon4			AGACCCGGTTCAT	BC025784	CCDS7595.1	10q26.12	2006-07-04			ENSG00000187021	ENSG00000187021			9156	protein-coding gene	gene with protein product		604422				1379598	Standard	NM_006229		Approved	PLRP1	uc001lco.1	P54315	OTTHUMG00000019109	ENST00000528052.1:c.269G>T	chr10.hg19:g.118351992G>T	ENSP00000433933:p.Arg90Leu	96.0	0.0		90.0	22.0	NM_006229	Q68D83|Q68DR6|Q8TAU2|Q9BS82	Missense_Mutation	SNP	ENST00000528052.1	hg19	CCDS7595.1	.	.	.	.	.	.	.	.	.	.	G	15.08	2.726545	0.48833	.	.	ENSG00000187021	ENST00000531984;ENST00000358834;ENST00000528052;ENST00000442761;ENST00000530319;ENST00000527980;ENST00000471549;ENST00000534537	D;D;D;D;D;D;D;D	0.88896	-2.44;-2.44;-2.44;-2.44;-2.44;-2.44;-2.44;-2.44	5.21	4.3	0.51218	Lipase, N-terminal (1);	0.000000	0.64402	D	0.000003	D	0.95956	0.8683	H	0.96080	3.765	0.40664	D	0.982154	D;D	0.89917	1.0;0.994	D;D	0.77557	0.99;0.914	D	0.97114	0.9806	10	0.87932	D	0	-7.899	12.9869	0.58596	0.0801:0.0:0.9199:0.0	.	90;90	P54315;P54315-2	LIPR1_HUMAN;.	L	90	ENSP00000436123:R90L;ENSP00000351695:R90L;ENSP00000433933:R90L;ENSP00000400963:R90L;ENSP00000437263:R90L;ENSP00000433785:R90L;ENSP00000431207:R90L;ENSP00000434159:R90L	ENSP00000351695:R90L	R	+	2	0	PNLIPRP1	118341982	0.988000	0.35896	0.908000	0.35775	0.192000	0.23643	5.700000	0.68318	1.326000	0.45319	0.655000	0.94253	CGG	.	G|1.000;A|0.000		0.493	PNLIPRP1-011	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384633.1	NM_006229		T	118351992	G	T	118351992	3	4	355	1	0	0	0	0	1	0	0	0	12159	1116	39	1	279	1	PNLIPRP1	10	118351992	Missense_Mutation	SNP	G	TCGA-WX-AA46-01A-11D-A38X-10	19610033	118351992	17182755	28	50097										
CPSF7	79869	hgsc.bcm.edu	37	chr11	61183611	61183611	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	atagggggcagaggccttcaTgtaagtatctggtggaggcc	16	7	2	1	rs143271041		TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr11:61183611T>C	ENST00000394888.4	-	6	1103	c.931A>G	c.(931-933)Atg>Gtg	p.M311V	CPSF7_ENST00000448745.1_Missense_Mutation_p.M302V|CPSF7_ENST00000340437.4_Missense_Mutation_p.M354V|CPSF7_ENST00000439958.3_Missense_Mutation_p.M302V	NM_001136040.2	NP_001129512.1	Q8N684	CPSF7_HUMAN	cleavage and polyadenylation specific factor 7, 59kDa	311	Pro-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|protein tetramerization (GO:0051262)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)|mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	22						GAGGCCTTCATGTAAGTATCT	0.517																																					p.M354V		Atlas-SNP	.											.	CPSF7	46	.	0			c.A1060G						.	T	VAL/MET,VAL/MET,VAL/MET	0,4404		0,0,2202	58	65	62		931,904,1060	5.6	1	11	dbSNP_134	62	1,8591	1.2+/-3.3	0,1,4295	no	missense,missense,missense	CPSF7	NM_001136040.2,NM_001142565.1,NM_024811.3	21,21,21	0,1,6497	CC,CT,TT		0.0116,0.0,0.0077	benign,benign,benign	311/472,302/463,354/515	61183611	1,12995	2202	4296	6498	SO:0001583	missense	79869	exon6			CCTTCATGTAAGT		CCDS8006.2, CCDS44619.1, CCDS44620.1	11q12.2	2013-06-18			ENSG00000149532	ENSG00000149532		"RNA binding motif (RRM) containing"	30098	protein-coding gene	gene with protein product	"pre mRNA cleavage factor I, 59 kDa subunit", "cleavage factor Im complex 59 kDa subunit"					12477932	Standard	NM_024811		Approved	FLJ12529	uc001nrp.3	Q8N684	OTTHUMG00000168198	ENST00000394888.4:c.931A>G	chr11.hg19:g.61183611T>C	ENSP00000378352:p.Met311Val	91.0	0.0		62.0	10.0	NM_024811	B3KU04|C9K0Q4|Q7Z3H9|Q9H025|Q9H9V1	Missense_Mutation	SNP	ENST00000394888.4	hg19	CCDS44619.1	.	.	.	.	.	.	.	.	.	.	T	10.61	1.398025	0.25205	0.0	1.16E-4	ENSG00000149532	ENST00000340437;ENST00000394888;ENST00000439958;ENST00000448745;ENST00000544147;ENST00000477890	D;D;D;D;D	0.86230	-2.09;-2.09;-2.09;-2.09;-2.09	5.61	5.61	0.85477	.	0.461453	0.25383	N	0.031071	T	0.70605	0.3243	N	0.03608	-0.345	0.80722	D	1	B;B;B;B	0.06786	0.0;0.0;0.001;0.0	B;B;B;B	0.10450	0.002;0.002;0.002;0.005	T	0.66360	-0.5943	10	0.16896	T	0.51	-4.9219	10.9315	0.47220	0.0:0.0747:0.0:0.9253	.	302;311;354;302	B4DGF8;Q8N684;Q8N684-3;Q8N684-2	.;CPSF7_HUMAN;.;.	V	354;311;302;302;77;235	ENSP00000345412:M354V;ENSP00000378352:M311V;ENSP00000397203:M302V;ENSP00000407394:M302V;ENSP00000437860:M235V	ENSP00000345412:M354V	M	-	1	0	CPSF7	60940187	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.786000	0.47790	2.126000	0.65437	0.528000	0.53228	ATG	.	T|1.000;C|0.000		0.517	CPSF7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347835.2	NM_024811		C	61183611	T	C	61183611	3	2	355	1	0	0	0	0	1	0	0	0	3832	1464	51	2	500	2	CPSF7	11	61183611	Missense_Mutation	SNP	T	TCGA-WX-AA46-01A-11D-A38X-10		61183611	73822905	29	50098										
CARNS1	57571	hgsc.bcm.edu	37	chr11	67191670	67191670	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	atcgagatcaacccccgcatGggtggcttctacctgcgtga	11	13	2	2			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr11:67191670G>A	ENST00000307823.3	+	9	2534	c.2082G>A	c.(2080-2082)atG>atA	p.M694I	CARNS1_ENST00000531040.1_Missense_Mutation_p.M791I|CARNS1_ENST00000423745.2_Missense_Mutation_p.M694I|CARNS1_ENST00000445895.2_Missense_Mutation_p.M817I	NM_020811.1	NP_065862.1	A5YM72	CRNS1_HUMAN	carnosine synthase 1	694	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.				ATP catabolic process (GO:0006200)|carnosine biosynthetic process (GO:0035499)		ATP binding (GO:0005524)|ATPase activity (GO:0016887)|carnosine synthase activity (GO:0047730)|metal ion binding (GO:0046872)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)	11						ACCCCCGCATGGGTGGCTTCT	0.617																																					p.M817I		Atlas-SNP	.											.	CARNS1	60	.	0			c.G2451A						.						35	39	38					11																	67191670		2131	4238	6369	SO:0001583	missense	57571	exon10			CCGCATGGGTGGC		CCDS44658.1, CCDS53667.1	11q13.1	2010-03-25	2010-03-25	2010-03-25	ENSG00000172508	ENSG00000172508			29268	protein-coding gene	gene with protein product		613368	"ATP-grasp domain containing 1"	ATPGD1		20097752	Standard	NM_020811		Approved	KIAA1394	uc010rpr.2	A5YM72		ENST00000307823.3:c.2082G>A	chr11.hg19:g.67191670G>A	ENSP00000308268:p.Met694Ile	156.0	0.0		114.0	31.0	NM_001166222	A8K1M3|B4DFC6|E9PK38|F5H427|Q8N467|Q9P2F3	Missense_Mutation	SNP	ENST00000307823.3	hg19	CCDS44658.1	.	.	.	.	.	.	.	.	.	.	g	21.0	4.088690	0.76756	.	.	ENSG00000172508	ENST00000531040;ENST00000307823;ENST00000542831;ENST00000423745;ENST00000445895	T;T;T;T	0.28666	1.6;1.6;1.6;1.6	5.54	5.54	0.83059	ATP-grasp fold (1);ATP-grasp fold, DUF201-type (1);ATP-grasp fold, subdomain 2 (1);	0.144148	0.46145	D	0.000306	T	0.52677	0.1749	M	0.66297	2.02	0.46609	D	0.999121	P;P	0.51791	0.948;0.899	P;P	0.60117	0.869;0.73	T	0.51779	-0.8662	10	0.59425	D	0.04	-41.5132	18.2385	0.89958	0.0:0.0:1.0:0.0	.	694;833	A5YM72;A5YM72-3	CRNS1_HUMAN;.	I	791;694;791;694;817	ENSP00000431670:M791I;ENSP00000308268:M694I;ENSP00000401519:M694I;ENSP00000389009:M817I	ENSP00000308268:M694I	M	+	3	0	CARNS1	66948246	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.860000	0.75473	2.614000	0.88457	0.543000	0.68304	ATG	.	.		0.617	CARNS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395501.1	NM_020811		A	67191670	G	A	67191670	3	1	355	1	0	0	0	0	1	0	0	0	2658	1348	47	3	2485	3	CARNS1	11	67191670	Missense_Mutation	SNP	G	TCGA-WX-AA46-01A-11D-A38X-10	6008059	67191670	67814846	30	50099										
TYR	7299	hgsc.bcm.edu	37	chr11	88924399	88924399	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	agccgattggaggagtacaaCagccatcagtctttatgcaa	10	9	2	0			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr11:88924399C>T	ENST00000263321.5	+	2	1351	c.849C>T	c.(847-849)aaC>aaT	p.N283N	TYR_ENST00000526139.1_3'UTR	NM_000372.4	NP_000363.1	P14679	TYRO_HUMAN	tyrosinase	283					cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process from tyrosine (GO:0006583)|thymus development (GO:0048538)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)	copper ion binding (GO:0005507)|monophenol monooxygenase activity (GO:0004503)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.0033)			Azelaic Acid(DB00548)|Mimosine(DB01055)|Monobenzone(DB00600)	AGGAGTACAACAGCCATCAGT	0.483																																					p.N283N		Atlas-SNP	.											.	TYR	130	.	0			c.C849T						.						133	121	125					11																	88924399		2201	4299	6500	SO:0001819	synonymous_variant	7299	exon2			GTACAACAGCCAT	M27160	CCDS8284.1	11q14.3	2013-09-27	2012-09-28		ENSG00000077498	ENSG00000077498	1.14.18.1		12442	protein-coding gene	gene with protein product	"oculocutaneous albinism IA"	606933					Standard	NM_000372		Approved	OCAIA, OCA1A, OCA1	uc001pcs.3	P14679	OTTHUMG00000167294	ENST00000263321.5:c.849C>T	chr11.hg19:g.88924399C>T		141.0	0.0		167.0	55.0	NM_000372	Q15675|Q15676|Q15680|Q8TAK4|Q9BYY0|Q9BZX1	Silent	SNP	ENST00000263321.5	hg19	CCDS8284.1																																																																																			.	.		0.483	TYR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394045.2	NM_000372		T	88924399	C	T	88924399	2	4	355	1	0	0	0	0	0	0	0	1	16828	477	17	3		3	TYR	11	88924399	Silent	SNP	C	TCGA-WX-AA46-01A-11D-A38X-10	21732729	88924399	46082117	31	50100										
SNX19	399979	hgsc.bcm.edu	37	chr11	130773191	130773191	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	ataagacgaagaaacttttgCatgttttcggtacatagcca	8	7	0	2			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr11:130773191C>A	ENST00000265909.4	-	8	3101	c.2532G>T	c.(2530-2532)atG>atT	p.M844I	SNX19_ENST00000530356.1_Missense_Mutation_p.M224I|SNX19_ENST00000528555.1_Missense_Mutation_p.M224I|SNX19_ENST00000534726.1_Missense_Mutation_p.M84I|SNX19_ENST00000545537.1_Missense_Mutation_p.M84I|SNX19_ENST00000539184.1_Missense_Mutation_p.M287I|SNX19_ENST00000533318.1_5'UTR	NM_014758.2	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19	844					protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(8)|ovary(3)|prostate(1)|skin(6)|urinary_tract(1)	35	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		GAAACTTTTGCATGTTTTCGG	0.448																																					p.M844I		Atlas-SNP	.											.	SNX19	84	.	0			c.G2532T						.						139	123	129					11																	130773191		2201	4297	6498	SO:0001583	missense	399979	exon8			CTTTTGCATGTTT	D87443	CCDS31721.1, CCDS73416.1	11q25	2010-04-20			ENSG00000120451	ENSG00000120451		"Sorting nexins"	21532	protein-coding gene	gene with protein product							Standard	NM_014758		Approved	KIAA0254, CHET8	uc001qgk.4	Q92543	OTTHUMG00000165663	ENST00000265909.4:c.2532G>T	chr11.hg19:g.130773191C>A	ENSP00000265909:p.Met844Ile	129.0	0.0		123.0	5.0	NM_014758	E9PKB9|Q8IV55	Missense_Mutation	SNP	ENST00000265909.4	hg19	CCDS31721.1	.	.	.	.	.	.	.	.	.	.	C	7.853	0.724442	0.15439	.	.	ENSG00000120451	ENST00000265909;ENST00000534726;ENST00000545537;ENST00000528555;ENST00000530356;ENST00000539184	T;T;T;T;T;T	0.24350	1.86;1.86;1.86;1.86;1.86;1.86	5.77	3.91	0.45181	Sorting nexin, C-terminal (1);	0.297494	0.47455	D	0.000229	T	0.13200	0.0320	N	0.17082	0.46	0.39660	D	0.9706	B;B	0.09022	0.002;0.001	B;B	0.14023	0.002;0.01	T	0.09292	-1.0681	10	0.08599	T	0.76	-6.4731	9.3858	0.38342	0.0:0.7375:0.1267:0.1358	.	287;844	F5H5D1;Q92543	.;SNX19_HUMAN	I	844;84;84;224;224;287	ENSP00000265909:M844I;ENSP00000433699:M84I;ENSP00000437982:M84I;ENSP00000435122:M224I;ENSP00000432307:M224I;ENSP00000443480:M287I	ENSP00000265909:M844I	M	-	3	0	SNX19	130278401	0.997000	0.39634	1.000000	0.80357	0.964000	0.63967	0.339000	0.19875	0.905000	0.36596	0.655000	0.94253	ATG	.	.		0.448	SNX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385649.1	NM_014758		A	130773191	C	A	130773191	3	1	355	1	0	0	0	0	1	0	0	0	14905	710	25	3	462	3	SNX19	11	130773191	Missense_Mutation	SNP	C	TCGA-WX-AA46-01A-11D-A38X-10	41848792	130773191	4233325	32	50101										
CS	1431	hgsc.bcm.edu	37	chr12	56667010	56667010	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	acaccccaaacaggaccgtgTagtaattcatctccgtcatg	7	13	3	0			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr12:56667010T>C	ENST00000351328.3	-	11	1449	c.1259A>G	c.(1258-1260)tAc>tGc	p.Y420C	CS_ENST00000548567.1_Missense_Mutation_p.Y354C|CS_ENST00000542324.2_Missense_Mutation_p.Y407C	NM_004077.2	NP_004068.2	O75390	CISY_HUMAN	citrate synthase	420					carbohydrate metabolic process (GO:0005975)|cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	citrate (Si)-synthase activity (GO:0004108)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	17		Myeloproliferative disorder(1001;0.000374)		BRCA - Breast invasive adenocarcinoma(357;6.17e-07)		CAGGACCGTGTAGTAATTCAT	0.478																																					p.Y420C		Atlas-SNP	.											.	CS	44	.	0			c.A1259G						.						97	88	91					12																	56667010		2203	4300	6503	SO:0001583	missense	1431	exon11			ACCGTGTAGTAAT		CCDS8913.1	12q13.2	2012-10-02				ENSG00000062485	2.3.3.1		2422	protein-coding gene	gene with protein product		118950					Standard	NM_004077		Approved		uc001sks.1	O75390	OTTHUMG00000170344	ENST00000351328.3:c.1259A>G	chr12.hg19:g.56667010T>C	ENSP00000342056:p.Tyr420Cys	174.0	0.0		152.0	34.0	NM_004077	Q71UT9|Q7KZH0|Q96FZ8|Q9BWN8	Missense_Mutation	SNP	ENST00000351328.3	hg19	CCDS8913.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.056042	0.76074	.	.	ENSG00000062485	ENST00000548567;ENST00000351328;ENST00000548746;ENST00000542324	.	.	.	5.33	5.33	0.75918	Citrate synthase-like, core (1);	0.000000	0.85682	D	0.000000	D	0.88362	0.6416	H	0.97829	4.085	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.993;0.996	D	0.92482	0.5993	9	0.87932	D	0	-9.2794	14.6005	0.68438	0.0:0.0:0.0:1.0	.	407;375;420	B4DJV2;B3KTN4;O75390	.;.;CISY_HUMAN	C	354;420;93;407	.	ENSP00000342056:Y420C	Y	-	2	0	CS	54953277	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.277000	0.78572	2.137000	0.66172	0.528000	0.53228	TAC	.	.		0.478	CS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408588.2	NM_004077		C	56667010	T	C	56667010	3	2	355	1	0	0	0	0	1	0	0	0	3926	1638	57	2	145	2	CS	12	56667010	Missense_Mutation	SNP	T	TCGA-WX-AA46-01A-11D-A38X-10		56667010	77184885	33	50102										
N4BP2L2	10443	hgsc.bcm.edu	37	chr13	33109968	33109968	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	agaataagtaacttctgcaaTttatttaacttttcctcttg	4	7	2	1			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr13:33109968T>A	ENST00000267068.3	-	2	1361	c.1197A>T	c.(1195-1197)aaA>aaT	p.K399N	N4BP2L2_ENST00000446957.2_Missense_Mutation_p.K399N|N4BP2L2_ENST00000399396.3_Intron|N4BP2L2_ENST00000357505.6_Intron|N4BP2L2_ENST00000504114.1_Intron	NM_014887.2	NP_055702.1	Q92802	N42L2_HUMAN	NEDD4 binding protein 2-like 2	399					negative regulation of hematopoietic stem cell differentiation (GO:1902037)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of hematopoietic stem cell proliferation (GO:1902035)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptional repressor complex (GO:0017053)	enzyme binding (GO:0019899)|RNA polymerase II transcription corepressor activity (GO:0001106)			kidney(4)|large_intestine(3)|liver(1)|lung(6)|skin(1)|urinary_tract(1)	16		Lung SC(185;0.0262)		all cancers(112;9.5e-07)|Epithelial(112;5.07e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00196)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.243)		ACTTCTGCAATTTATTTAACT	0.373																																					p.K399N		Atlas-SNP	.											.	N4BP2L2	90	.	0			c.A1197T						.						90	90	90					13																	33109968		2203	4300	6503	SO:0001583	missense	10443	exon2			CTGCAATTTATTT	U50532	CCDS9346.1, CCDS45024.1, CCDS61307.1	13q13.1	2010-12-02			ENSG00000244754	ENSG00000244754			26916	protein-coding gene	gene with protein product	"phosphonoformate immuno-associated protein 5"	615788				8812419	Standard	NM_014887		Approved	CG005, PFAAP5	uc010abe.1	Q92802	OTTHUMG00000016700	ENST00000267068.3:c.1197A>T	chr13.hg19:g.33109968T>A	ENSP00000267068:p.Lys399Asn	90.0	0.0		92.0	5.0	NM_014887	A3KME8	Missense_Mutation	SNP	ENST00000267068.3	hg19	CCDS9346.1	.	.	.	.	.	.	.	.	.	.	T	13.23	2.175795	0.38413	.	.	ENSG00000244754	ENST00000446957;ENST00000505213;ENST00000267068	T;T;T	0.47528	0.84;0.85;0.84	5.08	2.67	0.31697	.	.	.	.	.	T	0.43634	0.1256	L	0.31157	0.91	0.80722	D	1	D;D	0.64830	0.994;0.994	P;P	0.56278	0.795;0.795	T	0.23190	-1.0195	9	0.33940	T	0.23	-23.4899	5.8979	0.18949	0.2751:0.0753:0.0:0.6497	.	399;399	D6R968;Q92802	.;N42L2_HUMAN	N	399	ENSP00000394239:K399N;ENSP00000423362:K399N;ENSP00000267068:K399N	ENSP00000267068:K399N	K	-	3	2	N4BP2L2	32007968	0.985000	0.35326	1.000000	0.80357	0.992000	0.81027	0.566000	0.23593	0.991000	0.38814	0.528000	0.53228	AAA	.	.		0.373	N4BP2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044421.1	NM_014887		A	33109968	T	A	33109968	3	1	355	1	0	0	0	0	1	0	0	0	10121	1490	52	4	2435	4	N4BP2L2	13	33109968	Missense_Mutation	SNP	T	TCGA-WX-AA46-01A-11D-A38X-10		33109968	82059910	34	50103										
SPG20	23111	hgsc.bcm.edu	37	chr13	36905735	36905735	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	gatataaccagtcacaaaccTgaaaggattcattagaagaa	7	7	2	3			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr13:36905735T>C	ENST00000451493.1	-	3	1028		c.e3-2		SPG20_ENST00000438666.2_Splice_Site|SPG20_ENST00000495510.1_Splice_Site|SPG20_ENST00000494062.2_Splice_Site|SPG20_ENST00000355182.4_Splice_Site	NM_001142295.1	NP_001135767.1	Q8N0X7	SPG20_HUMAN	spastic paraplegia 20 (Troyer syndrome)						abscission (GO:0009838)|adipose tissue development (GO:0060612)|cell death (GO:0008219)|cell division (GO:0051301)|lipid particle organization (GO:0034389)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of collateral sprouting in absence of injury (GO:0048698)|neuromuscular process (GO:0050905)|regulation of mitochondrial membrane potential (GO:0051881)	cytoplasm (GO:0005737)|lipid particle (GO:0005811)|midbody (GO:0030496)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	27		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;2.42e-08)|Epithelial(112;1.58e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00128)|BRCA - Breast invasive adenocarcinoma(63;0.0125)|GBM - Glioblastoma multiforme(144;0.026)		GTCACAAACCTGAAAGGATTC	0.308																																					.		Atlas-SNP	.											.	SPG20	87	.	0			c.811-2A>G						.						43	43	43					13																	36905735		2203	4300	6503	SO:0001630	splice_region_variant	23111	exon4			CAAACCTGAAAGG	AB011182	CCDS9356.1	13q13.1	2008-07-04	2007-04-23		ENSG00000133104	ENSG00000133104			18514	protein-coding gene	gene with protein product	"spartin"	607111				6022528, 12134148	Standard	NM_001142294		Approved	KIAA0610, TAHCCP1	uc001uvm.3	Q8N0X7	OTTHUMG00000016730	ENST00000451493.1:c.811-2A>G	chr13.hg19:g.36905735T>C		83.0	0.0		92.0	30.0	NM_015087	O60349|Q86Y67|Q9H1T2|Q9H1T3	Splice_Site	SNP	ENST00000451493.1	hg19	CCDS9356.1	.	.	.	.	.	.	.	.	.	.	T	14.61	2.586730	0.46110	.	.	ENSG00000133104	ENST00000438666;ENST00000355182;ENST00000451493;ENST00000423217	.	.	.	5.69	4.49	0.54785	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.0141	0.53303	0.1296:0.0:0.0:0.8704	.	.	.	.	.	-1	.	.	.	-	.	.	SPG20	35803735	1.000000	0.71417	0.818000	0.32626	0.612000	0.37316	7.283000	0.78640	0.957000	0.37930	0.459000	0.35465	.	.	.		0.308	SPG20-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044494.2		Intron	C	36905735	T	C	36905735	5	2	355	1	0	0	0	0	0	0	1	0	15057	1594	55	2	1219	2	SPG20	13	36905735	Splice_Site	SNP	T	TCGA-WX-AA46-01A-11D-A38X-10	3795767	36905735	78264143	35	50104										
POSTN	10631	hgsc.bcm.edu	37	chr13	38153242	38153242	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	ttgatttcaattcattcaccAgaagtgtatcatttacctat	4	8	4	2			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr13:38153242A>G	ENST00000379747.4	-	14	1925	c.1808T>C	c.(1807-1809)cTg>cCg	p.L603P	POSTN_ENST00000379742.4_Missense_Mutation_p.L603P|POSTN_ENST00000379743.4_Missense_Mutation_p.L603P|POSTN_ENST00000541481.1_Missense_Mutation_p.L603P|POSTN_ENST00000541179.1_Missense_Mutation_p.L603P|POSTN_ENST00000379749.4_Missense_Mutation_p.L603P	NM_006475.2	NP_006466.2	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor	603	FAS1 4. {ECO:0000255|PROSITE- ProRule:PRU00082, ECO:0000305}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of Notch signaling pathway (GO:0008593)|skeletal system development (GO:0001501)|tissue development (GO:0009888)	proteinaceous extracellular matrix (GO:0005578)|trans-Golgi network (GO:0005802)	heparin binding (GO:0008201)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(16)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	59		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)		TTCATTCACCAGAAGTGTATC	0.308																																					p.L603P		Atlas-SNP	.											.	POSTN	161	.	0			c.T1808C						.						81	73	76					13																	38153242		2201	4297	6498	SO:0001583	missense	10631	exon14			TTCACCAGAAGTG	D13665	CCDS9364.1, CCDS45034.1, CCDS53864.1, CCDS66530.1, CCDS66531.1	13q13.3	2008-02-05			ENSG00000133110	ENSG00000133110			16953	protein-coding gene	gene with protein product		608777				8363580, 12235007	Standard	NM_006475		Approved	OSF-2, PN, periostin	uc001uwo.4	Q15063	OTTHUMG00000016751	ENST00000379747.4:c.1808T>C	chr13.hg19:g.38153242A>G	ENSP00000369071:p.Leu603Pro	107.0	0.0		154.0	21.0	NM_006475	B1ALD8|C0IMJ1|C0IMJ2|C0IMJ4|D2KRH7|F5H628|Q15064|Q29XZ0|Q3KPJ5|Q5VSY5|Q8IZF9	Missense_Mutation	SNP	ENST00000379747.4	hg19	CCDS9364.1	.	.	.	.	.	.	.	.	.	.	A	14.39	2.521274	0.44866	.	.	ENSG00000133110	ENST00000541179;ENST00000379749;ENST00000379747;ENST00000379743;ENST00000379742;ENST00000541481	D;D;D;D;D;D	0.90844	-2.74;-2.74;-2.74;-2.74;-2.74;-2.74	5.23	5.23	0.72850	FAS1 domain (5);	0.282386	0.32533	N	0.005968	D	0.93625	0.7964	M	0.73598	2.24	0.80722	D	1	D;P;P;P;D;P;P	0.54601	0.96;0.951;0.86;0.915;0.967;0.731;0.86	P;P;P;P;P;P;P	0.58077	0.832;0.742;0.723;0.635;0.67;0.477;0.723	D	0.93060	0.6473	10	0.37606	T	0.19	.	15.1173	0.72413	1.0:0.0:0.0:0.0	.	603;603;603;603;603;603;603	C0IMJ4;F5H628;B1ALD8;Q15063-3;Q15063-4;Q15063-2;Q15063	.;.;.;.;.;.;POSTN_HUMAN	P	603	ENSP00000437959:L603P;ENSP00000369073:L603P;ENSP00000369071:L603P;ENSP00000369067:L603P;ENSP00000369066:L603P;ENSP00000437953:L603P	ENSP00000369066:L603P	L	-	2	0	POSTN	37051242	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	6.294000	0.72738	1.971000	0.57363	0.383000	0.25322	CTG	.	.		0.308	POSTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044566.2	NM_006475		G	38153242	A	G	38153242	3	3	355	1	0	0	0	0	1	0	0	0	12268	188	7	2	742	2	POSTN	13	38153242	Missense_Mutation	SNP	A	TCGA-WX-AA46-01A-11D-A38X-10	1247507	38153242	77016636	36	50105										
COL4A2	1284	hgsc.bcm.edu	37	chr13	111125290	111125290	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	ttttagggttcataggacccCgaggatccaaaggtgcagtg	13	8	1	0			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr13:111125290C>T	ENST00000360467.5	+	29	2524	c.2218C>T	c.(2218-2220)Cga>Tga	p.R740*		NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	740	Triple-helical region.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	extracellular matrix structural constituent (GO:0005201)			NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	80	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			CATAGGACCCCGAGGATCCAA	0.592																																					p.R740X		Atlas-SNP	.											.	COL4A2	178	.	0			c.C2218T						.						9	9	9					13																	111125290		1800	4036	5836	SO:0001587	stop_gained	1284	exon29			GGACCCCGAGGAT	AK025912	CCDS41907.1	13q34	2013-09-05			ENSG00000134871	ENSG00000134871		"Collagens"	2203	protein-coding gene	gene with protein product	"canstatin", "collagen type IV alpha 2"	120090				2439508, 3025878	Standard	NM_001846		Approved	FLJ22259, DKFZp686I14213	uc001vqx.3	P08572	OTTHUMG00000017344	ENST00000360467.5:c.2218C>T	chr13.hg19:g.111125290C>T	ENSP00000353654:p.Arg740*	207.0	0.0		198.0	14.0	NM_001846	Q14052|Q548C3|Q5VZA9|Q66K23	Nonsense_Mutation	SNP	ENST00000360467.5	hg19	CCDS41907.1	.	.	.	.	.	.	.	.	.	.	C	42	9.381156	0.99155	.	.	ENSG00000134871	ENST00000360467;ENST00000257309	.	.	.	5.37	4.43	0.53597	.	0.000000	0.43747	D	0.000533	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09084	T	0.74	.	13.9817	0.64308	0.2362:0.7638:0.0:0.0	.	.	.	.	X	740	.	ENSP00000257309:R740X	R	+	1	2	COL4A2	109923291	0.995000	0.38212	1.000000	0.80357	0.854000	0.48673	0.941000	0.29005	2.516000	0.84829	0.563000	0.77884	CGA	.	.		0.592	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846		T	111125290	C	T	111125290	4	4	355	1	0	0	0	0	0	1	0	0	3692	644	23	1	2328	1	COL4A2	13	111125290	Nonsense_Mutation	SNP	C	TCGA-WX-AA46-01A-11D-A38X-10	72972048	111125290	4044588	37	50106										
PSMC6	5706	hgsc.bcm.edu	37	chr14	53175062	53175062	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	aagaacttaccaagcagtatGaaaagtctgaaaatgatctg	8	6	2	4			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr14:53175062G>T	ENST00000606149.1	+	2	137	c.121G>T	c.(121-123)Gaa>Taa	p.E41*	PSMC6_ENST00000445930.2_Nonsense_Mutation_p.E55*	NM_002806.3	NP_002797.3	P62333	PRS10_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 6	41					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|protein binding, bridging (GO:0030674)			breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	19	Breast(41;0.176)					CAAGCAGTATGAAAAGTCTGA	0.363																																					p.E55X		Atlas-SNP	.											.	PSMC6	71	.	0			c.G163T						.						112	110	111					14																	53175062		2203	4300	6503	SO:0001587	stop_gained	5706	exon2			CAGTATGAAAAGT		CCDS9710.2	14q22.1	2010-04-21			ENSG00000100519	ENSG00000100519		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9553	protein-coding gene	gene with protein product		602708				8674546, 9473509	Standard	NM_002806		Approved	p42	uc010tqx.2	P62333	OTTHUMG00000152333	ENST00000606149.1:c.121G>T	chr14.hg19:g.53175062G>T	ENSP00000475721:p.Glu41*	147.0	0.0		132.0	42.0	NM_002806	B2R975|P49719|Q6IBU3|Q92524	Nonsense_Mutation	SNP	ENST00000606149.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	27.0|27.0	4.788983|4.788983	0.90367|0.90367	.|.	.|.	ENSG00000100519|ENSG00000100519	ENST00000445930|ENST00000556813	.|.	.|.	.|.	5.17|5.17	5.17|5.17	0.71159|0.71159	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|.	.|.	.|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.25106|.	T|.	0.35|.	.|.	19.0331|19.0331	0.92965|0.92965	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|L	55|40	.|.	ENSP00000401802:E55X|.	E|X	+|+	1|2	0|2	PSMC6|PSMC6	52244812|52244812	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.913000|0.913000	0.54294|0.54294	9.378000|9.378000	0.97191|0.97191	2.570000|2.570000	0.86706|0.86706	0.561000|0.561000	0.74099|0.74099	GAA|TGA	.	.		0.363	PSMC6-018	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000470741.1	NM_002806		T	53175062	G	T	53175062	4	4	355	1	0	0	0	0	0	1	0	0	12703	1291	45	3	169	3	PSMC6	14	53175062	Nonsense_Mutation	SNP	G	TCGA-WX-AA46-01A-11D-A38X-10		53175062	54174478	38	50107										
PPP2R5C	5527	hgsc.bcm.edu	37	chr14	102356589	102356590	+	Frame_Shift_Del	DEL	AG	AG	-													0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	tctaggtttatttatgaaacAgagcatcataatggcatagc					rs4617782		TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr14:102356589_102356590delAG	ENST00000334743.5	+	6	693_694	c.645_646delAG	c.(643-648)acagagfs	p.E216fs	PPP2R5C_ENST00000445439.3_Frame_Shift_Del_p.E216fs|PPP2R5C_ENST00000350249.3_Frame_Shift_Del_p.E216fs|PPP2R5C_ENST00000422945.2_Frame_Shift_Del_p.E247fs|PPP2R5C_ENST00000328724.5_Frame_Shift_Del_p.E271fs|PPP2R5C_ENST00000557095.1_Frame_Shift_Del_p.E216fs	NM_002719.3	NP_002710.2	Q13362	2A5G_HUMAN	protein phosphatase 2, regulatory subunit B', gamma	216					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of cell proliferation (GO:0008285)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	chromosome, centromeric region (GO:0000775)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	20						TTTATGAAACAGAGCATCATAA	0.386																																					p.270_270del		Atlas-INDEL	.											.	PPP2R5C	74	.	0			c.809_810del						.																																			SO:0001589	frameshift_variant	5527	exon8			.	L42375	CCDS9964.1, CCDS9965.1, CCDS45163.1, CCDS53911.1, CCDS53912.1	14q32.31	2010-06-18	2010-04-14		ENSG00000078304	ENSG00000078304		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9311	protein-coding gene	gene with protein product		601645	"protein phosphatase 2, regulatory subunit B (B56), gamma isoform", "protein phosphatase 2, regulatory subunit B', gamma isoform"			7592815	Standard	NM_002719		Approved	B56G, PR61G	uc001ykk.3	Q13362		ENST00000334743.5:c.645_646delAG	chr14.hg19:g.102356591_102356592delAG	ENSP00000333905:p.Glu216fs	137.0	0.0		115.0	27.0	NM_001161726	B4DYJ8|B5BUA5|F5GWP3|Q14391|Q15060|Q15174|Q6ZN33	Frame_Shift_Del	DEL	ENST00000334743.5	hg19	CCDS9964.1																																																																																			.	.		0.386	PPP2R5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414373.2	NM_002719		-	102356590	AG	-	102356589	7	5	355	1	0	1	0	1	0	0	0	0	12406	175	7	0	1036	0	PPP2R5C	14	102356589	Frame_Shift_Del	DEL	AG	TCGA-WX-AA46-01A-11D-A38X-10	49181527	102356589	4992951	39	50108										
GCNT3	9245	hgsc.bcm.edu	37	chr15	59911450	59911450	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	cctctgggccacccttcagcGtgcacggtggatgcctggct	13	15	2	0	rs142393489		TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr15:59911450G>A	ENST00000396065.1	+	3	1461	c.1013G>A	c.(1012-1014)cGt>cAt	p.R338H	GCNT3_ENST00000560585.1_Missense_Mutation_p.R338H	NM_004751.2	NP_004742.1	O95395	GCNT3_HUMAN	glucosaminyl (N-acetyl) transferase 3, mucin type	338					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|immunoglobulin production in mucosal tissue (GO:0002426)|intestinal absorption (GO:0050892)|kidney morphogenesis (GO:0060993)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|tissue morphogenesis (GO:0048729)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylgalactosaminyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0047225)|beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)|N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)			central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						ACCCTTCAGCGTGCACGGTGG	0.507																																					p.R338H		Atlas-SNP	.											GCNT3,NS,carcinoma,+1,1	GCNT3	42	.	0			c.G1013A						.						120	111	114					15																	59911450		2190	4290	6480	SO:0001583	missense	9245	exon3			TTCAGCGTGCACG	AF102542	CCDS10172.1	15q22	2013-02-25			ENSG00000140297	ENSG00000140297	2.4.1.102, 2.4.1.150	"Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	4205	protein-coding gene	gene with protein product		606836				9915862, 9988682	Standard	NM_004751		Approved	C2GnT-M, C2/4GnT, C2GnT2	uc002age.3	O95395	OTTHUMG00000132726	ENST00000396065.1:c.1013G>A	chr15.hg19:g.59911450G>A	ENSP00000379377:p.Arg338His	109.0	0.0		135.0	7.0	NM_004751		Missense_Mutation	SNP	ENST00000396065.1	hg19	CCDS10172.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.991162	0.93106	.	.	ENSG00000140297	ENST00000396065	T	0.11277	2.79	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.40322	0.1112	M	0.84846	2.72	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.27054	-1.0085	10	0.49607	T	0.09	.	19.4741	0.94979	0.0:0.0:1.0:0.0	.	338	O95395	GCNT3_HUMAN	H	338	ENSP00000379377:R338H	ENSP00000379377:R338H	R	+	2	0	GCNT3	57698742	1.000000	0.71417	0.997000	0.53966	0.990000	0.78478	9.869000	0.99810	2.595000	0.87683	0.655000	0.94253	CGT	.	G|1.000;C|0.000		0.507	GCNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256068.1	NM_004751		A	59911450	G	A	59911450	3	1	355	1	0	0	0	0	1	0	0	0	6310	1145	40	1	1015	1	GCNT3	15	59911450	Missense_Mutation	SNP	G	TCGA-WX-AA46-01A-11D-A38X-10		59911450	42619942	40	50109										
TBL3	10607	hgsc.bcm.edu	37	chr16	2025894	2025894	+	Missense_Mutation	SNP	G	G	T													0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	cgtggcctccaatagcccctGcctaaaagtgtttgagctgc							TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr16:2025894G>T	ENST00000568546.1	+	11	1201	c.1073G>T	c.(1072-1074)tGc>tTc	p.C358F		NM_006453.2	NP_006444.2	Q12788	TBL3_HUMAN	transducin (beta)-like 3	358					G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|intracellular signal transduction (GO:0035556)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)			breast(1)|endometrium(2)|kidney(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	18						AATAGCCCCTGCCTAAAAGTG	0.637																																					p.C358F	Melanoma(118;616 1651 35077 38081 48633)	Atlas-SNP	.											.	TBL3	54	.	0			c.G1073T						.						70	68	69					16																	2025894		2198	4300	6498	SO:0001583	missense	10607	exon11			GCCCCTGCCTAAA	U02609	CCDS10453.1	16p13.3	2013-01-10			ENSG00000183751	ENSG00000183751		"WD repeat domain containing"	11587	protein-coding gene	gene with protein product		605915				8307582	Standard	NM_006453		Approved	SAZD, UTP13	uc002cnu.1	Q12788	OTTHUMG00000128710	ENST00000568546.1:c.1073G>T	chr16.hg19:g.2025894G>T	ENSP00000454836:p.Cys358Phe	209.0	0.0		113.0	18.0	NM_006453	Q59GD6|Q8IVB7|Q96A78	Missense_Mutation	SNP	ENST00000568546.1	hg19	CCDS10453.1	.	.	.	.	.	.	.	.	.	.	G	14.20	2.465845	0.43839	.	.	ENSG00000183751	ENST00000332704	.	.	.	4.75	3.78	0.43462	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (2);WD40-repeat-containing domain (1);	0.715221	0.13405	N	0.390350	T	0.31451	0.0797	N	0.22421	0.69	0.40625	D	0.981806	B;B	0.30439	0.001;0.279	B;B	0.27608	0.0;0.081	T	0.13791	-1.0496	9	0.15499	T	0.54	-14.1595	5.077	0.14636	0.289:0.0:0.711:0.0	.	120;358	A0JLS5;Q12788	.;TBL3_HUMAN	F	358	.	ENSP00000331815:C358F	C	+	2	0	TBL3	1965895	1.000000	0.71417	1.000000	0.80357	0.871000	0.50021	6.045000	0.71020	2.194000	0.70268	0.561000	0.74099	TGC	.	.		0.637	TBL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250615.3	NM_006453		T	2025894	G	T	2025894	3	4	355	1	0	0	0	0	1	0	0	0	15658	1319	46	3	1115	3	TBL3	16	2025894	Missense_Mutation	SNP	G	TCGA-WX-AA46-01A-11D-A38X-10		2025894	88328859	41	50110	259	2								
TBL3	10607	hgsc.bcm.edu	37	chr16	2025898	2025898	+	Silent	SNP	A	A	G													0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	gcctccaatagcccctgcctAaaagtgtttgagctgcagac					rs556701886		TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr16:2025898A>G	ENST00000568546.1	+	11	1205	c.1077A>G	c.(1075-1077)ctA>ctG	p.L359L		NM_006453.2	NP_006444.2	Q12788	TBL3_HUMAN	transducin (beta)-like 3	359					G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|intracellular signal transduction (GO:0035556)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)			breast(1)|endometrium(2)|kidney(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	18						GCCCCTGCCTAAAAGTGTTTG	0.637																																					p.L359L	Melanoma(118;616 1651 35077 38081 48633)	Atlas-SNP	.											.	TBL3	54	.	0			c.A1077G						.						68	66	66					16																	2025898		2198	4300	6498	SO:0001819	synonymous_variant	10607	exon11			CTGCCTAAAAGTG	U02609	CCDS10453.1	16p13.3	2013-01-10			ENSG00000183751	ENSG00000183751		"WD repeat domain containing"	11587	protein-coding gene	gene with protein product		605915				8307582	Standard	NM_006453		Approved	SAZD, UTP13	uc002cnu.1	Q12788	OTTHUMG00000128710	ENST00000568546.1:c.1077A>G	chr16.hg19:g.2025898A>G		208.0	0.0		120.0	20.0	NM_006453	Q59GD6|Q8IVB7|Q96A78	Silent	SNP	ENST00000568546.1	hg19	CCDS10453.1																																																																																			.	.		0.637	TBL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250615.3	NM_006453		G	2025898	A	G	2025898	2	3	355	1	0	0	0	0	0	0	0	1	15658	349	13	2		2	TBL3	16	2025898	Silent	SNP	A	TCGA-WX-AA46-01A-11D-A38X-10	4	2025898	88328855	42	50111	259	2								
MT1H	4496	hgsc.bcm.edu	37	chr16	56704900	56704900	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	gaagtgcagctgctgtgcctGatgtcgggacagccctgctg	15	11	0	1			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr16:56704900G>A	ENST00000332374.4	+	3	256	c.185G>A	c.(184-186)tGa>tAa	p.*62*	MT1G_ENST00000379811.3_5'Flank|MT1G_ENST00000444837.2_5'Flank|MT1H_ENST00000569155.1_3'UTR|MT1G_ENST00000568675.1_5'Flank|MT1G_ENST00000569500.1_5'Flank	NM_005951.2	NP_005942.1	P80294	MT1H_HUMAN	metallothionein 1H	0					cellular response to cadmium ion (GO:0071276)|cellular response to zinc ion (GO:0071294)|negative regulation of growth (GO:0045926)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			lung(5)	5						TGCTGTGCCTGATGTCGGGAC	0.512																																					p.X62X		Atlas-SNP	.											.	MT1H	19	.	0			c.G185A						.						87	81	83					16																	56704900		2198	4300	6498	SO:0001819	synonymous_variant	4496	exon3			GTGCCTGATGTCG	BC008408	CCDS10767.1	16q13	2008-02-05			ENSG00000205358	ENSG00000205358		"Metallothioneins"	7400	protein-coding gene	gene with protein product		156354		MT1		2286373, 8049263	Standard	NM_005951		Approved		uc002ejw.3	P80294	OTTHUMG00000133283	ENST00000332374.4:c.185G>A	chr16.hg19:g.56704900G>A		62.0	0.0		44.0	8.0	NM_005951	B2RUY6	Silent	SNP	ENST00000332374.4	hg19	CCDS10767.1																																																																																			.	.		0.512	MT1H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257063.1	NM_005951		A	56704900	G	A	56704900	2	1	355	1	0	0	0	0	0	0	0	1	9911	1285	45	3		3	MT1H	16	56704900	Silent	SNP	G	TCGA-WX-AA46-01A-11D-A38X-10	54679002	56704900	33649853	43	50112										
C16orf7	9605	hgsc.bcm.edu	37	chr16	89783145	89783145	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	gcaggagacccaccaagcttGgcggccgtcgactgggccct	14	15	0	1			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr16:89783145G>T	ENST00000389386.3	-	3	385	c.261C>A	c.(259-261)gcC>gcA	p.A87A	VPS9D1-AS1_ENST00000562298.1_RNA|VPS9D1-AS1_ENST00000562866.1_RNA|VPS9D1_ENST00000561976.1_Silent_p.A17A	NM_004913.2	NP_004904.2	Q9Y2B5	VP9D1_HUMAN	VPS9 domain containing 1	87					ATP synthesis coupled proton transport (GO:0015986)		GTPase activator activity (GO:0005096)|transporter activity (GO:0005215)										CACCAAGCTTGGCGGCCGTCG	0.647																																					p.A87A		Atlas-SNP	.											.	.	.	.	0			c.C261A						.						23	29	27					16																	89783145		1915	4111	6026	SO:0001819	synonymous_variant	9605	exon3			AAGCTTGGCGGCC	AB018551	CCDS42220.1	16q24.3	2012-10-09	2012-10-09	2012-10-09	ENSG00000075399	ENSG00000075399			13526	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 7"	C16orf7		10231027	Standard	NM_004913		Approved	ATP-BL	uc002fom.1	Q9Y2B5	OTTHUMG00000173219	ENST00000389386.3:c.261C>A	chr16.hg19:g.89783145G>T		89.0	0.0		82.0	4.0	NM_004913		Silent	SNP	ENST00000389386.3	hg19	CCDS42220.1																																																																																			.	.		0.647	VPS9D1-002	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422508.1	NM_004913		T	89783145	G	T	89783145	2	4	355	1	0	0	0	0	0	0	0	1	1830	1335	47	3		3	C16orf7	16	89783145	Silent	SNP	G	TCGA-WX-AA46-01A-11D-A38X-10	33078245	89783145	571608	44	50113										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11515011	11515011	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	taatcaactgagaacaataaCggtgaggggcatggccaagc	12	8	1	2			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr17:11515011C>G	ENST00000262442.4	+	4	886	c.818C>G	c.(817-819)aCg>aGg	p.T273R	DNAH9_ENST00000579828.1_Missense_Mutation_p.T273R|DNAH9_ENST00000454412.2_Missense_Mutation_p.T273R	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	273	Stem. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		AGAACAATAACGGTGAGGGGC	0.448																																					p.T273R		Atlas-SNP	.											.	DNAH9	695	.	0			c.C818G						.						144	129	134					17																	11515011		2203	4300	6503	SO:0001583	missense	1770	exon4			CAATAACGGTGAG	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.818C>G	chr17.hg19:g.11515011C>G	ENSP00000262442:p.Thr273Arg	139.0	0.0		127.0	10.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	hg19	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	C	0.004	-2.312430	0.00237	.	.	ENSG00000007174	ENST00000262442;ENST00000454412	T;T	0.53857	0.6;0.6	5.69	2.32	0.28847	Dynein heavy chain, domain-1 (1);	0.476491	0.22576	N	0.058271	T	0.13756	0.0333	N	0.00446	-1.495	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.09377	0.002;0.004	T	0.30446	-0.9978	10	0.07482	T	0.82	.	4.8323	0.13447	0.56:0.1552:0.2848:0.0	.	273;273	Q9NYC9;E7EP17	DYH9_HUMAN;.	R	273	ENSP00000262442:T273R;ENSP00000414874:T273R	ENSP00000262442:T273R	T	+	2	0	DNAH9	11455736	0.994000	0.37717	0.004000	0.12327	0.010000	0.07245	2.496000	0.45346	0.443000	0.26582	-0.311000	0.09066	ACG	.	.		0.448	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		G	11515011	C	G	11515011	3	3	355	1	0	0	0	0	1	0	0	0	4610	536	19	4	832	4	DNAH9	17	11515011	Missense_Mutation	SNP	C	TCGA-WX-AA46-01A-11D-A38X-10		11515011	69680199	45	50114										
SEPT4	5414	hgsc.bcm.edu	37	chr17	56604304	56604304	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	ttcacgaacttgctcagttcTccatcatccgtggtgtcctc	7	14	4	0			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr17:56604304T>A	ENST00000317268.3	-	2	272	c.96A>T	c.(94-96)ggA>ggT	p.G32G	SEPT4_ENST00000317256.6_Silent_p.G13G|SEPT4_ENST00000580791.1_5'UTR|SEPT4_ENST00000579371.1_Intron|SEPT4_ENST00000580844.1_Intron|SEPT4_ENST00000580809.1_Intron|SEPT4_ENST00000583114.1_5'UTR|SEPT4_ENST00000426861.1_Silent_p.G13G|RP11-112H10.4_ENST00000580769.1_RNA|RP11-112H10.4_ENST00000578022.1_RNA|SEPT4_ENST00000412945.3_Silent_p.G24G|SEPT4_ENST00000393086.1_Silent_p.G13G|RP11-112H10.4_ENST00000580589.1_RNA|SEPT4_ENST00000457347.2_Silent_p.G47G	NM_004574.3	NP_004565.1	O43236	SEPT4_HUMAN	septin 4	32					apoptotic process (GO:0006915)|brain development (GO:0007420)|cell cycle (GO:0007049)|cell division (GO:0051301)|GTP catabolic process (GO:0006184)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of protein ubiquitination (GO:0031398)|regulation of apoptotic process (GO:0042981)|sperm capacitation (GO:0048240)|sperm mitochondrion organization (GO:0030382)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|sperm annulus (GO:0097227)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)			NS(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	18	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TGCTCAGTTCTCCATCATCCG	0.592																																					p.G47G		Atlas-SNP	.											.	SEPT4	48	.	0			c.A141T						.						76	82	80					17																	56604304		2203	4300	6503	SO:0001819	synonymous_variant	5414	exon3			CAGTTCTCCATCA	AF073312	CCDS11609.1, CCDS11610.1, CCDS45743.1, CCDS56041.1, CCDS58581.1, CCDS58582.1	17q22	2013-01-21	2005-01-11	2005-01-12	ENSG00000108387	ENSG00000108387		"Septins"	9165	protein-coding gene	gene with protein product	"bradeoin", "septin-M"	603696	"peanut-like 2 (Drosophila)"	PNUTL2		9889007	Standard	NM_001198713		Approved	H5, CE5B3, hucep-7, ARTS, hCDCREL-2, MART	uc002iwm.2	O43236		ENST00000317268.3:c.96A>T	chr17.hg19:g.56604304T>A		82.0	0.0		57.0	14.0	NM_001256782	B2RD42|B3KSX9|B4DXC6|B4DXV5|Q6IAP3|Q9H315|Q9UM58	Silent	SNP	ENST00000317268.3	hg19	CCDS11610.1																																																																																			.	.		0.592	SEPT4-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445420.1	NM_080417		A	56604304	T	A	56604304	2	1	355	1	0	0	0	0	0	0	0	1	14081	1538	54	4		4	SEPT4	17	56604304	Silent	SNP	T	TCGA-WX-AA46-01A-11D-A38X-10	45089293	56604304	24590906	46	50115										
CLTC	1213	hgsc.bcm.edu	37	chr17	57724931	57724931	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	gagtctcagccagtgaaaatGtttgatcgccattctagcct	9	10	2	2			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr17:57724931G>A	ENST00000269122.3	+	3	697	c.423G>A	c.(421-423)atG>atA	p.M141I	CLTC_ENST00000393043.1_Missense_Mutation_p.M141I|CLTC_ENST00000579456.1_Intron	NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	141	Globular terminal domain.|WD40-like repeat 3.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)		CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					CAGTGAAAATGTTTGATCGCC	0.418			T	"ALK, TFE3"	"ALCL, renal "																																p.M141I		Atlas-SNP	.		Dom	yes		17	17q11-qter	1213	"clathrin, heavy polypeptide (Hc)"		L	.	CLTC	124	.	0			c.G423A						.						177	162	168					17																	57724931		2203	4300	6503	SO:0001583	missense	1213	exon3			GAAAATGTTTGAT	X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367			2092	protein-coding gene	gene with protein product		118955	"clathrin, heavy polypeptide (Hc)", "clathrin, heavy chain", "clathrin, heavy polypeptide-like 2"	CLTCL2		1765375, 7584026	Standard	NM_004859		Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.423G>A	chr17.hg19:g.57724931G>A	ENSP00000269122:p.Met141Ile	168.0	0.0		186.0	13.0	NM_004859	D3DU00|Q6N0A0|Q86TF2	Missense_Mutation	SNP	ENST00000269122.3	hg19	CCDS32696.1	.	.	.	.	.	.	.	.	.	.	G	11.47	1.649531	0.29336	.	.	ENSG00000141367	ENST00000269122;ENST00000393043	T;T	0.20332	2.08;2.08	5.79	5.79	0.91817	Clathrin, heavy chain, propeller, N-terminal (1);Clathrin, heavy chain, linker/propeller domain (1);	0.047357	0.85682	D	0.000000	T	0.18130	0.0435	L	0.28740	0.885	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.10450	0.005;0.003	T	0.10200	-1.0640	10	0.11182	T	0.66	.	20.0411	0.97590	0.0:0.0:1.0:0.0	.	141;141	Q00610;Q00610-2	CLH1_HUMAN;.	I	141	ENSP00000269122:M141I;ENSP00000376763:M141I	ENSP00000269122:M141I	M	+	3	0	CLTC	55079713	1.000000	0.71417	1.000000	0.80357	0.732000	0.41865	3.453000	0.52978	2.739000	0.93911	0.655000	0.94253	ATG	.	.		0.418	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258859.1	NM_004859		A	57724931	G	A	57724931	3	1	355	1	0	0	0	0	1	0	0	0	3568	1377	48	3	433	3	CLTC	17	57724931	Missense_Mutation	SNP	G	TCGA-WX-AA46-01A-11D-A38X-10	1120627	57724931	23470279	47	50116										
CCDC46	201134	hgsc.bcm.edu	37	chr17	64128831	64128831	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	gtccatcttctctgtgagttGgactcaaggagtgtgatctc	11	9	4	2			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr17:64128831G>T	ENST00000392769.2	-	5	739	c.521C>A	c.(520-522)cCa>cAa	p.P174Q	CEP112_ENST00000537949.1_Missense_Mutation_p.P174Q|CEP112_ENST00000535342.2_Missense_Mutation_p.P174Q	NM_145036.3	NP_659473.2	Q8N8E3	CE112_HUMAN	centrosomal protein 112kDa	174					receptor localization to synapse (GO:0097120)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(8)|lung(11)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	28						TCTGTGAGTTGGACTCAAGGA	0.383																																					p.P174Q		Atlas-SNP	.											.	CEP112	192	.	0			c.C521A						.						108	100	103					17																	64128831		2203	4300	6503	SO:0001583	missense	201134	exon5			TGAGTTGGACTCA	AF458591	CCDS32710.1, CCDS32711.1	17q24.2	2014-02-20	2011-05-06	2011-05-06	ENSG00000154240	ENSG00000154240			28514	protein-coding gene	gene with protein product			"coiled-coil domain containing 46"	CCDC46		21399614	Standard	NM_145036		Approved	MGC33887	uc002jfl.3	Q8N8E3		ENST00000392769.2:c.521C>A	chr17.hg19:g.64128831G>T	ENSP00000376522:p.Pro174Gln	89.0	0.0		112.0	5.0	NM_001199165	Q6PIB5|Q8NCR4|Q8NFR4	Missense_Mutation	SNP	ENST00000392769.2	hg19	CCDS32710.1	.	.	.	.	.	.	.	.	.	.	G	11.83	1.755511	0.31046	.	.	ENSG00000154240	ENST00000535342;ENST00000392769;ENST00000537949	T;T;T	0.47528	0.92;0.92;0.84	4.82	3.85	0.44370	.	0.439424	0.19202	N	0.120158	T	0.50274	0.1606	M	0.67953	2.075	0.80722	D	1	P;P	0.41131	0.739;0.739	P;P	0.45232	0.474;0.474	T	0.50964	-0.8765	10	0.52906	T	0.07	-4.6798	9.1486	0.36948	0.1024:0.0:0.8976:0.0	.	174;174	F5GYE8;Q8N8E3	.;CE112_HUMAN	Q	174	ENSP00000442784:P174Q;ENSP00000376522:P174Q;ENSP00000440775:P174Q	ENSP00000376522:P174Q	P	-	2	0	CEP112	61559293	1.000000	0.71417	0.625000	0.29200	0.561000	0.35649	3.465000	0.53064	1.161000	0.42604	0.655000	0.94253	CCA	.	.		0.383	CEP112-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446582.1	NM_145036		T	64128831	G	T	64128831	3	4	355	1	0	0	0	0	1	0	0	0	2819	1348	47	3	2604	3	CCDC46	17	64128831	Missense_Mutation	SNP	G	TCGA-WX-AA46-01A-11D-A38X-10	6403900	64128831	17066379	48	50117										
BPTF	2186	hgsc.bcm.edu	37	chr17	65916145	65916145	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	ccatagaaacatccgaaactGaaatcacaacaacagaaata	4	10	1	3			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr17:65916145G>T	ENST00000321892.4	+	15	5882	c.5821G>T	c.(5821-5823)Gaa>Taa	p.E1941*	BPTF_ENST00000306378.6_Nonsense_Mutation_p.E1815*|BPTF_ENST00000424123.3_Nonsense_Mutation_p.E1802*|BPTF_ENST00000335221.5_Nonsense_Mutation_p.E1941*			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	1941					anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			ATCCGAAACTGAAATCACAAC	0.343																																					p.E1941X		Atlas-SNP	.											.	BPTF	415	.	0			c.G5821T						.						117	120	119					17																	65916145		2203	4300	6503	SO:0001587	stop_gained	2186	exon15			GAAACTGAAATCA	AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"Zinc fingers, PHD-type"	3581	protein-coding gene	gene with protein product		601819	"fetal Alzheimer antigen"	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.5821G>T	chr17.hg19:g.65916145G>T	ENSP00000315454:p.Glu1941*	93.0	0.0		82.0	4.0	NM_004459	Q6NX67|Q7Z7D6|Q9UIG2	Nonsense_Mutation	SNP	ENST00000321892.4	hg19		.	.	.	.	.	.	.	.	.	.	G	48	14.022587	0.99775	.	.	ENSG00000171634	ENST00000306378;ENST00000335221;ENST00000321892	.	.	.	5.65	5.65	0.86999	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-19.2322	19.7228	0.96150	0.0:0.0:1.0:0.0	.	.	.	.	X	1815;1941;1941	.	ENSP00000307208:E1815X	E	+	1	0	BPTF	63346607	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	8.023000	0.88764	2.667000	0.90743	0.655000	0.94253	GAA	.	.		0.343	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459		T	65916145	G	T	65916145	4	4	355	1	0	0	0	0	0	1	0	0	1497	1291	45	3	5879	3	BPTF	17	65916145	Nonsense_Mutation	SNP	G	TCGA-WX-AA46-01A-11D-A38X-10	1787314	65916145	15279065	49	50118										
ELAC1	55520	hgsc.bcm.edu	37	chr18	48510826	48510826	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	tctgtttgatgatgaacaatTtgttgtaaaagcatttcgcc	8	6	1	3			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr18:48510826T>G	ENST00000269466.3	+	3	625	c.518T>G	c.(517-519)tTt>tGt	p.F173C	ELAC1_ENST00000591429.1_Missense_Mutation_p.F173C|RP11-729L2.2_ENST00000588256.1_Intron|RP11-729L2.2_ENST00000590722.2_Intron|ELAC1_ENST00000588577.1_Intron|SMAD4_ENST00000452201.2_Intron	NM_018696.2	NP_061166.1	Q9H777	RNZ1_HUMAN	elaC ribonuclease Z 1	173					tRNA 3'-trailer cleavage (GO:0042779)	cytosol (GO:0005829)|nucleus (GO:0005634)	endoribonuclease activity, producing 5'-phosphomonoesters (GO:0016891)|metal ion binding (GO:0046872)	p.F173C(1)		kidney(1)|large_intestine(4)|prostate(1)	6		Colorectal(6;0.0269)|all_epithelial(6;0.0729)		Colorectal(21;0.000943)|COAD - Colon adenocarcinoma(17;0.0398)|READ - Rectum adenocarcinoma(32;0.0894)|STAD - Stomach adenocarcinoma(97;0.18)		GATGAACAATTTGTTGTAAAA	0.398																																					p.F173C		Atlas-SNP	.											ELAC1,colon,carcinoma,0,1	ELAC1	17	.	1	Substitution - Missense(1)	large_intestine(1)	c.T518G						.						66	65	65					18																	48510826		2203	4300	6503	SO:0001583	missense	55520	exon3			AACAATTTGTTGT	AB029151	CCDS11949.1	18q21	2013-05-24	2013-05-24		ENSG00000141642	ENSG00000141642	3.1.26.11		14197	protein-coding gene	gene with protein product	"tRNA Z (short form)", "RNaseZ(S)"	608079	"elaC (E. coli) homolog 1", "elaC homolog 1 (E. coli)"			12711671, 21559454	Standard	NM_018696		Approved	D29	uc002lez.3	Q9H777	OTTHUMG00000132695	ENST00000269466.3:c.518T>G	chr18.hg19:g.48510826T>G	ENSP00000269466:p.Phe173Cys	113.0	0.0		138.0	14.0	NM_018696	Q9NS99	Missense_Mutation	SNP	ENST00000269466.3	hg19	CCDS11949.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.295390	0.81025	.	.	ENSG00000141642	ENST00000269466	T	0.77229	-1.08	5.95	5.95	0.96441	Beta-lactamase-like (1);	0.000000	0.85682	D	0.000000	D	0.86973	0.6062	M	0.70903	2.155	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.70487	0.969;0.969	D	0.88267	0.2927	10	0.87932	D	0	.	15.4149	0.74960	0.0:0.0:0.0:1.0	.	173;173	Q53EY2;Q9H777	.;RNZ1_HUMAN	C	173	ENSP00000269466:F173C	ENSP00000269466:F173C	F	+	2	0	ELAC1	46764824	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.906000	0.75719	2.281000	0.76405	0.528000	0.53228	TTT	.	.		0.398	ELAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255992.2			G	48510826	T	G	48510826	3	3	355	1	0	0	0	0	1	0	0	0	5048	1841	64	5	524	5	ELAC1	18	48510826	Missense_Mutation	SNP	T	TCGA-WX-AA46-01A-11D-A38X-10		48510826	29566422	50	50119										
SERPINB3	6317	hgsc.bcm.edu	37	chr18	61323171	61323171	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	ccattcccatggttctcaacGtgtccttgaggtcatagctc	8	13	2	1	rs377088096		TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr18:61323171G>A	ENST00000283752.5	-	8	1036	c.893C>T	c.(892-894)aCg>aTg	p.T298M	SERPINB11_ENST00000489748.1_RNA|SERPINB3_ENST00000332821.8_Missense_Mutation_p.T246M	NM_006919.2	NP_008850.1	P29508	SPB3_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 3	298					negative regulation of catalytic activity (GO:0043086)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)|virus receptor activity (GO:0001618)	p.T298M(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	36						GGTTCTCAACGTGTCCTTGAG	0.488																																					p.T298M		Atlas-SNP	.											SERPINB3,NS,carcinoma,0,1	SERPINB3	90	.	1	Substitution - Missense(1)	lung(1)	c.C893T						.	G	MET/THR	1,4405	2.1+/-5.4	0,1,2202	180	154	163		893	-3.2	0	18		163	0,8600		0,0,4300	no	missense	SERPINB3	NM_006919.2	81	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	298/391	61323171	1,13005	2203	4300	6503	SO:0001583	missense	6317	exon8			CTCAACGTGTCCT	U19568	CCDS11987.1	18q21.3	2014-02-18	2005-08-18		ENSG00000057149	ENSG00000057149		"Serine (or cysteine) peptidase inhibitors"	10569	protein-coding gene	gene with protein product		600517	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3"	SCC, SCCA1		7724531, 24172014	Standard	NM_006919		Approved	T4-A, HsT1196	uc002lji.3	P29508	OTTHUMG00000060403	ENST00000283752.5:c.893C>T	chr18.hg19:g.61323171G>A	ENSP00000283752:p.Thr298Met	114.0	0.0		147.0	24.0	NM_006919	A6NDM2|B2RBT5|B3W5Y6|Q53H28|Q53YB5|Q86VF3|Q86W04|Q8IWL4|Q8IXI3|Q96J21|Q9BYF8	Missense_Mutation	SNP	ENST00000283752.5	hg19	CCDS11987.1	.	.	.	.	.	.	.	.	.	.	G	8.978	0.974626	0.18736	2.27E-4	0.0	ENSG00000057149	ENST00000283752;ENST00000332821	D;D	0.84800	-1.9;-1.9	3.07	-3.17	0.05202	Serpin domain (3);	1.383540	0.04944	N	0.459085	D	0.87732	0.6251	M	0.80746	2.51	0.09310	N	1	B;D	0.55385	0.334;0.971	B;P	0.47941	0.146;0.562	T	0.81123	-0.1076	10	0.66056	D	0.02	.	11.7335	0.51752	0.6699:0.0:0.3301:0.0	.	246;298	P29508-2;P29508	.;SPB3_HUMAN	M	298;246	ENSP00000283752:T298M;ENSP00000329498:T246M	ENSP00000283752:T298M	T	-	2	0	SERPINB3	59474151	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-3.514000	0.00445	-0.831000	0.04256	-0.403000	0.06358	ACG	.	.		0.488	SERPINB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133791.1	NM_006919		A	61323171	G	A	61323171	3	1	355	1	0	0	0	0	1	0	0	0	14117	1145	40	1	283	1	SERPINB3	18	61323171	Missense_Mutation	SNP	G	TCGA-WX-AA46-01A-11D-A38X-10	12812345	61323171	16754077	51	50120										
ZNF407	55628	hgsc.bcm.edu	37	chr18	72344756	72344756	+	Nonsense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	cctgagttgtcagtgttgttCatttatatccttggatgaaa	9	6	2	2			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr18:72344756C>G	ENST00000299687.5	+	1	1781	c.1781C>G	c.(1780-1782)tCa>tGa	p.S594*	ZNF407_ENST00000582337.1_Nonsense_Mutation_p.S594*|ZNF407_ENST00000577538.1_Nonsense_Mutation_p.S594*|ZNF407_ENST00000309902.6_Nonsense_Mutation_p.S594*	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	594					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		CAGTGTTGTTCATTTATATCC	0.378																																					p.S594X		Atlas-SNP	.											.	ZNF407	231	.	0			c.C1781G						.						158	162	161					18																	72344756		1900	4118	6018	SO:0001587	stop_gained	55628	exon1			GTTGTTCATTTAT	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"Zinc fingers, C2H2-type"	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.1781C>G	chr18.hg19:g.72344756C>G	ENSP00000299687:p.Ser594*	110.0	0.0		117.0	7.0	NM_001146190	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Nonsense_Mutation	SNP	ENST00000299687.5	hg19	CCDS45885.1	.	.	.	.	.	.	.	.	.	.	C	39	7.389618	0.98255	.	.	ENSG00000215421	ENST00000299687;ENST00000309902	.	.	.	5.76	4.89	0.63831	.	0.178214	0.23696	U	0.045466	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	.	14.8311	0.70149	0.0:0.931:0.0:0.069	.	.	.	.	X	594	.	ENSP00000299687:S594X	S	+	2	0	ZNF407	70473744	0.977000	0.34250	0.001000	0.08648	0.793000	0.44817	3.184000	0.50926	-1.847000	0.01173	-0.710000	0.03640	TCA	.	.		0.378	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757		G	72344756	C	G	72344756	4	3	355	1	0	0	0	0	0	1	0	0	17902	838	29	4	1783	4	ZNF407	18	72344756	Nonsense_Mutation	SNP	C	TCGA-WX-AA46-01A-11D-A38X-10	11021585	72344756	5732492	52	50121										
DPF1	8193	hgsc.bcm.edu	37	chr19	38713312	38713312	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	cgcgcgttgtaactgcggcaGtgctcgatggcctcgcggta	15	12	0	0			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr19:38713312G>C	ENST00000420980.2	-	2	173	c.147C>G	c.(145-147)caC>caG	p.H49Q	DPF1_ENST00000456296.1_Missense_Mutation_p.H23Q|DPF1_ENST00000414789.1_5'UTR|DPF1_ENST00000412732.1_5'UTR|DPF1_ENST00000355526.4_Missense_Mutation_p.H49Q|DPF1_ENST00000416611.1_Missense_Mutation_p.H23Q	NM_004647.2	NP_004638.2	Q92782	DPF1_HUMAN	D4, zinc and double PHD fingers family 1	49					apoptotic process (GO:0006915)|nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nBAF complex (GO:0071565)	zinc ion binding (GO:0008270)			large_intestine(1)|lung(4)|ovary(1)|skin(1)	7	all_cancers(60;1.24e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			AACTGCGGCAGTGCTCGATGG	0.687																																					p.H49Q		Atlas-SNP	.											.	DPF1	54	.	0			c.C147G						.						26	26	26					19																	38713312		2200	4298	6498	SO:0001583	missense	8193	exon2			GCGGCAGTGCTCG	U43843	CCDS33008.2, CCDS46064.1, CCDS46065.1	19q13.12	2013-01-28			ENSG00000011332	ENSG00000011332		"Zinc fingers, PHD-type"	20225	protein-coding gene	gene with protein product		601670				8812431	Standard	XM_005259288		Approved	neuro-d4, NEUD4, BAF45b	uc002ohm.3	Q92782	OTTHUMG00000157164	ENST00000420980.2:c.147C>G	chr19.hg19:g.38713312G>C	ENSP00000397354:p.His49Gln	164.0	0.0		121.0	23.0	NM_001135155	B3KSY8|Q08AJ0	Missense_Mutation	SNP	ENST00000420980.2	hg19	CCDS33008.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	7.524|7.524	0.657360|0.657360	0.14580|0.14580	.|.	.|.	ENSG00000011332|ENSG00000011332	ENST00000420980;ENST00000437720;ENST00000416611;ENST00000456296;ENST00000434076|ENST00000355526	D;D;D|.	0.89123|.	-2.02;-2.0;-2.47|.	3.36|3.36	3.36|3.36	0.38483|0.38483	.|.	0.078481|.	0.48767|.	N|.	0.000168|.	T|T	0.32224|0.32224	0.0822|0.0822	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	B;B;D;P;B|.	0.89917|.	0.004;0.004;1.0;0.916;0.379|.	B;B;D;P;B|.	0.97110|.	0.007;0.012;1.0;0.821;0.241|.	T|T	0.08166|0.08166	-1.0735|-1.0735	10|5	0.13108|.	T|.	0.6|.	-17.1432|-17.1432	8.1585|8.1585	0.31185|0.31185	0.1178:0.0:0.8822:0.0|0.1178:0.0:0.8822:0.0	.|.	23;23;22;49;49|.	B4DMQ8;E9PDV3;C8C3P2;Q92782-2;Q92782|.	.;.;.;.;DPF1_HUMAN|.	Q|V	49;49;23;23;23|42	ENSP00000397354:H49Q;ENSP00000390223:H23Q;ENSP00000411569:H23Q|.	ENSP00000390223:H23Q|.	H|L	-|-	3|1	2|2	DPF1|DPF1	43405152|43405152	0.997000|0.997000	0.39634|0.39634	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	0.351000|0.351000	0.20096|0.20096	1.902000|1.902000	0.55061|0.55061	0.394000|0.394000	0.25966|0.25966	CAC|CTG	.	.		0.687	DPF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347721.1			C	38713312	G	C	38713312	3	2	355	1	0	0	0	0	1	0	0	0	4718	1020	36	4	1171	4	DPF1	19	38713312	Missense_Mutation	SNP	G	TCGA-WX-AA46-01A-11D-A38X-10		38713312	20415671	53	50122										
EID2B	126272	hgsc.bcm.edu	37	chr19	40023135	40023135	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	atctgaccggaatcatggagCtaccatccagatactcgcgg	10	12	2	2			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr19:40023135C>A	ENST00000326282.4	-	1	359	c.308G>T	c.(307-309)aGc>aTc	p.S103I	CTB-60E11.9_ENST00000594676.1_RNA|EID2B_ENST00000601837.1_Intron	NM_152361.1	NP_689574.1			EP300 interacting inhibitor of differentiation 2B											endometrium(1)|lung(1)|urinary_tract(1)	3	all_cancers(60;4.04e-06)|all_lung(34;1.77e-07)|Lung NSC(34;2.09e-07)|all_epithelial(25;1.13e-05)|Ovarian(47;0.159)		Epithelial(26;8.61e-26)|all cancers(26;2.76e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			AATCATGGAGCTACCATCCAG	0.592																																					p.S103I		Atlas-SNP	.											.	EID2B	9	.	0			c.G308T						.						50	52	52					19																	40023135		2203	4300	6503	SO:0001583	missense	126272	exon1			ATGGAGCTACCAT	AK096263	CCDS12539.1	19q13.2	2008-02-05				ENSG00000176401			26796	protein-coding gene	gene with protein product						15970276	Standard	NM_152361		Approved	EID-3, FLJ38944	uc002olz.1	Q96D98		ENST00000326282.4:c.308G>T	chr19.hg19:g.40023135C>A	ENSP00000317564:p.Ser103Ile	350.0	0.0		324.0	30.0	NM_152361		Missense_Mutation	SNP	ENST00000326282.4	hg19	CCDS12539.1	.	.	.	.	.	.	.	.	.	.	C	16.25	3.070823	0.55539	.	.	ENSG00000176401	ENST00000326282	T	0.32023	1.47	2.23	-4.47	0.03525	.	.	.	.	.	T	0.11452	0.0279	N	0.14661	0.345	0.09310	N	1	P	0.35821	0.523	B	0.22601	0.04	T	0.10847	-1.0612	9	0.45353	T	0.12	.	4.6015	0.12356	0.0:0.2675:0.179:0.5535	.	103	Q96D98	EID2B_HUMAN	I	103	ENSP00000317564:S103I	ENSP00000317564:S103I	S	-	2	0	EID2B	44714975	0.000000	0.05858	0.000000	0.03702	0.950000	0.60333	-1.118000	0.03280	-1.268000	0.02439	0.306000	0.20318	AGC	.	.		0.592	EID2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464961.1	NM_152361		A	40023135	C	A	40023135	3	1	355	1	0	0	0	0	1	0	0	0	4990	797	28	3	181	3	EID2B	19	40023135	Missense_Mutation	SNP	C	TCGA-WX-AA46-01A-11D-A38X-10	1309823	40023135	19105848	54	50123										
PANK2	80025	hgsc.bcm.edu	37	chr20	3897669	3897669	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	catcaccaacaacattggctCaatagcaagaatgtgtgccc	7	12	2	1			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr20:3897669C>T	ENST00000316562.4	+	5	1514	c.1508C>T	c.(1507-1509)tCa>tTa	p.S503L	PANK2_ENST00000497424.1_Missense_Mutation_p.S212L|MIR103A2_ENST00000362154.1_RNA|PANK2_ENST00000610179.1_Missense_Mutation_p.S380L|PANK2_ENST00000464452.1_3'UTR	NM_153638.2	NP_705902.2	Q9BZ23	PANK2_HUMAN	pantothenate kinase 2	503					aerobic respiration (GO:0009060)|cell death (GO:0008219)|coenzyme A biosynthetic process (GO:0015937)|coenzyme biosynthetic process (GO:0009108)|mitochondrion morphogenesis (GO:0070584)|pantothenate metabolic process (GO:0015939)|regulation of mitochondrial membrane potential (GO:0051881)|small molecule metabolic process (GO:0044281)|spermatid development (GO:0007286)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial intermembrane space (GO:0005758)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						AACATTGGCTCAATAGCAAGA	0.453																																					p.S503L		Atlas-SNP	.											.	PANK2	37	.	0			c.C1508T						.						144	121	129					20																	3897669		2203	4300	6503	SO:0001583	missense	80025	exon5			TTGGCTCAATAGC	AK021791	CCDS13071.2, CCDS13072.1	20p13	2008-07-31	2008-07-31	2002-09-06	ENSG00000125779	ENSG00000125779	2.7.1.33		15894	protein-coding gene	gene with protein product	"Hallervorden-Spatz syndrome"	606157	"neurodegeneration with brain iron accumulation 1 (Hallervorden-Spatz syndrome)"	C20orf48, NBIA1		8944032, 11479594	Standard	XM_005260835		Approved	HSS, FLJ11729, PKAN, HARP	uc002wkc.3	Q9BZ23	OTTHUMG00000031768	ENST00000316562.4:c.1508C>T	chr20.hg19:g.3897669C>T	ENSP00000313377:p.Ser503Leu	166.0	0.0		133.0	25.0	NM_153638	B1AK33|B2Z3X0|D3DVZ0|Q5T7I2|Q5T7I4|Q7RTX5|Q8N7Q4|Q8TCR5|Q9BYW5|Q9HAF2	Missense_Mutation	SNP	ENST00000316562.4	hg19	CCDS13071.2	.	.	.	.	.	.	.	.	.	.	C	34	5.383593	0.95967	.	.	ENSG00000125779	ENST00000497424;ENST00000316562;ENST00000399552	D;D	0.99548	-6.14;-6.14	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	D	0.99468	0.9811	M	0.63208	1.945	0.58432	D	0.999999	D	0.89917	1.0	D	0.85130	0.997	D	0.98446	1.0589	10	0.66056	D	0.02	.	16.3012	0.82816	0.0:1.0:0.0:0.0	.	503	Q9BZ23	PANK2_HUMAN	L	212;503;319	ENSP00000417609:S212L;ENSP00000313377:S503L	ENSP00000313377:S503L	S	+	2	0	PANK2	3845669	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	7.579000	0.82511	2.713000	0.92767	0.655000	0.94253	TCA	.	.		0.453	PANK2-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077793.2	NM_024960		T	3897669	C	T	3897669	3	4	355	1	0	0	0	0	1	0	0	0	11426	838	29	3	1526	3	PANK2	20	3897669	Missense_Mutation	SNP	C	TCGA-WX-AA46-01A-11D-A38X-10		3897669	59127851	55	50124										
TCFL5	10732	hgsc.bcm.edu	37	chr20	61491546	61491546	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	gtaaacagtgggtatgtaaaTtgcaaagcagtagttgtagc	12	4	0	0			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr20:61491546T>C	ENST00000335351.3	-	2	854	c.762A>G	c.(760-762)caA>caG	p.Q254Q	TCFL5_ENST00000217162.5_Silent_p.Q206Q	NM_006602.2	NP_006593.2	Q9UL49	TCFL5_HUMAN	transcription factor-like 5 (basic helix-loop-helix)	254					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)	male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|large_intestine(5)|lung(1)|urinary_tract(1)	9	Breast(26;5.68e-08)					GGTATGTAAATTGCAAAGCAG	0.373																																					p.Q254Q		Atlas-SNP	.											.	TCFL5	43	.	0			c.A762G						.						152	147	149					20																	61491546		2203	4300	6503	SO:0001819	synonymous_variant	10732	exon2			TGTAAATTGCAAA	AB012124	CCDS13506.1	20q13.33	2013-09-19			ENSG00000101190	ENSG00000101190		"Basic helix-loop-helix proteins"	11646	protein-coding gene	gene with protein product	"HPV-16 E2 binding protein 1"	604745				9763657	Standard	XM_005260185		Approved	Figlb, E2BP-1, CHA, bHLHe82	uc002ydp.3	Q9UL49	OTTHUMG00000032939	ENST00000335351.3:c.762A>G	chr20.hg19:g.61491546T>C		163.0	0.0		130.0	23.0	NM_006602	O94771|Q9BYW0	Silent	SNP	ENST00000335351.3	hg19	CCDS13506.1																																																																																			.	.		0.373	TCFL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080079.2	NM_006602		C	61491546	T	C	61491546	2	2	355	1	0	0	0	0	0	0	0	1	15714	1490	52	2		2	TCFL5	20	61491546	Silent	SNP	T	TCGA-WX-AA46-01A-11D-A38X-10	57593877	61491546	1533974	56	50125										
AP1B1	162	hgsc.bcm.edu	37	chr22	29727788	29727788	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0892857142857143	5	1	1.57773952954676	2.83993115318417	0.946643717728055	1	1	0	gaacccacctggaggttgttCagaggctccatcttcatgac	10	12	3	2			TCGA-WX-AA46-01A-11D-A38X-10	TCGA-WX-AA46-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c32ea52-9c54-4776-ac95-a5a2a4a6d084	3ca4659e-8911-4dee-b019-29b5cf9bc842	g.chr22:29727788C>G	ENST00000405198.1	-	17	2458	c.2427G>C	c.(2425-2427)ctG>ctC	p.L809L	AP1B1_ENST00000472057.1_5'UTR|SNORD125_ENST00000459538.1_RNA|AP1B1_ENST00000317368.7_Silent_p.L782L|AP1B1_ENST00000415447.1_Silent_p.L802L|AP1B1_ENST00000357586.2_Silent_p.L809L|AP1B1_ENST00000402502.1_Silent_p.L802L|AP1B1_ENST00000356015.2_Silent_p.L802L|AP1B1_ENST00000432560.2_Silent_p.L802L			Q10567	AP1B1_HUMAN	adaptor-related protein complex 1, beta 1 subunit	809					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|trans-Golgi network membrane (GO:0032588)	protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			endometrium(3)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						GGAGGTTGTTCAGAGGCTCCA	0.652																																					p.L809L		Atlas-SNP	.											.	AP1B1	72	.	0			c.G2427C						.						71	66	68					22																	29727788		2203	4300	6503	SO:0001819	synonymous_variant	162	exon18			GTTGTTCAGAGGC	L13939	CCDS13855.1, CCDS13856.1, CCDS13856.2, CCDS54515.1	22q12.2	2010-06-18			ENSG00000100280	ENSG00000100280			554	protein-coding gene	gene with protein product		600157		ADTB1, CLAPB2		7987321, 8812422	Standard	NM_145730		Approved	BAM22, AP105A	uc003afj.3	Q10567	OTTHUMG00000151109	ENST00000405198.1:c.2427G>C	chr22.hg19:g.29727788C>G		143.0	0.0		94.0	12.0	NM_001127	C9JRD1|F8WDL0|P78436|Q20WL3|Q86X54	Silent	SNP	ENST00000405198.1	hg19	CCDS13855.1																																																																																			.	.		0.652	AP1B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321374.1	NM_001127		G	29727788	C	G	29727788	2	3	355	1	0	0	0	0	0	0	0	1	731	813	29	4		4	AP1B1	22	29727788	Silent	SNP	C	TCGA-WX-AA46-01A-11D-A38X-10		29727788	21576778	57	50126										
CSMD2	114784	hgsc.bcm.edu	37	chr1	34209061	34209061	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	gaaatcaaactgaggctccaCgtcaatgtcgttgaaggcca	10	10	2	2			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr1:34209061C>G	ENST00000373381.4	-	14	2169	c.1993G>C	c.(1993-1995)Gtg>Ctg	p.V665L		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	625	CUB 4. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.V625M(1)		NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				TGAGGCTCCACGTCAATGTCG	0.602																																					p.V625L		Atlas-SNP	.											CSMD2,caecum,carcinoma,0,1	CSMD2	946	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1873C						.						84	84	84					1																	34209061		2203	4300	6503	SO:0001583	missense	114784	exon14			GCTCCACGTCAAT	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.1993G>C	chr1.hg19:g.34209061C>G	ENSP00000362479:p.Val665Leu	60.0	0.0		71.0	23.0	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373381.4	hg19		.	.	.	.	.	.	.	.	.	.	C	13.80	2.345427	0.41498	.	.	ENSG00000121904	ENST00000373381	T	0.15256	2.44	5.58	5.58	0.84498	CUB (5);	0.055186	0.64402	D	0.000001	T	0.08492	0.0211	N	0.02120	-0.675	0.80722	D	1	B;B	0.23990	0.095;0.01	B;B	0.33846	0.171;0.079	T	0.16100	-1.0414	10	0.02654	T	1	.	18.9334	0.92576	0.0:1.0:0.0:0.0	.	625;665	Q7Z408;E7EUA6	CSMD2_HUMAN;.	L	665	ENSP00000362479:V665L	ENSP00000241312:V625L	V	-	1	0	CSMD2	33981648	1.000000	0.71417	0.968000	0.41197	0.989000	0.77384	4.839000	0.62810	2.782000	0.95742	0.655000	0.94253	GTG	.	.		0.602	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896		G	34209061	C	G	34209061	3	3	356	1	0	0	0	0	1	0	0	0	3947	536	19	4	8814	4	CSMD2	1	34209061	Missense_Mutation	SNP	C	TCGA-WX-AA47-01A-11D-A38X-10		34209061	215041560	1	50127										
COL24A1	255631	hgsc.bcm.edu	37	chr1	86200503	86200503	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	aatctggccattccatccctTgaaaccaataggcaatcctg	6	13	1	1			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr1:86200503T>A	ENST00000370571.2	-	59	5293	c.4927A>T	c.(4927-4929)Aag>Tag	p.K1643*	COL24A1_ENST00000436319.1_Nonsense_Mutation_p.K1622*	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	1643	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				extracellular matrix organization (GO:0030198)|hematopoietic progenitor cell differentiation (GO:0002244)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			NS(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(9)|liver(1)|lung(56)|ovary(4)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	101				all cancers(265;0.0627)|Epithelial(280;0.0689)		TTCCATCCCTTGAAACCAATA	0.433																																					p.K1643X		Atlas-SNP	.											.	COL24A1	202	.	0			c.A4927T						.						177	170	172					1																	86200503		1891	4117	6008	SO:0001587	stop_gained	255631	exon59			ATCCCTTGAAACC	AF410793	CCDS41353.1	1p22.3-p22.2	2013-01-16			ENSG00000171502	ENSG00000171502		"Collagens"	20821	protein-coding gene	gene with protein product		610025					Standard	NM_152890		Approved		uc001dlj.3	Q17RW2	OTTHUMG00000010629	ENST00000370571.2:c.4927A>T	chr1.hg19:g.86200503T>A	ENSP00000359603:p.Lys1643*	187.0	0.0		200.0	77.0	NM_152890	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Nonsense_Mutation	SNP	ENST00000370571.2	hg19	CCDS41353.1	.	.	.	.	.	.	.	.	.	.	T	42	9.714598	0.99245	.	.	ENSG00000171502	ENST00000370571;ENST00000436319	.	.	.	5.23	5.23	0.72850	.	0.000000	0.38720	N	0.001589	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.2771	0.73750	0.0:0.0:0.0:1.0	.	.	.	.	X	1643;1622	.	ENSP00000359603:K1643X	K	-	1	0	COL24A1	85973091	1.000000	0.71417	1.000000	0.80357	0.864000	0.49448	2.664000	0.46783	2.191000	0.70037	0.528000	0.53228	AAG	.	.		0.433	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	NM_152890		A	86200503	T	A	86200503	4	1	356	1	0	0	0	0	0	1	0	0	3685	1821	63	4	225	4	COL24A1	1	86200503	Nonsense_Mutation	SNP	T	TCGA-WX-AA47-01A-11D-A38X-10	51991442	86200503	163050118	2	50128										
ANKRD35	148741	hgsc.bcm.edu	37	chr1	145562472	145562472	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	ggcgagaggagtgcacaaagCaaagcagcggagtccctgga	16	9	0	1			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr1:145562472C>T	ENST00000355594.4	+	10	2247	c.2160C>T	c.(2158-2160)agC>agT	p.S720S		NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	720										NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(16)|ovary(4)|prostate(3)|skin(2)|urinary_tract(1)	47	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GTGCACAAAGCAAAGCAGCGG	0.662																																					p.S720S	Melanoma(9;127 754 22988 51047)	Atlas-SNP	.											.	ANKRD35	96	.	0			c.C2160T						.						22	26	25					1																	145562472		2203	4300	6503	SO:0001819	synonymous_variant	148741	exon10			ACAAAGCAAAGCA	AK091120	CCDS72867.1, CCDS72868.1	1q21.1	2013-01-10			ENSG00000198483	ENSG00000198483		"Ankyrin repeat domain containing"	26323	protein-coding gene	gene with protein product							Standard	NM_144698		Approved	FLJ25124	uc001eob.1	Q8N283	OTTHUMG00000013743	ENST00000355594.4:c.2160C>T	chr1.hg19:g.145562472C>T		163.0	0.0		185.0	52.0	NM_144698	A6NEU0|B4DL62|Q3MJ10|Q96LS3	Silent	SNP	ENST00000355594.4	hg19	CCDS919.1																																																																																			.	.		0.662	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	NM_144698		T	145562472	C	T	145562472	2	4	356	1	0	0	0	0	0	0	0	1	664	709	25	3		3	ANKRD35	1	145562472	Silent	SNP	C	TCGA-WX-AA47-01A-11D-A38X-10	59361969	145562472	103688149	3	50129										
YY1AP1	55249	hgsc.bcm.edu	37	chr1	155640243	155640243	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	ccacttgctttggcaaacagGgaaattcattggctataaga	9	8	1	1			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr1:155640243G>C	ENST00000295566.4	-	8	817	c.794C>G	c.(793-795)cCc>cGc	p.P265R	YY1AP1_ENST00000368330.2_Missense_Mutation_p.P199R|YY1AP1_ENST00000368339.5_Missense_Mutation_p.P337R|YY1AP1_ENST00000311573.5_Missense_Mutation_p.P188R|YY1AP1_ENST00000476093.1_5'UTR|YY1AP1_ENST00000438245.2_Intron|YY1AP1_ENST00000407221.1_Missense_Mutation_p.P188R|YY1AP1_ENST00000361831.5_Missense_Mutation_p.P188R|YY1AP1_ENST00000368340.5_Missense_Mutation_p.P337R|YY1AP1_ENST00000347088.5_Missense_Mutation_p.P199R|YY1AP1_ENST00000359205.5_Missense_Mutation_p.P188R|YY1AP1_ENST00000404643.1_Missense_Mutation_p.P199R|MSTO1_ENST00000538143.1_Intron|YY1AP1_ENST00000355499.4_Missense_Mutation_p.P199R|YY1AP1_ENST00000535662.1_Missense_Mutation_p.P65R|MSTO1_ENST00000452804.2_Intron|YY1AP1_ENST00000405763.3_Missense_Mutation_p.P337R	NM_001198906.1|NM_139118.2	NP_001185835.1|NP_620829.1	Q9H869	YYAP1_HUMAN	YY1 associated protein 1	265					regulation of cell cycle (GO:0051726)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(7)|ovary(2)|skin(2)|urinary_tract(2)	31	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)					TGGCAAACAGGGAAATTCATT	0.408																																					p.P337R		Atlas-SNP	.											.	YY1AP1	104	.	0			c.C1010G						.						85	83	84					1																	155640243		2203	4300	6503	SO:0001583	missense	55249	exon7			AAACAGGGAAATT	BC008766	CCDS1115.1, CCDS1116.1, CCDS55643.1, CCDS55644.1, CCDS55645.1	1q22	2009-05-07			ENSG00000163374	ENSG00000163374			30935	protein-coding gene	gene with protein product		607860				11710830	Standard	NM_139119		Approved	YY1AP, HCCA2, YAP		Q9H869	OTTHUMG00000035437	ENST00000295566.4:c.794C>G	chr1.hg19:g.155640243G>C	ENSP00000295566:p.Pro265Arg	124.0	0.0		148.0	41.0	NM_001198904	B0QZ54|B4DMP2|B4E0I0|D3DV96|D3DV98|H7BY62|Q5VYZ1|Q5VYZ4|Q5VYZ7|Q7L4C3|Q7L5E2|Q8IXA6|Q8TEW5|Q8TF04|Q96HB6|Q9BQ64|Q9NV84	Missense_Mutation	SNP	ENST00000295566.4	hg19	CCDS1115.1	.	.	.	.	.	.	.	.	.	.	G	15.00	2.703830	0.48412	.	.	ENSG00000163374	ENST00000359205;ENST00000355499;ENST00000311573;ENST00000347088;ENST00000361831;ENST00000368340;ENST00000295566;ENST00000368330;ENST00000407221;ENST00000404643;ENST00000368339;ENST00000535662;ENST00000405763;ENST00000443231	T;T;T;T;T;T;T;T;T;T;T;T	0.27256	1.71;1.71;1.79;1.71;1.71;1.78;1.79;1.71;1.79;1.81;1.68;1.81	3.17	3.17	0.36434	.	0.071494	0.56097	D	0.000029	T	0.31949	0.0813	M	0.73962	2.25	0.80722	D	1	P;P;P;P;D;P;D	0.64830	0.551;0.944;0.919;0.929;0.978;0.933;0.994	P;P;P;P;P;P;P	0.60682	0.516;0.714;0.587;0.586;0.716;0.668;0.878	T	0.13629	-1.0502	10	0.72032	D	0.01	.	7.8062	0.29204	0.123:0.0:0.877:0.0	.	265;337;199;337;265;199;337	B4DQQ0;B4DMP2;Q9H869-4;B0QZ55;Q9H869;Q9H869-2;Q5VYZ1	.;.;.;.;YYAP1_HUMAN;.;.	R	188;199;188;199;188;337;265;199;188;199;337;65;337;188	ENSP00000352134:P188R;ENSP00000347686:P199R;ENSP00000311138:P188R;ENSP00000316079:P199R;ENSP00000355298:P188R;ENSP00000357324:P337R;ENSP00000295566:P265R;ENSP00000357314:P199R;ENSP00000385791:P188R;ENSP00000385390:P199R;ENSP00000357323:P337R;ENSP00000437926:P65R	ENSP00000295566:P265R	P	-	2	0	YY1AP1	153906867	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.786000	0.47790	1.756000	0.51951	0.557000	0.71058	CCC	.	.		0.408	YY1AP1-043	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000086027.1	NM_139118		C	155640243	G	C	155640243	3	2	356	1	0	0	0	0	1	0	0	0	17523	1232	43	4	1672	4	YY1AP1	1	155640243	Missense_Mutation	SNP	G	TCGA-WX-AA47-01A-11D-A38X-10	10077771	155640243	93610378	4	50130										
KIAA1804	84451	hgsc.bcm.edu	37	chr1	233489695	233489695	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	ctgagccgtttgccaagctcAtgaaaggtattgtgtgtgtg	13	7	1	2			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr1:233489695A>G	ENST00000366624.3	+	3	1390	c.1129A>G	c.(1129-1131)Atg>Gtg	p.M377V	MLK4_ENST00000366623.3_Missense_Mutation_p.M377V	NM_032435.2	NP_115811.2																					TGCCAAGCTCATGAAAGGTAT	0.448																																					p.M377V		Atlas-SNP	.											.	KIAA1804	129	.	0			c.A1129G						.						121	106	111					1																	233489695		2203	4300	6503	SO:0001583	missense	0	exon3			AAGCTCATGAAAG																												ENST00000366624.3:c.1129A>G	chr1.hg19:g.233489695A>G	ENSP00000355583:p.Met377Val	90.0	0.0		127.0	75.0	NM_032435		Missense_Mutation	SNP	ENST00000366624.3	hg19	CCDS1598.1	.	.	.	.	.	.	.	.	.	.	A	16.70	3.195953	0.58126	.	.	ENSG00000143674	ENST00000366623;ENST00000366624	D;D	0.86366	-2.11;-2.11	4.91	4.91	0.64330	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.86033	0.5836	N	0.16098	0.37	0.80722	D	1	P;P	0.45474	0.859;0.575	P;B	0.58620	0.842;0.343	D	0.87394	0.2365	10	0.48119	T	0.1	.	14.7177	0.69284	1.0:0.0:0.0:0.0	.	377;377	Q5TCX8;Q5TCX8-2	M3KL4_HUMAN;.	V	377	ENSP00000355582:M377V;ENSP00000355583:M377V	ENSP00000355582:M377V	M	+	1	0	RP5-862P8.2	231556318	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.263000	0.78421	2.053000	0.61076	0.460000	0.39030	ATG	.	.		0.448	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1			G	233489695	A	G	233489695	3	3	356	1	0	0	0	0	1	0	0	0	8268	217	8	2	1139	2	KIAA1804	1	233489695	Missense_Mutation	SNP	A	TCGA-WX-AA47-01A-11D-A38X-10	77849452	233489695	15760926	5	50131										
CCDC121	79635	hgsc.bcm.edu	37	chr2	27849931	27849931	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	attatgacttccttgcagtcTctgcctcgcctggattaagg	9	11	1	1			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr2:27849931T>A	ENST00000324364.3	-	2	916	c.736A>T	c.(736-738)Aga>Tga	p.R246*	GPN1_ENST00000407583.3_5'Flank|ZNF512_ENST00000556601.1_Intron|GPN1_ENST00000515877.1_5'Flank|GPN1_ENST00000503738.1_5'Flank|GPN1_ENST00000424214.1_5'Flank|GPN1_ENST00000610189.1_5'Flank|CCDC121_ENST00000394775.3_Nonsense_Mutation_p.R408*|GPN1_ENST00000458167.2_5'Flank|RP11-158I13.2_ENST00000505973.1_RNA|GPN1_ENST00000264718.3_5'Flank	NM_024584.4	NP_078860.2	Q6ZUS5	CC121_HUMAN	coiled-coil domain containing 121	246										breast(1)|endometrium(3)|large_intestine(2)|lung(6)|prostate(2)	14	Acute lymphoblastic leukemia(172;0.155)					CCTTGCAGTCTCTGCCTCGCC	0.478																																					p.R408X		Atlas-SNP	.											.	CCDC121	43	.	0			c.A1222T						.						121	114	116					2																	27849931		2203	4300	6503	SO:0001587	stop_gained	79635	exon2			GCAGTCTCTGCCT	AK125354	CCDS1759.1, CCDS46247.1	2p23.2	2008-02-05			ENSG00000176714	ENSG00000176714			25833	protein-coding gene	gene with protein product							Standard	NM_024584		Approved	FLJ43364, FLJ13646	uc002rld.3	Q6ZUS5	OTTHUMG00000128427	ENST00000324364.3:c.736A>T	chr2.hg19:g.27849931T>A	ENSP00000339087:p.Arg246*	87.0	0.0		75.0	34.0	NM_001142683	B3KW66|J3KQZ8|Q9H8G6	Nonsense_Mutation	SNP	ENST00000324364.3	hg19	CCDS1759.1	.	.	.	.	.	.	.	.	.	.	T	16.61	3.172399	0.57584	.	.	ENSG00000176714	ENST00000324364;ENST00000394775	.	.	.	5.24	2.22	0.28083	.	1.730580	0.03530	N	0.222357	.	.	.	.	.	.	0.49213	D	0.999765	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.8964	11.4413	0.50099	0.0:0.0:0.4601:0.5399	.	.	.	.	X	246;408	.	ENSP00000339087:R246X	R	-	1	2	CCDC121	27703435	0.001000	0.12720	0.002000	0.10522	0.001000	0.01503	0.493000	0.22451	0.117000	0.18138	-0.435000	0.05868	AGA	.	.		0.478	CCDC121-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250215.1	NM_024584		A	27849931	T	A	27849931	4	1	356	1	0	0	0	0	0	1	0	0	2759	1559	54	4	104	4	CCDC121	2	27849931	Nonsense_Mutation	SNP	T	TCGA-WX-AA47-01A-11D-A38X-10		27849931	215349442	6	50132										
CDKL4	344387	hgsc.bcm.edu	37	chr2	39452979	39452979	+	Splice_Site	DEL	C	C	-													0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	ttcagtttccagattacttaCccatttgggtttctttccag							TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr2:39452979delC	ENST00000395035.3	-	2	290		c.e2+1		CDKL4_ENST00000378803.1_Splice_Site			Q5MAI5	CDKL4_HUMAN	cyclin-dependent kinase-like 4							cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			breast(1)|large_intestine(2)|liver(1)|lung(7)|ovary(1)	12		all_hematologic(82;0.248)				AGATTACTTACCCATTTGGGT	0.373																																					.		Atlas-INDEL	.											.	CDKL4	30	.	0			c.290+2G>-						.						66	65	65					2																	39452979		2202	4299	6501	SO:0001630	splice_region_variant	344387	exon3			.		CCDS33184.1	2p22.3	2011-11-04			ENSG00000205111	ENSG00000205111		"Cyclin-dependent kinases"	19287	protein-coding gene	gene with protein product							Standard	NM_001009565		Approved		uc002rrm.3	Q5MAI5	OTTHUMG00000133574	ENST00000395035.3:c.290+1G>-	chr2.hg19:g.39452979delC		59.0	0.0		73.0	26.0	NM_001009565	Q2NME9	Splice_Site	DEL	ENST00000395035.3	hg19																																																																																				.	.		0.373	CDKL4-002	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000331655.1	XM_293029	Intron	-	39452979	C	-	39452979	8	5	356	1	0	1	0	1	0	0	1	0	3158	521	18	0	684	0	CDKL4	2	39452979	Splice_Site	DEL	C	TCGA-WX-AA47-01A-11D-A38X-10	11603048	39452979	203746394	7	50133										
CLK1	1195	hgsc.bcm.edu	37	chr2	201726515	201726515	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	ttcttttatgactgctgctgCtcctccattttccataatcc	4	13	1	1			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr2:201726515C>G	ENST00000321356.4	-	2	206	c.71G>C	c.(70-72)aGc>aCc	p.S24T	CLK1_ENST00000492793.1_Intron|Y_RNA_ENST00000516950.1_RNA|CLK1_ENST00000434813.2_Missense_Mutation_p.S66T	NM_004071.3	NP_004062.2	P49759	CLK1_HUMAN	CDC-like kinase 1	24					cell proliferation (GO:0008283)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|regulation of RNA splicing (GO:0043484)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			NS(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(12)|ovary(1)|pancreas(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33						ACTGCTGCTGCTCCTCCATTT	0.413																																					p.S66T		Atlas-SNP	.											.	CLK1	103	.	0			c.G197C						.						191	179	183					2																	201726515		2203	4300	6503	SO:0001583	missense	1195	exon2			CTGCTGCTCCTCC	L29219	CCDS2331.1, CCDS54427.1	2q33	2008-05-02			ENSG00000013441	ENSG00000013441		"CDC-like kinases"	2068	protein-coding gene	gene with protein product		601951				9856501	Standard	NM_004071		Approved		uc002uwe.2	P49759	OTTHUMG00000132784	ENST00000321356.4:c.71G>C	chr2.hg19:g.201726515C>G	ENSP00000326830:p.Ser24Thr	107.0	0.0		86.0	38.0	NM_001162407	B4DFW7|Q0P694|Q8N5V8	Missense_Mutation	SNP	ENST00000321356.4	hg19	CCDS2331.1	.	.	.	.	.	.	.	.	.	.	C	13.54	2.266578	0.40095	.	.	ENSG00000013441	ENST00000321356;ENST00000357369;ENST00000434813	T;T	0.67523	-0.2;-0.27	5.27	5.27	0.74061	.	0.000000	0.64402	D	0.000003	T	0.65026	0.2652	M	0.63428	1.95	0.32787	N	0.501672	B;B	0.27823	0.19;0.094	B;B	0.29077	0.098;0.046	T	0.68326	-0.5438	10	0.23302	T	0.38	.	17.0516	0.86520	0.0:1.0:0.0:0.0	.	66;24	B4DFW7;P49759	.;CLK1_HUMAN	T	24;24;66	ENSP00000326830:S24T;ENSP00000394734:S66T	ENSP00000326830:S24T	S	-	2	0	CLK1	201434760	0.414000	0.25408	1.000000	0.80357	0.753000	0.42808	1.376000	0.34306	2.613000	0.88420	0.637000	0.83480	AGC	.	.		0.413	CLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256192.2			G	201726515	C	G	201726515	3	3	356	1	0	0	0	0	1	0	0	0	3538	797	28	4	1431	4	CLK1	2	201726515	Missense_Mutation	SNP	C	TCGA-WX-AA47-01A-11D-A38X-10	162273536	201726515	41472858	8	50134										
ATG9A	79065	hgsc.bcm.edu	37	chr2	220087067	220087067	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	cagcggggagaaggagcgcaGggcagaggcgacttcagccc	18	11	1	2			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr2:220087067G>C	ENST00000409618.1	-	12	2393	c.1954C>G	c.(1954-1956)Ctg>Gtg	p.L652V	ATG9A_ENST00000361242.4_Missense_Mutation_p.L652V|AC068946.1_ENST00000408417.1_RNA|ATG9A_ENST00000396761.2_Missense_Mutation_p.L652V|ATG9A_ENST00000409422.1_Missense_Mutation_p.L591V			Q7Z3C6	ATG9A_HUMAN	autophagy related 9A	652					autophagic vacuole assembly (GO:0000045)|late nucleophagy (GO:0044805)|mitochondrion degradation (GO:0000422)|piecemeal microautophagy of nucleus (GO:0034727)|protein localization to pre-autophagosomal structure (GO:0034497)|protein transport (GO:0015031)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)				endometrium(2)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|stomach(1)	13		Renal(207;0.0474)		Epithelial(149;1.37e-06)|all cancers(144;0.000222)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AAGGAGCGCAGGGCAGAGGCG	0.662																																					p.L652V		Atlas-SNP	.											.	ATG9A	50	.	0			c.C1954G						.						49	58	55					2																	220087067		1979	4151	6130	SO:0001583	missense	79065	exon12			AGCGCAGGGCAGA	AK021732	CCDS42820.1	2q35	2014-02-12	2012-06-06	2005-09-11	ENSG00000198925	ENSG00000198925			22408	protein-coding gene	gene with protein product		612204	"APG9 autophagy 9-like 1 (S. cerevisiae)", "ATG9 autophagy related 9 homolog A (S. cerevisiae)"	APG9L1			Standard	NM_024085		Approved	FLJ22169	uc002vkf.1	Q7Z3C6	OTTHUMG00000154557	ENST00000409618.1:c.1954C>G	chr2.hg19:g.220087067G>C	ENSP00000386710:p.Leu652Val	143.0	0.0		107.0	31.0	NM_001077198	Q3ZAQ6|Q6P0N7|Q7Z317|Q7Z320|Q8NDK6|Q8WU65|Q9BVL5|Q9H6L1|Q9HAG7	Missense_Mutation	SNP	ENST00000409618.1	hg19	CCDS42820.1	.	.	.	.	.	.	.	.	.	.	G	16.47	3.133382	0.56828	.	.	ENSG00000198925	ENST00000396761;ENST00000409618;ENST00000361242;ENST00000409422;ENST00000429920	T;T;T;T;T	0.38722	1.8;1.8;1.8;1.38;1.12	5.35	4.48	0.54585	.	0.145153	0.47455	D	0.000237	T	0.56247	0.1972	M	0.71581	2.175	0.46586	D	0.999112	D	0.63880	0.993	D	0.67548	0.952	T	0.54944	-0.8217	10	0.15499	T	0.54	-7.6341	10.2144	0.43160	0.1499:0.0:0.8501:0.0	.	652	Q7Z3C6	ATG9A_HUMAN	V	652;652;652;591;211	ENSP00000379983:L652V;ENSP00000386710:L652V;ENSP00000355173:L652V;ENSP00000386535:L591V;ENSP00000400234:L211V	ENSP00000355173:L652V	L	-	1	2	ATG9A	219795311	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.352000	0.44080	1.503000	0.48686	0.591000	0.81541	CTG	.	.		0.662	ATG9A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335930.1	NM_024085		C	220087067	G	C	220087067	3	2	356	1	0	0	0	0	1	0	0	0	1102	991	35	4	585	4	ATG9A	2	220087067	Missense_Mutation	SNP	G	TCGA-WX-AA47-01A-11D-A38X-10	18360552	220087067	23112306	9	50135										
SCN10A	6336	hgsc.bcm.edu	37	chr3	38797307	38797307	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	gctggttgtaaggatcagagCggggtgatttgttgtcttct	15	5	3	2			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr3:38797307C>A	ENST00000449082.2	-	10	1432	c.1433G>T	c.(1432-1434)cGc>cTc	p.R478L		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	478					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	AGGATCAGAGCGGGGTGATTT	0.488																																					p.R478L		Atlas-SNP	.											SCN10A,colon,carcinoma,0,2	SCN10A	359	.	0			c.G1433T						.						276	231	246					3																	38797307		2203	4300	6503	SO:0001583	missense	6336	exon10			TCAGAGCGGGGTG	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10582	protein-coding gene	gene with protein product		604427	"sodium channel, voltage-gated, type X, alpha polypeptide"			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.1433G>T	chr3.hg19:g.38797307C>A	ENSP00000390600:p.Arg478Leu	107.0	1.0		102.0	41.0	NM_006514	A6NDQ1	Missense_Mutation	SNP	ENST00000449082.2	hg19	CCDS33736.1	.	.	.	.	.	.	.	.	.	.	C	3.042	-0.197227	0.06259	.	.	ENSG00000185313	ENST00000449082	D	0.95756	-3.8	5.34	-0.209	0.13180	.	.	.	.	.	D	0.87669	0.6235	N	0.17082	0.46	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.77365	-0.2615	9	0.66056	D	0.02	.	1.8994	0.03264	0.1318:0.1499:0.1374:0.581	.	478	Q9Y5Y9	SCNAA_HUMAN	L	478	ENSP00000390600:R478L	ENSP00000390600:R478L	R	-	2	0	SCN10A	38772311	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.031000	0.12287	-0.056000	0.13221	-1.099000	0.02127	CGC	.	.		0.488	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		A	38797307	C	A	38797307	3	1	356	1	0	0	0	0	1	0	0	0	13927	768	27	1	4509	1	SCN10A	3	38797307	Missense_Mutation	SNP	C	TCGA-WX-AA47-01A-11D-A38X-10		38797307	159225123	10	50136										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266136	41266136	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	gtgccactaccacagctcctTctctgagtggtaaaggcaat	9	12	1	1	rs121913407		TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr3:41266136T>C	ENST00000349496.5	+	3	413	c.133T>C	c.(133-135)Tct>Cct	p.S45P	CTNNB1_ENST00000396183.3_Missense_Mutation_p.S45P|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S45P|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S45P|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S38P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	45			Missing (in colorectal cancer). {ECO:0000269|PubMed:9065402}.|S -> F (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> P (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S45P(168)|p.A5_A80del(53)|p.S45del(50)|p.S45A(11)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.S45_G48del(1)|p.Q28_Q61del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.S45_L46del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.P44_N51del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.T40_L46del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.S45E(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.S45T(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.T42_K49>Q(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CACAGCTCCTTCTCTGAGTGG	0.502		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S45P	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,carcinoma,0,1	CTNNB1	4904	.	355	Substitution - Missense(181)|Deletion - In frame(149)|Complex - deletion inframe(18)|Unknown(7)	liver(151)|kidney(53)|soft_tissue(47)|large_intestine(37)|adrenal_gland(28)|endometrium(9)|stomach(7)|skin(6)|pituitary(3)|prostate(3)|thyroid(2)|small_intestine(2)|bone(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)	c.T133C						.						84	74	78					3																	41266136		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	GCTCCTTCTCTGA	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.133T>C	chr3.hg19:g.41266136T>C	ENSP00000344456:p.Ser45Pro	119.0	0.0		146.0	68.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.440246	0.83993	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.65903	0.2736	M	0.65677	2.01	0.80722	D	1	D	0.60575	0.988	P	0.62649	0.905	T	0.69083	-0.5239	10	0.87932	D	0	-13.6823	16.3453	0.83126	0.0:0.0:0.0:1.0	.	45	P35222	CTNB1_HUMAN	P	38;45;45;45;45;38;45;45;45	ENSP00000400508:S38P;ENSP00000385604:S45P;ENSP00000412219:S45P;ENSP00000379486:S45P;ENSP00000344456:S45P;ENSP00000411226:S38P;ENSP00000379488:S45P;ENSP00000409302:S45P;ENSP00000401599:S45P	ENSP00000344456:S45P	S	+	1	0	CTNNB1	41241140	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.261000	0.74972	0.533000	0.62120	TCT	.	.		0.502	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41266136	T	C	41266136	3	2	356	1	0	0	0	0	1	0	0	0	4018	1783	62	2	139	2	CTNNB1	3	41266136	Missense_Mutation	SNP	T	TCGA-WX-AA47-01A-11D-A38X-10	2468829	41266136	156756294	11	50137										
TTC14	151613	hgsc.bcm.edu	37	chr3	180328329	180328329	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	aggaaataagtcaaaaaattAatacaccaaggatatcggca	7	6	1	0			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr3:180328329A>G	ENST00000296015.4	+	12	2444	c.2312A>G	c.(2311-2313)tAa>tGa	p.*771*	TTC14_ENST00000382584.4_Intron|TTC14_ENST00000412756.2_3'UTR	NM_133462.3	NP_597719.1	Q96N46	TTC14_HUMAN	tetratricopeptide repeat domain 14	0							RNA binding (GO:0003723)			endometrium(3)|kidney(5)|large_intestine(9)|lung(24)|ovary(2)|pancreas(1)|skin(1)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			TCAAAAAATTAATACACCAAG	0.299																																					p.X771X		Atlas-SNP	.											.	TTC14	112	.	0			c.A2312G						.						31	37	35					3																	180328329		2079	4231	6310	SO:0001819	synonymous_variant	151613	exon12			AAAATTAATACAC	AB075860	CCDS3237.1, CCDS46963.1, CCDS75055.1	3q27.2	2013-01-10			ENSG00000163728	ENSG00000163728		"Tetratricopeptide (TTC) repeat domain containing"	24697	protein-coding gene	gene with protein product						11853319	Standard	NM_001042601		Approved	FLJ00166, KIAA1980	uc003fkk.3	Q96N46	OTTHUMG00000157859	ENST00000296015.4:c.2312A>G	chr3.hg19:g.180328329A>G		139.0	0.0		129.0	64.0	NM_133462	G5E9X0|Q6UWJ7|Q8TF22	Silent	SNP	ENST00000296015.4	hg19	CCDS3237.1																																																																																			.	.		0.299	TTC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349786.1	NM_133462		G	180328329	A	G	180328329	2	3	356	1	0	0	0	0	0	0	0	1	16696	369	13	2		2	TTC14	3	180328329	Silent	SNP	A	TCGA-WX-AA47-01A-11D-A38X-10	139062193	180328329	17694101	12	50138										
LRRC33	375387	hgsc.bcm.edu	37	chr3	196387632	196387632	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	gcttcacattcgggagcacgAgccccccggagcgctcaccg	12	17	2	0			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr3:196387632A>G	ENST00000328557.4	+	3	1321	c.1118A>G	c.(1117-1119)gAg>gGg	p.E373G		NM_198565.1	NP_940967.1	Q86YC3	NRROS_HUMAN	negative regulator of reactive oxygen species	373					immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|superoxide metabolic process (GO:0006801)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)											CGGGAGCACGAGCCCCCCGGA	0.642																																					p.E373G		Atlas-SNP	.											.	LRRC33	91	.	0			c.A1118G						.						64	68	66					3																	196387632		2203	4300	6503	SO:0001583	missense	375387	exon3			AGCACGAGCCCCC	AY358322	CCDS3319.1	3q29	2013-07-02	2013-07-02	2013-07-02	ENSG00000174004	ENSG00000174004			24613	protein-coding gene	gene with protein product		615322	"leucine rich repeat containing 33"	LRRC33		12975309	Standard	NM_198565		Approved	UNQ3030, ELLP3030, MGC50789, GARPL1	uc003fwv.3	Q86YC3	OTTHUMG00000155569	ENST00000328557.4:c.1118A>G	chr3.hg19:g.196387632A>G	ENSP00000328625:p.Glu373Gly	77.0	0.0		69.0	32.0	NM_198565		Missense_Mutation	SNP	ENST00000328557.4	hg19	CCDS3319.1	.	.	.	.	.	.	.	.	.	.	A	10.41	1.341592	0.24339	.	.	ENSG00000174004	ENST00000328557	T	0.58940	0.3	6.17	5.03	0.67393	.	0.586814	0.18714	N	0.133219	T	0.30665	0.0772	N	0.02334	-0.595	0.26626	N	0.972567	P	0.43231	0.801	B	0.38106	0.265	T	0.11542	-1.0583	10	0.34782	T	0.22	.	11.8368	0.52330	0.9327:0.0:0.0673:0.0	.	373	Q86YC3	LRC33_HUMAN	G	373	ENSP00000328625:E373G	ENSP00000328625:E373G	E	+	2	0	LRRC33	197872029	0.999000	0.42202	0.993000	0.49108	0.267000	0.26476	4.157000	0.58144	2.371000	0.80710	0.533000	0.62120	GAG	.	.		0.642	NRROS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340676.1	NM_198565		G	196387632	A	G	196387632	3	3	356	1	0	0	0	0	1	0	0	0	8997	304	11	2	1124	2	LRRC33	3	196387632	Missense_Mutation	SNP	A	TCGA-WX-AA47-01A-11D-A38X-10	16059303	196387632	1634798	13	50139										
SENP5	205564	hgsc.bcm.edu	37	chr3	196612404	196612404	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	tcctgagactccaagcagagAagctgttgtcatcagcaaag	10	10	2	2			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr3:196612404A>G	ENST00000323460.5	+	2	601	c.352A>G	c.(352-354)Aag>Gag	p.K118E	SENP5_ENST00000419026.1_Intron|SENP5_ENST00000445299.2_Missense_Mutation_p.K118E	NM_152699.4	NP_689912.2	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5	118					cell cycle (GO:0007049)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)			NS(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(9)|lung(14)|skin(1)	32	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.14e-24)|all cancers(36;2.1e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.004)		CCAAGCAGAGAAGCTGTTGTC	0.403																																					p.K118E	Ovarian(47;891 1095 11174 13858 51271)	Atlas-SNP	.											.	SENP5	68	.	0			c.A352G						.						61	62	62					3																	196612404		2203	4300	6503	SO:0001583	missense	205564	exon2			GCAGAGAAGCTGT	BC030705	CCDS3322.1	3q29	2005-08-17	2005-08-17		ENSG00000119231	ENSG00000119231			28407	protein-coding gene	gene with protein product		612845	"SUMO1/sentrin specific protease 5"			12477932	Standard	NM_152699		Approved	MGC27076	uc003fwz.4	Q96HI0	OTTHUMG00000155527	ENST00000323460.5:c.352A>G	chr3.hg19:g.196612404A>G	ENSP00000327197:p.Lys118Glu	108.0	0.0		86.0	31.0	NM_152699	B4DY82|Q96SA5	Missense_Mutation	SNP	ENST00000323460.5	hg19	CCDS3322.1	.	.	.	.	.	.	.	.	.	.	A	10.54	1.379178	0.24944	.	.	ENSG00000119231	ENST00000323460;ENST00000445299	T;T	0.25085	2.16;1.82	5.18	4.0	0.46444	.	1.206240	0.05724	N	0.598271	T	0.21718	0.0523	N	0.24115	0.695	0.80722	D	1	B;B	0.20052	0.041;0.041	B;B	0.16722	0.016;0.016	T	0.02553	-1.1142	10	0.62326	D	0.03	-2.1309	10.0949	0.42469	0.8493:0.0:0.0:0.1506	.	118;118	B4DY82;Q96HI0	.;SENP5_HUMAN	E	118	ENSP00000327197:K118E;ENSP00000390231:K118E	ENSP00000327197:K118E	K	+	1	0	SENP5	198096801	1.000000	0.71417	0.626000	0.29213	0.450000	0.32258	5.992000	0.70609	1.031000	0.39867	0.533000	0.62120	AAG	.	.		0.403	SENP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340524.1	NM_152699		G	196612404	A	G	196612404	3	3	356	1	0	0	0	0	1	0	0	0	14064	247	9	2	354	2	SENP5	3	196612404	Missense_Mutation	SNP	A	TCGA-WX-AA47-01A-11D-A38X-10	224772	196612404	1410026	14	50140										
CWH43	80157	hgsc.bcm.edu	37	chr4	49005762	49005762	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	tcacaaacaggaacagcttcAgctgcggggctcctttacct	9	13	2	0			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr4:49005762A>G	ENST00000226432.4	+	7	996	c.813A>G	c.(811-813)tcA>tcG	p.S271S	CWH43_ENST00000513409.1_Silent_p.S244S	NM_025087.2	NP_079363.2	Q9H720	PG2IP_HUMAN	cell wall biogenesis 43 C-terminal homolog (S. cerevisiae)	271					GPI anchor biosynthetic process (GO:0006506)	integral component of membrane (GO:0016021)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(26)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43						GAACAGCTTCAGCTGCGGGGC	0.502																																					p.S271S		Atlas-SNP	.											.	CWH43	101	.	0			c.A813G						.						78	79	78					4																	49005762		2203	4300	6503	SO:0001819	synonymous_variant	80157	exon7			AGCTTCAGCTGCG		CCDS3486.1, CCDS68697.1	4p12-p11	2010-09-21			ENSG00000109182	ENSG00000109182			26133	protein-coding gene	gene with protein product						17714445, 17761529	Standard	NM_025087		Approved	FLJ21511, CWH43-C	uc003gyv.3	Q9H720	OTTHUMG00000128627	ENST00000226432.4:c.813A>G	chr4.hg19:g.49005762A>G		80.0	0.0		70.0	32.0	NM_025087	B2RPD7	Silent	SNP	ENST00000226432.4	hg19	CCDS3486.1																																																																																			.	.		0.502	CWH43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250496.2	NM_025087		G	49005762	A	G	49005762	2	3	356	1	0	0	0	0	0	0	0	1	4075	175	7	2		2	CWH43	4	49005762	Silent	SNP	A	TCGA-WX-AA47-01A-11D-A38X-10		49005762	142148514	15	50141										
BMP2K	55589	hgsc.bcm.edu	37	chr4	79792095	79792115	+	In_Frame_Del	DEL	CAGCAGCAGCAGCAACAGCAA	CAGCAGCAGCAGCAACAGCAA	-													0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	atcctcaccagcagcagcagCagcagcagcagcaacagcaa					rs375179282|rs534035187|rs553571896	byFrequency	TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	CAGCAGCAGCAGCAACAGCAA	CAGCAGCAGCAGCAACAGCAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr4:79792095_79792115delCAGCAGCAGCAGCAACAGCAA	ENST00000335016.5	+	11	1556_1576	c.1390_1410delCAGCAGCAGCAGCAACAGCAA	c.(1390-1410)cagcagcagcagcaacagcaadel	p.QQQQQQQ478del	BMP2K_ENST00000502871.1_In_Frame_Del_p.QQQQQQQ478del	NM_198892.1	NP_942595.1	Q9NSY1	BMP2K_HUMAN	BMP2 inducible kinase	478	Gln/His-rich.			Missing (in Ref. 2; CAB70863). {ECO:0000305}.|Q -> R (in Ref. 4; AAH36021). {ECO:0000305}.	regulation of bone mineralization (GO:0030500)	nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatase regulator activity (GO:0019208)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	13						gcagcagcagcagcagcagcagcaacagcaacagcagcagc	0.557																																					p.463_470del		Atlas-INDEL	.											.	BMP2K	169	.	0			c.1389_1409del						.																																			SO:0001651	inframe_deletion	55589	exon11			.	AB015331	CCDS34019.1, CCDS47083.1	4q21.21	2008-05-15			ENSG00000138756	ENSG00000138756			18041	protein-coding gene	gene with protein product							Standard	NM_017593		Approved	DKFZp434K0614, BIKe	uc003hlk.3	Q9NSY1	OTTHUMG00000160900	ENST00000335016.5:c.1390_1410delCAGCAGCAGCAGCAACAGCAA	chr4.hg19:g.79792095_79792115delCAGCAGCAGCAGCAACAGCAA	ENSP00000334836:p.Gln478_Gln484del	27.0	0.0		34.0	10.0	NM_017593	O94791|Q4W5H2|Q8IYF2|Q8N2G7|Q8NHG9|Q9NTG8	In_Frame_Del	DEL	ENST00000335016.5	hg19	CCDS47083.1																																																																																			.	.		0.557	BMP2K-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_017593		-	79792115	CAGCAGCAGCAGCAACAGCAA	-	79792095	7	5	356	1	0	1	0	1	0	0	0	0	1460	711	25	0	1432	0	BMP2K	4	79792095	In_Frame_Del	DEL	CAGCAGCAGCAGCAACAGCAA	TCGA-WX-AA47-01A-11D-A38X-10	30786333	79792095	111362181	16	50142										
CENPE	1062	hgsc.bcm.edu	37	chr4	104065618	104065618	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	caaggttttcatgtagtatcTgagtcaaccttatattctcc	6	9	4	1			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr4:104065618T>C	ENST00000265148.3	-	33	5104	c.5015A>G	c.(5014-5016)cAg>cGg	p.Q1672R	CENPE_ENST00000380026.3_Missense_Mutation_p.Q1647R	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	1672					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)			NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		ATGTAGTATCTGAGTCAACCT	0.393																																					p.Q1672R		Atlas-SNP	.											.	CENPE	253	.	0			c.A5015G						.						184	176	179					4																	104065618		2203	4300	6503	SO:0001583	missense	1062	exon33			AGTATCTGAGTCA	Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"Kinesins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1856	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 61"	117143	"centromere protein E (312kD)"			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.5015A>G	chr4.hg19:g.104065618T>C	ENSP00000265148:p.Gln1672Arg	77.0	0.0		109.0	44.0	NM_001813	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	hg19	CCDS34042.1	.	.	.	.	.	.	.	.	.	.	T	15.65	2.897007	0.52121	.	.	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026	T;T	0.71698	-0.59;-0.59	5.13	5.13	0.70059	.	.	.	.	.	D	0.83358	0.5237	M	0.77313	2.365	0.27375	N	0.955571	D;D	0.69078	0.997;0.995	D;D	0.79784	0.993;0.965	T	0.76429	-0.2962	9	0.49607	T	0.09	.	13.2046	0.59788	0.0:0.0:0.0:1.0	.	1647;1672	Q02224-3;Q02224	.;CENPE_HUMAN	R	1672;1672;1647	ENSP00000265148:Q1672R;ENSP00000369365:Q1647R	ENSP00000265148:Q1672R	Q	-	2	0	CENPE	104285067	0.995000	0.38212	0.345000	0.25642	0.503000	0.33858	4.162000	0.58177	1.948000	0.56530	0.445000	0.29226	CAG	.	.		0.393	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	104065618	T	C	104065618	3	2	356	1	0	0	0	0	1	0	0	0	3232	1580	55	2	3158	2	CENPE	4	104065618	Missense_Mutation	SNP	T	TCGA-WX-AA47-01A-11D-A38X-10	24273523	104065618	87088658	17	50143										
BASP1	10409	hgsc.bcm.edu	37	chr5	17275402	17275403	+	Frame_Shift_Ins	INS	-	-	CGAGGGCG													0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	aaggagaaagacaagaaggcINScgagggcgcggcgacggaag							TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr5:17275402_17275403insCGAGGGCG	ENST00000322611.3	+	2	337_338	c.77_78insCGAGGGCG	c.(76-81)gccgagfs	p.-29fs		NM_001271606.1|NM_006317.3	NP_001258535.1|NP_006308.3	P80723	BASP1_HUMAN	brain abundant, membrane attached signal protein 1						diaphragm development (GO:0060539)|glomerular visceral epithelial cell differentiation (GO:0072112)|gonad development (GO:0008406)|mesenchymal to epithelial transition (GO:0060231)|metanephric mesenchyme development (GO:0072075)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of heart growth (GO:0060421)|positive regulation of metanephric ureteric bud development (GO:2001076)|substantia nigra development (GO:0021762)|thorax and anterior abdomen determination (GO:0007356)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|lung(8)	9						GACAAGAAGGCCGAGGGCGCGG	0.614																																					p.A26fs		Atlas-INDEL	.											.	BASP1	29	.	0			c.77_78insCGAGGGCG						.																																			SO:0001589	frameshift_variant	10409	exon2			.	AF039656	CCDS3888.1	5p15.1	2010-12-03			ENSG00000176788	ENSG00000176788			957	protein-coding gene	gene with protein product		605940				9310187, 9749536	Standard	NM_001271606		Approved	NAP-22, NAP22, CAP23, CAP-23	uc031siz.1	P80723	OTTHUMG00000131061	ENST00000322611.3:c.78_85dupCGAGGGCG	chr5.hg19:g.17275403_17275410dupCGAGGGCG	ENSP00000319281:p.Ala29fs	327.0	0.0		393.0	52.0	NM_006317	B4DJA8|D3DTD5|O43596|Q5U0S0|Q9BWA5	Frame_Shift_Ins	INS	ENST00000322611.3	hg19	CCDS3888.1																																																																																			.	.		0.614	BASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253716.2			CGAGGGCG	17275403	-	CGAGGGCG	17275402	7	5	356	1	0	1	1	0	0	0	0	0	1317	739	26	0	79	0	BASP1	5	17275402	Frame_Shift_Ins	INS	-	TCGA-WX-AA47-01A-11D-A38X-10		17275402	163639858	18	50144										
IL6ST	3572	hgsc.bcm.edu	37	chr5	55260054	55260065	+	In_Frame_Del	DEL	TTGACAAAATAC	TTGACAAAATAC	-													0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	cttctacccagacttcaatgTtgacaaaatacacagtagaa							TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	TTGACAAAATAC	TTGACAAAATAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr5:55260054_55260065delTTGACAAAATAC	ENST00000381298.2	-	6	879_890	c.567_578delGTATTTTGTCAA	c.(565-579)gtgtattttgtcaac>gtc	p.YFVN190del	IL6ST_ENST00000381293.2_Intron|IL6ST_ENST00000522633.2_In_Frame_Del_p.YFVN190del|IL6ST_ENST00000381294.3_In_Frame_Del_p.YFVN190del|IL6ST_ENST00000577363.1_5'UTR|IL6ST_ENST00000536319.1_In_Frame_Del_p.YFVN190del|IL6ST_ENST00000336909.5_In_Frame_Del_p.YFVN190del|IL6ST_ENST00000381286.3_Intron|IL6ST_ENST00000381287.4_In_Frame_Del_p.YFVN190del|IL6ST_ENST00000502326.3_In_Frame_Del_p.YFVN190del|IL6ST_ENST00000396816.1_In_Frame_Del_p.47_51CILST>S	NM_001190981.1|NM_002184.3|NM_175767.2	NP_001177910.1|NP_002175.2|NP_786943.1	P40189	IL6RB_HUMAN	interleukin 6 signal transducer	190	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|glycogen metabolic process (GO:0005977)|interleukin-27-mediated signaling pathway (GO:0070106)|interleukin-6-mediated signaling pathway (GO:0070102)|leukemia inhibitory factor signaling pathway (GO:0048861)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of Notch signaling pathway (GO:0008593)|response to cytokine (GO:0034097)|viral process (GO:0016032)	ciliary neurotrophic factor receptor complex (GO:0070110)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|interleukin-6 receptor complex (GO:0005896)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|oncostatin-M receptor complex (GO:0005900)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|interleukin-11 receptor activity (GO:0004921)|interleukin-27 receptor activity (GO:0045509)|protein homodimerization activity (GO:0042803)	p.N193delN(1)|p.Y186_Y190delYSTVY(1)		breast(2)|endometrium(5)|kidney(5)|large_intestine(4)|liver(2)|lung(1)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)				GACTTCAATGTTGACAAAATACACAGTAGAAT	0.368			O		hepatocellular ca																																p.190_193del		Atlas-INDEL	.		Dom	yes		5	5q11	3572	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"		E	.,1	IL6ST	75	.	2	Deletion - In frame(2)	liver(2)	c.568_579del						.																																			SO:0001651	inframe_deletion	3572	exon6			.	M57230	CCDS3971.1, CCDS47209.1, CCDS54856.1	5q11.2	2014-04-04	2014-04-04		ENSG00000134352	ENSG00000134352		"Interleukins and interleukin receptors", "CD molecules", "Fibronectin type III domain containing"	6021	protein-coding gene	gene with protein product	"gp130, oncostatin M receptor"	600694	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"			2261637	Standard	NM_002184		Approved	GP130, CD130	uc003jqq.3	P40189	OTTHUMG00000097043	ENST00000381298.2:c.567_578delGTATTTTGTCAA	chr5.hg19:g.55260054_55260065delTTGACAAAATAC	ENSP00000370698:p.Tyr190_Asn193del	165.0	0.0		193.0	73.0	NM_002184	A0N0L4|Q5FC04|Q9UQ41	In_Frame_Del	DEL	ENST00000381298.2	hg19	CCDS3971.1																																																																																			.	.		0.368	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184		-	55260065	TTGACAAAATAC	-	55260054	7	5	356	1	0	1	0	1	0	0	0	0	7712	1725	60	0	2226	0	IL6ST	5	55260054	In_Frame_Del	DEL	TTGACAAAATAC	TCGA-WX-AA47-01A-11D-A38X-10	37984652	55260054	125655206	19	50145										
SGTB	54557	hgsc.bcm.edu	37	chr5	64976566	64976566	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	ttcagggtcaagatctaatgCcttttgataacttgtaactg	8	7	3	2			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr5:64976566C>T	ENST00000381007.4	-	7	770	c.535G>A	c.(535-537)Gca>Aca	p.A179T		NM_019072.2	NP_061945.1	Q96EQ0	SGTB_HUMAN	small glutamine-rich tetratricopeptide repeat (TPR)-containing, beta	179										large_intestine(3)|lung(3)|skin(3)	9		Lung NSC(167;3.24e-06)|Prostate(74;0.0138)|Ovarian(174;0.0545)|Breast(144;0.174)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0657)|Lung(70;0.00487)		AGATCTAATGCCTTTTGATAA	0.348																																					p.A179T		Atlas-SNP	.											.	SGTB	22	.	0			c.G535A						.						140	140	140					5																	64976566		2203	4300	6503	SO:0001583	missense	54557	exon7			CTAATGCCTTTTG	AK096321	CCDS3988.1	5q12.3	2013-01-10			ENSG00000197860	ENSG00000197860		"Tetratricopeptide (TTC) repeat domain containing"	23567	protein-coding gene	gene with protein product						12477932	Standard	XM_005248548		Approved	Sgt2, FLJ39002	uc003jud.3	Q96EQ0	OTTHUMG00000097801	ENST00000381007.4:c.535G>A	chr5.hg19:g.64976566C>T	ENSP00000370395:p.Ala179Thr	98.0	0.0		121.0	9.0	NM_019072		Missense_Mutation	SNP	ENST00000381007.4	hg19	CCDS3988.1	.	.	.	.	.	.	.	.	.	.	C	35	5.449249	0.96205	.	.	ENSG00000197860	ENST00000381007;ENST00000506816	D;D	0.83837	-1.77;-1.77	5.31	5.31	0.75309	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	D	0.93481	0.7920	M	0.93016	3.37	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.94799	0.7969	10	0.87932	D	0	-18.9877	18.9824	0.92760	0.0:1.0:0.0:0.0	.	179	Q96EQ0	SGTB_HUMAN	T	179	ENSP00000370395:A179T;ENSP00000421447:A179T	ENSP00000370395:A179T	A	-	1	0	SGTB	65012322	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.463000	0.80869	2.496000	0.84212	0.557000	0.71058	GCA	.	.		0.348	SGTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215057.2	NM_019072		T	64976566	C	T	64976566	3	4	356	1	0	0	0	0	1	0	0	0	14241	739	26	3	399	3	SGTB	5	64976566	Missense_Mutation	SNP	C	TCGA-WX-AA47-01A-11D-A38X-10	9716512	64976566	115938694	20	50146										
ARL10	285598	hgsc.bcm.edu	37	chr5	175798739	175798739	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	acccaggacctgagcgaggcCatgagtatgggggagctgca	16	10	0	2			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr5:175798739C>T	ENST00000310389.5	+	4	672	c.576C>T	c.(574-576)gcC>gcT	p.A192A		NM_173664.4	NP_775935.1	Q8N8L6	ARL10_HUMAN	ADP-ribosylation factor-like 10	192					small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)			endometrium(2)|lung(1)|ovary(1)	4	all_cancers(89;0.0064)|Renal(175;0.000269)|Lung NSC(126;0.0105)|all_lung(126;0.0168)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	Kidney(146;0.0965)		TGAGCGAGGCCATGAGTATGG	0.562																																					p.A192A		Atlas-SNP	.											.	ARL10	19	.	0			c.C576T						.						92	99	96					5																	175798739		2203	4300	6503	SO:0001819	synonymous_variant	285598	exon4			CGAGGCCATGAGT	BK001673	CCDS4400.1	5q35.3	2014-05-09	2005-11-03	2005-11-03	ENSG00000175414	ENSG00000175414		"ADP-ribosylation factors-like", "ADP-ribosylation factors"	22042	protein-coding gene	gene with protein product			"ADP-ribosylation factor-like 10A"	ARL10A			Standard	NM_173664		Approved		uc003mec.1	Q8N8L6	OTTHUMG00000130655	ENST00000310389.5:c.576C>T	chr5.hg19:g.175798739C>T		115.0	0.0		157.0	8.0	NM_173664		Silent	SNP	ENST00000310389.5	hg19	CCDS4400.1																																																																																			.	.		0.562	ARL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253145.2	NM_173664		T	175798739	C	T	175798739	2	4	356	1	0	0	0	0	0	0	0	1	926	581	21	3		3	ARL10	5	175798739	Silent	SNP	C	TCGA-WX-AA47-01A-11D-A38X-10	110822173	175798739	5116521	21	50147										
RXRB	6257	hgsc.bcm.edu	37	chr6	33162491	33162491	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	atggggagcctcaagcatctCcatgaggaaggtgtcgatgg	15	8	2	1			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr6:33162491C>A	ENST00000374680.3	-	10	1781	c.1570G>T	c.(1570-1572)Gag>Tag	p.E524*	RXRB_ENST00000374685.4_Nonsense_Mutation_p.E528*|COL11A2_ENST00000374714.1_5'Flank|COL11A2_ENST00000374712.1_5'Flank|COL11A2_ENST00000374713.1_5'Flank|COL11A2_ENST00000361917.1_5'Flank|COL11A2_ENST00000374708.4_5'Flank|COL11A2_ENST00000341947.2_5'Flank|COL11A2_ENST00000395194.1_5'Flank|COL11A2_ENST00000357486.1_5'Flank|COL11A2_ENST00000395197.1_5'Flank|RXRB_ENST00000544186.1_Nonsense_Mutation_p.E338*	NM_001270401.1|NM_021976.4	NP_001257330.1|NP_068811.1	P28702	RXRB_HUMAN	retinoid X receptor, beta	524	Ligand-binding. {ECO:0000250}.				cardiac muscle cell proliferation (GO:0060038)|cellular response to retinoic acid (GO:0071300)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|maternal placenta development (GO:0001893)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	9-cis retinoic acid receptor activity (GO:0004886)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(1)|skin(2)	15					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Tazarotene(DB00799)|Tretinoin(DB00755)	TCAAGCATCTCCATGAGGAAG	0.557																																					p.E528X		Atlas-SNP	.											.	RXRB	34	.	0			c.G1582T						.						86	80	82					6																	33162491		1511	2709	4220	SO:0001587	stop_gained	6257	exon10			GCATCTCCATGAG	M84820	CCDS4768.1, CCDS59007.1	6p21.3	2013-01-16			ENSG00000204231	ENSG00000204231		"Nuclear hormone receptors"	10478	protein-coding gene	gene with protein product	"nuclear receptor subfamily 2 group B member 2"	180246				8257090	Standard	NM_021976		Approved	NR2B2, H-2RIIBP, RCoR-1	uc003odc.4	P28702	OTTHUMG00000031298	ENST00000374680.3:c.1570G>T	chr6.hg19:g.33162491C>A	ENSP00000363812:p.Glu524*	87.0	0.0		66.0	34.0	NM_001270401	P28703|Q59G65|Q5JP92|Q5STQ1	Nonsense_Mutation	SNP	ENST00000374680.3	hg19	CCDS4768.1	.	.	.	.	.	.	.	.	.	.	C	39	7.389040	0.98252	.	.	ENSG00000204231	ENST00000374685;ENST00000374680;ENST00000544186	.	.	.	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	16.1569	0.81675	0.0:1.0:0.0:0.0	.	.	.	.	X	528;524;338	.	ENSP00000363812:E524X	E	-	1	0	RXRB	33270469	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.644000	0.83416	2.674000	0.91012	0.551000	0.68910	GAG	.	.		0.557	RXRB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076642.2	NM_021976		A	33162491	C	A	33162491	4	1	356	1	0	0	0	0	0	1	0	0	13779	864	30	3	35	3	RXRB	6	33162491	Nonsense_Mutation	SNP	C	TCGA-WX-AA47-01A-11D-A38X-10		33162491	137952576	22	50148										
FZD1	8321	hgsc.bcm.edu	37	chr7	90895843	90895843	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	tgtacactgtgccagccaccAtcgtcatcgcctgctacttc	7	16	1	0			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr7:90895843A>G	ENST00000287934.2	+	1	2061	c.1648A>G	c.(1648-1650)Atc>Gtc	p.I550V		NM_003505.1	NP_003496.1	Q9UP38	FZD1_HUMAN	frizzled class receptor 1	550					autocrine signaling (GO:0035425)|axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation (GO:0044338)|canonical Wnt signaling pathway involved in osteoblast differentiation (GO:0044339)|cell-cell signaling (GO:0007267)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hard palate development (GO:0060022)|lung alveolus development (GO:0048286)|membranous septum morphogenesis (GO:0003149)|muscular septum morphogenesis (GO:0003150)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron differentiation (GO:0030182)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|response to drug (GO:0042493)|vasculature development (GO:0001944)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|receptor binding (GO:0005102)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24	all_cancers(62;3.1e-10)|all_epithelial(64;1.66e-08)|Breast(17;0.000635)|Lung NSC(181;0.153)|all_lung(186;0.154)|all_hematologic(106;0.215)		STAD - Stomach adenocarcinoma(171;0.0134)			GCCAGCCACCATCGTCATCGC	0.607																																					p.I550V		Atlas-SNP	.											.	FZD1	64	.	0			c.A1648G						.						93	72	79					7																	90895843		2203	4300	6503	SO:0001583	missense	8321	exon1			GCCACCATCGTCA	AB017363	CCDS5620.1	7q21	2014-01-29	2014-01-29		ENSG00000157240	ENSG00000157240		"GPCR / Class F : Frizzled receptors"	4038	protein-coding gene	gene with protein product	"Wnt receptor", "frizzled, Drosophila, homolog of, 1"	603408	"frizzled (Drosophila) homolog 1", "frizzled homolog 1 (Drosophila)", "frizzled 1, seven transmembrane spanning receptor", "frizzled family receptor 1"			9813155	Standard	NM_003505		Approved	DKFZp564G072	uc003ula.3	Q9UP38	OTTHUMG00000023046	ENST00000287934.2:c.1648A>G	chr7.hg19:g.90895843A>G	ENSP00000287934:p.Ile550Val	58.0	0.0		48.0	23.0	NM_003505	A4D1E8|O94815|Q549T8	Missense_Mutation	SNP	ENST00000287934.2	hg19	CCDS5620.1	.	.	.	.	.	.	.	.	.	.	A	16.43	3.122341	0.56613	.	.	ENSG00000157240	ENST00000287934	T	0.81247	-1.47	5.03	5.03	0.67393	GPCR, family 2-like (1);	0.000000	0.64402	D	0.000003	T	0.77644	0.4161	L	0.41824	1.3	0.54753	D	0.999986	P	0.36683	0.565	B	0.42882	0.401	T	0.75889	-0.3158	10	0.31617	T	0.26	.	14.9189	0.70818	1.0:0.0:0.0:0.0	.	550	Q9UP38	FZD1_HUMAN	V	550	ENSP00000287934:I550V	ENSP00000287934:I550V	I	+	1	0	FZD1	90733779	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.270000	0.78493	2.107000	0.64212	0.533000	0.62120	ATC	.	.		0.607	FZD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059367.2	NM_003505		G	90895843	A	G	90895843	3	3	356	1	0	0	0	0	1	0	0	0	6136	217	8	2	1650	2	FZD1	7	90895843	Missense_Mutation	SNP	A	TCGA-WX-AA47-01A-11D-A38X-10		90895843	68242820	23	50149										
MYC	4609	hgsc.bcm.edu	37	chr8	128750607	128750607	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	gaggaggagaacttctaccaGcagcagcagcagagcgagct	14	10	1	2	rs61752959	byFrequency	TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr8:128750607G>C	ENST00000259523.6	+	2	1304	c.99G>C	c.(97-99)caG>caC	p.Q33H	MYC_ENST00000524013.1_Missense_Mutation_p.Q47H|MYC_ENST00000377970.2_Missense_Mutation_p.Q48H			P01106	MYC_HUMAN	v-myc avian myelocytomatosis viral oncogene homolog	33	Poly-Gln.				branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|cell cycle arrest (GO:0007050)|cellular iron ion homeostasis (GO:0006879)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|chromosome organization (GO:0051276)|energy reserve metabolic process (GO:0006112)|fibroblast apoptotic process (GO:0044346)|gene expression (GO:0010467)|MAPK cascade (GO:0000165)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell division (GO:0051782)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of monocyte differentiation (GO:0045656)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|oxygen transport (GO:0015671)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of metanephric cap mesenchymal cell proliferation (GO:0090096)|positive regulation of response to DNA damage stimulus (GO:2001022)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of telomere maintenance (GO:0032204)|response to drug (GO:0042493)|response to gamma radiation (GO:0010332)|response to growth factor (GO:0070848)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|protein complex binding (GO:0032403)|repressing transcription factor binding (GO:0070491)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.Q33H(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|lung(7)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	16	all_cancers(1;6.19e-134)|all_epithelial(1;1.75e-119)|all_lung(1;5.66e-51)|Breast(1;1.08e-22)|all_neural(1;4.45e-21)|Medulloblastoma(1;1.88e-20)|Colorectal(1;1.92e-09)|Lung SC(1;4.52e-07)|Ovarian(5;0.000122)|Esophageal squamous(12;0.000995)|Renal(1;0.0921)|Hepatocellular(40;0.108)|Myeloproliferative disorder(2;0.135)|Melanoma(291;0.185)	Myeloproliferative disorder(644;0.0255)|Ovarian(118;0.0654)|Breast(495;0.212)|Acute lymphoblastic leukemia(644;0.22)	Epithelial(1;1.63e-94)|all cancers(1;5.82e-87)|OV - Ovarian serous cystadenocarcinoma(1;2.12e-71)|BRCA - Breast invasive adenocarcinoma(1;4.3e-14)|Lung(2;0.000381)|Colorectal(2;0.0102)|LUAD - Lung adenocarcinoma(14;0.0172)|READ - Rectum adenocarcinoma(2;0.0723)|LUSC - Lung squamous cell carcinoma(258;0.151)	KIRC - Kidney renal clear cell carcinoma(542;0.248)	Nadroparin(DB08813)	ACTTCTACCAGCAGCAGCAGC	0.612		3	"A, T"	"IGK@, BCL5, BCL7A , BTG1, TRA@, IGH@"	"Burkitt lymphoma,  amplified in other cancers, B-CLL"						OREG0018982	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q48H		Atlas-SNP	.		Dom	yes		8	8q24.12-q24.13	4609	v-myc myelocytomatosis viral oncogene homolog (avian)		"L, E"	MYC,trunk,malignant_melanoma,0,1	MYC	168	.	1	Substitution - Missense(1)	skin(1)	c.G144C						.						44	46	45					8																	128750607		2203	4300	6503	SO:0001583	missense	4609	exon2			CTACCAGCAGCAG		CCDS6359.2	8q24	2013-07-09	2013-07-09		ENSG00000136997	ENSG00000136997		"Basic helix-loop-helix proteins"	7553	protein-coding gene	gene with protein product		190080					Standard	NM_002467		Approved	c-Myc, bHLHe39, MYCC	uc003ysi.3	P01106	OTTHUMG00000128475	ENST00000259523.6:c.99G>C	chr8.hg19:g.128750607G>C	ENSP00000259523:p.Gln33His	88.0	1.0	1567	87.0	4.0	NM_002467	A8WFE7|P01107|Q14026	Missense_Mutation	SNP	ENST00000259523.6	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.18|10.18	1.279178|1.279178	0.23307|0.23307	.|.	.|.	ENSG00000136997|ENSG00000136997	ENST00000259523;ENST00000517291;ENST00000377970;ENST00000524013|ENST00000520751	T;T;T;T|.	0.16073|.	2.37;2.37;2.37;2.37|.	5.08|5.08	0.863|0.863	0.19062|0.19062	Transcription regulator Myc, N-terminal (1);|.	0.789352|.	0.11848|.	N|.	0.523582|.	T|T	0.36276|0.36276	0.0961|0.0961	N|N	0.11927|0.11927	0.2|0.2	0.23266|0.23266	N|N	0.998011|0.998011	B|.	0.02656|.	0.0|.	B|.	0.08055|.	0.003|.	T|T	0.47509|0.47509	-0.9112|-0.9112	10|6	0.11485|0.87932	T|D	0.65|0	-6.8285|-6.8285	19.6165|19.6165	0.95636|0.95636	0.0:0.7294:0.2705:0.0|0.0:0.7294:0.2705:0.0	.|.	33|.	P01106|.	MYC_HUMAN|.	H|T	33;47;48;47|22	ENSP00000259523:Q33H;ENSP00000429441:Q47H;ENSP00000367207:Q48H;ENSP00000430235:Q47H|.	ENSP00000259523:Q33H|ENSP00000430226:S22T	Q|S	+|+	3|2	2|0	MYC|MYC	128819789|128819789	0.000000|0.000000	0.05858|0.05858	0.997000|0.997000	0.53966|0.53966	0.870000|0.870000	0.49936|0.49936	-0.054000|-0.054000	0.11826|0.11826	-0.043000|-0.043000	0.13513|0.13513	0.561000|0.561000	0.74099|0.74099	CAG|AGC	.	G|0.985;A|0.015		0.612	MYC-002	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000250278.1			C	128750607	G	C	128750607	3	2	356	1	0	0	0	0	1	0	0	0	10025	962	34	4	150	4	MYC	8	128750607	Missense_Mutation	SNP	G	TCGA-WX-AA47-01A-11D-A38X-10		128750607	17613415	24	50150										
KANK1	23189	hgsc.bcm.edu	37	chr9	713335	713335	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	aagctttcggggaacctcacTcacagatgggctccctcaac	9	14	3	1			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr9:713335T>G	ENST00000382303.1	+	7	3221	c.2569T>G	c.(2569-2571)Tca>Gca	p.S857A	KANK1_ENST00000382293.3_Missense_Mutation_p.S699A|KANK1_ENST00000382297.2_Missense_Mutation_p.S857A|KANK1_ENST00000489369.1_3'UTR	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	857					negative regulation of actin filament polymerization (GO:0030837)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lamellipodium morphogenesis (GO:2000393)|negative regulation of neuron projection development (GO:0010977)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of wound healing (GO:0090303)|regulation of establishment of cell polarity (GO:2000114)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	beta-catenin binding (GO:0008013)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|stomach(4)|upper_aerodigestive_tract(1)	43		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		GGAACCTCACTCACAGATGGG	0.517																																					p.S857A		Atlas-SNP	.											.	KANK1	231	.	0			c.T2569G						.						130	123	126					9																	713335		2203	4300	6503	SO:0001583	missense	23189	exon7			CCTCACTCACAGA	AL833161	CCDS6441.1, CCDS34976.1	9p24.3	2013-01-10	2008-01-29	2008-01-29	ENSG00000107104	ENSG00000107104		"KN motif and ankyrin repeat domain containing", "Ankyrin repeat domain containing"	19309	protein-coding gene	gene with protein product		607704	"ankyrin repeat domain 15"	ANKRD15		12133830, 17996375, 19554261	Standard	NM_015158		Approved	KIAA0172, KANK	uc003zgn.2	Q14678	OTTHUMG00000019434	ENST00000382303.1:c.2569T>G	chr9.hg19:g.713335T>G	ENSP00000371740:p.Ser857Ala	111.0	0.0		106.0	39.0	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Missense_Mutation	SNP	ENST00000382303.1	hg19	CCDS34976.1	.	.	.	.	.	.	.	.	.	.	T	15.82	2.945167	0.53079	.	.	ENSG00000107104	ENST00000382303;ENST00000354485;ENST00000382297;ENST00000382293	T;T;T	0.75704	-0.96;-0.96;-0.96	5.79	4.59	0.56863	.	0.151922	0.31071	N	0.008313	T	0.68686	0.3028	L	0.46157	1.445	0.80722	D	1	B;B	0.23591	0.088;0.034	B;B	0.27380	0.079;0.022	T	0.68922	-0.5281	10	0.56958	D	0.05	-11.0127	12.661	0.56813	0.0:0.0:0.1377:0.8623	.	857;857	Q5W0W1;Q14678	.;KANK1_HUMAN	A	857;857;857;699	ENSP00000371740:S857A;ENSP00000371734:S857A;ENSP00000371730:S699A	ENSP00000346479:S857A	S	+	1	0	KANK1	703335	1.000000	0.71417	0.918000	0.36340	0.991000	0.79684	3.931000	0.56529	2.208000	0.71279	0.533000	0.62120	TCA	.	.		0.517	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158		G	713335	T	G	713335	3	3	356	1	0	0	0	0	1	0	0	0	7985	1551	54	5	2575	5	KANK1	9	713335	Missense_Mutation	SNP	T	TCGA-WX-AA47-01A-11D-A38X-10		713335	140500096	25	50151										
FRMPD1	22844	hgsc.bcm.edu	37	chr9	37746177	37746177	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	ggttctgccctggaggcctgCccgagcccacagctgcacca	12	17	1	0			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr9:37746177C>A	ENST00000539465.1	+	16	4741	c.4148C>A	c.(4147-4149)gCc>gAc	p.A1383D	RP11-613M10.9_ENST00000540557.1_Intron|FRMPD1_ENST00000377765.3_Missense_Mutation_p.A1383D			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	1383						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		TGGAGGCCTGCCCGAGCCCAC	0.652																																					p.A1383D		Atlas-SNP	.											.	FRMPD1	237	.	0			c.C4148A						.						43	51	48					9																	37746177		2203	4300	6503	SO:0001583	missense	22844	exon16			GGCCTGCCCGAGC	AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.4148C>A	chr9.hg19:g.37746177C>A	ENSP00000444411:p.Ala1383Asp	80.0	0.0		54.0	25.0	NM_014907	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	hg19	CCDS6612.1	.	.	.	.	.	.	.	.	.	.	C	11.77	1.739027	0.30774	.	.	ENSG00000070601	ENST00000377765;ENST00000539465	T;T	0.08102	3.13;3.13	5.52	3.65	0.41850	.	0.740008	0.13361	N	0.393680	T	0.06600	0.0169	N	0.24115	0.695	0.80722	D	1	P	0.42409	0.779	B	0.39299	0.296	T	0.38090	-0.9677	10	0.52906	T	0.07	-1.1614	8.8199	0.35018	0.0:0.7631:0.1534:0.0834	.	1383	Q5SYB0	FRPD1_HUMAN	D	1383	ENSP00000366995:A1383D;ENSP00000444411:A1383D	ENSP00000366995:A1383D	A	+	2	0	FRMPD1	37736177	0.001000	0.12720	0.977000	0.42913	0.300000	0.27592	0.557000	0.23454	1.307000	0.44944	0.655000	0.94253	GCC	.	.		0.652	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907		A	37746177	C	A	37746177	3	1	356	1	0	0	0	0	1	0	0	0	6065	739	26	3	4206	3	FRMPD1	9	37746177	Missense_Mutation	SNP	C	TCGA-WX-AA47-01A-11D-A38X-10	37032842	37746177	103467254	26	50152										
CDK9	1025	hgsc.bcm.edu	37	chr9	130550509	130550509	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	gcagatcctgcatagggacaTgaaggctgctaatgtgctta	12	8	0	2			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr9:130550509T>C	ENST00000373264.4	+	5	549	c.449T>C	c.(448-450)aTg>aCg	p.M150T	CDK9_ENST00000480353.1_3'UTR|MIR3960_ENST00000583311.1_RNA|CDK9_ENST00000373265.2_Missense_Mutation_p.M267T	NM_001261.3	NP_001252.1	P50750	CDK9_HUMAN	cyclin-dependent kinase 9	150	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|cellular response to cytokine stimulus (GO:0071345)|DNA repair (GO:0006281)|gene expression (GO:0010467)|negative regulation of cell cycle arrest (GO:0071157)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|regulation of DNA repair (GO:0006282)|regulation of histone modification (GO:0031056)|replication fork arrest (GO:0043111)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|positive transcription elongation factor complex b (GO:0008024)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|DNA binding (GO:0003677)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)|snRNA binding (GO:0017069)|transcription regulatory region DNA binding (GO:0044212)			lung(1)	1						CATAGGGACATGAAGGCTGCT	0.602																																					p.M150T		Atlas-SNP	.											.	CDK9	22	.	0			c.T449C						.						59	50	53					9																	130550509		2203	4300	6503	SO:0001583	missense	1025	exon5			GGGACATGAAGGC	L25676	CCDS6879.1	9q34.1	2011-11-08	2007-11-21		ENSG00000136807	ENSG00000136807		"Cyclin-dependent kinases"	1780	protein-coding gene	gene with protein product		603251	"cyclin-dependent kinase 9 (CDC2-related kinase)"	CDC2L4		8170997, 9356449	Standard	NM_001261		Approved	PITALRE, C-2k, TAK	uc004bse.2	P50750	OTTHUMG00000020715	ENST00000373264.4:c.449T>C	chr9.hg19:g.130550509T>C	ENSP00000362361:p.Met150Thr	83.0	0.0		64.0	23.0	NM_001261	Q5JU24|Q5JU25|Q5U006|Q96TF1	Missense_Mutation	SNP	ENST00000373264.4	hg19	CCDS6879.1	.	.	.	.	.	.	.	.	.	.	T	18.49	3.634584	0.67130	.	.	ENSG00000136807	ENST00000373265;ENST00000373264	T;T	0.44482	0.92;0.92	5.35	5.35	0.76521	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.64670	0.2619	L	0.46157	1.445	0.80722	D	1	B	0.31318	0.319	D	0.71656	0.974	T	0.67197	-0.5731	10	0.87932	D	0	-12.7817	14.5075	0.67762	0.0:0.0:0.0:1.0	.	150	P50750	CDK9_HUMAN	T	267;150	ENSP00000362362:M267T;ENSP00000362361:M150T	ENSP00000362361:M150T	M	+	2	0	CDK9	129590330	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	7.636000	0.83301	2.019000	0.59389	0.443000	0.29094	ATG	.	.		0.602	CDK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054235.1			C	130550509	T	C	130550509	3	2	356	1	0	0	0	0	1	0	0	0	3153	1464	51	2	467	2	CDK9	9	130550509	Missense_Mutation	SNP	T	TCGA-WX-AA47-01A-11D-A38X-10	92804332	130550509	10662922	27	50153										
TPP1	6881	hgsc.bcm.edu	37	chr11	6636106	6636107	+	5'Flank	INS	-	-	C													0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	ccatacttacatcaaagagtINScctgccccatgctgctggta					rs1128396	byFrequency	TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr11:6636106_6636107insC	ENST00000299424.4	-	0	0				TPP1_ENST00000534644.1_5'Flank|TAF10_ENST00000531760.1_5'Flank|TPP1_ENST00000533371.1_Frame_Shift_Ins_p.G271fs|TPP1_ENST00000299427.6_Frame_Shift_Ins_p.G514fs	NM_006284.3	NP_006275.1	Q12962	TAF10_HUMAN	TAF10 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 30kDa						chromatin organization (GO:0006325)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone deubiquitination (GO:0016578)|histone H3 acetylation (GO:0043966)|protein homooligomerization (GO:0051260)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|perinuclear region of cytoplasm (GO:0048471)|STAGA complex (GO:0030914)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|RNA polymerase binding (GO:0070063)|transcription coactivator activity (GO:0003713)						Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.0481)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.129)		CATCAAAGAGTCCTGCCCCATG	0.535																																					p.G514fs		Atlas-INDEL	.											.	TPP1	71	.	0			c.1542_1543insG						.																																			SO:0001631	upstream_gene_variant	1200	exon12			.	U13991, U25816	CCDS7769.1	11p15.5-p15.2	2006-11-14	2002-08-29	2001-12-07	ENSG00000166337	ENSG00000166337			11543	protein-coding gene	gene with protein product		600475	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, H, 30kD"	TAF2H, TAF2A		7923369	Standard	NM_006284		Approved	TAFII30	uc001mej.2	Q12962	OTTHUMG00000133402		chr11.hg19:g.6636108_6636108dupC	Exception_encountered	97.0	0.0		72.0	27.0	NM_000391	O00703|Q13175|Q6FH13	Frame_Shift_Ins	INS	ENST00000299424.4	hg19	CCDS7769.1																																																																																			.	.		0.535	TAF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257259.2	NM_006284		C	6636107	-	C	6636106	6	5	356	0	1	1	1	0	0	0	0	0	16426	1654	58	0		0	TPP1	11	6636106	5'Flank	INS	-	TCGA-WX-AA47-01A-11D-A38X-10		6636106	128370410	28	50154										
RPS13	6207	hgsc.bcm.edu	37	chr11	17099170	17099170	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	gatgccccgagctcacccggGagcatgcatgcgacccatga	12	15	1	1			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr11:17099170G>A	ENST00000525634.1	-	1	164	c.19C>T	c.(19-21)Ccc>Tcc	p.P7S	SNORD14B_ENST00000364533.1_RNA|PIK3C2A_ENST00000531428.1_5'Flank|SNORD14A_ENST00000606526.1_RNA|RPS13_ENST00000228140.2_Missense_Mutation_p.P7S|RPS13_ENST00000526895.1_5'UTR			P62277	RS13_HUMAN	ribosomal protein S13	7					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|negative regulation of RNA splicing (GO:0033119)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribosome (GO:0005840)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)	5						GCTCACCCGGGAGCATGCATG	0.647																																					p.P7S		Atlas-SNP	.											RPS13,NS,carcinoma,+2,1	RPS13	14	.	0			c.C19T						.						36	44	42					11																	17099170		2200	4294	6494	SO:0001583	missense	6207	exon1			ACCCGGGAGCATG	X79239	CCDS7823.1	11p	2011-04-05			ENSG00000110700	ENSG00000110700		"S ribosomal proteins"	10386	protein-coding gene	gene with protein product	"40S ribosomal protein S13"	180476				8332508, 9582194	Standard	NM_001017		Approved	S13	uc001mmp.3	P62277	OTTHUMG00000165988	ENST00000525634.1:c.19C>T	chr11.hg19:g.17099170G>A	ENSP00000435777:p.Pro7Ser	258.0	0.0		235.0	110.0	NM_001017	B2R549|P19116|Q02546|Q29200|Q498Y0	Missense_Mutation	SNP	ENST00000525634.1	hg19	CCDS7823.1	.	.	.	.	.	.	.	.	.	.	G	32	5.141462	0.94560	.	.	ENSG00000110700	ENST00000228140;ENST00000525634;ENST00000533969	T	0.22134	1.97	6.07	6.07	0.98685	Ribosomal protein S13/S15, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.20210	0.0486	L	0.35644	1.08	0.80722	D	1	B	0.02656	0.0	B	0.11329	0.006	T	0.03818	-1.1001	10	0.22706	T	0.39	.	18.417	0.90574	0.0:0.0:1.0:0.0	.	7	P62277	RS13_HUMAN	S	7	ENSP00000432096:P7S	ENSP00000228140:P7S	P	-	1	0	RPS13	17055746	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.305000	0.96197	2.884000	0.98904	0.655000	0.94253	CCC	.	.		0.647	RPS13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387320.2	NM_001017		A	17099170	G	A	17099170	3	1	356	1	0	0	0	0	1	0	0	0	13638	1174	41	3	460	3	RPS13	11	17099170	Missense_Mutation	SNP	G	TCGA-WX-AA47-01A-11D-A38X-10	10463064	17099170	117907346	29	50155										
ZNF202	7753	hgsc.bcm.edu	37	chr11	123598282	123598282	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	ctctaacctgggagatctcaTcaggtctggggattggaaat	12	8	4	1			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr11:123598282T>A	ENST00000529691.1	-	6	1073	c.854A>T	c.(853-855)gAt>gTt	p.D285V	ZNF202_ENST00000336139.4_Missense_Mutation_p.D285V|ZNF202_ENST00000530393.1_Missense_Mutation_p.D285V			O95125	ZN202_HUMAN	zinc finger protein 202	285	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.03)		GGAGATCTCATCAGGTCTGGG	0.473																																					p.D285V		Atlas-SNP	.											.	ZNF202	72	.	0			c.A854T						.						96	93	94					11																	123598282		2202	4299	6501	SO:0001583	missense	7753	exon8			ATCTCATCAGGTC	AF027219	CCDS8443.1	11q23.3	2013-01-09				ENSG00000166261		"Zinc fingers, C2H2-type", "-", "-", "-"	12994	protein-coding gene	gene with protein product		603430				9790754	Standard	XM_005271659		Approved	ZKSCAN10, ZSCAN42	uc001pzd.1	O95125		ENST00000529691.1:c.854A>T	chr11.hg19:g.123598282T>A	ENSP00000433881:p.Asp285Val	57.0	0.0		57.0	26.0	NM_003455	B0LPH9|Q4JG21|Q9H1B9|Q9NSM4	Missense_Mutation	SNP	ENST00000529691.1	hg19	CCDS8443.1	.	.	.	.	.	.	.	.	.	.	T	17.64	3.438843	0.62955	.	.	ENSG00000166261	ENST00000336139;ENST00000530393;ENST00000529691	T;T;T	0.00976	5.48;5.48;5.48	4.73	4.73	0.59995	Krueppel-associated box (3);	0.266360	0.26816	N	0.022344	T	0.01387	0.0045	L	0.55213	1.73	0.58432	D	0.999993	B	0.29085	0.232	B	0.32533	0.147	T	0.58399	-0.7643	10	0.51188	T	0.08	-4.1193	6.9389	0.24483	0.0:0.1009:0.0:0.8991	.	285	O95125	ZN202_HUMAN	V	285	ENSP00000337724:D285V;ENSP00000432504:D285V;ENSP00000433881:D285V	ENSP00000337724:D285V	D	-	2	0	ZNF202	123103492	0.002000	0.14202	1.000000	0.80357	0.997000	0.91878	0.227000	0.17795	1.987000	0.57996	0.454000	0.30748	GAT	.	.		0.473	ZNF202-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387419.1	NM_003455		A	123598282	T	A	123598282	3	1	356	1	0	0	0	0	1	0	0	0	17778	1435	50	4	1100	4	ZNF202	11	123598282	Missense_Mutation	SNP	T	TCGA-WX-AA47-01A-11D-A38X-10	106499112	123598282	11408234	30	50156										
FARP1	10160	hgsc.bcm.edu	37	chr13	98896955	98896956	+	Intron	INS	-	-	T													0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	cactgaagagcttcttaatcINSttttttgagtcaggacttga							TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr13:98896955_98896956insT	ENST00000319562.6	+	2	436				FARP1_ENST00000376586.2_Intron|FARP1_ENST00000595437.1_Intron|FARP1_ENST00000376581.5_Frame_Shift_Ins_p.L128fs	NM_005766.2	NP_005757.1	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)						dendrite morphogenesis (GO:0048813)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|synapse assembly (GO:0007416)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|synapse (GO:0045202)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|endometrium(6)|kidney(6)|large_intestine(13)|lung(16)|ovary(1)|skin(3)|urinary_tract(1)	49	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			GCTTCTTAATCTTTTTTGAGTC	0.381																																					p.L128fs		Atlas-INDEL	.											.	FARP1	207	.	0			c.382_383insT						.																																			SO:0001627	intron_variant	10160	exon3			.	AB008430	CCDS9487.1, CCDS32000.1, CCDS66572.1	13q32.2	2013-01-10			ENSG00000152767	ENSG00000152767		"Rho guanine nucleotide exchange factors", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Pleckstrin homology (PH) domain containing"	3591	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 75"	602654				9425278	Standard	NM_005766		Approved	CDEP, PLEKHC2, MGC87400, PPP1R75	uc001vnj.3	Q9Y4F1	OTTHUMG00000017248	ENST00000319562.6:c.171+31288->T	chr13.hg19:g.98896961_98896961dupT		84.0	0.0		75.0	23.0	NM_001001715	Q5JVI9|Q6IQ29	Frame_Shift_Ins	INS	ENST00000319562.6	hg19	CCDS9487.1																																																																																			.	.		0.381	FARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045541.3	NM_005766		T	98896956	-	T	98896955	6	5	356	0	1	1	1	0	0	0	0	0	5684	913	32	0		0	FARP1	13	98896955	Intron	INS	-	TCGA-WX-AA47-01A-11D-A38X-10		98896955	16272923	31	50157										
SMG1	23049	hgsc.bcm.edu	37	chr16	18937327	18937327	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	ggtgccgccgccgccgccgcCgctgctcagccgagaccccg	14	21	1	1			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr16:18937327C>T	ENST00000446231.2	-	1	449	c.37G>A	c.(37-39)Ggc>Agc	p.G13S	SMG1_ENST00000567737.1_5'UTR|CTD-2288F12.1_ENST00000565782.1_RNA|SMG1_ENST00000389467.3_Missense_Mutation_p.G13S			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	13	Interaction with SMG8 and SMG9.				DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						ccgccgccgccgctgcTCAGC	0.736																																					p.G13S		Atlas-SNP	.											.	SMG1	401	.	0			c.G37A						.						2	3	3					16																	18937327		1046	2801	3847	SO:0001583	missense	23049	exon1			CGCCGCCGCTGCT	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase-related kinase"	607032	"smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.37G>A	chr16.hg19:g.18937327C>T	ENSP00000402515:p.Gly13Ser	78.0	0.0		92.0	5.0	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	ENST00000446231.2	hg19	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	c	16.19	3.051895	0.55218	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	T;T	0.01240	5.12;5.12	4.27	3.31	0.37934	.	0.832224	0.10596	N	0.656220	T	0.00998	0.0033	N	0.14661	0.345	0.31512	N	0.663496	B	0.22346	0.068	B	0.08055	0.003	T	0.29912	-0.9996	10	0.12766	T	0.61	.	6.0417	0.19738	0.0:0.7231:0.0:0.2769	.	13	Q96Q15	SMG1_HUMAN	S	13	ENSP00000402515:G13S;ENSP00000374118:G13S	ENSP00000374118:G13S	G	-	1	0	SMG1	18844828	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.149000	0.42244	0.999000	0.39023	0.455000	0.32223	GGC	.	.		0.736	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		T	18937327	C	T	18937327	3	4	356	1	0	0	0	0	1	0	0	0	14810	652	23	1	11200	1	SMG1	16	18937327	Missense_Mutation	SNP	C	TCGA-WX-AA47-01A-11D-A38X-10		18937327	71417426	32	50158										
ZNF267	10308	hgsc.bcm.edu	37	chr16	31896500	31896500	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	aggtcttgttgtctctaagcCggacctgatcacctttttgg	10	10	3	1			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr16:31896500C>T	ENST00000300870.10	+	3	358	c.149C>T	c.(148-150)cCg>cTg	p.P50L	ZNF267_ENST00000394846.3_Missense_Mutation_p.P50L	NM_001265588.1|NM_003414.5	NP_001252517.1|NP_003405	Q14586	ZN267_HUMAN	zinc finger protein 267	50	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(5)|kidney(1)|large_intestine(14)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	41						GTCTCTAAGCCGGACCTGATC	0.408																																					p.P50L		Atlas-SNP	.											.	ZNF267	94	.	0			c.C149T						.						57	56	56					16																	31896500		2197	4300	6497	SO:0001583	missense	10308	exon3			CTAAGCCGGACCT	X78925	CCDS32440.1	16p11.2	2013-01-08			ENSG00000185947	ENSG00000185947		"Zinc fingers, C2H2-type", "-"	13060	protein-coding gene	gene with protein product		604752				7865130	Standard	NM_003414		Approved	HZF2	uc002ecs.5	Q14586		ENST00000300870.10:c.149C>T	chr16.hg19:g.31896500C>T	ENSP00000300870:p.Pro50Leu	127.0	0.0		105.0	7.0	NM_003414	A0JNZ9|Q8NE41|Q9NRJ0	Missense_Mutation	SNP	ENST00000300870.10	hg19	CCDS32440.1	.	.	.	.	.	.	.	.	.	.	c	0.003	-2.488876	0.00161	.	.	ENSG00000185947	ENST00000300870;ENST00000394846	T;T	0.01025	5.43;5.43	0.675	-0.981	0.10269	Krueppel-associated box (3);	.	.	.	.	T	0.03915	0.0110	M	0.86651	2.83	0.09310	N	1	D	0.76494	0.999	D	0.63283	0.913	T	0.21759	-1.0236	8	0.38643	T	0.18	.	.	.	.	.	50	Q14586	ZN267_HUMAN	L	50	ENSP00000300870:P50L;ENSP00000461286:P50L	ENSP00000300870:P50L	P	+	2	0	ZNF267	31804001	0.004000	0.15560	0.001000	0.08648	0.007000	0.05969	0.442000	0.21628	-0.418000	0.07450	-0.339000	0.08088	CCG	.	.		0.408	ZNF267-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432446.2	NM_003414		T	31896500	C	T	31896500	3	4	356	1	0	0	0	0	1	0	0	0	17821	652	23	1	159	1	ZNF267	16	31896500	Missense_Mutation	SNP	C	TCGA-WX-AA47-01A-11D-A38X-10	12959173	31896500	58458253	33	50159										
ZFP90	146198	hgsc.bcm.edu	37	chr16	68598406	68598406	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	tcatctctcattcagcatgaGagaactcatactggagagaa	8	9	5	3			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr16:68598406G>C	ENST00000570495.1	+	5	2008	c.1716G>C	c.(1714-1716)gaG>gaC	p.E572D	ZFP90_ENST00000563169.2_Missense_Mutation_p.E572D|ZFP90_ENST00000398253.2_Missense_Mutation_p.E572D			Q8TF47	ZFP90_HUMAN	ZFP90 zinc finger protein	572					negative regulation of DNA binding (GO:0043392)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(2)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	27		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00233)|Epithelial(162;0.0184)|all cancers(182;0.0946)		TTCAGCATGAGAGAACTCATA	0.428																																					p.E572D		Atlas-SNP	.											.	ZFP90	67	.	0			c.G1716C						.						100	114	110					16																	68598406		2189	4297	6486	SO:0001583	missense	146198	exon4			GCATGAGAGAACT	AK074332	CCDS42183.1	16q22.1	2013-01-08	2012-11-27			ENSG00000184939		"Zinc fingers, C2H2-type", "-"	23329	protein-coding gene	gene with protein product		609451	"zinc finger protein 90 homolog (mouse)"			7576184	Standard	NM_133458		Approved	KIAA1954, NK10, ZNF756	uc002ewc.3	Q8TF47		ENST00000570495.1:c.1716G>C	chr16.hg19:g.68598406G>C	ENSP00000460547:p.Glu572Asp	151.0	0.0		124.0	48.0	NM_133458	B2RU00|B3KVE7|Q49AD1|Q96MQ6	Missense_Mutation	SNP	ENST00000570495.1	hg19	CCDS42183.1	.	.	.	.	.	.	.	.	.	.	G	18.14	3.556705	0.65425	.	.	ENSG00000184939	ENST00000398253	T	0.18502	2.21	5.97	5.01	0.66863	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.23846	0.0577	L	0.55990	1.75	0.29328	N	0.866888	P	0.52692	0.955	P	0.49085	0.6	T	0.14062	-1.0486	9	0.87932	D	0	-12.1166	8.4866	0.33076	0.1754:0.0:0.8246:0.0	.	572	Q8TF47	ZFP90_HUMAN	D	572	ENSP00000381304:E572D	ENSP00000381304:E572D	E	+	3	2	ZFP90	67155907	0.998000	0.40836	1.000000	0.80357	0.994000	0.84299	2.078000	0.41567	1.509000	0.48786	0.561000	0.74099	GAG	.	.		0.428	ZFP90-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436217.3	XM_085375		C	68598406	G	C	68598406	3	2	356	1	0	0	0	0	1	0	0	0	17669	933	33	4	1730	4	ZFP90	16	68598406	Missense_Mutation	SNP	G	TCGA-WX-AA47-01A-11D-A38X-10	36701906	68598406	21756347	34	50160										
GSG2	83903	hgsc.bcm.edu	37	chr17	3629472	3629472	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	tgtgctctggttacattaccTgacagacaagatgctgaaac	9	9	1	4			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr17:3629472T>C	ENST00000325418.4	+	1	2262	c.2243T>C	c.(2242-2244)cTg>cCg	p.L748P	ITGAE_ENST00000571185.1_Intron|ITGAE_ENST00000263087.4_Intron	NM_031965.2	NP_114171.2	Q8TF76	HASP_HUMAN	germ cell associated 2 (haspin)	748	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159, ECO:0000305}.				histone H3-T3 phosphorylation involved in chromosome passenger complex localization to kinetochore (GO:2000751)|intracellular signal transduction (GO:0035556)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|protein localization to chromosome, centromeric region (GO:0071459)|protein phosphorylation (GO:0006468)|regulation of spindle checkpoint (GO:0090231)	centrosome (GO:0005813)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|histone kinase activity (H3-T3 specific) (GO:0072354)|protein kinase activity (GO:0004672)										TTACATTACCTGACAGACAAG	0.418																																					p.L748P		Atlas-SNP	.											.	GSG2	48	.	0			c.T2243C						.						87	84	85					17																	3629472		2203	4300	6503	SO:0001583	missense	83903	exon1			ATTACCTGACAGA	AB039834	CCDS11036.1	17p13	2005-01-19			ENSG00000177602	ENSG00000177602			19682	protein-coding gene	gene with protein product		609240					Standard	NM_031965		Approved	haspin	uc002fwp.3	Q8TF76	OTTHUMG00000090703	ENST00000325418.4:c.2243T>C	chr17.hg19:g.3629472T>C	ENSP00000325290:p.Leu748Pro	122.0	0.0		100.0	4.0	NM_031965	Q5U5K3|Q96MN1|Q9BXS7	Missense_Mutation	SNP	ENST00000325418.4	hg19	CCDS11036.1	.	.	.	.	.	.	.	.	.	.	T	16.77	3.213988	0.58452	.	.	ENSG00000177602	ENST00000325418	T	0.13778	2.56	5.41	5.41	0.78517	Protein kinase-like domain (1);Domain of unknown function DUF3635 (1);Protein kinase, catalytic domain (1);	0.000000	0.56097	D	0.000029	T	0.43722	0.1260	M	0.89414	3.03	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.51576	-0.8688	10	0.87932	D	0	-24.1108	13.4721	0.61287	0.0:0.0:0.0:1.0	.	748	Q8TF76	HASP_HUMAN	P	748	ENSP00000325290:L748P	ENSP00000325290:L748P	L	+	2	0	GSG2	3576221	1.000000	0.71417	1.000000	0.80357	0.799000	0.45148	5.780000	0.68956	2.184000	0.69523	0.533000	0.62120	CTG	.	.		0.418	GSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207391.1	NM_031965		C	3629472	T	C	3629472	3	2	356	1	0	0	0	0	1	0	0	0	6831	1580	55	2	2245	2	GSG2	17	3629472	Missense_Mutation	SNP	T	TCGA-WX-AA47-01A-11D-A38X-10		3629472	77565738	35	50161										
CCDC144NL	339184	hgsc.bcm.edu	37	chr17	20768818	20768818	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	ctttgctcatgcagatgacaAtactcttgaaaatggtggca	9	8	2	3			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr17:20768818A>G	ENST00000327925.5	-	4	695	c.576T>C	c.(574-576)taT>taC	p.Y192Y	CCDC144NL_ENST00000539484.1_5'UTR|RP11-344E13.3_ENST00000439794.2_RNA|RP11-344E13.3_ENST00000577537.1_RNA|RP11-344E13.3_ENST00000417232.2_RNA	NM_001004306.1	NP_001004306.1	Q6NUI1	C144L_HUMAN	coiled-coil domain containing 144 family, N-terminal like	192										large_intestine(3)|lung(3)|skin(1)	7						GCAGATGACAATACTCTTGAA	0.358																																					p.Y192Y		Atlas-SNP	.											.	CCDC144NL	34	.	0			c.T576C						.						73	67	69					17																	20768818		2203	4300	6503	SO:0001819	synonymous_variant	339184	exon4			ATGACAATACTCT		CCDS32591.1	17p11.2	2009-01-15			ENSG00000205212	ENSG00000205212			33735	protein-coding gene	gene with protein product							Standard	NM_001004306		Approved	MGC87631	uc002gyf.3	Q6NUI1	OTTHUMG00000132271	ENST00000327925.5:c.576T>C	chr17.hg19:g.20768818A>G		19.0	0.0		25.0	5.0	NM_001004306		Silent	SNP	ENST00000327925.5	hg19	CCDS32591.1																																																																																			.	.		0.358	CCDC144NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255361.2	NM_001004306		G	20768818	A	G	20768818	2	3	356	1	0	0	0	0	0	0	0	1	2781	108	4	2		2	CCDC144NL	17	20768818	Silent	SNP	A	TCGA-WX-AA47-01A-11D-A38X-10	17139346	20768818	60426392	36	50162										
OR1M1	125963	hgsc.bcm.edu	37	chr19	9204711	9204711	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	cgtctatctgtgtccctcctCggtcctcaccactgtgaagg	9	15	3	1			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr19:9204711C>T	ENST00000429566.3	+	1	857	c.791C>T	c.(790-792)tCg>tTg	p.S264L		NM_001004456.1	NP_001004456.1	Q8NGA1	OR1M1_HUMAN	olfactory receptor, family 1, subfamily M, member 1	264						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|large_intestine(3)|lung(17)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32						TGTCCCTCCTCGGTCCTCACC	0.557																																					p.S264L		Atlas-SNP	.											.	OR1M1	52	.	0			c.C791T						.						149	134	139					19																	9204711		2203	4300	6503	SO:0001583	missense	125963	exon1			CCTCCTCGGTCCT		CCDS32896.1	19p13.2	2013-09-20			ENSG00000170929	ENSG00000170929		"GPCR / Class A : Olfactory receptors"	8220	protein-coding gene	gene with protein product							Standard	NM_001004456		Approved	OR19-6	uc010xkj.2	Q8NGA1	OTTHUMG00000179930	ENST00000429566.3:c.791C>T	chr19.hg19:g.9204711C>T	ENSP00000401966:p.Ser264Leu	76.0	0.0		68.0	7.0	NM_001004456	B9EHA6|Q6IFJ3|Q96R91	Missense_Mutation	SNP	ENST00000429566.3	hg19	CCDS32896.1	.	.	.	.	.	.	.	.	.	.	c	17.14	3.312329	0.60414	.	.	ENSG00000170929	ENST00000305465;ENST00000429566	T	0.00216	8.53	3.71	1.55	0.23275	GPCR, rhodopsin-like superfamily (1);	0.118256	0.38837	N	0.001550	T	0.00356	0.0011	M	0.84585	2.705	0.09310	N	1	D	0.57571	0.98	P	0.51999	0.687	T	0.41106	-0.9527	10	0.54805	T	0.06	.	8.6371	0.33955	0.0:0.8057:0.0:0.1943	.	264	Q8NGA1	OR1M1_HUMAN	L	267;264	ENSP00000401966:S264L	ENSP00000303195:S267L	S	+	2	0	OR1M1	9065711	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-0.376000	0.07465	0.376000	0.24707	0.580000	0.79431	TCG	.	.		0.557	OR1M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448993.1			T	9204711	C	T	9204711	3	4	356	1	0	0	0	0	1	0	0	0	10977	893	31	1	793	1	OR1M1	19	9204711	Missense_Mutation	SNP	C	TCGA-WX-AA47-01A-11D-A38X-10		9204711	49924272	37	50163										
SIX5	147912	hgsc.bcm.edu	37	chr19	46270086	46270086	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	agagaggtcttggtctcgctGgccccctgagggctgggctg	17	11	2	2			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr19:46270086G>A	ENST00000317578.6	-	2	1512	c.1131C>T	c.(1129-1131)gcC>gcT	p.A377A	SIX5_ENST00000560168.1_3'UTR|AC074212.5_ENST00000592217.2_RNA|AC074212.5_ENST00000559756.1_RNA|AC074212.6_ENST00000590076.1_RNA	NM_175875.4	NP_787071	Q8N196	SIX5_HUMAN	SIX homeobox 5	377					lens development in camera-type eye (GO:0002088)|negative regulation of cell proliferation (GO:0008285)|regulation of transcription, DNA-templated (GO:0006355)|spermatid development (GO:0007286)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	8		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00783)|GBM - Glioblastoma multiforme(486;0.0802)|Epithelial(262;0.235)		TGGTCTCGCTGGCCCCCTGAG	0.721																																					p.A377A		Atlas-SNP	.											.	SIX5	35	.	0			c.C1131T						.						4	4	4					19																	46270086		2064	3995	6059	SO:0001819	synonymous_variant	147912	exon2			CTCGCTGGCCCCC	L08835	CCDS12673.1	19q13.32	2011-06-20	2007-07-13			ENSG00000177045		"Homeoboxes / SINE class"	10891	protein-coding gene	gene with protein product		600963	"sine oculis homeobox (Drosophila) homolog 5", "sine oculis homeobox homolog 5 (Drosophila)"	DMAHP		8595416	Standard	NM_175875		Approved		uc002pdb.3	Q8N196		ENST00000317578.6:c.1131C>T	chr19.hg19:g.46270086G>A		81.0	0.0		55.0	20.0	NM_175875		Silent	SNP	ENST00000317578.6	hg19	CCDS12673.1																																																																																			.	.		0.721	SIX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417341.3	NM_175875		A	46270086	G	A	46270086	2	1	356	1	0	0	0	0	0	0	0	1	14365	1335	47	3		3	SIX5	19	46270086	Silent	SNP	G	TCGA-WX-AA47-01A-11D-A38X-10	37065375	46270086	12858897	38	50164										
ZSCAN4	201516	hgsc.bcm.edu	37	chr19	58189641	58189641	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	tttccctaatcatcatccagGaagagaacggtcctaggcct	8	12	2	1			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr19:58189641G>A	ENST00000318203.5	+	5	1367	c.670G>A	c.(670-672)Gaa>Aaa	p.E224K		NM_152677.2	NP_689890.1	Q8NAM6	ZSCA4_HUMAN	zinc finger and SCAN domain containing 4	224					telomere maintenance via telomere lengthening (GO:0010833)|transcription, DNA-templated (GO:0006351)	nuclear chromosome, telomeric region (GO:0000784)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|large_intestine(5)|liver(2)|lung(17)|ovary(1)|skin(1)|stomach(1)	30		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		CATCATCCAGGAAGAGAACGG	0.423																																					p.E224K		Atlas-SNP	.											.	ZSCAN4	72	.	0			c.G670A						.						74	70	72					19																	58189641		2203	4300	6503	SO:0001583	missense	201516	exon5			ATCCAGGAAGAGA	AK092424	CCDS12958.1	19q13.43	2013-01-08	2004-11-01	2004-11-02		ENSG00000180532		"-", "Zinc fingers, C2H2-type"	23709	protein-coding gene	gene with protein product		613419	"zinc finger protein 494"	ZNF494			Standard	NM_152677		Approved	FLJ35105	uc002qpu.3	Q8NAM6		ENST00000318203.5:c.670G>A	chr19.hg19:g.58189641G>A	ENSP00000321963:p.Glu224Lys	99.0	0.0		115.0	51.0	NM_152677	Q3MIQ2	Missense_Mutation	SNP	ENST00000318203.5	hg19	CCDS12958.1	.	.	.	.	.	.	.	.	.	.	G	7.554	0.663292	0.14710	.	.	ENSG00000180532	ENST00000318203	T	0.06849	3.25	4.13	-0.41	0.12374	.	0.950149	0.08717	N	0.904015	T	0.04407	0.0121	N	0.22421	0.69	0.09310	N	1	B	0.21452	0.056	B	0.15870	0.014	T	0.47114	-0.9142	10	0.10902	T	0.67	-2.7827	3.8628	0.09004	0.3062:0.1809:0.5129:0.0	.	224	Q8NAM6	ZSCA4_HUMAN	K	224	ENSP00000321963:E224K	ENSP00000321963:E224K	E	+	1	0	ZSCAN4	62881453	0.404000	0.25328	0.000000	0.03702	0.010000	0.07245	0.479000	0.22228	0.039000	0.15632	-0.150000	0.13652	GAA	.	.		0.423	ZSCAN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466812.1	NM_152677		A	58189641	G	A	58189641	3	1	356	1	0	0	0	0	1	0	0	0	18252	1175	41	3	680	3	ZSCAN4	19	58189641	Missense_Mutation	SNP	G	TCGA-WX-AA47-01A-11D-A38X-10	11919555	58189641	939342	39	50165										
EDN3	1908	hgsc.bcm.edu	37	chr20	57899428	57899428	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	gcaagcaggctttagacctcCaccatccaaagctcatgccc	7	16	1	1			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr20:57899428C>T	ENST00000337938.2	+	5	1017	c.631C>T	c.(631-633)Cac>Tac	p.H211Y	EDN3_ENST00000311585.7_3'UTR|EDN3_ENST00000395654.3_Missense_Mutation_p.H197Y|EDN3_ENST00000371028.2_Missense_Mutation_p.H211Y|EDN3_ENST00000371025.3_3'UTR	NM_207034.1	NP_996917.1	P14138	EDN3_HUMAN	endothelin 3	211					blood circulation (GO:0008015)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|inositol phosphate-mediated signaling (GO:0048016)|melanocyte differentiation (GO:0030318)|multicellular organismal development (GO:0007275)|neural crest cell migration (GO:0001755)|neuron differentiation (GO:0030182)|neutrophil chemotaxis (GO:0030593)|peptide hormone secretion (GO:0030072)|positive regulation of cell proliferation (GO:0008284)|positive regulation of heart rate (GO:0010460)|positive regulation of hormone secretion (GO:0046887)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|regulation of developmental pigmentation (GO:0048070)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|signal transduction (GO:0007165)|vasoconstriction (GO:0042310)|vein smooth muscle contraction (GO:0014826)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone activity (GO:0005179)|receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	19	all_lung(29;0.0115)					TTTAGACCTCCACCATCCAAA	0.532																																					p.H211Y		Atlas-SNP	.											.	EDN3	83	.	0			c.C631T						.						108	111	110					20																	57899428		2203	4300	6503	SO:0001583	missense	1908	exon5			GACCTCCACCATC	X52001	CCDS13477.1, CCDS13478.1, CCDS13479.1	20q13.2-q13.3	2013-02-26			ENSG00000124205	ENSG00000124205		"Endogenous ligands"	3178	protein-coding gene	gene with protein product		131242					Standard	NM_000114		Approved	ET3	uc002yaq.3	P14138	OTTHUMG00000032867	ENST00000337938.2:c.631C>T	chr20.hg19:g.57899428C>T	ENSP00000337128:p.His211Tyr	143.0	0.0		127.0	60.0	NM_207034	E1P5I5|Q03229|Q7Z6D2|Q9UGT7	Missense_Mutation	SNP	ENST00000337938.2	hg19	CCDS13477.1	.	.	.	.	.	.	.	.	.	.	C	11.06	1.528713	0.27387	.	.	ENSG00000124205	ENST00000337938;ENST00000371028;ENST00000395654	D;D;D	0.95949	-2.13;-2.13;-3.86	4.78	2.84	0.33178	.	315.406000	0.00166	N	0.000000	D	0.92740	0.7692	L	0.34521	1.04	0.09310	N	1	P;P	0.42518	0.782;0.675	B;B	0.40444	0.329;0.176	D	0.84887	0.0834	10	0.52906	T	0.07	.	7.5959	0.28048	0.0:0.8062:0.0:0.1938	.	197;211	P14138-2;P14138	.;EDN3_HUMAN	Y	211;211;197	ENSP00000337128:H211Y;ENSP00000360067:H211Y;ENSP00000379015:H197Y	ENSP00000337128:H211Y	H	+	1	0	EDN3	57332823	0.000000	0.05858	0.001000	0.08648	0.013000	0.08279	0.215000	0.17562	0.733000	0.32492	-0.140000	0.14226	CAC	.	.		0.532	EDN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079919.2	NM_000114		T	57899428	C	T	57899428	3	4	356	1	0	0	0	0	1	0	0	0	4920	594	21	3	688	3	EDN3	20	57899428	Missense_Mutation	SNP	C	TCGA-WX-AA47-01A-11D-A38X-10		57899428	5126092	40	50166										
FBLN1	2192	hgsc.bcm.edu	37	chr22	45937218	45937218	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	gtgcccaactgtggccgtggCtaccatctcaacgaggaggg	14	12	1	0			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr22:45937218C>T	ENST00000327858.6	+	9	1127	c.1032C>T	c.(1030-1032)ggC>ggT	p.G344G	FBLN1_ENST00000442170.2_Silent_p.G344G|FBLN1_ENST00000348697.2_Silent_p.G344G|FBLN1_ENST00000402984.3_Silent_p.G382G|FBLN1_ENST00000476366.1_3'UTR|FBLN1_ENST00000262722.7_Silent_p.G344G|FBLN1_ENST00000340923.5_Silent_p.G344G	NM_006486.2	NP_006477	P23142	FBLN1_HUMAN	fibulin 1	344	EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|viral process (GO:0016032)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)|peptidase activator activity (GO:0016504)			biliary_tract(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)	30		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		GTGGCCGTGGCTACCATCTCA	0.527																																					p.G344G		Atlas-SNP	.											.	FBLN1	143	.	0			c.C1032T						.						119	97	105					22																	45937218		2203	4300	6503	SO:0001819	synonymous_variant	2192	exon9			CCGTGGCTACCAT		CCDS14067.1, CCDS14068.1, CCDS14069.1, CCDS43028.1	22q13.31	2010-06-15			ENSG00000077942	ENSG00000077942		"Fibulins"	3600	protein-coding gene	gene with protein product		135820				2269669, 1400330	Standard	NM_006485		Approved	FBLN	uc003bgj.1	P23142	OTTHUMG00000151340	ENST00000327858.6:c.1032C>T	chr22.hg19:g.45937218C>T		108.0	0.0		108.0	40.0	NM_006487	B0QY42|B1AHL4|P23143|P23144|P37888|Q5TIC4|Q8TBH8|Q9HBQ5|Q9UC21|Q9UGR4|Q9UH41	Silent	SNP	ENST00000327858.6	hg19	CCDS14067.1																																																																																			.	.		0.527	FBLN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322287.1	NM_006486		T	45937218	C	T	45937218	2	4	356	1	0	0	0	0	0	0	0	1	5706	784	28	3		3	FBLN1	22	45937218	Silent	SNP	C	TCGA-WX-AA47-01A-11D-A38X-10		45937218	5367348	41	50167										
CELSR1	9620	hgsc.bcm.edu	37	chr22	46930896	46930896	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	ttccgggtgttgccgcctgtGagctggtaggtaatcacact	13	10	1	1			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr22:46930896G>A	ENST00000262738.3	-	1	2171	c.2172C>T	c.(2170-2172)ctC>ctT	p.L724L	CELSR1_ENST00000497509.1_5'Flank|CELSR1_ENST00000395964.1_Silent_p.L724L	NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	724	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		TGCCGCCTGTGAGCTGGTAGG	0.637																																					p.L724L		Atlas-SNP	.											.	CELSR1	242	.	0			c.C2172T						.						57	39	45					22																	46930896		2201	4299	6500	SO:0001819	synonymous_variant	9620	exon1			GCCTGTGAGCTGG	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	1850	protein-coding gene	gene with protein product	"flamingo homolog 2 (Drosophila)"	604523	"cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.2172C>T	chr22.hg19:g.46930896G>A		54.0	0.0		33.0	14.0	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Silent	SNP	ENST00000262738.3	hg19	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	G	0.128	-1.117159	0.01799	.	.	ENSG00000075275	ENST00000454637	.	.	.	4.51	0.798	0.18660	.	.	.	.	.	T	0.58836	0.2150	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54576	-0.8273	4	.	.	.	.	11.0373	0.47808	0.0846:0.4365:0.4788:0.0	.	.	.	.	L	99	.	.	S	-	2	0	CELSR1	45309560	0.999000	0.42202	0.993000	0.49108	0.070000	0.16714	0.393000	0.20817	0.315000	0.23110	0.305000	0.20034	TCA	.	.		0.637	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		A	46930896	G	A	46930896	2	1	356	1	0	0	0	0	0	0	0	1	3223	1277	45	3		3	CELSR1	22	46930896	Silent	SNP	G	TCGA-WX-AA47-01A-11D-A38X-10	993678	46930896	4373670	42	50168										
PLXNB2	23654	hgsc.bcm.edu	37	chr22	50718956	50718956	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	gggttcttggccaccacgtaCtgctccaggagctccaggaa	12	13	1	0			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chr22:50718956C>G	ENST00000449103.1	-	25	4277	c.4137G>C	c.(4135-4137)caG>caC	p.Q1379H	PLXNB2_ENST00000496720.1_5'Flank|PLXNB2_ENST00000359337.4_Missense_Mutation_p.Q1379H			O15031	PLXB2_HUMAN	plexin B2	1379					brain development (GO:0007420)|neural tube closure (GO:0001843)|neuroblast proliferation (GO:0007405)|positive regulation of axonogenesis (GO:0050772)|regulation of cell shape (GO:0008360)|regulation of neuron migration (GO:2001222)|regulation of protein phosphorylation (GO:0001932)|regulation of Rho GTPase activity (GO:0032319)|semaphorin-plexin signaling pathway (GO:0071526)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	GTPase activator activity (GO:0005096)|semaphorin receptor activity (GO:0017154)			breast(2)|central_nervous_system(4)|cervix(2)|endometrium(11)|kidney(4)|large_intestine(3)|liver(1)|lung(20)|ovary(5)|prostate(6)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	66		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|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)		CCACCACGTACTGCTCCAGGA	0.672																																					p.Q1379H		Atlas-SNP	.											.	PLXNB2	172	.	0			c.G4137C						.						82	88	86					22																	50718956		2191	4295	6486	SO:0001583	missense	23654	exon25			CACGTACTGCTCC		CCDS43035.1	22q13.33	2008-06-12			ENSG00000196576	ENSG00000196576		"Plexins"	9104	protein-coding gene	gene with protein product		604293				10520995, 12183458	Standard	NM_012401		Approved	MM1, KIAA0315, PLEXB2	uc003bkv.4	O15031	OTTHUMG00000150219	ENST00000449103.1:c.4137G>C	chr22.hg19:g.50718956C>G	ENSP00000409171:p.Gln1379His	59.0	0.0		54.0	17.0	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Missense_Mutation	SNP	ENST00000449103.1	hg19	CCDS43035.1	.	.	.	.	.	.	.	.	.	.	C	14.53	2.562678	0.45694	.	.	ENSG00000196576	ENST00000449103;ENST00000359337;ENST00000399964	T;T	0.12255	2.7;2.7	4.28	4.28	0.50868	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.000000	0.64402	D	0.000003	T	0.23410	0.0566	L	0.51422	1.61	0.44234	D	0.997079	P	0.45428	0.858	P	0.57960	0.83	T	0.00380	-1.1776	10	0.37606	T	0.19	.	8.4285	0.32744	0.0:0.8239:0.0:0.1761	.	1379	O15031	PLXB2_HUMAN	H	1379;1379;11	ENSP00000409171:Q1379H;ENSP00000352288:Q1379H	ENSP00000352288:Q1379H	Q	-	3	2	PLXNB2	49061083	0.989000	0.36119	1.000000	0.80357	0.988000	0.76386	0.289000	0.18957	2.366000	0.80165	0.561000	0.74099	CAG	.	.		0.672	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401		G	50718956	C	G	50718956	3	3	356	1	0	0	0	0	1	0	0	0	12133	564	20	4	1431	4	PLXNB2	22	50718956	Missense_Mutation	SNP	C	TCGA-WX-AA47-01A-11D-A38X-10	3788060	50718956	585610	43	50169										
KAL1	3730	hgsc.bcm.edu	37	chrX	8504916	8504916	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	ccttggagtgactttttggcCgtattggttggacagtcacc	12	9	1	1			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chrX:8504916C>T	ENST00000262648.3	-	11	1666	c.1517G>A	c.(1516-1518)cGg>cAg	p.R506Q	KAL1_ENST00000481896.1_5'UTR	NM_000216.2	NP_000207.2	P23352	KALM_HUMAN	Kallmann syndrome 1 sequence	506	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|liver(1)|lung(6)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(1)	32						ACTTTTTGGCCGTATTGGTTG	0.443																																					p.R506Q		Atlas-SNP	.											.	KAL1	78	.	0			c.G1517A						.						132	109	117					X																	8504916		2203	4300	6503	SO:0001583	missense	3730	exon11			TTTGGCCGTATTG		CCDS14130.1	Xp22.32	2013-02-11			ENSG00000011201	ENSG00000011201		"WAP four-disulfide core domain containing", "Fibronectin type III domain containing"	6211	protein-coding gene	gene with protein product	"anosmin-1", "WAP four-disulfide core domain 19"	300836		KAL, ADMLX		11463336	Standard	NM_000216		Approved	KALIG-1, WFDC19	uc004csf.3	P23352	OTTHUMG00000021107	ENST00000262648.3:c.1517G>A	chrX.hg19:g.8504916C>T	ENSP00000262648:p.Arg506Gln	217.0	0.0		211.0	83.0	NM_000216	B2RPF8	Missense_Mutation	SNP	ENST00000262648.3	hg19	CCDS14130.1	.	.	.	.	.	.	.	.	.	.	C	4.781	0.145252	0.09134	.	.	ENSG00000011201	ENST00000262648	T	0.53857	0.6	3.99	2.14	0.27477	Fibronectin, type III (2);	0.434585	0.26079	N	0.026467	T	0.38639	0.1048	M	0.62723	1.935	0.22926	N	0.998559	P	0.37233	0.588	B	0.29942	0.109	T	0.20371	-1.0277	10	0.22706	T	0.39	-6.8111	4.9608	0.14065	0.0:0.6052:0.1733:0.2215	.	506	P23352	KALM_HUMAN	Q	506	ENSP00000262648:R506Q	ENSP00000262648:R506Q	R	-	2	0	KAL1	8464916	0.851000	0.29673	0.010000	0.14722	0.136000	0.21042	0.573000	0.23699	0.087000	0.17167	-0.198000	0.12761	CGG	.	.		0.443	KAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055692.1	NM_000216		T	8504916	C	T	8504916	3	4	356	1	0	0	0	0	1	0	0	0	7983	652	23	1	541	1	KAL1	23	8504916	Missense_Mutation	SNP	C	TCGA-WX-AA47-01A-11D-A38X-10		8504916	146765644	44	50170										
CFP	5199	hgsc.bcm.edu	37	chrX	47483694	47483694	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	ttagagttcctcttcctcagGgtctttgcaagcaggcacgt	10	11	3	1			TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chrX:47483694G>T	ENST00000396992.3	-	9	1510	c.1390C>A	c.(1390-1392)Cct>Act	p.P464T	CFP_ENST00000247153.3_Missense_Mutation_p.P464T	NM_001145252.1	NP_001138724.1	P27918	PROP_HUMAN	complement factor properdin	464					complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|defense response to bacterium (GO:0042742)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	18						TCTTCCTCAGGGTCTTTGCAA	0.542																																					p.P464T		Atlas-SNP	.											.	CFP	43	.	0			c.C1390A						.						259	177	204					X																	47483694		2203	4300	6503	SO:0001583	missense	5199	exon9			CCTCAGGGTCTTT	M83652	CCDS14282.1	Xp11.4	2014-09-17	2006-03-02	2006-03-02	ENSG00000126759	ENSG00000126759		"Complement system"	8864	protein-coding gene	gene with protein product		300383	"properdin P factor, complement"	PFC		1783405	Standard	NM_001145252		Approved		uc004dih.3	P27918	OTTHUMG00000021451	ENST00000396992.3:c.1390C>A	chrX.hg19:g.47483694G>T	ENSP00000380189:p.Pro464Thr	151.0	0.0		147.0	63.0	NM_001145252	O15134|O15135|O15136|O75826	Missense_Mutation	SNP	ENST00000396992.3	hg19	CCDS14282.1	.	.	.	.	.	.	.	.	.	.	G	17.87	3.495704	0.64186	.	.	ENSG00000126759	ENST00000396992;ENST00000247153	T;T	0.43294	0.95;0.95	5.01	5.01	0.66863	.	0.000000	0.64402	D	0.000001	T	0.60327	0.2260	M	0.64997	1.995	0.35791	D	0.822416	D	0.76494	0.999	D	0.85130	0.997	T	0.70249	-0.4924	10	0.72032	D	0.01	.	12.5877	0.56426	0.0:0.0:1.0:0.0	.	464	P27918	PROP_HUMAN	T	464	ENSP00000380189:P464T;ENSP00000247153:P464T	ENSP00000247153:P464T	P	-	1	0	CFP	47368638	1.000000	0.71417	0.972000	0.41901	0.699000	0.40488	2.579000	0.46059	2.465000	0.83290	0.529000	0.55759	CCT	.	.		0.542	CFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056435.2	NM_002621		T	47483694	G	T	47483694	3	4	356	1	0	0	0	0	1	0	0	0	3295	1232	43	3	23	3	CFP	23	47483694	Missense_Mutation	SNP	G	TCGA-WX-AA47-01A-11D-A38X-10	38978778	47483694	107786866	45	50171										
STARD8	9754	hgsc.bcm.edu	37	chrX	67938119	67938126	+	Frame_Shift_Del	DEL	TGGGCCCA	TGGGCCCA	-													0.0434782608695652	2	1	0.743478260869565	1.06211180124224	0.57190635451505	1	1	0	cccatggagagtccccagccTgggcccaggctgaagtccag							TCGA-WX-AA47-01A-11D-A38X-10	TCGA-WX-AA47-10A-01D-A38X-10	TGGGCCCA	TGGGCCCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dab9728a-5871-4bb0-9ae4-8c6b4885000f	e0c88f8e-49d8-413f-be0d-85b5e3e27b15	g.chrX:67938119_67938126delTGGGCCCA	ENST00000252336.6	+	5	1495_1502	c.1123_1130delTGGGCCCA	c.(1123-1131)tgggcccagfs	p.WAQ375fs	STARD8_ENST00000374599.3_Frame_Shift_Del_p.WAQ455fs|STARD8_ENST00000374597.3_Frame_Shift_Del_p.WAQ375fs	NM_014725.4	NP_055540.2	Q92502	STAR8_HUMAN	StAR-related lipid transfer (START) domain containing 8	375					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)			NS(2)|breast(5)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(2)	50						GTCCCCAGCCTGGGCCCAGGCTGAAGTC	0.644																																					p.454_457del		Atlas-INDEL	.											.	STARD8	282	.	0			c.1362_1369del						.																																			SO:0001589	frameshift_variant	9754	exon6			.	D80011	CCDS14390.1, CCDS48134.1	Xq13.1	2011-09-13	2007-08-16		ENSG00000130052	ENSG00000130052		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	19161	protein-coding gene	gene with protein product		300689	"START domain containing 8"			8724849	Standard	NM_001142504		Approved	KIAA0189, ARHGAP38	uc004dxb.3	Q92502	OTTHUMG00000021748	ENST00000252336.6:c.1123_1130delTGGGCCCA	chrX.hg19:g.67938119_67938126delTGGGCCCA	ENSP00000252336:p.Trp375fs	190.0	0.0		175.0	60.0	NM_001142503	A8K6T2|D3DVT9|Q5JST0|Q68DG7	Frame_Shift_Del	DEL	ENST00000252336.6	hg19	CCDS14390.1																																																																																			.	.		0.644	STARD8-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057026.2	NM_014725		-	67938126	TGGGCCCA	-	67938119	7	5	356	1	0	1	0	1	0	0	0	0	15278	1580	55	0	1385	0	STARD8	23	67938119	Frame_Shift_Del	DEL	TGGGCCCA	TCGA-WX-AA47-01A-11D-A38X-10	20454425	67938119	87332441	46	50172										
DOCK7	85440	hgsc.bcm.edu	37	chr1	62958432	62958432	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	acaagtcctgactcagtaaaGtattttccagagcagatacc	7	10	1	3			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr1:62958432G>A	ENST00000340370.5	-	40	5228	c.5211C>T	c.(5209-5211)taC>taT	p.Y1737Y	DOCK7_ENST00000251157.5_Silent_p.Y1759Y	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	1768	DHR-2.				activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						ACTCAGTAAAGTATTTTCCAG	0.388																																					p.Y1759Y		Atlas-SNP	.											.	DOCK7	184	.	0			c.C5277T						.						110	103	105					1																	62958432		2203	4300	6503	SO:0001819	synonymous_variant	85440	exon41			AGTAAAGTATTTT		CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.5211C>T	chr1.hg19:g.62958432G>A		353.0	0.0		227.0	171.0	NM_001271999	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Silent	SNP	ENST00000340370.5	hg19	CCDS30734.1	.	.	.	.	.	.	.	.	.	.	G	8.518	0.868061	0.17250	.	.	ENSG00000116641	ENST00000454575	.	.	.	5.52	5.52	0.82312	.	.	.	.	.	T	0.57636	0.2067	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56498	-0.7969	4	.	.	.	.	7.2236	0.26002	0.2058:0.0:0.7942:0.0	.	.	.	.	F	931	.	.	L	-	1	0	DOCK7	62731020	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.485000	0.53208	2.596000	0.87737	0.585000	0.79938	CTT	.	.		0.388	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407		A	62958432	G	A	62958432	2	1	357	1	0	0	0	0	0	0	0	1	4694	1024	36	3		3	DOCK7	1	62958432	Silent	SNP	G	TCGA-XR-A8TC-01A-11D-A35Z-10		62958432	186292189	1	50173										
ATXN7L2	127002	hgsc.bcm.edu	37	chr1	110034053	110034053	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	aatggggccaagagtgaagcGggcagggcccctggactgtc	17	10	0	2	rs377112437		TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr1:110034053G>A	ENST00000369870.3	+	10	1883	c.1868G>A	c.(1867-1869)cGg>cAg	p.R623Q	CYB561D1_ENST00000420578.2_5'Flank|CYB561D1_ENST00000528785.1_5'Flank|CYB561D1_ENST00000369868.3_5'Flank|CYB561D1_ENST00000310611.4_5'Flank|CYB561D1_ENST00000527072.1_5'Flank|CYB561D1_ENST00000496961.1_5'Flank|CYB561D1_ENST00000393709.3_5'Flank|CYB561D1_ENST00000430195.2_5'Flank|ATXN7L2_ENST00000459635.1_3'UTR|CYB561D1_ENST00000533024.1_5'Flank	NM_153340.4	NP_699171.3	Q5T6C5	AT7L2_HUMAN	ataxin 7-like 2	623										breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)	17		all_epithelial(167;0.00197)|all_lung(203;0.00291)|Lung NSC(277;0.00453)		Colorectal(144;0.0129)|Lung(183;0.0426)|Epithelial(280;0.0675)|READ - Rectum adenocarcinoma(129;0.0693)|all cancers(265;0.071)|LUSC - Lung squamous cell carcinoma(189;0.228)		AGAGTGAAGCGGGCAGGGCCC	0.607																																					p.R623Q		Atlas-SNP	.											ATXN7L2,colon,carcinoma,0,1	ATXN7L2	60	.	0			c.G1868A						.	G	GLN/ARG	0,4406		0,0,2203	37	43	41		1868	5.4	1	1		41	1,8599	1.2+/-3.3	0,1,4299	no	missense	ATXN7L2	NM_153340.4	43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	623/723	110034053	1,13005	2203	4300	6503	SO:0001583	missense	127002	exon10			TGAAGCGGGCAGG	BC037582	CCDS30794.1	1p13.2	2008-02-05			ENSG00000162650	ENSG00000162650			28713	protein-coding gene	gene with protein product						12477932	Standard	NM_153340		Approved	MGC46534, FLJ00381	uc001dxr.3	Q5T6C5	OTTHUMG00000011027	ENST00000369870.3:c.1868G>A	chr1.hg19:g.110034053G>A	ENSP00000358886:p.Arg623Gln	192.0	0.0		110.0	69.0	NM_153340		Missense_Mutation	SNP	ENST00000369870.3	hg19	CCDS30794.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.172916	0.78452	0.0	1.16E-4	ENSG00000162650	ENST00000369870;ENST00000369869	T	0.32515	1.45	5.36	5.36	0.76844	.	0.573844	0.15973	N	0.235687	T	0.26340	0.0643	N	0.19112	0.55	0.33363	D	0.572545	D;D	0.76494	0.998;0.999	D;D	0.72625	0.929;0.978	T	0.02553	-1.1142	10	0.16420	T	0.52	-5.1715	16.1282	0.81408	0.0:0.0:1.0:0.0	.	250;623	Q5T6C4;Q5T6C5	.;AT7L2_HUMAN	Q	623;250	ENSP00000358886:R623Q	ENSP00000358885:R250Q	R	+	2	0	ATXN7L2	109835576	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.533000	0.67160	2.793000	0.96121	0.561000	0.74099	CGG	.	.		0.607	ATXN7L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030331.1	NM_153340		A	110034053	G	A	110034053	3	1	357	1	0	0	0	0	1	0	0	0	1217	1116	39	1	1906	1	ATXN7L2	1	110034053	Missense_Mutation	SNP	G	TCGA-XR-A8TC-01A-11D-A35Z-10	47075621	110034053	139216568	2	50174										
FMO4	2329	hgsc.bcm.edu	37	chr1	171289026	171289026	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	cctctcctccatcaaatgctGtgtggatgaggacctggagc	11	12	2	1			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr1:171289026G>A	ENST00000367749.3	+	3	392	c.62G>A	c.(61-63)tGt>tAt	p.C21Y		NM_002022.1	NP_002013.1	P31512	FMO4_HUMAN	flavin containing monooxygenase 4	21					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	33	all_cancers(6;3.9e-08)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					ATCAAATGCTGTGTGGATGAG	0.473																																					p.C21Y	Pancreas(24;816 862 7754 7993 32832)	Atlas-SNP	.											.	FMO4	64	.	0			c.G62A						.						235	218	224					1																	171289026		2203	4300	6503	SO:0001583	missense	2329	exon3			AATGCTGTGTGGA	BC002780	CCDS1295.1	1q24.3	2011-08-04			ENSG00000076258	ENSG00000076258	1.14.13.8		3772	protein-coding gene	gene with protein product		136131		FMO2		8311461	Standard	NM_002022		Approved		uc001gho.3	P31512	OTTHUMG00000035506	ENST00000367749.3:c.62G>A	chr1.hg19:g.171289026G>A	ENSP00000356723:p.Cys21Tyr	77.0	0.0		175.0	90.0	NM_002022	Q53XR0	Missense_Mutation	SNP	ENST00000367749.3	hg19	CCDS1295.1	.	.	.	.	.	.	.	.	.	.	G	19.51	3.840706	0.71488	.	.	ENSG00000076258	ENST00000367749	T	0.64991	-0.13	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	D	0.83078	0.5176	H	0.94734	3.575	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88063	0.2795	10	0.87932	D	0	-17.2113	17.477	0.87661	0.0:0.0:1.0:0.0	.	21	P31512	FMO4_HUMAN	Y	21	ENSP00000356723:C21Y	ENSP00000356723:C21Y	C	+	2	0	FMO4	169555650	1.000000	0.71417	1.000000	0.80357	0.419000	0.31324	9.396000	0.97270	2.404000	0.81709	0.650000	0.86243	TGT	.	.		0.473	FMO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086223.1	NM_002022		A	171289026	G	A	171289026	3	1	357	1	0	0	0	0	1	0	0	0	5965	1377	48	3	64	3	FMO4	1	171289026	Missense_Mutation	SNP	G	TCGA-XR-A8TC-01A-11D-A35Z-10	61254973	171289026	77961595	3	50175										
GPR52	9293	hgsc.bcm.edu	37	chr1	174417781	174417781	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	taattttcttgccttcctttTttggctgggggaaacctggt	10	8	1	0			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr1:174417781T>C	ENST00000367685.2	+	1	570	c.532T>C	c.(532-534)Ttt>Ctt	p.F178L	RABGAP1L_ENST00000367689.3_Intron|RABGAP1L_ENST00000357444.6_Intron|RABGAP1L_ENST00000251507.4_Intron	NM_005684.4	NP_005675.3	Q9Y2T5	GPR52_HUMAN	G protein-coupled receptor 52	178					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(3)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|prostate(1)|skin(2)	20						GCCTTCCTTTTTTGGCTGGGG	0.433																																					p.F178L	Ovarian(92;924 1390 1930 16467 40583)	Atlas-SNP	.											.	GPR52	40	.	0			c.T532C						.						204	199	201					1																	174417781		2203	4300	6503	SO:0001583	missense	9293	exon1			TCCTTTTTTGGCT	AF096784	CCDS30941.1	1q24	2012-08-21			ENSG00000203737	ENSG00000203737		"GPCR / Class A : Orphans"	4508	protein-coding gene	gene with protein product		604106				9931487	Standard	NM_005684		Approved		uc001gka.1	Q9Y2T5	OTTHUMG00000034901	ENST00000367685.2:c.532T>C	chr1.hg19:g.174417781T>C	ENSP00000356658:p.Phe178Leu	70.0	0.0		142.0	25.0	NM_005684	O75654|Q4VBL6|Q6ISM0	Missense_Mutation	SNP	ENST00000367685.2	hg19	CCDS30941.1	.	.	.	.	.	.	.	.	.	.	T	7.181	0.589605	0.13812	.	.	ENSG00000203737	ENST00000367685	T	0.36340	1.26	5.9	5.9	0.94986	GPCR, rhodopsin-like superfamily (1);	0.072916	0.53938	N	0.000041	T	0.22437	0.0541	N	0.10945	0.07	0.43766	D	0.996286	B	0.23650	0.089	B	0.26517	0.07	T	0.11060	-1.0603	10	0.12766	T	0.61	-12.3619	16.3322	0.83039	0.0:0.0:0.0:1.0	.	178	Q9Y2T5	GPR52_HUMAN	L	178	ENSP00000356658:F178L	ENSP00000356658:F178L	F	+	1	0	GPR52	172684404	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.634000	0.83273	2.251000	0.74343	0.528000	0.53228	TTT	.	.		0.433	GPR52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084511.1	NM_005684		C	174417781	T	C	174417781	3	2	357	1	0	0	0	0	1	0	0	0	6706	1841	64	2	534	2	GPR52	1	174417781	Missense_Mutation	SNP	T	TCGA-XR-A8TC-01A-11D-A35Z-10	3128755	174417781	74832840	4	50176										
INTS7	25896	hgsc.bcm.edu	37	chr1	212161330	212161330	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	gtcataaggagtctggagggCacactcacaaagtgcctgga	13	9	3	0			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr1:212161330C>T	ENST00000366994.3	-	8	999	c.895G>A	c.(895-897)Gcc>Acc	p.A299T	INTS7_ENST00000440600.2_Missense_Mutation_p.A250T|INTS7_ENST00000366993.3_Missense_Mutation_p.A299T|INTS7_ENST00000469606.1_5'UTR|INTS7_ENST00000366992.3_Missense_Mutation_p.A299T	NM_001199811.1|NM_001199812.1|NM_015434.3	NP_001186740.1|NP_001186741.1|NP_056249.1	Q9NVH2	INT7_HUMAN	integrator complex subunit 7	299					cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|snRNA processing (GO:0016180)	chromosome (GO:0005694)|integrator complex (GO:0032039)				NS(1)|breast(1)|kidney(1)|large_intestine(8)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20				OV - Ovarian serous cystadenocarcinoma(81;0.00584)|all cancers(67;0.0318)|Epithelial(68;0.0852)		GTCTGGAGGGCACACTCACAA	0.393																																					p.A299T		Atlas-SNP	.											.	INTS7	68	.	0			c.G895A						.						107	95	99					1																	212161330		2203	4300	6503	SO:0001583	missense	25896	exon8			GGAGGGCACACTC	AK022509	CCDS1501.1, CCDS55684.1, CCDS55683.1, CCDS55685.1	1q32.3	2008-02-05	2006-03-15	2006-03-15	ENSG00000143493	ENSG00000143493			24484	protein-coding gene	gene with protein product		611350	"chromosome 1 open reading frame 73"	C1orf73		16239144	Standard	NM_015434		Approved	DKFZP434B168, INT7	uc001hiw.2	Q9NVH2	OTTHUMG00000037119	ENST00000366994.3:c.895G>A	chr1.hg19:g.212161330C>T	ENSP00000355961:p.Ala299Thr	64.0	0.0		124.0	32.0	NM_015434	B4DLZ6|B7WNP6|B7WPB6|Q8N4K7|Q8WUH5|Q9H9V3|Q9NVU5|Q9UFC6|Q9UFM3	Missense_Mutation	SNP	ENST00000366994.3	hg19	CCDS1501.1	.	.	.	.	.	.	.	.	.	.	C	16.13	3.036277	0.54896	.	.	ENSG00000143493	ENST00000366994;ENST00000366993;ENST00000366992;ENST00000440600	T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.16	4.94	4.94	0.65067	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.66723	0.2818	N	0.16166	0.38	0.80722	D	1	D;D;D;D	0.67145	0.996;0.996;0.969;0.969	D;D;P;P	0.77557	0.99;0.99;0.685;0.766	T	0.61252	-0.7100	10	0.08599	T	0.76	-9.4479	18.1681	0.89734	0.0:1.0:0.0:0.0	.	250;299;299;299	B4DLZ6;Q9NVH2-3;Q9NVH2-2;Q9NVH2	.;.;.;INT7_HUMAN	T	299;299;299;250	ENSP00000355961:A299T;ENSP00000355960:A299T;ENSP00000355959:A299T;ENSP00000388908:A250T	ENSP00000355959:A299T	A	-	1	0	INTS7	210227953	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.295000	0.65692	2.292000	0.77174	0.591000	0.81541	GCC	.	.		0.393	INTS7-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090142.1	NM_015434		T	212161330	C	T	212161330	3	4	357	1	0	0	0	0	1	0	0	0	7792	710	25	3	2045	3	INTS7	1	212161330	Missense_Mutation	SNP	C	TCGA-XR-A8TC-01A-11D-A35Z-10	37743549	212161330	37089291	5	50177										
CDC42BPA	8476	hgsc.bcm.edu	37	chr1	227300124	227300124	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	gcttctgtatgaacttccagCtttaaaacagaatgaaaaat	6	7	1	3			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr1:227300124C>T	ENST00000366769.3	-	14	3182		c.e14-1		CDC42BPA_ENST00000535525.1_Splice_Site|CDC42BPA_ENST00000366765.3_Splice_Site|CDC42BPA_ENST00000366766.2_Splice_Site|CDC42BPA_ENST00000366764.2_Splice_Site|CDC42BPA_ENST00000366767.3_Splice_Site|CDC42BPA_ENST00000334218.5_Splice_Site	NM_003607.3	NP_003598.2			CDC42 binding protein kinase alpha (DMPK-like)											NS(1)|breast(4)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(12)|lung(32)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|urinary_tract(2)	77		all_cancers(173;0.156)|Prostate(94;0.0792)				GAACTTCCAGCTTTAAAACAG	0.353																																					.		Atlas-SNP	.											.	CDC42BPA	528	.	0			c.1891-1G>A						.						130	128	129					1																	227300124		2203	4300	6503	SO:0001630	splice_region_variant	8476	exon15			TTCCAGCTTTAAA	U59305	CCDS1558.1, CCDS1559.1	1q42.11	2011-11-23	2001-11-28		ENSG00000143776	ENSG00000143776			1737	protein-coding gene	gene with protein product	"myotonic dystrophy kinase-related Cdc42-binding kinase"	603412	"CDC42-binding protein kinase alpha (DMPK-like)"				Standard	NM_003607		Approved	MRCKA, PK428, FLJ23347, KIAA0451, MRCK	uc001hqr.3	Q5VT25	OTTHUMG00000037618	ENST00000366769.3:c.1891-1G>A	chr1.hg19:g.227300124C>T		63.0	0.0		107.0	25.0	NM_003607		Splice_Site	SNP	ENST00000366769.3	hg19	CCDS1558.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.945207	0.73672	.	.	ENSG00000143776	ENST00000366769;ENST00000366767;ENST00000334218;ENST00000366766;ENST00000366764;ENST00000535525;ENST00000366765	.	.	.	5.52	5.52	0.82312	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.4394	0.94811	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CDC42BPA	225366747	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	6.063000	0.71162	2.572000	0.86782	0.585000	0.79938	.	.	.		0.353	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	NM_014826	Intron	T	227300124	C	T	227300124	5	4	357	1	0	0	0	0	0	0	1	0	3074	811	28	3	3361	3	CDC42BPA	1	227300124	Splice_Site	SNP	C	TCGA-XR-A8TC-01A-11D-A35Z-10	15138794	227300124	21950497	6	50178										
HADHA	3030	hgsc.bcm.edu	37	chr2	26416510	26416510	+	Frame_Shift_Del	DEL	A	A	-													0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	ccacctccaaaccgctccccAaagactttgcccagatcttc							TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr2:26416510delA	ENST00000380649.3	-	17	1950	c.1821delT	c.(1819-1821)tttfs	p.F607fs		NM_000182.4	NP_000173.2	P40939	ECHA_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), alpha subunit	607					cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acetyltransferase activity (GO:0003985)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)			autonomic_ganglia(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(4)|skin(1)	30	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ACCGCTCCCCAAAGACTTTGC	0.522																																					p.G608fs		Atlas-INDEL	.											.	HADHA	87	.	0			c.1822delG						.						167	160	163					2																	26416510		2203	4300	6503	SO:0001589	frameshift_variant	3030	exon17			.	D16480	CCDS1721.1	2p23	2014-09-17	2010-04-30		ENSG00000084754	ENSG00000084754	1.1.1.211, 4.2.1.17		4801	protein-coding gene	gene with protein product	"gastrin-binding protein", "long-chain-3-hydroxyacyl-CoA dehydrogenase", "long-chain 2-enoyl-CoA hydratase", "mitochondrial trifunctional protein, alpha subunit"	600890	"hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit"			9605857, 7918661	Standard	NM_000182		Approved	GBP, LCEH, LCHAD, MTPA	uc002rgy.3	P40939	OTTHUMG00000096979	ENST00000380649.3:c.1821delT	chr2.hg19:g.26416510delA	ENSP00000370023:p.Phe607fs	154.0	0.0		136.0	46.0	NM_000182	B2R7L4|B4DYP2|Q16679|Q53T69|Q53TA2|Q96GT7|Q9UQC5	Frame_Shift_Del	DEL	ENST00000380649.3	hg19	CCDS1721.1																																																																																			.	.		0.522	HADHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214051.1	NM_000182		-	26416510	A	-	26416510	7	5	357	1	0	1	0	1	0	0	0	0	6952	127	5	0	486	0	HADHA	2	26416510	Frame_Shift_Del	DEL	A	TCGA-XR-A8TC-01A-11D-A35Z-10		26416510	216782863	7	50179	260	2								
HADHA	3030	hgsc.bcm.edu	37	chr2	26416514	26416514	+	Missense_Mutation	SNP	A	A	G													0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	ctccaaaccgctccccaaagActttgcccagatcttccgcc							TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr2:26416514A>G	ENST00000380649.3	-	17	1946	c.1817T>C	c.(1816-1818)gTc>gCc	p.V606A		NM_000182.4	NP_000173.2	P40939	ECHA_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), alpha subunit	606					cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acetyltransferase activity (GO:0003985)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)			autonomic_ganglia(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(4)|skin(1)	30	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTCCCCAAAGACTTTGCCCAG	0.537																																					p.V606A		Atlas-SNP	.											.	HADHA	87	.	0			c.T1817C						.						172	163	166					2																	26416514		2203	4300	6503	SO:0001583	missense	3030	exon17			CCAAAGACTTTGC	D16480	CCDS1721.1	2p23	2014-09-17	2010-04-30		ENSG00000084754	ENSG00000084754	1.1.1.211, 4.2.1.17		4801	protein-coding gene	gene with protein product	"gastrin-binding protein", "long-chain-3-hydroxyacyl-CoA dehydrogenase", "long-chain 2-enoyl-CoA hydratase", "mitochondrial trifunctional protein, alpha subunit"	600890	"hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit"			9605857, 7918661	Standard	NM_000182		Approved	GBP, LCEH, LCHAD, MTPA	uc002rgy.3	P40939	OTTHUMG00000096979	ENST00000380649.3:c.1817T>C	chr2.hg19:g.26416514A>G	ENSP00000370023:p.Val606Ala	152.0	0.0		137.0	47.0	NM_000182	B2R7L4|B4DYP2|Q16679|Q53T69|Q53TA2|Q96GT7|Q9UQC5	Missense_Mutation	SNP	ENST00000380649.3	hg19	CCDS1721.1	.	.	.	.	.	.	.	.	.	.	A	7.150	0.583637	0.13749	.	.	ENSG00000084754	ENST00000380649;ENST00000492433	D;D	0.88741	-2.42;-2.42	5.97	3.11	0.35812	3-hydroxyacyl-CoA dehydrogenase, C-terminal (1);Dehydrogenase, multihelical (1);6-phosphogluconate dehydrogenase, C-terminal-like (1);	0.148266	0.64402	N	0.000009	T	0.61899	0.2384	N	0.00633	-1.31	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.59177	-0.7503	10	0.02654	T	1	-37.444	7.8159	0.29258	0.1411:0.0:0.7267:0.1321	.	606;606	E9KL44;P40939	.;ECHA_HUMAN	A	606;92	ENSP00000370023:V606A;ENSP00000438039:V92A	ENSP00000370023:V606A	V	-	2	0	HADHA	26270018	1.000000	0.71417	0.999000	0.59377	0.981000	0.71138	4.743000	0.62110	0.413000	0.25759	-0.177000	0.13119	GTC	.	.		0.537	HADHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214051.1	NM_000182		G	26416514	A	G	26416514	3	3	357	1	0	0	0	0	1	0	0	0	6952	275	10	2	490	2	HADHA	2	26416514	Missense_Mutation	SNP	A	TCGA-XR-A8TC-01A-11D-A35Z-10	4	26416514	216782859	8	50180	260	2								
DRD3	1814	hgsc.bcm.edu	37	chr3	113890665	113890665	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	gttggtggtagtctgcagggCccgctccttcagcacagcca	13	13	2	0			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr3:113890665C>A	ENST00000460779.1	-	3	464	c.175G>T	c.(175-177)Gcc>Tcc	p.A59S	DRD3_ENST00000295881.7_Missense_Mutation_p.A59S|DRD3_ENST00000467632.1_Missense_Mutation_p.A59S|DRD3_ENST00000383673.2_Missense_Mutation_p.A59S	NM_001282563.1	NP_001269492.1	P35462	DRD3_HUMAN	dopamine receptor D3	59					acid secretion (GO:0046717)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|arachidonic acid secretion (GO:0050482)|behavioral response to cocaine (GO:0048148)|cellular calcium ion homeostasis (GO:0006874)|circadian regulation of gene expression (GO:0032922)|dopamine metabolic process (GO:0042417)|G-protein coupled receptor internalization (GO:0002031)|G-protein coupled receptor signaling pathway (GO:0007186)|gastric emptying (GO:0035483)|learning (GO:0007612)|learning or memory (GO:0007611)|locomotory behavior (GO:0007626)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of blood pressure (GO:0045776)|negative regulation of dopamine receptor signaling pathway (GO:0060160)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein secretion (GO:0050709)|negative regulation of sodium:proton antiporter activity (GO:0032416)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of mitosis (GO:0045840)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prepulse inhibition (GO:0060134)|regulation of blood volume by renin-angiotensin (GO:0002016)|regulation of cAMP metabolic process (GO:0030814)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|regulation of dopamine secretion (GO:0014059)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of lipid metabolic process (GO:0019216)|regulation of locomotion involved in locomotory behavior (GO:0090325)|regulation of multicellular organism growth (GO:0040014)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to histamine (GO:0034776)|response to morphine (GO:0043278)|social behavior (GO:0035176)|synaptic transmission, dopaminergic (GO:0001963)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|cell projection (GO:0042995)|endocytic vesicle (GO:0030139)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity, coupled via Gi/Go (GO:0001591)|drug binding (GO:0008144)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(23)|ovary(1)|pancreas(1)|skin(1)	36					Amisulpride(DB06288)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Clozapine(DB00363)|Domperidone(DB01184)|Dopamine(DB00988)|Haloperidol(DB00502)|Iloperidone(DB04946)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Pimozide(DB01100)|Pramipexole(DB00413)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sulpiride(DB00391)|Yohimbine(DB01392)|Ziprasidone(DB00246)	GTCTGCAGGGCCCGCTCCTTC	0.612																																					p.A59S		Atlas-SNP	.											.	DRD3	76	.	0			c.G175T						.						101	89	93					3																	113890665		2203	4300	6503	SO:0001583	missense	1814	exon2			GCAGGGCCCGCTC		CCDS2978.1, CCDS33829.1	3q13.3	2012-08-08			ENSG00000151577	ENSG00000151577		"GPCR / Class A : Dopamine receptors"	3024	protein-coding gene	gene with protein product		126451				1916765	Standard	XM_005247171		Approved		uc003ebc.1	P35462	OTTHUMG00000159334	ENST00000460779.1:c.175G>T	chr3.hg19:g.113890665C>A	ENSP00000419402:p.Ala59Ser	128.0	0.0		144.0	61.0	NM_033663	A1A4V5|Q4VBM8	Missense_Mutation	SNP	ENST00000460779.1	hg19	CCDS2978.1	.	.	.	.	.	.	.	.	.	.	C	12.88	2.071838	0.36566	.	.	ENSG00000151577	ENST00000460779;ENST00000467632;ENST00000383673;ENST00000281274;ENST00000295881	T;T;T;T	0.71341	-0.56;-0.56;-0.56;-0.56	5.0	3.07	0.35406	GPCR, rhodopsin-like superfamily (1);	0.266401	0.38778	N	0.001576	T	0.49047	0.1534	N	0.12961	0.28	0.38964	D	0.958611	B;B;B;B	0.14438	0.01;0.01;0.01;0.0	B;B;B;B	0.28385	0.089;0.089;0.089;0.006	T	0.37549	-0.9701	10	0.23891	T	0.37	.	5.0636	0.14570	0.1778:0.6045:0.0:0.2177	.	59;59;59;59	A1A4V4;A8K8E4;P35462;E9PCM4	.;.;DRD3_HUMAN;.	S	59	ENSP00000419402:A59S;ENSP00000420662:A59S;ENSP00000373169:A59S;ENSP00000295881:A59S	ENSP00000281274:A59S	A	-	1	0	DRD3	115373355	0.121000	0.22262	0.940000	0.37924	0.951000	0.60555	0.626000	0.24492	1.351000	0.45789	-0.126000	0.14955	GCC	.	.		0.612	DRD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354699.1	NM_000796.3		A	113890665	C	A	113890665	3	1	357	1	0	0	0	0	1	0	0	0	4760	739	26	3	1051	3	DRD3	3	113890665	Missense_Mutation	SNP	C	TCGA-XR-A8TC-01A-11D-A35Z-10		113890665	84131765	9	50181										
CCKAR	886	hgsc.bcm.edu	37	chr4	26483375	26483376	+	Missense_Mutation	DNP	GG	GG	TT													0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	ccctcgcccctgggggaccaGgattggggcagcaggggaag							TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr4:26483375_26483376GG>TT	ENST00000295589.3	-	5	1365_1366	c.1171_1172CC>AA	c.(1171-1173)CCt>AAt	p.P391N		NM_000730.2	NP_000721.1	P32238	CCKAR_HUMAN	cholecystokinin A receptor	391					axonogenesis (GO:0007409)|cholecystokinin signaling pathway (GO:0038188)|digestion (GO:0007586)|feeding behavior (GO:0007631)|forebrain development (GO:0030900)|neuron migration (GO:0001764)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|response to nutrient (GO:0007584)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cholecystokinin receptor activity (GO:0004951)			NS(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|liver(1)|lung(14)|pancreas(1)|skin(1)	29		Breast(46;0.0503)			Ceruletide(DB00403)	TGGGGGACCAGGATTGGGGCAG	0.624																																					p.P391H|p.P391T		Atlas-SNP	.											.	CCKAR	74	.	0			c.C1172A|c.C1171A						.																																			SO:0001583	missense	886	exon5			GGACCAGGATTGG|GACCAGGATTGGG	L19315	CCDS3438.1	4p15.2	2013-09-20			ENSG00000163394	ENSG00000163394		"GPCR / Class A : Cholecystokinin receptors"	1570	protein-coding gene	gene with protein product		118444					Standard	NM_000730		Approved		uc003gse.1	P32238	OTTHUMG00000128567	ENST00000295589.3:c.1171_1172delinsTT	chr4.hg19:g.26483375_26483376delinsTT	ENSP00000295589:p.Pro391Asn	136.0	0.0		168.0|169.0	57.0|59.0	NM_000730	B2R9Z5	Missense_Mutation	SNP	ENST00000295589.3	hg19	CCDS3438.1																																																																																			.	.		0.624	CCKAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250418.2			TT	26483376	GG	TT	26483375	3	4	357	1	0	0	0	0	1	0	0	0	2882	1000	35	3	118	3	CCKAR	4	26483375	Missense_Mutation	DNP	GG	TCGA-XR-A8TC-01A-11D-A35Z-10		26483375	164670901	10	50182										
IQGAP2	10788	hgsc.bcm.edu	37	chr5	75991366	75991366	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	agcatagccaatctatgattGaagatgcacagctgcctctt	8	10	2	3			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr5:75991366G>C	ENST00000274364.6	+	32	4378	c.4081G>C	c.(4081-4083)Gaa>Caa	p.E1361Q	IQGAP2_ENST00000396234.3_Missense_Mutation_p.E857Q|IQGAP2_ENST00000379730.3_Missense_Mutation_p.E863Q|IQGAP2_ENST00000502745.1_Missense_Mutation_p.E857Q|CTD-2384B11.2_ENST00000507514.1_RNA	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	1361					negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		ATCTATGATTGAAGATGCACA	0.458																																					p.E1361Q		Atlas-SNP	.											.	IQGAP2	186	.	0			c.G4081C						.						97	87	90					5																	75991366		2203	4300	6503	SO:0001583	missense	10788	exon32			ATGATTGAAGATG	U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.4081G>C	chr5.hg19:g.75991366G>C	ENSP00000274364:p.Glu1361Gln	336.0	0.0		374.0	156.0	NM_006633	A8K4V1|B7Z8A4|J3KR91	Missense_Mutation	SNP	ENST00000274364.6	hg19	CCDS34188.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.012935	0.75161	.	.	ENSG00000145703	ENST00000274364;ENST00000379730;ENST00000505766;ENST00000396234;ENST00000502745	T;T;T;T;T	0.02916	4.24;4.11;4.24;4.11;4.11	5.48	4.61	0.57282	.	0.154446	0.56097	D	0.000028	T	0.06142	0.0159	M	0.69823	2.125	0.80722	D	1	B;B;B	0.33000	0.393;0.393;0.273	B;B;B	0.35813	0.211;0.211;0.105	T	0.21724	-1.0237	10	0.38643	T	0.18	-15.9353	13.8002	0.63194	0.0734:0.0:0.9266:0.0	.	863;857;1361	F5H7S7;Q13576-2;Q13576	.;.;IQGA2_HUMAN	Q	1361;863;1311;857;857	ENSP00000274364:E1361Q;ENSP00000442313:E863Q;ENSP00000421097:E1311Q;ENSP00000379535:E857Q;ENSP00000426027:E857Q	ENSP00000274364:E1361Q	E	+	1	0	IQGAP2	76027122	1.000000	0.71417	0.501000	0.27601	0.751000	0.42716	7.920000	0.87521	1.306000	0.44926	0.655000	0.94253	GAA	.	.		0.458	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633		C	75991366	G	C	75991366	3	2	357	1	0	0	0	0	1	0	0	0	7824	1291	45	4	4207	4	IQGAP2	5	75991366	Missense_Mutation	SNP	G	TCGA-XR-A8TC-01A-11D-A35Z-10		75991366	104923894	11	50183										
APC	324	hgsc.bcm.edu	37	chr5	112162900	112162901	+	Missense_Mutation	DNP	GG	GG	AT													0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	ttacactaagacgatatgctGgaatggctttgacaaacttg							TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr5:112162900_112162901GG>AT	ENST00000457016.1	+	12	1884_1885	c.1504_1505GG>AT	c.(1504-1506)GGa>ATa	p.G502I	APC_ENST00000257430.4_Missense_Mutation_p.G502I|APC_ENST00000508376.2_Missense_Mutation_p.G502I|CTC-554D6.1_ENST00000520401.1_5'Flank			P25054	APC_HUMAN	adenomatous polyposis coli	502	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		ACGATATGCTGGAATGGCTTTG	0.366		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											p.G502R|p.G502V	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-SNP	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	.	APC	4158	.	1	Unknown(1)	skin(1)	c.G1504A|c.G1505T						.																																			SO:0001583	missense	324	exon13	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	TATGCTGGAATGG|ATGCTGGAATGGC	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	Exception_encountered	chr5.hg19:g.112162900_112162901delinsAT	ENSP00000413133:p.Gly502Ile	138.0	0.0		123.0	51.0	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	hg19	CCDS4107.1																																																																																			.	.		0.366	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		AT	112162901	GG	AT	112162900	3	1	357	1	0	0	0	0	1	0	0	0	763	1349	47	3	1546	3	APC	5	112162900	Missense_Mutation	DNP	GG	TCGA-XR-A8TC-01A-11D-A35Z-10	36171534	112162900	68752360	12	50184										
HLA-C	3107	hgsc.bcm.edu	37	chr6	31239099	31239099	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	gtcgggccccaggtcgcagcCagacatcctctggagggtgt	15	13	1	1			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr6:31239099C>G	ENST00000376228.5	-	3	384	c.370G>C	c.(370-372)Ggc>Cgc	p.G124R	HLA-C_ENST00000383329.3_Missense_Mutation_p.G124R	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	124	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						AGGTCGCAGCCAGACATCCTC	0.721																																					p.G124R		Atlas-SNP	.											.	HLA-C	92	.	0			c.G370C						.						22	21	21					6																	31239099		2157	4193	6350	SO:0001583	missense	3107	exon3			CGCAGCCAGACAT	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4933	protein-coding gene	gene with protein product		142840	"psoriasis susceptibility 1"	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.370G>C	chr6.hg19:g.31239099C>G	ENSP00000365402:p.Gly124Arg	83.0	0.0		214.0	21.0	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	hg19	CCDS34393.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	13.38|13.38	2.219532|2.219532	0.39201|0.39201	.|.	.|.	ENSG00000204525|ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307|ENST00000415537	T;T|.	0.02916|.	4.11;4.11|.	2.81|2.81	1.9|1.9	0.25705|0.25705	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);|.	0.000000|.	0.37012|.	U|.	0.002289|.	T|T	0.75989|0.75989	0.3925|0.3925	H|H	0.99058|0.99058	4.415|4.415	0.30556|0.30556	N|N	0.764949|0.764949	D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D|.	0.97110|.	1.0;1.0;1.0;1.0;1.0|.	T|T	0.72007|0.72007	-0.4420|-0.4420	10|6	0.87932|0.87932	D|D	0|0	.|.	9.0174|9.0174	0.36179|0.36179	0.2222:0.7778:0.0:0.0|0.2222:0.7778:0.0:0.0	.|.	124;99;124;124;124|.	A2AEA4;Q92671;A6H578;A2AEA2;P10321|.	.;.;.;.;1C07_HUMAN|.	R|S	124;124;124;161|123	ENSP00000365402:G124R;ENSP00000372819:G124R|.	ENSP00000365402:G124R|ENSP00000365412:W118S	G|W	-|-	1|2	0|0	HLA-C|HLA-C	31347078|31347078	0.987000|0.987000	0.35691|0.35691	0.126000|0.126000	0.21872|0.21872	0.004000|0.004000	0.04260|0.04260	3.034000|3.034000	0.49751|0.49751	0.722000|0.722000	0.32252|0.32252	0.305000|0.305000	0.20034|0.20034	GGC|TGG	.	.		0.721	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117		G	31239099	C	G	31239099	3	3	357	1	0	0	0	0	1	0	0	0	7206	594	21	4	754	4	HLA-C	6	31239099	Missense_Mutation	SNP	C	TCGA-XR-A8TC-01A-11D-A35Z-10		31239099	139875968	13	50185										
BTNL2	56244	hgsc.bcm.edu	37	chr6	32369565	32369565	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	cagcacctcgtacttacccaGctcagtctggagtttctctg	8	14	3	0			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr6:32369565G>T	ENST00000374993.1	-	4	726	c.727C>A	c.(727-729)Ctg>Atg	p.L243M	BTNL2_ENST00000544175.1_De_novo_Start_InFrame|BTNL2_ENST00000454136.3_Missense_Mutation_p.L243M|BTNL2_ENST00000540315.1_Intron|BTNL2_ENST00000374995.3_Intron|BTNL2_ENST00000414363.1_Missense_Mutation_p.L33M|BTNL2_ENST00000429232.2_Intron	NM_019602.1	NP_062548.1	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2 (MHC class II associated)	243	Ig-like V-type 3.					integral component of membrane (GO:0016021)				central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)|urinary_tract(1)	19						TACTTACCCAGCTCAGTCTGG	0.468																																					p.L243M		Atlas-SNP	.											.	BTNL2	50	.	0			c.C727A						.						49	51	50					6																	32369565		2203	4300	6503	SO:0001583	missense	56244	exon4			TACCCAGCTCAGT	AF186588		6p21.3	2014-01-14			ENSG00000204290	ENSG00000204290		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Butyrophilins"	1142	protein-coding gene	gene with protein product		606000				10803852, 15735647	Standard	XM_006726138		Approved	HSBLMHC1, BTL-II, BTN7	uc003obg.1	Q9UIR0	OTTHUMG00000031102	ENST00000374993.1:c.727C>A	chr6.hg19:g.32369565G>T	ENSP00000364132:p.Leu243Met	62.0	0.0		153.0	13.0	NM_019602	A0PJV5|B0UYW9|B0V0N6|O98261|Q08E96|Q58R22|Q58R23|Q5JYF9|Q5MP42|Q5MP43|Q5RIF8|Q5SP08|Q5SP09|Q5SRW3|Q5SRW4|Q5SU36|Q95HK0	Missense_Mutation	SNP	ENST00000374993.1	hg19		.	.	.	.	.	.	.	.	.	.	G	8.623	0.891864	0.17613	.	.	ENSG00000204290	ENST00000468270;ENST00000414363;ENST00000374993	T;T	0.04234	4.26;3.67	5.16	-0.234	0.13074	Immunoglobulin-like (1);	0.409388	0.18106	N	0.151532	T	0.01835	0.0058	L	0.53780	1.695	0.80722	D	1	B;B	0.27380	0.112;0.177	B;B	0.23716	0.048;0.03	T	0.44832	-0.9302	10	0.33141	T	0.24	.	9.2919	0.37791	0.0747:0.0:0.2703:0.6549	.	33;243	Q9UIR0-4;Q9UIR0	.;BTNL2_HUMAN	M	243;33;243	ENSP00000390512:L33M;ENSP00000364132:L243M	ENSP00000364132:L243M	L	-	1	2	BTNL2	32477543	0.998000	0.40836	0.884000	0.34674	0.428000	0.31595	0.455000	0.21843	-0.258000	0.09446	-0.211000	0.12701	CTG	.	.		0.468	BTNL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_019602		T	32369565	G	T	32369565	3	4	357	1	0	0	0	0	1	0	0	0	1567	962	34	3	652	3	BTNL2	6	32369565	Missense_Mutation	SNP	G	TCGA-XR-A8TC-01A-11D-A35Z-10	1130466	32369565	138745502	14	50186										
CDKN1A	1026	hgsc.bcm.edu	37	chr6	36652015	36652015	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	gggctgcatccaggaggcccGtgagcgatggaacttcgact	15	11	0	1			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr6:36652015G>T	ENST00000405375.1	+	2	372	c.137G>T	c.(136-138)cGt>cTt	p.R46L	CDKN1A_ENST00000373711.2_Missense_Mutation_p.R46L|CDKN1A_ENST00000478800.1_3'UTR|CDKN1A_ENST00000244741.5_Missense_Mutation_p.R46L|CDKN1A_ENST00000448526.2_Missense_Mutation_p.R80L	NM_001220778.1	NP_001207707.1	P38936	CDN1A_HUMAN	cyclin-dependent kinase inhibitor 1A (p21, Cip1)	46					cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to extracellular stimulus (GO:0031668)|cellular response to ionizing radiation (GO:0071479)|cellular senescence (GO:0090398)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle (GO:0000278)|mitotic cell cycle arrest (GO:0071850)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of gene expression (GO:0010629)|negative regulation of phosphorylation (GO:0042326)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ regeneration (GO:0031100)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of DNA biosynthetic process (GO:2000278)|regulation of protein import into nucleus, translocation (GO:0033158)|response to arsenic-containing substance (GO:0046685)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to hyperoxia (GO:0055093)|response to organonitrogen compound (GO:0010243)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|stress-induced premature senescence (GO:0090400)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCNA-p21 complex (GO:0070557)	cyclin-dependent protein kinase activating kinase activity (GO:0019912)|cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|urinary_tract(5)	15						CAGGAGGCCCGTGAGCGATGG	0.662																																					p.R46L		Atlas-SNP	.											.	CDKN1A	27	.	0			c.G137T						.						51	46	48					6																	36652015		2203	4300	6503	SO:0001583	missense	1026	exon2			AGGCCCGTGAGCG	U03106	CCDS4824.1	6p21.1	2009-01-21			ENSG00000124762	ENSG00000124762			1784	protein-coding gene	gene with protein product		116899		CDKN1			Standard	NM_000389		Approved	P21, CIP1, WAF1, SDI1, CAP20, p21CIP1, p21Cip1/Waf1	uc021yzb.1	P38936	OTTHUMG00000014603	ENST00000405375.1:c.137G>T	chr6.hg19:g.36652015G>T	ENSP00000384849:p.Arg46Leu	47.0	0.0		75.0	41.0	NM_001220778	Q14010|Q6FI05|Q9BUT4	Missense_Mutation	SNP	ENST00000405375.1	hg19	CCDS4824.1	.	.	.	.	.	.	.	.	.	.	G	11.96	1.795480	0.31777	.	.	ENSG00000124762	ENST00000448526;ENST00000244741;ENST00000405375;ENST00000373711	D;D;D;D	0.83673	-1.75;-1.75;-1.75;-1.75	5.06	4.11	0.48088	.	0.506057	0.17321	N	0.178490	T	0.63954	0.2555	L	0.46157	1.445	0.28243	N	0.925595	P;B;P	0.39282	0.666;0.165;0.524	B;B;B	0.36922	0.236;0.118;0.153	T	0.58769	-0.7578	10	0.44086	T	0.13	-5.9852	7.5934	0.28033	0.1161:0.0:0.8839:0.0	.	80;46;46	B4DQP9;P38936;Q96LE1	.;CDN1A_HUMAN;.	L	80;46;46;46	ENSP00000409259:R80L;ENSP00000244741:R46L;ENSP00000384849:R46L;ENSP00000362815:R46L	ENSP00000244741:R46L	R	+	2	0	CDKN1A	36759993	0.581000	0.26741	0.906000	0.35671	0.400000	0.30750	2.014000	0.40951	2.642000	0.89623	0.561000	0.74099	CGT	.	.		0.662	CDKN1A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040354.1	NM_078467		T	36652015	G	T	36652015	3	4	357	1	0	0	0	0	1	0	0	0	3160	1145	40	1	139	1	CDKN1A	6	36652015	Missense_Mutation	SNP	G	TCGA-XR-A8TC-01A-11D-A35Z-10	4282450	36652015	134463052	15	50187										
RBM28	55131	hgsc.bcm.edu	37	chr7	127964620	127964620	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	ctccctactcacagccttctCgggccagatagagattccgg	9	15	2	2			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr7:127964620C>A	ENST00000223073.2	-	12	1445	c.1331G>T	c.(1330-1332)cGa>cTa	p.R444L	RBM28_ENST00000415472.2_Missense_Mutation_p.R303L	NM_018077.2	NP_060547.2	Q9NW13	RBM28_HUMAN	RNA binding motif protein 28	444					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleolus (GO:0005730)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|kidney(7)|large_intestine(3)|lung(8)|ovary(2)	21						ACAGCCTTCTCGGGCCAGATA	0.517																																					p.R444L		Atlas-SNP	.											.	RBM28	71	.	0			c.G1331T						.						137	132	133					7																	127964620		2203	4300	6503	SO:0001583	missense	55131	exon12			CCTTCTCGGGCCA	AK001239	CCDS5801.1, CCDS55159.1	7q32.2	2013-02-12			ENSG00000106344	ENSG00000106344		"RNA binding motif (RRM) containing"	21863	protein-coding gene	gene with protein product		612074					Standard	NM_018077		Approved	FLJ10377	uc003vmp.2	Q9NW13	OTTHUMG00000157711	ENST00000223073.2:c.1331G>T	chr7.hg19:g.127964620C>A	ENSP00000223073:p.Arg444Leu	113.0	0.0		118.0	40.0	NM_018077	A4D100|B4DU52|E9PDD9|Q53H65|Q96CV3	Missense_Mutation	SNP	ENST00000223073.2	hg19	CCDS5801.1	.	.	.	.	.	.	.	.	.	.	C	32	5.105540	0.94245	.	.	ENSG00000106344	ENST00000223073;ENST00000415472	T;T	0.22336	2.9;1.96	5.63	5.63	0.86233	.	0.118400	0.53938	D	0.000045	T	0.48003	0.1476	M	0.77486	2.375	0.80722	D	1	P;D;P	0.69078	0.457;0.997;0.457	P;D;P	0.76071	0.485;0.987;0.485	T	0.39231	-0.9624	10	0.51188	T	0.08	-9.3348	15.5476	0.76118	0.0:1.0:0.0:0.0	.	303;444;303	E9PDD9;Q9NW13;B4DU52	.;RBM28_HUMAN;.	L	444;303	ENSP00000223073:R444L;ENSP00000390517:R303L	ENSP00000223073:R444L	R	-	2	0	RBM28	127751856	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.107000	0.71517	2.826000	0.97356	0.655000	0.94253	CGA	.	.		0.517	RBM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349442.2	NM_018077		A	127964620	C	A	127964620	3	1	357	1	0	0	0	0	1	0	0	0	13143	884	31	1	980	1	RBM28	7	127964620	Missense_Mutation	SNP	C	TCGA-XR-A8TC-01A-11D-A35Z-10		127964620	31174043	16	50188										
WHSC1L1	54904	hgsc.bcm.edu	37	chr8	38146244	38146244	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	ctctgacaggtcagcaacctGgatctgcacctttcctatta	7	13	3	1			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr8:38146244G>A	ENST00000317025.8	-	19	3779	c.3262C>T	c.(3262-3264)Cag>Tag	p.Q1088*	WHSC1L1_ENST00000527502.1_Nonsense_Mutation_p.Q1088*|WHSC1L1_ENST00000433384.2_Nonsense_Mutation_p.Q1039*	NM_023034.1	NP_075447.1	Q9BZ95	NSD3_HUMAN	Wolf-Hirschhorn syndrome candidate 1-like 1	1088					histone lysine methylation (GO:0034968)|histone methylation (GO:0016571)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)			TCAGCAACCTGGATCTGCACC	0.478			T	NUP98	AML																																p.Q1088X		Atlas-SNP	.		Dom	yes		8	8p12	54904	Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3)		L	.	WHSC1L1	137	.	0			c.C3262T						.						90	88	89					8																	38146244		1980	4192	6172	SO:0001587	stop_gained	54904	exon19			CAACCTGGATCTG	AF332469	CCDS6105.1, CCDS43729.1	8p11.2	2013-05-20			ENSG00000147548	ENSG00000147548			12767	protein-coding gene	gene with protein product		607083				10802047, 23269674	Standard	NM_023034		Approved	FLJ20353, NSD3	uc003xli.3	Q9BZ95		ENST00000317025.8:c.3262C>T	chr8.hg19:g.38146244G>A	ENSP00000313983:p.Gln1088*	97.0	0.0		159.0	51.0	NM_023034	B7ZL11|D3DSX1|Q1RMD3|Q3B796|Q6ZSA5|Q9BYU8|Q9BYU9|Q9H2M8|Q9H9W9|Q9NXA6	Nonsense_Mutation	SNP	ENST00000317025.8	hg19	CCDS43729.1	.	.	.	.	.	.	.	.	.	.	G	45	11.868959	0.99612	.	.	ENSG00000147548	ENST00000433384;ENST00000317025;ENST00000446459;ENST00000527502	.	.	.	6.17	6.17	0.99709	.	0.295611	0.23977	U	0.042714	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	.	.	.	X	1039;1088;1025;1088	.	ENSP00000313983:Q1088X	Q	-	1	0	WHSC1L1	38265401	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.062000	0.89475	2.941000	0.99782	0.655000	0.94253	CAG	.	.		0.478	WHSC1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381924.3	NM_023034		A	38146244	G	A	38146244	4	1	357	1	0	0	0	0	0	1	0	0	17378	1357	47	3	1075	3	WHSC1L1	8	38146244	Nonsense_Mutation	SNP	G	TCGA-XR-A8TC-01A-11D-A35Z-10		38146244	108217778	17	50189										
STK3	6788	hgsc.bcm.edu	37	chr8	99608325	99608325	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	caaacactttttaacaaaatCggtgaaatcatcggaccaaa	5	9	1	1			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr8:99608325C>T	ENST00000419617.2	-	7	897	c.757G>A	c.(757-759)Gat>Aat	p.D253N	STK3_ENST00000521768.1_5'UTR|STK3_ENST00000523601.1_Missense_Mutation_p.D281N	NM_006281.3	NP_006272.2	Q13188	STK3_HUMAN	serine/threonine kinase 3	253	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell differentiation involved in embryonic placenta development (GO:0060706)|central nervous system development (GO:0007417)|endocardium development (GO:0003157)|hepatocyte apoptotic process (GO:0097284)|hippo signaling (GO:0035329)|intracellular signal transduction (GO:0035556)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of organ growth (GO:0046621)|neural tube formation (GO:0001841)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|primitive hemopoiesis (GO:0060215)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein dimerization activity (GO:0046983)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	17	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)		TTAACAAAATCGGTGAAATCA	0.398																																					p.D281N		Atlas-SNP	.											.	STK3	47	.	0			c.G841A						.						79	76	77					8																	99608325		1846	4100	5946	SO:0001583	missense	6788	exon9			CAAAATCGGTGAA	BC010640	CCDS47900.1, CCDS59108.1, CCDS75774.1	8q22.2	2011-05-24	2010-06-25		ENSG00000104375	ENSG00000104375			11406	protein-coding gene	gene with protein product		605030	"serine/threonine kinase 3 (Ste20, yeast homolog)"			8816758	Standard	NM_006281		Approved	MST2, KRS1	uc003yip.4	Q13188	OTTHUMG00000164651	ENST00000419617.2:c.757G>A	chr8.hg19:g.99608325C>T	ENSP00000390500:p.Asp253Asn	199.0	0.0		315.0	87.0	NM_001256312	A8K722|B3KYA7|Q15445|Q15801|Q96FM6	Missense_Mutation	SNP	ENST00000419617.2	hg19	CCDS47900.1	.	.	.	.	.	.	.	.	.	.	C	18.77	3.695478	0.68386	.	.	ENSG00000104375	ENST00000419617;ENST00000523601;ENST00000518165	T;T;T	0.16597	2.33;2.33;2.92	5.28	5.28	0.74379	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.26774	0.0655	L	0.50919	1.6	0.80722	D	1	P;P;P	0.52061	0.95;0.709;0.836	P;B;B	0.48227	0.571;0.308;0.378	T	0.00778	-1.1570	10	0.52906	T	0.07	.	19.2729	0.94018	0.0:1.0:0.0:0.0	.	142;253;281	E5RFQ9;Q13188;B3KYA7	.;STK3_HUMAN;.	N	253;281;142	ENSP00000390500:D253N;ENSP00000429744:D281N;ENSP00000428014:D142N	ENSP00000390500:D253N	D	-	1	0	STK3	99677501	1.000000	0.71417	0.991000	0.47740	0.983000	0.72400	7.776000	0.85560	2.638000	0.89438	0.467000	0.42956	GAT	.	.		0.398	STK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379635.1	NM_006281		T	99608325	C	T	99608325	3	4	357	1	0	0	0	0	1	0	0	0	15310	884	31	1	738	1	STK3	8	99608325	Missense_Mutation	SNP	C	TCGA-XR-A8TC-01A-11D-A35Z-10	61462081	99608325	46755697	18	50190										
DOCK8	81704	hgsc.bcm.edu	37	chr9	396879	396879	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	tttcatggatgacataactaCtattgttaatgtggtcacct	7	7	2	1			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr9:396879C>T	ENST00000453981.1	+	25	3177	c.3065C>T	c.(3064-3066)aCt>aTt	p.T1022I	DOCK8_ENST00000382331.1_Missense_Mutation_p.T324I|DOCK8_ENST00000382329.1_Missense_Mutation_p.T489I|DOCK8_ENST00000469391.1_Missense_Mutation_p.T922I|DOCK8_ENST00000432829.2_Missense_Mutation_p.T954I			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	1022					blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		GACATAACTACTATTGTTAAT	0.413																																					p.T1022I		Atlas-SNP	.											.	DOCK8	401	.	0			c.C3065T						.						167	160	162					9																	396879		2203	4300	6503	SO:0001583	missense	81704	exon25			TAACTACTATTGT	AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.3065C>T	chr9.hg19:g.396879C>T	ENSP00000408464:p.Thr1022Ile	198.0	0.0		185.0	66.0	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Missense_Mutation	SNP	ENST00000453981.1	hg19	CCDS6440.2	.	.	.	.	.	.	.	.	.	.	C	28.7	4.941247	0.92526	.	.	ENSG00000107099	ENST00000453981;ENST00000287364;ENST00000432829;ENST00000469391;ENST00000382331;ENST00000382329	T;T;T;T;T	0.23147	1.92;1.92;1.92;1.92;1.92	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.57080	0.2029	M	0.82517	2.595	0.80722	D	1	D;P;P;D	0.89917	1.0;0.935;0.935;0.967	D;P;P;P	0.91635	0.999;0.512;0.615;0.661	T	0.56032	-0.8046	10	0.41790	T	0.15	.	19.8411	0.96685	0.0:1.0:0.0:0.0	.	324;922;489;1022	A2A370;E9PH09;A2A369;Q8NF50	.;.;.;DOCK8_HUMAN	I	1022;990;954;922;324;489	ENSP00000408464:T1022I;ENSP00000394888:T954I;ENSP00000419438:T922I;ENSP00000371768:T324I;ENSP00000371766:T489I	ENSP00000287364:T990I	T	+	2	0	DOCK8	386879	1.000000	0.71417	0.980000	0.43619	0.782000	0.44232	7.663000	0.83820	2.683000	0.91414	0.655000	0.94253	ACT	.	.		0.413	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307		T	396879	C	T	396879	3	4	357	1	0	0	0	0	1	0	0	0	4695	565	20	3	3163	3	DOCK8	9	396879	Missense_Mutation	SNP	C	TCGA-XR-A8TC-01A-11D-A35Z-10		396879	140816552	19	50191										
KCNV2	169522	hgsc.bcm.edu	37	chr9	2718363	2718363	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	tgcttcgaggagcggcgcgaCgagctgagcgaacggctcaa	16	11	1	1			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr9:2718363C>T	ENST00000382082.3	+	1	862	c.624C>T	c.(622-624)gaC>gaT	p.D208D		NM_133497.3	NP_598004.1	Q8TDN2	KCNV2_HUMAN	potassium channel, subfamily V, member 2	208					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(2)	35				GBM - Glioblastoma multiforme(50;0.0257)		AGCGGCGCGACGAGCTGAGCG	0.692																																					p.D208D		Atlas-SNP	.											.	KCNV2	72	.	0			c.C624T						.						9	8	8					9																	2718363		2119	4191	6310	SO:0001819	synonymous_variant	169522	exon1			GCGCGACGAGCTG	AF348983	CCDS6447.1	9p24.2	2011-07-05			ENSG00000168263	ENSG00000168263		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	19698	protein-coding gene	gene with protein product		607604				12060745, 16382104	Standard	NM_133497		Approved	Kv8.2	uc003zho.2	Q8TDN2	OTTHUMG00000019449	ENST00000382082.3:c.624C>T	chr9.hg19:g.2718363C>T		58.0	0.0		86.0	37.0	NM_133497	Q5T6X0	Silent	SNP	ENST00000382082.3	hg19	CCDS6447.1																																																																																			.	.		0.692	KCNV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051528.1	NM_133497		T	2718363	C	T	2718363	2	4	357	1	0	0	0	0	0	0	0	1	8104	535	19	1		1	KCNV2	9	2718363	Silent	SNP	C	TCGA-XR-A8TC-01A-11D-A35Z-10	2321484	2718363	138495068	20	50192										
NANS	54187	hgsc.bcm.edu	37	chr9	100823187	100823187	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	agacgtacggggagcacaaaCgacatctggagttcagccat	12	10	2	1			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr9:100823187C>T	ENST00000210444.5	+	2	326	c.256C>T	c.(256-258)Cga>Tga	p.R86*		NM_018946.3	NP_061819.2	Q9NR45	SIAS_HUMAN	N-acetylneuraminic acid synthase	86					lipopolysaccharide biosynthetic process (GO:0009103)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	N-acetylneuraminate synthase activity (GO:0050462)|N-acylneuraminate cytidylyltransferase activity (GO:0008781)|N-acylneuraminate-9-phosphate synthase activity (GO:0047444)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	11		Acute lymphoblastic leukemia(62;0.0559)				GGAGCACAAACGACATCTGGA	0.537																																					p.R86X		Atlas-SNP	.											.	NANS	24	.	0			c.C256T						.						223	206	212					9																	100823187		2203	4300	6503	SO:0001587	stop_gained	54187	exon2			CACAAACGACATC	AF161387	CCDS6733.1	9p24.1-p23	2008-07-31	2008-07-31		ENSG00000095380	ENSG00000095380			19237	protein-coding gene	gene with protein product	"sialic acid synthase"	605202				10749855	Standard	NM_018946		Approved	SAS	uc004ayc.3	Q9NR45	OTTHUMG00000020341	ENST00000210444.5:c.256C>T	chr9.hg19:g.100823187C>T	ENSP00000210444:p.Arg86*	140.0	0.0		162.0	62.0	NM_018946	B2RE98|Q8WUV9|Q9BWS6|Q9NVD4	Nonsense_Mutation	SNP	ENST00000210444.5	hg19	CCDS6733.1	.	.	.	.	.	.	.	.	.	.	C	34	5.346147	0.95807	.	.	ENSG00000095380	ENST00000210444	.	.	.	5.73	4.83	0.62350	.	0.094643	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.7221	14.1947	0.65662	0.1509:0.8491:0.0:0.0	.	.	.	.	X	86	.	ENSP00000210444:R86X	R	+	1	2	NANS	99863008	1.000000	0.71417	0.930000	0.37139	0.806000	0.45545	5.470000	0.66756	1.556000	0.49512	-0.181000	0.13052	CGA	.	.		0.537	NANS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053359.1	NM_018946		T	100823187	C	T	100823187	4	4	357	1	0	0	0	0	0	1	0	0	10164	528	19	1	262	1	NANS	9	100823187	Nonsense_Mutation	SNP	C	TCGA-XR-A8TC-01A-11D-A35Z-10	98104824	100823187	40390244	21	50193										
GARNL3	84253	hgsc.bcm.edu	37	chr9	130104554	130104554	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	catttgcccagaaacgtcggCgtaccctggatatgttgatt	10	10	0	2			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr9:130104554C>T	ENST00000373387.4	+	14	1544	c.1192C>T	c.(1192-1194)Cgt>Tgt	p.R398C	GARNL3_ENST00000314904.5_Missense_Mutation_p.R398C|GARNL3_ENST00000435213.2_Missense_Mutation_p.R376C	NM_032293.4	NP_115669.3	Q5VVW2	GARL3_HUMAN	GTPase activating Rap/RanGAP domain-like 3	398	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)|small GTPase regulator activity (GO:0005083)			NS(1)|central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(24)|ovary(1)|skin(1)|urinary_tract(2)	41						GAAACGTCGGCGTACCCTGGA	0.388																																					p.R398C		Atlas-SNP	.											.	GARNL3	83	.	0			c.C1192T						.						160	150	154					9																	130104554		2203	4300	6503	SO:0001583	missense	84253	exon14			CGTCGGCGTACCC	BC034983	CCDS6869.2, CCDS69663.1	9q34.13	2009-09-14	2004-08-09		ENSG00000136895	ENSG00000136895			25425	protein-coding gene	gene with protein product			"GTPase activating RANGAP domain-like 3"			11230166	Standard	NM_032293		Approved	DKFZp761J1523, bA356B19.1	uc011mae.2	Q5VVW2	OTTHUMG00000020700	ENST00000373387.4:c.1192C>T	chr9.hg19:g.130104554C>T	ENSP00000362485:p.Arg398Cys	107.0	0.0		108.0	40.0	NM_032293	B4DEP7|B7Z3Q6|Q8IYU1|Q8N951|Q8ND89|Q9BQH6	Missense_Mutation	SNP	ENST00000373387.4	hg19	CCDS6869.2	.	.	.	.	.	.	.	.	.	.	C	24.8	4.572632	0.86542	.	.	ENSG00000136895	ENST00000435213;ENST00000314904;ENST00000373387	D;D;D	0.95588	-3.75;-3.75;-3.75	5.38	4.45	0.53987	Rap/ran-GAP (2);	0.000000	0.85682	D	0.000000	D	0.98150	0.9389	M	0.93594	3.435	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.98805	1.0741	9	.	.	.	.	14.2203	0.65823	0.1496:0.8504:0.0:0.0	.	398;376;339	Q5VVW2;B7Z3Q6;Q5VVW4	GARL3_HUMAN;.;.	C	376;398;398	ENSP00000396205:R376C;ENSP00000313970:R398C;ENSP00000362485:R398C	.	R	+	1	0	GARNL3	129144375	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.661000	0.68025	2.491000	0.84063	0.650000	0.86243	CGT	.	.		0.388	GARNL3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054151.3	NM_032293		T	130104554	C	T	130104554	3	4	357	1	0	0	0	0	1	0	0	0	6249	768	27	1	1246	1	GARNL3	9	130104554	Missense_Mutation	SNP	C	TCGA-XR-A8TC-01A-11D-A35Z-10	29281367	130104554	11108877	22	50194										
CXCL12	6387	hgsc.bcm.edu	37	chr10	44880397	44880397	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	cgccgagcgcacttaccgtcGctgaggcagagcgcggtcag	15	14	1	2			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr10:44880397G>C	ENST00000374429.2	-	1	143	c.57C>G	c.(55-57)agC>agG	p.S19R	CXCL12_ENST00000496375.1_Intron|CXCL12_ENST00000395794.2_Missense_Mutation_p.S19R|CXCL12_ENST00000395795.4_Missense_Mutation_p.S19R|CXCL12_ENST00000343575.6_Missense_Mutation_p.S19R|CXCL12_ENST00000395793.3_Missense_Mutation_p.S19R|CXCL12_ENST00000374426.2_Missense_Mutation_p.S19R	NM_000609.5|NM_001277990.1	NP_000600.1|NP_001264919.1	P48061	SDF1_HUMAN	chemokine (C-X-C motif) ligand 12	19					adult locomotory behavior (GO:0008344)|ameboidal cell migration (GO:0001667)|blood circulation (GO:0008015)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cellular calcium ion homeostasis (GO:0006874)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|germ cell development (GO:0007281)|germ cell migration (GO:0008354)|immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|motor neuron axon guidance (GO:0008045)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of leukocyte apoptotic process (GO:2000107)|negative regulation of leukocyte tethering or rolling (GO:1903237)|neuron migration (GO:0001764)|organ regeneration (GO:0031100)|patterning of blood vessels (GO:0001569)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cell adhesion (GO:0045785)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of T cell migration (GO:2000406)|regulation of actin polymerization or depolymerization (GO:0008064)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to peptide hormone (GO:0043434)|response to radiation (GO:0009314)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation (GO:0042098)|telencephalon cell migration (GO:0022029)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	chemokine activity (GO:0008009)|chemokine receptor binding (GO:0042379)|CXCR chemokine receptor binding (GO:0045236)|receptor binding (GO:0005102)			endometrium(1)|large_intestine(1)|lung(3)|skin(1)	6					Tinzaparin(DB06822)	ACTTACCGTCGCTGAGGCAGA	0.766																																					p.S19R		Atlas-SNP	.											.	CXCL12	37	.	0			c.C57G						.						6	7	7					10																	44880397		2015	4006	6021	SO:0001583	missense	6387	exon1			ACCGTCGCTGAGG	L36033	CCDS7207.1, CCDS31186.1, CCDS44373.1, CCDS53527.1, CCDS60518.1	10q11.1	2013-02-28	2010-05-11	2002-08-23	ENSG00000107562	ENSG00000107562		"Endogenous ligands"	10672	protein-coding gene	gene with protein product		600835	"stromal cell-derived factor 1"	SDF1A, SDF1B, SDF1		7490086	Standard	NM_001033886		Approved	SCYB12, SDF-1a, SDF-1b, PBSF, TLSF-a, TLSF-b, TPAR1	uc021ppm.1	P48061	OTTHUMG00000018054	ENST00000374429.2:c.57C>G	chr10.hg19:g.44880397G>C	ENSP00000363551:p.Ser19Arg	38.0	0.0		51.0	22.0	NM_199168	B2R4G0|E7EVL0|H7BYN8|Q2L985|Q2L986|Q2L988|Q5IT36|Q6ICW0|Q9H554	Missense_Mutation	SNP	ENST00000374429.2	hg19	CCDS44373.1	.	.	.	.	.	.	.	.	.	.	G	19.60	3.858620	0.71834	.	.	ENSG00000107562	ENST00000395795;ENST00000374429;ENST00000395793;ENST00000374426;ENST00000343575;ENST00000395794	T;T;T;T;T	0.26660	1.72;1.75;1.77;1.73;1.72	5.37	-1.72	0.08107	.	0.143577	0.64402	D	0.000004	T	0.13543	0.0328	.	.	.	0.38404	D	0.945757	B;B	0.09022	0.001;0.002	B;B	0.09377	0.002;0.004	T	0.11567	-1.0582	9	0.66056	D	0.02	.	0.3982	0.00421	0.2598:0.1405:0.3126:0.2871	.	19;19	P48061-3;P48061	.;SDF1_HUMAN	R	19	ENSP00000379141:S19R;ENSP00000363551:S19R;ENSP00000363548:S19R;ENSP00000339913:S19R;ENSP00000379140:S19R	ENSP00000339913:S19R	S	-	3	2	CXCL12	44200403	0.889000	0.30405	0.994000	0.49952	0.422000	0.31414	-0.253000	0.08794	-0.180000	0.10637	-0.181000	0.13052	AGC	.	.		0.766	CXCL12-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047738.2	NM_000609		C	44880397	G	C	44880397	3	2	357	1	0	0	0	0	1	0	0	0	4082	1078	38	4	503	4	CXCL12	10	44880397	Missense_Mutation	SNP	G	TCGA-XR-A8TC-01A-11D-A35Z-10		44880397	90654350	23	50195										
H2AFY2	55506	hgsc.bcm.edu	37	chr10	71835496	71835496	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	tcatctttccagtggggaggCtgatgcgttatctgaagaaa	12	7	3	3			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr10:71835496C>G	ENST00000373255.4	+	2	346	c.82C>G	c.(82-84)Ctg>Gtg	p.L28V		NM_018649.2	NP_061119.1	Q9P0M6	H2AW_HUMAN	H2A histone family, member Y2	28	Histone H2A.				brain development (GO:0007420)|chromatin modification (GO:0016568)|dosage compensation (GO:0007549)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901837)|nucleosome assembly (GO:0006334)	Barr body (GO:0001740)|extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|transcription regulatory region DNA binding (GO:0044212)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(4)|skin(1)	15						AGTGGGGAGGCTGATGCGTTA	0.547																																					p.L28V		Atlas-SNP	.											.	H2AFY2	30	.	0			c.C82G						.						184	147	159					10																	71835496		2203	4300	6503	SO:0001583	missense	55506	exon2			GGGAGGCTGATGC	AF336304	CCDS7296.1	10q22.1	2011-01-27			ENSG00000099284	ENSG00000099284		"Histones / Replication-independent"	14453	protein-coding gene	gene with protein product						11331621, 11262398	Standard	NM_018649		Approved	macroH2A2	uc001jqm.3	Q9P0M6	OTTHUMG00000018396	ENST00000373255.4:c.82C>G	chr10.hg19:g.71835496C>G	ENSP00000362352:p.Leu28Val	186.0	0.0		242.0	147.0	NM_018649	Q5SQT2	Missense_Mutation	SNP	ENST00000373255.4	hg19	CCDS7296.1	.	.	.	.	.	.	.	.	.	.	C	11.69	1.712714	0.30413	.	.	ENSG00000099284	ENST00000373255;ENST00000395046;ENST00000455786	T;T	0.64803	-0.12;-0.12	5.82	2.69	0.31865	Histone-fold (2);Histone core (1);Histone H2A (2);	0.046830	0.85682	D	0.000000	T	0.21962	0.0529	N	0.00525	-1.395	0.40353	D	0.979153	B	0.15473	0.013	B	0.18871	0.023	T	0.03423	-1.1038	10	0.12103	T	0.63	.	4.7294	0.12957	0.3537:0.4558:0.0:0.1905	.	28	Q9P0M6	H2AW_HUMAN	V	28	ENSP00000362352:L28V;ENSP00000404584:L28V	ENSP00000362352:L28V	L	+	1	2	H2AFY2	71505502	1.000000	0.71417	0.996000	0.52242	0.968000	0.65278	3.943000	0.56621	0.792000	0.33850	-0.258000	0.10820	CTG	.	.		0.547	H2AFY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048480.2	NM_018649		G	71835496	C	G	71835496	3	3	357	1	0	0	0	0	1	0	0	0	6939	796	28	4	84	4	H2AFY2	10	71835496	Missense_Mutation	SNP	C	TCGA-XR-A8TC-01A-11D-A35Z-10	26955099	71835496	63699251	24	50196										
MUC5B	727897	hgsc.bcm.edu	37	chr11	1282675	1282675	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	cacctgctgccaggagaggcGggtccacgaggagacggtgc	17	12	0	2	rs372911529		TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr11:1282675G>A	ENST00000529681.1	+	49	17184	c.17126G>A	c.(17125-17127)cGg>cAg	p.R5709Q	MUC5B_ENST00000447027.1_Missense_Mutation_p.R5712Q	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	5709	CTCK. {ECO:0000255|PROSITE- ProRule:PRU00039}.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CAGGAGAGGCGGGTCCACGAG	0.652													G|||	1	0.000199681	8e-04	0	5008	,	,		18334	0		0	False		,,,				2504	0				p.R5709Q		Atlas-SNP	.											.	MUC5B	473	.	0			c.G17126A						.	G	GLN/ARG	1,4333		0,1,2166	26	38	34		17126	-2	0	11		34	0,8460		0,0,4230	no	missense	MUC5B	NM_002458.2	43	0,1,6396	AA,AG,GG		0.0,0.0231,0.0078	benign	5709/5763	1282675	1,12793	2167	4230	6397	SO:0001583	missense	727897	exon49			AGAGGCGGGTCCA	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.17126G>A	chr11.hg19:g.1282675G>A	ENSP00000436812:p.Arg5709Gln	34.0	0.0		35.0	16.0	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	hg19	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	G	5.261	0.233574	0.09969	2.31E-4	0.0	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000546052;ENST00000406844	T;T	0.16073	2.37;2.55	4.31	-2.02	0.07388	.	.	.	.	.	T	0.06917	0.0176	N	0.16708	0.43	0.09310	N	1	B;P	0.35011	0.319;0.48	B;B	0.17979	0.018;0.02	T	0.25187	-1.0139	9	0.87932	D	0	.	3.6219	0.08099	0.4318:0.0:0.2859:0.2823	.	6046;5712	A7Y9J9;E9PBJ0	.;.	Q	5709;5712;5653;608;5421	ENSP00000436812:R5709Q;ENSP00000415793:R5712Q	ENSP00000343037:R5653Q	R	+	2	0	MUC5B	1239251	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	-0.757000	0.04772	-0.303000	0.08856	-0.254000	0.11334	CGG	.	.		0.652	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		A	1282675	G	A	1282675	3	1	357	1	0	0	0	0	1	0	0	0	9988	1116	39	1	17329	1	MUC5B	11	1282675	Missense_Mutation	SNP	G	TCGA-XR-A8TC-01A-11D-A35Z-10		1282675	133723841	25	50197										
ST5	6764	hgsc.bcm.edu	37	chr11	8734241	8734241	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	cgtgcgatagctgggggcgcGcttcagcatcgactggatgt	16	10	1	0			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr11:8734241G>A	ENST00000534127.1	-	12	2414	c.2029C>T	c.(2029-2031)Cgc>Tgc	p.R677C	ST5_ENST00000526099.1_Missense_Mutation_p.R190C|ST5_ENST00000530438.1_Missense_Mutation_p.R257C|ST5_ENST00000357665.1_Missense_Mutation_p.R677C|ST5_ENST00000313726.6_Missense_Mutation_p.R677C|ST5_ENST00000530991.1_Missense_Mutation_p.R149C|RPL27A_ENST00000531102.1_Intron|ST5_ENST00000526757.1_Missense_Mutation_p.R257C	NM_005418.3	NP_005409.3	P78524	ST5_HUMAN	suppression of tumorigenicity 5	677					positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(13)|liver(1)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	39				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)		CTGGGGGCGCGCTTCAGCATC	0.587																																					p.R677C		Atlas-SNP	.											.	ST5	85	.	0			c.C2029T						.						46	41	43					11																	8734241		2201	4296	6497	SO:0001583	missense	6764	exon12			GGGCGCGCTTCAG	U15131	CCDS7791.1, CCDS7792.1	11p15	2012-10-04				ENSG00000166444		"DENN/MADD domain containing"	11350	protein-coding gene	gene with protein product	"DENN/MADD domain containing 2B"	140750				1390339	Standard	NM_005418		Approved	HTS1, DENND2B, p126	uc001mgt.3	P78524		ENST00000534127.1:c.2029C>T	chr11.hg19:g.8734241G>A	ENSP00000433528:p.Arg677Cys	30.0	0.0		38.0	9.0	NM_005418	B2R6X7|B3KXQ6|P78523|Q16492|Q7KYY2|Q7KZ12|Q8NE12|Q9BQQ6	Missense_Mutation	SNP	ENST00000534127.1	hg19	CCDS7791.1	.	.	.	.	.	.	.	.	.	.	G	16.73	3.205042	0.58234	.	.	ENSG00000166444	ENST00000526757;ENST00000534127;ENST00000313726;ENST00000530991;ENST00000357665;ENST00000526099;ENST00000530438;ENST00000533020;ENST00000447053;ENST00000530593;ENST00000528527	T;T;T;T;T;T;T;T;T;T	0.39997	2.88;2.88;2.88;2.88;2.88;2.88;2.88;2.88;1.05;2.88	5.28	4.31	0.51392	.	0.000000	0.85682	D	0.000000	T	0.35941	0.0949	L	0.58810	1.83	0.80722	D	1	B;P;P	0.38148	0.028;0.539;0.62	B;B;B	0.28709	0.013;0.071;0.093	T	0.45804	-0.9236	10	0.87932	D	0	-8.1483	13.2376	0.59979	0.0:0.0:0.7611:0.2389	.	190;257;677	B4DDL8;P78524-2;P78524	.;.;ST5_HUMAN	C	257;677;677;149;677;190;257;149;287;134;149	ENSP00000435097:R257C;ENSP00000433528:R677C;ENSP00000319678:R677C;ENSP00000432887:R149C;ENSP00000350294:R677C;ENSP00000436808:R190C;ENSP00000436802:R257C;ENSP00000433588:R149C;ENSP00000437096:R134C;ENSP00000431580:R149C	ENSP00000319678:R677C	R	-	1	0	ST5	8690817	1.000000	0.71417	0.998000	0.56505	0.920000	0.55202	3.142000	0.50601	2.467000	0.83353	0.655000	0.94253	CGC	.	.		0.587	ST5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386518.1	NM_005418		A	8734241	G	A	8734241	3	1	357	1	0	0	0	0	1	0	0	0	15235	1087	38	1	1432	1	ST5	11	8734241	Missense_Mutation	SNP	G	TCGA-XR-A8TC-01A-11D-A35Z-10	7451566	8734241	126272275	26	50198										
CORO1B	57175	hgsc.bcm.edu	37	chr11	67209971	67209971	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	accgccaggaacttggggttGacggcgcagaaggtgctgtc	16	10	0	2			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr11:67209971G>C	ENST00000341356.5	-	2	239	c.129C>G	c.(127-129)gtC>gtG	p.V43V	CORO1B_ENST00000539724.1_5'Flank|CORO1B_ENST00000453768.2_Silent_p.V43V|CORO1B_ENST00000545016.1_Silent_p.V43V|CORO1B_ENST00000393893.1_Silent_p.V43V	NM_020441.2	NP_065174.1	Q9BR76	COR1B_HUMAN	coronin, actin binding protein, 1B	43					actin cytoskeleton organization (GO:0030036)|actin filament branching (GO:0090135)|actin filament bundle assembly (GO:0051017)|cell migration (GO:0016477)|endothelial cell chemotaxis (GO:0035767)|negative regulation of Arp2/3 complex-mediated actin nucleation (GO:0034316)|positive regulation of lamellipodium morphogenesis (GO:2000394)|protein localization to cell leading edge (GO:1902463)|ruffle organization (GO:0031529)|wound healing (GO:0042060)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)|Arp2/3 complex binding (GO:0071933)|identical protein binding (GO:0042802)			cervix(1)|endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	13			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)			ACTTGGGGTTGACGGCGCAGA	0.607																																					p.V43V		Atlas-SNP	.											.	CORO1B	30	.	0			c.C129G						.						98	75	83					11																	67209971		2199	4295	6494	SO:0001819	synonymous_variant	57175	exon2			GGGGTTGACGGCG	AK000860	CCDS8164.1	11q13.1	2013-01-10	2001-11-28		ENSG00000172725	ENSG00000172725		"Coronins", "WD repeat domain containing"	2253	protein-coding gene	gene with protein product		609849	"coronin, actin-binding protein, 1B"			9778037	Standard	NM_001018070		Approved	coronin-2	uc001olk.1	Q9BR76	OTTHUMG00000167775	ENST00000341356.5:c.129C>G	chr11.hg19:g.67209971G>C		98.0	0.0		82.0	33.0	NM_020441	B2RD45	Silent	SNP	ENST00000341356.5	hg19	CCDS8164.1																																																																																			.	.		0.607	CORO1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396220.1	NM_020441		C	67209971	G	C	67209971	2	2	357	1	0	0	0	0	0	0	0	1	3756	1277	45	4		4	CORO1B	11	67209971	Silent	SNP	G	TCGA-XR-A8TC-01A-11D-A35Z-10	58475730	67209971	67796545	27	50199										
CHD4	1108	hgsc.bcm.edu	37	chr12	6701864	6701864	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	agataaacacatacttactgGaacctctcgggggtgagaaa	10	8	1	2			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr12:6701864G>C	ENST00000357008.2	-	18	2935	c.2772C>G	c.(2770-2772)ttC>ttG	p.F924L	CHD4_ENST00000309577.6_Missense_Mutation_p.F924L|CHD4_ENST00000544040.1_Missense_Mutation_p.F917L|CHD4_ENST00000544484.1_Missense_Mutation_p.F921L	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	924					ATP-dependent chromatin remodeling (GO:0043044)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|RNA polymerase II repressing transcription factor binding (GO:0001103)|zinc ion binding (GO:0008270)			central_nervous_system(2)	2						ATACTTACTGGAACCTCTCGG	0.433																																					p.F924L	Colon(32;586 792 4568 16848 45314)	Atlas-SNP	.											.	CHD4	539	.	0			c.C2772G						.						117	116	116					12																	6701864		2203	4300	6503	SO:0001583	missense	1108	exon18			TTACTGGAACCTC	X86691	CCDS8552.1	12p13	2013-01-28				ENSG00000111642		"Zinc fingers, PHD-type"	1919	protein-coding gene	gene with protein product		603277				7575689, 8843877	Standard	XM_006718958		Approved	Mi-2b, Mi2-BETA	uc001qpo.3	Q14839		ENST00000357008.2:c.2772C>G	chr12.hg19:g.6701864G>C	ENSP00000349508:p.Phe924Leu	91.0	0.0		103.0	48.0	NM_001273	Q8IXZ5	Missense_Mutation	SNP	ENST00000357008.2	hg19	CCDS8552.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.632359	0.87660	.	.	ENSG00000111642	ENST00000544484;ENST00000544040;ENST00000309577;ENST00000357008;ENST00000537464	D;D;D;D	0.92699	-3.09;-3.09;-3.09;-3.09	5.66	4.78	0.61160	DEAD-like helicase (1);SNF2-related (1);	0.000000	0.85682	D	0.000000	D	0.92916	0.7746	L	0.35542	1.07	0.80722	D	1	D;D;D	0.63046	0.992;0.973;0.974	D;D;D	0.75484	0.986;0.961;0.969	D	0.93303	0.6678	10	0.87932	D	0	-5.0299	11.6259	0.51145	0.1421:0.0:0.8579:0.0	.	924;924;917	Q14839-2;Q14839;F5GWX5	.;CHD4_HUMAN;.	L	921;917;924;924;898	ENSP00000440392:F921L;ENSP00000440542:F917L;ENSP00000312419:F924L;ENSP00000349508:F924L	ENSP00000312419:F924L	F	-	3	2	CHD4	6572125	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	4.944000	0.63561	1.396000	0.46663	0.557000	0.71058	TTC	.	.		0.433	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001273		C	6701864	G	C	6701864	3	2	357	1	0	0	0	0	1	0	0	0	3329	1165	41	4	3058	4	CHD4	12	6701864	Missense_Mutation	SNP	G	TCGA-XR-A8TC-01A-11D-A35Z-10		6701864	127150031	28	50200										
STAB2	55576	hgsc.bcm.edu	37	chr12	104056724	104056724	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	agttctcattcctccctccaTtgtcccgattctgccccatc	4	18	2	0			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr12:104056724T>C	ENST00000388887.2	+	18	2174	c.1970T>C	c.(1969-1971)aTt>aCt	p.I657T		NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						CCTCCCTCCATTGTCCCGATT	0.453																																					p.I657T		Atlas-SNP	.											.	STAB2	370	.	0			c.T1970C						.						146	140	142					12																	104056724		2203	4300	6503	SO:0001583	missense	55576	exon18			CCTCCATTGTCCC	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"hyaluronic acid receptor for endocytosis"	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.1970T>C	chr12.hg19:g.104056724T>C	ENSP00000373539:p.Ile657Thr	128.0	0.0		218.0	137.0	NM_017564		Missense_Mutation	SNP	ENST00000388887.2	hg19	CCDS31888.1	.	.	.	.	.	.	.	.	.	.	T	15.96	2.987176	0.53934	.	.	ENSG00000136011	ENST00000388887	T	0.66280	-0.2	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.73961	0.3654	M	0.83603	2.65	0.48975	D	0.999732	D	0.63880	0.993	P	0.52109	0.69	T	0.78388	-0.2223	10	0.52906	T	0.07	.	14.9618	0.71161	0.0:0.0:0.0:1.0	.	657	Q8WWQ8	STAB2_HUMAN	T	657	ENSP00000373539:I657T	ENSP00000373539:I657T	I	+	2	0	STAB2	102580854	1.000000	0.71417	0.900000	0.35374	0.204000	0.24138	6.656000	0.74396	2.006000	0.58801	0.533000	0.62120	ATT	.	.		0.453	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			C	104056724	T	C	104056724	3	2	357	1	0	0	0	0	1	0	0	0	15253	1493	52	2	2040	2	STAB2	12	104056724	Missense_Mutation	SNP	T	TCGA-XR-A8TC-01A-11D-A35Z-10	97354860	104056724	29795171	29	50201										
DDX54	79039	hgsc.bcm.edu	37	chr12	113600779	113600779	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	tcgtcaggttctgggcttcaTcccccatcaagtccaggaca	9	14	4	0			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr12:113600779T>C	ENST00000306014.5	-	17	2180	c.2153A>G	c.(2152-2154)gAt>gGt	p.D718G	DDX54_ENST00000314045.7_Missense_Mutation_p.D718G|DDX54_ENST00000549271.1_5'Flank	NM_024072.3	NP_076977.3	Q8TDD1	DDX54_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 54	718					ATP catabolic process (GO:0006200)|intracellular estrogen receptor signaling pathway (GO:0030520)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						CTGGGCTTCATCCCCCATCAA	0.627																																					p.D718G		Atlas-SNP	.											.	DDX54	73	.	0			c.A2153G						.						60	53	56					12																	113600779		2203	4300	6503	SO:0001583	missense	79039	exon17			GCTTCATCCCCCA	AF144056	CCDS31907.1, CCDS44984.1	12q24.11	2006-01-30				ENSG00000123064		"DEAD-boxes"	20084	protein-coding gene	gene with protein product		611665				12466272	Standard	NM_001111322		Approved	MGC2835, APR-5, DP97	uc001tuq.4	Q8TDD1	OTTHUMG00000169676	ENST00000306014.5:c.2153A>G	chr12.hg19:g.113600779T>C	ENSP00000304072:p.Asp718Gly	24.0	0.0		45.0	5.0	NM_024072	Q86YT8|Q9BRZ1	Missense_Mutation	SNP	ENST00000306014.5	hg19	CCDS31907.1	.	.	.	.	.	.	.	.	.	.	T	29.9	5.047035	0.93740	.	.	ENSG00000123064	ENST00000314045;ENST00000306014	T;T	0.32272	1.46;1.54	5.41	5.41	0.78517	DBP10CT (2);	0.046715	0.85682	D	0.000000	T	0.63295	0.2499	M	0.90483	3.12	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	T	0.72014	-0.4418	10	0.72032	D	0.01	.	15.1093	0.72343	0.0:0.0:0.0:1.0	.	718;718	Q8TDD1-2;Q8TDD1	.;DDX54_HUMAN	G	718	ENSP00000323858:D718G;ENSP00000304072:D718G	ENSP00000304072:D718G	D	-	2	0	DDX54	112085162	1.000000	0.71417	0.979000	0.43373	0.927000	0.56198	7.616000	0.83018	2.043000	0.60533	0.523000	0.50628	GAT	.	.		0.627	DDX54-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405435.1	NM_024072		C	113600779	T	C	113600779	3	2	357	1	0	0	0	0	1	0	0	0	4374	1435	50	2	511	2	DDX54	12	113600779	Missense_Mutation	SNP	T	TCGA-XR-A8TC-01A-11D-A35Z-10	9544055	113600779	20251116	30	50202										
FERMT2	10979	hgsc.bcm.edu	37	chr14	53360119	53360119	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	atctctgggtttctttaagaGagaaagttcttcggggtgtc	12	6	3	2			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr14:53360119G>C	ENST00000395631.2	-	4	634	c.418C>G	c.(418-420)Ctc>Gtc	p.L140V	FERMT2_ENST00000553373.1_Missense_Mutation_p.L140V|FERMT2_ENST00000341590.3_Missense_Mutation_p.L140V|FERMT2_ENST00000399304.3_Missense_Mutation_p.L140V|FERMT2_ENST00000343279.4_Missense_Mutation_p.L140V			Q96AC1	FERM2_HUMAN	fermitin family member 2	140					cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|focal adhesion assembly (GO:0048041)|integrin activation (GO:0033622)|integrin-mediated signaling pathway (GO:0007229)|protein localization to membrane (GO:0072657)|regulation of cell shape (GO:0008360)|substrate adhesion-dependent cell spreading (GO:0034446)|transforming growth factor beta receptor signaling pathway (GO:0007179)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|stress fiber (GO:0001725)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)		ERO1L/FERMT2(2)	NS(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	20	Breast(41;0.0342)					TTCTTTAAGAGAGAAAGTTCT	0.338																																					p.L140V		Atlas-SNP	.											.	FERMT2	59	.	0			c.C418G						.						72	78	76					14																	53360119		2203	4300	6503	SO:0001583	missense	10979	exon4			TTAAGAGAGAAAG	Z24725	CCDS9713.1, CCDS45107.1, CCDS45108.1	14q22.1	2013-01-10	2010-06-24	2007-12-14	ENSG00000073712	ENSG00000073712		"Fermitins", "Pleckstrin homology (PH) domain containing"	15767	protein-coding gene	gene with protein product	"kindlin-2"	607746	"pleckstrin homology domain containing, family C (with FERM domain) member 1", "fermitin family homolog 2 (Drosophila)"	PLEKHC1		8175911, 12697302	Standard	NM_006832		Approved	mig-2, KIND2, UNC112B	uc001xac.3	Q96AC1	OTTHUMG00000140309	ENST00000395631.2:c.418C>G	chr14.hg19:g.53360119G>C	ENSP00000378993:p.Leu140Val	54.0	0.0		60.0	27.0	NM_001135000	B5TJY2|Q14840|Q86TY7	Missense_Mutation	SNP	ENST00000395631.2	hg19	CCDS9713.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.680462	0.88542	.	.	ENSG00000073712	ENST00000395631;ENST00000341590;ENST00000554152;ENST00000343279;ENST00000553373;ENST00000399304;ENST00000554288;ENST00000555692;ENST00000554712	D;D;D;D;D;D;T;T	0.89415	-2.51;-2.51;-2.51;-2.51;-2.51;-2.51;0.67;0.44	5.73	5.73	0.89815	FERM, N-terminal (1);Band 4.1 domain (1);	0.000000	0.85682	D	0.000000	D	0.91462	0.7305	L	0.49126	1.545	0.80722	D	1	P;P;P	0.41848	0.72;0.763;0.763	P;P;P	0.51453	0.54;0.507;0.67	D	0.91514	0.5229	10	0.72032	D	0.01	.	19.959	0.97233	0.0:0.0:1.0:0.0	.	140;140;140	Q96AC1-2;Q96AC1;B5TJY2	.;FERM2_HUMAN;.	V	140;140;82;140;140;140;35;96;140	ENSP00000378993:L140V;ENSP00000340391:L140V;ENSP00000450741:L82V;ENSP00000342858:L140V;ENSP00000451084:L140V;ENSP00000382243:L140V;ENSP00000451268:L35V;ENSP00000452472:L96V	ENSP00000340391:L140V	L	-	1	0	FERMT2	52429869	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.271000	0.78506	2.720000	0.93068	0.644000	0.83932	CTC	.	.		0.338	FERMT2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276907.2	NM_006832		C	53360119	G	C	53360119	3	2	357	1	0	0	0	0	1	0	0	0	5826	942	33	4	1709	4	FERMT2	14	53360119	Missense_Mutation	SNP	G	TCGA-XR-A8TC-01A-11D-A35Z-10		53360119	53989421	31	50203										
C14orf135	64430	hgsc.bcm.edu	37	chr14	60590986	60590986	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	actgcagaagctcgcagagtTgatgaagtttttgaagatgc	12	6	0	6			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr14:60590986T>G	ENST00000406854.1	+	9	2651	c.2097T>G	c.(2095-2097)gtT>gtG	p.V699V	PCNXL4_ENST00000404681.2_Silent_p.V699V|PCNXL4_ENST00000317623.4_Silent_p.V465V|PCNXL4_ENST00000535349.1_5'UTR|PCNXL4_ENST00000406949.1_Silent_p.V465V			Q63HM2	PCX4_HUMAN	pecanex-like 4 (Drosophila)	699						integral component of membrane (GO:0016021)											CTCGCAGAGTTGATGAAGTTT	0.353																																					p.V465V		Atlas-SNP	.											.	.	.	.	0			c.T1395G						.						50	48	48					14																	60590986		2203	4300	6503	SO:0001819	synonymous_variant	64430	exon8			CAGAGTTGATGAA	AK022861		14q23.1	2012-07-18	2012-07-18	2012-07-18	ENSG00000126773	ENSG00000126773			20349	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 135"	C14orf135			Standard	NM_022495		Approved		uc001xer.4	Q63HM2	OTTHUMG00000150361	ENST00000406854.1:c.2097T>G	chr14.hg19:g.60590986T>G		89.0	0.0		116.0	37.0	NM_022495	A8MXM2|Q9BQG8|Q9H9F2	Silent	SNP	ENST00000406854.1	hg19		.	.	.	.	.	.	.	.	.	.	T	8.974	0.973726	0.18736	.	.	ENSG00000126773	ENST00000554534	.	.	.	5.71	4.58	0.56647	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.0216	0.30412	0.0:0.0737:0.1478:0.7785	.	.	.	.	G	118	.	.	X	+	1	0	C14orf135	59660739	0.930000	0.31532	1.000000	0.80357	0.997000	0.91878	-0.086000	0.11233	2.180000	0.69256	0.528000	0.53228	TGA	.	.		0.353	PCNXL4-005	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000317847.1	NM_022495		G	60590986	T	G	60590986	2	3	357	1	0	0	0	0	0	0	0	1	1747	1799	63	5		5	C14orf135	14	60590986	Silent	SNP	T	TCGA-XR-A8TC-01A-11D-A35Z-10	7230867	60590986	46758554	32	50204										
PDE8A	5151	hgsc.bcm.edu	37	chr15	85656625	85656625	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	cagtttccagccagagacgaCactcttccatggcccggata	9	14	1	1			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr15:85656625C>G	ENST00000310298.4	+	14	1384	c.1132C>G	c.(1132-1134)Cac>Gac	p.H378D	PDE8A_ENST00000557957.1_Missense_Mutation_p.H306D|PDE8A_ENST00000339708.5_Missense_Mutation_p.H332D|PDE8A_ENST00000557819.2_3'UTR|PDE8A_ENST00000394553.1_Missense_Mutation_p.H378D			O60658	PDE8A_HUMAN	phosphodiesterase 8A	378					cAMP catabolic process (GO:0006198)|cyclic nucleotide metabolic process (GO:0009187)|phosphorelay signal transduction system (GO:0000160)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	25	Colorectal(223;0.227)		BRCA - Breast invasive adenocarcinoma(143;0.0608)		Caffeine(DB00201)|Ketotifen(DB00920)	CCAGAGACGACACTCTTCCAT	0.532																																					p.H378D		Atlas-SNP	.											.	PDE8A	50	.	0			c.C1132G						.						166	138	148					15																	85656625		2203	4299	6502	SO:0001583	missense	5151	exon13			AGACGACACTCTT	AF056490	CCDS10336.1, CCDS10337.1, CCDS58397.1	15q25.3	2008-05-14			ENSG00000073417	ENSG00000073417	3.1.4.17	"Phosphodiesterases"	8793	protein-coding gene	gene with protein product		602972				9618252	Standard	NM_001243137		Approved	HsT19550	uc002blh.3	O60658	OTTHUMG00000148670	ENST00000310298.4:c.1132C>G	chr15.hg19:g.85656625C>G	ENSP00000311453:p.His378Asp	66.0	0.0		105.0	48.0	NM_002605	B3KXE6|H0YMZ7|Q6P9H3|Q969I1|Q96PC9|Q96PD0|Q96PD1|Q96T71|Q9UMB7|Q9UMC3	Missense_Mutation	SNP	ENST00000310298.4	hg19	CCDS10336.1	.	.	.	.	.	.	.	.	.	.	C	12.86	2.065415	0.36470	.	.	ENSG00000073417	ENST00000310298;ENST00000394553;ENST00000339708	T;T;T	0.69561	-0.41;-0.41;-0.41	4.92	4.92	0.64577	.	0.419670	0.25032	N	0.033662	T	0.74245	0.3691	M	0.68317	2.08	0.53688	D	0.999978	P;P	0.51351	0.823;0.944	P;P	0.52109	0.69;0.644	T	0.77357	-0.2618	10	0.62326	D	0.03	.	15.6911	0.77453	0.0:1.0:0.0:0.0	.	332;378	O60658-2;O60658	.;PDE8A_HUMAN	D	378;378;332	ENSP00000311453:H378D;ENSP00000378056:H378D;ENSP00000340679:H332D	ENSP00000311453:H378D	H	+	1	0	PDE8A	83457629	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	3.378000	0.52432	2.550000	0.86006	0.655000	0.94253	CAC	.	.		0.532	PDE8A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000309018.1	NM_002605		G	85656625	C	G	85656625	3	3	357	1	0	0	0	0	1	0	0	0	11662	478	17	4	1182	4	PDE8A	15	85656625	Missense_Mutation	SNP	C	TCGA-XR-A8TC-01A-11D-A35Z-10		85656625	16874767	33	50205										
AXIN1	8312	hgsc.bcm.edu	37	chr16	347849	347849	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	ctgggccctgcgggtggcctCggcctccacctgctccttgg	14	17	0	0			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr16:347849C>A	ENST00000262320.3	-	6	2028	c.1657G>T	c.(1657-1659)Gag>Tag	p.E553*	AXIN1_ENST00000354866.3_Nonsense_Mutation_p.E553*|AXIN1_ENST00000481769.1_5'UTR	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	553	Interaction with RNF111.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				CGGGTGGCCTCGGCCTCCACC	0.706																																					p.E553X		Atlas-SNP	.											.	AXIN1	290	.	0			c.G1657T						.						41	38	39					16																	347849		2201	4298	6499	SO:0001587	stop_gained	8312	exon6			TGGCCTCGGCCTC	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.1657G>T	chr16.hg19:g.347849C>A	ENSP00000262320:p.Glu553*	52.0	0.0		37.0	28.0	NM_181050	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Nonsense_Mutation	SNP	ENST00000262320.3	hg19	CCDS10405.1	.	.	.	.	.	.	.	.	.	.	C	35	5.528516	0.96446	.	.	ENSG00000103126	ENST00000262320;ENST00000354866	.	.	.	5.37	5.37	0.77165	.	0.123114	0.64402	D	0.000016	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-34.046	19.0878	0.93212	0.0:1.0:0.0:0.0	.	.	.	.	X	553	.	ENSP00000262320:E553X	E	-	1	0	AXIN1	287850	1.000000	0.71417	0.879000	0.34478	0.160000	0.22226	7.003000	0.76310	2.531000	0.85337	0.478000	0.44815	GAG	.	.		0.706	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3			A	347849	C	A	347849	4	1	357	1	0	0	0	0	0	1	0	0	1236	893	31	1	955	1	AXIN1	16	347849	Nonsense_Mutation	SNP	C	TCGA-XR-A8TC-01A-11D-A35Z-10		347849	90006904	34	50206										
KRT33A	3883	hgsc.bcm.edu	37	chr17	39506783	39506783	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	ttctccagctccgcgttgtcCcgctccagctgacgcacctt	8	18	1	1			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr17:39506783C>A	ENST00000007735.3	-	1	281	c.237G>T	c.(235-237)cgG>cgT	p.R79R		NM_004138.3	NP_004129.2	O76009	KT33A_HUMAN	keratin 33A	79	Coil 1A.|Rod.					extracellular space (GO:0005615)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	21		Breast(137;0.000496)				CCGCGTTGTCCCGCTCCAGCT	0.602																																					p.R79R		Atlas-SNP	.											.	KRT33A	53	.	0			c.G237T						.						94	88	90					17																	39506783		2203	4300	6503	SO:0001819	synonymous_variant	3883	exon1			GTTGTCCCGCTCC	Y16788	CCDS11388.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000006059	ENSG00000006059		"-", "Intermediate filaments type I, keratins (acidic)"	6450	protein-coding gene	gene with protein product	"hard keratin type I 3I"	602761	"keratin, hair, acidic, 3A"	KRTHA3A		7565656, 16831889	Standard	NM_004138		Approved	Ha-3I, Krt1-3	uc002hwk.2	O76009	OTTHUMG00000133432	ENST00000007735.3:c.237G>T	chr17.hg19:g.39506783C>A		126.0	0.0		119.0	44.0	NM_004138	B2RA87|Q6NTB9|Q6ZZB9	Silent	SNP	ENST00000007735.3	hg19	CCDS11388.1																																																																																			.	.		0.602	KRT33A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257295.1	NM_004138		A	39506783	C	A	39506783	2	1	357	1	0	0	0	0	0	0	0	1	8478	610	22	3		3	KRT33A	17	39506783	Silent	SNP	C	TCGA-XR-A8TC-01A-11D-A35Z-10		39506783	41688427	35	50207										
ADAM11	4185	hgsc.bcm.edu	37	chr17	42853002	42853002	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	aagaaatgcaccctgactcaCgacgccatgtgcagcgacgg	11	13	1	2			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr17:42853002C>A	ENST00000200557.6	+	17	1612	c.1443C>A	c.(1441-1443)caC>caA	p.H481Q	ADAM11_ENST00000535346.1_Missense_Mutation_p.H281Q	NM_002390.4	NP_002381.2	O75078	ADA11_HUMAN	ADAM metallopeptidase domain 11	481	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				integrin-mediated signaling pathway (GO:0007229)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(15)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33		Prostate(33;0.0959)				CCCTGACTCACGACGCCATGT	0.682																																					p.H481Q		Atlas-SNP	.											.	ADAM11	118	.	0			c.C1443A						.						10	9	10					17																	42853002		2185	4261	6446	SO:0001583	missense	4185	exon17			GACTCACGACGCC	D17390	CCDS11486.1	17q21.3	2014-08-12	2005-08-18		ENSG00000073670			"ADAM metallopeptidase domain containing"	189	protein-coding gene	gene with protein product	"metalloproteinase-like, disintegrin-like, cysteine-rich protein"	155120	"a disintegrin and metalloproteinase domain 11"	MDC		8252040	Standard	XM_005257373		Approved		uc002ihh.3	O75078	OTTHUMG00000179038	ENST00000200557.6:c.1443C>A	chr17.hg19:g.42853002C>A	ENSP00000200557:p.His481Gln	60.0	0.0		71.0	26.0	NM_002390	Q14808|Q14809|Q14810	Missense_Mutation	SNP	ENST00000200557.6	hg19	CCDS11486.1	.	.	.	.	.	.	.	.	.	.	C	4.406	0.075076	0.08485	.	.	ENSG00000073670	ENST00000200557;ENST00000535346;ENST00000355638	T;T	0.10382	2.88;2.88	4.42	1.38	0.22167	Blood coagulation inhibitor, Disintegrin (4);	0.000000	0.85682	D	0.000000	T	0.04724	0.0128	N	0.04275	-0.24	0.54753	D	0.999981	B;P	0.37781	0.051;0.608	B;B	0.41946	0.085;0.371	T	0.49799	-0.8901	10	0.12766	T	0.61	.	6.8839	0.24189	0.0:0.527:0.0:0.473	.	281;481	B4DKD2;O75078	.;ADA11_HUMAN	Q	481;281;381	ENSP00000200557:H481Q;ENSP00000443773:H281Q	ENSP00000200557:H481Q	H	+	3	2	ADAM11	40208528	0.010000	0.17322	0.999000	0.59377	0.940000	0.58332	-1.022000	0.03611	0.146000	0.19002	-0.272000	0.10252	CAC	.	.		0.682	ADAM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444531.1	NM_002390		A	42853002	C	A	42853002	3	1	357	1	0	0	0	0	1	0	0	0	235	535	19	1	1509	1	ADAM11	17	42853002	Missense_Mutation	SNP	C	TCGA-XR-A8TC-01A-11D-A35Z-10	3346219	42853002	38342208	36	50208										
HOXB2	3212	hgsc.bcm.edu	37	chr17	46620730	46620730	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	gctaaaggccgggggtccgcGcttaaggcccccggcaccac	14	16	0	0			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr17:46620730G>C	ENST00000330070.4	-	2	1938	c.771C>G	c.(769-771)agC>agG	p.S257R	HOXB-AS1_ENST00000508688.1_RNA|HOXB-AS1_ENST00000504972.3_RNA|HOXB2_ENST00000504772.3_5'Flank|HOXB-AS1_ENST00000435312.1_RNA	NM_002145.3	NP_002136.1	P14652	HXB2_HUMAN	homeobox B2	257					anterior/posterior pattern specification (GO:0009952)|blood circulation (GO:0008015)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|facial nerve structural organization (GO:0021612)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|neural nucleus development (GO:0048857)|rhombomere 3 development (GO:0021569)|rhombomere 4 development (GO:0021570)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)	11						GGGGGTCCGCGCTTAAGGCCC	0.786																																					p.S257R		Atlas-SNP	.											.	HOXB2	23	.	0			c.C771G						.						5	8	7					17																	46620730		1750	3505	5255	SO:0001583	missense	3212	exon2			GTCCGCGCTTAAG		CCDS11527.1	17q21.32	2012-02-22	2005-12-22		ENSG00000173917	ENSG00000173917		"Homeoboxes / ANTP class : HOXL subclass"	5113	protein-coding gene	gene with protein product		142967	"homeo box B2"	HOX2, HOX2H		1973146, 1358459	Standard	XM_005257276		Approved		uc002inm.3	P14652	OTTHUMG00000159930	ENST00000330070.4:c.771C>G	chr17.hg19:g.46620730G>C	ENSP00000331741:p.Ser257Arg	55.0	0.0		57.0	24.0	NM_002145	P10913|P17485	Missense_Mutation	SNP	ENST00000330070.4	hg19	CCDS11527.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	2.970|2.970	-0.212559|-0.212559	0.06140|0.06140	.|.	.|.	ENSG00000173917|ENSG00000173917	ENST00000326226|ENST00000330070	.|D	.|0.88818	.|-2.43	4.06|4.06	0.491|0.491	0.16867|0.16867	.|.	.|1.635550	.|0.03482	.|N	.|0.215219	T|T	0.76278|0.76278	0.3965|0.3965	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B	.|0.06786	.|0.001	.|B	.|0.04013	.|0.001	T|T	0.64441|0.64441	-0.6407|-0.6407	6|10	0.20519|0.40728	T|T	0.43|0.16	.|.	2.6608|2.6608	0.05026|0.05026	0.1061:0.3428:0.3759:0.1752|0.1061:0.3428:0.3759:0.1752	.|.	.|257	.|P14652	.|HXB2_HUMAN	G|R	165|257	.|ENSP00000331741:S257R	ENSP00000316334:R165G|ENSP00000331741:S257R	R|S	-|-	1|3	0|2	HOXB2|HOXB2	43975729|43975729	0.000000|0.000000	0.05858|0.05858	0.022000|0.022000	0.16811|0.16811	0.030000|0.030000	0.12068|0.12068	0.022000|0.022000	0.13511|0.13511	0.432000|0.432000	0.26286|0.26286	0.556000|0.556000	0.70494|0.70494	CGC|AGC	.	.		0.786	HOXB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358384.2			C	46620730	G	C	46620730	3	2	357	1	0	0	0	0	1	0	0	0	7310	1078	38	4	303	4	HOXB2	17	46620730	Missense_Mutation	SNP	G	TCGA-XR-A8TC-01A-11D-A35Z-10	3767728	46620730	34574480	37	50209										
PRAC	84366	hgsc.bcm.edu	37	chr17	46799700	46799700	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	cttattagagagaaaagcacTcttggaggtagtaagatggg	13	4	1	3			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr17:46799700T>C	ENST00000290294.3	-	1	184	c.55A>G	c.(55-57)Agt>Ggt	p.S19G	PRAC2_ENST00000432056.1_RNA|MIR3185_ENST00000583892.1_RNA|PRAC2_ENST00000422730.2_RNA	NM_032391.2	NP_115767.1	Q96KF2	PRAC1_HUMAN	prostate cancer susceptibility candidate 1	19						nucleus (GO:0005634)											AGAAAAGCACTCTTGGAGGTA	0.537																																					p.S19G		Atlas-SNP	.											.	PRAC	6	.	0			c.A55G						.						104	94	98					17																	46799700		2203	4300	6503	SO:0001583	missense	84366	exon1			AAGCACTCTTGGA	AF331165	CCDS11535.1	17q21	2013-08-29	2013-08-29	2013-08-29	ENSG00000159182	ENSG00000159182			30591	protein-coding gene	gene with protein product	"prostate, rectum and colon"	609819	"chromosome 17 open reading frame 92", "prostate cancer susceptibility candidate"	C17orf92, PRAC		11340635	Standard	NM_032391		Approved		uc002iny.3	Q96KF2	OTTHUMG00000159899	ENST00000290294.3:c.55A>G	chr17.hg19:g.46799700T>C	ENSP00000290294:p.Ser19Gly	82.0	0.0		96.0	37.0	NM_032391		Missense_Mutation	SNP	ENST00000290294.3	hg19	CCDS11535.1	.	.	.	.	.	.	.	.	.	.	T	10.39	1.337740	0.24253	.	.	ENSG00000159182	ENST00000290294	T	0.58358	0.34	3.78	0.227	0.15359	.	.	.	.	.	T	0.36193	0.0958	.	.	.	0.09310	N	1	B	0.17038	0.02	B	0.13407	0.009	T	0.32824	-0.9892	8	0.87932	D	0	.	3.2764	0.06899	0.0:0.2312:0.2115:0.5573	.	19	Q96KF2	PRAC_HUMAN	G	19	ENSP00000290294:S19G	ENSP00000290294:S19G	S	-	1	0	PRAC	44154699	0.143000	0.22626	0.001000	0.08648	0.394000	0.30568	0.626000	0.24492	-0.003000	0.14444	0.482000	0.46254	AGT	.	.		0.537	PRAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358086.1	NM_032391		C	46799700	T	C	46799700	3	2	357	1	0	0	0	0	1	0	0	0	12433	1551	54	2	126	2	PRAC	17	46799700	Missense_Mutation	SNP	T	TCGA-XR-A8TC-01A-11D-A35Z-10	178970	46799700	34395510	38	50210										
UNK	85451	hgsc.bcm.edu	37	chr17	73808617	73808617	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	ggccagtcggctggggctgcGagccatgccatgatagaaaa	15	10	0	2			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr17:73808617G>A	ENST00000589666.1	+	4	683	c.573G>A	c.(571-573)gcG>gcA	p.A191A	UNK_ENST00000293218.3_Silent_p.A267A	NM_001080419.2	NP_001073888.2	Q9C0B0	UNK_HUMAN	unkempt family zinc finger	191							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			cervix(3)|endometrium(8)|kidney(2)|large_intestine(5)|lung(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	25			all cancers(21;2.61e-06)|Epithelial(20;7.39e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|LUSC - Lung squamous cell carcinoma(166;0.154)			CTGGGGCTGCGAGCCATGCCA	0.607																																					p.A191A		Atlas-SNP	.											.	UNK	87	.	0			c.G573A						.						35	42	40					17																	73808617		2034	4190	6224	SO:0001819	synonymous_variant	85451	exon4			GGCTGCGAGCCAT	AB051540	CCDS45778.1, CCDS45778.2	17q25.3	2013-10-17	2013-10-17	2007-02-06		ENSG00000132478		"Zinc fingers, CCCH-type domain containing"	29369	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 5", "zinc finger CCCH-type containing 5", "unkempt homolog (Drosophila)"	ZC3HDC5, ZC3H5		11214970	Standard	NM_001080419		Approved	KIAA1753	uc021udd.2	Q9C0B0		ENST00000589666.1:c.573G>A	chr17.hg19:g.73808617G>A		116.0	0.0		89.0	41.0	NM_001080419		Silent	SNP	ENST00000589666.1	hg19	CCDS45778.2																																																																																			.	.		0.607	UNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448835.1	NM_001080419		A	73808617	G	A	73808617	2	1	357	1	0	0	0	0	0	0	0	1	17015	1045	37	1		1	UNK	17	73808617	Silent	SNP	G	TCGA-XR-A8TC-01A-11D-A35Z-10	27008917	73808617	7386593	39	50211										
RPTOR	57521	hgsc.bcm.edu	37	chr17	78931502	78931503	+	Missense_Mutation	DNP	GG	GG	TT													0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	cgtgcggatcgtccggatctGggacacagaccgtgagatga							TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr17:78931502_78931503GG>TT	ENST00000306801.3	+	29	3811_3812	c.3449_3450GG>TT	c.(3448-3450)tGG>tTT	p.W1150F	RPTOR_ENST00000575542.1_3'UTR|RPTOR_ENST00000544334.2_Missense_Mutation_p.W992F	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	1150					cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nutrient levels (GO:0031669)|insulin receptor signaling pathway (GO:0008286)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|regulation of cell size (GO:0008361)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|TORC1 complex (GO:0031931)	14-3-3 protein binding (GO:0071889)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	44						GTCCGGATCTGGGACACAGACC	0.619																																					p.W1150L|p.W1150C		Atlas-SNP	.											RPTOR,colon,carcinoma,0,1|.	RPTOR	122	.	0			c.G3449T|c.G3450T						.																																			SO:0001583	missense	57521	exon29			GGATCTGGGACAC|GATCTGGGACACA		CCDS11773.1, CCDS54175.1	17q25.3	2013-01-10				ENSG00000141564		"WD repeat domain containing"	30287	protein-coding gene	gene with protein product	"regulatory associated protein of mTOR"	607130				10718198, 12150926	Standard	NM_001163034		Approved	KOG1, Mip1, KIAA1303, raptor	uc002jyt.1	Q8N122		Exception_encountered	chr17.hg19:g.78931502_78931503delinsTT	ENSP00000307272:p.Trp1150Phe	57.0|56.0	0.0		52.0|51.0	22.0|21.0	NM_020761	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Missense_Mutation	SNP	ENST00000306801.3	hg19	CCDS11773.1																																																																																			.	.		0.619	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761		TT	78931503	GG	TT	78931502	3	4	357	1	0	0	0	0	1	0	0	0	13680	1357	47	3	3563	3	RPTOR	17	78931502	Missense_Mutation	DNP	GG	TCGA-XR-A8TC-01A-11D-A35Z-10	5122885	78931502	2263708	40	50212										
PSG6	5675	hgsc.bcm.edu	37	chr19	43420327	43420327	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	ctcctccagtcccatcgcctCgctttatgatgtgtaaggtg	9	13	0	1			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr19:43420327C>T	ENST00000292125.2	-	2	421	c.377G>A	c.(376-378)cGa>cAa	p.R126Q	PSG6_ENST00000187910.2_Missense_Mutation_p.R126Q|PSG6_ENST00000402603.4_Missense_Mutation_p.R126Q|PSG6_ENST00000601833.1_Missense_Mutation_p.R55Q	NM_002782.4	NP_002773.1	Q00889	PSG6_HUMAN	pregnancy specific beta-1-glycoprotein 6	126	Ig-like V-type.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.R126Q(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(19)|ovary(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	44		Prostate(69;0.00899)				CCCATCGCCTCGCTTTATGAT	0.498																																					p.R126Q		Atlas-SNP	.											PSG6,NS,carcinoma,0,1	PSG6	89	.	1	Substitution - Missense(1)	prostate(1)	c.G377A						.						301	266	278					19																	43420327		2201	4299	6500	SO:0001583	missense	5675	exon2			TCGCCTCGCTTTA		CCDS12613.1, CCDS33038.1	19q13.2	2013-01-29			ENSG00000170848	ENSG00000170848		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9523	protein-coding gene	gene with protein product		176395				1690992	Standard	NM_002782		Approved			Q00889	OTTHUMG00000151127	ENST00000292125.2:c.377G>A	chr19.hg19:g.43420327C>T	ENSP00000292125:p.Arg126Gln	70.0	0.0		91.0	8.0	NM_001031850	O75244|Q15224|Q15235|Q549K1	Missense_Mutation	SNP	ENST00000292125.2	hg19	CCDS12613.1	.	.	.	.	.	.	.	.	.	.	N	1.797	-0.478133	0.04414	.	.	ENSG00000170848	ENST00000187910;ENST00000402603;ENST00000292125;ENST00000402456	T;T;T	0.64803	-0.12;-0.12;-0.12	2.24	-4.48	0.03515	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.33089	0.0851	N	0.16037	0.36	0.09310	N	1	P;B;B	0.42584	0.784;0.132;0.128	B;B;B	0.37508	0.252;0.024;0.152	T	0.26018	-1.0115	9	0.22109	T	0.4	.	3.76	0.08601	0.1727:0.2354:0.0:0.5919	.	126;126;126	Q00889;Q00889-2;B5MCE1	PSG6_HUMAN;.;.	Q	126	ENSP00000187910:R126Q;ENSP00000385736:R126Q;ENSP00000292125:R126Q	ENSP00000187910:R126Q	R	-	2	0	PSG6	48112167	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.320000	0.00513	-1.530000	0.01751	-1.111000	0.02071	CGA	.	.		0.498	PSG6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321436.1	NM_002782		T	43420327	C	T	43420327	3	4	357	1	0	0	0	0	1	0	0	0	12671	884	31	1	989	1	PSG6	19	43420327	Missense_Mutation	SNP	C	TCGA-XR-A8TC-01A-11D-A35Z-10		43420327	15708656	41	50213										
ERCC2	2068	hgsc.bcm.edu	37	chr19	45867148	45867148	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	ccaggaaatgctcggccgtgCggatggagccaggcactgcc	15	13	0	0			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr19:45867148C>G	ENST00000391945.4	-	11	1048	c.971G>C	c.(970-972)cGc>cCc	p.R324P	ERCC2_ENST00000485403.2_Missense_Mutation_p.R300P|ERCC2_ENST00000391944.3_Missense_Mutation_p.R246P|ERCC2_ENST00000391940.4_Missense_Mutation_p.R300P|ERCC2_ENST00000221481.6_3'UTR	NM_000400.3	NP_000391.1	P18074	ERCC2_HUMAN	excision repair cross-complementation group 2	324					7-methylguanosine mRNA capping (GO:0006370)|aging (GO:0007568)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|central nervous system myelin formation (GO:0032289)|chromosome segregation (GO:0007059)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|embryonic cleavage (GO:0040016)|erythrocyte maturation (GO:0043249)|extracellular matrix organization (GO:0030198)|gene expression (GO:0010467)|hair cell differentiation (GO:0035315)|hair follicle maturation (GO:0048820)|hematopoietic stem cell differentiation (GO:0060218)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|spinal cord development (GO:0021510)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)|viral process (GO:0016032)	cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|MMXD complex (GO:0071817)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			large_intestine(4)|lung(2)|ovary(1)|pancreas(1)|stomach(1)	9		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		CTCGGCCGTGCGGATGGAGCC	0.701			"Mis, N, F, S"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.R324P		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (D)	19	19q13.2-q13.3	2068	"excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D)"		E	.	ERCC2	78	.	0			c.G971C						.						12	13	13					19																	45867148		2175	4249	6424	SO:0001583	missense	2068	exon11	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	GCCGTGCGGATGG		CCDS33049.1, CCDS46112.1	19q13.3	2014-09-17	2014-03-07		ENSG00000104884	ENSG00000104884	3.6.4.12	"General transcription factor IIH complex subunits"	3434	protein-coding gene	gene with protein product	"excision repair cross-complementing rodent repair deficiency, complementation group 2 protein", "TFIIH basal transcription factor complex helicase XPB subunit"	126340	"xeroderma pigmentosum complementary group D", "excision repair cross-complementing rodent repair deficiency, complementation group 2"	XPD		8413672, 2184031	Standard	NM_000400		Approved	MAG, EM9, MGC102762, MGC126218, MGC126219, TFIIH	uc002pbj.2	P18074	OTTHUMG00000048190	ENST00000391945.4:c.971G>C	chr19.hg19:g.45867148C>G	ENSP00000375809:p.Arg324Pro	20.0	0.0		30.0	16.0	NM_000400	Q2TB78|Q2YDY2|Q7KZU6|Q8N721	Missense_Mutation	SNP	ENST00000391945.4	hg19	CCDS33049.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.955504	0.92726	.	.	ENSG00000104884	ENST00000391941;ENST00000391942;ENST00000391945;ENST00000391944;ENST00000391940	D;D;D	0.84370	-1.84;-1.84;-1.84	5.62	5.62	0.85841	Domain of unknown function DUF1227 (1);	0.099070	0.64402	D	0.000001	D	0.94850	0.8336	H	0.95539	3.685	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	D	0.96014	0.9004	10	0.87932	D	0	-25.3123	17.1426	0.86758	0.0:1.0:0.0:0.0	.	246;300;324	E7EVE9;Q7KZU6;P18074	.;.;ERCC2_HUMAN	P	274;300;324;246;300	ENSP00000375809:R324P;ENSP00000375808:R246P;ENSP00000375804:R300P	ENSP00000375804:R300P	R	-	2	0	ERCC2	50558988	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	5.052000	0.64263	2.637000	0.89404	0.561000	0.74099	CGC	.	.		0.701	ERCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109626.2	NM_000400		G	45867148	C	G	45867148	3	3	357	1	0	0	0	0	1	0	0	0	5215	768	27	4	1420	4	ERCC2	19	45867148	Missense_Mutation	SNP	C	TCGA-XR-A8TC-01A-11D-A35Z-10	2446821	45867148	13261835	42	50214										
COL18A1	80781	hgsc.bcm.edu	37	chr21	46875754	46875756	+	In_Frame_Del	DEL	GAG	GAG	-													0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	ccgagagcccggacgcgccaGaggagaacattgccggtgtc					rs377623821	byFrequency	TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr21:46875754_46875756delGAG	ENST00000359759.4	+	1	331_333	c.310_312delGAG	c.(310-312)gagdel	p.E105del	COL18A1_ENST00000400337.2_Intron|COL18A1_ENST00000355480.5_In_Frame_Del_p.E105del			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	105					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		GGACGCGCCAGAGGAGAACATTG	0.64																																					p.103_104del		Atlas-INDEL	.											.	COL18A1	129	.	0			c.309_311del						.																																			SO:0001651	inframe_deletion	80781	exon1			.		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"Collagens"	2195	protein-coding gene	gene with protein product	"endostatin"	120328	"Knobloch syndrome, type 1"	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.310_312delGAG	chr21.hg19:g.46875757_46875759delGAG	ENSP00000352798:p.Glu105del	108.0	0.0		104.0	39.0	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	In_Frame_Del	DEL	ENST00000359759.4	hg19																																																																																				.	.		0.64	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1			-	46875756	GAG	-	46875754	7	5	357	1	0	1	0	1	0	0	0	0	3677	943	33	0	426	0	COL18A1	21	46875754	In_Frame_Del	DEL	GAG	TCGA-XR-A8TC-01A-11D-A35Z-10		46875754	1254141	43	50215										
TBC1D10A	83874	hgsc.bcm.edu	37	chr22	30722679	30722679	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	cacgcgccctcggcgccctgCgagcccacgatgaagccgaa	12	18	0	1	rs375400780		TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chr22:30722679C>A	ENST00000215790.7	-	1	356	c.192G>T	c.(190-192)tcG>tcT	p.S64S	TBC1D10A_ENST00000403477.3_Silent_p.S64S|TBC1D10A_ENST00000490449.1_5'UTR	NM_031937.2	NP_114143.1	Q9BXI6	TB10A_HUMAN	TBC1 domain family, member 10A	64					activation of cysteine-type endopeptidase activity (GO:0097202)|positive regulation of proteolysis (GO:0045862)|retrograde transport, endosome to Golgi (GO:0042147)	extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rab GTPase activator activity (GO:0005097)			cervix(2)|endometrium(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	23						CGGCGCCCTGCGAGCCCACGA	0.716																																					p.S64S		Atlas-SNP	.											.	TBC1D10A	49	.	0			c.G192T						.	C	,	2,4384		0,2,2191	17	22	20		192,192	-5	0.9	22		20	0,8550		0,0,4275	no	coding-synonymous,coding-synonymous	TBC1D10A	NM_001204240.1,NM_031937.2	,	0,2,6466	AA,AC,CC		0.0,0.0456,0.0155	,	64/516,64/509	30722679	2,12934	2193	4275	6468	SO:0001819	synonymous_variant	83874	exon1			GCCCTGCGAGCCC	AF331038	CCDS13874.1, CCDS56227.1	22q12.2	2013-07-09	2005-03-10	2005-03-10	ENSG00000099992	ENSG00000099992			23609	protein-coding gene	gene with protein product	"EBP50-PDZ interactor of 64 kD"	610020	"TBC1 domain family, member 10"	TBC1D10		11285285, 20404108	Standard	NM_001204240		Approved	EPI64, AC004997.C22.2	uc010gvu.3	Q9BXI6	OTTHUMG00000150924	ENST00000215790.7:c.192G>T	chr22.hg19:g.30722679C>A		119.0	0.0		108.0	54.0	NM_031937	B3KXT8|O76053|Q20WK7|Q543A2	Silent	SNP	ENST00000215790.7	hg19	CCDS13874.1																																																																																			.	.		0.716	TBC1D10A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320550.1	NM_031937		A	30722679	C	A	30722679	2	1	357	1	0	0	0	0	0	0	0	1	15613	755	27	1		1	TBC1D10A	22	30722679	Silent	SNP	C	TCGA-XR-A8TC-01A-11D-A35Z-10		30722679	20581887	44	50216										
RBM10	8241	hgsc.bcm.edu	37	chrX	47030582	47030582	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	gaggaggaggaggaggaggaGgatgaggaggaggaggagaa	25	0	0	2			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chrX:47030582G>T	ENST00000377604.3	+	4	1099	c.357G>T	c.(355-357)gaG>gaT	p.E119D	RBM10_ENST00000345781.6_Intron|RBM10_ENST00000329236.7_Intron	NM_001204467.1|NM_001204468.1|NM_005676.4	NP_001191396.1|NP_001191397.1|NP_005667.2	P98175	RBM10_HUMAN	RNA binding motif protein 10	119	Poly-Glu.				3'-UTR-mediated mRNA stabilization (GO:0070935)|mRNA processing (GO:0006397)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	48						aggaggaggaggatgaggagg	0.662																																					p.E184D	Melanoma(171;120 2705 19495 39241)	Atlas-SNP	.											.	RBM10	117	.	0			c.G552T						.						20	19	19					X																	47030582		2202	4294	6496	SO:0001583	missense	8241	exon4			GGAGGAGGATGAG	U35373	CCDS14274.1, CCDS56600.1, CCDS75969.1	Xp11.3	2014-06-09			ENSG00000182872	ENSG00000182872		"Zinc fingers, RAN-binding domain containing", "G patch domain containing", "RNA binding motif (RRM) containing"	9896	protein-coding gene	gene with protein product		300080				8590280, 8808293	Standard	NM_005676		Approved	DXS8237E, KIAA0122, GPATC9, ZRANB5, GPATCH9	uc004dhi.3	P98175	OTTHUMG00000021432	ENST00000377604.3:c.357G>T	chrX.hg19:g.47030582G>T	ENSP00000366829:p.Glu119Asp	99.0	0.0		110.0	5.0	NM_001204468	C4AM81|Q14136|Q5JRR2|Q9BTE4|Q9BTX0|Q9NTB1	Missense_Mutation	SNP	ENST00000377604.3	hg19	CCDS14274.1	.	.	.	.	.	.	.	.	.	.	G	7.514	0.655267	0.14580	.	.	ENSG00000182872	ENST00000377604	T	0.11169	2.8	3.1	1.15	0.20763	Nucleotide-binding, alpha-beta plait (1);	0.859005	0.09469	N	0.797951	T	0.04815	0.0130	N	0.08118	0	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.38628	-0.9652	10	0.11182	T	0.66	-1.7872	6.9396	0.24486	0.0:0.0:0.4873:0.5127	.	184;119;119	Q7Z3D7;P98175-2;P98175	.;.;RBM10_HUMAN	D	119	ENSP00000366829:E119D	ENSP00000366829:E119D	E	+	3	2	RBM10	46915526	1.000000	0.71417	0.776000	0.31678	0.914000	0.54420	0.961000	0.29267	0.165000	0.19558	0.502000	0.49764	GAG	.	.		0.662	RBM10-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056381.1	NM_005676		T	47030582	G	T	47030582	3	4	357	1	0	0	0	0	1	0	0	0	13126	991	35	3	367	3	RBM10	23	47030582	Missense_Mutation	SNP	G	TCGA-XR-A8TC-01A-11D-A35Z-10		47030582	108239978	45	50217										
SUV39H1	6839	hgsc.bcm.edu	37	chrX	48558697	48558697	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	aaggccaagcagaggcgggcGctccgtcgctgggagcagga	18	11	0	1			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chrX:48558697G>C	ENST00000376687.3	+	3	571	c.381G>C	c.(379-381)gcG>gcC	p.A127A	AF196970.3_ENST00000416061.1_RNA|SUV39H1_ENST00000453214.2_Intron|SUV39H1_ENST00000337852.6_Silent_p.A138A	NM_003173.2	NP_003164.1	O43463	SUV91_HUMAN	suppressor of variegation 3-9 homolog 1 (Drosophila)	127					cell cycle (GO:0007049)|cell differentiation (GO:0030154)|chromatin organization (GO:0006325)|chromatin silencing at rDNA (GO:0000183)|histone H3-K9 dimethylation (GO:0036123)|histone H3-K9 trimethylation (GO:0036124)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|rRNA processing (GO:0006364)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin silencing complex (GO:0005677)|chromosome, centromeric region (GO:0000775)|condensed nuclear chromosome (GO:0000794)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|rDNA heterochromatin (GO:0033553)	chromatin binding (GO:0003682)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|protein N-terminus binding (GO:0047485)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	14						AGAGGCGGGCGCTCCGTCGCT	0.662																																					p.A127A		Atlas-SNP	.											.	SUV39H1	36	.	0			c.G381C						.						25	22	23					X																	48558697		2201	4299	6500	SO:0001819	synonymous_variant	6839	exon3			GCGGGCGCTCCGT	AF019968	CCDS14304.1, CCDS65252.1	Xp11.23	2011-07-01	2001-11-28		ENSG00000101945	ENSG00000101945		"Chromatin-modifying enzymes / K-methyltransferases"	11479	protein-coding gene	gene with protein product		300254	"suppressor of variegation 3-9 (Drosophila) homolog 1"	SUV39H		10202156	Standard	NM_001282166		Approved	KMT1A	uc004dkn.3	O43463	OTTHUMG00000022701	ENST00000376687.3:c.381G>C	chrX.hg19:g.48558697G>C		179.0	0.0		188.0	78.0	NM_003173	B2R6E8|B4DST0|Q53G60|Q6FHK6	Silent	SNP	ENST00000376687.3	hg19	CCDS14304.1	.	.	.	.	.	.	.	.	.	.	G	2.233	-0.375765	0.05034	.	.	ENSG00000101945	ENST00000448548	.	.	.	4.82	-9.65	0.00537	.	0.191102	0.44902	D	0.000408	T	0.44265	0.1285	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57562	-0.7790	6	0.30854	T	0.27	.	5.8447	0.18659	0.6066:0.2217:0.0944:0.0773	.	.	.	.	P	127	.	ENSP00000410043:A127P	A	+	1	0	SUV39H1	48443641	0.000000	0.05858	0.073000	0.20177	0.568000	0.35870	-2.881000	0.00715	-2.425000	0.00561	-1.189000	0.01698	GCT	.	.		0.662	SUV39H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058909.1	NM_003173		C	48558697	G	C	48558697	2	2	357	1	0	0	0	0	0	0	0	1	15427	1074	38	4		4	SUV39H1	23	48558697	Silent	SNP	G	TCGA-XR-A8TC-01A-11D-A35Z-10	1528115	48558697	106711863	46	50218										
VSIG4	11326	hgsc.bcm.edu	37	chrX	65242305	65242305	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0652173913043478	3	1	1.02539912917271	2.42367066895369	0	0.1	0.617038875103394	0	tgcgaagatggccaccctcaTggtttctccagagtcgttgg	12	11	2	2			TCGA-XR-A8TC-01A-11D-A35Z-10	TCGA-XR-A8TC-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f6f8eb64-43ca-4cbb-996d-6a32332040cb	7fbbfbff-4266-4236-98a1-03b439b86b0a	g.chrX:65242305T>A	ENST00000374737.4	-	8	1108	c.1000A>T	c.(1000-1002)Atg>Ttg	p.M334L	VSIG4_ENST00000455586.2_3'UTR|VSIG4_ENST00000412866.2_Missense_Mutation_p.M240L	NM_001257403.1|NM_007268.2	NP_001244332.1|NP_009199.1	Q9Y279	VSIG4_HUMAN	V-set and immunoglobulin domain containing 4	334					complement activation, alternative pathway (GO:0006957)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of T cell proliferation (GO:0042130)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						GCCACCCTCATGGTTTCTCCA	0.567																																					p.M334L		Atlas-SNP	.											.	VSIG4	54	.	0			c.A1000T						.						59	42	47					X																	65242305		2203	4300	6503	SO:0001583	missense	11326	exon8			CCCTCATGGTTTC	AJ132502	CCDS14383.1, CCDS48132.1, CCDS55435.1	Xq12-q13.3	2013-01-29			ENSG00000155659	ENSG00000155659		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17032	protein-coding gene	gene with protein product		300353				10899594, 11004523, 17016555, 17016562	Standard	NM_007268		Approved	Z39IG	uc004dwh.2	Q9Y279	OTTHUMG00000021727	ENST00000374737.4:c.1000A>T	chrX.hg19:g.65242305T>A	ENSP00000363869:p.Met334Leu	100.0	0.0		112.0	28.0	NM_007268	Q6UXI4	Missense_Mutation	SNP	ENST00000374737.4	hg19	CCDS14383.1	.	.	.	.	.	.	.	.	.	.	T	0.593	-0.832346	0.02713	.	.	ENSG00000155659	ENST00000374737;ENST00000412866	T;T	0.25414	1.8;2.27	4.51	-1.35	0.09114	.	0.845481	0.10185	N	0.705309	T	0.20007	0.0481	L	0.51422	1.61	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.30909	-0.9962	10	0.56958	D	0.05	-1.622	4.7901	0.13245	0.5245:0.0:0.1633:0.3121	.	240;334	Q9Y279-3;Q9Y279	.;VSIG4_HUMAN	L	334;240	ENSP00000363869:M334L;ENSP00000394143:M240L	ENSP00000363869:M334L	M	-	1	0	VSIG4	65159030	0.010000	0.17322	0.004000	0.12327	0.023000	0.10783	0.202000	0.17295	-0.099000	0.12263	-0.567000	0.04161	ATG	.	.		0.567	VSIG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056986.1	NM_007268		A	65242305	T	A	65242305	3	1	357	1	0	0	0	0	1	0	0	0	17240	1464	51	4	203	4	VSIG4	23	65242305	Missense_Mutation	SNP	T	TCGA-XR-A8TC-01A-11D-A35Z-10	16683608	65242305	90028255	47	50219										
AJAP1	55966	hgsc.bcm.edu	37	chr1	4829928	4829928	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	tccaggtctggctgtccatcAgatcatcaccatcaccgtct	7	15	6	1			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr1:4829928A>G	ENST00000378191.4	+	3	1226	c.845A>G	c.(844-846)cAg>cGg	p.Q282R	AJAP1_ENST00000378190.3_Missense_Mutation_p.Q282R	NM_018836.3	NP_061324.1	Q9UKB5	AJAP1_HUMAN	adherens junctions associated protein 1	282					cell adhesion (GO:0007155)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|urinary_tract(1)	24	all_cancers(77;0.071)|Ovarian(185;0.0721)	all_cancers(23;1.77e-36)|all_epithelial(116;1.26e-21)|all_lung(118;3.51e-08)|Lung NSC(185;3.47e-06)|all_neural(13;8.84e-06)|all_hematologic(16;7.61e-05)|Breast(487;0.000507)|Renal(390;0.0007)|Colorectal(325;0.00117)|Hepatocellular(190;0.0071)|Glioma(11;0.0155)|Myeloproliferative disorder(586;0.0258)|Ovarian(437;0.0409)|Lung SC(97;0.133)|Medulloblastoma(700;0.215)		Epithelial(90;3.89e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.97e-19)|GBM - Glioblastoma multiforme(42;3.71e-19)|Colorectal(212;4.57e-06)|COAD - Colon adenocarcinoma(227;0.00019)|Kidney(185;0.000969)|BRCA - Breast invasive adenocarcinoma(365;0.00122)|STAD - Stomach adenocarcinoma(132;0.00578)|KIRC - Kidney renal clear cell carcinoma(229;0.0126)|READ - Rectum adenocarcinoma(331;0.0689)		GCTGTCCATCAGATCATCACC	0.552																																					p.Q282R		Atlas-SNP	.											.	AJAP1	68	.	0			c.A845G						.						216	196	203					1																	4829928		2203	4300	6503	SO:0001583	missense	55966	exon3			TCCATCAGATCAT	AF175409	CCDS54.1	1p36.32	2008-02-05	2008-01-08		ENSG00000196581	ENSG00000196581			30801	protein-coding gene	gene with protein product	"transmembrane protein SHREW1"	610972				14595118	Standard	NM_001042478		Approved	SHREW1, SHREW-1, MOT8	uc001aln.3	Q9UKB5	OTTHUMG00000000645	ENST00000378191.4:c.845A>G	chr1.hg19:g.4829928A>G	ENSP00000367433:p.Gln282Arg	62.0	0.0		75.0	16.0	NM_018836	Q9Y229	Missense_Mutation	SNP	ENST00000378191.4	hg19	CCDS54.1	.	.	.	.	.	.	.	.	.	.	A	17.15	3.315334	0.60524	.	.	ENSG00000196581	ENST00000378190;ENST00000378191	T;T	0.50548	0.74;0.74	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.58264	0.2110	L	0.32530	0.975	0.54753	D	0.999984	D	0.71674	0.998	D	0.80764	0.994	T	0.61257	-0.7099	10	0.62326	D	0.03	-28.3985	14.7407	0.69451	1.0:0.0:0.0:0.0	.	282	Q9UKB5	AJAP1_HUMAN	R	282	ENSP00000367432:Q282R;ENSP00000367433:Q282R	ENSP00000367432:Q282R	Q	+	2	0	AJAP1	4729788	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.613000	0.90913	2.081000	0.62600	0.383000	0.25322	CAG	.	.		0.552	AJAP1-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001542.3	NM_018836		G	4829928	A	G	4829928	3	3	358	1	0	0	0	0	1	0	0	0	438	188	7	2	855	2	AJAP1	1	4829928	Missense_Mutation	SNP	A	TCGA-XR-A8TD-01A-12D-A38X-10		4829928	244420693	1	50220										
OR10R2	343406	hgsc.bcm.edu	37	chr1	158449910	158449910	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	ctccacacaccaatgtacttCttccttggcattctctcaac	3	16	3	0			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr1:158449910C>A	ENST00000368152.1	+	1	243	c.243C>A	c.(241-243)ttC>ttA	p.F81L	RP11-144L1.4_ENST00000426251.1_RNA|RP11-144L1.4_ENST00000419738.1_RNA	NM_001004472.1	NP_001004472.1	Q8NGX6	O10R2_HUMAN	olfactory receptor, family 10, subfamily R, member 2	81						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F81F(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(26)|pancreas(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	41	all_hematologic(112;0.0378)					CAATGTACTTCTTCCTTGGCA	0.413																																					p.F81L		Atlas-SNP	.											OR10R2,NS,carcinoma,0,1	OR10R2	81	.	1	Substitution - coding silent(1)	lung(1)	c.C243A						.						272	232	246					1																	158449910		2203	4300	6503	SO:0001583	missense	343406	exon1			GTACTTCTTCCTT	AB065640	CCDS30898.1	1q23.1	2012-08-09			ENSG00000198965	ENSG00000198965		"GPCR / Class A : Olfactory receptors"	14820	protein-coding gene	gene with protein product							Standard	NM_001004472		Approved	OR10R2Q	uc010pik.2	Q8NGX6	OTTHUMG00000019632	ENST00000368152.1:c.243C>A	chr1.hg19:g.158449910C>A	ENSP00000357134:p.Phe81Leu	119.0	0.0		125.0	39.0	NM_001004472	Q5VWM8|Q6IFS1|Q96R61	Missense_Mutation	SNP	ENST00000368152.1	hg19	CCDS30898.1	.	.	.	.	.	.	.	.	.	.	c	13.86	2.362679	0.41902	.	.	ENSG00000198965	ENST00000368152	T	0.00269	8.37	4.28	2.41	0.29592	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00039	0.0001	L	0.43923	1.385	0.25427	N	0.988216	P	0.37548	0.599	B	0.35607	0.206	T	0.00406	-1.1759	9	0.52906	T	0.07	.	3.1243	0.06402	0.1901:0.5082:0.0:0.3018	.	81	Q8NGX6	O10R2_HUMAN	L	81	ENSP00000357134:F81L	ENSP00000357134:F81L	F	+	3	2	OR10R2	156716534	0.000000	0.05858	0.991000	0.47740	0.799000	0.45148	-0.984000	0.03755	0.429000	0.26202	0.655000	0.94253	TTC	.	.		0.413	OR10R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051847.2	NM_001004472		A	158449910	C	A	158449910	3	1	358	1	0	0	0	0	1	0	0	0	10926	912	32	3	245	3	OR10R2	1	158449910	Missense_Mutation	SNP	C	TCGA-XR-A8TD-01A-12D-A38X-10	153619982	158449910	90800711	2	50221										
RGS13	6003	hgsc.bcm.edu	37	chr1	192613528	192613528	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	aatctaagaggcccccttcaAagtaagtagcatttaagttt	7	8	2	1			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr1:192613528A>G	ENST00000391995.2	+	4	352	c.64A>G	c.(64-66)Aac>Gac	p.N22D	RGS13_ENST00000543215.1_Splice_Site_p.N22D	NM_002927.4	NP_002918.1	O14921	RGS13_HUMAN	regulator of G-protein signaling 13	22					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			endometrium(1)|kidney(1)|large_intestine(4)|lung(12)|skin(1)	19						GCCCCCTTCAAAGTAAGTAGC	0.294																																					p.N22D		Atlas-SNP	.											.	RGS13	31	.	0			c.A64G						.						113	126	121					1																	192613528		2203	4299	6502	SO:0001630	splice_region_variant	6003	exon4			CCTTCAAAGTAAG	AF030107	CCDS1376.1	1q31.2	2008-02-05	2007-08-14		ENSG00000127074	ENSG00000127074		"Regulators of G-protein signaling"	9995	protein-coding gene	gene with protein product		607190	"regulator of G-protein signalling 13"			11875076	Standard	NM_144766		Approved		uc001gsk.3	O14921	OTTHUMG00000035601	ENST00000391995.2:c.65+1A>G	chr1.hg19:g.192613528A>G		564.0	0.0		747.0	260.0	NM_002927	Q6PGR2|Q8TD63|Q9BX45	Missense_Mutation	SNP	ENST00000391995.2	hg19	CCDS1376.1	.	.	.	.	.	.	.	.	.	.	A	12.58	1.980030	0.34942	.	.	ENSG00000127074	ENST00000391995;ENST00000543215	T;T	0.28069	1.63;1.63	5.62	5.62	0.85841	.	0.584107	0.17614	N	0.167974	T	0.20210	0.0486	N	0.14661	0.345	0.30090	N	0.808437	B	0.06786	0.001	B	0.09377	0.004	T	0.08411	-1.0723	10	0.45353	T	0.12	.	12.4878	0.55883	1.0:0.0:0.0:0.0	.	22	O14921	RGS13_HUMAN	D	22	ENSP00000375853:N22D;ENSP00000442837:N22D	ENSP00000375853:N22D	N	+	1	0	RGS13	190880151	1.000000	0.71417	1.000000	0.80357	0.810000	0.45777	1.707000	0.37888	2.255000	0.74692	0.533000	0.62120	AAC	.	.		0.294	RGS13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086400.1	NM_002927	Missense_Mutation	G	192613528	A	G	192613528	5	3	358	1	0	0	0	0	0	0	1	0	13311	28	1	2	66	2	RGS13	1	192613528	Splice_Site	SNP	A	TCGA-XR-A8TD-01A-12D-A38X-10	34163618	192613528	56637093	3	50222										
SPATA17	128153	hgsc.bcm.edu	37	chr1	217856682	217856682	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	agagtacctgaaagtcgtttCagagaccaatgatgcaatta	9	7	1	4			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr1:217856682C>T	ENST00000366933.4	+	5	429	c.374C>T	c.(373-375)tCa>tTa	p.S125L		NM_138796.2	NP_620151.1	Q96L03	SPT17_HUMAN	spermatogenesis associated 17	125						cytoplasm (GO:0005737)		p.S125*(1)		endometrium(1)|kidney(1)|large_intestine(9)|lung(6)|pancreas(2)|prostate(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(81;0.0516)|all cancers(67;0.0891)|GBM - Glioblastoma multiforme(131;0.117)		AAAGTCGTTTCAGAGACCAAT	0.353																																					p.S125L		Atlas-SNP	.											SPATA17,NS,carcinoma,0,2	SPATA17	59	.	1	Substitution - Nonsense(1)	pancreas(1)	c.C374T						.						94	109	104					1																	217856682		2201	4300	6501	SO:0001583	missense	128153	exon5			TCGTTTCAGAGAC	AK098591	CCDS1519.1	1q41	2008-02-05			ENSG00000162814	ENSG00000162814			25184	protein-coding gene	gene with protein product	"IQ motif containing H"	611032				16395525	Standard	NM_138796		Approved	IQCH	uc001hlh.1	Q96L03	OTTHUMG00000037875	ENST00000366933.4:c.374C>T	chr1.hg19:g.217856682C>T	ENSP00000355900:p.Ser125Leu	423.0	0.0		459.0	86.0	NM_138796	A5D6N2	Missense_Mutation	SNP	ENST00000366933.4	hg19	CCDS1519.1	.	.	.	.	.	.	.	.	.	.	C	15.95	2.984252	0.53827	.	.	ENSG00000162814	ENST00000366933	T	0.46063	0.88	5.43	5.43	0.79202	.	0.296074	0.32401	N	0.006152	T	0.42787	0.1218	M	0.68317	2.08	0.39486	D	0.967964	B	0.25563	0.129	B	0.24394	0.053	T	0.43637	-0.9379	10	0.09338	T	0.73	-14.4113	19.2545	0.93940	0.0:1.0:0.0:0.0	.	125	Q96L03	SPT17_HUMAN	L	125	ENSP00000355900:S125L	ENSP00000355900:S125L	S	+	2	0	SPATA17	215923305	0.998000	0.40836	1.000000	0.80357	0.446000	0.32137	4.485000	0.60279	2.537000	0.85549	0.555000	0.69702	TCA	.	.		0.353	SPATA17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092433.2	NM_138796		T	217856682	C	T	217856682	3	4	358	1	0	0	0	0	1	0	0	0	15017	838	29	3	392	3	SPATA17	1	217856682	Missense_Mutation	SNP	C	TCGA-XR-A8TD-01A-12D-A38X-10	25243154	217856682	31393939	4	50223										
THADA	63892	hgsc.bcm.edu	37	chr2	43801925	43801926	+	Nonsense_Mutation	DNP	CC	CC	AA													0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	agggacgaaatctgcaccttCcacagtgagccggtgcattt							TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr2:43801925_43801926CC>AA	ENST00000405006.4	-	11	1629_1630	c.1278_1279GG>TT	c.(1276-1281)gtGGaa>gtTTaa	p.E427*	THADA_ENST00000415080.2_Nonsense_Mutation_p.E137*|THADA_ENST00000330266.7_Nonsense_Mutation_p.E137*|THADA_ENST00000405975.2_Nonsense_Mutation_p.E427*|THADA_ENST00000403856.1_Nonsense_Mutation_p.E427*|THADA_ENST00000402360.2_Nonsense_Mutation_p.E427*|THADA_ENST00000404790.1_Nonsense_Mutation_p.E427*	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	427										breast(1)|endometrium(9)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	66		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				TCTGCACCTTCCACAGTGAGCC	0.431																																					p.E427X|p.V426V		Atlas-SNP	.											.	THADA	131	.	0			c.G1279T|c.G1278T						.																																			SO:0001587	stop_gained	63892	exon11			CACCTTCCACAGT|ACCTTCCACAGTG	AY149629	CCDS46268.1, CCDS62901.1, CCDS62902.1	2p21	2008-02-05			ENSG00000115970	ENSG00000115970			19217	protein-coding gene	gene with protein product		611800				12063398, 11214970	Standard	NM_022065		Approved	FLJ21877, KIAA1767, GITA	uc002rsx.4	Q6YHU6	OTTHUMG00000152398	ENST00000405006.4:c.1278_1279delinsAA	chr2.hg19:g.43801925_43801926delinsAA	ENSP00000385995:p.Glu427*	113.0|114.0	0.0		172.0	40.0	NM_001083953	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Nonsense_Mutation|Silent	SNP	ENST00000405006.4	hg19	CCDS46268.1																																																																																			.	.		0.431	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326070.3	NM_022065		AA	43801926	CC	AA	43801925	4	1	358	1	0	0	0	0	0	1	0	0	15855	864	30	3	4694	3	THADA	2	43801925	Nonsense_Mutation	DNP	CC	TCGA-XR-A8TD-01A-12D-A38X-10		43801925	199397448	5	50224										
ANKRD53	79998	hgsc.bcm.edu	37	chr2	71212146	71212146	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	ggcacggcggtgcgcggctgCacacagtggacggccactgg	18	13	0	0			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr2:71212146C>T	ENST00000360589.3	+	6	1343	c.1309C>T	c.(1309-1311)Cac>Tac	p.H437Y	ANKRD53_ENST00000441349.1_3'UTR|ANKRD53_ENST00000457410.1_Missense_Mutation_p.H403Y|AC007040.11_ENST00000606025.1_Intron|ANKRD53_ENST00000272421.6_3'UTR	NM_001115116.1	NP_001108588.1	Q8N9V6	ANR53_HUMAN	ankyrin repeat domain 53	437										endometrium(2)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	11						TGCGCGGCTGCACACAGTGGA	0.662											OREG0014687	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.H437Y		Atlas-SNP	.											.,1	ANKRD53	55	.	0			c.C1309T						.						6	10	9					2																	71212146		674	1560	2234	SO:0001583	missense	79998	exon6			CGGCTGCACACAG	BC035234	CCDS1913.1, CCDS46321.1	2p13.3	2013-01-10			ENSG00000144031	ENSG00000144031		"Ankyrin repeat domain containing"	25691	protein-coding gene	gene with protein product							Standard	NM_024933		Approved	FLJ12056, FLJ36160	uc002shl.4	Q8N9V6	OTTHUMG00000129712	ENST00000360589.3:c.1309C>T	chr2.hg19:g.71212146C>T	ENSP00000353796:p.His437Tyr	64.0	0.0	1128	88.0	16.0	NM_001115116	Q8IYP8	Missense_Mutation	SNP	ENST00000360589.3	hg19	CCDS46321.1	.	.	.	.	.	.	.	.	.	.	C	15.67	2.902713	0.52227	.	.	ENSG00000144031	ENST00000457410;ENST00000360589	T;T	0.63255	0.05;-0.03	5.56	2.47	0.30058	.	1.366400	0.04579	N	0.394573	T	0.41213	0.1149	N	0.14661	0.345	0.09310	N	1	B	0.15473	0.013	B	0.09377	0.004	T	0.25779	-1.0122	10	0.02654	T	1	-3.9471	7.4216	0.27075	0.0:0.698:0.0:0.302	.	437	Q8N9V6	ANR53_HUMAN	Y	403;437	ENSP00000407004:H403Y;ENSP00000353796:H437Y	ENSP00000353796:H437Y	H	+	1	0	ANKRD53	71065654	0.000000	0.05858	0.037000	0.18230	0.053000	0.15095	-0.598000	0.05706	0.257000	0.21650	0.561000	0.74099	CAC	.	.		0.662	ANKRD53-004	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330275.2	NM_024933		T	71212146	C	T	71212146	3	4	358	1	0	0	0	0	1	0	0	0	679	710	25	3	1462	3	ANKRD53	2	71212146	Missense_Mutation	SNP	C	TCGA-XR-A8TD-01A-12D-A38X-10	27410221	71212146	171987227	6	50225										
ALMS1	7840	hgsc.bcm.edu	37	chr2	73613065	73613065	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	gaggaggaggaggaggaggaGgaggaagaggaggaggctgc	25	2	0	1			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr2:73613065G>A	ENST00000264448.6	+	1	180	c.69G>A	c.(67-69)gaG>gaA	p.E23E	ALMS1_ENST00000377715.1_Silent_p.E23E|ALMS1_ENST00000409009.1_Silent_p.E23E	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	23	Glu-rich.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				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						aggaggaggaggaggaagagg	0.687																																					p.E23E		Atlas-SNP	.											.	ALMS1	384	.	0			c.G69A						.						6	9	8					2																	73613065		1849	3831	5680	SO:0001819	synonymous_variant	7840	exon1			GGAGGAGGAGGAA	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.69G>A	chr2.hg19:g.73613065G>A		450.0	0.0		501.0	34.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	hg19	CCDS42697.1																																																																																			.	.		0.687	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		A	73613065	G	A	73613065	2	1	358	1	0	0	0	0	0	0	0	1	535	991	35	3		3	ALMS1	2	73613065	Silent	SNP	G	TCGA-XR-A8TD-01A-12D-A38X-10	2400919	73613065	169586308	7	50226										
DGKD	8527	hgsc.bcm.edu	37	chr2	234355412	234355412	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	cggcaggcctcctcctctacCgtcaccgaagacttcagcga	9	17	3	1			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr2:234355412C>T	ENST00000264057.2	+	12	1401	c.1389C>T	c.(1387-1389)acC>acT	p.T463T	DGKD_ENST00000409813.3_Silent_p.T419T	NM_152879.2	NP_690618.2	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa	463					blood coagulation (GO:0007596)|cell growth (GO:0016049)|diacylglycerol metabolic process (GO:0046339)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|multicellular organismal development (GO:0007275)|platelet activation (GO:0030168)|protein homooligomerization (GO:0051260)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein transport (GO:0015031)|response to organic substance (GO:0010033)|second-messenger-mediated signaling (GO:0019932)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol binding (GO:0019992)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(13)|lung(15)|ovary(1)|pancreas(1)|skin(1)	38		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Phosphatidylserine(DB00144)	CCTCCTCTACCGTCACCGAAG	0.602																																					p.T463T		Atlas-SNP	.											.	DGKD	106	.	0			c.C1389T						.						105	87	93					2																	234355412		2203	4300	6503	SO:0001819	synonymous_variant	8527	exon12			CTCTACCGTCACC	D63479	CCDS2504.1, CCDS46546.1	2q37	2013-01-10	2002-08-29		ENSG00000077044	ENSG00000077044		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	2851	protein-coding gene	gene with protein product	"diglyceride kinase"	601826	"diacylglycerol kinase, delta (130kD)"			8626538, 12810723	Standard	NM_003648		Approved	KIAA0145, DGKdelta	uc002vui.1	Q16760	OTTHUMG00000133290	ENST00000264057.2:c.1389C>T	chr2.hg19:g.234355412C>T		77.0	0.0		62.0	22.0	NM_152879	Q14158|Q6PK55|Q8NG53	Silent	SNP	ENST00000264057.2	hg19	CCDS2504.1																																																																																			.	.		0.602	DGKD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257072.2	NM_003648		T	234355412	C	T	234355412	2	4	358	1	0	0	0	0	0	0	0	1	4469	639	23	1		1	DGKD	2	234355412	Silent	SNP	C	TCGA-XR-A8TD-01A-12D-A38X-10	160742347	234355412	8843961	8	50227										
ACPP	55	hgsc.bcm.edu	37	chr3	132061467	132061467	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	tttggaatttggagtaaagtCtacgaccctttatattgtga	9	5	1	1			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr3:132061467C>A	ENST00000336375.5	+	6	717	c.627C>A	c.(625-627)gtC>gtA	p.V209V	ACPP_ENST00000351273.7_Silent_p.V209V|ACPP_ENST00000475741.1_Silent_p.V176V	NM_001099.4	NP_001090.2	P15309	PPAP_HUMAN	acid phosphatase, prostate	209					adenosine metabolic process (GO:0046085)|dephosphorylation (GO:0016311)|nucleotide metabolic process (GO:0009117)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|purine nucleobase metabolic process (GO:0006144)|regulation of sensory perception of pain (GO:0051930)|thiamine metabolic process (GO:0006772)	apical part of cell (GO:0045177)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi cisterna (GO:0031985)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|vesicle membrane (GO:0012506)	5'-nucleotidase activity (GO:0008253)|acid phosphatase activity (GO:0003993)|choline binding (GO:0033265)|identical protein binding (GO:0042802)|lysophosphatidic acid phosphatase activity (GO:0052642)|phosphatase activity (GO:0016791)|thiamine phosphate phosphatase activity (GO:0042131)			NS(1)|breast(1)|endometrium(2)|large_intestine(5)|lung(13)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	27						GGAGTAAAGTCTACGACCCTT	0.313																																					p.V209V		Atlas-SNP	.											.	ACPP	118	.	0			c.C627A						.						101	106	104					3																	132061467		2203	4300	6503	SO:0001819	synonymous_variant	55	exon6			TAAAGTCTACGAC		CCDS3073.1, CCDS46916.1	3q22.1	2012-05-16			ENSG00000014257	ENSG00000014257	3.1.3.2		125	protein-coding gene	gene with protein product		171790					Standard	NM_001099		Approved	ACP3, ACP-3	uc003eop.4	P15309	OTTHUMG00000159650	ENST00000336375.5:c.627C>A	chr3.hg19:g.132061467C>A		97.0	0.0		62.0	9.0	NM_001099	D3DNC6|Q5FBY0|Q96KY0|Q96QK9|Q96QM0	Silent	SNP	ENST00000336375.5	hg19	CCDS3073.1																																																																																			.	.		0.313	ACPP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000356699.2	NM_001099		A	132061467	C	A	132061467	2	1	358	1	0	0	0	0	0	0	0	1	167	900	32	3		3	ACPP	3	132061467	Silent	SNP	C	TCGA-XR-A8TD-01A-12D-A38X-10		132061467	65960963	9	50228										
NLGN1	22871	hgsc.bcm.edu	37	chr3	173998485	173998485	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	atctcaatgacatttctcagTatacctctacaacaactaaa	2	11	3	1			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr3:173998485T>G	ENST00000457714.1	+	7	2293	c.1864T>G	c.(1864-1866)Tat>Gat	p.Y622D	NLGN1_ENST00000401917.3_Missense_Mutation_p.Y662D|NLGN1_ENST00000361589.4_Missense_Mutation_p.Y622D|NLGN1_ENST00000545397.1_Missense_Mutation_p.Y622D	NM_014932.2	NP_055747.1	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	639					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|calcium-dependent cell-cell adhesion (GO:0016339)|cytoskeletal matrix organization at active zone (GO:0048789)|establishment of protein localization (GO:0045184)|heterophilic cell-cell adhesion (GO:0007157)|N-methyl-D-aspartate receptor clustering (GO:0097114)|nervous system development (GO:0007399)|neurexin clustering (GO:0097115)|neuron cell-cell adhesion (GO:0007158)|neuronal signal transduction (GO:0023041)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|positive regulation of synaptic vesicle exocytosis (GO:2000302)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|protein homooligomerization (GO:0051260)|protein localization to synapse (GO:0035418)|protein targeting (GO:0006605)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuron differentiation (GO:0045664)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|synapse assembly (GO:0007416)|synaptic vesicle clustering (GO:0097091)|synaptic vesicle targeting (GO:0016080)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|filopodium tip (GO:0032433)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|PDZ domain binding (GO:0030165)|protein dimerization activity (GO:0046983)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(2)|lung(54)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	83	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			CATTTCTCAGTATACCTCTAC	0.413																																					p.Y622D		Atlas-SNP	.											.	NLGN1	209	.	0			c.T1864G						.						123	121	122					3																	173998485		2203	4300	6503	SO:0001583	missense	22871	exon7			TCTCAGTATACCT	AB028993	CCDS3222.1	3q26.32	2008-07-18			ENSG00000169760	ENSG00000169760			14291	protein-coding gene	gene with protein product		600568				10767552, 10819331	Standard	NM_014932		Approved	KIAA1070	uc003fio.1	Q8N2Q7	OTTHUMG00000157005	ENST00000457714.1:c.1864T>G	chr3.hg19:g.173998485T>G	ENSP00000392500:p.Tyr622Asp	132.0	0.0		136.0	31.0	NM_014932	Q9UPT2	Missense_Mutation	SNP	ENST00000457714.1	hg19	CCDS3222.1	.	.	.	.	.	.	.	.	.	.	T	10.37	1.332296	0.24167	.	.	ENSG00000169760	ENST00000457714;ENST00000361589;ENST00000545397;ENST00000401917	T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.18	5.59	5.59	0.84812	.	0.146153	0.48767	D	0.000165	T	0.55114	0.1900	L	0.39245	1.2	0.37444	D	0.914541	B	0.11235	0.004	B	0.10450	0.005	T	0.57619	-0.7780	10	0.52906	T	0.07	.	14.6374	0.68699	0.0:0.0:0.0:1.0	.	622	Q8N2Q7-2	.	D	622;622;622;662	ENSP00000392500:Y622D;ENSP00000354541:Y622D;ENSP00000441108:Y622D;ENSP00000385750:Y662D	ENSP00000354541:Y622D	Y	+	1	0	NLGN1	175481179	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.266000	0.43320	2.246000	0.74042	0.533000	0.62120	TAT	.	.		0.413	NLGN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347054.3	NM_014932		G	173998485	T	G	173998485	3	3	358	1	0	0	0	0	1	0	0	0	10470	1638	57	5	1882	5	NLGN1	3	173998485	Missense_Mutation	SNP	T	TCGA-XR-A8TD-01A-12D-A38X-10	41937018	173998485	24023945	10	50229										
CCNA2	890	hgsc.bcm.edu	37	chr4	122743628	122743628	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	ccaggtaaactaatggctgaAttaaaagccagggcatcttc	9	9	1	1			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr4:122743628A>C	ENST00000274026.5	-	2	690	c.387T>G	c.(385-387)aaT>aaG	p.N129K		NM_001237.3	NP_001228	P20248	CCNA2_HUMAN	cyclin A2	129					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic G2 DNA damage checkpoint (GO:0007095)|mitotic nuclear division (GO:0007067)|organ regeneration (GO:0031100)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|response to estradiol (GO:0032355)|response to glucagon (GO:0033762)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	12						TAATGGCTGAATTAAAAGCCA	0.413																																					p.N129K		Atlas-SNP	.											.	CCNA2	30	.	0			c.T387G						.						98	96	96					4																	122743628		2203	4300	6503	SO:0001583	missense	890	exon2			GGCTGAATTAAAA		CCDS3723.1	4q27	2012-07-12			ENSG00000145386	ENSG00000145386			1578	protein-coding gene	gene with protein product		123835		CCNA, CCN1		1675006	Standard	NM_001237		Approved		uc003iec.4	P20248	OTTHUMG00000133072	ENST00000274026.5:c.387T>G	chr4.hg19:g.122743628A>C	ENSP00000274026:p.Asn129Lys	154.0	0.0		131.0	14.0	NM_001237	A8K7B6|Q2M3U6|Q4W5P4|Q6LER8	Missense_Mutation	SNP	ENST00000274026.5	hg19	CCDS3723.1	.	.	.	.	.	.	.	.	.	.	A	8.312	0.822373	0.16678	.	.	ENSG00000145386	ENST00000274026	T	0.14144	2.53	5.5	-2.16	0.07080	.	0.647659	0.14346	N	0.325384	T	0.07999	0.0200	L	0.55481	1.735	0.09310	N	1	B	0.19200	0.034	B	0.15870	0.014	T	0.44329	-0.9335	10	0.05436	T	0.98	.	2.4874	0.04601	0.5139:0.1113:0.2667:0.1081	.	129	P20248	CCNA2_HUMAN	K	129	ENSP00000274026:N129K	ENSP00000274026:N129K	N	-	3	2	CCNA2	122963078	0.462000	0.25791	0.351000	0.25721	0.772000	0.43724	0.723000	0.25939	-0.188000	0.10499	0.533000	0.62120	AAT	.	.		0.413	CCNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256712.2	NM_001237		C	122743628	A	C	122743628	3	2	358	1	0	0	0	0	1	0	0	0	2912	98	4	5	939	5	CCNA2	4	122743628	Missense_Mutation	SNP	A	TCGA-XR-A8TD-01A-12D-A38X-10		122743628	68410648	11	50230										
USP38	84640	hgsc.bcm.edu	37	chr4	144135474	144135474	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	tgtgagaaggaaaattttagAcaatgtatcactgccactgg	10	6	1	2			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr4:144135474A>G	ENST00000307017.4	+	9	2851	c.2345A>G	c.(2344-2346)gAc>gGc	p.D782G	USP38_ENST00000510377.1_Missense_Mutation_p.D782G	NM_032557.5	NP_115946.2	Q8NB14	UBP38_HUMAN	ubiquitin specific peptidase 38	782	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	33	all_hematologic(180;0.158)					AAAATTTTAGACAATGTATCA	0.363																																					p.D782G		Atlas-SNP	.											.	USP38	92	.	0			c.A2345G						.						54	53	54					4																	144135474		2203	4300	6503	SO:0001583	missense	84640	exon9			TTTTAGACAATGT	AF211481	CCDS3758.1	4q31.1	2008-02-05	2005-08-08		ENSG00000170185	ENSG00000170185		"Ubiquitin-specific peptidases"	20067	protein-coding gene	gene with protein product			"ubiquitin specific protease 38"			12838346	Standard	NM_032557		Approved	KIAA1891, HP43.8KD	uc003ijb.3	Q8NB14	OTTHUMG00000161420	ENST00000307017.4:c.2345A>G	chr4.hg19:g.144135474A>G	ENSP00000303434:p.Asp782Gly	119.0	0.0		114.0	25.0	NM_032557	B3KX93|Q3ZCV1|Q8NDF5|Q96DK6|Q96PZ6|Q9BY55	Missense_Mutation	SNP	ENST00000307017.4	hg19	CCDS3758.1	.	.	.	.	.	.	.	.	.	.	A	17.87	3.495155	0.64186	.	.	ENSG00000170185	ENST00000510377;ENST00000307017	T;T	0.33865	1.39;1.39	5.78	5.78	0.91487	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.049173	0.85682	D	0.000000	T	0.60038	0.2238	M	0.71206	2.165	0.58432	D	0.999998	D;D	0.89917	0.974;1.0	P;D	0.80764	0.88;0.994	T	0.61342	-0.7082	10	0.51188	T	0.08	-3.4351	16.1082	0.81241	1.0:0.0:0.0:0.0	.	782;782	Q8NB14;Q3ZCV1	UBP38_HUMAN;.	G	782	ENSP00000427647:D782G;ENSP00000303434:D782G	ENSP00000303434:D782G	D	+	2	0	USP38	144354924	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.355000	0.79434	2.205000	0.71048	0.482000	0.46254	GAC	.	.		0.363	USP38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364869.1	NM_032557		G	144135474	A	G	144135474	3	3	358	1	0	0	0	0	1	0	0	0	17084	275	10	2	2379	2	USP38	4	144135474	Missense_Mutation	SNP	A	TCGA-XR-A8TD-01A-12D-A38X-10	21391846	144135474	47018802	12	50231										
POU4F2	5458	hgsc.bcm.edu	37	chr4	147560457	147560457	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	agctcgagcaacgctggtggTggcggcggcggcggcggcgg	22	11	0	0	rs530695040|rs5862765		TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr4:147560457T>C	ENST00000281321.3	+	1	413	c.165T>C	c.(163-165)ggT>ggC	p.G55G	AC093887.1_ENST00000584185.1_RNA	NM_004575.2	NP_004566.2	Q12837	PO4F2_HUMAN	POU class 4 homeobox 2	55	Poly-Gly.				axon extension (GO:0048675)|axon guidance (GO:0007411)|intracellular estrogen receptor signaling pathway (GO:0030520)|MAPK cascade (GO:0000165)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|retinal ganglion cell axon guidance (GO:0031290)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	33	all_hematologic(180;0.151)					ACGCTggtggtggcggcggcg	0.761																																					p.G55G		Atlas-SNP	.											.	POU4F2	83	.	0			c.T165C						.						3	3	3					4																	147560457		1733	3503	5236	SO:0001819	synonymous_variant	5458	exon1			TGGTGGTGGCGGC	U06233	CCDS34074.1	4q31.22	2011-06-20	2007-07-13					"Homeoboxes / POU class"	9219	protein-coding gene	gene with protein product		113725	"POU domain, class 4, transcription factor 2", "POU domain class 4, transcription factor 2"	BRN3B		8332509	Standard	NM_004575		Approved	Brn-3b	uc003ikv.3	Q12837		ENST00000281321.3:c.165T>C	chr4.hg19:g.147560457T>C		121.0	0.0		122.0	5.0	NM_004575	B1PJR6|B2RC84|Q13883|Q14987	Silent	SNP	ENST00000281321.3	hg19	CCDS34074.1																																																																																			.	.		0.761	POU4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367020.1	NM_004575		C	147560457	T	C	147560457	2	2	358	1	0	0	0	0	0	0	0	1	12288	1683	59	2		2	POU4F2	4	147560457	Silent	SNP	T	TCGA-XR-A8TD-01A-12D-A38X-10	3424983	147560457	43593819	13	50232										
SPOCK3	50859	hgsc.bcm.edu	37	chr4	167675697	167675697	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	agtagcaccactcattattaGatattaaactgtccttgtat	5	8	1	1			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr4:167675697G>T	ENST00000357154.3	-	9	1039	c.902C>A	c.(901-903)tCt>tAt	p.S301Y	SPOCK3_ENST00000504953.1_Missense_Mutation_p.S298Y|SPOCK3_ENST00000502330.1_Missense_Mutation_p.S301Y|SPOCK3_ENST00000421836.2_Missense_Mutation_p.S250Y|SPOCK3_ENST00000507137.1_5'UTR|SPOCK3_ENST00000357545.4_Missense_Mutation_p.S298Y|SPOCK3_ENST00000506886.1_Missense_Mutation_p.S301Y|SPOCK3_ENST00000541637.1_Missense_Mutation_p.S203Y|SPOCK3_ENST00000535728.1_Missense_Mutation_p.S169Y|SPOCK3_ENST00000511269.1_Missense_Mutation_p.S298Y|SPOCK3_ENST00000512648.1_Missense_Mutation_p.S298Y|SPOCK3_ENST00000512681.1_Missense_Mutation_p.S203Y|SPOCK3_ENST00000541354.1_Missense_Mutation_p.S181Y|SPOCK3_ENST00000510741.1_Missense_Mutation_p.S258Y|SPOCK3_ENST00000511531.1_Missense_Mutation_p.S301Y|SPOCK3_ENST00000534949.1_Missense_Mutation_p.S205Y	NM_016950.2	NP_058646.2	Q9BQ16	TICN3_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 3	301					negative regulation of endopeptidase activity (GO:0010951)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|glycosaminoglycan binding (GO:0005539)|metalloendopeptidase inhibitor activity (GO:0008191)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	38	all_hematologic(180;0.221)	Prostate(90;0.0181)|Renal(120;0.0184)|Melanoma(52;0.0198)		GBM - Glioblastoma multiforme(119;0.02)		CTCATTATTAGATATTAAACT	0.383																																					p.S301Y		Atlas-SNP	.											.	SPOCK3	90	.	0			c.C902A						.						133	123	127					4																	167675697		2203	4300	6503	SO:0001583	missense	50859	exon9			TTATTAGATATTA	AJ001454	CCDS34095.1, CCDS54817.1, CCDS56343.1, CCDS56344.1, CCDS56346.1, CCDS56347.1, CCDS58931.1, CCDS75207.1	4q32.3	2011-10-10			ENSG00000196104	ENSG00000196104			13565	protein-coding gene	gene with protein product		607989				11751414	Standard	NM_001204352		Approved	testican-3	uc003iri.1	Q9BQ16	OTTHUMG00000161190	ENST00000357154.3:c.902C>A	chr4.hg19:g.167675697G>T	ENSP00000349677:p.Ser301Tyr	86.0	0.0		92.0	11.0	NM_016950	B2R7M7|B3KR67|B4DGK5|B4DHB4|B4DHV3|B4DI46|B4DJY3|E7EP61|F5H099|O75705|Q6UW53|Q96Q26	Missense_Mutation	SNP	ENST00000357154.3	hg19	CCDS54817.1	.	.	.	.	.	.	.	.	.	.	G	17.97	3.517725	0.64634	.	.	ENSG00000196104	ENST00000357154;ENST00000357545;ENST00000504953;ENST00000506886;ENST00000511531;ENST00000502330;ENST00000510741;ENST00000541354;ENST00000512681;ENST00000511269;ENST00000535728;ENST00000421836;ENST00000541637;ENST00000534949;ENST00000512648	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;1.84	5.64	5.64	0.86602	SPARC/Testican, calcium-binding domain (1);EF-hand-like domain (1);	0.057382	0.64402	D	0.000001	D	0.84079	0.5393	M	0.90425	3.115	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	0.999;1.0;1.0;0.999;0.999;1.0;1.0;0.999	D;D;D;D;D;D;D;D	0.91635	0.981;0.991;0.997;0.998;0.998;0.991;0.999;0.998	D	0.86420	0.1754	10	0.87932	D	0	-1.8575	20.0723	0.97728	0.0:0.0:1.0:0.0	.	203;205;250;310;258;301;298;301	B4DGK5;F5H099;B4DHB4;B4DFW5;E7EP61;Q9BQ16-2;Q9BQ16-1;Q9BQ16	.;.;.;.;.;.;.;TICN3_HUMAN	Y	301;298;298;301;301;301;258;181;203;298;169;250;203;205;298	ENSP00000349677:S301Y;ENSP00000350153:S298Y;ENSP00000425570:S298Y;ENSP00000420920:S301Y;ENSP00000423421:S301Y;ENSP00000423606:S301Y;ENSP00000426716:S258Y;ENSP00000444789:S181Y;ENSP00000426318:S203Y;ENSP00000425502:S298Y;ENSP00000441396:S169Y;ENSP00000411344:S250Y;ENSP00000445430:S203Y;ENSP00000438142:S205Y;ENSP00000426177:S298Y	ENSP00000349677:S301Y	S	-	2	0	SPOCK3	167912272	1.000000	0.71417	1.000000	0.80357	0.226000	0.24999	9.697000	0.98697	2.819000	0.97034	0.650000	0.86243	TCT	.	.		0.383	SPOCK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364091.1			T	167675697	G	T	167675697	3	4	358	1	0	0	0	0	1	0	0	0	15096	942	33	3	424	3	SPOCK3	4	167675697	Missense_Mutation	SNP	G	TCGA-XR-A8TD-01A-12D-A38X-10	20115240	167675697	23478579	14	50233										
GALNTL6	442117	hgsc.bcm.edu	37	chr4	173734692	173734692	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	ttgtgctttcatttttcagaCcaaattgcactaaaccacaa	4	10	2	1			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr4:173734692C>G	ENST00000506823.1	+	7	1398	c.741C>G	c.(739-741)aaC>aaG	p.N247K	GALNTL6_ENST00000508122.1_Splice_Site_p.N230K	NM_001034845.2	NP_001030017.2	Q49A17	GLTL6_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 6	247	Catalytic subdomain A.				protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(2)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	45						ATTTTTCAGACCAAATTGCAC	0.438																																					p.N247K		Atlas-SNP	.											.	GALNTL6	102	.	0			c.C741G						.						87	74	78					4																	173734692		2203	4300	6503	SO:0001630	splice_region_variant	442117	exon7			TTCAGACCAAATT		CCDS34104.1	4q34.1	2014-03-13	2014-03-13		ENSG00000174473	ENSG00000174473		"Glycosyltransferase family 2 domain containing"	33844	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase-like 6"	615138	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 6"				Standard	NM_001034845		Approved	GALNT17, GalNAc-T6L	uc003isv.3	Q49A17	OTTHUMG00000160807	ENST00000506823.1:c.740-1C>G	chr4.hg19:g.173734692C>G		79.0	0.0		88.0	18.0	NM_001034845	Q2L4S6	Missense_Mutation	SNP	ENST00000506823.1	hg19	CCDS34104.1	.	.	.	.	.	.	.	.	.	.	C	15.13	2.741642	0.49151	.	.	ENSG00000174473	ENST00000506823;ENST00000508122	T;T	0.58358	0.34;0.34	5.97	5.13	0.70059	Glycosyl transferase, family 2 (1);	0.000000	0.64402	D	0.000002	T	0.37732	0.1014	N	0.17379	0.485	0.54753	D	0.999988	B	0.27013	0.166	B	0.31101	0.124	T	0.22556	-1.0213	10	0.42905	T	0.14	.	11.7205	0.51678	0.0:0.8648:0.0:0.1352	.	247	Q49A17	GLTL6_HUMAN	K	247;230	ENSP00000423313:N247K;ENSP00000423827:N230K	ENSP00000423313:N247K	N	+	3	2	GALNTL6	173971267	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.685000	0.46959	2.836000	0.97738	0.655000	0.94253	AAC	.	.		0.438	GALNTL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362395.1	NM_001034845	Missense_Mutation	G	173734692	C	G	173734692	5	3	358	1	0	0	0	0	0	0	1	0	6233	521	18	4	763	4	GALNTL6	4	173734692	Splice_Site	SNP	C	TCGA-XR-A8TD-01A-12D-A38X-10	6058995	173734692	17419584	15	50234										
KIAA0947	23379	hgsc.bcm.edu	37	chr5	5463128	5463128	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	aagcaaccctgtgaggaagaAacacttggaacctgtgaaga	11	8	0	4			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr5:5463128A>G	ENST00000296564.7	+	13	3903	c.3681A>G	c.(3679-3681)gaA>gaG	p.E1227E		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		1227					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						GTGAGGAAGAAACACTTGGAA	0.368																																					p.E1227E		Atlas-SNP	.											.	KIAA0947	301	.	0			c.A3681G						.						48	48	48					5																	5463128		1847	4087	5934	SO:0001819	synonymous_variant	23379	exon13			GGAAGAAACACTT																												ENST00000296564.7:c.3681A>G	chr5.hg19:g.5463128A>G		171.0	0.0		165.0	42.0	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Silent	SNP	ENST00000296564.7	hg19	CCDS47187.1																																																																																			.	.		0.368	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1			G	5463128	A	G	5463128	2	3	358	1	0	0	0	0	0	0	0	1	8211	11	1	2		2	KIAA0947	5	5463128	Silent	SNP	A	TCGA-XR-A8TD-01A-12D-A38X-10		5463128	175452132	16	50235										
SRD5A1	6715	hgsc.bcm.edu	37	chr5	6633889	6633889	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	gctgccctcgctggccctgcCgctctaccagtacgccagcg	11	19	1	0			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr5:6633889C>A	ENST00000274192.5	+	1	434	c.200C>A	c.(199-201)cCg>cAg	p.P67Q	SRD5A1_ENST00000538824.1_Missense_Mutation_p.R76S|NSUN2_ENST00000264670.6_5'Flank|SRD5A1_ENST00000504286.1_3'UTR|NSUN2_ENST00000506139.1_5'Flank|NSUN2_ENST00000539938.1_5'Flank|SRD5A1_ENST00000537411.1_Missense_Mutation_p.R76S	NM_001047.2	NP_001038.1	P18405	S5A1_HUMAN	steroid-5-alpha-reductase, alpha polypeptide 1 (3-oxo-5 alpha-steroid delta 4-dehydrogenase alpha 1)	67				Missing (in Ref. 4; AAF14869). {ECO:0000305}.	androgen biosynthetic process (GO:0006702)|cell differentiation (GO:0030154)|sex determination (GO:0007530)|sex differentiation (GO:0007548)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	3-oxo-5-alpha-steroid 4-dehydrogenase activity (GO:0003865)|cholestenone 5-alpha-reductase activity (GO:0047751)|electron carrier activity (GO:0009055)			endometrium(3)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19					Dutasteride(DB01126)|Finasteride(DB01216)|Levonorgestrel(DB00367)|Spironolactone(DB00421)	CTGGCCCTGCCGCTCTACCAG	0.706																																					p.P67Q		Atlas-SNP	.											.	SRD5A1	31	.	0			c.C200A						.						15	16	16					5																	6633889		2164	4230	6394	SO:0001583	missense	6715	exon1			CCCTGCCGCTCTA	M32313	CCDS3870.1	5p15.31	2008-02-05			ENSG00000145545	ENSG00000145545	1.3.99.5		11284	protein-coding gene	gene with protein product		184753				1686016	Standard	XR_427663		Approved		uc003jdw.3	P18405	OTTHUMG00000090456	ENST00000274192.5:c.200C>A	chr5.hg19:g.6633889C>A	ENSP00000274192:p.Pro67Gln	10.0	0.0		17.0	7.0	NM_001047	B2R7Q1|Q9UHY4|Q9UP36|Q9UP37	Missense_Mutation	SNP	ENST00000274192.5	hg19	CCDS3870.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.7|22.7	4.322329|4.322329	0.81580|0.81580	.|.	.|.	ENSG00000145545|ENSG00000145545	ENST00000274192|ENST00000537411;ENST00000538824	T|T	0.25085|0.23950	1.82|1.88	3.6|3.6	3.6|3.6	0.41247|0.41247	.|.	0.059678|.	0.64402|.	D|.	0.000002|.	T|T	0.48840|0.48840	0.1522|0.1522	M|M	0.85197|0.85197	2.74|2.74	0.34530|0.34530	D|D	0.70915|0.70915	D|D	0.55605|0.59767	0.972|0.986	D|P	0.65573|0.58780	0.936|0.845	T|T	0.68345|0.68345	-0.5433|-0.5433	10|9	0.52906|0.87932	T|D	0.07|0	-11.7956|-11.7956	12.6006|12.6006	0.56494|0.56494	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	67|76	P18405|F5GXK9	S5A1_HUMAN|.	Q|S	67|76	ENSP00000274192:P67Q|ENSP00000440186:R76S	ENSP00000274192:P67Q|ENSP00000446275:R76S	P|R	+|+	2|1	0|0	SRD5A1|SRD5A1	6686889|6686889	0.854000|0.854000	0.29725|0.29725	0.996000|0.996000	0.52242|0.52242	0.912000|0.912000	0.54170|0.54170	1.846000|1.846000	0.39289|0.39289	2.005000|2.005000	0.58758|0.58758	0.643000|0.643000	0.83706|0.83706	CCG|CGC	.	.		0.706	SRD5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206903.1	NM_001047		A	6633889	C	A	6633889	3	1	358	1	0	0	0	0	1	0	0	0	15153	652	23	1	202	1	SRD5A1	5	6633889	Missense_Mutation	SNP	C	TCGA-XR-A8TD-01A-12D-A38X-10	1170761	6633889	174281371	17	50236										
OCLN	100506658	hgsc.bcm.edu	37	chr5	68805179	68805179	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	cctgtgtggcctccacgcttGcctgggacagaggctatgga	14	12	0	1			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr5:68805179G>T	ENST00000355237.2	+	3	698	c.262G>T	c.(262-264)Gcc>Tcc	p.A88S	OCLN_ENST00000538151.1_Intron|OCLN_ENST00000380766.2_Missense_Mutation_p.A88S|OCLN_ENST00000396442.2_Missense_Mutation_p.A88S|OCLN_ENST00000542132.1_Intron	NM_002538.3	NP_002529.1	Q16625	OCLN_HUMAN	occludin	88	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				apoptotic process (GO:0006915)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|protein complex assembly (GO:0006461)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethionine metabolic process (GO:0046500)|tight junction assembly (GO:0070830)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	protein domain specific binding (GO:0019904)|structural molecule activity (GO:0005198)|thiopurine S-methyltransferase activity (GO:0008119)			endometrium(2)|large_intestine(1)|liver(1)|prostate(1)|skin(1)	6		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)		CTCCACGCTTGCCTGGGACAG	0.507																																					p.A88S		Atlas-SNP	.											.	OCLN	22	.	0			c.G262T						.						189	178	182					5																	68805179		2203	4300	6503	SO:0001583	missense	100506658	exon3			ACGCTTGCCTGGG	U49184	CCDS4006.1, CCDS54864.1	5q13.1	2014-06-13			ENSG00000197822	ENSG00000197822			8104	protein-coding gene	gene with protein product	"tight junction protein occludin TM4 minus", "phosphatase 1, regulatory subunit 115"	602876				8601611	Standard	NM_002538		Approved	PPP1R115	uc003jwu.3	Q16625	OTTHUMG00000099356	ENST00000355237.2:c.262G>T	chr5.hg19:g.68805179G>T	ENSP00000347379:p.Ala88Ser	128.0	0.0		163.0	29.0	NM_001205254	B5BU70|D2DU64|D2DU65|D2IGC0|D2IGC1|E2CYV9|Q5U1V4|Q8N6K1	Missense_Mutation	SNP	ENST00000355237.2	hg19	CCDS4006.1	.	.	.	.	.	.	.	.	.	.	G	15.90	2.968669	0.53614	.	.	ENSG00000197822	ENST00000355237;ENST00000396442;ENST00000380766	T;T;T	0.60040	0.22;0.22;1.73	6.04	6.04	0.98038	Marvel (1);MARVEL-like domain (1);	0.146506	0.64402	D	0.000009	T	0.69314	0.3097	M	0.79475	2.455	0.80722	D	1	P	0.43024	0.798	P	0.50378	0.639	T	0.71563	-0.4555	10	0.62326	D	0.03	-29.4195	14.0093	0.64486	0.0:0.2528:0.7472:0.0	.	88	Q16625	OCLN_HUMAN	S	88	ENSP00000347379:A88S;ENSP00000379719:A88S;ENSP00000370143:A88S	ENSP00000347379:A88S	A	+	1	0	OCLN	68840935	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.110000	0.57831	2.873000	0.98535	0.563000	0.77884	GCC	.	.		0.507	OCLN-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216794.1	NM_002538		T	68805179	G	T	68805179	3	4	358	1	0	0	0	0	1	0	0	0	10829	1319	46	3	268	3	OCLN	5	68805179	Missense_Mutation	SNP	G	TCGA-XR-A8TD-01A-12D-A38X-10	62171290	68805179	112110081	18	50237										
PCDHA3	56145	hgsc.bcm.edu	37	chr5	140182420	140182420	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	gcgggcgtgccgcctctgggCagcaacgtgacgctgcaggt	17	13	1	1			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr5:140182420C>A	ENST00000522353.2	+	1	1638	c.1638C>A	c.(1636-1638)ggC>ggA	p.G546G	PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000532566.2_Silent_p.G546G|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000520672.2_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	546	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGCCTCTGGGCAGCAACGTGA	0.677																																					p.G546G		Atlas-SNP	.											.	PCDHA3	396	.	0			c.C1638A						.						88	89	89					5																	140182420		2203	4298	6501	SO:0001819	synonymous_variant	56145	exon1			TCTGGGCAGCAAC	AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"Cadherins / Protocadherins : Clustered"	8669	other	complex locus constituent	"KIAA0345-like 11"	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.1638C>A	chr5.hg19:g.140182420C>A		54.0	0.0		55.0	13.0	NM_031497	O75286	Silent	SNP	ENST00000522353.2	hg19	CCDS54915.1																																																																																			.	.		0.677	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906		A	140182420	C	A	140182420	2	1	358	1	0	0	0	0	0	0	0	1	11534	697	25	3		3	PCDHA3	5	140182420	Silent	SNP	C	TCGA-XR-A8TD-01A-12D-A38X-10	71377241	140182420	40732840	19	50238										
SPRY4	81848	hgsc.bcm.edu	37	chr5	141694360	141694361	+	In_Frame_Ins	INS	-	-	TGC													0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	gagccgttggtcagaggatgINStgctgctgctgctgctcaca							TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr5:141694360_141694361insTGC	ENST00000434127.2	-	2	556_557	c.313_314insGCA	c.(313-315)aca>aGCAca	p.104_105insS	SPRY4_ENST00000503582.1_5'Flank|SPRY4_ENST00000344120.4_In_Frame_Ins_p.127_128insS	NM_001127496.1	NP_001120968.1	Q9C004	SPY4_HUMAN	sprouty homolog 4 (Drosophila)	104	Poly-Ser.				multicellular organismal development (GO:0007275)|negative regulation of MAP kinase activity (GO:0043407)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(7)|ovary(1)	18		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTCAGAGGATGTGCTGCTGCTG	0.658									Testicular Cancer, Familial Clustering of																												p.T128delinsST		Atlas-INDEL	.											.	SPRY4	31	.	0			c.383_384insGCA						.		,	1,4263		0,1,2131					,	5.8	1			70	2,8250		0,2,4124	no	coding,coding	SPRY4	NM_030964.3,NM_001127496.1	,	0,3,6255	A1A1,A1R,RR		0.0242,0.0235,0.024	,	,		3,12513				SO:0001652	inframe_insertion	81848	exon3	Familial Cancer Database		.	AF227516	CCDS4274.1, CCDS47296.1	5q31.3	2010-08-05			ENSG00000187678	ENSG00000187678			15533	protein-coding gene	gene with protein product		607984				16465403	Standard	NM_030964		Approved		uc010jgi.1	Q9C004	OTTHUMG00000129663	ENST00000434127.2:c.311_313dupGCA	chr5.hg19:g.141694367_141694369dupTGC	ENSP00000399468:p.Ser106_Ser107dup	55.0	0.0		66.0	11.0	NM_030964	A4FVB2|A4FVB3|Q6QIX2|Q9C003	In_Frame_Ins	INS	ENST00000434127.2	hg19	CCDS47296.1																																																																																			.	.		0.658	SPRY4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370652.1			TGC	141694361	-	TGC	141694360	7	5	358	1	0	1	1	0	0	0	0	0	15123	1377	48	0	589	0	SPRY4	5	141694360	In_Frame_Ins	INS	-	TCGA-XR-A8TD-01A-12D-A38X-10	1511940	141694360	39220900	20	50239										
CDKN1A	1026	hgsc.bcm.edu	37	chr6	36652098	36652098	+	Frame_Shift_Del	DEL	C	C	-													0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	gtgtgcggggccttggcctgCccaagctctaccttcccacg							TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr6:36652098delC	ENST00000405375.1	+	2	455	c.220delC	c.(220-222)cccfs	p.P74fs	CDKN1A_ENST00000373711.2_Frame_Shift_Del_p.P74fs|CDKN1A_ENST00000478800.1_3'UTR|CDKN1A_ENST00000244741.5_Frame_Shift_Del_p.P74fs|CDKN1A_ENST00000448526.2_Frame_Shift_Del_p.P108fs	NM_001220778.1	NP_001207707.1	P38936	CDN1A_HUMAN	cyclin-dependent kinase inhibitor 1A (p21, Cip1)	74					cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to extracellular stimulus (GO:0031668)|cellular response to ionizing radiation (GO:0071479)|cellular senescence (GO:0090398)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle (GO:0000278)|mitotic cell cycle arrest (GO:0071850)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of gene expression (GO:0010629)|negative regulation of phosphorylation (GO:0042326)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ regeneration (GO:0031100)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of DNA biosynthetic process (GO:2000278)|regulation of protein import into nucleus, translocation (GO:0033158)|response to arsenic-containing substance (GO:0046685)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to hyperoxia (GO:0055093)|response to organonitrogen compound (GO:0010243)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|stress-induced premature senescence (GO:0090400)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCNA-p21 complex (GO:0070557)	cyclin-dependent protein kinase activating kinase activity (GO:0019912)|cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|urinary_tract(5)	15						CCTTGGCCTGCCCAAGCTCTA	0.672																																					p.L73fs		Atlas-INDEL	.											.	CDKN1A	27	.	0			c.219delG						.						39	36	37					6																	36652098		2203	4300	6503	SO:0001589	frameshift_variant	1026	exon2			.	U03106	CCDS4824.1	6p21.1	2009-01-21			ENSG00000124762	ENSG00000124762			1784	protein-coding gene	gene with protein product		116899		CDKN1			Standard	NM_000389		Approved	P21, CIP1, WAF1, SDI1, CAP20, p21CIP1, p21Cip1/Waf1	uc021yzb.1	P38936	OTTHUMG00000014603	ENST00000405375.1:c.220delC	chr6.hg19:g.36652098delC	ENSP00000384849:p.Pro74fs	59.0	0.0		71.0	30.0	NM_000389	Q14010|Q6FI05|Q9BUT4	Frame_Shift_Del	DEL	ENST00000405375.1	hg19	CCDS4824.1																																																																																			.	.		0.672	CDKN1A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040354.1	NM_078467		-	36652098	C	-	36652098	7	5	358	1	0	1	0	1	0	0	0	0	3160	739	26	0	222	0	CDKN1A	6	36652098	Frame_Shift_Del	DEL	C	TCGA-XR-A8TD-01A-12D-A38X-10		36652098	134462969	21	50240										
KCNK16	83795	hgsc.bcm.edu	37	chr6	39286869	39286870	+	Frame_Shift_Del	DEL	CC	CC	-													0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	tgctggggttggtagagttgCctttggggttcacacctttc					rs146890431		TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	CC	CC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr6:39286869_39286870delCC	ENST00000373229.5	-	2	266_267	c.253_254delGG	c.(253-255)ggcfs	p.G85fs	KCNK16_ENST00000373227.4_Frame_Shift_Del_p.G85fs|KCNK16_ENST00000507712.1_Frame_Shift_Del_p.G20fs|KCNK16_ENST00000437525.2_Frame_Shift_Del_p.G85fs|KCNK16_ENST00000425054.2_Frame_Shift_Del_p.G85fs	NM_032115.3	NP_115491.1	Q96T55	KCNKG_HUMAN	potassium channel, subfamily K, member 16	85					potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)	13						GGTAGAGTTGCCTTTGGGGTTC	0.545																																					p.85_85del		Atlas-INDEL	.											.	KCNK16	59	.	0			c.254_255del						.																																			SO:0001589	frameshift_variant	83795	exon2			.	AF358909	CCDS4843.1, CCDS47420.1, CCDS47421.1, CCDS47422.1	6p21.2-p21.1	2012-03-07			ENSG00000095981	ENSG00000095981		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	14464	protein-coding gene	gene with protein product		607369				11263999, 16382106	Standard	NM_032115		Approved	K2p16.1, TALK-1, TALK1	uc003ooq.3	Q96T55	OTTHUMG00000014645	ENST00000373229.5:c.253_254delGG	chr6.hg19:g.39286869_39286870delCC	ENSP00000362326:p.Gly85fs	61.0	0.0		81.0	38.0	NM_001135106	B5TJL9|Q2M2N9|Q5TCF3|Q6X6Z3|Q6X6Z4|Q6X6Z5|Q9H591	Frame_Shift_Del	DEL	ENST00000373229.5	hg19	CCDS4843.1																																																																																			.	.		0.545	KCNK16-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040452.2	NM_032115		-	39286870	CC	-	39286869	7	5	358	1	0	1	0	1	0	0	0	0	8072	739	26	0	1080	0	KCNK16	6	39286869	Frame_Shift_Del	DEL	CC	TCGA-XR-A8TD-01A-12D-A38X-10	2634771	39286869	131828198	22	50241										
EYS	346007	hgsc.bcm.edu	37	chr6	66204853	66204853	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	tgatggaccacttgccataaCtgtgataaaataatgtgtcc	8	8	0	2			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr6:66204853C>A	ENST00000370621.3	-	4	977	c.451G>T	c.(451-453)Gtt>Ttt	p.V151F	EYS_ENST00000342421.5_Missense_Mutation_p.V151F|EYS_ENST00000393380.2_Missense_Mutation_p.V151F|EYS_ENST00000370616.2_Missense_Mutation_p.V151F|EYS_ENST00000503581.1_Missense_Mutation_p.V151F|EYS_ENST00000370618.3_Missense_Mutation_p.V151F			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	151					detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						CTTGCCATAACTGTGATAAAA	0.428																																					p.V151F		Atlas-SNP	.											.	EYS	527	.	0			c.G451T						.						73	64	67					6																	66204853		2203	4300	6503	SO:0001583	missense	346007	exon4			CCATAACTGTGAT		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.451G>T	chr6.hg19:g.66204853C>A	ENSP00000359655:p.Val151Phe	128.0	0.0		156.0	65.0	NM_001142801	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	hg19		.	.	.	.	.	.	.	.	.	.	C	12.21	1.868234	0.32977	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616;ENST00000393380;ENST00000342421;ENST00000370618	D;D;D;D;D;D	0.87809	-2.3;-2.3;-2.3;-2.3;-2.3;-2.3	4.73	3.85	0.44370	.	.	.	.	.	T	0.77987	0.4213	N	0.08118	0	0.18873	N	0.999984	D;D;D	0.67145	0.996;0.996;0.994	D;D;D	0.71414	0.952;0.973;0.941	T	0.73000	-0.4120	9	0.35671	T	0.21	.	11.8543	0.52429	0.0:0.6615:0.3385:0.0	.	151;151;151	Q5T1H1-1;Q5T1H1-2;Q5SZM4	.;.;.	F	151	ENSP00000424243:V151F;ENSP00000359655:V151F;ENSP00000359650:V151F;ENSP00000377042:V151F;ENSP00000341818:V151F;ENSP00000359652:V151F	ENSP00000341818:V151F	V	-	1	0	EYS	66261574	0.019000	0.18553	0.929000	0.37066	0.948000	0.59901	0.112000	0.15479	1.074000	0.40909	0.591000	0.81541	GTT	.	.		0.428	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		A	66204853	C	A	66204853	3	1	358	1	0	0	0	0	1	0	0	0	5334	565	20	3	9105	3	EYS	6	66204853	Missense_Mutation	SNP	C	TCGA-XR-A8TD-01A-12D-A38X-10	26917984	66204853	104910214	23	50242										
BAI3	577	hgsc.bcm.edu	37	chr6	70070994	70070994	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	tgaaaaaagaaaatagtgaaTtgcggagaactgtgtactta	10	3	0	4			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr6:70070994T>A	ENST00000370598.1	+	29	4650	c.3829T>A	c.(3829-3831)Ttg>Atg	p.L1277M	BAI3_ENST00000546190.1_Missense_Mutation_p.L241M|BAI3_ENST00000238918.8_Missense_Mutation_p.L483M	NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	1277					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				AAATAGTGAATTGCGGAGAAC	0.398																																					p.L1277M		Atlas-SNP	.											.	BAI3	451	.	0			c.T3829A						.						90	87	88					6																	70070994		2203	4298	6501	SO:0001583	missense	577	exon29			AGTGAATTGCGGA	AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"-", "GPCR / Class B : Orphans"	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.3829T>A	chr6.hg19:g.70070994T>A	ENSP00000359630:p.Leu1277Met	82.0	0.0		98.0	30.0	NM_001704	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	ENST00000370598.1	hg19	CCDS4968.1	.	.	.	.	.	.	.	.	.	.	T	7.343	0.621257	0.14193	.	.	ENSG00000135298	ENST00000370598;ENST00000238918;ENST00000546190	T;T;T	0.07114	3.22;3.22;3.22	5.34	2.55	0.30701	.	0.060503	0.64402	D	0.000002	T	0.01287	0.0042	N	0.05383	-0.06	0.32378	N	0.554921	B;B	0.21520	0.057;0.007	B;B	0.16289	0.015;0.002	T	0.49143	-0.8970	10	0.33141	T	0.24	.	9.0313	0.36260	0.0:0.2645:0.0:0.7355	.	483;1277	B7Z356;O60242	.;BAI3_HUMAN	M	1277;483;241	ENSP00000359630:L1277M;ENSP00000238918:L483M;ENSP00000441821:L241M	ENSP00000238918:L483M	L	+	1	2	BAI3	70127715	0.889000	0.30405	0.996000	0.52242	0.729000	0.41735	0.051000	0.14141	0.283000	0.22279	-0.376000	0.06991	TTG	.	.		0.398	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			A	70070994	T	A	70070994	3	1	358	1	0	0	0	0	1	0	0	0	1300	1490	52	4	3935	4	BAI3	6	70070994	Missense_Mutation	SNP	T	TCGA-XR-A8TD-01A-12D-A38X-10	3866141	70070994	101044073	24	50243										
EPHA7	2045	hgsc.bcm.edu	37	chr6	93955017	93955017	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	tttaagagtttaagcttactCaatagtcatcctggctactg	7	8	2	1			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr6:93955017C>A	ENST00000369303.4	-	16	3065	c.2881G>T	c.(2881-2883)Gag>Tag	p.E961*		NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	961	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|ephrin receptor signaling pathway (GO:0048013)|negative chemotaxis (GO:0050919)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cell-cell adhesion (GO:0022407)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of protein autophosphorylation (GO:0031952)|retinal ganglion cell axon guidance (GO:0031290)	dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|chemorepellent activity (GO:0045499)|GPI-linked ephrin receptor activity (GO:0005004)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(1)|central_nervous_system(7)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|lung(43)|ovary(8)|pancreas(1)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(13)|urinary_tract(1)	112		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		TAAGCTTACTCAATAGTCATC	0.313																																					p.E961X		Atlas-SNP	.											.	EPHA7	251	.	0			c.G2881T						.						47	51	50					6																	93955017		2203	4300	6503	SO:0001630	splice_region_variant	2045	exon16			CTTACTCAATAGT	L36642	CCDS5031.1, CCDS75494.1	6q16.3	2013-02-11	2004-10-28		ENSG00000135333	ENSG00000135333		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3390	protein-coding gene	gene with protein product		602190	"EphA7"			9267020	Standard	NM_004440		Approved	Hek11	uc003poe.3	Q15375	OTTHUMG00000015228	ENST00000369303.4:c.2882+1G>T	chr6.hg19:g.93955017C>A		46.0	0.0		54.0	17.0	NM_004440	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Nonsense_Mutation	SNP	ENST00000369303.4	hg19	CCDS5031.1	.	.	.	.	.	.	.	.	.	.	C	42	9.561575	0.99205	.	.	ENSG00000135333	ENST00000369303	.	.	.	5.95	5.95	0.96441	.	0.106709	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	20.3812	0.98933	0.0:1.0:0.0:0.0	.	.	.	.	X	961	.	ENSP00000358309:E961X	E	-	1	0	EPHA7	94011738	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.818000	0.86416	2.821000	0.97095	0.650000	0.86243	GAG	.	.		0.313	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1		Nonsense_Mutation	A	93955017	C	A	93955017	5	1	358	1	0	0	0	0	0	0	1	0	5174	840	29	3	123	3	EPHA7	6	93955017	Splice_Site	SNP	C	TCGA-XR-A8TD-01A-12D-A38X-10	23884023	93955017	77160050	25	50244										
GPER	2852	hgsc.bcm.edu	37	chr7	1131626	1131626	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	tggtggtgaacatcagcttcCgcgagaagatgaccatcccc	11	12	1	4			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr7:1131626C>T	ENST00000297469.3	+	2	953	c.262C>T	c.(262-264)Cgc>Tgc	p.R88C	C7orf50_ENST00000397100.2_Intron|GPER1_ENST00000397088.3_Missense_Mutation_p.R88C|C7orf50_ENST00000357429.6_Intron|C7orf50_ENST00000397098.3_Intron|C7orf50_ENST00000488073.1_Intron|GPER1_ENST00000397092.1_Missense_Mutation_p.R88C|GPER1_ENST00000401670.1_Missense_Mutation_p.R88C	NM_001505.2	NP_001496.1	Q99527	GPER1_HUMAN	G protein-coupled estrogen receptor 1	88					apoptotic chromosome condensation (GO:0030263)|cell cycle (GO:0007049)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucose stimulus (GO:0071333)|cellular response to mineralocorticoid stimulus (GO:0071389)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to tumor necrosis factor (GO:0071356)|cytosolic calcium ion homeostasis (GO:0051480)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA metabolic process (GO:0051053)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gene expression (GO:0010629)|negative regulation of inflammatory response (GO:0050728)|negative regulation of leukocyte activation (GO:0002695)|negative regulation of lipid biosynthetic process (GO:0051055)|neuronal action potential (GO:0019228)|nuclear fragmentation involved in apoptotic nuclear change (GO:0030264)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of gene expression (GO:0010628)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of insulin secretion (GO:0032024)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neurogenesis (GO:0050769)|positive regulation of neurotransmitter secretion (GO:0001956)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of uterine smooth muscle contraction (GO:0070474)|positive regulation of vasodilation (GO:0045909)|steroid hormone mediated signaling pathway (GO:0043401)	axon (GO:0030424)|axon terminus (GO:0043679)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|dendritic spine head (GO:0044327)|dendritic spine membrane (GO:0032591)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|keratin filament (GO:0045095)|mitochondrial membrane (GO:0031966)|neuronal postsynaptic density (GO:0097481)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	chromatin binding (GO:0003682)|estrogen receptor activity (GO:0030284)|G-protein coupled receptor activity (GO:0004930)|mineralocorticoid receptor activity (GO:0017082)|steroid binding (GO:0005496)										CATCAGCTTCCGCGAGAAGAT	0.572																																					p.R88C		Atlas-SNP	.											.	GPER	25	.	0			c.C262T						.						150	125	133					7																	1131626		2203	4300	6503	SO:0001583	missense	2852	exon2			AGCTTCCGCGAGA	U63917	CCDS5322.1	7p22	2013-08-14	2007-07-03	2013-08-14	ENSG00000164850	ENSG00000164850			4485	protein-coding gene	gene with protein product		601805	"G protein-coupled receptor 30"	CMKRL2, GPR30, GPER		9479505, 17655271	Standard	NM_001098201		Approved	FEG-1, GPCR-Br, LERGU, LERGU2, DRY12, LyGPR, CEPR	uc003skb.2	Q99527	OTTHUMG00000023680	ENST00000297469.3:c.262C>T	chr7.hg19:g.1131626C>T	ENSP00000297469:p.Arg88Cys	137.0	0.0		125.0	41.0	NM_001505	A8K6C5|B5BUJ1|O00143|O43494|Q13631|Q6FHL1|Q96F42|Q99981	Missense_Mutation	SNP	ENST00000297469.3	hg19	CCDS5322.1	.	.	.	.	.	.	.	.	.	.	C	19.35	3.810061	0.70797	.	.	ENSG00000164850	ENST00000401670;ENST00000397092;ENST00000297469;ENST00000397088;ENST00000508834	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	5.48	5.48	0.80851	GPCR, rhodopsin-like superfamily (1);	0.114379	0.56097	D	0.000021	T	0.70509	0.3232	M	0.87180	2.865	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	T	0.76011	-0.3115	10	0.87932	D	0	-19.7876	18.349	0.90331	0.0:1.0:0.0:0.0	.	88	Q99527	GPER_HUMAN	C	88	ENSP00000385151:R88C;ENSP00000380281:R88C;ENSP00000297469:R88C;ENSP00000380277:R88C	ENSP00000297469:R88C	R	+	1	0	GPER	1098152	1.000000	0.71417	0.993000	0.49108	0.918000	0.54935	4.453000	0.60061	2.584000	0.87258	0.643000	0.83706	CGC	.	.		0.572	GPER1-030	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060001.1	NM_001039966		T	1131626	C	T	1131626	3	4	358	1	0	0	0	0	1	0	0	0	6615	652	23	1	264	1	GPER	7	1131626	Missense_Mutation	SNP	C	TCGA-XR-A8TD-01A-12D-A38X-10		1131626	158007037	26	50245										
GLI3	2737	hgsc.bcm.edu	37	chr7	42005709	42005709	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	cggctgcaggtggcgccgccCgtagccgtgggctcccccgt	16	17	0	0			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr7:42005709C>T	ENST00000395925.3	-	15	3046	c.2962G>A	c.(2962-2964)Ggg>Agg	p.G988R	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	988					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						TGGCGCCGCCCGTAGCCGTGG	0.761									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																												p.G988R		Atlas-SNP	.											.	GLI3	312	.	0			c.G2962A						.						4	5	4					7																	42005709		1829	3699	5528	SO:0001583	missense	2737	exon15	Familial Cancer Database	;	GCCGCCCGTAGCC		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"Zinc fingers, C2H2-type"	4319	protein-coding gene	gene with protein product	"zinc finger protein GLI3", "oncogene GLI3", "DNA-binding protein"	165240	"Greig cephalopolysyndactyly syndrome", "GLI-Kruppel family member GLI3", "glioma-associated oncogene family zinc finger 3"	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.2962G>A	chr7.hg19:g.42005709C>T	ENSP00000379258:p.Gly988Arg	591.0	0.0		697.0	169.0	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Missense_Mutation	SNP	ENST00000395925.3	hg19	CCDS5465.1	.	.	.	.	.	.	.	.	.	.	C	10.12	1.264134	0.23136	.	.	ENSG00000106571	ENST00000395925	T	0.14391	2.51	4.98	2.47	0.30058	.	0.372049	0.34200	N	0.004164	T	0.09818	0.0241	L	0.35854	1.095	0.80722	D	1	B	0.19331	0.035	B	0.15484	0.013	T	0.21930	-1.0231	10	0.27082	T	0.32	.	7.8654	0.29535	0.0:0.5894:0.0:0.4106	.	988	P10071	GLI3_HUMAN	R	988	ENSP00000379258:G988R	ENSP00000379258:G988R	G	-	1	0	GLI3	41972234	0.042000	0.20092	0.311000	0.25182	0.874000	0.50279	0.353000	0.20130	0.194000	0.20326	0.563000	0.77884	GGG	.	.		0.761	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168		T	42005709	C	T	42005709	3	4	358	1	0	0	0	0	1	0	0	0	6447	652	23	1	1784	1	GLI3	7	42005709	Missense_Mutation	SNP	C	TCGA-XR-A8TD-01A-12D-A38X-10	40874083	42005709	117132954	27	50246										
ANKRD7	56311	hgsc.bcm.edu	37	chr7	117879966	117879966	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	cgtaatttcctttatagataGatacccacaattcactgcga	5	10	1	2			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr7:117879966G>A	ENST00000265224.4	+	6	871	c.716G>A	c.(715-717)aGa>aAa	p.R239K	ANKRD7_ENST00000477532.1_3'UTR|ANKRD7_ENST00000357099.4_Missense_Mutation_p.R259K|ANKRD7_ENST00000417525.1_Splice_Site|ANKRD7_ENST00000433239.1_Missense_Mutation_p.R186K	NM_019644.3	NP_062618.2	Q92527	ANKR7_HUMAN	ankyrin repeat domain 7	239					male gonad development (GO:0008584)	nucleus (GO:0005634)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)	29						TTTATAGATAGATACCCACAA	0.373																																					p.R239K		Atlas-SNP	.											ANKRD7,NS,carcinoma,0,1	ANKRD7	44	.	0			c.G716A						.						102	94	96					7																	117879966		1874	4109	5983	SO:0001583	missense	56311	exon6			TAGATAGATACCC	D78334	CCDS43638.1	7q31	2013-01-10			ENSG00000106013	ENSG00000106013		"Ankyrin repeat domain containing"	18588	protein-coding gene	gene with protein product	"testis-specific ankyrin motif containing protein"	610731				8812458	Standard	NM_019644		Approved	TSA806	uc003vji.3	Q92527	OTTHUMG00000156960	ENST00000265224.4:c.716G>A	chr7.hg19:g.117879966G>A	ENSP00000265224:p.Arg239Lys	48.0	0.0		56.0	18.0	NM_019644	B4DYF5|Q96QN1|Q9UDM3	Missense_Mutation	SNP	ENST00000265224.4	hg19	CCDS43638.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.655|8.655	0.899133|0.899133	0.17686|0.17686	.|.	.|.	ENSG00000106013|ENSG00000106013	ENST00000417525|ENST00000357099;ENST00000265224;ENST00000433239	.|T;T;T	.|0.38077	.|1.18;1.29;1.16	4.01|4.01	4.01|4.01	0.46588|0.46588	.|.	.|1.421560	.|0.05562	.|U	.|0.569396	.|T	.|0.28863	.|0.0716	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	N|N	1|1	.|D	.|0.61080	.|0.989	.|B	.|0.42916	.|0.402	.|T	.|0.10474	.|-1.0628	.|10	.|0.22109	.|T	.|0.4	.|0.1982	11.8083|11.8083	0.52169|0.52169	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|239	.|Q92527	.|ANKR7_HUMAN	.|K	-1|259;239;186	.|ENSP00000349612:R259K;ENSP00000265224:R239K;ENSP00000388473:R186K	.|ENSP00000265224:R239K	.|R	+|+	.|2	.|0	ANKRD7|ANKRD7	117667202|117667202	0.835000|0.835000	0.29415|0.29415	0.098000|0.098000	0.21074|0.21074	0.045000|0.045000	0.14185|0.14185	2.060000|2.060000	0.41394|0.41394	2.241000|2.241000	0.73720|0.73720	0.455000|0.455000	0.32223|0.32223	.|AGA	.	.		0.373	ANKRD7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346826.1	NM_001077708		A	117879966	G	A	117879966	3	1	358	1	0	0	0	0	1	0	0	0	686	942	33	3	738	3	ANKRD7	7	117879966	Missense_Mutation	SNP	G	TCGA-XR-A8TD-01A-12D-A38X-10	75874257	117879966	41258697	28	50247										
ZC3HAV1	56829	hgsc.bcm.edu	37	chr7	138764367	138764367	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	taatttaaggatctggtagaAgttatatctgtggccactcc	9	7	2	1			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr7:138764367A>C	ENST00000242351.5	-	4	1636	c.1320T>G	c.(1318-1320)acT>acG	p.T440T	ZC3HAV1_ENST00000464606.1_Silent_p.T440T|ZC3HAV1_ENST00000471652.1_Silent_p.T440T	NM_020119.3	NP_064504.2	Q7Z2W4	ZCCHV_HUMAN	zinc finger CCCH-type, antiviral 1	440					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of mRNA catabolic process (GO:0061014)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(4)|skin(1)	37						ATCTGGTAGAAGTTATATCTG	0.458																																					p.T440T		Atlas-SNP	.											.	ZC3HAV1	75	.	0			c.T1320G						.						106	107	107					7																	138764367		2203	4300	6503	SO:0001819	synonymous_variant	56829	exon4			GGTAGAAGTTATA	BX571742	CCDS5851.1, CCDS55171.1	7q34	2012-07-05			ENSG00000105939	ENSG00000105939		"Zinc fingers, CCCH-type domain containing", "Poly (ADP-ribose) polymerases"	23721	protein-coding gene	gene with protein product	"zinc finger antiviral protein", " CCCH-type zinc finger antiviral protein"	607312				12215647, 12851707	Standard	NM_024625		Approved	ZAP, FLB6421, FLJ13288, MGC48898, ZC3HDC2, ZC3H2, PARP13	uc003vun.3	Q7Z2W4	OTTHUMG00000157471	ENST00000242351.5:c.1320T>G	chr7.hg19:g.138764367A>C		130.0	0.0		111.0	29.0	NM_024625	A4D1R2|A4D1S4|Q8IW57|Q8TAJ3|Q96N79|Q9H8R9|Q9P0Y7	Silent	SNP	ENST00000242351.5	hg19	CCDS5851.1																																																																																			.	.		0.458	ZC3HAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348915.1	NM_020119		C	138764367	A	C	138764367	2	2	358	1	0	0	0	0	0	0	0	1	17590	59	3	5		5	ZC3HAV1	7	138764367	Silent	SNP	A	TCGA-XR-A8TD-01A-12D-A38X-10	20884401	138764367	20374296	29	50248										
SFTPC	649	hgsc.bcm.edu	37	chr8	22021530	22021530	+	5'Flank	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	gccgtgagcaccctgtgtggCgaggtgccgctctactacat	13	13	1	1	rs529959941	byFrequency	TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr8:22021530C>T	ENST00000306385.5	+	0	0				BMP1_ENST00000354870.5_5'Flank|BMP1_ENST00000397814.3_5'Flank|BMP1_ENST00000397816.3_5'Flank|BMP1_ENST00000306349.8_5'Flank|SFTPC_ENST00000524255.1_Silent_p.G137G|SFTPC_ENST00000437090.2_3'UTR|SFTPC_ENST00000520605.1_Intron|SFTPC_ENST00000521315.1_Silent_p.G184G|SFTPC_ENST00000318561.3_Silent_p.G190G	NM_006129.4	NP_006120.1	P13497	BMP1_HUMAN	bone morphogenetic protein 1						cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lipoprotein metabolic process (GO:0042157)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of cartilage development (GO:0061036)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(3)	30				Colorectal(74;0.00229)|COAD - Colon adenocarcinoma(73;0.0661)|READ - Rectum adenocarcinoma(644;0.11)		CCCTGTGTGGCGAGGTGCCGC	0.692													C|||	5	0.000998403	0	0	5008	,	,		16831	0		0	False		,,,				2504	0.0051				p.G190G		Atlas-SNP	.											.	SFTPC	19	.	0			c.C570T						.						41	49	47					8																	22021530		2051	4182	6233	SO:0001631	upstream_gene_variant	6440	exon5			GTGTGGCGAGGTG		CCDS6026.1, CCDS34856.1	8p21	2013-02-06	2004-08-09		ENSG00000168487	ENSG00000168487	3.4.24.19	"Bone morphogenetic proteins"	1067	protein-coding gene	gene with protein product	"procollagen C-endopeptidase"	112264	"procollagen C-endopeptidase"	PCOLC		2004778	Standard	NM_006129		Approved		uc003xbg.3	P13497	OTTHUMG00000097761		chr8.hg19:g.22021530C>T	Exception_encountered	153.0	0.0		129.0	38.0	NM_003018	A8K6F5|B2RN46|D3DSR0|Q13292|Q13872|Q14874|Q99421|Q99422|Q99423|Q9UL38	Silent	SNP	ENST00000306385.5	hg19	CCDS6026.1																																																																																			.	.		0.692	BMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214995.2	NM_006132		T	22021530	C	T	22021530	1	4	358	0	1	0	0	0	0	0	0	0	14207	755	27	1		1	SFTPC	8	22021530	5'Flank	SNP	C	TCGA-XR-A8TD-01A-12D-A38X-10		22021530	124342492	30	50249										
ADAM18	8749	hgsc.bcm.edu	37	chr8	39537657	39537657	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	atatattcaagaccatgtatGtgtatctatagccactggtt	7	7	2	1			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr8:39537657G>T	ENST00000265707.5	+	16	1778	c.1733G>T	c.(1732-1734)tGt>tTt	p.C578F	ADAM18_ENST00000541111.1_5'UTR|ADAM18_ENST00000379866.1_Missense_Mutation_p.C554F	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	578	Cys-rich.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(31)|ovary(1)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)	71		all_cancers(7;1.32e-05)|all_epithelial(6;3.08e-10)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00769)|Breast(189;0.0112)	LUSC - Lung squamous cell carcinoma(45;0.000199)			GACCATGTATGTGTATCTATA	0.393																																					p.C578F		Atlas-SNP	.											.	ADAM18	169	.	0			c.G1733T						.						107	95	99					8																	39537657		2203	4300	6503	SO:0001583	missense	8749	exon16			ATGTATGTGTATC	AJ133004	CCDS6113.1, CCDS55225.1	8p11.22	2008-08-07	2005-08-18		ENSG00000168619	ENSG00000168619		"ADAM metallopeptidase domain containing"	196	protein-coding gene	gene with protein product			"a disintegrin and metalloproteinase domain 18"			12200459	Standard	NM_014237		Approved	tMDCIII, ADAM27	uc003xni.3	Q9Y3Q7	OTTHUMG00000164040	ENST00000265707.5:c.1733G>T	chr8.hg19:g.39537657G>T	ENSP00000265707:p.Cys578Phe	112.0	0.0		118.0	30.0	NM_014237	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Missense_Mutation	SNP	ENST00000265707.5	hg19	CCDS6113.1	.	.	.	.	.	.	.	.	.	.	G	13.40	2.225280	0.39300	.	.	ENSG00000168619	ENST00000265707;ENST00000379866;ENST00000522198	T;T	0.63580	-0.05;-0.05	3.85	3.85	0.44370	ADAM, cysteine-rich (2);	0.000000	0.41712	D	0.000821	D	0.82852	0.5127	H	0.94423	3.535	0.53005	D	0.999963	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.86556	0.1838	10	0.87932	D	0	.	11.5792	0.50881	0.0:0.0:1.0:0.0	.	554;578	Q9Y3Q7-2;Q9Y3Q7	.;ADA18_HUMAN	F	578;554;510	ENSP00000265707:C578F;ENSP00000369195:C554F	ENSP00000265707:C578F	C	+	2	0	ADAM18	39656814	0.802000	0.28943	0.055000	0.19348	0.010000	0.07245	3.770000	0.55310	2.451000	0.82905	0.563000	0.77884	TGT	.	.		0.393	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237		T	39537657	G	T	39537657	3	4	358	1	0	0	0	0	1	0	0	0	239	1377	48	3	1795	3	ADAM18	8	39537657	Missense_Mutation	SNP	G	TCGA-XR-A8TD-01A-12D-A38X-10	17516127	39537657	106826365	31	50250										
ARFGEF1	10565	hgsc.bcm.edu	37	chr8	68208769	68208769	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	tgcttgctaagtagatattgTaacatgttctcacagcttgc	8	8	1	1			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr8:68208769T>C	ENST00000262215.3	-	5	925	c.536A>G	c.(535-537)tAc>tGc	p.Y179C		NM_006421.4	NP_006412.2	Q9Y6D6	BIG1_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)	179	DCB; DCB:DCB domain and DCB:HUS domain interaction.				endomembrane system organization (GO:0010256)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein glycosylation in Golgi (GO:0090284)|positive regulation of wound healing (GO:0090303)|protein transport (GO:0015031)|regulation of ARF protein signal transduction (GO:0032012)|regulation of establishment of cell polarity (GO:2000114)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|small nuclear ribonucleoprotein complex (GO:0030532)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|guanyl-nucleotide exchange factor activity (GO:0005085)|myosin binding (GO:0017022)|protein kinase A regulatory subunit binding (GO:0034237)			breast(1)|endometrium(14)|kidney(4)|large_intestine(17)|lung(20)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)			GTAGATATTGTAACATGTTCT	0.363																																					p.Y179C		Atlas-SNP	.											.	ARFGEF1	196	.	0			c.A536G						.						192	170	177					8																	68208769		2203	4300	6503	SO:0001583	missense	10565	exon5			ATATTGTAACATG	AF084520	CCDS6199.1	8q13	2011-08-18	2011-08-18		ENSG00000066777	ENSG00000066777			15772	protein-coding gene	gene with protein product		604141				10212200, 8917509	Standard	NM_006421		Approved	DKFZP434L057, BIG1, ARFGEP1, p200	uc003xxo.2	Q9Y6D6	OTTHUMG00000164626	ENST00000262215.3:c.536A>G	chr8.hg19:g.68208769T>C	ENSP00000262215:p.Tyr179Cys	90.0	0.0		93.0	23.0	NM_006421	Q9NV46|Q9UFV2|Q9UNL0	Missense_Mutation	SNP	ENST00000262215.3	hg19	CCDS6199.1	.	.	.	.	.	.	.	.	.	.	T	19.31	3.802530	0.70682	.	.	ENSG00000066777	ENST00000262215	T	0.40476	1.03	4.89	3.7	0.42460	Armadillo-type fold (1);	0.067502	0.64402	D	0.000008	T	0.73329	0.3573	H	0.96142	3.775	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.79715	-0.1687	10	0.87932	D	0	.	11.8351	0.52319	0.0:0.0:0.1463:0.8537	.	179	Q9Y6D6	BIG1_HUMAN	C	179	ENSP00000262215:Y179C	ENSP00000262215:Y179C	Y	-	2	0	ARFGEF1	68371323	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.103000	0.71492	0.694000	0.31654	0.477000	0.44152	TAC	.	.		0.363	ARFGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379441.4	NM_006421		C	68208769	T	C	68208769	3	2	358	1	0	0	0	0	1	0	0	0	852	1638	57	2	5153	2	ARFGEF1	8	68208769	Missense_Mutation	SNP	T	TCGA-XR-A8TD-01A-12D-A38X-10	28671112	68208769	78155253	32	50251										
ZDHHC12	84885	hgsc.bcm.edu	37	chr9	131484347	131484347	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	tggaggaaccatggctgtctGctcctctttgagctcctcct	10	13	2	1			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr9:131484347G>C	ENST00000372663.4	-	3	268	c.256C>G	c.(256-258)Cag>Gag	p.Q86E	ZDHHC12_ENST00000467312.1_5'UTR|ZDHHC12_ENST00000372667.5_Missense_Mutation_p.Q100E|ZDHHC12_ENST00000372672.2_Missense_Mutation_p.Q86E|RP11-545E17.3_ENST00000443631.1_RNA	NM_032799.4	NP_116188	Q96GR4	ZDH12_HUMAN	zinc finger, DHHC-type containing 12	86					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			central_nervous_system(1)|ovary(2)|upper_aerodigestive_tract(1)	4						ATGGCTGTCTGCTCCTCTTTG	0.622																																					p.Q86E		Atlas-SNP	.											.	ZDHHC12	14	.	0			c.C256G						.						132	111	118					9																	131484347		2203	4300	6503	SO:0001583	missense	84885	exon3			CTGTCTGCTCCTC	AK027430	CCDS6909.1	9q34.11	2008-02-05			ENSG00000160446	ENSG00000160446		"Zinc fingers, DHHC-type"	19159	protein-coding gene	gene with protein product							Standard	NM_032799		Approved	ZNF400, FLJ14524	uc004bvy.3	Q96GR4	OTTHUMG00000020756	ENST00000372663.4:c.256C>G	chr9.hg19:g.131484347G>C	ENSP00000361748:p.Gln86Glu	103.0	0.0		115.0	23.0	NM_032799	A6NH95|B2RE03|Q5T265|Q5T267|Q5T268|Q86VT5|Q96T09	Missense_Mutation	SNP	ENST00000372663.4	hg19	CCDS6909.1	.	.	.	.	.	.	.	.	.	.	G	8.339	0.828352	0.16749	.	.	ENSG00000160446	ENST00000372663;ENST00000372672;ENST00000372667;ENST00000372664;ENST00000452105;ENST00000406904	T;T;T;T	0.25085	1.82;1.82;1.82;1.82	4.21	4.21	0.49690	.	0.263978	0.37906	N	0.001890	T	0.19525	0.0469	L	0.56280	1.765	0.26449	N	0.975632	B;B	0.33000	0.218;0.393	B;B	0.29077	0.059;0.098	T	0.24440	-1.0160	10	0.02654	T	1	.	12.4505	0.55675	0.0:0.0:1.0:0.0	.	141;86	Q96GR4-3;Q96GR4	.;ZDH12_HUMAN	E	86;86;100;86;86;141	ENSP00000361748:Q86E;ENSP00000361752:Q100E;ENSP00000387587:Q86E;ENSP00000384205:Q141E	ENSP00000361748:Q86E	Q	-	1	0	ZDHHC12	130524168	0.989000	0.36119	1.000000	0.80357	0.475000	0.33008	3.606000	0.54095	2.074000	0.62210	0.456000	0.33151	CAG	.	.		0.622	ZDHHC12-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054484.1	NM_032799		C	131484347	G	C	131484347	3	2	358	1	0	0	0	0	1	0	0	0	17617	1328	46	4	559	4	ZDHHC12	9	131484347	Missense_Mutation	SNP	G	TCGA-XR-A8TD-01A-12D-A38X-10		131484347	9729084	33	50252										
KIAA1217	56243	hgsc.bcm.edu	37	chr10	24816985	24816985	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	agtcaataccaaatctggagAtgccgccagccacaggccca	9	14	2	1			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr10:24816985A>T	ENST00000376454.3	+	14	3049	c.3019A>T	c.(3019-3021)Atg>Ttg	p.M1007L	KIAA1217_ENST00000396445.1_Missense_Mutation_p.M690L|KIAA1217_ENST00000430453.2_3'UTR|KIAA1217_ENST00000376452.3_Missense_Mutation_p.M972L|KIAA1217_ENST00000376462.1_Missense_Mutation_p.M927L|KIAA1217_ENST00000458595.1_Missense_Mutation_p.M972L|KIAA1217_ENST00000307544.6_Missense_Mutation_p.M690L|KIAA1217_ENST00000396446.1_Missense_Mutation_p.M690L|KIAA1217_ENST00000376451.2_Missense_Mutation_p.M690L	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	1007					embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						AAATCTGGAGATGCCGCCAGC	0.488																																					p.M1007L		Atlas-SNP	.											.	KIAA1217	235	.	0			c.A3019T						.						69	71	71					10																	24816985		2203	4300	6503	SO:0001583	missense	56243	exon14			CTGGAGATGCCGC	BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"sickle tail"					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.3019A>T	chr10.hg19:g.24816985A>T	ENSP00000365637:p.Met1007Leu	144.0	0.0		162.0	34.0	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Missense_Mutation	SNP	ENST00000376454.3	hg19	CCDS31165.1	.	.	.	.	.	.	.	.	.	.	A	17.46	3.394783	0.62066	.	.	ENSG00000120549	ENST00000376462;ENST00000458595;ENST00000442879;ENST00000376454;ENST00000376452;ENST00000307544;ENST00000450158;ENST00000396445;ENST00000376451;ENST00000396446	T;T;T;T;T;T;T;T	0.46819	0.86;0.86;0.86;0.86;0.86;0.86;0.86;0.86	6.11	4.98	0.66077	.	0.214995	0.52532	D	0.000077	T	0.38348	0.1037	L	0.59436	1.845	0.31062	N	0.714028	B;B;B;B;P;B;P;B	0.44006	0.169;0.126;0.066;0.08;0.824;0.447;0.649;0.264	B;B;B;B;B;B;B;B	0.38880	0.082;0.035;0.049;0.074;0.284;0.108;0.266;0.131	T	0.39961	-0.9588	10	0.10902	T	0.67	.	9.1493	0.36953	0.8619:0.0:0.1381:0.0	.	972;972;690;690;690;690;1007;1007	Q5T5P2-7;A6NLF3;Q5T5P2-4;Q5T5P2-8;Q5T5P2-3;Q5T5P2-6;Q5T5P2;Q5T5P2-2	.;.;.;.;.;.;SKT_HUMAN;.	L	927;972;690;1007;972;690;690;690;690;690	ENSP00000365645:M927L;ENSP00000392625:M972L;ENSP00000365637:M1007L;ENSP00000365635:M972L;ENSP00000302343:M690L;ENSP00000379722:M690L;ENSP00000365634:M690L;ENSP00000379723:M690L	ENSP00000302343:M690L	M	+	1	0	KIAA1217	24856991	1.000000	0.71417	1.000000	0.80357	0.815000	0.46073	3.179000	0.50887	1.142000	0.42291	0.533000	0.62120	ATG	.	.		0.488	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590		T	24816985	A	T	24816985	3	4	358	1	0	0	0	0	1	0	0	0	8225	333	12	4	3073	4	KIAA1217	10	24816985	Missense_Mutation	SNP	A	TCGA-XR-A8TD-01A-12D-A38X-10		24816985	110717762	34	50253										
OR51L1	119682	hgsc.bcm.edu	37	chr11	5020793	5020793	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	aagattatcctgtacagatgCcaggaccaacagtatttatg	8	8	0	2			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr11:5020793C>G	ENST00000321543.1	+	1	581	c.581C>G	c.(580-582)gCc>gGc	p.A194G		NM_001004755.1	NP_001004755.1	Q8NGJ5	O51L1_HUMAN	olfactory receptor, family 51, subfamily L, member 1	194						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A194D(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(19)|skin(2)|stomach(1)	31		Medulloblastoma(188;0.0061)|all_neural(188;0.0479)|Breast(177;0.086)		Epithelial(150;1.75e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGTACAGATGCCAGGACCAAC	0.428																																					p.A194G		Atlas-SNP	.											OR51L1,NS,carcinoma,0,1	OR51L1	60	.	1	Substitution - Missense(1)	lung(1)	c.C581G						.						223	190	202					11																	5020793		2201	4298	6499	SO:0001583	missense	119682	exon1			CAGATGCCAGGAC	AB065799	CCDS31369.1	11p15.4	2012-08-09			ENSG00000176798	ENSG00000176798		"GPCR / Class A : Olfactory receptors"	14759	protein-coding gene	gene with protein product							Standard	NM_001004755		Approved		uc010qyu.2	Q8NGJ5	OTTHUMG00000066605	ENST00000321543.1:c.581C>G	chr11.hg19:g.5020793C>G	ENSP00000322156:p.Ala194Gly	154.0	0.0		131.0	27.0	NM_001004755	Q6IFE5	Missense_Mutation	SNP	ENST00000321543.1	hg19	CCDS31369.1	.	.	.	.	.	.	.	.	.	.	C	12.22	1.871682	0.33069	.	.	ENSG00000176798	ENST00000321543	T	0.00158	8.65	5.18	5.18	0.71444	GPCR, rhodopsin-like superfamily (1);	0.157082	0.29916	N	0.010875	T	0.00328	0.0010	L	0.59436	1.845	0.09310	N	0.999999	D	0.67145	0.996	P	0.60173	0.87	T	0.56944	-0.7895	10	0.87932	D	0	.	10.9225	0.47174	0.0:0.9145:0.0:0.0855	.	194	Q8NGJ5	O51L1_HUMAN	G	194	ENSP00000322156:A194G	ENSP00000322156:A194G	A	+	2	0	OR51L1	4977369	0.000000	0.05858	0.992000	0.48379	0.029000	0.11900	-0.288000	0.08377	2.685000	0.91497	0.557000	0.71058	GCC	.	.		0.428	OR51L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142812.1	NM_001004755		G	5020793	C	G	5020793	3	3	358	1	0	0	0	0	1	0	0	0	11111	739	26	4	583	4	OR51L1	11	5020793	Missense_Mutation	SNP	C	TCGA-XR-A8TD-01A-12D-A38X-10		5020793	129985723	35	50254										
OR52W1	120787	hgsc.bcm.edu	37	chr11	6221115	6221115	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	ggatattctgggtatcactgGctcctatggactcattgccc	10	11	3	0			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr11:6221115G>T	ENST00000311352.2	+	1	740	c.662G>T	c.(661-663)gGc>gTc	p.G221V	RP11-290F24.6_ENST00000600308.1_lincRNA	NM_001005178.1	NP_001005178.1	Q6IF63	O52W1_HUMAN	olfactory receptor, family 52, subfamily W, member 1	221						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|kidney(2)|large_intestine(1)|lung(6)	11		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;2.13e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGTATCACTGGCTCCTATGGA	0.522																																					p.G221V		Atlas-SNP	.											OR52W1,NS,carcinoma,0,1	OR52W1	33	.	0			c.G662T						.						193	171	178					11																	6221115		2201	4296	6497	SO:0001583	missense	120787	exon1			TCACTGGCTCCTA	AB065511	CCDS31407.1	11p15.4	2012-08-09		2004-03-10	ENSG00000175485	ENSG00000175485		"GPCR / Class A : Olfactory receptors"	15239	protein-coding gene	gene with protein product				OR52W1P			Standard	NM_001005178		Approved		uc010qzz.2	Q6IF63	OTTHUMG00000165378	ENST00000311352.2:c.662G>T	chr11.hg19:g.6221115G>T	ENSP00000309673:p.Gly221Val	98.0	0.0		91.0	26.0	NM_001005178	Q8NH78	Missense_Mutation	SNP	ENST00000311352.2	hg19	CCDS31407.1	.	.	.	.	.	.	.	.	.	.	G	0.719	-0.784427	0.02907	.	.	ENSG00000175485	ENST00000311352	T	0.32753	1.44	4.7	1.54	0.23209	GPCR, rhodopsin-like superfamily (1);	0.401855	0.18065	N	0.152812	T	0.09949	0.0244	N	0.02876	-0.465	0.21355	N	0.999714	B	0.17268	0.021	B	0.15870	0.014	T	0.37103	-0.9720	10	0.02654	T	1	.	8.7092	0.34374	0.0:0.2509:0.463:0.2861	.	221	Q6IF63	O52W1_HUMAN	V	221	ENSP00000309673:G221V	ENSP00000309673:G221V	G	+	2	0	OR52W1	6177691	0.001000	0.12720	0.002000	0.10522	0.755000	0.42902	1.018000	0.30002	0.211000	0.20683	0.563000	0.77884	GGC	.	.		0.522	OR52W1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383758.1	NM_001005178		T	6221115	G	T	6221115	3	4	358	1	0	0	0	0	1	0	0	0	11141	1203	42	3	664	3	OR52W1	11	6221115	Missense_Mutation	SNP	G	TCGA-XR-A8TD-01A-12D-A38X-10	1200322	6221115	128785401	36	50255										
MAP3K11	399909	hgsc.bcm.edu	37	chr11	65380603	65380603	+	5'Flank	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	cagcacatggggaggcacgcGccgcccggccagagctcggc	16	16	0	1			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr11:65380603G>A	ENST00000355703.3	+	0	0				MAP3K11_ENST00000309100.3_Missense_Mutation_p.R209C|MAP3K11_ENST00000530153.1_5'Flank	NM_032223.2	NP_115599.2	Q9H6A9	PCX3_HUMAN	pecanex-like 3 (Drosophila)							integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)	13						GGAGGCACGCGCCGCCCGGCC	0.657																																					p.R209C		Atlas-SNP	.											.	MAP3K11	67	.	0			c.C625T						.						46	46	46					11																	65380603		2200	4297	6497	SO:0001631	upstream_gene_variant	4296	exon1			GCACGCGCCGCCC	BX640978	CCDS44650.1	11q12.1	2008-07-21			ENSG00000197136	ENSG00000197136			18760	protein-coding gene	gene with protein product						15146197	Standard	NM_032223		Approved	FLJ22427	uc001oey.2	Q9H6A9	OTTHUMG00000166539		chr11.hg19:g.65380603G>A	Exception_encountered	57.0	0.0		69.0	16.0	NM_002419	Q6MZN8	Missense_Mutation	SNP	ENST00000355703.3	hg19	CCDS44650.1	.	.	.	.	.	.	.	.	.	.	G	11.99	1.802406	0.31869	.	.	ENSG00000173327	ENST00000309100	D	0.94092	-3.35	3.92	2.95	0.34219	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000004	D	0.95367	0.8496	M	0.73753	2.245	0.37551	D	0.9187	D	0.89917	1.0	D	0.74348	0.983	D	0.95631	0.8689	10	0.87932	D	0	.	9.0887	0.36596	0.0:0.0:0.6396:0.3604	.	209	Q16584	M3K11_HUMAN	C	209	ENSP00000309597:R209C	ENSP00000309597:R209C	R	-	1	0	MAP3K11	65137179	0.961000	0.32948	0.965000	0.40720	0.059000	0.15707	1.863000	0.39459	2.027000	0.59764	0.655000	0.94253	CGC	.	.		0.657	PCNXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390321.1	NM_032223		A	65380603	G	A	65380603	1	1	358	0	1	0	0	0	0	0	0	0	9254	1087	38	1		1	MAP3K11	11	65380603	5'Flank	SNP	G	TCGA-XR-A8TD-01A-12D-A38X-10	59159488	65380603	69625913	37	50256										
OR10G4	390264	hgsc.bcm.edu	37	chr11	123886314	123886314	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	agcctcgtgacagcattcatCctcacaggccttccccatgc	7	17	2	1			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr11:123886314C>T	ENST00000320891.4	+	1	33	c.33C>T	c.(31-33)atC>atT	p.I11I		NM_001004462.1	NP_001004462.1	Q8NGN3	O10G4_HUMAN	olfactory receptor, family 10, subfamily G, member 4	11						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)|skin(4)|stomach(6)|upper_aerodigestive_tract(1)	48		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0401)		CAGCATTCATCCTCACAGGCC	0.547																																					p.I11I		Atlas-SNP	.											.	OR10G4	77	.	0			c.C33T						.						147	103	118					11																	123886314		2202	4299	6501	SO:0001819	synonymous_variant	390264	exon1			ATTCATCCTCACA	AB065757	CCDS31702.1	11q24.1	2012-08-09			ENSG00000254737	ENSG00000254737		"GPCR / Class A : Olfactory receptors"	14809	protein-coding gene	gene with protein product							Standard	NM_001004462		Approved		uc010sac.2	Q8NGN3	OTTHUMG00000165966	ENST00000320891.4:c.33C>T	chr11.hg19:g.123886314C>T		114.0	0.0		114.0	30.0	NM_001004462	Q6IEW0	Silent	SNP	ENST00000320891.4	hg19	CCDS31702.1																																																																																			.	.		0.547	OR10G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387268.1	NM_001004462		T	123886314	C	T	123886314	2	4	358	1	0	0	0	0	0	0	0	1	10910	845	30	3		3	OR10G4	11	123886314	Silent	SNP	C	TCGA-XR-A8TD-01A-12D-A38X-10	58505711	123886314	11120202	38	50257										
C12orf40	283461	hgsc.bcm.edu	37	chr12	40076537	40076537	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	actcaatacagcatatttggGggaaaaatggaaaggaagtt	11	4	1	0			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr12:40076537G>T	ENST00000324616.5	+	8	965	c.811G>T	c.(811-813)Ggg>Tgg	p.G271W	C12orf40_ENST00000398716.1_Missense_Mutation_p.G194W|C12orf40_ENST00000405531.3_Missense_Mutation_p.G271W	NM_001031748.2	NP_001026918.2	Q86WS4	CL040_HUMAN	chromosome 12 open reading frame 40	271										breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(6)|prostate(1)|skin(2)	38						GCATATTTGGGGGAAAAATGG	0.348																																					p.G271W		Atlas-SNP	.											C12orf40,trunk,malignant_melanoma,-1,1	C12orf40	118	.	0			c.G811T						.						135	135	135					12																	40076537		1841	4083	5924	SO:0001583	missense	283461	exon8			ATTTGGGGGAAAA	AK097445	CCDS41770.1	12q12	2008-08-04			ENSG00000180116	ENSG00000180116			26846	protein-coding gene	gene with protein product						12477932	Standard	XM_005268806		Approved	FLJ40126	uc001rmc.3	Q86WS4	OTTHUMG00000133567	ENST00000324616.5:c.811G>T	chr12.hg19:g.40076537G>T	ENSP00000317671:p.Gly271Trp	107.0	0.0		124.0	21.0	NM_001031748	B7WNU1|Q8IXY6|Q8N818|V9HW02	Missense_Mutation	SNP	ENST00000324616.5	hg19	CCDS41770.1	.	.	.	.	.	.	.	.	.	.	G	7.838	0.721194	0.15372	.	.	ENSG00000180116	ENST00000405531;ENST00000398716;ENST00000324616	T;T	0.53206	0.63;0.64	5.26	3.42	0.39159	.	0.894443	0.09527	N	0.790054	T	0.53610	0.1807	L	0.27053	0.805	0.09310	N	1	D	0.57257	0.979	P	0.59948	0.866	T	0.49560	-0.8927	10	0.72032	D	0.01	.	12.644	0.56723	0.1515:0.0:0.8485:0.0	.	271	Q86WS4	CL040_HUMAN	W	271;194;271	ENSP00000383897:G271W;ENSP00000317671:G271W	ENSP00000317671:G271W	G	+	1	0	C12orf40	38362804	0.030000	0.19436	0.000000	0.03702	0.001000	0.01503	0.930000	0.28858	0.445000	0.26639	-1.094000	0.02160	GGG	.	.		0.348	C12orf40-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257664.2	NM_173599		T	40076537	G	T	40076537	3	4	358	1	0	0	0	0	1	0	0	0	1688	1232	43	3	841	3	C12orf40	12	40076537	Missense_Mutation	SNP	G	TCGA-XR-A8TD-01A-12D-A38X-10		40076537	93775358	39	50258										
ARID2	196528	hgsc.bcm.edu	37	chr12	46254732	46254732	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	tctgtggcagtcttgtaaaaAgtaaatggcaattttatttg	9	4	2	0			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr12:46254732A>C	ENST00000334344.6	+	16	5094	c.4922A>C	c.(4921-4923)aAg>aCg	p.K1641T	ARID2_ENST00000457135.1_Splice_Site_p.K249T|ARID2_ENST00000444670.1_Splice_Site_p.K1251T|ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000422737.1_Splice_Site_p.K1492T	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	1641					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		TCTTGTAAAAAGTAAATGGCA	0.343			"N, S, F"		hepatocellular carcinoma																																p.K1641T		Atlas-SNP	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	311	.	0			c.A4922C						.						44	46	45					12																	46254732		2203	4300	6503	SO:0001630	splice_region_variant	196528	exon16			GTAAAAAGTAAAT		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.4922+1A>C	chr12.hg19:g.46254732A>C		75.0	0.0		53.0	14.0	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Missense_Mutation	SNP	ENST00000334344.6	hg19	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	A	17.52	3.411379	0.62399	.	.	ENSG00000189079	ENST00000334344;ENST00000549153;ENST00000338636;ENST00000422737;ENST00000444670;ENST00000457135	T;T	0.35048	1.33;1.52	5.86	5.86	0.93980	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	0.052017	0.64402	D	0.000001	T	0.52869	0.1761	L	0.49126	1.545	0.58432	D	0.999998	D;D;P	0.67145	0.996;0.996;0.783	P;P;B	0.61874	0.895;0.851;0.285	T	0.54695	-0.8255	10	0.87932	D	0	-8.3742	16.2644	0.82568	1.0:0.0:0.0:0.0	.	1641;1251;1641	Q68CP9-3;F8W108;Q68CP9	.;.;ARID2_HUMAN	T	1641;758;758;1492;1251;249	ENSP00000335044:K1641T;ENSP00000388357:K249T	ENSP00000335044:K1641T	K	+	2	0	ARID2	44540999	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.024000	0.76443	2.244000	0.73946	0.528000	0.53228	AAG	.	.		0.343	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875	Missense_Mutation	C	46254732	A	C	46254732	5	2	358	1	0	0	0	0	0	0	1	0	915	86	3	5	4984	5	ARID2	12	46254732	Splice_Site	SNP	A	TCGA-XR-A8TD-01A-12D-A38X-10	6178195	46254732	87597163	40	50259										
NCKAP1L	3071	hgsc.bcm.edu	37	chr12	54910690	54910690	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	tcttccttagtggccagtttCattgtcaacggcggcaattt	9	10	3	0			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr12:54910690C>T	ENST00000293373.6	+	11	1088	c.1009C>T	c.(1009-1011)Cat>Tat	p.H337Y	NCKAP1L_ENST00000545638.2_Missense_Mutation_p.H287Y|NCKAP1L_ENST00000552211.1_3'UTR	NM_005337.4	NP_005328.2	P55160	NCKPL_HUMAN	NCK-associated protein 1-like	337					actin polymerization-dependent cell motility (GO:0070358)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|chemotaxis (GO:0006935)|cortical actin cytoskeleton organization (GO:0030866)|erythrocyte development (GO:0048821)|maintenance of cell polarity (GO:0030011)|myeloid cell homeostasis (GO:0002262)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of myosin-light-chain-phosphatase activity (GO:0035509)|neutrophil chemotaxis (GO:0030593)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of CD8-positive, alpha-beta T cell differentiation (GO:0043378)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of lymphocyte differentiation (GO:0045621)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of T cell proliferation (GO:0042102)|protein complex assembly (GO:0006461)|response to drug (GO:0042493)|T cell homeostasis (GO:0043029)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|SCAR complex (GO:0031209)	protein complex binding (GO:0032403)|protein kinase activator activity (GO:0030295)|Rac GTPase activator activity (GO:0030675)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(37)|ovary(3)|prostate(3)|skin(3)|stomach(2)	80						TGGCCAGTTTCATTGTCAACG	0.498																																					p.H337Y		Atlas-SNP	.											NCKAP1L,NS,lymphoid_neoplasm,0,1	NCKAP1L	180	.	0			c.C1009T						.						122	114	117					12																	54910690		2203	4300	6503	SO:0001583	missense	3071	exon11			CAGTTTCATTGTC	AI924363	CCDS31813.1, CCDS53799.1	12q13.1	2005-10-11	2005-10-11	2005-10-11		ENSG00000123338			4862	protein-coding gene	gene with protein product		141180	"hematopoietic protein 1"	HEM1		1932118	Standard	NM_005337		Approved		uc001sgc.4	P55160	OTTHUMG00000169843	ENST00000293373.6:c.1009C>T	chr12.hg19:g.54910690C>T	ENSP00000293373:p.His337Tyr	121.0	0.0		105.0	26.0	NM_005337	B4DUT5|Q52LW0	Missense_Mutation	SNP	ENST00000293373.6	hg19	CCDS31813.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808739	0.90707	.	.	ENSG00000123338	ENST00000293373;ENST00000545638	T;T	0.56444	0.46;0.46	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	T	0.71771	0.3379	M	0.79011	2.435	0.54753	D	0.999982	D	0.63046	0.992	D	0.64042	0.921	T	0.75792	-0.3193	10	0.87932	D	0	-18.2617	16.554	0.84481	0.0:1.0:0.0:0.0	.	337	P55160	NCKPL_HUMAN	Y	337;287	ENSP00000293373:H337Y;ENSP00000445596:H287Y	ENSP00000293373:H337Y	H	+	1	0	NCKAP1L	53196957	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.252000	0.78309	2.578000	0.87016	0.591000	0.81541	CAT	.	.		0.498	NCKAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406195.1	NM_005337		T	54910690	C	T	54910690	3	4	358	1	0	0	0	0	1	0	0	0	10231	826	29	3	1051	3	NCKAP1L	12	54910690	Missense_Mutation	SNP	C	TCGA-XR-A8TD-01A-12D-A38X-10	8655958	54910690	78941205	41	50260										
NAV3	89795	hgsc.bcm.edu	37	chr12	78553012	78553012	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	gtagcagcttttgaaaagagCttagggaatatgactggccg	13	6	0	3			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr12:78553012C>A	ENST00000397909.2	+	23	4988	c.4815C>A	c.(4813-4815)agC>agA	p.S1605R	NAV3_ENST00000536525.2_Missense_Mutation_p.S1605R|NAV3_ENST00000266692.7_Missense_Mutation_p.S1428R|NAV3_ENST00000228327.6_Missense_Mutation_p.S1605R			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1605						membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						TTGAAAAGAGCTTAGGGAATA	0.393										HNSCC(70;0.22)																											p.S1605R		Atlas-SNP	.											.	NAV3	506	.	0			c.C4815A						.						124	114	117					12																	78553012		1853	4091	5944	SO:0001583	missense	89795	exon23			AAAGAGCTTAGGG	AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.4815C>A	chr12.hg19:g.78553012C>A	ENSP00000381007:p.Ser1605Arg	61.0	0.0		70.0	15.0	NM_014903	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.27|18.27	3.587294|3.587294	0.66105|0.66105	.|.	.|.	ENSG00000067798|ENSG00000067798	ENST00000552895|ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692;ENST00000378640;ENST00000550788	.|D;D;D;D;D	.|0.94650	.|-3.48;-3.48;-3.48;-3.48;-3.48	5.44|5.44	-0.251|-0.251	0.13003|0.13003	.|.	.|0.000000	.|0.47852	.|U	.|0.000215	D|D	0.95984|0.95984	0.8692|0.8692	M|M	0.78049|0.78049	2.395|2.395	0.80722|0.80722	D|D	1|1	.|D;D;P;D	.|0.76494	.|0.983;0.997;0.954;0.999	.|P;D;B;D	.|0.80764	.|0.796;0.991;0.393;0.994	D|D	0.94241|0.94241	0.7485|0.7485	5|10	.|0.87932	.|D	.|0	-17.1767|-17.1767	8.7911|8.7911	0.34852|0.34852	0.0:0.6348:0.0:0.3652|0.0:0.6348:0.0:0.3652	.|.	.|1605;1428;1605;1605	.|E7EUC6;Q8IVL0-3;Q8IVL0;Q8IVL0-2	.|.;.;NAV3_HUMAN;.	I|R	500|1605;1605;1605;1428;226;234	.|ENSP00000446132:S1605R;ENSP00000381007:S1605R;ENSP00000228327:S1605R;ENSP00000266692:S1428R;ENSP00000448303:S234R	.|ENSP00000228327:S1605R	L|S	+|+	1|3	0|2	NAV3|NAV3	77077143|77077143	0.999000|0.999000	0.42202|0.42202	0.997000|0.997000	0.53966|0.53966	0.995000|0.995000	0.86356|0.86356	0.636000|0.636000	0.24644|0.24644	0.122000|0.122000	0.18314|0.18314	-0.290000|-0.290000	0.09829|0.09829	CTT|AGC	.	.		0.393	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		A	78553012	C	A	78553012	3	1	358	1	0	0	0	0	1	0	0	0	10194	796	28	3	4905	3	NAV3	12	78553012	Missense_Mutation	SNP	C	TCGA-XR-A8TD-01A-12D-A38X-10	23642322	78553012	55298883	42	50261										
EIF2AK4	440275	hgsc.bcm.edu	37	chr15	40265138	40265138	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	cttggatgacaaggaaagatGgagtccccagcagttgttga	13	7	0	3			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr15:40265138G>T	ENST00000263791.5	+	10	1626	c.1583G>T	c.(1582-1584)tGg>tTg	p.W528L	EIF2AK4_ENST00000382727.2_Missense_Mutation_p.W528L|EIF2AK4_ENST00000559624.1_Missense_Mutation_p.W528L	NM_001013703.2	NP_001013725.2	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha kinase 4	528	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to starvation (GO:0009267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of translation (GO:0017148)|protein phosphorylation (GO:0006468)|regulation of translational initiation (GO:0006446)|regulation of translational initiation in response to stress (GO:0043558)	cytosolic ribosome (GO:0022626)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)	40		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		AAGGAAAGATGGAGTCCCCAG	0.423																																					p.W528L		Atlas-SNP	.											.	EIF2AK4	107	.	0			c.G1583T						.						116	112	114					15																	40265138		1895	4131	6026	SO:0001583	missense	440275	exon10			AAAGATGGAGTCC	AB037759	CCDS42016.1	15q13.3	2008-08-18				ENSG00000128829			19687	protein-coding gene	gene with protein product		609280				10504407	Standard	XM_005254392		Approved	GCN2, KIAA1338	uc001zkm.1	Q9P2K8		ENST00000263791.5:c.1583G>T	chr15.hg19:g.40265138G>T	ENSP00000263791:p.Trp528Leu	116.0	0.0		160.0	30.0	NM_001013703	C9JEC4|Q69YL7|Q6DC97|Q96GN6|Q9H5K1|Q9NSQ3|Q9NSZ5|Q9UJ56	Missense_Mutation	SNP	ENST00000263791.5	hg19	CCDS42016.1	.	.	.	.	.	.	.	.	.	.	G	19.02	3.745444	0.69418	.	.	ENSG00000128829	ENST00000263791;ENST00000382727	T;T	0.71461	-0.57;-0.57	5.84	5.84	0.93424	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.75317	0.3833	N	0.25825	0.765	0.80722	D	1	D;D	0.89917	1.0;0.995	D;D	0.91635	0.999;0.959	T	0.67130	-0.5748	10	0.10377	T	0.69	-9.6195	20.1336	0.98010	0.0:0.0:1.0:0.0	.	528;528	Q9P2K8;Q9P2K8-3	E2AK4_HUMAN;.	L	528	ENSP00000263791:W528L;ENSP00000372174:W528L	ENSP00000263791:W528L	W	+	2	0	EIF2AK4	38052430	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.179000	0.89692	2.767000	0.95098	0.591000	0.81541	TGG	.	.		0.423	EIF2AK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418395.1			T	40265138	G	T	40265138	3	4	358	1	0	0	0	0	1	0	0	0	5001	1357	47	3	1621	3	EIF2AK4	15	40265138	Missense_Mutation	SNP	G	TCGA-XR-A8TD-01A-12D-A38X-10		40265138	62266254	43	50262										
TLN2	83660	hgsc.bcm.edu	37	chr15	63011973	63011973	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	ttgccttctgcaggcagtggCtgatcacatccctcagctgg	11	13	3	1			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr15:63011973C>A	ENST00000561311.1	+	24	3115	c.2885C>A	c.(2884-2886)gCt>gAt	p.A962D	TLN2_ENST00000306829.6_Missense_Mutation_p.A962D			Q9Y4G6	TLN2_HUMAN	talin 2	962	Ala-rich.				cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						CAGGCAGTGGCTGATCACATC	0.537																																					p.A962D		Atlas-SNP	.											.	TLN2	253	.	0			c.C2885A						.						60	48	52					15																	63011973		2203	4300	6503	SO:0001583	missense	83660	exon22			CAGTGGCTGATCA	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.2885C>A	chr15.hg19:g.63011973C>A	ENSP00000453508:p.Ala962Asp	23.0	0.0		29.0	10.0	NM_015059	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	hg19	CCDS32261.1	.	.	.	.	.	.	.	.	.	.	C	33	5.218013	0.95104	.	.	ENSG00000171914	ENST00000306829	T	0.69926	-0.44	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	D	0.82595	0.5071	M	0.78637	2.42	0.80722	D	1	D	0.69078	0.997	D	0.68943	0.961	D	0.83420	0.0032	10	0.62326	D	0.03	-12.2663	19.9103	0.97024	0.0:1.0:0.0:0.0	.	962	Q9Y4G6	TLN2_HUMAN	D	962	ENSP00000303476:A962D	ENSP00000303476:A962D	A	+	2	0	TLN2	60799265	1.000000	0.71417	0.999000	0.59377	0.926000	0.56050	7.772000	0.85439	2.765000	0.95021	0.650000	0.86243	GCT	.	.		0.537	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			A	63011973	C	A	63011973	3	1	358	1	0	0	0	0	1	0	0	0	15963	797	28	3	2971	3	TLN2	15	63011973	Missense_Mutation	SNP	C	TCGA-XR-A8TD-01A-12D-A38X-10	22746835	63011973	39519419	44	50263										
CLPX	10845	hgsc.bcm.edu	37	chr15	65472498	65472498	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	aatctgagtttcaaatgtccCaagccttcctaaaactgaca	5	11	2	2			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr15:65472498C>T	ENST00000300107.3	-	2	312	c.124G>A	c.(124-126)Ggg>Agg	p.G42R		NM_006660.3	NP_006651.2	O76031	CLPX_HUMAN	caseinolytic mitochondrial matrix peptidase chaperone subunit	42					ATP catabolic process (GO:0006200)|positive regulation of peptidase activity (GO:0010952)|protein folding (GO:0006457)|proteolysis involved in cellular protein catabolic process (GO:0051603)	endopeptidase Clp complex (GO:0009368)|mitochondrial endopeptidase Clp complex (GO:0009841)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|metal ion binding (GO:0046872)|peptidase activator activity (GO:0016504)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(4)|prostate(1)|skin(2)	16						TCAAATGTCCCAAGCCTTCCT	0.388																																					p.G42R		Atlas-SNP	.											.	CLPX	49	.	0			c.G124A						.						91	93	92					15																	65472498		2202	4299	6501	SO:0001583	missense	10845	exon2			ATGTCCCAAGCCT	AJ006267	CCDS10202.1	15q22.31	2013-09-12	2013-09-12		ENSG00000166855	ENSG00000166855		"ATPases / AAA-type"	2088	protein-coding gene	gene with protein product		615611	"ClpX (caseinolytic protease X, E. coli) homolog", "ClpX caseinolytic protease X homolog (E. coli)", "ClpX caseinolytic peptidase X homolog (E. coli)"			22841477	Standard	NM_006660		Approved		uc002aom.3	O76031	OTTHUMG00000133139	ENST00000300107.3:c.124G>A	chr15.hg19:g.65472498C>T	ENSP00000300107:p.Gly42Arg	104.0	0.0		155.0	39.0	NM_006660	A1L428|A8K8F1|B9EGI8|Q9H4D9	Missense_Mutation	SNP	ENST00000300107.3	hg19	CCDS10202.1	.	.	.	.	.	.	.	.	.	.	C	15.29	2.789190	0.49997	.	.	ENSG00000166855	ENST00000300107;ENST00000546194	T	0.17691	2.26	6.17	5.25	0.73442	.	0.101965	0.64402	D	0.000002	T	0.12178	0.0296	N	0.22421	0.69	0.47308	D	0.999384	B;B	0.14805	0.011;0.006	B;B	0.15052	0.012;0.012	T	0.08700	-1.0709	10	0.35671	T	0.21	.	11.0179	0.47701	0.0:0.8037:0.13:0.0663	.	42;42	Q9H072;O76031	.;CLPX_HUMAN	R	42	ENSP00000300107:G42R	ENSP00000300107:G42R	G	-	1	0	CLPX	63259551	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.705000	0.54823	1.616000	0.50265	0.655000	0.94253	GGG	.	.		0.388	CLPX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256828.2	NM_006660		T	65472498	C	T	65472498	3	4	358	1	0	0	0	0	1	0	0	0	3558	594	21	3	1829	3	CLPX	15	65472498	Missense_Mutation	SNP	C	TCGA-XR-A8TD-01A-12D-A38X-10	2460525	65472498	37058894	45	50264										
ANKFN1	162282	hgsc.bcm.edu	37	chr17	54535228	54535228	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	atgccttcttttgcagctgtCttgtatgtgggaagatataa	10	6	2	1			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr17:54535228C>T	ENST00000318698.2	+	13	1489	c.1454C>T	c.(1453-1455)tCt>tTt	p.S485F	ANKFN1_ENST00000566473.2_Missense_Mutation_p.S485F	NM_153228.2	NP_694960.2	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain containing 1	485										NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(11)|lung(27)|ovary(1)|prostate(1)|skin(1)	53						TTGCAGCTGTCTTGTATGTGG	0.473																																					p.S485F		Atlas-SNP	.											.	ANKFN1	115	.	0			c.C1454T						.						180	148	159					17																	54535228		2203	4300	6503	SO:0001583	missense	162282	exon13			AGCTGTCTTGTAT	AK095654	CCDS32686.1	17q23.2	2014-02-12	2005-11-15		ENSG00000153930	ENSG00000153930		"Ankyrin repeat domain containing", "Fibronectin type III domain containing"	26766	protein-coding gene	gene with protein product							Standard	NM_153228		Approved	FLJ38335	uc002iun.1	Q8N957	OTTHUMG00000155010	ENST00000318698.2:c.1454C>T	chr17.hg19:g.54535228C>T	ENSP00000321627:p.Ser485Phe	52.0	0.0		75.0	21.0	NM_153228		Missense_Mutation	SNP	ENST00000318698.2	hg19	CCDS32686.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.405288	0.83230	.	.	ENSG00000153930	ENST00000318698	T	0.29397	1.57	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.60431	0.2268	M	0.78637	2.42	0.80722	D	1	D	0.89917	1.0	D	0.71184	0.972	T	0.60198	-0.7310	10	0.87932	D	0	-12.508	20.8794	0.99867	0.0:1.0:0.0:0.0	.	485	Q8N957	ANKF1_HUMAN	F	485	ENSP00000321627:S485F	ENSP00000321627:S485F	S	+	2	0	ANKFN1	51890227	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.487000	0.81328	2.941000	0.99782	0.655000	0.94253	TCT	.	.		0.473	ANKFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338043.1	NM_153228		T	54535228	C	T	54535228	3	4	358	1	0	0	0	0	1	0	0	0	625	913	32	3	1504	3	ANKFN1	17	54535228	Missense_Mutation	SNP	C	TCGA-XR-A8TD-01A-12D-A38X-10		54535228	26659982	46	50265										
AKAP1	8165	hgsc.bcm.edu	37	chr17	55182885	55182885	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	cctgggatgctggcgctcctCggctggtggtggtttttctc	15	11	1	0			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr17:55182885C>T	ENST00000337714.3	+	2	293	c.60C>T	c.(58-60)ctC>ctT	p.L20L	AKAP1_ENST00000314126.3_Silent_p.L20L|AKAP1_ENST00000572557.1_Silent_p.L20L|AKAP1_ENST00000571629.1_Silent_p.L20L|AKAP1_ENST00000539273.1_Silent_p.L20L	NM_003488.3	NP_003479.1	Q92667	AKAP1_HUMAN	A kinase (PRKA) anchor protein 1	20					blood coagulation (GO:0007596)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.L20L(1)		endometrium(2)|liver(1)|lung(7)|ovary(2)|pancreas(1)|skin(1)	14	Breast(9;5.46e-08)					TGGCGCTCCTCGGCTGGTGGT	0.577																																					p.L20L		Atlas-SNP	.											AKAP1,NS,carcinoma,0,1	AKAP1	73	.	1	Substitution - coding silent(1)	endometrium(1)	c.C60T						.						61	58	59					17																	55182885		2203	4300	6503	SO:0001819	synonymous_variant	8165	exon3			GCTCCTCGGCTGG	X97335	CCDS11594.1	17q22	2013-01-23			ENSG00000121057	ENSG00000121057		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Tudor domain containing"	367	protein-coding gene	gene with protein product	"protein kinase anchoring protein 1", "dual specificity A-kinase-anchoring protein 1", "protein phosphatase 1, regulatory subunit 43", "tudor domain containing 17"	602449		PRKA1		8769136, 7499250	Standard	NM_003488		Approved	AKAP121, AKAP149, SAKAP84, S-AKAP84, AKAP84, D-AKAP1, PPP1R43, TDRD17	uc002iux.3	Q92667	OTTHUMG00000140369	ENST00000337714.3:c.60C>T	chr17.hg19:g.55182885C>T		63.0	0.0		116.0	21.0	NM_001242902	A8K8Q1|D3DTZ0|Q13320|Q9BW14	Silent	SNP	ENST00000337714.3	hg19	CCDS11594.1																																																																																			.	.		0.577	AKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277069.1			T	55182885	C	T	55182885	2	4	358	1	0	0	0	0	0	0	0	1	445	871	31	1		1	AKAP1	17	55182885	Silent	SNP	C	TCGA-XR-A8TD-01A-12D-A38X-10	647657	55182885	26012325	47	50266										
MED13	9969	hgsc.bcm.edu	37	chr17	60024360	60024360	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	gtcagattgcactgaaggcaCgtggaggtgcaaagaggcct	15	8	1	3			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr17:60024360C>A	ENST00000397786.2	-	29	6386	c.6310G>T	c.(6310-6312)Gtg>Ttg	p.V2104L		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	2104					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						ACTGAAGGCACGTGGAGGTGC	0.418																																					p.V2104L		Atlas-SNP	.											.	MED13	181	.	0			c.G6310T						.						133	135	135					17																	60024360		1979	4172	6151	SO:0001583	missense	9969	exon29			AAGGCACGTGGAG	AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"thyroid hormone receptor associated protein 1"	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.6310G>T	chr17.hg19:g.60024360C>A	ENSP00000380888:p.Val2104Leu	101.0	0.0		128.0	24.0	NM_005121	B2RU05|O60334	Missense_Mutation	SNP	ENST00000397786.2	hg19	CCDS42366.1	.	.	.	.	.	.	.	.	.	.	C	33	5.224811	0.95173	.	.	ENSG00000108510	ENST00000397786;ENST00000262436	D	0.86562	-2.14	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	D	0.92277	0.7550	L	0.60455	1.87	0.80722	D	1	D	0.69078	0.997	D	0.80764	0.994	D	0.91963	0.5580	10	0.48119	T	0.1	-8.027	18.9301	0.92561	0.0:1.0:0.0:0.0	.	2104	Q9UHV7	MED13_HUMAN	L	2104;2103	ENSP00000380888:V2104L	ENSP00000262436:V2103L	V	-	1	0	MED13	57379142	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.429000	0.80309	2.464000	0.83262	0.467000	0.42956	GTG	.	.		0.418	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121		A	60024360	C	A	60024360	3	1	358	1	0	0	0	0	1	0	0	0	9439	536	19	1	222	1	MED13	17	60024360	Missense_Mutation	SNP	C	TCGA-XR-A8TD-01A-12D-A38X-10	4841475	60024360	21170850	48	50267										
C18orf34	374864	hgsc.bcm.edu	37	chr18	30847217	30847217	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	tactgattttcatgacttttTtgcttccaggttagttggtc	8	7	1	2			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr18:30847217T>G	ENST00000383096.3	-	13	1403	c.1221A>C	c.(1219-1221)caA>caC	p.Q407H	CCDC178_ENST00000300227.8_Missense_Mutation_p.Q407H|CCDC178_ENST00000579916.1_Intron|CCDC178_ENST00000402325.1_Missense_Mutation_p.Q407H|CCDC178_ENST00000403303.1_Missense_Mutation_p.Q407H|CCDC178_ENST00000583930.1_Missense_Mutation_p.Q407H|CCDC178_ENST00000406524.2_Missense_Mutation_p.Q407H|CCDC178_ENST00000579947.1_Missense_Mutation_p.Q407H			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178	407																	CATGACTTTTTTGCTTCCAGG	0.338																																					p.Q407H		Atlas-SNP	.											.	.	.	.	0			c.A1221C						.						78	81	80					18																	30847217		2203	4296	6499	SO:0001583	missense	374864	exon12			ACTTTTTTGCTTC	AK126038	CCDS11906.1, CCDS42424.1	18q12.1	2012-10-15	2012-10-15	2012-10-15	ENSG00000166960	ENSG00000166960			29588	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 34"	C18orf34			Standard	NM_198995		Approved	FLJ44050	uc002kxn.2	Q5BJE1	OTTHUMG00000132279	ENST00000383096.3:c.1221A>C	chr18.hg19:g.30847217T>G	ENSP00000372576:p.Gln407His	146.0	0.0		199.0	49.0	NM_001105528	A6NDC6|J3KS92|Q6ZP67|Q6ZU20	Missense_Mutation	SNP	ENST00000383096.3	hg19	CCDS42424.1	.	.	.	.	.	.	.	.	.	.	T	5.640	0.302692	0.10678	.	.	ENSG00000166960	ENST00000403303;ENST00000383096;ENST00000300227;ENST00000406524;ENST00000402325	T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97	4.17	0.49	0.16861	.	.	.	.	.	T	0.33789	0.0875	L	0.34521	1.04	0.09310	N	1	P;P;P;P	0.40794	0.729;0.729;0.729;0.729	P;P;P;P	0.45138	0.471;0.471;0.471;0.471	T	0.17837	-1.0356	9	0.45353	T	0.12	-4.6522	5.9326	0.19148	0.0:0.3638:0.0:0.6362	.	407;407;407;407	F8W7A7;B5MD75;Q5BJE1-2;Q5BJE1	.;.;.;CR034_HUMAN	H	407	ENSP00000385591:Q407H;ENSP00000372576:Q407H;ENSP00000300227:Q407H;ENSP00000385867:Q407H;ENSP00000385234:Q407H	ENSP00000300227:Q407H	Q	-	3	2	C18orf34	29101215	0.063000	0.20901	0.002000	0.10522	0.032000	0.12392	0.237000	0.17985	0.080000	0.16959	0.383000	0.25322	CAA	.	.		0.338	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255373.2	NM_198995		G	30847217	T	G	30847217	3	3	358	1	0	0	0	0	1	0	0	0	1904	1838	64	5	1426	5	C18orf34	18	30847217	Missense_Mutation	SNP	T	TCGA-XR-A8TD-01A-12D-A38X-10		30847217	47230031	49	50268										
WDR7	23335	hgsc.bcm.edu	37	chr18	54687994	54687994	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	agacaatccatggacacaagGgaccaatcactgcagtggct	10	11	1	1			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr18:54687994G>A	ENST00000254442.3	+	27	4394	c.4183G>A	c.(4183-4185)Gga>Aga	p.G1395R	WDR7_ENST00000589935.1_Intron|WDR7_ENST00000357574.3_Missense_Mutation_p.G1362R	NM_015285.2	NP_056100.2	Q9Y4E6	WDR7_HUMAN	WD repeat domain 7	1395					hematopoietic progenitor cell differentiation (GO:0002244)					NS(1)|breast(5)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(37)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	78				Lung(128;0.0238)|Colorectal(16;0.0296)		TGGACACAAGGGACCAATCAC	0.393																																					p.G1395R		Atlas-SNP	.											.	WDR7	166	.	0			c.G4183A						.						156	135	142					18																	54687994		2203	4300	6503	SO:0001583	missense	23335	exon27			CACAAGGGACCAA	AB011113	CCDS11962.1, CCDS11963.1	18q21.31	2013-01-09			ENSG00000091157	ENSG00000091157		"WD repeat domain containing"	13490	protein-coding gene	gene with protein product		613473				10828621	Standard	XM_005266674		Approved	KIAA0541, TRAG	uc002lgk.1	Q9Y4E6	OTTHUMG00000132721	ENST00000254442.3:c.4183G>A	chr18.hg19:g.54687994G>A	ENSP00000254442:p.Gly1395Arg	107.0	0.0		110.0	23.0	NM_015285	A7E2C8|Q86UX5|Q86VP2|Q96PS7	Missense_Mutation	SNP	ENST00000254442.3	hg19	CCDS11962.1	.	.	.	.	.	.	.	.	.	.	G	32	5.144545	0.94603	.	.	ENSG00000091157	ENST00000254442;ENST00000357574;ENST00000444065;ENST00000398311	T;T	0.61859	0.07;0.07	6.17	6.17	0.99709	WD40/YVTN repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.72819	0.3508	L	0.46567	1.45	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.69815	-0.5043	10	0.51188	T	0.08	.	20.4745	0.99168	0.0:0.0:1.0:0.0	.	1362;1395	Q9Y4E6-2;Q9Y4E6	.;WDR7_HUMAN	R	1395;1362;720;1362	ENSP00000254442:G1395R;ENSP00000350187:G1362R	ENSP00000254442:G1395R	G	+	1	0	WDR7	52838992	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.693000	0.98684	2.941000	0.99782	0.655000	0.94253	GGA	.	.		0.393	WDR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256062.1			A	54687994	G	A	54687994	3	1	358	1	0	0	0	0	1	0	0	0	17335	1233	43	3	4285	3	WDR7	18	54687994	Missense_Mutation	SNP	G	TCGA-XR-A8TD-01A-12D-A38X-10	23840777	54687994	23389254	50	50269										
SALL3	27164	hgsc.bcm.edu	37	chr18	76753074	76753074	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	gcgcccggcctgccaagtccGcttctacctcagacttccgc	9	19	2	1	rs377646222		TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr18:76753074G>A	ENST00000537592.2	+	2	1083	c.1083G>A	c.(1081-1083)ccG>ccA	p.P361P	SALL3_ENST00000536229.3_Silent_p.P228P|SALL3_ENST00000575389.2_Silent_p.P361P	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	361					forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|negative regulation of smoothened signaling pathway (GO:0045879)|olfactory bulb interneuron development (GO:0021891)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(40)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)		TGCCAAGTCCGCTTCTACCTC	0.726																																					p.P361P		Atlas-SNP	.											.	SALL3	162	.	0			c.G1083A						.	G		1,4335		0,1,2167	12	13	13		1083	-8.7	0.2	18		13	0,8518		0,0,4259	no	coding-synonymous	SALL3	NM_171999.2		0,1,6426	AA,AG,GG		0.0,0.0231,0.0078		361/1301	76753074	1,12853	2168	4259	6427	SO:0001819	synonymous_variant	27164	exon2			AAGTCCGCTTCTA	AJ007421	CCDS12013.1	18q23	2013-10-17	2013-10-17		ENSG00000256463	ENSG00000256463		"Zinc fingers, C2H2-type"	10527	protein-coding gene	gene with protein product		605079	"sal (Drosophila)-like 3", "sal-like 3 (Drosophila)"			10610715	Standard	NM_171999		Approved	ZNF796	uc002lmt.3	Q9BXA9	OTTHUMG00000132896	ENST00000537592.2:c.1083G>A	chr18.hg19:g.76753074G>A		62.0	0.0		77.0	19.0	NM_171999	Q9UGH1	Silent	SNP	ENST00000537592.2	hg19	CCDS12013.1																																																																																			.	.		0.726	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256397.1	NM_171999		A	76753074	G	A	76753074	2	1	358	1	0	0	0	0	0	0	0	1	13827	1074	38	1		1	SALL3	18	76753074	Silent	SNP	G	TCGA-XR-A8TD-01A-12D-A38X-10	22065080	76753074	1324174	51	50270										
COL5A3	50509	hgsc.bcm.edu	37	chr19	10097061	10097061	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	gccccttcggcccctcaggaCcatcctctccccggggacct	9	21	2	0			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr19:10097061C>A	ENST00000264828.3	-	30	2367	c.2282G>T	c.(2281-2283)gGt>gTt	p.G761V		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	761	Triple-helical region.				axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			CCCCTCAGGACCATCCTCTCC	0.612																																					p.G761V		Atlas-SNP	.											.	COL5A3	243	.	0			c.G2282T						.						21	26	24					19																	10097061		2201	4300	6501	SO:0001583	missense	50509	exon30			TCAGGACCATCCT	AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573		"Collagens"	14864	protein-coding gene	gene with protein product		120216				10722718	Standard	NM_015719		Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.2282G>T	chr19.hg19:g.10097061C>A	ENSP00000264828:p.Gly761Val	73.0	0.0		59.0	8.0	NM_015719	Q9NZQ6	Missense_Mutation	SNP	ENST00000264828.3	hg19	CCDS12222.1	.	.	.	.	.	.	.	.	.	.	C	19.45	3.829691	0.71258	.	.	ENSG00000080573	ENST00000264828	D	0.99637	-6.29	4.2	4.2	0.49525	.	0.000000	0.64402	D	0.000001	D	0.99764	0.9904	H	0.97758	4.07	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96942	0.9688	10	0.72032	D	0.01	.	14.3955	0.67007	0.0:1.0:0.0:0.0	.	761	P25940	CO5A3_HUMAN	V	761	ENSP00000264828:G761V	ENSP00000264828:G761V	G	-	2	0	COL5A3	9958061	1.000000	0.71417	0.990000	0.47175	0.724000	0.41520	6.969000	0.76092	2.024000	0.59613	0.462000	0.41574	GGT	.	.		0.612	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719		A	10097061	C	A	10097061	3	1	358	1	0	0	0	0	1	0	0	0	3700	507	18	3	3107	3	COL5A3	19	10097061	Missense_Mutation	SNP	C	TCGA-XR-A8TD-01A-12D-A38X-10		10097061	49031922	52	50271										
ZNF536	9745	hgsc.bcm.edu	37	chr19	31048062	31048062	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	aaatctgcacattttcttgcAggtaagtgacactccctgtc	7	11	2	1			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr19:31048062A>T	ENST00000355537.3	+	5	4042		c.e5-1			NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536						negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					ATTTTCTTGCAGGTAAGTGAC	0.458																																					.		Atlas-SNP	.											.	ZNF536	424	.	0			c.3896-2A>T						.						312	267	282					19																	31048062		2203	4300	6503	SO:0001630	splice_region_variant	9745	exon5			TCTTGCAGGTAAG		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"Zinc fingers, C2H2-type"	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.3896-1A>T	chr19.hg19:g.31048062A>T		142.0	0.0		164.0	40.0	NM_014717	A2RU18	Splice_Site	SNP	ENST00000355537.3	hg19	CCDS32984.1	.	.	.	.	.	.	.	.	.	.	A	13.94	2.387433	0.42308	.	.	ENSG00000198597	ENST00000355537	.	.	.	5.76	5.76	0.90799	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.4668	0.55764	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ZNF536	35739902	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	4.684000	0.61686	2.195000	0.70347	0.533000	0.62120	.	.	.		0.458	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717	Intron	T	31048062	A	T	31048062	5	4	358	1	0	0	0	0	0	0	1	0	17989	202	7	4	3908	4	ZNF536	19	31048062	Splice_Site	SNP	A	TCGA-XR-A8TD-01A-12D-A38X-10	20951001	31048062	28080921	53	50272										
ZNF880	400713	hgsc.bcm.edu	37	chr19	52887731	52887731	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	agaaaccttacaaatgtaatGagtgtggcaaggtcttcaac	9	7	2	2			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr19:52887731G>A	ENST00000422689.2	+	4	913	c.898G>A	c.(898-900)Gag>Aag	p.E300K		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	300					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						CAAATGTAATGAGTGTGGCAA	0.398																																					p.E300K		Atlas-SNP	.											.	ZNF880	45	.	0			c.G898A						.						71	64	66					19																	52887731		1568	3582	5150	SO:0001583	missense	400713	exon4			TGTAATGAGTGTG	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"Zinc fingers, C2H2-type", "-"	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.898G>A	chr19.hg19:g.52887731G>A	ENSP00000406318:p.Glu300Lys	96.0	0.0		137.0	18.0	NM_001145434	B4DNA6	Missense_Mutation	SNP	ENST00000422689.2	hg19	CCDS46164.1	.	.	.	.	.	.	.	.	.	.	G	3.908	-0.020580	0.07634	.	.	ENSG00000221923	ENST00000422689	T	0.07327	3.2	1.89	-0.678	0.11353	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12178	0.0296	L	0.37466	1.105	0.09310	N	1	P	0.51147	0.942	P	0.57244	0.816	T	0.24012	-1.0172	8	.	.	.	.	6.6328	0.22867	0.2778:0.0:0.7222:0.0	.	300	Q6PDB4	ZN880_HUMAN	K	300	ENSP00000406318:E300K	.	E	+	1	0	ZNF880	57579543	0.000000	0.05858	0.123000	0.21794	0.081000	0.17604	-0.261000	0.08694	-0.261000	0.09405	-0.404000	0.06349	GAG	.	.		0.398	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434		A	52887731	G	A	52887731	3	1	358	1	0	0	0	0	1	0	0	0	18212	1291	45	3	912	3	ZNF880	19	52887731	Missense_Mutation	SNP	G	TCGA-XR-A8TD-01A-12D-A38X-10	21839669	52887731	6241252	54	50273										
SIGLEC1	6614	hgsc.bcm.edu	37	chr20	3684557	3684557	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	tagacgccagcatcgctccaGgctgcctggggcaggtgcag	15	13	0	1	rs2122216		TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr20:3684557G>A	ENST00000344754.4	-	4	887	c.888C>T	c.(886-888)gcC>gcT	p.A296A	SIGLEC1_ENST00000202578.4_Silent_p.A296A	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	296	Ig-like C2-type 2.				cell-matrix adhesion (GO:0007160)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of T cell apoptotic process (GO:0070234)|single organismal cell-cell adhesion (GO:0016337)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|liver(2)|lung(24)|ovary(3)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)	70						CATCGCTCCAGGCTGCCTGGG	0.582																																					p.A296A		Atlas-SNP	.											.	SIGLEC1	210	.	0			c.C888T						.						86	65	72					20																	3684557		2203	4300	6503	SO:0001819	synonymous_variant	6614	exon4			GCTCCAGGCTGCC	AF230073	CCDS13060.1	20p13	2013-01-29	2006-01-19	2006-01-19	ENSG00000088827	ENSG00000088827		"CD molecules", "Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	11127	protein-coding gene	gene with protein product		600751	"sialoadhesin"	SN		8530048	Standard	XM_006723610		Approved	SIGLEC-1, CD169, FLJ00051, FLJ00055, FLJ00073, FLJ32150, dJ1009E24.1, sialoadhesin	uc002wja.3	Q9BZZ2	OTTHUMG00000031757	ENST00000344754.4:c.888C>T	chr20.hg19:g.3684557G>A		74.0	0.0		39.0	8.0	NM_023068	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Silent	SNP	ENST00000344754.4	hg19	CCDS13060.1																																																																																			.	.		0.582	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068		A	3684557	G	A	3684557	2	1	358	1	0	0	0	0	0	0	0	1	14320	987	35	3		3	SIGLEC1	20	3684557	Silent	SNP	G	TCGA-XR-A8TD-01A-12D-A38X-10		3684557	59340963	55	50274										
SLPI	6590	hgsc.bcm.edu	37	chr20	43882264	43882264	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	gcatttgatgccacaagtgtCaggacaacatctcttcttcc	7	12	3	1			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr20:43882264C>T	ENST00000338380.2	-	2	216	c.196G>A	c.(196-198)Gac>Aac	p.D66N		NM_003064.2	NP_003055.1	P03973	SLPI_HUMAN	secretory leukocyte peptidase inhibitor	66	Trypsin inhibitory domain.|WAP 1. {ECO:0000255|PROSITE- ProRule:PRU00722}.				negative regulation of protein binding (GO:0032091)|negative regulation of viral genome replication (GO:0045071)	extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|enzyme binding (GO:0019899)|serine-type endopeptidase inhibitor activity (GO:0004867)			lung(3)|ovary(1)	4		Myeloproliferative disorder(115;0.0122)				CCACAAGTGTCAGGACAACAT	0.527																																					p.D66N	GBM(64;162 1089 31780 33427 34538)	Atlas-SNP	.											.	SLPI	13	.	0			c.G196A						.						116	98	104					20																	43882264		2203	4300	6503	SO:0001583	missense	6590	exon2			AAGTGTCAGGACA	X04502	CCDS13347.1	20q13.12	2013-01-21	2005-08-17		ENSG00000124107	ENSG00000124107		"WAP four-disulfide core domain containing"	11092	protein-coding gene	gene with protein product	"antileukoproteinase"	107285	"secretory leukocyte protease inhibitor (antileukoproteinase)"			3640338, 12206714	Standard	NM_003064		Approved	HUSI-I, ALK1, ALP, BLPI, HUSI, WAP4, WFDC4	uc002xnm.1	P03973	OTTHUMG00000033075	ENST00000338380.2:c.196G>A	chr20.hg19:g.43882264C>T	ENSP00000342082:p.Asp66Asn	124.0	0.0		141.0	20.0	NM_003064	B2R5H8|P07757	Missense_Mutation	SNP	ENST00000338380.2	hg19	CCDS13347.1	.	.	.	.	.	.	.	.	.	.	C	14.24	2.476336	0.44044	.	.	ENSG00000124107	ENST00000338380	T	0.70399	-0.48	5.05	1.43	0.22495	Whey acidic protein, 4-disulphide core (5);4-disulphide core (1);	0.674594	0.12875	N	0.431916	T	0.61489	0.2351	L	0.31476	0.935	0.09310	N	1	D	0.54772	0.968	P	0.49999	0.628	T	0.50074	-0.8870	10	0.27082	T	0.32	.	7.1501	0.25606	0.2344:0.4569:0.3087:0.0	.	66	P03973	SLPI_HUMAN	N	66	ENSP00000342082:D66N	ENSP00000342082:D66N	D	-	1	0	SLPI	43315678	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.368000	0.20399	0.620000	0.30215	-0.304000	0.09214	GAC	.	.		0.527	SLPI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080494.3			T	43882264	C	T	43882264	3	4	358	1	0	0	0	0	1	0	0	0	14768	826	29	3	214	3	SLPI	20	43882264	Missense_Mutation	SNP	C	TCGA-XR-A8TD-01A-12D-A38X-10	40197707	43882264	19143256	56	50275										
CABIN1	23523	hgsc.bcm.edu	37	chr22	24492014	24492014	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	aaggaccctttgccaggggcGaggagaagaacacacccaaa	12	11	0	2	rs193920999		TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chr22:24492014G>A	ENST00000398319.2	+	25	4292	c.3907G>A	c.(3907-3909)Gag>Aag	p.E1303K	CABIN1_ENST00000405822.2_Missense_Mutation_p.E1253K|CABIN1_ENST00000263119.5_Missense_Mutation_p.E1303K	NM_001199281.1	NP_001186210.1	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	1303					cell surface receptor signaling pathway (GO:0007166)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of catalytic activity (GO:0043086)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)			breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(13)|liver(1)|lung(18)|ovary(5)|pancreas(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						TGCCAGGGGCGAGGAGAAGAA	0.552																																					p.E1303K		Atlas-SNP	.											CABIN1,NS,adenoma,0,1	CABIN1	153	.	0			c.G3907A						.						121	125	124					22																	24492014		2203	4300	6503	SO:0001583	missense	23523	exon25			AGGGGCGAGGAGA	AF072441	CCDS13823.1, CCDS74830.1	22q11.23	2008-09-16			ENSG00000099991	ENSG00000099991			24187	protein-coding gene	gene with protein product		604251				9655484, 9205841	Standard	NM_001199281		Approved	KIAA0330, PPP3IN	uc002zzi.1	Q9Y6J0	OTTHUMG00000150797	ENST00000398319.2:c.3907G>A	chr22.hg19:g.24492014G>A	ENSP00000381364:p.Glu1303Lys	107.0	0.0		68.0	24.0	NM_001199281	G5E9F3|Q6PHY0|Q9Y460	Missense_Mutation	SNP	ENST00000398319.2	hg19	CCDS13823.1	.	.	.	.	.	.	.	.	.	.	G	17.97	3.518608	0.64634	.	.	ENSG00000099991	ENST00000263119;ENST00000405822;ENST00000398319	T;T;T	0.65178	0.0;-0.14;0.0	4.91	4.91	0.64330	.	0.000000	0.85682	D	0.000000	T	0.44519	0.1297	L	0.28740	0.885	0.80722	D	1	P;P	0.40638	0.725;0.605	B;B	0.26770	0.073;0.033	T	0.44620	-0.9316	10	0.18276	T	0.48	.	17.5248	0.87796	0.0:0.0:1.0:0.0	.	1253;1303	G5E9F3;Q9Y6J0	.;CABIN_HUMAN	K	1303;1253;1303	ENSP00000263119:E1303K;ENSP00000384694:E1253K;ENSP00000381364:E1303K	ENSP00000263119:E1303K	E	+	1	0	CABIN1	22822014	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	8.616000	0.90924	2.468000	0.83385	0.650000	0.86243	GAG	.	.		0.552	CABIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320161.2	NM_012295		A	24492014	G	A	24492014	3	1	358	1	0	0	0	0	1	0	0	0	2530	1059	37	1	4001	1	CABIN1	22	24492014	Missense_Mutation	SNP	G	TCGA-XR-A8TD-01A-12D-A38X-10		24492014	26812552	57	50276										
CXorf22	170063	hgsc.bcm.edu	37	chrX	35988970	35988970	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	aaaaacagcaaaagaaattaCatgaaaactattatgcaatg	5	5	0	2	rs17852470		TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chrX:35988970C>T	ENST00000297866.5	+	11	1966	c.1900C>T	c.(1900-1902)Cat>Tat	p.H634Y		NM_152632.3	NP_689845.2	Q6ZTR5	CX022_HUMAN	chromosome X open reading frame 22	634			H -> Y (in dbSNP:rs17852470). {ECO:0000269|PubMed:15489334}.							breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(3)	44						AAAGAAATTACATGAAAACTA	0.303																																					p.H634Y		Atlas-SNP	.											.	CXorf22	272	.	0			c.C1900T						.						40	36	37					X																	35988970		2202	4293	6495	SO:0001583	missense	170063	exon11			AAATTACATGAAA	BC027936	CCDS14237.2	Xp21.1	2014-08-07			ENSG00000165164	ENSG00000165164			28546	protein-coding gene	gene with protein product						12477932	Standard	NM_152632		Approved	MGC34831	uc004ddj.3	Q6ZTR5	OTTHUMG00000021350	ENST00000297866.5:c.1900C>T	chrX.hg19:g.35988970C>T	ENSP00000297866:p.His634Tyr	697.0	1.0		767.0	163.0	NM_152632	Q5JRM8|Q8N6X8	Missense_Mutation	SNP	ENST00000297866.5	hg19	CCDS14237.2	.	.	.	.	.	.	.	.	.	.	C	13.38	2.221188	0.39201	.	.	ENSG00000165164	ENST00000297866	T	0.18810	2.19	5.0	2.96	0.34315	.	0.255981	0.37809	N	0.001927	T	0.37812	0.1017	M	0.74881	2.28	0.09310	N	1	D	0.76494	0.999	D	0.66979	0.948	T	0.16335	-1.0406	10	0.20519	T	0.43	-35.2732	8.5209	0.33275	0.5292:0.4708:0.0:0.0	rs17852470	634	Q6ZTR5	CX022_HUMAN	Y	634	ENSP00000297866:H634Y	ENSP00000297866:H634Y	H	+	1	0	CXorf22	35898891	0.001000	0.12720	0.012000	0.15200	0.003000	0.03518	-0.515000	0.06290	0.865000	0.35603	0.589000	0.80489	CAT	.	C|1.000;|0.000		0.303	CXorf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056216.2	NM_152632		T	35988970	C	T	35988970	3	4	358	1	0	0	0	0	1	0	0	0	4104	478	17	3	1942	3	CXorf22	23	35988970	Missense_Mutation	SNP	C	TCGA-XR-A8TD-01A-12D-A38X-10		35988970	119281590	58	50277										
HUWE1	10075	hgsc.bcm.edu	37	chrX	53579402	53579402	+	Splice_Site	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	tcagaggatgcaggtggggaGctgagggaaatcatgctcag	17	6	3	2			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chrX:53579402G>T	ENST00000342160.3	-	62	9208	c.8751C>A	c.(8749-8751)agC>agA	p.S2917R	HUWE1_ENST00000262854.6_Splice_Site_p.S2917R			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	2917					base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						CAGGTGGGGAGCTGAGGGAAA	0.488																																					p.S2917R		Atlas-SNP	.											.	HUWE1	724	.	0			c.C8751A						.						49	44	46					X																	53579402		2203	4300	6503	SO:0001630	splice_region_variant	10075	exon63			TGGGGAGCTGAGG	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"HECT, UBA and WWE domain containing 1"			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.8751-1C>A	chrX.hg19:g.53579402G>T		303.0	0.0		303.0	61.0	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	hg19	CCDS35301.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.94|14.94	2.685282|2.685282	0.47991|0.47991	.|.	.|.	ENSG00000086758|ENSG00000086758	ENST00000427052|ENST00000342160;ENST00000262854	.|T;T	.|0.35973	.|1.28;1.28	5.95|5.95	5.95|5.95	0.96441|0.96441	.|.	.|0.642748	.|0.17050	.|N	.|0.188954	T|T	0.25568|0.25568	0.0622|0.0622	N|N	0.14661|0.14661	0.345|0.345	0.45183|0.45183	D|D	0.998197|0.998197	.|B;B	.|0.21905	.|0.022;0.062	.|B;B	.|0.23716	.|0.004;0.048	T|T	0.10405|0.10405	-1.0631|-1.0631	5|10	.|0.13470	.|T	.|0.59	.|.	18.0042|18.0042	0.89205|0.89205	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|2917;2917	.|Q7Z6Z7;Q7Z6Z7-2	.|HUWE1_HUMAN;.	I|R	1951|2917	.|ENSP00000340648:S2917R;ENSP00000262854:S2917R	.|ENSP00000262854:S2917R	L|S	-|-	1|3	0|2	HUWE1|HUWE1	53596127|53596127	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.936000|0.936000	0.57629|0.57629	2.999000|2.999000	0.49473|0.49473	2.528000|2.528000	0.85240|0.85240	0.529000|0.529000	0.55759|0.55759	CTC|AGC	.	.		0.488	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119	Missense_Mutation	T	53579402	G	T	53579402	5	4	358	1	0	0	0	0	0	0	1	0	7470	985	34	3	4461	3	HUWE1	23	53579402	Splice_Site	SNP	G	TCGA-XR-A8TD-01A-12D-A38X-10	17590432	53579402	101691158	59	50278										
FAM120C	54954	hgsc.bcm.edu	37	chrX	54209302	54209302	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	cgggccccgggcagctgaggGggcggcggcggcggcagcgg	24	13	0	1			TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chrX:54209302G>C	ENST00000375180.2	-	1	386	c.330C>G	c.(328-330)ccC>ccG	p.P110P	FAM120C_ENST00000497680.1_5'Flank|FAM120C_ENST00000477084.1_Silent_p.P110P|FAM120C_ENST00000328235.4_Silent_p.P110P	NM_017848.4	NP_060318.3	Q9NX05	F120C_HUMAN	family with sequence similarity 120C	110							poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28						GCAGCTGAGGGGGCGGCGGCG	0.746																																					p.P110P		Atlas-SNP	.											.	FAM120C	89	.	0			c.C330G						.						3	4	3					X																	54209302		1733	3249	4982	SO:0001819	synonymous_variant	54954	exon1			CTGAGGGGGCGGC	AY150025	CCDS14356.1, CCDS55421.1, CCDS75987.1	Xp11.22	2011-04-13	2006-07-04	2006-07-04	ENSG00000184083	ENSG00000184083			16949	protein-coding gene	gene with protein product		300741	"chromosome X open reading frame 17"	CXorf17		14585507	Standard	XM_006724589		Approved	ORF34, FLJ20506	uc004dsz.4	Q9NX05	OTTHUMG00000021625	ENST00000375180.2:c.330C>G	chrX.hg19:g.54209302G>C		95.0	0.0		111.0	5.0	NM_017848	B2RMT7	Silent	SNP	ENST00000375180.2	hg19	CCDS14356.1																																																																																			.	.		0.746	FAM120C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056795.2	NM_017848		C	54209302	G	C	54209302	2	2	358	1	0	0	0	0	0	0	0	1	5423	1219	43	4		4	FAM120C	23	54209302	Silent	SNP	G	TCGA-XR-A8TD-01A-12D-A38X-10	629900	54209302	101061258	60	50279			1	68		2	2	17	N	G_A	3.152737e-05
FAM120C	54954	hgsc.bcm.edu	37	chrX	54209318	54209318	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0983606557377049	6	1	1.93771812080537	0	2.30680728667306	0.0108359133126935	0.241259836031806	0	gagggggcggcggcggcggcAgcggagggtgcagcccgggc	25	11	0	0	rs199506922		TCGA-XR-A8TD-01A-12D-A38X-10	TCGA-XR-A8TD-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	76dab338-0a6f-42fe-a0f3-d9427f704348	156d13f3-f11c-4ebf-9efe-80eab3ac25e7	g.chrX:54209318A>G	ENST00000375180.2	-	1	370	c.314T>C	c.(313-315)cTg>cCg	p.L105P	FAM120C_ENST00000497680.1_5'Flank|FAM120C_ENST00000477084.1_Missense_Mutation_p.L105P|FAM120C_ENST00000328235.4_Missense_Mutation_p.L105P	NM_017848.4	NP_060318.3	Q9NX05	F120C_HUMAN	family with sequence similarity 120C	105							poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28						CGGCGGCGGCAGCGGAGGGTG	0.746													a|||	2	0.000529801	0	0	3775	,	,		7371	0		0.001	False		,,,				2504	0.001				p.L105P		Atlas-SNP	.											.	FAM120C	89	.	0			c.T314C						.						3	4	3					X																	54209318		1477	2706	4183	SO:0001583	missense	54954	exon1			GGCGGCAGCGGAG	AY150025	CCDS14356.1, CCDS55421.1, CCDS75987.1	Xp11.22	2011-04-13	2006-07-04	2006-07-04	ENSG00000184083	ENSG00000184083			16949	protein-coding gene	gene with protein product		300741	"chromosome X open reading frame 17"	CXorf17		14585507	Standard	XM_006724589		Approved	ORF34, FLJ20506	uc004dsz.4	Q9NX05	OTTHUMG00000021625	ENST00000375180.2:c.314T>C	chrX.hg19:g.54209318A>G	ENSP00000364324:p.Leu105Pro	99.0	0.0		100.0	9.0	NM_017848	B2RMT7	Missense_Mutation	SNP	ENST00000375180.2	hg19	CCDS14356.1	.	.	.	.	.	.	.	.	.	.	a	9.339	1.062497	0.19987	.	.	ENSG00000184083	ENST00000375180;ENST00000328235;ENST00000477084	T;T;T	0.47869	1.82;1.36;0.83	2.73	1.45	0.22620	.	0.278989	0.27531	N	0.018943	T	0.19327	0.0464	N	0.03608	-0.345	0.47476	D	0.999433	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.03008	-1.1083	10	0.32370	T	0.25	0.3639	4.7246	0.12935	0.4324:0.0:0.5676:0.0	.	105;105;105	F8W881;Q9NX05-2;Q9NX05	.;.;F120C_HUMAN	P	105	ENSP00000364324:L105P;ENSP00000329896:L105P;ENSP00000420718:L105P	ENSP00000329896:L105P	L	-	2	0	FAM120C	54226043	0.970000	0.33590	0.968000	0.41197	0.426000	0.31534	0.267000	0.18552	0.262000	0.21774	0.378000	0.23410	CTG	.	.		0.746	FAM120C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056795.2	NM_017848		G	54209318	A	G	54209318	3	3	358	1	0	0	0	0	1	0	0	0	5423	188	7	2	3062	2	FAM120C	23	54209318	Missense_Mutation	SNP	A	TCGA-XR-A8TD-01A-12D-A38X-10	16	54209318	101061242	61	50280			1	68		2	2	17	N	G_A	3.152737e-05
NADK	65220	hgsc.bcm.edu	37	chr1	1684346	1684346	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctggataggggcttgacctaGccctcctcctcctcctcctc	8	18	0	1			TCGA-XR-A8TE-01A-11D-A35Z-10	TCGA-XR-A8TE-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52ed1382-9a5b-4ac9-95ff-e59c6d6c48ff	2d84231b-c606-494f-9df7-68b2f88ac114	g.chr1:1684346G>C	ENST00000341426.5	-	12	1559	c.1338C>G	c.(1336-1338)ggC>ggG	p.G446G	NADK_ENST00000378625.1_Silent_p.G591G|NADK_ENST00000342348.5_Silent_p.G414G|NADK_ENST00000344463.4_Silent_p.G591G|NADK_ENST00000341991.3_Silent_p.G446G	NM_023018.4	NP_075394.3	O95544	NADK_HUMAN	NAD kinase	446				G -> EG (in Ref. 3; BAH12420). {ECO:0000305}.	ATP metabolic process (GO:0046034)|NAD metabolic process (GO:0019674)|NADP biosynthetic process (GO:0006741)|phosphorylation (GO:0016310)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			NS(1)|autonomic_ganglia(1)|endometrium(4)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)|stomach(1)|urinary_tract(1)	17	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.61e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;8.75e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.33e-23)|GBM - Glioblastoma multiforme(42;1.35e-07)|Colorectal(212;0.000203)|COAD - Colon adenocarcinoma(227;0.000225)|Kidney(185;0.00265)|STAD - Stomach adenocarcinoma(132;0.00655)|BRCA - Breast invasive adenocarcinoma(365;0.00855)|KIRC - Kidney renal clear cell carcinoma(229;0.0382)|Lung(427;0.207)		GCTTGACCTAGCcctcctcct	0.627																																					p.G591G		Atlas-SNP	.											.	NADK	79	.	0			c.C1773G						.						26	23	24					1																	1684346		2202	4300	6502	SO:0001819	synonymous_variant	65220	exon14			GACCTAGCCCTCC	BC001709	CCDS30565.1, CCDS55561.1, CCDS55562.1	1p36.33	2013-04-29			ENSG00000008130	ENSG00000008130	2.7.1.23		29831	protein-coding gene	gene with protein product		611616				11594753	Standard	NM_023018		Approved	FLJ13052	uc001aie.3	O95544	OTTHUMG00000000942	ENST00000341426.5:c.1338C>G	chr1.hg19:g.1684346G>C		99.0	0.0		65.0	6.0	NM_001198994	A6NNN3|A8K296|B7Z434|F5GXR5|Q5QPS4|Q9H2P2|Q9H931	Silent	SNP	ENST00000341426.5	hg19	CCDS30565.1																																																																																			.	.		0.627	NADK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002769.1	NM_023018		C	1684346	G	C	1684346	2	2	359	1	0	0	0	0	0	0	0	1	10146	958	34	4		4	NADK	1	1684346	Silent	SNP	G	TCGA-XR-A8TE-01A-11D-A35Z-10		1684346	247566275	1	50281										
CLIP4	79745	hgsc.bcm.edu	37	chr2	29366594	29366594	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gaatgacaaaggacagatccCtgctgatgttgttccagacc	10	10	0	4			TCGA-XR-A8TE-01A-11D-A35Z-10	TCGA-XR-A8TE-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52ed1382-9a5b-4ac9-95ff-e59c6d6c48ff	2d84231b-c606-494f-9df7-68b2f88ac114	g.chr2:29366594C>A	ENST00000320081.5	+	7	923	c.668C>A	c.(667-669)cCt>cAt	p.P223H	CLIP4_ENST00000404424.1_Missense_Mutation_p.P223H|CLIP4_ENST00000401617.2_Missense_Mutation_p.P116H|CLIP4_ENST00000401605.1_Missense_Mutation_p.P223H	NM_024692.4	NP_078968.3	Q8N3C7	CLIP4_HUMAN	CAP-GLY domain containing linker protein family, member 4	223										endometrium(4)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|prostate(1)|skin(1)	26	Acute lymphoblastic leukemia(172;0.155)					GGACAGATCCCTGCTGATGTT	0.418																																					p.P223H		Atlas-SNP	.											.	CLIP4	69	.	0			c.C668A						.						83	85	84					2																	29366594		2203	4300	6503	SO:0001583	missense	79745	exon7			AGATCCCTGCTGA	AK024722	CCDS1770.1, CCDS74502.1	2p23	2013-01-10	2007-01-04	2007-01-04	ENSG00000115295	ENSG00000115295		"Ankyrin repeat domain containing"	26108	protein-coding gene	gene with protein product			"restin-like 2"	RSNL2			Standard	XM_005264562		Approved	FLJ21069	uc002rmv.3	Q8N3C7	OTTHUMG00000097837	ENST00000320081.5:c.668C>A	chr2.hg19:g.29366594C>A	ENSP00000327009:p.Pro223His	177.0	0.0		129.0	57.0	NM_024692	A0AV10|B2RMQ3|B7Z7N8|Q7Z4U3|Q96BR7|Q96MA5|Q9H7C0	Missense_Mutation	SNP	ENST00000320081.5	hg19	CCDS1770.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.543573	0.86022	.	.	ENSG00000115295	ENST00000401605;ENST00000401617;ENST00000404424;ENST00000402240;ENST00000320081;ENST00000379543;ENST00000530644	T;T;T;T	0.61274	0.12;0.12;0.12;0.12	5.5	5.5	0.81552	Ankyrin repeat-containing domain (3);	0.052984	0.85682	D	0.000000	T	0.75824	0.3902	M	0.75264	2.295	0.80722	D	1	D;D	0.71674	0.998;0.998	P;D	0.63703	0.879;0.917	T	0.78507	-0.2177	10	0.87932	D	0	.	19.3951	0.94604	0.0:1.0:0.0:0.0	.	223;223	A8K6D0;Q8N3C7	.;CLIP4_HUMAN	H	223;116;223;223;223;224;205	ENSP00000384242:P223H;ENSP00000385148:P116H;ENSP00000385594:P223H;ENSP00000327009:P223H	ENSP00000327009:P223H	P	+	2	0	CLIP4	29220098	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	7.818000	0.86416	2.571000	0.86741	0.655000	0.94253	CCT	.	.		0.418	CLIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215123.2	NM_024692		A	29366594	C	A	29366594	3	1	359	1	0	0	0	0	1	0	0	0	3537	681	24	3	690	3	CLIP4	2	29366594	Missense_Mutation	SNP	C	TCGA-XR-A8TE-01A-11D-A35Z-10		29366594	213832779	2	50282										
SIX2	10736	hgsc.bcm.edu	37	chr2	45235916	45235916	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	cggcagcgggaatttgcggcGcacgcggtatttgcccacgg	16	12	0	0			TCGA-XR-A8TE-01A-11D-A35Z-10	TCGA-XR-A8TE-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52ed1382-9a5b-4ac9-95ff-e59c6d6c48ff	2d84231b-c606-494f-9df7-68b2f88ac114	g.chr2:45235916G>A	ENST00000303077.6	-	1	653	c.334C>T	c.(334-336)Cgc>Tgc	p.R112C		NM_016932.4	NP_058628.3	Q9NPC8	SIX2_HUMAN	SIX homeobox 2	112					anatomical structure morphogenesis (GO:0009653)|anterior/posterior axis specification (GO:0009948)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|chondrocyte differentiation (GO:0002062)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|kidney development (GO:0001822)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|mesenchymal stem cell maintenance involved in nephron morphogenesis (GO:0072038)|mesenchymal stem cell proliferation (GO:0097168)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|mesodermal cell fate specification (GO:0007501)|middle ear morphogenesis (GO:0042474)|nephron development (GO:0072006)|nephron morphogenesis (GO:0072028)|positive regulation of chondrocyte proliferation (GO:1902732)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein import into nucleus (GO:0006606)|regulation of branching involved in ureteric bud morphogenesis (GO:0090189)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(6)|large_intestine(3)|lung(8)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	22		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				AATTTGCGGCGCACGCGGTAT	0.657																																					p.R112C		Atlas-SNP	.											.	SIX2	39	.	0			c.C334T						.						40	44	42					2																	45235916		2203	4300	6503	SO:0001583	missense	10736	exon1			TGCGGCGCACGCG	AF136939	CCDS1822.1	2p21	2011-06-20	2007-07-13		ENSG00000170577	ENSG00000170577		"Homeoboxes / SINE class"	10888	protein-coding gene	gene with protein product		604994	"sine oculis homeobox (Drosophila) homolog 2", "sine oculis homeobox homolog 2 (Drosophila)"				Standard	NM_016932		Approved		uc002ruo.3	Q9NPC8	OTTHUMG00000152421	ENST00000303077.6:c.334C>T	chr2.hg19:g.45235916G>A	ENSP00000304502:p.Arg112Cys	103.0	0.0		102.0	6.0	NM_016932	Q9BXH7	Missense_Mutation	SNP	ENST00000303077.6	hg19	CCDS1822.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.980571	0.92982	.	.	ENSG00000170577	ENST00000303077	D	0.91740	-2.9	4.58	4.58	0.56647	.	0.000000	0.85682	D	0.000000	D	0.97504	0.9183	H	0.96633	3.855	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.99331	1.0909	10	0.87932	D	0	-31.7345	16.9715	0.86301	0.0:0.0:1.0:0.0	.	112;112	Q8TBA2;Q9NPC8	.;SIX2_HUMAN	C	112	ENSP00000304502:R112C	ENSP00000304502:R112C	R	-	1	0	SIX2	45089420	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.674000	0.74487	2.081000	0.62600	0.462000	0.41574	CGC	.	.		0.657	SIX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326188.2			A	45235916	G	A	45235916	3	1	359	1	0	0	0	0	1	0	0	0	14362	1087	38	1	549	1	SIX2	2	45235916	Missense_Mutation	SNP	G	TCGA-XR-A8TE-01A-11D-A35Z-10	15869322	45235916	197963457	3	50283										
MMRN1	22915	hgsc.bcm.edu	37	chr4	90857798	90857798	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	acttgttgtatagatcgatcGttgcctggtagtctggcaaa	11	7	1	1			TCGA-XR-A8TE-01A-11D-A35Z-10	TCGA-XR-A8TE-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52ed1382-9a5b-4ac9-95ff-e59c6d6c48ff	2d84231b-c606-494f-9df7-68b2f88ac114	g.chr4:90857798G>A	ENST00000394980.1	+	7	3286	c.2967G>A	c.(2965-2967)tcG>tcA	p.S989S	MMRN1_ENST00000508372.1_Silent_p.S731S|MMRN1_ENST00000264790.2_Silent_p.S989S|MMRN1_ENST00000394981.1_Intron			Q13201	MMRN1_HUMAN	multimerin 1	989					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)				breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|liver(2)|lung(34)|ovary(5)|prostate(1)|skin(6)|stomach(1)|urinary_tract(2)	72		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)		TAGATCGATCGTTGCCTGGTA	0.353																																					p.S989S		Atlas-SNP	.											.	MMRN1	174	.	0			c.G2967A						.						59	63	62					4																	90857798		2203	4298	6501	SO:0001819	synonymous_variant	22915	exon6			TCGATCGTTGCCT	U27109	CCDS3635.1	4q22	2008-02-05	2004-03-02	2004-03-02	ENSG00000138722	ENSG00000138722		"EMI domain containing"	7178	protein-coding gene	gene with protein product	"glycoprotein Ia*"	601456	"multimerin"	MMRN		7629143, 10828608	Standard	NM_007351		Approved	ECM, EMILIN4, GPIa*	uc003hst.3	Q13201	OTTHUMG00000130947	ENST00000394980.1:c.2967G>A	chr4.hg19:g.90857798G>A		215.0	0.0		173.0	33.0	NM_007351	Q4W5L1|Q6P3T8|Q6ZUL9	Silent	SNP	ENST00000394980.1	hg19	CCDS3635.1																																																																																			.	.		0.353	MMRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253546.2	NM_007351		A	90857798	G	A	90857798	2	1	359	1	0	0	0	0	0	0	0	1	9679	1132	40	1		1	MMRN1	4	90857798	Silent	SNP	G	TCGA-XR-A8TE-01A-11D-A35Z-10		90857798	100296478	4	50284										
GPM6A	2823	hgsc.bcm.edu	37	chr4	176556161	176556161	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tacttctgcatccggcaggcGtctttcacataggcccagtt	9	13	3	0	rs141777363	byFrequency	TCGA-XR-A8TE-01A-11D-A35Z-10	TCGA-XR-A8TE-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52ed1382-9a5b-4ac9-95ff-e59c6d6c48ff	2d84231b-c606-494f-9df7-68b2f88ac114	g.chr4:176556161G>A	ENST00000280187.7	-	8	777	c.732C>T	c.(730-732)gaC>gaT	p.D244D	GPM6A_ENST00000393658.2_Silent_p.D244D|GPM6A_ENST00000506219.1_5'UTR|GPM6A_ENST00000515090.1_Silent_p.D237D|GPM6A_ENST00000506894.1_Silent_p.D233D	NM_005277.4	NP_005268.1	P51674	GPM6A_HUMAN	glycoprotein M6A	244					neural retina development (GO:0003407)|neuron migration (GO:0001764)|neuron projection morphogenesis (GO:0048812)|positive regulation of filopodium assembly (GO:0051491)|stem cell differentiation (GO:0048863)|synapse assembly (GO:0007416)	axonal growth cone (GO:0044295)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	calcium channel activity (GO:0005262)			NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(16)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	33		Breast(14;7.35e-05)|Melanoma(52;0.00909)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;9.21e-19)|Epithelial(43;3.01e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.02e-09)|STAD - Stomach adenocarcinoma(60;0.00083)|GBM - Glioblastoma multiforme(59;0.00168)|LUSC - Lung squamous cell carcinoma(193;0.0388)		TCCGGCAGGCGTCTTTCACAT	0.428													G|||	2	0.000399361	8e-04	0	5008	,	,		17428	0		0	False		,,,				2504	0.001				p.D244D		Atlas-SNP	.											.	GPM6A	70	.	0			c.C732T						.	G	,,	0,4406		0,0,2203	85	78	80		732,732,699	0.3	1	4	dbSNP_134	80	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	GPM6A	NM_005277.3,NM_201591.1,NM_201592.1	,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,	244/279,244/279,233/268	176556161	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	2823	exon7			GCAGGCGTCTTTC		CCDS3824.1, CCDS54822.1, CCDS58936.1	4q34	2008-08-29				ENSG00000150625			4460	protein-coding gene	gene with protein product		601275		GPM6		8661015, 18574501	Standard	NM_005277		Approved		uc003iug.4	P51674		ENST00000280187.7:c.732C>T	chr4.hg19:g.176556161G>A		69.0	0.0		48.0	15.0	NM_201591	B7Z642|E9PHI5|Q92602	Silent	SNP	ENST00000280187.7	hg19	CCDS3824.1																																																																																			.	G|1.000;A|0.000		0.428	GPM6A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362163.1			A	176556161	G	A	176556161	2	1	359	1	0	0	0	0	0	0	0	1	6623	1136	40	1		1	GPM6A	4	176556161	Silent	SNP	G	TCGA-XR-A8TE-01A-11D-A35Z-10	85698363	176556161	14598115	5	50285										
EIF2AK1	27102	hgsc.bcm.edu	37	chr7	6064424	6064424	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	attatcttcatctgtagggtGaggttaacctgtaaggagaa	11	5	3	2			TCGA-XR-A8TE-01A-11D-A35Z-10	TCGA-XR-A8TE-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52ed1382-9a5b-4ac9-95ff-e59c6d6c48ff	2d84231b-c606-494f-9df7-68b2f88ac114	g.chr7:6064424G>T	ENST00000199389.6	-	15	1919	c.1773C>A	c.(1771-1773)ctC>ctA	p.L591L	EIF2AK1_ENST00000536084.1_Silent_p.L467L	NM_001134335.1|NM_014413.3	NP_001127807.1|NP_055228.2	Q9BQI3	E2AK1_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 1	591					negative regulation of cell proliferation (GO:0008285)|negative regulation of hemoglobin biosynthetic process (GO:0046986)|negative regulation of translational initiation by iron (GO:0045993)|protein autophosphorylation (GO:0046777)|protoporphyrinogen IX metabolic process (GO:0046501)|regulation of eIF2 alpha phosphorylation by heme (GO:0010999)|response to external stimulus (GO:0009605)|response to stress (GO:0006950)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|heme binding (GO:0020037)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	27		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.106)|OV - Ovarian serous cystadenocarcinoma(56;5.22e-14)		TCTGTAGGGTGAGGTTAACCT	0.383																																					p.L591L		Atlas-SNP	.											.	EIF2AK1	76	.	0			c.C1773A						.						121	105	110					7																	6064424		2203	4300	6503	SO:0001819	synonymous_variant	27102	exon15			TAGGGTGAGGTTA	BC006524	CCDS5345.1	7p22	2005-01-20			ENSG00000086232	ENSG00000086232			24921	protein-coding gene	gene with protein product	"heme regulated initiation factor 2 alpha kinase"	613635				7709427, 10718198	Standard	NM_014413		Approved	HRI, KIAA1369	uc003spp.3	Q9BQI3	OTTHUMG00000090689	ENST00000199389.6:c.1773C>A	chr7.hg19:g.6064424G>T		65.0	0.0		76.0	4.0	NM_014413	A8K2R2|Q549K6|Q8NBW3|Q9HC02|Q9NYE0|Q9P0V6|Q9P1J5|Q9P2H8|Q9UHG4	Silent	SNP	ENST00000199389.6	hg19	CCDS5345.1	.	.	.	.	.	.	.	.	.	.	G	2.091	-0.408431	0.04832	.	.	ENSG00000086232	ENST00000422786	.	.	.	5.49	1.14	0.20703	.	.	.	.	.	T	0.24812	0.0602	.	.	.	0.27146	N	0.961534	.	.	.	.	.	.	T	0.24693	-1.0153	4	.	.	.	-11.5986	4.6152	0.12422	0.444:0.1642:0.3918:0.0	.	.	.	.	N	43	.	.	H	-	1	0	EIF2AK1	6030950	0.960000	0.32886	0.886000	0.34754	0.459000	0.32528	0.550000	0.23345	0.040000	0.15660	-0.262000	0.10625	CAC	.	.		0.383	EIF2AK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207373.2	NM_014413		T	6064424	G	T	6064424	2	4	359	1	0	0	0	0	0	0	0	1	4998	1277	45	3		3	EIF2AK1	7	6064424	Silent	SNP	G	TCGA-XR-A8TE-01A-11D-A35Z-10		6064424	153074239	6	50286										
AHR	196	hgsc.bcm.edu	37	chr7	17362177	17362177	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ggaggccaggataactgtagAgcagcaaatttcagagaagg	14	6	1	2			TCGA-XR-A8TE-01A-11D-A35Z-10	TCGA-XR-A8TE-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52ed1382-9a5b-4ac9-95ff-e59c6d6c48ff	2d84231b-c606-494f-9df7-68b2f88ac114	g.chr7:17362177A>G	ENST00000242057.4	+	3	949	c.306A>G	c.(304-306)agA>agG	p.R102R		NM_001621.4	NP_001612.1	P35869	AHR_HUMAN	aryl hydrocarbon receptor	102					apoptotic process (GO:0006915)|blood vessel development (GO:0001568)|cell cycle (GO:0007049)|circadian regulation of gene expression (GO:0032922)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|regulation of B cell proliferation (GO:0030888)|regulation of gene expression (GO:0010468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to toxic substance (GO:0009636)|response to xenobiotic stimulus (GO:0009410)|transcription from RNA polymerase II promoter (GO:0006366)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosolic aryl hydrocarbon receptor complex (GO:0034752)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|Hsp90 protein binding (GO:0051879)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(11)|ovary(1)|pancreas(1)|urinary_tract(3)	33	Lung NSC(10;0.0392)|all_lung(11;0.0754)				Atorvastatin(DB01076)|Flutamide(DB00499)|Ginseng(DB01404)|Leflunomide(DB01097)|Mexiletine(DB00379)|Nimodipine(DB00393)	ATAACTGTAGAGCAGCAAATT	0.333																																					p.R102R		Atlas-SNP	.											.	AHR	89	.	0			c.A306G						.						67	68	68					7																	17362177		2203	4299	6502	SO:0001819	synonymous_variant	196	exon3			CTGTAGAGCAGCA	L19872	CCDS5366.1	7p15	2013-05-21			ENSG00000106546	ENSG00000106546		"Basic helix-loop-helix proteins"	348	protein-coding gene	gene with protein product		600253				8125016	Standard	NM_001621		Approved	bHLHe76	uc011jxz.1	P35869	OTTHUMG00000149967	ENST00000242057.4:c.306A>G	chr7.hg19:g.17362177A>G		567.0	0.0		641.0	30.0	NM_001621	A4D130|Q13728|Q13803|Q13804	Silent	SNP	ENST00000242057.4	hg19	CCDS5366.1																																																																																			.	.		0.333	AHR-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314620.2	NM_001621		G	17362177	A	G	17362177	2	3	359	1	0	0	0	0	0	0	0	1	416	301	11	2		2	AHR	7	17362177	Silent	SNP	A	TCGA-XR-A8TE-01A-11D-A35Z-10	11297753	17362177	141776486	7	50287										
LRRC4	64101	hgsc.bcm.edu	37	chr7	127669904	127669904	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttccacaagtgaagccagccCgtcaaaagcattccgctcaa	7	14	2	1			TCGA-XR-A8TE-01A-11D-A35Z-10	TCGA-XR-A8TE-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52ed1382-9a5b-4ac9-95ff-e59c6d6c48ff	2d84231b-c606-494f-9df7-68b2f88ac114	g.chr7:127669904C>T	ENST00000249363.3	-	2	1047	c.790G>A	c.(790-792)Ggg>Agg	p.G264R	SND1_ENST00000354725.3_Intron	NM_022143.4	NP_071426.1	Q9HBW1	LRRC4_HUMAN	leucine rich repeat containing 4	264					postsynaptic density protein 95 clustering (GO:0097119)|regulation of synapse organization (GO:0050807)|synapse organization (GO:0050808)	cell junction (GO:0030054)|dendritic spine (GO:0043197)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)		p.G264W(1)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(6)|lung(4)|pancreas(1)|skin(2)	26				Lung(243;0.124)		GAAGCCAGCCCGTCAAAAGCA	0.547																																					p.G264R		Atlas-SNP	.											LRRC4,colon,carcinoma,0,1	LRRC4	72	.	1	Substitution - Missense(1)	large_intestine(1)	c.G790A						.						68	51	57					7																	127669904		2203	4299	6502	SO:0001583	missense	64101	exon2			CCAGCCCGTCAAA	AF196976	CCDS5799.1	7q31	2013-01-14	2003-11-19		ENSG00000128594	ENSG00000128594		"Immunoglobulin superfamily / I-set domain containing"	15586	protein-coding gene	gene with protein product		610486	"leucine-rich repeat-containing 4"			12969517	Standard	NM_022143		Approved	NAG14	uc003vmk.3	Q9HBW1	OTTHUMG00000157563	ENST00000249363.3:c.790G>A	chr7.hg19:g.127669904C>T	ENSP00000249363:p.Gly264Arg	145.0	0.0		122.0	27.0	NM_022143	A4D0Y9|Q14DU9|Q6ZMI8|Q96A85	Missense_Mutation	SNP	ENST00000249363.3	hg19	CCDS5799.1	.	.	.	.	.	.	.	.	.	.	C	17.75	3.466287	0.63625	.	.	ENSG00000128594	ENST00000249363	T	0.62364	0.03	4.7	4.7	0.59300	.	0.331492	0.27340	N	0.019812	T	0.65048	0.2654	M	0.66939	2.045	0.50632	D	0.999886	D	0.55800	0.973	P	0.46389	0.515	T	0.67043	-0.5770	10	0.37606	T	0.19	.	15.1891	0.73028	0.0:1.0:0.0:0.0	.	264	Q9HBW1	LRRC4_HUMAN	R	264	ENSP00000249363:G264R	ENSP00000249363:G264R	G	-	1	0	LRRC4	127457140	0.998000	0.40836	0.998000	0.56505	0.988000	0.76386	3.954000	0.56708	2.408000	0.81797	0.655000	0.94253	GGG	.	.		0.547	LRRC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349170.1	NM_022143		T	127669904	C	T	127669904	3	4	359	1	0	0	0	0	1	0	0	0	9006	652	23	1	1175	1	LRRC4	7	127669904	Missense_Mutation	SNP	C	TCGA-XR-A8TE-01A-11D-A35Z-10	110307727	127669904	31468759	8	50288										
IRF5	3663	hgsc.bcm.edu	37	chr7	128587359	128587359	+	Missense_Mutation	SNP	A	A	G													0	0	1	0	0	0	1	1	0	caagtggccgcccactctgcAgccgcccactctgcggccgc					rs566635242|rs199508964|rs60344245	byFrequency	TCGA-XR-A8TE-01A-11D-A35Z-10	TCGA-XR-A8TE-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52ed1382-9a5b-4ac9-95ff-e59c6d6c48ff	2d84231b-c606-494f-9df7-68b2f88ac114	g.chr7:128587359A>G	ENST00000402030.2	+	6	581	c.509A>G	c.(508-510)cAg>cGg	p.Q170R	IRF5_ENST00000473745.1_Missense_Mutation_p.Q170R|IRF5_ENST00000357234.5_Missense_Mutation_p.Q186R|IRF5_ENST00000477535.1_Intron|IRF5_ENST00000249375.4_Missense_Mutation_p.Q170R	NM_001098629.1|NM_001098630.1	NP_001092099.1|NP_001092100.1	Q13568	IRF5_HUMAN	interferon regulatory factor 5	170					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to muramyl dipeptide (GO:0032495)|response to peptidoglycan (GO:0032494)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.?(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(1)|prostate(1)	15						CCCACTCTGCAGCCGCCCACT	0.657													A|||	1	0.000199681	0	0.0014	5008	,	,		13852	0		0	False		,,,				2504	0				p.Q186R		Atlas-SNP	.											.	IRF5	40	.	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	c.A557G						.						9	11	10					7																	128587359		2119	4233	6352	SO:0001583	missense	3663	exon6			CTCTGCAGCCGCC		CCDS5808.1, CCDS43645.1, CCDS56512.1	7q32	2008-07-18			ENSG00000128604	ENSG00000128604			6120	protein-coding gene	gene with protein product		607218					Standard	XM_005250317		Approved		uc003vog.3	Q13568	OTTHUMG00000158410	ENST00000402030.2:c.509A>G	chr7.hg19:g.128587359A>G	ENSP00000385352:p.Gln170Arg	145.0	0.0		131.0	10.0	NM_001098629	A4D1J8|A8DUA8|A8DUA9|E7EQ16|E7EW54|Q1A7B4|Q64GA9|Q64GB1|Q64GB2|Q6RCM8|Q9BQF0	Missense_Mutation	SNP	ENST00000402030.2	hg19	CCDS5808.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	1.282|1.282	-0.609995|-0.609995	0.03690|0.03690	.|.	.|.	ENSG00000128604|ENSG00000128604	ENST00000357234;ENST00000402030;ENST00000249375;ENST00000473745;ENST00000412326|ENST00000430204	D;D;D;D|.	0.97328|.	-4.34;-4.31;-4.31;-4.31|.	0.128|0.128	0.128|0.128	0.14733|0.14733	.|.	2.402420|.	0.02158|.	N|.	0.058537|.	T|T	0.23451|0.23451	0.0567|0.0567	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	N|N	1|1	B;.|.	0.02656|.	0.0;.|.	B;.|.	0.01281|.	0.0;.|.	T|T	0.27020|0.27020	-1.0086|-1.0086	9|5	0.10636|0.30854	T|T	0.68|0.27	.|.	.|.	.|.	.|.	.|.	170;186|159	Q13568;Q13568-2|E9PC81	IRF5_HUMAN;.|.	R|G	186;170;170;170;170|159	ENSP00000349770:Q186R;ENSP00000385352:Q170R;ENSP00000249375:Q170R;ENSP00000419149:Q170R|.	ENSP00000249375:Q170R|ENSP00000409106:S159G	Q|S	+|+	2|1	0|0	IRF5|IRF5	128374595|128374595	0.021000|0.021000	0.18746|0.18746	0.470000|0.470000	0.27216|0.27216	0.091000|0.091000	0.18340|0.18340	0.271000|0.271000	0.18626|0.18626	0.243000|0.243000	0.21327|0.21327	0.240000|0.240000	0.17902|0.17902	CAG|AGC	.	.		0.657	IRF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350934.1	NM_001098627		G	128587359	A	G	128587359	3	3	359	1	0	0	0	0	1	0	0	0	7842	188	7	2	575	2	IRF5	7	128587359	Missense_Mutation	SNP	A	TCGA-XR-A8TE-01A-11D-A35Z-10	917455	128587359	30551304	9	50289	261	2								
IRF5	3663	hgsc.bcm.edu	37	chr7	128587366	128587366	+	Silent	SNP	C	C	T													0	0	1	0	0	0	1	1	0	ccgcccactctgcagccgccCactctgcggccgcctactct					rs534043449|rs199508964|rs60344245	byFrequency	TCGA-XR-A8TE-01A-11D-A35Z-10	TCGA-XR-A8TE-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52ed1382-9a5b-4ac9-95ff-e59c6d6c48ff	2d84231b-c606-494f-9df7-68b2f88ac114	g.chr7:128587366C>T	ENST00000402030.2	+	6	588	c.516C>T	c.(514-516)ccC>ccT	p.P172P	IRF5_ENST00000473745.1_Silent_p.P172P|IRF5_ENST00000357234.5_Silent_p.P188P|IRF5_ENST00000477535.1_Intron|IRF5_ENST00000249375.4_Silent_p.P172P	NM_001098629.1|NM_001098630.1	NP_001092099.1|NP_001092100.1	Q13568	IRF5_HUMAN	interferon regulatory factor 5	172					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to muramyl dipeptide (GO:0032495)|response to peptidoglycan (GO:0032494)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.?(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(1)|prostate(1)	15						TGCAGCCGCCCACTCTGCGGC	0.657													C|||	3	0.000599042	0	0.0014	5008	,	,		12915	0.001		0.001	False		,,,				2504	0				p.P188P		Atlas-SNP	.											.	IRF5	40	.	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	c.C564T						.						8	9	9					7																	128587366		2090	4208	6298	SO:0001819	synonymous_variant	3663	exon6			GCCGCCCACTCTG		CCDS5808.1, CCDS43645.1, CCDS56512.1	7q32	2008-07-18			ENSG00000128604	ENSG00000128604			6120	protein-coding gene	gene with protein product		607218					Standard	XM_005250317		Approved		uc003vog.3	Q13568	OTTHUMG00000158410	ENST00000402030.2:c.516C>T	chr7.hg19:g.128587366C>T		129.0	0.0		131.0	17.0	NM_001098629	A4D1J8|A8DUA8|A8DUA9|E7EQ16|E7EW54|Q1A7B4|Q64GA9|Q64GB1|Q64GB2|Q6RCM8|Q9BQF0	Silent	SNP	ENST00000402030.2	hg19	CCDS5808.1	.	.	.	.	.	.	.	.	.	.	C	3.008	-0.204506	0.06180	.	.	ENSG00000128604	ENST00000430204	.	.	.	.	.	.	.	0.400804	0.18480	N	0.139975	T	0.13286	0.0322	.	.	.	0.19775	N	0.999958	.	.	.	.	.	.	T	0.29792	-1.0000	4	0.07644	T	0.81	.	.	.	.	.	161	E9PC81	.	L	161	.	ENSP00000409106:P161L	P	+	2	0	IRF5	128374602	0.023000	0.18921	0.251000	0.24312	0.062000	0.15995	0.105000	0.15333	0.119000	0.18210	0.121000	0.15741	CCA	.	.		0.657	IRF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350934.1	NM_001098627		T	128587366	C	T	128587366	2	4	359	1	0	0	0	0	0	0	0	1	7842	581	21	3		3	IRF5	7	128587366	Silent	SNP	C	TCGA-XR-A8TE-01A-11D-A35Z-10	7	128587366	30551297	10	50290	261	2								
PODXL	5420	hgsc.bcm.edu	37	chr7	131241035	131241035	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	tcaccattctgggagggcgaCggcgacggcgacggcgacga	17	12	2	0	rs11277659|rs547816245|rs532078953	byFrequency	TCGA-XR-A8TE-01A-11D-A35Z-10	TCGA-XR-A8TE-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52ed1382-9a5b-4ac9-95ff-e59c6d6c48ff	2d84231b-c606-494f-9df7-68b2f88ac114	g.chr7:131241035C>G	ENST00000378555.3	-	1	331	c.84G>C	c.(82-84)ccG>ccC	p.P28P	PODXL_ENST00000465001.1_Intron|PODXL_ENST00000537928.1_Silent_p.P28P|PODXL_ENST00000322985.9_Silent_p.P28P|PODXL_ENST00000541194.1_Silent_p.P28P			O00592	PODXL_HUMAN	podocalyxin-like	28					cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)		p.P30_S31delPS(2)		NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					GGGAGggcgacggcgacggcg	0.741																																					p.P28P		Atlas-SNP	.											.	PODXL	53	.	2	Deletion - In frame(2)	prostate(2)	c.G84C						.																																			SO:0001819	synonymous_variant	5420	exon1			GGGCGACGGCGAC		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.84G>C	chr7.hg19:g.131241035C>G		60.0	0.0		105.0	5.0	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Silent	SNP	ENST00000378555.3	hg19	CCDS34755.1																																																																																			.	.		0.741	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111		G	131241035	C	G	131241035	2	3	359	1	0	0	0	0	0	0	0	1	12189	523	19	4		4	PODXL	7	131241035	Silent	SNP	C	TCGA-XR-A8TE-01A-11D-A35Z-10	2653669	131241035	27897628	11	50291										
XKR4	114786	hgsc.bcm.edu	37	chr8	56270341	56270341	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	atgagtatgcggatgtgagtAtgctgcatttgctagccacc	12	8	0	2			TCGA-XR-A8TE-01A-11D-A35Z-10	TCGA-XR-A8TE-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52ed1382-9a5b-4ac9-95ff-e59c6d6c48ff	2d84231b-c606-494f-9df7-68b2f88ac114	g.chr8:56270341A>C	ENST00000327381.6	+	2	1010	c.910A>C	c.(910-912)Atg>Ctg	p.M304L		NM_052898.1	NP_443130.1	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related family, member 4	304						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(3)|large_intestine(4)|liver(2)|lung(12)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	34			Epithelial(17;0.000117)|all cancers(17;0.000836)			GGATGTGAGTATGCTGCATTT	0.463																																					p.M304L		Atlas-SNP	.											.	XKR4	104	.	0			c.A910C						.						176	155	162					8																	56270341		2203	4300	6503	SO:0001583	missense	114786	exon2			GTGAGTATGCTGC	AY534241	CCDS34893.1	8q12.1	2006-01-12	2006-01-12		ENSG00000206579	ENSG00000206579			29394	protein-coding gene	gene with protein product			"X Kell blood group precursor-related family, member 4"				Standard	NM_052898		Approved	KIAA1889	uc003xsf.3	Q5GH76	OTTHUMG00000164288	ENST00000327381.6:c.910A>C	chr8.hg19:g.56270341A>C	ENSP00000328326:p.Met304Leu	128.0	0.0		109.0	13.0	NM_052898	Q96PZ8	Missense_Mutation	SNP	ENST00000327381.6	hg19	CCDS34893.1	.	.	.	.	.	.	.	.	.	.	A	16.28	3.078412	0.55753	.	.	ENSG00000206579	ENST00000327381;ENST00000543752	T	0.66638	-0.22	5.96	5.96	0.96718	.	0.040138	0.85682	D	0.000000	T	0.65801	0.2726	L	0.35723	1.085	0.54753	D	0.99998	P	0.34934	0.476	B	0.43386	0.418	T	0.64356	-0.6427	10	0.38643	T	0.18	-0.4388	16.4447	0.83919	1.0:0.0:0.0:0.0	.	304	Q5GH76	XKR4_HUMAN	L	304	ENSP00000328326:M304L	ENSP00000328326:M304L	M	+	1	0	XKR4	56432895	1.000000	0.71417	0.995000	0.50966	0.697000	0.40408	9.339000	0.96797	2.284000	0.76573	0.528000	0.53228	ATG	.	.		0.463	XKR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378129.2	NM_052898		C	56270341	A	C	56270341	3	2	359	1	0	0	0	0	1	0	0	0	17448	449	16	5	916	5	XKR4	8	56270341	Missense_Mutation	SNP	A	TCGA-XR-A8TE-01A-11D-A35Z-10		56270341	90093681	12	50292										
CNTNAP3	79937	hgsc.bcm.edu	37	chr9	39078814	39078814	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gaggggccgctggggcgcagCgccgccttcaggggagcagc	20	13	1	0			TCGA-XR-A8TE-01A-11D-A35Z-10	TCGA-XR-A8TE-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52ed1382-9a5b-4ac9-95ff-e59c6d6c48ff	2d84231b-c606-494f-9df7-68b2f88ac114	g.chr9:39078814C>A	ENST00000297668.6	-	22	3619	c.3546G>T	c.(3544-3546)gcG>gcT	p.A1182A	CNTNAP3_ENST00000377656.2_Silent_p.A1101A	NM_033655.3	NP_387504.2	Q9BZ76	CNTP3_HUMAN	contactin associated protein-like 3	1182	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell recognition (GO:0008037)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	24				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		TGGGGCGCAGCGCCGCCTTCA	0.791																																					p.A1182A		Atlas-SNP	.											CNTNAP3,NS,carcinoma,0,1	CNTNAP3	82	.	0			c.G3546T						.						1	1	1					9																	39078814		22	91	113	SO:0001819	synonymous_variant	79937	exon22			GCGCAGCGCCGCC	AF333769	CCDS6616.1	9q12	2008-02-05			ENSG00000106714	ENSG00000106714			13834	protein-coding gene	gene with protein product	"cell recognition molecule CASPR3 (FLJ14195, KIAA1714)"	610517				12093160	Standard	NM_033655		Approved	CASPR3, KIAA1714, FLJ14195, CNTNAP3A	uc004abi.3	Q9BZ76	OTTHUMG00000019954	ENST00000297668.6:c.3546G>T	chr9.hg19:g.39078814C>A		12.0	1.0		6.0	2.0	NM_033655	B1AMA0|Q9C0E9	Silent	SNP	ENST00000297668.6	hg19	CCDS6616.1																																																																																			.	.		0.791	CNTNAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052511.1	NM_033655		A	39078814	C	A	39078814	2	1	359	1	0	0	0	0	0	0	0	1	3650	755	27	1		1	CNTNAP3	9	39078814	Silent	SNP	C	TCGA-XR-A8TE-01A-11D-A35Z-10		39078814	102134617	13	50293										
GNA14	9630	hgsc.bcm.edu	37	chr9	80144156	80144156	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ttgataaaggtgcttttcccActttcaccagttcctataag	6	10	1	1			TCGA-XR-A8TE-01A-11D-A35Z-10	TCGA-XR-A8TE-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52ed1382-9a5b-4ac9-95ff-e59c6d6c48ff	2d84231b-c606-494f-9df7-68b2f88ac114	g.chr9:80144156A>G	ENST00000341700.6	-	2	651	c.138T>C	c.(136-138)agT>agC	p.S46S	RP11-466A17.1_ENST00000439145.1_RNA	NM_004297.3	NP_004288.1	O95837	GNA14_HUMAN	guanine nucleotide binding protein (G protein), alpha 14	46					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			endometrium(3)|kidney(1)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	24						TGCTTTTCCCACTTTCACCAG	0.438																																					p.S46S		Atlas-SNP	.											.	GNA14	50	.	0			c.T138C						.						190	186	187					9																	80144156		2203	4300	6503	SO:0001819	synonymous_variant	9630	exon2			TTTCCCACTTTCA	AF105201	CCDS6657.1	9q21	2008-05-23			ENSG00000156049	ENSG00000156049			4382	protein-coding gene	gene with protein product		604397				10191087, 17620339	Standard	NM_004297		Approved		uc004aku.3	O95837	OTTHUMG00000020058	ENST00000341700.6:c.138T>C	chr9.hg19:g.80144156A>G		102.0	0.0		76.0	10.0	NM_004297	B1ALW3	Silent	SNP	ENST00000341700.6	hg19	CCDS6657.1																																																																																			.	.		0.438	GNA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052759.1			G	80144156	A	G	80144156	2	3	359	1	0	0	0	0	0	0	0	1	6510	156	6	2		2	GNA14	9	80144156	Silent	SNP	A	TCGA-XR-A8TE-01A-11D-A35Z-10	41065342	80144156	61069275	14	50294										
SMPD1	6609	hgsc.bcm.edu	37	chr11	6411972	6411972	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gcgctggcgctggcgctggcTctgtctgactctcgggttct	15	13	4	1	rs281860676		TCGA-XR-A8TE-01A-11D-A35Z-10	TCGA-XR-A8TE-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52ed1382-9a5b-4ac9-95ff-e59c6d6c48ff	2d84231b-c606-494f-9df7-68b2f88ac114	g.chr11:6411972T>G	ENST00000342245.4	+	1	312	c.144T>G	c.(142-144)gcT>gcG	p.A48A	SMPD1_ENST00000356761.2_Silent_p.A48A|SMPD1_ENST00000299397.3_Silent_p.A48A|SMPD1_ENST00000527275.1_Silent_p.A48A|SMPD1_ENST00000533196.1_3'UTR	NM_000543.4|NM_001007593.2	NP_000534.3|NP_001007594.2	P17405	ASM_HUMAN	sphingomyelin phosphodiesterase 1, acid lysosomal	47					cell death (GO:0008219)|ceramide biosynthetic process (GO:0046513)|glycosphingolipid metabolic process (GO:0006687)|negative regulation of MAP kinase activity (GO:0043407)|nervous system development (GO:0007399)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein dephosphorylation (GO:0035307)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)|sphingomyelin metabolic process (GO:0006684)|termination of signal transduction (GO:0023021)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lamellar body (GO:0042599)|lysosomal lumen (GO:0043202)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(3)	23		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;4.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	Amlodipine(DB00381)|Chlorpromazine(DB00477)|Desipramine(DB01151)	tggcgctggcTCTGTCTGACT	0.697																																					p.A48A		Atlas-SNP	.											.	SMPD1	108	.	0			c.T144G						.						25	28	27					11																	6411972		2201	4296	6497	SO:0001819	synonymous_variant	6609	exon1			GCTGGCTCTGTCT	AB209775	CCDS31409.1, CCDS44531.1, CCDS31409.2	11p15.4-p15.1	2010-04-28	2008-02-04		ENSG00000166311	ENSG00000166311	3.1.4.12		11120	protein-coding gene	gene with protein product	"acid sphingomyelinase"	607608				1711683	Standard	NM_000543		Approved	ASM	uc001mcw.3	P17405	OTTHUMG00000165453	ENST00000342245.4:c.144T>G	chr11.hg19:g.6411972T>G		112.0	0.0		69.0	6.0	NM_000543	A8K8M3|E9PKS3|P17406|Q13811|Q16837|Q16841	Silent	SNP	ENST00000342245.4	hg19	CCDS44531.1																																																																																			.	.		0.697	SMPD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384205.1	NM_000543		G	6411972	T	G	6411972	2	3	359	1	0	0	0	0	0	0	0	1	14819	1538	54	5		5	SMPD1	11	6411972	Silent	SNP	T	TCGA-XR-A8TE-01A-11D-A35Z-10		6411972	128594544	15	50295										
MUC15	143662	hgsc.bcm.edu	37	chr11	26582625	26582625	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gttagttctatacagaagtaCgaagtggaggtatgtcatcc	11	6	2	1	rs560016592		TCGA-XR-A8TE-01A-11D-A35Z-10	TCGA-XR-A8TE-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52ed1382-9a5b-4ac9-95ff-e59c6d6c48ff	2d84231b-c606-494f-9df7-68b2f88ac114	g.chr11:26582625C>T	ENST00000455601.2	-	4	1110	c.992G>A	c.(991-993)cGt>cAt	p.R331H	ANO3_ENST00000529242.1_Intron|MUC15_ENST00000436318.2_Missense_Mutation_p.R358H|ANO3_ENST00000531568.1_Intron|MUC15_ENST00000527569.1_Missense_Mutation_p.R308H|ANO3_ENST00000256737.3_Intron|ANO3_ENST00000525139.1_Intron|MUC15_ENST00000281268.8_Missense_Mutation_p.R308H|ANO3_ENST00000537978.1_Intron|MUC15_ENST00000529533.1_Missense_Mutation_p.R358H	NM_145650.3	NP_663625.2	Q8N387	MUC15_HUMAN	mucin 15, cell surface associated	331					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R331H(2)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	25						TACAGAAGTACGAAGTGGAGG	0.378																																					p.R358H		Atlas-SNP	.											MUC15_ENST00000436318,NS,carcinoma,0,3	MUC15	88	.	2	Substitution - Missense(2)	lung(1)|kidney(1)	c.G1073A						.						178	163	168					11																	26582625		2203	4300	6503	SO:0001583	missense	143662	exon5			GAAGTACGAAGTG	AJ417818	CCDS7859.1, CCDS44556.1, CCDS44557.1	11p14.3	2007-01-17	2006-03-14					"Mucins"	14956	protein-coding gene	gene with protein product		608566				12047385	Standard	NM_145650		Approved		uc001mqw.3	Q8N387		ENST00000455601.2:c.992G>A	chr11.hg19:g.26582625C>T	ENSP00000397339:p.Arg331His	99.0	0.0		88.0	26.0	NM_001135091	B3KY00|E9PII6|F8W945|Q6UWS3|Q8IXI8|Q8WW41	Missense_Mutation	SNP	ENST00000455601.2	hg19	CCDS7859.1	.	.	.	.	.	.	.	.	.	.	C	12.64	1.997644	0.35226	.	.	ENSG00000169550	ENST00000455601;ENST00000436318;ENST00000281268;ENST00000529533;ENST00000527569	T;T;T;T;T	0.39787	1.11;1.06;1.11;1.06;1.11	5.33	2.29	0.28610	.	0.000000	0.49916	D	0.000136	T	0.36663	0.0975	L	0.32530	0.975	0.09310	N	0.999999	D;P;P	0.69078	0.997;0.917;0.917	P;B;B	0.52598	0.703;0.291;0.291	T	0.15435	-1.0437	10	0.87932	D	0	-10.0199	4.5326	0.12013	0.1475:0.539:0.0:0.3135	.	308;331;358	F8W945;Q8N387;E9PII6	.;MUC15_HUMAN;.	H	331;358;308;358;308	ENSP00000397339:R331H;ENSP00000416753:R358H;ENSP00000281268:R308H;ENSP00000431983:R358H;ENSP00000431945:R308H	ENSP00000281268:R308H	R	-	2	0	MUC15	26539201	0.450000	0.25697	0.686000	0.30086	0.099000	0.18886	0.682000	0.25335	0.755000	0.32990	-0.186000	0.12905	CGT	.	.		0.378	MUC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387866.1	NM_145650		T	26582625	C	T	26582625	3	4	359	1	0	0	0	0	1	0	0	0	9981	536	19	1	16	1	MUC15	11	26582625	Missense_Mutation	SNP	C	TCGA-XR-A8TE-01A-11D-A35Z-10	20170653	26582625	108423891	16	50296										
SYT7	9066	hgsc.bcm.edu	37	chr11	61290591	61290591	+	Frame_Shift_Del	DEL	C	C	-													0	0	1	0	0	0	1	1	0	gagcttgtccttgtccatgaCagtgatgatgatggtcgtct							TCGA-XR-A8TE-01A-11D-A35Z-10	TCGA-XR-A8TE-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52ed1382-9a5b-4ac9-95ff-e59c6d6c48ff	2d84231b-c606-494f-9df7-68b2f88ac114	g.chr11:61290591delC	ENST00000263846.4	-	8	1390	c.1063delG	c.(1063-1065)gtcfs	p.V355fs	SYT7_ENST00000540677.1_Frame_Shift_Del_p.V430fs|SYT7_ENST00000540831.1_5'Flank|SYT7_ENST00000542836.1_Frame_Shift_Del_p.V399fs|SYT7_ENST00000535826.1_Frame_Shift_Del_p.V474fs|SYT7_ENST00000539008.1_Frame_Shift_Del_p.V638fs|SYT7_ENST00000542670.1_Frame_Shift_Del_p.V563fs	NM_004200.3	NP_004191.2	O43581	SYT7_HUMAN	synaptotagmin VII	355	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|plasma membrane repair (GO:0001778)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of insulin secretion (GO:0050796)	cell junction (GO:0030054)|dense core granule (GO:0031045)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			kidney(2)|large_intestine(3)|lung(4)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						TTGTCCATGACAGTGATGATG	0.577																																					p.V430fs		Atlas-INDEL	.											.	SYT7	39	.	0			c.1289delT						.						282	220	241					11																	61290591		2202	4299	6501	SO:0001589	frameshift_variant	9066	exon9			.	AF038535	CCDS31577.1, CCDS58139.1, CCDS73298.1	11q12-q13.1	2013-01-21			ENSG00000011347	ENSG00000011347		"Synaptotagmins"	11514	protein-coding gene	gene with protein product		604146	"prostate cancer associated protein 7"	PCANAP7		9615227	Standard	NM_001252065		Approved	IPCA-7, SYT-VII, MGC150517	uc009ynr.3	O43581	OTTHUMG00000168199	ENST00000263846.4:c.1063delG	chr11.hg19:g.61290591delC	ENSP00000263846:p.Val355fs	96.0	0.0		72.0	23.0	NM_001252065	F5GZU9|Q08AH6	Frame_Shift_Del	DEL	ENST00000263846.4	hg19	CCDS31577.1																																																																																			.	.		0.577	SYT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398733.1	NM_004200		-	61290591	C	-	61290591	7	5	359	1	0	1	0	1	0	0	0	0	15494	478	17	0	156	0	SYT7	11	61290591	Frame_Shift_Del	DEL	C	TCGA-XR-A8TE-01A-11D-A35Z-10	34707966	61290591	73715925	17	50297										
PYGM	5837	hgsc.bcm.edu	37	chr11	64522206	64522206	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	gttcgtgcgcacgggatcacGgcagccgaacttggaagact	14	11	1	1			TCGA-XR-A8TE-01A-11D-A35Z-10	TCGA-XR-A8TE-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52ed1382-9a5b-4ac9-95ff-e59c6d6c48ff	2d84231b-c606-494f-9df7-68b2f88ac114	g.chr11:64522206G>T	ENST00000164139.3	-	8	1356	c.958C>A	c.(958-960)Cgt>Agt	p.R320S	PYGM_ENST00000462303.1_5'Flank|PYGM_ENST00000377432.3_Missense_Mutation_p.R232S	NM_005609.2	NP_005600.1	P11217	PYGM_HUMAN	phosphorylase, glycogen, muscle	320					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glycogen phosphorylase activity (GO:0008184)|nucleotide binding (GO:0000166)|pyridoxal phosphate binding (GO:0030170)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						ACGGGATCACGGCAGCCGAAC	0.592																																					p.R320S		Atlas-SNP	.											.	PYGM	77	.	0			c.C958A						.						81	62	69					11																	64522206		2201	4297	6498	SO:0001583	missense	5837	exon8			GATCACGGCAGCC		CCDS8079.1, CCDS53659.1	11q12-q13.2	2013-03-01	2008-07-31		ENSG00000068976	ENSG00000068976	2.4.1.1	"Glycogen phosphorylases"	9726	protein-coding gene	gene with protein product	"McArdle syndrome", "glycogen storage disease type V", "glycogen phosphorylase, muscle form"	608455	"phosphorylase, glycogen; muscle"				Standard	NM_005609		Approved		uc001oax.4	P11217	OTTHUMG00000066835	ENST00000164139.3:c.958C>A	chr11.hg19:g.64522206G>T	ENSP00000164139:p.Arg320Ser	94.0	0.0		71.0	4.0	NM_005609	A0AVK1|A6NDY6	Missense_Mutation	SNP	ENST00000164139.3	hg19	CCDS8079.1	.	.	.	.	.	.	.	.	.	.	G	16.57	3.159235	0.57368	.	.	ENSG00000068976	ENST00000377432;ENST00000164139;ENST00000540450	D;D	0.92965	-3.08;-3.14	4.89	4.89	0.63831	.	0.361992	0.24215	N	0.040489	D	0.90566	0.7043	M	0.73962	2.25	0.54753	D	0.999989	B;B	0.12630	0.001;0.006	B;B	0.15484	0.013;0.013	D	0.87674	0.2543	10	0.52906	T	0.07	-6.7916	10.6027	0.45375	0.0:0.0:0.8083:0.1917	.	232;320	A6NDY6;P11217	.;PYGM_HUMAN	S	232;320;301	ENSP00000366650:R232S;ENSP00000164139:R320S	ENSP00000164139:R320S	R	-	1	0	PYGM	64278782	0.784000	0.28713	0.993000	0.49108	0.984000	0.73092	1.059000	0.30517	2.551000	0.86045	0.561000	0.74099	CGT	.	.		0.592	PYGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143254.2	NM_005609		T	64522206	G	T	64522206	3	4	359	1	0	0	0	0	1	0	0	0	12877	1116	39	1	1622	1	PYGM	11	64522206	Missense_Mutation	SNP	G	TCGA-XR-A8TE-01A-11D-A35Z-10	3231615	64522206	70484310	18	50298										
KLRC1	3821	hgsc.bcm.edu	37	chr12	10603179	10603179	+	Splice_Site	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	ctctggagctgatggtaaatCtgcagggagagaaatgggaa	15	5	2	2			TCGA-XR-A8TE-01A-11D-A35Z-10	TCGA-XR-A8TE-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52ed1382-9a5b-4ac9-95ff-e59c6d6c48ff	2d84231b-c606-494f-9df7-68b2f88ac114	g.chr12:10603179C>A	ENST00000359151.3	-	3	369		c.e3-1		KLRC1_ENST00000536188.1_Splice_Site|KLRC1_ENST00000408006.3_Splice_Site|KLRC1_ENST00000544822.1_Splice_Site|KLRC1_ENST00000347831.5_Splice_Site	NM_002259.4	NP_002250	P26715	NKG2A_HUMAN	killer cell lectin-like receptor subfamily C, member 1						cell surface receptor signaling pathway (GO:0007166)|regulation of immune response (GO:0050776)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(8)|skin(1)	16						GATGGTAAATCTGCAGGGAGA	0.438																																					.		Atlas-SNP	.											.	KLRC1	33	.	0			c.188-1G>T						.						88	85	86					12																	10603179		2203	4300	6503	SO:0001630	splice_region_variant	3821	exon4			GTAAATCTGCAGG	U54782	CCDS8625.1, CCDS8626.1	12p13	2010-06-30			ENSG00000134545	ENSG00000134545		"Killer cell lectin-like receptors", "CD molecules"	6374	protein-coding gene	gene with protein product	"NKG2-1/B activating NK receptor"	161555		NKG2		9598306	Standard	NM_002259		Approved	NKG2-A, NKG2-B, CD159a	uc001qyl.3	P26715		ENST00000359151.3:c.188-1G>T	chr12.hg19:g.10603179C>A		85.0	0.0		68.0	14.0	NM_002259		Splice_Site	SNP	ENST00000359151.3	hg19	CCDS8625.1	.	.	.	.	.	.	.	.	.	.	c	7.057	0.565618	0.13560	.	.	ENSG00000134545	ENST00000536188;ENST00000359151;ENST00000408006;ENST00000347831;ENST00000544822	.	.	.	3.45	1.27	0.21489	.	.	.	.	.	.	.	.	.	.	.	0.19300	N	0.999975	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.0722	0.19895	0.241:0.5726:0.1864:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	KLRC1	10494446	0.039000	0.19947	0.001000	0.08648	0.191000	0.23601	0.190000	0.17057	0.178000	0.19917	0.467000	0.42956	.	.	.		0.438	KLRC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400115.1	NM_002259	Intron	A	10603179	C	A	10603179	5	1	359	1	0	0	0	0	0	0	1	0	8424	927	32	3	534	3	KLRC1	12	10603179	Splice_Site	SNP	C	TCGA-XR-A8TE-01A-11D-A35Z-10		10603179	123248716	19	50299										
WNK4	65266	hgsc.bcm.edu	37	chr17	40933030	40933030	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	accgcctagctccaaagaacCccccgagggcacgtggaccg	11	17	0	1			TCGA-XR-A8TE-01A-11D-A35Z-10	TCGA-XR-A8TE-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52ed1382-9a5b-4ac9-95ff-e59c6d6c48ff	2d84231b-c606-494f-9df7-68b2f88ac114	g.chr17:40933030C>A	ENST00000246914.5	+	1	335	c.314C>A	c.(313-315)cCc>cAc	p.P105H		NM_032387.4	NP_115763.2	Q96J92	WNK4_HUMAN	WNK lysine deficient protein kinase 4	105					chloride transport (GO:0006821)|distal tubule morphogenesis (GO:0072156)|intracellular signal transduction (GO:0035556)|ion homeostasis (GO:0050801)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)|renal sodium ion absorption (GO:0070294)	cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|prostate(1)|skin(5)|stomach(1)	35		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.0749)		TCCAAAGAACCCCCCGAGGGC	0.726																																					p.P105H	Esophageal Squamous(6;201 374 4964 23855 42828)	Atlas-SNP	.											.	WNK4	182	.	0			c.C314A						.						10	13	12					17																	40933030		2170	4279	6449	SO:0001583	missense	65266	exon1			AAGAACCCCCCGA	AJ309861	CCDS11439.1	17q21-q22	2005-01-19	2005-01-19	2005-01-19		ENSG00000126562			14544	protein-coding gene	gene with protein product		601844	"protein kinase, lysine deficient 4"	PRKWNK4			Standard	NM_032387		Approved		uc002ibj.3	Q96J92		ENST00000246914.5:c.314C>A	chr17.hg19:g.40933030C>A	ENSP00000246914:p.Pro105His	107.0	0.0		82.0	10.0	NM_032387	B0LPI0|Q8N8X3|Q8N8Z2|Q96DT8|Q9BYS5	Missense_Mutation	SNP	ENST00000246914.5	hg19	CCDS11439.1	.	.	.	.	.	.	.	.	.	.	C	6.725	0.502455	0.12822	.	.	ENSG00000126562	ENST00000246914	T	0.72394	-0.65	4.85	-1.53	0.08611	.	0.879409	0.09637	N	0.775451	T	0.52964	0.1767	L	0.29908	0.895	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.40365	-0.9567	10	0.42905	T	0.14	-2.29	5.6348	0.17530	0.3006:0.5463:0.0:0.1531	.	105	Q96J92	WNK4_HUMAN	H	105	ENSP00000246914:P105H	ENSP00000246914:P105H	P	+	2	0	WNK4	38186556	0.492000	0.26027	0.025000	0.17156	0.002000	0.02628	0.898000	0.28404	-0.044000	0.13491	0.563000	0.77884	CCC	.	.		0.726	WNK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452389.1			A	40933030	C	A	40933030	3	1	359	1	0	0	0	0	1	0	0	0	17395	623	22	3	316	3	WNK4	17	40933030	Missense_Mutation	SNP	C	TCGA-XR-A8TE-01A-11D-A35Z-10		40933030	40262180	20	50300										
MBD3L1	85509	hgsc.bcm.edu	37	chr19	8953859	8953859	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	agacagtcagagagagactcGcaatagcactgattgcggat	12	8	1	4			TCGA-XR-A8TE-01A-11D-A35Z-10	TCGA-XR-A8TE-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52ed1382-9a5b-4ac9-95ff-e59c6d6c48ff	2d84231b-c606-494f-9df7-68b2f88ac114	g.chr19:8953859G>A	ENST00000595891.1	+	3	736	c.505G>A	c.(505-507)Gca>Aca	p.A169T	MBD3L1_ENST00000305625.2_Missense_Mutation_p.A169T			Q8WWY6	MB3L1_HUMAN	methyl-CpG binding domain protein 3-like 1	169					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.A169T(1)		NS(1)|cervix(1)|large_intestine(5)|liver(1)|lung(2)|skin(2)	12						AGAGAGACTCGCAATAGCACT	0.473																																					p.A169T		Atlas-SNP	.											MBD3L1,colon,carcinoma,0,1	MBD3L1	24	.	1	Substitution - Missense(1)	large_intestine(1)	c.G505A						.						44	41	42					19																	8953859		2203	4297	6500	SO:0001583	missense	85509	exon1			AGACTCGCAATAG	AY038022	CCDS12209.1	19p13.2	2011-01-31	2003-03-19	2003-03-21	ENSG00000170948	ENSG00000170948			15774	protein-coding gene	gene with protein product		607963	"methyl-CpG binding domain protein 3-like"	MBD3L		12504854	Standard	NM_145208		Approved		uc002mko.2	Q8WWY6		ENST00000595891.1:c.505G>A	chr19.hg19:g.8953859G>A	ENSP00000471575:p.Ala169Thr	65.0	0.0		40.0	12.0	NM_145208	B5BUM6|Q2M291	Missense_Mutation	SNP	ENST00000595891.1	hg19	CCDS12209.1	.	.	.	.	.	.	.	.	.	.	G	8.182	0.793989	0.16327	.	.	ENSG00000170948	ENST00000305625	T	0.49432	0.78	3.92	0.577	0.17385	.	0.646825	0.12885	N	0.431113	T	0.38506	0.1043	M	0.72894	2.215	0.09310	N	1	B	0.33612	0.419	B	0.28385	0.089	T	0.22661	-1.0210	10	0.34782	T	0.22	-14.2204	4.3308	0.11062	0.2079:0.1861:0.606:0.0	.	169	Q8WWY6	MB3L1_HUMAN	T	169	ENSP00000304198:A169T	ENSP00000304198:A169T	A	+	1	0	MBD3L1	8814859	0.329000	0.24696	0.137000	0.22149	0.007000	0.05969	1.118000	0.31246	0.230000	0.21059	-0.165000	0.13383	GCA	.	.		0.473	MBD3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459973.1	NM_145208		A	8953859	G	A	8953859	3	1	359	1	0	0	0	0	1	0	0	0	9354	1087	38	1	507	1	MBD3L1	19	8953859	Missense_Mutation	SNP	G	TCGA-XR-A8TE-01A-11D-A35Z-10		8953859	50175124	21	50301										
PTCHD2	57540	hgsc.bcm.edu	37	chr1	11561824	11561824	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	gcgcctcgcgctgggactacTcgcgcgcctatgtgagtgcc	14	15	0	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr1:11561824T>A	ENST00000294484.6	+	2	913	c.775T>A	c.(775-777)Tcg>Acg	p.S259T	PTCHD2_ENST00000389575.3_Missense_Mutation_p.S259T	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	259					cholesterol homeostasis (GO:0042632)|regulation of lipid transport (GO:0032368)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hedgehog receptor activity (GO:0008158)			NS(3)|breast(2)|endometrium(9)|kidney(4)|large_intestine(5)|lung(34)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	76	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		CTGGGACTACTCGCGCGCCTA	0.682																																					p.S259T		Atlas-SNP	.											.	PTCHD2	193	.	0			c.T775A						.						9	10	10					1																	11561824		1968	4129	6097	SO:0001583	missense	57540	exon2			GACTACTCGCGCG	AB037758	CCDS41247.1	1p36.22	2010-02-17			ENSG00000204624	ENSG00000204624			29251	protein-coding gene	gene with protein product		611251				15738394	Standard	NM_020780		Approved	KIAA1337, DISP3	uc001ash.4	Q9P2K9	OTTHUMG00000002074	ENST00000294484.6:c.775T>A	chr1.hg19:g.11561824T>A	ENSP00000294484:p.Ser259Thr	125.0	0.0		78.0	5.0	NM_020780	Q5VTU9|Q9UJD6	Missense_Mutation	SNP	ENST00000294484.6	hg19	CCDS41247.1	.	.	.	.	.	.	.	.	.	.	T	10.45	1.353496	0.24512	.	.	ENSG00000204624	ENST00000294484;ENST00000389575	T;T	0.24538	1.85;1.85	5.67	4.51	0.55191	.	0.354453	0.28566	N	0.014894	T	0.15825	0.0381	L	0.27053	0.805	0.32304	N	0.564635	B	0.31026	0.304	B	0.29716	0.106	T	0.18935	-1.0321	10	0.25106	T	0.35	-11.2912	7.3622	0.26752	0.1437:0.0:0.1503:0.706	.	259	Q9P2K9	PTHD2_HUMAN	T	259	ENSP00000294484:S259T;ENSP00000374226:S259T	ENSP00000294484:S259T	S	+	1	0	PTCHD2	11484411	0.997000	0.39634	0.949000	0.38748	0.250000	0.25880	1.666000	0.37460	0.936000	0.37367	0.533000	0.62120	TCG	.	.		0.682	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561		A	11561824	T	A	11561824	3	1	360	1	0	0	0	0	1	0	0	0	12745	1551	54	4	777	4	PTCHD2	1	11561824	Missense_Mutation	SNP	T	TCGA-XR-A8TF-01A-11D-A35Z-10		11561824	237688797	1	50302										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27107072	27107075	+	Frame_Shift_Del	DEL	TGGA	TGGA	-													0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	accctttgagccaactagtgTggacatgatgcggcgggctg					rs573998153		TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	TGGA	TGGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr1:27107072_27107075delTGGA	ENST00000324856.7	+	20	7054_7057	c.6683_6686delTGGA	c.(6682-6687)gtggacfs	p.VD2228fs	ARID1A_ENST00000540690.1_Frame_Shift_Del_p.VD556fs|ARID1A_ENST00000457599.2_Frame_Shift_Del_p.VD2011fs|ARID1A_ENST00000374152.2_Frame_Shift_Del_p.VD1845fs	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	2228					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		CCAACTAGTGTGGACATGATGCGG	0.603			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.2228_2229del		Atlas-INDEL	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.6682_6685del						.																																			SO:0001589	frameshift_variant	8289	exon20			.	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.6683_6686delTGGA	chr1.hg19:g.27107072_27107075delTGGA	ENSP00000320485:p.Val2228fs	92.0	0.0		28.0	18.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Del	DEL	ENST00000324856.7	hg19	CCDS285.1																																																																																			.	.		0.603	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		-	27107075	TGGA	-	27107072	7	5	360	1	0	1	0	1	0	0	0	0	913	1696	59	0	6761	0	ARID1A	1	27107072	Frame_Shift_Del	DEL	TGGA	TCGA-XR-A8TF-01A-11D-A35Z-10	15545248	27107072	222143549	2	50303	262	2								
ARID1A	8289	hgsc.bcm.edu	37	chr1	27107078	27107095	+	In_Frame_Del	DEL	TGATGCGGCGGGCTGCCC	TGATGCGGCGGGCTGCCC	-													0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	tgagccaactagtgtggacaTgatgcggcgggctgcccgcg					rs142878055		TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	TGATGCGGCGGGCTGCCC	TGATGCGGCGGGCTGCCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr1:27107078_27107095delTGATGCGGCGGGCTGCCC	ENST00000324856.7	+	20	7060_7077	c.6689_6706delTGATGCGGCGGGCTGCCC	c.(6688-6708)atgatgcggcgggctgcccgc>agc	p.2230_2236MMRRAAR>S	ARID1A_ENST00000540690.1_In_Frame_Del_p.558_564MMRRAAR>S|ARID1A_ENST00000457599.2_In_Frame_Del_p.2013_2019MMRRAAR>S|ARID1A_ENST00000374152.2_In_Frame_Del_p.1847_1853MMRRAAR>S	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	2230					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)	p.A2235fs*32(1)|p.M2231fs*32(1)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		AGTGTGGACATGATGCGGCGGGCTGCCCGCGCGCTGCT	0.587			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.2230_2235del		Atlas-INDEL	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	2	Deletion - Frameshift(2)	ovary(1)|liver(1)	c.6688_6705del						.																																			SO:0001651	inframe_deletion	8289	exon20			.	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.6689_6706delTGATGCGGCGGGCTGCCC	chr1.hg19:g.27107078_27107095delTGATGCGGCGGGCTGCCC	ENSP00000320485:p.Met2230_Arg2236delinsSer	89.0	0.0		26.0	18.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	In_Frame_Del	DEL	ENST00000324856.7	hg19	CCDS285.1																																																																																			.	.		0.587	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		-	27107095	TGATGCGGCGGGCTGCCC	-	27107078	7	5	360	1	0	1	0	1	0	0	0	0	913	1464	51	0	6767	0	ARID1A	1	27107078	In_Frame_Del	DEL	TGATGCGGCGGGCTGCCC	TCGA-XR-A8TF-01A-11D-A35Z-10	6	27107078	222143543	3	50304	262	2								
ZCCHC11	23318	hgsc.bcm.edu	37	chr1	52897111	52897111	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	tggaaatggctgaggctgagGagaataagatggtgattcag	16	3	1	5			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr1:52897111G>A	ENST00000371544.3	-	28	4544	c.4282C>T	c.(4282-4284)Cct>Tct	p.P1428S	ZCCHC11_ENST00000257177.4_Missense_Mutation_p.P1429S	NM_001009881.2|NM_015269.2	NP_001009881.1|NP_056084.1	Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11	1428	Gln-rich.|Pro-rich.				cytokine production (GO:0001816)|miRNA catabolic process (GO:0010587)|miRNA metabolic process (GO:0010586)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|pre-miRNA processing (GO:0031054)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|RNA 3'-end processing (GO:0031123)|stem cell maintenance (GO:0019827)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(17)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	58						TGAGGCTGAGGAGAATAAGAT	0.363																																					p.P1429S		Atlas-SNP	.											.	ZCCHC11	151	.	0			c.C4285T						.						27	25	26					1																	52897111		2202	4297	6499	SO:0001583	missense	23318	exon28			GCTGAGGAGAATA	D83776	CCDS30715.1, CCDS30716.1	1p32.3	2014-03-05			ENSG00000134744	ENSG00000134744		"Zinc fingers, CCHC domain containing"	28981	protein-coding gene	gene with protein product	"TUTase4"	613692				8724849, 12239557	Standard	NM_015269		Approved	KIAA0191, PAPD3, TUT4	uc001cty.2	Q5TAX3	OTTHUMG00000008200	ENST00000371544.3:c.4282C>T	chr1.hg19:g.52897111G>A	ENSP00000360599:p.Pro1428Ser	142.0	0.0		179.0	85.0	NM_001009881	A2RRP0|B7Z8J5|D3DQ35|Q12764|Q5TAX2|Q5TAX4|Q86XZ3	Missense_Mutation	SNP	ENST00000371544.3	hg19	CCDS30716.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.3|22.3	4.271025|4.271025	0.80469|0.80469	.|.	.|.	ENSG00000134744|ENSG00000134744	ENST00000257177;ENST00000371544;ENST00000531722|ENST00000474453	T;T|.	0.57595|.	0.39;0.4|.	5.27|5.27	5.27|5.27	0.74061|0.74061	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.60011|0.60011	0.2236|0.2236	L|L	0.27053|0.27053	0.805|0.805	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.85130|.	0.997|.	T|T	0.63229|0.63229	-0.6684|-0.6684	10|6	0.35671|0.59425	T|D	0.21|0.04	.|.	18.8838|18.8838	0.92367|0.92367	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1428|.	Q5TAX3|.	TUT4_HUMAN|.	S|F	1429;1428;266|273	ENSP00000257177:P1429S;ENSP00000360599:P1428S|.	ENSP00000257177:P1429S|ENSP00000433711:S273F	P|S	-|-	1|2	0|0	ZCCHC11|ZCCHC11	52669699|52669699	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	8.849000|8.849000	0.92178|0.92178	2.459000|2.459000	0.83118|0.83118	0.557000|0.557000	0.71058|0.71058	CCT|TCC	.	.		0.363	ZCCHC11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022462.1	XM_038288		A	52897111	G	A	52897111	3	1	360	1	0	0	0	0	1	0	0	0	17595	1174	41	3	664	3	ZCCHC11	1	52897111	Missense_Mutation	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10	25790033	52897111	196353510	4	50305										
DPYD	1806	hgsc.bcm.edu	37	chr1	98015193	98015193	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	tgtagtgttagccaaaccaaCgacatcaccacctgcaaata	6	12	1	0	rs141439344		TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr1:98015193C>T	ENST00000370192.3	-	12	1547	c.1447G>A	c.(1447-1449)Gtt>Att	p.V483I		NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	483					beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase catabolic process (GO:0006145)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymidine catabolic process (GO:0006214)|thymine catabolic process (GO:0006210)|UMP biosynthetic process (GO:0006222)|uracil catabolic process (GO:0006212)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|dihydroorotate dehydrogenase activity (GO:0004152)|dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(18)|lung(30)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	GCCAAACCAACGACATCACCA	0.433																																					p.V483I		Atlas-SNP	.											.	DPYD	219	.	0			c.G1447A						.	C	ILE/VAL	2,4404	4.2+/-10.8	0,2,2201	177	146	157		1447	4.3	1	1	dbSNP_134	157	0,8600		0,0,4300	no	missense	DPYD	NM_000110.3	29	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	benign	483/1026	98015193	2,13004	2203	4300	6503	SO:0001583	missense	1806	exon12			AACCAACGACATC	U20938	CCDS30777.1, CCDS53346.1	1p22	2014-09-17			ENSG00000188641	ENSG00000188641	1.3.1.2		3012	protein-coding gene	gene with protein product		612779				7713523	Standard	NM_000110		Approved	DPD	uc001drv.3	Q12882	OTTHUMG00000039683	ENST00000370192.3:c.1447G>A	chr1.hg19:g.98015193C>T	ENSP00000359211:p.Val483Ile	132.0	0.0		105.0	30.0	NM_000110	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Missense_Mutation	SNP	ENST00000370192.3	hg19	CCDS30777.1	.	.	.	.	.	.	.	.	.	.	C	6.853	0.526762	0.13066	4.54E-4	0.0	ENSG00000188641	ENST00000370192	D	0.82526	-1.62	6.16	4.31	0.51392	.	0.416154	0.26863	N	0.022106	T	0.67887	0.2941	L	0.50919	1.6	0.80722	D	1	B	0.09022	0.002	B	0.08055	0.003	T	0.62310	-0.6881	10	0.45353	T	0.12	-19.0706	13.5794	0.61893	0.0:0.7708:0.0:0.2292	.	483	Q12882	DPYD_HUMAN	I	483	ENSP00000359211:V483I	ENSP00000359211:V483I	V	-	1	0	DPYD	97787781	1.000000	0.71417	0.977000	0.42913	0.007000	0.05969	3.082000	0.50128	0.502000	0.28037	-0.813000	0.03139	GTT	.	C|1.000;T|0.000		0.433	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110		T	98015193	C	T	98015193	3	4	360	1	0	0	0	0	1	0	0	0	4747	536	19	1	1678	1	DPYD	1	98015193	Missense_Mutation	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10	45118082	98015193	151235428	5	50306										
CSF1	1435	hgsc.bcm.edu	37	chr1	110466107	110466107	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	ccctctgtcggggccttcaaCcccgggatggaggatattct	12	13	3	0			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr1:110466107C>T	ENST00000329608.6	+	6	1255	c.864C>T	c.(862-864)aaC>aaT	p.N288N	CSF1_ENST00000369801.1_Silent_p.N288N|CSF1_ENST00000369802.3_Silent_p.N288N|CSF1_ENST00000420111.2_Intron|CSF1_ENST00000344188.5_Silent_p.N288N	NM_000757.5|NM_172211.3	NP_000748|NP_757350.1	P09603	CSF1_HUMAN	colony stimulating factor 1 (macrophage)	288					branching involved in mammary gland duct morphogenesis (GO:0060444)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|developmental process involved in reproduction (GO:0003006)|hemopoiesis (GO:0030097)|homeostasis of number of cells within a tissue (GO:0048873)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary duct terminal end bud growth (GO:0060763)|mammary gland fat development (GO:0060611)|monocyte activation (GO:0042117)|odontogenesis (GO:0042476)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|osteoclast proliferation (GO:0002158)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of gene expression (GO:0010628)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of monocyte differentiation (GO:0045657)|positive regulation of mononuclear cell proliferation (GO:0032946)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of odontogenesis of dentin-containing tooth (GO:0042488)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of macrophage derived foam cell differentiation (GO:0010743)|regulation of ossification (GO:0030278)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|macrophage colony-stimulating factor receptor binding (GO:0005157)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(3)|large_intestine(3)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	20		all_epithelial(167;3.58e-05)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Acute lymphoblastic leukemia(138;0.204)		Lung(183;0.0238)|Colorectal(144;0.112)|all cancers(265;0.117)|Epithelial(280;0.127)|LUSC - Lung squamous cell carcinoma(189;0.135)		GGGCCTTCAACCCCGGGATGG	0.602											OREG0013645	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N288N		Atlas-SNP	.											.	CSF1	40	.	0			c.C864T						.						37	41	40					1																	110466107		2203	4300	6503	SO:0001819	synonymous_variant	1435	exon6			CTTCAACCCCGGG	BC021117	CCDS816.1, CCDS817.1, CCDS30797.1	1p13.3	2012-09-20			ENSG00000184371	ENSG00000184371			2432	protein-coding gene	gene with protein product		120420				1540160	Standard	NM_172210		Approved	M-CSF, MCSF, MGC31930	uc001dyw.4	P09603	OTTHUMG00000011646	ENST00000329608.6:c.864C>T	chr1.hg19:g.110466107C>T		119.0	0.0	1427	100.0	31.0	NM_172210	A8K6J5|Q13130|Q14086|Q14806|Q5VVF3|Q5VVF4|Q9UQR8	Silent	SNP	ENST00000329608.6	hg19	CCDS816.1																																																																																			.	.		0.602	CSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032208.1	NM_000757		T	110466107	C	T	110466107	2	4	360	1	0	0	0	0	0	0	0	1	3933	506	18	3		3	CSF1	1	110466107	Silent	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10	12450914	110466107	138784514	6	50307										
SYCP1	6847	hgsc.bcm.edu	37	chr1	115438077	115438077	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	tgctcattttagaagagatgActaagcttacaaataacaaa	6	6	1	3			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr1:115438077A>T	ENST00000369522.3	+	16	1507	c.1267A>T	c.(1267-1269)Act>Tct	p.T423S	SYCP1_ENST00000369518.1_Missense_Mutation_p.T423S	NM_001282541.1|NM_003176.2	NP_001269470.1|NP_003167.2	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1	423					chiasma assembly (GO:0051026)|lateral element assembly (GO:0051878)|meiotic DNA repair synthesis (GO:0000711)|reciprocal meiotic recombination (GO:0007131)|regulation of protein localization (GO:0032880)|sperm chromatin condensation (GO:0035092)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)|male germ cell nucleus (GO:0001673)|transverse filament (GO:0000802)	DNA binding (GO:0003677)		RGS22/SYCP1(2)	NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		AGAAGAGATGACTAAGCTTAC	0.294																																					p.T423S		Atlas-SNP	.											.	SYCP1	149	.	0			c.A1267T						.						25	25	25					1																	115438077		2153	4258	6411	SO:0001583	missense	6847	exon16			GAGATGACTAAGC	D67035	CCDS879.1, CCDS72840.1	1p13-p12	2009-03-12			ENSG00000198765	ENSG00000198765			11487	protein-coding gene	gene with protein product	"cancer/testis antigen 8"	602162				9560255	Standard	XM_005271154		Approved	HOM-TES-14, SCP1, CT8	uc001efr.3	Q15431	OTTHUMG00000012057	ENST00000369522.3:c.1267A>T	chr1.hg19:g.115438077A>T	ENSP00000358535:p.Thr423Ser	583.0	1.0		567.0	352.0	NM_003176	O14963|Q5VXJ6	Missense_Mutation	SNP	ENST00000369522.3	hg19	CCDS879.1	.	.	.	.	.	.	.	.	.	.	A	9.033	0.987831	0.18966	.	.	ENSG00000198765	ENST00000369522;ENST00000536734;ENST00000455987;ENST00000369518	T;T;T	0.53857	0.6;0.6;0.6	4.94	1.08	0.20341	.	0.909246	0.09420	N	0.804584	T	0.17959	0.0431	L	0.50333	1.59	0.26261	N	0.978572	B;B	0.19583	0.037;0.037	B;B	0.25614	0.062;0.062	T	0.27400	-1.0075	10	0.11182	T	0.66	1.8418	2.9289	0.05793	0.6139:0.0:0.2027:0.1834	.	423;423	B7ZLS9;Q15431	.;SYCP1_HUMAN	S	423	ENSP00000358535:T423S;ENSP00000410011:T423S;ENSP00000358531:T423S	ENSP00000358531:T423S	T	+	1	0	SYCP1	115239600	0.962000	0.33011	0.585000	0.28666	0.900000	0.52787	0.593000	0.23999	0.336000	0.23639	0.528000	0.53228	ACT	.	.		0.294	SYCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033386.1	NM_003176		T	115438077	A	T	115438077	3	4	360	1	0	0	0	0	1	0	0	0	15446	275	10	4	1325	4	SYCP1	1	115438077	Missense_Mutation	SNP	A	TCGA-XR-A8TF-01A-11D-A35Z-10	4971970	115438077	133812544	7	50308										
SPAG17	200162	hgsc.bcm.edu	37	chr1	118640441	118640441	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	aagttttaagctcttttatgGcattttctttcttcaatttt	4	6	4	0			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr1:118640441G>A	ENST00000336338.5	-	7	928	c.863C>T	c.(862-864)gCc>gTc	p.A288V		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	288						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		CTCTTTTATGGCATTTTCTTT	0.328																																					p.A288V		Atlas-SNP	.											.	SPAG17	263	.	0			c.C863T						.						120	114	116					1																	118640441		2203	4300	6503	SO:0001583	missense	200162	exon7			TTTATGGCATTTT		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.863C>T	chr1.hg19:g.118640441G>A	ENSP00000337804:p.Ala288Val	133.0	0.0		110.0	28.0	NM_206996	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	hg19	CCDS899.1	.	.	.	.	.	.	.	.	.	.	G	10.45	1.354228	0.24512	.	.	ENSG00000155761	ENST00000336338	T	0.37584	1.19	5.3	-3.69	0.04450	.	1.572630	0.03310	N	0.190387	T	0.09774	0.0240	L	0.38175	1.15	0.09310	N	1	B	0.16396	0.017	B	0.10450	0.005	T	0.31833	-0.9929	10	0.49607	T	0.09	.	3.297	0.06970	0.1524:0.0954:0.2313:0.5208	.	288	Q6Q759	SPG17_HUMAN	V	288	ENSP00000337804:A288V	ENSP00000337804:A288V	A	-	2	0	SPAG17	118441964	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.042000	0.13949	-0.344000	0.08338	0.650000	0.86243	GCC	.	.		0.328	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		A	118640441	G	A	118640441	3	1	360	1	0	0	0	0	1	0	0	0	14994	1203	42	3	5976	3	SPAG17	1	118640441	Missense_Mutation	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10	3202364	118640441	130610180	8	50309										
NBPF7	343505	hgsc.bcm.edu	37	chr1	120384152	120384152	+	IGR	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	tcagtgagtgggaggcatctCtcccttcccgtaacttctcc	9	14	3	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr1:120384152C>G								REG4 (29869 upstream) : ADAM30 (52003 downstream)																							GGAGGCATCTCTCCCTTCCCG	0.498																																					p.R137T		Atlas-SNP	.											NBPF7,right_upper_lobe,carcinoma,0,1	NBPF7	46	.	0			c.G410C						.						136	152	146					1																	120384152		2203	4300	6503	SO:0001628	intergenic_variant	343505	exon3			GCATCTCTCCCTT																													chr1.hg19:g.120384152C>G		168.0	0.0		147.0	40.0	NM_001047980		Missense_Mutation	SNP		hg19																																																																																				.	.	0	0.498									G	120384152	C	G	120384152	1	3	360	0	1	0	0	0	0	0	0	0	10207	913	32	4		4	NBPF7	1	120384152	IGR	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10	1743711	120384152	128866469	9	50310										
TCHH	7062	hgsc.bcm.edu	37	chr1	152084224	152084224	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	gcctctcctcctcctcgagcTtcagccaacgttcgcgcctc	7	20	2	0			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr1:152084224T>C	ENST00000368804.1	-	2	1468	c.1469A>G	c.(1468-1470)aAg>aGg	p.K490R		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	490	9 X 28 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTCCTCGAGCTTCAGCCAACG	0.672																																					p.K490R		Atlas-SNP	.											.	TCHH	275	.	0			c.A1469G						.						65	71	69					1																	152084224		2109	4224	6333	SO:0001583	missense	7062	exon3			TCGAGCTTCAGCC	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"EF-hand domain containing"	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.1469A>G	chr1.hg19:g.152084224T>C	ENSP00000357794:p.Lys490Arg	37.0	0.0		59.0	5.0	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	hg19	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	t	8.419	0.845945	0.16963	.	.	ENSG00000159450	ENST00000368804	T	0.04654	3.58	2.98	-5.97	0.02227	.	.	.	.	.	T	0.00524	0.0017	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48547	-0.9026	9	0.09590	T	0.72	.	5.0277	0.14393	0.1398:0.4054:0.0:0.4548	.	490	Q07283	TRHY_HUMAN	R	490	ENSP00000357794:K490R	ENSP00000357794:K490R	K	-	2	0	TCHH	150350848	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.247000	0.00266	-1.053000	0.03218	-1.396000	0.01147	AAG	.	.		0.672	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		C	152084224	T	C	152084224	3	2	360	1	0	0	0	0	1	0	0	0	15715	1609	56	2	4366	2	TCHH	1	152084224	Missense_Mutation	SNP	T	TCGA-XR-A8TF-01A-11D-A35Z-10	31700072	152084224	97166397	10	50311										
KCNN3	3782	hgsc.bcm.edu	37	chr1	154841900	154841900	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	gggcttcatgaccccaccgcTatacttgcaggagctcatgg	11	13	2	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr1:154841900T>A	ENST00000271915.4	-	1	856	c.541A>T	c.(541-543)Agc>Tgc	p.S181C	KCNN3_ENST00000358505.2_5'Flank	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	186					potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	ACCCCACCGCTATACTTGCAG	0.677																																					p.S181C		Atlas-SNP	.											.	KCNN3	141	.	0			c.A541T						.						41	44	43					1																	154841900		2203	4300	6503	SO:0001583	missense	3782	exon1			CACCGCTATACTT	AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.541A>T	chr1.hg19:g.154841900T>A	ENSP00000271915:p.Ser181Cys	98.0	0.0		110.0	48.0	NM_001204087	B1ANX0|O43517|Q86VF9|Q8WXG7	Missense_Mutation	SNP	ENST00000271915.4	hg19	CCDS30880.1	.	.	.	.	.	.	.	.	.	.	T	19.64	3.864790	0.71949	.	.	ENSG00000143603	ENST00000271915	D	0.95821	-3.82	4.75	4.75	0.60458	.	0.262866	0.27227	N	0.020326	D	0.90293	0.6964	N	0.14661	0.345	0.80722	D	1	D;D	0.64830	0.994;0.983	P;P	0.51355	0.667;0.533	D	0.92589	0.6081	10	0.87932	D	0	-20.1914	12.2631	0.54661	0.0:0.0:0.0:1.0	.	187;186	Q6JXY2;Q9UGI6	.;KCNN3_HUMAN	C	181	ENSP00000271915:S181C	ENSP00000271915:S181C	S	-	1	0	KCNN3	153108524	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.928000	0.70088	1.992000	0.58205	0.460000	0.39030	AGC	.	.		0.677	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249		A	154841900	T	A	154841900	3	1	360	1	0	0	0	0	1	0	0	0	8089	1522	53	4	1708	4	KCNN3	1	154841900	Missense_Mutation	SNP	T	TCGA-XR-A8TF-01A-11D-A35Z-10	2757676	154841900	94408721	11	50312										
SLC25A44	9673	hgsc.bcm.edu	37	chr1	156170105	156170105	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	tcaggtgcgggggaacccagAgggacaaggggtagttgcct	18	8	1	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr1:156170105A>G	ENST00000359511.4	+	2	639	c.467A>G	c.(466-468)gAg>gGg	p.E156G	SLC25A44_ENST00000423538.2_Missense_Mutation_p.E133G|SLC25A44_ENST00000469537.1_3'UTR	NM_014655.2	NP_055470.1	Q96H78	S2544_HUMAN	solute carrier family 25, member 44	156					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				breast(3)|kidney(2)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14	Hepatocellular(266;0.158)					GGGAACCCAGAGGGACAAGGG	0.562																																					p.E156G		Atlas-SNP	.											.	SLC25A44	30	.	0			c.A467G						.						90	80	83					1																	156170105		2203	4300	6503	SO:0001583	missense	9673	exon2			ACCCAGAGGGACA	AB007915	CCDS1133.1, CCDS72943.1	1q22	2013-05-22			ENSG00000160785	ENSG00000160785		"Solute carriers"	29036	protein-coding gene	gene with protein product		610824				16949250	Standard	NM_001286184		Approved	FLJ90431, KIAA0446	uc001fnp.3	Q96H78	OTTHUMG00000014816	ENST00000359511.4:c.467A>G	chr1.hg19:g.156170105A>G	ENSP00000352497:p.Glu156Gly	82.0	0.0		123.0	39.0	NM_014655	O75034	Missense_Mutation	SNP	ENST00000359511.4	hg19	CCDS1133.1	.	.	.	.	.	.	.	.	.	.	A	10.02	1.234832	0.22626	.	.	ENSG00000160785	ENST00000359511;ENST00000423538	T;T	0.79247	-1.25;-1.13	5.55	5.55	0.83447	Mitochondrial carrier domain (2);	0.396482	0.27609	N	0.018607	T	0.38188	0.1031	N	0.02916	-0.46	0.44603	D	0.997574	B;B;B	0.10296	0.003;0.002;0.002	B;B;B	0.11329	0.004;0.006;0.004	T	0.40194	-0.9576	10	0.17832	T	0.49	-8.6994	13.7027	0.62620	1.0:0.0:0.0:0.0	.	133;133;156	E9PGQ0;B4DGC4;Q96H78	.;.;S2544_HUMAN	G	156;133	ENSP00000352497:E156G;ENSP00000407560:E133G	ENSP00000352497:E156G	E	+	2	0	SLC25A44	154436729	0.929000	0.31497	0.921000	0.36526	0.675000	0.39556	3.136000	0.50554	2.333000	0.79357	0.482000	0.46254	GAG	.	.		0.562	SLC25A44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040856.1	NM_014655		G	156170105	A	G	156170105	3	3	360	1	0	0	0	0	1	0	0	0	14524	304	11	2	469	2	SLC25A44	1	156170105	Missense_Mutation	SNP	A	TCGA-XR-A8TF-01A-11D-A35Z-10	1328205	156170105	93080516	12	50313										
CD5L	922	hgsc.bcm.edu	37	chr1	157805704	157805704	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	cactgagccaatgtatcttcTgttcctgtgcaactgactga	8	11	2	3			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr1:157805704T>G	ENST00000368174.4	-	3	393	c.297A>C	c.(295-297)acA>acC	p.T99T	CD5L_ENST00000484609.1_5'Flank	NM_005894.2	NP_005885.1	O43866	CD5L_HUMAN	CD5 molecule-like	99	SRCR 1. {ECO:0000255|PROSITE- ProRule:PRU00196}.				apoptotic process (GO:0006915)|cellular defense response (GO:0006968)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	scavenger receptor activity (GO:0005044)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	52	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			ATGTATCTTCTGTTCCTGTGC	0.493																																					p.T99T		Atlas-SNP	.											CD5L,NS,carcinoma,0,1	CD5L	112	.	0			c.A297C						.						227	232	230					1																	157805704		2203	4300	6503	SO:0001819	synonymous_variant	922	exon3			ATCTTCTGTTCCT	U82812	CCDS1171.1	1q21-q23	2008-02-05	2006-03-28		ENSG00000073754	ENSG00000073754			1690	protein-coding gene	gene with protein product		602592	"apoptosis inhibitor 6", "CD5 antigen-like (scavenger receptor cysteine rich family)"	API6		9045627	Standard	NM_005894		Approved	Spalpha	uc001frk.4	O43866	OTTHUMG00000022440	ENST00000368174.4:c.297A>C	chr1.hg19:g.157805704T>G		86.0	0.0		96.0	30.0	NM_005894	A8K7M5|Q6UX63	Silent	SNP	ENST00000368174.4	hg19	CCDS1171.1																																																																																			.	.		0.493	CD5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058346.1	NM_005894		G	157805704	T	G	157805704	2	3	360	1	0	0	0	0	0	0	0	1	3029	1567	55	5		5	CD5L	1	157805704	Silent	SNP	T	TCGA-XR-A8TF-01A-11D-A35Z-10	1635599	157805704	91444917	13	50314										
IL10	3586	hgsc.bcm.edu	37	chr1	206945657	206945657	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	gaaggcatctcggagatctcGaagcatgttaggcaggttgc	14	8	2	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr1:206945657G>A	ENST00000423557.1	-	1	182	c.124C>T	c.(124-126)Cga>Tga	p.R42*	IL10_ENST00000471071.1_5'Flank	NM_000572.2	NP_000563.1	P22301	IL10_HUMAN	interleukin 10	42					B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|cell-cell signaling (GO:0007267)|cellular response to estradiol stimulus (GO:0071392)|cellular response to lipopolysaccharide (GO:0071222)|cytoplasmic sequestering of NF-kappaB (GO:0007253)|defense response to bacterium (GO:0042742)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|leukocyte chemotaxis (GO:0030595)|negative regulation of apoptotic process (GO:0043066)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of chronic inflammatory response to antigenic stimulus (GO:0002875)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interferon-alpha biosynthetic process (GO:0045355)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of myeloid dendritic cell activation (GO:0030886)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|negative regulation of tumor necrosis factor production (GO:0032720)|positive regulation of B cell apoptotic process (GO:0002904)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor biosynthetic process (GO:0032800)|regulation of gene expression (GO:0010468)|regulation of isotype switching (GO:0045191)|regulation of sensory perception of pain (GO:0051930)|response to activity (GO:0014823)|response to carbon monoxide (GO:0034465)|response to drug (GO:0042493)|response to glucocorticoid (GO:0051384)|response to inactivity (GO:0014854)|response to insulin (GO:0032868)|response to molecule of bacterial origin (GO:0002237)|type 2 immune response (GO:0042092)	extracellular space (GO:0005615)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|interleukin-10 receptor binding (GO:0005141)			endometrium(1)|large_intestine(6)|lung(4)|prostate(1)	12	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.211)			CGGAGATCTCGAAGCATGTTA	0.552																																					p.R42X		Atlas-SNP	.											.	IL10	22	.	0			c.C124T						.						123	101	108					1																	206945657		2203	4300	6503	SO:0001587	stop_gained	3586	exon1			GATCTCGAAGCAT	M57627	CCDS1467.1	1q31-q32	2011-07-14			ENSG00000136634	ENSG00000136634		"Interleukins and interleukin receptors"	5962	protein-coding gene	gene with protein product	"cytokine synthesis inhibitory factor", "T-cell growth inhibitory factor"	124092				9162098	Standard	NM_000572		Approved	CSIF, TGIF, IL10A, IL-10	uc001hen.1	P22301	OTTHUMG00000036386	ENST00000423557.1:c.124C>T	chr1.hg19:g.206945657G>A	ENSP00000412237:p.Arg42*	71.0	0.0		139.0	66.0	NM_000572		Nonsense_Mutation	SNP	ENST00000423557.1	hg19	CCDS1467.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.422291	0.83559	.	.	ENSG00000136634	ENST00000423557	.	.	.	5.86	3.89	0.44902	.	0.305675	0.33161	N	0.005215	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.8814	6.8794	0.24164	0.087:0.0:0.7406:0.1724	.	.	.	.	X	42	.	ENSP00000412237:R42X	R	-	1	2	IL10	205012280	0.482000	0.25948	0.451000	0.26982	0.376000	0.30014	1.684000	0.37649	1.484000	0.48361	0.655000	0.94253	CGA	.	.		0.552	IL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088564.3	NM_000572		A	206945657	G	A	206945657	4	1	360	1	0	0	0	0	0	1	0	0	7628	1066	37	1	432	1	IL10	1	206945657	Nonsense_Mutation	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10	49139953	206945657	42304964	14	50315										
ESRRG	2104	hgsc.bcm.edu	37	chr1	216850491	216850491	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	tagtggtacccagaagcgatGtcaccacacactaaacacag	8	12	1	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr1:216850491G>C	ENST00000408911.3	-	2	552	c.399C>G	c.(397-399)gaC>gaG	p.D133E	ESRRG_ENST00000463665.1_Missense_Mutation_p.D110E|ESRRG_ENST00000361395.2_Missense_Mutation_p.D110E|ESRRG_ENST00000493603.1_Missense_Mutation_p.D110E|ESRRG_ENST00000366937.1_Missense_Mutation_p.D138E|ESRRG_ENST00000366938.2_Missense_Mutation_p.D110E|ESRRG_ENST00000366940.2_Missense_Mutation_p.D110E|ESRRG_ENST00000493748.1_Missense_Mutation_p.D110E|ESRRG_ENST00000361525.3_Missense_Mutation_p.D110E|ESRRG_ENST00000391890.3_Missense_Mutation_p.D110E|ESRRG_ENST00000487276.1_Missense_Mutation_p.D110E|ESRRG_ENST00000360012.3_Missense_Mutation_p.D110E|ESRRG_ENST00000359162.2_Missense_Mutation_p.D110E	NM_001438.3	NP_001429.2	P62508	ERR3_HUMAN	estrogen-related receptor gamma	133					gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	AF-2 domain binding (GO:0050682)|retinoic acid receptor activity (GO:0003708)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(29)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)	CAGAAGCGATGTCACCACACA	0.483																																					p.D138E		Atlas-SNP	.											.	ESRRG	111	.	0			c.C414G						.						194	170	178					1																	216850491		2203	4300	6503	SO:0001583	missense	2104	exon3			AGCGATGTCACCA	AF058291	CCDS1517.1, CCDS41468.1, CCDS58060.1, CCDS58061.1	1q41	2014-02-18			ENSG00000196482	ENSG00000196482		"Nuclear hormone receptors"	3474	protein-coding gene	gene with protein product		602969				9676434, 10072763	Standard	NM_001243505		Approved	NR3B3	uc001hkw.2	P62508	OTTHUMG00000037025	ENST00000408911.3:c.399C>G	chr1.hg19:g.216850491G>C	ENSP00000386171:p.Asp133Glu	113.0	0.0		224.0	80.0	NM_001243518	A8K4I0|A8K6I2|B3KY84|E9PGB7|F8W8J3|O75454|O96021|Q68DA0|Q6P274|Q6PK28|Q6TS38|Q9R1F3|Q9UNJ4	Missense_Mutation	SNP	ENST00000408911.3	hg19	CCDS41468.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.457957	0.84317	.	.	ENSG00000196482	ENST00000361525;ENST00000366940;ENST00000366937;ENST00000408911;ENST00000359162;ENST00000361395;ENST00000366938;ENST00000360012;ENST00000493603;ENST00000391890;ENST00000463665;ENST00000487276;ENST00000354407;ENST00000493748;ENST00000475275	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.98135	-4.74;-4.74;-4.74;-4.74;-4.74;-4.74;-4.74;-4.74;-4.74;-4.74;-4.74;-4.74;-4.74;-4.74	6.01	4.92	0.64577	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (5);	0.000000	0.85682	D	0.000000	D	0.98563	0.9520	M	0.82823	2.61	0.58432	D	0.999999	D;D;D	0.71674	0.998;0.99;0.992	D;D;D	0.79108	0.923;0.98;0.992	D	0.98614	1.0664	10	0.87932	D	0	.	13.85	0.63489	0.1234:0.0:0.8766:0.0	.	110;138;133	E9PGB7;F8W8J3;P62508	.;.;ERR3_HUMAN	E	110;110;138;133;110;110;110;110;110;110;110;110;110;110;110	ENSP00000355225:D110E;ENSP00000355907:D110E;ENSP00000355904:D138E;ENSP00000386171:D133E;ENSP00000352077:D110E;ENSP00000354584:D110E;ENSP00000355905:D110E;ENSP00000353108:D110E;ENSP00000419594:D110E;ENSP00000375761:D110E;ENSP00000418629:D110E;ENSP00000419155:D110E;ENSP00000417374:D110E;ENSP00000419514:D110E	ENSP00000346386:D110E	D	-	3	2	ESRRG	214917114	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.135000	0.57997	2.861000	0.98227	0.650000	0.86243	GAC	.	.		0.483	ESRRG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089882.2	NM_206595		C	216850491	G	C	216850491	3	2	360	1	0	0	0	0	1	0	0	0	5264	1368	48	4	1001	4	ESRRG	1	216850491	Missense_Mutation	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10	9904834	216850491	32400130	15	50316										
TRIM67	440730	hgsc.bcm.edu	37	chr1	231344891	231344891	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	cgccttcggggtggccagggCcagcgtggtcaaggacatga	17	11	1	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr1:231344891C>T	ENST00000366653.5	+	8	2018	c.2018C>T	c.(2017-2019)gCc>gTc	p.A673V	TRIM67_ENST00000366652.2_Missense_Mutation_p.A673V|TRIM67_ENST00000449018.3_Missense_Mutation_p.A611V|TRIM67_ENST00000444294.3_Missense_Mutation_p.A671V			Q6ZTA4	TRI67_HUMAN	tripartite motif containing 67	673	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Breast(184;0.0871)	all_cancers(173;0.189)|Prostate(94;0.167)				GTGGCCAGGGCCAGCGTGGTC	0.627																																					p.A673V		Atlas-SNP	.											.	TRIM67	160	.	0			c.C2018T						.						85	94	91					1																	231344891		2195	4298	6493	SO:0001583	missense	440730	exon8			CCAGGGCCAGCGT	AK126782	CCDS44333.1, CCDS73048.1	1q42.2	2014-02-17	2011-01-25		ENSG00000119283	ENSG00000119283		"Tripartite motif containing / Tripartite motif containing", "Fibronectin type III domain containing", "RING-type (C3HC4) zinc fingers"	31859	protein-coding gene	gene with protein product		610584	"tripartite motif-containing 67"				Standard	NM_001004342		Approved	TNL	uc009xfn.1	Q6ZTA4	OTTHUMG00000037958	ENST00000366653.5:c.2018C>T	chr1.hg19:g.231344891C>T	ENSP00000355613:p.Ala673Val	160.0	0.0		296.0	112.0	NM_001004342	Q5TER7|Q5TER8|Q7Z4K7	Missense_Mutation	SNP	ENST00000366653.5	hg19	CCDS44333.1	.	.	.	.	.	.	.	.	.	.	C	12.96	2.095422	0.36952	.	.	ENSG00000119283	ENST00000444294;ENST00000366652;ENST00000449018;ENST00000366653	T;T;T;T	0.68331	-0.32;-0.32;-0.32;-0.32	5.73	2.33	0.28932	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.213831	0.43416	N	0.000575	T	0.45013	0.1321	N	0.17379	0.485	0.31046	N	0.715771	B	0.12013	0.005	B	0.15870	0.014	T	0.38845	-0.9642	10	0.30854	T	0.27	.	7.4988	0.27505	0.0:0.6079:0.0:0.3921	.	673	Q6ZTA4	TRI67_HUMAN	V	671;673;611;673	ENSP00000412124:A671V;ENSP00000355612:A673V;ENSP00000400163:A611V;ENSP00000355613:A673V	ENSP00000355612:A673V	A	+	2	0	TRIM67	229411514	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.353000	0.52247	0.637000	0.30526	0.655000	0.94253	GCC	.	.		0.627	TRIM67-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092649.3	NM_001004342		T	231344891	C	T	231344891	3	4	360	1	0	0	0	0	1	0	0	0	16555	739	26	3	2048	3	TRIM67	1	231344891	Missense_Mutation	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10	14494400	231344891	17905730	16	50317										
FMN2	56776	hgsc.bcm.edu	37	chr1	240256430	240256430	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	cggccggagcccccgtgcgaGgggctggggacacggatgag	20	12	0	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr1:240256430G>A	ENST00000319653.9	+	1	1251	c.1021G>A	c.(1021-1023)Ggg>Agg	p.G341R		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	341					cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CCCCGTGCGAGGGGCTGGGGA	0.731																																					p.G341R		Atlas-SNP	.											.	FMN2	451	.	0			c.G1021A						.						4	5	5					1																	240256430		1568	3405	4973	SO:0001583	missense	56776	exon1			GTGCGAGGGGCTG	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.1021G>A	chr1.hg19:g.240256430G>A	ENSP00000318884:p.Gly341Arg	29.0	0.0		69.0	24.0	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	hg19	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	G	2.889	-0.230026	0.06022	.	.	ENSG00000155816	ENST00000319653	T	0.27557	1.66	2.97	2.05	0.26809	.	0.729752	0.12526	N	0.461216	T	0.24547	0.0595	L	0.54323	1.7	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.19679	-1.0298	10	0.31617	T	0.26	.	4.4116	0.11436	0.1324:0.2338:0.6338:0.0	.	341	Q9NZ56	FMN2_HUMAN	R	341	ENSP00000318884:G341R	ENSP00000318884:G341R	G	+	1	0	FMN2	238323053	0.010000	0.17322	0.001000	0.08648	0.485000	0.33311	1.824000	0.39072	0.813000	0.34350	-0.481000	0.04817	GGG	.	.		0.731	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		A	240256430	G	A	240256430	3	1	360	1	0	0	0	0	1	0	0	0	5958	1000	35	3	1023	3	FMN2	1	240256430	Missense_Mutation	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10	8911539	240256430	8994191	17	50318										
OR2T34	127068	hgsc.bcm.edu	37	chr1	248737365	248737365	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	gccggcggcagaattcatccTgtggatgagatgcaggatga	15	8	1	3			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr1:248737365T>A	ENST00000328782.2	-	1	715	c.694A>T	c.(694-696)Agg>Tgg	p.R232W		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	232						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R232W(1)		breast(1)|endometrium(1)|large_intestine(6)|lung(28)|ovary(2)|skin(2)|stomach(3)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GAATTCATCCTGTGGATGAGA	0.547																																					p.R232W		Atlas-SNP	.											OR2T34,NS,carcinoma,+1,1	OR2T34	72	.	1	Substitution - Missense(1)	lung(1)	c.A694T						.						112	128	122					1																	248737365		2176	4300	6476	SO:0001583	missense	127068	exon1			TCATCCTGTGGAT	BK004477	CCDS31120.1	1q44	2012-08-09			ENSG00000183310	ENSG00000183310		"GPCR / Class A : Olfactory receptors"	31256	protein-coding gene	gene with protein product							Standard	NM_001001821		Approved		uc001iep.1	Q8NGX1	OTTHUMG00000040387	ENST00000328782.2:c.694A>T	chr1.hg19:g.248737365T>A	ENSP00000330904:p.Arg232Trp	284.0	1.0		536.0	167.0	NM_001001821	B2RNJ8|Q6IEY5|Q96R31	Missense_Mutation	SNP	ENST00000328782.2	hg19	CCDS31120.1	.	.	.	.	.	.	.	.	.	.	.	18.33	3.600295	0.66332	.	.	ENSG00000183310	ENST00000328782	T	0.00269	8.37	2.37	2.37	0.29283	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00815	0.0027	H	0.96269	3.795	0.23036	N	0.998395	D	0.76494	0.999	D	0.83275	0.996	T	0.25222	-1.0138	9	0.87932	D	0	.	9.2409	0.37495	0.0:0.0:0.0:1.0	.	232	Q8NGX1	O2T34_HUMAN	W	232	ENSP00000330904:R232W	ENSP00000330904:R232W	R	-	1	2	OR2T34	246803988	0.001000	0.12720	0.140000	0.22221	0.165000	0.22458	0.844000	0.27654	0.964000	0.38108	0.104000	0.15600	AGG	.	.		0.547	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821		A	248737365	T	A	248737365	3	1	360	1	0	0	0	0	1	0	0	0	11034	1579	55	4	266	4	OR2T34	1	248737365	Missense_Mutation	SNP	T	TCGA-XR-A8TF-01A-11D-A35Z-10	8480935	248737365	513256	18	50319										
NTSR2	23620	hgsc.bcm.edu	37	chr2	11809668	11809668	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	agcgcggtgcggctcaccagCaccgtgcacactcgcgaggc	14	16	1	0			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr2:11809668C>A	ENST00000306928.5	-	1	622	c.588G>T	c.(586-588)gtG>gtT	p.V196V		NM_012344.3	NP_036476	O95665	NTR2_HUMAN	neurotensin receptor 2	196					cell surface receptor signaling pathway (GO:0007166)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|regulation of membrane potential (GO:0042391)|sensory perception (GO:0007600)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled neurotensin receptor activity (GO:0016492)|G-protein coupled receptor activity (GO:0004930)			breast(1)|large_intestine(7)|lung(7)|prostate(1)|urinary_tract(1)	17	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.129)|OV - Ovarian serous cystadenocarcinoma(76;0.24)	Levocabastine(DB01106)	GGCTCACCAGCACCGTGCACA	0.711																																					p.V196V		Atlas-SNP	.											.	NTSR2	36	.	0			c.G588T						.						11	13	13					2																	11809668		1729	3414	5143	SO:0001819	synonymous_variant	23620	exon1			CACCAGCACCGTG	Y10148	CCDS1681.1	2p25.1	2012-08-08			ENSG00000169006	ENSG00000169006		"GPCR / Class A : Neurotensin receptors"	8040	protein-coding gene	gene with protein product		605538				8647296, 9851594	Standard	NM_012344		Approved	NTR2	uc002rbq.4	O95665	OTTHUMG00000119083	ENST00000306928.5:c.588G>T	chr2.hg19:g.11809668C>A		32.0	0.0		31.0	20.0	NM_012344	Q53QQ5|Q57Z87|Q8IY58|Q8TBH6	Silent	SNP	ENST00000306928.5	hg19	CCDS1681.1																																																																																			.	.		0.711	NTSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239297.1			A	11809668	C	A	11809668	2	1	360	1	0	0	0	0	0	0	0	1	10720	697	25	3		3	NTSR2	2	11809668	Silent	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10		11809668	231389705	19	50320										
LPIN1	23175	hgsc.bcm.edu	37	chr2	11913854	11913854	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	taccctaattcggatagagaGtggtcacccactcccaggta	9	12	1	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr2:11913854G>T	ENST00000256720.2	+	5	798	c.705G>T	c.(703-705)gaG>gaT	p.E235D	LPIN1_ENST00000449576.2_Missense_Mutation_p.E284D|LPIN1_ENST00000396099.1_Missense_Mutation_p.E241D|LPIN1_ENST00000396098.1_Missense_Mutation_p.E241D|LPIN1_ENST00000425416.2_Missense_Mutation_p.E241D	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	235					cellular lipid metabolic process (GO:0044255)|fatty acid catabolic process (GO:0009062)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)|triglyceride mobilization (GO:0006642)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(15)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	45	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		CGGATAGAGAGTGGTCACCCA	0.463																																					p.E284D		Atlas-SNP	.											.	LPIN1	99	.	0			c.G852T						.						126	123	124					2																	11913854		2203	4300	6503	SO:0001583	missense	23175	exon6			TAGAGAGTGGTCA	D80010	CCDS1682.1, CCDS58699.1, CCDS58700.1, CCDS58701.1	2p25.1	2008-05-23			ENSG00000134324	ENSG00000134324			13345	protein-coding gene	gene with protein product		605518				11138012, 8724849, 16950137	Standard	NM_145693		Approved	KIAA0188	uc010yjm.3	Q14693	OTTHUMG00000119082	ENST00000256720.2:c.705G>T	chr2.hg19:g.11913854G>T	ENSP00000256720:p.Glu235Asp	81.0	0.0		60.0	20.0	NM_001261428	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Missense_Mutation	SNP	ENST00000256720.2	hg19	CCDS1682.1	.	.	.	.	.	.	.	.	.	.	G	11.54	1.668814	0.29604	.	.	ENSG00000134324	ENST00000449576;ENST00000396098;ENST00000396099;ENST00000425416;ENST00000256720	T;D;T;T;T	0.88664	-1.41;-2.41;-1.4;-1.44;-1.44	5.33	2.47	0.30058	.	0.260548	0.44483	D	0.000444	T	0.80330	0.4603	L	0.45137	1.4	0.80722	D	1	B;B;B	0.19445	0.004;0.004;0.036	B;B;B	0.22386	0.02;0.012;0.039	T	0.66304	-0.5957	10	0.18276	T	0.48	-29.8864	3.764	0.08615	0.2861:0.192:0.5219:0.0	.	284;235;241	F5GY24;Q14693;A8MU38	.;LPIN1_HUMAN;.	D	284;241;241;241;235	ENSP00000397908:E284D;ENSP00000379405:E241D;ENSP00000379406:E241D;ENSP00000401522:E241D;ENSP00000256720:E235D	ENSP00000256720:E235D	E	+	3	2	LPIN1	11831305	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	0.756000	0.26419	0.595000	0.29777	0.467000	0.42956	GAG	.	.		0.463	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693		T	11913854	G	T	11913854	3	4	360	1	0	0	0	0	1	0	0	0	8927	1020	36	3	719	3	LPIN1	2	11913854	Missense_Mutation	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10	104186	11913854	231285519	20	50321										
SMEK2	57223	hgsc.bcm.edu	37	chr2	55825633	55825633	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	aaattctcttcaaaaacagaTggtgtgggcaaaatgatgtc	9	6	2	2			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr2:55825633T>C	ENST00000345102.5	-	4	1141	c.840A>G	c.(838-840)ccA>ccG	p.P280P	SMEK2_ENST00000407823.3_Silent_p.P280P|SMEK2_ENST00000272313.5_Silent_p.P280P	NM_001122964.1	NP_001116436	Q5MIZ7	P4R3B_HUMAN	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	280					positive regulation of gluconeogenesis (GO:0045722)|protein dephosphorylation (GO:0006470)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)				kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	16			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			CAAAAACAGATGGTGTGGGCA	0.348																																					p.P280P		Atlas-SNP	.											.	SMEK2	86	.	0			c.A840G						.						83	82	83					2																	55825633		2203	4300	6503	SO:0001819	synonymous_variant	57223	exon4			AACAGATGGTGTG	AB037808	CCDS1855.1, CCDS46289.1, CCDS62913.1	2p16.1	2008-09-15			ENSG00000138041				29267	protein-coding gene	gene with protein product		610352				16085932, 18614045	Standard	NM_001122964		Approved	PSY2, FLFL2, KIAA1387, FLJ31474	uc002rzc.3	Q5MIZ7	OTTHUMG00000129336	ENST00000345102.5:c.840A>G	chr2.hg19:g.55825633T>C		396.0	0.0		319.0	103.0	NM_001122964	Q6P9B0|Q86XB8|Q9BQJ0|Q9BRK2|Q9H913|Q9P2G0	Silent	SNP	ENST00000345102.5	hg19	CCDS46289.1																																																																																			.	.		0.348	SMEK2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251483.1	NM_020463		C	55825633	T	C	55825633	2	2	360	1	0	0	0	0	0	0	0	1	14809	1451	51	2		2	SMEK2	2	55825633	Silent	SNP	T	TCGA-XR-A8TF-01A-11D-A35Z-10	43911779	55825633	187373740	21	50322										
EGR4	1961	hgsc.bcm.edu	37	chr2	73519494	73519494	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	gcgggaggcgcccggaggccGggcttgacgtcgggcgggga	23	11	0	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr2:73519494G>A	ENST00000545030.1	-	2	935	c.861C>T	c.(859-861)ccC>ccT	p.P287P	EGR4_ENST00000436467.2_Silent_p.P184P	NM_001965.3	NP_001956.3	Q05215	EGR4_HUMAN	early growth response 4	287	Pro-rich.				cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						CCCGGAGGCCGGGCTTGACGT	0.716																																					p.P287P		Atlas-SNP	.											EGR4_ENST00000545030,NS,adenocarcinoma,0,2	EGR4	52	.	0			c.C861T						.						6	9	8					2																	73519494		2116	4184	6300	SO:0001819	synonymous_variant	1961	exon2			GAGGCCGGGCTTG		CCDS1925.2	2p13	2013-01-08			ENSG00000135625	ENSG00000135625		"Zinc fingers, C2H2-type"	3241	protein-coding gene	gene with protein product		128992				1584812	Standard	NM_001965		Approved	NGFI-C, PAT133	uc010yrj.2	Q05215	OTTHUMG00000129774	ENST00000545030.1:c.861C>T	chr2.hg19:g.73519494G>A		144.0	0.0		111.0	61.0	NM_001965	B2RAE3|G3V1T5|Q2Z1P5	Silent	SNP	ENST00000545030.1	hg19	CCDS1925.2																																																																																			.	.		0.716	EGR4-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001965		A	73519494	G	A	73519494	2	1	360	1	0	0	0	0	0	0	0	1	4976	1103	39	1		1	EGR4	2	73519494	Silent	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10	17693861	73519494	169679879	22	50323										
ATOH8	84913	hgsc.bcm.edu	37	chr2	85981926	85981926	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	aatttacaataaccaccaggAttcctccgcgtcgcctagga	7	13	0	0			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr2:85981926A>G	ENST00000306279.3	+	1	910	c.614A>G	c.(613-615)gAt>gGt	p.D205G	ATOH8_ENST00000463422.1_3'UTR	NM_032827.6	NP_116216.2	Q96SQ7	ATOH8_HUMAN	atonal homolog 8 (Drosophila)	205					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(1)|large_intestine(1)|lung(2)	5						AACCACCAGGATTCCTCCGCG	0.647																																					p.D205G		Atlas-SNP	.											.	ATOH8	15	.	0			c.A614G						.						45	54	51					2																	85981926		2189	4271	6460	SO:0001583	missense	84913	exon1			ACCAGGATTCCTC	AK074681	CCDS1985.1	2p11.2	2013-05-21			ENSG00000168874	ENSG00000168874		"Basic helix-loop-helix proteins"	24126	protein-coding gene	gene with protein product	"basic helix loop helix transcription factor 6"					12419857	Standard	NM_032827		Approved	HATH6, FLJ14708, bHLHa21	uc002sqn.3	Q96SQ7	OTTHUMG00000130178	ENST00000306279.3:c.614A>G	chr2.hg19:g.85981926A>G	ENSP00000304676:p.Asp205Gly	161.0	0.0		157.0	88.0	NM_032827	Q504S2|Q659B0	Missense_Mutation	SNP	ENST00000306279.3	hg19	CCDS1985.1	.	.	.	.	.	.	.	.	.	.	A	14.76	2.632542	0.46944	.	.	ENSG00000168874	ENST00000306279	D	0.94613	-3.47	3.78	2.6	0.31112	.	0.257225	0.29646	N	0.011563	D	0.83248	0.5213	N	0.08118	0	0.30024	N	0.814115	P;P	0.47409	0.895;0.879	B;B	0.36464	0.191;0.225	T	0.80596	-0.1312	10	0.32370	T	0.25	-10.9615	8.056	0.30606	0.8183:0.0:0.0:0.1817	.	205;205	Q96SQ7;Q96SQ7-2	ATOH8_HUMAN;.	G	205	ENSP00000304676:D205G	ENSP00000304676:D205G	D	+	2	0	ATOH8	85835437	0.986000	0.35501	1.000000	0.80357	0.984000	0.73092	0.869000	0.27996	0.790000	0.33803	0.374000	0.22700	GAT	.	.		0.647	ATOH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252496.1	NM_032827		G	85981926	A	G	85981926	3	3	360	1	0	0	0	0	1	0	0	0	1114	333	12	2	616	2	ATOH8	2	85981926	Missense_Mutation	SNP	A	TCGA-XR-A8TF-01A-11D-A35Z-10	12462432	85981926	157217447	23	50324										
TTN	7273	hgsc.bcm.edu	37	chr2	179399523	179399542	+	Frame_Shift_Del	DEL	ATGTCAAAGTGTCCAATATT	ATGTCAAAGTGTCCAATATT	-													0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	aaatgatattttctggtctaAtgtcaaagtgtccaatatta					rs184789288|rs56376197|rs76106451	byFrequency	TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	ATGTCAAAGTGTCCAATATT	ATGTCAAAGTGTCCAATATT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr2:179399523_179399542delATGTCAAAGTGTCCAATATT	ENST00000591111.1	-	308	97101_97120	c.96877_96896delAATATTGGACACTTTGACAT	c.(96877-96897)aatattggacactttgacattfs	p.NIGHFDI32293fs	TTN_ENST00000460472.2_Frame_Shift_Del_p.NIGHFDI24869fs|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Frame_Shift_Del_p.NIGHFDI25061fs|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Frame_Shift_Del_p.NIGHFDI31366fs|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN_ENST00000589042.1_Frame_Shift_Del_p.NIGHFDI33934fs|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN_ENST00000359218.5_Frame_Shift_Del_p.NIGHFDI24994fs|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000415561.1_RNA|TTN-AS1_ENST00000588257.1_RNA			Q8WZ42	TITIN_HUMAN	titin	32293	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTCTGGTCTAATGTCAAAGTGTCCAATATTATGACTGTGT	0.373																																					p.33934_33940del		Atlas-INDEL	.											.	TTN	18412	.	0			c.101801_101820del						.																																			SO:0001589	frameshift_variant	7273	exon358			.	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.96877_96896delAATATTGGACACTTTGACAT	chr2.hg19:g.179399523_179399542delATGTCAAAGTGTCCAATATT	ENSP00000465570:p.Asn32293fs	49.0	0.0		46.0	10.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Frame_Shift_Del	DEL	ENST00000591111.1	hg19																																																																																				.	.		0.373	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		-	179399542	ATGTCAAAGTGTCCAATATT	-	179399523	7	5	360	1	0	1	0	1	0	0	0	0	16750	101	4	0	6180	0	TTN	2	179399523	Frame_Shift_Del	DEL	ATGTCAAAGTGTCCAATATT	TCGA-XR-A8TF-01A-11D-A35Z-10	93417597	179399523	63799850	24	50325										
CERKL	375298	hgsc.bcm.edu	37	chr2	182468567	182468567	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	ccatgaggagtacttacctgCcaatattttcttgaactgtc	7	10	1	2			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr2:182468567C>T	ENST00000339098.5	-	2	477	c.478G>A	c.(478-480)Gca>Aca	p.A160T	CERKL_ENST00000410087.3_Missense_Mutation_p.A160T|CERKL_ENST00000374970.2_Missense_Mutation_p.A160T|CERKL_ENST00000374969.2_Missense_Mutation_p.A160T|CERKL_ENST00000479558.1_5'UTR|CERKL_ENST00000409440.3_Missense_Mutation_p.A160T			Q49MI3	CERKL_HUMAN	ceramide kinase-like	160					negative regulation of apoptotic process (GO:0043066)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(13)|ovary(3)|skin(3)	32			OV - Ovarian serous cystadenocarcinoma(117;0.088)			TACTTACCTGCCAATATTTTC	0.308																																					p.A160T		Atlas-SNP	.											.	CERKL	138	.	0			c.G478A						.						70	77	74					2																	182468567		2203	4296	6499	SO:0001583	missense	375298	exon2			TACCTGCCAATAT	BC020465	CCDS33340.1, CCDS33341.1, CCDS42789.1, CCDS46466.1, CCDS54425.1	2q31.3	2005-01-04			ENSG00000188452	ENSG00000188452			21699	protein-coding gene	gene with protein product			"retinitis pigmentosa 26 (autosomal recessive)"	RP26		14681825	Standard	NR_027689		Approved		uc002uny.3	Q49MI3	OTTHUMG00000154315	ENST00000339098.5:c.478G>A	chr2.hg19:g.182468567C>T	ENSP00000341159:p.Ala160Thr	133.0	0.0		101.0	29.0	NM_001160277	B2RPL2|B4DEY1|Q49MH9|Q49MI0|Q49MI1|Q49MI2|Q5DVJ2|Q5DVJ4|Q5DVJ5|Q6UZF6|Q6ZP59	Missense_Mutation	SNP	ENST00000339098.5	hg19	CCDS42789.1	.	.	.	.	.	.	.	.	.	.	C	4.943	0.175269	0.09391	.	.	ENSG00000188452	ENST00000410087;ENST00000409440;ENST00000374969;ENST00000339098;ENST00000374970	T;T;T;T;T	0.29655	2.26;2.57;2.47;2.57;1.56	4.95	3.82	0.43975	.	0.918265	0.09119	N	0.846016	T	0.26048	0.0635	N	0.08118	0	0.23913	N	0.996485	B;D;B;B;B	0.76494	0.017;0.999;0.063;0.004;0.013	B;D;B;B;B	0.64687	0.002;0.928;0.017;0.004;0.003	T	0.26710	-1.0095	10	0.14252	T	0.57	.	3.8515	0.08957	0.0:0.6468:0.0:0.3532	.	160;160;160;160;160	B4DEY1;Q49MI3-4;Q49MI3-3;Q49MI3-2;Q49MI3	.;.;.;.;CERKL_HUMAN	T	160	ENSP00000386725:A160T;ENSP00000387080:A160T;ENSP00000364108:A160T;ENSP00000341159:A160T;ENSP00000364109:A160T	ENSP00000341159:A160T	A	-	1	0	CERKL	182176812	1.000000	0.71417	1.000000	0.80357	0.705000	0.40729	3.155000	0.50700	2.455000	0.83008	0.655000	0.94253	GCA	.	.		0.308	CERKL-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334811.1			T	182468567	C	T	182468567	3	4	360	1	0	0	0	0	1	0	0	0	3270	739	26	3	1250	3	CERKL	2	182468567	Missense_Mutation	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10	3069044	182468567	60730806	25	50326										
RQCD1	9125	hgsc.bcm.edu	37	chr2	219447779	219447779	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	ttgcaatgctctggcattacTgcaatgtgtagcatcacatc	8	10	2	0			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr2:219447779T>C	ENST00000273064.6	+	3	665	c.290T>C	c.(289-291)cTg>cCg	p.L97P	RQCD1_ENST00000509807.2_Missense_Mutation_p.L97P|RQCD1_ENST00000295701.5_Missense_Mutation_p.L97P|RQCD1_ENST00000542068.1_Missense_Mutation_p.L97P	NM_005444.2	NP_005435.1	Q92600	RCD1_HUMAN	RCD1 required for cell differentiation1 homolog (S. pombe)	97					cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of ligand-dependent nuclear receptor transcription coactivator activity (GO:2000327)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|sex differentiation (GO:0007548)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)|prostate(3)|skin(1)	15		Renal(207;0.0915)		Epithelial(149;1.13e-06)|all cancers(144;0.000192)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CTGGCATTACTGCAATGTGTA	0.393																																					p.L97P		Atlas-SNP	.											.	RQCD1	32	.	0			c.T290C						.						136	121	126					2																	219447779		2203	4300	6503	SO:0001583	missense	9125	exon3			CATTACTGCAATG	D87957	CCDS33379.1, CCDS63123.1	2q35	2010-04-23	2001-11-28		ENSG00000144580	ENSG00000144580			10445	protein-coding gene	gene with protein product	"cancer/testis antigen 129"	612054	"rcd1 (required for cell differentiation, S.pombe) homolog 1"			9447985	Standard	NM_001271634		Approved	RCD1, RCD1+, CNOT9, CT129	uc010zki.3	Q92600	OTTHUMG00000154750	ENST00000273064.6:c.290T>C	chr2.hg19:g.219447779T>C	ENSP00000273064:p.Leu97Pro	125.0	0.0		133.0	69.0	NM_001271634	B2RPI0|B5MDQ4|B7Z1E5|Q96IX4	Missense_Mutation	SNP	ENST00000273064.6	hg19	CCDS33379.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.794802	0.90453	.	.	ENSG00000144580	ENST00000273064;ENST00000509807;ENST00000542068;ENST00000295701	T;T;T;T	0.72835	-0.69;-0.35;-0.69;-0.69	5.78	5.78	0.91487	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.90270	0.6957	H	0.97829	4.085	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.992;1.0;0.999	D	0.93668	0.6987	10	0.72032	D	0.01	-15.1264	16.3979	0.83621	0.0:0.0:0.0:1.0	.	97;97;97	B7Z1E5;Q92600;B5MDQ4	.;RCD1_HUMAN;.	P	97	ENSP00000273064:L97P;ENSP00000441357:L97P;ENSP00000443687:L97P;ENSP00000295701:L97P	ENSP00000273064:L97P	L	+	2	0	RQCD1	219156023	1.000000	0.71417	0.997000	0.53966	0.944000	0.59088	7.997000	0.88414	2.333000	0.79357	0.533000	0.62120	CTG	.	.		0.393	RQCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336920.1	NM_005444		C	219447779	T	C	219447779	3	2	360	1	0	0	0	0	1	0	0	0	13685	1580	55	2	300	2	RQCD1	2	219447779	Missense_Mutation	SNP	T	TCGA-XR-A8TF-01A-11D-A35Z-10	36979212	219447779	23751594	26	50327										
COL4A4	1286	hgsc.bcm.edu	37	chr2	228009257	228009257	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	atacatattgtacagaaaagAgaatgagtataagtgaccta	8	4	0	4			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr2:228009257A>C	ENST00000396625.3	-	3	296	c.89T>G	c.(88-90)cTc>cGc	p.L30R	COL4A4_ENST00000329662.7_Missense_Mutation_p.L30R	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	30					axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		TACAGAAAAGAGAATGAGTAT	0.289																																					p.L30R		Atlas-SNP	.											.	COL4A4	215	.	0			c.T89G						.						90	85	86					2																	228009257		1811	4073	5884	SO:0001583	missense	1286	exon3			GAAAAGAGAATGA		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"Collagens"	2206	protein-coding gene	gene with protein product	"collagen of basement membrane, alpha-4 chain"	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.89T>G	chr2.hg19:g.228009257A>C	ENSP00000379866:p.Leu30Arg	1177.0	0.0		932.0	550.0	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Missense_Mutation	SNP	ENST00000396625.3	hg19	CCDS42828.1	.	.	.	.	.	.	.	.	.	.	A	12.95	2.090108	0.36855	.	.	ENSG00000081052	ENST00000396625;ENST00000329662	D;D	0.91351	-2.83;-2.78	4.71	4.71	0.59529	.	.	.	.	.	D	0.88930	0.6571	N	0.14661	0.345	0.36174	D	0.84895	D	0.71674	0.998	P	0.62649	0.905	D	0.91211	0.4999	9	0.62326	D	0.03	.	10.5174	0.44898	1.0:0.0:0.0:0.0	.	30	P53420	CO4A4_HUMAN	R	30	ENSP00000379866:L30R;ENSP00000328553:L30R	ENSP00000328553:L30R	L	-	2	0	COL4A4	227717501	0.348000	0.24861	0.632000	0.29296	0.423000	0.31445	3.944000	0.56629	1.970000	0.57323	0.455000	0.32223	CTC	.	.		0.289	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092		C	228009257	A	C	228009257	3	2	360	1	0	0	0	0	1	0	0	0	3695	304	11	5	5167	5	COL4A4	2	228009257	Missense_Mutation	SNP	A	TCGA-XR-A8TF-01A-11D-A35Z-10	8561478	228009257	15190116	27	50328										
CNTN6	27255	hgsc.bcm.edu	37	chr3	1414520	1414520	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	atttctccctttctgtctgcAggaatctgttggggatttga	10	8	4	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr3:1414520A>T	ENST00000446702.2	+	14	2295		c.e14-1		CNTN6_ENST00000350110.2_Splice_Site|CNTN6_ENST00000539053.1_Splice_Site			Q9UQ52	CNTN6_HUMAN	contactin 6						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		TTCTGTCTGCAGGAATCTGTT	0.353																																					.		Atlas-SNP	.											CNTN6,NS,malignant_melanoma,0,1	CNTN6	245	.	0			c.1669-2A>T						.						141	148	146					3																	1414520		2203	4300	6503	SO:0001630	splice_region_variant	27255	exon14			GTCTGCAGGAATC	AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	2176	protein-coding gene	gene with protein product	"neural adhesion molecule"	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.1669-1A>T	chr3.hg19:g.1414520A>T		67.0	0.0		68.0	16.0	NM_014461	Q2KHM2	Splice_Site	SNP	ENST00000446702.2	hg19	CCDS2557.1	.	.	.	.	.	.	.	.	.	.	A	18.89	3.719325	0.68844	.	.	ENSG00000134115	ENST00000446702;ENST00000539053;ENST00000350110	.	.	.	5.51	5.51	0.81932	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9209	0.79570	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CNTN6	1389520	1.000000	0.71417	0.988000	0.46212	0.714000	0.41099	6.797000	0.75150	2.210000	0.71456	0.533000	0.62120	.	.	.		0.353	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461	Intron	T	1414520	A	T	1414520	5	4	360	1	0	0	0	0	0	0	1	0	3647	202	7	4	1717	4	CNTN6	3	1414520	Splice_Site	SNP	A	TCGA-XR-A8TF-01A-11D-A35Z-10		1414520	196607910	28	50329										
CMTM7	112616	hgsc.bcm.edu	37	chr3	32433454	32433454	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	cagcagcggcagcgcgctcgGacccggggccggcgcggccc	18	18	0	0			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr3:32433454G>A	ENST00000334983.5	+	1	292	c.56G>A	c.(55-57)gGa>gAa	p.G19E	CMTM7_ENST00000349718.4_Missense_Mutation_p.G19E	NM_138410.2	NP_612419.1	Q96FZ5	CKLF7_HUMAN	CKLF-like MARVEL transmembrane domain containing 7	19					chemotaxis (GO:0006935)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|large_intestine(1)|lung(2)	4						AGCGCGCTCGGACCCGGGGCC	0.771																																					p.G19E		Atlas-SNP	.											.	CMTM7	14	.	0			c.G56A						.						1	1	1					3																	32433454		820	1756	2576	SO:0001583	missense	112616	exon1			CGCTCGGACCCGG	AF479263	CCDS33730.1, CCDS33731.1	3p22.2	2005-11-08	2005-11-08	2005-11-08	ENSG00000153551	ENSG00000153551			19178	protein-coding gene	gene with protein product		607890	"chemokine-like factor super family 7", "chemokine-like factor superfamily 7"	CKLFSF7			Standard	NM_138410		Approved	FLJ30992	uc003cey.1	Q96FZ5	OTTHUMG00000155869	ENST00000334983.5:c.56G>A	chr3.hg19:g.32433454G>A	ENSP00000335605:p.Gly19Glu	30.0	0.0		27.0	10.0	NM_138410	Q5VLK1	Missense_Mutation	SNP	ENST00000334983.5	hg19	CCDS33730.1	.	.	.	.	.	.	.	.	.	.	G	15.22	2.768064	0.49680	.	.	ENSG00000153551	ENST00000334983;ENST00000349718	T	0.30448	1.53	3.91	0.8	0.18672	.	1.336160	0.05327	U	0.527675	T	0.23133	0.0559	N	0.24115	0.695	0.09310	N	1	P;P	0.47677	0.899;0.838	P;B	0.45099	0.469;0.218	T	0.22906	-1.0203	10	0.15952	T	0.53	.	7.9518	0.30019	0.0:0.3141:0.5262:0.1597	.	19;19	Q5VLK1;Q96FZ5	.;CKLF7_HUMAN	E	19	ENSP00000335605:G19E	ENSP00000335605:G19E	G	+	2	0	CMTM7	32408458	0.026000	0.19158	0.008000	0.14137	0.752000	0.42762	1.005000	0.29834	0.824000	0.34613	0.305000	0.20034	GGA	.	.		0.771	CMTM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342084.1			A	32433454	G	A	32433454	3	1	360	1	0	0	0	0	1	0	0	0	3590	1174	41	3	58	3	CMTM7	3	32433454	Missense_Mutation	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10	31018934	32433454	165588976	29	50330										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266101	41266101	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	gcaacagtcttacctggactCtggaatccattctggtgcca	9	12	3	0	rs121913416|rs121913400		TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr3:41266101C>T	ENST00000349496.5	+	3	378	c.98C>T	c.(97-99)tCt>tTt	p.S33F	CTNNB1_ENST00000396183.3_Missense_Mutation_p.S33F|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S33F|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S26F|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S33F	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	33			Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> F (in PTR, MDB and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10666372}.|S -> L (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> Y (in colorectal cancer and PTR; enhances transactivation of target genes). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:9065402}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S33C(168)|p.S33F(97)|p.S33Y(60)|p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.S33L(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S33N(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.D32fs*9(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.S29_H36del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.D32_H36>D(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TACCTGGACTCTGGAATCCAT	0.488	S33C(SKMEL1_SKIN)|S33F(SW1573_LUNG)|S33Y(SW48_LARGE_INTESTINE)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S33F	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,0,359	CTNNB1	4904	.	468	Substitution - Missense(331)|Deletion - In frame(111)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(165)|central_nervous_system(82)|large_intestine(40)|endometrium(37)|stomach(32)|skin(21)|ovary(20)|pituitary(19)|pancreas(12)|lung(7)|biliary_tract(6)|soft_tissue(4)|bone(4)|breast(3)|prostate(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|parathyroid(2)|small_intestine(2)|thyroid(1)|NS(1)|urinary_tract(1)|adrenal_gland(1)	c.C98T						.						92	77	82					3																	41266101		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	TGGACTCTGGAAT	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.98C>T	chr3.hg19:g.41266101C>T	ENSP00000344456:p.Ser33Phe	220.0	1.0		148.0	50.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.498846	0.85069	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.50813	0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.72053	0.3413	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74188	-0.3746	10	0.87932	D	0	-10.7796	19.9596	0.97236	0.0:1.0:0.0:0.0	.	33	P35222	CTNB1_HUMAN	F	26;33;33;33;33;26;33;33;33	ENSP00000400508:S26F;ENSP00000385604:S33F;ENSP00000412219:S33F;ENSP00000379486:S33F;ENSP00000344456:S33F;ENSP00000411226:S26F;ENSP00000379488:S33F;ENSP00000409302:S33F;ENSP00000401599:S33F	ENSP00000344456:S33F	S	+	2	0	CTNNB1	41241105	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.726000	0.93360	0.655000	0.94253	TCT	.	.		0.488	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41266101	C	T	41266101	3	4	360	1	0	0	0	0	1	0	0	0	4018	913	32	3	104	3	CTNNB1	3	41266101	Missense_Mutation	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10	8832647	41266101	156756329	30	50331										
CCR5	1234	hgsc.bcm.edu	37	chr3	46415374	46415374	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	tgcaaatgctgttctattttCcagcaagaggctcccgagcg	10	11	1	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr3:46415374C>T	ENST00000292303.4	+	2	1127	c.981C>T	c.(979-981)ttC>ttT	p.F327F	RP11-24F11.2_ENST00000451485.1_RNA|CCR5_ENST00000445772.1_Silent_p.F327F|CCR5_ENST00000343801.4_Silent_p.F327F	NM_001100168.1	NP_001093638.1	P51681	CCR5_HUMAN	chemokine (C-C motif) receptor 5 (gene/pseudogene)	327					calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|entry into host cell (GO:0030260)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|MAPK cascade (GO:0000165)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to cholesterol (GO:0070723)|signaling (GO:0023052)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|C-C chemokine binding (GO:0019957)|C-C chemokine receptor activity (GO:0016493)|chemokine (C-C motif) ligand 5 binding (GO:0071791)|chemokine receptor activity (GO:0004950)|coreceptor activity (GO:0015026)|phosphatidylinositol phospholipase C activity (GO:0004435)			central_nervous_system(1)|large_intestine(2)|lung(13)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20				BRCA - Breast invasive adenocarcinoma(193;0.00112)|KIRC - Kidney renal clear cell carcinoma(197;0.017)|Kidney(197;0.02)	Maraviroc(DB04835)	GTTCTATTTTCCAGCAAGAGG	0.502																																					p.F327F		Atlas-SNP	.											.	CCR5	128	.	0			c.C981T						.						108	107	108					3																	46415374		2203	4296	6499	SO:0001819	synonymous_variant	1234	exon3			TATTTTCCAGCAA		CCDS2739.1	3p21	2012-08-08	2012-01-23		ENSG00000160791	ENSG00000160791		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1606	protein-coding gene	gene with protein product		601373	"chemokine (C-C motif) receptor 5"	CMKBR5		8639485	Standard	NM_001100168		Approved	CKR-5, CC-CKR-5, CKR5, CD195, IDDM22	uc003cpo.4	P51681	OTTHUMG00000133481	ENST00000292303.4:c.981C>T	chr3.hg19:g.46415374C>T		96.0	0.0		109.0	71.0	NM_000579	O14692|O14693|O14695|O14696|O14697|O14698|O14699|O14700|O14701|O14702|O14703|O14704|O14705|O14706|O14707|O14708|O15538|Q9UPA4	Silent	SNP	ENST00000292303.4	hg19	CCDS2739.1																																																																																			.	.		0.502	CCR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257377.2	NM_000579		T	46415374	C	T	46415374	2	4	360	1	0	0	0	0	0	0	0	1	2946	854	30	3		3	CCR5	3	46415374	Silent	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10	5149273	46415374	151607056	31	50332										
STAB1	23166	hgsc.bcm.edu	37	chr3	52554832	52554832	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	tggcccagggcagccctgagGcctgctggcgcttctacccg	14	16	1	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr3:52554832G>T	ENST00000321725.6	+	55	5795	c.5719G>T	c.(5719-5721)Gcc>Tcc	p.A1907S		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	1907					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)			breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		CAGCCCTGAGGCCTGCTGGCG	0.657																																					p.A1907S		Atlas-SNP	.											.	STAB1	178	.	0			c.G5719T						.						127	151	143					3																	52554832		2203	4300	6503	SO:0001583	missense	23166	exon55			CCTGAGGCCTGCT	AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"MS-1 antigen", "fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1", "common lymphatic endothelial and vascular endothelial receptor-1"	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.5719G>T	chr3.hg19:g.52554832G>T	ENSP00000312946:p.Ala1907Ser	69.0	0.0		33.0	14.0	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Missense_Mutation	SNP	ENST00000321725.6	hg19	CCDS33768.1	.	.	.	.	.	.	.	.	.	.	G	4.341	0.062627	0.08388	.	.	ENSG00000010327	ENST00000321725	D	0.84516	-1.86	5.49	-3.57	0.04612	.	1.755180	0.02221	N	0.064051	T	0.70002	0.3174	N	0.24115	0.695	0.09310	N	1	B	0.19583	0.037	B	0.19391	0.025	T	0.58132	-0.7690	10	0.09338	T	0.73	.	2.3425	0.04263	0.3871:0.1188:0.3737:0.1204	.	1907	Q9NY15	STAB1_HUMAN	S	1907	ENSP00000312946:A1907S	ENSP00000312946:A1907S	A	+	1	0	STAB1	52529872	0.001000	0.12720	0.218000	0.23776	0.805000	0.45488	-0.908000	0.04063	-0.701000	0.05063	0.655000	0.94253	GCC	.	.		0.657	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136		T	52554832	G	T	52554832	3	4	360	1	0	0	0	0	1	0	0	0	15252	1203	42	3	5937	3	STAB1	3	52554832	Missense_Mutation	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10	6139458	52554832	145467598	32	50333										
APPL1	26060	hgsc.bcm.edu	37	chr3	57282291	57282291	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	aggatttggaagtagccagtGatcccttatatgtgcctgac	11	8	0	2			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr3:57282291G>T	ENST00000288266.3	+	10	922	c.775G>T	c.(775-777)Gat>Tat	p.D259Y		NM_012096.2	NP_036228.1	Q9UKG1	DP13A_HUMAN	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 1	259	Required for RAB5A binding.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|insulin receptor signaling pathway (GO:0008286)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic process (GO:0042981)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|regulation of glucose import (GO:0046324)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle membrane (GO:0012506)	identical protein binding (GO:0042802)|protein kinase B binding (GO:0043422)			breast(3)|endometrium(3)|kidney(3)|large_intestine(10)|liver(2)|lung(4)|prostate(2)	27				KIRC - Kidney renal clear cell carcinoma(284;0.0124)|Kidney(284;0.0144)		AGTAGCCAGTGATCCCTTATA	0.413																																					p.D259Y		Atlas-SNP	.											.	APPL1	59	.	0			c.G775T						.						118	111	114					3																	57282291		2203	4300	6503	SO:0001583	missense	26060	exon10			GCCAGTGATCCCT	AB037849	CCDS2882.1	3p21.1-p14.3	2013-01-11			ENSG00000157500	ENSG00000157500		"Pleckstrin homology (PH) domain containing"	24035	protein-coding gene	gene with protein product		604299				10490823, 17030088	Standard	NM_012096		Approved	APPL	uc003dio.3	Q9UKG1	OTTHUMG00000133756	ENST00000288266.3:c.775G>T	chr3.hg19:g.57282291G>T	ENSP00000288266:p.Asp259Tyr	263.0	0.0		267.0	168.0	NM_012096	Q9P2B9	Missense_Mutation	SNP	ENST00000288266.3	hg19	CCDS2882.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.633918	0.87660	.	.	ENSG00000157500	ENST00000288266	T	0.11604	2.76	5.94	5.94	0.96194	.	0.044796	0.85682	D	0.000000	T	0.28001	0.0690	M	0.63843	1.955	0.80722	D	1	P;P	0.52316	0.905;0.952	P;P	0.54815	0.678;0.761	T	0.00078	-1.2114	10	0.72032	D	0.01	-15.5856	20.3552	0.98837	0.0:0.0:1.0:0.0	.	242;259	B4DQX8;Q9UKG1	.;DP13A_HUMAN	Y	259	ENSP00000288266:D259Y	ENSP00000288266:D259Y	D	+	1	0	APPL1	57257331	1.000000	0.71417	1.000000	0.80357	0.816000	0.46133	9.807000	0.99171	2.812000	0.96745	0.557000	0.71058	GAT	.	.		0.413	APPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258196.2	NM_012096		T	57282291	G	T	57282291	3	4	360	1	0	0	0	0	1	0	0	0	817	1290	45	3	813	3	APPL1	3	57282291	Missense_Mutation	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10	4727459	57282291	140740139	33	50334										
TMEM39A	55254	hgsc.bcm.edu	37	chr3	119155803	119155803	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	tgaggtgctcacatgaccagCgcatgtcatagtactgggta	12	9	2	2			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr3:119155803C>A	ENST00000319172.5	-	7	1367	c.947G>T	c.(946-948)cGc>cTc	p.R316L	TMEM39A_ENST00000486159.1_5'Flank	NM_018266.1	NP_060736.1	Q9NV64	TM39A_HUMAN	transmembrane protein 39A	316						integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|skin(1)	13				GBM - Glioblastoma multiforme(114;0.244)		ACATGACCAGCGCATGTCATA	0.453																																					p.R316L		Atlas-SNP	.											.	TMEM39A	36	.	0			c.G947T						.						198	179	186					3																	119155803		2203	4300	6503	SO:0001583	missense	55254	exon7			GACCAGCGCATGT	BC021277	CCDS2987.1	3q13.33	2005-01-10			ENSG00000176142	ENSG00000176142			25600	protein-coding gene	gene with protein product						12477932	Standard	NM_018266		Approved	FLJ10902	uc003eck.2	Q9NV64	OTTHUMG00000159361	ENST00000319172.5:c.947G>T	chr3.hg19:g.119155803C>A	ENSP00000326063:p.Arg316Leu	124.0	0.0		110.0	23.0	NM_018266	D3DN80|Q53FN4|Q53GI1|Q6PKB5	Missense_Mutation	SNP	ENST00000319172.5	hg19	CCDS2987.1	.	.	.	.	.	.	.	.	.	.	C	14.55	2.570205	0.45798	.	.	ENSG00000176142	ENST00000319172;ENST00000491685	T	0.45668	0.89	5.16	4.29	0.51040	.	0.000000	0.85682	D	0.000000	T	0.46073	0.1374	L	0.40543	1.245	0.80722	D	1	D	0.56521	0.976	P	0.58780	0.845	T	0.27054	-1.0085	10	0.11794	T	0.64	-11.3742	12.867	0.57946	0.0:0.9221:0.0:0.0779	.	316	Q9NV64	TM39A_HUMAN	L	316;162	ENSP00000326063:R316L	ENSP00000326063:R316L	R	-	2	0	TMEM39A	120638493	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.588000	0.67517	1.420000	0.47138	0.650000	0.86243	CGC	.	.		0.453	TMEM39A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354941.3	NM_018266		A	119155803	C	A	119155803	3	1	360	1	0	0	0	0	1	0	0	0	16176	768	27	1	531	1	TMEM39A	3	119155803	Missense_Mutation	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10	61873512	119155803	78866627	34	50335										
STXBP5L	9515	hgsc.bcm.edu	37	chr3	121126301	121126301	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	ataatctgctcagaaaaacaAgccaaagtcttctcactgcc	5	12	4	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr3:121126301A>T	ENST00000273666.6	+	24	3142	c.2871A>T	c.(2869-2871)caA>caT	p.Q957H	STXBP5L_ENST00000492541.1_Missense_Mutation_p.Q957H|STXBP5L_ENST00000471454.1_Missense_Mutation_p.Q933H|STXBP5L_ENST00000472879.1_Missense_Mutation_p.Q933H|STXBP5L_ENST00000497029.1_Missense_Mutation_p.Q931H	NM_014980.2	NP_055795.1	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	957					exocytosis (GO:0006887)|glucose homeostasis (GO:0042593)|negative regulation of insulin secretion (GO:0046676)|positive regulation of protein secretion (GO:0050714)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(12)|lung(28)|ovary(7)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				GBM - Glioblastoma multiforme(114;0.0694)		CAGAAAAACAAGCCAAAGTCT	0.383																																					p.Q957H		Atlas-SNP	.											.	STXBP5L	159	.	0			c.A2871T						.						135	131	132					3																	121126301		1925	4123	6048	SO:0001583	missense	9515	exon24			AAAACAAGCCAAA	AB023223	CCDS43137.1	3q13.33-q21.1	2013-01-10			ENSG00000145087	ENSG00000145087		"WD repeat domain containing"	30757	protein-coding gene	gene with protein product		609381				10231032, 14767561	Standard	NM_014980		Approved	KIAA1006, LLGL4	uc003eec.4	Q9Y2K9	OTTHUMG00000159426	ENST00000273666.6:c.2871A>T	chr3.hg19:g.121126301A>T	ENSP00000273666:p.Gln957His	149.0	0.0		126.0	31.0	NM_014980	Q4G1B4|Q6PIC3	Missense_Mutation	SNP	ENST00000273666.6	hg19	CCDS43137.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.203209	0.79127	.	.	ENSG00000145087	ENST00000273666;ENST00000471454;ENST00000472879;ENST00000497029;ENST00000492541;ENST00000471262	T;T;T;T;T;T	0.30448	1.53;1.53;1.53;1.53;1.53;1.53	5.33	5.33	0.75918	Lethal giant larvae (Lgl)-like, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.63534	0.2519	M	0.89904	3.07	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.85130	0.997;0.997	T	0.72507	-0.4272	10	0.87932	D	0	-13.8021	15.5893	0.76512	1.0:0.0:0.0:0.0	.	933;957	E9PFI2;Q9Y2K9	.;STB5L_HUMAN	H	957;933;933;931;957;900	ENSP00000273666:Q957H;ENSP00000420019:Q933H;ENSP00000419627:Q933H;ENSP00000420287:Q931H;ENSP00000420666:Q957H;ENSP00000420167:Q900H	ENSP00000273666:Q957H	Q	+	3	2	STXBP5L	122608991	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.952000	0.70282	2.149000	0.67028	0.528000	0.53228	CAA	.	.		0.383	STXBP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355256.3			T	121126301	A	T	121126301	3	4	360	1	0	0	0	0	1	0	0	0	15372	69	3	4	2961	4	STXBP5L	3	121126301	Missense_Mutation	SNP	A	TCGA-XR-A8TF-01A-11D-A35Z-10	1970498	121126301	76896129	35	50336										
CCDC48	79825	hgsc.bcm.edu	37	chr3	128720898	128720898	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	agccgccggagctcaccttcCgccagttccacgcgcgcctc	10	20	1	0			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr3:128720898C>T	ENST00000480450.1	+	1	427	c.427C>T	c.(427-429)Cgc>Tgc	p.R143C	KIAA1257_ENST00000510149.1_Intron|EFCC1_ENST00000436022.2_5'UTR			Q9HA90	EFCC1_HUMAN	EF-hand and coiled-coil domain containing 1	143							calcium ion binding (GO:0005509)										GCTCACCTTCCGCCAGTTCCA	0.731																																					p.R143C		Atlas-SNP	.											.	.	.	.	0			c.C427T						.						2	4	4					3																	128720898		407	1211	1618	SO:0001583	missense	79825	exon1			ACCTTCCGCCAGT	AK022119	CCDS3054.1, CCDS3054.2	3q21.3	2013-01-11	2013-01-11	2013-01-11	ENSG00000114654	ENSG00000114654		"EF-hand domain containing"	25692	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 73", "coiled-coil domain containing 48"	C3orf73, CCDC48			Standard	NM_024768		Approved	FLJ12057	uc011bkt.2	Q9HA90	OTTHUMG00000158996	ENST00000480450.1:c.427C>T	chr3.hg19:g.128720898C>T	ENSP00000420075:p.Arg143Cys	113.0	0.0		79.0	29.0	NM_024768	A8MYE2	Missense_Mutation	SNP	ENST00000480450.1	hg19	CCDS3054.2	.	.	.	.	.	.	.	.	.	.	C	15.66	2.898598	0.52227	.	.	ENSG00000114654	ENST00000480450	T	0.58797	0.31	3.43	3.43	0.39272	.	0.000000	0.64402	U	0.000003	T	0.71187	0.3310	M	0.62723	1.935	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.74725	-0.3568	10	0.87932	D	0	-8.647	12.4012	0.55414	0.0:1.0:0.0:0.0	.	143	Q9HA90	CCD48_HUMAN	C	143	ENSP00000420075:R143C	ENSP00000420075:R143C	R	+	1	0	CCDC48	130203588	1.000000	0.71417	1.000000	0.80357	0.305000	0.27757	1.657000	0.37366	1.458000	0.47871	0.306000	0.20318	CGC	.	.		0.731	EFCC1-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352832.1	NM_024768		T	128720898	C	T	128720898	3	4	360	1	0	0	0	0	1	0	0	0	2821	652	23	1	429	1	CCDC48	3	128720898	Missense_Mutation	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10	7594597	128720898	69301532	36	50337										
PLS1	5357	hgsc.bcm.edu	37	chr3	142388377	142388377	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	aacaaagatggcaaaatcagTtttgaagagtttgtgtcagt	10	4	2	3			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr3:142388377T>G	ENST00000337777.3	+	3	429	c.216T>G	c.(214-216)agT>agG	p.S72R	PLS1_ENST00000457734.2_Missense_Mutation_p.S72R|PLS1_ENST00000497002.1_Missense_Mutation_p.S72R	NM_002670.2	NP_002661.2	Q14651	PLSI_HUMAN	plastin 1	72	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	27						GCAAAATCAGTTTTGAAGAGT	0.403																																					p.S72R		Atlas-SNP	.											.	PLS1	71	.	0			c.T216G						.						178	186	183					3																	142388377		2203	4300	6503	SO:0001583	missense	5357	exon3			AATCAGTTTTGAA	L20826	CCDS3125.1	3q23	2013-01-10	2010-02-10		ENSG00000120756	ENSG00000120756		"EF-hand domain containing"	9090	protein-coding gene	gene with protein product		602734	"plastin 1 (I isoform)"			8139549	Standard	NM_002670		Approved	I-plastin, Plastin-1	uc003euz.3	Q14651	OTTHUMG00000159292	ENST00000337777.3:c.216T>G	chr3.hg19:g.142388377T>G	ENSP00000336831:p.Ser72Arg	118.0	0.0		125.0	7.0	NM_001172312	A8K2Q1|D3DNG3|Q8NEG6	Missense_Mutation	SNP	ENST00000337777.3	hg19	CCDS3125.1	.	.	.	.	.	.	.	.	.	.	T	15.48	2.846534	0.51164	.	.	ENSG00000120756	ENST00000457734;ENST00000475296;ENST00000464320;ENST00000337777;ENST00000497002	T;T;T;T;T	0.76709	-1.04;-1.04;-1.04;-1.04;-1.04	5.16	0.407	0.16371	EF-hand-like domain (1);	0.204788	0.64402	N	0.000013	T	0.79215	0.4408	M	0.88377	2.95	0.48135	D	0.999593	B	0.02656	0.0	B	0.08055	0.003	T	0.74850	-0.3524	10	0.87932	D	0	-15.057	12.7818	0.57480	0.0:0.8314:0.0:0.1686	.	72	Q14651	PLSI_HUMAN	R	72	ENSP00000387890:S72R;ENSP00000417311:S72R;ENSP00000418880:S72R;ENSP00000336831:S72R;ENSP00000418700:S72R	ENSP00000336831:S72R	S	+	3	2	PLS1	143871067	1.000000	0.71417	0.988000	0.46212	0.991000	0.79684	1.258000	0.32944	-0.160000	0.11002	0.528000	0.53228	AGT	.	.		0.403	PLS1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354435.1	NM_002670		G	142388377	T	G	142388377	3	3	360	1	0	0	0	0	1	0	0	0	12116	1722	60	5	222	5	PLS1	3	142388377	Missense_Mutation	SNP	T	TCGA-XR-A8TF-01A-11D-A35Z-10	13667479	142388377	55634053	37	50338										
RAP2B	5912	hgsc.bcm.edu	37	chr3	152880629	152880629	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	gagattgaggtggactcgtcGccgtcggtgctggagatcct	16	9	0	3			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr3:152880629G>T	ENST00000323534.2	+	1	601	c.147G>T	c.(145-147)tcG>tcT	p.S49S	RP11-529G21.2_ENST00000487827.1_RNA	NM_002886.2	NP_002877.2	P61225	RAP2B_HUMAN	RAP2B, member of RAS oncogene family	49					GTP catabolic process (GO:0006184)|negative regulation of cell migration (GO:0030336)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of protein autophosphorylation (GO:0031954)|Rap protein signal transduction (GO:0032486)|regulation of protein tyrosine kinase activity (GO:0061097)|signal transduction (GO:0007165)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	GDP binding (GO:0019003)|GTP binding (GO:0005525)			NS(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0628)|Lung(72;0.11)			TGGACTCGTCGCCGTCGGTGC	0.597																																					p.S49S		Atlas-SNP	.											.	RAP2B	20	.	0			c.G147T						.						108	106	107					3																	152880629		2203	4300	6503	SO:0001819	synonymous_variant	5912	exon1			CTCGTCGCCGTCG		CCDS3170.1	3q25.2	2014-05-09			ENSG00000181467	ENSG00000181467			9862	protein-coding gene	gene with protein product	"Ras-related protein RAP-2B", "small GTP binding protein", "Ras family small GTP binding protein RAP2B"	179541				2118648	Standard	NM_002886		Approved		uc003ezr.3	P61225	OTTHUMG00000159655	ENST00000323534.2:c.147G>T	chr3.hg19:g.152880629G>T		138.0	0.0		137.0	40.0	NM_002886	P17964|Q96EG5|Q9CXG0	Silent	SNP	ENST00000323534.2	hg19	CCDS3170.1																																																																																			.	.		0.597	RAP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356707.1	NM_002886		T	152880629	G	T	152880629	2	4	360	1	0	0	0	0	0	0	0	1	13056	1074	38	1		1	RAP2B	3	152880629	Silent	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10	10492252	152880629	45141801	38	50339										
FXR1	8087	hgsc.bcm.edu	37	chr3	180652981	180652981	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	ttagattaccaccaccacctGatataaaaaaagaaattagt	4	8	0	3			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr3:180652981G>T	ENST00000357559.4	+	3	544	c.160G>T	c.(160-162)Gat>Tat	p.D54Y	FXR1_ENST00000468861.1_5'UTR|FXR1_ENST00000445140.2_Missense_Mutation_p.D54Y|FXR1_ENST00000480918.1_Missense_Mutation_p.D41Y|FXR1_ENST00000305586.7_5'UTR|FXR1_ENST00000491062.1_Intron	NM_001013438.2|NM_005087.3	NP_001013456.1|NP_005078.2	P51114	FXR1_HUMAN	fragile X mental retardation, autosomal homolog 1	54					apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|muscle organ development (GO:0007517)|negative regulation of translation (GO:0017148)	costamere (GO:0043034)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|polysome (GO:0005844)	G-quadruplex RNA binding (GO:0002151)|mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|endometrium(4)|large_intestine(5)|lung(12)|skin(2)	26	all_cancers(143;6.07e-14)|Ovarian(172;0.0212)		Epithelial(37;3.05e-35)|OV - Ovarian serous cystadenocarcinoma(80;2.4e-22)			ACCACCACCTGATATAAAAAA	0.284																																					p.D54Y		Atlas-SNP	.											.	FXR1	75	.	0			c.G160T						.						63	65	64					3																	180652981		2203	4300	6503	SO:0001583	missense	8087	exon3			CCACCTGATATAA	M67468	CCDS3238.1, CCDS33894.1, CCDS46965.1	3q28	2014-01-28			ENSG00000114416	ENSG00000114416			4023	protein-coding gene	gene with protein product		600819				7781595, 9642279	Standard	NM_005087		Approved		uc003fkq.3	P51114	OTTHUMG00000158138	ENST00000357559.4:c.160G>T	chr3.hg19:g.180652981G>T	ENSP00000350170:p.Asp54Tyr	358.0	0.0		256.0	129.0	NM_001013438	A8K9B8|Q7Z450|Q8N6R8	Missense_Mutation	SNP	ENST00000357559.4	hg19	CCDS3238.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.764166	0.89932	.	.	ENSG00000114416	ENST00000357559;ENST00000445140;ENST00000480918;ENST00000484042	T;T;T;T	0.48522	1.81;1.14;1.61;0.81	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.67776	0.2929	M	0.70595	2.14	0.80722	D	1	D;P;D	0.76494	0.999;0.658;0.971	D;P;P	0.63033	0.91;0.476;0.667	T	0.69738	-0.5064	10	0.72032	D	0.01	-8.0643	19.4329	0.94778	0.0:0.0:1.0:0.0	.	41;54;54	B4DXZ6;P51114-2;P51114	.;.;FXR1_HUMAN	Y	54;54;41;58	ENSP00000350170:D54Y;ENSP00000388828:D54Y;ENSP00000418097:D41Y;ENSP00000417513:D58Y	ENSP00000350170:D54Y	D	+	1	0	FXR1	182135675	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.583000	0.90794	2.763000	0.94921	0.557000	0.71058	GAT	.	.		0.284	FXR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350265.5			T	180652981	G	T	180652981	3	4	360	1	0	0	0	0	1	0	0	0	6123	1290	45	3	170	3	FXR1	3	180652981	Missense_Mutation	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10	27772352	180652981	17369449	39	50340										
LRBA	987	hgsc.bcm.edu	37	chr4	151773243	151773243	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	cttcccttcctccagcatctGaccaaggtctgattctacag	6	15	3	2			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr4:151773243G>C	ENST00000357115.3	-	23	3862	c.3619C>G	c.(3619-3621)Cag>Gag	p.Q1207E	LRBA_ENST00000510413.1_Missense_Mutation_p.Q1207E|LRBA_ENST00000535741.1_Missense_Mutation_p.Q1207E|LRBA_ENST00000507224.1_Missense_Mutation_p.Q1207E	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	1207						cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					TCCAGCATCTGACCAAGGTCT	0.408																																					p.Q1207E		Atlas-SNP	.											.	LRBA	253	.	0			c.C3619G						.						113	109	110					4																	151773243		2203	4300	6503	SO:0001583	missense	987	exon23			GCATCTGACCAAG	AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"WD repeat domain containing"	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.3619C>G	chr4.hg19:g.151773243G>C	ENSP00000349629:p.Gln1207Glu	127.0	0.0		67.0	23.0	NM_006726	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Missense_Mutation	SNP	ENST00000357115.3	hg19	CCDS3773.1	.	.	.	.	.	.	.	.	.	.	G	0	-2.748877	0.00086	.	.	ENSG00000198589	ENST00000535741;ENST00000510413;ENST00000357115;ENST00000507224	T;T;T;T	0.53640	1.02;1.17;1.02;0.61	5.78	4.02	0.46733	.	1.403590	0.04133	N	0.318263	T	0.25531	0.0621	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.32402	-0.9908	10	0.02654	T	1	.	5.8662	0.18777	0.0725:0.3908:0.4035:0.1332	.	1207;1207	P50851;P50851-2	LRBA_HUMAN;.	E	1207	ENSP00000446299:Q1207E;ENSP00000421552:Q1207E;ENSP00000349629:Q1207E;ENSP00000422180:Q1207E	ENSP00000349629:Q1207E	Q	-	1	0	LRBA	151992693	0.166000	0.22962	0.008000	0.14137	0.097000	0.18754	1.589000	0.36644	0.861000	0.35504	0.591000	0.81541	CAG	.	.		0.408	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			C	151773243	G	C	151773243	3	2	360	1	0	0	0	0	1	0	0	0	8940	1299	45	4	5116	4	LRBA	4	151773243	Missense_Mutation	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10		151773243	39381033	40	50341										
SPEF2	79925	hgsc.bcm.edu	37	chr5	35700832	35700832	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	gtttcagatacttcctcaatGagtcgcatgaatgatattat	7	7	2	4			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr5:35700832G>A	ENST00000356031.3	+	16	2530	c.2376G>A	c.(2374-2376)atG>atA	p.M792I	CTD-2113L7.1_ENST00000510433.1_RNA|SPEF2_ENST00000509059.1_Missense_Mutation_p.M787I|SPEF2_ENST00000440995.2_Missense_Mutation_p.M787I	NM_024867.3	NP_079143.3	Q9C093	SPEF2_HUMAN	sperm flagellar 2	792					axoneme assembly (GO:0035082)|brain morphogenesis (GO:0048854)|embryonic neurocranium morphogenesis (GO:0048702)|fertilization (GO:0009566)|immune system development (GO:0002520)|multicellular organismal aging (GO:0010259)|respiratory system development (GO:0060541)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)|manchette (GO:0002177)|sperm midpiece (GO:0097225)				breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	37	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			CTTCCTCAATGAGTCGCATGA	0.358																																					p.M792I		Atlas-SNP	.											SPEF2_ENST00000356031,NS,carcinoma,0,1	SPEF2	324	.	0			c.G2376A						.						91	82	85					5																	35700832		1844	4078	5922	SO:0001583	missense	79925	exon16			CTCAATGAGTCGC	AB051557	CCDS3910.1, CCDS43309.1	5p13.2	2010-05-04			ENSG00000152582	ENSG00000152582			26293	protein-coding gene	gene with protein product	"cancer/testis antigen 122"	610172				11214970, 16549801, 17610085	Standard	NM_024867		Approved	KPL2, FLJ23577, CT122	uc003jjo.3	Q9C093	OTTHUMG00000131111	ENST00000356031.3:c.2376G>A	chr5.hg19:g.35700832G>A	ENSP00000348314:p.Met792Ile	115.0	0.0		127.0	24.0	NM_024867	Q2TAC9|Q96LL6|Q9H5C7|Q9H5Q7	Missense_Mutation	SNP	ENST00000356031.3	hg19	CCDS43309.1	.	.	.	.	.	.	.	.	.	.	G	6.568	0.473146	0.12461	.	.	ENSG00000152582	ENST00000356031;ENST00000509059;ENST00000440995;ENST00000504054	T;T;T;T	0.27402	1.67;1.67;1.67;1.67	5.79	1.02	0.19986	.	0.583392	0.16116	N	0.228844	T	0.18882	0.0453	N	0.22421	0.69	0.23036	N	0.998399	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.001;0.003;0.0	T	0.17592	-1.0364	10	0.48119	T	0.1	.	8.6755	0.34176	0.3692:0.0:0.6308:0.0	.	787;787;792	D6REZ4;Q9C093-2;Q9C093	.;.;SPEF2_HUMAN	I	792;787;787;298	ENSP00000348314:M792I;ENSP00000421593:M787I;ENSP00000412125:M787I;ENSP00000421744:M298I	ENSP00000348314:M792I	M	+	3	0	SPEF2	35736589	0.796000	0.28864	0.004000	0.12327	0.055000	0.15305	1.206000	0.32321	0.098000	0.17522	0.650000	0.86243	ATG	.	.		0.358	SPEF2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367199.1	NM_144722		A	35700832	G	A	35700832	3	1	360	1	0	0	0	0	1	0	0	0	15050	1290	45	3	2459	3	SPEF2	5	35700832	Missense_Mutation	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10		35700832	145214428	41	50342										
NAIP	4671	hgsc.bcm.edu	37	chr5	70280580	70280583	+	Frame_Shift_Del	DEL	CCTG	CCTG	-													0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	cagtcccaaatcttgatgttCctgcctatctgaatccagga							TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	CCTG	CCTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr5:70280580_70280583delCCTG	ENST00000517649.1	-	12	2583_2586	c.2293_2296delCAGG	c.(2293-2298)caggaafs	p.QE765fs	NAIP_ENST00000523981.1_Frame_Shift_Del_p.QE603fs|NAIP_ENST00000503719.2_Frame_Shift_Del_p.QE603fs|NAIP_ENST00000194097.4_Frame_Shift_Del_p.QE765fs|NAIP_ENST00000508426.2_Frame_Shift_Del_p.QE765fs	NM_004536.2	NP_004527.2	Q13075	BIRC1_HUMAN	NLR family, apoptosis inhibitory protein	765					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|metal ion binding (GO:0046872)			central_nervous_system(1)	1		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)		TCTTGATGTTCCTGCCTATCTGAA	0.441																																					p.765_766del		Atlas-INDEL	.											.	NAIP	38	.	0			c.2294_2297del						.																																			SO:0001589	frameshift_variant	4671	exon12			.	U19251	CCDS4009.1, CCDS43327.1	5q13.2	2010-06-16	2006-12-08	2006-12-08	ENSG00000249437	ENSG00000249437		"Baculoviral IAP repeat containing", "Nucleotide-binding domain and leucine rich repeat containing"	7634	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and BIR domain containing 1", "NLR family, BIR domain containing 1"	600355	"baculoviral IAP repeat-containing 1"	BIRC1		7813013	Standard	NM_022892		Approved	NLRB1	uc003jyj.1	Q13075	OTTHUMG00000163318	ENST00000517649.1:c.2293_2296delCAGG	chr5.hg19:g.70280580_70280583delCCTG	ENSP00000428657:p.Gln765fs	189.0	0.0		84.0	17.0	NM_004536	B9EG72|E9PHD1|O75857|Q13730|Q59GI6|Q8TDZ4|Q99796	Frame_Shift_Del	DEL	ENST00000517649.1	hg19	CCDS4009.1																																																																																			.	.		0.441	NAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372649.6	NM_004536		-	70280583	CCTG	-	70280580	7	5	360	1	0	1	0	1	0	0	0	0	10156	864	30	0	1939	0	NAIP	5	70280580	Frame_Shift_Del	DEL	CCTG	TCGA-XR-A8TF-01A-11D-A35Z-10	34579748	70280580	110634680	42	50343										
REEP2	51308	hgsc.bcm.edu	37	chr5	137780496	137780496	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	aagagctatgagaccatgatGagggtgggcaagaggggcct	17	6	0	5			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr5:137780496G>A	ENST00000254901.5	+	5	479	c.357G>A	c.(355-357)atG>atA	p.M119I	REEP2_ENST00000378339.2_Missense_Mutation_p.M119I|REEP2_ENST00000506158.1_Missense_Mutation_p.M81I	NM_016606.2	NP_057690.2	Q9BRK0	REEP2_HUMAN	receptor accessory protein 2	119					cell death (GO:0008219)|endoplasmic reticulum tubular network organization (GO:0071786)|protein transport into membrane raft (GO:0032596)|regulation of intracellular transport (GO:0032386)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	12			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			AGACCATGATGAGGGTGGGCA	0.612																																					p.M119I		Atlas-SNP	.											.	REEP2	21	.	0			c.G357A						.						72	63	66					5																	137780496		2203	4300	6503	SO:0001583	missense	51308	exon5			CATGATGAGGGTG	AK056193	CCDS4205.1, CCDS64259.1	5q31	2014-03-12	2006-02-07	2006-02-07	ENSG00000132563	ENSG00000132563		"Receptor accessory proteins"	17975	protein-coding gene	gene with protein product		609347	"chromosome 5 open reading frame 19"	C5orf19		16271481, 15550249, 24388663	Standard	NM_016606		Approved	SGC32445, SPG72	uc003lda.4	Q9BRK0	OTTHUMG00000129205	ENST00000254901.5:c.357G>A	chr5.hg19:g.137780496G>A	ENSP00000254901:p.Met119Ile	136.0	0.0		164.0	29.0	NM_016606	Q53EM8|Q9NYF2	Missense_Mutation	SNP	ENST00000254901.5	hg19	CCDS4205.1	.	.	.	.	.	.	.	.	.	.	G	19.87	3.907712	0.72868	.	.	ENSG00000132563	ENST00000378339;ENST00000254901;ENST00000506158	D;D;T	0.87966	-2.31;-2.32;-1.47	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	D	0.84442	0.5473	L	0.46157	1.445	0.80722	D	1	B;B	0.19200	0.012;0.034	B;B	0.20955	0.014;0.032	T	0.80466	-0.1370	10	0.45353	T	0.12	-6.4081	17.4692	0.87641	0.0:0.0:1.0:0.0	.	119;119	A8K3D2;Q9BRK0	.;REEP2_HUMAN	I	119;119;81	ENSP00000367590:M119I;ENSP00000254901:M119I;ENSP00000422530:M81I	ENSP00000254901:M119I	M	+	3	0	REEP2	137808395	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.523000	0.98034	2.670000	0.90874	0.650000	0.86243	ATG	.	.		0.612	REEP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251284.1	NM_016606		A	137780496	G	A	137780496	3	1	360	1	0	0	0	0	1	0	0	0	13220	1290	45	3	375	3	REEP2	5	137780496	Missense_Mutation	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10	67499916	137780496	43134764	43	50344										
NDUFA2	4695	hgsc.bcm.edu	37	chr5	140027159	140027159	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	gactcctcgacttgctgcggCcgccgccatccttgttaata	9	15	0	0	rs370015250		TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr5:140027159C>T	ENST00000252102.4	-	1	211	c.10G>A	c.(10-12)Gcc>Acc	p.A4T	NDUFA2_ENST00000512088.1_Missense_Mutation_p.A4T|MIR3655_ENST00000581765.1_RNA|IK_ENST00000417647.2_5'Flank|NDUFA2_ENST00000510680.1_5'Flank	NM_001185012.1|NM_002488.4	NP_001171941.1|NP_002479.1	O43678	NDUA2_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 2, 8kDa	4					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(3)|large_intestine(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTTGCTGCGGCCGCCGCCATC	0.622																																					p.A4T		Atlas-SNP	.											.	NDUFA2	13	.	0			c.G10A						.	C	THR/ALA,THR/ALA	1,4379		0,1,2189	15	16	16		10,10	1	0	5		16	0,8564		0,0,4282	no	missense,missense	NDUFA2	NM_002488.4,NM_001185012.1	58,58	0,1,6471	TT,TC,CC		0.0,0.0228,0.0077	benign,benign	4/100,4/77	140027159	1,12943	2190	4282	6472	SO:0001583	missense	4695	exon1			CTGCGGCCGCCGC	AF047185	CCDS4234.1, CCDS54911.1	5q31.2	2011-07-04	2002-08-29		ENSG00000131495	ENSG00000131495		"Mitochondrial respiratory chain complex / Complex I"	7685	protein-coding gene	gene with protein product	"complex I B8 subunit"	602137	"NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 2 (8kD, B8)"			9425316, 9763676	Standard	NM_002488		Approved	B8	uc003lgp.3	O43678	OTTHUMG00000129505	ENST00000252102.4:c.10G>A	chr5.hg19:g.140027159C>T	ENSP00000252102:p.Ala4Thr	51.0	0.0		67.0	37.0	NM_001185012	D6RJD6|Q6IAY8	Missense_Mutation	SNP	ENST00000252102.4	hg19	CCDS4234.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.180132	0.78564	2.28E-4	0.0	ENSG00000131495	ENST00000252102;ENST00000512088	.	.	.	5.8	0.998	0.19857	.	0.148745	0.64402	D	0.000012	T	0.42944	0.1225	.	.	.	0.80722	D	1	B	0.06786	0.001	B	0.08055	0.003	T	0.18808	-1.0325	8	0.42905	T	0.14	-0.473	7.5555	0.27822	0.0:0.6431:0.1076:0.2493	.	4	O43678	NDUA2_HUMAN	T	4	.	ENSP00000252102:A4T	A	-	1	0	NDUFA2	140007343	0.979000	0.34478	0.002000	0.10522	0.009000	0.06853	2.463000	0.45058	0.119000	0.18210	-1.002000	0.02502	GCC	.	.		0.622	NDUFA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251679.2	NM_002488		T	140027159	C	T	140027159	3	4	360	1	0	0	0	0	1	0	0	0	10273	739	26	3	328	3	NDUFA2	5	140027159	Missense_Mutation	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10	2246663	140027159	40888101	44	50345										
PCDHGA12	26025	hgsc.bcm.edu	37	chr5	140810476	140810476	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	agggtgggcgacatctccagGgacctggggctggagccccg	18	12	1	0			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr5:140810476G>A	ENST00000252085.3	+	1	292	c.150G>A	c.(148-150)agG>agA	p.R50R	PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGB8P_ENST00000502926.1_RNA|PCDHGA7_ENST00000518325.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA9_ENST00000573521.1_Intron	NM_003735.2|NM_032094.1	NP_003726.1|NP_115265.1	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12	50	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(23)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	58			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACATCTCCAGGGACCTGGGGC	0.642																																					p.R50R		Atlas-SNP	.											.	PCDHGA12	271	.	0			c.G150A						.						65	79	74					5																	140810476		2203	4300	6503	SO:0001819	synonymous_variant	26025	exon1			CTCCAGGGACCTG	AF152506	CCDS4260.1, CCDS75346.1	5q31	2010-01-26	2002-05-23		ENSG00000253159	ENSG00000253159		"Cadherins / Protocadherins : Clustered"	8699	other	protocadherin	"fibroblast cadherin FIB3"	603059	"cadherin 21"	CDH21		10380929	Standard	NM_003735		Approved	KIAA0588, FIB3, PCDH-GAMMA-A12		O60330	OTTHUMG00000129611	ENST00000252085.3:c.150G>A	chr5.hg19:g.140810476G>A		254.0	0.0		308.0	145.0	NM_032094	O15100|Q6UW70|Q9Y5D7	Silent	SNP	ENST00000252085.3	hg19	CCDS4260.1																																																																																			.	.		0.642	PCDHGA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251806.2	NM_003735		A	140810476	G	A	140810476	2	1	360	1	0	0	0	0	0	0	0	1	11562	1223	43	3		3	PCDHGA12	5	140810476	Silent	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10	783317	140810476	40104784	45	50346										
GLRA1	2741	hgsc.bcm.edu	37	chr5	151271886	151271886	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	ctctacctttaaaattgggcCtgatcctggcatcatatccg	7	12	2	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr5:151271886C>A	ENST00000455880.2	-	2	456	c.170G>T	c.(169-171)aGg>aTg	p.R57M	GLRA1_ENST00000274576.4_Missense_Mutation_p.R57M|GLRA1_ENST00000471351.2_5'UTR|GLRA1_ENST00000545569.1_Intron			P23415	GLRA1_HUMAN	glycine receptor, alpha 1	57					acrosome reaction (GO:0007340)|action potential (GO:0001508)|adult walking behavior (GO:0007628)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|muscle contraction (GO:0006936)|negative regulation of transmission of nerve impulse (GO:0051970)|neuromuscular process controlling posture (GO:0050884)|neuropeptide signaling pathway (GO:0007218)|positive regulation of acrosome reaction (GO:2000344)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of membrane potential (GO:0042391)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|righting reflex (GO:0060013)|startle response (GO:0001964)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|external side of plasma membrane (GO:0009897)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glycine-gated chloride channel activity (GO:0016934)|glycine binding (GO:0016594)|taurine binding (GO:0030977)|transmitter-gated ion channel activity (GO:0022824)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	23		all_hematologic(541;0.0341)|Medulloblastoma(196;0.0912)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Ethanol(DB00898)|Ginkgo biloba(DB01381)|Glycine(DB00145)|Halothane(DB01159)|Isoflurane(DB00753)|Lindane(DB00431)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	AAAATTGGGCCTGATCCTGGC	0.498																																					p.R57M		Atlas-SNP	.											.	GLRA1	61	.	0			c.G170T						.						101	91	94					5																	151271886		2203	4300	6503	SO:0001583	missense	2741	exon2			TTGGGCCTGATCC		CCDS4320.1, CCDS54942.1	5q33.1	2012-02-07	2008-01-24		ENSG00000145888	ENSG00000145888		"Ligand-gated ion channels / Glycine receptors"	4326	protein-coding gene	gene with protein product	"startle disease/hyperekplexia", "stiff person syndrome"	138491	"glycine receptor, alpha 1 (startle disease/hyperekplexia)"	STHE		1355335, 8298642	Standard	NM_000171		Approved		uc003lut.3	P23415	OTTHUMG00000130121	ENST00000455880.2:c.170G>T	chr5.hg19:g.151271886C>A	ENSP00000411593:p.Arg57Met	132.0	0.0		167.0	81.0	NM_000171	B2R6T3|Q14C77|Q6DJV9	Missense_Mutation	SNP	ENST00000455880.2	hg19	CCDS54942.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.743030	0.89663	.	.	ENSG00000145888	ENST00000274576;ENST00000455880	D;D	0.83419	-1.72;-1.72	5.48	5.48	0.80851	Neurotransmitter-gated ion-channel ligand-binding (3);	0.105778	0.64402	D	0.000006	D	0.94212	0.8142	H	0.95224	3.64	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.95553	0.8622	10	0.87932	D	0	.	19.3497	0.94378	0.0:1.0:0.0:0.0	.	57;57	P23415;P23415-2	GLRA1_HUMAN;.	M	57	ENSP00000274576:R57M;ENSP00000411593:R57M	ENSP00000274576:R57M	R	-	2	0	GLRA1	151252079	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.311000	0.78958	2.583000	0.87209	0.591000	0.81541	AGG	.	.		0.498	GLRA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000373959.1			A	151271886	C	A	151271886	3	1	360	1	0	0	0	0	1	0	0	0	6462	681	24	3	1235	3	GLRA1	5	151271886	Missense_Mutation	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10	10461410	151271886	29643374	46	50347										
HAND1	9421	hgsc.bcm.edu	37	chr5	153857306	153857306	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	gccggccaagacggccgccaAgcgcctccagccgcccgggg	15	19	0	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr5:153857306A>T	ENST00000231121.2	-	1	518	c.263T>A	c.(262-264)cTt>cAt	p.L88H		NM_004821.2	NP_004812.1	O96004	HAND1_HUMAN	heart and neural crest derivatives expressed 1	88					angiogenesis (GO:0001525)|blastocyst development (GO:0001824)|cardiac left ventricle formation (GO:0003218)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cartilage morphogenesis (GO:0060536)|embryonic heart tube development (GO:0035050)|embryonic heart tube formation (GO:0003144)|heart development (GO:0007507)|heart looping (GO:0001947)|mesenchyme development (GO:0060485)|mesoderm formation (GO:0001707)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)|trophectodermal cell differentiation (GO:0001829)|trophoblast giant cell differentiation (GO:0060707)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)	6	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)			ACGGCCGCCAAGCGCCTCCAG	0.716																																					p.L88H		Atlas-SNP	.											.	HAND1	21	.	0			c.T263A						.						14	17	16					5																	153857306		2202	4289	6491	SO:0001583	missense	9421	exon1			CCGCCAAGCGCCT	AF061756	CCDS4327.1	5q33	2013-05-21			ENSG00000113196	ENSG00000113196		"Basic helix-loop-helix proteins"	4807	protein-coding gene	gene with protein product		602406				9337404, 9931445	Standard	NM_004821		Approved	eHand, Thing1, Hxt, bHLHa27	uc003lvn.3	O96004	OTTHUMG00000130193	ENST00000231121.2:c.263T>A	chr5.hg19:g.153857306A>T	ENSP00000231121:p.Leu88His	59.0	0.0		65.0	38.0	NM_004821		Missense_Mutation	SNP	ENST00000231121.2	hg19	CCDS4327.1	.	.	.	.	.	.	.	.	.	.	A	13.20	2.165780	0.38217	.	.	ENSG00000113196	ENST00000231121	D	0.95518	-3.73	4.98	4.98	0.66077	.	0.000000	0.64402	D	0.000001	D	0.90776	0.7104	L	0.36672	1.1	0.48511	D	0.999664	P	0.46327	0.876	B	0.36289	0.221	D	0.90420	0.4416	10	0.41790	T	0.15	-19.501	12.6267	0.56634	1.0:0.0:0.0:0.0	.	88	O96004	HAND1_HUMAN	H	88	ENSP00000231121:L88H	ENSP00000231121:L88H	L	-	2	0	HAND1	153837499	0.690000	0.27699	0.933000	0.37362	0.677000	0.39632	1.898000	0.39809	1.866000	0.54105	0.260000	0.18958	CTT	.	.		0.716	HAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252511.1	NM_004821		T	153857306	A	T	153857306	3	4	360	1	0	0	0	0	1	0	0	0	6958	72	3	4	392	4	HAND1	5	153857306	Missense_Mutation	SNP	A	TCGA-XR-A8TF-01A-11D-A35Z-10	2585420	153857306	27057954	47	50348										
CANX	821	hgsc.bcm.edu	37	chr5	179146764	179146764	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	gtacgtacctgatccagacgCagagaaacctgaggattggt	12	9	0	4			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr5:179146764C>G	ENST00000247461.4	+	9	1207	c.1007C>G	c.(1006-1008)gCa>gGa	p.A336G	CANX_ENST00000415618.2_Missense_Mutation_p.A371G|CANX_ENST00000452673.2_Missense_Mutation_p.A336G|CANX_ENST00000512607.2_Missense_Mutation_p.A228G|CANX_ENST00000504734.1_Missense_Mutation_p.A336G	NM_001746.3	NP_001737.1	P27824	CALX_HUMAN	calnexin	336	4 X approximate repeats.|Interaction with PPIB. {ECO:0000250}.|P domain (Extended arm). {ECO:0000250}.				aging (GO:0007568)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|chaperone-mediated protein folding (GO:0061077)|clathrin-mediated endocytosis (GO:0072583)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|protein secretion (GO:0009306)|synaptic vesicle endocytosis (GO:0048488)	axon (GO:0030424)|dendrite cytoplasm (GO:0032839)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|ER-mitochondrion membrane contact site (GO:0044233)|extracellular vesicular exosome (GO:0070062)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)|ribosome (GO:0005840)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|kidney(4)|large_intestine(2)|lung(7)|prostate(2)|urinary_tract(3)	22	all_cancers(89;0.000129)|all_epithelial(37;5.59e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0413)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Antihemophilic Factor(DB00025)|Tenecteplase(DB00031)	GATCCAGACGCAGAGAAACCT	0.418																																					p.A336G		Atlas-SNP	.											.	CANX	47	.	0			c.C1007G						.						69	70	70					5																	179146764		2203	4300	6503	SO:0001583	missense	821	exon9			CAGACGCAGAGAA	L18887	CCDS4447.1	5q35	2008-07-18			ENSG00000127022	ENSG00000127022			1473	protein-coding gene	gene with protein product	"major histocompatibility complex class I antigen-binding protein p88"	114217				1326756, 8136357	Standard	NM_001746		Approved	CNX, IP90, P90	uc003mkl.3	P27824	OTTHUMG00000130910	ENST00000247461.4:c.1007C>G	chr5.hg19:g.179146764C>G	ENSP00000247461:p.Ala336Gly	237.0	0.0		270.0	113.0	NM_001746	B2R5V8|B4DGP8|B4E2T8|D3DWQ3|D6R9K3	Missense_Mutation	SNP	ENST00000247461.4	hg19	CCDS4447.1	.	.	.	.	.	.	.	.	.	.	C	17.83	3.485958	0.63962	.	.	ENSG00000127022	ENST00000504734;ENST00000415618;ENST00000452673;ENST00000247461;ENST00000502673;ENST00000512607;ENST00000376953	T;T;T;T;T;T	0.57595	0.39;0.39;0.39;0.39;0.39;0.39	5.35	4.48	0.54585	Calreticulin/calnexin, conserved site (1);Calreticulin/calnexin, P (2);	0.000000	0.85682	D	0.000000	T	0.65417	0.2689	H	0.94385	3.53	0.80722	D	1	B;B;B	0.32051	0.1;0.046;0.354	B;B;B	0.32393	0.145;0.043;0.145	T	0.72475	-0.4282	10	0.87932	D	0	-23.0612	14.2121	0.65771	0.0:0.9272:0.0:0.0728	.	371;272;336	B4DGP8;Q6ZP56;P27824	.;.;CALX_HUMAN	G	336;371;336;336;272;228;272	ENSP00000424063:A336G;ENSP00000394817:A371G;ENSP00000391646:A336G;ENSP00000247461:A336G;ENSP00000421107:A272G;ENSP00000423588:A228G	ENSP00000247461:A336G	A	+	2	0	CANX	179079370	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.570000	0.82390	1.256000	0.44068	0.561000	0.74099	GCA	.	.		0.418	CANX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253500.2	NM_001024649		G	179146764	C	G	179146764	3	3	360	1	0	0	0	0	1	0	0	0	2620	710	25	4	1037	4	CANX	5	179146764	Missense_Mutation	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10	25289458	179146764	1768496	48	50349										
DST	667	hgsc.bcm.edu	37	chr6	56505183	56505183	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	ggaagtcatccctgatgacaGgccagaagtcatactagaag	11	9	2	4			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr6:56505183G>A	ENST00000361203.3	-	14	1622	c.1615C>T	c.(1615-1617)Ctg>Ttg	p.L539L	DST_ENST00000370754.5_Silent_p.L717L|DST_ENST00000446842.2_Silent_p.L213L|DST_ENST00000244364.6_Silent_p.L213L|DST_ENST00000312431.6_Silent_p.L539L|DST_ENST00000370769.4_Silent_p.L539L|DST_ENST00000518935.1_Silent_p.L213L|DST_ENST00000370788.2_Silent_p.L539L|DST_ENST00000421834.2_Silent_p.L539L|DST_ENST00000370765.6_Silent_p.L213L			Q03001	DYST_HUMAN	dystonin	539					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			CCTGATGACAGGCCAGAAGTC	0.473																																					p.L213L		Atlas-SNP	.											.	DST	1427	.	0			c.C637T						.						143	146	145					6																	56505183		2203	4300	6503	SO:0001819	synonymous_variant	667	exon4			ATGACAGGCCAGA	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.1615C>T	chr6.hg19:g.56505183G>A		153.0	0.0		213.0	106.0	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000361203.3	hg19																																																																																				.	.		0.473	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		A	56505183	G	A	56505183	2	1	360	1	0	0	0	0	0	0	0	1	4785	991	35	3		3	DST	6	56505183	Silent	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10		56505183	114609884	49	50350										
GPR63	81491	hgsc.bcm.edu	37	chr6	97247593	97247593	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	gtatggaacgcagtcaacacTgccgagaagaccatggtttc	11	10	1	2			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr6:97247593T>A	ENST00000229955.3	-	2	360	c.15A>T	c.(13-15)gcA>gcT	p.A5A	GPR63_ENST00000417980.1_Silent_p.A5A	NM_001143957.2|NM_030784.3	NP_001137429.1|NP_110411.1	Q9BZJ6	GPR63_HUMAN	G protein-coupled receptor 63	5						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			kidney(1)|large_intestine(5)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(76;6.89e-05)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.0618)|Colorectal(196;0.0721)		BRCA - Breast invasive adenocarcinoma(108;0.0912)		CAGTCAACACTGCCGAGAAGA	0.463																																					p.A5A		Atlas-SNP	.											.	GPR63	60	.	0			c.A15T						.						108	99	102					6																	97247593		2203	4300	6503	SO:0001819	synonymous_variant	81491	exon2			CAACACTGCCGAG	AF317654	CCDS5036.1	6q16.1-q16.3	2012-08-21			ENSG00000112218	ENSG00000112218		"GPCR / Class A : Orphans"	13302	protein-coding gene	gene with protein product		606915					Standard	NM_030784		Approved	PSP24(beta), PSP24B	uc003pou.3	Q9BZJ6	OTTHUMG00000015245	ENST00000229955.3:c.15A>T	chr6.hg19:g.97247593T>A		104.0	0.0		87.0	74.0	NM_030784	Q9UJH3	Silent	SNP	ENST00000229955.3	hg19	CCDS5036.1																																																																																			.	.		0.463	GPR63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041566.2			A	97247593	T	A	97247593	2	1	360	1	0	0	0	0	0	0	0	1	6712	1567	55	4		4	GPR63	6	97247593	Silent	SNP	T	TCGA-XR-A8TF-01A-11D-A35Z-10	40742410	97247593	73867474	50	50351										
ALDH8A1	64577	hgsc.bcm.edu	37	chr6	135239910	135239910	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	gtgggaagcataaagtagccTgcctggttcctggcagggag	16	8	0	0			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr6:135239910T>C	ENST00000265605.2	-	7	1175	c.1107A>G	c.(1105-1107)gcA>gcG	p.A369A	ALDH8A1_ENST00000367847.2_Silent_p.A319A|ALDH8A1_ENST00000367845.2_Silent_p.A315A	NM_022568.3	NP_072090.1	Q9H2A2	AL8A1_HUMAN	aldehyde dehydrogenase 8 family, member A1	369					9-cis-retinoic acid biosynthetic process (GO:0042904)|retinal metabolic process (GO:0042574)|retinoic acid metabolic process (GO:0042573)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	retinal dehydrogenase activity (GO:0001758)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	36	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00401)|GBM - Glioblastoma multiforme(68;0.0058)		TAAAGTAGCCTGCCTGGTTCC	0.517																																					p.A369A		Atlas-SNP	.											.	ALDH8A1	68	.	0			c.A1107G						.						115	112	113					6																	135239910		2203	4300	6503	SO:0001819	synonymous_variant	64577	exon7			GTAGCCTGCCTGG	AL021939	CCDS5171.1, CCDS5172.1, CCDS55057.1	6q24.1-q25.1	2008-07-03			ENSG00000118514	ENSG00000118514		"Aldehyde dehydrogenases"	15471	protein-coding gene	gene with protein product		606467				11007799	Standard	NM_001193480		Approved	ALDH12	uc003qew.3	Q9H2A2	OTTHUMG00000015623	ENST00000265605.2:c.1107A>G	chr6.hg19:g.135239910T>C		116.0	0.0		72.0	61.0	NM_022568	B7Z521|O60793|Q24JS9|Q53GT3|Q5TI80	Silent	SNP	ENST00000265605.2	hg19	CCDS5171.1																																																																																			.	.		0.517	ALDH8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042334.2			C	135239910	T	C	135239910	2	2	360	1	0	0	0	0	0	0	0	1	505	1567	55	2		2	ALDH8A1	6	135239910	Silent	SNP	T	TCGA-XR-A8TF-01A-11D-A35Z-10	37992317	135239910	35875157	51	50352										
C6orf97	80129	hgsc.bcm.edu	37	chr6	151936741	151936741	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	taaagaaagggccagaaacaTgatagaagtggtaaccagtg	12	5	0	4			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr6:151936741T>C	ENST00000239374.7	+	10	1973	c.1874T>C	c.(1873-1875)aTg>aCg	p.M625T	CCDC170_ENST00000367290.5_Missense_Mutation_p.M632T|RNU6-813P_ENST00000384691.1_RNA	NM_025059.3	NP_079335.2	Q8IYT3	CC170_HUMAN	coiled-coil domain containing 170	625																	GCCAGAAACATGATAGAAGTG	0.403																																					p.M625T		Atlas-SNP	.											.	.	.	.	0			c.T1874C						.						151	146	147					6																	151936741		1848	4093	5941	SO:0001583	missense	80129	exon10			GAAACATGATAGA	AK026958	CCDS43515.1	6q25.1	2012-03-26	2012-03-26	2012-03-26	ENSG00000120262	ENSG00000120262			21177	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 97"	C6orf97			Standard	NM_025059		Approved	FLJ23305, bA282P11.1	uc003qol.3	Q8IYT3	OTTHUMG00000015839	ENST00000239374.7:c.1874T>C	chr6.hg19:g.151936741T>C	ENSP00000239374:p.Met625Thr	347.0	0.0		220.0	192.0	NM_025059	Q5VXB7|Q6P9E4|Q96KA9|Q9H5M3	Missense_Mutation	SNP	ENST00000239374.7	hg19	CCDS43515.1	.	.	.	.	.	.	.	.	.	.	T	9.258	1.042412	0.19748	.	.	ENSG00000120262	ENST00000239374;ENST00000367290	T;T	0.08193	3.13;3.12	6.16	3.82	0.43975	.	0.196579	0.56097	N	0.000040	T	0.02610	0.0079	L	0.45137	1.4	0.36427	D	0.864708	B	0.09022	0.002	B	0.08055	0.003	T	0.33317	-0.9873	10	0.17832	T	0.49	-11.4716	10.1543	0.42814	0.0:0.1329:0.0:0.8671	.	625	Q8IYT3	CF097_HUMAN	T	625;632	ENSP00000239374:M625T;ENSP00000356259:M632T	ENSP00000239374:M625T	M	+	2	0	C6orf97	151978434	0.972000	0.33761	0.284000	0.24805	0.765000	0.43378	2.051000	0.41307	1.152000	0.42452	0.528000	0.53228	ATG	.	.		0.403	CCDC170-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042727.2	NM_025059		C	151936741	T	C	151936741	3	2	360	1	0	0	0	0	1	0	0	0	2376	1464	51	2	1912	2	C6orf97	6	151936741	Missense_Mutation	SNP	T	TCGA-XR-A8TF-01A-11D-A35Z-10	16696831	151936741	19178326	52	50353										
FNDC1	84624	hgsc.bcm.edu	37	chr6	159642682	159642682	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	tccatgaactctcagggccgGagccaaccagtctacagggc	11	14	2	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr6:159642682G>T	ENST00000297267.9	+	6	920	c.720G>T	c.(718-720)cgG>cgT	p.R240R	FNDC1_ENST00000340366.6_Silent_p.R240R|FNDC1_ENST00000480856.1_3'UTR	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	240	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		CTCAGGGCCGGAGCCAACCAG	0.498																																					p.R240R		Atlas-SNP	.											.	FNDC1	250	.	0			c.G720T						.						109	118	115					6																	159642682		1984	4158	6142	SO:0001819	synonymous_variant	84624	exon6			GGGCCGGAGCCAA	AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"Fibronectin type III domain containing"	21184	protein-coding gene	gene with protein product		609991	"fibronectin type III domain containing 2"	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.720G>T	chr6.hg19:g.159642682G>T		103.0	0.0		57.0	50.0	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Silent	SNP	ENST00000297267.9	hg19	CCDS47512.1	.	.	.	.	.	.	.	.	.	.	G	10.79	1.450093	0.26074	.	.	ENSG00000164694	ENST00000329629	.	.	.	6.17	5.28	0.74379	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-1.963	9.8425	0.41006	0.0698:0.2659:0.6643:0.0	.	.	.	.	X	199	.	.	E	+	1	0	FNDC1	159562670	0.999000	0.42202	0.964000	0.40570	0.976000	0.68499	2.835000	0.48175	1.565000	0.49641	0.655000	0.94253	GAG	.	.		0.498	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532		T	159642682	G	T	159642682	2	4	360	1	0	0	0	0	0	0	0	1	5976	1161	41	3		3	FNDC1	6	159642682	Silent	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10	7705941	159642682	11472385	53	50354										
PRR18	285800	hgsc.bcm.edu	37	chr6	166721359	166721359	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	agcctgccggccggggcgggGcgcacgtggctggggcccgc	21	15	0	0			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr6:166721359G>A	ENST00000322583.3	-	1	512	c.272C>T	c.(271-273)gCc>gTc	p.A91V		NM_175922.3	NP_787118.2	Q8N4B5	PRR18_HUMAN	proline rich 18	91	Pro-rich.									haematopoietic_and_lymphoid_tissue(2)|lung(1)	3		Breast(66;2.35e-05)|Ovarian(120;0.0606)|Prostate(117;0.0959)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-19)|BRCA - Breast invasive adenocarcinoma(81;4.45e-06)|GBM - Glioblastoma multiforme(31;7.96e-05)		ccggggcggggcgcacgtggc	0.831																																					p.A91V		Atlas-SNP	.											.	PRR18	4	.	0			c.C272T						.						1	1	1					6																	166721359		430	1138	1568	SO:0001583	missense	285800	exon1			GGCGGGGCGCACG	BC034775	CCDS5291.1	6q27	2009-01-27	2009-01-27						28574	protein-coding gene	gene with protein product			"proline rich region 18"			12477932	Standard	NM_175922		Approved	MGC35308	uc003quw.1	Q8N4B5		ENST00000322583.3:c.272C>T	chr6.hg19:g.166721359G>A	ENSP00000319590:p.Ala91Val	13.0	0.0		35.0	19.0	NM_175922		Missense_Mutation	SNP	ENST00000322583.3	hg19	CCDS5291.1	.	.	.	.	.	.	.	.	.	.	G	11.89	1.772267	0.31411	.	.	ENSG00000176381	ENST00000322583;ENST00000529616	T	0.44482	0.92	3.02	3.02	0.34903	.	0.816969	0.09878	U	0.744100	T	0.18383	0.0441	N	0.19112	0.55	0.09310	N	1	P	0.43938	0.822	P	0.45428	0.48	T	0.09596	-1.0667	10	0.41790	T	0.15	.	11.4293	0.50029	0.0:0.0:1.0:0.0	.	91	Q8N4B5	PRR18_HUMAN	V	91	ENSP00000319590:A91V	ENSP00000319590:A91V	A	-	2	0	PRR18	166641349	0.001000	0.12720	0.413000	0.26509	0.027000	0.11550	0.424000	0.21330	1.202000	0.43218	0.484000	0.47621	GCC	.	.		0.831	PRR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392563.3	NM_175922		A	166721359	G	A	166721359	3	1	360	1	0	0	0	0	1	0	0	0	12602	1203	42	3	619	3	PRR18	6	166721359	Missense_Mutation	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10	7078677	166721359	4393708	54	50355										
WDR27	253769	hgsc.bcm.edu	37	chr6	170043854	170043854	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	acgagtaacagatggttggcCaacccacaggccagccactg	11	13	0	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr6:170043854C>A	ENST00000448612.1	-	17	1795	c.1686G>T	c.(1684-1686)ttG>ttT	p.L562F	WDR27_ENST00000546525.1_5'UTR|WDR27_ENST00000423258.1_Missense_Mutation_p.L435F|WDR27_ENST00000333572.6_Missense_Mutation_p.L562F	NM_182552.4	NP_872358.4	A2RRH5	WDR27_HUMAN	WD repeat domain 27	532						nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|skin(1)	12		Breast(66;1.53e-05)|Ovarian(120;0.216)		OV - Ovarian serous cystadenocarcinoma(33;6.48e-20)|BRCA - Breast invasive adenocarcinoma(81;3.56e-07)|GBM - Glioblastoma multiforme(31;0.00168)		GATGGTTGGCCAACCCACAGG	0.418																																					p.L562F		Atlas-SNP	.											.	WDR27	129	.	0			c.G1686T						.						49	54	52					6																	170043854		1873	4093	5966	SO:0001583	missense	253769	exon17			GTTGGCCAACCCA	AK131435	CCDS47520.1, CCDS47520.2, CCDS56459.1	6q27	2013-01-09	2003-06-18		ENSG00000184465	ENSG00000184465		"WD repeat domain containing"	21248	protein-coding gene	gene with protein product							Standard	NM_182552		Approved	MGC43690	uc003qwx.3	A2RRH5	OTTHUMG00000016061	ENST00000448612.1:c.1686G>T	chr6.hg19:g.170043854C>A	ENSP00000416289:p.Leu562Phe	115.0	0.0		91.0	39.0	NM_182552	A5PLM8|C9JGV0|Q5T066	Missense_Mutation	SNP	ENST00000448612.1	hg19	CCDS47520.2	.	.	.	.	.	.	.	.	.	.	C	9.881	1.201495	0.22121	.	.	ENSG00000184465	ENST00000448612;ENST00000333572;ENST00000423258	T;T;T	0.39787	1.07;1.06;4.98	5.19	-1.45	0.08828	.	0.000000	0.47852	D	0.000208	T	0.17704	0.0425	M	0.62723	1.935	0.80722	D	1	B;P;P	0.48407	0.105;0.617;0.91	B;B;P	0.45428	0.042;0.28;0.48	T	0.31052	-0.9957	10	0.12430	T	0.62	-9.8639	4.8836	0.13692	0.1369:0.3538:0.0:0.5092	.	562;435;562	F2Z2U5;A2RRH5-2;C9JGV0	.;.;.	F	562;562;435	ENSP00000416289:L562F;ENSP00000330265:L562F;ENSP00000397869:L435F	ENSP00000330265:L562F	L	-	3	2	WDR27	169785779	0.245000	0.23899	0.144000	0.22314	0.024000	0.10985	-0.609000	0.05635	-0.252000	0.09528	-0.293000	0.09583	TTG	.	.		0.418	WDR27-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000407334.1	NM_182552		A	170043854	C	A	170043854	3	1	360	1	0	0	0	0	1	0	0	0	17299	593	21	3	923	3	WDR27	6	170043854	Missense_Mutation	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10	3322495	170043854	1071213	55	50356										
MTERF	7978	hgsc.bcm.edu	37	chr7	91503579	91503579	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	gaggaactttatattattctCtaagtttaggttgttattgg	9	3	1	0			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr7:91503579C>A	ENST00000351870.3	-	3	622	c.529G>T	c.(529-531)Gag>Tag	p.E177*	MTERF_ENST00000419292.1_Nonsense_Mutation_p.E157*|MTERF_ENST00000481516.1_5'Flank|MTERF_ENST00000406735.2_Nonsense_Mutation_p.E157*	NM_006980.3	NP_008911.1	Q99551	MTEF1_HUMAN		177					DNA geometric change (GO:0032392)|DNA-templated transcription, termination (GO:0006353)|gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of mitochondrial transcription (GO:0006393)|transcription from mitochondrial promoter (GO:0006390)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|liver(1)|lung(2)|skin(1)	14	all_cancers(62;2.28e-09)|all_epithelial(64;1.07e-07)|Breast(17;0.00371)|all_hematologic(106;0.091)|all_lung(186;0.178)|Lung NSC(181;0.235)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.0993)|Kidney(17;0.118)|Epithelial(20;0.136)|LUSC - Lung squamous cell carcinoma(200;0.176)			ATATTATTCTCTAAGTTTAGG	0.388																																					p.E177X		Atlas-SNP	.											.	MTERF	32	.	0			c.G529T						.						75	77	76					7																	91503579		2203	4300	6503	SO:0001587	stop_gained	7978	exon3			TATTCTCTAAGTT																												ENST00000351870.3:c.529G>T	chr7.hg19:g.91503579C>A	ENSP00000248643:p.Glu177*	140.0	0.0		204.0	58.0	NM_006980	A4D1E3|Q32NF8|Q53H51|Q9BVR7	Nonsense_Mutation	SNP	ENST00000351870.3	hg19	CCDS5621.1	.	.	.	.	.	.	.	.	.	.	C	17.10	3.302166	0.60195	.	.	ENSG00000127989	ENST00000419292;ENST00000351870;ENST00000406735	.	.	.	4.62	4.62	0.57501	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.7868	12.2646	0.54670	0.0:0.7167:0.2833:0.0	.	.	.	.	X	157;177;157	.	ENSP00000248643:E177X	E	-	1	0	MTERF	91341515	0.993000	0.37304	1.000000	0.80357	0.997000	0.91878	1.011000	0.29911	2.503000	0.84419	0.591000	0.81541	GAG	.	.		0.388	MTERF-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000342896.1			A	91503579	C	A	91503579	4	1	360	1	0	0	0	0	0	1	0	0	9927	922	32	3	674	3	MTERF	7	91503579	Nonsense_Mutation	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10		91503579	67635084	56	50357										
STAG3	10734	hgsc.bcm.edu	37	chr7	99797925	99797925	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	agttgactgagcacctcatcCccctgctgccccagctcctg	8	18	1	2			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr7:99797925C>T	ENST00000426455.1	+	17	2151	c.1744C>T	c.(1744-1746)Ccc>Tcc	p.P582S	GATS_ENST00000543273.1_RNA|STAG3_ENST00000394018.2_Missense_Mutation_p.P524S|STAG3_ENST00000440830.1_3'UTR|STAG3_ENST00000317296.5_Missense_Mutation_p.P582S	NM_001282716.1	NP_001269645.1	Q9UJ98	STAG3_HUMAN	stromal antigen 3	582					chromosome segregation (GO:0007059)|synaptonemal complex assembly (GO:0007130)	chromosome, centromeric region (GO:0000775)|extracellular space (GO:0005615)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)|nucleolus (GO:0005730)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)|transverse filament (GO:0000802)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(11)|lung(30)|ovary(5)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	66	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GCACCTCATCCCCCTGCTGCC	0.597																																					p.P582S		Atlas-SNP	.											.	STAG3	121	.	0			c.C1744T						.						67	56	60					7																	99797925		2203	4300	6503	SO:0001583	missense	10734	exon17			CTCATCCCCCTGC	AJ007798	CCDS34703.1, CCDS64730.1, CCDS75642.1	7q22	2008-02-01			ENSG00000066923	ENSG00000066923			11356	protein-coding gene	gene with protein product		608489				10698974	Standard	XM_005250116		Approved		uc003utx.1	Q9UJ98	OTTHUMG00000155183	ENST00000426455.1:c.1744C>T	chr7.hg19:g.99797925C>T	ENSP00000400359:p.Pro582Ser	95.0	0.0		132.0	28.0	NM_012447	A6H8Z1|B4DZ10|D6W5U8|H7BYK9|Q8NDP3	Missense_Mutation	SNP	ENST00000426455.1	hg19	CCDS34703.1	.	.	.	.	.	.	.	.	.	.	.	19.52	3.843073	0.71488	.	.	ENSG00000066923	ENST00000426455;ENST00000394018;ENST00000339784;ENST00000317296	T;T;T	0.22743	1.94;1.94;1.94	5.3	5.3	0.74995	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.52532	D	0.000063	T	0.23094	0.0558	L	0.49455	1.56	0.38969	D	0.958701	P;P	0.41597	0.756;0.58	B;B	0.41466	0.358;0.304	T	0.02352	-1.1172	10	0.59425	D	0.04	-20.0884	12.062	0.53568	0.0:0.827:0.173:0.0	.	524;582	B4DZ10;Q9UJ98	.;STAG3_HUMAN	S	582;524;540;582	ENSP00000400359:P582S;ENSP00000377586:P524S;ENSP00000319318:P582S	ENSP00000319318:P582S	P	+	1	0	STAG3	99635861	0.000000	0.05858	0.999000	0.59377	0.955000	0.61496	0.133000	0.15912	2.757000	0.94681	0.655000	0.94253	CCC	.	.		0.597	STAG3-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338734.2	NM_012447		T	99797925	C	T	99797925	3	4	360	1	0	0	0	0	1	0	0	0	15259	623	22	3	1806	3	STAG3	7	99797925	Missense_Mutation	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10	8294346	99797925	59340738	57	50358										
FLJ36031	168455	hgsc.bcm.edu	37	chr7	106301219	106301220	+	Frame_Shift_Del	DEL	AC	AC	-													0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	cgacagttgcgaccgcgagtAcaccaccttctcctcccgcg							TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr7:106301219_106301220delAC	ENST00000523505.1	-	1	222_223	c.123_124delGT	c.(121-126)gtgtacfs	p.Y42fs		NM_175884.4	NP_787080.2	Q8N9Z2	CC71L_HUMAN	coiled-coil domain containing 71-like	42										endometrium(1)	1						GACCGCGAGTACACCACCTTCT	0.718																																					p.42_42del		Atlas-INDEL	.											.	CCDC71L	2	.	0			c.124_125del						.																																			SO:0001589	frameshift_variant	168455	exon1			.		CCDS55151.1	7q22.3	2011-12-12	2011-12-12	2011-12-12	ENSG00000253276	ENSG00000253276			26685	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 74"	C7orf74		12477932	Standard	NM_175884		Approved	FLJ36031	uc003vdt.3	Q8N9Z2	OTTHUMG00000164150	ENST00000523505.1:c.123_124delGT	chr7.hg19:g.106301221_106301222delAC	ENSP00000430897:p.Tyr42fs	90.0	0.0		111.0	36.0	NM_175884	Q7Z756	Frame_Shift_Del	DEL	ENST00000523505.1	hg19	CCDS55151.1																																																																																			.	.		0.718	CCDC71L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377493.1	NM_175884		-	106301220	AC	-	106301219	7	5	360	1	0	1	0	1	0	0	0	0	5936	391	14	0	587	0	FLJ36031	7	106301219	Frame_Shift_Del	DEL	AC	TCGA-XR-A8TF-01A-11D-A35Z-10	6503294	106301219	52837444	58	50359										
GPR37	2861	hgsc.bcm.edu	37	chr7	124404436	124404436	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	cgccagtccattggccgtctTggacaggggcttgtggtggg	17	10	1	0			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr7:124404436T>A	ENST00000303921.2	-	1	1245	c.595A>T	c.(595-597)Aag>Tag	p.K199*		NM_005302.3	NP_005293.1	O15354	GPR37_HUMAN	G protein-coupled receptor 37 (endothelin receptor type B-like)	199					dopamine biosynthetic process (GO:0042416)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotion involved in locomotory behavior (GO:0031987)|positive regulation of dopamine metabolic process (GO:0045964)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|ubiquitin ligase complex (GO:0000151)	G-protein coupled receptor activity (GO:0004930)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						TTGGCCGTCTTGGACAGGGGC	0.617																																					p.K199X		Atlas-SNP	.											.	GPR37	89	.	0			c.A595T						.						45	52	50					7																	124404436		2203	4299	6502	SO:0001587	stop_gained	2861	exon1			CCGTCTTGGACAG		CCDS5792.1	7q31	2012-08-21			ENSG00000170775	ENSG00000170775		"GPCR / Class A : Orphans"	4494	protein-coding gene	gene with protein product		602583				9339362	Standard	NM_005302		Approved	EDNRBL, hET(B)R-LP, PAELR	uc003vli.4	O15354	OTTHUMG00000157197	ENST00000303921.2:c.595A>T	chr7.hg19:g.124404436T>A	ENSP00000306449:p.Lys199*	116.0	0.0		105.0	44.0	NM_005302	A4D0Y6|O00348|O14768|Q8TD39	Nonsense_Mutation	SNP	ENST00000303921.2	hg19	CCDS5792.1	.	.	.	.	.	.	.	.	.	.	T	39	7.525840	0.98339	.	.	ENSG00000170775	ENST00000303921	.	.	.	4.81	2.37	0.29283	.	0.572470	0.19041	N	0.124286	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05721	T	0.95	-24.8929	3.5298	0.07773	0.1957:0.1036:0.0:0.7007	.	.	.	.	X	199	.	ENSP00000306449:K199X	K	-	1	0	GPR37	124191672	0.706000	0.27856	0.387000	0.26183	0.187000	0.23431	2.110000	0.41873	2.033000	0.60031	0.529000	0.55759	AAG	.	.		0.617	GPR37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347873.1	NM_005302		A	124404436	T	A	124404436	4	1	360	1	0	0	0	0	0	1	0	0	6699	1821	63	4	1254	4	GPR37	7	124404436	Nonsense_Mutation	SNP	T	TCGA-XR-A8TF-01A-11D-A35Z-10	18103217	124404436	34734227	59	50360										
PODXL	5420	hgsc.bcm.edu	37	chr7	131241035	131241035	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	tcaccattctgggagggcgaCggcgacggcgacggcgacga	17	12	2	0	rs11277659|rs547816245|rs532078953	byFrequency	TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr7:131241035C>G	ENST00000378555.3	-	1	331	c.84G>C	c.(82-84)ccG>ccC	p.P28P	PODXL_ENST00000322985.9_Silent_p.P28P|PODXL_ENST00000541194.1_Silent_p.P28P|PODXL_ENST00000537928.1_Silent_p.P28P|PODXL_ENST00000465001.1_Intron			O00592	PODXL_HUMAN	podocalyxin-like	28					cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)		p.P30_S31delPS(2)		NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					GGGAGggcgacggcgacggcg	0.741																																					p.P28P		Atlas-SNP	.											.	PODXL	53	.	2	Deletion - In frame(2)	prostate(2)	c.G84C						.																																			SO:0001819	synonymous_variant	5420	exon1			GGGCGACGGCGAC		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.84G>C	chr7.hg19:g.131241035C>G		67.0	0.0		106.0	8.0	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Silent	SNP	ENST00000378555.3	hg19	CCDS34755.1																																																																																			.	.		0.741	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111		G	131241035	C	G	131241035	2	3	360	1	0	0	0	0	0	0	0	1	12189	523	19	4		4	PODXL	7	131241035	Silent	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10	6836599	131241035	27897628	60	50361										
CRYGN	155051	hgsc.bcm.edu	37	chr7	151127230	151127230	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	tgaagagagctgctcagctgGaagtcctcagctccgaagct	12	11	2	2			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr7:151127230G>C	ENST00000337323.2	-	4	579	c.453C>G	c.(451-453)ttC>ttG	p.F151L	CRYGN_ENST00000476631.1_5'UTR|CRYGN_ENST00000491928.1_3'UTR|RP4-555L14.4_ENST00000465549.1_RNA	NM_144727.1	NP_653328.1	Q8WXF5	CRGN_HUMAN	crystallin, gamma N	151										central_nervous_system(1)|kidney(1)|large_intestine(1)|liver(1)|lung(4)	8			OV - Ovarian serous cystadenocarcinoma(82;0.00358)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TGCTCAGCTGGAAGTCCTCAG	0.562																																					p.F151L		Atlas-SNP	.											.	CRYGN	15	.	0			c.C453G						.						183	145	158					7																	151127230		2203	4300	6503	SO:0001583	missense	155051	exon4			CAGCTGGAAGTCC	AF445455	CCDS5926.1	7q36.1	2003-02-25			ENSG00000127377	ENSG00000127377			20458	protein-coding gene	gene with protein product		609603					Standard	NM_144727		Approved		uc003wke.3	Q8WXF5	OTTHUMG00000157353	ENST00000337323.2:c.453C>G	chr7.hg19:g.151127230G>C	ENSP00000338613:p.Phe151Leu	136.0	0.0		140.0	59.0	NM_144727	Q496G6	Missense_Mutation	SNP	ENST00000337323.2	hg19	CCDS5926.1	.	.	.	.	.	.	.	.	.	.	G	13.67	2.307033	0.40795	.	.	ENSG00000127377	ENST00000337323	T	0.78595	-1.19	1.91	1.91	0.25777	.	0.563161	0.18877	N	0.128688	T	0.68668	0.3026	L	0.49126	1.545	0.09310	N	1	B	0.10296	0.003	B	0.15052	0.012	T	0.63817	-0.6551	10	0.87932	D	0	.	7.3297	0.26575	0.0:0.0:1.0:0.0	.	151	Q8WXF5	CRGN_HUMAN	L	151	ENSP00000338613:F151L	ENSP00000338613:F151L	F	-	3	2	CRYGN	150758163	0.007000	0.16637	0.011000	0.14972	0.015000	0.08874	0.673000	0.25203	1.394000	0.46624	0.561000	0.74099	TTC	.	.		0.562	CRYGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348553.1			C	151127230	G	C	151127230	3	2	360	1	0	0	0	0	1	0	0	0	3920	1165	41	4	99	4	CRYGN	7	151127230	Missense_Mutation	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10	19886195	151127230	8011433	61	50362										
CSMD1	64478	hgsc.bcm.edu	37	chr8	3046418	3046418	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	caaggactcacctgaattccCgagccctccgtaactatgat	7	14	1	2	rs541557117		TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr8:3046418C>A	ENST00000520002.1	-	36	6072	c.5517G>T	c.(5515-5517)tcG>tcT	p.S1839S	CSMD1_ENST00000542608.1_Silent_p.S1838S|CSMD1_ENST00000602557.1_Silent_p.S1839S|CSMD1_ENST00000523387.1_5'UTR|CSMD1_ENST00000537824.1_Silent_p.S1838S|CSMD1_ENST00000602723.1_Silent_p.S1839S|CSMD1_ENST00000400186.3_Silent_p.S1839S|CSMD1_ENST00000539096.1_Silent_p.S1838S			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1839	CUB 11. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CCTGAATTCCCGAGCCCTCCG	0.468																																					p.S1838S		Atlas-SNP	.											.	CSMD1	1469	.	0			c.G5514T						.						55	52	53					8																	3046418		1879	4098	5977	SO:0001819	synonymous_variant	64478	exon35			AATTCCCGAGCCC			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.5517G>T	chr8.hg19:g.3046418C>A		141.0	0.0		136.0	85.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	hg19		.	.	.	.	.	.	.	.	.	.	C	0.245	-1.011072	0.02095	.	.	ENSG00000183117	ENST00000335551	.	.	.	5.53	-10.3	0.00346	.	.	.	.	.	T	0.46034	0.1372	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55736	-0.8094	4	.	.	.	.	8.2452	0.31684	0.0:0.3839:0.2804:0.3357	.	.	.	.	W	1319	.	.	G	-	1	0	CSMD1	3033825	0.020000	0.18652	0.046000	0.18839	0.050000	0.14768	-1.027000	0.03592	-1.907000	0.01087	-1.169000	0.01745	GGG	.	.		0.468	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		A	3046418	C	A	3046418	2	1	360	1	0	0	0	0	0	0	0	1	3946	639	23	1		1	CSMD1	8	3046418	Silent	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10		3046418	143317604	62	50363										
LZTS1	11178	hgsc.bcm.edu	37	chr8	20110855	20110855	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	tgggtcccacgggtgtgaccAgcgggtccagctggtagctg	17	11	0	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr8:20110855A>T	ENST00000381569.1	-	3	944	c.587T>A	c.(586-588)cTg>cAg	p.L196Q	LZTS1_ENST00000522290.1_Missense_Mutation_p.L196Q|LZTS1_ENST00000265801.6_Missense_Mutation_p.L196Q			Q9Y250	LZTS1_HUMAN	leucine zipper, putative tumor suppressor 1	196					cell cycle (GO:0007049)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of macroautophagy (GO:0016242)|positive regulation of type I interferon production (GO:0032481)|regulation of dendrite morphogenesis (GO:0048814)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|nucleoplasm (GO:0005654)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(16)|ovary(2)|skin(1)|urinary_tract(1)	29				Colorectal(74;0.0511)|COAD - Colon adenocarcinoma(73;0.207)		GGGTGTGACCAGCGGGTCCAG	0.642																																					p.L196Q		Atlas-SNP	.											.	LZTS1	72	.	0			c.T587A						.						39	47	44					8																	20110855		2200	4297	6497	SO:0001583	missense	11178	exon2			GTGACCAGCGGGT	AF123659	CCDS6015.1	8p22	2012-10-05			ENSG00000061337	ENSG00000061337			13861	protein-coding gene	gene with protein product		606551	"F37/Esophageal cancer-related gene-coding leucine-zipper motif"			10097140, 17349584	Standard	NM_021020		Approved	FEZ1	uc003wzr.3	Q9Y250	OTTHUMG00000097027	ENST00000381569.1:c.587T>A	chr8.hg19:g.20110855A>T	ENSP00000370981:p.Leu196Gln	83.0	0.0		58.0	9.0	NM_021020	D3DSQ6|Q9Y5V7|Q9Y5V8|Q9Y5V9|Q9Y5W0|Q9Y5W1|Q9Y5W2	Missense_Mutation	SNP	ENST00000381569.1	hg19	CCDS6015.1	.	.	.	.	.	.	.	.	.	.	A	13.86	2.363030	0.41902	.	.	ENSG00000061337	ENST00000381569;ENST00000265801;ENST00000522290;ENST00000360248	T;T;T	0.26223	2.07;2.07;1.75	5.93	5.93	0.95920	.	0.212647	0.39407	N	0.001363	T	0.39200	0.1069	L	0.42245	1.32	0.41912	D	0.990472	D;B	0.89917	1.0;0.278	D;B	0.68943	0.961;0.072	T	0.10753	-1.0616	10	0.10902	T	0.67	-23.1903	15.2069	0.73186	1.0:0.0:0.0:0.0	.	196;196	Q9Y250-4;Q9Y250	.;LZTS1_HUMAN	Q	196	ENSP00000370981:L196Q;ENSP00000265801:L196Q;ENSP00000429263:L196Q	ENSP00000265801:L196Q	L	-	2	0	LZTS1	20155135	1.000000	0.71417	0.999000	0.59377	0.971000	0.66376	8.962000	0.93254	2.271000	0.75665	0.459000	0.35465	CTG	.	.		0.642	LZTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214122.1	NM_021020		T	20110855	A	T	20110855	3	4	360	1	0	0	0	0	1	0	0	0	9147	188	7	4	1211	4	LZTS1	8	20110855	Missense_Mutation	SNP	A	TCGA-XR-A8TF-01A-11D-A35Z-10	17064437	20110855	126253167	63	50364										
ELP3	55140	hgsc.bcm.edu	37	chr8	27957343	27957343	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	atgtgagatgctttactttcAgggtgaaaaccaagacagct	10	7	1	3			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr8:27957343A>T	ENST00000256398.8	+	3	496		c.e3-1		ELP3_ENST00000521015.1_Splice_Site|ELP3_ENST00000524103.1_Splice_Site|ELP3_ENST00000523760.1_Splice_Site|ELP3_ENST00000537665.1_Splice_Site|ELP3_ENST00000380353.4_Intron|ELP3_ENST00000542181.1_Intron	NM_001284220.1|NM_001284226.1|NM_018091.5	NP_001271149.1|NP_001271155.1|NP_060561.3	Q9H9T3	ELP3_HUMAN	elongator acetyltransferase complex subunit 3						chromatin organization (GO:0006325)|positive regulation of cell migration (GO:0030335)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	histone acetyltransferase activity (GO:0004402)|iron-sulfur cluster binding (GO:0051536)|metal ion binding (GO:0046872)|phosphorylase kinase regulator activity (GO:0008607)			kidney(2)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.151)|Colorectal(74;0.183)		CTTTACTTTCAGGGTGAAAAC	0.448																																					.		Atlas-SNP	.											.	ELP3	36	.	0			c.120-2A>T						.						96	90	92					8																	27957343		2203	4300	6503	SO:0001630	splice_region_variant	55140	exon3			ACTTTCAGGGTGA		CCDS6065.1, CCDS64860.1, CCDS64861.1, CCDS75717.1, CCDS75718.1	8p21.1	2012-08-14	2012-08-08		ENSG00000134014	ENSG00000134014		"Chromatin-modifying enzymes / K-acetyltransferases", "Elongator acetyltransferase complex subunits"	20696	protein-coding gene	gene with protein product		612722	"elongation protein 3 homolog (S. cerevisiae)"			11714725	Standard	NM_018091		Approved	FLJ10422, KAT9	uc003xgo.4	Q9H9T3	OTTHUMG00000102124	ENST00000256398.8:c.120-1A>T	chr8.hg19:g.27957343A>T		71.0	0.0		71.0	44.0	NM_018091	B4DE19|B4DIG1|E2QRI5|Q53G84|Q6AWB0|Q9BVF7|Q9NVZ1	Splice_Site	SNP	ENST00000256398.8	hg19	CCDS6065.1	.	.	.	.	.	.	.	.	.	.	A	20.5	3.994140	0.74703	.	.	ENSG00000134014	ENST00000520270;ENST00000521015;ENST00000521570;ENST00000256398;ENST00000524024;ENST00000520288;ENST00000521099	.	.	.	5.33	5.33	0.75918	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5348	0.61641	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ELP3	28013262	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	8.432000	0.90288	2.147000	0.66899	0.482000	0.46254	.	.	.		0.448	ELP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219963.2	NM_018091	Intron	T	27957343	A	T	27957343	5	4	360	1	0	0	0	0	0	0	1	0	5083	202	7	4	128	4	ELP3	8	27957343	Splice_Site	SNP	A	TCGA-XR-A8TF-01A-11D-A35Z-10	7846488	27957343	118406679	64	50365										
CPA6	57094	hgsc.bcm.edu	37	chr8	68430279	68430279	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	actgctgggctgccacaggtCcacctgtagtgcaggaacca	12	13	0	0			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr8:68430279C>T	ENST00000297770.4	-	3	411	c.196G>A	c.(196-198)Gac>Aac	p.D66N	CPA6_ENST00000518549.1_Missense_Mutation_p.D66N|CPA6_ENST00000297769.4_5'UTR	NM_020361.4	NP_065094.3	Q8N4T0	CBPA6_HUMAN	carboxypeptidase A6	66						proteinaceous extracellular matrix (GO:0005578)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(5)	26			Epithelial(68;0.04)|OV - Ovarian serous cystadenocarcinoma(28;0.0593)|all cancers(69;0.136)			TGCCACAGGTCCACCTGTAGT	0.453																																					p.D66N		Atlas-SNP	.											CPA6,right_upper_lobe,carcinoma,0,1	CPA6	69	.	0			c.G196A						.						92	83	86					8																	68430279		2203	4300	6503	SO:0001583	missense	57094	exon3			ACAGGTCCACCTG	AF221594	CCDS6200.1	8q12.3	2012-02-10			ENSG00000165078	ENSG00000165078			17245	protein-coding gene	gene with protein product		609562				11836249	Standard	NM_020361		Approved	CPAH	uc003xxq.4	Q8N4T0	OTTHUMG00000164575	ENST00000297770.4:c.196G>A	chr8.hg19:g.68430279C>T	ENSP00000297770:p.Asp66Asn	168.0	0.0		171.0	34.0	NM_020361	Q8NEX8|Q8TDE8|Q9NRI9	Missense_Mutation	SNP	ENST00000297770.4	hg19	CCDS6200.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.947866	0.92593	.	.	ENSG00000165078	ENST00000297770;ENST00000518549	T;T	0.21031	2.03;2.03	6.06	6.06	0.98353	Proteinase inhibitor, propeptide (1);Proteinase inhibitor, carboxypeptidase propeptide (2);	0.047994	0.85682	D	0.000000	T	0.48333	0.1494	M	0.68593	2.085	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.971	T	0.17349	-1.0372	10	0.46703	T	0.11	.	20.2159	0.98296	0.0:1.0:0.0:0.0	.	66;66	Q8N4T0-2;Q8N4T0	.;CBPA6_HUMAN	N	66	ENSP00000297770:D66N;ENSP00000431112:D66N	ENSP00000297770:D66N	D	-	1	0	CPA6	68592833	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.994000	0.70623	2.882000	0.98803	0.655000	0.94253	GAC	.	.		0.453	CPA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379296.2	NM_020361		T	68430279	C	T	68430279	3	4	360	1	0	0	0	0	1	0	0	0	3796	855	30	3	1153	3	CPA6	8	68430279	Missense_Mutation	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10	40472936	68430279	77933743	65	50366										
PRDM14	63978	hgsc.bcm.edu	37	chr8	70970978	70970978	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	aacagggaaatttcctatcgCccttgtccacacagggggtg	11	11	0	0			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr8:70970978C>A	ENST00000276594.2	-	6	1484	c.1283G>T	c.(1282-1284)gGc>gTc	p.G428V		NM_024504.3	NP_078780.1	Q9GZV8	PRD14_HUMAN	PR domain containing 14	428					cell fate specification (GO:0001708)|cell morphogenesis (GO:0000902)|fertilization (GO:0009566)|germ cell development (GO:0007281)|germ-line stem cell maintenance (GO:0030718)|histone H3-R26 methylation (GO:0034972)|homeostasis of number of cells within a tissue (GO:0048873)|inner cell mass cell fate commitment (GO:0001827)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|regulation of DNA methylation (GO:0044030)|regulation of gene expression, epigenetic (GO:0040029)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Breast(64;0.193)		Epithelial(68;0.00508)|all cancers(69;0.0259)|OV - Ovarian serous cystadenocarcinoma(28;0.0405)			TTTCCTATCGCCCTTGTCCAC	0.483																																					p.G428V	NSCLC(129;99 1813 5906 40656 46114)	Atlas-SNP	.											.	PRDM14	102	.	0			c.G1283T						.						115	104	108					8																	70970978		2203	4300	6503	SO:0001583	missense	63978	exon6			CTATCGCCCTTGT	AF319458	CCDS6206.1	8q13.3	2013-01-08			ENSG00000147596	ENSG00000147596		"Zinc fingers, C2H2-type"	14001	protein-coding gene	gene with protein product		611781					Standard	NM_024504		Approved		uc003xym.3	Q9GZV8	OTTHUMG00000150495	ENST00000276594.2:c.1283G>T	chr8.hg19:g.70970978C>A	ENSP00000276594:p.Gly428Val	110.0	0.0		123.0	61.0	NM_024504	Q86UX9	Missense_Mutation	SNP	ENST00000276594.2	hg19	CCDS6206.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.855070	0.91355	.	.	ENSG00000147596	ENST00000276594	T	0.14266	2.52	5.73	5.73	0.89815	Zinc finger, C2H2 (1);	0.000000	0.85682	D	0.000000	T	0.49626	0.1568	M	0.90977	3.165	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.59139	-0.7510	10	0.87932	D	0	-23.4223	19.9036	0.96999	0.0:1.0:0.0:0.0	.	428	Q9GZV8	PRD14_HUMAN	V	428	ENSP00000276594:G428V	ENSP00000276594:G428V	G	-	2	0	PRDM14	71133532	1.000000	0.71417	0.966000	0.40874	0.871000	0.50021	7.343000	0.79319	2.706000	0.92434	0.655000	0.94253	GGC	.	.		0.483	PRDM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318505.1			A	70970978	C	A	70970978	3	1	360	1	0	0	0	0	1	0	0	0	12467	739	26	3	444	3	PRDM14	8	70970978	Missense_Mutation	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10	2540699	70970978	75393044	66	50367										
PTK2	5747	hgsc.bcm.edu	37	chr8	141678423	141678423	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	gctggattttactggacatcTcgatgacagctttcaccagg	10	10	2	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr8:141678423T>G	ENST00000522684.1	-	30	3039	c.2810A>C	c.(2809-2811)gAg>gCg	p.E937A	PTK2_ENST00000519465.1_Missense_Mutation_p.E565A|PTK2_ENST00000538769.1_Missense_Mutation_p.E605A|PTK2_ENST00000517712.1_5'UTR|PTK2_ENST00000340930.3_Missense_Mutation_p.E950A|PTK2_ENST00000517887.1_Missense_Mutation_p.E981A|PTK2_ENST00000535192.1_Missense_Mutation_p.E891A|PTK2_ENST00000395218.2_Missense_Mutation_p.E950A|PTK2_ENST00000519419.1_Missense_Mutation_p.E981A|PTK2_ENST00000430260.2_Missense_Mutation_p.E247A|PTK2_ENST00000521059.1_Missense_Mutation_p.E937A	NM_153831.3	NP_722560.1	Q05397	FAK1_HUMAN	protein tyrosine kinase 2	937	Interaction with ARHGEF28. {ECO:0000250}.|Interaction with TGFB1I1.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell motility (GO:0048870)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|central nervous system neuron axonogenesis (GO:0021955)|embryo development (GO:0009790)|endothelial cell migration (GO:0043542)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|establishment of nucleus localization (GO:0040023)|extracellular matrix organization (GO:0030198)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|growth hormone receptor signaling pathway (GO:0060396)|heart morphogenesis (GO:0003007)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of organ growth (GO:0046621)|negative regulation of synapse assembly (GO:0051964)|netrin-activated signaling pathway (GO:0038007)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|placenta development (GO:0001890)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|regulation of endothelial cell migration (GO:0010594)|regulation of focal adhesion assembly (GO:0051893)|regulation of osteoblast differentiation (GO:0045667)|regulation of Rho GTPase activity (GO:0032319)|signal complex assembly (GO:0007172)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)	apical plasma membrane (GO:0016324)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|stress fiber (GO:0001725)	actin binding (GO:0003779)|ATP binding (GO:0005524)|JUN kinase binding (GO:0008432)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(6)|lung(23)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	48	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)			ACTGGACATCTCGATGACAGC	0.498											OREG0019022	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E959A		Atlas-SNP	.											.	PTK2	311	.	0			c.A2876C						.						114	100	105					8																	141678423		2203	4300	6503	SO:0001583	missense	5747	exon30			GACATCTCGATGA	L13616	CCDS6381.1, CCDS56557.1	8q24.3	2013-02-18	2013-02-18		ENSG00000169398	ENSG00000169398	2.7.10.1	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9611	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 71"	600758	"PTK2 protein tyrosine kinase 2"			8422239	Standard	NM_153831		Approved	FAK, FADK, FAK1, PPP1R71	uc003yvt.3	Q05397	OTTHUMG00000067438	ENST00000522684.1:c.2810A>C	chr8.hg19:g.141678423T>G	ENSP00000429911:p.Glu937Ala	158.0	0.0	1665	142.0	40.0	NM_005607	B4E2N6|F5H4S4|Q14291|Q9UD85	Missense_Mutation	SNP	ENST00000522684.1	hg19	CCDS6381.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.402679	0.83230	.	.	ENSG00000169398	ENST00000522684;ENST00000535192;ENST00000519465;ENST00000517887;ENST00000521059;ENST00000395214;ENST00000395218;ENST00000354438;ENST00000395221;ENST00000523539;ENST00000340930;ENST00000538769;ENST00000519419;ENST00000430260;ENST00000521986	T;T;T;T;T;T;T;T;T;T;T;T	0.32988	1.43;1.43;1.43;1.43;1.43;1.43;1.43;1.43;1.43;1.43;1.43;1.43	5.62	5.62	0.85841	Focal adhesion kinase, targeting (FAT) domain (3);	0.000000	0.85682	D	0.000000	T	0.40448	0.1117	N	0.25890	0.77	0.58432	D	0.999996	D;D;B;D;B;D;P;P;B;B	0.76494	0.999;0.999;0.246;0.999;0.374;0.999;0.565;0.537;0.246;0.374	D;D;B;D;B;D;P;B;B;B	0.91635	0.998;0.999;0.268;0.997;0.097;0.996;0.456;0.219;0.194;0.097	T	0.13335	-1.0513	10	0.12430	T	0.62	.	15.8239	0.78683	0.0:0.0:0.0:1.0	.	950;635;860;937;959;891;892;764;605;565	B4E2N6;B4DH13;Q59GN8;Q05397;Q658W2;Q8IYN9;Q59GM6;Q05397-2;Q8N9D7;E9PEI4	.;.;.;FAK1_HUMAN;.;.;.;.;.;.	A	937;891;565;981;937;892;950;861;635;609;950;605;981;247;638	ENSP00000429911:E937A;ENSP00000438009:E891A;ENSP00000429170:E565A;ENSP00000429082:E981A;ENSP00000429474:E937A;ENSP00000378644:E950A;ENSP00000428492:E609A;ENSP00000341189:E950A;ENSP00000445742:E605A;ENSP00000429129:E981A;ENSP00000403416:E247A;ENSP00000430603:E638A	ENSP00000341189:E950A	E	-	2	0	PTK2	141747605	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	7.810000	0.86072	2.135000	0.66039	0.533000	0.62120	GAG	.	.		0.498	PTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378054.5	NM_005607		G	141678423	T	G	141678423	3	3	360	1	0	0	0	0	1	0	0	0	12775	1551	54	5	360	5	PTK2	8	141678423	Missense_Mutation	SNP	T	TCGA-XR-A8TF-01A-11D-A35Z-10	70707445	141678423	4685599	67	50368										
MAFA	389692	hgsc.bcm.edu	37	chr8	144512551	144512551	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	gcgggctgctgggcagctcgGcgcccatcgccagctccgcg	16	17	0	0			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr8:144512551G>T	ENST00000333480.2	-	1	25	c.26C>A	c.(25-27)gCc>gAc	p.A9D	MAFA_ENST00000528185.1_5'Flank	NM_201589.3	NP_963883.2	Q8NHW3	MAFA_HUMAN	v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog A	9					insulin secretion (GO:0030073)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to glucose (GO:0009749)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|lung(1)|upper_aerodigestive_tract(2)	4	all_cancers(97;7.39e-11)|all_epithelial(106;5.44e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.237)			GGGCAGCTCGGCGCCCATCGC	0.741										HNSCC(29;0.082)																											p.A9D		Atlas-SNP	.											.	MAFA	9	.	0			c.C26A						.						12	10	11					8																	144512551		2120	4193	6313	SO:0001583	missense	389692	exon1			AGCTCGGCGCCCA	AY083269	CCDS34955.1	8q24.3	2013-07-09	2013-07-09			ENSG00000182759			23145	protein-coding gene	gene with protein product		610303					Standard	NM_201589		Approved	RIPE3b1, hMafA	uc003yyc.2	Q8NHW3		ENST00000333480.2:c.26C>A	chr8.hg19:g.144512551G>T	ENSP00000328364:p.Ala9Asp	43.0	0.0		41.0	11.0	NM_201589		Missense_Mutation	SNP	ENST00000333480.2	hg19	CCDS34955.1	.	.	.	.	.	.	.	.	.	.	g	13.82	2.351261	0.41700	.	.	ENSG00000182759	ENST00000333480	D	0.98362	-4.89	3.06	0.888	0.19206	.	0.085474	0.43110	U	0.000602	D	0.92087	0.7492	N	0.08118	0	0.31181	N	0.702042	B	0.34015	0.435	B	0.33196	0.159	D	0.90874	0.4748	10	0.49607	T	0.09	.	6.3367	0.21300	0.2052:0.1816:0.6132:0.0	.	9	Q8NHW3	MAFA_HUMAN	D	9	ENSP00000328364:A9D	ENSP00000328364:A9D	A	-	2	0	MAFA	144583694	0.957000	0.32711	0.703000	0.30354	0.823000	0.46562	2.781000	0.47750	1.255000	0.44051	0.409000	0.27619	GCC	.	.		0.741	MAFA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381511.2	NM_201589		T	144512551	G	T	144512551	3	4	360	1	0	0	0	0	1	0	0	0	9166	1203	42	3	1039	3	MAFA	8	144512551	Missense_Mutation	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10	2834128	144512551	1851471	68	50369										
NRBP2	340371	hgsc.bcm.edu	37	chr8	144917879	144917879	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	gaaggtgctctccaggaaggCggccagcttcatccggtcgt	14	12	2	0	rs372417243		TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr8:144917879C>T	ENST00000442628.2	-	18	1598	c.1459G>A	c.(1459-1461)Gcc>Acc	p.A487T	NRBP2_ENST00000327830.5_Missense_Mutation_p.A244T|RP11-299M14.2_ENST00000534006.1_RNA	NM_178564.3	NP_848659.2			nuclear receptor binding protein 2											central_nervous_system(2)|kidney(1)|large_intestine(2)	5	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;6.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			TCCAGGAAGGCGGCCAGCTTC	0.746																																					p.A487T		Atlas-SNP	.											.	NRBP2	20	.	0			c.G1459A						.	C	THR/ALA	0,4402		0,0,2201	35	35	35		1459	-1.2	0.2	8		35	1,8597	1.2+/-3.3	0,1,4298	no	missense	NRBP2	NM_178564.3	58	0,1,6499	TT,TC,CC		0.0116,0.0,0.0077	benign	487/502	144917879	1,12999	2201	4299	6500	SO:0001583	missense	340371	exon18			GGAAGGCGGCCAG	BC037396	CCDS34959.1, CCDS34959.2	8q24.3	2005-01-24							19339	protein-coding gene	gene with protein product		615563				14702039	Standard	NM_178564		Approved	DKFZp434P086	uc011lkt.2	Q9NSY0		ENST00000442628.2:c.1459G>A	chr8.hg19:g.144917879C>T	ENSP00000414055:p.Ala487Thr	138.0	0.0		103.0	28.0	NM_178564		Missense_Mutation	SNP	ENST00000442628.2	hg19	CCDS34959.2	.	.	.	.	.	.	.	.	.	.	C	11.36	1.615690	0.28801	0.0	1.16E-4	ENSG00000185189	ENST00000442628;ENST00000327830	T;T	0.30448	4.6;1.53	3.8	-1.24	0.09435	.	1.880630	0.03156	N	0.168547	T	0.15305	0.0369	N	0.11427	0.14	0.09310	N	1	B;B;B	0.24618	0.107;0.014;0.015	B;B;B	0.15484	0.013;0.011;0.005	T	0.19160	-1.0314	10	0.08381	T	0.77	-10.2363	8.9368	0.35704	0.0:0.6002:0.0:0.3998	.	487;155;279	Q9NSY0;B3KSN6;Q9NSY0-2	NRBP2_HUMAN;.;.	T	487;244	ENSP00000414055:A487T;ENSP00000330271:A244T	ENSP00000330271:A244T	A	-	1	0	NRBP2	144989867	0.000000	0.05858	0.218000	0.23776	0.780000	0.44128	-1.022000	0.03611	-0.603000	0.05767	-0.982000	0.02568	GCC	.	.		0.746	NRBP2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382247.1	NM_178564		T	144917879	C	T	144917879	3	4	360	1	0	0	0	0	1	0	0	0	10652	768	27	1	50	1	NRBP2	8	144917879	Missense_Mutation	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10	405328	144917879	1446143	69	50370										
UNC13B	10497	hgsc.bcm.edu	37	chr9	35399446	35399446	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	gccatctttccaaactcaagGtactctgggtgtggggtcct	11	11	3	0			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr9:35399446G>A	ENST00000378495.3	+	34	4230		c.e34+1		UNC13B_ENST00000396787.1_Splice_Site|UNC13B_ENST00000378496.4_Splice_Site	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)						apoptotic process (GO:0006915)|excretion (GO:0007588)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synaptic vesicle priming (GO:0010808)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|terminal bouton (GO:0043195)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(16)|liver(2)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			CAAACTCAAGGTACTCTGGGT	0.562																																					.		Atlas-SNP	.											.	UNC13B	153	.	0			c.4008+1G>A						.						94	81	85					9																	35399446		2203	4300	6503	SO:0001630	splice_region_variant	10497	exon34			CTCAAGGTACTCT	AF020202	CCDS6579.1	9p13.3	2008-05-15	2003-10-17	2003-10-17	ENSG00000198722	ENSG00000198722			12566	protein-coding gene	gene with protein product		605836	"unc-13-like (C. elegans)"	UNC13		9607201	Standard	NM_006377		Approved	hmunc13, Unc13h2	uc003zwq.3	O14795	OTTHUMG00000019856	ENST00000378495.3:c.4008+1G>A	chr9.hg19:g.35399446G>A		65.0	0.0		50.0	33.0	NM_006377	Q5VYM8	Splice_Site	SNP	ENST00000378495.3	hg19	CCDS6579.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.342116	0.81911	.	.	ENSG00000198722	ENST00000396787;ENST00000378495;ENST00000378496;ENST00000535471	.	.	.	5.29	5.29	0.74685	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.1113	0.93317	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	UNC13B	35389446	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.169000	0.94788	2.761000	0.94854	0.655000	0.94253	.	.	.		0.562	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377	Intron	A	35399446	G	A	35399446	5	1	360	1	0	0	0	0	0	0	1	0	17000	1275	44	3	4143	3	UNC13B	9	35399446	Splice_Site	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10		35399446	105813985	70	50371										
TLE1	7088	hgsc.bcm.edu	37	chr9	84268953	84268953	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	atctcttggcgatttcagtcTataaagacaaagccacacaa	6	10	3	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr9:84268953T>A	ENST00000376499.3	-	5	1299		c.e5-2		TLE1_ENST00000376463.1_Splice_Site|TLE1_ENST00000376472.1_Splice_Site	NM_005077.3	NP_005068.2	Q04724	TLE1_HUMAN	transducin-like enhancer of split 1 (E(sp1) homolog, Drosophila)						multicellular organismal development (GO:0007275)|negative regulation of anoikis (GO:2000811)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation of gene expression (GO:0010628)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription factor binding (GO:0008134)			NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	29						GATTTCAGTCTATAAAGACAA	0.378																																					.	NSCLC(155;1437 1995 30668 39354 45875)|Melanoma(16;266 781 14000 47728 51870)	Atlas-SNP	.											.	TLE1	81	.	0			c.235-2A>T						.						112	104	107					9																	84268953		2203	4300	6503	SO:0001630	splice_region_variant	7088	exon6			TCAGTCTATAAAG		CCDS6661.1	9q21.32	2013-01-10	2001-11-28		ENSG00000196781	ENSG00000196781		"WD repeat domain containing"	11837	protein-coding gene	gene with protein product	"enhancer of split groucho 1"	600189	"transducin-like enhancer of split 1, homolog of Drosophila E(sp1)"			8365415, 8808280	Standard	NM_005077		Approved	ESG1, GRG1, ESG	uc004aly.3	Q04724	OTTHUMG00000021008	ENST00000376499.3:c.235-2A>T	chr9.hg19:g.84268953T>A		87.0	0.0		69.0	38.0	NM_005077	A8K495|Q5T3G4|Q969V9	Splice_Site	SNP	ENST00000376499.3	hg19	CCDS6661.1	.	.	.	.	.	.	.	.	.	.	T	16.46	3.129151	0.56721	.	.	ENSG00000196781	ENST00000376499;ENST00000355002;ENST00000418319;ENST00000376463	.	.	.	5.93	5.93	0.95920	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3943	0.83563	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	TLE1	83458773	1.000000	0.71417	0.997000	0.53966	0.439000	0.31926	8.040000	0.89188	2.281000	0.76405	0.533000	0.62120	.	.	.		0.378	TLE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055407.1	NM_005077	Intron	A	84268953	T	A	84268953	5	1	360	1	0	0	0	0	0	0	1	0	15953	1536	53	4	2143	4	TLE1	9	84268953	Splice_Site	SNP	T	TCGA-XR-A8TF-01A-11D-A35Z-10	48869507	84268953	56944478	71	50372										
CTSL1	1514	hgsc.bcm.edu	37	chr9	90342523	90342523	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	tcctaggttttaaaacatgaAtcctacactcatccttgctg	5	11	1	1	rs112682750	byFrequency	TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr9:90342523A>G	ENST00000343150.5	+	2	895	c.5A>G	c.(4-6)aAt>aGt	p.N2S	CTSL_ENST00000342020.5_Missense_Mutation_p.N2S|CTSL_ENST00000340342.6_Missense_Mutation_p.N2S|CTSL_ENST00000495822.1_3'UTR			P07711	CATL1_HUMAN	cathepsin L	2					adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to thyroid hormone stimulus (GO:0097067)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|macrophage apoptotic process (GO:0071888)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|nucleus (GO:0005634)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|fibronectin binding (GO:0001968)|histone binding (GO:0042393)|proteoglycan binding (GO:0043394)										TAAAACATGAATCCTACACTC	0.448																																					p.N2S		Atlas-SNP	.											.	CTSL1	43	.	0			c.A5G						.						120	111	114					9																	90342523		2203	4300	6503	SO:0001583	missense	1514	exon2			ACATGAATCCTAC	X12451	CCDS6675.1	9q21.33	2013-06-27	2013-06-27	2013-06-27	ENSG00000135047	ENSG00000135047	3.4.22.15	"Cathepsins"	2537	protein-coding gene	gene with protein product		116880	"cathepsin L1"	CTSL1		8419312, 2835398	Standard	NM_145918		Approved	FLJ31037	uc004apk.4	P07711	OTTHUMG00000020149	ENST00000343150.5:c.5A>G	chr9.hg19:g.90342523A>G	ENSP00000345344:p.Asn2Ser	91.0	0.0		115.0	39.0	NM_145918	Q6IAV1|Q96QJ0	Missense_Mutation	SNP	ENST00000343150.5	hg19	CCDS6675.1	.	.	.	.	.	.	.	.	.	.	A	3.478	-0.106430	0.06924	.	.	ENSG00000135047	ENST00000343150;ENST00000340342;ENST00000342020;ENST00000539280	T;T;T	0.70164	-0.46;-0.46;0.01	3.76	1.2	0.21068	.	0.475967	0.25517	N	0.030136	T	0.49098	0.1537	L	0.29908	0.895	0.09310	N	1	B	0.20887	0.049	B	0.12156	0.007	T	0.34279	-0.9835	10	0.39692	T	0.17	.	8.3874	0.32508	0.589:0.4109:0.0:0.0	.	2	P07711	CATL1_HUMAN	S	2	ENSP00000345344:N2S;ENSP00000365061:N2S;ENSP00000340470:N2S	ENSP00000365061:N2S	N	+	2	0	CTSL1	89532343	0.636000	0.27207	0.413000	0.26509	0.323000	0.28346	0.684000	0.25364	0.040000	0.15660	0.397000	0.26171	AAT	.	A|0.996;C|0.004		0.448	CTSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052936.1	NM_001912		G	90342523	A	G	90342523	3	3	360	1	0	0	0	0	1	0	0	0	4040	101	4	2	7	2	CTSL1	9	90342523	Missense_Mutation	SNP	A	TCGA-XR-A8TF-01A-11D-A35Z-10	6073570	90342523	50870908	72	50373										
KIAA1529	100499483	hgsc.bcm.edu	37	chr9	100105753	100105753	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	tgtaggaagtcccattccacCttctcagccatgttcatcaa	6	13	3	0			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr9:100105753C>T	ENST00000357054.1	+	33	3890	c.2955C>T	c.(2953-2955)acC>acT	p.T985T	CCDC180_ENST00000411667.2_Silent_p.T843T|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000529487.1_Silent_p.T846T|CCDC180_ENST00000460482.2_3'UTR|CCDC180_ENST00000375202.2_Silent_p.T846T|CCDC180_ENST00000395220.1_3'UTR			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	985						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											CCCATTCCACCTTCTCAGCCA	0.403																																					p.T846T		Atlas-SNP	.											.	.	.	.	0			c.C2538T						.						115	107	110					9																	100105753		2203	4300	6503	SO:0001819	synonymous_variant	0	exon19			TTCCACCTTCTCA	AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"Behcet's Disease Associated Gene 1"		"KIAA1529", "chromosome 9 open reading frame 174"	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.2955C>T	chr9.hg19:g.100105753C>T		132.0	0.0		102.0	24.0	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Silent	SNP	ENST00000357054.1	hg19																																																																																				.	.		0.403	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893		T	100105753	C	T	100105753	2	4	360	1	0	0	0	0	0	0	0	1	8249	668	24	3		3	KIAA1529	9	100105753	Silent	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10	9763230	100105753	41107678	73	50374										
ANKS6	203286	hgsc.bcm.edu	37	chr9	101539738	101539738	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	cctcttgtgctcccaggaccTgagagacaaatggaaatttc	9	11	1	2			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr9:101539738T>A	ENST00000353234.4	-	8	1615		c.e8-2		ANKS6_ENST00000375018.1_Splice_Site|ANKS6_ENST00000375019.2_Splice_Site|ANKS6_ENST00000540940.1_Splice_Site			Q68DC2	ANKS6_HUMAN	ankyrin repeat and sterile alpha motif domain containing 6							cilium (GO:0005929)|cytoplasm (GO:0005737)				endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	21		Acute lymphoblastic leukemia(62;0.0527)				TCCCAGGACCTGAGAGACAAA	0.483																																					.		Atlas-SNP	.											.	ANKS6	59	.	0			c.1568-2A>T						.						117	110	112					9																	101539738		1901	4114	6015	SO:0001630	splice_region_variant	203286	exon9			AGGACCTGAGAGA	AK094247	CCDS43856.1	9q31.1	2013-09-10	2006-02-17	2006-02-17	ENSG00000165138	ENSG00000165138		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	26724	protein-coding gene	gene with protein product		615370	"sterile alpha motif domain containing 6", "ankyrin repeat domain 14"	SAMD6, ANKRD14		23793029	Standard	XM_005251793		Approved	FLJ36928, NPHP16	uc004ayu.3	Q68DC2	OTTHUMG00000020347	ENST00000353234.4:c.1568-2A>T	chr9.hg19:g.101539738T>A		132.0	0.0		116.0	45.0	NM_173551	A0SE62|Q5VSL0|Q5VSL2|Q5VSL3|Q5VSL4|Q68DB8|Q6P2R2|Q8N9L6|Q96D62	Splice_Site	SNP	ENST00000353234.4	hg19	CCDS43856.1	.	.	.	.	.	.	.	.	.	.	T	19.54	3.846742	0.71603	.	.	ENSG00000165138	ENST00000375019;ENST00000375018;ENST00000353234;ENST00000540940	.	.	.	5.65	5.65	0.86999	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.2705	0.54704	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	ANKS6	100579559	1.000000	0.71417	0.985000	0.45067	0.986000	0.74619	5.633000	0.67825	2.139000	0.66308	0.533000	0.62120	.	.	.		0.483	ANKS6-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277053.1	NM_173551	Intron	A	101539738	T	A	101539738	5	1	360	1	0	0	0	0	0	0	1	0	692	1594	55	4	1081	4	ANKS6	9	101539738	Splice_Site	SNP	T	TCGA-XR-A8TF-01A-11D-A35Z-10	1433985	101539738	39673693	74	50375										
ZNF462	58499	hgsc.bcm.edu	37	chr9	109687122	109687122	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	gaccatgaatgctgcaagccGggagatacccaatactaccg	10	12	0	2			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr9:109687122G>A	ENST00000277225.5	+	3	1218	c.929G>A	c.(928-930)cGg>cAg	p.R310Q	ZNF462_ENST00000457913.1_Missense_Mutation_p.R310Q|ZNF462_ENST00000441147.2_5'Flank			Q96JM2	ZN462_HUMAN	zinc finger protein 462	310					chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						GCTGCAAGCCGGGAGATACCC	0.512																																					p.R310Q		Atlas-SNP	.											.	ZNF462	322	.	0			c.G929A						.						67	63	64					9																	109687122		2203	4300	6503	SO:0001583	missense	58499	exon3			CAAGCCGGGAGAT	AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"Zinc fingers, C2H2-type"	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.929G>A	chr9.hg19:g.109687122G>A	ENSP00000277225:p.Arg310Gln	177.0	0.0		160.0	36.0	NM_021224	Q5T0T4|Q8N408	Missense_Mutation	SNP	ENST00000277225.5	hg19	CCDS35096.1	.	.	.	.	.	.	.	.	.	.	G	15.70	2.910093	0.52439	.	.	ENSG00000148143	ENST00000277225;ENST00000457913	T;T	0.05996	3.36;3.81	5.91	4.84	0.62591	.	0.189972	0.52532	D	0.000075	T	0.04543	0.0124	N	0.24115	0.695	0.80722	D	1	P;B	0.35155	0.487;0.355	B;B	0.27608	0.081;0.037	T	0.53711	-0.8400	9	.	.	.	.	14.2337	0.65911	0.0803:0.0:0.9197:0.0	.	310;310	Q96JM2-3;Q96JM2	.;ZN462_HUMAN	Q	310	ENSP00000277225:R310Q;ENSP00000414570:R310Q	.	R	+	2	0	ZNF462	108726943	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.882000	0.48546	2.808000	0.96608	0.655000	0.94253	CGG	.	.		0.512	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224		A	109687122	G	A	109687122	3	1	360	1	0	0	0	0	1	0	0	0	17941	1116	39	1	935	1	ZNF462	9	109687122	Missense_Mutation	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10	8147384	109687122	31526309	75	50376										
COL5A1	1289	hgsc.bcm.edu	37	chr9	137658880	137658880	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	gcctggccccccaggacagcAgggtaatccaggcgcccagg	14	16	0	0			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr9:137658880A>T	ENST00000371817.3	+	23	2582	c.2168A>T	c.(2167-2169)cAg>cTg	p.Q723L		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	723	Triple-helical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		CCAGGACAGCAGGGTAATCCA	0.652																																					p.Q723L		Atlas-SNP	.											.	COL5A1	323	.	0			c.A2168T						.						35	38	37					9																	137658880		2203	4300	6503	SO:0001583	missense	1289	exon23			GACAGCAGGGTAA	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"Collagens"	2209	protein-coding gene	gene with protein product	"alpha 1 type V collagen"	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.2168A>T	chr9.hg19:g.137658880A>T	ENSP00000360882:p.Gln723Leu	159.0	0.0		118.0	35.0	NM_000093	Q15094|Q5SUX4	Missense_Mutation	SNP	ENST00000371817.3	hg19	CCDS6982.1	.	.	.	.	.	.	.	.	.	.	A	17.07	3.294232	0.60086	.	.	ENSG00000130635	ENST00000371817	D	0.95788	-3.81	5.18	5.18	0.71444	.	0.000000	0.64402	U	0.000001	D	0.95701	0.8602	L	0.54908	1.71	0.50467	D	0.99987	P	0.45126	0.851	P	0.55391	0.775	D	0.94991	0.8134	10	0.44086	T	0.13	.	11.3986	0.49858	1.0:0.0:0.0:0.0	.	723	P20908	CO5A1_HUMAN	L	723	ENSP00000360882:Q723L	ENSP00000360882:Q723L	Q	+	2	0	COL5A1	136798701	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.806000	0.62569	1.939000	0.56221	0.533000	0.62120	CAG	.	.		0.652	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093		T	137658880	A	T	137658880	3	4	360	1	0	0	0	0	1	0	0	0	3698	188	7	4	2258	4	COL5A1	9	137658880	Missense_Mutation	SNP	A	TCGA-XR-A8TF-01A-11D-A35Z-10	27971758	137658880	3554551	76	50377										
COBRA1	25920	hgsc.bcm.edu	37	chr9	140151494	140151494	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	agtccttcccccaagaccagGcgccagggcgaggtgagggg	16	13	0	2			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr9:140151494G>T	ENST00000343053.4	+	4	922	c.585G>T	c.(583-585)agG>agT	p.R195S		NM_015456.3	NP_056271.2	Q8WX92	NELFB_HUMAN	negative elongation factor complex member B	195					gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|NELF complex (GO:0032021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											CCAAGACCAGGCGCCAGGGCG	0.622																																					p.R195S		Atlas-SNP	.											.	.	.	.	0			c.G585T						.						55	53	54					9																	140151494		2203	4300	6503	SO:0001583	missense	25920	exon4			GACCAGGCGCCAG	AF464935	CCDS7040.1	9q34	2013-01-31	2013-01-31	2013-01-31	ENSG00000188986	ENSG00000188986			24324	protein-coding gene	gene with protein product		611180	"cofactor of BRCA1"	COBRA1		11230166, 10574461, 17910036, 17659869	Standard	NM_015456		Approved	KIAA1182, NELF-B	uc004cmm.4	Q8WX92	OTTHUMG00000131778	ENST00000343053.4:c.585G>T	chr9.hg19:g.140151494G>T	ENSP00000339495:p.Arg195Ser	49.0	0.0		37.0	21.0	NM_015456	A2BFA3|Q96EW5|Q9H9R4|Q9ULN8|Q9Y3W0	Missense_Mutation	SNP	ENST00000343053.4	hg19	CCDS7040.1	.	.	.	.	.	.	.	.	.	.	G	19.09	3.759794	0.69763	.	.	ENSG00000188986	ENST00000343053	.	.	.	5.2	0.0162	0.14107	.	0.000000	0.85682	D	0.000000	T	0.69993	0.3173	M	0.81942	2.565	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.66905	-0.5805	9	0.87932	D	0	-53.3232	5.3017	0.15781	0.44:0.0:0.4288:0.1312	.	195	Q8WX92	NELFB_HUMAN	S	195	.	ENSP00000339495:R195S	R	+	3	2	COBRA1	139271315	0.734000	0.28142	0.920000	0.36463	0.977000	0.68977	-0.073000	0.11468	-0.031000	0.13781	-0.258000	0.10820	AGG	.	.		0.622	NELFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254710.1	NM_015456		T	140151494	G	T	140151494	3	4	360	1	0	0	0	0	1	0	0	0	3657	1194	42	3	599	3	COBRA1	9	140151494	Missense_Mutation	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10	2492614	140151494	1061937	77	50378										
SFMBT2	57713	hgsc.bcm.edu	37	chr10	7409744	7409744	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	tagcgcagaagcagcagctgCccgcacgtggtaatgatcgt	13	11	0	2			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr10:7409744C>A	ENST00000361972.4	-	4	393	c.303G>T	c.(301-303)ggG>ggT	p.G101G	SFMBT2_ENST00000397160.3_Silent_p.G101G|SFMBT2_ENST00000397167.1_Silent_p.G101G|SFMBT2_ENST00000379711.2_Silent_p.G101G|SFMBT2_ENST00000379713.3_Silent_p.G101G	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	101					negative regulation of gene expression (GO:0010629)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	histone binding (GO:0042393)			NS(2)|breast(3)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(26)|lung(34)|ovary(5)|pancreas(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	99						GCAGCAGCTGCCCGCACGTGG	0.577																																					p.G101G		Atlas-SNP	.											.	SFMBT2	209	.	0			c.G303T						.						88	84	85					10																	7409744		2203	4300	6503	SO:0001819	synonymous_variant	57713	exon4			CAGCTGCCCGCAC	AB046837	CCDS31138.1	10p15.1	2013-01-10	2003-11-14		ENSG00000198879	ENSG00000198879		"Sterile alpha motif (SAM) domain containing"	20256	protein-coding gene	gene with protein product		615392	"Scm-related gene containing four mbt domains 2"			10997877	Standard	NM_001029880		Approved	KIAA1617	uc009xio.2	Q5VUG0	OTTHUMG00000017630	ENST00000361972.4:c.303G>T	chr10.hg19:g.7409744C>A		153.0	0.0		141.0	29.0	NM_001029880	A7MD09|Q9HCF5	Silent	SNP	ENST00000361972.4	hg19	CCDS31138.1																																																																																			.	.		0.577	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046673.1	NM_001029880		A	7409744	C	A	7409744	2	1	360	1	0	0	0	0	0	0	0	1	14173	726	26	3		3	SFMBT2	10	7409744	Silent	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10		7409744	128125003	78	50379										
SLC39A12	221074	hgsc.bcm.edu	37	chr10	18254573	18254573	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	tccccagactactttacagaAtatattttcagttccttgaa	4	10	1	3			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr10:18254573A>T	ENST00000377369.2	+	4	978	c.705A>T	c.(703-705)gaA>gaT	p.E235D	SLC39A12_ENST00000377374.4_Missense_Mutation_p.E235D|SLC39A12_ENST00000539911.1_Missense_Mutation_p.E101D|SLC39A12_ENST00000377371.3_Missense_Mutation_p.E235D	NM_001145195.1|NM_001282733.1|NM_001282734.1	NP_001138667.1|NP_001269662.1|NP_001269663.1	Q504Y0	S39AC_HUMAN	solute carrier family 39 (zinc transporter), member 12	235					regulation of microtubule polymerization (GO:0031113)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)|zinc ion transmembrane import (GO:0071578)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	zinc ion transmembrane transporter activity (GO:0005385)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(5)|lung(38)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	60						ACTTTACAGAATATATTTTCA	0.423																																					p.E235D		Atlas-SNP	.											.	SLC39A12	181	.	0			c.A705T						.						63	61	62					10																	18254573		2203	4300	6503	SO:0001583	missense	221074	exon4			TACAGAATATATT		CCDS7124.1, CCDS44362.1, CCDS60493.1, CCDS60494.1	10p12.33	2013-05-22			ENSG00000148482	ENSG00000148482		"Solute carriers"	20860	protein-coding gene	gene with protein product		608734	"solute carrier family 39 (metal ion transporter), member 12"			12659941	Standard	NM_152725		Approved	FLJ30499	uc001ipo.2	Q504Y0	OTTHUMG00000017759	ENST00000377369.2:c.705A>T	chr10.hg19:g.18254573A>T	ENSP00000366586:p.Glu235Asp	113.0	0.0		127.0	64.0	NM_152725	B7ZL35|C9JJL4|Q49AN8|Q4G0L3|Q5VWV8|Q5VWV9|Q6NZY5|Q96NN4	Missense_Mutation	SNP	ENST00000377369.2	hg19	CCDS44362.1	.	.	.	.	.	.	.	.	.	.	A	0.088	-1.171317	0.01660	.	.	ENSG00000148482	ENST00000377369;ENST00000377374;ENST00000377371;ENST00000539911;ENST00000425219	T;T;T;T	0.60171	0.36;0.32;0.36;0.21	5.81	-11.0	0.00169	.	0.402119	0.30347	N	0.009838	T	0.28665	0.0710	L	0.43152	1.355	0.21553	N	0.999647	B;B;B	0.13594	0.008;0.003;0.008	B;B;B	0.15052	0.012;0.005;0.012	T	0.51505	-0.8697	10	0.02654	T	1	-2.6034	4.8868	0.13706	0.3389:0.4168:0.1627:0.0817	.	235;235;235	Q504Y0-4;Q504Y0;Q504Y0-3	.;S39AC_HUMAN;.	D	235;235;235;101;155	ENSP00000366586:E235D;ENSP00000366591:E235D;ENSP00000366588:E235D;ENSP00000440445:E101D	ENSP00000366586:E235D	E	+	3	2	SLC39A12	18294579	0.061000	0.20836	0.014000	0.15608	0.169000	0.22640	-0.890000	0.04140	-1.849000	0.01171	-1.647000	0.00761	GAA	.	.		0.423	SLC39A12-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_152725		T	18254573	A	T	18254573	3	4	360	1	0	0	0	0	1	0	0	0	14630	98	4	4	715	4	SLC39A12	10	18254573	Missense_Mutation	SNP	A	TCGA-XR-A8TF-01A-11D-A35Z-10	10844829	18254573	117280174	79	50380										
ANKRD30A	91074	hgsc.bcm.edu	37	chr10	37507926	37507926	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	aggtttctcacactcatgaaAatgaaaattatctcttacat	4	8	3	2			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr10:37507926A>T	ENST00000602533.1	+	34	3217	c.3118A>T	c.(3118-3120)Aat>Tat	p.N1040Y	ANKRD30A_ENST00000361713.1_Missense_Mutation_p.N1040Y|ANKRD30A_ENST00000374660.1_Missense_Mutation_p.N1159Y			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	1096					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						CACTCATGAAAATGAAAATTA	0.318																																					p.N1040Y		Atlas-SNP	.											.	ANKRD30A	448	.	0			c.A3118T						.						29	27	28					10																	37507926		1790	4037	5827	SO:0001583	missense	91074	exon34			CATGAAAATGAAA	AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"Ankyrin repeat domain containing"	17234	protein-coding gene	gene with protein product	"breast cancer antigen NY-BR-1"	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.3118A>T	chr10.hg19:g.37507926A>T	ENSP00000473551:p.Asn1040Tyr	315.0	0.0		406.0	197.0	NM_052997	Q5W025	Missense_Mutation	SNP	ENST00000602533.1	hg19		.	.	.	.	.	.	.	.	.	.	a	6.191	0.403492	0.11754	.	.	ENSG00000148513	ENST00000361713;ENST00000374660	T;T	0.17691	2.26;2.26	2.07	0.878	0.19150	.	.	.	.	.	T	0.09862	0.0242	N	0.24115	0.695	0.18873	N	0.999988	P	0.44734	0.842	B	0.38378	0.272	T	0.19976	-1.0289	9	0.72032	D	0.01	.	5.1158	0.14833	0.8311:0.0:0.1689:0.0	.	1096	Q9BXX3	AN30A_HUMAN	Y	1040;1159	ENSP00000354432:N1040Y;ENSP00000363792:N1159Y	ENSP00000354432:N1040Y	N	+	1	0	ANKRD30A	37547932	0.998000	0.40836	0.007000	0.13788	0.010000	0.07245	2.586000	0.46119	0.094000	0.17404	0.381000	0.24937	AAT	.	.		0.318	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997		T	37507926	A	T	37507926	3	4	360	1	0	0	0	0	1	0	0	0	658	14	1	4	3252	4	ANKRD30A	10	37507926	Missense_Mutation	SNP	A	TCGA-XR-A8TF-01A-11D-A35Z-10	19253353	37507926	98026821	80	50381										
RTKN2	219790	hgsc.bcm.edu	37	chr10	63957897	63957897	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	agacgatgtctgagatacacTtgtttttccccagttgtcct	8	10	1	2			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr10:63957897T>A	ENST00000373789.3	-	12	1696	c.1600A>T	c.(1600-1602)Agt>Tgt	p.S534C	RTKN2_ENST00000315289.2_Intron|RTKN2_ENST00000395265.1_Intron	NM_145307.2	NP_660350.2	Q8IZC4	RTKN2_HUMAN	rhotekin 2	534					hemopoiesis (GO:0030097)|positive regulation of cell proliferation (GO:0008284)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Prostate(12;0.0297)|all_hematologic(501;0.215)					TGAGATACACTTGTTTTTCCC	0.423																																					p.S534C		Atlas-SNP	.											.	RTKN2	68	.	0			c.A1600T						.						266	249	255					10																	63957897		2203	4300	6503	SO:0001583	missense	219790	exon12			ATACACTTGTTTT	BC025765	CCDS7263.1, CCDS73140.1	10q21.3	2013-01-10	2007-12-14	2007-12-14	ENSG00000182010	ENSG00000182010		"Pleckstrin homology (PH) domain containing"	19364	protein-coding gene	gene with protein product			"pleckstrin homology domain containing, family K member 1"	PLEKHK1		15504364	Standard	NM_001282941		Approved	Em:AC024597.2, bA531F24.1, FLJ39352	uc001jlw.3	Q8IZC4	OTTHUMG00000018299	ENST00000373789.3:c.1600A>T	chr10.hg19:g.63957897T>A	ENSP00000362894:p.Ser534Cys	170.0	0.0		204.0	80.0	NM_145307	Q3ZCR1|Q68DZ6|Q8N8K1|Q8TAV2	Missense_Mutation	SNP	ENST00000373789.3	hg19	CCDS7263.1	.	.	.	.	.	.	.	.	.	.	T	9.099	1.003623	0.19121	.	.	ENSG00000182010	ENST00000373789	T	0.33654	1.4	5.61	-2.11	0.07187	.	0.716416	0.15065	N	0.282553	T	0.27313	0.0670	L	0.46157	1.445	0.09310	N	1	P	0.40660	0.726	B	0.40101	0.319	T	0.14671	-1.0464	10	0.54805	T	0.06	-0.3926	6.7969	0.23731	0.13:0.4623:0.0:0.4077	.	534	Q8IZC4	RTKN2_HUMAN	C	534	ENSP00000362894:S534C	ENSP00000362894:S534C	S	-	1	0	RTKN2	63627903	0.000000	0.05858	0.009000	0.14445	0.629000	0.37895	-0.113000	0.10774	-0.385000	0.07833	0.533000	0.62120	AGT	.	.		0.423	RTKN2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091618.1	NM_145307		A	63957897	T	A	63957897	3	1	360	1	0	0	0	0	1	0	0	0	13738	1609	56	4	233	4	RTKN2	10	63957897	Missense_Mutation	SNP	T	TCGA-XR-A8TF-01A-11D-A35Z-10	26449971	63957897	71576850	81	50382										
CPEB3	22849	hgsc.bcm.edu	37	chr10	93841114	93841114	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	tgtgctgaagctgcacaaaaCgagcgctgatggctgcaatg	13	9	0	2			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr10:93841114C>T	ENST00000265997.4	-	9	2004	c.1832G>A	c.(1831-1833)cGt>cAt	p.R611H	CPEB3_ENST00000412050.4_Missense_Mutation_p.R597H	NM_014912.4	NP_055727.3	Q8NE35	CPEB3_HUMAN	cytoplasmic polyadenylation element binding protein 3	611	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				3'-UTR-mediated mRNA destabilization (GO:0061158)|cellular response to amino acid stimulus (GO:0071230)|long-term memory (GO:0007616)|negative regulation of cytoplasmic translational elongation (GO:1900248)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translation (GO:0017148)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of mRNA polyadenylation (GO:1900365)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|regulation of dendritic spine development (GO:0060998)|regulation of synaptic plasticity (GO:0048167)|translation (GO:0006412)	apical dendrite (GO:0097440)|CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuron projection (GO:0043005)|nucleus (GO:0005634)|synapse (GO:0045202)	mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)|translation factor activity, nucleic acid binding (GO:0008135)|translation repressor activity, nucleic acid binding (GO:0000900)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.0869)				CTGCACAAAACGAGCGCTGAT	0.488																																					p.R611H		Atlas-SNP	.											.	CPEB3	43	.	0			c.G1832A						.						155	140	145					10																	93841114		2203	4300	6503	SO:0001583	missense	22849	exon9			ACAAAACGAGCGC	AB023157	CCDS31246.1, CCDS53553.1	10q23.33	2013-02-12			ENSG00000107864	ENSG00000107864		"RNA binding motif (RRM) containing"	21746	protein-coding gene	gene with protein product		610606				10231032, 12672660	Standard	NM_014912		Approved	KIAA0940	uc001khw.2	Q8NE35	OTTHUMG00000018756	ENST00000265997.4:c.1832G>A	chr10.hg19:g.93841114C>T	ENSP00000265997:p.Arg611His	98.0	0.0		118.0	6.0	NM_014912	Q5T389|Q9NQJ7|Q9Y2E9	Missense_Mutation	SNP	ENST00000265997.4	hg19	CCDS31246.1	.	.	.	.	.	.	.	.	.	.	C	36	5.630965	0.96682	.	.	ENSG00000107864	ENST00000394210;ENST00000412050;ENST00000265997	T;T	0.21734	1.99;1.99	5.81	5.81	0.92471	RNA recognition motif domain (2);	0.000000	0.85682	D	0.000000	T	0.44498	0.1296	L	0.50333	1.59	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.80764	0.982;0.987;0.994	T	0.18967	-1.0320	10	0.72032	D	0.01	-9.8615	20.0782	0.97758	0.0:1.0:0.0:0.0	.	611;597;597	Q8NE35;Q5QP71;Q8NE35-2	CPEB3_HUMAN;.;.	H	597;597;611	ENSP00000398310:R597H;ENSP00000265997:R611H	ENSP00000265997:R611H	R	-	2	0	CPEB3	93831094	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.818000	0.86416	2.746000	0.94184	0.655000	0.94253	CGT	.	.		0.488	CPEB3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049387.2	NM_014912		T	93841114	C	T	93841114	3	4	360	1	0	0	0	0	1	0	0	0	3804	536	19	1	272	1	CPEB3	10	93841114	Missense_Mutation	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10	29883217	93841114	41693633	82	50383										
PI4K2A	55361	hgsc.bcm.edu	37	chr10	99433469	99433492	+	In_Frame_Del	DEL	GAGCCGGAAGCCCTTCTTTTCATG	GAGCCGGAAGCCCTTCTTTTCATG	-													0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	tcctacacacagagctttcaGagccggaagcccttcttttc							TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	GAGCCGGAAGCCCTTCTTTTCATG	GAGCCGGAAGCCCTTCTTTTCATG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr10:99433469_99433492delGAGCCGGAAGCCCTTCTTTTCATG	ENST00000370631.3	+	9	1467_1490	c.1410_1433delGAGCCGGAAGCCCTTCTTTTCATG	c.(1408-1434)cagagccggaagcccttcttttcatgg>cag	p.SRKPFFSW471del	PI4K2A_ENST00000370649.3_In_Frame_Del_p.SRKPFFSW441del|PI4K2A_ENST00000555577.1_In_Frame_Del_p.SRKPFFSW441del	NM_018425.2	NP_060895.1	Q9BTU6	P4K2A_HUMAN	phosphatidylinositol 4-kinase type 2 alpha	471					basophil degranulation (GO:0002561)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|early endosome membrane (GO:0031901)|endosome (GO:0005768)|exocytic vesicle (GO:0070382)|Golgi apparatus (GO:0005794)|growing cell tip (GO:0035838)|host cell presynaptic membrane (GO:0044231)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|presynaptic membrane (GO:0042734)|protein complex (GO:0043234)|synaptic vesicle membrane (GO:0030672)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|AP-3 adaptor complex binding (GO:0035651)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)			endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(1)	12		Colorectal(252;0.162)		Epithelial(162;1.24e-10)|all cancers(201;1.2e-08)		AGAGCTTTCAGAGCCGGAAGCCCTTCTTTTCATGGTGGTAGCTC	0.58																																					p.470_478del		Atlas-INDEL	.											.	PI4K2A	57	.	0			c.1409_1432del						.																																			SO:0001651	inframe_deletion	55361	exon9			.	AF070611	CCDS7469.1	10q24	2011-02-09			ENSG00000155252	ENSG00000155252			30031	protein-coding gene	gene with protein product		609763				11244087, 11279162	Standard	NM_018425		Approved	PI4KII, DKFZP761G1923, PIK42A	uc001kog.1	Q9BTU6	OTTHUMG00000018863	ENST00000370631.3:c.1410_1433delGAGCCGGAAGCCCTTCTTTTCATG	chr10.hg19:g.99433469_99433492delGAGCCGGAAGCCCTTCTTTTCATG	ENSP00000359665:p.Ser471_Trp478del	66.0	0.0		83.0	16.0	NM_018425	D3DR59|Q9NSG8	In_Frame_Del	DEL	ENST00000370631.3	hg19	CCDS7469.1																																																																																			.	.		0.58	PI4K2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049735.1	NM_018425		-	99433492	GAGCCGGAAGCCCTTCTTTTCATG	-	99433469	7	5	360	1	0	1	0	1	0	0	0	0	11880	933	33	0	1444	0	PI4K2A	10	99433469	In_Frame_Del	DEL	GAGCCGGAAGCCCTTCTTTTCATG	TCGA-XR-A8TF-01A-11D-A35Z-10	5592355	99433469	36101278	83	50384										
CTSD	1509	hgsc.bcm.edu	37	chr11	1785050	1785050	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	cgcggaggcgggtgcagccaGcaggcagagggcgagcggca	21	11	0	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr11:1785050G>A	ENST00000236671.2	-	1	172	c.40C>T	c.(40-42)Ctg>Ttg	p.L14L	AC068580.1_ENST00000580120.1_RNA|AC068580.5_ENST00000446489.1_RNA|AC068580.6_ENST00000449248.1_RNA	NM_001909.4	NP_001900.1	P07339	CATD_HUMAN	cathepsin D	14					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|autophagic vacuole assembly (GO:0000045)|cell death (GO:0008219)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|mitochondrion (GO:0005739)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(1)|large_intestine(4)|lung(8)	13		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00136)|Lung(200;0.0684)|LUSC - Lung squamous cell carcinoma(625;0.0822)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	GGTGCAGCCAGCAGGCAGAGG	0.756																																					p.L14L		Atlas-SNP	.											.	CTSD	26	.	0			c.C40T						.						4	6	6					11																	1785050		1534	2828	4362	SO:0001819	synonymous_variant	1509	exon1			CAGCCAGCAGGCA	M11233	CCDS7725.1	11p15.5	2009-06-26	2006-12-05		ENSG00000117984	ENSG00000117984	3.4.23.5	"Cathepsins"	2529	protein-coding gene	gene with protein product	"ceroid-lipofuscinosis, neuronal 10"	116840	"cathepsin D (lysosomal aspartyl protease)"	CPSD		3927292	Standard	NM_001909		Approved	CLN10	uc001luc.2	P07339	OTTHUMG00000044760	ENST00000236671.2:c.40C>T	chr11.hg19:g.1785050G>A		82.0	0.0		60.0	42.0	NM_001909	Q6IB57	Silent	SNP	ENST00000236671.2	hg19	CCDS7725.1																																																																																			.	.		0.756	CTSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104272.5	NM_001909		A	1785050	G	A	1785050	2	1	360	1	0	0	0	0	0	0	0	1	4034	962	34	3		3	CTSD	11	1785050	Silent	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10		1785050	133221466	84	50385										
OSBPL5	114879	hgsc.bcm.edu	37	chr11	3113775	3113775	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	ggcgatgtccttcagggggtCccaggggctgtggctggagg	20	9	1	0			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr11:3113775C>A	ENST00000263650.7	-	19	2305	c.2146G>T	c.(2146-2148)Gac>Tac	p.D716Y	OSBPL5_ENST00000348039.5_Missense_Mutation_p.D648Y|OSBPL5_ENST00000542243.1_Missense_Mutation_p.D347Y|OSBPL5_ENST00000478260.1_Missense_Mutation_p.D170Y|OSBPL5_ENST00000389989.3_Missense_Mutation_p.D648Y|OSBPL5_ENST00000525498.1_Missense_Mutation_p.D627Y	NM_020896.3	NP_065947.1	Q9H0X9	OSBL5_HUMAN	oxysterol binding protein-like 5	716					cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|Golgi to plasma membrane transport (GO:0006893)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	cholesterol binding (GO:0015485)|oxysterol binding (GO:0008142)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	25		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)		TTCAGGGGGTCCCAGGGGCTG	0.677																																					p.D716Y		Atlas-SNP	.											.	OSBPL5	78	.	0			c.G2146T						.						23	20	21					11																	3113775		2194	4289	6483	SO:0001583	missense	114879	exon19			GGGGGTCCCAGGG	AF392453	CCDS31343.1, CCDS31344.1	11p15.4	2013-01-10			ENSG00000021762	ENSG00000021762		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16392	protein-coding gene	gene with protein product		606733					Standard	NM_145638		Approved	KIAA1534, ORP5	uc001lxk.2	Q9H0X9	OTTHUMG00000011702	ENST00000263650.7:c.2146G>T	chr11.hg19:g.3113775C>A	ENSP00000263650:p.Asp716Tyr	106.0	0.0		79.0	27.0	NM_020896	A6NDP0|A6NJS8|Q54A90|Q8N596|Q9BZB0|Q9P1Z4	Missense_Mutation	SNP	ENST00000263650.7	hg19	CCDS31344.1	.	.	.	.	.	.	.	.	.	.	C	19.96	3.922762	0.73213	.	.	ENSG00000021762	ENST00000478260;ENST00000263650;ENST00000389989;ENST00000534454;ENST00000525498;ENST00000542243;ENST00000348039;ENST00000357352	T;T;T;T;T;T;T	0.33216	1.42;1.42;1.42;1.42;1.42;1.42;1.42	4.47	2.59	0.31030	.	0.064974	0.64402	D	0.000013	T	0.61413	0.2345	M	0.93283	3.4	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.65315	-0.6198	10	0.87932	D	0	-13.9727	9.4578	0.38764	0.0:0.8223:0.0:0.1777	.	627;648;716	B4DVB0;Q8N596;Q9H0X9	.;.;OSBL5_HUMAN	Y	170;716;648;269;627;347;648;335	ENSP00000437141:D170Y;ENSP00000263650:D716Y;ENSP00000374639:D648Y;ENSP00000431412:D269Y;ENSP00000433342:D627Y;ENSP00000441551:D347Y;ENSP00000302872:D648Y	ENSP00000263650:D716Y	D	-	1	0	OSBPL5	3070351	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	3.900000	0.56295	0.361000	0.24292	0.561000	0.74099	GAC	.	.		0.677	OSBPL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032332.2			A	3113775	C	A	3113775	3	1	360	1	0	0	0	0	1	0	0	0	11289	855	30	3	509	3	OSBPL5	11	3113775	Missense_Mutation	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10	1328725	3113775	131892741	85	50386										
SLC17A6	57084	hgsc.bcm.edu	37	chr11	22396318	22396318	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	caggttggtatgctatctgcTgtgccacacttagtaatgac	10	9	1	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr11:22396318T>A	ENST00000263160.3	+	9	1496	c.1059T>A	c.(1057-1059)gcT>gcA	p.A353A		NM_020346.2	NP_065079.1	Q9P2U8	VGLU2_HUMAN	solute carrier family 17 (vesicular glutamate transporter), member 6	353					ion transport (GO:0006811)|neurotransmitter uptake (GO:0001504)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|synaptic vesicle membrane (GO:0030672)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(28)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)	50						TGCTATCTGCTGTGCCACACT	0.373																																					p.A353A		Atlas-SNP	.											.	SLC17A6	135	.	0			c.T1059A						.						233	226	229					11																	22396318		2203	4300	6503	SO:0001819	synonymous_variant	57084	exon9			ATCTGCTGTGCCA	AB032435	CCDS7856.1	11p14.3	2013-07-18	2013-07-18		ENSG00000091664	ENSG00000091664		"Solute carriers"	16703	protein-coding gene	gene with protein product	"vesicular glutamate transporter 2", "differentiation-associated Na-dependent inorganic phosphate cotransporter"	607563	"solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6"			11306821	Standard	NM_020346		Approved	DNPI, VGLUT2	uc001mqk.3	Q9P2U8	OTTHUMG00000166063	ENST00000263160.3:c.1059T>A	chr11.hg19:g.22396318T>A		94.0	0.0		79.0	44.0	NM_020346	A6NKS2	Silent	SNP	ENST00000263160.3	hg19	CCDS7856.1																																																																																			.	.		0.373	SLC17A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387671.1	NM_020346		A	22396318	T	A	22396318	2	1	360	1	0	0	0	0	0	0	0	1	14436	1567	55	4		4	SLC17A6	11	22396318	Silent	SNP	T	TCGA-XR-A8TF-01A-11D-A35Z-10	19282543	22396318	112610198	86	50387										
OR4A47	403253	hgsc.bcm.edu	37	chr11	48510756	48510757	+	Frame_Shift_Del	DEL	GT	GT	-													0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	tggttatcatgagacaatggGtgtgtgttgtgctgctggta							TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	GT	GT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr11:48510756_48510757delGT	ENST00000446524.1	+	1	488_489	c.412_413delGT	c.(412-414)gtgfs	p.V138fs		NM_001005512.2	NP_001005512.2	Q6IF82	O4A47_HUMAN	olfactory receptor, family 4, subfamily A, member 47	138						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(18)|ovary(1)|skin(1)|urinary_tract(2)	29						GAGACAATGGGTGTGTGTTGTG	0.475																																					p.137_138del		Atlas-INDEL	.											.	OR4A47	72	.	0			c.411_412del						.																																			SO:0001589	frameshift_variant	403253	exon1			.	BK004380	CCDS31490.1	11p11.2	2012-08-09			ENSG00000237388	ENSG00000237388		"GPCR / Class A : Olfactory receptors"	31266	protein-coding gene	gene with protein product							Standard	NM_001005512		Approved		uc010rhx.2	Q6IF82	OTTHUMG00000166581	ENST00000446524.1:c.412_413delGT	chr11.hg19:g.48510762_48510763delGT	ENSP00000412752:p.Val138fs	74.0	0.0		88.0	23.0	NM_001005512		Frame_Shift_Del	DEL	ENST00000446524.1	hg19	CCDS31490.1																																																																																			.	.		0.475	OR4A47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390559.1	NM_001005512		-	48510757	GT	-	48510756	7	5	360	1	0	1	0	1	0	0	0	0	11051	1261	44	0	414	0	OR4A47	11	48510756	Frame_Shift_Del	DEL	GT	TCGA-XR-A8TF-01A-11D-A35Z-10	26114438	48510756	86495760	87	50388										
MMP8	4317	hgsc.bcm.edu	37	chr11	102595576	102595576	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	gcagaaatggaagcgtcttcAgggagaacatgatcttctct	11	8	4	3			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr11:102595576A>T	ENST00000236826.3	-	1	109	c.11T>A	c.(10-12)cTg>cAg	p.L4Q		NM_002424.2	NP_002415.1	P22894	MMP8_HUMAN	matrix metallopeptidase 8 (neutrophil collagenase)	4					collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(4)|skin(6)|stomach(1)|urinary_tract(1)	32	all_cancers(8;0.00092)|all_epithelial(12;0.00389)|Lung NSC(15;0.227)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0555)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.189)	BRCA - Breast invasive adenocarcinoma(274;0.0141)	Marimastat(DB00786)	AAGCGTCTTCAGGGAGAACAT	0.468																																					p.L4Q		Atlas-SNP	.											.	MMP8	68	.	0			c.T11A						.						150	157	155					11																	102595576		2203	4299	6502	SO:0001583	missense	4317	exon1			GTCTTCAGGGAGA	J05556	CCDS8320.1	11q21-q22	2008-02-05	2005-08-08		ENSG00000118113	ENSG00000118113	3.4.24.34		7175	protein-coding gene	gene with protein product		120355	"matrix metalloproteinase 8 (neutrophil collagenase)"	CLG1			Standard	NM_002424		Approved		uc001phe.2	P22894	OTTHUMG00000167587	ENST00000236826.3:c.11T>A	chr11.hg19:g.102595576A>T	ENSP00000236826:p.Leu4Gln	314.0	1.0		278.0	95.0	NM_002424	Q45F99	Missense_Mutation	SNP	ENST00000236826.3	hg19	CCDS8320.1	.	.	.	.	.	.	.	.	.	.	A	11.61	1.689556	0.29962	.	.	ENSG00000118113	ENST00000236826	T	0.15256	2.44	5.26	2.79	0.32731	.	5.107090	0.00357	N	0.000034	T	0.22781	0.0550	L	0.43152	1.355	0.09310	N	0.999996	D	0.54207	0.965	P	0.47402	0.546	T	0.12116	-1.0560	10	0.87932	D	0	.	5.6196	0.17450	0.7634:0.0:0.0859:0.1507	.	4	P22894	MMP8_HUMAN	Q	4	ENSP00000236826:L4Q	ENSP00000236826:L4Q	L	-	2	0	MMP8	102100786	0.749000	0.28305	0.019000	0.16419	0.003000	0.03518	2.291000	0.43540	0.944000	0.37579	0.533000	0.62120	CTG	.	.		0.468	MMP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395223.1	NM_002424		T	102595576	A	T	102595576	3	4	360	1	0	0	0	0	1	0	0	0	9677	188	7	4	1432	4	MMP8	11	102595576	Missense_Mutation	SNP	A	TCGA-XR-A8TF-01A-11D-A35Z-10	54084820	102595576	32410940	88	50389										
ARHGAP20	57569	hgsc.bcm.edu	37	chr11	110450147	110450147	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	gtcgcagaccactgtaggccCtgagtctgggctggtcgcat	14	12	1	2			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr11:110450147C>G	ENST00000260283.4	-	16	3807	c.3523G>C	c.(3523-3525)Ggg>Cgg	p.G1175R	ARHGAP20_ENST00000533353.1_Missense_Mutation_p.G1149R|ARHGAP20_ENST00000524756.1_Missense_Mutation_p.G1152R|ARHGAP20_ENST00000357139.3_Missense_Mutation_p.G1149R|ARHGAP20_ENST00000529591.1_Missense_Mutation_p.G718R|ARHGAP20_ENST00000527598.1_Missense_Mutation_p.G1139R|ARHGAP20_ENST00000528829.1_Missense_Mutation_p.G1139R	NM_020809.3	NP_065860.2	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20	1175					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(18)|lung(13)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	60		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;3.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|all cancers(92;0.000147)|OV - Ovarian serous cystadenocarcinoma(223;0.0475)		ACTGTAGGCCCTGAGTCTGGG	0.483																																					p.G1175R		Atlas-SNP	.											.	ARHGAP20	150	.	0			c.G3523C						.						125	130	128					11																	110450147		2201	4298	6499	SO:0001583	missense	57569	exon16			TAGGCCCTGAGTC	AB037812	CCDS31673.1, CCDS58175.1, CCDS58176.1, CCDS58177.1	11q23.2	2011-06-29			ENSG00000137727	ENSG00000137727		"Rho GTPase activating proteins"	18357	protein-coding gene	gene with protein product		609568				14532992	Standard	NM_020809		Approved	KIAA1391	uc001pkz.2	Q9P2F6	OTTHUMG00000166590	ENST00000260283.4:c.3523G>C	chr11.hg19:g.110450147C>G	ENSP00000260283:p.Gly1175Arg	94.0	0.0		97.0	49.0	NM_020809	A8K8C5|B0YIW7|B0YIW8|Q6RJU1|Q6RJU2|Q6RJU3|Q6RJU5|Q8IXS1	Missense_Mutation	SNP	ENST00000260283.4	hg19	CCDS31673.1	.	.	.	.	.	.	.	.	.	.	C	6.888	0.533390	0.13188	.	.	ENSG00000137727	ENST00000260283;ENST00000357139;ENST00000529591;ENST00000524756;ENST00000528829;ENST00000533353;ENST00000527598	T;T;T;T;T;T;T	0.09350	2.99;2.99;3.03;2.99;2.99;2.99;2.99	5.62	3.73	0.42828	.	0.544729	0.16797	N	0.199152	T	0.11750	0.0286	L	0.54323	1.7	0.09310	N	1	B;B;B	0.15473	0.013;0.008;0.013	B;B;B	0.17433	0.018;0.007;0.015	T	0.14062	-1.0486	10	0.38643	T	0.18	.	9.4276	0.38590	0.0:0.8322:0.0:0.1677	.	1149;1175;1152	Q9P2F6-2;Q9P2F6;Q9P2F6-3	.;RHG20_HUMAN;.	R	1175;1149;718;1152;1139;1149;1139	ENSP00000260283:G1175R;ENSP00000349660:G1149R;ENSP00000437905:G718R;ENSP00000432076:G1152R;ENSP00000436319:G1139R;ENSP00000436522:G1149R;ENSP00000431399:G1139R	ENSP00000260283:G1175R	G	-	1	0	ARHGAP20	109955357	0.018000	0.18449	0.003000	0.11579	0.067000	0.16453	2.358000	0.44134	1.341000	0.45600	0.655000	0.94253	GGG	.	.		0.483	ARHGAP20-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390628.1	NM_020809		G	110450147	C	G	110450147	3	3	360	1	0	0	0	0	1	0	0	0	870	681	24	4	56	4	ARHGAP20	11	110450147	Missense_Mutation	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10	7854571	110450147	24556369	89	50390										
STT3A	3703	hgsc.bcm.edu	37	chr11	125472792	125472792	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	tgtgtgttcctggcccctctCttctcctccttcaccaccat	5	18	3	0			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr11:125472792C>T	ENST00000529196.1	+	6	572	c.366C>T	c.(364-366)ctC>ctT	p.L122L	STT3A_ENST00000531491.1_Silent_p.L30L|STT3A_ENST00000392708.4_Silent_p.L122L			P46977	STT3A_HUMAN	STT3A, subunit of the oligosaccharyltransferase complex (catalytic)	122					cellular protein metabolic process (GO:0044267)|co-translational protein modification (GO:0043686)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			NS(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	33	all_hematologic(175;0.228)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0919)|all_lung(97;0.0994)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0996)		TGGCCCCTCTCTTCTCCTCCT	0.478																																					p.L122L		Atlas-SNP	.											.	STT3A	52	.	0			c.C366T						.						219	178	192					11																	125472792		2201	4299	6500	SO:0001819	synonymous_variant	3703	exon5			CCCTCTCTTCTCC	BC020965	CCDS8458.1, CCDS60998.1	11q23.3	2013-03-06	2013-03-06	2006-02-07	ENSG00000134910	ENSG00000134910	2.4.99.18		6172	protein-coding gene	gene with protein product	"dolichyl-diphosphooligosaccharide protein glycotransferase"	601134	"integral membrane protein 1", "STT3, subunit of the oligosaccharyltransferase complex, homolog A (S. cerevisiae)", "STT3A, cataylic subunit of the oligosaccharyltransferase complex"	ITM1		8941377, 8634329, 10234787	Standard	NM_152713		Approved	TMC, MGC9042, STT3-A	uc001qcd.2	P46977	OTTHUMG00000165852	ENST00000529196.1:c.366C>T	chr11.hg19:g.125472792C>T		135.0	0.0		143.0	31.0	NM_152713	B4DJ24|E9PNQ1|Q86XU9|Q8TE35|Q8WUB4	Silent	SNP	ENST00000529196.1	hg19	CCDS8458.1																																																																																			.	.		0.478	STT3A-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386691.1	NM_152713		T	125472792	C	T	125472792	2	4	360	1	0	0	0	0	0	0	0	1	15348	900	32	3		3	STT3A	11	125472792	Silent	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10	15022645	125472792	9533724	90	50391										
KCNA6	3742	hgsc.bcm.edu	37	chr12	4920532	4920532	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	aaagatcgtgggctcgctgtGtgccatcgctggggtcctca	14	11	1	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr12:4920532G>T	ENST00000280684.3	+	1	2191	c.1325G>T	c.(1324-1326)tGt>tTt	p.C442F	RP11-234B24.4_ENST00000542988.1_lincRNA|KCNA6_ENST00000433855.1_Missense_Mutation_p.C442F			P17658	KCNA6_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 6	442					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(3)|endometrium(5)|large_intestine(6)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(5)	49					Dalfampridine(DB06637)	GGCTCGCTGTGTGCCATCGCT	0.597										HNSCC(72;0.22)																											p.C442F		Atlas-SNP	.											.	KCNA6	122	.	0			c.G1325T						.						150	129	136					12																	4920532		2203	4300	6503	SO:0001583	missense	3742	exon1			CGCTGTGTGCCAT	X17622	CCDS8534.1	12p13	2014-06-12						"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6225	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 96"	176257				16382104	Standard	NM_002235		Approved	Kv1.6, HBK2, PPP1R96	uc001qng.3	P17658		ENST00000280684.3:c.1325G>T	chr12.hg19:g.4920532G>T	ENSP00000280684:p.Cys442Phe	121.0	0.0		154.0	40.0	NM_002235		Missense_Mutation	SNP	ENST00000280684.3	hg19	CCDS8534.1	.	.	.	.	.	.	.	.	.	.	G	19.91	3.915152	0.73098	.	.	ENSG00000151079	ENST00000433855;ENST00000280684	D;D	0.98264	-4.83;-4.83	5.18	5.18	0.71444	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99089	0.9687	M	0.88640	2.97	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99581	1.0973	10	0.87932	D	0	.	17.8587	0.88775	0.0:0.0:1.0:0.0	.	442	P17658	KCNA6_HUMAN	F	442	ENSP00000408321:C442F;ENSP00000280684:C442F	ENSP00000280684:C442F	C	+	2	0	KCNA6	4790793	1.000000	0.71417	0.967000	0.41034	0.950000	0.60333	9.565000	0.98154	2.688000	0.91661	0.655000	0.94253	TGT	.	.		0.597	KCNA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398909.1	NM_002235		T	4920532	G	T	4920532	3	4	360	1	0	0	0	0	1	0	0	0	8016	1377	48	3	1327	3	KCNA6	12	4920532	Missense_Mutation	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10		4920532	128931363	91	50392										
NCAPD2	9918	hgsc.bcm.edu	37	chr12	6635520	6635520	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	caggttgtttgagcgactgcGggagacagtcacaaaaggtg	15	7	1	2			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr12:6635520G>A	ENST00000315579.5	+	20	3348	c.2549G>A	c.(2548-2550)cGg>cAg	p.R850Q	NCAPD2_ENST00000542492.1_3'UTR|NCAPD2_ENST00000545962.1_Missense_Mutation_p.R805Q	NM_014865.3	NP_055680.3	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	850					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|condensin core heterodimer (GO:0000797)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|pronucleus (GO:0045120)	histone binding (GO:0042393)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	48						GAGCGACTGCGGGAGACAGTC	0.562																																					p.R850Q		Atlas-SNP	.											.	NCAPD2	99	.	0			c.G2549A						.						78	77	77					12																	6635520		2203	4300	6503	SO:0001583	missense	9918	exon20			GACTGCGGGAGAC	D63880	CCDS8548.1	12p13.31	2008-02-04			ENSG00000010292	ENSG00000010292			24305	protein-coding gene	gene with protein product	"chromosome condensation related SMC associated protein 1"	615638				8590280, 10958694	Standard	NM_014865		Approved	CNAP1, hCAP-D2, CAP-D2, KIAA0159	uc001qoo.2	Q15021	OTTHUMG00000168513	ENST00000315579.5:c.2549G>A	chr12.hg19:g.6635520G>A	ENSP00000325017:p.Arg850Gln	120.0	0.0		119.0	20.0	NM_014865	D3DUR4|Q8N6U3	Missense_Mutation	SNP	ENST00000315579.5	hg19	CCDS8548.1	.	.	.	.	.	.	.	.	.	.	G	5.659	0.306235	0.10733	.	.	ENSG00000010292	ENST00000315579;ENST00000382457;ENST00000545962;ENST00000535602	T;T;T	0.43688	0.94;0.94;0.94	5.39	-10.8	0.00216	Armadillo-type fold (1);	0.982473	0.08360	N	0.957858	T	0.18087	0.0434	N	0.11560	0.145	0.09310	N	1	B;B;B	0.15141	0.012;0.0;0.001	B;B;B	0.09377	0.004;0.002;0.002	T	0.36866	-0.9730	10	0.11485	T	0.65	-0.5211	14.6822	0.69026	0.7242:0.0834:0.1924:0.0	.	805;811;850	F5GZJ1;B3KY03;Q15021	.;.;CND1_HUMAN	Q	850;722;805;722	ENSP00000325017:R850Q;ENSP00000371895:R722Q;ENSP00000444417:R805Q	ENSP00000325017:R850Q	R	+	2	0	NCAPD2	6505781	0.000000	0.05858	0.000000	0.03702	0.341000	0.28922	-1.492000	0.02300	-2.524000	0.00495	-0.982000	0.02568	CGG	.	.		0.562	NCAPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399964.1	NM_014865		A	6635520	G	A	6635520	3	1	360	1	0	0	0	0	1	0	0	0	10214	1116	39	1	2623	1	NCAPD2	12	6635520	Missense_Mutation	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10	1714988	6635520	127216375	92	50393										
A2ML1	144568	hgsc.bcm.edu	37	chr12	9027081	9027081	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	aaagtgtgctggtcaccaacTtgaaaccagcaaccatcaag	8	11	2	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr12:9027081T>A	ENST00000299698.7	+	34	4462	c.4282T>A	c.(4282-4284)Ttg>Atg	p.L1428M	A2ML1_ENST00000539547.1_Missense_Mutation_p.L937M	NM_001282424.1|NM_144670.4	NP_001269353.1|NP_653271			alpha-2-macroglobulin-like 1											NS(2)|breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(2)|lung(36)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	80						GGTCACCAACTTGAAACCAGC	0.448																																					p.L1428M		Atlas-SNP	.											.	A2ML1	199	.	0			c.T4282A						.						138	134	135					12																	9027081		2015	4167	6182	SO:0001583	missense	144568	exon34			ACCAACTTGAAAC	AK057908	CCDS8596.2, CCDS73439.1	12p13	2010-12-14	2005-09-01	2005-09-01	ENSG00000166535	ENSG00000166535			23336	protein-coding gene	gene with protein product		610627	"C3 and PZP-like, alpha-2-macroglobulin domain containing 9"	CPAMD9		16298998	Standard	NM_144670		Approved	FLJ25179	uc001quz.5	A8K2U0	OTTHUMG00000128499	ENST00000299698.7:c.4282T>A	chr12.hg19:g.9027081T>A	ENSP00000299698:p.Leu1428Met	85.0	0.0		85.0	34.0	NM_144670		Missense_Mutation	SNP	ENST00000299698.7	hg19	CCDS8596.2	.	.	.	.	.	.	.	.	.	.	t	16.25	3.069744	0.55539	.	.	ENSG00000166535	ENST00000299698;ENST00000539161;ENST00000541459;ENST00000539547	T;T;T	0.25749	1.78;1.78;1.78	3.32	-2.08	0.07254	Alpha-macroglobulin, receptor-binding (3);	0.000000	0.35708	N	0.003021	T	0.44623	0.1302	M	0.78049	2.395	0.26427	N	0.976002	D	0.89917	1.0	D	0.87578	0.998	T	0.33854	-0.9852	10	0.72032	D	0.01	.	9.3268	0.37997	0.0:0.5694:0.0:0.4306	.	1428	A8K2U0	A2ML1_HUMAN	M	1428;1428;978;937	ENSP00000299698:L1428M;ENSP00000443174:L978M;ENSP00000438292:L937M	ENSP00000299698:L1428M	L	+	1	2	A2ML1	8918348	0.214000	0.23563	0.976000	0.42696	0.973000	0.67179	0.120000	0.15647	-0.482000	0.06782	-1.008000	0.02478	TTG	.	.		0.448	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250304.3	NM_144670		A	9027081	T	A	9027081	3	1	360	1	0	0	0	0	1	0	0	0	5	1606	56	4	4416	4	A2ML1	12	9027081	Missense_Mutation	SNP	T	TCGA-XR-A8TF-01A-11D-A35Z-10	2391561	9027081	124824814	93	50394										
C12orf12	196477	hgsc.bcm.edu	37	chr12	91348095	91348095	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	cgcggcctctgcggccccagCgcttcttcctgcctgggggc	14	18	2	0			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr12:91348095C>T	ENST00000358859.2	-	1	858	c.425G>A	c.(424-426)cGc>cAc	p.R142H	CCER1_ENST00000548187.1_Intron	NM_152638.2	NP_689851.1	Q8TC90	CCER1_HUMAN	coiled-coil glutamate-rich protein 1	142																	GCGGCCCCAGCGCTTCTTCCT	0.701																																					p.R142H		Atlas-SNP	.											C12orf12,NS,carcinoma,0,1	.	.	.	0			c.G425A						.						14	17	16					12																	91348095		2198	4287	6485	SO:0001583	missense	196477	exon1			CCCCAGCGCTTCT	BC024183	CCDS9036.1	12q21.33	2012-05-30	2012-05-30	2012-05-30	ENSG00000197651	ENSG00000197651			28373	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 12"	C12orf12		17967063	Standard	NM_152638		Approved	MGC26598	uc001tbj.3	Q8TC90	OTTHUMG00000170070	ENST00000358859.2:c.425G>A	chr12.hg19:g.91348095C>T	ENSP00000351727:p.Arg142His	34.0	0.0		30.0	13.0	NM_152638	Q8TC47	Missense_Mutation	SNP	ENST00000358859.2	hg19	CCDS9036.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.173783	0.78452	.	.	ENSG00000197651	ENST00000358859	T	0.39997	1.05	4.62	3.73	0.42828	.	0.000000	0.33023	N	0.005378	T	0.29288	0.0729	L	0.29908	0.895	0.31812	N	0.627021	P	0.44877	0.845	B	0.39027	0.288	T	0.38802	-0.9644	10	0.52906	T	0.07	-13.9974	10.0901	0.42443	0.0:0.9055:0.0:0.0945	.	142	Q8TC90	CL012_HUMAN	H	142	ENSP00000351727:R142H	ENSP00000351727:R142H	R	-	2	0	C12orf12	89872226	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	2.434000	0.44802	1.152000	0.42452	0.462000	0.41574	CGC	.	.		0.701	CCER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407142.2	NM_152638		T	91348095	C	T	91348095	3	4	360	1	0	0	0	0	1	0	0	0	1678	768	27	1	799	1	C12orf12	12	91348095	Missense_Mutation	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10	82321014	91348095	42503800	94	50395										
NUP37	79023	hgsc.bcm.edu	37	chr12	102512142	102512142	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	tgcagttttgtagactaaccTgaaacgtacacgtgccaatg	9	9	0	2			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr12:102512142T>A	ENST00000552283.1	-	2	294	c.155A>T	c.(154-156)cAg>cTg	p.Q52L	PARPBP_ENST00000541394.1_5'Flank|NUP37_ENST00000251074.1_Splice_Site_p.Q52L|PARPBP_ENST00000358383.5_5'Flank|PARPBP_ENST00000392911.2_5'Flank|PARPBP_ENST00000543784.1_5'Flank|PARPBP_ENST00000378128.3_5'Flank|PARPBP_ENST00000327680.2_5'Flank|PARPBP_ENST00000537257.1_5'Flank|NUP37_ENST00000543021.1_5'UTR			Q8NFH4	NUP37_HUMAN	nucleoporin 37kDa	52					carbohydrate metabolic process (GO:0005975)|chromosome segregation (GO:0007059)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)|nucleus (GO:0005634)				endometrium(3)|large_intestine(3)|lung(10)|ovary(1)	17						TAGACTAACCTGAAACGTACA	0.368																																					p.Q52L		Atlas-SNP	.											.	NUP37	26	.	0			c.A155T						.						205	185	192					12																	102512142		2203	4300	6503	SO:0001630	splice_region_variant	79023	exon1			CTAACCTGAAACG	AF514994	CCDS9089.1	12q23.2	2014-08-12			ENSG00000075188	ENSG00000075188		"WD repeat domain containing"	29929	protein-coding gene	gene with protein product		609264				12196509	Standard	NM_024057		Approved	MGC5585, FLJ22618	uc001tjc.3	Q8NFH4	OTTHUMG00000170478	ENST00000552283.1:c.156+1A>T	chr12.hg19:g.102512142T>A		117.0	0.0		153.0	53.0	NM_024057	Q9H644	Missense_Mutation	SNP	ENST00000552283.1	hg19	CCDS9089.1	.	.	.	.	.	.	.	.	.	.	T	19.00	3.742024	0.69418	.	.	ENSG00000075188	ENST00000552283;ENST00000251074;ENST00000551744	T;T;T	0.69685	-0.42;-0.42;2.85	5.55	5.55	0.83447	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.050915	0.85682	D	0.000000	T	0.66228	0.2768	M	0.73598	2.24	0.80722	D	1	P;P	0.40144	0.704;0.651	B;B	0.36922	0.236;0.198	T	0.66818	-0.5827	10	0.27785	T	0.31	-8.1022	15.6948	0.77488	0.0:0.0:0.0:1.0	.	52;52	B4DKV8;Q8NFH4	.;NUP37_HUMAN	L	52	ENSP00000448054:Q52L;ENSP00000251074:Q52L;ENSP00000448086:Q52L	ENSP00000251074:Q52L	Q	-	2	0	NUP37	101036272	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.185000	0.77714	2.109000	0.64355	0.528000	0.53228	CAG	.	.		0.368	NUP37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409330.1	NM_024057	Missense_Mutation	A	102512142	T	A	102512142	5	1	360	1	0	0	0	0	0	0	1	0	10773	1594	55	4	861	4	NUP37	12	102512142	Splice_Site	SNP	T	TCGA-XR-A8TF-01A-11D-A35Z-10	11164047	102512142	31339753	95	50396										
ANKRD13A	88455	hgsc.bcm.edu	37	chr12	110456257	110456257	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	gatttgaaaacatgagctggAtaagagggaggcgtagtttt	14	3	0	3			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr12:110456257A>G	ENST00000261739.4	+	5	674	c.508A>G	c.(508-510)Ata>Gta	p.I170V	ANKRD13A_ENST00000550404.1_3'UTR	NM_033121.1	NP_149112.1	Q8IZ07	AN13A_HUMAN	ankyrin repeat domain 13A	170						endosome (GO:0005768)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(8)|lung(3)|urinary_tract(1)	16						CATGAGCTGGATAAGAGGGAG	0.418																																					p.I170V		Atlas-SNP	.											.	ANKRD13A	39	.	0			c.A508G						.						138	138	138					12																	110456257		2203	4300	6503	SO:0001583	missense	88455	exon5			AGCTGGATAAGAG	AF064604	CCDS9140.1	12q24.12	2013-01-10	2006-06-30	2006-06-30		ENSG00000076513		"Ankyrin repeat domain containing"	21268	protein-coding gene	gene with protein product		615123	"ankyrin repeat domain 13"	ANKRD13		10508479	Standard	NM_033121		Approved	NY-REN-25	uc001tpx.3	Q8IZ07	OTTHUMG00000169314	ENST00000261739.4:c.508A>G	chr12.hg19:g.110456257A>G	ENSP00000261739:p.Ile170Val	222.0	0.0		251.0	105.0	NM_033121	O60736	Missense_Mutation	SNP	ENST00000261739.4	hg19	CCDS9140.1	.	.	.	.	.	.	.	.	.	.	A	12.08	1.830347	0.32329	.	.	ENSG00000076513	ENST00000261739	T	0.41758	0.99	5.63	4.49	0.54785	.	0.135399	0.64402	N	0.000004	T	0.33990	0.0882	N	0.21448	0.665	0.80722	D	1	P;B;P	0.41643	0.758;0.003;0.758	B;B;P	0.46208	0.426;0.007;0.507	T	0.10730	-1.0617	10	0.49607	T	0.09	-8.0922	8.0558	0.30604	0.8295:0.0:0.1705:0.0	.	170;170;170	B4DYP5;Q3ZTS7;Q8IZ07	.;.;AN13A_HUMAN	V	170	ENSP00000261739:I170V	ENSP00000261739:I170V	I	+	1	0	ANKRD13A	108940640	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.405000	0.52630	0.981000	0.38548	0.533000	0.62120	ATA	.	.		0.418	ANKRD13A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403430.1	NM_033121		G	110456257	A	G	110456257	3	3	360	1	0	0	0	0	1	0	0	0	641	333	12	2	526	2	ANKRD13A	12	110456257	Missense_Mutation	SNP	A	TCGA-XR-A8TF-01A-11D-A35Z-10	7944115	110456257	23395638	96	50397										
PTPN11	5781	hgsc.bcm.edu	37	chr12	112942513	112942513	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	ctccagaatgagagaagacaGtgctagagtctatgaaaacg	11	7	1	6			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr12:112942513G>T	ENST00000351677.2	+	15	1925	c.1727G>T	c.(1726-1728)aGt>aTt	p.S576I		NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	580					abortive mitotic cell cycle (GO:0033277)|activation of MAPK activity (GO:0000187)|atrioventricular canal development (GO:0036302)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage checkpoint (GO:0000077)|ephrin receptor signaling pathway (GO:0048013)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|genitalia development (GO:0048806)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|multicellular organismal reproductive process (GO:0048609)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cortisol secretion (GO:0051463)|negative regulation of growth hormone secretion (GO:0060125)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ growth (GO:0035265)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of hormone secretion (GO:0046887)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of multicellular organism growth (GO:0040014)|regulation of protein export from nucleus (GO:0046825)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	insulin receptor binding (GO:0005158)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3)	451						AGAGAAGACAGTGCTAGAGTC	0.363			Mis		"JMML, AML, MDS"		Noonan Syndrome		Noonan syndrome																												p.S576I		Atlas-SNP	.		Dom	yes		12	12q24.1	5781	"protein tyrosine phosphatase, non-receptor type 11"	yes	L	.	PTPN11	623	.	0			c.G1727T						.						46	43	44					12																	112942513		2203	4300	6503	SO:0001583	missense	5781	exon15	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	AAGACAGTGCTAG	D13540	CCDS9163.1, CCDS58280.1	12q24.1	2014-09-17	2008-07-31		ENSG00000179295	ENSG00000179295		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor", "SH2 domain containing"	9644	protein-coding gene	gene with protein product		176876	"Noonan syndrome 1"	NS1		7894486, 1280823	Standard	NM_080601		Approved	BPTP3, SH-PTP2, SHP-2, PTP2C, SHP2	uc001ttx.3	Q06124	OTTHUMG00000134334	ENST00000351677.2:c.1727G>T	chr12.hg19:g.112942513G>T	ENSP00000340944:p.Ser576Ile	406.0	0.0		497.0	210.0	NM_002834	A8K1D9|Q96HD7	Missense_Mutation	SNP	ENST00000351677.2	hg19	CCDS9163.1	.	.	.	.	.	.	.	.	.	.	G	15.43	2.830161	0.50845	.	.	ENSG00000179295	ENST00000351677	T	0.10860	2.83	5.8	-0.274	0.12910	.	0.314416	0.37348	N	0.002131	T	0.06645	0.0170	N	0.24115	0.695	0.44024	D	0.996749	B	0.13145	0.007	B	0.10450	0.005	T	0.24048	-1.0171	10	0.72032	D	0.01	.	7.6148	0.28152	0.3303:0.1351:0.5347:0.0	.	576	Q06124-2	.	I	576	ENSP00000340944:S576I	ENSP00000340944:S576I	S	+	2	0	PTPN11	111426896	1.000000	0.71417	0.992000	0.48379	0.984000	0.73092	1.446000	0.35090	0.035000	0.15519	-0.300000	0.09419	AGT	.	.		0.363	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259496.2			T	112942513	G	T	112942513	3	4	360	1	0	0	0	0	1	0	0	0	12793	1029	36	3	1785	3	PTPN11	12	112942513	Missense_Mutation	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10	2486256	112942513	20909382	97	50398										
CCNA1	8900	hgsc.bcm.edu	37	chr13	37012886	37012886	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	tggaggttggggaagaatatAaacttcgagcagagaccctg	14	6	0	2			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr13:37012886A>G	ENST00000255465.4	+	5	1039	c.775A>G	c.(775-777)Aaa>Gaa	p.K259E	CCNA1_ENST00000449823.1_Missense_Mutation_p.K215E|CCNA1_ENST00000418263.1_Missense_Mutation_p.K258E|CCNA1_ENST00000440264.1_Missense_Mutation_p.K215E			P78396	CCNA1_HUMAN	cyclin A1	259					G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|male meiosis I (GO:0007141)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)				breast(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(2)|urinary_tract(1)	35		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.91e-07)|Epithelial(112;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0119)|GBM - Glioblastoma multiforme(144;0.0242)		GGAAGAATATAAACTTCGAGC	0.517																																					p.K259E		Atlas-SNP	.											.	CCNA1	91	.	0			c.A775G						.						145	126	132					13																	37012886		2203	4300	6503	SO:0001583	missense	8900	exon5			GAATATAAACTTC	U66838	CCDS9357.1, CCDS45031.1	13q12.3-q13	2014-01-21			ENSG00000133101	ENSG00000133101			1577	protein-coding gene	gene with protein product		604036				9041194	Standard	NM_003914		Approved	CT146	uc001uvr.4	P78396	OTTHUMG00000016733	ENST00000255465.4:c.775A>G	chr13.hg19:g.37012886A>G	ENSP00000255465:p.Lys259Glu	231.0	0.0		125.0	53.0	NM_003914	B7Z7E3|Q5T3V0|Q5U0G2|Q8IY91	Missense_Mutation	SNP	ENST00000255465.4	hg19	CCDS9357.1	.	.	.	.	.	.	.	.	.	.	A	16.81	3.226606	0.58668	.	.	ENSG00000133101	ENST00000440264;ENST00000449823;ENST00000418263;ENST00000255465	T;T;T;T	0.17691	2.26;2.26;2.26;2.26	5.33	4.15	0.48705	Cyclin, N-terminal (2);Cyclin-like (3);	0.187288	0.56097	D	0.000026	T	0.24661	0.0598	L	0.39566	1.225	0.54753	D	0.999984	P;B	0.38048	0.616;0.277	B;P	0.49528	0.423;0.614	T	0.01652	-1.1303	10	0.54805	T	0.06	.	12.55	0.56222	0.8521:0.1479:0.0:0.0	.	258;259	P78396-2;P78396	.;CCNA1_HUMAN	E	215;215;258;259	ENSP00000400666:K215E;ENSP00000409873:K215E;ENSP00000396479:K258E;ENSP00000255465:K259E	ENSP00000255465:K259E	K	+	1	0	CCNA1	35910886	1.000000	0.71417	0.002000	0.10522	0.439000	0.31926	5.892000	0.69790	0.955000	0.37878	0.528000	0.53228	AAA	.	.		0.517	CCNA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044514.2	NM_003914		G	37012886	A	G	37012886	3	3	360	1	0	0	0	0	1	0	0	0	2911	363	13	2	793	2	CCNA1	13	37012886	Missense_Mutation	SNP	A	TCGA-XR-A8TF-01A-11D-A35Z-10		37012886	78156992	98	50399										
POSTN	10631	hgsc.bcm.edu	37	chr13	38159034	38159034	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	ataatagactcagaacactgGagagtatttaagatgtggta	10	4	1	4			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr13:38159034G>T	ENST00000379747.4	-	8	1044	c.927C>A	c.(925-927)ctC>ctA	p.L309L	POSTN_ENST00000541179.1_Silent_p.L309L|POSTN_ENST00000379742.4_Silent_p.L309L|POSTN_ENST00000541481.1_Silent_p.L309L|POSTN_ENST00000379743.4_Silent_p.L309L|POSTN_ENST00000379749.4_Silent_p.L309L	NM_006475.2	NP_006466.2	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor	309	FAS1 2. {ECO:0000255|PROSITE- ProRule:PRU00082, ECO:0000305}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of Notch signaling pathway (GO:0008593)|skeletal system development (GO:0001501)|tissue development (GO:0009888)	proteinaceous extracellular matrix (GO:0005578)|trans-Golgi network (GO:0005802)	heparin binding (GO:0008201)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(16)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	59		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)		CAGAACACTGGAGAGTATTTA	0.393																																					p.L309L		Atlas-SNP	.											.	POSTN	161	.	0			c.C927A						.						110	103	106					13																	38159034		2203	4300	6503	SO:0001819	synonymous_variant	10631	exon8			ACACTGGAGAGTA	D13665	CCDS9364.1, CCDS45034.1, CCDS53864.1, CCDS66530.1, CCDS66531.1	13q13.3	2008-02-05			ENSG00000133110	ENSG00000133110			16953	protein-coding gene	gene with protein product		608777				8363580, 12235007	Standard	NM_006475		Approved	OSF-2, PN, periostin	uc001uwo.4	Q15063	OTTHUMG00000016751	ENST00000379747.4:c.927C>A	chr13.hg19:g.38159034G>T		91.0	0.0		40.0	21.0	NM_006475	B1ALD8|C0IMJ1|C0IMJ2|C0IMJ4|D2KRH7|F5H628|Q15064|Q29XZ0|Q3KPJ5|Q5VSY5|Q8IZF9	Silent	SNP	ENST00000379747.4	hg19	CCDS9364.1																																																																																			.	.		0.393	POSTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044566.2	NM_006475		T	38159034	G	T	38159034	2	4	360	1	0	0	0	0	0	0	0	1	12268	1161	41	3		3	POSTN	13	38159034	Silent	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10	1146148	38159034	77010844	99	50400										
JUB	84962	hgsc.bcm.edu	37	chr14	23444239	23444239	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	aagtccactgtgaaggggatGccatccaggcacttgttgca	12	10	0	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr14:23444239G>A	ENST00000262713.2	-	5	1689	c.1314C>T	c.(1312-1314)ggC>ggT	p.G438G	RP11-298I3.5_ENST00000555074.1_Intron|AJUBA_ENST00000361265.4_Silent_p.G438G|AJUBA_ENST00000397388.3_Silent_p.G21G	NM_032876.4	NP_116265.1	Q96IF1	AJUBA_HUMAN	ajuba LIM protein	438	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				calcium-dependent cell-cell adhesion (GO:0016339)|cellular protein localization (GO:0034613)|focal adhesion assembly (GO:0048041)|G2/M transition of mitotic cell cycle (GO:0000086)|gene silencing by miRNA (GO:0035195)|glycerophospholipid biosynthetic process (GO:0046474)|lamellipodium assembly (GO:0030032)|mitotic cell cycle (GO:0000278)|negative regulation of hippo signaling (GO:0035331)|negative regulation of kinase activity (GO:0033673)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cellular biosynthetic process (GO:0031328)|positive regulation of gene silencing by miRNA (GO:2000637)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein complex assembly (GO:0031334)|regulation of cell migration (GO:0030334)|regulation of cellular response to hypoxia (GO:1900037)|regulation of GTPase activity (GO:0043087)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)|wound healing, spreading of epidermal cells (GO:0035313)	cell-cell junction (GO:0005911)|cytoplasmic mRNA processing body (GO:0000932)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|transcription factor complex (GO:0005667)	alpha-catenin binding (GO:0045294)|chromatin binding (GO:0003682)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)										TGAAGGGGATGCCATCCAGGC	0.522																																					p.G438G		Atlas-SNP	.											.	.	.	.	0			c.C1314T						.						159	145	150					14																	23444239		2203	4300	6503	SO:0001819	synonymous_variant	84962	exon5			GGGGATGCCATCC	AK025567	CCDS9581.1, CCDS9582.1	14q11.2	2011-11-10	2011-11-10	2011-11-10	ENSG00000129474	ENSG00000129474			20250	protein-coding gene	gene with protein product		609066	"jub, ajuba homolog (Xenopus laevis)"	JUB		10330178	Standard	NM_032876		Approved	MGC15563	uc001whz.3	Q96IF1	OTTHUMG00000028711	ENST00000262713.2:c.1314C>T	chr14.hg19:g.23444239G>A		75.0	0.0		82.0	26.0	NM_032876	A8MX18|D3DS37	Silent	SNP	ENST00000262713.2	hg19	CCDS9581.1																																																																																			.	.		0.522	AJUBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071685.2			A	23444239	G	A	23444239	2	1	360	1	0	0	0	0	0	0	0	1	7977	1306	46	3		3	JUB	14	23444239	Silent	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10		23444239	83905301	100	50401										
HEATR5A	25938	hgsc.bcm.edu	37	chr14	31814462	31814462	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	gcagaatcaatgatcaatgaTagagaatgtaatgcccaggt	10	6	2	4			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr14:31814462T>C	ENST00000389961.3	-	19	2870	c.2871A>G	c.(2869-2871)ctA>ctG	p.L957L	HEATR5A_ENST00000439348.1_Silent_p.L957L|HEATR5A_ENST00000439727.1_Silent_p.L670L|HEATR5A_ENST00000404677.3_Silent_p.L963L|HEATR5A_ENST00000543095.2_Silent_p.L963L			Q86XA9	HTR5A_HUMAN	HEAT repeat containing 5A	957										breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)	26	Hepatocellular(127;0.0877)|Breast(36;0.137)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.0797)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0059)		TGATCAATGATAGAGAATGTA	0.333																																					p.L963L		Atlas-SNP	.											.	HEATR5A	181	.	0			c.A2889G						.						89	84	86					14																	31814462		1879	4095	5974	SO:0001819	synonymous_variant	25938	exon20			CAATGATAGAGAA	AB037737		14q12	2012-04-19	2007-01-02	2007-01-02	ENSG00000129493	ENSG00000129493			20276	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 125"	C14orf125			Standard	NM_015473		Approved	DKFZP434I1735	uc001wrf.4	Q86XA9	OTTHUMG00000169043	ENST00000389961.3:c.2871A>G	chr14.hg19:g.31814462T>C		107.0	0.0		125.0	44.0	NM_015473	Q68DD8|Q6P3S5|Q6P5R9|Q9H8D7|Q9NXB7|Q9P2N0|Q9UFQ3	Silent	SNP	ENST00000389961.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	8.257|8.257	0.810209|0.810209	0.16537|0.16537	.|.	.|.	ENSG00000129493|ENSG00000129493	ENST00000550366|ENST00000538864	.|.	.|.	.|.	5.41|5.41	-10.8|-10.8	0.00216|0.00216	.|.	.|.	.|.	.|.	.|.	T|T	0.47967|0.47967	0.1474|0.1474	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.60880|0.60880	-0.7175|-0.7175	4|4	.|.	.|.	.|.	.|.	10.5804|10.5804	0.45252|0.45252	0.0757:0.5897:0.2397:0.0949|0.0757:0.5897:0.2397:0.0949	.|.	.|.	.|.	.|.	V|C	606|591	.|.	.|.	I|Y	-|-	1|2	0|0	HEATR5A|HEATR5A	30884213|30884213	0.003000|0.003000	0.15002|0.15002	0.103000|0.103000	0.21229|0.21229	0.865000|0.865000	0.49528|0.49528	-1.191000|-1.191000	0.03055|0.03055	-1.913000|-1.913000	0.01079|0.01079	-0.250000|-0.250000	0.11733|0.11733	ATC|TAT	.	.		0.333	HEATR5A-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015473		C	31814462	T	C	31814462	2	2	360	1	0	0	0	0	0	0	0	1	7040	1393	49	2		2	HEATR5A	14	31814462	Silent	SNP	T	TCGA-XR-A8TF-01A-11D-A35Z-10	8370223	31814462	75535078	101	50402										
CTAGE5	4253	hgsc.bcm.edu	37	chr14	39819413	39819413	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	tgagttcccctcaggtttgaTtccaccttcaaatgagcctg	8	12	2	3			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr14:39819413T>G	ENST00000280083.3	+	24	2674	c.2360T>G	c.(2359-2361)aTt>aGt	p.I787S	CTAGE5_ENST00000553383.1_3'UTR|CTAGE5_ENST00000341502.5_Intron|CTAGE5_ENST00000553352.1_Missense_Mutation_p.I758S|RP11-407N17.3_ENST00000603904.1_Missense_Mutation_p.I758S|CTAGE5_ENST00000557038.1_Missense_Mutation_p.I707S|CTAGE5_ENST00000348007.3_Missense_Mutation_p.I744S|RP11-407N17.3_ENST00000553728.1_Missense_Mutation_p.I1322S|CTAGE5_ENST00000341749.3_Missense_Mutation_p.I775S|CTAGE5_ENST00000396165.4_Missense_Mutation_p.I758S|CTAGE5_ENST00000396158.2_Missense_Mutation_p.I792S|CTAGE5_ENST00000556148.1_Missense_Mutation_p.I712S			O15320	CTGE5_HUMAN	CTAGE family, member 5	787	Pro-rich.				positive regulation of catalytic activity (GO:0043085)	membrane (GO:0016020)	enzyme activator activity (GO:0008047)		CTAGE5/SIP1(2)	breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0475)		TCAGGTTTGATTCCACCTTCA	0.453																																					p.I792S		Atlas-SNP	.											.	CTAGE5	75	.	0			c.T2375G						.						90	91	91					14																	39819413		2203	4300	6503	SO:0001583	missense	4253	exon24			GTTTGATTCCACC	U94780	CCDS9673.1, CCDS9674.1, CCDS9675.1, CCDS9676.1, CCDS58316.1, CCDS58317.1	14q21.1	2009-09-11	2004-08-24	2004-08-26	ENSG00000150527	ENSG00000150527			7057	protein-coding gene	gene with protein product		602132	"meningioma expressed antigen 6 (coiled-coil proline-rich)"	MGEA, MGEA6		9356211, 11149944	Standard	NM_203355		Approved	MEA6, cTAGE-5A, cTAGE-5B, cTAGE-5C, cTAGE-5D, MGEA11	uc001wvi.4	O15320	OTTHUMG00000140258	ENST00000280083.3:c.2360T>G	chr14.hg19:g.39819413T>G	ENSP00000280083:p.Ile787Ser	187.0	0.0		157.0	88.0	NM_001247989	B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Missense_Mutation	SNP	ENST00000280083.3	hg19	CCDS9674.1	.	.	.	.	.	.	.	.	.	.	T	10.10	1.258866	0.23051	.	.	ENSG00000258941;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527	ENST00000553728;ENST00000341749;ENST00000557038;ENST00000382245;ENST00000396165;ENST00000396158;ENST00000280083;ENST00000556148;ENST00000348007;ENST00000553352	T;T;T;T;T;T;T;T;T	0.08458	3.27;3.1;3.09;3.1;3.39;3.39;3.1;3.44;3.1	5.61	-8.4	0.00965	.	0.492488	0.15133	N	0.278742	T	0.04318	0.0119	N	0.25890	0.77	0.09310	N	1	B;B;B;B;B	0.10296	0.003;0.002;0.003;0.002;0.003	B;B;B;B;B	0.12156	0.007;0.005;0.007;0.005;0.007	T	0.33343	-0.9872	9	.	.	.	.	10.8927	0.47004	0.0:0.5518:0.2266:0.2216	.	792;744;787;715;775	O15320-5;O15320-2;O15320;O15320-7;G3XAC5	.;.;CTGE5_HUMAN;.;.	S	1322;775;707;655;758;792;787;712;744;758	ENSP00000452252:I1322S;ENSP00000343897:I775S;ENSP00000450869:I707S;ENSP00000379468:I758S;ENSP00000379462:I792S;ENSP00000280083:I787S;ENSP00000452562:I712S;ENSP00000343912:I744S;ENSP00000450449:I758S	.	I	+	2	0	CTAGE5;RP11-407N17.3	38889164	0.000000	0.05858	0.000000	0.03702	0.729000	0.41735	-0.743000	0.04845	-1.762000	0.01308	0.460000	0.39030	ATT	.	.		0.453	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930		G	39819413	T	G	39819413	3	3	360	1	0	0	0	0	1	0	0	0	3996	1493	52	5	2485	5	CTAGE5	14	39819413	Missense_Mutation	SNP	T	TCGA-XR-A8TF-01A-11D-A35Z-10	8004951	39819413	67530127	102	50403										
FLRT2	23768	hgsc.bcm.edu	37	chr14	86089243	86089243	+	Frame_Shift_Del	DEL	T	T	-													0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	gaaaatgggccacagtttagTagggggcatcgttcaggagc					rs139260862		TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr14:86089243delT	ENST00000330753.4	+	2	2152	c.1385delT	c.(1384-1386)gtafs	p.V462fs	FLRT2_ENST00000554746.1_Frame_Shift_Del_p.V462fs	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	462	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		CACAGTTTAGTAGGGGGCATC	0.488																																					p.V462X		Atlas-INDEL	.											.	FLRT2	168	.	0			c.1384delG						.						105	95	98					14																	86089243		2203	4300	6503	SO:0001589	frameshift_variant	23768	exon2			.	AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070		"Fibronectin type III domain containing"	3761	protein-coding gene	gene with protein product		604807				10644439, 16872596	Standard	XM_005267490		Approved		uc001xvr.3	O43155		ENST00000330753.4:c.1385delT	chr14.hg19:g.86089243delT	ENSP00000332879:p.Val462fs	141.0	0.0		127.0	71.0	NM_013231	A0AV84|B7ZLP3	Frame_Shift_Del	DEL	ENST00000330753.4	hg19	CCDS9877.1																																																																																			.	.		0.488	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1			-	86089243	T	-	86089243	7	5	360	1	0	1	0	1	0	0	0	0	5947	1638	57	0	1387	0	FLRT2	14	86089243	Frame_Shift_Del	DEL	T	TCGA-XR-A8TF-01A-11D-A35Z-10	46269830	86089243	21260297	103	50404										
KIAA1409	57578	hgsc.bcm.edu	37	chr14	94088968	94088968	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	ttcccgaagatgcagagaacCccacagaaagtgagaagcct	10	11	0	4			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr14:94088968C>A	ENST00000393151.2	+	30	5389	c.5389C>A	c.(5389-5391)Ccc>Acc	p.P1797T	UNC79_ENST00000256339.4_Missense_Mutation_p.P1620T|UNC79_ENST00000553484.1_Missense_Mutation_p.P1819T|UNC79_ENST00000555664.1_Missense_Mutation_p.P1797T			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	1797					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						TGCAGAGAACCCCACAGAAAG	0.522																																					p.P1620T		Atlas-SNP	.											.	UNC79	366	.	0			c.C4858A						.						66	60	62					14																	94088968		2203	4300	6503	SO:0001583	missense	57578	exon30			GAGAACCCCACAG	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"KIAA1409"	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.5389C>A	chr14.hg19:g.94088968C>A	ENSP00000376858:p.Pro1797Thr	218.0	0.0		200.0	60.0	NM_020818	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	hg19		.	.	.	.	.	.	.	.	.	.	C	3.270	-0.149306	0.06585	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.17370	2.28;2.28;2.28;2.28	5.57	4.67	0.58626	.	0.238613	0.42964	D	0.000629	T	0.12347	0.0300	N	0.19112	0.55	0.09310	N	1	B	0.14438	0.01	B	0.18561	0.022	T	0.19418	-1.0306	10	0.15499	T	0.54	-2.5733	16.5969	0.84799	0.0:0.8698:0.1302:0.0	.	1819	C9JQL1	.	T	1620;1797;1819;1797;1819	ENSP00000256339:P1620T;ENSP00000450868:P1797T;ENSP00000451360:P1819T;ENSP00000376858:P1797T	ENSP00000256339:P1620T	P	+	1	0	KIAA1409	93158721	0.827000	0.29292	0.013000	0.15412	0.454000	0.32378	3.109000	0.50345	1.329000	0.45376	0.484000	0.47621	CCC	.	.		0.522	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		A	94088968	C	A	94088968	3	1	360	1	0	0	0	0	1	0	0	0	8239	623	22	3	4964	3	KIAA1409	14	94088968	Missense_Mutation	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10	7999725	94088968	13260572	104	50405										
TRPM1	4308	hgsc.bcm.edu	37	chr15	31323191	31323191	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	gaattctactcttacggtctAtctggtctgcaaacacctct	6	12	6	0			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr15:31323191A>G	ENST00000256552.6	-	23	3269	c.3122T>C	c.(3121-3123)aTa>aCa	p.I1041T	TRPM1_ENST00000542188.1_Missense_Mutation_p.I1058T|RP11-348B17.1_ENST00000561299.1_RNA|TRPM1_ENST00000397795.2_Missense_Mutation_p.I1019T|RP11-348B17.1_ENST00000558755.1_RNA	NM_001252024.1	NP_001238953.1			transient receptor potential cation channel, subfamily M, member 1											NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		CTTACGGTCTATCTGGTCTGC	0.428																																					p.I1058T		Atlas-SNP	.											.	TRPM1	183	.	0			c.T3173C						.						126	129	128					15																	31323191		2159	4287	6446	SO:0001583	missense	4308	exon22			CGGTCTATCTGGT	AF071787	CCDS10024.2, CCDS58345.1, CCDS58346.1, CCDS58347.1	15q13.3	2014-01-28		2002-01-18	ENSG00000134160	ENSG00000134160		"Voltage-gated ion channels / Transient receptor potential cation channels"	7146	protein-coding gene	gene with protein product		603576	"melastatin 1"	MLSN1		9806836, 9537257, 16382100	Standard	NM_001252020		Approved	LTRPC1, CSNB1C	uc021sia.1	Q7Z4N2	OTTHUMG00000129267	ENST00000256552.6:c.3122T>C	chr15.hg19:g.31323191A>G	ENSP00000256552:p.Ile1041Thr	123.0	0.0		133.0	81.0	NM_001252020		Missense_Mutation	SNP	ENST00000256552.6	hg19	CCDS58346.1	.	.	.	.	.	.	.	.	.	.	A	16.28	3.078174	0.55753	.	.	ENSG00000134160	ENST00000397795;ENST00000542188;ENST00000256552;ENST00000397793	D;D;D	0.98512	-4.97;-4.97;-4.97	6.05	4.93	0.64822	Ion transport (1);	0.087042	0.85682	N	0.000000	D	0.98416	0.9473	M	0.72576	2.205	0.50813	D	0.999897	D;P	0.71674	0.998;0.931	D;P	0.62955	0.909;0.817	D	0.98628	1.0670	10	0.87932	D	0	-22.2619	12.1212	0.53893	0.9334:0.0:0.0666:0.0	.	1013;1019	Q7Z4N2-3;Q7Z4N2	.;TRPM1_HUMAN	T	1019;1058;1041;1019	ENSP00000380897:I1019T;ENSP00000437849:I1058T;ENSP00000256552:I1041T	ENSP00000256552:I1041T	I	-	2	0	TRPM1	29110483	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.472000	0.80996	1.113000	0.41760	0.528000	0.53228	ATA	.	.		0.428	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420		G	31323191	A	G	31323191	3	3	360	1	0	0	0	0	1	0	0	0	16600	449	16	2	1779	2	TRPM1	15	31323191	Missense_Mutation	SNP	A	TCGA-XR-A8TF-01A-11D-A35Z-10		31323191	71208201	105	50406										
FBN1	2200	hgsc.bcm.edu	37	chr15	48829987	48829987	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	ggttgctgatcacagtaaaaCatgggcctgtcctgtaatct	10	9	2	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr15:48829987C>T	ENST00000316623.5	-	7	1012	c.557G>A	c.(556-558)tGt>tAt	p.C186Y		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	186	TB 1.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		CACAGTAAAACATGGGCCTGT	0.493																																					p.C186Y		Atlas-SNP	.											.	FBN1	310	.	0			c.G557A						.						62	64	63					15																	48829987		2197	4296	6493	SO:0001583	missense	2200	exon7			GTAAAACATGGGC	X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.557G>A	chr15.hg19:g.48829987C>T	ENSP00000325527:p.Cys186Tyr	116.0	0.0		114.0	7.0	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	hg19	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.262391	0.80358	.	.	ENSG00000166147	ENST00000316623;ENST00000544030;ENST00000537463	D;D	0.98060	-4.69;-4.69	5.14	5.14	0.70334	Matrix fibril-associated (2);TGF-beta binding (1);	0.000000	0.85682	D	0.000000	D	0.98811	0.9599	M	0.86028	2.79	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.99517	1.0957	10	0.72032	D	0.01	.	19.143	0.93452	0.0:1.0:0.0:0.0	.	186	P35555	FBN1_HUMAN	Y	186	ENSP00000325527:C186Y;ENSP00000440294:C186Y	ENSP00000325527:C186Y	C	-	2	0	FBN1	46617279	1.000000	0.71417	0.973000	0.42090	0.965000	0.64279	7.606000	0.82863	2.814000	0.96858	0.655000	0.94253	TGT	.	.		0.493	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			T	48829987	C	T	48829987	3	4	360	1	0	0	0	0	1	0	0	0	5710	478	17	3	8298	3	FBN1	15	48829987	Missense_Mutation	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10	17506796	48829987	53701405	106	50407										
LARP6	55323	hgsc.bcm.edu	37	chr15	71124522	71124522	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	ggagagcaggggactcgtacCggggcttttctcctgggtcc	16	11	1	1	rs146941351		TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr15:71124522C>T	ENST00000299213.8	-	3	1415	c.1345G>A	c.(1345-1347)Ggt>Agt	p.G449S	RP11-138H8.7_ENST00000592096.1_lincRNA	NM_018357.2	NP_060827.2	Q9BRS8	LARP6_HUMAN	La ribonucleoprotein domain family, member 6	449					regulation of translation (GO:0006417)|RNA processing (GO:0006396)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	19						GGACTCGTACCGGGGCTTTTC	0.617																																					p.G449S		Atlas-SNP	.											.	LARP6	43	.	0			c.G1345A						.						69	73	72					15																	71124522		2199	4297	6496	SO:0001583	missense	55323	exon3			TCGTACCGGGGCT	BC009446	CCDS10236.1, CCDS32281.1	15q23	2012-11-19			ENSG00000166173	ENSG00000166173		"La ribonucleoprotein domain containing"	24012	protein-coding gene	gene with protein product		611300				12477932	Standard	NM_018357		Approved	acheron, FLJ11196	uc002ass.3	Q9BRS8	OTTHUMG00000172179	ENST00000299213.8:c.1345G>A	chr15.hg19:g.71124522C>T	ENSP00000299213:p.Gly449Ser	129.0	0.0		102.0	35.0	NM_018357	Q5XKE4|Q8N3N2|Q9NUR0	Missense_Mutation	SNP	ENST00000299213.8	hg19	CCDS32281.1	.	.	.	.	.	.	.	.	.	.	C	5.204	0.223079	0.09863	.	.	ENSG00000166173	ENST00000299213	T	0.39997	1.05	5.3	2.19	0.27852	.	0.242826	0.40908	D	0.000983	T	0.18257	0.0438	N	0.08118	0	0.25583	N	0.986774	B	0.18863	0.031	B	0.14023	0.01	T	0.20739	-1.0266	10	0.17369	T	0.5	-11.2105	6.5295	0.22320	0.0:0.6889:0.1436:0.1675	.	449	Q9BRS8	LARP6_HUMAN	S	449	ENSP00000299213:G449S	ENSP00000299213:G449S	G	-	1	0	LARP6	68911576	0.022000	0.18835	0.001000	0.08648	0.311000	0.27955	1.794000	0.38774	0.159000	0.19401	0.555000	0.69702	GGT	.	C|1.000;A|0.000		0.617	LARP6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417197.2	NM_018357		T	71124522	C	T	71124522	3	4	360	1	0	0	0	0	1	0	0	0	8641	652	23	1	134	1	LARP6	15	71124522	Missense_Mutation	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10	22294535	71124522	31406870	107	50408										
NEO1	4756	hgsc.bcm.edu	37	chr15	73541947	73541947	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	gttgatgtttcaagtcactcTtacaccattaatgggttgaa	8	7	3	2			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr15:73541947T>G	ENST00000339362.5	+	12	2226	c.1779T>G	c.(1777-1779)tcT>tcG	p.S593S	NEO1_ENST00000560262.1_Silent_p.S593S|NEO1_ENST00000261908.6_Silent_p.S593S|NEO1_ENST00000560352.1_3'UTR|NEO1_ENST00000558964.1_Silent_p.S593S			Q92859	NEO1_HUMAN	neogenin 1	593	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|iron ion homeostasis (GO:0055072)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of transcription, DNA-templated (GO:0006355)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(9)|lung(26)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	57						CAAGTCACTCTTACACCATTA	0.348																																					p.S593S		Atlas-SNP	.											.	NEO1	102	.	0			c.T1779G						.						103	98	100					15																	73541947		2198	4297	6495	SO:0001819	synonymous_variant	4756	exon11			TCACTCTTACACC	U61262	CCDS10247.1, CCDS53957.1, CCDS58378.1	15q22.3-q23	2014-06-20	2010-06-24		ENSG00000067141	ENSG00000067141		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7754	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 2"	601907	"neogenin (chicken) homolog 1"			9121761	Standard	NM_002499		Approved	NGN, HsT17534, IGDCC2, NTN1R2	uc002avm.4	Q92859	OTTHUMG00000133509	ENST00000339362.5:c.1779T>G	chr15.hg19:g.73541947T>G		134.0	0.0		121.0	34.0	NM_001172623	B7ZKM9|B7ZKN0|O00340|Q17RX1	Silent	SNP	ENST00000339362.5	hg19	CCDS10247.1																																																																																			.	.		0.348	NEO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257472.2	NM_002499		G	73541947	T	G	73541947	2	3	360	1	0	0	0	0	0	0	0	1	10345	1596	56	5		5	NEO1	15	73541947	Silent	SNP	T	TCGA-XR-A8TF-01A-11D-A35Z-10	2417425	73541947	28989445	108	50409										
AXIN1	8312	hgsc.bcm.edu	37	chr16	396840	396840	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	cccaggtccagatccgagcgCctcggagtggccgtcgaagt	14	14	0	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr16:396840C>A	ENST00000262320.3	-	2	557	c.186G>T	c.(184-186)agG>agT	p.R62S	AXIN1_ENST00000481769.1_Intron|AXIN1_ENST00000354866.3_Missense_Mutation_p.R62S	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	62					activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				GATCCGAGCGCCTCGGAGTGG	0.607											OREG0003698	type=REGULATORY REGION|Gene=AXIN1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.R62S		Atlas-SNP	.											.	AXIN1	290	.	0			c.G186T						.						37	36	36					16																	396840		2203	4300	6503	SO:0001583	missense	8312	exon2			CGAGCGCCTCGGA	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.186G>T	chr16.hg19:g.396840C>A	ENSP00000262320:p.Arg62Ser	86.0	0.0	588	35.0	17.0	NM_181050	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Missense_Mutation	SNP	ENST00000262320.3	hg19	CCDS10405.1	.	.	.	.	.	.	.	.	.	.	C	16.64	3.179822	0.57800	.	.	ENSG00000103126	ENST00000262320;ENST00000354866	T;T	0.64991	-0.13;-0.12	5.34	3.37	0.38596	.	0.000000	0.85682	D	0.000000	T	0.77611	0.4156	M	0.81341	2.54	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.78250	-0.2277	10	0.72032	D	0.01	-19.0395	10.6745	0.45778	0.0:0.8434:0.0:0.1566	.	62;62	O15169-2;O15169	.;AXIN1_HUMAN	S	62	ENSP00000262320:R62S;ENSP00000346935:R62S	ENSP00000262320:R62S	R	-	3	2	AXIN1	336841	0.999000	0.42202	0.979000	0.43373	0.885000	0.51271	0.798000	0.27014	0.625000	0.30304	0.655000	0.94253	AGG	.	.		0.607	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3			A	396840	C	A	396840	3	1	360	1	0	0	0	0	1	0	0	0	1236	738	26	3	2442	3	AXIN1	16	396840	Missense_Mutation	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10		396840	89957913	109	50410										
SSTR5	6755	hgsc.bcm.edu	37	chr16	1129724	1129724	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	agcccgcctccgccggcctcTacttcttcgtggtcatcctc	8	19	3	0			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr16:1129724T>C	ENST00000293897.4	+	1	944	c.856T>C	c.(856-858)Tac>Cac	p.Y286H	SSTR5-AS1_ENST00000569832.1_RNA|SSTR5_ENST00000562758.1_Intron|SSTR5_ENST00000397547.2_Missense_Mutation_p.Y286H	NM_001053.3	NP_001044.1	P35346	SSR5_HUMAN	somatostatin receptor 5	286					G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose homeostasis (GO:0042593)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cytokinesis (GO:0032467)|regulation of insulin secretion (GO:0050796)|somatostatin signaling pathway (GO:0038170)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			endometrium(2)|lung(5)|prostate(1)|skin(1)	9		Hepatocellular(780;0.00369)			Octreotide(DB00104)|Pasireotide(DB06663)|Vapreotide(DB04894)	CGCCGGCCTCTACTTCTTCGT	0.617																																					p.Y286H		Atlas-SNP	.											.	SSTR5	36	.	0			c.T856C						.						74	84	80					16																	1129724		2193	4296	6489	SO:0001583	missense	6755	exon2			GGCCTCTACTTCT	D16827	CCDS10429.1	16p13.3	2012-08-08			ENSG00000162009	ENSG00000162009		"GPCR / Class A : Somatostatin receptors"	11334	protein-coding gene	gene with protein product		182455				7607700	Standard	NM_001053		Approved		uc021taf.1	P35346	OTTHUMG00000047842	ENST00000293897.4:c.856T>C	chr16.hg19:g.1129724T>C	ENSP00000293897:p.Tyr286His	63.0	0.0		48.0	22.0	NM_001172560	P34988|Q541E0|Q9UJI5	Missense_Mutation	SNP	ENST00000293897.4	hg19	CCDS10429.1	.	.	.	.	.	.	.	.	.	.	T	10.04	1.242590	0.22796	.	.	ENSG00000162009	ENST00000397547;ENST00000293897	T;T	0.73047	-0.71;-0.71	4.76	4.76	0.60689	GPCR, rhodopsin-like superfamily (1);	0.136393	0.51477	D	0.000097	T	0.72811	0.3507	L	0.61218	1.895	0.36314	D	0.857852	P	0.37636	0.603	B	0.44278	0.445	T	0.78866	-0.2035	10	0.44086	T	0.13	.	13.4447	0.61134	0.0:0.0:0.0:1.0	.	286	P35346	SSR5_HUMAN	H	286	ENSP00000380680:Y286H;ENSP00000293897:Y286H	ENSP00000293897:Y286H	Y	+	1	0	SSTR5	1069725	1.000000	0.71417	0.997000	0.53966	0.030000	0.12068	7.813000	0.86123	1.786000	0.52430	0.459000	0.35465	TAC	.	.		0.617	SSTR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420836.1			C	1129724	T	C	1129724	3	2	360	1	0	0	0	0	1	0	0	0	15216	1522	53	2	858	2	SSTR5	16	1129724	Missense_Mutation	SNP	T	TCGA-XR-A8TF-01A-11D-A35Z-10	732884	1129724	89225029	110	50411										
IL21R	50615	hgsc.bcm.edu	37	chr16	27448987	27448987	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	actactcccaggagtgtggcAgctttctcctggctgagagc	12	12	1	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr16:27448987A>T	ENST00000337929.3	+	4	804	c.331A>T	c.(331-333)Agc>Tgc	p.S111C	IL21R_ENST00000395755.1_Missense_Mutation_p.S111C|IL21R_ENST00000564089.1_Missense_Mutation_p.S111C|IL21R_ENST00000395754.4_Missense_Mutation_p.S111C	NM_181078.2	NP_851564.1	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor	111	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				interleukin-21-mediated signaling pathway (GO:0038114)|natural killer cell activation (GO:0030101)	integral component of membrane (GO:0016021)	interleukin-21 receptor activity (GO:0001532)			breast(2)|large_intestine(3)|lung(1)|ovary(2)	8						GGAGTGTGGCAGCTTTCTCCT	0.557			T	BCL6	NHL																																p.S133C		Atlas-SNP	.		Dom	yes		16	16p11	50615	interleukin 21 receptor		L	.	IL21R	95	.	0			c.A397T						.						116	88	98					16																	27448987		2197	4300	6497	SO:0001583	missense	50615	exon5			TGTGGCAGCTTTC	AF254067	CCDS10630.1	16p11	2014-09-17			ENSG00000103522	ENSG00000103522		"Interleukins and interleukin receptors", "CD molecules"	6006	protein-coding gene	gene with protein product		605383				11081504	Standard	NM_181078		Approved	CD360	uc002dos.2	Q9HBE5	OTTHUMG00000131675	ENST00000337929.3:c.331A>T	chr16.hg19:g.27448987A>T	ENSP00000338010:p.Ser111Cys	78.0	0.0		52.0	27.0	NM_181079	A8K9E8|D3DWF7|Q96HZ1|Q9HB91	Missense_Mutation	SNP	ENST00000337929.3	hg19	CCDS10630.1	.	.	.	.	.	.	.	.	.	.	A	13.44	2.236641	0.39498	.	.	ENSG00000103522	ENST00000337929;ENST00000395755;ENST00000395754	T;T;T	0.57752	0.38;0.38;0.38	4.79	0.789	0.18607	Fibronectin, type III (1);	0.778148	0.12653	N	0.450337	T	0.59810	0.2221	M	0.69823	2.125	0.32605	N	0.525403	D	0.67145	0.996	P	0.56216	0.794	T	0.64584	-0.6373	10	0.59425	D	0.04	-9.8773	5.7655	0.18224	0.5212:0.3223:0.0:0.1565	.	111	Q9HBE5	IL21R_HUMAN	C	111	ENSP00000338010:S111C;ENSP00000379104:S111C;ENSP00000379103:S111C	ENSP00000338010:S111C	S	+	1	0	IL21R	27356488	0.964000	0.33143	0.990000	0.47175	0.073000	0.16967	0.210000	0.17455	0.227000	0.20999	-0.478000	0.04885	AGC	.	.		0.557	IL21R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254578.2	NM_181078		T	27448987	A	T	27448987	3	4	360	1	0	0	0	0	1	0	0	0	7680	188	7	4	341	4	IL21R	16	27448987	Missense_Mutation	SNP	A	TCGA-XR-A8TF-01A-11D-A35Z-10	26319263	27448987	62905766	111	50412										
LONP2	83752	hgsc.bcm.edu	37	chr16	48295405	48295405	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	agaagatgaagatgaagatgAagataatgatgacattgtca	11	2	1	10			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr16:48295405A>T	ENST00000285737.4	+	5	887	c.794A>T	c.(793-795)gAa>gTa	p.E265V	LONP2_ENST00000535754.1_Missense_Mutation_p.E221V	NM_031490.2	NP_113678.2			lon peptidase 2, peroxisomal											breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						GATGAAGATGAAGATAATGAT	0.353																																					p.E265V		Atlas-SNP	.											.	LONP2	63	.	0			c.A794T						.						151	150	150					16																	48295405		2200	4300	6500	SO:0001583	missense	83752	exon5			AAGATGAAGATAA	AJ548761	CCDS10734.1, CCDS73880.1	16q12.1	2010-04-21			ENSG00000102910	ENSG00000102910		"ATPases / AAA-type"	20598	protein-coding gene	gene with protein product						14561759	Standard	XM_005256191		Approved	MGC4840, LONP, LONPL	uc002efi.1	Q86WA8	OTTHUMG00000133144	ENST00000285737.4:c.794A>T	chr16.hg19:g.48295405A>T	ENSP00000285737:p.Glu265Val	296.0	0.0		174.0	67.0	NM_031490		Missense_Mutation	SNP	ENST00000285737.4	hg19	CCDS10734.1	.	.	.	.	.	.	.	.	.	.	A	28.3	4.905543	0.92107	.	.	ENSG00000102910	ENST00000285737;ENST00000535754;ENST00000416006	T;T	0.34275	1.37;1.39	5.88	5.88	0.94601	.	0.159786	0.56097	D	0.000024	T	0.48314	0.1493	M	0.81112	2.525	0.80722	D	1	P;P	0.49961	0.93;0.93	P;P	0.44860	0.462;0.462	T	0.56860	-0.7909	10	0.62326	D	0.03	-30.4383	16.2898	0.82742	1.0:0.0:0.0:0.0	.	221;265	B7ZKL7;Q86WA8	.;LONP2_HUMAN	V	265;221;221	ENSP00000285737:E265V;ENSP00000445426:E221V	ENSP00000285737:E265V	E	+	2	0	LONP2	46852906	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.984000	0.88150	2.250000	0.74265	0.482000	0.46254	GAA	.	.		0.353	LONP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256839.2	NM_031490		T	48295405	A	T	48295405	3	4	360	1	0	0	0	0	1	0	0	0	8902	246	9	4	812	4	LONP2	16	48295405	Missense_Mutation	SNP	A	TCGA-XR-A8TF-01A-11D-A35Z-10	20846418	48295405	42059348	112	50413										
NLRC5	84166	hgsc.bcm.edu	37	chr16	57062007	57062007	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	taagagcaggaagtgtggggAtgcctttgcagaagccctct	14	8	1	2			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr16:57062007A>G	ENST00000262510.6	+	7	2324	c.2099A>G	c.(2098-2100)gAt>gGt	p.D700G	NLRC5_ENST00000436936.1_Missense_Mutation_p.D700G|NLRC5_ENST00000308149.7_Missense_Mutation_p.D700G|NLRC5_ENST00000539144.1_Missense_Mutation_p.D700G	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	700					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				AAGTGTGGGGATGCCTTTGCA	0.577																																					p.D700G		Atlas-SNP	.											.	NLRC5	186	.	0			c.A2099G						.						48	44	45					16																	57062007		2198	4300	6498	SO:0001583	missense	84166	exon6			GTGGGGATGCCTT	AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"Nucleotide-binding domain and leucine rich repeat containing"	29933	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5", "NOD-like receptor C5"	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.2099A>G	chr16.hg19:g.57062007A>G	ENSP00000262510:p.Asp700Gly	70.0	0.0		38.0	21.0	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Missense_Mutation	SNP	ENST00000262510.6	hg19	CCDS10773.1	.	.	.	.	.	.	.	.	.	.	A	15.16	2.749607	0.49257	.	.	ENSG00000140853	ENST00000262510;ENST00000308149;ENST00000436936;ENST00000327982;ENST00000539144;ENST00000538110;ENST00000543030	T;T;T;T;T;T	0.57273	0.41;0.41;0.41;0.41;0.41;0.41	5.31	5.31	0.75309	.	0.000000	0.33401	N	0.004947	T	0.69314	0.3097	M	0.65975	2.015	0.40836	D	0.98363	D;D;D;B	0.89917	1.0;1.0;0.994;0.161	D;D;D;B	0.97110	1.0;1.0;0.941;0.174	T	0.72896	-0.4153	10	0.59425	D	0.04	.	12.6503	0.56757	1.0:0.0:0.0:0.0	.	700;700;700;700	Q86WI3-5;Q86WI3-4;Q86WI3-6;Q86WI3	.;.;.;NLRC5_HUMAN	G	700;700;700;174;700;207;55	ENSP00000262510:D700G;ENSP00000308886:D700G;ENSP00000389739:D700G;ENSP00000441727:D700G;ENSP00000441597:D207G;ENSP00000440153:D55G	ENSP00000262510:D700G	D	+	2	0	NLRC5	55619508	1.000000	0.71417	0.910000	0.35882	0.046000	0.14306	5.874000	0.69652	2.028000	0.59812	0.533000	0.62120	GAT	.	.		0.577	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206		G	57062007	A	G	57062007	3	3	360	1	0	0	0	0	1	0	0	0	10479	333	12	2	2117	2	NLRC5	16	57062007	Missense_Mutation	SNP	A	TCGA-XR-A8TF-01A-11D-A35Z-10	8766602	57062007	33292746	113	50414										
ENO3	2027	hgsc.bcm.edu	37	chr17	4857083	4857083	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	gcagctgagaagggggtcccCctgtaccgccacatcgcaga	13	14	0	2			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr17:4857083C>T	ENST00000323997.6	+	6	519	c.387C>T	c.(385-387)ccC>ccT	p.P129P	ENO3_ENST00000519584.1_Silent_p.P86P|ENO3_ENST00000518175.1_Silent_p.P129P	NM_001976.4|NM_053013.3	NP_001967.3|NP_443739.3	P13929	ENOB_HUMAN	enolase 3 (beta, muscle)	129					aging (GO:0007568)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|response to drug (GO:0042493)|skeletal muscle tissue regeneration (GO:0043403)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|phosphopyruvate hydratase complex (GO:0000015)|plasma membrane (GO:0005886)	magnesium ion binding (GO:0000287)|phosphopyruvate hydratase activity (GO:0004634)			cervix(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)	15						AGGGGGTCCCCCTGTACCGCC	0.622																																					p.P129P		Atlas-SNP	.											.	ENO3	36	.	0			c.C387T						.						110	97	102					17																	4857083		2203	4300	6503	SO:0001819	synonymous_variant	2027	exon6			GGTCCCCCTGTAC	X16504	CCDS11062.1, CCDS54070.1	17p13.2	2013-09-19	2004-11-22		ENSG00000108515	ENSG00000108515	4.2.1.11		3354	protein-coding gene	gene with protein product		131370	"enolase 3, (beta, muscle)"				Standard	NM_001976		Approved		uc002gab.4	P13929	OTTHUMG00000099394	ENST00000323997.6:c.387C>T	chr17.hg19:g.4857083C>T		118.0	0.0		68.0	15.0	NM_001976	B4DUI6|B4DUM6|D3DTL2|E7ENK8|Q96AE2	Silent	SNP	ENST00000323997.6	hg19	CCDS11062.1																																																																																			.	.		0.622	ENO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216851.2			T	4857083	C	T	4857083	2	4	360	1	0	0	0	0	0	0	0	1	5125	610	22	3		3	ENO3	17	4857083	Silent	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10		4857083	76338127	114	50415										
AMAC1L3	643664	hgsc.bcm.edu	37	chr17	7385340	7385340	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	cctacttgaacccgcctgacTccacacacccatcgccgccc	5	22	0	2			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr17:7385340T>G	ENST00000412468.2	+	2	152	c.37T>G	c.(37-39)Tcc>Gcc	p.S13A	ZBTB4_ENST00000380599.4_5'Flank|POLR2A_ENST00000572844.1_5'Flank|POLR2A_ENST00000322644.6_5'Flank|ZBTB4_ENST00000311403.4_Intron	NM_001102614.1	NP_001096084.1	P0C7Q6	S35G6_HUMAN	solute carrier family 35, member G6	13						integral component of membrane (GO:0016021)											CCCGCCTGACTCCACACACCC	0.672																																					p.S13A		Atlas-SNP	.											.	.	.	.	0			c.T37G						.						51	54	53					17																	7385340		2203	4300	6503	SO:0001583	missense	643664	exon2			CCTGACTCCACAC		CCDS45603.1	17p13.1	2013-05-22	2011-08-03	2011-08-03		ENSG00000259224		"Solute carriers"	31351	protein-coding gene	gene with protein product			"transmembrane protein 21B", "acyl-malonyl condensing enzyme 1-like 3"	TMEM21B, AMAC1L3			Standard	NM_001102614		Approved		uc010cmj.1	P0C7Q6		ENST00000412468.2:c.37T>G	chr17.hg19:g.7385340T>G	ENSP00000396523:p.Ser13Ala	81.0	0.0		88.0	52.0	NM_001102614		Missense_Mutation	SNP	ENST00000412468.2	hg19	CCDS45603.1	.	.	.	.	.	.	.	.	.	.	T	0.006	-2.028742	0.00410	.	.	ENSG00000181222	ENST00000412468	T	0.27104	1.69	4.21	3.12	0.35913	.	.	.	.	.	T	0.10380	0.0254	N	0.08118	0	0.09310	N	0.999994	B	0.09022	0.002	B	0.09377	0.004	T	0.32877	-0.9890	9	0.06625	T	0.88	-5.403	7.0163	0.24890	0.0:0.1102:0.0:0.8898	.	13	P0C7Q6	S35G6_HUMAN	A	13	ENSP00000396523:S13A	ENSP00000396523:S13A	S	+	1	0	SLC35G6	7326064	1.000000	0.71417	1.000000	0.80357	0.008000	0.06430	1.164000	0.31810	1.681000	0.50988	0.379000	0.24179	TCC	.	.		0.672	SLC35G6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001102614		G	7385340	T	G	7385340	3	3	360	1	0	0	0	0	1	0	0	0	561	1551	54	5	43	5	AMAC1L3	17	7385340	Missense_Mutation	SNP	T	TCGA-XR-A8TF-01A-11D-A35Z-10	2528257	7385340	73809870	115	50416										
AMAC1L3	643664	hgsc.bcm.edu	37	chr17	7385382	7385382	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	ccgctccacccagcctccgcTggcaccagtgctgccagccc	9	22	0	0			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr17:7385382T>C	ENST00000412468.2	+	2	194	c.79T>C	c.(79-81)Tgg>Cgg	p.W27R	ZBTB4_ENST00000380599.4_5'Flank|POLR2A_ENST00000572844.1_5'Flank|POLR2A_ENST00000322644.6_5'Flank|ZBTB4_ENST00000311403.4_Intron	NM_001102614.1	NP_001096084.1	P0C7Q6	S35G6_HUMAN	solute carrier family 35, member G6	27						integral component of membrane (GO:0016021)											CAGCCTCCGCTGGCACCAGTG	0.662																																					p.W27R		Atlas-SNP	.											.	.	.	.	0			c.T79C						.						45	51	49					17																	7385382		2202	4298	6500	SO:0001583	missense	643664	exon2			CTCCGCTGGCACC		CCDS45603.1	17p13.1	2013-05-22	2011-08-03	2011-08-03		ENSG00000259224		"Solute carriers"	31351	protein-coding gene	gene with protein product			"transmembrane protein 21B", "acyl-malonyl condensing enzyme 1-like 3"	TMEM21B, AMAC1L3			Standard	NM_001102614		Approved		uc010cmj.1	P0C7Q6		ENST00000412468.2:c.79T>C	chr17.hg19:g.7385382T>C	ENSP00000396523:p.Trp27Arg	71.0	0.0		81.0	48.0	NM_001102614		Missense_Mutation	SNP	ENST00000412468.2	hg19	CCDS45603.1	.	.	.	.	.	.	.	.	.	.	T	3.764	-0.049064	0.07407	.	.	ENSG00000181222	ENST00000412468	T	0.26373	1.74	4.21	1.96	0.26148	.	.	.	.	.	T	0.10680	0.0261	N	0.08118	0	0.19575	N	0.999967	B	0.29085	0.232	B	0.23574	0.047	T	0.28933	-1.0028	9	0.25106	T	0.35	6.0E-4	5.2846	0.15694	0.0:0.2418:0.0:0.7582	.	27	P0C7Q6	S35G6_HUMAN	R	27	ENSP00000396523:W27R	ENSP00000396523:W27R	W	+	1	0	SLC35G6	7326106	0.006000	0.16342	0.093000	0.20910	0.519000	0.34347	0.409000	0.21082	0.608000	0.30000	0.379000	0.24179	TGG	.	.		0.662	SLC35G6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001102614		C	7385382	T	C	7385382	3	2	360	1	0	0	0	0	1	0	0	0	561	1580	55	2	85	2	AMAC1L3	17	7385382	Missense_Mutation	SNP	T	TCGA-XR-A8TF-01A-11D-A35Z-10	42	7385382	73809828	116	50417										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11593507	11593507	+	Silent	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	cagtatgagccccacccacgGaccaatgtccccctcctgtg	8	18	0	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr17:11593507G>A	ENST00000262442.4	+	20	4436	c.4368G>A	c.(4366-4368)cgG>cgA	p.R1456R	DNAH9_ENST00000454412.2_Silent_p.R1456R	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	1456	Stem. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.R1456R(1)		NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		CCCACCCACGGACCAATGTCC	0.493																																					p.R1456R		Atlas-SNP	.											DNAH9,NS,carcinoma,0,1	DNAH9	695	.	1	Substitution - coding silent(1)	lung(1)	c.G4368A						.						81	79	80					17																	11593507		2203	4300	6503	SO:0001819	synonymous_variant	1770	exon20			CCCACGGACCAAT	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.4368G>A	chr17.hg19:g.11593507G>A		116.0	0.0		119.0	47.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	hg19	CCDS11160.1																																																																																			.	.		0.493	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		A	11593507	G	A	11593507	2	1	360	1	0	0	0	0	0	0	0	1	4610	1161	41	3		3	DNAH9	17	11593507	Silent	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10	4208125	11593507	69601703	117	50418										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11833232	11833232	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	caccctggagaagaagctggAggagcacagtgagaacagcc	14	10	0	3			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr17:11833232A>T	ENST00000262442.4	+	63	11995	c.11927A>T	c.(11926-11928)gAg>gTg	p.E3976V	DNAH9_ENST00000396001.2_3'UTR|DNAH9_ENST00000454412.2_Intron|DNAH9_ENST00000608377.1_Missense_Mutation_p.E288V	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	3976	AAA 6. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		AAGAAGCTGGAGGAGCACAGT	0.592																																					p.E3976V		Atlas-SNP	.											.	DNAH9	695	.	0			c.A11927T						.						74	57	63					17																	11833232		2203	4300	6503	SO:0001583	missense	1770	exon63			AGCTGGAGGAGCA	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.11927A>T	chr17.hg19:g.11833232A>T	ENSP00000262442:p.Glu3976Val	144.0	0.0		154.0	44.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	hg19	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.005631	0.74932	.	.	ENSG00000007174	ENST00000262442;ENST00000396001	T;T	0.10099	2.91;2.91	5.19	4.1	0.47936	Dynein heavy chain (1);	0.053068	0.64402	D	0.000001	T	0.41811	0.1175	M	0.94142	3.5	0.58432	D	0.999999	D	0.60575	0.988	D	0.73708	0.981	T	0.52866	-0.8518	10	0.87932	D	0	.	11.2692	0.49129	0.7083:0.2917:0.0:0.0	.	3976	Q9NYC9	DYH9_HUMAN	V	3976;288	ENSP00000262442:E3976V;ENSP00000379323:E288V	ENSP00000262442:E3976V	E	+	2	0	DNAH9	11773957	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.227000	0.78070	0.973000	0.38340	0.460000	0.39030	GAG	.	.		0.592	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		T	11833232	A	T	11833232	3	4	360	1	0	0	0	0	1	0	0	0	4610	304	11	4	12177	4	DNAH9	17	11833232	Missense_Mutation	SNP	A	TCGA-XR-A8TF-01A-11D-A35Z-10	239725	11833232	69361978	118	50419										
PPP1R1B	84152	hgsc.bcm.edu	37	chr17	37791873	37791873	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	tccccagctgggcaaaagacAacctgtggccagggtctgga	13	12	1	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr17:37791873A>T	ENST00000254079.4	+	6	928	c.459A>T	c.(457-459)acA>acT	p.T153T	PPP1R1B_ENST00000394267.2_Silent_p.T117T|PPP1R1B_ENST00000394265.1_Silent_p.T117T|STARD3_ENST00000580611.1_5'Flank|PPP1R1B_ENST00000579000.1_Silent_p.T120T|STARD3_ENST00000394250.4_5'Flank|STARD3_ENST00000336308.5_5'Flank|PPP1R1B_ENST00000580825.1_Silent_p.T153T|STARD3_ENST00000544210.2_5'Flank	NM_032192.3	NP_115568.2	Q9UD71	PPR1B_HUMAN	protein phosphatase 1, regulatory (inhibitor) subunit 1B	153					intracellular signal transduction (GO:0035556)|negative regulation of catalytic activity (GO:0043086)|negative regulation of female receptivity (GO:0007621)|negative regulation of protein kinase activity (GO:0006469)|regulation of catalytic activity (GO:0050790)|response to amphetamine (GO:0001975)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	protein kinase inhibitor activity (GO:0004860)|protein phosphatase inhibitor activity (GO:0004864)|protein phosphatase type 1 regulator activity (GO:0008599)			kidney(1)|large_intestine(1)|liver(1)|lung(2)	5	Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;1.04e-44)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			GGCAAAAGACAACCTGTGGCC	0.587																																					p.T153T		Atlas-SNP	.											.	PPP1R1B	9	.	0			c.A459T						.						84	96	92					17																	37791873		2203	4300	6503	SO:0001819	synonymous_variant	84152	exon6			AAAGACAACCTGT	AI124650	CCDS11339.1, CCDS11340.1	17q12	2012-04-17	2008-07-31		ENSG00000131771	ENSG00000131771	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9287	protein-coding gene	gene with protein product	"dopamine and cAMP regulated phosphoprotein"	604399				8120638	Standard	NM_032192		Approved	DARPP-32, FLJ20940	uc002hrz.3	Q9UD71	OTTHUMG00000133210	ENST00000254079.4:c.459A>T	chr17.hg19:g.37791873A>T		107.0	0.0		106.0	45.0	NM_032192	Q547V9|Q547W0|Q9H7G1	Silent	SNP	ENST00000254079.4	hg19	CCDS11339.1																																																																																			.	.		0.587	PPP1R1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256925.2	NM_032192		T	37791873	A	T	37791873	2	4	360	1	0	0	0	0	0	0	0	1	12380	117	5	4		4	PPP1R1B	17	37791873	Silent	SNP	A	TCGA-XR-A8TF-01A-11D-A35Z-10	25958641	37791873	43403337	119	50420										
KRT9	3857	hgsc.bcm.edu	37	chr17	39726458	39726458	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	agagttttgttgttgcccacTgtcaggtccacaatctgaaa	9	9	2	2			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr17:39726458T>A	ENST00000246662.4	-	2	722	c.657A>T	c.(655-657)acA>acT	p.T219T	KRT9_ENST00000588431.1_5'UTR	NM_000226.3	NP_000217.2	P35527	K1C9_HUMAN	keratin 9	219	Coil 1B.|Rod.				epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		Breast(137;0.000307)				TGTTGCCCACTGTCAGGTCCA	0.502																																					p.T219T		Atlas-SNP	.											.	KRT9	78	.	0			c.A657T						.						272	230	244					17																	39726458		2203	4300	6503	SO:0001819	synonymous_variant	3857	exon2			GCCCACTGTCAGG		CCDS32654.1	17q21.2	2013-06-20	2008-08-01		ENSG00000171403	ENSG00000171403		"-", "Intermediate filaments type I, keratins (acidic)"	6447	protein-coding gene	gene with protein product	"cytokeratin 9", "type I cytoskeletal 9", "epidermolytic palmoplantar keratoderma"	607606				7512862, 16831889	Standard	NM_000226		Approved	EPPK, K9, CK-9	uc002hxe.4	P35527	OTTHUMG00000133599	ENST00000246662.4:c.657A>T	chr17.hg19:g.39726458T>A		145.0	0.0		116.0	36.0	NM_000226	O00109|Q0IJ47|Q14665	Silent	SNP	ENST00000246662.4	hg19	CCDS32654.1																																																																																			.	.		0.502	KRT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257707.1	NM_000226		A	39726458	T	A	39726458	2	1	360	1	0	0	0	0	0	0	0	1	8510	1567	55	4		4	KRT9	17	39726458	Silent	SNP	T	TCGA-XR-A8TF-01A-11D-A35Z-10	1934585	39726458	41468752	120	50421										
KCNH4	23415	hgsc.bcm.edu	37	chr17	40330239	40330239	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	tggctccccttctaccaaggGagttttctgttgggaagaaa	11	9	2	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr17:40330239G>T	ENST00000264661.3	-	4	796	c.464C>A	c.(463-465)tCc>tAc	p.S155Y	KCNH4_ENST00000607371.1_Missense_Mutation_p.S155Y	NM_012285.2	NP_036417.1	Q9UQ05	KCNH4_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 4	155					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(15)|skin(2)|urinary_tract(1)	32		all_cancers(22;1.24e-06)|all_epithelial(22;4.33e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.126)		TCTACCAAGGGAGTTTTCTGT	0.592																																					p.S155Y	NSCLC(117;707 1703 2300 21308 31858)	Atlas-SNP	.											.	KCNH4	105	.	0			c.C464A						.						73	72	73					17																	40330239		2203	4300	6503	SO:0001583	missense	23415	exon4			CCAAGGGAGTTTT	AB022698	CCDS11420.1	17q21	2012-07-05				ENSG00000089558		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6253	protein-coding gene	gene with protein product		604528				10455180, 16382104	Standard	NM_012285		Approved	Kv12.3, elk1	uc002hzb.2	Q9UQ05		ENST00000264661.3:c.464C>A	chr17.hg19:g.40330239G>T	ENSP00000264661:p.Ser155Tyr	91.0	0.0		85.0	50.0	NM_012285		Missense_Mutation	SNP	ENST00000264661.3	hg19	CCDS11420.1	.	.	.	.	.	.	.	.	.	.	G	7.853	0.724445	0.15439	.	.	ENSG00000089558	ENST00000264661	D	0.98792	-5.14	4.99	4.02	0.46733	.	0.195495	0.25517	N	0.030123	D	0.95683	0.8596	L	0.43152	1.355	0.21604	N	0.999623	B	0.12630	0.006	B	0.14578	0.011	D	0.88790	0.3277	10	0.30078	T	0.28	.	4.541	0.12058	0.179:0.0:0.6311:0.1899	.	155	Q9UQ05	KCNH4_HUMAN	Y	155	ENSP00000264661:S155Y	ENSP00000264661:S155Y	S	-	2	0	KCNH4	37583765	1.000000	0.71417	0.996000	0.52242	0.183000	0.23260	2.203000	0.42752	1.326000	0.45319	0.563000	0.77884	TCC	.	.		0.592	KCNH4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449791.2	NM_012285		T	40330239	G	T	40330239	3	4	360	1	0	0	0	0	1	0	0	0	8043	1174	41	3	2641	3	KCNH4	17	40330239	Missense_Mutation	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10	603781	40330239	40864971	121	50422										
PGS1	9489	hgsc.bcm.edu	37	chr17	76374876	76374894	+	Splice_Site	DEL	CGCCAGCGCAGGAGGTGAG	CGCCAGCGCAGGAGGTGAG	-													0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	gcctcggcaggaaccgggacCgccagcgcaggaggtgagag					rs368468919		TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	CGCCAGCGCAGGAGGTGAG	CGCCAGCGCAGGAGGTGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr17:76374876_76374894delCGCCAGCGCAGGAGGTGAG	ENST00000262764.6	+	1	156_169	c.130_143delCGCCAGCGCAGGAGGTGAG	c.(130-144)cgccagcgcaggagg>g	p.RQRRR44fs	PGS1_ENST00000329897.7_5'UTR	NM_024419.3	NP_077733.3	Q32NB8	PGPS1_HUMAN	phosphatidylglycerophosphate synthase 1	44					cardiolipin biosynthetic process (GO:0032049)|diacylglycerol metabolic process (GO:0046339)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity (GO:0008444)			cervix(2)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	10			BRCA - Breast invasive adenocarcinoma(99;0.00144)|OV - Ovarian serous cystadenocarcinoma(97;0.031)			GAACCGGGACCGCCAGCGCAGGAGGTGAGAGGGGCGGCC	0.758																																					p.43_48del	Esophageal Squamous(45;182 1126 10685 43198)	Atlas-INDEL	.											.	PGS1	30	.	0			c.129_143del						.																																			SO:0001630	splice_region_variant	9489	exon1			.		CCDS42391.1	17q25.3	2006-02-09							30029	protein-coding gene	gene with protein product		614942				9880566	Standard	XR_243691		Approved	DKFZP762M186	uc002jvm.3	Q32NB8		ENST00000262764.6:c.143+1CGCCAGCGCAGGAGGTGAG>-	chr17.hg19:g.76374876_76374894delCGCCAGCGCAGGAGGTGAG		68.0	0.0		55.0	33.0	NM_024419	B7ZA32|Q8IYK9|Q8TA85|Q96A75|Q9H7G9|Q9NPW7	In_Frame_Del	DEL	ENST00000262764.6	hg19	CCDS42391.1																																																																																			.	.		0.758	PGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437301.1	NM_024419	Frame_Shift_Del	-	76374894	CGCCAGCGCAGGAGGTGAG	-	76374876	8	5	360	1	0	1	0	1	0	0	1	0	11817	652	23	0	132	0	PGS1	17	76374876	Splice_Site	DEL	CGCCAGCGCAGGAGGTGAG	TCGA-XR-A8TF-01A-11D-A35Z-10	36044637	76374876	4820334	122	50423										
KIAA1632	57724	hgsc.bcm.edu	37	chr18	43462411	43462412	+	Frame_Shift_Ins	INS	-	-	A													0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	gaagcctggtacgatcagacINSagaggaggtttagtggcgct							TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr18:43462411_43462412insA	ENST00000282041.5	-	31	5379_5380	c.5345_5346insT	c.(5344-5346)ctgfs	p.L1782fs	EPG5_ENST00000585906.1_5'UTR	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	1782					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)					NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						TACGATCAGACAGAGGAGGTTT	0.391																																					p.L1782fs		Atlas-INDEL	.											.	EPG5	199	.	0			c.5346_5347insT						.																																			SO:0001589	frameshift_variant	57724	exon31			.	AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"KIAA1632"	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.5346dupT	chr18.hg19:g.43462412_43462412dupA	ENSP00000282041:p.Leu1782fs	192.0	0.0		168.0	49.0	NM_020964	A2BDF3|Q9H8C8	Frame_Shift_Ins	INS	ENST00000282041.5	hg19	CCDS11926.2																																																																																			.	.		0.391	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		A	43462412	-	A	43462411	7	5	360	1	0	1	1	0	0	0	0	0	8258	465	17	0	2449	0	KIAA1632	18	43462411	Frame_Shift_Ins	INS	-	TCGA-XR-A8TF-01A-11D-A35Z-10		43462411	34614837	123	50424										
CDH19	28513	hgsc.bcm.edu	37	chr18	64239248	64239248	+	Splice_Site	DEL	T	T	-													0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	attttaaataaataagtaccTggccgatgtgatgactagtc							TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr18:64239248delT	ENST00000540086.1	-	2	440	c.194delA	c.(193-195)cag>cg	p.Q65fs	CDH19_ENST00000262150.2_Splice_Site_p.Q65fs	NM_001271028.1	NP_001257957.1	Q96JQ0	PCD16_HUMAN	cadherin 19, type 2	165	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(22)|ovary(1)|prostate(3)|skin(7)	61		Esophageal squamous(42;0.0132)				AATAAGTACCTGGCCGATGTG	0.378																																					p.Q65fs		Atlas-INDEL	.											.	CDH19	141	.	0			c.195delG						.						67	64	65					18																	64239248		2202	4300	6502	SO:0001630	splice_region_variant	28513	exon2			.	AJ007607	CCDS11994.1, CCDS59325.1	18q22.1	2010-01-26			ENSG00000071991	ENSG00000071991		"Cadherins / Major cadherins"	1758	protein-coding gene	gene with protein product		603016				10995570	Standard	NM_021153		Approved	CDH7	uc002lkc.2	Q9H159	OTTHUMG00000132802	ENST00000540086.1:c.195+1A>-	chr18.hg19:g.64239248delT		84.0	0.0		80.0	27.0	NM_021153	O15098	Frame_Shift_Del	DEL	ENST00000540086.1	hg19	CCDS59325.1																																																																																			.	.		0.378	CDH19-005	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000442285.1	NM_021153	Frame_Shift_Del	-	64239248	T	-	64239248	8	5	360	1	0	1	0	1	0	0	1	0	3106	1594	55	0	2168	0	CDH19	18	64239248	Splice_Site	DEL	T	TCGA-XR-A8TF-01A-11D-A35Z-10	20776837	64239248	13838000	124	50425										
ZNF556	80032	hgsc.bcm.edu	37	chr19	2877959	2877959	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	catccttacacaaacacgcgAgaacgcatgctaaaaagaaa	6	11	0	2			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr19:2877959A>T	ENST00000307635.2	+	4	1090	c.1003A>T	c.(1003-1005)Aga>Tga	p.R335*	ZNF556_ENST00000586426.1_Nonsense_Mutation_p.R334*	NM_024967.1	NP_079243.1	Q9HAH1	ZN556_HUMAN	zinc finger protein 556	335					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(3)|skin(7)	31				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CAAACACGCGAGAACGCATGC	0.507																																					p.R335X		Atlas-SNP	.											.	ZNF556	73	.	0			c.A1003T						.						43	41	41					19																	2877959		2203	4300	6503	SO:0001587	stop_gained	80032	exon4			CACGCGAGAACGC	BC009374	CCDS12097.1, CCDS74254.1	19p13.3	2013-09-20			ENSG00000172000	ENSG00000172000		"Zinc fingers, C2H2-type", "-"	25669	protein-coding gene	gene with protein product						12477932	Standard	XM_005259647		Approved	FLJ11637	uc002lwp.1	Q9HAH1	OTTHUMG00000180501	ENST00000307635.2:c.1003A>T	chr19.hg19:g.2877959A>T	ENSP00000302603:p.Arg335*	154.0	0.0		127.0	69.0	NM_024967	Q96GM3	Nonsense_Mutation	SNP	ENST00000307635.2	hg19	CCDS12097.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.107895	0.77096	.	.	ENSG00000172000	ENST00000307635	.	.	.	2.13	2.13	0.27403	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.5549	0.27819	1.0:0.0:0.0:0.0	.	.	.	.	X	335	.	ENSP00000302603:R335X	R	+	1	2	ZNF556	2828959	0.000000	0.05858	0.002000	0.10522	0.003000	0.03518	-1.875000	0.01634	0.826000	0.34661	0.334000	0.21626	AGA	.	.		0.507	ZNF556-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451638.2	NM_024967		T	2877959	A	T	2877959	4	4	360	1	0	0	0	0	0	1	0	0	18002	296	11	4	1017	4	ZNF556	19	2877959	Nonsense_Mutation	SNP	A	TCGA-XR-A8TF-01A-11D-A35Z-10		2877959	56251024	125	50426										
ITGB1BP3	27231	hgsc.bcm.edu	37	chr19	3942230	3942230	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	ccggacgcggatgcggccacAgaacggccaggcctgcagcg	16	15	0	1	rs143940174	byFrequency	TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr19:3942230A>G	ENST00000168977.2	+	8	942	c.652A>G	c.(652-654)Aga>Gga	p.R218G	NMRK2_ENST00000593949.1_Missense_Mutation_p.R223G|NMRK2_ENST00000599576.1_3'UTR	NM_170678.2	NP_733778.1	Q9NPI5	NRK2_HUMAN	nicotinamide riboside kinase 2	218					NAD biosynthetic process (GO:0009435)|negative regulation of myoblast differentiation (GO:0045662)	intracellular (GO:0005622)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|ribosylnicotinamide kinase activity (GO:0050262)										ATGCGGCCACAGAACGGCCAG	0.657																																					p.R218G		Atlas-SNP	.											.	.	.	.	0			c.A652G						.						21	21	21					19																	3942230		2201	4297	6498	SO:0001583	missense	27231	exon8			GGCCACAGAACGG	AF190819	CCDS12115.1, CCDS74259.1	19p13.3	2013-10-28	2012-05-31	2012-05-31	ENSG00000077009	ENSG00000077009			17871	protein-coding gene	gene with protein product	"muscle-specific beta 1 integrin binding protein", "nicotinamide riboside kinase 2"	608705	"integrin beta 1 binding protein 3"	ITGB1BP3		10613898, 15137942	Standard	NM_170678		Approved	MIBP, NRK2	uc002lyz.4	Q9NPI5	OTTHUMG00000181758	ENST00000168977.2:c.652A>G	chr19.hg19:g.3942230A>G	ENSP00000168977:p.Arg218Gly	89.0	0.0		93.0	30.0	NM_170678	B7ZKR3|Q52M81|Q9NZK3	Missense_Mutation	SNP	ENST00000168977.2	hg19	CCDS12115.1	.	.	.	.	.	.	.	.	.	.	A	4.796	0.148092	0.09134	.	.	ENSG00000077009	ENST00000168977;ENST00000395034	T	0.44881	0.91	2.42	-0.334	0.12666	.	.	.	.	.	T	0.18087	0.0434	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.17531	-1.0366	9	0.46703	T	0.11	2.9665	1.4237	0.02318	0.4205:0.0:0.2593:0.3202	.	223;218	B7ZKR3;Q9NPI5	.;NRK2_HUMAN	G	218;174	ENSP00000168977:R218G	ENSP00000168977:R218G	R	+	1	2	ITGB1BP3	3893230	0.000000	0.05858	0.018000	0.16275	0.153000	0.21895	0.013000	0.13310	0.188000	0.20168	0.397000	0.26171	AGA	.	A|0.999;C|0.001		0.657	NMRK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457492.1	NM_014446, NM_170678		G	3942230	A	G	3942230	3	3	360	1	0	0	0	0	1	0	0	0	7902	180	7	2	678	2	ITGB1BP3	19	3942230	Missense_Mutation	SNP	A	TCGA-XR-A8TF-01A-11D-A35Z-10	1064271	3942230	55186753	126	50427										
SH2D3A	10045	hgsc.bcm.edu	37	chr19	6755305	6755305	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	tgctcgttcggggcaaggcaGatatgggcatggtggaggct	18	7	0	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr19:6755305G>C	ENST00000245908.6	-	5	787	c.518C>G	c.(517-519)tCt>tGt	p.S173C	SH2D3A_ENST00000599563.1_5'UTR|SH2D3A_ENST00000437152.3_Missense_Mutation_p.S51C	NM_005490.2	NP_005481.2	Q9BRG2	SH23A_HUMAN	SH2 domain containing 3A	173					JNK cascade (GO:0007254)|positive regulation of signal transduction (GO:0009967)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)|SH3/SH2 adaptor activity (GO:0005070)			breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|skin(3)|urinary_tract(1)	24						GGGCAAGGCAGATATGGGCAT	0.587																																					p.S173C		Atlas-SNP	.											.	SH2D3A	53	.	0			c.C518G						.						89	93	91					19																	6755305		2203	4300	6503	SO:0001583	missense	10045	exon5			AAGGCAGATATGG	AF124249	CCDS12173.1	19p13.3	2013-02-14	2002-01-14			ENSG00000125731		"SH2 domain containing"	16885	protein-coding gene	gene with protein product		604721	"SH2 domain-containing 3A"			10187783	Standard	NM_005490		Approved	NSP1	uc002mft.3	Q9BRG2		ENST00000245908.6:c.518C>G	chr19.hg19:g.6755305G>C	ENSP00000245908:p.Ser173Cys	155.0	0.0		143.0	50.0	NM_005490	A8K9R6|B4DRS7|Q9Y2X4	Missense_Mutation	SNP	ENST00000245908.6	hg19	CCDS12173.1	.	.	.	.	.	.	.	.	.	.	G	8.921	0.961100	0.18583	.	.	ENSG00000125731	ENST00000245908;ENST00000437152	T;T	0.42131	2.58;0.98	4.1	-1.33	0.09172	.	0.774326	0.10546	N	0.662111	T	0.29850	0.0746	L	0.42245	1.32	0.09310	N	1	B;B	0.14438	0.01;0.001	B;B	0.11329	0.006;0.001	T	0.31364	-0.9946	10	0.59425	D	0.04	-0.0312	4.0897	0.09963	0.2536:0.3715:0.3748:0.0	.	51;173	B4DRS7;Q9BRG2	.;SH23A_HUMAN	C	173;51	ENSP00000245908:S173C;ENSP00000393303:S51C	ENSP00000245908:S173C	S	-	2	0	SH2D3A	6706305	0.033000	0.19621	0.043000	0.18650	0.080000	0.17528	1.826000	0.39092	-0.089000	0.12484	0.313000	0.20887	TCT	.	.		0.587	SH2D3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458016.1	NM_005490		C	6755305	G	C	6755305	3	2	360	1	0	0	0	0	1	0	0	0	14248	942	33	4	1236	4	SH2D3A	19	6755305	Missense_Mutation	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10	2813075	6755305	52373678	127	50428										
MUC16	94025	hgsc.bcm.edu	37	chr19	9066432	9066432	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	ttcttgtggatatttctggcAaaactgtggactgagaaggg	13	5	2	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr19:9066432A>C	ENST00000397910.4	-	3	21217	c.21014T>G	c.(21013-21015)tTg>tGg	p.L7005W		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	7007	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TATTTCTGGCAAAACTGTGGA	0.512																																					p.L7005W		Atlas-SNP	.											.	MUC16	4315	.	0			c.T21014G						.						291	268	276					19																	9066432		1988	4173	6161	SO:0001583	missense	94025	exon3			TCTGGCAAAACTG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.21014T>G	chr19.hg19:g.9066432A>C	ENSP00000381008:p.Leu7005Trp	106.0	0.0		117.0	36.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	a	3.961	-0.010309	0.07727	.	.	ENSG00000181143	ENST00000397910	T	0.03301	3.98	3.05	-0.419	0.12340	.	.	.	.	.	T	0.04182	0.0116	L	0.29908	0.895	.	.	.	P	0.47106	0.89	P	0.46362	0.514	T	0.37174	-0.9717	8	0.87932	D	0	.	7.597	0.28054	0.2532:0.0:0.7468:0.0	.	7005	B5ME49	.	W	7005	ENSP00000381008:L7005W	ENSP00000381008:L7005W	L	-	2	0	MUC16	8927432	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.470000	0.22084	0.012000	0.14892	-1.615000	0.00797	TTG	.	.		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	9066432	A	C	9066432	3	2	360	1	0	0	0	0	1	0	0	0	9982	131	5	5	22837	5	MUC16	19	9066432	Missense_Mutation	SNP	A	TCGA-XR-A8TF-01A-11D-A35Z-10	2311127	9066432	50062551	128	50429										
MAP1S	55201	hgsc.bcm.edu	37	chr19	17838628	17838629	+	Frame_Shift_Del	DEL	AC	AC	-													0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	tgcggcagactcagacgaagAcacagagggctttggagtcc							TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr19:17838628_17838629delAC	ENST00000324096.4	+	5	2586_2587	c.2435_2436delAC	c.(2434-2436)gacfs	p.D812fs	MAP1S_ENST00000544059.2_Frame_Shift_Del_p.D786fs|CTD-3149D2.4_ENST00000595363.1_RNA|MAP1S_ENST00000597681.1_3'UTR	NM_018174.4	NP_060644.4	Q66K74	MAP1S_HUMAN	microtubule-associated protein 1S	812	Necessary for association with microtubules.|Necessary for interaction with RASSF1 isoform A and isoform C.|Pro-rich.				apoptotic DNA fragmentation (GO:0006309)|brain development (GO:0007420)|execution phase of apoptosis (GO:0097194)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|nervous system development (GO:0007399)|neuron projection morphogenesis (GO:0048812)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	actin filament binding (GO:0051015)|beta-tubulin binding (GO:0048487)|DNA binding (GO:0003677)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	25						TCAGACGAAGACACAGAGGGCT	0.673																																					p.812_812del		Atlas-INDEL	.											.	MAP1S	74	.	0			c.2434_2435del						.																																			SO:0001589	frameshift_variant	55201	exon5			.	BC067115	CCDS32954.1	19p13.12	2008-02-05	2006-07-04	2006-07-04		ENSG00000130479			15715	protein-coding gene	gene with protein product		607573	"chromosome 19 open reading frame 5", "VCY2 interacting protein 1", "BPY2 interacting protein 1"	C19orf5, VCY2IP1, BPY2IP1		11827465, 15528209, 16297881, 14627543	Standard	NM_018174		Approved	FLJ10669, MAP8	uc002nhe.1	Q66K74		ENST00000324096.4:c.2435_2436delAC	chr19.hg19:g.17838630_17838631delAC	ENSP00000325313:p.Asp812fs	119.0	0.0		119.0	34.0	NM_018174	B4DH53|Q27QB1|Q6NXF1|Q8N3L8|Q8N3W5|Q8NI88|Q96H94|Q96IT4|Q96SP8|Q9BRC6|Q9H928|Q9NVK7	Frame_Shift_Del	DEL	ENST00000324096.4	hg19	CCDS32954.1																																																																																			.	.		0.673	MAP1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466027.1	NM_018174		-	17838629	AC	-	17838628	7	5	360	1	0	1	0	1	0	0	0	0	9243	275	10	0	2453	0	MAP1S	19	17838628	Frame_Shift_Del	DEL	AC	TCGA-XR-A8TF-01A-11D-A35Z-10	8772196	17838628	41290355	129	50430										
INSL3	3640	hgsc.bcm.edu	37	chr19	17932271	17932271	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	cccaacgcgaacaccagggcAgggcccagcagcaccagcgc	12	18	0	0			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr19:17932271A>T	ENST00000317306.7	-	1	61	c.45T>A	c.(43-45)ccT>ccA	p.P15P	INSL3_ENST00000379695.5_Silent_p.P15P	NM_005543.3	NP_005534.2	P51460	INSL3_HUMAN	insulin-like 3 (Leydig cell)	15					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cell-cell signaling (GO:0007267)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|oocyte maturation (GO:0001556)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell proliferation (GO:0008284)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|perinuclear region of cytoplasm (GO:0048471)	insulin receptor binding (GO:0005158)|protease binding (GO:0002020)|receptor binding (GO:0005102)			breast(1)|lung(1)	2						ACACCAGGGCAGGGCCCAGCA	0.731																																					p.P15P		Atlas-SNP	.											.	INSL3	8	.	0			c.T45A						.						4	7	6					19																	17932271		1709	3178	4887	SO:0001819	synonymous_variant	3640	exon1			CAGGGCAGGGCCC		CCDS12365.1, CCDS58655.1	19p13.2-p12	2013-02-26	2003-05-13			ENSG00000248099		"Endogenous ligands"	6086	protein-coding gene	gene with protein product	"prepro-INSL3"	146738	"relaxin-like factor"	RLNL		8020942	Standard	NM_001265587		Approved	RLF, MGC119818, MGC119819	uc010ebf.2	P51460		ENST00000317306.7:c.45T>A	chr19.hg19:g.17932271A>T		166.0	0.0		153.0	79.0	NM_005543	B4DZ72|G3XAG0|Q3KPI5|Q3KPI6|Q6YNB5|Q9UEA2|Q9UPH6	Silent	SNP	ENST00000317306.7	hg19	CCDS12365.1																																																																																			.	.		0.731	INSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466836.1	NM_005543		T	17932271	A	T	17932271	2	4	360	1	0	0	0	0	0	0	0	1	7776	175	7	4		4	INSL3	19	17932271	Silent	SNP	A	TCGA-XR-A8TF-01A-11D-A35Z-10	93643	17932271	41196712	130	50431										
KCNN1	3780	hgsc.bcm.edu	37	chr19	18092673	18092673	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	cggctggccttcacgtacgcGccctcggtggccgaggccga	15	16	1	0	rs371311512		TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr19:18092673G>T	ENST00000222249.9	+	5	973	c.654G>T	c.(652-654)gcG>gcT	p.A218A		NM_002248.3	NP_002239.2	Q92952	KCNN1_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 1	218					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			endometrium(1)|kidney(1)|lung(5)|urinary_tract(1)	8					Miconazole(DB01110)|Procaine(DB00721)	TCACGTACGCGCCCTCGGTGG	0.657																																					p.A218A		Atlas-SNP	.											.	KCNN1	74	.	0			c.G654T						.						27	29	28					19																	18092673		2200	4290	6490	SO:0001819	synonymous_variant	3780	exon5			GTACGCGCCCTCG	U69883	CCDS67611.1	19p13.1	2012-07-05				ENSG00000105642		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6290	protein-coding gene	gene with protein product		602982				8781233, 10516439, 16382103	Standard	NM_002248		Approved	KCa2.1, hSK1	uc002nht.3	Q92952		ENST00000222249.9:c.654G>T	chr19.hg19:g.18092673G>T		71.0	0.0		71.0	20.0	NM_002248	Q5KR10|Q6DJU4	Silent	SNP	ENST00000222249.9	hg19																																																																																				.	.		0.657	KCNN1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471896.2	NM_002248		T	18092673	G	T	18092673	2	4	360	1	0	0	0	0	0	0	0	1	8087	1074	38	1		1	KCNN1	19	18092673	Silent	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10	160402	18092673	41036310	131	50432										
ZNF90	7643	hgsc.bcm.edu	37	chr19	20228890	20228890	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	aaaaaaacctttcaaatgtaTagaatgtggcaaagctttca	6	6	2	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr19:20228890T>A	ENST00000418063.2	+	4	639	c.527T>A	c.(526-528)aTa>aAa	p.I176K	ZNF90_ENST00000474284.1_Intron	NM_007138.1	NP_009069.1	Q03938	ZNF90_HUMAN	zinc finger protein 90	176					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|lung(2)|ovary(1)|skin(1)	5						TTCAAATGTATAGAATGTGGC	0.338																																					p.I176K		Atlas-SNP	.											.	ZNF90	93	.	0			c.T527A						.						33	30	31					19																	20228890		692	1591	2283	SO:0001583	missense	7643	exon4			AATGTATAGAATG	M61870	CCDS46028.1	19p12	2013-01-08	2006-02-01		ENSG00000213988	ENSG00000213988		"Zinc fingers, C2H2-type", "-"	13165	protein-coding gene	gene with protein product		603973	"zinc finger protein 90 (HTF9)"			8467795	Standard	NM_007138		Approved	HTF9	uc002nor.2	Q03938	OTTHUMG00000158057	ENST00000418063.2:c.527T>A	chr19.hg19:g.20228890T>A	ENSP00000410466:p.Ile176Lys	151.0	0.0		162.0	7.0	NM_007138	B9EH87	Missense_Mutation	SNP	ENST00000418063.2	hg19	CCDS46028.1	.	.	.	.	.	.	.	.	.	.	T	0.061	-1.223539	0.01530	.	.	ENSG00000213988	ENST00000418063	T	0.15834	2.39	1.18	-1.08	0.09936	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04952	0.0133	N	0.00201	-1.865	0.09310	N	1	D	0.53151	0.958	P	0.54590	0.756	T	0.09400	-1.0676	8	.	.	.	.	1.5824	0.02637	0.3582:0.2957:0.0:0.3462	.	176	Q03938	ZNF90_HUMAN	K	176	ENSP00000410466:I176K	.	I	+	2	0	ZNF90	20089890	0.000000	0.05858	0.023000	0.16930	0.023000	0.10783	-3.899000	0.00339	0.251000	0.21505	0.248000	0.18094	ATA	.	.		0.338	ZNF90-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350101.1	NM_007138		A	20228890	T	A	20228890	3	1	360	1	0	0	0	0	1	0	0	0	18214	1406	49	4	541	4	ZNF90	19	20228890	Missense_Mutation	SNP	T	TCGA-XR-A8TF-01A-11D-A35Z-10	2136217	20228890	38900093	132	50433										
UPK1A	11045	hgsc.bcm.edu	37	chr19	36166776	36166776	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	cacatctggtcccatggactGggtgaacttcacgtcagcct	10	13	3	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr19:36166776G>T	ENST00000222275.2	+	5	503	c.503G>T	c.(502-504)tGg>tTg	p.W168L	UPK1A-AS1_ENST00000443196.1_RNA|UPK1A_ENST00000379013.2_Missense_Mutation_p.W168L	NM_007000.2	NP_008931.1	O00322	UPK1A_HUMAN	uroplakin 1A	168					epithelial cell differentiation (GO:0030855)|protein oligomerization (GO:0051259)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	monosaccharide binding (GO:0048029)|protein homodimerization activity (GO:0042803)			breast(1)|large_intestine(4)|lung(2)|stomach(2)	9	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CCCATGGACTGGGTGAACTTC	0.617																																					p.W168L		Atlas-SNP	.											.	UPK1A	23	.	0			c.G503T						.						76	66	69					19																	36166776		2203	4300	6503	SO:0001583	missense	11045	exon5			TGGACTGGGTGAA	AF085807	CCDS12470.1, CCDS62640.1	19q13.1	2013-02-14			ENSG00000105668	ENSG00000105668		"Tetraspanins"	12577	protein-coding gene	gene with protein product		611557				9846985, 10404304	Standard	NM_007000		Approved	TSPAN21	uc002oaw.3	O00322	OTTHUMG00000048115	ENST00000222275.2:c.503G>T	chr19.hg19:g.36166776G>T	ENSP00000222275:p.Trp168Leu	54.0	0.0		43.0	12.0	NM_007000	Q3KNU5|Q3KNU6	Missense_Mutation	SNP	ENST00000222275.2	hg19	CCDS12470.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.625855	0.87560	.	.	ENSG00000105668	ENST00000222275;ENST00000379013	T;T	0.81330	-1.48;-1.48	5.22	5.22	0.72569	Tetraspanin, EC2 domain (1);	0.000000	0.64402	D	0.000001	D	0.88503	0.6454	M	0.66939	2.045	0.54753	D	0.999985	D;D	0.69078	0.993;0.997	P;D	0.79108	0.857;0.992	D	0.89641	0.3862	10	0.87932	D	0	0.8394	16.2551	0.82510	0.0:0.0:1.0:0.0	.	168;168	O00322-2;O00322	.;UPK1A_HUMAN	L	168	ENSP00000222275:W168L;ENSP00000368298:W168L	ENSP00000222275:W168L	W	+	2	0	UPK1A	40858616	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.340000	0.72973	2.433000	0.82419	0.549000	0.68633	TGG	.	.		0.617	UPK1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109486.3			T	36166776	G	T	36166776	3	4	360	1	0	0	0	0	1	0	0	0	17022	1357	47	3	521	3	UPK1A	19	36166776	Missense_Mutation	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10	15937886	36166776	22962207	133	50434										
ZNF382	84911	hgsc.bcm.edu	37	chr19	37117233	37117233	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	tgatggaaaagttttgaaaaAtatttcagaactagtcatta	7	3	2	3			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr19:37117233A>G	ENST00000292928.2	+	5	547	c.434A>G	c.(433-435)aAt>aGt	p.N145S	ZNF382_ENST00000435416.1_Missense_Mutation_p.N144S|ZNF382_ENST00000423582.1_Missense_Mutation_p.N96S|CTD-3234P18.2_ENST00000585467.1_lincRNA|ZNF382_ENST00000439428.1_Missense_Mutation_p.N144S	NM_001256838.1|NM_032825.4	NP_001243767.1|NP_116214.2	Q96SR6	ZN382_HUMAN	zinc finger protein 382	145	Represses transcription. {ECO:0000250}.				negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	34	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			GTTTTGAAAAATATTTCAGAA	0.323																																					p.N145S		Atlas-SNP	.											.	ZNF382	87	.	0			c.A434G						.						63	71	69					19																	37117233		2190	4292	6482	SO:0001583	missense	84911	exon5			TGAAAAATATTTC	AF513816	CCDS33004.1, CCDS58659.1	19q13.13	2013-01-08			ENSG00000161298	ENSG00000161298		"Zinc fingers, C2H2-type", "-"	17409	protein-coding gene	gene with protein product		609516					Standard	NM_032825		Approved	FLJ14686, KS1	uc010efb.4	Q96SR6	OTTHUMG00000048153	ENST00000292928.2:c.434A>G	chr19.hg19:g.37117233A>G	ENSP00000292928:p.Asn145Ser	406.0	0.0		326.0	194.0	NM_032825	A3KMP6|A8MT55|C9K0V5|Q53ZY8|Q5JPJ2	Missense_Mutation	SNP	ENST00000292928.2	hg19	CCDS33004.1	.	.	.	.	.	.	.	.	.	.	A	5.998	0.368011	0.11352	.	.	ENSG00000161298	ENST00000423582;ENST00000292928;ENST00000439428;ENST00000435416	T;T;T;T	0.06068	3.35;3.55;3.56;3.56	4.83	4.83	0.62350	.	0.000000	0.45867	D	0.000337	T	0.04679	0.0127	N	0.16098	0.37	0.27857	N	0.940528	P;P;P	0.50528	0.936;0.936;0.895	P;P;B	0.47645	0.553;0.553;0.351	T	0.14671	-1.0464	10	0.05436	T	0.98	.	10.9744	0.47456	1.0:0.0:0.0:0.0	.	144;144;145	Q96SR6-2;Q96SR6-3;Q96SR6	.;.;ZN382_HUMAN	S	96;145;144;144	ENSP00000389722:N96S;ENSP00000292928:N145S;ENSP00000407593:N144S;ENSP00000410113:N144S	ENSP00000292928:N145S	N	+	2	0	ZNF382	41809073	0.388000	0.25197	1.000000	0.80357	0.908000	0.53690	1.778000	0.38614	2.163000	0.67991	0.460000	0.39030	AAT	.	.		0.323	ZNF382-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109562.2	NM_032825		G	37117233	A	G	37117233	3	3	360	1	0	0	0	0	1	0	0	0	17888	101	4	2	444	2	ZNF382	19	37117233	Missense_Mutation	SNP	A	TCGA-XR-A8TF-01A-11D-A35Z-10	950457	37117233	22011750	134	50435										
GRIK5	2901	hgsc.bcm.edu	37	chr19	42507596	42507596	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	aaatgccaccaatgttctccAtgcccaaacctggagggcga	9	13	1	0			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr19:42507596A>T	ENST00000262895.3	-	18	2401	c.2402T>A	c.(2401-2403)aTg>aAg	p.M801K	GRIK5_ENST00000301218.4_Missense_Mutation_p.M801K|GRIK5_ENST00000593562.1_Missense_Mutation_p.M801K	NM_002088.4	NP_002079.3	Q16478	GRIK5_HUMAN	glutamate receptor, ionotropic, kainate 5	801					cellular response to glucose stimulus (GO:0071333)|establishment of localization in cell (GO:0051649)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|positive regulation of neuron apoptotic process (GO:0043525)|protein retention in ER lumen (GO:0006621)|receptor clustering (GO:0043113)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic vesicle fusion to presynaptic membrane (GO:0031630)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(11)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	35		Prostate(69;0.059)				AATGTTCTCCATGCCCAAACC	0.577																																					p.M801K		Atlas-SNP	.											.	GRIK5	220	.	0			c.T2402A						.						96	80	85					19																	42507596		2203	4300	6503	SO:0001583	missense	2901	exon18			TTCTCCATGCCCA		CCDS12595.1	19q13.2	2012-08-29			ENSG00000105737	ENSG00000105737		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4583	protein-coding gene	gene with protein product		600283		GRIK2		7527545	Standard	NM_002088		Approved	GluK5, KA2	uc002osj.2	Q16478	OTTHUMG00000044573	ENST00000262895.3:c.2402T>A	chr19.hg19:g.42507596A>T	ENSP00000262895:p.Met801Lys	108.0	0.0		103.0	63.0	NM_002088	Q8WWG8	Missense_Mutation	SNP	ENST00000262895.3	hg19	CCDS12595.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.76|19.76	3.887112|3.887112	0.72410|0.72410	.|.	.|.	ENSG00000105737|ENSG00000105737	ENST00000454993|ENST00000262895;ENST00000301218	.|T;T	.|0.54479	.|0.57;0.57	4.06|4.06	4.06|4.06	0.47325|0.47325	.|Ionotropic glutamate receptor (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.54663|0.54663	0.1872|0.1872	L|L	0.49571|0.49571	1.57|1.57	0.53688|0.53688	D|D	0.999974|0.999974	.|B	.|0.31859	.|0.343	.|B	.|0.42361	.|0.385	T|T	0.60850|0.60850	-0.7181|-0.7181	5|10	.|0.87932	.|D	.|0	.|.	12.1313|12.1313	0.53944|0.53944	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|801	.|Q16478	.|GRIK5_HUMAN	Q|K	177|801	.|ENSP00000262895:M801K;ENSP00000301218:M801K	.|ENSP00000262895:M801K	H|M	-|-	3|2	2|0	GRIK5|GRIK5	47199436|47199436	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.928000|0.928000	0.56348|0.56348	8.842000|8.842000	0.92136|0.92136	1.697000|1.697000	0.51169|0.51169	0.454000|0.454000	0.30748|0.30748	CAT|ATG	.	.		0.577	GRIK5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463453.1			T	42507596	A	T	42507596	3	4	360	1	0	0	0	0	1	0	0	0	6786	217	8	4	548	4	GRIK5	19	42507596	Missense_Mutation	SNP	A	TCGA-XR-A8TF-01A-11D-A35Z-10	5390363	42507596	16621387	135	50436										
PRKCG	5582	hgsc.bcm.edu	37	chr19	54393251	54393251	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	ggagatccgggctcccacagCagatgagatccacgtaactg	12	12	0	3			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr19:54393251C>T	ENST00000263431.3	+	5	791	c.509C>T	c.(508-510)gCa>gTa	p.A170V	PRKCG_ENST00000542049.1_Missense_Mutation_p.A57V|PRKCG_ENST00000536044.1_Missense_Mutation_p.A170V|PRKCG_ENST00000540413.1_Missense_Mutation_p.A170V	NM_002739.3	NP_002730.1	P05129	KPCG_HUMAN	protein kinase C, gamma	170	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cell death (GO:0008219)|chemosensory behavior (GO:0007635)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein ubiquitination (GO:0031397)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of mismatch repair (GO:0032425)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to morphine (GO:0043278)|response to pain (GO:0048265)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic membrane (GO:0097060)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(4)|ovary(2)|pancreas(2)|skin(1)	10	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)	Tamoxifen(DB00675)	GCTCCCACAGCAGATGAGATC	0.711																																					p.A170V		Atlas-SNP	.											.	PRKCG	246	.	0			c.C509T						.						11	13	12					19																	54393251		2172	4244	6416	SO:0001583	missense	5582	exon5			CCACAGCAGATGA	M13977	CCDS12867.1	19q13.4	2014-09-17			ENSG00000126583	ENSG00000126583	2.7.11.1		9402	protein-coding gene	gene with protein product	"PKC-gamma"	176980		PKCG, SCA14		8432525, 3755548	Standard	NM_002739		Approved	PKCC, MGC57564	uc002qcq.1	P05129	OTTHUMG00000064846	ENST00000263431.3:c.509C>T	chr19.hg19:g.54393251C>T	ENSP00000263431:p.Ala170Val	93.0	0.0		76.0	18.0	NM_002739	B7Z8Q0	Missense_Mutation	SNP	ENST00000263431.3	hg19	CCDS12867.1	.	.	.	.	.	.	.	.	.	.	c	9.550	1.115735	0.20795	.	.	ENSG00000126583	ENST00000536044;ENST00000540413;ENST00000263431;ENST00000542049	T;T;T;T	0.41065	1.01;1.01;1.01;1.01	4.75	2.23	0.28157	C2 membrane targeting protein (1);C2 calcium/lipid-binding domain, CaLB (1);	.	.	.	.	T	0.30510	0.0767	L	0.45352	1.415	0.09310	N	1	B;B;B;B;B	0.21688	0.059;0.009;0.002;0.004;0.0	B;B;B;B;B	0.08055	0.003;0.002;0.001;0.001;0.0	T	0.15292	-1.0442	8	.	.	.	.	6.6773	0.23102	0.1816:0.5574:0.261:0.0	.	57;170;170;170;170	B7Z8Q0;F5H5C4;B7Z870;B7Z3W6;P05129	.;.;.;.;KPCG_HUMAN	V	170;170;170;57	ENSP00000440541:A170V;ENSP00000443493:A170V;ENSP00000263431:A170V;ENSP00000438090:A57V	.	A	+	2	0	PRKCG	59085063	0.000000	0.05858	0.001000	0.08648	0.024000	0.10985	0.820000	0.27323	1.090000	0.41315	0.651000	0.88453	GCA	.	.		0.711	PRKCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139233.3	NM_002739		T	54393251	C	T	54393251	3	4	360	1	0	0	0	0	1	0	0	0	12524	710	25	3	527	3	PRKCG	19	54393251	Missense_Mutation	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10	11885655	54393251	4735732	136	50437										
ATRN	8455	hgsc.bcm.edu	37	chr20	3619493	3619493	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	agcaacttcttcgagagatgCaacagatggccagccgtccc	10	13	1	2			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr20:3619493C>T	ENST00000262919.5	+	27	4029	c.3961C>T	c.(3961-3963)Caa>Taa	p.Q1321*		NM_139321.2	NP_647537.1	O75882	ATRN_HUMAN	attractin	1321					cerebellum development (GO:0021549)|inflammatory response (GO:0006954)|myelination (GO:0042552)|pigmentation (GO:0043473)|regulation of multicellular organism growth (GO:0040014)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			breast(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	59						TCGAGAGATGCAACAGATGGC	0.423																																					p.Q1321X		Atlas-SNP	.											.	ATRN	118	.	0			c.C3961T						.						86	79	82					20																	3619493		2203	4300	6503	SO:0001587	stop_gained	8455	exon27			GAGATGCAACAGA	AF034957	CCDS13053.1, CCDS13054.1	20p13	2008-07-02			ENSG00000088812	ENSG00000088812			885	protein-coding gene	gene with protein product	"mahogany protein"	603130				9736737, 8596018	Standard	NM_139321		Approved	DPPT-L, MGCA	uc002wim.2	O75882	OTTHUMG00000031746	ENST00000262919.5:c.3961C>T	chr20.hg19:g.3619493C>T	ENSP00000262919:p.Gln1321*	82.0	0.0		96.0	43.0	NM_139321	A8KAE5|O60295|O95414|Q3MIT3|Q5TDA2|Q5TDA4|Q5VYW3|Q9NTQ3|Q9NTQ4|Q9NU01|Q9NZ57|Q9NZ58|Q9UC75|Q9UDF5	Nonsense_Mutation	SNP	ENST00000262919.5	hg19	CCDS13053.1	.	.	.	.	.	.	.	.	.	.	C	43	10.275521	0.99373	.	.	ENSG00000088812	ENST00000262919	.	.	.	5.09	5.09	0.68999	.	0.202236	0.43747	D	0.000531	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-10.1928	16.0325	0.80588	0.0:1.0:0.0:0.0	.	.	.	.	X	1321	.	ENSP00000262919:Q1321X	Q	+	1	0	ATRN	3567493	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.242000	0.78210	2.638000	0.89438	0.650000	0.86243	CAA	.	.		0.423	ATRN-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077740.2	NM_139321		T	3619493	C	T	3619493	4	4	360	1	0	0	0	0	0	1	0	0	1206	711	25	3	4089	3	ATRN	20	3619493	Nonsense_Mutation	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10		3619493	59406027	137	50438										
DHX35	60625	hgsc.bcm.edu	37	chr20	37647529	37647529	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	aatcccatgtttgccaaaatGctgcttgaatcaggtgggta	10	8	1	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr20:37647529G>C	ENST00000252011.3	+	15	1518	c.1485G>C	c.(1483-1485)atG>atC	p.M495I	DHX35_ENST00000373325.2_Missense_Mutation_p.M495I|DHX35_ENST00000373323.4_Missense_Mutation_p.M464I	NM_021931.3	NP_068750.2	Q9H5Z1	DHX35_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 35	495					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(13)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	40		Myeloproliferative disorder(115;0.00878)				TTGCCAAAATGCTGCTTGAAT	0.453																																					p.M495I		Atlas-SNP	.											.	DHX35	82	.	0			c.G1485C						.						167	156	160					20																	37647529		2203	4300	6503	SO:0001583	missense	60625	exon15			CAAAATGCTGCTT	AK026412	CCDS13310.1, CCDS54463.1	20q11.22-q12	2003-06-13	2003-06-13	2003-06-13	ENSG00000101452	ENSG00000101452		"DEAH-boxes"	15861	protein-coding gene	gene with protein product			"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 35"	C20orf15, DDX35			Standard	NM_001190809		Approved	FLJ22759, KAIA0875	uc002xjh.3	Q9H5Z1	OTTHUMG00000032463	ENST00000252011.3:c.1485G>C	chr20.hg19:g.37647529G>C	ENSP00000252011:p.Met495Ile	110.0	0.0		126.0	64.0	NM_021931	A2RTX3|B4E0J0|F5GXM6|Q5THR0|Q9H4H7|Q9H6T6	Missense_Mutation	SNP	ENST00000252011.3	hg19	CCDS13310.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.514404	0.85389	.	.	ENSG00000101452	ENST00000373325;ENST00000252011;ENST00000373323;ENST00000373321	T;T;T	0.34275	1.37;1.37;1.37	5.94	5.94	0.96194	Helicase-associated domain (2);	0.000000	0.85682	D	0.000000	T	0.46776	0.1410	L	0.45137	1.4	0.80722	D	1	B;P	0.50528	0.415;0.936	B;P	0.50970	0.198;0.655	T	0.36504	-0.9745	10	0.72032	D	0.01	.	20.3594	0.98849	0.0:0.0:1.0:0.0	.	464;495	F5GXM6;Q9H5Z1	.;DHX35_HUMAN	I	495;495;464;1	ENSP00000362422:M495I;ENSP00000252011:M495I;ENSP00000362420:M464I	ENSP00000252011:M495I	M	+	3	0	DHX35	37080943	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.816000	0.99350	2.816000	0.96949	0.563000	0.77884	ATG	.	.		0.453	DHX35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079212.2	NM_021931		C	37647529	G	C	37647529	3	2	360	1	0	0	0	0	1	0	0	0	4510	1319	46	4	1543	4	DHX35	20	37647529	Missense_Mutation	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10	34028036	37647529	25377991	138	50439										
OSBPL2	9885	hgsc.bcm.edu	37	chr20	60854388	60854388	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	gaggcaccatcaccctggagCtgctcaagtgagtgtcggtg	14	11	2	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr20:60854388C>T	ENST00000313733.3	+	7	869	c.667C>T	c.(667-669)Ctg>Ttg	p.L223L	OSBPL2_ENST00000439951.2_Silent_p.L131L|OSBPL2_ENST00000358053.2_Silent_p.L211L	NM_144498.1	NP_653081.1	Q9H1P3	OSBL2_HUMAN	oxysterol binding protein-like 2	223					lipid transport (GO:0006869)		cholesterol binding (GO:0015485)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	17	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;1.33e-06)			CACCCTGGAGCTGCTCAAGTG	0.567																																					p.L223L		Atlas-SNP	.											.	OSBPL2	51	.	0			c.C667T						.						76	64	68					20																	60854388		2203	4300	6503	SO:0001819	synonymous_variant	9885	exon7			CTGGAGCTGCTCA	AB018315	CCDS13494.1, CCDS13495.1, CCDS63323.1	20q13.3	2008-08-01	2001-11-28		ENSG00000130703	ENSG00000130703		"Oxysterol binding proteins"	15761	protein-coding gene	gene with protein product		606731	"oxysterol-binding protein-like 2"			10588946, 11861666	Standard	NM_144498		Approved	KIAA0772, ORP-2	uc002yck.1	Q9H1P3	OTTHUMG00000032909	ENST00000313733.3:c.667C>T	chr20.hg19:g.60854388C>T		103.0	0.0		114.0	48.0	NM_144498	A8K736|Q6IBT0|Q9BZB1|Q9Y4B8	Silent	SNP	ENST00000313733.3	hg19	CCDS13495.1																																																																																			.	.		0.567	OSBPL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080021.1	NM_014835		T	60854388	C	T	60854388	2	4	360	1	0	0	0	0	0	0	0	1	11287	796	28	3		3	OSBPL2	20	60854388	Silent	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10	23206859	60854388	2171132	139	50440										
DEPDC5	9681	hgsc.bcm.edu	37	chr22	32266715	32266715	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	acagggctactcctccacaaActccagtgacagcaggtgag	10	13	0	2			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr22:32266715A>C	ENST00000382112.3	+	33	3513	c.3443A>C	c.(3442-3444)aAc>aCc	p.N1148T	DEPDC5_ENST00000400246.1_Missense_Mutation_p.N1157T|DEPDC5_ENST00000539165.1_5'UTR|DEPDC5_ENST00000382111.2_Missense_Mutation_p.N1157T|DEPDC5_ENST00000382105.2_Missense_Mutation_p.N1079T|DEPDC5_ENST00000400248.2_Missense_Mutation_p.N1126T|DEPDC5_ENST00000494060.1_3'UTR|DEPDC5_ENST00000266091.3_Missense_Mutation_p.N1135T|DEPDC5_ENST00000535622.1_Missense_Mutation_p.N1057T|DEPDC5_ENST00000400249.2_Missense_Mutation_p.N1126T	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	1157					intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						TCCTCCACAAACTCCAGTGAC	0.532																																					p.N1157T		Atlas-SNP	.											.	DEPDC5	266	.	0			c.A3470C						.						88	90	90					22																	32266715		1997	4172	6169	SO:0001583	missense	9681	exon34			CCACAAACTCCAG	AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.3443A>C	chr22.hg19:g.32266715A>C	ENSP00000371546:p.Asn1148Thr	138.0	0.0		139.0	8.0	NM_001242896	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Missense_Mutation	SNP	ENST00000382112.3	hg19	CCDS46692.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.73|12.73	2.026962|2.026962	0.35797|0.35797	.|.	.|.	ENSG00000100150|ENSG00000100150	ENST00000433147|ENST00000535622;ENST00000266091;ENST00000400249;ENST00000382109;ENST00000400246;ENST00000382105;ENST00000382112;ENST00000382111;ENST00000400248	.|T;T;T;T;T;T;T;T	.|0.32272	.|1.46;1.88;1.88;1.85;1.47;1.88;1.85;1.88	5.95|5.95	3.81|3.81	0.43845|0.43845	.|.	.|0.488018	.|0.22083	.|N	.|0.064865	T|T	0.20577|0.20577	0.0495|0.0495	L|L	0.27053|0.27053	0.805|0.805	0.22468|0.22468	N|N	0.999079|0.999079	.|P;B;B;P;B;B;B	.|0.35923	.|0.528;0.049;0.102;0.515;0.066;0.049;0.09	.|B;B;B;B;B;B;B	.|0.41332	.|0.167;0.042;0.034;0.354;0.05;0.042;0.028	T|T	0.14699|0.14699	-1.0463|-1.0463	5|10	.|0.12103	.|T	.|0.63	.|.	6.6623|6.6623	0.23020|0.23020	0.7651:0.0:0.2349:0.0|0.7651:0.0:0.2349:0.0	.|.	.|478;1157;1057;543;1135;1148;1126	.|B4DSS1;B9EGN9;B4DH93;O75140-7;O75140-4;A8MPX9;O75140	.|.;.;.;.;.;.;DEPD5_HUMAN	N|T	532|1057;1135;1126;1057;1157;1079;1148;1157;1126	.|ENSP00000440210:N1057T;ENSP00000266091:N1135T;ENSP00000383108:N1126T;ENSP00000383105:N1157T;ENSP00000371539:N1079T;ENSP00000371546:N1148T;ENSP00000371545:N1157T;ENSP00000383107:N1126T	.|ENSP00000266091:N1135T	K|N	+|+	3|2	2|0	DEPDC5|DEPDC5	30596715|30596715	0.910000|0.910000	0.30920|0.30920	0.847000|0.847000	0.33407|0.33407	0.985000|0.985000	0.73830|0.73830	1.825000|1.825000	0.39081|0.39081	1.034000|1.034000	0.39945|0.39945	0.533000|0.533000	0.62120|0.62120	AAA|AAC	.	.		0.532	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662		C	32266715	A	C	32266715	3	2	360	1	0	0	0	0	1	0	0	0	4444	43	2	5	3591	5	DEPDC5	22	32266715	Missense_Mutation	SNP	A	TCGA-XR-A8TF-01A-11D-A35Z-10		32266715	19037851	140	50441										
TRIOBP	11078	hgsc.bcm.edu	37	chr22	38121212	38121212	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	aatctgagaccatcatctccCcaccgctccactcaatggaa	5	16	4	1	rs374255684		TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr22:38121212C>T	ENST00000406386.3	+	7	2904	c.2649C>T	c.(2647-2649)ccC>ccT	p.P883P		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	883					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					CATCATCTCCCCACCGCTCCA	0.537																																					p.P883P		Atlas-SNP	.											.	TRIOBP	262	.	0			c.C2649T						.						139	152	147					22																	38121212		2036	4165	6201	SO:0001819	synonymous_variant	11078	exon7			ATCTCCCCACCGC	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"Pleckstrin homology (PH) domain containing"	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.2649C>T	chr22.hg19:g.38121212C>T		160.0	0.0		149.0	42.0	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Silent	SNP	ENST00000406386.3	hg19	CCDS43015.1																																																																																			.	.		0.537	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2			T	38121212	C	T	38121212	2	4	360	1	0	0	0	0	0	0	0	1	16568	610	22	3		3	TRIOBP	22	38121212	Silent	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10	5854497	38121212	13183354	141	50442										
DDX17	10521	hgsc.bcm.edu	37	chr22	38888102	38888102	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	ctgtagcaataaggatgggtGcctttccagaacggaactct	11	9	1	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chr22:38888102G>T	ENST00000396821.3	-	11	1505	c.1406C>A	c.(1405-1407)gCa>gAa	p.A469E	DDX17_ENST00000432525.1_5'UTR|DDX17_ENST00000381633.3_Missense_Mutation_p.A390E	NM_001098504.1|NM_006386.4	NP_001091974|NP_006377.2	Q92841	DDX17_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 17	469	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of skeletal muscle cell differentiation (GO:2001014)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA helicase activity (GO:0003724)|RNA-dependent ATPase activity (GO:0008186)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(6)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	25	Melanoma(58;0.0286)					AAGGATGGGTGCCTTTCCAGA	0.363																																					p.A469E	Ovarian(55;1085 1454 6392 21425)	Atlas-SNP	.											.	DDX17	73	.	0			c.C1406A						.						93	74	81					22																	38888102		2203	4300	6503	SO:0001583	missense	10521	exon11			ATGGGTGCCTTTC	U59321	CCDS33646.1, CCDS46706.1	22q13.1	2012-02-23	2012-02-23		ENSG00000100201	ENSG00000100201		"DEAD-boxes"	2740	protein-coding gene	gene with protein product		608469	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 17 (72kD)", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 17"			8871553, 17226766	Standard	NM_006386		Approved	P72	uc003avy.4	Q92841	OTTHUMG00000151136	ENST00000396821.3:c.1406C>A	chr22.hg19:g.38888102G>T	ENSP00000380033:p.Ala469Glu	113.0	0.0		94.0	4.0	NM_006386	B1AHM0|Q69YT1|Q6ICD6	Missense_Mutation	SNP	ENST00000396821.3	hg19	CCDS46706.1	.	.	.	.	.	.	.	.	.	.	G	31	5.076927	0.94000	.	.	ENSG00000100201	ENST00000396821;ENST00000381633;ENST00000403230;ENST00000404499	T;T;T	0.05025	3.51;3.51;3.51	6.17	6.17	0.99709	Helicase, C-terminal (3);	0.088322	0.85682	D	0.000000	T	0.22166	0.0534	L	0.49513	1.565	0.80722	D	1	D;P;P	0.63880	0.993;0.916;0.897	D;P;P	0.66497	0.944;0.642;0.51	T	0.00002	-1.2636	10	0.72032	D	0.01	-14.5753	20.8794	0.99867	0.0:0.0:1.0:0.0	.	390;471;469	Q92841;Q59F66;Q92841-4	DDX17_HUMAN;.;.	E	469;390;469;471	ENSP00000380033:A469E;ENSP00000371046:A390E;ENSP00000385536:A469E	ENSP00000371046:A390E	A	-	2	0	DDX17	37218048	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.429000	0.97481	2.941000	0.99782	0.655000	0.94253	GCA	.	.		0.363	DDX17-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321476.2	NM_030881		T	38888102	G	T	38888102	3	4	360	1	0	0	0	0	1	0	0	0	4346	1319	46	3	801	3	DDX17	22	38888102	Missense_Mutation	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10	766890	38888102	12416464	142	50443										
ASMTL	8623	hgsc.bcm.edu	37	chrX	1571669	1571669	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	tgaggatctcctgacggcgtGgggaggcgctggccagcacc	17	12	1	2			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chrX:1571669G>A	ENST00000381317.3	-	1	97	c.65C>T	c.(64-66)cCa>cTa	p.P22L	ASMTL_ENST00000534940.1_Intron|ASMTL_ENST00000416733.2_5'UTR|ASMTL_ENST00000381333.4_Missense_Mutation_p.P22L	NM_004192.3	NP_004183.2	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like	22	MAF-like.					cytoplasm (GO:0005737)	O-methyltransferase activity (GO:0008171)			NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(9)|pancreas(1)|soft_tissue(1)	23		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				CTGACGGCGTGGGGAGGCGCT	0.726																																					p.P22L		Atlas-SNP	.											.	ASMTL	56	.	0			c.C65T						.						16	22	21					X																	1571669		1943	4117	6060	SO:0001583	missense	8623	exon1			CGGCGTGGGGAGG	Y15521	CCDS43917.1, CCDS55362.1, CCDS55363.1	Xp22.3 and Yp11.3	2008-02-05			ENSG00000169093	ENSG00000169093		"Pseudoautosomal regions / PAR1"	751	protein-coding gene	gene with protein product		300162, 400011				9736779	Standard	NM_004192		Approved		uc004cpx.2	O95671	OTTHUMG00000021057	ENST00000381317.3:c.65C>T	chrX.hg19:g.1571669G>A	ENSP00000370718:p.Pro22Leu	58.0	0.0		65.0	17.0	NM_001173474	B4DX75|F5GXH4|J3JS33|Q5JQ53|Q8NBH5|Q96G02|Q9BUL6	Missense_Mutation	SNP	ENST00000381317.3	hg19	CCDS43917.1	.	.	.	.	.	.	.	.	.	.	N	12.06	1.823775	0.32237	.	.	ENSG00000169093	ENST00000381333;ENST00000381317	T;T	0.04360	3.64;3.82	2.12	2.12	0.27331	.	0.000000	0.64402	U	0.000001	T	0.24890	0.0604	H	0.96301	3.8	0.42202	D	0.991772	D;D	0.60575	0.97;0.988	P;D	0.66084	0.467;0.941	T	0.01824	-1.1266	10	0.87932	D	0	.	6.0088	0.19562	0.1731:0.0:0.8269:0.0	.	22;22	O95671-2;O95671	.;ASML_HUMAN	L	22	ENSP00000370734:P22L;ENSP00000370718:P22L	ENSP00000370718:P22L	P	-	2	0	ASMTL	1531669	0.977000	0.34250	0.990000	0.47175	0.777000	0.43975	2.237000	0.43061	0.649000	0.30751	0.272000	0.19324	CCA	.	.		0.726	ASMTL-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055595.1	NM_004192		A	1571669	G	A	1571669	3	1	360	1	0	0	0	0	1	0	0	0	1046	1348	47	3	1852	3	ASMTL	23	1571669	Missense_Mutation	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10		1571669	153698891	143	50444										
ZBED1	9189	hgsc.bcm.edu	37	chrX	2408474	2408474	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	gggacgactcgggcttcagcTtggagaaggcggtggcgaag	19	8	1	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chrX:2408474T>A	ENST00000381223.4	-	2	490	c.287A>T	c.(286-288)aAg>aTg	p.K96M	ZBED1_ENST00000381218.3_Missense_Mutation_p.K96M|ZBED1_ENST00000381222.2_Missense_Mutation_p.K96M|ZBED1_ENST00000515319.1_5'Flank|DHRSX_ENST00000334651.5_Intron	NM_001171135.1|NM_001171136.1|NM_004729.3	NP_001164606.1|NP_001164607.1|NP_004720.1	O96006	ZBED1_HUMAN	zinc finger, BED-type containing 1	96					metabolic process (GO:0008152)	nuclear chromosome (GO:0000228)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transposase activity (GO:0004803)			endometrium(8)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|upper_aerodigestive_tract(1)	25		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GGGCTTCAGCTTGGAGAAGGC	0.647																																					p.K96M		Atlas-SNP	.											.	ZBED1	64	.	0			c.A287T						.						116	109	112					X																	2408474		2203	4296	6499	SO:0001583	missense	9189	exon2			TTCAGCTTGGAGA	AB018328	CCDS14118.1	Xp22.33 and Yp11	2013-05-03	2004-01-14	2004-01-16	ENSG00000214717	ENSG00000214717		"Pseudoautosomal regions / PAR1", "Zinc fingers, BED-type"	447	protein-coding gene	gene with protein product		300178	"Ac-like transposable element"	ALTE		9872452, 9887332, 23533661	Standard	NM_001171135		Approved	TRAMP, KIAA0785, DREF, hDREF	uc004cqh.2	O96006	OTTHUMG00000021069	ENST00000381223.4:c.287A>T	chrX.hg19:g.2408474T>A	ENSP00000370621:p.Lys96Met	231.0	0.0		185.0	56.0	NM_001171135	Q96BY4	Missense_Mutation	SNP	ENST00000381223.4	hg19	CCDS14118.1	.	.	.	.	.	.	.	.	.	.	T	14.00	2.403463	0.42613	.	.	ENSG00000214717	ENST00000381223;ENST00000381222;ENST00000381218;ENST00000461691	.	.	.	2.62	2.62	0.31277	.	0.087637	0.42294	U	0.000731	T	0.34337	0.0894	.	.	.	0.09310	N	1	P	0.51791	0.948	P	0.46543	0.52	T	0.13602	-1.0503	8	0.45353	T	0.12	-19.7652	10.2814	0.43541	0.0:0.0:0.0:1.0	.	96	O96006	ZBED1_HUMAN	M	96	.	ENSP00000370616:K96M	K	-	2	0	ZBED1	2418474	1.000000	0.71417	0.997000	0.53966	0.720000	0.41350	2.499000	0.45372	0.888000	0.36160	0.347000	0.21830	AAG	.	.		0.647	ZBED1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144310.3	NM_004729		A	2408474	T	A	2408474	3	1	360	1	0	0	0	0	1	0	0	0	17532	1609	56	4	1801	4	ZBED1	23	2408474	Missense_Mutation	SNP	T	TCGA-XR-A8TF-01A-11D-A35Z-10	836805	2408474	152862086	144	50445										
TLR7	51284	hgsc.bcm.edu	37	chrX	12903873	12903873	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	cacataccagacatctccccAgcgtcctttcacagactgga	6	16	2	2			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chrX:12903873A>T	ENST00000380659.3	+	3	385	c.246A>T	c.(244-246)ccA>ccT	p.P82P		NM_016562.3	NP_057646.1	Q9NYK1	TLR7_HUMAN	toll-like receptor 7	82					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of chemokine production (GO:0032722)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|toll-like receptor 7 signaling pathway (GO:0034154)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	cytoplasm (GO:0005737)|early phagosome (GO:0032009)|endolysosome membrane (GO:0036020)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|single-stranded RNA binding (GO:0003727)|siRNA binding (GO:0035197)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(4)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	44					Hydroxychloroquine(DB01611)|Imiquimod(DB00724)	ACATCTCCCCAGCGTCCTTTC	0.483																																					p.P82P		Atlas-SNP	.											.	TLR7	125	.	0			c.A246T						.						145	135	138					X																	12903873		2203	4300	6503	SO:0001819	synonymous_variant	51284	exon3			CTCCCCAGCGTCC	AF240467	CCDS14151.1	Xp22.3	2008-02-05			ENSG00000196664	ENSG00000196664			15631	protein-coding gene	gene with protein product		300365				11022119	Standard	NM_016562		Approved		uc004cvc.3	Q9NYK1	OTTHUMG00000021137	ENST00000380659.3:c.246A>T	chrX.hg19:g.12903873A>T		178.0	0.0		215.0	201.0	NM_016562	D1CS69|Q9NR98	Silent	SNP	ENST00000380659.3	hg19	CCDS14151.1																																																																																			.	.		0.483	TLR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055769.1	NM_016562		T	12903873	A	T	12903873	2	4	360	1	0	0	0	0	0	0	0	1	15971	175	7	4		4	TLR7	23	12903873	Silent	SNP	A	TCGA-XR-A8TF-01A-11D-A35Z-10	10495399	12903873	142366687	145	50446										
DDX53	168400	hgsc.bcm.edu	37	chrX	23019572	23019572	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	ttcgtagagaacatgtcaccCaacgacaaagtcatcatgtt	7	10	3	1			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chrX:23019572C>T	ENST00000327968.5	+	1	1486	c.1398C>T	c.(1396-1398)ccC>ccT	p.P466P	RP11-40F8.2_ENST00000455399.1_lincRNA	NM_182699.3	NP_874358.2	Q86TM3	DDX53_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 53	466	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|RNA binding (GO:0003723)			breast(2)|endometrium(5)|kidney(4)|large_intestine(3)|lung(15)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	35						ACATGTCACCCAACGACAAAG	0.383																																					p.P466P		Atlas-SNP	.											.	DDX53	76	.	0			c.C1398T						.						108	96	100					X																	23019572		2203	4300	6503	SO:0001819	synonymous_variant	168400	exon1			GTCACCCAACGAC	AY039237	CCDS35214.1	Xp22.13	2009-03-25			ENSG00000184735	ENSG00000184735		"DEAD-boxes"	20083	protein-coding gene	gene with protein product	"cancer associated gene", "cancer/testis antigen 26"						Standard	NM_182699		Approved	CAGE, CT26	uc004daj.3	Q86TM3	OTTHUMG00000021248	ENST00000327968.5:c.1398C>T	chrX.hg19:g.23019572C>T		169.0	0.0		202.0	10.0	NM_182699	Q0D2N2|Q6NVV4	Silent	SNP	ENST00000327968.5	hg19	CCDS35214.1																																																																																			.	.		0.383	DDX53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056043.1	NM_182699		T	23019572	C	T	23019572	2	4	360	1	0	0	0	0	0	0	0	1	4373	581	21	3		3	DDX53	23	23019572	Silent	SNP	C	TCGA-XR-A8TF-01A-11D-A35Z-10	10115699	23019572	132250988	146	50447										
LANCL3	347404	hgsc.bcm.edu	37	chrX	37431397	37431397	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	tcgccacggcccgggaacgcTacctgcgctcggctaagcgc	13	17	0	0			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chrX:37431397T>A	ENST00000378619.3	+	1	493	c.274T>A	c.(274-276)Tac>Aac	p.Y92N	LANCL3_ENST00000378621.3_Missense_Mutation_p.Y92N|TM4SF2_ENST00000465127.1_Intron	NM_001170331.1	NP_001163802.1	Q6ZV70	LANC3_HUMAN	LanC lantibiotic synthetase component C-like 3 (bacterial)	92							catalytic activity (GO:0003824)			lung(4)|pancreas(1)	5						CCGGGAACGCTACCTGCGCTC	0.716																																					p.Y92N		Atlas-SNP	.											.	LANCL3	42	.	0			c.T274A						.						9	8	9					X																	37431397		2054	4009	6063	SO:0001583	missense	347404	exon1			GAACGCTACCTGC	AK124915	CCDS14240.1, CCDS55398.1	Xp21.1	2008-02-05			ENSG00000147036	ENSG00000147036			24767	protein-coding gene	gene with protein product							Standard	NM_198511		Approved	FLJ42925	uc011mkd.2	Q6ZV70	OTTHUMG00000033177	ENST00000378619.3:c.274T>A	chrX.hg19:g.37431397T>A	ENSP00000367882:p.Tyr92Asn	36.0	0.0		36.0	33.0	NM_001170331	A6NHE3	Missense_Mutation	SNP	ENST00000378619.3	hg19	CCDS55398.1	.	.	.	.	.	.	.	.	.	.	T	17.94	3.511046	0.64522	.	.	ENSG00000147036	ENST00000378621;ENST00000378619	T;T	0.51817	0.69;0.69	4.62	4.62	0.57501	.	0.000000	0.64402	D	0.000001	T	0.63177	0.2489	M	0.79805	2.47	0.58432	D	0.999999	D;D	0.67145	0.996;0.981	P;P	0.57846	0.828;0.74	T	0.64402	-0.6416	10	0.30078	T	0.28	-13.7322	12.9836	0.58579	0.0:0.0:0.0:1.0	.	92;92	Q6ZV70;Q6ZV70-2	LANC3_HUMAN;.	N	92	ENSP00000367885:Y92N;ENSP00000367882:Y92N	ENSP00000367882:Y92N	Y	+	1	0	LANCL3	37316316	1.000000	0.71417	1.000000	0.80357	0.277000	0.26821	6.742000	0.74843	1.513000	0.48852	0.388000	0.25769	TAC	.	.		0.716	LANCL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080885.1	NM_198511		A	37431397	T	A	37431397	3	1	360	1	0	0	0	0	1	0	0	0	8631	1522	53	4	276	4	LANCL3	23	37431397	Missense_Mutation	SNP	T	TCGA-XR-A8TF-01A-11D-A35Z-10	14411825	37431397	117839163	147	50448										
TSPYL2	64061	hgsc.bcm.edu	37	chrX	53112112	53112112	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	agcagttttggtggagagggGgccctagaaacctgtagcgc	16	8	0	2	rs376774006		TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chrX:53112112G>A	ENST00000375442.4	+	1	564	c.432G>A	c.(430-432)ggG>ggA	p.G144G		NM_022117.3	NP_071400.1	Q9H2G4	TSYL2_HUMAN	TSPY-like 2	144					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell cycle (GO:0007049)|cellular protein metabolic process (GO:0044267)|chromatin modification (GO:0016568)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA replication (GO:0008156)|nucleosome assembly (GO:0006334)|regulation of protein kinase activity (GO:0045859)|regulation of signal transduction (GO:0009966)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	rDNA binding (GO:0000182)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(1)	19						GTGGAGAGGGGGCCCTAGAAA	0.592																																					p.G144G		Atlas-SNP	.											.	TSPYL2	53	.	0			c.G432A						.			0,3831		0,0,1630,571	26	29	28		432	2.6	0.9	X		28	1,6726		0,1,2427,1871	no	coding-synonymous	TSPYL2	NM_022117.3		0,1,4057,2442	AA,AG,GG,G		0.0149,0.0,0.0095		144/694	53112112	1,10557	2201	4299	6500	SO:0001819	synonymous_variant	64061	exon1			AGAGGGGGCCCTA	AF273046	CCDS14350.1	Xp11	2014-06-09			ENSG00000184205	ENSG00000184205			24358	protein-coding gene	gene with protein product		300564				11318608, 11395479	Standard	NM_022117		Approved	SE20-4, HRIHFB2216, CTCL, DENTT, CDA1, CINAP, TSPX	uc004drw.3	Q9H2G4	OTTHUMG00000021597	ENST00000375442.4:c.432G>A	chrX.hg19:g.53112112G>A		145.0	0.0		191.0	11.0	NM_022117	O94799|Q96DG7|Q9BZW6	Silent	SNP	ENST00000375442.4	hg19	CCDS14350.1																																																																																			.	.		0.592	TSPYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056718.1	NM_022117		A	53112112	G	A	53112112	2	1	360	1	0	0	0	0	0	0	0	1	16675	1219	43	3		3	TSPYL2	23	53112112	Silent	SNP	G	TCGA-XR-A8TF-01A-11D-A35Z-10	15680715	53112112	102158448	148	50449										
LRCH2	57631	hgsc.bcm.edu	37	chrX	114414316	114414316	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0472972972972973	7	1	1.12042571039111	2.72103386809269	0.777438248026483	1	1	0	tctcattgcagctaatatccTaaggagaacaataaaacaga	6	8	1	2			TCGA-XR-A8TF-01A-11D-A35Z-10	TCGA-XR-A8TF-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ff0de221-788c-40f3-ba51-eb71a52ccfa5	bf67ce8b-0bd6-4d14-9747-17eb2471d622	g.chrX:114414316T>A	ENST00000317135.8	-	4	652		c.e4-2		LRCH2_ENST00000538422.1_Splice_Site	NM_020871.3	NP_065922.3	Q5VUJ6	LRCH2_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 2											breast(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	19						GCTAATATCCTAAGGAGAACA	0.269																																					.		Atlas-SNP	.											.	LRCH2	138	.	0			c.622-2A>T						.						40	32	35					X																	114414316		1785	4045	5830	SO:0001630	splice_region_variant	57631	exon5			ATATCCTAAGGAG	AB040928	CCDS48155.1, CCDS59175.1	Xq24	2008-02-05			ENSG00000130224	ENSG00000130224			29292	protein-coding gene	gene with protein product						10819331	Standard	NM_020871		Approved	KIAA1495	uc010nqe.3	Q5VUJ6	OTTHUMG00000022233	ENST00000317135.8:c.622-2A>T	chrX.hg19:g.114414316T>A		207.0	0.0		253.0	235.0	NM_001243963	F5H2T1|Q08AD5|Q9HA88|Q9P233	Splice_Site	SNP	ENST00000317135.8	hg19	CCDS48155.1	.	.	.	.	.	.	.	.	.	.	T	17.43	3.388682	0.61956	.	.	ENSG00000130224	ENST00000317135;ENST00000538422	.	.	.	5.27	5.27	0.74061	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.1402	0.59430	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	LRCH2	114320572	1.000000	0.71417	1.000000	0.80357	0.799000	0.45148	7.452000	0.80683	1.850000	0.53721	0.437000	0.28790	.	.	.		0.269	LRCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057971.2	NM_020871	Intron	A	114414316	T	A	114414316	5	1	360	1	0	0	0	0	0	0	1	0	8942	1536	53	4	1749	4	LRCH2	23	114414316	Splice_Site	SNP	T	TCGA-XR-A8TF-01A-11D-A35Z-10	61302204	114414316	40856244	149	50450										
LSM10	84967	hgsc.bcm.edu	37	chr1	36859597	36859597	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	tgttcatgaaagcatcgacaTtgtctatgcgtccgtgggcc	11	10	2	1			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr1:36859597T>A	ENST00000315732.2	-	2	283	c.134A>T	c.(133-135)aAt>aTt	p.N45I	LSM10_ENST00000476041.1_5'UTR	NM_032881.1	NP_116270.1	Q969L4	LSM10_HUMAN	LSM10, U7 small nuclear RNA associated	45					gene expression (GO:0010467)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U7 snRNP (GO:0005683)	histone pre-mRNA DCP binding (GO:0071208)			upper_aerodigestive_tract(1)|urinary_tract(1)	2		Myeloproliferative disorder(586;0.0393)				AGCATCGACATTGTCTATGCG	0.577																																					p.N45I		Atlas-SNP	.											.	LSM10	9	.	0			c.A134T						.						172	137	149					1																	36859597		2203	4300	6503	SO:0001583	missense	84967	exon2			TCGACATTGTCTA	AF394685	CCDS408.1	1p34.3	2008-02-05			ENSG00000181817	ENSG00000181817			17562	protein-coding gene	gene with protein product						11574479	Standard	NM_032881		Approved	MGC15749	uc001cao.1	Q969L4	OTTHUMG00000008140	ENST00000315732.2:c.134A>T	chr1.hg19:g.36859597T>A	ENSP00000319341:p.Asn45Ile	74.0	0.0		105.0	40.0	NM_032881		Missense_Mutation	SNP	ENST00000315732.2	hg19	CCDS408.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.937724	0.73557	.	.	ENSG00000181817	ENST00000315732	T	0.43294	0.95	6.11	6.11	0.99139	Like-Sm ribonucleoprotein (LSM) domain (1);Like-Sm ribonucleoprotein (LSM)-related domain (1);	0.040882	0.85682	D	0.000000	T	0.57007	0.2024	M	0.65975	2.015	0.80722	D	1	D	0.54397	0.966	P	0.58331	0.837	T	0.59899	-0.7367	10	0.59425	D	0.04	-36.5114	11.7047	0.51592	0.0:0.0701:0.0:0.9299	.	45	Q969L4	LSM10_HUMAN	I	45	ENSP00000319341:N45I	ENSP00000319341:N45I	N	-	2	0	LSM10	36632184	1.000000	0.71417	0.939000	0.37840	0.854000	0.48673	3.627000	0.54252	2.343000	0.79666	0.496000	0.49642	AAT	.	.		0.577	LSM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022294.1	NM_032881		A	36859597	T	A	36859597	3	1	361	1	0	0	0	0	1	0	0	0	9060	1493	52	4	241	4	LSM10	1	36859597	Missense_Mutation	SNP	T	TCGA-XR-A8TG-01A-11D-A35Z-10		36859597	212391024	1	50451										
ZC3H12A	80149	hgsc.bcm.edu	37	chr1	37945929	37945929	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	cttctcctgccggggcatccTgctggcagtgaactggtttc	12	13	1	1			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr1:37945929T>A	ENST00000373087.6	+	3	598	c.482T>A	c.(481-483)cTg>cAg	p.L161Q		NM_025079.2	NP_079355.2			zinc finger CCCH-type containing 12A											NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				CGGGGCATCCTGCTGGCAGTG	0.627																																					p.L161Q		Atlas-SNP	.											.	ZC3H12A	58	.	0			c.T482A						.						84	74	77					1																	37945929		2203	4300	6503	SO:0001583	missense	80149	exon3			GCATCCTGCTGGC		CCDS417.1	1p34.3	2012-07-05			ENSG00000163874	ENSG00000163874		"Zinc fingers, CCCH-type domain containing"	26259	protein-coding gene	gene with protein product	"MCP induced protein 1"	610562				18178554, 22055188	Standard	NM_025079		Approved	FLJ23231, MCPIP1	uc001cbb.4	Q5D1E8	OTTHUMG00000004221	ENST00000373087.6:c.482T>A	chr1.hg19:g.37945929T>A	ENSP00000362179:p.Leu161Gln	62.0	0.0		76.0	28.0	NM_025079		Missense_Mutation	SNP	ENST00000373087.6	hg19	CCDS417.1	.	.	.	.	.	.	.	.	.	.	T	16.81	3.225566	0.58668	.	.	ENSG00000163874	ENST00000373087;ENST00000373082	T	0.45276	0.9	4.8	4.8	0.61643	Ribonuclease Zc3h12a-like (1);	0.156336	0.43579	D	0.000556	T	0.22126	0.0533	N	0.01446	-0.86	0.49213	D	0.999765	B	0.24963	0.115	B	0.37989	0.262	T	0.17501	-1.0367	10	0.10377	T	0.69	-19.9641	14.6504	0.68792	0.0:0.0:0.0:1.0	.	161	Q5D1E8	ZC12A_HUMAN	Q	161	ENSP00000362179:L161Q	ENSP00000362174:L161Q	L	+	2	0	ZC3H12A	37718516	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.993000	0.49425	1.934000	0.56057	0.460000	0.39030	CTG	.	.		0.627	ZC3H12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012154.2	NM_025079		A	37945929	T	A	37945929	3	1	361	1	0	0	0	0	1	0	0	0	17576	1580	55	4	488	4	ZC3H12A	1	37945929	Missense_Mutation	SNP	T	TCGA-XR-A8TG-01A-11D-A35Z-10	1086332	37945929	211304692	2	50452										
FAAH	2166	hgsc.bcm.edu	37	chr1	46876499	46876499	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	tgtgcagctgccaaggctgtCagctttcctcagcaacatga	10	12	2	1			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr1:46876499C>T	ENST00000243167.8	+	11	1373	c.1289C>T	c.(1288-1290)tCa>tTa	p.S430L		NM_001441.2	NP_001432.2	O00519	FAAH1_HUMAN	fatty acid amide hydrolase	430					fatty acid catabolic process (GO:0009062)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|organelle membrane (GO:0031090)	acylglycerol lipase activity (GO:0047372)|carbon-nitrogen ligase activity, with glutamine as amido-N-donor (GO:0016884)|fatty acid amide hydrolase activity (GO:0017064)			breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	22	Acute lymphoblastic leukemia(166;0.155)				Propofol(DB00818)|Thiopental(DB00599)	CCAAGGCTGTCAGCTTTCCTC	0.597																																					p.S430L		Atlas-SNP	.											.	FAAH	36	.	0			c.C1289T						.						97	85	89					1																	46876499		2203	4300	6503	SO:0001583	missense	2166	exon11			GGCTGTCAGCTTT	U82535	CCDS535.1	1p35-p34	2008-02-05			ENSG00000117480	ENSG00000117480			3553	protein-coding gene	gene with protein product		602935				9122178	Standard	NM_001441		Approved	FAAH-1	uc001cpu.2	O00519	OTTHUMG00000007811	ENST00000243167.8:c.1289C>T	chr1.hg19:g.46876499C>T	ENSP00000243167:p.Ser430Leu	55.0	0.0		53.0	10.0	NM_001441	D3DQ19|Q52M86|Q5TDF8	Missense_Mutation	SNP	ENST00000243167.8	hg19	CCDS535.1	.	.	.	.	.	.	.	.	.	.	C	10.61	1.398996	0.25291	.	.	ENSG00000117480	ENST00000243167;ENST00000396325	T	0.55052	0.54	5.28	3.37	0.38596	Amidase signature domain (2);	0.475716	0.22230	N	0.062822	T	0.46054	0.1373	L	0.41415	1.275	0.18873	N	0.999982	B	0.26318	0.146	B	0.36186	0.219	T	0.48007	-0.9072	10	0.66056	D	0.02	-17.4305	8.3105	0.32068	0.0:0.8167:0.0:0.1833	.	430	O00519	FAAH1_HUMAN	L	430;137	ENSP00000243167:S430L	ENSP00000243167:S430L	S	+	2	0	FAAH	46649086	0.005000	0.15991	0.755000	0.31263	0.174000	0.22865	1.579000	0.36536	1.472000	0.48140	-0.140000	0.14226	TCA	.	.		0.597	FAAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021443.1	NM_001441		T	46876499	C	T	46876499	3	4	361	1	0	0	0	0	1	0	0	0	5358	838	29	3	1331	3	FAAH	1	46876499	Missense_Mutation	SNP	C	TCGA-XR-A8TG-01A-11D-A35Z-10	8930570	46876499	202374122	3	50453										
SFRS11	9295	hgsc.bcm.edu	37	chr1	70716344	70716345	+	Frame_Shift_Ins	INS	-	-	A													0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	ggtatgacagtgagaaagagINSaaaaaagaagagaagaaacc							TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr1:70716344_70716345insA	ENST00000370950.3	+	13	1393_1394	c.1311_1312insA	c.(1312-1314)aaafs	p.K438fs	SRSF11_ENST00000405432.1_Frame_Shift_Ins_p.K438fs|SRSF11_ENST00000370949.1_Frame_Shift_Ins_p.K378fs|SRSF11_ENST00000484162.1_3'UTR|SRSF11_ENST00000370951.1_Frame_Shift_Ins_p.K437fs			Q05519	SRS11_HUMAN	serine/arginine-rich splicing factor 11	438					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			large_intestine(3)|ovary(2)|skin(1)	6						GTGAGAAAGAGAAAAAAGAAGA	0.371																																					p.E437fs		Atlas-INDEL	.											.	SRSF11	68	.	0			c.1311_1312insA						.																																			SO:0001589	frameshift_variant	9295	exon13			.	M74002	CCDS647.1, CCDS53332.1	1p31.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000116754	ENSG00000116754		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10782	protein-coding gene	gene with protein product	"SR splicing factor 11"	602010	"splicing factor, arginine/serine-rich 11"	SFRS11		1896467, 20516191	Standard	NM_004768		Approved	p54, NET2	uc001des.3	Q05519	OTTHUMG00000009342	ENST00000370950.3:c.1317dupA	chr1.hg19:g.70716350_70716350dupA	ENSP00000359988:p.Lys438fs	181.0	0.0		234.0	89.0	NM_004768	Q5T758|Q8IWE6	Frame_Shift_Ins	INS	ENST00000370950.3	hg19	CCDS647.1																																																																																			.	.		0.371	SRSF11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025889.1	NM_004768		A	70716345	-	A	70716344	7	5	361	1	0	1	1	0	0	0	0	0	14181	933	33	0	1357	0	SFRS11	1	70716344	Frame_Shift_Ins	INS	-	TCGA-XR-A8TG-01A-11D-A35Z-10	23839845	70716344	178534277	4	50454										
GSTM3	2947	hgsc.bcm.edu	37	chr1	110280323	110280323	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	ttccccagaaacatggagaaTtgtttcagttgtccaggtag	10	8	1	2			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr1:110280323T>C	ENST00000540225.1	-	7	733	c.423A>G	c.(421-423)caA>caG	p.Q141Q	GSTM3_ENST00000361066.2_Silent_p.Q141Q|GSTM3_ENST00000256594.3_Silent_p.Q141Q|GSTM3_ENST00000488824.1_5'UTR|RP4-735C1.4_ENST00000431955.1_RNA			P21266	GSTM3_HUMAN	glutathione S-transferase mu 3 (brain)	141	GST C-terminal.				cellular detoxification of nitrogen compound (GO:0070458)|establishment of blood-nerve barrier (GO:0008065)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|nitrobenzene metabolic process (GO:0018916)|response to estrogen (GO:0043627)|small molecule metabolic process (GO:0044281)|xenobiotic catabolic process (GO:0042178)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)	enzyme binding (GO:0019899)|glutathione binding (GO:0043295)|glutathione transferase activity (GO:0004364)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|skin(1)	9		all_epithelial(167;1.95e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)		Colorectal(144;0.0339)|Lung(183;0.0426)|all cancers(265;0.113)|Epithelial(280;0.125)|COAD - Colon adenocarcinoma(174;0.134)|LUSC - Lung squamous cell carcinoma(189;0.228)	Glutathione(DB00143)|Vitamin E(DB00163)	ACATGGAGAATTGTTTCAGTT	0.423																																					p.Q141Q		Atlas-SNP	.											.	GSTM3	21	.	0			c.A423G						.						121	136	131					1																	110280323		2203	4300	6503	SO:0001819	synonymous_variant	2947	exon7			GGAGAATTGTTTC	BC000088	CCDS812.1	1p13.3	2012-06-21	2008-11-26		ENSG00000134202	ENSG00000134202	2.5.1.18	"Glutathione S-transferases / Soluble"	4635	protein-coding gene	gene with protein product		138390	"glutathione S-transferase M3 (brain)"			2345169	Standard	NM_000849		Approved	GST5	uc001dyo.2	P21266	OTTHUMG00000011640	ENST00000540225.1:c.423A>G	chr1.hg19:g.110280323T>C		191.0	0.0		267.0	110.0	NM_000849	O60550|Q96HA3	Silent	SNP	ENST00000540225.1	hg19	CCDS812.1																																																																																			.	.		0.423	GSTM3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032182.1	NM_000849		C	110280323	T	C	110280323	2	2	361	1	0	0	0	0	0	0	0	1	6848	1490	52	2		2	GSTM3	1	110280323	Silent	SNP	T	TCGA-XR-A8TG-01A-11D-A35Z-10	39563979	110280323	138970298	5	50455										
CHD1L	9557	hgsc.bcm.edu	37	chr1	146765405	146765405	+	Splice_Site	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	ttagcagcaaaaaagaagaaAggtaagctcttccacctgtg	9	8	1	2			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr1:146765405A>C	ENST00000369258.4	+	21	2525	c.2505A>C	c.(2503-2505)aaA>aaC	p.K835N	CHD1L_ENST00000369259.3_Splice_Site_p.K631N|CHD1L_ENST00000361293.5_Splice_Site_p.K554N|CHD1L_ENST00000431239.1_Splice_Site_p.K741N|CHD1L_ENST00000467213.1_3'UTR	NM_001256336.1|NM_004284.4|NM_024568.2	NP_001243265.1|NP_004275.4|NP_078844.2	Q86WJ1	CHD1L_HUMAN	chromodomain helicase DNA binding protein 1-like	835	Macro. {ECO:0000255|PROSITE- ProRule:PRU00490}.				ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|nucleotide binding (GO:0000166)			breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(923;0.0487)					AAAAGAAGAAAGGTAAGCTCT	0.428																																					p.K835N		Atlas-SNP	.											.	CHD1L	72	.	0			c.A2505C						.						94	94	94					1																	146765405		2203	4300	6503	SO:0001630	splice_region_variant	9557	exon21			GAAGAAAGGTAAG	AF054177	CCDS927.1, CCDS58021.1, CCDS58022.1, CCDS72882.1	1q21.1	2008-02-05			ENSG00000131778	ENSG00000131778			1916	protein-coding gene	gene with protein product		613039				9653160	Standard	NM_004284		Approved	ALC1	uc001epm.5	Q86WJ1	OTTHUMG00000150271	ENST00000369258.4:c.2506+1A>C	chr1.hg19:g.146765405A>C		46.0	0.0		82.0	5.0	NM_004284	A5YM64|B4DDE1|B5MDZ7|Q53EZ3|Q5VXX7|Q6DD94|Q6PK83|Q86XH3|Q96HF7|Q96SP3|Q9BVJ1|Q9NVV8	Missense_Mutation	SNP	ENST00000369258.4	hg19	CCDS927.1	.	.	.	.	.	.	.	.	.	.	A	10.73	1.431463	0.25813	.	.	ENSG00000131778	ENST00000431239;ENST00000369259;ENST00000369258;ENST00000361293	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	5.27	2.85	0.33270	Appr-1-p processing (1);	0.099970	0.64402	D	0.000002	T	0.09598	0.0236	N	0.16903	0.455	0.47819	D	0.999528	B;B;B	0.28783	0.222;0.047;0.012	B;B;B	0.33196	0.159;0.033;0.016	T	0.10428	-1.0630	10	0.10111	T	0.7	.	4.5306	0.12002	0.7002:0.2001:0.0997:0.0	.	741;631;835	Q86WJ1-2;Q86WJ1-3;Q86WJ1	.;.;CHD1L_HUMAN	N	741;631;835;554	ENSP00000389031:K741N;ENSP00000358263:K631N;ENSP00000358262:K835N;ENSP00000355100:K554N	ENSP00000355100:K554N	K	+	3	2	CHD1L	145232029	0.998000	0.40836	1.000000	0.80357	0.905000	0.53344	0.595000	0.24029	2.118000	0.64928	0.455000	0.32223	AAA	.	.		0.428	CHD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040377.1	NM_004284	Missense_Mutation	C	146765405	A	C	146765405	5	2	361	1	0	0	0	0	0	0	1	0	3326	86	3	5	2587	5	CHD1L	1	146765405	Splice_Site	SNP	A	TCGA-XR-A8TG-01A-11D-A35Z-10	36485082	146765405	102485216	6	50456										
FLG2	388698	hgsc.bcm.edu	37	chr1	152328015	152328015	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	gaggattgtcctgagccagaCccatgttgtccaaagccaga	11	11	0	3			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr1:152328015C>G	ENST00000388718.5	-	3	2319	c.2247G>C	c.(2245-2247)ggG>ggC	p.G749G	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	749	Ser-rich.				establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGAGCCAGACCCATGTTGTC	0.507																																					p.G749G		Atlas-SNP	.											.	FLG2	431	.	0			c.G2247C						.						290	274	279					1																	152328015		2203	4300	6503	SO:0001819	synonymous_variant	388698	exon3			GCCAGACCCATGT	AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"EF-hand domain containing"	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.2247G>C	chr1.hg19:g.152328015C>G		125.0	0.0		210.0	107.0	NM_001014342	Q9H4U1	Silent	SNP	ENST00000388718.5	hg19	CCDS30861.1																																																																																			.	.		0.507	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		G	152328015	C	G	152328015	2	3	361	1	0	0	0	0	0	0	0	1	5931	494	18	4		4	FLG2	1	152328015	Silent	SNP	C	TCGA-XR-A8TG-01A-11D-A35Z-10	5562610	152328015	96922606	7	50457										
SSR2	6746	hgsc.bcm.edu	37	chr1	155984782	155984782	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	ccatcctcctgggccaggtaAgtaattgttgccgaggtgaa	12	10	0	1			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr1:155984782A>C	ENST00000295702.4	-	4	404	c.333T>G	c.(331-333)acT>acG	p.T111T	SSR2_ENST00000529008.1_Intron|SSR2_ENST00000480567.1_Silent_p.T111T|SSR2_ENST00000496742.1_Intron	NM_003145.3	NP_003136.1	P43308	SSRB_HUMAN	signal sequence receptor, beta (translocon-associated protein beta)	111					cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|gene expression (GO:0010467)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|stomach(1)	10	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					GGGCCAGGTAAGTAATTGTTG	0.527																																					p.T111T		Atlas-SNP	.											.	SSR2	20	.	0			c.T333G						.						95	86	89					1																	155984782		2203	4300	6503	SO:0001819	synonymous_variant	6746	exon4			CAGGTAAGTAATT	BC000341	CCDS1126.1	1q21-q23	2008-02-05			ENSG00000163479	ENSG00000163479			11324	protein-coding gene	gene with protein product		600867				7789174	Standard	NM_003145		Approved	TLAP, TRAPB	uc001fmx.3	P43308	OTTHUMG00000017456	ENST00000295702.4:c.333T>G	chr1.hg19:g.155984782A>C		96.0	0.0		261.0	51.0	NM_003145	B2R9K9|D3DVA7|Q53HI0|Q5VY95|Q5VY96|Q6IB31|Q9BWE4	Silent	SNP	ENST00000295702.4	hg19	CCDS1126.1																																																																																			.	.		0.527	SSR2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046172.2	NM_003145		C	155984782	A	C	155984782	2	2	361	1	0	0	0	0	0	0	0	1	15206	59	3	5		5	SSR2	1	155984782	Silent	SNP	A	TCGA-XR-A8TG-01A-11D-A35Z-10	3656767	155984782	93265839	8	50458										
CEP350	9857	hgsc.bcm.edu	37	chr1	180000501	180000501	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	cagaactcacttcttgatgaGgaaaaagcagaacgtggctc	10	9	2	4			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr1:180000501G>C	ENST00000367607.3	+	15	4015	c.3597G>C	c.(3595-3597)gaG>gaC	p.E1199D		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	1199	Ser-rich.				microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						TTCTTGATGAGGAAAAAGCAG	0.378																																					p.E1199D		Atlas-SNP	.											.	CEP350	418	.	0			c.G3597C						.						59	61	60					1																	180000501		2203	4300	6503	SO:0001583	missense	9857	exon15			TGATGAGGAAAAA	AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"centrosome associated protein 350"					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.3597G>C	chr1.hg19:g.180000501G>C	ENSP00000356579:p.Glu1199Asp	280.0	0.0		564.0	310.0	NM_014810	O75068|Q8TDK3|Q8WY20	Missense_Mutation	SNP	ENST00000367607.3	hg19	CCDS1336.1	.	.	.	.	.	.	.	.	.	.	G	18.17	3.564312	0.65651	.	.	ENSG00000135837	ENST00000367607	T	0.59364	0.27	5.93	0.141	0.14811	.	0.000000	0.47455	D	0.000223	T	0.56717	0.2004	L	0.32530	0.975	0.35699	D	0.815498	D;D	0.69078	0.994;0.997	D;D	0.72625	0.97;0.978	T	0.58825	-0.7568	9	.	.	.	.	5.6332	0.17522	0.5918:0.1616:0.2466:0.0	.	1199;1199	E7EU22;Q5VT06	.;CE350_HUMAN	D	1199	ENSP00000356579:E1199D	.	E	+	3	2	CEP350	178267124	1.000000	0.71417	0.997000	0.53966	0.751000	0.42716	0.678000	0.25277	0.109000	0.17891	-0.142000	0.14014	GAG	.	.		0.378	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810		C	180000501	G	C	180000501	3	2	361	1	0	0	0	0	1	0	0	0	3256	991	35	4	3651	4	CEP350	1	180000501	Missense_Mutation	SNP	G	TCGA-XR-A8TG-01A-11D-A35Z-10	24015719	180000501	69250120	9	50459										
TPR	7175	hgsc.bcm.edu	37	chr1	186322973	186322973	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	ccttcaacattatcttgcagCatttcataactggtatgaaa	5	9	3	1			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr1:186322973C>A	ENST00000367478.4	-	18	2477	c.2181G>T	c.(2179-2181)atG>atT	p.M727I	TPR_ENST00000474852.1_5'UTR	NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	727					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		TATCTTGCAGCATTTCATAAC	0.343			T	NTRK1	papillary thyroid																																p.M727I		Atlas-SNP	.		Dom	yes		1	1q25	7175	translocated promoter region		E	.	TPR	441	.	0			c.G2181T						.						179	154	162					1																	186322973		1871	4106	5977	SO:0001583	missense	7175	exon18			TTGCAGCATTTCA	U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"translocated promoter region (to activated MET oncogene)"			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.2181G>T	chr1.hg19:g.186322973C>A	ENSP00000356448:p.Met727Ile	31.0	0.0		81.0	14.0	NM_003292	Q15655|Q5SWY0|Q99968	Missense_Mutation	SNP	ENST00000367478.4	hg19	CCDS41446.1	.	.	.	.	.	.	.	.	.	.	C	18.79	3.698055	0.68386	.	.	ENSG00000047410	ENST00000367478	T	0.16743	2.32	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.24198	0.0586	M	0.65975	2.015	0.80722	D	1	B	0.30824	0.296	B	0.28991	0.097	T	0.01666	-1.1300	10	0.33940	T	0.23	.	20.1162	0.97934	0.0:1.0:0.0:0.0	.	727	P12270	TPR_HUMAN	I	727	ENSP00000356448:M727I	ENSP00000356448:M727I	M	-	3	0	TPR	184589596	1.000000	0.71417	0.998000	0.56505	0.972000	0.66771	7.445000	0.80570	2.756000	0.94617	0.655000	0.94253	ATG	.	.		0.343	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292		A	186322973	C	A	186322973	3	1	361	1	0	0	0	0	1	0	0	0	16431	710	25	3	5046	3	TPR	1	186322973	Missense_Mutation	SNP	C	TCGA-XR-A8TG-01A-11D-A35Z-10	6322472	186322973	62927648	10	50460										
KIAA1804	84451	hgsc.bcm.edu	37	chr1	233514789	233514789	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	cctcttgggaaagatgctcaGagagagaatcctgcagaagc	12	9	2	4			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr1:233514789G>T	ENST00000366624.3	+	9	2298	c.2037G>T	c.(2035-2037)caG>caT	p.Q679H	MLK4_ENST00000366622.1_Missense_Mutation_p.Q125H	NM_032435.2	NP_115811.2												p.N682fs*21(1)									AAGATGCTCAGAGAGAGAATC	0.458																																					p.Q679H		Atlas-SNP	.											.	KIAA1804	129	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.G2037T						.						64	70	68					1																	233514789		2203	4300	6503	SO:0001583	missense	0	exon9			TGCTCAGAGAGAG																												ENST00000366624.3:c.2037G>T	chr1.hg19:g.233514789G>T	ENSP00000355583:p.Gln679His	211.0	0.0		259.0	20.0	NM_032435		Missense_Mutation	SNP	ENST00000366624.3	hg19	CCDS1598.1	.	.	.	.	.	.	.	.	.	.	G	7.118	0.577427	0.13686	.	.	ENSG00000143674	ENST00000366624;ENST00000366622	T;T	0.30182	1.54;1.54	4.95	3.08	0.35506	.	0.479096	0.19657	N	0.109078	T	0.27866	0.0686	L	0.59436	1.845	0.28267	N	0.924563	B;B	0.17268	0.021;0.012	B;B	0.18561	0.021;0.022	T	0.22382	-1.0218	10	0.56958	D	0.05	.	6.8224	0.23864	0.1654:0.163:0.6716:0.0	.	126;679	Q5TCX8-3;Q5TCX8	.;M3KL4_HUMAN	H	679;125	ENSP00000355583:Q679H;ENSP00000355581:Q125H	ENSP00000355581:Q125H	Q	+	3	2	RP5-862P8.2	231581412	1.000000	0.71417	0.491000	0.27477	0.253000	0.25986	2.447000	0.44917	0.680000	0.31366	0.655000	0.94253	CAG	.	.		0.458	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1			T	233514789	G	T	233514789	3	4	361	1	0	0	0	0	1	0	0	0	8268	933	33	3	2071	3	KIAA1804	1	233514789	Missense_Mutation	SNP	G	TCGA-XR-A8TG-01A-11D-A35Z-10	47191816	233514789	15735832	11	50461										
EHD3	30845	hgsc.bcm.edu	37	chr2	31472315	31472315	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	ccagggatcctctctggggaGaagcagaggatcagccgggg	17	10	2	2			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr2:31472315G>A	ENST00000322054.5	+	3	768	c.483G>A	c.(481-483)gaG>gaA	p.E161E	EHD3_ENST00000541626.1_Silent_p.E161E	NM_014600.2	NP_055415.1	Q9NZN3	EHD3_HUMAN	EH-domain containing 3	161	Dynamin-type G.				blood coagulation (GO:0007596)|endocytic recycling (GO:0032456)|protein homooligomerization (GO:0051260)|protein targeting to plasma membrane (GO:0072661)|regulation of cardiac muscle cell membrane potential (GO:0086036)	cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|nucleic acid binding (GO:0003676)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(11)|lung(12)|ovary(1)|skin(3)	33	Acute lymphoblastic leukemia(172;0.155)					TCTCTGGGGAGAAGCAGAGGA	0.577																																					p.E161E		Atlas-SNP	.											.	EHD3	90	.	0			c.G483A						.						95	86	89					2																	31472315		2203	4300	6503	SO:0001819	synonymous_variant	30845	exon3			TGGGGAGAAGCAG	AF181264	CCDS1774.1	2p21	2013-01-10			ENSG00000013016	ENSG00000013016		"EF-hand domain containing"	3244	protein-coding gene	gene with protein product		605891		PAST3		10673336	Standard	NM_014600		Approved		uc002rnu.3	Q9NZN3	OTTHUMG00000099365	ENST00000322054.5:c.483G>A	chr2.hg19:g.31472315G>A		61.0	0.0		69.0	37.0	NM_014600	B4DFR5|D6W574|Q8N514|Q9NZB3	Silent	SNP	ENST00000322054.5	hg19	CCDS1774.1																																																																																			.	.		0.577	EHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216810.1	NM_014600		A	31472315	G	A	31472315	2	1	361	1	0	0	0	0	0	0	0	1	4981	933	33	3		3	EHD3	2	31472315	Silent	SNP	G	TCGA-XR-A8TG-01A-11D-A35Z-10		31472315	211727058	12	50462										
BIRC6	57448	hgsc.bcm.edu	37	chr2	32689764	32689764	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	ttttatgactccaccactcaCtccacccaatgaagcagttt	4	14	1	2			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr2:32689764C>G	ENST00000421745.2	+	25	5263	c.5129C>G	c.(5128-5130)aCt>aGt	p.T1710S		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	1710					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					CCACCACTCACTCCACCCAAT	0.483																																					p.T1710S	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.C5129G						.						148	139	142					2																	32689764		2203	4300	6503	SO:0001583	missense	57448	exon25			CACTCACTCCACC	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.5129C>G	chr2.hg19:g.32689764C>G	ENSP00000393596:p.Thr1710Ser	119.0	0.0		112.0	46.0	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	hg19	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	C	31	5.096664	0.94197	.	.	ENSG00000115760	ENST00000421745	T	0.74947	-0.89	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.79885	0.4523	L	0.31065	0.9	0.80722	D	1	D	0.63880	0.993	D	0.68192	0.956	T	0.75878	-0.3162	10	0.28530	T	0.3	.	20.1551	0.98106	0.0:1.0:0.0:0.0	.	1710	Q9NR09	BIRC6_HUMAN	S	1710	ENSP00000393596:T1710S	ENSP00000393596:T1710S	T	+	2	0	BIRC6	32543268	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.818000	0.86416	2.760000	0.94817	0.655000	0.94253	ACT	.	.		0.483	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		G	32689764	C	G	32689764	3	3	361	1	0	0	0	0	1	0	0	0	1438	565	20	4	5227	4	BIRC6	2	32689764	Missense_Mutation	SNP	C	TCGA-XR-A8TG-01A-11D-A35Z-10	1217449	32689764	210509609	13	50463										
PCBP1	5093	hgsc.bcm.edu	37	chr2	70315913	70315913	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	cagtatctaatcaatgccagGctttcctctgagaagggcat	9	10	3	1			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr2:70315913G>T	ENST00000303577.5	+	1	1329	c.1038G>T	c.(1036-1038)agG>agT	p.R346S	PCBP1-AS1_ENST00000366234.3_RNA|PCBP1-AS1_ENST00000449178.1_RNA|PCBP1-AS1_ENST00000421843.1_RNA|PCBP1-AS1_ENST00000422515.1_RNA|PCBP1-AS1_ENST00000416395.1_RNA|PCBP1-AS1_ENST00000416068.1_RNA|PCBP1-AS1_ENST00000594548.1_RNA|PCBP1-AS1_ENST00000601396.1_RNA|PCBP1-AS1_ENST00000413069.1_RNA|PCBP1-AS1_ENST00000411429.1_RNA|PCBP1-AS1_ENST00000610168.1_RNA|PCBP1-AS1_ENST00000415742.1_RNA|PCBP1-AS1_ENST00000457770.1_RNA|PCBP1-AS1_ENST00000432604.1_RNA|PCBP1-AS1_ENST00000442040.1_RNA|PCBP1-AS1_ENST00000596573.1_RNA|PCBP1-AS1_ENST00000415222.1_RNA|PCBP1-AS1_ENST00000439892.1_RNA|PCBP1-AS1_ENST00000458686.1_RNA|PCBP1-AS1_ENST00000423402.1_RNA|PCBP1-AS1_ENST00000420309.1_RNA|PCBP1-AS1_ENST00000609075.1_RNA|PCBP1-AS1_ENST00000413791.1_RNA|PCBP1-AS1_ENST00000599673.1_RNA|PCBP1-AS1_ENST00000437456.1_RNA|PCBP1-AS1_ENST00000418564.1_RNA|PCBP1-AS1_ENST00000437019.1_RNA|PCBP1-AS1_ENST00000452431.1_RNA|PCBP1-AS1_ENST00000444410.1_RNA|PCBP1-AS1_ENST00000429599.2_RNA|PCBP1-AS1_ENST00000425333.1_RNA|PCBP1-AS1_ENST00000415060.2_RNA|PCBP1-AS1_ENST00000413436.1_RNA|PCBP1-AS1_ENST00000596028.1_RNA|PCBP1-AS1_ENST00000596665.1_RNA|PCBP1-AS1_ENST00000458698.2_RNA|PCBP1-AS1_ENST00000425601.1_RNA|PCBP1-AS1_ENST00000435880.2_RNA|PCBP1-AS1_ENST00000418308.1_RNA|PCBP1-AS1_ENST00000457076.1_RNA|PCBP1-AS1_ENST00000595459.1_RNA|PCBP1-AS1_ENST00000419963.1_RNA|AC016700.2_ENST00000455541.1_lincRNA|PCBP1-AS1_ENST00000456161.1_RNA|PCBP1-AS1_ENST00000444320.1_RNA|PCBP1-AS1_ENST00000434781.1_RNA|PCBP1-AS1_ENST00000439670.2_RNA	NM_006196.3	NP_006187.2	Q15365	PCBP1_HUMAN	poly(rC) binding protein 1	346					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|skin(1)	12						TCAATGCCAGGCTTTCCTCTG	0.498																																					p.R346S	Colon(85;1146 1307 3484 18706 25380)	Atlas-SNP	.											.	PCBP1	28	.	0			c.G1038T						.						34	36	35					2																	70315913		2203	4300	6503	SO:0001583	missense	5093	exon1			TGCCAGGCTTTCC		CCDS1898.1	2p13-p12	2013-07-16	2001-11-28		ENSG00000169564	ENSG00000169564			8647	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein E1"	601209	"poly(rC)-binding protein 1"			8833161	Standard	NM_006196		Approved	HNRPE1, hnRNP-E1, HNRPX, hnRNP-X	uc002sgf.3	Q15365	OTTHUMG00000129645	ENST00000303577.5:c.1038G>T	chr2.hg19:g.70315913G>T	ENSP00000305556:p.Arg346Ser	60.0	0.0		64.0	34.0	NM_006196	Q13157|Q14975	Missense_Mutation	SNP	ENST00000303577.5	hg19	CCDS1898.1	.	.	.	.	.	.	.	.	.	.	G	12.37	1.918614	0.33908	.	.	ENSG00000169564	ENST00000303577	T	0.36157	1.27	3.66	3.66	0.41972	K Homology (1);	0.180691	0.32901	N	0.005520	T	0.31167	0.0788	L	0.52823	1.66	0.80722	D	1	B	0.17268	0.021	B	0.15870	0.014	T	0.08848	-1.0702	10	0.25106	T	0.35	.	11.1467	0.48434	0.0:0.0:1.0:0.0	.	346	Q15365	PCBP1_HUMAN	S	346	ENSP00000305556:R346S	ENSP00000305556:R346S	R	+	3	2	PCBP1	70169417	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.512000	0.98008	2.345000	0.79718	0.563000	0.77884	AGG	.	.		0.498	PCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251844.1	NM_006196		T	70315913	G	T	70315913	3	4	361	1	0	0	0	0	1	0	0	0	11509	1194	42	3	1040	3	PCBP1	2	70315913	Missense_Mutation	SNP	G	TCGA-XR-A8TG-01A-11D-A35Z-10	37626149	70315913	172883460	14	50464										
REG3G	130120	hgsc.bcm.edu	37	chr2	79254181	79254181	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	tggcttgccagaagcggcccTctggaaaactggtgtctgtg	14	10	2	1			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr2:79254181T>C	ENST00000272324.5	+	4	401	c.217T>C	c.(217-219)Tct>Cct	p.S73P	REG3G_ENST00000409471.1_Intron|REG3G_ENST00000393897.2_Missense_Mutation_p.S73P	NM_001008387.2	NP_001008388.1	Q6UW15	REG3G_HUMAN	regenerating islet-derived 3 gamma	73	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				acute-phase response (GO:0006953)|defense response to Gram-positive bacterium (GO:0050830)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of keratinocyte differentiation (GO:0045617)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of wound healing (GO:0090303)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(27)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GAAGCGGCCCTCTGGAAAACT	0.557																																					p.S73P		Atlas-SNP	.											.	REG3G	67	.	0			c.T217C						.						138	135	136					2																	79254181		2203	4300	6503	SO:0001583	missense	130120	exon4			CGGCCCTCTGGAA	AY359047	CCDS1962.1, CCDS58714.1	2p12	2005-02-11			ENSG00000143954	ENSG00000143954			29595	protein-coding gene	gene with protein product		609933				12975309	Standard	NM_001008387		Approved	UNQ429, LPPM429, PAP1B	uc002snx.4	Q6UW15	OTTHUMG00000130018	ENST00000272324.5:c.217T>C	chr2.hg19:g.79254181T>C	ENSP00000272324:p.Ser73Pro	74.0	0.0		90.0	4.0	NM_198448	A8K980|D6W5J6|Q3SYE4|Q3SYE6|Q6FH18	Missense_Mutation	SNP	ENST00000272324.5	hg19	CCDS1962.1	.	.	.	.	.	.	.	.	.	.	T	16.31	3.088220	0.55968	.	.	ENSG00000143954	ENST00000393897;ENST00000272324	T;T	0.19938	2.11;2.11	4.83	3.65	0.41850	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.336224	0.21857	N	0.068091	T	0.49474	0.1559	M	0.93283	3.4	0.19300	N	0.999971	P	0.51537	0.946	P	0.61132	0.884	T	0.48175	-0.9058	10	0.59425	D	0.04	.	8.6682	0.34134	0.0:0.0:0.1933:0.8067	.	73	Q6UW15	REG3G_HUMAN	P	73	ENSP00000377475:S73P;ENSP00000272324:S73P	ENSP00000272324:S73P	S	+	1	0	REG3G	79107689	0.004000	0.15560	0.035000	0.18076	0.789000	0.44602	1.200000	0.32247	0.949000	0.37715	0.533000	0.62120	TCT	.	.		0.557	REG3G-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328247.1	NM_198448		C	79254181	T	C	79254181	3	2	361	1	0	0	0	0	1	0	0	0	13228	1551	54	2	227	2	REG3G	2	79254181	Missense_Mutation	SNP	T	TCGA-XR-A8TG-01A-11D-A35Z-10	8938268	79254181	163945192	15	50465										
IL18RAP	8807	hgsc.bcm.edu	37	chr2	103057777	103057777	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	gttttcatctttcagtgggaGacactaaactcaaaccagat	7	9	4	2			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr2:103057777G>A	ENST00000264260.2	+	7	1325	c.736G>A	c.(736-738)Gac>Aac	p.D246N	AC007278.3_ENST00000450893.1_RNA|IL18RAP_ENST00000409369.1_Missense_Mutation_p.D104N	NM_003853.2	NP_003844.1	O95256	I18RA_HUMAN	interleukin 18 receptor accessory protein	246					cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|inflammatory response (GO:0006954)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(5)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(4)	37						TTCAGTGGGAGACACTAAACT	0.438																																					p.D246N		Atlas-SNP	.											.	IL18RAP	102	.	0			c.G736A						.						122	106	112					2																	103057777		2203	4300	6503	SO:0001583	missense	8807	exon7			GTGGGAGACACTA	AF077346	CCDS2061.1	2q12.1	2013-01-11			ENSG00000115607	ENSG00000115607		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5989	protein-coding gene	gene with protein product		604509				9792649	Standard	XM_005264034		Approved	AcPL, CD218b	uc002tbx.3	O95256	OTTHUMG00000130777	ENST00000264260.2:c.736G>A	chr2.hg19:g.103057777G>A	ENSP00000264260:p.Asp246Asn	48.0	0.0		68.0	32.0	NM_003853	B2RPJ3|Q3KPE7|Q3KPE8|Q53TT4|Q53TU5	Missense_Mutation	SNP	ENST00000264260.2	hg19	CCDS2061.1	.	.	.	.	.	.	.	.	.	.	G	0.096	-1.159443	0.01686	.	.	ENSG00000115607	ENST00000264260;ENST00000409369	T;T	0.02421	4.37;4.3	5.31	-1.3	0.09259	.	0.951031	0.08821	N	0.888745	T	0.01835	0.0058	N	0.19112	0.55	0.19575	N	0.999967	B	0.02656	0.0	B	0.04013	0.001	T	0.49588	-0.8924	10	0.17369	T	0.5	.	4.6111	0.12402	0.6157:0.0:0.2154:0.1688	.	246	O95256	I18RA_HUMAN	N	246;104	ENSP00000264260:D246N;ENSP00000387201:D104N	ENSP00000264260:D246N	D	+	1	0	IL18RAP	102424209	0.008000	0.16893	0.073000	0.20177	0.220000	0.24768	-0.095000	0.11077	-0.138000	0.11434	0.491000	0.48974	GAC	.	.		0.438	IL18RAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253291.2	NM_003853		A	103057777	G	A	103057777	3	1	361	1	0	0	0	0	1	0	0	0	7657	942	33	3	754	3	IL18RAP	2	103057777	Missense_Mutation	SNP	G	TCGA-XR-A8TG-01A-11D-A35Z-10	23803596	103057777	140141596	16	50466										
GRB14	2888	hgsc.bcm.edu	37	chr2	165350963	165350964	+	Frame_Shift_Ins	INS	-	-	T													0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	tataatttgaaagtgctttaINSttttttgtccatgactcatt							TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr2:165350963_165350964insT	ENST00000263915.3	-	13	1991_1992	c.1453_1454insA	c.(1453-1455)atafs	p.I485fs	GRB14_ENST00000543549.1_Frame_Shift_Ins_p.I398fs|GRB14_ENST00000497306.1_Intron	NM_004490.2	NP_004481.2	Q14449	GRB14_HUMAN	growth factor receptor-bound protein 14	485	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				blood coagulation (GO:0007596)|leukocyte migration (GO:0050900)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			breast(3)|endometrium(2)|large_intestine(6)|lung(10)|ovary(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	32						AAAGTGCTTTATTTTTTGTCCA	0.332																																					p.I485fs		Atlas-INDEL	.											.	GRB14	73	.	0			c.1454_1455insA						.																																			SO:0001589	frameshift_variant	2888	exon13			.		CCDS2222.1	2q22-q24	2013-02-14			ENSG00000115290	ENSG00000115290		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	4565	protein-coding gene	gene with protein product		601524				8812444	Standard	XM_005246477		Approved		uc002ucl.3	Q14449	OTTHUMG00000132135	ENST00000263915.3:c.1454dupA	chr2.hg19:g.165350969_165350969dupT	ENSP00000263915:p.Ile485fs	209.0	0.0		295.0	51.0	NM_004490	B7Z7F9|Q7Z6I1	Frame_Shift_Ins	INS	ENST00000263915.3	hg19	CCDS2222.1																																																																																			.	.		0.332	GRB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255180.2			T	165350964	-	T	165350963	7	5	361	1	0	1	1	0	0	0	0	0	6766	449	16	0	176	0	GRB14	2	165350963	Frame_Shift_Ins	INS	-	TCGA-XR-A8TG-01A-11D-A35Z-10	62293186	165350963	77848410	17	50467										
HOXD12	3238	hgsc.bcm.edu	37	chr2	176964607	176964607	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	tcgccagactctttctacttCtccaacctgaggccgaatgg	8	14	3	2			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr2:176964607C>T	ENST00000406506.2	+	1	150	c.78C>T	c.(76-78)ttC>ttT	p.F26F	HOXD12_ENST00000404162.2_Silent_p.F26F			P35452	HXD12_HUMAN	homeobox D12	26					embryonic digit morphogenesis (GO:0042733)|pattern specification process (GO:0007389)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|large_intestine(1)|lung(7)|ovary(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0521)|READ - Rectum adenocarcinoma(9;0.0678)		CTTTCTACTTCTCCAACCTGA	0.657																																					p.F26F		Atlas-SNP	.											.	HOXD12	25	.	0			c.C78T						.						55	60	59					2																	176964607		1860	4076	5936	SO:0001819	synonymous_variant	3238	exon1			CTACTTCTCCAAC		CCDS46456.1	2q31.1	2011-06-20	2005-12-22		ENSG00000170178	ENSG00000170178		"Homeoboxes / ANTP class : HOXL subclass"	5135	protein-coding gene	gene with protein product		142988	"homeo box D12"	HOX4H		1675198, 1973146	Standard	NM_021193		Approved		uc010zev.1	P35452	OTTHUMG00000150358	ENST00000406506.2:c.78C>T	chr2.hg19:g.176964607C>T		80.0	0.0		99.0	35.0	NM_021193	B5MCP0|Q0VAD7|Q0VAD8|Q9NS03	Silent	SNP	ENST00000406506.2	hg19	CCDS46456.1																																																																																			.	.		0.657	HOXD12-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359253.2	NM_021193		T	176964607	C	T	176964607	2	4	361	1	0	0	0	0	0	0	0	1	7330	912	32	3		3	HOXD12	2	176964607	Silent	SNP	C	TCGA-XR-A8TG-01A-11D-A35Z-10	11613644	176964607	66234766	18	50468										
FSIP2	401024	hgsc.bcm.edu	37	chr2	186673007	186673007	+	Missense_Mutation	SNP	T	T	G													0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	tatggaaaaagtgatcaaaaTtattgatgaacttaagtcta							TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr2:186673007T>G	ENST00000424728.1	+	17	18974	c.18974T>G	c.(18973-18975)aTt>aGt	p.I6325S	FSIP2_ENST00000343098.5_Missense_Mutation_p.I6414S			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	6325										NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						GTGATCAAAATTATTGATGAA	0.338																																					p.I6414S		Atlas-SNP	.											FSIP2_ENST00000343098,colon,carcinoma,0,2	FSIP2	251	.	0			c.T19241G						.						33	32	33					2																	186673007		1808	4051	5859	SO:0001583	missense	401024	exon17			TCAAAATTATTGA	AK092099	CCDS54426.1	2q32.1	2010-06-18			ENSG00000188738	ENSG00000188738			21675	protein-coding gene	gene with protein product		615796				14702039	Standard	NM_173651		Approved	FLJ34780	uc002upl.3	Q5CZC0	OTTHUMG00000153874	ENST00000424728.1:c.18974T>G	chr2.hg19:g.186673007T>G	ENSP00000401306:p.Ile6325Ser	182.0	0.0		253.0	45.0	NM_173651	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Missense_Mutation	SNP	ENST00000424728.1	hg19		.	.	.	.	.	.	.	.	.	.	T	14.20	2.465493	0.43839	.	.	ENSG00000188738	ENST00000343098;ENST00000424728	T;T	0.58358	0.34;0.34	5.21	5.21	0.72293	.	0.112312	0.40144	N	0.001173	T	0.54870	0.1885	L	0.47190	1.495	0.37090	D	0.899402	.	.	.	.	.	.	T	0.59963	-0.7355	8	0.35671	T	0.21	.	11.3941	0.49832	0.0:0.0:0.0:1.0	.	.	.	.	S	6414;6325	ENSP00000344403:I6414S;ENSP00000401306:I6325S	ENSP00000344403:I6414S	I	+	2	0	FSIP2	186381252	0.996000	0.38824	0.868000	0.34077	0.489000	0.33432	1.615000	0.36922	2.188000	0.69820	0.482000	0.46254	ATT	.	.		0.338	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651		G	186673007	T	G	186673007	3	3	361	1	0	0	0	0	1	0	0	0	6083	1493	52	5	19307	5	FSIP2	2	186673007	Missense_Mutation	SNP	T	TCGA-XR-A8TG-01A-11D-A35Z-10	9708400	186673007	56526366	19	50469	263	2								
FSIP2	401024	hgsc.bcm.edu	37	chr2	186673014	186673014	+	Missense_Mutation	SNP	T	T	A													0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	aaagtgatcaaaattattgaTgaacttaagtctaaggaaaa							TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr2:186673014T>A	ENST00000424728.1	+	17	18981	c.18981T>A	c.(18979-18981)gaT>gaA	p.D6327E	FSIP2_ENST00000343098.5_Missense_Mutation_p.D6416E			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	6327										NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						AAATTATTGATGAACTTAAGT	0.333																																					p.D6416E		Atlas-SNP	.											.	FSIP2	251	.	0			c.T19248A						.						33	32	32					2																	186673014		1810	4051	5861	SO:0001583	missense	401024	exon17			TATTGATGAACTT	AK092099	CCDS54426.1	2q32.1	2010-06-18			ENSG00000188738	ENSG00000188738			21675	protein-coding gene	gene with protein product		615796				14702039	Standard	NM_173651		Approved	FLJ34780	uc002upl.3	Q5CZC0	OTTHUMG00000153874	ENST00000424728.1:c.18981T>A	chr2.hg19:g.186673014T>A	ENSP00000401306:p.Asp6327Glu	183.0	0.0		255.0	45.0	NM_173651	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Missense_Mutation	SNP	ENST00000424728.1	hg19		.	.	.	.	.	.	.	.	.	.	T	11.36	1.614971	0.28712	.	.	ENSG00000188738	ENST00000343098;ENST00000424728	T;T	0.51574	0.7;0.7	5.17	1.22	0.21188	.	0.234668	0.30159	N	0.010263	T	0.35008	0.0917	L	0.49778	1.585	0.09310	N	0.999998	.	.	.	.	.	.	T	0.15122	-1.0448	8	0.11794	T	0.64	.	3.9746	0.09468	0.3217:0.0893:0.0:0.589	.	.	.	.	E	6416;6327	ENSP00000344403:D6416E;ENSP00000401306:D6327E	ENSP00000344403:D6416E	D	+	3	2	FSIP2	186381259	0.981000	0.34729	0.228000	0.23943	0.146000	0.21551	1.031000	0.30165	0.409000	0.25649	-0.353000	0.07706	GAT	.	.		0.333	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651		A	186673014	T	A	186673014	3	1	361	1	0	0	0	0	1	0	0	0	6083	1461	51	4	19314	4	FSIP2	2	186673014	Missense_Mutation	SNP	T	TCGA-XR-A8TG-01A-11D-A35Z-10	7	186673014	56526359	20	50470	263	2								
LAMB2	3913	hgsc.bcm.edu	37	chr3	49169137	49169138	+	Missense_Mutation	DNP	AT	AT	CA													0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	ctgctgagcgttccaccagcAtggcagcagggcgaaatgtc							TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	A|T	A|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr3:49169137_49169138AT>CA	ENST00000418109.1	-	6	642_643	c.478_479AT>TG	c.(478-480)ATg>TGg	p.M160W	LAMB2_ENST00000305544.4_Missense_Mutation_p.M160W	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	160	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		TTCCACCAGCATGGCAGCAGGG	0.599																																					p.M160R|p.M160L		Atlas-SNP	.											.	LAMB2	156	.	0			c.T479G|c.A478T						.																																			SO:0001583	missense	3913	exon5			ACCAGCATGGCAG|CCAGCATGGCAGC		CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"Laminins"	6487	protein-coding gene	gene with protein product	"laminin S"	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.478_479delinsCA	chr3.hg19:g.49169137_49169138delinsCA	ENSP00000388325:p.Met160Trp	50.0	0.0		83.0|82.0	6.0	NM_002292	Q16321	Missense_Mutation	SNP	ENST00000418109.1	hg19	CCDS2789.1																																																																																			.	.		0.599	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292		CA	49169138	AT	CA	49169137	3	2	361	1	0	0	0	0	1	0	0	0	8620	217	8	5	5029	5	LAMB2	3	49169137	Missense_Mutation	DNP	AT	TCGA-XR-A8TG-01A-11D-A35Z-10		49169137	148853293	21	50471										
PEX5L	51555	hgsc.bcm.edu	37	chr3	179689381	179689381	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	tgtacgtaagtattcacttaCctgcttttgatcaacaatta	5	8	2	1			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr3:179689381C>T	ENST00000467460.1	-	2	424		c.e2+1		PEX5L_ENST00000485199.1_Splice_Site|PEX5L_ENST00000464614.1_Splice_Site|PEX5L_ENST00000465751.1_Intron|PEX5L_ENST00000468741.1_Splice_Site|PEX5L_ENST00000263962.8_Intron|PEX5L_ENST00000476138.1_Splice_Site|PEX5L_ENST00000472994.1_Intron	NM_001256751.1|NM_016559.2	NP_001243680.1|NP_057643.1	Q8IYB4	PEX5R_HUMAN	peroxisomal biogenesis factor 5-like						maintenance of protein location (GO:0045185)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome matrix, docking (GO:0016560)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of membrane potential (GO:0042391)	cytosol (GO:0005829)|dendrite (GO:0030425)|peroxisomal membrane (GO:0005778)|receptor complex (GO:0043235)	peroxisome matrix targeting signal-1 binding (GO:0005052)|peroxisome targeting sequence binding (GO:0000268)|small GTPase binding (GO:0031267)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(23)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	all_cancers(143;3.94e-14)|Ovarian(172;0.0338)|Breast(254;0.183)		OV - Ovarian serous cystadenocarcinoma(80;1.75e-26)|GBM - Glioblastoma multiforme(14;0.000518)			tattcacttacctgcttttga	0.343																																					.		Atlas-SNP	.											.	PEX5L	104	.	0			c.93+1G>A						.						192	181	185					3																	179689381		2203	4299	6502	SO:0001630	splice_region_variant	51555	exon3			CACTTACCTGCTT	AJ245503	CCDS3236.1, CCDS58861.1, CCDS58862.1, CCDS58863.1, CCDS58864.1, CCDS58865.1, CCDS58866.1, CCDS58867.1	3q27.1	2013-01-10			ENSG00000114757	ENSG00000114757		"Tetratricopeptide (TTC) repeat domain containing"	30024	protein-coding gene	gene with protein product		611058				11463335	Standard	NM_016559		Approved	PEX5R, PXR2	uc003fki.2	Q8IYB4	OTTHUMG00000157363	ENST00000467460.1:c.93+1G>A	chr3.hg19:g.179689381C>T		56.0	0.0		78.0	31.0	NM_001256752	B7Z2A5|B7Z305|B7Z318|B7Z5Z5|B7Z8P2|E7EUV8|E7EUZ0|E9PEC1|E9PH97|Q9NQD1|Q9P2U3|Q9P2U4	Splice_Site	SNP	ENST00000467460.1	hg19	CCDS3236.1																																																																																			.	.		0.343	PEX5L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348577.1	NM_016559	Intron	T	179689381	C	T	179689381	5	4	361	1	0	0	0	0	0	0	1	0	11758	521	18	3	1842	3	PEX5L	3	179689381	Splice_Site	SNP	C	TCGA-XR-A8TG-01A-11D-A35Z-10	130520244	179689381	18333049	22	50472										
ADD1	118	hgsc.bcm.edu	37	chr4	2909499	2909499	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	gaggatggacatagaacttcCacctctgctgtccctaacct	8	13	1	1			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr4:2909499C>A	ENST00000398129.1	+	10	1463	c.1443C>A	c.(1441-1443)tcC>tcA	p.S481S	ADD1_ENST00000446856.1_Silent_p.S481S|ADD1_ENST00000398123.2_Silent_p.S512S|ADD1_ENST00000513328.2_Silent_p.S481S|ADD1_ENST00000355842.3_Silent_p.S481S|ADD1_ENST00000503455.2_Silent_p.S512S|ADD1_ENST00000264758.7_Silent_p.S512S|ADD1_ENST00000398125.1_Silent_p.S512S			P35611	ADDA_HUMAN	adducin 1 (alpha)	481					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|barbed-end actin filament capping (GO:0051016)|cell morphogenesis (GO:0000902)|cell volume homeostasis (GO:0006884)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to retinoic acid (GO:0071300)|endoplasmic reticulum unfolded protein response (GO:0030968)|erythrocyte differentiation (GO:0030218)|hemoglobin metabolic process (GO:0020027)|homeostasis of number of cells within a tissue (GO:0048873)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein binding (GO:0032092)	cytosol (GO:0005829)|dendritic spine (GO:0043197)|F-actin capping protein complex (GO:0008290)|focal adhesion (GO:0005925)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|spectrin binding (GO:0030507)|structural molecule activity (GO:0005198)|transcription factor binding (GO:0008134)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		ATAGAACTTCCACCTCTGCTG	0.448																																					p.S512S	Esophageal Squamous(71;505 1201 20414 34538 37449)	Atlas-SNP	.											.	ADD1	56	.	0			c.C1536A						.						213	188	196					4																	2909499		2203	4300	6503	SO:0001819	synonymous_variant	118	exon11			AACTTCCACCTCT	L07261	CCDS3363.1, CCDS3364.1, CCDS43205.1, CCDS75094.1	4p16.3	2009-04-22			ENSG00000087274	ENSG00000087274			243	protein-coding gene	gene with protein product		102680				1840603	Standard	NM_001119		Approved		uc003gfq.3	P35611	OTTHUMG00000122080	ENST00000398129.1:c.1443C>A	chr4.hg19:g.2909499C>A		102.0	0.0		159.0	17.0	NM_176801	A2A3N8|A2A3P0|B4DI79|D3DVR3|D3DVR4|D3DVR5|Q13734|Q14729|Q16156|Q86XM2|Q9UJB6	Silent	SNP	ENST00000398129.1	hg19	CCDS43205.1	.	.	.	.	.	.	.	.	.	.	C	10.27	1.303737	0.23736	.	.	ENSG00000087274	ENST00000514940	.	.	.	5.59	5.59	0.84812	.	.	.	.	.	T	0.76557	0.4004	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.74228	-0.3733	4	.	.	.	-26.4874	19.9513	0.97200	0.0:1.0:0.0:0.0	.	.	.	.	Q	218	.	.	P	+	2	0	ADD1	2879297	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.628000	0.67791	2.790000	0.95986	0.655000	0.94253	CCA	.	.		0.448	ADD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242840.1	NM_014189		A	2909499	C	A	2909499	2	1	361	1	0	0	0	0	0	0	0	1	304	581	21	3		3	ADD1	4	2909499	Silent	SNP	C	TCGA-XR-A8TG-01A-11D-A35Z-10		2909499	188244777	23	50473										
SLAIN2	57606	hgsc.bcm.edu	37	chr4	48385695	48385695	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	cgcagtcttccaaacctgtcCcgaacatctaatacacaagt	5	14	2	0			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr4:48385695C>A	ENST00000264313.6	+	6	1672	c.1254C>A	c.(1252-1254)tcC>tcA	p.S418S	SLAIN2_ENST00000512093.1_Silent_p.S225S	NM_020846.1	NP_065897.1	Q9P270	SLAI2_HUMAN	SLAIN motif family, member 2	418					cytoplasmic microtubule organization (GO:0031122)|microtubule nucleation (GO:0007020)|positive regulation of microtubule polymerization (GO:0031116)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|prostate(1)	13						CAAACCTGTCCCGAACATCTA	0.358																																					p.S418S		Atlas-SNP	.											.	SLAIN2	31	.	0			c.C1254A						.						53	48	50					4																	48385695		1841	4094	5935	SO:0001819	synonymous_variant	57606	exon6			CCTGTCCCGAACA	BC006139	CCDS47051.1	4p12	2008-02-05	2006-09-12	2006-09-12	ENSG00000109171	ENSG00000109171			29282	protein-coding gene	gene with protein product		610492	"KIAA1458"	KIAA1458		16546155	Standard	NM_020846		Approved	FLJ21611	uc003gya.4	Q9P270	OTTHUMG00000161701	ENST00000264313.6:c.1254C>A	chr4.hg19:g.48385695C>A		240.0	0.0		485.0	21.0	NM_020846	A8K4P1|Q8N5R3	Silent	SNP	ENST00000264313.6	hg19	CCDS47051.1	.	.	.	.	.	.	.	.	.	.	C	8.966	0.971715	0.18736	.	.	ENSG00000109171	ENST00000510595	.	.	.	5.55	3.82	0.43975	.	.	.	.	.	T	0.69940	0.3167	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.66060	-0.6017	4	.	.	.	-6.8365	14.8188	0.70055	0.0:0.869:0.0:0.131	.	.	.	.	T	1	.	.	P	+	1	0	SLAIN2	48080452	0.998000	0.40836	1.000000	0.80357	0.976000	0.68499	0.478000	0.22212	0.321000	0.23259	-1.134000	0.01955	CCG	.	.		0.358	SLAIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365807.4	NM_020846		A	48385695	C	A	48385695	2	1	361	1	0	0	0	0	0	0	0	1	14381	610	22	3		3	SLAIN2	4	48385695	Silent	SNP	C	TCGA-XR-A8TG-01A-11D-A35Z-10	45476196	48385695	142768581	24	50474										
YTHDC1	91746	hgsc.bcm.edu	37	chr4	69179869	69179869	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	ctctgtctcgatcacataatCgctctctttctctttctcta	3	14	6	0			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr4:69179869C>A	ENST00000344157.4	-	17	2467	c.2132G>T	c.(2131-2133)cGa>cTa	p.R711L	YTHDC1_ENST00000579690.1_Missense_Mutation_p.R719L|YTHDC1_ENST00000355665.3_Missense_Mutation_p.R693L	NM_001031732.2	NP_001026902.1	Q96MU7	YTDC1_HUMAN	YTH domain containing 1	711	Arg-rich.				mRNA splice site selection (GO:0006376)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	30						atcacataatcgctctctttc	0.463																																					p.R711L		Atlas-SNP	.											YTHDC1,NS,carcinoma,0,1	YTHDC1	81	.	0			c.G2132T						.						78	72	74					4																	69179869		2203	4300	6503	SO:0001583	missense	91746	exon17			CATAATCGCTCTC	AK098515	CCDS3522.2, CCDS33992.1	4q13.3	2009-01-14			ENSG00000083896	ENSG00000083896			30626	protein-coding gene	gene with protein product						12368078, 10564280	Standard	XM_005265706		Approved	YT521, KIAA1966, YT521-B	uc003hdx.3	Q96MU7	OTTHUMG00000129306	ENST00000344157.4:c.2132G>T	chr4.hg19:g.69179869C>A	ENSP00000339245:p.Arg711Leu	82.0	0.0		123.0	28.0	NM_001031732	Q4W5Q3|Q7Z622|Q8TF35	Missense_Mutation	SNP	ENST00000344157.4	hg19	CCDS33992.1	.	.	.	.	.	.	.	.	.	.	C	17.01	3.279710	0.59758	.	.	ENSG00000083896	ENST00000344157;ENST00000355665	T;T	0.34667	1.38;1.35	5.56	5.56	0.83823	.	0.222920	0.44285	D	0.000480	T	0.40743	0.1129	N	0.24115	0.695	0.49582	D	0.999803	D;P	0.56035	0.974;0.956	P;P	0.52481	0.7;0.504	T	0.35574	-0.9783	10	0.87932	D	0	.	19.1452	0.93463	0.0:1.0:0.0:0.0	.	693;711	Q96MU7-2;Q96MU7	.;YTDC1_HUMAN	L	711;693	ENSP00000339245:R711L;ENSP00000347888:R693L	ENSP00000339245:R711L	R	-	2	0	YTHDC1	68862464	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.795000	0.69074	2.619000	0.88677	0.467000	0.42956	CGA	.	.		0.463	YTHDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251437.1	NM_133370		A	69179869	C	A	69179869	3	1	361	1	0	0	0	0	1	0	0	0	17511	884	31	1	55	1	YTHDC1	4	69179869	Missense_Mutation	SNP	C	TCGA-XR-A8TG-01A-11D-A35Z-10	20794174	69179869	121974407	25	50475										
ANK2	287	hgsc.bcm.edu	37	chr4	114274408	114274408	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	gaaggctgctgaggaagagcCaggagagccttttgaaatcg	15	7	0	4			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr4:114274408C>G	ENST00000357077.4	+	38	4687	c.4634C>G	c.(4633-4635)cCa>cGa	p.P1545R	ANK2_ENST00000510275.2_Intron|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000394537.3_Intron|ANK2_ENST00000264366.6_Missense_Mutation_p.P1512R|ANK2_ENST00000506722.1_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	1545					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		GAGGAAGAGCCAGGAGAGCCT	0.438																																					p.P1545R		Atlas-SNP	.											.	ANK2	576	.	0			c.C4634G						.						54	56	55					4																	114274408		2203	4300	6503	SO:0001583	missense	287	exon38			AAGAGCCAGGAGA	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.4634C>G	chr4.hg19:g.114274408C>G	ENSP00000349588:p.Pro1545Arg	138.0	0.0		107.0	84.0	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	hg19	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	C	19.35	3.810136	0.70797	.	.	ENSG00000145362	ENST00000503423;ENST00000504454;ENST00000357077;ENST00000264366	T;T;T;T	0.67698	-0.02;-0.16;-0.28;-0.27	5.62	5.62	0.85841	.	0.000000	0.53938	D	0.000044	T	0.78929	0.4361	L	0.51422	1.61	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.74023	0.943;0.982	T	0.78145	-0.2318	10	0.51188	T	0.08	.	19.662	0.95877	0.0:1.0:0.0:0.0	.	1512;1545	Q01484;Q01484-4	ANK2_HUMAN;.	R	1458;1560;1545;1512	ENSP00000421011:P1458R;ENSP00000424722:P1560R;ENSP00000349588:P1545R;ENSP00000264366:P1512R	ENSP00000264366:P1512R	P	+	2	0	ANK2	114493857	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.079000	0.71291	2.649000	0.89929	0.650000	0.86243	CCA	.	.		0.438	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		G	114274408	C	G	114274408	3	3	361	1	0	0	0	0	1	0	0	0	621	594	21	4	4849	4	ANK2	4	114274408	Missense_Mutation	SNP	C	TCGA-XR-A8TG-01A-11D-A35Z-10	45094539	114274408	76879868	26	50476										
LARP1B	55132	hgsc.bcm.edu	37	chr4	129019441	129019441	+	Nonsense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	tttccctgattgctggttttCagcgtgttcaggctctcact	9	11	3	1			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr4:129019441C>T	ENST00000326639.6	+	8	980	c.769C>T	c.(769-771)Cag>Tag	p.Q257*	LARP1B_ENST00000354456.3_5'UTR|LARP1B_ENST00000394288.3_Nonsense_Mutation_p.Q257*|LARP1B_ENST00000432347.2_Nonsense_Mutation_p.Q257*|LARP1B_ENST00000512292.1_Nonsense_Mutation_p.Q257*|LARP1B_ENST00000427266.1_Nonsense_Mutation_p.Q257*|LARP1B_ENST00000264584.5_Nonsense_Mutation_p.Q210*|LARP1B_ENST00000441387.1_Nonsense_Mutation_p.Q257*	NM_018078.2	NP_060548.2	Q659C4	LAR1B_HUMAN	La ribonucleoprotein domain family, member 1B	257	HTH La-type RNA-binding. {ECO:0000255|PROSITE-ProRule:PRU00332}.					nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|lung(11)|ovary(1)|prostate(3)	34						TGCTGGTTTTCAGCGTGTTCA	0.378																																					p.Q257X		Atlas-SNP	.											.	LARP1B	120	.	0			c.C769T						.						96	83	87					4																	129019441		2203	4300	6503	SO:0001587	stop_gained	55132	exon8			GGTTTTCAGCGTG		CCDS3738.1, CCDS47133.1, CCDS64057.1	4q28.2	2009-06-09	2009-06-09	2009-06-09	ENSG00000138709	ENSG00000138709		"La ribonucleoprotein domain containing"	24704	protein-coding gene	gene with protein product			"La ribonucleoprotein domain family, member 2"	LARP2		12045101	Standard	NM_018078		Approved	FLJ10378, DKFZp434K245, DKFZp686E0316	uc003iga.3	Q659C4	OTTHUMG00000133343	ENST00000326639.6:c.769C>T	chr4.hg19:g.129019441C>T	ENSP00000321997:p.Gln257*	40.0	0.0		72.0	14.0	NM_032239	Q2YDB6|Q4W599|Q4W5B2|Q659A0|Q6P5X2|Q7Z3F7|Q86VK7|Q8N6F4|Q8N7H4|Q8NAF2|Q9H5E7|Q9NW12	Nonsense_Mutation	SNP	ENST00000326639.6	hg19	CCDS3738.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	37|37	6.180200|6.180200	0.97352|0.97352	.|.	.|.	ENSG00000138709|ENSG00000138709	ENST00000326639;ENST00000512292;ENST00000508819;ENST00000394288;ENST00000432347;ENST00000264584;ENST00000441387;ENST00000427266|ENST00000507377	.|.	.|.	.|.	5.27|5.27	5.27|5.27	0.74061|0.74061	.|.	0.114305|.	0.64402|.	D|.	0.000015|.	.|T	.|0.64148	.|0.2572	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.61252	.|-0.7100	.|4	0.20046|.	T|.	0.44|.	.|.	12.0742|12.0742	0.53634|0.53634	0.0:0.9213:0.0:0.0787|0.0:0.9213:0.0:0.0787	.|.	.|.	.|.	.|.	X|L	257;257;210;257;257;210;257;257|225	.|.	ENSP00000264584:Q210X|.	Q|S	+|+	1|2	0|0	LARP1B|LARP1B	129238891|129238891	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	5.535000|5.535000	0.67173|0.67173	2.732000|2.732000	0.93576|0.93576	0.650000|0.650000	0.86243|0.86243	CAG|TCA	.	.		0.378	LARP1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257173.2	NM_018078		T	129019441	C	T	129019441	4	4	361	1	0	0	0	0	0	1	0	0	8638	827	29	3	791	3	LARP1B	4	129019441	Nonsense_Mutation	SNP	C	TCGA-XR-A8TG-01A-11D-A35Z-10	14745033	129019441	62134835	27	50477										
ZNF827	152485	hgsc.bcm.edu	37	chr4	146823924	146823924	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	cagaacactgagctgctgggCgtggtgggaaggcggggaaa	19	7	0	2	rs139372039		TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr4:146823924C>A	ENST00000508784.1	-	2	714	c.487G>T	c.(487-489)Gcc>Tcc	p.A163S	ZNF827_ENST00000379448.4_Missense_Mutation_p.A163S|ZNF827_ENST00000513320.1_Intron			Q17R98	ZN827_HUMAN	zinc finger protein 827	163					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	all_hematologic(180;0.151)					AGCTGCTGGGCGTGGTGGGAA	0.537																																					p.A163S		Atlas-SNP	.											.	ZNF827	102	.	0			c.G487T						.						77	68	71					4																	146823924		2203	4300	6503	SO:0001583	missense	152485	exon2			GCTGGGCGTGGTG	AK091130	CCDS34072.1	4q31.22	2013-01-08			ENSG00000151612	ENSG00000151612		"Zinc fingers, C2H2-type"	27193	protein-coding gene	gene with protein product						12477932	Standard	NM_178835		Approved		uc003ikm.3	Q17R98	OTTHUMG00000161362	ENST00000508784.1:c.487G>T	chr4.hg19:g.146823924C>A	ENSP00000421863:p.Ala163Ser	45.0	0.0		57.0	28.0	NM_178835	B7ZL52|Q7Z4S7|Q8N279	Missense_Mutation	SNP	ENST00000508784.1	hg19		.	.	.	.	.	.	.	.	.	.	C	18.39	3.613722	0.66672	.	.	ENSG00000151612	ENST00000508784;ENST00000379448;ENST00000281318	T;T	0.16597	2.33;2.38	5.84	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.21631	0.0521	L	0.27053	0.805	0.46078	D	0.998851	P;P	0.46621	0.811;0.881	P;P	0.50934	0.452;0.654	T	0.01734	-1.1285	10	0.87932	D	0	-22.6858	14.9737	0.71254	0.0:0.9316:0.0:0.0684	.	163;163	Q17R98;Q17R98-2	ZN827_HUMAN;.	S	163;163;162	ENSP00000421863:A163S;ENSP00000368761:A163S	ENSP00000281318:A162S	A	-	1	0	ZNF827	147043374	1.000000	0.71417	0.991000	0.47740	0.734000	0.41952	7.416000	0.80143	1.483000	0.48342	-0.258000	0.10820	GCC	.	C|1.000;T|0.000		0.537	ZNF827-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000364654.2	NM_178835		A	146823924	C	A	146823924	3	1	361	1	0	0	0	0	1	0	0	0	18195	768	27	1	2794	1	ZNF827	4	146823924	Missense_Mutation	SNP	C	TCGA-XR-A8TG-01A-11D-A35Z-10	17804483	146823924	44330352	28	50478										
AGA	175	hgsc.bcm.edu	37	chr4	178355598	178355598	+	Frame_Shift_Del	DEL	G	G	-													0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	gcggctgcccctgcagtatcGtcagcataggctccagctcc					rs148052291	byFrequency	TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr4:178355598delG	ENST00000264595.2	-	7	871	c.744delC	c.(742-744)gacfs	p.D249fs	AGA_ENST00000506853.1_5'UTR	NM_000027.3|NM_001171988.1	NP_000018.2|NP_001165459.1	P20933	ASPG_HUMAN	aspartylglucosaminidase	249					protein deglycosylation (GO:0006517)|protein maturation (GO:0051604)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity (GO:0003948)|peptidase activity (GO:0008233)	p.D248D(1)		endometrium(1)|kidney(2)|large_intestine(6)|lung(5)|skin(2)	16		all_lung(41;1.27e-09)|Lung NSC(41;1.1e-08)|Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Hepatocellular(41;0.148)|all_neural(102;0.164)|Colorectal(36;0.245)		all cancers(43;1.37e-22)|Epithelial(43;3.86e-20)|OV - Ovarian serous cystadenocarcinoma(60;3.8e-11)|Colorectal(24;6.98e-05)|GBM - Glioblastoma multiforme(59;0.000362)|COAD - Colon adenocarcinoma(29;0.000462)|STAD - Stomach adenocarcinoma(60;0.0029)|LUSC - Lung squamous cell carcinoma(193;0.0328)|READ - Rectum adenocarcinoma(43;0.163)		CTGCAGTATCGTCAGCATAGG	0.468																																					p.D249fs		Atlas-INDEL	.											.	AGA	39	.	1	Substitution - coding silent(1)	large_intestine(1)	c.745delG						.						111	105	107					4																	178355598		2203	4300	6503	SO:0001589	frameshift_variant	175	exon7			.	X55330	CCDS3829.1	4q34.3	2014-06-23			ENSG00000038002	ENSG00000038002	3.5.1.26		318	protein-coding gene	gene with protein product	"glycosylasparaginase", "N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase"	613228					Standard	NM_000027		Approved	ASRG	uc003iuu.2	P20933	OTTHUMG00000160723	ENST00000264595.2:c.744delC	chr4.hg19:g.178355598delG	ENSP00000264595:p.Asp249fs	197.0	0.0		386.0	119.0	NM_000027	B2R7H2|D3DP47|Q4W5Q2|Q6FHN6|Q9UCK6|Q9UCK7|Q9UCK8	Frame_Shift_Del	DEL	ENST00000264595.2	hg19	CCDS3829.1																																																																																			.	.		0.468	AGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361916.1	NM_000027		-	178355598	G	-	178355598	7	5	361	1	0	1	0	1	0	0	0	0	365	1136	40	0	308	0	AGA	4	178355598	Frame_Shift_Del	DEL	G	TCGA-XR-A8TG-01A-11D-A35Z-10	31531674	178355598	12798678	29	50479										
ODZ3	55714	hgsc.bcm.edu	37	chr4	183721246	183721246	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	cgctacggcatgaccctggaCgaggagaaggcgcgcatcct	14	13	0	2			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr4:183721246C>T	ENST00000511685.1	+	28	7965	c.7842C>T	c.(7840-7842)gaC>gaT	p.D2614D	TENM3_ENST00000406950.2_Silent_p.D2614D			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	2614					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										TGACCCTGGACGAGGAGAAGG	0.746																																					p.D2614D		Atlas-SNP	.											.	.	.	.	0			c.C7842T						.						12	14	13					4																	183721246		2130	4235	6365	SO:0001819	synonymous_variant	55714	exon27			CCTGGACGAGGAG	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.7842C>T	chr4.hg19:g.183721246C>T		51.0	0.0		95.0	35.0	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Silent	SNP	ENST00000511685.1	hg19	CCDS47165.1																																																																																			.	.		0.746	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			T	183721246	C	T	183721246	2	4	361	1	0	0	0	0	0	0	0	1	10845	535	19	1		1	ODZ3	4	183721246	Silent	SNP	C	TCGA-XR-A8TG-01A-11D-A35Z-10	5365648	183721246	7433030	30	50480										
GCNT4	51301	hgsc.bcm.edu	37	chr5	74325466	74325466	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	gacaaccaaagaataggctaTtgggaagcttttctcctcct	8	10	1	1			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr5:74325466T>G	ENST00000322348.4	-	1	1258	c.397A>C	c.(397-399)Ata>Cta	p.I133L		NM_016591.2	NP_057675.1	Q9P109	GCNT4_HUMAN	glucosaminyl (N-acetyl) transferase 4, core 2	133					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|homeostasis of number of cells (GO:0048872)|inter-male aggressive behavior (GO:0002121)|kidney morphogenesis (GO:0060993)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|thyroid hormone metabolic process (GO:0042403)|tissue morphogenesis (GO:0048729)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)|N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(2)|skin(1)|stomach(2)	19		all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;8.44e-57)		GAATAGGCTATTGGGAAGCTT	0.393																																					p.I133L		Atlas-SNP	.											.	GCNT4	46	.	0			c.A397C						.						134	129	131					5																	74325466		2203	4300	6503	SO:0001583	missense	51301	exon1			AGGCTATTGGGAA	AF132035	CCDS4026.1	5q12	2013-02-25	2010-03-16		ENSG00000176928	ENSG00000176928	2.4.1.102	"Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	17973	protein-coding gene	gene with protein product	"core 2 beta-1,6-N-acetylglucosaminyltransferase 3", "beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 4"		"glucosaminyl (N-acetyl) transferase 4, core 2 (beta-1,6-N-acetylglucosaminyltransferase)"			10753916	Standard	NM_016591		Approved	C2GNT3	uc003kdn.3	Q9P109	OTTHUMG00000131272	ENST00000322348.4:c.397A>C	chr5.hg19:g.74325466T>G	ENSP00000317027:p.Ile133Leu	55.0	0.0		90.0	6.0	NM_016591		Missense_Mutation	SNP	ENST00000322348.4	hg19	CCDS4026.1	.	.	.	.	.	.	.	.	.	.	.	10.05	1.244533	0.22796	.	.	ENSG00000176928	ENST00000322348	T	0.12147	2.71	6.17	3.71	0.42584	.	0.100808	0.64402	D	0.000003	T	0.05914	0.0154	N	0.16066	0.365	0.32426	N	0.548674	B	0.10296	0.003	B	0.14023	0.01	T	0.33599	-0.9862	10	0.07030	T	0.85	-16.0138	4.9956	0.14237	0.1163:0.0633:0.1217:0.6987	.	133	Q9P109	GCNT4_HUMAN	L	133	ENSP00000317027:I133L	ENSP00000317027:I133L	I	-	1	0	GCNT4	74361222	0.315000	0.24571	0.702000	0.30337	0.952000	0.60782	0.539000	0.23175	0.524000	0.28502	-0.313000	0.08912	ATA	.	.		0.393	GCNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254040.1	NM_016591		G	74325466	T	G	74325466	3	3	361	1	0	0	0	0	1	0	0	0	6311	1493	52	5	968	5	GCNT4	5	74325466	Missense_Mutation	SNP	T	TCGA-XR-A8TG-01A-11D-A35Z-10		74325466	106589794	31	50481										
CHD1	1105	hgsc.bcm.edu	37	chr5	98192416	98192416	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	cagttttctgtgtttctctcTgtcactgtaatatctaataa	5	8	5	0			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr5:98192416T>A	ENST00000284049.3	-	35	4950	c.4801A>T	c.(4801-4803)Aga>Tga	p.R1601*		NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	1601					chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	49		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	TGTTTCTCTCTGTCACTGTAA	0.294																																					p.R1601X		Atlas-SNP	.											.	CHD1	137	.	0			c.A4801T						.						67	66	66					5																	98192416		2202	4299	6501	SO:0001587	stop_gained	1105	exon35			TCTCTCTGTCACT	AF006513	CCDS34204.1	5q15-q21	2008-07-18			ENSG00000153922	ENSG00000153922			1915	protein-coding gene	gene with protein product		602118				8460153, 9326634	Standard	XM_005271866		Approved		uc003knf.3	O14646	OTTHUMG00000162744	ENST00000284049.3:c.4801A>T	chr5.hg19:g.98192416T>A	ENSP00000284049:p.Arg1601*	78.0	0.0		110.0	43.0	NM_001270	Q17RZ3	Nonsense_Mutation	SNP	ENST00000284049.3	hg19	CCDS34204.1	.	.	.	.	.	.	.	.	.	.	T	43	10.137175	0.99344	.	.	ENSG00000153922	ENST00000422663;ENST00000284049	.	.	.	5.7	3.18	0.36537	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.4484	0.55664	0.0:0.0:0.2537:0.7463	.	.	.	.	X	191;1601	.	ENSP00000284049:R1601X	R	-	1	2	CHD1	98220316	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	2.786000	0.47790	0.375000	0.24679	0.533000	0.62120	AGA	.	.		0.294	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270		A	98192416	T	A	98192416	4	1	361	1	0	0	0	0	0	1	0	0	3325	1588	55	4	335	4	CHD1	5	98192416	Nonsense_Mutation	SNP	T	TCGA-XR-A8TG-01A-11D-A35Z-10	23866950	98192416	82722844	32	50482										
ODZ2	57451	hgsc.bcm.edu	37	chr5	167525124	167525124	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	aggatttctaggagcagactGtgctaaaggtatgtgccgcc	13	8	1	1			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr5:167525124G>C	ENST00000518659.1	+	9	1844	c.1805G>C	c.(1804-1806)tGt>tCt	p.C602S	TENM2_ENST00000520394.1_Missense_Mutation_p.C370S|CTB-178M22.1_ENST00000517408.1_RNA|TENM2_ENST00000545108.1_Missense_Mutation_p.C602S|TENM2_ENST00000519204.1_Missense_Mutation_p.C481S|TENM2_ENST00000403607.2_Missense_Mutation_p.C435S	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	602	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.|EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										GGAGCAGACTGTGCTAAAGGT	0.517																																					p.C602S		Atlas-SNP	.											.	.	.	.	0			c.G1805C						.						127	125	126					5																	167525124		2042	4189	6231	SO:0001583	missense	57451	exon9			CAGACTGTGCTAA	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"odz, odd Oz/ten-m homolog 2 (Drosophila)"	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.1805G>C	chr5.hg19:g.167525124G>C	ENSP00000429430:p.Cys602Ser	77.0	0.0		140.0	33.0	NM_001122679	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	hg19		.	.	.	.	.	.	.	.	.	.	G	17.09	3.301418	0.60195	.	.	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	T;T;T;T;T	0.20200	2.09;2.09;2.09;2.09;2.09	5.11	5.11	0.69529	EGF, extracellular (1);Epidermal growth factor-like (1);EGF-like region, conserved site (2);Epidermal growth factor-like, type 3 (1);	0.046763	0.85682	D	0.000000	T	0.68522	0.3010	H	0.99368	4.535	0.80722	D	1	D;D;D	0.89917	1.0;0.984;1.0	D;D;D	0.91635	0.997;0.974;0.999	D	0.84155	0.0425	10	0.87932	D	0	.	18.9359	0.92584	0.0:0.0:1.0:0.0	.	602;370;481	Q9NT68;F8VNQ3;G3V106	TEN2_HUMAN;.;.	S	602;602;481;370;435	ENSP00000429430:C602S;ENSP00000438635:C602S;ENSP00000428964:C481S;ENSP00000427874:C370S;ENSP00000384905:C435S	ENSP00000384905:C435S	C	+	2	0	ODZ2	167457702	1.000000	0.71417	0.997000	0.53966	0.075000	0.17131	9.420000	0.97426	2.538000	0.85594	0.650000	0.86243	TGT	.	.		0.517	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		C	167525124	G	C	167525124	3	2	361	1	0	0	0	0	1	0	0	0	10844	1377	48	4	1839	4	ODZ2	5	167525124	Missense_Mutation	SNP	G	TCGA-XR-A8TG-01A-11D-A35Z-10	69332708	167525124	13390136	33	50483										
TNXB	7148	hgsc.bcm.edu	37	chr6	32047000	32047000	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	aaagagtcgaagctgccctgGgggacggtccagaagaggct	16	9	0	3			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr6:32047000G>A	ENST00000375244.3	-	11	4386	c.4185C>T	c.(4183-4185)ccC>ccT	p.P1395P	TNXB_ENST00000375247.2_Silent_p.P1395P|RNA5SP206_ENST00000516703.1_RNA			P22105	TENX_HUMAN	tenascin XB	1482	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						AGCTGCCCTGGGGGACGGTCC	0.677																																					p.P1395P		Atlas-SNP	.											.	TNXB	553	.	0			c.C4185T						.						117	129	125					6																	32047000		1260	2540	3800	SO:0001819	synonymous_variant	7148	exon11			GCCCTGGGGGACG	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.4185C>T	chr6.hg19:g.32047000G>A		62.0	0.0		77.0	11.0	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Silent	SNP	ENST00000375244.3	hg19																																																																																				.	.		0.677	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		A	32047000	G	A	32047000	2	1	361	1	0	0	0	0	0	0	0	1	16361	1219	43	3		3	TNXB	6	32047000	Silent	SNP	G	TCGA-XR-A8TG-01A-11D-A35Z-10		32047000	139068067	34	50484										
PACSIN1	29993	hgsc.bcm.edu	37	chr6	34494117	34494117	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	cgatgaggcctcactggcgcCagaggagaccaccgacagct	13	14	1	3			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr6:34494117C>A	ENST00000538621.1	+	2	280	c.35C>A	c.(34-36)cCa>cAa	p.P12Q	PACSIN1_ENST00000374043.2_5'UTR|PACSIN1_ENST00000486120.1_3'UTR|PACSIN1_ENST00000244458.2_Missense_Mutation_p.P12Q	NM_001199583.2	NP_001186512.1	Q9BY11	PACN1_HUMAN	protein kinase C and casein kinase substrate in neurons 1	12	F-BAR domain.				actin filament organization (GO:0007015)|establishment of protein localization to plasma membrane (GO:0090002)|membrane tubulation (GO:0097320)|neuron projection morphogenesis (GO:0048812)|positive regulation of dendrite development (GO:1900006)|protein localization to membrane (GO:0072657)|synaptic vesicle endocytosis (GO:0048488)	axon terminus (GO:0043679)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|synapse (GO:0045202)	phospholipid binding (GO:0005543)			endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|prostate(2)	13						TCACTGGCGCCAGAGGAGACC	0.627																																					p.P12Q		Atlas-SNP	.											.	PACSIN1	42	.	0			c.C35A						.						55	51	53					6																	34494117		2203	4300	6503	SO:0001583	missense	29993	exon2			TGGCGCCAGAGGA	AB037800	CCDS4793.1	6p21.3	2008-02-05			ENSG00000124507	ENSG00000124507			8570	protein-coding gene	gene with protein product	"syndapin I"	606512				11179684	Standard	NM_020804		Approved	SDPI	uc003ojp.4	Q9BY11	OTTHUMG00000014547	ENST00000538621.1:c.35C>A	chr6.hg19:g.34494117C>A	ENSP00000439639:p.Pro12Gln	37.0	0.0		73.0	40.0	NM_020804	Q9P2G8	Missense_Mutation	SNP	ENST00000538621.1	hg19	CCDS4793.1	.	.	.	.	.	.	.	.	.	.	C	11.35	1.612398	0.28712	.	.	ENSG00000124507	ENST00000244458;ENST00000436831;ENST00000538621	T;T	0.48522	0.81;0.81	5.09	4.09	0.47781	.	0.906697	0.09497	N	0.794108	T	0.10723	0.0262	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.17440	-1.0369	10	0.13470	T	0.59	-2.7758	9.8093	0.40812	0.0:0.8616:0.0:0.1384	.	12	Q9BY11	PACN1_HUMAN	Q	12	ENSP00000244458:P12Q;ENSP00000439639:P12Q	ENSP00000244458:P12Q	P	+	2	0	PACSIN1	34602095	0.001000	0.12720	0.996000	0.52242	0.994000	0.84299	1.023000	0.30065	2.372000	0.80975	0.561000	0.74099	CCA	.	.		0.627	PACSIN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040236.1			A	34494117	C	A	34494117	3	1	361	1	0	0	0	0	1	0	0	0	11383	594	21	3	37	3	PACSIN1	6	34494117	Missense_Mutation	SNP	C	TCGA-XR-A8TG-01A-11D-A35Z-10	2447117	34494117	136620950	35	50485										
DNAH8	1769	hgsc.bcm.edu	37	chr6	38743590	38743590	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	tgagtaattctaccatagaaGgaatagatattatggcaata	8	4	1	3			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr6:38743590G>A	ENST00000359357.3	+	11	1428	c.1174G>A	c.(1174-1176)Gga>Aga	p.G392R	DNAH8_ENST00000441566.1_Missense_Mutation_p.G392R|DNAH8_ENST00000449981.2_Missense_Mutation_p.G609R			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	392					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						TACCATAGAAGGAATAGATAT	0.294																																					p.G609R		Atlas-SNP	.											.	DNAH8	1239	.	0			c.G1825A						.						49	56	54					6																	38743590		2196	4285	6481	SO:0001583	missense	1769	exon13			ATAGAAGGAATAG	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.1174G>A	chr6.hg19:g.38743590G>A	ENSP00000352312:p.Gly392Arg	374.0	0.0		493.0	181.0	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	hg19		.	.	.	.	.	.	.	.	.	.	G	24.5	4.536989	0.85812	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.57436	0.4;0.4;0.4	5.8	5.8	0.92144	Dynein heavy chain, domain-1 (1);	0.000000	0.85682	D	0.000000	T	0.70996	0.3288	M	0.80332	2.49	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.74028	-0.3796	10	0.87932	D	0	.	17.8277	0.88671	0.0:0.0:1.0:0.0	.	392	Q96JB1	DYH8_HUMAN	R	597;597;392;392	ENSP00000333363:G597R;ENSP00000352312:G392R;ENSP00000402294:G392R	ENSP00000333363:G597R	G	+	1	0	DNAH8	38851568	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.641000	0.83368	2.758000	0.94735	0.643000	0.83706	GGA	.	.		0.294	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		A	38743590	G	A	38743590	3	1	361	1	0	0	0	0	1	0	0	0	4609	1001	35	3	1208	3	DNAH8	6	38743590	Missense_Mutation	SNP	G	TCGA-XR-A8TG-01A-11D-A35Z-10	4249473	38743590	132371477	36	50486										
FILIP1	27145	hgsc.bcm.edu	37	chr6	76072567	76072567	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	ctctggctccgcagacccgtAatgagcctccagaacctcag	9	16	2	3			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr6:76072567A>G	ENST00000237172.7	-	3	673	c.343T>C	c.(343-345)Tac>Cac	p.Y115H	RP11-415D17.3_ENST00000609544.1_RNA|RP11-415D17.3_ENST00000588761.1_RNA|RP11-415D17.3_ENST00000440220.1_RNA|RP11-415D17.3_ENST00000419709.1_RNA|RP11-415D17.3_ENST00000415457.2_RNA|FILIP1_ENST00000393004.2_Missense_Mutation_p.Y115H|RP11-415D17.3_ENST00000591821.2_RNA|FILIP1_ENST00000370020.1_Missense_Mutation_p.Y16H	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	115										breast(3)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)	80						GCAGACCCGTAATGAGCCTCC	0.507																																					p.Y115H		Atlas-SNP	.											.	FILIP1	173	.	0			c.T343C						.						130	130	130					6																	76072567		2203	4300	6503	SO:0001583	missense	27145	exon3			ACCCGTAATGAGC	AB033101	CCDS4984.1, CCDS75480.1	6q14.1	2008-02-05			ENSG00000118407	ENSG00000118407			21015	protein-coding gene	gene with protein product		607307				10574462	Standard	XM_005248713		Approved	FILIP, KIAA1275	uc003pia.3	Q7Z7B0	OTTHUMG00000015056	ENST00000237172.7:c.343T>C	chr6.hg19:g.76072567A>G	ENSP00000237172:p.Tyr115His	69.0	0.0		63.0	33.0	NM_015687	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Missense_Mutation	SNP	ENST00000237172.7	hg19	CCDS4984.1	.	.	.	.	.	.	.	.	.	.	A	32	5.134986	0.94517	.	.	ENSG00000118407	ENST00000393004;ENST00000237172;ENST00000370020	T;T;T	0.67345	-0.26;-0.26;-0.26	5.99	5.99	0.97316	Cortactin-binding protein-2, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.82171	0.4979	M	0.88570	2.965	0.80722	D	1	D;D;D	0.89917	1.0;0.984;0.981	D;D;P	0.91635	0.999;0.927;0.881	D	0.85222	0.1027	10	0.59425	D	0.04	-14.6073	16.4943	0.84223	1.0:0.0:0.0:0.0	.	115;115;115	A8K2G7;Q7Z7B0;Q7Z7B0-2	.;FLIP1_HUMAN;.	H	115;115;16	ENSP00000376728:Y115H;ENSP00000237172:Y115H;ENSP00000359037:Y16H	ENSP00000237172:Y115H	Y	-	1	0	FILIP1	76129287	1.000000	0.71417	1.000000	0.80357	0.843000	0.47879	9.339000	0.96797	2.291000	0.77112	0.533000	0.62120	TAC	.	.		0.507	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179		G	76072567	A	G	76072567	3	3	361	1	0	0	0	0	1	0	0	0	5902	362	13	2	3314	2	FILIP1	6	76072567	Missense_Mutation	SNP	A	TCGA-XR-A8TG-01A-11D-A35Z-10	37328977	76072567	95042500	37	50487										
BVES	11149	hgsc.bcm.edu	37	chr6	105564646	105564646	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	cttttccaataagatacctaAagatttcatacaagaaaggt	5	7	1	3			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr6:105564646A>C	ENST00000314641.5	-	6	962	c.746T>G	c.(745-747)tTt>tGt	p.F249C	BVES_ENST00000336775.5_Missense_Mutation_p.F249C|BVES_ENST00000446408.2_Missense_Mutation_p.F249C	NM_001199563.1	NP_001186492.1	Q8NE79	POPD1_HUMAN	blood vessel epicardial substance	249					epithelial cell-cell adhesion (GO:0090136)|hematopoietic progenitor cell differentiation (GO:0002244)|muscle organ development (GO:0007517)|positive regulation of locomotion (GO:0040017)|positive regulation of receptor recycling (GO:0001921)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|regulation of Rac GTPase activity (GO:0032314)|sinoatrial node cell development (GO:0060931)|substrate adhesion-dependent cell spreading (GO:0034446)|vesicle-mediated transport (GO:0016192)	integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	cAMP binding (GO:0030552)|structural molecule activity (GO:0005198)			NS(2)|large_intestine(6)|lung(9)|prostate(2)|skin(1)|urinary_tract(1)	21		all_cancers(87;2.83e-05)|Acute lymphoblastic leukemia(125;1.95e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0101)|Colorectal(196;0.204)|Lung NSC(302;0.238)				AAGATACCTAAAGATTTCATA	0.323																																					p.F249C		Atlas-SNP	.											.	BVES	33	.	0			c.T746G						.						74	69	71					6																	105564646		2202	4295	6497	SO:0001583	missense	11149	exon6			TACCTAAAGATTT	AF124512	CCDS5051.1	6q21	2008-11-25			ENSG00000112276	ENSG00000112276			1152	protein-coding gene	gene with protein product	"popeye domain containing 1"	604577				10441744, 10882522	Standard	NM_147147		Approved	HBVES, POP1, POPDC1	uc003pqx.3	Q8NE79	OTTHUMG00000015291	ENST00000314641.5:c.746T>G	chr6.hg19:g.105564646A>C	ENSP00000313172:p.Phe249Cys	97.0	0.0		108.0	40.0	NM_001199563	A8K1R4|E1P5D8|Q5T550|Q5T551|Q8IWC6|Q9HBV0|Q9UNG6	Missense_Mutation	SNP	ENST00000314641.5	hg19	CCDS5051.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.321008	0.81580	.	.	ENSG00000112276	ENST00000314641;ENST00000336775;ENST00000446408	T;T;T	0.52754	0.65;0.65;0.65	5.55	5.55	0.83447	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);	0.000000	0.85682	D	0.000000	T	0.65291	0.2677	M	0.81682	2.555	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.71484	-0.4579	10	0.87932	D	0	-18.5597	15.9824	0.80121	1.0:0.0:0.0:0.0	.	249	Q8NE79	POPD1_HUMAN	C	249	ENSP00000313172:F249C;ENSP00000337259:F249C;ENSP00000397310:F249C	ENSP00000313172:F249C	F	-	2	0	BVES	105671339	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.287000	0.95975	2.234000	0.73211	0.528000	0.53228	TTT	.	.		0.323	BVES-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406075.1	NM_147147		C	105564646	A	C	105564646	3	2	361	1	0	0	0	0	1	0	0	0	1577	14	1	5	348	5	BVES	6	105564646	Missense_Mutation	SNP	A	TCGA-XR-A8TG-01A-11D-A35Z-10	29492079	105564646	65550421	38	50488										
CITED2	10370	hgsc.bcm.edu	37	chr6	139694788	139694788	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	ctggccaccgggggacccatGaactgggagttgttaaacct	13	11	0	1			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr6:139694788G>T	ENST00000367651.2	-	2	509	c.294C>A	c.(292-294)ttC>ttA	p.F98L	CITED2_ENST00000537332.1_Missense_Mutation_p.F98L|CITED2_ENST00000536159.1_Missense_Mutation_p.F98L	NM_006079.4	NP_006070.2	Q99967	CITE2_HUMAN	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	98					adrenal cortex formation (GO:0035802)|bone morphogenesis (GO:0060349)|cardiac neural crest cell development involved in heart development (GO:0061308)|cell aging (GO:0007569)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|cranial nerve morphogenesis (GO:0021602)|decidualization (GO:0046697)|determination of left/right symmetry (GO:0007368)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|endocardial cushion development (GO:0003197)|erythrocyte development (GO:0048821)|granulocyte differentiation (GO:0030851)|heart development (GO:0007507)|heart looping (GO:0001947)|hematopoietic progenitor cell differentiation (GO:0002244)|left/right axis specification (GO:0070986)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell migration (GO:0030336)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900164)|outflow tract morphogenesis (GO:0003151)|peripheral nervous system development (GO:0007422)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of gene expression (GO:0010628)|positive regulation of male gonad development (GO:2000020)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|pulmonary artery morphogenesis (GO:0061156)|regulation of organ formation (GO:0003156)|regulation of RNA biosynthetic process (GO:2001141)|response to estrogen (GO:0043627)|response to fluid shear stress (GO:0034405)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|sex determination (GO:0007530)|skeletal muscle cell differentiation (GO:0035914)|spleen development (GO:0048536)|thymus development (GO:0048538)|transforming growth factor beta receptor signaling pathway (GO:0007179)|trophectodermal cell differentiation (GO:0001829)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|LBD domain binding (GO:0050693)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			large_intestine(1)|lung(4)	5	Breast(32;0.226)			GBM - Glioblastoma multiforme(68;0.000171)|OV - Ovarian serous cystadenocarcinoma(155;0.00134)		GGGGACCCATGAACTGGGAGT	0.667																																					p.F103L	NSCLC(98;1219 1550 33720 43229 49330)	Atlas-SNP	.											.	CITED2	16	.	0			c.C309A						.						41	47	45					6																	139694788		2191	4287	6478	SO:0001583	missense	10370	exon2			ACCCATGAACTGG	U65093	CCDS5195.1, CCDS75530.1	6q23.3	2008-08-29			ENSG00000164442	ENSG00000164442			1987	protein-coding gene	gene with protein product		602937				8901575, 10552932	Standard	NM_006079		Approved	MRG1	uc021zfz.2	Q99967	OTTHUMG00000015691	ENST00000367651.2:c.294C>A	chr6.hg19:g.139694788G>T	ENSP00000356623:p.Phe98Leu	38.0	0.0		57.0	21.0	NM_001168389	O95426|Q5VTF4	Missense_Mutation	SNP	ENST00000367651.2	hg19	CCDS5195.1	.	.	.	.	.	.	.	.	.	.	G	12.93	2.086869	0.36855	.	.	ENSG00000164442	ENST00000367651;ENST00000536159;ENST00000537332;ENST00000392312	T;T;T	0.73681	-0.77;-0.77;-0.77	5.28	5.28	0.74379	.	0.000000	0.64402	D	0.000001	T	0.56016	0.1957	L	0.50333	1.59	0.52099	D	0.99994	B	0.34349	0.45	B	0.34138	0.176	T	0.58679	-0.7594	9	.	.	.	-2.7	12.2935	0.54831	0.0778:0.0:0.9222:0.0	.	98	Q99967	CITE2_HUMAN	L	98	ENSP00000356623:F98L;ENSP00000442831:F98L;ENSP00000444198:F98L	.	F	-	3	2	CITED2	139736481	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	2.724000	0.47285	2.488000	0.83962	0.462000	0.41574	TTC	.	.		0.667	CITED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042463.1			T	139694788	G	T	139694788	3	4	361	1	0	0	0	0	1	0	0	0	3442	1281	45	3	522	3	CITED2	6	139694788	Missense_Mutation	SNP	G	TCGA-XR-A8TG-01A-11D-A35Z-10	34130142	139694788	31420279	39	50489										
GRM1	2911	hgsc.bcm.edu	37	chr6	146755516	146755516	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	cggtgctggcaggccccggtGgtcccgggaacgggctgcgg	20	13	0	0			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr6:146755516G>T	ENST00000282753.1	+	8	3404	c.3169G>T	c.(3169-3171)Ggt>Tgt	p.G1057C	GRM1_ENST00000361719.2_Missense_Mutation_p.G1057C|GRM1_ENST00000355289.4_3'UTR|GRM1_ENST00000492807.2_3'UTR|GRM1_ENST00000507907.1_3'UTR|GRM1_ENST00000392299.2_3'UTR			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	1057					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		AGGCCCCGGTGGTCCCGGGAA	0.667																																					p.G1057C		Atlas-SNP	.											.	GRM1	419	.	0			c.G3169T						.						19	24	22					6																	146755516		2194	4283	6477	SO:0001583	missense	2911	exon9			CCCGGTGGTCCCG	U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4593	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 85"	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	ENST00000282753.1:c.3169G>T	chr6.hg19:g.146755516G>T	ENSP00000282753:p.Gly1057Cys	120.0	0.0		134.0	61.0	NM_000838	B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Missense_Mutation	SNP	ENST00000282753.1	hg19	CCDS5209.1	.	.	.	.	.	.	.	.	.	.	G	15.75	2.924433	0.52653	.	.	ENSG00000152822	ENST00000361719;ENST00000282753	D;D	0.88277	-2.36;-2.36	5.5	4.62	0.57501	.	0.995451	0.08147	N	0.990731	T	0.76371	0.3978	L	0.29908	0.895	0.80722	D	1	P	0.39576	0.679	B	0.38500	0.275	T	0.71517	-0.4569	10	0.54805	T	0.06	.	9.4856	0.38928	0.0994:0.0:0.9005:0.0	.	1057	Q13255	GRM1_HUMAN	C	1057	ENSP00000354896:G1057C;ENSP00000282753:G1057C	ENSP00000282753:G1057C	G	+	1	0	GRM1	146797209	0.944000	0.32072	0.218000	0.23776	0.764000	0.43329	1.439000	0.35013	1.318000	0.45170	0.456000	0.33151	GGT	.	.		0.667	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838		T	146755516	G	T	146755516	3	4	361	1	0	0	0	0	1	0	0	0	6805	1348	47	3	3264	3	GRM1	6	146755516	Missense_Mutation	SNP	G	TCGA-XR-A8TG-01A-11D-A35Z-10	7060728	146755516	24359551	40	50490										
MICALL2	79778	hgsc.bcm.edu	37	chr7	1484708	1484708	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	cacgagggcggactttccccTccgtgggagtgggggccagg	18	12	0	0			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr7:1484708T>A	ENST00000297508.7	-	6	1173	c.998A>T	c.(997-999)gAg>gTg	p.E333V	MICALL2_ENST00000405088.4_Missense_Mutation_p.E121V	NM_182924.3	NP_891554.1	Q8IY33	MILK2_HUMAN	MICAL-like 2	333	Mediates targeting to the cell plasma membrane. {ECO:0000250}.|Necessary and sufficient for interaction with actinins. {ECO:0000250}.				actin cytoskeleton reorganization (GO:0031532)|actin filament polymerization (GO:0030041)|endocytic recycling (GO:0032456)|neuron projection development (GO:0031175)|substrate adhesion-dependent cell spreading (GO:0034446)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|stress fiber (GO:0001725)|tight junction (GO:0005923)	actin filament binding (GO:0051015)|filamin binding (GO:0031005)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(8)|ovary(2)|skin(2)	19		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;6.01e-15)		GACTTTCCCCTCCGTGGGAGT	0.711																																					p.E333V		Atlas-SNP	.											.	MICALL2	63	.	0			c.A998T						.						9	9	9					7																	1484708		2027	4079	6106	SO:0001583	missense	79778	exon6			TTCCCCTCCGTGG	BC037988	CCDS5324.1	7p22.3	2006-11-24			ENSG00000164877	ENSG00000164877			29672	protein-coding gene	gene with protein product	"junctional Rab13-binding protein"					12110185, 16525024	Standard	NM_182924		Approved	MGC46023, FLJ23471, MICAL-L2, JRAB	uc003skj.4	Q8IY33	OTTHUMG00000119021	ENST00000297508.7:c.998A>T	chr7.hg19:g.1484708T>A	ENSP00000297508:p.Glu333Val	44.0	0.0		57.0	23.0	NM_182924	D3YTD2|Q7RTP4|Q7Z655|Q8TEQ4|Q9H5F9	Missense_Mutation	SNP	ENST00000297508.7	hg19	CCDS5324.1	.	.	.	.	.	.	.	.	.	.	T	9.563	1.118944	0.20877	.	.	ENSG00000164877	ENST00000405088;ENST00000297508	T;T	0.69685	2.48;-0.42	3.28	-1.31	0.09230	.	1.676740	0.04204	N	0.330530	T	0.42449	0.1203	N	0.19112	0.55	0.09310	N	1	P	0.38978	0.652	B	0.26693	0.072	T	0.25187	-1.0139	10	0.29301	T	0.29	.	4.5177	0.11943	0.0:0.555:0.2139:0.2311	.	333	Q8IY33	MILK2_HUMAN	V	121;333	ENSP00000385928:E121V;ENSP00000297508:E333V	ENSP00000297508:E333V	E	-	2	0	MICALL2	1451234	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.745000	0.04834	-0.453000	0.07076	-0.451000	0.05528	GAG	.	.		0.711	MICALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239223.2	NM_182924		A	1484708	T	A	1484708	3	1	361	1	0	0	0	0	1	0	0	0	9583	1551	54	4	1764	4	MICALL2	7	1484708	Missense_Mutation	SNP	T	TCGA-XR-A8TG-01A-11D-A35Z-10		1484708	157653955	41	50491										
SDK1	221935	hgsc.bcm.edu	37	chr7	4150329	4150329	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	cgacgaggaggagtgggtcaCcctctatgaagaggagaatg	16	7	2	3			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr7:4150329C>T	ENST00000404826.2	+	23	3498	c.3359C>T	c.(3358-3360)aCc>aTc	p.T1120I	SDK1_ENST00000389531.3_Missense_Mutation_p.T1120I	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	1120	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		GAGTGGGTCACCCTCTATGAA	0.552																																					p.T1120I		Atlas-SNP	.											.	SDK1	361	.	0			c.C3359T						.						172	136	148					7																	4150329		2203	4300	6503	SO:0001583	missense	221935	exon23			GGGTCACCCTCTA	AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19307	protein-coding gene	gene with protein product		607216	"sidekick homolog 1 (chicken)", "sidekick homolog 1, cell adhesion molecule (chicken)"			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.3359C>T	chr7.hg19:g.4150329C>T	ENSP00000385899:p.Thr1120Ile	51.0	0.0		63.0	19.0	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	hg19	CCDS34590.1	.	.	.	.	.	.	.	.	.	.	C	9.811	1.183059	0.21870	.	.	ENSG00000146555	ENST00000404826;ENST00000389531	T;T	0.58652	0.32;0.32	5.51	0.358	0.16084	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.697831	0.14119	N	0.340183	T	0.44829	0.1312	L	0.31752	0.955	0.09310	N	1	B;B	0.14012	0.009;0.008	B;B	0.12156	0.005;0.007	T	0.26815	-1.0092	10	0.35671	T	0.21	.	14.3466	0.66668	0.0:0.5558:0.2759:0.1682	.	1120;1120	F8W6X9;Q7Z5N4	.;SDK1_HUMAN	I	1120	ENSP00000385899:T1120I;ENSP00000374182:T1120I	ENSP00000374182:T1120I	T	+	2	0	SDK1	4116855	0.002000	0.14202	0.270000	0.24601	0.967000	0.64934	0.329000	0.19698	-0.238000	0.09724	-0.176000	0.13171	ACC	.	.		0.552	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744		T	4150329	C	T	4150329	3	4	361	1	0	0	0	0	1	0	0	0	13983	507	18	3	3449	3	SDK1	7	4150329	Missense_Mutation	SNP	C	TCGA-XR-A8TG-01A-11D-A35Z-10	2665621	4150329	154988334	42	50492										
IGFBP3	3486	hgsc.bcm.edu	37	chr7	45954471	45954471	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	cctccttccccttggtggtgTagcctgggagaggctgccca	13	14	0	1	rs45490491		TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr7:45954471T>C	ENST00000275521.6	-	4	957	c.824A>G	c.(823-825)tAc>tGc	p.Y275C	IGFBP3_ENST00000465642.1_5'Flank|IGFBP3_ENST00000381083.4_Missense_Mutation_p.Y281C|IGFBP3_ENST00000381086.5_Missense_Mutation_p.Y178C	NM_000598.4|NM_001013398.1	NP_000589.2|NP_001013416.1	P17936	IBP3_HUMAN	insulin-like growth factor binding protein 3	275	Thyroglobulin type-1. {ECO:0000255|PROSITE-ProRule:PRU00500}.				apoptotic process (GO:0006915)|cellular protein metabolic process (GO:0044267)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of signal transduction (GO:0009968)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell proliferation (GO:0048662)|osteoblast differentiation (GO:0001649)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of myoblast differentiation (GO:0045663)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of glucose metabolic process (GO:0010906)|type B pancreatic cell proliferation (GO:0044342)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|insulin-like growth factor binding protein complex (GO:0016942)|nucleus (GO:0005634)	insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|metal ion binding (GO:0046872)|protein tyrosine phosphatase activator activity (GO:0008160)			large_intestine(6)|lung(7)|pancreas(1)|prostate(3)	17					Mecasermin(DB01277)	CTTGGTGGTGTAGCCTGGGAG	0.597																																					p.Y281C		Atlas-SNP	.											.	IGFBP3	40	.	0			c.A842G						.						77	63	68					7																	45954471		2203	4300	6503	SO:0001583	missense	3486	exon4			GTGGTGTAGCCTG		CCDS5505.1, CCDS34632.1	7p12.3	2014-09-17			ENSG00000146674	ENSG00000146674			5472	protein-coding gene	gene with protein product	"growth hormone-dependent binding protein", "acid stable subunit of the 140 K IGF complex", "binding protein 53", "binding protein 29", "IGF-binding protein 3"	146732				1695633	Standard	NM_000598		Approved	IBP3, BP-53	uc003tnr.3	P17936	OTTHUMG00000023769	ENST00000275521.6:c.824A>G	chr7.hg19:g.45954471T>C	ENSP00000275521:p.Tyr275Cys	62.0	0.0		83.0	30.0	NM_001013398	A4D2F5|D3DVM0|Q2V509|Q6P1M6|Q9UCL4	Missense_Mutation	SNP	ENST00000275521.6	hg19	CCDS5505.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.00|14.00	2.403640|2.403640	0.42613|0.42613	.|.	.|.	ENSG00000146674|ENSG00000146674	ENST00000428530|ENST00000545032;ENST00000275521;ENST00000381086;ENST00000438491;ENST00000442142;ENST00000381083;ENST00000433047	.|T;T;T	.|0.63255	.|-0.03;-0.03;-0.03	5.29|5.29	-0.433|-0.433	0.12287|0.12287	.|Thyroglobulin type-1 (5);	.|0.343146	.|0.31660	.|N	.|0.007273	T|T	0.66577|0.66577	0.2803|0.2803	L|L	0.54323|0.54323	1.7|1.7	0.24740|0.24740	N|N	0.993049|0.993049	.|D;D;D	.|0.71674	.|0.998;0.998;0.996	.|D;D;D	.|0.70227	.|0.954;0.968;0.956	T|T	0.57423|0.57423	-0.7814|-0.7814	5|10	.|0.45353	.|T	.|0.12	-15.1114|-15.1114	5.7833|5.7833	0.18318|0.18318	0.4564:0.0:0.1376:0.406|0.4564:0.0:0.1376:0.406	.|.	.|178;275;260	.|B3KWK7;P17936;B4DN53	.|.;IBP3_HUMAN;.	A|C	127|252;275;178;261;173;281;247	.|ENSP00000275521:Y275C;ENSP00000370476:Y178C;ENSP00000370473:Y281C	.|ENSP00000275521:Y275C	T|Y	-|-	1|2	0|0	IGFBP3|IGFBP3	45920996|45920996	0.945000|0.945000	0.32115|0.32115	0.044000|0.044000	0.18714|0.18714	0.631000|0.631000	0.37964|0.37964	1.263000|1.263000	0.33004|0.33004	-0.330000|-0.330000	0.08514|0.08514	0.533000|0.533000	0.62120|0.62120	ACA|TAC	.	.		0.597	IGFBP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251356.3	NM_001013398		C	45954471	T	C	45954471	3	2	361	1	0	0	0	0	1	0	0	0	7589	1638	57	2	55	2	IGFBP3	7	45954471	Missense_Mutation	SNP	T	TCGA-XR-A8TG-01A-11D-A35Z-10	41804142	45954471	113184192	43	50493										
PCMTD1	115294	hgsc.bcm.edu	37	chr8	52733033	52733033	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	cattgcttcattgtgatcttTttcctcctcttctttgttat	4	10	4	1			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr8:52733033T>G	ENST00000360540.5	-	7	1358	c.952A>C	c.(952-954)Aaa>Caa	p.K318Q	PCMTD1_ENST00000522514.1_Missense_Mutation_p.K318Q|PCMTD1_ENST00000519559.1_5'UTR|PCMTD1_ENST00000544451.1_Missense_Mutation_p.K242Q	NM_052937.2	NP_443169.2	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	318						cytoplasm (GO:0005737)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)			NS(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(17)|prostate(2)|skin(8)|soft_tissue(1)	37		Lung NSC(129;0.0795)|all_lung(136;0.144)				TTGTGAtctttttcctcctct	0.388																																					p.K318Q		Atlas-SNP	.											.	PCMTD1	73	.	0			c.A952C						.						108	89	95					8																	52733033		2203	4300	6503	SO:0001583	missense	115294	exon6			GATCTTTTTCCTC		CCDS6148.1, CCDS69480.1	8q11.23	2010-08-05			ENSG00000168300	ENSG00000168300			30483	protein-coding gene	gene with protein product							Standard	XM_005251146		Approved	FLJ10883	uc003xqx.4	Q96MG8	OTTHUMG00000164246	ENST00000360540.5:c.952A>C	chr8.hg19:g.52733033T>G	ENSP00000353739:p.Lys318Gln	64.0	0.0		107.0	9.0	NM_052937	Q96FK9	Missense_Mutation	SNP	ENST00000360540.5	hg19	CCDS6148.1	.	.	.	.	.	.	.	.	.	.	T	12.81	2.050034	0.36181	.	.	ENSG00000168300	ENST00000360540;ENST00000544451;ENST00000522514	T;T;T	0.47528	1.47;0.84;1.47	5.97	4.79	0.61399	.	0.648513	0.16477	N	0.212690	T	0.32315	0.0825	N	0.14661	0.345	0.43512	D	0.99577	P;P;B	0.39282	0.666;0.493;0.048	B;B;B	0.37508	0.252;0.116;0.012	T	0.05683	-1.0870	10	0.34782	T	0.22	-20.6325	13.5036	0.61471	0.0:0.0:0.1301:0.8699	.	188;242;318	B4E2B4;F5H1M8;Q96MG8	.;.;PCMD1_HUMAN	Q	318;242;318	ENSP00000353739:K318Q;ENSP00000444026:K242Q;ENSP00000428099:K318Q	ENSP00000353739:K318Q	K	-	1	0	PCMTD1	52895586	1.000000	0.71417	0.719000	0.30619	0.281000	0.26958	4.310000	0.59141	1.041000	0.40125	0.533000	0.62120	AAA	.	.		0.388	PCMTD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377909.2	NM_052937		G	52733033	T	G	52733033	3	3	361	1	0	0	0	0	1	0	0	0	11595	1850	64	5	125	5	PCMTD1	8	52733033	Missense_Mutation	SNP	T	TCGA-XR-A8TG-01A-11D-A35Z-10		52733033	93630989	44	50494										
CRH	1392	hgsc.bcm.edu	37	chr8	67089349	67089363	+	In_Frame_Del	DEL	GCAGCAGCAGCTGCT	GCAGCAGCAGCTGCT	-													0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	gctgtcgagcgagcgccgagGcagcagcagctgctgcagca							TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	GCAGCAGCAGCTGCT	GCAGCAGCAGCTGCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr8:67089349_67089363delGCAGCAGCAGCTGCT	ENST00000276571.3	-	2	796_810	c.350_364delAGCAGCTGCTGCTGC	c.(349-366)cagcagctgctgctgcct>cct	p.QQLLL117del		NM_000756.2	NP_000747.1	P06850	CRF_HUMAN	corticotropin releasing hormone	117					adrenal gland development (GO:0030325)|associative learning (GO:0008306)|cellular response to cocaine (GO:0071314)|cellular response to dexamethasone stimulus (GO:0071549)|diterpenoid metabolic process (GO:0016101)|feeding behavior (GO:0007631)|female pregnancy (GO:0007565)|ferulate metabolic process (GO:0033494)|glucocorticoid biosynthetic process (GO:0006704)|hormone-mediated apoptotic signaling pathway (GO:0008628)|hypothalamus development (GO:0021854)|inflammatory response (GO:0006954)|ion homeostasis (GO:0050801)|learning or memory (GO:0007611)|locomotory exploration behavior (GO:0035641)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|lung development (GO:0030324)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell death (GO:0060548)|negative regulation of circadian sleep/wake cycle, REM sleep (GO:0042322)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of gene expression (GO:0010629)|negative regulation of glucagon secretion (GO:0070093)|negative regulation of luteinizing hormone secretion (GO:0033685)|negative regulation of norepinephrine secretion (GO:0010700)|parturition (GO:0007567)|positive regulation of behavioral fear response (GO:2000987)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|positive regulation of circadian sleep/wake cycle, wakefulness (GO:0010841)|positive regulation of corticosterone secretion (GO:2000854)|positive regulation of corticotropin secretion (GO:0051461)|positive regulation of cortisol secretion (GO:0051464)|positive regulation of digestive system process (GO:0060456)|positive regulation of gene expression (GO:0010628)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of protein phosphorylation (GO:0001934)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of serotonin secretion (GO:0014062)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to ether (GO:0045472)|response to immobilization stress (GO:0035902)|response to pain (GO:0048265)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, dopaminergic (GO:0001963)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|perikaryon (GO:0043204)|varicosity (GO:0043196)	hormone activity (GO:0005179)|neuropeptide hormone activity (GO:0005184)|receptor binding (GO:0005102)			breast(1)|endometrium(1)|lung(2)|urinary_tract(1)	5		all_cancers(86;2.58e-06)|all_epithelial(80;6.27e-09)|all_lung(136;0.000414)|Lung NSC(129;0.0011)	Epithelial(68;0.0136)|all cancers(69;0.0507)|BRCA - Breast invasive adenocarcinoma(89;0.0628)|OV - Ovarian serous cystadenocarcinoma(28;0.0904)		Corticotropin(DB01285)	GAGCGCCGAGGCAGCAGCAGCTGCTGCAGCAACAC	0.726											OREG0018805	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.117_122del		Atlas-INDEL	.											.	CRH	8	.	0			c.351_365del						.																																			SO:0001651	inframe_deletion	1392	exon2			.		CCDS6188.1	8q13	2013-02-25				ENSG00000147571		"Endogenous ligands"	2355	protein-coding gene	gene with protein product	"corticotropin-releasing factor", "corticoliberin"	122560					Standard	NM_000756		Approved	CRF	uc003xvy.2	P06850		ENST00000276571.3:c.350_364delAGCAGCTGCTGCTGC	chr8.hg19:g.67089349_67089363delGCAGCAGCAGCTGCT	ENSP00000276571:p.Gln117_Leu121del	51.0	0.0	1096	54.0	20.0	NM_000756	B3KQS4	In_Frame_Del	DEL	ENST00000276571.3	hg19	CCDS6188.1																																																																																			.	.		0.726	CRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378926.1	NM_000756		-	67089363	GCAGCAGCAGCTGCT	-	67089349	7	5	361	1	0	1	0	1	0	0	0	0	3871	1203	42	0	230	0	CRH	8	67089349	In_Frame_Del	DEL	GCAGCAGCAGCTGCT	TCGA-XR-A8TG-01A-11D-A35Z-10	14356316	67089349	79274673	45	50495										
PREX2	80243	hgsc.bcm.edu	37	chr8	69104690	69104690	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	cttctggggttggactgctgTcagtttcctcggagctgtgc	14	10	2	0			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr8:69104690T>C	ENST00000288368.4	+	37	4811	c.4534T>C	c.(4534-4536)Tca>Cca	p.S1512P		NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	1512					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						TGGACTGCTGTCAGTTTCCTC	0.562																																					p.S1512P		Atlas-SNP	.											.	PREX2	614	.	0			c.T4534C						.						69	56	61					8																	69104690		2203	4300	6503	SO:0001583	missense	80243	exon37			CTGCTGTCAGTTT	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.4534T>C	chr8.hg19:g.69104690T>C	ENSP00000288368:p.Ser1512Pro	38.0	0.0		65.0	11.0	NM_024870	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	hg19	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	T	5.499	0.277037	0.10403	.	.	ENSG00000046889	ENST00000288368	T	0.59083	0.29	4.89	4.89	0.63831	.	0.080287	0.52532	D	0.000069	T	0.42810	0.1219	N	0.17082	0.46	0.52501	D	0.999954	B	0.02656	0.0	B	0.06405	0.002	T	0.30707	-0.9969	10	0.44086	T	0.13	.	14.8053	0.69948	0.0:0.0:0.0:1.0	.	1512	Q70Z35	PREX2_HUMAN	P	1512	ENSP00000288368:S1512P	ENSP00000288368:S1512P	S	+	1	0	PREX2	69267244	1.000000	0.71417	0.993000	0.49108	0.918000	0.54935	3.477000	0.53151	1.965000	0.57142	0.383000	0.25322	TCA	.	.		0.562	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		C	69104690	T	C	69104690	3	2	361	1	0	0	0	0	1	0	0	0	12489	1667	58	2	4909	2	PREX2	8	69104690	Missense_Mutation	SNP	T	TCGA-XR-A8TG-01A-11D-A35Z-10	2015341	69104690	77259332	46	50496										
JPH1	56704	hgsc.bcm.edu	37	chr8	75227529	75227529	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	gtcgctgcggacagagctgcGcttgctcgagatggaagact	15	10	0	3			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr8:75227529G>A	ENST00000342232.4	-	2	746	c.706C>T	c.(706-708)Cgc>Tgc	p.R236C		NM_020647.2	NP_065698.1	Q9HDC5	JPH1_HUMAN	junctophilin 1	236	Ser-rich.				calcium ion transport into cytosol (GO:0060402)|muscle organ development (GO:0007517)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	24	Breast(64;0.00576)		BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.0728)|all cancers(69;0.176)			ACAGAGCTGCGCTTGCTCGAG	0.562																																					p.R236C		Atlas-SNP	.											.	JPH1	77	.	0			c.C706T						.						72	76	74					8																	75227529		2203	4300	6503	SO:0001583	missense	56704	exon2			AGCTGCGCTTGCT	AB042634	CCDS6217.1	8q21	2008-07-03			ENSG00000104369	ENSG00000104369			14201	protein-coding gene	gene with protein product		605266				10891348, 10949023	Standard	XM_005251273		Approved	JP-1	uc003yae.3	Q9HDC5	OTTHUMG00000164524	ENST00000342232.4:c.706C>T	chr8.hg19:g.75227529G>A	ENSP00000344488:p.Arg236Cys	107.0	0.0		147.0	17.0	NM_020647	B2RTZ0	Missense_Mutation	SNP	ENST00000342232.4	hg19	CCDS6217.1	.	.	.	.	.	.	.	.	.	.	G	17.56	3.421215	0.62622	.	.	ENSG00000104369	ENST00000342232	T	0.61392	0.11	4.89	4.01	0.46588	.	0.051769	0.85682	D	0.000000	T	0.68979	0.3060	M	0.72118	2.19	0.80722	D	1	D	0.76494	0.999	P	0.56088	0.791	T	0.73341	-0.4013	10	0.56958	D	0.05	.	14.6516	0.68800	0.0:0.0:0.8535:0.1465	.	236	Q9HDC5	JPH1_HUMAN	C	236	ENSP00000344488:R236C	ENSP00000344488:R236C	R	-	1	0	JPH1	75390084	1.000000	0.71417	1.000000	0.80357	0.787000	0.44495	3.462000	0.53042	1.247000	0.43917	-0.182000	0.12963	CGC	.	.		0.562	JPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379102.1			A	75227529	G	A	75227529	3	1	361	1	0	0	0	0	1	0	0	0	7969	1087	38	1	1295	1	JPH1	8	75227529	Missense_Mutation	SNP	G	TCGA-XR-A8TG-01A-11D-A35Z-10	6122839	75227529	71136493	47	50497										
CDKN2A	1029	hgsc.bcm.edu	37	chr9	21971209	21971209	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	cgctgcccatcatcatgaccTgccagagagaacagaatggt	10	12	2	4			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr9:21971209T>A	ENST00000304494.5	-	2	421		c.e2-2		CDKN2A_ENST00000479692.2_Splice_Site|CDKN2A_ENST00000361570.3_Splice_Site|CDKN2A_ENST00000497750.1_Splice_Site|CDKN2A_ENST00000494262.1_Splice_Site|CDKN2A_ENST00000578845.2_5'UTR|CDKN2A_ENST00000446177.1_Splice_Site|CDKN2A_ENST00000498124.1_Splice_Site|CDKN2A_ENST00000579755.1_Splice_Site|CDKN2A_ENST00000579122.1_Splice_Site|CDKN2A_ENST00000530628.2_Splice_Site|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000498628.2_Splice_Site	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A						cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular senescence (GO:2000774)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|Ras protein signal transduction (GO:0007265)|replicative senescence (GO:0090399)|senescence-associated heterochromatin focus assembly (GO:0035986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|senescence-associated heterochromatin focus (GO:0035985)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.0?(1315)|p.?(23)|p.0(1)|p.V28_V51del(1)		NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		CATCATGACCTGCCAGAGAGA	0.667		17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)																											.		Atlas-SNP	.											CDKN2A_ENST00000498124,bladder,carcinoma,0,17	CDKN2A	4810	.	1340	Whole gene deletion(1316)|Unknown(23)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(277)|skin(168)|central_nervous_system(163)|lung(146)|urinary_tract(91)|bone(74)|soft_tissue(57)|upper_aerodigestive_tract(52)|pleura(51)|oesophagus(49)|ovary(34)|kidney(30)|breast(30)|pancreas(29)|thyroid(13)|NS(12)|biliary_tract(12)|stomach(12)|autonomic_ganglia(7)|meninges(7)|large_intestine(6)|liver(6)|salivary_gland(4)|thymus(4)|vulva(2)|endometrium(2)|prostate(2)	c.151-2A>T	GRCh37	CS014762	CDKN2A	S		.						8	9	8					9																	21971209		2066	4135	6201	SO:0001630	splice_region_variant	1029	exon3			ATGACCTGCCAGA	L27211	CCDS6510.1, CCDS6511.1, CCDS6511.2, CCDS56565.1	9p21	2014-09-17	2012-03-08		ENSG00000147889	ENSG00000147889			1787	protein-coding gene	gene with protein product		600160	"cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)"	CDKN2, MLM		8152487, 7606716	Standard	NM_058195		Approved	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf	uc003zpk.3	P42771	OTTHUMG00000019686	ENST00000304494.5:c.151-2A>T	chr9.hg19:g.21971209T>A		37.0	0.0		43.0	16.0	NM_001195132	A5X2G7|D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	Splice_Site	SNP	ENST00000304494.5	hg19	CCDS6510.1	.	.	.	.	.	.	.	.	.	.	T	15.20	2.762210	0.49468	.	.	ENSG00000147889	ENST00000361570;ENST00000304494;ENST00000530628;ENST00000446177	.	.	.	5.74	5.74	0.90152	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.022	0.71637	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	CDKN2A	21961209	1.000000	0.71417	0.993000	0.49108	0.550000	0.35303	7.014000	0.76380	2.181000	0.69327	0.454000	0.30748	.	.	.		0.667	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	NM_000077	Intron	A	21971209	T	A	21971209	5	1	361	1	0	0	0	0	0	0	1	0	3163	1594	55	4	329	4	CDKN2A	9	21971209	Splice_Site	SNP	T	TCGA-XR-A8TG-01A-11D-A35Z-10		21971209	119242222	48	50498										
AGTPBP1	23287	hgsc.bcm.edu	37	chr9	88162138	88162138	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	tctaactcatcattactttcTgcactgtaatcaacttcttc	2	12	6	0			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr9:88162138T>C	ENST00000357081.3	-	26	3711	c.3567A>G	c.(3565-3567)gcA>gcG	p.A1189A	AGTPBP1_ENST00000376109.3_Silent_p.A1201A|AGTPBP1_ENST00000337006.4_3'UTR|AGTPBP1_ENST00000376083.3_Silent_p.A1149A|AGTPBP1_ENST00000432218.1_Missense_Mutation_p.Q638R			Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	1189					adult walking behavior (GO:0007628)|C-terminal protein deglutamylation (GO:0035609)|cerebellar Purkinje cell differentiation (GO:0021702)|eye photoreceptor cell differentiation (GO:0001754)|mitochondrion organization (GO:0007005)|neuromuscular process (GO:0050905)|neurotransmitter metabolic process (GO:0042133)|olfactory bulb development (GO:0021772)|protein side chain deglutamylation (GO:0035610)|retina development in camera-type eye (GO:0060041)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(12)|ovary(5)|skin(2)|urinary_tract(3)	44						CATTACTTTCTGCACTGTAAT	0.383																																					p.A1149A		Atlas-SNP	.											.	AGTPBP1	128	.	0			c.A3447G						.						157	142	147					9																	88162138		2203	4300	6503	SO:0001819	synonymous_variant	23287	exon26			ACTTTCTGCACTG	AB028958	CCDS6672.1, CCDS75854.1	9q21.33	2014-06-23			ENSG00000135049	ENSG00000135049			17258	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 1", "tubulinyl-Tyr carboxypeptidase", "carboxypeptidase-tubulin", "tyrosine carboxypeptidase", "soluble carboxypeptidase"	606830				11083920	Standard	NM_015239		Approved	KIAA1035, Nna1, CCP1	uc010mqc.3	Q9UPW5	OTTHUMG00000020124	ENST00000357081.3:c.3567A>G	chr9.hg19:g.88162138T>C		86.0	0.0		98.0	42.0	NM_015239	B4DIT6|B4DRZ8|Q5VV80|Q63HM7|Q658P5|Q6P9D6|Q9H8U6|Q9H9W8|Q9NVK1	Silent	SNP	ENST00000357081.3	hg19		.	.	.	.	.	.	.	.	.	.	T	14.72	2.619031	0.46736	.	.	ENSG00000135049	ENST00000432218	T	0.42900	0.96	5.89	4.74	0.60224	.	.	.	.	.	T	0.58538	0.2129	.	.	.	0.80722	D	1	D	0.63046	0.992	P	0.57009	0.811	T	0.63484	-0.6627	8	0.87932	D	0	-24.3728	13.251	0.60052	0.0:0.0:0.1326:0.8674	.	638	B4DHX2	.	R	638	ENSP00000402804:Q638R	ENSP00000402804:Q638R	Q	-	2	0	AGTPBP1	87351958	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.705000	0.47127	1.027000	0.39758	0.459000	0.35465	CAG	.	.		0.383	AGTPBP1-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052893.1	NM_015239		C	88162138	T	C	88162138	2	2	361	1	0	0	0	0	0	0	0	1	400	1567	55	2		2	AGTPBP1	9	88162138	Silent	SNP	T	TCGA-XR-A8TG-01A-11D-A35Z-10	66190929	88162138	53051293	49	50499										
ABCA2	20	hgsc.bcm.edu	37	chr9	139910208	139910208	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	cgtgggctcgtccaggatgaTggcgcgagagccgcccacga	16	13	0	2			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr9:139910208T>C	ENST00000371605.3	-	22	3577	c.3430A>G	c.(3430-3432)Atc>Gtc	p.I1144V	ABCA2_ENST00000492260.1_5'Flank|ABCA2_ENST00000341511.6_Missense_Mutation_p.I1145V|ABCA2_ENST00000265662.5_Missense_Mutation_p.I1145V			Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 2	1144	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				ATP catabolic process (GO:0006200)|cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|regulation of intracellular cholesterol transport (GO:0032383)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|nucleotide binding (GO:0000166)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|liver(1)|lung(25)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	41	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		TCCAGGATGATGGCGCGAGAG	0.657																																					p.I1175V		Atlas-SNP	.											.	ABCA2	113	.	0			c.A3523G						.						28	34	32					9																	139910208		2169	4266	6435	SO:0001583	missense	20	exon23			GGATGATGGCGCG	U18235	CCDS43909.1	9q34	2012-03-14			ENSG00000107331	ENSG00000107331		"ATP binding cassette transporters / subfamily A"	32	protein-coding gene	gene with protein product		600047		ABC2		8088782	Standard	NM_212533		Approved		uc022bpy.1	Q9BZC7	OTTHUMG00000020958	ENST00000371605.3:c.3430A>G	chr9.hg19:g.139910208T>C	ENSP00000360666:p.Ile1144Val	61.0	0.0		95.0	38.0	NM_212533	A6NED5|Q5SPY5|Q5W9G5|Q76MW7|Q9HC28	Missense_Mutation	SNP	ENST00000371605.3	hg19		.	.	.	.	.	.	.	.	.	.	T	0.050	-1.252815	0.01469	.	.	ENSG00000107331	ENST00000265662;ENST00000371605;ENST00000355090;ENST00000341511	D;D;D	0.93712	-3.27;-3.27;-3.27	4.2	3.05	0.35203	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.139902	0.46442	N	0.000285	T	0.81574	0.4851	N	0.13272	0.32	0.29949	N	0.820374	B;B	0.10296	0.003;0.003	B;B	0.14023	0.01;0.007	T	0.67632	-0.5621	10	0.02654	T	1	.	5.5655	0.17168	0.0:0.3972:0.0:0.6028	.	1144;1175	Q9BZC7;E7ETC3	ABCA2_HUMAN;.	V	1145;1144;1175;1145	ENSP00000265662:I1145V;ENSP00000360666:I1144V;ENSP00000344155:I1145V	ENSP00000265662:I1145V	I	-	1	0	ABCA2	139030029	1.000000	0.71417	0.996000	0.52242	0.247000	0.25773	3.841000	0.55850	0.499000	0.27970	0.260000	0.18958	ATC	.	.		0.657	ABCA2-202	KNOWN	basic	protein_coding	protein_coding		NM_001606		C	139910208	T	C	139910208	3	2	361	1	0	0	0	0	1	0	0	0	32	1464	51	2	3985	2	ABCA2	9	139910208	Missense_Mutation	SNP	T	TCGA-XR-A8TG-01A-11D-A35Z-10	51748070	139910208	1303223	50	50500										
ASCC1	51008	hgsc.bcm.edu	37	chr10	73857193	73857193	+	3'UTR	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	cagctttagggagccaaagtAgaagttctcaaacaactgaa	9	8	1	2			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr10:73857193A>T	ENST00000342444.4	-	0	1355				ASCC1_ENST00000317126.4_Missense_Mutation_p.Y325N|ASCC1_ENST00000394919.1_Missense_Mutation_p.Y325N|ASCC1_ENST00000317168.6_Missense_Mutation_p.Y325N|ASCC1_ENST00000545550.1_Missense_Mutation_p.Y347N	NM_001198799.2	NP_001185728.1	Q8N9N2	ASCC1_HUMAN	activating signal cointegrator 1 complex subunit 1						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|transcription factor complex (GO:0005667)	catalytic activity (GO:0003824)|RNA binding (GO:0003723)			endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|lung(2)|skin(1)	7						GAGCCAAAGTAGAAGTTCTCA	0.353																																					p.Y325N		Atlas-SNP	.											.	ASCC1	18	.	0			c.T973A						.						67	66	67					10																	73857193		2203	4300	6503	SO:0001624	3_prime_UTR_variant	51008	exon10			CAAAGTAGAAGTT	AY013290	CCDS31219.1, CCDS55713.1	10q22.1	2012-09-20			ENSG00000138303	ENSG00000138303			24268	protein-coding gene	gene with protein product		614215				10810093, 12077347	Standard	NM_001198799		Approved	CGI-18, ASC1p50, Em:AC022392.3	uc001jst.2	Q8N9N2	OTTHUMG00000018434	ENST00000342444.4:c.*51T>A	chr10.hg19:g.73857193A>T		107.0	0.0		171.0	14.0	NM_001198798	Q5SW06|Q5SW07|Q96EI8|Q9Y307	Missense_Mutation	SNP	ENST00000342444.4	hg19	CCDS55713.1	.	.	.	.	.	.	.	.	.	.	A	10.54	1.378864	0.24944	.	.	ENSG00000138303	ENST00000394919;ENST00000317168;ENST00000373101;ENST00000317126;ENST00000545550	T;T;T;T	0.61980	0.06;0.06;0.06;0.06	5.47	2.99	0.34606	.	.	.	.	.	T	0.42381	0.1200	L	0.31926	0.97	0.80722	D	1	B	0.15141	0.012	B	0.10450	0.005	T	0.25882	-1.0119	9	0.13470	T	0.59	.	4.2651	0.10759	0.6767:0.0:0.1477:0.1756	.	347	F5H874	.	N	325;325;325;325;347	ENSP00000378377:Y325N;ENSP00000320810:Y325N;ENSP00000320461:Y325N;ENSP00000442121:Y347N	ENSP00000320461:Y325N	Y	-	1	0	ASCC1	73527199	0.969000	0.33509	1.000000	0.80357	0.882000	0.50991	0.699000	0.25586	2.074000	0.62210	0.402000	0.26972	TAC	.	.		0.353	ASCC1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048573.2	NM_015947		T	73857193	A	T	73857193	1	4	361	0	1	0	0	0	0	0	0	0	1031	420	15	4		4	ASCC1	10	73857193	3'UTR	SNP	A	TCGA-XR-A8TG-01A-11D-A35Z-10		73857193	61677554	51	50501										
ATRNL1	26033	hgsc.bcm.edu	37	chr10	117154258	117154258	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	gaataaaaggtgaccaatgcCaattgtaagtaagaatgact	9	5	0	3			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr10:117154258C>T	ENST00000355044.3	+	20	3391	c.3265C>T	c.(3265-3267)Caa>Taa	p.Q1089*	ATRNL1_ENST00000303745.7_5'UTR|ATRNL1_ENST00000423111.2_Nonsense_Mutation_p.Q140*	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	1089	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.				G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(11)|liver(2)|lung(44)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		TGACCAATGCCAATTGTAAGT	0.333																																					p.Q1089X		Atlas-SNP	.											ATRNL1,NS,lymphoid_neoplasm,0,1	ATRNL1	219	.	0			c.C3265T						.						110	103	105					10																	117154258		2203	4299	6502	SO:0001587	stop_gained	26033	exon20			CAATGCCAATTGT	AB011106	CCDS7592.1, CCDS73204.1	10q26	2004-03-04			ENSG00000107518	ENSG00000107518			29063	protein-coding gene	gene with protein product		612869				9628581	Standard	NM_001276282		Approved	KIAA0534, FLJ45344, ALP	uc001lcg.3	Q5VV63	OTTHUMG00000019096	ENST00000355044.3:c.3265C>T	chr10.hg19:g.117154258C>T	ENSP00000347152:p.Gln1089*	93.0	0.0		87.0	31.0	NM_207303	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Nonsense_Mutation	SNP	ENST00000355044.3	hg19	CCDS7592.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.3|25.3	4.627380|4.627380	0.87560|0.87560	.|.	.|.	ENSG00000107518|ENSG00000107518	ENST00000526373|ENST00000355044;ENST00000423111	.|.	.|.	.|.	5.61|5.61	5.61|5.61	0.85477|0.85477	.|.	.|0.110458	.|0.64402	.|D	.|0.000004	T|.	0.74772|.	0.3760|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.76759|.	-0.2841|.	4|.	.|0.66056	.|D	.|0.02	-14.7681|-14.7681	15.1377|15.1377	0.72583|0.72583	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	L|X	172|1089;140	.|.	.|ENSP00000347152:Q1089X	P|Q	+|+	2|1	0|0	ATRNL1|ATRNL1	117144248|117144248	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.790000|0.790000	0.44656|0.44656	6.050000|6.050000	0.71063|0.71063	2.640000|2.640000	0.89533|0.89533	0.655000|0.655000	0.94253|0.94253	CCA|CAA	.	.		0.333	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349		T	117154258	C	T	117154258	4	4	361	1	0	0	0	0	0	1	0	0	1207	595	21	3	3343	3	ATRNL1	10	117154258	Nonsense_Mutation	SNP	C	TCGA-XR-A8TG-01A-11D-A35Z-10	43297065	117154258	18380489	52	50502										
USH1C	10083	hgsc.bcm.edu	37	chr11	17542918	17542918	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	catctccttccggtatctctCattttcctctgctgccttct	4	16	5	0			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr11:17542918C>T	ENST00000318024.4	-	13	1168	c.1060G>A	c.(1060-1062)Gag>Aag	p.E354K	USH1C_ENST00000527020.1_Missense_Mutation_p.E335K|USH1C_ENST00000005226.7_Missense_Mutation_p.E354K|USH1C_ENST00000527720.1_Missense_Mutation_p.E323K	NM_005709.3	NP_005700.2	Q9Y6N9	USH1C_HUMAN	Usher syndrome 1C (autosomal recessive, severe)	354					auditory receptor cell differentiation (GO:0042491)|equilibrioception (GO:0050957)|G2/M transition of mitotic cell cycle (GO:0000086)|inner ear morphogenesis (GO:0042472)|parallel actin filament bundle assembly (GO:0030046)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	spectrin binding (GO:0030507)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	48						CGGTATCTCTCATTTTCCTCT	0.498																																					p.E354K		Atlas-SNP	.											USH1C_ENST00000318024,colon,carcinoma,0,2	USH1C	157	.	0			c.G1060A						.						315	256	276					11																	17542918		2200	4293	6493	SO:0001583	missense	10083	exon13			ATCTCTCATTTTC	AB006955	CCDS7825.1, CCDS31438.1, CCDS73265.1	11p14.3	2013-06-19	2004-05-19		ENSG00000006611	ENSG00000006611			12597	protein-coding gene	gene with protein product	"harmonin"	605242	"deafness, autosomal recessive 18"	DFNB18		10973247, 12107438	Standard	NM_005709		Approved	PDZ73, harmonin, NY-CO-37, NY-CO-38, PDZ-73, AIE-75, PDZD7C	uc001mne.3	Q9Y6N9	OTTHUMG00000166323	ENST00000318024.4:c.1060G>A	chr11.hg19:g.17542918C>T	ENSP00000317018:p.Glu354Lys	85.0	0.0		99.0	23.0	NM_005709	A8K423|Q7RTU8|Q96B29|Q9UM04|Q9UM17|Q9UPC3	Missense_Mutation	SNP	ENST00000318024.4	hg19	CCDS31438.1	.	.	.	.	.	.	.	.	.	.	C	32	5.117405	0.94385	.	.	ENSG00000006611	ENST00000318024;ENST00000527720;ENST00000527020;ENST00000005226	T;T;T;T	0.65178	1.71;1.7;1.8;-0.14	5.72	5.72	0.89469	.	0.048412	0.85682	D	0.000000	T	0.64148	0.2572	L	0.34521	1.04	0.58432	D	0.999997	D;P;D	0.62365	0.971;0.952;0.991	P;P;P	0.53102	0.654;0.452;0.718	T	0.59553	-0.7433	10	0.29301	T	0.29	.	18.651	0.91430	0.0:1.0:0.0:0.0	.	335;354;354	Q9Y6N9-4;Q9Y6N9;Q7RTU8	.;USH1C_HUMAN;.	K	354;323;335;354	ENSP00000317018:E354K;ENSP00000432944:E323K;ENSP00000436934:E335K;ENSP00000005226:E354K	ENSP00000005226:E354K	E	-	1	0	USH1C	17499494	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.118000	0.71583	2.703000	0.92315	0.650000	0.86243	GAG	.	.		0.498	USH1C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389146.1	NM_005709		T	17542918	C	T	17542918	3	4	361	1	0	0	0	0	1	0	0	0	17049	835	29	3	1777	3	USH1C	11	17542918	Missense_Mutation	SNP	C	TCGA-XR-A8TG-01A-11D-A35Z-10		17542918	117463598	53	50503										
PRMT3	10196	hgsc.bcm.edu	37	chr11	20473685	20473685	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	tttttatgcagggctattttCttctgtttgagtctatgtta	8	5	3	1			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr11:20473685C>T	ENST00000331079.6	+	11	1220	c.1003C>T	c.(1003-1005)Ctt>Ttt	p.L335F	PRMT3_ENST00000437750.2_Missense_Mutation_p.L273F	NM_001145167.1|NM_005788.3	NP_001138639.1|NP_005779	O60678	ANM3_HUMAN	protein arginine methyltransferase 3	335	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				histone arginine methylation (GO:0034969)|negative regulation of protein ubiquitination (GO:0031397)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|ribosome (GO:0005840)	histone-arginine N-methyltransferase activity (GO:0008469)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|modified amino acid binding (GO:0072341)|protein-arginine N-methyltransferase activity (GO:0016274)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)			endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|prostate(1)	17						GGGCTATTTTCTTCTGTTTGA	0.333																																					p.L335F		Atlas-SNP	.											.	PRMT3	50	.	0			c.C1003T						.						154	147	150					11																	20473685		2203	4300	6503	SO:0001583	missense	10196	exon11			TATTTTCTTCTGT	AF059531	CCDS7853.1, CCDS44554.1	11p15.1	2008-02-05	2006-02-16	2006-02-16	ENSG00000185238	ENSG00000185238		"Protein arginine methyltransferases"	30163	protein-coding gene	gene with protein product		603190	"HMT1 hnRNP methyltransferase-like 3 (S. cerevisiae)"	HRMT1L3		9642256	Standard	NM_005788		Approved		uc001mqb.3	O60678	OTTHUMG00000166022	ENST00000331079.6:c.1003C>T	chr11.hg19:g.20473685C>T	ENSP00000331879:p.Leu335Phe	73.0	0.0		91.0	36.0	NM_005788	B4DUC7	Missense_Mutation	SNP	ENST00000331079.6	hg19	CCDS7853.1	.	.	.	.	.	.	.	.	.	.	C	16.98	3.270695	0.59540	.	.	ENSG00000185238	ENST00000331079;ENST00000541255;ENST00000437750	T;T	0.27402	1.67;1.67	5.69	4.78	0.61160	.	0.057109	0.64402	N	0.000002	T	0.49983	0.1589	L	0.49126	1.545	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.52668	-0.8545	10	0.87932	D	0	-18.8309	14.6779	0.68996	0.0:0.9295:0.0:0.0705	.	273;335	O60678-2;O60678	.;ANM3_HUMAN	F	335;335;273	ENSP00000331879:L335F;ENSP00000397766:L273F	ENSP00000331879:L335F	L	+	1	0	PRMT3	20430261	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	3.249000	0.51437	1.418000	0.47098	-0.139000	0.14373	CTT	.	.		0.333	PRMT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387489.1	NM_005788		T	20473685	C	T	20473685	3	4	361	1	0	0	0	0	1	0	0	0	12550	913	32	3	1045	3	PRMT3	11	20473685	Missense_Mutation	SNP	C	TCGA-XR-A8TG-01A-11D-A35Z-10	2930767	20473685	114532831	54	50504										
OR4S2	219431	hgsc.bcm.edu	37	chr11	55418847	55418847	+	Silent	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	gggttcttacactccattatCcaagtggctctggtagtcca	9	11	2	0			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr11:55418847C>A	ENST00000312422.2	+	1	468	c.468C>A	c.(466-468)atC>atA	p.I156I		NM_001004059.2	NP_001004059.2	Q8NH73	OR4S2_HUMAN	olfactory receptor, family 4, subfamily S, member 2	156						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(4)|lung(28)|ovary(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_epithelial(135;0.0748)				ACTCCATTATCCAAGTGGCTC	0.433																																					p.I156I		Atlas-SNP	.											.	OR4S2	89	.	0			c.C468A						.						217	172	188					11																	55418847		2181	4040	6221	SO:0001819	synonymous_variant	219431	exon1			CATTATCCAAGTG	BK004390	CCDS31505.1	11q11	2012-08-09	2002-11-13	2002-11-15	ENSG00000174982	ENSG00000174982		"GPCR / Class A : Olfactory receptors"	15183	protein-coding gene	gene with protein product			"olfactory receptor, family 4, subfamily S, member 2 pseudogene"	OR4S2P			Standard	NM_001004059		Approved	OST725	uc001nhs.1	Q8NH73	OTTHUMG00000166799	ENST00000312422.2:c.468C>A	chr11.hg19:g.55418847C>A		152.0	0.0		176.0	79.0	NM_001004059	Q6IF72	Silent	SNP	ENST00000312422.2	hg19	CCDS31505.1																																																																																			.	.		0.433	OR4S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391503.1	NM_001004059		A	55418847	C	A	55418847	2	1	361	1	0	0	0	0	0	0	0	1	11092	845	30	3		3	OR4S2	11	55418847	Silent	SNP	C	TCGA-XR-A8TG-01A-11D-A35Z-10	34945162	55418847	79587669	55	50505										
AHNAK	79026	hgsc.bcm.edu	37	chr11	62292058	62292058	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	ggcatcttcagttttggaccTtttaatttggcatctgggcc	10	9	3	0			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr11:62292058T>C	ENST00000378024.4	-	5	10105	c.9831A>G	c.(9829-9831)aaA>aaG	p.K3277K	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	3277					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				GTTTTGGACCTTTTAATTTGG	0.413																																					p.K3277K		Atlas-SNP	.											.	AHNAK	532	.	0			c.A9831G						.						136	126	130					11																	62292058		2202	4299	6501	SO:0001819	synonymous_variant	79026	exon5			TGGACCTTTTAAT	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.9831A>G	chr11.hg19:g.62292058T>C		67.0	0.0		92.0	43.0	NM_001620	A1A586	Silent	SNP	ENST00000378024.4	hg19	CCDS31584.1																																																																																			.	.		0.413	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		C	62292058	T	C	62292058	2	2	361	1	0	0	0	0	0	0	0	1	414	1606	56	2		2	AHNAK	11	62292058	Silent	SNP	T	TCGA-XR-A8TG-01A-11D-A35Z-10	6873211	62292058	72714458	56	50506										
UBTFL1	0	hgsc.bcm.edu	37	chr11	89819558	89819558	+	IGR	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	ctcccagagcagatgaaacaGaaatatattcaggatttccg	8	9	1	4			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr11:89819558G>T								TRIM49C (13000 upstream) : SNORD56 (32000 downstream)																							AGATGAAACAGAAATATATTC	0.443																																					p.Q147H		Atlas-SNP	.											.	.	.	.	0			c.G441T						.						29	21	23					11																	89819558		675	1510	2185	SO:0001628	intergenic_variant	642623	exon1			GAAACAGAAATAT																													chr11.hg19:g.89819558G>T		172.0	0.0		236.0	39.0	NM_001143975		Missense_Mutation	SNP		hg19																																																																																				.	.	0	0.443									T	89819558	G	T	89819558	1	4	361	0	1	0	0	0	0	0	0	0	16925	933	33	3		3	UBTFL1	11	89819558	IGR	SNP	G	TCGA-XR-A8TG-01A-11D-A35Z-10	27527500	89819558	45186958	57	50507										
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	103039593	103039593	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	gttcatacaactgaagactgGgcttggaaaaaacaacttag	9	7	1	2			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr11:103039593G>T	ENST00000375735.2	+	32	5016	c.4872G>T	c.(4870-4872)tgG>tgT	p.W1624C	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.W1624C|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	1624	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		CTGAAGACTGGGCTTGGAAAA	0.328																																					p.W1624C		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.G4872T						.						96	93	94					11																	103039593		1826	4082	5908	SO:0001583	missense	79659	exon32			AGACTGGGCTTGG	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.4872G>T	chr11.hg19:g.103039593G>T	ENSP00000364887:p.Trp1624Cys	95.0	0.0		114.0	12.0	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	hg19	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	G	18.12	3.554110	0.65425	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.28454	1.61;1.61	6.05	5.13	0.70059	.	0.000000	0.33938	U	0.004402	T	0.65491	0.2696	M	0.91561	3.22	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.75836	-0.3177	10	0.87932	D	0	.	17.3526	0.87328	0.0:0.1251:0.8749:0.0	.	1624;1624	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	C	1624	ENSP00000364887:W1624C;ENSP00000381167:W1624C	ENSP00000364887:W1624C	W	+	3	0	DYNC2H1	102544803	1.000000	0.71417	1.000000	0.80357	0.766000	0.43426	9.471000	0.97696	1.539000	0.49286	0.650000	0.86243	TGG	.	.		0.328	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		T	103039593	G	T	103039593	3	4	361	1	0	0	0	0	1	0	0	0	4848	1241	43	3	4998	3	DYNC2H1	11	103039593	Missense_Mutation	SNP	G	TCGA-XR-A8TG-01A-11D-A35Z-10	13220035	103039593	31966923	58	50508										
OR8B4	283162	hgsc.bcm.edu	37	chr11	124294728	124294728	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	ctgttctgataatcccacaaGgataaactcagtcactgagg	8	10	3	2			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr11:124294728G>C	ENST00000356130.3	-	1	61	c.40C>G	c.(40-42)Ctt>Gtt	p.L14V		NM_001005196.1	NP_001005196.1	Q96RC9	OR8B4_HUMAN	olfactory receptor, family 8, subfamily B, member 4	14						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(1)|urinary_tract(1)	32		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		AATCCCACAAGGATAAACTCA	0.493																																					p.L14V		Atlas-SNP	.											.	OR8B4	60	.	0			c.C40G						.						47	45	46					11																	124294728		2201	4298	6499	SO:0001583	missense	283162	exon1			CCACAAGGATAAA	AB065831	CCDS31710.1	11q24	2012-08-09		2001-06-29	ENSG00000198657	ENSG00000198657		"GPCR / Class A : Olfactory receptors"	8473	protein-coding gene	gene with protein product				OR8B4P			Standard	NM_001005196		Approved		uc010sak.2	Q96RC9	OTTHUMG00000165916	ENST00000356130.3:c.40C>G	chr11.hg19:g.124294728G>C	ENSP00000348449:p.Leu14Val	64.0	0.0		68.0	31.0	NM_001005196	B2RNF8|Q6IFQ7	Missense_Mutation	SNP	ENST00000356130.3	hg19	CCDS31710.1	.	.	.	.	.	.	.	.	.	.	g	14.71	2.615266	0.46631	.	.	ENSG00000198657	ENST00000356130	T	0.00563	6.58	4.62	1.74	0.24563	.	0.294190	0.24429	N	0.038611	T	0.02380	0.0073	M	0.94021	3.485	0.31020	N	0.718231	D	0.64830	0.994	P	0.61201	0.885	T	0.02179	-1.1200	10	0.87932	D	0	.	9.8764	0.41207	0.227:0.0:0.773:0.0	.	14	Q96RC9	OR8B4_HUMAN	V	14	ENSP00000348449:L14V	ENSP00000348449:L14V	L	-	1	0	OR8B4	123799938	0.984000	0.35163	0.848000	0.33437	0.812000	0.45895	0.923000	0.28757	0.297000	0.22615	-0.748000	0.03510	CTT	.	.		0.493	OR8B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387055.1	NM_001005196		C	124294728	G	C	124294728	3	2	361	1	0	0	0	0	1	0	0	0	11238	1000	35	4	891	4	OR8B4	11	124294728	Missense_Mutation	SNP	G	TCGA-XR-A8TG-01A-11D-A35Z-10	21255135	124294728	10711788	59	50509										
GYS2	2998	hgsc.bcm.edu	37	chr12	21713390	21713390	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	atttgtcttggcaggcataaTgaaaaacaccatcactgtga	8	8	2	2			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr12:21713390T>C	ENST00000261195.2	-	8	1353	c.1099A>G	c.(1099-1101)Att>Gtt	p.I367V		NM_021957.3	NP_068776.2	P54840	GYS2_HUMAN	glycogen synthase 2 (liver)	367					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|ectoplasm (GO:0043265)	glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein homodimerization activity (GO:0042803)			NS(1)|breast(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(14)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						GCAGGCATAATGAAAAACACC	0.373																																					p.I367V	Colon(149;9 1820 3690 10544 50424)	Atlas-SNP	.											.	GYS2	110	.	0			c.A1099G						.						192	174	180					12																	21713390		2203	4300	6503	SO:0001583	missense	2998	exon8			GCATAATGAAAAA		CCDS8690.1	12p12.2-p11.2	2013-02-22			ENSG00000111713	ENSG00000111713	2.4.1.11	"Glycosyltransferase group 1 domain containing"	4707	protein-coding gene	gene with protein product		138571					Standard	NM_021957		Approved		uc001rfb.3	P54840	OTTHUMG00000169135	ENST00000261195.2:c.1099A>G	chr12.hg19:g.21713390T>C	ENSP00000261195:p.Ile367Val	71.0	0.0		87.0	30.0	NM_021957	A0AVD8	Missense_Mutation	SNP	ENST00000261195.2	hg19	CCDS8690.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.178868	0.78564	.	.	ENSG00000111713	ENST00000261195	T	0.69435	-0.4	4.87	4.87	0.63330	.	0.000000	0.85682	D	0.000000	T	0.79885	0.4523	M	0.83852	2.665	0.80722	D	1	P	0.46020	0.871	P	0.56612	0.802	T	0.82125	-0.0612	10	0.51188	T	0.08	-24.7952	14.628	0.68635	0.0:0.0:0.0:1.0	.	367	P54840	GYS2_HUMAN	V	367	ENSP00000261195:I367V	ENSP00000261195:I367V	I	-	1	0	GYS2	21604657	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	7.854000	0.86942	2.046000	0.60703	0.460000	0.39030	ATT	.	.		0.373	GYS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402396.1	NM_021957		C	21713390	T	C	21713390	3	2	361	1	0	0	0	0	1	0	0	0	6922	1464	51	2	1048	2	GYS2	12	21713390	Missense_Mutation	SNP	T	TCGA-XR-A8TG-01A-11D-A35Z-10		21713390	112138505	60	50510										
KRT6A	3853	hgsc.bcm.edu	37	chr12	52886815	52886815	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	tgcggctgccaaagccagctCctccacatgcaccacccagg	9	18	0	0			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr12:52886815C>T	ENST00000330722.6	-	1	226	c.158G>A	c.(157-159)gGa>gAa	p.G53E		NM_005554.3	NP_005545.1	P02538	K2C6A_HUMAN	keratin 6A	53	Head.				cell differentiation (GO:0030154)|positive regulation of cell proliferation (GO:0008284)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	39				BRCA - Breast invasive adenocarcinoma(357;0.189)		AAAGCCAGCTCCTCCACATGC	0.662																																					p.G53E		Atlas-SNP	.											.	KRT6A	89	.	0			c.G158A						.						16	21	20					12																	52886815		2029	4038	6067	SO:0001583	missense	3853	exon1			CCAGCTCCTCCAC	BC014152, L42593, L42610	CCDS41786.1	12q13.13	2013-01-16			ENSG00000205420	ENSG00000205420		"-", "Intermediate filaments type II, keratins (basic)"	6443	protein-coding gene	gene with protein product		148041	"keratin 6C", "keratin 6D"	KRT6C, KRT6D		1713141, 16831889	Standard	NM_005554		Approved	CK6C, K6C, CK6D, K6D	uc001sam.3	P02538	OTTHUMG00000169597	ENST00000330722.6:c.158G>A	chr12.hg19:g.52886815C>T	ENSP00000369317:p.Gly53Glu	166.0	0.0		194.0	77.0	NM_005554	A4QPC1|P48667|Q08AR4|Q6NT67|Q96CL4	Missense_Mutation	SNP	ENST00000330722.6	hg19	CCDS41786.1	.	.	.	.	.	.	.	.	.	.	C	16.46	3.128182	0.56721	.	.	ENSG00000205420	ENST00000330722	D	0.94966	-3.57	5.24	5.24	0.73138	.	0.000000	0.64402	D	0.000016	D	0.97604	0.9215	M	0.88105	2.93	0.48452	D	0.999656	D	0.89917	1.0	D	0.91635	0.999	D	0.96743	0.9548	10	0.30854	T	0.27	.	19.2638	0.93979	0.0:1.0:0.0:0.0	.	53	P02538	K2C6A_HUMAN	E	53	ENSP00000369317:G53E	ENSP00000369317:G53E	G	-	2	0	KRT6A	51173082	0.144000	0.22641	0.998000	0.56505	0.799000	0.45148	2.143000	0.42187	2.626000	0.88956	0.549000	0.68633	GGA	.	.		0.662	KRT6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404978.2	NM_005554		T	52886815	C	T	52886815	3	4	361	1	0	0	0	0	1	0	0	0	8489	855	30	3	1572	3	KRT6A	12	52886815	Missense_Mutation	SNP	C	TCGA-XR-A8TG-01A-11D-A35Z-10	31173425	52886815	80965080	61	50511										
TDG	6996	hgsc.bcm.edu	37	chr12	104379458	104379458	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	catatggtggtgcttacggaGaaaatccatgcagcagtgaa	12	7	0	2			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr12:104379458G>T	ENST00000392872.3	+	9	1276	c.1042G>T	c.(1042-1044)Gaa>Taa	p.E348*	TDG_ENST00000544861.1_Nonsense_Mutation_p.E205*|TDG_ENST00000266775.9_Nonsense_Mutation_p.E344*|AC078819.1_ENST00000401157.1_RNA|TDG_ENST00000542036.1_Nonsense_Mutation_p.E144*	NM_003211.4	NP_003202.3	Q13569	TDG_HUMAN	thymine-DNA glycosylase	348					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|chromatin modification (GO:0016568)|depyrimidination (GO:0045008)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|embryo development (GO:0009790)|mismatch repair (GO:0006298)|negative regulation of chromatin binding (GO:0035562)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression, epigenetic (GO:0040029)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|double-stranded DNA binding (GO:0003690)|mismatched DNA binding (GO:0030983)|protein homodimerization activity (GO:0042803)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|RNA polymerase II transcription cofactor activity (GO:0001104)|structure-specific DNA binding (GO:0043566)			large_intestine(2)|lung(14)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(302;0.00114)		TGCTTACGGAGAAAATCCATG	0.433								Base excision repair (BER), DNA glycosylases																													p.E348X		Atlas-SNP	.											.	TDG	43	.	0			c.G1042T						.						181	162	168					12																	104379458		2203	4300	6503	SO:0001587	stop_gained	6996	exon9			TACGGAGAAAATC	U51166	CCDS9095.1	12q24.1	2014-05-14			ENSG00000139372	ENSG00000139372	3.2.2.29		11700	protein-coding gene	gene with protein product	"G/T mismatch-specific thymine DNA glycosylase"	601423				8662714, 9299239	Standard	NM_003211		Approved		uc001tkg.3	Q13569	OTTHUMG00000168418	ENST00000392872.3:c.1042G>T	chr12.hg19:g.104379458G>T	ENSP00000376611:p.Glu348*	94.0	0.0		131.0	16.0	NM_003211	Q8IUZ6|Q8IZM3	Nonsense_Mutation	SNP	ENST00000392872.3	hg19	CCDS9095.1	.	.	.	.	.	.	.	.	.	.	G	32	5.155488	0.94686	.	.	ENSG00000139372	ENST00000392872;ENST00000266775;ENST00000544861;ENST00000542036	.	.	.	5.7	5.7	0.88788	.	0.266936	0.41396	D	0.000888	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.45353	T	0.12	-9.8938	16.346	0.83133	0.0:0.1406:0.8594:0.0	.	.	.	.	X	348;344;205;144	.	ENSP00000266775:E344X	E	+	1	0	TDG	102903588	1.000000	0.71417	0.013000	0.15412	0.216000	0.24613	6.729000	0.74775	2.692000	0.91855	0.655000	0.94253	GAA	.	.		0.433	TDG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399673.2			T	104379458	G	T	104379458	4	4	361	1	0	0	0	0	0	1	0	0	15740	943	33	3	1076	3	TDG	12	104379458	Nonsense_Mutation	SNP	G	TCGA-XR-A8TG-01A-11D-A35Z-10	51492643	104379458	29472437	62	50512										
OAS3	4940	hgsc.bcm.edu	37	chr12	113405240	113405240	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	caggccagctggtctctggcTccaggcccagctctcaagtc	11	16	2	0			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr12:113405240T>C	ENST00000228928.7	+	13	2886	c.2707T>C	c.(2707-2709)Tcc>Ccc	p.S903P	RP1-71H24.1_ENST00000552784.1_RNA	NM_006187.2	NP_006178.2	Q9Y6K5	OAS3_HUMAN	2'-5'-oligoadenylate synthetase 3, 100kDa	903	OAS domain 3.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|nucleobase-containing compound metabolic process (GO:0006139)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|skin(2)	27						GGTCTCTGGCTCCAGGCCCAG	0.562																																					p.S903P		Atlas-SNP	.											.	OAS3	63	.	0			c.T2707C						.						40	42	41					12																	113405240		2034	4216	6250	SO:0001583	missense	4940	exon13			TCTGGCTCCAGGC	AF063613	CCDS44981.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111331			8088	protein-coding gene	gene with protein product		603351	"2'-5'-oligoadenylate synthetase 3 (100 kD)"			9790745	Standard	NM_006187		Approved		uc001tug.3	Q9Y6K5	OTTHUMG00000169795	ENST00000228928.7:c.2707T>C	chr12.hg19:g.113405240T>C	ENSP00000228928:p.Ser903Pro	83.0	0.0		129.0	57.0	NM_006187	Q2HJ14|Q9H3P5	Missense_Mutation	SNP	ENST00000228928.7	hg19	CCDS44981.1	.	.	.	.	.	.	.	.	.	.	T	12.54	1.968387	0.34754	.	.	ENSG00000111331	ENST00000228928;ENST00000323881	T	0.08720	3.06	4.26	-3.32	0.04973	-oligoadenylate synthetase 1, domain 2/C-terminal (2);-5&apos (2);2&apos (2);	6.218310	0.00926	U	0.002648	T	0.12860	0.0312	M	0.67397	2.05	0.09310	N	1	P	0.52577	0.954	P	0.48952	0.596	T	0.34477	-0.9827	10	0.36615	T	0.2	.	1.1569	0.01797	0.2763:0.0986:0.3433:0.2818	.	903	Q9Y6K5	OAS3_HUMAN	P	903;902	ENSP00000228928:S903P	ENSP00000228928:S903P	S	+	1	0	OAS3	111889623	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.220000	0.09215	-0.290000	0.09025	-0.471000	0.05019	TCC	.	.		0.562	OAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405920.1			C	113405240	T	C	113405240	3	2	361	1	0	0	0	0	1	0	0	0	10810	1551	54	2	2757	2	OAS3	12	113405240	Missense_Mutation	SNP	T	TCGA-XR-A8TG-01A-11D-A35Z-10	9025782	113405240	20446655	63	50513										
SETD8	387893	hgsc.bcm.edu	37	chr12	123874057	123874057	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	cagcgacggccccgggcccgGagatggtggagcggaggggc	21	12	0	1			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr12:123874057G>C	ENST00000402868.3	+	2	514	c.88G>C	c.(88-90)Gag>Cag	p.E30Q	SETD8_ENST00000330479.4_Missense_Mutation_p.E30Q|SETD8_ENST00000478781.2_Intron			Q9NQR1	SETD8_HUMAN	SET domain containing (lysine methyltransferase) 8	71	Ala-rich.|Poly-Arg.				histone lysine methylation (GO:0034968)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine monomethylation (GO:0018026)|regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043516)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|urinary_tract(1)	13	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.00101)|Epithelial(86;0.00425)		CCCGGGCCCGGAGATGGTGGA	0.811																																					p.E30Q		Atlas-SNP	.											.	SETD8	35	.	0			c.G88C						.						1	1	1					12																	123874057		123	314	437	SO:0001583	missense	387893	exon2			GGCCCGGAGATGG	AY102937	CCDS9247.1	12q24.31	2011-07-01			ENSG00000183955	ENSG00000183955		"Chromatin-modifying enzymes / K-methyltransferases"	29489	protein-coding gene	gene with protein product		607240				15933070, 12086618, 12121615	Standard	NM_020382		Approved	SET8, SET07, PR-Set7, KMT5A	uc001uew.3	Q9NQR1	OTTHUMG00000150477	ENST00000402868.3:c.88G>C	chr12.hg19:g.123874057G>C	ENSP00000384629:p.Glu30Gln	0.0	0.0		13.0	7.0	NM_020382	A8K9D0|Q86W83|Q8TD09	Missense_Mutation	SNP	ENST00000402868.3	hg19	CCDS9247.1	.	.	.	.	.	.	.	.	.	.	G	15.51	2.854477	0.51376	.	.	ENSG00000183955	ENST00000402868;ENST00000330479	D;D	0.98666	-5.06;-5.06	1.77	1.77	0.24775	.	130.389000	0.00622	U	0.000447	D	0.94558	0.8247	N	0.14661	0.345	0.21473	N	0.999678	P	0.50710	0.938	B	0.37451	0.25	D	0.93140	0.6540	10	0.17832	T	0.49	-0.2818	6.9164	0.24361	0.0:0.0:1.0:0.0	.	30	Q9NQR1-2	.	Q	30	ENSP00000384629:E30Q;ENSP00000332995:E30Q	ENSP00000332995:E30Q	E	+	1	0	SETD8	122440010	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	1.377000	0.34317	0.987000	0.38709	0.163000	0.16589	GAG	.	.		0.811	SETD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318263.1	NM_020382		C	123874057	G	C	123874057	3	2	361	1	0	0	0	0	1	0	0	0	14152	1175	41	4	94	4	SETD8	12	123874057	Missense_Mutation	SNP	G	TCGA-XR-A8TG-01A-11D-A35Z-10	10468817	123874057	9977838	64	50514										
TMEM132B	114795	hgsc.bcm.edu	37	chr12	126135432	126135432	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	gttcatgaaggtggaggagcCgaaaatcgctcagttacagg	14	7	2	1	rs149523266	byFrequency	TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr12:126135432C>T	ENST00000299308.3	+	7	1840	c.1832C>T	c.(1831-1833)cCg>cTg	p.P611L	TMEM132B_ENST00000535886.1_Missense_Mutation_p.P123L	NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	611						integral component of membrane (GO:0016021)				NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		GTGGAGGAGCCGAAAATCGCT	0.602																																					p.P611L		Atlas-SNP	.											.	TMEM132B	207	.	0			c.C1832T						.						64	69	68					12																	126135432		2077	4205	6282	SO:0001583	missense	114795	exon7			AGGAGCCGAAAAT	AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.1832C>T	chr12.hg19:g.126135432C>T	ENSP00000299308:p.Pro611Leu	97.0	0.0		132.0	61.0	NM_052907	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Missense_Mutation	SNP	ENST00000299308.3	hg19	CCDS41859.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.048572	0.93740	.	.	ENSG00000139364	ENST00000299308;ENST00000535886	T;T	0.20738	2.05;2.05	5.14	5.14	0.70334	.	0.192832	0.37012	N	0.002288	T	0.30324	0.0761	M	0.73962	2.25	0.80722	D	1	P	0.46987	0.888	B	0.40565	0.333	T	0.31943	-0.9925	10	0.72032	D	0.01	.	18.6079	0.91273	0.0:1.0:0.0:0.0	.	611	Q14DG7	T132B_HUMAN	L	611;123	ENSP00000299308:P611L;ENSP00000440436:P123L	ENSP00000299308:P611L	P	+	2	0	TMEM132B	124701385	0.970000	0.33590	0.881000	0.34555	0.943000	0.58893	7.562000	0.82300	2.358000	0.79984	0.650000	0.86243	CCG	.	C|0.999;A|0.001		0.602	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907		T	126135432	C	T	126135432	3	4	361	1	0	0	0	0	1	0	0	0	16061	652	23	1	1858	1	TMEM132B	12	126135432	Missense_Mutation	SNP	C	TCGA-XR-A8TG-01A-11D-A35Z-10	2261375	126135432	7716463	65	50515										
DDHD1	80821	hgsc.bcm.edu	37	chr14	53619420	53619420	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	ggaccctcctgtcgcgccgcCgccccccgagttcgtcggga	13	19	0	0			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr14:53619420C>T	ENST00000323669.5	-	1	396	c.397G>A	c.(397-399)Ggc>Agc	p.G133S	RP11-547D23.1_ENST00000554235.1_RNA|AL356020.1_ENST00000584587.1_RNA|DDHD1_ENST00000395606.1_Missense_Mutation_p.G133S|DDHD1_ENST00000357758.3_Missense_Mutation_p.G133S	NM_001160148.1	NP_001153620.1	Q8NEL9	DDHD1_HUMAN	DDHD domain containing 1	133					cell death (GO:0008219)|lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)	25	Breast(41;0.037)					GTCGCGCCGCCGCCCCCCGAG	0.741																																					p.G133S		Atlas-SNP	.											.	DDHD1	202	.	0			c.G397A						.						10	11	11					14																	53619420		2171	4228	6399	SO:0001583	missense	80821	exon1			CGCCGCCGCCCCC	AB051492	CCDS9714.1, CCDS53895.1, CCDS53896.1	14q21	2012-11-23			ENSG00000100523	ENSG00000100523			19714	protein-coding gene	gene with protein product	"phosphatidic acid-preferring phospholipase A1"	614603	"spastic paraplegia 28 (autosomal recessive)"	SPG28		11214970, 20359546	Standard	NM_030637		Approved	KIAA1705, PA-PLA1	uc001xai.3	Q8NEL9	OTTHUMG00000140305	ENST00000323669.5:c.397G>A	chr14.hg19:g.53619420C>T	ENSP00000327104:p.Gly133Ser	89.0	0.0		75.0	4.0	NM_001160147	G5E9D1|Q8WVH3|Q96LL2|Q9C0F8	Missense_Mutation	SNP	ENST00000323669.5	hg19	CCDS53895.1	.	.	.	.	.	.	.	.	.	.	C	13.61	2.289660	0.40494	.	.	ENSG00000100523	ENST00000323669;ENST00000395606;ENST00000357758	.	.	.	3.78	2.88	0.33553	.	0.306105	0.25944	U	0.027297	T	0.37237	0.0996	L	0.29908	0.895	0.29342	N	0.865948	B;D;B	0.89917	0.027;1.0;0.027	B;D;B	0.78314	0.006;0.991;0.006	T	0.21724	-1.0237	9	0.11485	T	0.65	-5.2152	5.4996	0.16821	0.0:0.6251:0.1807:0.1942	.	133;133;133	G5E9D1;Q8NEL9;Q8NEL9-2	.;DDHD1_HUMAN;.	S	133	.	ENSP00000327104:G133S	G	-	1	0	DDHD1	52689170	0.825000	0.29262	0.998000	0.56505	0.632000	0.37999	0.111000	0.15458	0.774000	0.33427	0.462000	0.41574	GGC	.	.		0.741	DDHD1-003	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276901.1			T	53619420	C	T	53619420	3	4	361	1	0	0	0	0	1	0	0	0	4328	652	23	1	2382	1	DDHD1	14	53619420	Missense_Mutation	SNP	C	TCGA-XR-A8TG-01A-11D-A35Z-10		53619420	53730120	66	50516										
VSX2	338917	hgsc.bcm.edu	37	chr14	74727333	74727333	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	gctggaggcagcagccgagtCggggaggaagcccgaggggg	22	9	0	0			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr14:74727333C>T	ENST00000261980.2	+	5	887	c.797C>T	c.(796-798)tCg>tTg	p.S266L		NM_182894.2	NP_878314.1	P58304	VSX2_HUMAN	visual system homeobox 2	266					cell fate commitment (GO:0045165)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to stimulus (GO:0050896)|retinal bipolar neuron differentiation (GO:0060040)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	7				BRCA - Breast invasive adenocarcinoma(234;0.00154)		GCAGCCGAGTCGGGGAGGAAG	0.597																																					p.S266L		Atlas-SNP	.											.	VSX2	32	.	0			c.C797T						.						11	13	12					14																	74727333		2193	4297	6490	SO:0001583	missense	338917	exon5			CCGAGTCGGGGAG	AC005519	CCDS9827.1	14q24.3	2011-06-20	2007-08-21	2007-08-21		ENSG00000119614		"Homeoboxes / PRD class"	1975	protein-coding gene	gene with protein product		142993	"C elegans ceh-10 homeo domain-containing homolog", "ceh-10 homeo domain containing homolog (C. elegans)", "ceh-10 homeodomain containing homolog (C. elegans)"	HOX10, CHX10		1973146	Standard	NM_182894		Approved	RET1	uc001xpq.3	P58304		ENST00000261980.2:c.797C>T	chr14.hg19:g.74727333C>T	ENSP00000261980:p.Ser266Leu	337.0	0.0		384.0	33.0	NM_182894	A1A4X6	Missense_Mutation	SNP	ENST00000261980.2	hg19	CCDS9827.1	.	.	.	.	.	.	.	.	.	.	C	16.15	3.041954	0.55003	.	.	ENSG00000119614	ENST00000261980	D	0.91237	-2.81	4.93	4.93	0.64822	.	0.644709	0.15920	N	0.238169	D	0.82861	0.5129	N	0.21194	0.64	0.35847	D	0.826451	B	0.31413	0.322	B	0.21917	0.037	D	0.83580	0.0117	10	0.31617	T	0.26	.	14.0026	0.64442	0.0:0.8487:0.1513:0.0	.	266	P58304	VSX2_HUMAN	L	266	ENSP00000261980:S266L	ENSP00000261980:S266L	S	+	2	0	VSX2	73797086	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.497000	0.53295	2.550000	0.86006	0.655000	0.94253	TCG	.	.		0.597	VSX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412323.1	NM_182894		T	74727333	C	T	74727333	3	4	361	1	0	0	0	0	1	0	0	0	17247	893	31	1	815	1	VSX2	14	74727333	Missense_Mutation	SNP	C	TCGA-XR-A8TG-01A-11D-A35Z-10	21107913	74727333	32622207	67	50517										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105413863	105413863	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	tgaacttgctatctttggctGtcacacccttgtcggccagg	10	12	2	1	rs371234619		TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr14:105413863G>A	ENST00000333244.5	-	7	8044	c.7925C>T	c.(7924-7926)aCa>aTa	p.T2642I	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2642						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				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)			ATCTTTGGCTGTCACACCCTT	0.592																																					p.T2642I		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C7925T						.						218	237	231					14																	105413863		1997	4158	6155	SO:0001583	missense	113146	exon7			TTGGCTGTCACAC	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.7925C>T	chr14.hg19:g.105413863G>A	ENSP00000353114:p.Thr2642Ile	110.0	0.0		144.0	16.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	hg19	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	c	11.91	1.780972	0.31502	.	.	ENSG00000185567	ENST00000333244	T	0.00902	5.56	3.26	0.711	0.18162	.	.	.	.	.	T	0.01454	0.0047	M	0.67953	2.075	0.09310	N	1	B	0.24258	0.1	B	0.21546	0.035	T	0.39231	-0.9624	9	0.37606	T	0.19	.	8.0014	0.30299	0.0:0.0:0.306:0.694	.	2642	Q8IVF2	AHNK2_HUMAN	I	2642	ENSP00000353114:T2642I	ENSP00000353114:T2642I	T	-	2	0	AHNAK2	104484908	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.128000	0.15810	-0.076000	0.12775	0.306000	0.20318	ACA	.	.		0.592	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105413863	G	A	105413863	3	1	361	1	0	0	0	0	1	0	0	0	415	1377	48	3	9466	3	AHNAK2	14	105413863	Missense_Mutation	SNP	G	TCGA-XR-A8TG-01A-11D-A35Z-10	30686530	105413863	1935677	68	50518										
HAUS2	55142	hgsc.bcm.edu	37	chr15	42858922	42858922	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	cttgtatccccaaaatattaGctgaagaaagttatctttat	5	7	1	2			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr15:42858922G>T	ENST00000260372.3	+	6	679	c.616G>T	c.(616-618)Gct>Tct	p.A206S	RP11-265N6.2_ENST00000567089.1_RNA|RP11-265N6.2_ENST00000561902.1_RNA|HAUS2_ENST00000568876.1_Missense_Mutation_p.A175S	NM_018097.2	NP_060567.1	Q9NVX0	HAUS2_HUMAN	HAUS augmin-like complex, subunit 2	206					centrosome organization (GO:0051297)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|HAUS complex (GO:0070652)|microtubule (GO:0005874)|nucleus (GO:0005634)				endometrium(1)|large_intestine(1)|lung(1)	3						CAAAATATTAGCTGAAGAAAG	0.343																																					p.A206S		Atlas-SNP	.											.	HAUS2	12	.	0			c.G616T						.						73	72	73					15																	42858922		2203	4299	6502	SO:0001583	missense	55142	exon6			ATATTAGCTGAAG	AK001322	CCDS10090.1, CCDS45247.1	15q15.1	2014-02-20	2009-04-20	2009-04-20	ENSG00000137814	ENSG00000137814		"HAUS augmin-like complex subunits"	25530	protein-coding gene	gene with protein product		613429	"chromosome 15 open reading frame 25", "centrosomal protein 27kDa"	C15orf25, CEP27		14702039, 14654843, 19427217	Standard	NM_018097		Approved	FLJ10460, HsT17025	uc001zqe.3	Q9NVX0	OTTHUMG00000130678	ENST00000260372.3:c.616G>T	chr15.hg19:g.42858922G>T	ENSP00000260372:p.Ala206Ser	118.0	0.0		142.0	43.0	NM_018097	C9JH36|Q9H9B3	Missense_Mutation	SNP	ENST00000260372.3	hg19	CCDS10090.1	.	.	.	.	.	.	.	.	.	.	G	11.60	1.685533	0.29872	.	.	ENSG00000137814	ENST00000260372;ENST00000391623	T	0.41758	0.99	6.17	-2.41	0.06562	.	0.563980	0.17875	N	0.159059	T	0.23171	0.0560	L	0.35414	1.06	0.22762	N	0.998762	B;B	0.22003	0.013;0.063	B;B	0.17979	0.007;0.02	T	0.08973	-1.0696	10	0.36615	T	0.2	0.0501	3.6903	0.08343	0.3308:0.0:0.2479:0.4214	.	175;206	Q9NVX0-3;Q9NVX0	.;HAUS2_HUMAN	S	206;175	ENSP00000260372:A206S	ENSP00000260372:A206S	A	+	1	0	HAUS2	40646214	0.836000	0.29430	0.916000	0.36221	0.732000	0.41865	-0.308000	0.08156	-0.069000	0.12931	0.655000	0.94253	GCT	.	.		0.343	HAUS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253173.1	NM_018097		T	42858922	G	T	42858922	3	4	361	1	0	0	0	0	1	0	0	0	6975	971	34	3	638	3	HAUS2	15	42858922	Missense_Mutation	SNP	G	TCGA-XR-A8TG-01A-11D-A35Z-10		42858922	59672470	69	50519										
C16orf71	146562	hgsc.bcm.edu	37	chr16	4787921	4787921	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	acaagtccagggcctgggtcGctgcagctgaagagtccctt	13	12	0	2			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr16:4787921G>C	ENST00000299320.5	+	3	728	c.250G>C	c.(250-252)Gct>Cct	p.A84P	RP11-127I20.7_ENST00000588099.1_RNA|C16orf71_ENST00000590191.1_Missense_Mutation_p.A84P	NM_139170.2	NP_631909.2	Q8IYS4	CP071_HUMAN	chromosome 16 open reading frame 71	84										breast(1)|central_nervous_system(1)|large_intestine(4)|lung(4)|ovary(1)	11						GGCCTGGGTCGCTGCAGCTGA	0.552																																					p.A84P		Atlas-SNP	.											.	C16orf71	46	.	0			c.G250C						.						72	68	69					16																	4787921		2197	4300	6497	SO:0001583	missense	146562	exon3			TGGGTCGCTGCAG	AF447587	CCDS10521.1	16p13.3	2008-02-05			ENSG00000166246	ENSG00000166246			25081	protein-coding gene	gene with protein product						12477932	Standard	XM_005255144		Approved	FLJ43261, DKFZp686H2240	uc002cxn.3	Q8IYS4	OTTHUMG00000129480	ENST00000299320.5:c.250G>C	chr16.hg19:g.4787921G>C	ENSP00000299320:p.Ala84Pro	105.0	0.0		89.0	35.0	NM_139170	Q8NCV0	Missense_Mutation	SNP	ENST00000299320.5	hg19	CCDS10521.1	.	.	.	.	.	.	.	.	.	.	G	14.57	2.575344	0.45902	.	.	ENSG00000166246	ENST00000299320	T	0.06933	3.24	3.95	-7.9	0.01169	.	1.473130	0.04778	N	0.429214	T	0.07773	0.0195	L	0.43152	1.355	0.09310	N	1	B	0.12013	0.005	B	0.08055	0.003	T	0.25847	-1.0120	10	0.54805	T	0.06	5.5624	9.5592	0.39357	0.1509:0.3931:0.456:0.0	.	84	Q8IYS4	CP071_HUMAN	P	84	ENSP00000299320:A84P	ENSP00000299320:A84P	A	+	1	0	C16orf71	4727922	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.241000	0.02911	-2.751000	0.00374	-1.078000	0.02229	GCT	.	.		0.552	C16orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251644.1	NM_139170		C	4787921	G	C	4787921	3	2	361	1	0	0	0	0	1	0	0	0	1832	1087	38	4	256	4	C16orf71	16	4787921	Missense_Mutation	SNP	G	TCGA-XR-A8TG-01A-11D-A35Z-10		4787921	85566832	70	50520										
PDZD9	255762	hgsc.bcm.edu	37	chr16	21995781	21995781	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	tcatcacgtcacaattaatgTcttttcctacactaatagta	3	10	4	0			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr16:21995781T>C	ENST00000424898.2	-	4	664	c.602A>G	c.(601-603)gAc>gGc	p.D201G	PDZD9_ENST00000286143.6_Missense_Mutation_p.D139G|PDZD9_ENST00000537222.2_Missense_Mutation_p.D141G			Q8IXQ8	PDZD9_HUMAN	PDZ domain containing 9	201										breast(3)|endometrium(2)|lung(3)|pancreas(1)	9						ACAATTAATGTCTTTTCCTAC	0.443																																					p.D141G		Atlas-SNP	.											.	PDZD9	18	.	0			c.A422G						.						213	194	200					16																	21995781		2198	4300	6498	SO:0001583	missense	255762	exon3			TTAATGTCTTTTC	BC039562	CCDS10602.1, CCDS10602.2	16p12.1	2010-04-14	2010-04-14	2010-04-14	ENSG00000155714	ENSG00000155714			28740	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 65"	C16orf65		12477932	Standard	NM_173806		Approved	MGC50721	uc021ter.1	Q8IXQ8	OTTHUMG00000131586	ENST00000424898.2:c.602A>G	chr16.hg19:g.21995781T>C	ENSP00000400514:p.Asp201Gly	125.0	0.0		131.0	23.0	NM_173806	F5GWW8	Missense_Mutation	SNP	ENST00000424898.2	hg19		.	.	.	.	.	.	.	.	.	.	T	14.80	2.644166	0.47258	.	.	ENSG00000155714	ENST00000424898;ENST00000537222;ENST00000286143	T	0.59224	0.28	5.43	4.33	0.51752	.	0.289846	0.29587	N	0.011730	T	0.54046	0.1834	M	0.66939	2.045	0.26686	N	0.971445	B	0.15930	0.015	B	0.19946	0.027	T	0.54543	-0.8278	10	0.87932	D	0	-6.1257	8.1798	0.31305	0.0:0.0913:0.0:0.9087	.	139	Q8IXQ8-2	.	G	201;141;139	ENSP00000400514:D201G	ENSP00000286143:D139G	D	-	2	0	PDZD9	21903282	0.562000	0.26586	0.024000	0.17045	0.405000	0.30901	2.176000	0.42500	0.888000	0.36160	0.460000	0.39030	GAC	.	.		0.443	PDZD9-003	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000381652.1	NM_173806		C	21995781	T	C	21995781	3	2	361	1	0	0	0	0	1	0	0	0	11715	1667	58	2	196	2	PDZD9	16	21995781	Missense_Mutation	SNP	T	TCGA-XR-A8TG-01A-11D-A35Z-10	17207860	21995781	68358972	71	50521										
CES1	1066	hgsc.bcm.edu	37	chr16	55866943	55866943	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	cgcggaagcagagagagtggCcaggataaaggcacggagcc	17	9	0	2			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr16:55866943C>T	ENST00000361503.4	-	1	155	c.25G>A	c.(25-27)Gcc>Acc	p.A9T	CES1_ENST00000360526.3_Missense_Mutation_p.A9T|CES1_ENST00000422046.2_Missense_Mutation_p.A9T			P23141	EST1_HUMAN	carboxylesterase 1	9					epithelial cell differentiation (GO:0030855)|metabolic process (GO:0008152)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)	carboxylic ester hydrolase activity (GO:0052689)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)								all cancers(182;0.13)|Epithelial(162;0.137)	Benzocaine(DB01086)|Capecitabine(DB01101)|Ciclesonide(DB01410)|Clopidogrel(DB00758)|Cyclandelate(DB04838)|Dabigatran etexilate(DB06695)|Indomethacin(DB00328)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Mycophenolate mofetil(DB00688)|Oseltamivir(DB00198)|Probucol(DB01599)|Rufinamide(DB06201)|Tamoxifen(DB00675)|Trandolapril(DB00519)	GAGAGAGTGGCCAGGATAAAG	0.592																																					p.A9T	NSCLC(162;1801 2756 42904 52896)	Atlas-SNP	.											.	CES1	78	.	0			c.G25A						.						73	62	66					16																	55866943		2160	4195	6355	SO:0001583	missense	1066	exon1			GAGTGGCCAGGAT	BC012418	CCDS32450.1, CCDS45488.1, CCDS45489.1	16q22.2	2010-10-12	2010-10-12		ENSG00000198848	ENSG00000198848	3.1.1.1	"Carboxylesterases"	1863	protein-coding gene	gene with protein product	"human monocyte/macrophage serine esterase 1"	114835	"carboxylesterase 1 (monocyte/macrophage serine esterase 1)"			2070086, 20931200	Standard	XM_005255774		Approved	HMSE, CES2, HMSE1, SES1, CEH, CES1A1, CES1A2	uc002eil.3	P23141		ENST00000361503.4:c.25G>A	chr16.hg19:g.55866943C>T	ENSP00000355193:p.Ala9Thr	295.0	0.0		344.0	139.0	NM_001025195	A6NIM1|A8K3K8|A8K844|E9PAU8|P82127|Q00015|Q13657|Q14062|Q16737|Q16788|Q549X7|Q549X8|Q86UK2|Q96EE8|Q9UC52|Q9UDG8|Q9UK77|Q9ULY2	Missense_Mutation	SNP	ENST00000361503.4	hg19	CCDS45488.1	.	.	.	.	.	.	.	.	.	.	.	5.505	0.278120	0.10403	.	.	ENSG00000198848	ENST00000360526;ENST00000361503;ENST00000422046	T;T;T	0.68479	-0.33;-0.33;-0.33	3.81	-3.75	0.04372	Carboxylesterase, type B (1);	3.397390	0.01003	N	0.003715	T	0.48714	0.1515	L	0.32530	0.975	0.09310	N	1	B;B;B	0.09022	0.002;0.002;0.001	B;B;B	0.15052	0.012;0.012;0.005	T	0.12941	-1.0528	10	0.14656	T	0.56	.	2.5395	0.04722	0.1406:0.2275:0.4399:0.1919	.	9;9;9	E9PAU8;P23141;P23141-2	.;EST1_HUMAN;.	T	9	ENSP00000353720:A9T;ENSP00000355193:A9T;ENSP00000390492:A9T	ENSP00000353720:A9T	A	-	1	0	CES1	54424444	0.000000	0.05858	0.000000	0.03702	0.104000	0.19210	-1.338000	0.02655	-0.684000	0.05183	0.644000	0.83932	GCC	.	.		0.592	CES1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000433285.1	NM_001266		T	55866943	C	T	55866943	3	4	361	1	0	0	0	0	1	0	0	0	3271	739	26	3	1737	3	CES1	16	55866943	Missense_Mutation	SNP	C	TCGA-XR-A8TG-01A-11D-A35Z-10	33871162	55866943	34487810	72	50522										
LCAT	3931	hgsc.bcm.edu	37	chr16	67976467	67976468	+	Frame_Shift_Ins	INS	-	-	CC													0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	tccaccagccctgcgagcttINSgcggtagtactcctcctgct							TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr16:67976467_67976468insCC	ENST00000264005.5	-	5	575_576	c.546_547insGG	c.(544-549)cgcaagfs	p.K183fs	CTC-479C5.17_ENST00000590594.1_lincRNA	NM_000229.1	NP_000220.1	P04180	LCAT_HUMAN	lecithin-cholesterol acyltransferase	183					cholesterol esterification (GO:0034435)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|high-density lipoprotein particle remodeling (GO:0034375)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein metabolic process (GO:0042157)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|regulation of high-density lipoprotein particle assembly (GO:0090107)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|very-low-density lipoprotein particle remodeling (GO:0034372)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)	apolipoprotein A-I binding (GO:0034186)|phosphatidylcholine-sterol O-acyltransferase activity (GO:0004607)			cervix(4)|endometrium(4)|large_intestine(1)|lung(6)|ovary(1)	16		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00418)|Epithelial(162;0.0183)|all cancers(182;0.12)		CCTGCGAGCTTGCGGTAGTACT	0.634																																					p.K183fs		Atlas-INDEL	.											.	LCAT	31	.	0			c.547_548insGG						.																																			SO:0001589	frameshift_variant	3931	exon5			.		CCDS10854.1	16q22.1	2012-10-02			ENSG00000213398	ENSG00000213398	2.3.1.43		6522	protein-coding gene	gene with protein product		606967					Standard	NM_000229		Approved		uc002euy.1	P04180	OTTHUMG00000137551	ENST00000264005.5:c.546_547insGG	chr16.hg19:g.67976467_67976468insCC	ENSP00000264005:p.Lys183fs	146.0	0.0		152.0	45.0	NM_000229	Q53XQ3	Frame_Shift_Ins	INS	ENST00000264005.5	hg19	CCDS10854.1																																																																																			.	.		0.634	LCAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268885.3			CC	67976468	-	CC	67976467	7	5	361	1	0	1	1	0	0	0	0	0	8667	1821	63	0	783	0	LCAT	16	67976467	Frame_Shift_Ins	INS	-	TCGA-XR-A8TG-01A-11D-A35Z-10	12109524	67976467	22378286	73	50523	264	2								
LCAT	3931	hgsc.bcm.edu	37	chr16	67976468	67976468	+	Silent	SNP	G	G	C													0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	tccaccagccctgcgagcttGcggtagtactcctcctgctg							TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr16:67976468G>C	ENST00000264005.5	-	5	575	c.546C>G	c.(544-546)cgC>cgG	p.R182R	CTC-479C5.17_ENST00000590594.1_lincRNA	NM_000229.1	NP_000220.1	P04180	LCAT_HUMAN	lecithin-cholesterol acyltransferase	182			R -> C. {ECO:0000269|PubMed:8318557, ECO:0000269|PubMed:8432868}.		cholesterol esterification (GO:0034435)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|high-density lipoprotein particle remodeling (GO:0034375)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein metabolic process (GO:0042157)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|regulation of high-density lipoprotein particle assembly (GO:0090107)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|very-low-density lipoprotein particle remodeling (GO:0034372)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)	apolipoprotein A-I binding (GO:0034186)|phosphatidylcholine-sterol O-acyltransferase activity (GO:0004607)			cervix(4)|endometrium(4)|large_intestine(1)|lung(6)|ovary(1)	16		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00418)|Epithelial(162;0.0183)|all cancers(182;0.12)		CTGCGAGCTTGCGGTAGTACT	0.637																																					p.R182R		Atlas-SNP	.											.	LCAT	31	.	0			c.C546G						.						57	49	52					16																	67976468		2198	4300	6498	SO:0001819	synonymous_variant	3931	exon5			GAGCTTGCGGTAG		CCDS10854.1	16q22.1	2012-10-02			ENSG00000213398	ENSG00000213398	2.3.1.43		6522	protein-coding gene	gene with protein product		606967					Standard	NM_000229		Approved		uc002euy.1	P04180	OTTHUMG00000137551	ENST00000264005.5:c.546C>G	chr16.hg19:g.67976468G>C		144.0	0.0		145.0	45.0	NM_000229	Q53XQ3	Silent	SNP	ENST00000264005.5	hg19	CCDS10854.1																																																																																			.	.		0.637	LCAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268885.3			C	67976468	G	C	67976468	2	2	361	1	0	0	0	0	0	0	0	1	8667	1306	46	4		4	LCAT	16	67976468	Silent	SNP	G	TCGA-XR-A8TG-01A-11D-A35Z-10	1	67976468	22378285	74	50524	264	2								
PRPF8	10594	hgsc.bcm.edu	37	chr17	1554097	1554097	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	gcaggaggcagggaaacggtCaggcatacaggtcctcccga	15	11	1	0			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr17:1554097C>T	ENST00000572621.1	-	42	7272	c.7007G>A	c.(7006-7008)tGa>tAa	p.*2336*	PRPF8_ENST00000575116.1_5'Flank|PRPF8_ENST00000304992.6_Silent_p.*2336*|RILP_ENST00000301336.6_5'Flank			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	0					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		GGGAAACGGTCAGGCATACAG	0.602																																					p.X2336X		Atlas-SNP	.											PRPF8,NS,carcinoma,0,1	PRPF8	169	.	0			c.G7007A						.						107	88	95					17																	1554097		2203	4300	6503	SO:0001819	synonymous_variant	10594	exon43			AACGGTCAGGCAT	AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231			17340	protein-coding gene	gene with protein product		607300	"PRP8 pre-mRNA processing factor 8 homolog (yeast)", "PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)"	RP13		11468273, 10411133	Standard	NM_006445		Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.7007G>A	chr17.hg19:g.1554097C>T		67.0	0.0		49.0	6.0	NM_006445	O14547|O75965	Silent	SNP	ENST00000572621.1	hg19	CCDS11010.1																																																																																			.	.		0.602	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2			T	1554097	C	T	1554097	2	4	361	1	0	0	0	0	0	0	0	1	12587	837	29	3		3	PRPF8	17	1554097	Silent	SNP	C	TCGA-XR-A8TG-01A-11D-A35Z-10		1554097	79641113	75	50525										
TP53	7157	hgsc.bcm.edu	37	chr17	7574033	7574033	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	gaagcgctcacgcccacggaTctgcagcaacagaggagggg	15	12	2	1			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr17:7574033T>A	ENST00000269305.4	-	10	1183	c.994A>T	c.(994-996)Atc>Ttc	p.I332F	TP53_ENST00000359597.4_Intron|TP53_ENST00000445888.2_Splice_Site_p.I332F|TP53_ENST00000420246.2_3'UTR|TP53_ENST00000455263.2_3'UTR|TP53_ENST00000413465.2_Intron	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	332	Interaction with CARM1.|Interaction with HIPK1. {ECO:0000250}.|Interaction with HIPK2.|Oligomerization.		I -> V (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.I332fs*49(1)|p.?(1)|p.I332V(1)|p.I332fs*5(1)|p.I332fs*13(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CGCCCACGGATCTGCAGCAAC	0.512		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.I332F	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53,NS,carcinoma,0,1	TP53	33396	.	13	Whole gene deletion(8)|Deletion - Frameshift(2)|Substitution - Missense(1)|Unknown(1)|Insertion - Frameshift(1)	bone(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|breast(2)|large_intestine(1)|stomach(1)|ovary(1)	c.A994T						.						45	37	39					17																	7574033		2203	4300	6503	SO:0001630	splice_region_variant	7157	exon10	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	CACGGATCTGCAG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.994-1A>T	chr17.hg19:g.7574033T>A		92.0	0.0		78.0	20.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	15.87	2.961350	0.53400	.	.	ENSG00000141510	ENST00000269305;ENST00000445888;ENST00000396473	D;D	0.95885	-3.84;-3.84	5.43	5.43	0.79202	p53, tetramerisation domain (3);	0.119653	0.56097	D	0.000028	D	0.97417	0.9155	M	0.83012	2.62	0.58432	D	0.999991	D	0.63046	0.992	D	0.65874	0.939	D	0.98034	1.0378	10	0.87932	D	0	-36.4786	13.43	0.61049	0.0:0.0:0.0:1.0	.	332	P04637	P53_HUMAN	F	332;332;321	ENSP00000269305:I332F;ENSP00000391478:I332F	ENSP00000269305:I332F	I	-	1	0	TP53	7514758	1.000000	0.71417	1.000000	0.80357	0.150000	0.21749	1.211000	0.32382	2.061000	0.61500	0.459000	0.35465	ATC	.	.		0.512	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	Missense_Mutation	A	7574033	T	A	7574033	5	1	361	1	0	0	0	0	0	0	1	0	16396	1449	50	4	195	4	TP53	17	7574033	Splice_Site	SNP	T	TCGA-XR-A8TG-01A-11D-A35Z-10	6019936	7574033	73621177	76	50526										
TP53	7157	hgsc.bcm.edu	37	chr17	7577538	7577538	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	tgatggtgaggatgggcctcCggttcatgccgcccatgcag	15	11	1	2	rs11540652		TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr17:7577538C>T	ENST00000269305.4	-	7	932	c.743G>A	c.(742-744)cGg>cAg	p.R248Q	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.R248Q|TP53_ENST00000445888.2_Missense_Mutation_p.R248Q|TP53_ENST00000420246.2_Missense_Mutation_p.R248Q|TP53_ENST00000455263.2_Missense_Mutation_p.R248Q|TP53_ENST00000413465.2_Missense_Mutation_p.R248Q	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	248	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.		NR -> IP (in a sporadic cancer; somatic mutation).|NR -> KW (in sporadic cancers; somatic mutation).|R -> C (in a sporadic cancer; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:7682763}.|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs11540652). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:2263646, ECO:0000269|PubMed:7682763, ECO:0000269|PubMed:7887414}.|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:8829627}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R248Q(580)|p.R248L(75)|p.R248P(19)|p.R155Q(18)|p.0?(8)|p.?(5)|p.R155L(3)|p.R155P(2)|p.N247_R248delNR(2)|p.R248fs*16(2)|p.M246_P250delMNRRP(2)|p.R248_P250delRRP(1)|p.unknown(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*96(1)|p.R248fs*>39(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GATGGGCCTCCGGTTCATGCC	0.572	R248Q(BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(HCC1143_BREAST)|R248Q(HCC70_BREAST)|R248Q(HEC1A_ENDOMETRIUM)|R248Q(HS683_CENTRAL_NERVOUS_SYSTEM)|R248Q(HSC4_UPPER_AERODIGESTIVE_TRACT)|R248Q(KASUMI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KYSE150_OESOPHAGUS)|R248Q(MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NAMALWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NCIH211_LUNG)|R248Q(NCIN87_STOMACH)|R248Q(NIHOVCAR3_OVARY)|R248Q(NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(P12ICHIKAWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(PANC0203_PANCREAS)|R248Q(PC14_LUNG)|R248Q(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(RT112_URINARY_TRACT)|R248Q(SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SF295_CENTRAL_NERVOUS_SYSTEM)|R248Q(SKUT1_SOFT_TISSUE)|R248Q(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SW1463_LARGE_INTESTINE)|R248Q(WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.R248Q	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,adenocarcinoma,0,4	TP53	33396	.	725	Substitution - Missense(698)|Whole gene deletion(8)|Deletion - In frame(7)|Unknown(6)|Insertion - Frameshift(3)|Deletion - Frameshift(2)|Complex - compound substitution(1)	large_intestine(138)|breast(83)|haematopoietic_and_lymphoid_tissue(74)|lung(71)|upper_aerodigestive_tract(63)|central_nervous_system(46)|oesophagus(37)|urinary_tract(37)|ovary(36)|stomach(35)|endometrium(23)|skin(18)|prostate(11)|bone(10)|biliary_tract(9)|liver(9)|pancreas(7)|vulva(3)|kidney(3)|cervix(3)|peritoneum(2)|thyroid(2)|soft_tissue(1)|pituitary(1)|adrenal_gland(1)|small_intestine(1)|thymus(1)	c.G743A	GRCh37	CM920675	TP53	M	rs11540652	.	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	152	112	126	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	743,743,743,743,347,347,347	3.7	1	17	dbSNP_120	126	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense,missense	TP53	NM_000546.4,NM_001126112.1,NM_001126113.1,NM_001126114.1,NM_001126115.1,NM_001126116.1,NM_001126117.1	43,43,43,43,43,43,43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	248/394,248/394,248/347,248/342,116/262,116/210,116/215	7577538	1,13005	2203	4300	6503	SO:0001583	missense	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GGCCTCCGGTTCA	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.743G>A	chr17.hg19:g.7577538C>T	ENSP00000269305:p.Arg248Gln	68.0	0.0		49.0	11.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.822907	0.90873	0.0	1.16E-4	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99864	-7.28;-7.28;-7.28;-7.28;-7.28;-7.28;-7.28;-7.28	4.62	3.65	0.41850	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99840	0.9927	M	0.88640	2.97	0.58432	A	0.999994	D;D;D;D;D;D	0.89917	1.0;0.994;1.0;1.0;1.0;1.0	D;P;D;D;D;D	0.91635	0.996;0.882;0.999;0.995;0.996;0.995	D	0.96819	0.9602	9	0.72032	D	0.01	-9.5643	10.6687	0.45745	0.0:0.9059:0.0:0.0941	rs11540652;rs11540652	248;248;155;248;248;248	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	Q	248;248;248;248;248;248;237;155;116;155	ENSP00000410739:R248Q;ENSP00000352610:R248Q;ENSP00000269305:R248Q;ENSP00000398846:R248Q;ENSP00000391127:R248Q;ENSP00000391478:R248Q;ENSP00000425104:R116Q;ENSP00000423862:R155Q	ENSP00000269305:R248Q	R	-	2	0	TP53	7518263	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	5.884000	0.69729	1.305000	0.44909	0.462000	0.41574	CGG	.	.		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7577538	C	T	7577538	3	4	361	1	0	0	0	0	1	0	0	0	16396	652	23	1	547	1	TP53	17	7577538	Missense_Mutation	SNP	C	TCGA-XR-A8TG-01A-11D-A35Z-10	3505	7577538	73617672	77	50527										
KRT38	8687	hgsc.bcm.edu	37	chr17	39594488	39594488	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	agctgctcctccacgttgctGatgaggctctgcatctgggc	12	13	2	2			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr17:39594488G>A	ENST00000246646.3	-	6	1097	c.1098C>T	c.(1096-1098)atC>atT	p.I366I		NM_006771.3	NP_006762.3	O76015	KRT38_HUMAN	keratin 38	366	Coil 2.|Rod.					extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	29		Breast(137;0.000496)				CCACGTTGCTGATGAGGCTCT	0.597																																					p.I366I		Atlas-SNP	.											.	KRT38	63	.	0			c.C1098T						.						68	62	64					17																	39594488		2203	4300	6503	SO:0001819	synonymous_variant	8687	exon6			GTTGCTGATGAGG	Y16794	CCDS11392.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000171360	ENSG00000171360		"-", "Intermediate filaments type I, keratins (acidic)"	6456	protein-coding gene	gene with protein product		604542	"keratin, hair, acidic, 8"	KRTHA8		9756910, 16831889	Standard	NM_006771		Approved		uc002hwq.1	O76015	OTTHUMG00000133439	ENST00000246646.3:c.1098C>T	chr17.hg19:g.39594488G>A		49.0	0.0		82.0	29.0	NM_006771	A2RRM5|Q6A164	Silent	SNP	ENST00000246646.3	hg19	CCDS11392.1																																																																																			.	.		0.597	KRT38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257307.2	NM_006771		A	39594488	G	A	39594488	2	1	361	1	0	0	0	0	0	0	0	1	8484	1280	45	3		3	KRT38	17	39594488	Silent	SNP	G	TCGA-XR-A8TG-01A-11D-A35Z-10	32016950	39594488	41600722	78	50528										
C17orf71	55181	hgsc.bcm.edu	37	chr17	57289158	57289158	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	tgtgtgcacaaatttcactcAttacctaaatcaggtagcta	6	9	3	0			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr17:57289158A>G	ENST00000543872.2	+	2	2010	c.1746A>G	c.(1744-1746)tcA>tcG	p.S582S	SMG8_ENST00000300917.5_Silent_p.S582S|CTD-2510F5.6_ENST00000577660.1_Intron|SMG8_ENST00000580498.1_Intron|SMG8_ENST00000578922.1_Silent_p.S582S			Q8ND04	SMG8_HUMAN	SMG8 nonsense mediated mRNA decay factor	582					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of protein kinase activity (GO:0045859)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)				NS(1)|breast(5)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(1)	33						AATTTCACTCATTACCTAAAT	0.358																																					p.S582S		Atlas-SNP	.											.	SMG8	79	.	0			c.A1746G						.						86	78	81					17																	57289158		2203	4300	6503	SO:0001819	synonymous_variant	55181	exon1			TCACTCATTACCT	AL834490	CCDS11615.1	17q23.2	2013-07-02	2013-07-02	2011-06-21					25551	protein-coding gene	gene with protein product		613175	"chromosome 17 open reading frame 71", "smg-8 homolog, nonsense mediated mRNA decay factor (C. elegans)"	C17orf71		19417104	Standard	NM_018149		Approved	FLJ10587, FLJ23205	uc002ixi.3	Q8ND04		ENST00000543872.2:c.1746A>G	chr17.hg19:g.57289158A>G		29.0	0.0		36.0	17.0	NM_018149	Q8N5U5|Q8TDN0|Q9H5P5|Q9NVQ1	Silent	SNP	ENST00000543872.2	hg19	CCDS11615.1																																																																																			.	.		0.358	SMG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445960.2	NM_018149		G	57289158	A	G	57289158	2	3	361	1	0	0	0	0	0	0	0	1	1880	204	8	2		2	C17orf71	17	57289158	Silent	SNP	A	TCGA-XR-A8TG-01A-11D-A35Z-10	17694670	57289158	23906052	79	50529										
CD300E	342510	hgsc.bcm.edu	37	chr17	72613261	72613261	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	tgaggggagctcttacctggGgaaacatacaccctaaccag	11	11	1	1			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr17:72613261G>A	ENST00000328630.3	-	2	424	c.384C>T	c.(382-384)tcC>tcT	p.S128S	CD300E_ENST00000392619.1_Silent_p.S155S|CD300E_ENST00000426295.2_Silent_p.S169S			Q496F6	CLM2_HUMAN	CD300e molecule	128					innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|kidney(3)|large_intestine(4)|lung(4)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	19						TCTTACCTGGGGAAACATACA	0.542																																					p.S128S		Atlas-SNP	.											.	CD300E	70	.	0			c.C384T						.						91	82	85					17																	72613261		2203	4300	6503	SO:0001819	synonymous_variant	342510	exon2			ACCTGGGGAAACA	BX648376	CCDS11702.1	17q25.1	2013-01-11	2006-03-28	2006-02-22	ENSG00000186407	ENSG00000186407		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	28874	protein-coding gene	gene with protein product		609801	"CD300 antigen like family member E", "CD300e antigen"	CD300LE		15549731, 15557162	Standard	NM_181449		Approved	IREM2, CLM2	uc002jlb.2	Q496F6	OTTHUMG00000067605	ENST00000328630.3:c.384C>T	chr17.hg19:g.72613261G>A		69.0	0.0		90.0	39.0	NM_181449	B4DNS1|Q7Z7I3	Silent	SNP	ENST00000328630.3	hg19	CCDS11702.1																																																																																			.	.		0.542	CD300E-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_181449		A	72613261	G	A	72613261	2	1	361	1	0	0	0	0	0	0	0	1	3000	1219	43	3		3	CD300E	17	72613261	Silent	SNP	G	TCGA-XR-A8TG-01A-11D-A35Z-10	15324103	72613261	8581949	80	50530										
ITGB4	3691	hgsc.bcm.edu	37	chr17	73738810	73738810	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	cactgccaccctcggccgccGcctggtaaacatcaccatca	7	19	2	0			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr17:73738810G>T	ENST00000200181.3	+	25	3117	c.2930G>T	c.(2929-2931)cGc>cTc	p.R977L	ITGB4_ENST00000339591.3_Missense_Mutation_p.R977L|ITGB4_ENST00000579662.1_Missense_Mutation_p.R977L|ITGB4_ENST00000450894.3_Missense_Mutation_p.R977L|ITGB4_ENST00000449880.2_Missense_Mutation_p.R977L	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	977					amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			CTCGGCCGCCGCCTGGTAAAC	0.647																																					p.R977L		Atlas-SNP	.											.	ITGB4	165	.	0			c.G2930T						.						37	33	34					17																	73738810		2202	4298	6500	SO:0001583	missense	3691	exon25			GCCGCCGCCTGGT		CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"CD molecules", "Integrins", "Fibronectin type III domain containing"	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.2930G>T	chr17.hg19:g.73738810G>T	ENSP00000200181:p.Arg977Leu	28.0	0.0		47.0	16.0	NM_001005731	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Missense_Mutation	SNP	ENST00000200181.3	hg19	CCDS11727.1	.	.	.	.	.	.	.	.	.	.	G	15.09	2.730858	0.48939	.	.	ENSG00000132470	ENST00000200181;ENST00000339591;ENST00000449880	T;T;T	0.75589	-0.95;-0.9;-0.9	5.34	5.34	0.76211	.	0.139500	0.46758	D	0.000270	T	0.74876	0.3774	L	0.27053	0.805	0.48901	D	0.99972	D;D;D	0.60160	0.987;0.977;0.977	P;P;P	0.59487	0.858;0.725;0.725	T	0.77675	-0.2499	10	0.87932	D	0	.	12.4566	0.55708	0.0767:0.0:0.9233:0.0	.	977;977;977	P16144-3;A0AVL6;P16144	.;.;ITB4_HUMAN	L	977	ENSP00000200181:R977L;ENSP00000344079:R977L;ENSP00000400217:R977L	ENSP00000200181:R977L	R	+	2	0	ITGB4	71250405	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	4.803000	0.62546	2.546000	0.85860	0.556000	0.70494	CGC	.	.		0.647	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1			T	73738810	G	T	73738810	3	4	361	1	0	0	0	0	1	0	0	0	7906	1087	38	1	3024	1	ITGB4	17	73738810	Missense_Mutation	SNP	G	TCGA-XR-A8TG-01A-11D-A35Z-10	1125549	73738810	7456400	81	50531										
ACAA2	10449	hgsc.bcm.edu	37	chr18	47329197	47329197	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	tccgtaagctccaaagggcgTtcgcttagcagcaactacaa	9	12	0	0			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr18:47329197T>C	ENST00000285093.10	-	2	518	c.43A>G	c.(43-45)Acg>Gcg	p.T15A	ACAA2_ENST00000589432.1_5'UTR|RP11-886H22.1_ENST00000590532.2_3'UTR|ACAA2_ENST00000587994.1_Missense_Mutation_p.T12A	NM_006111.2	NP_006102.2	P42765	THIM_HUMAN	acetyl-CoA acyltransferase 2	15					cellular response to hypoxia (GO:0071456)|cholesterol biosynthetic process (GO:0006695)|fatty acid metabolic process (GO:0006631)|negative regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902109)|negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901029)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	acetyl-CoA C-acyltransferase activity (GO:0003988)|poly(A) RNA binding (GO:0044822)			large_intestine(2)|lung(7)|ovary(1)	10						CCAAAGGGCGTTCGCTTAGCA	0.453																																					p.T15A		Atlas-SNP	.											.	ACAA2	29	.	0			c.A43G						.						104	95	98					18																	47329197		2203	4300	6503	SO:0001583	missense	10449	exon2			AGGGCGTTCGCTT	D16294	CCDS11939.1	18q21	2010-04-30	2010-04-30		ENSG00000167315	ENSG00000167315	2.3.1.16		83	protein-coding gene	gene with protein product	"mitochondrial 3-oxoacyl-Coenzyme A thiolase"	604770	"acetyl-Coenzyme A acyltransferase 2"			8241273	Standard	NM_006111		Approved	DSAEC	uc002ldw.4	P42765	OTTHUMG00000132667	ENST00000285093.10:c.43A>G	chr18.hg19:g.47329197T>C	ENSP00000285093:p.Thr15Ala	95.0	0.0		179.0	54.0	NM_006111	Q9BUT6	Missense_Mutation	SNP	ENST00000285093.10	hg19	CCDS11939.1	.	.	.	.	.	.	.	.	.	.	T	25.4	4.630287	0.87660	.	.	ENSG00000167315	ENST00000285093	D	0.96300	-3.97	5.64	5.64	0.86602	Thiolase-like, subgroup (1);Thiolase, N-terminal (1);Thiolase-like (1);	0.000000	0.85682	D	0.000000	D	0.98836	0.9607	H	0.97707	4.06	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.78314	0.99;0.991	D	0.99609	1.0980	10	0.87932	D	0	-23.5008	15.535	0.75996	0.0:0.0:0.0:1.0	.	15;15	B2RB23;P42765	.;THIM_HUMAN	A	15	ENSP00000285093:T15A	ENSP00000285093:T15A	T	-	1	0	ACAA2	45583195	1.000000	0.71417	0.819000	0.32651	0.779000	0.44077	7.911000	0.87458	2.149000	0.67028	0.533000	0.62120	ACG	.	.		0.453	ACAA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255921.2	NM_006111		C	47329197	T	C	47329197	3	2	361	1	0	0	0	0	1	0	0	0	105	1725	60	2	1186	2	ACAA2	18	47329197	Missense_Mutation	SNP	T	TCGA-XR-A8TG-01A-11D-A35Z-10		47329197	30748051	82	50532										
VPS4B	9525	hgsc.bcm.edu	37	chr18	61067937	61067937	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	cctccaaggtgttctcttgcCtaaaatttagatttagaaaa	6	8	1	2			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr18:61067937C>A	ENST00000238497.5	-	6	688		c.e6-1		VPS4B_ENST00000591383.1_Splice_Site	NM_004869.3	NP_004860.2	O75351	VPS4B_HUMAN	vacuolar protein sorting 4 homolog B (S. cerevisiae)						ATP catabolic process (GO:0006200)|cell cycle (GO:0007049)|cell division (GO:0051301)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|intracellular cholesterol transport (GO:0032367)|membrane organization (GO:0061024)|positive regulation of viral release from host cell (GO:1902188)|potassium ion transport (GO:0006813)|protein transport (GO:0015031)|regulation of viral process (GO:0050792)|response to lipid (GO:0033993)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|nucleus (GO:0005634)|vacuolar membrane (GO:0005774)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)			breast(1)|large_intestine(3)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	13						GTTCTCTTGCCTAAAATTTAG	0.378																																					.		Atlas-SNP	.											.	VPS4B	33	.	0			c.485-1G>T						.						64	64	64					18																	61067937		2203	4300	6503	SO:0001630	splice_region_variant	9525	exon7			TCTTGCCTAAAAT	AF038960	CCDS11983.1	18q21.33	2010-04-21	2006-04-04	2002-06-14	ENSG00000119541	ENSG00000119541		"ATPases / AAA-type"	10895	protein-coding gene	gene with protein product		609983	"suppressor of K+ transport defect 1", "vacuolar protein sorting 4B (yeast)"	SKD1		11563910	Standard	XM_006722582		Approved	VPS4-2, SKD1B	uc002lix.3	O75351	OTTHUMG00000132790	ENST00000238497.5:c.485-1G>T	chr18.hg19:g.61067937C>A		85.0	0.0		106.0	32.0	NM_004869	Q69HW4|Q9GZS7	Splice_Site	SNP	ENST00000238497.5	hg19	CCDS11983.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.647207	0.87958	.	.	ENSG00000119541	ENST00000238497	.	.	.	5.8	5.8	0.92144	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.418	0.99029	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	VPS4B	59218917	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.692000	0.84203	2.902000	0.99343	0.650000	0.86243	.	.	.		0.378	VPS4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256198.2	NM_004869	Intron	A	61067937	C	A	61067937	5	1	361	1	0	0	0	0	0	0	1	0	17228	695	24	3	874	3	VPS4B	18	61067937	Splice_Site	SNP	C	TCGA-XR-A8TG-01A-11D-A35Z-10	13738740	61067937	17009311	83	50533										
SHD	56961	hgsc.bcm.edu	37	chr19	4288320	4288320	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	aggcagctacctagtgcggcTcagtgagaccaacccccagg	12	14	1	1			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr19:4288320T>G	ENST00000543264.2	+	5	2260	c.797T>G	c.(796-798)cTc>cGc	p.L266R	SHD_ENST00000599689.1_Intron	NM_020209.3	NP_064594.3	Q96IW2	SHD_HUMAN	Src homology 2 domain containing transforming protein D	266	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.									breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|stomach(1)	14				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0337)|STAD - Stomach adenocarcinoma(1328;0.18)		CTAGTGCGGCTCAGTGAGACC	0.582																																					p.L266R		Atlas-SNP	.											.	SHD	33	.	0			c.T797G						.						84	71	75					19																	4288320		2203	4300	6503	SO:0001583	missense	56961	exon5			TGCGGCTCAGTGA	BC007206	CCDS12125.1	19p13.3	2013-02-14				ENSG00000105251		"SH2 domain containing"	30633	protein-coding gene	gene with protein product		610481				9315092	Standard	NM_020209		Approved		uc002lzw.2	Q96IW2		ENST00000543264.2:c.797T>G	chr19.hg19:g.4288320T>G	ENSP00000446058:p.Leu266Arg	76.0	0.0		109.0	31.0	NM_020209	Q96NC2	Missense_Mutation	SNP	ENST00000543264.2	hg19	CCDS12125.1	.	.	.	.	.	.	.	.	.	.	T	15.90	2.970664	0.53614	.	.	ENSG00000105251	ENST00000543264;ENST00000221852	D	0.88354	-2.37	4.91	3.85	0.44370	SH2 motif (5);	0.314114	0.29609	N	0.011677	T	0.77239	0.4101	N	0.12502	0.225	0.38167	D	0.939229	B	0.12630	0.006	B	0.25759	0.063	T	0.72623	-0.4237	10	0.33141	T	0.24	-20.2727	7.2661	0.26229	0.2933:0.0:0.0:0.7067	.	266	Q96IW2	SHD_HUMAN	R	266;181	ENSP00000446058:L266R	ENSP00000221852:L181R	L	+	2	0	SHD	4239320	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	5.004000	0.63966	2.075000	0.62263	0.454000	0.30748	CTC	.	.		0.582	SHD-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458082.1	NM_020209		G	4288320	T	G	4288320	3	3	361	1	0	0	0	0	1	0	0	0	14290	1551	54	5	815	5	SHD	19	4288320	Missense_Mutation	SNP	T	TCGA-XR-A8TG-01A-11D-A35Z-10		4288320	54840663	84	50534										
KANK2	25959	hgsc.bcm.edu	37	chr19	11304443	11304444	+	Missense_Mutation	DNP	GG	GG	CA													0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	atactgagggtagaagccacGgccgcagtaggaataggctg							TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr19:11304443_11304444GG>CA	ENST00000586659.1	-	4	626_627	c.312_313CC>TG	c.(310-315)ggCCgt>ggTGgt	p.R105G	KANK2_ENST00000589894.1_Missense_Mutation_p.R105G|KANK2_ENST00000432929.2_Missense_Mutation_p.R105G|KANK2_ENST00000589359.1_Missense_Mutation_p.R105G|KANK2_ENST00000355150.5_Missense_Mutation_p.R105G			Q63ZY3	KANK2_HUMAN	KN motif and ankyrin repeat domains 2	105					apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)				endometrium(2)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						TAGAAGCCACGGCCGCAGTAGG	0.668																																					p.R105G|p.G104G		Atlas-SNP	.											.	KANK2	47	.	0			c.C313G|c.C312T						.																																			SO:0001583	missense	25959	exon2			AGCCACGGCCGCA|GCCACGGCCGCAG	AK000011	CCDS12255.1, CCDS54219.1	19p13.2	2013-01-10	2008-01-29	2008-01-29		ENSG00000197256		"KN motif and ankyrin repeat domain containing", "Ankyrin repeat domain containing"	29300	protein-coding gene	gene with protein product		614610	"matrix-remodelling associated 3", "ankyrin repeat domain 25"	MXRA3, ANKRD25		10819331, 17996375, 19554261	Standard	NM_015493		Approved	KIAA1518	uc002mqm.3	Q63ZY3		ENST00000586659.1:c.312_313delinsCA	chr19.hg19:g.11304443_11304444delinsCA	ENSP00000465650:p.Arg105Gly	129.0|128.0	0.0		242.0|241.0	34.0|31.0	NM_015493	B0I1P4|Q3KQZ3|Q6GUF5|Q9H8S4|Q9NUP0|Q9P210	Missense_Mutation|Silent	SNP	ENST00000586659.1	hg19	CCDS12255.1																																																																																			.	.		0.668	KANK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453066.2	NM_015493		CA	11304444	GG	CA	11304443	3	2	361	1	0	0	0	0	1	0	0	0	7986	1116	39	4	2306	4	KANK2	19	11304443	Missense_Mutation	DNP	GG	TCGA-XR-A8TG-01A-11D-A35Z-10	7016123	11304443	47824540	85	50535										
CILP2	148113	hgsc.bcm.edu	37	chr19	19654688	19654688	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	ctctgtgcgccgtctggagaGaagggagattcactgccctg	14	11	3	2			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr19:19654688G>T	ENST00000291495.5	+	8	1419	c.1334G>T	c.(1333-1335)aGa>aTa	p.R445I	CILP2_ENST00000586018.1_Missense_Mutation_p.R451I	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	445						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				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						CGTCTGGAGAGAAGGGAGATT	0.706																																					p.R445I		Atlas-SNP	.											.	CILP2	84	.	0			c.G1334T						.						53	50	51					19																	19654688		2201	4300	6501	SO:0001583	missense	148113	exon8			TGGAGAGAAGGGA	AF542080	CCDS12405.1	19p13.11	2013-01-14				ENSG00000160161		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	24213	protein-coding gene	gene with protein product		612419				12477932	Standard	NM_153221		Approved	MGC45771	uc002nmv.4	Q8IUL8		ENST00000291495.5:c.1334G>T	chr19.hg19:g.19654688G>T	ENSP00000291495:p.Arg445Ile	121.0	0.0		123.0	11.0	NM_153221	Q6NV88|Q8N4A6|Q8WV21	Missense_Mutation	SNP	ENST00000291495.5	hg19	CCDS12405.1	.	.	.	.	.	.	.	.	.	.	G	11.49	1.655304	0.29425	.	.	ENSG00000160161	ENST00000291495	T	0.51574	0.7	4.21	0.489	0.16854	.	0.425372	0.24483	N	0.038137	T	0.22859	0.0552	N	0.08118	0	0.21325	N	0.999725	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.17018	-1.0383	10	0.41790	T	0.15	-2.2175	7.4391	0.27172	0.0:0.4986:0.3418:0.1596	.	445;445	B2RAJ0;Q8IUL8	.;CILP2_HUMAN	I	445	ENSP00000291495:R445I	ENSP00000291495:R445I	R	+	2	0	CILP2	19515688	0.002000	0.14202	0.709000	0.30452	0.612000	0.37316	0.168000	0.16622	0.734000	0.32515	0.423000	0.28283	AGA	.	.		0.706	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221		T	19654688	G	T	19654688	3	4	361	1	0	0	0	0	1	0	0	0	3432	942	33	3	1364	3	CILP2	19	19654688	Missense_Mutation	SNP	G	TCGA-XR-A8TG-01A-11D-A35Z-10	8350245	19654688	39474295	86	50536										
ZNF43	7594	hgsc.bcm.edu	37	chr19	21992333	21992333	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	atttgaaaagttttttttcaGtatggcttatcttatgtctg	7	4	3	1			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr19:21992333G>T	ENST00000354959.4	-	4	675	c.506C>A	c.(505-507)aCt>aAt	p.T169N	ZNF43_ENST00000595461.1_Missense_Mutation_p.T163N|ZNF43_ENST00000598381.1_Missense_Mutation_p.T163N|ZNF43_ENST00000594012.1_Missense_Mutation_p.T163N	NM_003423.3	NP_003414.2	P17038	ZNF43_HUMAN	zinc finger protein 43	169					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2)	51		Renal(1328;0.000219)|Hepatocellular(1079;0.121)		GBM - Glioblastoma multiforme(1328;5.97e-05)|STAD - Stomach adenocarcinoma(1328;0.0127)		TTTTTTTTCAGTATGGCTTAT	0.318																																					p.T178N		Atlas-SNP	.											.	ZNF43	152	.	0			c.C533A						.						37	37	37					19																	21992333		2201	4297	6498	SO:0001583	missense	7594	exon4			TTTTCAGTATGGC	X59244	CCDS12413.2, CCDS59367.1, CCDS74321.1	19p13.1-p12	2013-01-08	2006-05-11		ENSG00000198521	ENSG00000198521		"Zinc fingers, C2H2-type", "-"	13109	protein-coding gene	gene with protein product		603972	"zinc finger protein 39-like 1 (KOX 27)", "zinc finger protein 43 (HTF6)"	ZNF39L1		1711675	Standard	NM_001256649		Approved	HTF6, KOX27	uc031rka.1	P17038	OTTHUMG00000128543	ENST00000354959.4:c.506C>A	chr19.hg19:g.21992333G>T	ENSP00000347045:p.Thr169Asn	101.0	0.0		123.0	50.0	NM_001256653	A8K5N8|P28160|Q53XQ2|Q5H9T3|Q96DG1	Missense_Mutation	SNP	ENST00000354959.4	hg19	CCDS12413.2	.	.	.	.	.	.	.	.	.	.	G	10.08	1.251617	0.22880	.	.	ENSG00000198521	ENST00000397148;ENST00000354959	T	0.26067	1.76	1.5	-1.72	0.08107	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.41096	0.1144	M	0.70275	2.135	0.09310	N	1	D	0.63880	0.993	D	0.65140	0.932	T	0.25847	-1.0120	9	0.52906	T	0.07	.	6.7676	0.23576	0.2642:0.0:0.7358:0.0	.	169	P17038	ZNF43_HUMAN	N	168;169	ENSP00000347045:T169N	ENSP00000347045:T169N	T	-	2	0	ZNF43	21784173	0.003000	0.15002	0.000000	0.03702	0.004000	0.04260	0.566000	0.23593	-0.555000	0.06142	-0.350000	0.07774	ACT	.	.		0.318	ZNF43-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250380.2	NM_003423		T	21992333	G	T	21992333	3	4	361	1	0	0	0	0	1	0	0	0	17918	1029	36	3	1927	3	ZNF43	19	21992333	Missense_Mutation	SNP	G	TCGA-XR-A8TG-01A-11D-A35Z-10	2337645	21992333	37136650	87	50537										
FLT3LG	2323	hgsc.bcm.edu	37	chr19	49983824	49983824	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	cacaggtgccccccgtccccAgtccccaggacctgctgctt	9	20	0	0			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr19:49983824A>T	ENST00000594009.1	+	7	755	c.676A>T	c.(676-678)Agt>Tgt	p.S226C	CTD-3148I10.15_ENST00000595815.1_RNA|FLT3LG_ENST00000597551.1_Missense_Mutation_p.S226C|FLT3LG_ENST00000595510.1_Missense_Mutation_p.S144C|FLT3LG_ENST00000596435.1_Missense_Mutation_p.S208C|FLT3LG_ENST00000204637.2_Missense_Mutation_p.S144C|FLT3LG_ENST00000600429.1_Missense_Mutation_p.S226C|CTD-3148I10.9_ENST00000599536.1_Intron	NM_001204503.1	NP_001191432.1	P49771	FLT3L_HUMAN	fms-related tyrosine kinase 3 ligand	226					embryonic hemopoiesis (GO:0035162)|lymphocyte differentiation (GO:0030098)|positive regulation of cell proliferation (GO:0008284)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of protein phosphorylation (GO:0001934)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|intrinsic component of external side of plasma membrane (GO:0031233)|membrane (GO:0016020)	receptor binding (GO:0005102)			large_intestine(2)|lung(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	10		all_lung(116;1.62e-07)|Lung NSC(112;8.47e-07)|all_neural(266;0.0381)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00154)|GBM - Glioblastoma multiforme(486;0.0246)		CCCCGTCCCCAGTCCCCAGGA	0.657																																					p.S226C		Atlas-SNP	.											.	FLT3LG	22	.	0			c.A676T						.						37	34	35					19																	49983824		2203	4300	6503	SO:0001583	missense	2323	exon7			GTCCCCAGTCCCC	U04806	CCDS12767.1, CCDS62753.1	19q13.3	2014-01-30				ENSG00000090554		"Endogenous ligands"	3766	protein-coding gene	gene with protein product		600007				8145851, 7824267	Standard	NM_001204502		Approved		uc010yau.2	P49771		ENST00000594009.1:c.676A>T	chr19.hg19:g.49983824A>T	ENSP00000469613:p.Ser226Cys	84.0	0.0		80.0	34.0	NM_001204503	A0AVC2|B9EGH2|Q05C96	Missense_Mutation	SNP	ENST00000594009.1	hg19	CCDS12767.1	.	.	.	.	.	.	.	.	.	.	A	14.85	2.657994	0.47467	.	.	ENSG00000090554	ENST00000204637	.	.	.	4.22	-5.81	0.02340	.	1.159090	0.06320	N	0.704297	T	0.22666	0.0547	N	0.22421	0.69	0.09310	N	0.999999	B	0.09022	0.002	B	0.04013	0.001	T	0.21177	-1.0253	9	0.51188	T	0.08	-11.0515	2.7293	0.05222	0.2713:0.4365:0.1769:0.1154	.	226	P49771	FLT3L_HUMAN	C	226	.	ENSP00000204637:S226C	S	+	1	0	FLT3LG	54675636	0.000000	0.05858	0.000000	0.03702	0.222000	0.24845	-0.222000	0.09190	-1.196000	0.02676	-0.496000	0.04628	AGT	.	.		0.657	FLT3LG-007	KNOWN	alternative_3_UTR|alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465305.1			T	49983824	A	T	49983824	3	4	361	1	0	0	0	0	1	0	0	0	5951	188	7	4	702	4	FLT3LG	19	49983824	Missense_Mutation	SNP	A	TCGA-XR-A8TG-01A-11D-A35Z-10	27991491	49983824	9145159	88	50538										
ZNF444	55311	hgsc.bcm.edu	37	chr19	56669904	56669904	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	gggtcgtcagcaacgagggtGcctcaggatgtgacgcaggg	18	9	2	1			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr19:56669904G>A	ENST00000337080.3	+	4	706	c.339G>A	c.(337-339)gtG>gtA	p.V113V	ZNF444_ENST00000592171.1_3'UTR|ZNF444_ENST00000592949.1_Silent_p.V113V	NM_001253792.1|NM_018337.3	NP_001240721.1|NP_060807.2	Q8N0Y2	ZN444_HUMAN	zinc finger protein 444	113					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(1)|endometrium(1)|lung(5)	7		Colorectal(82;3.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0531)		CAACGAGGGTGCCTCAGGATG	0.597																																					p.V113V		Atlas-SNP	.											.	ZNF444	15	.	0			c.G339A						.						83	69	74					19																	56669904		2203	4300	6503	SO:0001819	synonymous_variant	55311	exon4			GAGGGTGCCTCAG	AB052954	CCDS12939.1, CCDS59426.1	19q13.43	2013-01-09			ENSG00000167685	ENSG00000167685		"-", "Zinc fingers, C2H2-type"	16052	protein-coding gene	gene with protein product		607874				11978792, 19760602	Standard	NM_001253792		Approved	ZSCAN17, FLJ11137, EZF2	uc002qmm.3	Q8N0Y2		ENST00000337080.3:c.339G>A	chr19.hg19:g.56669904G>A		139.0	0.0		195.0	8.0	NM_001253792	Q8TEQ9|Q8WU35|Q9NUU1	Silent	SNP	ENST00000337080.3	hg19	CCDS12939.1																																																																																			.	.		0.597	ZNF444-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457503.1	NM_018337		A	56669904	G	A	56669904	2	1	361	1	0	0	0	0	0	0	0	1	17932	1306	46	3		3	ZNF444	19	56669904	Silent	SNP	G	TCGA-XR-A8TG-01A-11D-A35Z-10	6686080	56669904	2459079	89	50539										
SEC23B	10483	hgsc.bcm.edu	37	chr20	18491519	18491519	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	tcatccagcagaatgaagaaCgggatggtgtgcgttttagt	13	6	1	3	rs121918222		TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr20:18491519C>T	ENST00000336714.3	+	2	472	c.40C>T	c.(40-42)Cgg>Tgg	p.R14W	SEC23B_ENST00000377475.3_Missense_Mutation_p.R14W|SEC23B_ENST00000262544.2_Missense_Mutation_p.R14W|SEC23B_ENST00000377465.1_Missense_Mutation_p.R14W	NM_006363.4|NM_032985.4|NM_032986.3	NP_006354.2|NP_116780.1|NP_116781.1	Q15437	SC23B_HUMAN	Sec23 homolog B (S. cerevisiae)	14			R -> W (in CDAN2; the mutant protein is unstable with less than 5% of protein detectable compared to wild-type). {ECO:0000269|PubMed:19561605, ECO:0000269|PubMed:19621418}.		ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	32						GAATGAAGAACGGGATGGTGT	0.448																																					p.R14W		Atlas-SNP	.											.	SEC23B	70	.	0			c.C40T						.	C	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	155	138	144	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	40,40,40,40,40	4.1	1	20	dbSNP_133	144	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense,missense,missense	SEC23B	NM_001172745.1,NM_001172746.1,NM_006363.4,NM_032985.4,NM_032986.3	101,101,101,101,101	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	14/768,14/750,14/768,14/768,14/768	18491519	3,13003	2203	4300	6503	SO:0001583	missense	10483	exon2			GAAGAACGGGATG	X97065	CCDS13137.1	20p11.23	2010-02-09	2001-11-28		ENSG00000101310	ENSG00000101310			10702	protein-coding gene	gene with protein product		610512	"Sec23 (S. cerevisiae) homolog B", "congenital dyserythropoietic anemia, type II"	CDAN2		8898360, 10329445, 19621418	Standard	NM_032985		Approved	CDA-II, CDAII, HEMPAS	uc002wrb.2	Q15437	OTTHUMG00000031976	ENST00000336714.3:c.40C>T	chr20.hg19:g.18491519C>T	ENSP00000338844:p.Arg14Trp	167.0	0.0		302.0	14.0	NM_032985	D3DW33|Q503A9|Q5W183|Q9BS15|Q9BSI2|Q9H1D7	Missense_Mutation	SNP	ENST00000336714.3	hg19	CCDS13137.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.150161	0.78001	2.27E-4	2.33E-4	ENSG00000101310	ENST00000450074;ENST00000336714;ENST00000262544;ENST00000377475;ENST00000377465	D;D;D;D;D	0.83075	-1.68;-1.68;-1.68;-1.68;-1.68	5.08	4.12	0.48240	.	0.060523	0.64402	D	0.000003	D	0.89774	0.6812	M	0.82056	2.57	0.80722	A	1	D;D	0.76494	0.999;0.999	P;P	0.62184	0.899;0.856	D	0.92798	0.6254	9	0.72032	D	0.01	-11.6695	13.9573	0.64157	0.1525:0.8475:0.0:0.0	.	14;14	B4DJW8;Q15437	.;SC23B_HUMAN	W	14	ENSP00000403971:R14W;ENSP00000338844:R14W;ENSP00000262544:R14W;ENSP00000366695:R14W;ENSP00000366685:R14W	ENSP00000262544:R14W	R	+	1	2	SEC23B	18439519	1.000000	0.71417	0.963000	0.40424	0.988000	0.76386	3.052000	0.49893	1.333000	0.45449	0.655000	0.94253	CGG	.	C|1.000;T|0.000		0.448	SEC23B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078184.5			T	18491519	C	T	18491519	3	4	361	1	0	0	0	0	1	0	0	0	14007	527	19	1	42	1	SEC23B	20	18491519	Missense_Mutation	SNP	C	TCGA-XR-A8TG-01A-11D-A35Z-10		18491519	44534001	90	50540										
C20orf117	140710	hgsc.bcm.edu	37	chr20	35414900	35414900	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	ctgctctgtcactcgctgggGgggagtgccctctcctcccc	12	17	3	0			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr20:35414900G>T	ENST00000357779.3	-	15	4586	c.4260C>A	c.(4258-4260)ccC>ccA	p.P1420P	SOGA1_ENST00000456801.2_Silent_p.P1261P|SOGA1_ENST00000237536.4_Silent_p.P1658P|SOGA1_ENST00000279034.6_Intron			O94964	SOGA1_HUMAN	suppressor of glucose, autophagy associated 1	1420					insulin receptor signaling pathway (GO:0008286)|negative regulation of gluconeogenesis (GO:0045721)|regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				endometrium(5)|kidney(1)|lung(21)|urinary_tract(1)	28						ACTCGCTGGGGGGGAGTGCCC	0.667																																					p.P1658P		Atlas-SNP	.											.	SOGA1	136	.	0			c.C4974A						.						31	37	35					20																	35414900		692	1591	2283	SO:0001819	synonymous_variant	140710	exon15			GCTGGGGGGGAGT	AK126630	CCDS46598.1, CCDS54459.1	20q11.23	2012-03-01	2012-02-27	2012-02-27	ENSG00000149639	ENSG00000149639			16111	protein-coding gene	gene with protein product	"suppressor of glucose by autophagy", "suppressor of glucose from autophagy"		"chromosome 20 open reading frame 117", "KIAA0889"	C20orf117, KIAA0889		20813965	Standard	NM_080627		Approved	dJ132F21.1, FLJ44670, SOGA	uc021wcx.1	O94964	OTTHUMG00000032395	ENST00000357779.3:c.4260C>A	chr20.hg19:g.35414900G>T		28.0	0.0		37.0	13.0	NM_080627	A6NK10|Q14DB2|Q5JW51|Q6ZTG8	Silent	SNP	ENST00000357779.3	hg19																																																																																				.	.		0.667	SOGA1-201	KNOWN	basic	protein_coding	protein_coding		NM_199181		T	35414900	G	T	35414900	2	4	361	1	0	0	0	0	0	0	0	1	2085	1219	43	3		3	C20orf117	20	35414900	Silent	SNP	G	TCGA-XR-A8TG-01A-11D-A35Z-10	16923381	35414900	27610620	91	50541										
PSMG1	8624	hgsc.bcm.edu	37	chr21	40549463	40549463	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	gtataacacaagtacagaatTgctgggattttccatacttg	8	7	0	1			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr21:40549463T>C	ENST00000331573.3	-	6	1155	c.690A>G	c.(688-690)gcA>gcG	p.A230A	PSMG1_ENST00000380900.2_Silent_p.A209A	NM_001261824.1|NM_003720.3	NP_001248753.1|NP_003711.1	O95456	PSMG1_HUMAN	proteasome (prosome, macropain) assembly chaperone 1	230					cerebellar granule cell precursor proliferation (GO:0021930)|proteasome assembly (GO:0043248)|proteasome core complex assembly (GO:0080129)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)				autonomic_ganglia(1)|endometrium(2)|large_intestine(1)|lung(1)|skin(1)|urinary_tract(2)	8		Prostate(19;8.44e-08)				AGTACAGAATTGCTGGGATTT	0.323																																					p.A230A		Atlas-SNP	.											.	PSMG1	11	.	0			c.A690G						.						74	70	71					21																	40549463		2202	4300	6502	SO:0001819	synonymous_variant	8624	exon6			CAGAATTGCTGGG	AJ006291	CCDS13660.1, CCDS13661.1	21q22.3	2007-10-23	2007-10-23	2007-10-23	ENSG00000183527	ENSG00000183527			3043	protein-coding gene	gene with protein product		605296	"Down syndrome critical region gene 2"	DSCR2		10872820, 17189198	Standard	NM_003720		Approved	c21-LRP, LRPC21, PAC1	uc002yxi.4	O95456	OTTHUMG00000066034	ENST00000331573.3:c.690A>G	chr21.hg19:g.40549463T>C		78.0	0.0		89.0	39.0	NM_003720	B5BUN2|Q6FHA3|Q6FHD3|Q6S713	Silent	SNP	ENST00000331573.3	hg19	CCDS13660.1	.	.	.	.	.	.	.	.	.	.	T	8.043	0.764242	0.15914	.	.	ENSG00000183527	ENST00000440607	.	.	.	5.73	-11.0	0.00169	.	.	.	.	.	T	0.42743	0.1216	.	.	.	0.58432	D	0.999996	.	.	.	.	.	.	T	0.51764	-0.8664	4	.	.	.	-28.1142	6.4678	0.21991	0.1007:0.1621:0.5813:0.156	.	.	.	.	D	87	.	.	N	-	1	0	PSMG1	39471333	0.000000	0.05858	0.000000	0.03702	0.764000	0.43329	-1.316000	0.02710	-1.955000	0.01023	0.455000	0.32223	AAT	.	.		0.323	PSMG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141404.2	NM_003720		C	40549463	T	C	40549463	2	2	361	1	0	0	0	0	0	0	0	1	12723	1799	63	2		2	PSMG1	21	40549463	Silent	SNP	T	TCGA-XR-A8TG-01A-11D-A35Z-10		40549463	7580432	92	50542										
MYO18B	84700	hgsc.bcm.edu	37	chr22	26298630	26298630	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	tgagtcagtgtttgagaaggGtctccgtgagaaagtgaccc	14	7	2	4			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chr22:26298630G>A	ENST00000407587.2	+	30	5046	c.4877G>A	c.(4876-4878)gGt>gAt	p.G1626D	CTA-125H2.2_ENST00000453457.3_RNA|CTA-125H2.2_ENST00000599080.1_RNA|CTA-125H2.2_ENST00000607895.1_RNA|MYO18B_ENST00000536101.1_Missense_Mutation_p.G1625D|CTA-125H2.2_ENST00000609570.1_RNA|CTA-125H2.2_ENST00000609889.1_RNA|CTA-125H2.2_ENST00000595093.1_RNA|CTA-125H2.2_ENST00000608257.1_RNA|CTA-125H2.2_ENST00000597548.1_RNA|CTA-125H2.2_ENST00000609823.1_RNA|CTA-125H2.2_ENST00000609157.1_RNA|CTA-125H2.2_ENST00000597284.1_RNA|CTA-125H2.2_ENST00000600269.1_RNA|CTA-125H2.2_ENST00000608115.1_RNA|CTA-125H2.2_ENST00000609275.1_RNA|MYO18B_ENST00000536204.1_3'UTR|CTA-125H2.2_ENST00000600211.1_RNA|MYO18B_ENST00000335473.7_Missense_Mutation_p.G1625D|CTA-125H2.2_ENST00000594585.1_RNA|CTA-125H2.2_ENST00000599792.1_RNA			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	1625	Tail.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						TTTGAGAAGGGTCTCCGTGAG	0.607																																					p.G1625D		Atlas-SNP	.											.	MYO18B	322	.	0			c.G4874A						.						46	50	49					22																	26298630		1997	4176	6173	SO:0001583	missense	84700	exon30			AGAAGGGTCTCCG	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.4877G>A	chr22.hg19:g.26298630G>A	ENSP00000386096:p.Gly1626Asp	78.0	0.0		100.0	11.0	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	hg19		.	.	.	.	.	.	.	.	.	.	G	13.81	2.348380	0.41599	.	.	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.86297	-2.08;-2.08;-2.1	5.11	4.1	0.47936	.	0.453258	0.23660	N	0.045839	T	0.80944	0.4721	L	0.38531	1.155	0.27028	N	0.964313	B;B;D;B	0.56746	0.029;0.314;0.977;0.441	B;B;P;B	0.48030	0.015;0.031;0.564;0.068	T	0.71965	-0.4433	10	0.02654	T	1	.	11.2411	0.48970	0.0894:0.0:0.9106:0.0	.	1138;1625;1626;1625	Q8IUG5-2;Q8IUG5;F5GXR6;F5GYU7	.;MY18B_HUMAN;.;.	D	1625;1625;1626	ENSP00000441229:G1625D;ENSP00000334563:G1625D;ENSP00000386096:G1626D	ENSP00000334563:G1625D	G	+	2	0	MYO18B	24628630	0.984000	0.35163	0.977000	0.42913	0.981000	0.71138	1.960000	0.40422	1.136000	0.42199	0.655000	0.94253	GGT	.	.		0.607	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		A	26298630	G	A	26298630	3	1	361	1	0	0	0	0	1	0	0	0	10075	1261	44	3	4988	3	MYO18B	22	26298630	Missense_Mutation	SNP	G	TCGA-XR-A8TG-01A-11D-A35Z-10		26298630	25005936	93	50543										
DMD	1756	hgsc.bcm.edu	37	chrX	32429887	32429887	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	gcctgggcttcctgaggcatTtgagctgcgtccaccttgtc	12	13	0	2			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chrX:32429887T>C	ENST00000357033.4	-	30	4421	c.4215A>G	c.(4213-4215)caA>caG	p.Q1405Q	DMD_ENST00000378677.2_Silent_p.Q1401Q	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	1405					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				CCTGAGGCATTTGAGCTGCGT	0.413																																					p.Q1405Q		Atlas-SNP	.											.	DMD	2127	.	0			c.A4215G						.						118	86	97					X																	32429887		2202	4300	6502	SO:0001819	synonymous_variant	1756	exon30			AGGCATTTGAGCT	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.4215A>G	chrX.hg19:g.32429887T>C		37.0	0.0		70.0	21.0	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Silent	SNP	ENST00000357033.4	hg19	CCDS14233.1																																																																																			.	.		0.413	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		C	32429887	T	C	32429887	2	2	361	1	0	0	0	0	0	0	0	1	4582	1838	64	2		2	DMD	23	32429887	Silent	SNP	T	TCGA-XR-A8TG-01A-11D-A35Z-10		32429887	122840673	94	50544										
MAP7D3	79649	hgsc.bcm.edu	37	chrX	135318419	135318419	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	taaccacgtggcttcctttcGgcttgttctttatcagtaga	8	10	2	1			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chrX:135318419G>A	ENST00000316077.9	-	7	940	c.720C>T	c.(718-720)gcC>gcT	p.A240A	MAP7D3_ENST00000370661.1_Silent_p.A205A|MAP7D3_ENST00000370663.5_Silent_p.A222A	NM_024597.3	NP_078873.2	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	240					microtubule cytoskeleton organization (GO:0000226)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(1)	44	Acute lymphoblastic leukemia(192;0.000127)					GCTTCCTTTCGGCTTGTTCTT	0.333																																					p.A240A		Atlas-SNP	.											.	MAP7D3	102	.	0			c.C720T						.						99	89	92					X																	135318419		1824	4070	5894	SO:0001819	synonymous_variant	79649	exon7			CCTTTCGGCTTGT	AL832120	CCDS44004.1, CCDS55508.1, CCDS55509.1	Xq26.3	2014-08-13			ENSG00000129680	ENSG00000129680			25742	protein-coding gene	gene with protein product		300930				24927501	Standard	NM_001173516		Approved	FLJ12649	uc004ezt.3	Q8IWC1	OTTHUMG00000022507	ENST00000316077.9:c.720C>T	chrX.hg19:g.135318419G>A		61.0	0.0		60.0	6.0	NM_024597	A2A2J0|A6NCZ7|A6NHR4|B4DWD2|H7BY77|Q5JXI5|Q5JXI6|Q6P2S1|Q9H9M8	Silent	SNP	ENST00000316077.9	hg19	CCDS44004.1																																																																																			.	.		0.333	MAP7D3-001	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058487.2			A	135318419	G	A	135318419	2	1	361	1	0	0	0	0	0	0	0	1	9278	1103	39	1		1	MAP7D3	23	135318419	Silent	SNP	G	TCGA-XR-A8TG-01A-11D-A35Z-10	102888532	135318419	19952141	95	50545										
ATP2B3	492	hgsc.bcm.edu	37	chrX	152815622	152815622	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0957446808510638	9	1	1.77220077220077	0	2.27854384997242	0.000579710144927536	0.0216231884057971	0	gtgcgcgagcagatcccggaAgacaagctttacaaagtgta	12	9	0	2			TCGA-XR-A8TG-01A-11D-A35Z-10	TCGA-XR-A8TG-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	81b78069-7129-494c-9209-e00ecf75cced	110d65ad-5d6c-4db6-beb6-720ee7d7b871	g.chrX:152815622A>C	ENST00000349466.2	+	11	2027	c.1701A>C	c.(1699-1701)gaA>gaC	p.E567D	ATP2B3_ENST00000370186.1_Missense_Mutation_p.E553D|ATP2B3_ENST00000370181.2_Missense_Mutation_p.E553D|ATP2B3_ENST00000263519.4_Missense_Mutation_p.E567D|ATP2B3_ENST00000393842.1_Missense_Mutation_p.E553D|ATP2B3_ENST00000359149.3_Missense_Mutation_p.E567D			Q16720	AT2B3_HUMAN	ATPase, Ca++ transporting, plasma membrane 3	567					blood coagulation (GO:0007596)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			NS(2)|breast(5)|endometrium(7)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|skin(3)	50	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					AGATCCCGGAAGACAAGCTTT	0.617																																					p.E567D		Atlas-SNP	.											.	ATP2B3	552	.	0			c.A1701C						.						107	76	86					X																	152815622		2203	4300	6503	SO:0001583	missense	492	exon10			CCCGGAAGACAAG	U60414	CCDS14722.1, CCDS35440.1	Xq28	2014-07-18			ENSG00000067842	ENSG00000067842	3.6.3.8	"ATPases / P-type"	816	protein-coding gene	gene with protein product	"plasma membrane calcium-transporting ATPase 3", "cilia and flagella associated protein 39"	300014	"spinocerebellar ataxia, X-linked 1", "cerebellar ataxia 2 (X-linked)"	SCAX1, CLA2		8187550, 22912398	Standard	NM_021949		Approved	PMCA3, CFAP39	uc004fht.1	Q16720	OTTHUMG00000024202	ENST00000349466.2:c.1701A>C	chrX.hg19:g.152815622A>C	ENSP00000343886:p.Glu567Asp	69.0	0.0		95.0	83.0	NM_001001344	B7WNR8|B7WNY5|Q12995|Q16858	Missense_Mutation	SNP	ENST00000349466.2	hg19	CCDS35440.1	.	.	.	.	.	.	.	.	.	.	a	20.7	4.032583	0.75504	.	.	ENSG00000067842	ENST00000370186;ENST00000349466;ENST00000393842;ENST00000359149;ENST00000263519;ENST00000370181	D;D;D;D;D;D	0.95980	-3.87;-3.87;-3.87;-3.87;-3.87;-3.87	5.02	1.32	0.21799	ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.111235	0.64402	D	0.000010	D	0.93148	0.7818	L	0.46885	1.475	0.40141	D	0.976836	P;P	0.51351	0.637;0.944	P;P	0.49085	0.515;0.6	D	0.90074	0.4165	10	0.59425	D	0.04	-17.8623	7.2612	0.26203	0.3555:0.0:0.6445:0.0	.	567;567	Q16720;Q16720-2	AT2B3_HUMAN;.	D	553;567;553;567;567;553	ENSP00000359205:E553D;ENSP00000343886:E567D;ENSP00000377425:E553D;ENSP00000352062:E567D;ENSP00000263519:E567D;ENSP00000359200:E553D	ENSP00000263519:E567D	E	+	3	2	ATP2B3	152468816	0.959000	0.32827	0.780000	0.31762	0.876000	0.50452	0.117000	0.15583	0.155000	0.19261	0.480000	0.44947	GAA	.	.		0.617	ATP2B3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060957.1	NM_021949		C	152815622	A	C	152815622	3	2	361	1	0	0	0	0	1	0	0	0	1141	69	3	5	1739	5	ATP2B3	23	152815622	Missense_Mutation	SNP	A	TCGA-XR-A8TG-01A-11D-A35Z-10	17497203	152815622	2454938	96	50546										
PRAMEF4	400735	hgsc.bcm.edu	37	chr1	12942173	12942173	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	tcctcttggcattgaggaagCacccatgggccatagcttca	10	12	2	1	rs201789683		TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr1:12942173C>G	ENST00000235349.5	-	3	447	c.377G>C	c.(376-378)tGc>tCc	p.C126S		NM_001009611.2	NP_001009611.1	O60810	PRAM4_HUMAN	PRAME family member 4	126					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(3)|skin(1)	24	Ovarian(185;0.249)	Lung NSC(185;3.67e-05)|all_lung(284;4.03e-05)|Renal(390;0.000147)|Breast(348;0.000278)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		ATTGAGGAAGCACCCATGGGC	0.493																																					p.C126S		Atlas-SNP	.											PRAMEF4,NS,carcinoma,0,1	PRAMEF4	62	.	0			c.G377C						.						44	56	52					1																	12942173		1381	2629	4010	SO:0001583	missense	400735	exon3			AGGAAGCACCCAT		CCDS30592.1	1p36.21	2013-01-17			ENSG00000243073	ENSG00000243073		"-"	31971	protein-coding gene	gene with protein product							Standard	NM_001009611		Approved	RP5-845O24.6	uc001aun.2	O60810	OTTHUMG00000001987	ENST00000235349.5:c.377G>C	chr1.hg19:g.12942173C>G	ENSP00000235349:p.Cys126Ser	25.0	1.0		32.0	3.0	NM_001009611	Q5LJB5	Missense_Mutation	SNP	ENST00000235349.5	hg19	CCDS30592.1	.	.	.	.	.	.	.	.	.	.	c	8.575	0.881031	0.17467	.	.	ENSG00000243073	ENST00000235349	T	0.18016	2.24	1.35	0.315	0.15852	.	1.371720	0.04624	N	0.402516	T	0.19406	0.0466	L	0.53671	1.685	0.09310	N	1	P	0.50272	0.933	P	0.44811	0.461	T	0.23190	-1.0195	10	0.33940	T	0.23	.	5.2546	0.15540	0.0:0.6297:0.3703:0.0	.	126	O60810	PRAM4_HUMAN	S	126	ENSP00000235349:C126S	ENSP00000235349:C126S	C	-	2	0	PRAMEF4	12864760	0.002000	0.14202	0.003000	0.11579	0.008000	0.06430	0.188000	0.17018	0.112000	0.17975	0.194000	0.17425	TGC	.	C|0.500;G|0.500		0.493	PRAMEF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005518.1	NM_001009611		G	12942173	C	G	12942173	3	3	362	1	0	0	0	0	1	0	0	0	12449	710	25	4	1067	4	PRAMEF4	1	12942173	Missense_Mutation	SNP	C	TCGA-YA-A8S7-01A-11D-A36X-10		12942173	236308448	1	50547										
PLEKHM2	23207	hgsc.bcm.edu	37	chr1	16055169	16055169	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	ggtttcctctctcaggggccAcagagaagccatacctggtg	12	12	2	1			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr1:16055169A>G	ENST00000375799.3	+	12	2154	c.1927A>G	c.(1927-1929)Aca>Gca	p.T643A	PLEKHM2_ENST00000375793.2_Missense_Mutation_p.T623A|RP11-288I21.1_ENST00000453804.1_RNA	NM_015164.2	NP_055979.2	Q8IWE5	PKHM2_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 2	643					Golgi organization (GO:0007030)	cytoplasm (GO:0005737)	kinesin binding (GO:0019894)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.000259)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00057)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		CTCAGGGGCCACAGAGAAGCC	0.562																																					p.T643A		Atlas-SNP	.											.	PLEKHM2	94	.	0			c.A1927G						.						39	46	44					1																	16055169		1939	4128	6067	SO:0001583	missense	23207	exon12			GGGGCCACAGAGA	AB020649	CCDS44063.1	1p36.13	2013-01-10			ENSG00000116786	ENSG00000116786		"Pleckstrin homology (PH) domain containing"	29131	protein-coding gene	gene with protein product		609613				10048485	Standard	NM_015164		Approved	KIAA0842	uc010obo.2	Q8IWE5	OTTHUMG00000003062	ENST00000375799.3:c.1927A>G	chr1.hg19:g.16055169A>G	ENSP00000364956:p.Thr643Ala	130.0	0.0		151.0	36.0	NM_015164	O94928|Q5VT65|Q6NUH9|Q7L8G1|Q8IVT7|Q8N2T4|Q96AY0|Q9NTF7	Missense_Mutation	SNP	ENST00000375799.3	hg19	CCDS44063.1	.	.	.	.	.	.	.	.	.	.	A	7.659	0.684463	0.14973	.	.	ENSG00000116786	ENST00000375799;ENST00000375793	T;T	0.42513	0.98;0.97	5.51	3.15	0.36227	.	0.235147	0.45867	N	0.000327	T	0.14141	0.0342	N	0.02916	-0.46	0.30768	N	0.743383	B	0.02656	0.0	B	0.04013	0.001	T	0.32903	-0.9889	10	0.02654	T	1	-0.9871	6.8392	0.23953	0.6555:0.0:0.3445:0.0	.	643	Q8IWE5	PKHM2_HUMAN	A	643;623	ENSP00000364956:T643A;ENSP00000364950:T623A	ENSP00000364950:T623A	T	+	1	0	PLEKHM2	15927756	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.530000	0.67141	0.376000	0.24707	-0.290000	0.09829	ACA	.	.		0.562	PLEKHM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008463.1	NM_015164		G	16055169	A	G	16055169	3	3	362	1	0	0	0	0	1	0	0	0	12090	159	6	2	1973	2	PLEKHM2	1	16055169	Missense_Mutation	SNP	A	TCGA-YA-A8S7-01A-11D-A36X-10	3112996	16055169	233195452	2	50548										
USP24	23358	hgsc.bcm.edu	37	chr1	55604390	55604390	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	ttcgtggaacagagtaaaaaTccttaaaaaacgaataagtc	7	6	0	1			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr1:55604390T>A	ENST00000294383.6	-	26	2818	c.2819A>T	c.(2818-2820)gAt>gTt	p.D940V	USP24_ENST00000407756.1_Splice_Site_p.D780V	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	940					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						AGAGTAAAAATCCTTAAAAAA	0.338																																					p.D940V		Atlas-SNP	.											.	USP24	323	.	0			c.A2819T						.						57	55	56					1																	55604390		1899	4123	6022	SO:0001630	splice_region_variant	23358	exon26			TAAAAATCCTTAA	AB028980	CCDS44154.1, CCDS44154.2	1p32.3	2008-04-11	2005-08-08		ENSG00000162402	ENSG00000162402		"Ubiquitin-specific peptidases"	12623	protein-coding gene	gene with protein product		610569	"ubiquitin specific protease 24"			12838346	Standard	NM_015306		Approved	KIAA1057	uc021onw.1	Q9UPU5	OTTHUMG00000008135	ENST00000294383.6:c.2818-1A>T	chr1.hg19:g.55604390T>A		79.0	0.0		100.0	31.0	NM_015306	Q6ZSY2|Q8N2Y4|Q9NXD1	Missense_Mutation	SNP	ENST00000294383.6	hg19	CCDS44154.2	.	.	.	.	.	.	.	.	.	.	T	23.8	4.454380	0.84209	.	.	ENSG00000162402	ENST00000294383;ENST00000407756	T;T	0.02446	4.29;4.29	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.11153	0.0272	L	0.53249	1.67	0.80722	D	1	D	0.76494	0.999	D	0.69307	0.963	T	0.18999	-1.0319	10	0.27785	T	0.31	.	16.3197	0.82945	0.0:0.0:0.0:1.0	rs34039649	780	B7WPF4	.	V	940;780	ENSP00000294383:D940V;ENSP00000385700:D780V	ENSP00000294383:D940V	D	-	2	0	USP24	55376978	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	7.655000	0.83696	2.302000	0.77476	0.533000	0.62120	GAT	.	.		0.338	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2		Missense_Mutation	A	55604390	T	A	55604390	5	1	362	1	0	0	0	0	0	0	1	0	17070	1449	50	4	5215	4	USP24	1	55604390	Splice_Site	SNP	T	TCGA-YA-A8S7-01A-11D-A36X-10	39549221	55604390	193646231	3	50549										
LRRIQ3	127255	hgsc.bcm.edu	37	chr1	74540431	74540431	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	aaatagatgacacatgttttCtgtgttcactggaatttttt	7	5	2	2			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr1:74540431C>A	ENST00000395089.1	-	5	910	c.911G>T	c.(910-912)aGa>aTa	p.R304I	LRRIQ3_ENST00000354431.4_Missense_Mutation_p.R304I			A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	304										NS(2)|breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(13)|liver(1)|lung(27)|ovary(3)|prostate(1)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(5)	73						CACATGTTTTCTGTGTTCACT	0.264																																					p.R304I		Atlas-SNP	.											.	LRRIQ3	146	.	0			c.G911T						.						50	43	45					1																	74540431		1768	4022	5790	SO:0001583	missense	127255	exon6			TGTTTTCTGTGTT	BX647210	CCDS41350.1	1p31.1	2008-06-12	2008-06-12	2008-06-12	ENSG00000162620	ENSG00000162620			28318	protein-coding gene	gene with protein product			"leucine rich repeat containing 44"	LRRC44		12477932	Standard	NM_001105659		Approved	MGC22773	uc001dfy.4	A6PVS8	OTTHUMG00000009508	ENST00000395089.1:c.911G>T	chr1.hg19:g.74540431C>A	ENSP00000378524:p.Arg304Ile	321.0	0.0		320.0	75.0	NM_001105659	A6PVS9|Q6P5P7|Q6ZMV4|Q8WUE0	Missense_Mutation	SNP	ENST00000395089.1	hg19	CCDS41350.1	.	.	.	.	.	.	.	.	.	.	C	5.722	0.317619	0.10845	.	.	ENSG00000162620	ENST00000417067;ENST00000395089;ENST00000354431	T;T	0.11821	2.74;2.74	4.62	0.617	0.17619	.	0.413516	0.17863	N	0.159453	T	0.03263	0.0095	L	0.44542	1.39	0.09310	N	1	B	0.15930	0.015	B	0.12837	0.008	T	0.37126	-0.9719	10	0.62326	D	0.03	.	3.1262	0.06408	0.1894:0.5081:0.0:0.3025	.	304	A6PVS8	LRIQ3_HUMAN	I	15;304;304	ENSP00000378524:R304I;ENSP00000346414:R304I	ENSP00000346414:R304I	R	-	2	0	LRRIQ3	74313019	0.001000	0.12720	0.002000	0.10522	0.002000	0.02628	-0.942000	0.03921	0.234000	0.21139	-0.899000	0.02877	AGA	.	.		0.264	LRRIQ3-008	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316539.1	NM_145258		A	74540431	C	A	74540431	3	1	362	1	0	0	0	0	1	0	0	0	9039	913	32	3	975	3	LRRIQ3	1	74540431	Missense_Mutation	SNP	C	TCGA-YA-A8S7-01A-11D-A36X-10	18936041	74540431	174710190	4	50550										
PALMD	54873	hgsc.bcm.edu	37	chr1	100152711	100152711	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	aggttaaggaaggagataaaTgaagaaaaagaagatgatga	13	0	0	7			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr1:100152711T>C	ENST00000263174.4	+	6	855	c.480T>C	c.(478-480)aaT>aaC	p.N160N	PALMD_ENST00000605497.1_Silent_p.N160N	NM_017734.4	NP_060204.1	Q9NP74	PALMD_HUMAN	palmdelphin	160					regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|membrane (GO:0016020)				central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(8)|ovary(6)|pancreas(1)|prostate(2)	31		all_epithelial(167;0.000813)|all_lung(203;0.0214)|Lung NSC(277;0.0216)		Epithelial(280;0.067)|all cancers(265;0.117)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)		AGGAGATAAATGAAGAAAAAG	0.328																																					p.N160N		Atlas-SNP	.											.	PALMD	64	.	0			c.T480C						.						76	83	81					1																	100152711		2201	4297	6498	SO:0001819	synonymous_variant	54873	exon6			GATAAATGAAGAA	AJ312214	CCDS758.1	1p22-p21	2008-07-18			ENSG00000099260	ENSG00000099260			15846	protein-coding gene	gene with protein product		610182		C1orf11		11478809	Standard	NM_017734		Approved	FLJ20271, PALML	uc001dsg.3	Q9NP74	OTTHUMG00000010764	ENST00000263174.4:c.480T>C	chr1.hg19:g.100152711T>C		336.0	0.0		362.0	81.0	NM_017734	Q9H7E6|Q9NPM5|Q9NPM6|Q9NPS0	Silent	SNP	ENST00000263174.4	hg19	CCDS758.1																																																																																			.	.		0.328	PALMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029672.1	NM_017734		C	100152711	T	C	100152711	2	2	362	1	0	0	0	0	0	0	0	1	11420	1461	51	2		2	PALMD	1	100152711	Silent	SNP	T	TCGA-YA-A8S7-01A-11D-A36X-10	25612280	100152711	149097910	5	50551										
TSPAN2	10100	hgsc.bcm.edu	37	chr1	115615540	115615540	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	actcacccacatagaaatacTctggggacttgtcctctgat	7	12	3	2	rs570453338		TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr1:115615540T>C	ENST00000369516.2	-	2	189	c.158A>G	c.(157-159)gAg>gGg	p.E53G	TSPAN2_ENST00000369514.2_Missense_Mutation_p.E53G|TSPAN2_ENST00000369515.2_Missense_Mutation_p.E53G	NM_005725.4	NP_005716.2	O60636	TSN2_HUMAN	tetraspanin 2	53					astrocyte development (GO:0014002)|axon development (GO:0061564)|brain development (GO:0007420)|inflammatory response (GO:0006954)|microglia development (GO:0014005)|myelination (GO:0042552)|oligodendrocyte differentiation (GO:0048709)	integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|plasma membrane (GO:0005886)				central_nervous_system(1)|large_intestine(4)|lung(3)|pancreas(1)|prostate(1)	10	Lung SC(450;0.211)	all_cancers(81;2.9e-07)|all_epithelial(167;1.42e-06)|all_lung(203;6.72e-06)|Lung NSC(69;1.13e-05)|Acute lymphoblastic leukemia(138;0.191)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|all cancers(265;0.159)|Epithelial(280;0.179)		ATAGAAATACTCTGGGGACTT	0.502													T|||	1	0.000199681	0	0	5008	,	,		19445	0		0	False		,,,				2504	0.001				p.E53G		Atlas-SNP	.											.	TSPAN2	37	.	0			c.A158G						.						113	104	107					1																	115615540		2203	4300	6503	SO:0001583	missense	10100	exon2			AAATACTCTGGGG	AF054839	CCDS881.1	1p13.1	2013-02-14			ENSG00000134198	ENSG00000134198		"Tetraspanins"	20659	protein-coding gene	gene with protein product		613133				9714763, 11739647	Standard	NM_005725		Approved	TSPAN-2, TSN2, FLJ12082	uc001eft.3	O60636	OTTHUMG00000011878	ENST00000369516.2:c.158A>G	chr1.hg19:g.115615540T>C	ENSP00000358529:p.Glu53Gly	68.0	0.0		76.0	13.0	NM_005725	D6PTH4|Q5TET2|Q8WU05	Missense_Mutation	SNP	ENST00000369516.2	hg19	CCDS881.1	.	.	.	.	.	.	.	.	.	.	T	18.39	3.612481	0.66672	.	.	ENSG00000134198	ENST00000369516;ENST00000369515;ENST00000433172;ENST00000369514	T;T;T;T	0.79749	-1.3;-1.3;-1.3;-1.3	5.35	5.35	0.76521	.	0.871613	0.10262	N	0.695783	T	0.73560	0.3602	L	0.27053	0.805	0.53688	D	0.999977	D	0.63880	0.993	D	0.63192	0.912	T	0.66826	-0.5825	10	0.13108	T	0.6	.	12.8614	0.57915	0.0:0.0:0.0:1.0	.	53	O60636	TSN2_HUMAN	G	53;53;47;53	ENSP00000358529:E53G;ENSP00000358528:E53G;ENSP00000415256:E47G;ENSP00000358527:E53G	ENSP00000358527:E53G	E	-	2	0	TSPAN2	115417063	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.529000	0.60588	2.021000	0.59480	0.533000	0.62120	GAG	.	.		0.502	TSPAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032828.1	NM_005725		C	115615540	T	C	115615540	3	2	362	1	0	0	0	0	1	0	0	0	16659	1551	54	2	535	2	TSPAN2	1	115615540	Missense_Mutation	SNP	T	TCGA-YA-A8S7-01A-11D-A36X-10	15462829	115615540	133635081	6	50552										
PRUNE	58497	hgsc.bcm.edu	37	chr1	151006653	151006653	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	tctgctgaggccgtcttcgaGaagtgcagtcagatctcact	11	11	4	3			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr1:151006653G>T	ENST00000271620.3	+	8	1461	c.1305G>T	c.(1303-1305)gaG>gaT	p.E435D	PRUNE_ENST00000368934.1_Missense_Mutation_p.E200D|BNIPL_ENST00000295294.7_5'Flank|PRUNE_ENST00000368936.1_Missense_Mutation_p.E253D|BNIPL_ENST00000368931.3_5'Flank|PRUNE_ENST00000368935.1_Missense_Mutation_p.E150D|PRUNE_ENST00000368937.1_Missense_Mutation_p.E200D|PRUNE_ENST00000271619.8_Missense_Mutation_p.E223D	NM_021222.1	NP_067045.1	Q86TP1	PRUNE_HUMAN	prune exopolyphosphatase	435						cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	inorganic diphosphatase activity (GO:0004427)|metal ion binding (GO:0046872)			NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	14	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			CCGTCTTCGAGAAGTGCAGTC	0.582																																					p.E435D		Atlas-SNP	.											.	PRUNE	40	.	0			c.G1305T						.						148	130	136					1																	151006653		2203	4300	6503	SO:0001583	missense	58497	exon8			CTTCGAGAAGTGC	U67085	CCDS977.1	1q21.2	2013-04-29	2013-04-29		ENSG00000143363	ENSG00000143363	3.6.1.11		13420	protein-coding gene	gene with protein product			"prune homolog (Drosophila)"			10602478, 11687967, 18700747	Standard	NM_021222		Approved	DRES-17, HTCD37	uc001ewh.1	Q86TP1	OTTHUMG00000035062	ENST00000271620.3:c.1305G>T	chr1.hg19:g.151006653G>T	ENSP00000271620:p.Glu435Asp	65.0	0.0		83.0	4.0	NM_021222	B2RCH8|B4DFL7|Q5SZF9|Q659E5|Q6P4E0|Q8N654|Q96JU5|Q9C071|Q9C072|Q9UIV0	Missense_Mutation	SNP	ENST00000271620.3	hg19	CCDS977.1	.	.	.	.	.	.	.	.	.	.	G	16.56	3.157966	0.57368	.	.	ENSG00000143363	ENST00000271620;ENST00000302413;ENST00000271619;ENST00000368937;ENST00000368936;ENST00000368935;ENST00000368934	T;T;T;T;T;T	0.38077	1.38;1.17;1.16;1.29;1.21;1.16	5.58	3.62	0.41486	.	0.063063	0.64402	D	0.000008	T	0.16557	0.0398	N	0.17082	0.46	0.35444	D	0.795098	P;P	0.48089	0.905;0.603	P;B	0.52793	0.709;0.184	T	0.03534	-1.1027	9	.	.	.	.	7.0318	0.24970	0.2854:0.0:0.7145:0.0	.	223;435	E9PCU1;Q86TP1	.;PRUNE_HUMAN	D	435;368;223;200;253;150;200	ENSP00000271620:E435D;ENSP00000271619:E223D;ENSP00000357933:E200D;ENSP00000357932:E253D;ENSP00000357931:E150D;ENSP00000357930:E200D	.	E	+	3	2	PRUNE	149273277	1.000000	0.71417	1.000000	0.80357	0.620000	0.37586	1.561000	0.36342	1.513000	0.48852	0.655000	0.94253	GAG	.	.		0.582	PRUNE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084885.1	NM_021222		T	151006653	G	T	151006653	3	4	362	1	0	0	0	0	1	0	0	0	12652	933	33	3	1335	3	PRUNE	1	151006653	Missense_Mutation	SNP	G	TCGA-YA-A8S7-01A-11D-A36X-10	35391113	151006653	98243968	7	50553										
SNX27	81609	hgsc.bcm.edu	37	chr1	151641091	151641091	+	Frame_Shift_Del	DEL	G	G	-													0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	taaatgacaatgaccttgctGttacctacttctttcatcag							TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr1:151641091delG	ENST00000458013.2	+	7	1249	c.1129delG	c.(1129-1131)gttfs	p.V377fs	SNX27_ENST00000482791.1_3'UTR|SNX27_ENST00000368838.1_Frame_Shift_Del_p.V284fs|SNX27_ENST00000368843.3_Frame_Shift_Del_p.V377fs			Q96L92	SNX27_HUMAN	sorting nexin family member 27	377	FERM-like region F2.				endosomal transport (GO:0016197)|endosome to lysosome transport (GO:0008333)|establishment of natural killer cell polarity (GO:0001770)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to plasma membrane (GO:1990126)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|immunological synapse (GO:0001772)|nucleus (GO:0005634)	phosphatidylinositol-3-phosphate binding (GO:0032266)			central_nervous_system(1)|large_intestine(2)|ovary(2)	5	Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			TGACCTTGCTGTTACCTACTT	0.368																																					p.A376fs	Colon(46;291 966 40145 41237 41888)	Atlas-INDEL	.											.	SNX27	44	.	0			c.1128delT						.						72	71	71					1																	151641091		2203	4300	6503	SO:0001589	frameshift_variant	81609	exon7			.	AB007957	CCDS1001.1	1q21.3	2008-03-11			ENSG00000143376	ENSG00000143376		"Sorting nexins"	20073	protein-coding gene	gene with protein product		611541				12461558	Standard	XM_005245509		Approved	MY014, KIAA0488, MGC20471	uc001eyn.1	Q96L92	OTTHUMG00000013052	ENST00000458013.2:c.1129delG	chr1.hg19:g.151641091delG	ENSP00000400333:p.Val377fs	102.0	0.0		170.0	83.0	NM_030918	Q32Q36|Q4AEJ5|Q5VWB0|Q5VWB1|Q5VWB2|Q6IPP6|Q86UB1|Q96D79|Q9H3K8	Frame_Shift_Del	DEL	ENST00000458013.2	hg19																																																																																				.	.		0.368	SNX27-003	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000036624.3	NM_030918		-	151641091	G	-	151641091	7	5	362	1	0	1	0	1	0	0	0	0	14912	1377	48	0	1155	0	SNX27	1	151641091	Frame_Shift_Del	DEL	G	TCGA-YA-A8S7-01A-11D-A36X-10	634438	151641091	97609530	8	50554										
LCE1D	353134	hgsc.bcm.edu	37	chr1	152770563	152770563	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	ctgcagccagccctcgggggGctccagctgctgcggtgggg	18	14	0	0			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr1:152770563G>T	ENST00000326233.6	+	2	336	c.293G>T	c.(292-294)gGc>gTc	p.G98V		NM_178352.2	NP_848129.1	Q5T752	LCE1D_HUMAN	late cornified envelope 1D	98	Cys-rich.				cellular response to calcium ion (GO:0071277)|cognition (GO:0050890)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)				large_intestine(1)	1	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCCTCGGGGGGCTCCAGCTGC	0.652																																					p.G98V		Atlas-SNP	.											.	LCE1D	19	.	0			c.G293T						.						39	35	37					1																	152770563		2015	3734	5749	SO:0001583	missense	353134	exon2			CGGGGGGCTCCAG		CCDS1025.1	1q21.3	2008-02-05			ENSG00000172155	ENSG00000172155		"Late cornified envelopes"	29465	protein-coding gene	gene with protein product		612606				11698679	Standard	NM_178352		Approved	LEP4	uc009wnp.3	Q5T752	OTTHUMG00000012444	ENST00000326233.6:c.293G>T	chr1.hg19:g.152770563G>T	ENSP00000316737:p.Gly98Val	374.0	0.0		590.0	161.0	NM_178352		Missense_Mutation	SNP	ENST00000326233.6	hg19	CCDS1025.1	.	.	.	.	.	.	.	.	.	.	G	7.299	0.612726	0.14066	.	.	ENSG00000172155	ENST00000326233	T	0.04454	3.62	4.26	4.26	0.50523	.	0.000000	0.36268	N	0.002697	T	0.07683	0.0193	M	0.82823	2.61	0.45704	D	0.998613	P	0.51351	0.944	P	0.47645	0.553	T	0.01537	-1.1330	10	0.87932	D	0	.	12.8829	0.58028	0.0:0.0:1.0:0.0	.	98	Q5T752	LCE1D_HUMAN	V	98	ENSP00000316737:G98V	ENSP00000316737:G98V	G	+	2	0	LCE1D	151037187	1.000000	0.71417	0.995000	0.50966	0.330000	0.28571	1.936000	0.40183	2.307000	0.77673	0.555000	0.69702	GGC	.	.		0.652	LCE1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034657.2	NM_178352		T	152770563	G	T	152770563	3	4	362	1	0	0	0	0	1	0	0	0	8671	1203	42	3	295	3	LCE1D	1	152770563	Missense_Mutation	SNP	G	TCGA-YA-A8S7-01A-11D-A36X-10	1129472	152770563	96480058	9	50555										
BCAN	63827	hgsc.bcm.edu	37	chr1	156618414	156618414	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	gacattggaggaagcacgggCgtactgccaggagcggggtg	19	8	0	0			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr1:156618414C>T	ENST00000329117.5	+	6	1160	c.824C>T	c.(823-825)gCg>gTg	p.A275V	RP11-284F21.7_ENST00000448869.1_RNA|BCAN_ENST00000361588.5_Missense_Mutation_p.A275V	NM_021948.4	NP_068767.3	Q96GW7	PGCB_HUMAN	brevican	275	Link 2. {ECO:0000255|PROSITE- ProRule:PRU00323}.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hippocampus development (GO:0021766)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	55	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GAAGCACGGGCGTACTGCCAG	0.612																																					p.A275V		Atlas-SNP	.											.	BCAN	174	.	0			c.C824T						.						84	80	82					1																	156618414		2203	4300	6503	SO:0001583	missense	63827	exon6			CACGGGCGTACTG	BC027971	CCDS1149.1, CCDS1150.1	1q31	2013-05-07			ENSG00000132692	ENSG00000132692		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	23059	protein-coding gene	gene with protein product	"chondroitin sulfate proteoglycan 7", "brevican proteoglycan"	600347				11054543, 11873941	Standard	NM_021948		Approved	BEHAB, MGC13038, CSPG7	uc001fpp.3	Q96GW7	OTTHUMG00000033322	ENST00000329117.5:c.824C>T	chr1.hg19:g.156618414C>T	ENSP00000331210:p.Ala275Val	121.0	0.0		181.0	82.0	NM_198427	D3DVC2|Q5SZ10|Q5T3I5|Q8TBB9|Q9HBK1|Q9HBK4	Missense_Mutation	SNP	ENST00000329117.5	hg19	CCDS1149.1	.	.	.	.	.	.	.	.	.	.	C	10.42	1.345214	0.24426	.	.	ENSG00000132692	ENST00000255029;ENST00000329117;ENST00000424639;ENST00000361588	T;T;T	0.32272	2.82;1.46;2.82	4.66	1.52	0.23074	C-type lectin fold (1);Link (3);C-type lectin-like (1);	0.671285	0.12836	N	0.435203	T	0.16685	0.0401	M	0.62154	1.92	0.09310	N	1	P;P	0.41345	0.746;0.489	B;B	0.39840	0.311;0.132	T	0.05022	-1.0911	10	0.54805	T	0.06	2.0E-4	12.3362	0.55069	0.5933:0.4067:0.0:0.0	.	275;275	Q96GW7;Q96GW7-2	PGCB_HUMAN;.	V	216;275;173;275	ENSP00000331210:A275V;ENSP00000401709:A173V;ENSP00000354925:A275V	ENSP00000255029:A216V	A	+	2	0	BCAN	154885038	0.000000	0.05858	0.022000	0.16811	0.829000	0.46940	-0.397000	0.07269	0.127000	0.18452	0.561000	0.74099	GCG	.	.		0.612	BCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081844.2	NM_021948		T	156618414	C	T	156618414	3	4	362	1	0	0	0	0	1	0	0	0	1345	768	27	1	842	1	BCAN	1	156618414	Missense_Mutation	SNP	C	TCGA-YA-A8S7-01A-11D-A36X-10	3847851	156618414	92632207	10	50556										
SUSD4	55061	hgsc.bcm.edu	37	chr1	223396698	223396698	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	tgctctcttggcacctgggaGgtgaatacagactttggagc	13	9	1	2			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr1:223396698G>A	ENST00000343846.3	-	7	1970	c.1337C>T	c.(1336-1338)cCt>cTt	p.P446L	SUSD4_ENST00000484758.2_Missense_Mutation_p.P377L|SUSD4_ENST00000454695.2_Missense_Mutation_p.P286L|SUSD4_ENST00000494793.2_Missense_Mutation_p.P446L|SUSD4_ENST00000478605.1_5'UTR|SUSD4_ENST00000366878.4_Missense_Mutation_p.P446L			Q5VX71	SUSD4_HUMAN	sushi domain containing 4	446						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|skin(1)	17				GBM - Glioblastoma multiforme(131;0.0611)		GCACCTGGGAGGTGAATACAG	0.597																																					p.P446L		Atlas-SNP	.											.	SUSD4	82	.	0			c.C1337T						.						60	67	65					1																	223396698		2065	4204	6269	SO:0001583	missense	55061	exon8			CTGGGAGGTGAAT	AK096265	CCDS31034.1, CCDS41471.1	1q41	2008-05-14			ENSG00000143502	ENSG00000143502			25470	protein-coding gene	gene with protein product		615827				12477932	Standard	NM_017982		Approved	FLJ10052	uc001hny.4	Q5VX71	OTTHUMG00000037936	ENST00000343846.3:c.1337C>T	chr1.hg19:g.223396698G>A	ENSP00000344219:p.Pro446Leu	45.0	0.0		48.0	10.0	NM_017982	D3DTB9|Q6UX62|Q9BSR0|Q9NWG0	Missense_Mutation	SNP	ENST00000343846.3	hg19	CCDS41471.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.71|10.71	1.427792|1.427792	0.25726|0.25726	.|.	.|.	ENSG00000143502|ENSG00000143502	ENST00000271787|ENST00000343846;ENST00000366878;ENST00000542750;ENST00000454695	.|T;T;T	.|0.30182	.|1.54;1.54;1.63	5.16|5.16	4.25|4.25	0.50352|0.50352	.|.	.|0.424789	.|0.20246	.|N	.|0.096182	T|T	0.28863|0.28863	0.0716|0.0716	L|L	0.43152|0.43152	1.355|1.355	0.80722|0.80722	D|D	1|1	.|B	.|0.17038	.|0.02	.|B	.|0.16722	.|0.016	T|T	0.07597|0.07597	-1.0764|-1.0764	6|10	0.34782|0.72032	T|D	0.22|0.01	0.173|0.173	13.3163|13.3163	0.60409|0.60409	0.0773:0.0:0.9227:0.0|0.0773:0.0:0.9227:0.0	.|.	.|446	.|Q5VX71	.|SUSD4_HUMAN	F|L	221|446;446;377;286	.|ENSP00000344219:P446L;ENSP00000355843:P446L;ENSP00000399288:P286L	ENSP00000271787:L221F|ENSP00000344219:P446L	L|P	-|-	1|2	0|0	SUSD4|SUSD4	221463321|221463321	1.000000|1.000000	0.71417|0.71417	0.292000|0.292000	0.24919|0.24919	0.067000|0.067000	0.16453|0.16453	5.921000|5.921000	0.70028|0.70028	1.178000|1.178000	0.42870|0.42870	0.655000|0.655000	0.94253|0.94253	CTC|CCT	.	.		0.597	SUSD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092592.2	NM_017982		A	223396698	G	A	223396698	3	1	362	1	0	0	0	0	1	0	0	0	15425	1000	35	3	143	3	SUSD4	1	223396698	Missense_Mutation	SNP	G	TCGA-YA-A8S7-01A-11D-A36X-10	66778284	223396698	25853923	11	50557										
RYR2	6262	hgsc.bcm.edu	37	chr1	237729909	237729909	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	cggcaccggggaaaggttccGaatcttccgtgccgagaaga	14	11	1	2			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr1:237729909G>A	ENST00000366574.2	+	28	3574	c.3257G>A	c.(3256-3258)cGa>cAa	p.R1086Q	RYR2_ENST00000542537.1_Missense_Mutation_p.R1070Q|RYR2_ENST00000360064.6_Missense_Mutation_p.R1084Q	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1086	4 X approximate repeats.|B30.2/SPRY 2. {ECO:0000255|PROSITE- ProRule:PRU00548}.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GAAAGGTTCCGAATCTTCCGT	0.542																																					p.R1086Q		Atlas-SNP	.											.	RYR2	1273	.	0			c.G3257A						.						80	80	80					1																	237729909		1917	4133	6050	SO:0001583	missense	6262	exon28			GGTTCCGAATCTT	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.3257G>A	chr1.hg19:g.237729909G>A	ENSP00000355533:p.Arg1086Gln	117.0	0.0		125.0	11.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	G	35	5.518913	0.96416	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.97186	-4.28;-4.25;-4.27	5.29	5.29	0.74685	B30.2/SPRY domain (1);	0.000000	0.56097	D	0.000037	D	0.97870	0.9300	M	0.87682	2.9	0.80722	D	1	D	0.67145	0.996	P	0.50570	0.644	D	0.98703	1.0701	10	0.72032	D	0.01	.	18.9442	0.92615	0.0:0.0:1.0:0.0	.	1086	Q92736	RYR2_HUMAN	Q	1086;1084;1070	ENSP00000355533:R1086Q;ENSP00000353174:R1084Q;ENSP00000443798:R1070Q	ENSP00000353174:R1084Q	R	+	2	0	RYR2	235796532	1.000000	0.71417	0.992000	0.48379	0.881000	0.50899	9.807000	0.99171	2.465000	0.83290	0.655000	0.94253	CGA	.	.		0.542	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		A	237729909	G	A	237729909	3	1	362	1	0	0	0	0	1	0	0	0	13784	1058	37	1	3367	1	RYR2	1	237729909	Missense_Mutation	SNP	G	TCGA-YA-A8S7-01A-11D-A36X-10	14333211	237729909	11520712	12	50558										
OR2G3	81469	hgsc.bcm.edu	37	chr1	247768926	247768926	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	agttccctaatggatttcatCcttctaggcttctcagacca	6	12	3	1			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr1:247768926C>T	ENST00000320002.2	+	1	71	c.39C>T	c.(37-39)atC>atT	p.I13I	RP11-978I15.10_ENST00000446347.1_RNA|RNU6-691P_ENST00000516585.1_RNA|RP11-978I15.10_ENST00000435333.1_RNA	NM_001001914.1	NP_001001914.1	Q8NGZ4	OR2G3_HUMAN	olfactory receptor, family 2, subfamily G, member 3	13						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(2)|liver(1)|lung(31)|skin(5)	50	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			TGGATTTCATCCTTCTAGGCT	0.468																																					p.I13I		Atlas-SNP	.											.	OR2G3	108	.	0			c.C39T						.						162	166	165					1																	247768926		2203	4300	6503	SO:0001819	synonymous_variant	81469	exon1			TTTCATCCTTCTA	BK004417	CCDS31093.1	1q44	2012-08-09			ENSG00000177476	ENSG00000177476		"GPCR / Class A : Olfactory receptors"	15008	protein-coding gene	gene with protein product							Standard	NM_001001914		Approved		uc010pyz.2	Q8NGZ4	OTTHUMG00000040576	ENST00000320002.2:c.39C>T	chr1.hg19:g.247768926C>T		93.0	0.0		94.0	4.0	NM_001001914	B2RN64|Q5JQT1|Q6IF45	Silent	SNP	ENST00000320002.2	hg19	CCDS31093.1																																																																																			.	.		0.468	OR2G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097624.1			T	247768926	C	T	247768926	2	4	362	1	0	0	0	0	0	0	0	1	11008	845	30	3		3	OR2G3	1	247768926	Silent	SNP	C	TCGA-YA-A8S7-01A-11D-A36X-10	10039017	247768926	1481695	13	50559										
APOB	338	hgsc.bcm.edu	37	chr2	21236200	21236201	+	Frame_Shift_Ins	INS	-	-	T													0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	agaacacccaggagaggcacINSttgcagttgatacaacttgg					rs371083133		TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr2:21236200_21236201insT	ENST00000233242.1	-	25	4174_4175	c.4047_4048insA	c.(4045-4050)caagtgfs	p.V1350fs		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	1350					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGGAGAGGCACTTGCAGTTGAT	0.505																																					p.V1350fs		Atlas-INDEL	.											.	APOB	761	.	0			c.4048_4049insA						.																																			SO:0001589	frameshift_variant	338	exon25			.	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.4048dupA	chr2.hg19:g.21236202_21236202dupT	ENSP00000233242:p.Val1350fs	119.0	0.0		113.0	25.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Frame_Shift_Ins	INS	ENST00000233242.1	hg19	CCDS1703.1																																																																																			.	.		0.505	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			T	21236201	-	T	21236200	7	5	362	1	0	1	1	0	0	0	0	0	785	565	20	0	9663	0	APOB	2	21236200	Frame_Shift_Ins	INS	-	TCGA-YA-A8S7-01A-11D-A36X-10		21236200	221963173	14	50560										
YSK4	80122	hgsc.bcm.edu	37	chr2	135763003	135763003	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	atcaaggagtaaagcccagtAccttctgtcctgggttgcca	10	11	2	0			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr2:135763003A>G	ENST00000375845.3	-	3	266		c.e3+1		MAP3K19_ENST00000392917.3_Splice_Site|MAP3K19_ENST00000358371.4_Splice_Site|MAP3K19_ENST00000375844.3_Splice_Site|MAP3K19_ENST00000315513.3_Splice_Site|MAP3K19_ENST00000392918.3_Splice_Site|MAP3K19_ENST00000392915.1_Splice_Site	NM_001018044.2|NM_025052.3	NP_001018054.1|NP_079328.3	Q56UN5	M3K19_HUMAN	mitogen-activated protein kinase kinase kinase 19								ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)										AAAGCCCAGTACCTTCTGTCC	0.433																																					.		Atlas-SNP	.											.	.	.	.	0			c.235+2T>C						.						151	136	141					2																	135763003		2203	4300	6503	SO:0001630	splice_region_variant	80122	exon4			CCCAGTACCTTCT	AK026727	CCDS2176.2, CCDS33293.1, CCDS63021.1, CCDS63020.1, CCDS63022.1	2q21.3	2012-10-16	2012-10-16	2012-10-16	ENSG00000176601	ENSG00000176601		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	26249	protein-coding gene	gene with protein product			"Yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)", "yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)", "YSK4 Sps1/Ste20-related kinase homolog (S. cerevisiae)"	YSK4		12477932	Standard	NM_001282883		Approved	FLJ23074	uc002tue.1	Q56UN5	OTTHUMG00000074083	ENST00000375845.3:c.235+1T>C	chr2.hg19:g.135763003A>G		63.0	0.0		75.0	4.0	NM_001018046	B2RP57|B7ZMH9|E2QRE3|Q56UN1|Q56UN2|Q56UN3|Q56UN4|Q8N4E9|Q9H5T2	Splice_Site	SNP	ENST00000375845.3	hg19	CCDS2176.2	.	.	.	.	.	.	.	.	.	.	A	12.01	1.808973	0.31961	.	.	ENSG00000176601	ENST00000375845;ENST00000358371;ENST00000375844;ENST00000392918;ENST00000392917;ENST00000392915;ENST00000425952	.	.	.	5.08	3.9	0.45041	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.1577	0.31178	0.8215:0.0:0.0:0.1785	.	.	.	.	.	-1	.	.	.	-	.	.	YSK4	135479473	1.000000	0.71417	0.951000	0.38953	0.448000	0.32197	3.873000	0.56093	1.029000	0.39812	0.379000	0.24179	.	.	.		0.433	MAP3K19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000158244.1	NM_025052	Intron	G	135763003	A	G	135763003	5	3	362	1	0	0	0	0	0	0	1	0	17510	405	14	2	3781	2	YSK4	2	135763003	Splice_Site	SNP	A	TCGA-YA-A8S7-01A-11D-A36X-10	114526803	135763003	107436370	15	50561										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196788420	196788420	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	atctctagcatggacatccaGtaccacaagtgctcccagag	8	13	1	1			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr2:196788420G>A	ENST00000312428.6	-	23	3824	c.3724C>T	c.(3724-3726)Ctg>Ttg	p.L1242L		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	1242	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						TGGACATCCAGTACCACAAGT	0.403																																					p.L1242L		Atlas-SNP	.											.	DNAH7	512	.	0			c.C3724T						.						124	115	118					2																	196788420		1981	4162	6143	SO:0001819	synonymous_variant	56171	exon23			CATCCAGTACCAC	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.3724C>T	chr2.hg19:g.196788420G>A		263.0	0.0		308.0	88.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Silent	SNP	ENST00000312428.6	hg19	CCDS42794.1																																																																																			.	.		0.403	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		A	196788420	G	A	196788420	2	1	362	1	0	0	0	0	0	0	0	1	4608	1020	36	3		3	DNAH7	2	196788420	Silent	SNP	G	TCGA-YA-A8S7-01A-11D-A36X-10	61025417	196788420	46410953	16	50562										
SLC6A11	6538	hgsc.bcm.edu	37	chr3	10976791	10976791	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	cacctacccagcctggggctAtggcattggctggctcatgg	13	13	1	0			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr3:10976791A>G	ENST00000254488.2	+	13	1718	c.1652A>G	c.(1651-1653)tAt>tGt	p.Y551C		NM_014229.1	NP_055044.1	P48066	S6A11_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 11	551					brain development (GO:0007420)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter binding (GO:0042165)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(13)|ovary(1)|skin(4)	35				OV - Ovarian serous cystadenocarcinoma(96;0.229)	Clobazam(DB00349)	GCCTGGGGCTATGGCATTGGC	0.562																																					p.Y551C		Atlas-SNP	.											.	SLC6A11	87	.	0			c.A1652G						.						194	172	179					3																	10976791		2203	4300	6503	SO:0001583	missense	6538	exon13			GGGGCTATGGCAT	S75989	CCDS2602.1	3p25.3	2013-07-19	2013-07-19		ENSG00000132164	ENSG00000132164		"Solute carriers"	11044	protein-coding gene	gene with protein product	"GABA transporter 3"	607952	"solute carrier family 6 (neurotransmitter transporter, GABA), member 11"			7874447	Standard	NM_014229		Approved	GAT3	uc003bvz.3	P48066	OTTHUMG00000129718	ENST00000254488.2:c.1652A>G	chr3.hg19:g.10976791A>G	ENSP00000254488:p.Tyr551Cys	137.0	0.0		127.0	24.0	NM_014229	B2R6U6|Q8IYC9	Missense_Mutation	SNP	ENST00000254488.2	hg19	CCDS2602.1	.	.	.	.	.	.	.	.	.	.	A	18.04	3.535097	0.64972	.	.	ENSG00000132164	ENST00000254488	T	0.74842	-0.88	4.19	4.19	0.49359	.	0.000000	0.64402	D	0.000001	D	0.87629	0.6225	M	0.93550	3.43	0.80722	D	1	P	0.49961	0.93	P	0.61275	0.886	D	0.89080	0.3475	10	0.39692	T	0.17	.	13.7375	0.62827	1.0:0.0:0.0:0.0	.	551	P48066	S6A11_HUMAN	C	551	ENSP00000254488:Y551C	ENSP00000254488:Y551C	Y	+	2	0	SLC6A11	10951791	1.000000	0.71417	0.883000	0.34634	0.837000	0.47467	8.941000	0.92964	1.904000	0.55121	0.533000	0.62120	TAT	.	.		0.562	SLC6A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251927.1	NM_014229		G	10976791	A	G	10976791	3	3	362	1	0	0	0	0	1	0	0	0	14689	449	16	2	1702	2	SLC6A11	3	10976791	Missense_Mutation	SNP	A	TCGA-YA-A8S7-01A-11D-A36X-10		10976791	187045639	17	50563										
SETD2	29072	hgsc.bcm.edu	37	chr3	47165806	47165806	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	gagtcgagtctacctgaagaGgtacagctggagggtttgga	16	6	1	2			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr3:47165806G>A	ENST00000409792.3	-	3	362	c.320C>T	c.(319-321)cCt>cTt	p.P107L		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	107					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TACCTGAAGAGGTACAGCTGG	0.428			"N, F, S, Mis"		clear cell renal carcinoma																																p.P107L		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.C320T						.						212	180	190					3																	47165806		692	1591	2283	SO:0001583	missense	29072	exon3			TGAAGAGGTACAG	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.320C>T	chr3.hg19:g.47165806G>A	ENSP00000386759:p.Pro107Leu	110.0	0.0		107.0	21.0	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	hg19	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	G	6.095	0.385853	0.11524	.	.	ENSG00000181555	ENST00000451092;ENST00000543224;ENST00000409792;ENST00000412450	D;T	0.90844	-2.74;1.15	5.42	4.53	0.55603	.	.	.	.	.	D	0.82733	0.5101	N	0.19112	0.55	0.38060	D	0.936058	B;B	0.28128	0.201;0.09	B;B	0.22386	0.039;0.024	T	0.82010	-0.0669	9	0.87932	D	0	.	11.1243	0.48308	0.0:0.1392:0.716:0.1447	.	107;107	F2Z317;Q9BYW2	.;SETD2_HUMAN	L	107;107;107;63	ENSP00000386759:P107L;ENSP00000416401:P63L	ENSP00000386759:P107L	P	-	2	0	SETD2	47140810	1.000000	0.71417	0.997000	0.53966	0.095000	0.18619	3.367000	0.52350	1.262000	0.44165	-0.302000	0.09304	CCT	.	.		0.428	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		A	47165806	G	A	47165806	3	1	362	1	0	0	0	0	1	0	0	0	14146	1000	35	3	7450	3	SETD2	3	47165806	Missense_Mutation	SNP	G	TCGA-YA-A8S7-01A-11D-A36X-10	36189015	47165806	150856624	18	50564										
IP6K1	9807	hgsc.bcm.edu	37	chr3	49785257	49785257	+	Frame_Shift_Del	DEL	A	A	-													0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	ggccagtgactgacctttgtAttcaggggtgaactccttca							TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr3:49785257delA	ENST00000321599.4	-	2	518	c.217delT	c.(217-219)tacfs	p.Y73fs	IP6K1_ENST00000468463.1_Frame_Shift_Del_p.Y73fs|IP6K1_ENST00000395238.1_Intron|IP6K1_ENST00000498149.1_5'Flank|IP6K1_ENST00000460540.1_Intron	NM_001242829.1|NM_153273.3	NP_001229758.1|NP_695005.1	Q92551	IP6K1_HUMAN	inositol hexakisphosphate kinase 1	73					inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol phosphorylation (GO:0046854)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(2)|skin(2)	15						TGACCTTTGTATTCAGGGGTG	0.493																																					p.Y73fs		Atlas-INDEL	.											.	IP6K1	41	.	0			c.218delA						.						52	50	51					3																	49785257		2203	4300	6503	SO:0001589	frameshift_variant	9807	exon2			.	D87452	CCDS33760.1, CCDS43092.1	3p21.31	2009-01-05	2009-01-05	2008-12-22	ENSG00000176095	ENSG00000176095			18360	protein-coding gene	gene with protein product		606991	"inositol hexaphosphate kinase 1"	IHPK1			Standard	NM_001242829		Approved	KIAA0263	uc003cxm.1	Q92551	OTTHUMG00000158197	ENST00000321599.4:c.217delT	chr3.hg19:g.49785257delA	ENSP00000323780:p.Tyr73fs	127.0	0.0		132.0	26.0	NM_153273	A8K157|A8MUX4|Q7L3I7|Q96E38	Frame_Shift_Del	DEL	ENST00000321599.4	hg19	CCDS33760.1																																																																																			.	.		0.493	IP6K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350380.1	NM_153273		-	49785257	A	-	49785257	7	5	362	1	0	1	0	1	0	0	0	0	7797	449	16	0	1128	0	IP6K1	3	49785257	Frame_Shift_Del	DEL	A	TCGA-YA-A8S7-01A-11D-A36X-10	2619451	49785257	148237173	19	50565										
ARGFX	503582	hgsc.bcm.edu	37	chr3	121303907	121303907	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	tcgacctaccggagtcaacaGtaaaggtctgatcccctgtg	10	12	2	1			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr3:121303907G>C	ENST00000334384.3	+	3	374	c.364G>C	c.(364-366)Gta>Cta	p.V122L		NM_001012659.1	NP_001012677.1	A6NJG6	ARGFX_HUMAN	arginine-fifty homeobox	122					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	15				GBM - Glioblastoma multiforme(114;0.152)		GGAGTCAACAGTAAAGGTCTG	0.507																																					p.V122L		Atlas-SNP	.											ARGFX,NS,carcinoma,0,1	ARGFX	36	.	0			c.G364C						.						79	80	80					3																	121303907		2203	4300	6503	SO:0001583	missense	503582	exon4			TCAACAGTAAAGG		CCDS33834.1	3q13.33	2011-06-20			ENSG00000186103	ENSG00000186103		"Homeoboxes / PRD class"	30146	protein-coding gene	gene with protein product		611164					Standard	XM_005247505		Approved		uc003eef.3	A6NJG6	OTTHUMG00000159395	ENST00000334384.3:c.364G>C	chr3.hg19:g.121303907G>C	ENSP00000335578:p.Val122Leu	62.0	0.0		77.0	16.0	NM_001012659		Missense_Mutation	SNP	ENST00000334384.3	hg19	CCDS33834.1	.	.	.	.	.	.	.	.	.	.	G	17.60	3.430688	0.62844	.	.	ENSG00000186103	ENST00000334384	D	0.98958	-5.27	2.92	0.0615	0.14341	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.411364	0.17853	N	0.159762	D	0.97192	0.9082	L	0.58101	1.795	0.09310	N	1	P	0.46395	0.877	P	0.48488	0.579	D	0.93681	0.6998	10	0.87932	D	0	-0.818	5.3905	0.16242	0.4102:0.0:0.5898:0.0	.	122	A6NJG6	ARGFX_HUMAN	L	122	ENSP00000335578:V122L	ENSP00000335578:V122L	V	+	1	0	ARGFX	122786597	0.636000	0.27207	0.092000	0.20876	0.639000	0.38242	0.227000	0.17795	-0.001000	0.14495	0.555000	0.69702	GTA	.	.		0.507	ARGFX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355096.2	NM_001012659		C	121303907	G	C	121303907	3	2	362	1	0	0	0	0	1	0	0	0	859	1029	36	4	374	4	ARGFX	3	121303907	Missense_Mutation	SNP	G	TCGA-YA-A8S7-01A-11D-A36X-10	71518650	121303907	76718523	20	50566										
DNAJC13	23317	hgsc.bcm.edu	37	chr3	132172975	132172975	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	attgaatttataaaagggcaAgtacggaaatattcttcaac	7	5	2	1			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr3:132172975A>G	ENST00000260818.6	+	9	1154	c.906A>G	c.(904-906)caA>caG	p.Q302Q	DNAJC13_ENST00000486798.1_3'UTR	NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	302					osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)		p.Q302Q(1)		breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						TAAAAGGGCAAGTACGGAAAT	0.313																																					p.Q302Q		Atlas-SNP	.											DNAJC13_ENST00000260818,NS,carcinoma,0,1	DNAJC13	253	.	1	Substitution - coding silent(1)	prostate(1)	c.A906G						.						77	91	86					3																	132172975		2201	4285	6486	SO:0001819	synonymous_variant	23317	exon9			AGGGCAAGTACGG	AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"Heat shock proteins / DNAJ (HSP40)"	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.906A>G	chr3.hg19:g.132172975A>G		410.0	1.0		391.0	79.0	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Silent	SNP	ENST00000260818.6	hg19	CCDS33857.1																																																																																			.	.		0.313	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268		G	132172975	A	G	132172975	2	3	362	1	0	0	0	0	0	0	0	1	4634	69	3	2		2	DNAJC13	3	132172975	Silent	SNP	A	TCGA-YA-A8S7-01A-11D-A36X-10	10869068	132172975	65849455	21	50567										
SLC2A2	6514	hgsc.bcm.edu	37	chr3	170725003	170725003	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	ccaagtgctcccctgagagcGgttggagcaatttcaccgat	11	12	1	1			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr3:170725003G>A	ENST00000314251.3	-	5	625	c.546C>T	c.(544-546)acC>acT	p.T182T	SLC2A2_ENST00000382808.4_Silent_p.T63T	NM_000340.1	NP_000331.1	P11168	GTR2_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 2	182					carbohydrate metabolic process (GO:0005975)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transmembrane transport (GO:0035428)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	brush border (GO:0005903)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|hexose transmembrane transporter activity (GO:0015149)			central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)		Streptozocin(DB00428)	CCCTGAGAGCGGTTGGAGCAA	0.458																																					p.T182T		Atlas-SNP	.											.	SLC2A2	71	.	0			c.C546T						.						88	80	83					3																	170725003		2203	4300	6503	SO:0001819	synonymous_variant	6514	exon5			GAGAGCGGTTGGA	J03810	CCDS3215.1	3q26.2-q27	2013-05-22			ENSG00000163581	ENSG00000163581		"Solute carriers"	11006	protein-coding gene	gene with protein product		138160		GLUT2		1852621	Standard	NM_000340		Approved		uc003fhe.1	P11168	OTTHUMG00000158997	ENST00000314251.3:c.546C>T	chr3.hg19:g.170725003G>A		112.0	0.0		131.0	23.0	NM_000340	A8K481|B2R936|B7Z547|F8W8V8|Q9UCW9	Silent	SNP	ENST00000314251.3	hg19	CCDS3215.1																																																																																			.	.		0.458	SLC2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352834.1	NM_000340		A	170725003	G	A	170725003	2	1	362	1	0	0	0	0	0	0	0	1	14559	1103	39	1		1	SLC2A2	3	170725003	Silent	SNP	G	TCGA-YA-A8S7-01A-11D-A36X-10	38552028	170725003	27297427	22	50568										
ECT2	1894	hgsc.bcm.edu	37	chr3	172473092	172473092	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	tacattttaacagaagagatGcctcagattgaaacaagagt	8	6	1	5			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr3:172473092G>C	ENST00000392692.3	+	3	314	c.138G>C	c.(136-138)atG>atC	p.M46I	ECT2_ENST00000441497.2_Missense_Mutation_p.M46I|ECT2_ENST00000540509.1_Missense_Mutation_p.M46I|ECT2_ENST00000232458.5_Missense_Mutation_p.M46I|ECT2_ENST00000427830.1_Missense_Mutation_p.M46I|ECT2_ENST00000417960.1_Missense_Mutation_p.M45I	NM_001258315.1	NP_001245244.1	Q9H8V3	ECT2_HUMAN	epithelial cell transforming 2	46					activation of protein kinase activity (GO:0032147)|activation of Rac GTPase activity (GO:0032863)|activation of Rho GTPase activity (GO:0032862)|apoptotic signaling pathway (GO:0097190)|cell morphogenesis (GO:0000902)|cellular response to calcium ion (GO:0071277)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to ionizing radiation (GO:0071479)|cytokinesis (GO:0000910)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of cytokinesis (GO:0032467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of Rho GTPase activity (GO:0032321)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|centralspindlin complex (GO:0097149)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|tight junction (GO:0005923)	GTPase activator activity (GO:0005096)|protein homodimerization activity (GO:0042803)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.33e-14)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)			CAGAAGAGATGCCTCAGATTG	0.313																																					p.M46I		Atlas-SNP	.											.	ECT2	79	.	0			c.G138C						.						89	93	92					3																	172473092		2203	4296	6499	SO:0001583	missense	1894	exon3			AGAGATGCCTCAG	AA206473	CCDS3220.1, CCDS58860.1	3q26.1-q26.2	2014-03-11	2014-03-11		ENSG00000114346	ENSG00000114346		"Rho guanine nucleotide exchange factors"	3155	protein-coding gene	gene with protein product		600586	"epithelial cell transforming sequence 2 oncogene"			8464478, 10579713	Standard	NM_018098		Approved	ARHGEF31	uc003fil.2	Q9H8V3	OTTHUMG00000156762	ENST00000392692.3:c.138G>C	chr3.hg19:g.172473092G>C	ENSP00000376457:p.Met46Ile	369.0	0.0		311.0	76.0	NM_001258315	Q0MT80|Q2M269|Q6U836|Q9NSV8|Q9NVW9	Missense_Mutation	SNP	ENST00000392692.3	hg19	CCDS58860.1	.	.	.	.	.	.	.	.	.	.	G	14.26	2.482213	0.44147	.	.	ENSG00000114346	ENST00000232458;ENST00000392692;ENST00000427830;ENST00000417960;ENST00000428567;ENST00000426894;ENST00000366090;ENST00000415665;ENST00000438041;ENST00000441497;ENST00000540509	T;T;T;T;T;T;T;T;T;T;T	0.68903	-0.3;-0.19;-0.36;-0.26;0.8;0.8;0.83;0.81;0.85;-0.3;-0.19	5.58	5.58	0.84498	.	0.045058	0.85682	D	0.000000	T	0.62171	0.2406	L	0.50333	1.59	0.58432	D	0.999991	B;B;B;B	0.23990	0.036;0.095;0.011;0.007	B;B;B;B	0.23574	0.012;0.047;0.013;0.008	T	0.58171	-0.7683	10	0.12430	T	0.62	-19.3201	19.5631	0.95380	0.0:0.0:1.0:0.0	.	46;46;46;45	Q9H8V3;Q9H8V3-3;G5E9L8;Q9H8V3-2	ECT2_HUMAN;.;.;.	I	46;46;46;45;45;46;46;46;46;46;46	ENSP00000232458:M46I;ENSP00000376457:M46I;ENSP00000401910:M46I;ENSP00000415876:M45I;ENSP00000403501:M45I;ENSP00000412331:M46I;ENSP00000403446:M46I;ENSP00000412028:M46I;ENSP00000389108:M46I;ENSP00000412259:M46I;ENSP00000443160:M46I	ENSP00000232458:M46I	M	+	3	0	ECT2	173955786	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	6.049000	0.71053	2.628000	0.89032	0.491000	0.48974	ATG	.	.		0.313	ECT2-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000345994.2	NM_018098		C	172473092	G	C	172473092	3	2	362	1	0	0	0	0	1	0	0	0	4903	1319	46	4	144	4	ECT2	3	172473092	Missense_Mutation	SNP	G	TCGA-YA-A8S7-01A-11D-A36X-10	1748089	172473092	25549338	23	50569										
EVC2	132884	hgsc.bcm.edu	37	chr4	5691040	5691040	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	gttaacaagcagccatatgcGggctgtctgtgcttcactcg	11	11	2	0			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr4:5691040G>C	ENST00000344408.5	-	5	603	c.550C>G	c.(550-552)Cgc>Ggc	p.R184G	EVC2_ENST00000310917.2_Missense_Mutation_p.R104G|EVC2_ENST00000344938.1_Missense_Mutation_p.R184G	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	184					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						AGCCATATGCGGGCTGTCTGT	0.542																																					p.R184G		Atlas-SNP	.											.	EVC2	202	.	0			c.C550G						.						88	73	78					4																	5691040		2203	4300	6503	SO:0001583	missense	132884	exon5			ATATGCGGGCTGT	AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.550C>G	chr4.hg19:g.5691040G>C	ENSP00000342144:p.Arg184Gly	90.0	0.0		56.0	8.0	NM_147127	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	hg19	CCDS3382.2	.	.	.	.	.	.	.	.	.	.	G	0.873	-0.731442	0.03135	.	.	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	T;T;T	0.74002	-0.8;-0.79;-0.8	4.54	2.65	0.31530	.	0.777031	0.11710	N	0.537047	T	0.49081	0.1536	N	0.08118	0	0.09310	N	1	B	0.18166	0.026	B	0.14023	0.01	T	0.24512	-1.0158	10	0.27082	T	0.32	-0.8185	4.4327	0.11535	0.1144:0.0:0.6611:0.2245	.	184	Q86UK5	LBN_HUMAN	G	184;104;184	ENSP00000339954:R184G;ENSP00000311683:R104G;ENSP00000342144:R184G	ENSP00000311683:R104G	R	-	1	0	EVC2	5741941	0.003000	0.15002	0.004000	0.12327	0.011000	0.07611	1.368000	0.34216	2.250000	0.74265	0.561000	0.74099	CGC	.	.		0.542	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127		C	5691040	G	C	5691040	3	2	362	1	0	0	0	0	1	0	0	0	5288	1116	39	4	3448	4	EVC2	4	5691040	Missense_Mutation	SNP	G	TCGA-YA-A8S7-01A-11D-A36X-10		5691040	185463236	24	50570										
DSPP	1834	hgsc.bcm.edu	37	chr4	88537208	88537216	+	In_Frame_Del	DEL	AGCAGTGAT	AGCAGTGAT	-													0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	acagcagtgacagcagcgacAgcagtgatagcagtgacagc					rs546380675|rs151217478|rs200679221|rs551655835	byFrequency	TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	AGCAGTGAT	AGCAGTGAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr4:88537208_88537216delAGCAGTGAT	ENST00000282478.7	+	4	3427_3435	c.3394_3402delAGCAGTGAT	c.(3394-3402)agcagtgatdel	p.SSD1135del	DSPP_ENST00000399271.1_In_Frame_Del_p.SSD1135del|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1135	Asp/Ser-rich.			Missing (in Ref. 1; AAF42472 and 3; AAD16120). {ECO:0000305}.	biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			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)		cagcagcgacagcagtgatagcagtgaca	0.565																																					p.1131_1134del		Atlas-INDEL	.											.	DSPP	174	.	0			c.3393_3401del						.																																			SO:0001651	inframe_deletion	1834	exon5			.	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3394_3402delAGCAGTGAT	chr4.hg19:g.88537208_88537216delAGCAGTGAT	ENSP00000282478:p.Ser1135_Asp1137del	127.0	0.0		98.0	58.0	NM_014208	A8MUI0|O95815	In_Frame_Del	DEL	ENST00000282478.7	hg19	CCDS43248.1																																																																																			.	.		0.565	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		-	88537216	AGCAGTGAT	-	88537208	7	5	362	1	0	1	0	1	0	0	0	0	4784	188	7	0	3408	0	DSPP	4	88537208	In_Frame_Del	DEL	AGCAGTGAT	TCGA-YA-A8S7-01A-11D-A36X-10	82846168	88537208	102617068	25	50571										
ZNF827	152485	hgsc.bcm.edu	37	chr4	146806895	146806895	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	cctggctgaacaatgctgacGcactgttggccacatactcg	10	13	0	2			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr4:146806895G>A	ENST00000508784.1	-	4	1909	c.1682C>T	c.(1681-1683)gCg>gTg	p.A561V	ZNF827_ENST00000379448.4_Missense_Mutation_p.A561V|ZNF827_ENST00000513320.1_Missense_Mutation_p.A211V			Q17R98	ZN827_HUMAN	zinc finger protein 827	561					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	all_hematologic(180;0.151)					CAATGCTGACGCACTGTTGGC	0.502																																					p.A561V		Atlas-SNP	.											.	ZNF827	102	.	0			c.C1682T						.						100	99	100					4																	146806895		2203	4300	6503	SO:0001583	missense	152485	exon4			GCTGACGCACTGT	AK091130	CCDS34072.1	4q31.22	2013-01-08			ENSG00000151612	ENSG00000151612		"Zinc fingers, C2H2-type"	27193	protein-coding gene	gene with protein product						12477932	Standard	NM_178835		Approved		uc003ikm.3	Q17R98	OTTHUMG00000161362	ENST00000508784.1:c.1682C>T	chr4.hg19:g.146806895G>A	ENSP00000421863:p.Ala561Val	134.0	0.0		128.0	7.0	NM_178835	B7ZL52|Q7Z4S7|Q8N279	Missense_Mutation	SNP	ENST00000508784.1	hg19		.	.	.	.	.	.	.	.	.	.	G	22.3	4.269972	0.80469	.	.	ENSG00000151612	ENST00000508784;ENST00000513320;ENST00000379448;ENST00000281318;ENST00000440280	T;T;T	0.09911	3.0;2.93;3.04	5.29	5.29	0.74685	.	0.094424	0.64402	D	0.000001	T	0.14270	0.0345	L	0.40543	1.245	0.58432	D	0.999994	D;P;D	0.54772	0.968;0.947;0.968	P;B;P	0.44772	0.46;0.271;0.46	T	0.01305	-1.1390	10	0.44086	T	0.13	-1.7467	18.9492	0.92635	0.0:0.0:1.0:0.0	.	211;561;561	G5E9Z1;Q17R98;Q17R98-2	.;ZN827_HUMAN;.	V	561;211;561;560;211	ENSP00000421863:A561V;ENSP00000423130:A211V;ENSP00000368761:A561V	ENSP00000281318:A560V	A	-	2	0	ZNF827	147026345	1.000000	0.71417	0.997000	0.53966	0.983000	0.72400	6.778000	0.75043	2.472000	0.83506	0.555000	0.69702	GCG	.	.		0.502	ZNF827-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000364654.2	NM_178835		A	146806895	G	A	146806895	3	1	362	1	0	0	0	0	1	0	0	0	18195	1087	38	1	1591	1	ZNF827	4	146806895	Missense_Mutation	SNP	G	TCGA-YA-A8S7-01A-11D-A36X-10	58269687	146806895	44347381	26	50572										
ETFDH	2110	hgsc.bcm.edu	37	chr4	159627390	159627390	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	ttgaagaactcatgggtatgGaaagagctatattctgttag	11	4	2	3			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr4:159627390G>A	ENST00000511912.1	+	11	1667	c.1335G>A	c.(1333-1335)tgG>tgA	p.W445*	ETFDH_ENST00000307738.5_Nonsense_Mutation_p.W398*	NM_001281738.1|NM_004453.2	NP_001268667.1|NP_004444.2	Q16134	ETFD_HUMAN	electron-transferring-flavoprotein dehydrogenase	445					cellular metabolic process (GO:0044237)|electron transport chain (GO:0022900)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|respiratory electron transport chain (GO:0022904)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	integral component of mitochondrial inner membrane (GO:0031305)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)	4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|electron-transferring-flavoprotein dehydrogenase activity (GO:0004174)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, oxidizing metal ions with flavin as acceptor (GO:0043783)|quinone binding (GO:0048038)|ubiquinone binding (GO:0048039)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|prostate(1)|skin(3)	28	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0172)		CATGGGTATGGAAAGAGCTAT	0.373																																					p.W445X		Atlas-SNP	.											.	ETFDH	57	.	0			c.G1335A						.						99	102	101					4																	159627390		2203	4300	6503	SO:0001587	stop_gained	2110	exon11			GGTATGGAAAGAG	S69232	CCDS3800.1, CCDS64090.1	4q32-q35	2008-08-26			ENSG00000171503	ENSG00000171503			3483	protein-coding gene	gene with protein product		231675					Standard	NM_004453		Approved	ETFQO	uc003iqb.3	Q16134	OTTHUMG00000161684	ENST00000511912.1:c.1335G>A	chr4.hg19:g.159627390G>A	ENSP00000426638:p.Trp445*	88.0	0.0		78.0	29.0	NM_004453	B4E3R9|J3KND9|Q7Z347	Nonsense_Mutation	SNP	ENST00000511912.1	hg19	CCDS3800.1	.	.	.	.	.	.	.	.	.	.	G	37	6.456944	0.97581	.	.	ENSG00000171503	ENST00000511912;ENST00000307738	.	.	.	5.89	5.03	0.67393	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.5324	16.9456	0.86229	0.0:0.128:0.872:0.0	.	.	.	.	X	445;398	.	ENSP00000303552:W398X	W	+	3	0	ETFDH	159846840	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	9.869000	0.99810	1.463000	0.47967	0.591000	0.81541	TGG	.	.		0.373	ETFDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365718.2			A	159627390	G	A	159627390	4	1	362	1	0	0	0	0	0	1	0	0	5273	1183	41	3	1377	3	ETFDH	4	159627390	Nonsense_Mutation	SNP	G	TCGA-YA-A8S7-01A-11D-A36X-10	12820495	159627390	31526886	27	50573										
SLCO6A1	133482	hgsc.bcm.edu	37	chr5	101815950	101815950	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	agcacataaaagtgatccaaGtcctattaaaaaggaggaag	9	6	0	1			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr5:101815950G>C	ENST00000506729.1	-	2	718	c.547C>G	c.(547-549)Ctt>Gtt	p.L183V	SLCO6A1_ENST00000514551.1_Intron|SLCO6A1_ENST00000379807.3_Missense_Mutation_p.L183V|SLCO6A1_ENST00000389019.3_Missense_Mutation_p.L183V|SLCO6A1_ENST00000379810.1_Missense_Mutation_p.L183V|SLCO6A1_ENST00000513675.1_Missense_Mutation_p.L183V			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	183						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(17)|lung(22)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	60		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)		AGTGATCCAAGTCCTATTAAA	0.318																																					p.L183V		Atlas-SNP	.											.	SLCO6A1	153	.	0			c.C547G						.						101	104	103					5																	101815950		2203	4298	6501	SO:0001583	missense	133482	exon2			ATCCAAGTCCTAT	AF505657	CCDS34206.1, CCDS75282.1	5q21.2	2013-05-22			ENSG00000205359	ENSG00000205359		"Solute carriers"	23613	protein-coding gene	gene with protein product	"cancer/testis antigen 48"	613365					Standard	XM_005271874		Approved	OATP6A1, OATPY, MGC26949, CT48	uc003knp.3	Q86UG4	OTTHUMG00000162759	ENST00000506729.1:c.547C>G	chr5.hg19:g.101815950G>C	ENSP00000421339:p.Leu183Val	81.0	0.0		83.0	22.0	NM_173488	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Missense_Mutation	SNP	ENST00000506729.1	hg19	CCDS34206.1	.	.	.	.	.	.	.	.	.	.	G	9.816	1.184358	0.21870	.	.	ENSG00000205359	ENST00000506729;ENST00000379807;ENST00000389019;ENST00000513675;ENST00000379810	D;D;D;D;D	0.81659	-1.52;-1.52;-1.52;-1.52;-1.52	4.46	-6.11	0.02131	Major facilitator superfamily domain, general substrate transporter (1);	1.056360	0.07386	N	0.888314	T	0.79482	0.4453	M	0.72118	2.19	0.19575	N	0.999969	P;B;P	0.45531	0.532;0.261;0.86	B;B;P	0.52957	0.376;0.07;0.714	T	0.69064	-0.5244	10	0.30078	T	0.28	.	2.1464	0.03788	0.2352:0.2695:0.3632:0.1321	.	183;183;183	Q86UG4-2;C9J020;Q86UG4	.;.;SO6A1_HUMAN	V	183	ENSP00000421339:L183V;ENSP00000369135:L183V;ENSP00000373671:L183V;ENSP00000421990:L183V;ENSP00000369138:L183V	ENSP00000369135:L183V	L	-	1	0	SLCO6A1	101843849	0.000000	0.05858	0.062000	0.19696	0.012000	0.07955	-1.737000	0.01843	-1.370000	0.02144	-0.469000	0.05056	CTT	.	.		0.318	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488		C	101815950	G	C	101815950	3	2	362	1	0	0	0	0	1	0	0	0	14747	1029	36	4	1660	4	SLCO6A1	5	101815950	Missense_Mutation	SNP	G	TCGA-YA-A8S7-01A-11D-A36X-10		101815950	79099310	28	50574										
EEF1A1	1915	hgsc.bcm.edu	37	chr6	74229620	74229620	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	acatacctcagcagcctcctTctcaaatttttcaatggttc	4	13	3	0			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr6:74229620T>C	ENST00000316292.9	-	1	1121	c.130A>G	c.(130-132)Aag>Gag	p.K44E	EEF1A1_ENST00000331523.2_Missense_Mutation_p.K44E|EEF1A1_ENST00000309268.6_Missense_Mutation_p.K44E|EEF1A1_ENST00000491404.1_5'Flank	NM_001402.5	NP_001393.1	P68104	EF1A1_HUMAN	eukaryotic translation elongation factor 1 alpha 1	44	tr-type G.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation elongation factor activity (GO:0003746)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(6)|prostate(2)|skin(3)	18						GCAGCCTCCTTCTCAAATTTT	0.423																																					p.K44E		Atlas-SNP	.											.	EEF1A1	56	.	0			c.A130G						.						127	129	128					6																	74229620		2203	4300	6503	SO:0001583	missense	1915	exon2			CCTCCTTCTCAAA	BC019669	CCDS4980.1	6q14.1	2010-06-30	2004-11-19		ENSG00000156508	ENSG00000156508			3189	protein-coding gene	gene with protein product		130590	"leukocyte receptor cluster (LRC) member 7"	EF1A, EEF1A, LENG7		8812466, 10941842	Standard	NM_001402		Approved	EE1A1	uc003phj.3	P68104	OTTHUMG00000015031	ENST00000316292.9:c.130A>G	chr6.hg19:g.74229620T>C	ENSP00000339063:p.Lys44Glu	35.0	0.0		33.0	6.0	NM_001402	P04719|P04720|Q6IQ15	Missense_Mutation	SNP	ENST00000316292.9	hg19	CCDS4980.1	.	.	.	.	.	.	.	.	.	.	T	13.92	2.380554	0.42207	.	.	ENSG00000156508	ENST00000316292;ENST00000358190;ENST00000309268;ENST00000331523;ENST00000391977;ENST00000456206;ENST00000356303;ENST00000455918	T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91	4.15	4.15	0.48705	Protein synthesis factor, GTP-binding (2);	0.000000	0.85682	U	0.000000	T	0.23965	0.0580	L	0.39326	1.205	0.80722	D	1	B;B;B;B;B	0.14012	0.002;0.009;0.009;0.009;0.009	B;B;B;B;B	0.26416	0.013;0.069;0.069;0.069;0.069	T	0.21999	-1.0229	10	0.87932	D	0	.	13.6597	0.62359	0.0:0.0:0.0:1.0	.	44;44;44;44;44	A6PW80;P68104;Q53HR5;Q6IPS9;Q5VTE0	.;EF1A1_HUMAN;.;.;EF1A3_HUMAN	E	44	ENSP00000339063:K44E;ENSP00000339053:K44E;ENSP00000330054:K44E;ENSP00000348651:K44E;ENSP00000392366:K44E	ENSP00000339053:K44E	K	-	1	0	EEF1A1	74286341	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	7.669000	0.83911	1.874000	0.54306	0.454000	0.30748	AAG	.	.		0.423	EEF1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041210.2	NM_001402		C	74229620	T	C	74229620	3	2	362	1	0	0	0	0	1	0	0	0	4925	1792	62	2	1286	2	EEF1A1	6	74229620	Missense_Mutation	SNP	T	TCGA-YA-A8S7-01A-11D-A36X-10		74229620	96885447	29	50575										
COL12A1	1303	hgsc.bcm.edu	37	chr6	75904617	75904617	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	tttgcccatgacatatgaacAgtattttcatctataatttt	4	7	2	2			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr6:75904617A>T	ENST00000322507.8	-	3	429	c.120T>A	c.(118-120)acT>acA	p.T40T	COL12A1_ENST00000345356.6_Intron|COL12A1_ENST00000416123.2_Silent_p.T40T|COL12A1_ENST00000483888.2_Silent_p.T40T	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	40	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						ACATATGAACAGTATTTTCAT	0.363																																					p.T40T		Atlas-SNP	.											.	COL12A1	385	.	0			c.T120A						.						93	89	91					6																	75904617		1814	4075	5889	SO:0001819	synonymous_variant	1303	exon3			ATGAACAGTATTT	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.120T>A	chr6.hg19:g.75904617A>T		74.0	0.0		92.0	38.0	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Silent	SNP	ENST00000322507.8	hg19	CCDS43482.1																																																																																			.	.		0.363	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		T	75904617	A	T	75904617	2	4	362	1	0	0	0	0	0	0	0	1	3671	175	7	4		4	COL12A1	6	75904617	Silent	SNP	A	TCGA-YA-A8S7-01A-11D-A36X-10	1674997	75904617	95210450	30	50576										
DOPEY1	23033	hgsc.bcm.edu	37	chr6	83847837	83847837	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	aggatctcgaaaatctcccaAtttcaacattcatcctctct	3	13	5	0	rs145538359		TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr6:83847837A>G	ENST00000349129.2	+	21	4336	c.4076A>G	c.(4075-4077)aAt>aGt	p.N1359S	DOPEY1_ENST00000484282.1_3'UTR|DOPEY1_ENST00000369739.3_Missense_Mutation_p.N1350S|DOPEY1_ENST00000237163.5_Missense_Mutation_p.N1340S	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	1359					protein transport (GO:0015031)					breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(16)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	67		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		AAATCTCCCAATTTCAACATT	0.428																																					p.N1359S		Atlas-SNP	.											.	DOPEY1	190	.	0			c.A4076G						.	G	SER/ASN,SER/ASN	1,4405	825.1+/-416.5	0,1,2202	113	117	115		4049,4076	-9.9	0.1	6	dbSNP_134	115	0,8598		0,0,4299	no	missense,missense	DOPEY1	NM_001199942.1,NM_015018.3	46,46	0,1,6501	GG,GA,AA		0.0,0.0227,0.0077	benign,benign	1350/2477,1359/2466	83847837	1,13003	2203	4299	6502	SO:0001583	missense	23033	exon21			CTCCCAATTTCAA	AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097			21194	protein-coding gene	gene with protein product			"KIAA1117"	KIAA1117		16301316, 16303751, 10931277	Standard	NM_015018		Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365	ENST00000349129.2:c.4076A>G	chr6.hg19:g.83847837A>G	ENSP00000195654:p.Asn1359Ser	98.0	0.0		122.0	11.0	NM_015018	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Missense_Mutation	SNP	ENST00000349129.2	hg19	CCDS4996.1	.	.	.	.	.	.	.	.	.	.	G	0.546	-0.851409	0.02651	2.27E-4	0.0	ENSG00000083097	ENST00000349129;ENST00000237163;ENST00000369739	T;T	0.20881	2.04;2.05	5.96	-9.85	0.00476	.	0.538426	0.23081	N	0.052147	T	0.01870	0.0059	N	0.08118	0	0.32598	N	0.526339	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.32322	-0.9911	10	0.07990	T	0.79	.	14.1367	0.65291	0.4447:0.0:0.4839:0.0714	.	1250;1350;1359	E1P545;B2RWN9;Q5JWR5	.;.;DOP1_HUMAN	S	1359;1340;1340	ENSP00000195654:N1359S;ENSP00000237163:N1340S	ENSP00000237163:N1340S	N	+	2	0	DOPEY1	83904556	0.001000	0.12720	0.050000	0.19076	0.778000	0.44026	-0.214000	0.09292	-2.382000	0.00593	-2.352000	0.00242	AAT	.	A|1.000;G|0.000		0.428	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018		G	83847837	A	G	83847837	3	3	362	1	0	0	0	0	1	0	0	0	4709	101	4	2	4150	2	DOPEY1	6	83847837	Missense_Mutation	SNP	A	TCGA-YA-A8S7-01A-11D-A36X-10	7943220	83847837	87267230	31	50577										
FUT9	10690	hgsc.bcm.edu	37	chr6	96651692	96651692	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	aaatccatacctacgggcaaGcatttggagaatatgtcaat	8	8	1	1			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr6:96651692G>C	ENST00000302103.5	+	3	987	c.661G>C	c.(661-663)Gca>Cca	p.A221P		NM_006581.3	NP_006572.2	Q9Y231	FUT9_HUMAN	fucosyltransferase 9 (alpha (1,3) fucosyltransferase)	221					carbohydrate metabolic process (GO:0005975)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|nervous system development (GO:0007399)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|liver(2)|lung(10)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(2)	34		all_cancers(76;4.77e-07)|Acute lymphoblastic leukemia(125;4.01e-09)|all_hematologic(75;1.25e-06)|all_epithelial(107;0.00279)|Colorectal(196;0.0356)		BRCA - Breast invasive adenocarcinoma(108;0.08)		CTACGGGCAAGCATTTGGAGA	0.368																																					p.A221P	Melanoma(98;1369 1476 6592 22940 26587)	Atlas-SNP	.											.	FUT9	79	.	0			c.G661C						.						54	53	53					6																	96651692		2203	4300	6503	SO:0001583	missense	10690	exon3			GGGCAAGCATTTG	AB023021	CCDS5033.1	6q16	2013-02-26			ENSG00000172461	ENSG00000172461		"Fucosyltransferases"	4020	protein-coding gene	gene with protein product		606865				10386598, 10575236	Standard	NM_006581		Approved	Fuc-TIX	uc003pop.4	Q9Y231	OTTHUMG00000015236	ENST00000302103.5:c.661G>C	chr6.hg19:g.96651692G>C	ENSP00000302599:p.Ala221Pro	83.0	0.0		86.0	12.0	NM_006581	Q5T0W4	Missense_Mutation	SNP	ENST00000302103.5	hg19	CCDS5033.1	.	.	.	.	.	.	.	.	.	.	G	18.72	3.683913	0.68157	.	.	ENSG00000172461	ENST00000302103	T	0.26223	1.75	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.36690	0.0976	M	0.75884	2.315	0.80722	D	1	B	0.33477	0.413	P	0.46479	0.518	T	0.14811	-1.0459	10	0.66056	D	0.02	-12.7125	18.9407	0.92604	0.0:0.0:1.0:0.0	.	221	Q9Y231	FUT9_HUMAN	P	221	ENSP00000302599:A221P	ENSP00000302599:A221P	A	+	1	0	FUT9	96758413	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.476000	0.97823	2.719000	0.93026	0.655000	0.94253	GCA	.	.		0.368	FUT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041554.2	NM_006581		C	96651692	G	C	96651692	3	2	362	1	0	0	0	0	1	0	0	0	6119	971	34	4	663	4	FUT9	6	96651692	Missense_Mutation	SNP	G	TCGA-YA-A8S7-01A-11D-A36X-10	12803855	96651692	74463375	32	50578										
MAN1A1	4121	hgsc.bcm.edu	37	chr6	119510970	119510970	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	ggtcaggtggcccatcttgtGctccaggaggccccctttcc	12	15	2	0			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr6:119510970G>A	ENST00000368468.3	-	10	1846	c.1405C>T	c.(1405-1407)Cac>Tac	p.H469Y		NM_005907.3	NP_005898.2	P33908	MA1A1_HUMAN	mannosidase, alpha, class 1A, member 1	469					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|mannosidase activity (GO:0015923)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(8)|ovary(2)|prostate(2)|skin(3)	24		all_epithelial(87;0.173)		OV - Ovarian serous cystadenocarcinoma(136;0.0612)|GBM - Glioblastoma multiforme(226;0.0702)|all cancers(137;0.115)		CCCATCTTGTGCTCCAGGAGG	0.552																																					p.H469Y	Ovarian(136;8 1825 12608 33541 47587)	Atlas-SNP	.											.	MAN1A1	77	.	0			c.C1405T						.						82	77	79					6																	119510970		2203	4300	6503	SO:0001583	missense	4121	exon10			TCTTGTGCTCCAG	AK025599	CCDS5122.1	6q22	2008-08-29			ENSG00000111885	ENSG00000111885	3.2.1.113		6821	protein-coding gene	gene with protein product		604344				8223597	Standard	NM_005907		Approved		uc003pym.2	P33908	OTTHUMG00000015472	ENST00000368468.3:c.1405C>T	chr6.hg19:g.119510970G>A	ENSP00000357453:p.His469Tyr	134.0	0.0		131.0	57.0	NM_005907	E7EU32|Q6P052|Q9NU44|Q9UJI3	Missense_Mutation	SNP	ENST00000368468.3	hg19	CCDS5122.1	.	.	.	.	.	.	.	.	.	.	G	28.6	4.937048	0.92458	.	.	ENSG00000111885	ENST00000368468	T	0.71461	-0.57	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.76579	0.4007	L	0.56769	1.78	0.80722	D	1	D	0.69078	0.997	P	0.60012	0.867	T	0.76242	-0.3031	10	0.49607	T	0.09	-36.6344	19.4267	0.94743	0.0:0.0:1.0:0.0	.	469	P33908	MA1A1_HUMAN	Y	469	ENSP00000357453:H469Y	ENSP00000357453:H469Y	H	-	1	0	MAN1A1	119552669	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.863000	0.87023	2.596000	0.87737	0.655000	0.94253	CAC	.	.		0.552	MAN1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042015.1	NM_005907		A	119510970	G	A	119510970	3	1	362	1	0	0	0	0	1	0	0	0	9219	1319	46	3	572	3	MAN1A1	6	119510970	Missense_Mutation	SNP	G	TCGA-YA-A8S7-01A-11D-A36X-10	22859278	119510970	51604097	33	50579										
ZNF479	90827	hgsc.bcm.edu	37	chr7	57188114	57188114	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	tgtctagtaaggtttgaggaCcagctaaaggctttgccaca	11	8	1	1			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr7:57188114C>G	ENST00000331162.4	-	5	1278	c.1008G>C	c.(1006-1008)tgG>tgC	p.W336C		NM_033273.1	NP_150376.1	Q96JC4	ZN479_HUMAN	zinc finger protein 479	336					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(53)|ovary(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	84			GBM - Glioblastoma multiforme(1;9.18e-12)			GGTTTGAGGACCAGCTAAAGG	0.453																																					p.W336C		Atlas-SNP	.											.	ZNF479	193	.	0			c.G1008C						.						17	18	18					7																	57188114		2037	4221	6258	SO:0001583	missense	90827	exon5			TGAGGACCAGCTA	AF277624	CCDS43590.1	7p11.2	2013-01-08			ENSG00000185177	ENSG00000185177		"Zinc fingers, C2H2-type", "-"	23258	protein-coding gene	gene with protein product						11410164	Standard	NM_033273		Approved	KR19	uc010kzo.3	Q96JC4	OTTHUMG00000156682	ENST00000331162.4:c.1008G>C	chr7.hg19:g.57188114C>G	ENSP00000333776:p.Trp336Cys	203.0	0.0		262.0	83.0	NM_033273		Missense_Mutation	SNP	ENST00000331162.4	hg19	CCDS43590.1	.	.	.	.	.	.	.	.	.	.	t	0	-2.749784	0.00086	.	.	ENSG00000185177	ENST00000331162	T	0.07567	3.18	1.01	-2.03	0.07365	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03651	0.0104	N	0.04880	-0.145	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36407	-0.9749	9	0.37606	T	0.19	.	6.028	0.19665	0.0:0.6308:0.2019:0.1673	.	336	Q96JC4	ZN479_HUMAN	C	336	ENSP00000333776:W336C	ENSP00000333776:W336C	W	-	3	0	ZNF479	57192056	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.972000	0.00087	-3.137000	0.00234	-3.214000	0.00053	TGG	.	.		0.453	ZNF479-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345302.1	XM_291202		G	57188114	C	G	57188114	3	3	362	1	0	0	0	0	1	0	0	0	17948	508	18	4	570	4	ZNF479	7	57188114	Missense_Mutation	SNP	C	TCGA-YA-A8S7-01A-11D-A36X-10		57188114	101950549	34	50580										
ANKRD7	56311	hgsc.bcm.edu	37	chr7	117876954	117876954	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	tgtggattcacagctgaggaAtatgtttatttccatggttt	10	5	1	1			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr7:117876954A>C	ENST00000265224.4	+	5	841	c.686A>C	c.(685-687)aAt>aCt	p.N229T	ANKRD7_ENST00000357099.4_Missense_Mutation_p.N249T|ANKRD7_ENST00000433239.1_Missense_Mutation_p.N176T|ANKRD7_ENST00000417525.1_Missense_Mutation_p.N176T|ANKRD7_ENST00000477532.1_3'UTR	NM_019644.3	NP_062618.2	Q92527	ANKR7_HUMAN	ankyrin repeat domain 7	229					male gonad development (GO:0008584)	nucleus (GO:0005634)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)	29						CAGCTGAGGAATATGTTTATT	0.388																																					p.N229T		Atlas-SNP	.											.	ANKRD7	44	.	0			c.A686C						.						298	276	283					7																	117876954		1900	4120	6020	SO:0001583	missense	56311	exon5			TGAGGAATATGTT	D78334	CCDS43638.1	7q31	2013-01-10			ENSG00000106013	ENSG00000106013		"Ankyrin repeat domain containing"	18588	protein-coding gene	gene with protein product	"testis-specific ankyrin motif containing protein"	610731				8812458	Standard	NM_019644		Approved	TSA806	uc003vji.3	Q92527	OTTHUMG00000156960	ENST00000265224.4:c.686A>C	chr7.hg19:g.117876954A>C	ENSP00000265224:p.Asn229Thr	132.0	0.0		133.0	17.0	NM_019644	B4DYF5|Q96QN1|Q9UDM3	Missense_Mutation	SNP	ENST00000265224.4	hg19	CCDS43638.1	.	.	.	.	.	.	.	.	.	.	A	8.617	0.890390	0.17613	.	.	ENSG00000106013	ENST00000357099;ENST00000265224;ENST00000417525;ENST00000433239	T;T;T;T	0.39592	1.08;1.18;1.12;1.07	4.35	0.115	0.14643	.	1.317880	0.05170	N	0.499413	T	0.27063	0.0663	L	0.36672	1.1	0.20563	N	0.999889	B	0.26081	0.141	B	0.19666	0.026	T	0.13845	-1.0494	10	0.16420	T	0.52	0.6552	1.696	0.02862	0.4111:0.3301:0.0984:0.1604	.	229	Q92527	ANKR7_HUMAN	T	249;229;176;176	ENSP00000349612:N249T;ENSP00000265224:N229T;ENSP00000395595:N176T;ENSP00000388473:N176T	ENSP00000265224:N229T	N	+	2	0	ANKRD7	117664190	0.994000	0.37717	1.000000	0.80357	0.083000	0.17756	0.068000	0.14531	0.167000	0.19631	0.254000	0.18369	AAT	.	.		0.388	ANKRD7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346826.1	NM_001077708		C	117876954	A	C	117876954	3	2	362	1	0	0	0	0	1	0	0	0	686	101	4	5	704	5	ANKRD7	7	117876954	Missense_Mutation	SNP	A	TCGA-YA-A8S7-01A-11D-A36X-10	60688840	117876954	41261709	35	50581										
C7orf58	79974	hgsc.bcm.edu	37	chr7	120782177	120782177	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	cccttgtttgaggccttcacAgcatgtggttttgtgcaggt	12	9	1	1			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr7:120782177A>G	ENST00000310396.5	+	16	2504	c.2037A>G	c.(2035-2037)acA>acG	p.T679T	CPED1_ENST00000450913.2_Silent_p.T679T|CPED1_ENST00000423795.1_Silent_p.T459T	NM_024913.4	NP_079189.4	A4D0V7	CPED1_HUMAN	cadherin-like and PC-esterase domain containing 1	679						endoplasmic reticulum (GO:0005783)											AGGCCTTCACAGCATGTGGTT	0.443																																					p.T679T		Atlas-SNP	.											.	.	.	.	0			c.A2037G						.						183	161	169					7																	120782177		2203	4299	6502	SO:0001819	synonymous_variant	79974	exon15			CTTCACAGCATGT		CCDS34739.1, CCDS47690.1	7q31.31	2012-06-12	2012-06-12	2012-06-12	ENSG00000106034	ENSG00000106034			26159	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 58"	C7orf58		20056006	Standard	NM_024913		Approved	FLJ21986	uc003vjq.4	A4D0V7	OTTHUMG00000156982	ENST00000310396.5:c.2037A>G	chr7.hg19:g.120782177A>G		111.0	0.0		144.0	51.0	NM_001105533	A8K1R3|Q6UXT1|Q86T76|Q86T84|Q8N2T5|Q96NC9	Silent	SNP	ENST00000310396.5	hg19	CCDS34739.1																																																																																			.	.		0.443	CPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346959.1	NM_024913		G	120782177	A	G	120782177	2	3	362	1	0	0	0	0	0	0	0	1	2407	175	7	2		2	C7orf58	7	120782177	Silent	SNP	A	TCGA-YA-A8S7-01A-11D-A36X-10	2905223	120782177	38356486	36	50582										
ADAM2	2515	hgsc.bcm.edu	37	chr8	39695697	39695697	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	cgctgagcagaaacaagacgCgccacatggcttgaagtcct	11	12	0	4			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr8:39695697C>T	ENST00000265708.4	-	1	111	c.8G>A	c.(7-9)cGc>cAc	p.R3H	ADAM2_ENST00000523181.1_5'UTR|ADAM2_ENST00000347580.4_Missense_Mutation_p.R3H|ADAM2_ENST00000521880.1_Missense_Mutation_p.R3H|ADAM2_ENST00000379853.2_Missense_Mutation_p.R3H	NM_001464.3	NP_001455.3	Q99965	ADAM2_HUMAN	ADAM metallopeptidase domain 2	3				Missing (in Ref. 2; AAD04206). {ECO:0000305}.	adult behavior (GO:0030534)|binding of sperm to zona pellucida (GO:0007339)|cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|visual learning (GO:0008542)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R3H(1)		haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(29)|ovary(3)|prostate(1)|skin(5)|urinary_tract(1)	53		all_cancers(7;2.38e-28)|all_epithelial(6;8.85e-21)|all_lung(54;1.24e-07)|Lung NSC(58;1.94e-07)|Hepatocellular(245;0.00745)|Breast(189;0.00908)|Renal(179;0.0183)|Colorectal(162;0.246)	LUSC - Lung squamous cell carcinoma(45;0.000149)	READ - Rectum adenocarcinoma(644;0.0689)|Kidney(114;0.162)		AAACAAGACGCGCCACATGGC	0.617																																					p.R3H		Atlas-SNP	.											ADAM2,face,carcinoma,0,1	ADAM2	124	.	1	Substitution - Missense(1)	skin(1)	c.G8A						.						74	75	75					8																	39695697		2203	4300	6503	SO:0001583	missense	2515	exon1			AAGACGCGCCACA	U52370	CCDS34884.1, CCDS64882.1, CCDS64883.1	8p11.2	2009-03-25	2008-07-31		ENSG00000104755	ENSG00000104755		"ADAM metallopeptidase domain containing"	198	protein-coding gene	gene with protein product	"cancer/testis antigen 15"	601533	"fertilin beta"	FTNB		8702389, 9070941	Standard	NM_001278113		Approved	PH-30b, PH30, CT15	uc003xnj.4	Q99965	OTTHUMG00000164041	ENST00000265708.4:c.8G>A	chr8.hg19:g.39695697C>T	ENSP00000265708:p.Arg3His	160.0	0.0		130.0	13.0	NM_001464	P78326|Q9UQQ8	Missense_Mutation	SNP	ENST00000265708.4	hg19	CCDS34884.1	.	.	.	.	.	.	.	.	.	.	C	11.64	1.699800	0.30142	.	.	ENSG00000104755	ENST00000347580;ENST00000379853;ENST00000265708;ENST00000521880	T;T;T;T	0.02177	5.03;4.41;5.27;5.23	3.27	2.39	0.29439	.	.	.	.	.	T	0.01976	0.0062	L	0.39898	1.24	0.09310	N	1	B;P;B;P	0.50819	0.002;0.928;0.032;0.939	B;B;B;B	0.36719	0.001;0.211;0.008;0.231	T	0.50972	-0.8764	8	.	.	.	.	6.4652	0.21977	0.0:0.8654:0.0:0.1346	.	3;3;3;3	B4DWY7;Q6P2G0;Q99965-2;Q99965	.;.;.;ADAM2_HUMAN	H	3	ENSP00000343854:R3H;ENSP00000369182:R3H;ENSP00000265708:R3H;ENSP00000429352:R3H	.	R	-	2	0	ADAM2	39814854	0.000000	0.05858	0.002000	0.10522	0.045000	0.14185	0.552000	0.23376	0.942000	0.37525	0.467000	0.42956	CGC	.	.		0.617	ADAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376926.1	NM_001464		T	39695697	C	T	39695697	3	4	362	1	0	0	0	0	1	0	0	0	241	768	27	1	2279	1	ADAM2	8	39695697	Missense_Mutation	SNP	C	TCGA-YA-A8S7-01A-11D-A36X-10		39695697	106668325	37	50583										
CYP7A1	1581	hgsc.bcm.edu	37	chr8	59404951	59404951	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	tctggatctaagtgcattaaCtgtgggtaaagagctatgat	11	5	2	2			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr8:59404951C>T	ENST00000301645.3	-	5	1313	c.1176G>A	c.(1174-1176)caG>caA	p.Q392Q		NM_000780.3	NP_000771.2	P22680	CP7A1_HUMAN	cytochrome P450, family 7, subfamily A, polypeptide 1	392					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to glucose stimulus (GO:0071333)|cholesterol catabolic process (GO:0006707)|cholesterol homeostasis (GO:0042632)|regulation of bile acid biosynthetic process (GO:0070857)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	cholesterol 7-alpha-monooxygenase activity (GO:0008123)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(4)|endometrium(1)|kidney(2)|large_intestine(5)|lung(19)|ovary(1)|prostate(1)|urinary_tract(1)	34		all_lung(136;0.0271)|Lung NSC(129;0.0351)|all_epithelial(80;0.0554)				AGTGCATTAACTGTGGGTAAA	0.438									Neonatal Giant Cell Hepatitis																												p.Q392Q		Atlas-SNP	.											.	CYP7A1	76	.	0			c.G1176A						.						184	161	169					8																	59404951		2203	4300	6503	SO:0001819	synonymous_variant	1581	exon5	Familial Cancer Database	Neonatal Hemochromatosis	CATTAACTGTGGG	M89803	CCDS6171.1	8q11-q12	2010-05-04	2003-01-14		ENSG00000167910	ENSG00000167910	1.14.13.17	"Cytochrome P450s"	2651	protein-coding gene	gene with protein product	"cholesterol 7 alpha-monooxygenase"	118455	"cytochrome P450, subfamily VIIA (cholesterol 7 alpha-monooxygenase), polypeptide 1"	CYP7		1358792	Standard	NM_000780		Approved		uc003xtm.4	P22680	OTTHUMG00000164301	ENST00000301645.3:c.1176G>A	chr8.hg19:g.59404951C>T		186.0	0.0		278.0	26.0	NM_000780	P78454|Q3MIL8|Q7KZ19	Silent	SNP	ENST00000301645.3	hg19	CCDS6171.1																																																																																			.	.		0.438	CYP7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378190.1	NM_000780		T	59404951	C	T	59404951	2	4	362	1	0	0	0	0	0	0	0	1	4198	564	20	3		3	CYP7A1	8	59404951	Silent	SNP	C	TCGA-YA-A8S7-01A-11D-A36X-10	19709254	59404951	86959071	38	50584										
RBM12B	389677	hgsc.bcm.edu	37	chr8	94747750	94747750	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	gaaatttcttaaatctctttCgtcaatactgagggacagat	7	7	3	2			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr8:94747750C>T	ENST00000399300.2	-	3	1102	c.889G>A	c.(889-891)Gaa>Aaa	p.E297K	RBM12B_ENST00000517700.1_Missense_Mutation_p.E297K|RP11-10N23.4_ENST00000517998.1_RNA|RBM12B_ENST00000520961.1_Intron	NM_203390.2	NP_976324.2	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B	297	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.						nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	30	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			AAATCTCTTTCGTCAATACTG	0.338																																					p.E297K		Atlas-SNP	.											.	RBM12B	78	.	0			c.G889A						.						64	61	62					8																	94747750		1806	4071	5877	SO:0001583	missense	389677	exon3			CTCTTTCGTCAAT		CCDS43755.1	8q22	2014-05-20			ENSG00000183808	ENSG00000183808		"RNA binding motif (RRM) containing"	32310	protein-coding gene	gene with protein product							Standard	NM_203390		Approved		uc003yfz.3	Q8IXT5	OTTHUMG00000164317	ENST00000399300.2:c.889G>A	chr8.hg19:g.94747750C>T	ENSP00000382239:p.Glu297Lys	82.0	0.0		126.0	20.0	NM_203390	A8MYB5	Missense_Mutation	SNP	ENST00000399300.2	hg19	CCDS43755.1	.	.	.	.	.	.	.	.	.	.	C	0.017	-1.501601	0.01001	.	.	ENSG00000183808	ENST00000399300;ENST00000517700	T;T	0.36520	1.25;1.25	5.26	2.9	0.33743	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.078542	0.53938	N	0.000050	T	0.10380	0.0254	N	0.01352	-0.895	0.28387	N	0.919275	B	0.06786	0.001	B	0.04013	0.001	T	0.35748	-0.9776	10	0.02654	T	1	-18.9042	9.0783	0.36536	0.0:0.1534:0.0:0.8466	.	297	Q8IXT5	RB12B_HUMAN	K	297	ENSP00000382239:E297K;ENSP00000427729:E297K	ENSP00000382239:E297K	E	-	1	0	RBM12B	94816926	1.000000	0.71417	0.945000	0.38365	0.460000	0.32559	5.932000	0.70121	0.411000	0.25702	-0.469000	0.05056	GAA	.	.		0.338	RBM12B-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383603.1	NM_203390		T	94747750	C	T	94747750	3	4	362	1	0	0	0	0	1	0	0	0	13129	893	31	1	2120	1	RBM12B	8	94747750	Missense_Mutation	SNP	C	TCGA-YA-A8S7-01A-11D-A36X-10	35342799	94747750	51616272	39	50585										
DCAF13	81034	hgsc.bcm.edu	37	chr8	104427710	104427710	+	5'Flank	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	ctgagccggaatccggacaaTtatgtccgcgaaaccaagtt	10	11	0	1			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr8:104427710T>C	ENST00000297578.4	-	0	0				DCAF13_ENST00000521999.1_3'UTR|DCAF13_ENST00000519682.1_Silent_p.N8N|DCAF13_ENST00000297579.5_Silent_p.N164N|DCAF13_ENST00000521716.1_Silent_p.N8N|DCAF13_ENST00000521971.1_Silent_p.N8N|SLC25A32_ENST00000543107.1_5'Flank	NM_030780.3	NP_110407.2	Q9H2D1	MFTC_HUMAN	solute carrier family 25 (mitochondrial folate carrier), member 32						folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|mitochondrial transport (GO:0006839)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	folic acid transporter activity (GO:0008517)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	9			OV - Ovarian serous cystadenocarcinoma(57;2.79e-06)|STAD - Stomach adenocarcinoma(118;0.197)		Folic Acid(DB00158)	ATCCGGACAATTATGTCCGCG	0.567																																					p.N164N		Atlas-SNP	.											.	DCAF13	66	.	0			c.T492C						.						30	34	32					8																	104427710		2203	4300	6503	SO:0001631	upstream_gene_variant	25879	exon1			GGACAATTATGTC	AF283645	CCDS6300.1	8q22.3	2013-05-22	2013-03-15		ENSG00000164933	ENSG00000164933		"Solute carriers"	29683	protein-coding gene	gene with protein product		610815	"solute carrier family 25, member 32"			10978331	Standard	NM_030780		Approved	MFTC	uc003yll.4	Q9H2D1	OTTHUMG00000164790		chr8.hg19:g.104427710T>C	Exception_encountered	116.0	0.0		153.0	15.0	NM_015420	Q96JZ6|Q96SU7	Silent	SNP	ENST00000297578.4	hg19	CCDS6300.1																																																																																			.	.		0.567	SLC25A32-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380290.2	NM_030780		C	104427710	T	C	104427710	1	2	362	0	1	0	0	0	0	0	0	0	4268	1490	52	2		2	DCAF13	8	104427710	5'Flank	SNP	T	TCGA-YA-A8S7-01A-11D-A36X-10	9679960	104427710	41936312	40	50586										
KANK1	23189	hgsc.bcm.edu	37	chr9	711084	711084	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	aacaagcagtgccccaacttCctcatagccagaagtcaagt	7	13	2	1			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr9:711084C>A	ENST00000382303.1	+	7	970	c.318C>A	c.(316-318)ttC>ttA	p.F106L	KANK1_ENST00000382293.3_5'UTR|KANK1_ENST00000489369.1_3'UTR|KANK1_ENST00000382297.2_Missense_Mutation_p.F106L	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	106					negative regulation of actin filament polymerization (GO:0030837)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lamellipodium morphogenesis (GO:2000393)|negative regulation of neuron projection development (GO:0010977)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of wound healing (GO:0090303)|regulation of establishment of cell polarity (GO:2000114)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	beta-catenin binding (GO:0008013)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|stomach(4)|upper_aerodigestive_tract(1)	43		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		GCCCCAACTTCCTCATAGCCA	0.507																																					p.F106L		Atlas-SNP	.											.	KANK1	231	.	0			c.C318A						.						150	117	128					9																	711084		2203	4300	6503	SO:0001583	missense	23189	exon7			CAACTTCCTCATA	AL833161	CCDS6441.1, CCDS34976.1	9p24.3	2013-01-10	2008-01-29	2008-01-29	ENSG00000107104	ENSG00000107104		"KN motif and ankyrin repeat domain containing", "Ankyrin repeat domain containing"	19309	protein-coding gene	gene with protein product		607704	"ankyrin repeat domain 15"	ANKRD15		12133830, 17996375, 19554261	Standard	NM_015158		Approved	KIAA0172, KANK	uc003zgn.2	Q14678	OTTHUMG00000019434	ENST00000382303.1:c.318C>A	chr9.hg19:g.711084C>A	ENSP00000371740:p.Phe106Leu	115.0	0.0		93.0	30.0	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Missense_Mutation	SNP	ENST00000382303.1	hg19	CCDS34976.1	.	.	.	.	.	.	.	.	.	.	C	7.285	0.609960	0.14066	.	.	ENSG00000107104	ENST00000382303;ENST00000354485;ENST00000382297	T;T	0.38240	1.15;1.15	5.99	3.19	0.36642	.	0.000000	0.53938	D	0.000057	T	0.25606	0.0623	L	0.38838	1.175	0.80722	D	1	B;B	0.24317	0.101;0.075	B;B	0.29663	0.105;0.042	T	0.03840	-1.0999	10	0.09843	T	0.71	-0.065	9.536	0.39222	0.0:0.7352:0.0:0.2648	.	106;106	Q5W0W1;Q14678	.;KANK1_HUMAN	L	106	ENSP00000371740:F106L;ENSP00000371734:F106L	ENSP00000346479:F106L	F	+	3	2	KANK1	701084	0.997000	0.39634	0.998000	0.56505	0.398000	0.30690	0.839000	0.27586	0.435000	0.26365	0.655000	0.94253	TTC	.	.		0.507	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158		A	711084	C	A	711084	3	1	362	1	0	0	0	0	1	0	0	0	7985	854	30	3	324	3	KANK1	9	711084	Missense_Mutation	SNP	C	TCGA-YA-A8S7-01A-11D-A36X-10		711084	140502347	41	50587										
VPS13A	23230	hgsc.bcm.edu	37	chr9	79971726	79971726	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	ttagagagagaatttaaggaAtatactgaatcttctccttc	7	6	2	3			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr9:79971726A>G	ENST00000360280.3	+	55	8009	c.7749A>G	c.(7747-7749)gaA>gaG	p.E2583E	VPS13A_ENST00000376636.3_Silent_p.E2544E|VPS13A_ENST00000376634.4_Silent_p.E2583E|VPS13A_ENST00000357409.5_Silent_p.E2583E	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	2583					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						AATTTAAGGAATATACTGAAT	0.358																																					p.E2583E		Atlas-SNP	.											.	VPS13A	735	.	0			c.A7749G						.						81	83	83					9																	79971726		2203	4299	6502	SO:0001819	synonymous_variant	23230	exon55			TAAGGAATATACT	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"chorein"	605978	"chorea acanthocytosis", "vacuolar protein sorting 13A (yeast)"	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.7749A>G	chr9.hg19:g.79971726A>G		79.0	0.0		75.0	9.0	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Silent	SNP	ENST00000360280.3	hg19	CCDS6655.1																																																																																			.	.		0.358	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		G	79971726	A	G	79971726	2	3	362	1	0	0	0	0	0	0	0	1	17204	98	4	2		2	VPS13A	9	79971726	Silent	SNP	A	TCGA-YA-A8S7-01A-11D-A36X-10	79260642	79971726	61241705	42	50588										
NODAL	4838	hgsc.bcm.edu	37	chr10	72195099	72195099	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	ccaacaggattaggacactcGccctcacagcgataggcgtt	10	13	1	0			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr10:72195099G>A	ENST00000287139.3	-	2	833	c.834C>T	c.(832-834)ggC>ggT	p.G278G	AC022532.1_ENST00000420338.2_Missense_Mutation_p.A16T	NM_018055.4	NP_060525.3	Q96S42	NODAL_HUMAN	nodal growth differentiation factor	278					axial mesodermal cell fate specification (GO:0048327)|brain development (GO:0007420)|cell migration involved in gastrulation (GO:0042074)|digestive tract morphogenesis (GO:0048546)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic pattern specification (GO:0009880)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|endodermal cell differentiation (GO:0035987)|epiblast cell-extraembryonic ectoderm cell signaling involved in anterior/posterior axis specification (GO:0060802)|floor plate morphogenesis (GO:0033505)|formation of anatomical boundary (GO:0048859)|growth (GO:0040007)|heart looping (GO:0001947)|inhibition of neuroepithelial cell differentiation (GO:0002085)|left lung morphogenesis (GO:0060460)|liver development (GO:0001889)|maternal placenta development (GO:0001893)|maternal process involved in parturition (GO:0060137)|mesendoderm development (GO:0048382)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of chorionic trophoblast cell proliferation (GO:1901383)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of trophoblast cell migration (GO:1901164)|neural fold formation (GO:0001842)|nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900164)|placenta development (GO:0001890)|polarity specification of proximal/distal axis (GO:0010085)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900224)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of gastrulation (GO:0010470)|regulation of stem cell maintenance (GO:2000036)|SMAD protein signal transduction (GO:0060395)|stem cell maintenance (GO:0019827)|transforming growth factor beta receptor signaling pathway involved in primitive streak formation (GO:0090010)|trophectodermal cellular morphogenesis (GO:0001831)|vasculature development (GO:0001944)	extracellular space (GO:0005615)	morphogen activity (GO:0016015)|type I activin receptor binding (GO:0070698)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(2)	15						TAGGACACTCGCCCTCACAGC	0.572																																					p.G278G		Atlas-SNP	.											.	NODAL	32	.	0			c.C834T						.						87	67	74					10																	72195099		2203	4300	6503	SO:0001819	synonymous_variant	4838	exon2			ACACTCGCCCTCA	BC033585	CCDS7304.1	10q22.1	2012-12-07	2012-12-07		ENSG00000156574	ENSG00000156574			7865	protein-coding gene	gene with protein product		601265	"nodal, mouse, homolog", "nodal homolog (mouse)"			9354794	Standard	NM_018055		Approved		uc001jrc.2	Q96S42	OTTHUMG00000018408	ENST00000287139.3:c.834C>T	chr10.hg19:g.72195099G>A		103.0	0.0		92.0	41.0	NM_018055	Q2M3A5|Q8N4V3	Silent	SNP	ENST00000287139.3	hg19	CCDS7304.1	.	.	.	.	.	.	.	.	.	.	G	16.19	3.053779	0.55218	.	.	ENSG00000197604	ENST00000420338	.	.	.	5.88	1.37	0.22104	.	.	.	.	.	T	0.60560	0.2278	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59674	-0.7410	5	0.87932	D	0	.	6.412	0.21696	0.149:0.0:0.4186:0.4324	.	.	.	.	T	16	.	ENSP00000411125:A16T	A	+	1	0	AC022532.1	71865105	0.000000	0.05858	1.000000	0.80357	0.948000	0.59901	-0.860000	0.04272	0.354000	0.24105	0.655000	0.94253	GCC	.	.		0.572	NODAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048511.1	NM_018055		A	72195099	G	A	72195099	2	1	362	1	0	0	0	0	0	0	0	1	10527	1074	38	1		1	NODAL	10	72195099	Silent	SNP	G	TCGA-YA-A8S7-01A-11D-A36X-10		72195099	63339648	43	50589										
LHPP	64077	hgsc.bcm.edu	37	chr10	126150467	126150467	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	aagcggctggctggcgtgcgCggggtgctgcttgacatctc	17	11	1	1			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr10:126150467C>T	ENST00000368842.5	+	1	64	c.36C>T	c.(34-36)cgC>cgT	p.R12R	LHPP_ENST00000368839.1_Silent_p.R12R|LHPP_ENST00000392757.4_Silent_p.R12R	NM_022126.3	NP_071409.3	Q9H008	LHPP_HUMAN	phospholysine phosphohistidine inorganic pyrophosphate phosphatase	12					phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	inorganic diphosphatase activity (GO:0004427)|magnesium ion binding (GO:0000287)|phosphohistidine phosphatase activity (GO:0008969)|protein homodimerization activity (GO:0042803)			large_intestine(2)|lung(2)	4		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.163)|Colorectal(40;0.187)		CTGGCGTGCGCGGGGTGCTGC	0.786																																					p.R12R	GBM(165;1980 2715 15999 18454)	Atlas-SNP	.											.	LHPP	18	.	0			c.C36T						.						7	6	7					10																	126150467		1921	3823	5744	SO:0001819	synonymous_variant	64077	exon1			CGTGCGCGGGGTG	AB049629	CCDS7640.1, CCDS53587.1	10q26.2	2010-02-17			ENSG00000107902	ENSG00000107902	3.6.1.1		30042	protein-coding gene	gene with protein product						12801912, 16430861	Standard	NM_022126		Approved	HDHD2B	uc001lhs.2	Q9H008	OTTHUMG00000019214	ENST00000368842.5:c.36C>T	chr10.hg19:g.126150467C>T		55.0	0.0		59.0	34.0	NM_022126	B3KP20|Q2TBE9|Q5VUV9|Q5VUW0	Silent	SNP	ENST00000368842.5	hg19	CCDS7640.1																																																																																			.	.		0.786	LHPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050870.1	NM_022126		T	126150467	C	T	126150467	2	4	362	1	0	0	0	0	0	0	0	1	8778	755	27	1		1	LHPP	10	126150467	Silent	SNP	C	TCGA-YA-A8S7-01A-11D-A36X-10	53955368	126150467	9384280	44	50590										
OR5M10	390167	hgsc.bcm.edu	37	chr11	56344592	56344592	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	cttgagagagtaaagcctgcAactacaaacattgccatctt	7	10	1	2			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr11:56344592A>G	ENST00000526812.2	-	1	671	c.606T>C	c.(604-606)gtT>gtC	p.V202V		NM_001004741.1	NP_001004741.1	Q6IEU7	OR5MA_HUMAN	olfactory receptor, family 5, subfamily M, member 10	202						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(15)|upper_aerodigestive_tract(2)|urinary_tract(2)	25						TAAAGCCTGCAACTACAAACA	0.463																																					p.V202V		Atlas-SNP	.											.	OR5M10	56	.	0			c.T606C						.						83	80	81					11																	56344592		1929	4122	6051	SO:0001819	synonymous_variant	390167	exon1			GCCTGCAACTACA	BK004515	CCDS53630.1	11q11	2012-08-09				ENSG00000254834		"GPCR / Class A : Olfactory receptors"	15290	protein-coding gene	gene with protein product							Standard	NM_001004741		Approved		uc001niz.1	Q6IEU7		ENST00000526812.2:c.606T>C	chr11.hg19:g.56344592A>G		322.0	0.0		254.0	36.0	NM_001004741	B9EIL9	Silent	SNP	ENST00000526812.2	hg19	CCDS53630.1																																																																																			.	.		0.463	OR5M10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391609.1	NM_001004741		G	56344592	A	G	56344592	2	3	362	1	0	0	0	0	0	0	0	1	11182	117	5	2		2	OR5M10	11	56344592	Silent	SNP	A	TCGA-YA-A8S7-01A-11D-A36X-10		56344592	78661924	45	50591										
AHNAK	79026	hgsc.bcm.edu	37	chr11	62298786	62298786	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	cagatctggagcattagtatCtacttttggtgcagaaatgt	10	6	2	2			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr11:62298786C>A	ENST00000378024.4	-	5	3377	c.3103G>T	c.(3103-3105)Gat>Tat	p.D1035Y	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	1035					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				GCATTAGTATCTACTTTTGGT	0.463																																					p.D1035Y		Atlas-SNP	.											.	AHNAK	532	.	0			c.G3103T						.						91	89	90					11																	62298786		2202	4299	6501	SO:0001583	missense	79026	exon5			TAGTATCTACTTT	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.3103G>T	chr11.hg19:g.62298786C>A	ENSP00000367263:p.Asp1035Tyr	135.0	0.0		99.0	35.0	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	hg19	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	-	12.39	1.923144	0.33908	.	.	ENSG00000124942	ENST00000378024	T	0.03035	4.07	4.63	3.7	0.42460	.	0.182863	0.46442	D	0.000300	T	0.26521	0.0648	H	0.96269	3.795	0.36492	D	0.868466	D	0.89917	1.0	D	0.91635	0.999	T	0.50533	-0.8817	10	0.66056	D	0.02	-13.8139	12.5834	0.56403	0.0:0.9113:0.0:0.0887	.	1035	Q09666	AHNK_HUMAN	Y	1035	ENSP00000367263:D1035Y	ENSP00000367263:D1035Y	D	-	1	0	AHNAK	62055362	0.929000	0.31497	0.995000	0.50966	0.362000	0.29581	1.692000	0.37731	2.285000	0.76669	0.555000	0.69702	GAT	.	.		0.463	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		A	62298786	C	A	62298786	3	1	362	1	0	0	0	0	1	0	0	0	414	913	32	3	14689	3	AHNAK	11	62298786	Missense_Mutation	SNP	C	TCGA-YA-A8S7-01A-11D-A36X-10	5954194	62298786	72707730	46	50592										
PPP1CA	5499	hgsc.bcm.edu	37	chr11	67166283	67166283	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	ttgggagctgagaaaagtgtCaccagctgccgcttggcaaa	13	9	1	1			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr11:67166283C>T	ENST00000376745.4	-	6	940	c.792G>A	c.(790-792)gtG>gtA	p.V264V	PPP1CA_ENST00000532446.1_5'UTR|PPP1CA_ENST00000358239.4_Silent_p.V220V|PPP1CA_ENST00000312989.7_Silent_p.V275V	NM_001008709.1|NM_002708.3	NP_001008709.1|NP_002699.1	P62136	PP1A_HUMAN	protein phosphatase 1, catalytic subunit, alpha isozyme	264					branching morphogenesis of an epithelial tube (GO:0048754)|cell cycle (GO:0007049)|cell division (GO:0051301)|circadian regulation of gene expression (GO:0032922)|entrainment of circadian clock by photoperiod (GO:0043153)|glycogen metabolic process (GO:0005977)|lung development (GO:0030324)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|protein dephosphorylation (GO:0006470)|regulation of circadian rhythm (GO:0042752)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of glycogen catabolic process (GO:0005981)|small molecule metabolic process (GO:0044281)|transforming growth factor beta receptor signaling pathway (GO:0007179)|triglyceride catabolic process (GO:0019433)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|MLL5-L complex (GO:0070688)|nucleus (GO:0005634)|perikaryon (GO:0043204)|protein phosphatase type 1 complex (GO:0000164)|PTW/PP1 phosphatase complex (GO:0072357)	metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)|protein serine/threonine phosphatase activity (GO:0004722)|ribonucleoprotein complex binding (GO:0043021)			breast(1)|lung(2)|pancreas(1)|urinary_tract(3)	7			BRCA - Breast invasive adenocarcinoma(15;8.53e-07)			AGAAAAGTGTCACCAGCTGCC	0.597																																					p.V275V		Atlas-SNP	.											.	PPP1CA	83	.	0			c.G825A						.						93	92	93					11																	67166283		2200	4295	6495	SO:0001819	synonymous_variant	5499	exon6			AAGTGTCACCAGC		CCDS8160.1, CCDS8161.1, CCDS31618.1	11q13	2013-01-18	2010-03-05			ENSG00000172531	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9281	protein-coding gene	gene with protein product		176875	"protein phosphatase 1, catalytic subunit, alpha isoform"	PPP1A			Standard	NM_002708		Approved	PP1A, PP-1A, PP1alpha	uc001oku.1	P62136		ENST00000376745.4:c.792G>A	chr11.hg19:g.67166283C>T		52.0	0.0		47.0	19.0	NM_001008709	A6NNR3|B2R908|P08129|P20653|P22802|Q07161	Silent	SNP	ENST00000376745.4	hg19	CCDS8160.1																																																																																			.	.		0.597	PPP1CA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395487.1	NM_002708		T	67166283	C	T	67166283	2	4	362	1	0	0	0	0	0	0	0	1	12361	813	29	3		3	PPP1CA	11	67166283	Silent	SNP	C	TCGA-YA-A8S7-01A-11D-A36X-10	4867497	67166283	67840233	47	50593										
PITPNM1	9600	hgsc.bcm.edu	37	chr11	67265462	67265462	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	gcagagtgcatcaaagcccaGgatgccaccaacaccatctc	8	15	2	1			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr11:67265462G>C	ENST00000534749.1	-	11	1896	c.1708C>G	c.(1708-1710)Ctg>Gtg	p.L570V	PITPNM1_ENST00000436757.2_Missense_Mutation_p.L570V|PITPNM1_ENST00000356404.3_Missense_Mutation_p.L570V			O00562	PITM1_HUMAN	phosphatidylinositol transfer protein, membrane-associated 1	570					brain development (GO:0007420)|lipid metabolic process (GO:0006629)|phospholipid transport (GO:0015914)|phototransduction (GO:0007602)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lipid particle (GO:0005811)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphatidylinositol transporter activity (GO:0008526)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(3)	18						TCAAAGCCCAGGATGCCACCA	0.642																																					p.L570V	GBM(28;144 709 4607 5525)	Atlas-SNP	.											.	PITPNM1	84	.	0			c.C1708G						.						56	51	53					11																	67265462		2200	4295	6495	SO:0001583	missense	9600	exon12			AGCCCAGGATGCC	X98654	CCDS31620.1, CCDS44659.1	11q13	2008-07-21		2003-05-16	ENSG00000110697	ENSG00000110697			9003	protein-coding gene	gene with protein product	"PYK2 N-terminal domain-interacting receptor 2", "retinal degeneration B alpha 1"	608794		PITPNM		9680295	Standard	NM_004910		Approved	DRES9, NIR2, RDGB1, RDGBA1, Rd9, RDGB	uc001oly.3	O00562	OTTHUMG00000167675	ENST00000534749.1:c.1708C>G	chr11.hg19:g.67265462G>C	ENSP00000437286:p.Leu570Val	44.0	0.0		36.0	10.0	NM_001130848	A6NME4|Q6T7X3|Q8TBN3|Q9BZ73	Missense_Mutation	SNP	ENST00000534749.1	hg19	CCDS31620.1	.	.	.	.	.	.	.	.	.	.	g	16.56	3.157199	0.57259	.	.	ENSG00000110697	ENST00000534749;ENST00000436757;ENST00000356404	T;T;T	0.64260	-0.07;-0.09;-0.07	3.98	3.98	0.46160	.	0.000000	0.33938	N	0.004413	T	0.79736	0.4497	M	0.84326	2.69	0.39340	D	0.965565	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.996	D	0.83408	0.0026	10	0.52906	T	0.07	-25.3043	15.1894	0.73032	0.0:0.0:1.0:0.0	.	570;570	O00562-2;O00562	.;PITM1_HUMAN	V	570	ENSP00000437286:L570V;ENSP00000398787:L570V;ENSP00000348772:L570V	ENSP00000348772:L570V	L	-	1	2	PITPNM1	67022038	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	5.217000	0.65252	2.235000	0.73313	0.556000	0.70494	CTG	.	.		0.642	PITPNM1-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395520.1	NM_004910		C	67265462	G	C	67265462	3	2	362	1	0	0	0	0	1	0	0	0	11959	991	35	4	2078	4	PITPNM1	11	67265462	Missense_Mutation	SNP	G	TCGA-YA-A8S7-01A-11D-A36X-10	99179	67265462	67741054	48	50594										
FAT3	120114	hgsc.bcm.edu	37	chr11	92564913	92564913	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	agcagcagtcttcgtacaacAtcagcgtgcgggccactgac	11	13	2	1	rs139337740	byFrequency	TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr11:92564913A>T	ENST00000298047.6	+	13	9624	c.9607A>T	c.(9607-9609)Atc>Ttc	p.I3203F	FAT3_ENST00000409404.2_Missense_Mutation_p.I3203F|FAT3_ENST00000525166.1_Missense_Mutation_p.I3053F			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	3203	Cadherin 29. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				TTCGTACAACATCAGCGTGCG	0.562										TCGA Ovarian(4;0.039)																											p.I3203F		Atlas-SNP	.											.	FAT3	1822	.	0			c.A9607T						.						69	76	74					11																	92564913		2166	4270	6436	SO:0001583	missense	120114	exon13			TACAACATCAGCG	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.9607A>T	chr11.hg19:g.92564913A>T	ENSP00000298047:p.Ile3203Phe	66.0	0.0		61.0	12.0	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	hg19		.	.	.	.	.	.	.	.	.	.	A	14.56	2.571711	0.45798	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.61859	0.07;0.07;0.07	5.19	4.04	0.47022	.	.	.	.	.	T	0.35248	0.0925	N	0.10972	0.075	0.80722	D	1	P	0.34639	0.461	B	0.32805	0.153	T	0.27157	-1.0082	9	0.87932	D	0	.	7.7134	0.28690	0.7862:0.1413:0.0726:0.0	.	3203	Q8TDW7-3	.	F	3203;3203;3053	ENSP00000298047:I3203F;ENSP00000387040:I3203F;ENSP00000432586:I3053F	ENSP00000298047:I3203F	I	+	1	0	FAT3	92204561	1.000000	0.71417	0.998000	0.56505	0.762000	0.43233	1.833000	0.39161	0.894000	0.36317	0.533000	0.62120	ATC	.	A|0.999;G|0.001		0.562	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		T	92564913	A	T	92564913	3	4	362	1	0	0	0	0	1	0	0	0	5699	217	8	4	9657	4	FAT3	11	92564913	Missense_Mutation	SNP	A	TCGA-YA-A8S7-01A-11D-A36X-10	25299451	92564913	42441603	49	50595										
OR6X1	390260	hgsc.bcm.edu	37	chr11	123625085	123625085	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	ttgtagcctgggctcagcccAcacagtggcaataataagcc	10	12	1	0			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr11:123625085A>G	ENST00000327930.2	-	1	168	c.142T>C	c.(142-144)Tgg>Cgg	p.W48R		NM_001005188.1	NP_001005188.1	Q8NH79	OR6X1_HUMAN	olfactory receptor, family 6, subfamily X, member 1	48						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(3)|endometrium(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(2)	23		Breast(109;0.0109)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		GGCTCAGCCCACACAGTGGCA	0.438																																					p.W48R		Atlas-SNP	.											.	OR6X1	54	.	0			c.T142C						.						94	91	92					11																	123625085		2202	4299	6501	SO:0001583	missense	390260	exon1			CAGCCCACACAGT	AB065510	CCDS31695.1	11q24.1	2012-08-09			ENSG00000221931	ENSG00000221931		"GPCR / Class A : Olfactory receptors"	14737	protein-coding gene	gene with protein product							Standard	NM_001005188		Approved		uc010rzy.2	Q8NH79	OTTHUMG00000166011	ENST00000327930.2:c.142T>C	chr11.hg19:g.123625085A>G	ENSP00000333724:p.Trp48Arg	119.0	0.0		129.0	38.0	NM_001005188	B9EGW9|Q6IFA0	Missense_Mutation	SNP	ENST00000327930.2	hg19	CCDS31695.1	.	.	.	.	.	.	.	.	.	.	A	12.12	1.841155	0.32513	.	.	ENSG00000221931	ENST00000327930	T	0.03801	3.8	4.08	2.95	0.34219	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.02610	0.0079	N	0.05124	-0.11	0.28141	N	0.92981	B	0.26081	0.141	B	0.20767	0.031	T	0.41305	-0.9516	9	0.41790	T	0.15	-3.6195	7.5173	0.27608	0.8938:0.0:0.1062:0.0	.	48	Q8NH79	OR6X1_HUMAN	R	48	ENSP00000333724:W48R	ENSP00000333724:W48R	W	-	1	0	OR6X1	123130295	0.000000	0.05858	0.887000	0.34795	0.844000	0.47949	-0.004000	0.12878	0.628000	0.30357	0.528000	0.53228	TGG	.	.		0.438	OR6X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387436.1	NM_001005188		G	123625085	A	G	123625085	3	3	362	1	0	0	0	0	1	0	0	0	11221	159	6	2	798	2	OR6X1	11	123625085	Missense_Mutation	SNP	A	TCGA-YA-A8S7-01A-11D-A36X-10	31060172	123625085	11381431	50	50596										
DCP1B	196513	hgsc.bcm.edu	37	chr12	2062188	2062188	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	ttttcaggcagctctgacaaTgggtggaggtctgcgctcct	13	10	3	1			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr12:2062188T>C	ENST00000280665.6	-	7	997	c.918A>G	c.(916-918)ccA>ccG	p.P306P	DCP1B_ENST00000397173.4_Silent_p.P204P|DCP1B_ENST00000540622.1_Silent_p.P180P|DCP1B_ENST00000541700.1_5'UTR	NM_152640.3	NP_689853.3	Q8IZD4	DCP1B_HUMAN	decapping mRNA 1B	306					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	hydrolase activity (GO:0016787)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(3)|lung(10)|skin(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00193)			GCTCTGACAATGGGTGGAGGT	0.537																																					p.P306P		Atlas-SNP	.											.	DCP1B	63	.	0			c.A918G						.						83	89	87					12																	2062188		2203	4300	6503	SO:0001819	synonymous_variant	196513	exon7			TGACAATGGGTGG	AY146652	CCDS31727.1	12p13.33	2013-05-02	2013-05-02		ENSG00000151065	ENSG00000151065			24451	protein-coding gene	gene with protein product		609843	"DCP1 decapping enzyme homolog B (S. cerevisiae)"			12417715, 15067023	Standard	NM_152640		Approved	FLJ31638	uc001qjx.1	Q8IZD4	OTTHUMG00000168113	ENST00000280665.6:c.918A>G	chr12.hg19:g.2062188T>C		55.0	0.0		48.0	12.0	NM_152640	B4DRD1|Q86XH9|Q96BP8|Q96MZ8	Silent	SNP	ENST00000280665.6	hg19	CCDS31727.1																																																																																			.	.		0.537	DCP1B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398244.1	NM_152640		C	2062188	T	C	2062188	2	2	362	1	0	0	0	0	0	0	0	1	4301	1451	51	2		2	DCP1B	12	2062188	Silent	SNP	T	TCGA-YA-A8S7-01A-11D-A36X-10		2062188	131789707	51	50597										
C12orf64	283310	hgsc.bcm.edu	37	chr12	80752454	80752454	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	gtaatttttctttttagtatGtgaaccaaacctttgtccta	5	7	1	1			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr12:80752454G>A	ENST00000547103.1	+	50	6068	c.6062G>A	c.(6061-6063)tGt>tAt	p.C2021Y	OTOGL_ENST00000458043.2_Missense_Mutation_p.C2033Y|OTOGL_ENST00000546620.1_Missense_Mutation_p.C52Y			Q3ZCN5	OTOGL_HUMAN	otogelin-like	2021	Cys-rich.				L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						TTTTTAGTATGTGAACCAAAC	0.353																																					p.C2033Y		Atlas-SNP	.											.	OTOGL	235	.	0			c.G6098A						.						95	94	95					12																	80752454		2203	4300	6503	SO:0001583	missense	283310	exon50			TAGTATGTGAACC	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"chromosome 12 open reading frame 64"	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.6062G>A	chr12.hg19:g.80752454G>A	ENSP00000447211:p.Cys2021Tyr	42.0	0.0		48.0	13.0	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.13|17.13	3.309777|3.309777	0.60414|0.60414	.|.	.|.	ENSG00000165899|ENSG00000165899	ENST00000547103;ENST00000458043;ENST00000546620;ENST00000550182|ENST00000298820	T;T;T;T|.	0.31247|.	1.5;1.5;1.5;1.5|.	5.08|5.08	5.08|5.08	0.68730|0.68730	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.82664|0.82664	0.5086|0.5086	M|M	0.84846|0.84846	2.72|2.72	0.44611|0.44611	D|D	0.997583|0.997583	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	D|D	0.84493|0.84493	0.0612|0.0612	10|5	0.62326|.	D|.	0.03|.	.|.	18.8344|18.8344	0.92155|0.92155	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	398|.	Q3ZCN5|.	OTOGL_HUMAN|.	Y|M	2021;2033;52;50|476	ENSP00000447211:C2021Y;ENSP00000400895:C2033Y;ENSP00000449094:C52Y;ENSP00000449641:C50Y|.	ENSP00000400895:C2033Y|.	C|V	+|+	2|1	0|0	OTOGL|OTOGL	79276585|79276585	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.524000|0.524000	0.34500|0.34500	8.327000|8.327000	0.90012|0.90012	2.526000|2.526000	0.85167|0.85167	0.591000|0.591000	0.81541|0.81541	TGT|GTG	.	.		0.353	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591		A	80752454	G	A	80752454	3	1	362	1	0	0	0	0	1	0	0	0	1709	1377	48	3	6296	3	C12orf64	12	80752454	Missense_Mutation	SNP	G	TCGA-YA-A8S7-01A-11D-A36X-10	78690266	80752454	53099441	52	50598										
FGD6	55785	hgsc.bcm.edu	37	chr12	95500747	95500747	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	caccttcattccagccagtgAgagcatgttgttcagtttat	8	10	2	1			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr12:95500747A>C	ENST00000343958.4	-	13	3623	c.3400T>G	c.(3400-3402)Tca>Gca	p.S1134A	FGD6_ENST00000549499.1_Missense_Mutation_p.S1134A|FGD6_ENST00000546711.1_Missense_Mutation_p.S1134A	NM_018351.3	NP_060821.3	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	1134	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(14)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56						CCAGCCAGTGAGAGCATGTTG	0.388																																					p.S1134A		Atlas-SNP	.											.	FGD6	127	.	0			c.T3400G						.						190	176	181					12																	95500747		2203	4300	6503	SO:0001583	missense	55785	exon13			CCAGTGAGAGCAT	AB037783	CCDS31878.1	12q23.1	2013-01-10				ENSG00000180263		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	21740	protein-coding gene	gene with protein product		613520					Standard	NM_018351		Approved	ZFYVE24, FLJ11183	uc001tdp.4	Q6ZV73	OTTHUMG00000170133	ENST00000343958.4:c.3400T>G	chr12.hg19:g.95500747A>C	ENSP00000344446:p.Ser1134Ala	183.0	0.0		173.0	24.0	NM_018351	Q6ZR53|Q7Z2Z7|Q96D44|Q9NUR8|Q9P2I5	Missense_Mutation	SNP	ENST00000343958.4	hg19	CCDS31878.1	.	.	.	.	.	.	.	.	.	.	A	8.501	0.864219	0.17250	.	.	ENSG00000180263	ENST00000343958;ENST00000546711;ENST00000551521;ENST00000549499	T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07	6.02	6.02	0.97574	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.38326	N	0.001739	T	0.79896	0.4525	N	0.20574	0.59	0.58432	D	0.999996	P;D	0.71674	0.537;0.998	B;D	0.71870	0.316;0.975	T	0.79242	-0.1884	10	0.32370	T	0.25	-16.3161	16.5494	0.84464	1.0:0.0:0.0:0.0	.	1134;1134	Q6ZV73-2;Q6ZV73	.;FGD6_HUMAN	A	1134;1134;130;1134	ENSP00000344446:S1134A;ENSP00000450342:S1134A;ENSP00000450240:S130A;ENSP00000449005:S1134A	ENSP00000344446:S1134A	S	-	1	0	FGD6	94024878	1.000000	0.71417	0.802000	0.32245	0.848000	0.48234	7.133000	0.77259	2.299000	0.77371	0.528000	0.53228	TCA	.	.		0.388	FGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407600.1	NM_018351		C	95500747	A	C	95500747	3	2	362	1	0	0	0	0	1	0	0	0	5845	304	11	5	928	5	FGD6	12	95500747	Missense_Mutation	SNP	A	TCGA-YA-A8S7-01A-11D-A36X-10	14748293	95500747	38351148	53	50599										
CCDC60	160777	hgsc.bcm.edu	37	chr12	119909929	119909929	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	gaaataaattccagccagccGaaaagatctcagaaatccac	6	11	1	2			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr12:119909929G>A	ENST00000327554.2	+	3	766	c.301G>A	c.(301-303)Gaa>Aaa	p.E101K	CCDC60_ENST00000546345.1_3'UTR|RP11-768F21.1_ENST00000509470.2_lincRNA	NM_178499.3	NP_848594.2	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60	101								p.E101K(2)		endometrium(4)|kidney(3)|large_intestine(8)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)		CCAGCCAGCCGAAAAGATCTC	0.423																																					p.E101K		Atlas-SNP	.											CCDC60,NS,malignant_melanoma,0,4	CCDC60	84	.	2	Substitution - Missense(2)	lung(1)|skin(1)	c.G301A						.						160	166	164					12																	119909929		2203	4300	6503	SO:0001583	missense	160777	exon3			CCAGCCGAAAAGA	BC040553	CCDS9190.1	12q24.23	2006-02-03			ENSG00000183273	ENSG00000183273			28610	protein-coding gene	gene with protein product						12477932	Standard	NM_178499		Approved	MGC39827	uc001txe.3	Q8IWA6	OTTHUMG00000168943	ENST00000327554.2:c.301G>A	chr12.hg19:g.119909929G>A	ENSP00000333374:p.Glu101Lys	119.0	0.0		138.0	17.0	NM_178499		Missense_Mutation	SNP	ENST00000327554.2	hg19	CCDS9190.1	.	.	.	.	.	.	.	.	.	.	G	1.545	-0.540681	0.04053	.	.	ENSG00000183273	ENST00000327554	T	0.21361	2.01	5.22	2.8	0.32819	.	0.477213	0.19451	N	0.113928	T	0.06325	0.0163	N	0.01705	-0.755	0.33283	D	0.562555	B	0.09022	0.002	B	0.04013	0.001	T	0.26780	-1.0093	9	.	.	.	-6.4841	4.9568	0.14046	0.715:0.1871:0.0978:0.0	.	101	Q8IWA6	CCD60_HUMAN	K	101	ENSP00000333374:E101K	.	E	+	1	0	CCDC60	118394312	0.704000	0.27836	0.569000	0.28460	0.315000	0.28087	1.025000	0.30090	0.289000	0.22422	-0.481000	0.04817	GAA	.	.		0.423	CCDC60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401680.1	NM_178499		A	119909929	G	A	119909929	3	1	362	1	0	0	0	0	1	0	0	0	2833	1059	37	1	311	1	CCDC60	12	119909929	Missense_Mutation	SNP	G	TCGA-YA-A8S7-01A-11D-A36X-10	24409182	119909929	13941966	54	50600										
GPR109B	8843	hgsc.bcm.edu	37	chr12	123201235	123201235	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	catctcggaacacacagcagTtcttcttgtctatttccaga	6	12	4	1			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr12:123201235T>A	ENST00000528880.2	-	1	204	c.50A>T	c.(49-51)aAc>aTc	p.N17I	HCAR1_ENST00000356987.2_Intron|RP11-324E6.6_ENST00000543611.1_lincRNA	NM_006018.2	NP_006009.2	P49019	HCAR3_HUMAN	hydroxycarboxylic acid receptor 3	17					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	9					Niacin(DB00627)	CACACAGCAGTTCTTCTTGTC	0.542																																					p.N17I		Atlas-SNP	.											.	HCAR3	49	.	0			c.A50T						.						88	81	83					12																	123201235		2203	4300	6503	SO:0001583	missense	8843	exon1			CAGCAGTTCTTCT	D10923	CCDS53842.1	12q24.31	2012-08-08	2011-05-30	2011-05-30		ENSG00000255398		"GPCR / Class A : Hydroxy-carboxylic acid receptors"	16824	protein-coding gene	gene with protein product		606039	"G protein-coupled receptor 109B"	GPR109B		7505609, 9205127, 18983141, 21454438	Standard	NM_006018		Approved	HCA3, HM74	uc001ucy.4	P49019		ENST00000528880.2:c.50A>T	chr12.hg19:g.123201235T>A	ENSP00000436714:p.Asn17Ile	91.0	0.0		93.0	8.0	NM_006018	A8K4G5|B2R830|E9PI97|Q8NGE4	Missense_Mutation	SNP	ENST00000528880.2	hg19	CCDS53842.1	.	.	.	.	.	.	.	.	.	.	T	9.314	1.056359	0.19907	.	.	ENSG00000255398	ENST00000528880	T	0.63580	-0.05	3.27	0.255	0.15561	.	.	.	.	.	T	0.48732	0.1516	L	0.46157	1.445	0.23533	N	0.997476	P	0.36683	0.565	B	0.35550	0.205	T	0.41305	-0.9516	9	0.52906	T	0.07	.	4.0878	0.09955	0.0:0.1302:0.4373:0.4325	.	17	E9PI97	.	I	17	ENSP00000436714:N17I	ENSP00000436714:N17I	N	-	2	0	HCAR3	121767188	1.000000	0.71417	0.174000	0.22961	0.513000	0.34164	0.374000	0.20501	0.238000	0.21222	0.155000	0.16302	AAC	.	.		0.542	HCAR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387549.2	NM_006018		A	123201235	T	A	123201235	3	1	362	1	0	0	0	0	1	0	0	0	6634	1725	60	4	1117	4	GPR109B	12	123201235	Missense_Mutation	SNP	T	TCGA-YA-A8S7-01A-11D-A36X-10	3291306	123201235	10650660	55	50601										
PARP4	143	hgsc.bcm.edu	37	chr13	25021314	25021314	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	gagaacatagcctggtcattTggtcttctatctatttataa	7	7	4	1			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr13:25021314T>C	ENST00000381989.3	-	26	3230	c.3125A>G	c.(3124-3126)cAa>cGa	p.Q1042R		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	1042	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		CCTGGTCATTTGGTCTTCTAT	0.428																																					p.Q1042R		Atlas-SNP	.											.	PARP4	142	.	0			c.A3125G						.						49	49	49					13																	25021314		2203	4300	6503	SO:0001583	missense	143	exon26			GTCATTTGGTCTT	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"Poly (ADP-ribose) polymerases"	271	protein-coding gene	gene with protein product	"von Willebrand factor A domain containing 5C"	607519	"ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.3125A>G	chr13.hg19:g.25021314T>C	ENSP00000371419:p.Gln1042Arg	188.0	0.0		133.0	38.0	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	hg19	CCDS9307.1	.	.	.	.	.	.	.	.	.	.	T	17.72	3.459965	0.63401	.	.	ENSG00000102699	ENST00000381989	T	0.21543	2.0	4.71	4.71	0.59529	von Willebrand factor, type A (2);	0.057132	0.64402	D	0.000001	T	0.48241	0.1489	M	0.85542	2.76	0.45822	D	0.998692	D	0.65815	0.995	D	0.69307	0.963	T	0.54728	-0.8250	10	0.66056	D	0.02	-18.7938	12.4962	0.55929	0.0:0.0:0.0:1.0	.	1042	Q9UKK3	PARP4_HUMAN	R	1042	ENSP00000371419:Q1042R	ENSP00000371419:Q1042R	Q	-	2	0	PARP4	23919314	1.000000	0.71417	0.877000	0.34402	0.713000	0.41058	5.285000	0.65633	2.113000	0.64589	0.524000	0.50904	CAA	.	.		0.428	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437		C	25021314	T	C	25021314	3	2	362	1	0	0	0	0	1	0	0	0	11472	1812	63	2	2085	2	PARP4	13	25021314	Missense_Mutation	SNP	T	TCGA-YA-A8S7-01A-11D-A36X-10		25021314	90148564	56	50602										
FRY	10129	hgsc.bcm.edu	37	chr13	32759191	32759191	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	gtggacttgacccgcatgctCctagaagctgaaaatgacaa	10	10	0	4			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr13:32759191C>T	ENST00000380250.3	+	26	3721	c.3225C>T	c.(3223-3225)ctC>ctT	p.L1075L		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	1075						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		CCCGCATGCTCCTAGAAGCTG	0.438																																					p.L1075L		Atlas-SNP	.											.	FRY	312	.	0			c.C3225T						.						129	125	126					13																	32759191		1861	4090	5951	SO:0001819	synonymous_variant	10129	exon26			CATGCTCCTAGAA	AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"chromosome 13 open reading frame 14"	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.3225C>T	chr13.hg19:g.32759191C>T		144.0	0.0		97.0	29.0	NM_023037	Q9Y3N6	Silent	SNP	ENST00000380250.3	hg19	CCDS41875.1																																																																																			.	.		0.438	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037		T	32759191	C	T	32759191	2	4	362	1	0	0	0	0	0	0	0	1	6071	842	30	3		3	FRY	13	32759191	Silent	SNP	C	TCGA-YA-A8S7-01A-11D-A36X-10	7737877	32759191	82410687	57	50603										
GRK1	6011	hgsc.bcm.edu	37	chr13	114324085	114324085	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	tatgcgtttgaaaccaaagcCgacctctgtctggtgatgac	10	10	2	3	rs370686602		TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr13:114324085C>A	ENST00000335678.6	+	2	1015	c.783C>A	c.(781-783)gcC>gcA	p.A261A		NM_002929.2	NP_002920.1	Q15835	RK_HUMAN	G protein-coupled receptor kinase 1	261	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of apoptotic process (GO:0043066)|photoreceptor cell morphogenesis (GO:0008594)|phototransduction, visible light (GO:0007603)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)|protein autophosphorylation (GO:0046777)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|protein kinase activity (GO:0004672)|rhodopsin kinase activity (GO:0050254)			ovary(2)	2	Lung NSC(43;0.0113)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.00696)|all_epithelial(44;0.00347)|all_lung(25;0.0221)|Breast(118;0.0411)|Lung NSC(25;0.0839)	all cancers(43;0.234)			AAACCAAAGCCGACCTCTGTC	0.552																																					p.A261A		Atlas-SNP	.											.	GRK1	41	.	0			c.C783A						.						150	153	152					13																	114324085		2042	4193	6235	SO:0001819	synonymous_variant	6011	exon2			CAAAGCCGACCTC			13q34	2013-09-02	2004-03-23	2004-03-24	ENSG00000185974	ENSG00000185974	2.7.11.14		10013	protein-coding gene	gene with protein product		180381	"rhodopsin kinase"	RHOK		8812493, 15057823	Standard	NM_002929		Approved	GPRK1, RK	uc010tkf.2	Q15835	OTTHUMG00000185528	ENST00000335678.6:c.783C>A	chr13.hg19:g.114324085C>A		49.0	0.0		64.0	15.0	NM_002929	Q53X14	Silent	SNP	ENST00000335678.6	hg19																																																																																				.	.		0.552	GRK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470655.1	NM_002929		A	114324085	C	A	114324085	2	1	362	1	0	0	0	0	0	0	0	1	6799	639	23	1		1	GRK1	13	114324085	Silent	SNP	C	TCGA-YA-A8S7-01A-11D-A36X-10	81564894	114324085	845793	58	50604										
IPO4	79711	hgsc.bcm.edu	37	chr14	24649686	24649686	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	agcctggagctcctgagcctTgtcaacaggcagtgagccca	12	13	1	2			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr14:24649686T>G	ENST00000354464.6	-	30	3384	c.3208A>C	c.(3208-3210)Aag>Cag	p.K1070Q	RP11-468E2.2_ENST00000561419.1_3'UTR	NM_024658.3	NP_078934.3	Q8TEX9	IPO4_HUMAN	importin 4	1070					DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|stomach(2)|urinary_tract(1)	33				GBM - Glioblastoma multiforme(265;0.0087)		TCCTGAGCCTTGTCAACAGGC	0.597																																					p.K1070Q		Atlas-SNP	.											.	IPO4	74	.	0			c.A3208C						.						44	47	46					14																	24649686		2040	4183	6223	SO:0001583	missense	79711	exon30			GAGCCTTGTCAAC	AF411122	CCDS9616.1	14q11.2	2003-03-10			ENSG00000196497	ENSG00000196497		"Importins"	19426	protein-coding gene	gene with protein product						11823430	Standard	NR_051979		Approved	Imp4, FLJ23338	uc001wmv.1	Q8TEX9	OTTHUMG00000028801	ENST00000354464.6:c.3208A>C	chr14.hg19:g.24649686T>G	ENSP00000346453:p.Lys1070Gln	51.0	0.0		58.0	12.0	NM_024658	B2RN95|Q2NL96|Q86TZ9|Q8NCG8|Q96SJ3|Q9BTI4|Q9H5L0	Missense_Mutation	SNP	ENST00000354464.6	hg19	CCDS9616.1	.	.	.	.	.	.	.	.	.	.	T	11.05	1.524698	0.27299	.	.	ENSG00000196497	ENST00000354464;ENST00000399536	T	0.08984	3.03	5.84	5.84	0.93424	Armadillo-like helical (1);	0.187146	0.47093	D	0.000257	T	0.05410	0.0143	N	0.16368	0.405	0.35392	D	0.790833	B;B	0.13145	0.004;0.007	B;B	0.11329	0.003;0.006	T	0.27365	-1.0076	10	0.08381	T	0.77	-31.4907	12.5963	0.56472	0.0:0.0:0.0:1.0	.	1070;1072	Q8TEX9;Q8TEX9-2	IPO4_HUMAN;.	Q	1070;746	ENSP00000346453:K1070Q	ENSP00000346453:K1070Q	K	-	1	0	IPO4	23719526	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.120000	0.41968	2.234000	0.73211	0.459000	0.35465	AAG	.	.		0.597	IPO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071931.4	NM_024658		G	24649686	T	G	24649686	3	3	362	1	0	0	0	0	1	0	0	0	7804	1821	63	5	41	5	IPO4	14	24649686	Missense_Mutation	SNP	T	TCGA-YA-A8S7-01A-11D-A36X-10		24649686	82699854	59	50605										
NKX2-1	7080	hgsc.bcm.edu	37	chr14	36988348	36988348	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	agagctggggcacccccgccGccgtcatgtggtaggcggcg	17	14	1	1	rs546402304		TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr14:36988348G>T	ENST00000518149.1	-	2	820	c.215C>A	c.(214-216)gCg>gAg	p.A72E	NKX2-1_ENST00000498187.2_Missense_Mutation_p.A72E|NKX2-1_ENST00000522719.2_Missense_Mutation_p.A72E|NKX2-1-AS1_ENST00000521292.2_RNA|RP11-896J10.3_ENST00000521945.1_RNA|NKX2-1_ENST00000354822.5_Missense_Mutation_p.A102E			P43699	NKX21_HUMAN	NK2 homeobox 1	72					anatomical structure formation involved in morphogenesis (GO:0048646)|axon guidance (GO:0007411)|brain development (GO:0007420)|cerebral cortex cell migration (GO:0021795)|cerebral cortex GABAergic interneuron differentiation (GO:0021892)|Clara cell differentiation (GO:0060486)|developmental induction (GO:0031128)|endoderm development (GO:0007492)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|forebrain development (GO:0030900)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain neuron fate commitment (GO:0021877)|globus pallidus development (GO:0021759)|hippocampus development (GO:0021766)|Leydig cell differentiation (GO:0033327)|locomotory behavior (GO:0007626)|lung development (GO:0030324)|lung saccule development (GO:0060430)|menarche (GO:0042696)|negative regulation of cell migration (GO:0030336)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron migration (GO:0001764)|oligodendrocyte differentiation (GO:0048709)|phospholipid metabolic process (GO:0006644)|pituitary gland development (GO:0021983)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|rhythmic process (GO:0048511)|thyroid gland development (GO:0030878)|Type II pneumocyte differentiation (GO:0060510)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(2)	7	all_cancers(3;4.47e-51)|Hepatocellular(127;0.158)|Esophageal squamous(585;0.164)|Breast(36;0.165)		Lung(8;1.8e-08)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.014)|all cancers(34;0.0366)|LUSC - Lung squamous cell carcinoma(13;0.132)	GBM - Glioblastoma multiforme(112;0.0171)		CACCCCCGCCGCCGTCATGTG	0.726			A		NSCLC																																p.A102E		Atlas-SNP	.		Dom	yes		14	14q13	7080	NK2 homeobox 1		E	.	NKX2-1	21	.	0			c.C305A						.						8	10	9					14																	36988348		1801	3920	5721	SO:0001583	missense	7080	exon2			CCCGCCGCCGTCA		CCDS9659.1, CCDS41945.1	14q13.3	2012-03-09	2007-07-26	2007-07-26	ENSG00000136352	ENSG00000136352		"Homeoboxes / ANTP class : NKL subclass"	11825	protein-coding gene	gene with protein product		600635	"benign chorea", "thyroid transcription factor 1"	NKX2A, BCH, TITF1		1976511	Standard	NM_001079668		Approved	TTF-1, TTF1	uc001wtu.3	P43699	OTTHUMG00000140225	ENST00000518149.1:c.215C>A	chr14.hg19:g.36988348G>T	ENSP00000428341:p.Ala72Glu	46.0	0.0		55.0	15.0	NM_001079668	D3DSA3|O14954|O14955|Q7KZF6|Q9BRJ8	Missense_Mutation	SNP	ENST00000518149.1	hg19	CCDS9659.1	.	.	.	.	.	.	.	.	.	.	G	19.85	3.903642	0.72754	.	.	ENSG00000136352	ENST00000354822;ENST00000498187;ENST00000518149;ENST00000522719	T;T;T;T	0.71698	-0.59;-0.59;-0.59;-0.59	4.59	4.59	0.56863	.	0.058788	0.64402	D	0.000002	T	0.80984	0.4729	M	0.67953	2.075	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.992	T	0.76383	-0.2979	10	0.10902	T	0.67	.	17.5585	0.87900	0.0:0.0:1.0:0.0	.	102;72	P43699-3;P43699	.;NKX21_HUMAN	E	102;72;72;72	ENSP00000346879:A102E;ENSP00000429607:A72E;ENSP00000428341:A72E;ENSP00000429519:A72E	ENSP00000346879:A102E	A	-	2	0	NKX2-1	36058099	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.946000	0.92992	2.381000	0.81170	0.462000	0.41574	GCG	.	.		0.726	NKX2-1-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376225.2	NM_003317		T	36988348	G	T	36988348	3	4	362	1	0	0	0	0	1	0	0	0	10458	1087	38	1	908	1	NKX2-1	14	36988348	Missense_Mutation	SNP	G	TCGA-YA-A8S7-01A-11D-A36X-10	12338662	36988348	70361192	60	50606										
PSEN1	5663	hgsc.bcm.edu	37	chr14	73637640	73637640	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	aagaagatgaggagctgacaTtgaaatatggcgccaagcat	12	6	0	5			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr14:73637640T>C	ENST00000324501.5	+	4	495	c.223T>C	c.(223-225)Ttg>Ctg	p.L75L	PSEN1_ENST00000557511.1_Silent_p.L75L|PSEN1_ENST00000344094.3_Silent_p.L75L|PSEN1_ENST00000357710.4_Silent_p.L71L|PSEN1_ENST00000406768.1_5'UTR|PSEN1_ENST00000394157.3_Silent_p.L75L|PSEN1_ENST00000261970.3_Silent_p.L75L|PSEN1_ENST00000394164.1_Silent_p.L71L	NM_000021.3|NM_007318.2	NP_000012.1|NP_015557.2	P49768	PSN1_HUMAN	presenilin 1	75					activation of MAPKK activity (GO:0000186)|amyloid precursor protein catabolic process (GO:0042987)|anagen (GO:0042640)|autophagic vacuole assembly (GO:0000045)|beta-amyloid formation (GO:0034205)|beta-amyloid metabolic process (GO:0050435)|blood vessel development (GO:0001568)|brain morphogenesis (GO:0048854)|Cajal-Retzius cell differentiation (GO:0021870)|calcium ion transmembrane transport (GO:0070588)|canonical Wnt signaling pathway (GO:0060070)|cell fate specification (GO:0001708)|cellular response to DNA damage stimulus (GO:0006974)|cerebral cortex cell migration (GO:0021795)|choline transport (GO:0015871)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic limb morphogenesis (GO:0030326)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart looping (GO:0001947)|hematopoietic progenitor cell differentiation (GO:0002244)|intracellular signal transduction (GO:0035556)|L-glutamate transport (GO:0015813)|membrane protein ectodomain proteolysis (GO:0006509)|memory (GO:0007613)|mitochondrial transport (GO:0006839)|myeloid leukocyte differentiation (GO:0002573)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of axonogenesis (GO:0050771)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|neuron migration (GO:0001764)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|positive regulation of coagulation (GO:0050820)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of receptor recycling (GO:0001921)|post-embryonic development (GO:0009791)|protein glycosylation (GO:0006486)|protein processing (GO:0016485)|protein transport (GO:0015031)|regulation of phosphorylation (GO:0042325)|regulation of protein binding (GO:0043393)|regulation of resting membrane potential (GO:0060075)|regulation of synaptic plasticity (GO:0048167)|regulation of synaptic transmission, glutamatergic (GO:0051966)|response to oxidative stress (GO:0006979)|single organismal cell-cell adhesion (GO:0016337)|skeletal system morphogenesis (GO:0048705)|skin morphogenesis (GO:0043589)|smooth endoplasmic reticulum calcium ion homeostasis (GO:0051563)|somitogenesis (GO:0001756)|synaptic vesicle targeting (GO:0016080)|T cell activation involved in immune response (GO:0002286)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cell cortex (GO:0005938)|cell surface (GO:0009986)|centrosome (GO:0005813)|ciliary rootlet (GO:0035253)|cytoplasmic vesicle (GO:0031410)|dendritic shaft (GO:0043198)|endoplasmic reticulum (GO:0005783)|gamma-secretase complex (GO:0070765)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|kinetochore (GO:0000776)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nuclear outer membrane (GO:0005640)|perinuclear region of cytoplasm (GO:0048471)|rough endoplasmic reticulum (GO:0005791)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	aspartic-type endopeptidase activity (GO:0004190)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|calcium channel activity (GO:0005262)|endopeptidase activity (GO:0004175)|PDZ domain binding (GO:0030165)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.075)		GGAGCTGACATTGAAATATGG	0.527																																					p.L75L		Atlas-SNP	.											.	PSEN1	38	.	0			c.T223C						.						156	132	140					14																	73637640		2203	4300	6503	SO:0001819	synonymous_variant	5663	exon4			CTGACATTGAAAT	AJ008005	CCDS9812.1, CCDS9813.1	14q24.3	2014-09-17	2008-07-28		ENSG00000080815	ENSG00000080815			9508	protein-coding gene	gene with protein product		104311	"Alzheimer disease 3"	AD3		1411576	Standard	NM_007318		Approved	FAD, S182, PS1	uc001xnr.3	P49768	OTTHUMG00000141279	ENST00000324501.5:c.223T>C	chr14.hg19:g.73637640T>C		138.0	0.0		173.0	59.0	NM_000021	B2R6D3|O95465|Q14762|Q15719|Q15720|Q96P33|Q9UIF0	Silent	SNP	ENST00000324501.5	hg19	CCDS9812.1																																																																																			.	.		0.527	PSEN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280500.2			C	73637640	T	C	73637640	2	2	362	1	0	0	0	0	0	0	0	1	12662	1490	52	2		2	PSEN1	14	73637640	Silent	SNP	T	TCGA-YA-A8S7-01A-11D-A36X-10	36649292	73637640	33711900	61	50607										
GPR65	8477	hgsc.bcm.edu	37	chr14	88477913	88477913	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	ttttgtcttatgctttactcCctttcatgtgatgttgctga	7	8	2	2			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr14:88477913C>A	ENST00000267549.3	+	2	1280	c.722C>A	c.(721-723)cCc>cAc	p.P241H	RP11-300J18.2_ENST00000554433.1_RNA	NM_003608.3	NP_003599.2	Q8IYL9	PSYR_HUMAN	G protein-coupled receptor 65	241					actin cytoskeleton reorganization (GO:0031532)|activation of Rho GTPase activity (GO:0032862)|apoptotic process (GO:0006915)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|multicellular organismal development (GO:0007275)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of stress fiber assembly (GO:0051496)|response to acidic pH (GO:0010447)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|prostate(1)	16						TGCTTTACTCCCTTTCATGTG	0.408																																					p.P241H		Atlas-SNP	.											.	GPR65	48	.	0			c.C722A						.						82	78	79					14																	88477913		2203	4300	6503	SO:0001583	missense	8477	exon2			TTACTCCCTTTCA	U95218	CCDS9879.1	14q31-q32.1	2012-08-21			ENSG00000140030	ENSG00000140030		"GPCR / Class A : Orphans"	4517	protein-coding gene	gene with protein product		604620				9655242	Standard	NM_003608		Approved	hTDAG8, TDAG8	uc001xvv.3	Q8IYL9	OTTHUMG00000028648	ENST00000267549.3:c.722C>A	chr14.hg19:g.88477913C>A	ENSP00000267549:p.Pro241His	120.0	0.0		160.0	42.0	NM_003608	O75819	Missense_Mutation	SNP	ENST00000267549.3	hg19	CCDS9879.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.638001	0.87760	.	.	ENSG00000140030	ENST00000267549	T	0.80393	-1.37	6.16	6.16	0.99307	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000032	D	0.93294	0.7863	H	0.94183	3.505	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93870	0.7161	10	0.87932	D	0	.	20.8598	0.99761	0.0:1.0:0.0:0.0	.	241	Q8IYL9	PSYR_HUMAN	H	241	ENSP00000267549:P241H	ENSP00000267549:P241H	P	+	2	0	GPR65	87547666	1.000000	0.71417	0.996000	0.52242	0.899000	0.52679	7.587000	0.82613	2.937000	0.99478	0.650000	0.86243	CCC	.	.		0.408	GPR65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071564.4			A	88477913	C	A	88477913	3	1	362	1	0	0	0	0	1	0	0	0	6714	623	22	3	724	3	GPR65	14	88477913	Missense_Mutation	SNP	C	TCGA-YA-A8S7-01A-11D-A36X-10	14840273	88477913	18871627	62	50608										
GABRA5	2558	hgsc.bcm.edu	37	chr15	27159962	27159962	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	tttttcagcttgaccatctcTgcagagtgccccatgcagct	8	13	2	2			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr15:27159962T>G	ENST00000335625.5	+	7	1398	c.510T>G	c.(508-510)tcT>tcG	p.S170S	GABRA5_ENST00000355395.5_Silent_p.S170S|GABRB3_ENST00000541819.2_Intron|GABRA5_ENST00000400081.3_Silent_p.S170S|GABRA5_ENST00000557449.1_3'UTR	NM_000810.3	NP_000801.1	P31644	GBRA5_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 5	170					associative learning (GO:0008306)|behavioral fear response (GO:0001662)|brain development (GO:0007420)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(1)|upper_aerodigestive_tract(1)	49		all_lung(180;4.59e-13)|Breast(32;0.000563)|Colorectal(260;0.227)		all cancers(64;1.45e-08)|Epithelial(43;4.96e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0232)|Lung(196;0.182)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zopiclone(DB01198)	TGACCATCTCTGCAGAGTGCC	0.473																																					p.S170S		Atlas-SNP	.											.	GABRA5	127	.	0			c.T510G						.						77	77	77					15																	27159962		1966	4168	6134	SO:0001819	synonymous_variant	2558	exon7			CATCTCTGCAGAG		CCDS45194.1	15q12	2012-06-22			ENSG00000186297	ENSG00000186297		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4079	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 5"	137142				1321750	Standard	NM_000810		Approved		uc021sgi.1	P31644	OTTHUMG00000171824	ENST00000335625.5:c.510T>G	chr15.hg19:g.27159962T>G		67.0	0.0		49.0	21.0	NM_001165037	A8K338|Q14DC2|Q53XL6|Q9NYT3|Q9NYT4|Q9NYT5	Silent	SNP	ENST00000335625.5	hg19	CCDS45194.1																																																																																			.	.		0.473	GABRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415234.1			G	27159962	T	G	27159962	2	3	362	1	0	0	0	0	0	0	0	1	6172	1567	55	5		5	GABRA5	15	27159962	Silent	SNP	T	TCGA-YA-A8S7-01A-11D-A36X-10		27159962	75371430	63	50609										
ADCY9	115	hgsc.bcm.edu	37	chr16	4015980	4015980	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	agagatgtcttgtccacataCtggacagaaggcaccaggtt	11	9	1	2	rs370863551		TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr16:4015980C>A	ENST00000294016.3	-	11	4396	c.3858G>T	c.(3856-3858)caG>caT	p.Q1286H		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	1286					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						TGTCCACATACTGGACAGAAG	0.602																																					p.Q1286H		Atlas-SNP	.											.	ADCY9	151	.	0			c.G3858T						.						100	88	93					16																	4015980		2197	4300	6497	SO:0001583	missense	115	exon11			CACATACTGGACA	AF036927	CCDS32382.1	16p13.3	2013-02-04				ENSG00000162104	4.6.1.1	"Adenylate cyclases"	240	protein-coding gene	gene with protein product		603302				9628827	Standard	NM_001116		Approved	AC9	uc002cvx.3	O60503		ENST00000294016.3:c.3858G>T	chr16.hg19:g.4015980C>A	ENSP00000294016:p.Gln1286His	74.0	0.0		62.0	7.0	NM_001116	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Missense_Mutation	SNP	ENST00000294016.3	hg19	CCDS32382.1	.	.	.	.	.	.	.	.	.	.	C	11.71	1.721068	0.30503	.	.	ENSG00000162104	ENST00000294016	D	0.83250	-1.7	5.67	3.62	0.41486	.	0.206543	0.43110	D	0.000614	T	0.68879	0.3049	N	0.17082	0.46	0.32166	N	0.582351	B	0.02656	0.0	B	0.04013	0.001	T	0.69034	-0.5252	10	0.37606	T	0.19	.	10.4262	0.44380	0.0:0.7935:0.1335:0.073	.	1286	O60503	ADCY9_HUMAN	H	1286	ENSP00000294016:Q1286H	ENSP00000294016:Q1286H	Q	-	3	2	ADCY9	3955981	0.986000	0.35501	0.573000	0.28510	0.926000	0.56050	2.141000	0.42168	1.541000	0.49316	0.655000	0.94253	CAG	.	.		0.602	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1			A	4015980	C	A	4015980	3	1	362	1	0	0	0	0	1	0	0	0	301	564	20	3	207	3	ADCY9	16	4015980	Missense_Mutation	SNP	C	TCGA-YA-A8S7-01A-11D-A36X-10		4015980	86338773	64	50610										
AKTIP	64400	hgsc.bcm.edu	37	chr16	53529086	53529086	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	gaatattactccaaaccacaCtgtaggaaaaaataaaagag	6	7	0	1			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr16:53529086C>T	ENST00000394657.7	-	5	488		c.e5-1		AKTIP_ENST00000570004.1_Splice_Site|AKTIP_ENST00000300245.4_Splice_Site	NM_001012398.1|NM_022476.2	NP_001012398.1|NP_071921.1	Q9H8T0	AKTIP_HUMAN	AKT interacting protein						apoptotic process (GO:0006915)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|protein transport (GO:0015031)	FHF complex (GO:0070695)|plasma membrane (GO:0005886)	acid-amino acid ligase activity (GO:0016881)			large_intestine(1)|lung(2)|prostate(2)	5		all_cancers(37;0.14)				CCAAACCACACTGTAGGAAAA	0.383																																					.		Atlas-SNP	.											.	AKTIP	16	.	0			c.314-1G>A						.						116	118	118					16																	53529086		2198	4300	6498	SO:0001630	splice_region_variant	64400	exon6			ACCACACTGTAGG	AK023320	CCDS10749.1	16q12.2	2010-01-14	2007-01-16	2007-01-16	ENSG00000166971	ENSG00000166971		"Ubiquitin-conjugating enzymes E2"	16710	protein-coding gene	gene with protein product		608483	"fused toes (mouse) homolog", "fused toes homolog (mouse)"	FTS		7818539, 8626685	Standard	XM_005256094		Approved	FLJ13258	uc002ehl.3	Q9H8T0	OTTHUMG00000133199	ENST00000394657.7:c.314-1G>A	chr16.hg19:g.53529086C>T		171.0	0.0		251.0	31.0	NM_001012398	Q503B1|Q53H38	Splice_Site	SNP	ENST00000394657.7	hg19	CCDS10749.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.301396	0.81136	.	.	ENSG00000166971	ENST00000394657;ENST00000300245	.	.	.	5.88	5.88	0.94601	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.2279	0.98344	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	AKTIP	52086587	1.000000	0.71417	0.999000	0.59377	0.770000	0.43624	7.721000	0.84768	2.778000	0.95560	0.655000	0.94253	.	.	.		0.383	AKTIP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256909.4	NM_022476	Intron	T	53529086	C	T	53529086	5	4	362	1	0	0	0	0	0	0	1	0	482	579	20	3	589	3	AKTIP	16	53529086	Splice_Site	SNP	C	TCGA-YA-A8S7-01A-11D-A36X-10	49513106	53529086	36825667	65	50611										
ZC3H18	124245	hgsc.bcm.edu	37	chr16	88677881	88677881	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	ccggcagcaccgtgaccgcgAccgggagaaggagcgggaga	18	12	0	3			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr16:88677881A>T	ENST00000301011.5	+	8	1612	c.1412A>T	c.(1411-1413)gAc>gTc	p.D471V	ZC3H18_ENST00000452588.2_Missense_Mutation_p.D495V	NM_144604.3	NP_653205.3	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	471						nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(9)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	42				BRCA - Breast invasive adenocarcinoma(80;0.0542)		CGTGACCGCGACCGggagaag	0.701																																					p.D471V	Ovarian(121;375 2276 20373 38669)	Atlas-SNP	.											.	ZC3H18	90	.	0			c.A1412T						.						49	39	42					16																	88677881		1780	3422	5202	SO:0001583	missense	124245	exon8			ACCGCGACCGGGA	BC001584	CCDS10967.1, CCDS73924.1	16q24.2-q24.3	2012-07-05			ENSG00000158545	ENSG00000158545		"Zinc fingers, CCCH-type domain containing"	25091	protein-coding gene	gene with protein product						17579712	Standard	NM_144604		Approved	NHN1	uc002fky.3	Q86VM9	OTTHUMG00000137679	ENST00000301011.5:c.1412A>T	chr16.hg19:g.88677881A>T	ENSP00000301011:p.Asp471Val	269.0	1.0		320.0	158.0	NM_144604	Q96DG4|Q96MP7	Missense_Mutation	SNP	ENST00000301011.5	hg19	CCDS10967.1	.	.	.	.	.	.	.	.	.	.	a	12.93	2.086639	0.36855	.	.	ENSG00000158545	ENST00000301011;ENST00000289509;ENST00000452588	T;T	0.54279	0.58;0.58	3.61	3.61	0.41365	.	1.035860	0.07564	N	0.917518	T	0.52158	0.1717	L	0.50333	1.59	0.51482	D	0.999928	P;B;P	0.44429	0.835;0.403;0.835	B;B;B	0.43018	0.405;0.405;0.405	T	0.50215	-0.8854	10	0.66056	D	0.02	-2.2907	10.0554	0.42241	1.0:0.0:0.0:0.0	.	495;495;471	E7ERS3;B4DTK7;Q86VM9	.;.;ZCH18_HUMAN	V	471;439;495	ENSP00000301011:D471V;ENSP00000416951:D495V	ENSP00000289509:D439V	D	+	2	0	ZC3H18	87205382	0.998000	0.40836	0.219000	0.23793	0.703000	0.40648	4.178000	0.58284	1.411000	0.46957	0.370000	0.22315	GAC	.	.		0.701	ZC3H18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000269168.1	NM_144604		T	88677881	A	T	88677881	3	4	362	1	0	0	0	0	1	0	0	0	17583	275	10	4	1438	4	ZC3H18	16	88677881	Missense_Mutation	SNP	A	TCGA-YA-A8S7-01A-11D-A36X-10	35148795	88677881	1676872	66	50612										
TP53	7157	hgsc.bcm.edu	37	chr17	7578235	7578235	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	aagtgtttctgtcatccaaaTactccacacgcaaatttcct	4	12	2	0			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr17:7578235T>G	ENST00000269305.4	-	6	803	c.614A>C	c.(613-615)tAt>tCt	p.Y205S	TP53_ENST00000359597.4_Missense_Mutation_p.Y205S|TP53_ENST00000420246.2_Missense_Mutation_p.Y205S|TP53_ENST00000574684.1_Intron|TP53_ENST00000413465.2_Missense_Mutation_p.Y205S|TP53_ENST00000455263.2_Missense_Mutation_p.Y205S|TP53_ENST00000445888.2_Missense_Mutation_p.Y205S	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	205	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		Y -> C (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1459726}.|Y -> D (in sporadic cancers; somatic mutation).|Y -> F (in sporadic cancers; somatic mutation).|Y -> H (in sporadic cancers; somatic mutation).|Y -> N (in sporadic cancers; somatic mutation).|Y -> S (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Y205C(68)|p.Y205S(14)|p.Y205F(8)|p.0?(8)|p.Y112C(5)|p.?(5)|p.Y73C(5)|p.Y73S(1)|p.Y112S(1)|p.E204fs*39(1)|p.E204_N210delEYLDDRN(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GTCATCCAAATACTCCACACG	0.542		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.Y205S	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,temporoparietal,glioma,0,24	TP53	33396	.	117	Substitution - Missense(102)|Whole gene deletion(8)|Unknown(5)|Deletion - In frame(1)|Deletion - Frameshift(1)	lung(20)|upper_aerodigestive_tract(19)|central_nervous_system(10)|large_intestine(9)|biliary_tract(8)|breast(6)|ovary(6)|haematopoietic_and_lymphoid_tissue(5)|endometrium(5)|urinary_tract(5)|bone(5)|soft_tissue(4)|oesophagus(4)|stomach(3)|liver(3)|pancreas(2)|vulva(1)|skin(1)|prostate(1)	c.A614C						.						136	121	126					17																	7578235		2203	4300	6503	SO:0001583	missense	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	TCCAAATACTCCA	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.614A>C	chr17.hg19:g.7578235T>G	ENSP00000269305:p.Tyr205Ser	175.0	0.0		152.0	54.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	19.82	3.897640	0.72639	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99868	-7.32;-7.32;-7.32;-7.32;-7.32;-7.32;-7.32;-7.32	5.41	4.33	0.51752	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99843	0.9928	M	0.92738	3.34	0.58432	D	0.999999	P;D;P;P;D;P;P	0.58268	0.766;0.982;0.89;0.954;0.974;0.853;0.943	P;P;P;P;P;P;P	0.61940	0.714;0.829;0.681;0.781;0.896;0.781;0.623	D	0.97292	0.9925	10	0.87932	D	0	-5.8058	9.707	0.40222	0.0:0.0827:0.0:0.9173	.	166;205;205;112;205;205;205	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	S	205;205;205;205;205;205;194;112;73;112;73	ENSP00000410739:Y205S;ENSP00000352610:Y205S;ENSP00000269305:Y205S;ENSP00000398846:Y205S;ENSP00000391127:Y205S;ENSP00000391478:Y205S;ENSP00000425104:Y73S;ENSP00000423862:Y112S	ENSP00000269305:Y205S	Y	-	2	0	TP53	7518960	1.000000	0.71417	0.137000	0.22149	0.045000	0.14185	7.996000	0.88334	1.001000	0.39076	-0.256000	0.11100	TAT	.	.		0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		G	7578235	T	G	7578235	3	3	362	1	0	0	0	0	1	0	0	0	16396	1406	49	5	680	5	TP53	17	7578235	Missense_Mutation	SNP	T	TCGA-YA-A8S7-01A-11D-A36X-10		7578235	73616975	67	50613										
GUCY2D	3000	hgsc.bcm.edu	37	chr17	7909969	7909969	+	Frame_Shift_Del	DEL	G	G	-													0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	cccggatgcacttcccgcgtGggggatcagcacccggacct					rs140638938		TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr17:7909969delG	ENST00000254854.4	+	4	1465	c.1315delG	c.(1315-1317)gggfs	p.G440fs		NM_000180.3	NP_000171.1	Q02846	GUC2D_HUMAN	guanylate cyclase 2D, membrane (retina-specific)	440					intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)			skin(1)	1		Prostate(122;0.157)				CTTCCCGCGTGGGGGATCAGC	0.647																																					p.R438fs		Atlas-INDEL	.											.	GUCY2D	82	.	0			c.1314delT						.						23	22	23					17																	7909969		2203	4300	6503	SO:0001589	frameshift_variant	3000	exon4			.	L26921	CCDS11127.1	17p13.1	2013-06-06			ENSG00000132518	ENSG00000132518			4689	protein-coding gene	gene with protein product		600179	"cone rod dystrophy 6"	CORD6, LCA, GUC2D, GUC1A4		1356371, 12552567	Standard	NM_000180		Approved	retGC, RETGC-1, ROS-GC1, CYGD, LCA1	uc002gjt.2	Q02846	OTTHUMG00000108169	ENST00000254854.4:c.1315delG	chr17.hg19:g.7909969delG	ENSP00000254854:p.Gly440fs	57.0	0.0		33.0	12.0	NM_000180	Q6LEA7	Frame_Shift_Del	DEL	ENST00000254854.4	hg19	CCDS11127.1																																																																																			.	.		0.647	GUCY2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226973.2			-	7909969	G	-	7909969	7	5	362	1	0	1	0	1	0	0	0	0	6906	1348	47	0	1325	0	GUCY2D	17	7909969	Frame_Shift_Del	DEL	G	TCGA-YA-A8S7-01A-11D-A36X-10	331734	7909969	73285241	68	50614										
KRTAP4-5	85289	hgsc.bcm.edu	37	chr17	39305781	39305782	+	In_Frame_Ins	INS	-	-	AGCTGGGGCGGCAGC													0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	gcagcaggtggtctggcagcINSagcaggggcggcagcagctg							TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr17:39305781_39305782insAGCTGGGGCGGCAGC	ENST00000343246.4	-	1	272_273	c.238_239insGCTGCCGCCCCAGCT	c.(238-240)tgc>tGCTGCCGCCCCAGCTgc	p.80_80C>CCRPSC		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	80	26 X 5 AA repeats of C-C-[GRQVCHIEK]- [SPTR]-[VSTQYC].		C -> CCCRPS.		aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(4)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			ggtctggcagcagcaggggcgg	0.653																																					p.C80delinsCCRPSC		Atlas-INDEL	.											.	KRTAP4-5	34	.	0			c.239_240insGCTGCCGCCCCAGCT						.																																			SO:0001652	inframe_insertion	85289	exon1			.	AJ406937	CCDS32650.1	17q21.2	2013-06-25			ENSG00000198271	ENSG00000198271		"Keratin associated proteins"	18899	protein-coding gene	gene with protein product						11279113	Standard	NM_033188		Approved	KAP4.5	uc002hwb.3	Q9BYR2	OTTHUMG00000133638	ENST00000343246.4:c.238_239insGCTGCCGCCCCAGCT	chr17.hg19:g.39305781_39305782insAGCTGGGGCGGCAGC	Exception_encountered	65.0	0.0		48.0	22.0	NM_033188		In_Frame_Ins	INS	ENST00000343246.4	hg19	CCDS32650.1																																																																																			.	.		0.653	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1			AGCTGGGGCGGCAGC	39305782	-	AGCTGGGGCGGCAGC	39305781	7	5	362	1	0	1	1	0	0	0	0	0	8563	710	25	0	310	0	KRTAP4-5	17	39305781	In_Frame_Ins	INS	-	TCGA-YA-A8S7-01A-11D-A36X-10	31395812	39305781	41889429	69	50615										
MRC2	9902	hgsc.bcm.edu	37	chr17	60758227	60758227	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	tgagcaccactccacgtgggCgcaggcgcagcgcatctgca	13	15	1	1			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr17:60758227C>T	ENST00000303375.5	+	17	2942	c.2540C>T	c.(2539-2541)gCg>gTg	p.A847V	MRC2_ENST00000446119.2_5'Flank	NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	847	C-type lectin 5. {ECO:0000255|PROSITE- ProRule:PRU00040}.				collagen catabolic process (GO:0030574)|endocytosis (GO:0006897)|osteoblast differentiation (GO:0001649)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|collagen binding (GO:0005518)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(11)|lung(28)|ovary(2)|prostate(1)|skin(3)	53						TCCACGTGGGCGCAGGCGCAG	0.672																																					p.A847V		Atlas-SNP	.											.	MRC2	126	.	0			c.C2540T						.						26	25	25					17																	60758227		2201	4299	6500	SO:0001583	missense	9902	exon17			CGTGGGCGCAGGC	AB014609	CCDS11634.1	17q23	2011-08-30				ENSG00000011028		"CD molecules", "C-type lectin domain containing"	16875	protein-coding gene	gene with protein product		612264				9734811, 8702911	Standard	NM_006039		Approved	KIAA0709, ENDO180, CLEC13E, CD280	uc002jad.4	Q9UBG0		ENST00000303375.5:c.2540C>T	chr17.hg19:g.60758227C>T	ENSP00000307513:p.Ala847Val	82.0	0.0		72.0	25.0	NM_006039	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	Missense_Mutation	SNP	ENST00000303375.5	hg19	CCDS11634.1	.	.	.	.	.	.	.	.	.	.	C	15.60	2.882540	0.51908	.	.	ENSG00000011028	ENST00000303375	T	0.19806	2.12	4.9	-1.13	0.09775	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.756743	0.12961	N	0.425011	T	0.10594	0.0259	N	0.17674	0.51	0.80722	D	1	B	0.09022	0.002	B	0.04013	0.001	T	0.16188	-1.0411	10	0.32370	T	0.25	-4.3242	5.3093	0.15821	0.0:0.2466:0.1806:0.5728	.	847	Q9UBG0	MRC2_HUMAN	V	847	ENSP00000307513:A847V	ENSP00000307513:A847V	A	+	2	0	MRC2	58111959	0.031000	0.19500	0.904000	0.35570	0.985000	0.73830	0.288000	0.18939	0.131000	0.18576	-0.291000	0.09656	GCG	.	.		0.672	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1			T	60758227	C	T	60758227	3	4	362	1	0	0	0	0	1	0	0	0	9767	768	27	1	2606	1	MRC2	17	60758227	Missense_Mutation	SNP	C	TCGA-YA-A8S7-01A-11D-A36X-10	21452446	60758227	20436983	70	50616										
SF3A2	8175	hgsc.bcm.edu	37	chr19	2245549	2245549	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	gaagatcggccgcccgggctAcaaaggtgagtctgcccgca	14	13	1	2			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr19:2245549A>G	ENST00000221494.5	+	5	768	c.350A>G	c.(349-351)tAc>tGc	p.Y117C		NM_007165.4	NP_009096.2	Q15428	SF3A2_HUMAN	splicing factor 3a, subunit 2, 66kDa	117					gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(1)|lung(2)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CGCCCGGGCTACAAAGGTGAG	0.647																																					p.Y117C		Atlas-SNP	.											.	SF3A2	22	.	0			c.A350G						.						28	35	32					19																	2245549		1641	3000	4641	SO:0001583	missense	8175	exon5			CGGGCTACAAAGG	L21990	CCDS12084.1	19p13.3	2012-10-02	2002-08-29		ENSG00000104897	ENSG00000104897			10766	protein-coding gene	gene with protein product		600796	"splicing factor 3a, subunit 2, 66kD"			8211113, 8541848	Standard	NM_007165		Approved	SF3a66, SAP62, PRPF11, Prp11	uc002lvg.3	Q15428	OTTHUMG00000180414	ENST00000221494.5:c.350A>G	chr19.hg19:g.2245549A>G	ENSP00000221494:p.Tyr117Cys	174.0	0.0		160.0	40.0	NM_007165	B2RBU1|D6W605|O75245	Missense_Mutation	SNP	ENST00000221494.5	hg19	CCDS12084.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.173739	0.78452	.	.	ENSG00000104897	ENST00000221494	T	0.56444	0.46	4.48	4.48	0.54585	.	0.000000	0.85682	D	0.000000	T	0.73713	0.3622	M	0.85373	2.75	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.77667	-0.2502	10	0.54805	T	0.06	-47.2792	12.9781	0.58547	1.0:0.0:0.0:0.0	.	117	Q15428	SF3A2_HUMAN	C	117	ENSP00000221494:Y117C	ENSP00000221494:Y117C	Y	+	2	0	SF3A2	2196549	1.000000	0.71417	0.997000	0.53966	0.895000	0.52256	8.421000	0.90259	1.658000	0.50742	0.459000	0.35465	TAC	.	.		0.647	SF3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451268.3			G	2245549	A	G	2245549	3	3	362	1	0	0	0	0	1	0	0	0	14162	391	14	2	364	2	SF3A2	19	2245549	Missense_Mutation	SNP	A	TCGA-YA-A8S7-01A-11D-A36X-10		2245549	56883434	71	50617										
LPHN1	22859	hgsc.bcm.edu	37	chr19	14274022	14274022	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	ttgggcaggcggtaggtggtGgtgtggcgggcggccacgta	22	7	0	0			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr19:14274022G>T	ENST00000340736.6	-	6	903	c.606C>A	c.(604-606)acC>acA	p.T202T	CTB-55O6.12_ENST00000588387.1_RNA|LPHN1_ENST00000361434.3_Silent_p.T197T|LPHN1_ENST00000591528.1_5'UTR|CTB-55O6.12_ENST00000592086.1_RNA	NM_001008701.2	NP_001008701.1	O94910	LPHN1_HUMAN	latrophilin 1	202	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|heterophilic cell-cell adhesion (GO:0007157)|neuropeptide signaling pathway (GO:0007218)|positive regulation of synapse maturation (GO:0090129)	axon (GO:0030424)|cell junction (GO:0030054)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)			central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						GGTAGGTGGTGGTGTGGCGGG	0.622																																					p.T202T		Atlas-SNP	.											.	LPHN1	107	.	0			c.C606A						.						99	77	84					19																	14274022		2203	4300	6503	SO:0001819	synonymous_variant	22859	exon6			GGTGGTGGTGTGG	AB020628	CCDS12307.1, CCDS32928.1	19p13.2	2014-08-08				ENSG00000072071		"-", "GPCR / Class B : Orphans"	20973	protein-coding gene	gene with protein product						10994649	Standard	NM_014921		Approved	KIAA0821, CIRL1, LEC2	uc010xnn.2	O94910		ENST00000340736.6:c.606C>A	chr19.hg19:g.14274022G>T		74.0	0.0		52.0	18.0	NM_001008701	Q96IE7|Q9BU07|Q9HAR3	Silent	SNP	ENST00000340736.6	hg19	CCDS32928.1																																																																																			.	.		0.622	LPHN1-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459696.1	NM_014921		T	14274022	G	T	14274022	2	4	362	1	0	0	0	0	0	0	0	1	8924	1335	47	3		3	LPHN1	19	14274022	Silent	SNP	G	TCGA-YA-A8S7-01A-11D-A36X-10	12028473	14274022	44854961	72	50618										
SFRS16	11129	hgsc.bcm.edu	37	chr19	45567465	45567465	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	cagcctggcggccccgccccGggacgtaatgccagcgcccg	14	19	0	0			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr19:45567465G>A	ENST00000221455.3	+	12	1199	c.1101G>A	c.(1099-1101)ccG>ccA	p.P367P	CLASRP_ENST00000544944.2_Silent_p.P367P|CLASRP_ENST00000391953.4_Silent_p.P305P	NM_007056.2	NP_008987	Q8N2M8	CLASR_HUMAN	CLK4-associating serine/arginine rich protein	367					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|pancreas(2)|prostate(1)	16						GCCCCGCCCCGGGACGTAATG	0.756																																					p.P367P		Atlas-SNP	.											.	CLASRP	44	.	0			c.G1101A						.						5	7	6					19																	45567465		2027	3961	5988	SO:0001819	synonymous_variant	11129	exon12			CGCCCCGGGACGT	AF042800	CCDS12652.2, CCDS62710.1	19q13.3	2010-09-21	2010-09-21	2010-09-21	ENSG00000104859	ENSG00000104859			17731	protein-coding gene	gene with protein product	"Clk4 associating SR-related protein"		"splicing factor, arginine/serine-rich 16"	SFRS16		12169693	Standard	NM_007056		Approved	SWAP2, CLASP	uc002pak.3	Q8N2M8	OTTHUMG00000150189	ENST00000221455.3:c.1101G>A	chr19.hg19:g.45567465G>A		117.0	0.0		129.0	8.0	NM_007056	B4DDT8|F8WAG9|O96026|Q6UW71|Q96DX2	Silent	SNP	ENST00000221455.3	hg19	CCDS12652.2																																																																																			.	.		0.756	CLASRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316749.1	NM_007056		A	45567465	G	A	45567465	2	1	362	1	0	0	0	0	0	0	0	1	14187	1103	39	1		1	SFRS16	19	45567465	Silent	SNP	G	TCGA-YA-A8S7-01A-11D-A36X-10	31293443	45567465	13561518	73	50619										
CCDC9	26093	hgsc.bcm.edu	37	chr19	47763963	47763963	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	cggcatgggccgagcatcgcGcagctgggagggcagccccg	18	14	0	0	rs368381443		TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr19:47763963G>T	ENST00000221922.6	+	5	551	c.329G>T	c.(328-330)cGc>cTc	p.R110L		NM_015603.2	NP_056418.1	Q9Y3X0	CCDC9_HUMAN	coiled-coil domain containing 9	110	Gly-rich.						poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|urinary_tract(1)	12		all_cancers(25;0.0432)|all_epithelial(76;0.00812)|Medulloblastoma(540;0.0208)|all_neural(266;0.0416)|Hepatocellular(1079;0.114)		OV - Ovarian serous cystadenocarcinoma(262;8.51e-95)|Epithelial(262;1.15e-92)|all cancers(93;7.67e-84)|GBM - Glioblastoma multiforme(486;0.024)|STAD - Stomach adenocarcinoma(1328;0.183)		CGAGCATCGCGCAGCTGGGAG	0.761																																					p.R110L		Atlas-SNP	.											.	CCDC9	37	.	0			c.G329T						.						11	14	13					19																	47763963		2055	4135	6190	SO:0001583	missense	26093	exon5			CATCGCGCAGCTG	AL050284	CCDS12698.1	19q13.33	2008-02-05				ENSG00000105321			24560	protein-coding gene	gene with protein product						11230166	Standard	NM_015603		Approved	DKFZP586M1019	uc010xym.2	Q9Y3X0		ENST00000221922.6:c.329G>T	chr19.hg19:g.47763963G>T	ENSP00000221922:p.Arg110Leu	52.0	0.0		66.0	11.0	NM_015603		Missense_Mutation	SNP	ENST00000221922.6	hg19	CCDS12698.1	.	.	.	.	.	.	.	.	.	.	-	10.46	1.356895	0.24598	.	.	ENSG00000105321	ENST00000221922;ENST00000504556	T	0.25579	1.79	3.32	0.336	0.15958	.	1.182760	0.06421	N	0.722298	T	0.20373	0.0490	L	0.47716	1.5	0.09310	N	1	P	0.35226	0.491	B	0.32805	0.153	T	0.25152	-1.0140	10	0.31617	T	0.26	-3.3954	5.3138	0.15845	0.374:0.0:0.626:0.0	.	110	Q9Y3X0	CCDC9_HUMAN	L	110	ENSP00000221922:R110L	ENSP00000221922:R110L	R	+	2	0	CCDC9	52455803	0.046000	0.20272	0.001000	0.08648	0.464000	0.32679	0.758000	0.26447	0.036000	0.15547	0.431000	0.28591	CGC	.	.		0.761	CCDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466917.1	NM_015603		T	47763963	G	T	47763963	3	4	362	1	0	0	0	0	1	0	0	0	2869	1087	38	1	343	1	CCDC9	19	47763963	Missense_Mutation	SNP	G	TCGA-YA-A8S7-01A-11D-A36X-10	2196498	47763963	11365020	74	50620										
PPFIA3	8541	hgsc.bcm.edu	37	chr19	49652850	49652850	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	cccatcctggcggaagatgtTccgggagaaggacctccgag	14	12	0	2			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr19:49652850T>C	ENST00000334186.4	+	28	3750	c.3401T>C	c.(3400-3402)tTc>tCc	p.F1134S	PPFIA3_ENST00000602351.1_Missense_Mutation_p.F1125S	NM_003660.2	NP_003651.1	O75145	LIPA3_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 3	1134					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|presynaptic active zone (GO:0048786)				NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(16)|pancreas(1)|prostate(1)|skin(4)|urinary_tract(1)	35		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.36e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000203)|GBM - Glioblastoma multiforme(486;0.00307)|Epithelial(262;0.00677)		CGGAAGATGTTCCGGGAGAAG	0.642																																					p.F1134S		Atlas-SNP	.											.	PPFIA3	71	.	0			c.T3401C						.						40	41	41					19																	49652850		2203	4300	6503	SO:0001583	missense	8541	exon28			AGATGTTCCGGGA	AF034800	CCDS12758.1	19q13.33	2013-09-23			ENSG00000177380	ENSG00000177380		"Sterile alpha motif (SAM) domain containing"	9247	protein-coding gene	gene with protein product	"protein tyrosine phosphatase, receptor type, f polypeptide, alpha 3", "liprin-alpha 3", "liprin"	603144				9624153, 9734811	Standard	NM_003660		Approved	KIAA0654, LPNA3, MGC126567, MGC126569	uc002pmr.3	O75145	OTTHUMG00000183213	ENST00000334186.4:c.3401T>C	chr19.hg19:g.49652850T>C	ENSP00000335614:p.Phe1134Ser	171.0	0.0		182.0	44.0	NM_003660	A8K142|Q3MJA0|Q9H8B5|Q9UEW4	Missense_Mutation	SNP	ENST00000334186.4	hg19	CCDS12758.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.701402	0.88924	.	.	ENSG00000177380	ENST00000334186	T	0.22539	1.95	4.12	4.12	0.48240	.	0.000000	0.48286	U	0.000185	T	0.41282	0.1152	M	0.69358	2.11	0.80722	D	1	P;D	0.76494	0.919;0.999	P;D	0.66351	0.615;0.943	T	0.36841	-0.9731	10	0.72032	D	0.01	-17.3063	12.5337	0.56131	0.0:0.0:0.0:1.0	.	1125;1134	O75145-2;O75145	.;LIPA3_HUMAN	S	1134	ENSP00000335614:F1134S	ENSP00000335614:F1134S	F	+	2	0	PPFIA3	54344662	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.678000	0.84035	1.863000	0.54032	0.379000	0.24179	TTC	.	.		0.642	PPFIA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465688.1	NM_003660		C	49652850	T	C	49652850	3	2	362	1	0	0	0	0	1	0	0	0	12320	1783	62	2	3507	2	PPFIA3	19	49652850	Missense_Mutation	SNP	T	TCGA-YA-A8S7-01A-11D-A36X-10	1888887	49652850	9476133	75	50621										
NFATC2	4773	hgsc.bcm.edu	37	chr20	50048660	50048675	+	Frame_Shift_Del	DEL	GGTAATACTTCCTTTT	GGTAATACTTCCTTTT	-													0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	gtttaatggtcacccccgcaGgtaatacttccttttggtca					rs6067777	byFrequency	TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	GGTAATACTTCCTTTT	GGTAATACTTCCTTTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr20:50048660_50048675delGGTAATACTTCCTTTT	ENST00000396009.3	-	9	2870_2885	c.2651_2666delAAAAGGAAGTATTACC	c.(2650-2667)caaaaggaagtattacctfs	p.QKEVLP884fs	NFATC2_ENST00000609943.1_Frame_Shift_Del_p.QKEVLP864fs|NFATC2_ENST00000371564.3_Frame_Shift_Del_p.QKEVLP884fs|NFATC2_ENST00000609507.1_Frame_Shift_Del_p.QKEVLP665fs|NFATC2_ENST00000414705.1_Frame_Shift_Del_p.QKEVLP864fs|NFATC2_ENST00000610033.1_Frame_Shift_Del_p.QKEVLP665fs	NM_001258297.1|NM_173091.3	NP_001245226.1|NP_775114.1	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	884					B cell receptor signaling pathway (GO:0050853)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear transcription factor complex (GO:0044798)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.V887A(1)	EWSR1/NFATC2(9)	breast(2)|endometrium(7)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	53	Hepatocellular(150;0.248)					CACCCCCGCAGGTAATACTTCCTTTTGGTCACTGAC	0.542																																					p.884_889del		Atlas-INDEL	.											.	NFATC2	112	.	1	Substitution - Missense(1)	lung(1)	c.2652_2667del						.																																			SO:0001589	frameshift_variant	4773	exon9			.	U43342, U43341	CCDS13437.1, CCDS33488.1, CCDS46614.1, CCDS68156.1, CCDS68157.1	20q13.2	2009-11-24			ENSG00000101096	ENSG00000101096		"Nuclear factor of activated T-cells"	7776	protein-coding gene	gene with protein product		600490				8202141	Standard	NM_012340		Approved	NF-ATP, NFATp, NFAT1	uc002xwd.4	Q13469	OTTHUMG00000032747	ENST00000396009.3:c.2651_2666delAAAAGGAAGTATTACC	chr20.hg19:g.50048660_50048675delGGTAATACTTCCTTTT	ENSP00000379330:p.Gln884fs	131.0	0.0		115.0	14.0	NM_012340	B5B2N8|B5B2N9|B5B2P0|B5B2P2|B5B2P3|Q13468|Q5TFW7|Q5TFW8|Q9NPX6|Q9NQH3|Q9UJR2	Frame_Shift_Del	DEL	ENST00000396009.3	hg19	CCDS13437.1																																																																																			.	.		0.542	NFATC2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079730.2	NM_012340		-	50048675	GGTAATACTTCCTTTT	-	50048660	7	5	362	1	0	1	0	1	0	0	0	0	10371	1000	35	0	167	0	NFATC2	20	50048660	Frame_Shift_Del	DEL	GGTAATACTTCCTTTT	TCGA-YA-A8S7-01A-11D-A36X-10		50048660	12976860	76	50622										
ZNF831	128611	hgsc.bcm.edu	37	chr20	57767596	57767596	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	tcaccaggagcaactcgctgCccttcgtcgagggctccagg	12	15	1	0			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr20:57767596C>G	ENST00000371030.2	+	1	1522	c.1522C>G	c.(1522-1524)Ccc>Gcc	p.P508A		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	508							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					CAACTCGCTGCCCTTCGTCGA	0.697																																					p.P508A		Atlas-SNP	.											.	ZNF831	287	.	0			c.C1522G						.						14	17	16					20																	57767596		1926	4093	6019	SO:0001583	missense	128611	exon1			TCGCTGCCCTTCG	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 174"	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.1522C>G	chr20.hg19:g.57767596C>G	ENSP00000360069:p.Pro508Ala	112.0	0.0		132.0	19.0	NM_178457	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	hg19	CCDS42894.1	.	.	.	.	.	.	.	.	.	.	C	16.88	3.244634	0.59103	.	.	ENSG00000124203	ENST00000371030	T	0.23754	1.89	5.21	5.21	0.72293	.	.	.	.	.	T	0.52980	0.1768	M	0.75615	2.305	0.32959	D	0.520812	D	0.89917	1.0	D	0.74674	0.984	T	0.65676	-0.6110	9	0.87932	D	0	-16.3529	17.7439	0.88414	0.0:1.0:0.0:0.0	.	508	Q5JPB2	ZN831_HUMAN	A	508	ENSP00000360069:P508A	ENSP00000360069:P508A	P	+	1	0	ZNF831	57200991	1.000000	0.71417	0.997000	0.53966	0.816000	0.46133	4.615000	0.61190	2.423000	0.82170	0.655000	0.94253	CCC	.	.		0.697	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		G	57767596	C	G	57767596	3	3	362	1	0	0	0	0	1	0	0	0	18200	739	26	4	1524	4	ZNF831	20	57767596	Missense_Mutation	SNP	C	TCGA-YA-A8S7-01A-11D-A36X-10	7718936	57767596	5257924	77	50623										
NEFH	4744	hgsc.bcm.edu	37	chr22	29885572	29885573	+	In_Frame_Ins	INS	-	-	CCCTGAGAAGGCCAAGTC													0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	acgaaggaggaagcaaagtcINSccctgagaaggccaagtccc							TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chr22:29885572_29885573insCCCTGAGAAGGCCAAGTC	ENST00000310624.6	+	4	1976_1977	c.1943_1944insCCCTGAGAAGGCCAAGTC	c.(1942-1947)tcccct>tcCCCTGAGAAGGCCAAGTCccct	p.648_649SP>SPEKAKSP		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	654	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.			Missing (in Ref. 1; CAA33366 and 5; AC000035). {ECO:0000305}.	axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						GAAGCAAAGTCCCCTGAGAAGG	0.569																																					p.S648delinsSPEKAKS		Atlas-INDEL	.											.	NEFH	178	.	0			c.1943_1944insCCCTGAGAAGGCCAAGTC						.																																			SO:0001652	inframe_insertion	4744	exon4			.		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1944_1961dupCCCTGAGAAGGCCAAGTC	chr22.hg19:g.29885572_29885573insCCCTGAGAAGGCCAAGTC	ENSP00000311997:p.Pro643_Ser648dup	234.0	0.0		280.0	45.0	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Ins	INS	ENST00000310624.6	hg19	CCDS13858.1																																																																																			.	.		0.569	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		CCCTGAGAAGGCCAAGTC	29885573	-	CCCTGAGAAGGCCAAGTC	29885572	7	5	362	1	0	1	1	0	0	0	0	0	10323	855	30	0	1957	0	NEFH	22	29885572	In_Frame_Ins	INS	-	TCGA-YA-A8S7-01A-11D-A36X-10		29885572	21418994	78	50624										
AR	367	hgsc.bcm.edu	37	chrX	66765173	66765173	+	Missense_Mutation	SNP	A	A	T													0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	gctgctgcagcagcagcagcAgcagcagcagcagcagcagc							TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chrX:66765173A>T	ENST00000374690.3	+	1	709	c.185A>T	c.(184-186)cAg>cTg	p.Q62L	AR_ENST00000513847.1_3'UTR|AR_ENST00000504326.1_Missense_Mutation_p.Q62L|AR_ENST00000396044.3_Missense_Mutation_p.Q62L	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	62	Gln-rich.|Modulating.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	cagcagcagcagcagcagcag	0.677									Androgen Insensitivity Syndrome																												p.Q62L		Atlas-SNP	.											.	AR	249	.	0			c.A185T						.						5	9	7					X																	66765173		1734	3384	5118	SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	AGCAGCAGCAGCA	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.185A>T	chrX.hg19:g.66765173A>T	ENSP00000363822:p.Gln62Leu	124.0	0.0		132.0	6.0	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	hg19	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	a	13.85	2.358892	0.41801	.	.	ENSG00000169083	ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	T;T;T	0.69306	-0.39;-0.39;-0.39	.	.	.	.	1.296110	0.05656	N	0.585987	T	0.58850	0.2151	N	0.19112	0.55	0.09310	N	0.999999	P;P;.	0.43431	0.807;0.458;.	P;B;.	0.53518	0.728;0.245;.	T	0.51180	-0.8738	8	0.11485	T	0.65	.	.	.	.	.	62;62;60	E7EVX6;D3YPQ2;P10275	.;.;ANDR_HUMAN	L	62	ENSP00000363822:Q62L;ENSP00000421155:Q62L;ENSP00000379359:Q62L	ENSP00000363822:Q62L	Q	+	2	0	AR	66681898	0.984000	0.35163	0.863000	0.33907	0.539000	0.34962	1.220000	0.32491	0.000000	0.14550	0.000000	0.15137	CAG	.	.		0.677	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		T	66765173	A	T	66765173	3	4	362	1	0	0	0	0	1	0	0	0	836	188	7	4	187	4	AR	23	66765173	Missense_Mutation	SNP	A	TCGA-YA-A8S7-01A-11D-A36X-10		66765173	88505387	79	50625	265	3	1	69		4	2	35	N	G_A	8.895892e-05
AR	367	hgsc.bcm.edu	37	chrX	66765176	66765176	+	Missense_Mutation	SNP	A	A	T													0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	gctgcagcagcagcagcagcAgcagcagcagcagcagcagc					rs62636527		TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chrX:66765176A>T	ENST00000374690.3	+	1	712	c.188A>T	c.(187-189)cAg>cTg	p.Q63L	AR_ENST00000513847.1_3'UTR|AR_ENST00000504326.1_Missense_Mutation_p.Q63L|AR_ENST00000396044.3_Missense_Mutation_p.Q63L	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	63	Gln-rich.|Modulating.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	cagcagcagcagcagcagcag	0.672									Androgen Insensitivity Syndrome																												p.Q63L		Atlas-SNP	.											.	AR	249	.	0			c.A188T						.						5	8	7					X																	66765176		1640	3236	4876	SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	AGCAGCAGCAGCA	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.188A>T	chrX.hg19:g.66765176A>T	ENSP00000363822:p.Gln63Leu	122.0	0.0		131.0	9.0	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	hg19	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	a	11.08	1.532203	0.27387	.	.	ENSG00000169083	ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	T;T;T	0.78246	-1.16;-1.16;-1.16	.	.	.	.	0.479323	0.15343	U	0.267412	T	0.62624	0.2443	N	0.19112	0.55	0.09310	N	0.999992	P;D;.	0.58268	0.755;0.982;.	B;P;.	0.48627	0.089;0.584;.	T	0.56408	-0.7984	8	0.17832	T	0.49	.	.	.	.	rs62636527	63;63;61	E7EVX6;D3YPQ2;P10275	.;.;ANDR_HUMAN	L	63	ENSP00000363822:Q63L;ENSP00000421155:Q63L;ENSP00000379359:Q63L	ENSP00000363822:Q63L	Q	+	2	0	AR	66681901	0.810000	0.29049	0.871000	0.34182	0.555000	0.35460	1.078000	0.30754	0.000000	0.14550	0.000000	0.15137	CAG	.	A|0.982;T|0.018		0.672	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		T	66765176	A	T	66765176	3	4	362	1	0	0	0	0	1	0	0	0	836	188	7	4	190	4	AR	23	66765176	Missense_Mutation	SNP	A	TCGA-YA-A8S7-01A-11D-A36X-10	3	66765176	88505384	80	50626	265	3	1	69		4	2	35	N	G_A	8.895892e-05
AR	367	hgsc.bcm.edu	37	chrX	66765179	66765179	+	Missense_Mutation	SNP	A	A	T													0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	gcagcagcagcagcagcagcAgcagcagcagcagcagcagc							TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chrX:66765179A>T	ENST00000374690.3	+	1	715	c.191A>T	c.(190-192)cAg>cTg	p.Q64L	AR_ENST00000513847.1_3'UTR|AR_ENST00000504326.1_Missense_Mutation_p.Q64L|AR_ENST00000396044.3_Missense_Mutation_p.Q64L	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	64	Gln-rich.|Modulating.|Poly-Gln.		Q -> R (in prostate cancer).		androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	cagcagcagcagcagcagcag	0.677									Androgen Insensitivity Syndrome																												p.Q64L		Atlas-SNP	.											.	AR	249	.	0			c.A191T						.						4	8	7					X																	66765179		1590	3143	4733	SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	AGCAGCAGCAGCA	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.191A>T	chrX.hg19:g.66765179A>T	ENSP00000363822:p.Gln64Leu	116.0	0.0		131.0	12.0	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	hg19	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	a	11.28	1.591655	0.28357	.	.	ENSG00000169083	ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	T;T;T	0.67865	-0.29;-0.29;-0.29	.	.	.	.	1.847110	0.03494	N	0.217131	T	0.56124	0.1964	N	0.19112	0.55	0.09310	N	0.999991	P;D;.	0.58268	0.755;0.982;.	B;P;.	0.48627	0.089;0.584;.	T	0.50381	-0.8835	8	0.38643	T	0.18	.	.	.	.	.	64;64;62	E7EVX6;D3YPQ2;P10275	.;.;ANDR_HUMAN	L	64	ENSP00000363822:Q64L;ENSP00000421155:Q64L;ENSP00000379359:Q64L	ENSP00000363822:Q64L	Q	+	2	0	AR	66681904	0.024000	0.19004	0.883000	0.34634	0.574000	0.36063	-0.145000	0.10265	0.000000	0.14550	0.000000	0.15137	CAG	.	.		0.677	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		T	66765179	A	T	66765179	3	4	362	1	0	0	0	0	1	0	0	0	836	188	7	4	193	4	AR	23	66765179	Missense_Mutation	SNP	A	TCGA-YA-A8S7-01A-11D-A36X-10	3	66765179	88505381	81	50627	265	3	1	69		4	2	35	N	G_A	8.895892e-05
AR	367	hgsc.bcm.edu	37	chrX	66765207	66765207	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	cagcagcagcagcagcagcaGcagcagcagcagcagcagca	13	14	0	0			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chrX:66765207G>A	ENST00000374690.3	+	1	743	c.219G>A	c.(217-219)caG>caA	p.Q73Q	AR_ENST00000513847.1_3'UTR|AR_ENST00000504326.1_Silent_p.Q73Q|AR_ENST00000396044.3_Silent_p.Q73Q	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	73	Gln-rich.|Modulating.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	agcagcagcagcagcagcagc	0.672									Androgen Insensitivity Syndrome																												p.Q73Q		Atlas-SNP	.											.	AR	249	.	0			c.G219A						.						5	6	6					X																	66765207		1961	3776	5737	SO:0001819	synonymous_variant	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	GCAGCAGCAGCAG	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.219G>A	chrX.hg19:g.66765207G>A		107.0	0.0		103.0	8.0	NM_000044	A2RUN2|B1AKD7|Q9UD95	Silent	SNP	ENST00000374690.3	hg19	CCDS14387.1																																																																																			.	.		0.672	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		A	66765207	G	A	66765207	2	1	362	1	0	0	0	0	0	0	0	1	836	962	34	3		3	AR	23	66765207	Silent	SNP	G	TCGA-YA-A8S7-01A-11D-A36X-10	28	66765207	88505353	82	50628			1	69		4	2	35	N	G_A	8.895892e-05
DLG3	1741	hgsc.bcm.edu	37	chrX	69712085	69712085	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0123456790123457	1	1	0.222073677956031	0	0.318627450980392	1	1	0	gtggcaggcaaggctggtgaCcccacacggagaaagtgagc	16	10	0	3			TCGA-YA-A8S7-01A-11D-A36X-10	TCGA-YA-A8S7-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0669d47b-cc46-4b77-ad30-b3f1adbbfd9f	71d7d669-128a-455a-b4c9-898b7e7a4a61	g.chrX:69712085C>G	ENST00000374360.3	+	11	1882	c.1649C>G	c.(1648-1650)aCc>aGc	p.T550S	DLG3_ENST00000194900.4_Missense_Mutation_p.T568S|DLG3_ENST00000374355.3_Missense_Mutation_p.T213S|DLG3_ENST00000542398.1_Missense_Mutation_p.T67S	NM_021120.3	NP_066943.2	Q92796	DLG3_HUMAN	discs, large homolog 3 (Drosophila)	550	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				axon guidance (GO:0007411)|establishment of planar polarity (GO:0001736)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|negative regulation of cell proliferation (GO:0008285)|negative regulation of phosphatase activity (GO:0010923)|synaptic transmission (GO:0007268)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|extracellular space (GO:0005615)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)|tight junction (GO:0005923)	phosphatase binding (GO:0019902)			endometrium(4)|kidney(1)|large_intestine(10)|lung(5)|pancreas(1)|urinary_tract(1)	22	Renal(35;0.156)					AGGCTGGTGACCCCACACGGA	0.532																																					p.T550S		Atlas-SNP	.											.	DLG3	100	.	0			c.C1649G						.						85	71	75					X																	69712085		2203	4300	6503	SO:0001583	missense	1741	exon11			TGGTGACCCCACA	U49089	CCDS14403.1, CCDS43967.1, CCDS55439.1	Xq13.1	2014-06-12	2008-12-15		ENSG00000082458	ENSG00000082458			2902	protein-coding gene	gene with protein product	"neuroendocrine-dlg", "protein phosphatase 1, regulatory subunit 82"	300189	"discs, large homolog 3 (neuroendocrine-dlg, Drosophila)"			9598320	Standard	NM_021120		Approved	NE-Dlg, SAP102, SAP-102, NEDLG, KIAA1232, MRX90, PPP1R82	uc004dyi.2	Q92796	OTTHUMG00000021778	ENST00000374360.3:c.1649C>G	chrX.hg19:g.69712085C>G	ENSP00000363480:p.Thr550Ser	112.0	0.0		153.0	11.0	NM_021120	B4E0H1|D3DVU5|Q5JUW6|Q5JUW7|Q9ULI8	Missense_Mutation	SNP	ENST00000374360.3	hg19	CCDS14403.1	.	.	.	.	.	.	.	.	.	.	C	12.63	1.995471	0.35226	.	.	ENSG00000082458	ENST00000194900;ENST00000374360;ENST00000374355;ENST00000542398	D;D;D;D	0.81739	-1.53;-1.53;-1.53;-1.53	5.15	5.15	0.70609	Src homology-3 domain (4);	0.000000	0.85682	D	0.000000	T	0.68348	0.2991	N	0.16602	0.42	0.80722	D	1	B;B;B	0.24186	0.08;0.099;0.002	B;B;B	0.25405	0.05;0.06;0.007	T	0.63761	-0.6564	9	.	.	.	.	16.6272	0.84974	0.0:1.0:0.0:0.0	.	67;213;550	B4E0H1;Q5JUW6;Q92796	.;.;DLG3_HUMAN	S	568;550;213;67	ENSP00000194900:T568S;ENSP00000363480:T550S;ENSP00000363475:T213S;ENSP00000441393:T67S	.	T	+	2	0	DLG3	69628810	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	7.651000	0.83577	2.389000	0.81357	0.600000	0.82982	ACC	.	.		0.532	DLG3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057074.2	NM_021120		G	69712085	C	G	69712085	3	3	362	1	0	0	0	0	1	0	0	0	4558	507	18	4	1829	4	DLG3	23	69712085	Missense_Mutation	SNP	C	TCGA-YA-A8S7-01A-11D-A36X-10	2946878	69712085	85558475	83	50629										
MAP3K6	9064	hgsc.bcm.edu	37	chr1	27686481	27686481	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	gaccgcagcaaggaggacagGctgcctgggtggggacagtc	18	10	0	0			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr1:27686481G>A	ENST00000493901.1	-	18	2426	c.2187C>T	c.(2185-2187)agC>agT	p.S729S	MAP3K6_ENST00000357582.2_Silent_p.S729S|MAP3K6_ENST00000374040.3_Silent_p.S721S	NM_004672.3	NP_004663.3	O95382	M3K6_HUMAN	mitogen-activated protein kinase kinase kinase 6	729	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)			breast(4)|central_nervous_system(2)|lung(3)|ovary(1)	10		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.69e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00132)|KIRC - Kidney renal clear cell carcinoma(1967;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		AGGAGGACAGGCTGCCTGGGT	0.597																																					p.S729S		Atlas-SNP	.											.	MAP3K6	134	.	0			c.C2187T						.						97	96	96					1																	27686481		2203	4300	6503	SO:0001819	synonymous_variant	9064	exon17			GGACAGGCTGCCT	AF100318	CCDS299.1, CCDS72738.1	1p36.11	2011-06-09			ENSG00000142733	ENSG00000142733		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6858	protein-coding gene	gene with protein product	"apoptosis signal regulating kinase 2"	604468				9875215	Standard	XM_005246029		Approved	MAPKKK6, ASK2, MEKK6	uc001bny.1	O95382	OTTHUMG00000004631	ENST00000493901.1:c.2187C>T	chr1.hg19:g.27686481G>A		76.0	0.0		69.0	8.0	NM_004672	A2ACE8|A2VDG4|A2VDG5|Q59HF4|Q5SSD4|Q75PK3|Q96B75	Silent	SNP	ENST00000493901.1	hg19	CCDS299.1	.	.	.	.	.	.	.	.	.	.	G	9.396	1.076745	0.20227	.	.	ENSG00000142733	ENST00000472410	.	.	.	5.03	3.16	0.36331	.	.	.	.	.	T	0.57504	0.2058	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51671	-0.8676	4	.	.	.	.	7.8465	0.29428	0.2581:0.0:0.7419:0.0	.	.	.	.	V	453	.	.	A	-	2	0	MAP3K6	27559068	1.000000	0.71417	1.000000	0.80357	0.834000	0.47266	1.414000	0.34736	0.709000	0.31976	0.561000	0.74099	GCC	.	.		0.597	MAP3K6-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000013469.2	NM_004672		A	27686481	G	A	27686481	2	1	363	1	0	0	0	0	0	0	0	1	9263	1194	42	3		3	MAP3K6	1	27686481	Silent	SNP	G	TCGA-ZP-A9CV-01A-11D-A382-10		27686481	221564140	1	50630										
PUM1	9698	hgsc.bcm.edu	37	chr1	31414910	31414910	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	gagtgtctggtcagggagacAgtgctccaggattctctgaa	14	8	3	2			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr1:31414910A>G	ENST00000257075.5	-	19	3142	c.3049T>C	c.(3049-3051)Tgt>Cgt	p.C1017R	PUM1_ENST00000440538.2_Missense_Mutation_p.C993R|PUM1_ENST00000424085.2_Missense_Mutation_p.C775R|PUM1_ENST00000373741.4_Missense_Mutation_p.C1055R|PUM1_ENST00000423018.2_Missense_Mutation_p.C875R|PUM1_ENST00000373742.2_Missense_Mutation_p.C958R|PUM1_ENST00000426105.2_Missense_Mutation_p.C1019R|PUM1_ENST00000373747.3_Missense_Mutation_p.C1020R	NM_014676.2	NP_055491.1	Q14671	PUM1_HUMAN	pumilio RNA-binding family member 1	1017	PUM-HD. {ECO:0000255|PROSITE- ProRule:PRU00318}.				membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(17)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)		TCAGGGAGACAGTGCTCCAGG	0.483																																					p.C1019R		Atlas-SNP	.											.	PUM1	107	.	0			c.T3055C						.						103	97	99					1																	31414910		2203	4300	6503	SO:0001583	missense	9698	exon19			GGAGACAGTGCTC	AF315592	CCDS338.1, CCDS44099.1	1p35.2	2013-09-02	2013-09-02		ENSG00000134644	ENSG00000134644			14957	protein-coding gene	gene with protein product		607204	"pumilio (Drosophila) homolog 1", "pumilio homolog 1 (Drosophila)"				Standard	NM_001020658		Approved	PUMH1, KIAA0099	uc001bsh.1	Q14671	OTTHUMG00000003795	ENST00000257075.5:c.3049T>C	chr1.hg19:g.31414910A>G	ENSP00000257075:p.Cys1017Arg	119.0	0.0		92.0	4.0	NM_001020658	A8K6W4|B4DG92|D3DPN3|E9PCJ0|Q53HH5|Q5VXY7|Q9HAN1	Missense_Mutation	SNP	ENST00000257075.5	hg19	CCDS338.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.7|20.7	4.037592|4.037592	0.75617|0.75617	.|.	.|.	ENSG00000134644|ENSG00000134644	ENST00000424085;ENST00000257075;ENST00000373747;ENST00000373749;ENST00000426105;ENST00000440538;ENST00000373741;ENST00000423018;ENST00000373742|ENST00000525843;ENST00000498419	T;T;T;T;T;T;T;T|.	0.14640|.	2.49;2.49;2.49;2.49;2.49;2.49;2.49;2.49|.	5.53|5.53	4.4|4.4	0.53042|0.53042	Armadillo-like helical (1);Armadillo-type fold (1);|.	0.043496|.	0.85682|.	D|.	0.000000|.	D|D	0.87059|0.87059	0.6083|0.6083	H|H	0.97635|0.97635	4.045|4.045	0.80722|0.80722	D|D	1|1	D;D;P;D;D;D;D;D|.	0.89917|.	0.999;1.0;0.879;1.0;0.994;0.995;0.994;0.994|.	D;D;P;D;D;D;D;D|.	0.87578|.	0.991;0.998;0.787;0.975;0.977;0.946;0.982;0.982|.	D|D	0.89551|0.89551	0.3799|0.3799	10|5	0.87932|.	D|.	0|.	-6.3069|-6.3069	11.2503|11.2503	0.49022|0.49022	0.9275:0.0:0.0725:0.0|0.9275:0.0:0.0725:0.0	.|.	958;875;1055;993;1017;1019;1020;1019|.	B4DG92;E7EWT3;Q5T1Z8;Q14671-2;Q14671;E9PCJ0;Q5T1Z4;Q53HH5|.	.;.;.;.;PUM1_HUMAN;.;.;.|.	R|P	775;1017;1020;757;1019;993;1055;875;958|955;730	ENSP00000400141:C775R;ENSP00000257075:C1017R;ENSP00000362852:C1020R;ENSP00000391723:C1019R;ENSP00000401777:C993R;ENSP00000362846:C1055R;ENSP00000399440:C875R;ENSP00000362847:C958R|.	ENSP00000257075:C1017R|.	C|L	-|-	1|2	0|0	PUM1|PUM1	31187497|31187497	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.287000|9.287000	0.95975|0.95975	1.031000|1.031000	0.39867|0.39867	0.528000|0.528000	0.53228|0.53228	TGT|CTG	.	.		0.483	PUM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000010671.1			G	31414910	A	G	31414910	3	3	363	1	0	0	0	0	1	0	0	0	12840	188	7	2	527	2	PUM1	1	31414910	Missense_Mutation	SNP	A	TCGA-ZP-A9CV-01A-11D-A382-10	3728429	31414910	217835711	2	50631										
JAK1	3716	hgsc.bcm.edu	37	chr1	65316572	65316573	+	Missense_Mutation	DNP	GC	GC	AA													0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	actcctgggctttcttagtaGccaccagcaggttggagatt							TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr1:65316572_65316573GC>AA	ENST00000342505.4	-	12	1917_1918	c.1669_1670GC>TT	c.(1669-1671)GCt>TTt	p.A557F	JAK1_ENST00000465376.1_5'Flank	NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	557					cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	TTTCTTAGTAGCCACCAGCAGG	0.584			Mis		ALL																																p.A557V|p.A557S		Atlas-SNP	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	.	JAK1	209	.	0			c.C1670T|c.G1669T						.																																			SO:0001583	missense	3716	exon12			TTAGTAGCCACCA|TAGTAGCCACCAG	M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.1669_1670delinsAA	chr1.hg19:g.65316572_65316573delinsAA	ENSP00000343204:p.Ala557Phe	79.0|78.0	0.0		70.0|71.0	11.0	NM_002227	Q59GQ2|Q9UD26	Missense_Mutation	SNP	ENST00000342505.4	hg19	CCDS41346.1																																																																																			.	.		0.584	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227		AA	65316573	GC	AA	65316572	3	1	363	1	0	0	0	0	1	0	0	0	7946	971	34	3	1850	3	JAK1	1	65316572	Missense_Mutation	DNP	GC	TCGA-ZP-A9CV-01A-11D-A382-10	33901662	65316572	183934049	3	50632										
ELTD1	64123	hgsc.bcm.edu	37	chr1	79387445	79387445	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	ggtgagtaattccaaaatgcAcatagactcctatacctatc	6	10	0	2			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr1:79387445A>G	ENST00000370742.3	-	9	1173	c.1110T>C	c.(1108-1110)tgT>tgC	p.C370C		NM_022159.3	NP_071442.2	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain containing 1	370	GPS. {ECO:0000255|PROSITE- ProRule:PRU00098}.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(45)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	69				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)		TCCAAAATGCACATAGACTCC	0.378																																					p.C370C		Atlas-SNP	.											.	ELTD1	143	.	0			c.T1110C						.						116	109	112					1																	79387445		1942	4135	6077	SO:0001819	synonymous_variant	64123	exon9			AAATGCACATAGA	AF192403	CCDS41352.1	1p33-p32	2014-08-08			ENSG00000162618	ENSG00000162618		"-", "GPCR / Class B : Orphans"	20822	protein-coding gene	gene with protein product						11050079	Standard	NM_022159		Approved	ETL	uc001diq.4	Q9HBW9	OTTHUMG00000009738	ENST00000370742.3:c.1110T>C	chr1.hg19:g.79387445A>G		246.0	0.0		247.0	88.0	NM_022159	B1AR71|Q5KU34	Silent	SNP	ENST00000370742.3	hg19	CCDS41352.1																																																																																			.	.		0.378	ELTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026859.1	NM_022159		G	79387445	A	G	79387445	2	3	363	1	0	0	0	0	0	0	0	1	5086	157	6	2		2	ELTD1	1	79387445	Silent	SNP	A	TCGA-ZP-A9CV-01A-11D-A382-10	14070873	79387445	169863176	4	50633										
PDZK1	5174	hgsc.bcm.edu	37	chr1	145748530	145748530	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	aaacttggacccagccccggCtctgctatctcgtgaaggaa	10	13	2	1			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr1:145748530C>G	ENST00000344770.2	+	3	476	c.403C>G	c.(403-405)Ctc>Gtc	p.L135V	PDZK1_ENST00000451928.2_Missense_Mutation_p.L135V|PDZK1_ENST00000417171.1_Missense_Mutation_p.L135V	NM_002614.4	NP_002605.2	Q5T2W1	NHRF3_HUMAN	PDZ domain containing 1	135	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				carnitine transport (GO:0015879)|cell proliferation (GO:0008283)|drug transport (GO:0015893)|establishment of protein localization to plasma membrane (GO:0090002)|positive regulation of ion transmembrane transport (GO:0034767)|positive regulation of protein targeting to membrane (GO:0090314)|regulation of anion transport (GO:0044070)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|transporter activity (GO:0005215)			NS(1)|endometrium(1)|large_intestine(1)|lung(3)|pancreas(1)	7	all_hematologic(18;0.00473)|Acute lymphoblastic leukemia(18;0.0786)		KIRC - Kidney renal clear cell carcinoma(6;0.0764)|Kidney(552;0.118)|Colorectal(543;0.229)			CCAGCCCCGGCTCTGCTATCT	0.517																																					p.L135V		Atlas-SNP	.											.	PDZK1	15	.	0			c.C403G						.						63	68	66					1																	145748530		2203	4300	6503	SO:0001583	missense	5174	exon4			CCCCGGCTCTGCT	AF012281	CCDS72859.1, CCDS72860.1	1q21	2009-08-21			ENSG00000174827	ENSG00000174827			8821	protein-coding gene	gene with protein product		603831				9461128	Standard	NM_002614		Approved	PDZD1, NHERF3	uc001eoo.2	Q5T2W1	OTTHUMG00000013735	ENST00000344770.2:c.403C>G	chr1.hg19:g.145748530C>G	ENSP00000342143:p.Leu135Val	359.0	0.0		522.0	212.0	NM_002614	B4DPB9|E7EU02|O60450|Q5T5P6|Q9BQ41	Missense_Mutation	SNP	ENST00000344770.2	hg19	CCDS924.1	.	.	.	.	.	.	.	.	.	.	C	13.86	2.362039	0.41902	.	.	ENSG00000174827	ENST00000443667;ENST00000417171;ENST00000451928;ENST00000344770	T;T;T;T	0.33654	1.4;1.58;1.53;1.58	5.84	2.97	0.34412	PDZ/DHR/GLGF (2);	0.065664	0.64402	D	0.000014	T	0.34832	0.0911	M	0.65677	2.01	0.25018	N	0.991357	B;D	0.71674	0.017;0.998	B;D	0.71184	0.013;0.972	T	0.14727	-1.0462	10	0.19147	T	0.46	-2.7934	9.7601	0.40526	0.0:0.7956:0.0:0.2044	.	135;135	E7EU02;Q5T2W1	.;NHRF3_HUMAN	V	135	ENSP00000409291:L135V;ENSP00000394485:L135V;ENSP00000403422:L135V;ENSP00000342143:L135V	ENSP00000342143:L135V	L	+	1	0	PDZK1	144459887	1.000000	0.71417	0.912000	0.35992	0.128000	0.20619	1.314000	0.33597	0.818000	0.34468	0.591000	0.81541	CTC	.	.		0.517	PDZK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038502.2	NM_002614		G	145748530	C	G	145748530	3	3	363	1	0	0	0	0	1	0	0	0	11716	797	28	4	409	4	PDZK1	1	145748530	Missense_Mutation	SNP	C	TCGA-ZP-A9CV-01A-11D-A382-10	66361085	145748530	103502091	5	50634										
DCST2	127579	hgsc.bcm.edu	37	chr1	155003072	155003072	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	gagaagtggtgggtggctgtCatgttgaactcaaactcctg	14	7	2	2			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr1:155003072C>T	ENST00000368424.3	-	6	913	c.855G>A	c.(853-855)atG>atA	p.M285I	DCST2_ENST00000295536.5_Missense_Mutation_p.M285I	NM_144622.2	NP_653223.2	Q5T1A1	DCST2_HUMAN	DC-STAMP domain containing 2	285						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(13)|ovary(3)|prostate(1)|skin(1)	38	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			GGGTGGCTGTCATGTTGAACT	0.592																																					p.M285I		Atlas-SNP	.											.	DCST2	80	.	0			c.G855A						.						80	56	65					1																	155003072		2203	4300	6503	SO:0001583	missense	127579	exon6			GGCTGTCATGTTG	AK057496	CCDS1082.2	1q22	2008-02-05		2005-08-09	ENSG00000163354	ENSG00000163354			26562	protein-coding gene	gene with protein product							Standard	NM_144622		Approved	FLJ32934	uc001fgm.3	Q5T1A1	OTTHUMG00000037371	ENST00000368424.3:c.855G>A	chr1.hg19:g.155003072C>T	ENSP00000357409:p.Met285Ile	260.0	0.0		404.0	67.0	NM_144622	Q2M2R2|Q8N810|Q96M03	Missense_Mutation	SNP	ENST00000368424.3	hg19	CCDS1082.2	.	.	.	.	.	.	.	.	.	.	C	3.637	-0.074336	0.07184	.	.	ENSG00000163354	ENST00000368424;ENST00000295536	T;T	0.18502	2.21;2.26	5.08	1.93	0.25924	.	0.634759	0.14777	N	0.299009	T	0.01940	0.0061	N	0.12182	0.205	0.24817	N	0.992607	B	0.02656	0.0	B	0.01281	0.0	T	0.46898	-0.9158	10	0.06099	T	0.92	-8.5874	8.6799	0.34203	0.0:0.6319:0.2842:0.0839	.	285	Q5T1A1	DCST2_HUMAN	I	285	ENSP00000357409:M285I;ENSP00000295536:M285I	ENSP00000295536:M285I	M	-	3	0	DCST2	153269696	0.977000	0.34250	0.974000	0.42286	0.983000	0.72400	0.029000	0.13666	0.636000	0.30508	0.655000	0.94253	ATG	.	.		0.592	DCST2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090953.3	NM_144622		T	155003072	C	T	155003072	3	4	363	1	0	0	0	0	1	0	0	0	4305	826	29	3	1506	3	DCST2	1	155003072	Missense_Mutation	SNP	C	TCGA-ZP-A9CV-01A-11D-A382-10	9254542	155003072	94247549	6	50635										
OR6K6	128371	hgsc.bcm.edu	37	chr1	158725375	158725375	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	agtgattctgggaatgcactCagctgaaggtcatcacaagg	12	8	4	2			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr1:158725375C>T	ENST00000368144.2	+	1	866	c.770C>T	c.(769-771)tCa>tTa	p.S257L		NM_001005184.1	NP_001005184.1	Q8NGW6	OR6K6_HUMAN	olfactory receptor, family 6, subfamily K, member 6	257						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(5)|lung(17)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_hematologic(112;0.0378)					GGAATGCACTCAGCTGAAGGT	0.463																																					p.S257L		Atlas-SNP	.											.	OR6K6	81	.	0			c.C770T						.						250	203	219					1																	158725375		2203	4300	6503	SO:0001583	missense	128371	exon1			TGCACTCAGCTGA	BK004198	CCDS30904.1	1q23.1	2012-08-09			ENSG00000180433	ENSG00000180433		"GPCR / Class A : Olfactory receptors"	15033	protein-coding gene	gene with protein product							Standard	NM_001005184		Approved		uc001fsw.1	Q8NGW6	OTTHUMG00000022772	ENST00000368144.2:c.770C>T	chr1.hg19:g.158725375C>T	ENSP00000357126:p.Ser257Leu	155.0	0.0		270.0	44.0	NM_001005184	B9EIM8|Q5VUU9|Q6IFR4	Missense_Mutation	SNP	ENST00000368144.2	hg19	CCDS30904.1	.	.	.	.	.	.	.	.	.	.	C	17.23	3.337308	0.60963	.	.	ENSG00000180433	ENST00000368144	T	0.00330	8.08	5.48	5.48	0.80851	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37530	N	0.002053	T	0.00875	0.0029	H	0.94620	3.56	0.45806	D	0.998687	D	0.89917	1.0	D	0.97110	1.0	T	0.55373	-0.8151	10	0.87932	D	0	-8.391	18.27	0.90065	0.0:1.0:0.0:0.0	.	257	Q8NGW6	OR6K6_HUMAN	L	257	ENSP00000357126:S257L	ENSP00000357126:S257L	S	+	2	0	OR6K6	156991999	0.006000	0.16342	0.883000	0.34634	0.043000	0.13939	2.164000	0.42387	2.848000	0.98002	0.655000	0.94253	TCA	.	.		0.463	OR6K6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059065.2	NM_001005184		T	158725375	C	T	158725375	3	4	363	1	0	0	0	0	1	0	0	0	11213	838	29	3	772	3	OR6K6	1	158725375	Missense_Mutation	SNP	C	TCGA-ZP-A9CV-01A-11D-A382-10	3722303	158725375	90525246	7	50636										
SERTAD4	56256	hgsc.bcm.edu	37	chr1	210414919	210414919	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	gtagaccatctcaatttttgAggaacgagcccacatccttt	7	11	1	2			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr1:210414919A>C	ENST00000367012.3	+	4	538	c.308A>C	c.(307-309)gAg>gCg	p.E103A	SERTAD4_ENST00000490620.1_3'UTR	NM_019605.3	NP_062551.1	Q9NUC0	SRTD4_HUMAN	SERTA domain containing 4	103	SERTA. {ECO:0000255|PROSITE- ProRule:PRU00396}.					nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(81;0.0237)|all cancers(67;0.127)		TCAATTTTTGAGGAACGAGCC	0.328																																					p.E103A		Atlas-SNP	.											.	SERTAD4	53	.	0			c.A308C						.						56	59	58					1																	210414919		2203	4300	6503	SO:0001583	missense	56256	exon4			TTTTTGAGGAACG	BC012083	CCDS1494.1	1q32.1-q41	2008-02-05			ENSG00000082497	ENSG00000082497			25236	protein-coding gene	gene with protein product						12477932	Standard	NM_019605		Approved	DJ667H12.2	uc001hhy.3	Q9NUC0	OTTHUMG00000036391	ENST00000367012.3:c.308A>C	chr1.hg19:g.210414919A>C	ENSP00000355979:p.Glu103Ala	126.0	0.0		187.0	61.0	NM_019605	B2RD32	Missense_Mutation	SNP	ENST00000367012.3	hg19	CCDS1494.1	.	.	.	.	.	.	.	.	.	.	A	16.55	3.155832	0.57259	.	.	ENSG00000082497	ENST00000367012	.	.	.	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.76190	0.3953	L	0.58101	1.795	0.47584	D	0.99946	D	0.63880	0.993	D	0.74674	0.984	T	0.78635	-0.2127	9	0.87932	D	0	-11.7237	15.9023	0.79387	1.0:0.0:0.0:0.0	.	103	Q9NUC0	SRTD4_HUMAN	A	103	.	ENSP00000355979:E103A	E	+	2	0	SERTAD4	208481542	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.452000	0.80683	2.153000	0.67306	0.533000	0.62120	GAG	.	.		0.328	SERTAD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088577.1	NM_019605		C	210414919	A	C	210414919	3	2	363	1	0	0	0	0	1	0	0	0	14138	304	11	5	318	5	SERTAD4	1	210414919	Missense_Mutation	SNP	A	TCGA-ZP-A9CV-01A-11D-A382-10	51689544	210414919	38835702	8	50637										
TTC13	79573	hgsc.bcm.edu	37	chr1	231048481	231048481	+	Frame_Shift_Del	DEL	A	A	-													0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	cttccgtggtttgagtttccAcagaaaataatatattgcca							TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr1:231048481delA	ENST00000366661.4	-	19	2124	c.2117delT	c.(2116-2118)gtgfs	p.V706fs	TTC13_ENST00000366662.4_Frame_Shift_Del_p.V652fs|TTC13_ENST00000414259.1_Frame_Shift_Del_p.V653fs	NM_024525.4	NP_078801.3	Q8NBP0	TTC13_HUMAN	tetratricopeptide repeat domain 13	706										central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	39	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)		COAD - Colon adenocarcinoma(196;0.243)		TTGAGTTTCCACAGAAAATAA	0.294																																					p.V706fs		Atlas-INDEL	.											.	TTC13	74	.	0			c.2118delG						.						115	118	117					1																	231048481		2202	4300	6502	SO:0001589	frameshift_variant	79573	exon19			.		CCDS1588.1, CCDS44332.1, CCDS44332.2	1q42.2	2013-01-10			ENSG00000143643	ENSG00000143643		"Tetratricopeptide (TTC) repeat domain containing"	26204	protein-coding gene	gene with protein product							Standard	NM_024525		Approved	FLJ22584	uc001huf.4	Q8NBP0	OTTHUMG00000037788	ENST00000366661.4:c.2117delT	chr1.hg19:g.231048481delA	ENSP00000355621:p.Val706fs	83.0	0.0		110.0	47.0	NM_024525	B1AQI1|B1AQI2|Q8IVP8|Q8NBI0|Q8ND20	Frame_Shift_Del	DEL	ENST00000366661.4	hg19	CCDS1588.1																																																																																			.	.		0.294	TTC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092229.2	NM_024525		-	231048481	A	-	231048481	7	5	363	1	0	1	0	1	0	0	0	0	16695	159	6	0	485	0	TTC13	1	231048481	Frame_Shift_Del	DEL	A	TCGA-ZP-A9CV-01A-11D-A382-10	20633562	231048481	18202140	9	50638										
ZNF670	93474	hgsc.bcm.edu	37	chr1	247201279	247201279	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	ccagtatgagttctttcatgTtcacgaagataacttgaata	7	7	3	3			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr1:247201279T>C	ENST00000366503.2	-	4	800	c.642A>G	c.(640-642)gaA>gaG	p.E214E		NM_001204220.1|NM_033213.4	NP_001191149.1|NP_149990.1	Q9BS34	ZN670_HUMAN	zinc finger protein 670	214					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	17	all_cancers(71;4.01e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00427)			TTCTTTCATGTTCACGAAGAT	0.348																																					p.E214E		Atlas-SNP	.											.	ZNF670	52	.	0			c.A642G						.						68	69	69					1																	247201279		2203	4300	6503	SO:0001819	synonymous_variant	93474	exon4			TTCATGTTCACGA		CCDS31087.1	1q44	2013-01-08			ENSG00000135747	ENSG00000135747		"Zinc fingers, C2H2-type", "-"	28167	protein-coding gene	gene with protein product						12477932	Standard	NM_033213		Approved	MGC12466	uc001icd.2	Q9BS34	OTTHUMG00000040868	ENST00000366503.2:c.642A>G	chr1.hg19:g.247201279T>C		86.0	0.0		161.0	27.0	NM_033213		Silent	SNP	ENST00000366503.2	hg19	CCDS31087.1																																																																																			.	.		0.348	ZNF670-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098183.3	NM_033213		C	247201279	T	C	247201279	2	2	363	1	0	0	0	0	0	0	0	1	18092	1722	60	2		2	ZNF670	1	247201279	Silent	SNP	T	TCGA-ZP-A9CV-01A-11D-A382-10	16152798	247201279	2049342	10	50639										
RTN4	57142	hgsc.bcm.edu	37	chr2	55253876	55253876	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	gctcctgaacgatcctttatAccttctggcgtactggggaa	10	11	1	1			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr2:55253876A>G	ENST00000337526.6	-	3	1602	c.1359T>C	c.(1357-1359)ggT>ggC	p.G453G	RTN4_ENST00000394611.2_Silent_p.G247G|RTN4_ENST00000317610.7_Intron|RTN4_ENST00000402434.2_Intron|RTN4_ENST00000357376.3_Silent_p.G247G|RTN4_ENST00000357732.4_Intron|RTN4_ENST00000405240.1_Silent_p.G247G|RTN4_ENST00000404909.1_Silent_p.G247G|RTN4_ENST00000354474.6_Silent_p.G221G	NM_020532.4	NP_065393.1	Q9NQC3	RTN4_HUMAN	reticulon 4	453					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonal fasciculation (GO:0007413)|cardiac epithelial to mesenchymal transition (GO:0060317)|cerebral cortex radial glia guided migration (GO:0021801)|endoplasmic reticulum tubular network organization (GO:0071786)|negative regulation of axon extension (GO:0030517)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell growth (GO:0030308)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of apoptotic process (GO:0042981)|regulation of axonogenesis (GO:0050770)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of cell migration (GO:0030334)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of endoplasmic reticulum membrane (GO:0030176)|intracellular (GO:0005622)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(1)|skin(1)|stomach(1)	36						GATCCTTTATACCTTCTGGCG	0.393																																					p.G453G		Atlas-SNP	.											.	RTN4	189	.	0			c.T1359C						.						204	193	197					2																	55253876		2202	4300	6502	SO:0001819	synonymous_variant	57142	exon3			CTTTATACCTTCT	AF087901	CCDS1851.1, CCDS1852.1, CCDS42683.1, CCDS42684.1, CCDS42685.1	2p14-p13	2008-05-23			ENSG00000115310	ENSG00000115310			14085	protein-coding gene	gene with protein product		604475				10667797, 10773680	Standard	NM_020532		Approved	NSP-CL, KIAA0886, NOGO, ASY	uc002rye.3	Q9NQC3	OTTHUMG00000129337	ENST00000337526.6:c.1359T>C	chr2.hg19:g.55253876A>G		80.0	0.0		82.0	27.0	NM_020532	O94962|Q7L7Q5|Q7L7Q6|Q7L7Q8|Q8IUA4|Q96B16|Q9BXG5|Q9H212|Q9H3I3|Q9UQ42|Q9Y293|Q9Y2Y7|Q9Y5U6	Silent	SNP	ENST00000337526.6	hg19	CCDS42684.1																																																																																			.	.		0.393	RTN4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251484.1			G	55253876	A	G	55253876	2	3	363	1	0	0	0	0	0	0	0	1	13743	378	14	2		2	RTN4	2	55253876	Silent	SNP	A	TCGA-ZP-A9CV-01A-11D-A382-10		55253876	187945497	11	50640										
CCDC85A	114800	hgsc.bcm.edu	37	chr2	56611449	56611449	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	caggttcgtgtcctggaattAggcaacatttgtcaggaaac	11	8	1	0			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr2:56611449A>C	ENST00000407595.2	+	6	2123	c.1621A>C	c.(1621-1623)Agg>Cgg	p.R541R	RP11-482H16.1_ENST00000607540.1_RNA	NM_001080433.1	NP_001073902.1	Q96PX6	CC85A_HUMAN	coiled-coil domain containing 85A	541										breast(6)|cervix(2)|endometrium(5)|kidney(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)	38			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			TCCTGGAATTAGGCAACATTT	0.413																																					p.R541R		Atlas-SNP	.											.	CCDC85A	70	.	0			c.A1621C						.						106	104	105					2																	56611449		1951	4140	6091	SO:0001819	synonymous_variant	114800	exon6			GGAATTAGGCAAC	AB067499	CCDS46290.1	2p16.1	2006-03-29			ENSG00000055813	ENSG00000055813			29400	protein-coding gene	gene with protein product						11572484	Standard	NM_001080433		Approved	KIAA1912	uc002rzn.3	Q96PX6	OTTHUMG00000152033	ENST00000407595.2:c.1621A>C	chr2.hg19:g.56611449A>C		86.0	0.0		87.0	30.0	NM_001080433		Silent	SNP	ENST00000407595.2	hg19	CCDS46290.1																																																																																			.	.		0.413	CCDC85A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324993.1			C	56611449	A	C	56611449	2	2	363	1	0	0	0	0	0	0	0	1	2861	411	15	5		5	CCDC85A	2	56611449	Silent	SNP	A	TCGA-ZP-A9CV-01A-11D-A382-10	1357573	56611449	186587924	12	50641										
ADD2	119	hgsc.bcm.edu	37	chr2	70910804	70910804	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	ataggcccaaaggtgctcccGgcccactgcacggagcccac	11	17	0	0	rs376528363		TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr2:70910804G>A	ENST00000264436.4	-	10	1488	c.1044C>T	c.(1042-1044)gcC>gcT	p.A348A	ADD2_ENST00000430656.1_Silent_p.A364A|ADD2_ENST00000355733.3_Silent_p.A348A|ADD2_ENST00000407644.2_Silent_p.A348A|ADD2_ENST00000413157.2_Silent_p.A348A	NM_001617.3	NP_001608.1	P35612	ADDB_HUMAN	adducin 2 (beta)	348					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|barbed-end actin filament capping (GO:0051016)|hemopoiesis (GO:0030097)|positive regulation of protein binding (GO:0032092)|protein complex assembly (GO:0006461)	cytoplasmic membrane-bounded vesicle (GO:0016023)|F-actin capping protein complex (GO:0008290)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|spectrin binding (GO:0030507)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(11)|lung(13)|ovary(3)|pancreas(1)|skin(2)	36						AGGTGCTCCCGGCCCACTGCA	0.627																																					p.A364A		Atlas-SNP	.											ADD2_ENST00000430656,NS,carcinoma,0,3	ADD2	261	.	0			c.C1092T						.	G	,,,,	1,4405	2.1+/-5.4	0,1,2202	43	41	42		1044,1092,1044,1044,1044	-9.7	0	2		42	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ADD2	NM_001185054.1,NM_001185055.1,NM_001617.3,NM_017482.3,NM_017488.3	,,,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,,,	348/727,364/576,348/727,348/560,348/644	70910804	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	119	exon9			GCTCCCGGCCCAC	X58199	CCDS1906.1, CCDS1909.1, CCDS46318.1, CCDS54365.1	2p13.3	2008-02-05			ENSG00000075340	ENSG00000075340			244	protein-coding gene	gene with protein product		102681				1840603	Standard	NM_001617		Approved	ADDB	uc021vjc.1	P35612	OTTHUMG00000129710	ENST00000264436.4:c.1044C>T	chr2.hg19:g.70910804G>A		231.0	0.0		210.0	55.0	NM_001185055	A8K4P2|B4DM17|D6W5G7|D6W5G8|Q13482|Q16412|Q59G82|Q5U5P4|Q6P0P2|Q6PGQ4|Q7Z688|Q7Z689|Q7Z690|Q7Z691	Silent	SNP	ENST00000264436.4	hg19	CCDS1906.1																																																																																			.	.		0.627	ADD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251918.4	NM_001617		A	70910804	G	A	70910804	2	1	363	1	0	0	0	0	0	0	0	1	305	1103	39	1		1	ADD2	2	70910804	Silent	SNP	G	TCGA-ZP-A9CV-01A-11D-A382-10	14299355	70910804	172288569	13	50642										
LASS6	253782	hgsc.bcm.edu	37	chr2	169626068	169626068	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	agtctagctcagatgaggagGactcagaacctccgggaaag	13	9	3	3			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr2:169626068G>T	ENST00000305747.6	+	10	1638	c.1051G>T	c.(1051-1053)Gac>Tac	p.D351Y	CERS6_ENST00000392687.4_Missense_Mutation_p.D359Y|CERS6-AS1_ENST00000425636.2_RNA	NM_203463.2	NP_982288.1	Q6ZMG9	CERS6_HUMAN	ceramide synthase 6	351					ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										AGATGAGGAGGACTCAGAACC	0.507																																					p.D359Y		Atlas-SNP	.											.	.	.	.	0			c.G1075T						.						112	107	109					2																	169626068		2203	4300	6503	SO:0001583	missense	253782	exon11			GAGGAGGACTCAG	BX393696	CCDS2228.1, CCDS58734.1	2q31	2011-07-11	2011-07-08	2011-07-08	ENSG00000172292	ENSG00000172292		"Homeoboxes / CERS class"	23826	protein-coding gene	gene with protein product		615336	"LAG1 longevity assurance homolog 6 (S. cerevisiae)", "LAG1 homolog, ceramide synthase 6"	LASS6			Standard	NM_203463		Approved		uc002uec.2	Q6ZMG9	OTTHUMG00000132183	ENST00000305747.6:c.1051G>T	chr2.hg19:g.169626068G>T	ENSP00000306579:p.Asp351Tyr	167.0	0.0		139.0	39.0	NM_001256126	Q32M63|Q8N617	Missense_Mutation	SNP	ENST00000305747.6	hg19	CCDS2228.1	.	.	.	.	.	.	.	.	.	.	G	18.54	3.645239	0.67358	.	.	ENSG00000172292	ENST00000305747;ENST00000392687	T;T	0.13089	2.79;2.62	5.97	5.97	0.96955	.	0.261937	0.48767	D	0.000162	T	0.31040	0.0784	M	0.89601	3.045	0.58432	D	0.999998	P;P	0.44090	0.826;0.826	P;P	0.45037	0.467;0.467	T	0.15665	-1.0429	10	0.59425	D	0.04	-11.6636	14.5506	0.68065	0.0697:0.0:0.9303:0.0	.	359;351	Q32M63;Q6ZMG9	.;CERS6_HUMAN	Y	351;359	ENSP00000306579:D351Y;ENSP00000376453:D359Y	ENSP00000306579:D351Y	D	+	1	0	CERS6	169334314	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	7.348000	0.79366	2.831000	0.97527	0.655000	0.94253	GAC	.	.		0.507	CERS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255235.2	NM_203463		T	169626068	G	T	169626068	3	4	363	1	0	0	0	0	1	0	0	0	8652	1174	41	3	1089	3	LASS6	2	169626068	Missense_Mutation	SNP	G	TCGA-ZP-A9CV-01A-11D-A382-10	98715264	169626068	73573305	14	50643										
GORASP2	26003	hgsc.bcm.edu	37	chr2	171822386	171822386	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	ccgagttcctcccgtcattcCccttggttccagagagctct	8	16	2	1			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr2:171822386C>G	ENST00000234160.4	+	10	1920	c.1105C>G	c.(1105-1107)Ccc>Gcc	p.P369A	GORASP2_ENST00000452526.2_Missense_Mutation_p.P381A|GORASP2_ENST00000493692.1_3'UTR	NM_001201428.1|NM_015530.4	NP_001188357.1|NP_056345.3	Q9H8Y8	GORS2_HUMAN	golgi reassembly stacking protein 2, 55kDa	369	Pro-rich.				mitotic cell cycle (GO:0000278)|organelle organization (GO:0006996)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(3)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	14						CCCGTCATTCCCCTTGGTTCC	0.597																																					p.P369A		Atlas-SNP	.											.	GORASP2	40	.	0			c.C1105G						.						154	120	132					2																	171822386		2203	4300	6503	SO:0001583	missense	26003	exon10			TCATTCCCCTTGG		CCDS33325.1	2q31.1	2012-09-20	2002-08-29		ENSG00000115806	ENSG00000115806			17500	protein-coding gene	gene with protein product		608693	"golgi reassembly stacking protein 2, 55 kDa"			10487747	Standard	NM_015530		Approved	GRASP55, GRS2, GOLPH6	uc002ugj.3	Q9H8Y8	OTTHUMG00000154072	ENST00000234160.4:c.1105C>G	chr2.hg19:g.171822386C>G	ENSP00000234160:p.Pro369Ala	68.0	0.0		80.0	33.0	NM_015530	B4DKT0|Q53TE3|Q96I74|Q96K84|Q9H946|Q9UFW4	Missense_Mutation	SNP	ENST00000234160.4	hg19	CCDS33325.1	.	.	.	.	.	.	.	.	.	.	C	19.73	3.882262	0.72294	.	.	ENSG00000115806	ENST00000234160;ENST00000452526	T;T	0.59364	0.38;0.27	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.75882	0.3910	M	0.67953	2.075	0.50813	D	0.99989	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.80764	0.994;0.994;0.994	T	0.73697	-0.3901	10	0.45353	T	0.12	-13.8958	20.1649	0.98147	0.0:1.0:0.0:0.0	.	325;381;369	B4DNR1;B4DKT0;Q9H8Y8	.;.;GORS2_HUMAN	A	369;381	ENSP00000234160:P369A;ENSP00000410208:P381A	ENSP00000234160:P369A	P	+	1	0	GORASP2	171530632	1.000000	0.71417	1.000000	0.80357	0.815000	0.46073	5.114000	0.64648	2.753000	0.94483	0.655000	0.94253	CCC	.	.		0.597	GORASP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333719.2			G	171822386	C	G	171822386	3	3	363	1	0	0	0	0	1	0	0	0	6584	623	22	4	1143	4	GORASP2	2	171822386	Missense_Mutation	SNP	C	TCGA-ZP-A9CV-01A-11D-A382-10	2196318	171822386	71376987	15	50644										
PASK	23178	hgsc.bcm.edu	37	chr2	242054738	242054738	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	gtgctccaccctggatagaaTtgcgatctctaaagtaactt	8	10	1	1			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr2:242054738T>C	ENST00000405260.1	-	13	3861	c.3163A>G	c.(3163-3165)Att>Gtt	p.I1055V	PASK_ENST00000544142.1_Missense_Mutation_p.I869V|PASK_ENST00000234040.4_Missense_Mutation_p.I1055V|PASK_ENST00000475666.1_5'Flank|PASK_ENST00000358649.4_Missense_Mutation_p.I1055V|PASK_ENST00000403638.3_Missense_Mutation_p.I1055V|PASK_ENST00000539818.1_Missense_Mutation_p.I839V	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	1055	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of glycogen biosynthetic process (GO:0045719)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of energy homeostasis (GO:2000505)|regulation of glucagon secretion (GO:0070092)|regulation of respiratory gaseous exchange (GO:0043576)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(20)|ovary(4)|prostate(4)|skin(1)|stomach(1)|urinary_tract(2)	53		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		CTGGATAGAATTGCGATCTCT	0.428																																					p.I1055V		Atlas-SNP	.											.	PASK	230	.	0			c.A3163G						.						175	159	164					2																	242054738		2203	4300	6503	SO:0001583	missense	23178	exon13			ATAGAATTGCGAT	U79240	CCDS2545.1, CCDS58758.1, CCDS58759.1	2q37.3	2008-05-23			ENSG00000115687	ENSG00000115687			17270	protein-coding gene	gene with protein product		607505				11688972, 11459942, 15148392	Standard	NM_001252119		Approved	PASKIN, KIAA0135, STK37	uc010fzl.2	Q96RG2	OTTHUMG00000133392	ENST00000405260.1:c.3163A>G	chr2.hg19:g.242054738T>C	ENSP00000384016:p.Ile1055Val	141.0	0.0		122.0	32.0	NM_015148	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Missense_Mutation	SNP	ENST00000405260.1	hg19	CCDS2545.1	.	.	.	.	.	.	.	.	.	.	T	18.39	3.613407	0.66672	.	.	ENSG00000115687	ENST00000234040;ENST00000544142;ENST00000405260;ENST00000358649;ENST00000539818;ENST00000403638	T;T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18;-0.18	5.39	5.39	0.77823	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.53938	D	0.000058	T	0.69178	0.3082	L	0.31526	0.94	0.48087	D	0.999586	B;B;B;P;B	0.52842	0.227;0.334;0.19;0.956;0.227	P;B;B;D;P	0.66716	0.5;0.324;0.367;0.946;0.5	T	0.72947	-0.4137	10	0.72032	D	0.01	.	15.3955	0.74790	0.0:0.0:0.0:1.0	.	1020;869;1055;1055;1055	B7Z7R6;F5GYW7;Q96RG2-2;G5E9F1;Q96RG2	.;.;.;.;PASK_HUMAN	V	1055;869;1055;1055;839;1055	ENSP00000234040:I1055V;ENSP00000441374:I869V;ENSP00000384016:I1055V;ENSP00000351475:I1055V;ENSP00000443083:I839V;ENSP00000384438:I1055V	ENSP00000234040:I1055V	I	-	1	0	PASK	241703411	1.000000	0.71417	0.174000	0.22961	0.536000	0.34869	4.716000	0.61916	2.040000	0.60383	0.460000	0.39030	ATT	.	.		0.428	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148		C	242054738	T	C	242054738	3	2	363	1	0	0	0	0	1	0	0	0	11481	1493	52	2	832	2	PASK	2	242054738	Missense_Mutation	SNP	T	TCGA-ZP-A9CV-01A-11D-A382-10	70232352	242054738	1144635	16	50645										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266137	41266137	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	tgccactaccacagctccttCtctgagtggtaaaggcaatc	8	13	1	1	rs121913409		TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr3:41266137C>T	ENST00000349496.5	+	3	414	c.134C>T	c.(133-135)tCt>tTt	p.S45F	CTNNB1_ENST00000405570.1_Missense_Mutation_p.S45F|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S45F|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S38F|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S45F	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	45			Missing (in colorectal cancer). {ECO:0000269|PubMed:9065402}.|S -> F (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> P (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S45F(384)|p.S45del(53)|p.A5_A80del(53)|p.S45C(19)|p.S45Y(17)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.S45_S47>C(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.S45_G48del(1)|p.Q28_Q61del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.S45_L46del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.P44_N51del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.S45fs*2(1)|p.T40_L46del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.S45E(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.T42_K49>Q(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		ACAGCTCCTTCTCTGAGTGGT	0.498	S45F(HCC15_LUNG)|S45F(LS180_LARGE_INTESTINE)	15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.S45F	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,carcinoma,+1,2	CTNNB1	4904	.	601	Substitution - Missense(421)|Deletion - In frame(152)|Complex - deletion inframe(20)|Unknown(7)|Deletion - Frameshift(1)	soft_tissue(233)|liver(141)|large_intestine(85)|kidney(74)|endometrium(16)|skin(11)|adrenal_gland(9)|stomach(7)|biliary_tract(5)|ovary(4)|lung(3)|central_nervous_system(2)|cervix(2)|small_intestine(2)|haematopoietic_and_lymphoid_tissue(2)|urinary_tract(1)|pituitary(1)|prostate(1)|bone(1)|pancreas(1)	c.C134T						.						84	74	77					3																	41266137		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	CTCCTTCTCTGAG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.134C>T	chr3.hg19:g.41266137C>T	ENSP00000344456:p.Ser45Phe	161.0	0.0		114.0	35.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.569754	0.86439	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.68165	0.2971	M	0.65677	2.01	0.80722	D	1	D	0.67145	0.996	D	0.64687	0.928	T	0.68895	-0.5288	10	0.87932	D	0	-13.6823	20.2983	0.98569	0.0:1.0:0.0:0.0	.	45	P35222	CTNB1_HUMAN	F	38;45;45;45;45;38;45;45;45	ENSP00000400508:S38F;ENSP00000385604:S45F;ENSP00000412219:S45F;ENSP00000379486:S45F;ENSP00000344456:S45F;ENSP00000411226:S38F;ENSP00000379488:S45F;ENSP00000409302:S45F;ENSP00000401599:S45F	ENSP00000344456:S45F	S	+	2	0	CTNNB1	41241141	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.802000	0.96397	0.655000	0.94253	TCT	.	.		0.498	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41266137	C	T	41266137	3	4	363	1	0	0	0	0	1	0	0	0	4018	913	32	3	140	3	CTNNB1	3	41266137	Missense_Mutation	SNP	C	TCGA-ZP-A9CV-01A-11D-A382-10		41266137	156756293	17	50646										
TRAK1	22906	hgsc.bcm.edu	37	chr3	42264841	42264841	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	cctgagggaagtgagagaaaAgaacgtccgcagcagcgaga	15	8	0	5			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr3:42264841A>G	ENST00000327628.5	+	16	2874	c.2474A>G	c.(2473-2475)aAg>aGg	p.K825R	TRAK1_ENST00000396175.1_Missense_Mutation_p.K767R|TRAK1_ENST00000487159.1_3'UTR|RNU4-78P_ENST00000410940.1_RNA	NM_001042646.2	NP_001036111.1	Q9UPV9	TRAK1_HUMAN	trafficking protein, kinesin binding 1	825					endosome to lysosome transport (GO:0008333)|protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	22						GTGAGAGAAAAGAACGTCCGC	0.572																																					p.K825R	GBM(44;195 884 22595 31865 41850)	Atlas-SNP	.											.	TRAK1	188	.	0			c.A2474G						.						47	53	51					3																	42264841		2025	4184	6209	SO:0001583	missense	22906	exon16			GAGAAAAGAACGT		CCDS2695.1, CCDS43072.1, CCDS58826.1, CCDS74922.1	3p22.1	2012-03-05			ENSG00000182606	ENSG00000182606			29947	protein-coding gene	gene with protein product	"OGT(O Glc NAc transferase) interacting protein 106 KDa", "O-linked N-acetylglucosamine transferase interacting protein 106", "milton homolog 1 (Drosophila)"	608112				10470851, 12435728, 16380713, 20230862	Standard	NM_014965		Approved	OIP106, KIAA1042, MILT1	uc003cky.4	Q9UPV9	OTTHUMG00000131795	ENST00000327628.5:c.2474A>G	chr3.hg19:g.42264841A>G	ENSP00000328998:p.Lys825Arg	86.0	0.0		65.0	5.0	NM_001042646	E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	Missense_Mutation	SNP	ENST00000327628.5	hg19	CCDS43072.1	.	.	.	.	.	.	.	.	.	.	A	11.25	1.583426	0.28268	.	.	ENSG00000182606	ENST00000327628;ENST00000396175	T;T	0.42513	0.97;0.97	5.11	2.65	0.31530	Trafficking kinesin-binding protein domain (1);	0.439904	0.23314	N	0.049534	T	0.19087	0.0458	N	0.08118	0	0.80722	D	1	B;B	0.09022	0.002;0.0	B;B	0.10450	0.005;0.001	T	0.05435	-1.0885	10	0.11485	T	0.65	.	8.6073	0.33782	0.8391:0.0:0.1609:0.0	.	767;825	C9JC32;Q9UPV9	.;TRAK1_HUMAN	R	825;767	ENSP00000328998:K825R;ENSP00000379478:K767R	ENSP00000328998:K825R	K	+	2	0	TRAK1	42239845	1.000000	0.71417	0.940000	0.37924	0.984000	0.73092	3.002000	0.49496	0.756000	0.33013	0.482000	0.46254	AAG	.	.		0.572	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343413.1	NM_014965		G	42264841	A	G	42264841	3	3	363	1	0	0	0	0	1	0	0	0	16464	72	3	2	2924	2	TRAK1	3	42264841	Missense_Mutation	SNP	A	TCGA-ZP-A9CV-01A-11D-A382-10	998704	42264841	155757589	18	50647										
KALRN	8997	hgsc.bcm.edu	37	chr3	124201708	124201708	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	atctcttcctacctaattaaGcctgtccaaaggatcaccaa	4	13	2	0			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr3:124201708G>A	ENST00000240874.3	+	28	4396	c.4239G>A	c.(4237-4239)aaG>aaA	p.K1413K	KALRN_ENST00000460856.1_Silent_p.K1404K|KALRN_ENST00000360013.3_Silent_p.K1413K	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1413	DH 1. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						ACCTAATTAAGCCTGTCCAAA	0.537																																					p.K1413K		Atlas-SNP	.											.	KALRN	556	.	0			c.G4239A						.						254	202	219					3																	124201708		2203	4300	6503	SO:0001819	synonymous_variant	8997	exon28			AATTAAGCCTGTC	U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	4814	protein-coding gene	gene with protein product	"serine/threonine kinase with Dbl and pleckstrin homology domains"	604605	"huntingtin-associated protein interacting protein (duo)"	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000240874.3:c.4239G>A	chr3.hg19:g.124201708G>A		152.0	0.0		92.0	38.0	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000240874.3	hg19	CCDS3027.1	.	.	.	.	.	.	.	.	.	.	G	9.327	1.059575	0.19987	.	.	ENSG00000160145	ENST00000354186	.	.	.	5.31	3.52	0.40303	.	.	.	.	.	T	0.57961	0.2089	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52815	-0.8525	4	.	.	.	.	8.0062	0.30325	0.3046:0.0:0.6954:0.0	.	.	.	.	N	1382	.	.	S	+	2	0	KALRN	125684398	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	0.813000	0.27225	0.813000	0.34350	0.655000	0.94253	AGC	.	.		0.537	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947		A	124201708	G	A	124201708	2	1	363	1	0	0	0	0	0	0	0	1	7984	962	34	3		3	KALRN	3	124201708	Silent	SNP	G	TCGA-ZP-A9CV-01A-11D-A382-10	81936867	124201708	73820722	19	50648										
PRR23A	729627	hgsc.bcm.edu	37	chr3	138724705	138724705	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	gaagacttcctgctcaacgaCgacgtcctccctgagagcgc	10	15	1	2			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr3:138724705C>T	ENST00000383163.2	-	1	405	c.406G>A	c.(406-408)Gtc>Atc	p.V136I	MRPS22_ENST00000495075.1_5'UTR	NM_001134659.1	NP_001128131.1	A6NEV1	PR23A_HUMAN	proline rich 23A	136										endometrium(3)|kidney(1)|lung(7)	11						TGCTCAACGACGACGTCCTCC	0.632																																					p.V136I		Atlas-SNP	.											.	PRR23A	35	.	0			c.G406A						.						53	50	51					3																	138724705		692	1591	2283	SO:0001583	missense	729627	exon1			CAACGACGACGTC		CCDS46923.1	3q22.3	2014-06-03				ENSG00000206260			37172	protein-coding gene	gene with protein product							Standard	NM_001134659		Approved		uc011bms.2	A6NEV1		ENST00000383163.2:c.406G>A	chr3.hg19:g.138724705C>T	ENSP00000372649:p.Val136Ile	192.0	0.0		198.0	63.0	NM_001134659		Missense_Mutation	SNP	ENST00000383163.2	hg19	CCDS46923.1	.	.	.	.	.	.	.	.	.	.	C	11.29	1.594299	0.28445	.	.	ENSG00000206260	ENST00000383163	.	.	.	2.92	-1.28	0.09318	.	0.261619	0.20067	N	0.099951	T	0.25717	0.0626	M	0.64997	1.995	0.09310	N	1	P	0.43519	0.809	B	0.36289	0.221	T	0.15867	-1.0422	9	0.56958	D	0.05	.	4.0248	0.09682	0.0:0.369:0.3856:0.2454	.	136	A6NEV1	PR23A_HUMAN	I	136	.	ENSP00000372649:V136I	V	-	1	0	PRR23A	140207395	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.264000	0.08658	-0.294000	0.08973	-1.185000	0.01705	GTC	.	.		0.632	PRR23A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361503.1	NM_001134659		T	138724705	C	T	138724705	3	4	363	1	0	0	0	0	1	0	0	0	12606	536	19	1	398	1	PRR23A	3	138724705	Missense_Mutation	SNP	C	TCGA-ZP-A9CV-01A-11D-A382-10	14522997	138724705	59297725	20	50649										
SEC31A	22872	hgsc.bcm.edu	37	chr4	83778256	83778267	+	In_Frame_Del	DEL	AAAGCCTGAGTA	AAAGCCTGAGTA	-													0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	tctcaaaattgcccgtcagcAaagcctgagtaattaaacca							TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	AAAGCCTGAGTA	AAAGCCTGAGTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr4:83778256_83778267delAAAGCCTGAGTA	ENST00000395310.2	-	16	1901_1912	c.1719_1730delTACTCAGGCTTT	c.(1717-1731)attactcaggctttg>atg	p.573_577ITQAL>M	SEC31A_ENST00000326950.5_In_Frame_Del_p.534_538ITQAL>M|SEC31A_ENST00000355196.2_In_Frame_Del_p.573_577ITQAL>M|SEC31A_ENST00000448323.1_In_Frame_Del_p.573_577ITQAL>M|SEC31A_ENST00000311785.7_In_Frame_Del_p.573_577ITQAL>M|SEC31A_ENST00000508502.1_In_Frame_Del_p.573_577ITQAL>M|SEC31A_ENST00000505984.1_In_Frame_Del_p.534_538ITQAL>M|SEC31A_ENST00000505472.1_In_Frame_Del_p.573_577ITQAL>M|SEC31A_ENST00000513858.1_In_Frame_Del_p.534_538ITQAL>M|SEC31A_ENST00000509142.1_In_Frame_Del_p.573_577ITQAL>M|SEC31A_ENST00000500777.2_In_Frame_Del_p.534_538ITQAL>M|SEC31A_ENST00000264405.5_In_Frame_Del_p.306_310ITQAL>M|SEC31A_ENST00000443462.2_In_Frame_Del_p.568_572ITQAL>M|SEC31A_ENST00000348405.4_In_Frame_Del_p.534_538ITQAL>M|SEC31A_ENST00000432794.1_In_Frame_Del_p.573_577ITQAL>M|SEC31A_ENST00000508479.1_In_Frame_Del_p.573_577ITQAL>M	NM_001077207.2|NM_001077208.2|NM_014933.3	NP_001070675.1|NP_001070676.1|NP_055748.2	O94979	SC31A_HUMAN	SEC31 homolog A (S. cerevisiae)	573					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)|response to calcium ion (GO:0051592)	COPII vesicle coat (GO:0030127)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle (GO:0030134)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|vesicle coat (GO:0030120)	calcium-dependent protein binding (GO:0048306)		SEC31A/ALK(3)|SEC31A/JAK2(4)	breast(1)	1		Hepatocellular(203;0.114)				GCCCGTCAGCAAAGCCTGAGTAATTAAACCAT	0.373																																					p.574_577del		Atlas-INDEL	.											.	SEC31A	227	.	0			c.1720_1731del						.																																			SO:0001651	inframe_deletion	22872	exon16			.	AB018358	CCDS3596.1, CCDS3597.1, CCDS43244.1, CCDS47088.1, CCDS54773.1, CCDS75155.1, CCDS75156.1	4q21.3	2013-01-10	2006-10-05	2006-09-07	ENSG00000138674	ENSG00000138674		"WD repeat domain containing"	17052	protein-coding gene	gene with protein product		610257	"SEC31-like 1 (S. cerevisiae)", "Sec31 homolog A (S. cerevisiae)"	SEC31L1		10048485, 10788476	Standard	NM_001077206		Approved	KIAA0905, ABP125, ABP130	uc003hnh.3	O94979	OTTHUMG00000130297	ENST00000395310.2:c.1719_1730delTACTCAGGCTTT	chr4.hg19:g.83778256_83778267delAAAGCCTGAGTA	ENSP00000378721:p.Ile573_Leu577delinsMet	237.0	0.0		167.0	34.0	NM_001077206	B4DIW6|B7ZKZ7|B7ZL00|H7C2W3|Q17RR5|Q5H9P6|Q5XG74|Q659G7|Q6ZU90|Q7LCX9|Q86TJ0|Q8IZH4|Q9P048|Q9P0A6|Q9UM05|Q9UM06	In_Frame_Del	DEL	ENST00000395310.2	hg19	CCDS3596.1																																																																																			.	.		0.373	SEC31A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252640.1	NM_016211		-	83778267	AAAGCCTGAGTA	-	83778256	7	5	363	1	0	1	0	1	0	0	0	0	14013	131	5	0	1980	0	SEC31A	4	83778256	In_Frame_Del	DEL	AAAGCCTGAGTA	TCGA-ZP-A9CV-01A-11D-A382-10		83778256	107376020	21	50650										
DSPP	1834	hgsc.bcm.edu	37	chr4	88535923	88535925	+	In_Frame_Del	DEL	TAG	TAG	-													0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	aatagcagtgagagcagtgaTagtagtgacagcagtgatag							TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	TAG	TAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr4:88535923_88535925delTAG	ENST00000282478.7	+	4	2142_2144	c.2109_2111delTAG	c.(2107-2112)gatagt>gat	p.S705del	DSPP_ENST00000399271.1_In_Frame_Del_p.S705del|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	705	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			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)		agagcagtgatagtagtgacagc	0.488																																					p.703_704del		Atlas-INDEL	.											.	DSPP	174	.	0			c.2108_2110del						.																																			SO:0001651	inframe_deletion	1834	exon5			.	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2109_2111delTAG	chr4.hg19:g.88535926_88535928delTAG	ENSP00000282478:p.Ser705del	230.0	0.0		198.0	32.0	NM_014208	A8MUI0|O95815	In_Frame_Del	DEL	ENST00000282478.7	hg19	CCDS43248.1																																																																																			.	.		0.488	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		-	88535925	TAG	-	88535923	7	5	363	1	0	1	0	1	0	0	0	0	4784	1403	49	0	2123	0	DSPP	4	88535923	In_Frame_Del	DEL	TAG	TCGA-ZP-A9CV-01A-11D-A382-10	4757667	88535923	102618353	22	50651			1	70		2	2	18	N	TAG_-	6.205246e-05
DSPP	1834	hgsc.bcm.edu	37	chr4	88535940	88535941	+	In_Frame_Ins	INS	-	-	TAG													0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	gatagtagtgacagcagtgaINStagtgacagcagtgatagta							TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr4:88535940_88535941insTAG	ENST00000282478.7	+	4	2159_2160	c.2126_2127insTAG	c.(2125-2130)gatagt>gaTAGtagt	p.710_711insS	DSPP_ENST00000399271.1_In_Frame_Ins_p.710_711insS|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	710	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			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)		gacagcagtgatagtgacagca	0.49																																					p.D709delinsDS		Atlas-INDEL	.											.	DSPP	174	.	0			c.2126_2127insTAG						.																																			SO:0001652	inframe_insertion	1834	exon5			.	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2127_2129dupTAG	chr4.hg19:g.88535941_88535943dupTAG	ENSP00000282478:p.Ser712_Ser713dup	231.0	0.0		204.0	14.0	NM_014208	A8MUI0|O95815	In_Frame_Ins	INS	ENST00000282478.7	hg19	CCDS43248.1																																																																																			.	.		0.49	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		TAG	88535941	-	TAG	88535940	7	5	363	1	0	1	1	0	0	0	0	0	4784	333	12	0	2140	0	DSPP	4	88535940	In_Frame_Ins	INS	-	TCGA-ZP-A9CV-01A-11D-A382-10	17	88535940	102618336	23	50652			1	70		2	2	18	N	TAG_-	6.205246e-05
PCDH18	54510	hgsc.bcm.edu	37	chr4	138451883	138451883	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	gtcattgatatcattgatttGaactgtaaaatgtttcactg	7	5	3	3			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr4:138451883G>T	ENST00000344876.4	-	1	1746	c.1360C>A	c.(1360-1362)Caa>Aaa	p.Q454K	PCDH18_ENST00000511115.1_Intron|PCDH18_ENST00000412923.2_Missense_Mutation_p.Q454K|PCDH18_ENST00000510305.1_Intron|PCDH18_ENST00000507846.1_Missense_Mutation_p.Q234K	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	454	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				brain development (GO:0007420)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(27)|lung(21)|ovary(2)|pancreas(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86	all_hematologic(180;0.24)					TCATTGATTTGAACTGTAAAA	0.413																																					p.Q454K		Atlas-SNP	.											.	PCDH18	229	.	0			c.C1360A						.						142	135	137					4																	138451883		2203	4300	6503	SO:0001583	missense	54510	exon1			TGATTTGAACTGT	AL137471	CCDS34064.1, CCDS75193.1	4q28.3	2010-01-26			ENSG00000189184	ENSG00000189184		"Cadherins / Protocadherins : Non-clustered"	14268	protein-coding gene	gene with protein product		608287				10835267, 11549318	Standard	XM_005263070		Approved	KIAA1562, PCDH68L	uc003ihe.4	Q9HCL0	OTTHUMG00000161348	ENST00000344876.4:c.1360C>A	chr4.hg19:g.138451883G>T	ENSP00000355082:p.Gln454Lys	85.0	0.0		91.0	27.0	NM_019035	A8K7K3|B7ZKT1|Q52LS2	Missense_Mutation	SNP	ENST00000344876.4	hg19	CCDS34064.1	.	.	.	.	.	.	.	.	.	.	G	11.12	1.545241	0.27652	.	.	ENSG00000189184	ENST00000344876;ENST00000412923;ENST00000507846	T;T;T	0.49432	0.78;0.78;0.78	6.04	6.04	0.98038	Cadherin (5);Cadherin conserved site (1);Cadherin-like (1);	0.000000	0.41938	D	0.000784	T	0.39545	0.1082	N	0.26130	0.795	0.80722	D	1	B;B;P	0.41345	0.32;0.036;0.746	B;B;B	0.40702	0.248;0.059;0.338	T	0.09100	-1.0690	10	0.11794	T	0.64	.	20.5948	0.99439	0.0:0.0:1.0:0.0	.	234;454;454	D6RIG4;Q9HCL0-2;Q9HCL0	.;.;PCD18_HUMAN	K	454;454;234	ENSP00000355082:Q454K;ENSP00000390688:Q454K;ENSP00000425903:Q234K	ENSP00000355082:Q454K	Q	-	1	0	PCDH18	138671333	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.824000	0.86668	2.873000	0.98535	0.563000	0.77884	CAA	.	.		0.413	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035		T	138451883	G	T	138451883	3	4	363	1	0	0	0	0	1	0	0	0	11522	1299	45	3	2063	3	PCDH18	4	138451883	Missense_Mutation	SNP	G	TCGA-ZP-A9CV-01A-11D-A382-10	49915943	138451883	52702393	24	50653										
ODZ3	55714	hgsc.bcm.edu	37	chr4	183658118	183658118	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	tcttatggtagctgtagtagGaagactcttccaaaagtggt	11	6	2	1			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr4:183658118G>A	ENST00000511685.1	+	17	3248	c.3125G>A	c.(3124-3126)gGa>gAa	p.G1042E	TENM3_ENST00000502950.1_3'UTR|TENM3_ENST00000406950.2_Missense_Mutation_p.G1042E			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1042					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										GCTGTAGTAGGAAGACTCTTC	0.388																																					p.G1042E		Atlas-SNP	.											.	.	.	.	0			c.G3125A						.						127	120	122					4																	183658118		1827	4088	5915	SO:0001583	missense	55714	exon16			TAGTAGGAAGACT	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.3125G>A	chr4.hg19:g.183658118G>A	ENSP00000424226:p.Gly1042Glu	161.0	0.0		202.0	11.0	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	hg19	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.659031	0.88154	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	D;D	0.99207	-5.56;-5.56	4.48	4.48	0.54585	.	.	.	.	.	D	0.99501	0.9822	M	0.89601	3.045	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.98221	1.0478	9	0.87932	D	0	.	17.3322	0.87268	0.0:0.0:1.0:0.0	.	1042	Q9P273	TEN3_HUMAN	E	1042	ENSP00000424226:G1042E;ENSP00000385276:G1042E	ENSP00000385276:G1042E	G	+	2	0	ODZ3	183895112	1.000000	0.71417	0.993000	0.49108	0.991000	0.79684	9.611000	0.98342	2.326000	0.78906	0.561000	0.74099	GGA	.	.		0.388	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			A	183658118	G	A	183658118	3	1	363	1	0	0	0	0	1	0	0	0	10845	1174	41	3	3187	3	ODZ3	4	183658118	Missense_Mutation	SNP	G	TCGA-ZP-A9CV-01A-11D-A382-10	45206235	183658118	7496158	25	50654										
FAT1	2195	hgsc.bcm.edu	37	chr4	187628067	187628067	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	gtttatccacatcgaagtttCcttctccgtggtccagaagg	9	11	1	1			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr4:187628067C>G	ENST00000441802.2	-	2	3124	c.2915G>C	c.(2914-2916)gGa>gCa	p.G972A		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	972	Cadherin 8. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						ATCGAAGTTTCCTTCTCCGTG	0.483										HNSCC(5;0.00058)																											p.G972A	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.G2915C						.						167	161	163					4																	187628067		1931	4141	6072	SO:0001583	missense	2195	exon2			AAGTTTCCTTCTC	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.2915G>C	chr4.hg19:g.187628067C>G	ENSP00000406229:p.Gly972Ala	140.0	0.0		110.0	6.0	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	hg19	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	C	16.10	3.027527	0.54683	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.53857	0.6	4.67	4.67	0.58626	Cadherin (4);Cadherin-like (1);	0.052914	0.85682	D	0.000000	T	0.68476	0.3005	L	0.55017	1.72	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.67078	-0.5761	10	0.40728	T	0.16	.	18.1062	0.89520	0.0:1.0:0.0:0.0	.	972	Q14517	FAT1_HUMAN	A	972	ENSP00000406229:G972A	ENSP00000260147:G972A	G	-	2	0	FAT1	187865061	1.000000	0.71417	0.954000	0.39281	0.035000	0.12851	4.713000	0.61895	2.579000	0.87056	0.491000	0.48974	GGA	.	.		0.483	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		G	187628067	C	G	187628067	3	3	363	1	0	0	0	0	1	0	0	0	5697	855	30	4	10955	4	FAT1	4	187628067	Missense_Mutation	SNP	C	TCGA-ZP-A9CV-01A-11D-A382-10	3969949	187628067	3526209	26	50655										
TRIML2	205860	hgsc.bcm.edu	37	chr4	189022387	189022387	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	tcagactcaatcatctttttAaaattttgttcctcttcctt	2	10	5	1			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr4:189022387A>T	ENST00000512729.1	-	3	527	c.153T>A	c.(151-153)ttT>ttA	p.F51L	TRIML2_ENST00000326754.3_Missense_Mutation_p.F51L|TRIML2_ENST00000536972.1_Missense_Mutation_p.F101L	NM_173553.1	NP_775824.1	Q8N7C3	TRIMM_HUMAN	tripartite motif family-like 2	51					protein ubiquitination (GO:0016567)|response to retinoic acid (GO:0032526)		ligase activity (GO:0016874)			central_nervous_system(2)|kidney(1)|large_intestine(7)|lung(25)|prostate(3)|urinary_tract(1)	39		all_cancers(14;3.11e-44)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|all_hematologic(60;0.0202)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)		OV - Ovarian serous cystadenocarcinoma(60;1.79e-11)|BRCA - Breast invasive adenocarcinoma(30;4.52e-06)|GBM - Glioblastoma multiforme(59;1.62e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.0091)|READ - Rectum adenocarcinoma(43;0.163)		TCATCTTTTTAAAATTTTGTT	0.363																																					p.F51L		Atlas-SNP	.											.	TRIML2	80	.	0			c.T153A						.						135	123	127					4																	189022387		2203	4300	6503	SO:0001583	missense	205860	exon3			CTTTTTAAAATTT	AK098667	CCDS3850.1	4q35.2	2014-02-12	2007-12-14		ENSG00000179046	ENSG00000179046			26378	protein-coding gene	gene with protein product	"SPRY domain containing 6"						Standard	NM_173553		Approved	FLJ25801, SPRYD6	uc003izl.2	Q8N7C3	OTTHUMG00000160225	ENST00000512729.1:c.153T>A	chr4.hg19:g.189022387A>T	ENSP00000422581:p.Phe51Leu	70.0	0.0		74.0	23.0	NM_173553	B7Z6J6	Missense_Mutation	SNP	ENST00000512729.1	hg19	CCDS3850.1	.	.	.	.	.	.	.	.	.	.	A	4.425	0.078590	0.08533	.	.	ENSG00000179046	ENST00000512729;ENST00000326754;ENST00000536972	T;T;T	0.56103	0.66;0.48;4.08	5.23	3.96	0.45880	.	0.810801	0.10621	N	0.653331	T	0.31420	0.0796	N	0.25201	0.72	0.28399	N	0.918739	B;B;B	0.31459	0.324;0.012;0.034	B;B;B	0.27076	0.076;0.012;0.006	T	0.20739	-1.0266	10	0.02654	T	1	.	8.5702	0.33565	0.8051:0.1949:0.0:0.0	.	101;51;51	B7Z6J6;B7ZLC3;Q8N7C3	.;.;TRIMM_HUMAN	L	51;51;101	ENSP00000422581:F51L;ENSP00000317498:F51L;ENSP00000441236:F101L	ENSP00000317498:F51L	F	-	3	2	TRIML2	189259381	1.000000	0.71417	1.000000	0.80357	0.734000	0.41952	0.555000	0.23422	2.279000	0.76181	0.533000	0.62120	TTT	.	.		0.363	TRIML2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359733.1	NM_173553		T	189022387	A	T	189022387	3	4	363	1	0	0	0	0	1	0	0	0	16566	359	13	4	1030	4	TRIML2	4	189022387	Missense_Mutation	SNP	A	TCGA-ZP-A9CV-01A-11D-A382-10	1394320	189022387	2131889	27	50656										
FBXL7	23194	hgsc.bcm.edu	37	chr5	15928342	15928342	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	ccgcggctctggaggactatCcgcctgacgggcgagaccat	14	14	1	2			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr5:15928342C>T	ENST00000504595.1	+	3	952	c.471C>T	c.(469-471)atC>atT	p.I157I	FBXL7_ENST00000510662.1_Silent_p.I110I|FBXL7_ENST00000329673.7_Silent_p.I145I	NM_001278317.1|NM_012304.3	NP_001265246.1|NP_036436.1	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7	157	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(13)|lung(33)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	60						GGAGGACTATCCGCCTGACGG	0.657																																					p.I157I		Atlas-SNP	.											.	FBXL7	138	.	0			c.C471T						.						18	23	21					5																	15928342		2084	4204	6288	SO:0001819	synonymous_variant	23194	exon3			GACTATCCGCCTG	AB020647	CCDS54833.1, CCDS64129.1	5p15.1	2011-06-09				ENSG00000183580		"F-boxes / Leucine-rich repeats"	13604	protein-coding gene	gene with protein product		605656				10048485, 10531035	Standard	NM_012304		Approved	KIAA0840, FBL7, FBL6	uc003jfn.1	Q9UJT9		ENST00000504595.1:c.471C>T	chr5.hg19:g.15928342C>T		92.0	0.0		65.0	18.0	NM_012304	B9EGF1|D6RDY7|O94926	Silent	SNP	ENST00000504595.1	hg19	CCDS54833.1																																																																																			.	.		0.657	FBXL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366117.1	NM_012304		T	15928342	C	T	15928342	2	4	363	1	0	0	0	0	0	0	0	1	5732	845	30	3		3	FBXL7	5	15928342	Silent	SNP	C	TCGA-ZP-A9CV-01A-11D-A382-10		15928342	164986918	28	50657										
FYB	2533	hgsc.bcm.edu	37	chr5	39141216	39141216	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	ccatcagagtgcgtgacaccAtcttgattgtcttcattgac	8	11	4	4	rs533406048		TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr5:39141216A>G	ENST00000351578.6	-	4	1510	c.1320T>C	c.(1318-1320)gaT>gaC	p.D440D	FYB_ENST00000505428.1_Silent_p.D440D|FYB_ENST00000540520.1_Silent_p.D450D|FYB_ENST00000512982.1_Silent_p.D440D|FYB_ENST00000515010.1_Silent_p.D440D	NM_199335.3	NP_955367.1	O15117	FYB_HUMAN	FYN binding protein	440	Interaction with SKAP1.				immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|NLS-bearing protein import into nucleus (GO:0006607)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	receptor binding (GO:0005102)			endometrium(2)|kidney(4)|large_intestine(6)|liver(1)|lung(29)|ovary(2)|upper_aerodigestive_tract(1)	45	all_lung(31;0.000343)		Epithelial(62;0.235)			GCGTGACACCATCTTGATTGT	0.358													a|||	1	0.000199681	0	0	5008	,	,		19531	0.001		0	False		,,,				2504	0				p.D450D		Atlas-SNP	.											.	FYB	354	.	0			c.T1350C						.						66	59	61					5																	39141216		1880	4122	6002	SO:0001819	synonymous_variant	2533	exon4			GACACCATCTTGA	U93049	CCDS47200.1, CCDS54848.1	5p13.1	2012-05-04	2010-05-04		ENSG00000082074	ENSG00000082074			4036	protein-coding gene	gene with protein product		602731	"FYN-binding protein (FYB-120/130)"			9115214, 9207119	Standard	NM_001465		Approved	SLAP-130, FYB-120/130	uc011cpl.2	O15117	OTTHUMG00000162071	ENST00000351578.6:c.1320T>C	chr5.hg19:g.39141216A>G		350.0	0.0		302.0	99.0	NM_001243093	A8K2Y8|B4DLN2|E9PBV9|O00359|Q9NZI9	Silent	SNP	ENST00000351578.6	hg19	CCDS47200.1																																																																																			.	.		0.358	FYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367098.1	NM_001465		G	39141216	A	G	39141216	2	3	363	1	0	0	0	0	0	0	0	1	6132	214	8	2		2	FYB	5	39141216	Silent	SNP	A	TCGA-ZP-A9CV-01A-11D-A382-10	23212874	39141216	141774044	29	50658										
FCHSD1	89848	hgsc.bcm.edu	37	chr5	141027040	141027040	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	tccagctcagtgtggctcagGgaggtcagggggtccctcaa	15	11	4	0			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr5:141027040G>C	ENST00000435817.2	-	9	803	c.753C>G	c.(751-753)tcC>tcG	p.S251S	FCHSD1_ENST00000522126.1_Silent_p.S175S|FCHSD1_ENST00000522783.1_Silent_p.S249S|FCHSD1_ENST00000523856.1_5'UTR	NM_033449.2	NP_258260.1	Q86WN1	FCSD1_HUMAN	FCH and double SH3 domains 1	251									FCHSD1/BRAF(2)	central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGTGGCTCAGGGAGGTCAGGG	0.612																																					p.S251S		Atlas-SNP	.											.	FCHSD1	51	.	0			c.C753G						.						35	39	38					5																	141027040		1930	4141	6071	SO:0001819	synonymous_variant	89848	exon9			GCTCAGGGAGGTC	AK027281	CCDS47295.1	5q31.3	2008-02-05			ENSG00000197948	ENSG00000197948			25463	protein-coding gene	gene with protein product						11214971, 15067381	Standard	NM_033449		Approved	FLJ00007	uc003llk.3	Q86WN1	OTTHUMG00000163762	ENST00000435817.2:c.753C>G	chr5.hg19:g.141027040G>C		149.0	0.0		121.0	41.0	NM_033449	Q6UX75|Q86Y77|Q9NXX8	Silent	SNP	ENST00000435817.2	hg19	CCDS47295.1																																																																																			.	.		0.612	FCHSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375282.2	NM_033449		C	141027040	G	C	141027040	2	2	363	1	0	0	0	0	0	0	0	1	5797	1219	43	4		4	FCHSD1	5	141027040	Silent	SNP	G	TCGA-ZP-A9CV-01A-11D-A382-10	101885824	141027040	39888220	30	50659										
SH3RF2	153769	hgsc.bcm.edu	37	chr5	145435595	145435595	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	cctggtctctacaccacatgGacgttatccacctcctctgt	6	16	2	0			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr5:145435595G>A	ENST00000511217.1	+	7	1426	c.1374G>A	c.(1372-1374)tgG>tgA	p.W458*	SH3RF2_ENST00000359120.4_Nonsense_Mutation_p.W458*|SH3RF2_ENST00000511705.1_3'UTR			Q8TEC5	SH3R2_HUMAN	SH3 domain containing ring finger 2	458					negative regulation of phosphatase activity (GO:0010923)|protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|phosphatase binding (GO:0019902)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase inhibitor activity (GO:0004864)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(9)|ovary(1)|prostate(1)|skin(2)|stomach(1)	22			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ACACCACATGGACGTTATCCA	0.463																																					p.W458X		Atlas-SNP	.											.	SH3RF2	58	.	0			c.G1374A						.						178	177	177					5																	145435595		2203	4300	6503	SO:0001587	stop_gained	153769	exon8			CACATGGACGTTA	AL833297	CCDS4280.1	5q32	2013-01-09	2011-11-04	2011-11-04	ENSG00000156463	ENSG00000156463		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	26299	protein-coding gene	gene with protein product	"heart protein phosphatase 1-binding protein", "POSH-eliminating RING protein"	613377	"protein phosphatase 1, regulatory subunit 39"	PPP1R39		22128169	Standard	NM_152550		Approved	FLJ23654, RNF158, Hepp1, POSHER	uc003lnt.3	Q8TEC5	OTTHUMG00000129685	ENST00000511217.1:c.1374G>A	chr5.hg19:g.145435595G>A	ENSP00000424497:p.Trp458*	105.0	0.0		109.0	46.0	NM_152550	A8K961|Q08AM9|Q6GMR9|Q8N5S8|Q96LP8	Nonsense_Mutation	SNP	ENST00000511217.1	hg19	CCDS4280.1	.	.	.	.	.	.	.	.	.	.	G	40	8.270784	0.98735	.	.	ENSG00000156463	ENST00000359120;ENST00000511217	.	.	.	5.67	5.67	0.87782	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18710	T	0.47	-14.5098	18.5412	0.91029	0.0:0.0:1.0:0.0	.	.	.	.	X	458	.	ENSP00000352028:W458X	W	+	3	0	SH3RF2	145415788	1.000000	0.71417	1.000000	0.80357	0.869000	0.49853	6.313000	0.72844	2.659000	0.90383	0.655000	0.94253	TGG	.	.		0.463	SH3RF2-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372804.1	NM_152550		A	145435595	G	A	145435595	4	1	363	1	0	0	0	0	0	1	0	0	14274	1183	41	3	1400	3	SH3RF2	5	145435595	Nonsense_Mutation	SNP	G	TCGA-ZP-A9CV-01A-11D-A382-10	4408555	145435595	35479665	31	50660										
CLK4	57396	hgsc.bcm.edu	37	chr5	178043943	178043943	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	cttcacccaaagtgtccacgAtttcatctagagtgaggagg	10	10	3	2			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr5:178043943A>C	ENST00000316308.4	-	5	650	c.482T>G	c.(481-483)aTc>aGc	p.I161S	CLK4_ENST00000522749.1_5'UTR|RN7SKP70_ENST00000516655.1_RNA	NM_020666.2	NP_065717.1	Q9HAZ1	CLK4_HUMAN	CDC-like kinase 4	161	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein autophosphorylation (GO:0046777)|regulation of RNA splicing (GO:0043484)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(2)	21	all_cancers(89;0.000969)|Renal(175;0.000159)|all_epithelial(37;0.000451)|Lung NSC(126;0.00545)|all_lung(126;0.00918)	all_cancers(40;0.0272)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.235)		AGTGTCCACGATTTCATCTAG	0.368																																					p.I161S		Atlas-SNP	.											.	CLK4	103	.	0			c.T482G						.						100	93	95					5																	178043943		2203	4300	6503	SO:0001583	missense	57396	exon5			TCCACGATTTCAT	AF294429	CCDS4437.1	5q35	2008-05-02			ENSG00000113240	ENSG00000113240		"CDC-like kinases"	13659	protein-coding gene	gene with protein product		607969				11170754	Standard	NM_020666		Approved		uc003mjf.1	Q9HAZ1	OTTHUMG00000130893	ENST00000316308.4:c.482T>G	chr5.hg19:g.178043943A>C	ENSP00000316948:p.Ile161Ser	313.0	0.0		304.0	89.0	NM_020666		Missense_Mutation	SNP	ENST00000316308.4	hg19	CCDS4437.1	.	.	.	.	.	.	.	.	.	.	A	15.02	2.709522	0.48517	.	.	ENSG00000113240	ENST00000316308;ENST00000536763	T	0.23348	1.91	5.38	5.38	0.77491	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.49915	0.1585	M	0.71920	2.185	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.53308	-0.8457	10	0.87932	D	0	.	13.3639	0.60671	1.0:0.0:0.0:0.0	.	161;161;161	B7ZL31;B9EG64;Q9HAZ1	.;.;CLK4_HUMAN	S	161	ENSP00000316948:I161S	ENSP00000316948:I161S	I	-	2	0	CLK4	177976549	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.157000	0.94714	2.047000	0.60756	0.528000	0.53228	ATC	.	.		0.368	CLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253479.2			C	178043943	A	C	178043943	3	2	363	1	0	0	0	0	1	0	0	0	3541	333	12	5	999	5	CLK4	5	178043943	Missense_Mutation	SNP	A	TCGA-ZP-A9CV-01A-11D-A382-10	32608348	178043943	2871317	32	50661										
BTN2A2	10385	hgsc.bcm.edu	37	chr6	26388421	26388421	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	tgacggcctcttcatggtcaCcacagctgtgatcatcagag	10	12	5	3			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr6:26388421C>T	ENST00000356709.4	+	4	734	c.623C>T	c.(622-624)aCc>aTc	p.T208I	BTN2A2_ENST00000432533.2_Intron|BTN2A2_ENST00000352867.2_Missense_Mutation_p.T92I|BTN2A2_ENST00000469230.1_Missense_Mutation_p.T208I|BTN2A2_ENST00000416795.2_Missense_Mutation_p.T208I|BTN2A2_ENST00000482536.1_Intron	NM_001197240.1|NM_006995.4	NP_001184169.1|NP_008926.2	Q8WVV5	BT2A2_HUMAN	butyrophilin, subfamily 2, member A2	208	Ig-like C2-type.				negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of cellular metabolic process (GO:0031324)|negative regulation of cytokine secretion (GO:0050710)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|large_intestine(5)|lung(13)	23						TTCATGGTCACCACAGCTGTG	0.542																																					p.T208I		Atlas-SNP	.											.	BTN2A2	87	.	0			c.C623T						.						163	136	145					6																	26388421		2203	4300	6503	SO:0001583	missense	10385	exon4			TGGTCACCACAGC	U90550	CCDS4606.1, CCDS4607.1, CCDS56401.1, CCDS56402.1, CCDS56403.1	6p22.1	2014-01-14			ENSG00000124508	ENSG00000124508		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Butyrophilins"	1137	protein-coding gene	gene with protein product		613591				10354554, 9149941	Standard	NM_006995		Approved	BTF2, BT2.2, BTN2.2	uc003nhq.3	Q8WVV5	OTTHUMG00000014452	ENST00000356709.4:c.623C>T	chr6.hg19:g.26388421C>T	ENSP00000349143:p.Thr208Ile	110.0	0.0		109.0	37.0	NM_001197238	A6NM84|B4DE97|B4DQ01|E9PH07|O00480	Missense_Mutation	SNP	ENST00000356709.4	hg19	CCDS4606.1	.	.	.	.	.	.	.	.	.	.	c	16.01	3.000407	0.54147	.	.	ENSG00000124508	ENST00000469230;ENST00000490025;ENST00000356709;ENST00000352867;ENST00000493275;ENST00000472507;ENST00000482842;ENST00000416795;ENST00000483410	T;T;T;T;T;T;T;T;T	0.56103	2.53;0.48;2.53;2.53;2.53;2.53;2.13;2.53;2.53	4.11	2.16	0.27623	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like fold (1);	0.391203	0.22451	N	0.059894	T	0.52141	0.1716	M	0.67953	2.075	0.09310	N	1	D;D;D;P	0.71674	0.998;0.99;0.991;0.707	D;P;P;P	0.73380	0.98;0.843;0.903;0.703	T	0.38607	-0.9653	10	0.51188	T	0.08	.	8.4152	0.32668	0.174:0.6576:0.1684:0.0	.	92;208;92;208	B4E3J1;Q8WVV5-2;A6NM84;Q8WVV5	.;.;.;BT2A2_HUMAN	I	208;3;208;92;208;92;3;208;92	ENSP00000417472:T208I;ENSP00000418965:T3I;ENSP00000349143:T208I;ENSP00000337117:T92I;ENSP00000418857:T208I;ENSP00000419226:T92I;ENSP00000417676:T3I;ENSP00000399308:T208I;ENSP00000418176:T92I	ENSP00000337117:T92I	T	+	2	0	BTN2A2	26496400	0.000000	0.05858	0.101000	0.21167	0.023000	0.10783	-0.160000	0.10041	0.705000	0.31890	0.454000	0.30748	ACC	.	.		0.542	BTN2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040117.1			T	26388421	C	T	26388421	3	4	363	1	0	0	0	0	1	0	0	0	1563	507	18	3	633	3	BTN2A2	6	26388421	Missense_Mutation	SNP	C	TCGA-ZP-A9CV-01A-11D-A382-10		26388421	144726646	33	50662										
GPR110	266977	hgsc.bcm.edu	37	chr6	46977900	46977900	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	agtcaatgaatttccgagaaAaattcagaggaagagctgtc	10	6	2	4			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr6:46977900A>C	ENST00000371253.2	-	11	1486	c.1271T>G	c.(1270-1272)tTt>tGt	p.F424C	GPR110_ENST00000449332.2_5'UTR|GPR110_ENST00000283297.5_Missense_Mutation_p.F227C	NM_153840.2	NP_722582.2	Q5T601	GP110_HUMAN	G protein-coupled receptor 110	424					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	29						TTTCCGAGAAAAATTCAGAGG	0.428																																					p.F424C		Atlas-SNP	.											.	GPR110	102	.	0			c.T1271G						.						78	76	77					6																	46977900		2203	4300	6503	SO:0001583	missense	266977	exon11			CGAGAAAAATTCA	AB083618	CCDS4920.1, CCDS34471.1	6p21.1	2014-08-08			ENSG00000153292	ENSG00000153292		"-", "GPCR / Class B : Orphans"	18990	protein-coding gene	gene with protein product						12435584, 14623098	Standard	XM_005249006		Approved	hGPCR36, PGR19	uc003oyt.3	Q5T601	OTTHUMG00000014795	ENST00000371253.2:c.1271T>G	chr6.hg19:g.46977900A>C	ENSP00000360299:p.Phe424Cys	141.0	0.0		105.0	43.0	NM_153840	Q5KU15|Q5T5Z9|Q5T600|Q86SM1|Q8IXE3|Q8IZF8|Q96DQ1|Q9H615	Missense_Mutation	SNP	ENST00000371253.2	hg19	CCDS34471.1	.	.	.	.	.	.	.	.	.	.	A	14.91	2.677028	0.47886	.	.	ENSG00000153292	ENST00000371252;ENST00000371253;ENST00000283297	T;T	0.35048	1.34;1.33	5.35	5.35	0.76521	.	0.343109	0.25408	N	0.030888	T	0.23094	0.0558	L	0.59436	1.845	0.34765	D	0.73309	P	0.51791	0.948	B	0.43155	0.41	T	0.28996	-1.0026	10	0.66056	D	0.02	-5.3984	9.1886	0.37184	0.796:0.0:0.0:0.204	.	424	Q5T601	GP110_HUMAN	C	424;424;227	ENSP00000360299:F424C;ENSP00000283297:F227C	ENSP00000283297:F227C	F	-	2	0	GPR110	47085859	0.958000	0.32768	0.701000	0.30321	0.501000	0.33797	4.207000	0.58480	2.150000	0.67090	0.454000	0.30748	TTT	.	.		0.428	GPR110-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040810.2	NM_153840		C	46977900	A	C	46977900	3	2	363	1	0	0	0	0	1	0	0	0	6635	14	1	5	1481	5	GPR110	6	46977900	Missense_Mutation	SNP	A	TCGA-ZP-A9CV-01A-11D-A382-10	20589479	46977900	124137167	34	50663										
SNX14	57231	hgsc.bcm.edu	37	chr6	86277255	86277255	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	ttatagaaagaacatacctgTaccacggataaacaaagttt	6	7	0	2			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr6:86277255T>A	ENST00000314673.3	-	5	634	c.458A>T	c.(457-459)tAc>tTc	p.Y153F	SNX14_ENST00000508980.1_5'UTR|SNX14_ENST00000505648.1_Missense_Mutation_p.Y101F|SNX14_ENST00000369627.2_Missense_Mutation_p.Y153F|RP11-321N4.5_ENST00000503906.1_3'UTR|SNX14_ENST00000513865.1_Missense_Mutation_p.Y153F|SNX14_ENST00000346348.3_Intron	NM_153816.3	NP_722523.1	Q9Y5W7	SNX14_HUMAN	sorting nexin 14	153	PXA. {ECO:0000255|PROSITE- ProRule:PRU00147, ECO:0000255|PROSITE- ProRule:PRU00553}.				protein transport (GO:0015031)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	integral component of membrane (GO:0016021)	phosphatidylinositol binding (GO:0035091)			NS(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(11)|skin(1)	22		all_cancers(76;4.83e-07)|Acute lymphoblastic leukemia(125;3.3e-08)|Prostate(29;2.55e-07)|all_hematologic(105;3.66e-05)|all_epithelial(107;0.000695)|Lung NSC(302;0.197)|all_lung(197;0.24)		BRCA - Breast invasive adenocarcinoma(108;0.0423)		AACATACCTGTACCACGGATA	0.269																																					p.Y153F		Atlas-SNP	.											.	SNX14	58	.	0			c.A458T						.						74	77	76					6																	86277255		2203	4298	6501	SO:0001583	missense	57231	exon5			TACCTGTACCACG	AF121863	CCDS5003.1, CCDS5004.1, CCDS75490.1	6q15	2008-10-22			ENSG00000135317	ENSG00000135317		"Sorting nexins"	14977	protein-coding gene	gene with protein product						11485546, 11736640	Standard	XM_005248738		Approved	RGS-PX2	uc003pkr.3	Q9Y5W7	OTTHUMG00000015140	ENST00000314673.3:c.458A>T	chr6.hg19:g.86277255T>A	ENSP00000313121:p.Tyr153Phe	807.0	0.0		704.0	221.0	NM_153816	B4DI55|Q4VBR3|Q5TCF9|Q5TCG0|Q6NUI7|Q6PI37|Q9BSD1	Missense_Mutation	SNP	ENST00000314673.3	hg19	CCDS5004.1	.	.	.	.	.	.	.	.	.	.	T	26.6	4.754308	0.89843	.	.	ENSG00000135317	ENST00000314673;ENST00000513865;ENST00000505648;ENST00000369627;ENST00000515216;ENST00000514419	T;T;T;T;T	0.64260	0.24;-0.09;0.29;0.25;0.28	5.77	5.77	0.91146	Phox-associated domain (2);	0.000000	0.85682	D	0.000000	T	0.59487	0.2197	L	0.50993	1.605	0.80722	D	1	B;P;B	0.39883	0.22;0.693;0.22	B;P;B	0.48982	0.108;0.597;0.1	T	0.63791	-0.6557	10	0.54805	T	0.06	.	16.1043	0.81209	0.0:0.0:0.0:1.0	.	153;153;101	Q9Y5W7-4;Q9Y5W7;Q9Y5W7-3	.;SNX14_HUMAN;.	F	153;153;101;153;80;152	ENSP00000313121:Y153F;ENSP00000420938:Y153F;ENSP00000427380:Y101F;ENSP00000358641:Y153F;ENSP00000425630:Y80F	ENSP00000313121:Y153F	Y	-	2	0	SNX14	86333974	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.501000	0.81600	2.201000	0.70794	0.528000	0.53228	TAC	.	.		0.269	SNX14-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041393.2	NM_153816		A	86277255	T	A	86277255	3	1	363	1	0	0	0	0	1	0	0	0	14900	1638	57	4	2482	4	SNX14	6	86277255	Missense_Mutation	SNP	T	TCGA-ZP-A9CV-01A-11D-A382-10	39299355	86277255	84837812	35	50664										
TPD52L1	7164	hgsc.bcm.edu	37	chr6	125584049	125584049	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	tcagctccacggcccatgccAgtgcccagagcttggcagga	12	15	1	1			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr6:125584049A>G	ENST00000534000.1	+	7	852	c.556A>G	c.(556-558)Agt>Ggt	p.S186G	TPD52L1_ENST00000524679.1_3'UTR|TPD52L1_ENST00000532429.1_Missense_Mutation_p.S157G|HDDC2_ENST00000608456.1_Intron|TPD52L1_ENST00000392482.2_3'UTR|TPD52L1_ENST00000530868.1_3'UTR|TPD52L1_ENST00000527711.1_Missense_Mutation_p.S173G|TPD52L1_ENST00000368388.2_3'UTR|TPD52L1_ENST00000368402.5_3'UTR|TPD52L1_ENST00000304877.13_Missense_Mutation_p.S191G|TPD52L1_ENST00000534199.1_3'UTR|TPD52L1_ENST00000528193.1_3'UTR	NM_003287.2	NP_003278.1	Q16890	TPD53_HUMAN	tumor protein D52-like 1	186					G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAP kinase activity (GO:0043406)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(2)|large_intestine(2)|prostate(1)	5			LUSC - Lung squamous cell carcinoma(4;0.0263)|Lung(4;0.0828)	GBM - Glioblastoma multiforme(226;0.0265)		GGCCCATGCCAGTGCCCAGAG	0.582																																					p.S186G		Atlas-SNP	.											.	TPD52L1	14	.	0			c.A556G						.						51	47	49					6																	125584049		2203	4300	6503	SO:0001583	missense	7164	exon7			CATGCCAGTGCCC	U44427	CCDS5130.1, CCDS34527.1, CCDS34528.1, CCDS43502.1, CCDS75513.1, CCDS75514.1	6q22-q23	2008-07-29			ENSG00000111907	ENSG00000111907			12006	protein-coding gene	gene with protein product		604069				8812487, 16112108	Standard	NM_003287		Approved	D53, hD53	uc003pzu.1	Q16890	OTTHUMG00000015505	ENST00000534000.1:c.556A>G	chr6.hg19:g.125584049A>G	ENSP00000434142:p.Ser186Gly	98.0	0.0		79.0	28.0	NM_003287	A8K757|A8K772|A8MUD2|A8MUJ7|A8MW70|F6V707|O43397|Q5TC99|Q5TDQ0|Q9BUQ6|Q9C054	Missense_Mutation	SNP	ENST00000534000.1	hg19	CCDS5130.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.237369	0.79800	.	.	ENSG00000111907	ENST00000304877;ENST00000534000;ENST00000527711;ENST00000532429;ENST00000392484	T;T;T;T	0.37915	1.17;1.17;1.17;1.17	5.53	5.53	0.82687	.	0.038889	0.85682	D	0.000000	T	0.44993	0.1320	M	0.70275	2.135	0.80722	D	1	D	0.63046	0.992	D	0.76071	0.987	T	0.41124	-0.9526	10	0.17832	T	0.49	-3.3036	13.1952	0.59734	1.0:0.0:0.0:0.0	.	186	Q16890	TPD53_HUMAN	G	191;186;173;157;186	ENSP00000306285:S191G;ENSP00000434142:S186G;ENSP00000436953:S173G;ENSP00000435447:S157G	ENSP00000306285:S191G	S	+	1	0	TPD52L1	125625748	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	4.115000	0.57865	2.104000	0.64026	0.528000	0.53228	AGT	.	.		0.582	TPD52L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042065.2			G	125584049	A	G	125584049	3	3	363	1	0	0	0	0	1	0	0	0	16413	188	7	2	582	2	TPD52L1	6	125584049	Missense_Mutation	SNP	A	TCGA-ZP-A9CV-01A-11D-A382-10	39306794	125584049	45531018	36	50665										
LAMA2	3908	hgsc.bcm.edu	37	chr6	129468191	129468191	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	gtccacttgatccagcgacaAatgtatgtatatttatagga	8	7	0	1			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr6:129468191A>T	ENST00000421865.2	+	6	956	c.907A>T	c.(907-909)Aat>Tat	p.N303Y		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	303	Laminin EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		TCCAGCGACAAATGTATGTAT	0.428																																					p.N303Y		Atlas-SNP	.											.	LAMA2	481	.	0			c.A907T						.						167	157	161					6																	129468191		2203	4299	6502	SO:0001583	missense	3908	exon6			GCGACAAATGTAT	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"Laminins"	6482	protein-coding gene	gene with protein product	"merosin", "congenital muscular dystrophy"	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.907A>T	chr6.hg19:g.129468191A>T	ENSP00000400365:p.Asn303Tyr	120.0	0.0		72.0	26.0	NM_000426	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	hg19	CCDS5138.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.353406	0.82243	.	.	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865	T	0.63744	-0.06	5.61	5.61	0.85477	EGF-like, laminin (3);	0.054064	0.64402	D	0.000001	T	0.58495	0.2126	N	0.16266	0.395	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.71184	0.972;0.948	T	0.68168	-0.5480	10	0.72032	D	0.01	.	16.101	0.81172	1.0:0.0:0.0:0.0	.	303;303	A6NF00;P24043	.;LAMA2_HUMAN	Y	303	ENSP00000400365:N303Y	ENSP00000346769:N303Y	N	+	1	0	LAMA2	129509884	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.851000	0.92205	2.263000	0.75096	0.528000	0.53228	AAT	.	.		0.428	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			T	129468191	A	T	129468191	3	4	363	1	0	0	0	0	1	0	0	0	8615	14	1	4	929	4	LAMA2	6	129468191	Missense_Mutation	SNP	A	TCGA-ZP-A9CV-01A-11D-A382-10	3884142	129468191	41646876	37	50666										
LFNG	3955	hgsc.bcm.edu	37	chr7	2559888	2559888	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	ttccaccgcgcgcgcctcgaCctgctgctggagacctggat	12	16	0	1			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr7:2559888C>T	ENST00000222725.5	+	1	413	c.393C>T	c.(391-393)gaC>gaT	p.D131D	LFNG_ENST00000402045.1_Intron|LFNG_ENST00000338732.3_Intron|LFNG_ENST00000359574.3_Silent_p.D131D|LFNG_ENST00000402506.1_Intron	NM_001040167.1	NP_001035257.1	Q8NES3	LFNG_HUMAN	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	131					compartment pattern specification (GO:0007386)|female meiotic division (GO:0007143)|metabolic process (GO:0008152)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|ovarian follicle development (GO:0001541)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of protein binding (GO:0032092)|regulation of Notch signaling pathway (GO:0008593)|regulation of somitogenesis (GO:0014807)|somitogenesis (GO:0001756)	extracellular region (GO:0005576)|integral component of Golgi membrane (GO:0030173)|vesicle (GO:0031982)	metal ion binding (GO:0046872)|O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity (GO:0033829)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)|urinary_tract(2)	6		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.54e-14)		CGCGCCTCGACCTGCTGCTGG	0.721																																					p.D131D		Atlas-SNP	.											.	LFNG	57	.	0			c.C393T						.						18	23	21					7																	2559888		2063	4182	6245	SO:0001819	synonymous_variant	3955	exon1			CCTCGACCTGCTG	BC014851	CCDS34586.1, CCDS34587.1, CCDS55081.1, CCDS55082.1	7p22.3	2013-02-19	2006-11-13		ENSG00000106003	ENSG00000106003	2.4.1.222	"Beta 3-glycosyltransferases"	6560	protein-coding gene	gene with protein product		602576	"lunatic fringe (Drosophila) homolog", "lunatic fringe homolog (Drosophila)"			9878264, 9187150	Standard	NM_001166355		Approved	SCDO3	uc003smf.3	Q8NES3	OTTHUMG00000152043	ENST00000222725.5:c.393C>T	chr7.hg19:g.2559888C>T		1341.0	2.0		1149.0	358.0	NM_001040167	B3KTY6|B5MCR5|O00589|Q96C39|Q9UJW5	Silent	SNP	ENST00000222725.5	hg19	CCDS34587.1																																																																																			.	.		0.721	LFNG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325021.1	NM_002304		T	2559888	C	T	2559888	2	4	363	1	0	0	0	0	0	0	0	1	8746	506	18	3		3	LFNG	7	2559888	Silent	SNP	C	TCGA-ZP-A9CV-01A-11D-A382-10		2559888	156578775	38	50667										
RFC2	5982	hgsc.bcm.edu	37	chr7	73663436	73663436	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	aatgcttgtggtcttgccggTtcctggagggccctgggaat	15	9	1	0			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr7:73663436T>A	ENST00000055077.3	-	4	298	c.238A>T	c.(238-240)Acc>Tcc	p.T80S	RFC2_ENST00000352131.3_Missense_Mutation_p.T80S	NM_181471.1	NP_852136.1	P35250	RFC2_HUMAN	replication factor C (activator 1) 2, 40kDa	80					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor C complex (GO:0005663)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(3)	8						GTCTTGCCGGTTCCTGGAGGG	0.527																																					p.T80S		Atlas-SNP	.											.	RFC2	27	.	0			c.A238T						.						69	73	72					7																	73663436		2203	4300	6503	SO:0001583	missense	5982	exon4			TGCCGGTTCCTGG		CCDS5567.1, CCDS5568.1, CCDS75618.1	7q11.23	2010-04-21	2002-08-29		ENSG00000049541	ENSG00000049541		"ATPases / AAA-type"	9970	protein-coding gene	gene with protein product	"activator 1"	600404	"replication factor C (activator 1) 2 (40kD)"			1313560, 7774928	Standard	NM_181471		Approved	A1, RFC40	uc003uaj.3	P35250	OTTHUMG00000023239	ENST00000055077.3:c.238A>T	chr7.hg19:g.73663436T>A	ENSP00000055077:p.Thr80Ser	48.0	0.0		53.0	15.0	NM_181471	B5BU07|D3DXG3|P32846|Q9BU93	Missense_Mutation	SNP	ENST00000055077.3	hg19	CCDS5568.1	.	.	.	.	.	.	.	.	.	.	T	17.98	3.520300	0.64747	.	.	ENSG00000049541	ENST00000352131;ENST00000055077	T;D	0.94650	0.96;-3.48	4.65	4.65	0.58169	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.094647	0.64402	D	0.000001	D	0.92368	0.7578	L	0.31578	0.945	0.58432	D	0.999999	B;B;P	0.37276	0.38;0.434;0.589	B;P;B	0.46208	0.373;0.507;0.41	D	0.92806	0.6260	10	0.87932	D	0	.	11.7504	0.51845	0.0:0.0:0.0:1.0	.	80;80;80	P35250-2;Q75MT5;P35250	.;.;RFC2_HUMAN	S	80	ENSP00000275627:T80S;ENSP00000055077:T80S	ENSP00000055077:T80S	T	-	1	0	RFC2	73301372	1.000000	0.71417	0.728000	0.30774	0.518000	0.34316	7.656000	0.83736	1.879000	0.54435	0.374000	0.22700	ACC	.	.		0.527	RFC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252459.2	NM_181471		A	73663436	T	A	73663436	3	1	363	1	0	0	0	0	1	0	0	0	13260	1725	60	4	858	4	RFC2	7	73663436	Missense_Mutation	SNP	T	TCGA-ZP-A9CV-01A-11D-A382-10	71103548	73663436	85475227	39	50668										
MUC17	140453	hgsc.bcm.edu	37	chr7	100681407	100681407	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	gccggtagttacttctgaggCtagcaccctttcagcaactc	9	13	2	1	rs201523803		TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr7:100681407C>T	ENST00000306151.4	+	3	6774	c.6710C>T	c.(6709-6711)gCt>gTt	p.A2237V		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2237	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					ACTTCTGAGGCTAGCACCCTT	0.502																																					p.A2237V		Atlas-SNP	.											.	MUC17	804	.	0			c.C6710T						.						346	342	343					7																	100681407		2203	4300	6503	SO:0001583	missense	140453	exon3			CTGAGGCTAGCAC	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.6710C>T	chr7.hg19:g.100681407C>T	ENSP00000302716:p.Ala2237Val	81.0	0.0		82.0	7.0	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	0.948	-0.707469	0.03230	.	.	ENSG00000169876	ENST00000306151	T	0.02656	4.21	1.3	-2.61	0.06171	.	.	.	.	.	T	0.01765	0.0056	L	0.27053	0.805	0.09310	N	1	B	0.21821	0.061	B	0.10450	0.005	T	0.46992	-0.9151	9	0.21014	T	0.42	.	2.1159	0.03713	0.2458:0.3783:0.0:0.3758	.	2237	Q685J3	MUC17_HUMAN	V	2237	ENSP00000302716:A2237V	ENSP00000302716:A2237V	A	+	2	0	MUC17	100468127	0.003000	0.15002	0.000000	0.03702	0.001000	0.01503	0.508000	0.22692	-1.786000	0.01269	-1.404000	0.01136	GCT	.	.		0.502	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		T	100681407	C	T	100681407	3	4	363	1	0	0	0	0	1	0	0	0	9983	797	28	3	6720	3	MUC17	7	100681407	Missense_Mutation	SNP	C	TCGA-ZP-A9CV-01A-11D-A382-10	27017971	100681407	58457256	40	50669										
RNF133	168433	hgsc.bcm.edu	37	chr7	122338822	122338822	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	tcccaactctgacaacacatGattcccaacatgaaatgata	4	12	1	4			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr7:122338822G>A	ENST00000340112.2	-	1	388	c.151C>T	c.(151-153)Cat>Tat	p.H51Y	CADPS2_ENST00000313070.7_Intron|CADPS2_ENST00000412584.2_Intron|CADPS2_ENST00000334010.7_Intron|CADPS2_ENST00000449022.2_Intron	NM_139175.1	NP_631914.1	Q8WVZ7	RN133_HUMAN	ring finger protein 133	51					protein autoubiquitination (GO:0051865)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	21						GACAACACATGATTCCCAACA	0.423																																					p.H51Y	Colon(198;1778 2057 7449 19869 45985)	Atlas-SNP	.											.	RNF133	41	.	0			c.C151T						.						118	115	116					7																	122338822		2203	4300	6503	SO:0001583	missense	168433	exon1			ACACATGATTCCC	AF447589	CCDS5784.1	7q31.33	2013-01-09			ENSG00000188050	ENSG00000188050		"RING-type (C3HC4) zinc fingers"	21154	protein-coding gene	gene with protein product							Standard	NM_139175		Approved		uc003vkj.1	Q8WVZ7	OTTHUMG00000157092	ENST00000340112.2:c.151C>T	chr7.hg19:g.122338822G>A	ENSP00000344489:p.His51Tyr	111.0	0.0		88.0	25.0	NM_139175	A4D0W2|Q8N7G7	Missense_Mutation	SNP	ENST00000340112.2	hg19	CCDS5784.1	.	.	.	.	.	.	.	.	.	.	G	8.492	0.862178	0.17178	.	.	ENSG00000188050	ENST00000340112	T	0.13657	2.57	6.06	6.06	0.98353	.	0.238580	0.32444	N	0.006082	T	0.07188	0.0182	N	0.08118	0	0.28435	N	0.917088	B	0.02656	0.0	B	0.01281	0.0	T	0.26744	-1.0094	10	0.09590	T	0.72	.	14.0173	0.64531	0.0:0.0:0.7505:0.2495	.	51	Q8WVZ7	RN133_HUMAN	Y	51	ENSP00000344489:H51Y	ENSP00000344489:H51Y	H	-	1	0	RNF133	122126058	0.503000	0.26115	0.971000	0.41717	0.555000	0.35460	1.719000	0.38011	2.882000	0.98803	0.655000	0.94253	CAT	.	.		0.423	RNF133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347413.1	NM_139175		A	122338822	G	A	122338822	3	1	363	1	0	0	0	0	1	0	0	0	13454	1290	45	3	983	3	RNF133	7	122338822	Missense_Mutation	SNP	G	TCGA-ZP-A9CV-01A-11D-A382-10	21657415	122338822	36799841	41	50670										
DNAJB6	10049	hgsc.bcm.edu	37	chr7	157155909	157155909	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	aaaaatcctgagaataaagaAgaagcagagagaaaattcaa	8	4	1	5			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr7:157155909A>C	ENST00000262177.4	+	3	325	c.120A>C	c.(118-120)gaA>gaC	p.E40D	DNAJB6_ENST00000429029.2_Missense_Mutation_p.E40D|DNAJB6_ENST00000443280.1_Missense_Mutation_p.E40D|DNAJB6_ENST00000452797.2_Intron	NM_058246.3	NP_490647.1	O75190	DNJB6_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 6	40	Interaction with HSP70.|J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				intermediate filament organization (GO:0045109)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of ATPase activity (GO:0032781)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	ATPase activator activity (GO:0001671)|chaperone binding (GO:0051087)|heat shock protein binding (GO:0031072)|unfolded protein binding (GO:0051082)			central_nervous_system(1)|lung(1)|ovary(2)|stomach(1)	5	all_neural(206;0.181)	all_epithelial(9;0.000606)|all_hematologic(28;0.00287)|Acute lymphoblastic leukemia(9;0.0647)|Ovarian(593;0.196)	OV - Ovarian serous cystadenocarcinoma(82;0.00399)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		AGAATAAAGAAGAAGCAGAGA	0.453																																					p.E40D	Esophageal Squamous(46;195 967 1350 20350 43814)	Atlas-SNP	.											.	DNAJB6	39	.	0			c.A120C						.						46	46	46					7																	157155909		2203	4297	6500	SO:0001583	missense	10049	exon3			TAAAGAAGAAGCA	AB014888	CCDS5946.1, CCDS47755.1	7q36.3	2014-02-03			ENSG00000105993	ENSG00000105993		"Heat shock proteins / DNAJ (HSP40)"	14888	protein-coding gene	gene with protein product		611332	"limb girdle muscular dystrophy 1D (autosomal dominant)"	LGMD1D		10319584, 9915854, 22366786	Standard	NM_005494		Approved	MRJ	uc003wnk.3	O75190	OTTHUMG00000157242	ENST00000262177.4:c.120A>C	chr7.hg19:g.157155909A>C	ENSP00000262177:p.Glu40Asp	168.0	0.0		179.0	58.0	NM_058246	A4D232|A8K7D8|A8KAG0|B4DN73|E9PCZ2|O95806|Q53EN8|Q59EF2|Q6FIC8|Q75MA2|Q9UIK6	Missense_Mutation	SNP	ENST00000262177.4	hg19	CCDS5946.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.957214	0.73902	.	.	ENSG00000105993	ENST00000441561;ENST00000429029;ENST00000262177;ENST00000417758;ENST00000443280;ENST00000421417;ENST00000437030;ENST00000412557;ENST00000453383;ENST00000439402	T;T;T;T;T;T;T;T;T	0.75704	1.41;1.41;1.41;1.41;1.41;1.41;1.41;1.41;-0.96	4.78	2.31	0.28768	Heat shock protein DnaJ, N-terminal (5);	0.603238	0.13016	U	0.420467	T	0.74726	0.3754	L	0.37561	1.115	0.80722	D	1	B;D;D;B	0.64830	0.196;0.994;0.988;0.0	B;D;D;B	0.66847	0.38;0.922;0.947;0.002	T	0.68108	-0.5496	10	0.42905	T	0.14	.	4.0204	0.09664	0.4009:0.0:0.1582:0.441	.	40;40;40;40	E9PH18;A8KAG0;O75190;O75190-2	.;.;DNJB6_HUMAN;.	D	40	ENSP00000410643:E40D;ENSP00000397556:E40D;ENSP00000262177:E40D;ENSP00000400665:E40D;ENSP00000396267:E40D;ENSP00000391690:E40D;ENSP00000403407:E40D;ENSP00000396240:E40D;ENSP00000389599:E40D	ENSP00000262177:E40D	E	+	3	2	DNAJB6	156848670	0.081000	0.21417	1.000000	0.80357	0.984000	0.73092	-0.832000	0.04400	0.255000	0.21593	0.528000	0.53228	GAA	.	.		0.453	DNAJB6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000348119.2			C	157155909	A	C	157155909	3	2	363	1	0	0	0	0	1	0	0	0	4626	69	3	5	126	5	DNAJB6	7	157155909	Missense_Mutation	SNP	A	TCGA-ZP-A9CV-01A-11D-A382-10	34817087	157155909	1982754	42	50671										
RP1L1	94137	hgsc.bcm.edu	37	chr8	10466108	10466108	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	agcctccggggcctctatgcCttcggccccatcactctgtc	9	18	3	0			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr8:10466108C>T	ENST00000382483.3	-	4	5723	c.5500G>A	c.(5500-5502)Ggc>Agc	p.G1834S		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1914					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		GCCTCTATGCCTTCGGCCCCA	0.637																																					p.G1834S		Atlas-SNP	.											.	RP1L1	453	.	0			c.G5500A						.						149	166	161					8																	10466108		2007	4158	6165	SO:0001583	missense	94137	exon4			CTATGCCTTCGGC	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.5500G>A	chr8.hg19:g.10466108C>T	ENSP00000371923:p.Gly1834Ser	54.0	0.0		27.0	11.0	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	hg19	CCDS43708.1	.	.	.	.	.	.	.	.	.	.	C	3.788	-0.044322	0.07452	.	.	ENSG00000183638	ENST00000382483	T	0.03772	3.81	2.95	2.95	0.34219	.	.	.	.	.	T	0.02494	0.0076	N	0.14661	0.345	0.09310	N	1	P	0.41524	0.753	B	0.35688	0.208	T	0.26155	-1.0111	9	0.07030	T	0.85	.	9.2877	0.37766	0.0:1.0:0.0:0.0	.	1834	A6NKC6	.	S	1834	ENSP00000371923:G1834S	ENSP00000371923:G1834S	G	-	1	0	RP1L1	10503518	.	.	0.007000	0.13788	0.026000	0.11368	.	.	1.156000	0.42514	0.455000	0.32223	GGC	.	.		0.637	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			T	10466108	C	T	10466108	3	4	363	1	0	0	0	0	1	0	0	0	13548	681	24	3	1706	3	RP1L1	8	10466108	Missense_Mutation	SNP	C	TCGA-ZP-A9CV-01A-11D-A382-10		10466108	135897914	43	50672										
PURG	29942	hgsc.bcm.edu	37	chr8	30890148	30890148	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	gatttcggctgcgcccccggCctgattaggggtggctgagg	17	11	0	2			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr8:30890148C>T	ENST00000475541.1	-	1	1083	c.151G>A	c.(151-153)Gcc>Acc	p.A51T	PURG_ENST00000339382.2_Missense_Mutation_p.A51T|WRN_ENST00000298139.5_5'Flank	NM_013357.2	NP_037489.1	Q9UJV8	PURG_HUMAN	purine-rich element binding protein G	51						nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(3)|lung(5)|ovary(2)|urinary_tract(1)	12				KIRC - Kidney renal clear cell carcinoma(542;0.0895)|Kidney(114;0.108)		GCGCCCCCGGCCTGATTAGGG	0.597																																					p.A51T		Atlas-SNP	.											.	PURG	79	.	0			c.G151A						.						23	25	24					8																	30890148		2203	4300	6503	SO:0001583	missense	29942	exon1			CCCCGGCCTGATT	AF195513	CCDS34878.1, CCDS6081.1	8p11	2004-02-09			ENSG00000172733	ENSG00000172733			17930	protein-coding gene	gene with protein product						12034829	Standard	NM_013357		Approved	PURG-A, PURG-B	uc003xin.3	Q9UJV8	OTTHUMG00000157357	ENST00000475541.1:c.151G>A	chr8.hg19:g.30890148C>T	ENSP00000418721:p.Ala51Thr	83.0	0.0		48.0	23.0	NM_013357	Q8TE64	Missense_Mutation	SNP	ENST00000475541.1	hg19	CCDS6081.1	.	.	.	.	.	.	.	.	.	.	C	10.93	1.488962	0.26686	.	.	ENSG00000172733	ENST00000339382;ENST00000475541	T;T	0.22134	1.97;1.98	4.9	-0.777	0.10981	.	0.836318	0.10506	N	0.666717	T	0.07863	0.0197	N	0.08118	0	0.21740	N	0.999569	B;B	0.02656	0.0;0.0	B;B	0.06405	0.0;0.002	T	0.35574	-0.9783	10	0.23891	T	0.37	2.8603	1.8219	0.03112	0.2532:0.3665:0.2348:0.1455	.	51;51	Q9UJV8;Q9UJV8-2	PURG_HUMAN;.	T	51	ENSP00000345168:A51T;ENSP00000418721:A51T	ENSP00000345168:A51T	A	-	1	0	PURG	31009690	0.424000	0.25490	0.199000	0.23439	0.950000	0.60333	-0.158000	0.10070	-0.204000	0.10235	0.313000	0.20887	GCC	.	.		0.597	PURG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348565.1	NM_013357		T	30890148	C	T	30890148	3	4	363	1	0	0	0	0	1	0	0	0	12844	739	26	3	1005	3	PURG	8	30890148	Missense_Mutation	SNP	C	TCGA-ZP-A9CV-01A-11D-A382-10	20424040	30890148	115473874	44	50673										
C8orf41	80185	hgsc.bcm.edu	37	chr8	33356779	33356779	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	tgtcttcacagctttggggaAttttggccaggagaccctga	12	9	2	2			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr8:33356779A>T	ENST00000431156.2	-	8	2057	c.1439T>A	c.(1438-1440)aTt>aAt	p.I480N	TTI2_ENST00000519356.1_Intron|TTI2_ENST00000360742.5_Missense_Mutation_p.I480N|MAK16_ENST00000360128.6_3'UTR|TTI2_ENST00000520636.1_Missense_Mutation_p.I449N	NM_001102401.2	NP_001095871.1	Q6NXR4	TTI2_HUMAN	TELO2 interacting protein 2	480																	GCTTTGGGGAATTTTGGCCAG	0.388																																					p.I480N		Atlas-SNP	.											.	.	.	.	0			c.T1439A						.						86	85	86					8																	33356779		2203	4300	6503	SO:0001583	missense	80185	exon8			TGGGGAATTTTGG	AK026916	CCDS6090.1	8p12	2011-11-10	2011-11-10	2011-09-22		ENSG00000129696			26262	protein-coding gene	gene with protein product		614426	"chromosome 8 open reading frame 41", "Tel2 interacting protein 2 homolog (S. pombe)"	C8orf41		20801936, 20810650	Standard	NM_025115		Approved	FLJ23263	uc003xjm.5	Q6NXR4		ENST00000431156.2:c.1439T>A	chr8.hg19:g.33356779A>T	ENSP00000411169:p.Ile480Asn	121.0	0.0		81.0	39.0	NM_001265581	D3DSV7|Q96IM2|Q9H5N4	Missense_Mutation	SNP	ENST00000431156.2	hg19	CCDS6090.1	.	.	.	.	.	.	.	.	.	.	A	12.00	1.805625	0.31961	.	.	ENSG00000129696	ENST00000360742;ENST00000431156;ENST00000522668;ENST00000520636;ENST00000520397	T;T;T	0.61040	0.14;0.14;0.16	5.94	1.91	0.25777	.	0.318102	0.28470	N	0.015238	T	0.47303	0.1438	M	0.67953	2.075	0.09310	N	1	P;P;P	0.45902	0.718;0.779;0.868	B;B;B	0.36808	0.125;0.233;0.233	T	0.49133	-0.8971	10	0.87932	D	0	-6.4158	6.0646	0.19856	0.6804:0.1512:0.1684:0.0	.	315;480;449	E5RH83;Q6NXR4;E5RIH5	.;TTI2_HUMAN;.	N	480;480;469;449;315	ENSP00000353971:I480N;ENSP00000411169:I480N;ENSP00000428401:I449N	ENSP00000353971:I480N	I	-	2	0	C8orf41	33476321	0.000000	0.05858	0.026000	0.17262	0.656000	0.38851	0.329000	0.19698	0.507000	0.28148	0.460000	0.39030	ATT	.	.		0.388	TTI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376555.1	NM_025115		T	33356779	A	T	33356779	3	4	363	1	0	0	0	0	1	0	0	0	2429	101	4	4	91	4	C8orf41	8	33356779	Missense_Mutation	SNP	A	TCGA-ZP-A9CV-01A-11D-A382-10	2466631	33356779	113007243	45	50674										
DPYS	1807	hgsc.bcm.edu	37	chr8	105456619	105456619	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	cctctgggcggcacagctcgTggccctcagggcctgttatc	13	15	2	0			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr8:105456619T>A	ENST00000351513.2	-	4	782	c.650A>T	c.(649-651)cAc>cTc	p.H217L		NM_001385.2	NP_001376.1	Q14117	DPYS_HUMAN	dihydropyrimidinase	217					beta-alanine metabolic process (GO:0019482)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein homotetramerization (GO:0051289)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymine catabolic process (GO:0006210)|uracil catabolic process (GO:0006212)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|dihydropyrimidinase activity (GO:0004157)|thymine binding (GO:0002059)|uracil binding (GO:0002058)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(57;1.61e-06)|STAD - Stomach adenocarcinoma(118;0.229)			GCACAGCTCGTGGCCCTCAGG	0.532																																					p.H217L		Atlas-SNP	.											.	DPYS	107	.	0			c.A650T						.						63	60	61					8																	105456619		2203	4300	6503	SO:0001583	missense	1807	exon4			AGCTCGTGGCCCT	D78011	CCDS6302.1	8q22	2004-01-22			ENSG00000147647	ENSG00000147647			3013	protein-coding gene	gene with protein product		613326				8973361	Standard	NM_001385		Approved	DHPase	uc003yly.4	Q14117	OTTHUMG00000164891	ENST00000351513.2:c.650A>T	chr8.hg19:g.105456619T>A	ENSP00000276651:p.His217Leu	89.0	0.0		89.0	18.0	NM_001385		Missense_Mutation	SNP	ENST00000351513.2	hg19	CCDS6302.1	.	.	.	.	.	.	.	.	.	.	T	33	5.226619	0.95173	.	.	ENSG00000147647	ENST00000351513	D	0.91124	-2.79	5.67	5.67	0.87782	Amidohydrolase 1 (1);	0.000000	0.85682	D	0.000000	D	0.95689	0.8598	M	0.85041	2.73	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96225	0.9163	10	0.72032	D	0.01	-16.638	15.9141	0.79496	0.0:0.0:0.0:1.0	.	217	Q14117	DPYS_HUMAN	L	217	ENSP00000276651:H217L	ENSP00000276651:H217L	H	-	2	0	DPYS	105525795	1.000000	0.71417	0.955000	0.39395	0.979000	0.70002	7.543000	0.82106	2.154000	0.67381	0.533000	0.62120	CAC	.	.		0.532	DPYS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380814.1	NM_001385		A	105456619	T	A	105456619	3	1	363	1	0	0	0	0	1	0	0	0	4748	1696	59	4	933	4	DPYS	8	105456619	Missense_Mutation	SNP	T	TCGA-ZP-A9CV-01A-11D-A382-10	72099840	105456619	40907403	46	50675										
ASAP1	50807	hgsc.bcm.edu	37	chr8	131146576	131146576	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	ctcatcttctgcctgaaagtGatatgttctattatctaaaa	5	8	5	2			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr8:131146576G>A	ENST00000518721.1	-	15	1410	c.1183C>T	c.(1183-1185)Cac>Tac	p.H395Y	ASAP1_ENST00000357668.1_Missense_Mutation_p.H395Y	NM_001247996.1|NM_018482.3	NP_001234925.1|NP_060952.2	Q9ULH1	ASAP1_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 1	395	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cilium morphogenesis (GO:0060271)|regulation of ARF GTPase activity (GO:0032312)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|zinc ion binding (GO:0008270)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(22)|ovary(6)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	68						GCCTGAAAGTGATATGTTCTA	0.343																																					p.H395Y		Atlas-SNP	.											.	ASAP1	133	.	0			c.C1183T						.						123	112	115					8																	131146576		2202	4300	6502	SO:0001583	missense	50807	exon15			GAAAGTGATATGT	AB033075	CCDS6362.1, CCDS75788.1	8q24.1-q24.2	2013-01-11	2008-09-22	2008-09-22	ENSG00000153317	ENSG00000153317		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	2720	protein-coding gene	gene with protein product	"centaurin, beta 4"	605953	"development and differentiation enhancing factor 1"	DDEF1		9819391	Standard	NM_018482		Approved	PAP, KIAA1249, ZG14P, CENTB4	uc003yta.2	Q9ULH1	OTTHUMG00000164772	ENST00000518721.1:c.1183C>T	chr8.hg19:g.131146576G>A	ENSP00000429900:p.His395Tyr	80.0	0.0		92.0	25.0	NM_018482	B2RNV3	Missense_Mutation	SNP	ENST00000518721.1	hg19	CCDS6362.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.7|26.7	4.766829|4.766829	0.90020|0.90020	.|.	.|.	ENSG00000153317|ENSG00000153317	ENST00000343135;ENST00000357668;ENST00000518721|ENST00000524124	T;T|.	0.74526|.	-0.85;-0.85|.	5.95|5.95	5.95|5.95	0.96441|0.96441	Pleckstrin homology-type (1);Pleckstrin homology domain (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72011|0.72011	0.3408|0.3408	L|L	0.53671|0.53671	1.685|1.685	0.80722|0.80722	D|D	1|1	D;D;D|.	0.62365|.	0.991;0.991;0.988|.	D;D;D|.	0.74348|.	0.933;0.933;0.983|.	T|T	0.66881|0.66881	-0.5811|-0.5811	10|5	0.87932|.	D|.	0|.	.|.	19.3579|19.3579	0.94422|0.94422	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	395;395;398|.	B2RNV3;Q9ULH1;Q9ULH1-2|.	.;ASAP1_HUMAN;.|.	Y|L	398;395;395|215	ENSP00000350297:H395Y;ENSP00000429900:H395Y|.	ENSP00000344591:H398Y|.	H|S	-|-	1|2	0|0	ASAP1|ASAP1	131215758|131215758	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.959000|0.959000	0.62525|0.62525	9.230000|9.230000	0.95299|0.95299	2.811000|2.811000	0.96726|0.96726	0.655000|0.655000	0.94253|0.94253	CAC|TCA	.	.		0.343	ASAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380170.1	NM_018482		A	131146576	G	A	131146576	3	1	363	1	0	0	0	0	1	0	0	0	1010	1290	45	3	2270	3	ASAP1	8	131146576	Missense_Mutation	SNP	G	TCGA-ZP-A9CV-01A-11D-A382-10	25689957	131146576	15217446	47	50676										
JRK	8629	hgsc.bcm.edu	37	chr8	143746721	143746721	+	RNA	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	attcccctgggccttataggCgacgggcaggtgctggatgc	15	11	0	0			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr8:143746721C>T	ENST00000507178.2	-	0	1089							O75564	JERKY_HUMAN	Jrk homolog (mouse)							nucleus (GO:0005634)	DNA binding (GO:0003677)					all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)				gccttataggcgacgggcagg	0.577																																					p.A253T		Atlas-SNP	.											.	.	.	.	0			c.G757A						.						13	16	15					8																	143746721		1390	2781	4171			8629	exon2			TATAGGCGACGGG	AF072467	CCDS75796.1, CCDS75797.1	8q24.3	2014-03-28	2014-03-28			ENSG00000234616			6199	protein-coding gene	gene with protein product		603210	"jerky (mouse) homolog", "jerky homolog (mouse)"			9675132	Standard	NM_003724		Approved	JH8, jerky	uc003ywo.3	O75564			chr8.hg19:g.143746721C>T		101.0	0.0		132.0	27.0	NM_003724	O75565	Missense_Mutation	SNP	ENST00000507178.2	hg19																																																																																				.	.		0.577	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724		T	143746721	C	T	143746721	1	4	363	0	1	0	0	0	0	0	0	0	7973	768	27	1		1	JRK	8	143746721	RNA	SNP	C	TCGA-ZP-A9CV-01A-11D-A382-10	12600145	143746721	2617301	48	50677										
FAM75A3	727830	hgsc.bcm.edu	37	chr9	40702834	40702834	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	tcaagccaagcatcctcaggAtctggcctccaccccatcac	6	18	4	0			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr9:40702834A>T	ENST00000356699.5	+	4	520	c.491A>T	c.(490-492)gAt>gTt	p.D164V	SPATA31A3_ENST00000463536.1_3'UTR|RP11-395E19.5_ENST00000432614.1_lincRNA	NM_001083124.1	NP_001076593.1	Q5VYP0	S31A3_HUMAN	SPATA31 subfamily A, member 3	164	Pro-rich.				cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)		p.D164A(4)									CATCCTCAGGATCTGGCCTCC	0.587																																					p.D164V		Atlas-SNP	.											FAM75A3_ENST00000356699,NS,carcinoma,0,2	.	.	.	4	Substitution - Missense(4)	lung(4)	c.A491T						.						35	42	40					9																	40702834		1903	4100	6003	SO:0001583	missense	727830	exon4			CTCAGGATCTGGC			9p12	2012-10-15	2012-10-12	2012-10-12	ENSG00000147926				32003	protein-coding gene	gene with protein product			"family with sequence similarity 75, member A3"	FAM75A3		20850414	Standard	NM_001083124		Approved	OTTHUMG00000013164, DKFZp434B204	uc010mmj.3	Q5VYP0	OTTHUMG00000013164	ENST00000356699.5:c.491A>T	chr9.hg19:g.40702834A>T	ENSP00000349132:p.Asp164Val	233.0	0.0		211.0	40.0	NM_001083124		Missense_Mutation	SNP	ENST00000356699.5	hg19	CCDS47969.1	.	.	.	.	.	.	.	.	.	.	A	3.105	-0.183859	0.06340	.	.	ENSG00000147926	ENST00000356699	T	0.04551	3.6	2.19	-1.07	0.09968	.	3.930080	0.00819	N	0.001570	T	0.03305	0.0096	L	0.34521	1.04	0.09310	N	1	P	0.41910	0.764	B	0.33295	0.161	T	0.37865	-0.9687	10	0.16420	T	0.52	0.3962	2.2476	0.04035	0.2503:0.4255:0.0:0.3242	.	164	Q5VYP0	F75A3_HUMAN	V	164	ENSP00000349132:D164V	ENSP00000349132:D164V	D	+	2	0	FAM75A3	40692834	0.020000	0.18652	0.002000	0.10522	0.019000	0.09904	-0.177000	0.09796	-0.262000	0.09392	-0.836000	0.03065	GAT	.	.		0.587	SPATA31A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036919.1	NM_001083124		T	40702834	A	T	40702834	3	4	363	1	0	0	0	0	1	0	0	0	5629	333	12	4	505	4	FAM75A3	9	40702834	Missense_Mutation	SNP	A	TCGA-ZP-A9CV-01A-11D-A382-10		40702834	100510597	49	50678										
NTRK2	4915	hgsc.bcm.edu	37	chr9	87359941	87359941	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	ccacgaacagaagtaatgaaAtcccttccacagacgtcact	6	13	1	3			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr9:87359941A>T	ENST00000323115.4	+	10	1602	c.1249A>T	c.(1249-1251)Atc>Ttc	p.I417F	NTRK2_ENST00000304053.6_Missense_Mutation_p.I417F|NTRK2_ENST00000395882.1_Missense_Mutation_p.I417F|NTRK2_ENST00000277120.3_Missense_Mutation_p.I417F|NTRK2_ENST00000376214.1_Missense_Mutation_p.I417F|NTRK2_ENST00000376208.1_Missense_Mutation_p.I417F|NTRK2_ENST00000376213.1_Missense_Mutation_p.I417F|NTRK2_ENST00000395866.2_Missense_Mutation_p.I261F|NTRK2_ENST00000359847.3_Missense_Mutation_p.I417F			Q16620	NTRK2_HUMAN	neurotrophic tyrosine kinase, receptor, type 2	417					activation of adenylate cyclase activity (GO:0007190)|aging (GO:0007568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|central nervous system neuron development (GO:0021954)|cerebral cortex development (GO:0021987)|circadian rhythm (GO:0007623)|feeding behavior (GO:0007631)|glutamate secretion (GO:0014047)|learning (GO:0007612)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mechanoreceptor differentiation (GO:0042490)|negative regulation of anoikis (GO:2000811)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular junction development (GO:0007528)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peripheral nervous system neuron development (GO:0048935)|positive regulation of axonogenesis (GO:0050772)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|regulation of dendrite development (GO:0050773)|regulation of neurotransmitter secretion (GO:0046928)|regulation of protein kinase B signaling (GO:0051896)|regulation of Rac GTPase activity (GO:0032314)|response to auditory stimulus (GO:0010996)|retinal rod cell development (GO:0046548)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vasculogenesis (GO:0001570)	cell surface (GO:0009986)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endosome (GO:0005768)|excitatory synapse (GO:0060076)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|receptor complex (GO:0043235)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|brain-derived neurotrophic factor binding (GO:0048403)|brain-derived neurotrophic factor-activated receptor activity (GO:0060175)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	46					Amitriptyline(DB00321)	AAGTAATGAAATCCCTTCCAC	0.458										TSP Lung(25;0.17)																											p.I417F		Atlas-SNP	.											.	NTRK2	331	.	0			c.A1249T						.						191	177	181					9																	87359941		2203	4300	6503	SO:0001583	missense	4915	exon11			AATGAAATCCCTT	AF410902	CCDS6671.1, CCDS35050.1, CCDS35051.1, CCDS35052.1, CCDS35053.1	9q22.1	2013-01-11			ENSG00000148053	ENSG00000148053	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing"	8032	protein-coding gene	gene with protein product		600456				7789988	Standard	NM_001018065		Approved	TRKB	uc004anz.1	Q16620	OTTHUMG00000020120	ENST00000323115.4:c.1249A>T	chr9.hg19:g.87359941A>T	ENSP00000314586:p.Ile417Phe	183.0	0.0		175.0	44.0	NM_001018065	B1ANZ4|B4DFV9|Q16675|Q59GJ1|Q8WXJ5|Q8WXJ6|Q8WXJ7	Missense_Mutation	SNP	ENST00000323115.4	hg19	CCDS35050.1	.	.	.	.	.	.	.	.	.	.	A	11.48	1.652788	0.29336	.	.	ENSG00000148053	ENST00000376214;ENST00000376213;ENST00000395882;ENST00000376208;ENST00000304053;ENST00000277120;ENST00000323115;ENST00000359847;ENST00000395866	T;T;T;T;T;T;T;T;T	0.74315	-0.83;-0.83;-0.45;-0.44;-0.43;-0.83;-0.83;-0.45;-0.43	6.17	6.17	0.99709	.	0.549739	0.20726	N	0.086818	T	0.61924	0.2386	L	0.28115	0.83	0.46981	D	0.999279	B;B;B;B;B;B;B;B	0.28258	0.041;0.041;0.068;0.13;0.0;0.021;0.103;0.205	B;B;B;B;B;B;B;B	0.32342	0.023;0.077;0.093;0.068;0.0;0.021;0.035;0.144	T	0.60449	-0.7261	10	0.39692	T	0.17	.	7.7612	0.28953	0.8522:0.0:0.1478:0.0	.	261;417;417;417;417;417;463;417	B4DFV9;Q16620-3;Q16620-5;Q5VWE5;Q16620;Q16620-4;Q59GJ1;Q16620-2	.;.;.;.;NTRK2_HUMAN;.;.;.	F	417;417;417;417;417;417;417;417;261	ENSP00000365387:I417F;ENSP00000365386:I417F;ENSP00000379221:I417F;ENSP00000365381:I417F;ENSP00000306167:I417F;ENSP00000277120:I417F;ENSP00000314586:I417F;ENSP00000352906:I417F;ENSP00000379207:I261F	ENSP00000277120:I417F	I	+	1	0	NTRK2	86549761	0.987000	0.35691	0.956000	0.39512	0.429000	0.31625	2.992000	0.49417	2.371000	0.80710	0.533000	0.62120	ATC	.	.		0.458	NTRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052882.1			T	87359941	A	T	87359941	3	4	363	1	0	0	0	0	1	0	0	0	10716	101	4	4	1287	4	NTRK2	9	87359941	Missense_Mutation	SNP	A	TCGA-ZP-A9CV-01A-11D-A382-10	46657107	87359941	53853490	50	50679										
NCBP1	4686	hgsc.bcm.edu	37	chr9	100403939	100403963	+	Splice_Site	DEL	TACAGTGTATGTATGCAAAAGATTT	TACAGTGTATGTATGCAAAAGATTT	-													0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	aagatcttaaggcttctttgTacagtgtatgtatgcaaaag					rs141438765	byFrequency	TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	TACAGTGTATGTATGCAAAAGATTT	TACAGTGTATGTATGCAAAAGATTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr9:100403939_100403963delTACAGTGTATGTATGCAAAAGATTT	ENST00000375147.3	+	3	475_480	c.219_224delTACAGTGTATGTATGCAAAAGATTT	c.(217-225)tgtacagtg>tgg	p.CTV73fs		NM_002486.4	NP_002477.1	Q09161	NCBP1_HUMAN	nuclear cap binding protein subunit 1, 80kDa	73	MIF4G.				7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA cis splicing, via spliceosome (GO:0045292)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of viral transcription (GO:0050434)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|spliceosomal snRNP assembly (GO:0000387)|termination of RNA polymerase II transcription (GO:0006369)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|mRNA cap binding complex (GO:0005845)|nuclear cap binding complex (GO:0005846)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA cap binding (GO:0000339)			NS(1)|central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)	19		Acute lymphoblastic leukemia(62;0.158)				GGCTTCTTTGTACAGTGTATGTATGCAAAAGATTTATGAATCCAG	0.378																																					p.73_75del	Ovarian(36;879 898 2893 44212 50307)	Atlas-INDEL	.											.	NCBP1	64	.	0			c.218_224del						.																																			SO:0001630	splice_region_variant	4686	exon3			.	BC001450	CCDS6728.1	9q34.1	2010-01-26	2002-08-29		ENSG00000136937	ENSG00000136937			7658	protein-coding gene	gene with protein product		600469	"nuclear cap binding protein subunit 1, 80kD"	NCBP		7937105, 8812508	Standard	NM_002486		Approved	CBP80, Sto1	uc004axq.3	Q09161	OTTHUMG00000020332	ENST00000375147.3:c.224+1TACAGTGTATGTATGCAAAAGATTT>-	chr9.hg19:g.100403939_100403963delTACAGTGTATGTATGCAAAAGATTT		68.0	0.0		52.0	10.0	NM_002486	B2R718|Q59G76|Q5T1V0|Q5T7X2	Frame_Shift_Del	DEL	ENST00000375147.3	hg19	CCDS6728.1																																																																																			.	.		0.378	NCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053337.1	NM_002486	Frame_Shift_Del	-	100403963	TACAGTGTATGTATGCAAAAGATTT	-	100403939	8	5	363	1	0	1	0	1	0	0	1	0	10220	1644	57	0	229	0	NCBP1	9	100403939	Splice_Site	DEL	TACAGTGTATGTATGCAAAAGATTT	TCGA-ZP-A9CV-01A-11D-A382-10	13043998	100403939	40809492	51	50680										
C9orf30	91283	hgsc.bcm.edu	37	chr9	103212870	103212870	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	gtttcaaatagagaactgtgCgatgatgagaaagagttcat	11	4	2	4			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr9:103212870C>A	ENST00000395067.2	+	3	721	c.450C>A	c.(448-450)tgC>tgA	p.C150*	MSANTD3_ENST00000374885.1_3'UTR|MSANTD3-TMEFF1_ENST00000502978.1_Intron|TMEFF1_ENST00000334943.6_Intron|MSANTD3_ENST00000489377.1_3'UTR	NM_001198805.1|NM_001198806.1|NM_080655.2	NP_001185734.1|NP_001185735.1|NP_542386.1	Q96H12	MSD3_HUMAN	Myb/SANT-like DNA-binding domain containing 3	150										endometrium(2)|lung(2)	4						GAGAACTGTGCGATGATGAGA	0.368																																					p.C150X		Atlas-SNP	.											.	MSANTD3	10	.	0			c.C450A						.						55	55	55					9																	103212870		2203	4300	6503	SO:0001587	stop_gained	91283	exon3			ACTGTGCGATGAT	BC008993	CCDS6749.1, CCDS56579.1	9q31.1	2012-03-13	2012-03-13	2012-03-13	ENSG00000066697	ENSG00000066697			23370	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 30"	C9orf30			Standard	NM_080655		Approved	MGC17337		Q96H12	OTTHUMG00000020365	ENST00000395067.2:c.450C>A	chr9.hg19:g.103212870C>A	ENSP00000378506:p.Cys150*	144.0	0.0		134.0	54.0	NM_001198805	B2RC35|Q5T726|Q5T727|Q5T728	Nonsense_Mutation	SNP	ENST00000395067.2	hg19	CCDS6749.1	.	.	.	.	.	.	.	.	.	.	C	19.29	3.799719	0.70567	.	.	ENSG00000066697	ENST00000395067;ENST00000374886	.	.	.	5.55	3.68	0.42216	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-17.7043	6.2738	0.20969	0.0:0.7226:0.0:0.2774	.	.	.	.	X	150	.	ENSP00000364021:C150X	C	+	3	2	C9orf30	102252691	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.635000	0.46537	2.604000	0.88044	0.467000	0.42956	TGC	.	.		0.368	MSANTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053410.1	NM_080655		A	103212870	C	A	103212870	4	1	363	1	0	0	0	0	0	1	0	0	2480	776	27	1	456	1	C9orf30	9	103212870	Nonsense_Mutation	SNP	C	TCGA-ZP-A9CV-01A-11D-A382-10	2808931	103212870	38000561	52	50681										
KIAA0368	23392	hgsc.bcm.edu	37	chr9	114182326	114182326	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	gcagccagtagcagcaaataTctggaagggatatgatctga	12	7	2	2			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr9:114182326T>C	ENST00000338205.5	-	15	1749	c.1530A>G	c.(1528-1530)agA>agG	p.R510R	KIAA0368_ENST00000259335.4_Silent_p.R688R			Q5VYK3	ECM29_HUMAN	KIAA0368	516					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)				NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						GCAGCAAATATCTGGAAGGGA	0.358																																					p.R688R		Atlas-SNP	.											.	KIAA0368	144	.	0			c.A2064G						.						99	95	96					9																	114182326		1865	4105	5970	SO:0001819	synonymous_variant	23392	exon17			CAAATATCTGGAA	AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"ECM29 homolog (S. cerevisiae)"					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.1530A>G	chr9.hg19:g.114182326T>C		166.0	0.0		131.0	40.0	NM_001080398	O15074|Q8WU82	Silent	SNP	ENST00000338205.5	hg19																																																																																				.	.		0.358	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686		C	114182326	T	C	114182326	2	2	363	1	0	0	0	0	0	0	0	1	8180	1432	50	2		2	KIAA0368	9	114182326	Silent	SNP	T	TCGA-ZP-A9CV-01A-11D-A382-10	10969456	114182326	27031105	53	50682										
TNC	3371	hgsc.bcm.edu	37	chr9	117848857	117848857	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	ccgcccgtctacacagcggcCacgattgtgacagtcagcag	11	15	2	1			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr9:117848857C>T	ENST00000350763.4	-	3	1564	c.1153G>A	c.(1153-1155)Ggc>Agc	p.G385S	TNC_ENST00000346706.3_Missense_Mutation_p.G385S|TNC_ENST00000340094.3_Missense_Mutation_p.G385S|TNC_ENST00000423613.2_Missense_Mutation_p.G385S|TNC_ENST00000542877.1_Missense_Mutation_p.G385S|TNC_ENST00000345230.3_Missense_Mutation_p.G385S|TNC_ENST00000341037.4_Missense_Mutation_p.G385S|TNC_ENST00000535648.1_Missense_Mutation_p.G385S|TNC_ENST00000537320.1_Missense_Mutation_p.G385S	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	385	EGF-like 8. {ECO:0000255|PROSITE- ProRule:PRU00076}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)			NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						ACACAGCGGCCACGATTGTGA	0.607																																					p.G385S		Atlas-SNP	.											.	TNC	282	.	0			c.G1153A						.						127	111	117					9																	117848857		2203	4300	6503	SO:0001583	missense	3371	exon3			AGCGGCCACGATT		CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	5318	protein-coding gene	gene with protein product	"hexabrachion (tenascin)"	187380	"hexabrachion (tenascin C, cytotactin)", "deafness, autosomal dominant 56"	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.1153G>A	chr9.hg19:g.117848857C>T	ENSP00000265131:p.Gly385Ser	43.0	0.0		61.0	8.0	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	ENST00000350763.4	hg19	CCDS6811.1	.	.	.	.	.	.	.	.	.	.	C	18.39	3.613747	0.66672	.	.	ENSG00000041982	ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000442945;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877	D;D;D;D;D;D;D;D;D	0.85411	-1.98;-1.98;-1.98;-1.98;-1.98;-1.98;-1.98;-1.98;-1.98	5.44	5.44	0.79542	EGF, extracellular (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.93979	0.8072	M	0.90145	3.09	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.94737	0.7915	10	0.87932	D	0	.	18.6123	0.91290	0.0:1.0:0.0:0.0	.	385;385	E9PC84;P24821	.;TENA_HUMAN	S	385	ENSP00000344400:G385S;ENSP00000438152:G385S;ENSP00000344555:G385S;ENSP00000345861:G385S;ENSP00000265131:G385S;ENSP00000339553:G385S;ENSP00000411406:G385S;ENSP00000443478:G385S;ENSP00000442242:G385S	ENSP00000344400:G385S	G	-	1	0	TNC	116888678	1.000000	0.71417	0.964000	0.40570	0.015000	0.08874	7.745000	0.85046	2.712000	0.92718	0.563000	0.77884	GGC	.	.		0.607	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160		T	117848857	C	T	117848857	3	4	363	1	0	0	0	0	1	0	0	0	16285	594	21	3	5556	3	TNC	9	117848857	Missense_Mutation	SNP	C	TCGA-ZP-A9CV-01A-11D-A382-10	3666531	117848857	23364574	54	50683										
SMNDC1	10285	hgsc.bcm.edu	37	chr10	112055050	112055050	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	gccatttcactttctggtccTctctttcctgctcaagttct	5	14	5	0			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr10:112055050T>C	ENST00000369603.5	-	5	718	c.515A>G	c.(514-516)gAg>gGg	p.E172G	SMNDC1_ENST00000471297.1_5'Flank|SMNDC1_ENST00000369592.1_Missense_Mutation_p.E172G	NM_005871.3	NP_005862.1	O75940	SPF30_HUMAN	survival motor neuron domain containing 1	172					apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(1)|lung(2)|skin(1)	4		Breast(234;0.174)		Epithelial(162;6.86e-05)|all cancers(201;0.00149)|BRCA - Breast invasive adenocarcinoma(275;0.119)		TTTCTGGTCCTCTCTTTCCTG	0.343																																					p.E172G		Atlas-SNP	.											.	SMNDC1	9	.	0			c.A515G						.						125	114	118					10																	112055050		2202	4299	6501	SO:0001583	missense	10285	exon5			TGGTCCTCTCTTT	AF083385	CCDS7565.1	10q23	2013-01-23			ENSG00000119953	ENSG00000119953		"Tudor domain containing"	16900	protein-coding gene	gene with protein product	"splicing factor 30, survival of motor neuron-related", "tudor domain containing 16C"	603519				9731529, 9817934	Standard	NM_005871		Approved	SPF30, SMNR, TDRD16C	uc001kzc.4	O75940	OTTHUMG00000019036	ENST00000369603.5:c.515A>G	chr10.hg19:g.112055050T>C	ENSP00000358616:p.Glu172Gly	116.0	0.0		103.0	23.0	NM_005871	B2RA27|D3DRB1|Q5T3K6	Missense_Mutation	SNP	ENST00000369603.5	hg19	CCDS7565.1	.	.	.	.	.	.	.	.	.	.	T	29.7	5.026528	0.93518	.	.	ENSG00000119953	ENST00000369603;ENST00000369592	D;D	0.88818	-2.43;-2.43	5.76	5.76	0.90799	.	0.113338	0.64402	D	0.000004	D	0.94689	0.8287	M	0.83118	2.625	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	D	0.95248	0.8357	10	0.72032	D	0.01	-16.0076	16.0701	0.80919	0.0:0.0:0.0:1.0	.	172	O75940	SPF30_HUMAN	G	172	ENSP00000358616:E172G;ENSP00000358605:E172G	ENSP00000358605:E172G	E	-	2	0	SMNDC1	112045040	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.008000	0.88588	2.196000	0.70406	0.533000	0.62120	GAG	.	.		0.343	SMNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050325.2	NM_005871		C	112055050	T	C	112055050	3	2	363	1	0	0	0	0	1	0	0	0	14814	1551	54	2	209	2	SMNDC1	10	112055050	Missense_Mutation	SNP	T	TCGA-ZP-A9CV-01A-11D-A382-10		112055050	23479697	55	50684										
TUBGCP2	10844	hgsc.bcm.edu	37	chr10	135101696	135101696	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	cgcagcgccagctccaggagCgcttccaggcgagggggcgt	17	14	0	0			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr10:135101696C>T	ENST00000252936.3	-	10	1698	c.1659G>A	c.(1657-1659)gcG>gcA	p.A553A	TUBGCP2_ENST00000543663.1_Silent_p.A581A|TUBGCP2_ENST00000417178.2_Silent_p.A423A|TUBGCP2_ENST00000368563.2_Silent_p.A553A|TUBGCP2_ENST00000368562.1_Silent_p.A146A			Q9BSJ2	GCP2_HUMAN	tubulin, gamma complex associated protein 2	553					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|protein complex assembly (GO:0006461)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(16)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	35		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.87e-06)|all cancers(32;8.98e-06)|Epithelial(32;1.15e-05)		GCTCCAGGAGCGCTTCCAGGC	0.667																																					p.A581A		Atlas-SNP	.											.	TUBGCP2	79	.	0			c.G1743A						.						61	59	60					10																	135101696		2203	4300	6503	SO:0001819	synonymous_variant	10844	exon12			CAGGAGCGCTTCC	AF042379	CCDS7676.1, CCDS58104.1, CCDS58105.1	10q26.3	2008-07-28			ENSG00000130640	ENSG00000130640			18599	protein-coding gene	gene with protein product						9566967	Standard	NM_001256617		Approved	GCP2, Spc97p, SPBC97	uc010qvc.2	Q9BSJ2	OTTHUMG00000019319	ENST00000252936.3:c.1659G>A	chr10.hg19:g.135101696C>T		109.0	0.0		92.0	6.0	NM_001256617	B4DM18|B7ZKL8|F5H4E0|F5H4L0|O43632|Q5VWX7	Silent	SNP	ENST00000252936.3	hg19	CCDS7676.1																																																																																			.	.		0.667	TUBGCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051148.1			T	135101696	C	T	135101696	2	4	363	1	0	0	0	0	0	0	0	1	16781	755	27	1		1	TUBGCP2	10	135101696	Silent	SNP	C	TCGA-ZP-A9CV-01A-11D-A382-10	23046646	135101696	433051	56	50685										
MUC2	4583	hgsc.bcm.edu	37	chr11	1092602	1092619	+	In_Frame_Del	DEL	CCACCACTCCCAGCCCTC	CCACCACTCCCAGCCCTC	-													0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	caccactcccagccctccaaCcaccactcccagccctccaa					rs201595190|rs201608750|rs547682241	byFrequency	TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	CCACCACTCCCAGCCCTC	CCACCACTCCCAGCCCTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr11:1092602_1092619delCCACCACTCCCAGCCCTC	ENST00000441003.2	+	30	4448_4465	c.4421_4438delCCACCACTCCCAGCCCTC	c.(4420-4440)accaccactcccagccctcca>aca	p.TTPSPP1475del	MUC2_ENST00000359061.5_In_Frame_Del_p.TTPSPP1476del|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_5'Flank	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4210	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	agccctccaaccaccactcccagccctccaaccaccac	0.628																																					p.1474_1479del		Atlas-INDEL	.											.	MUC2	614	.	0			c.4420_4437del						.			764,1992		44,676,658						-2.6	0		dbSNP_134	244	1546,3660		46,1454,1103	no	coding	MUC2	NM_002457.2		90,2130,1761	A1A1,A1R,RR		29.6965,27.7213,29.0128				2310,5652				SO:0001651	inframe_deletion	4583	exon30			.	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4421_4438delCCACCACTCCCAGCCCTC	chr11.hg19:g.1092602_1092619delCCACCACTCCCAGCCCTC	ENSP00000415183:p.Thr1475_Pro1480del	110.0	0.0		83.0	11.0	NM_002457	Q14878	In_Frame_Del	DEL	ENST00000441003.2	hg19																																																																																				.	.		0.628	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		-	1092619	CCACCACTCCCAGCCCTC	-	1092602	7	5	363	1	0	1	0	1	0	0	0	0	9984	507	18	0	4539	0	MUC2	11	1092602	In_Frame_Del	DEL	CCACCACTCCCAGCCCTC	TCGA-ZP-A9CV-01A-11D-A382-10		1092602	133913914	57	50686										
OR5P3	120066	hgsc.bcm.edu	37	chr11	7847513	7847513	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	cacagtggtgtcatttccagTccccatctatattgggaatg	9	10	2	0			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr11:7847513T>C	ENST00000328375.1	-	1	6	c.7A>G	c.(7-9)Act>Gct	p.T3A	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153445.1	NP_703146.1	Q8WZ94	OR5P3_HUMAN	olfactory receptor, family 5, subfamily P, member 3	3						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(2)|upper_aerodigestive_tract(1)	15				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		TCATTTCCAGTCCCCATCTAT	0.328																																					p.T3A		Atlas-SNP	.											.	OR5P3	44	.	0			c.A7G						.						34	33	34					11																	7847513		2006	4067	6073	SO:0001583	missense	120066	exon1			TTCCAGTCCCCAT	AF158377	CCDS7783.1	11p15.4	2012-08-09			ENSG00000182334	ENSG00000182334		"GPCR / Class A : Olfactory receptors"	14784	protein-coding gene	gene with protein product							Standard	NM_153445		Approved	JCG1	uc010rbg.2	Q8WZ94	OTTHUMG00000165669	ENST00000328375.1:c.7A>G	chr11.hg19:g.7847513T>C	ENSP00000332068:p.Thr3Ala	61.0	0.0		64.0	24.0	NM_153445	Q6IFE1|Q8NGM2	Missense_Mutation	SNP	ENST00000328375.1	hg19	CCDS7783.1	.	.	.	.	.	.	.	.	.	.	T	2.387	-0.340713	0.05243	.	.	ENSG00000182334	ENST00000328375	T	0.00573	6.48	5.1	-5.8	0.02347	.	1.251370	0.05929	U	0.634871	T	0.00300	0.0009	N	0.04994	-0.135	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.42799	-0.9430	10	0.09590	T	0.72	-5.849	3.7724	0.08647	0.2374:0.4727:0.121:0.169	.	3	Q8WZ94	OR5P3_HUMAN	A	3	ENSP00000332068:T3A	ENSP00000332068:T3A	T	-	1	0	OR5P3	7804089	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.155000	0.03163	-0.941000	0.03700	0.477000	0.44152	ACT	.	.		0.328	OR5P3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385697.1	NM_153445		C	7847513	T	C	7847513	3	2	363	1	0	0	0	0	1	0	0	0	11188	1667	58	2	931	2	OR5P3	11	7847513	Missense_Mutation	SNP	T	TCGA-ZP-A9CV-01A-11D-A382-10	6754911	7847513	127159003	58	50687										
ABCC8	6833	hgsc.bcm.edu	37	chr11	17496572	17496572	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	cttggagctctgacttccccAtcctgcagggagagacagtc	11	13	1	2			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr11:17496572A>G	ENST00000389817.3	-	2	219	c.151T>C	c.(151-153)Tgg>Cgg	p.W51R	ABCC8_ENST00000302539.4_Missense_Mutation_p.W51R			Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 8	51					carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium ion transmembrane transporter activity (GO:0015079)|sulfonylurea receptor activity (GO:0008281)			NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(38)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	67				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Chlorpropamide(DB00672)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Gliquidone(DB01251)|Glyburide(DB01016)|Glycodiazine(DB01382)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)|Tolbutamide(DB01124)	TGACTTCCCCATCCTGCAGGG	0.577																																					p.W51R		Atlas-SNP	.											.	ABCC8	170	.	0			c.T151C						.						153	96	116					11																	17496572		2200	4293	6493	SO:0001583	missense	6833	exon2			TTCCCCATCCTGC	L78207	CCDS31437.1, CCDS73264.1	11p15.1	2014-09-17			ENSG00000006071	ENSG00000006071		"ATP binding cassette transporters / subfamily C"	59	protein-coding gene	gene with protein product	"sulfonylurea receptor (hyperinsulinemia)"	600509		SUR, HRINS		7920639, 7716548	Standard	NM_000352		Approved	HI, PHHI, SUR1, MRP8, ABC36, HHF1, TNDM2	uc001mnc.3	Q09428	OTTHUMG00000166316	ENST00000389817.3:c.151T>C	chr11.hg19:g.17496572A>G	ENSP00000374467:p.Trp51Arg	93.0	0.0		108.0	34.0	NM_000352	A6NMX8|E3UYX6|O75948|Q16583	Missense_Mutation	SNP	ENST00000389817.3	hg19	CCDS31437.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.944147	0.73672	.	.	ENSG00000006071	ENST00000389817;ENST00000302539;ENST00000379493	D;D	0.96104	-3.91;-3.91	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	D	0.95617	0.8575	M	0.63843	1.955	0.80722	D	1	P;D	0.56035	0.931;0.974	P;P	0.58577	0.566;0.841	D	0.94106	0.7366	10	0.02654	T	1	.	15.0494	0.71854	1.0:0.0:0.0:0.0	.	51;51	B7Z4N0;Q09428	.;ABCC8_HUMAN	R	51;51;65	ENSP00000374467:W51R;ENSP00000303960:W51R	ENSP00000303960:W51R	W	-	1	0	ABCC8	17453148	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	9.325000	0.96381	1.955000	0.56771	0.477000	0.44152	TGG	.	.		0.577	ABCC8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389093.1	NM_000352		G	17496572	A	G	17496572	3	3	363	1	0	0	0	0	1	0	0	0	58	217	8	2	4746	2	ABCC8	11	17496572	Missense_Mutation	SNP	A	TCGA-ZP-A9CV-01A-11D-A382-10	9649059	17496572	117509944	59	50688										
C11orf41	25758	hgsc.bcm.edu	37	chr11	33628362	33628362	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	gagtcatcggcagtcctcaaCggcgaggtaagtgcctggag	15	10	2	0	rs375293606		TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr11:33628362C>T	ENST00000321505.4	+	13	4344	c.4164C>T	c.(4162-4164)aaC>aaT	p.N1388N	KIAA1549L_ENST00000389726.3_Silent_p.N1394N			Q6ZVL6	K154L_HUMAN	KIAA1549-like	1388						integral component of membrane (GO:0016021)		p.N1388N(1)									CAGTCCTCAACGGCGAGGTAA	0.587													C|||	1	0.000199681	0	0.0014	5008	,	,		17845	0		0	False		,,,				2504	0				p.N1388N		Atlas-SNP	.											C11orf41_ENST00000321505,rectum,carcinoma,0,1	.	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4164T						.	C		5,4069		0,5,2032	20	22	21		4164	-6.9	0.9	11		21	1,8395		0,1,4197	no	coding-synonymous	C11orf41	NM_012194.2		0,6,6229	TT,TC,CC		0.0119,0.1227,0.0481		1388/1850	33628362	6,12464	2037	4198	6235	SO:0001819	synonymous_variant	25758	exon13			CCTCAACGGCGAG	U10991	CCDS44565.1, CCDS44565.2	11p13	2012-08-09	2012-08-09	2012-08-09	ENSG00000110427	ENSG00000110427			24836	protein-coding gene	gene with protein product		612297	"chromosome 11 open reading frame 69", "chromosome 11 open reading frame 41"	C11orf69, C11orf41			Standard	NM_012194		Approved	G2, MGC34830	uc021qfs.1	Q6ZVL6	OTTHUMG00000150410	ENST00000321505.4:c.4164C>T	chr11.hg19:g.33628362C>T		116.0	0.0		79.0	23.0	NM_012194	B0QYU0	Silent	SNP	ENST00000321505.4	hg19	CCDS44565.2	.	.	.	.	.	.	.	.	.	.	C	4.733	0.136376	0.09032	0.001227	1.19E-4	ENSG00000110427	ENST00000526400	.	.	.	5.42	-6.9	0.01655	.	.	.	.	.	T	0.59542	0.2201	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63350	-0.6657	4	.	.	.	-17.5858	13.4248	0.61020	0.0:0.486:0.0:0.514	.	.	.	.	M	786	.	.	T	+	2	0	C11orf41	33584938	0.001000	0.12720	0.917000	0.36280	0.325000	0.28411	-2.225000	0.01212	-1.148000	0.02847	-0.263000	0.10527	ACG	.	.		0.587	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194		T	33628362	C	T	33628362	2	4	363	1	0	0	0	0	0	0	0	1	1642	535	19	1		1	C11orf41	11	33628362	Silent	SNP	C	TCGA-ZP-A9CV-01A-11D-A382-10	16131790	33628362	101378154	60	50689										
OR5M3	219482	hgsc.bcm.edu	37	chr11	56237304	56237304	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	ttctgctgagcgcattcgcaGaatggcaatgaggatgaata	12	7	1	4			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr11:56237304G>A	ENST00000312240.2	-	1	710	c.670C>T	c.(670-672)Ctg>Ttg	p.L224L		NM_001004742.2	NP_001004742.2	Q8NGP4	OR5M3_HUMAN	olfactory receptor, family 5, subfamily M, member 3	224						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(7)|lung(15)|ovary(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	37	Esophageal squamous(21;0.00448)					CGCATTCGCAGAATGGCAATG	0.403																																					p.L224L		Atlas-SNP	.											.	OR5M3	103	.	0			c.C670T						.						69	68	68					11																	56237304		2201	4292	6493	SO:0001819	synonymous_variant	219482	exon1			TTCGCAGAATGGC	AB065746	CCDS31532.1	11q11	2012-08-09			ENSG00000174937	ENSG00000174937		"GPCR / Class A : Olfactory receptors"	14806	protein-coding gene	gene with protein product							Standard	NM_001004742		Approved		uc010rjk.2	Q8NGP4	OTTHUMG00000166875	ENST00000312240.2:c.670C>T	chr11.hg19:g.56237304G>A		229.0	0.0		208.0	69.0	NM_001004742	B2RNM7|Q6IEW4|Q96RC0	Silent	SNP	ENST00000312240.2	hg19	CCDS31532.1																																																																																			.	.		0.403	OR5M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391639.1	NM_001004742		A	56237304	G	A	56237304	2	1	363	1	0	0	0	0	0	0	0	1	11184	933	33	3		3	OR5M3	11	56237304	Silent	SNP	G	TCGA-ZP-A9CV-01A-11D-A382-10	22608942	56237304	78769212	61	50690										
SLC43A1	8501	hgsc.bcm.edu	37	chr11	57258721	57258721	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	catctccgaggacagtgcccTgagttggggcgtccacgcag	14	13	1	1			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr11:57258721T>C	ENST00000278426.3	-	11	1524	c.1169A>G	c.(1168-1170)cAg>cGg	p.Q390R	SLC43A1_ENST00000528450.1_Missense_Mutation_p.Q390R|SLC43A1_ENST00000533515.1_5'Flank	NM_003627.5	NP_003618.1			solute carrier family 43 (amino acid system L transporter), member 1											breast(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	19						GACAGTGCCCTGAGTTGGGGC	0.572																																					p.Q390R		Atlas-SNP	.											.	SLC43A1	48	.	0			c.A1169G						.						57	51	53					11																	57258721		2201	4296	6497	SO:0001583	missense	8501	exon11			GTGCCCTGAGTTG	AF045584	CCDS7958.1	11q12.1	2013-07-17	2013-07-17	2003-09-12	ENSG00000149150	ENSG00000149150		"Solute carriers"	9225	protein-coding gene	gene with protein product		603733	"prostate cancer overexpressed gene 1"	POV1		9255310, 9722952	Standard	NM_003627		Approved	R00504, PB39	uc001nkk.3	O75387	OTTHUMG00000167030	ENST00000278426.3:c.1169A>G	chr11.hg19:g.57258721T>C	ENSP00000278426:p.Gln390Arg	130.0	0.0		118.0	40.0	NM_001198810		Missense_Mutation	SNP	ENST00000278426.3	hg19	CCDS7958.1	.	.	.	.	.	.	.	.	.	.	T	13.37	2.218096	0.39201	.	.	ENSG00000149150	ENST00000278426;ENST00000528450	T;T	0.21734	1.99;1.99	5.43	3.05	0.35203	Major facilitator superfamily domain, general substrate transporter (1);	1.192340	0.06122	N	0.668993	T	0.10852	0.0265	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.37619	-0.9698	10	0.20046	T	0.44	-2.6129	5.4052	0.16318	0.0:0.0915:0.1766:0.732	.	390	O75387	LAT3_HUMAN	R	390	ENSP00000278426:Q390R;ENSP00000435673:Q390R	ENSP00000278426:Q390R	Q	-	2	0	SLC43A1	57015297	0.001000	0.12720	0.110000	0.21437	0.193000	0.23685	0.841000	0.27613	0.345000	0.23873	0.454000	0.30748	CAG	.	.		0.572	SLC43A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392541.1	NM_003627		C	57258721	T	C	57258721	3	2	363	1	0	0	0	0	1	0	0	0	14647	1580	55	2	530	2	SLC43A1	11	57258721	Missense_Mutation	SNP	T	TCGA-ZP-A9CV-01A-11D-A382-10	1021417	57258721	77747795	62	50691										
MS4A5	64232	hgsc.bcm.edu	37	chr11	60197289	60197289	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	aattatttgctagaaaaatgAaaatcttaggggtaagtaag	9	2	1	2			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr11:60197289A>G	ENST00000300190.2	+	1	228	c.142A>G	c.(142-144)Aaa>Gaa	p.K48E	MS4A5_ENST00000534071.1_3'UTR	NM_023945.2	NP_076434.2	Q9H3V2	MS4A5_HUMAN	membrane-spanning 4-domains, subfamily A, member 5	48						integral component of membrane (GO:0016021)				large_intestine(7)|lung(7)|ovary(1)|skin(1)	16						TAGAAAAATGAAAATCTTAGG	0.413																																					p.K48E		Atlas-SNP	.											.	MS4A5	35	.	0			c.A142G						.						57	62	60					11																	60197289		2203	4300	6503	SO:0001583	missense	64232	exon1			AAAATGAAAATCT	AB013103	CCDS7987.1	11q12	2008-03-25			ENSG00000166930	ENSG00000166930			13374	protein-coding gene	gene with protein product		606499				11245982, 11401424	Standard	NM_023945		Approved	CD20L2	uc001npo.3	Q9H3V2	OTTHUMG00000167613	ENST00000300190.2:c.142A>G	chr11.hg19:g.60197289A>G	ENSP00000300190:p.Lys48Glu	86.0	0.0		77.0	28.0	NM_023945	Q9BZH1	Missense_Mutation	SNP	ENST00000300190.2	hg19	CCDS7987.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	8.380|8.380	0.837376|0.837376	0.16891|0.16891	.|.	.|.	ENSG00000166930|ENSG00000166930	ENST00000528905;ENST00000528093|ENST00000300190	.|T	.|0.14766	.|2.48	4.66|4.66	3.49|3.49	0.39957|0.39957	.|.	.|0.380794	.|0.27595	.|N	.|0.018664	T|T	0.08935|0.08935	0.0221|0.0221	N|N	0.20986|0.20986	0.625|0.625	0.22591|0.22591	N|N	0.998956|0.998956	.|B	.|0.21225	.|0.053	.|B	.|0.20184	.|0.028	T|T	0.24190|0.24190	-1.0167|-1.0167	5|10	.|0.46703	.|T	.|0.11	-5.4078|-5.4078	7.4129|7.4129	0.27027|0.27027	0.8993:0.0:0.1007:0.0|0.8993:0.0:0.1007:0.0	.|.	.|48	.|Q9H3V2	.|MS4A5_HUMAN	G|E	21;14|48	.|ENSP00000300190:K48E	.|ENSP00000300190:K48E	E|K	+|+	2|1	0|0	MS4A5|MS4A5	59953865|59953865	0.997000|0.997000	0.39634|0.39634	0.941000|0.941000	0.38009|0.38009	0.124000|0.124000	0.20399|0.20399	2.321000|2.321000	0.43805|0.43805	0.872000|0.872000	0.35775|0.35775	0.383000|0.383000	0.25322|0.25322	GAA|AAA	.	.		0.413	MS4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395392.1			G	60197289	A	G	60197289	3	3	363	1	0	0	0	0	1	0	0	0	9872	247	9	2	144	2	MS4A5	11	60197289	Missense_Mutation	SNP	A	TCGA-ZP-A9CV-01A-11D-A382-10	2938568	60197289	74809227	63	50692										
RCOR2	283248	hgsc.bcm.edu	37	chr11	63680390	63680390	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	ccctccagggcttggcgcagGctgctgttcgtctgcttcat	12	14	2	0			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr11:63680390G>A	ENST00000301459.4	-	9	1308	c.921C>T	c.(919-921)agC>agT	p.S307S	RCOR2_ENST00000473926.2_5'Flank	NM_173587.3	NP_775858.2	Q8IZ40	RCOR2_HUMAN	REST corepressor 2	307					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			kidney(2)|large_intestine(3)|liver(1)|lung(5)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	17						CTTGGCGCAGGCTGCTGTTCG	0.587																																					p.S307S		Atlas-SNP	.											.	RCOR2	43	.	0			c.C921T						.						56	44	48					11																	63680390		2201	4297	6498	SO:0001819	synonymous_variant	283248	exon9			GCGCAGGCTGCTG	BC010608	CCDS8052.1	11q13.1	2008-02-05			ENSG00000167771	ENSG00000167771			27455	protein-coding gene	gene with protein product						12477932	Standard	NM_173587		Approved		uc001nyc.3	Q8IZ40	OTTHUMG00000150472	ENST00000301459.4:c.921C>T	chr11.hg19:g.63680390G>A		104.0	0.0		74.0	27.0	NM_173587	Q96FP3	Silent	SNP	ENST00000301459.4	hg19	CCDS8052.1																																																																																			.	.		0.587	RCOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318233.1	NM_173587		A	63680390	G	A	63680390	2	1	363	1	0	0	0	0	0	0	0	1	13198	1194	42	3		3	RCOR2	11	63680390	Silent	SNP	G	TCGA-ZP-A9CV-01A-11D-A382-10	3483101	63680390	71326126	64	50693										
RPS6KA4	8986	hgsc.bcm.edu	37	chr11	64137353	64137353	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	tcctgcgacctctggagcctGggcgtcattctggtatggga	14	11	3	0			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr11:64137353G>A	ENST00000334205.4	+	14	1850	c.1785G>A	c.(1783-1785)ctG>ctA	p.L595L	MIR1237_ENST00000408346.1_RNA|RPS6KA4_ENST00000294261.4_Intron|RPS6KA4_ENST00000528057.1_Silent_p.L588L	NM_003942.2	NP_003933.1	O75676	KS6A4_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 4	595	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-S28 phosphorylation (GO:0043988)|histone phosphorylation (GO:0016572)|inflammatory response (GO:0006954)|interleukin-1-mediated signaling pathway (GO:0070498)|intracellular signal transduction (GO:0035556)|negative regulation of cytokine production (GO:0001818)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|mitogen-activated protein kinase p38 binding (GO:0048273)|protein serine/threonine kinase activity (GO:0004674)|ribosomal protein S6 kinase activity (GO:0004711)			breast(1)|endometrium(3)|lung(7)|ovary(1)|prostate(1)	13						TCTGGAGCCTGGGCGTCATTC	0.687																																					p.L595L		Atlas-SNP	.											.	RPS6KA4	85	.	0			c.G1785A						.						17	18	18					11																	64137353		2145	4185	6330	SO:0001819	synonymous_variant	8986	exon14			GAGCCTGGGCGTC	AJ010119	CCDS8073.1, CCDS73313.1	11q11-q13	2011-04-05	2002-08-29		ENSG00000162302	ENSG00000162302			10433	protein-coding gene	gene with protein product		603606	"ribosomal protein S6 kinase, 90kD, polypeptide 4"			9792677, 9687510	Standard	XM_005274379		Approved	RSK-B, MSK2	uc001oae.3	O75676	OTTHUMG00000046094	ENST00000334205.4:c.1785G>A	chr11.hg19:g.64137353G>A		75.0	0.0		60.0	21.0	NM_003942	A8K7Z8|O75585|Q53ES8	Silent	SNP	ENST00000334205.4	hg19	CCDS8073.1																																																																																			.	.		0.687	RPS6KA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106246.2	NM_003942		A	64137353	G	A	64137353	2	1	363	1	0	0	0	0	0	0	0	1	13668	1335	47	3		3	RPS6KA4	11	64137353	Silent	SNP	G	TCGA-ZP-A9CV-01A-11D-A382-10	456963	64137353	70869163	65	50694										
GPR152	390212	hgsc.bcm.edu	37	chr11	67220107	67220107	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	ccaggaagaccgtgtcccagCcaccttgggggtaggagtcc	14	13	0	1			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr11:67220107C>G	ENST00000312457.2	-	1	93	c.89G>C	c.(88-90)gGc>gCc	p.G30A	CABP4_ENST00000542025.2_3'UTR|CABP4_ENST00000325656.5_5'Flank|CABP4_ENST00000438189.2_5'UTR	NM_206997.1	NP_996880.1	Q8TDT2	GP152_HUMAN	G protein-coupled receptor 152	30						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	16			BRCA - Breast invasive adenocarcinoma(15;8.18e-06)			CGTGTCCCAGCCACCTTGGGG	0.657																																					p.G30A	Pancreas(102;800 1581 2723 7382 33622)	Atlas-SNP	.											.	GPR152	41	.	0			c.G89C						.						49	50	49					11																	67220107		2196	4289	6485	SO:0001583	missense	390212	exon1			TCCCAGCCACCTT	AY255600	CCDS8165.1	11q13.2	2013-09-20			ENSG00000175514	ENSG00000175514		"GPCR / Class A : Orphans"	23622	protein-coding gene	gene with protein product						12679517	Standard	NM_206997		Approved	PGR5	uc001olm.3	Q8TDT2	OTTHUMG00000168032	ENST00000312457.2:c.89G>C	chr11.hg19:g.67220107C>G	ENSP00000310255:p.Gly30Ala	184.0	0.0		222.0	64.0	NM_206997	Q0VD88|Q86SM0	Missense_Mutation	SNP	ENST00000312457.2	hg19	CCDS8165.1	.	.	.	.	.	.	.	.	.	.	C	12.38	1.921591	0.33908	.	.	ENSG00000175514	ENST00000312457	T	0.14516	2.5	5.28	4.36	0.52297	.	0.174032	0.27522	N	0.019000	T	0.06962	0.0177	N	0.19112	0.55	0.80722	D	1	P	0.38597	0.639	B	0.28916	0.096	T	0.40289	-0.9571	10	0.16420	T	0.52	.	10.8249	0.46627	0.3444:0.6556:0.0:0.0	.	30	Q8TDT2	GP152_HUMAN	A	30	ENSP00000310255:G30A	ENSP00000310255:G30A	G	-	2	0	GPR152	66976683	0.974000	0.33945	1.000000	0.80357	0.988000	0.76386	1.790000	0.38734	1.440000	0.47531	0.561000	0.74099	GGC	.	.		0.657	GPR152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397623.1			G	67220107	C	G	67220107	3	3	363	1	0	0	0	0	1	0	0	0	6666	739	26	4	1327	4	GPR152	11	67220107	Missense_Mutation	SNP	C	TCGA-ZP-A9CV-01A-11D-A382-10	3082754	67220107	67786409	66	50695										
LRRC32	2615	hgsc.bcm.edu	37	chr11	76372166	76372166	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	aggcgagtcagactgttctcCgccagtgagagggtatgcag	15	9	2	2			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr11:76372166C>T	ENST00000407242.2	-	3	713	c.471G>A	c.(469-471)gcG>gcA	p.A157A	LRRC32_ENST00000404995.1_Silent_p.A157A|AP001189.4_ENST00000447519.1_RNA|LRRC32_ENST00000260061.5_Silent_p.A157A|LRRC32_ENST00000464145.1_Intron	NM_005512.2	NP_005503.1	Q14392	LRC32_HUMAN	leucine rich repeat containing 32	157					negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of cytokine secretion (GO:0050710)|positive regulation of gene expression (GO:0010628)	integral component of plasma membrane (GO:0005887)		p.A157A(1)		endometrium(1)|large_intestine(3)|lung(26)|upper_aerodigestive_tract(1)	31						GACTGTTCTCCGCCAGTGAGA	0.642																																					p.A157A		Atlas-SNP	.											.	LRRC32	74	.	1	Substitution - coding silent(1)	lung(1)	c.G471A						.						66	68	67					11																	76372166		2200	4292	6492	SO:0001819	synonymous_variant	2615	exon3			GTTCTCCGCCAGT	Z24680	CCDS8245.1	11q13.5-q14	2008-02-05	2005-02-25	2005-02-25	ENSG00000137507	ENSG00000137507			4161	protein-coding gene	gene with protein product		137207	"glycoprotein A repetitions predominant"	D11S833E, GARP		8180135, 1543912	Standard	NM_005512		Approved		uc001oxq.4	Q14392	OTTHUMG00000133687	ENST00000407242.2:c.471G>A	chr11.hg19:g.76372166C>T		58.0	0.0		40.0	9.0	NM_005512	Q86V06	Silent	SNP	ENST00000407242.2	hg19	CCDS8245.1																																																																																			.	.		0.642	LRRC32-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257926.2	NM_005512		T	76372166	C	T	76372166	2	4	363	1	0	0	0	0	0	0	0	1	8996	639	23	1		1	LRRC32	11	76372166	Silent	SNP	C	TCGA-ZP-A9CV-01A-11D-A382-10	9152059	76372166	58634350	67	50696										
ARHGEF12	23365	hgsc.bcm.edu	37	chr11	120280158	120280158	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	gagagtagatccgagatataTggtaagctaatgtagctaat	11	4	0	3			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr11:120280158T>C	ENST00000397843.2	+	4	364	c.198T>C	c.(196-198)taT>taC	p.Y66Y	ARHGEF12_ENST00000532993.1_5'UTR|ARHGEF12_ENST00000356641.3_Intron	NM_015313.2	NP_056128.1	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12	66					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(5)|endometrium(6)|kidney(5)|large_intestine(13)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(2)	61		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)		CCGAGATATATGGTAAGCTAA	0.388			T	MLL	AML																																p.Y66Y		Atlas-SNP	.		Dom	yes		11	11q23.3	23365	RHO guanine nucleotide exchange factor (GEF) 12 (LARG)		L	.	ARHGEF12	133	.	0			c.T198C						.						136	134	135					11																	120280158		1877	4099	5976	SO:0001630	splice_region_variant	23365	exon4			GATATATGGTAAG	AF180681	CCDS41727.1, CCDS55794.1	11q23.3	2011-11-16			ENSG00000196914	ENSG00000196914		"Rho guanine nucleotide exchange factors"	14193	protein-coding gene	gene with protein product		604763				10681437, 9205841	Standard	NM_001198665		Approved	KIAA0382, LARG	uc001pxl.2	Q9NZN5	OTTHUMG00000166143	ENST00000397843.2:c.199+1T>C	chr11.hg19:g.120280158T>C		75.0	0.0		77.0	29.0	NM_015313	O15086|Q6P526	Silent	SNP	ENST00000397843.2	hg19	CCDS41727.1																																																																																			.	.		0.388	ARHGEF12-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388052.1	NM_015313	Silent	C	120280158	T	C	120280158	5	2	363	1	0	0	0	0	0	0	1	0	897	1478	51	2	212	2	ARHGEF12	11	120280158	Splice_Site	SNP	T	TCGA-ZP-A9CV-01A-11D-A382-10	43907992	120280158	14726358	68	50697										
CD163	9332	hgsc.bcm.edu	37	chr12	7639354	7639354	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	caggagccctcatgatagatCtctactctcccagcacagcg	8	15	3	2			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr12:7639354C>T	ENST00000359156.4	-	10	2401	c.2199G>A	c.(2197-2199)gaG>gaA	p.E733E	CD163_ENST00000396620.3_Silent_p.E766E|CD163_ENST00000539632.1_5'Flank|CD163_ENST00000432237.2_Silent_p.E733E|CD163_ENST00000541972.1_Silent_p.E721E	NM_004244.5	NP_004235.4	Q86VB7	C163A_HUMAN	CD163 molecule	733	SRCR 7. {ECO:0000255|PROSITE- ProRule:PRU00196}.				acute-phase response (GO:0006953)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(6)|pancreas(2)|prostate(1)|skin(5)|urinary_tract(4)	76					WF10(DB05389)	CATGATAGATCTCTACTCTCC	0.507																																					p.E733E		Atlas-SNP	.											.	CD163	221	.	0			c.G2199A						.						99	95	97					12																	7639354		2203	4300	6503	SO:0001819	synonymous_variant	9332	exon10			ATAGATCTCTACT	Z22968	CCDS8578.1, CCDS53742.1	12p13	2006-03-28	2006-03-28		ENSG00000177575	ENSG00000177575		"CD molecules"	1631	protein-coding gene	gene with protein product		605545	"CD163 antigen"			10403791, 8370408	Standard	NM_004244		Approved	M130, MM130	uc001qsz.3	Q86VB7	OTTHUMG00000168353	ENST00000359156.4:c.2199G>A	chr12.hg19:g.7639354C>T		113.0	0.0		79.0	19.0	NM_203416	C9JIG2|Q07898|Q07899|Q07900|Q07901|Q2VLH7	Silent	SNP	ENST00000359156.4	hg19	CCDS8578.1																																																																																			.	.		0.507	CD163-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399396.2	NM_004244, NM_203416		T	7639354	C	T	7639354	2	4	363	1	0	0	0	0	0	0	0	1	2969	912	32	3		3	CD163	12	7639354	Silent	SNP	C	TCGA-ZP-A9CV-01A-11D-A382-10		7639354	126212541	69	50698										
PDZRN4	29951	hgsc.bcm.edu	37	chr12	41961651	41961651	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	agttaaacttggagatgttgGaagaagagcataatgaagca	12	3	0	4			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr12:41961651G>T	ENST00000402685.2	+	9	1542	c.1534G>T	c.(1534-1536)Gaa>Taa	p.E512*	PDZRN4_ENST00000298919.7_Nonsense_Mutation_p.E252*|PDZRN4_ENST00000539469.2_Nonsense_Mutation_p.E254*	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	512							ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				GGAGATGTTGGAAGAAGAGCA	0.393																																					p.E512X		Atlas-SNP	.											.	PDZRN4	346	.	0			c.G1534T						.						102	91	95					12																	41961651		2203	4300	6503	SO:0001587	stop_gained	29951	exon9			ATGTTGGAAGAAG	AK094690	CCDS8739.1, CCDS53777.1	12q12	2008-08-14	2008-08-14			ENSG00000165966		"RING-type (C3HC4) zinc fingers"	30552	protein-coding gene	gene with protein product	"similar to semaF cytoplasmic domain associated protein 3"	609730				11230166, 15010864	Standard	NM_013377		Approved	DKFZp434B0417, LNX4, FLJ33777, IMAGE5767589	uc010skn.2	Q6ZMN7		ENST00000402685.2:c.1534G>T	chr12.hg19:g.41961651G>T	ENSP00000384197:p.Glu512*	95.0	0.0		96.0	27.0	NM_001164595	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Nonsense_Mutation	SNP	ENST00000402685.2	hg19	CCDS53777.1	.	.	.	.	.	.	.	.	.	.	G	39	7.685975	0.98431	.	.	ENSG00000165966	ENST00000402685;ENST00000539469;ENST00000298919	.	.	.	4.85	3.96	0.45880	.	0.153041	0.45126	D	0.000396	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-12.4928	13.7702	0.63019	0.0762:0.0:0.9238:0.0	.	.	.	.	X	512;254;252	.	ENSP00000298919:E252X	E	+	1	0	PDZRN4	40247918	1.000000	0.71417	0.994000	0.49952	0.867000	0.49689	7.802000	0.85969	1.358000	0.45922	-0.225000	0.12378	GAA	.	.		0.393	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377		T	41961651	G	T	41961651	4	4	363	1	0	0	0	0	0	1	0	0	11719	1175	41	3	1641	3	PDZRN4	12	41961651	Nonsense_Mutation	SNP	G	TCGA-ZP-A9CV-01A-11D-A382-10	34322297	41961651	91890244	70	50699										
ARID2	196528	hgsc.bcm.edu	37	chr12	46230548	46230548	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	tacatcaggagaatggatttGggagtctttatttcatccac	9	7	3	1			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr12:46230548G>A	ENST00000334344.6	+	8	969	c.797G>A	c.(796-798)tGg>tAg	p.W266*	ARID2_ENST00000444670.1_5'Flank|ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000422737.1_Nonsense_Mutation_p.W117*	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	266					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		GAATGGATTTGGGAGTCTTTA	0.333			"N, S, F"		hepatocellular carcinoma																																p.W266X		Atlas-SNP	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	311	.	0			c.G797A						.						124	126	125					12																	46230548		2203	4300	6503	SO:0001587	stop_gained	196528	exon8			GGATTTGGGAGTC		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.797G>A	chr12.hg19:g.46230548G>A	ENSP00000335044:p.Trp266*	231.0	0.0		210.0	62.0	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Nonsense_Mutation	SNP	ENST00000334344.6	hg19	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	G	39	7.715201	0.98450	.	.	ENSG00000189079	ENST00000334344;ENST00000422737	.	.	.	5.87	5.87	0.94306	.	0.056138	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	-2.9687	20.2009	0.98259	0.0:0.0:1.0:0.0	.	.	.	.	X	266;117	.	ENSP00000335044:W266X	W	+	2	0	ARID2	44516815	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.245000	0.65405	2.767000	0.95098	0.591000	0.81541	TGG	.	.		0.333	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		A	46230548	G	A	46230548	4	1	363	1	0	0	0	0	0	1	0	0	915	1357	47	3	827	3	ARID2	12	46230548	Nonsense_Mutation	SNP	G	TCGA-ZP-A9CV-01A-11D-A382-10	4268897	46230548	87621347	71	50700										
H1FNT	341567	hgsc.bcm.edu	37	chr12	48723425	48723425	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	gtcagcggcagcgacgccgcCggctacttcagggtctggaa	15	13	3	0	rs372377328		TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr12:48723425C>T	ENST00000335017.1	+	1	663	c.351C>T	c.(349-351)gcC>gcT	p.A117A		NM_181788.1	NP_861453.1	Q75WM6	H1FNT_HUMAN	H1 histone family, member N, testis-specific	117					chromosome condensation (GO:0030261)|multicellular organismal development (GO:0007275)|sperm chromatin condensation (GO:0035092)|spermatid nucleus elongation (GO:0007290)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	13						GCGACGCCGCCGGCTACTTCA	0.721																																					p.A117A		Atlas-SNP	.											.	H1FNT	30	.	0			c.C351T						.	C		0,4390		0,0,2195	11	15	13		351	-10.3	0	12		13	2,8566		0,2,4282	no	coding-synonymous	H1FNT	NM_181788.1		0,2,6477	TT,TC,CC		0.0233,0.0,0.0154		117/256	48723425	2,12956	2195	4284	6479	SO:0001819	synonymous_variant	341567	exon1			CGCCGCCGGCTAC	AY302593	CCDS8762.1	12q13.11	2011-01-27				ENSG00000187166		"Histones / Replication-independent"	24893	protein-coding gene	gene with protein product						15710904	Standard	NM_181788		Approved	HANP1, H1T2	uc001rrm.3	Q75WM6		ENST00000335017.1:c.351C>T	chr12.hg19:g.48723425C>T		134.0	0.0		143.0	43.0	NM_181788	Q147U8|Q5GKZ5|Q7Z694	Silent	SNP	ENST00000335017.1	hg19	CCDS8762.1																																																																																			.	.		0.721	H1FNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406516.1	NM_181788		T	48723425	C	T	48723425	2	4	363	1	0	0	0	0	0	0	0	1	6930	639	23	1		1	H1FNT	12	48723425	Silent	SNP	C	TCGA-ZP-A9CV-01A-11D-A382-10	2492877	48723425	85128470	72	50701										
TIMELESS	8914	hgsc.bcm.edu	37	chr12	56812013	56812013	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	tacagtgctcctcatcagagCcttgctctccagggacttta	8	13	3	1			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr12:56812013C>T	ENST00000553532.1	-	27	3509	c.3359G>A	c.(3358-3360)gGc>gAc	p.G1120D	TIMELESS_ENST00000229201.4_Missense_Mutation_p.G1119D|TIMELESS_ENST00000554616.1_Missense_Mutation_p.G617D					timeless circadian clock											NS(1)|breast(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(8)|lung(14)|ovary(7)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	49						CTCATCAGAGCCTTGCTCTCC	0.582																																					p.G1120D		Atlas-SNP	.											.	TIMELESS	107	.	0			c.G3359A						.						138	147	144					12																	56812013		2203	4300	6503	SO:0001583	missense	8914	exon27			TCAGAGCCTTGCT	AF098162	CCDS8918.1	12q13.3	2012-12-14	2012-12-14		ENSG00000111602	ENSG00000111602			11813	protein-coding gene	gene with protein product	"Tof1 homolog (S. cerevisiae)", "timeless circadian clock 1"	603887	"timeless (Drosophila) homolog", "timeless homolog (Drosophila)"			9856465	Standard	NM_003920		Approved	hTIM, TIM, TIM1	uc001slf.2	Q9UNS1	OTTHUMG00000170600	ENST00000553532.1:c.3359G>A	chr12.hg19:g.56812013C>T	ENSP00000450607:p.Gly1120Asp	104.0	0.0		83.0	28.0	NM_003920		Missense_Mutation	SNP	ENST00000553532.1	hg19	CCDS8918.1	.	.	.	.	.	.	.	.	.	.	C	4.591	0.109816	0.08780	.	.	ENSG00000111602	ENST00000229201;ENST00000553532;ENST00000554616	T;T;T	0.11277	3.33;3.33;2.79	5.26	-2.64	0.06114	Timeless C-terminal (1);	1.903580	0.02229	N	0.064696	T	0.05502	0.0145	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.22977	-1.0201	10	0.05833	T	0.94	0.0407	1.3823	0.02233	0.1217:0.2779:0.2379:0.3625	.	1120	Q9UNS1	TIM_HUMAN	D	1119;1120;617	ENSP00000229201:G1119D;ENSP00000450607:G1120D;ENSP00000450848:G617D	ENSP00000229201:G1120D	G	-	2	0	TIMELESS	55098280	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.614000	0.05604	-0.819000	0.04323	-0.137000	0.14449	GGC	.	.		0.582	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920		T	56812013	C	T	56812013	3	4	363	1	0	0	0	0	1	0	0	0	15919	739	26	3	279	3	TIMELESS	12	56812013	Missense_Mutation	SNP	C	TCGA-ZP-A9CV-01A-11D-A382-10	8088588	56812013	77039882	73	50702										
DNAH10	196385	hgsc.bcm.edu	37	chr12	124358197	124358197	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	gaaaagcgaaccaaagatacTtacggcccacccatgggaaa	9	11	0	1			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr12:124358197T>C	ENST00000409039.3	+	45	7549	c.7524T>C	c.(7522-7524)acT>acC	p.T2508T		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2508	AAA 3. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		CCAAAGATACTTACGGCCCAC	0.478																																					p.T2508T		Atlas-SNP	.											.	DNAH10	888	.	0			c.T7524C						.						62	59	60					12																	124358197		1929	4142	6071	SO:0001819	synonymous_variant	196385	exon45			AGATACTTACGGC	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.7524T>C	chr12.hg19:g.124358197T>C		138.0	0.0		97.0	34.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	hg19	CCDS9255.2																																																																																			.	.		0.478	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			C	124358197	T	C	124358197	2	2	363	1	0	0	0	0	0	0	0	1	4600	1596	56	2		2	DNAH10	12	124358197	Silent	SNP	T	TCGA-ZP-A9CV-01A-11D-A382-10	67546184	124358197	9493698	74	50703										
DNAH10	196385	hgsc.bcm.edu	37	chr12	124413834	124413834	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	ttctgaaggttgtcaccgagCcacccaatgggctgaaactc	10	12	2	2			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr12:124413834C>T	ENST00000409039.3	+	70	11990	c.11965C>T	c.(11965-11967)Cca>Tca	p.P3989S	DNAH10OS_ENST00000514254.2_3'UTR|CCDC92_ENST00000544798.1_Intron	NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	3989	AAA 6. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		TGTCACCGAGCCACCCAATGG	0.537																																					p.P3989S		Atlas-SNP	.											.	DNAH10	888	.	0			c.C11965T						.						27	28	28					12																	124413834		2049	4194	6243	SO:0001583	missense	196385	exon70			ACCGAGCCACCCA	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.11965C>T	chr12.hg19:g.124413834C>T	ENSP00000386770:p.Pro3989Ser	84.0	0.0		85.0	29.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	hg19	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	C	24.1	4.496467	0.85069	.	.	ENSG00000197653	ENST00000409039	T	0.14766	2.48	5.09	4.13	0.48395	Dynein heavy chain (1);	0.060979	0.64402	D	0.000002	T	0.42108	0.1188	M	0.86343	2.81	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	T	0.50642	-0.8804	10	0.87932	D	0	.	15.3131	0.74053	0.0:0.8599:0.1401:0.0	.	3989	Q8IVF4	DYH10_HUMAN	S	3989	ENSP00000386770:P3989S	ENSP00000386770:P3989S	P	+	1	0	DNAH10	122979787	1.000000	0.71417	0.998000	0.56505	0.973000	0.67179	6.001000	0.70685	2.528000	0.85240	0.591000	0.81541	CCA	.	.		0.537	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			T	124413834	C	T	124413834	3	4	363	1	0	0	0	0	1	0	0	0	4600	739	26	3	12243	3	DNAH10	12	124413834	Missense_Mutation	SNP	C	TCGA-ZP-A9CV-01A-11D-A382-10	55637	124413834	9438061	75	50704										
FLT3	2322	hgsc.bcm.edu	37	chr13	28601301	28601301	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	aatctctgtccaagtcctgtGaaatttttctcttttacttc	4	10	2	1			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr13:28601301G>A	ENST00000241453.7	-	17	2212	c.2131C>T	c.(2131-2133)Cac>Tac	p.H711Y	FLT3_ENST00000380982.4_Missense_Mutation_p.H711Y|FLT3_ENST00000537084.1_Missense_Mutation_p.H711Y	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	711	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell differentiation (GO:0030183)|cellular response to cytokine stimulus (GO:0071345)|common myeloid progenitor cell proliferation (GO:0035726)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell differentiation (GO:0097028)|hemopoiesis (GO:0030097)|leukocyte homeostasis (GO:0001776)|lymphocyte proliferation (GO:0046651)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|pro-B cell differentiation (GO:0002328)|pro-T cell differentiation (GO:0002572)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor signaling pathway (GO:0038084)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|cytokine receptor activity (GO:0004896)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(12329)|kidney(2)|large_intestine(8)|lung(30)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12390	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Ponatinib(DB08901)|Sorafenib(DB00398)|Sunitinib(DB01268)	CAAGTCCTGTGAAATTTTTCT	0.363			"Mis, O"		"AML, ALL"																																p.H711Y		Atlas-SNP	.		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	.	FLT3	15525	.	0			c.C2131T						.						142	146	144					13																	28601301		2203	4300	6503	SO:0001583	missense	2322	exon17			TCCTGTGAAATTT	U02687	CCDS31953.1	13q12	2014-09-17			ENSG00000122025	ENSG00000122025	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3765	protein-coding gene	gene with protein product		136351				8394751	Standard	NM_004119		Approved	STK1, FLK2, CD135	uc001urw.3	P36888	OTTHUMG00000016646	ENST00000241453.7:c.2131C>T	chr13.hg19:g.28601301G>A	ENSP00000241453:p.His711Tyr	132.0	0.0		120.0	6.0	NM_004119	A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	Missense_Mutation	SNP	ENST00000241453.7	hg19	CCDS31953.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.002385	0.74932	.	.	ENSG00000122025	ENST00000241453;ENST00000380982;ENST00000537084	D;D;D	0.88818	-2.43;-2.43;-2.43	6.03	6.03	0.97812	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.91563	0.7335	L	0.36672	1.1	0.49389	D	0.999781	D;D	0.89917	1.0;0.995	D;D	0.85130	0.997;0.976	D	0.86981	0.2104	10	0.13853	T	0.58	.	20.5568	0.99304	0.0:0.0:1.0:0.0	.	711;711	P36888-2;P36888	.;FLT3_HUMAN	Y	711	ENSP00000241453:H711Y;ENSP00000370369:H711Y;ENSP00000438139:H711Y	ENSP00000241453:H711Y	H	-	1	0	FLT3	27499301	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.786000	0.62425	2.861000	0.98227	0.655000	0.94253	CAC	.	.		0.363	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044319.2			A	28601301	G	A	28601301	3	1	363	1	0	0	0	0	1	0	0	0	5950	1290	45	3	882	3	FLT3	13	28601301	Missense_Mutation	SNP	G	TCGA-ZP-A9CV-01A-11D-A382-10		28601301	86568577	76	50705										
MYH7	4625	hgsc.bcm.edu	37	chr14	23884310	23884310	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	cattctccagctcccgcaccCgcgcttccagcttctgcagc	7	20	2	0			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr14:23884310C>G	ENST00000355349.3	-	37	5615	c.5453G>C	c.(5452-5454)cGg>cCg	p.R1818P	CTD-2201G16.1_ENST00000557368.1_RNA|MIR208B_ENST00000401172.1_RNA	NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	1818					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		CTCCCGCACCCGCGCTTCCAG	0.622																																					p.R1818P		Atlas-SNP	.											.	MYH7	349	.	0			c.G5453C						.						87	87	87					14																	23884310		2203	4300	6503	SO:0001583	missense	4625	exon37			CGCACCCGCGCTT	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.5453G>C	chr14.hg19:g.23884310C>G	ENSP00000347507:p.Arg1818Pro	36.0	0.0		44.0	15.0	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Missense_Mutation	SNP	ENST00000355349.3	hg19	CCDS9601.1	.	.	.	.	.	.	.	.	.	.	C	19.80	3.895207	0.72639	.	.	ENSG00000092054	ENST00000355349;ENST00000544444	D	0.84800	-1.9	5.27	5.27	0.74061	Myosin tail (1);	.	.	.	.	D	0.94447	0.8213	H	0.95712	3.71	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.95442	0.8526	9	0.87932	D	0	.	14.369	0.66826	0.0:0.927:0.0:0.073	.	1818	P12883	MYH7_HUMAN	P	1818;1823	ENSP00000347507:R1818P	ENSP00000347507:R1818P	R	-	2	0	MYH7	22954150	0.605000	0.26941	1.000000	0.80357	0.775000	0.43874	1.362000	0.34148	2.750000	0.94351	0.563000	0.77884	CGG	.	.		0.622	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257		G	23884310	C	G	23884310	3	3	363	1	0	0	0	0	1	0	0	0	10048	652	23	4	370	4	MYH7	14	23884310	Missense_Mutation	SNP	C	TCGA-ZP-A9CV-01A-11D-A382-10		23884310	83465230	77	50706										
SFTA3	253970	hgsc.bcm.edu	37	chr14	36943085	36943085	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	atgcagtatgaataattaacAtctgaaaatgcagaacaaaa	6	5	1	3			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr14:36943085A>T	ENST00000518529.2	-	4	938	c.263T>A	c.(262-264)aTg>aAg	p.M88K	RP11-896J10.3_ENST00000521945.1_RNA|SFTA3_ENST00000518987.1_5'Flank	NM_001101341.1	NP_001094811.1	P0C7M3	SFTA3_HUMAN	surfactant associated 3	88										breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|skin(1)	7						AATAATTAACATCTGAAAATG	0.373																																					p.M88K		Atlas-SNP	.											.	SFTA3	9	.	0			c.T263A						.						83	75	78					14																	36943085		1856	4105	5961	SO:0001630	splice_region_variant	253970	exon4			ATTAACATCTGAA	AY102071	CCDS45097.1	14q13.3	2014-06-19	2008-08-26	2008-08-26	ENSG00000229415	ENSG00000229415			18387	protein-coding gene	gene with protein product			"surfactant associated protein H"	SFTPH			Standard	NM_001101341		Approved	NANCI	uc001wtr.3	P0C7M3	OTTHUMG00000170540	ENST00000518529.2:c.262-1T>A	chr14.hg19:g.36943085A>T		229.0	0.0		217.0	68.0	NM_001101341		Missense_Mutation	SNP	ENST00000518529.2	hg19	CCDS45097.1	.	.	.	.	.	.	.	.	.	.	A	12.79	2.042307	0.35989	.	.	ENSG00000229415	ENST00000518529	.	.	.	4.23	3.07	0.35406	.	.	.	.	.	T	0.27765	0.0683	.	.	.	0.23747	N	0.99696	P	0.36535	0.557	B	0.33521	0.165	T	0.16630	-1.0396	7	0.87932	D	0	.	7.9443	0.29976	0.7914:0.2086:0.0:0.0	.	88	P0C7M3	SFTA3_HUMAN	K	88	.	ENSP00000428331:M88K	M	-	2	0	SFTA3	36012836	1.000000	0.71417	0.998000	0.56505	0.966000	0.64601	1.423000	0.34837	0.937000	0.37394	0.482000	0.46254	ATG	.	.		0.373	SFTA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376217.2	NM_001101341	Missense_Mutation	T	36943085	A	T	36943085	5	4	363	1	0	0	0	0	0	0	1	0	14203	231	8	4	25	4	SFTA3	14	36943085	Splice_Site	SNP	A	TCGA-ZP-A9CV-01A-11D-A382-10	13058775	36943085	70406455	78	50707										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64608713	64608713	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	atcacagaaatgattagctgGatgaacaatgtggagcatca	10	6	2	3			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr14:64608713G>T	ENST00000344113.4	+	82	15425	c.15213G>T	c.(15211-15213)tgG>tgT	p.W5071C	SYNE2_ENST00000394768.2_Missense_Mutation_p.W1456C|SYNE2_ENST00000554584.1_Missense_Mutation_p.W4988C|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000555002.1_Missense_Mutation_p.W1705C|SYNE2_ENST00000358025.3_Missense_Mutation_p.W5071C|SYNE2_ENST00000357395.3_Missense_Mutation_p.W1456C	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	5071					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		TGATTAGCTGGATGAACAATG	0.373																																					p.W5071C		Atlas-SNP	.											.	SYNE2	577	.	0			c.G15213T						.						88	80	83					14																	64608713		2203	4300	6503	SO:0001583	missense	23224	exon82			TAGCTGGATGAAC	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.15213G>T	chr14.hg19:g.64608713G>T	ENSP00000341781:p.Trp5071Cys	301.0	0.0		234.0	66.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	hg19	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.168251	0.78339	.	.	ENSG00000054654	ENST00000358025;ENST00000357395;ENST00000344113;ENST00000554584;ENST00000261678;ENST00000555002;ENST00000394768	T;T;T;T;T;T	0.70749	-0.48;-0.51;-0.48;-0.48;-0.48;-0.51	5.93	5.93	0.95920	.	0.000000	0.50627	D	0.000110	D	0.85168	0.5635	M	0.75777	2.31	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.97110	1.0;0.999;0.994;0.999	D	0.85515	0.1200	10	0.87932	D	0	.	20.3422	0.98769	0.0:0.0:1.0:0.0	.	1456;4988;5071;5071	Q8WXH0-7;G3V5X4;Q8WXH0;Q8WXH0-2	.;.;SYNE2_HUMAN;.	C	5071;1456;5071;4988;4994;1705;1456	ENSP00000350719:W5071C;ENSP00000349969:W1456C;ENSP00000341781:W5071C;ENSP00000452570:W4988C;ENSP00000450831:W1705C;ENSP00000378249:W1456C	ENSP00000261678:W4994C	W	+	3	0	SYNE2	63678466	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.751000	0.98889	2.810000	0.96702	0.655000	0.94253	TGG	.	.		0.373	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		T	64608713	G	T	64608713	3	4	363	1	0	0	0	0	1	0	0	0	15461	1183	41	3	15535	3	SYNE2	14	64608713	Missense_Mutation	SNP	G	TCGA-ZP-A9CV-01A-11D-A382-10	27665628	64608713	42740827	79	50708										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105409536	105409536	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	tcaggggctgtcacttccgcCttggggcctttcaggtccag	13	13	3	0			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr14:105409536C>A	ENST00000333244.5	-	7	12371	c.12252G>T	c.(12250-12252)aaG>aaT	p.K4084N	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4084						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				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)			TCACTTCCGCCTTGGGGCCTT	0.597																																					p.K4084N		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G12252T						.						158	162	161					14																	105409536		1868	4093	5961	SO:0001583	missense	113146	exon7			TTCCGCCTTGGGG	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.12252G>T	chr14.hg19:g.105409536C>A	ENSP00000353114:p.Lys4084Asn	258.0	0.0		226.0	60.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	hg19	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	-	13.58	2.280285	0.40294	.	.	ENSG00000185567	ENST00000333244	T	0.00711	5.8	4.13	-2.2	0.06994	.	0.238084	0.20122	U	0.098795	T	0.02380	0.0073	M	0.83692	2.655	0.09310	N	1	D	0.65815	0.995	D	0.68943	0.961	T	0.41016	-0.9532	10	0.23302	T	0.38	.	4.1823	0.10381	0.2641:0.4368:0.0:0.2991	.	4084	Q8IVF2	AHNK2_HUMAN	N	4084	ENSP00000353114:K4084N	ENSP00000353114:K4084N	K	-	3	2	AHNAK2	104480581	0.000000	0.05858	0.001000	0.08648	0.060000	0.15804	-2.709000	0.00819	-0.024000	0.13941	0.485000	0.47835	AAG	.	.		0.597	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105409536	C	A	105409536	3	1	363	1	0	0	0	0	1	0	0	0	415	680	24	3	5139	3	AHNAK2	14	105409536	Missense_Mutation	SNP	C	TCGA-ZP-A9CV-01A-11D-A382-10	40800823	105409536	1940004	80	50709										
GABPB1	2553	hgsc.bcm.edu	37	chr15	50578220	50578220	+	Intron	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	gacaaaaaaaattgaatttaTtttggatgactgcggcaaag	9	4	0	2			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr15:50578220T>C	ENST00000220429.8	-	8	1204				GABPB1_ENST00000396464.3_Silent_p.K348K|GABPB1_ENST00000560825.1_Silent_p.K347K|GABPB1_ENST00000429662.2_Silent_p.K360K|GABPB1_ENST00000359031.4_Silent_p.K348K|GABPB1_ENST00000543881.1_Intron|GABPB1_ENST00000380877.3_Intron			Q06547	GABP1_HUMAN	GA binding protein transcription factor, beta subunit 1						positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			cervix(1)|endometrium(1)|large_intestine(7)|lung(5)	14						ATTGAATTTATTTTGGATGAC	0.318																																					p.K360K		Atlas-SNP	.											.	GABPB1	33	.	0			c.A1080G						.						83	87	86					15																	50578220		2195	4294	6489	SO:0001627	intron_variant	2553	exon8			AATTTATTTTGGA	D13316	CCDS10135.1, CCDS10136.1, CCDS32239.1, CCDS45258.1	15q21.2	2013-01-10	2008-02-25	2008-02-25	ENSG00000104064	ENSG00000104064		"Ankyrin repeat domain containing"	4074	protein-coding gene	gene with protein product		600610	"GA binding protein transcription factor, beta subunit 2"	GABPB2		7958862	Standard	NM_016655		Approved	E4TF1-47, GABPB	uc001zyb.3	Q06547	OTTHUMG00000131642	ENST00000220429.8:c.1035+44A>G	chr15.hg19:g.50578220T>C		91.0	0.0		85.0	30.0	NM_002041	A8IE52|Q06545|Q12940|Q12941|Q12942|Q8IYD0	Silent	SNP	ENST00000220429.8	hg19	CCDS32239.1																																																																																			.	.		0.318	GABPB1-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000418294.1			C	50578220	T	C	50578220	1	2	363	0	1	0	0	0	0	0	0	0	6166	1490	52	2		2	GABPB1	15	50578220	Intron	SNP	T	TCGA-ZP-A9CV-01A-11D-A382-10		50578220	51953172	81	50710										
TLE3	7090	hgsc.bcm.edu	37	chr15	70366931	70366931	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	ggcgcgctccactgcctgcgCcacctgctgctggtgctgga	14	16	0	0			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr15:70366931C>T	ENST00000558939.1	-	6	1690	c.313G>A	c.(313-315)Gcg>Acg	p.A105T	TLE3_ENST00000559929.1_Missense_Mutation_p.A105T|TLE3_ENST00000558379.1_Missense_Mutation_p.A105T|TLE3_ENST00000539550.1_Missense_Mutation_p.A39T|TLE3_ENST00000451782.2_Missense_Mutation_p.A105T|TLE3_ENST00000440567.3_Missense_Mutation_p.A98T|TLE3_ENST00000317509.8_Missense_Mutation_p.A105T|TLE3_ENST00000560589.1_Missense_Mutation_p.A49T|TLE3_ENST00000442299.2_Missense_Mutation_p.A105T|TLE3_ENST00000559191.1_Intron|TLE3_ENST00000557997.1_Missense_Mutation_p.A105T|TLE3_ENST00000559048.1_Missense_Mutation_p.A111T|TLE3_ENST00000558201.1_Missense_Mutation_p.A111T|TLE3_ENST00000557907.1_Missense_Mutation_p.A105T|TLE3_ENST00000560939.1_Missense_Mutation_p.A111T	NM_001282979.1|NM_001282980.1|NM_001282981.1	NP_001269908.1|NP_001269909.1|NP_001269910.1	Q04726	TLE3_HUMAN	transducin-like enhancer of split 3	105	Gln-rich.				Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						ACTGCCTGCGCCACCTGCTGC	0.617																																					p.A105T		Atlas-SNP	.											TLE3_ENST00000558939,NS,carcinoma,0,2	TLE3	104	.	0			c.G313A						.						51	56	55					15																	70366931		2190	4294	6484	SO:0001583	missense	7090	exon6			CCTGCGCCACCTG	M99438	CCDS45293.1, CCDS45294.1, CCDS58375.1, CCDS61689.1, CCDS61691.1, CCDS61692.1, CCDS73747.1	15q22	2014-03-07	2014-03-07			ENSG00000140332		"WD repeat domain containing"	11839	protein-coding gene	gene with protein product		600190	"transducin-like enhancer of split 3, homolog of Drosophila E(sp1)", "transducin-like enhancer of split 3 (E(sp1) homolog, Drosophila)"			8365415	Standard	XM_005254623		Approved	ESG, ESG3, KIAA1547, HsT18976, GRG3	uc002asm.2	Q04726		ENST00000558939.1:c.313G>A	chr15.hg19:g.70366931C>T	ENSP00000452871:p.Ala105Thr	56.0	0.0		45.0	12.0	NM_001105192	B4DPT0|E9PD64|F8W964|Q6PI57|Q8IVV6|Q8WVR2|Q9HCM5	Missense_Mutation	SNP	ENST00000558939.1	hg19	CCDS45293.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.370315	0.82573	.	.	ENSG00000140332	ENST00000442299;ENST00000451782;ENST00000317509;ENST00000440567;ENST00000539550;ENST00000537387	T;T;T;T;T	0.57595	0.66;0.69;0.75;0.69;0.39	5.41	5.41	0.78517	Groucho/TLE, N-terminal Q-rich domain (1);	0.000000	0.85682	D	0.000000	T	0.71753	0.3377	M	0.89353	3.025	0.54753	D	0.999984	P;P;P;P;P;P;P;P	0.46512	0.604;0.803;0.604;0.803;0.855;0.879;0.731;0.731	P;P;P;P;P;P;B;B	0.51516	0.462;0.672;0.543;0.672;0.516;0.672;0.287;0.381	T	0.76179	-0.3054	10	0.49607	T	0.09	-4.8715	19.1972	0.93695	0.0:1.0:0.0:0.0	.	98;105;105;105;105;105;111;39	F8W964;E9PD64;Q04726-3;Q6PI57;Q04726-2;Q04726;Q04726-4;F5H7D6	.;.;.;.;.;TLE3_HUMAN;.;.	T	105;105;105;98;39;2	ENSP00000390007:A105T;ENSP00000394717:A105T;ENSP00000319233:A105T;ENSP00000415057:A98T;ENSP00000442594:A39T	ENSP00000319233:A105T	A	-	1	0	TLE3	68153985	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	5.963000	0.70372	2.537000	0.85549	0.561000	0.74099	GCG	.	.		0.617	TLE3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416913.1	NM_005078		T	70366931	C	T	70366931	3	4	363	1	0	0	0	0	1	0	0	0	15955	739	26	3	2065	3	TLE3	15	70366931	Missense_Mutation	SNP	C	TCGA-ZP-A9CV-01A-11D-A382-10	19788711	70366931	32164461	82	50711										
NMRAL1	57407	hgsc.bcm.edu	37	chr16	4511950	4511950	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	agccaagcttttcgtagtccTcaggagtcatctggaagcag	11	10	3	0			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr16:4511950T>G	ENST00000574733.1	-	6	1460	c.731A>C	c.(730-732)gAg>gCg	p.E244A	NMRAL1_ENST00000404295.3_Missense_Mutation_p.E244A|NMRAL1_ENST00000574425.1_Missense_Mutation_p.E244A|NMRAL1_ENST00000283429.6_Missense_Mutation_p.E244A|NMRAL1_ENST00000572391.1_5'Flank			Q9HBL8	NMRL1_HUMAN	NmrA-like family domain containing 1	244						cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|prostate(2)|stomach(1)	15						TTCGTAGTCCTCAGGAGTCAT	0.652																																					p.E244A		Atlas-SNP	.											.	NMRAL1	31	.	0			c.A731C						.						82	85	84					16																	4511950		2197	4300	6497	SO:0001583	missense	57407	exon6			TAGTCCTCAGGAG	AF225419	CCDS10516.1	16p13.3	2013-10-11			ENSG00000153406	ENSG00000153406		"Short chain dehydrogenase/reductase superfamily / Atypical members"	24987	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 48A, member 1"					19027726	Standard	NM_020677		Approved	FLJ25918, HSCARG, SDR48A1	uc002cwo.3	Q9HBL8	OTTHUMG00000129468	ENST00000574733.1:c.731A>C	chr16.hg19:g.4511950T>G	ENSP00000458762:p.Glu244Ala	130.0	0.0		129.0	39.0	NM_020677		Missense_Mutation	SNP	ENST00000574733.1	hg19	CCDS10516.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.065908	0.76187	.	.	ENSG00000153406	ENST00000283429;ENST00000404295	T;T	0.34072	1.38;1.38	5.7	5.7	0.88788	.	0.065640	0.64402	D	0.000007	T	0.43634	0.1256	L	0.53780	1.695	0.50632	D	0.999882	D	0.55605	0.972	P	0.49708	0.62	T	0.35076	-0.9803	10	0.48119	T	0.1	-38.0139	13.7109	0.62667	0.0:0.0:0.0:1.0	.	244	Q9HBL8	NMRL1_HUMAN	A	244	ENSP00000283429:E244A;ENSP00000383962:E244A	ENSP00000283429:E244A	E	-	2	0	NMRAL1	4451951	1.000000	0.71417	1.000000	0.80357	0.761000	0.43186	2.932000	0.48940	2.189000	0.69895	0.459000	0.35465	GAG	.	.		0.652	NMRAL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438579.1	NM_020677		G	4511950	T	G	4511950	3	3	363	1	0	0	0	0	1	0	0	0	10510	1551	54	5	172	5	NMRAL1	16	4511950	Missense_Mutation	SNP	T	TCGA-ZP-A9CV-01A-11D-A382-10		4511950	85842803	83	50712										
XPO6	23214	hgsc.bcm.edu	37	chr16	28188641	28188641	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	ctatttgctgggcaaagttaTtaagaagctcctctggaaaa	9	7	1	1			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr16:28188641T>C	ENST00000304658.5	-	3	607	c.107A>G	c.(106-108)aAt>aGt	p.N36S	XPO6_ENST00000565698.1_Missense_Mutation_p.N22S|SNORA25_ENST00000363782.1_RNA	NM_015171.3	NP_055986.1	Q96QU8	XPO6_HUMAN	exportin 6	36	Importin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00115}.				protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	25						GGCAAAGTTATTAAGAAGCTC	0.353																																					p.N36S		Atlas-SNP	.											.	XPO6	177	.	0			c.A107G						.						63	57	59					16																	28188641		1796	4070	5866	SO:0001583	missense	23214	exon3			AAGTTATTAAGAA	AY026388	CCDS42135.1, CCDS59266.1	16p11.2	2011-04-13	2003-03-11	2003-03-14		ENSG00000169180		"Exportins"	19733	protein-coding gene	gene with protein product		608411	"RAN binding protein 20"	RANBP20		14592989	Standard	NM_001270940		Approved	KIAA0370, FLJ22519	uc002dpa.2	Q96QU8		ENST00000304658.5:c.107A>G	chr16.hg19:g.28188641T>C	ENSP00000302790:p.Asn36Ser	187.0	0.0		206.0	68.0	NM_015171	A1L3W4|D3DWF9|Q2YDX3|Q53G88|Q68G50|Q76N88|Q96CP8|Q9BT21	Missense_Mutation	SNP	ENST00000304658.5	hg19	CCDS42135.1	.	.	.	.	.	.	.	.	.	.	T	15.04	2.715405	0.48622	.	.	ENSG00000169180	ENST00000304658	T	0.68025	-0.3	5.95	5.95	0.96441	Armadillo-like helical (1);Armadillo-type fold (1);Importin-beta, N-terminal (3);	0.045103	0.85682	D	0.000000	T	0.57607	0.2065	L	0.38175	1.15	0.58432	D	0.999999	B;P	0.44090	0.203;0.826	B;B	0.41946	0.123;0.371	T	0.55062	-0.8199	10	0.18276	T	0.48	-11.4385	14.359	0.66757	0.0:0.0:0.0:1.0	.	36;36	B7ZM10;Q96QU8	.;XPO6_HUMAN	S	36	ENSP00000302790:N36S	ENSP00000302790:N36S	N	-	2	0	XPO6	28096142	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.831000	0.86748	2.272000	0.75746	0.460000	0.39030	AAT	.	.		0.353	XPO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433732.1	XM_055195		C	28188641	T	C	28188641	3	2	363	1	0	0	0	0	1	0	0	0	17463	1493	52	2	3358	2	XPO6	16	28188641	Missense_Mutation	SNP	T	TCGA-ZP-A9CV-01A-11D-A382-10	23676691	28188641	62166112	84	50713										
MAZ	4150	hgsc.bcm.edu	37	chr16	29819111	29819111	+	Frame_Shift_Del	DEL	G	G	-													0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	catgacggcgctgtgcacaaGccctacaactgctcccactg							TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr16:29819111delG	ENST00000322945.6	+	2	1170	c.1005delG	c.(1003-1005)aagfs	p.K335fs	AC009133.14_ENST00000563806.1_RNA|MAZ_ENST00000568544.1_5'Flank|AC009133.14_ENST00000569981.1_RNA|MAZ_ENST00000569978.1_5'Flank|AC009133.15_ENST00000566537.1_RNA|MAZ_ENST00000219782.6_Frame_Shift_Del_p.K335fs|AC009133.20_ENST00000569039.1_RNA|MAZ_ENST00000568282.1_5'Flank|MAZ_ENST00000566906.2_Intron|MAZ_ENST00000562337.1_Intron|MAZ_ENST00000563402.1_Intron|MAZ_ENST00000545521.1_Frame_Shift_Del_p.K312fs	NM_002383.2	NP_002374.2	P56270	MAZ_HUMAN	MYC-associated zinc finger protein (purine-binding transcription factor)	335					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|termination of RNA polymerase II transcription (GO:0006369)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			endometrium(3)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	10						CTGTGCACAAGCCCTACAACT	0.682																																					p.K335fs	Colon(72;875 1167 15364 30899 37091)	Atlas-INDEL	.											.	MAZ	48	.	0			c.1004delA						.																																			SO:0001589	frameshift_variant	4150	exon2			.	M93339	CCDS42143.1, CCDS42144.1, CCDS61902.1, CCDS61903.1	16p11.2	2013-01-08			ENSG00000103495	ENSG00000103495		"Zinc fingers, C2H2-type"	6914	protein-coding gene	gene with protein product		600999				1567856, 1502157	Standard	NM_001276275		Approved	ZF87, Pur-1, Zif87, ZNF801	uc002dtx.4	P56270	OTTHUMG00000132119	ENST00000322945.6:c.1005delG	chr16.hg19:g.29819111delG	ENSP00000313362:p.Lys335fs	50.0	0.0		52.0	21.0	NM_002383	A8QJL9|C6G496|G5E927|H3BQD6|Q15703|Q8NFN7|Q99443	Frame_Shift_Del	DEL	ENST00000322945.6	hg19	CCDS42143.1																																																																																			.	.		0.682	MAZ-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000435536.1	NM_002383		-	29819111	G	-	29819111	7	5	363	1	0	1	0	1	0	0	0	0	9349	962	34	0	1011	0	MAZ	16	29819111	Frame_Shift_Del	DEL	G	TCGA-ZP-A9CV-01A-11D-A382-10	1630470	29819111	60535642	85	50714										
SRCAP	10847	hgsc.bcm.edu	37	chr16	30731600	30731600	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	gggtactgttagaagtggctActgctcctgaccccccaccc	10	15	0	2			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr16:30731600A>G	ENST00000262518.4	+	19	3320	c.2935A>G	c.(2935-2937)Act>Gct	p.T979A	SRCAP_ENST00000344771.4_Missense_Mutation_p.T979A|SRCAP_ENST00000395059.2_Missense_Mutation_p.T979A	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	979					histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			AGAAGTGGCTACTGCTCCTGA	0.547																																					p.T979A		Atlas-SNP	.											.	SRCAP	298	.	0			c.A2935G						.						109	119	116					16																	30731600		2197	4300	6497	SO:0001583	missense	10847	exon19			GTGGCTACTGCTC	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.2935A>G	chr16.hg19:g.30731600A>G	ENSP00000262518:p.Thr979Ala	95.0	0.0		107.0	45.0	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	hg19	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	A	17.28	3.348819	0.61183	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	D;D;D	0.90955	-2.76;-2.71;-2.69	5.45	5.45	0.79879	.	0.122741	0.37136	N	0.002221	T	0.80076	0.4557	N	0.12182	0.205	0.23984	N	0.996266	B;B;B	0.16166	0.016;0.016;0.006	B;B;B	0.15484	0.013;0.013;0.006	T	0.67852	-0.5563	10	0.45353	T	0.12	-7.6062	6.9074	0.24317	0.8334:0.0:0.1665:0.0	.	979;979;979	Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2	.;.;SRCAP_HUMAN	A	979	ENSP00000262518:T979A;ENSP00000378499:T979A;ENSP00000343042:T979A	ENSP00000262518:T979A	T	+	1	0	SRCAP	30639101	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.722000	0.68485	2.062000	0.61559	0.477000	0.44152	ACT	.	.		0.547	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		G	30731600	A	G	30731600	3	3	363	1	0	0	0	0	1	0	0	0	15150	391	14	2	3001	2	SRCAP	16	30731600	Missense_Mutation	SNP	A	TCGA-ZP-A9CV-01A-11D-A382-10	912489	30731600	59623153	86	50715										
EDC4	23644	hgsc.bcm.edu	37	chr16	67916665	67916665	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	ctgtgctagcccagctgcggGgcctggtcagcacactgcag	14	14	1	0			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr16:67916665G>A	ENST00000358933.5	+	26	3765	c.3526G>A	c.(3526-3528)Ggc>Agc	p.G1176S	CTC-479C5.10_ENST00000572067.1_lincRNA|NRN1L_ENST00000339176.3_5'Flank|NRN1L_ENST00000576147.1_5'Flank	NM_014329.4	NP_055144.3	Q6P2E9	EDC4_HUMAN	enhancer of mRNA decapping 4	1176					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	41		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)		CCAGCTGCGGGGCCTGGTCAG	0.642											OREG0023890	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G1176S		Atlas-SNP	.											.	EDC4	101	.	0			c.G3526A						.						52	53	53					16																	67916665		2198	4300	6498	SO:0001583	missense	23644	exon26			CTGCGGGGCCTGG	U17474	CCDS10849.1	16q22.1	2008-02-05			ENSG00000038358	ENSG00000038358			17157	protein-coding gene	gene with protein product		606030				9067524	Standard	NM_014329		Approved	RCD-8, Ge-1, HEDLS	uc002eur.3	Q6P2E9	OTTHUMG00000137543	ENST00000358933.5:c.3526G>A	chr16.hg19:g.67916665G>A	ENSP00000351811:p.Gly1176Ser	114.0	0.0	1103	109.0	35.0	NM_014329	A6NGM1|A8K4T4|Q13025|Q13826|Q6ZR12|Q7Z6H7	Missense_Mutation	SNP	ENST00000358933.5	hg19	CCDS10849.1	.	.	.	.	.	.	.	.	.	.	G	14.05	2.420838	0.42918	.	.	ENSG00000038358	ENST00000358933	.	.	.	5.74	4.78	0.61160	.	0.099971	0.64402	D	0.000002	T	0.29783	0.0744	L	0.36672	1.1	0.33204	D	0.552521	B	0.34015	0.435	B	0.24974	0.057	T	0.35895	-0.9770	9	0.09338	T	0.73	-23.0541	9.415	0.38517	0.0792:0.2486:0.6722:0.0	.	1176	Q6P2E9	EDC4_HUMAN	S	1176	.	ENSP00000351811:G1176S	G	+	1	0	EDC4	66474166	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.607000	0.61133	1.437000	0.47472	0.591000	0.81541	GGC	.	.		0.642	EDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268874.2	NM_014329		A	67916665	G	A	67916665	3	1	363	1	0	0	0	0	1	0	0	0	4910	1232	43	3	3628	3	EDC4	16	67916665	Missense_Mutation	SNP	G	TCGA-ZP-A9CV-01A-11D-A382-10	37185065	67916665	22438088	87	50716										
GPS2	2874	hgsc.bcm.edu	37	chr17	7216083	7216095	+	Frame_Shift_Del	DEL	GGTAGAATCGCGG	GGTAGAATCGCGG	-													0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	ataatctgatggtcacttgtGgtagaatcgcgggttctggc					rs3180570|rs147653865|rs201341909|rs142252898		TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	GGTAGAATCGCGG	GGTAGAATCGCGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr17:7216083_7216095delGGTAGAATCGCGG	ENST00000380728.2	-	11	1264_1276	c.964_976delCCGCGATTCTACC	c.(964-978)ccgcgattctaccacfs	p.PRFYH322fs	GPS2_ENST00000391950.3_Intron|GPS2_ENST00000389167.5_Frame_Shift_Del_p.PRFYH322fs|RP11-542C16.2_ENST00000575474.1_3'UTR			Q13227	GPS2_HUMAN	G protein pathway suppressor 2	322					cell cycle (GO:0007049)|inactivation of MAPK activity (GO:0000188)|JNK cascade (GO:0007254)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	GTPase inhibitor activity (GO:0005095)|transcription corepressor activity (GO:0003714)	p.R323*(1)		breast(1)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(4)	24		Prostate(122;0.157)				GGTCACTTGTGGTAGAATCGCGGGTTCTGGCTG	0.559																																					p.322_326del		Atlas-INDEL	.											.	GPS2	44	.	1	Substitution - Nonsense(1)	endometrium(1)	c.965_977del						.																																			SO:0001589	frameshift_variant	2874	exon11			.	U28963	CCDS11100.1	17p13.1	2006-04-29			ENSG00000132522	ENSG00000132522			4550	protein-coding gene	gene with protein product		601935				8943324	Standard	NM_004489		Approved		uc002gfx.1	Q13227	OTTHUMG00000102198	ENST00000380728.2:c.964_976delCCGCGATTCTACC	chr17.hg19:g.7216083_7216095delGGTAGAATCGCGG	ENSP00000370104:p.Pro322fs	62.0	0.0		57.0	10.0	NM_004489	B4DXA1|Q6FHM8	Frame_Shift_Del	DEL	ENST00000380728.2	hg19	CCDS11100.1																																																																																			.	.		0.559	GPS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220048.4	NM_004489		-	7216095	GGTAGAATCGCGG	-	7216083	7	5	363	1	0	1	0	1	0	0	0	0	6742	1348	47	0	11	0	GPS2	17	7216083	Frame_Shift_Del	DEL	GGTAGAATCGCGG	TCGA-ZP-A9CV-01A-11D-A382-10		7216083	73979127	88	50717										
DNAH9	1770	hgsc.bcm.edu	37	chr17	11593239	11593239	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	aagcactgtgtggaacacgcTgagctccctgagggcagtag	14	10	0	2			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr17:11593239T>C	ENST00000262442.4	+	20	4168	c.4100T>C	c.(4099-4101)cTg>cCg	p.L1367P	DNAH9_ENST00000454412.2_Missense_Mutation_p.L1367P	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	1367	Stem. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		TGGAACACGCTGAGCTCCCTG	0.592																																					p.L1367P		Atlas-SNP	.											.	DNAH9	695	.	0			c.T4100C						.						28	22	24					17																	11593239		2203	4300	6503	SO:0001583	missense	1770	exon20			ACACGCTGAGCTC	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.4100T>C	chr17.hg19:g.11593239T>C	ENSP00000262442:p.Leu1367Pro	102.0	0.0		109.0	5.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	hg19	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	T	14.44	2.537292	0.45176	.	.	ENSG00000007174	ENST00000262442;ENST00000454412	T;T	0.62498	0.02;0.02	5.72	5.72	0.89469	Dynein heavy chain, domain-2 (1);	0.000000	0.64402	D	0.000009	D	0.83926	0.5360	M	0.94101	3.495	0.80722	D	1	D	0.63880	0.993	D	0.70935	0.971	D	0.87659	0.2533	10	0.56958	D	0.05	.	16.0168	0.80445	0.0:0.0:0.0:1.0	.	1367	Q9NYC9	DYH9_HUMAN	P	1367	ENSP00000262442:L1367P;ENSP00000414874:L1367P	ENSP00000262442:L1367P	L	+	2	0	DNAH9	11533964	1.000000	0.71417	0.449000	0.26957	0.002000	0.02628	7.997000	0.88414	2.194000	0.70268	0.528000	0.53228	CTG	.	.		0.592	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		C	11593239	T	C	11593239	3	2	363	1	0	0	0	0	1	0	0	0	4610	1580	55	2	4178	2	DNAH9	17	11593239	Missense_Mutation	SNP	T	TCGA-ZP-A9CV-01A-11D-A382-10	4377156	11593239	69601971	89	50718										
EVI2B	2124	hgsc.bcm.edu	37	chr17	29632116	29632116	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	gtgaatttttgacagttgatGttggttgtgtggatggatta	14	1	0	3			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr17:29632116G>A	ENST00000330927.4	-	2	666	c.512C>T	c.(511-513)aCa>aTa	p.T171I	EVI2B_ENST00000544462.1_Missense_Mutation_p.T186I|NF1_ENST00000358273.4_Intron|NF1_ENST00000356175.3_Intron|EVI2B_ENST00000577894.1_Missense_Mutation_p.T171I	NM_006495.3	NP_006486.3	P34910	EVI2B_HUMAN	ecotropic viral integration site 2B	171						integral component of plasma membrane (GO:0005887)		p.0?(8)|p.?(3)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|urinary_tract(1)	12		all_cancers(10;6.97e-11)|all_epithelial(10;0.0051)|all_hematologic(16;0.0149)|Breast(31;0.0155)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|all_lung(9;0.0468)|Lung NSC(157;0.094)		UCEC - Uterine corpus endometrioid carcinoma (4;6.64e-05)|all cancers(4;6.88e-13)|Epithelial(4;8.95e-12)|OV - Ovarian serous cystadenocarcinoma(4;1.01e-11)|GBM - Glioblastoma multiforme(4;0.184)		GACAGTTGATGTTGGTTGTGT	0.343																																					p.T171I		Atlas-SNP	.											.	EVI2B	33	.	11	Whole gene deletion(8)|Unknown(3)	soft_tissue(7)|autonomic_ganglia(2)|lung(1)|central_nervous_system(1)	c.C512T						.						202	199	200					17																	29632116		2203	4300	6503	SO:0001583	missense	2124	exon2			GTTGATGTTGGTT		CCDS11266.1	17q11.2	2011-08-11			ENSG00000185862	ENSG00000185862		"CD molecules"	3500	protein-coding gene	gene with protein product		158381				1903357	Standard	NM_006495		Approved	D17S376, EVDB, CD361	uc002hgk.2	P34910	OTTHUMG00000132869	ENST00000330927.4:c.512C>T	chr17.hg19:g.29632116G>A	ENSP00000333779:p.Thr171Ile	308.0	0.0		245.0	76.0	NM_006495	B7Z4A7	Missense_Mutation	SNP	ENST00000330927.4	hg19	CCDS11266.1	.	.	.	.	.	.	.	.	.	.	G	9.806	1.181903	0.21787	.	.	ENSG00000185862	ENST00000330927;ENST00000544462	T;T	0.59906	0.24;0.23	5.55	-1.28	0.09318	.	0.843555	0.10035	N	0.724172	T	0.51517	0.1679	M	0.69823	2.125	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.003	T	0.42766	-0.9432	10	0.42905	T	0.14	-10.9741	6.7321	0.23388	0.3401:0.0:0.5486:0.1113	.	186;171	B7Z4A7;P34910	.;EVI2B_HUMAN	I	171;186	ENSP00000333779:T171I;ENSP00000439738:T186I	ENSP00000333779:T171I	T	-	2	0	EVI2B	26656242	0.000000	0.05858	0.000000	0.03702	0.032000	0.12392	-0.208000	0.09371	-0.756000	0.04703	-1.134000	0.01955	ACA	.	.		0.343	EVI2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256349.2	NM_006495		A	29632116	G	A	29632116	3	1	363	1	0	0	0	0	1	0	0	0	5290	1377	48	3	838	3	EVI2B	17	29632116	Missense_Mutation	SNP	G	TCGA-ZP-A9CV-01A-11D-A382-10	18038877	29632116	51563094	90	50719										
ERBB2	2064	hgsc.bcm.edu	37	chr17	37882886	37882886	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	aattctcccgcatggccaggGacccccagcgctttgtggtc	11	15	1	0			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr17:37882886G>T	ENST00000269571.5	+	24	3103	c.2944G>T	c.(2944-2946)Gac>Tac	p.D982Y	ERBB2_ENST00000584450.1_Missense_Mutation_p.D982Y|MIEN1_ENST00000474210.1_5'Flank|ERBB2_ENST00000445658.2_Missense_Mutation_p.D706Y|ERBB2_ENST00000541774.1_Missense_Mutation_p.D967Y|ERBB2_ENST00000406381.2_Missense_Mutation_p.D952Y|MIR4728_ENST00000580969.1_RNA|ERBB2_ENST00000584601.1_Missense_Mutation_p.D952Y|ERBB2_ENST00000540147.1_Missense_Mutation_p.D952Y			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	982	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	CATGGCCAGGGACCCCCAGCG	0.597		1	"A, Mis, O"		"breast, ovarian, other tumour types, NSCLC, gastric"					TCGA GBM(5;<1E-08)																											p.D982Y		Atlas-SNP	.		Dom	yes		17	17q21.1	2064	"v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"		E	.	ERBB2	429	.	0			c.G2944T						.						114	95	101					17																	37882886		2203	4300	6503	SO:0001583	missense	2064	exon24			GCCAGGGACCCCC	X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"CD molecules"	3430	protein-coding gene	gene with protein product	"neuro/glioblastoma derived oncogene homolog"	164870	"v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.2944G>T	chr17.hg19:g.37882886G>T	ENSP00000269571:p.Asp982Tyr	103.0	0.0		94.0	28.0	NM_004448	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Missense_Mutation	SNP	ENST00000269571.5	hg19	CCDS32642.1	.	.	.	.	.	.	.	.	.	.	G	15.90	2.970485	0.53614	.	.	ENSG00000141736	ENST00000406381;ENST00000541774;ENST00000445658;ENST00000269571;ENST00000540147	T;T;T;T;T	0.62364	0.03;0.03;0.03;0.03;0.03	5.29	5.29	0.74685	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.81702	0.4878	M	0.85197	2.74	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.994;0.977;0.994	D	0.84855	0.0816	9	0.87932	D	0	.	17.7407	0.88406	0.0:0.0:1.0:0.0	.	706;967;982	B4DTR1;P04626-4;P04626	.;.;ERBB2_HUMAN	Y	952;967;706;982;952	ENSP00000385185:D952Y;ENSP00000446466:D967Y;ENSP00000404047:D706Y;ENSP00000269571:D982Y;ENSP00000443562:D952Y	ENSP00000269571:D982Y	D	+	1	0	ERBB2	35136412	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.860000	0.99555	2.473000	0.83533	0.655000	0.94253	GAC	.	.		0.597	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2			T	37882886	G	T	37882886	3	4	363	1	0	0	0	0	1	0	0	0	5208	1174	41	3	3038	3	ERBB2	17	37882886	Missense_Mutation	SNP	G	TCGA-ZP-A9CV-01A-11D-A382-10	8250770	37882886	43312324	91	50720										
MED24	9862	hgsc.bcm.edu	37	chr17	38189360	38189360	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	accagggactgcgtctcgccTgtcaggttcatggtgccctc	12	14	3	0			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr17:38189360T>C	ENST00000394128.2	-	8	852	c.771A>G	c.(769-771)acA>acG	p.T257T	MED24_ENST00000501516.3_Silent_p.T276T|MED24_ENST00000394126.1_Silent_p.T282T|MED24_ENST00000394127.2_Silent_p.T244T|MED24_ENST00000356271.3_Silent_p.T244T|MED24_ENST00000479829.1_5'Flank	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	257					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	41	Colorectal(19;0.000442)					GCGTCTCGCCTGTCAGGTTCA	0.637																																					p.T257T		Atlas-SNP	.											.	MED24	89	.	0			c.A771G						.						61	52	55					17																	38189360		2203	4300	6503	SO:0001819	synonymous_variant	9862	exon8			CTCGCCTGTCAGG	AF055995	CCDS11359.1, CCDS42315.1	17q21.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000008838	ENSG00000008838			22963	protein-coding gene	gene with protein product		607000	"thyroid hormone receptor associated protein 4", "cofactor required for Sp1 transcriptional activation, subunit 4, 100kDa"	THRAP4, CRSP4			Standard	NM_001079518		Approved	TRAP100, KIAA0130, DRIP100, CRSP100	uc002htt.3	O75448	OTTHUMG00000133329	ENST00000394128.2:c.771A>G	chr17.hg19:g.38189360T>C		51.0	0.0		44.0	18.0	NM_014815	A8K4S5|B3KMR9|Q14143|Q9NNY5	Silent	SNP	ENST00000394128.2	hg19	CCDS11359.1																																																																																			.	.		0.637	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815		C	38189360	T	C	38189360	2	2	363	1	0	0	0	0	0	0	0	1	9451	1567	55	2		2	MED24	17	38189360	Silent	SNP	T	TCGA-ZP-A9CV-01A-11D-A382-10	306474	38189360	43005850	92	50721										
SPATA20	64847	hgsc.bcm.edu	37	chr17	48625802	48625802	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	cctcctacaacatgcctacaAtcctgtggactggtgagcac	8	14	0	1			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr17:48625802A>G	ENST00000356488.4	+	2	319	c.236A>G	c.(235-237)aAt>aGt	p.N79S	SPATA20_ENST00000006658.6_Missense_Mutation_p.N95S|SPATA20_ENST00000511937.1_3'UTR|SPATA20_ENST00000393244.3_Missense_Mutation_p.N35S	NM_001258372.1	NP_001245301.1	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20	79					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)	catalytic activity (GO:0003824)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;9.38e-09)			CATGCCTACAATCCTGTGGAC	0.622																																					p.N95S		Atlas-SNP	.											.	SPATA20	59	.	0			c.A284G						.						115	104	108					17																	48625802		2203	4300	6503	SO:0001583	missense	64847	exon3			CCTACAATCCTGT		CCDS11571.1, CCDS58563.1, CCDS58564.1	17q21.33	2011-03-17			ENSG00000006282	ENSG00000006282			26125	protein-coding gene	gene with protein product	"hypothetical protein FLJ21347"	613939				12477932	Standard	NM_022827		Approved	FLJ21347, SSP411, Tisp78	uc002ird.3	Q8TB22	OTTHUMG00000162162	ENST00000356488.4:c.236A>G	chr17.hg19:g.48625802A>G	ENSP00000348878:p.Asn79Ser	92.0	0.0		78.0	8.0	NM_022827	Q2TA99|Q2XUZ6|Q6P0P1|Q8WVW3|Q9H747	Missense_Mutation	SNP	ENST00000356488.4	hg19	CCDS58563.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.702713	0.88924	.	.	ENSG00000006282	ENST00000006658;ENST00000356488;ENST00000393244	T;T;T	0.48522	0.81;0.81;0.81	4.73	4.73	0.59995	Thioredoxin-like fold (2);Domain of unknown function DUF255 (1);	0.000000	0.85682	D	0.000000	T	0.74344	0.3704	M	0.91249	3.19	0.53688	D	0.999974	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.997	T	0.81378	-0.0960	10	0.87932	D	0	-21.8816	14.384	0.66931	1.0:0.0:0.0:0.0	.	79;79;95	B4DZC5;Q8TB22;Q8TB22-2	.;SPT20_HUMAN;.	S	95;79;35	ENSP00000006658:N95S;ENSP00000348878:N79S;ENSP00000376935:N35S	ENSP00000006658:N95S	N	+	2	0	SPATA20	45980801	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	8.687000	0.91255	1.988000	0.58038	0.459000	0.35465	AAT	.	.		0.622	SPATA20-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367651.1	NM_022827		G	48625802	A	G	48625802	3	3	363	1	0	0	0	0	1	0	0	0	15021	101	4	2	294	2	SPATA20	17	48625802	Missense_Mutation	SNP	A	TCGA-ZP-A9CV-01A-11D-A382-10	10436442	48625802	32569408	93	50722										
SMARCD2	6603	hgsc.bcm.edu	37	chr17	61911879	61911879	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	gtgcacttgacgttgaggtcTccaggccgttttacttggaa	12	9	1	2			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr17:61911879T>C	ENST00000448276.2	-	7	1141	c.876A>G	c.(874-876)ggA>ggG	p.G292G	SMARCD2_ENST00000225742.9_Silent_p.G217G|SMARCD2_ENST00000323347.10_Silent_p.G244G	NM_001098426.1	NP_001091896.1	Q92925	SMRD2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2	292					ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|nucleosome disassembly (GO:0006337)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(1)	8						CGTTGAGGTCTCCAGGCCGTT	0.612											OREG0024642	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G292G		Atlas-SNP	.											.	SMARCD2	29	.	0			c.A876G						.						171	164	166					17																	61911879		2051	4224	6275	SO:0001819	synonymous_variant	6603	exon7			GAGGTCTCCAGGC	U66618	CCDS45756.1	17q23.3	2014-07-16			ENSG00000108604	ENSG00000108604			11107	protein-coding gene	gene with protein product	"mammalian chromatin remodeling complex BRG1-associated factor 60B", "Swp73-like protein", "chromatin remodeling complex BAF60B subunit", "SWI/SNF complex 60 kDa subunit B"	601736				8804307, 9693044	Standard	NM_001098426		Approved	BAF60B, Rsc6p, CRACD2, PRO2451	uc010deb.1	Q92925	OTTHUMG00000179045	ENST00000448276.2:c.876A>G	chr17.hg19:g.61911879T>C		76.0	0.0	1057	82.0	23.0	NM_001098426	A5PLL5|A6NNQ7|B4DV56|B4E1R6|Q7L2I6|Q9UHZ1	Silent	SNP	ENST00000448276.2	hg19	CCDS45756.1																																																																																			.	.		0.612	SMARCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444544.1	NM_001098426		C	61911879	T	C	61911879	2	2	363	1	0	0	0	0	0	0	0	1	14793	1538	54	2		2	SMARCD2	17	61911879	Silent	SNP	T	TCGA-ZP-A9CV-01A-11D-A382-10	13286077	61911879	19283331	94	50723										
ABCA10	10349	hgsc.bcm.edu	37	chr17	67212380	67212380	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	aagaaaggccatataagctaTagagtgtgaatatcaccatg	9	6	1	3			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr17:67212380T>C	ENST00000269081.4	-	8	1559	c.650A>G	c.(649-651)tAt>tGt	p.Y217C	ABCA10_ENST00000416101.2_Missense_Mutation_p.Y217C|ABCA10_ENST00000432313.2_Missense_Mutation_p.Y217C	NM_080282.3	NP_525021.3	Q8WWZ4	ABCAA_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 10	217					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(34)|ovary(2)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	81	Breast(10;6.95e-12)					ATATAAGCTATAGAGTGTGAA	0.343																																					p.Y217C		Atlas-SNP	.											.	ABCA10	209	.	0			c.A650G						.						156	161	159					17																	67212380		2203	4300	6503	SO:0001583	missense	10349	exon8			AAGCTATAGAGTG	AY247065	CCDS11684.1	17q24	2012-03-14			ENSG00000154263	ENSG00000154263		"ATP binding cassette transporters / subfamily A"	30	protein-coding gene	gene with protein product		612508				12821155, 11435397	Standard	NM_080282		Approved	EST698739	uc010dfa.1	Q8WWZ4	OTTHUMG00000164716	ENST00000269081.4:c.650A>G	chr17.hg19:g.67212380T>C	ENSP00000269081:p.Tyr217Cys	252.0	0.0		241.0	72.0	NM_080282	C9JZH2|C9K035|Q6PIQ6|Q7Z2I9|Q7Z7P7|Q86TD2	Missense_Mutation	SNP	ENST00000269081.4	hg19	CCDS11684.1	.	.	.	.	.	.	.	.	.	.	A	14.82	2.650649	0.47362	.	.	ENSG00000154263	ENST00000269081;ENST00000416101;ENST00000432313	D;D;D	0.87887	-2.31;-2.31;-2.31	3.34	3.34	0.38264	.	0.000000	0.34906	U	0.003581	D	0.82504	0.5051	N	0.14661	0.345	0.09310	N	1	B;P	0.40282	0.365;0.711	B;P	0.52627	0.062;0.704	T	0.73720	-0.3894	10	0.87932	D	0	.	6.757	0.23520	0.7904:0.0:0.0:0.2096	.	217;217	E5RFP5;Q8WWZ4	.;ABCAA_HUMAN	C	217	ENSP00000269081:Y217C;ENSP00000407772:Y217C;ENSP00000387674:Y217C	ENSP00000269081:Y217C	Y	-	2	0	ABCA10	64723975	0.019000	0.18553	0.002000	0.10522	0.493000	0.33554	1.342000	0.33919	0.379000	0.24794	-0.311000	0.09066	TAT	.	.		0.343	ABCA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379881.4	NM_080282		C	67212380	T	C	67212380	3	2	363	1	0	0	0	0	1	0	0	0	29	1406	49	2	4113	2	ABCA10	17	67212380	Missense_Mutation	SNP	T	TCGA-ZP-A9CV-01A-11D-A382-10	5300501	67212380	13982830	95	50724										
ELAC1	55520	hgsc.bcm.edu	37	chr18	48500817	48500820	+	Frame_Shift_Del	DEL	CCAT	CCAT	-													0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	tggggacgggtgcagcatacCcatctccaacccggggtgcc							TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	CCAT	CCAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr18:48500817_48500820delCCAT	ENST00000269466.3	+	2	150_153	c.43_46delCCAT	c.(43-48)ccatctfs	p.PS15fs	RP11-729L2.2_ENST00000590722.2_Frame_Shift_Del_p.PS15fs|SMAD4_ENST00000452201.2_5'UTR|ELAC1_ENST00000591429.1_Frame_Shift_Del_p.PS15fs|ELAC1_ENST00000588577.1_Frame_Shift_Del_p.PS15fs|RP11-729L2.2_ENST00000588256.1_3'UTR	NM_018696.2	NP_061166.1	Q9H777	RNZ1_HUMAN	elaC ribonuclease Z 1	15					tRNA 3'-trailer cleavage (GO:0042779)	cytosol (GO:0005829)|nucleus (GO:0005634)	endoribonuclease activity, producing 5'-phosphomonoesters (GO:0016891)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(4)|prostate(1)	6		Colorectal(6;0.0269)|all_epithelial(6;0.0729)		Colorectal(21;0.000943)|COAD - Colon adenocarcinoma(17;0.0398)|READ - Rectum adenocarcinoma(32;0.0894)|STAD - Stomach adenocarcinoma(97;0.18)		TGCAGCATACCCATCTCCAACCCG	0.515																																					p.14_15del		Atlas-INDEL	.											.	ELAC1	17	.	0			c.42_45del						.																																			SO:0001589	frameshift_variant	55520	exon2			.	AB029151	CCDS11949.1	18q21	2013-05-24	2013-05-24		ENSG00000141642	ENSG00000141642	3.1.26.11		14197	protein-coding gene	gene with protein product	"tRNA Z (short form)", "RNaseZ(S)"	608079	"elaC (E. coli) homolog 1", "elaC homolog 1 (E. coli)"			12711671, 21559454	Standard	NM_018696		Approved	D29	uc002lez.3	Q9H777	OTTHUMG00000132695	ENST00000269466.3:c.43_46delCCAT	chr18.hg19:g.48500817_48500820delCCAT	ENSP00000269466:p.Pro15fs	129.0	0.0		111.0	36.0	NM_018696	Q9NS99	Frame_Shift_Del	DEL	ENST00000269466.3	hg19	CCDS11949.1																																																																																			.	.		0.515	ELAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255992.2			-	48500820	CCAT	-	48500817	7	5	363	1	0	1	0	1	0	0	0	0	5048	623	22	0	45	0	ELAC1	18	48500817	Frame_Shift_Del	DEL	CCAT	TCGA-ZP-A9CV-01A-11D-A382-10		48500817	29576431	96	50725										
PKN1	5585	hgsc.bcm.edu	37	chr19	14580605	14580605	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	gctgggcctacagtttcttcAcgaacacaagatcgtctaca	8	12	3	1			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr19:14580605A>G	ENST00000242783.6	+	17	2360	c.2195A>G	c.(2194-2196)cAc>cGc	p.H732R	PKN1_ENST00000342216.4_Missense_Mutation_p.H738R	NM_002741.3	NP_002732.3	Q16512	PKN1_HUMAN	protein kinase N1	732	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|epithelial cell migration (GO:0010631)|histone H3-T11 phosphorylation (GO:0035407)|hyperosmotic response (GO:0006972)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|GTP-Rho binding (GO:0017049)|histone binding (GO:0042393)|histone deacetylase binding (GO:0042826)|histone kinase activity (H3-T11 specific) (GO:0035402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|Rac GTPase binding (GO:0048365)			breast(3)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)	31						CAGTTTCTTCACGAACACAAG	0.597																																					p.H738R	NSCLC(185;2539 2965 10733 52867)	Atlas-SNP	.											.	PKN1	99	.	0			c.A2213G						.						128	130	129					19																	14580605		2093	4214	6307	SO:0001583	missense	5585	exon17			TTCTTCACGAACA	S75546	CCDS42513.1, CCDS42514.1	19p13.12	2008-05-14	2004-07-01	2004-07-01	ENSG00000123143	ENSG00000123143			9405	protein-coding gene	gene with protein product		601032	"protein kinase C-like 1"	PRKCL1		9570957	Standard	NM_002741		Approved	DBK, PRK1, PKN, MGC46204, PAK1	uc002myq.3	Q16512	OTTHUMG00000039611	ENST00000242783.6:c.2195A>G	chr19.hg19:g.14580605A>G	ENSP00000242783:p.His732Arg	87.0	0.0		57.0	4.0	NM_213560	A8K7W5|B2R9R4|B3KVN3|Q15143|Q504U4|Q8IUV5|Q9UD44	Missense_Mutation	SNP	ENST00000242783.6	hg19	CCDS42513.1	.	.	.	.	.	.	.	.	.	.	A	16.08	3.020478	0.54576	.	.	ENSG00000123143	ENST00000242783;ENST00000342216	D;D	0.84516	-1.86;-1.86	4.06	4.06	0.47325	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	U	0.000001	D	0.92691	0.7677	M	0.90145	3.09	0.45580	D	0.998527	D;D	0.76494	0.999;0.999	D;D	0.81914	0.991;0.995	D	0.93591	0.6921	10	0.87932	D	0	-23.9526	11.2607	0.49080	1.0:0.0:0.0:0.0	.	738;732	Q16512-2;Q16512	.;PKN1_HUMAN	R	732;738	ENSP00000242783:H732R;ENSP00000343325:H738R	ENSP00000242783:H732R	H	+	2	0	PKN1	14441605	1.000000	0.71417	0.976000	0.42696	0.332000	0.28634	8.362000	0.90100	1.828000	0.53243	0.402000	0.26972	CAC	.	.		0.597	PKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095510.1	NM_002741, NM_213560		G	14580605	A	G	14580605	3	3	363	1	0	0	0	0	1	0	0	0	11988	159	6	2	2304	2	PKN1	19	14580605	Missense_Mutation	SNP	A	TCGA-ZP-A9CV-01A-11D-A382-10		14580605	44548378	97	50726										
C19orf2	8725	hgsc.bcm.edu	37	chr19	30496346	30496346	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	tgaattcacagaagatttgcAgaaaatgagcgatgtgagta	11	4	1	6			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr19:30496346A>G	ENST00000542441.2	+	5	743	c.446A>G	c.(445-447)cAg>cGg	p.Q149R	URI1_ENST00000360605.4_Missense_Mutation_p.Q131R|URI1_ENST00000392271.1_Missense_Mutation_p.Q73R|URI1_ENST00000312051.6_Missense_Mutation_p.Q109R|URI1_ENST00000574176.1_3'UTR			O94763	RMP_HUMAN	URI1, prefoldin-like chaperone	149					cellular response to growth factor stimulus (GO:0071363)|cellular response to steroid hormone stimulus (GO:0071383)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of phosphatase activity (GO:0010923)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein folding (GO:0006457)|regulation of cell growth (GO:0001558)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to virus (GO:0009615)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, core complex (GO:0005665)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|prefoldin complex (GO:0016272)	chromatin binding (GO:0003682)|protein phosphatase inhibitor activity (GO:0004864)|RNA polymerase II transcription corepressor activity (GO:0001106)										GAAGATTTGCAGAAAATGAGC	0.274																																					p.Q149R		Atlas-SNP	.											.	.	.	.	0			c.A446G						.						47	49	48					19																	30496346		2202	4294	6496	SO:0001583	missense	8725	exon5			ATTTGCAGAAAAT	AF091095	CCDS12420.1, CCDS58658.1	19q12	2012-04-17	2011-11-21	2011-11-21	ENSG00000105176	ENSG00000105176		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	13236	protein-coding gene	gene with protein product	"unconventional prefoldin RPB5 interactor", "RPB5-mediating protein", "protein phosphatase 1, regulatory subunit 19"	603494	"chromosome 19 open reading frame 2"	C19orf2		9878255, 9819440	Standard	NM_003796		Approved	RMP, NNX3, FLJ10575, URI, PPP1R19	uc002nsr.3	O94763		ENST00000542441.2:c.446A>G	chr19.hg19:g.30496346A>G	ENSP00000442436:p.Gln149Arg	468.0	0.0		417.0	129.0	NM_003796	A8K805|H7BY42|Q8TC23|Q9UNU3	Missense_Mutation	SNP	ENST00000542441.2	hg19	CCDS12420.1	.	.	.	.	.	.	.	.	.	.	A	14.75	2.629006	0.46944	.	.	ENSG00000105176	ENST00000360605;ENST00000392271;ENST00000542441;ENST00000312051	T;T;T	0.08008	3.14;3.14;3.14	5.53	5.53	0.82687	Prefoldin (1);	0.156761	0.64402	D	0.000020	T	0.12008	0.0292	L	0.54323	1.7	0.43255	D	0.995187	P;B;P	0.51057	0.818;0.075;0.941	B;B;P	0.45167	0.311;0.076;0.472	T	0.21177	-1.0253	10	0.15066	T	0.55	-16.7344	15.6521	0.77104	1.0:0.0:0.0:0.0	.	109;149;147	F8W9T0;O94763;Q8TC23	.;RMP_HUMAN;.	R	147;73;149;109	ENSP00000376097:Q73R;ENSP00000442436:Q149R;ENSP00000312530:Q109R	ENSP00000312530:Q109R	Q	+	2	0	C19orf2	35188186	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.602000	0.90868	2.096000	0.63516	0.454000	0.30748	CAG	.	.		0.274	URI1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439756.1	NM_134447		G	30496346	A	G	30496346	3	3	363	1	0	0	0	0	1	0	0	0	1913	188	7	2	464	2	C19orf2	19	30496346	Missense_Mutation	SNP	A	TCGA-ZP-A9CV-01A-11D-A382-10	15915741	30496346	28632637	98	50727										
TSHZ3	57616	hgsc.bcm.edu	37	chr19	31768721	31768721	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	gctgcggaagcccccatcgcTggatgcctccatcttgatgg	12	14	1	1			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr19:31768721T>C	ENST00000240587.4	-	2	2305	c.1978A>G	c.(1978-1980)Agc>Ggc	p.S660G		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	660					in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					CCCCCATCGCTGGATGCCTCC	0.657																																					p.S660G		Atlas-SNP	.											.	TSHZ3	549	.	0			c.A1978G						.						15	17	16					19																	31768721		2190	4279	6469	SO:0001583	missense	57616	exon2			CATCGCTGGATGC	AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	30700	protein-coding gene	gene with protein product	"teashirt 3"	614119	"zinc finger protein 537", "teashirt family zinc finger 3"	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.1978A>G	chr19.hg19:g.31768721T>C	ENSP00000240587:p.Ser660Gly	53.0	0.0		45.0	19.0	NM_020856	Q9H0G6|Q9P254	Missense_Mutation	SNP	ENST00000240587.4	hg19	CCDS12421.2	.	.	.	.	.	.	.	.	.	.	T	6.024	0.372807	0.11409	.	.	ENSG00000121297	ENST00000240587	T	0.40756	1.02	5.5	2.3	0.28687	.	0.520911	0.24373	N	0.039081	T	0.27169	0.0666	L	0.27053	0.805	0.26666	N	0.971811	B	0.02656	0.0	B	0.01281	0.0	T	0.14952	-1.0454	10	0.33141	T	0.24	-11.4673	9.1577	0.37002	0.0:0.2066:0.0:0.7934	.	660	Q63HK5	TSH3_HUMAN	G	660	ENSP00000240587:S660G	ENSP00000240587:S660G	S	-	1	0	TSHZ3	36460561	1.000000	0.71417	0.051000	0.19133	0.266000	0.26442	2.296000	0.43584	0.074000	0.16767	0.528000	0.53228	AGC	.	.		0.657	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856		C	31768721	T	C	31768721	3	2	363	1	0	0	0	0	1	0	0	0	16640	1580	55	2	1271	2	TSHZ3	19	31768721	Missense_Mutation	SNP	T	TCGA-ZP-A9CV-01A-11D-A382-10	1272375	31768721	27360262	99	50728										
CEBPA	1050	hgsc.bcm.edu	37	chr19	33792731	33792731	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	gggcggccaggtgcgcgggcGgcgggtgcgggtgcgggtgc	26	10	0	0			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr19:33792731G>T	ENST00000498907.2	-	1	739	c.590C>A	c.(589-591)cCg>cAg	p.P197Q	CTD-2540B15.11_ENST00000589932.1_RNA|CEBPA-AS1_ENST00000592982.2_RNA|CTD-2540B15.7_ENST00000587312.1_RNA	NM_004364.3	NP_004355.2	P49715	CEBPA_HUMAN	CCAAT/enhancer binding protein (C/EBP), alpha	197					acute-phase response (GO:0006953)|brown fat cell differentiation (GO:0050873)|cell maturation (GO:0048469)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|cholesterol metabolic process (GO:0008203)|cytokine-mediated signaling pathway (GO:0019221)|embryonic placenta development (GO:0001892)|generation of precursor metabolites and energy (GO:0006091)|inner ear development (GO:0048839)|liver development (GO:0001889)|lung development (GO:0030324)|macrophage differentiation (GO:0030225)|mitochondrion organization (GO:0007005)|myeloid cell differentiation (GO:0030099)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ regeneration (GO:0031100)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|response to glucocorticoid (GO:0051384)|response to vitamin B2 (GO:0033274)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|urea cycle (GO:0000050)|viral process (GO:0016032)|white fat cell differentiation (GO:0050872)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|Rb-E2F complex (GO:0035189)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.P185_P197del(1)|p.S190_P198del(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(912)|lung(5)|prostate(1)|stomach(1)	920	Esophageal squamous(110;0.137)					GTGCGCGGGCGGCGGGTGCGG	0.771			"Mis, N, F"		"AML, MDS"				Acute Myeloid Leukemia, Familial, associated with CEBPA germline mutation																												p.P197Q		Atlas-SNP	.		Dom	yes		19	19q13.1	1050	"CCAAT/enhancer binding protein (C/EBP), alpha"		L	.	CEBPA	986	.	2	Deletion - In frame(2)	haematopoietic_and_lymphoid_tissue(2)	c.C590A						.						2	2	2					19																	33792731		646	1482	2128	SO:0001583	missense	1050	exon1	Familial Cancer Database	Familial AML	GCGGGCGGCGGGT	M37197	CCDS54243.1	19q13.1	2014-09-17				ENSG00000245848		"basic leucine zipper proteins"	1833	protein-coding gene	gene with protein product		116897		CEBP		1535333, 1840554	Standard	NM_004364		Approved	C/EBP-alpha	uc002nun.3	P49715		ENST00000498907.2:c.590C>A	chr19.hg19:g.33792731G>T	ENSP00000427514:p.Pro197Gln	323.0	0.0		183.0	13.0	NM_004364	A7LNP2|P78319|Q05CA4	Missense_Mutation	SNP	ENST00000498907.2	hg19	CCDS54243.1	.	.	.	.	.	.	.	.	.	.	G	5.481	0.273783	0.10403	.	.	ENSG00000245848	ENST00000498907	T	0.18174	2.23	4.04	4.04	0.47022	.	.	.	.	.	T	0.07863	0.0197	N	0.08118	0	0.26767	N	0.969872	B	0.26147	0.143	B	0.17979	0.02	T	0.28776	-1.0033	9	0.14252	T	0.57	.	9.2485	0.37541	0.0:0.0:0.7839:0.2161	.	197	P49715	CEBPA_HUMAN	Q	197	ENSP00000427514:P197Q	ENSP00000427514:P197Q	P	-	2	0	CEBPA	38484571	0.997000	0.39634	0.974000	0.42286	0.061000	0.15899	3.946000	0.56644	1.799000	0.52666	0.289000	0.19496	CCG	.	.		0.771	CEBPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365012.1	NM_004364		T	33792731	G	T	33792731	3	4	363	1	0	0	0	0	1	0	0	0	3201	1116	39	1	490	1	CEBPA	19	33792731	Missense_Mutation	SNP	G	TCGA-ZP-A9CV-01A-11D-A382-10	2024010	33792731	25336252	100	50729										
CCDC114	93233	hgsc.bcm.edu	37	chr19	48821778	48821778	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	cttgacctggttctgggctgCgctgatctgcacctggagat	13	11	2	3	rs376555574		TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr19:48821778C>T	ENST00000315396.7	-	3	797	c.115G>A	c.(115-117)Gca>Aca	p.A39T	CCDC114_ENST00000497803.1_5'UTR	NM_144577.3	NP_653178.3	Q96M63	CC114_HUMAN	coiled-coil domain containing 114	39					outer dynein arm assembly (GO:0036158)	cilium (GO:0005929)|outer dynein arm (GO:0036157)				cervix(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|stomach(1)	24		all_epithelial(76;9.64e-05)|all_lung(116;0.000147)|Lung NSC(112;0.000251)|Prostate(7;0.0187)|all_neural(266;0.0228)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000162)|Epithelial(262;0.0134)|GBM - Glioblastoma multiforme(486;0.0143)		TTCTGGGCTGCGCTGATCTGC	0.657																																					p.A39T		Atlas-SNP	.											.	CCDC114	100	.	0			c.G115A						.	C	THR/ALA	1,1383		0,1,691	27	29	29		115	-1.6	0	19		29	0,3182		0,0,1591	no	missense	CCDC114	NM_144577.3	58	0,1,2282	TT,TC,CC		0.0,0.0723,0.0219	benign	39/671	48821778	1,4565	692	1591	2283	SO:0001583	missense	93233	exon3			GGGCTGCGCTGAT	BC025752	CCDS12714.2	19q13.32	2013-02-22			ENSG00000105479	ENSG00000105479			26560	protein-coding gene	gene with protein product		615038				23261302, 23261303	Standard	NM_144577		Approved	FLJ32926, CILD20	uc002pir.2	Q96M63	OTTHUMG00000156161	ENST00000315396.7:c.115G>A	chr19.hg19:g.48821778C>T	ENSP00000318429:p.Ala39Thr	43.0	0.0		35.0	5.0	NM_144577	Q6ZRL4|Q96M06|Q9UFG8	Missense_Mutation	SNP	ENST00000315396.7	hg19	CCDS12714.2	.	.	.	.	.	.	.	.	.	.	C	10.35	1.326454	0.24080	7.23E-4	0.0	ENSG00000105479	ENST00000315396	T	0.22743	1.94	4.56	-1.63	0.08345	.	.	.	.	.	T	0.09069	0.0224	N	0.14661	0.345	0.09310	N	1	P;P	0.47302	0.893;0.745	B;B	0.35182	0.197;0.123	T	0.27434	-1.0074	9	0.42905	T	0.14	-6.7784	7.666	0.28432	0.0:0.4221:0.0:0.5779	.	39;39	Q96M63;Q96M63-5	CC114_HUMAN;.	T	39	ENSP00000318429:A39T	ENSP00000318429:A39T	A	-	1	0	CCDC114	53513590	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.043000	0.03535	-0.039000	0.13602	-0.482000	0.04802	GCA	.	.		0.657	CCDC114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343207.1	NM_144577		T	48821778	C	T	48821778	3	4	363	1	0	0	0	0	1	0	0	0	2753	768	27	1	1945	1	CCDC114	19	48821778	Missense_Mutation	SNP	C	TCGA-ZP-A9CV-01A-11D-A382-10	15029047	48821778	10307205	101	50730										
MYH14	79784	hgsc.bcm.edu	37	chr19	50812373	50812373	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	ggctgcagcgtgagctggaaGatgtcacagagtcggccgag	17	9	1	3			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr19:50812373G>A	ENST00000596571.1	+	39	5776	c.5776G>A	c.(5776-5778)Gat>Aat	p.D1926N	MYH14_ENST00000440075.2_Missense_Mutation_p.D1967N|MYH14_ENST00000262269.8_Missense_Mutation_p.D1967N|MYH14_ENST00000376970.2_Missense_Mutation_p.D1959N|MYH14_ENST00000601313.1_Missense_Mutation_p.D1967N|MYH14_ENST00000598205.1_Missense_Mutation_p.D1934N|MYH14_ENST00000425460.1_Missense_Mutation_p.D1934N|CTB-191K22.5_ENST00000595563.1_RNA			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	1926					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		TGAGCTGGAAGATGTCACAGA	0.642																																					p.D1967N		Atlas-SNP	.											.	MYH14	261	.	0			c.G5899A						.						83	86	85					19																	50812373		2103	4231	6334	SO:0001583	missense	79784	exon42			CTGGAAGATGTCA	AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"Myosins / Myosin superfamily : Class II"	23212	protein-coding gene	gene with protein product		608568	"myosin, heavy polypeptide 14", "myosin, heavy chain 14"	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.5776G>A	chr19.hg19:g.50812373G>A	ENSP00000472819:p.Asp1926Asn	221.0	0.0		194.0	64.0	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Missense_Mutation	SNP	ENST00000596571.1	hg19	CCDS59411.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.847853	0.91277	.	.	ENSG00000105357	ENST00000440075;ENST00000376970;ENST00000425460;ENST00000376965;ENST00000262269	T;T;T;T	0.80480	-1.38;-1.38;-1.38;-1.38	3.82	3.82	0.43975	Myosin tail (1);	.	.	.	.	D	0.86719	0.6000	M	0.72118	2.19	0.52501	D	0.99995	D;D;D	0.59357	0.968;0.974;0.985	P;P;P	0.61003	0.57;0.842;0.882	D	0.88467	0.3059	9	0.87932	D	0	.	13.5874	0.61940	0.0:0.0:1.0:0.0	.	1967;1926;1934	Q7Z406-2;Q7Z406;Q7Z406-6	.;MYH14_HUMAN;.	N	1967;1959;1934;1710;1967	ENSP00000406273:D1967N;ENSP00000366169:D1959N;ENSP00000407879:D1934N;ENSP00000262269:D1967N	ENSP00000262269:D1967N	D	+	1	0	MYH14	55504185	1.000000	0.71417	0.999000	0.59377	0.925000	0.55904	9.003000	0.93577	2.151000	0.67156	0.462000	0.41574	GAT	.	.		0.642	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729		A	50812373	G	A	50812373	3	1	363	1	0	0	0	0	1	0	0	0	10042	942	33	3	6061	3	MYH14	19	50812373	Missense_Mutation	SNP	G	TCGA-ZP-A9CV-01A-11D-A382-10	1990595	50812373	8316610	102	50731										
ZNF321	399669	hgsc.bcm.edu	37	chr19	53432469	53432469	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	cagtcaactctttgatttctGtcatgggtgcttcgtgacca	9	10	4	2			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chr19:53432469G>A	ENST00000391777.3	-	4	510	c.389C>T	c.(388-390)aCa>aTa	p.T130I	ZNF816-ZNF321P_ENST00000313956.4_RNA|ZNF816_ENST00000434371.2_Missense_Mutation_p.T130I|ZNF816_ENST00000549216.1_Missense_Mutation_p.T61I			Q8N8H1	ZN321_HUMAN	zinc finger protein 321, pseudogene	61										endometrium(1)|large_intestine(1)|lung(1)|ovary(1)	4						TTTGATTTCTGTCATGGGTGC	0.408																																					p.T130I		Atlas-SNP	.											.	.	.	.	0			c.C389T						.						186	186	186					19																	53432469		2203	4300	6503	SO:0001583	missense	100529240	exon4			ATTTCTGTCATGG	AK096828		19q13.4	2013-01-08	2011-04-19	2011-04-19	ENSG00000221874	ENSG00000221874			13827	pseudogene	pseudogene			"zinc finger protein 321"	ZNF321			Standard	NR_037805		Approved	MGC35402		Q8N8H1	OTTHUMG00000167760	ENST00000391777.3:c.389C>T	chr19.hg19:g.53432469G>A	ENSP00000375656:p.Thr130Ile	111.0	0.0		97.0	40.0	NM_001202473	B7ZB38|Q68DZ0|Q86SS5	Missense_Mutation	SNP	ENST00000391777.3	hg19	CCDS56101.1	.	.	.	.	.	.	.	.	.	.	g	10.51	1.371635	0.24771	.	.	ENSG00000180257;ENSG00000180257;ENSG00000221874	ENST00000549216;ENST00000434371;ENST00000391777	T;T;T	0.02280	4.36;5.64;5.64	1.23	0.147	0.14838	.	.	.	.	.	T	0.05731	0.0150	L	0.58810	1.83	0.09310	N	1	D	0.61697	0.99	P	0.61592	0.891	T	0.36578	-0.9742	9	0.36615	T	0.2	.	3.4192	0.07386	0.2802:0.0:0.7198:0.0	.	61	Q8N8H1	ZN321_HUMAN	I	61;130;130	ENSP00000449832:T61I;ENSP00000438519:T130I;ENSP00000375656:T130I	ENSP00000375656:T130I	T	-	2	0	ZNF321P;ZNF816	58124281	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	0.173000	0.16724	0.107000	0.17824	0.134000	0.15878	ACA	.	.		0.408	ZNF321P-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000396130.1	NR_037805		A	53432469	G	A	53432469	3	1	363	1	0	0	0	0	1	0	0	0	17855	1377	48	3	316	3	ZNF321	19	53432469	Missense_Mutation	SNP	G	TCGA-ZP-A9CV-01A-11D-A382-10	2620096	53432469	5696514	103	50732										
XG	7499	hgsc.bcm.edu	37	chrX	2724766	2724766	+	Intron	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	agggggctatagactcaactCtcgttatggaaatacttatg	10	7	2	1			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chrX:2724766C>T	ENST00000381174.5	+	8	598				XG_ENST00000426774.1_Intron|XG_ENST00000419513.2_Missense_Mutation_p.S133F			P55808	XG_HUMAN	Xg blood group							integral component of plasma membrane (GO:0005887)				endometrium(1)|large_intestine(3)|lung(3)|ovary(1)	8		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				AGACTCAACTCTCGTTATGGA	0.408																																					p.S133F		Atlas-SNP	.											.	XG	22	.	0			c.C398T						.						151	106	120					X																	2724766		692	1590	2282	SO:0001627	intron_variant	7499	exon8			TCAACTCTCGTTA	AF380356	CCDS14120.1, CCDS48073.1	Xp22.32	2014-07-19	2006-01-12		ENSG00000124343	ENSG00000124343		"Blood group antigens", "Pseudoautosomal regions / PAR1"	12806	protein-coding gene	gene with protein product		300879	"Xg blood group (pseudoautosomal boundary-divided on the X chromosome)"	PBDX		8054981	Standard	NM_175569		Approved		uc004cqp.3	P55808	OTTHUMG00000021075	ENST00000381174.5:c.374-1460C>T	chrX.hg19:g.2724766C>T		259.0	0.0		223.0	30.0	NM_001141919	E9PCH1|Q496N8|Q496N9|Q496P0|Q71BZ5	Missense_Mutation	SNP	ENST00000381174.5	hg19	CCDS14120.1	.	.	.	.	.	.	.	.	.	.	C	0.025	-1.376260	0.01214	.	.	ENSG00000124343	ENST00000419513	T	0.47177	0.85	1.93	1.93	0.25924	.	0.857039	0.10061	U	0.720940	T	0.41419	0.1158	N	0.14661	0.345	0.19775	N	0.999957	D	0.58620	0.983	P	0.55303	0.773	T	0.24083	-1.0170	10	0.59425	D	0.04	.	7.0818	0.25235	0.0:1.0:0.0:0.0	.	133	P55808-3	.	F	133	ENSP00000411004:S133F	ENSP00000411004:S133F	S	+	2	0	XG	2734766	0.001000	0.12720	0.005000	0.12908	0.061000	0.15899	0.366000	0.20365	1.034000	0.39945	0.384000	0.25694	TCT	.	.		0.408	XG-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055633.2	NM_175569		T	2724766	C	T	2724766	1	4	363	0	1	0	0	0	0	0	0	0	17442	913	32	3		3	XG	23	2724766	Intron	SNP	C	TCGA-ZP-A9CV-01A-11D-A382-10		2724766	152545794	104	50733										
AP1S2	8905	hgsc.bcm.edu	37	chrX	15864090	15864090	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	tttccagggtaattagttcaTtgtcctgatcctcaatagca	7	9	2	1			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chrX:15864090T>C	ENST00000329235.2	-	3	467	c.224A>G	c.(223-225)aAt>aGt	p.N75S	AP1S2_ENST00000421527.2_Missense_Mutation_p.N117S|AP1S2_ENST00000380291.1_Missense_Mutation_p.N75S|AP1S2_ENST00000479184.1_5'Flank|AP1S2_ENST00000545766.1_Missense_Mutation_p.N117S	NM_001272071.1|NM_003916.3	NP_001259000.1|NP_003907.3	P56377	AP1S2_HUMAN	adaptor-related protein complex 1, sigma 2 subunit	75					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	AP-type membrane coat adaptor complex (GO:0030119)|coated pit (GO:0005905)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|trans-Golgi network membrane (GO:0032588)	protein transporter activity (GO:0008565)			large_intestine(1)	1	Hepatocellular(33;0.183)					AATTAGTTCATTGTCCTGATC	0.313																																					p.N75S		Atlas-SNP	.											.	AP1S2	9	.	0			c.A224G						.						86	88	88					X																	15864090		2202	4294	6496	SO:0001583	missense	8905	exon3			AGTTCATTGTCCT	AB015320	CCDS14173.1, CCDS75958.1	Xp22	2014-01-31			ENSG00000182287	ENSG00000182287			560	protein-coding gene	gene with protein product		300629	"mental retardation, X-linked 59", "mental retardation, X-linked, syndromic 5", "Pettigrew X-linked mental retardation syndrome"	MRX59, MRXS5, PGS		9733768, 17186471, 23756445	Standard	NM_003916		Approved	SIGMA1B	uc010nex.4	P56377	OTTHUMG00000021186	ENST00000329235.2:c.224A>G	chrX.hg19:g.15864090T>C	ENSP00000328789:p.Asn75Ser	375.0	1.0		297.0	194.0	NM_001272071	B4DSU4|O95326|Q9H2N6	Missense_Mutation	SNP	ENST00000329235.2	hg19	CCDS14173.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	18.66|18.66	3.671407|3.671407	0.67814|0.67814	.|.	.|.	ENSG00000182287|ENSG00000182287	ENST00000450644|ENST00000329235;ENST00000380291;ENST00000545766;ENST00000421527;ENST00000340245	.|.	.|.	.|.	5.87|5.87	5.87|5.87	0.94306|0.94306	.|Longin-like (1);AP complex, mu/sigma subunit (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.66426|0.66426	0.2788|0.2788	M|M	0.74467|0.74467	2.265|2.265	0.80722|0.80722	D|D	1|1	.|B;P;B;P;P;P	.|0.49862	.|0.012;0.929;0.066;0.62;0.62;0.58	.|B;P;B;P;P;B	.|0.49226	.|0.078;0.529;0.154;0.603;0.603;0.377	T|T	0.68202|0.68202	-0.5471|-0.5471	5|9	.|0.40728	.|T	.|0.16	-24.5985|-24.5985	15.1946|15.1946	0.73078|0.73078	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|75;117;117;75;75;72	.|B7Z853;B4DSU4;B7Z3M9;Q549M9;P56377;E9PE78	.|.;.;.;.;AP1S2_HUMAN;.	V|S	68|75;75;117;117;72	.|.	.|ENSP00000328789:N75S	M|N	-|-	1|2	0|0	AP1S2|AP1S2	15774011|15774011	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	7.606000|7.606000	0.82863|0.82863	1.971000|1.971000	0.57363|0.57363	0.483000|0.483000	0.47432|0.47432	ATG|AAT	.	.		0.313	AP1S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055893.1	NM_003916		C	15864090	T	C	15864090	3	2	363	1	0	0	0	0	1	0	0	0	737	1493	52	2	261	2	AP1S2	23	15864090	Missense_Mutation	SNP	T	TCGA-ZP-A9CV-01A-11D-A382-10	13139324	15864090	139406470	105	50734										
RPS6KA3	6197	hgsc.bcm.edu	37	chrX	20187600	20187600	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	tgttgggtctctcttgctttTatcaataatctaaaaggcaa	7	7	4	0			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chrX:20187600T>A	ENST00000379565.3	-	16	1570	c.1363A>T	c.(1363-1365)Aaa>Taa	p.K455*	RPS6KA3_ENST00000479809.1_5'UTR|RPS6KA3_ENST00000544447.1_Nonsense_Mutation_p.K427*|RPS6KA3_ENST00000379548.4_Nonsense_Mutation_p.K425*|RPS6KA3_ENST00000540702.1_Nonsense_Mutation_p.K426*	NM_004586.2	NP_004577.1	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 3	455	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|central nervous system development (GO:0007417)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(14)|lung(7)|ovary(1)|stomach(1)	41					Acetylsalicylic acid(DB00945)	CTCTTGCTTTTATCAATAATC	0.308																																					p.K455X		Atlas-SNP	.											.	RPS6KA3	110	.	0			c.A1363T						.						133	130	131					X																	20187600		2203	4300	6503	SO:0001587	stop_gained	6197	exon16			TGCTTTTATCAAT	U08316	CCDS14197.1	Xp22.2-p22.1	2013-06-03	2002-08-29		ENSG00000177189	ENSG00000177189			10432	protein-coding gene	gene with protein product		300075	"ribosomal protein S6 kinase, 90kD, polypeptide 3", "mental retardation, X-linked 19", "Coffin-Lowry syndrome"	MRX19, CLS		8141249, 11896450, 16879200	Standard	XM_005274573		Approved	RSK, RSK2, HU-3	uc004czu.3	P51812	OTTHUMG00000021231	ENST00000379565.3:c.1363A>T	chrX.hg19:g.20187600T>A	ENSP00000368884:p.Lys455*	75.0	0.0		67.0	7.0	NM_004586	B2R9V4|Q4VAP3|Q59H26|Q5JPK8|Q7Z3Z7	Nonsense_Mutation	SNP	ENST00000379565.3	hg19	CCDS14197.1	.	.	.	.	.	.	.	.	.	.	T	38	7.191203	0.98125	.	.	ENSG00000177189	ENST00000379565;ENST00000544447;ENST00000379548;ENST00000540702	.	.	.	5.41	4.21	0.49690	.	0.112294	0.64402	D	0.000015	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.7149	0.51647	0.0:0.0:0.1459:0.8541	.	.	.	.	X	455;427;425;426	.	ENSP00000368865:K425X	K	-	1	0	RPS6KA3	20097521	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.934000	0.87649	0.756000	0.33013	0.486000	0.48141	AAA	.	.		0.308	RPS6KA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056011.3	NM_004586		A	20187600	T	A	20187600	4	1	363	1	0	0	0	0	0	1	0	0	13667	1763	61	4	887	4	RPS6KA3	23	20187600	Nonsense_Mutation	SNP	T	TCGA-ZP-A9CV-01A-11D-A382-10	4323510	20187600	135082960	106	50735										
ZNF630	57232	hgsc.bcm.edu	37	chrX	47918452	47918452	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	ccttcccacagtcagtacacAcataaggtttttctcctgta	5	13	2	0			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chrX:47918452A>G	ENST00000409324.3	-	5	1605	c.1379T>C	c.(1378-1380)gTg>gCg	p.V460A	ZNF630_ENST00000276054.4_Missense_Mutation_p.V336A|ZNF630-AS1_ENST00000436124.1_RNA|ZNF630_ENST00000442455.3_Missense_Mutation_p.V446A	NM_001037735.2	NP_001032824.2	Q2M218	ZN630_HUMAN	zinc finger protein 630	460					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(6)|lung(11)|ovary(1)	19						GTCAGTACACACATAAGGTTT	0.443																																					p.V460A		Atlas-SNP	.											.	ZNF630	71	.	0			c.T1379C						.						66	65	65					X																	47918452		2194	4287	6481	SO:0001583	missense	57232	exon5			GTACACACATAAG	AK000580	CCDS35237.2, CCDS75971.1	Xp11.3-p11.1	2013-01-08			ENSG00000221994	ENSG00000221994		"Zinc fingers, C2H2-type", "-"	28855	protein-coding gene	gene with protein product		300819					Standard	NM_001037735		Approved	BC037316, dJ54B20.2, FLJ20573, MGC138344	uc004div.4	Q2M218	OTTHUMG00000021463	ENST00000409324.3:c.1379T>C	chrX.hg19:g.47918452A>G	ENSP00000386393:p.Val460Ala	49.0	0.0		56.0	33.0	NM_001037735	F8WAG4|Q5H8Z5	Missense_Mutation	SNP	ENST00000409324.3	hg19	CCDS35237.2	.	.	.	.	.	.	.	.	.	.	.	0.010	-1.750664	0.00669	.	.	ENSG00000221994	ENST00000442455;ENST00000276054;ENST00000409324	T;T;T	0.37411	3.22;1.2;3.22	2.38	-2.75	0.05914	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.15825	0.0381	N	0.11651	0.15	0.09310	N	1	B	0.18863	0.031	B	0.19391	0.025	T	0.21484	-1.0244	9	0.51188	T	0.08	.	2.5065	0.04646	0.264:0.0:0.3169:0.4191	.	460	Q2M218	ZN630_HUMAN	A	446;336;460	ENSP00000393163:V446A;ENSP00000354683:V336A;ENSP00000386393:V460A	ENSP00000354683:V336A	V	-	2	0	ZNF630	47803396	0.000000	0.05858	0.031000	0.17742	0.166000	0.22503	-1.982000	0.01489	-0.322000	0.08615	0.433000	0.28618	GTG	.	.		0.443	ZNF630-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327254.1	NM_001037735		G	47918452	A	G	47918452	3	3	363	1	0	0	0	0	1	0	0	0	18069	159	6	2	598	2	ZNF630	23	47918452	Missense_Mutation	SNP	A	TCGA-ZP-A9CV-01A-11D-A382-10	27730852	47918452	107352108	107	50736										
TEX11	56159	hgsc.bcm.edu	37	chrX	69960592	69960592	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	attgagagccttatcataatAtttggtgtcatcccaatcca	6	9	2	1			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chrX:69960592A>G	ENST00000395889.2	-	12	1002	c.847T>C	c.(847-849)Tat>Cat	p.Y283H	TEX11_ENST00000374333.2_Missense_Mutation_p.Y268H|TEX11_ENST00000344304.3_Missense_Mutation_p.Y283H	NM_001003811.1	NP_001003811.1	Q8IYF3	TEX11_HUMAN	testis expressed 11	283					chiasma assembly (GO:0051026)|fertilization (GO:0009566)|male gonad development (GO:0008584)|male meiosis chromosome segregation (GO:0007060)|meiotic gene conversion (GO:0006311)|negative regulation of apoptotic process (GO:0043066)|reciprocal meiotic recombination (GO:0007131)|resolution of meiotic recombination intermediates (GO:0000712)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)				breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(13)|ovary(3)|prostate(3)|skin(3)	48	Renal(35;0.156)					TTATCATAATATTTGGTGTCA	0.323																																					p.Y283H		Atlas-SNP	.											.	TEX11	132	.	0			c.T847C						.						94	81	85					X																	69960592		2203	4300	6503	SO:0001583	missense	56159	exon12			CATAATATTTGGT	AF285594	CCDS35323.1, CCDS43968.1	Xp11	2008-02-05	2007-03-13		ENSG00000120498	ENSG00000120498			11733	protein-coding gene	gene with protein product		300311	"testis expressed sequence 11"			11279525	Standard	NM_001003811		Approved	TSGA3, TGC1	uc004dyl.3	Q8IYF3	OTTHUMG00000021782	ENST00000395889.2:c.847T>C	chrX.hg19:g.69960592A>G	ENSP00000379226:p.Tyr283His	185.0	0.0		158.0	95.0	NM_001003811	A8K8V6|Q5JQQ8|Q96LZ4|Q96M47|Q9BXU6	Missense_Mutation	SNP	ENST00000395889.2	hg19	CCDS35323.1	.	.	.	.	.	.	.	.	.	.	A	13.72	2.320604	0.41096	.	.	ENSG00000120498	ENST00000374333;ENST00000395889;ENST00000344304	T;T;T	0.32515	1.45;1.46;1.46	4.74	3.57	0.40892	Tetratricopeptide-like helical (1);	0.077576	0.53938	D	0.000042	T	0.42966	0.1226	M	0.68952	2.095	0.26533	N	0.974213	P;P	0.52316	0.94;0.952	P;P	0.58130	0.798;0.833	T	0.28004	-1.0057	9	.	.	.	-9.438	6.0842	0.19958	0.8836:0.0:0.1164:0.0	.	268;283	Q8IYF3-3;Q8IYF3	.;TEX11_HUMAN	H	268;283;283	ENSP00000363453:Y268H;ENSP00000379226:Y283H;ENSP00000340995:Y283H	.	Y	-	1	0	TEX11	69877317	0.967000	0.33354	0.820000	0.32676	0.386000	0.30323	1.592000	0.36676	0.656000	0.30886	0.417000	0.27973	TAT	.	.		0.323	TEX11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359072.1			G	69960592	A	G	69960592	3	3	363	1	0	0	0	0	1	0	0	0	15789	449	16	2	2055	2	TEX11	23	69960592	Missense_Mutation	SNP	A	TCGA-ZP-A9CV-01A-11D-A382-10	22042140	69960592	85309968	108	50737										
ITM2A	9452	hgsc.bcm.edu	37	chrX	78616864	78616864	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	gacgaaggcggaaggactttCtgttattgcaaagttggtaa	13	5	1	0			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chrX:78616864C>T	ENST00000373298.2	-	5	808	c.665G>A	c.(664-666)aGa>aAa	p.R222K	ITM2A_ENST00000434584.2_Missense_Mutation_p.R178K|ITM2A_ENST00000469541.1_5'UTR	NM_004867.4	NP_004858.1	O43736	ITM2A_HUMAN	integral membrane protein 2A	222	BRICHOS. {ECO:0000255|PROSITE- ProRule:PRU00255}.					integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	18						GAAGGACTTTCTGTTATTGCA	0.443																																					p.R222K		Atlas-SNP	.											.	ITM2A	51	.	0			c.G665A						.						106	91	96					X																	78616864		2203	4299	6502	SO:0001583	missense	9452	exon5			GACTTTCTGTTAT	BC034485	CCDS14444.1, CCDS55455.1	Xq13.3-q21.2	2012-10-10			ENSG00000078596	ENSG00000078596		"BRICHOS domain containing"	6173	protein-coding gene	gene with protein product	"BRICHOS domain containing 2A"	300222				9892734, 8702637	Standard	NM_004867		Approved	BRICD2A, E25A	uc004edh.3	O43736	OTTHUMG00000021900	ENST00000373298.2:c.665G>A	chrX.hg19:g.78616864C>T	ENSP00000362395:p.Arg222Lys	273.0	0.0		302.0	58.0	NM_004867	B2R7X5|B4E062|Q6IBC9	Missense_Mutation	SNP	ENST00000373298.2	hg19	CCDS14444.1	.	.	.	.	.	.	.	.	.	.	C	0.553	-0.848467	0.02651	.	.	ENSG00000078596	ENST00000373298;ENST00000434584	T;T	0.78707	-1.2;-1.2	4.11	2.95	0.34219	BRICHOS (2);	0.135951	0.43919	D	0.000520	T	0.45796	0.1360	N	0.02802	-0.49	0.37139	D	0.901612	B;B	0.10296	0.003;0.001	B;B	0.11329	0.006;0.006	T	0.47195	-0.9136	10	0.06365	T	0.9	-8.3944	5.8741	0.18819	0.0:0.7284:0.0:0.2716	.	178;222	B4E062;O43736	.;ITM2A_HUMAN	K	222;178	ENSP00000362395:R222K;ENSP00000415533:R178K	ENSP00000362395:R222K	R	-	2	0	ITM2A	78503520	0.989000	0.36119	0.984000	0.44739	0.527000	0.34593	0.722000	0.25925	1.789000	0.52484	0.513000	0.50165	AGA	.	.		0.443	ITM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057329.1	NM_004867		T	78616864	C	T	78616864	3	4	363	1	0	0	0	0	1	0	0	0	7921	913	32	3	134	3	ITM2A	23	78616864	Missense_Mutation	SNP	C	TCGA-ZP-A9CV-01A-11D-A382-10	8656272	78616864	76653696	109	50738										
ARMCX3	51566	hgsc.bcm.edu	37	chrX	100880946	100880946	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	agaaaatgaacctactcagaAtcaattcggtgaaggttcac	8	8	3	4			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chrX:100880946A>G	ENST00000341189.4	+	5	1843	c.977A>G	c.(976-978)aAt>aGt	p.N326S	ARMCX3_ENST00000537169.1_Missense_Mutation_p.N326S|RP4-545K15.5_ENST00000564612.1_RNA|ARMCX3-AS1_ENST00000454228.1_RNA|ARMCX3_ENST00000471229.2_Missense_Mutation_p.N326S	NM_016607.3	NP_057691.1	Q9UH62	ARMX3_HUMAN	armadillo repeat containing, X-linked 3	326					cellular protein localization (GO:0034613)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	integral component of mitochondrial outer membrane (GO:0031307)				endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)	11						CCTACTCAGAATCAATTCGGT	0.303																																					p.N326S		Atlas-SNP	.											.	ARMCX3	33	.	0			c.A977G						.						49	54	52					X																	100880946		2190	4289	6479	SO:0001583	missense	51566	exon5			CTCAGAATCAATT	AY359079	CCDS14489.1	Xq22.1	2014-03-21			ENSG00000102401	ENSG00000102401		"Armadillo repeat containing"	24065	protein-coding gene	gene with protein product		300364				11162520, 11042152, 19304657, 16221301, 22569362	Standard	NM_016607		Approved	ALEX3, GASP6	uc004eia.1	Q9UH62	OTTHUMG00000022035	ENST00000341189.4:c.977A>G	chrX.hg19:g.100880946A>G	ENSP00000340672:p.Asn326Ser	163.0	0.0		296.0	244.0	NM_016607	Q53HC6|Q7LCF5|Q9NPE4	Missense_Mutation	SNP	ENST00000341189.4	hg19	CCDS14489.1	.	.	.	.	.	.	.	.	.	.	A	1.383	-0.583008	0.03827	.	.	ENSG00000102401	ENST00000341189;ENST00000537169	T;T	0.28895	1.59;1.59	4.44	3.26	0.37387	Armadillo-type fold (1);	0.477766	0.25711	N	0.028803	T	0.14442	0.0349	N	0.08118	0	0.24920	N	0.991989	B	0.17852	0.024	B	0.28385	0.089	T	0.27773	-1.0064	9	.	.	.	-7.3172	6.3575	0.21410	0.7779:0.0:0.0:0.2221	.	326	Q9UH62	ARMX3_HUMAN	S	326	ENSP00000340672:N326S;ENSP00000439032:N326S	.	N	+	2	0	ARMCX3	100767602	1.000000	0.71417	0.987000	0.45799	0.980000	0.70556	1.053000	0.30442	0.797000	0.33971	0.486000	0.48141	AAT	.	.		0.303	ARMCX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057568.2	NM_016607		G	100880946	A	G	100880946	3	3	363	1	0	0	0	0	1	0	0	0	961	101	4	2	979	2	ARMCX3	23	100880946	Missense_Mutation	SNP	A	TCGA-ZP-A9CV-01A-11D-A382-10	22264082	100880946	54389614	110	50739										
SLITRK4	139065	hgsc.bcm.edu	37	chrX	142718332	142718333	+	Frame_Shift_Ins	INS	-	-	C													0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	acggccaatgtgttccagaaINSccccgatataagggagcttc							TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chrX:142718332_142718333insC	ENST00000381779.4	-	2	817_818	c.592_593insG	c.(592-594)gttfs	p.V198fs	SLITRK4_ENST00000338017.4_Frame_Shift_Ins_p.V198fs|SLITRK4_ENST00000356928.1_Frame_Shift_Ins_p.V198fs	NM_001184749.2|NM_001184750.1|NM_173078.4	NP_001171678.1|NP_001171679.1|NP_775101.1	Q8IW52	SLIK4_HUMAN	SLIT and NTRK-like family, member 4	198						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(27)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	60	Acute lymphoblastic leukemia(192;6.56e-05)					GTGTTCCAGAACCCCGATATAA	0.436																																					p.V198fs		Atlas-INDEL	.											.	SLITRK4	162	.	0			c.593_594insG						.																																			SO:0001589	frameshift_variant	139065	exon2			.	BC040986	CCDS14679.1	Xq27.3	2004-06-23			ENSG00000179542	ENSG00000179542			23502	protein-coding gene	gene with protein product		300562				14557068	Standard	NM_001184749		Approved	DKFZp547M2010	uc004fby.3	Q8IW52	OTTHUMG00000022580	ENST00000381779.4:c.593dupG	chrX.hg19:g.142718336_142718336dupC	ENSP00000371198:p.Val198fs	150.0	0.0		228.0	159.0	NM_173078	Q5JXG3|Q8TCM8|Q96DL3	Frame_Shift_Ins	INS	ENST00000381779.4	hg19	CCDS14679.1																																																																																			.	.		0.436	SLITRK4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058617.1	NM_173078		C	142718333	-	C	142718332	7	5	363	1	0	1	1	0	0	0	0	0	14760	43	2	0	1924	0	SLITRK4	23	142718332	Frame_Shift_Ins	INS	-	TCGA-ZP-A9CV-01A-11D-A382-10	41837386	142718332	12552228	111	50740	266	3								
SLITRK4	139065	hgsc.bcm.edu	37	chrX	142718337	142718337	+	Silent	SNP	G	G	A													0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	ccaatgtgttccagaaccccGatataagggagcttctggat							TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chrX:142718337G>A	ENST00000381779.4	-	2	813	c.588C>T	c.(586-588)atC>atT	p.I196I	SLITRK4_ENST00000338017.4_Silent_p.I196I|SLITRK4_ENST00000356928.1_Silent_p.I196I	NM_001184749.2|NM_001184750.1|NM_173078.4	NP_001171678.1|NP_001171679.1|NP_775101.1	Q8IW52	SLIK4_HUMAN	SLIT and NTRK-like family, member 4	196						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(27)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	60	Acute lymphoblastic leukemia(192;6.56e-05)					CCAGAACCCCGATATAAGGGA	0.433																																					p.I196I		Atlas-SNP	.											.	SLITRK4	162	.	0			c.C588T						.						78	75	76					X																	142718337		2203	4300	6503	SO:0001819	synonymous_variant	139065	exon2			AACCCCGATATAA	BC040986	CCDS14679.1	Xq27.3	2004-06-23			ENSG00000179542	ENSG00000179542			23502	protein-coding gene	gene with protein product		300562				14557068	Standard	NM_001184749		Approved	DKFZp547M2010	uc004fby.3	Q8IW52	OTTHUMG00000022580	ENST00000381779.4:c.588C>T	chrX.hg19:g.142718337G>A		153.0	0.0		224.0	163.0	NM_001184750	Q5JXG3|Q8TCM8|Q96DL3	Silent	SNP	ENST00000381779.4	hg19	CCDS14679.1																																																																																			.	.		0.433	SLITRK4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058617.1	NM_173078		A	142718337	G	A	142718337	2	1	363	1	0	0	0	0	0	0	0	1	14760	1048	37	1		1	SLITRK4	23	142718337	Silent	SNP	G	TCGA-ZP-A9CV-01A-11D-A382-10	5	142718337	12552223	112	50741	266	3								
SLITRK4	139065	hgsc.bcm.edu	37	chrX	142718339	142718339	+	Missense_Mutation	SNP	T	T	A													0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	aatgtgttccagaaccccgaTataagggagcttctggattc							TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chrX:142718339T>A	ENST00000381779.4	-	2	811	c.586A>T	c.(586-588)Atc>Ttc	p.I196F	SLITRK4_ENST00000338017.4_Missense_Mutation_p.I196F|SLITRK4_ENST00000356928.1_Missense_Mutation_p.I196F	NM_001184749.2|NM_001184750.1|NM_173078.4	NP_001171678.1|NP_001171679.1|NP_775101.1	Q8IW52	SLIK4_HUMAN	SLIT and NTRK-like family, member 4	196						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(27)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	60	Acute lymphoblastic leukemia(192;6.56e-05)					AGAACCCCGATATAAGGGAGC	0.428																																					p.I196F		Atlas-SNP	.											.	SLITRK4	162	.	0			c.A586T						.						78	75	76					X																	142718339		2203	4300	6503	SO:0001583	missense	139065	exon2			CCCCGATATAAGG	BC040986	CCDS14679.1	Xq27.3	2004-06-23			ENSG00000179542	ENSG00000179542			23502	protein-coding gene	gene with protein product		300562				14557068	Standard	NM_001184749		Approved	DKFZp547M2010	uc004fby.3	Q8IW52	OTTHUMG00000022580	ENST00000381779.4:c.586A>T	chrX.hg19:g.142718339T>A	ENSP00000371198:p.Ile196Phe	152.0	0.0		221.0	162.0	NM_001184750	Q5JXG3|Q8TCM8|Q96DL3	Missense_Mutation	SNP	ENST00000381779.4	hg19	CCDS14679.1	.	.	.	.	.	.	.	.	.	.	T	11.02	1.517065	0.27123	.	.	ENSG00000179542	ENST00000381779;ENST00000356928;ENST00000338017	T;T;T	0.53206	0.63;0.63;0.63	5.59	5.59	0.84812	.	0.067032	0.56097	D	0.000030	T	0.33789	0.0875	N	0.11845	0.185	0.53005	D	0.999968	P	0.38195	0.622	B	0.39299	0.296	T	0.31420	-0.9944	10	0.54805	T	0.06	-10.3098	13.5237	0.61582	0.0:0.0:0.0:1.0	.	196	Q8IW52	SLIK4_HUMAN	F	196	ENSP00000371198:I196F;ENSP00000349400:I196F;ENSP00000336627:I196F	ENSP00000336627:I196F	I	-	1	0	SLITRK4	142546005	0.998000	0.40836	0.991000	0.47740	0.986000	0.74619	2.207000	0.42788	1.877000	0.54381	0.486000	0.48141	ATC	.	.		0.428	SLITRK4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058617.1	NM_173078		A	142718339	T	A	142718339	3	1	363	1	0	0	0	0	1	0	0	0	14760	1406	49	4	1931	4	SLITRK4	23	142718339	Missense_Mutation	SNP	T	TCGA-ZP-A9CV-01A-11D-A382-10	2	142718339	12552221	113	50742	266	3								
CNGA2	1260	hgsc.bcm.edu	37	chrX	150912121	150912121	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	tccaacatgaatgccacccgGgcagagttccaggctaagat	10	12	0	3			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chrX:150912121G>T	ENST00000329903.4	+	6	1179	c.1146G>T	c.(1144-1146)cgG>cgT	p.R382R		NM_005140.1	NP_005131.1	Q16280	CNGA2_HUMAN	cyclic nucleotide gated channel alpha 2	382					phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sensory perception of smell (GO:0007608)	integral component of plasma membrane (GO:0005887)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			breast(4)|endometrium(4)|large_intestine(5)|lung(34)|prostate(2)	49	Acute lymphoblastic leukemia(192;6.56e-05)					ATGCCACCCGGGCAGAGTTCC	0.498																																					p.R382R		Atlas-SNP	.											.	CNGA2	136	.	0			c.G1146T						.						108	99	102					X																	150912121		2203	4300	6503	SO:0001819	synonymous_variant	1260	exon7			CACCCGGGCAGAG	S76067	CCDS14701.1	Xq27	2011-07-05			ENSG00000183862	ENSG00000183862		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2149	protein-coding gene	gene with protein product		300338		CNCA1, CNCA		7532814, 16382102	Standard	NM_005140		Approved	CNG2, OCNC1, OCNCa, OCNCALPHA, OCNCalpha, FLJ46312	uc004fey.1	Q16280	OTTHUMG00000024173	ENST00000329903.4:c.1146G>T	chrX.hg19:g.150912121G>T		45.0	0.0		66.0	28.0	NM_005140	A0AVD0	Silent	SNP	ENST00000329903.4	hg19	CCDS14701.1																																																																																			.	.		0.498	CNGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060888.1	NM_005140		T	150912121	G	T	150912121	2	4	363	1	0	0	0	0	0	0	0	1	3599	1219	43	3		3	CNGA2	23	150912121	Silent	SNP	G	TCGA-ZP-A9CV-01A-11D-A382-10	8193782	150912121	4358439	114	50743			2	71		2	2	20	N	G_A	6.935249e-05
CNGA2	1260	hgsc.bcm.edu	37	chrX	150912140	150912140	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0973451327433628	11	1	1.5855454238433	0	1.82947548904996	9.61482991365884e-06	0.00276632013778537	0	gggcagagttccaggctaagAtcgatgccgtgaaacactac	12	10	0	3			TCGA-ZP-A9CV-01A-11D-A382-10	TCGA-ZP-A9CV-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41039f88-9d78-4c6c-b429-d1c87cd8e568	917fa983-ed0a-4cee-b281-caabdc37221b	g.chrX:150912140A>G	ENST00000329903.4	+	6	1198	c.1165A>G	c.(1165-1167)Atc>Gtc	p.I389V		NM_005140.1	NP_005131.1	Q16280	CNGA2_HUMAN	cyclic nucleotide gated channel alpha 2	389					phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sensory perception of smell (GO:0007608)	integral component of plasma membrane (GO:0005887)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			breast(4)|endometrium(4)|large_intestine(5)|lung(34)|prostate(2)	49	Acute lymphoblastic leukemia(192;6.56e-05)					CCAGGCTAAGATCGATGCCGT	0.507																																					p.I389V		Atlas-SNP	.											.	CNGA2	136	.	0			c.A1165G						.						109	98	102					X																	150912140		2203	4300	6503	SO:0001583	missense	1260	exon7			GCTAAGATCGATG	S76067	CCDS14701.1	Xq27	2011-07-05			ENSG00000183862	ENSG00000183862		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2149	protein-coding gene	gene with protein product		300338		CNCA1, CNCA		7532814, 16382102	Standard	NM_005140		Approved	CNG2, OCNC1, OCNCa, OCNCALPHA, OCNCalpha, FLJ46312	uc004fey.1	Q16280	OTTHUMG00000024173	ENST00000329903.4:c.1165A>G	chrX.hg19:g.150912140A>G	ENSP00000328478:p.Ile389Val	44.0	0.0		63.0	48.0	NM_005140	A0AVD0	Missense_Mutation	SNP	ENST00000329903.4	hg19	CCDS14701.1	.	.	.	.	.	.	.	.	.	.	A	9.324	1.058721	0.19987	.	.	ENSG00000183862	ENST00000329903	D	0.96685	-4.09	4.96	4.96	0.65561	Cyclic nucleotide-binding-like (1);	0.000000	0.85682	D	0.000000	D	0.91516	0.7321	N	0.21508	0.67	0.40174	D	0.97721	B	0.21753	0.06	B	0.18263	0.021	D	0.88493	0.3077	10	0.30078	T	0.28	.	11.7614	0.51905	1.0:0.0:0.0:0.0	.	389	Q16280	CNGA2_HUMAN	V	389	ENSP00000328478:I389V	ENSP00000328478:I389V	I	+	1	0	CNGA2	150662796	1.000000	0.71417	0.983000	0.44433	0.833000	0.47200	5.956000	0.70315	1.749000	0.51849	0.430000	0.28490	ATC	.	.		0.507	CNGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060888.1	NM_005140		G	150912140	A	G	150912140	3	3	363	1	0	0	0	0	1	0	0	0	3599	333	12	2	1187	2	CNGA2	23	150912140	Missense_Mutation	SNP	A	TCGA-ZP-A9CV-01A-11D-A382-10	19	150912140	4358420	115	50744			2	71		2	2	20	N	G_A	6.935249e-05
CSMD2	114784	hgsc.bcm.edu	37	chr1	34291374	34291374	+	Splice_Site	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	ttcaactcaatttgcttcttGactagagaggaggtaagagg	11	6	3	3			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr1:34291374G>T	ENST00000373381.4	-	7	1211	c.1035C>A	c.(1033-1035)gtC>gtA	p.V345V		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	305	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				TTTGCTTCTTGACTAGAGAGG	0.517																																					p.V305V		Atlas-SNP	.											.	CSMD2	946	.	0			c.C915A						.						96	72	80					1																	34291374		2203	4300	6503	SO:0001630	splice_region_variant	114784	exon7			CTTCTTGACTAGA	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.1034-1C>A	chr1.hg19:g.34291374G>T		33.0	0.0		46.0	19.0	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Silent	SNP	ENST00000373381.4	hg19																																																																																				.	.		0.517	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896	Silent	T	34291374	G	T	34291374	5	4	364	1	0	0	0	0	0	0	1	0	3947	1304	45	3	9800	3	CSMD2	1	34291374	Splice_Site	SNP	G	TCGA-ZP-A9CY-01A-11D-A382-10		34291374	214959247	1	50745										
REG4	83998	hgsc.bcm.edu	37	chr1	120345731	120345731	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	tcagcttcctgaagtaaccaTagcaattggacttgtggtaa	9	8	1	1			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr1:120345731T>C	ENST00000354219.1	-	4	564	c.125A>G	c.(124-126)tAt>tGt	p.Y42C	REG4_ENST00000256585.5_Missense_Mutation_p.Y42C|REG4_ENST00000530654.1_Missense_Mutation_p.Y42C|REG4_ENST00000369401.4_Missense_Mutation_p.Y42C	NM_001159352.1	NP_001152824.1	Q9BYZ8	REG4_HUMAN	regenerating islet-derived family, member 4	42	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.					cytoplasm (GO:0005737)|extracellular region (GO:0005576)	heparin binding (GO:0008201)|mannan binding (GO:2001065)			central_nervous_system(1)|large_intestine(1)|lung(8)|ovary(2)|prostate(1)|skin(2)	15	all_cancers(5;4.81e-10)|all_epithelial(5;7.98e-11)|Melanoma(3;1.93e-05)|Breast(55;0.218)|all_neural(166;0.219)	all_lung(203;8.1e-07)|Lung NSC(69;5.89e-06)|all_epithelial(167;0.000959)		Lung(183;0.011)|LUSC - Lung squamous cell carcinoma(189;0.0588)		GAAGTAACCATAGCAATTGGA	0.473																																					p.Y42C		Atlas-SNP	.											.	REG4	36	.	0			c.A125G						.						73	66	68					1																	120345731		2203	4300	6503	SO:0001583	missense	83998	exon3			TAACCATAGCAAT	AY007243	CCDS906.1, CCDS53354.1	1p13.1-p12	2008-02-05			ENSG00000134193	ENSG00000134193			22977	protein-coding gene	gene with protein product	"regenerating gene type IV", " gastrointestinal secretory protein"	609846				11311942, 12455032	Standard	NM_032044		Approved	REG-IV, RELP, GISP	uc001eif.3	Q9BYZ8	OTTHUMG00000012175	ENST00000354219.1:c.125A>G	chr1.hg19:g.120345731T>C	ENSP00000346158:p.Tyr42Cys	128.0	0.0		141.0	43.0	NM_001159353	Q8NER6|Q8NER7	Missense_Mutation	SNP	ENST00000354219.1	hg19	CCDS906.1	.	.	.	.	.	.	.	.	.	.	T	13.93	2.384577	0.42308	.	.	ENSG00000134193	ENST00000354219;ENST00000256585;ENST00000369402;ENST00000530654;ENST00000369401	T;T;T;T	0.42513	1.64;1.64;0.97;0.97	5.08	5.08	0.68730	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (2);	0.096438	0.45361	D	0.000376	T	0.69169	0.3081	H	0.97051	3.93	0.39594	D	0.969624	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.79736	-0.1678	10	0.87932	D	0	-17.0463	11.2157	0.48825	0.0:0.0:0.0:1.0	.	42;42	Q9BYZ8-2;Q9BYZ8	.;REG4_HUMAN	C	42	ENSP00000346158:Y42C;ENSP00000256585:Y42C;ENSP00000437135:Y42C;ENSP00000358409:Y42C	ENSP00000256585:Y42C	Y	-	2	0	REG4	120147254	0.930000	0.31532	0.994000	0.49952	0.156000	0.22039	1.373000	0.34272	2.145000	0.66743	0.529000	0.55759	TAT	.	.		0.473	REG4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033675.1	NM_032044		C	120345731	T	C	120345731	3	2	364	1	0	0	0	0	1	0	0	0	13229	1406	49	2	607	2	REG4	1	120345731	Missense_Mutation	SNP	T	TCGA-ZP-A9CY-01A-11D-A382-10	86054357	120345731	128904890	2	50746										
DISP1	84976	hgsc.bcm.edu	37	chr1	223177664	223177664	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	agcaatctggagttctatgaCctccaggatagcctctccga	9	12	3	1			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr1:223177664C>A	ENST00000284476.6	+	8	3089	c.2925C>A	c.(2923-2925)gaC>gaA	p.D975E		NM_032890.3	NP_116279.2	Q96F81	DISP1_HUMAN	dispatched homolog 1 (Drosophila)	975					determination of left/right symmetry (GO:0007368)|diaphragm development (GO:0060539)|dorsal/ventral pattern formation (GO:0009953)|embryonic pattern specification (GO:0009880)|patched ligand maturation (GO:0007225)|peptide transport (GO:0015833)|protein homotrimerization (GO:0070207)|regulation of protein secretion (GO:0050708)|smoothened signaling pathway (GO:0007224)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)|peptide transporter activity (GO:0015197)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(20)|lung(25)|prostate(4)|skin(1)|stomach(1)|urinary_tract(5)	69				GBM - Glioblastoma multiforme(131;0.102)		AGTTCTATGACCTCCAGGATA	0.498																																					p.D975E		Atlas-SNP	.											.	DISP1	145	.	0			c.C2925A						.						77	65	69					1																	223177664		2203	4300	6503	SO:0001583	missense	84976	exon10			CTATGACCTCCAG	AK056569	CCDS1536.1	1q42.12	2008-02-05			ENSG00000154309	ENSG00000154309			19711	protein-coding gene	gene with protein product		607502				10619433	Standard	NM_032890		Approved	DISPA, MGC13130, DKFZP434I0428, MGC16796	uc001hnu.2	Q96F81	OTTHUMG00000037893	ENST00000284476.6:c.2925C>A	chr1.hg19:g.223177664C>A	ENSP00000284476:p.Asp975Glu	76.0	0.0		142.0	12.0	NM_032890	Q8N7C2|Q96I92|Q9H698|Q9H8H9|Q9UFA2	Missense_Mutation	SNP	ENST00000284476.6	hg19	CCDS1536.1	.	.	.	.	.	.	.	.	.	.	C	16.91	3.252200	0.59212	.	.	ENSG00000154309	ENST00000284476	D	0.91068	-2.78	5.58	4.47	0.54385	.	0.000000	0.85682	D	0.000000	D	0.88058	0.6335	N	0.12887	0.27	0.51012	D	0.999906	P	0.49696	0.927	P	0.58620	0.842	D	0.86197	0.1616	10	0.27082	T	0.32	-48.6543	14.3147	0.66440	0.0:0.8739:0.0:0.1261	.	975	Q96F81	DISP1_HUMAN	E	975	ENSP00000284476:D975E	ENSP00000284476:D975E	D	+	3	2	DISP1	221244287	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.521000	0.45563	2.639000	0.89480	0.491000	0.48974	GAC	.	.		0.498	DISP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092512.1	NM_032890		A	223177664	C	A	223177664	3	1	364	1	0	0	0	0	1	0	0	0	4541	506	18	3	2951	3	DISP1	1	223177664	Missense_Mutation	SNP	C	TCGA-ZP-A9CY-01A-11D-A382-10	102831933	223177664	26072957	3	50747										
PGBD5	79605	hgsc.bcm.edu	37	chr1	230492769	230492770	+	Frame_Shift_Ins	INS	-	-	T													0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	cgtggaagtacttgaggatcINSttctcgaagcgggcctggct							TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr1:230492769_230492770insT	ENST00000525115.1	-	2	445_446	c.422_423insA	c.(421-423)aagfs	p.K141fs	PGBD5_ENST00000321327.2_Frame_Shift_Ins_p.K240fs|PGBD5_ENST00000391860.1_Frame_Shift_Ins_p.K95fs			Q8N414	PGBD5_HUMAN	piggyBac transposable element derived 5	141						integral component of membrane (GO:0016021)				biliary_tract(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(2)|skin(1)	33	Breast(184;0.0397)	Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;0.201)		ACTTGAGGATCTTCTCGAAGCG	0.624																																					p.K210fs		Atlas-INDEL	.											.	PGBD5	73	.	0			c.630_631insA						.																																			SO:0001589	frameshift_variant	79605	exon2			.	AK021475		1q42.13	2008-02-05			ENSG00000177614	ENSG00000177614			19405	protein-coding gene	gene with protein product							Standard	NM_001258311		Approved	DKFZp761A0620, FLJ11413	uc031psq.1	Q8N414	OTTHUMG00000037759	ENST00000525115.1:c.423dupA	chr1.hg19:g.230492771_230492771dupT	ENSP00000431404:p.Lys141fs	92.0	0.0		156.0	70.0	NM_001258311	A0PJF3|B9EK58|Q5SR37|Q6PJN2	Frame_Shift_Ins	INS	ENST00000525115.1	hg19																																																																																				.	.		0.624	PGBD5-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000382617.1	NM_024554		T	230492770	-	T	230492769	7	5	364	1	0	1	1	0	0	0	0	0	11793	912	32	0	968	0	PGBD5	1	230492769	Frame_Shift_Ins	INS	-	TCGA-ZP-A9CY-01A-11D-A382-10	7315105	230492769	18757852	4	50748										
TUBA3E	112714	hgsc.bcm.edu	37	chr2	130951447	130951447	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	cattgacgtctttggggaccAcgtcccccctgtacaacatg	9	14	1	1			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr2:130951447A>G	ENST00000312988.7	-	4	1068	c.968T>C	c.(967-969)gTg>gCg	p.V323A		NM_207312.2	NP_997195	Q6PEY2	TBA3E_HUMAN	tubulin, alpha 3e	323					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(4)|kidney(7)|large_intestine(6)|lung(9)|skin(2)	28	Colorectal(110;0.1)					TTTGGGGACCACGTCCCCCCT	0.552																																					p.V323A		Atlas-SNP	.											.	TUBA3E	73	.	0			c.T968C						.						154	133	140					2																	130951447		2203	4300	6503	SO:0001583	missense	112714	exon4			GGGACCACGTCCC	BC057811	CCDS2158.1	2q21.1	2007-03-16			ENSG00000152086	ENSG00000152086		"Tubulins"	20765	protein-coding gene	gene with protein product							Standard	NM_207312		Approved		uc002tqv.3	Q6PEY2	OTTHUMG00000131626	ENST00000312988.7:c.968T>C	chr2.hg19:g.130951447A>G	ENSP00000318197:p.Val323Ala	92.0	0.0		128.0	32.0	NM_207312		Missense_Mutation	SNP	ENST00000312988.7	hg19	CCDS2158.1	.	.	.	.	.	.	.	.	.	.	a	13.77	2.334877	0.41297	.	.	ENSG00000152086	ENST00000312988	D	0.86030	-2.06	2.96	2.96	0.34315	Tubulin/FtsZ, 2-layer sandwich domain (3);Tubulin/FtsZ, C-terminal (1);	0.000000	0.44902	U	0.000418	D	0.94565	0.8249	H	0.98295	4.195	0.45528	D	0.998487	D	0.89917	1.0	D	0.97110	1.0	D	0.94373	0.7597	10	0.87932	D	0	.	9.3032	0.37858	1.0:0.0:0.0:0.0	.	323	Q6PEY2	TBA3E_HUMAN	A	323	ENSP00000318197:V323A	ENSP00000318197:V323A	V	-	2	0	TUBA3E	130667917	1.000000	0.71417	0.993000	0.49108	0.718000	0.41266	7.867000	0.87062	1.363000	0.46019	0.374000	0.22700	GTG	.	.		0.552	TUBA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254519.1	NM_207312		G	130951447	A	G	130951447	3	3	364	1	0	0	0	0	1	0	0	0	16763	159	6	2	392	2	TUBA3E	2	130951447	Missense_Mutation	SNP	A	TCGA-ZP-A9CY-01A-11D-A382-10		130951447	112247926	5	50749										
ACVR2A	92	hgsc.bcm.edu	37	chr2	148684717	148684722	+	In_Frame_Del	DEL	TGGATG	TGGATG	-													0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	gcagaagccaggttatcagcTggatgtgtaggtgaaagaat							TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	TGGATG	TGGATG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr2:148684717_148684722delTGGATG	ENST00000241416.7	+	11	2052_2057	c.1416_1421delTGGATG	c.(1414-1422)gctggatgt>gct	p.GC473del	ACVR2A_ENST00000495775.1_3'UTR|ACVR2A_ENST00000404590.1_In_Frame_Del_p.GC473del|ACVR2A_ENST00000535787.1_In_Frame_Del_p.GC365del	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	473	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)	p.G473fs*3(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		GGTTATCAGCTGGATGTGTAGGTGAA	0.413																																					p.472_474del		Atlas-INDEL	.											.	ACVR2A	125	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1415_1420del						.																																			SO:0001651	inframe_deletion	92	exon11			.		CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"activin A receptor, type II"	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.1416_1421delTGGATG	chr2.hg19:g.148684717_148684722delTGGATG	ENSP00000241416:p.Gly473_Cys474del	122.0	0.0		146.0	48.0	NM_001616	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	In_Frame_Del	DEL	ENST00000241416.7	hg19	CCDS33301.1																																																																																			.	.		0.413	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616		-	148684722	TGGATG	-	148684717	7	5	364	1	0	1	0	1	0	0	0	0	223	1567	55	0	1458	0	ACVR2A	2	148684717	In_Frame_Del	DEL	TGGATG	TCGA-ZP-A9CY-01A-11D-A382-10	17733270	148684717	94514656	6	50750										
XIRP2	129446	hgsc.bcm.edu	37	chr2	168102782	168102782	+	Frame_Shift_Del	DEL	A	A	-													0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	aagagagattttgattagtgAagaagagaagggaaatgtta							TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr2:168102782delA	ENST00000409195.1	+	9	4969	c.4880delA	c.(4879-4881)gaafs	p.E1629fs	XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000295237.9_Frame_Shift_Del_p.E1629fs|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409273.1_Frame_Shift_Del_p.E1407fs|XIRP2_ENST00000409605.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1454					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TTGATTAGTGAAGAAGAGAAG	0.328																																					p.E1627fs		Atlas-INDEL	.											.	XIRP2	914	.	0			c.4879delG						.						44	41	42					2																	168102782		1820	4067	5887	SO:0001589	frameshift_variant	129446	exon9			.	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.4880delA	chr2.hg19:g.168102782delA	ENSP00000386840:p.Glu1629fs	229.0	0.0		312.0	126.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Frame_Shift_Del	DEL	ENST00000409195.1	hg19	CCDS42769.1																																																																																			.	.		0.328	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		-	168102782	A	-	168102782	7	5	364	1	0	1	0	1	0	0	0	0	17445	246	9	0	4910	0	XIRP2	2	168102782	Frame_Shift_Del	DEL	A	TCGA-ZP-A9CY-01A-11D-A382-10	19418065	168102782	75096591	7	50751										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196825326	196825326	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	tggcctcccagtgcctggggCgcaaaccaggattacagatc	12	13	0	1	rs374382600		TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr2:196825326C>A	ENST00000312428.6	-	18	2649	c.2549G>T	c.(2548-2550)cGc>cTc	p.R850L		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	850	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						GTGCCTGGGGCGCAAACCAGG	0.453																																					p.R850L		Atlas-SNP	.											.	DNAH7	512	.	0			c.G2549T						.						123	125	125					2																	196825326		1936	4131	6067	SO:0001583	missense	56171	exon18			CTGGGGCGCAAAC	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.2549G>T	chr2.hg19:g.196825326C>A	ENSP00000311273:p.Arg850Leu	89.0	0.0		111.0	33.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	hg19	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	C	15.60	2.882636	0.51908	.	.	ENSG00000118997	ENST00000312428	T	0.62941	-0.01	5.74	3.93	0.45458	Dynein heavy chain, domain-2 (1);	0.125121	0.53938	D	0.000044	T	0.73860	0.3641	M	0.87758	2.905	0.80722	D	1	P	0.52316	0.952	P	0.56700	0.804	T	0.75811	-0.3186	10	0.59425	D	0.04	.	6.4969	0.22148	0.0:0.6773:0.1768:0.1459	.	850	Q8WXX0	DYH7_HUMAN	L	850	ENSP00000311273:R850L	ENSP00000311273:R850L	R	-	2	0	DNAH7	196533571	0.943000	0.32029	1.000000	0.80357	0.961000	0.63080	2.036000	0.41165	1.417000	0.47077	-0.172000	0.13284	CGC	.	.		0.453	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		A	196825326	C	A	196825326	3	1	364	1	0	0	0	0	1	0	0	0	4608	768	27	1	9717	1	DNAH7	2	196825326	Missense_Mutation	SNP	C	TCGA-ZP-A9CY-01A-11D-A382-10	28722544	196825326	46374047	8	50752										
EPHA4	2043	hgsc.bcm.edu	37	chr2	222365844	222365844	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	agctgtggggtgggcacttgGcacaggtggcatccgtggag	19	8	0	0			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr2:222365844G>C	ENST00000281821.2	-	4	913	c.872C>G	c.(871-873)gCc>gGc	p.A291G	EPHA4_ENST00000409938.1_Missense_Mutation_p.A291G|EPHA4_ENST00000392071.4_Missense_Mutation_p.A240G|EPHA4_ENST00000409854.1_Missense_Mutation_p.A291G	NM_004438.3	NP_004429.1	P54764	EPHA4_HUMAN	EPH receptor A4	291	Cys-rich.				adult walking behavior (GO:0007628)|cell adhesion (GO:0007155)|corticospinal tract morphogenesis (GO:0021957)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|glial cell migration (GO:0008347)|motor neuron axon guidance (GO:0008045)|negative regulation of axon regeneration (GO:0048681)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001108)|protein autophosphorylation (GO:0046777)|regulation of astrocyte differentiation (GO:0048710)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rap GTPase activity (GO:0032317)	axon (GO:0030424)|axon terminus (GO:0043679)|axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|DH domain binding (GO:0097161)|GPI-linked ephrin receptor activity (GO:0005004)|PH domain binding (GO:0042731)|protein kinase activity (GO:0004672)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		TGGGCACTTGGCACAGGTGGC	0.507																																					p.A291G		Atlas-SNP	.											.	EPHA4	263	.	0			c.C872G						.						91	82	85					2																	222365844		2203	4300	6503	SO:0001583	missense	2043	exon4			CACTTGGCACAGG	L36645	CCDS2447.1	2q36.3	2013-02-11	2004-10-28		ENSG00000116106	ENSG00000116106	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3388	protein-coding gene	gene with protein product		602188	"EphA4"	TYRO1		9267020	Standard	NM_004438		Approved	Hek8	uc002vmq.3	P54764	OTTHUMG00000133142	ENST00000281821.2:c.872C>G	chr2.hg19:g.222365844G>C	ENSP00000281821:p.Ala291Gly	69.0	0.0		104.0	6.0	NM_004438	A8K2P1|B2R601|B7Z6Q8|Q2M380	Missense_Mutation	SNP	ENST00000281821.2	hg19	CCDS2447.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.59|15.59	2.880025|2.880025	0.51801|0.51801	.|.	.|.	ENSG00000116106|ENSG00000116106	ENST00000281821;ENST00000409854;ENST00000409938;ENST00000392071|ENST00000441679	T;T;T;T|.	0.50001|.	0.76;0.76;0.76;0.76|.	6.07|6.07	6.07|6.07	0.98685|0.98685	.|.	0.103168|.	0.64402|.	D|.	0.000003|.	T|T	0.59197|0.59197	0.2176|0.2176	N|N	0.26130|0.26130	0.795|0.795	0.46499|0.46499	D|D	0.999074|0.999074	B|.	0.02656|.	0.0|.	B|.	0.04013|.	0.001|.	T|T	0.49899|0.49899	-0.8890|-0.8890	10|5	0.30078|.	T|.	0.28|.	.|.	20.6439|20.6439	0.99570|0.99570	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	291|.	P54764|.	EPHA4_HUMAN|.	G|A	291;291;291;240|28	ENSP00000281821:A291G;ENSP00000386276:A291G;ENSP00000386829:A291G;ENSP00000375923:A240G|.	ENSP00000281821:A291G|.	A|P	-|-	2|1	0|0	EPHA4|EPHA4	222074088|222074088	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.655000|7.655000	0.83696|0.83696	2.884000|2.884000	0.98904|0.98904	0.655000|0.655000	0.94253|0.94253	GCC|CCA	.	.		0.507	EPHA4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256836.3			C	222365844	G	C	222365844	3	2	364	1	0	0	0	0	1	0	0	0	5171	1203	42	4	2144	4	EPHA4	2	222365844	Missense_Mutation	SNP	G	TCGA-ZP-A9CY-01A-11D-A382-10	25540518	222365844	20833529	9	50753										
COL4A3	1285	hgsc.bcm.edu	37	chr2	228147228	228147228	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	aagaggatatccaggaaatcCgggaattttagggccaccag	12	8	0	1	rs368342782		TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr2:228147228C>T	ENST00000396578.3	+	32	2798	c.2636C>T	c.(2635-2637)cCg>cTg	p.P879L	AC097662.2_ENST00000439598.2_RNA|AC097662.2_ENST00000396588.2_RNA|AC097662.2_ENST00000433324.1_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	879	Triple-helical region.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|blood circulation (GO:0008015)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|collagen catabolic process (GO:0030574)|endothelial cell apoptotic process (GO:0072577)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|sensory perception of sound (GO:0007605)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metalloendopeptidase inhibitor activity (GO:0008191)|structural molecule activity (GO:0005198)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)		CCAGGAAATCCGGGAATTTTA	0.428													C|||	1	0.000199681	0	0	5008	,	,		3728	0		0	False		,,,				2504	0.001				p.P879L		Atlas-SNP	.											.	COL4A3	293	.	0			c.C2636T						.	C	LEU/PRO	1,3727		0,1,1863	129	126	127		2636	4	0.8	2		127	0,8186		0,0,4093	no	missense	COL4A3	NM_000091.4	98	0,1,5956	TT,TC,CC		0.0,0.0268,0.0084	probably-damaging	879/1671	228147228	1,11913	1864	4093	5957	SO:0001583	missense	1285	exon32			GAAATCCGGGAAT		CCDS42829.1	2q36-q37	2014-09-17			ENSG00000169031	ENSG00000169031		"Collagens"	2204	protein-coding gene	gene with protein product	"tumstatin"	120070				1737849	Standard	NM_000091		Approved		uc002vom.2	Q01955	OTTHUMG00000149891	ENST00000396578.3:c.2636C>T	chr2.hg19:g.228147228C>T	ENSP00000379823:p.Pro879Leu	171.0	0.0		191.0	58.0	NM_000091	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Missense_Mutation	SNP	ENST00000396578.3	hg19	CCDS42829.1	.	.	.	.	.	.	.	.	.	.	C	11.60	1.687028	0.29962	2.68E-4	0.0	ENSG00000169031	ENST00000396578;ENST00000328380;ENST00000335583;ENST00000396574;ENST00000315699	D	0.96685	-4.09	5.93	4.01	0.46588	.	0.208090	0.34178	N	0.004188	D	0.97359	0.9136	M	0.83953	2.67	0.58432	D	0.999999	D;D;D;D	0.69078	0.996;0.996;0.996;0.997	P;P;P;P	0.58077	0.742;0.797;0.742;0.832	D	0.97583	1.0112	10	0.72032	D	0.01	.	12.3675	0.55236	0.3057:0.6943:0.0:0.0	.	879;879;879;879	Q01955-5;Q01955-4;Q01955-2;Q01955	.;.;.;CO4A3_HUMAN	L	879	ENSP00000379823:P879L	ENSP00000323334:P879L	P	+	2	0	COL4A3	227855472	0.845000	0.29573	0.755000	0.31263	0.142000	0.21351	1.575000	0.36493	1.491000	0.48482	0.655000	0.94253	CCG	.	.		0.428	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091		T	228147228	C	T	228147228	3	4	364	1	0	0	0	0	1	0	0	0	3693	652	23	1	2762	1	COL4A3	2	228147228	Missense_Mutation	SNP	C	TCGA-ZP-A9CY-01A-11D-A382-10	5781384	228147228	15052145	10	50754										
DIS3L2	129563	hgsc.bcm.edu	37	chr2	233001275	233001275	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	gcgaactgtttaggaaatacGccctgttttctccctcagac	8	12	2	1			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr2:233001275G>T	ENST00000409307.1	+	7	796	c.796G>T	c.(796-798)Gcc>Tcc	p.A266S	DIS3L2_ENST00000360410.4_Silent_p.T285T|DIS3L2_ENST00000325385.7_Missense_Mutation_p.A266S|DIS3L2_ENST00000273009.6_Missense_Mutation_p.A266S					DIS3 like 3'-5' exoribonuclease 2											breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(2)|urinary_tract(1)	40		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)		TAGGAAATACGCCCTGTTTTC	0.468																																					p.A266S		Atlas-SNP	.											.	DIS3L2	77	.	0			c.G796T						.						190	177	181					2																	233001275		1890	4124	6014	SO:0001583	missense	129563	exon8			AAATACGCCCTGT	BC026166	CCDS42834.1, CCDS58752.1, CCDS58753.1	2q37.1	2014-09-17	2014-03-05		ENSG00000144535	ENSG00000144535			28648	protein-coding gene	gene with protein product		614184	"family with sequence similarity 6, member A", "DIS3 mitotic control homolog (S. cerevisiae)-like 2"	FAM6A		22306653, 23503588	Standard	NM_152383		Approved	FLJ36974, MGC42174	uc010fxz.3	Q8IYB7	OTTHUMG00000153385	ENST00000409307.1:c.796G>T	chr2.hg19:g.233001275G>T	ENSP00000386799:p.Ala266Ser	143.0	0.0		168.0	60.0	NM_152383		Missense_Mutation	SNP	ENST00000409307.1	hg19	CCDS42834.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.829740	0.91036	.	.	ENSG00000144535	ENST00000273009;ENST00000542873;ENST00000325385;ENST00000431466;ENST00000409307	T;T;T	0.28069	1.63;1.84;1.84	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.43322	0.1242	M	0.69185	2.1	0.80722	D	1	P	0.39071	0.658	B	0.43082	0.407	T	0.12016	-1.0564	10	0.40728	T	0.16	-20.8641	20.6525	0.99598	0.0:0.0:1.0:0.0	.	266	Q8IYB7	DI3L2_HUMAN	S	266	ENSP00000273009:A266S;ENSP00000315569:A266S;ENSP00000386799:A266S	ENSP00000273009:A266S	A	+	1	0	DIS3L2	232709519	1.000000	0.71417	0.987000	0.45799	0.946000	0.59487	8.025000	0.88777	2.890000	0.99128	0.585000	0.79938	GCC	.	.		0.468	DIS3L2-015	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330988.1	NM_152383		T	233001275	G	T	233001275	3	4	364	1	0	0	0	0	1	0	0	0	4539	1087	38	1	822	1	DIS3L2	2	233001275	Missense_Mutation	SNP	G	TCGA-ZP-A9CY-01A-11D-A382-10	4854047	233001275	10198098	11	50755										
OR6B2	389090	hgsc.bcm.edu	37	chr2	240969050	240969050	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	gcttgttggagctctgggaaTcaatggcttggggccggaca	16	8	2	0			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr2:240969050T>A	ENST00000402971.2	-	1	856	c.797A>T	c.(796-798)gAt>gTt	p.D266V		NM_001005853.1	NP_001005853.1	Q6IFH4	OR6B2_HUMAN	olfactory receptor, family 6, subfamily B, member 2	266						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(4)|lung(9)|prostate(1)	15		all_epithelial(40;1.64e-11)|Breast(86;0.000327)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.229)|Melanoma(123;0.238)		Epithelial(121;3.4e-29)|all cancers(36;2.08e-27)|OV - Ovarian serous cystadenocarcinoma(60;4.63e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.56e-05)|Lung(119;0.00344)|LUSC - Lung squamous cell carcinoma(224;0.0148)		GCTCTGGGAATCAATGGCTTG	0.507																																					p.D266V		Atlas-SNP	.											.	OR6B2	30	.	0			c.A797T						.						85	87	87					2																	240969050		1991	4157	6148	SO:0001583	missense	389090	exon1			TGGGAATCAATGG		CCDS46559.1	2q37.3	2012-08-09	2004-10-07	2004-10-07	ENSG00000182083	ENSG00000182083		"GPCR / Class A : Olfactory receptors"	15041	protein-coding gene	gene with protein product			"olfactory receptor, family 6, subfamily B, member 2 pseudogene"	OR6B2P			Standard	XM_005247004		Approved		uc010zoc.2	Q6IFH4	OTTHUMG00000152400	ENST00000402971.2:c.797A>T	chr2.hg19:g.240969050T>A	ENSP00000384563:p.Asp266Val	260.0	0.0		315.0	118.0	NM_001005853	B2RPR3|Q8NGW0	Missense_Mutation	SNP	ENST00000402971.2	hg19	CCDS46559.1	.	.	.	.	.	.	.	.	.	.	T	6.453	0.451703	0.12223	.	.	ENSG00000182083	ENST00000402971	T	0.00130	8.69	4.36	0.181	0.15073	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47852	D	0.000204	T	0.00144	0.0004	L	0.35854	1.095	0.09310	N	0.99999	P	0.39940	0.696	B	0.41374	0.355	T	0.43245	-0.9403	10	0.46703	T	0.11	.	11.9582	0.52993	0.0:0.0:0.641:0.359	.	266	Q6IFH4	OR6B2_HUMAN	V	266	ENSP00000384563:D266V	ENSP00000384563:D266V	D	-	2	0	OR6B2	240617723	0.001000	0.12720	0.010000	0.14722	0.662000	0.39071	0.880000	0.28159	-0.051000	0.13334	0.482000	0.46254	GAT	.	.		0.507	OR6B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326079.1	NM_001005853		A	240969050	T	A	240969050	3	1	364	1	0	0	0	0	1	0	0	0	11197	1435	50	4	143	4	OR6B2	2	240969050	Missense_Mutation	SNP	T	TCGA-ZP-A9CY-01A-11D-A382-10	7967775	240969050	2230323	12	50756										
ITIH4	3700	hgsc.bcm.edu	37	chr3	52855127	52855128	+	Frame_Shift_Del	DEL	AA	AA	-													0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	ccacactggactccgtttggAaagtgatgttctgtgtaggc							TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr3:52855127_52855128delAA	ENST00000266041.4	-	12	1654_1655	c.1558_1559delTT	c.(1558-1560)ttcfs	p.F520fs	ITIH4_ENST00000467462.1_5'UTR|ITIH4_ENST00000485816.1_Frame_Shift_Del_p.F520fs|ITIH4_ENST00000406595.1_Frame_Shift_Del_p.F520fs|ITIH4_ENST00000346281.5_Frame_Shift_Del_p.F520fs|ITIH4_ENST00000434759.3_Frame_Shift_Del_p.F432fs|RP5-966M1.6_ENST00000468472.1_3'UTR|ITIH4-AS1_ENST00000478366.1_RNA	NM_002218.4	NP_002209.2	Q14624	ITIH4_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 4	520					acute-phase response (GO:0006953)|hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)|response to cytokine (GO:0034097)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)		CTCCGTTTGGAAAGTGATGTTC	0.564											OREG0015616	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.520_520del		Atlas-INDEL	.											.	ITIH4	74	.	0			c.1559_1560del						.																																			SO:0001589	frameshift_variant	3700	exon12			.	D38535	CCDS2865.1, CCDS54596.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055955	ENSG00000055955			6169	protein-coding gene	gene with protein product	"plasma Kallikrein-sensitive glycoprotein"	600564	"inter-alpha (globulin) inhibitor H4 (plasma Kallikrein-sensitive glycoprotein)"	ITIHL1		9480842, 7805892	Standard	NM_002218		Approved	IHRP, H4P	uc003dfz.3	Q14624	OTTHUMG00000159023	ENST00000266041.4:c.1558_1559delTT	chr3.hg19:g.52855127_52855128delAA	ENSP00000266041:p.Phe520fs	48.0	0.0	988	74.0	22.0	NM_002218	B7Z545|E9PGN5|Q15135|Q9P190|Q9UQ54	Frame_Shift_Del	DEL	ENST00000266041.4	hg19	CCDS2865.1																																																																																			.	.		0.564	ITIH4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317715.1	NM_002218		-	52855128	AA	-	52855127	7	5	364	1	0	1	0	1	0	0	0	0	7915	246	9	0	1285	0	ITIH4	3	52855127	Frame_Shift_Del	DEL	AA	TCGA-ZP-A9CY-01A-11D-A382-10		52855127	145167303	13	50757										
UMPS	7372	hgsc.bcm.edu	37	chr3	124456869	124456886	+	In_Frame_Del	DEL	TCTATCTGCTGATGTTTC	TCTATCTGCTGATGTTTC	-													0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	aagaaggagaccaatctgtgTctatctgctgatgtttcact					rs200421426		TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	TCTATCTGCTGATGTTTC	TCTATCTGCTGATGTTTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr3:124456869_124456886delTCTATCTGCTGATGTTTC	ENST00000232607.2	+	3	871_888	c.765_782delTCTATCTGCTGATGTTTC	c.(763-783)tgtctatctgctgatgtttca>tga	p.255_261CLSADVS>*	UMPS_ENST00000538242.1_In_Frame_Del_p.77_83CLSADVS>*|UMPS_ENST00000413078.2_In_Frame_Del_p.77_83CLSADVS>*|UMPS_ENST00000498715.1_3'UTR|UMPS_ENST00000536109.1_In_Frame_Del_p.163_169CLSADVS>*	NM_000373.3	NP_000364.1	P11172	UMPS_HUMAN	uridine monophosphate synthetase	255	OMPdecase.				'de novo' pyrimidine nucleobase biosynthetic process (GO:0006207)|'de novo' UMP biosynthetic process (GO:0044205)|cellular response to drug (GO:0035690)|female pregnancy (GO:0007565)|lactation (GO:0007595)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside biosynthetic process (GO:0046134)|small molecule metabolic process (GO:0044281)|UMP biosynthetic process (GO:0006222)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	orotate phosphoribosyltransferase activity (GO:0004588)|orotidine-5'-phosphate decarboxylase activity (GO:0004590)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	16				GBM - Glioblastoma multiforme(114;0.146)	Fluorouracil(DB00544)	CCAATCTGTGTCTATCTGCTGATGTTTCACTGGCCAGA	0.472																																					p.255_261del		Atlas-INDEL	.											.	UMPS	43	.	0			c.764_781del						.																																			SO:0001651	inframe_deletion	7372	exon3			.		CCDS3029.1	3q13	2008-02-04	2008-02-04		ENSG00000114491	ENSG00000114491	2.4.2.10, 4.1.1.23		12563	protein-coding gene	gene with protein product	"orotate phosphoribosyl transferase and orotidine-5'-decarboxylase"	613891				2767686	Standard	NM_000373		Approved		uc003ehl.4	P11172	OTTHUMG00000159431	ENST00000232607.2:c.765_782delTCTATCTGCTGATGTTTC	chr3.hg19:g.124456869_124456886delTCTATCTGCTGATGTTTC	ENSP00000232607:p.Cys255_Ser261delins*	96.0	0.0		129.0	27.0	NM_000373	B5LY68|B5LY72|O00758|O00759|O00760|Q16862|Q9H3Q2|Q9UG49	In_Frame_Del	DEL	ENST00000232607.2	hg19	CCDS3029.1																																																																																			.	.		0.472	UMPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355271.1	NM_000373		-	124456886	TCTATCTGCTGATGTTTC	-	124456869	7	5	364	1	0	1	0	1	0	0	0	0	16996	1673	58	0	775	0	UMPS	3	124456869	In_Frame_Del	DEL	TCTATCTGCTGATGTTTC	TCGA-ZP-A9CY-01A-11D-A382-10	71601742	124456869	73565561	14	50758										
KBTBD12	166348	hgsc.bcm.edu	37	chr3	127642185	127642185	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	ttacatgtacaatgcagcttTggagatcaataatgccaatg	8	7	1	1			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr3:127642185T>C	ENST00000405109.1	+	2	748	c.281T>C	c.(280-282)tTg>tCg	p.L94S	KBTBD12_ENST00000343941.4_5'Flank|KBTBD12_ENST00000405256.1_Missense_Mutation_p.L94S|KBTBD12_ENST00000407609.3_Intron			Q3ZCT8	KBTBC_HUMAN	kelch repeat and BTB (POZ) domain containing 12	94	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.									endometrium(1)|large_intestine(6)|lung(5)|ovary(1)	13						AATGCAGCTTTGGAGATCAAT	0.383																																					p.L94S		Atlas-SNP	.											.	KBTBD12	41	.	0			c.T281C						.						77	73	74					3																	127642185		1925	4131	6056	SO:0001583	missense	166348	exon1			CAGCTTTGGAGAT		CCDS33848.2	3q21.3	2013-01-08	2009-10-01	2009-10-01	ENSG00000187715	ENSG00000187715		"BTB/POZ domain containing"	25731	protein-coding gene	gene with protein product			"kelch domain containing 6"	KLHDC6			Standard	NM_207335		Approved	FLJ46299	uc010hsr.3	Q3ZCT8	OTTHUMG00000150508	ENST00000405109.1:c.281T>C	chr3.hg19:g.127642185T>C	ENSP00000385957:p.Leu94Ser	130.0	0.0		176.0	54.0	NM_207335	B5MCC6|Q6ZRK1	Missense_Mutation	SNP	ENST00000405109.1	hg19	CCDS33848.2	.	.	.	.	.	.	.	.	.	.	T	18.58	3.655215	0.67472	.	.	ENSG00000187715	ENST00000405109;ENST00000405256	T;T	0.71934	-0.61;-0.61	5.75	5.75	0.90469	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	.	.	.	.	D	0.85813	0.5784	M	0.84773	2.715	0.47949	D	0.99955	D	0.89917	1.0	D	0.91635	0.999	D	0.88140	0.2844	9	0.87932	D	0	.	16.0656	0.80867	0.0:0.0:0.0:1.0	.	94	Q3ZCT8	KBTBC_HUMAN	S	94	ENSP00000385957:L94S;ENSP00000385879:L94S	ENSP00000385957:L94S	L	+	2	0	KBTBD12	129124875	1.000000	0.71417	0.711000	0.30485	0.729000	0.41735	7.698000	0.84413	2.203000	0.70933	0.377000	0.23210	TTG	.	.		0.383	KBTBD12-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318682.1	NM_207335		C	127642185	T	C	127642185	3	2	364	1	0	0	0	0	1	0	0	0	8000	1821	63	2	283	2	KBTBD12	3	127642185	Missense_Mutation	SNP	T	TCGA-ZP-A9CY-01A-11D-A382-10	3185316	127642185	70380245	15	50759										
DNAJC13	23317	hgsc.bcm.edu	37	chr3	132241675	132241675	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	caaacttcctcgtataggttCgaattacgttaatgaaattt	6	7	0	1			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr3:132241675C>T	ENST00000260818.6	+	49	5925	c.5677C>T	c.(5677-5679)Cga>Tga	p.R1893*		NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	1893					osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						CGTATAGGTTCGAATTACGTT	0.323																																					p.R1893X		Atlas-SNP	.											.	DNAJC13	253	.	0			c.C5677T						.						48	48	48					3																	132241675		2203	4299	6502	SO:0001587	stop_gained	23317	exon49			TAGGTTCGAATTA	AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"Heat shock proteins / DNAJ (HSP40)"	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.5677C>T	chr3.hg19:g.132241675C>T	ENSP00000260818:p.Arg1893*	184.0	0.0		247.0	49.0	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Nonsense_Mutation	SNP	ENST00000260818.6	hg19	CCDS33857.1	.	.	.	.	.	.	.	.	.	.	C	47	13.197359	0.99726	.	.	ENSG00000138246	ENST00000260818;ENST00000538066	.	.	.	6.08	4.12	0.48240	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.459	0.27283	0.3342:0.58:0.0:0.0858	.	.	.	.	X	1893;540	.	ENSP00000260818:R1893X	R	+	1	2	DNAJC13	133724365	1.000000	0.71417	1.000000	0.80357	0.576000	0.36127	3.821000	0.55700	1.562000	0.49601	0.655000	0.94253	CGA	.	.		0.323	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268		T	132241675	C	T	132241675	4	4	364	1	0	0	0	0	0	1	0	0	4634	876	31	1	5867	1	DNAJC13	3	132241675	Nonsense_Mutation	SNP	C	TCGA-ZP-A9CY-01A-11D-A382-10	4599490	132241675	65780755	16	50760										
STX18	53407	hgsc.bcm.edu	37	chr4	4421847	4421847	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	cacgcggaagccagcgttgtTtttaatggcctgggcaggga	15	9	0	0			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr4:4421847T>A	ENST00000306200.2	-	11	985	c.922A>T	c.(922-924)Aac>Tac	p.N308Y	STX18_ENST00000505286.1_Intron	NM_016930.2	NP_058626.1	Q9P2W9	STX18_HUMAN	syntaxin 18	308				N -> D (in Ref. 2; AAS47513). {ECO:0000305}.	ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	5				UCEC - Uterine corpus endometrioid carcinoma (64;0.0534)		CCAGCGTTGTTTTTAATGGCC	0.567																																					p.N308Y		Atlas-SNP	.											.	STX18	16	.	0			c.A922T						.						71	62	65					4																	4421847		2203	4300	6503	SO:0001583	missense	53407	exon11			CGTTGTTTTTAAT	AB028741	CCDS3377.1	4p16.3-p16.2	2013-09-23			ENSG00000168818	ENSG00000168818			15942	protein-coding gene	gene with protein product		606046				10788491	Standard	NM_016930		Approved	Ufe1	uc003gic.3	Q9P2W9	OTTHUMG00000090331	ENST00000306200.2:c.922A>T	chr4.hg19:g.4421847T>A	ENSP00000305810:p.Asn308Tyr	50.0	0.0		64.0	22.0	NM_016930	Q596L3|Q5TZP5	Missense_Mutation	SNP	ENST00000306200.2	hg19	CCDS3377.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.690896	0.88735	.	.	ENSG00000168818	ENST00000306200	T	0.24538	1.85	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	T	0.40670	0.1126	L	0.47716	1.5	0.80722	D	1	D	0.59357	0.985	P	0.58620	0.842	T	0.25222	-1.0138	10	0.72032	D	0.01	-0.4683	15.4307	0.75092	0.0:0.0:0.0:1.0	.	308	Q9P2W9	STX18_HUMAN	Y	308	ENSP00000305810:N308Y	ENSP00000305810:N308Y	N	-	1	0	STX18	4472748	1.000000	0.71417	0.985000	0.45067	0.976000	0.68499	7.329000	0.79170	2.044000	0.60594	0.459000	0.35465	AAC	.	.		0.567	STX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206696.1			A	4421847	T	A	4421847	3	1	364	1	0	0	0	0	1	0	0	0	15356	1841	64	4	89	4	STX18	4	4421847	Missense_Mutation	SNP	T	TCGA-ZP-A9CY-01A-11D-A382-10		4421847	186732429	17	50761										
PPEF2	5470	hgsc.bcm.edu	37	chr4	76797690	76797690	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	aggagccaagccgaaggggcGaagagggaagagagcggctt	19	7	0	2			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr4:76797690G>A	ENST00000286719.7	-	11	1426	c.1070C>T	c.(1069-1071)tCg>tTg	p.S357L		NM_006239.2	NP_006230.2	O14830	PPE2_HUMAN	protein phosphatase, EF-hand calcium binding domain 2	357	Catalytic.				detection of stimulus involved in sensory perception (GO:0050906)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|protein dephosphorylation (GO:0006470)|regulation of JUN kinase activity (GO:0043506)|regulation of MAP kinase activity (GO:0043405)|visual perception (GO:0007601)	cilium (GO:0005929)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|Hsp70 protein binding (GO:0030544)|Hsp90 protein binding (GO:0051879)|iron ion binding (GO:0005506)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	50			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			CCGAAGGGGCGAAGAGGGAAG	0.617																																					p.S357L	NSCLC(105;1359 1603 15961 44567 47947)	Atlas-SNP	.											.	PPEF2	108	.	0			c.C1070T						.						65	66	66					4																	76797690		2203	4300	6503	SO:0001583	missense	5470	exon11			AGGGGCGAAGAGG	AF023456	CCDS34013.1	4q21.1	2013-01-10			ENSG00000156194	ENSG00000156194		"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits", "EF-hand domain containing"	9244	protein-coding gene	gene with protein product	"protein phosphatase 7, catalytic subunit, beta isozyme"	602256				9326663, 12051765	Standard	NM_006239		Approved	PPP7CB	uc003hix.3	O14830	OTTHUMG00000160915	ENST00000286719.7:c.1070C>T	chr4.hg19:g.76797690G>A	ENSP00000286719:p.Ser357Leu	90.0	0.0		128.0	48.0	NM_006239	O14831	Missense_Mutation	SNP	ENST00000286719.7	hg19	CCDS34013.1	.	.	.	.	.	.	.	.	.	.	G	13.35	2.210553	0.39102	.	.	ENSG00000156194	ENST00000286719;ENST00000337500	T	0.40476	1.03	4.7	3.84	0.44239	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (1);Metallophosphoesterase domain (1);	1.386770	0.04471	N	0.376022	T	0.45736	0.1357	L	0.27053	0.805	0.09310	N	1	D;D	0.63880	0.98;0.993	B;P	0.52189	0.383;0.692	T	0.44907	-0.9297	10	0.33940	T	0.23	-0.8082	12.6384	0.56696	0.0:0.168:0.832:0.0	.	357;357	O14830-2;O14830	.;PPE2_HUMAN	L	357	ENSP00000286719:S357L	ENSP00000286719:S357L	S	-	2	0	PPEF2	77016714	0.010000	0.17322	0.005000	0.12908	0.003000	0.03518	1.484000	0.35508	0.966000	0.38159	0.491000	0.48974	TCG	.	.		0.617	PPEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362929.1	NM_006239		A	76797690	G	A	76797690	3	1	364	1	0	0	0	0	1	0	0	0	12317	1059	37	1	1219	1	PPEF2	4	76797690	Missense_Mutation	SNP	G	TCGA-ZP-A9CY-01A-11D-A382-10	72375843	76797690	114356586	18	50762										
DSPP	1834	hgsc.bcm.edu	37	chr4	88536436	88536436	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	agcgatagcagtgacagcagCaacagcagtgacagcagtga	13	9	0	3			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr4:88536436C>T	ENST00000282478.7	+	4	2655	c.2622C>T	c.(2620-2622)agC>agT	p.S874S	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.S874S			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	874	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			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)		gtgacagcagcaacagcagtg	0.502																																					p.S874S		Atlas-SNP	.											.	DSPP	174	.	0			c.C2622T						.						70	85	79					4																	88536436		1641	2936	4577	SO:0001819	synonymous_variant	1834	exon5			CAGCAGCAACAGC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2622C>T	chr4.hg19:g.88536436C>T		206.0	0.0		312.0	29.0	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	hg19	CCDS43248.1																																																																																			.	.		0.502	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		T	88536436	C	T	88536436	2	4	364	1	0	0	0	0	0	0	0	1	4784	709	25	3		3	DSPP	4	88536436	Silent	SNP	C	TCGA-ZP-A9CY-01A-11D-A382-10	11738746	88536436	102617840	19	50763										
DSPP	1834	hgsc.bcm.edu	37	chr4	88537513	88537513	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	gacagcagtgacagcaatgaAagcagcgacagcagtgacag	13	9	0	3	rs112275895		TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr4:88537513A>C	ENST00000282478.7	+	4	3732	c.3699A>C	c.(3697-3699)gaA>gaC	p.E1233D	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Missense_Mutation_p.E1233D			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1233	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			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)		acagcaatgaaagcagcgaca	0.547																																					p.E1233D		Atlas-SNP	.											.	DSPP	174	.	0			c.A3699C						.																																			SO:0001583	missense	1834	exon5			CAATGAAAGCAGC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3699A>C	chr4.hg19:g.88537513A>C	ENSP00000282478:p.Glu1233Asp	270.0	0.0		396.0	40.0	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	hg19	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	A	0.010	-1.785366	0.00628	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.88741	-2.42;-2.42	2.61	-5.21	0.02815	.	.	.	.	.	T	0.57213	0.2038	N	0.01048	-1.04	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.57347	-0.7827	9	0.02654	T	1	.	0.7125	0.00926	0.2623:0.1881:0.1298:0.4197	.	1233	Q9NZW4	DSPP_HUMAN	D	1233	ENSP00000382213:E1233D;ENSP00000282478:E1233D	ENSP00000282478:E1233D	E	+	3	2	DSPP	88756537	0.003000	0.15002	0.000000	0.03702	0.000000	0.00434	-2.769000	0.00780	-2.252000	0.00699	-3.496000	0.00033	GAA	.	A|0.500;C|0.500		0.547	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		C	88537513	A	C	88537513	3	2	364	1	0	0	0	0	1	0	0	0	4784	11	1	5	3713	5	DSPP	4	88537513	Missense_Mutation	SNP	A	TCGA-ZP-A9CY-01A-11D-A382-10	1077	88537513	102616763	20	50764										
PCDH18	54510	hgsc.bcm.edu	37	chr4	138452550	138452550	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	tctgaaatgcttatttttagTatggatgagccagacctctg	9	7	2	3			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr4:138452550T>A	ENST00000344876.4	-	1	1079	c.693A>T	c.(691-693)atA>atT	p.I231I	PCDH18_ENST00000511115.1_Intron|PCDH18_ENST00000507846.1_Silent_p.I11I|PCDH18_ENST00000510305.1_Intron|PCDH18_ENST00000412923.2_Silent_p.I231I	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	231	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				brain development (GO:0007420)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(27)|lung(21)|ovary(2)|pancreas(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86	all_hematologic(180;0.24)					TTATTTTTAGTATGGATGAGC	0.458																																					p.I231I		Atlas-SNP	.											.	PCDH18	229	.	0			c.A693T						.						77	77	77					4																	138452550		2203	4300	6503	SO:0001819	synonymous_variant	54510	exon1			TTTTAGTATGGAT	AL137471	CCDS34064.1, CCDS75193.1	4q28.3	2010-01-26			ENSG00000189184	ENSG00000189184		"Cadherins / Protocadherins : Non-clustered"	14268	protein-coding gene	gene with protein product		608287				10835267, 11549318	Standard	XM_005263070		Approved	KIAA1562, PCDH68L	uc003ihe.4	Q9HCL0	OTTHUMG00000161348	ENST00000344876.4:c.693A>T	chr4.hg19:g.138452550T>A		47.0	0.0		82.0	30.0	NM_019035	A8K7K3|B7ZKT1|Q52LS2	Silent	SNP	ENST00000344876.4	hg19	CCDS34064.1																																																																																			.	.		0.458	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035		A	138452550	T	A	138452550	2	1	364	1	0	0	0	0	0	0	0	1	11522	1628	57	4		4	PCDH18	4	138452550	Silent	SNP	T	TCGA-ZP-A9CY-01A-11D-A382-10	49915037	138452550	52701726	21	50765										
ADAMTS12	81792	hgsc.bcm.edu	37	chr5	33534965	33534965	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	tttcttgcaggcctgctggtTgcattttttgaattctggag	11	7	2	1			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr5:33534965T>C	ENST00000504830.1	-	23	4914	c.4579A>G	c.(4579-4581)Aac>Gac	p.N1527D	ADAMTS12_ENST00000352040.3_Missense_Mutation_p.N1442D	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	1527	TSP type-1 8. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						GCCTGCTGGTTGCATTTTTTG	0.468										HNSCC(64;0.19)																											p.N1527D		Atlas-SNP	.											.	ADAMTS12	464	.	0			c.A4579G						.						149	140	143					5																	33534965		2203	4300	6503	SO:0001583	missense	81792	exon23			GCTGGTTGCATTT	AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"ADAM metallopeptidases with thrombospondin type 1 motif"	14605	protein-coding gene	gene with protein product		606184	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.4579A>G	chr5.hg19:g.33534965T>C	ENSP00000422554:p.Asn1527Asp	62.0	0.0		112.0	40.0	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	hg19	CCDS34140.1	.	.	.	.	.	.	.	.	.	.	T	15.08	2.726111	0.48833	.	.	ENSG00000151388	ENST00000504830;ENST00000352040	T;T	0.52983	0.64;0.64	5.13	3.96	0.45880	.	0.248692	0.45867	D	0.000339	T	0.51432	0.1674	M	0.82923	2.615	0.80722	D	1	P;P	0.42078	0.728;0.77	B;P	0.45377	0.346;0.478	T	0.49615	-0.8921	10	0.15952	T	0.53	.	7.9855	0.30210	0.0:0.094:0.0:0.906	.	1442;1527	P58397-3;P58397	.;ATS12_HUMAN	D	1527;1442	ENSP00000422554:N1527D;ENSP00000344847:N1442D	ENSP00000344847:N1442D	N	-	1	0	ADAMTS12	33570722	1.000000	0.71417	0.999000	0.59377	0.932000	0.56968	1.279000	0.33191	0.896000	0.36366	0.460000	0.39030	AAC	.	.		0.468	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		C	33534965	T	C	33534965	3	2	364	1	0	0	0	0	1	0	0	0	257	1812	63	2	213	2	ADAMTS12	5	33534965	Missense_Mutation	SNP	T	TCGA-ZP-A9CY-01A-11D-A382-10		33534965	147380295	22	50766										
MAP3K1	4214	hgsc.bcm.edu	37	chr5	56161727	56161727	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	gctccatctcgtaacaccatCcagaagtttgtttcacgcat	6	13	2	1			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr5:56161727C>G	ENST00000399503.3	+	6	1224	c.1224C>G	c.(1222-1224)atC>atG	p.I408M		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	408					activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		GTAACACCATCCAGAAGTTTG	0.373																																					p.I408M		Atlas-SNP	.											.	MAP3K1	355	.	0			c.C1224G						.						121	118	119					5																	56161727		1900	4122	6022	SO:0001583	missense	4214	exon6			CACCATCCAGAAG	U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6848	protein-coding gene	gene with protein product		600982	"mitogen-activated protein kinase kinase kinase 1"	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.1224C>G	chr5.hg19:g.56161727C>G	ENSP00000382423:p.Ile408Met	130.0	0.0		195.0	58.0	NM_005921		Missense_Mutation	SNP	ENST00000399503.3	hg19	CCDS43318.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.719616	0.89205	.	.	ENSG00000095015	ENST00000399503	T	0.68903	-0.36	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.76083	0.3938	L	0.34521	1.04	0.80722	D	1	D	0.71674	0.998	D	0.78314	0.991	T	0.77376	-0.2611	10	0.66056	D	0.02	.	19.8765	0.96875	0.0:1.0:0.0:0.0	.	408	Q13233	M3K1_HUMAN	M	408	ENSP00000382423:I408M	ENSP00000382423:I408M	I	+	3	3	MAP3K1	56197484	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.066000	0.64351	2.695000	0.91970	0.650000	0.86243	ATC	.	.		0.373	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066		G	56161727	C	G	56161727	3	3	364	1	0	0	0	0	1	0	0	0	9252	845	30	4	1246	4	MAP3K1	5	56161727	Missense_Mutation	SNP	C	TCGA-ZP-A9CY-01A-11D-A382-10	22626762	56161727	124753533	23	50767										
CCNB1	891	hgsc.bcm.edu	37	chr5	68471253	68471253	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	gagcaacatactttggccaaAtacctgatggaactaactat	7	9	0	1			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr5:68471253A>G	ENST00000256442.5	+	7	1225	c.972A>G	c.(970-972)aaA>aaG	p.K324K	snoU13_ENST00000459230.1_RNA	NM_031966.3	NP_114172.1	P14635	CCNB1_HUMAN	cyclin B1	324					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|cellular response to iron(III) ion (GO:0071283)|cellular response to organic cyclic compound (GO:0071407)|digestive tract development (GO:0048565)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle checkpoint (GO:0071174)|mitotic spindle stabilization (GO:0043148)|negative regulation of gene expression (GO:0010629)|negative regulation of protein phosphorylation (GO:0001933)|oocyte maturation (GO:0001556)|positive regulation of attachment of spindle microtubules to kinetochore (GO:0051987)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|regulation of chromosome condensation (GO:0060623)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to DDT (GO:0046680)|response to drug (GO:0042493)|response to mechanical stimulus (GO:0009612)|spermatogenesis (GO:0007283)|tissue regeneration (GO:0042246)|ventricular cardiac muscle cell development (GO:0055015)	centrosome (GO:0005813)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	kinase activity (GO:0016301)|patched binding (GO:0005113)|protein kinase binding (GO:0019901)			large_intestine(2)|lung(5)|skin(1)	8		Lung NSC(167;5.51e-05)|Prostate(74;0.00634)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)		CTTTGGCCAAATACCTGATGG	0.403																																					p.K324K		Atlas-SNP	.											.	CCNB1	36	.	0			c.A972G						.						175	162	166					5																	68471253		2203	4300	6503	SO:0001819	synonymous_variant	891	exon7			GGCCAAATACCTG	U22364	CCDS3997.1	5q12	2008-07-18			ENSG00000134057	ENSG00000134057			1579	protein-coding gene	gene with protein product	"G2/mitotic-specific cyclin B1"	123836		CCNB		1386342	Standard	NM_031966		Approved		uc003jvm.3	P14635	OTTHUMG00000097817	ENST00000256442.5:c.972A>G	chr5.hg19:g.68471253A>G		123.0	0.0		167.0	51.0	NM_031966	A8K066|Q5TZP9	Silent	SNP	ENST00000256442.5	hg19	CCDS3997.1																																																																																			.	.		0.403	CCNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215084.1	NM_031966		G	68471253	A	G	68471253	2	3	364	1	0	0	0	0	0	0	0	1	2913	98	4	2		2	CCNB1	5	68471253	Silent	SNP	A	TCGA-ZP-A9CY-01A-11D-A382-10	12309526	68471253	112444007	24	50768										
GPR98	84059	hgsc.bcm.edu	37	chr5	90078941	90078941	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	attccaagttcccattacagTggaggaagatgttgggctga	12	7	0	2			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr5:90078941T>A	ENST00000405460.2	+	66	13328	c.13232T>A	c.(13231-13233)gTg>gAg	p.V4411E	GPR98_ENST00000425867.2_Splice_Site_p.V72E	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	4411	Calx-beta 30. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		CCCATTACAGTGGAGGAAGAT	0.428																																					p.V4411E		Atlas-SNP	.											.	GPR98	605	.	0			c.T13232A						.						176	169	171					5																	90078941		2008	4182	6190	SO:0001630	splice_region_variant	84059	exon66			TTACAGTGGAGGA	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.13232-1T>A	chr5.hg19:g.90078941T>A		108.0	0.0		127.0	35.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	T	27.7	4.855748	0.91355	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.39056	1.1;1.1	6.17	6.17	0.99709	Na-Ca exchanger/integrin-beta4 (2);	0.000000	0.85682	D	0.000000	T	0.73560	0.3602	M	0.92784	3.345	0.47862	D	0.999538	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.99;0.999	T	0.80238	-0.1465	9	.	.	.	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	72;4411;72	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	E	4411;4411;72	ENSP00000384582:V4411E;ENSP00000392618:V72E	.	V	+	2	0	GPR98	90114697	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	6.044000	0.71012	2.371000	0.80710	0.533000	0.62120	GTG	.	.		0.428	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	Missense_Mutation	A	90078941	T	A	90078941	5	1	364	1	0	0	0	0	0	0	1	0	6730	1710	59	4	13494	4	GPR98	5	90078941	Splice_Site	SNP	T	TCGA-ZP-A9CY-01A-11D-A382-10	21607688	90078941	90836319	25	50769										
PCDHGB6	56100	hgsc.bcm.edu	37	chr5	140787904	140787904	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	gaggagctggccaagggctcGgtggtggggaacctcgctaa	18	9	0	0			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr5:140787904G>T	ENST00000520790.1	+	1	135	c.135G>T	c.(133-135)tcG>tcT	p.S45S	PCDHGA7_ENST00000518325.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB3_ENST00000576222.1_Intron	NM_018926.2|NM_032100.1	NP_061749.1|NP_115271.1	Q9Y5F9	PCDGI_HUMAN	protocadherin gamma subfamily B, 6	45	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)	48			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCAAGGGCTCGGTGGTGGGGA	0.617																																					p.S45S		Atlas-SNP	.											.	PCDHGB6	120	.	0			c.G135T						.						48	53	51					5																	140787904		1953	4138	6091	SO:0001819	synonymous_variant	56100	exon1			GGGCTCGGTGGTG	AF152522	CCDS54929.1, CCDS75342.1	5q31	2010-01-26				ENSG00000253305		"Cadherins / Protocadherins : Clustered"	8713	other	protocadherin		606303				10380929	Standard	NM_018926		Approved	PCDH-GAMMA-B6		Q9Y5F9		ENST00000520790.1:c.135G>T	chr5.hg19:g.140787904G>T		108.0	0.0		146.0	18.0	NM_032100	Q9Y5C5	Silent	SNP	ENST00000520790.1	hg19	CCDS54929.1																																																																																			.	.		0.617	PCDHGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374746.1	NM_018926		T	140787904	G	T	140787904	2	4	364	1	0	0	0	0	0	0	0	1	11576	1103	39	1		1	PCDHGB6	5	140787904	Silent	SNP	G	TCGA-ZP-A9CY-01A-11D-A382-10	50708963	140787904	40127356	26	50770										
PCDHGB6	56100	hgsc.bcm.edu	37	chr5	140789789	140789789	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	acttgcaagagatactgccaGacctcagcgaccgccctgta	9	14	1	2			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr5:140789789G>T	ENST00000520790.1	+	1	2020	c.2020G>T	c.(2020-2022)Gac>Tac	p.D674Y	PCDHGA7_ENST00000518325.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA10_ENST00000398610.2_5'Flank|PCDHGA3_ENST00000253812.6_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB3_ENST00000576222.1_Intron	NM_018926.2|NM_032100.1	NP_061749.1|NP_115271.1	Q9Y5F9	PCDGI_HUMAN	protocadherin gamma subfamily B, 6	674	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)	48			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GATACTGCCAGACCTCAGCGA	0.607																																					p.D674Y		Atlas-SNP	.											.	PCDHGB6	120	.	0			c.G2020T						.						91	99	96					5																	140789789		2120	4241	6361	SO:0001583	missense	56100	exon1			CTGCCAGACCTCA	AF152522	CCDS54929.1, CCDS75342.1	5q31	2010-01-26				ENSG00000253305		"Cadherins / Protocadherins : Clustered"	8713	other	protocadherin		606303				10380929	Standard	NM_018926		Approved	PCDH-GAMMA-B6		Q9Y5F9		ENST00000520790.1:c.2020G>T	chr5.hg19:g.140789789G>T	ENSP00000428603:p.Asp674Tyr	63.0	0.0		107.0	37.0	NM_032100	Q9Y5C5	Missense_Mutation	SNP	ENST00000520790.1	hg19	CCDS54929.1	.	.	.	.	.	.	.	.	.	.	g	16.84	3.234620	0.58886	.	.	ENSG00000253305	ENST00000520790	T	0.52754	0.65	5.18	4.31	0.51392	Cadherin (1);	.	.	.	.	T	0.72890	0.3517	M	0.88377	2.95	0.21652	N	0.999604	D;D	0.89917	0.996;1.0	D;D	0.76071	0.957;0.987	T	0.66756	-0.5843	9	0.87932	D	0	.	13.6668	0.62401	0.0744:0.0:0.9256:0.0	.	674;674	Q9Y5F9;Q9Y5F9-2	PCDGI_HUMAN;.	Y	674	ENSP00000428603:D674Y	ENSP00000428603:D674Y	D	+	1	0	PCDHGB6	140769973	1.000000	0.71417	0.173000	0.22940	0.008000	0.06430	7.290000	0.78711	1.187000	0.43000	0.563000	0.77884	GAC	.	.		0.607	PCDHGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374746.1	NM_018926		T	140789789	G	T	140789789	3	4	364	1	0	0	0	0	1	0	0	0	11576	942	33	3	2022	3	PCDHGB6	5	140789789	Missense_Mutation	SNP	G	TCGA-ZP-A9CY-01A-11D-A382-10	1885	140789789	40125471	27	50771										
SLC34A1	6569	hgsc.bcm.edu	37	chr5	176821180	176821180	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	caagtggccaaggtcatccaGaaggtcatcaatacgggtga	12	9	3	2			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr5:176821180G>T	ENST00000324417.5	+	10	1249	c.1158G>T	c.(1156-1158)caG>caT	p.Q386H	SLC34A1_ENST00000513614.1_Intron	NM_003052.4	NP_003043.3	Q06495	NPT2A_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 1	386					arsenate ion transmembrane transport (GO:1901684)|bone remodeling (GO:0046849)|cellular response to metal ion (GO:0071248)|cellular response to parathyroid hormone stimulus (GO:0071374)|cellular response to staurosporine (GO:0072734)|dentinogenesis (GO:0097187)|gentamycin metabolic process (GO:1901128)|glycoprotein metabolic process (GO:0009100)|indole metabolic process (GO:0042431)|ion transport (GO:0006811)|kidney development (GO:0001822)|ossification (GO:0001503)|phosphate ion homeostasis (GO:0055062)|phosphate ion transport (GO:0006817)|positive regulation of membrane potential (GO:0045838)|positive regulation of phosphate transmembrane transport (GO:2000187)|positive regulation of sodium-dependent phosphate transport (GO:2000120)|protein homooligomerization (GO:0051260)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to growth hormone (GO:0060416)|response to lead ion (GO:0010288)|response to magnesium ion (GO:0032026)|response to mercury ion (GO:0046689)|response to potassium ion (GO:0035864)|response to thyroid hormone (GO:0097066)|response to vitamin A (GO:0033189)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|tricarboxylic acid metabolic process (GO:0072350)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|membrane-bounded vesicle (GO:0031988)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|symporter activity (GO:0015293)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGGTCATCCAGAAGGTCATCA	0.582																																					p.Q386H		Atlas-SNP	.											.	SLC34A1	73	.	0			c.G1158T						.						134	126	129					5																	176821180		2203	4300	6503	SO:0001583	missense	6569	exon10			CATCCAGAAGGTC	L13258	CCDS4418.1, CCDS54953.1	5q35.3	2013-07-17	2013-07-17		ENSG00000131183	ENSG00000131183		"Solute carriers"	11019	protein-coding gene	gene with protein product	"sodium/phosphate co-transporter", "solute carrier family 17 (sodium phosphate), member 2", "Na+-phosphate cotransporter type II"	182309	"solute carrier family 34 (sodium phosphate), member 1"	NPT2, SLC17A2		8327470, 8693007	Standard	NM_003052		Approved	NAPI-3, NPTIIa, SLC11	uc003mgk.4	Q06495	OTTHUMG00000130857	ENST00000324417.5:c.1158G>T	chr5.hg19:g.176821180G>T	ENSP00000321424:p.Gln386His	96.0	0.0		139.0	48.0	NM_003052	B4DPE3	Missense_Mutation	SNP	ENST00000324417.5	hg19	CCDS4418.1	.	.	.	.	.	.	.	.	.	.	G	13.89	2.371960	0.42003	.	.	ENSG00000131183	ENST00000324417	D	0.86097	-2.07	5.34	5.34	0.76211	.	0.314463	0.31061	N	0.008329	T	0.76097	0.3940	N	0.11000	0.08	0.39156	D	0.962321	B	0.06786	0.001	B	0.18561	0.022	T	0.73357	-0.4008	10	0.87932	D	0	-31.5828	18.6545	0.91445	0.0:0.0:1.0:0.0	.	386	Q06495	NPT2A_HUMAN	H	386	ENSP00000321424:Q386H	ENSP00000321424:Q386H	Q	+	3	2	SLC34A1	176753786	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	3.720000	0.54933	2.495000	0.84180	0.462000	0.41574	CAG	.	.		0.582	SLC34A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253431.1	NM_003052		T	176821180	G	T	176821180	3	4	364	1	0	0	0	0	1	0	0	0	14582	933	33	3	1283	3	SLC34A1	5	176821180	Missense_Mutation	SNP	G	TCGA-ZP-A9CY-01A-11D-A382-10	36031391	176821180	4094080	28	50772										
ZFP57	4340	hgsc.bcm.edu	37	chr6	29641190	29641190	+	IGR	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	aggtcttgtcacagagcgtgCaacagaagggcctctcccca	11	13	3	2			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr6:29641190C>T	ENST00000376917.3	+	0	2160				ZFP57_ENST00000376881.3_Missense_Mutation_p.C213Y|ZFP57_ENST00000488757.1_Missense_Mutation_p.C233Y|ZFP57_ENST00000376883.1_Missense_Mutation_p.C213Y	NM_002433.4|NM_206809.3	NP_002424.3|NP_996532.2	Q16653	MOG_HUMAN	myelin oligodendrocyte glycoprotein						cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|positive regulation of MyD88-dependent toll-like receptor signaling pathway (GO:0034126)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)|skin(2)	19						ACAGAGCGTGCAACAGAAGGG	0.557																																					p.C233Y		Atlas-SNP	.											.	ZFP57	80	.	0			c.G698A						.						77	87	84					6																	29641190		1375	2614	3989	SO:0001628	intergenic_variant	346171	exon4			AGCGTGCAACAGA		CCDS4667.1, CCDS34366.1, CCDS34367.1, CCDS34368.1, CCDS34369.1, CCDS34370.1, CCDS47394.1, CCDS47395.1, CCDS47395.2, CCDS54977.1	6p22.1	2014-01-16			ENSG00000204655	ENSG00000204655		"Immunoglobulin superfamily / V-set domain containing", "Butyrophilins"	7197	protein-coding gene	gene with protein product		159465					Standard	NM_002433		Approved	BTN6, BTNL11	uc003nne.3	Q16653	OTTHUMG00000031099		chr6.hg19:g.29641190C>T		98.0	0.0		117.0	35.0	NM_001109809	A6NDR4|A6NNJ9|A8MY31|B0UZR9|E9PGF0|F8W9D5|O00713|O00714|O00715|Q13054|Q13055|Q14855|Q29ZN8|Q56UY0|Q5JNX7|Q5JNY1|Q5JNY2|Q5JNY4|Q5SSB5|Q5SSB6|Q5STL9|Q5STM0|Q5STM1|Q5STM2|Q5STM5|Q5SUK5|Q5SUK7|Q5SUK8|Q5SUK9|Q5SUL0|Q5SUL1|Q8IYG5|Q92891|Q92892|Q92893|Q92894|Q92895|Q93053|Q96KU9|Q96KV0|Q96KV1|Q99605	Missense_Mutation	SNP	ENST00000376917.3	hg19	CCDS34370.1	.	.	.	.	.	.	.	.	.	.	C	14.70	2.614850	0.46631	.	.	ENSG00000204644	ENST00000488757;ENST00000376881;ENST00000376883	D;D;D	0.85088	-1.94;-1.94;-1.94	4.51	3.63	0.41609	.	0.000000	0.50627	D	0.000104	D	0.93103	0.7804	H	0.97186	3.955	0.45415	D	0.998392	D;D	0.69078	0.997;0.997	D;D	0.67725	0.953;0.953	D	0.93621	0.6948	10	0.87932	D	0	-18.7952	10.3332	0.43835	0.0:0.9:0.0:0.1	.	233;213	Q9NU63-3;Q9NU63-2	.;.	Y	233;213;213	ENSP00000418259:C233Y;ENSP00000366078:C213Y;ENSP00000366080:C213Y	ENSP00000366078:C213Y	C	-	2	0	ZFP57	29749169	1.000000	0.71417	0.108000	0.21378	0.170000	0.22686	5.515000	0.67049	2.498000	0.84270	0.558000	0.71614	TGC	.	.		0.557	MOG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076160.3	NM_002433		T	29641190	C	T	29641190	1	4	364	0	1	0	0	0	0	0	0	0	17666	710	25	3		3	ZFP57	6	29641190	IGR	SNP	C	TCGA-ZP-A9CY-01A-11D-A382-10		29641190	141473877	29	50773										
DOM3Z	1797	hgsc.bcm.edu	37	chr6	31938745	31938745	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	acataagctcccggaggagcGgtggccgagcaagcctctgg	15	12	1	0	rs558849573	byFrequency	TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr6:31938745G>A	ENST00000375349.3	-	3	947	c.536C>T	c.(535-537)cCg>cTg	p.P179L	DXO_ENST00000478221.1_5'UTR|DXO_ENST00000337523.5_Missense_Mutation_p.P179L|STK19_ENST00000375333.2_5'Flank|STK19_ENST00000375331.2_5'Flank|DXO_ENST00000375356.3_Missense_Mutation_p.P179L			O77932	DXO_HUMAN	decapping exoribonuclease	179					metabolic process (GO:0008152)|mRNA catabolic process (GO:0006402)|nuclear mRNA surveillance (GO:0071028)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA destabilization (GO:0050779)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|magnesium ion binding (GO:0000287)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|RNA pyrophosphohydrolase activity (GO:0034353)										CCGGAGGAGCGGTGGCCGAGC	0.597													G|||	2	0.000399361	0	0.0029	5008	,	,		15226	0		0	False		,,,				2504	0				p.P179L		Atlas-SNP	.											.	DOM3Z	20	.	0			c.C536T						.						78	92	87					6																	31938745		1509	2707	4216	SO:0001583	missense	1797	exon3			AGGAGCGGTGGCC	AF059252	CCDS4732.1	6p21.3	2013-09-11	2013-09-11	2013-09-11	ENSG00000204348	ENSG00000204348			2992	protein-coding gene	gene with protein product		605996	"DOM-3 (C. elegans) homolog Z", "dom-3 homolog Z (C. elegans)"	DOM3Z		9799600, 23523372	Standard	NM_005510		Approved		uc003nyp.1	O77932	OTTHUMG00000031272	ENST00000375349.3:c.536C>T	chr6.hg19:g.31938745G>A	ENSP00000364498:p.Pro179Leu	36.0	0.0		60.0	23.0	NM_005510	A2CER3|B0UZ80|O15004|O78127|O78128|Q5ST60|Q6IPZ2|Q9NPK4	Missense_Mutation	SNP	ENST00000375349.3	hg19	CCDS4732.1	.	.	.	.	.	.	.	.	.	.	G	10.36	1.329086	0.24167	.	.	ENSG00000204348	ENST00000337523;ENST00000375349;ENST00000375356	T;T;T	0.19938	2.11;2.11;2.11	5.23	3.45	0.39498	.	0.191692	0.44902	D	0.000414	T	0.05640	0.0148	L	0.49455	1.56	0.09310	N	0.999994	B;B	0.28971	0.229;0.039	B;B	0.12156	0.007;0.003	T	0.21484	-1.0244	10	0.38643	T	0.18	-14.8551	4.2437	0.10662	0.1756:0.0:0.5376:0.2867	.	179;179	F8WC68;O77932	.;DOM3Z_HUMAN	L	179	ENSP00000337759:P179L;ENSP00000364498:P179L;ENSP00000364505:P179L	ENSP00000337759:P179L	P	-	2	0	DOM3Z	32046724	0.995000	0.38212	0.977000	0.42913	0.705000	0.40729	2.827000	0.48112	1.201000	0.43203	-0.254000	0.11334	CCG	.	.		0.597	DXO-006	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076592.3			A	31938745	G	A	31938745	3	1	364	1	0	0	0	0	1	0	0	0	4707	1116	39	1	674	1	DOM3Z	6	31938745	Missense_Mutation	SNP	G	TCGA-ZP-A9CY-01A-11D-A382-10	2297555	31938745	139176322	30	50774										
EEF1A1	1915	hgsc.bcm.edu	37	chr6	74229110	74229110	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	aaagtctctgtgtcctggggCatcaatgatagtcacatagt	10	8	3	1			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr6:74229110C>T	ENST00000316292.9	-	2	1265	c.274G>A	c.(274-276)Gcc>Acc	p.A92T	EEF1A1_ENST00000331523.2_Missense_Mutation_p.A92T|EEF1A1_ENST00000309268.6_Missense_Mutation_p.A92T|EEF1A1_ENST00000491404.1_5'UTR	NM_001402.5	NP_001393.1	P68104	EF1A1_HUMAN	eukaryotic translation elongation factor 1 alpha 1	92	G3. {ECO:0000250}.|tr-type G.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation elongation factor activity (GO:0003746)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(6)|prostate(2)|skin(3)	18						TGTCCTGGGGCATCAATGATA	0.408											OREG0003890	type=REGULATORY REGION|Gene=LOC477388|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.A92T		Atlas-SNP	.											.	EEF1A1	56	.	0			c.G274A						.						95	107	103					6																	74229110		2203	4298	6501	SO:0001583	missense	1915	exon3			CTGGGGCATCAAT	BC019669	CCDS4980.1	6q14.1	2010-06-30	2004-11-19		ENSG00000156508	ENSG00000156508			3189	protein-coding gene	gene with protein product		130590	"leukocyte receptor cluster (LRC) member 7"	EF1A, EEF1A, LENG7		8812466, 10941842	Standard	NM_001402		Approved	EE1A1	uc003phj.3	P68104	OTTHUMG00000015031	ENST00000316292.9:c.274G>A	chr6.hg19:g.74229110C>T	ENSP00000339063:p.Ala92Thr	39.0	0.0	1151	76.0	29.0	NM_001402	P04719|P04720|Q6IQ15	Missense_Mutation	SNP	ENST00000316292.9	hg19	CCDS4980.1	.	.	.	.	.	.	.	.	.	.	C	13.98	2.398406	0.42512	.	.	ENSG00000156508	ENST00000316292;ENST00000358190;ENST00000309268;ENST00000331523;ENST00000391977;ENST00000356303;ENST00000455918	T;T;T;T;T	0.27557	1.66;1.66;1.66;1.66;1.66	3.93	3.93	0.45458	Protein synthesis factor, GTP-binding (4);	0.000000	0.64402	U	0.000001	T	0.19087	0.0458	L	0.33137	0.985	0.80722	D	1	B;B;B;P	0.36378	0.162;0.162;0.162;0.55	B;B;B;B	0.40534	0.158;0.158;0.158;0.332	T	0.14448	-1.0472	10	0.87932	D	0	.	16.5844	0.84724	0.0:1.0:0.0:0.0	.	92;92;92;92	P68104;Q53HR5;Q6IPS9;Q5VTE0	EF1A1_HUMAN;.;.;EF1A3_HUMAN	T	92	ENSP00000339063:A92T;ENSP00000339053:A92T;ENSP00000330054:A92T;ENSP00000348651:A92T;ENSP00000392366:A92T	ENSP00000339053:A92T	A	-	1	0	EEF1A1	74285831	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.344000	0.79328	2.202000	0.70862	0.549000	0.68633	GCC	.	.		0.408	EEF1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041210.2	NM_001402		T	74229110	C	T	74229110	3	4	364	1	0	0	0	0	1	0	0	0	4925	710	25	3	1138	3	EEF1A1	6	74229110	Missense_Mutation	SNP	C	TCGA-ZP-A9CY-01A-11D-A382-10	42290365	74229110	96885957	31	50775										
SLC2A12	154091	hgsc.bcm.edu	37	chr6	134350236	134350236	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	ttcctcagttgtatctgagaGtgctcttaaccttccaagaa	7	10	3	2			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr6:134350236G>C	ENST00000275230.5	-	2	882	c.727C>G	c.(727-729)Ctc>Gtc	p.L243V		NM_145176.2	NP_660159.1	Q8TD20	GTR12_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 12	243					glucose transport (GO:0015758)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			NS(1)|breast(1)|large_intestine(6)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	17	Breast(56;0.214)|Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0101)|GBM - Glioblastoma multiforme(68;0.0123)		GTATCTGAGAGTGCTCTTAAC	0.438																																					p.L243V	Melanoma(122;1663 1672 14489 35294 41228)	Atlas-SNP	.											.	SLC2A12	43	.	0			c.C727G						.						74	74	74					6																	134350236		2203	4300	6503	SO:0001583	missense	154091	exon2			CTGAGAGTGCTCT	AL035699	CCDS5169.1	6q23.2	2013-05-22			ENSG00000146411	ENSG00000146411		"Solute carriers"	18067	protein-coding gene	gene with protein product		610372				11780753, 11832379	Standard	XM_006715349		Approved	GLUT12, GLUT8	uc003qem.1	Q8TD20	OTTHUMG00000015611	ENST00000275230.5:c.727C>G	chr6.hg19:g.134350236G>C	ENSP00000275230:p.Leu243Val	134.0	0.0		152.0	45.0	NM_145176	B3KV17|Q7Z6U3|Q96MR8	Missense_Mutation	SNP	ENST00000275230.5	hg19	CCDS5169.1	.	.	.	.	.	.	.	.	.	.	G	1.976	-0.435356	0.04669	.	.	ENSG00000146411	ENST00000275230	T	0.73363	-0.74	5.4	-2.89	0.05665	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.030380	0.07605	N	0.924261	T	0.20047	0.0482	N	0.01824	-0.7	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.10823	-1.0613	10	0.25751	T	0.34	-5.1749	5.8477	0.18675	0.0:0.2874:0.2507:0.4619	.	243	Q8TD20	GTR12_HUMAN	V	243	ENSP00000275230:L243V	ENSP00000275230:L243V	L	-	1	0	SLC2A12	134391929	0.003000	0.15002	0.012000	0.15200	0.490000	0.33462	-0.009000	0.12765	-0.505000	0.06568	-0.518000	0.04402	CTC	.	.		0.438	SLC2A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042302.1			C	134350236	G	C	134350236	3	2	364	1	0	0	0	0	1	0	0	0	14556	1029	36	4	1142	4	SLC2A12	6	134350236	Missense_Mutation	SNP	G	TCGA-ZP-A9CY-01A-11D-A382-10	60121126	134350236	36764831	32	50776										
GPR126	57211	hgsc.bcm.edu	37	chr6	142738477	142738477	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	aatgaagtctatggaaaagaAagttatgggaaagaaaaagg	12	1	1	3			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr6:142738477A>T	ENST00000230173.6	+	21	3482	c.3006A>T	c.(3004-3006)gaA>gaT	p.E1002D	GPR126_ENST00000367608.2_Missense_Mutation_p.E974D|GPR126_ENST00000296932.8_Missense_Mutation_p.E974D|GPR126_ENST00000367609.3_Missense_Mutation_p.E1002D	NM_020455.5	NP_065188	Q86SQ4	GP126_HUMAN	G protein-coupled receptor 126	1002					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(12)|lung(10)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)		ATGGAAAAGAAAGTTATGGGA	0.348																																					p.E1002D		Atlas-SNP	.											.	GPR126	192	.	0			c.A3006T						.						106	96	99					6																	142738477		1825	4085	5910	SO:0001583	missense	57211	exon21			AAAAGAAAGTTAT	AK027843	CCDS47489.1, CCDS47490.1, CCDS47491.1, CCDS55064.1	6q23.1-q24.3	2014-08-08			ENSG00000112414	ENSG00000112414		"-", "GPCR / Class B : Orphans"	13841	protein-coding gene	gene with protein product		612243				12565841	Standard	NM_001032395		Approved	FLJ14937	uc010khe.3	Q86SQ4	OTTHUMG00000015709	ENST00000230173.6:c.3006A>T	chr6.hg19:g.142738477A>T	ENSP00000230173:p.Glu1002Asp	171.0	0.0		227.0	71.0	NM_198569	Q5TGN7|Q6DHZ4|Q6F3F5|Q6F3F6|Q6F3F7|Q6F3F8|Q6MZU7|Q8IXA4|Q8NC14|Q96JW0	Missense_Mutation	SNP	ENST00000230173.6	hg19	CCDS47490.1	.	.	.	.	.	.	.	.	.	.	A	4.276	0.050297	0.08243	.	.	ENSG00000112414	ENST00000230173;ENST00000367608;ENST00000296932;ENST00000367609	T;T;T;T	0.37058	1.22;1.22;1.22;1.22	5.28	0.167	0.15006	GPCR, family 2-like (1);	0.673685	0.14623	N	0.308272	T	0.03651	0.0104	N	0.04275	-0.24	0.09310	N	1	B;B;B;B;B	0.10296	0.001;0.002;0.002;0.002;0.003	B;B;B;B;B	0.16289	0.008;0.005;0.005;0.009;0.015	T	0.42378	-0.9455	10	0.16896	T	0.51	.	2.6723	0.05070	0.3838:0.127:0.366:0.1232	.	62;974;1002;974;1002	B4DSK4;Q86SQ4-4;Q86SQ4-3;Q86SQ4-2;Q86SQ4	.;.;.;.;GP126_HUMAN	D	1002;974;974;1002	ENSP00000230173:E1002D;ENSP00000356580:E974D;ENSP00000296932:E974D;ENSP00000356581:E1002D	ENSP00000230173:E1002D	E	+	3	2	GPR126	142780170	0.000000	0.05858	0.270000	0.24601	0.289000	0.27227	-0.598000	0.05706	-0.095000	0.12351	-0.297000	0.09499	GAA	.	.		0.348	GPR126-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042487.2			T	142738477	A	T	142738477	3	4	364	1	0	0	0	0	1	0	0	0	6648	11	1	4	3088	4	GPR126	6	142738477	Missense_Mutation	SNP	A	TCGA-ZP-A9CY-01A-11D-A382-10	8388241	142738477	28376590	33	50777										
TTYH3	80727	hgsc.bcm.edu	37	chr7	2689555	2689555	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	cgcccacctcagggctccagCgacttctgtgtggaccctga	11	16	2	1			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr7:2689555C>T	ENST00000258796.7	+	7	1009	c.804C>T	c.(802-804)agC>agT	p.S268S	TTYH3_ENST00000403167.1_Silent_p.S97S|TTYH3_ENST00000477439.1_3'UTR|TTYH3_ENST00000407643.1_Silent_p.S236S	NM_025250.2	NP_079526.1	Q9C0H2	TTYH3_HUMAN	tweety family member 3	268					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)|intracellular calcium activated chloride channel activity (GO:0005229)			kidney(1)|large_intestine(3)|lung(9)|prostate(2)|upper_aerodigestive_tract(2)	17		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.04e-14)		AGGGCTCCAGCGACTTCTGTG	0.627																																					p.S268S		Atlas-SNP	.											.	TTYH3	36	.	0			c.C804T						.						96	84	88					7																	2689555		2203	4300	6503	SO:0001819	synonymous_variant	80727	exon7			CTCCAGCGACTTC		CCDS34588.1	7p22	2013-09-02	2013-09-02		ENSG00000136295	ENSG00000136295			22222	protein-coding gene	gene with protein product		608919	"tweety homolog 3 (Drosophila)"				Standard	NM_025250		Approved	KIAA1691	uc003smp.3	Q9C0H2	OTTHUMG00000152050	ENST00000258796.7:c.804C>T	chr7.hg19:g.2689555C>T		59.0	0.0		95.0	7.0	NM_025250	A4D201|B7WP98|Q6L749|Q6ZVG3|Q8TEG6	Silent	SNP	ENST00000258796.7	hg19	CCDS34588.1																																																																																			.	.		0.627	TTYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325082.2	XM_166523		T	2689555	C	T	2689555	2	4	364	1	0	0	0	0	0	0	0	1	16756	767	27	1		1	TTYH3	7	2689555	Silent	SNP	C	TCGA-ZP-A9CY-01A-11D-A382-10		2689555	156449108	34	50778										
CACNA2D1	781	hgsc.bcm.edu	37	chr7	81689806	81689806	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	catttcggagacagatgttcGgatcagtttaagtgtcaatc	10	7	2	2			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr7:81689806G>T	ENST00000356253.5	-	10	1072	c.817C>A	c.(817-819)Cga>Aga	p.R273R	CACNA2D1_ENST00000423588.1_Silent_p.R273R|CACNA2D1_ENST00000356860.3_Silent_p.R273R			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	273	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				calcium ion transport (GO:0006816)|regulation of calcium ion transport (GO:0051924)	extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81					Amlodipine(DB00381)|Cyclandelate(DB04838)|Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)	ACAGATGTTCGGATCAGTTTA	0.348																																					p.R273R		Atlas-SNP	.											.	CACNA2D1	191	.	0			c.C817A						.						135	117	123					7																	81689806		2203	4300	6503	SO:0001819	synonymous_variant	781	exon10			ATGTTCGGATCAG	M76559	CCDS5598.1	7q21-q22	2014-09-17			ENSG00000153956	ENSG00000153956		"Calcium channel subunits"	1399	protein-coding gene	gene with protein product		114204	"long intergenic non-protein coding RNA 1112"	CACNL2A, CACNA2, MHS3, LINC01112		8188232	Standard	XM_005250570		Approved	lncRNA-N3	uc003uhr.1	P54289	OTTHUMG00000023622	ENST00000356253.5:c.817C>A	chr7.hg19:g.81689806G>T		72.0	0.0		108.0	38.0	NM_000722	Q17R45|Q9UD80|Q9UD81|Q9UD82	Silent	SNP	ENST00000356253.5	hg19																																																																																				.	.		0.348	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding				T	81689806	G	T	81689806	2	4	364	1	0	0	0	0	0	0	0	1	2550	1124	39	1		1	CACNA2D1	7	81689806	Silent	SNP	G	TCGA-ZP-A9CY-01A-11D-A382-10	79000251	81689806	77448857	35	50779										
TMEM66	51669	hgsc.bcm.edu	37	chr8	29927547	29927547	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	cagtttttccaaatttgtatGcaatatctaagtccgtctta	5	8	2	0			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr8:29927547G>C	ENST00000256255.6	-	3	568	c.311C>G	c.(310-312)gCa>gGa	p.A104G	TMEM66_ENST00000536273.1_5'UTR|TMEM66_ENST00000545648.1_5'UTR	NM_016127.4	NP_057211.4	Q96BY9	SARAF_HUMAN		104					calcium ion transport (GO:0006816)|regulation of store-operated calcium entry (GO:2001256)	integral component of endoplasmic reticulum membrane (GO:0030176)				endometrium(2)|large_intestine(1)|lung(11)	14				KIRC - Kidney renal clear cell carcinoma(542;0.0993)|Kidney(114;0.119)		AAATTTGTATGCAATATCTAA	0.358																																					p.A104G		Atlas-SNP	.											.	TMEM66	23	.	0			c.C311G						.						149	163	158					8																	29927547		2203	4300	6503	SO:0001583	missense	51669	exon3			TTGTATGCAATAT																												ENST00000256255.6:c.311C>G	chr8.hg19:g.29927547G>C	ENSP00000256255:p.Ala104Gly	31.0	0.0		39.0	15.0	NM_016127	B3KQQ4|B7Z9J1|D3DSU7|H9MHJ8|H9MHJ9|Q53HE8|Q9UNZ3|Q9Y683	Missense_Mutation	SNP	ENST00000256255.6	hg19	CCDS6074.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.51|11.51	1.660157|1.660157	0.29515|0.29515	.|.	.|.	ENSG00000133872|ENSG00000133872	ENST00000256255;ENST00000541035;ENST00000523127;ENST00000522794;ENST00000523761|ENST00000521265	T;T;T;T|.	0.45668|.	0.89;0.89;0.89;0.89|.	5.72|5.72	5.72|5.72	0.89469|0.89469	.|.	0.373490|.	0.30830|.	N|.	0.008781|.	T|T	0.71651|0.71651	0.3365|0.3365	L|L	0.56769|0.56769	1.78|1.78	0.80722|0.80722	D|D	1|1	D;D|.	0.67145|.	0.996;0.996|.	D;D|.	0.65573|.	0.936;0.936|.	T|T	0.68413|0.68413	-0.5415|-0.5415	10|5	0.37606|.	T|.	0.19|.	-23.8231|-23.8231	17.3623|17.3623	0.87354|0.87354	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	104;104|.	B3KQQ4;Q96BY9|.	.;TMM66_HUMAN|.	G|D	104;68;2;68;95|104	ENSP00000256255:A104G;ENSP00000428323:A2G;ENSP00000429630:A68G;ENSP00000428832:A95G|.	ENSP00000256255:A104G|.	A|H	-|-	2|1	0|0	TMEM66|TMEM66	30047089|30047089	0.998000|0.998000	0.40836|0.40836	0.308000|0.308000	0.25141|0.25141	0.398000|0.398000	0.30690|0.30690	5.082000|5.082000	0.64450|0.64450	2.715000|2.715000	0.92844|0.92844	0.585000|0.585000	0.79938|0.79938	GCA|CAT	.	.		0.358	TMEM66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257254.4			C	29927547	G	C	29927547	3	2	364	1	0	0	0	0	1	0	0	0	16210	1319	46	4	724	4	TMEM66	8	29927547	Missense_Mutation	SNP	G	TCGA-ZP-A9CY-01A-11D-A382-10		29927547	116436475	36	50780										
LYN	4067	hgsc.bcm.edu	37	chr8	56866505	56866505	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	ggagtccatcaagttggtgaAaaggcttggcgctgggcagt	16	7	1	1			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr8:56866505A>G	ENST00000519728.1	+	8	1048	c.752A>G	c.(751-753)aAa>aGa	p.K251R	LYN_ENST00000520220.2_Missense_Mutation_p.K230R	NM_002350.3	NP_002341.1	P07948	LYN_HUMAN	LYN proto-oncogene, Src family tyrosine kinase	251	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to extracellular stimulus (GO:0031668)|cellular response to heat (GO:0034605)|cellular response to retinoic acid (GO:0071300)|cytokine secretion (GO:0050663)|dendritic cell differentiation (GO:0097028)|erythrocyte differentiation (GO:0030218)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|Fc receptor mediated stimulatory signaling pathway (GO:0002431)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|histamine secretion by mast cell (GO:0002553)|immune response-regulating cell surface receptor signaling pathway (GO:0002768)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|leukocyte migration (GO:0050900)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of immune response (GO:0050777)|negative regulation of intracellular signal transduction (GO:1902532)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of mast cell proliferation (GO:0070667)|negative regulation of myeloid leukocyte differentiation (GO:0002762)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|neuron projection development (GO:0031175)|oligodendrocyte development (GO:0014003)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060369)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of mast cell proliferation (GO:0070668)|positive regulation of neuron projection development (GO:0010976)|positive regulation of oligodendrocyte progenitor proliferation (GO:0070447)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of stress-activated protein kinase signaling cascade (GO:0070304)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of B cell apoptotic process (GO:0002902)|regulation of B cell receptor signaling pathway (GO:0050855)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cytokine production (GO:0001817)|regulation of cytokine secretion (GO:0050707)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of erythrocyte differentiation (GO:0045646)|regulation of inflammatory response (GO:0050727)|regulation of mast cell activation (GO:0033003)|regulation of mast cell degranulation (GO:0043304)|regulation of monocyte chemotaxis (GO:0090025)|regulation of platelet aggregation (GO:0090330)|regulation of protein phosphorylation (GO:0001932)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|response to amino acid (GO:0043200)|response to axon injury (GO:0048678)|response to carbohydrate (GO:0009743)|response to drug (GO:0042493)|response to hormone (GO:0009725)|response to insulin (GO:0032868)|response to organic cyclic compound (GO:0014070)|response to sterol depletion (GO:0006991)|response to toxic substance (GO:0009636)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|T cell costimulation (GO:0031295)|tolerance induction to self antigen (GO:0002513)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integrin alpha2-beta1 complex (GO:0034666)|mast cell granule (GO:0042629)|membrane raft (GO:0045121)|mitochondrial crista (GO:0030061)|mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|glycosphingolipid binding (GO:0043208)|ion channel binding (GO:0044325)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	22		all_lung(136;0.0555)|Lung NSC(129;0.0726)|all_epithelial(80;0.0772)	Epithelial(17;0.000834)|all cancers(17;0.00598)		Bosutinib(DB06616)|Ponatinib(DB08901)	AAGTTGGTGAAAAGGCTTGGC	0.527																																					p.K251R		Atlas-SNP	.											.	LYN	54	.	0			c.A752G						.						108	106	107					8																	56866505		2203	4300	6503	SO:0001583	missense	4067	exon8			TGGTGAAAAGGCT	M16038	CCDS6162.1, CCDS47859.1	8q13	2014-06-25	2014-06-25		ENSG00000254087	ENSG00000254087		"SH2 domain containing"	6735	protein-coding gene	gene with protein product		165120	"v-yes-1 Yamaguchi sarcoma viral related oncogene homolog"			3561390	Standard	NM_002350		Approved	JTK8	uc003xsk.4	P07948	OTTHUMG00000044345	ENST00000519728.1:c.752A>G	chr8.hg19:g.56866505A>G	ENSP00000428924:p.Lys251Arg	131.0	0.0		200.0	63.0	NM_002350	A0AVQ5	Missense_Mutation	SNP	ENST00000519728.1	hg19	CCDS6162.1	.	.	.	.	.	.	.	.	.	.	A	9.355	1.066606	0.20067	.	.	ENSG00000254087	ENST00000519728;ENST00000520220	T;T	0.11495	2.77;2.77	5.08	5.08	0.68730	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);SH2 motif (1);Protein kinase, catalytic domain (1);	0.041699	0.85682	D	0.000000	T	0.05593	0.0147	N	0.05199	-0.095	0.80722	D	1	B;B	0.12630	0.006;0.002	B;B	0.20577	0.03;0.02	T	0.22730	-1.0208	10	0.07030	T	0.85	.	15.1358	0.72566	1.0:0.0:0.0:0.0	.	321;251	Q6NUK7;P07948	.;LYN_HUMAN	R	251;230	ENSP00000428924:K251R;ENSP00000428424:K230R	ENSP00000428924:K251R	K	+	2	0	LYN	57029059	1.000000	0.71417	0.961000	0.40146	0.414000	0.31173	7.363000	0.79516	2.049000	0.60858	0.528000	0.53228	AAA	.	.		0.527	LYN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378155.1	NM_002350		G	56866505	A	G	56866505	3	3	364	1	0	0	0	0	1	0	0	0	9116	14	1	2	778	2	LYN	8	56866505	Missense_Mutation	SNP	A	TCGA-ZP-A9CY-01A-11D-A382-10	26938958	56866505	89497517	37	50781										
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110509162	110509162	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	tccaaggccagtttaatcctGtggaaaagtggtttgacaat	10	7	0	1	rs562593738		TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr8:110509162G>C	ENST00000378402.5	+	64	10446	c.10342G>C	c.(10342-10344)Gtg>Ctg	p.V3448L		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	3448					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			GTTTAATCCTGTGGAAAAGTG	0.363										HNSCC(38;0.096)																											p.V3448L		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.G10342C						.						147	139	141					8																	110509162		1814	4078	5892	SO:0001583	missense	93035	exon64			AATCCTGTGGAAA	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.10342G>C	chr8.hg19:g.110509162G>C	ENSP00000367655:p.Val3448Leu	82.0	0.0		115.0	37.0	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	hg19	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	G	10.55	1.381104	0.24944	.	.	ENSG00000205038	ENST00000378402;ENST00000526472	T;T	0.80214	-1.35;-1.35	5.64	-7.4	0.01397	Pectin lyase fold/virulence factor (1);	1.157390	0.06179	N	0.679125	T	0.64994	0.2649	L	0.43152	1.355	0.09310	N	1	B	0.06786	0.001	B	0.11329	0.006	T	0.47736	-0.9094	10	0.26408	T	0.33	.	1.9622	0.03388	0.1516:0.2546:0.3643:0.2295	.	3448	Q86WI1	PKHL1_HUMAN	L	3448;376	ENSP00000367655:V3448L;ENSP00000437376:V376L	ENSP00000367655:V3448L	V	+	1	0	PKHD1L1	110578338	0.002000	0.14202	0.000000	0.03702	0.211000	0.24417	-0.063000	0.11655	-1.258000	0.02471	-0.806000	0.03193	GTG	.	.		0.363	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		C	110509162	G	C	110509162	3	2	364	1	0	0	0	0	1	0	0	0	11981	1377	48	4	10596	4	PKHD1L1	8	110509162	Missense_Mutation	SNP	G	TCGA-ZP-A9CY-01A-11D-A382-10	53642657	110509162	35854860	38	50782										
KANK1	23189	hgsc.bcm.edu	37	chr9	730216	730216	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	tacgctgtctccagtgaaccTgacagacgaccagatcgccg	10	14	1	4			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr9:730216T>A	ENST00000382303.1	+	8	3516	c.2864T>A	c.(2863-2865)cTg>cAg	p.L955Q	KANK1_ENST00000382293.3_Missense_Mutation_p.L797Q|KANK1_ENST00000489369.1_3'UTR|KANK1_ENST00000382297.2_Missense_Mutation_p.L955Q	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	955					negative regulation of actin filament polymerization (GO:0030837)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lamellipodium morphogenesis (GO:2000393)|negative regulation of neuron projection development (GO:0010977)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of wound healing (GO:0090303)|regulation of establishment of cell polarity (GO:2000114)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	beta-catenin binding (GO:0008013)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|stomach(4)|upper_aerodigestive_tract(1)	43		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		CCAGTGAACCTGACAGACGAC	0.532																																					p.L955Q		Atlas-SNP	.											.	KANK1	231	.	0			c.T2864A						.						74	63	67					9																	730216		2203	4300	6503	SO:0001583	missense	23189	exon8			TGAACCTGACAGA	AL833161	CCDS6441.1, CCDS34976.1	9p24.3	2013-01-10	2008-01-29	2008-01-29	ENSG00000107104	ENSG00000107104		"KN motif and ankyrin repeat domain containing", "Ankyrin repeat domain containing"	19309	protein-coding gene	gene with protein product		607704	"ankyrin repeat domain 15"	ANKRD15		12133830, 17996375, 19554261	Standard	NM_015158		Approved	KIAA0172, KANK	uc003zgn.2	Q14678	OTTHUMG00000019434	ENST00000382303.1:c.2864T>A	chr9.hg19:g.730216T>A	ENSP00000371740:p.Leu955Gln	77.0	0.0		132.0	52.0	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Missense_Mutation	SNP	ENST00000382303.1	hg19	CCDS34976.1	.	.	.	.	.	.	.	.	.	.	T	9.970	1.225126	0.22457	.	.	ENSG00000107104	ENST00000382303;ENST00000354485;ENST00000382297;ENST00000382293	T;T;T	0.18960	2.18;2.18;2.18	5.91	4.71	0.59529	.	0.163209	0.29280	N	0.012607	T	0.14141	0.0342	L	0.31664	0.95	0.80722	D	1	P;B	0.38617	0.64;0.067	B;B	0.32465	0.146;0.011	T	0.03818	-1.1001	10	0.52906	T	0.07	-0.2898	10.8049	0.46512	0.1408:0.0:0.0:0.8592	.	955;955	Q5W0W1;Q14678	.;KANK1_HUMAN	Q	955;955;955;797	ENSP00000371740:L955Q;ENSP00000371734:L955Q;ENSP00000371730:L797Q	ENSP00000346479:L955Q	L	+	2	0	KANK1	720216	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	2.295000	0.43576	2.266000	0.75297	0.533000	0.62120	CTG	.	.		0.532	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158		A	730216	T	A	730216	3	1	364	1	0	0	0	0	1	0	0	0	7985	1580	55	4	2874	4	KANK1	9	730216	Missense_Mutation	SNP	T	TCGA-ZP-A9CY-01A-11D-A382-10		730216	140483215	39	50783										
RANBP6	26953	hgsc.bcm.edu	37	chr9	6015125	6015125	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	ccaggaaagtgccagaaaacGtgaagtgcaacttcccatag	10	10	0	2	rs149927185		TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr9:6015125G>T	ENST00000259569.5	-	1	493	c.483C>A	c.(481-483)caC>caA	p.H161Q	RANBP6_ENST00000485372.1_Intron	NM_001243202.1|NM_001243203.1|NM_012416.3	NP_001230131.1|NP_001230132.1|NP_036548.1	O60518	RNBP6_HUMAN	RAN binding protein 6	161					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(5)|large_intestine(8)|lung(9)|ovary(7)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	51		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00522)|Lung(218;0.101)		GCCAGAAAACGTGAAGTGCAA	0.433																																					p.H161Q		Atlas-SNP	.											.	RANBP6	127	.	0			c.C483A						.						57	56	56					9																	6015125		2203	4300	6503	SO:0001583	missense	26953	exon1			GAAAACGTGAAGT	AF039023	CCDS6467.1	9p24.1	2008-03-26			ENSG00000137040	ENSG00000137040			9851	protein-coding gene	gene with protein product							Standard	NM_001243202		Approved		uc003zjr.3	O60518	OTTHUMG00000019512	ENST00000259569.5:c.483C>A	chr9.hg19:g.6015125G>T	ENSP00000259569:p.His161Gln	90.0	0.0		128.0	38.0	NM_012416	Q5T7X4|Q7Z3V2|Q96E78	Missense_Mutation	SNP	ENST00000259569.5	hg19	CCDS6467.1	.	.	.	.	.	.	.	.	.	.	G	6.613	0.481597	0.12581	.	.	ENSG00000137040	ENST00000259569	T	0.66995	-0.24	4.51	-0.395	0.12431	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.44519	0.1297	N	0.25890	0.77	0.50313	D	0.99986	B	0.33919	0.432	B	0.28465	0.09	T	0.12708	-1.0537	10	0.29301	T	0.29	-6.4829	8.7868	0.34825	0.4187:0.0:0.5813:0.0	.	161	O60518	RNBP6_HUMAN	Q	161	ENSP00000259569:H161Q	ENSP00000259569:H161Q	H	-	3	2	RANBP6	6005125	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	1.025000	0.30090	-0.068000	0.12953	0.561000	0.74099	CAC	.	G|1.000;A|0.000		0.433	RANBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051650.1	NM_012416		T	6015125	G	T	6015125	3	4	364	1	0	0	0	0	1	0	0	0	13046	1136	40	1	2838	1	RANBP6	9	6015125	Missense_Mutation	SNP	G	TCGA-ZP-A9CY-01A-11D-A382-10	5284909	6015125	135198306	40	50784										
KIAA1958	158405	hgsc.bcm.edu	37	chr9	115337345	115337345	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	gtatccccttgtctgccctgCagctgcctggacaggatgag	12	13	1	1			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr9:115337345C>T	ENST00000337530.6	+	2	1281	c.985C>T	c.(985-987)Cag>Tag	p.Q329*	KIAA1958_ENST00000374244.3_Nonsense_Mutation_p.Q329*|KIAA1958_ENST00000536272.1_Nonsense_Mutation_p.Q329*	NM_133465.2	NP_597722.1	Q8N8K9	K1958_HUMAN	KIAA1958	329										endometrium(1)|large_intestine(9)|lung(10)|prostate(2)|skin(3)	25						GTCTGCCCTGCAGCTGCCTGG	0.552																																					p.Q329X		Atlas-SNP	.											.	KIAA1958	52	.	0			c.C985T						.						226	213	217					9																	115337345		2203	4300	6503	SO:0001587	stop_gained	158405	exon2			GCCCTGCAGCTGC	AB075838	CCDS35108.1, CCDS69642.1	9q33.1	2009-09-22			ENSG00000165185	ENSG00000165185			23427	protein-coding gene	gene with protein product							Standard	NM_001287038		Approved	FLJ39294	uc004bgf.1	Q8N8K9	OTTHUMG00000020508	ENST00000337530.6:c.985C>T	chr9.hg19:g.115337345C>T	ENSP00000336940:p.Gln329*	42.0	0.0		55.0	16.0	NM_133465	B7ZKW6|Q2M336|Q5T252|Q8TF43|Q96N02	Nonsense_Mutation	SNP	ENST00000337530.6	hg19	CCDS35108.1	.	.	.	.	.	.	.	.	.	.	C	36	5.657210	0.96724	.	.	ENSG00000165185	ENST00000337530;ENST00000374244;ENST00000536272	.	.	.	5.92	5.92	0.95590	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.36615	T	0.2	-14.168	20.3214	0.98679	0.0:1.0:0.0:0.0	.	.	.	.	X	329	.	ENSP00000336940:Q329X	Q	+	1	0	KIAA1958	114377166	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.786000	0.69006	2.804000	0.96469	0.655000	0.94253	CAG	.	.		0.552	KIAA1958-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053690.1	NM_133465		T	115337345	C	T	115337345	4	4	364	1	0	0	0	0	0	1	0	0	8273	711	25	3	987	3	KIAA1958	9	115337345	Nonsense_Mutation	SNP	C	TCGA-ZP-A9CY-01A-11D-A382-10	109322220	115337345	25876086	41	50785										
RGS3	5998	hgsc.bcm.edu	37	chr9	116303703	116303703	+	Intron	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	accaggacagactctgattgGctgagcaaacccaagggcgg	13	11	1	3			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr9:116303703G>T	ENST00000374140.2	+	20	2246				RGS3_ENST00000462143.1_Intron|RGS3_ENST00000350696.5_Intron|RGS3_ENST00000394646.3_Intron|RGS3_ENST00000317613.6_Missense_Mutation_p.G602V|RGS3_ENST00000343817.5_Intron|RGS3_ENST00000374136.1_Missense_Mutation_p.G340V	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3						inactivation of MAPK activity (GO:0000188)|positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			cervix(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	48						ACTCTGATTGGCTGAGCAAAC	0.552																																					p.G602V		Atlas-SNP	.											.	RGS3	251	.	0			c.G1805T						.						156	164	162					9																	116303703		2203	4300	6503	SO:0001627	intron_variant	5998	exon18			TGATTGGCTGAGC	AF006610	CCDS6797.1, CCDS6798.1, CCDS35113.1, CCDS35114.1, CCDS43869.1, CCDS65111.1	9q32	2008-02-05	2007-08-14		ENSG00000138835	ENSG00000138835		"Regulators of G-protein signaling"	9999	protein-coding gene	gene with protein product		602189	"regulator of G-protein signalling 3"			8602223, 11034339	Standard	NM_001276260		Approved	C2PA, FLJ20370, PDZ-RGS3	uc004bhq.4	P49796	OTTHUMG00000021048	ENST00000374140.2:c.2037+4505G>T	chr9.hg19:g.116303703G>T		75.0	0.0		120.0	41.0	NM_017790	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Missense_Mutation	SNP	ENST00000374140.2	hg19	CCDS43869.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.604822	0.87157	.	.	ENSG00000138835	ENST00000317613;ENST00000374136	T	0.40476	1.03	5.5	5.5	0.81552	.	.	.	.	.	T	0.55146	0.1902	L	0.36672	1.1	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.56980	-0.7889	9	0.87932	D	0	.	14.887	0.70575	0.0:0.0:1.0:0.0	.	340;602	Q5VXC0;P49796-5	.;.	V	602;340	ENSP00000312844:G602V	ENSP00000312844:G602V	G	+	2	0	RGS3	115343524	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.540000	0.53611	2.578000	0.87016	0.650000	0.86243	GGC	.	.		0.552	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790		T	116303703	G	T	116303703	1	4	364	0	1	0	0	0	0	0	0	0	13321	1203	42	3		3	RGS3	9	116303703	Intron	SNP	G	TCGA-ZP-A9CY-01A-11D-A382-10	966358	116303703	24909728	42	50786										
COL5A1	1289	hgsc.bcm.edu	37	chr9	137688730	137688730	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	aaggacccacaggatttcctGgaccaaagggcccccctgta	10	14	0	0			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr9:137688730G>A	ENST00000371817.3	+	36	3295	c.2881G>A	c.(2881-2883)Gga>Aga	p.G961R		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	961	Triple-helical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		AGGATTTCCTGGACCAAAGGG	0.592																																					p.G961R		Atlas-SNP	.											.	COL5A1	323	.	0			c.G2881A						.						66	76	72					9																	137688730		2203	4300	6503	SO:0001583	missense	1289	exon36			TTTCCTGGACCAA	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"Collagens"	2209	protein-coding gene	gene with protein product	"alpha 1 type V collagen"	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.2881G>A	chr9.hg19:g.137688730G>A	ENSP00000360882:p.Gly961Arg	94.0	0.0		122.0	35.0	NM_000093	Q15094|Q5SUX4	Missense_Mutation	SNP	ENST00000371817.3	hg19	CCDS6982.1	.	.	.	.	.	.	.	.	.	.	g	18.48	3.633692	0.67130	.	.	ENSG00000130635	ENST00000371817	D	0.99186	-5.53	4.72	4.72	0.59763	.	0.000000	0.85682	U	0.000000	D	0.99582	0.9849	H	0.97707	4.06	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97641	1.0148	10	0.87932	D	0	.	17.6509	0.88163	0.0:0.0:1.0:0.0	.	961	P20908	CO5A1_HUMAN	R	961	ENSP00000360882:G961R	ENSP00000360882:G961R	G	+	1	0	COL5A1	136828551	1.000000	0.71417	0.998000	0.56505	0.845000	0.48019	9.493000	0.97960	2.149000	0.67028	0.443000	0.29094	GGA	.	.		0.592	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093		A	137688730	G	A	137688730	3	1	364	1	0	0	0	0	1	0	0	0	3698	1349	47	3	3023	3	COL5A1	9	137688730	Missense_Mutation	SNP	G	TCGA-ZP-A9CY-01A-11D-A382-10	21385027	137688730	3524701	43	50787										
MYO3A	53904	hgsc.bcm.edu	37	chr10	26462696	26462696	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	atctgtagtgaagacttccaCtttcaaacctgaagaggaaa	8	8	2	4			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr10:26462696C>A	ENST00000265944.5	+	30	3669	c.3503C>A	c.(3502-3504)aCt>aAt	p.T1168N	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	1168					ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						AAGACTTCCACTTTCAAACCT	0.368																																					p.T1168N		Atlas-SNP	.											.	MYO3A	371	.	0			c.C3503A						.						56	55	56					10																	26462696		2203	4300	6503	SO:0001583	missense	53904	exon30			CTTCCACTTTCAA	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.3503C>A	chr10.hg19:g.26462696C>A	ENSP00000265944:p.Thr1168Asn	177.0	0.0		222.0	75.0	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	hg19	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	C	4.130	0.022448	0.08006	.	.	ENSG00000095777	ENST00000265944	T	0.76709	-1.04	5.42	1.2	0.21068	.	1.502560	0.02945	N	0.140997	T	0.62962	0.2471	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40308	-0.9570	10	0.17832	T	0.49	.	2.5718	0.04797	0.1145:0.4507:0.2172:0.2176	.	1168	Q8NEV4	MYO3A_HUMAN	N	1168	ENSP00000265944:T1168N	ENSP00000265944:T1168N	T	+	2	0	MYO3A	26502702	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	0.582000	0.23834	0.334000	0.23590	0.655000	0.94253	ACT	.	.		0.368	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		A	26462696	C	A	26462696	3	1	364	1	0	0	0	0	1	0	0	0	10085	565	20	3	3613	3	MYO3A	10	26462696	Missense_Mutation	SNP	C	TCGA-ZP-A9CY-01A-11D-A382-10		26462696	109072051	44	50788										
LRRC20	55222	hgsc.bcm.edu	37	chr10	72061218	72061218	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	agtgggttgaagcggaggttGatgctgcgcaaggctggcat	18	6	0	2			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr10:72061218G>A	ENST00000355790.4	-	5	924	c.447C>T	c.(445-447)atC>atT	p.I149I	LRRC20_ENST00000373224.1_Silent_p.I149I|LRRC20_ENST00000395010.1_Silent_p.I93I|LRRC20_ENST00000358141.2_Silent_p.I99I|LRRC20_ENST00000395011.1_Silent_p.I99I	NM_001278212.1|NM_001278214.1|NM_207119.1	NP_001265141.1|NP_001265143.1|NP_997002.1	Q8TCA0	LRC20_HUMAN	leucine rich repeat containing 20	149										endometrium(2)|large_intestine(4)|lung(2)|urinary_tract(1)	9						AGCGGAGGTTGATGCTGCGCA	0.602																																					p.I149I		Atlas-SNP	.											.	LRRC20	19	.	0			c.C447T						.						125	120	122					10																	72061218		2203	4300	6503	SO:0001819	synonymous_variant	55222	exon5			GAGGTTGATGCTG	BC024001	CCDS7300.1, CCDS7301.1, CCDS7302.1, CCDS73145.1	10q22.2	2004-04-15			ENSG00000172731	ENSG00000172731			23421	protein-coding gene	gene with protein product							Standard	NM_207119		Approved	FLJ10751, FLJ10844	uc031pvr.1	Q8TCA0	OTTHUMG00000018407	ENST00000355790.4:c.447C>T	chr10.hg19:g.72061218G>A		45.0	0.0		61.0	17.0	NM_207119	Q5T6D4|Q5T6D6|Q9NVA6|Q9NVG3	Silent	SNP	ENST00000355790.4	hg19	CCDS7302.1																																																																																			.	.		0.602	LRRC20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048510.1	NM_018239		A	72061218	G	A	72061218	2	1	364	1	0	0	0	0	0	0	0	1	8986	1280	45	3		3	LRRC20	10	72061218	Silent	SNP	G	TCGA-ZP-A9CY-01A-11D-A382-10	45598522	72061218	63473529	45	50789										
SORCS1	114815	hgsc.bcm.edu	37	chr10	108339004	108339004	+	Intron	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	cataaacattaatccccgggAtcttcctaaaatattaatag	4	9	1	0			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr10:108339004A>G	ENST00000263054.6	-	25	3379				SORCS1_ENST00000369698.1_Missense_Mutation_p.I661T|SORCS1_ENST00000344440.6_Missense_Mutation_p.I1126T	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1						neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		AATCCCCGGGATCTTCCTAAA	0.463																																					p.I1126T		Atlas-SNP	.											.	SORCS1	534	.	0			c.T3377C						.						136	131	132					10																	108339004		2203	4300	6503	SO:0001627	intron_variant	114815	exon26			CCCGGGATCTTCC	AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.3371+122T>C	chr10.hg19:g.108339004A>G		56.0	0.0		77.0	6.0	NM_001206572	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	hg19	CCDS7559.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.47|16.47	3.132160|3.132160	0.56828|0.56828	.|.	.|.	ENSG00000108018|ENSG00000108018	ENST00000369698;ENST00000344440|ENST00000452214	T;T|.	0.25749|.	1.78;2.35|.	5.68|5.68	5.68|5.68	0.88126|0.88126	.|.	0.418903|.	0.24720|.	N|.	0.036157|.	T|T	0.68403|0.68403	0.2997|0.2997	L|L	0.50333|0.50333	1.59|1.59	0.49798|0.49798	D|D	0.999827|0.999827	D;D|.	0.71674|.	0.998;0.973|.	D;P|.	0.72982|.	0.979;0.885|.	T|T	0.66097|0.66097	-0.6008|-0.6008	9|5	.|.	.|.	.|.	-4.822|-4.822	15.9315|15.9315	0.79663|0.79663	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	1126;1126|.	Q8WY21-3;Q8WY21-2|.	.;.|.	T|P	661;1126|141	ENSP00000358712:I661T;ENSP00000345964:I1126T|.	.|.	I|S	-|-	2|1	0|0	SORCS1|SORCS1	108328994|108328994	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.979000|0.979000	0.70002|0.70002	8.962000|8.962000	0.93254|0.93254	2.176000|2.176000	0.68965|0.68965	0.455000|0.455000	0.32223|0.32223	ATC|TCC	.	.		0.463	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918		G	108339004	A	G	108339004	1	3	364	0	1	0	0	0	0	0	0	0	14945	333	12	2		2	SORCS1	10	108339004	Intron	SNP	A	TCGA-ZP-A9CY-01A-11D-A382-10	36277786	108339004	27195743	46	50790										
OR5L1	219437	hgsc.bcm.edu	37	chr11	55579715	55579715	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	ccatggaacagtcctttccaTttattgcaggcccagttcag	8	12	1	0			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr11:55579715T>G	ENST00000333973.2	+	1	862	c.773T>G	c.(772-774)aTt>aGt	p.I258S		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, member 1	258						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(4)|liver(4)|lung(36)|ovary(2)|pancreas(1)|prostate(5)|skin(9)|stomach(4)|upper_aerodigestive_tract(3)	78		all_epithelial(135;0.208)				GTCCTTTCCATTTATTGCAGG	0.512																																					p.I258S		Atlas-SNP	.											.	OR5L1	145	.	0			c.T773G						.						121	104	110					11																	55579715		2200	4296	6496	SO:0001583	missense	219437	exon1			TTTCCATTTATTG	AB065780	CCDS31509.1	11q11	2012-08-09			ENSG00000186117	ENSG00000186117		"GPCR / Class A : Olfactory receptors"	8350	protein-coding gene	gene with protein product							Standard	NM_001004738		Approved	OST262	uc001nhw.1	Q8NGL2	OTTHUMG00000166810	ENST00000333973.2:c.773T>G	chr11.hg19:g.55579715T>G	ENSP00000335529:p.Ile258Ser	70.0	0.0		112.0	33.0	NM_001004738	B2RNK6|Q6IFD0	Missense_Mutation	SNP	ENST00000333973.2	hg19	CCDS31509.1	.	.	.	.	.	.	.	.	.	.	t	9.996	1.232216	0.22626	.	.	ENSG00000186117	ENST00000333973	T	0.00145	8.67	4.12	2.96	0.34315	GPCR, rhodopsin-like superfamily (1);	0.509225	0.18083	N	0.152222	T	0.00178	0.0005	L	0.54965	1.715	0.09310	N	1	B	0.15473	0.013	B	0.23018	0.043	T	0.33854	-0.9852	10	0.62326	D	0.03	-12.5116	7.1659	0.25689	0.0:0.1959:0.0:0.8041	.	258	Q8NGL2	OR5L1_HUMAN	S	258	ENSP00000335529:I258S	ENSP00000335529:I258S	I	+	2	0	OR5L1	55336291	0.000000	0.05858	0.001000	0.08648	0.090000	0.18270	0.264000	0.18497	0.472000	0.27344	0.352000	0.21897	ATT	.	.		0.512	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738		G	55579715	T	G	55579715	3	3	364	1	0	0	0	0	1	0	0	0	11179	1493	52	5	775	5	OR5L1	11	55579715	Missense_Mutation	SNP	T	TCGA-ZP-A9CY-01A-11D-A382-10		55579715	79426801	47	50791										
HEPHL1	341208	hgsc.bcm.edu	37	chr11	93836112	93836112	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	cttatagatggaatatccctAaaagatccggtccagggcct	9	10	0	2			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr11:93836112A>G	ENST00000315765.9	+	15	2616	c.2608A>G	c.(2608-2610)Aaa>Gaa	p.K870E		NM_001098672.1	NP_001092142.1	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	870	Plastocyanin-like 5.				copper ion transport (GO:0006825)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	61		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				GAATATCCCTAAAAGATCCGG	0.338																																					p.K870E		Atlas-SNP	.											.	HEPHL1	144	.	0			c.A2608G						.						72	68	70					11																	93836112		1796	4056	5852	SO:0001583	missense	341208	exon15			ATCCCTAAAAGAT	BX641008	CCDS44710.1	11q21	2008-02-05			ENSG00000181333	ENSG00000181333			30477	protein-coding gene	gene with protein product							Standard	NM_001098672		Approved	DKFZp686F22190	uc001pep.2	Q6MZM0	OTTHUMG00000167751	ENST00000315765.9:c.2608A>G	chr11.hg19:g.93836112A>G	ENSP00000313699:p.Lys870Glu	68.0	0.0		86.0	32.0	NM_001098672	Q3C1W7	Missense_Mutation	SNP	ENST00000315765.9	hg19	CCDS44710.1	.	.	.	.	.	.	.	.	.	.	A	1.891	-0.455586	0.04540	.	.	ENSG00000181333	ENST00000315765	D	0.97850	-4.57	5.16	4.04	0.47022	Cupredoxin (2);Multicopper oxidase, type 3 (1);	0.155825	0.64402	D	0.000020	D	0.88466	0.6444	N	0.02854	-0.475	0.31325	N	0.685564	B	0.15930	0.015	B	0.19946	0.027	T	0.81254	-0.1016	10	0.02654	T	1	-16.266	4.0378	0.09737	0.5707:0.1749:0.2544:0.0	.	870	Q6MZM0	HPHL1_HUMAN	E	870	ENSP00000313699:K870E	ENSP00000313699:K870E	K	+	1	0	HEPHL1	93475760	0.993000	0.37304	0.997000	0.53966	0.839000	0.47603	2.238000	0.43070	0.816000	0.34421	-0.256000	0.11100	AAA	.	.		0.338	HEPHL1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396103.2	XM_291947		G	93836112	A	G	93836112	3	3	364	1	0	0	0	0	1	0	0	0	7064	363	13	2	2666	2	HEPHL1	11	93836112	Missense_Mutation	SNP	A	TCGA-ZP-A9CY-01A-11D-A382-10	38256397	93836112	41170404	48	50792										
ZNF202	7753	hgsc.bcm.edu	37	chr11	123599920	123599920	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	tgggtcctcgggcactgggaCctctatgaagaaaagaaggc	14	9	1	3			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr11:123599920C>A	ENST00000529691.1	-	4	835	c.616G>T	c.(616-618)Gtc>Ttc	p.V206F	ZNF202_ENST00000336139.4_Missense_Mutation_p.V206F|ZNF202_ENST00000530393.1_Missense_Mutation_p.V206F			O95125	ZN202_HUMAN	zinc finger protein 202	206					lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.03)		GGCACTGGGACCTCTATGAAG	0.517																																					p.V206F		Atlas-SNP	.											.	ZNF202	72	.	0			c.G616T						.						58	55	56					11																	123599920		2202	4299	6501	SO:0001583	missense	7753	exon6			CTGGGACCTCTAT	AF027219	CCDS8443.1	11q23.3	2013-01-09				ENSG00000166261		"Zinc fingers, C2H2-type", "-", "-", "-"	12994	protein-coding gene	gene with protein product		603430				9790754	Standard	XM_005271659		Approved	ZKSCAN10, ZSCAN42	uc001pzd.1	O95125		ENST00000529691.1:c.616G>T	chr11.hg19:g.123599920C>A	ENSP00000433881:p.Val206Phe	30.0	0.0		47.0	21.0	NM_003455	B0LPH9|Q4JG21|Q9H1B9|Q9NSM4	Missense_Mutation	SNP	ENST00000529691.1	hg19	CCDS8443.1	.	.	.	.	.	.	.	.	.	.	C	12.23	1.874620	0.33069	.	.	ENSG00000166261	ENST00000336139;ENST00000530393;ENST00000529691	T;T;T	0.06371	3.31;3.31;3.31	5.32	1.07	0.20283	.	0.637749	0.12998	N	0.421874	T	0.04588	0.0125	L	0.29908	0.895	0.24721	N	0.993142	B	0.25719	0.132	B	0.21917	0.037	T	0.44314	-0.9336	10	0.15066	T	0.55	-2.8232	9.0697	0.36484	0.1507:0.364:0.4853:0.0	.	206	O95125	ZN202_HUMAN	F	206	ENSP00000337724:V206F;ENSP00000432504:V206F;ENSP00000433881:V206F	ENSP00000337724:V206F	V	-	1	0	ZNF202	123105130	0.069000	0.21087	0.516000	0.27786	0.639000	0.38242	0.012000	0.13287	0.597000	0.29811	-0.312000	0.09012	GTC	.	.		0.517	ZNF202-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387419.1	NM_003455		A	123599920	C	A	123599920	3	1	364	1	0	0	0	0	1	0	0	0	17778	507	18	3	1346	3	ZNF202	11	123599920	Missense_Mutation	SNP	C	TCGA-ZP-A9CY-01A-11D-A382-10	29763808	123599920	11406596	49	50793										
PRMT8	56341	hgsc.bcm.edu	37	chr12	3692299	3692299	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	gcctgcagatacagcgcaacGactacgtccacgccctggtc	10	16	0	1			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr12:3692299G>A	ENST00000382622.3	+	8	1294	c.904G>A	c.(904-906)Gac>Aac	p.D302N	PRMT8_ENST00000452611.2_Missense_Mutation_p.D293N|PRMT8_ENST00000261252.4_3'UTR	NM_019854.4	NP_062828.3	Q9NR22	ANM8_HUMAN	protein arginine methyltransferase 8	302	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				histone arginine methylation (GO:0034969)|histone H4-R3 methylation (GO:0043985)|histone methylation (GO:0016571)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|regulation of protein binding (GO:0043393)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	histone methyltransferase activity (H4-R3 specific) (GO:0044020)|histone-arginine N-methyltransferase activity (GO:0008469)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(9)|lung(14)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)	37			OV - Ovarian serous cystadenocarcinoma(31;0.0109)|COAD - Colon adenocarcinoma(12;0.0264)			ACAGCGCAACGACTACGTCCA	0.483																																					p.D302N		Atlas-SNP	.											.	PRMT8	97	.	0			c.G904A						.						119	94	102					12																	3692299		2203	4300	6503	SO:0001583	missense	56341	exon8			CGCAACGACTACG	AF263539	CCDS8521.2, CCDS58200.1	12p13.3	2006-03-03	2006-02-16	2006-02-16	ENSG00000111218	ENSG00000111218		"Protein arginine methyltransferases"	5188	protein-coding gene	gene with protein product		610086	"HMT1 hnRNP methyltransferase-like 3 (S. cerevisiae)", "HMT1 hnRNP methyltransferase-like 4 (S. cerevisiae)"	HRMT1L3, HRMT1L4		16051612	Standard	NM_019854		Approved		uc001qmf.4	Q9NR22	OTTHUMG00000128493	ENST00000382622.3:c.904G>A	chr12.hg19:g.3692299G>A	ENSP00000372067:p.Asp302Asn	69.0	0.0		108.0	40.0	NM_019854	B2RDP0|Q8TBJ8	Missense_Mutation	SNP	ENST00000382622.3	hg19	CCDS8521.2	.	.	.	.	.	.	.	.	.	.	G	20.9	4.062770	0.76187	.	.	ENSG00000111218	ENST00000452611;ENST00000382622	D;D	0.84660	-1.88;-1.88	5.55	5.55	0.83447	.	0.134229	0.64402	D	0.000003	D	0.93854	0.8034	M	0.93241	3.395	0.80722	D	1	D;D	0.76494	0.999;0.997	P;P	0.62649	0.905;0.841	D	0.95141	0.8264	10	0.87932	D	0	.	17.0578	0.86539	0.0:0.0:1.0:0.0	.	293;302	Q9NR22-2;Q9NR22	.;ANM8_HUMAN	N	293;302	ENSP00000414507:D293N;ENSP00000372067:D302N	ENSP00000372067:D302N	D	+	1	0	PRMT8	3562560	1.000000	0.71417	0.992000	0.48379	0.322000	0.28314	9.869000	0.99810	2.625000	0.88918	0.650000	0.86243	GAC	.	.		0.483	PRMT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250297.2	NM_019854		A	3692299	G	A	3692299	3	1	364	1	0	0	0	0	1	0	0	0	12554	1058	37	1	934	1	PRMT8	12	3692299	Missense_Mutation	SNP	G	TCGA-ZP-A9CY-01A-11D-A382-10		3692299	130159596	50	50794										
BHLHE41	79365	hgsc.bcm.edu	37	chr12	26275865	26275865	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	ggcggccgcggacccggcggCcgagggagcgccggtgcctt	20	15	0	0			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr12:26275865C>T	ENST00000242728.4	-	5	930	c.583G>A	c.(583-585)Gcc>Acc	p.A195T	RP11-283G6.3_ENST00000545819.1_RNA|RP11-283G6.3_ENST00000535914.1_RNA	NM_030762.2	NP_110389.1	Q9C0J9	BHE41_HUMAN	basic helix-loop-helix family, member e41	195					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|circadian regulation of gene expression (GO:0032922)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)	nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|histone deacetylase binding (GO:0042826)|MRF binding (GO:0043426)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|transcription corepressor activity (GO:0003714)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(1)	5						GACCCGGCGGCCGAGGGAGCG	0.711																																					p.A195T		Atlas-SNP	.											.	BHLHE41	20	.	0			c.G583A						.						6	9	8					12																	26275865		2055	4080	6135	SO:0001583	missense	79365	exon5			CGGCGGCCGAGGG	AB044088	CCDS8706.1	12p12.1	2011-12-05	2009-01-12	2009-01-12	ENSG00000123095	ENSG00000123095		"Basic helix-loop-helix proteins"	16617	protein-coding gene	gene with protein product	"differentially expressed in chondrocytes 2", "Enhancer-of-split and hairy-related protein 1"	606200	"basic helix-loop-helix domain containing, class B, 3"	BHLHB3		11162494, 18557763	Standard	NM_030762		Approved	DEC2, SHARP-1, SHARP1, bHLHe41	uc001rhb.3	Q9C0J9	OTTHUMG00000169174	ENST00000242728.4:c.583G>A	chr12.hg19:g.26275865C>T	ENSP00000242728:p.Ala195Thr	121.0	0.0		161.0	50.0	NM_030762	A2I2N8	Missense_Mutation	SNP	ENST00000242728.4	hg19	CCDS8706.1	.	.	.	.	.	.	.	.	.	.	C	4.963	0.178855	0.09443	.	.	ENSG00000123095	ENST00000242728;ENST00000540731	T	0.55588	0.51	2.74	0.376	0.16193	.	1.818110	0.03319	U	0.191646	T	0.27798	0.0684	N	0.08118	0	0.58432	D	0.999999	B	0.26935	0.164	B	0.22753	0.041	T	0.39187	-0.9626	10	0.19590	T	0.45	-6.3677	1.5786	0.02629	0.1967:0.4512:0.1958:0.1562	.	195	Q9C0J9	BHE41_HUMAN	T	195	ENSP00000242728:A195T	ENSP00000242728:A195T	A	-	1	0	BHLHE41	26167132	0.812000	0.29077	0.046000	0.18839	0.407000	0.30961	1.368000	0.34216	0.235000	0.21160	0.313000	0.20887	GCC	.	.		0.711	BHLHE41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402714.1	NM_030762		T	26275865	C	T	26275865	3	4	364	1	0	0	0	0	1	0	0	0	1424	739	26	3	869	3	BHLHE41	12	26275865	Missense_Mutation	SNP	C	TCGA-ZP-A9CY-01A-11D-A382-10	22583566	26275865	107576030	51	50795										
CCDC53	51019	hgsc.bcm.edu	37	chr12	102455087	102455087	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	tgtgcaccacaaattggtttAgaaaagccaccgttcttttc	7	10	1	1			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr12:102455087A>G	ENST00000240079.6	-	2	250	c.89T>C	c.(88-90)cTa>cCa	p.L30P	RP11-554E23.4_ENST00000552707.1_RNA|CCDC53_ENST00000539515.1_5'UTR|CCDC53_ENST00000545679.1_Missense_Mutation_p.L30P	NM_016053.2	NP_057137.1	Q9Y3C0	CCD53_HUMAN	coiled-coil domain containing 53	30						actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|WASH complex (GO:0071203)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4						AAATTGGTTTAGAAAAGCCAC	0.433																																					p.L30P		Atlas-SNP	.											.	CCDC53	14	.	0			c.T89C						.						114	103	106					12																	102455087		1924	4129	6053	SO:0001583	missense	51019	exon2			TGGTTTAGAAAAG	AF151874	CCDS44959.1, CCDS73512.1	12q23.3	2014-05-09			ENSG00000120860	ENSG00000120860			24256	protein-coding gene	gene with protein product						10810093, 20498093	Standard	XM_005268939		Approved	CGI-116	uc010svw.2	Q9Y3C0	OTTHUMG00000168187	ENST00000240079.6:c.89T>C	chr12.hg19:g.102455087A>G	ENSP00000240079:p.Leu30Pro	119.0	0.0		155.0	59.0	NM_016053	B2RC74|Q53FF0|Q6IAI4|Q96QK0	Missense_Mutation	SNP	ENST00000240079.6	hg19	CCDS44959.1	.	.	.	.	.	.	.	.	.	.	A	29.0	4.970400	0.92919	.	.	ENSG00000120860	ENST00000240079;ENST00000545679	.	.	.	5.93	5.93	0.95920	.	0.062101	0.64402	D	0.000004	T	0.80523	0.4639	M	0.81802	2.56	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.78314	0.975;0.991	T	0.83172	-0.0093	9	0.87932	D	0	-8.1961	16.3943	0.83563	1.0:0.0:0.0:0.0	.	30;30	F5GZ97;Q9Y3C0	.;CCD53_HUMAN	P	30	.	ENSP00000240079:L30P	L	-	2	0	CCDC53	100979217	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.673000	0.91186	2.281000	0.76405	0.533000	0.62120	CTA	.	.		0.433	CCDC53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398685.1	NM_016053		G	102455087	A	G	102455087	3	3	364	1	0	0	0	0	1	0	0	0	2825	420	15	2	450	2	CCDC53	12	102455087	Missense_Mutation	SNP	A	TCGA-ZP-A9CY-01A-11D-A382-10	76179222	102455087	31396808	52	50796										
C12orf76	400073	hgsc.bcm.edu	37	chr12	110496826	110496826	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	ccgaacaaactgtggtatgaAtgaagcgagaagcttgtcca	11	8	0	3			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr12:110496826A>T	ENST00000309050.5	-	3	522	c.158T>A	c.(157-159)aTt>aAt	p.I53N	C12orf76_ENST00000548936.1_Intron|C12orf76_ENST00000548191.1_Intron	NM_207435.1	NP_997318.1	Q8N812	CL076_HUMAN	chromosome 12 open reading frame 76	53										endometrium(1)|large_intestine(2)|lung(2)|ovary(1)	6						tgtggtatgaatgaagcgaga	0.463																																					p.I53N		Atlas-SNP	.											.	C12orf76	10	.	0			c.T158A						.						111	94	100					12																	110496826		1327	2309	3636	SO:0001583	missense	400073	exon3			GTATGAATGAAGC	BC041968	CCDS9141.1	12q24.11	2012-08-16			ENSG00000174456	ENSG00000174456			33790	protein-coding gene	gene with protein product							Standard	NM_207435		Approved	FLJ40142	uc001tqe.2	Q8N812	OTTHUMG00000169315	ENST00000309050.5:c.158T>A	chr12.hg19:g.110496826A>T	ENSP00000308368:p.Ile53Asn	153.0	0.0		213.0	65.0	NM_207435		Missense_Mutation	SNP	ENST00000309050.5	hg19	CCDS9141.1	.	.	.	.	.	.	.	.	.	.	A	6.471	0.455129	0.12283	.	.	ENSG00000174456	ENST00000309050	.	.	.	1.07	1.07	0.20283	.	.	.	.	.	T	0.11153	0.0272	N	0.14661	0.345	0.09310	N	1	D	0.53885	0.963	B	0.36534	0.227	T	0.17410	-1.0370	8	0.87932	D	0	.	4.3477	0.11141	1.0:0.0:0.0:0.0	.	53	Q8N812	CL076_HUMAN	N	53	.	ENSP00000308368:I53N	I	-	2	0	C12orf76	108981209	0.002000	0.14202	0.001000	0.08648	0.024000	0.10985	1.518000	0.35877	0.713000	0.32060	0.260000	0.18958	ATT	.	.		0.463	C12orf76-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403439.2	NM_207435		T	110496826	A	T	110496826	3	4	364	1	0	0	0	0	1	0	0	0	1717	101	4	4	261	4	C12orf76	12	110496826	Missense_Mutation	SNP	A	TCGA-ZP-A9CY-01A-11D-A382-10	8041739	110496826	23355069	53	50797										
PTPN11	5781	hgsc.bcm.edu	37	chr12	112915714	112915714	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	cccaaaaagagttacattgcCacacaaggctgcctgcaaaa	7	12	0	1			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr12:112915714C>A	ENST00000351677.2	+	9	1185	c.987C>A	c.(985-987)gcC>gcA	p.A329A	PTPN11_ENST00000392597.1_Silent_p.A329A	NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	329	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				abortive mitotic cell cycle (GO:0033277)|activation of MAPK activity (GO:0000187)|atrioventricular canal development (GO:0036302)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage checkpoint (GO:0000077)|ephrin receptor signaling pathway (GO:0048013)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|genitalia development (GO:0048806)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|multicellular organismal reproductive process (GO:0048609)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cortisol secretion (GO:0051463)|negative regulation of growth hormone secretion (GO:0060125)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ growth (GO:0035265)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of hormone secretion (GO:0046887)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of multicellular organism growth (GO:0040014)|regulation of protein export from nucleus (GO:0046825)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	insulin receptor binding (GO:0005158)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3)	451						GTTACATTGCCACACAAGGCT	0.413			Mis		"JMML, AML, MDS"		Noonan Syndrome		Noonan syndrome																												p.A329A		Atlas-SNP	.		Dom	yes		12	12q24.1	5781	"protein tyrosine phosphatase, non-receptor type 11"	yes	L	.	PTPN11	623	.	0			c.C987A						.						62	55	57					12																	112915714		2203	4300	6503	SO:0001819	synonymous_variant	5781	exon9	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	CATTGCCACACAA	D13540	CCDS9163.1, CCDS58280.1	12q24.1	2014-09-17	2008-07-31		ENSG00000179295	ENSG00000179295		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor", "SH2 domain containing"	9644	protein-coding gene	gene with protein product		176876	"Noonan syndrome 1"	NS1		7894486, 1280823	Standard	NM_080601		Approved	BPTP3, SH-PTP2, SHP-2, PTP2C, SHP2	uc001ttx.3	Q06124	OTTHUMG00000134334	ENST00000351677.2:c.987C>A	chr12.hg19:g.112915714C>A		165.0	0.0		198.0	78.0	NM_080601	A8K1D9|Q96HD7	Silent	SNP	ENST00000351677.2	hg19	CCDS9163.1																																																																																			.	.		0.413	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259496.2			A	112915714	C	A	112915714	2	1	364	1	0	0	0	0	0	0	0	1	12793	581	21	3		3	PTPN11	12	112915714	Silent	SNP	C	TCGA-ZP-A9CY-01A-11D-A382-10	2418888	112915714	20936181	54	50798										
BRCA2	675	hgsc.bcm.edu	37	chr13	32936724	32936724	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	gaatttgggtttataatcacTatagatggatcatatggaaa	9	3	2	1	rs397507942		TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr13:32936724T>A	ENST00000380152.3	+	17	8103	c.7870T>A	c.(7870-7872)Tat>Aat	p.Y2624N	BRCA2_ENST00000544455.1_Missense_Mutation_p.Y2624N			P51587	BRCA2_HUMAN	breast cancer 2, early onset	2624					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TTATAATCACTATAGATGGAT	0.378			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											p.Y2624N	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	.	BRCA2	812	.	0			c.T7870A						.						102	102	102					13																	32936724		2203	4300	6503	SO:0001583	missense	675	exon17	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	AATCACTATAGAT	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.7870T>A	chr13.hg19:g.32936724T>A	ENSP00000369497:p.Tyr2624Asn	117.0	0.0		182.0	35.0	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	hg19	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.761987	0.89932	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	D;D	0.89415	-2.51;-2.51	5.66	5.66	0.87406	DNA recombination/repair protein BRCA2, helical domain (2);	0.000000	0.85682	D	0.000000	D	0.95306	0.8477	M	0.89095	3.005	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96037	0.9021	10	0.87932	D	0	.	16.1819	0.81915	0.0:0.0:0.0:1.0	.	2624	P51587	BRCA2_HUMAN	N	2624	ENSP00000369497:Y2624N;ENSP00000439902:Y2624N	ENSP00000369497:Y2624N	Y	+	1	0	BRCA2	31834724	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.978000	0.88095	2.279000	0.76181	0.533000	0.62120	TAT	.	.		0.378	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		A	32936724	T	A	32936724	3	1	364	1	0	0	0	0	1	0	0	0	1501	1522	53	4	7932	4	BRCA2	13	32936724	Missense_Mutation	SNP	T	TCGA-ZP-A9CY-01A-11D-A382-10		32936724	82233154	55	50799										
TPP2	7174	hgsc.bcm.edu	37	chr13	103268744	103268744	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	ggtaatttttctgtctttgcAgaaagaacggaaggaaaaaa	10	4	2	2			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr13:103268744A>T	ENST00000376065.4	+	4	426		c.e4-1		TPP2_ENST00000376052.3_Splice_Site	NM_003291.2	NP_003282.2	P29144	TPP2_HUMAN	tripeptidyl peptidase II						antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)|tripeptidyl-peptidase activity (GO:0008240)			breast(2)|endometrium(5)|kidney(2)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	52	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					CTGTCTTTGCAGAAAGAACGG	0.413																																					.		Atlas-SNP	.											.	TPP2	124	.	0			c.391-2A>T						.						77	85	83					13																	103268744		2203	4300	6503	SO:0001630	splice_region_variant	7174	exon4			CTTTGCAGAAAGA	M55169	CCDS9502.1	13q32-q33	2008-02-05			ENSG00000134900	ENSG00000134900	3.4.14.10		12016	protein-coding gene	gene with protein product		190470				1670990	Standard	NM_003291		Approved		uc001vpi.4	P29144	OTTHUMG00000017305	ENST00000376065.4:c.391-1A>T	chr13.hg19:g.103268744A>T		77.0	0.0		133.0	57.0	NM_003291	Q5VZU8	Splice_Site	SNP	ENST00000376065.4	hg19	CCDS9502.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.972224	0.74246	.	.	ENSG00000134900	ENST00000376065;ENST00000376052	.	.	.	5.54	5.54	0.83059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9801	0.80102	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TPP2	102066745	1.000000	0.71417	1.000000	0.80357	0.773000	0.43773	8.883000	0.92426	2.230000	0.72887	0.528000	0.53228	.	.	.		0.413	TPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045683.2		Intron	T	103268744	A	T	103268744	5	4	364	1	0	0	0	0	0	0	1	0	16427	202	7	4	403	4	TPP2	13	103268744	Splice_Site	SNP	A	TCGA-ZP-A9CY-01A-11D-A382-10	70332020	103268744	11901134	56	50800										
FAM155A	728215	hgsc.bcm.edu	37	chr13	107822876	107822876	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	tggttgagttttcttccagcGtgttgatgcctccaaagctc	10	10	1	2			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr13:107822876G>T	ENST00000375915.2	-	3	1484	c.1346C>A	c.(1345-1347)aCg>aAg	p.T449K		NM_001080396.2	NP_001073865.1	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A	449						integral component of membrane (GO:0016021)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33						TTCTTCCAGCGTGTTGATGCC	0.517																																					p.T449K		Atlas-SNP	.											.	FAM155A	82	.	0			c.C1346A						.						119	102	108					13																	107822876		2203	4300	6503	SO:0001583	missense	728215	exon3			TCCAGCGTGTTGA	L10374	CCDS32006.1	13q33.3	2008-04-15			ENSG00000204442	ENSG00000204442			33877	protein-coding gene	gene with protein product							Standard	NM_001080396		Approved		uc001vql.3	B1AL88	OTTHUMG00000017326	ENST00000375915.2:c.1346C>A	chr13.hg19:g.107822876G>T	ENSP00000365080:p.Thr449Lys	26.0	0.0		43.0	13.0	NM_001080396	B2RUV1|B7Z334	Missense_Mutation	SNP	ENST00000375915.2	hg19	CCDS32006.1	.	.	.	.	.	.	.	.	.	.	G	12.67	2.007445	0.35415	.	.	ENSG00000204442	ENST00000375915	T	0.12465	2.68	5.55	5.55	0.83447	.	0.564912	0.19081	N	0.123254	T	0.10337	0.0253	N	0.14661	0.345	0.34797	D	0.73633	B	0.27416	0.178	B	0.31946	0.138	T	0.18935	-1.0321	10	0.49607	T	0.09	.	12.0487	0.53495	0.0782:0.0:0.9218:0.0	.	449	B1AL88	F155A_HUMAN	K	449	ENSP00000365080:T449K	ENSP00000365080:T449K	T	-	2	0	FAM155A	106620877	1.000000	0.71417	0.291000	0.24904	0.206000	0.24218	5.929000	0.70096	2.638000	0.89438	0.638000	0.83543	ACG	.	.		0.517	FAM155A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045736.2	NM_001080396		T	107822876	G	T	107822876	3	4	364	1	0	0	0	0	1	0	0	0	5470	1145	40	1	34	1	FAM155A	13	107822876	Missense_Mutation	SNP	G	TCGA-ZP-A9CY-01A-11D-A382-10	4554132	107822876	7347002	57	50801										
ING1	3621	hgsc.bcm.edu	37	chr13	111367802	111367802	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	ttggctgtgatgtccttcgtGgaatgtccttatcattcccc	9	11	1	1			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr13:111367802G>T	ENST00000375774.3	+	1	474	c.12G>T	c.(10-12)gtG>gtT	p.V4V	CARS2_ENST00000535398.1_5'Flank|ING1_ENST00000375775.3_Intron|ING1_ENST00000464141.1_3'UTR|ING1_ENST00000338450.7_Intron|ING1_ENST00000333219.7_Intron	NM_005537.4	NP_005528.3	Q9UK53	ING1_HUMAN	inhibitor of growth family, member 1	4					cell cycle (GO:0007049)|chromatin modification (GO:0016568)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell death (GO:0010941)	nucleus (GO:0005634)	methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(6)|lung(1)|ovary(1)	12	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.188)			TGTCCTTCGTGGAATGTCCTT	0.527																																					p.V4V		Atlas-SNP	.											.	ING1	106	.	0			c.G12T						.						113	108	110					13																	111367802		2203	4300	6503	SO:0001819	synonymous_variant	3621	exon1			CTTCGTGGAATGT		CCDS9515.1, CCDS9516.1, CCDS9517.1, CCDS9518.1	13q34	2013-01-28			ENSG00000153487	ENSG00000153487		"Zinc fingers, PHD-type"	6062	protein-coding gene	gene with protein product	"inhibitor of growth 1", "tumor suppressor ING1", "growth inhibitor ING1", "growth inhibitory protein ING1"	601566				8944021, 9186514	Standard	NM_198219		Approved	p33ING1, p33ING1b, p24ING1c, p33, p47, p47ING1a	uc001vri.3	Q9UK53	OTTHUMG00000017346	ENST00000375774.3:c.12G>T	chr13.hg19:g.111367802G>T		56.0	0.0		73.0	26.0	NM_001267728	O00532|O43658|Q53ZR3|Q5T9G8|Q5T9G9|Q5T9H0|Q5T9H1|Q9H007|Q9HD98|Q9HD99|Q9NS83|Q9P0U6|Q9UBC6|Q9UIJ1|Q9UIJ2|Q9UIJ3|Q9UIJ4|Q9UK52	Silent	SNP	ENST00000375774.3	hg19	CCDS9517.1																																																																																			.	.		0.527	ING1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045770.2	NM_005537		T	111367802	G	T	111367802	2	4	364	1	0	0	0	0	0	0	0	1	7744	1335	47	3		3	ING1	13	111367802	Silent	SNP	G	TCGA-ZP-A9CY-01A-11D-A382-10	3544926	111367802	3802076	58	50802										
RTN1	6252	hgsc.bcm.edu	37	chr14	60212764	60212764	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	gtttaattgagatgtcagtgTctttattcttaaagtccaag	8	5	3	1			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr14:60212764T>C	ENST00000267484.5	-	2	1012	c.677A>G	c.(676-678)gAc>gGc	p.D226G		NM_021136.2	NP_066959.1	Q16799	RTN1_HUMAN	reticulon 1	226					neuron differentiation (GO:0030182)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)				central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(30)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(108;0.0968)		GATGTCAGTGTCTTTATTCTT	0.433																																					p.D226G		Atlas-SNP	.											.	RTN1	139	.	0			c.A677G						.						228	225	226					14																	60212764		2203	4300	6503	SO:0001583	missense	6252	exon2			TCAGTGTCTTTAT	L10333	CCDS9740.1, CCDS9741.1	14q21-q22	2008-08-29			ENSG00000139970	ENSG00000139970			10467	protein-coding gene	gene with protein product		600865	"neuroendocrine-specific protein"	NSP		8275708	Standard	NM_206852		Approved		uc001xen.1	Q16799	OTTHUMG00000028947	ENST00000267484.5:c.677A>G	chr14.hg19:g.60212764T>C	ENSP00000267484:p.Asp226Gly	143.0	0.0		163.0	51.0	NM_021136	Q16800|Q16801|Q5BKZ4|Q9BQ59	Missense_Mutation	SNP	ENST00000267484.5	hg19	CCDS9740.1	.	.	.	.	.	.	.	.	.	.	T	9.821	1.185836	0.21870	.	.	ENSG00000139970	ENST00000267484;ENST00000433623	T	0.23147	1.92	5.48	3.15	0.36227	.	0.541566	0.18398	N	0.142433	T	0.19846	0.0477	L	0.50919	1.6	0.09310	N	1	B	0.16166	0.016	B	0.10450	0.005	T	0.26503	-1.0101	10	0.12766	T	0.61	.	8.2271	0.31575	0.0:0.2581:0.0:0.7419	.	226	Q16799	RTN1_HUMAN	G	226;152	ENSP00000267484:D226G	ENSP00000267484:D226G	D	-	2	0	RTN1	59282517	0.001000	0.12720	0.989000	0.46669	0.818000	0.46254	0.233000	0.17911	0.920000	0.36970	0.455000	0.32223	GAC	.	.		0.433	RTN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000072278.2			C	60212764	T	C	60212764	3	2	364	1	0	0	0	0	1	0	0	0	13740	1667	58	2	1750	2	RTN1	14	60212764	Missense_Mutation	SNP	T	TCGA-ZP-A9CY-01A-11D-A382-10		60212764	47136776	59	50803										
C14orf102	55051	hgsc.bcm.edu	37	chr14	90756941	90756941	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	tcaaagattgcccaatatcaTcaaacaacacctgcaacaaa	3	12	3	1			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr14:90756941T>A	ENST00000354366.3	-	10	2085	c.1853A>T	c.(1852-1854)gAt>gTt	p.D618V	NRDE2_ENST00000357904.3_Missense_Mutation_p.D387V	NM_017970.3	NP_060440.2	Q9H7Z3	NRDE2_HUMAN	NRDE-2, necessary for RNA interference, domain containing	618																	CCCAATATCATCAAACAACAC	0.423																																					p.D618V		Atlas-SNP	.											.	.	.	.	0			c.A1853T						.						74	76	75					14																	90756941		2203	4300	6503	SO:0001583	missense	55051	exon10			ATATCATCAAACA	AK000870	CCDS9890.1	14q32.11	2012-12-14	2012-09-25	2012-09-25	ENSG00000119720	ENSG00000119720			20186	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 102"	C14orf102			Standard	NM_017970		Approved	FLJ14051	uc001xyi.2	Q9H7Z3	OTTHUMG00000171020	ENST00000354366.3:c.1853A>T	chr14.hg19:g.90756941T>A	ENSP00000346335:p.Asp618Val	141.0	0.0		186.0	66.0	NM_017970	B4DH71|Q4G0A7|Q9NWH6	Missense_Mutation	SNP	ENST00000354366.3	hg19	CCDS9890.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.482300	0.84747	.	.	ENSG00000119720	ENST00000354366;ENST00000357904;ENST00000554464	T;T	0.33654	1.4;1.4	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	T	0.63780	0.2540	M	0.82056	2.57	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.68281	-0.5450	10	0.72032	D	0.01	-26.717	16.3322	0.83039	0.0:0.0:0.0:1.0	.	618	Q9H7Z3	CN102_HUMAN	V	618;387;197	ENSP00000346335:D618V;ENSP00000350579:D387V	ENSP00000346335:D618V	D	-	2	0	C14orf102	89826694	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	7.211000	0.77933	2.251000	0.74343	0.528000	0.53228	GAT	.	.		0.423	NRDE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411264.1	NM_017970		A	90756941	T	A	90756941	3	1	364	1	0	0	0	0	1	0	0	0	1737	1435	50	4	1661	4	C14orf102	14	90756941	Missense_Mutation	SNP	T	TCGA-ZP-A9CY-01A-11D-A382-10	30544177	90756941	16592599	60	50804										
DPP8	54878	hgsc.bcm.edu	37	chr15	65746732	65746732	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	atattggagtccttccacctGatcgtcaatttctatttgac	6	10	2	2			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr15:65746732G>A	ENST00000341861.5	-	17	3768	c.2188C>T	c.(2188-2190)Cag>Tag	p.Q730*	DPP8_ENST00000559233.1_Nonsense_Mutation_p.Q730*|DPP8_ENST00000358939.4_Intron|DPP8_ENST00000560048.2_5'UTR|DPP8_ENST00000321118.7_Nonsense_Mutation_p.Q681*|DPP8_ENST00000321147.6_Intron|DPP8_ENST00000300141.6_Nonsense_Mutation_p.Q714*|DPP8_ENST00000339244.5_Nonsense_Mutation_p.Q557*	NM_197960.2	NP_932064.1	Q6V1X1	DPP8_HUMAN	dipeptidyl-peptidase 8	730					immune response (GO:0006955)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(2)|endometrium(3)|large_intestine(11)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						CCTTCCACCTGATCGTCAATT	0.408																																					p.Q730X		Atlas-SNP	.											.	DPP8	78	.	0			c.C2188T						.						110	97	102					15																	65746732		2201	4299	6500	SO:0001587	stop_gained	54878	exon18			CCACCTGATCGTC	AF221634	CCDS10207.1, CCDS10208.1, CCDS10209.1, CCDS10210.1	15q22	2008-07-18	2006-01-12		ENSG00000074603	ENSG00000074603			16490	protein-coding gene	gene with protein product	"dipeptidyl peptidase VIII", "dipeptidyl peptidase IV-related protein-1", "prolyl dipeptidase DPP8"	606819	"dipeptidylpeptidase 8"			11012666	Standard	XM_005254500		Approved	DP8, DPRP1, MSTP141, FLJ14920, FLJ20283, MGC26191	uc002aox.3	Q6V1X1	OTTHUMG00000133150	ENST00000341861.5:c.2188C>T	chr15.hg19:g.65746732G>A	ENSP00000339208:p.Gln730*	95.0	0.0		103.0	32.0	NM_197960	Q7Z4C8|Q7Z4D3|Q7Z4E1|Q8IWG7|Q8NEM5|Q96JX1|Q9HBM2|Q9HBM3|Q9HBM4|Q9HBM5|Q9NXF4	Nonsense_Mutation	SNP	ENST00000341861.5	hg19	CCDS10207.1	.	.	.	.	.	.	.	.	.	.	G	35	5.448426	0.96205	.	.	ENSG00000074603	ENST00000341861;ENST00000300141;ENST00000321118;ENST00000339244	.	.	.	5.27	5.27	0.74061	.	0.000000	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-41.6308	18.9065	0.92464	0.0:0.0:1.0:0.0	.	.	.	.	X	730;714;681;557	.	ENSP00000300141:Q714X	Q	-	1	0	DPP8	63533785	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	9.869000	0.99810	2.436000	0.82500	0.655000	0.94253	CAG	.	.		0.408	DPP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256847.1	NM_017743		A	65746732	G	A	65746732	4	1	364	1	0	0	0	0	0	1	0	0	4734	1299	45	3	524	3	DPP8	15	65746732	Nonsense_Mutation	SNP	G	TCGA-ZP-A9CY-01A-11D-A382-10		65746732	36784660	61	50805										
LOXL1	4016	hgsc.bcm.edu	37	chr15	74235244	74235244	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	tatgtgcaagcatccacttaTgtgcagagagcccacctgta	9	11	0	1			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr15:74235244T>C	ENST00000261921.7	+	2	1478	c.1152T>C	c.(1150-1152)taT>taC	p.Y384Y		NM_005576.2	NP_005567.2	Q08397	LOXL1_HUMAN	lysyl oxidase-like 1	384	Lysyl-oxidase like.				extracellular matrix organization (GO:0030198)|oxidation-reduction process (GO:0055114)|protein deamination (GO:0018277)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	copper ion binding (GO:0005507)|oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor (GO:0016641)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10						CATCCACTTATGTGCAGAGAG	0.577																																					p.Y384Y		Atlas-SNP	.											.	LOXL1	25	.	0			c.T1152C						.						227	207	214					15																	74235244		2198	4297	6495	SO:0001819	synonymous_variant	4016	exon2			CACTTATGTGCAG	L21186	CCDS10253.1	15q24-q25	2008-07-18			ENSG00000129038	ENSG00000129038			6665	protein-coding gene	gene with protein product		153456				7689553	Standard	NM_005576		Approved	LOXL, LOL	uc002awc.1	Q08397	OTTHUMG00000137595	ENST00000261921.7:c.1152T>C	chr15.hg19:g.74235244T>C		67.0	0.0		98.0	33.0	NM_005576	Q6NUL3|Q96BW7	Silent	SNP	ENST00000261921.7	hg19	CCDS10253.1																																																																																			.	.		0.577	LOXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268995.2	NM_005576		C	74235244	T	C	74235244	2	2	364	1	0	0	0	0	0	0	0	1	8908	1471	51	2		2	LOXL1	15	74235244	Silent	SNP	T	TCGA-ZP-A9CY-01A-11D-A382-10	8488512	74235244	28296148	62	50806										
IL16	3603	hgsc.bcm.edu	37	chr15	81598333	81598333	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	ttctttccatcaacggcaagTctctcaaggggaccacgcac	8	14	4	0			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr15:81598333T>C	ENST00000302987.4	+	16	3505	c.3505T>C	c.(3505-3507)Tct>Cct	p.S1169P	IL16_ENST00000394660.2_Missense_Mutation_p.S1169P|RP11-761I4.4_ENST00000607019.1_RNA|IL16_ENST00000394652.2_Missense_Mutation_p.S468P			Q14005	IL16_HUMAN	interleukin 16	1169	Interaction with PPP1R12A, PPP1R12B and PPP1R12C.|PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						CAACGGCAAGTCTCTCAAGGG	0.552																																					p.S1169P		Atlas-SNP	.											.	IL16	254	.	0			c.T3505C						.						167	170	169					15																	81598333		2203	4300	6503	SO:0001583	missense	3603	exon17			GGCAAGTCTCTCA	U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"Interleukins and interleukin receptors"	5980	protein-coding gene	gene with protein product	"prointerleukin 16", "lymphocyte chemoattractant factor"	603035	"interleukin 16 (lymphocyte chemoattractant factor)"			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.3505T>C	chr15.hg19:g.81598333T>C	ENSP00000302935:p.Ser1169Pro	81.0	0.0		114.0	41.0	NM_001172128	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Missense_Mutation	SNP	ENST00000302987.4	hg19	CCDS42069.1	.	.	.	.	.	.	.	.	.	.	T	13.55	2.270556	0.40194	.	.	ENSG00000172349	ENST00000394660;ENST00000355368;ENST00000302987;ENST00000329842;ENST00000394653;ENST00000394652;ENST00000394656	T;T;T	0.27256	1.68;1.68;1.68	4.64	4.64	0.57946	PDZ/DHR/GLGF (4);	0.000000	0.46145	D	0.000312	T	0.47783	0.1464	M	0.64170	1.965	0.47037	D	0.999298	D;D;D;D;D;D	0.76494	0.998;0.998;0.999;0.998;0.996;0.979	D;D;D;D;D;D	0.87578	0.998;0.991;0.99;0.997;0.994;0.968	T	0.48681	-0.9014	10	0.59425	D	0.04	.	14.225	0.65853	0.0:0.0:0.0:1.0	.	1001;662;706;559;1169;1169	F8W7Z5;Q6ZTT5;B7Z8M3;B3KY62;Q14005;Q14005-2	.;.;.;.;IL16_HUMAN;.	P	1169;1001;1169;706;559;468;468	ENSP00000378155:S1169P;ENSP00000302935:S1169P;ENSP00000378147:S468P	ENSP00000302935:S1169P	S	+	1	0	IL16	79385388	1.000000	0.71417	0.995000	0.50966	0.009000	0.06853	2.603000	0.46266	1.933000	0.56026	0.533000	0.62120	TCT	.	.		0.552	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217		C	81598333	T	C	81598333	3	2	364	1	0	0	0	0	1	0	0	0	7642	1667	58	2	3567	2	IL16	15	81598333	Missense_Mutation	SNP	T	TCGA-ZP-A9CY-01A-11D-A382-10	7363089	81598333	20933059	63	50807										
GRIN2A	2903	hgsc.bcm.edu	37	chr16	9892293	9892293	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	agccttgtaattcaagactgCggcatcgtagatgaaagcgt	11	8	1	3			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr16:9892293C>T	ENST00000396573.2	-	12	2506	c.2197G>A	c.(2197-2199)Gca>Aca	p.A733T	GRIN2A_ENST00000404927.2_Missense_Mutation_p.A733T|GRIN2A_ENST00000330684.3_Missense_Mutation_p.A733T|GRIN2A_ENST00000535259.1_Missense_Mutation_p.A576T|GRIN2A_ENST00000396575.2_Missense_Mutation_p.A733T|GRIN2A_ENST00000562109.1_Missense_Mutation_p.A733T	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	733					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	TTCAAGACTGCGGCATCGTAG	0.562																																					p.A733T		Atlas-SNP	.											.	GRIN2A	366	.	0			c.G2197A						.						92	75	80					16																	9892293		2197	4300	6497	SO:0001583	missense	2903	exon12			AGACTGCGGCATC		CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.2197G>A	chr16.hg19:g.9892293C>T	ENSP00000379818:p.Ala733Thr	84.0	0.0		131.0	26.0	NM_000833	O00669|Q17RZ6	Missense_Mutation	SNP	ENST00000396573.2	hg19	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	C	17.91	3.504573	0.64410	.	.	ENSG00000183454	ENST00000396573;ENST00000404927;ENST00000535259;ENST00000330684;ENST00000396575	T;T;T;T;T	0.27104	1.69;1.69;1.69;1.69;1.69	5.18	5.18	0.71444	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.104112	0.64402	D	0.000004	T	0.39937	0.1097	L	0.31294	0.92	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	P;D;D	0.87578	0.9;0.967;0.998	T	0.10064	-1.0646	9	.	.	.	.	17.6555	0.88176	0.0:1.0:0.0:0.0	.	576;733;733	F5GZ52;Q17RZ6;Q12879	.;.;NMDE1_HUMAN	T	733;733;576;733;733	ENSP00000379818:A733T;ENSP00000385872:A733T;ENSP00000441572:A576T;ENSP00000332549:A733T;ENSP00000379820:A733T	.	A	-	1	0	GRIN2A	9799794	1.000000	0.71417	0.079000	0.20413	0.019000	0.09904	7.681000	0.84073	2.412000	0.81896	0.557000	0.71058	GCA	.	.		0.562	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			T	9892293	C	T	9892293	3	4	364	1	0	0	0	0	1	0	0	0	6788	768	27	1	2209	1	GRIN2A	16	9892293	Missense_Mutation	SNP	C	TCGA-ZP-A9CY-01A-11D-A382-10		9892293	80462460	64	50808										
SPN	6693	hgsc.bcm.edu	37	chr16	29675057	29675057	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	tgtttgcctggaaatggccaCgcttctccttctccttgggg	11	12	2	0			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr16:29675057C>T	ENST00000360121.3	+	2	100	c.8C>T	c.(7-9)aCg>aTg	p.T3M	SPN_ENST00000395389.2_Missense_Mutation_p.T3M	NM_001030288.2|NM_003123.4	NP_001025459.1|NP_003114.1	O75398	DEAF1_HUMAN	sialophorin	0	Ala-rich.				anatomical structure morphogenesis (GO:0009653)|embryonic skeletal system development (GO:0048706)|germ cell development (GO:0007281)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|skin(2)|stomach(1)	15						GAAATGGCCACGCTTCTCCTT	0.632																																					p.T3M		Atlas-SNP	.											SPN,NS,carcinoma,0,1	SPN	44	.	0			c.C8T						.						118	129	125					16																	29675057		2197	4300	6497	SO:0001583	missense	6693	exon2			TGGCCACGCTTCT	J04536	CCDS10650.1	16p11.2	2008-07-31	2008-07-31		ENSG00000197471	ENSG00000197471		"CD molecules"	11249	protein-coding gene	gene with protein product	"leukosialin"	182160	"sialophorin (gpL115, leukosialin, CD43)"			2784859, 2521952	Standard	NM_001030288		Approved	LSN, CD43, GPL115	uc002dtm.4	P16150	OTTHUMG00000097765	ENST00000360121.3:c.8C>T	chr16.hg19:g.29675057C>T	ENSP00000353238:p.Thr3Met	62.0	0.0		67.0	23.0	NM_001030288	A8K1F8|A8K5R8|C7T5V5|O15152|O75399|O75510|O75511|O75512|O75513|Q9UET1	Missense_Mutation	SNP	ENST00000360121.3	hg19	CCDS10650.1	.	.	.	.	.	.	.	.	.	.	.	9.054	0.992699	0.18966	.	.	ENSG00000197471	ENST00000395389;ENST00000436527;ENST00000360121	T;T;T	0.31769	1.48;1.48;1.48	4.51	1.1	0.20463	.	2.276340	0.02812	N	0.124479	T	0.17874	0.0429	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.22208	-1.0223	10	0.51188	T	0.08	1.0E-4	5.7104	0.17931	0.0:0.3389:0.0:0.6611	.	3	P16150	LEUK_HUMAN	M	3	ENSP00000378787:T3M;ENSP00000412907:T3M;ENSP00000353238:T3M	ENSP00000353238:T3M	T	+	2	0	SPN	29582558	0.001000	0.12720	0.096000	0.21009	0.007000	0.05969	0.333000	0.19768	0.335000	0.23614	-0.340000	0.08031	ACG	.	.		0.632	SPN-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215001.2			T	29675057	C	T	29675057	3	4	364	1	0	0	0	0	1	0	0	0	15088	536	19	1	10	1	SPN	16	29675057	Missense_Mutation	SNP	C	TCGA-ZP-A9CY-01A-11D-A382-10	19782764	29675057	60679696	65	50809										
MTSS1L	92154	hgsc.bcm.edu	37	chr16	70698645	70698645	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	catggccaggtcactggcggCgggggacacctcctcaccgt	14	15	2	0			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr16:70698645C>A	ENST00000338779.6	-	14	1601	c.1327G>T	c.(1327-1329)Gcc>Tcc	p.A443S	FLJ00418_ENST00000597002.1_5'UTR	NM_138383.2	NP_612392.1	Q765P7	MTSSL_HUMAN	metastasis suppressor 1-like	443					filopodium assembly (GO:0046847)|signal transduction (GO:0007165)					breast(1)|central_nervous_system(2)|endometrium(1)|liver(1)|lung(1)|skin(1)	7						TCACTGGCGGCGGGGGACACC	0.672																																					p.A443S		Atlas-SNP	.											.	MTSS1L	22	.	0			c.G1327T						.						28	26	26					16																	70698645		2198	4298	6496	SO:0001583	missense	92154	exon14			TGGCGGCGGGGGA		CCDS32476.1	16q22.1	2008-12-16				ENSG00000132613			25094	protein-coding gene	gene with protein product	"actin-bundling protein with BAIAP2 homology"					12477932	Standard	XM_006721335		Approved	ABBA-1, LOC92154	uc002ezj.3	Q765P7		ENST00000338779.6:c.1327G>T	chr16.hg19:g.70698645C>A	ENSP00000341171:p.Ala443Ser	105.0	0.0		108.0	19.0	NM_138383	A6NJI7|Q9BUA8	Missense_Mutation	SNP	ENST00000338779.6	hg19	CCDS32476.1	.	.	.	.	.	.	.	.	.	.	C	13.35	2.212109	0.39102	.	.	ENSG00000132613	ENST00000338779	T	0.36340	1.26	4.89	3.94	0.45596	.	0.245478	0.40469	N	0.001085	T	0.36110	0.0955	M	0.63428	1.95	0.40467	D	0.980309	P	0.39940	0.696	B	0.41917	0.37	T	0.14952	-1.0454	10	0.11794	T	0.64	-16.434	12.6675	0.56849	0.0:0.9182:0.0:0.0818	.	443	Q765P7	MTSSL_HUMAN	S	443	ENSP00000341171:A443S	ENSP00000341171:A443S	A	-	1	0	MTSS1L	69256146	1.000000	0.71417	0.090000	0.20809	0.117000	0.20001	6.039000	0.70972	1.044000	0.40200	0.462000	0.41574	GCC	.	.		0.672	MTSS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434927.3	NM_138383		A	70698645	C	A	70698645	3	1	364	1	0	0	0	0	1	0	0	0	9972	768	27	1	924	1	MTSS1L	16	70698645	Missense_Mutation	SNP	C	TCGA-ZP-A9CY-01A-11D-A382-10	41023588	70698645	19656108	66	50810										
OR1E2	8388	hgsc.bcm.edu	37	chr17	3336671	3336671	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	gtggtcagcacccaggacagCgccaccacggagagacagag	14	13	1	2			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr17:3336671C>T	ENST00000248384.1	-	1	464	c.465G>A	c.(463-465)gcG>gcA	p.A155A		NM_003554.1	NP_003545.1	P47887	OR1E2_HUMAN	olfactory receptor, family 1, subfamily E, member 2	155					sensory perception of chemical stimulus (GO:0007606)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)|receptor activity (GO:0004872)			endometrium(3)|large_intestine(3)|lung(3)	9						CCCAGGACAGCGCCACCACGG	0.547											OREG0006785	type=TRANSCRIPTION FACTOR BINDING SITE|Gene=OR1E2|TFbs=REST|Dataset=NRSF/REST ChIPSeq sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.A155A		Atlas-SNP	.											.	OR1E2	25	.	0			c.G465A						.						81	72	75					17																	3336671		2203	4300	6503	SO:0001819	synonymous_variant	8388	exon1			GGACAGCGCCACC	U04686	CCDS11026.1	17p13.3	2012-08-09			ENSG00000127780	ENSG00000127780		"GPCR / Class A : Olfactory receptors"	8190	protein-coding gene	gene with protein product				OR1E4		8004088, 9500546	Standard	NM_003554		Approved	OR17-93, OR17-135	uc010vre.2	P47887	OTTHUMG00000090651	ENST00000248384.1:c.465G>A	chr17.hg19:g.3336671C>T		164.0	0.0	610	207.0	31.0	NM_003554	O43877|O95632|Q0VAD5|Q0VAD6|Q9UL13	Silent	SNP	ENST00000248384.1	hg19	CCDS11026.1																																																																																			.	.		0.547	OR1E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207311.1			T	3336671	C	T	3336671	2	4	364	1	0	0	0	0	0	0	0	1	10964	755	27	1		1	OR1E2	17	3336671	Silent	SNP	C	TCGA-ZP-A9CY-01A-11D-A382-10		3336671	77858539	67	50811										
TBX4	9496	hgsc.bcm.edu	37	chr17	59557244	59557244	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	tgtgttttctccccacagatCacccagctgaaaattgagaa	7	11	2	3			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr17:59557244C>A	ENST00000240335.1	+	6	750	c.705C>A	c.(703-705)atC>atA	p.I235I	TBX4_ENST00000393853.4_Silent_p.I235I|TBX4_ENST00000589449.1_3'UTR	NM_018488.2	NP_060958.2	P57082	TBX4_HUMAN	T-box 4	235					angiogenesis (GO:0001525)|embryonic limb morphogenesis (GO:0030326)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(15)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						CCCCACAGATCACCCAGCTGA	0.517																																					p.I235I		Atlas-SNP	.											.	TBX4	69	.	0			c.C705A						.						104	96	99					17																	59557244		2203	4300	6503	SO:0001819	synonymous_variant	9496	exon6			ACAGATCACCCAG	AF188703	CCDS11629.1	17q21-q22	2005-10-11				ENSG00000121075		"T-boxes"	11603	protein-coding gene	gene with protein product		601719				10945475	Standard	NM_018488		Approved		uc002izi.3	P57082		ENST00000240335.1:c.705C>A	chr17.hg19:g.59557244C>A		108.0	0.0		170.0	19.0	NM_018488	A5PKU7|B2RMT1|B7ZLV3	Silent	SNP	ENST00000240335.1	hg19	CCDS11629.1																																																																																			.	.		0.517	TBX4-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449649.1	NM_018488		A	59557244	C	A	59557244	2	1	364	1	0	0	0	0	0	0	0	1	15675	816	29	3		3	TBX4	17	59557244	Silent	SNP	C	TCGA-ZP-A9CY-01A-11D-A382-10	56220573	59557244	21637966	68	50812										
SERPINB8	5271	hgsc.bcm.edu	37	chr18	61654510	61654510	+	Nonstop_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	gtggcaggttctcttctccgTaaagaggagcaattgctgta	12	8	2	1			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr18:61654510T>C	ENST00000397985.2	+	7	1379	c.1123T>C	c.(1123-1125)Taa>Caa	p.*375Q	SERPINB8_ENST00000542677.1_Nonstop_Mutation_p.*193Q|SERPINB8_ENST00000493661.1_Intron|SERPINB8_ENST00000353706.2_Nonstop_Mutation_p.*375Q	NM_001276490.1	NP_001263419.1	P50452	SPB8_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 8	0					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|kidney(1)|large_intestine(4)|lung(9)|skin(1)	17		Esophageal squamous(42;0.129)				CTCTTCTCCGTAAAGAGGAGC	0.458																																					p.X375Q		Atlas-SNP	.											.	SERPINB8	42	.	0			c.T1123C						.						78	80	79					18																	61654510		2203	4300	6503	SO:0001578	stop_lost	5271	exon7			TCTCCGTAAAGAG	L40377	CCDS11991.1, CCDS42442.1, CCDS62460.1	18q22.1	2014-02-18	2005-08-18		ENSG00000166401	ENSG00000166401		"Serine (or cysteine) peptidase inhibitors"	8952	protein-coding gene	gene with protein product	"cytoplasmic antiproteinase 2"	601697	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 8"	PI8		8530382, 9268635, 24172014	Standard	NM_198833		Approved	CAP2	uc002lju.3	P50452	OTTHUMG00000060596	ENST00000397985.2:c.1123T>C	chr18.hg19:g.61654510T>C	ENSP00000381072:p.*375Glnext*19	58.0	0.0		83.0	4.0	NM_198833	B4DTW2|Q7Z2V6|Q8N178	Missense_Mutation	SNP	ENST00000397985.2	hg19	CCDS11991.1	.	.	.	.	.	.	.	.	.	.	T	11.69	1.714724	0.30413	.	.	ENSG00000166401	ENST00000397985;ENST00000353706;ENST00000542677	.	.	.	5.25	5.25	0.73442	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5025	0.67732	0.0:0.0:0.0:1.0	.	.	.	.	Q	375;375;193	.	.	X	+	1	0	SERPINB8	59805490	0.003000	0.15002	0.003000	0.11579	0.042000	0.13812	1.386000	0.34419	2.200000	0.70718	0.460000	0.39030	TAA	.	.		0.458	SERPINB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134014.1	NM_001031848		C	61654510	T	C	61654510	4	2	364	1	0	0	0	0	0	0	0	0	14122	1651	57	2	1158	2	SERPINB8	18	61654510	Nonstop_Mutation	SNP	T	TCGA-ZP-A9CY-01A-11D-A382-10		61654510	16422738	69	50813										
AP1M1	8907	hgsc.bcm.edu	37	chr19	16314322	16314322	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	ggacatgtcagaggtggagcActtcatgcccatcctgatgg	13	10	2	2			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr19:16314322A>G	ENST00000291439.3	+	2	544	c.95A>G	c.(94-96)cAc>cGc	p.H32R	AP1M1_ENST00000429941.2_Missense_Mutation_p.H32R|AP1M1_ENST00000541844.1_Intron|AP1M1_ENST00000444449.2_Missense_Mutation_p.H32R|AP1M1_ENST00000590756.1_Intron	NM_032493.3	NP_115882.1	Q9BXS5	AP1M1_HUMAN	adaptor-related protein complex 1, mu 1 subunit	32					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|endosome to melanosome transport (GO:0035646)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|trans-Golgi network membrane (GO:0032588)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|ovary(3)|prostate(2)	21						GAGGTGGAGCACTTCATGCCC	0.562																																					p.H32R		Atlas-SNP	.											.	AP1M1	48	.	0			c.A95G						.						102	86	91					19																	16314322		2203	4300	6503	SO:0001583	missense	8907	exon2			TGGAGCACTTCAT		CCDS12342.1, CCDS46008.1	19p13.12	2008-05-23							13667	protein-coding gene	gene with protein product		603535				9653655, 17988225	Standard	NM_032493		Approved	AP47, CLAPM2	uc002ndv.2	Q9BXS5		ENST00000291439.3:c.95A>G	chr19.hg19:g.16314322A>G	ENSP00000291439:p.His32Arg	74.0	0.0		97.0	29.0	NM_001130524	Q4TTY5	Missense_Mutation	SNP	ENST00000291439.3	hg19	CCDS12342.1	.	.	.	.	.	.	.	.	.	.	A	10.30	1.312322	0.23908	.	.	ENSG00000072958	ENST00000444449;ENST00000291439;ENST00000429941	T;T;T	0.61980	0.65;0.65;0.06	4.59	4.59	0.56863	Longin-like (1);AP complex, mu/sigma subunit (1);	0.000000	0.85682	D	0.000000	T	0.41511	0.1162	N	0.12443	0.215	0.80722	D	1	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.09377	0.0;0.004;0.004	T	0.26677	-1.0096	10	0.14656	T	0.56	-40.567	13.1508	0.59488	1.0:0.0:0.0:0.0	.	32;32;32	E7ENJ6;Q4TTY5;Q9BXS5	.;.;AP1M1_HUMAN	R	32	ENSP00000388996:H32R;ENSP00000291439:H32R;ENSP00000411498:H32R	ENSP00000291439:H32R	H	+	2	0	AP1M1	16175322	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.993000	0.76245	1.715000	0.51383	0.533000	0.62120	CAC	.	.		0.562	AP1M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460492.1	NM_032493		G	16314322	A	G	16314322	3	3	364	1	0	0	0	0	1	0	0	0	734	159	6	2	101	2	AP1M1	19	16314322	Missense_Mutation	SNP	A	TCGA-ZP-A9CY-01A-11D-A382-10		16314322	42814661	70	50814										
ZNF737	100129842	hgsc.bcm.edu	37	chr19	20728081	20728081	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	ttcacatttgtagggtttctCtccgctatgaattatcttat	6	8	3	1			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr19:20728081C>T	ENST00000427401.4	-	4	1022	c.928G>A	c.(928-930)Gag>Aag	p.E310K		NM_001159293.1	NP_001152765.1	O75373	ZN737_HUMAN	zinc finger protein 737	310					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|kidney(1)|lung(7)|ovary(1)|stomach(1)|urinary_tract(1)	13						TAGGGTTTCTCTCCGCTATGA	0.413																																					p.E310K		Atlas-SNP	.											.	ZNF737	50	.	0			c.G928A						.						40	39	39					19																	20728081		692	1591	2283	SO:0001583	missense	100129842	exon4			GTTTCTCTCCGCT	BC015765	CCDS54238.1	19p12	2013-01-08						"Zinc fingers, C2H2-type", "-"	32468	protein-coding gene	gene with protein product		603984					Standard	NM_001159293		Approved	ZNF102	uc002npa.3	O75373		ENST00000427401.4:c.928G>A	chr19.hg19:g.20728081C>T	ENSP00000395733:p.Glu310Lys	87.0	0.0		119.0	6.0	NM_001159293	C9JHM3	Missense_Mutation	SNP	ENST00000427401.4	hg19	CCDS54238.1	.	.	.	.	.	.	.	.	.	.	-	15.35	2.806492	0.50421	.	.	ENSG00000237440	ENST00000427401	T	0.24350	1.86	0.801	0.801	0.18679	.	.	.	.	.	T	0.32285	0.0824	L	0.53671	1.685	0.29096	N	0.881784	D	0.55605	0.972	P	0.53360	0.724	T	0.19516	-1.0303	9	0.59425	D	0.04	.	6.955	0.24565	0.0:1.0:0.0:0.0	.	310	C9JHM3	.	K	310	ENSP00000395733:E310K	ENSP00000395733:E310K	E	-	1	0	ZNF737	20519921	0.828000	0.29307	0.061000	0.19648	0.061000	0.15899	3.485000	0.53208	0.170000	0.19704	0.173000	0.16961	GAG	.	.		0.413	ZNF737-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447844.2	NM_145289		T	20728081	C	T	20728081	3	4	364	1	0	0	0	0	1	0	0	0	18141	922	32	3	686	3	ZNF737	19	20728081	Missense_Mutation	SNP	C	TCGA-ZP-A9CY-01A-11D-A382-10	4413759	20728081	38400902	71	50815										
EGLN2	112398	hgsc.bcm.edu	37	chr19	41307313	41307313	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	cagctatgtcatcaacgggcGcaccaaggtaaggctaggtg	13	10	2	0			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr19:41307313G>T	ENST00000593726.1	+	1	1864	c.836G>T	c.(835-837)cGc>cTc	p.R279L	RAB4B-EGLN2_ENST00000594136.1_3'UTR|EGLN2_ENST00000594140.1_5'Flank|EGLN2_ENST00000406058.2_Missense_Mutation_p.R279L|CTC-490E21.12_ENST00000601627.1_Missense_Mutation_p.A38S|EGLN2_ENST00000303961.4_Missense_Mutation_p.R279L			Q96KS0	EGLN2_HUMAN	egl-9 family hypoxia-inducible factor 2	279	Fe2OG dioxygenase. {ECO:0000255|PROSITE- ProRule:PRU00805}.				cell redox homeostasis (GO:0045454)|cellular response to hypoxia (GO:0071456)|intracellular estrogen receptor signaling pathway (GO:0030520)|peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)|positive regulation of protein catabolic process (GO:0045732)|regulation of cell growth (GO:0001558)|regulation of neuron apoptotic process (GO:0043523)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to hypoxia (GO:0001666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ferrous iron binding (GO:0008198)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|oxygen sensor activity (GO:0019826)|peptidyl-proline 4-dioxygenase activity (GO:0031545)			breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	10			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Vitamin C(DB00126)	ATCAACGGGCGCACCAAGGTA	0.612																																					p.R279L		Atlas-SNP	.											.	EGLN2	31	.	0			c.G836T						.						37	39	38					19																	41307313		2190	4280	6470	SO:0001583	missense	112398	exon2			ACGGGCGCACCAA	AJ310544	CCDS12567.1	19q13.2	2013-08-21	2013-08-21		ENSG00000269858	ENSG00000269858			14660	protein-coding gene	gene with protein product	"HIF prolyl hydroxylase 1"	606424	"EGL nine (C.elegans) homolog 2", "egl nine homolog 2 (C. elegans)"				Standard	NM_080732		Approved	PHD1, HIFPH1	uc002oph.3	Q96KS0		ENST00000593726.1:c.836G>T	chr19.hg19:g.41307313G>T	ENSP00000469686:p.Arg279Leu	36.0	0.0		60.0	15.0	NM_053046	A8K5S0|Q8WWY4|Q9BV14	Missense_Mutation	SNP	ENST00000593726.1	hg19	CCDS12567.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.834998	0.91117	.	.	ENSG00000171570	ENST00000303961;ENST00000406058	D;D	0.87650	-2.28;-2.28	4.25	4.25	0.50352	Oxoglutarate/iron-dependent oxygenase (1);Prolyl 4-hydroxylase, alpha subunit (1);	0.000000	0.85682	D	0.000000	D	0.95101	0.8413	H	0.94964	3.605	0.80722	D	1	D	0.76494	0.999	D	0.76575	0.988	D	0.96268	0.9196	10	0.66056	D	0.02	-15.4074	15.9613	0.79933	0.0:0.0:1.0:0.0	.	279	Q96KS0	EGLN2_HUMAN	L	279	ENSP00000307080:R279L;ENSP00000385253:R279L	ENSP00000307080:R279L	R	+	2	0	EGLN2	45999153	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.488000	0.97947	2.368000	0.80403	0.655000	0.94253	CGC	.	.		0.612	EGLN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463218.1			T	41307313	G	T	41307313	3	4	364	1	0	0	0	0	1	0	0	0	4971	1087	38	1	838	1	EGLN2	19	41307313	Missense_Mutation	SNP	G	TCGA-ZP-A9CY-01A-11D-A382-10	20579232	41307313	17821670	72	50816										
ZNF415	55786	hgsc.bcm.edu	37	chr19	53612770	53612770	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	gaagaaattatttggggtggTgaaactgaggaaccatggtt	14	3	0	3			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr19:53612770T>C	ENST00000500065.4	-	4	861	c.528A>G	c.(526-528)tcA>tcG	p.S176S	ZNF415_ENST00000448501.1_Silent_p.S224S|ZNF415_ENST00000597748.1_3'UTR|ZNF415_ENST00000455735.2_Silent_p.S224S|ZNF415_ENST00000440291.1_Silent_p.S163S|ZNF415_ENST00000243643.4_Silent_p.S176S|ZNF415_ENST00000421033.1_Silent_p.S188S|ZNF415_ENST00000597503.1_3'UTR|ZNF415_ENST00000594011.1_3'UTR|ZNF415_ENST00000595193.1_3'UTR|ZNF415_ENST00000601493.1_5'UTR	NM_001136038.2	NP_001129510.2	Q09FC8	ZN415_HUMAN	zinc finger protein 415	224					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				GBM - Glioblastoma multiforme(134;0.0191)		TTTGGGGTGGTGAAACTGAGG	0.378																																					p.S176S		Atlas-SNP	.											.	ZNF415	68	.	0			c.A528G						.						111	107	109					19																	53612770		2203	4300	6503	SO:0001819	synonymous_variant	55786	exon4			GGGTGGTGAAACT	AK002053	CCDS12860.1, CCDS54313.1	19q13.42	2014-03-18			ENSG00000170954	ENSG00000170954		"Zinc fingers, C2H2-type", "-"	20636	protein-coding gene	gene with protein product						14702039	Standard	NM_001136038		Approved		uc002qaw.3	Q09FC8	OTTHUMG00000182865	ENST00000500065.4:c.528A>G	chr19.hg19:g.53612770T>C		114.0	0.0		155.0	29.0	NM_018355	F5H287|Q09FC7|Q09FC9|Q09FD0|Q6NSZ2|Q6P3S0|Q9NUR2	Silent	SNP	ENST00000500065.4	hg19	CCDS54313.1																																																																																			.	.		0.378	ZNF415-025	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464043.1	NM_018355		C	53612770	T	C	53612770	2	2	364	1	0	0	0	0	0	0	0	1	17907	1683	59	2		2	ZNF415	19	53612770	Silent	SNP	T	TCGA-ZP-A9CY-01A-11D-A382-10	12305457	53612770	5516213	73	50817										
RRBP1	6238	hgsc.bcm.edu	37	chr20	17596112	17596112	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	tcctctgtttctgaagactcTagggggccggctgtgcggag	15	10	3	2			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr20:17596112T>C	ENST00000377813.1	-	23	4317	c.4014A>G	c.(4012-4014)ctA>ctG	p.L1338L	RRBP1_ENST00000470422.1_5'UTR|RRBP1_ENST00000246043.4_Silent_p.L1338L|RRBP1_ENST00000455029.2_Silent_p.L679L|RRBP1_ENST00000360807.4_Silent_p.L905L|RRBP1_ENST00000377807.2_Silent_p.L905L			Q9P2E9	RRBP1_HUMAN	ribosome binding protein 1	1338					osteoblast differentiation (GO:0001649)|protein transport (GO:0015031)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(6)	28						CTGAAGACTCTAGGGGGCCGG	0.627																																					p.L905L		Atlas-SNP	.											.	RRBP1	157	.	0			c.A2715G						.						45	47	47					20																	17596112		2203	4300	6503	SO:0001819	synonymous_variant	6238	exon23			AGACTCTAGGGGG	AB037819	CCDS13128.1	20p12	2012-12-07	2012-12-07		ENSG00000125844	ENSG00000125844			10448	protein-coding gene	gene with protein product		601418	"ribosome binding protein 1 (dog 180kD homolog)", "ribosome binding protein 1 homolog 180kDa (dog)"			8812507	Standard	NM_001042576		Approved	ES/130, hES	uc002wpw.1	Q9P2E9	OTTHUMG00000031945	ENST00000377813.1:c.4014A>G	chr20.hg19:g.17596112T>C		30.0	0.0		39.0	18.0	NM_004587	A2A2S6|A6NCN6|O75300|O75301|Q5W165|Q96SB2|Q9BWP1|Q9H476	Silent	SNP	ENST00000377813.1	hg19																																																																																				.	.		0.627	RRBP1-002	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000078125.1	NM_001042576		C	17596112	T	C	17596112	2	2	364	1	0	0	0	0	0	0	0	1	13693	1509	53	2		2	RRBP1	20	17596112	Silent	SNP	T	TCGA-ZP-A9CY-01A-11D-A382-10		17596112	45429408	74	50818										
C20orf135	140701	hgsc.bcm.edu	37	chr20	62493842	62493842	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	acccggggccggtgctgctgCtccgacgcacgcaggatgac	15	15	0	1			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr20:62493842C>T	ENST00000369916.3	+	1	1277	c.949C>T	c.(949-951)Ctc>Ttc	p.L317F	TPD52L2_ENST00000346249.4_5'Flank|TPD52L2_ENST00000351424.4_5'Flank|C20ORF135_ENST00000601296.1_5'Flank|TPD52L2_ENST00000358548.4_5'Flank|TPD52L2_ENST00000348257.5_5'Flank|TPD52L2_ENST00000369927.4_5'Flank|TPD52L2_ENST00000217121.5_5'Flank|TPD52L2_ENST00000352482.4_5'Flank	NM_080622.3	NP_542189.1	Q9H3Z7	ABHGB_HUMAN	abhydrolase domain containing 16B	317							hydrolase activity (GO:0016787)			endometrium(2)|kidney(1)|lung(3)	6						GGTGCTGCTGCTCCGACGCAC	0.692																																					p.L317F		Atlas-SNP	.											.	ABHD16B	22	.	0			c.C949T						.						10	11	11					20																	62493842		2180	4267	6447	SO:0001583	missense	140701	exon1			CTGCTGCTCCGAC		CCDS13539.1	20q13.33	2013-01-17	2010-12-09	2010-12-09	ENSG00000183260	ENSG00000183260		"Abhydrolase domain containing"	16128	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 135"	C20orf135			Standard	NM_080622		Approved	dJ591C20.1	uc002ygx.1	Q9H3Z7	OTTHUMG00000033010	ENST00000369916.3:c.949C>T	chr20.hg19:g.62493842C>T	ENSP00000358932:p.Leu317Phe	43.0	0.0		73.0	28.0	NM_080622		Missense_Mutation	SNP	ENST00000369916.3	hg19	CCDS13539.1	.	.	.	.	.	.	.	.	.	.	C	11.90	1.775764	0.31411	.	.	ENSG00000183260	ENST00000369916	T	0.38077	1.16	5.04	4.03	0.46877	.	0.215659	0.36268	N	0.002691	T	0.26521	0.0648	N	0.12182	0.205	0.39436	D	0.967165	B	0.33964	0.434	B	0.43018	0.405	T	0.15723	-1.0427	10	0.51188	T	0.08	-3.851	9.0601	0.36429	0.2775:0.7225:0.0:0.0	.	317	Q9H3Z7	ABHGB_HUMAN	F	317	ENSP00000358932:L317F	ENSP00000358932:L317F	L	+	1	0	ABHD16B	61964286	1.000000	0.71417	0.981000	0.43875	0.114000	0.19823	4.018000	0.57174	2.341000	0.79615	0.591000	0.81541	CTC	.	.		0.692	ABHD16B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080254.1			T	62493842	C	T	62493842	3	4	364	1	0	0	0	0	1	0	0	0	2090	797	28	3	951	3	C20orf135	20	62493842	Missense_Mutation	SNP	C	TCGA-ZP-A9CY-01A-11D-A382-10	44897730	62493842	531678	75	50819										
BPIL2	254240	hgsc.bcm.edu	37	chr22	32827371	32827371	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	gcagaccagtctttgtcccaAaataaccaggccaacactgg	8	13	1	1	rs370427363		TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr22:32827371A>G	ENST00000397452.1	-	12	1290	c.1180T>C	c.(1180-1182)Ttg>Ctg	p.L394L	BPIFC_ENST00000534972.1_Silent_p.L118L|BPIFC_ENST00000300399.3_Silent_p.L394L|BPIFC_ENST00000432451.2_Silent_p.L151L			Q8NFQ6	BPIFC_HUMAN	BPI fold containing family C	394						extracellular region (GO:0005576)	lipopolysaccharide binding (GO:0001530)|phospholipid binding (GO:0005543)										CTTTGTCCCAAAATAACCAGG	0.393																																					p.L394L		Atlas-SNP	.											.	.	.	.	0			c.T1180C						.	A		1,4405	2.1+/-5.4	0,1,2202	77	62	67		1180	1.6	0.8	22		67	0,8600		0,0,4300	no	coding-synonymous	BPIFC	NM_174932.2		0,1,6502	GG,GA,AA		0.0,0.0227,0.0077		394/508	32827371	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	254240	exon11			GTCCCAAAATAAC	AF465766	CCDS13906.1	22q12.3	2011-08-04	2011-08-01	2011-08-01	ENSG00000184459	ENSG00000184459		"BPI fold containing"	16503	protein-coding gene	gene with protein product		614109	"bactericidal/permeability-increasing protein-like 2"	BPIL2			Standard	NM_174932		Approved	dJ149A16.7	uc003amn.2	Q8NFQ6	OTTHUMG00000058273	ENST00000397452.1:c.1180T>C	chr22.hg19:g.32827371A>G		234.0	0.0		301.0	93.0	NM_174932	A2RRF1	Silent	SNP	ENST00000397452.1	hg19	CCDS13906.1																																																																																			.	.		0.393	BPIFC-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129029.2	NM_174932		G	32827371	A	G	32827371	2	3	364	1	0	0	0	0	0	0	0	1	1494	11	1	2		2	BPIL2	22	32827371	Silent	SNP	A	TCGA-ZP-A9CY-01A-11D-A382-10		32827371	18477195	76	50820										
ZC3H7B	23264	hgsc.bcm.edu	37	chr22	41751769	41751769	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	tctgtcctgcagctggaccaAggagcggcgggtccttctgg	15	12	2	0			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chr22:41751769A>G	ENST00000352645.4	+	19	2434	c.2177A>G	c.(2176-2178)aAg>aGg	p.K726R	ZC3H7B_ENST00000351589.4_Missense_Mutation_p.K726R	NM_017590.4	NP_060060.3	Q9UGR2	Z3H7B_HUMAN	zinc finger CCCH-type containing 7B	742					viral process (GO:0016032)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	38						AGCTGGACCAAGGAGCGGCGG	0.592																																					p.K726R		Atlas-SNP	.											.	ZC3H7B	82	.	0			c.A2177G						.						43	42	42					22																	41751769		2202	4300	6502	SO:0001583	missense	23264	exon19			GGACCAAGGAGCG		CCDS14013.1	22q13.2	2013-01-10		2005-08-09	ENSG00000100403	ENSG00000100403		"Zinc fingers, CCCH-type domain containing", "Tetratricopeptide (TTC) repeat domain containing"	30869	protein-coding gene	gene with protein product						10470851, 11230166	Standard	NM_017590		Approved	RoXaN, FLJ13787, DKFZp434K0920, KIAA1031	uc003azw.4	Q9UGR2	OTTHUMG00000150969	ENST00000352645.4:c.2177A>G	chr22.hg19:g.41751769A>G	ENSP00000345793:p.Lys726Arg	80.0	0.0		116.0	44.0	NM_017590	A7YY88|B2RCA4|Q5TFX9|Q8TBT9|Q9H8B6|Q9UGQ9|Q9UGR0|Q9UGR1|Q9UK03|Q9UPW9	Missense_Mutation	SNP	ENST00000352645.4	hg19	CCDS14013.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.034038	0.75504	.	.	ENSG00000100403	ENST00000352645;ENST00000351589	T;T	0.15017	2.46;2.46	5.14	5.14	0.70334	.	0.050485	0.85682	N	0.000000	T	0.22551	0.0544	L	0.54323	1.7	0.52099	D	0.999941	B	0.20459	0.045	B	0.31869	0.137	T	0.02893	-1.1097	10	0.38643	T	0.18	-12.5875	15.0062	0.71513	1.0:0.0:0.0:0.0	.	726	Q9UGR2-2	.	R	726	ENSP00000345793:K726R;ENSP00000263243:K726R	ENSP00000263243:K726R	K	+	2	0	ZC3H7B	40081715	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.930000	0.92872	1.948000	0.56530	0.454000	0.30748	AAG	.	.		0.592	ZC3H7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320696.1	NM_017590		G	41751769	A	G	41751769	3	3	364	1	0	0	0	0	1	0	0	0	17588	72	3	2	2247	2	ZC3H7B	22	41751769	Missense_Mutation	SNP	A	TCGA-ZP-A9CY-01A-11D-A382-10	8924398	41751769	9552797	77	50821										
CASK	8573	hgsc.bcm.edu	37	chrX	41379791	41379791	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	taattgtgagatcgaagtagTgtgcatatgttctctgtaag	11	4	1	1			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chrX:41379791T>A	ENST00000378163.1	-	27	3137	c.2663A>T	c.(2662-2664)cAc>cTc	p.H888L	CASK_ENST00000421587.2_Missense_Mutation_p.H859L|CASK_ENST00000442742.2_Missense_Mutation_p.H860L|CASK-AS1_ENST00000451126.1_RNA|CASK_ENST00000318588.9_Missense_Mutation_p.H883L|CASK_ENST00000378166.4_Missense_Mutation_p.H883L|CASK_ENST00000378158.1_Missense_Mutation_p.H871L|CASK_ENST00000361962.4_Missense_Mutation_p.H871L			O14936	CSKP_HUMAN	calcium/calmodulin-dependent serine protein kinase (MAGUK family)	888	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				calcium ion import (GO:0070509)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of wound healing (GO:0061045)|nucleotide phosphorylation (GO:0046939)|positive regulation of calcium ion import (GO:0090280)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	actin cytoskeleton (GO:0015629)|basement membrane (GO:0005604)|basolateral plasma membrane (GO:0016323)|cell-cell junction (GO:0005911)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nuclear lamina (GO:0005652)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	ATP binding (GO:0005524)|guanylate kinase activity (GO:0004385)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(5)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|ovary(3)|prostate(1)|stomach(1)	32						ATCGAAGTAGTGTGCATATGT	0.473																																					p.H883L	NSCLC(42;104 1086 3090 27189 35040)	Atlas-SNP	.											.	CASK	93	.	0			c.A2648T						.						157	127	137					X																	41379791		2203	4300	6503	SO:0001583	missense	8573	exon27			AAGTAGTGTGCAT	AF035582	CCDS14257.1, CCDS48094.1, CCDS48095.1	Xp11.4	2010-02-09			ENSG00000147044	ENSG00000147044			1497	protein-coding gene	gene with protein product		300172	"trinucleotide repeat containing 8"	TNRC8		9722958	Standard	NM_003688		Approved	LIN2, CAGH39, FGS4	uc004dfl.4	O14936	OTTHUMG00000021378	ENST00000378163.1:c.2663A>T	chrX.hg19:g.41379791T>A	ENSP00000367405:p.His888Leu	50.0	0.0		87.0	36.0	NM_003688	A6NES1|B7ZKY0|O43215|Q17RI4|Q59HA0|Q5VT16|Q5VT17|Q5VT18|Q5VT19|Q66T42|Q9BYH6|Q9NYB2|Q9NYB3	Missense_Mutation	SNP	ENST00000378163.1	hg19		.	.	.	.	.	.	.	.	.	.	T	16.59	3.165180	0.57476	.	.	ENSG00000147044	ENST00000421587;ENST00000318588;ENST00000361962;ENST00000378163;ENST00000378179;ENST00000378168;ENST00000378158;ENST00000378166;ENST00000442742	T;T;T;T;T;T;T;T;T	0.18810	2.19;2.19;2.19;2.19;2.19;2.19;2.19;2.19;2.19	5.52	5.52	0.82312	Guanylate kinase/L-type calcium channel (1);Guanylate kinase (2);	0.000000	0.64402	D	0.000012	T	0.53498	0.1800	M	0.88450	2.955	0.80722	D	1	D;P;D;D;D	0.89917	1.0;0.812;0.999;1.0;0.999	D;P;D;D;D	0.91635	0.997;0.642;0.982;0.999;0.99	T	0.63301	-0.6668	10	0.87932	D	0	.	14.885	0.70560	0.0:0.0:0.0:1.0	.	859;860;883;888;480	O14936-3;O14936-4;O14936-2;O14936;Q5JS72	.;.;.;CSKP_HUMAN;.	L	859;883;871;888;480;343;871;883;860	ENSP00000400526:H859L;ENSP00000322727:H883L;ENSP00000354641:H871L;ENSP00000367405:H888L;ENSP00000367421:H480L;ENSP00000367410:H343L;ENSP00000367400:H871L;ENSP00000367408:H883L;ENSP00000398007:H860L	ENSP00000322727:H883L	H	-	2	0	CASK	41264735	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.655000	0.83696	1.965000	0.57142	0.486000	0.48141	CAC	.	.		0.473	CASK-007	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000056285.1	NM_003688		A	41379791	T	A	41379791	3	1	364	1	0	0	0	0	1	0	0	0	2667	1696	59	4	121	4	CASK	23	41379791	Missense_Mutation	SNP	T	TCGA-ZP-A9CY-01A-11D-A382-10		41379791	113890769	78	50822										
RIBC1	158787	hgsc.bcm.edu	37	chrX	53455601	53455616	+	Intron	DEL	AGAGACCTGAGGCCTA	AGAGACCTGAGGCCTA	-													0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	cagcccggccctccagactcAgagacctgaggcctagtggg							TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	AGAGACCTGAGGCCTA	AGAGACCTGAGGCCTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chrX:53455601_53455616delAGAGACCTGAGGCCTA	ENST00000375327.3	+	5	697				RIBC1_ENST00000457095.1_Stop_Codon_Del|RIBC1_ENST00000414955.2_Intron|RIBC1_ENST00000490702.1_Intron	NM_001031745.2	NP_001026915.1	Q8N443	RIBC1_HUMAN	RIB43A domain with coiled-coils 1											lung(2)	2						CTCCAGACTCAGAGACCTGAGGCCTAGTGGGGATCT	0.537																																					p.190_193del		Atlas-INDEL	.											.	RIBC1	20	.	0			c.569_817del						.																																			SO:0001627	intron_variant	158787	exon5			.	AK057345	CCDS14353.1, CCDS35299.1, CCDS59168.1	Xp11.23	2006-04-12			ENSG00000158423	ENSG00000158423			26537	protein-coding gene	gene with protein product							Standard	NM_144968		Approved	FLJ32783	uc004dsk.4	Q8N443	OTTHUMG00000021615	ENST00000375327.3:c.544+26AGAGACCTGAGGCCTA>-	chrX.hg19:g.53455601_53455616delAGAGACCTGAGGCCTA		278.0	0.0		350.0	80.0	NM_144968	B4E297|E9PDU2|Q5H931|Q96A80	Frame_Shift_Del	DEL	ENST00000375327.3	hg19	CCDS35299.1																																																																																			.	.		0.537	RIBC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056762.1	NM_144968		-	53455616	AGAGACCTGAGGCCTA	-	53455601	6	5	364	0	1	1	0	1	0	0	0	0	13367	175	7	0		0	RIBC1	23	53455601	Intron	DEL	AGAGACCTGAGGCCTA	TCGA-ZP-A9CY-01A-11D-A382-10	12075810	53455601	101814959	79	50823										
HUWE1	10075	hgsc.bcm.edu	37	chrX	53574709	53574709	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	gacaatggtggaaatagccgTggcagcaaccagggctggag	16	8	0	0			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chrX:53574709T>C	ENST00000342160.3	-	67	11018	c.10561A>G	c.(10561-10563)Acg>Gcg	p.T3521A	HUWE1_ENST00000262854.6_Missense_Mutation_p.T3521A|HUWE1_ENST00000474288.1_5'UTR			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	3521	Thr-rich.				base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						GAAATAGCCGTGGCAGCAACC	0.582																																					p.T3521A		Atlas-SNP	.											.	HUWE1	724	.	0			c.A10561G						.						93	71	79					X																	53574709		2203	4300	6503	SO:0001583	missense	10075	exon68			TAGCCGTGGCAGC	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"HECT, UBA and WWE domain containing 1"			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.10561A>G	chrX.hg19:g.53574709T>C	ENSP00000340648:p.Thr3521Ala	139.0	0.0		174.0	32.0	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	hg19	CCDS35301.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	8.369|8.369	0.834950|0.834950	0.16820|0.16820	.|.	.|.	ENSG00000086758|ENSG00000086758	ENST00000427052;ENST00000426907|ENST00000342160;ENST00000262854	.|T;T	.|0.34859	.|1.34;1.34	5.09|5.09	1.22|1.22	0.21188|0.21188	.|.	.|1.238120	.|0.05397	.|N	.|0.540001	T|T	0.11239|0.11239	0.0274|0.0274	N|N	0.01352|0.01352	-0.895|-0.895	0.29085|0.29085	N|N	0.882461|0.882461	.|B;B	.|0.06786	.|0.0;0.001	.|B;B	.|0.06405	.|0.0;0.002	T|T	0.35674|0.35674	-0.9779|-0.9779	5|10	.|0.06236	.|T	.|0.91	.|.	4.0809|4.0809	0.09925|0.09925	0.1583:0.1865:0.0:0.6552|0.1583:0.1865:0.0:0.6552	.|.	.|3521;3505	.|Q7Z6Z7;Q7Z6Z7-2	.|HUWE1_HUMAN;.	R|A	2554;358|3521	.|ENSP00000340648:T3521A;ENSP00000262854:T3521A	.|ENSP00000262854:T3521A	H|T	-|-	2|1	0|0	HUWE1|HUWE1	53591434|53591434	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.952000|0.952000	0.60782|0.60782	1.143000|1.143000	0.31553|0.31553	0.216000|0.216000	0.20781|0.20781	0.409000|0.409000	0.27619|0.27619	CAC|ACG	.	.		0.582	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		C	53574709	T	C	53574709	3	2	364	1	0	0	0	0	1	0	0	0	7470	1696	59	2	2631	2	HUWE1	23	53574709	Missense_Mutation	SNP	T	TCGA-ZP-A9CY-01A-11D-A382-10	119108	53574709	101695851	80	50824										
IRS4	8471	hgsc.bcm.edu	37	chrX	107978082	107978082	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	ggccacctcctgagccccggCcatttcctgagccccaattg	9	18	0	2			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chrX:107978082C>T	ENST00000372129.2	-	1	1569	c.1493G>A	c.(1492-1494)gGc>gAc	p.G498D	RP6-24A23.3_ENST00000608811.1_RNA|RP6-24A23.6_ENST00000563887.1_5'Flank|RP6-24A23.3_ENST00000436013.1_RNA	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	498					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						TGAGCCCCGGCCATTTCCTGA	0.582																																					p.G498D		Atlas-SNP	.											.	IRS4	253	.	0			c.G1493A						.						124	117	119					X																	107978082		2203	4300	6503	SO:0001583	missense	8471	exon1			CCCCGGCCATTTC	AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.1493G>A	chrX.hg19:g.107978082C>T	ENSP00000361202:p.Gly498Asp	121.0	0.0		151.0	58.0	NM_003604		Missense_Mutation	SNP	ENST00000372129.2	hg19	CCDS14544.1	.	.	.	.	.	.	.	.	.	.	C	11.88	1.769312	0.31320	.	.	ENSG00000133124	ENST00000372129	T	0.37752	1.18	3.93	3.93	0.45458	.	0.144833	0.45867	D	0.000328	T	0.24044	0.0582	L	0.32530	0.975	0.37325	D	0.909708	P	0.38473	0.633	B	0.32805	0.153	T	0.20405	-1.0276	10	0.42905	T	0.14	-14.2995	10.427	0.44385	0.0:1.0:0.0:0.0	.	498	O14654	IRS4_HUMAN	D	498	ENSP00000361202:G498D	ENSP00000361202:G498D	G	-	2	0	IRS4	107864738	1.000000	0.71417	1.000000	0.80357	0.836000	0.47400	2.468000	0.45102	2.219000	0.72066	0.596000	0.82720	GGC	.	.		0.582	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604		T	107978082	C	T	107978082	3	4	364	1	0	0	0	0	1	0	0	0	7851	739	26	3	2284	3	IRS4	23	107978082	Missense_Mutation	SNP	C	TCGA-ZP-A9CY-01A-11D-A382-10	54403373	107978082	47292478	81	50825										
GPR112	139378	hgsc.bcm.edu	37	chrX	135429239	135429239	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	tcctgtgacagctaaggctgAgaccacccttttctctacct	7	14	1	2			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chrX:135429239A>G	ENST00000394143.1	+	6	3665	c.3374A>G	c.(3373-3375)gAg>gGg	p.E1125G	GPR112_ENST00000287534.4_Missense_Mutation_p.E1062G|GPR112_ENST00000394141.1_Missense_Mutation_p.E920G|GPR112_ENST00000412101.1_Missense_Mutation_p.E920G|GPR112_ENST00000370652.1_Missense_Mutation_p.E1125G	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	1125					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					GCTAAGGCTGAGACCACCCTT	0.493																																					p.E1125G		Atlas-SNP	.											.	GPR112	459	.	0			c.A3374G						.						153	119	130					X																	135429239		2203	4300	6503	SO:0001583	missense	139378	exon6			AGGCTGAGACCAC	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"-", "GPCR / Class B : Orphans"	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.3374A>G	chrX.hg19:g.135429239A>G	ENSP00000377699:p.Glu1125Gly	144.0	0.0		181.0	52.0	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	hg19	CCDS35409.1	.	.	.	.	.	.	.	.	.	.	A	10.73	1.431287	0.25813	.	.	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.29397	1.6;1.6;1.57;1.71;1.57	2.7	1.38	0.22167	.	.	.	.	.	T	0.18215	0.0437	N	0.24115	0.695	0.09310	N	1	P;B;B	0.40834	0.73;0.187;0.118	B;B;B	0.38755	0.281;0.073;0.033	T	0.11397	-1.0589	9	0.54805	T	0.06	.	4.5943	0.12322	0.6987:0.0:0.0:0.3013	.	1062;920;1125	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	G	1125;1125;920;1062;920	ENSP00000377699:E1125G;ENSP00000359686:E1125G;ENSP00000416526:E920G;ENSP00000287534:E1062G;ENSP00000377697:E920G	ENSP00000287534:E1062G	E	+	2	0	GPR112	135256905	0.000000	0.05858	0.017000	0.16124	0.062000	0.15995	-0.050000	0.11904	0.109000	0.17891	0.356000	0.21956	GAG	.	.		0.493	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1			G	135429239	A	G	135429239	3	3	364	1	0	0	0	0	1	0	0	0	6637	304	11	2	3384	2	GPR112	23	135429239	Missense_Mutation	SNP	A	TCGA-ZP-A9CY-01A-11D-A382-10	27451157	135429239	19841321	82	50826										
DKC1	1736	hgsc.bcm.edu	37	chrX	153991251	153991251	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.036144578313253	3	1	0.927715500579822	0	1.14860014357502	0.192307692307692	0.751940625889747	0	gcagggtaacatggcggatgCggaaggtaagggctgcaggc	19	7	0	0			TCGA-ZP-A9CY-01A-11D-A382-10	TCGA-ZP-A9CY-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a74a213-3d11-481d-80af-c56a90e932ad	e224c0c8-8493-4ce1-855b-34fc11453c98	g.chrX:153991251C>T	ENST00000369550.5	+	1	221	c.11C>T	c.(10-12)gCg>gTg	p.A4V		NM_001142463.1|NM_001363.3	NP_001135935.1|NP_001354.1	O60832	DKC1_HUMAN	dyskeratosis congenita 1, dyskerin	4	Nucleolar localization.				cell proliferation (GO:0008283)|pseudouridine synthesis (GO:0001522)|RNA processing (GO:0006396)|rRNA processing (GO:0006364)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)|telomerase activity (GO:0003720)			breast(2)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|prostate(1)	15	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					ATGGCGGATGCGGAAGGTAAG	0.726									Congenital Dyskeratosis																												p.A4V		Atlas-SNP	.											.	DKC1	41	.	0			c.C11T						.						41	34	36					X																	153991251		2161	4222	6383	SO:0001583	missense	1736	exon1	Familial Cancer Database	Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita	CGGATGCGGAAGG	AJ224481	CCDS14761.1, CCDS76062.1	Xq28	2014-09-17			ENSG00000130826	ENSG00000130826			2890	protein-coding gene	gene with protein product		300126		DKC		9590285, 9888995	Standard	NM_001142463		Approved	XAP101, dyskerin, NAP57, NOLA4	uc004fmm.3	O60832	OTTHUMG00000024242	ENST00000369550.5:c.11C>T	chrX.hg19:g.153991251C>T	ENSP00000358563:p.Ala4Val	273.0	0.0		362.0	127.0	NM_001363	F5BSB3|O43845|Q96G67|Q9Y505	Missense_Mutation	SNP	ENST00000369550.5	hg19	CCDS14761.1	.	.	.	.	.	.	.	.	.	.	C	11.05	1.523512	0.27299	.	.	ENSG00000130826	ENST00000369550;ENST00000413910	D;D	0.97480	-4.31;-4.4	3.74	-1.84	0.07809	.	.	.	.	.	D	0.87908	0.6296	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.78521	-0.2172	9	0.20046	T	0.44	.	0.2288	0.00177	0.3336:0.2607:0.1617:0.2439	.	4;4	A8MUT5;O60832	.;DKC1_HUMAN	V	4	ENSP00000358563:A4V;ENSP00000400542:A4V	ENSP00000358563:A4V	A	+	2	0	DKC1	153644445	0.482000	0.25948	0.053000	0.19242	0.425000	0.31504	0.189000	0.17037	-0.594000	0.05836	-0.233000	0.12211	GCG	.	.		0.726	DKC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061180.5	NM_001363		T	153991251	C	T	153991251	3	4	364	1	0	0	0	0	1	0	0	0	4544	768	27	1	13	1	DKC1	23	153991251	Missense_Mutation	SNP	C	TCGA-ZP-A9CY-01A-11D-A382-10	18562012	153991251	1279309	83	50827										
AGTRAP	57085	hgsc.bcm.edu	37	chr1	11808647	11808647	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	catgtaccgggagcgcggggGtgagctcctggtccacactg	16	12	0	1	rs141868096		TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr1:11808647G>T	ENST00000314340.5	+	4	398	c.344G>T	c.(343-345)gGt>gTt	p.G115V	AGTRAP_ENST00000491346.1_Splice_Site|AGTRAP_ENST00000510878.1_Missense_Mutation_p.V80L|AGTRAP_ENST00000400895.2_Silent_p.G147G|AGTRAP_ENST00000376627.2_Silent_p.G159G|AGTRAP_ENST00000376629.4_Splice_Site|AGTRAP_ENST00000452018.2_Splice_Site|AGTRAP_ENST00000376637.3_Splice_Site	NM_020350.4	NP_065083.3	Q6RW13	ATRAP_HUMAN	angiotensin II receptor-associated protein	115	Interaction with AGTR1.				regulation of blood pressure (GO:0008217)|response to hypoxia (GO:0001666)	cell cortex (GO:0005938)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	angiotensin type II receptor activity (GO:0004945)		AGTRAP/BRAF(2)	endometrium(1)|lung(3)|prostate(1)	5	Ovarian(185;0.249)	Lung NSC(185;4.15e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.46e-06)|COAD - Colon adenocarcinoma(227;0.000256)|BRCA - Breast invasive adenocarcinoma(304;0.0003)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0649)		GAGCGCGGGGGTGAGCTCCTG	0.662																																					p.G115V		Atlas-SNP	.											.	AGTRAP	9	.	0			c.G344T						.						57	48	51					1																	11808647		2203	4300	6503	SO:0001583	missense	57085	exon4			GCGGGGGTGAGCT	AF165187	CCDS136.1, CCDS30585.1, CCDS30586.1, CCDS41248.1, CCDS44056.1	1p36.22	2008-02-05			ENSG00000177674	ENSG00000177674			13539	protein-coding gene	gene with protein product		608729				11733189	Standard	NM_001040194		Approved	ATRAP	uc001asv.3	Q6RW13	OTTHUMG00000002230	ENST00000314340.5:c.344G>T	chr1.hg19:g.11808647G>T	ENSP00000319713:p.Gly115Val	31.0	0.0		26.0	11.0	NM_020350	A8MVQ5|Q5SNV4|Q5SNV5|Q96AC0|Q96PL4|Q9NRW9	Missense_Mutation	SNP	ENST00000314340.5	hg19	CCDS136.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	18.33|18.33|18.33	3.601366|3.601366|3.601366	0.66445|0.66445|0.66445	.|.|.	.|.|.	ENSG00000177674|ENSG00000177674|ENSG00000177674	ENST00000376637;ENST00000376629;ENST00000452018|ENST00000314340|ENST00000510878	.|T|.	.|0.69685|.	.|-0.42|.	3.93|3.93|3.93	3.93|3.93|3.93	0.45458|0.45458|0.45458	.|.|.	.|0.000000|.	.|0.64402|.	.|U|.	.|0.000001|.	.|T|T	.|0.48554|0.48554	.|0.1506|0.1506	.|.|.	.|.|.	.|.|.	0.28240|0.28240|0.28240	N|N|N	0.925738|0.925738|0.925738	.|D|.	.|0.89917|.	.|1.0|.	.|D|.	.|0.97110|.	.|1.0|.	.|T|T	.|0.41324|0.41324	.|-0.9515|-0.9515	.|8|4	.|.|.	.|.|.	.|.|.	.|-2.2315|-2.2315	13.8422|13.8422|13.8422	0.63446|0.63446|0.63446	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.|.	.|115|.	.|Q6RW13|.	.|ATRAP_HUMAN|.	.|V|L	-1|115|80	.|ENSP00000319713:G115V|.	.|.|.	.|G|V	+|+|+	.|2|1	.|0|0	AGTRAP|AGTRAP|AGTRAP	11731234|11731234|11731234	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.898000|0.898000|0.898000	0.35279|0.35279|0.35279	0.891000|0.891000|0.891000	0.51852|0.51852|0.51852	8.330000|8.330000|8.330000	0.90019|0.90019|0.90019	2.208000|2.208000|2.208000	0.71279|0.71279|0.71279	0.462000|0.462000|0.462000	0.41574|0.41574|0.41574	.|GGT|GTG	.	G|1.000;A|0.000		0.662	AGTRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006335.1	NM_020350		T	11808647	G	T	11808647	3	4	365	1	0	0	0	0	1	0	0	0	403	1275	44	3	459	3	AGTRAP	1	11808647	Missense_Mutation	SNP	G	TCGA-ZP-A9CZ-01A-11D-A382-10		11808647	237441974	1	50828										
TMEM39B	55116	hgsc.bcm.edu	37	chr1	32566142	32566142	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	aacgtggctatcccctctgaCgtctcccacttccgcttcca	6	18	2	1	rs373923538		TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr1:32566142C>T	ENST00000336294.5	+	8	1361	c.1215C>T	c.(1213-1215)gaC>gaT	p.D405D	TMEM39B_ENST00000487305.1_3'UTR|TMEM39B_ENST00000427288.1_Silent_p.D290D|TMEM39B_ENST00000456834.2_3'UTR|TMEM39B_ENST00000373634.4_Silent_p.D206D	NM_018056.2	NP_060526.2	Q9GZU3	TM39B_HUMAN	transmembrane protein 39B	405						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|lung(5)|ovary(1)|prostate(2)	11		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				TCCCCTCTGACGTCTCCCACT	0.592																																					p.D405D		Atlas-SNP	.											.	TMEM39B	66	.	0			c.C1215T						.	C		0,4406		0,0,2203	80	69	72		1215	-10	0	1		72	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TMEM39B	NM_018056.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		405/493	32566142	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	55116	exon8			CTCTGACGTCTCC	AL136695	CCDS351.2	1p35.1	2008-02-05			ENSG00000121775	ENSG00000121775			25510	protein-coding gene	gene with protein product						12477932	Standard	NM_018056		Approved	FLJ10315	uc010ogv.2	Q9GZU3	OTTHUMG00000004020	ENST00000336294.5:c.1215C>T	chr1.hg19:g.32566142C>T		113.0	0.0		88.0	9.0	NM_018056	B4DKN8|B4DQE6|B4DTN8|D3DPP4|Q6IA44	Silent	SNP	ENST00000336294.5	hg19	CCDS351.2																																																																																			.	.		0.592	TMEM39B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011489.2	NM_018056		T	32566142	C	T	32566142	2	4	365	1	0	0	0	0	0	0	0	1	16177	535	19	1		1	TMEM39B	1	32566142	Silent	SNP	C	TCGA-ZP-A9CZ-01A-11D-A382-10	20757495	32566142	216684479	2	50829										
INADL	10207	hgsc.bcm.edu	37	chr1	62299331	62299331	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	tctttggtatttcaggttgaCcacaatatggatgtcaatac	8	7	3	1			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr1:62299331C>T	ENST00000371158.2	+	17	2100	c.1986C>T	c.(1984-1986)gaC>gaT	p.D662D	INADL_ENST00000316485.6_Silent_p.D662D	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	662					cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						TTCAGGTTGACCACAATATGG	0.363																																					p.D662D		Atlas-SNP	.											.	INADL	179	.	0			c.C1986T						.						110	104	106					1																	62299331		2203	4300	6503	SO:0001819	synonymous_variant	10207	exon17			GGTTGACCACAAT	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.1986C>T	chr1.hg19:g.62299331C>T		164.0	0.0		195.0	36.0	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Silent	SNP	ENST00000371158.2	hg19	CCDS617.2																																																																																			.	.		0.363	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		T	62299331	C	T	62299331	2	4	365	1	0	0	0	0	0	0	0	1	7740	506	18	3		3	INADL	1	62299331	Silent	SNP	C	TCGA-ZP-A9CZ-01A-11D-A382-10	29733189	62299331	186951290	3	50830										
ADCY10	55811	hgsc.bcm.edu	37	chr1	167825481	167825481	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	tgtcgttaggctgtactgcaCcaatgacaatgtaggtggtg	13	7	0	1			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr1:167825481C>T	ENST00000367851.4	-	17	2277	c.2093G>A	c.(2092-2094)gGt>gAt	p.G698D	ADCY10_ENST00000367848.1_Missense_Mutation_p.G606D|ADCY10_ENST00000545172.1_Missense_Mutation_p.G545D	NM_018417.4	NP_060887.2	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10 (soluble)	698					cAMP biosynthetic process (GO:0006171)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|spermatogenesis (GO:0007283)	apical part of cell (GO:0045177)|axon (GO:0030424)|basal part of cell (GO:0045178)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)			autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(26)|ovary(2)|prostate(4)|skin(6)|stomach(1)|urinary_tract(1)	63						CTGTACTGCACCAATGACAAT	0.458																																					p.G698D		Atlas-SNP	.											.	ADCY10	175	.	0			c.G2093A						.						309	259	276					1																	167825481		2203	4300	6503	SO:0001583	missense	55811	exon17			ACTGCACCAATGA	AF271058	CCDS1265.1, CCDS53426.1, CCDS72977.1	1q24	2013-02-04			ENSG00000143199	ENSG00000143199	4.6.1.1	"Adenylate cyclases"	21285	protein-coding gene	gene with protein product	"soluble adenylyl cyclase", "Hypercalciuria, absorptive, 2"	605205					Standard	XM_006711449		Approved	SAC, Sacy, SACI, HCA2, RP1-313L4.2	uc001ger.3	Q96PN6	OTTHUMG00000034573	ENST00000367851.4:c.2093G>A	chr1.hg19:g.167825481C>T	ENSP00000356825:p.Gly698Asp	188.0	0.0		278.0	13.0	NM_018417	B4DZF0|F5GWS5|O95558|Q5R329|Q5R330|Q8WXV4|Q9NNX0	Missense_Mutation	SNP	ENST00000367851.4	hg19	CCDS1265.1	.	.	.	.	.	.	.	.	.	.	C	13.07	2.126709	0.37533	.	.	ENSG00000143199	ENST00000545172;ENST00000367851;ENST00000367848	T;T;T	0.34275	1.37;1.38;1.38	5.16	5.16	0.70880	.	0.110120	0.41938	D	0.000798	T	0.45577	0.1349	M	0.68317	2.08	0.30578	N	0.762778	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.975;0.946	T	0.34675	-0.9819	9	0.21014	T	0.42	-17.3898	14.1528	0.65398	0.0:1.0:0.0:0.0	.	545;606;698	F5GWS5;Q96PN6-2;Q96PN6	.;.;ADCYA_HUMAN	D	545;698;606	ENSP00000441992:G545D;ENSP00000356825:G698D;ENSP00000356822:G606D	ENSP00000356822:G606D	G	-	2	0	ADCY10	166092105	0.023000	0.18921	0.070000	0.20053	0.003000	0.03518	1.668000	0.37481	2.421000	0.82119	0.563000	0.77884	GGT	.	.		0.458	ADCY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083663.1	NM_018417		T	167825481	C	T	167825481	3	4	365	1	0	0	0	0	1	0	0	0	293	507	18	3	2807	3	ADCY10	1	167825481	Missense_Mutation	SNP	C	TCGA-ZP-A9CZ-01A-11D-A382-10	105526150	167825481	81425140	4	50831										
ZNF648	127665	hgsc.bcm.edu	37	chr1	182026606	182026606	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	gagttccctgcggacgtgtcTacacttttgtgcgcacagag	12	11	1	1			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr1:182026606T>C	ENST00000339948.3	-	2	747	c.540A>G	c.(538-540)gtA>gtG	p.V180V		NM_001009992.1	NP_001009992.1	Q5T619	ZN648_HUMAN	zinc finger protein 648	180					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(7)|large_intestine(10)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	40						CGGACGTGTCTACACTTTTGT	0.582																																					p.V180V	NSCLC(71;908 1374 5429 20458 35642)	Atlas-SNP	.											.	ZNF648	111	.	0			c.A540G						.						65	68	67					1																	182026606		2203	4300	6503	SO:0001819	synonymous_variant	127665	exon2			CGTGTCTACACTT	AK128654	CCDS30952.1	1q25.3	2013-01-08			ENSG00000179930	ENSG00000179930		"Zinc fingers, C2H2-type"	18190	protein-coding gene	gene with protein product							Standard	NM_001009992		Approved	FLJ46813	uc001goz.3	Q5T619	OTTHUMG00000037302	ENST00000339948.3:c.540A>G	chr1.hg19:g.182026606T>C		73.0	0.0		83.0	25.0	NM_001009992	B2RP16	Silent	SNP	ENST00000339948.3	hg19	CCDS30952.1																																																																																			.	.		0.582	ZNF648-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090794.1	XM_060597		C	182026606	T	C	182026606	2	2	365	1	0	0	0	0	0	0	0	1	18078	1509	53	2		2	ZNF648	1	182026606	Silent	SNP	T	TCGA-ZP-A9CZ-01A-11D-A382-10	14201125	182026606	67224015	5	50832										
ALMS1	7840	hgsc.bcm.edu	37	chr2	73613036	73613037	+	Missense_Mutation	DNP	GA	GA	CT													0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	catggccgggcgagctggagGaggaggaggaggaggaggag					rs61156725|rs72319667|rs3074417	byFrequency	TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr2:73613036_73613037GA>CT	ENST00000264448.6	+	1	151_152	c.40_41GA>CT	c.(40-42)GAg>CTg	p.E14L	ALMS1_ENST00000409009.1_Missense_Mutation_p.E14L|ALMS1_ENST00000377715.1_Missense_Mutation_p.E14L	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	14	Glu-rich.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.E27_E28delEE(1)		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						CGAGCTggaggaggaggaggag	0.693																																					p.E14Q|p.E14V		Atlas-SNP	.											.	ALMS1	384	.	1	Deletion - In frame(1)	ovary(1)	c.G40C|c.A41T						.																																			SO:0001583	missense	7840	exon1			CTGGAGGAGGAGG|TGGAGGAGGAGGA	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	Exception_encountered	chr2.hg19:g.73613036_73613037delinsCT	ENSP00000264448:p.Glu14Leu	181.0|178.0	0.0		230.0|231.0	12.0|19.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1																																																																																			.	.		0.693	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		CT	73613037	GA	CT	73613036	3	2	365	1	0	0	0	0	1	0	0	0	535	1175	41	4	42	4	ALMS1	2	73613036	Missense_Mutation	DNP	GA	TCGA-ZP-A9CZ-01A-11D-A382-10		73613036	169586337	6	50833										
RGPD4	285190	hgsc.bcm.edu	37	chr2	108453116	108453116	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	tgaagctaaagaatatgatcTtgctaaaaagtaagtacaaa	7	4	1	3			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr2:108453116T>C	ENST00000408999.3	+	2	208	c.131T>C	c.(130-132)cTt>cCt	p.L44P	RGPD4_ENST00000354986.4_Missense_Mutation_p.L44P	NM_182588.2	NP_872394.2	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4	44					protein targeting to Golgi (GO:0000042)					breast(1)|endometrium(7)|kidney(4)|lung(23)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(3)	43						GAATATGATCTTGCTAAAAAG	0.249																																					p.L44P		Atlas-SNP	.											.	RGPD4	112	.	0			c.T131C						.																																			SO:0001583	missense	285190	exon2			ATGATCTTGCTAA	BX537861	CCDS46381.1	2q12.3	2013-01-10			ENSG00000196862	ENSG00000196862		"Tetratricopeptide (TTC) repeat domain containing"	32417	protein-coding gene	gene with protein product		612707				15710750, 15815621	Standard	NM_182588		Approved	RGP4, DKFZp686P0288	uc010ywk.2	Q7Z3J3	OTTHUMG00000153208	ENST00000408999.3:c.131T>C	chr2.hg19:g.108453116T>C	ENSP00000386810:p.Leu44Pro	381.0	1.0		383.0	103.0	NM_182588	B9A029	Missense_Mutation	SNP	ENST00000408999.3	hg19	CCDS46381.1	.	.	.	.	.	.	.	.	.	.	t	9.842	1.191238	0.21954	.	.	ENSG00000196862	ENST00000354986;ENST00000408999	T;T	0.37915	1.17;1.17	2.35	2.35	0.29111	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	.	.	.	.	T	0.49490	0.1560	L	0.53249	1.67	0.54753	D	0.999983	D	0.64830	0.994	D	0.79784	0.993	T	0.41233	-0.9520	9	0.40728	T	0.16	-21.0283	9.2374	0.37475	0.0:0.0:0.0:1.0	.	44	Q7Z3J3	RGPD4_HUMAN	P	44	ENSP00000347081:L44P;ENSP00000386810:L44P	ENSP00000347081:L44P	L	+	2	0	RGPD4	107819548	1.000000	0.71417	1.000000	0.80357	0.601000	0.36947	6.117000	0.71577	1.080000	0.41073	0.155000	0.16302	CTT	.	.		0.249	RGPD4-001	NOVEL	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330096.2	XM_496581		C	108453116	T	C	108453116	3	2	365	1	0	0	0	0	1	0	0	0	13303	1609	56	2	137	2	RGPD4	2	108453116	Missense_Mutation	SNP	T	TCGA-ZP-A9CZ-01A-11D-A382-10	34840080	108453116	134746257	7	50834										
PPIG	9360	hgsc.bcm.edu	37	chr2	170471112	170471112	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	taggcatcatgttgtttttgGacaagtaatctctggtcaag	10	6	3	0			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr2:170471112G>A	ENST00000260970.3	+	9	645	c.425G>A	c.(424-426)gGa>gAa	p.G142E	PPIG_ENST00000462903.1_Missense_Mutation_p.G142E|PPIG_ENST00000409714.3_Missense_Mutation_p.G127E|PPIG_ENST00000448752.2_Missense_Mutation_p.G142E	NM_004792.2	NP_004783.2	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G (cyclophilin G)	142	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				protein folding (GO:0006457)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(17)|ovary(2)|stomach(1)|urinary_tract(1)	43					L-Proline(DB00172)	GTTGTTTTTGGACAAGTAATC	0.318																																					p.G142E		Atlas-SNP	.											.	PPIG	100	.	0			c.G425A						.						98	102	101					2																	170471112		2203	4300	6503	SO:0001583	missense	9360	exon9			TTTTTGGACAAGT	X99717	CCDS2235.1	2q31.1	2010-07-23	2006-01-12		ENSG00000138398	ENSG00000138398	6.1.1.16		14650	protein-coding gene	gene with protein product	"SR-related CTD-associated factor 10"	606093	"peptidyl-prolyl isomerase G (cyclophilin G)"			8973360, 9153302	Standard	NM_004792		Approved	CARS-Cyp, SRCyp, SCAF10	uc002uez.3	Q13427	OTTHUMG00000132206	ENST00000260970.3:c.425G>A	chr2.hg19:g.170471112G>A	ENSP00000260970:p.Gly142Glu	420.0	1.0		403.0	132.0	NM_004792	D3DPC5|D3DPC6|O00706|Q53R40|Q53SN4|Q96DG9	Missense_Mutation	SNP	ENST00000260970.3	hg19	CCDS2235.1	.	.	.	.	.	.	.	.	.	.	G	18.91	3.723290	0.68959	.	.	ENSG00000138398	ENST00000260970;ENST00000530133;ENST00000433207;ENST00000409714;ENST00000462903;ENST00000448752;ENST00000414307	D;D;D;D;D;D	0.87256	-2.23;-2.23;-2.23;-2.23;-2.23;-2.23	5.37	5.37	0.77165	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (4);Cyclophilin-like (1);	0.000000	0.85682	D	0.000000	D	0.96898	0.8987	H	0.99555	4.625	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	D	0.98847	1.0757	10	0.87932	D	0	-11.2017	19.1154	0.93336	0.0:0.0:1.0:0.0	.	138;127;127;142;142	C9JM79;E9PG73;Q2NKQ6;Q13427-2;Q13427	.;.;.;.;PPIG_HUMAN	E	142;142;138;127;142;142;142	ENSP00000260970:G142E;ENSP00000408683:G138E;ENSP00000386245:G127E;ENSP00000435987:G142E;ENSP00000407083:G142E;ENSP00000402222:G142E	ENSP00000260970:G142E	G	+	2	0	PPIG	170179358	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	9.869000	0.99810	2.511000	0.84671	0.491000	0.48974	GGA	.	.		0.318	PPIG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255264.2			A	170471112	G	A	170471112	3	1	365	1	0	0	0	0	1	0	0	0	12336	1174	41	3	451	3	PPIG	2	170471112	Missense_Mutation	SNP	G	TCGA-ZP-A9CZ-01A-11D-A382-10	62017996	170471112	72728261	8	50835										
KIF1A	547	hgsc.bcm.edu	37	chr2	241700204	241700204	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	gcggcctctgggggcagcagGtcgggtggcagaggggagta	22	8	1	1			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr2:241700204G>T	ENST00000320389.7	-	24	2453	c.2295C>A	c.(2293-2295)gaC>gaA	p.D765E	KIF1A_ENST00000498729.2_Missense_Mutation_p.D774E	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A	765					anterograde axon cargo transport (GO:0008089)|ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			NS(1)|central_nervous_system(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(25)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	66		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		GGGGCAGCAGGTCGGGTGGCA	0.632																																					p.D774E		Atlas-SNP	.											.	KIF1A	152	.	0			c.C2322A						.						43	49	47					2																	241700204		1957	4127	6084	SO:0001583	missense	547	exon25			CAGCAGGTCGGGT	AF004425	CCDS46561.1, CCDS58757.1	2q37.2	2014-09-17	2004-01-09	2004-01-14	ENSG00000130294	ENSG00000130294		"Kinesins", "Pleckstrin homology (PH) domain containing"	888	protein-coding gene	gene with protein product		601255	"axonal transport of synaptic vesicles", "chromosome 2 open reading frame 20", "spastic paraplegia 30 (autosomal recessive)"	ATSV, C2orf20, SPG30		7539720, 10323250, 22258533	Standard	NM_001244008		Approved	UNC104	uc010fzk.3	Q12756	OTTHUMG00000151940	ENST00000320389.7:c.2295C>A	chr2.hg19:g.241700204G>T	ENSP00000322791:p.Asp765Glu	278.0	1.0		291.0	107.0	NM_001244008	B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	Missense_Mutation	SNP	ENST00000320389.7	hg19	CCDS46561.1	.	.	.	.	.	.	.	.	.	.	G	6.888	0.533288	0.13188	.	.	ENSG00000130294	ENST00000320389;ENST00000498729;ENST00000373308;ENST00000404283	T;T;T	0.74315	-0.83;-0.83;-0.83	4.94	1.64	0.23874	.	0.000000	0.85682	U	0.000000	T	0.52322	0.1727	N	0.17474	0.49	0.53688	D	0.999972	B;B;B	0.26195	0.002;0.144;0.033	B;B;B	0.29785	0.009;0.107;0.041	T	0.44574	-0.9319	10	0.02654	T	1	.	10.4463	0.44497	0.3256:0.0:0.6744:0.0	.	774;774;765	F5H045;Q12756-2;Q12756	.;.;KIF1A_HUMAN	E	765;774;774;774	ENSP00000322791:D765E;ENSP00000438388:D774E;ENSP00000384231:D774E	ENSP00000322791:D765E	D	-	3	2	KIF1A	241348877	1.000000	0.71417	0.992000	0.48379	0.968000	0.65278	1.501000	0.35693	0.510000	0.28216	-0.324000	0.08512	GAC	.	.		0.632	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3	NM_138483		T	241700204	G	T	241700204	3	4	365	1	0	0	0	0	1	0	0	0	8292	1252	44	3	2873	3	KIF1A	2	241700204	Missense_Mutation	SNP	G	TCGA-ZP-A9CZ-01A-11D-A382-10	71229092	241700204	1499169	9	50836										
TRPC3	7222	hgsc.bcm.edu	37	chr4	122833233	122833233	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	aaacttcataaaagggcttcGcagaattttccccagctgta	7	10	1	1			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr4:122833233G>A	ENST00000379645.3	-	5	1430	c.1357C>T	c.(1357-1359)Cga>Tga	p.R453*	TRPC3_ENST00000264811.5_Nonsense_Mutation_p.R380*|TRPC3_ENST00000513531.1_Nonsense_Mutation_p.R325*	NM_001130698.1	NP_001124170.1	Q13507	TRPC3_HUMAN	transient receptor potential cation channel, subfamily C, member 3	368					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|phototransduction (GO:0007602)|platelet activation (GO:0030168)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cardiac muscle hypertrophy in response to stress (GO:1903244)|response to ATP (GO:0033198)|response to calcium ion (GO:0051592)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(12)|lung(13)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						AAAGGGCTTCGCAGAATTTTC	0.413																																					p.R453X		Atlas-SNP	.											.	TRPC3	201	.	0			c.C1357T						.						53	62	59					4																	122833233		2203	4300	6503	SO:0001587	stop_gained	7222	exon5			GGCTTCGCAGAAT	Y13758	CCDS3725.1, CCDS47130.1	4q27	2011-12-14			ENSG00000138741	ENSG00000138741		"Voltage-gated ion channels / Transient receptor potential cation channels"	12335	protein-coding gene	gene with protein product		602345				8646775, 16382100	Standard	NM_003305		Approved		uc003ieg.2	Q13507	OTTHUMG00000133069	ENST00000379645.3:c.1357C>T	chr4.hg19:g.122833233G>A	ENSP00000368966:p.Arg453*	68.0	0.0		53.0	17.0	NM_001130698	A7VJS1|E9PCJ9|O00593|Q15660|Q52M35|Q5G1L5	Nonsense_Mutation	SNP	ENST00000379645.3	hg19	CCDS47130.1	.	.	.	.	.	.	.	.	.	.	G	42	9.596350	0.99214	.	.	ENSG00000138741	ENST00000264811;ENST00000379645;ENST00000513531	.	.	.	5.21	4.34	0.51931	.	0.097830	0.44285	D	0.000467	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-46.5027	14.8638	0.70399	0.0:0.0:0.8551:0.1449	.	.	.	.	X	380;453;325	.	ENSP00000264811:R380X	R	-	1	2	TRPC3	123052683	1.000000	0.71417	0.999000	0.59377	0.987000	0.75469	4.759000	0.62227	1.144000	0.42321	0.455000	0.32223	CGA	.	.		0.413	TRPC3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364252.1	NM_003305		A	122833233	G	A	122833233	4	1	365	1	0	0	0	0	0	1	0	0	16594	1095	38	1	1440	1	TRPC3	4	122833233	Nonsense_Mutation	SNP	G	TCGA-ZP-A9CZ-01A-11D-A382-10		122833233	68321043	10	50837										
CDH9	1007	hgsc.bcm.edu	37	chr5	26915756	26915756	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	accgactccagacatttcagGaacactggcagtgtataagt	9	10	1	1			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr5:26915756G>A	ENST00000231021.4	-	3	677	c.505C>T	c.(505-507)Cct>Tct	p.P169S		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	169	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						GACATTTCAGGAACACTGGCA	0.348																																					p.P169S	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											.	CDH9	305	.	0			c.C505T						.						73	73	73					5																	26915756		2203	4300	6503	SO:0001583	missense	1007	exon3			TTTCAGGAACACT	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"Cadherins / Major cadherins"	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.505C>T	chr5.hg19:g.26915756G>A	ENSP00000231021:p.Pro169Ser	97.0	0.0		160.0	75.0	NM_016279	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	hg19	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.162476	0.78226	.	.	ENSG00000113100	ENST00000231021	T	0.52983	0.64	4.77	4.77	0.60923	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.56790	0.2009	L	0.43701	1.375	0.58432	D	0.999999	D	0.57899	0.981	P	0.58820	0.846	T	0.54214	-0.8327	9	.	.	.	.	16.74	0.85456	0.0:0.0:1.0:0.0	.	169	Q9ULB4	CADH9_HUMAN	S	169	ENSP00000231021:P169S	.	P	-	1	0	CDH9	26951513	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.703000	0.98714	2.352000	0.79861	0.650000	0.86243	CCT	.	.		0.348	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		A	26915756	G	A	26915756	3	1	365	1	0	0	0	0	1	0	0	0	3119	1174	41	3	1904	3	CDH9	5	26915756	Missense_Mutation	SNP	G	TCGA-ZP-A9CZ-01A-11D-A382-10		26915756	153999504	11	50838										
ITGA2	3673	hgsc.bcm.edu	37	chr5	52370309	52370309	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	tttaaagagagaacaacaggTacaacttgcatttcatcctc	6	9	1	2			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr5:52370309T>C	ENST00000296585.5	+	21	2807		c.e21+2			NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)						axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular response to hormone stimulus (GO:0032870)|collagen-activated signaling pathway (GO:0038065)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|hepatocyte differentiation (GO:0070365)|hypotonic response (GO:0006971)|integrin-mediated signaling pathway (GO:0007229)|mammary gland development (GO:0030879)|mesodermal cell differentiation (GO:0048333)|organ morphogenesis (GO:0009887)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell projection organization (GO:0031346)|positive regulation of collagen binding (GO:0033343)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA binding (GO:0043388)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|response to amine (GO:0014075)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to muscle activity (GO:0014850)|response to organic cyclic compound (GO:0014070)|skin morphogenesis (GO:0043589)|substrate-dependent cell migration (GO:0006929)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	axon terminus (GO:0043679)|basal part of cell (GO:0045178)|cell outer membrane (GO:0009279)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin alpha2-beta1 complex (GO:0034666)|integrin complex (GO:0008305)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)			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)				GAACAACAGGTACAACTTGCA	0.438																																					.		Atlas-SNP	.											.	ITGA2	211	.	0			c.2664+2T>C						.						161	133	143					5																	52370309		2203	4300	6503	SO:0001630	splice_region_variant	3673	exon21			AACAGGTACAACT		CCDS3957.1	5q11.2	2010-03-23			ENSG00000164171	ENSG00000164171		"CD molecules", "Integrins"	6137	protein-coding gene	gene with protein product		192974		CD49B			Standard	NM_002203		Approved	CD49b	uc003joy.3	P17301	OTTHUMG00000131165	ENST00000296585.5:c.2664+2T>C	chr5.hg19:g.52370309T>C		91.0	0.0		137.0	6.0	NM_002203	Q14595	Splice_Site	SNP	ENST00000296585.5	hg19	CCDS3957.1	.	.	.	.	.	.	.	.	.	.	T	11.26	1.585762	0.28268	.	.	ENSG00000164171	ENST00000296585	.	.	.	5.01	5.01	0.66863	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.7407	0.62847	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	ITGA2	52406066	1.000000	0.71417	0.996000	0.52242	0.050000	0.14768	5.090000	0.64498	2.224000	0.72417	0.528000	0.53228	.	.	.		0.438	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203	Intron	C	52370309	T	C	52370309	5	2	365	1	0	0	0	0	0	0	1	0	7884	1652	57	2	2748	2	ITGA2	5	52370309	Splice_Site	SNP	T	TCGA-ZP-A9CZ-01A-11D-A382-10	25454553	52370309	128544951	12	50839										
CATSPER3	347732	hgsc.bcm.edu	37	chr5	134343827	134343827	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	tcaccctcttcagcttggccAcggtactgtgtttgggaaca	10	12	3	0			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr5:134343827A>T	ENST00000282611.6	+	4	759	c.673A>T	c.(673-675)Acg>Tcg	p.T225S		NM_178019.2	NP_821138.1	Q86XQ3	CTSR3_HUMAN	cation channel, sperm associated 3	225					calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|endoplasmic reticulum (GO:0005783)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|stomach(1)|urinary_tract(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CAGCTTGGCCACGGTACTGTG	0.562																																					p.T225S		Atlas-SNP	.											.	CATSPER3	38	.	0			c.A673T						.						82	76	78					5																	134343827		2203	4300	6503	SO:0001583	missense	347732	exon4			TTGGCCACGGTAC	AF432876	CCDS4181.1	5q31.2	2011-07-05			ENSG00000152705	ENSG00000152705		"Voltage-gated ion channels / Cation channels, sperm associated"	20819	protein-coding gene	gene with protein product		609120				12646162, 12932298, 17227845, 16382101	Standard	NM_178019		Approved	CACRC	uc003lag.3	Q86XQ3	OTTHUMG00000129137	ENST00000282611.6:c.673A>T	chr5.hg19:g.134343827A>T	ENSP00000282611:p.Thr225Ser	101.0	0.0		137.0	10.0	NM_178019	Q86XS6	Missense_Mutation	SNP	ENST00000282611.6	hg19	CCDS4181.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.270117	0.80469	.	.	ENSG00000152705	ENST00000282611	D	0.98400	-4.91	4.46	4.46	0.54185	Ion transport (1);	0.000000	0.56097	D	0.000035	D	0.98566	0.9521	M	0.74258	2.255	0.38616	D	0.951025	D	0.76494	0.999	D	0.85130	0.997	D	0.99874	1.1101	9	.	.	.	-25.7976	11.9375	0.52882	1.0:0.0:0.0:0.0	.	225	Q86XQ3	CTSR3_HUMAN	S	225	ENSP00000282611:T225S	.	T	+	1	0	CATSPER3	134371726	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.599000	0.67592	1.950000	0.56595	0.460000	0.39030	ACG	.	.		0.562	CATSPER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251191.2	NM_178019		T	134343827	A	T	134343827	3	4	365	1	0	0	0	0	1	0	0	0	2691	159	6	4	687	4	CATSPER3	5	134343827	Missense_Mutation	SNP	A	TCGA-ZP-A9CZ-01A-11D-A382-10	81973518	134343827	46571433	13	50840										
PCDHA4	56144	hgsc.bcm.edu	37	chr5	140188506	140188506	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	ggcactggtggcgcagtgagCgagctggtgccatggtcggt	19	9	0	1			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr5:140188506C>T	ENST00000530339.1	+	1	1734	c.1734C>T	c.(1732-1734)agC>agT	p.S578S	PCDHA1_ENST00000504120.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000356878.4_Silent_p.S578S|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Silent_p.S578S|PCDHA2_ENST00000526136.1_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	578					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGCAGTGAGCGAGCTGGTGC	0.662																																					p.S578S		Atlas-SNP	.											.	PCDHA4	419	.	0			c.C1734T						.						95	89	91					5																	140188506		2202	4299	6501	SO:0001819	synonymous_variant	56144	exon1			AGTGAGCGAGCTG	AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"Cadherins / Protocadherins : Clustered"	8670	other	complex locus constituent	"ortholog of mouse CNR1, KIAA0345-like 10"	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.1734C>T	chr5.hg19:g.140188506C>T		77.0	0.0		65.0	17.0	NM_031500	O75285|Q2M253	Silent	SNP	ENST00000530339.1	hg19	CCDS54916.1																																																																																			.	.		0.662	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907		T	140188506	C	T	140188506	2	4	365	1	0	0	0	0	0	0	0	1	11535	767	27	1		1	PCDHA4	5	140188506	Silent	SNP	C	TCGA-ZP-A9CZ-01A-11D-A382-10	5844679	140188506	40726754	14	50841										
GRIA1	2890	hgsc.bcm.edu	37	chr5	153190694	153190694	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	cggcagtggagagaatggtcGggtggtcagccatgacttcc	16	9	1	2			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr5:153190694G>A	ENST00000285900.5	+	16	2973	c.2630G>A	c.(2629-2631)cGg>cAg	p.R877Q	GRIA1_ENST00000518142.1_Missense_Mutation_p.R797Q|GRIA1_ENST00000518783.1_Missense_Mutation_p.R887Q|GRIA1_ENST00000340592.5_Missense_Mutation_p.R877Q|GRIA1_ENST00000521843.2_Missense_Mutation_p.R808Q|GRIA1_ENST00000448073.4_Missense_Mutation_p.R887Q	NM_000827.3|NM_001258019.1	NP_000818.2|NP_001244948.1	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1	877					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|axonal spine (GO:0044308)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|neuron spine (GO:0044309)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|PDZ domain binding (GO:0030165)			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)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Perampanel(DB08883)|Sevoflurane(DB01236)	GAGAATGGTCGGGTGGTCAGC	0.592																																					p.R887Q		Atlas-SNP	.											.	GRIA1	321	.	0			c.G2660A						.						55	54	55					5																	153190694		2203	4300	6503	SO:0001583	missense	2890	exon16			ATGGTCGGGTGGT		CCDS4322.1, CCDS47318.1, CCDS58986.1, CCDS58987.1, CCDS58988.1, CCDS58989.1	5q33	2012-08-29			ENSG00000155511	ENSG00000155511		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4571	protein-coding gene	gene with protein product		138248		GLUR1		1652753, 1319477	Standard	NM_000827		Approved	GluA1, GLURA	uc011dcy.2	P42261	OTTHUMG00000130148	ENST00000285900.5:c.2630G>A	chr5.hg19:g.153190694G>A	ENSP00000285900:p.Arg877Gln	232.0	0.0		255.0	66.0	NM_001258021	B7Z2S0|B7Z2W8|B7Z3F6|B7Z9G9|D3DQI4|E7ESV8|Q2NKM6	Missense_Mutation	SNP	ENST00000285900.5	hg19	CCDS4322.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.288962	0.80914	.	.	ENSG00000155511	ENST00000285900;ENST00000544403;ENST00000518142;ENST00000340592;ENST00000521843;ENST00000544794;ENST00000518783;ENST00000448073	T;T;T;T;T;T;T	0.12984	2.68;2.64;2.69;2.64;2.63;2.66;2.66	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.25044	0.0608	L	0.41236	1.265	0.58432	D	0.999999	P;P;D;P;D	0.71674	0.918;0.918;0.998;0.951;0.997	B;B;P;B;P	0.56648	0.17;0.17;0.665;0.32;0.803	T	0.01004	-1.1484	10	0.87932	D	0	.	17.3487	0.87316	0.0:0.0:1.0:0.0	.	887;887;797;877;877	E7ESV8;B7Z9G9;B7Z3F6;P42261-2;P42261	.;.;.;.;GRIA1_HUMAN	Q	877;877;797;877;810;808;887;887	ENSP00000285900:R877Q;ENSP00000427920:R797Q;ENSP00000339343:R877Q;ENSP00000427864:R810Q;ENSP00000442108:R808Q;ENSP00000428994:R887Q;ENSP00000415569:R887Q	ENSP00000285900:R877Q	R	+	2	0	GRIA1	153170887	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.242000	0.95408	2.330000	0.79161	0.561000	0.74099	CGG	.	.		0.592	GRIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252456.3			A	153190694	G	A	153190694	3	1	365	1	0	0	0	0	1	0	0	0	6776	1116	39	1	2811	1	GRIA1	5	153190694	Missense_Mutation	SNP	G	TCGA-ZP-A9CZ-01A-11D-A382-10	13002188	153190694	27724566	15	50842										
SYNGAP1	8831	hgsc.bcm.edu	37	chr6	33412344	33412344	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	cccacatcgagcgggaagagTacaagctcaaggagtactca	11	11	2	1			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr6:33412344T>C	ENST00000418600.2	+	16	3633	c.3532T>C	c.(3532-3534)Tac>Cac	p.Y1178H	SYNGAP1_ENST00000496374.1_3'UTR|SYNGAP1_ENST00000428982.2_Missense_Mutation_p.Y1119H|SYNGAP1_ENST00000293748.5_Missense_Mutation_p.Y1178H	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	1178					dendrite development (GO:0016358)|negative regulation of axonogenesis (GO:0050771)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|pattern specification process (GO:0007389)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|receptor clustering (GO:0043113)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of MAPK cascade (GO:0043408)|regulation of synapse structure and activity (GO:0050803)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Rab GTPase activator activity (GO:0005097)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(15)|ovary(7)|pancreas(1)|stomach(1)|urinary_tract(1)	43						GCGGGAAGAGTACAAGCTCAA	0.567																																					p.Y1178H		Atlas-SNP	.											.	SYNGAP1	202	.	0			c.T3532C						.						78	64	69					6																	33412344		2203	4300	6503	SO:0001583	missense	8831	exon16			GAAGAGTACAAGC	AB067525	CCDS34434.2	6p21.3	2010-06-25	2010-06-25		ENSG00000197283	ENSG00000197283			11497	protein-coding gene	gene with protein product		603384	"synaptic Ras GTPase activating protein 1 homolog (rat)"			9581761, 18323856	Standard	NM_006772		Approved	SYNGAP, RASA5, KIAA1938	uc011dri.2	Q96PV0	OTTHUMG00000031096	ENST00000418600.2:c.3532T>C	chr6.hg19:g.33412344T>C	ENSP00000403636:p.Tyr1178His	96.0	0.0		102.0	29.0	NM_006772	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Missense_Mutation	SNP	ENST00000418600.2	hg19	CCDS34434.2	.	.	.	.	.	.	.	.	.	.	T	17.17	3.320222	0.60634	.	.	ENSG00000197283	ENST00000293748;ENST00000418600;ENST00000449372;ENST00000428982	T;T;T	0.80994	-1.44;-1.44;-1.44	4.61	4.61	0.57282	.	0.150213	0.45606	D	0.000341	T	0.73265	0.3565	L	0.36672	1.1	0.34971	D	0.753149	D;D;D	0.65815	0.995;0.987;0.994	P;P;P	0.61658	0.892;0.693;0.827	T	0.70651	-0.4813	10	0.15499	T	0.54	.	12.0081	0.53272	0.0:0.0:0.0:1.0	.	1178;1178;1178	Q96PV0;Q96PV0-2;Q96PV0-4	SYGP1_HUMAN;.;.	H	1178;1178;1164;1119	ENSP00000293748:Y1178H;ENSP00000403636:Y1178H;ENSP00000412475:Y1119H	ENSP00000293748:Y1178H	Y	+	1	0	SYNGAP1	33520322	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.034000	0.76511	1.936000	0.56123	0.533000	0.62120	TAC	.	.		0.567	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407		C	33412344	T	C	33412344	3	2	365	1	0	0	0	0	1	0	0	0	15462	1638	57	2	3594	2	SYNGAP1	6	33412344	Missense_Mutation	SNP	T	TCGA-ZP-A9CZ-01A-11D-A382-10		33412344	137702723	16	50843										
SNAP91	9892	hgsc.bcm.edu	37	chr6	84303250	84303250	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	tggcggtggcagcggaggtgGtggtagtggtggtggcagcg	24	5	0	0			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr6:84303250G>A	ENST00000439399.2	-	18	1959	c.1643C>T	c.(1642-1644)aCc>aTc	p.T548I	SNAP91_ENST00000521743.1_Missense_Mutation_p.T548I|SNAP91_ENST00000195649.6_Missense_Mutation_p.T548I|SNAP91_ENST00000369694.2_Missense_Mutation_p.T548I|SNAP91_ENST00000520302.1_Missense_Mutation_p.T546I|SNAP91_ENST00000521485.1_Missense_Mutation_p.T548I|SNAP91_ENST00000428679.2_Missense_Mutation_p.T548I|SNAP91_ENST00000520213.1_Intron|SNAP91_ENST00000437520.1_Intron	NM_014841.2	NP_055656.1	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa	548	Ala-rich.|Thr-rich.				clathrin coat assembly (GO:0048268)|protein transport (GO:0015031)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|protein kinase binding (GO:0019901)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(22)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		agcggaggtggtggtagtggt	0.577																																					p.T548I		Atlas-SNP	.											.	SNAP91	199	.	0			c.C1643T						.						19	23	22					6																	84303250		2091	4148	6239	SO:0001583	missense	9892	exon17			GAGGTGGTGGTAG	AB014556	CCDS47455.1, CCDS56437.1, CCDS56438.1	6q15	2012-12-07	2012-12-07		ENSG00000065609	ENSG00000065609			14986	protein-coding gene	gene with protein product		607923	"synaptosomal-associated protein, 91 kDa (mouse) homolog", "synaptosomal-associated protein, 91kDa homolog (mouse)"			9734811, 12493563, 10436022	Standard	NM_014841		Approved	KIAA0656, AP180, CALM	uc003pka.3	O60641	OTTHUMG00000015114	ENST00000439399.2:c.1643C>T	chr6.hg19:g.84303250G>A	ENSP00000400459:p.Thr548Ile	138.0	0.0		142.0	43.0	NM_001242792	A8K0L7|E5RI02|Q5JX13|Q68DL9|Q6P9D3|Q9NTY7	Missense_Mutation	SNP	ENST00000439399.2	hg19	CCDS47455.1	.	.	.	.	.	.	.	.	.	.	G	14.89	2.671805	0.47781	.	.	ENSG00000065609	ENST00000521485;ENST00000369694;ENST00000439399;ENST00000195649;ENST00000428679;ENST00000520302;ENST00000521743	T;T;T;T;T;T;T	0.15372	2.46;2.45;2.45;2.46;2.46;2.43;2.45	5.3	5.3	0.74995	.	1.080100	0.07004	N	0.823920	T	0.07593	0.0191	N	0.14661	0.345	0.80722	D	1	P;B;P;B	0.41313	0.745;0.392;0.622;0.392	B;B;B;B	0.36418	0.224;0.11;0.149;0.11	T	0.40646	-0.9552	10	0.72032	D	0.01	-0.0231	18.5672	0.91120	0.0:0.0:1.0:0.0	.	429;546;548;546	B7Z2N2;E5RI02;O60641;E1P549	.;.;AP180_HUMAN;.	I	548;548;548;548;548;546;548	ENSP00000429776:T548I;ENSP00000358708:T548I;ENSP00000400459:T548I;ENSP00000195649:T548I;ENSP00000412492:T548I;ENSP00000428511:T546I;ENSP00000428215:T548I	ENSP00000195649:T548I	T	-	2	0	SNAP91	84359969	1.000000	0.71417	0.990000	0.47175	0.934000	0.57294	6.245000	0.72398	2.476000	0.83614	0.462000	0.41574	ACC	.	.		0.577	SNAP91-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375296.1			A	84303250	G	A	84303250	3	1	365	1	0	0	0	0	1	0	0	0	14848	1261	44	3	1128	3	SNAP91	6	84303250	Missense_Mutation	SNP	G	TCGA-ZP-A9CZ-01A-11D-A382-10	50890906	84303250	86811817	17	50844										
FUCA2	2519	hgsc.bcm.edu	37	chr6	143823511	143823511	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	ccttcaccaattcttcaattGtaagatagtcagagattcca	5	10	4	2			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr6:143823511G>A	ENST00000002165.6	-	4	999	c.944C>T	c.(943-945)aCa>aTa	p.T315I	FUCA2_ENST00000367585.1_Intron|RP1-20N2.6_ENST00000589489.1_RNA|RP1-20N2.6_ENST00000591892.1_RNA|RP1-20N2.6_ENST00000593045.1_RNA|RP1-20N2.6_ENST00000589563.1_RNA|RP1-20N2.6_ENST00000610068.1_RNA|RP1-20N2.6_ENST00000593175.1_RNA|RP1-20N2.6_ENST00000590703.1_RNA|FUCA2_ENST00000438118.2_Intron|RP1-20N2.6_ENST00000591189.1_RNA|RP1-20N2.6_ENST00000415586.1_RNA	NM_032020.4	NP_114409.2	Q9BTY2	FUCO2_HUMAN	fucosidase, alpha-L- 2, plasma	315					fucose metabolic process (GO:0006004)|glycoside catabolic process (GO:0016139)|regulation of entry of bacterium into host cell (GO:2000535)|response to bacterium (GO:0009617)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-L-fucosidase activity (GO:0004560)|fucose binding (GO:0042806)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				OV - Ovarian serous cystadenocarcinoma(155;7.45e-06)|GBM - Glioblastoma multiforme(68;0.0142)		TTCTTCAATTGTAAGATAGTC	0.388																																					p.T315I		Atlas-SNP	.											.	FUCA2	28	.	0			c.C944T						.						164	153	156					6																	143823511		2203	4300	6503	SO:0001583	missense	2519	exon4			TCAATTGTAAGAT	BC003060	CCDS5200.1	6q24	2012-10-02			ENSG00000001036	ENSG00000001036	3.2.1.51		4008	protein-coding gene	gene with protein product		136820				6590153	Standard	NM_032020		Approved	MGC1314, dJ20N2.5	uc003qjm.3	Q9BTY2	OTTHUMG00000015728	ENST00000002165.6:c.944C>T	chr6.hg19:g.143823511G>A	ENSP00000002165:p.Thr315Ile	113.0	0.0		113.0	39.0	NM_032020	E9PEB6|Q7Z6V1|Q7Z6Y2|Q8NBK4	Missense_Mutation	SNP	ENST00000002165.6	hg19	CCDS5200.1	.	.	.	.	.	.	.	.	.	.	G	17.60	3.430817	0.62844	.	.	ENSG00000001036	ENST00000002165	T	0.59502	0.26	5.62	5.62	0.85841	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.143965	0.64402	D	0.000010	D	0.83589	0.5287	H	0.97611	4.04	0.53688	D	0.999974	D	0.64830	0.994	D	0.71656	0.974	D	0.89043	0.3450	10	0.87932	D	0	-9.7956	19.6689	0.95903	0.0:0.0:1.0:0.0	.	315	Q9BTY2	FUCO2_HUMAN	I	315	ENSP00000002165:T315I	ENSP00000002165:T315I	T	-	2	0	FUCA2	143865204	1.000000	0.71417	0.213000	0.23690	0.980000	0.70556	4.359000	0.59449	2.642000	0.89623	0.655000	0.94253	ACA	.	.		0.388	FUCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042521.2	NM_032020		A	143823511	G	A	143823511	3	1	365	1	0	0	0	0	1	0	0	0	6103	1377	48	3	475	3	FUCA2	6	143823511	Missense_Mutation	SNP	G	TCGA-ZP-A9CZ-01A-11D-A382-10	59520261	143823511	27291556	18	50845										
C7orf10	79783	hgsc.bcm.edu	37	chr7	40234654	40234654	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	tcacatcatctattgttccaTcacaggtatttcaaccccac	3	14	5	0			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr7:40234654T>C	ENST00000335693.4	+	6	523	c.500T>C	c.(499-501)aTc>aCc	p.I167T	C7orf10_ENST00000540834.1_Missense_Mutation_p.I160T|C7orf10_ENST00000401647.2_Missense_Mutation_p.I167T|C7orf10_ENST00000309930.5_Missense_Mutation_p.I167T	NM_001193313.1	NP_001180242.1	Q9HAC7	SUCHY_HUMAN		167					metabolic process (GO:0008152)	mitochondrion (GO:0005739)	succinate-hydroxymethylglutarate CoA-transferase activity (GO:0047369)			endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)	18						TATTGTTCCATCACAGGTATT	0.393																																					p.I167T		Atlas-SNP	.											.	C7orf10	99	.	0			c.T500C						.						270	266	267					7																	40234654		1902	4120	6022	SO:0001583	missense	79783	exon6			GTTCCATCACAGG																												ENST00000335693.4:c.500T>C	chr7.hg19:g.40234654T>C	ENSP00000338475:p.Ile167Thr	56.0	0.0		67.0	15.0	NM_001193313	A4D1W5|B4DR73|Q4KMW4|Q4KMW8|Q4KMZ0|Q8TE00|Q8TEY1	Missense_Mutation	SNP	ENST00000335693.4	hg19	CCDS55105.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	23.5|23.5	4.426576|4.426576	0.83667|0.83667	.|.	.|.	ENSG00000175600|ENSG00000175600	ENST00000309930;ENST00000401647;ENST00000335693;ENST00000540834|ENST00000416370	T;T;T;T|.	0.60171|.	0.21;0.21;0.21;2.5|.	5.81|5.81	5.81|5.81	0.92471|0.92471	CoA-transferase family III domain (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.85852|0.85852	0.5793|0.5793	M|M	0.93283|0.93283	3.4|3.4	0.50632|0.50632	D|D	0.999885|0.999885	D;D;D|.	0.54601|.	0.967;0.967;0.959|.	P;P;P|.	0.58391|.	0.838;0.838;0.749|.	D|D	0.89525|0.89525	0.3781|0.3781	10|5	0.87932|.	D|.	0|.	-14.1537|-14.1537	15.1388|15.1388	0.72595|0.72595	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	167;167;130|.	Q4KMW8;Q9HAC7;Q9HAC7-2|.	.;CG010_HUMAN;.|.	T|P	167;167;167;160|162	ENSP00000312054:I167T;ENSP00000385222:I167T;ENSP00000338475:I167T;ENSP00000445521:I160T|.	ENSP00000312054:I167T|.	I|S	+|+	2|1	0|0	C7orf10|C7orf10	40201179|40201179	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	6.548000|6.548000	0.73896|0.73896	2.210000|2.210000	0.71456|0.71456	0.533000|0.533000	0.62120|0.62120	ATC|TCA	.	.		0.393	C7orf10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000338388.1			C	40234654	T	C	40234654	3	2	365	1	0	0	0	0	1	0	0	0	2378	1435	50	2	411	2	C7orf10	7	40234654	Missense_Mutation	SNP	T	TCGA-ZP-A9CZ-01A-11D-A382-10		40234654	118904009	19	50846										
ZNF804B	219578	hgsc.bcm.edu	37	chr7	88966180	88966180	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	tacagcatttattcctacatTgtttggtcctcacttaaatc	4	10	1	0			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr7:88966180T>A	ENST00000333190.4	+	4	4493	c.3884T>A	c.(3883-3885)tTg>tAg	p.L1295*		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	1295							metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			ATTCCTACATTGTTTGGTCCT	0.443										HNSCC(36;0.09)																											p.L1295X		Atlas-SNP	.											.	ZNF804B	322	.	0			c.T3884A						.						203	189	194					7																	88966180		2203	4300	6503	SO:0001587	stop_gained	219578	exon4			CTACATTGTTTGG	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"zinc finger 804B"				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.3884T>A	chr7.hg19:g.88966180T>A	ENSP00000329638:p.Leu1295*	131.0	0.0		120.0	25.0	NM_181646	B2RTV2|Q7Z714|Q96MN7	Nonsense_Mutation	SNP	ENST00000333190.4	hg19	CCDS5613.1	.	.	.	.	.	.	.	.	.	.	T	44	11.041769	0.99507	.	.	ENSG00000182348	ENST00000333190	.	.	.	5.41	5.41	0.78517	.	0.126543	0.36002	N	0.002848	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.3995	15.6016	0.76628	0.0:0.0:0.0:1.0	.	.	.	.	X	1295	.	ENSP00000329638:L1295X	L	+	2	0	ZNF804B	88804116	1.000000	0.71417	0.958000	0.39756	0.495000	0.33615	7.181000	0.77682	2.258000	0.74832	0.533000	0.62120	TTG	.	.		0.443	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646		A	88966180	T	A	88966180	4	1	365	1	0	0	0	0	0	1	0	0	18186	1821	63	4	3898	4	ZNF804B	7	88966180	Nonsense_Mutation	SNP	T	TCGA-ZP-A9CZ-01A-11D-A382-10	48731526	88966180	70172483	20	50847										
TSGA13	114960	hgsc.bcm.edu	37	chr7	130356523	130356523	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	tctttcctcatatctctctcAtggactggagcaaaggtgag	9	10	4	1			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr7:130356523A>G	ENST00000456951.1	-	8	1487	c.636T>C	c.(634-636)caT>caC	p.H212H	TSGA13_ENST00000356588.3_Silent_p.H212H|COPG2_ENST00000445977.2_5'Flank			Q96PP4	TSG13_HUMAN	testis specific, 13	212										endometrium(1)|kidney(3)|large_intestine(3)|lung(6)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	18	Melanoma(18;0.0435)					TATCTCTCTCATGGACTGGAG	0.433																																					p.H212H		Atlas-SNP	.											.	TSGA13	35	.	0			c.T636C						.						233	223	226					7																	130356523		2203	4300	6503	SO:0001819	synonymous_variant	114960	exon7			TCTCTCATGGACT	AK093329	CCDS5824.1	7q32	2008-02-04			ENSG00000213265	ENSG00000213265			12369	protein-coding gene	gene with protein product							Standard	NM_052933		Approved		uc003vqi.3	Q96PP4	OTTHUMG00000154999	ENST00000456951.1:c.636T>C	chr7.hg19:g.130356523A>G		92.0	0.0		109.0	41.0	NM_052933	B3KSC9	Silent	SNP	ENST00000456951.1	hg19	CCDS5824.1																																																																																			.	.		0.433	TSGA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337997.1	NM_052933		G	130356523	A	G	130356523	2	3	365	1	0	0	0	0	0	0	0	1	16634	214	8	2		2	TSGA13	7	130356523	Silent	SNP	A	TCGA-ZP-A9CZ-01A-11D-A382-10	41390343	130356523	28782140	21	50848										
PODXL	5420	hgsc.bcm.edu	37	chr7	131241029	131241029	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	ggccactcaccattctgggaGggcgacggcgacggcgacgg	17	13	2	0	rs11277659|rs547816245|rs532078953|rs79759078|rs571821675	byFrequency	TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr7:131241029G>C	ENST00000378555.3	-	1	337	c.90C>G	c.(88-90)ccC>ccG	p.P30P	PODXL_ENST00000541194.1_Silent_p.P30P|PODXL_ENST00000537928.1_Silent_p.P30P|PODXL_ENST00000465001.1_Intron|PODXL_ENST00000322985.9_Silent_p.P30P			O00592	PODXL_HUMAN	podocalyxin-like	30					cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					CATTCTGGGAGggcgacggcg	0.751																																					p.P30P		Atlas-SNP	.											.	PODXL	53	.	0			c.C90G						.						5	7	6					7																	131241029		1981	3946	5927	SO:0001819	synonymous_variant	5420	exon1			CTGGGAGGGCGAC		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.90C>G	chr7.hg19:g.131241029G>C		101.0	0.0		119.0	13.0	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Silent	SNP	ENST00000378555.3	hg19	CCDS34755.1																																																																																			.	.		0.751	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111		C	131241029	G	C	131241029	2	2	365	1	0	0	0	0	0	0	0	1	12189	987	35	4		4	PODXL	7	131241029	Silent	SNP	G	TCGA-ZP-A9CZ-01A-11D-A382-10	884506	131241029	27897634	22	50849										
SCRIB	23513	hgsc.bcm.edu	37	chr8	144873558	144873558	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	cccagcccggccccaactcaCcagggctgggagatggttcc	12	17	1	1			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr8:144873558C>T	ENST00000320476.3	-	35	4754		c.e35+1		RP11-429J17.8_ENST00000532625.1_RNA|RP11-429J17.8_ENST00000527139.1_RNA|RP11-429J17.8_ENST00000534089.1_RNA|SCRIB_ENST00000546337.1_5'Flank|SCRIB_ENST00000356994.2_Splice_Site|SCRIB_ENST00000377533.3_Splice_Site	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein						activation of Rac GTPase activity (GO:0032863)|apoptotic process involved in morphogenesis (GO:0060561)|astrocyte cell migration (GO:0043615)|asymmetric protein localization (GO:0008105)|auditory receptor cell stereocilium organization (GO:0060088)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cochlear nucleus development (GO:0021747)|establishment of apical/basal cell polarity (GO:0035089)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of mitotic cell cycle (GO:0045930)|neural tube closure (GO:0001843)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of receptor recycling (GO:0001921)|protein localization to adherens junction (GO:0071896)|single organismal cell-cell adhesion (GO:0016337)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle targeting (GO:0016080)|viral process (GO:0016032)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)|Scrib-APC-beta-catenin complex (GO:0034750)				NS(1)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(20)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	42	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			CCCCAACTCACCAGGGCTGGG	0.667																																					.	Pancreas(51;966 1133 10533 14576 29674)	Atlas-SNP	.											.	SCRIB	192	.	0			c.4822+1G>A						.						25	23	23					8																	144873558		2195	4298	6493	SO:0001630	splice_region_variant	23513	exon37			AACTCACCAGGGC	AY062238	CCDS6411.1, CCDS6412.1	8q24.3	2013-03-05	2013-03-05		ENSG00000180900	ENSG00000180900			30377	protein-coding gene	gene with protein product		607733	"scribbled homolog (Drosophila)"			11027293, 14681682	Standard	NM_182706		Approved	KIAA0147, SCRB1, Vartul	uc003yzo.1	Q14160	OTTHUMG00000165154	ENST00000320476.3:c.4747+1G>A	chr8.hg19:g.144873558C>T		265.0	0.0		228.0	145.0	NM_182706	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Splice_Site	SNP	ENST00000320476.3	hg19	CCDS6411.1	.	.	.	.	.	.	.	.	.	.	C	11.71	1.719434	0.30503	.	.	ENSG00000180900	ENST00000356994;ENST00000320476;ENST00000526832;ENST00000377533	.	.	.	4.24	4.24	0.50183	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.9849	0.53142	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SCRIB	144945546	0.000000	0.05858	0.968000	0.41197	0.459000	0.32528	0.384000	0.20668	2.209000	0.71365	0.486000	0.48141	.	.	.		0.667	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356	Intron	T	144873558	C	T	144873558	5	4	365	1	0	0	0	0	0	0	1	0	13952	521	18	3	152	3	SCRIB	8	144873558	Splice_Site	SNP	C	TCGA-ZP-A9CZ-01A-11D-A382-10		144873558	1490464	23	50850										
A1CF	29974	hgsc.bcm.edu	37	chr10	52601663	52601663	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	tgcttgattgcattcttggcTtccactttatttgaaaatgt	7	7	1	2			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr10:52601663T>A	ENST00000373993.1	-	3	368	c.324A>T	c.(322-324)gaA>gaT	p.E108D	A1CF_ENST00000395495.1_Missense_Mutation_p.E108D|A1CF_ENST00000373997.3_Missense_Mutation_p.E108D|A1CF_ENST00000374001.2_Missense_Mutation_p.E108D|A1CF_ENST00000373995.3_Missense_Mutation_p.E116D|A1CF_ENST00000395489.2_Missense_Mutation_p.E101D|A1CF_ENST00000282641.2_Missense_Mutation_p.E108D			Q9NQ94	A1CF_HUMAN	APOBEC1 complementation factor	108	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cytidine to uridine editing (GO:0016554)|gene expression (GO:0010467)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|protein stabilization (GO:0050821)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			NS(1)|breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(14)|prostate(2)|skin(3)	29						CATTCTTGGCTTCCACTTTAT	0.318																																					p.E116D		Atlas-SNP	.											.	A1CF	190	.	0			c.A348T						.						159	147	151					10																	52601663		2201	4299	6500	SO:0001583	missense	29974	exon6			CTTGGCTTCCACT	AF271790	CCDS7241.1, CCDS7242.1, CCDS7243.1, CCDS73133.1	10q21.1	2013-02-12			ENSG00000148584	ENSG00000148584		"RNA binding motif (RRM) containing"	24086	protein-coding gene	gene with protein product						11815617, 11072063	Standard	NM_014576		Approved	ACF, ASP, ACF64, ACF65, APOBEC1CF	uc001jjj.3	Q9NQ94	OTTHUMG00000018240	ENST00000373993.1:c.324A>T	chr10.hg19:g.52601663T>A	ENSP00000363105:p.Glu108Asp	85.0	0.0		72.0	28.0	NM_001198820	A1L4F2|A8K7G7|B7ZM14|Q5SZQ0|Q9NQ93|Q9NQX8|Q9NQX9|Q9NXC9|Q9NZD3	Missense_Mutation	SNP	ENST00000373993.1	hg19	CCDS7242.1	.	.	.	.	.	.	.	.	.	.	T	10.73	1.432096	0.25813	.	.	ENSG00000148584	ENST00000374001;ENST00000373993;ENST00000373997;ENST00000373995;ENST00000282641;ENST00000395495;ENST00000395488;ENST00000395489;ENST00000414883	T;T;T;T;T;T;T;T	0.39056	1.1;1.1;1.1;2.56;1.1;2.56;2.56;2.56	5.76	0.87	0.19102	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.090773	0.85682	N	0.000000	T	0.11965	0.0291	N	0.02120	-0.675	0.49299	D	0.99977	B;B;B;B	0.17038	0.001;0.0;0.02;0.001	B;B;B;B	0.16722	0.003;0.004;0.016;0.003	T	0.06041	-1.0849	10	0.16896	T	0.51	-11.4567	1.0491	0.01576	0.1459:0.221:0.1512:0.4818	.	101;108;108;116	F8W9F8;Q9NQ94;Q9NQ94-2;Q9NQ94-4	.;A1CF_HUMAN;.;.	D	108;108;108;116;108;108;91;101;108	ENSP00000363113:E108D;ENSP00000363105:E108D;ENSP00000363109:E108D;ENSP00000363107:E116D;ENSP00000282641:E108D;ENSP00000378873:E108D;ENSP00000378868:E101D;ENSP00000397953:E108D	ENSP00000282641:E108D	E	-	3	2	A1CF	52271669	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	1.086000	0.30853	0.431000	0.26258	0.383000	0.25322	GAA	.	.		0.318	A1CF-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048086.2	NM_014576		A	52601663	T	A	52601663	3	1	365	1	0	0	0	0	1	0	0	0	2	1606	56	4	1496	4	A1CF	10	52601663	Missense_Mutation	SNP	T	TCGA-ZP-A9CZ-01A-11D-A382-10		52601663	82933084	24	50851										
PRKG1	5592	hgsc.bcm.edu	37	chr10	54042052	54042052	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	ctactggtcactgggaatccTaatgtatgaactcctgactg	9	10	1	2			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr10:54042052T>C	ENST00000401604.2	+	14	1834	c.1640T>C	c.(1639-1641)cTa>cCa	p.L547P	PRKG1-AS1_ENST00000452247.2_RNA|PRKG1_ENST00000373980.4_Missense_Mutation_p.L562P|PRKG1_ENST00000373985.1_Missense_Mutation_p.L535P|PRKG1_ENST00000373975.2_Missense_Mutation_p.L265P|PRKG1-AS1_ENST00000426785.2_RNA			Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I	547	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|dendrite development (GO:0016358)|forebrain development (GO:0030900)|negative regulation of platelet aggregation (GO:0090331)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|regulation of GTPase activity (GO:0043087)|relaxation of vascular smooth muscle (GO:0060087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	53		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		CTGGGAATCCTAATGTATGAA	0.453																																					p.L562P		Atlas-SNP	.											.	PRKG1	167	.	0			c.T1685C						.						100	88	92					10																	54042052		2203	4300	6503	SO:0001583	missense	5592	exon14			GAATCCTAATGTA		CCDS7244.1	10q11.2	2009-07-10			ENSG00000185532	ENSG00000185532	2.7.11.1		9414	protein-coding gene	gene with protein product		176894		PRKGR1B, PRKG1B		2792381, 1544322	Standard	NM_001098512		Approved	PGK, PKG	uc001jjo.3	Q13976	OTTHUMG00000018248	ENST00000401604.2:c.1640T>C	chr10.hg19:g.54042052T>C	ENSP00000384200:p.Leu547Pro	140.0	0.0		137.0	49.0	NM_006258	A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	Missense_Mutation	SNP	ENST00000401604.2	hg19	CCDS44399.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.484595	0.84854	.	.	ENSG00000185532	ENST00000401604;ENST00000373985;ENST00000373980;ENST00000332193;ENST00000373975	T;T;T	0.68765	-0.35;-0.35;-0.35	5.63	5.63	0.86233	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.85915	0.5808	M	0.92169	3.28	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.998;0.999	D	0.89359	0.3666	10	0.87932	D	0	-9.8148	15.791	0.78364	0.0:0.0:0.0:1.0	.	265;562;547	B3KSF3;Q13976-2;Q13976	.;.;KGP1_HUMAN	P	547;535;562;265;159	ENSP00000384200:L547P;ENSP00000363097:L535P;ENSP00000363092:L562P	ENSP00000327642:L265P	L	+	2	0	PRKG1	53712058	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.990000	0.88215	2.270000	0.75569	0.460000	0.39030	CTA	.	.		0.453	PRKG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	54042052	T	C	54042052	3	2	365	1	0	0	0	0	1	0	0	0	12534	1522	53	2	2009	2	PRKG1	10	54042052	Missense_Mutation	SNP	T	TCGA-ZP-A9CZ-01A-11D-A382-10	1440389	54042052	81492695	25	50852										
SLIT1	6585	hgsc.bcm.edu	37	chr10	98924583	98924583	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	accccatactcacagcacccGcagctgcttgagccccgcaa	7	19	1	1			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr10:98924583G>A	ENST00000266058.4	-	2	507	c.262C>T	c.(262-264)Cgg>Tgg	p.R88W	ARHGAP19-SLIT1_ENST00000453547.2_Silent_p.C513C|SLIT1_ENST00000371041.3_Missense_Mutation_p.R88W|SLIT1_ENST00000456008.2_5'UTR|SLIT1_ENST00000371070.4_Missense_Mutation_p.R88W	NM_003061.2	NP_003052.2	O75093	SLIT1_HUMAN	slit homolog 1 (Drosophila)	88					axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|dorsal/ventral axon guidance (GO:0033563)|establishment of nucleus localization (GO:0040023)|forebrain morphogenesis (GO:0048853)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of synapse assembly (GO:0051964)|retinal ganglion cell axon guidance (GO:0031290)|spinal cord development (GO:0021510)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(37)|ovary(5)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	78		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		CACAGCACCCGCAGCTGCTTG	0.612																																					p.R88W		Atlas-SNP	.											.	SLIT1	154	.	0			c.C262T						.						140	121	128					10																	98924583		2203	4300	6503	SO:0001583	missense	6585	exon2			GCACCCGCAGCTG	AB011537	CCDS7453.1	10q23.3-q24	2008-08-01	2001-11-28		ENSG00000187122	ENSG00000187122			11085	protein-coding gene	gene with protein product		603742	"slit (Drosophila) homolog 1"	SLIL1		9693030, 9813312	Standard	NM_003061		Approved	slit1, MEGF4, Slit-1, SLIT3	uc001kmw.2	O75093	OTTHUMG00000018843	ENST00000266058.4:c.262C>T	chr10.hg19:g.98924583G>A	ENSP00000266058:p.Arg88Trp	52.0	0.0		69.0	18.0	NM_003061	Q5T0V1|Q8WWZ2|Q9UIL7	Missense_Mutation	SNP	ENST00000266058.4	hg19	CCDS7453.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.080403	0.76528	.	.	ENSG00000187122	ENST00000266058;ENST00000371057;ENST00000371054;ENST00000371070;ENST00000314867;ENST00000456008;ENST00000371041	T;T;T;T	0.59083	0.29;0.29;0.29;0.29	4.79	4.79	0.61399	.	0.000000	0.85682	D	0.000000	T	0.70666	0.3250	L	0.58583	1.82	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.996;0.95	T	0.73081	-0.4095	10	0.87932	D	0	.	11.9031	0.52694	0.0:0.0:0.8255:0.1745	.	88;88;88	E7EWQ8;O75093-2;O75093	.;.;SLIT1_HUMAN	W	88;88;88;88;71;88;88	ENSP00000266058:R88W;ENSP00000360109:R88W;ENSP00000315005:R71W;ENSP00000360080:R88W	ENSP00000266058:R88W	R	-	1	2	SLIT1	98914573	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.616000	0.54174	2.474000	0.83562	0.561000	0.74099	CGG	.	.		0.612	SLIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049636.1	NM_003061		A	98924583	G	A	98924583	3	1	365	1	0	0	0	0	1	0	0	0	14754	1086	38	1	4486	1	SLIT1	10	98924583	Missense_Mutation	SNP	G	TCGA-ZP-A9CZ-01A-11D-A382-10	44882531	98924583	36610164	26	50853										
SMPD1	6609	hgsc.bcm.edu	37	chr11	6411944	6411944	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	gatgggcctggtgctggcgcTggcgctggcgctggcgctgg	21	11	0	0	rs550067660	byFrequency	TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr11:6411944T>C	ENST00000342245.4	+	1	284	c.116T>C	c.(115-117)cTg>cCg	p.L39P	SMPD1_ENST00000533196.1_3'UTR|SMPD1_ENST00000356761.2_Missense_Mutation_p.L39P|SMPD1_ENST00000527275.1_Missense_Mutation_p.L39P|SMPD1_ENST00000299397.3_Missense_Mutation_p.L39P	NM_000543.4|NM_001007593.2	NP_000534.3|NP_001007594.2	P17405	ASM_HUMAN	sphingomyelin phosphodiesterase 1, acid lysosomal	39					cell death (GO:0008219)|ceramide biosynthetic process (GO:0046513)|glycosphingolipid metabolic process (GO:0006687)|negative regulation of MAP kinase activity (GO:0043407)|nervous system development (GO:0007399)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein dephosphorylation (GO:0035307)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)|sphingomyelin metabolic process (GO:0006684)|termination of signal transduction (GO:0023021)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lamellar body (GO:0042599)|lysosomal lumen (GO:0043202)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(3)	23		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;4.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	Amlodipine(DB00381)|Chlorpromazine(DB00477)|Desipramine(DB01151)	gtgctggcgctggcgctggcg	0.711																																					p.L39P		Atlas-SNP	.											.	SMPD1	108	.	0			c.T116C						.						14	18	17					11																	6411944		2190	4281	6471	SO:0001583	missense	6609	exon1			TGGCGCTGGCGCT	AB209775	CCDS31409.1, CCDS44531.1, CCDS31409.2	11p15.4-p15.1	2010-04-28	2008-02-04		ENSG00000166311	ENSG00000166311	3.1.4.12		11120	protein-coding gene	gene with protein product	"acid sphingomyelinase"	607608				1711683	Standard	NM_000543		Approved	ASM	uc001mcw.3	P17405	OTTHUMG00000165453	ENST00000342245.4:c.116T>C	chr11.hg19:g.6411944T>C	ENSP00000340409:p.Leu39Pro	114.0	0.0		117.0	39.0	NM_000543	A8K8M3|E9PKS3|P17406|Q13811|Q16837|Q16841	Missense_Mutation	SNP	ENST00000342245.4	hg19	CCDS44531.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.414709	0.83449	.	.	ENSG00000166311	ENST00000299397;ENST00000356761;ENST00000342245;ENST00000527275	T;T;T;T	0.11063	2.81;2.81;2.83;2.83	4.97	3.76	0.43208	.	.	.	.	.	T	0.12390	0.0301	N	0.08118	0	0.35645	D	0.811284	D;D;D	0.69078	0.995;0.997;0.995	P;D;P	0.65010	0.854;0.931;0.854	T	0.24404	-1.0161	9	0.72032	D	0.01	.	8.3318	0.32191	0.0:0.0:0.1998:0.8002	.	39;39;37	E9PKS3;G3XAB5;P17405	.;.;ASM_HUMAN	P	39	ENSP00000299397:L39P;ENSP00000349203:L39P;ENSP00000340409:L39P;ENSP00000435350:L39P	ENSP00000299397:L39P	L	+	2	0	SMPD1	6368520	0.415000	0.25416	0.956000	0.39512	0.093000	0.18481	0.928000	0.28831	1.982000	0.57802	0.460000	0.39030	CTG	.	.		0.711	SMPD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384205.1	NM_000543		C	6411944	T	C	6411944	3	2	365	1	0	0	0	0	1	0	0	0	14819	1580	55	2	118	2	SMPD1	11	6411944	Missense_Mutation	SNP	T	TCGA-ZP-A9CZ-01A-11D-A382-10		6411944	128594572	27	50854										
EHF	26298	hgsc.bcm.edu	37	chr11	34680176	34680176	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	atgggaagaccgatctgaggGcgtcttcaggttcttgaaat	13	7	4	3			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr11:34680176G>A	ENST00000533754.1	+	8	921	c.704G>A	c.(703-705)gGc>gAc	p.G235D	EHF_ENST00000531794.1_Missense_Mutation_p.G257D|EHF_ENST00000257831.3_Missense_Mutation_p.G235D|EHF_ENST00000450654.2_Missense_Mutation_p.G212D|EHF_ENST00000530286.1_Missense_Mutation_p.G235D					ets homologous factor										NFIA/EHF(2)	autonomic_ganglia(1)|cervix(1)|endometrium(3)|kidney(3)|lung(8)|upper_aerodigestive_tract(1)	17		all_hematologic(20;0.117)	Epithelial(1;0.055)|all cancers(1;0.137)|STAD - Stomach adenocarcinoma(6;0.235)			CGATCTGAGGGCGTCTTCAGG	0.488																																					p.G257D		Atlas-SNP	.											.	EHF	38	.	0			c.G770A						.						89	93	92					11																	34680176		2202	4298	6500	SO:0001583	missense	26298	exon8			CTGAGGGCGTCTT	AF170583	CCDS7894.1, CCDS55752.1, CCDS55753.1	11p12	2008-07-18				ENSG00000135373			3246	protein-coding gene	gene with protein product	"epithelium-specific ets factor 3", "ESE3 transcription factor"	605439				10527851	Standard	NM_012153		Approved	ESE3, ESEJ	uc021qfu.1	Q9NZC4		ENST00000533754.1:c.704G>A	chr11.hg19:g.34680176G>A	ENSP00000435837:p.Gly235Asp	144.0	0.0		156.0	45.0	NM_001206616		Missense_Mutation	SNP	ENST00000533754.1	hg19	CCDS7894.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.922457	0.92319	.	.	ENSG00000135373	ENST00000257831;ENST00000450654;ENST00000530286;ENST00000533754;ENST00000531794	T;T;T;T;T	0.15834	2.39;2.39;2.39;2.39;2.39	5.7	5.7	0.88788	Winged helix-turn-helix transcription repressor DNA-binding (1);Ets (4);	0.000000	0.85682	D	0.000000	T	0.57036	0.2026	H	0.94734	3.575	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.998;1.0	T	0.69131	-0.5226	10	0.87932	D	0	.	19.8388	0.96673	0.0:0.0:1.0:0.0	.	257;212;235	E9PSB2;Q9NZC4-2;Q9NZC4	.;.;EHF_HUMAN	D	235;212;235;235;257	ENSP00000257831:G235D;ENSP00000399733:G212D;ENSP00000433508:G235D;ENSP00000435837:G235D;ENSP00000435835:G257D	ENSP00000257831:G235D	G	+	2	0	EHF	34636752	1.000000	0.71417	1.000000	0.80357	0.837000	0.47467	9.869000	0.99810	2.695000	0.91970	0.561000	0.74099	GGC	.	.		0.488	EHF-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000389855.1	NM_012153		A	34680176	G	A	34680176	3	1	365	1	0	0	0	0	1	0	0	0	4983	1203	42	3	730	3	EHF	11	34680176	Missense_Mutation	SNP	G	TCGA-ZP-A9CZ-01A-11D-A382-10	28268232	34680176	100326340	28	50855										
SF3B2	10992	hgsc.bcm.edu	37	chr11	65828119	65828119	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	ctaagatgggcaaaattgacAtcgactaccagaaactgcat	8	9	0	3			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr11:65828119A>G	ENST00000322535.6	+	14	1745	c.1696A>G	c.(1696-1698)Atc>Gtc	p.I566V	SF3B2_ENST00000528302.1_Missense_Mutation_p.I549V	NM_006842.2	NP_006833.2	Q13435	SF3B2_HUMAN	splicing factor 3b, subunit 2, 145kDa	566					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	41						CAAAATTGACATCGACTACCA	0.493																																					p.I566V		Atlas-SNP	.											.	SF3B2	85	.	0			c.A1696G						.						145	127	133					11																	65828119		2201	4295	6496	SO:0001583	missense	10992	exon14			ATTGACATCGACT	U41371	CCDS31612.1	11q13	2010-07-21	2002-08-29		ENSG00000087365	ENSG00000087365			10769	protein-coding gene	gene with protein product		605591	"splicing factor 3b, subunit 2, 145kD"			8566756	Standard	XM_005273726		Approved	SAP145, SF3b1, Cus1, SF3b145	uc001ogy.1	Q13435	OTTHUMG00000166751	ENST00000322535.6:c.1696A>G	chr11.hg19:g.65828119A>G	ENSP00000318861:p.Ile566Val	136.0	0.0		144.0	49.0	NM_006842	A8K485|B4DT19|Q7L4T5|Q7Z627|Q969K1|Q96CM6|Q9BWD2	Missense_Mutation	SNP	ENST00000322535.6	hg19	CCDS31612.1	.	.	.	.	.	.	.	.	.	.	A	25.6	4.653305	0.88056	.	.	ENSG00000087365	ENST00000528302;ENST00000322535;ENST00000355456	.	.	.	5.82	5.82	0.92795	Domain of unknown function DUF382 (1);	0.000000	0.85682	D	0.000000	T	0.72486	0.3466	M	0.80183	2.485	0.80722	D	1	P	0.37083	0.581	P	0.45946	0.498	T	0.75811	-0.3186	9	0.66056	D	0.02	-21.0583	14.1327	0.65266	1.0:0.0:0.0:0.0	.	566	Q13435	SF3B2_HUMAN	V	549;566;470	.	ENSP00000318861:I566V	I	+	1	0	SF3B2	65584695	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.319000	0.89992	2.221000	0.72209	0.528000	0.53228	ATC	.	.		0.493	SF3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391352.2			G	65828119	A	G	65828119	3	3	365	1	0	0	0	0	1	0	0	0	14166	217	8	2	1750	2	SF3B2	11	65828119	Missense_Mutation	SNP	A	TCGA-ZP-A9CZ-01A-11D-A382-10	31147943	65828119	69178397	29	50856										
MYO7A	4647	hgsc.bcm.edu	37	chr11	76909563	76909563	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	ccagtctccccaagaacgacGtcatcgtggccgtcaactgg	10	15	3	1			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr11:76909563G>A	ENST00000409709.3	+	34	4737	c.4465G>A	c.(4465-4467)Gtc>Atc	p.V1489I	MYO7A_ENST00000458637.2_Missense_Mutation_p.V1489I|MYO7A_ENST00000409619.2_Missense_Mutation_p.V1478I	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	1489	FERM 1. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						CAAGAACGACGTCATCGTGGC	0.607																																					p.V1489I		Atlas-SNP	.											MYO7A,NS,carcinoma,0,1	MYO7A	164	.	0			c.G4465A						.						73	81	78					11																	76909563		2084	4188	6272	SO:0001583	missense	4647	exon34			AACGACGTCATCG	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"A-kinase anchor proteins", "Myosins / Myosin superfamily : Class VII"	7606	protein-coding gene	gene with protein product		276903	"myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.4465G>A	chr11.hg19:g.76909563G>A	ENSP00000386331:p.Val1489Ile	54.0	0.0		44.0	15.0	NM_000260	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Missense_Mutation	SNP	ENST00000409709.3	hg19	CCDS53683.1	.	.	.	.	.	.	.	.	.	.	G	12.23	1.876425	0.33162	.	.	ENSG00000137474	ENST00000409709;ENST00000458637;ENST00000409619;ENST00000545136;ENST00000358342;ENST00000343356;ENST00000341717;ENST00000458169;ENST00000544424	D;D;D;D	0.91351	-2.83;-2.83;-2.83;-2.83	5.06	5.06	0.68205	FERM domain (1);	0.067374	0.64402	D	0.000017	D	0.89677	0.6784	M	0.78049	2.395	0.80722	D	1	P;P;B	0.43662	0.545;0.814;0.343	B;B;B	0.35413	0.161;0.202;0.086	D	0.89739	0.3932	10	0.34782	T	0.22	.	18.6167	0.91305	0.0:0.0:1.0:0.0	.	1478;1489;1489	B9A011;F8VUN5;Q13402	.;.;MYO7A_HUMAN	I	1489;1489;1478;700;1488;1458;1365;670;142	ENSP00000386331:V1489I;ENSP00000392185:V1489I;ENSP00000386635:V1478I;ENSP00000417017:V670I	ENSP00000345075:V1365I	V	+	1	0	MYO7A	76587211	1.000000	0.71417	0.556000	0.28293	0.082000	0.17680	4.164000	0.58190	2.624000	0.88883	0.655000	0.94253	GTC	.	.		0.607	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260		A	76909563	G	A	76909563	3	1	365	1	0	0	0	0	1	0	0	0	10091	1145	40	1	4629	1	MYO7A	11	76909563	Missense_Mutation	SNP	G	TCGA-ZP-A9CZ-01A-11D-A382-10	11081444	76909563	58096953	30	50857										
APOA4	337	hgsc.bcm.edu	37	chr11	116692001	116692001	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	gccgcagctcctcggcactgGccgagatcctggccttgagc	13	16	0	2			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr11:116692001G>C	ENST00000357780.3	-	3	887	c.773C>G	c.(772-774)gCc>gGc	p.A258G		NM_000482.3	NP_000473.2	P06727	APOA4_HUMAN	apolipoprotein A-IV	258	13 X 22 AA approximate tandem repeats.				cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|chylomicron assembly (GO:0034378)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle remodeling (GO:0034375)|hydrogen peroxide catabolic process (GO:0042744)|innate immune response in mucosa (GO:0002227)|leukocyte cell-cell adhesion (GO:0007159)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|multicellular organismal lipid catabolic process (GO:0044240)|negative regulation of plasma lipoprotein particle oxidation (GO:0034445)|phosphatidylcholine metabolic process (GO:0046470)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of triglyceride catabolic process (GO:0010898)|protein-lipid complex assembly (GO:0065005)|regulation of cholesterol transport (GO:0032374)|regulation of intestinal cholesterol absorption (GO:0030300)|removal of superoxide radicals (GO:0019430)|response to lipid hydroperoxide (GO:0006982)|response to stilbenoid (GO:0035634)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|very-low-density lipoprotein particle remodeling (GO:0034372)	blood microparticle (GO:0072562)|chylomicron (GO:0042627)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	antioxidant activity (GO:0016209)|cholesterol transporter activity (GO:0017127)|copper ion binding (GO:0005507)|lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)|phosphatidylcholine binding (GO:0031210)|phosphatidylcholine-sterol O-acyltransferase activator activity (GO:0060228)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(2)|lung(10)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(158;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|Epithelial(105;1.62e-05)|all cancers(92;0.000165)|OV - Ovarian serous cystadenocarcinoma(223;0.148)		CTCGGCACTGGCCGAGATCCT	0.642																																					p.A258G		Atlas-SNP	.											.	APOA4	51	.	0			c.C773G						.						51	55	54					11																	116692001		2201	4292	6493	SO:0001583	missense	337	exon3			GCACTGGCCGAGA		CCDS31681.1	11q23.3	2013-01-24			ENSG00000110244	ENSG00000110244		"Apolipoproteins"	602	protein-coding gene	gene with protein product		107690					Standard	NM_000482		Approved		uc001pps.1	P06727	OTTHUMG00000046110	ENST00000357780.3:c.773C>G	chr11.hg19:g.116692001G>C	ENSP00000350425:p.Ala258Gly	61.0	0.0		40.0	18.0	NM_000482	A8MSL6|Q14CW8|Q6Q787	Missense_Mutation	SNP	ENST00000357780.3	hg19	CCDS31681.1	.	.	.	.	.	.	.	.	.	.	G	11.63	1.696713	0.30142	.	.	ENSG00000110244	ENST00000357780	T	0.74421	-0.84	4.96	-0.127	0.13510	Apolipoprotein/apolipophorin (1);	0.715917	0.12970	N	0.424246	T	0.82006	0.4943	M	0.83852	2.665	0.09310	N	1	D	0.58970	0.984	P	0.60345	0.873	T	0.71097	-0.4691	10	0.30854	T	0.27	-7.5352	9.7132	0.40258	0.0:0.3156:0.471:0.2134	.	258	P06727	APOA4_HUMAN	G	258	ENSP00000350425:A258G	ENSP00000350425:A258G	A	-	2	0	APOA4	116197211	0.045000	0.20229	0.000000	0.03702	0.026000	0.11368	2.350000	0.44063	0.097000	0.17492	0.563000	0.77884	GCC	.	.		0.642	APOA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106279.2	NM_000482		C	116692001	G	C	116692001	3	2	365	1	0	0	0	0	1	0	0	0	783	1203	42	4	421	4	APOA4	11	116692001	Missense_Mutation	SNP	G	TCGA-ZP-A9CZ-01A-11D-A382-10	39782438	116692001	18314515	31	50858										
LDHB	3945	hgsc.bcm.edu	37	chr12	21799847	21799847	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	aattacctttatctgccacaAttttaggtgtctgaagaaat	6	7	2	2			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr12:21799847A>C	ENST00000396076.1	-	3	565	c.233T>G	c.(232-234)aTt>aGt	p.I78S	LDHB_ENST00000350669.1_Missense_Mutation_p.I78S	NM_001174097.1	NP_001167568.1	P07195	LDHB_HUMAN	lactate dehydrogenase B	78					cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|lactate metabolic process (GO:0006089)|NAD metabolic process (GO:0019674)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	L-lactate dehydrogenase activity (GO:0004459)|NAD binding (GO:0051287)			breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	26						ATCTGCCACAATTTTAGGTGT	0.373																																					p.I78S		Atlas-SNP	.											.	LDHB	47	.	0			c.T233G						.						119	106	111					12																	21799847		2203	4300	6503	SO:0001583	missense	3945	exon3			GCCACAATTTTAG		CCDS8691.1	12p12.2-p12.1	2012-10-02			ENSG00000111716	ENSG00000111716	1.1.1.27		6541	protein-coding gene	gene with protein product		150100					Standard	NM_002300		Approved		uc001rfe.3	P07195	OTTHUMG00000133760	ENST00000396076.1:c.233T>G	chr12.hg19:g.21799847A>C	ENSP00000379386:p.Ile78Ser	55.0	0.0		62.0	17.0	NM_002300		Missense_Mutation	SNP	ENST00000396076.1	hg19	CCDS8691.1	.	.	.	.	.	.	.	.	.	.	A	18.46	3.629126	0.67015	.	.	ENSG00000111716	ENST00000396076;ENST00000350669;ENST00000396075;ENST00000450584;ENST00000539782	D;D;D;D;D	0.90900	-2.75;-2.75;-2.75;-2.75;-2.75	4.96	4.96	0.65561	Lactate/malate dehydrogenase, N-terminal (1);NAD(P)-binding domain (1);	0.045811	0.85682	D	0.000000	D	0.94974	0.8374	M	0.89287	3.02	0.80722	D	1	P	0.39737	0.685	P	0.53266	0.722	D	0.95668	0.8721	10	0.72032	D	0.01	.	14.6699	0.68937	1.0:0.0:0.0:0.0	.	78	P07195	LDHB_HUMAN	S	78	ENSP00000379386:I78S;ENSP00000229319:I78S;ENSP00000379385:I78S;ENSP00000398015:I78S;ENSP00000442680:I78S	ENSP00000229319:I78S	I	-	2	0	LDHB	21691114	1.000000	0.71417	1.000000	0.80357	0.845000	0.48019	9.157000	0.94714	1.858000	0.53909	0.460000	0.39030	ATT	.	.		0.373	LDHB-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258220.2	NM_002300		C	21799847	A	C	21799847	3	2	365	1	0	0	0	0	1	0	0	0	8710	101	4	5	795	5	LDHB	12	21799847	Missense_Mutation	SNP	A	TCGA-ZP-A9CZ-01A-11D-A382-10		21799847	112052048	32	50859										
R3HDM2	22864	hgsc.bcm.edu	37	chr12	57674222	57674222	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	agttgctgctgctgctgctgCtgttgctgctgggcagtaca	14	10	0	0			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr12:57674222C>T	ENST00000347140.3	-	14	1611	c.1221G>A	c.(1219-1221)caG>caA	p.Q407Q	R3HDM2_ENST00000413953.2_Silent_p.Q134Q|R3HDM2_ENST00000403821.2_Silent_p.Q407Q|RP11-123K3.4_ENST00000548184.1_3'UTR|R3HDM2_ENST00000402412.1_Silent_p.Q421Q|R3HDM2_ENST00000441731.2_Silent_p.Q68Q|R3HDM2_ENST00000358907.2_Silent_p.Q407Q			Q9Y2K5	R3HD2_HUMAN	R3H domain containing 2	407	Gln-rich.					nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	22						gctgctgctgctgttgctgct	0.567																																					p.Q407Q		Atlas-SNP	.											.	R3HDM2	125	.	0			c.G1221A						.						104	93	97					12																	57674222		2203	4300	6503	SO:0001819	synonymous_variant	22864	exon12			CTGCTGCTGTTGC	AB023219	CCDS8937.2	12q13.3	2012-11-19			ENSG00000179912	ENSG00000179912			29167	protein-coding gene	gene with protein product							Standard	NM_014925		Approved	KIAA1002	uc009zpm.1	Q9Y2K5	OTTHUMG00000171568	ENST00000347140.3:c.1221G>A	chr12.hg19:g.57674222C>T		64.0	0.0		79.0	5.0	NM_014925	Q2M1T9|Q3ZCT5	Silent	SNP	ENST00000347140.3	hg19	CCDS8937.2	.	.	.	.	.	.	.	.	.	.	C	12.71	2.018308	0.35606	.	.	ENSG00000179912	ENST00000466401	.	.	.	4.49	1.62	0.23740	.	.	.	.	.	T	0.51719	0.1691	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.36768	-0.9734	4	.	.	.	1.0729	5.4164	0.16376	0.0:0.5998:0.1455:0.2548	.	.	.	.	N	5	.	.	S	-	2	0	R3HDM2	55960489	0.030000	0.19436	0.992000	0.48379	0.921000	0.55340	-1.132000	0.03235	0.156000	0.19299	-0.294000	0.09567	AGC	.	.		0.567	R3HDM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326570.2	NM_014925		T	57674222	C	T	57674222	2	4	365	1	0	0	0	0	0	0	0	1	12903	796	28	3		3	R3HDM2	12	57674222	Silent	SNP	C	TCGA-ZP-A9CZ-01A-11D-A382-10	35874375	57674222	76177673	33	50860										
C12orf24	29902	hgsc.bcm.edu	37	chr12	110924510	110924510	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	ttccctttggcggccagtgaGaaacaaagaagggtctgttt	12	8	1	2			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr12:110924510G>A	ENST00000377673.5	+	5	1120	c.608G>A	c.(607-609)aGa>aAa	p.R203K		NM_013300.2	NP_037432.2	Q8WUB2	F216A_HUMAN	family with sequence similarity 216, member A	203																	CGGCCAGTGAGAAACAAAGAA	0.468																																					p.R203K		Atlas-SNP	.											.	.	.	.	0			c.G608A						.						81	87	85					12																	110924510		2203	4300	6503	SO:0001583	missense	29902	exon5			CAGTGAGAAACAA	U79274	CCDS31899.1	12q24.11	2012-02-07	2012-02-07	2012-02-07	ENSG00000204856	ENSG00000204856			30180	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 24"	C12orf24			Standard	NM_013300		Approved	HSU79274	uc001tqu.4	Q8WUB2	OTTHUMG00000169526	ENST00000377673.5:c.608G>A	chr12.hg19:g.110924510G>A	ENSP00000366901:p.Arg203Lys	81.0	0.0		119.0	26.0	NM_013300	A6NH30|Q99776	Missense_Mutation	SNP	ENST00000377673.5	hg19	CCDS31899.1	.	.	.	.	.	.	.	.	.	.	G	18.96	3.733588	0.69189	.	.	ENSG00000204856	ENST00000377673;ENST00000538285;ENST00000548869;ENST00000546396	T	0.57907	0.37	4.32	3.43	0.39272	.	0.000000	0.44688	D	0.000437	T	0.34308	0.0893	N	0.24115	0.695	0.80722	D	1	P;P;P	0.45957	0.496;0.869;0.869	B;B;B	0.38842	0.196;0.283;0.283	T	0.21348	-1.0248	10	0.87932	D	0	-7.5831	7.9714	0.30130	0.1118:0.0:0.8882:0.0	.	203;203;203	B4DJX7;F5GZE4;Q8WUB2	.;.;CL024_HUMAN	K	203;203;109;12	ENSP00000366901:R203K	ENSP00000366901:R203K	R	+	2	0	C12orf24	109408893	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	2.253000	0.43205	1.038000	0.40049	0.467000	0.42956	AGA	.	.		0.468	FAM216A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404616.1	NM_013300		A	110924510	G	A	110924510	3	1	365	1	0	0	0	0	1	0	0	0	1680	942	33	3	626	3	C12orf24	12	110924510	Missense_Mutation	SNP	G	TCGA-ZP-A9CZ-01A-11D-A382-10	53250288	110924510	22927385	34	50861										
KL	9365	hgsc.bcm.edu	37	chr13	33591317	33591317	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	cctacgtggtggcctggcacGgctacgccaccgggcgcctg	15	16	0	0			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr13:33591317G>A	ENST00000380099.3	+	1	747	c.739G>A	c.(739-741)Ggc>Agc	p.G247S	KL_ENST00000487852.1_3'UTR|KL_ENST00000426690.2_Intron	NM_004795.3	NP_004786.2	Q9UEF7	KLOT_HUMAN	klotho	247	Glycosyl hydrolase-1 1.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|calcium ion homeostasis (GO:0055074)|carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-glucosidase activity (GO:0008422)|beta-glucuronidase activity (GO:0004566)|fibroblast growth factor binding (GO:0017134)|signal transducer activity (GO:0004871)|vitamin D binding (GO:0005499)			breast(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|skin(5)	41	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		GGCCTGGCACGGCTACGCCAC	0.692																																					p.G247S		Atlas-SNP	.											.	KL	106	.	0			c.G739A						.						17	16	16					13																	33591317		2101	4091	6192	SO:0001583	missense	9365	exon1			TGGCACGGCTACG	AB005142	CCDS9347.1	13q12	2008-02-05			ENSG00000133116	ENSG00000133116			6344	protein-coding gene	gene with protein product		604824				9464267	Standard	NM_004795		Approved		uc001uus.3	Q9UEF7	OTTHUMG00000017408	ENST00000380099.3:c.739G>A	chr13.hg19:g.33591317G>A	ENSP00000369442:p.Gly247Ser	36.0	0.0		66.0	20.0	NM_004795	Q5VZ95|Q96KV5|Q96KW5|Q9UEI9|Q9Y4F0	Missense_Mutation	SNP	ENST00000380099.3	hg19	CCDS9347.1	.	.	.	.	.	.	.	.	.	.	G	29.5	5.011954	0.93346	.	.	ENSG00000133116	ENST00000380099	T	0.35048	1.33	4.55	4.55	0.56014	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	T	0.62221	0.2410	M	0.78456	2.415	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.66602	-0.5882	10	0.54805	T	0.06	-26.5644	17.4992	0.87727	0.0:0.0:1.0:0.0	.	247	Q9UEF7	KLOT_HUMAN	S	247	ENSP00000369442:G247S	ENSP00000369442:G247S	G	+	1	0	KL	32489317	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.256000	0.95535	2.357000	0.79964	0.563000	0.77884	GGC	.	.		0.692	KL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045987.1			A	33591317	G	A	33591317	3	1	365	1	0	0	0	0	1	0	0	0	8340	1116	39	1	741	1	KL	13	33591317	Missense_Mutation	SNP	G	TCGA-ZP-A9CZ-01A-11D-A382-10		33591317	81578561	35	50862										
NFATC4	4776	hgsc.bcm.edu	37	chr14	24845611	24845611	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	accacccaggcccccctaccCctcctatccccatgaagacc	4	23	0	2			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr14:24845611C>T	ENST00000250373.4	+	9	2309	c.2168C>T	c.(2167-2169)cCc>cTc	p.P723L	NFATC4_ENST00000554966.1_Missense_Mutation_p.P736L|NFATC4_ENST00000554591.1_Missense_Mutation_p.P786L|NFATC4_ENST00000555393.1_Missense_Mutation_p.P11L|NFATC4_ENST00000555453.1_Missense_Mutation_p.P711L|NFATC4_ENST00000413692.2_Missense_Mutation_p.P786L|NFATC4_ENST00000556279.1_Missense_Mutation_p.P755L|NFATC4_ENST00000539237.2_Missense_Mutation_p.P755L|NFATC4_ENST00000422617.3_Missense_Mutation_p.P711L|NFATC4_ENST00000554661.1_Missense_Mutation_p.P653L|NFATC4_ENST00000554050.1_Missense_Mutation_p.P723L|NFATC4_ENST00000555802.1_Missense_Mutation_p.P11L|NFATC4_ENST00000554473.1_Missense_Mutation_p.P258L|NFATC4_ENST00000556759.1_Missense_Mutation_p.P258L|NFATC4_ENST00000554344.1_Missense_Mutation_p.P653L|NFATC4_ENST00000555167.1_Missense_Mutation_p.P258L|NFATC4_ENST00000553708.1_Missense_Mutation_p.P723L|NFATC4_ENST00000424781.2_Missense_Mutation_p.P736L|NFATC4_ENST00000553469.1_Missense_Mutation_p.P755L|NFATC4_ENST00000557451.1_Missense_Mutation_p.P653L|NFATC4_ENST00000556169.1_Missense_Mutation_p.P711L|NFATC4_ENST00000557767.1_Missense_Mutation_p.P11L|NFATC4_ENST00000553879.1_Missense_Mutation_p.P653L|NFATC4_ENST00000555590.1_Missense_Mutation_p.P736L	NM_004554.4	NP_004545.2	Q14934	NFAC4_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4	723	Pro-rich.				cellular respiration (GO:0045333)|cellular response to lithium ion (GO:0071285)|cellular response to UV (GO:0034644)|heart development (GO:0007507)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of synaptic plasticity (GO:0048167)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription coactivator activity (GO:0003713)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(7)|liver(4)|lung(12)|ovary(1)|skin(2)	34				GBM - Glioblastoma multiforme(265;0.018)		CCCCCCTACCCCTCCTATCCC	0.617																																					p.P786L		Atlas-SNP	.											.	NFATC4	115	.	0			c.C2357T						.						61	68	65					14																	24845611		2203	4300	6503	SO:0001583	missense	4776	exon10			CCTACCCCTCCTA	BC053855	CCDS9629.1, CCDS45089.1, CCDS55909.1, CCDS55910.1, CCDS55911.1, CCDS73625.1	14q11.2	2009-11-24			ENSG00000100968	ENSG00000100968		"Nuclear factor of activated T-cells"	7778	protein-coding gene	gene with protein product		602699				7749981	Standard	NM_004554		Approved	NFAT3	uc010tok.2	Q14934	OTTHUMG00000029351	ENST00000250373.4:c.2168C>T	chr14.hg19:g.24845611C>T	ENSP00000250373:p.Pro723Leu	101.0	0.0		127.0	23.0	NM_001198967	B4DDG5|B4DY55|B5B2U7|B5B2U8|B5B2U9|B5B2V0|B5B2V1|B5B2V2|B5B2V3|B5B2V4|B5B2V5|B5B2V7|B5B2V8|B5B2V9|B5B2W0|B5B2W1|B5B2W2|B5B2W3|B5B2W4|B5B2W5|B5B2W6|B5B2W7|B5B2W8|B5B2W9|B5B2X0|Q7Z598|Q96H68	Missense_Mutation	SNP	ENST00000250373.4	hg19	CCDS9629.1	.	.	.	.	.	.	.	.	.	.	C	14.90	2.674926	0.47781	.	.	ENSG00000100968	ENST00000413692;ENST00000554591;ENST00000555590;ENST00000554966;ENST00000424781;ENST00000539237;ENST00000556279;ENST00000553469;ENST00000554050;ENST00000250373;ENST00000553708;ENST00000553879;ENST00000554344;ENST00000554661;ENST00000556169;ENST00000557451;ENST00000422617;ENST00000555453;ENST00000554473;ENST00000556759;ENST00000555167;ENST00000557767;ENST00000555393;ENST00000555802	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.51325	3.16;3.02;3.19;3.03;3.21;3.2;3.18;3.01;3.03;3.18;3.18;2.88;2.88;2.77;2.7;2.9;2.88;2.86;1.38;1.51;1.48;0.79;0.71	5.13	5.13	0.70059	.	0.213578	0.33895	N	0.004445	T	0.29028	0.0721	N	0.14661	0.345	0.47441	D	0.999426	B;B;B;B;B;B;B;B;B;B;B;B;B	0.26547	0.065;0.007;0.027;0.027;0.027;0.027;0.027;0.152;0.152;0.007;0.027;0.152;0.016	B;B;B;B;B;B;B;B;B;B;B;B;B	0.24006	0.023;0.015;0.025;0.035;0.025;0.025;0.025;0.05;0.05;0.015;0.035;0.05;0.011	T	0.10200	-1.0640	10	0.12103	T	0.63	-6.9713	13.9397	0.64048	0.0:1.0:0.0:0.0	.	711;711;755;755;736;736;736;786;786;711;755;786;723	Q14934-17;Q14934-9;Q14934-14;Q14934-4;Q14934-15;Q14934-6;Q14934-7;Q14934-2;Q14934-3;Q14934-10;Q14934-5;Q14934-11;Q14934	.;.;.;.;.;.;.;.;.;.;.;.;NFAC4_HUMAN	L	786;786;736;736;736;755;755;755;723;723;723;653;653;653;711;653;711;711;258;258;258;11;11;11	ENSP00000388910:P786L;ENSP00000452039:P786L;ENSP00000451224:P736L;ENSP00000450644:P736L;ENSP00000388668:P736L;ENSP00000439350:P755L;ENSP00000452270:P755L;ENSP00000451502:P755L;ENSP00000451151:P723L;ENSP00000250373:P723L;ENSP00000450590:P723L;ENSP00000452349:P653L;ENSP00000450469:P653L;ENSP00000450733:P653L;ENSP00000451454:P711L;ENSP00000451284:P653L;ENSP00000396788:P711L;ENSP00000450686:P711L;ENSP00000450810:P258L;ENSP00000451183:P258L;ENSP00000451395:P258L;ENSP00000451801:P11L;ENSP00000451590:P11L	ENSP00000250373:P723L	P	+	2	0	NFATC4	23915451	0.994000	0.37717	1.000000	0.80357	0.993000	0.82548	3.423000	0.52756	2.667000	0.90743	0.561000	0.74099	CCC	.	.		0.617	NFATC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073206.6	NM_004554		T	24845611	C	T	24845611	3	4	365	1	0	0	0	0	1	0	0	0	10374	623	22	3	2395	3	NFATC4	14	24845611	Missense_Mutation	SNP	C	TCGA-ZP-A9CZ-01A-11D-A382-10		24845611	82503929	36	50863										
GPHN	10243	hgsc.bcm.edu	37	chr14	67525478	67525478	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	ctggagatgactccggtgctTgggacagaaatcatcaatta	11	8	2	3			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr14:67525478T>A	ENST00000315266.5	+	10	2141	c.1020T>A	c.(1018-1020)ctT>ctA	p.L340L	GPHN_ENST00000459628.1_Silent_p.L355L|GPHN_ENST00000543237.1_Silent_p.L386L|GPHN_ENST00000544752.2_3'UTR|GPHN_ENST00000305960.9_Silent_p.L309L|GPHN_ENST00000478722.1_Silent_p.L373L	NM_001024218.1	NP_001019389.1	Q9NQX3	GEPH_HUMAN	gephyrin	340	MPT adenylyltransferase.				establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycine receptor clustering (GO:0072579)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|molybdopterin adenylyltransferase activity (GO:0061598)|molybdopterin molybdotransferase activity (GO:0061599)|transferase activity (GO:0016740)			large_intestine(8)|liver(1)|ovary(2)|stomach(1)	12		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		CTCCGGTGCTTGGGACAGAAA	0.398			T	MLL	AL																																p.L373L		Atlas-SNP	.		Dom	yes		14	14q24	10243	gephyrin (GPH)		L	.	GPHN	79	.	0			c.T1119A						.						173	166	168					14																	67525478		2203	4300	6503	SO:0001819	synonymous_variant	10243	exon11			GGTGCTTGGGACA	AB037806	CCDS9777.1, CCDS32103.1	14q23.3	2008-04-22			ENSG00000171723	ENSG00000171723			15465	protein-coding gene	gene with protein product		603930				1319186, 10325225, 18403029	Standard	XM_005267250		Approved	KIAA1385	uc001xix.3	Q9NQX3	OTTHUMG00000029785	ENST00000315266.5:c.1020T>A	chr14.hg19:g.67525478T>A		45.0	0.0		51.0	17.0	NM_020806	Q9H4E9|Q9P2G2	Silent	SNP	ENST00000315266.5	hg19	CCDS32103.1																																																																																			.	.		0.398	GPHN-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000074299.2	NM_020806		A	67525478	T	A	67525478	2	1	365	1	0	0	0	0	0	0	0	1	6618	1799	63	4		4	GPHN	14	67525478	Silent	SNP	T	TCGA-ZP-A9CZ-01A-11D-A382-10	42679867	67525478	39824062	37	50864										
CIITA	4261	hgsc.bcm.edu	37	chr16	10989526	10989526	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	caagggacttttcctcccagAacccgacacagacaccatca	6	16	1	2	rs200879588		TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr16:10989526A>T	ENST00000324288.8	+	3	333	c.200A>T	c.(199-201)gAa>gTa	p.E67V	CIITA_ENST00000537380.1_3'UTR|CIITA_ENST00000381835.5_Splice_Site_p.E67V	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	67	Asp/Glu-rich (acidic).				aging (GO:0007568)|cellular response to electrical stimulus (GO:0071257)|cellular response to exogenous dsRNA (GO:0071360)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to antibiotic (GO:0046677)|response to interferon-gamma (GO:0034341)|transcription, DNA-templated (GO:0006351)	cell surface (GO:0009986)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|GTP binding (GO:0005525)|kinase activity (GO:0016301)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transferase activity, transferring acyl groups (GO:0016746)			central_nervous_system(1)|large_intestine(7)|ovary(1)|skin(1)|stomach(2)	12						TTCCTCCCAGAACCCGACACA	0.552			T	"FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"	"PMBL, Hodgkin Lymphona, "																																p.E67V		Atlas-SNP	.		Dom	yes		16	16p13	4261	"class II, major histocompatibility complex, transactivator"		L	.	CIITA	92	.	0			c.A200T						.						77	75	75					16																	10989526		2197	4300	6497	SO:0001630	splice_region_variant	4261	exon3			TCCCAGAACCCGA	U18259	CCDS10544.1, CCDS66943.1, CCDS73826.1	16p13	2014-09-17	2005-08-12	2005-08-12	ENSG00000179583	ENSG00000179583		"Nucleotide-binding domain and leucine rich repeat containing"	7067	protein-coding gene	gene with protein product	"NLR family, acid domain containing", "nucleotide-binding oligomerization domain, leucine rich repeat and acid domain containing"	600005	"MHC class II transactivator"	MHC2TA		8402893	Standard	NM_000246		Approved	C2TA, NLRA	uc002dai.4	P33076	OTTHUMG00000129753	ENST00000324288.8:c.200-1A>T	chr16.hg19:g.10989526A>T		121.0	0.0		120.0	32.0	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Missense_Mutation	SNP	ENST00000324288.8	hg19	CCDS10544.1	.	.	.	.	.	.	.	.	.	.	A	19.86	3.904970	0.72868	.	.	ENSG00000179583	ENST00000324288;ENST00000381835;ENST00000388910;ENST00000537380	T;T	0.77489	-1.1;1.25	4.78	4.78	0.61160	.	0.326457	0.21745	N	0.069773	T	0.82235	0.4993	L	0.48642	1.525	0.31959	N	0.608646	D;D;P;P;D;D	0.76494	0.999;0.997;0.954;0.954;0.987;0.993	D;P;P;P;P;P	0.70487	0.969;0.829;0.572;0.572;0.809;0.776	T	0.83045	-0.0155	9	.	.	.	.	10.7295	0.46087	1.0:0.0:0.0:0.0	.	67;67;67;67;67;67	F5H2J4;E9PFE0;A0N0N9;P33076;F2Z2G8;Q96KL4	.;.;.;C2TA_HUMAN;.;.	V	67	ENSP00000316328:E67V;ENSP00000371257:E67V	.	E	+	2	0	CIITA	10897027	0.996000	0.38824	0.840000	0.33206	0.833000	0.47200	4.088000	0.57678	1.801000	0.52704	0.533000	0.62120	GAA	.	A|0.999;G|0.001		0.552	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246	Missense_Mutation	T	10989526	A	T	10989526	5	4	365	1	0	0	0	0	0	0	1	0	3430	260	9	4	210	4	CIITA	16	10989526	Splice_Site	SNP	A	TCGA-ZP-A9CZ-01A-11D-A382-10		10989526	79365227	38	50865										
POLR3E	55718	hgsc.bcm.edu	37	chr16	22325438	22325438	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	atgaggcggaagacgatgttAagcagatcacggtgagccct	14	8	1	4			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr16:22325438A>G	ENST00000299853.5	+	8	678	c.511A>G	c.(511-513)Aag>Gag	p.K171E	POLR3E_ENST00000359210.4_Missense_Mutation_p.K171E|POLR3E_ENST00000564209.1_Missense_Mutation_p.K171E|POLR3E_ENST00000418581.2_Missense_Mutation_p.K135E	NM_001258033.1|NM_001258035.1|NM_018119.3	NP_001244962.1|NP_001244964.1|NP_060589.1	Q9NVU0	RPC5_HUMAN	polymerase (RNA) III (DNA directed) polypeptide E (80kD)	171					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	centrosome (GO:0005813)|cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA-directed RNA polymerase activity (GO:0003899)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27				GBM - Glioblastoma multiforme(48;0.012)		AGACGATGTTAAGCAGATCAC	0.617																																					p.K171E		Atlas-SNP	.											.	POLR3E	62	.	0			c.A511G						.						61	49	53					16																	22325438		2197	4300	6497	SO:0001583	missense	55718	exon8			GATGTTAAGCAGA	AY092085	CCDS10605.1, CCDS58432.1, CCDS58433.1, CCDS58434.1, CCDS73845.1	16p12	2013-01-21			ENSG00000058600	ENSG00000058600		"RNA polymerase subunits"	30347	protein-coding gene	gene with protein product						10819331, 10521666	Standard	NM_018119		Approved	RPC5, SIN, FLJ10509	uc002dkk.4	Q9NVU0	OTTHUMG00000094779	ENST00000299853.5:c.511A>G	chr16.hg19:g.22325438A>G	ENSP00000299853:p.Lys171Glu	67.0	0.0		79.0	4.0	NM_001258033	B4DL24|B4DUP6|H3BT11|Q9BWF7|Q9H8W8|Q9H907|Q9P276	Missense_Mutation	SNP	ENST00000299853.5	hg19	CCDS10605.1	.	.	.	.	.	.	.	.	.	.	A	34	5.292316	0.95546	.	.	ENSG00000058600	ENST00000299853;ENST00000359210;ENST00000418581	T;T;T	0.44881	0.91;0.91;0.91	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.61073	0.2318	L	0.56769	1.78	0.80722	D	1	D;P;D;D;D;D	0.67145	0.996;0.926;0.993;0.995;0.996;0.991	D;P;D;D;D;D	0.69479	0.964;0.802;0.951;0.919;0.951;0.919	T	0.63637	-0.6592	10	0.87932	D	0	-35.7917	16.0282	0.80558	1.0:0.0:0.0:0.0	.	115;135;171;171;171;171	B4DDR0;B4DL24;B4DUP6;Q9NVU0-2;Q9NVU0;Q9NVU0-3	.;.;.;.;RPC5_HUMAN;.	E	171;171;135	ENSP00000299853:K171E;ENSP00000352140:K171E;ENSP00000399254:K135E	ENSP00000299853:K171E	K	+	1	0	POLR3E	22232939	1.000000	0.71417	0.992000	0.48379	0.934000	0.57294	8.636000	0.91010	2.268000	0.75426	0.454000	0.30748	AAG	.	.		0.617	POLR3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211590.1	NM_018119		G	22325438	A	G	22325438	3	3	365	1	0	0	0	0	1	0	0	0	12241	363	13	2	537	2	POLR3E	16	22325438	Missense_Mutation	SNP	A	TCGA-ZP-A9CZ-01A-11D-A382-10	11335912	22325438	68029315	39	50866										
RBL2	5934	hgsc.bcm.edu	37	chr16	53487516	53487517	+	Frame_Shift_Ins	INS	-	-	A													0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	ctatattaggaaactttatgINSaaaaaaaggtttgtaagtag							TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr16:53487516_53487517insA	ENST00000262133.6	+	6	1056_1057	c.919_920insA	c.(919-921)gaafs	p.E307fs	RBL2_ENST00000379935.4_3'UTR|RBL2_ENST00000544545.1_Frame_Shift_Ins_p.E91fs	NM_005611.3	NP_005602.3	Q08999	RBL2_HUMAN	retinoblastoma-like 2	307					chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						GAAACTTTATGAAAAAAAGGTT	0.337																																					p.E307fs		Atlas-INDEL	.											.	RBL2	115	.	0			c.919_920insA						.																																			SO:0001589	frameshift_variant	5934	exon6			.	X74594	CCDS10748.1	16q12.2	2014-03-11	2014-03-11		ENSG00000103479	ENSG00000103479			9894	protein-coding gene	gene with protein product		180203				8361765, 8643454	Standard	NM_005611		Approved	Rb2, p130	uc002ehi.4	Q08999	OTTHUMG00000133198	ENST00000262133.6:c.926dupA	chr16.hg19:g.53487523_53487523dupA	ENSP00000262133:p.Glu307fs	224.0	0.0		145.0	71.0	NM_005611	B7Z913|Q15073|Q16084|Q8NE70|Q92812	Frame_Shift_Ins	INS	ENST00000262133.6	hg19	CCDS10748.1																																																																																			.	.		0.337	RBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256908.3	NM_005611		A	53487517	-	A	53487516	7	5	365	1	0	1	1	0	0	0	0	0	13125	1291	45	0	941	0	RBL2	16	53487516	Frame_Shift_Ins	INS	-	TCGA-ZP-A9CZ-01A-11D-A382-10	31162078	53487516	36867237	40	50867										
ATMIN	23300	hgsc.bcm.edu	37	chr16	81075037	81075037	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	ctgctgtccaattgaaggctGccccagaggccctgagagac	12	13	0	4			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr16:81075037G>A	ENST00000299575.4	+	2	437	c.413G>A	c.(412-414)tGc>tAc	p.C138Y	ATMIN_ENST00000564241.1_5'UTR|ATMIN_ENST00000539819.1_3'UTR|ATMIN_ENST00000566488.1_5'UTR	NM_015251.2	NP_056066.2	O43313	ATMIN_HUMAN	ATM interactor	138					cellular response to DNA damage stimulus (GO:0006974)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dynein binding (GO:0045502)|metal ion binding (GO:0046872)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	20						ATTGAAGGCTGCCCCAGAGGC	0.403																																					p.C138Y		Atlas-SNP	.											.	ATMIN	50	.	0			c.G413A						.						124	128	127					16																	81075037		2202	4300	6502	SO:0001583	missense	23300	exon2			AAGGCTGCCCCAG	BC002701	CCDS32494.1, CCDS73917.1	16q23.2	2013-01-07			ENSG00000166454	ENSG00000166454		"Zinc fingers, C2H2-type"	29034	protein-coding gene	gene with protein product	"ATM/ATR-Substrate Chk2-Interacting Zn++-finger protein", "ATM INteracting protein"	614693				15933716, 17525732, 19001856	Standard	XM_005255866		Approved	ASCIZ, KIAA0431, ZNF822	uc002ffz.1	O43313	OTTHUMG00000176469	ENST00000299575.4:c.413G>A	chr16.hg19:g.81075037G>A	ENSP00000299575:p.Cys138Tyr	374.0	0.0		267.0	122.0	NM_015251	A8K4H8|Q68DC9	Missense_Mutation	SNP	ENST00000299575.4	hg19	CCDS32494.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.884502	0.91814	.	.	ENSG00000166454	ENST00000299575	T	0.67698	-0.28	5.51	5.51	0.81932	Zinc finger, C2H2-like (1);	0.000000	0.85682	D	0.000000	T	0.76212	0.3956	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.78048	-0.2356	10	0.87932	D	0	-12.6354	19.7859	0.96437	0.0:0.0:1.0:0.0	.	138	O43313	ATMIN_HUMAN	Y	138	ENSP00000299575:C138Y	ENSP00000299575:C138Y	C	+	2	0	ATMIN	79632538	1.000000	0.71417	0.998000	0.56505	0.942000	0.58702	9.720000	0.98763	2.746000	0.94184	0.655000	0.94253	TGC	.	.		0.403	ATMIN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432140.1	NM_015251		A	81075037	G	A	81075037	3	1	365	1	0	0	0	0	1	0	0	0	1110	1319	46	3	419	3	ATMIN	16	81075037	Missense_Mutation	SNP	G	TCGA-ZP-A9CZ-01A-11D-A382-10	27587521	81075037	9279716	41	50868										
EPN2	22905	hgsc.bcm.edu	37	chr17	19186882	19186882	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	agggcccaggctctcaaaacCaaagagcgcatggcccaggt	12	13	1	1			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr17:19186882C>G	ENST00000314728.5	+	3	934	c.450C>G	c.(448-450)acC>acG	p.T150T	EPN2_ENST00000395626.1_Silent_p.T150T|EPN2_ENST00000347697.2_Silent_p.T150T|EPN2_ENST00000575595.1_Intron|EPN2_ENST00000395620.2_Silent_p.T150T|EPN2_ENST00000395618.3_Intron|EPN2_ENST00000571254.1_Silent_p.T150T	NM_014964.4	NP_055779.2	O95208	EPN2_HUMAN	epsin 2	150					embryonic organ development (GO:0048568)|endocytosis (GO:0006897)|in utero embryonic development (GO:0001701)|Notch signaling pathway (GO:0007219)	clathrin coat of endocytic vesicle (GO:0030128)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	lipid binding (GO:0008289)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	19	all_cancers(12;3.11e-05)|all_epithelial(12;0.00121)|Hepatocellular(7;0.00345)|Breast(13;0.143)					CTCTCAAAACCAAAGAGCGCA	0.602																																					p.T150T		Atlas-SNP	.											.	EPN2	52	.	0			c.C450G						.						51	52	52					17																	19186882		2203	4300	6503	SO:0001819	synonymous_variant	22905	exon3			CAAAACCAAAGAG	AB028988	CCDS11203.1, CCDS11204.1, CCDS42277.1	17p11.2	2012-11-19			ENSG00000072134	ENSG00000072134			18639	protein-coding gene	gene with protein product	"Eps15 binding protein"	607263				10567358	Standard	NM_014964		Approved	KIAA1065, EHB21	uc002gvd.4	O95208	OTTHUMG00000178447	ENST00000314728.5:c.450C>G	chr17.hg19:g.19186882C>G		88.0	0.0		92.0	26.0	NM_148921	A8MTV8|B3KRX8|E9PBC2|O95207|Q52LD0|Q9H7Z2|Q9UPT7	Silent	SNP	ENST00000314728.5	hg19	CCDS11203.1																																																																																			.	.		0.602	EPN2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132283.3	NM_014964		G	19186882	C	G	19186882	2	3	365	1	0	0	0	0	0	0	0	1	5188	581	21	4		4	EPN2	17	19186882	Silent	SNP	C	TCGA-ZP-A9CZ-01A-11D-A382-10		19186882	62008328	42	50869										
NF1	4763	hgsc.bcm.edu	37	chr17	29588781	29588781	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	ataagatggcaacacttcttGcatacctgggtcctccagag	9	11	1	2			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr17:29588781G>A	ENST00000358273.4	+	35	5013	c.4630G>A	c.(4630-4632)Gca>Aca	p.A1544T	NF1_ENST00000356175.3_Missense_Mutation_p.A1523T	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	1544					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		AACACTTCTTGCATACCTGGG	0.408			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																											p.A1544T		Atlas-SNP	.	yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	.	NF1	1586	.	12	Whole gene deletion(8)|Unknown(4)	soft_tissue(7)|autonomic_ganglia(2)|central_nervous_system(2)|lung(1)	c.G4630A						.						118	104	109					17																	29588781		2203	4300	6503	SO:0001583	missense	4763	exon35	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	CTTCTTGCATACC		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.4630G>A	chr17.hg19:g.29588781G>A	ENSP00000351015:p.Ala1544Thr	192.0	0.0		304.0	86.0	NM_001042492	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	hg19	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	G	36	5.690594	0.96793	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735	D;D;D	0.81579	-1.51;-1.51;-1.51	5.68	5.68	0.88126	Rho GTPase activation protein (1);Armadillo-type fold (1);Ras GTPase-activating protein (1);	0.054740	0.64402	D	0.000001	D	0.87051	0.6081	L	0.46157	1.445	0.80722	D	1	D;P;D	0.58620	0.973;0.844;0.983	P;P;D	0.70016	0.729;0.501;0.967	D	0.87090	0.2172	10	0.59425	D	0.04	.	18.7806	0.91930	0.0:0.0:1.0:0.0	.	573;1523;1544	Q59FX3;P21359-2;P21359	.;.;NF1_HUMAN	T	1544;1523;1189	ENSP00000351015:A1544T;ENSP00000348498:A1523T;ENSP00000389907:A1189T	ENSP00000348498:A1523T	A	+	1	0	NF1	26612907	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.196000	0.94978	2.681000	0.91329	0.650000	0.86243	GCA	.	.		0.408	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		A	29588781	G	A	29588781	3	1	365	1	0	0	0	0	1	0	0	0	10365	1319	46	3	4829	3	NF1	17	29588781	Missense_Mutation	SNP	G	TCGA-ZP-A9CZ-01A-11D-A382-10	10401899	29588781	51606429	43	50870										
SUZ12	23512	hgsc.bcm.edu	37	chr17	30321616	30321616	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	gtgctaggatagatgtttctAtcaatgagtgttatgatggc	12	4	2	3			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr17:30321616A>G	ENST00000322652.5	+	13	1700	c.1471A>G	c.(1471-1473)Atc>Gtc	p.I491V	SUZ12_ENST00000580398.1_Missense_Mutation_p.I468V	NM_015355.2	NP_056170.2	Q15022	SUZ12_HUMAN	SUZ12 polycomb repressive complex 2 subunit	491					histone ubiquitination (GO:0016574)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|histone methyltransferase activity (GO:0042054)|metal ion binding (GO:0046872)|methylated histone binding (GO:0035064)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)		SSH2/SUZ12(2)|JAZF1/SUZ12(133)	breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|lung(5)|skin(1)	21		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.041)|Ovarian(249;0.182)|Breast(31;0.231)				AGATGTTTCTATCAATGAGTG	0.358			T	JAZF1	endometrial stromal tumours																																p.I491V		Atlas-SNP	.		Dom	yes		17	17q11.2	23512	suppressor of zeste 12 homolog (Drosophila)		M	.	SUZ12	61	.	0			c.A1471G						.						98	87	91					17																	30321616		2203	4300	6503	SO:0001583	missense	23512	exon13			GTTTCTATCAATG	D63881	CCDS11270.1	17q21	2013-06-05	2013-06-05		ENSG00000178691	ENSG00000178691		"Zinc fingers, C2H2-type"	17101	protein-coding gene	gene with protein product		606245	"suppressor of zeste 12 homolog (Drosophila)"			8590280, 11371647, 18784248	Standard	NM_015355		Approved	JJAZ1, KIAA0160, CHET9	uc002hgs.2	Q15022	OTTHUMG00000132813	ENST00000322652.5:c.1471A>G	chr17.hg19:g.30321616A>G	ENSP00000316578:p.Ile491Val	84.0	0.0		126.0	60.0	NM_015355	Q96BD9	Missense_Mutation	SNP	ENST00000322652.5	hg19	CCDS11270.1	.	.	.	.	.	.	.	.	.	.	a	12.60	1.986490	0.35036	.	.	ENSG00000178691	ENST00000322652	T	0.44083	0.93	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	T	0.37812	0.1017	L	0.46157	1.445	0.54753	D	0.999984	B;B	0.25521	0.059;0.128	B;B	0.23716	0.023;0.048	T	0.15578	-1.0432	10	0.33141	T	0.24	-7.7038	14.8417	0.70230	1.0:0.0:0.0:0.0	.	491;491	A8K1U9;Q15022	.;SUZ12_HUMAN	V	491	ENSP00000316578:I491V	ENSP00000316578:I491V	I	+	1	0	SUZ12	27345729	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.572000	0.82409	1.894000	0.54839	0.523000	0.50628	ATC	.	.		0.358	SUZ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256260.2	NM_015355		G	30321616	A	G	30321616	3	3	365	1	0	0	0	0	1	0	0	0	15431	449	16	2	1521	2	SUZ12	17	30321616	Missense_Mutation	SNP	A	TCGA-ZP-A9CZ-01A-11D-A382-10	732835	30321616	50873594	44	50871										
PSMC5	5705	hgsc.bcm.edu	37	chr17	61908427	61908427	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	gtgagggagctgtttgtcatGgcacgggaacatgctccatc	14	9	1	1			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr17:61908427G>A	ENST00000310144.6	+	8	1019	c.711G>A	c.(709-711)atG>atA	p.M237I	PSMC5_ENST00000580864.1_Missense_Mutation_p.M229I|PSMC5_ENST00000581882.1_Missense_Mutation_p.M229I|FTSJ3_ENST00000580295.1_5'Flank|PSMC5_ENST00000375812.4_Missense_Mutation_p.M229I	NM_002805.5	NP_002796.4	P62195	PRS8_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 5	237	May mediate interaction with PRPF9. {ECO:0000250|UniProtKB:P62196}.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of inclusion body assembly (GO:0090261)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|nuclear proteasome complex (GO:0031595)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|thyrotropin-releasing hormone receptor binding (GO:0031531)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			endometrium(3)|kidney(2)|large_intestine(8)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	20						TGTTTGTCATGGCACGGGAAC	0.562																																					p.M237I		Atlas-SNP	.											.	PSMC5	41	.	0			c.G711A						.						81	78	79					17																	61908427		2203	4300	6503	SO:0001583	missense	5705	exon8			TGTCATGGCACGG	L38810	CCDS11645.1, CCDS56043.1	17q23.3	2010-04-21			ENSG00000087191	ENSG00000087191		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9552	protein-coding gene	gene with protein product		601681				9473509, 9048938	Standard	NM_002805		Approved	SUG1, p45/SUG, TBP10, p45, S8, TRIP1, SUG-1	uc002jcb.3	P62195		ENST00000310144.6:c.711G>A	chr17.hg19:g.61908427G>A	ENSP00000310572:p.Met237Ile	74.0	0.0		109.0	45.0	NM_002805	A8K3Z3|A8K763|O35051|O43208|P47210|P52915|P52916	Missense_Mutation	SNP	ENST00000310144.6	hg19	CCDS11645.1	.	.	.	.	.	.	.	.	.	.	G	18.88	3.716511	0.68844	.	.	ENSG00000087191	ENST00000310144;ENST00000375812	D;D	0.92699	-3.09;-3.09	5.64	5.64	0.86602	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.87645	0.6229	N	0.05574	-0.02	0.80722	D	1	B;B	0.30889	0.299;0.167	B;B	0.40782	0.34;0.14	D	0.86779	0.1978	10	0.62326	D	0.03	.	17.243	0.87019	0.0:0.0:1.0:0.0	.	229;237	A8K3Z3;P62195	.;PRS8_HUMAN	I	237;229	ENSP00000310572:M237I;ENSP00000364970:M229I	ENSP00000310572:M237I	M	+	3	0	PSMC5	59262159	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	9.592000	0.98245	2.937000	0.99478	0.650000	0.86243	ATG	.	.		0.562	PSMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444404.1	NM_002805		A	61908427	G	A	61908427	3	1	365	1	0	0	0	0	1	0	0	0	12702	1348	47	3	741	3	PSMC5	17	61908427	Missense_Mutation	SNP	G	TCGA-ZP-A9CZ-01A-11D-A382-10	31586811	61908427	19286783	45	50872										
EEF2	1938	hgsc.bcm.edu	37	chr19	3980917	3980917	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	ggccgtcacaggggagggcaGgtggatggtgatcatctgca	18	8	3	1			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr19:3980917G>C	ENST00000309311.6	-	8	1160	c.1072C>G	c.(1072-1074)Ctg>Gtg	p.L358V	EEF2_ENST00000600720.1_5'Flank|SNORD37_ENST00000384048.1_RNA	NM_001961.3	NP_001952.1	P13639	EF2_HUMAN	eukaryotic translation elongation factor 2	358	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|hematopoietic progenitor cell differentiation (GO:0002244)|positive regulation of gene expression (GO:0010628)|positive regulation of translation (GO:0045727)|translation (GO:0006412)|translational elongation (GO:0006414)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation activator activity (GO:0008494)|translation elongation factor activity (GO:0003746)			endometrium(4)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|GBM - Glioblastoma multiforme(1328;0.0223)|STAD - Stomach adenocarcinoma(1328;0.18)		GGGGAGGGCAGGTGGATGGTG	0.692																																					p.L358V	Colon(165;1804 1908 4071 6587 18799)	Atlas-SNP	.											.	EEF2	57	.	0			c.C1072G						.																																			SO:0001583	missense	1938	exon8			AGGGCAGGTGGAT	Z11692	CCDS12117.1	19p13.3	2012-09-20			ENSG00000167658	ENSG00000167658			3214	protein-coding gene	gene with protein product	"polypeptidyl-tRNA translocase"	130610		EF2		2610926, 6427766	Standard	NM_001961		Approved	EEF-2	uc002lze.3	P13639		ENST00000309311.6:c.1072C>G	chr19.hg19:g.3980917G>C	ENSP00000307940:p.Leu358Val	39.0	0.0		62.0	18.0	NM_001961	B2RMP5|D6W618|Q58J86	Missense_Mutation	SNP	ENST00000309311.6	hg19	CCDS12117.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.127675	0.77549	.	.	ENSG00000167658	ENST00000543343;ENST00000309311	T	0.34275	1.37	5.4	4.36	0.52297	.	0.141721	0.48286	D	0.000197	T	0.56156	0.1966	M	0.75615	2.305	0.80722	D	1	D	0.69078	0.997	D	0.79108	0.992	T	0.58476	-0.7630	10	0.66056	D	0.02	-33.3889	8.8252	0.35050	0.1724:0.0:0.8276:0.0	.	358	P13639	EF2_HUMAN	V	358	ENSP00000307940:L358V	ENSP00000307940:L358V	L	-	1	2	EEF2	3931917	1.000000	0.71417	0.996000	0.52242	0.891000	0.51852	4.014000	0.57145	1.243000	0.43853	0.561000	0.74099	CTG	.	.		0.692	EEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457615.2	NM_001961		C	3980917	G	C	3980917	3	2	365	1	0	0	0	0	1	0	0	0	4931	991	35	4	1536	4	EEF2	19	3980917	Missense_Mutation	SNP	G	TCGA-ZP-A9CZ-01A-11D-A382-10		3980917	55148066	46	50873										
ARHGEF18	23370	hgsc.bcm.edu	37	chr19	7528790	7528790	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	gcagctccacaggcccgcccAggagggctgagaccttcgcg	14	16	0	1			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr19:7528790A>C	ENST00000359920.6	+	12	2411	c.2158A>C	c.(2158-2160)Agg>Cgg	p.R720R	CTD-2207O23.3_ENST00000593531.1_Silent_p.P677P|ARHGEF18_ENST00000319670.9_Silent_p.R562R	NM_001130955.1	NP_001124427.1	Q6ZSZ5	ARHGI_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 18	720					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transforming growth factor beta receptor signaling pathway (GO:0007179)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	23		Renal(5;0.0902)				AGGCCCGCCCAGGAGGGCTGA	0.682																																					p.R720R		Atlas-SNP	.											.	ARHGEF18	129	.	0			c.A2158C						.						21	22	22					19																	7528790		2192	4285	6477	SO:0001819	synonymous_variant	23370	exon12			CCGCCCAGGAGGG	AK074372	CCDS12177.1, CCDS45946.1	19p13.3	2013-01-10	2009-06-12			ENSG00000104880		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	17090	protein-coding gene	gene with protein product	"Rho-specific guanine nucleotide exchange factor p114"		"rho/rac guanine nucleotide exchange factor (GEF) 18"			9628581, 11318610	Standard	NM_015318		Approved	P114-RhoGEF, KIAA0521, MGC15913	uc002mgi.3	Q6ZSZ5		ENST00000359920.6:c.2158A>C	chr19.hg19:g.7528790A>C		208.0	0.0		231.0	12.0	NM_001130955	A8MV62|B5ME81|O60274|Q6DD92	Silent	SNP	ENST00000359920.6	hg19	CCDS45946.1																																																																																			.	.		0.682	ARHGEF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436340.1	NM_015318		C	7528790	A	C	7528790	2	2	365	1	0	0	0	0	0	0	0	1	901	179	7	5		5	ARHGEF18	19	7528790	Silent	SNP	A	TCGA-ZP-A9CZ-01A-11D-A382-10	3547873	7528790	51600193	47	50874										
MUC16	94025	hgsc.bcm.edu	37	chr19	9075042	9075042	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	gacctttgctaaagagagtgGtcttctctgagtatgtaaat	10	6	2	2			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr19:9075042G>C	ENST00000397910.4	-	3	12607	c.12404C>G	c.(12403-12405)aCc>aGc	p.T4135S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4137	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AAAGAGAGTGGTCTTCTCTGA	0.502																																					p.T4135S		Atlas-SNP	.											.	MUC16	4315	.	0			c.C12404G						.						142	133	136					19																	9075042		2062	4189	6251	SO:0001583	missense	94025	exon3			AGAGTGGTCTTCT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.12404C>G	chr19.hg19:g.9075042G>C	ENSP00000381008:p.Thr4135Ser	154.0	0.0		131.0	6.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	8.820	0.937406	0.18206	.	.	ENSG00000181143	ENST00000397910	T	0.27720	1.65	1.93	-1.97	0.07503	.	.	.	.	.	T	0.11580	0.0282	N	0.04018	-0.295	.	.	.	B	0.27166	0.17	B	0.28709	0.093	T	0.24621	-1.0155	8	0.87932	D	0	.	0.7984	0.01070	0.1625:0.235:0.3636:0.2388	.	4135	B5ME49	.	S	4135	ENSP00000381008:T4135S	ENSP00000381008:T4135S	T	-	2	0	MUC16	8936042	0.000000	0.05858	0.002000	0.10522	0.653000	0.38743	-0.281000	0.08456	-0.390000	0.07774	0.313000	0.20887	ACC	.	.		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	9075042	G	C	9075042	3	2	365	1	0	0	0	0	1	0	0	0	9982	1261	44	4	31447	4	MUC16	19	9075042	Missense_Mutation	SNP	G	TCGA-ZP-A9CZ-01A-11D-A382-10	1546252	9075042	50053941	48	50875										
LENG9	94059	hgsc.bcm.edu	37	chr19	54974339	54974339	+	Frame_Shift_Del	DEL	C	C	-													0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	ggaagcggaagaagcgcacgCggtgctggggcactgccagc							TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr19:54974339delC	ENST00000333834.4	-	1	555	c.437delG	c.(436-438)cgcfs	p.R146fs		NM_198988.1	NP_945339.2	Q96B70	LENG9_HUMAN	leukocyte receptor cluster (LRC) member 9	146							catalytic activity (GO:0003824)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)	11	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.134)		GAAGCGCACGCGGTGCTGGGG	0.731																																					p.R146fs		Atlas-INDEL	.											.	LENG9	46	.	0			c.438delC						.						5	7	6					19																	54974339		2071	4126	6197	SO:0001589	frameshift_variant	94059	exon1			.	AF211976		19q13.4	2014-05-06			ENSG00000182909	ENSG00000275183			16306	protein-coding gene	gene with protein product						10941842	Standard	NM_198988		Approved		uc010yez.2	Q96B70	OTTHUMG00000188273	ENST00000333834.4:c.437delG	chr19.hg19:g.54974339delC	ENSP00000331647:p.Arg146fs	92.0	0.0		92.0	31.0	NM_198988	B2VAM3	Frame_Shift_Del	DEL	ENST00000333834.4	hg19	CCDS12895.2																																																																																			.	.		0.731	LENG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140806.3	NM_198988		-	54974339	C	-	54974339	7	5	365	1	0	1	0	1	0	0	0	0	8734	768	27	0	1072	0	LENG9	19	54974339	Frame_Shift_Del	DEL	C	TCGA-ZP-A9CZ-01A-11D-A382-10	45899297	54974339	4154644	49	50876										
MYT1	4661	hgsc.bcm.edu	37	chr20	62843408	62843408	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	tgttctcttacagtcttagcCatgcatgagaacgtgctgaa	9	9	2	2			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr20:62843408C>T	ENST00000328439.1	+	9	1798	c.1434C>T	c.(1432-1434)gcC>gcT	p.A478A	MYT1_ENST00000536311.1_Silent_p.A478A|MYT1_ENST00000360149.4_Silent_p.A180A	NM_004535.2	NP_004526.1	Q99640	PMYT1_HUMAN	myelin transcription factor 1	0	Interaction with CDC2-CCNB1.|Interaction with PIN1.				G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(12)|liver(1)|lung(17)|ovary(5)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					CAGTCTTAGCCATGCATGAGA	0.607																																					p.A478A	GBM(59;481 1041 20555 21139 33705)	Atlas-SNP	.											.	MYT1	152	.	0			c.C1434T						.						147	133	138					20																	62843408		2203	4300	6503	SO:0001819	synonymous_variant	4661	exon9			CTTAGCCATGCAT	M96980	CCDS13558.1	20q13.33	2014-03-24			ENSG00000196132	ENSG00000196132		"Zinc fingers, C2HC-type containing"	7622	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 2"	600379		PLPB1		1280325, 9268380	Standard	NM_004535		Approved	MTF1, MYTI, ZC2HC4A, NZF2	uc002yii.3	Q01538	OTTHUMG00000149988	ENST00000328439.1:c.1434C>T	chr20.hg19:g.62843408C>T		31.0	0.0		26.0	9.0	NM_004535	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Silent	SNP	ENST00000328439.1	hg19	CCDS13558.1																																																																																			.	.		0.607	MYT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080297.1	NM_004535		T	62843408	C	T	62843408	2	4	365	1	0	0	0	0	0	0	0	1	10115	581	21	3		3	MYT1	20	62843408	Silent	SNP	C	TCGA-ZP-A9CZ-01A-11D-A382-10		62843408	182112	50	50877										
PLAC4	25825	hgsc.bcm.edu	37	chr21	42551226	42551226	+	Intron	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	gagtccagggtgaggattgaGggtgtcagggtgagtgagag	21	3	1	4			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr21:42551226G>C	ENST00000330333.6	+	1	775				PLAC4_ENST00000414699.1_RNA|PLAC4_ENST00000440221.2_RNA|PLAC4_ENST00000536486.1_RNA|BACE2_ENST00000328735.6_Intron|BACE2_ENST00000347667.5_Intron|PLAC4_ENST00000430327.2_RNA|BACE2-IT1_ENST00000433378.1_RNA	NM_012105.3	NP_036237.2	Q9Y5Z0	BACE2_HUMAN	beta-site APP-cleaving enzyme 2						membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(2)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14		Prostate(19;1.57e-07)|all_epithelial(19;0.0251)				tgaggattgagggtgtcaggg	0.602																																					p.P110P		Atlas-SNP	.											.	.	.	.	0			c.C330G						.						152	132	139					21																	42551226		2190	4254	6444	SO:0001627	intron_variant	191585	exon1			GATTGAGGGTGTC	AF117892	CCDS13668.1, CCDS13669.1, CCDS13670.1	21q22.3	2011-08-11			ENSG00000182240	ENSG00000182240			934	protein-coding gene	gene with protein product		605668		AEPLC		10965118, 10830953	Standard	NM_138991		Approved	CEAP1, DRAP, ALP56	uc002yyw.3	Q9Y5Z0	OTTHUMG00000086742	ENST00000330333.6:c.312+10724G>C	chr21.hg19:g.42551226G>C		145.0	0.0		143.0	40.0	NM_182832	A8K7P1|Q5DIH8|Q8N2D4|Q9H2V8|Q9NZL1|Q9NZL2|Q9UJT6	Silent	SNP	ENST00000330333.6	hg19	CCDS13668.1																																																																																			.	.		0.602	BACE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195056.1			C	42551226	G	C	42551226	1	2	365	0	1	0	0	0	0	0	0	0	12023	987	35	4		4	PLAC4	21	42551226	Intron	SNP	G	TCGA-ZP-A9CZ-01A-11D-A382-10		42551226	5578669	51	50878										
PLA2G6	8398	hgsc.bcm.edu	37	chr22	38525570	38525570	+	Splice_Site	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	atcatctccacgttgtctttCtgttggagatggagagagga	12	7	4	2			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr22:38525570C>G	ENST00000332509.3	-	8	1261		c.e8-1		PLA2G6_ENST00000402064.1_Splice_Site|PLA2G6_ENST00000335539.3_Splice_Site|PLA2G6_ENST00000490473.1_5'Flank	NM_003560.2	NP_003551.2	O60733	PLPL9_HUMAN	phospholipase A2, group VI (cytosolic, calcium-independent)						cardiolipin acyl-chain remodeling (GO:0035965)|cardiolipin biosynthetic process (GO:0032049)|cell death (GO:0008219)|chemotaxis (GO:0006935)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|glycerophospholipid biosynthetic process (GO:0046474)|innate immune response (GO:0045087)|lipid catabolic process (GO:0016042)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phospholipid metabolic process (GO:0006644)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of ceramide biosynthetic process (GO:2000304)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of exocytosis (GO:0045921)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of vasodilation (GO:0045909)|regulation of store-operated calcium channel activity (GO:1901339)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|urinary bladder smooth muscle contraction (GO:0014832)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipase A2 activity (GO:0004623)			breast(2)|endometrium(6)|kidney(1)|large_intestine(4)|liver(1)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	24	Melanoma(58;0.045)				Quinacrine(DB01103)	CGTTGTCTTTCTGTTGGAGAT	0.557																																					.		Atlas-SNP	.											.	PLA2G6	54	.	0			c.1078-1G>C						.						132	115	121					22																	38525570		2203	4300	6503	SO:0001630	splice_region_variant	8398	exon9			GTCTTTCTGTTGG	AF064594	CCDS13967.1, CCDS33645.1	22q13.1	2013-01-10			ENSG00000184381	ENSG00000184381	3.1.1.4	"Patatin-like phospholipase domain containing", "Parkinson disease", "Ankyrin repeat domain containing"	9039	protein-coding gene	gene with protein product	"neurodegeneration with brain iron accumulation 2"	603604				9417066, 16799181, 19029121	Standard	NM_001199562		Approved	iPLA2, PNPLA9, PARK14, iPLA2beta, NBIA2	uc003aux.1	O60733	OTTHUMG00000151246	ENST00000332509.3:c.1078-1G>C	chr22.hg19:g.38525570C>G		129.0	0.0		119.0	33.0	NM_001199562	A8K597|B0QYE8|O75645|Q8N452|Q9UG29|Q9UIT0|Q9Y671	Splice_Site	SNP	ENST00000332509.3	hg19	CCDS13967.1	.	.	.	.	.	.	.	.	.	.	C	17.18	3.323836	0.60634	.	.	ENSG00000184381	ENST00000332509;ENST00000419848;ENST00000335539;ENST00000402064;ENST00000335538;ENST00000396860;ENST00000452794;ENST00000451461;ENST00000427114;ENST00000427453;ENST00000452542	.	.	.	5.34	4.32	0.51571	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.408	0.67096	0.0:0.9282:0.0:0.0718	.	.	.	.	.	-1	.	.	.	-	.	.	PLA2G6	36855516	1.000000	0.71417	0.996000	0.52242	0.868000	0.49771	6.783000	0.75078	1.372000	0.46190	0.655000	0.94253	.	.	.		0.557	PLA2G6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321860.1	NM_001004426	Intron	G	38525570	C	G	38525570	5	3	365	1	0	0	0	0	0	0	1	0	12017	927	32	4	1383	4	PLA2G6	22	38525570	Splice_Site	SNP	C	TCGA-ZP-A9CZ-01A-11D-A382-10		38525570	12778996	52	50879										
CACNA1I	8911	hgsc.bcm.edu	37	chr22	40080333	40080333	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	caagtcccttctccccggatGcctccagccctctcctgccc	6	22	2	0			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr22:40080333G>A	ENST00000402142.3	+	36	5857	c.5857G>A	c.(5857-5859)Gcc>Acc	p.A1953T	CACNA1I_ENST00000404898.1_Missense_Mutation_p.A1918T|CACNA1I_ENST00000336649.4_Missense_Mutation_p.A1959T|CACNA1I_ENST00000401624.1_Missense_Mutation_p.A1953T|CACNA1I_ENST00000407673.1_Missense_Mutation_p.A1918T|CACNA1I_ENST00000400164.3_Missense_Mutation_p.A1918T	NM_021096.3	NP_066919.2	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type, alpha 1I subunit	1953					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|signal transduction (GO:0007165)|sleep (GO:0030431)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(2)|lung(27)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Melanoma(58;0.0749)				Cinnarizine(DB00568)|Flunarizine(DB04841)|Paramethadione(DB00617)|Spironolactone(DB00421)|Verapamil(DB00661)|Zonisamide(DB00909)	CTCCCCGGATGCCTCCAGCCC	0.642																																					p.A1953T		Atlas-SNP	.											.	CACNA1I	264	.	0			c.G5857A						.						43	50	48					22																	40080333		2034	4156	6190	SO:0001583	missense	8911	exon36			CCGGATGCCTCCA	AF129133	CCDS46710.1, CCDS46711.1	22q13.1	2012-03-07	2007-02-16		ENSG00000100346	ENSG00000100346		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1396	protein-coding gene	gene with protein product		608230				10454147, 16382099	Standard	NM_021096		Approved	Cav3.3	uc003ayd.3	Q9P0X4	OTTHUMG00000151096	ENST00000402142.3:c.5857G>A	chr22.hg19:g.40080333G>A	ENSP00000385019:p.Ala1953Thr	80.0	0.0		80.0	18.0	NM_021096	B0QY12|B0QY13|B0QY14|O95504|Q5JZ88|Q7Z6S9|Q8NFX6|Q9NZC8|Q9UH15|Q9UH30|Q9ULU9|Q9UNE6	Missense_Mutation	SNP	ENST00000402142.3	hg19	CCDS46710.1	.	.	.	.	.	.	.	.	.	.	G	7.192	0.591814	0.13812	.	.	ENSG00000100346	ENST00000402142;ENST00000404898;ENST00000401624;ENST00000407673;ENST00000336649;ENST00000400164	D;D;D;D;D;D	0.96716	-4.03;-4.0;-4.1;-4.07;-4.05;-3.96	5.05	4.03	0.46877	.	4.434490	0.00481	N	0.000123	D	0.90731	0.7091	N	0.08118	0	0.09310	N	1	B;B;B;B	0.06786	0.0;0.0;0.001;0.001	B;B;B;B	0.08055	0.001;0.001;0.003;0.001	T	0.80919	-0.1167	10	0.14656	T	0.56	.	8.8533	0.35212	0.225:0.0:0.775:0.0	.	1918;1953;1918;1953	Q9P0X4-3;Q9P0X4-2;Q9P0X4-4;Q9P0X4	.;.;.;CAC1I_HUMAN	T	1953;1918;1953;1918;1959;1918	ENSP00000385019:A1953T;ENSP00000384093:A1918T;ENSP00000383887:A1953T;ENSP00000385680:A1918T;ENSP00000337829:A1959T;ENSP00000383028:A1918T	ENSP00000337829:A1959T	A	+	1	0	CACNA1I	38410279	0.002000	0.14202	0.694000	0.30210	0.562000	0.35680	0.644000	0.24766	2.334000	0.79466	0.561000	0.74099	GCC	.	.		0.642	CACNA1I-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321290.1	NM_001003406		A	40080333	G	A	40080333	3	1	365	1	0	0	0	0	1	0	0	0	2548	1319	46	3	5999	3	CACNA1I	22	40080333	Missense_Mutation	SNP	G	TCGA-ZP-A9CZ-01A-11D-A382-10	1554763	40080333	11224233	53	50880										
MXRA5	25878	hgsc.bcm.edu	37	chrX	3235461	3235461	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	aactgcgaggggcggatctgGgtaccgtccccgagcaccca	14	14	1	0			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chrX:3235461G>C	ENST00000217939.6	-	6	6415	c.6261C>G	c.(6259-6261)acC>acG	p.T2087T		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	2087	Ig-like C2-type 5.					extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				GGCGGATCTGGGTACCGTCCC	0.647																																					p.T2087T		Atlas-SNP	.											.	MXRA5	815	.	0			c.C6261G						.						32	28	29					X																	3235461		2194	4288	6482	SO:0001819	synonymous_variant	25878	exon6			GATCTGGGTACCG	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7539	protein-coding gene	gene with protein product	"adlican"					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.6261C>G	chrX.hg19:g.3235461G>C		69.0	0.0		61.0	34.0	NM_015419	Q6P1M7|Q9Y3Y8	Silent	SNP	ENST00000217939.6	hg19	CCDS14124.1																																																																																			.	.		0.647	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		C	3235461	G	C	3235461	2	2	365	1	0	0	0	0	0	0	0	1	10012	1219	43	4		4	MXRA5	23	3235461	Silent	SNP	G	TCGA-ZP-A9CZ-01A-11D-A382-10		3235461	152035099	54	50881										
NXF5	55998	hgsc.bcm.edu	37	chrX	101092559	101092559	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0363636363636364	2	1	0.486842105263158	0.943256578947368	0.328089244851259	1	1	0	gtgaagtcatgctgagtttcAggcaatgcactgagggagtc	14	7	2	3			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chrX:101092559A>T	ENST00000361708.2	-	15	1346	c.987T>A	c.(985-987)ccT>ccA	p.P329P	NXF5_ENST00000473265.2_Silent_p.P329P|NXF5_ENST00000537026.1_Silent_p.P329P			Q9H1B4	NXF5_HUMAN	nuclear RNA export factor 5	329	NTF2; truncated.				mRNA export from nucleus (GO:0006406)|multicellular organismal development (GO:0007275)|RNA transport (GO:0050658)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|skin(1)	30						GCTGAGTTTCAGGCAATGCAC	0.547																																					p.P329P		Atlas-SNP	.											.	NXF5	65	.	0			c.T987A						.						201	158	173					X																	101092559		2203	4300	6503	SO:0001819	synonymous_variant	55998	exon15			AGTTTCAGGCAAT	AJ277654	CCDS14491.1, CCDS14491.2	Xq22	2008-07-28			ENSG00000126952	ENSG00000126952			8075	protein-coding gene	gene with protein product		300319				11566096	Standard	NM_032946		Approved		uc011mrk.1	Q9H1B4	OTTHUMG00000022042	ENST00000361708.2:c.987T>A	chrX.hg19:g.101092559A>T		241.0	0.0		249.0	177.0	NM_032946	A2RRM0|B1AV82|B1AV83|B1AV84|B1AV85|Q9H1B0|Q9H1B1|Q9H1B2|Q9H1B3	Silent	SNP	ENST00000361708.2	hg19																																																																																				.	.		0.547	NXF5-201	KNOWN	basic	protein_coding	protein_coding				T	101092559	A	T	101092559	2	4	365	1	0	0	0	0	0	0	0	1	10795	175	7	4		4	NXF5	23	101092559	Silent	SNP	A	TCGA-ZP-A9CZ-01A-11D-A382-10	97857098	101092559	54178001	55	50882										
TNFRSF18	8784	hgsc.bcm.edu	37	chr1	1140775	1140775	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	gactgtaccccctggcctggGggacaagggtggtgccggca	17	12	0	0			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr1:1140775G>C	ENST00000379268.2	-	2	404	c.285C>G	c.(283-285)ccC>ccG	p.P95P	TNFRSF18_ENST00000379265.5_Silent_p.P95P|TNFRSF18_ENST00000328596.6_Silent_p.P95P|TNFRSF18_ENST00000486728.1_Silent_p.P23P	NM_004195.2|NM_148902.1	NP_004186.1|NP_683700.1	Q9Y5U5	TNR18_HUMAN	tumor necrosis factor receptor superfamily, member 18	95					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|signal transduction (GO:0007165)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	tumor necrosis factor-activated receptor activity (GO:0005031)			lung(1)	1	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;3.73e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.01e-21)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		CCTGGCCTGGGGGACAAGGGT	0.657																																					p.P95P	GBM(157;472 1934 13810 14591 35952)	Atlas-SNP	.											.	TNFRSF18	13	.	0			c.C285G						.						46	41	43					1																	1140775		2200	4292	6492	SO:0001819	synonymous_variant	8784	exon2			GCCTGGGGGACAA	AF125304	CCDS9.1, CCDS10.1, CCDS30552.1	1p36.3	2011-08-11			ENSG00000186891	ENSG00000186891		"Tumor necrosis factor receptor superfamily", "CD molecules"	11914	protein-coding gene	gene with protein product		603905				9177197, 10037686	Standard	NM_004195		Approved	AITR, GITR, CD357	uc001add.3	Q9Y5U5	OTTHUMG00000001414	ENST00000379268.2:c.285C>G	chr1.hg19:g.1140775G>C		374.0	0.0		323.0	111.0	NM_148902	B1AME1|O95851|Q5U0I4|Q9NYJ9	Silent	SNP	ENST00000379268.2	hg19	CCDS10.1																																																																																			.	.		0.657	TNFRSF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004083.2	NM_004195		C	1140775	G	C	1140775	2	2	366	1	0	0	0	0	0	0	0	1	16306	1219	43	4		4	TNFRSF18	1	1140775	Silent	SNP	G	TCGA-ZP-A9D0-01A-11D-A36X-10		1140775	248109846	1	50883										
ACAP3	116983	hgsc.bcm.edu	37	chr1	1229084	1229084	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	ctccgccatgcgcgccagacGgagcctacggggaggcacag	15	15	0	1			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr1:1229084G>A	ENST00000354700.5	-	24	2567	c.2365C>T	c.(2365-2367)Cgt>Tgt	p.R789C	ACAP3_ENST00000353662.3_Missense_Mutation_p.R714C|ACAP3_ENST00000379037.2_5'Flank	NM_030649.2	NP_085152.2	Q96P50	ACAP3_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 3	789					regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			endometrium(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	14						CGCGCCAGACGGAGCCTACGG	0.781																																					p.R789C		Atlas-SNP	.											.	ACAP3	87	.	0			c.C2365T						.						3	3	3					1																	1229084		1697	3296	4993	SO:0001583	missense	116983	exon24			CCAGACGGAGCCT	AF411981	CCDS19.2	1p36	2013-01-10	2008-09-22	2008-09-22	ENSG00000131584	ENSG00000131584		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16754	protein-coding gene	gene with protein product			"centaurin, beta 5"	CENTB5			Standard	NM_030649		Approved	KIAA1716	uc001aeb.2	Q96P50	OTTHUMG00000002235	ENST00000354700.5:c.2365C>T	chr1.hg19:g.1229084G>A	ENSP00000346733:p.Arg789Cys	16.0	0.0		14.0	9.0	NM_030649	B1AMF5|Q5TA42|Q5TA43|Q86UT3|Q9BSR9|Q9C0E7	Missense_Mutation	SNP	ENST00000354700.5	hg19	CCDS19.2	.	.	.	.	.	.	.	.	.	.	G	19.09	3.759323	0.69763	.	.	ENSG00000131584	ENST00000354700;ENST00000353662	T;T	0.34275	1.37;1.37	4.26	4.26	0.50523	Ankyrin repeat-containing domain (2);	0.136297	0.50627	D	0.000110	T	0.65739	0.2720	M	0.89414	3.03	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.989;0.995	T	0.74808	-0.3539	10	0.87932	D	0	.	15.8335	0.78778	0.0:0.0:1.0:0.0	.	789;714	Q96P50;Q96P50-1	ACAP3_HUMAN;.	C	789;714	ENSP00000346733:R789C;ENSP00000321139:R714C	ENSP00000321139:R714C	R	-	1	0	ACAP3	1218947	1.000000	0.71417	0.988000	0.46212	0.102000	0.19082	3.947000	0.56652	2.195000	0.70347	0.549000	0.68633	CGT	.	.		0.781	ACAP3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006366.2	NM_030649		A	1229084	G	A	1229084	3	1	366	1	0	0	0	0	1	0	0	0	120	1116	39	1	143	1	ACAP3	1	1229084	Missense_Mutation	SNP	G	TCGA-ZP-A9D0-01A-11D-A36X-10	88309	1229084	248021537	2	50884										
STX6	10228	hgsc.bcm.edu	37	chr1	180991796	180991796	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	ctttcaccacaaagaaggggTcctccatggacatggcgtcc	10	13	1	1			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr1:180991796T>A	ENST00000258301.5	-	1	251	c.14A>T	c.(13-15)gAc>gTc	p.D5V	STX6_ENST00000542060.1_5'UTR	NM_005819.4	NP_005810.1	O43752	STX6_HUMAN	syntaxin 6	5					endosome organization (GO:0007032)|Golgi vesicle transport (GO:0048193)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147)|vesicle fusion (GO:0006906)	clathrin-coated vesicle (GO:0030136)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|SNARE complex (GO:0031201)|trans-Golgi network membrane (GO:0032588)	SNAP receptor activity (GO:0005484)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)	10						AAAGAAGGGGTCCTCCATGGA	0.706																																					p.D5V		Atlas-SNP	.											.	STX6	21	.	0			c.A14T						.						26	28	27					1																	180991796		2202	4300	6502	SO:0001583	missense	10228	exon1			AAGGGGTCCTCCA	AJ002078	CCDS1341.1, CCDS65738.1	1q25.3	2008-02-05			ENSG00000135823	ENSG00000135823			11441	protein-coding gene	gene with protein product		603944				10080545	Standard	XM_005244824		Approved		uc021pfr.1	O43752	OTTHUMG00000035179	ENST00000258301.5:c.14A>T	chr1.hg19:g.180991796T>A	ENSP00000258301:p.Asp5Val	177.0	0.0		234.0	48.0	NM_005819	B2R652|B4DR17|Q5VY08|Q6FH83	Missense_Mutation	SNP	ENST00000258301.5	hg19	CCDS1341.1	.	.	.	.	.	.	.	.	.	.	T	15.12	2.739505	0.49045	.	.	ENSG00000135823	ENST00000258301	.	.	.	5.09	3.95	0.45737	t-SNARE (1);Syntaxin 6, N-terminal (1);	0.102848	0.64402	D	0.000004	T	0.81612	0.4859	M	0.93150	3.385	0.45035	D	0.998054	D	0.71674	0.998	D	0.74023	0.982	D	0.86832	0.2011	8	0.87932	D	0	-7.69	8.9399	0.35722	0.0:0.0:0.1883:0.8117	.	5	O43752	STX6_HUMAN	V	5	.	ENSP00000258301:D5V	D	-	2	0	STX6	179258419	1.000000	0.71417	1.000000	0.80357	0.106000	0.19336	3.680000	0.54641	0.763000	0.33175	-0.648000	0.03929	GAC	.	.		0.706	STX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085143.1	NM_005819		A	180991796	T	A	180991796	3	1	366	1	0	0	0	0	1	0	0	0	15364	1667	58	4	785	4	STX6	1	180991796	Missense_Mutation	SNP	T	TCGA-ZP-A9D0-01A-11D-A36X-10	179762712	180991796	68258825	3	50885										
ARPC5	10092	hgsc.bcm.edu	37	chr1	183602268	183602268	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	gggttcttcagagctgcctgTagggcagctgtcatgtttcc	13	10	3	1			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr1:183602268T>C	ENST00000359856.6	-	2	231	c.165A>G	c.(163-165)ctA>ctG	p.L55L	RGL1_ENST00000304685.4_5'Flank|ARPC5_ENST00000367534.1_Silent_p.L55L|RGL1_ENST00000536277.1_5'Flank|ARPC5_ENST00000294742.6_Silent_p.L58L|ARPC5_ENST00000462965.1_5'UTR	NM_005717.3	NP_005708.1	O15511	ARPC5_HUMAN	actin related protein 2/3 complex, subunit 5, 16kDa	55					actin cytoskeleton organization (GO:0030036)|Arp2/3 complex-mediated actin nucleation (GO:0034314)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	structural constituent of cytoskeleton (GO:0005200)			cervix(1)|large_intestine(1)|lung(2)	4						GAGCTGCCTGTAGGGCAGCTG	0.463																																					p.L58L	Melanoma(136;1596 1789 3041 4830 41075)	Atlas-SNP	.											.	ARPC5	6	.	0			c.A174G						.						132	134	133					1																	183602268		2203	4300	6503	SO:0001819	synonymous_variant	10092	exon2			TGCCTGTAGGGCA	AF017807	CCDS1357.1, CCDS58050.1	1q	2011-07-06	2002-08-29		ENSG00000162704	ENSG00000162704		"Actin related protein 2/3 complex subunits"	708	protein-coding gene	gene with protein product	"Arp2/3 protein complex subunit p16"	604227	"actin related protein 2/3 complex, subunit 5 (16 kD)"			9359840, 9230079	Standard	NM_005717		Approved	p16-Arc, ARC16, dJ127C7.3	uc021pgb.2	O15511	OTTHUMG00000035326	ENST00000359856.6:c.165A>G	chr1.hg19:g.183602268T>C		121.0	0.0		220.0	39.0	NM_001270439	A6NEC4|Q6PG42	Silent	SNP	ENST00000359856.6	hg19	CCDS1357.1																																																																																			.	.		0.463	ARPC5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000085477.1	NM_005717		C	183602268	T	C	183602268	2	2	366	1	0	0	0	0	0	0	0	1	974	1625	57	2		2	ARPC5	1	183602268	Silent	SNP	T	TCGA-ZP-A9D0-01A-11D-A36X-10	2610472	183602268	65648353	4	50886										
CR1	1378	hgsc.bcm.edu	37	chr1	207748949	207748949	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	tttgcctttaggcaccgactCattggtcactcatctgctga	8	12	4	1			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr1:207748949C>T	ENST00000367049.4	+	28	4461	c.4461C>T	c.(4459-4461)ctC>ctT	p.L1487L	CR1_ENST00000367052.1_Silent_p.L1037L|CR1_ENST00000367053.1_Silent_p.L1037L|RP11-78B10.2_ENST00000596003.1_RNA|CR1_ENST00000367051.1_Silent_p.L1037L|RP11-78B10.2_ENST00000597497.1_RNA|CR1_ENST00000400960.2_Silent_p.L1037L	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1037	Sushi 23. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						GGCACCGACTCATTGGTCACT	0.443																																					p.L1487L		Atlas-SNP	.											.	CR1	354	.	0			c.C4461T						.						329	317	321					1																	207748949		1936	4140	6076	SO:0001819	synonymous_variant	1378	exon28			CCGACTCATTGGT	Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"CD molecules", "Blood group antigens", "Complement system"	2334	protein-coding gene	gene with protein product		120620	"complement component (3b/4b) receptor 1, including Knops blood group system"			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.4461C>T	chr1.hg19:g.207748949C>T		281.0	0.0		474.0	97.0	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Silent	SNP	ENST00000367049.4	hg19	CCDS44308.1																																																																																			.	.		0.443	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573		T	207748949	C	T	207748949	2	4	366	1	0	0	0	0	0	0	0	1	3842	813	29	3		3	CR1	1	207748949	Silent	SNP	C	TCGA-ZP-A9D0-01A-11D-A36X-10	24146681	207748949	41501672	5	50887										
AHCTF1	25909	hgsc.bcm.edu	37	chr1	247024559	247024559	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	actggaactgcacattttttAggtgtagtaaatacttctaa	7	6	1	0			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr1:247024559A>C	ENST00000391829.2	-	29	3897	c.3774T>G	c.(3772-3774)ccT>ccG	p.P1258P	AHCTF1_ENST00000470300.1_5'UTR|AHCTF1_ENST00000326225.3_Silent_p.P1267P|AHCTF1_ENST00000366508.1_Silent_p.P1293P			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	1258	Disordered. {ECO:0000250}.|Necessary for nuclear localization. {ECO:0000250}.				cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(6)|cervix(3)|endometrium(8)|kidney(6)|large_intestine(12)|liver(2)|lung(21)|ovary(5)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	74	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			CACATTTTTTAGGTGTAGTAA	0.353																																					p.P1267P	Colon(145;197 1800 4745 15099 26333)	Atlas-SNP	.											.	AHCTF1	187	.	0			c.T3801G						.						30	29	29					1																	247024559		2203	4296	6499	SO:0001819	synonymous_variant	25909	exon29			TTTTTTAGGTGTA		CCDS1629.1, CCDS1629.2	1q44	2008-09-09			ENSG00000153207	ENSG00000153207			24618	protein-coding gene	gene with protein product	"ELYS transcription factor like protein TMBS62"	610853				11952839	Standard	NM_015446		Approved	ELYS	uc001ibv.2	Q8WYP5	OTTHUMG00000040706	ENST00000391829.2:c.3774T>G	chr1.hg19:g.247024559A>C		203.0	0.0		387.0	170.0	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Silent	SNP	ENST00000391829.2	hg19																																																																																				.	.		0.353	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446		C	247024559	A	C	247024559	2	2	366	1	0	0	0	0	0	0	0	1	408	407	15	5		5	AHCTF1	1	247024559	Silent	SNP	A	TCGA-ZP-A9D0-01A-11D-A36X-10	39275610	247024559	2226062	6	50888										
FAM179A	165186	hgsc.bcm.edu	37	chr2	29222198	29222198	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	cccaggaacctcagggccttGtctttgggggaccagcccct	12	15	2	0			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr2:29222198G>C	ENST00000379558.4	+	4	642	c.291G>C	c.(289-291)ttG>ttC	p.L97F	FAM179A_ENST00000403861.2_Missense_Mutation_p.L97F	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	97										breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						TCAGGGCCTTGTCTTTGGGGG	0.612																																					p.L97F		Atlas-SNP	.											.	FAM179A	106	.	0			c.G291C						.						36	41	39					2																	29222198		2198	4296	6494	SO:0001583	missense	165186	exon4			GGCCTTGTCTTTG	AK125239, AK125744	CCDS1769.2	2p23.2	2008-10-30			ENSG00000189350	ENSG00000189350			33715	protein-coding gene	gene with protein product						16344560	Standard	NM_199280		Approved	FLJ43249, LOC165186	uc010ezl.3	Q6ZUX3	OTTHUMG00000128432	ENST00000379558.4:c.291G>C	chr2.hg19:g.29222198G>C	ENSP00000368876:p.Leu97Phe	179.0	0.0		133.0	51.0	NM_199280	Q6ZUF5	Missense_Mutation	SNP	ENST00000379558.4	hg19	CCDS1769.2	.	.	.	.	.	.	.	.	.	.	G	16.79	3.221506	0.58560	.	.	ENSG00000189350	ENST00000379558;ENST00000403861	T;T	0.12147	2.9;2.71	5.73	2.87	0.33458	.	.	.	.	.	T	0.19208	0.0461	L	0.29908	0.895	0.09310	N	1	D;D	0.65815	0.995;0.993	D;P	0.66497	0.944;0.797	T	0.09640	-1.0665	8	.	.	.	.	5.2693	0.15617	0.194:0.2144:0.5916:0.0	.	97;97	F8W8E4;Q6ZUX3	.;F179A_HUMAN	F	97	ENSP00000368876:L97F;ENSP00000384699:L97F	.	L	+	3	2	FAM179A	29075702	0.005000	0.15991	0.008000	0.14137	0.095000	0.18619	0.549000	0.23329	0.771000	0.33359	0.478000	0.44815	TTG	.	.		0.612	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280		C	29222198	G	C	29222198	3	2	366	1	0	0	0	0	1	0	0	0	5510	1368	48	4	301	4	FAM179A	2	29222198	Missense_Mutation	SNP	G	TCGA-ZP-A9D0-01A-11D-A36X-10		29222198	213977175	7	50889										
SFXN5	94097	hgsc.bcm.edu	37	chr2	73250320	73250320	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	atccaaaactggattacctgCttgattttctgtgcactcca	6	11	1	1			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr2:73250320C>T	ENST00000272433.2	-	4	403	c.273G>A	c.(271-273)aaG>aaA	p.K91K	SFXN5_ENST00000474528.1_5'UTR|SFXN5_ENST00000410065.1_Silent_p.K91K	NM_144579.2	NP_653180.1	Q8TD22	SFXN5_HUMAN	sideroflexin 5	91					iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)|citrate transmembrane transporter activity (GO:0015137)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)	9						GGATTACCTGCTTGATTTTCT	0.463																																					p.K91K		Atlas-SNP	.											.	SFXN5	31	.	0			c.G273A						.						75	78	77					2																	73250320		2203	4300	6503	SO:0001819	synonymous_variant	94097	exon4			TACCTGCTTGATT	AY044437	CCDS1922.1	2p13	2008-05-21			ENSG00000144040	ENSG00000144040		"Sideroflexins"	16073	protein-coding gene	gene with protein product		615572				12039050, 12150972	Standard	XM_005264648		Approved	BBG-TCC	uc002siq.3	Q8TD22	OTTHUMG00000129775	ENST00000272433.2:c.273G>A	chr2.hg19:g.73250320C>T		73.0	0.0		39.0	13.0	NM_144579	A8K116|Q494Y3|Q53T29	Silent	SNP	ENST00000272433.2	hg19	CCDS1922.1	.	.	.	.	.	.	.	.	.	.	C	9.185	1.024484	0.19433	.	.	ENSG00000144040	ENST00000411783	.	.	.	5.24	2.34	0.29019	.	.	.	.	.	T	0.54838	0.1883	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44467	-0.9326	4	.	.	.	-23.0405	6.7519	0.23491	0.0:0.7062:0.0:0.2938	.	.	.	.	T	81	.	.	A	-	1	0	SFXN5	73103828	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	1.530000	0.36007	0.297000	0.22615	-0.312000	0.09012	GCA	.	.		0.463	SFXN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251991.1	NM_144579		T	73250320	C	T	73250320	2	4	366	1	0	0	0	0	0	0	0	1	14213	796	28	3		3	SFXN5	2	73250320	Silent	SNP	C	TCGA-ZP-A9D0-01A-11D-A36X-10	44028122	73250320	169949053	8	50890										
CNTNAP5	129684	hgsc.bcm.edu	37	chr2	125555843	125555843	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	cccaggcacccagtcttttgCtctttatcaattcttcttct	4	14	6	0			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr2:125555843C>T	ENST00000431078.1	+	19	3524	c.3160C>T	c.(3160-3162)Ctc>Ttc	p.L1054F		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	1054	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		CAGTCTTTTGCTCTTTATCAA	0.473																																					p.L1054F		Atlas-SNP	.											CNTNAP5,right_upper_lobe,carcinoma,0,1	CNTNAP5	405	.	0			c.C3160T						.						148	145	146					2																	125555843		1970	4152	6122	SO:0001583	missense	129684	exon19			CTTTTGCTCTTTA	AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.3160C>T	chr2.hg19:g.125555843C>T	ENSP00000399013:p.Leu1054Phe	123.0	0.0		108.0	27.0	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Missense_Mutation	SNP	ENST00000431078.1	hg19	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	C	16.72	3.201791	0.58234	.	.	ENSG00000155052	ENST00000431078	D	0.85556	-2.0	5.92	3.04	0.35103	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.156540	0.29376	N	0.012333	D	0.85256	0.5655	M	0.81614	2.55	0.54753	D	0.999981	B	0.30482	0.281	B	0.34931	0.192	T	0.82741	-0.0307	10	0.45353	T	0.12	.	11.0798	0.48053	0.0:0.808:0.0:0.192	.	1054	Q8WYK1	CNTP5_HUMAN	F	1054	ENSP00000399013:L1054F	ENSP00000399013:L1054F	L	+	1	0	CNTNAP5	125272313	1.000000	0.71417	0.998000	0.56505	0.972000	0.66771	1.787000	0.38704	0.786000	0.33708	-0.312000	0.09012	CTC	.	.		0.473	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			T	125555843	C	T	125555843	3	4	366	1	0	0	0	0	1	0	0	0	3652	797	28	3	3234	3	CNTNAP5	2	125555843	Missense_Mutation	SNP	C	TCGA-ZP-A9D0-01A-11D-A36X-10	52305523	125555843	117643530	9	50891										
SCN1A	6323	hgsc.bcm.edu	37	chr2	166852580	166852580	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	cctaattttttcattgcattAtagtatttcttctgttcttc	3	8	4	0			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr2:166852580A>G	ENST00000303395.4	-	24	4523	c.4524T>C	c.(4522-4524)taT>taC	p.Y1508Y	SCN1A_ENST00000423058.2_Silent_p.Y1508Y|AC010127.3_ENST00000595647.1_RNA|AC010127.3_ENST00000597623.1_RNA|SCN1A_ENST00000375405.3_Silent_p.Y1497Y|SCN1A_ENST00000409050.1_Silent_p.Y1480Y			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1508					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TCATTGCATTATAGTATTTCT	0.318																																					p.Y1508Y		Atlas-SNP	.											.	SCN1A	641	.	0			c.T4524C						.						130	124	126					2																	166852580		2202	4300	6502	SO:0001819	synonymous_variant	6323	exon24			TGCATTATAGTAT	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10585	protein-coding gene	gene with protein product		182389	"febrile convulsions 3"	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.4524T>C	chr2.hg19:g.166852580A>G		168.0	0.0		156.0	57.0	NM_001165963	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Silent	SNP	ENST00000303395.4	hg19	CCDS54413.1																																																																																			.	.		0.318	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		G	166852580	A	G	166852580	2	3	366	1	0	0	0	0	0	0	0	1	13929	456	16	2		2	SCN1A	2	166852580	Silent	SNP	A	TCGA-ZP-A9D0-01A-11D-A36X-10	41296737	166852580	76346793	10	50892										
FSIP2	401024	hgsc.bcm.edu	37	chr2	186670241	186670241	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	acttttttcaggagactggtCttccaccttcttttcatttc	5	11	4	1			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr2:186670241C>T	ENST00000424728.1	+	17	16208	c.16208C>T	c.(16207-16209)tCt>tTt	p.S5403F	FSIP2_ENST00000343098.5_Missense_Mutation_p.S5492F			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	5403										NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						GGAGACTGGTCTTCCACCTTC	0.393																																					p.S5492F		Atlas-SNP	.											.	FSIP2	251	.	0			c.C16475T						.						104	95	98					2																	186670241		1850	4087	5937	SO:0001583	missense	401024	exon17			ACTGGTCTTCCAC	AK092099	CCDS54426.1	2q32.1	2010-06-18			ENSG00000188738	ENSG00000188738			21675	protein-coding gene	gene with protein product		615796				14702039	Standard	NM_173651		Approved	FLJ34780	uc002upl.3	Q5CZC0	OTTHUMG00000153874	ENST00000424728.1:c.16208C>T	chr2.hg19:g.186670241C>T	ENSP00000401306:p.Ser5403Phe	231.0	0.0		238.0	89.0	NM_173651	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Missense_Mutation	SNP	ENST00000424728.1	hg19		.	.	.	.	.	.	.	.	.	.	C	11.37	1.617792	0.28801	.	.	ENSG00000188738	ENST00000343098;ENST00000424728	T;T	0.44881	0.91;0.91	5.13	2.07	0.26955	.	.	.	.	.	T	0.22742	0.0549	L	0.27053	0.805	0.25818	N	0.984311	.	.	.	.	.	.	T	0.24012	-1.0172	7	0.08179	T	0.78	.	3.9741	0.09467	0.0:0.563:0.2124:0.2246	.	.	.	.	F	5492;5403	ENSP00000344403:S5492F;ENSP00000401306:S5403F	ENSP00000344403:S5492F	S	+	2	0	FSIP2	186378486	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	0.861000	0.27885	0.720000	0.32209	0.460000	0.39030	TCT	.	.		0.393	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651		T	186670241	C	T	186670241	3	4	366	1	0	0	0	0	1	0	0	0	6083	913	32	3	16541	3	FSIP2	2	186670241	Missense_Mutation	SNP	C	TCGA-ZP-A9D0-01A-11D-A36X-10	19817661	186670241	56529132	11	50893										
PVRL3	25945	hgsc.bcm.edu	37	chr3	110837591	110837591	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	gccatttgcatcgcagccacTggaaaacccgttgcacatat	8	13	0	0			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr3:110837591T>G	ENST00000485303.1	+	3	866	c.591T>G	c.(589-591)acT>acG	p.T197T	PVRL3_ENST00000319792.3_Silent_p.T197T|PVRL3_ENST00000493615.1_Silent_p.T174T	NM_001243286.1|NM_015480.2	NP_001230215.1|NP_056295.1	Q9NQS3	PVRL3_HUMAN	poliovirus receptor-related 3	197	Ig-like C2-type 1.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|fertilization (GO:0009566)|homophilic cell adhesion (GO:0007156)|lens morphogenesis in camera-type eye (GO:0002089)|retina morphogenesis in camera-type eye (GO:0060042)|single organismal cell-cell adhesion (GO:0016337)	apical junction complex (GO:0043296)|cell-cell adherens junction (GO:0005913)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	cell adhesion molecule binding (GO:0050839)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(3)	19						TCGCAGCCACTGGAAAACCCG	0.423																																					p.T197T		Atlas-SNP	.											.	PVRL3	78	.	0			c.T591G						.						60	51	54					3																	110837591		2203	4300	6503	SO:0001819	synonymous_variant	25945	exon3			AGCCACTGGAAAA	AF282874	CCDS2957.1, CCDS58842.1, CCDS58843.1	3q13	2013-01-29			ENSG00000177707	ENSG00000177707		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17664	protein-coding gene	gene with protein product		607147				11024295	Standard	NM_015480		Approved	nectin-3, PPR3, PVRR3, DKFZP566B0846, CDw113, CD113	uc003dxt.2	Q9NQS3	OTTHUMG00000159239	ENST00000485303.1:c.591T>G	chr3.hg19:g.110837591T>G		198.0	0.0		199.0	72.0	NM_001243286	E9PFR0|Q6NVZ3|Q8NC05|Q8WVU4|Q9BVA9|Q9Y412	Silent	SNP	ENST00000485303.1	hg19	CCDS2957.1																																																																																			.	.		0.423	PVRL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354045.1	NM_015480		G	110837591	T	G	110837591	2	3	366	1	0	0	0	0	0	0	0	1	12856	1567	55	5		5	PVRL3	3	110837591	Silent	SNP	T	TCGA-ZP-A9D0-01A-11D-A36X-10		110837591	87184839	12	50894										
DSPP	1834	hgsc.bcm.edu	37	chr4	88537513	88537513	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	gacagcagtgacagcaatgaAagcagcgacagcagtgacag	13	9	0	3	rs112275895		TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr4:88537513A>C	ENST00000282478.7	+	4	3732	c.3699A>C	c.(3697-3699)gaA>gaC	p.E1233D	DSPP_ENST00000399271.1_Missense_Mutation_p.E1233D|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1233	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			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)		acagcaatgaaagcagcgaca	0.547																																					p.E1233D		Atlas-SNP	.											.	DSPP	174	.	0			c.A3699C						.																																			SO:0001583	missense	1834	exon5			CAATGAAAGCAGC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3699A>C	chr4.hg19:g.88537513A>C	ENSP00000282478:p.Glu1233Asp	347.0	0.0		383.0	39.0	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	hg19	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	A	0.010	-1.785366	0.00628	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.88741	-2.42;-2.42	2.61	-5.21	0.02815	.	.	.	.	.	T	0.57213	0.2038	N	0.01048	-1.04	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.57347	-0.7827	9	0.02654	T	1	.	0.7125	0.00926	0.2623:0.1881:0.1298:0.4197	.	1233	Q9NZW4	DSPP_HUMAN	D	1233	ENSP00000382213:E1233D;ENSP00000282478:E1233D	ENSP00000282478:E1233D	E	+	3	2	DSPP	88756537	0.003000	0.15002	0.000000	0.03702	0.000000	0.00434	-2.769000	0.00780	-2.252000	0.00699	-3.496000	0.00033	GAA	.	A|0.500;C|0.500		0.547	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		C	88537513	A	C	88537513	3	2	366	1	0	0	0	0	1	0	0	0	4784	11	1	5	3713	5	DSPP	4	88537513	Missense_Mutation	SNP	A	TCGA-ZP-A9D0-01A-11D-A36X-10		88537513	102616763	13	50895										
PITX2	5308	hgsc.bcm.edu	37	chr4	111543434	111543434	+	Intron	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	gcggcctccgggctggaggtGtcggagatggtgtgcacctc	18	11	0	1			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr4:111543434G>T	ENST00000354925.2	-	6	1890				PITX2_ENST00000355080.5_Intron|PITX2_ENST00000394598.2_Intron|PITX2_ENST00000394595.3_Intron|PITX2_ENST00000306732.3_Missense_Mutation_p.D61E|PITX2_ENST00000557119.2_Missense_Mutation_p.D61E|PITX2_ENST00000556049.1_5'Flank	NM_001204397.1	NP_001191326.1	Q99697	PITX2_HUMAN	paired-like homeodomain 2						atrial cardiac muscle tissue morphogenesis (GO:0055009)|atrioventricular valve development (GO:0003171)|camera-type eye development (GO:0043010)|cardiac neural crest cell migration involved in outflow tract morphogenesis (GO:0003253)|cell proliferation involved in outflow tract morphogenesis (GO:0061325)|deltoid tuberosity development (GO:0035993)|determination of left/right symmetry (GO:0007368)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic hindlimb morphogenesis (GO:0035116)|endodermal digestive tract morphogenesis (GO:0061031)|extraocular skeletal muscle development (GO:0002074)|female gonad development (GO:0008585)|hair cell differentiation (GO:0035315)|hypothalamus cell migration (GO:0021855)|in utero embryonic development (GO:0001701)|iris morphogenesis (GO:0061072)|left lung morphogenesis (GO:0060460)|left/right axis specification (GO:0070986)|male gonad development (GO:0008584)|myoblast fusion (GO:0007520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|odontogenesis (GO:0042476)|odontogenesis of dentin-containing tooth (GO:0042475)|patterning of blood vessels (GO:0001569)|positive regulation of DNA binding (GO:0043388)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prolactin secreting cell differentiation (GO:0060127)|pulmonary myocardium development (GO:0003350)|pulmonary vein morphogenesis (GO:0060577)|regulation of cell migration (GO:0030334)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to hormone (GO:0009725)|response to vitamin A (GO:0033189)|somatotropin secreting cell differentiation (GO:0060126)|spleen development (GO:0048536)|subthalamic nucleus development (GO:0021763)|superior vena cava morphogenesis (GO:0060578)|vascular smooth muscle cell differentiation (GO:0035886)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell development (GO:0055015)|ventricular septum morphogenesis (GO:0060412)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin DNA binding (GO:0031490)|phosphoprotein binding (GO:0051219)|protein homodimerization activity (GO:0042803)|ribonucleoprotein complex binding (GO:0043021)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|endometrium(3)|large_intestine(1)|lung(5)	10		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00222)		GGCTGGAGGTGTCGGAGATGG	0.687																																					p.D61E		Atlas-SNP	.											.	PITX2	73	.	0			c.C183A						.						16	17	17					4																	111543434		2189	4271	6460	SO:0001627	intron_variant	5308	exon1			GGAGGTGTCGGAG	U69961	CCDS3692.1, CCDS3693.1, CCDS3694.1	4q25	2011-06-20	2007-07-12		ENSG00000164093	ENSG00000164093		"Homeoboxes / PRD class"	9005	protein-coding gene	gene with protein product		601542	"paired-like homeodomain transcription factor 2"	IRID2, IHG2, RIEG, RIEG1, RGS		9539779, 7581385	Standard	NM_000325		Approved	IGDS, RS, Brx1, Otlx2, ARP1	uc021xqr.1	Q99697	OTTHUMG00000132837	ENST00000354925.2:c.185-909C>A	chr4.hg19:g.111543434G>T		205.0	0.0		182.0	79.0	NM_000325	A8K6C6|B2RA02|B3KXS0|O60578|O60579|O60580|Q3KQX9|Q9BY17	Missense_Mutation	SNP	ENST00000354925.2	hg19	CCDS3692.1	.	.	.	.	.	.	.	.	.	.	G	16.25	3.069630	0.55539	.	.	ENSG00000164093	ENST00000306732	D	0.91124	-2.79	5.17	4.32	0.51571	.	0.345833	0.33092	N	0.005290	T	0.79563	0.4467	.	.	.	0.80722	D	1	B	0.13145	0.007	B	0.17979	0.02	T	0.70905	-0.4745	9	0.02654	T	1	.	12.429	0.55563	0.084:0.0:0.916:0.0	.	61	Q99697-2	.	E	61	ENSP00000304169:D61E	ENSP00000304169:D61E	D	-	3	2	PITX2	111762883	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.169000	0.71913	1.138000	0.42230	0.655000	0.94253	GAC	.	.		0.687	PITX2-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256308.2			T	111543434	G	T	111543434	1	4	366	0	1	0	0	0	0	0	0	0	11964	1368	48	3		3	PITX2	4	111543434	Intron	SNP	G	TCGA-ZP-A9D0-01A-11D-A36X-10	23005921	111543434	79610842	14	50896										
RASA1	5921	hgsc.bcm.edu	37	chr5	86668007	86668007	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	ggacatccaataaacgccttCgtcaggtgaagcttaatttt	8	9	1	1			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr5:86668007C>G	ENST00000274376.6	+	13	2335	c.1771C>G	c.(1771-1773)Cgt>Ggt	p.R591G	RASA1_ENST00000506290.1_Missense_Mutation_p.R425G|RASA1_ENST00000456692.2_Missense_Mutation_p.R414G|RASA1_ENST00000512763.1_Missense_Mutation_p.R424G	NM_002890.2	NP_002881.1	P20936	RASA1_HUMAN	RAS p21 protein activator (GTPase activating protein) 1	591	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				blood vessel morphogenesis (GO:0048514)|embryo development (GO:0009790)|intracellular signal transduction (GO:0035556)|mitotic cytokinesis (GO:0000281)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|regulation of RNA metabolic process (GO:0051252)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|ruffle (GO:0001726)	glycoprotein binding (GO:0001948)|GTPase binding (GO:0051020)|potassium channel inhibitor activity (GO:0019870)|Ras GTPase activator activity (GO:0005099)|receptor binding (GO:0005102)			NS(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(12)|lung(13)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	48		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		TAAACGCCTTCGTCAGGTGAA	0.353																																					p.R591G		Atlas-SNP	.											.	RASA1	213	.	0			c.C1771G						.						85	86	86					5																	86668007		2203	4300	6503	SO:0001583	missense	5921	exon13			CGCCTTCGTCAGG		CCDS34200.1, CCDS47243.1	5q13	2013-02-14			ENSG00000145715	ENSG00000145715		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	9871	protein-coding gene	gene with protein product	"capillary malformation-arteriovenous malformation"	139150		RASA		15917201	Standard	NM_022650		Approved	GAP, CM-AVM, p120GAP, p120RASGAP	uc003kiw.3	P20936	OTTHUMG00000162605	ENST00000274376.6:c.1771C>G	chr5.hg19:g.86668007C>G	ENSP00000274376:p.Arg591Gly	148.0	0.0		158.0	48.0	NM_002890	B2R6W3|Q9UDI1	Missense_Mutation	SNP	ENST00000274376.6	hg19	CCDS34200.1	.	.	.	.	.	.	.	.	.	.	C	19.36	3.812121	0.70797	.	.	ENSG00000145715	ENST00000274376;ENST00000534133;ENST00000456692;ENST00000512763;ENST00000506290	D;T;T;T	0.81821	-1.54;-1.44;-1.43;-1.44	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	D	0.89100	0.6619	M	0.71581	2.175	0.80722	D	1	D;D;D;D;D	0.76494	0.993;0.999;0.993;0.996;0.986	P;D;P;D;P	0.67382	0.87;0.951;0.87;0.939;0.775	D	0.89999	0.4113	10	0.87932	D	0	.	19.1952	0.93684	0.0:1.0:0.0:0.0	.	425;424;425;414;591	E9PGC0;B4DTL2;B4DTX4;P20936-2;P20936	.;.;.;.;RASA1_HUMAN	G	591;624;414;424;425	ENSP00000274376:R591G;ENSP00000411221:R414G;ENSP00000422008:R424G;ENSP00000420905:R425G	ENSP00000274376:R591G	R	+	1	0	RASA1	86703763	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.486000	0.53215	2.531000	0.85337	0.650000	0.86243	CGT	.	.		0.353	RASA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369729.1	NM_002890		G	86668007	C	G	86668007	3	3	366	1	0	0	0	0	1	0	0	0	13075	884	31	4	1833	4	RASA1	5	86668007	Missense_Mutation	SNP	C	TCGA-ZP-A9D0-01A-11D-A36X-10		86668007	94247253	15	50897										
RFESD	317671	hgsc.bcm.edu	37	chr5	94991973	94991973	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	taagtgtgactctgatttttAtgccactggagacttcaaag	9	7	2	3			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr5:94991973A>T	ENST00000311364.4	+	5	1851	c.434A>T	c.(433-435)tAt>tTt	p.Y145F	SPATA9_ENST00000477047.2_Intron|RFESD_ENST00000513950.2_3'UTR|RFESD_ENST00000458310.1_Missense_Mutation_p.Y198F|RFESD_ENST00000380005.4_Missense_Mutation_p.Y198F	NM_173362.3	NP_775498.1	Q8TAC1	RFESD_HUMAN	Rieske (Fe-S) domain containing	145							2 iron, 2 sulfur cluster binding (GO:0051537)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)			autonomic_ganglia(2)|endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(1)	6		all_cancers(142;0.000215)|all_epithelial(76;7.43e-07)|all_lung(232;0.0318)|Lung NSC(167;0.041)|Ovarian(225;0.051)|Colorectal(57;0.162)		all cancers(79;5.94e-17)		TCTGATTTTTATGCCACTGGA	0.308																																					p.Y198F		Atlas-SNP	.											.	RFESD	22	.	0			c.A593T						.						60	70	66					5																	94991973		2203	4300	6503	SO:0001583	missense	317671	exon6			ATTTTTATGCCAC	BC035110	CCDS4075.1, CCDS47248.1	5q15	2010-12-07			ENSG00000175449	ENSG00000175449			29587	protein-coding gene	gene with protein product						12477932	Standard	NM_173362		Approved		uc003klg.3	Q8TAC1	OTTHUMG00000121168	ENST00000311364.4:c.434A>T	chr5.hg19:g.94991973A>T	ENSP00000309229:p.Tyr145Phe	84.0	0.0		71.0	26.0	NM_001131066	J3KPH1	Missense_Mutation	SNP	ENST00000311364.4	hg19	CCDS4075.1	.	.	.	.	.	.	.	.	.	.	A	16.70	3.196803	0.58126	.	.	ENSG00000175449	ENST00000380005;ENST00000311364;ENST00000458310	.	.	.	5.44	5.44	0.79542	.	0.056927	0.64402	D	0.000001	T	0.58090	0.2098	M	0.67517	2.055	0.80722	D	1	B	0.22683	0.073	B	0.18561	0.022	T	0.55302	-0.8162	8	.	.	.	-5.8305	11.212	0.48804	0.8627:0.0:0.0:0.1373	.	145	Q8TAC1	RFESD_HUMAN	F	198;145;198	.	.	Y	+	2	0	RFESD	95017729	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.793000	0.55484	2.070000	0.61991	0.383000	0.25322	TAT	.	.		0.308	RFESD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241654.1	NM_173362		T	94991973	A	T	94991973	3	4	366	1	0	0	0	0	1	0	0	0	13264	449	16	4	611	4	RFESD	5	94991973	Missense_Mutation	SNP	A	TCGA-ZP-A9D0-01A-11D-A36X-10	8323966	94991973	85923287	16	50898										
FTMT	94033	hgsc.bcm.edu	37	chr5	121187819	121187819	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	ccccctggccgcagccgcctCctcccgggaccctaccgggc	11	23	0	0			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr5:121187819C>A	ENST00000321339.1	+	1	170	c.161C>A	c.(160-162)tCc>tAc	p.S54Y		NM_177478.1	NP_803431.1	Q8N4E7	FTMT_HUMAN	ferritin mitochondrial	54					cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)|positive regulation of cell proliferation (GO:0008284)|positive regulation of lyase activity (GO:0051349)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of transferase activity (GO:0051347)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ferric iron binding (GO:0008199)|ferroxidase activity (GO:0004322)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	33		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	Epithelial(69;0.000171)|OV - Ovarian serous cystadenocarcinoma(64;0.000188)|all cancers(49;0.0027)		GCAGCCGCCTCCTCCCGGGAC	0.766																																					p.S54Y		Atlas-SNP	.											.	FTMT	71	.	0			c.C161A						.						7	9	9					5																	121187819		2142	4198	6340	SO:0001583	missense	94033	exon1			CCGCCTCCTCCCG	BC034419	CCDS4128.1	5q23.1	2008-02-05			ENSG00000181867	ENSG00000181867			17345	protein-coding gene	gene with protein product		608847				11323407	Standard	NM_177478		Approved	MtF	uc003kss.3	Q8N4E7	OTTHUMG00000128912	ENST00000321339.1:c.161C>A	chr5.hg19:g.121187819C>A	ENSP00000313691:p.Ser54Tyr	43.0	0.0		52.0	21.0	NM_177478		Missense_Mutation	SNP	ENST00000321339.1	hg19	CCDS4128.1	.	.	.	.	.	.	.	.	.	.	C	5.474	0.272473	0.10349	.	.	ENSG00000181867	ENST00000321339	T	0.64991	-0.13	3.23	1.32	0.21799	.	.	.	.	.	T	0.38161	0.1030	L	0.27053	0.805	0.09310	N	1	B	0.30406	0.278	B	0.28385	0.089	T	0.29181	-1.0020	9	0.02654	T	1	.	5.2817	0.15678	0.0:0.5856:0.0:0.4144	.	54	Q8N4E7	FTMT_HUMAN	Y	54	ENSP00000313691:S54Y	ENSP00000313691:S54Y	S	+	2	0	FTMT	121215718	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.239000	0.18023	0.337000	0.23665	0.655000	0.94253	TCC	.	.		0.766	FTMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250884.1	NM_177478		A	121187819	C	A	121187819	3	1	366	1	0	0	0	0	1	0	0	0	6093	855	30	3	163	3	FTMT	5	121187819	Missense_Mutation	SNP	C	TCGA-ZP-A9D0-01A-11D-A36X-10	26195846	121187819	59727441	17	50899										
ANKHD1	54882	hgsc.bcm.edu	37	chr5	139908010	139908010	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	caacgttatctacgttccagCccgctaataaacttaataag	5	11	1	0			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr5:139908010C>T	ENST00000360839.2	+	29	5633	c.5479C>T	c.(5479-5481)Ccc>Tcc	p.P1827S	SNORD45_ENST00000363181.1_RNA|ANKHD1_ENST00000297183.6_Missense_Mutation_p.P1827S|ANKHD1-EIF4EBP3_ENST00000532219.1_Missense_Mutation_p.P1827S|ANKHD1_ENST00000544120.1_Missense_Mutation_p.P210S	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	1827						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TACGTTCCAGCCCGCTAATAA	0.438																																					p.P1827S		Atlas-SNP	.											.	ANKHD1	233	.	0			c.C5479T						.						150	147	148					5																	139908010		2203	4300	6503	SO:0001583	missense	54882	exon29			TTCCAGCCCGCTA	AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503		"Ankyrin repeat domain containing"	24714	protein-coding gene	gene with protein product		610500				10470851, 11230166, 16098192	Standard	NM_017747		Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.5479C>T	chr5.hg19:g.139908010C>T	ENSP00000354085:p.Pro1827Ser	151.0	0.0		143.0	58.0	NM_017747	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Missense_Mutation	SNP	ENST00000360839.2	hg19	CCDS4225.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.75|10.75	1.438920|1.438920	0.25900|0.25900	.|.	.|.	ENSG00000131503|ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000254996	ENST00000435794;ENST00000432301|ENST00000360839;ENST00000297183;ENST00000253810;ENST00000431508;ENST00000536646;ENST00000433049;ENST00000544120;ENST00000532219	.|T;T;T;T;T;T	.|0.63096	.|0.02;-0.02;2.12;2.17;1.77;-0.02	4.99|4.99	3.2|3.2	0.36748|0.36748	.|.	.|0.366825	.|0.28659	.|N	.|0.014565	T|T	0.44891|0.44891	0.1315|0.1315	L|L	0.28274|0.28274	0.84|0.84	0.36827|0.36827	D|D	0.886704|0.886704	.|B;B;B;B;B	.|0.02656	.|0.0;0.0;0.0;0.0;0.0	.|B;B;B;B;B	.|0.04013	.|0.001;0.0;0.001;0.001;0.001	T|T	0.43228|0.43228	-0.9404|-0.9404	5|10	.|0.56958	.|D	.|0.05	.|.	6.5559|6.5559	0.22460|0.22460	0.0:0.5672:0.2815:0.1512|0.0:0.5672:0.2815:0.1512	.|.	.|210;257;1827;1827;1827	.|Q8IWG5;Q9H059;E9PF56;Q8IWZ2;Q8IWZ3	.|.;.;.;.;ANKH1_HUMAN	V|S	317;277|1827;1827;1827;483;262;349;210;1827	.|ENSP00000354085:P1827S;ENSP00000297183:P1827S;ENSP00000393204:P483S;ENSP00000390034:P349S;ENSP00000437687:P210S;ENSP00000432016:P1827S	.|ENSP00000432016:P1827S	A|P	+|+	2|1	0|0	ANKHD1|ANKHD1-EIF4EBP3;ANKHD1	139888194|139888194	0.995000|0.995000	0.38212|0.38212	0.998000|0.998000	0.56505|0.56505	0.914000|0.914000	0.54420|0.54420	0.506000|0.506000	0.22658|0.22658	0.687000|0.687000	0.31509|0.31509	0.655000|0.655000	0.94253|0.94253	GCC|CCC	.	.		0.438	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747		T	139908010	C	T	139908010	3	4	366	1	0	0	0	0	1	0	0	0	628	739	26	3	5699	3	ANKHD1	5	139908010	Missense_Mutation	SNP	C	TCGA-ZP-A9D0-01A-11D-A36X-10	18720191	139908010	41007250	18	50900										
PCDHGA11	56105	hgsc.bcm.edu	37	chr5	140801283	140801283	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	aatgctagggatccagatgtGggcgtgaactccctccagag	13	10	0	3			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr5:140801283G>A	ENST00000398587.2	+	1	522	c.489G>A	c.(487-489)gtG>gtA	p.V163V	PCDHGA8_ENST00000398604.2_Intron|PCDHGA11_ENST00000518882.1_Silent_p.V163V|PCDHGA3_ENST00000253812.6_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron	NM_018914.2|NM_032092.1	NP_061737.1|NP_114481.1	Q9Y5H2	PCDGB_HUMAN	protocadherin gamma subfamily A, 11	163	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(8)|kidney(3)|large_intestine(9)|lung(22)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATCCAGATGTGGGCGTGAACT	0.542																																					p.V163V		Atlas-SNP	.											.	PCDHGA11	128	.	0			c.G489A						.						35	37	36					5																	140801283		1951	4156	6107	SO:0001819	synonymous_variant	56105	exon1			AGATGTGGGCGTG	AF152505	CCDS47294.1, CCDS54930.1, CCDS75345.1	5q31	2010-01-26			ENSG00000253873	ENSG00000253873		"Cadherins / Protocadherins : Clustered"	8698	other	protocadherin		606298				10380929	Standard	NM_018914		Approved	PCDH-GAMMA-A11		Q9Y5H2	OTTHUMG00000164055	ENST00000398587.2:c.489G>A	chr5.hg19:g.140801283G>A		125.0	0.0		124.0	35.0	NM_032091	B7ZVY8|Q9Y5D8|Q9Y5D9	Silent	SNP	ENST00000398587.2	hg19	CCDS47294.1																																																																																			.	.		0.542	PCDHGA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376974.1	NM_018914		A	140801283	G	A	140801283	2	1	366	1	0	0	0	0	0	0	0	1	11561	1335	47	3		3	PCDHGA11	5	140801283	Silent	SNP	G	TCGA-ZP-A9D0-01A-11D-A36X-10	893273	140801283	40113977	19	50901										
GALNT10	55568	hgsc.bcm.edu	37	chr5	153570579	153570579	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	gcggcggtggcgccggcggcGggacaggtgagtccccccgt	20	14	0	1			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr5:153570579G>A	ENST00000297107.6	+	1	290	c.153G>A	c.(151-153)gcG>gcA	p.A51A	MFAP3_ENST00000519325.1_Intron|GALNT10_ENST00000377661.2_Silent_p.A51A|GALNT10_ENST00000425427.2_Silent_p.A51A	NM_198321.3	NP_938080.1	Q86SR1	GLT10_HUMAN	polypeptide N-acetylgalactosaminyltransferase 10	51					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(12)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	32	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)|all_hematologic(541;0.21)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)			cgccggcggcgggACAGGTGA	0.697																																					p.A51A		Atlas-SNP	.											.	GALNT10	70	.	0			c.G153A						.						2	3	3					5																	153570579		1372	2906	4278	SO:0001819	synonymous_variant	55568	exon1			GGCGGCGGGACAG	AK023782	CCDS4325.1	5q34	2014-03-13	2014-03-13		ENSG00000164574	ENSG00000164574	2.4.1.41	"Glycosyltransferase family 2 domain containing"	19873	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 10"	608043	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 10 (GalNAc-T10)"			12417297	Standard	NM_198321		Approved	GalNAc-T10	uc003lvh.3	Q86SR1	OTTHUMG00000130145	ENST00000297107.6:c.153G>A	chr5.hg19:g.153570579G>A		54.0	0.0		38.0	11.0	NM_198321	B3KXC9|Q6IN56|Q86VP8|Q8IXJ2|Q8TEJ2|Q96IV2|Q9H8E1|Q9Y4M4	Silent	SNP	ENST00000297107.6	hg19	CCDS4325.1																																																																																			.	.		0.697	GALNT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252453.1	NM_198321		A	153570579	G	A	153570579	2	1	366	1	0	0	0	0	0	0	0	1	6216	1103	39	1		1	GALNT10	5	153570579	Silent	SNP	G	TCGA-ZP-A9D0-01A-11D-A36X-10	12769296	153570579	27344681	20	50902										
ERGIC1	57222	hgsc.bcm.edu	37	chr5	172359459	172359459	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	ccctggcctcccacgactacAtcctgaagattgtgcccacg	8	17	0	2	rs140909162		TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr5:172359459A>C	ENST00000393784.3	+	8	701	c.562A>C	c.(562-564)Atc>Ctc	p.I188L		NM_001031711.2	NP_001026881.1	Q969X5	ERGI1_HUMAN	endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1	188					ER to Golgi vesicle-mediated transport (GO:0006888)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(2)	9	Renal(175;0.000159)|Lung NSC(126;0.00344)|all_lung(126;0.00594)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CCACGACTACATCCTGAAGAT	0.597											OREG0017050	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I188L		Atlas-SNP	.											.	ERGIC1	35	.	0			c.A562C						.	A	LEU/ILE	0,4406		0,0,2203	71	59	63		562	4.9	1	5	dbSNP_134	63	1,8599	1.2+/-3.3	0,1,4299	no	missense	ERGIC1	NM_001031711.2	5	0,1,6502	CC,CA,AA		0.0116,0.0,0.0077	benign	188/291	172359459	1,13005	2203	4300	6503	SO:0001583	missense	57222	exon8			GACTACATCCTGA	AF267855	CCDS34292.1	5q35.1	2009-11-06			ENSG00000113719	ENSG00000113719			29205	protein-coding gene	gene with protein product						10574461, 15308636	Standard	NM_001031711		Approved	ERGIC32, ERGIC-32, KIAA1181, NET24	uc003mbw.4	Q969X5	OTTHUMG00000130520	ENST00000393784.3:c.562A>C	chr5.hg19:g.172359459A>C	ENSP00000377374:p.Ile188Leu	72.0	0.0	237	65.0	25.0	NM_001031711	Q9H0L0|Q9H2J2|Q9ULN9	Missense_Mutation	SNP	ENST00000393784.3	hg19	CCDS34292.1	.	.	.	.	.	.	.	.	.	.	A	18.22	3.576391	0.65878	0.0	1.16E-4	ENSG00000113719	ENST00000393784	.	.	.	4.9	4.9	0.64082	Domain of unknown function DUF1692 (1);	0.046408	0.85682	D	0.000000	T	0.50667	0.1629	L	0.50919	1.6	0.80722	D	1	B;B	0.28178	0.202;0.201	B;B	0.29942	0.109;0.081	T	0.54241	-0.8323	9	0.62326	D	0.03	-27.4274	8.8988	0.35481	0.9152:0.0:0.0848:0.0	.	133;188	B4E0N6;Q969X5	.;ERGI1_HUMAN	L	188	.	ENSP00000377374:I188L	I	+	1	0	ERGIC1	172292065	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.273000	0.78527	1.844000	0.53588	0.533000	0.62120	ATC	.	A|1.000;C|0.000		0.597	ERGIC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252938.3	NM_020462		C	172359459	A	C	172359459	3	2	366	1	0	0	0	0	1	0	0	0	5225	217	8	5	592	5	ERGIC1	5	172359459	Missense_Mutation	SNP	A	TCGA-ZP-A9D0-01A-11D-A36X-10	18788880	172359459	8555801	21	50903										
B4GALT7	11285	hgsc.bcm.edu	37	chr5	177036620	177036620	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	ccgcactgccctgtctgtggGcggggccccctgcactgtcc	13	18	1	0			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr5:177036620G>A	ENST00000029410.5	+	6	1019	c.908G>A	c.(907-909)gGc>gAc	p.G303D	RP11-1277A3.1_ENST00000499900.2_RNA	NM_007255.2	NP_009186.1	Q9UBV7	B4GT7_HUMAN	xylosylprotein beta 1,4-galactosyltransferase, polypeptide 7	303					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|chondroitin sulfate metabolic process (GO:0030204)|extracellular fibril organization (GO:0043206)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|negative regulation of fibroblast proliferation (GO:0048147)|protein N-linked glycosylation (GO:0006487)|proteoglycan metabolic process (GO:0006029)|small molecule metabolic process (GO:0044281)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|galactosyltransferase activity (GO:0008378)|manganese ion binding (GO:0030145)|xylosylprotein 4-beta-galactosyltransferase activity (GO:0046525)			endometrium(2)|large_intestine(1)|lung(1)|pancreas(1)|skin(1)|urinary_tract(1)	7	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTGTCTGTGGGCGGGGCCCCC	0.592																																					p.G303D		Atlas-SNP	.											.	B4GALT7	21	.	0			c.G908A						.						80	77	78					5																	177036620		2203	4300	6503	SO:0001583	missense	11285	exon6			CTGTGGGCGGGGC	AB028600	CCDS4429.1	5q35.1-q35.3	2013-02-19	2012-07-18		ENSG00000027847	ENSG00000027847		"Beta 4-glycosyltransferases"	930	protein-coding gene	gene with protein product	"galactosyltransferase I"	604327				10438455, 10473568	Standard	NM_007255		Approved	XGALT-1, beta4Gal-T7	uc003mhy.3	Q9UBV7	OTTHUMG00000130851	ENST00000029410.5:c.908G>A	chr5.hg19:g.177036620G>A	ENSP00000029410:p.Gly303Asp	137.0	0.0		127.0	48.0	NM_007255	B3KN39|Q9UHN2	Missense_Mutation	SNP	ENST00000029410.5	hg19	CCDS4429.1	.	.	.	.	.	.	.	.	.	.	.	4.285	0.052114	0.08291	.	.	ENSG00000027847	ENST00000029410;ENST00000541139	T	0.69040	-0.37	5.21	0.886	0.19194	.	0.362657	0.34362	N	0.004032	T	0.47002	0.1422	N	0.21097	0.63	0.39543	D	0.968851	B	0.06786	0.001	B	0.06405	0.002	T	0.47522	-0.9111	10	0.02654	T	1	-14.3041	16.3216	0.82953	0.0:0.4968:0.5032:0.0	.	303	Q9UBV7	B4GT7_HUMAN	D	303;189	ENSP00000029410:G303D	ENSP00000029410:G303D	G	+	2	0	B4GALT7	176969226	0.996000	0.38824	0.979000	0.43373	0.889000	0.51656	2.345000	0.44018	0.228000	0.21019	0.561000	0.74099	GGC	.	.		0.592	B4GALT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253421.1	NM_007255		A	177036620	G	A	177036620	3	1	366	1	0	0	0	0	1	0	0	0	1276	1203	42	3	930	3	B4GALT7	5	177036620	Missense_Mutation	SNP	G	TCGA-ZP-A9D0-01A-11D-A36X-10	4677161	177036620	3878640	22	50904										
HSF2	3298	hgsc.bcm.edu	37	chr6	122744789	122744789	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	gaggacttccaggccatgctAtcaggaagacaatttagcat	10	9	1	1	rs201391717		TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr6:122744789A>G	ENST00000368455.4	+	10	1326	c.1134A>G	c.(1132-1134)ctA>ctG	p.L378L	HSF2_ENST00000452194.1_Silent_p.L378L	NM_004506.3	NP_004497.1	Q03933	HSF2_HUMAN	heat shock transcription factor 2	378	Hydrophobic repeat HR-C.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to stress (GO:0006950)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding (GO:0001162)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			large_intestine(4)|lung(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				OV - Ovarian serous cystadenocarcinoma(136;0.00371)|all cancers(137;0.0299)|GBM - Glioblastoma multiforme(226;0.0586)		AGGCCATGCTATCAGGAAGAC	0.348																																					p.L378L		Atlas-SNP	.											.	HSF2	43	.	0			c.A1134G						.						144	130	135					6																	122744789		2203	4300	6503	SO:0001819	synonymous_variant	3298	exon10			CATGCTATCAGGA	M65217	CCDS5124.1, CCDS47470.1	6q22	2008-08-29			ENSG00000025156	ENSG00000025156			5225	protein-coding gene	gene with protein product		140581				1871106	Standard	NM_004506		Approved		uc003pyu.2	Q03933	OTTHUMG00000016216	ENST00000368455.4:c.1134A>G	chr6.hg19:g.122744789A>G		88.0	0.0		78.0	29.0	NM_004506	B4DGJ4|Q0VAH9|Q2M1K4|Q9H445	Silent	SNP	ENST00000368455.4	hg19	CCDS5124.1																																																																																			.	A|1.000;C|0.000		0.348	HSF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043520.1	NM_004506		G	122744789	A	G	122744789	2	3	366	1	0	0	0	0	0	0	0	1	7405	436	16	2		2	HSF2	6	122744789	Silent	SNP	A	TCGA-ZP-A9D0-01A-11D-A36X-10		122744789	48370278	23	50905										
NOS3	4846	hgsc.bcm.edu	37	chr7	150710398	150710405	+	Frame_Shift_Del	DEL	GAACGCCC	GAACGCCC	-													0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	ctctaccgcgacgaggtgcaGaacgcccagcagcgcggggt					rs141415941		TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	GAACGCCC	GAACGCCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr7:150710398_150710405delGAACGCCC	ENST00000297494.3	+	25	3543_3550	c.3186_3193delGAACGCCC	c.(3184-3195)cagaacgcccagfs	p.QNAQ1062fs	NOS3_ENST00000477227.1_3'UTR|ATG9B_ENST00000444312.1_3'UTR|ATG9B_ENST00000605938.1_3'UTR|ATG9B_ENST00000377974.2_3'UTR|NOS3_ENST00000461406.1_Frame_Shift_Del_p.QNAQ856fs|ATG9B_ENST00000494791.1_5'UTR	NM_000603.4	NP_000594.2	P60323	NANO3_HUMAN	nitric oxide synthase 3 (endothelial cell)	0					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|oogenesis (GO:0048477)|regulation of cell cycle (GO:0051726)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(11)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	50	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		ACGAGGTGCAGAACGCCCAGCAGCGCGG	0.62											OREG0018443	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.1062_1064del		Atlas-INDEL	.											.	NOS3	131	.	0			c.3185_3192del						.																																			SO:0001589	frameshift_variant	4846	exon25			.		CCDS5912.1, CCDS55182.1, CCDS55183.1	7q36	2007-02-15			ENSG00000164867	ENSG00000164867	1.14.13.39		7876	protein-coding gene	gene with protein product	"endothelial nitric oxide synthase"	163729				1379542	Standard	NM_000603		Approved	ECNOS, eNOS	uc003wif.3	P29474	OTTHUMG00000158343	ENST00000297494.3:c.3186_3193delGAACGCCC	chr7.hg19:g.150710398_150710405delGAACGCCC	ENSP00000297494:p.Gln1062fs	70.0	0.0	1734	52.0	15.0	NM_000603	Q495E5	Frame_Shift_Del	DEL	ENST00000297494.3	hg19	CCDS5912.1																																																																																			.	.		0.62	NOS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350750.2	NM_000603		-	150710405	GAACGCCC	-	150710398	7	5	366	1	0	1	0	1	0	0	0	0	10553	933	33	0	3562	0	NOS3	7	150710398	Frame_Shift_Del	DEL	GAACGCCC	TCGA-ZP-A9D0-01A-11D-A36X-10		150710398	8428265	24	50906										
PRKAG2	51422	hgsc.bcm.edu	37	chr7	151329170	151329170	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	ctcaccttcgtcctcgaactCcagcttctccagcatgccgg	7	18	2	0	rs397517281		TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr7:151329170C>A	ENST00000287878.4	-	5	1243	c.739G>T	c.(739-741)Gag>Tag	p.E247*	PRKAG2_ENST00000418337.2_Nonsense_Mutation_p.E6*|PRKAG2_ENST00000392801.2_Nonsense_Mutation_p.E203*|PRKAG2_ENST00000433631.2_Nonsense_Mutation_p.E123*|PRKAG2_ENST00000492843.1_Nonsense_Mutation_p.E123*	NM_016203.3	NP_057287.2	Q9UGJ0	AAKG2_HUMAN	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	247					ATP biosynthetic process (GO:0006754)|carnitine shuttle (GO:0006853)|cell cycle arrest (GO:0007050)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|glycogen metabolic process (GO:0005977)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase activity (GO:0045860)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of fatty acid metabolic process (GO:0019217)|regulation of fatty acid oxidation (GO:0046320)|regulation of glucose import (GO:0046324)|regulation of glycolytic process (GO:0006110)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)	ADP binding (GO:0043531)|AMP binding (GO:0016208)|ATP binding (GO:0005524)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|phosphorylase kinase regulator activity (GO:0008607)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|upper_aerodigestive_tract(1)	26	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)	Acetylsalicylic acid(DB00945)	TCCTCGAACTCCAGCTTCTCC	0.771																																					p.E247X		Atlas-SNP	.											.	PRKAG2	86	.	0			c.G739T						.						7	10	9					7																	151329170		2093	4133	6226	SO:0001587	stop_gained	51422	exon5			CGAACTCCAGCTT	AF087875	CCDS5928.1, CCDS43683.1, CCDS47752.1	7q35-q36	2014-09-17			ENSG00000106617	ENSG00000106617			9386	protein-coding gene	gene with protein product	"AMPK gamma2"	602743				8557660, 8621499	Standard	NM_024429		Approved	AAKG, AAKG2, H91620p, WPWS, CMH6	uc003wkk.3	Q9UGJ0	OTTHUMG00000157324	ENST00000287878.4:c.739G>T	chr7.hg19:g.151329170C>A	ENSP00000287878:p.Glu247*	54.0	0.0		47.0	9.0	NM_016203	Q53Y07|Q6NUI0|Q75MP4|Q9NUZ9|Q9UDN8|Q9ULX8	Nonsense_Mutation	SNP	ENST00000287878.4	hg19	CCDS5928.1	.	.	.	.	.	.	.	.	.	.	C	41	8.792104	0.98956	.	.	ENSG00000106617	ENST00000418337;ENST00000287878;ENST00000492843;ENST00000433631;ENST00000392801;ENST00000476632	.	.	.	3.36	3.36	0.38483	.	0.854162	0.10081	U	0.718430	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09843	T	0.71	.	10.2143	0.43160	0.0:1.0:0.0:0.0	.	.	.	.	X	6;247;123;123;203;6	.	ENSP00000287878:E247X	E	-	1	0	PRKAG2	150960103	0.997000	0.39634	0.020000	0.16555	0.136000	0.21042	1.540000	0.36115	1.417000	0.47077	0.467000	0.42956	GAG	.	.		0.771	PRKAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348440.2	NM_016203		A	151329170	C	A	151329170	4	1	366	1	0	0	0	0	0	1	0	0	12513	864	30	3	1018	3	PRKAG2	7	151329170	Nonsense_Mutation	SNP	C	TCGA-ZP-A9D0-01A-11D-A36X-10	618772	151329170	7809493	25	50907										
DOCK5	80005	hgsc.bcm.edu	37	chr8	25240239	25240239	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	cattaaggcaatgaggcctcAgcctgaatactttgctgttg	10	9	1	2			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr8:25240239A>G	ENST00000276440.7	+	40	4120	c.4076A>G	c.(4075-4077)cAg>cGg	p.Q1359R		NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	1359	DHR-2.				positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		ATGAGGCCTCAGCCTGAATAC	0.448																																					p.Q1359R	Pancreas(145;34 1887 3271 10937 30165)	Atlas-SNP	.											.	DOCK5	167	.	0			c.A4076G						.						117	105	109					8																	25240239		2203	4300	6503	SO:0001583	missense	80005	exon40			GGCCTCAGCCTGA		CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459			23476	protein-coding gene	gene with protein product						12432077	Standard	NM_024940		Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.4076A>G	chr8.hg19:g.25240239A>G	ENSP00000276440:p.Gln1359Arg	135.0	0.0		74.0	40.0	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Missense_Mutation	SNP	ENST00000276440.7	hg19	CCDS6047.1	.	.	.	.	.	.	.	.	.	.	A	18.23	3.577519	0.65878	.	.	ENSG00000147459	ENST00000276440	T	0.03889	3.77	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.08492	0.0211	L	0.50333	1.59	0.58432	D	0.999996	B;B;B	0.28584	0.216;0.002;0.002	B;B;B	0.32928	0.155;0.005;0.005	T	0.07635	-1.0762	10	0.62326	D	0.03	.	15.9599	0.79923	1.0:0.0:0.0:0.0	.	148;1349;1359	Q6ZP32;D3DSS6;Q9H7D0	.;.;DOCK5_HUMAN	R	1359	ENSP00000276440:Q1359R	ENSP00000276440:Q1359R	Q	+	2	0	DOCK5	25296156	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.339000	0.96797	2.162000	0.67917	0.533000	0.62120	CAG	.	.		0.448	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940		G	25240239	A	G	25240239	3	3	366	1	0	0	0	0	1	0	0	0	4692	188	7	2	4234	2	DOCK5	8	25240239	Missense_Mutation	SNP	A	TCGA-ZP-A9D0-01A-11D-A36X-10		25240239	121123783	26	50908										
ZHX1	11244	hgsc.bcm.edu	37	chr8	124266377	124266377	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	tcttctggtaagtttggtttGtgcccttaacctatttaatt	7	7	2	0			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr8:124266377G>C	ENST00000522655.1	-	3	2350	c.1810C>G	c.(1810-1812)Caa>Gaa	p.Q604E	ZHX1-C8ORF76_ENST00000357082.4_Intron|ZHX1_ENST00000522595.1_5'Flank|ZHX1_ENST00000395571.3_Missense_Mutation_p.Q604E|ZHX1_ENST00000297857.2_Missense_Mutation_p.Q604E			Q9UKY1	ZHX1_HUMAN	zinc fingers and homeoboxes 1	604					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(37;1.25e-09)|Ovarian(258;0.0154)		STAD - Stomach adenocarcinoma(47;0.00527)			AGTTTGGTTTGTGCCCTTAAC	0.363																																					p.Q604E		Atlas-SNP	.											.	ZHX1	89	.	0			c.C1810G						.						101	99	100					8																	124266377		2203	4300	6503	SO:0001583	missense	11244	exon3			TGGTTTGTGCCCT	AF106862	CCDS6342.1	8q24.13	2012-03-09	2004-01-23		ENSG00000165156	ENSG00000165156		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	12871	protein-coding gene	gene with protein product		604764	"zinc-fingers and homeoboxes 1"			10441475	Standard	NM_001017926		Approved		uc003yqe.3	Q9UKY1	OTTHUMG00000165088	ENST00000522655.1:c.1810C>G	chr8.hg19:g.124266377G>C	ENSP00000428821:p.Gln604Glu	91.0	0.0		81.0	31.0	NM_007222	Q8IWD8	Missense_Mutation	SNP	ENST00000522655.1	hg19	CCDS6342.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.637|0.637	-0.815039|-0.815039	0.02776|0.02776	.|.	.|.	ENSG00000165156|ENSG00000165156	ENST00000520474|ENST00000297857;ENST00000395571;ENST00000522655	.|D;D;D	.|0.96073	.|-3.9;-3.9;-3.9	5.3|5.3	5.3|5.3	0.74995|0.74995	.|Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	.|0.178458	.|0.49305	.|D	.|0.000147	D|D	0.88775|0.88775	0.6528|0.6528	.|.	.|.	.|.	0.48975|0.48975	D|D	0.999734|0.999734	.|B	.|0.09022	.|0.002	.|B	.|0.10450	.|0.005	T|T	0.83194|0.83194	-0.0082|-0.0082	4|9	.|0.02654	.|T	.|1	-15.6398|-15.6398	16.0406|16.0406	0.80679|0.80679	0.0:0.1989:0.8011:0.0|0.0:0.1989:0.8011:0.0	.|.	.|604	.|Q9UKY1	.|ZHX1_HUMAN	Q|E	288|604	.|ENSP00000297857:Q604E;ENSP00000378938:Q604E;ENSP00000428821:Q604E	.|ENSP00000297857:Q604E	H|Q	-|-	3|1	2|0	ZHX1|ZHX1	124335558|124335558	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	4.036000|4.036000	0.57304|0.57304	2.763000|2.763000	0.94921|0.94921	0.555000|0.555000	0.69702|0.69702	CAC|CAA	.	.		0.363	ZHX1-003	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000381759.1			C	124266377	G	C	124266377	3	2	366	1	0	0	0	0	1	0	0	0	17690	1386	48	4	815	4	ZHX1	8	124266377	Missense_Mutation	SNP	G	TCGA-ZP-A9D0-01A-11D-A36X-10	99026138	124266377	22097645	27	50909										
PRUNE2	158471	hgsc.bcm.edu	37	chr9	79319694	79319694	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	taccatttggtggtcctatgTctccacctgctggtaaatca	8	11	2	0			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr9:79319694T>G	ENST00000376718.3	-	8	7619	c.7496A>C	c.(7495-7497)gAc>gCc	p.D2499A	PRUNE2_ENST00000428286.1_Missense_Mutation_p.D2140A	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	2499					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						TGGTCCTATGTCTCCACCTGC	0.418											OREG0019258	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D2499A		Atlas-SNP	.											.	PRUNE2	331	.	0			c.A7496C						.						72	59	63					9																	79319694		1567	3577	5144	SO:0001583	missense	158471	exon8			CCTATGTCTCCAC	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.7496A>C	chr9.hg19:g.79319694T>G	ENSP00000365908:p.Asp2499Ala	139.0	0.0	1190	75.0	34.0	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	hg19	CCDS47982.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.77|18.77	3.694587|3.694587	0.68386|0.68386	.|.	.|.	ENSG00000106772|ENSG00000106772	ENST00000376718;ENST00000428286;ENST00000422033|ENST00000426088	T;T|.	0.59502|.	0.26;0.29|.	6.08|6.08	4.95|4.95	0.65309|0.65309	.|.	0.000000|.	0.64402|.	D|.	0.000010|.	T|T	0.65186|0.65186	0.2667|0.2667	M|M	0.64997|0.64997	1.995|1.995	0.80722|0.80722	D|D	1|1	D|.	0.76494|.	0.999|.	D|.	0.65874|.	0.939|.	T|T	0.64330|0.64330	-0.6433|-0.6433	10|5	0.42905|.	T|.	0.14|.	-26.2698|-26.2698	11.6879|11.6879	0.51497|0.51497	0.0:0.0683:0.0:0.9317|0.0:0.0683:0.0:0.9317	.|.	2499|.	Q8WUY3|.	PRUN2_HUMAN|.	A|S	2499;2140;2498|1820	ENSP00000365908:D2499A;ENSP00000397425:D2140A|.	ENSP00000365908:D2499A|.	D|R	-|-	2|3	0|2	PRUNE2|PRUNE2	78509514|78509514	0.982000|0.982000	0.34865|0.34865	0.998000|0.998000	0.56505|0.56505	0.997000|0.997000	0.91878|0.91878	0.657000|0.657000	0.24963|0.24963	2.333000|2.333000	0.79357|0.79357	0.533000|0.533000	0.62120|0.62120	GAC|AGA	.	.		0.418	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		G	79319694	T	G	79319694	3	3	366	1	0	0	0	0	1	0	0	0	12653	1667	58	5	1818	5	PRUNE2	9	79319694	Missense_Mutation	SNP	T	TCGA-ZP-A9D0-01A-11D-A36X-10		79319694	61893737	28	50910										
SVEP1	79987	hgsc.bcm.edu	37	chr9	113170387	113170387	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	aaatctccttgggtttcaggCactcaatggctttacatgtt	8	9	3	0			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr9:113170387C>T	ENST00000401783.2	-	38	7829	c.7493G>A	c.(7492-7494)tGc>tAc	p.C2498Y	SVEP1_ENST00000297826.5_Missense_Mutation_p.C424Y|SVEP1_ENST00000374469.1_Missense_Mutation_p.C2475Y	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2498	Sushi 19. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						GGGTTTCAGGCACTCAATGGC	0.473																																					p.C2498Y		Atlas-SNP	.											.	SVEP1	326	.	0			c.G7493A						.						50	50	50					9																	113170387		1922	4125	6047	SO:0001583	missense	79987	exon38			TTCAGGCACTCAA	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.7493G>A	chr9.hg19:g.113170387C>T	ENSP00000384917:p.Cys2498Tyr	78.0	0.0		67.0	36.0	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	hg19	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	C	14.79	2.640702	0.47153	.	.	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826;ENST00000374463	D;D;D	0.99784	-6.74;-6.74;-6.74	5.85	5.85	0.93711	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.85682	D	0.000000	D	0.99904	0.9954	H	0.99130	4.44	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96282	0.9207	10	0.87932	D	0	.	20.1577	0.98120	0.0:1.0:0.0:0.0	.	2498	Q4LDE5	SVEP1_HUMAN	Y	2498;2475;424;170	ENSP00000384917:C2498Y;ENSP00000363593:C2475Y;ENSP00000297826:C424Y	ENSP00000297826:C424Y	C	-	2	0	SVEP1	112210208	1.000000	0.71417	0.994000	0.49952	0.214000	0.24535	7.624000	0.83124	2.767000	0.95098	0.655000	0.94253	TGC	.	.		0.473	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	113170387	C	T	113170387	3	4	366	1	0	0	0	0	1	0	0	0	15435	710	25	3	3266	3	SVEP1	9	113170387	Missense_Mutation	SNP	C	TCGA-ZP-A9D0-01A-11D-A36X-10	33850693	113170387	28043044	29	50911										
REXO4	57109	hgsc.bcm.edu	37	chr9	136272184	136272184	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	gtacagcctcattgctgcctGggcatcctgaatctagacga	10	12	2	2			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr9:136272184G>A	ENST00000371942.3	-	8	1361	c.1162C>T	c.(1162-1164)Cag>Tag	p.Q388*	REXO4_ENST00000371935.2_Nonsense_Mutation_p.Q216*	NM_020385.2	NP_065118.2	Q9GZR2	REXO4_HUMAN	REX4, RNA exonuclease 4 homolog (S. cerevisiae)	388	Exonuclease.				regulation of transcription, DNA-templated (GO:0006355)	nucleolus (GO:0005730)|nucleus (GO:0005634)	exonuclease activity (GO:0004527)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(4)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	15				OV - Ovarian serous cystadenocarcinoma(145;8.58e-08)|Epithelial(140;9.55e-07)|all cancers(34;1.05e-05)		ATTGCTGCCTGGGCATCCTGA	0.592											OREG0019587	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q388X		Atlas-SNP	.											.	REXO4	27	.	0			c.C1162T						.						153	118	130					9																	136272184		2203	4300	6503	SO:0001587	stop_gained	57109	exon8			CTGCCTGGGCATC	AF273304	CCDS6969.1, CCDS65179.1	9q34	2008-02-05	2005-08-22	2005-08-22	ENSG00000148300	ENSG00000148300			12820	protein-coding gene	gene with protein product		602930	"Xenopus prevents mitotic catatrophe 2 homolog", "XPMC2 prevents mitotic catastrophe 2 homolog (Xenopus laevis)"	XPMC2H		9325058	Standard	NM_020385		Approved		uc004cdm.3	Q9GZR2	OTTHUMG00000020870	ENST00000371942.3:c.1162C>T	chr9.hg19:g.136272184G>A	ENSP00000361010:p.Gln388*	40.0	0.0	1624	26.0	17.0	NM_020385	B2RAT2|Q5T8S4|Q5T8S5|Q5T8S6|Q9GZW3	Nonsense_Mutation	SNP	ENST00000371942.3	hg19	CCDS6969.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.68|16.68	3.190936|3.190936	0.58017|0.58017	.|.	.|.	ENSG00000148300|ENSG00000148300	ENST00000453165|ENST00000371942;ENST00000371935;ENST00000454825	T|.	0.21932|.	1.98|.	5.27|5.27	5.27|5.27	0.74061|0.74061	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.68577|.	0.3016|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.64495|.	-0.6394|.	6|.	0.66056|0.27785	D|T	0.02|0.31	.|.	16.0348|16.0348	0.80617|0.80617	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	L|X	343|388;216;216	ENSP00000403272:P343L|.	ENSP00000403272:P343L|ENSP00000361003:Q216X	P|Q	-|-	2|1	0|0	REXO4|REXO4	135262005|135262005	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.074000|0.074000	0.17049|0.17049	7.064000|7.064000	0.76721|0.76721	2.451000|2.451000	0.82905|0.82905	0.561000|0.561000	0.74099|0.74099	CCA|CAG	.	.		0.592	REXO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054899.1			A	136272184	G	A	136272184	4	1	366	1	0	0	0	0	0	1	0	0	13258	1357	47	3	110	3	REXO4	9	136272184	Nonsense_Mutation	SNP	G	TCGA-ZP-A9D0-01A-11D-A36X-10	23101797	136272184	4941247	30	50912										
ANKRD26	22852	hgsc.bcm.edu	37	chr10	27313387	27313390	+	Frame_Shift_Del	DEL	TCTT	TCTT	-													0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	aaatcttacccagttatctcTctttctaattcaacattttt							TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	TCTT	TCTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr10:27313387_27313390delTCTT	ENST00000376087.4	-	28	4236_4239	c.4071_4074delAAGA	c.(4069-4074)gaaagafs	p.ER1357fs	ANKRD26_ENST00000436985.2_Frame_Shift_Del_p.ER1373fs|ANKRD26_ENST00000376070.3_Frame_Shift_Del_p.ER914fs	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	1356					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						CAGTTATCTCTCTTTCTAATTCAA	0.24																																					p.1358_1359del		Atlas-INDEL	.											.	ANKRD26	179	.	0			c.4072_4075del						.																																			SO:0001589	frameshift_variant	22852	exon28			.	AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"Ankyrin repeat domain containing"	29186	protein-coding gene	gene with protein product		610855	"thrombocytopenia 2 (autosomal dominant)"	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.4071_4074delAAGA	chr10.hg19:g.27313387_27313390delTCTT	ENSP00000365255:p.Glu1357fs	295.0	0.0		269.0	103.0	NM_014915	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Frame_Shift_Del	DEL	ENST00000376087.4	hg19	CCDS41499.1																																																																																			.	.		0.24	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1			-	27313390	TCTT	-	27313387	7	5	366	1	0	1	0	1	0	0	0	0	654	1548	54	0	1086	0	ANKRD26	10	27313387	Frame_Shift_Del	DEL	TCTT	TCGA-ZP-A9D0-01A-11D-A36X-10		27313387	108221360	31	50913										
ANK3	288	hgsc.bcm.edu	37	chr10	61832026	61832026	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	acatcatgaacaagtacatgCgaaagtttttctttctgaga	7	7	3	2			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr10:61832026C>A	ENST00000280772.2	-	37	8804	c.8613G>T	c.(8611-8613)tcG>tcT	p.S2871S	ANK3_ENST00000373827.2_Intron|ANK3_ENST00000355288.2_Intron|ANK3_ENST00000503366.1_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	2871					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						CAAGTACATGCGAAAGTTTTT	0.403																																					p.S2871S		Atlas-SNP	.											.	ANK3	703	.	0			c.G8613T						.						82	86	84					10																	61832026		2203	4299	6502	SO:0001819	synonymous_variant	288	exon37			TACATGCGAAAGT	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.8613G>T	chr10.hg19:g.61832026C>A		84.0	0.0		83.0	36.0	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Silent	SNP	ENST00000280772.2	hg19	CCDS7258.1																																																																																			.	.		0.403	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		A	61832026	C	A	61832026	2	1	366	1	0	0	0	0	0	0	0	1	622	755	27	1		1	ANK3	10	61832026	Silent	SNP	C	TCGA-ZP-A9D0-01A-11D-A36X-10	34518639	61832026	73702721	32	50914										
CCAR1	55749	hgsc.bcm.edu	37	chr10	70482318	70482319	+	Frame_Shift_Ins	INS	-	-	A													0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	ctactcagtttacagccactINSgcagtatcacagccaggtca							TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr10:70482318_70482319insA	ENST00000265872.6	+	2	176_177	c.57_58insA	c.(58-60)gcafs	p.A20fs	CCAR1_ENST00000535016.1_Frame_Shift_Ins_p.A20fs|CCAR1_ENST00000543719.1_Frame_Shift_Ins_p.A20fs	NM_001282959.1|NM_001282960.1|NM_018237.2	NP_001269888.1|NP_001269889.1|NP_060707.2	Q8IX12	CCAR1_HUMAN	cell division cycle and apoptosis regulator 1	20					apoptotic process (GO:0006915)|cell cycle (GO:0007049)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|lung(13)|ovary(7)|skin(3)	56						TTACAGCCACTGCAGTATCACA	0.46																																					p.T19fs		Atlas-INDEL	.											.	CCAR1	118	.	0			c.57_58insA						.																																			SO:0001589	frameshift_variant	55749	exon2			.	AY249140	CCDS7282.1, CCDS60547.1	10q22.1	2004-02-19			ENSG00000060339	ENSG00000060339			24236	protein-coding gene	gene with protein product		612569				12816952	Standard	NM_018237		Approved	FLJ10590, CARP-1, CARP1	uc001joo.3	Q8IX12	OTTHUMG00000018361	Exception_encountered	chr10.hg19:g.70482318_70482319insA	ENSP00000265872:p.Ala20fs	69.0	0.0		98.0	34.0	NM_018237	A0JLT7|A1L4P7|A8K9D4|B4DNP8|B4DRK8|Q32NE3|Q5EBM3|Q5VUP6|Q6PIZ0|Q6X935|Q9H8N4|Q9NVA7|Q9NVQ0|Q9NWM6	Frame_Shift_Ins	INS	ENST00000265872.6	hg19	CCDS7282.1																																																																																			.	.		0.46	CCAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048356.2	NM_018237		A	70482319	-	A	70482318	7	5	366	1	0	1	1	0	0	0	0	0	2732	1567	55	0	59	0	CCAR1	10	70482318	Frame_Shift_Ins	INS	-	TCGA-ZP-A9D0-01A-11D-A36X-10	8650292	70482318	65052429	33	50915										
IFIT3	3437	hgsc.bcm.edu	37	chr10	91099865	91099865	+	Frame_Shift_Del	DEL	A	A	-													0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	gtcccagagagctcctctctAactcagagcaactgaactga							TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr10:91099865delA	ENST00000371818.4	+	2	1633	c.1453delA	c.(1453-1455)aacfs	p.N485fs	LIPA_ENST00000371837.1_Intron|IFIT3_ENST00000371811.4_Frame_Shift_Del_p.N485fs|LIPA_ENST00000487618.1_Intron	NM_001549.4	NP_001540.2	O14879	IFIT3_HUMAN	interferon-induced protein with tetratricopeptide repeats 3	485					cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)	identical protein binding (GO:0042802)			breast(1)|central_nervous_system(3)|endometrium(1)|large_intestine(4)|lung(3)|skin(2)|urinary_tract(1)	15						GCTCCTCTCTAACTCAGAGCA	0.547																																					p.S484fs		Atlas-INDEL	.											.	IFIT3	36	.	0			c.1452delT						.						45	50	48					10																	91099865		2203	4300	6503	SO:0001589	frameshift_variant	3437	exon2			.	U52513	CCDS7402.1, CCDS31241.1	10q23.31	2014-05-22	2004-07-16	2004-07-16	ENSG00000119917	ENSG00000119917		"Tetratricopeptide (TTC) repeat domain containing"	5411	protein-coding gene	gene with protein product		604650	"interferon-induced protein with tetratricopeptide repeats 4"	IFIT4		9828129, 9391139	Standard	NM_001031683		Approved	ISG60, RIG-G, CIG-49, IFI60, GARG-49, IRG2	uc001kgg.3	O14879	OTTHUMG00000018708	ENST00000371818.4:c.1453delA	chr10.hg19:g.91099865delA	ENSP00000360883:p.Asn485fs	81.0	0.0		91.0	33.0	NM_001549	Q99634|Q9BSK7	Frame_Shift_Del	DEL	ENST00000371818.4	hg19	CCDS7402.1																																																																																			.	.		0.547	IFIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049294.1	NM_001549		-	91099865	A	-	91099865	7	5	366	1	0	1	0	1	0	0	0	0	7533	362	13	0	1468	0	IFIT3	10	91099865	Frame_Shift_Del	DEL	A	TCGA-ZP-A9D0-01A-11D-A36X-10	20617547	91099865	44434882	34	50916										
SLC5A12	159963	hgsc.bcm.edu	37	chr11	26725171	26725171	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	gccaagtaaaagttcctcccActgtgatagtccaaaaagtg	8	10	0	1			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr11:26725171A>T	ENST00000396005.3	-	6	1037	c.728T>A	c.(727-729)gTg>gAg	p.V243E	SLC5A12_ENST00000280467.6_Missense_Mutation_p.V243E	NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	243					sodium ion transport (GO:0006814)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)	35						AGTTCCTCCCACTGTGATAGT	0.408																																					p.V243E		Atlas-SNP	.											SLC5A12_ENST00000280467,right_upper_lobe,carcinoma,0,2	SLC5A12	134	.	0			c.T728A						.						129	124	125					11																	26725171		2203	4299	6502	SO:0001583	missense	159963	exon6			CCTCCCACTGTGA	BC049207	CCDS7860.2	11p14.2	2013-07-19	2013-07-19		ENSG00000148942	ENSG00000148942		"Solute carriers"	28750	protein-coding gene	gene with protein product		612455	"solute carrier family 5 (sodium/glucose cotransporter), member 12"			12477932	Standard	NM_178498		Approved	MGC52019, SMCT2	uc001mra.2	Q1EHB4	OTTHUMG00000150706	ENST00000396005.3:c.728T>A	chr11.hg19:g.26725171A>T	ENSP00000379326:p.Val243Glu	101.0	0.0		90.0	36.0	NM_178498	Q86UC7	Missense_Mutation	SNP	ENST00000396005.3	hg19	CCDS7860.2	.	.	.	.	.	.	.	.	.	.	A	25.8	4.670489	0.88348	.	.	ENSG00000148942	ENST00000396005;ENST00000280467;ENST00000533617	D;D;D	0.88741	-2.42;-2.42;-2.42	5.51	5.51	0.81932	.	0.361911	0.23870	N	0.043760	D	0.94745	0.8304	M	0.87682	2.9	0.23271	N	0.99801	P;D	0.64830	0.676;0.994	P;D	0.65987	0.776;0.94	D	0.89846	0.4006	10	0.87932	D	0	.	15.6015	0.76628	1.0:0.0:0.0:0.0	.	243;243	Q1EHB4-2;Q1EHB4	.;SC5AC_HUMAN	E	243;243;55	ENSP00000379326:V243E;ENSP00000280467:V243E;ENSP00000435053:V55E	ENSP00000280467:V243E	V	-	2	0	SLC5A12	26681747	0.976000	0.34144	0.885000	0.34714	0.965000	0.64279	9.287000	0.95975	2.094000	0.63399	0.477000	0.44152	GTG	.	.		0.408	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319681.1	NM_178498		T	26725171	A	T	26725171	3	4	366	1	0	0	0	0	1	0	0	0	14679	159	6	4	1168	4	SLC5A12	11	26725171	Missense_Mutation	SNP	A	TCGA-ZP-A9D0-01A-11D-A36X-10		26725171	108281345	35	50917										
GRM5	2915	hgsc.bcm.edu	37	chr11	88242143	88242143	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	cggggcgccgacgccggggcTgggggccgcggtggacagca	22	13	0	0			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr11:88242143T>A	ENST00000305447.4	-	9	3405	c.3256A>T	c.(3256-3258)Agc>Tgc	p.S1086C	GRM5-AS1_ENST00000526448.1_RNA|GRM5-AS1_ENST00000531994.1_RNA|GRM5_ENST00000305432.5_Missense_Mutation_p.S1054C|GRM5_ENST00000393297.1_Intron|GRM5_ENST00000455756.2_Missense_Mutation_p.S1054C|GRM5_ENST00000418177.2_Missense_Mutation_p.S1086C	NM_001143831.2	NP_001137303.1	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5	1086					activation of MAPKKK activity (GO:0000185)|cognition (GO:0050890)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|learning (GO:0007612)|locomotory behavior (GO:0007626)|negative regulation of locomotion (GO:0040013)|phospholipase C-activating G-protein coupled glutamate receptor signaling pathway (GO:0007206)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(1)|breast(5)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(18)|lung(40)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)|Rufinamide(DB06201)	ACGCCGGGGCTGGGGGCCGCG	0.642																																					p.S1086C		Atlas-SNP	.											.	GRM5	414	.	0			c.A3256T						.						12	15	14					11																	88242143		2195	4291	6486	SO:0001583	missense	2915	exon9			CGGGGCTGGGGGC	D28538	CCDS8283.1, CCDS44694.1	11q14.3	2014-06-12			ENSG00000168959	ENSG00000168959		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4597	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 86"	604102				7908515	Standard	NM_001143831		Approved	MGLUR5, GPRC1E, mGlu5, PPP1R86	uc001pcq.3	P41594	OTTHUMG00000134306	ENST00000305447.4:c.3256A>T	chr11.hg19:g.88242143T>A	ENSP00000306138:p.Ser1086Cys	160.0	0.0		133.0	45.0	NM_001143831	Q6J164	Missense_Mutation	SNP	ENST00000305447.4	hg19	CCDS44694.1	.	.	.	.	.	.	.	.	.	.	T	12.57	1.977921	0.34942	.	.	ENSG00000168959	ENST00000418177;ENST00000455756;ENST00000305432;ENST00000305447	D;D;D;D	0.89123	-2.44;-2.47;-2.47;-2.44	4.72	3.79	0.43588	.	0.455544	0.23125	N	0.051649	T	0.79009	0.4374	N	0.14661	0.345	0.23346	N	0.997869	P;P	0.44946	0.846;0.761	B;B	0.40329	0.326;0.221	T	0.68930	-0.5279	9	.	.	.	.	12.0581	0.53546	0.0:0.9136:0.0:0.0864	.	1054;1086	P41594-2;P41594	.;GRM5_HUMAN	C	1086;1054;1054;1086	ENSP00000402912:S1086C;ENSP00000405690:S1054C;ENSP00000305905:S1054C;ENSP00000306138:S1086C	.	S	-	1	0	GRM5	87881791	0.155000	0.22806	0.171000	0.22900	0.377000	0.30045	0.515000	0.22801	0.928000	0.37168	-0.468000	0.05107	AGC	.	.		0.642	GRM5-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259226.1	NM_000842		A	88242143	T	A	88242143	3	1	366	1	0	0	0	0	1	0	0	0	6809	1580	55	4	386	4	GRM5	11	88242143	Missense_Mutation	SNP	T	TCGA-ZP-A9D0-01A-11D-A36X-10	61516972	88242143	46764373	36	50918										
MFAP5	8076	hgsc.bcm.edu	37	chr12	8800725	8800725	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	ctgcaaatccacattttcacAgggaggaagtcggaagtaat	10	8	1	0			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr12:8800725A>T	ENST00000359478.2	-	10	671	c.484T>A	c.(484-486)Tgt>Agt	p.C162S	MFAP5_ENST00000433590.2_Missense_Mutation_p.C137S|MFAP5_ENST00000543369.1_Missense_Mutation_p.C140S|MFAP5_ENST00000396549.2_Missense_Mutation_p.C152S|MFAP5_ENST00000540087.1_Missense_Mutation_p.C152S|MFAP5_ENST00000535336.1_Missense_Mutation_p.C98S	NM_003480.2	NP_003471.1	Q13361	MFAP5_HUMAN	microfibrillar associated protein 5	162					extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|microfibril (GO:0001527)	extracellular matrix structural constituent (GO:0005201)			breast(1)|endometrium(2)|large_intestine(4)|lung(5)|skin(1)	13	Lung SC(5;0.184)					ACATTTTCACAGGGAGGAAGT	0.478																																					p.C162S		Atlas-SNP	.											.	MFAP5	34	.	0			c.T484A						.						89	87	87					12																	8800725		2203	4300	6503	SO:0001583	missense	8076	exon10			TTTCACAGGGAGG	AK124368	CCDS8595.1, CCDS73437.1	12p13.1-p12.3	2004-04-05				ENSG00000197614			29673	protein-coding gene	gene with protein product		601103				9792630, 8557636	Standard	XM_005253485		Approved	MAGP2, MP25	uc001qut.1	Q13361		ENST00000359478.2:c.484T>A	chr12.hg19:g.8800725A>T	ENSP00000352455:p.Cys162Ser	267.0	0.0		286.0	99.0	NM_003480	B0AZL6|D3DUV1|Q7Z490	Missense_Mutation	SNP	ENST00000359478.2	hg19	CCDS8595.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.221392	0.79464	.	.	ENSG00000197614	ENST00000543467;ENST00000359478;ENST00000433590;ENST00000396549;ENST00000543369;ENST00000535336;ENST00000540087	.	.	.	4.79	4.79	0.61399	.	0.068358	0.64402	D	0.000009	T	0.59918	0.2229	L	0.32530	0.975	0.36278	D	0.855596	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.78314	0.991;0.991;0.991	T	0.68895	-0.5288	9	0.87932	D	0	-13.1712	10.894	0.47012	1.0:0.0:0.0:0.0	.	137;162;152	B3KW70;Q13361;Q7Z490	.;MFAP5_HUMAN;.	S	68;162;137;152;140;98;152	.	ENSP00000352455:C162S	C	-	1	0	MFAP5	8691992	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	4.493000	0.60341	2.138000	0.66242	0.460000	0.39030	TGT	.	.		0.478	MFAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400656.2	NM_003480		T	8800725	A	T	8800725	3	4	366	1	0	0	0	0	1	0	0	0	9527	188	7	4	41	4	MFAP5	12	8800725	Missense_Mutation	SNP	A	TCGA-ZP-A9D0-01A-11D-A36X-10		8800725	125051170	37	50919										
UTP20	27340	hgsc.bcm.edu	37	chr12	101779827	101779827	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	aagcaaagaagagaaagataGagttcctgcgtccaggatat	11	6	0	4			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr12:101779827G>C	ENST00000261637.4	+	62	8458	c.8284G>C	c.(8284-8286)Gag>Cag	p.E2762Q		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	2762	Nuclear localization signal.				endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						GAGAAAGATAGAGTTCCTGCG	0.373																																					p.E2762Q		Atlas-SNP	.											.	UTP20	222	.	0			c.G8284C						.						127	134	132					12																	101779827		2203	4300	6503	SO:0001583	missense	27340	exon62			AAGATAGAGTTCC	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"down regulated in metastasis"	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.8284G>C	chr12.hg19:g.101779827G>C	ENSP00000261637:p.Glu2762Gln	343.0	0.0		349.0	122.0	NM_014503	Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	hg19	CCDS9081.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.676759	0.88445	.	.	ENSG00000120800	ENST00000261637	T	0.19806	2.12	5.93	5.05	0.67936	.	0.049132	0.85682	D	0.000000	T	0.36853	0.0982	L	0.51422	1.61	0.52501	D	0.999956	D	0.71674	0.998	D	0.63597	0.916	T	0.05162	-1.0902	10	0.38643	T	0.18	-13.7632	13.4138	0.60958	0.0721:0.0:0.9279:0.0	.	2762	O75691	UTP20_HUMAN	Q	2762	ENSP00000261637:E2762Q	ENSP00000261637:E2762Q	E	+	1	0	UTP20	100303958	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.276000	0.95745	1.527000	0.49086	-0.148000	0.13756	GAG	.	.		0.373	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		C	101779827	G	C	101779827	3	2	366	1	0	0	0	0	1	0	0	0	17114	943	33	4	8530	4	UTP20	12	101779827	Missense_Mutation	SNP	G	TCGA-ZP-A9D0-01A-11D-A36X-10	92979102	101779827	32072068	38	50920										
ATP2A2	488	hgsc.bcm.edu	37	chr12	110782702	110782716	+	In_Frame_Del	DEL	GCTGCTACCGTGGGT	GCTGCTACCGTGGGT	-													0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	tgttcccaggttacgtcggcGctgctaccgtgggtgctgct					rs150843644|rs375275623		TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	GCTGCTACCGTGGGT	GCTGCTACCGTGGGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr12:110782702_110782716delGCTGCTACCGTGGGT	ENST00000539276.2	+	17	2642_2656	c.2533_2547delGCTGCTACCGTGGGT	c.(2533-2547)gctgctaccgtgggtdel	p.AATVG845del	ATP2A2_ENST00000395494.2_In_Frame_Del_p.AATVG818del|ATP2A2_ENST00000308664.6_In_Frame_Del_p.AATVG845del			P16615	AT2A2_HUMAN	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	845					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|epidermis development (GO:0008544)|ER-nucleus signaling pathway (GO:0006984)|ion transmembrane transport (GO:0034220)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart rate (GO:0010460)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|calcium-transporting ATPase activity involved in regulation of cardiac muscle cell membrane potential (GO:0086039)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|S100 protein binding (GO:0044548)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(10)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	38						TTACGTCGGCGCTGCTACCGTGGGTGCTGCTGCAT	0.563																																					p.844_849del		Atlas-INDEL	.											.	ATP2A2	78	.	0			c.2532_2546del						.																																			SO:0001651	inframe_deletion	488	exon17			.		CCDS9143.1, CCDS9144.1	12q24.11	2012-10-22			ENSG00000174437	ENSG00000174437	3.6.3.8	"ATPases / P-type"	812	protein-coding gene	gene with protein product	"sarcoplasmic/endoplasmic reticulum calcium ATPase 2", "calcium pump 2"	108740		ATP2B, DAR		10080178	Standard	NM_170665		Approved	SERCA2	uc001tqk.4	P16615	OTTHUMG00000169327	ENST00000539276.2:c.2533_2547delGCTGCTACCGTGGGT	chr12.hg19:g.110782702_110782716delGCTGCTACCGTGGGT	ENSP00000440045:p.Ala845_Gly849del	120.0	0.0		82.0	26.0	NM_170665	A6NDN7|B4DF05|P16614|Q86VJ2	In_Frame_Del	DEL	ENST00000539276.2	hg19	CCDS9144.1																																																																																			.	.		0.563	ATP2A2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403539.1	NM_001681		-	110782716	GCTGCTACCGTGGGT	-	110782702	7	5	366	1	0	1	0	1	0	0	0	0	1137	1087	38	0	2599	0	ATP2A2	12	110782702	In_Frame_Del	DEL	GCTGCTACCGTGGGT	TCGA-ZP-A9D0-01A-11D-A36X-10	9002875	110782702	23069193	39	50921										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64600832	64600832	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	atgcatctcttgaaaaggacCtggaaattcttatatctaca	6	8	3	1			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr14:64600832C>A	ENST00000344113.4	+	78	14772	c.14560C>A	c.(14560-14562)Ctg>Atg	p.L4854M	ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000555002.1_Missense_Mutation_p.L1488M|SYNE2_ENST00000358025.3_Missense_Mutation_p.L4854M|SYNE2_ENST00000357395.3_Missense_Mutation_p.L1239M|SYNE2_ENST00000394768.2_Missense_Mutation_p.L1239M|SYNE2_ENST00000554584.1_Missense_Mutation_p.L4771M	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	4854					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		TGAAAAGGACCTGGAAATTCT	0.373																																					p.L4854M		Atlas-SNP	.											.	SYNE2	577	.	0			c.C14560A						.						138	143	142					14																	64600832		2203	4300	6503	SO:0001583	missense	23224	exon78			AAGGACCTGGAAA	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.14560C>A	chr14.hg19:g.64600832C>A	ENSP00000341781:p.Leu4854Met	143.0	0.0		130.0	54.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	hg19	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	C	12.26	1.883853	0.33255	.	.	ENSG00000054654	ENST00000358025;ENST00000357395;ENST00000344113;ENST00000554584;ENST00000261678;ENST00000555002;ENST00000394768	T;T;T;T;T;T	0.70164	-0.43;2.77;-0.46;-0.38;2.78;2.77	5.95	5.05	0.67936	.	0.000000	0.40818	N	0.001003	T	0.78698	0.4324	M	0.76328	2.33	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	T	0.79621	-0.1727	10	0.72032	D	0.01	.	8.6131	0.33815	0.0:0.7946:0.0:0.2054	.	1239;4854;4854	Q8WXH0-7;Q8WXH0;Q8WXH0-2	.;SYNE2_HUMAN;.	M	4854;1239;4854;4771;4771;1488;1239	ENSP00000350719:L4854M;ENSP00000349969:L1239M;ENSP00000341781:L4854M;ENSP00000452570:L4771M;ENSP00000450831:L1488M;ENSP00000378249:L1239M	ENSP00000261678:L4771M	L	+	1	2	SYNE2	63670585	0.940000	0.31905	1.000000	0.80357	0.975000	0.68041	1.399000	0.34566	2.821000	0.97095	0.561000	0.74099	CTG	.	.		0.373	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		A	64600832	C	A	64600832	3	1	366	1	0	0	0	0	1	0	0	0	15461	680	24	3	14866	3	SYNE2	14	64600832	Missense_Mutation	SNP	C	TCGA-ZP-A9D0-01A-11D-A36X-10		64600832	42748708	40	50922										
NRXN3	9369	hgsc.bcm.edu	37	chr14	80271457	80271457	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	tctctttgacataaacagccAacatcagatgatcttgtttc	5	10	3	3			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr14:80271457A>G	ENST00000557594.1	+	5	1865	c.912A>G	c.(910-912)ccA>ccG	p.P304P	NRXN3_ENST00000556003.1_Intron|NRXN3_ENST00000281127.7_Silent_p.P304P|NRXN3_ENST00000335750.5_Silent_p.P936P|NRXN3_ENST00000554719.1_Silent_p.P936P|NRXN3_ENST00000428277.2_Silent_p.P334P	NM_001272020.1	NP_001258949.1	Q9HDB5	NRX3B_HUMAN	neurexin 3	304					adult behavior (GO:0030534)|angiogenesis (GO:0001525)|learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(23)|lung(40)|ovary(3)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(9)|urinary_tract(1)	104		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		ATAAACAGCCAACATCAGATG	0.383																																					p.P936P		Atlas-SNP	.											.	NRXN3	342	.	0			c.A2808G						.						208	187	194					14																	80271457		2203	4300	6503	SO:0001819	synonymous_variant	9369	exon16			ACAGCCAACATCA	AB018286	CCDS9870.1, CCDS9871.1, CCDS45145.1, CCDS61515.1	14q31	2010-01-19				ENSG00000021645			8010	protein-coding gene	gene with protein product		600567	"chromosome 14 open reading frame 60"	C14orf60		11944992, 12379233	Standard	NM_004796		Approved	KIAA0743	uc001xun.4	Q9HDB5		ENST00000557594.1:c.912A>G	chr14.hg19:g.80271457A>G		74.0	0.0		56.0	25.0	NM_004796	A5PKW8|A8MPU5|B3KPM7|Q6NUR0|Q8IUD8	Silent	SNP	ENST00000557594.1	hg19																																																																																				.	.		0.383	NRXN3-004	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000413790.1	NM_001105250		G	80271457	A	G	80271457	2	3	366	1	0	0	0	0	0	0	0	1	10676	117	5	2		2	NRXN3	14	80271457	Silent	SNP	A	TCGA-ZP-A9D0-01A-11D-A36X-10	15670625	80271457	27078083	41	50923										
PRPF8	10594	hgsc.bcm.edu	37	chr17	1577803	1577803	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	ggggtgggcagcctcagtggCtatgtcctggaaactgagaa	16	8	1	1			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr17:1577803C>T	ENST00000572621.1	-	20	3497	c.3232G>A	c.(3232-3234)Gcc>Acc	p.A1078T	PRPF8_ENST00000304992.6_Missense_Mutation_p.A1078T			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	1078	Reverse transcriptase homology domain.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		GCCTCAGTGGCTATGTCCTGG	0.527																																					p.A1078T		Atlas-SNP	.											.	PRPF8	169	.	0			c.G3232A						.						155	149	151					17																	1577803		2203	4300	6503	SO:0001583	missense	10594	exon21			CAGTGGCTATGTC	AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231			17340	protein-coding gene	gene with protein product		607300	"PRP8 pre-mRNA processing factor 8 homolog (yeast)", "PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)"	RP13		11468273, 10411133	Standard	NM_006445		Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.3232G>A	chr17.hg19:g.1577803C>T	ENSP00000460348:p.Ala1078Thr	183.0	0.0		177.0	62.0	NM_006445	O14547|O75965	Missense_Mutation	SNP	ENST00000572621.1	hg19	CCDS11010.1	.	.	.	.	.	.	.	.	.	.	C	13.40	2.227054	0.39399	.	.	ENSG00000174231	ENST00000304992	T	0.80033	-1.33	5.25	5.25	0.73442	.	0.104865	0.64402	D	0.000004	T	0.75213	0.3819	L	0.41961	1.31	0.53688	D	0.999974	B	0.06786	0.001	B	0.08055	0.003	T	0.68484	-0.5396	10	0.19147	T	0.46	.	19.0491	0.93036	0.0:1.0:0.0:0.0	.	1078	Q6P2Q9	PRP8_HUMAN	T	1078	ENSP00000304350:A1078T	ENSP00000304350:A1078T	A	-	1	0	PRPF8	1524553	0.998000	0.40836	1.000000	0.80357	0.856000	0.48823	3.858000	0.55979	2.740000	0.93945	0.313000	0.20887	GCC	.	.		0.527	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2			T	1577803	C	T	1577803	3	4	366	1	0	0	0	0	1	0	0	0	12587	797	28	3	3867	3	PRPF8	17	1577803	Missense_Mutation	SNP	C	TCGA-ZP-A9D0-01A-11D-A36X-10		1577803	79617407	42	50924										
SLFN11	91607	hgsc.bcm.edu	37	chr17	33680389	33680389	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	cagaggctggttttcacaaaCgtagagaattctgtgtgcct	11	8	2	2			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr17:33680389C>T	ENST00000394566.1	-	6	2160	c.1888G>A	c.(1888-1890)Gtt>Att	p.V630I	SLFN11_ENST00000308377.4_Missense_Mutation_p.V630I	NM_001104587.1|NM_001104588.1|NM_001104589.1|NM_001104590.1	NP_001098057.1|NP_001098058.1|NP_001098059.1|NP_001098060.1	Q7Z7L1	SLN11_HUMAN	schlafen family member 11	630					defense response to virus (GO:0051607)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|tRNA binding (GO:0000049)			autonomic_ganglia(1)|breast(1)|kidney(3)|large_intestine(14)|lung(17)|ovary(1)|prostate(4)|skin(2)|stomach(5)|upper_aerodigestive_tract(2)	50		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TTTTCACAAACGTAGAGAATT	0.423																																					p.V630I		Atlas-SNP	.											.	SLFN11	112	.	0			c.G1888A						.						58	57	57					17																	33680389		2202	4297	6499	SO:0001583	missense	91607	exon4			CACAAACGTAGAG	AK074184	CCDS11294.1	17q12	2006-04-05			ENSG00000172716	ENSG00000172716			26633	protein-coding gene	gene with protein product		614953				12477932	Standard	NM_001104587		Approved	FLJ34922	uc010ctr.3	Q7Z7L1	OTTHUMG00000132948	ENST00000394566.1:c.1888G>A	chr17.hg19:g.33680389C>T	ENSP00000378067:p.Val630Ile	563.0	0.0		586.0	123.0	NM_152270	E1P643|Q8N3S8|Q8N762|Q8TEE0	Missense_Mutation	SNP	ENST00000394566.1	hg19	CCDS11294.1	.	.	.	.	.	.	.	.	.	.	c	0.018	-1.481177	0.01027	.	.	ENSG00000172716	ENST00000308377;ENST00000394566	D;D	0.83250	-1.7;-1.7	3.69	-7.39	0.01402	Domain of unknown function DUF2075 (1);	1.014740	0.07917	N	0.975160	T	0.56746	0.2006	N	0.03071	-0.42	0.09310	N	1	B	0.15141	0.012	B	0.17098	0.017	T	0.57791	-0.7750	10	0.02654	T	1	.	14.3428	0.66639	0.0:0.184:0.0:0.816	.	630	Q7Z7L1	SLN11_HUMAN	I	630	ENSP00000312402:V630I;ENSP00000378067:V630I	ENSP00000312402:V630I	V	-	1	0	SLFN11	30704502	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-1.746000	0.01829	-1.872000	0.01136	-0.792000	0.03331	GTT	.	.		0.423	SLFN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256480.1	NM_152270		T	33680389	C	T	33680389	3	4	366	1	0	0	0	0	1	0	0	0	14748	536	19	1	825	1	SLFN11	17	33680389	Missense_Mutation	SNP	C	TCGA-ZP-A9D0-01A-11D-A36X-10	32102586	33680389	47514821	43	50925										
SMCHD1	23347	hgsc.bcm.edu	37	chr18	2728559	2728559	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	ttttagatgaatcagacaacAtaacagcacaaccaaaattg	5	8	1	3	rs9961682	byFrequency	TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr18:2728559A>C	ENST00000320876.6	+	23	3216	c.2878A>C	c.(2878-2880)Ata>Cta	p.I960L	SMCHD1_ENST00000261598.8_Missense_Mutation_p.I960L|SMCHD1_ENST00000609587.1_3'UTR|RP11-703M24.5_ENST00000583546.1_RNA	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	960			I -> V (in dbSNP:rs9961682).		chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						ATCAGACAACATAACAGCACA	0.358																																					p.I960L		Atlas-SNP	.											.	SMCHD1	88	.	0			c.A2878C						.						104	100	101					18																	2728559		1862	4100	5962	SO:0001583	missense	23347	exon23			GACAACATAACAG	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.2878A>C	chr18.hg19:g.2728559A>C	ENSP00000326603:p.Ile960Leu	157.0	0.0		139.0	51.0	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Missense_Mutation	SNP	ENST00000320876.6	hg19	CCDS45822.1	.	.	.	.	.	.	.	.	.	.	A	11.32	1.603959	0.28534	.	.	ENSG00000101596	ENST00000320876;ENST00000261598	T;T	0.24538	1.85;1.85	5.84	-3.46	0.04767	.	0.509376	0.22250	N	0.062565	T	0.14743	0.0356	L	0.36672	1.1	0.27499	N	0.952033	B	0.02656	0.0	B	0.04013	0.001	T	0.29119	-1.0022	10	0.17832	T	0.49	-4.6572	9.6361	0.39809	0.3166:0.2087:0.4747:0.0	.	960	A6NHR9	SMHD1_HUMAN	L	960	ENSP00000326603:I960L;ENSP00000261598:I960L	ENSP00000261598:I960L	I	+	1	0	SMCHD1	2718559	0.830000	0.29337	0.936000	0.37596	0.999000	0.98932	-0.076000	0.11412	-0.889000	0.03950	0.528000	0.53228	ATA	.	A|0.969;G|0.031		0.358	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			C	2728559	A	C	2728559	3	2	366	1	0	0	0	0	1	0	0	0	14803	217	8	5	2968	5	SMCHD1	18	2728559	Missense_Mutation	SNP	A	TCGA-ZP-A9D0-01A-11D-A36X-10		2728559	75348689	44	50926										
ZNF397OS	100101467	hgsc.bcm.edu	37	chr18	32833559	32833559	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	agctctgattgaaggattttCcacattcattacattcataa	5	8	3	2			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr18:32833559C>G	ENST00000420878.3	-	5	1795	c.1340G>C	c.(1339-1341)gGa>gCa	p.G447A	ZNF397_ENST00000592264.1_Intron|ZSCAN30_ENST00000333206.5_Missense_Mutation_p.G447A|ZNF397_ENST00000589420.1_Intron|ZNF397_ENST00000355632.4_Intron|ZNF397_ENST00000261333.6_Intron	NM_001166012.1	NP_001159484.1	Q86W11	ZSC30_HUMAN	zinc finger and SCAN domain containing 30	447					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(5)|lung(3)|urinary_tract(1)	9						GAAGGATTTTCCACATTCATT	0.393																																					p.G447A		Atlas-SNP	.											.	ZSCAN30	34	.	0			c.G1340C						.						108	100	102					18																	32833559		1568	3582	5150	SO:0001583	missense	100101467	exon5			GATTTTCCACATT	AY234408	CCDS42427.1, CCDS74207.1	18q12.2	2013-01-08	2010-07-23	2010-07-23	ENSG00000186814	ENSG00000186814		"-", "Zinc fingers, C2H2-type"	33517	protein-coding gene	gene with protein product			"zinc finger protein 397 opposite strand", "ZNF397 opposite strand"	ZNF397OS		12801647	Standard	NM_001166012		Approved	ZNF917	uc002kym.3	Q86W11		ENST00000420878.3:c.1340G>C	chr18.hg19:g.32833559C>G	ENSP00000392371:p.Gly447Ala	139.0	0.0		131.0	61.0	NM_001166012	B4E0N0|Q6ZNB3|Q96PN3	Missense_Mutation	SNP	ENST00000420878.3	hg19	CCDS42427.1	.	.	.	.	.	.	.	.	.	.	C	17.45	3.391790	0.62066	.	.	ENSG00000186814	ENST00000420878;ENST00000333206;ENST00000360932	T;T	0.01464	4.86;4.86	4.19	3.32	0.38043	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.35436	N	0.003216	T	0.05868	0.0153	M	0.82056	2.57	0.80722	D	1	D	0.57571	0.98	P	0.51487	0.671	T	0.09862	-1.0655	10	0.87932	D	0	.	10.0114	0.41988	0.0:0.8991:0.0:0.1008	.	447	Q86W11	ZSC30_HUMAN	A	447;447;382	ENSP00000392371:G447A;ENSP00000329738:G447A	ENSP00000329738:G447A	G	-	2	0	ZSCAN30	31087557	0.989000	0.36119	1.000000	0.80357	0.980000	0.70556	2.799000	0.47892	1.107000	0.41642	0.655000	0.94253	GGA	.	.		0.393	ZSCAN30-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442510.1	NM_001112734		G	32833559	C	G	32833559	3	3	366	1	0	0	0	0	1	0	0	0	17899	855	30	4	148	4	ZNF397OS	18	32833559	Missense_Mutation	SNP	C	TCGA-ZP-A9D0-01A-11D-A36X-10	30105000	32833559	45243689	45	50927										
ZNF681	148213	hgsc.bcm.edu	37	chr19	23938228	23938228	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	atattgaagttatcctcaccCaagaagaccaggtttctgta	7	9	2	3			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr19:23938228C>A	ENST00000402377.3	-	2	270	c.129G>T	c.(127-129)ttG>ttT	p.L43F	ZNF681_ENST00000395385.3_Intron	NM_138286.2	NP_612143.2	Q96N22	ZN681_HUMAN	zinc finger protein 681	43	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(3)	21		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				TATCCTCACCCAAGAAGACCA	0.343																																					p.L43F		Atlas-SNP	.											.	ZNF681	76	.	0			c.G129T						.						101	111	108					19																	23938228		2203	4300	6503	SO:0001630	splice_region_variant	148213	exon2			CTCACCCAAGAAG	AK056088	CCDS12414.2	19p12	2013-01-08			ENSG00000196172	ENSG00000196172		"Zinc fingers, C2H2-type", "-"	26457	protein-coding gene	gene with protein product	"hypothetical protein FLJ31526"						Standard	NM_138286		Approved	FLJ31526	uc002nrk.4	Q96N22	OTTHUMG00000150831	ENST00000402377.3:c.130+1G>T	chr19.hg19:g.23938228C>A		568.0	0.0		539.0	172.0	NM_138286	B3KVF7	Missense_Mutation	SNP	ENST00000402377.3	hg19	CCDS12414.2	.	.	.	.	.	.	.	.	.	.	.	9.460	1.092941	0.20471	.	.	ENSG00000196172	ENST00000402377	T	0.02787	4.16	1.05	1.05	0.20165	Krueppel-associated box (4);	.	.	.	.	T	0.16171	0.0389	M	0.93375	3.41	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.00496	-1.1705	9	0.87932	D	0	.	5.3007	0.15776	0.0:1.0:0.0:0.0	.	43	Q96N22	ZN681_HUMAN	F	43	ENSP00000384000:L43F	ENSP00000384000:L43F	L	-	3	2	ZNF681	23730068	0.685000	0.27652	0.327000	0.25402	0.331000	0.28603	0.108000	0.15396	0.452000	0.26830	0.460000	0.39030	TTG	.	.		0.343	ZNF681-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320248.2	NM_138286	Missense_Mutation	A	23938228	C	A	23938228	5	1	366	1	0	0	0	0	0	0	1	0	18103	608	21	3	1820	3	ZNF681	19	23938228	Splice_Site	SNP	C	TCGA-ZP-A9D0-01A-11D-A36X-10		23938228	35190755	46	50928										
HSPA12B	116835	hgsc.bcm.edu	37	chr20	3723019	3723019	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	gtctagtggctatgctttcaGctttgccagtgaccctgagg	12	10	2	2			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr20:3723019G>C	ENST00000254963.2	+	4	375	c.230G>C	c.(229-231)aGc>aCc	p.S77T	HSPA12B_ENST00000542646.1_Intron	NM_001197327.1|NM_052970.4	NP_001184256.1|NP_443202.3	Q96MM6	HS12B_HUMAN	heat shock 70kD protein 12B	77							ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	14						TATGCTTTCAGCTTTGCCAGT	0.597																																					p.S77T		Atlas-SNP	.											.	HSPA12B	43	.	0			c.G230C						.						62	57	59					20																	3723019		2203	4300	6503	SO:0001583	missense	116835	exon4			CTTTCAGCTTTGC	AK056712	CCDS13061.1	20p13	2011-09-02	2003-04-10	2003-04-10	ENSG00000132622	ENSG00000132622		"Heat shock proteins / HSP70"	16193	protein-coding gene	gene with protein product		610702	"chromosome 20 open reading frame 60"	C20orf60		12552099	Standard	NM_052970		Approved	dJ1009E24.2	uc002wjd.3	Q96MM6	OTTHUMG00000031755	ENST00000254963.2:c.230G>C	chr20.hg19:g.3723019G>C	ENSP00000254963:p.Ser77Thr	64.0	0.0		60.0	20.0	NM_052970	D3DVX7|Q2TAK3|Q9BR52	Missense_Mutation	SNP	ENST00000254963.2	hg19	CCDS13061.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.815939	0.90790	.	.	ENSG00000132622	ENST00000254963	T	0.03801	3.8	4.73	4.73	0.59995	.	0.000000	0.85682	D	0.000000	T	0.16385	0.0394	M	0.69463	2.115	0.80722	D	1	P;D	0.60575	0.933;0.988	P;P	0.61800	0.728;0.894	T	0.00512	-1.1696	10	0.34782	T	0.22	.	15.5958	0.76578	0.0:0.0:1.0:0.0	.	77;77	B7ZLP2;Q96MM6	.;HS12B_HUMAN	T	77	ENSP00000254963:S77T	ENSP00000254963:S77T	S	+	2	0	HSPA12B	3671019	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.493000	0.97960	2.626000	0.88956	0.655000	0.94253	AGC	.	.		0.597	HSPA12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077756.2	NM_052970		C	3723019	G	C	3723019	3	2	366	1	0	0	0	0	1	0	0	0	7414	971	34	4	240	4	HSPA12B	20	3723019	Missense_Mutation	SNP	G	TCGA-ZP-A9D0-01A-11D-A36X-10		3723019	59302501	47	50929										
PREX1	57580	hgsc.bcm.edu	37	chr20	47262565	47262565	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	gatgcgtcgcaggacccaccCgaggtgggctctgtgatggt	16	11	1	1			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr20:47262565C>T	ENST00000371941.3	-	26	3358	c.3336G>A	c.(3334-3336)tcG>tcA	p.S1112S	PREX1_ENST00000396220.1_Silent_p.S1112S	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	1112					actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			AGGACCCACCCGAGGTGGGCT	0.587																																					p.S1112S		Atlas-SNP	.											.	PREX1	441	.	0			c.G3336A						.						68	62	64					20																	47262565		2203	4300	6503	SO:0001819	synonymous_variant	57580	exon26			CCCACCCGAGGTG	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.3336G>A	chr20.hg19:g.47262565C>T		43.0	0.0		35.0	18.0	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Silent	SNP	ENST00000371941.3	hg19	CCDS13410.1																																																																																			.	.		0.587	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		T	47262565	C	T	47262565	2	4	366	1	0	0	0	0	0	0	0	1	12488	639	23	1		1	PREX1	20	47262565	Silent	SNP	C	TCGA-ZP-A9D0-01A-11D-A36X-10	43539546	47262565	15762955	48	50930										
CASS4	57091	hgsc.bcm.edu	37	chr20	55025670	55025670	+	Frame_Shift_Del	DEL	C	C	-													0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	cccaggagccagagaagcagCagttatatgacataccagcc							TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr20:55025670delC	ENST00000360314.3	+	5	802	c.577delC	c.(577-579)cagfs	p.Q193fs	CASS4_ENST00000434344.1_Frame_Shift_Del_p.Q193fs|CASS4_ENST00000371336.3_Frame_Shift_Del_p.Q193fs	NM_001164116.1	NP_001157588.1	Q9NQ75	CASS4_HUMAN	Cas scaffolding protein family member 4	193					cell adhesion (GO:0007155)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)			breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(4)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	54						AGAGAAGCAGCAGTTATATGA	0.488																																					p.Q192fs		Atlas-INDEL	.											.	CASS4	121	.	0			c.576delG						.						92	72	78					20																	55025670		2203	4300	6503	SO:0001589	frameshift_variant	57091	exon4			.	AJ276678	CCDS33492.1, CCDS54475.1	20q13.31	2011-04-13	2008-04-14	2008-04-15	ENSG00000087589	ENSG00000087589		"Cas scaffolding proteins"	15878	protein-coding gene	gene with protein product	"HEF-like protein", "HEF1-Efs-p130Cas-like"		"chromosome 20 open reading frame 32"	C20orf32			Standard	NM_020356		Approved	HEFL, HEPL	uc002xxr.2	Q9NQ75	OTTHUMG00000032788	ENST00000360314.3:c.577delC	chr20.hg19:g.55025670delC	ENSP00000353462:p.Gln193fs	123.0	0.0		108.0	42.0	NM_001164115	E1P5Z8|Q5QPD6|Q96K09|Q9BYL5	Frame_Shift_Del	DEL	ENST00000360314.3	hg19	CCDS33492.1																																																																																			.	.		0.488	CASS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079789.2	NM_020356		-	55025670	C	-	55025670	7	5	366	1	0	1	0	1	0	0	0	0	2685	711	25	0	591	0	CASS4	20	55025670	Frame_Shift_Del	DEL	C	TCGA-ZP-A9D0-01A-11D-A36X-10	7763105	55025670	7999850	49	50931										
CLDN5	7122	hgsc.bcm.edu	37	chr22	19511459	19511459	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	tggccgggcccggggccacgCaggtggtgcactgcgcgccc	18	16	0	0			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chr22:19511459C>T	ENST00000406028.1	-	2	1635	c.575G>A	c.(574-576)tGc>tAc	p.C192Y	CLDN5_ENST00000413119.2_Missense_Mutation_p.C192Y|CLDN5_ENST00000403084.1_Missense_Mutation_p.C192Y			O00501	CLD5_HUMAN	claudin 5	107					calcium-independent cell-cell adhesion (GO:0016338)|myelination (GO:0042552)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			liver(1)|lung(2)|prostate(1)	4	Colorectal(54;0.0993)					CGGGGCCACGCAGGTGGTGCA	0.731																																					p.C192Y		Atlas-SNP	.											.	CLDN5	22	.	0			c.G575A						.						7	8	8					22																	19511459		2161	4229	6390	SO:0001583	missense	7122	exon1			GCCACGCAGGTGG	AF000959	CCDS13763.2	22q11.21	2008-08-01	2008-08-01		ENSG00000184113	ENSG00000184113		"Claudins"	2047	protein-coding gene	gene with protein product		602101	"transmembrane protein deleted in velocardiofacial syndrome"	AWAL, TMVCF		9441748, 9192844	Standard	NM_003277		Approved	CPETRL1, BEC1	uc002zpu.2	O00501	OTTHUMG00000150441	ENST00000406028.1:c.575G>A	chr22.hg19:g.19511459C>T	ENSP00000385477:p.Cys192Tyr	72.0	0.0		81.0	24.0	NM_001130861	B3KS11|Q53XW2|Q8WUW3	Missense_Mutation	SNP	ENST00000406028.1	hg19	CCDS13763.2	.	.	.	.	.	.	.	.	.	.	C	20.7	4.033652	0.75504	.	.	ENSG00000184113	ENST00000406028;ENST00000403084;ENST00000413119	D;D;D	0.89050	-2.46;-2.46;-2.46	4.96	3.91	0.45181	.	0.000000	0.85682	D	0.000000	D	0.94686	0.8286	M	0.92219	3.285	0.80722	D	1	D	0.59767	0.986	D	0.67548	0.952	D	0.94506	0.7714	10	0.87932	D	0	.	9.6628	0.39965	0.0:0.7764:0.1431:0.0805	.	192	D3DX19	.	Y	192	ENSP00000385477:C192Y;ENSP00000384554:C192Y;ENSP00000400612:C192Y	ENSP00000384554:C192Y	C	-	2	0	CLDN5	17891459	1.000000	0.71417	1.000000	0.80357	0.814000	0.46013	4.899000	0.63245	1.049000	0.40321	0.462000	0.41574	TGC	.	.		0.731	CLDN5-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318122.3	NM_003277		T	19511459	C	T	19511459	3	4	366	1	0	0	0	0	1	0	0	0	3490	710	25	3	340	3	CLDN5	22	19511459	Missense_Mutation	SNP	C	TCGA-ZP-A9D0-01A-11D-A36X-10		19511459	31793107	50	50932										
FAM48B2	170067	hgsc.bcm.edu	37	chrX	24329899	24329900	+	IGR	INS	-	-	AGCAGC													0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	gctaaagcaggagcagcagcINSaggagcaggagcaggagcag							TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chrX:24329899_24329900insAGCAGC								AC096509.1 (25105 upstream) : AC004552.1 (37025 downstream)																							ggagcagcagcaggagcaggag	0.609																																					p.A512delinsAAA		Atlas-INDEL	.											.	.	.	.	0			c.1534_1535insGCTGCT						.																																			SO:0001628	intergenic_variant	170067	exon1			.																													chrX.hg19:g.24329894_24329899dupAGCAGC		295.0	0.0		300.0	30.0	NM_001136233		In_Frame_Ins	INS		hg19																																																																																				.	.	0	0.609									AGCAGC	24329900	-	AGCAGC	24329899	6	5	366	0	1	1	1	0	0	0	0	0	5582	710	25	0		0	FAM48B2	23	24329899	IGR	INS	-	TCGA-ZP-A9D0-01A-11D-A36X-10		24329899	130940661	51	50933										
TAB3	257397	hgsc.bcm.edu	37	chrX	30873586	30873586	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	taaaaggcgatttctattcaTcctattgtcatctggactat	6	8	4	0			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chrX:30873586T>A	ENST00000378933.1	-	3	373	c.196A>T	c.(196-198)Atg>Ttg	p.M66L	TAB3_ENST00000288422.2_Missense_Mutation_p.M66L|TAB3_ENST00000378932.2_Missense_Mutation_p.M66L|TAB3-AS2_ENST00000445240.1_RNA|TAB3_ENST00000378930.3_Missense_Mutation_p.M66L|TAB3_ENST00000378928.1_5'Flank	NM_152787.3	NP_690000.2	Q8N5C8	TAB3_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 3	66					activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|skin(1)	27						TTTCTATTCATCCTATTGTCA	0.433																																					p.M66L	Pancreas(164;1598 1985 29022 43301 49529)	Atlas-SNP	.											.	TAB3	82	.	0			c.A196T						.						61	54	56					X																	30873586		2202	4300	6502	SO:0001583	missense	257397	exon6			TATTCATCCTATT	AY331591	CCDS14226.1	Xp21.2	2010-02-05	2010-02-05	2010-02-05	ENSG00000157625	ENSG00000157625			30681	protein-coding gene	gene with protein product	"TAK1 binding protein 3"	300480	"mitogen-activated protein kinase kinase kinase 7 interacting protein 3"	MAP3K7IP3		14633987, 14670075	Standard	XM_005274482		Approved		uc004dcj.3	Q8N5C8	OTTHUMG00000021329	ENST00000378933.1:c.196A>T	chrX.hg19:g.30873586T>A	ENSP00000368215:p.Met66Leu	171.0	0.0		161.0	52.0	NM_152787	A6NDD9|Q6VQR0	Missense_Mutation	SNP	ENST00000378933.1	hg19	CCDS14226.1	.	.	.	.	.	.	.	.	.	.	T	2.713	-0.268450	0.05716	.	.	ENSG00000157625	ENST00000378933;ENST00000378930;ENST00000288422;ENST00000378932	T;T;T;T	0.70399	-0.48;-0.48;-0.48;-0.48	5.44	4.27	0.50696	.	0.192203	0.56097	D	0.000029	T	0.47116	0.1428	N	0.11427	0.14	0.30810	N	0.738987	B;B	0.09022	0.002;0.001	B;B	0.04013	0.001;0.0	T	0.42378	-0.9455	10	0.14656	T	0.56	-2.84	10.0701	0.42328	0.0:0.08:0.0:0.92	.	66;66	Q8N5C8-2;Q8N5C8	.;TAB3_HUMAN	L	66	ENSP00000368215:M66L;ENSP00000368212:M66L;ENSP00000288422:M66L;ENSP00000368214:M66L	ENSP00000288422:M66L	M	-	1	0	TAB3	30783507	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.600000	0.46240	1.923000	0.55706	0.486000	0.48141	ATG	.	.		0.433	TAB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056173.1	NM_152787		A	30873586	T	A	30873586	3	1	366	1	0	0	0	0	1	0	0	0	15512	1435	50	4	1966	4	TAB3	23	30873586	Missense_Mutation	SNP	T	TCGA-ZP-A9D0-01A-11D-A36X-10	6543687	30873586	124396974	52	50934										
STAG2	10735	hgsc.bcm.edu	37	chrX	123197040	123197040	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0566037735849057	3	1	1.07851239669421	1.12987012987013	1.05454545454545	1	1	0	gatttggaaatatataccacTggacgattagaaaaggtaag	10	4	0	1			TCGA-ZP-A9D0-01A-11D-A36X-10	TCGA-ZP-A9D0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b293a3fc-fa50-456a-a8cc-42ede95b381c	67df7979-ba2c-424e-b4f2-bffcd8828c05	g.chrX:123197040T>C	ENST00000371160.1	+	19	2096	c.1806T>C	c.(1804-1806)acT>acC	p.T602T	STAG2_ENST00000354548.5_Silent_p.T533T|STAG2_ENST00000371157.3_Silent_p.T602T|STAG2_ENST00000371144.3_Silent_p.T602T|STAG2_ENST00000218089.9_Silent_p.T602T|STAG2_ENST00000371145.3_Silent_p.T602T|STAG2_ENST00000469481.1_Intron	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	602					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						TATATACCACTGGACGATTAG	0.289																																					p.T602T		Atlas-SNP	.											.	STAG2	309	.	0			c.T1806C						.						58	56	57					X																	123197040		2203	4300	6503	SO:0001819	synonymous_variant	10735	exon19			TACCACTGGACGA	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.1806T>C	chrX.hg19:g.123197040T>C		370.0	0.0		403.0	127.0	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Silent	SNP	ENST00000371160.1	hg19	CCDS14607.1																																																																																			.	.		0.289	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		C	123197040	T	C	123197040	2	2	366	1	0	0	0	0	0	0	0	1	15258	1567	55	2		2	STAG2	23	123197040	Silent	SNP	T	TCGA-ZP-A9D0-01A-11D-A36X-10	92323454	123197040	32073520	53	50935										
NPHP4	261734	hgsc.bcm.edu	37	chr1	5927958	5927958	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	cactcgctcggaacaagaccTgtgaggaggccacgctgagt	13	12	0	3			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr1:5927958T>G	ENST00000378156.4	-	24	3581		c.e24-2		NPHP4_ENST00000478423.2_Splice_Site	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4						actin cytoskeleton organization (GO:0030036)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(4)	47	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		GAACAAGACCTGTGAGGAGGC	0.602																																					.		Atlas-SNP	.											.	NPHP4	119	.	0			c.3316-2A>C						.						49	57	55					1																	5927958		2163	4260	6423	SO:0001630	splice_region_variant	261734	exon25			AAGACCTGTGAGG	AB014573	CCDS44052.1	1p36	2010-03-26			ENSG00000131697	ENSG00000131697			19104	protein-coding gene	gene with protein product	"nephroretinin", "nephrocystin-4", "POC10 centriolar protein homolog (Chlamydomonas)"	607215				11920287, 12205563	Standard	XR_244787		Approved	SLSN4, KIAA0673, POC10	uc001alq.2	O75161	OTTHUMG00000000701	ENST00000378156.4:c.3316-2A>C	chr1.hg19:g.5927958T>G		99.0	0.0		67.0	35.0	NM_015102	Q8IWC0	Splice_Site	SNP	ENST00000378156.4	hg19	CCDS44052.1	.	.	.	.	.	.	.	.	.	.	T	12.21	1.870377	0.33069	.	.	ENSG00000131697	ENST00000378156	.	.	.	5.57	5.57	0.84162	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.9117	0.70761	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	NPHP4	5850545	1.000000	0.71417	0.994000	0.49952	0.052000	0.14988	7.900000	0.87376	2.117000	0.64856	0.459000	0.35465	.	.	.		0.602	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2		Intron	G	5927958	T	G	5927958	5	3	367	1	0	0	0	0	0	0	1	0	10590	1594	55	5	994	5	NPHP4	1	5927958	Splice_Site	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10		5927958	243322663	1	50936										
ERRFI1	54206	hgsc.bcm.edu	37	chr1	8073423	8073423	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ccatttgtttcttctgcttcCctaaaaaatttttcatattt	2	9	3	0			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr1:8073423C>A	ENST00000377482.5	-	4	1459	c.1236G>T	c.(1234-1236)agG>agT	p.R412S	ERRFI1_ENST00000474874.1_Intron	NM_018948.3	NP_061821.1	Q9UJM3	ERRFI_HUMAN	ERBB receptor feedback inhibitor 1	412					lung alveolus development (GO:0048286)|lung epithelium development (GO:0060428)|lung vasculature development (GO:0060426)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of protein autophosphorylation (GO:0031953)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of keratinocyte differentiation (GO:0045616)|response to stress (GO:0006950)|skin morphogenesis (GO:0043589)	cytoplasm (GO:0005737)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|Rho GTPase activator activity (GO:0005100)			breast(1)|endometrium(2)|large_intestine(3)|liver(3)|lung(3)|ovary(1)|prostate(1)|skin(2)	16	Ovarian(185;0.06)|all_lung(157;0.151)	all_epithelial(116;1.76e-16)|all_lung(118;3.66e-05)|Lung NSC(185;0.000163)|Renal(390;0.000469)|Colorectal(325;0.0033)|Breast(348;0.0044)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.11)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;2.33e-70)|GBM - Glioblastoma multiforme(8;8.05e-37)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;6.9e-06)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.000985)|READ - Rectum adenocarcinoma(331;0.0642)		CTTCTGCTTCCCTAAAAAATT	0.408																																					p.R412S		Atlas-SNP	.											.	ERRFI1	42	.	0			c.G1236T						.						144	140	141					1																	8073423		2203	4300	6503	SO:0001583	missense	54206	exon4			TGCTTCCCTAAAA	BC025337	CCDS94.1	1p36.23	2008-02-05			ENSG00000116285	ENSG00000116285			18185	protein-coding gene	gene with protein product		608069				10749885, 2780291, 12226756, 11003669	Standard	NM_018948		Approved	MIG-6, GENE-33, RALT	uc001aoz.3	Q9UJM3	OTTHUMG00000001221	ENST00000377482.5:c.1236G>T	chr1.hg19:g.8073423C>A	ENSP00000366702:p.Arg412Ser	158.0	0.0		129.0	47.0	NM_018948	B2RDX9|Q9NTG9|Q9UD05	Missense_Mutation	SNP	ENST00000377482.5	hg19	CCDS94.1	.	.	.	.	.	.	.	.	.	.	C	15.07	2.724773	0.48833	.	.	ENSG00000116285	ENST00000377482	T	0.18338	2.22	5.9	4.0	0.46444	.	0.141384	0.48286	D	0.000200	T	0.17152	0.0412	L	0.57536	1.79	0.80722	D	1	B	0.19706	0.038	B	0.14023	0.01	T	0.03534	-1.1027	10	0.72032	D	0.01	-3.5302	7.6674	0.28439	0.0:0.7082:0.1371:0.1547	.	412	Q9UJM3	ERRFI_HUMAN	S	412	ENSP00000366702:R412S	ENSP00000366702:R412S	R	-	3	2	ERRFI1	7996010	0.978000	0.34361	0.736000	0.30914	0.923000	0.55619	1.818000	0.39012	0.802000	0.34089	0.650000	0.86243	AGG	.	.		0.408	ERRFI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003617.1	NM_018948		A	8073423	C	A	8073423	3	1	367	1	0	0	0	0	1	0	0	0	5246	622	22	3	156	3	ERRFI1	1	8073423	Missense_Mutation	SNP	C	TCGA-ZP-A9D1-01A-11D-A382-10	2145465	8073423	241177198	2	50937										
PADI1	29943	hgsc.bcm.edu	37	chr1	17555182	17555182	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	agtgtctgtcctatgaagttGagcgacagccaggggagcag	15	8	1	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr1:17555182G>T	ENST00000375471.4	+	7	807	c.715G>T	c.(715-717)Gag>Tag	p.E239*		NM_013358.2	NP_037490.2	Q9ULC6	PADI1_HUMAN	peptidyl arginine deiminase, type I	239					protein citrullination (GO:0018101)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|skin(1)|stomach(1)|urinary_tract(1)	28		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00054)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00522)|BRCA - Breast invasive adenocarcinoma(304;1.3e-05)|COAD - Colon adenocarcinoma(227;1.31e-05)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(196;0.0069)|READ - Rectum adenocarcinoma(331;0.0681)|Lung(427;0.197)	L-Citrulline(DB00155)	CTATGAAGTTGAGCGACAGCC	0.567																																					p.E239X	Esophageal Squamous(80;414 1257 4580 27746 50832)	Atlas-SNP	.											.	PADI1	77	.	0			c.G715T						.						147	156	153					1																	17555182		2203	4300	6503	SO:0001587	stop_gained	29943	exon7			GAAGTTGAGCGAC	AB033768	CCDS178.1	1p36.13	2008-07-18			ENSG00000142623	ENSG00000142623	3.5.3.15	"Peptidyl arginine deiminases"	18367	protein-coding gene	gene with protein product	"peptidylarginine deiminase type I", "protein-arginine deiminase type-1", "hPAD-colony 10"	607934				12416996	Standard	NM_013358		Approved	HPAD10, PDI1, PDI, PAD1	uc001bah.1	Q9ULC6	OTTHUMG00000002294	ENST00000375471.4:c.715G>T	chr1.hg19:g.17555182G>T	ENSP00000364620:p.Glu239*	109.0	0.0		71.0	19.0	NM_013358	A1L4K6|Q70SX6	Nonsense_Mutation	SNP	ENST00000375471.4	hg19	CCDS178.1	.	.	.	.	.	.	.	.	.	.	G	15.98	2.991974	0.54041	.	.	ENSG00000142623	ENST00000375471	.	.	.	4.83	1.85	0.25348	.	0.553031	0.19267	N	0.118520	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	0.07030	T	0.85	-13.3718	5.5782	0.17235	0.2492:0.1406:0.6102:0.0	.	.	.	.	X	239	.	ENSP00000364620:E239X	E	+	1	0	PADI1	17427769	0.001000	0.12720	0.017000	0.16124	0.065000	0.16274	0.323000	0.19593	0.441000	0.26529	0.561000	0.74099	GAG	.	.		0.567	PADI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006621.1	NM_013358		T	17555182	G	T	17555182	4	4	367	1	0	0	0	0	0	1	0	0	11386	1291	45	3	741	3	PADI1	1	17555182	Nonsense_Mutation	SNP	G	TCGA-ZP-A9D1-01A-11D-A382-10	9481759	17555182	231695439	3	50938										
LRRC41	10489	hgsc.bcm.edu	37	chr1	46751145	46751145	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	gaatagctccaaggtggagaTgctgcggaatctttgtgaag	14	6	1	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr1:46751145T>C	ENST00000343304.6	-	4	1669	c.1384A>G	c.(1384-1386)Atc>Gtc	p.I462V	LRRC41_ENST00000472710.1_5'UTR	NM_006369.4	NP_006360.3	Q15345	LRC41_HUMAN	leucine rich repeat containing 41	462					protein ubiquitination (GO:0016567)	membrane (GO:0016020)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(7)|ovary(3)|pancreas(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Acute lymphoblastic leukemia(166;0.155)					AAGGTGGAGATGCTGCGGAAT	0.557																																					p.I462V		Atlas-SNP	.											.	LRRC41	74	.	0			c.A1384G						.						101	95	97					1																	46751145		2203	4300	6503	SO:0001583	missense	10489	exon4			TGGAGATGCTGCG	AK024051	CCDS533.1	1p34.1	2008-02-05			ENSG00000132128	ENSG00000132128			16917	protein-coding gene	gene with protein product						11384984	Standard	XM_005270376		Approved	MUF1	uc001cpn.3	Q15345	OTTHUMG00000007810	ENST00000343304.6:c.1384A>G	chr1.hg19:g.46751145T>C	ENSP00000343298:p.Ile462Val	74.0	0.0		50.0	25.0	NM_006369	A8K5G8|Q3MJ96|Q5TDF5|Q71RA8|Q9BSM0	Missense_Mutation	SNP	ENST00000343304.6	hg19	CCDS533.1	.	.	.	.	.	.	.	.	.	.	t	1.866	-0.461401	0.04508	.	.	ENSG00000132128	ENST00000343304;ENST00000371972	T	0.53640	0.61	5.16	4.04	0.47022	.	0.089161	0.46145	D	0.000317	T	0.17323	0.0416	N	0.03608	-0.345	0.26917	N	0.966763	B;B;B	0.18461	0.013;0.028;0.013	B;B;B	0.22386	0.019;0.039;0.011	T	0.34378	-0.9831	10	0.02654	T	1	8.1046	4.3228	0.11025	0.0:0.3013:0.0:0.6987	.	462;440;462	Q15345-3;E9PE58;Q15345	.;.;LRC41_HUMAN	V	462;440	ENSP00000343298:I462V	ENSP00000343298:I462V	I	-	1	0	LRRC41	46523732	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	2.472000	0.45136	1.962000	0.57031	0.370000	0.22315	ATC	.	.		0.557	LRRC41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021438.1	NM_006369		C	46751145	T	C	46751145	3	2	367	1	0	0	0	0	1	0	0	0	9008	1464	51	2	1082	2	LRRC41	1	46751145	Missense_Mutation	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	29195963	46751145	202499476	4	50939										
OLFM3	118427	hgsc.bcm.edu	37	chr1	102271685	102271685	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	catccaagcaccaaatcgggTtccagatgtcttgactgtaa	8	11	1	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr1:102271685T>C	ENST00000338858.5	-	5	705	c.706A>G	c.(706-708)Acc>Gcc	p.T236A	OLFM3_ENST00000462354.1_5'UTR|OLFM3_ENST00000536598.1_3'UTR|OLFM3_ENST00000370103.4_Missense_Mutation_p.T216A			Q96PB7	NOE3_HUMAN	olfactomedin 3	236	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				eye photoreceptor cell development (GO:0042462)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)				breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(24)|ovary(3)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	43		all_epithelial(167;1.87e-06)|all_lung(203;8.12e-05)|Lung NSC(277;0.000189)		all cancers(265;0.0843)|Epithelial(280;0.0921)|COAD - Colon adenocarcinoma(174;0.145)		CCAAATCGGGTTCCAGATGTC	0.418																																					p.T216A		Atlas-SNP	.											.	OLFM3	178	.	0			c.A646G						.						166	150	155					1																	102271685		2203	4300	6503	SO:0001583	missense	118427	exon5			ATCGGGTTCCAGA	AF397392	CCDS30781.1, CCDS72832.1	1p22	2008-05-23			ENSG00000118733	ENSG00000118733			17990	protein-coding gene	gene with protein product	"optimedin"	607567				12019210, 16115881	Standard	NM_001288821		Approved	NOE3	uc001dug.2	Q96PB7	OTTHUMG00000010941	ENST00000338858.5:c.706A>G	chr1.hg19:g.102271685T>C	ENSP00000345192:p.Thr236Ala	95.0	0.0		103.0	47.0	NM_058170	Q5T3V6|Q6IMI7|Q6IMI8|Q6IMI9|Q6IMJ1|Q8TBG1|Q96PB2|Q96PB3|Q96PB4|Q96PB5|Q96PB6	Missense_Mutation	SNP	ENST00000338858.5	hg19		.	.	.	.	.	.	.	.	.	.	T	15.13	2.742796	0.49151	.	.	ENSG00000118733	ENST00000424771;ENST00000370103;ENST00000338858	D;D	0.88431	-2.38;-2.38	5.17	5.17	0.71159	Olfactomedin-like (3);	0.050460	0.85682	D	0.000000	T	0.76730	0.4028	L	0.42245	1.32	0.80722	D	1	B;B	0.20052	0.019;0.041	B;B	0.26614	0.071;0.063	T	0.73322	-0.4019	10	0.23891	T	0.37	.	11.0763	0.48034	0.0:0.0:0.1551:0.8449	.	216;236	Q5T3V6;Q96PB7	.;NOE3_HUMAN	A	87;216;236	ENSP00000359121:T216A;ENSP00000345192:T236A	ENSP00000345192:T236A	T	-	1	0	OLFM3	102044273	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.979000	0.56888	1.962000	0.57031	0.482000	0.46254	ACC	.	.		0.418	OLFM3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000030142.1			C	102271685	T	C	102271685	3	2	367	1	0	0	0	0	1	0	0	0	10863	1725	60	2	738	2	OLFM3	1	102271685	Missense_Mutation	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	55520540	102271685	146978936	5	50940										
C1orf103	55791	hgsc.bcm.edu	37	chr1	111494486	111494486	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	gatcgcgtcccactaggatcGatggtactcaatggtggcat	12	10	1	0			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr1:111494486G>T	ENST00000369763.4	-	2	1410	c.1020C>A	c.(1018-1020)atC>atA	p.I340I	LRIF1_ENST00000494675.1_Intron|LRIF1_ENST00000485275.2_Intron|RP11-96K19.2_ENST00000440689.1_RNA	NM_018372.3	NP_060842.3	Q5T3J3	LRIF1_HUMAN	ligand dependent nuclear receptor interacting factor 1	340					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)				endometrium(2)|kidney(2)|large_intestine(7)|lung(12)|ovary(2)|skin(1)|urinary_tract(2)	28						CACTAGGATCGATGGTACTCA	0.338																																					p.I340I		Atlas-SNP	.											.	LRIF1	65	.	0			c.C1020A						.						72	74	73					1																	111494486		2202	4300	6502	SO:0001819	synonymous_variant	55791	exon2			AGGATCGATGGTA	AY190122	CCDS30800.1, CCDS41366.1	1p13.3	2011-04-15	2011-04-15	2011-04-15	ENSG00000121931	ENSG00000121931			30299	protein-coding gene	gene with protein product	"receptor interacting factor 1"	615354	"chromosome 1 open reading frame 103"	C1orf103		17455211	Standard	NM_018372		Approved	RIF1, FLJ11269	uc001eaa.3	Q5T3J3	OTTHUMG00000011913	ENST00000369763.4:c.1020C>A	chr1.hg19:g.111494486G>T		68.0	0.0		46.0	22.0	NM_018372	Q86XS4|Q8N3B6|Q96HT4|Q9NUM5|Q9NV32	Silent	SNP	ENST00000369763.4	hg19	CCDS30800.1																																																																																			.	.		0.338	LRIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000032932.2	NM_018372		T	111494486	G	T	111494486	2	4	367	1	0	0	0	0	0	0	0	1	1979	1048	37	1		1	C1orf103	1	111494486	Silent	SNP	G	TCGA-ZP-A9D1-01A-11D-A382-10	9222801	111494486	137756135	6	50941										
BCL9	607	hgsc.bcm.edu	37	chr1	147092530	147092530	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	tggcaggcagccaggtgcatTccccaggcattaaccctctg	11	14	1	0			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr1:147092530T>C	ENST00000234739.3	+	8	3309	c.2569T>C	c.(2569-2571)Tcc>Ccc	p.S857P		NM_004326.2	NP_004317.2	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	857	Pro-rich.				canonical Wnt signaling pathway (GO:0060070)|myotube differentiation involved in skeletal muscle regeneration (GO:0014908)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				breast(1)|large_intestine(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	7	all_hematologic(923;0.115)					CCAGGTGCATTCCCCAGGCAT	0.612			T	"IGH@, IGL@"	B-ALL																																p.S857P		Atlas-SNP	.		Dom	yes		1	1q21	607	B-cell CLL/lymphoma 9		L	.	BCL9	150	.	0			c.T2569C						.						64	62	63					1																	147092530		2203	4300	6503	SO:0001583	missense	607	exon8			GTGCATTCCCCAG	Y13620	CCDS30833.1	1q21	2008-02-05			ENSG00000116128	ENSG00000116128			1008	protein-coding gene	gene with protein product		602597				9490669	Standard	NM_004326		Approved		uc001epq.3	O00512	OTTHUMG00000014031	ENST00000234739.3:c.2569T>C	chr1.hg19:g.147092530T>C	ENSP00000234739:p.Ser857Pro	39.0	0.0		69.0	21.0	NM_004326	Q5T489	Missense_Mutation	SNP	ENST00000234739.3	hg19	CCDS30833.1	.	.	.	.	.	.	.	.	.	.	T	15.35	2.807150	0.50421	.	.	ENSG00000116128	ENST00000234739	T	0.63744	-0.06	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.65133	0.2662	L	0.36672	1.1	0.58432	D	0.999999	D;D	0.71674	0.998;0.998	D;D	0.78314	0.991;0.991	T	0.70662	-0.4810	10	0.87932	D	0	-16.7505	15.5185	0.75846	0.0:0.0:0.0:1.0	.	857;857	Q1JQ81;O00512	.;BCL9_HUMAN	P	857	ENSP00000234739:S857P	ENSP00000234739:S857P	S	+	1	0	BCL9	145559154	1.000000	0.71417	0.990000	0.47175	0.245000	0.25701	6.113000	0.71553	2.246000	0.74042	0.533000	0.62120	TCC	.	.		0.612	BCL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039468.1	NM_004326		C	147092530	T	C	147092530	3	2	367	1	0	0	0	0	1	0	0	0	1381	1783	62	2	2587	2	BCL9	1	147092530	Missense_Mutation	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	35598044	147092530	102158091	7	50942										
TCHH	7062	hgsc.bcm.edu	37	chr1	152083351	152083351	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	gcctggccgacagcctctgaCggcccctctcgctcttttcc	9	19	3	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr1:152083351C>A	ENST00000368804.1	-	2	2341	c.2342G>T	c.(2341-2343)cGt>cTt	p.R781L		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	781					keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CAGCCTCTGACGGCCCCTCTC	0.687																																					p.R781L		Atlas-SNP	.											.	TCHH	275	.	0			c.G2342T						.						24	32	29					1																	152083351		2032	4197	6229	SO:0001583	missense	7062	exon3			CTCTGACGGCCCC	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"EF-hand domain containing"	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.2342G>T	chr1.hg19:g.152083351C>A	ENSP00000357794:p.Arg781Leu	65.0	0.0		96.0	27.0	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	hg19	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	c	2.502	-0.314972	0.05422	.	.	ENSG00000159450	ENST00000368804	T	0.07216	3.21	2.98	1.93	0.25924	.	.	.	.	.	T	0.02380	0.0073	N	0.24115	0.695	0.09310	N	1	P	0.52842	0.956	P	0.46110	0.504	T	0.46978	-0.9152	9	0.25106	T	0.35	.	7.2234	0.26002	0.0:0.7212:0.2788:0.0	.	781	Q07283	TRHY_HUMAN	L	781	ENSP00000357794:R781L	ENSP00000357794:R781L	R	-	2	0	TCHH	150349975	0.000000	0.05858	0.088000	0.20740	0.006000	0.05464	-1.409000	0.02483	1.681000	0.50988	0.306000	0.20318	CGT	.	.		0.687	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		A	152083351	C	A	152083351	3	1	367	1	0	0	0	0	1	0	0	0	15715	536	19	1	3493	1	TCHH	1	152083351	Missense_Mutation	SNP	C	TCGA-ZP-A9D1-01A-11D-A382-10	4990821	152083351	97167270	8	50943										
FLG	2312	hgsc.bcm.edu	37	chr1	152281292	152281292	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	tgcagatgaagcttgtccatGcccaatgcctgagtgtctgg	12	10	1	3			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr1:152281292G>A	ENST00000368799.1	-	3	6105	c.6070C>T	c.(6070-6072)Cat>Tat	p.H2024Y	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2024	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCTTGTCCATGCCCAATGCCT	0.537									Ichthyosis																												p.H2024Y		Atlas-SNP	.											.	FLG	900	.	0			c.C6070T						.						623	519	554					1																	152281292		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GTCCATGCCCAAT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.6070C>T	chr1.hg19:g.152281292G>A	ENSP00000357789:p.His2024Tyr	102.0	0.0		145.0	16.0	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	hg19	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	g	6.483	0.457222	0.12342	.	.	ENSG00000143631	ENST00000368799	T	0.03717	3.83	3.73	2.8	0.32819	.	.	.	.	.	T	0.00724	0.0024	N	0.08118	0	0.09310	N	1	B	0.22541	0.071	B	0.25759	0.063	T	0.48080	-0.9066	9	0.26408	T	0.33	-7.6777	7.4586	0.27280	0.1229:0.0:0.8771:0.0	.	2024	P20930	FILA_HUMAN	Y	2024	ENSP00000357789:H2024Y	ENSP00000357789:H2024Y	H	-	1	0	FLG	150547916	0.013000	0.17824	0.001000	0.08648	0.001000	0.01503	2.227000	0.42972	0.896000	0.36366	0.485000	0.47835	CAT	.	.		0.537	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152281292	G	A	152281292	3	1	367	1	0	0	0	0	1	0	0	0	5930	1319	46	3	6119	3	FLG	1	152281292	Missense_Mutation	SNP	G	TCGA-ZP-A9D1-01A-11D-A382-10	197941	152281292	96969329	9	50944										
LCE2D	353141	hgsc.bcm.edu	37	chr1	152636635	152636635	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ccccctcccaaatgtcctccCaagtgtaccccaaaatgtcc	4	19	0	0			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr1:152636635C>A	ENST00000368784.1	+	2	109	c.54C>A	c.(52-54)ccC>ccA	p.P18P		NM_178430.2	NP_848517.1	Q5TA82	LCE2D_HUMAN	late cornified envelope 2D	18	Cys-rich.				keratinization (GO:0031424)					large_intestine(1)|lung(7)|prostate(2)	10	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			AATGTCCTCCCAAGTGTACCC	0.522																																					p.P18P		Atlas-SNP	.											.	LCE2D	26	.	0			c.C54A						.						107	113	111					1																	152636635		2203	4300	6503	SO:0001819	synonymous_variant	353141	exon2			TCCTCCCAAGTGT	BI670513	CCDS1018.1	1q21.3	2008-02-05	2004-10-11	2004-10-15	ENSG00000187223	ENSG00000187223		"Late cornified envelopes"	16518	protein-coding gene	gene with protein product		612612	"small proline rich-like (epidermal differentiation complex) 1A"	SPRL1A		11698679	Standard	NM_178430		Approved	LEP12	uc001fag.4	Q5TA82	OTTHUMG00000014400	ENST00000368784.1:c.54C>A	chr1.hg19:g.152636635C>A		207.0	0.0		275.0	59.0	NM_178430	A1L4M8	Silent	SNP	ENST00000368784.1	hg19	CCDS1018.1																																																																																			.	.		0.522	LCE2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040058.1	NM_178430		A	152636635	C	A	152636635	2	1	367	1	0	0	0	0	0	0	0	1	8677	581	21	3		3	LCE2D	1	152636635	Silent	SNP	C	TCGA-ZP-A9D1-01A-11D-A382-10	355343	152636635	96613986	10	50945										
PYGO2	90780	hgsc.bcm.edu	37	chr1	154931793	154931793	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ggagcccctgaccaggtctcTggagaggagaagggccaaaa	15	10	1	3			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr1:154931793T>A	ENST00000368457.2	-	3	854	c.683A>T	c.(682-684)cAg>cTg	p.Q228L	RP11-307C12.12_ENST00000605085.1_RNA|PYGO2_ENST00000368456.1_Missense_Mutation_p.Q191L|PYGO2_ENST00000483463.1_5'Flank	NM_138300.3	NP_612157.1	Q9BRQ0	PYGO2_HUMAN	pygopus family PHD finger 2	228	Pro-rich.				brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|developmental growth (GO:0048589)|in utero embryonic development (GO:0001701)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|mammary gland development (GO:0030879)|palate development (GO:0060021)|positive regulation of chromatin binding (GO:0035563)|post-embryonic development (GO:0009791)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|spermatid nucleus differentiation (GO:0007289)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone acetyltransferase regulator activity (GO:0035034)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(3)|skin(2)|urinary_tract(1)	10	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			ACCAGGTCTCTGGAGAGGAGA	0.637																																					p.Q228L	NSCLC(87;357 1460 1955 21029 23522)	Atlas-SNP	.											.	PYGO2	32	.	0			c.A683T						.						29	34	32					1																	154931793		2203	4300	6503	SO:0001583	missense	90780	exon3			GGTCTCTGGAGAG	BC006132	CCDS1075.1	1q22	2013-10-09	2013-10-09		ENSG00000163348	ENSG00000163348		"Zinc fingers, PHD-type"	30257	protein-coding gene	gene with protein product		606903	"pygopus homolog 2 (Drosophila)"			11988739	Standard	NM_138300		Approved		uc001fft.3	Q9BRQ0	OTTHUMG00000037370	ENST00000368457.2:c.683A>T	chr1.hg19:g.154931793T>A	ENSP00000357442:p.Gln228Leu	134.0	0.0		183.0	42.0	NM_138300	Q8WYZ4|Q96CY2	Missense_Mutation	SNP	ENST00000368457.2	hg19	CCDS1075.1	.	.	.	.	.	.	.	.	.	.	T	13.41	2.227446	0.39399	.	.	ENSG00000163348	ENST00000368457;ENST00000368456	T;T	0.48522	0.81;0.83	4.72	4.72	0.59763	.	0.383874	0.21678	N	0.070764	T	0.17408	0.0418	N	0.19112	0.55	0.45962	D	0.998789	P	0.37864	0.61	B	0.34873	0.191	T	0.05354	-1.0890	10	0.31617	T	0.26	-4.3103	11.8504	0.52407	0.0:0.0:0.0:1.0	.	228	Q9BRQ0	PYGO2_HUMAN	L	228;191	ENSP00000357442:Q228L;ENSP00000357441:Q191L	ENSP00000357441:Q191L	Q	-	2	0	PYGO2	153198417	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.648000	0.46647	1.988000	0.58038	0.379000	0.24179	CAG	.	.		0.637	PYGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090949.1	NM_138300		A	154931793	T	A	154931793	3	1	367	1	0	0	0	0	1	0	0	0	12879	1580	55	4	541	4	PYGO2	1	154931793	Missense_Mutation	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	2295158	154931793	94318828	11	50946										
RUSC1	23623	hgsc.bcm.edu	37	chr1	155292300	155292300	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	cagagaaaactaaagctgaaTggaaaaccactgaaaacaat	7	7	0	3			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr1:155292300T>C	ENST00000368352.5	+	2	887	c.736T>C	c.(736-738)Tgg>Cgg	p.W246R	RUSC1-AS1_ENST00000543656.1_RNA|RUSC1_ENST00000292254.4_5'Flank|RUSC1-AS1_ENST00000443642.1_RNA|RUSC1-AS1_ENST00000450199.1_RNA|RUSC1_ENST00000368349.4_5'Flank|RUSC1-AS1_ENST00000446880.1_RNA|RUSC1_ENST00000368347.4_5'Flank|RUSC1_ENST00000368354.3_Missense_Mutation_p.W246R	NM_001105203.1	NP_001098673.1	Q9BVN2	RUSC1_HUMAN	RUN and SH3 domain containing 1	246					positive regulation of signal transduction (GO:0009967)|protein polyubiquitination (GO:0000209)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(2)|skin(1)|urinary_tract(1)	21	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;1.55e-10)|all cancers(21;4.15e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)			TAAAGCTGAATGGAAAACCAC	0.413																																					p.W246R		Atlas-SNP	.											.	RUSC1	85	.	0			c.T736C						.						98	100	99					1																	155292300		1844	4076	5920	SO:0001583	missense	23623	exon2			GCTGAATGGAAAA	AB026894	CCDS1112.1, CCDS41410.1, CCDS41411.1, CCDS41412.1	1q21-q22	2011-04-28			ENSG00000160753	ENSG00000160753			17153	protein-coding gene	gene with protein product						10760598	Standard	NM_001105203		Approved	NESCA	uc001fkj.2	Q9BVN2	OTTHUMG00000013910	ENST00000368352.5:c.736T>C	chr1.hg19:g.155292300T>C	ENSP00000357336:p.Trp246Arg	252.0	0.0		349.0	92.0	NM_001105203	B3KWM9|Q5T9U9|Q5T9V0|Q5T9V1|Q5T9V2|Q9UPY4|Q9Y4T5	Missense_Mutation	SNP	ENST00000368352.5	hg19	CCDS41410.1	.	.	.	.	.	.	.	.	.	.	T	7.491	0.650587	0.14516	.	.	ENSG00000160753	ENST00000368354;ENST00000368352	T;T	0.38887	1.19;1.11	4.6	2.13	0.27403	.	0.599178	0.14252	N	0.331411	T	0.13670	0.0331	L	0.29908	0.895	0.45594	D	0.998532	P	0.36616	0.561	B	0.34242	0.178	T	0.06232	-1.0838	10	0.72032	D	0.01	-11.3603	5.1765	0.15137	0.0:0.0969:0.3538:0.5493	.	246	Q9BVN2	RUSC1_HUMAN	R	246	ENSP00000357338:W246R;ENSP00000357336:W246R	ENSP00000357336:W246R	W	+	1	0	RUSC1	153558924	0.931000	0.31567	0.459000	0.27081	0.045000	0.14185	1.110000	0.31147	0.747000	0.32809	0.454000	0.30748	TGG	.	.		0.413	RUSC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039071.1			C	155292300	T	C	155292300	3	2	367	1	0	0	0	0	1	0	0	0	13765	1464	51	2	738	2	RUSC1	1	155292300	Missense_Mutation	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	360507	155292300	93958321	12	50947										
FAM5B	57795	hgsc.bcm.edu	37	chr1	177199111	177199111	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ctgcctggctgggtgttggcTgtctcagccacggcggctgc	16	13	1	0			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr1:177199111T>A	ENST00000361539.4	+	2	411	c.99T>A	c.(97-99)gcT>gcA	p.A33A		NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	33					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	extracellular region (GO:0005576)											GGGTGTTGGCTGTCTCAGCCA	0.692																																					p.A33A		Atlas-SNP	.											.	FAM5B	191	.	0			c.T99A						.						28	33	32					1																	177199111		2202	4298	6500	SO:0001819	synonymous_variant	57795	exon2			GTTGGCTGTCTCA		CCDS1320.1	1q24	2013-08-06	2013-08-06	2013-07-31	ENSG00000198797	ENSG00000198797			13746	protein-coding gene	gene with protein product			"family with sequence similarity 5, member B"	FAM5B		15193423	Standard	NM_021165		Approved	DBCCR1L2	uc001glf.3	Q9C0B6	OTTHUMG00000034953	ENST00000361539.4:c.99T>A	chr1.hg19:g.177199111T>A		222.0	0.0		301.0	93.0	NM_021165	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Silent	SNP	ENST00000361539.4	hg19	CCDS1320.1																																																																																			.	.		0.692	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1	NM_021165		A	177199111	T	A	177199111	2	1	367	1	0	0	0	0	0	0	0	1	5601	1567	55	4		4	FAM5B	1	177199111	Silent	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	21906811	177199111	72051510	13	50948										
C1orf49	84066	hgsc.bcm.edu	37	chr1	178485749	178485749	+	Splice_Site	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	catgcctttcttccttgttaGataaaggatctaatggacaa	7	8	2	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr1:178485749G>T	ENST00000319416.2	+	5	328		c.e5-1		TEX35_ENST00000367643.3_Splice_Site|TEX35_ENST00000258298.2_Splice_Site|TEX35_ENST00000367639.1_Splice_Site|TEX35_ENST00000367641.3_Splice_Site|TEX35_ENST00000367642.3_Intron	NM_032126.4	NP_115502.2			testis expressed 35																		TTCCTTGTTAGATAAAGGATC	0.408																																					.		Atlas-SNP	.											C1orf49_ENST00000367643,NS,carcinoma,0,2	TEX35	15	.	0			c.217-1G>T						.						124	105	111					1																	178485749		2203	4300	6503	SO:0001630	splice_region_variant	84066	exon5			TTGTTAGATAAAG	AL136694	CCDS1323.1, CCDS53433.1, CCDS53434.1	1q25.2	2014-01-28	2012-06-29	2012-06-29	ENSG00000240021	ENSG00000240021			25366	protein-coding gene	gene with protein product	"Testis-Specific Conserved gene 24kDa"		"chromosome 1 open reading frame 49"	C1orf49		11230166, 17077512	Standard	NM_032126		Approved	DKFZP564J047, TSC24	uc001glt.2	Q5T0J7	OTTHUMG00000035023	ENST00000319416.2:c.217-1G>T	chr1.hg19:g.178485749G>T		114.0	0.0		170.0	43.0	NM_001170724		Splice_Site	SNP	ENST00000319416.2	hg19	CCDS1323.1	.	.	.	.	.	.	.	.	.	.	G	9.408	1.079864	0.20309	.	.	ENSG00000240021	ENST00000319416;ENST00000367643;ENST00000367641;ENST00000367639	.	.	.	5.12	5.12	0.69794	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4459	0.67349	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	C1orf49	176752372	1.000000	0.71417	0.996000	0.52242	0.048000	0.14542	4.225000	0.58600	2.542000	0.85734	0.655000	0.94253	.	.	.		0.408	TEX35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084917.1	NM_032126	Intron	T	178485749	G	T	178485749	5	4	367	1	0	0	0	0	0	0	1	0	2043	956	33	3	258	3	C1orf49	1	178485749	Splice_Site	SNP	G	TCGA-ZP-A9D1-01A-11D-A382-10	1286638	178485749	70764872	14	50949										
TPR	7175	hgsc.bcm.edu	37	chr1	186329450	186329450	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	actatcttagctacagctgcTgcagtaggagacatggcggc	12	10	1	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr1:186329450T>C	ENST00000367478.4	-	11	1442	c.1146A>G	c.(1144-1146)gcA>gcG	p.A382A	TPR_ENST00000474852.1_5'UTR	NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	382					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		CTACAGCTGCTGCAGTAGGAG	0.368			T	NTRK1	papillary thyroid																																p.A382A		Atlas-SNP	.		Dom	yes		1	1q25	7175	translocated promoter region		E	.	TPR	441	.	0			c.A1146G						.						76	77	77					1																	186329450		1850	4106	5956	SO:0001819	synonymous_variant	7175	exon11			AGCTGCTGCAGTA	U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"translocated promoter region (to activated MET oncogene)"			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.1146A>G	chr1.hg19:g.186329450T>C		374.0	0.0		592.0	66.0	NM_003292	Q15655|Q5SWY0|Q99968	Silent	SNP	ENST00000367478.4	hg19	CCDS41446.1																																																																																			.	.		0.368	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292		C	186329450	T	C	186329450	2	2	367	1	0	0	0	0	0	0	0	1	16431	1567	55	2		2	TPR	1	186329450	Silent	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	7843701	186329450	62921171	15	50950										
RGS1	5996	hgsc.bcm.edu	37	chr1	192548402	192548402	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	atcccaggttcctcaaatcaGatatttacttaaatcttcta	3	10	4	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr1:192548402G>T	ENST00000367459.3	+	5	646	c.580G>T	c.(580-582)Gat>Tat	p.D194Y		NM_002922.3	NP_002913.3	Q08116	RGS1_HUMAN	regulator of G-protein signaling 1	194	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.			D -> H (in Ref. 5; CAA51826). {ECO:0000305}.	adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|immune response (GO:0006955)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)			kidney(8)|large_intestine(1)|lung(13)	22		Breast(1374;0.188)				CCTCAAATCAGATATTTACTT	0.398																																					p.D194Y		Atlas-SNP	.											.	RGS1	75	.	0			c.G580T						.						63	66	65					1																	192548402		2203	4300	6503	SO:0001583	missense	5996	exon5			AAATCAGATATTT	AF493925	CCDS1375.2	1q31	2008-02-05	2007-08-14		ENSG00000090104	ENSG00000090104		"Regulators of G-protein signaling"	9991	protein-coding gene	gene with protein product		600323	"regulator of G-protein signalling 1"	IER1		8241276, 8602223	Standard	NM_002922		Approved	1R20, IR20, BL34	uc001gsi.1	Q08116	OTTHUMG00000035598	ENST00000367459.3:c.580G>T	chr1.hg19:g.192548402G>T	ENSP00000356429:p.Asp194Tyr	340.0	1.0		549.0	252.0	NM_002922	B2RDM9|B4DZY0|Q07918|Q9H1W2	Missense_Mutation	SNP	ENST00000367459.3	hg19	CCDS1375.2	.	.	.	.	.	.	.	.	.	.	G	20.5	3.995080	0.74703	.	.	ENSG00000090104	ENST00000367459	T	0.02140	4.43	5.68	0.195	0.15151	Regulator of G protein signalling (3);Regulator of G protein signalling superfamily (1);Regulator of G-protein signaling, domain 1 (1);	0.491930	0.21786	N	0.069138	T	0.10594	0.0259	M	0.87381	2.88	0.80722	D	1	P	0.47302	0.893	P	0.60286	0.872	T	0.00516	-1.1694	10	0.72032	D	0.01	.	9.9548	0.41660	0.4975:0.0:0.5025:0.0	.	194	Q08116	RGS1_HUMAN	Y	194	ENSP00000356429:D194Y	ENSP00000356429:D194Y	D	+	1	0	RGS1	190815025	0.932000	0.31603	0.989000	0.46669	0.996000	0.88848	1.163000	0.31798	-0.156000	0.11079	0.591000	0.81541	GAT	.	.		0.398	RGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086391.1	NM_002922		T	192548402	G	T	192548402	3	4	367	1	0	0	0	0	1	0	0	0	13307	942	33	3	598	3	RGS1	1	192548402	Missense_Mutation	SNP	G	TCGA-ZP-A9D1-01A-11D-A382-10	6218952	192548402	56702219	16	50951										
KIF14	9928	hgsc.bcm.edu	37	chr1	200550340	200550340	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	attactcacctgccaaaaacAtagtatgttttcaatttgct	4	9	2	0			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr1:200550340A>G	ENST00000367350.4	-	20	3762	c.3324T>C	c.(3322-3324)taT>taC	p.Y1108Y		NM_014875.2	NP_055690.1	Q15058	KIF14_HUMAN	kinesin family member 14	1108	Required for CIT-binding.				ATP catabolic process (GO:0006200)|cytoskeleton-dependent intracellular transport (GO:0030705)|establishment of protein localization (GO:0045184)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of integrin activation (GO:0033624)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of Rap protein signal transduction (GO:0032487)|substrate adhesion-dependent cell spreading (GO:0034446)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|PDZ domain binding (GO:0030165)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(8)|kidney(8)|large_intestine(15)|lung(13)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	61						TGCCAAAAACATAGTATGTTT	0.313																																					p.Y1108Y		Atlas-SNP	.											.	KIF14	156	.	0			c.T3324C						.						89	91	91					1																	200550340		2202	4300	6502	SO:0001819	synonymous_variant	9928	exon20			AAAAACATAGTAT	D26361	CCDS30963.1	1q32.1	2008-03-03			ENSG00000118193	ENSG00000118193		"Kinesins"	19181	protein-coding gene	gene with protein product		611279				7584044	Standard	NM_014875		Approved	KIAA0042	uc010ppk.1	Q15058	OTTHUMG00000035723	ENST00000367350.4:c.3324T>C	chr1.hg19:g.200550340A>G		190.0	0.0		335.0	67.0	NM_014875	Q14CI8|Q4G0A5|Q5T1W3	Silent	SNP	ENST00000367350.4	hg19	CCDS30963.1																																																																																			.	.		0.313	KIF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086878.1	NM_014875		G	200550340	A	G	200550340	2	3	367	1	0	0	0	0	0	0	0	1	8285	224	8	2		2	KIF14	1	200550340	Silent	SNP	A	TCGA-ZP-A9D1-01A-11D-A382-10	8001938	200550340	48700281	17	50952										
PFKFB2	5208	hgsc.bcm.edu	37	chr1	207245694	207245694	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	cagccctctccgtgcccaggAcatgcaagaaggggccgact	12	15	1	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr1:207245694A>T	ENST00000367080.3	+	15	1620	c.1496A>T	c.(1495-1497)gAc>gTc	p.D499V	PFKFB2_ENST00000411990.2_Intron|PFKFB2_ENST00000541914.1_Intron|PFKFB2_ENST00000545806.1_Missense_Mutation_p.D466V|PFKFB2_ENST00000367079.2_Intron|PFKFB2_ENST00000473310.1_Intron	NM_006212.2	NP_006203.2	O60825	F262_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2	499	Fructose-2,6-bisphosphatase.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|glucose catabolic process (GO:0006007)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|lactate metabolic process (GO:0006089)|positive regulation of glucokinase activity (GO:0033133)|positive regulation of insulin secretion (GO:0032024)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)|protein kinase binding (GO:0019901)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	20	Prostate(682;0.19)					CGTGCCCAGGACATGCAAGAA	0.567																																					p.D499V		Atlas-SNP	.											.	PFKFB2	70	.	0			c.A1496T						.						49	54	52					1																	207245694		2203	4300	6503	SO:0001583	missense	5208	exon15			CCCAGGACATGCA		CCDS31003.1, CCDS31004.1	1q31-q32.2	2012-07-13			ENSG00000123836	ENSG00000123836	2.7.1.105, 3.1.3.46		8873	protein-coding gene	gene with protein product		171835					Standard	XM_005273162		Approved		uc001hfg.3	O60825	OTTHUMG00000036033	ENST00000367080.3:c.1496A>T	chr1.hg19:g.207245694A>T	ENSP00000356047:p.Asp499Val	140.0	0.0		237.0	60.0	NM_006212	O60824|Q5VVQ3|Q5VVQ4|Q9H3P1	Missense_Mutation	SNP	ENST00000367080.3	hg19	CCDS31004.1	.	.	.	.	.	.	.	.	.	.	A	16.71	3.198715	0.58126	.	.	ENSG00000123836	ENST00000367080;ENST00000545806	.	.	.	5.46	5.46	0.80206	.	0.183413	0.49305	D	0.000159	T	0.38161	0.1030	N	0.22421	0.69	0.80722	D	1	P	0.37015	0.578	B	0.33196	0.159	T	0.38714	-0.9648	9	0.54805	T	0.06	.	13.2546	0.60070	1.0:0.0:0.0:0.0	.	499	O60825	F262_HUMAN	V	499;466	.	ENSP00000356047:D499V	D	+	2	0	PFKFB2	205312317	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	2.396000	0.44468	2.215000	0.71742	0.529000	0.55759	GAC	.	.		0.567	PFKFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087838.1			T	207245694	A	T	207245694	3	4	367	1	0	0	0	0	1	0	0	0	11770	275	10	4	1550	4	PFKFB2	1	207245694	Missense_Mutation	SNP	A	TCGA-ZP-A9D1-01A-11D-A382-10	6695354	207245694	42004927	18	50953										
CR2	1380	hgsc.bcm.edu	37	chr1	207643282	207643282	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ctgcggttcagtgtccacatCcccagatcctaagaggccga	10	14	1	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr1:207643282C>A	ENST00000367058.3	+	6	1249	c.1060C>A	c.(1060-1062)Ccc>Acc	p.P354T	CR2_ENST00000367059.3_Missense_Mutation_p.P354T|CR2_ENST00000367057.3_Missense_Mutation_p.P354T|CR2_ENST00000458541.2_Missense_Mutation_p.P354T	NM_001877.4	NP_001868.2	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus) receptor 2	354	Sushi 6. {ECO:0000255|PROSITE- ProRule:PRU00302}.				B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|complement activation, classical pathway (GO:0006958)|immune response (GO:0006955)|innate immune response (GO:0045087)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	complement binding (GO:0001848)|complement receptor activity (GO:0004875)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|breast(3)|endometrium(4)|kidney(3)|large_intestine(12)|lung(26)|ovary(1)|pancreas(1)|prostate(1)|skin(12)|upper_aerodigestive_tract(3)|urinary_tract(1)	69						GTGTCCACATCCCCAGATCCT	0.502																																					p.P354T		Atlas-SNP	.											.	CR2	164	.	0			c.C1060A						.						137	121	126					1																	207643282		2203	4300	6503	SO:0001583	missense	1380	exon6			CCACATCCCCAGA	M26004	CCDS1478.1, CCDS31007.1	1q32	2014-09-17			ENSG00000117322	ENSG00000117322		"CD molecules", "Complement system"	2336	protein-coding gene	gene with protein product		120650					Standard	NM_001006658		Approved	CD21	uc001hfv.3	P20023	OTTHUMG00000036307	ENST00000367058.3:c.1060C>A	chr1.hg19:g.207643282C>A	ENSP00000356025:p.Pro354Thr	110.0	0.0		216.0	27.0	NM_001006658	C9JHD2|Q13866|Q14212|Q53EL2|Q5BKT9|Q5SR46|Q5SR48	Missense_Mutation	SNP	ENST00000367058.3	hg19	CCDS1478.1	.	.	.	.	.	.	.	.	.	.	C	14.19	2.462109	0.43736	.	.	ENSG00000117322	ENST00000367058;ENST00000367057;ENST00000367059;ENST00000458541	D;D;D;D	0.84800	-1.9;-1.9;-1.9;-1.9	5.09	5.09	0.68999	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	D	0.93822	0.8024	M	0.92219	3.285	0.38394	D	0.945491	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.95446	0.8530	9	0.87932	D	0	.	14.7242	0.69332	0.0:1.0:0.0:0.0	.	354;354;354	Q5SR47;P20023;P20023-3	.;CR2_HUMAN;.	T	354	ENSP00000356025:P354T;ENSP00000356024:P354T;ENSP00000356026:P354T;ENSP00000404222:P354T	ENSP00000356024:P354T	P	+	1	0	CR2	205709905	0.806000	0.28996	0.214000	0.23707	0.092000	0.18411	3.970000	0.56824	2.756000	0.94617	0.561000	0.74099	CCC	.	.		0.502	CR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000088274.1	NM_001877		A	207643282	C	A	207643282	3	1	367	1	0	0	0	0	1	0	0	0	3844	855	30	3	1082	3	CR2	1	207643282	Missense_Mutation	SNP	C	TCGA-ZP-A9D1-01A-11D-A382-10	397588	207643282	41607339	19	50954										
ZP4	57829	hgsc.bcm.edu	37	chr1	238048573	238048573	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	agatccaaggctttctggacAgggatcagctgggtctgata	13	8	3	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr1:238048573A>T	ENST00000366570.4	-	9	1361	c.1203T>A	c.(1201-1203)ccT>ccA	p.P401P	RP11-193H5.1_ENST00000450451.1_RNA	NM_021186.3	NP_067009.1	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4	401	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				acrosomal vesicle exocytosis (GO:0060478)|binding of sperm to zona pellucida (GO:0007339)|intracellular signal transduction (GO:0035556)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of humoral immune response (GO:0002922)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of T cell proliferation (GO:0042102)|protein kinase A signaling (GO:0010737)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	acrosin binding (GO:0032190)|signal transducer activity (GO:0004871)			breast(6)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(42)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	73	Ovarian(103;0.103)	all_cancers(173;0.00175)|all_epithelial(177;0.162)|all_neural(198;0.164)|Melanoma(53;0.211)|Prostate(94;0.214)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			CTTTCTGGACAGGGATCAGCT	0.517																																					p.P401P	NSCLC(166;160 2029 11600 18754 19936)	Atlas-SNP	.											.	ZP4	161	.	0			c.T1203A						.						75	74	74					1																	238048573		2203	4300	6503	SO:0001819	synonymous_variant	57829	exon9			CTGGACAGGGATC	U05781	CCDS1615.1	1q43	2013-01-17			ENSG00000116996	ENSG00000116996		"Zona pellucida glycoproteins"	15770	protein-coding gene	gene with protein product		613514				7841460	Standard	NM_021186		Approved	ZPB	uc001hym.3	Q12836	OTTHUMG00000039586	ENST00000366570.4:c.1203T>A	chr1.hg19:g.238048573A>T		171.0	0.0		274.0	129.0	NM_021186	B2RAE1	Silent	SNP	ENST00000366570.4	hg19	CCDS1615.1																																																																																			.	.		0.517	ZP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095476.1			T	238048573	A	T	238048573	2	4	367	1	0	0	0	0	0	0	0	1	18233	175	7	4		4	ZP4	1	238048573	Silent	SNP	A	TCGA-ZP-A9D1-01A-11D-A382-10	30405291	238048573	11202048	20	50955										
FMN2	56776	hgsc.bcm.edu	37	chr1	240601442	240601442	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ccaaatgctttcttcagtatCtggcatgaattcagctctga	7	10	5	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr1:240601442C>A	ENST00000319653.9	+	16	5222	c.4992C>A	c.(4990-4992)atC>atA	p.I1664I	FMN2_ENST00000545751.1_Silent_p.I260I	NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1664	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			TCTTCAGTATCTGGCATGAAT	0.388																																					p.I1664I		Atlas-SNP	.											.	FMN2	451	.	0			c.C4992A						.						132	129	130					1																	240601442		2203	4300	6503	SO:0001819	synonymous_variant	56776	exon16			CAGTATCTGGCAT	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.4992C>A	chr1.hg19:g.240601442C>A		85.0	0.0		142.0	39.0	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	hg19	CCDS31069.2																																																																																			.	.		0.388	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		A	240601442	C	A	240601442	2	1	367	1	0	0	0	0	0	0	0	1	5958	903	32	3		3	FMN2	1	240601442	Silent	SNP	C	TCGA-ZP-A9D1-01A-11D-A382-10	2552869	240601442	8649179	21	50956										
MYT1L	23040	hgsc.bcm.edu	37	chr2	1926174	1926174	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	tcatattgtccctcctcccaGcttccatggccatcttctcc	4	18	3	0			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr2:1926174G>A	ENST00000399161.2	-	10	2114	c.1367C>T	c.(1366-1368)gCt>gTt	p.A456V	MYT1L_ENST00000428368.2_Missense_Mutation_p.A456V	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	456					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		CCTCCTCCCAGCTTCCATGGC	0.527																																					p.A456V		Atlas-SNP	.											.	MYT1L	241	.	0			c.C1367T						.						181	176	178					2																	1926174		2002	4159	6161	SO:0001583	missense	23040	exon10			CTCCCAGCTTCCA	AF036943	CCDS46222.1	2p25.3	2013-01-10			ENSG00000186487	ENSG00000186487		"Zinc fingers, C2HC-type containing"	7623	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 1"	613084				9373037	Standard	XM_006711862		Approved	KIAA1106, NZF1, ZC2HC4B	uc002qxd.3	Q9UL68	OTTHUMG00000151407	ENST00000399161.2:c.1367C>T	chr2.hg19:g.1926174G>A	ENSP00000382114:p.Ala456Val	86.0	0.0		105.0	43.0	NM_015025	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Missense_Mutation	SNP	ENST00000399161.2	hg19		.	.	.	.	.	.	.	.	.	.	G	13.88	2.370526	0.42003	.	.	ENSG00000186487	ENST00000399161;ENST00000295067;ENST00000428368	T;T	0.45668	0.9;0.89	5.91	5.91	0.95273	.	0.158944	0.56097	D	0.000033	T	0.32285	0.0824	L	0.27053	0.805	0.80722	D	1	B;B	0.29988	0.172;0.264	B;B	0.21151	0.015;0.033	T	0.05852	-1.0860	10	0.21014	T	0.42	-28.3964	20.2936	0.98544	0.0:0.0:1.0:0.0	.	456;456	Q9UL68;Q9UL68-4	MYT1L_HUMAN;.	V	456;404;456	ENSP00000382114:A456V;ENSP00000396103:A456V	ENSP00000295067:A404V	A	-	2	0	MYT1L	1905181	1.000000	0.71417	0.351000	0.25721	0.045000	0.14185	9.781000	0.99029	2.801000	0.96364	0.655000	0.94253	GCT	.	.		0.527	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025		A	1926174	G	A	1926174	3	1	367	1	0	0	0	0	1	0	0	0	10116	971	34	3	2251	3	MYT1L	2	1926174	Missense_Mutation	SNP	G	TCGA-ZP-A9D1-01A-11D-A382-10		1926174	241273199	22	50957										
KIDINS220	57498	hgsc.bcm.edu	37	chr2	8919137	8919137	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	aggcaagtggactatgttgcGcatgtagtcatggccattta	12	7	1	0			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr2:8919137G>T	ENST00000256707.3	-	19	2684	c.2503C>A	c.(2503-2505)Cgc>Agc	p.R835S	KIDINS220_ENST00000319688.5_Missense_Mutation_p.R836S|KIDINS220_ENST00000427284.1_Missense_Mutation_p.R835S|KIDINS220_ENST00000418530.1_Missense_Mutation_p.R793S|KIDINS220_ENST00000473731.1_Missense_Mutation_p.R835S	NM_020738.2	NP_065789.1	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate, 220kDa	835	KAP NTPase.				activation of MAPKK activity (GO:0000186)|cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|dendrite morphogenesis (GO:0048813)|in utero embryonic development (GO:0001701)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of neuron projection development (GO:0010976)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|protein complex (GO:0043234)	PDZ domain binding (GO:0030165)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(25)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	60	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					ACTATGTTGCGCATGTAGTCA	0.403																																					p.R835S		Atlas-SNP	.											KIDINS220,NS,carcinoma,0,1	KIDINS220	136	.	0			c.C2503A						.						250	224	232					2																	8919137		1894	4122	6016	SO:0001583	missense	57498	exon19			TGTTGCGCATGTA	AK025528	CCDS42650.1	2p24	2013-01-10			ENSG00000134313	ENSG00000134313		"Ankyrin repeat domain containing"	29508	protein-coding gene	gene with protein product	"ankyrin repeat-rich membrane-spanning protein"	615759				10998417, 10574462	Standard	NM_020738		Approved	ARMS	uc002qzc.2	Q9ULH0	OTTHUMG00000151658	ENST00000256707.3:c.2503C>A	chr2.hg19:g.8919137G>T	ENSP00000256707:p.Arg835Ser	67.0	0.0		82.0	30.0	NM_020738	A1L4N4|Q4VC08|Q6MZU2|Q9H889|Q9H9E4|Q9NT37|Q9UF42	Missense_Mutation	SNP	ENST00000256707.3	hg19	CCDS42650.1	.	.	.	.	.	.	.	.	.	.	G	16.82	3.228423	0.58777	.	.	ENSG00000134313	ENST00000496383;ENST00000541927;ENST00000256707;ENST00000427284;ENST00000418530;ENST00000473731;ENST00000489024;ENST00000319688	T;T;T;T;T;T;T	0.32272	1.46;1.46;1.46;1.46;1.46;1.46;1.46	5.64	5.64	0.86602	KAP P-loop (1);	0.000000	0.85682	D	0.000000	T	0.54255	0.1847	M	0.66939	2.045	0.80722	D	1	D;D;D;D	0.89917	0.999;0.989;1.0;1.0	D;P;D;D	0.97110	0.997;0.854;0.999;1.0	T	0.51100	-0.8748	10	0.52906	T	0.07	.	15.6595	0.77174	0.0:0.0:0.8623:0.1377	.	836;836;793;835	B4DK94;E9PH70;Q9ULH0-2;Q9ULH0	.;.;.;KDIS_HUMAN	S	582;519;835;835;793;835;836;836	ENSP00000420364:R582S;ENSP00000256707:R835S;ENSP00000411849:R835S;ENSP00000414923:R793S;ENSP00000418974:R835S;ENSP00000419964:R836S;ENSP00000319947:R836S	ENSP00000256707:R835S	R	-	1	0	KIDINS220	8836588	1.000000	0.71417	1.000000	0.80357	0.328000	0.28507	4.165000	0.58196	2.820000	0.97059	0.650000	0.86243	CGC	.	.		0.403	KIDINS220-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323408.2	NM_020738		T	8919137	G	T	8919137	3	4	367	1	0	0	0	0	1	0	0	0	8280	1087	38	1	2860	1	KIDINS220	2	8919137	Missense_Mutation	SNP	G	TCGA-ZP-A9D1-01A-11D-A382-10	6992963	8919137	234280236	23	50958										
DTNB	1838	hgsc.bcm.edu	37	chr2	25819006	25819006	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	tctgtgtaaccaaaagatggCccttcaaagacagctgttgg	10	9	2	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr2:25819006C>T	ENST00000406818.3	-	6	801	c.552G>A	c.(550-552)ggG>ggA	p.G184G	DTNB_ENST00000288642.8_Silent_p.G184G|DTNB_ENST00000496972.2_Silent_p.G127G|DTNB_ENST00000405222.1_Silent_p.G184G|DTNB_ENST00000404103.3_Silent_p.G184G|DTNB_ENST00000545439.1_Intron|DTNB_ENST00000407186.1_Silent_p.G184G|DTNB_ENST00000407038.3_Silent_p.G184G|DTNB_ENST00000407661.3_Silent_p.G184G|DTNB_ENST00000472690.1_5'UTR	NM_001256303.1|NM_021907.4	NP_001243232.1|NP_068707.1	O60941	DTNB_HUMAN	dystrobrevin, beta	184						cytoplasm (GO:0005737)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CAAAAGATGGCCCTTCAAAGA	0.453																																					p.G184G		Atlas-SNP	.											.	DTNB	43	.	0			c.G552A						.						71	70	70					2																	25819006		1856	4106	5962	SO:0001819	synonymous_variant	1838	exon6			AGATGGCCCTTCA	AF022728	CCDS46233.1, CCDS46234.1, CCDS46235.1, CCDS46236.1, CCDS46237.1, CCDS58702.1, CCDS74496.1	2p23.2	2008-05-15			ENSG00000138101	ENSG00000138101			3058	protein-coding gene	gene with protein product		602415				9419360	Standard	NM_021907		Approved		uc002rgh.4	O60941	OTTHUMG00000152129	ENST00000406818.3:c.552G>A	chr2.hg19:g.25819006C>T		143.0	0.0		146.0	25.0	NM_021907	B7Z733|F5GZG4|G5E9F6|O43782|O60881|O75538|Q86VR4|Q96AW0|Q9UE14|Q9UE15|Q9UE16	Silent	SNP	ENST00000406818.3	hg19	CCDS46237.1																																																																																			.	.		0.453	DTNB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325361.1	NM_033147		T	25819006	C	T	25819006	2	4	367	1	0	0	0	0	0	0	0	1	4791	726	26	3		3	DTNB	2	25819006	Silent	SNP	C	TCGA-ZP-A9D1-01A-11D-A382-10	16899869	25819006	217380367	24	50959										
EFEMP1	2202	hgsc.bcm.edu	37	chr2	56098002	56098002	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	atgtatttgtagactattgaCtggggcagttctcggcacat	11	7	1	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr2:56098002C>A	ENST00000394555.2	-	10	1608	c.1173G>T	c.(1171-1173)caG>caT	p.Q391H	EFEMP1_ENST00000394554.1_Missense_Mutation_p.Q391H|EFEMP1_ENST00000424836.2_Missense_Mutation_p.Q253H|EFEMP1_ENST00000355426.3_Missense_Mutation_p.Q391H	NM_001039348.2|NM_001039349.2	NP_001034437.1|NP_001034438.1	Q12805	FBLN3_HUMAN	EGF containing fibulin-like extracellular matrix protein 1	391	Mediates interaction with TIMP3.				epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|negative regulation of chondrocyte differentiation (GO:0032331)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|epidermal growth factor-activated receptor activity (GO:0005006)			NS(1)|breast(2)|endometrium(4)|large_intestine(6)|lung(5)|ovary(5)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			AGACTATTGACTGGGGCAGTT	0.448																																					p.Q391H	GBM(92;934 1319 7714 28760 40110)	Atlas-SNP	.											.	EFEMP1	81	.	0			c.G1173T						.						95	93	94					2																	56098002		2203	4300	6503	SO:0001583	missense	2202	exon10			TATTGACTGGGGC	U03877	CCDS1857.1	2p16	2013-01-08	2011-01-25		ENSG00000115380	ENSG00000115380		"Fibulins"	3218	protein-coding gene	gene with protein product	"fibulin 3"	601548	"fibrillin-like", "EGF-containing fibulin-like extracellular matrix protein 1"	DHRD, FBNL		8812496, 7799918	Standard	NM_001039348		Approved	S1-5, FBLN3, MTLV	uc002rzi.3	Q12805	OTTHUMG00000129343	ENST00000394555.2:c.1173G>T	chr2.hg19:g.56098002C>A	ENSP00000378058:p.Gln391His	119.0	0.0		152.0	48.0	NM_001039349	A8K3I4|B4DW75|D6W5D2|Q541U7	Missense_Mutation	SNP	ENST00000394555.2	hg19	CCDS1857.1	.	.	.	.	.	.	.	.	.	.	C	11.73	1.726567	0.30593	.	.	ENSG00000115380	ENST00000394555;ENST00000394554;ENST00000405693;ENST00000424836;ENST00000355426	D;D;T;D	0.83992	-1.79;-1.79;-1.26;-1.79	5.65	1.76	0.24704	.	0.199045	0.35585	N	0.003117	T	0.69495	0.3117	N	0.14661	0.345	0.30058	N	0.811164	D;P	0.53312	0.959;0.788	P;B	0.49301	0.606;0.406	T	0.65360	-0.6187	10	0.15499	T	0.54	.	6.3334	0.21282	0.0:0.4565:0.213:0.3305	.	253;391	B4DW75;Q12805	.;FBLN3_HUMAN	H	391;391;247;253;391	ENSP00000378058:Q391H;ENSP00000378057:Q391H;ENSP00000399145:Q253H;ENSP00000347596:Q391H	ENSP00000347596:Q391H	Q	-	3	2	EFEMP1	55951506	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.550000	0.23345	0.404000	0.25506	0.655000	0.94253	CAG	.	.		0.448	EFEMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251491.2			A	56098002	C	A	56098002	3	1	367	1	0	0	0	0	1	0	0	0	4943	564	20	3	316	3	EFEMP1	2	56098002	Missense_Mutation	SNP	C	TCGA-ZP-A9D1-01A-11D-A382-10	30278996	56098002	187101371	25	50960										
ARHGEF4	50649	hgsc.bcm.edu	37	chr2	131797621	131797621	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	caggacgagcccgcggatgaCgacgcccctctggccgggaa	15	15	1	1	rs150958124		TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr2:131797621C>T	ENST00000326016.5	+	7	1299	c.780C>T	c.(778-780)gaC>gaT	p.D260D	ARHGEF4_ENST00000409303.1_Silent_p.D260D|ARHGEF4_ENST00000392953.3_Silent_p.D260D|ARHGEF4_ENST00000355771.3_Silent_p.D189D|ARHGEF4_ENST00000439368.2_3'UTR|ARHGEF4_ENST00000428230.2_Intron|ARHGEF4_ENST00000525839.1_Silent_p.D260D	NM_015320.2	NP_056135.2	Q9NR80	ARHG4_HUMAN	Rho guanine nucleotide exchange factor (GEF) 4	260					apoptotic signaling pathway (GO:0097190)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein domain specific binding (GO:0019904)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(4)	29		Prostate(154;0.055)		BRCA - Breast invasive adenocarcinoma(221;0.097)		CCGCGGATGACGACGCCCCTC	0.701																																					p.D260D		Atlas-SNP	.											ARHGEF4_ENST00000392953,NS,carcinoma,0,2	ARHGEF4	89	.	0			c.C780T						.						31	33	32					2																	131797621		2188	4282	6470	SO:0001819	synonymous_variant	50649	exon7			GGATGACGACGCC	AL137289	CCDS2165.1, CCDS42754.1	2q22	2013-01-10			ENSG00000136002	ENSG00000136002		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	684	protein-coding gene	gene with protein product	"APC-stimulated guanine nucleotide exchange factor"	605216				10873612	Standard	NM_015320		Approved	STM6, KIAA1112, ASEF	uc002tsa.1	Q9NR80	OTTHUMG00000131657	ENST00000326016.5:c.780C>T	chr2.hg19:g.131797621C>T		127.0	1.0		165.0	7.0	NM_032995	Q9HDC6|Q9UPP0	Silent	SNP	ENST00000326016.5	hg19	CCDS2165.1																																																																																			.	C|1.000;A|0.000		0.701	ARHGEF4-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254554.4			T	131797621	C	T	131797621	2	4	367	1	0	0	0	0	0	0	0	1	908	535	19	1		1	ARHGEF4	2	131797621	Silent	SNP	C	TCGA-ZP-A9D1-01A-11D-A382-10	75699619	131797621	111401752	26	50961										
NEB	4703	hgsc.bcm.edu	37	chr2	152473927	152473927	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ctaacatgatttctggtgtaTcaggcatgacatgaatagtt	9	6	2	3			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr2:152473927T>A	ENST00000172853.10	-	71	10550	c.10403A>T	c.(10402-10404)gAt>gTt	p.D3468V	NEB_ENST00000603639.1_Missense_Mutation_p.D3711V|NEB_ENST00000397345.3_Missense_Mutation_p.D3711V|NEB_ENST00000604864.1_Missense_Mutation_p.D3711V|NEB_ENST00000427231.2_Missense_Mutation_p.D3711V|NEB_ENST00000409198.1_Missense_Mutation_p.D3468V			P20929	NEBU_HUMAN	nebulin	3468					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TTCTGGTGTATCAGGCATGAC	0.338																																					p.D3711V		Atlas-SNP	.											.	NEB	1697	.	0			c.A11132T						.						138	121	127					2																	152473927		1868	4105	5973	SO:0001583	missense	4703	exon75			GGTGTATCAGGCA	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.10403A>T	chr2.hg19:g.152473927T>A	ENSP00000172853:p.Asp3468Val	44.0	0.0		51.0	17.0	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	hg19		.	.	.	.	.	.	.	.	.	.	T	21.1	4.099029	0.76870	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.68903	-0.36;-0.36;-0.36;-0.36	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	D	0.85401	0.5688	M	0.92367	3.3	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.88488	0.3073	10	0.54805	T	0.06	.	15.3854	0.74695	0.0:0.0:0.0:1.0	.	3468	P20929	NEBU_HUMAN	V	3468;3711;3711;3468	ENSP00000386259:D3468V;ENSP00000380505:D3711V;ENSP00000416578:D3711V;ENSP00000172853:D3468V	ENSP00000172853:D3468V	D	-	2	0	NEB	152182173	1.000000	0.71417	0.979000	0.43373	0.984000	0.73092	4.011000	0.57124	2.100000	0.63781	0.482000	0.46254	GAT	.	.		0.338	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		A	152473927	T	A	152473927	3	1	367	1	0	0	0	0	1	0	0	0	10311	1435	50	4	14986	4	NEB	2	152473927	Missense_Mutation	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	20676306	152473927	90725446	27	50962										
NEB	4703	hgsc.bcm.edu	37	chr2	152534508	152534508	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	tgaccacatcctgggctttcTtagccgccacgacattgaac	8	14	1	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr2:152534508T>A	ENST00000172853.10	-	33	3596	c.3449A>T	c.(3448-3450)aAg>aTg	p.K1150M	NEB_ENST00000603639.1_Missense_Mutation_p.K1150M|NEB_ENST00000397345.3_Missense_Mutation_p.K1150M|NEB_ENST00000604864.1_Missense_Mutation_p.K1150M|NEB_ENST00000427231.2_Missense_Mutation_p.K1150M|NEB_ENST00000409198.1_Missense_Mutation_p.K1150M			P20929	NEBU_HUMAN	nebulin	1150					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		CTGGGCTTTCTTAGCCGCCAC	0.453																																					p.K1150M		Atlas-SNP	.											.	NEB	1697	.	0			c.A3449T						.						105	112	110					2																	152534508		2004	4171	6175	SO:0001583	missense	4703	exon33			GCTTTCTTAGCCG	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.3449A>T	chr2.hg19:g.152534508T>A	ENSP00000172853:p.Lys1150Met	108.0	0.0		110.0	25.0	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	hg19		.	.	.	.	.	.	.	.	.	.	T	23.9	4.468036	0.84533	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.39229	1.09;1.09;1.09;1.09	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.65903	0.2736	M	0.78637	2.42	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.70912	-0.4743	10	0.87932	D	0	.	15.1962	0.73092	0.0:0.0:0.0:1.0	.	1150	P20929	NEBU_HUMAN	M	1150	ENSP00000386259:K1150M;ENSP00000380505:K1150M;ENSP00000416578:K1150M;ENSP00000172853:K1150M	ENSP00000172853:K1150M	K	-	2	0	NEB	152242754	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	5.114000	0.64648	2.134000	0.65973	0.533000	0.62120	AAG	.	.		0.453	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		A	152534508	T	A	152534508	3	1	367	1	0	0	0	0	1	0	0	0	10311	1609	56	4	22837	4	NEB	2	152534508	Missense_Mutation	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	60581	152534508	90664865	28	50963										
COBLL1	22837	hgsc.bcm.edu	37	chr2	165557052	165557052	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	tgtccatctgtgcttttagtTtcttgtttttcttccatgga	7	8	3	0			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr2:165557052T>G	ENST00000392717.2	-	11	1675	c.1671A>C	c.(1669-1671)gaA>gaC	p.E557D	COBLL1_ENST00000194871.6_Missense_Mutation_p.E585D|COBLL1_ENST00000342193.4_Missense_Mutation_p.E519D|COBLL1_ENST00000375458.2_Missense_Mutation_p.E480D|COBLL1_ENST00000409184.3_Missense_Mutation_p.E518D|COBLL1_ENST00000491126.2_5'Flank			Q53SF7	COBL1_HUMAN	cordon-bleu WH2 repeat protein-like 1	557						extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	47						TGCTTTTAGTTTCTTGTTTTT	0.363																																					p.E519D		Atlas-SNP	.											.	COBLL1	122	.	0			c.A1557C						.						143	128	133					2																	165557052		2203	4300	6503	SO:0001583	missense	22837	exon10			TTTAGTTTCTTGT	AB023194	CCDS2223.2, CCDS63045.1	2q24.3	2012-12-07	2012-12-07		ENSG00000082438	ENSG00000082438			23571	protein-coding gene	gene with protein product		610318	"COBL-like 1"				Standard	NM_001278458		Approved	KIAA0977	uc002ucp.3	Q53SF7	OTTHUMG00000074019	ENST00000392717.2:c.1671A>C	chr2.hg19:g.165557052T>G	ENSP00000376478:p.Glu557Asp	111.0	0.0		102.0	22.0	NM_014900	A6NMZ3|Q6IQ33|Q7Z3I6|Q9BRH4|Q9UG88|Q9Y2I3	Missense_Mutation	SNP	ENST00000392717.2	hg19		.	.	.	.	.	.	.	.	.	.	T	11.80	1.746627	0.30955	.	.	ENSG00000082438	ENST00000375458;ENST00000342193;ENST00000409184;ENST00000392717;ENST00000194871	.	.	.	5.22	4.03	0.46877	.	0.345007	0.28312	N	0.015801	T	0.35480	0.0933	L	0.34521	1.04	0.31727	N	0.637501	B;B;B	0.26577	0.153;0.028;0.047	B;B;B	0.24974	0.057;0.027;0.054	T	0.38929	-0.9638	9	0.37606	T	0.19	-5.8748	10.5183	0.44903	0.1442:0.0:0.0:0.8558	.	557;585;518	Q53SF7;B7Z2P5;Q53SF7-2	COBL1_HUMAN;.;.	D	480;519;518;557;585	.	ENSP00000194871:E585D	E	-	3	2	COBLL1	165265298	1.000000	0.71417	0.532000	0.27989	0.272000	0.26649	1.251000	0.32862	0.899000	0.36444	0.260000	0.18958	GAA	.	.		0.363	COBLL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014900		G	165557052	T	G	165557052	3	3	367	1	0	0	0	0	1	0	0	0	3656	1838	64	5	1963	5	COBLL1	2	165557052	Missense_Mutation	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	13022544	165557052	77642321	29	50964										
PLCL1	5334	hgsc.bcm.edu	37	chr2	198953586	198953586	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	gttttcttcctcacagaatgCaatcgtgtctattaaggaac	7	9	3	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr2:198953586C>A	ENST00000428675.1	+	3	3118	c.2720C>A	c.(2719-2721)gCa>gAa	p.A907E	PLCL1_ENST00000437704.2_Missense_Mutation_p.A809E	NM_006226.3	NP_006217.3	Q15111	PLCL1_HUMAN	phospholipase C-like 1	907					gamma-aminobutyric acid signaling pathway (GO:0007214)|intracellular signal transduction (GO:0035556)|lipid metabolic process (GO:0006629)|positive regulation of receptor binding (GO:1900122)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|inositol 1,4,5 trisphosphate binding (GO:0070679)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(14)|lung(44)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	80					Quinacrine(DB01103)	TCACAGAATGCAATCGTGTCT	0.443																																					p.A907E		Atlas-SNP	.											.	PLCL1	358	.	0			c.C2720A						.						386	387	386					2																	198953586		2203	4300	6503	SO:0001583	missense	5334	exon3			AGAATGCAATCGT	D42108	CCDS2326.1, CCDS2326.2	2q33	2014-06-13	2002-02-18	2002-02-22	ENSG00000115896	ENSG00000115896			9063	protein-coding gene	gene with protein product	"phospholipase C related, but catalytically inactive protein", "protein phosphatase 1, regulatory subunit 127"	600597	"phospholipase C, epsilon"	PLCE		7633416	Standard	NM_006226		Approved	PLC-L, PLCL, PRIP, PPP1R127	uc010fsp.3	Q15111	OTTHUMG00000132750	ENST00000428675.1:c.2720C>A	chr2.hg19:g.198953586C>A	ENSP00000402861:p.Ala907Glu	77.0	0.0		66.0	18.0	NM_006226	Q3MJ90|Q53SD3|Q7Z3S3	Missense_Mutation	SNP	ENST00000428675.1	hg19	CCDS2326.2	.	.	.	.	.	.	.	.	.	.	C	16.55	3.155596	0.57259	.	.	ENSG00000115896	ENST00000428675;ENST00000437704	T;T	0.22539	1.95;2.02	5.13	5.13	0.70059	.	0.000000	0.64402	D	0.000017	T	0.48554	0.1506	M	0.79805	2.47	0.80722	D	1	D;D	0.62365	0.991;0.991	D;D	0.64321	0.924;0.924	T	0.47947	-0.9077	9	.	.	.	.	18.7752	0.91908	0.0:1.0:0.0:0.0	.	907;833	Q15111;B4DYZ4	PLCL1_HUMAN;.	E	907;809	ENSP00000402861:A907E;ENSP00000414138:A809E	.	A	+	2	0	PLCL1	198661831	1.000000	0.71417	0.403000	0.26384	0.051000	0.14879	7.641000	0.83368	2.661000	0.90470	0.650000	0.86243	GCA	.	.		0.443	PLCL1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340210.1	NM_006226		A	198953586	C	A	198953586	3	1	367	1	0	0	0	0	1	0	0	0	12048	710	25	3	2730	3	PLCL1	2	198953586	Missense_Mutation	SNP	C	TCGA-ZP-A9D1-01A-11D-A382-10	33396534	198953586	44245787	30	50965										
COL6A3	1293	hgsc.bcm.edu	37	chr2	238287845	238287845	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	caacgttggctgatccatccAaaagaaagatgatatccctt	7	10	0	4			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr2:238287845A>G	ENST00000295550.4	-	6	2383	c.1931T>C	c.(1930-1932)tTg>tCg	p.L644S	COL6A3_ENST00000346358.4_Intron|COL6A3_ENST00000353578.4_Missense_Mutation_p.L438S|COL6A3_ENST00000392004.3_Missense_Mutation_p.L438S|COL6A3_ENST00000392003.2_Missense_Mutation_p.L237S|COL6A3_ENST00000472056.1_Intron|COL6A3_ENST00000409809.1_Missense_Mutation_p.L438S|COL6A3_ENST00000347401.3_Missense_Mutation_p.L443S	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	644	Nonhelical region.|VWFA 4. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		TGATCCATCCAAAAGAAAGAT	0.388																																					p.L644S		Atlas-SNP	.											.	COL6A3	608	.	0			c.T1931C						.						61	60	61					2																	238287845		2203	4300	6503	SO:0001583	missense	1293	exon6			CCATCCAAAAGAA	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.1931T>C	chr2.hg19:g.238287845A>G	ENSP00000295550:p.Leu644Ser	224.0	0.0		222.0	45.0	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	hg19	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	A	23.6	4.439223	0.83885	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000409809;ENST00000392004;ENST00000392003	D;D;D;D;D;D	0.84298	-1.83;-1.83;-1.83;-1.83;-1.83;-1.83	5.52	5.52	0.82312	von Willebrand factor, type A (3);	0.000000	0.39146	U	0.001454	D	0.94082	0.8103	M	0.92219	3.285	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.997;1.0;1.0;0.99	D	0.95404	0.8492	10	0.87932	D	0	.	15.6766	0.77332	1.0:0.0:0.0:0.0	.	237;438;438;644	A8MT30;E9PGQ9;P12111-2;P12111	.;.;.;CO6A3_HUMAN	S	644;443;438;438;438;237	ENSP00000295550:L644S;ENSP00000315609:L443S;ENSP00000315873:L438S;ENSP00000386844:L438S;ENSP00000375861:L438S;ENSP00000375860:L237S	ENSP00000295550:L644S	L	-	2	0	COL6A3	237952584	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.262000	0.95591	2.099000	0.63709	0.533000	0.62120	TTG	.	.		0.388	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		G	238287845	A	G	238287845	3	3	367	1	0	0	0	0	1	0	0	0	3703	131	5	2	7805	2	COL6A3	2	238287845	Missense_Mutation	SNP	A	TCGA-ZP-A9D1-01A-11D-A382-10	39334259	238287845	4911528	31	50966										
CCDC54	84692	hgsc.bcm.edu	37	chr3	107097090	107097090	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	aatttctccccaaatgaaaaCtctgaagaaacgtaaccatc	4	11	2	3			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr3:107097090C>A	ENST00000261058.1	+	1	903	c.656C>A	c.(655-657)aCt>aAt	p.T219N		NM_032600.2	NP_115989.1	Q8NEL0	CCD54_HUMAN	coiled-coil domain containing 54	219										NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	19						CAAATGAAAACTCTGAAGAAA	0.383																																					p.T219N		Atlas-SNP	.											.	CCDC54	56	.	0			c.C656A						.						71	73	73					3																	107097090		2203	4300	6503	SO:0001583	missense	84692	exon1			TGAAAACTCTGAA	AF367469	CCDS2949.1	3q13.12	2013-10-11			ENSG00000138483	ENSG00000138483			30703	protein-coding gene	gene with protein product	"sperm protein 17"					15257753	Standard	NM_032600		Approved	NYD-SP17, FLJ25362, SP17	uc003dwi.1	Q8NEL0	OTTHUMG00000159169	ENST00000261058.1:c.656C>A	chr3.hg19:g.107097090C>A	ENSP00000261058:p.Thr219Asn	325.0	0.0		251.0	130.0	NM_032600	Q96A43	Missense_Mutation	SNP	ENST00000261058.1	hg19	CCDS2949.1	.	.	.	.	.	.	.	.	.	.	C	10.38	1.335225	0.24253	.	.	ENSG00000138483	ENST00000261058	T	0.48522	0.81	5.09	3.23	0.37069	.	0.272597	0.26048	N	0.026653	T	0.42291	0.1196	L	0.59436	1.845	0.09310	N	1	B	0.26809	0.16	B	0.31290	0.127	T	0.41752	-0.9491	10	0.56958	D	0.05	-0.4695	6.5026	0.22178	0.1771:0.7279:0.0:0.095	.	219	Q8NEL0	CCD54_HUMAN	N	219	ENSP00000261058:T219N	ENSP00000261058:T219N	T	+	2	0	CCDC54	108579780	0.093000	0.21703	0.016000	0.15963	0.236000	0.25371	0.781000	0.26774	1.141000	0.42275	0.460000	0.39030	ACT	.	.		0.383	CCDC54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353651.1	NM_032600		A	107097090	C	A	107097090	3	1	367	1	0	0	0	0	1	0	0	0	2826	565	20	3	658	3	CCDC54	3	107097090	Missense_Mutation	SNP	C	TCGA-ZP-A9D1-01A-11D-A382-10		107097090	90925340	32	50967										
HTR3C	170572	hgsc.bcm.edu	37	chr3	183776324	183776324	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ctcttgggcatcaacaaggcCaccccaaagatgtccatggg	10	13	2	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr3:183776324C>A	ENST00000318351.1	+	6	703	c.669C>A	c.(667-669)gcC>gcA	p.A223A		NM_130770.2	NP_570126.2	Q8WXA8	5HT3C_HUMAN	5-hydroxytryptamine (serotonin) receptor 3C, ionotropic	223					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(2)	32	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)		Ergoloid mesylate(DB01049)	TCAACAAGGCCACCCCAAAGA	0.532																																					p.A223A		Atlas-SNP	.											.	HTR3C	65	.	0			c.C669A						.						125	116	119					3																	183776324		2203	4300	6503	SO:0001819	synonymous_variant	170572	exon6			CAAGGCCACCCCA	AF459285	CCDS3250.1	3q27	2012-05-22	2012-02-03		ENSG00000178084	ENSG00000178084		"5-HT (serotonin) receptors", "Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"	24003	protein-coding gene	gene with protein product		610121	"5-hydroxytryptamine (serotonin) receptor 3, family member C"			12801637, 15157181	Standard	NM_130770		Approved		uc003fmk.3	Q8WXA8	OTTHUMG00000156862	ENST00000318351.1:c.669C>A	chr3.hg19:g.183776324C>A		194.0	0.0		147.0	41.0	NM_130770	A2RRR5	Silent	SNP	ENST00000318351.1	hg19	CCDS3250.1																																																																																			.	.		0.532	HTR3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346296.1	NM_130770		A	183776324	C	A	183776324	2	1	367	1	0	0	0	0	0	0	0	1	7455	581	21	3		3	HTR3C	3	183776324	Silent	SNP	C	TCGA-ZP-A9D1-01A-11D-A382-10	76679234	183776324	14246106	33	50968										
TADA2B	93624	hgsc.bcm.edu	37	chr4	7045509	7045509	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ctgggggcccgaggccgaggGcggctggaccagtcgcgagg	21	12	0	0			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr4:7045509G>A	ENST00000310074.7	+	1	392	c.203G>A	c.(202-204)gGc>gAc	p.G68D	RP11-367J11.2_ENST00000500031.1_RNA|TADA2B_ENST00000512388.1_Intron|CCDC96_ENST00000310085.4_5'Flank	NM_152293.2	NP_689506.2	Q86TJ2	TAD2B_HUMAN	transcriptional adaptor 2B	68	SANT. {ECO:0000255|PROSITE- ProRule:PRU00624}.				chromatin organization (GO:0006325)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	SAGA-type complex (GO:0070461)|STAGA complex (GO:0030914)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)	18						GAGGCCGAGGGCGGCTGGACC	0.731																																					p.G68D		Atlas-SNP	.											.	TADA2B	29	.	0			c.G203A						.						8	10	10					4																	7045509		1879	4006	5885	SO:0001583	missense	93624	exon1			CCGAGGGCGGCTG	AK026299	CCDS47007.1	4p16.1	2009-10-02			ENSG00000173011	ENSG00000173011			30781	protein-coding gene	gene with protein product		608790				12972612, 18936164	Standard	NM_152293		Approved	MGC21874	uc003gjw.4	Q86TJ2	OTTHUMG00000159983	ENST00000310074.7:c.203G>A	chr4.hg19:g.7045509G>A	ENSP00000308022:p.Gly68Asp	84.0	0.0		96.0	37.0	NM_152293	A0AUJ8|A4QMR7|B3KSN0|B3KU86|Q6MZG9	Missense_Mutation	SNP	ENST00000310074.7	hg19	CCDS47007.1	.	.	.	.	.	.	.	.	.	.	G	17.62	3.434180	0.62955	.	.	ENSG00000173011	ENST00000310074	T	0.41758	0.99	3.13	2.16	0.27623	Myb, DNA-binding (1);SANT domain, DNA binding (1);Homeodomain-related (1);Homeodomain-like (1);SANT, eukarya (1);	0.067384	0.64402	U	0.000015	T	0.31104	0.0786	L	0.31371	0.925	0.80722	D	1	P	0.45240	0.854	P	0.46144	0.505	T	0.03103	-1.1072	10	0.13853	T	0.58	-26.8665	9.6762	0.40043	0.0:0.0:0.7916:0.2084	.	68	Q86TJ2	TAD2B_HUMAN	D	68	ENSP00000308022:G68D	ENSP00000308022:G68D	G	+	2	0	TADA2B	7096410	1.000000	0.71417	1.000000	0.80357	0.440000	0.31957	6.163000	0.71880	1.446000	0.47643	0.484000	0.47621	GGC	.	.		0.731	TADA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358687.2	NM_152293		A	7045509	G	A	7045509	3	1	367	1	0	0	0	0	1	0	0	0	15526	1203	42	3	205	3	TADA2B	4	7045509	Missense_Mutation	SNP	G	TCGA-ZP-A9D1-01A-11D-A382-10		7045509	184108767	34	50969										
CPEB2	132864	hgsc.bcm.edu	37	chr4	15004505	15004505	+	5'Flank	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	cccccttctccgtccccctcGgcggcggcgcgggcagcccg	13	22	1	0			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr4:15004505G>A	ENST00000507071.1	+	0	0				CPEB2_ENST00000541112.1_Missense_Mutation_p.G70S|CPEB2_ENST00000538197.1_Missense_Mutation_p.G70S|CPEB2_ENST00000345451.3_5'Flank|RP11-665G4.1_ENST00000502344.1_RNA|CPEB2_ENST00000382395.3_5'Flank|CPEB2_ENST00000382401.3_5'Flank|CPEB2_ENST00000259997.5_5'Flank|CPEB2_ENST00000442003.2_Missense_Mutation_p.G70S			Q7Z5Q1	CPEB2_HUMAN	cytoplasmic polyadenylation element binding protein 2						cellular response to arsenic-containing substance (GO:0071243)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|cellular response to oxidative stress (GO:0034599)|negative regulation of cytoplasmic translation (GO:2000766)|negative regulation of cytoplasmic translational elongation (GO:1900248)|negative regulation of GTPase activity (GO:0034260)	cytoplasm (GO:0005737)|messenger ribonucleoprotein complex (GO:1990124)|nucleus (GO:0005634)	GTPase inhibitor activity (GO:0005095)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ribosomal large subunit binding (GO:0043023)|ribosomal small subunit binding (GO:0043024)|ribosome binding (GO:0043022)|translation repressor activity, nucleic acid binding (GO:0000900)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|skin(3)	14						CGTCCCCCTcggcggcggcgc	0.711																																					p.G70S		Atlas-SNP	.											.	CPEB2	77	.	0			c.G208A						.																																			SO:0001631	upstream_gene_variant	132864	exon1			CCCCTCGGCGGCG	AY247744	CCDS56325.1, CCDS56326.1	4p15.33	2013-02-12			ENSG00000137449	ENSG00000137449		"RNA binding motif (RRM) containing"	21745	protein-coding gene	gene with protein product		610605				12672660	Standard	NM_182485		Approved		uc003gnk.2	Q7Z5Q1	OTTHUMG00000090669		chr4.hg19:g.15004505G>A	Exception_encountered	1.0	0.0		5.0	5.0	NM_001177381	E7EPM3|F5H160|Q3B8N6|Q3MI89|Q3MI90|Q3MI92|Q7Z5Q0	Missense_Mutation	SNP	ENST00000507071.1	hg19		.	.	.	.	.	.	.	.	.	.	G	10.26	1.301768	0.23736	.	.	ENSG00000137449	ENST00000538197;ENST00000541112;ENST00000442003	T;T;T	0.55588	0.51;0.51;0.53	2.51	2.51	0.30379	.	.	.	.	.	T	0.36608	0.0973	N	0.08118	0	0.25027	N	0.991299	.	.	.	.	.	.	T	0.38329	-0.9666	7	0.87932	D	0	.	10.723	0.46050	0.0:0.0:1.0:0.0	.	.	.	.	S	70	ENSP00000443985:G70S;ENSP00000437884:G70S;ENSP00000414270:G70S	ENSP00000414270:G70S	G	+	1	0	CPEB2	14613603	0.234000	0.23783	0.956000	0.39512	0.945000	0.59286	0.315000	0.19451	1.398000	0.46701	0.416000	0.27883	GGC	.	.		0.711	CPEB2-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000207349.2	XM_059607		A	15004505	G	A	15004505	1	1	367	0	1	0	0	0	0	0	0	0	3803	1116	39	1		1	CPEB2	4	15004505	5'Flank	SNP	G	TCGA-ZP-A9D1-01A-11D-A382-10	7958996	15004505	176149771	35	50970										
WDR19	57728	hgsc.bcm.edu	37	chr4	39201126	39201126	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	actaagagaatcacttgtggAtgttggaatgcagaaaatct	10	5	2	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr4:39201126A>G	ENST00000399820.3	+	6	589	c.435A>G	c.(433-435)ggA>ggG	p.G145G	WDR19_ENST00000506503.1_Silent_p.G145G|WDR19_ENST00000288634.7_5'UTR	NM_025132.3	NP_079408.3	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19	145					ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium assembly (GO:0042384)|digestive system development (GO:0055123)|ear morphogenesis (GO:0042471)|embryonic camera-type eye development (GO:0031076)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|intraciliary retrograde transport (GO:0035721)|myotome development (GO:0061055)|neurological system process (GO:0050877)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|motile cilium (GO:0031514)|nonmotile primary cilium (GO:0031513)|photoreceptor connecting cilium (GO:0032391)				large_intestine(1)	1						TCACTTGTGGATGTTGGAATG	0.338																																					p.G145G		Atlas-SNP	.											.	WDR19	96	.	0			c.A435G						.						131	124	127					4																	39201126		1852	4088	5940	SO:0001819	synonymous_variant	57728	exon6			TTGTGGATGTTGG	AB046858, AY029257	CCDS47042.1	4p14	2014-02-21			ENSG00000157796	ENSG00000157796		"WD repeat domain containing", "Intraflagellar transport homologs"	18340	protein-coding gene	gene with protein product	"intraflagellar transport 144 homolog (Chlamydomonas)"	608151				12906858, 22019273	Standard	XM_005262658		Approved	Pwdmp, KIAA1638, FLJ23127, ORF26, DYF-2, Oseg6, IFT144, NPHP13	uc003gtv.3	Q8NEZ3	OTTHUMG00000160466	ENST00000399820.3:c.435A>G	chr4.hg19:g.39201126A>G		95.0	0.0		94.0	12.0	NM_025132	B5MEF2|Q8N5B4|Q9H5S0|Q9HCD4	Silent	SNP	ENST00000399820.3	hg19	CCDS47042.1																																																																																			.	.		0.338	WDR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360689.1			G	39201126	A	G	39201126	2	3	367	1	0	0	0	0	0	0	0	1	17294	320	12	2		2	WDR19	4	39201126	Silent	SNP	A	TCGA-ZP-A9D1-01A-11D-A382-10	24196621	39201126	151953150	36	50971										
N4BP2	55728	hgsc.bcm.edu	37	chr4	40123848	40123848	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	cgatggccaaatctctgaccAtagactgtctggaattggca	10	10	2	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr4:40123848A>G	ENST00000261435.6	+	9	4533	c.4117A>G	c.(4117-4119)Ata>Gta	p.I1373V		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	1373					nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|endonuclease activity (GO:0004519)			breast(4)|endometrium(3)|kidney(12)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	60						ATCTCTGACCATAGACTGTCT	0.408																																					p.I1373V		Atlas-SNP	.											.	N4BP2	166	.	0			c.A4117G						.						131	139	136					4																	40123848		2203	4300	6503	SO:0001583	missense	55728	exon9			CTGACCATAGACT	AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"BCL-3 binding protein"					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.4117A>G	chr4.hg19:g.40123848A>G	ENSP00000261435:p.Ile1373Val	325.0	0.0		363.0	82.0	NM_018177	A0AVR3|Q9NVK2|Q9P2D4	Missense_Mutation	SNP	ENST00000261435.6	hg19	CCDS3457.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.52|12.52	1.963130|1.963130	0.34659|0.34659	.|.	.|.	ENSG00000078177|ENSG00000078177	ENST00000513269|ENST00000261435;ENST00000381804	.|T	.|0.26660	.|1.72	5.96|5.96	5.96|5.96	0.96718|0.96718	.|.	.|0.124247	.|0.53938	.|D	.|0.000041	T|T	0.40956|0.40956	0.1138|0.1138	L|L	0.43152|0.43152	1.355|1.355	0.39022|0.39022	D|D	0.959766|0.959766	.|D;D	.|0.64830	.|0.994;0.99	.|D;D	.|0.69479	.|0.964;0.921	T|T	0.35992|0.35992	-0.9766|-0.9766	5|10	.|0.62326	.|D	.|0.03	-21.2043|-21.2043	11.4906|11.4906	0.50379|0.50379	0.866:0.0:0.0:0.134|0.866:0.0:0.0:0.134	.|.	.|1373;1373	.|Q86UW6-2;Q86UW6	.|.;N4BP2_HUMAN	R|V	1019|1373;1293	.|ENSP00000261435:I1373V	.|ENSP00000261435:I1373V	H|I	+|+	2|1	0|0	N4BP2|N4BP2	39800243|39800243	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.026000|0.026000	0.11368|0.11368	3.519000|3.519000	0.53458|0.53458	2.278000|2.278000	0.76064|0.76064	0.477000|0.477000	0.44152|0.44152	CAT|ATA	.	.		0.408	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177		G	40123848	A	G	40123848	3	3	367	1	0	0	0	0	1	0	0	0	10119	217	8	2	4143	2	N4BP2	4	40123848	Missense_Mutation	SNP	A	TCGA-ZP-A9D1-01A-11D-A382-10	922722	40123848	151030428	37	50972										
GRXCR1	389207	hgsc.bcm.edu	37	chr4	42965143	42965143	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ttgtgttcattgatggccatTaccttggggtaagtaagctg	12	6	1	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr4:42965143T>A	ENST00000399770.2	+	2	619	c.619T>A	c.(619-621)Tac>Aac	p.Y207N		NM_001080476.2	NP_001073945.1	A8MXD5	GRCR1_HUMAN	glutaredoxin, cysteine rich 1	207	Glutaredoxin. {ECO:0000255|PROSITE- ProRule:PRU00686}.				auditory receptor cell differentiation (GO:0042491)|cell redox homeostasis (GO:0045454)|inner ear receptor cell development (GO:0060119)|inner ear receptor stereocilium organization (GO:0060122)|negative regulation of phosphatase activity (GO:0010923)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of sound (GO:0007605)|vestibular receptor cell development (GO:0060118)	kinocilium (GO:0060091)|stereocilium (GO:0032420)	electron carrier activity (GO:0009055)|protein disulfide oxidoreductase activity (GO:0015035)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(22)|ovary(1)|prostate(2)|skin(1)	32						TGATGGCCATTACCTTGGGGT	0.438																																					p.Y207N		Atlas-SNP	.											.	GRXCR1	78	.	0			c.T619A						.						319	317	317					4																	42965143		1901	4122	6023	SO:0001583	missense	389207	exon2			GGCCATTACCTTG		CCDS43225.1	4p14	2014-06-12			ENSG00000215203	ENSG00000215203			31673	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 88"	613283	"deafness, autosomal recessive 25"	DFNB25		20137778	Standard	NM_001080476		Approved	PPP1R88	uc003gwt.3	A8MXD5	OTTHUMG00000160434	ENST00000399770.2:c.619T>A	chr4.hg19:g.42965143T>A	ENSP00000382670:p.Tyr207Asn	148.0	0.0		124.0	46.0	NM_001080476		Missense_Mutation	SNP	ENST00000399770.2	hg19	CCDS43225.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.331310	0.81690	.	.	ENSG00000215203	ENST00000399770	T	0.31769	1.48	5.98	5.98	0.97165	Glutaredoxin (2);Thioredoxin-like fold (2);	0.000000	0.64402	U	0.000006	T	0.59155	0.2173	M	0.80616	2.505	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.63844	-0.6545	10	0.72032	D	0.01	-13.9405	15.6508	0.77091	0.0:0.0:0.0:1.0	.	207	A8MXD5	GRCR1_HUMAN	N	207	ENSP00000382670:Y207N	ENSP00000382670:Y207N	Y	+	1	0	GRXCR1	42659900	1.000000	0.71417	0.999000	0.59377	0.876000	0.50452	7.698000	0.84413	2.289000	0.77006	0.482000	0.46254	TAC	.	.		0.438	GRXCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360576.1	NM_001080476		A	42965143	T	A	42965143	3	1	367	1	0	0	0	0	1	0	0	0	6821	1754	61	4	625	4	GRXCR1	4	42965143	Missense_Mutation	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	2841295	42965143	148189133	38	50973										
ENPP6	133121	hgsc.bcm.edu	37	chr4	185033941	185033941	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	gtagacagtcatgtgttccaCtgtgctcagtttgttatata	9	7	2	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr4:185033941C>A	ENST00000296741.2	-	6	1018	c.877G>T	c.(877-879)Gtg>Ttg	p.V293L		NM_153343.3	NP_699174.1	Q6UWR7	ENPP6_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 6	293					choline metabolic process (GO:0019695)|lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	glycerophosphocholine cholinephosphodiesterase activity (GO:0047390)|glycerophosphodiester phosphodiesterase activity (GO:0008889)|phosphoric diester hydrolase activity (GO:0008081)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|skin(2)	15		all_lung(41;7.99e-12)|Lung NSC(41;1.46e-11)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;4.98e-27)|Epithelial(43;3.15e-24)|OV - Ovarian serous cystadenocarcinoma(60;4.09e-12)|Colorectal(24;3.78e-05)|STAD - Stomach adenocarcinoma(60;4.5e-05)|COAD - Colon adenocarcinoma(29;0.000154)|GBM - Glioblastoma multiforme(59;0.000167)|BRCA - Breast invasive adenocarcinoma(30;0.000378)|LUSC - Lung squamous cell carcinoma(40;0.0151)		ATGTGTTCCACTGTGCTCAGT	0.403																																					p.V293L		Atlas-SNP	.											.	ENPP6	61	.	0			c.G877T						.						150	145	147					4																	185033941		2203	4300	6503	SO:0001583	missense	133121	exon6			GTTCCACTGTGCT	AK057370	CCDS3834.1	4q35.1	2008-02-05			ENSG00000164303	ENSG00000164303			23409	protein-coding gene	gene with protein product							Standard	NM_153343		Approved	MGC33971	uc003iwc.3	Q6UWR7	OTTHUMG00000160617	ENST00000296741.2:c.877G>T	chr4.hg19:g.185033941C>A	ENSP00000296741:p.Val293Leu	81.0	0.0		73.0	11.0	NM_153343	Q4W5Q1|Q96M57	Missense_Mutation	SNP	ENST00000296741.2	hg19	CCDS3834.1	.	.	.	.	.	.	.	.	.	.	C	14.39	2.520253	0.44866	.	.	ENSG00000164303	ENST00000296741	T	0.72051	-0.62	5.97	5.97	0.96955	Alkaline-phosphatase-like, core domain (1);	0.308954	0.35067	N	0.003472	T	0.60521	0.2275	N	0.25426	0.745	0.46011	D	0.998815	P	0.38223	0.623	B	0.41036	0.346	T	0.56829	-0.7914	10	0.22706	T	0.39	-37.5289	13.2716	0.60164	0.0:0.9274:0.0:0.0726	.	293	Q6UWR7	ENPP6_HUMAN	L	293	ENSP00000296741:V293L	ENSP00000296741:V293L	V	-	1	0	ENPP6	185270935	1.000000	0.71417	0.959000	0.39883	0.006000	0.05464	5.054000	0.64275	2.836000	0.97738	0.655000	0.94253	GTG	.	.		0.403	ENPP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361428.1	NM_153343		A	185033941	C	A	185033941	3	1	367	1	0	0	0	0	1	0	0	0	5136	565	20	3	457	3	ENPP6	4	185033941	Missense_Mutation	SNP	C	TCGA-ZP-A9D1-01A-11D-A382-10	142068798	185033941	6120335	39	50974										
CDH18	1016	hgsc.bcm.edu	37	chr5	19571838	19571838	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	caacaatgatcttcagcataGtagcatctttaaaaggaccc	6	10	3	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr5:19571838G>C	ENST00000507958.1	-	10	2093	c.1103C>G	c.(1102-1104)aCt>aGt	p.T368S	CDH18_ENST00000506372.1_Missense_Mutation_p.T368S|CDH18_ENST00000511273.1_Missense_Mutation_p.T368S|CDH18_ENST00000382275.1_Missense_Mutation_p.T368S|CDH18_ENST00000274170.4_Missense_Mutation_p.T368S|CDH18_ENST00000502796.1_Missense_Mutation_p.T368S			Q13634	CAD18_HUMAN	cadherin 18, type 2	368	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					CTTCAGCATAGTAGCATCTTT	0.408																																					p.T368S		Atlas-SNP	.											.	CDH18	561	.	0			c.C1103G						.						133	115	121					5																	19571838		2203	4300	6503	SO:0001583	missense	1016	exon8			AGCATAGTAGCAT	U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"Cadherins / Major cadherins"	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.1103C>G	chr5.hg19:g.19571838G>C	ENSP00000425093:p.Thr368Ser	198.0	0.0		237.0	70.0	NM_001167667	A8K0I2|B4DHG6|Q8N5Z2	Missense_Mutation	SNP	ENST00000507958.1	hg19	CCDS3889.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.568208	0.86439	.	.	ENSG00000145526	ENST00000382275;ENST00000507958;ENST00000542864;ENST00000274170;ENST00000506372;ENST00000502796;ENST00000515257;ENST00000511273	T;T;T;T;T;T;T	0.62364	0.1;0.1;0.1;0.08;0.09;0.28;0.03	5.17	5.17	0.71159	Cadherin (2);Cadherin-like (1);	0.052565	0.85682	D	0.000000	T	0.69033	0.3066	M	0.74389	2.26	0.51012	D	0.999905	B;P	0.36438	0.24;0.553	B;B	0.42959	0.403;0.392	T	0.68584	-0.5370	9	.	.	.	.	17.5963	0.88013	0.0:0.0:1.0:0.0	.	368;368	B4DHG6;Q13634	.;CAD18_HUMAN	S	368;368;368;368;368;368;314;368	ENSP00000371710:T368S;ENSP00000425093:T368S;ENSP00000274170:T368S;ENSP00000424931:T368S;ENSP00000422138:T368S;ENSP00000427383:T314S;ENSP00000425854:T368S	.	T	-	2	0	CDH18	19607595	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.312000	0.96287	2.591000	0.87537	0.655000	0.94253	ACT	.	.		0.408	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934		C	19571838	G	C	19571838	3	2	367	1	0	0	0	0	1	0	0	0	3105	1029	36	4	1293	4	CDH18	5	19571838	Missense_Mutation	SNP	G	TCGA-ZP-A9D1-01A-11D-A382-10		19571838	161343422	40	50975										
TAF9	6880	hgsc.bcm.edu	37	chr5	68651607	68651607	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ccttctctcatttggttatcTaactcatcaactacctgtaa	3	12	5	0			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr5:68651607T>C	ENST00000380822.4	-	4	246	c.195A>G	c.(193-195)ttA>ttG	p.L65L	TAF9_ENST00000380818.3_Silent_p.L62L|TAF9_ENST00000502819.1_Intron|TAF9_ENST00000512561.1_Silent_p.L34L	NM_016283.4	NP_057367.1	Q16594	TAF9_HUMAN	TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 32kDa	0					cellular response to DNA damage stimulus (GO:0006974)|chromatin organization (GO:0006325)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of cell growth (GO:0030307)|positive regulation of response to cytokine stimulus (GO:0060760)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein stabilization (GO:0050821)|response to interleukin-1 (GO:0070555)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|PCAF complex (GO:0000125)|pre-snoRNP complex (GO:0070761)|STAGA complex (GO:0030914)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	activating transcription factor binding (GO:0033613)|C2H2 zinc finger domain binding (GO:0070742)|DNA binding (GO:0003677)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(4)|urinary_tract(1)	8		Lung NSC(167;7.26e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.1e-56)|Epithelial(20;9.54e-53)|all cancers(19;2.2e-48)|Lung(70;0.0176)		TTTGGTTATCTAACTCATCAA	0.323																																					p.L65L		Atlas-SNP	.											.	TAF9	28	.	0			c.A195G						.						96	94	94					5																	68651607		2203	4300	6503	SO:0001819	synonymous_variant	6880	exon4			GTTATCTAACTCA	U21858	CCDS4001.1, CCDS4002.1, CCDS43324.1	5q13.2	2013-09-26	2002-08-29	2001-12-07	ENSG00000085231	ENSG00000085231			11542	protein-coding gene	gene with protein product		600822	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, G, 32kD"	TAF2G		10191103, 15630091, 16079131	Standard	NM_001015892		Approved	TAFII31, TAFII32, TAFIID32, MGC5067, CGI-137, MGC1603, MGC3647, AD-004	uc003jwa.3	Q16594	OTTHUMG00000099359	ENST00000380822.4:c.195A>G	chr5.hg19:g.68651607T>C		201.0	0.0		218.0	86.0	NM_016283	D3DWA3|Q5U0D1|Q9BTS1	Silent	SNP	ENST00000380822.4	hg19	CCDS4001.1																																																																																			.	.		0.323	TAF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216793.1	NM_003187		C	68651607	T	C	68651607	2	2	367	1	0	0	0	0	0	0	0	1	15550	1519	53	2		2	TAF9	5	68651607	Silent	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	49079769	68651607	112263653	41	50976										
MSH3	4437	hgsc.bcm.edu	37	chr5	79950745	79950745	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ccgcagcgcccccagcgcccCcagctcccgccttcccgccc	8	27	0	0	rs144629981|rs3045983|rs557874766	byFrequency	TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr5:79950745C>G	ENST00000265081.6	+	1	279	c.199C>G	c.(199-201)Cca>Gca	p.P67A	DHFR_ENST00000439211.2_5'UTR|DHFR_ENST00000504396.1_5'Flank|DHFR_ENST00000511032.1_5'Flank|DHFR_ENST00000513048.1_5'Flank|DHFR_ENST00000505337.1_5'Flank	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	67					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		CCCAGCGCCCCCAGCTCCCGC	0.731								Mismatch excision repair (MMR)					C|||	1091	0.217851	0.2678	0.1916	5008	,	,		6483	0.0476		0.2356	False		,,,				2504	0.3262				p.P67A	Melanoma(88;1010 1399 13793 26548 36275)	Atlas-SNP	.											MSH3,NS,carcinoma,0,1	MSH3	129	.	0			c.C199G						.						3	4	3					5																	79950745		1702	3410	5112	SO:0001583	missense	4437	exon1			GCGCCCCCAGCTC	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"Divergent upstream protein", "Mismatch repair protein 1"	600887	"mutS (E. coli) homolog 3", "mutS homolog 3 (E. coli)"				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.199C>G	chr5.hg19:g.79950745C>G	ENSP00000265081:p.Pro67Ala	67.0	0.0		71.0	9.0	NM_002439	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Missense_Mutation	SNP	ENST00000265081.6	hg19	CCDS34195.1	.	.	.	.	.	.	.	.	.	.	C	6.333	0.429466	0.11987	.	.	ENSG00000113318	ENST00000265081;ENST00000535995	D	0.85484	-1.99	.	.	.	.	.	.	.	.	T	0.70150	0.3191	N	0.19112	0.55	0.19945	N	0.999946	B	0.18741	0.03	B	0.17098	0.017	T	0.53507	-0.8429	6	.	.	.	0.6693	.	.	.	.	67	P20585	MSH3_HUMAN	A	67;58	ENSP00000265081:P67A	.	P	+	1	0	MSH3	79986501	0.560000	0.26570	0.857000	0.33713	0.119000	0.20118	0.055000	0.14229	0.064000	0.16427	0.064000	0.15345	CCA	.	.		0.731	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439		G	79950745	C	G	79950745	3	3	367	1	0	0	0	0	1	0	0	0	9880	623	22	4	201	4	MSH3	5	79950745	Missense_Mutation	SNP	C	TCGA-ZP-A9D1-01A-11D-A382-10	11299138	79950745	100964515	42	50977										
BRD8	10902	hgsc.bcm.edu	37	chr5	137485368	137485368	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ggctgaaaagtgtatccaccAagggagtctccttaatgtta	10	8	1	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr5:137485368A>G	ENST00000254900.5	-	23	3610	c.3239T>C	c.(3238-3240)tTg>tCg	p.L1080S		NM_139199.1	NP_631938	Q9H0E9	BRD8_HUMAN	bromodomain containing 8	1080					cell surface receptor signaling pathway (GO:0007166)|chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|intracellular receptor signaling pathway (GO:0030522)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Swr1 complex (GO:0000812)	sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid hormone receptor activity (GO:0004887)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(3)|urinary_tract(1)	35			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TGTATCCACCAAGGGAGTCTC	0.453																																					p.L1080S		Atlas-SNP	.											.	BRD8	192	.	0			c.T3239C						.						126	107	114					5																	137485368		2203	4300	6503	SO:0001583	missense	10902	exon23			TCCACCAAGGGAG	AF016270	CCDS4198.1, CCDS34241.1, CCDS54907.1	5q31	2008-02-05			ENSG00000112983	ENSG00000112983			19874	protein-coding gene	gene with protein product		602848				8611617, 9368056	Standard	NM_001164326		Approved	SMAP, p120	uc003lcf.1	Q9H0E9	OTTHUMG00000129204	ENST00000254900.5:c.3239T>C	chr5.hg19:g.137485368A>G	ENSP00000254900:p.Leu1080Ser	187.0	0.0		204.0	68.0	NM_139199	O43178|Q15355|Q58AB0|Q59GN0|Q969M9	Missense_Mutation	SNP	ENST00000254900.5	hg19	CCDS4198.1	.	.	.	.	.	.	.	.	.	.	A	12.81	2.048224	0.36181	.	.	ENSG00000112983	ENST00000254900;ENST00000427976	T;T	0.33216	1.77;1.42	5.13	5.13	0.70059	.	0.000000	0.36519	N	0.002552	T	0.29423	0.0733	L	0.29908	0.895	0.80722	D	1	D	0.53151	0.958	P	0.48873	0.593	T	0.01972	-1.1237	10	0.31617	T	0.26	-4.3791	12.9429	0.58357	1.0:0.0:0.0:0.0	.	1080	Q9H0E9	BRD8_HUMAN	S	1080;186	ENSP00000254900:L1080S;ENSP00000392646:L186S	ENSP00000254900:L1080S	L	-	2	0	BRD8	137513267	0.971000	0.33674	0.986000	0.45419	0.040000	0.13550	4.628000	0.61282	2.154000	0.67381	0.528000	0.53228	TTG	.	.		0.453	BRD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251282.3	NM_006696		G	137485368	A	G	137485368	3	3	367	1	0	0	0	0	1	0	0	0	1508	131	5	2	488	2	BRD8	5	137485368	Missense_Mutation	SNP	A	TCGA-ZP-A9D1-01A-11D-A382-10	57534623	137485368	43429892	43	50978										
PCDHB16	57717	hgsc.bcm.edu	37	chr5	140562308	140562308	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ctggggttggggttgacagaGatgtccacccgcaaggccag	16	10	0	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr5:140562308G>C	ENST00000361016.2	+	1	1329	c.174G>C	c.(172-174)gaG>gaC	p.E58D		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	58	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGTTGACAGAGATGTCCACCC	0.527																																					p.E58D		Atlas-SNP	.											.	PCDHB16	159	.	0			c.G174C						.						83	93	89					5																	140562308		2203	4300	6503	SO:0001583	missense	57717	exon1			GACAGAGATGTCC	AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"Cadherins / Protocadherins : Clustered"	14546	other	protocadherin	"cadherin ME1", "protocadherin-3x", "PCDHbeta 16"	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325	ENST00000361016.2:c.174G>C	chr5.hg19:g.140562308G>C	ENSP00000354293:p.Glu58Asp	129.0	0.0		133.0	45.0	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	hg19	CCDS4251.1	.	.	.	.	.	.	.	.	.	.	G	8.701	0.909785	0.17833	.	.	ENSG00000196963	ENST00000361016	T	0.32272	1.46	4.84	1.84	0.25277	Cadherin, N-terminal (1);Cadherin (1);	0.237484	0.21632	N	0.071469	T	0.22513	0.0543	L	0.41961	1.31	0.09310	N	1	B	0.02656	0.0	B	0.19391	0.025	T	0.18335	-1.0340	10	0.49607	T	0.09	.	4.8603	0.13581	0.077:0.2765:0.5041:0.1424	.	58	Q9NRJ7	PCDBG_HUMAN	D	58	ENSP00000354293:E58D	ENSP00000354293:E58D	E	+	3	2	PCDHB16	140542492	0.000000	0.05858	0.017000	0.16124	0.283000	0.27025	0.062000	0.14389	0.435000	0.26365	-0.140000	0.14226	GAG	.	.		0.527	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957		C	140562308	G	C	140562308	3	2	367	1	0	0	0	0	1	0	0	0	11550	933	33	4	176	4	PCDHB16	5	140562308	Missense_Mutation	SNP	G	TCGA-ZP-A9D1-01A-11D-A382-10	3076940	140562308	40352952	44	50979										
PCDHGB1	56104	hgsc.bcm.edu	37	chr5	140731163	140731163	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ccgacatcaacgacaatgcaCctgttttccatcaggcctcc	6	16	2	0			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr5:140731163C>A	ENST00000523390.1	+	1	1336	c.1336C>A	c.(1336-1338)Cct>Act	p.P446T	PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018922.2|NM_032095.1	NP_061745.1|NP_115266.1	Q9Y5G3	PCDGD_HUMAN	protocadherin gamma subfamily B, 1	446	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGACAATGCACCTGTTTTCCA	0.552																																					p.P446T		Atlas-SNP	.											.	PCDHGB1	198	.	0			c.C1336A						.						85	97	93					5																	140731163		2174	4275	6449	SO:0001583	missense	56104	exon1			AATGCACCTGTTT	AF152517	CCDS54923.1, CCDS75330.1	5q31	2010-01-26				ENSG00000254221		"Cadherins / Protocadherins : Clustered"	8708	other	protocadherin	"protocadherin gamma subfamily B, 1, isoform 2"	606299				10380929	Standard	NM_018922		Approved	PCDH-GAMMA-B1		Q9Y5G3		ENST00000523390.1:c.1336C>A	chr5.hg19:g.140731163C>A	ENSP00000429273:p.Pro446Thr	98.0	0.0		130.0	59.0	NM_018922	Q3SY75|Q9Y5C8	Missense_Mutation	SNP	ENST00000523390.1	hg19	CCDS54923.1	.	.	.	.	.	.	.	.	.	.	.	15.94	2.980371	0.53827	.	.	ENSG00000254221	ENST00000523390	D	0.84730	-1.89	5.49	4.62	0.57501	Cadherin (5);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	D	0.96200	0.8761	H	0.99732	4.735	0.38792	D	0.955004	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99840	1.1061	9	0.87932	D	0	.	16.3327	0.83049	0.0:0.8674:0.1326:0.0	.	446;446	Q9Y5G3-2;Q9Y5G3	.;PCDGD_HUMAN	T	446	ENSP00000429273:P446T	ENSP00000429273:P446T	P	+	1	0	PCDHGB1	140711347	1.000000	0.71417	0.052000	0.19188	0.683000	0.39861	5.956000	0.70315	1.431000	0.47355	0.563000	0.77884	CCT	.	.		0.552	PCDHGB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374740.1	NM_018922		A	140731163	C	A	140731163	3	1	367	1	0	0	0	0	1	0	0	0	11571	507	18	3	1338	3	PCDHGB1	5	140731163	Missense_Mutation	SNP	C	TCGA-ZP-A9D1-01A-11D-A382-10	168855	140731163	40184097	45	50980										
PCDHGA7	56108	hgsc.bcm.edu	37	chr5	140763436	140763436	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	tggaggttcaggctcaagatGgtcctggtagtctgacaaag	14	7	3	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr5:140763436G>T	ENST00000518325.1	+	1	970	c.970G>T	c.(970-972)Ggt>Tgt	p.G324C	PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA5_ENST00000518069.1_Intron	NM_018920.2	NP_061743.1	Q9Y5G6	PCDG7_HUMAN	protocadherin gamma subfamily A, 7	324	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|biliary_tract(1)|endometrium(8)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|skin(1)|stomach(3)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGCTCAAGATGGTCCTGGTAG	0.388																																					p.G324C		Atlas-SNP	.											.	PCDHGA7	130	.	0			c.G970T						.						102	100	101					5																	140763436		1940	4169	6109	SO:0001583	missense	56108	exon1			CAAGATGGTCCTG	AF152514	CCDS54927.1, CCDS75336.1	5q31	2010-01-26				ENSG00000253537		"Cadherins / Protocadherins : Clustered"	8705	other	protocadherin		606294				10380929	Standard	NM_018920		Approved	PCDH-GAMMA-A7		Q9Y5G6		ENST00000518325.1:c.970G>T	chr5.hg19:g.140763436G>T	ENSP00000430024:p.Gly324Cys	154.0	0.0		190.0	69.0	NM_032087	B2RN87|Q9Y5D0	Missense_Mutation	SNP	ENST00000518325.1	hg19	CCDS54927.1	.	.	.	.	.	.	.	.	.	.	.	16.62	3.174129	0.57692	.	.	ENSG00000253537	ENST00000518325	T	0.04603	3.59	5.15	4.27	0.50696	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.23410	0.0566	M	0.84683	2.71	0.33311	D	0.566079	D;D	0.64830	0.994;0.984	D;D	0.79108	0.992;0.924	T	0.23440	-1.0188	9	0.87932	D	0	.	13.1071	0.59253	0.0787:0.0:0.9213:0.0	.	324;324	Q9Y5G6;Q9Y5G6-2	PCDG7_HUMAN;.	C	324	ENSP00000430024:G324C	ENSP00000430024:G324C	G	+	1	0	PCDHGA7	140743620	0.010000	0.17322	0.992000	0.48379	0.799000	0.45148	1.359000	0.34113	2.546000	0.85860	0.655000	0.94253	GGT	.	.		0.388	PCDHGA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374744.1	NM_018920		T	140763436	G	T	140763436	3	4	367	1	0	0	0	0	1	0	0	0	11568	1348	47	3	972	3	PCDHGA7	5	140763436	Missense_Mutation	SNP	G	TCGA-ZP-A9D1-01A-11D-A382-10	32273	140763436	40151824	46	50981										
SLIT3	6586	hgsc.bcm.edu	37	chr5	168727673	168727673	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ccaaggccagcgccaggcggGcgcgcacggcggcgccgacc	17	18	0	0			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr5:168727673G>C	ENST00000519560.1	-	1	460	c.41C>G	c.(40-42)gCc>gGc	p.A14G	SLIT3_ENST00000521130.1_5'UTR|SLIT3_ENST00000332966.8_Missense_Mutation_p.A14G|SLIT3_ENST00000404867.3_Missense_Mutation_p.A14G	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	14					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CGCCAGGCGGGCGCGCACGGC	0.761																																					p.A14G	Ovarian(29;311 847 10864 17279 24903)	Atlas-SNP	.											.	SLIT3	224	.	0			c.C41G						.						2	3	3					5																	168727673		1252	2497	3749	SO:0001583	missense	6586	exon1			AGGCGGGCGCGCA	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"slit (Drosophila) homolog 3"	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.41C>G	chr5.hg19:g.168727673G>C	ENSP00000430333:p.Ala14Gly	55.0	0.0		74.0	22.0	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Missense_Mutation	SNP	ENST00000519560.1	hg19	CCDS4369.1	.	.	.	.	.	.	.	.	.	.	G	10.15	1.270324	0.23221	.	.	ENSG00000184347	ENST00000519560;ENST00000332966;ENST00000404867	T;T;T	0.76316	-1.01;-1.01;-1.0	3.55	1.52	0.23074	.	1.220170	0.06514	U	0.738493	T	0.55545	0.1927	N	0.08118	0	0.21220	N	0.99975	B;B	0.15141	0.009;0.012	B;B	0.16289	0.014;0.015	T	0.43261	-0.9402	10	0.18710	T	0.47	.	4.7619	0.13111	0.3114:0.0:0.6886:0.0	.	14;14	O75094-2;O75094	.;SLIT3_HUMAN	G	14	ENSP00000430333:A14G;ENSP00000332164:A14G;ENSP00000384890:A14G	ENSP00000332164:A14G	A	-	2	0	SLIT3	168660251	0.851000	0.29673	1.000000	0.80357	0.558000	0.35554	0.302000	0.19192	0.719000	0.32188	-0.344000	0.07964	GCC	.	.		0.761	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062		C	168727673	G	C	168727673	3	2	367	1	0	0	0	0	1	0	0	0	14756	1203	42	4	4674	4	SLIT3	5	168727673	Missense_Mutation	SNP	G	TCGA-ZP-A9D1-01A-11D-A382-10	27964237	168727673	12187587	47	50982										
DOCK2	1794	hgsc.bcm.edu	37	chr5	169267834	169267834	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	gaaccggacagtcatcaccaTgggccgggatcacattctga	11	12	4	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr5:169267834T>C	ENST00000256935.8	+	27	2857	c.2777T>C	c.(2776-2778)aTg>aCg	p.M926T	DOCK2_ENST00000520908.1_Missense_Mutation_p.M418T|DOCK2_ENST00000540750.1_5'UTR|DOCK2_ENST00000523351.1_3'UTR	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	926					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GTCATCACCATGGGCCGGGAT	0.453																																					p.M926T		Atlas-SNP	.											.	DOCK2	389	.	0			c.T2777C						.						132	112	119					5																	169267834		2203	4300	6503	SO:0001583	missense	1794	exon27			TCACCATGGGCCG	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.2777T>C	chr5.hg19:g.169267834T>C	ENSP00000256935:p.Met926Thr	89.0	0.0		99.0	38.0	NM_004946	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	hg19	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	T	14.43	2.532226	0.45073	.	.	ENSG00000134516	ENST00000256935;ENST00000343291;ENST00000520908;ENST00000519628	T;T	0.03635	3.86;3.86	5.28	5.28	0.74379	.	0.075281	0.85682	D	0.000000	T	0.04318	0.0119	L	0.38175	1.15	0.80722	D	1	B;B	0.17038	0.02;0.002	B;B	0.14023	0.01;0.003	T	0.45041	-0.9288	10	0.34782	T	0.22	.	12.7092	0.57080	0.0:0.0:0.0:1.0	.	418;926	E7ERW7;Q92608	.;DOCK2_HUMAN	T	926;307;418;130	ENSP00000256935:M926T;ENSP00000429283:M418T	ENSP00000256935:M926T	M	+	2	0	DOCK2	169200412	1.000000	0.71417	0.995000	0.50966	0.854000	0.48673	5.129000	0.64739	1.990000	0.58119	0.477000	0.44152	ATG	.	.		0.453	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		C	169267834	T	C	169267834	3	2	367	1	0	0	0	0	1	0	0	0	4689	1464	51	2	2883	2	DOCK2	5	169267834	Missense_Mutation	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	540161	169267834	11647426	48	50983										
FAM153B	202134	hgsc.bcm.edu	37	chr5	175530270	175530270	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	caggagctgtccagttacaaCggcgaggaggaggacccaga	15	10	0	1	rs367572504		TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr5:175530270C>T	ENST00000253490.4	+	13	762	c.705C>T	c.(703-705)aaC>aaT	p.N235N	FAM153B_ENST00000512862.1_Intron|FAM153B_ENST00000515817.1_Silent_p.N158N|FAM153B_ENST00000510151.1_Silent_p.N158N			P0C7A2	F153B_HUMAN	family with sequence similarity 153, member B	235										endometrium(3)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	16	all_cancers(89;0.00406)|Renal(175;0.000269)|Lung NSC(126;0.0103)|all_lung(126;0.0164)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)	Kidney(146;0.0965)		CCAGTTACAACGGCGAGGAGG	0.448													c|||	1	0.000199681	8e-04	0	5008	,	,		38352	0		0	False		,,,				2504	0				p.N158N		Atlas-SNP	.											.	FAM153B	28	.	0			c.C474T						.	C		1,4405	2.1+/-5.4	0,1,2202	293	301	298		705	-1.2	0	5		298	0,8600		0,0,4300	no	coding-synonymous	FAM153B	NM_001079529.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		235/388	175530270	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	202134	exon12			TTACAACGGCGAG	AK055006	CCDS43401.1, CCDS43401.2	5q35.2	2010-05-12			ENSG00000182230	ENSG00000182230			27323	protein-coding gene	gene with protein product							Standard	NM_001265615		Approved		uc031smb.1	P0C7A2	OTTHUMG00000163181	ENST00000253490.4:c.705C>T	chr5.hg19:g.175530270C>T		1266.0	0.0		1591.0	310.0	NM_001265615	A8MTI1	Silent	SNP	ENST00000253490.4	hg19																																																																																				.	.		0.448	FAM153B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_001079529		T	175530270	C	T	175530270	2	4	367	1	0	0	0	0	0	0	0	1	5466	535	19	1		1	FAM153B	5	175530270	Silent	SNP	C	TCGA-ZP-A9D1-01A-11D-A382-10	6262436	175530270	5384990	49	50984										
SYNGAP1	8831	hgsc.bcm.edu	37	chr6	33414444	33414444	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	tatgagcggaggctgctgtcCcaggaagaacaaaccagcaa	12	10	0	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr6:33414444C>A	ENST00000418600.2	+	17	3776	c.3675C>A	c.(3673-3675)tcC>tcA	p.S1225S	SYNGAP1_ENST00000496374.1_3'UTR|SYNGAP1_ENST00000428982.2_Silent_p.S1166S|SYNGAP1_ENST00000293748.5_Silent_p.S1225S	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	1225					dendrite development (GO:0016358)|negative regulation of axonogenesis (GO:0050771)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|pattern specification process (GO:0007389)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|receptor clustering (GO:0043113)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of MAPK cascade (GO:0043408)|regulation of synapse structure and activity (GO:0050803)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Rab GTPase activator activity (GO:0005097)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(15)|ovary(7)|pancreas(1)|stomach(1)|urinary_tract(1)	43						GGCTGCTGTCCCAGGAAGAAC	0.557																																					p.S1225S		Atlas-SNP	.											.	SYNGAP1	202	.	0			c.C3675A						.						102	81	88					6																	33414444		2203	4300	6503	SO:0001819	synonymous_variant	8831	exon17			GCTGTCCCAGGAA	AB067525	CCDS34434.2	6p21.3	2010-06-25	2010-06-25		ENSG00000197283	ENSG00000197283			11497	protein-coding gene	gene with protein product		603384	"synaptic Ras GTPase activating protein 1 homolog (rat)"			9581761, 18323856	Standard	NM_006772		Approved	SYNGAP, RASA5, KIAA1938	uc011dri.2	Q96PV0	OTTHUMG00000031096	ENST00000418600.2:c.3675C>A	chr6.hg19:g.33414444C>A		173.0	0.0		123.0	27.0	NM_006772	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Silent	SNP	ENST00000418600.2	hg19	CCDS34434.2																																																																																			.	.		0.557	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407		A	33414444	C	A	33414444	2	1	367	1	0	0	0	0	0	0	0	1	15462	610	22	3		3	SYNGAP1	6	33414444	Silent	SNP	C	TCGA-ZP-A9D1-01A-11D-A382-10		33414444	137700623	50	50985										
TTBK1	84630	hgsc.bcm.edu	37	chr6	43226800	43226800	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	gtcaatgtgacgccagtgccTggggacctgctccgggagaa	15	11	1	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr6:43226800T>A	ENST00000259750.4	+	11	1124	c.1041T>A	c.(1039-1041)ccT>ccA	p.P347P	TTBK1_ENST00000304139.5_Silent_p.P296P	NM_032538.1	NP_115927.1	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	347					substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(10)|liver(1)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)			CGCCAGTGCCTGGGGACCTGC	0.647																																					p.P347P		Atlas-SNP	.											.	TTBK1	124	.	0			c.T1041A						.						48	53	51					6																	43226800		2203	4300	6503	SO:0001819	synonymous_variant	84630	exon11			AGTGCCTGGGGAC	AB058758	CCDS34455.1	6p21.1	2008-02-05			ENSG00000146216	ENSG00000146216			19140	protein-coding gene	gene with protein product						11347906	Standard	XM_006715229		Approved	KIAA1855	uc003ouq.1	Q5TCY1	OTTHUMG00000014725	ENST00000259750.4:c.1041T>A	chr6.hg19:g.43226800T>A		186.0	0.0		123.0	28.0	NM_032538	A2A2U5|Q2L6C6|Q6ZNH0|Q8N444|Q96JH2	Silent	SNP	ENST00000259750.4	hg19	CCDS34455.1																																																																																			.	.		0.647	TTBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040584.3			A	43226800	T	A	43226800	2	1	367	1	0	0	0	0	0	0	0	1	16691	1567	55	4		4	TTBK1	6	43226800	Silent	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	9812356	43226800	127888267	51	50986										
PKHD1	5314	hgsc.bcm.edu	37	chr6	51917968	51917968	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ttgatctgatgaaccagcacTggggagtttgccggaggggg	17	7	1	3	rs4715271	byFrequency	TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr6:51917968T>A	ENST00000371117.3	-	21	2321	c.2046A>T	c.(2044-2046)ccA>ccT	p.P682P	PKHD1_ENST00000340994.4_Silent_p.P682P	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	682					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					GAACCAGCACTGGGGAGTTTG	0.527																																					p.P682P		Atlas-SNP	.											.	PKHD1	927	.	0			c.A2046T						.						71	73	72					6																	51917968		2203	4300	6503	SO:0001819	synonymous_variant	5314	exon21			CAGCACTGGGGAG	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.2046A>T	chr6.hg19:g.51917968T>A		166.0	0.0		141.0	30.0	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	hg19	CCDS4935.1																																																																																			.	T|0.921;G|0.079		0.527	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		A	51917968	T	A	51917968	2	1	367	1	0	0	0	0	0	0	0	1	11980	1567	55	4		4	PKHD1	6	51917968	Silent	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	8691168	51917968	119197099	52	50987										
EYS	346007	hgsc.bcm.edu	37	chr6	66005906	66005906	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	accgctacagttacaattgtGcgaaagggccaggcagaggc	13	10	0	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr6:66005906G>A	ENST00000370621.3	-	12	2399	c.1873C>T	c.(1873-1875)Cac>Tac	p.H625Y	EYS_ENST00000503581.1_Missense_Mutation_p.H625Y|EYS_ENST00000370616.2_Missense_Mutation_p.H625Y			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	625					detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						TTACAATTGTGCGAAAGGGCC	0.433																																					p.H625Y		Atlas-SNP	.											.	EYS	527	.	0			c.C1873T						.						144	112	122					6																	66005906		692	1591	2283	SO:0001583	missense	346007	exon12			AATTGTGCGAAAG		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.1873C>T	chr6.hg19:g.66005906G>A	ENSP00000359655:p.His625Tyr	122.0	0.0		78.0	18.0	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	hg19		.	.	.	.	.	.	.	.	.	.	.	0.946	-0.707923	0.03230	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	T;T;T	0.80304	-1.36;-1.36;-1.36	5.48	3.35	0.38373	.	.	.	.	.	T	0.44286	0.1286	N	0.08118	0	0.09310	N	0.999998	B	0.14438	0.01	B	0.17722	0.019	T	0.41106	-0.9527	9	0.41790	T	0.15	.	9.396	0.38404	0.091:0.1501:0.7588:0.0	.	625	Q5T1H1-1	.	Y	625	ENSP00000424243:H625Y;ENSP00000359655:H625Y;ENSP00000359650:H625Y	ENSP00000359650:H625Y	H	-	1	0	EYS	66062627	0.949000	0.32298	0.057000	0.19452	0.020000	0.10135	0.785000	0.26830	1.312000	0.45043	-0.226000	0.12346	CAC	.	.		0.433	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		A	66005906	G	A	66005906	3	1	367	1	0	0	0	0	1	0	0	0	5334	1319	46	3	7534	3	EYS	6	66005906	Missense_Mutation	SNP	G	TCGA-ZP-A9D1-01A-11D-A382-10	14087938	66005906	105109161	53	50988										
BAI3	577	hgsc.bcm.edu	37	chr6	69349286	69349286	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	gctgcaaaccacccaagtctGcaatcttaccagggaggcca	9	14	2	0			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr6:69349286G>C	ENST00000370598.1	+	3	1540	c.719G>C	c.(718-720)tGc>tCc	p.C240S		NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	240					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.C240Y(1)		NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				ACCCAAGTCTGCAATCTTACC	0.537																																					p.C240S		Atlas-SNP	.											BAI3,NS,carcinoma,0,1	BAI3	451	.	1	Substitution - Missense(1)	lung(1)	c.G719C						.						22	22	22					6																	69349286		2201	4299	6500	SO:0001583	missense	577	exon3			AAGTCTGCAATCT	AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"-", "GPCR / Class B : Orphans"	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.719G>C	chr6.hg19:g.69349286G>C	ENSP00000359630:p.Cys240Ser	55.0	0.0		26.0	6.0	NM_001704	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	ENST00000370598.1	hg19	CCDS4968.1	.	.	.	.	.	.	.	.	.	.	G	19.18	3.778475	0.70107	.	.	ENSG00000135298	ENST00000370598	T	0.19532	2.14	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.23133	0.0559	L	0.36672	1.1	0.80722	D	1	P	0.50156	0.932	P	0.60789	0.879	T	0.01360	-1.1375	10	0.18276	T	0.48	.	19.1668	0.93561	0.0:0.0:1.0:0.0	.	240	O60242	BAI3_HUMAN	S	240	ENSP00000359630:C240S	ENSP00000359630:C240S	C	+	2	0	BAI3	69406007	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.420000	0.97426	2.599000	0.87857	0.563000	0.77884	TGC	.	.		0.537	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			C	69349286	G	C	69349286	3	2	367	1	0	0	0	0	1	0	0	0	1300	1319	46	4	721	4	BAI3	6	69349286	Missense_Mutation	SNP	G	TCGA-ZP-A9D1-01A-11D-A382-10	3343380	69349286	101765781	54	50989										
MDN1	23195	hgsc.bcm.edu	37	chr6	90408665	90408665	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ttccacattagccagtactcTggatttgtggtcacagtact	8	10	2	0			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr6:90408665T>C	ENST00000369393.3	-	59	9202	c.9087A>G	c.(9085-9087)ccA>ccG	p.P3029P	MDN1_ENST00000428876.1_Silent_p.P3029P			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	3029					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		GCCAGTACTCTGGATTTGTGG	0.418																																					p.P3029P		Atlas-SNP	.											.	MDN1	478	.	0			c.A9087G						.						92	90	91					6																	90408665		2203	4300	6503	SO:0001819	synonymous_variant	23195	exon59			GTACTCTGGATTT	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.9087A>G	chr6.hg19:g.90408665T>C		74.0	0.0		71.0	19.0	NM_014611	O15019|Q5T794	Silent	SNP	ENST00000369393.3	hg19	CCDS5024.1																																																																																			.	.		0.418	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			C	90408665	T	C	90408665	2	2	367	1	0	0	0	0	0	0	0	1	9424	1567	55	2		2	MDN1	6	90408665	Silent	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	21059379	90408665	80706402	55	50990										
TRDN	10345	hgsc.bcm.edu	37	chr6	123696761	123696761	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	tcaacatacttgcttttactTgtttgtcacttggaactgtt	6	8	2	0			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr6:123696761T>A	ENST00000398178.3	-	19	1283	c.1262A>T	c.(1261-1263)cAa>cTa	p.Q421L	TRDN_ENST00000334268.4_Missense_Mutation_p.Q421L	NM_006073.3	NP_006064.2	Q13061	TRDN_HUMAN	triadin	421					cellular calcium ion homeostasis (GO:0006874)|cytoplasmic microtubule organization (GO:0031122)|endoplasmic reticulum membrane organization (GO:0090158)|heart contraction (GO:0060047)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|myotube differentiation (GO:0014902)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|positive regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901846)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to organic cyclic compound (GO:0014070)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)	ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	41				GBM - Glioblastoma multiforme(226;0.184)		TGCTTTTACTTGTTTGTCACT	0.284																																					p.Q422L		Atlas-SNP	.											.	TRDN	88	.	0			c.A1265T						.						58	60	60					6																	123696761		1773	3998	5771	SO:0001583	missense	10345	exon19			TTTACTTGTTTGT	U18985	CCDS59035.1, CCDS75511.1	6q22.31	2008-05-15			ENSG00000186439	ENSG00000186439			12261	protein-coding gene	gene with protein product		603283				7588753	Standard	NM_001251987		Approved		uc003pzj.2	Q13061	OTTHUMG00000015497	ENST00000398178.3:c.1262A>T	chr6.hg19:g.123696761T>A	ENSP00000381240:p.Gln421Leu	109.0	0.0		105.0	20.0	NM_001251987	A5D6W5|F5H2W7|Q6NSB8	Missense_Mutation	SNP	ENST00000398178.3	hg19	CCDS55053.1	.	.	.	.	.	.	.	.	.	.	T	11.21	1.572145	0.28092	.	.	ENSG00000186439	ENST00000398178;ENST00000398161;ENST00000334268	T;T	0.18810	2.19;2.19	5.5	3.07	0.35406	.	0.650503	0.13683	N	0.370051	T	0.03608	0.0103	N	0.12182	0.205	0.80722	D	1	B;B;B	0.10296	0.003;0.003;0.003	B;B;B	0.06405	0.002;0.002;0.002	T	0.28808	-1.0032	10	0.33141	T	0.24	-10.7856	4.9613	0.14068	0.1605:0.0858:0.0:0.7537	.	421;422;421	Q5SWK9;Q8IVK2;Q13061	.;.;TRDN_HUMAN	L	421;423;421	ENSP00000381240:Q421L;ENSP00000333984:Q421L	ENSP00000333984:Q421L	Q	-	2	0	TRDN	123738460	0.798000	0.28890	0.933000	0.37362	0.863000	0.49368	0.491000	0.22419	0.490000	0.27771	-0.263000	0.10527	CAA	.	.		0.284	TRDN-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				A	123696761	T	A	123696761	3	1	367	1	0	0	0	0	1	0	0	0	16483	1812	63	4	1019	4	TRDN	6	123696761	Missense_Mutation	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	33288096	123696761	47418306	56	50991										
PTPRK	5796	hgsc.bcm.edu	37	chr6	128388829	128388829	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	gcaaagtaatacggtgcaccCccactcatggcattttggta	9	11	1	0	rs150985952		TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr6:128388829C>T	ENST00000368215.3	-	12	1991	c.1992G>A	c.(1990-1992)ggG>ggA	p.G664G	PTPRK_ENST00000368226.4_Silent_p.G664G|PTPRK_ENST00000368210.3_Silent_p.G664G|PTPRK_ENST00000368213.5_Silent_p.G664G|PTPRK_ENST00000524481.1_5'UTR|RP11-103C16.2_ENST00000417390.1_RNA|PTPRK_ENST00000368227.3_Silent_p.G664G|PTPRK_ENST00000532331.1_Silent_p.G664G|PTPRK_ENST00000368207.3_Silent_p.G664G			Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	664	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to reactive oxygen species (GO:0034614)|cellular response to UV (GO:0034644)|focal adhesion assembly (GO:0048041)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)		PTPRK/RSPO3(10)	autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(14)|lung(24)|ovary(3)|pancreas(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	72				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		ACGGTGCACCCCCACTCATGG	0.542																																					p.G664G		Atlas-SNP	.											.	PTPRK	330	.	0			c.G1992A						.	C	,	0,4406		0,0,2203	110	109	110		1992,1992	-0.7	0.2	6	dbSNP_134	110	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	PTPRK	NM_001135648.1,NM_002844.3	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	664/1447,664/1441	128388829	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	5796	exon12			TGCACCCCCACTC	L77886	CCDS5137.1, CCDS47473.1, CCDS75517.1	6q22.2-q22.3	2013-02-11			ENSG00000152894	ENSG00000152894		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9674	protein-coding gene	gene with protein product		602545				9047348, 8663237	Standard	NM_002844		Approved	R-PTP-kappa	uc010kfc.3	Q15262	OTTHUMG00000015536	ENST00000368215.3:c.1992G>A	chr6.hg19:g.128388829C>T		96.0	0.0		78.0	20.0	NM_001135648	B2RTQ8|B7ZMG0|Q14763|Q5TG10|Q5TG11	Silent	SNP	ENST00000368215.3	hg19																																																																																				.	C|1.000;T|0.000		0.542	PTPRK-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000042163.1			T	128388829	C	T	128388829	2	4	367	1	0	0	0	0	0	0	0	1	12820	610	22	3		3	PTPRK	6	128388829	Silent	SNP	C	TCGA-ZP-A9D1-01A-11D-A382-10	4692068	128388829	42726238	57	50992										
FNDC1	84624	hgsc.bcm.edu	37	chr6	159654122	159654122	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	tgccctcccgagcccaccccAgggttccctctcactctgat	7	20	2	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr6:159654122A>G	ENST00000297267.9	+	11	2778	c.2578A>G	c.(2578-2580)Agg>Ggg	p.R860G	FNDC1_ENST00000340366.6_Missense_Mutation_p.R797G	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	860					cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		AGCCCACCCCAGGGTTCCCTC	0.617																																					p.R860G		Atlas-SNP	.											.	FNDC1	250	.	0			c.A2578G						.						23	28	26					6																	159654122		1964	4139	6103	SO:0001583	missense	84624	exon11			CACCCCAGGGTTC	AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"Fibronectin type III domain containing"	21184	protein-coding gene	gene with protein product		609991	"fibronectin type III domain containing 2"	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.2578A>G	chr6.hg19:g.159654122A>G	ENSP00000297267:p.Arg860Gly	70.0	0.0		60.0	16.0	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	hg19	CCDS47512.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.54|11.54	1.669276|1.669276	0.29604|0.29604	.|.	.|.	ENSG00000164694|ENSG00000164694	ENST00000329629|ENST00000297267;ENST00000340366	.|T;T	.|0.09073	.|3.02;3.77	4.61|4.61	0.675|0.675	0.17952|0.17952	.|.	.|0.571497	.|0.18148	.|N	.|0.150172	T|T	0.01592|0.01592	0.0051|0.0051	L|L	0.32530|0.32530	0.975|0.975	0.09310|0.09310	N|N	1|1	.|B;B	.|0.13594	.|0.008;0.002	.|B;B	.|0.13407	.|0.009;0.003	T|T	0.47420|0.47420	-0.9119|-0.9119	5|10	.|0.23891	.|T	.|0.37	-21.4251|-21.4251	5.7661|5.7661	0.18227|0.18227	0.5867:0.3252:0.0881:0.0|0.5867:0.3252:0.0881:0.0	.|.	.|797;860	.|Q4ZHG4-2;Q4ZHG4	.|.;FNDC1_HUMAN	R|G	755|860;797	.|ENSP00000297267:R860G;ENSP00000342460:R797G	.|ENSP00000297267:R860G	Q|R	+|+	2|1	0|2	FNDC1|FNDC1	159574112|159574112	0.762000|0.762000	0.28451|0.28451	0.020000|0.020000	0.16555|0.16555	0.006000|0.006000	0.05464|0.05464	1.253000|1.253000	0.32886|0.32886	-0.022000|-0.022000	0.13986|0.13986	-0.290000|-0.290000	0.09829|0.09829	CAG|AGG	.	.		0.617	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532		G	159654122	A	G	159654122	3	3	367	1	0	0	0	0	1	0	0	0	5976	179	7	2	2620	2	FNDC1	6	159654122	Missense_Mutation	SNP	A	TCGA-ZP-A9D1-01A-11D-A382-10	31265293	159654122	11460945	58	50993										
PDE1C	5137	hgsc.bcm.edu	37	chr7	31904592	31904592	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	tagaggaggtaatgcactgtCtgtgtaacatcggcagcgtg	14	7	1	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr7:31904592C>A	ENST00000396191.1	-	7	1169	c.714G>T	c.(712-714)caG>caT	p.Q238H	PDE1C_ENST00000321453.7_Missense_Mutation_p.Q238H|PDE1C_ENST00000396184.3_Missense_Mutation_p.Q238H|PDE1C_ENST00000396193.1_Missense_Mutation_p.Q298H|PDE1C_ENST00000396182.2_Missense_Mutation_p.Q238H	NM_001191057.1	NP_001177986.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	238	Catalytic. {ECO:0000250}.				activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)	cytosol (GO:0005829)	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	81			GBM - Glioblastoma multiforme(11;0.216)		Caffeine(DB00201)	AATGCACTGTCTGTGTAACAT	0.448																																					p.Q298H		Atlas-SNP	.											.	PDE1C	465	.	0			c.G894T						.						183	160	168					7																	31904592		2203	4300	6503	SO:0001583	missense	5137	exon8			CACTGTCTGTGTA	U40371	CCDS5437.1, CCDS55099.1, CCDS55100.1	7p15.1-p14.3	2008-05-15	2002-08-29		ENSG00000154678	ENSG00000154678	3.1.4.17	"Phosphodiesterases"	8776	protein-coding gene	gene with protein product		602987	"phosphodiesterase 1C, calmodulin-dependent (70kD)"			8557689	Standard	XM_005249769		Approved	Hcam3	uc003tco.2	Q14123	OTTHUMG00000023836	ENST00000396191.1:c.714G>T	chr7.hg19:g.31904592C>A	ENSP00000379494:p.Gln238His	105.0	0.0		177.0	48.0	NM_001191058	B3KPC6|E9PE92|Q14124|Q8NB10	Missense_Mutation	SNP	ENST00000396191.1	hg19	CCDS55099.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.638265	0.87760	.	.	ENSG00000154678	ENST00000396193;ENST00000396191;ENST00000321453;ENST00000396184;ENST00000396182	D;D;D;D;D	0.81739	-1.53;-1.53;-1.53;-1.53;-1.53	5.88	5.88	0.94601	Metal-dependent phosphohydrolase, HD domain (1);5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.000000	0.85682	D	0.000000	D	0.88451	0.6440	M	0.69823	2.125	0.80722	D	1	P;D;D	0.89917	0.924;0.969;1.0	P;P;D	0.81914	0.631;0.747;0.995	D	0.88276	0.2933	10	0.54805	T	0.06	.	14.3976	0.67022	0.0:0.9276:0.0:0.0724	.	238;298;238	Q14123-2;E9PE92;Q14123	.;.;PDE1C_HUMAN	H	298;238;238;238;238	ENSP00000379496:Q298H;ENSP00000379494:Q238H;ENSP00000318105:Q238H;ENSP00000379487:Q238H;ENSP00000379485:Q238H	ENSP00000318105:Q238H	Q	-	3	2	PDE1C	31871117	1.000000	0.71417	1.000000	0.80357	0.819000	0.46315	3.349000	0.52217	2.781000	0.95711	0.591000	0.81541	CAG	.	.		0.448	PDE1C-006	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328458.1			A	31904592	C	A	31904592	3	1	367	1	0	0	0	0	1	0	0	0	11644	912	32	3	1234	3	PDE1C	7	31904592	Missense_Mutation	SNP	C	TCGA-ZP-A9D1-01A-11D-A382-10		31904592	127234071	59	50994										
ZNF3	7551	hgsc.bcm.edu	37	chr7	99674959	99674959	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ggcctgaggttcctgagataCgagatcagcctgagtttcca	12	10	1	4	rs372465031		TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr7:99674959C>T	ENST00000424697.1	-	3	328	c.22G>A	c.(22-24)Gta>Ata	p.V8I	ZNF3_ENST00000413658.2_Missense_Mutation_p.V8I|ZNF3_ENST00000303915.6_Missense_Mutation_p.V8I|ZNF3_ENST00000299667.4_Missense_Mutation_p.V8I	NM_001278284.1|NM_001278287.1|NM_001278290.1|NM_001278291.1|NM_001278292.1|NM_032924.3	NP_001265213.1|NP_001265216.1|NP_001265219.1|NP_001265220.1|NP_001265221.1|NP_116313.3	P17036	ZNF3_HUMAN	zinc finger protein 3	8					cell differentiation (GO:0030154)|leukocyte activation (GO:0045321)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(8)|ovary(1)|skin(2)	25	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)	Ovarian(593;2.06e-05)|Myeloproliferative disorder(862;0.0122)|Breast(660;0.029)	STAD - Stomach adenocarcinoma(171;0.129)			TCCTGAGATACGAGATCAGCC	0.493																																					p.V8I		Atlas-SNP	.											.	ZNF3	54	.	0			c.G22A						.						151	155	154					7																	99674959		1997	4178	6175	SO:0001583	missense	7551	exon3			GAGATACGAGATC	AF027136	CCDS43618.1, CCDS43619.1	7q22.1	2013-01-08	2006-05-05					"Zinc fingers, C2H2-type", "-"	13089	protein-coding gene	gene with protein product		194510	"zinc finger protein 3 (A8-51)"				Standard	NM_032924		Approved	A8-51, KOX25, PP838, FLJ20216, HF.12, Zfp113	uc003usr.4	P17036		ENST00000424697.1:c.22G>A	chr7.hg19:g.99674959C>T	ENSP00000415358:p.Val8Ile	115.0	0.0		140.0	45.0	NM_032924	D6W5U0|P13683|Q9HBR4|Q9NNX8|Q9NXJ1|Q9UC15|Q9UC16	Missense_Mutation	SNP	ENST00000424697.1	hg19	CCDS43619.1	.	.	.	.	.	.	.	.	.	.	C	12.61	1.990662	0.35131	.	.	ENSG00000166526	ENST00000413658;ENST00000424697;ENST00000303915;ENST00000299667;ENST00000449785;ENST00000428683;ENST00000415068	T;T;T;T;T;T;T	0.06068	4.8;3.35;3.35;3.35;5.35;5.35;5.05	5.53	4.65	0.58169	.	0.398926	0.18433	N	0.141390	T	0.05686	0.0149	L	0.34521	1.04	0.09310	N	1	B;B	0.21821	0.001;0.061	B;B	0.17722	0.001;0.019	T	0.36065	-0.9763	10	0.22706	T	0.39	-4.8621	10.3091	0.43697	0.0:0.9117:0.0:0.0883	.	8;8	P17036;P17036-2	ZNF3_HUMAN;.	I	8	ENSP00000399951:V8I;ENSP00000415358:V8I;ENSP00000306372:V8I;ENSP00000299667:V8I;ENSP00000405970:V8I;ENSP00000388042:V8I;ENSP00000416686:V8I	ENSP00000299667:V8I	V	-	1	0	ZNF3	99512895	0.021000	0.18746	0.203000	0.23512	0.888000	0.51559	1.172000	0.31908	1.576000	0.49790	0.655000	0.94253	GTA	.	.		0.493	ZNF3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336247.3	NM_017715		T	99674959	C	T	99674959	3	4	367	1	0	0	0	0	1	0	0	0	17844	536	19	1	1463	1	ZNF3	7	99674959	Missense_Mutation	SNP	C	TCGA-ZP-A9D1-01A-11D-A382-10	67770367	99674959	59463704	60	50995										
CTTNBP2	83992	hgsc.bcm.edu	37	chr7	117375412	117375412	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ccgacagtgaagatttttctAaattttctaaaatgatgatg	7	5	2	4			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr7:117375412A>G	ENST00000160373.3	-	15	3690	c.3599T>C	c.(3598-3600)tTa>tCa	p.L1200S		NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	1200					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)				breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		AGATTTTTCTAAATTTTCTAA	0.363																																					p.L1200S		Atlas-SNP	.											.	CTTNBP2	200	.	0			c.T3599C						.						50	56	54					7																	117375412		2203	4299	6502	SO:0001583	missense	83992	exon15			TTTTCTAAATTTT		CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"Ankyrin repeat domain containing"	15679	protein-coding gene	gene with protein product		609772	"cortactin binding protein 2"	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.3599T>C	chr7.hg19:g.117375412A>G	ENSP00000160373:p.Leu1200Ser	158.0	0.0		189.0	29.0	NM_033427	O43389|Q7LG11|Q9C0A5	Missense_Mutation	SNP	ENST00000160373.3	hg19	CCDS5774.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.81|16.81	3.225843|3.225843	0.58668|0.58668	.|.	.|.	ENSG00000077063|ENSG00000077063	ENST00000160373|ENST00000435233	T|.	0.55760|.	0.5|.	5.52|5.52	5.52|5.52	0.82312|0.82312	.|.	0.063539|.	0.64402|.	D|.	0.000004|.	T|.	0.80065|.	0.4555|.	M|M	0.86805|0.86805	2.84|2.84	0.51012|0.51012	D|D	0.999908|0.999908	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	T|.	0.83029|.	-0.0163|.	10|.	0.87932|.	D|.	0|.	-0.2297|-0.2297	15.9458|15.9458	0.79792|0.79792	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	1200|.	Q8WZ74|.	CTTB2_HUMAN|.	S|Q	1200|185	ENSP00000160373:L1200S|.	ENSP00000160373:L1200S|.	L|X	-|-	2|1	0|0	CTTNBP2|CTTNBP2	117162648|117162648	0.998000|0.998000	0.40836|0.40836	1.000000|1.000000	0.80357|0.80357	0.934000|0.934000	0.57294|0.57294	6.361000|6.361000	0.73070|0.73070	2.216000|2.216000	0.71823|0.71823	0.533000|0.533000	0.62120|0.62120	TTA|TAG	.	.		0.363	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		G	117375412	A	G	117375412	3	3	367	1	0	0	0	0	1	0	0	0	4047	372	13	2	1428	2	CTTNBP2	7	117375412	Missense_Mutation	SNP	A	TCGA-ZP-A9D1-01A-11D-A382-10	17700453	117375412	41763251	61	50996										
MGAM	8972	hgsc.bcm.edu	37	chr7	141795408	141795408	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	tgttgcttttgtgaatatttCcagaactgtcctgcagacca	8	9	0	3			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr7:141795408C>A	ENST00000549489.2	+	41	4909	c.4814C>A	c.(4813-4815)tCc>tAc	p.S1605Y	MGAM_ENST00000475668.2_Missense_Mutation_p.S2501Y	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1605	Glucoamylase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	GTGAATATTTCCAGAACTGTC	0.493																																					p.S1605Y		Atlas-SNP	.											.	MGAM	767	.	0			c.C4814A						.						160	139	145					7																	141795408		1899	4129	6028	SO:0001583	missense	8972	exon41			ATATTTCCAGAAC	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.4814C>A	chr7.hg19:g.141795408C>A	ENSP00000447378:p.Ser1605Tyr	96.0	0.0		94.0	17.0	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	hg19	CCDS47727.1	.	.	.	.	.	.	.	.	.	.	C	17.53	3.413122	0.62511	.	.	ENSG00000257335	ENST00000549489;ENST00000475668	D	0.91577	-2.87	5.48	5.48	0.80851	Glycoside hydrolase, superfamily (1);	.	.	.	.	D	0.95345	0.8489	M	0.78801	2.425	0.45403	D	0.998388	D	0.89917	1.0	D	0.79108	0.992	D	0.95429	0.8514	9	0.72032	D	0.01	.	18.4728	0.90781	0.0:1.0:0.0:0.0	.	1605	O43451	MGA_HUMAN	Y	1605;2502	ENSP00000447378:S1605Y	ENSP00000373973:S1605Y	S	+	2	0	MGAM	141441877	1.000000	0.71417	0.957000	0.39632	0.132000	0.20833	4.833000	0.62766	2.724000	0.93272	0.655000	0.94253	TCC	.	.		0.493	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			A	141795408	C	A	141795408	3	1	367	1	0	0	0	0	1	0	0	0	9550	855	30	3	4972	3	MGAM	7	141795408	Missense_Mutation	SNP	C	TCGA-ZP-A9D1-01A-11D-A382-10	24419996	141795408	17343255	62	50997										
CUL1	8454	hgsc.bcm.edu	37	chr7	148484107	148484108	+	Missense_Mutation	DNP	CA	CA	TG													0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	gtcttcaagtacatagaagaCaaagacgtatttcagaagtt							TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C|A	C|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr7:148484107_148484108CA>TG	ENST00000325222.4	+	13	1653_1654	c.1374_1375CA>TG	c.(1372-1377)gaCAaa>gaTGaa	p.K459E	CUL1_ENST00000409469.1_Missense_Mutation_p.K459E|CUL1_ENST00000602748.1_Missense_Mutation_p.K459E	NM_003592.2	NP_003583.2	Q13616	CUL1_HUMAN	cullin 1	459					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic cell cycle (GO:0000278)|negative regulation of cell proliferation (GO:0008285)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|viral process (GO:0016032)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|SCF ubiquitin ligase complex (GO:0019005)				breast(2)|central_nervous_system(2)|endometrium(1)|kidney(5)|large_intestine(10)|liver(2)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	40	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)			ACATAGAAGACAAAGACGTATT	0.5																																					p.D458D|p.K459E		Atlas-SNP	.											.	CUL1	80	.	0			c.C1374T|c.A1375G						.																																			SO:0001583	missense	8454	exon13			AGAAGACAAAGAC|GAAGACAAAGACG	U58087	CCDS34772.1	7q36.1	2011-05-24			ENSG00000055130	ENSG00000055130			2551	protein-coding gene	gene with protein product		603134				8681378	Standard	NM_003592		Approved		uc003wey.3	Q13616	OTTHUMG00000152776	Exception_encountered	chr7.hg19:g.148484107_148484108delinsTG	ENSP00000326804:p.Lys459Glu	48.0|49.0	0.0		56.0	22.0	NM_003592	D3DWG3|O60719|Q08AL6|Q8IYW1	Silent|Missense_Mutation	SNP	ENST00000325222.4	hg19	CCDS34772.1																																																																																			.	.		0.5	CUL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467785.1	NM_003592		TG	148484108	CA	TG	148484107	3	4	367	1	0	0	0	0	1	0	0	0	4056	477	17	3	1420	3	CUL1	7	148484107	Missense_Mutation	DNP	CA	TCGA-ZP-A9D1-01A-11D-A382-10	6688699	148484107	10654556	63	50998										
GIMAP6	474344	hgsc.bcm.edu	37	chr7	150325099	150325099	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ccctgttgttgaagccgcaaTggcgccgtgcaagggtcaca	13	12	1	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr7:150325099T>C	ENST00000328902.5	-	3	803	c.587A>G	c.(586-588)cAt>cGt	p.H196R	GIMAP6_ENST00000493969.1_3'UTR	NM_001244072.1|NM_024711.5	NP_001231001.1|NP_078987.3	Q6P9H5	GIMA6_HUMAN	GTPase, IMAP family member 6	196	AIG1-type G.					cytosol (GO:0005829)	GTP binding (GO:0005525)			endometrium(4)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	29			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GAAGCCGCAATGGCGCCGTGC	0.587																																					p.H266R		Atlas-SNP	.											.	GIMAP6	60	.	0			c.A797G						.						118	123	121					7																	150325099		2203	4300	6503	SO:0001583	missense	474344	exon3			CCGCAATGGCGCC	AK026343	CCDS34778.1, CCDS59087.1, CCDS75676.1	7q36.1	2014-04-04			ENSG00000133561	ENSG00000133561		"GTPases, IMAP"	21918	protein-coding gene	gene with protein product	"immune-associated nucleotide-binding protein 6"					15474311	Standard	NM_001244072		Approved	FLJ22690, IAN6	uc022apv.1	Q6P9H5	OTTHUMG00000159137	ENST00000328902.5:c.587A>G	chr7.hg19:g.150325099T>C	ENSP00000330374:p.His196Arg	70.0	0.0		84.0	30.0	NM_001244072	C9J7B6|D3DWZ4|Q5ZPR6|Q9H612	Missense_Mutation	SNP	ENST00000328902.5	hg19	CCDS34778.1	.	.	.	.	.	.	.	.	.	.	T	12.84	2.058128	0.36277	.	.	ENSG00000133561	ENST00000328902;ENST00000392862	T	0.05081	3.5	4.29	4.29	0.51040	AIG1 (1);	0.063141	0.64402	D	0.000003	T	0.14527	0.0351	L	0.39633	1.23	0.80722	D	1	P;D	0.76494	0.904;0.999	P;D	0.74674	0.837;0.984	T	0.01232	-1.1411	10	0.48119	T	0.1	.	9.7378	0.40399	0.0:0.0:0.0:1.0	.	196;116	Q6P9H5;Q6P9H5-2	GIMA6_HUMAN;.	R	196;257	ENSP00000330374:H196R	ENSP00000330374:H196R	H	-	2	0	GIMAP6	149956032	1.000000	0.71417	1.000000	0.80357	0.042000	0.13812	3.009000	0.49552	1.820000	0.53075	0.459000	0.35465	CAT	.	.		0.587	GIMAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353457.1	NM_024711		C	150325099	T	C	150325099	3	2	367	1	0	0	0	0	1	0	0	0	6391	1464	51	2	295	2	GIMAP6	7	150325099	Missense_Mutation	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	1840992	150325099	8813564	64	50999										
RB1CC1	9821	hgsc.bcm.edu	37	chr8	53596502	53596502	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	cagccatgcattctcctccaTtgaccaccagcacctggtgt	7	16	1	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr8:53596502T>C	ENST00000025008.5	-	4	666	c.143A>G	c.(142-144)aAt>aGt	p.N48S	RB1CC1_ENST00000539297.1_Missense_Mutation_p.N48S|RB1CC1_ENST00000435644.2_Missense_Mutation_p.N48S|RB1CC1_ENST00000521611.1_Intron	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1	48					autophagic vacuole assembly (GO:0000045)|cell cycle (GO:0007049)|heart development (GO:0007507)|JNK cascade (GO:0007254)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell size (GO:0045793)|positive regulation of protein phosphorylation (GO:0001934)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)				NS(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(19)|ovary(8)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	60		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				TTCTCCTCCATTGACCACCAG	0.418																																					p.N48S	GBM(180;1701 2102 13475 42023 52570)	Atlas-SNP	.											.	RB1CC1	163	.	0			c.A143G						.						119	94	103					8																	53596502		2203	4300	6503	SO:0001583	missense	9821	exon4			CCTCCATTGACCA	AB059622	CCDS34892.1, CCDS47856.1	8q11	2014-06-13				ENSG00000023287			15574	protein-coding gene	gene with protein product	"200 kDa FAK family kinase-interacting protein", "phosphatase 1, regulatory subunit 131"	606837				11850849, 7724523, 18443221	Standard	NM_014781		Approved	KIAA0203, Cc1, DRAGOU14, FIP200, ATG17, PPP1R131	uc003xre.4	Q8TDY2		ENST00000025008.5:c.143A>G	chr8.hg19:g.53596502T>C	ENSP00000025008:p.Asn48Ser	69.0	0.0		88.0	44.0	NM_001083617	Q86YR4|Q8WVU9|Q92601	Missense_Mutation	SNP	ENST00000025008.5	hg19	CCDS34892.1	.	.	.	.	.	.	.	.	.	.	T	17.80	3.479187	0.63849	.	.	ENSG00000023287	ENST00000025008;ENST00000435644;ENST00000539297;ENST00000517963	T;T;T	0.41065	1.01;1.01;1.01	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	T	0.46268	0.1384	N	0.20401	0.57	0.80722	D	1	D;D	0.71674	0.998;0.997	D;D	0.80764	0.994;0.985	T	0.30060	-0.9991	10	0.13108	T	0.6	-21.6464	14.99	0.71381	0.0:0.0:0.0:1.0	.	48;48	Q8TDY2-2;Q8TDY2	.;RBCC1_HUMAN	S	48;48;48;44	ENSP00000025008:N48S;ENSP00000396067:N48S;ENSP00000445960:N48S	ENSP00000025008:N48S	N	-	2	0	RB1CC1	53759055	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.926000	0.70070	1.999000	0.58509	0.455000	0.32223	AAT	.	.		0.418	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378011.1	NM_014781		C	53596502	T	C	53596502	3	2	367	1	0	0	0	0	1	0	0	0	13114	1493	52	2	4725	2	RB1CC1	8	53596502	Missense_Mutation	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10		53596502	92767520	65	51000										
CCNE2	9134	hgsc.bcm.edu	37	chr8	95900175	95900175	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ctcaagtttggaagcaatgaAtaatgaggtaattccaatga	9	5	1	3			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr8:95900175A>G	ENST00000520509.1	-	7	832	c.580T>C	c.(580-582)Ttc>Ctc	p.F194L	RP11-347C18.5_ENST00000605911.1_RNA|CCNE2_ENST00000308108.4_Missense_Mutation_p.F194L|CCNE2_ENST00000396133.3_Missense_Mutation_p.F194L|CCNE2_ENST00000523476.1_5'UTR			O96020	CCNE2_HUMAN	cyclin E2	194					cell cycle checkpoint (GO:0000075)|cell division (GO:0051301)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			cervix(1)|endometrium(2)|large_intestine(3)|lung(4)|prostate(1)	11	Breast(36;8.75e-07)					GAAGCAATGAATAATGAGGTA	0.264																																					p.F194L		Atlas-SNP	.											.	CCNE2	29	.	0			c.T580C						.						59	65	63					8																	95900175		2198	4280	6478	SO:0001583	missense	9134	exon7			CAATGAATAATGA	AF091433	CCDS6264.1	8q22.1	2005-10-18			ENSG00000175305	ENSG00000175305			1590	protein-coding gene	gene with protein product		603775				9840927, 9840943	Standard	NM_057749		Approved	CYCE2	uc003yhc.3	O96020	OTTHUMG00000164696	ENST00000520509.1:c.580T>C	chr8.hg19:g.95900175A>G	ENSP00000429089:p.Phe194Leu	349.0	0.0		382.0	106.0	NM_057749	O95439	Missense_Mutation	SNP	ENST00000520509.1	hg19	CCDS6264.1	.	.	.	.	.	.	.	.	.	.	A	33	5.209567	0.95069	.	.	ENSG00000175305	ENST00000520509;ENST00000308108;ENST00000542725;ENST00000396133	T;T;T	0.10099	2.91;2.91;2.91	5.63	5.63	0.86233	Cyclin, N-terminal (1);Cyclin-like (3);	0.000000	0.85682	D	0.000000	T	0.25306	0.0615	L	0.50333	1.59	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.04885	-1.0920	10	0.11485	T	0.65	.	15.8419	0.78852	1.0:0.0:0.0:0.0	.	194;194	Q8WUE3;O96020	.;CCNE2_HUMAN	L	194;194;86;194	ENSP00000429089:F194L;ENSP00000309181:F194L;ENSP00000379437:F194L	ENSP00000309181:F194L	F	-	1	0	CCNE2	95969351	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.530000	0.81962	2.137000	0.66172	0.533000	0.62120	TTC	.	.		0.264	CCNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379808.1	NM_057749, NM_004702		G	95900175	A	G	95900175	3	3	367	1	0	0	0	0	1	0	0	0	2923	101	4	2	658	2	CCNE2	8	95900175	Missense_Mutation	SNP	A	TCGA-ZP-A9D1-01A-11D-A382-10	42303673	95900175	50463847	66	51001										
CNTFR	1271	hgsc.bcm.edu	37	chr9	34568951	34568951	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	cggcggcggcaagcacagcaCagcaggcccacgggacagga	16	14	0	0			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr9:34568951C>A	ENST00000378980.3	-	3	322	c.29G>T	c.(28-30)tGt>tTt	p.C10F	CNTFR-AS1_ENST00000438244.1_RNA|CNTFR-AS1_ENST00000454187.1_RNA|CNTFR-AS1_ENST00000453642.1_RNA|CNTFR_ENST00000351266.4_Missense_Mutation_p.C10F|CNTFR-AS1_ENST00000436360.1_RNA	NM_001207011.1|NM_147164.2	NP_001193940.1|NP_671693.1	P26992	CNTFR_HUMAN	ciliary neurotrophic factor receptor	10					brainstem development (GO:0003360)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)|positive regulation of cell proliferation (GO:0008284)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|skeletal muscle organ development (GO:0060538)|suckling behavior (GO:0001967)	anchored component of membrane (GO:0031225)|CNTFR-CLCF1 complex (GO:0097059)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|cytokine binding (GO:0019955)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(4)|skin(1)	15	all_epithelial(49;0.0899)		STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.00494)		AAGCACAGCACAGCAGGCCCA	0.677																																					p.C10F		Atlas-SNP	.											.	CNTFR	46	.	0			c.G29T						.						20	23	22					9																	34568951		2194	4291	6485	SO:0001583	missense	1271	exon3			ACAGCACAGCAGG	M73238	CCDS6558.1	9p13	2013-02-11			ENSG00000122756	ENSG00000122756		"Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2170	protein-coding gene	gene with protein product		118946				1648265	Standard	NM_001842		Approved		uc003zuq.2	P26992	OTTHUMG00000019821	ENST00000378980.3:c.29G>T	chr9.hg19:g.34568951C>A	ENSP00000368265:p.Cys10Phe	91.0	0.0		116.0	37.0	NM_147164	Q5U050	Missense_Mutation	SNP	ENST00000378980.3	hg19	CCDS6558.1	.	.	.	.	.	.	.	.	.	.	C	14.51	2.558315	0.45590	.	.	ENSG00000122756	ENST00000378980;ENST00000351266;ENST00000417345	T;T;T	0.30182	1.54;1.54;1.54	4.83	3.86	0.44501	.	0.085367	0.45126	D	0.000393	T	0.24586	0.0596	L	0.45581	1.43	0.40167	D	0.977139	B	0.02656	0.0	B	0.01281	0.0	T	0.17471	-1.0368	9	0.30854	T	0.27	.	9.3853	0.38338	0.2282:0.7718:0.0:0.0	.	10	P26992	CNTFR_HUMAN	F	10	ENSP00000368265:C10F;ENSP00000242338:C10F;ENSP00000388082:C10F	ENSP00000242338:C10F	C	-	2	0	CNTFR	34558951	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	2.011000	0.40922	2.504000	0.84457	0.655000	0.94253	TGT	.	.		0.677	CNTFR-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052176.1			A	34568951	C	A	34568951	3	1	367	1	0	0	0	0	1	0	0	0	3640	478	17	3	1121	3	CNTFR	9	34568951	Missense_Mutation	SNP	C	TCGA-ZP-A9D1-01A-11D-A382-10		34568951	106644480	67	51002										
CA9	768	hgsc.bcm.edu	37	chr9	35680975	35680975	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	cacacagaaggggaaccaaaGggggtgtgagctaccgccca	14	11	0	2	rs374397867		TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr9:35680975G>A	ENST00000378357.4	+	11	1437	c.1333G>A	c.(1333-1335)Ggg>Agg	p.G445R	CA9_ENST00000493245.1_3'UTR	NM_001216.2	NP_001207.2	Q16790	CAH9_HUMAN	carbonic anhydrase IX	445					bicarbonate transport (GO:0015701)|cellular response to hypoxia (GO:0071456)|morphogenesis of an epithelium (GO:0002009)|one-carbon metabolic process (GO:0006730)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to drug (GO:0042493)|response to testosterone (GO:0033574)|secretion (GO:0046903)|small molecule metabolic process (GO:0044281)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(3)|lung(5)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	17	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)		Benzthiazide(DB00562)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Zonisamide(DB00909)	GGGAACCAAAGGGGGTGTGAG	0.552																																					p.G445R		Atlas-SNP	.											.	CA9	48	.	0			c.G1333A						.						79	88	85					9																	35680975		2203	4300	6503	SO:0001583	missense	768	exon11			ACCAAAGGGGGTG	X66839	CCDS6585.1	9p13.3	2012-08-21			ENSG00000107159	ENSG00000107159		"Carbonic anhydrases"	1383	protein-coding gene	gene with protein product	"carbonic dehydratase", "RCC-associated protein G250"	603179				8661007, 9787087	Standard	NM_001216		Approved	MN, CAIX	uc003zxo.4	Q16790	OTTHUMG00000021029	ENST00000378357.4:c.1333G>A	chr9.hg19:g.35680975G>A	ENSP00000367608:p.Gly445Arg	56.0	0.0		57.0	6.0	NM_001216	Q5T4R1	Missense_Mutation	SNP	ENST00000378357.4	hg19	CCDS6585.1	.	.	.	.	.	.	.	.	.	.	G	10.57	1.387492	0.25031	.	.	ENSG00000107159	ENST00000378357	T	0.63255	-0.03	4.91	4.02	0.46733	.	0.629032	0.14957	N	0.288583	T	0.47097	0.1427	L	0.39898	1.24	0.29079	N	0.882839	P	0.36199	0.543	B	0.28916	0.096	T	0.40572	-0.9556	10	0.29301	T	0.29	.	9.1051	0.36692	0.0995:0.0:0.9005:0.0	.	445	Q16790	CAH9_HUMAN	R	445	ENSP00000367608:G445R	ENSP00000367608:G445R	G	+	1	0	CA9	35670975	0.996000	0.38824	0.884000	0.34674	0.022000	0.10575	2.849000	0.48286	1.427000	0.47276	0.591000	0.81541	GGG	.	.		0.552	CA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055479.1	NM_001216		A	35680975	G	A	35680975	3	1	367	1	0	0	0	0	1	0	0	0	2526	1000	35	3	1375	3	CA9	9	35680975	Missense_Mutation	SNP	G	TCGA-ZP-A9D1-01A-11D-A382-10	1112024	35680975	105532456	68	51003										
TOMM5	401505	hgsc.bcm.edu	37	chr9	37588927	37588927	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	caatttctttaagataaatgGagctgaaagaaaaacaaatc	6	5	1	3			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr9:37588927G>C	ENST00000321301.6	-	2	233	c.124C>G	c.(124-126)Cca>Gca	p.P42A	RP11-613M10.8_ENST00000537239.2_Missense_Mutation_p.P55A|TOMM5_ENST00000377773.5_Missense_Mutation_p.P76A|TOMM5_ENST00000401811.3_Missense_Mutation_p.S82C|FBXO10_ENST00000541829.1_5'Flank|TOMM5_ENST00000544379.1_3'UTR|RP11-613M10.9_ENST00000540557.1_3'UTR|RP11-613M10.8_ENST00000544475.1_5'Flank	NM_001001790.2	NP_001001790.1	Q8N4H5	TOM5_HUMAN	translocase of outer mitochondrial membrane 5 homolog (yeast)	42					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	integral component of membrane (GO:0016021)|mitochondrial outer membrane translocase complex (GO:0005742)|mitochondrion (GO:0005739)											AAGATAAATGGAGCTGAAAGA	0.328																																					p.P76A		Atlas-SNP	.											.	TOMM5	3	.	0			c.C226G						.						59	57	58					9																	37588927		1823	4081	5904	SO:0001583	missense	401505	exon2			TAAATGGAGCTGA	BC029423	CCDS43803.1, CCDS47967.1, CCDS47968.1	9p13.2	2008-08-21	2008-08-21	2008-08-21	ENSG00000175768	ENSG00000175768			31369	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 105"	C9orf105		18331822	Standard	NM_001001790		Approved	bA613M10.3	uc011lql.2	Q8N4H5	OTTHUMG00000019923	ENST00000321301.6:c.124C>G	chr9.hg19:g.37588927G>C	ENSP00000313584:p.Pro42Ala	70.0	0.0		96.0	29.0	NM_001134485	B2DG07|F6S928|Q5JRT7	Missense_Mutation	SNP	ENST00000321301.6	hg19	CCDS43803.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.1|21.1	4.095999|4.095999	0.76870|0.76870	.|.	.|.	ENSG00000175768|ENSG00000175768	ENST00000377773;ENST00000321301|ENST00000401811	.|.	.|.	.|.	5.14|5.14	5.14|5.14	0.70334|0.70334	.|.	0.072023|.	0.53938|.	D|.	0.000043|.	T|T	0.74045|0.74045	0.3665|0.3665	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	0.998;1.0|.	D;D|.	0.87578|.	0.994;0.998|.	T|T	0.76413|0.76413	-0.2968|-0.2968	8|5	0.87932|0.87932	D|D	0|0	.|.	14.2857|14.2857	0.66245|0.66245	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	42;76|.	Q8N4H5;Q5JRT7|.	TOM5_HUMAN;.|.	A|C	76;42|82	.|.	ENSP00000439443:P55A|ENSP00000384411:S82C	P|S	-|-	1|2	0|0	TOMM5|TOMM5	37578927|37578927	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.961000|0.961000	0.63080|0.63080	6.993000|6.993000	0.76245|0.76245	2.833000|2.833000	0.97629|0.97629	0.555000|0.555000	0.69702|0.69702	CCA|TCC	.	.		0.328	TOMM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052468.2			C	37588927	G	C	37588927	3	2	367	1	0	0	0	0	1	0	0	0	16375	1174	41	4	35	4	TOMM5	9	37588927	Missense_Mutation	SNP	G	TCGA-ZP-A9D1-01A-11D-A382-10	1907952	37588927	103624504	69	51004										
SFMBT2	57713	hgsc.bcm.edu	37	chr10	7318928	7318928	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	cagagtacatttccattcagAggccatcttcaaaggataga	8	9	3	3			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr10:7318928A>T	ENST00000361972.4	-	7	886	c.796T>A	c.(796-798)Tct>Act	p.S266T	SFMBT2_ENST00000397167.1_Missense_Mutation_p.S266T	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	266					negative regulation of gene expression (GO:0010629)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	histone binding (GO:0042393)			NS(2)|breast(3)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(26)|lung(34)|ovary(5)|pancreas(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	99						TTCCATTCAGAGGCCATCTTC	0.398																																					p.S266T		Atlas-SNP	.											.	SFMBT2	209	.	0			c.T796A						.						143	136	139					10																	7318928		2203	4300	6503	SO:0001583	missense	57713	exon7			ATTCAGAGGCCAT	AB046837	CCDS31138.1	10p15.1	2013-01-10	2003-11-14		ENSG00000198879	ENSG00000198879		"Sterile alpha motif (SAM) domain containing"	20256	protein-coding gene	gene with protein product		615392	"Scm-related gene containing four mbt domains 2"			10997877	Standard	NM_001029880		Approved	KIAA1617	uc009xio.2	Q5VUG0	OTTHUMG00000017630	ENST00000361972.4:c.796T>A	chr10.hg19:g.7318928A>T	ENSP00000355109:p.Ser266Thr	69.0	0.0		73.0	11.0	NM_001029880	A7MD09|Q9HCF5	Missense_Mutation	SNP	ENST00000361972.4	hg19	CCDS31138.1	.	.	.	.	.	.	.	.	.	.	A	10.80	1.452028	0.26074	.	.	ENSG00000198879	ENST00000361972;ENST00000397167	T;T	0.42513	0.97;0.97	5.83	4.68	0.58851	.	0.211412	0.51477	D	0.000090	T	0.34542	0.0901	L	0.56769	1.78	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.12528	-1.0544	10	0.15066	T	0.55	.	7.8787	0.29610	0.6425:0.1223:0.0:0.2352	.	266	Q5VUG0	SMBT2_HUMAN	T	266	ENSP00000355109:S266T;ENSP00000380353:S266T	ENSP00000355109:S266T	S	-	1	0	SFMBT2	7358934	1.000000	0.71417	0.998000	0.56505	0.975000	0.68041	3.332000	0.52083	1.006000	0.39211	0.533000	0.62120	TCT	.	.		0.398	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046673.1	NM_001029880		T	7318928	A	T	7318928	3	4	367	1	0	0	0	0	1	0	0	0	14173	304	11	4	1948	4	SFMBT2	10	7318928	Missense_Mutation	SNP	A	TCGA-ZP-A9D1-01A-11D-A382-10		7318928	128215819	70	51005										
PRF1	5551	hgsc.bcm.edu	37	chr10	72357836	72357836	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	acggccccactccggtttccTggaggctcccccagaagcat	10	17	0	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr10:72357836T>G	ENST00000441259.1	-	3	1801	c.1641A>C	c.(1639-1641)ccA>ccC	p.P547P	PRF1_ENST00000373209.2_Silent_p.P547P	NM_001083116.1|NM_005041.4	NP_001076585.1|NP_005032.2	P14222	PERF_HUMAN	perforin 1 (pore forming protein)	547					apoptotic process (GO:0006915)|cellular defense response (GO:0006968)|cytolysis (GO:0019835)|defense response to tumor cell (GO:0002357)|defense response to virus (GO:0051607)|immune response to tumor cell (GO:0002418)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)	cytolytic granule (GO:0044194)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|wide pore channel activity (GO:0022829)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(3)|urinary_tract(3)	23						TCCGGTTTCCTGGAGGCTCCC	0.587			M			"various leukaemia, lymphoma"	Type 2 familial hemophagocytic lymphohistiocytosis		Familial Hemophagocytic Lymphohistiocytosis																												p.P547P		Atlas-SNP	.	yes	Rec			10	10q22	5551	perforin 1 (pore forming protein)		L	.	PRF1	64	.	0			c.A1641C						.						50	53	52					10																	72357836		2203	4300	6503	SO:0001819	synonymous_variant	5551	exon3	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	GTTTCCTGGAGGC	BC047695	CCDS7305.1	10q22	2014-09-17			ENSG00000180644	ENSG00000180644			9360	protein-coding gene	gene with protein product	"Perforin", "perforin 1 (preforming protein)"	170280				1505959, 2592021	Standard	NM_005041		Approved	PFP, P1, HPLH2	uc001jrf.4	P14222	OTTHUMG00000018412	ENST00000441259.1:c.1641A>C	chr10.hg19:g.72357836T>G		50.0	0.0		52.0	6.0	NM_001083116	B2R6X4|Q59F57|Q86WX7	Silent	SNP	ENST00000441259.1	hg19	CCDS7305.1																																																																																			.	.		0.587	PRF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048517.2	NM_005041		G	72357836	T	G	72357836	2	3	367	1	0	0	0	0	0	0	0	1	12490	1567	55	5		5	PRF1	10	72357836	Silent	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	65038908	72357836	63176911	71	51006										
SYNPO2L	79933	hgsc.bcm.edu	37	chr10	75407632	75407632	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ctggggcaggcgcctctgggCgcgcagagggtcgcaaaggc	19	12	1	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr10:75407632C>T	ENST00000394810.2	-	4	1927	c.1778G>A	c.(1777-1779)cGc>cAc	p.R593H	SYNPO2L_ENST00000372873.4_Missense_Mutation_p.R369H	NM_001114133.1	NP_001107605.1	Q9H987	SYP2L_HUMAN	synaptopodin 2-like	593	Pro-rich.					cytoskeleton (GO:0005856)|nucleus (GO:0005634)|Z disc (GO:0030018)				breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Prostate(51;0.0112)					CGCCTCTGGGCGCGCAGAGGG	0.697																																					p.R593H		Atlas-SNP	.											.	SYNPO2L	118	.	0			c.G1778A						.						14	17	16					10																	75407632		2097	4222	6319	SO:0001583	missense	79933	exon4			TCTGGGCGCGCAG	AK022983	CCDS7331.1, CCDS44438.1	10q22.3	2007-12-19			ENSG00000166317	ENSG00000166317			23532	protein-coding gene	gene with protein product							Standard	XM_005270158		Approved	FLJ12921	uc001jut.4	Q9H987	OTTHUMG00000018471	ENST00000394810.2:c.1778G>A	chr10.hg19:g.75407632C>T	ENSP00000378289:p.Arg593His	124.0	0.0		90.0	15.0	NM_001114133	A5PKV9|Q68A20	Missense_Mutation	SNP	ENST00000394810.2	hg19	CCDS44438.1	.	.	.	.	.	.	.	.	.	.	C	1.653	-0.513599	0.04200	.	.	ENSG00000166317	ENST00000372873;ENST00000394810	T;T	0.23348	1.91;2.24	5.02	0.816	0.18768	.	0.704670	0.13824	N	0.360217	T	0.14184	0.0343	N	0.22421	0.69	0.09310	N	1	B;B	0.13594	0.008;0.008	B;B	0.06405	0.001;0.002	T	0.19614	-1.0300	10	0.41790	T	0.15	-6.1817	5.0297	0.14404	0.1467:0.4438:0.0:0.4095	.	593;369	Q9H987;Q9H987-2	SYP2L_HUMAN;.	H	369;593	ENSP00000361964:R369H;ENSP00000378289:R593H	ENSP00000361964:R369H	R	-	2	0	SYNPO2L	75077638	0.001000	0.12720	0.355000	0.25773	0.010000	0.07245	-0.169000	0.09911	0.318000	0.23185	-0.272000	0.10252	CGC	.	.		0.697	SYNPO2L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316562.2	NM_024875		T	75407632	C	T	75407632	3	4	367	1	0	0	0	0	1	0	0	0	15473	768	27	1	1159	1	SYNPO2L	10	75407632	Missense_Mutation	SNP	C	TCGA-ZP-A9D1-01A-11D-A382-10	3049796	75407632	60127115	72	51007										
SORCS3	22986	hgsc.bcm.edu	37	chr10	107006989	107006989	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ccctgcagaatatttccagtCccagcttttatcattctctc	4	14	2	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr10:107006989C>A	ENST00000369701.3	+	22	3232	c.3005C>A	c.(3004-3006)tCc>tAc	p.S1002Y	SORCS3_ENST00000369699.4_3'UTR	NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	1002					learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		TATTTCCAGTCCCAGCTTTTA	0.458																																					p.S1002Y	NSCLC(116;1497 1690 7108 13108 14106)	Atlas-SNP	.											.	SORCS3	282	.	0			c.C3005A						.						102	93	96					10																	107006989		2203	4300	6503	SO:0001583	missense	22986	exon22			TCCAGTCCCAGCT	AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.3005C>A	chr10.hg19:g.107006989C>A	ENSP00000358715:p.Ser1002Tyr	92.0	0.0		67.0	25.0	NM_014978	Q5VXF9|Q9NQJ2	Missense_Mutation	SNP	ENST00000369701.3	hg19	CCDS7558.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.635534	0.87760	.	.	ENSG00000156395	ENST00000369701	T	0.16457	2.34	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.45955	0.1368	M	0.78637	2.42	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.29731	-1.0002	9	.	.	.	.	19.7426	0.96238	0.0:1.0:0.0:0.0	.	1002	Q9UPU3	SORC3_HUMAN	Y	1002	ENSP00000358715:S1002Y	.	S	+	2	0	SORCS3	106996979	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	7.252000	0.78309	2.741000	0.93983	0.650000	0.86243	TCC	.	.		0.458	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978		A	107006989	C	A	107006989	3	1	367	1	0	0	0	0	1	0	0	0	14947	855	30	3	3091	3	SORCS3	10	107006989	Missense_Mutation	SNP	C	TCGA-ZP-A9D1-01A-11D-A382-10	31599357	107006989	28527758	73	51008										
FAM160B1	57700	hgsc.bcm.edu	37	chr10	116603573	116603573	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	gccagagcctgcggctgcaaAgtgccttacacagagcactt	11	13	0	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr10:116603573A>G	ENST00000369248.4	+	7	1225	c.890A>G	c.(889-891)aAg>aGg	p.K297R	FAM160B1_ENST00000369250.3_Missense_Mutation_p.K297R	NM_020940.3	NP_065991.3	Q5W0V3	F16B1_HUMAN	family with sequence similarity 160, member B1	297										NS(1)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|lung(13)	25						GCGGCTGCAAAGTGCCTTACA	0.473																																					p.K297R		Atlas-SNP	.											.	FAM160B1	107	.	0			c.A890G						.						99	82	87					10																	116603573		2203	4300	6503	SO:0001583	missense	57700	exon7			CTGCAAAGTGCCT	AB046820	CCDS31290.1, CCDS44480.1	10q26.11	2008-06-05	2008-06-05	2008-06-05	ENSG00000151553	ENSG00000151553			29320	protein-coding gene	gene with protein product			"KIAA1600"	KIAA1600		10997877	Standard	NM_020940		Approved	bA106M7.3	uc001lcb.3	Q5W0V3	OTTHUMG00000019092	ENST00000369248.4:c.890A>G	chr10.hg19:g.116603573A>G	ENSP00000358251:p.Lys297Arg	99.0	0.0		68.0	8.0	NM_020940	Q5H9P7|Q5W0V2|Q8IY76|Q9HCH2	Missense_Mutation	SNP	ENST00000369248.4	hg19	CCDS31290.1	.	.	.	.	.	.	.	.	.	.	A	18.45	3.625866	0.66901	.	.	ENSG00000151553	ENST00000369248;ENST00000369250	T;T	0.30981	1.51;1.51	5.39	3.07	0.35406	.	0.043310	0.85682	N	0.000000	T	0.30541	0.0768	L	0.50333	1.59	0.80722	D	1	P;P	0.49961	0.894;0.93	P;P	0.49301	0.606;0.53	T	0.09907	-1.0653	10	0.10111	T	0.7	-12.9582	9.3458	0.38107	0.855:0.0:0.145:0.0	.	297;297	Q5W0V3-2;Q5W0V3	.;F16B1_HUMAN	R	297	ENSP00000358251:K297R;ENSP00000358253:K297R	ENSP00000358251:K297R	K	+	2	0	FAM160B1	116593563	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	2.199000	0.42715	0.371000	0.24564	0.533000	0.62120	AAG	.	.		0.473	FAM160B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050499.1	XM_049351		G	116603573	A	G	116603573	3	3	367	1	0	0	0	0	1	0	0	0	5475	72	3	2	916	2	FAM160B1	10	116603573	Missense_Mutation	SNP	A	TCGA-ZP-A9D1-01A-11D-A382-10	9596584	116603573	18931174	74	51009										
KNDC1	85442	hgsc.bcm.edu	37	chr10	135009312	135009312	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	cccggagcggccgtccgcggCtgaggccatcaaggtaacca	14	15	1	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr10:135009312C>A	ENST00000304613.3	+	10	1742	c.1721C>A	c.(1720-1722)gCt>gAt	p.A574D	KNDC1_ENST00000368572.2_Missense_Mutation_p.A574D|KNDC1_ENST00000368571.2_Missense_Mutation_p.A509D			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	574	KIND 2. {ECO:0000255|PROSITE- ProRule:PRU00709}.				cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		CCGTCCGCGGCTGAGGCCATC	0.692																																					p.A574D		Atlas-SNP	.											.	KNDC1	155	.	0			c.C1721A						.						16	16	16					10																	135009312		2177	4275	6452	SO:0001583	missense	85442	exon10			CCGCGGCTGAGGC	AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"RasGEF domain family, member 2"	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.1721C>A	chr10.hg19:g.135009312C>A	ENSP00000304437:p.Ala574Asp	98.0	0.0		106.0	20.0	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	hg19	CCDS7674.1	.	.	.	.	.	.	.	.	.	.	C	15.33	2.802372	0.50315	.	.	ENSG00000171798	ENST00000304613;ENST00000368572;ENST00000368571	T;T;T	0.33216	1.42;1.42;1.42	4.84	4.84	0.62591	KIND (2);	0.393157	0.22150	N	0.063936	T	0.50154	0.1599	L	0.59436	1.845	0.51767	D	0.999938	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.989	T	0.32241	-0.9914	10	0.22109	T	0.4	-18.7477	15.8121	0.78573	0.0:1.0:0.0:0.0	.	509;574	Q76NI1-2;Q76NI1	.;VKIND_HUMAN	D	574;574;509	ENSP00000304437:A574D;ENSP00000357561:A574D;ENSP00000357560:A509D	ENSP00000304437:A574D	A	+	2	0	KNDC1	134859302	0.065000	0.20965	0.151000	0.22473	0.026000	0.11368	0.949000	0.29109	2.433000	0.82419	0.306000	0.20318	GCT	.	.		0.692	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643		A	135009312	C	A	135009312	3	1	367	1	0	0	0	0	1	0	0	0	8435	797	28	3	1759	3	KNDC1	10	135009312	Missense_Mutation	SNP	C	TCGA-ZP-A9D1-01A-11D-A382-10	18405739	135009312	525435	75	51010										
CDHR5	53841	hgsc.bcm.edu	37	chr11	621353	621353	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	tgacctgctcacccgcaccaGcagccagaaggtcatgttcg	10	15	2	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr11:621353G>A	ENST00000358353.3	-	7	932	c.610C>T	c.(610-612)Ctg>Ttg	p.L204L	CDHR5_ENST00000397542.2_Silent_p.L204L|CDHR5_ENST00000529337.1_5'Flank|CDHR5_ENST00000349570.7_Silent_p.L204L			Q9HBB8	CDHR5_HUMAN	cadherin-related family member 5	204	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043, ECO:0000305}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	23						ACCCGCACCAGCAGCCAGAAG	0.662																																					p.L204L		Atlas-SNP	.											.	CDHR5	77	.	0			c.C610T						.						39	43	42					11																	621353		2203	4300	6503	SO:0001819	synonymous_variant	53841	exon6			GCACCAGCAGCCA	AF258675	CCDS7707.1, CCDS7708.1	11p15.5	2011-07-01	2010-01-25	2010-01-25	ENSG00000099834	ENSG00000099834		"Cadherins / Cadherin-related"	7521	protein-coding gene	gene with protein product		606839	"mucin and cadherin-like", "mucin-like protocadherin"	MUCDHL, MUPCDH		11031102, 10801787	Standard	NM_021924		Approved	FLJ20219, MU-PCDH	uc001lqj.3	Q9HBB8	OTTHUMG00000132018	ENST00000358353.3:c.610C>T	chr11.hg19:g.621353G>A		70.0	0.0		77.0	20.0	NM_031264	C9J7X1|Q9H746|Q9HAU3|Q9HBB5|Q9HBB6|Q9HBB7|Q9NX86|Q9NXI9	Silent	SNP	ENST00000358353.3	hg19	CCDS7707.1																																																																																			.	.		0.662	CDHR5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255023.2	NM_021924		A	621353	G	A	621353	2	1	367	1	0	0	0	0	0	0	0	1	3124	962	34	3		3	CDHR5	11	621353	Silent	SNP	G	TCGA-ZP-A9D1-01A-11D-A382-10		621353	134385163	76	51011										
PRDM11	56981	hgsc.bcm.edu	37	chr11	45246411	45246411	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	gcaggtaagttggtttggatGagattattgtcggagggcag	17	3	0	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr11:45246411G>A	ENST00000530656.1	+	7	1488	c.1488G>A	c.(1486-1488)atG>atA	p.M496I	CTD-2560E9.3_ENST00000527450.1_RNA|PRDM11_ENST00000263765.4_Missense_Mutation_p.M496I|PRDM11_ENST00000528980.1_Intron|PRDM11_ENST00000424263.2_Missense_Mutation_p.M462I			Q9NQV5	PRD11_HUMAN	PR domain containing 11	496							methyltransferase activity (GO:0008168)			endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	26						TGGTTTGGATGAGATTATTGT	0.547																																					p.M462I	NSCLC(118;1511 1736 6472 36603 43224)	Atlas-SNP	.											.	PRDM11	53	.	0			c.G1386A						.						55	58	57					11																	45246411		2203	4299	6502	SO:0001583	missense	56981	exon7			TTGGATGAGATTA	AF275818	CCDS58130.1, CCDS73277.1	11p11	2008-07-21			ENSG00000019485	ENSG00000019485			13996	protein-coding gene	gene with protein product	"PR-domain containing protein 11"						Standard	NM_001256695		Approved	PFM8	uc031qab.1	Q9NQV5	OTTHUMG00000166478	ENST00000530656.1:c.1488G>A	chr11.hg19:g.45246411G>A	ENSP00000435976:p.Met496Ile	37.0	0.0		30.0	11.0	NM_001256696	Q8N9F1	Missense_Mutation	SNP	ENST00000530656.1	hg19		.	.	.	.	.	.	.	.	.	.	G	2.177	-0.388591	0.04932	.	.	ENSG00000019485	ENST00000263765;ENST00000530656;ENST00000424263	T;T;T	0.20332	2.08;2.08;2.08	5.45	3.58	0.41010	.	0.547731	0.17171	N	0.184296	T	0.10723	0.0262	N	0.14661	0.345	0.09310	N	0.999997	B	0.02656	0.0	B	0.04013	0.001	T	0.16041	-1.0416	10	0.72032	D	0.01	-14.0673	3.2445	0.06792	0.2802:0.0:0.5313:0.1885	.	496	Q9NQV5	PRD11_HUMAN	I	496;496;462	ENSP00000263765:M496I;ENSP00000435976:M496I;ENSP00000394314:M462I	ENSP00000263765:M496I	M	+	3	0	PRDM11	45202987	0.998000	0.40836	0.830000	0.32933	0.085000	0.17905	1.510000	0.35790	1.300000	0.44818	-0.140000	0.14226	ATG	.	.		0.547	PRDM11-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000389928.1	NM_020229		A	45246411	G	A	45246411	3	1	367	1	0	0	0	0	1	0	0	0	12464	1290	45	3	1514	3	PRDM11	11	45246411	Missense_Mutation	SNP	G	TCGA-ZP-A9D1-01A-11D-A382-10	44625058	45246411	89760105	77	51012										
PTPRJ	5795	hgsc.bcm.edu	37	chr11	48142579	48142579	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	cagtcctgtgtttgacattaAagctgtttccatcagtccaa	7	10	1	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr11:48142579A>G	ENST00000418331.2	+	4	729	c.377A>G	c.(376-378)aAa>aGa	p.K126R	PTPRJ_ENST00000440289.2_Missense_Mutation_p.K126R|PTPRJ_ENST00000526550.1_3'UTR	NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	126	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				contact inhibition (GO:0060242)|heart development (GO:0007507)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of vascular permeability (GO:0043116)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of cell adhesion (GO:0045785)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion (GO:0030155)|vasculogenesis (GO:0001570)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|mitogen-activated protein kinase binding (GO:0051019)|phosphatase activity (GO:0016791)|platelet-derived growth factor receptor binding (GO:0005161)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|endometrium(7)|kidney(7)|large_intestine(5)|lung(15)|ovary(1)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						TTTGACATTAAAGCTGTTTCC	0.338																																					p.K126R		Atlas-SNP	.											.	PTPRJ	225	.	0			c.A377G						.						66	60	62					11																	48142579		2201	4298	6499	SO:0001583	missense	5795	exon4			ACATTAAAGCTGT	U10886	CCDS7945.1, CCDS44596.1	11p11.2	2013-02-11			ENSG00000149177	ENSG00000149177		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9673	protein-coding gene	gene with protein product		600925				7937872, 7994032	Standard	NM_001098503		Approved	DEP1, HPTPeta, CD148	uc001ngp.4	Q12913	OTTHUMG00000166573	ENST00000418331.2:c.377A>G	chr11.hg19:g.48142579A>G	ENSP00000400010:p.Lys126Arg	209.0	0.0		173.0	71.0	NM_001098503	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Missense_Mutation	SNP	ENST00000418331.2	hg19	CCDS7945.1	.	.	.	.	.	.	.	.	.	.	A	12.57	1.977500	0.34848	.	.	ENSG00000149177	ENST00000278456;ENST00000418331;ENST00000440289;ENST00000534219	T;T;T	0.57436	0.4;0.4;0.4	5.41	5.41	0.78517	Fibronectin, type III (4);Immunoglobulin-like fold (1);	.	.	.	.	T	0.42359	0.1199	L	0.28115	0.83	0.22737	N	0.998798	P;P	0.36086	0.503;0.536	B;B	0.37144	0.242;0.145	T	0.39165	-0.9627	9	0.51188	T	0.08	.	11.8428	0.52364	1.0:0.0:0.0:0.0	.	126;126	Q12913;Q6P4H4	PTPRJ_HUMAN;.	R	126;126;126;47	ENSP00000400010:K126R;ENSP00000409733:K126R;ENSP00000432686:K47R	ENSP00000278456:K126R	K	+	2	0	PTPRJ	48099155	0.654000	0.27367	0.068000	0.19968	0.034000	0.12701	2.142000	0.42177	2.064000	0.61679	0.482000	0.46254	AAA	.	.		0.338	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1			G	48142579	A	G	48142579	3	3	367	1	0	0	0	0	1	0	0	0	12819	14	1	2	391	2	PTPRJ	11	48142579	Missense_Mutation	SNP	A	TCGA-ZP-A9D1-01A-11D-A382-10	2896168	48142579	86863937	78	51013										
PRPF19	27339	hgsc.bcm.edu	37	chr11	60670109	60670109	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ggcacaatgaggccagcctgTggtttcagggtagccagagc	15	10	1	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr11:60670109T>C	ENST00000227524.4	-	5	613	c.408A>G	c.(406-408)ccA>ccG	p.P136P		NM_014502.4	NP_055317.1			pre-mRNA processing factor 19											haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|urinary_tract(1)	22						GGCCAGCCTGTGGTTTCAGGG	0.552																																					p.P136P		Atlas-SNP	.											.	PRPF19	62	.	0			c.A408G						.						81	78	79					11																	60670109		2203	4299	6502	SO:0001819	synonymous_variant	27339	exon5			AGCCTGTGGTTTC	BC018698	CCDS7995.1	11q12.2	2014-05-20	2013-06-10	2005-04-01	ENSG00000110107	ENSG00000110107		"WD repeat domain containing", "U-box domain containing"	17896	protein-coding gene	gene with protein product	"nuclear matrix protein NMP200 related to splicing factor PRP19", "psoralen 4"	608330	"PRP19/PSO4 homolog (S. cerevisiae)", "PRP19/PSO4 pre-mRNA processing factor 19 homolog (S. cerevisiae)"	PRP19		12960389	Standard	NM_014502		Approved	UBOX4, NMP200, PSO4, hPSO4	uc001nqf.3	Q9UMS4	OTTHUMG00000167798	ENST00000227524.4:c.408A>G	chr11.hg19:g.60670109T>C		161.0	0.0		162.0	23.0	NM_014502		Silent	SNP	ENST00000227524.4	hg19	CCDS7995.1																																																																																			.	.		0.552	PRPF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396334.1	NM_014502		C	60670109	T	C	60670109	2	2	367	1	0	0	0	0	0	0	0	1	12576	1683	59	2		2	PRPF19	11	60670109	Silent	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	12527530	60670109	74336407	79	51014										
CDC42BPG	55561	hgsc.bcm.edu	37	chr11	64600763	64600763	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	cgaggtgcagcggagacactTggtcggggatgggaagctcc	18	9	0	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr11:64600763T>C	ENST00000342711.5	-	24	2670	c.2671A>G	c.(2671-2673)Aag>Gag	p.K891E	CDC42BPG_ENST00000491280.1_5'Flank	NM_017525.2	NP_059995.2			CDC42 binding protein kinase gamma (DMPK-like)											central_nervous_system(1)|lung(3)	4						CGGAGACACTTGGTCGGGGAT	0.697																																					p.K891E		Atlas-SNP	.											.	CDC42BPG	101	.	0			c.A2671G						.						17	17	17					11																	64600763		2004	3915	5919	SO:0001583	missense	55561	exon24			GACACTTGGTCGG	AY648038	CCDS31601.1	11q13	2013-01-10			ENSG00000171219	ENSG00000171219		"Pleckstrin homology (PH) domain containing"	29829	protein-coding gene	gene with protein product		613991				9341881, 15194684	Standard	NM_017525		Approved	HSMDPKIN, MRCKgamma, DMPK2, kappa-200	uc001obs.4	Q6DT37	OTTHUMG00000045365	ENST00000342711.5:c.2671A>G	chr11.hg19:g.64600763T>C	ENSP00000345133:p.Lys891Glu	110.0	0.0		91.0	30.0	NM_017525		Missense_Mutation	SNP	ENST00000342711.5	hg19	CCDS31601.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.186733	0.78789	.	.	ENSG00000171219	ENST00000342711	D	0.93307	-3.2	5.3	4.13	0.48395	Protein kinase C-like, phorbol ester/diacylglycerol binding (4);	0.147172	0.31821	N	0.007020	D	0.93759	0.8005	M	0.75447	2.3	0.34223	D	0.675595	D	0.53619	0.961	P	0.49752	0.621	D	0.95542	0.8613	10	0.87932	D	0	.	10.7102	0.45980	0.0:0.0:0.1603:0.8397	.	891	Q6DT37	MRCKG_HUMAN	E	891	ENSP00000345133:K891E	ENSP00000345133:K891E	K	-	1	0	CDC42BPG	64357339	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	0.922000	0.28734	0.919000	0.36945	0.454000	0.30748	AAG	.	.		0.697	CDC42BPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105352.4	XM_290516		C	64600763	T	C	64600763	3	2	367	1	0	0	0	0	1	0	0	0	3076	1821	63	2	2040	2	CDC42BPG	11	64600763	Missense_Mutation	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	3930654	64600763	70405753	80	51015										
ARHGEF17	9828	hgsc.bcm.edu	37	chr11	73068372	73068372	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	aagacgcagacatcatcaaaGgtgggtttgatgctaggggt	14	6	2	3			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr11:73068372G>C	ENST00000263674.3	+	9	4437	c.4087G>C	c.(4087-4089)Ggg>Cgg	p.G1363R	AP002761.1_ENST00000582555.1_RNA	NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	1363					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(2)	32						CATCATCAAAGGTGGGTTTGA	0.577																																					p.G1363R		Atlas-SNP	.											.	ARHGEF17	117	.	0			c.G4087C						.						41	43	43					11																	73068372		2200	4293	6493	SO:0001630	splice_region_variant	9828	exon9			ATCAAAGGTGGGT	AF378754	CCDS8221.1	11q13.3	2011-11-16			ENSG00000110237	ENSG00000110237		"Rho guanine nucleotide exchange factors"	21726	protein-coding gene	gene with protein product	"Rho-specific guanine-nucleotide exchange factor 164 kDa", "tumor endothelial marker 4"					11559528, 12071859	Standard	NM_014786		Approved	TEM4, KIAA0337, p164-RhoGEF	uc001otu.3	Q96PE2	OTTHUMG00000167971	ENST00000263674.3:c.4087+1G>C	chr11.hg19:g.73068372G>C		97.0	0.0		77.0	10.0	NM_014786	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Missense_Mutation	SNP	ENST00000263674.3	hg19	CCDS8221.1	.	.	.	.	.	.	.	.	.	.	G	18.27	3.587309	0.66105	.	.	ENSG00000110237	ENST00000263674	T	0.31247	1.5	5.44	5.44	0.79542	.	0.053182	0.85682	D	0.000000	T	0.50854	0.1640	L	0.50333	1.59	0.80722	D	1	D	0.76494	0.999	D	0.68765	0.96	T	0.48958	-0.8988	10	0.62326	D	0.03	-26.664	18.2609	0.90035	0.0:0.0:1.0:0.0	.	1363	Q96PE2	ARHGH_HUMAN	R	1363	ENSP00000263674:G1363R	ENSP00000263674:G1363R	G	+	1	0	ARHGEF17	72746020	1.000000	0.71417	1.000000	0.80357	0.595000	0.36748	7.077000	0.76814	2.559000	0.86315	0.591000	0.81541	GGG	.	.		0.577	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786	Missense_Mutation	C	73068372	G	C	73068372	5	2	367	1	0	0	0	0	0	0	1	0	900	1014	35	4	4121	4	ARHGEF17	11	73068372	Splice_Site	SNP	G	TCGA-ZP-A9D1-01A-11D-A382-10	8467609	73068372	61938144	81	51016										
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	103060402	103060402	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	tatatgccattttttttagtTacccagaaagagagcagtta	7	6	0	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr11:103060402T>C	ENST00000375735.2	+	45	7438	c.7294T>C	c.(7294-7296)Tac>Cac	p.Y2432H	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Splice_Site_p.Y2432H	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	2432	AAA 3. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		TTTTTTTAGTTACCCAGAAAG	0.313																																					p.Y2432H		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.T7294C						.						62	61	61					11																	103060402		1804	4067	5871	SO:0001630	splice_region_variant	79659	exon45			TTTAGTTACCCAG	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.7293-1T>C	chr11.hg19:g.103060402T>C		71.0	0.0		83.0	8.0	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	hg19	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	T	17.40	3.379663	0.61845	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.36878	1.23;1.23	5.46	4.33	0.51752	.	.	.	.	.	T	0.61148	0.2324	M	0.86268	2.805	0.49483	D	0.999799	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.987	T	0.63189	-0.6693	9	0.41790	T	0.15	.	11.657	0.51324	0.0:0.07:0.0:0.93	.	2432;2432	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	H	2432	ENSP00000364887:Y2432H;ENSP00000381167:Y2432H	ENSP00000364887:Y2432H	Y	+	1	0	DYNC2H1	102565612	1.000000	0.71417	1.000000	0.80357	0.695000	0.40330	4.666000	0.61554	1.009000	0.39289	-0.274000	0.10170	TAC	.	.		0.313	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	Missense_Mutation	C	103060402	T	C	103060402	5	2	367	1	0	0	0	0	0	0	1	0	4848	1768	61	2	7472	2	DYNC2H1	11	103060402	Splice_Site	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	29992030	103060402	31946114	82	51017										
MLL	4297	hgsc.bcm.edu	37	chr11	118376851	118376851	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	gtttccacaactggggacatCacagaccccctctactgctg	8	15	2	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr11:118376851C>T	ENST00000389506.5	+	27	10235	c.10235C>T	c.(10234-10236)tCa>tTa	p.S3412L	KMT2A_ENST00000534358.1_Missense_Mutation_p.S3415L|KMT2A_ENST00000354520.4_Missense_Mutation_p.S3374L			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	3412					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										CTGGGGACATCACAGACCCCC	0.532																																					p.S3415L		Atlas-SNP	.											.	MLL	548	.	0			c.C10244T						.						92	94	93					11																	118376851		2200	4295	6495	SO:0001583	missense	4297	exon27			GGACATCACAGAC	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.10235C>T	chr11.hg19:g.118376851C>T	ENSP00000374157:p.Ser3412Leu	104.0	0.0		87.0	19.0	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Missense_Mutation	SNP	ENST00000389506.5	hg19	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	C	14.09	2.433053	0.43224	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313	D;D;D	0.84660	-1.87;-1.88;-1.83	5.87	4.96	0.65561	.	0.152354	0.47093	N	0.000250	T	0.81370	0.4808	L	0.46157	1.445	0.54753	D	0.999987	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.76737	-0.2849	10	0.42905	T	0.14	.	15.0128	0.71562	0.0:0.9319:0.0:0.0681	.	3415;3412	E9PQG7;Q03164	.;MLL1_HUMAN	L	3415;3412;3374;2322	ENSP00000436786:S3415L;ENSP00000374157:S3412L;ENSP00000346516:S3374L	ENSP00000346516:S3374L	S	+	2	0	MLL	117882061	0.998000	0.40836	0.495000	0.27527	0.997000	0.91878	4.640000	0.61368	1.493000	0.48517	0.591000	0.81541	TCA	.	.		0.532	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		T	118376851	C	T	118376851	3	4	367	1	0	0	0	0	1	0	0	0	9629	838	29	3	10341	3	MLL	11	118376851	Missense_Mutation	SNP	C	TCGA-ZP-A9D1-01A-11D-A382-10	15316449	118376851	16629665	83	51018										
DDX6	1656	hgsc.bcm.edu	37	chr11	118650350	118650350	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ggttaacatacctgaataggAgatggcttttcccagcccat	9	10	0	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr11:118650350A>T	ENST00000526070.2	-	4	720	c.360T>A	c.(358-360)tcT>tcA	p.S120S	DDX6_ENST00000534980.1_Silent_p.S120S|DDX6_ENST00000264018.4_Silent_p.S120S	NM_001257191.1	NP_001244120.1	P26196	DDX6_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 6	120					cytoplasmic mRNA processing body assembly (GO:0033962)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|RISC complex (GO:0016442)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(1)|ovary(1)|prostate(1)	13	all_hematologic(175;0.0839)	Renal(330;0.0183)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)|Hepatocellular(160;0.0893)|Breast(348;0.0979)|all_hematologic(192;0.103)		OV - Ovarian serous cystadenocarcinoma(223;3.39e-06)|BRCA - Breast invasive adenocarcinoma(274;3.4e-05)|Colorectal(284;0.0377)		CCTGAATAGGAGATGGCTTTT	0.373			T	IGH@	B-NHL																																p.S120S		Atlas-SNP	.		Dom	yes		11	11q23.3	1656	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6		L	.	DDX6	64	.	0			c.T360A						.						79	71	73					11																	118650350		1842	4091	5933	SO:0001819	synonymous_variant	1656	exon4			AATAGGAGATGGC	D17532	CCDS44751.1	11q23.3	2012-02-23	2012-02-23		ENSG00000110367	ENSG00000110367		"DEAD-boxes"	2747	protein-coding gene	gene with protein product		600326	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 6 (RNA helicase, 54kD)", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 6"	HLR2		1579499, 11839790	Standard	NM_004397		Approved	RCK	uc001pub.2	P26196	OTTHUMG00000166411	ENST00000526070.2:c.360T>A	chr11.hg19:g.118650350A>T		295.0	0.0		272.0	49.0	NM_004397	Q5D048	Silent	SNP	ENST00000526070.2	hg19	CCDS44751.1																																																																																			.	.		0.373	DDX6-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000389647.2	NM_004397		T	118650350	A	T	118650350	2	4	367	1	0	0	0	0	0	0	0	1	4379	291	11	4		4	DDX6	11	118650350	Silent	SNP	A	TCGA-ZP-A9D1-01A-11D-A382-10	273499	118650350	16356166	84	51019										
BICD1	636	hgsc.bcm.edu	37	chr12	32491901	32491901	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	gcaaggaaaaaaggttaaccGtggctccaccaggtaaacat	10	9	0	0	rs141754177	byFrequency	TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr12:32491901G>T	ENST00000281474.5	+	8	2855	c.2752G>T	c.(2752-2754)Gtg>Ttg	p.V918L	BICD1_ENST00000548411.1_Intron	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	918					anatomical structure morphogenesis (GO:0009653)|intracellular mRNA localization (GO:0008298)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900737)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein localization to organelle (GO:0033365)|regulation of proteinase activated receptor activity (GO:1900276)|RNA processing (GO:0006396)|stress granule assembly (GO:0034063)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|host cell viral assembly compartment (GO:0072517)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	cytoskeletal adaptor activity (GO:0008093)|dynactin binding (GO:0034452)|dynein binding (GO:0045502)|proteinase activated receptor binding (GO:0031871)|Rab GTPase binding (GO:0017137)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			AAGGTTAACCGTGGCTCCACC	0.507																																					p.V918L		Atlas-SNP	.											.	BICD1	89	.	0			c.G2752T						.						51	52	52					12																	32491901		2203	4300	6503	SO:0001583	missense	636	exon8			TTAACCGTGGCTC	U90028	CCDS8726.1, CCDS44859.1	12p11.2-p11.1	2005-01-13	2001-11-28			ENSG00000151746			1049	protein-coding gene	gene with protein product		602204	"Bicaudal D (Drosophila) homolog 1"			9367685	Standard	NM_001714		Approved		uc001rku.3	Q96G01	OTTHUMG00000169307	ENST00000281474.5:c.2752G>T	chr12.hg19:g.32491901G>T	ENSP00000281474:p.Val918Leu	45.0	0.0		43.0	24.0	NM_001714	A8K2C3|F8W113|O43892|O43893	Missense_Mutation	SNP	ENST00000281474.5	hg19	CCDS8726.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.005308	0.74932	.	.	ENSG00000151746	ENST00000281474	T	0.50277	0.75	5.73	5.73	0.89815	.	0.000000	0.41500	D	0.000866	T	0.48642	0.1511	N	0.08118	0	0.80722	D	1	P	0.50066	0.931	P	0.60286	0.872	T	0.58702	-0.7590	10	0.87932	D	0	.	18.0686	0.89398	0.0:0.0:1.0:0.0	.	918	Q96G01	BICD1_HUMAN	L	918	ENSP00000281474:V918L	ENSP00000281474:V918L	V	+	1	0	BICD1	32383168	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.808000	0.69165	2.720000	0.93068	0.591000	0.81541	GTG	.	G|1.000;A|0.000		0.507	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403380.1	NM_001714		T	32491901	G	T	32491901	3	4	367	1	0	0	0	0	1	0	0	0	1428	1145	40	1	2782	1	BICD1	12	32491901	Missense_Mutation	SNP	G	TCGA-ZP-A9D1-01A-11D-A382-10		32491901	101359994	85	51020										
MLL2	8085	hgsc.bcm.edu	37	chr12	49433342	49433342	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ctgcagctgtttccttctccTgccgcagggtgttgcgctgg	13	13	1	0			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr12:49433342T>A	ENST00000301067.7	-	32	8104	c.8105A>T	c.(8104-8106)cAg>cTg	p.Q2702L	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	2702					chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										TTCCTTCTCCTGCCGCAGGGT	0.597																																					p.Q2702L		Atlas-SNP	.											.	MLL2	1173	.	0			c.A8105T						.						15	17	16					12																	49433342		2009	4184	6193	SO:0001583	missense	8085	exon32			TTCTCCTGCCGCA	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.8105A>T	chr12.hg19:g.49433342T>A	ENSP00000301067:p.Gln2702Leu	43.0	0.0		21.0	9.0	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	hg19	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	T	16.44	3.124905	0.56613	.	.	ENSG00000167548	ENST00000301067	D	0.94576	-3.46	5.53	5.53	0.82687	.	0.000000	0.36409	N	0.002604	D	0.95427	0.8515	L	0.38175	1.15	0.52099	D	0.999943	D	0.76494	0.999	D	0.78314	0.991	D	0.96070	0.9045	10	0.87932	D	0	.	14.9582	0.71135	0.0:0.0:0.0:1.0	.	2702	O14686	MLL2_HUMAN	L	2702	ENSP00000301067:Q2702L	ENSP00000301067:Q2702L	Q	-	2	0	MLL2	47719609	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.125000	0.77193	2.236000	0.73375	0.496000	0.49642	CAG	.	.		0.597	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			A	49433342	T	A	49433342	3	1	367	1	0	0	0	0	1	0	0	0	9630	1580	55	4	8600	4	MLL2	12	49433342	Missense_Mutation	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	16941441	49433342	84418553	86	51021										
CEP290	80184	hgsc.bcm.edu	37	chr12	88534999	88534999	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	gcaccttggataaggaaatcAataaattatctgccagttct	7	8	3	0			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr12:88534999A>T	ENST00000552810.1	-	2	429	c.86T>A	c.(85-87)tTg>tAg	p.L29*	CEP290_ENST00000309041.7_Nonsense_Mutation_p.L29*|TMTC3_ENST00000266712.6_5'Flank	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	29					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						TAAGGAAATCAATAAATTATC	0.294																																					p.L29X		Atlas-SNP	.											.	CEP290	195	.	0			c.T86A						.						96	84	87					12																	88534999		1812	4065	5877	SO:0001587	stop_gained	80184	exon2			GAAATCAATAAAT	AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"Joubert syndrome 5", "nephrocystin-6", "cancer/testis antigen 87", "POC3 centriolar protein homolog (Chlamydomonas)", "Meckel syndrome, type 4"	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.86T>A	chr12.hg19:g.88534999A>T	ENSP00000448012:p.Leu29*	346.0	0.0		326.0	70.0	NM_025114	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Nonsense_Mutation	SNP	ENST00000552810.1	hg19	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	A	37	5.993412	0.97184	.	.	ENSG00000198707	ENST00000552810;ENST00000309041;ENST00000536998;ENST00000550962	.	.	.	6.07	6.07	0.98685	.	0.250591	0.32952	N	0.005455	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.6817	0.51461	0.8679:0.0:0.0:0.1321	.	.	.	.	X	29	.	ENSP00000308021:L29X	L	-	2	0	CEP290	87059130	0.996000	0.38824	1.000000	0.80357	0.995000	0.86356	4.041000	0.57339	2.330000	0.79161	0.477000	0.44152	TTG	.	.		0.294	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		T	88534999	A	T	88534999	4	4	367	1	0	0	0	0	0	1	0	0	3255	131	5	4	7565	4	CEP290	12	88534999	Nonsense_Mutation	SNP	A	TCGA-ZP-A9D1-01A-11D-A382-10	39101657	88534999	45316896	87	51022										
ASCL4	121549	hgsc.bcm.edu	37	chr12	108168997	108168997	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	gtgtgctttccggcaaatgaTggagacgcgtaaaccggcgg	15	9	0	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr12:108168997T>C	ENST00000342331.4	+	1	836	c.5T>C	c.(4-6)aTg>aCg	p.M2T		NM_203436.2	NP_982260.2	Q6XD76	ASCL4_HUMAN	achaete-scute family bHLH transcription factor 4	1					regulation of transcription from RNA polymerase II promoter (GO:0006357)|skin development (GO:0043588)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(1)|large_intestine(3)|lung(6)|upper_aerodigestive_tract(1)	13						CGGCAAATGATGGAGACGCGT	0.592																																					p.M2T	GBM(170;776 3695 11650)	Atlas-SNP	.											.	ASCL4	28	.	0			c.T5C						.						74	82	79					12																	108168997		2203	4300	6503	SO:0001583	missense	121549	exon1			AAATGATGGAGAC	AY238895	CCDS31894.2	12q24.11	2013-10-17	2013-10-17		ENSG00000187855	ENSG00000187855		"Basic helix-loop-helix proteins"	24311	protein-coding gene	gene with protein product		609155	"achaete-scute complex-like 4 (Drosophila)", "achaete-scute complex homolog 4 (Drosophila)"				Standard	NM_203436		Approved	HASH4, bHLHa44	uc001tmr.3	Q6XD76	OTTHUMG00000156964	ENST00000342331.4:c.5T>C	chr12.hg19:g.108168997T>C	ENSP00000345420:p.Met2Thr	169.0	0.0		150.0	64.0	NM_203436	Q7RTS2	Missense_Mutation	SNP	ENST00000342331.4	hg19	CCDS31894.2	.	.	.	.	.	.	.	.	.	.	T	13.88	2.369072	0.42003	.	.	ENSG00000187855	ENST00000342331	D	0.96856	-4.15	4.74	4.74	0.60224	.	0.091646	0.48286	D	0.000197	D	0.96479	0.8851	.	.	.	0.31333	N	0.684587	D	0.58620	0.983	P	0.53401	0.725	D	0.96125	0.9088	9	0.72032	D	0.01	-11.7909	12.7764	0.57451	0.0:0.0:0.0:1.0	.	1	Q6XD76	ASCL4_HUMAN	T	2	ENSP00000345420:M2T	ENSP00000345420:M2T	M	+	2	0	ASCL4	106693127	1.000000	0.71417	0.996000	0.52242	0.053000	0.15095	4.085000	0.57657	1.906000	0.55180	0.397000	0.26171	ATG	.	.		0.592	ASCL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346845.1	NM_203436		C	108168997	T	C	108168997	3	2	367	1	0	0	0	0	1	0	0	0	1036	1464	51	2	7	2	ASCL4	12	108168997	Missense_Mutation	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	19633998	108168997	25682898	88	51023										
NCOR2	9612	hgsc.bcm.edu	37	chr12	124821697	124821697	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	caggtgggaatgtggcagccGggcgaacgggtgaggaggtg	22	6	0	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr12:124821697G>A	ENST00000405201.1	-	38	5717	c.5717C>T	c.(5716-5718)cCg>cTg	p.P1906L	NCOR2_ENST00000356219.3_Missense_Mutation_p.P1913L|NCOR2_ENST00000404121.2_Missense_Mutation_p.P1467L|NCOR2_ENST00000397355.1_Missense_Mutation_p.P1897L|NCOR2_ENST00000404621.1_Missense_Mutation_p.P1896L|NCOR2_ENST00000429285.2_Missense_Mutation_p.P1896L			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1917					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		TGTGGCAGCCGGGCGAACGGG	0.672																																					p.P1906L		Atlas-SNP	.											.	NCOR2	475	.	0			c.C5717T						.						11	16	15					12																	124821697		1948	3998	5946	SO:0001583	missense	9612	exon40			GCAGCCGGGCGAA	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"nuclear receptor co-repressor 2"			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.5717C>T	chr12.hg19:g.124821697G>A	ENSP00000384018:p.Pro1906Leu	158.0	0.0		112.0	45.0	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	hg19	CCDS41858.2	.	.	.	.	.	.	.	.	.	.	g	11.13	1.548590	0.27652	.	.	ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000429285	T;T;T;T;T;T	0.16457	2.34;2.6;2.34;2.6;2.34;2.6	4.36	3.46	0.39613	.	0.534882	0.16106	U	0.229337	T	0.10380	0.0254	N	0.14661	0.345	0.46044	D	0.99883	B;B;B	0.27068	0.167;0.064;0.038	B;B;B	0.17098	0.011;0.017;0.008	T	0.12604	-1.0541	10	0.44086	T	0.13	-13.2026	11.9482	0.52940	0.0856:0.0:0.9144:0.0	.	1897;1906;1917	C9J239;C9JFD3;Q9Y618	.;.;NCOR2_HUMAN	L	1906;1896;1913;1897;1905;1467;1896	ENSP00000384018:P1906L;ENSP00000384202:P1896L;ENSP00000348551:P1913L;ENSP00000380513:P1897L;ENSP00000385618:P1467L;ENSP00000400281:P1896L	ENSP00000348551:P1913L	P	-	2	0	NCOR2	123387650	1.000000	0.71417	0.776000	0.31678	0.799000	0.45148	5.844000	0.69430	0.810000	0.34279	0.556000	0.70494	CCG	.	.		0.672	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312		A	124821697	G	A	124821697	3	1	367	1	0	0	0	0	1	0	0	0	10245	1116	39	1	1867	1	NCOR2	12	124821697	Missense_Mutation	SNP	G	TCGA-ZP-A9D1-01A-11D-A382-10	16652700	124821697	9030198	89	51024										
ATP8A2	51761	hgsc.bcm.edu	37	chr13	26152991	26152991	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	agactttcaaaagactcaaaAtatatggaggaaacattatg	7	5	2	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr13:26152991A>T	ENST00000381655.2	+	21	1963	c.1821A>T	c.(1819-1821)aaA>aaT	p.K607N	ATP8A2_ENST00000255283.8_Missense_Mutation_p.K567N|ATP8A2_ENST00000491840.1_3'UTR	NM_016529.4	NP_057613.4	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8A, member 2	567					aging (GO:0007568)|axonogenesis (GO:0007409)|detection of light stimulus involved in visual perception (GO:0050908)|eating behavior (GO:0042755)|inner ear morphogenesis (GO:0042472)|involuntary skeletal muscle contraction (GO:0003011)|negative regulation of cell proliferation (GO:0008285)|neurofilament cytoskeleton organization (GO:0060052)|neuromuscular process controlling posture (GO:0050884)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phospholipid translocation (GO:0061092)|response to auditory stimulus (GO:0010996)|retina layer formation (GO:0010842)|skin development (GO:0043588)	cell projection (GO:0042995)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(17)|lung(31)|ovary(4)|skin(3)|stomach(1)|urinary_tract(1)	72		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		AAGACTCAAAATATATGGAGG	0.388																																					p.K607N		Atlas-SNP	.											.	ATP8A2	181	.	0			c.A1821T						.						127	120	122					13																	26152991		1853	4099	5952	SO:0001583	missense	51761	exon21			CTCAAAATATATG	AL137256	CCDS41873.1	13q12	2010-04-20	2010-03-31		ENSG00000132932	ENSG00000132932	3.6.3.1	"ATPases / P-type"	13533	protein-coding gene	gene with protein product		605870	"ATPase, aminophospholipid transporter-like, Class I, type 8A, member 2", "ATPase, aminophospholipid transporter-like, class I, type 8A, member 2"			11015572, 19778899	Standard	NM_016529		Approved	ATPIB, ML-1	uc001uqk.3	Q9NTI2	OTTHUMG00000016611	ENST00000381655.2:c.1821A>T	chr13.hg19:g.26152991A>T	ENSP00000371070:p.Lys607Asn	67.0	0.0		66.0	28.0	NM_016529	Q9H527|Q9NPU6|Q9NTL2|Q9NYM3	Missense_Mutation	SNP	ENST00000381655.2	hg19	CCDS41873.1	.	.	.	.	.	.	.	.	.	.	A	13.54	2.266536	0.40095	.	.	ENSG00000132932	ENST00000381655;ENST00000255283;ENST00000544544	T;T	0.70399	-0.48;-0.48	5.61	-2.11	0.07187	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.159237	0.56097	D	0.000025	T	0.57373	0.2049	N	0.25789	0.76	0.44395	D	0.997304	B;B;B	0.29805	0.195;0.257;0.195	B;B;B	0.35770	0.21;0.189;0.21	T	0.51012	-0.8759	10	0.40728	T	0.16	.	14.3082	0.66397	0.204:0.0:0.796:0.0	.	567;387;567	B7Z880;F5GZN5;Q9NTI2	.;.;AT8A2_HUMAN	N	607;567;387	ENSP00000371070:K607N;ENSP00000255283:K567N	ENSP00000255283:K567N	K	+	3	2	ATP8A2	25050991	1.000000	0.71417	0.997000	0.53966	0.984000	0.73092	1.288000	0.33296	-0.156000	0.11079	-0.250000	0.11733	AAA	.	.		0.388	ATP8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044236.2	NM_016529		T	26152991	A	T	26152991	3	4	367	1	0	0	0	0	1	0	0	0	1193	98	4	4	1903	4	ATP8A2	13	26152991	Missense_Mutation	SNP	A	TCGA-ZP-A9D1-01A-11D-A382-10		26152991	89016887	90	51025										
FRY	10129	hgsc.bcm.edu	37	chr13	32776494	32776494	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ctttcctacatctttatagaTccttgaagcaaagctttttg	5	9	1	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr13:32776494T>C	ENST00000380250.3	+	31	4344	c.3848T>C	c.(3847-3849)aTc>aCc	p.I1283T		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	1283						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		TCTTTATAGATCCTTGAAGCA	0.383																																					p.I1283T		Atlas-SNP	.											.	FRY	312	.	0			c.T3848C						.						71	71	71					13																	32776494		1828	4077	5905	SO:0001630	splice_region_variant	10129	exon31			TATAGATCCTTGA	AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"chromosome 13 open reading frame 14"	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.3847-1T>C	chr13.hg19:g.32776494T>C		168.0	0.0		139.0	63.0	NM_023037	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	hg19	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.084492	0.76642	.	.	ENSG00000073910	ENST00000380250;ENST00000380257	T	0.63913	-0.07	5.24	5.24	0.73138	.	0.116735	0.64402	D	0.000020	T	0.57844	0.2081	L	0.45137	1.4	0.80722	D	1	B	0.33940	0.433	B	0.39339	0.297	T	0.54009	-0.8357	10	0.19590	T	0.45	.	15.141	0.72609	0.0:0.0:0.0:1.0	.	1283	Q5TBA9	FRY_HUMAN	T	1283;122	ENSP00000369600:I1283T	ENSP00000369600:I1283T	I	+	2	0	FRY	31674494	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	7.640000	0.83355	1.996000	0.58369	0.374000	0.22700	ATC	.	.		0.383	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037	Missense_Mutation	C	32776494	T	C	32776494	5	2	367	1	0	0	0	0	0	0	1	0	6071	1449	50	2	3970	2	FRY	13	32776494	Splice_Site	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	6623503	32776494	82393384	91	51026										
THSD1	55901	hgsc.bcm.edu	37	chr13	52971697	52971697	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ggccaggtcaatgggtcctgTggaggtaatgactgagtctc	15	8	2	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr13:52971697T>C	ENST00000258613.4	-	3	869	c.691A>G	c.(691-693)Aca>Gca	p.T231A	RNY4P24_ENST00000362735.1_RNA|THSD1_ENST00000544466.1_Intron|THSD1_ENST00000349258.4_Missense_Mutation_p.T231A	NM_018676.3	NP_061146.1	Q9NS62	THSD1_HUMAN	thrombospondin, type I, domain containing 1	231					hematopoietic progenitor cell differentiation (GO:0002244)	cell periphery (GO:0071944)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Breast(56;0.000207)|Lung NSC(96;0.00145)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.8e-08)		ATGGGTCCTGTGGAGGTAATG	0.557																																					p.T231A		Atlas-SNP	.											.	THSD1	89	.	0			c.A691G						.						65	59	61					13																	52971697		2203	4300	6503	SO:0001583	missense	55901	exon3			GTCCTGTGGAGGT	AK096289	CCDS9432.1, CCDS9433.1	13q14.13	2010-04-20	2004-03-11		ENSG00000136114	ENSG00000136114			17754	protein-coding gene	gene with protein product			"thrombospondin, type I, domain 1"				Standard	NM_018676		Approved	TMTSP	uc001vgo.3	Q9NS62	OTTHUMG00000016963	ENST00000258613.4:c.691A>G	chr13.hg19:g.52971697T>C	ENSP00000258613:p.Thr231Ala	133.0	0.0		155.0	51.0	NM_018676	A2A3J3|B2RCF5|Q6P3U1|Q6UXZ2	Missense_Mutation	SNP	ENST00000258613.4	hg19	CCDS9432.1	.	.	.	.	.	.	.	.	.	.	T	11.42	1.632592	0.29068	.	.	ENSG00000136114	ENST00000349258;ENST00000258613;ENST00000378095	T;T	0.17213	2.29;2.47	5.48	1.13	0.20643	.	0.626866	0.15887	N	0.239723	T	0.16514	0.0397	M	0.68317	2.08	0.09310	N	1	P;B	0.37663	0.604;0.021	B;B	0.38264	0.269;0.012	T	0.12091	-1.0561	10	0.40728	T	0.16	-1.8223	4.0599	0.09834	0.1457:0.2091:0.0:0.6452	.	231;231	Q9NS62-2;Q9NS62	.;THSD1_HUMAN	A	231	ENSP00000340650:T231A;ENSP00000258613:T231A	ENSP00000258613:T231A	T	-	1	0	THSD1	51869698	0.000000	0.05858	0.001000	0.08648	0.980000	0.70556	0.482000	0.22276	0.272000	0.22027	0.459000	0.35465	ACA	.	.		0.557	THSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045058.3			C	52971697	T	C	52971697	3	2	367	1	0	0	0	0	1	0	0	0	15892	1696	59	2	1879	2	THSD1	13	52971697	Missense_Mutation	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	20195203	52971697	62198181	92	51027										
SYNE2	23224	hgsc.bcm.edu	37	chr14	64494342	64494342	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	gcaggagaagaaagctcagtTaaagatttataagaaattcc	9	5	1	4			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr14:64494342T>C	ENST00000344113.4	+	43	6757	c.6545T>C	c.(6544-6546)tTa>tCa	p.L2182S	SYNE2_ENST00000358025.3_Missense_Mutation_p.L2182S|SYNE2_ENST00000554584.1_Missense_Mutation_p.L2182S|SYNE2_ENST00000357395.3_5'UTR	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	2182					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		AAAGCTCAGTTAAAGATTTAT	0.383																																					p.L2182S		Atlas-SNP	.											.	SYNE2	577	.	0			c.T6545C						.						98	95	96					14																	64494342		1817	4079	5896	SO:0001583	missense	23224	exon43			CTCAGTTAAAGAT	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.6545T>C	chr14.hg19:g.64494342T>C	ENSP00000341781:p.Leu2182Ser	309.0	0.0		262.0	53.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	hg19	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	T	15.09	2.730511	0.48939	.	.	ENSG00000054654	ENST00000358025;ENST00000344113;ENST00000554584;ENST00000261678	T;T;T	0.50001	0.76;0.76;0.76	5.48	5.48	0.80851	.	0.000000	0.40818	N	0.001010	T	0.57036	0.2026	L	0.29908	0.895	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77557	0.976;0.99	T	0.61402	-0.7070	10	0.87932	D	0	.	14.1357	0.65287	0.0:0.0:0.0:1.0	.	2182;2182	Q8WXH0;Q8WXH0-2	SYNE2_HUMAN;.	S	2182	ENSP00000350719:L2182S;ENSP00000341781:L2182S;ENSP00000452570:L2182S	ENSP00000261678:L2182S	L	+	2	0	SYNE2	63564095	1.000000	0.71417	0.998000	0.56505	0.968000	0.65278	4.896000	0.63222	2.081000	0.62600	0.482000	0.46254	TTA	.	.		0.383	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		C	64494342	T	C	64494342	3	2	367	1	0	0	0	0	1	0	0	0	15461	1764	61	2	6711	2	SYNE2	14	64494342	Missense_Mutation	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10		64494342	42855198	93	51028										
DYNC1H1	1778	hgsc.bcm.edu	37	chr14	102446137	102446137	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	cttcacttgcagcaaaatatTgaaattccggagatcagcct	7	10	2	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr14:102446137T>C	ENST00000360184.4	+	4	764	c.600T>C	c.(598-600)atT>atC	p.I200I		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	200	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						AGCAAAATATTGAAATTCCGG	0.403																																					p.I200I		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.T600C						.						124	131	129					14																	102446137		2203	4300	6503	SO:0001819	synonymous_variant	1778	exon4			AAATATTGAAATT	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"Cytoplasmic dyneins"	2961	protein-coding gene	gene with protein product		600112	"dynein, cytoplasmic, heavy polypeptide 1"	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.600T>C	chr14.hg19:g.102446137T>C		173.0	0.0		152.0	26.0	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Silent	SNP	ENST00000360184.4	hg19	CCDS9966.1																																																																																			.	.		0.403	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		C	102446137	T	C	102446137	2	2	367	1	0	0	0	0	0	0	0	1	4843	1800	63	2		2	DYNC1H1	14	102446137	Silent	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	37951795	102446137	4903403	94	51029										
UNC13C	440279	hgsc.bcm.edu	37	chr15	54305889	54305889	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	gaaacagaactttctgaactAcgagggcacgtcaatgctct	9	10	3	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr15:54305889A>G	ENST00000260323.11	+	1	789	c.789A>G	c.(787-789)ctA>ctG	p.L263L	UNC13C_ENST00000537900.1_Silent_p.L263L|UNC13C_ENST00000545554.1_Silent_p.L263L	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	263					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		TTTCTGAACTACGAGGGCACG	0.453																																					p.L263L		Atlas-SNP	.											.	UNC13C	674	.	0			c.A789G						.						87	85	86					15																	54305889		1972	4161	6133	SO:0001819	synonymous_variant	440279	exon1			TGAACTACGAGGG	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.789A>G	chr15.hg19:g.54305889A>G		86.0	0.0		55.0	20.0	NM_001080534	Q0P613|Q8ND48|Q96NP3	Silent	SNP	ENST00000260323.11	hg19	CCDS45264.1																																																																																			.	.		0.453	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		G	54305889	A	G	54305889	2	3	367	1	0	0	0	0	0	0	0	1	17001	378	14	2		2	UNC13C	15	54305889	Silent	SNP	A	TCGA-ZP-A9D1-01A-11D-A382-10		54305889	48225503	95	51030										
MRPL46	26589	hgsc.bcm.edu	37	chr15	89003046	89003046	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	cctgggggaacttgaatgtgTagtgcccacagggtgcattt	14	8	0	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr15:89003046T>C	ENST00000312475.4	-	4	679	c.638A>G	c.(637-639)tAc>tGc	p.Y213C	MRPL46_ENST00000559538.1_5'UTR	NM_022163.3	NP_071446.2	Q9H2W6	RM46_HUMAN	mitochondrial ribosomal protein L46	213						mitochondrion (GO:0005739)|ribosome (GO:0005840)	hydrolase activity (GO:0016787)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)	5	Lung NSC(78;0.203)		BRCA - Breast invasive adenocarcinoma(143;0.188)			CTTGAATGTGTAGTGCCCACA	0.473																																					p.Y213C		Atlas-SNP	.											.	MRPL46	13	.	0			c.A638G						.						81	77	79					15																	89003046		2201	4299	6500	SO:0001583	missense	26589	exon4			AATGTGTAGTGCC	AF210056	CCDS10341.1	15q25.3	2012-10-08	2001-12-10	2001-12-14	ENSG00000259494	ENSG00000259494		"Mitochondrial ribosomal proteins / large subunits"	1192	protein-coding gene	gene with protein product		611851	"chromosome 15 open reading frame 4"	C15orf4		11761714, 11551941	Standard	NM_022163		Approved	LIECG2, P2ECSL	uc002bmj.2	Q9H2W6	OTTHUMG00000148683	ENST00000312475.4:c.638A>G	chr15.hg19:g.89003046T>C	ENSP00000312311:p.Tyr213Cys	81.0	0.0		83.0	20.0	NM_022163	B2RD75|Q9HBU8	Missense_Mutation	SNP	ENST00000312475.4	hg19	CCDS10341.1	.	.	.	.	.	.	.	.	.	.	T	15.25	2.779233	0.49891	.	.	ENSG00000173867	ENST00000312475	T	0.54279	0.58	6.17	5.04	0.67666	NUDIX hydrolase domain (1);	0.000000	0.85682	D	0.000000	T	0.76090	0.3939	M	0.89534	3.04	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.79617	-0.1729	10	0.56958	D	0.05	.	12.1762	0.54186	0.128:0.0:0.0:0.872	.	213	Q9H2W6	RM46_HUMAN	C	213	ENSP00000312311:Y213C	ENSP00000312311:Y213C	Y	-	2	0	MRPL46	86804050	1.000000	0.71417	1.000000	0.80357	0.149000	0.21700	7.572000	0.82409	1.129000	0.42072	-0.336000	0.08194	TAC	.	.		0.473	MRPL46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309073.1	NM_022163		C	89003046	T	C	89003046	3	2	367	1	0	0	0	0	1	0	0	0	9819	1638	57	2	205	2	MRPL46	15	89003046	Missense_Mutation	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	34697157	89003046	13528346	96	51031										
GSPT1	2935	hgsc.bcm.edu	37	chr16	11991860	11991860	+	5'UTR	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	tacatcattaccttcacacaAtgactgttcctcttgagagg	6	11	3	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr16:11991860A>G	ENST00000420576.2	-	0	73				RP11-166B2.8_ENST00000574364.1_RNA|GSPT1_ENST00000439887.2_Silent_p.L129L|GSPT1_ENST00000563468.1_5'Flank|GSPT1_ENST00000434724.2_Silent_p.L129L	NM_001130007.1	NP_001123479.1	P15170	ERF3A_HUMAN	G1 to S phase transition 1						G1/S transition of mitotic cell cycle (GO:0000082)|GTP catabolic process (GO:0006184)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein methylation (GO:0006479)|translational termination (GO:0006415)	intracellular (GO:0005622)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|translation release factor activity (GO:0003747)			breast(1)|central_nervous_system(1)|kidney(4)|lung(4)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	14						CCTTCACACAATGACTGTTCC	0.313																																					p.L129L		Atlas-SNP	.											.	GSPT1	71	.	0			c.T385C						.						83	68	73					16																	11991860		1560	3549	5109	SO:0001623	5_prime_UTR_variant	2935	exon2			CACACAATGACTG	BC008391	CCDS45412.1, CCDS45413.1, CCDS45414.1	16p13.1	2008-08-01							4621	protein-coding gene	gene with protein product		139259				2511002, 17700517	Standard	NM_002094		Approved	GST1, ETF3A, eRF3a	uc002dbt.3	P15170		ENST00000420576.2:c.-30T>C	chr16.hg19:g.11991860A>G		135.0	0.0		126.0	35.0	NM_001130006	J3KQG6|Q96GF2	Silent	SNP	ENST00000420576.2	hg19	CCDS45414.1																																																																																			.	.		0.313	GSPT1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000421514.1	NM_002094		G	11991860	A	G	11991860	1	3	367	0	1	0	0	0	0	0	0	0	6835	98	4	2		2	GSPT1	16	11991860	5'UTR	SNP	A	TCGA-ZP-A9D1-01A-11D-A382-10		11991860	78362893	97	51032										
ACSM2A	123876	hgsc.bcm.edu	37	chr16	20489989	20489989	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	caggcctataggcatcttctCtggctatgtggtgagaaact	11	9	2	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr16:20489989C>G	ENST00000573854.1	+	10	1385	c.1271C>G	c.(1270-1272)tCt>tGt	p.S424C	ACSM2A_ENST00000575690.1_Missense_Mutation_p.S424C|ACSM2A_ENST00000219054.6_Missense_Mutation_p.S424C|ACSM2A_ENST00000536134.1_Missense_Mutation_p.S196C|ACSM2A_ENST00000417235.2_Missense_Mutation_p.S345C|ACSM2A_ENST00000575558.1_3'UTR|ACSM2A_ENST00000396104.2_Missense_Mutation_p.S424C	NM_001010845.2	NP_001010845	Q08AH3	ACS2A_HUMAN	acyl-CoA synthetase medium-chain family member 2A	424					fatty acid metabolic process (GO:0006631)|glucose homeostasis (GO:0042593)|medium-chain fatty-acyl-CoA metabolic process (GO:0036112)|triglyceride homeostasis (GO:0070328)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(34)|ovary(1)|skin(6)|stomach(1)	51						GGCATCTTCTCTGGCTATGTG	0.517																																					p.S424C		Atlas-SNP	.											.	ACSM2A	120	.	0			c.C1271G						.						137	108	118					16																	20489989		2203	4300	6503	SO:0001583	missense	123876	exon11			TCTTCTCTGGCTA	AK091878, AK096039	CCDS32401.1	16p12.3	2014-08-08	2007-06-20	2007-06-20	ENSG00000183747	ENSG00000183747		"Acyl-CoA synthetase family"	32017	protein-coding gene	gene with protein product		614358	"acyl-CoA synthetase medium-chain family member 2"	ACSM2			Standard	NM_001010845		Approved	A-923A4.1, MGC150530	uc010bwe.3	Q08AH3	OTTHUMG00000177401	ENST00000573854.1:c.1271C>G	chr16.hg19:g.20489989C>G	ENSP00000459451:p.Ser424Cys	87.0	0.0		73.0	23.0	NM_001010845	B3KTT9|O75202	Missense_Mutation	SNP	ENST00000573854.1	hg19	CCDS32401.1	.	.	.	.	.	.	.	.	.	.	C	6.284	0.420551	0.11928	.	.	ENSG00000183747	ENST00000417235;ENST00000219054;ENST00000536134;ENST00000396104	T;T;T;T	0.46451	0.87;0.87;0.87;0.87	3.33	1.26	0.21427	AMP-dependent synthetase/ligase (1);	0.000000	0.49916	D	0.000139	T	0.34890	0.0913	L	0.53249	1.67	0.80722	D	1	B;B	0.20368	0.007;0.044	B;B	0.25506	0.011;0.061	T	0.12167	-1.0558	10	0.54805	T	0.06	-12.7384	6.8245	0.23874	0.0:0.7217:0.1754:0.1029	.	345;424	B7Z8R0;Q08AH3	.;ACS2A_HUMAN	C	345;424;196;424	ENSP00000392169:S345C;ENSP00000219054:S424C;ENSP00000445082:S196C;ENSP00000379411:S424C	ENSP00000219054:S424C	S	+	2	0	ACSM2A	20397490	0.000000	0.05858	0.973000	0.42090	0.384000	0.30261	0.306000	0.19279	0.082000	0.17018	-1.043000	0.02367	TCT	.	.		0.517	ACSM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436764.1	NM_001010845		G	20489989	C	G	20489989	3	3	367	1	0	0	0	0	1	0	0	0	183	913	32	4	1305	4	ACSM2A	16	20489989	Missense_Mutation	SNP	C	TCGA-ZP-A9D1-01A-11D-A382-10	8498129	20489989	69864764	98	51033										
VPS4A	27183	hgsc.bcm.edu	37	chr16	69353433	69353433	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	atctgatgtccaagtggctgGgggagagtgaaaagtaagtc	15	5	1	3			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr16:69353433G>T	ENST00000254950.11	+	6	763	c.607G>T	c.(607-609)Ggg>Tgg	p.G203W	COG8_ENST00000564419.1_5'Flank|RP11-343C2.11_ENST00000570054.2_Missense_Mutation_p.G227W	NM_013245.2	NP_037377.1			vacuolar protein sorting 4 homolog A (S. cerevisiae)											NS(1)|central_nervous_system(1)|large_intestine(2)|lung(3)	7		Ovarian(137;0.101)				CAAGTGGCTGGGGGAGAGTGA	0.597																																					p.G203W		Atlas-SNP	.											.	VPS4A	18	.	0			c.G607T						.						33	36	35					16																	69353433		2084	4224	6308	SO:0001583	missense	27183	exon6			TGGCTGGGGGAGA	AF112215	CCDS45517.1	16q23.1	2010-04-21	2006-04-04		ENSG00000132612	ENSG00000132612		"ATPases / AAA-type"	13488	protein-coding gene	gene with protein product		609982	"vacuolar protein sorting 4A (yeast homolog)", "vacuolar protein sorting 4A (yeast)"			10637304, 11563910	Standard	NM_013245		Approved	VPS4, VPS4-1, FLJ22197, SKD2, SKD1, SKD1A	uc002eww.3	Q9UN37		ENST00000254950.11:c.607G>T	chr16.hg19:g.69353433G>T	ENSP00000254950:p.Gly203Trp	68.0	0.0		68.0	13.0	NM_013245		Missense_Mutation	SNP	ENST00000254950.11	hg19	CCDS45517.1	.	.	.	.	.	.	.	.	.	.	G	31	5.068134	0.93950	.	.	ENSG00000132612	ENST00000254950	D	0.95272	-3.66	6.06	6.06	0.98353	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.98950	0.9643	H	0.99927	4.965	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98748	1.0719	10	0.87932	D	0	-43.4151	20.2159	0.98296	0.0:0.0:1.0:0.0	.	203	Q9UN37	VPS4A_HUMAN	W	203	ENSP00000254950:G203W	ENSP00000254950:G203W	G	+	1	0	VPS4A	67910934	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.858000	0.99539	2.882000	0.98803	0.655000	0.94253	GGG	.	.		0.597	VPS4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430563.3	NM_013245		T	69353433	G	T	69353433	3	4	367	1	0	0	0	0	1	0	0	0	17227	1232	43	3	629	3	VPS4A	16	69353433	Missense_Mutation	SNP	G	TCGA-ZP-A9D1-01A-11D-A382-10	48863444	69353433	21001320	99	51034										
GEMIN4	50628	hgsc.bcm.edu	37	chr17	650889	650889	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	atggcagatggtggtgggcaGggccatcaggagctggataa	18	6	1	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr17:650889G>T	ENST00000319004.5	-	2	512	c.394C>A	c.(394-396)Ctg>Atg	p.L132M	GEMIN4_ENST00000437269.1_Missense_Mutation_p.L132M|GEMIN4_ENST00000576778.1_Missense_Mutation_p.L121M	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	132					gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)				breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		GTGGTGGGCAGGGCCATCAGG	0.557																																					p.L132M		Atlas-SNP	.											.	GEMIN4	116	.	0			c.C394A						.						80	84	83					17																	650889		2030	4186	6216	SO:0001583	missense	50628	exon2			TGGGCAGGGCCAT	AF177341	CCDS45559.1	17p13.3	2008-07-18				ENSG00000179409			15717	protein-coding gene	gene with protein product	"HCC-associated protein 1", "component of gems 4"	606969				10725331	Standard	NM_015721		Approved	HHRF-1, DKFZP434B131, p97, DKFZP434D174, HC56, HCAP1	uc002frs.1	P57678		ENST00000319004.5:c.394C>A	chr17.hg19:g.650889G>T	ENSP00000321706:p.Leu132Met	192.0	0.0		111.0	5.0	NM_015721	Q9NZS7|Q9UG32|Q9Y4Q2	Missense_Mutation	SNP	ENST00000319004.5	hg19	CCDS45559.1	.	.	.	.	.	.	.	.	.	.	G	16.04	3.010800	0.54361	.	.	ENSG00000179409	ENST00000319004;ENST00000437269	T;T	0.36340	1.26;1.26	5.66	3.65	0.41850	.	0.069975	0.64402	D	0.000015	T	0.56016	0.1957	M	0.66939	2.045	0.43750	D	0.996254	D;D	0.89917	1.0;1.0	D;D	0.91635	0.995;0.999	T	0.57579	-0.7787	10	0.72032	D	0.01	-11.1415	11.807	0.52161	0.146:0.0:0.854:0.0	.	132;132	E7EN12;P57678	.;GEMI4_HUMAN	M	132	ENSP00000321706:L132M;ENSP00000392460:L132M	ENSP00000321706:L132M	L	-	1	2	GEMIN4	597639	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	2.701000	0.47094	0.744000	0.32741	0.655000	0.94253	CTG	.	.		0.557	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437181.1	NM_015721		T	650889	G	T	650889	3	4	367	1	0	0	0	0	1	0	0	0	6338	991	35	3	2786	3	GEMIN4	17	650889	Missense_Mutation	SNP	G	TCGA-ZP-A9D1-01A-11D-A382-10		650889	80544321	100	51035										
MYOCD	93649	hgsc.bcm.edu	37	chr17	12608447	12608447	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	aacactcccttttctaagttTtacagttaagacttcaacaa	3	10	2	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr17:12608447T>C	ENST00000343344.4	+	2	58	c.58T>C	c.(58-60)Tta>Cta	p.L20L	MYOCD_ENST00000425538.1_Silent_p.L20L|AC005358.3_ENST00000445508.1_RNA			Q8IZQ8	MYCD_HUMAN	myocardin	20					cardiac muscle cell differentiation (GO:0055007)|cardiac ventricle development (GO:0003231)|cardiocyte differentiation (GO:0035051)|cell growth involved in cardiac muscle cell development (GO:0061049)|cellular component maintenance (GO:0043954)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hypoxia (GO:0071456)|digestive tract development (GO:0048565)|ductus arteriosus closure (GO:0097070)|hepatic stellate cell activation (GO:0035733)|lung alveolus development (GO:0048286)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of skeletal muscle cell differentiation (GO:2001015)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cardiac vascular smooth muscle cell differentiation (GO:2000724)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cell growth by extracellular stimulus (GO:0001560)|regulation of histone acetylation (GO:0035065)|regulation of myoblast differentiation (GO:0045661)|regulation of smooth muscle cell differentiation (GO:0051150)|response to hypoxia (GO:0001666)|smooth muscle cell differentiation (GO:0051145)|urinary bladder development (GO:0060157)|uterus development (GO:0060065)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(2)|lung(33)|ovary(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	70				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)		TTTCTAAGTTTTACAGTTAAG	0.338																																					p.L20L		Atlas-SNP	.											.	MYOCD	291	.	0			c.T58C						.						99	83	88					17																	12608447		2203	4300	6503	SO:0001819	synonymous_variant	93649	exon2			TAAGTTTTACAGT	AF532596	CCDS11163.1, CCDS54091.1	17p11.2	2004-03-01			ENSG00000141052	ENSG00000141052			16067	protein-coding gene	gene with protein product		606127				11439182, 12397177	Standard	XM_005256863		Approved	MYCD	uc002gno.2	Q8IZQ8	OTTHUMG00000058767	ENST00000343344.4:c.58T>C	chr17.hg19:g.12608447T>C		364.0	0.0		295.0	88.0	NM_001146312	Q5UBU5|Q8N7Q1	Silent	SNP	ENST00000343344.4	hg19	CCDS11163.1																																																																																			.	.		0.338	MYOCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129950.1	NM_153604		C	12608447	T	C	12608447	2	2	367	1	0	0	0	0	0	0	0	1	10096	1838	64	2		2	MYOCD	17	12608447	Silent	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	11957558	12608447	68586763	101	51036										
PROCA1	6830	hgsc.bcm.edu	37	chr17	27030972	27030972	+	IGR	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	tttttcttctttaccttcttGatcaccttgctgccctgacc	4	14	4	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr17:27030972G>A	ENST00000314616.6	+	0	6518				PROCA1_ENST00000581289.1_3'UTR|PROCA1_ENST00000439862.3_Silent_p.I207I|PROCA1_ENST00000301039.2_Silent_p.I205I|PROCA1_ENST00000579650.1_5'Flank	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)						chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					ttaccttcttGATCACCTTGC	0.512																																					p.I205I		Atlas-SNP	.											.	PROCA1	28	.	0			c.C615T						.						43	42	43					17																	27030972		2203	4300	6503	SO:0001628	intergenic_variant	147011	exon4			CTTCTTGATCACC	U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"SH2 domain containing"	11470	protein-coding gene	gene with protein product		601333	"suppressor of Ty (S.cerevisiae) 6 homolog"			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85			chr17.hg19:g.27030972G>A		58.0	0.0		51.0	16.0	NM_152465	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Silent	SNP	ENST00000314616.6	hg19	CCDS32596.1																																																																																			.	.		0.512	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170		A	27030972	G	A	27030972	1	1	367	0	1	0	0	0	0	0	0	0	12558	1280	45	3		3	PROCA1	17	27030972	IGR	SNP	G	TCGA-ZP-A9D1-01A-11D-A382-10	14422525	27030972	54164238	102	51037										
LHX1	3975	hgsc.bcm.edu	37	chr17	35300131	35300131	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	tcctcgcaggcccagacaccAgtggacctacccttcgtgcc	9	18	0	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr17:35300131A>G	ENST00000254457.5	+	5	2335	c.924A>G	c.(922-924)ccA>ccG	p.P308P	RP11-445F12.2_ENST00000607336.1_RNA	NM_005568.3	NP_005559.2	P48742	LHX1_HUMAN	LIM homeobox 1	308					anatomical structure formation involved in morphogenesis (GO:0048646)|anatomical structure morphogenesis (GO:0009653)|anterior/posterior axis specification (GO:0009948)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell-cell signaling (GO:0007267)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation (GO:0021937)|cerebellum development (GO:0021549)|cervix development (GO:0060067)|comma-shaped body morphogenesis (GO:0072049)|dorsal/ventral pattern formation (GO:0009953)|ectoderm formation (GO:0001705)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|embryonic viscerocranium morphogenesis (GO:0048703)|endoderm formation (GO:0001706)|epithelium development (GO:0060429)|forebrain regionalization (GO:0021871)|gastrulation with mouth forming second (GO:0001702)|head development (GO:0060322)|horizontal cell localization (GO:0035852)|kidney development (GO:0001822)|lateral motor column neuron migration (GO:0097477)|mesonephric duct development (GO:0072177)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric glomerulus development (GO:0072224)|metanephric part of ureteric bud development (GO:0035502)|metanephric renal vesicle morphogenesis (GO:0072283)|metanephric S-shaped body morphogenesis (GO:0072284)|motor neuron axon guidance (GO:0008045)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct elongation (GO:0035849)|nephric duct morphogenesis (GO:0072178)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|oviduct development (GO:0060066)|oviduct epithelium development (GO:0035846)|paramesonephric duct development (GO:0061205)|pattern specification process (GO:0007389)|positive regulation of anterior head development (GO:2000744)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of embryonic development (GO:0040019)|positive regulation of gastrulation (GO:2000543)|positive regulation of nephron tubule epithelial cell differentiation (GO:2000768)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|primitive streak formation (GO:0090009)|pronephros development (GO:0048793)|regulation of gene expression (GO:0010468)|renal vesicle morphogenesis (GO:0072077)|retina layer formation (GO:0010842)|S-shaped body morphogenesis (GO:0072050)|somite rostral/caudal axis specification (GO:0032525)|spinal cord association neuron differentiation (GO:0021527)|telencephalon development (GO:0021537)|transcription from RNA polymerase II promoter (GO:0006366)|ureteric bud development (GO:0001657)|urogenital system development (GO:0001655)|uterine epithelium development (GO:0035847)|uterus development (GO:0060065)|vagina development (GO:0060068)|ventral spinal cord development (GO:0021517)	nucleus (GO:0005634)|protein complex (GO:0043234)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	16		Breast(25;0.00607)				CCCAGACACCAGTGGACCTAC	0.716																																					p.P308P		Atlas-SNP	.											.	LHX1	48	.	0			c.A924G						.						15	16	16					17																	35300131		2201	4293	6494	SO:0001819	synonymous_variant	3975	exon5			GACACCAGTGGAC	U14755	CCDS11316.1	17q12	2014-04-11			ENSG00000132130	ENSG00000273706		"Homeoboxes / LIM class"	6593	protein-coding gene	gene with protein product		601999				9212161	Standard	NM_005568		Approved	LIM-1, LIM1	uc002hnh.2	P48742	OTTHUMG00000188456	ENST00000254457.5:c.924A>G	chr17.hg19:g.35300131A>G		291.0	0.0		253.0	55.0	NM_005568	Q3MIW0	Silent	SNP	ENST00000254457.5	hg19	CCDS11316.1																																																																																			.	.		0.716	LHX1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256704.3	NM_005568		G	35300131	A	G	35300131	2	3	367	1	0	0	0	0	0	0	0	1	8779	175	7	2		2	LHX1	17	35300131	Silent	SNP	A	TCGA-ZP-A9D1-01A-11D-A382-10	8269159	35300131	45895079	103	51038										
KRT27	342574	hgsc.bcm.edu	37	chr17	38936060	38936060	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	aggtctaccccgggggccgcGttcatctccacgttcacgtt	11	15	4	0			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr17:38936060G>A	ENST00000301656.3	-	4	778	c.738C>T	c.(736-738)aaC>aaT	p.N246N	KRT27_ENST00000540723.1_5'Flank	NM_181537.3	NP_853515.2			keratin 27											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(3)|skin(1)|stomach(1)	21		Breast(137;0.000812)				CGGGGGCCGCGTTCATCTCCA	0.517																																					p.N246N		Atlas-SNP	.											.	KRT27	41	.	0			c.C738T						.						53	55	55					17																	38936060		2203	4300	6503	SO:0001819	synonymous_variant	342574	exon4			GGCCGCGTTCATC	AJ564206	CCDS11375.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000171446	ENSG00000171446		"-", "Intermediate filaments type I, keratins (acidic)"	30841	protein-coding gene	gene with protein product			"keratin 25C"	KRT25C		16831889	Standard	NM_181537		Approved		uc002hvg.3	Q7Z3Y8	OTTHUMG00000133371	ENST00000301656.3:c.738C>T	chr17.hg19:g.38936060G>A		124.0	0.0		81.0	24.0	NM_181537		Silent	SNP	ENST00000301656.3	hg19	CCDS11375.1																																																																																			.	.		0.517	KRT27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257216.1	NM_181537		A	38936060	G	A	38936060	2	1	367	1	0	0	0	0	0	0	0	1	8473	1136	40	1		1	KRT27	17	38936060	Silent	SNP	G	TCGA-ZP-A9D1-01A-11D-A382-10	3635929	38936060	42259150	104	51039										
HAP1	9001	hgsc.bcm.edu	37	chr17	39890781	39890781	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ctgcggctgcgcagagggctCcggagcgggactggctgagg	20	11	0	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr17:39890781C>A	ENST00000310778.5	-	1	115	c.106G>T	c.(106-108)Gag>Tag	p.E36*	HAP1_ENST00000393939.2_Nonsense_Mutation_p.E36*|JUP_ENST00000540235.1_Intron|HAP1_ENST00000341193.5_Nonsense_Mutation_p.E36*|HAP1_ENST00000347901.4_Nonsense_Mutation_p.E36*			P54257	HAP1_HUMAN	huntingtin-associated protein 1	36					anterograde axon cargo transport (GO:0008089)|autophagy (GO:0006914)|brain development (GO:0007420)|cell projection organization (GO:0030030)|exocytosis (GO:0006887)|negative regulation of beta-amyloid formation (GO:1902430)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|positive regulation of neurotrophin production (GO:0032901)|positive regulation of nonmotile primary cilium assembly (GO:1902857)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|protein localization (GO:0008104)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|regulation of organelle transport along microtubule (GO:1902513)|retrograde axon cargo transport (GO:0008090)|synaptic transmission (GO:0007268)|vesicle transport along microtubule (GO:0047496)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|inclusion body (GO:0016234)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|synapse (GO:0045202)	brain-derived neurotrophic factor binding (GO:0048403)|ion channel binding (GO:0044325)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(4)|skin(1)	21		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.0677)			GCAGAGGGCTCCGGAGCGGGA	0.711																																					p.E36X		Atlas-SNP	.											.	HAP1	48	.	0			c.G106T						.						13	14	14					17																	39890781		2158	4242	6400	SO:0001587	stop_gained	9001	exon1			AGGGCTCCGGAGC	AF040723	CCDS11406.1, CCDS42338.1, CCDS42339.1	17q21.2-q21.3	2008-04-23	2008-04-23		ENSG00000173805	ENSG00000173805			4812	protein-coding gene	gene with protein product	"neuroan 1"	600947		HAP2		7477378, 9668110	Standard	NM_177977		Approved	HLP, hHLP1, HIP5	uc002hxn.1	P54257	OTTHUMG00000133498	ENST00000310778.5:c.106G>T	chr17.hg19:g.39890781C>A	ENSP00000309392:p.Glu36*	78.0	0.0		75.0	19.0	NM_177977	A8MQB5|O75358|Q59GK4|Q9H4G3|Q9HA98|Q9NY90	Nonsense_Mutation	SNP	ENST00000310778.5	hg19		.	.	.	.	.	.	.	.	.	.	C	18.06	3.538931	0.65085	.	.	ENSG00000173805	ENST00000393939;ENST00000310778;ENST00000347901;ENST00000341193	.	.	.	2.63	1.65	0.23941	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-12.3453	5.4635	0.16630	0.0:0.8413:0.0:0.1587	.	.	.	.	X	36	.	ENSP00000309392:E36X	E	-	1	0	HAP1	37144307	0.000000	0.05858	0.435000	0.26784	0.036000	0.12997	0.299000	0.19138	0.670000	0.31165	0.467000	0.42956	GAG	.	.		0.711	HAP1-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000389619.1	NM_003949		A	39890781	C	A	39890781	4	1	367	1	0	0	0	0	0	1	0	0	6962	864	30	3	1821	3	HAP1	17	39890781	Nonsense_Mutation	SNP	C	TCGA-ZP-A9D1-01A-11D-A382-10	954721	39890781	41304429	105	51040										
CACNG4	27092	hgsc.bcm.edu	37	chr17	64961144	64961144	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	tggctgtactccagcgcgcaCatctgcaacggcaccaacct	9	16	1	0			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr17:64961144C>T	ENST00000262138.3	+	1	119	c.117C>T	c.(115-117)caC>caT	p.H39H		NM_014405.3	NP_055220.1	Q9UBN1	CCG4_HUMAN	calcium channel, voltage-dependent, gamma subunit 4	39					membrane depolarization (GO:0051899)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(3)	19	all_cancers(12;9.86e-11)		BRCA - Breast invasive adenocarcinoma(6;1.35e-07)			CCAGCGCGCACATCTGCAACG	0.701																																					p.H39H		Atlas-SNP	.											.	CACNG4	44	.	0			c.C117T						.						36	31	33					17																	64961144		2203	4300	6503	SO:0001819	synonymous_variant	27092	exon1			CGCGCACATCTGC	AH008289	CCDS11667.1	17q24	2006-01-23				ENSG00000075461		"Calcium channel subunits"	1408	protein-coding gene	gene with protein product		606404				10613843	Standard	NM_014405		Approved	MGC11138, MGC24983	uc002jft.2	Q9UBN1		ENST00000262138.3:c.117C>T	chr17.hg19:g.64961144C>T		185.0	0.0		152.0	42.0	NM_014405	B2RCK0	Silent	SNP	ENST00000262138.3	hg19	CCDS11667.1																																																																																			.	.		0.701	CACNG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447036.1	NM_014405		T	64961144	C	T	64961144	2	4	367	1	0	0	0	0	0	0	0	1	2561	477	17	3		3	CACNG4	17	64961144	Silent	SNP	C	TCGA-ZP-A9D1-01A-11D-A382-10	25070363	64961144	16234066	106	51041										
GRIN2C	2905	hgsc.bcm.edu	37	chr17	72842250	72842250	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	caggtctatggcccgcttccAgtgggagtccttctgcatgg	13	12	2	0			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr17:72842250A>T	ENST00000293190.5	-	11	2451	c.2305T>A	c.(2305-2307)Tgg>Agg	p.W769R	GRIN2C_ENST00000347612.4_Missense_Mutation_p.W769R	NM_000835.3	NP_000826.2	Q14957	NMDE3_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2C	769					directional locomotion (GO:0033058)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of protein catabolic process (GO:0042177)|neuromuscular process controlling balance (GO:0050885)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|response to wounding (GO:0009611)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	33	all_lung(278;0.172)|Lung NSC(278;0.207)				Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GCCCGCTTCCAGTGGGAGTCC	0.622																																					p.W769R		Atlas-SNP	.											.	GRIN2C	144	.	0			c.T2305A						.						166	125	139					17																	72842250		2203	4300	6503	SO:0001583	missense	2905	exon11			GCTTCCAGTGGGA		CCDS32724.1, CCDS62330.1	17q25.1	2012-08-29			ENSG00000161509	ENSG00000161509		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4587	protein-coding gene	gene with protein product		138254		NMDAR2C		9480759	Standard	NM_001278553		Approved	GluN2C	uc002jlt.1	Q14957	OTTHUMG00000044524	ENST00000293190.5:c.2305T>A	chr17.hg19:g.72842250A>T	ENSP00000293190:p.Trp769Arg	101.0	0.0		69.0	16.0	NM_000835	B2RTT1	Missense_Mutation	SNP	ENST00000293190.5	hg19	CCDS32724.1	.	.	.	.	.	.	.	.	.	.	A	13.88	2.368492	0.42003	.	.	ENSG00000161509	ENST00000293190;ENST00000347612	T	0.27890	1.64	4.45	4.45	0.53987	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.193708	0.48286	D	0.000181	T	0.53932	0.1827	M	0.72894	2.215	0.58432	D	0.999996	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.59386	-0.7464	10	0.87932	D	0	.	13.8334	0.63395	1.0:0.0:0.0:0.0	.	803;769	Q8IW23;Q14957	.;NMDE3_HUMAN	R	769;803	ENSP00000293190:W769R	ENSP00000293190:W769R	W	-	1	0	GRIN2C	70353845	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.075000	0.94004	1.980000	0.57719	0.459000	0.35465	TGG	.	.		0.622	GRIN2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103824.1			T	72842250	A	T	72842250	3	4	367	1	0	0	0	0	1	0	0	0	6790	188	7	4	1408	4	GRIN2C	17	72842250	Missense_Mutation	SNP	A	TCGA-ZP-A9D1-01A-11D-A382-10	7881106	72842250	8352960	107	51042										
PGS1	9489	hgsc.bcm.edu	37	chr17	76399940	76399940	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	caccactggctatttcaaccTgacccaggcctacatggacc	7	16	1	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr17:76399940T>C	ENST00000262764.6	+	7	1198	c.1172T>C	c.(1171-1173)cTg>cCg	p.L391P	PGS1_ENST00000329897.7_Missense_Mutation_p.L256P|PGS1_ENST00000588281.1_3'UTR	NM_024419.3	NP_077733.3	Q32NB8	PGPS1_HUMAN	phosphatidylglycerophosphate synthase 1	391					cardiolipin biosynthetic process (GO:0032049)|diacylglycerol metabolic process (GO:0046339)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity (GO:0008444)			cervix(2)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	10			BRCA - Breast invasive adenocarcinoma(99;0.00144)|OV - Ovarian serous cystadenocarcinoma(97;0.031)			TATTTCAACCTGACCCAGGCC	0.572																																					p.L391P	Esophageal Squamous(45;182 1126 10685 43198)	Atlas-SNP	.											.	PGS1	30	.	0			c.T1172C						.						97	101	100					17																	76399940		2022	4167	6189	SO:0001583	missense	9489	exon7			TCAACCTGACCCA		CCDS42391.1	17q25.3	2006-02-09							30029	protein-coding gene	gene with protein product		614942				9880566	Standard	XR_243691		Approved	DKFZP762M186	uc002jvm.3	Q32NB8		ENST00000262764.6:c.1172T>C	chr17.hg19:g.76399940T>C	ENSP00000262764:p.Leu391Pro	97.0	0.0		87.0	25.0	NM_024419	B7ZA32|Q8IYK9|Q8TA85|Q96A75|Q9H7G9|Q9NPW7	Missense_Mutation	SNP	ENST00000262764.6	hg19	CCDS42391.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.361570	0.82353	.	.	ENSG00000087157	ENST00000262764;ENST00000329897;ENST00000335081	D;D	0.92397	-3.03;-3.03	5.59	5.59	0.84812	.	0.000000	0.64402	D	0.000002	D	0.94653	0.8276	L	0.48986	1.54	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.95018	0.8158	10	0.62326	D	0.03	-14.5175	15.7604	0.78076	0.0:0.0:0.0:1.0	.	391	Q32NB8	PGPS1_HUMAN	P	391;256;256	ENSP00000262764:L391P;ENSP00000330039:L256P	ENSP00000262764:L391P	L	+	2	0	PGS1	73911535	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.646000	0.83445	2.125000	0.65367	0.460000	0.39030	CTG	.	.		0.572	PGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437301.1	NM_024419		C	76399940	T	C	76399940	3	2	367	1	0	0	0	0	1	0	0	0	11817	1580	55	2	1198	2	PGS1	17	76399940	Missense_Mutation	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	3557690	76399940	4795270	108	51043										
LAMA1	284217	hgsc.bcm.edu	37	chr18	6956653	6956653	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	actggaaaagcccggggctcTggcaagagcttgctgtcctc	13	12	1	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr18:6956653T>G	ENST00000389658.3	-	56	8169	c.8076A>C	c.(8074-8076)ccA>ccC	p.P2692P	RP11-781P6.1_ENST00000584722.1_RNA	NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2692				P -> R (in Ref. 1 and 4). {ECO:0000305}.	axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				CCCGGGGCTCTGGCAAGAGCT	0.567																																					p.P2692P		Atlas-SNP	.											.	LAMA1	458	.	0			c.A8076C						.						63	68	67					18																	6956653		2203	4300	6503	SO:0001819	synonymous_variant	284217	exon56			GGGCTCTGGCAAG	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.8076A>C	chr18.hg19:g.6956653T>G		40.0	0.0		67.0	19.0	NM_005559		Silent	SNP	ENST00000389658.3	hg19	CCDS32787.1																																																																																			.	.		0.567	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		G	6956653	T	G	6956653	2	3	367	1	0	0	0	0	0	0	0	1	8614	1567	55	5		5	LAMA1	18	6956653	Silent	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10		6956653	71120595	109	51044										
DSG4	147409	hgsc.bcm.edu	37	chr18	28992917	28992917	+	Frame_Shift_Del	DEL	T	T	-													0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	gcagttggattgtggatgacTtagatgaaagctgcatggaa							TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr18:28992917delT	ENST00000308128.4	+	16	2617	c.2482delT	c.(2482-2484)ttafs	p.L828fs	RP11-534N16.1_ENST00000581856.1_RNA|DSG4_ENST00000359747.4_Frame_Shift_Del_p.L847fs|RP11-534N16.1_ENST00000578477.1_RNA	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4	828					anagen (GO:0042640)|BMP signaling pathway (GO:0030509)|homophilic cell adhesion (GO:0007156)|keratinocyte differentiation (GO:0030216)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(6)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(11)|liver(2)|lung(35)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			TGTGGATGACTTAGATGAAAG	0.453																																					p.D846fs		Atlas-INDEL	.											.	DSG4	343	.	0			c.2538delC						.						135	125	128					18																	28992917		2203	4300	6503	SO:0001589	frameshift_variant	147409	exon15			.	AY177664, AY168788	CCDS11897.1, CCDS45845.1	18q12.1	2010-01-26			ENSG00000175065	ENSG00000175065		"Cadherins / Major cadherins"	21307	protein-coding gene	gene with protein product		607892				12648213	Standard	NM_001134453		Approved	CDHF13, LAH	uc002kwq.2	Q86SJ6	OTTHUMG00000131979	ENST00000308128.4:c.2482delT	chr18.hg19:g.28992917delT	ENSP00000311859:p.Leu828fs	84.0	0.0		121.0	40.0	NM_001134453	A2RUI1|Q6Y9L9|Q8IXV4	Frame_Shift_Del	DEL	ENST00000308128.4	hg19	CCDS11897.1																																																																																			.	.		0.453	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254941.1	NM_177986		-	28992917	T	-	28992917	7	5	367	1	0	1	0	1	0	0	0	0	4781	1606	56	0	2665	0	DSG4	18	28992917	Frame_Shift_Del	DEL	T	TCGA-ZP-A9D1-01A-11D-A382-10	22036264	28992917	49084331	110	51045										
CXXC1	30827	hgsc.bcm.edu	37	chr18	47809307	47809307	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	gcactggcgcttgggcaggcGgcagaagtcacccgtgagct	16	12	1	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr18:47809307G>A	ENST00000285106.6	-	14	2455	c.1741C>T	c.(1741-1743)Cgc>Tgc	p.R581C	MBD1_ENST00000353909.3_5'Flank|MBD1_ENST00000398495.2_5'Flank|MBD1_ENST00000424334.2_5'Flank|CXXC1_ENST00000412036.2_Missense_Mutation_p.R585C|MBD1_ENST00000436910.1_5'Flank|MBD1_ENST00000457839.2_5'Flank|MBD1_ENST00000591535.1_5'Flank|MBD1_ENST00000398493.1_5'Flank|MBD1_ENST00000585595.1_5'Flank|MBD1_ENST00000269471.5_5'Flank|MBD1_ENST00000588937.1_5'Flank|MBD1_ENST00000590208.1_5'Flank|CXXC1_ENST00000589940.1_Silent_p.A568A|MBD1_ENST00000347968.3_5'Flank|MBD1_ENST00000585672.1_5'Flank|MBD1_ENST00000587605.1_5'Flank|MBD1_ENST00000382948.5_5'Flank|MBD1_ENST00000591416.1_5'Flank|MBD1_ENST00000349085.2_5'Flank|MBD1_ENST00000339998.6_5'Flank|MBD1_ENST00000269468.5_5'Flank|MBD1_ENST00000398488.1_5'Flank	NM_001101654.1|NM_014593.3	NP_001095124.1|NP_055408.2	Q9P0U4	CXXC1_HUMAN	CXXC finger protein 1	581					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|histone H3-K4 methylation (GO:0051568)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	24						TTGGGCAGGCGGCAGAAGTCA	0.612																																					p.R585C		Atlas-SNP	.											.	CXXC1	50	.	0			c.C1753T						.						92	83	86					18																	47809307		2203	4300	6503	SO:0001583	missense	30827	exon14			GCAGGCGGCAGAA	BC014940	CCDS11945.1, CCDS45866.1	18q12	2014-02-20	2014-02-20		ENSG00000154832	ENSG00000154832		"Zinc fingers, PHD-type"	24343	protein-coding gene	gene with protein product	"CpG binding protein", "DNA-binding protein with PHD finger and CXXC domain", "zinc finger, CpG binding-type containing 1"	609150	"CXXC finger 1 (PHD domain)"			10799292, 10688657	Standard	NM_014593		Approved	HsT2645, PCCX1, hCGBP, PHF18, CGBP, SPP1, CFP1, ZCGPC1	uc002ler.4	Q9P0U4	OTTHUMG00000132670	ENST00000285106.6:c.1741C>T	chr18.hg19:g.47809307G>A	ENSP00000285106:p.Arg581Cys	93.0	0.0		108.0	20.0	NM_001101654	B2RC03|Q8N2W4|Q96BC8|Q9P2V7	Missense_Mutation	SNP	ENST00000285106.6	hg19	CCDS11945.1	.	.	.	.	.	.	.	.	.	.	G	14.58	2.579244	0.46006	.	.	ENSG00000154832	ENST00000285106;ENST00000412036	T;T	0.26660	1.73;1.72	4.2	4.2	0.49525	CpG binding protein, C-terminal (1);	0.066796	0.56097	D	0.000034	T	0.22781	0.0550	L	0.58428	1.81	0.80722	D	1	P;P;P	0.41131	0.694;0.739;0.487	B;B;B	0.34779	0.119;0.189;0.085	T	0.06232	-1.0838	10	0.62326	D	0.03	-5.6841	9.805	0.40789	0.0:0.0:0.7944:0.2056	.	585;581;448	Q9P0U4-2;Q9P0U4;Q59EC8	.;CXXC1_HUMAN;.	C	581;585	ENSP00000285106:R581C;ENSP00000390475:R585C	ENSP00000285106:R581C	R	-	1	0	CXXC1	46063305	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	3.569000	0.53827	2.033000	0.60031	0.453000	0.30009	CGC	.	.		0.612	CXXC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255927.2	NM_014593		A	47809307	G	A	47809307	3	1	367	1	0	0	0	0	1	0	0	0	4099	1116	39	1	237	1	CXXC1	18	47809307	Missense_Mutation	SNP	G	TCGA-ZP-A9D1-01A-11D-A382-10	18816390	47809307	30267941	111	51046										
CDH19	28513	hgsc.bcm.edu	37	chr18	64211362	64211362	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ctggatcttaatgaaagtggTggaagcctcagtgtggtact	13	6	2	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr18:64211362T>A	ENST00000540086.1	-	7	1306	c.1060A>T	c.(1060-1062)Acc>Tcc	p.T354S	CDH19_ENST00000262150.2_Missense_Mutation_p.T354S	NM_001271028.1	NP_001257957.1	Q96JQ0	PCD16_HUMAN	cadherin 19, type 2	456	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(22)|ovary(1)|prostate(3)|skin(7)	61		Esophageal squamous(42;0.0132)				ATGAAAGTGGTGGAAGCCTCA	0.423																																					p.T354S		Atlas-SNP	.											.	CDH19	141	.	0			c.A1060T						.						135	119	124					18																	64211362		2203	4300	6503	SO:0001583	missense	28513	exon7			AAGTGGTGGAAGC	AJ007607	CCDS11994.1, CCDS59325.1	18q22.1	2010-01-26			ENSG00000071991	ENSG00000071991		"Cadherins / Major cadherins"	1758	protein-coding gene	gene with protein product		603016				10995570	Standard	NM_021153		Approved	CDH7	uc002lkc.2	Q9H159	OTTHUMG00000132802	ENST00000540086.1:c.1060A>T	chr18.hg19:g.64211362T>A	ENSP00000439593:p.Thr354Ser	103.0	0.0		108.0	42.0	NM_021153	O15098	Missense_Mutation	SNP	ENST00000540086.1	hg19	CCDS59325.1	.	.	.	.	.	.	.	.	.	.	T	7.991	0.753203	0.15778	.	.	ENSG00000071991	ENST00000262150;ENST00000540086;ENST00000454642	T;T	0.55760	0.5;0.5	5.62	3.18	0.36537	Cadherin (4);Cadherin-like (1);	0.376285	0.30109	N	0.010387	T	0.50888	0.1642	M	0.69185	2.1	0.09310	N	1	B;B	0.32604	0.126;0.377	B;B	0.38616	0.053;0.277	T	0.48210	-0.9055	10	0.51188	T	0.08	.	6.8684	0.24106	0.1347:0.0741:0.0:0.7912	.	354;354	F5H1K0;Q9H159	.;CAD19_HUMAN	S	354;354;299	ENSP00000262150:T354S;ENSP00000439593:T354S	ENSP00000262150:T354S	T	-	1	0	CDH19	62362342	0.989000	0.36119	0.196000	0.23383	0.564000	0.35744	1.958000	0.40402	0.481000	0.27557	0.528000	0.53228	ACC	.	.		0.423	CDH19-005	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000442285.1	NM_021153		A	64211362	T	A	64211362	3	1	367	1	0	0	0	0	1	0	0	0	3106	1696	59	4	1282	4	CDH19	18	64211362	Missense_Mutation	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	16402055	64211362	13865886	112	51047										
SALL3	27164	hgsc.bcm.edu	37	chr18	76757118	76757118	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	aacaacgagatctccgtcatCcagaacggcggcatccccca	8	16	2	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr18:76757118C>T	ENST00000537592.2	+	3	3699	c.3699C>T	c.(3697-3699)atC>atT	p.I1233I	SALL3_ENST00000575389.2_Silent_p.I1161I|SALL3_ENST00000536229.3_Silent_p.I1028I	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	1233					forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|negative regulation of smoothened signaling pathway (GO:0045879)|olfactory bulb interneuron development (GO:0021891)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(40)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)		TCTCCGTCATCCAGAACGGCG	0.617																																					p.I1233I		Atlas-SNP	.											.	SALL3	162	.	0			c.C3699T						.						109	100	103					18																	76757118		2203	4300	6503	SO:0001819	synonymous_variant	27164	exon3			CGTCATCCAGAAC	AJ007421	CCDS12013.1	18q23	2013-10-17	2013-10-17		ENSG00000256463	ENSG00000256463		"Zinc fingers, C2H2-type"	10527	protein-coding gene	gene with protein product		605079	"sal (Drosophila)-like 3", "sal-like 3 (Drosophila)"			10610715	Standard	NM_171999		Approved	ZNF796	uc002lmt.3	Q9BXA9	OTTHUMG00000132896	ENST00000537592.2:c.3699C>T	chr18.hg19:g.76757118C>T		171.0	0.0		166.0	55.0	NM_171999	Q9UGH1	Silent	SNP	ENST00000537592.2	hg19	CCDS12013.1																																																																																			.	.		0.617	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256397.1	NM_171999		T	76757118	C	T	76757118	2	4	367	1	0	0	0	0	0	0	0	1	13827	845	30	3		3	SALL3	18	76757118	Silent	SNP	C	TCGA-ZP-A9D1-01A-11D-A382-10	12545756	76757118	1320130	113	51048										
ADAMTSL5	339366	hgsc.bcm.edu	37	chr19	1510211	1510211	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ggacagggcggccattgtacAgggcacactgtaggtctcgg	16	10	1	0			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr19:1510211A>C	ENST00000413997.2	-	5	328	c.329T>G	c.(328-330)cTg>cGg	p.L110R	CTB-25B13.9_ENST00000590252.1_RNA|ADAMTSL5_ENST00000590562.1_5'UTR|ADAMTSL5_ENST00000395467.2_5'UTR|ADAMTSL5_ENST00000330475.4_Missense_Mutation_p.L100R			Q6ZMM2	ATL5_HUMAN	ADAMTS-like 5	110						extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	10		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCCATTGTACAGGGCACACTG	0.627																																					p.L100R		Atlas-SNP	.											.	ADAMTSL5	24	.	0			c.T299G						.						39	39	39					19																	1510211		2202	4300	6502	SO:0001583	missense	339366	exon5			TTGTACAGGGCAC	BC040620	CCDS12071.1	19p13.3	2008-02-05	2006-02-07	2006-02-07		ENSG00000185761			27912	protein-coding gene	gene with protein product			"thrombospondin, type I, domain containing 6"	THSD6			Standard	NM_213604		Approved		uc002ltd.2	Q6ZMM2		ENST00000413997.2:c.329T>G	chr19.hg19:g.1510211A>C	ENSP00000399364:p.Leu110Arg	77.0	0.0		81.0	11.0	NM_213604	B4DXK7|Q8IW95	Missense_Mutation	SNP	ENST00000413997.2	hg19		.	.	.	.	.	.	.	.	.	.	A	7.769	0.706963	0.15239	.	.	ENSG00000185761	ENST00000413997;ENST00000330475	T;T	0.62498	0.02;0.02	4.6	4.6	0.57074	.	0.260088	0.31450	N	0.007635	T	0.54806	0.1881	N	0.20530	0.585	0.80722	D	1	D;D	0.54772	0.968;0.968	P;P	0.51016	0.656;0.656	T	0.57394	-0.7819	10	0.46703	T	0.11	.	11.3547	0.49609	1.0:0.0:0.0:0.0	.	110;100	B4DXK7;Q6ZMM2	.;ATL5_HUMAN	R	110;100	ENSP00000399364:L110R;ENSP00000327608:L100R	ENSP00000327608:L100R	L	-	2	0	ADAMTSL5	1461211	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	3.799000	0.55529	1.691000	0.51100	0.374000	0.22700	CTG	.	.		0.627	ADAMTSL5-202	KNOWN	basic	protein_coding	protein_coding		XM_294919		C	1510211	A	C	1510211	3	2	367	1	0	0	0	0	1	0	0	0	278	188	7	5	1148	5	ADAMTSL5	19	1510211	Missense_Mutation	SNP	A	TCGA-ZP-A9D1-01A-11D-A382-10		1510211	57618772	114	51049										
ATCAY	85300	hgsc.bcm.edu	37	chr19	3913803	3913803	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	cgtgcacagcttggaagaccTggagcaactcatccctatgg	11	12	1	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr19:3913803T>C	ENST00000450849.2	+	9	1381	c.914T>C	c.(913-915)cTg>cCg	p.L305P	ATCAY_ENST00000301260.6_Missense_Mutation_p.L305P|ATCAY_ENST00000398448.3_Missense_Mutation_p.L311P|ATCAY_ENST00000600960.1_Missense_Mutation_p.L305P	NM_033064.4	NP_149053.1	Q86WG3	ATCAY_HUMAN	ataxia, cerebellar, Cayman type	305	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.|Mediates interaction with GLS.				apoptotic process (GO:0006915)|mitochondrion distribution (GO:0048311)|negative regulation of glutamate metabolic process (GO:2000212)|neuron projection development (GO:0031175)|regulation of protein localization (GO:0032880)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrial membrane (GO:0031966)|neuron projection (GO:0043005)|synapse (GO:0045202)	kinesin binding (GO:0019894)			breast(1)|endometrium(2)|kidney(2)|lung(2)	7		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00485)|STAD - Stomach adenocarcinoma(1328;0.183)		TTGGAAGACCTGGAGCAACTC	0.577																																					p.L305P		Atlas-SNP	.											.	ATCAY	84	.	0			c.T914C						.						93	101	99					19																	3913803		2071	4198	6269	SO:0001583	missense	85300	exon9			AAGACCTGGAGCA		CCDS45923.1	19p13.3	2014-06-24	2008-07-18		ENSG00000167654	ENSG00000167654			779	protein-coding gene	gene with protein product	"Cayman ataxia", "caytaxin"	608179				8845847, 14556008	Standard	NM_033064		Approved		uc002lyy.4	Q86WG3	OTTHUMG00000181836	ENST00000450849.2:c.914T>C	chr19.hg19:g.3913803T>C	ENSP00000390941:p.Leu305Pro	79.0	0.0		82.0	24.0	NM_033064	Q8NAQ2|Q8TAQ3|Q96HC6|Q96JF5	Missense_Mutation	SNP	ENST00000450849.2	hg19	CCDS45923.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.097301	0.76870	.	.	ENSG00000167654	ENST00000450849;ENST00000301260;ENST00000357694;ENST00000398448;ENST00000539301	T;T;T	0.58506	0.33;0.33;0.33	4.4	4.4	0.53042	Cellular retinaldehyde-binding/triple function, C-terminal (4);	0.167610	0.40908	D	0.000995	D	0.82384	0.5025	H	0.96015	3.755	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.87554	0.2467	10	0.87932	D	0	.	12.7855	0.57502	0.0:0.0:0.0:1.0	.	311;305;305	B4DS11;Q86WG3-3;Q86WG3	.;.;ATCAY_HUMAN	P	305;305;305;311;283	ENSP00000390941:L305P;ENSP00000301260:L305P;ENSP00000381466:L311P	ENSP00000301260:L305P	L	+	2	0	ATCAY	3864803	1.000000	0.71417	1.000000	0.80357	0.858000	0.48976	7.767000	0.85331	1.629000	0.50426	0.247000	0.18012	CTG	.	.		0.577	ATCAY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457872.2			C	3913803	T	C	3913803	3	2	367	1	0	0	0	0	1	0	0	0	1077	1580	55	2	944	2	ATCAY	19	3913803	Missense_Mutation	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	2403592	3913803	55215180	115	51050										
ZNF506	440515	hgsc.bcm.edu	37	chr19	19906192	19906192	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	catttaaaagatttttttccAgtatctcttatcttatgttt	3	6	2	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr19:19906192A>T	ENST00000540806.2	-	4	592	c.504T>A	c.(502-504)acT>acA	p.T168T	ZNF506_ENST00000450683.2_Silent_p.T136T|CTC-559E9.4_ENST00000590274.1_lincRNA|ZNF506_ENST00000443905.2_Silent_p.T168T|ZNF506_ENST00000587461.1_Intron|CTC-559E9.6_ENST00000591884.1_RNA|CTC-559E9.6_ENST00000589657.1_RNA			Q5JVG8	ZN506_HUMAN	zinc finger protein 506	168					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|large_intestine(7)|lung(3)|skin(1)|stomach(1)	14						ATTTTTTTCCAGTATCTCTTA	0.289																																					p.T168T		Atlas-SNP	.											.	ZNF506	36	.	0			c.T504A						.						39	37	38					19																	19906192		1874	4127	6001	SO:0001819	synonymous_variant	440515	exon4			TTTTCCAGTATCT	AK095575	CCDS42531.1, CCDS46027.1	19p13.11	2013-01-08				ENSG00000081665		"Zinc fingers, C2H2-type", "-"	23780	protein-coding gene	gene with protein product							Standard	NM_001099269		Approved	DKFZp761G1812	uc010eci.2	Q5JVG8		ENST00000540806.2:c.504T>A	chr19.hg19:g.19906192A>T		102.0	0.0		118.0	37.0	NM_001099269	B3KTH6	Silent	SNP	ENST00000540806.2	hg19	CCDS42531.1																																																																																			.	.		0.289	ZNF506-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460794.1	XM_036218		T	19906192	A	T	19906192	2	4	367	1	0	0	0	0	0	0	0	1	17967	175	7	4		4	ZNF506	19	19906192	Silent	SNP	A	TCGA-ZP-A9D1-01A-11D-A382-10	15992389	19906192	39222791	116	51051										
TGFB1	80776	hgsc.bcm.edu	37	chr19	41858864	41858864	+	IGR	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	tagtcttgcaggtggatagtCccgcggccggccggccaggc	16	13	1	0	rs199758510|rs66551611	byFrequency	TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr19:41858864C>T	ENST00000243578.3	-	0	1027				TGFB1_ENST00000221930.5_Missense_Mutation_p.G29E|CTC-435M10.3_ENST00000604424.1_Intron|TMEM91_ENST00000604123.1_5'Flank|TMEM91_ENST00000539627.1_Intron	NM_030578.3	NP_085055.2	Q9BPU9	B9D2_HUMAN	B9 protein domain 2						cilium assembly (GO:0042384)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|TCTN-B9D complex (GO:0036038)	gamma-tubulin binding (GO:0043015)			large_intestine(1)|ovary(1)	2						GGTGGATAGTCCCGCGGCCGG	0.711													C|||	2	0.000399361	8e-04	0	5008	,	,		12405	0		0.001	False		,,,				2504	0				p.G29E		Atlas-SNP	.											.	TGFB1	27	.	0			c.G86A	GRCh37	CM090931|CM090932	TGFB1	M		.	C	GLU/GLY	2,4240		0,2,2119	13	10	11		86	1.3	1	19		11	3,8293		0,3,4145	yes	missense	TGFB1	NM_000660.4	98	0,5,6264	TT,TC,CC		0.0362,0.0471,0.0399	possibly-damaging	29/391	41858864	5,12533	2121	4148	6269	SO:0001628	intergenic_variant	7040	exon1			GATAGTCCCGCGG	BC004157	CCDS12579.1	19q13.2	2014-01-28				ENSG00000123810			28636	protein-coding gene	gene with protein product		611951				21763481	Standard	NM_030578		Approved	MGC4093, MKS10	uc002oqj.2	Q9BPU9			chr19.hg19:g.41858864C>T		54.0	0.0		65.0	22.0	NM_000660		Missense_Mutation	SNP	ENST00000243578.3	hg19	CCDS12579.1	.	.	.	.	.	.	.	.	.	.	C	18.97	3.735595	0.69189	4.71E-4	3.62E-4	ENSG00000105329	ENST00000221930	T	0.31769	1.48	3.74	1.29	0.21616	Transforming growth factor-beta, N-terminal (1);	0.473959	0.22160	N	0.063783	T	0.33585	0.0868	M	0.62723	1.935	0.80722	D	1	P	0.42161	0.772	B	0.43575	0.424	T	0.30149	-0.9988	10	0.49607	T	0.09	-15.6854	12.0894	0.53717	0.0:0.5772:0.4228:0.0	.	29	P01137	TGFB1_HUMAN	E	29	ENSP00000221930:G29E	ENSP00000221930:G29E	G	-	2	0	TGFB1	46550704	0.004000	0.15560	0.981000	0.43875	0.943000	0.58893	0.541000	0.23207	0.724000	0.32296	0.462000	0.41574	GGA	.	.		0.711	B9D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463489.1	NM_030578		T	41858864	C	T	41858864	1	4	367	0	1	0	0	0	0	0	0	0	15831	855	30	3		3	TGFB1	19	41858864	IGR	SNP	C	TCGA-ZP-A9D1-01A-11D-A382-10	21952672	41858864	17270119	117	51052										
ZNF229	7772	hgsc.bcm.edu	37	chr19	44933761	44933761	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	atatggtttctctccagtgtGgaccctctgatggacaagca	10	10	2	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr19:44933761G>T	ENST00000588931.1	-	6	1628	c.1195C>A	c.(1195-1197)Cac>Aac	p.H399N	ZNF229_ENST00000291187.4_Missense_Mutation_p.H393N|CTC-512J12.4_ENST00000588655.1_RNA|ZNF229_ENST00000591289.1_Intron	NM_014518.2	NP_055333.2	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	399					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|central_nervous_system(2)|endometrium(6)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	45		Prostate(69;0.0352)				TCTCCAGTGTGGACCCTCTGA	0.507																																					p.H399N		Atlas-SNP	.											.	ZNF229	123	.	0			c.C1195A						.						93	104	100					19																	44933761		2203	4300	6503	SO:0001583	missense	7772	exon6			CAGTGTGGACCCT	AF192979	CCDS42574.1, CCDS62706.1	19q13.2	2013-01-08				ENSG00000278318		"Zinc fingers, C2H2-type", "-"	13022	protein-coding gene	gene with protein product							Standard	XM_006723372		Approved		uc002oze.1	Q9UJW7		ENST00000588931.1:c.1195C>A	chr19.hg19:g.44933761G>T	ENSP00000466519:p.His399Asn	115.0	0.0		152.0	48.0	NM_014518	B2RWN3|Q59FV2|Q86WL9	Missense_Mutation	SNP	ENST00000588931.1	hg19	CCDS42574.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.998096	0.93227	.	.	ENSG00000167383	ENST00000291187	.	.	.	3.86	2.71	0.32032	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.76227	0.3958	M	0.93763	3.455	0.30332	N	0.786536	D	0.71674	0.998	D	0.66602	0.945	T	0.75470	-0.3306	8	0.87932	D	0	.	11.5979	0.50984	0.0:0.182:0.818:0.0	.	399	Q9UJW7	ZN229_HUMAN	N	399	.	ENSP00000291187:H399N	H	-	1	0	ZNF229	49625601	1.000000	0.71417	0.336000	0.25522	0.974000	0.67602	4.809000	0.62591	1.694000	0.51137	0.609000	0.83330	CAC	.	.		0.507	ZNF229-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460833.1	NM_014518		T	44933761	G	T	44933761	3	4	367	1	0	0	0	0	1	0	0	0	17797	1348	47	3	1286	3	ZNF229	19	44933761	Missense_Mutation	SNP	G	TCGA-ZP-A9D1-01A-11D-A382-10	3074897	44933761	14195222	118	51053										
NLRP4	147945	hgsc.bcm.edu	37	chr19	56388508	56388508	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	gtgtcgggctctgacgcataCggattgccgcttagagattc	13	10	1	2	rs572392165		TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr19:56388508C>T	ENST00000301295.6	+	8	3094	c.2672C>T	c.(2671-2673)aCg>aTg	p.T891M	NLRP4_ENST00000346986.5_Missense_Mutation_p.T835M|NLRP4_ENST00000587891.1_Missense_Mutation_p.T816M	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	891					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		CTGACGCATACGGATTGCCGC	0.473													C|||	1	0.000199681	0	0	5008	,	,		20970	0		0	False		,,,				2504	0.001				p.T891M		Atlas-SNP	.											.	NLRP4	331	.	0			c.C2672T						.						201	189	193					19																	56388508		2203	4300	6503	SO:0001583	missense	147945	exon8			CGCATACGGATTG	AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"Nucleotide-binding domain and leucine rich repeat containing"	22943	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4", "cancer/testis antigen 58"	609645	"NACHT, leucine rich repeat and PYD containing 4"	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.2672C>T	chr19.hg19:g.56388508C>T	ENSP00000301295:p.Thr891Met	151.0	0.0		153.0	36.0	NM_134444	Q86W87|Q96AY6	Missense_Mutation	SNP	ENST00000301295.6	hg19	CCDS12936.1	.	.	.	.	.	.	.	.	.	.	C	12.16	1.853296	0.32699	.	.	ENSG00000160505	ENST00000301295;ENST00000346986	T;T	0.48836	0.8;0.8	3.91	3.91	0.45181	.	.	.	.	.	T	0.40448	0.1117	L	0.38175	1.15	0.09310	N	1	P;P;P	0.52170	0.715;0.84;0.951	B;B;B	0.42798	0.231;0.398;0.224	T	0.33059	-0.9883	9	0.87932	D	0	.	11.6309	0.51173	0.0:1.0:0.0:0.0	.	835;816;891	Q96MN2-2;Q96MN2-3;Q96MN2	.;.;NALP4_HUMAN	M	891;835	ENSP00000301295:T891M;ENSP00000344787:T835M	ENSP00000301295:T891M	T	+	2	0	NLRP4	61080320	0.020000	0.18652	0.017000	0.16124	0.002000	0.02628	3.378000	0.52432	2.195000	0.70347	0.585000	0.79938	ACG	.	.		0.473	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444		T	56388508	C	T	56388508	3	4	367	1	0	0	0	0	1	0	0	0	10488	536	19	1	2698	1	NLRP4	19	56388508	Missense_Mutation	SNP	C	TCGA-ZP-A9D1-01A-11D-A382-10	11454747	56388508	2740475	119	51054										
NINL	22981	hgsc.bcm.edu	37	chr20	25478971	25478971	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ttcaccttctcgtccacgctGaagtccaggctctggaagca	9	14	3	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr20:25478971G>T	ENST00000278886.6	-	9	1117	c.1044C>A	c.(1042-1044)ttC>ttA	p.F348L	NINL_ENST00000422516.1_Missense_Mutation_p.F348L	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	348					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|microtubule (GO:0005874)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(13)|lung(25)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	57						CGTCCACGCTGAAGTCCAGGC	0.612																																					p.F348L		Atlas-SNP	.											.	NINL	148	.	0			c.C1044A						.						79	58	65					20																	25478971		2203	4300	6503	SO:0001583	missense	22981	exon9			CACGCTGAAGTCC		CCDS33452.1	20p11.22-p11.1	2013-01-10			ENSG00000101004	ENSG00000101004		"EF-hand domain containing"	29163	protein-coding gene	gene with protein product	"ninein-like protein"	609580				10231032	Standard	XM_005260678		Approved	KIAA0980, NLP	uc002wux.1	Q9Y2I6	OTTHUMG00000032127	ENST00000278886.6:c.1044C>A	chr20.hg19:g.25478971G>T	ENSP00000278886:p.Phe348Leu	41.0	0.0		39.0	15.0	NM_025176	A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	Missense_Mutation	SNP	ENST00000278886.6	hg19	CCDS33452.1	.	.	.	.	.	.	.	.	.	.	G	16.85	3.235389	0.58886	.	.	ENSG00000101004	ENST00000278886;ENST00000422516	T;T	0.41758	1.24;0.99	5.12	3.19	0.36642	.	0.000000	0.85682	D	0.000000	T	0.54143	0.1840	M	0.79258	2.445	0.54753	D	0.999986	D;D	0.59767	0.986;0.966	P;P	0.56163	0.793;0.452	T	0.54721	-0.8251	10	0.52906	T	0.07	-18.4003	8.1315	0.31029	0.2501:0.0:0.7499:0.0	.	348;348	Q9Y2I6-2;Q9Y2I6	.;NINL_HUMAN	L	348	ENSP00000278886:F348L;ENSP00000410431:F348L	ENSP00000278886:F348L	F	-	3	2	NINL	25426971	0.998000	0.40836	0.786000	0.31890	0.664000	0.39144	2.510000	0.45468	0.754000	0.32968	-0.251000	0.11542	TTC	.	.		0.612	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078445.3	NM_025176		T	25478971	G	T	25478971	3	4	367	1	0	0	0	0	1	0	0	0	10429	1281	45	3	3168	3	NINL	20	25478971	Missense_Mutation	SNP	G	TCGA-ZP-A9D1-01A-11D-A382-10		25478971	37546549	120	51055										
C20orf185	359710	hgsc.bcm.edu	37	chr20	31643273	31643273	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	gtggtccctgcttctgctctGgggcctggcgactccatgcc	13	15	2	0			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr20:31643273G>T	ENST00000375494.3	+	1	44	c.44G>T	c.(43-45)tGg>tTg	p.W15L	AL121756.1_ENST00000579962.1_RNA	NM_182658.1	NP_872599.1	P59826	BPIB3_HUMAN	BPI fold containing family B, member 3	15	Leu-rich.				innate immune response (GO:0045087)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										CTTCTGCTCTGGGGCCTGGCG	0.607																																					p.W15L		Atlas-SNP	.											.	.	.	.	0			c.G44T						.						103	99	100					20																	31643273		2203	4300	6503	SO:0001583	missense	359710	exon1			TGCTCTGGGGCCT	AF549189	CCDS13212.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186190	ENSG00000186190		"BPI fold containing"	16178	protein-coding gene	gene with protein product		615717	"chromosome 20 open reading frame 185"	C20orf185		11971875, 21787333	Standard	NM_182658		Approved	dJ726C3.4, LPLUNC3, RYA3	uc002wym.1	P59826	OTTHUMG00000032234	ENST00000375494.3:c.44G>T	chr20.hg19:g.31643273G>T	ENSP00000364643:p.Trp15Leu	49.0	0.0		63.0	9.0	NM_182658	Q5TDX7	Missense_Mutation	SNP	ENST00000375494.3	hg19	CCDS13212.1	.	.	.	.	.	.	.	.	.	.	G	18.82	3.705141	0.68615	.	.	ENSG00000186190	ENST00000375494	T	0.01287	5.05	4.9	3.89	0.44902	.	0.426267	0.20041	N	0.100509	T	0.01353	0.0044	L	0.44542	1.39	0.28072	N	0.932555	B	0.26935	0.164	B	0.25405	0.06	T	0.42799	-0.9430	10	0.02654	T	1	-3.5556	9.5259	0.39165	0.0:0.0:0.7748:0.2252	.	15	P59826	BPIB3_HUMAN	L	15	ENSP00000364643:W15L	ENSP00000364643:W15L	W	+	2	0	BPIFB3	31106934	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.785000	0.38684	2.548000	0.85928	0.655000	0.94253	TGG	.	.		0.607	BPIFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078654.2	NM_182658		T	31643273	G	T	31643273	3	4	367	1	0	0	0	0	1	0	0	0	2099	1357	47	3	46	3	C20orf185	20	31643273	Missense_Mutation	SNP	G	TCGA-ZP-A9D1-01A-11D-A382-10	6164302	31643273	31382247	121	51056										
CBFA2T2	9139	hgsc.bcm.edu	37	chr20	32207337	32207337	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	tttcagaactcaacagtgacAattgaggaattccactgtaa	7	8	2	3			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr20:32207337A>G	ENST00000346541.3	+	5	999	c.462A>G	c.(460-462)acA>acG	p.T154T	CBFA2T2_ENST00000397800.1_Silent_p.T125T|CBFA2T2_ENST00000344201.3_Silent_p.T125T|CBFA2T2_ENST00000397798.2_Silent_p.T125T|CBFA2T2_ENST00000375279.2_Silent_p.T154T|CBFA2T2_ENST00000342704.6_Silent_p.T145T|CBFA2T2_ENST00000492345.1_Silent_p.T125T|CBFA2T2_ENST00000359606.3_Silent_p.T164T	NM_005093.3	NP_005084.1	O43439	MTG8R_HUMAN	core-binding factor, runt domain, alpha subunit 2; translocated to, 2	154	TAFH. {ECO:0000255|PROSITE- ProRule:PRU00440}.				epithelial cell differentiation (GO:0030855)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)	20						CAACAGTGACAATTGAGGAAT	0.328																																					p.T154T	Esophageal Squamous(174;142 1955 14837 21276 28041)	Atlas-SNP	.											.	CBFA2T2	93	.	0			c.A462G						.						80	82	81					20																	32207337		2203	4300	6503	SO:0001819	synonymous_variant	9139	exon5			AGTGACAATTGAG	AF052210	CCDS13221.1, CCDS46590.1	20q11	2007-01-29			ENSG00000078699	ENSG00000078699		"Zinc fingers, MYND-type"	1536	protein-coding gene	gene with protein product		603672				9790752	Standard	XM_006723886		Approved	MTGR1, ZMYND3	uc002wze.1	O43439	OTTHUMG00000032261	ENST00000346541.3:c.462A>G	chr20.hg19:g.32207337A>G		101.0	0.0		103.0	22.0	NM_005093	B2RAE6|F8W6D7|Q5TGE4|Q5TGE5|Q5TGE6|Q5TGE7|Q8IWF3|Q96B06|Q96L00|Q9H436|Q9UJP8|Q9UJP9|Q9UP24	Silent	SNP	ENST00000346541.3	hg19	CCDS13221.1																																																																																			.	.		0.328	CBFA2T2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078708.2	NM_001032999		G	32207337	A	G	32207337	2	3	367	1	0	0	0	0	0	0	0	1	2699	117	5	2		2	CBFA2T2	20	32207337	Silent	SNP	A	TCGA-ZP-A9D1-01A-11D-A382-10	564064	32207337	30818183	122	51057										
MYBL2	4605	hgsc.bcm.edu	37	chr20	42343871	42343871	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	cttcttgcaggccaagcccgAgaaggcagcagtggcccaga	13	13	1	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr20:42343871A>T	ENST00000217026.4	+	13	2049	c.1922A>T	c.(1921-1923)gAg>gTg	p.E641V	MYBL2_ENST00000396863.4_Missense_Mutation_p.E617V	NM_002466.2	NP_002457.1	P10244	MYBB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 2	641					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|spindle assembly involved in mitosis (GO:0090307)	Myb complex (GO:0031523)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	46		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			GCCAAGCCCGAGAAGGCAGCA	0.597																																					p.E641V		Atlas-SNP	.											.	MYBL2	82	.	0			c.A1922T						.						136	144	142					20																	42343871		2203	4300	6503	SO:0001583	missense	4605	exon13			AGCCCGAGAAGGC		CCDS13322.1, CCDS63276.1	20q13.1	2013-07-09	2013-07-09		ENSG00000101057	ENSG00000101057			7548	protein-coding gene	gene with protein product		601415				8812502	Standard	NM_002466		Approved	BMYB, B-MYB	uc002xlb.1	P10244	OTTHUMG00000033062	ENST00000217026.4:c.1922A>T	chr20.hg19:g.42343871A>T	ENSP00000217026:p.Glu641Val	247.0	0.0		233.0	90.0	NM_002466	B2RBS5|B7Z8D9|F8W6N6|Q53F07	Missense_Mutation	SNP	ENST00000217026.4	hg19	CCDS13322.1	.	.	.	.	.	.	.	.	.	.	a	9.604	1.129558	0.21041	.	.	ENSG00000101057	ENST00000396863;ENST00000217026	T;T	0.15256	2.44;2.44	4.43	4.43	0.53597	.	1.462090	0.04095	N	0.311925	T	0.22781	0.0550	L	0.55481	1.735	0.31788	N	0.630056	B;B	0.34103	0.018;0.437	B;B	0.35470	0.047;0.203	T	0.18304	-1.0341	10	0.28530	T	0.3	-17.0091	11.5313	0.50612	1.0:0.0:0.0:0.0	.	617;641	F8W6N6;P10244	.;MYBB_HUMAN	V	617;641	ENSP00000380072:E617V;ENSP00000217026:E641V	ENSP00000217026:E641V	E	+	2	0	MYBL2	41777285	1.000000	0.71417	0.947000	0.38551	0.111000	0.19643	4.033000	0.57282	1.772000	0.52199	0.398000	0.26397	GAG	.	.		0.597	MYBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080408.1	NM_002466		T	42343871	A	T	42343871	3	4	367	1	0	0	0	0	1	0	0	0	10019	304	11	4	1972	4	MYBL2	20	42343871	Missense_Mutation	SNP	A	TCGA-ZP-A9D1-01A-11D-A382-10	10136534	42343871	20681649	123	51058										
PHACTR3	116154	hgsc.bcm.edu	37	chr20	58348348	58348348	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ccccaggccaagccacactcTtccaagcctccagcatgaag	7	18	1	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr20:58348348T>C	ENST00000371015.1	+	6	1233	c.766T>C	c.(766-768)Ttc>Ctc	p.F256L	PHACTR3_ENST00000359926.3_Missense_Mutation_p.F253L|PHACTR3_ENST00000355648.4_Missense_Mutation_p.F215L|PHACTR3_ENST00000541461.1_Missense_Mutation_p.F215L|PHACTR3_ENST00000395636.2_Missense_Mutation_p.F215L|PHACTR3_ENST00000361300.4_Missense_Mutation_p.F145L|PHACTR3_ENST00000395639.4_Missense_Mutation_p.F145L	NM_001281507.1|NM_080672.3	NP_001268436.1|NP_542403.1	Q96KR7	PHAR3_HUMAN	phosphatase and actin regulator 3	256						nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|liver(2)|lung(32)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	59	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)			AGCCACACTCTTCCAAGCCTC	0.622																																					p.F256L		Atlas-SNP	.											.	PHACTR3	104	.	0			c.T766C						.						83	86	85					20																	58348348		2203	4300	6503	SO:0001583	missense	116154	exon6			ACACTCTTCCAAG	AJ311122	CCDS13480.1, CCDS13481.1, CCDS42895.1, CCDS56202.1	20q13.32-q13.33	2014-06-13	2004-05-20	2004-05-20	ENSG00000087495	ENSG00000087495		"Phosphatase and actin regulators"	15833	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 123"	608725	"chromosome 20 open reading frame 101"	C20orf101		15107502	Standard	NM_001199505		Approved	PPP1R123	uc002yau.3	Q96KR7	OTTHUMG00000032869	ENST00000371015.1:c.766T>C	chr20.hg19:g.58348348T>C	ENSP00000360054:p.Phe256Leu	127.0	0.0		110.0	27.0	NM_080672	B1AKX0|B1AN68|B1AN69|B2RB46|Q32P33|Q707P6|Q9H4T4	Missense_Mutation	SNP	ENST00000371015.1	hg19	CCDS13480.1	.	.	.	.	.	.	.	.	.	.	T	7.847	0.723123	0.15439	.	.	ENSG00000087495	ENST00000359926;ENST00000371015;ENST00000395639;ENST00000541461;ENST00000355648;ENST00000395636;ENST00000361300	T;T;T;T;T;T;T	0.27890	2.02;2.05;1.64;2.03;2.03;2.03;1.64	5.02	3.92	0.45320	.	0.325285	0.34777	N	0.003686	T	0.29126	0.0724	M	0.63428	1.95	0.43688	D	0.996137	B;B;B	0.15141	0.012;0.003;0.003	B;B;B	0.12156	0.007;0.002;0.004	T	0.05566	-1.0877	10	0.27785	T	0.31	-14.4625	9.7549	0.40498	0.0:0.0815:0.0:0.9185	.	145;256;253	Q96KR7-3;Q96KR7;B1AKX0	.;PHAR3_HUMAN;.	L	253;256;145;215;215;215;145	ENSP00000353002:F253L;ENSP00000360054:F256L;ENSP00000379001:F145L;ENSP00000442483:F215L;ENSP00000347866:F215L;ENSP00000378998:F215L;ENSP00000354555:F145L	ENSP00000347866:F215L	F	+	1	0	PHACTR3	57781743	1.000000	0.71417	0.991000	0.47740	0.029000	0.11900	4.287000	0.59001	0.767000	0.33267	0.533000	0.62120	TTC	.	.		0.622	PHACTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079923.3	NM_080672		C	58348348	T	C	58348348	3	2	367	1	0	0	0	0	1	0	0	0	11820	1609	56	2	788	2	PHACTR3	20	58348348	Missense_Mutation	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	16004477	58348348	4677172	124	51059										
B3GALT5	10317	hgsc.bcm.edu	37	chr21	41032874	41032874	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	atttcctagacgtctattacAatctgaccctgaagaccatg	6	11	2	4			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr21:41032874A>G	ENST00000380620.4	+	5	980	c.388A>G	c.(388-390)Aat>Gat	p.N130D	B3GALT5_ENST00000343118.4_Missense_Mutation_p.N130D|B3GALT5_ENST00000398714.2_Missense_Mutation_p.N130D|AF064860.5_ENST00000416555.1_RNA|B3GALT5_ENST00000380618.1_Missense_Mutation_p.N130D			Q9Y2C3	B3GT5_HUMAN	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 5	130					protein glycosylation (GO:0006486)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity (GO:0008499)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	16		Prostate(19;2.55e-06)				CGTCTATTACAATCTGACCCT	0.512																																					p.N130D		Atlas-SNP	.											.	B3GALT5	40	.	0			c.A388G						.						103	102	102					21																	41032874		2203	4300	6503	SO:0001583	missense	10317	exon3			TATTACAATCTGA	AB020337	CCDS13667.1, CCDS74795.1	21q22.3	2013-02-19			ENSG00000183778	ENSG00000183778		"Beta 3-glycosyltransferases"	920	protein-coding gene	gene with protein product	"homolog of C. elegans Bt toxin resistance gene bre-5", "GlcNAc-beta-1,3-galactosyltransferase 5"	604066				10212226	Standard	NM_006057		Approved	beta3Gal-T5, B3GalT-V, GLCT5, B3T5	uc002yyj.1	Q9Y2C3	OTTHUMG00000086725	ENST00000380620.4:c.388A>G	chr21.hg19:g.41032874A>G	ENSP00000369994:p.Asn130Asp	103.0	0.0		87.0	14.0	NM_033170	A8KA86|D3DSI3|Q2M3L5|Q53Z19|Q9NY96|Q9P1X6|Q9P1X7	Missense_Mutation	SNP	ENST00000380620.4	hg19	CCDS13667.1	.	.	.	.	.	.	.	.	.	.	A	18.21	3.574278	0.65878	.	.	ENSG00000183778	ENST00000380620;ENST00000380618;ENST00000343118;ENST00000398714	T;T;T;T	0.47869	0.83;0.83;0.83;0.83	5.72	5.72	0.89469	.	0.000000	0.64402	D	0.000001	T	0.79070	0.4384	H	0.96301	3.8	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.86091	0.1550	10	0.87932	D	0	.	16.0156	0.80439	1.0:0.0:0.0:0.0	.	130	Q9Y2C3	B3GT5_HUMAN	D	130	ENSP00000369994:N130D;ENSP00000369992:N130D;ENSP00000343318:N130D;ENSP00000381699:N130D	ENSP00000343318:N130D	N	+	1	0	B3GALT5	39954744	1.000000	0.71417	0.115000	0.21578	0.044000	0.14063	9.144000	0.94629	2.189000	0.69895	0.533000	0.62120	AAT	.	.		0.512	B3GALT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195008.2	NM_033170		G	41032874	A	G	41032874	3	3	367	1	0	0	0	0	1	0	0	0	1250	130	5	2	390	2	B3GALT5	21	41032874	Missense_Mutation	SNP	A	TCGA-ZP-A9D1-01A-11D-A382-10		41032874	7097021	125	51060										
MCM3AP	8888	hgsc.bcm.edu	37	chr21	47692553	47692553	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	cgctggcacagaagacacccTtgtttctcaggtcctggtac	10	13	1	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr21:47692553T>G	ENST00000397708.1	-	9	2641	c.2387A>C	c.(2386-2388)aAg>aCg	p.K796T	MCM3AP_ENST00000291688.1_Missense_Mutation_p.K796T			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	796	SAC3 homology.				DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					GAAGACACCCTTGTTTCTCAG	0.488																																					p.K796T		Atlas-SNP	.											.	MCM3AP	146	.	0			c.A2387C						.						184	161	169					21																	47692553		2203	4300	6503	SO:0001583	missense	8888	exon8			ACACCCTTGTTTC	AB005543	CCDS13734.1	21q22.3	2012-12-19	2007-04-04		ENSG00000160294	ENSG00000160294			6946	protein-coding gene	gene with protein product	"germinal-centre associated nuclear protein"	603294	"minichromosome maintenance deficient (S. cerevisiae) 3-associated protein", "MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein"			9712829, 16914116, 21195085	Standard	XM_005261205		Approved	Map80, KIAA0572, GANP, SAC3	uc002zir.1	O60318	OTTHUMG00000090630	ENST00000397708.1:c.2387A>C	chr21.hg19:g.47692553T>G	ENSP00000380820:p.Lys796Thr	103.0	0.0		89.0	21.0	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Missense_Mutation	SNP	ENST00000397708.1	hg19	CCDS13734.1	.	.	.	.	.	.	.	.	.	.	T	12.29	1.892968	0.33442	.	.	ENSG00000160294	ENST00000397708;ENST00000291688	T;T	0.03889	3.77;3.77	5.93	-3.45	0.04781	.	0.579934	0.20128	N	0.098660	T	0.06781	0.0173	L	0.46157	1.445	0.19775	N	0.99996	B	0.34399	0.452	P	0.45138	0.471	T	0.24512	-1.0158	10	0.52906	T	0.07	-5.7953	7.9937	0.30256	0.1151:0.451:0.0:0.4339	.	796	O60318	MCM3A_HUMAN	T	796	ENSP00000380820:K796T;ENSP00000291688:K796T	ENSP00000291688:K796T	K	-	2	0	MCM3AP	46516981	0.215000	0.23574	0.024000	0.17045	0.001000	0.01503	0.439000	0.21575	-0.619000	0.05648	-0.336000	0.08194	AAG	.	.		0.488	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906		G	47692553	T	G	47692553	3	3	367	1	0	0	0	0	1	0	0	0	9397	1609	56	5	3639	5	MCM3AP	21	47692553	Missense_Mutation	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	6659679	47692553	437342	126	51061										
CRYBB2	1415	hgsc.bcm.edu	37	chr22	25627596	25627596	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ttggctaccagtaccccggcTaccgtgggctgcagtacctg	12	14	0	0			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr22:25627596T>A	ENST00000398215.2	+	6	646	c.475T>A	c.(475-477)Tac>Aac	p.Y159N		NM_000496.2	NP_000487.1	P43320	CRBB2_HUMAN	crystallin, beta B2	159	Beta/gamma crystallin 'Greek key' 4. {ECO:0000255|PROSITE-ProRule:PRU00028}.				camera-type eye development (GO:0043010)|response to stimulus (GO:0050896)|visual perception (GO:0007601)		identical protein binding (GO:0042802)|structural constituent of eye lens (GO:0005212)|structural molecule activity (GO:0005198)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)	10						GTACCCCGGCTACCGTGGGCT	0.642																																					p.Y159N		Atlas-SNP	.											.	CRYBB2	18	.	0			c.T475A						.						93	89	91					22																	25627596		2203	4300	6503	SO:0001583	missense	1415	exon6			CCCGGCTACCGTG		CCDS13831.1	22q11.23	2008-06-10			ENSG00000244752	ENSG00000244752			2398	protein-coding gene	gene with protein product		123620		CCA2, CRYB2A, CRYB2		9158139, 8224918	Standard	XM_006724141		Approved		uc003abp.1	P43320	OTTHUMG00000150905	ENST00000398215.2:c.475T>A	chr22.hg19:g.25627596T>A	ENSP00000381273:p.Tyr159Asn	176.0	0.0		184.0	44.0	NM_000496	Q9UCM8	Missense_Mutation	SNP	ENST00000398215.2	hg19	CCDS13831.1	.	.	.	.	.	.	.	.	.	.	t	15.62	2.886049	0.51908	.	.	ENSG00000244752	ENST00000398215	D	0.82893	-1.66	4.22	4.22	0.49857	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.000000	0.85682	D	0.000000	D	0.94032	0.8088	H	0.98199	4.17	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95433	0.8518	10	0.87932	D	0	.	12.4953	0.55925	0.0:0.0:0.0:1.0	.	159	P43320	CRBB2_HUMAN	N	159	ENSP00000381273:Y159N	ENSP00000381273:Y159N	Y	+	1	0	CRYBB2	23957596	1.000000	0.71417	0.998000	0.56505	0.065000	0.16274	7.664000	0.83830	1.535000	0.49220	0.379000	0.24179	TAC	.	.		0.642	CRYBB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320350.1	NM_000496		A	25627596	T	A	25627596	3	1	367	1	0	0	0	0	1	0	0	0	3913	1522	53	4	493	4	CRYBB2	22	25627596	Missense_Mutation	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10		25627596	25676970	127	51062										
CHEK2	11200	hgsc.bcm.edu	37	chr22	29130702	29130702	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	gagcctcaacatccgactccCgagacatcacgacctcaaaa	6	16	3	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr22:29130702C>T	ENST00000405598.1	-	3	199	c.8G>A	c.(7-9)cGg>cAg	p.R3Q	CHEK2_ENST00000382578.1_Missense_Mutation_p.R3Q|CHEK2_ENST00000404276.1_Missense_Mutation_p.R3Q|CHEK2_ENST00000382565.1_Missense_Mutation_p.R3Q|CHEK2_ENST00000544772.1_5'UTR|CHEK2_ENST00000382566.1_Missense_Mutation_p.R3Q|CHEK2_ENST00000402731.1_Missense_Mutation_p.R3Q|CHEK2_ENST00000328354.6_Missense_Mutation_p.R3Q|CHEK2_ENST00000348295.3_Missense_Mutation_p.R3Q|CHEK2_ENST00000382580.2_Missense_Mutation_p.R3Q|CHEK2_ENST00000403642.1_Missense_Mutation_p.R3Q			O96017	CHK2_HUMAN	checkpoint kinase 2	3					cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						ATCCGACTCCCGAGACATCAC	0.493			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																													p.R3Q		Atlas-SNP	.	yes	Rec		familial breast cancer	22	22q12.1	11200	CHK2 checkpoint homolog (S. pombe)		E	.	CHEK2	438	.	0			c.G8A						.						79	69	72					22																	29130702		2203	4300	6503	SO:0001583	missense	11200	exon2			GACTCCCGAGACA	AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"CHK2 (checkpoint, S.pombe) homolog", "CHK2 checkpoint homolog (S. pombe)"	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.8G>A	chr22.hg19:g.29130702C>T	ENSP00000386087:p.Arg3Gln	52.0	0.0		55.0	20.0	NM_145862	A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Missense_Mutation	SNP	ENST00000405598.1	hg19	CCDS13843.1	.	.	.	.	.	.	.	.	.	.	C	14.43	2.532779	0.45073	.	.	ENSG00000183765	ENST00000348295;ENST00000382578;ENST00000382565;ENST00000382563;ENST00000382566;ENST00000328354;ENST00000404276;ENST00000405598;ENST00000382580;ENST00000403642;ENST00000402731;ENST00000447421;ENST00000439200;ENST00000398017	T;T;T;D;T;T;T;T;T;T;T;D;D	0.95205	0.57;-0.24;-0.4;-3.63;-0.4;-0.4;-0.4;-0.5;-0.24;0.57;0.01;-3.64;-2.7	4.4	1.14	0.20703	.	0.550725	0.19541	N	0.111799	D	0.83225	0.5208	N	0.14661	0.345	0.25501	N	0.987555	B;B;B;B;B;P	0.45672	0.012;0.011;0.001;0.005;0.001;0.864	B;B;B;B;B;B	0.32624	0.003;0.005;0.001;0.003;0.001;0.149	T	0.76416	-0.2967	10	0.20519	T	0.43	.	8.9181	0.35594	0.0:0.6733:0.0:0.3267	.	3;3;3;3;3;3	O96017-7;O96017-4;A8JZZ5;O96017-12;O96017;O96017-9	.;.;.;.;CHK2_HUMAN;.	Q	3;3;3;3;3;3;3;3;3;3;3;3;3;13	ENSP00000329012:R3Q;ENSP00000372021:R3Q;ENSP00000372006:R3Q;ENSP00000372007:R3Q;ENSP00000329178:R3Q;ENSP00000385747:R3Q;ENSP00000386087:R3Q;ENSP00000372023:R3Q;ENSP00000384919:R3Q;ENSP00000384835:R3Q;ENSP00000397478:R3Q;ENSP00000408065:R3Q;ENSP00000381099:R13Q	ENSP00000329178:R3Q	R	-	2	0	CHEK2	27460702	0.163000	0.22920	0.993000	0.49108	0.978000	0.69477	0.131000	0.15870	0.222000	0.20900	0.563000	0.77884	CGG	.	.		0.493	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735		T	29130702	C	T	29130702	3	4	367	1	0	0	0	0	1	0	0	0	3337	652	23	1	1812	1	CHEK2	22	29130702	Missense_Mutation	SNP	C	TCGA-ZP-A9D1-01A-11D-A382-10	3503106	29130702	22173864	128	51063										
HMGXB4	10042	hgsc.bcm.edu	37	chr22	35661318	35661318	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	agttagtgatagatgattctTaccgagaaatcaagaagaaa	9	4	2	6			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr22:35661318T>C	ENST00000216106.5	+	5	1065	c.937T>C	c.(937-939)Tac>Cac	p.Y313H	HMGXB4_ENST00000444518.2_Missense_Mutation_p.Y204H	NM_001003681.2	NP_001003681.1	Q9UGU5	HMGX4_HUMAN	HMG box domain containing 4	313					endosome to lysosome transport (GO:0008333)|negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)	NURF complex (GO:0016589)	DNA binding (GO:0003677)			breast(1)|endometrium(1)|large_intestine(6)|liver(1)|lung(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						AGATGATTCTTACCGAGAAAT	0.418																																					p.Y313H		Atlas-SNP	.											.	HMGXB4	52	.	0			c.T937C						.						67	72	70					22																	35661318		2203	4300	6503	SO:0001583	missense	10042	exon5			GATTCTTACCGAG	AJ010069	CCDS33641.1	22q13	2011-07-01	2009-01-05	2009-01-05	ENSG00000100281	ENSG00000100281		"High mobility group / Non-canonical"	5003	protein-coding gene	gene with protein product		604702	"high-mobility group protein 2-like 1"	HMG2L1		10329004, 10591208, 20511232	Standard	NM_001003681		Approved	THC211630	uc003anl.3	Q9UGU5	OTTHUMG00000150439	ENST00000216106.5:c.937T>C	chr22.hg19:g.35661318T>C	ENSP00000216106:p.Tyr313His	151.0	0.0		153.0	27.0	NM_001003681	O75672|O75673|Q9UMT5	Missense_Mutation	SNP	ENST00000216106.5	hg19	CCDS33641.1	.	.	.	.	.	.	.	.	.	.	T	19.80	3.894945	0.72639	.	.	ENSG00000100281	ENST00000420166;ENST00000444518;ENST00000455359;ENST00000216106	T;T;T;T	0.63744	-0.05;2.0;-0.06;2.01	6.01	6.01	0.97437	.	0.360991	0.33382	N	0.004971	T	0.69433	0.3110	L	0.29908	0.895	0.44316	D	0.997197	D	0.76494	0.999	D	0.66196	0.942	T	0.72701	-0.4214	10	0.72032	D	0.01	-15.5509	16.5285	0.84344	0.0:0.0:0.0:1.0	.	313	Q9UGU5	HMGX4_HUMAN	H	204;204;204;313	ENSP00000401658:Y204H;ENSP00000398302:Y204H;ENSP00000415500:Y204H;ENSP00000216106:Y313H	ENSP00000216106:Y313H	Y	+	1	0	HMGXB4	33991318	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.940000	0.75917	2.307000	0.77673	0.528000	0.53228	TAC	.	.		0.418	HMGXB4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318104.2	NM_005487		C	35661318	T	C	35661318	3	2	367	1	0	0	0	0	1	0	0	0	7248	1754	61	2	951	2	HMGXB4	22	35661318	Missense_Mutation	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	6530616	35661318	15643248	129	51064										
SREBF2	6721	hgsc.bcm.edu	37	chr22	42280874	42280874	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	cctgcaggatccgcctgttcCgatgtacacatggcgttgtg	12	12	0	0	rs200493376		TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chr22:42280874C>T	ENST00000361204.4	+	11	2233	c.2067C>T	c.(2065-2067)tcC>tcT	p.S689S		NM_004599.2	NP_004590.2	Q12772	SRBP2_HUMAN	sterol regulatory element binding transcription factor 2	689					cellular lipid metabolic process (GO:0044255)|cellular response to laminar fluid shear stress (GO:0071499)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cholesterol homeostasis (GO:2000188)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|response to low-density lipoprotein particle (GO:0055098)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SREBP-SCAP-Insig complex (GO:0032937)	E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(6)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	38						CCGCCTGTTCCGATGTACACA	0.537																																					p.S689S		Atlas-SNP	.											.	SREBF2	99	.	0			c.C2067T						.						114	93	100					22																	42280874		2203	4300	6503	SO:0001819	synonymous_variant	6721	exon11			CTGTTCCGATGTA	U02031	CCDS14023.1	22q13.2	2013-05-21			ENSG00000198911	ENSG00000198911		"Basic helix-loop-helix proteins"	11290	protein-coding gene	gene with protein product		600481				7903453	Standard	NM_004599		Approved	SREBP2, bHLHd2	uc003bbi.3	Q12772	OTTHUMG00000151261	ENST00000361204.4:c.2067C>T	chr22.hg19:g.42280874C>T		122.0	0.0		116.0	26.0	NM_004599	Q05BD5|Q6GTH7|Q86V36|Q9UH04	Silent	SNP	ENST00000361204.4	hg19	CCDS14023.1																																																																																			.	C|0.999;T|0.001		0.537	SREBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321956.1	NM_004599		T	42280874	C	T	42280874	2	4	367	1	0	0	0	0	0	0	0	1	15157	639	23	1		1	SREBF2	22	42280874	Silent	SNP	C	TCGA-ZP-A9D1-01A-11D-A382-10	6619556	42280874	9023692	130	51065										
FRMPD4	9758	hgsc.bcm.edu	37	chrX	12516855	12516855	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	gggaacctggggcttgagccAggtgccgccctatggatggg	18	10	0	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chrX:12516855A>T	ENST00000380682.1	+	2	604	c.98A>T	c.(97-99)cAg>cTg	p.Q33L		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	33	WW. {ECO:0000255|PROSITE- ProRule:PRU00224}.				positive regulation of synapse structural plasticity (GO:0051835)	cytoskeleton (GO:0005856)|dendritic spine (GO:0043197)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						GGCTTGAGCCAGGTGCCGCCC	0.517																																					p.Q33L		Atlas-SNP	.											.	FRMPD4	214	.	0			c.A98T						.						64	61	62					X																	12516855		2203	4300	6503	SO:0001583	missense	9758	exon2			TGAGCCAGGTGCC	AB002314	CCDS35201.1	Xp22.31	2006-02-09	2006-02-09	2006-02-09	ENSG00000169933	ENSG00000169933			29007	protein-coding gene	gene with protein product		300838	"PDZ domain containing 10"	PDZK10, PDZD10		9205841	Standard	NM_014728		Approved	KIAA0316	uc004cuz.2	Q14CM0	OTTHUMG00000021138	ENST00000380682.1:c.98A>T	chrX.hg19:g.12516855A>T	ENSP00000370057:p.Gln33Leu	197.0	0.0		233.0	92.0	NM_014728	A8K0X9|O15032	Missense_Mutation	SNP	ENST00000380682.1	hg19	CCDS35201.1	.	.	.	.	.	.	.	.	.	.	A	16.00	2.999598	0.54147	.	.	ENSG00000169933	ENST00000380682;ENST00000429478;ENST00000304087	T	0.06218	3.33	5.13	5.13	0.70059	WW/Rsp5/WWP (1);	0.081862	0.49305	D	0.000141	T	0.15262	0.0368	L	0.54323	1.7	0.44337	D	0.997229	D;B	0.57257	0.979;0.061	P;B	0.54270	0.747;0.018	T	0.00412	-1.1755	10	0.62326	D	0.03	.	14.3389	0.66611	1.0:0.0:0.0:0.0	.	25;33	B7ZLE1;Q14CM0	.;FRPD4_HUMAN	L	33;24;22	ENSP00000370057:Q33L	ENSP00000304583:Q22L	Q	+	2	0	FRMPD4	12426776	1.000000	0.71417	1.000000	0.80357	0.814000	0.46013	7.978000	0.88095	1.834000	0.53371	0.486000	0.48141	CAG	.	.		0.517	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055771.1	XM_045712		T	12516855	A	T	12516855	3	4	367	1	0	0	0	0	1	0	0	0	6067	188	7	4	104	4	FRMPD4	23	12516855	Missense_Mutation	SNP	A	TCGA-ZP-A9D1-01A-11D-A382-10		12516855	142753705	131	51066										
PDHA1	5160	hgsc.bcm.edu	37	chrX	19367462	19367462	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	ctggtagcatcccgtaatttTgcaaatgatgctacatttga	8	8	0	2			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chrX:19367462T>G	ENST00000422285.2	+	2	195	c.90T>G	c.(88-90)ttT>ttG	p.F30L	PDHA1_ENST00000545074.1_Missense_Mutation_p.F30L|PDHA1_ENST00000379806.5_Missense_Mutation_p.F68L|PDHA1_ENST00000379805.3_Missense_Mutation_p.F30L|PDHA1_ENST00000540249.1_Missense_Mutation_p.F30L			P08559	ODPA_HUMAN	pyruvate dehydrogenase (lipoamide) alpha 1	30					acetyl-CoA biosynthetic process from pyruvate (GO:0006086)|cellular metabolic process (GO:0044237)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|pyruvate dehydrogenase complex (GO:0045254)	pyruvate dehydrogenase (acetyl-transferring) activity (GO:0004739)|pyruvate dehydrogenase activity (GO:0004738)			endometrium(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)	18	Hepatocellular(33;0.183)					CCCGTAATTTTGCAAATGATG	0.299																																					p.F68L		Atlas-SNP	.											.	PDHA1	85	.	0			c.T204G						.						81	72	75					X																	19367462		2203	4300	6503	SO:0001583	missense	5160	exon3			TAATTTTGCAAAT		CCDS14192.1, CCDS55380.1, CCDS55381.1, CCDS55382.1	Xp22.1	2008-02-05			ENSG00000131828	ENSG00000131828	1.2.4.1		8806	protein-coding gene	gene with protein product		300502		PDHA			Standard	NM_001173454		Approved		uc004czh.4	P08559	OTTHUMG00000021224	ENST00000422285.2:c.90T>G	chrX.hg19:g.19367462T>G	ENSP00000394382:p.Phe30Leu	349.0	0.0		354.0	104.0	NM_001173454	A5YVE9|B2R5P7|B7Z3T7|B7Z3X5|Q53H41|Q5JPT8|Q9NP12|Q9UBJ8|Q9UBU0|Q9UNG4|Q9UNG5	Missense_Mutation	SNP	ENST00000422285.2	hg19	CCDS14192.1	.	.	.	.	.	.	.	.	.	.	T	14.48	2.547046	0.45383	.	.	ENSG00000131828	ENST00000379806;ENST00000545074;ENST00000540249;ENST00000423505;ENST00000417819;ENST00000422285;ENST00000355808;ENST00000379815;ENST00000379805	D;D;D;D;D;D;D;D	0.98633	-4.55;-4.5;-4.37;-4.72;-3.2;-4.54;-5.04;-4.86	5.31	1.54	0.23209	.	0.106752	0.64402	D	0.000004	D	0.95837	0.8645	L	0.50333	1.59	0.46061	D	0.998846	B;B;B;B;B	0.22003	0.017;0.063;0.016;0.052;0.016	B;B;B;B;B	0.18263	0.021;0.011;0.008;0.016;0.008	D	0.90506	0.4477	10	0.11794	T	0.64	-27.1807	9.3325	0.38030	0.0:0.297:0.0:0.703	.	30;30;30;68;30	B7Z3X5;B7Z3T7;B2R5P7;A5YVE9;P08559	.;.;.;.;ODPA_HUMAN	L	68;30;30;68;58;30;30;58;30	ENSP00000369134:F68L;ENSP00000438550:F30L;ENSP00000440761:F30L;ENSP00000406473:F68L;ENSP00000404616:F58L;ENSP00000394382:F30L;ENSP00000348062:F30L;ENSP00000369133:F30L	ENSP00000348062:F30L	F	+	3	2	PDHA1	19277383	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.852000	0.27764	0.245000	0.21373	0.486000	0.48141	TTT	.	.		0.299	PDHA1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055977.1			G	19367462	T	G	19367462	3	3	367	1	0	0	0	0	1	0	0	0	11673	1809	63	5	214	5	PDHA1	23	19367462	Missense_Mutation	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	6850607	19367462	135903098	132	51067										
ARR3	407	hgsc.bcm.edu	37	chrX	69497340	69497340	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	atccgccgcttccttctgtcAgctcagcccctacaactcca	5	19	3	0			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chrX:69497340A>T	ENST00000307959.8	+	9	621	c.570A>T	c.(568-570)tcA>tcT	p.S190S	ARR3_ENST00000374495.3_Silent_p.S190S	NM_004312.2	NP_004303.2	P36575	ARRC_HUMAN	arrestin 3, retinal (X-arrestin)	190					endocytosis (GO:0006897)|regulation of protein phosphorylation (GO:0001932)|signal transduction (GO:0007165)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|synapse (GO:0045202)				endometrium(3)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|skin(1)	16						TCCTTCTGTCAGCTCAGCCCC	0.597																																					p.S190S		Atlas-SNP	.											.	ARR3	41	.	0			c.A570T						.						54	49	51					X																	69497340		2203	4300	6503	SO:0001819	synonymous_variant	407	exon9			TCTGTCAGCTCAG		CCDS14399.1	Xq13.1	2013-10-11			ENSG00000120500	ENSG00000120500			710	protein-coding gene	gene with protein product	"arrestin 4"	301770				8224247	Standard	NM_004312		Approved	ARRX	uc004dyb.2	P36575	OTTHUMG00000021768	ENST00000307959.8:c.570A>T	chrX.hg19:g.69497340A>T		337.0	1.0		388.0	119.0	NM_004312	B5B0B9|Q5JT23|Q5JT24|Q6IBF5|Q96EN2	Silent	SNP	ENST00000307959.8	hg19	CCDS14399.1																																																																																			.	.		0.597	ARR3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057055.2	NM_004312		T	69497340	A	T	69497340	2	4	367	1	0	0	0	0	0	0	0	1	979	175	7	4		4	ARR3	23	69497340	Silent	SNP	A	TCGA-ZP-A9D1-01A-11D-A382-10	50129878	69497340	85773220	133	51068										
CUL4B	8450	hgsc.bcm.edu	37	chrX	119677623	119677623	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	gtaataagtctgtctgcttcTtcttctagacgtttgttaac	7	8	5	1			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chrX:119677623T>C	ENST00000404115.3	-	10	1670	c.1269A>G	c.(1267-1269)gaA>gaG	p.E423E	snoU13_ENST00000605987.1_RNA|CUL4B_ENST00000371322.5_Silent_p.E405E|CUL4B_ENST00000336592.6_Silent_p.E410E	NM_003588.3	NP_003579.3	Q13620	CUL4B_HUMAN	cullin 4B	423					cell cycle (GO:0007049)|histone H2A monoubiquitination (GO:0035518)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of protein catabolic process (GO:0045732)|ubiquitin-dependent protein catabolic process (GO:0006511)|UV-damage excision repair (GO:0070914)	Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						TGTCTGCTTCTTCTTCTAGAC	0.343																																					p.E423E		Atlas-SNP	.											.	CUL4B	181	.	0			c.A1269G						.						252	243	246					X																	119677623		2203	4300	6503	SO:0001819	synonymous_variant	8450	exon10			TGCTTCTTCTTCT	U58091	CCDS35379.1, CCDS43987.1	Xq23	2011-05-24			ENSG00000158290	ENSG00000158290			2555	protein-coding gene	gene with protein product		300304				8681378	Standard	NM_003588		Approved		uc004esw.3	Q13620	OTTHUMG00000022302	ENST00000404115.3:c.1269A>G	chrX.hg19:g.119677623T>C		144.0	0.0		153.0	50.0	NM_003588	B1APK5|B3KVX4|B7Z5K8|Q6PIE4|Q6UP07|Q7Z673|Q9BY37|Q9UEB7|Q9UED7	Silent	SNP	ENST00000404115.3	hg19	CCDS35379.1																																																																																			.	.		0.343	CUL4B-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058103.1	NM_003588		C	119677623	T	C	119677623	2	2	367	1	0	0	0	0	0	0	0	1	4060	1606	56	2		2	CUL4B	23	119677623	Silent	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	50180283	119677623	35592937	134	51069										
SLITRK2	84631	hgsc.bcm.edu	37	chrX	144905172	144905172	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	actgcacttaggaaacaacaGgattgcagtcattcaggaag	10	8	2	0			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chrX:144905172G>T	ENST00000370490.1	+	1	5484	c.1229G>T	c.(1228-1230)aGg>aTg	p.R410M	SLITRK2_ENST00000434188.2_Missense_Mutation_p.R410M|SLITRK2_ENST00000413937.2_Missense_Mutation_p.R410M|SLITRK2_ENST00000447897.2_Missense_Mutation_p.R410M|SLITRK2_ENST00000428560.2_Missense_Mutation_p.R410M			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	410					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					GGAAACAACAGGATTGCAGTC	0.398																																					p.R410M		Atlas-SNP	.											.	SLITRK2	221	.	0			c.G1229T						.						112	107	108					X																	144905172		2203	4300	6503	SO:0001583	missense	84631	exon5			ACAACAGGATTGC	Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"slit-like 1 (Drosophila)"	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.1229G>T	chrX.hg19:g.144905172G>T	ENSP00000359521:p.Arg410Met	229.0	0.0		229.0	66.0	NM_001144005	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Missense_Mutation	SNP	ENST00000370490.1	hg19	CCDS14680.1	.	.	.	.	.	.	.	.	.	.	G	19.12	3.765441	0.69878	.	.	ENSG00000185985	ENST00000335565;ENST00000447897;ENST00000370490;ENST00000434188;ENST00000413937;ENST00000428560	T;T;T;T;T;T	0.60672	0.17;0.17;0.17;0.17;0.17;0.17	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.73721	0.3623	M	0.64997	1.995	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.76545	-0.2920	10	0.87932	D	0	-7.9199	15.6062	0.76672	0.0:0.0:1.0:0.0	.	410	Q9H156	SLIK2_HUMAN	M	410	ENSP00000334374:R410M;ENSP00000411681:R410M;ENSP00000359521:R410M;ENSP00000397015:R410M;ENSP00000407347:R410M;ENSP00000412010:R410M	ENSP00000334374:R410M	R	+	2	0	SLITRK2	144712864	1.000000	0.71417	0.998000	0.56505	0.860000	0.49131	9.869000	0.99810	2.280000	0.76307	0.594000	0.82650	AGG	.	.		0.398	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539		T	144905172	G	T	144905172	3	4	367	1	0	0	0	0	1	0	0	0	14758	1000	35	3	1231	3	SLITRK2	23	144905172	Missense_Mutation	SNP	G	TCGA-ZP-A9D1-01A-11D-A382-10	25227549	144905172	10365388	135	51070										
SLITRK2	84631	hgsc.bcm.edu	37	chrX	144906450	144906450	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0367647058823529	5	1	1.15063097821719	1.89854111405836	0.911299734748011	1	1	0	accggactacctcgaagttcTggaaaaacaaactgcaatca	7	11	2	0			TCGA-ZP-A9D1-01A-11D-A382-10	TCGA-ZP-A9D1-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2460c441-afaf-48ea-b29d-e1ec16a2b246	a8172d2a-1255-4865-938b-5a96f7faf691	g.chrX:144906450T>A	ENST00000370490.1	+	1	6762	c.2507T>A	c.(2506-2508)cTg>cAg	p.L836Q	SLITRK2_ENST00000434188.2_Missense_Mutation_p.L836Q|SLITRK2_ENST00000413937.2_Missense_Mutation_p.L836Q|SLITRK2_ENST00000447897.2_Missense_Mutation_p.L836Q|TMEM257_ENST00000408967.2_5'Flank|SLITRK2_ENST00000428560.2_Missense_Mutation_p.L836Q			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	836					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					CTCGAAGTTCTGGAAAAACAA	0.463																																					p.L836Q		Atlas-SNP	.											.	SLITRK2	221	.	0			c.T2507A						.						58	54	56					X																	144906450		2203	4300	6503	SO:0001583	missense	84631	exon5			AAGTTCTGGAAAA	Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"slit-like 1 (Drosophila)"	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.2507T>A	chrX.hg19:g.144906450T>A	ENSP00000359521:p.Leu836Gln	388.0	0.0		454.0	145.0	NM_001144005	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Missense_Mutation	SNP	ENST00000370490.1	hg19	CCDS14680.1	.	.	.	.	.	.	.	.	.	.	T	19.33	3.806306	0.70682	.	.	ENSG00000185985	ENST00000447897;ENST00000370490;ENST00000434188;ENST00000413937;ENST00000428560	T;T;T;T;T	0.72505	-0.66;-0.66;-0.66;-0.66;-0.66	5.38	5.38	0.77491	.	0.000000	0.64402	D	0.000004	T	0.81631	0.4863	M	0.65498	2.005	0.80722	D	1	D	0.76494	0.999	D	0.75484	0.986	D	0.83586	0.0120	10	0.87932	D	0	-4.179	12.2755	0.54733	0.0:0.0:0.0:1.0	.	836	Q9H156	SLIK2_HUMAN	Q	836	ENSP00000411681:L836Q;ENSP00000359521:L836Q;ENSP00000397015:L836Q;ENSP00000407347:L836Q;ENSP00000412010:L836Q	ENSP00000359521:L836Q	L	+	2	0	SLITRK2	144714142	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	1.803000	0.52742	0.486000	0.48141	CTG	.	.		0.463	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539		A	144906450	T	A	144906450	3	1	367	1	0	0	0	0	1	0	0	0	14758	1580	55	4	2509	4	SLITRK2	23	144906450	Missense_Mutation	SNP	T	TCGA-ZP-A9D1-01A-11D-A382-10	1278	144906450	10364110	136	51071										
ST6GALNAC5	81849	hgsc.bcm.edu	37	chr1	77334301	77334301	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	cagcagcagcagcagcagcaAcagcagcagcaggcgtcggc	14	14	0	0			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr1:77334301A>G	ENST00000477717.1	+	2	370	c.135A>G	c.(133-135)caA>caG	p.Q45Q	ST6GALNAC5_ENST00000496845.1_3'UTR	NM_030965.1	NP_112227.1	Q9BVH7	SIA7E_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	45	Poly-Gln.				glycosphingolipid biosynthetic process (GO:0006688)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	integral component of Golgi membrane (GO:0030173)	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity (GO:0001665)|sialyltransferase activity (GO:0008373)			endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	18						agcagcagcaacagcagcagc	0.716																																					p.Q45Q		Atlas-SNP	.											.	ST6GALNAC5	59	.	0			c.A135G						.						11	12	12					1																	77334301		2032	3963	5995	SO:0001819	synonymous_variant	81849	exon2			GCAGCAACAGCAG		CCDS673.1	1p31.1	2013-03-01	2005-02-07	2005-02-07	ENSG00000117069	ENSG00000117069		"Sialyltransferases"	19342	protein-coding gene	gene with protein product		610134	"sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) E"	SIAT7E		10521438, 10601645	Standard	NM_030965		Approved	MGC3184, ST6GalNAcV	uc001dhi.3	Q9BVH7	OTTHUMG00000009687	ENST00000477717.1:c.135A>G	chr1.hg19:g.77334301A>G		141.0	0.0		156.0	8.0	NM_030965	B1AK82	Silent	SNP	ENST00000477717.1	hg19	CCDS673.1																																																																																			.	.		0.716	ST6GALNAC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026692.2	NM_030965		G	77334301	A	G	77334301	2	3	368	1	0	0	0	0	0	0	0	1	15242	40	2	2		2	ST6GALNAC5	1	77334301	Silent	SNP	A	TCGA-ZP-A9D2-01A-11D-A382-10		77334301	171916320	1	51072										
CTTNBP2NL	55917	hgsc.bcm.edu	37	chr1	112999349	112999364	+	Frame_Shift_Del	DEL	CACTGTCTCCCAGCAG	CACTGTCTCCCAGCAG	-													0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	cctctcttccagtgggagctCactgtctcccagcagcactg							TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	CACTGTCTCCCAGCAG	CACTGTCTCCCAGCAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr1:112999349_112999364delCACTGTCTCCCAGCAG	ENST00000271277.6	+	6	1460_1475	c.1235_1250delCACTGTCTCCCAGCAG	c.(1234-1251)tcactgtctcccagcagcfs	p.SLSPSS412fs		NM_018704.2	NP_061174.1	Q9P2B4	CT2NL_HUMAN	CTTNBP2 N-terminal like	412					negative regulation of transmembrane transport (GO:0034763)|negative regulation of transporter activity (GO:0032410)|protein dephosphorylation (GO:0006470)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	protein phosphatase 2A binding (GO:0051721)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	29		all_cancers(81;0.00064)|all_epithelial(167;0.000415)|all_lung(203;0.00045)|Lung NSC(69;0.000705)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		AGTGGGAGCTCACTGTCTCCCAGCAGCACTGCCTCC	0.569																																					p.412_417del		Atlas-INDEL	.											.	CTTNBP2NL	65	.	0			c.1234_1249del						.																																			SO:0001589	frameshift_variant	55917	exon6			.	AB037854	CCDS845.1	1p13.2	2008-02-05			ENSG00000143079	ENSG00000143079			25330	protein-coding gene	gene with protein product		615100				10718198	Standard	NM_018704		Approved	DKFZp547A023	uc001ebx.3	Q9P2B4	OTTHUMG00000011154	ENST00000271277.6:c.1235_1250delCACTGTCTCCCAGCAG	chr1.hg19:g.112999349_112999364delCACTGTCTCCCAGCAG	ENSP00000271277:p.Ser412fs	103.0	0.0		60.0	28.0	NM_018704	B3KMS5|Q96B40	Frame_Shift_Del	DEL	ENST00000271277.6	hg19	CCDS845.1																																																																																			.	.		0.569	CTTNBP2NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030686.1	NM_018704		-	112999364	CACTGTCTCCCAGCAG	-	112999349	7	5	368	1	0	1	0	1	0	0	0	0	4048	838	29	0	1249	0	CTTNBP2NL	1	112999349	Frame_Shift_Del	DEL	CACTGTCTCCCAGCAG	TCGA-ZP-A9D2-01A-11D-A382-10	35665048	112999349	136251272	2	51073										
ARHGEF11	9826	hgsc.bcm.edu	37	chr1	156918128	156918128	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	cacctggtggagaggctggaGgtagaggacgaggctgactg	19	7	0	3			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr1:156918128G>A	ENST00000361409.2	-	22	2710	c.1968C>T	c.(1966-1968)acC>acT	p.T656T	ARHGEF11_ENST00000368194.3_Silent_p.T696T|ARHGEF11_ENST00000487682.1_5'Flank|ARHGEF11_ENST00000315174.8_Silent_p.T72T	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	656					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cytokinesis (GO:0000910)|establishment of cell polarity (GO:0030010)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)|striated muscle contraction (GO:0006941)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(27)|ovary(4)|pancreas(2)|pleura(1)|prostate(4)|skin(7)|stomach(1)|urinary_tract(2)	81	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					AGAGGCTGGAGGTAGAGGACG	0.612																																					p.T696T		Atlas-SNP	.											.	ARHGEF11	168	.	0			c.C2088T						.						97	85	89					1																	156918128		2203	4300	6503	SO:0001819	synonymous_variant	9826	exon23			GCTGGAGGTAGAG	AB002378	CCDS1162.1, CCDS1163.1	1q21	2011-11-16			ENSG00000132694	ENSG00000132694		"Rho guanine nucleotide exchange factors"	14580	protein-coding gene	gene with protein product		605708				10526156, 9205841	Standard	NM_014784		Approved	KIAA0380, GTRAP48, PDZ-RHOGEF	uc001fqn.3	O15085	OTTHUMG00000041292	ENST00000361409.2:c.1968C>T	chr1.hg19:g.156918128G>A		113.0	0.0		146.0	22.0	NM_198236	D3DVD0|Q5VY40|Q6PFW2	Silent	SNP	ENST00000361409.2	hg19	CCDS1162.1																																																																																			.	.		0.612	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236		A	156918128	G	A	156918128	2	1	368	1	0	0	0	0	0	0	0	1	896	987	35	3		3	ARHGEF11	1	156918128	Silent	SNP	G	TCGA-ZP-A9D2-01A-11D-A382-10	43918779	156918128	92332493	3	51074										
DCAF6	55827	hgsc.bcm.edu	37	chr1	167944101	167944101	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	ttcgttcagggcaccgagcaAacatatttagtgcaaagttc	9	9	1	0			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr1:167944101A>G	ENST00000312263.6	+	4	490	c.286A>G	c.(286-288)Aac>Gac	p.N96D	DCAF6_ENST00000367843.3_Missense_Mutation_p.N96D|DCAF6_ENST00000470919.1_3'UTR|DCAF6_ENST00000367840.3_Missense_Mutation_p.N96D|DCAF6_ENST00000432587.2_Missense_Mutation_p.N65D	NM_001017977.2	NP_001017977.1	Q58WW2	DCAF6_HUMAN	DDB1 and CUL4 associated factor 6	96					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	36						GCACCGAGCAAACATATTTAG	0.328																																					p.N96D		Atlas-SNP	.											.	DCAF6	99	.	0			c.A286G						.						103	98	100					1																	167944101		2203	4300	6503	SO:0001583	missense	55827	exon4			CGAGCAAACATAT	AL136738	CCDS1267.2, CCDS30933.1, CCDS55657.1, CCDS55658.1	1q23.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000143164	ENSG00000143164		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	30002	protein-coding gene	gene with protein product		610494	"IQ motif and WD repeats 1"	IQWD1		12032826	Standard	NM_018442		Approved	PC326	uc001gex.3	Q58WW2	OTTHUMG00000034572	ENST00000312263.6:c.286A>G	chr1.hg19:g.167944101A>G	ENSP00000311949:p.Asn96Asp	431.0	0.0		590.0	299.0	NM_001198956	A2A295|B4DNB8|Q7L8I0|Q8IXH3|Q8TB19	Missense_Mutation	SNP	ENST00000312263.6	hg19	CCDS30933.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.694303	0.88830	.	.	ENSG00000143164	ENST00000367843;ENST00000432587;ENST00000312263;ENST00000367840	T;T;T;T	0.81078	-1.45;-1.45;-1.45;-1.45	4.92	4.92	0.64577	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.099690	0.64402	D	0.000003	D	0.89396	0.6703	M	0.89478	3.035	0.80722	D	1.000000	D;D;D;D	0.76494	0.999;0.998;0.999;0.997	D;D;D;D	0.85130	0.995;0.991;0.997;0.981	D	0.91879	0.5514	9	0.87932	D	0	.	14.8612	0.70382	1.0:0.0:0.0:0.0	.	65;96;96;96	B4DNB8;Q58WW2-3;Q58WW2;Q58WW2-2	.;.;DCAF6_HUMAN;.	D	96;65;96;96	ENSP00000356817:N96D;ENSP00000396238:N65D;ENSP00000311949:N96D;ENSP00000356814:N96D	ENSP00000311949:N96D	N	+	1	0	DCAF6	166210725	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.648000	0.91062	1.954000	0.56735	0.454000	0.30748	AAC	.	.		0.328	DCAF6-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083661.2	NM_018442		G	167944101	A	G	167944101	3	3	368	1	0	0	0	0	1	0	0	0	4276	14	1	2	300	2	DCAF6	1	167944101	Missense_Mutation	SNP	A	TCGA-ZP-A9D2-01A-11D-A382-10	11025973	167944101	81306520	4	51075										
KIFAP3	22920	hgsc.bcm.edu	37	chr1	170003616	170003616	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	ccaattttatagtgagtaatAagtccatgaaattgagaaaa	7	4	0	3			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr1:170003616A>T	ENST00000361580.2	-	7	866	c.639T>A	c.(637-639)ctT>ctA	p.L213L	KIFAP3_ENST00000367767.1_Silent_p.L169L|KIFAP3_ENST00000490550.1_5'Flank|KIFAP3_ENST00000367765.1_Silent_p.L173L|KIFAP3_ENST00000538366.1_Silent_p.L135L	NM_014970.3	NP_055785.2	Q92845	KIFA3_HUMAN	kinesin-associated protein 3	213					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|membrane organization (GO:0061024)|microtubule-based movement (GO:0007018)|microtubule-based process (GO:0007017)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|plus-end-directed vesicle transport along microtubule (GO:0072383)|positive regulation of calcium-dependent cell-cell adhesion (GO:0046587)|protein complex assembly (GO:0006461)|protein localization (GO:0008104)|signal transduction (GO:0007165)	centrosome (GO:0005813)|condensed nuclear chromosome (GO:0000794)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|intraciliary transport particle (GO:0030990)|kinesin II complex (GO:0016939)|microtubule cytoskeleton (GO:0015630)	kinesin binding (GO:0019894)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(18)|prostate(2)|skin(3)|urinary_tract(2)	35	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					AGTGAGTAATAAGTCCATGAA	0.294																																					p.L213L		Atlas-SNP	.											.	KIFAP3	102	.	0			c.T639A						.						55	54	54					1																	170003616		2202	4295	6497	SO:0001819	synonymous_variant	22920	exon7			AGTAATAAGTCCA	U59919	CCDS1288.1, CCDS55659.1, CCDS55660.1, CCDS55661.1	1q24.2	2012-09-20			ENSG00000075945	ENSG00000075945			17060	protein-coding gene	gene with protein product	"Smg GDS"	601836				8900189	Standard	NM_014970		Approved	SMAP, KAP3, FLA3, KAP-1	uc001ggv.3	Q92845	OTTHUMG00000035947	ENST00000361580.2:c.639T>A	chr1.hg19:g.170003616A>T		438.0	0.0		561.0	133.0	NM_014970	B1AKU4|B1AKU5|B2RDL1|B7Z8A3|F5H591|Q8NHU7|Q9H416	Silent	SNP	ENST00000361580.2	hg19	CCDS1288.1																																																																																			.	.		0.294	KIFAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087568.1	NM_014970		T	170003616	A	T	170003616	2	4	368	1	0	0	0	0	0	0	0	1	8320	349	13	4		4	KIFAP3	1	170003616	Silent	SNP	A	TCGA-ZP-A9D2-01A-11D-A382-10	2059515	170003616	79247005	5	51076										
NFASC	23114	hgsc.bcm.edu	37	chr1	204985578	204985578	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	acggctccttcatcggccagTacacggtcaaaaaggacaag	10	12	2	0			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr1:204985578T>C	ENST00000401399.1	+	29	3833	c.3634T>C	c.(3634-3636)Tac>Cac	p.Y1212H	NFASC_ENST00000339876.6_Missense_Mutation_p.Y1212H|NFASC_ENST00000495396.1_3'UTR|NFASC_ENST00000404076.1_Missense_Mutation_p.Y1129H|NFASC_ENST00000367171.4_Missense_Mutation_p.Y1304H|NFASC_ENST00000338586.6_Missense_Mutation_p.Y1196H|NFASC_ENST00000539706.1_Missense_Mutation_p.Y1146H|NFASC_ENST00000513543.1_Missense_Mutation_p.Y1141H|NFASC_ENST00000367172.4_Missense_Mutation_p.Y1319H|NFASC_ENST00000338515.6_Missense_Mutation_p.Y1229H|NFASC_ENST00000404907.1_Missense_Mutation_p.Y1146H|NFASC_ENST00000367170.4_Missense_Mutation_p.Y1240H|NFASC_ENST00000367169.4_Missense_Mutation_p.Y1043H|NFASC_ENST00000360049.4_Missense_Mutation_p.Y1141H			O94856	NFASC_HUMAN	neurofascin	1319					axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			CATCGGCCAGTACACGGTCAA	0.572																																					p.Y1212H		Atlas-SNP	.											.	NFASC	396	.	0			c.T3634C						.						183	162	169					1																	204985578		2203	4300	6503	SO:0001583	missense	23114	exon30			GGCCAGTACACGG	AK027553	CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1	1q32.1	2013-02-11	2010-06-24		ENSG00000163531	ENSG00000163531		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	29866	protein-coding gene	gene with protein product		609145	"neurofascin homolog (chicken)"			1377696, 8672144	Standard	NM_015090		Approved	NRCAML, KIAA0756, FLJ46866, NF	uc001hbj.3	O94856	OTTHUMG00000151697	ENST00000401399.1:c.3634T>C	chr1.hg19:g.204985578T>C	ENSP00000385637:p.Tyr1212His	154.0	0.0		203.0	50.0	NM_001005388	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Missense_Mutation	SNP	ENST00000401399.1	hg19	CCDS53460.1	.	.	.	.	.	.	.	.	.	.	T	27.1	4.804331	0.90623	.	.	ENSG00000163531	ENST00000367172;ENST00000367171;ENST00000367170;ENST00000338515;ENST00000339876;ENST00000338586;ENST00000295776;ENST00000539706;ENST00000360049;ENST00000367169;ENST00000404076;ENST00000401399;ENST00000404907;ENST00000513543;ENST00000430393;ENST00000447819	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.94000	-3.33;-3.33;-3.33;-3.33;-3.33;-3.33;-3.33;-3.33;-3.33;-3.33;-3.33;-3.33;-3.33;-3.33;-3.33	5.34	5.34	0.76211	.	0.000000	0.46442	D	0.000299	D	0.96941	0.9001	M	0.87547	2.89	0.29834	N	0.829762	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;0.999;1.0	D;D;D;D;D;D;D	0.97110	0.999;1.0;1.0;0.997;0.994;0.997;1.0	D	0.94626	0.7817	10	0.87932	D	0	.	14.9906	0.71384	0.0:0.0:0.0:1.0	.	1319;1161;1146;1196;1038;1212;1141	O94856;O94856-11;O94856-8;F8W8X7;O94856-4;O94856-9;O94856-3	NFASC_HUMAN;.;.;.;.;.;.	H	1319;1304;1240;1229;1212;1196;1161;1146;1141;1043;1129;1212;1146;1141;1137;190	ENSP00000356140:Y1319H;ENSP00000356139:Y1304H;ENSP00000356138:Y1240H;ENSP00000342128:Y1229H;ENSP00000344786:Y1212H;ENSP00000343509:Y1196H;ENSP00000438614:Y1146H;ENSP00000353154:Y1141H;ENSP00000356137:Y1043H;ENSP00000385676:Y1129H;ENSP00000385637:Y1212H;ENSP00000384061:Y1146H;ENSP00000425908:Y1141H;ENSP00000415031:Y1137H;ENSP00000416891:Y190H	ENSP00000295776:Y1161H	Y	+	1	0	NFASC	203252201	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.013000	0.88655	2.011000	0.59026	0.460000	0.39030	TAC	.	.		0.572	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388		C	204985578	T	C	204985578	3	2	368	1	0	0	0	0	1	0	0	0	10368	1638	57	2	4157	2	NFASC	1	204985578	Missense_Mutation	SNP	T	TCGA-ZP-A9D2-01A-11D-A382-10	34981962	204985578	44265043	6	51077										
DSTYK	25778	hgsc.bcm.edu	37	chr1	205131199	205131199	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	tgcaaaagcctcgtgggaacTattgagccgagtccggaatt	12	9	0	1			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr1:205131199T>C	ENST00000367162.3	-	6	1813	c.1783A>G	c.(1783-1785)Agt>Ggt	p.S595G	DSTYK_ENST00000367161.3_Missense_Mutation_p.S595G|DSTYK_ENST00000367160.4_Intron	NM_015375.2	NP_056190.1	Q6XUX3	DUSTY_HUMAN	dual serine/threonine and tyrosine protein kinase	595					cellular response to fibroblast growth factor stimulus (GO:0044344)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of kinase activity (GO:0033674)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(2)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(2)	14						TCGTGGGAACTATTGAGCCGA	0.527																																					p.S595G		Atlas-SNP	.											.	DSTYK	87	.	0			c.A1783G						.						60	56	57					1																	205131199		2203	4300	6503	SO:0001583	missense	25778	exon6			GGGAACTATTGAG	AF068286	CCDS1451.1, CCDS1452.1	1q32	2008-12-18	2008-12-18	2008-12-18	ENSG00000133059	ENSG00000133059			29043	protein-coding gene	gene with protein product		612666	"receptor interacting protein kinase 5"	RIPK5		15178406	Standard	NM_015375		Approved	KIAA0472, DustyPK, RIP5	uc001hbw.3	Q6XUX3	OTTHUMG00000037102	ENST00000367162.3:c.1783A>G	chr1.hg19:g.205131199T>C	ENSP00000356130:p.Ser595Gly	133.0	0.0		209.0	55.0	NM_199462	B7ZL64|O75060|Q17R94|Q5RKT0|Q6IN87|Q6P997|Q86Y03|Q9P1S5	Missense_Mutation	SNP	ENST00000367162.3	hg19	CCDS1451.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.418841	0.83559	.	.	ENSG00000133059	ENST00000367161;ENST00000367162	T;T	0.80123	-1.26;-1.34	5.9	5.9	0.94986	.	0.085942	0.85682	D	0.000000	D	0.85767	0.5773	L	0.58101	1.795	0.80722	D	1	P;D;P	0.54601	0.628;0.967;0.902	B;P;P	0.57101	0.184;0.813;0.554	D	0.86915	0.2063	10	0.66056	D	0.02	-11.2991	15.9847	0.80142	0.0:0.0:0.0:1.0	.	56;595;595	Q6XUX3-4;Q6XUX3-2;Q6XUX3	.;.;DUSTY_HUMAN	G	595	ENSP00000356129:S595G;ENSP00000356130:S595G	ENSP00000356129:S595G	S	-	1	0	DSTYK	203397822	1.000000	0.71417	0.993000	0.49108	0.968000	0.65278	5.056000	0.64287	2.254000	0.74563	0.482000	0.46254	AGT	.	.		0.527	DSTYK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090345.1	NM_015375		C	205131199	T	C	205131199	3	2	368	1	0	0	0	0	1	0	0	0	4787	1522	53	2	1038	2	DSTYK	1	205131199	Missense_Mutation	SNP	T	TCGA-ZP-A9D2-01A-11D-A382-10	145621	205131199	44119422	7	51078										
MAL	4118	hgsc.bcm.edu	37	chr2	95719156	95719156	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	acatagccactctgctctacGtggtccatgcggtgttctct	9	13	3	0			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr2:95719156G>A	ENST00000309988.4	+	4	527	c.418G>A	c.(418-420)Gtg>Atg	p.V140M	MAL_ENST00000353004.3_Missense_Mutation_p.V98M|MAL_ENST00000349807.3_Missense_Mutation_p.V42M|MAL_ENST00000354078.3_Missense_Mutation_p.V84M|AC103563.9_ENST00000442200.1_RNA	NM_002371.3	NP_002362.1	P21145	MAL_HUMAN	mal, T-cell differentiation protein	140	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				apical protein localization (GO:0045176)|apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|central nervous system development (GO:0007417)|membrane raft polarization (GO:0001766)|myelination (GO:0042552)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extrinsic component of membrane (GO:0019898)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)	channel activity (GO:0015267)|lipid binding (GO:0008289)|peptidase activator activity involved in apoptotic process (GO:0016505)|structural constituent of myelin sheath (GO:0019911)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|prostate(2)	10				STAD - Stomach adenocarcinoma(1183;0.18)		TCTGCTCTACGTGGTCCATGC	0.512																																					p.V140M		Atlas-SNP	.											.	MAL	21	.	0			c.G418A						.						228	212	217					2																	95719156		2203	4300	6503	SO:0001583	missense	4118	exon4			CTCTACGTGGTCC		CCDS2006.1, CCDS2007.1, CCDS2008.1, CCDS2009.1	2q11.1	2008-07-29			ENSG00000172005	ENSG00000172005			6817	protein-coding gene	gene with protein product		188860					Standard	NM_002371		Approved		uc002stx.2	P21145	OTTHUMG00000132011	ENST00000309988.4:c.418G>A	chr2.hg19:g.95719156G>A	ENSP00000310880:p.Val140Met	63.0	0.0		71.0	47.0	NM_002371	Q6FH77	Missense_Mutation	SNP	ENST00000309988.4	hg19	CCDS2006.1	.	.	.	.	.	.	.	.	.	.	G	13.86	2.361864	0.41801	.	.	ENSG00000172005	ENST00000309988;ENST00000353004;ENST00000354078;ENST00000349807	T;T	0.45668	1.64;0.89	5.57	2.84	0.33178	Marvel (1);MARVEL-like domain (1);	0.229924	0.46145	D	0.000317	T	0.29321	0.0730	L	0.48642	1.525	0.21897	N	0.99948	B;P;P;P	0.46656	0.389;0.719;0.882;0.875	B;B;B;B	0.36766	0.023;0.104;0.232;0.218	T	0.12656	-1.0539	10	0.34782	T	0.22	.	7.9755	0.30153	0.2543:0.0:0.7457:0.0	.	42;98;84;140	P21145-4;P21145-2;P21145-3;P21145	.;.;.;MAL_HUMAN	M	140;98;84;42	ENSP00000310880:V140M;ENSP00000306568:V98M	ENSP00000310880:V140M	V	+	1	0	MAL	95082883	0.999000	0.42202	1.000000	0.80357	0.967000	0.64934	2.464000	0.45067	0.429000	0.26202	0.650000	0.86243	GTG	.	.		0.512	MAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254982.3	NM_002371		A	95719156	G	A	95719156	3	1	368	1	0	0	0	0	1	0	0	0	9208	1145	40	1	432	1	MAL	2	95719156	Missense_Mutation	SNP	G	TCGA-ZP-A9D2-01A-11D-A382-10		95719156	147480217	8	51079										
PRR21	643905	hgsc.bcm.edu	37	chr2	240982306	240982307	+	In_Frame_Ins	INS	-	-	AGG													0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	gggtgaagagccgtggatgaINSgccgtgggggaagagctgtt							TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr2:240982306_240982307insAGG	ENST00000408934.1	-	1	92_93	c.93_94insCCT	c.(91-96)ggctca>ggcCCTtca	p.31_32GS>GPS		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	31										NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(5)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	29						GCCGTGGATGAGCCGTGGGGGA	0.564																																					p.S32delinsPS		Atlas-INDEL	.											.	PRR21	53	.	0			c.94_95insCCT						.																																			SO:0001652	inframe_insertion	643905	exon1			.	AF453950	CCDS33417.1	2q37.3	2009-04-20			ENSG00000221961	ENSG00000221961			33866	protein-coding gene	gene with protein product							Standard	NM_001080835		Approved		uc010zod.2	Q8WXC7	OTTHUMG00000159174	ENST00000408934.1:c.93_94insCCT	chr2.hg19:g.240982306_240982307insAGG	ENSP00000386166:p.Gly31_Ser32insPro	72.0	0.0		100.0	11.0	NM_001080835		In_Frame_Ins	INS	ENST00000408934.1	hg19	CCDS33417.1																																																																																			.	.		0.564	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835		AGG	240982307	-	AGG	240982306	7	5	368	1	0	1	1	0	0	0	0	0	12604	304	11	0	1078	0	PRR21	2	240982306	In_Frame_Ins	INS	-	TCGA-ZP-A9D2-01A-11D-A382-10	145263150	240982306	2217067	9	51080										
CCDC13	152206	hgsc.bcm.edu	37	chr3	42750482	42750482	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	ggctgtcatcctattgcttgCctgtcttctgctgccgcagg	11	13	3	0			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr3:42750482C>A	ENST00000310232.6	-	16	2221	c.2138G>T	c.(2137-2139)gGc>gTc	p.G713V	HHATL-AS1_ENST00000600839.1_RNA	NM_144719.3	NP_653320.3	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13	713										endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	25						CTATTGCTTGCCTGTCTTCTG	0.597																																					p.G713V		Atlas-SNP	.											.	CCDC13	71	.	0			c.G2138T						.						93	88	89					3																	42750482		2203	4300	6503	SO:0001583	missense	152206	exon16			TGCTTGCCTGTCT	AK058196	CCDS2705.1	3p22.1	2005-01-25			ENSG00000244607	ENSG00000244607			26358	protein-coding gene	gene with protein product						12477932	Standard	NM_144719		Approved	FLJ25467	uc003cly.4	Q8IYE1	OTTHUMG00000133046	ENST00000310232.6:c.2138G>T	chr3.hg19:g.42750482C>A	ENSP00000309836:p.Gly713Val	30.0	0.0		34.0	11.0	NM_144719		Missense_Mutation	SNP	ENST00000310232.6	hg19	CCDS2705.1	.	.	.	.	.	.	.	.	.	.	C	9.641	1.139079	0.21205	.	.	ENSG00000244607	ENST00000310232	T	0.24538	1.85	3.71	2.55	0.30701	.	0.289069	0.32287	N	0.006317	T	0.15522	0.0374	N	0.19112	0.55	0.19775	N	0.999957	B	0.25105	0.118	B	0.31245	0.126	T	0.20672	-1.0268	10	0.30854	T	0.27	.	7.2759	0.26283	0.0:0.1846:0.0:0.8154	.	713	Q8IYE1	CCD13_HUMAN	V	713	ENSP00000309836:G713V	ENSP00000309836:G713V	G	-	2	0	CCDC13	42725486	0.884000	0.30299	0.116000	0.21606	0.014000	0.08584	2.525000	0.45598	0.774000	0.33427	-0.416000	0.06073	GGC	.	.		0.597	CCDC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256652.1	NM_144719		A	42750482	C	A	42750482	3	1	368	1	0	0	0	0	1	0	0	0	2767	739	26	3	13	3	CCDC13	3	42750482	Missense_Mutation	SNP	C	TCGA-ZP-A9D2-01A-11D-A382-10		42750482	155271948	10	51081										
CP	1356	hgsc.bcm.edu	37	chr3	148925166	148925166	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	ctacctttcagatggtttagAttctgacagctgagcatcca	8	10	2	4			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr3:148925166A>C	ENST00000264613.6	-	5	1282	c.1020T>G	c.(1018-1020)aaT>aaG	p.N340K		NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	340	F5/8 type A 1.|Plastocyanin-like 2.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)	chaperone binding (GO:0051087)|copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	GATGGTTTAGATTCTGACAGC	0.413																																					p.N340K		Atlas-SNP	.											.	CP	112	.	0			c.T1020G						.						104	100	101					3																	148925166		2203	4299	6502	SO:0001583	missense	1356	exon5			GTTTAGATTCTGA	M13536	CCDS3141.1	3q23-q25	2010-07-01			ENSG00000047457	ENSG00000047457	1.16.3.1		2295	protein-coding gene	gene with protein product		117700					Standard	NM_000096		Approved		uc003ewy.4	P00450	OTTHUMG00000159563	ENST00000264613.6:c.1020T>G	chr3.hg19:g.148925166A>C	ENSP00000264613:p.Asn340Lys	107.0	0.0		112.0	34.0	NM_000096	Q14063|Q2PP18|Q9UKS4	Missense_Mutation	SNP	ENST00000264613.6	hg19	CCDS3141.1	.	.	.	.	.	.	.	.	.	.	A	19.37	3.814159	0.70912	.	.	ENSG00000047457	ENST00000264613;ENST00000494544	D;D	0.99758	-6.65;-6.65	5.96	1.08	0.20341	Cupredoxin (2);Multicopper oxidase, type 1 (1);	0.106813	0.64402	D	0.000006	D	0.99336	0.9767	M	0.61703	1.905	0.29110	N	0.880911	D;D;D;D	0.65815	0.995;0.995;0.995;0.995	P;P;P;P	0.59595	0.86;0.792;0.86;0.823	D	0.99892	1.1137	10	0.30078	T	0.28	-29.9854	6.6893	0.23161	0.3781:0.1644:0.4575:0.0	.	340;340;340;340	A5PL27;A8K5A4;P00450;Q1L857	.;.;CERU_HUMAN;.	K	340;123	ENSP00000264613:N340K;ENSP00000420545:N123K	ENSP00000264613:N340K	N	-	3	2	CP	150407856	1.000000	0.71417	0.997000	0.53966	0.989000	0.77384	0.900000	0.28431	0.170000	0.19704	0.533000	0.62120	AAT	.	.		0.413	CP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317498.1	NM_000096		C	148925166	A	C	148925166	3	2	368	1	0	0	0	0	1	0	0	0	3789	330	12	5	2237	5	CP	3	148925166	Missense_Mutation	SNP	A	TCGA-ZP-A9D2-01A-11D-A382-10	106174684	148925166	49097264	11	51082										
LSG1	55341	hgsc.bcm.edu	37	chr3	194369468	194369468	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	cggtggggatcttcatcctcTctaggcgttatgatgttaat	11	8	3	1			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr3:194369468T>A	ENST00000265245.5	-	11	1799	c.1485A>T	c.(1483-1485)agA>agT	p.R495S	AC046143.2_ENST00000582474.1_RNA	NM_018385.2	NP_060855.2	Q9H089	LSG1_HUMAN	large 60S subunit nuclear export GTPase 1	495					GTP catabolic process (GO:0006184)|nuclear export (GO:0051168)|protein transport (GO:0015031)|ribosome biogenesis (GO:0042254)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(3)|large_intestine(2)|lung(9)	16	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;4.34e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;7.55e-06)		CTTCATCCTCTCTAGGCGTTA	0.418																																					p.R495S		Atlas-SNP	.											.	LSG1	38	.	0			c.A1485T						.						206	177	187					3																	194369468		2203	4300	6503	SO:0001583	missense	55341	exon11			ATCCTCTCTAGGC		CCDS33922.1	3q29	2013-08-21	2013-08-21		ENSG00000041802	ENSG00000041802			25652	protein-coding gene	gene with protein product		610780	"large subunit GTPase 1 homolog (S. cerevisiae)"			11230166	Standard	NM_018385		Approved	FLJ11301	uc003fui.3	Q9H089	OTTHUMG00000156021	ENST00000265245.5:c.1485A>T	chr3.hg19:g.194369468T>A	ENSP00000265245:p.Arg495Ser	107.0	0.0		108.0	35.0	NM_018385	A0JLT4|A0PJK3|A6NI18|Q7L9H8|Q9NUK8	Missense_Mutation	SNP	ENST00000265245.5	hg19	CCDS33922.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	8.389|8.389	0.839338|0.839338	0.16891|0.16891	.|.	.|.	ENSG00000041802|ENSG00000041802	ENST00000437613|ENST00000265245	.|T	.|0.13538	.|2.58	5.79|5.79	4.64|4.64	0.57946|0.57946	.|.	.|0.098489	.|0.64402	.|D	.|0.000002	T|T	0.06962|0.06962	0.0177|0.0177	N|N	0.12182|0.12182	0.205|0.205	0.58432|0.58432	D|D	0.999994|0.999994	.|B	.|0.16603	.|0.018	.|B	.|0.19666	.|0.026	T|T	0.21348|0.21348	-1.0248|-1.0248	5|10	.|0.09084	.|T	.|0.74	.|.	9.257|9.257	0.37590|0.37590	0.0:0.1556:0.0:0.8444|0.0:0.1556:0.0:0.8444	.|.	.|495	.|Q9H089	.|LSG1_HUMAN	V|S	212|495	.|ENSP00000265245:R495S	.|ENSP00000265245:R495S	E|R	-|-	2|3	0|2	LSG1|LSG1	195850757|195850757	1.000000|1.000000	0.71417|0.71417	0.974000|0.974000	0.42286|0.42286	0.378000|0.378000	0.30076|0.30076	1.796000|1.796000	0.38794|0.38794	1.037000|1.037000	0.40024|0.40024	0.528000|0.528000	0.53228|0.53228	GAG|AGA	.	.		0.418	LSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342740.1	NM_018385		A	194369468	T	A	194369468	3	1	368	1	0	0	0	0	1	0	0	0	9058	1548	54	4	507	4	LSG1	3	194369468	Missense_Mutation	SNP	T	TCGA-ZP-A9D2-01A-11D-A382-10	45444302	194369468	3652962	12	51083										
FAM193A	8603	hgsc.bcm.edu	37	chr4	2664933	2664933	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	gcccccaggggccccgaaggAagatggagtgctgggaagca	17	11	0	1			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr4:2664933A>C	ENST00000324666.5	+	10	1475	c.1124A>C	c.(1123-1125)gAa>gCa	p.E375A	FAM193A_ENST00000502458.1_Missense_Mutation_p.E397A|FAM193A_ENST00000545951.1_Missense_Mutation_p.E375A|FAM193A_ENST00000505311.1_Missense_Mutation_p.E375A|FAM193A_ENST00000382839.3_Missense_Mutation_p.E375A	NM_001256666.1	NP_001243595.1	P78312	F193A_HUMAN	family with sequence similarity 193, member A	375										NS(2)|breast(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(12)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	40						GCCCCGAAGGAAGATGGAGTG	0.577																																					p.E397A		Atlas-SNP	.											.	FAM193A	103	.	0			c.A1190C						.						53	65	61					4																	2664933		2203	4300	6503	SO:0001583	missense	8603	exon11			CGAAGGAAGATGG	AB000459	CCDS33943.1, CCDS58874.1, CCDS58875.1, CCDS58876.1	4p16.3	2009-09-04	2009-09-04	2009-09-04					16822	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 8"	C4orf8		9734812	Standard	NR_046335		Approved	RES4-22	uc010ick.3	P78312		ENST00000324666.5:c.1124A>C	chr4.hg19:g.2664933A>C	ENSP00000324587:p.Glu375Ala	472.0	0.0		312.0	176.0	NM_001256667	B7ZM85|B9EGR0|E9PFA1|O43607|P78311|P78313|Q9UEG8	Missense_Mutation	SNP	ENST00000324666.5	hg19	CCDS58875.1	.	.	.	.	.	.	.	.	.	.	A	11.52	1.661842	0.29515	.	.	ENSG00000125386	ENST00000382839;ENST00000324666;ENST00000545951;ENST00000502458;ENST00000513350	T;T;T;T;T	0.36520	1.26;1.66;1.25;1.25;1.25	5.57	4.36	0.52297	.	0.147796	0.64402	D	0.000011	T	0.33000	0.0848	L	0.51422	1.61	0.34498	D	0.705735	B;B;B;B;B	0.10296	0.003;0.003;0.003;0.001;0.001	B;B;B;B;B	0.09377	0.004;0.004;0.004;0.004;0.004	T	0.36529	-0.9744	10	0.45353	T	0.12	-16.1954	11.9581	0.52993	0.8548:0.1452:0.0:0.0	.	375;397;375;397;375	B9EGR0;E9PFA1;P78312;B7ZM85;P78312-2	.;.;F193A_HUMAN;.;.	A	375;375;375;397;229	ENSP00000372290:E375A;ENSP00000324587:E375A;ENSP00000443617:E375A;ENSP00000427505:E397A;ENSP00000427260:E229A	ENSP00000324587:E375A	E	+	2	0	FAM193A	2634731	1.000000	0.71417	0.376000	0.26042	0.016000	0.09150	4.343000	0.59348	0.903000	0.36546	0.528000	0.53228	GAA	.	.		0.577	FAM193A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360903.1	NM_003704		C	2664933	A	C	2664933	3	2	368	1	0	0	0	0	1	0	0	0	5529	246	9	5	1154	5	FAM193A	4	2664933	Missense_Mutation	SNP	A	TCGA-ZP-A9D2-01A-11D-A382-10		2664933	188489343	13	51084										
ENPEP	2028	hgsc.bcm.edu	37	chr4	111397874	111397874	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	acttcgtcaacccagtccacTacgacctgcacgtgaagccc	7	17	1	1			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr4:111397874T>C	ENST00000265162.5	+	1	646	c.304T>C	c.(304-306)Tac>Cac	p.Y102H		NM_001977.3	NP_001968.3	Q07075	AMPE_HUMAN	glutamyl aminopeptidase (aminopeptidase A)	102					angiogenesis (GO:0001525)|angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|glomerulus development (GO:0032835)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|brush border (GO:0005903)|cytoplasmic vesicle (GO:0031410)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metalloaminopeptidase activity (GO:0070006)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(22)|ovary(1)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(1)	54		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.0031)		CCCAGTCCACTACGACCTGCA	0.612																																					p.Y102H		Atlas-SNP	.											.	ENPEP	149	.	0			c.T304C						.						92	97	95					4																	111397874		2203	4300	6503	SO:0001583	missense	2028	exon1			GTCCACTACGACC	L12468	CCDS3691.1	4q25	2008-02-05			ENSG00000138792	ENSG00000138792	3.4.11.7	"CD molecules"	3355	protein-coding gene	gene with protein product		138297				9268642	Standard	NM_001977		Approved	gp160, CD249	uc003iab.4	Q07075	OTTHUMG00000132546	ENST00000265162.5:c.304T>C	chr4.hg19:g.111397874T>C	ENSP00000265162:p.Tyr102His	93.0	0.0		57.0	29.0	NM_001977	Q504U2	Missense_Mutation	SNP	ENST00000265162.5	hg19	CCDS3691.1	.	.	.	.	.	.	.	.	.	.	T	17.75	3.466308	0.63625	.	.	ENSG00000138792	ENST00000265162	T	0.04454	3.62	5.83	5.83	0.93111	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.41834	0.1176	H	0.99516	4.605	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.68078	-0.5504	10	0.87932	D	0	.	16.1922	0.82000	0.0:0.0:0.0:1.0	.	102	Q07075	AMPE_HUMAN	H	102	ENSP00000265162:Y102H	ENSP00000265162:Y102H	Y	+	1	0	ENPEP	111617323	1.000000	0.71417	1.000000	0.80357	0.037000	0.13140	7.633000	0.83260	2.226000	0.72624	0.459000	0.35465	TAC	.	.		0.612	ENPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255747.2			C	111397874	T	C	111397874	3	2	368	1	0	0	0	0	1	0	0	0	5130	1522	53	2	306	2	ENPEP	4	111397874	Missense_Mutation	SNP	T	TCGA-ZP-A9D2-01A-11D-A382-10	108732941	111397874	79756402	14	51085										
EXOC3	11336	hgsc.bcm.edu	37	chr5	457080	457080	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	agccattgctttctccacacGtggtctctgagctgcttgac	9	13	2	2			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr5:457080G>A	ENST00000512944.1	+	5	1312	c.1123G>A	c.(1123-1125)Gtg>Atg	p.V375M	EXOC3_ENST00000315013.5_Missense_Mutation_p.V375M	NM_007277.4	NP_009208.2	O60645	EXOC3_HUMAN	exocyst complex component 3	386					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|secretory granule membrane (GO:0030667)				breast(2)|cervix(1)|endometrium(4)|large_intestine(1)|lung(13)|ovary(1)|urinary_tract(1)	23		Ovarian(839;0.0563)	Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			TTCTCCACACGTGGTCTCTGA	0.567																																					p.V375M		Atlas-SNP	.											.	EXOC3	54	.	0			c.G1123A						.						94	98	96					5																	457080		2128	4225	6353	SO:0001583	missense	11336	exon5			CCACACGTGGTCT	BC034427	CCDS54830.1	5p15.33	2013-01-22	2005-11-01	2005-11-01	ENSG00000180104	ENSG00000180104			30378	protein-coding gene	gene with protein product		608186	"SEC6-like 1 (S. cerevisiae)"	SEC6L1		8619474	Standard	XM_005248238		Approved	Sec6p	uc003jba.3	O60645	OTTHUMG00000162205	ENST00000512944.1:c.1123G>A	chr5.hg19:g.457080G>A	ENSP00000425587:p.Val375Met	123.0	0.0		233.0	147.0	NM_007277	Q6P2E8|Q8TEN6|Q8WUW0|Q96DI4	Missense_Mutation	SNP	ENST00000512944.1	hg19	CCDS54830.1	.	.	.	.	.	.	.	.	.	.	G	12.28	1.890638	0.33348	.	.	ENSG00000180104	ENST00000512944;ENST00000315013	T;T	0.07216	3.21;3.21	5.87	4.07	0.47477	.	0.267034	0.36972	N	0.002313	T	0.07773	0.0195	L	0.54323	1.7	0.39155	D	0.9623	P	0.38551	0.636	B	0.30646	0.118	T	0.22836	-1.0205	10	0.45353	T	0.12	-35.1588	8.2681	0.31827	0.2439:0.0:0.7561:0.0	.	386	O60645	EXOC3_HUMAN	M	375	ENSP00000425587:V375M;ENSP00000323377:V375M	ENSP00000323377:V375M	V	+	1	0	EXOC3	510080	0.999000	0.42202	0.669000	0.29828	0.620000	0.37586	2.880000	0.48530	0.797000	0.33971	0.655000	0.94253	GTG	.	.		0.567	EXOC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367882.1	NM_007277		A	457080	G	A	457080	3	1	368	1	0	0	0	0	1	0	0	0	5305	1145	40	1	1137	1	EXOC3	5	457080	Missense_Mutation	SNP	G	TCGA-ZP-A9D2-01A-11D-A382-10		457080	180458180	15	51086										
IRX1	79192	hgsc.bcm.edu	37	chr5	3596440	3596440	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	ggggccgtacgcgggcgcgcCcaactacagcgccttcctgc	14	17	0	0			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr5:3596440C>A	ENST00000302006.3	+	1	273	c.221C>A	c.(220-222)cCc>cAc	p.P74H	CTD-2012M11.3_ENST00000559410.1_RNA	NM_024337.3	NP_077313.3	P78414	IRX1_HUMAN	iroquois homeobox 1	74					proximal/distal pattern formation involved in metanephric nephron development (GO:0072272)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			biliary_tract(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(18)|ovary(2)|pancreas(1)|prostate(5)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						GCGGGCGCGCCCAACTACAGC	0.751																																					p.P74H		Atlas-SNP	.											.	IRX1	106	.	0			c.C221A						.						8	10	9					5																	3596440		1892	3864	5756	SO:0001583	missense	79192	exon1			GCGCGCCCAACTA	U90307	CCDS34132.1	5p15.33	2011-12-16	2007-07-13		ENSG00000170549	ENSG00000170549		"Homeoboxes / TALE class"	14358	protein-coding gene	gene with protein product		606197					Standard	NM_024337		Approved	IRX-5	uc003jde.3	P78414	OTTHUMG00000161632	ENST00000302006.3:c.221C>A	chr5.hg19:g.3596440C>A	ENSP00000305244:p.Pro74His	35.0	0.0		92.0	12.0	NM_024337	Q7Z2F8|Q8N312	Missense_Mutation	SNP	ENST00000302006.3	hg19	CCDS34132.1	.	.	.	.	.	.	.	.	.	.	C	9.634	1.137173	0.21123	.	.	ENSG00000170549	ENST00000302006	T	0.58210	0.35	2.34	2.34	0.29019	.	0.062950	0.64402	U	0.000005	T	0.30823	0.0777	N	0.05510	-0.035	0.41829	D	0.990062	B	0.22851	0.076	B	0.19148	0.024	T	0.17992	-1.0351	10	0.44086	T	0.13	.	12.6417	0.56712	0.0:1.0:0.0:0.0	.	74	P78414	IRX1_HUMAN	H	74	ENSP00000305244:P74H	ENSP00000305244:P74H	P	+	2	0	IRX1	3649440	0.998000	0.40836	1.000000	0.80357	0.988000	0.76386	1.564000	0.36375	1.290000	0.44636	0.485000	0.47835	CCC	.	.		0.751	IRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365546.1	NM_024337		A	3596440	C	A	3596440	3	1	368	1	0	0	0	0	1	0	0	0	7852	623	22	3	223	3	IRX1	5	3596440	Missense_Mutation	SNP	C	TCGA-ZP-A9D2-01A-11D-A382-10	3139360	3596440	177318820	16	51087										
TRIO	7204	hgsc.bcm.edu	37	chr5	14304637	14304637	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	ccttccctcagagctgcaggAcctagaagatgccattcatc	8	14	2	3			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr5:14304637A>G	ENST00000344204.4	+	8	1460	c.1436A>G	c.(1435-1437)gAc>gGc	p.D479G	TRIO_ENST00000509967.2_Missense_Mutation_p.D430G|TRIO_ENST00000537187.1_Missense_Mutation_p.D479G	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	479					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118	Lung NSC(4;0.000742)					GAGCTGCAGGACCTAGAAGAT	0.413																																					p.D479G		Atlas-SNP	.											.	TRIO	305	.	0			c.A1436G						.						213	178	190					5																	14304637		2203	4300	6503	SO:0001583	missense	7204	exon8			TGCAGGACCTAGA	AF091395	CCDS3883.1	5p14-p15.1	2013-01-11	2012-07-12		ENSG00000038382	ENSG00000038382		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing"	12303	protein-coding gene	gene with protein product		601893	"triple functional domain (PTPRF interacting)"			8643598	Standard	NM_007118		Approved	ARHGEF23	uc003jff.3	O75962	OTTHUMG00000131057	ENST00000344204.4:c.1436A>G	chr5.hg19:g.14304637A>G	ENSP00000339299:p.Asp479Gly	150.0	0.0		292.0	51.0	NM_007118	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Missense_Mutation	SNP	ENST00000344204.4	hg19	CCDS3883.1	.	.	.	.	.	.	.	.	.	.	A	16.81	3.224747	0.58668	.	.	ENSG00000038382	ENST00000344204;ENST00000537187;ENST00000509967;ENST00000513206	T;T;T	0.65732	-0.17;-0.17;0.46	5.18	5.18	0.71444	.	0.052170	0.85682	D	0.000000	T	0.59918	0.2229	L	0.51422	1.61	0.80722	D	1	B;B;P	0.43392	0.112;0.167;0.805	B;B;B	0.43413	0.138;0.127;0.419	T	0.58651	-0.7599	10	0.28530	T	0.3	.	15.0541	0.71897	1.0:0.0:0.0:0.0	.	430;479;479	F5H228;O75962-5;O75962	.;.;TRIO_HUMAN	G	479;479;430;166	ENSP00000339299:D479G;ENSP00000446348:D479G;ENSP00000445592:D430G	ENSP00000339299:D479G	D	+	2	0	TRIO	14357637	1.000000	0.71417	0.996000	0.52242	0.984000	0.73092	9.307000	0.96226	1.966000	0.57179	0.528000	0.53228	GAC	.	.		0.413	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118		G	14304637	A	G	14304637	3	3	368	1	0	0	0	0	1	0	0	0	16567	275	10	2	1466	2	TRIO	5	14304637	Missense_Mutation	SNP	A	TCGA-ZP-A9D2-01A-11D-A382-10	10708197	14304637	166610623	17	51088										
PCDHB5	26167	hgsc.bcm.edu	37	chr5	140515199	140515199	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	ggggtgggggaactggccacTcggggcgcgcgaatgcatta	19	9	0	0			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr5:140515199T>A	ENST00000231134.5	+	1	400	c.183T>A	c.(181-183)acT>acA	p.T61T		NM_015669.2	NP_056484.1	Q9Y5E4	PCDB5_HUMAN	protocadherin beta 5	61	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|kidney(1)|large_intestine(18)|lung(25)|ovary(3)|prostate(6)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	81			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AACTGGCCACTCGGGGCGCGC	0.493																																					p.T61T		Atlas-SNP	.											.	PCDHB5	184	.	0			c.T183A						.						63	70	68					5																	140515199		2203	4300	6503	SO:0001819	synonymous_variant	26167	exon1			GGCCACTCGGGGC	AF152498	CCDS4247.1	5q31	2010-01-26			ENSG00000113209	ENSG00000113209		"Cadherins / Protocadherins : Clustered"	8690	other	protocadherin		606331				10380929	Standard	NM_015669		Approved	DKFZp586B0217, PCDH-BETA5	uc003liq.3	Q9Y5E4	OTTHUMG00000129616	ENST00000231134.5:c.183T>A	chr5.hg19:g.140515199T>A		160.0	0.0		101.0	38.0	NM_015669	Q549F4|Q9UFU9	Silent	SNP	ENST00000231134.5	hg19	CCDS4247.1																																																																																			.	.		0.493	PCDHB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251811.1	NM_015669		A	140515199	T	A	140515199	2	1	368	1	0	0	0	0	0	0	0	1	11554	1538	54	4		4	PCDHB5	5	140515199	Silent	SNP	T	TCGA-ZP-A9D2-01A-11D-A382-10	126210562	140515199	40400061	18	51089										
HIST1H4G	8369	hgsc.bcm.edu	37	chr6	26247104	26247104	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	tgccgggccaagcgccggatAgtgcacttggtaatgccctg	14	12	0	0			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr6:26247104A>G	ENST00000244537.4	-	1	155	c.102T>C	c.(100-102)acT>acC	p.T34T		NM_003547.2	NP_003538.1	Q99525	H4G_HUMAN	histone cluster 1, H4g	34						nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(1)|large_intestine(1)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	7		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)				AGCGCCGGATAGTGCACTTGG	0.562																																					p.T34T		Atlas-SNP	.											.	HIST1H4G	18	.	0			c.T102C						.						51	47	49					6																	26247104		2203	4300	6503	SO:0001819	synonymous_variant	8369	exon1			CCGGATAGTGCAC	Z80788	CCDS4599.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000124578	ENSG00000275663		"Histones / Replication-dependent"	4792	protein-coding gene	gene with protein product		602832	"H4 histone family, member L", "histone 1, H4g"	H4FL		9119399, 12408966	Standard	NM_003547		Approved	H4/l	uc003nhf.3	Q99525	OTTHUMG00000014444	ENST00000244537.4:c.102T>C	chr6.hg19:g.26247104A>G		76.0	0.0		98.0	35.0	NM_003547		Silent	SNP	ENST00000244537.4	hg19	CCDS4599.1																																																																																			.	.		0.562	HIST1H4G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040107.1	NM_003547		G	26247104	A	G	26247104	2	3	368	1	0	0	0	0	0	0	0	1	7180	407	15	2		2	HIST1H4G	6	26247104	Silent	SNP	A	TCGA-ZP-A9D2-01A-11D-A382-10		26247104	144867963	19	51090										
MDC1	9656	hgsc.bcm.edu	37	chr6	30672323	30672323	+	Missense_Mutation	SNP	G	G	A													0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	atgtgggctcaggggtgacaGgttggtctgtggaggtggaa							TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr6:30672323G>A	ENST00000376406.3	-	10	5284	c.4637C>T	c.(4636-4638)cCt>cTt	p.P1546L	MDC1_ENST00000376405.2_Missense_Mutation_p.P1282L|MDC1-AS1_ENST00000442150.1_RNA	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	1546	Interaction with the PRKDC complex.				DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intra-S DNA damage checkpoint (GO:0031573)	chromosome (GO:0005694)|focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	FHA domain binding (GO:0070975)|protein C-terminus binding (GO:0008022)			breast(2)|kidney(1)|ovary(1)	4						AGGGGTGACAGGTTGGTCTGT	0.572								Other conserved DNA damage response genes																													p.P1546L		Atlas-SNP	.											.	MDC1	218	.	0			c.C4637T						.						120	139	132					6																	30672323		2203	4300	6503	SO:0001583	missense	9656	exon10			GTGACAGGTTGGT	D79992	CCDS34384.1	6p21.3	2010-02-17	2009-06-12		ENSG00000137337	ENSG00000137337			21163	protein-coding gene	gene with protein product		607593				10975465, 12607005	Standard	NM_014641		Approved	NFBD1, KIAA0170, Em:AB023051.5	uc003nrg.4	Q14676	OTTHUMG00000031075	ENST00000376406.3:c.4637C>T	chr6.hg19:g.30672323G>A	ENSP00000365588:p.Pro1546Leu	147.0	0.0		146.0	32.0	NM_014641	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Missense_Mutation	SNP	ENST00000376406.3	hg19	CCDS34384.1	.	.	.	.	.	.	.	.	.	.	G	11.20	1.567538	0.28003	.	.	ENSG00000137337	ENST00000376406;ENST00000376405;ENST00000429610;ENST00000422104	T;T	0.23552	1.9;1.9	4.26	3.26	0.37387	.	.	.	.	.	T	0.30541	0.0768	M	0.72894	2.215	0.09310	N	1	D;B	0.89917	1.0;0.366	D;B	0.74023	0.982;0.038	T	0.04767	-1.0928	9	0.41790	T	0.15	.	7.9752	0.30151	0.1228:0.0:0.8772:0.0	.	1282;1546	Q14676-2;Q14676	.;MDC1_HUMAN	L	1546;1282;1259;1112	ENSP00000365588:P1546L;ENSP00000365587:P1282L	ENSP00000365587:P1282L	P	-	2	0	MDC1	30780302	0.006000	0.16342	0.007000	0.13788	0.014000	0.08584	0.108000	0.15396	1.239000	0.43787	0.449000	0.29647	CCT	.	.		0.572	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641		A	30672323	G	A	30672323	3	1	368	1	0	0	0	0	1	0	0	0	9412	1000	35	3	1656	3	MDC1	6	30672323	Missense_Mutation	SNP	G	TCGA-ZP-A9D2-01A-11D-A382-10	4425219	30672323	140442744	20	51091	267	2								
MDC1	9656	hgsc.bcm.edu	37	chr6	30672332	30672332	+	Missense_Mutation	SNP	G	G	C													0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	caggggtgacaggttggtctGtggaggtggaaggctggagc							TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr6:30672332G>C	ENST00000376406.3	-	10	5275	c.4628C>G	c.(4627-4629)aCa>aGa	p.T1543R	MDC1_ENST00000376405.2_Missense_Mutation_p.T1279R|MDC1-AS1_ENST00000442150.1_RNA	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	1543	Interaction with the PRKDC complex.				DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intra-S DNA damage checkpoint (GO:0031573)	chromosome (GO:0005694)|focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	FHA domain binding (GO:0070975)|protein C-terminus binding (GO:0008022)			breast(2)|kidney(1)|ovary(1)	4						AGGTTGGTCTGTGGAGGTGGA	0.572								Other conserved DNA damage response genes																													p.T1543R		Atlas-SNP	.											.	MDC1	218	.	0			c.C4628G						.						119	138	132					6																	30672332		2203	4300	6503	SO:0001583	missense	9656	exon10			TGGTCTGTGGAGG	D79992	CCDS34384.1	6p21.3	2010-02-17	2009-06-12		ENSG00000137337	ENSG00000137337			21163	protein-coding gene	gene with protein product		607593				10975465, 12607005	Standard	NM_014641		Approved	NFBD1, KIAA0170, Em:AB023051.5	uc003nrg.4	Q14676	OTTHUMG00000031075	ENST00000376406.3:c.4628C>G	chr6.hg19:g.30672332G>C	ENSP00000365588:p.Thr1543Arg	146.0	0.0		151.0	39.0	NM_014641	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Missense_Mutation	SNP	ENST00000376406.3	hg19	CCDS34384.1	.	.	.	.	.	.	.	.	.	.	G	9.207	1.029859	0.19512	.	.	ENSG00000137337	ENST00000376406;ENST00000376405;ENST00000429610;ENST00000422104	T;T	0.10099	2.91;2.91	4.06	-4.43	0.03568	.	.	.	.	.	T	0.08179	0.0204	M	0.71581	2.175	0.09310	N	1	D;P	0.65815	0.995;0.881	P;B	0.60609	0.877;0.164	T	0.05517	-1.0880	9	0.49607	T	0.09	.	0.7113	0.00925	0.2516:0.1202:0.2236:0.4046	.	1279;1543	Q14676-2;Q14676	.;MDC1_HUMAN	R	1543;1279;1256;1109	ENSP00000365588:T1543R;ENSP00000365587:T1279R	ENSP00000365587:T1279R	T	-	2	0	MDC1	30780311	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-2.104000	0.01340	-0.995000	0.03459	-0.398000	0.06409	ACA	.	.		0.572	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641		C	30672332	G	C	30672332	3	2	368	1	0	0	0	0	1	0	0	0	9412	1377	48	4	1665	4	MDC1	6	30672332	Missense_Mutation	SNP	G	TCGA-ZP-A9D2-01A-11D-A382-10	9	30672332	140442735	21	51092	267	2								
ZNF318	24149	hgsc.bcm.edu	37	chr6	43316238	43316238	+	Frame_Shift_Del	DEL	C	C	-													0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	ttcagattgcttcttttctgCctcttctgcctcttgccgta							TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr6:43316238delC	ENST00000361428.2	-	6	2973	c.2896delG	c.(2896-2898)gcafs	p.A966fs	ZNF318_ENST00000318149.3_Frame_Shift_Del_p.A966fs	NM_014345.2	NP_055160.2	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	966					meiotic nuclear division (GO:0007126)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(21)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	61			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)			TTCTTTTCTGCCTCTTCTGCC	0.463																																					p.A966fs		Atlas-INDEL	.											.	ZNF318	175	.	0			c.2897delC						.						255	224	234					6																	43316238		2203	4300	6503	SO:0001589	frameshift_variant	24149	exon6			.	AF090114	CCDS4895.2	6p21.1	2013-09-19			ENSG00000171467	ENSG00000171467		"Zinc fingers, C2H2-type"	13578	protein-coding gene	gene with protein product						10873617	Standard	NM_014345		Approved	HRIHFB2436, ZFP318	uc003oux.3	Q5VUA4	OTTHUMG00000014732	ENST00000361428.2:c.2896delG	chr6.hg19:g.43316238delC	ENSP00000354964:p.Ala966fs	74.0	0.0		126.0	34.0	NM_014345	O94796|Q4G0E4|Q8NEM6|Q9UNU8|Q9Y2W9	Frame_Shift_Del	DEL	ENST00000361428.2	hg19	CCDS4895.2																																																																																			.	.		0.463	ZNF318-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040601.2	NM_014345		-	43316238	C	-	43316238	7	5	368	1	0	1	0	1	0	0	0	0	17851	739	26	0	3963	0	ZNF318	6	43316238	Frame_Shift_Del	DEL	C	TCGA-ZP-A9D2-01A-11D-A382-10	12643906	43316238	127798829	22	51093										
ASCC3	10973	hgsc.bcm.edu	37	chr6	101073148	101073148	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	caattccaaagcagtaagacGagtttgacgtcttgatgaga	10	7	1	4			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr6:101073148G>A	ENST00000369162.2	-	30	5049	c.4705C>T	c.(4705-4707)Cgt>Tgt	p.R1569C		NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	1569	Helicase C-terminal 2. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		GCAGTAAGACGAGTTTGACGT	0.383																																					p.R1569C		Atlas-SNP	.											.	ASCC3	205	.	0			c.C4705T						.						113	107	109					6																	101073148		2203	4300	6503	SO:0001583	missense	10973	exon30			TAAGACGAGTTTG	AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"RNA helicase family"	614217	"helicase, ATP binding 1"	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.4705C>T	chr6.hg19:g.101073148G>A	ENSP00000358159:p.Arg1569Cys	153.0	0.0		146.0	43.0	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Missense_Mutation	SNP	ENST00000369162.2	hg19	CCDS5046.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.363799	0.82353	.	.	ENSG00000112249	ENST00000369162	D	0.85258	-1.96	5.87	4.99	0.66335	Helicase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.94079	0.8102	H	0.97465	4.01	0.80722	D	1	D	0.89917	1.0	D	0.70716	0.97	D	0.95933	0.8940	10	0.87932	D	0	.	14.248	0.66001	0.0:0.0:0.6752:0.3248	.	1569	Q8N3C0	HELC1_HUMAN	C	1569	ENSP00000358159:R1569C	ENSP00000358159:R1569C	R	-	1	0	ASCC3	101179869	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.389000	0.73199	1.461000	0.47929	0.585000	0.79938	CGT	.	.		0.383	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828		A	101073148	G	A	101073148	3	1	368	1	0	0	0	0	1	0	0	0	1033	1058	37	1	1955	1	ASCC3	6	101073148	Missense_Mutation	SNP	G	TCGA-ZP-A9D2-01A-11D-A382-10	57756910	101073148	70041919	23	51094										
UNC93A	54346	hgsc.bcm.edu	37	chr6	167705003	167705003	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	cagaagtctaaggaacgtccTtgtggtttcctttgggttcc	11	9	1	1	rs374730365		TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr6:167705003T>C	ENST00000230256.3	+	1	201	c.26T>C	c.(25-27)cTt>cCt	p.L9P	UNC93A_ENST00000366830.2_3'UTR|UNC93A_ENST00000366829.2_Missense_Mutation_p.L9P	NM_018974.3	NP_061847.2	Q86WB7	UN93A_HUMAN	unc-93 homolog A (C. elegans)	9						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	40		Breast(66;7.62e-05)|Ovarian(120;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		AGGAACGTCCTTGTGGTTTCC	0.453																																					p.L9P		Atlas-SNP	.											UNC93A,NS,carcinoma,0,1	UNC93A	66	.	0			c.T26C						.	T	PRO/LEU,PRO/LEU	0,4406		0,0,2203	208	188	195		26,26	5.6	0.1	6		195	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	UNC93A	NM_001143947.1,NM_018974.3	98,98	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	probably-damaging,probably-damaging	9/416,9/458	167705003	1,13005	2203	4300	6503	SO:0001583	missense	54346	exon1			ACGTCCTTGTGGT	AJ508812	CCDS5300.1, CCDS47515.1	6q27	2014-05-16	2001-11-28		ENSG00000112494	ENSG00000112494			12570	protein-coding gene	gene with protein product		607995	"unc93 (C.elegans) homolog A"			12381271	Standard	NM_001143947		Approved	dJ366N23.2, dJ366N23.1	uc003qvq.3	Q86WB7	OTTHUMG00000016021	ENST00000230256.3:c.26T>C	chr6.hg19:g.167705003T>C	ENSP00000230256:p.Leu9Pro	73.0	0.0		79.0	30.0	NM_018974	B3KRP5|Q4QQJ4|Q5JZD6	Missense_Mutation	SNP	ENST00000230256.3	hg19	CCDS5300.1	.	.	.	.	.	.	.	.	.	.	T	12.94	2.087996	0.36855	0.0	1.16E-4	ENSG00000112494	ENST00000503433;ENST00000230256;ENST00000366829	D;D;D	0.82526	-1.62;-1.62;-1.62	5.57	5.57	0.84162	Major facilitator superfamily domain, general substrate transporter (1);	0.162513	0.37304	N	0.002154	D	0.89199	0.6647	M	0.83012	2.62	0.50313	D	0.99986	D;D	0.76494	0.998;0.999	D;D	0.65573	0.915;0.936	D	0.90563	0.4517	10	0.59425	D	0.04	-27.3271	14.9068	0.70727	0.0:0.0:0.0:1.0	.	9;9	Q4QQJ4;Q86WB7	.;UN93A_HUMAN	P	9	ENSP00000421484:L9P;ENSP00000230256:L9P;ENSP00000355794:L9P	ENSP00000230256:L9P	L	+	2	0	UNC93A	167624993	0.844000	0.29557	0.065000	0.19835	0.005000	0.04900	6.317000	0.72862	2.123000	0.65237	0.533000	0.62120	CTT	.	.		0.453	UNC93A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043125.2	NM_018974		C	167705003	T	C	167705003	3	2	368	1	0	0	0	0	1	0	0	0	17011	1609	56	2	28	2	UNC93A	6	167705003	Missense_Mutation	SNP	T	TCGA-ZP-A9D2-01A-11D-A382-10	66631855	167705003	3410064	24	51095										
INTS1	26173	hgsc.bcm.edu	37	chr7	1510839	1510839	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	gcaacactcctcggccgagcTcatcagccgctgcaggttgg	12	15	2	0			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr7:1510839T>C	ENST00000404767.3	-	46	6362	c.6277A>G	c.(6277-6279)Agc>Ggc	p.S2093G	INTS1_ENST00000389470.4_Missense_Mutation_p.S2297G	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1	2093					inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	62		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		TCGGCCGAGCTCATCAGCCGC	0.672																																					p.S2093G		Atlas-SNP	.											.	INTS1	145	.	0			c.A6277G						.						13	19	17					7																	1510839		2045	4162	6207	SO:0001583	missense	26173	exon46			CCGAGCTCATCAG	AB037861	CCDS47526.1	7p22.3	2009-11-06			ENSG00000164880	ENSG00000164880			24555	protein-coding gene	gene with protein product		611345				16239144	Standard	NM_001080453		Approved	DKFZp586J0619, KIAA1440, INT1, NET28	uc003skn.2	Q8N201	OTTHUMG00000151449	ENST00000404767.3:c.6277A>G	chr7.hg19:g.1510839T>C	ENSP00000385722:p.Ser2093Gly	122.0	0.0		129.0	34.0	NM_001080453	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Missense_Mutation	SNP	ENST00000404767.3	hg19	CCDS47526.1	.	.	.	.	.	.	.	.	.	.	T	16.62	3.175221	0.57692	.	.	ENSG00000164880	ENST00000404767;ENST00000389470;ENST00000483196	T;T	0.66995	-0.24;-0.24	5.38	5.38	0.77491	.	0.166079	0.64402	D	0.000004	T	0.62756	0.2454	L	0.59436	1.845	0.40761	D	0.983006	B	0.28439	0.212	B	0.27380	0.079	T	0.60855	-0.7180	10	0.23891	T	0.37	.	15.375	0.74598	0.0:0.0:0.0:1.0	.	2093	Q8N201	INT1_HUMAN	G	2093;2297;106	ENSP00000385722:S2093G;ENSP00000374121:S2297G	ENSP00000374121:S2297G	S	-	1	0	INTS1	1477365	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.902000	0.56310	2.041000	0.60428	0.379000	0.24179	AGC	.	.		0.672	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1			C	1510839	T	C	1510839	3	2	368	1	0	0	0	0	1	0	0	0	7784	1551	54	2	307	2	INTS1	7	1510839	Missense_Mutation	SNP	T	TCGA-ZP-A9D2-01A-11D-A382-10		1510839	157627824	25	51096										
MACC1	346389	hgsc.bcm.edu	37	chr7	20199854	20199854	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	cggccaattgtgaagcaagtCtgggtcctggcattcttgtt	12	9	2	1			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr7:20199854C>A	ENST00000400331.5	-	5	438	c.130G>T	c.(130-132)Gac>Tac	p.D44Y	MACC1_ENST00000589011.1_Missense_Mutation_p.D44Y|MACC1_ENST00000332878.4_Missense_Mutation_p.D44Y	NM_182762.3	NP_877439.3	Q6ZN28	MACC1_HUMAN	metastasis associated in colon cancer 1	44					positive regulation of cell division (GO:0051781)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(15)|lung(12)|ovary(2)|prostate(1)|skin(3)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(1)	39						TGAAGCAAGTCTGGGTCCTGG	0.393																																					p.D44Y		Atlas-SNP	.											.	MACC1	99	.	0			c.G130T						.						74	76	75					7																	20199854		2202	4298	6500	SO:0001583	missense	346389	exon5			GCAAGTCTGGGTC		CCDS5369.1	7p15.3	2008-10-14			ENSG00000183742	ENSG00000183742			30215	protein-coding gene	gene with protein product		612646					Standard	NM_182762		Approved	7A5, SH3BP4L	uc003sus.4	Q6ZN28	OTTHUMG00000128415	ENST00000400331.5:c.130G>T	chr7.hg19:g.20199854C>A	ENSP00000383185:p.Asp44Tyr	53.0	0.0		49.0	15.0	NM_182762	A8MUS5|B2RNR9|Q6ZQN8|Q7Z5A5	Missense_Mutation	SNP	ENST00000400331.5	hg19	CCDS5369.1	.	.	.	.	.	.	.	.	.	.	C	6.964	0.547810	0.13312	.	.	ENSG00000183742	ENST00000400331;ENST00000332878	T;T	0.10860	2.83;2.83	5.61	-1.88	0.07713	.	1.250890	0.05323	N	0.526993	T	0.07098	0.0180	N	0.19112	0.55	0.09310	N	1	B	0.33448	0.412	B	0.35353	0.201	T	0.34428	-0.9829	10	0.72032	D	0.01	7.0831	2.3855	0.04364	0.1065:0.444:0.2068:0.2427	.	44	Q6ZN28	MACC1_HUMAN	Y	44	ENSP00000383185:D44Y;ENSP00000328410:D44Y	ENSP00000328410:D44Y	D	-	1	0	MACC1	20166379	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	-1.031000	0.03578	-0.410000	0.07542	0.585000	0.79938	GAC	.	.		0.393	MACC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250202.5	NM_182762		A	20199854	C	A	20199854	3	1	368	1	0	0	0	0	1	0	0	0	9152	913	32	3	2440	3	MACC1	7	20199854	Missense_Mutation	SNP	C	TCGA-ZP-A9D2-01A-11D-A382-10	18689015	20199854	138938809	26	51097										
CCDC129	223075	hgsc.bcm.edu	37	chr7	31618002	31618002	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	gactaacaagctcaagagctTgtctcatcttgcaggcaaag	9	10	3	1			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr7:31618002T>C	ENST00000407970.3	+	8	1162	c.1124T>C	c.(1123-1125)tTg>tCg	p.L375S	CCDC129_ENST00000409210.1_Missense_Mutation_p.L283S|CCDC129_ENST00000319386.3_Intron|CCDC129_ENST00000451887.2_Missense_Mutation_p.L401S	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	375										cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						CTCAAGAGCTTGTCTCATCTT	0.498																																					p.L401S		Atlas-SNP	.											.	CCDC129	127	.	0			c.T1202C						.						49	49	49					7																	31618002		1991	4165	6156	SO:0001583	missense	223075	exon8			AGAGCTTGTCTCA	AK128026	CCDS5435.2, CCDS59050.1, CCDS75577.1	7p14.3	2006-08-21			ENSG00000180347	ENSG00000180347			27363	protein-coding gene	gene with protein product						14702039	Standard	NM_001257967		Approved	FLJ38344	uc011kad.1	Q6ZRS4	OTTHUMG00000128611	ENST00000407970.3:c.1124T>C	chr7.hg19:g.31618002T>C	ENSP00000384416:p.Leu375Ser	86.0	0.0		138.0	56.0	NM_001257968	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Missense_Mutation	SNP	ENST00000407970.3	hg19	CCDS5435.2	.	.	.	.	.	.	.	.	.	.	T	15.04	2.716345	0.48622	.	.	ENSG00000180347	ENST00000407970;ENST00000451887;ENST00000538406;ENST00000409210	T;T;T	0.27256	1.94;1.94;1.68	5.61	1.93	0.25924	.	.	.	.	.	T	0.24812	0.0602	M	0.66939	2.045	0.09310	N	1	B;B;B	0.22683	0.073;0.073;0.073	B;B;B	0.23716	0.048;0.048;0.048	T	0.26744	-1.0094	8	.	.	.	-6.5141	5.7321	0.18047	0.0:0.1504:0.1551:0.6944	.	401;385;375	F5H3V5;F5H2J8;Q6ZRS4	.;.;CC129_HUMAN	S	375;401;385;283	ENSP00000384416:L375S;ENSP00000395835:L401S;ENSP00000387214:L283S	.	L	+	2	0	CCDC129	31584527	0.001000	0.12720	0.000000	0.03702	0.010000	0.07245	0.857000	0.27831	0.146000	0.19002	0.533000	0.62120	TTG	.	.		0.498	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300		C	31618002	T	C	31618002	3	2	368	1	0	0	0	0	1	0	0	0	2766	1821	63	2	1150	2	CCDC129	7	31618002	Missense_Mutation	SNP	T	TCGA-ZP-A9D2-01A-11D-A382-10	11418148	31618002	127520661	27	51098										
RELN	5649	hgsc.bcm.edu	37	chr7	103251167	103251167	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	tttctggggaagaagcactaTgactctcctccactgtgtaa	9	10	2	2			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr7:103251167T>C	ENST00000428762.1	-	22	3142	c.2983A>G	c.(2983-2985)Ata>Gta	p.I995V	RELN_ENST00000424685.2_Missense_Mutation_p.I995V|RELN_ENST00000343529.5_Missense_Mutation_p.I995V	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	995					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		AGAAGCACTATGACTCTCCTC	0.393																																					p.I995V	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.A2983G						.						176	141	153					7																	103251167		2203	4300	6503	SO:0001583	missense	5649	exon22			GCACTATGACTCT		CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.2983A>G	chr7.hg19:g.103251167T>C	ENSP00000392423:p.Ile995Val	59.0	0.0		57.0	19.0	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	hg19	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	T	15.68	2.905559	0.52333	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.21932	2.0;2.0;1.98	6.17	6.17	0.99709	.	0.296669	0.38111	N	0.001818	T	0.09686	0.0238	N	0.01352	-0.895	0.25587	N	0.986733	B;B	0.06786	0.001;0.001	B;B	0.10450	0.005;0.001	T	0.29181	-1.0020	10	0.62326	D	0.03	.	15.3933	0.74767	0.0:0.0:0.0:1.0	.	995;995	P78509-2;P78509	.;RELN_HUMAN	V	995	ENSP00000392423:I995V;ENSP00000345694:I995V;ENSP00000388446:I995V	ENSP00000345694:I995V	I	-	1	0	RELN	103038403	1.000000	0.71417	0.904000	0.35570	0.992000	0.81027	5.663000	0.68038	2.371000	0.80710	0.533000	0.62120	ATA	.	.		0.393	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		C	103251167	T	C	103251167	3	2	368	1	0	0	0	0	1	0	0	0	13235	1464	51	2	7575	2	RELN	7	103251167	Missense_Mutation	SNP	T	TCGA-ZP-A9D2-01A-11D-A382-10	71633165	103251167	55887496	28	51099										
PRSS1	5644	hgsc.bcm.edu	37	chr7	142460804	142460804	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	ctgtgcccagaagaacaagcCtggagtctacaccaaggtct	10	12	2	2			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr7:142460804C>T	ENST00000311737.7	+	5	683	c.677C>T	c.(676-678)cCt>cTt	p.P226L	PRSS1_ENST00000486171.1_Missense_Mutation_p.P240L	NM_002769.4	NP_002760.1	P07477	TRY1_HUMAN	protease, serine, 1 (trypsin 1)	226	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cobalamin metabolic process (GO:0009235)|digestion (GO:0007586)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(24)|prostate(2)	38	Melanoma(164;0.047)	all_cancers(3;2.14e-49)|Acute lymphoblastic leukemia(3;7.3e-185)|all_hematologic(3;1.1e-165)	all cancers(2;0.000126)|Colorectal(2;0.000157)|Epithelial(2;0.000191)|COAD - Colon adenocarcinoma(2;0.00189)		Aprotinin(DB06692)	AAGAACAAGCCTGGAGTCTAC	0.507																																					p.P226L		Atlas-SNP	.											.	PRSS1	68	.	0			c.C677T						.						86	87	87					7																	142460804		2203	4300	6503	SO:0001583	missense	5644	exon5			ACAAGCCTGGAGT	M22612	CCDS5872.1	7q34	2012-10-02			ENSG00000204983	ENSG00000204983	3.4.21.4	"Serine peptidases / Serine peptidases"	9475	protein-coding gene	gene with protein product		276000		TRY1			Standard	NM_002769		Approved		uc003wak.2	P07477	OTTHUMG00000158923	ENST00000311737.7:c.677C>T	chr7.hg19:g.142460804C>T	ENSP00000308720:p.Pro226Leu	249.0	0.0		316.0	125.0	NM_002769	A1A509|A6NJ71|B2R5I5|Q5NV57|Q7M4N3|Q7M4N4|Q92955|Q9HAN4|Q9HAN5|Q9HAN6|Q9HAN7	Missense_Mutation	SNP	ENST00000311737.7	hg19	CCDS5872.1	.	.	.	.	.	.	.	.	.	.	C	14.90	2.673440	0.47781	.	.	ENSG00000204983	ENST00000486171;ENST00000311737;ENST00000529243	D;D	0.95137	-3.62;-3.62	3.18	3.18	0.36537	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.85682	D	0.000000	D	0.97663	0.9234	M	0.94101	3.495	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.99;0.993	D	0.98507	1.0617	10	0.87932	D	0	.	13.7261	0.62759	0.0:1.0:0.0:0.0	.	240;226	E7EQ64;P07477	.;TRY1_HUMAN	L	240;226;216	ENSP00000417854:P240L;ENSP00000308720:P226L	ENSP00000308720:P226L	P	+	2	0	PRSS1	142140378	1.000000	0.71417	0.996000	0.52242	0.062000	0.15995	7.492000	0.81482	1.721000	0.51461	0.195000	0.17529	CCT	.	.		0.507	PRSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352538.2			T	142460804	C	T	142460804	3	4	368	1	0	0	0	0	1	0	0	0	12626	681	24	3	695	3	PRSS1	7	142460804	Missense_Mutation	SNP	C	TCGA-ZP-A9D2-01A-11D-A382-10	39209637	142460804	16677859	29	51100										
REPIN1	29803	hgsc.bcm.edu	37	chr7	150068831	150068835	+	Frame_Shift_Del	DEL	CCACC	CCACC	-													0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	cgagctcatctgcggcggtgCcaccctcccgccccggaggc							TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	CCACC	CCACC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr7:150068831_150068835delCCACC	ENST00000425389.2	+	1	579_583	c.501_505delCCACC	c.(499-507)tgccaccctfs	p.HP168fs	REPIN1_ENST00000444957.1_Frame_Shift_Del_p.HP168fs|REPIN1_ENST00000466559.1_3'UTR|REPIN1_ENST00000489432.2_Frame_Shift_Del_p.HP225fs|RP4-584D14.5_ENST00000488310.1_RNA|REPIN1_ENST00000482680.1_3'UTR|REPIN1_ENST00000540729.1_Frame_Shift_Del_p.HP168fs|REPIN1_ENST00000397281.2_Frame_Shift_Del_p.HP168fs|REPIN1_ENST00000479668.1_3'UTR	NM_014374.3	NP_055189.2	Q9BWE0	REPI1_HUMAN	replication initiator 1	168					DNA replication (GO:0006260)|regulation of fatty acid transport (GO:2000191)|regulation of glucose import in response to insulin stimulus (GO:2001273)	cytosolic ribosome (GO:0022626)|lipid particle (GO:0005811)|nuclear membrane (GO:0031965)|nuclear origin of replication recognition complex (GO:0005664)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			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)			TGCGGCGGTGCCACCCTCCCGCCCC	0.644																																					p.224_225del		Atlas-INDEL	.											.	REPIN1	74	.	0			c.671_675del						.																																			SO:0001589	frameshift_variant	29803	exon3			.	AF201303	CCDS43677.1, CCDS47745.1	7q36.1	2013-01-08	2003-08-07	2003-08-08				"Zinc fingers, C2H2-type"	17922	protein-coding gene	gene with protein product	"replication initiation region protein (60kD)", "zinc finger protein AP4", "zinc finger protein 464 (RIP60)"		"zinc finger protein 464 (RIP60)"	ZNF464		10606657	Standard	NM_013400		Approved	RIP60, AP4, H_DJ0584D14.12, Zfp464	uc010lpr.1	Q9BWE0		ENST00000425389.2:c.501_505delCCACC	chr7.hg19:g.150068831_150068835delCCACC	ENSP00000388287:p.His168fs	59.0	0.0		59.0	17.0	NM_001099695	C9J3L7|D3DWZ1|Q7LE03|Q9BUZ6|Q9NZH2|Q9UMP5	Frame_Shift_Del	DEL	ENST00000425389.2	hg19	CCDS43677.1																																																																																			.	.		0.644	REPIN1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376940.1	NM_014374		-	150068835	CCACC	-	150068831	7	5	368	1	0	1	0	1	0	0	0	0	13242	747	26	0	678	0	REPIN1	7	150068831	Frame_Shift_Del	DEL	CCACC	TCGA-ZP-A9D2-01A-11D-A382-10	7608027	150068831	9069832	30	51101										
TNFRSF10B	8795	hgsc.bcm.edu	37	chr8	22884792	22884792	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	attgtcctcagccccaggtcGttgtgagctctggaaaaaga	11	10	2	2	rs138183043		TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr8:22884792G>A	ENST00000276431.4	-	7	1074	c.790C>T	c.(790-792)Cga>Tga	p.R264*	TNFRSF10B_ENST00000347739.3_Nonsense_Mutation_p.R235*|TNFRSF10B_ENST00000519910.1_5'Flank|TNFRSF10B_ENST00000542226.1_Nonsense_Mutation_p.R84*	NM_003842.4|NM_147187.2	NP_003833.4|NP_671716.2	O14763	TR10B_HUMAN	tumor necrosis factor receptor superfamily, member 10b	264					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell surface receptor signaling pathway (GO:0007166)|cellular response to mechanical stimulus (GO:0071260)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of apoptotic process (GO:0042981)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to endoplasmic reticulum stress (GO:0034976)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|TRAIL binding (GO:0045569)			NS(1)|endometrium(2)|large_intestine(7)|liver(1)|lung(3)|skin(1)	15		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0179)|COAD - Colon adenocarcinoma(73;0.0703)		GCCCCAGGTCGTTGTGAGCTC	0.567																																					p.R264X	GBM(94;1064 1342 1839 21060 42553)	Atlas-SNP	.											.	TNFRSF10B	34	.	0			c.C790T						.	G	stop/ARG,stop/ARG	0,4406		0,0,2203	68	66	67		790,703	-0.2	0	8	dbSNP_134	67	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained,stop-gained	TNFRSF10B	NM_003842.4,NM_147187.2	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	264/441,235/412	22884792	1,13005	2203	4300	6503	SO:0001587	stop_gained	8795	exon7			CAGGTCGTTGTGA	AF012628	CCDS6035.1, CCDS6036.1	8p22-p21	2006-02-22			ENSG00000120889	ENSG00000120889		"Tumor necrosis factor receptor superfamily", "CD molecules"	11905	protein-coding gene	gene with protein product		603612				9285725, 9311998	Standard	NM_003842		Approved	DR5, KILLER, TRICK2A, TRAIL-R2, TRICKB, CD262	uc003xcu.2	O14763	OTTHUMG00000097826	ENST00000276431.4:c.790C>T	chr8.hg19:g.22884792G>A	ENSP00000276431:p.Arg264*	65.0	0.0		59.0	28.0	NM_003842	O14720|O15508|O15517|O15531|Q6UXM8|Q7Z360|Q9BVE0	Nonsense_Mutation	SNP	ENST00000276431.4	hg19	CCDS6035.1	.	.	.	.	.	.	.	.	.	.	g	16.59	3.166475	0.57476	0.0	1.16E-4	ENSG00000120889	ENST00000276431;ENST00000347739;ENST00000542226	.	.	.	1.77	-0.235	0.13071	.	9.625390	0.01527	U	0.018637	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.14252	T	0.57	.	3.0633	0.06206	0.0:0.5031:0.2997:0.1973	.	.	.	.	X	264;235;84	.	ENSP00000276431:R264X	R	-	1	2	TNFRSF10B	22940737	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.181000	0.09740	-0.081000	0.12662	-0.226000	0.12346	CGA	.	G|1.000;A|0.000		0.567	TNFRSF10B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215099.2	NM_147187		A	22884792	G	A	22884792	4	1	368	1	0	0	0	0	0	1	0	0	16296	1153	40	1	544	1	TNFRSF10B	8	22884792	Nonsense_Mutation	SNP	G	TCGA-ZP-A9D2-01A-11D-A382-10		22884792	123479230	31	51102										
FBXO43	286151	hgsc.bcm.edu	37	chr8	101153292	101153292	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	ggacaatctgcttttcctctTctgtctctgactgcgagctt	8	12	4	1			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr8:101153292T>G	ENST00000428847.2	-	2	1506	c.1190A>C	c.(1189-1191)gAa>gCa	p.E397A		NM_001029860.3	NP_001025031.2	Q4G163	FBX43_HUMAN	F-box protein 43	397					meiotic nuclear division (GO:0007126)|negative regulation of meiosis (GO:0045835)|negative regulation of protein catabolic process (GO:0042177)|protein ubiquitination (GO:0016567)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(5)|lung(14)|prostate(1)|skin(5)|urinary_tract(1)	31	all_cancers(14;0.000139)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000274)|all_lung(17;0.000798)		Epithelial(11;1.17e-09)|all cancers(13;1.34e-07)|OV - Ovarian serous cystadenocarcinoma(57;3.82e-05)|STAD - Stomach adenocarcinoma(118;0.0957)			CTTTTCCTCTTCTGTCTCTGA	0.507																																					p.E397A		Atlas-SNP	.											.	FBXO43	155	.	0			c.A1190C						.						114	111	112					8																	101153292		1989	4179	6168	SO:0001583	missense	286151	exon2			TCCTCTTCTGTCT	BC028709	CCDS47904.1	8q22.3	2004-08-24			ENSG00000156509	ENSG00000156509		"F-boxes /  "other""	28521	protein-coding gene	gene with protein product		609110					Standard	NR_036491		Approved	Fbx43	uc003yjd.3	Q4G163	OTTHUMG00000164803	ENST00000428847.2:c.1190A>C	chr8.hg19:g.101153292T>G	ENSP00000403293:p.Glu397Ala	103.0	0.0		109.0	31.0	NM_001029860		Missense_Mutation	SNP	ENST00000428847.2	hg19	CCDS47904.1	.	.	.	.	.	.	.	.	.	.	T	18.31	3.595499	0.66219	.	.	ENSG00000156509	ENST00000428847	T	0.40756	1.02	5.01	5.01	0.66863	.	0.114509	0.56097	D	0.000021	T	0.52419	0.1733	L	0.56769	1.78	0.46437	D	0.999042	D;D	0.62365	0.991;0.991	P;P	0.53760	0.734;0.734	T	0.54794	-0.8240	10	0.49607	T	0.09	-11.9298	15.0166	0.71591	0.0:0.0:0.0:1.0	.	363;397	C9J908;Q4G163	.;FBX43_HUMAN	A	397	ENSP00000403293:E397A	ENSP00000403293:E397A	E	-	2	0	FBXO43	101222468	1.000000	0.71417	0.997000	0.53966	0.963000	0.63663	7.069000	0.76755	2.003000	0.58678	0.533000	0.62120	GAA	.	.		0.507	FBXO43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380380.1	XM_209918		G	101153292	T	G	101153292	3	3	368	1	0	0	0	0	1	0	0	0	5760	1783	62	5	952	5	FBXO43	8	101153292	Missense_Mutation	SNP	T	TCGA-ZP-A9D2-01A-11D-A382-10	78268500	101153292	45210730	32	51103										
CSMD3	114788	hgsc.bcm.edu	37	chr8	113599446	113599446	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	aaattccttcattattcgttGcagatgcaccacattcagct	5	11	2	1			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr8:113599446G>C	ENST00000297405.5	-	23	3978	c.3734C>G	c.(3733-3735)gCa>gGa	p.A1245G	CSMD3_ENST00000352409.3_Missense_Mutation_p.A1245G|CSMD3_ENST00000343508.3_Missense_Mutation_p.A1205G|CSMD3_ENST00000455883.2_Missense_Mutation_p.A1141G	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1245	CUB 7. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						ATTATTCGTTGCAGATGCACC	0.348										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.A1245G		Atlas-SNP	.											.	CSMD3	2325	.	0			c.C3734G						.						110	105	107					8																	113599446		2203	4300	6503	SO:0001583	missense	114788	exon23			TTCGTTGCAGATG	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.3734C>G	chr8.hg19:g.113599446G>C	ENSP00000297405:p.Ala1245Gly	112.0	0.0		106.0	43.0	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	15.82	2.946786	0.53186	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.28666	1.6;1.6;1.6;1.6;1.6	4.14	4.14	0.48551	Complement control module (1);CUB (5);	0.167271	0.40640	N	0.001057	T	0.24198	0.0586	L	0.32530	0.975	0.29213	N	0.874458	P;B;B	0.37824	0.609;0.433;0.099	B;B;B	0.35413	0.185;0.202;0.096	T	0.09487	-1.0672	10	0.25751	T	0.34	.	16.9637	0.86280	0.0:0.0:1.0:0.0	.	1141;1245;1205	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	G	1205;1245;585;1141;1245	ENSP00000345799:A1205G;ENSP00000297405:A1245G;ENSP00000341558:A585G;ENSP00000412263:A1141G;ENSP00000343124:A1245G	ENSP00000297405:A1245G	A	-	2	0	CSMD3	113668622	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.161000	0.58170	2.303000	0.77524	0.591000	0.81541	GCA	.	.		0.348	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		C	113599446	G	C	113599446	3	2	368	1	0	0	0	0	1	0	0	0	3948	1319	46	4	7585	4	CSMD3	8	113599446	Missense_Mutation	SNP	G	TCGA-ZP-A9D2-01A-11D-A382-10	12446154	113599446	32764576	33	51104										
AKR1C3	8644	hgsc.bcm.edu	37	chr10	5136645	5136645	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	aagtgacagggaatggattcCaaacaccagtgtgtaaagct	11	7	0	1			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr10:5136645C>T	ENST00000380554.3	+	1	661	c.9C>T	c.(7-9)tcC>tcT	p.S3S	U8_ENST00000459536.1_RNA|AKR1C3_ENST00000439082.2_Intron|AKR1C3_ENST00000605149.1_Intron|AKR1C3_ENST00000470862.2_Intron	NM_001253908.1|NM_003739.5	NP_001240837.1|NP_003730.4	P42330	AK1C3_HUMAN	aldo-keto reductase family 1, member C3	3				S -> P (in Ref. 3; no nucleotide entry). {ECO:0000305}.	arachidonic acid metabolic process (GO:0019369)|cellular response to cadmium ion (GO:0071276)|cellular response to calcium ion (GO:0071277)|cellular response to corticosteroid stimulus (GO:0071384)|cellular response to jasmonic acid stimulus (GO:0071395)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to reactive oxygen species (GO:0034614)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|farnesol catabolic process (GO:0016488)|G-protein coupled receptor signaling pathway (GO:0007186)|keratinocyte differentiation (GO:0030216)|male gonad development (GO:0008584)|multicellular organismal macromolecule metabolic process (GO:0044259)|negative regulation of retinoic acid biosynthetic process (GO:1900053)|oxidation-reduction process (GO:0055114)|phototransduction, visible light (GO:0007603)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|progesterone metabolic process (GO:0042448)|prostaglandin metabolic process (GO:0006693)|protein import into nucleus, translocation (GO:0000060)|regulation of retinoic acid receptor signaling pathway (GO:0048385)|regulation of testosterone biosynthetic process (GO:2000224)|renal absorption (GO:0070293)|response to nutrient (GO:0007584)|response to prostaglandin (GO:0034694)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity (GO:0047020)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase activity (GO:0047023)|delta4-3-oxosteroid 5beta-reductase activity (GO:0047787)|dihydrotestosterone 17-beta-dehydrogenase activity (GO:0035410)|geranylgeranyl reductase activity (GO:0045550)|indanol dehydrogenase activity (GO:0047718)|ketoreductase activity (GO:0045703)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|prostaglandin D2 11-ketoreductase activity (GO:0036131)|prostaglandin F receptor activity (GO:0004958)|prostaglandin-F synthase activity (GO:0047017)|retinal dehydrogenase activity (GO:0001758)|retinol dehydrogenase activity (GO:0004745)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)|testosterone dehydrogenase (NAD+) activity (GO:0047035)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|skin(1)	14					Bimatoprost(DB00905)|Doxorubicin(DB00997)	GAATGGATTCCAAACACCAGT	0.458																																					p.S3S		Atlas-SNP	.											.	AKR1C3	21	.	0			c.C9T						.						208	180	190					10																	5136645		2203	4299	6502	SO:0001819	synonymous_variant	8644	exon1			GGATTCCAAACAC	L43839	CCDS7063.1, CCDS73062.1	10p15-p14	2012-12-04	2012-12-04		ENSG00000196139	ENSG00000196139	1.1.1.213, 1.1.1.188	"Aldo-keto reductases"	386	protein-coding gene	gene with protein product	"dihydrodiol dehydrogenase X", "prostaglandin F synthase", "3-alpha hydroxysteroid dehydrogenase, type II"	603966	"hydroxysteroid (17-beta) dehydrogenase 5", "aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II)"	HSD17B5		7650035, 9792917	Standard	NM_003739		Approved	KIAA0119, DDX, HAKRB, PGFS	uc021pml.1	P42330	OTTHUMG00000017585	ENST00000380554.3:c.9C>T	chr10.hg19:g.5136645C>T		108.0	0.0		113.0	38.0	NM_001253909	A8K2V0|B4DL37|Q5T2L1|Q96DJ1|Q96KI8|Q99530|Q9UCX1|Q9UII3|Q9UKL9	Silent	SNP	ENST00000380554.3	hg19	CCDS7063.1																																																																																			.	.		0.458	AKR1C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046533.2	NM_003739		T	5136645	C	T	5136645	2	4	368	1	0	0	0	0	0	0	0	1	471	581	21	3		3	AKR1C3	10	5136645	Silent	SNP	C	TCGA-ZP-A9D2-01A-11D-A382-10		5136645	130398102	34	51105										
PARD3	56288	hgsc.bcm.edu	37	chr10	34671515	34671515	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	tgcctatttttttggtgttaTaaccactgcttacagtcgta	7	8	0	0			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr10:34671515T>C	ENST00000374789.3	-	9	1677	c.1352A>G	c.(1351-1353)tAt>tGt	p.Y451C	PARD3_ENST00000544292.1_Missense_Mutation_p.Y181C|PARD3_ENST00000374776.1_Missense_Mutation_p.Y451C|PARD3_ENST00000340077.5_Missense_Mutation_p.Y451C|PARD3_ENST00000545260.1_Missense_Mutation_p.Y407C|PARD3_ENST00000545693.1_Missense_Mutation_p.Y451C|PARD3_ENST00000350537.4_Missense_Mutation_p.Y451C|PARD3_ENST00000374790.3_Missense_Mutation_p.Y407C|PARD3_ENST00000346874.4_Missense_Mutation_p.Y451C|PARD3_ENST00000374788.3_Missense_Mutation_p.Y451C|PARD3_ENST00000374794.3_Missense_Mutation_p.Y407C|PARD3_ENST00000374773.1_Missense_Mutation_p.Y451C	NM_019619.3	NP_062565.2	Q8TEW0	PARD3_HUMAN	par-3 family cell polarity regulator	451					apical constriction (GO:0003383)|asymmetric cell division (GO:0008356)|axonogenesis (GO:0007409)|cell cycle (GO:0007049)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|centrosome localization (GO:0051642)|establishment of epithelial cell polarity (GO:0090162)|establishment or maintenance of cell polarity (GO:0007163)|microtubule cytoskeleton organization (GO:0000226)|myelination in peripheral nervous system (GO:0022011)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|positive regulation of myelination (GO:0031643)|protein complex assembly (GO:0006461)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein targeting to membrane (GO:0006612)|regulation of actin filament-based process (GO:0032970)|regulation of cellular localization (GO:0060341)|tight junction assembly (GO:0070830)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing, spreading of cells (GO:0044319)	apical part of cell (GO:0045177)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|internode region of axon (GO:0033269)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|tight junction (GO:0005923)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	63		Breast(68;0.0707)				TTTGGTGTTATAACCACTGCT	0.443																																					p.Y451C		Atlas-SNP	.											.	PARD3	131	.	0			c.A1352G						.						121	116	118					10																	34671515		2203	4300	6503	SO:0001583	missense	56288	exon9			GTGTTATAACCAC	AF252293	CCDS7178.1, CCDS53509.1, CCDS53510.1, CCDS53511.1, CCDS53512.1, CCDS53513.1, CCDS53514.1, CCDS53515.1, CCDS53516.1	10p11.22	2014-06-13	2013-08-28		ENSG00000148498	ENSG00000148498			16051	protein-coding gene	gene with protein product	"atypical PKC isotype-specific interacting protein", "par-3 family cell polarity regulator alpha", "protein phosphatase 1, regulatory subunit 118"	606745	"par-3 (partitioning defective 3, C.elegans) homolog", "par-3 partitioning defective 3 homolog (C. elegans)"			10934474	Standard	NM_001184790		Approved	PAR3, PARD3A, Bazooka, Baz, ASIP, PPP1R118	uc010qej.2	Q8TEW0	OTTHUMG00000017948	ENST00000374789.3:c.1352A>G	chr10.hg19:g.34671515T>C	ENSP00000363921:p.Tyr451Cys	87.0	0.0		67.0	21.0	NM_001184788	F5H5T0|Q5T2U1|Q5VUA2|Q5VUA3|Q5VWV0|Q5VWV1|Q5VWV3|Q5VWV4|Q5VWV5|Q6IQ47|Q8TCZ9|Q8TEW1|Q8TEW2|Q8TEW3|Q96K28|Q96RM6|Q96RM7|Q9BY57|Q9BY58|Q9HC48|Q9NWL4|Q9NYE6	Missense_Mutation	SNP	ENST00000374789.3	hg19	CCDS7178.1	.	.	.	.	.	.	.	.	.	.	T	16.76	3.212609	0.58452	.	.	ENSG00000148498	ENST00000545693;ENST00000545260;ENST00000374789;ENST00000374788;ENST00000346874;ENST00000374794;ENST00000350537;ENST00000374790;ENST00000374776;ENST00000340077;ENST00000374773;ENST00000544292	T;T;T;T;T;T;T;T;T;T;T;T	0.18502	2.21;2.21;2.21;2.21;2.21;2.21;2.21;2.21;2.21;2.21;2.21;2.21	5.88	5.88	0.94601	PDZ/DHR/GLGF (1);	0.224065	0.47852	D	0.000210	T	0.39118	0.1066	M	0.62723	1.935	0.45762	D	0.998656	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.76494	0.997;0.999;0.999;0.997;0.999;0.997;0.997;0.963;0.963;0.994;0.998;0.987;0.984;0.991;0.966	P;D;D;P;D;P;P;P;P;P;P;P;P;P;P	0.71184	0.895;0.93;0.972;0.852;0.972;0.852;0.852;0.537;0.631;0.716;0.867;0.841;0.873;0.902;0.873	T	0.04565	-1.0942	10	0.37606	T	0.19	.	16.3009	0.82811	0.0:0.0:0.0:1.0	.	407;407;451;451;451;451;451;451;407;451;451;451;451;451;181	Q8TEW0-5;Q8TEW0-3;Q8TEW0-7;Q8TEW0-6;F5H5T0;Q8TEW0-4;Q8TEW0-2;Q8TEW0;Q5VWV2;Q6IQ47;Q5VWU8;Q8TEW0-8;Q8TEW0-9;Q8TEW0-10;F5GZI3	.;.;.;.;.;.;.;PARD3_HUMAN;.;.;.;.;.;.;.	C	451;407;451;451;451;407;451;407;451;451;451;181	ENSP00000443147:Y451C;ENSP00000440857:Y407C;ENSP00000363921:Y451C;ENSP00000363920:Y451C;ENSP00000340591:Y451C;ENSP00000363926:Y407C;ENSP00000311986:Y451C;ENSP00000363922:Y407C;ENSP00000363908:Y451C;ENSP00000341844:Y451C;ENSP00000363905:Y451C;ENSP00000444429:Y181C	ENSP00000341844:Y451C	Y	-	2	0	PARD3	34711521	1.000000	0.71417	0.650000	0.29550	0.655000	0.38815	5.210000	0.65214	2.246000	0.74042	0.533000	0.62120	TAT	.	.		0.443	PARD3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047527.1	NM_019619		C	34671515	T	C	34671515	3	2	368	1	0	0	0	0	1	0	0	0	11452	1406	49	2	2821	2	PARD3	10	34671515	Missense_Mutation	SNP	T	TCGA-ZP-A9D2-01A-11D-A382-10	29534870	34671515	100863232	35	51106										
TBC1D12	23232	hgsc.bcm.edu	37	chr10	96163102	96163102	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	gtcggcgccgggggtcccgaGgagggcgcgccccctgccac	18	17	0	0			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr10:96163102G>T	ENST00000225235.4	+	1	842	c.732G>T	c.(730-732)gaG>gaT	p.E244D		NM_015188.1	NP_056003.1	O60347	TBC12_HUMAN	TBC1 domain family, member 12	244							Rab GTPase activator activity (GO:0005097)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(2)	20		Colorectal(252;0.0429)				GGGGTCCCGAGGAGGGCGCGC	0.706																																					p.E244D		Atlas-SNP	.											.	TBC1D12	51	.	0			c.G732T						.						4	7	6					10																	96163102		1623	3594	5217	SO:0001583	missense	23232	exon1			TCCCGAGGAGGGC	AB011180	CCDS41553.1	10q23.33	2013-09-20			ENSG00000108239	ENSG00000108239			29082	protein-coding gene	gene with protein product						9628581	Standard	NM_015188		Approved	KIAA0608	uc001kjr.2	O60347	OTTHUMG00000018794	ENST00000225235.4:c.732G>T	chr10.hg19:g.96163102G>T	ENSP00000225235:p.Glu244Asp	203.0	0.0		210.0	79.0	NM_015188	Q5VYA6|Q8WX26|Q8WX59|Q9UG83	Missense_Mutation	SNP	ENST00000225235.4	hg19	CCDS41553.1	.	.	.	.	.	.	.	.	.	.	G	10.84	1.464795	0.26335	.	.	ENSG00000108239	ENST00000225235	T	0.05447	3.44	3.26	1.34	0.21922	.	1.938870	0.03361	U	0.197532	T	0.03871	0.0109	N	0.08118	0	0.09310	N	1	B	0.17667	0.023	B	0.12156	0.007	T	0.41680	-0.9495	10	0.15499	T	0.54	.	6.9076	0.24317	0.2459:0.0:0.7541:0.0	.	244	O60347	TBC12_HUMAN	D	244	ENSP00000225235:E244D	ENSP00000225235:E244D	E	+	3	2	TBC1D12	96153092	0.979000	0.34478	0.014000	0.15608	0.067000	0.16453	1.762000	0.38451	0.212000	0.20703	0.462000	0.41574	GAG	.	.		0.706	TBC1D12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049482.2			T	96163102	G	T	96163102	3	4	368	1	0	0	0	0	1	0	0	0	15616	991	35	3	734	3	TBC1D12	10	96163102	Missense_Mutation	SNP	G	TCGA-ZP-A9D2-01A-11D-A382-10	61491587	96163102	39371645	36	51107										
TRPM5	29850	hgsc.bcm.edu	37	chr11	2434047	2434047	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	agggtgacctcgggccctgaGgggccctgggggggcggcct	21	12	0	2			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr11:2434047G>A	ENST00000155858.6	-	15	2300	c.2292C>T	c.(2290-2292)ccC>ccT	p.P764P	TRPM5_ENST00000452833.1_Silent_p.P766P|TRPM5_ENST00000533060.1_Silent_p.P764P|TRPM5_ENST00000528453.1_Silent_p.P764P	NM_014555.3	NP_055370.1			transient receptor potential cation channel, subfamily M, member 5											breast(1)|central_nervous_system(1)|endometrium(4)|liver(1)|lung(8)|ovary(2)|prostate(2)|skin(2)|urinary_tract(2)	23		Medulloblastoma(188;0.0049)|Breast(177;0.00586)|all_epithelial(84;0.0075)|Ovarian(85;0.0256)|all_neural(188;0.0311)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|LUSC - Lung squamous cell carcinoma(625;0.191)		CGGGCCCTGAGGGGCCCTGGG	0.627																																					p.P764P	NSCLC(1;49 61 17205 18850 43201)	Atlas-SNP	.											.	TRPM5	86	.	0			c.C2292T						.						19	20	19					11																	2434047		2187	4294	6481	SO:0001819	synonymous_variant	29850	exon15			CCCTGAGGGGCCC	AF177473	CCDS31340.1	11p15.5	2011-12-14			ENSG00000070985	ENSG00000070985		"Voltage-gated ion channels / Transient receptor potential cation channels"	14323	protein-coding gene	gene with protein product		604600				10607831, 16382100	Standard	NM_014555		Approved	LTRPC5, MTR1	uc001lwm.4	Q9NZQ8	OTTHUMG00000009896	ENST00000155858.6:c.2292C>T	chr11.hg19:g.2434047G>A		153.0	0.0		148.0	44.0	NM_014555		Silent	SNP	ENST00000155858.6	hg19	CCDS31340.1																																																																																			.	.		0.627	TRPM5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000027378.1	NM_014555		A	2434047	G	A	2434047	2	1	368	1	0	0	0	0	0	0	0	1	16604	987	35	3		3	TRPM5	11	2434047	Silent	SNP	G	TCGA-ZP-A9D2-01A-11D-A382-10		2434047	132572469	37	51108										
MS4A6A	64231	hgsc.bcm.edu	37	chr11	59949192	59949192	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	gtctcattgggaacaggttgTgatgtcatgatggtgttgcc	14	6	2	2			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr11:59949192T>C	ENST00000530839.1	-	3	501	c.9A>G	c.(7-9)tcA>tcG	p.S3S	MS4A6A_ENST00000529054.1_Silent_p.S31S|MS4A6A_ENST00000533023.1_Silent_p.S3S|MS4A6A_ENST00000420732.2_Silent_p.S3S|MS4A6A_ENST00000412309.2_Silent_p.S31S|MS4A6A_ENST00000528851.1_Silent_p.S3S|MS4A6A_ENST00000529906.1_5'Flank|MS4A6A_ENST00000426738.2_Silent_p.S3S|MS4A6A_ENST00000323961.3_Silent_p.S3S|MS4A6A_ENST00000532169.1_Silent_p.S3S	NM_152852.2	NP_690591.1	Q9H2W1	M4A6A_HUMAN	membrane-spanning 4-domains, subfamily A, member 6A	3						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						GAACAGGTTGTGATGTCATGA	0.448																																					p.S31S		Atlas-SNP	.											.	MS4A6A	85	.	0			c.A93G						.						210	188	196					11																	59949192		2201	4295	6496	SO:0001819	synonymous_variant	64231	exon3			AGGTTGTGATGTC	AB013104	CCDS7981.1, CCDS44615.1, CCDS44616.1, CCDS58134.1	11q12.1	2008-03-25			ENSG00000110077	ENSG00000110077			13375	protein-coding gene	gene with protein product		606548		MS4A6		11245982, 11401424	Standard	NM_152852		Approved	CD20L3	uc010rla.2	Q9H2W1	OTTHUMG00000167241	ENST00000530839.1:c.9A>G	chr11.hg19:g.59949192T>C		185.0	0.0		173.0	60.0	NM_001247999	A8K755|F8W9K1|Q7Z4E8|Q8TBV7|Q8TEZ4|Q8TEZ5|Q96PG6|Q9H2L1|Q9H2N3|Q9H3V1|Q9HC76	Silent	SNP	ENST00000530839.1	hg19	CCDS7981.1																																																																																			.	.		0.448	MS4A6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393848.1			C	59949192	T	C	59949192	2	2	368	1	0	0	0	0	0	0	0	1	9873	1683	59	2		2	MS4A6A	11	59949192	Silent	SNP	T	TCGA-ZP-A9D2-01A-11D-A382-10	57515145	59949192	75057324	38	51109										
BAZ2A	11176	hgsc.bcm.edu	37	chr12	56993613	56993613	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	gaaactcatcattgtcacccTtccggcagactagacatgtc	7	13	3	2			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr12:56993613T>C	ENST00000551812.1	-	26	5244	c.5051A>G	c.(5050-5052)aAg>aGg	p.K1684R	BAZ2A_ENST00000553222.1_5'Flank|BAZ2A_ENST00000549884.1_Missense_Mutation_p.K1682R|BAZ2A_ENST00000179765.5_Missense_Mutation_p.K1652R|BAZ2A_ENST00000379441.3_Missense_Mutation_p.K1654R	NM_013449.3	NP_038477.2	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	1684					chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA methylation (GO:0006306)|heterochromatin assembly involved in chromatin silencing (GO:0070869)|histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|histone H4 deacetylation (GO:0070933)|histone H4-K20 methylation (GO:0034770)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|nucleolus (GO:0005730)|rDNA heterochromatin (GO:0033553)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|lysine-acetylated histone binding (GO:0070577)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(15)|urinary_tract(1)	31						ATTGTCACCCTTCCGGCAGAC	0.572																																					p.K1684R		Atlas-SNP	.											.	BAZ2A	263	.	0			c.A5051G						.						76	78	77					12																	56993613		2068	4212	6280	SO:0001583	missense	11176	exon26			TCACCCTTCCGGC	AB032254	CCDS44924.1, CCDS73483.1	12q13.3	2013-01-28				ENSG00000076108		"Zinc fingers, PHD-type"	962	protein-coding gene	gene with protein product	"TTF-I interacting peptide 5"	605682				10662543, 11532953	Standard	XM_005268596		Approved	KIAA0314, TIP5, WALp3	uc001slq.1	Q9UIF9	OTTHUMG00000170332	ENST00000551812.1:c.5051A>G	chr12.hg19:g.56993613T>C	ENSP00000446880:p.Lys1684Arg	89.0	0.0		100.0	29.0	NM_013449	B3KN66|O00536|O15030|Q68DI8|Q96H26	Missense_Mutation	SNP	ENST00000551812.1	hg19	CCDS44924.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.706213	0.89018	.	.	ENSG00000076108	ENST00000379441;ENST00000179765;ENST00000551812;ENST00000549787;ENST00000549884	D;D;D;D;D	0.84873	-1.91;-1.91;-1.91;-1.91;-1.91	5.01	5.01	0.66863	Zinc finger, PHD-finger (2);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.87845	0.6280	L	0.34521	1.04	0.58432	D	0.999998	D;P;P;D	0.89917	0.998;0.676;0.771;1.0	D;P;P;D	0.85130	0.991;0.711;0.644;0.997	D	0.87757	0.2596	10	0.44086	T	0.13	-22.0809	14.3902	0.66973	0.0:0.0:0.0:1.0	.	1682;1680;1684;1657	F8VU39;Q9UIF9-3;Q9UIF9;Q9UIF9-2	.;.;BAZ2A_HUMAN;.	R	1654;1652;1684;616;1682	ENSP00000368754:K1654R;ENSP00000179765:K1652R;ENSP00000446880:K1684R;ENSP00000448760:K616R;ENSP00000447941:K1682R	ENSP00000179765:K1652R	K	-	2	0	BAZ2A	55279880	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.602000	0.54066	2.177000	0.69029	0.533000	0.62120	AAG	.	.		0.572	BAZ2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408561.1	NM_013449		C	56993613	T	C	56993613	3	2	368	1	0	0	0	0	1	0	0	0	1331	1609	56	2	682	2	BAZ2A	12	56993613	Missense_Mutation	SNP	T	TCGA-ZP-A9D2-01A-11D-A382-10		56993613	76858282	39	51110										
ELK3	2004	hgsc.bcm.edu	37	chr12	96641039	96641039	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	ccgaagacagcccccccgtgGaagaagtcaggactgtgatc	12	13	1	3			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr12:96641039G>T	ENST00000228741.3	+	3	855	c.529G>T	c.(529-531)Gaa>Taa	p.E177*	ELK3_ENST00000552142.1_Intron	NM_005230.2	NP_005221.2	P41970	ELK3_HUMAN	ELK3, ETS-domain protein (SRF accessory protein 2)	177					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|wound healing (GO:0042060)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	purine-rich negative regulatory element binding (GO:0032422)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(5)|ovary(2)|prostate(1)|stomach(2)	20	all_cancers(2;0.00173)					CCCCCCCGTGGAAGAAGTCAG	0.597																																					p.E177X		Atlas-SNP	.											.	ELK3	36	.	0			c.G529T						.						55	57	56					12																	96641039		2203	4300	6503	SO:0001587	stop_gained	2004	exon3			CCCGTGGAAGAAG	BC017371	CCDS9060.1	12q23	2006-12-30				ENSG00000111145			3325	protein-coding gene	gene with protein product		600247				7851904	Standard	NM_005230		Approved	ERP, NET, SAP2	uc001teo.1	P41970		ENST00000228741.3:c.529G>T	chr12.hg19:g.96641039G>T	ENSP00000228741:p.Glu177*	90.0	0.0		90.0	38.0	NM_005230	B2R6S6|Q6FG57|Q6GU29|Q9UD17	Nonsense_Mutation	SNP	ENST00000228741.3	hg19	CCDS9060.1	.	.	.	.	.	.	.	.	.	.	G	39	7.612086	0.98390	.	.	ENSG00000111145	ENST00000228741	.	.	.	5.65	5.65	0.86999	.	0.382249	0.32343	N	0.006229	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	19.7205	0.96142	0.0:0.0:1.0:0.0	.	.	.	.	X	177	.	ENSP00000228741:E177X	E	+	1	0	ELK3	95165170	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	6.594000	0.74104	2.671000	0.90904	0.462000	0.41574	GAA	.	.		0.597	ELK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408694.1	NM_005230		T	96641039	G	T	96641039	4	4	368	1	0	0	0	0	0	1	0	0	5062	1175	41	3	535	3	ELK3	12	96641039	Nonsense_Mutation	SNP	G	TCGA-ZP-A9D2-01A-11D-A382-10	39647426	96641039	37210856	40	51111										
FZD10	11211	hgsc.bcm.edu	37	chr12	130648052	130648052	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	tgaaggacgggggccccgggCgcggcggctgcgacaacccg	19	14	0	1			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr12:130648052C>T	ENST00000229030.4	+	1	1049	c.565C>T	c.(565-567)Cgc>Tgc	p.R189C	FZD10-AS1_ENST00000505807.2_RNA|FZD10_ENST00000539839.1_Missense_Mutation_p.A156V			Q9ULW2	FZD10_HUMAN	frizzled class receptor 10	189					brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|gonad development (GO:0008406)|negative regulation of Rho GTPase activity (GO:0034259)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of actin cytoskeleton organization (GO:0032956)|vasculature development (GO:0001944)	cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|pancreas(1)|prostate(3)|urinary_tract(1)	35	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.3e-06)|Epithelial(86;1.66e-05)|all cancers(50;5.18e-05)		gggccccgggcgcggcggcTG	0.761																																					p.R189C		Atlas-SNP	.											.	FZD10	95	.	0			c.C565T						.						7	9	8					12																	130648052		2060	4016	6076	SO:0001583	missense	11211	exon1			CCCGGGCGCGGCG	AB027464	CCDS9267.1	12q24.33	2014-01-29	2014-01-29			ENSG00000111432		"GPCR / Class F : Frizzled receptors", "CD molecules"	4039	protein-coding gene	gene with protein product		606147	"frizzled (Drosophila) homolog 10", "frizzled homolog 10 (Drosophila)", "frizzled 10, seven transmembrane spanning receptor", "frizzled family receptor 10"			10448064	Standard	NM_007197		Approved	CD350	uc001uii.3	Q9ULW2		ENST00000229030.4:c.565C>T	chr12.hg19:g.130648052C>T	ENSP00000229030:p.Arg189Cys	98.0	0.0		79.0	9.0	NM_007197		Missense_Mutation	SNP	ENST00000229030.4	hg19	CCDS9267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.416|8.416	0.845394|0.845394	0.16963|0.16963	.|.	.|.	ENSG00000111432|ENSG00000111432	ENST00000539839|ENST00000229030	.|T	.|0.76968	.|-1.06	4.94|4.94	4.94|4.94	0.65067|0.65067	.|.	.|0.701794	.|0.11876	.|U	.|0.520940	T|T	0.70798|0.70798	0.3265|0.3265	L|L	0.44542|0.44542	1.39|1.39	0.53688|0.53688	D|D	0.999978|0.999978	.|B	.|0.16396	.|0.017	.|B	.|0.11329	.|0.006	T|T	0.64398|0.64398	-0.6417|-0.6417	6|10	0.87932|0.37606	D|T	0|0.19	.|.	11.1185|11.1185	0.48275|0.48275	0.2976:0.7024:0.0:0.0|0.2976:0.7024:0.0:0.0	.|.	.|189	.|Q9ULW2	.|FZD10_HUMAN	V|C	156|189	.|ENSP00000229030:R189C	ENSP00000438460:A156V|ENSP00000229030:R189C	A|R	+|+	2|1	0|0	FZD10|FZD10	129214005|129214005	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.289000|0.289000	0.27227|0.27227	3.350000|3.350000	0.52224|0.52224	2.270000|2.270000	0.75569|0.75569	0.491000|0.491000	0.48974|0.48974	GCG|CGC	.	.		0.761	FZD10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	130648052	C	T	130648052	3	4	368	1	0	0	0	0	1	0	0	0	6137	768	27	1	567	1	FZD10	12	130648052	Missense_Mutation	SNP	C	TCGA-ZP-A9D2-01A-11D-A382-10	34007013	130648052	3203843	41	51112										
MLH3	27030	hgsc.bcm.edu	37	chr14	75514826	75514826	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	aagtgacatggtgtctgaaaAgggcttaaaaacatttctaa	9	5	2	2			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr14:75514826A>G	ENST00000556740.1	-	1	1568	c.1533T>C	c.(1531-1533)ccT>ccC	p.P511P	MLH3_ENST00000238662.7_Silent_p.P511P|MLH3_ENST00000380968.2_5'UTR|MLH3_ENST00000555671.1_5'Flank|MLH3_ENST00000544985.1_5'Flank|MLH3_ENST00000355774.2_Silent_p.P511P|MLH3_ENST00000556257.1_Silent_p.P511P			Q9UHC1	MLH3_HUMAN	mutL homolog 3	511					ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44				BRCA - Breast invasive adenocarcinoma(234;0.00688)		GTGTCTGAAAAGGGCTTAAAA	0.378								Mismatch excision repair (MMR)																													p.P511P		Atlas-SNP	.											.	MLH3	200	.	0			c.T1533C						.						76	80	79					14																	75514826		2203	4300	6503	SO:0001819	synonymous_variant	27030	exon2			CTGAAAAGGGCTT	AF195657	CCDS9837.1, CCDS32123.1	14q24.3	2014-09-17	2013-09-12			ENSG00000119684			7128	protein-coding gene	gene with protein product		604395	"mutL (E. coli) homolog 3", "mutL homolog 3 (E. coli)"			10615123	Standard	XR_245681		Approved		uc001xrd.1	Q9UHC1		ENST00000556740.1:c.1533T>C	chr14.hg19:g.75514826A>G		129.0	0.0		90.0	4.0	NM_014381	P49751|Q56DK9|Q9P292|Q9UHC0	Silent	SNP	ENST00000556740.1	hg19	CCDS32123.1																																																																																			.	.		0.378	MLH3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415006.1	NM_014381		G	75514826	A	G	75514826	2	3	368	1	0	0	0	0	0	0	0	1	9627	59	3	2		2	MLH3	14	75514826	Silent	SNP	A	TCGA-ZP-A9D2-01A-11D-A382-10		75514826	31834714	42	51113										
COG8	84342	hgsc.bcm.edu	37	chr16	69368984	69368984	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	ggcacggtactgggtgatgaTatcaaagagatggacacggg	16	6	1	3			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr16:69368984T>C	ENST00000306875.4	-	3	967	c.853A>G	c.(853-855)Atc>Gtc	p.I285V	COG8_ENST00000562081.1_Missense_Mutation_p.I285V|RP11-343C2.12_ENST00000562949.1_5'Flank	NM_032382.4	NP_115758.3	Q96MW5	COG8_HUMAN	component of oligomeric golgi complex 8	285					protein transport (GO:0015031)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|kidney(1)|large_intestine(2)|ovary(2)|skin(1)	9						TGGGTGATGATATCAAAGAGA	0.522																																					p.I285V		Atlas-SNP	.											.	COG8	32	.	0			c.A853G						.						90	74	79					16																	69368984		2198	4300	6498	SO:0001583	missense	84342	exon3			TGATGATATCAAA	AK025968	CCDS10876.1	16q22.1	2011-05-31			ENSG00000213380	ENSG00000213380		"Components of oligomeric golgi complex"	18623	protein-coding gene	gene with protein product		606979				11980916	Standard	NM_032382		Approved	FLJ22315, DOR1	uc002ewy.2	Q96MW5	OTTHUMG00000154277	ENST00000306875.4:c.853A>G	chr16.hg19:g.69368984T>C	ENSP00000305459:p.Ile285Val	172.0	0.0		173.0	58.0	NM_032382	Q0VAK2|Q8WVV6|Q9H6F8	Missense_Mutation	SNP	ENST00000306875.4	hg19	CCDS10876.1	.	.	.	.	.	.	.	.	.	.	T	13.94	2.386123	0.42308	.	.	ENSG00000213380	ENST00000306875	T	0.47869	0.83	5.93	3.66	0.41972	Cullin repeat-like-containing domain (1);	0.137590	0.64402	N	0.000003	T	0.41026	0.1141	L	0.33189	0.99	0.44677	D	0.997665	B;B	0.26258	0.058;0.145	B;B	0.40825	0.152;0.341	T	0.18524	-1.0334	10	0.22706	T	0.39	11.3878	7.7494	0.28888	0.0:0.3213:0.0:0.6787	.	312;285	B4DYU2;Q96MW5	.;COG8_HUMAN	V	285	ENSP00000305459:I285V	ENSP00000305459:I285V	I	-	1	0	COG8	67926485	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.670000	0.37502	1.035000	0.39972	0.460000	0.39030	ATC	.	.		0.522	COG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268948.2	NM_032382		C	69368984	T	C	69368984	3	2	368	1	0	0	0	0	1	0	0	0	3666	1406	49	2	997	2	COG8	16	69368984	Missense_Mutation	SNP	T	TCGA-ZP-A9D2-01A-11D-A382-10		69368984	20985769	43	51114										
ANKRD11	29123	hgsc.bcm.edu	37	chr16	89348575	89348575	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	gtgtttctctctcttcttctTctcttttaggatgttgatgg	8	8	5	1			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr16:89348575T>C	ENST00000301030.4	-	9	4835	c.4375A>G	c.(4375-4377)Aag>Gag	p.K1459E	ANKRD11_ENST00000378330.2_Missense_Mutation_p.K1459E	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	1459	Lys-rich.				bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		ctcttcttcttctctttTAGG	0.468																																					p.K1459E		Atlas-SNP	.											.	ANKRD11	195	.	0			c.A4375G						.						109	76	87					16																	89348575		2198	4300	6498	SO:0001583	missense	29123	exon9			TCTTCTTCTCTTT	AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"Ankyrin repeat domain containing"	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.4375A>G	chr16.hg19:g.89348575T>C	ENSP00000301030:p.Lys1459Glu	62.0	0.0		63.0	20.0	NM_001256183	Q6NTG1|Q6QMF8	Missense_Mutation	SNP	ENST00000301030.4	hg19	CCDS32513.1	.	.	.	.	.	.	.	.	.	.	T	9.505	1.104280	0.20632	.	.	ENSG00000167522	ENST00000301030;ENST00000378330	T;T	0.47528	0.84;0.84	5.11	5.11	0.69529	.	0.125201	0.52532	D	0.000065	T	0.53318	0.1789	M	0.69823	2.125	0.80722	D	1	P	0.48694	0.914	P	0.48030	0.564	T	0.52245	-0.8601	10	0.18710	T	0.47	.	14.8585	0.70359	0.0:0.0:0.0:1.0	.	1459	Q6UB99	ANR11_HUMAN	E	1459	ENSP00000301030:K1459E;ENSP00000367581:K1459E	ENSP00000301030:K1459E	K	-	1	0	ANKRD11	87876076	1.000000	0.71417	0.986000	0.45419	0.073000	0.16967	5.767000	0.68850	2.045000	0.60652	0.460000	0.39030	AAG	.	.		0.468	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		C	89348575	T	C	89348575	3	2	368	1	0	0	0	0	1	0	0	0	639	1792	62	2	3636	2	ANKRD11	16	89348575	Missense_Mutation	SNP	T	TCGA-ZP-A9D2-01A-11D-A382-10	19979591	89348575	1006178	44	51115										
TP53	7157	hgsc.bcm.edu	37	chr17	7577099	7577099	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	cttcctctgtgcgccggtctCtcccaggacaggcacaaaca	9	16	2	0	rs121912660		TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr17:7577099C>T	ENST00000269305.4	-	8	1028	c.839G>A	c.(838-840)aGa>aAa	p.R280K	TP53_ENST00000359597.4_Missense_Mutation_p.R280K|TP53_ENST00000445888.2_Missense_Mutation_p.R280K|TP53_ENST00000420246.2_Missense_Mutation_p.R280K|TP53_ENST00000413465.2_Intron|TP53_ENST00000455263.2_Missense_Mutation_p.R280K|TP53_ENST00000574684.1_5'Flank	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	280	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> G (in sporadic cancers; somatic mutation).|R -> I (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|R -> K (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1694291}.|R -> P (in a sporadic cancer; somatic mutation).|R -> S (in sporadic cancers; somatic mutation).|R -> T (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1631151}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R280T(65)|p.R280K(49)|p.R280I(16)|p.0?(8)|p.?(2)|p.R280_D281delRD(2)|p.A276_R283delACPGRDRR(1)|p.C275fs*20(1)|p.A276fs*64(1)|p.L265_K305del41(1)|p.G279_R280delGR(1)|p.F270_D281del12(1)|p.G279fs*59(1)|p.D281fs*24(1)|p.R280fs*62(1)|p.S269fs*21(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCGCCGGTCTCTCCCAGGACA	0.542		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.R280K	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,NS,carcinoma,-1,147	TP53	33396	.	154	Substitution - Missense(130)|Deletion - In frame(8)|Whole gene deletion(8)|Deletion - Frameshift(6)|Unknown(2)	urinary_tract(50)|breast(22)|lung(20)|upper_aerodigestive_tract(14)|haematopoietic_and_lymphoid_tissue(8)|large_intestine(5)|central_nervous_system(5)|stomach(4)|biliary_tract(4)|oesophagus(4)|skin(4)|ovary(4)|bone(4)|prostate(3)|small_intestine(1)|endometrium(1)|vagina(1)	c.G839A	GRCh37	CM993218	TP53	M	rs121912660	.						77	67	70					17																	7577099		2203	4300	6503	SO:0001583	missense	7157	exon8	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	CGGTCTCTCCCAG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.839G>A	chr17.hg19:g.7577099C>T	ENSP00000269305:p.Arg280Lys	112.0	0.0		70.0	34.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	36	5.663043	0.96745	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99854	-7.19;-7.19;-7.19;-7.19;-7.19;-7.19	5.13	5.13	0.70059	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99885	0.9945	M	0.92649	3.33	0.80722	D	1	D;D;D;P	0.69078	0.972;0.997;0.977;0.896	D;D;D;D	0.85130	0.942;0.997;0.941;0.921	D	0.96400	0.9296	10	0.87932	D	0	-21.0303	16.1198	0.81342	0.0:1.0:0.0:0.0	.	280;280;280;280	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	K	280;280;280;280;280;269;148	ENSP00000352610:R280K;ENSP00000269305:R280K;ENSP00000398846:R280K;ENSP00000391127:R280K;ENSP00000391478:R280K;ENSP00000425104:R148K	ENSP00000269305:R280K	R	-	2	0	TP53	7517824	0.978000	0.34361	1.000000	0.80357	0.980000	0.70556	7.587000	0.82613	2.667000	0.90743	0.462000	0.41574	AGA	.	.		0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7577099	C	T	7577099	3	4	368	1	0	0	0	0	1	0	0	0	16396	913	32	3	447	3	TP53	17	7577099	Missense_Mutation	SNP	C	TCGA-ZP-A9D2-01A-11D-A382-10		7577099	73618111	45	51116										
POLG2	11232	hgsc.bcm.edu	37	chr17	62492649	62492649	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	agagtttctgcagaaactaaCctgaaggcactgtccccggg	11	11	1	3			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr17:62492649C>A	ENST00000539111.2	-	1	505	c.438G>T	c.(436-438)agG>agT	p.R146S		NM_007215.3	NP_009146.2	Q9UHN1	DPOG2_HUMAN	polymerase (DNA directed), gamma 2, accessory subunit	146					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)	extracellular vesicular exosome (GO:0070062)|mitochondrial chromosome (GO:0000262)|mitochondrial nucleoid (GO:0042645)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(4)|skin(2)|stomach(1)|urinary_tract(1)	15	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;4.97e-11)			CAGAAACTAACCTGAAGGCAC	0.507																																					p.R146S	Colon(3;18 21 435 17652 48887)	Atlas-SNP	.											.	POLG2	29	.	0			c.G438T						.						96	93	94					17																	62492649		2203	4300	6503	SO:0001583	missense	11232	exon1			AACTAACCTGAAG	U94703	CCDS32706.1	17q23.3	2012-05-18			ENSG00000256525	ENSG00000256525		"DNA polymerases"	9180	protein-coding gene	gene with protein product		604983				9153213	Standard	NM_007215		Approved	MTPOLB, HP55	uc002jei.3	Q9UHN1		ENST00000539111.2:c.438G>T	chr17.hg19:g.62492649C>A	ENSP00000442563:p.Arg146Ser	165.0	0.0		247.0	114.0	NM_007215	O00419|Q0IJ81|Q96GW2|Q9UK35|Q9UK94	Missense_Mutation	SNP	ENST00000539111.2	hg19	CCDS32706.1	.	.	.	.	.	.	.	.	.	.	C	17.43	3.386787	0.61956	.	.	ENSG00000256525	ENST00000539111	T	0.77358	-1.09	5.15	3.04	0.35103	.	0.217217	0.41396	D	0.000888	T	0.75481	0.3855	L	0.48642	1.525	0.50632	D	0.999888	P;P	0.47253	0.892;0.892	P;P	0.52598	0.703;0.703	T	0.72868	-0.4162	10	0.39692	T	0.17	-13.5186	7.3304	0.26580	0.1258:0.6789:0.1224:0.0729	.	146;146	E5KS15;Q9UHN1	.;DPOG2_HUMAN	S	146	ENSP00000442563:R146S	ENSP00000442563:R146S	R	-	3	2	POLG2	59923111	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.745000	0.38278	2.428000	0.82296	0.555000	0.69702	AGG	.	.		0.507	POLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443820.1	NM_007215		A	62492649	C	A	62492649	3	1	368	1	0	0	0	0	1	0	0	0	12210	506	18	3	1051	3	POLG2	17	62492649	Missense_Mutation	SNP	C	TCGA-ZP-A9D2-01A-11D-A382-10	54915550	62492649	18702561	46	51117										
CCDC45	90799	hgsc.bcm.edu	37	chr17	62522209	62522209	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	aaatgaaaacagagctacagCctcatcctgcaattcacctt	5	12	2	2			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr17:62522209C>T	ENST00000556440.2	+	10	1553	c.1043C>T	c.(1042-1044)gCc>gTc	p.A348V	CEP95_ENST00000553412.1_Missense_Mutation_p.A184V|CEP95_ENST00000577476.1_3'UTR	NM_138363.1	NP_612372.1	Q96GE4	CEP95_HUMAN	centrosomal protein 95kDa	348						centrosome (GO:0005813)|cytoplasm (GO:0005737)|spindle pole (GO:0000922)				endometrium(1)|kidney(3)|large_intestine(5)|lung(3)|ovary(1)	13						AGAGCTACAGCCTCATCCTGC	0.353																																					p.A348V		Atlas-SNP	.											.	CEP95	103	.	0			c.C1043T						.						116	113	114					17																	62522209		1848	4092	5940	SO:0001583	missense	90799	exon10			CTACAGCCTCATC	AL832822	CCDS45763.1	17q24.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000258890	ENSG00000258890			25141	protein-coding gene	gene with protein product			"coiled-coil domain containing 45"	CCDC45		21399614	Standard	NM_138363		Approved	DKFZp667E1824	uc002jem.3	Q96GE4	OTTHUMG00000179174	ENST00000556440.2:c.1043C>T	chr17.hg19:g.62522209C>T	ENSP00000450461:p.Ala348Val	140.0	0.0		183.0	33.0	NM_138363	B4DMD2|Q96M81	Missense_Mutation	SNP	ENST00000556440.2	hg19	CCDS45763.1	.	.	.	.	.	.	.	.	.	.	C	0.009	-1.806742	0.00606	.	.	ENSG00000258890	ENST00000553956;ENST00000556440;ENST00000553412	T;T	0.31247	1.5;1.5	5.19	-1.27	0.09347	.	1.613740	0.03097	N	0.160567	T	0.13756	0.0333	N	0.05383	-0.06	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.10474	-1.0628	10	0.26408	T	0.33	2.2769	0.8833	0.01239	0.2949:0.1364:0.1325:0.4363	.	348	Q96GE4	CEP95_HUMAN	V	283;348;184	ENSP00000450461:A348V;ENSP00000450906:A184V	ENSP00000438458:A283V	A	+	2	0	CEP95	59952671	0.103000	0.21917	0.007000	0.13788	0.021000	0.10359	0.056000	0.14256	-0.376000	0.07943	0.563000	0.77884	GCC	.	.		0.353	CEP95-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445100.2	NM_138363		T	62522209	C	T	62522209	3	4	368	1	0	0	0	0	1	0	0	0	2818	739	26	3	1081	3	CCDC45	17	62522209	Missense_Mutation	SNP	C	TCGA-ZP-A9D2-01A-11D-A382-10	29560	62522209	18673001	47	51118										
SLC25A41	8570	hgsc.bcm.edu	37	chr19	6427484	6427484	+	5'Flank	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	gccccttgtactggcccgtcCgacgcaaggtcaaccgcgtc	11	17	1	0	rs370967882	byFrequency	TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr19:6427484C>T	ENST00000398148.3	-	0	0				SLC25A41_ENST00000321510.6_Missense_Mutation_p.R218Q	NM_003685.2	NP_003676.2	Q92945	FUBP2_HUMAN	KH-type splicing regulatory protein						gene expression (GO:0010467)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|regulation of miRNA metabolic process (GO:2000628)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|transcription, DNA-templated (GO:0006351)	cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|liver(1)|lung(6)|skin(1)|soft_tissue(1)	17						CTGGCCCGTCCGACGCAAGGT	0.617													C|||	6	0.00119808	0	0.0014	5008	,	,		17211	0		0.002	False		,,,				2504	0.0031				p.R218Q	Colon(55;593 1006 2067 9135 22980)	Atlas-SNP	.											.	SLC25A41	26	.	0			c.G653A						.	C	GLN/ARG	0,4400		0,0,2200	21	25	24		653	1.8	0	19		24	1,8591		0,1,4295	no	missense	SLC25A41	NM_173637.3	43	0,1,6495	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	218/371	6427484	1,12991	2200	4296	6496	SO:0001631	upstream_gene_variant	284427	exon5			CCCGTCCGACGCA	U94832	CCDS45936.1	19p13.3	2010-11-23	2008-02-04		ENSG00000088247	ENSG00000088247			6316	protein-coding gene	gene with protein product	"FUSE binding protein 2"	603445				9136930, 8940189	Standard	NM_003685		Approved	KSRP, FBP2, FUBP2	uc002mer.4	Q92945			chr19.hg19:g.6427484C>T	Exception_encountered	163.0	0.0		153.0	46.0	NM_173637	O00301|Q59EZ9|Q5U4P6|Q9UNT5|Q9UQH5	Missense_Mutation	SNP	ENST00000398148.3	hg19	CCDS45936.1	.	.	.	.	.	.	.	.	.	.	C	12.57	1.976333	0.34848	0.0	1.16E-4	ENSG00000181240	ENST00000321510	T	0.78246	-1.16	4.07	1.82	0.25136	Mitochondrial carrier domain (2);	.	.	.	.	T	0.57888	0.2084	L	0.28608	0.87	0.80722	D	1	P	0.37083	0.581	B	0.28784	0.094	T	0.50448	-0.8827	9	0.44086	T	0.13	-12.87	4.9452	0.13985	0.1761:0.6309:0.0:0.1931	.	218	Q8N5S1	S2541_HUMAN	Q	218	ENSP00000322649:R218Q	ENSP00000322649:R218Q	R	-	2	0	SLC25A41	6378484	0.097000	0.21791	0.036000	0.18154	0.317000	0.28152	1.067000	0.30616	0.320000	0.23234	0.462000	0.41574	CGG	.	.		0.617	KHSRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453305.1			T	6427484	C	T	6427484	1	4	368	0	1	0	0	0	0	0	0	0	14521	652	23	1		1	SLC25A41	19	6427484	5'Flank	SNP	C	TCGA-ZP-A9D2-01A-11D-A382-10		6427484	52701499	48	51119										
MUC16	94025	hgsc.bcm.edu	37	chr19	9060294	9060294	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	atatgtcttgtgacattgtgGactgatcagggctaggtcct	12	7	2	2			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr19:9060294G>T	ENST00000397910.4	-	3	27355	c.27152C>A	c.(27151-27153)tCc>tAc	p.S9051Y		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9053	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGACATTGTGGACTGATCAGG	0.488																																					p.S9051Y		Atlas-SNP	.											.	MUC16	4315	.	0			c.C27152A						.						161	150	153					19																	9060294		2014	4192	6206	SO:0001583	missense	94025	exon3			ATTGTGGACTGAT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.27152C>A	chr19.hg19:g.9060294G>T	ENSP00000381008:p.Ser9051Tyr	77.0	0.0		94.0	26.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	7.963	0.747399	0.15710	.	.	ENSG00000181143	ENST00000397910	T	0.02737	4.18	1.53	1.53	0.23141	.	.	.	.	.	T	0.07369	0.0186	L	0.46157	1.445	.	.	.	D	0.62365	0.991	P	0.62649	0.905	T	0.17167	-1.0378	8	0.87932	D	0	.	6.4855	0.22087	0.0:0.0:1.0:0.0	.	9051	B5ME49	.	Y	9051	ENSP00000381008:S9051Y	ENSP00000381008:S9051Y	S	-	2	0	MUC16	8921294	0.000000	0.05858	0.001000	0.08648	0.536000	0.34869	-0.201000	0.09464	1.157000	0.42530	0.306000	0.20318	TCC	.	.		0.488	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9060294	G	T	9060294	3	4	368	1	0	0	0	0	1	0	0	0	9982	1174	41	3	16699	3	MUC16	19	9060294	Missense_Mutation	SNP	G	TCGA-ZP-A9D2-01A-11D-A382-10	2632810	9060294	50068689	49	51120										
PPAN	56342	hgsc.bcm.edu	37	chr19	10221280	10221280	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	agcgcaagcaggagcagcggGaggcccacaggtccaggcag	17	12	0	0			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr19:10221280G>T	ENST00000253107.7	+	10	1127	c.1021G>T	c.(1021-1023)Gag>Tag	p.E341*	PPAN-P2RY11_ENST00000393796.4_Nonsense_Mutation_p.E341*|SNORD105_ENST00000386910.1_RNA|PPAN-P2RY11_ENST00000428358.1_Nonsense_Mutation_p.E341*|SNORD105B_ENST00000458770.1_RNA|P2RY11_ENST00000321826.4_5'Flank|PPAN_ENST00000556468.1_Nonsense_Mutation_p.E341*|PPAN_ENST00000393793.1_Nonsense_Mutation_p.E288*	NM_020230.5	NP_064615.3	Q9NQ55	SSF1_HUMAN	peter pan homolog (Drosophila)	341					RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(3)|liver(2)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	15			OV - Ovarian serous cystadenocarcinoma(20;2.19e-08)|Epithelial(33;1.76e-05)|all cancers(31;3.54e-05)			GGAGCAGCGGGAGGCCCACAG	0.667																																					p.E341X		Atlas-SNP	.											.	PPAN	43	.	0			c.G1021T						.						12	16	15					19																	10221280		2189	4290	6479	SO:0001587	stop_gained	56342	exon10			CAGCGGGAGGCCC	BC033202	CCDS12225.1	19p13.2	2008-02-05	2001-11-28		ENSG00000130810	ENSG00000130810			9227	protein-coding gene	gene with protein product		607793	"peter pan (Drosophila) homolog"			10873382	Standard	NM_020230		Approved	SSF1, SSF2, SSF, BXDC3		Q9NQ55	OTTHUMG00000156826	ENST00000253107.7:c.1021G>T	chr19.hg19:g.10221280G>T	ENSP00000253107:p.Glu341*	114.0	0.0		142.0	44.0	NM_020230	C9J3F9|Q9BW97|Q9H170	Nonsense_Mutation	SNP	ENST00000253107.7	hg19	CCDS12225.1	.	.	.	.	.	.	.	.	.	.	G	38	6.747008	0.97809	.	.	ENSG00000243207;ENSG00000243207;ENSG00000130810;ENSG00000130810;ENSG00000130810;ENSG00000130810	ENST00000428358;ENST00000393796;ENST00000253107;ENST00000556468;ENST00000342696;ENST00000393793	.	.	.	4.78	4.78	0.61160	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11485	T	0.65	-42.6564	16.6071	0.84832	0.0:0.0:1.0:0.0	.	.	.	.	X	341;341;341;341;341;288	.	ENSP00000253107:E341X	E	+	1	0	PPAN;PPAN-P2RY11	10082280	1.000000	0.71417	0.990000	0.47175	0.580000	0.36256	3.364000	0.52328	2.203000	0.70933	0.561000	0.74099	GAG	.	.		0.667	PPAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316658.1	NM_020230		T	10221280	G	T	10221280	4	4	368	1	0	0	0	0	0	1	0	0	12297	1175	41	3	1059	3	PPAN	19	10221280	Nonsense_Mutation	SNP	G	TCGA-ZP-A9D2-01A-11D-A382-10	1160986	10221280	48907703	50	51121										
ZNF493	284443	hgsc.bcm.edu	37	chr19	21607547	21607547	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	aatgtggcaaaactttctacCgattctcaaaccttaatacg	5	10	2	0			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr19:21607547C>T	ENST00000355504.4	+	2	1968	c.1702C>T	c.(1702-1704)Cga>Tga	p.R568*	ZNF493_ENST00000392288.2_Nonsense_Mutation_p.R696*|CTD-2561J22.3_ENST00000600810.1_Intron	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	568					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						AACTTTCTACCGATTCTCAAA	0.343																																					p.R696X		Atlas-SNP	.											.	ZNF493	178	.	0			c.C2086T						.						32	35	34					19																	21607547		2202	4295	6497	SO:0001587	stop_gained	284443	exon4			TTCTACCGATTCT	AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"Zinc fingers, C2H2-type", "-"	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.1702C>T	chr19.hg19:g.21607547C>T	ENSP00000347691:p.Arg568*	281.0	0.0		257.0	78.0	NM_001076678	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Nonsense_Mutation	SNP	ENST00000355504.4	hg19	CCDS12412.1	.	.	.	.	.	.	.	.	.	.	N	22.0	4.225634	0.79576	.	.	ENSG00000196268	ENST00000392288;ENST00000355504	.	.	.	1.14	-2.28	0.06826	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.15499	T	0.54	.	3.0269	0.06094	0.2093:0.201:0.0:0.5898	.	.	.	.	X	696;568	.	ENSP00000347691:R568X	R	+	1	2	ZNF493	21399387	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-7.134000	0.00043	-1.207000	0.02637	-1.192000	0.01694	CGA	.	.		0.343	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910		T	21607547	C	T	21607547	4	4	368	1	0	0	0	0	0	1	0	0	17959	644	23	1	2163	1	ZNF493	19	21607547	Nonsense_Mutation	SNP	C	TCGA-ZP-A9D2-01A-11D-A382-10	11386267	21607547	37521436	51	51122										
ZNF227	7770	hgsc.bcm.edu	37	chr19	44740511	44740511	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	ctgtggtaagggcttcagtcAgtcctctggtcttcaatccc	10	12	5	0			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr19:44740511A>T	ENST00000313040.7	+	6	2133	c.1928A>T	c.(1927-1929)cAg>cTg	p.Q643L	ZNF227_ENST00000391961.2_Missense_Mutation_p.Q592L|ZNF227_ENST00000589005.1_Missense_Mutation_p.Q592L|ZNF235_ENST00000589799.1_3'UTR	NM_182490.1	NP_872296.1	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	643					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(2)|stomach(1)|urinary_tract(1)	24		Prostate(69;0.0435)				GGCTTCAGTCAGTCCTCTGGT	0.463																																					p.Q643L		Atlas-SNP	.											.	ZNF227	62	.	0			c.A1928T						.						66	67	67					19																	44740511		2203	4300	6503	SO:0001583	missense	7770	exon6			TCAGTCAGTCCTC	AK092253	CCDS12636.1, CCDS74388.1	19q13.32	2013-01-08						"Zinc fingers, C2H2-type", "-"	13020	protein-coding gene	gene with protein product							Standard	XM_005259232		Approved		uc002oyu.3	Q86WZ6		ENST00000313040.7:c.1928A>T	chr19.hg19:g.44740511A>T	ENSP00000321049:p.Gln643Leu	102.0	0.0		121.0	44.0	NM_182490	B3KRU7|B7Z5P9	Missense_Mutation	SNP	ENST00000313040.7	hg19	CCDS12636.1	.	.	.	.	.	.	.	.	.	.	A	16.88	3.243687	0.58995	.	.	ENSG00000131115	ENST00000313040;ENST00000328297;ENST00000391961;ENST00000418980;ENST00000377916	T;T	0.35236	1.32;1.32	4.07	3.02	0.34903	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.37376	0.1001	L	0.28649	0.875	0.80722	D	1	D;D;D;D	0.71674	0.998;0.988;0.988;0.998	D;P;P;D	0.63113	0.911;0.717;0.624;0.911	T	0.11743	-1.0575	9	0.32370	T	0.25	.	5.3507	0.16034	0.7093:0.0:0.2906:0.0	.	564;622;595;643	B7Z6M2;Q658S5;Q9NS43;Q86WZ6	.;.;.;ZN227_HUMAN	L	643;600;592;622;282	ENSP00000321049:Q643L;ENSP00000375823:Q592L	ENSP00000321049:Q643L	Q	+	2	0	ZNF227	49432351	0.000000	0.05858	0.963000	0.40424	0.997000	0.91878	0.127000	0.15790	1.625000	0.50366	0.455000	0.32223	CAG	.	.		0.463	ZNF227-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460720.1	NM_182490		T	44740511	A	T	44740511	3	4	368	1	0	0	0	0	1	0	0	0	17796	188	7	4	1942	4	ZNF227	19	44740511	Missense_Mutation	SNP	A	TCGA-ZP-A9D2-01A-11D-A382-10	23132964	44740511	14388472	52	51123										
SAPS1	22870	hgsc.bcm.edu	37	chr19	55756722	55756722	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	ggccgaggtgccaatgtgctGcagcagcaggtccacgaagt	15	11	0	0			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr19:55756722G>A	ENST00000412770.2	-	4	1029	c.463C>T	c.(463-465)Cag>Tag	p.Q155*	PPP6R1_ENST00000587283.1_Nonsense_Mutation_p.Q155*	NM_014931.3	NP_055746.3	Q9UPN7	PP6R1_HUMAN	protein phosphatase 6, regulatory subunit 1	155	Interaction with PPP6C.				regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)	protein phosphatase binding (GO:0019903)			breast(1)	1						CCAATGTGCTGCAGCAGCAGG	0.637																																					p.Q155X		Atlas-SNP	.											.	PPP6R1	63	.	0			c.C463T						.						43	50	47					19																	55756722		2168	4279	6447	SO:0001587	stop_gained	22870	exon4			TGTGCTGCAGCAG	AB029038	CCDS46186.1	19q13.42	2012-04-17	2010-06-28	2010-06-28	ENSG00000105063	ENSG00000105063		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"	29195	protein-coding gene	gene with protein product		610875	"KIAA1115", "SAPS domain family, member 1"	KIAA1115, SAPS1		16769727	Standard	NM_014931		Approved	SAP190	uc002qjw.4	Q9UPN7		ENST00000412770.2:c.463C>T	chr19.hg19:g.55756722G>A	ENSP00000414202:p.Gln155*	69.0	0.0		70.0	16.0	NM_014931	Q2M2H3|Q504V2|Q6NVJ6|Q9BU97	Nonsense_Mutation	SNP	ENST00000412770.2	hg19	CCDS46186.1	.	.	.	.	.	.	.	.	.	.	G	38	6.977884	0.97975	.	.	ENSG00000105063	ENST00000444538;ENST00000412770	.	.	.	4.95	2.7	0.31948	.	0.350692	0.23554	N	0.046939	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.8703	5.5798	0.17243	0.1792:0.0:0.6617:0.1591	.	.	.	.	X	155	.	ENSP00000414202:Q155X	Q	-	1	0	PPP6R1	60448534	0.970000	0.33590	0.998000	0.56505	0.991000	0.79684	2.322000	0.43814	0.711000	0.32018	0.655000	0.94253	CAG	.	.		0.637	PPP6R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452663.1	NM_014931		A	55756722	G	A	55756722	4	1	368	1	0	0	0	0	0	1	0	0	13851	1328	46	3	2266	3	SAPS1	19	55756722	Nonsense_Mutation	SNP	G	TCGA-ZP-A9D2-01A-11D-A382-10	11016211	55756722	3372261	53	51124										
HNF4A	3172	hgsc.bcm.edu	37	chr20	43052656	43052656	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	tgcccaccctcttccattgtAgatgccaaggggctgagcga	11	13	1	2			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr20:43052656A>T	ENST00000316099.4	+	8	981		c.e8-1		HNF4A_ENST00000415691.2_Splice_Site|AL132772.1_ENST00000581483.1_RNA|HNF4A_ENST00000443598.2_Splice_Site|HNF4A_ENST00000316673.4_Splice_Site|HNF4A_ENST00000457232.1_Splice_Site|HNF4A_ENST00000609795.1_Splice_Site	NM_000457.4|NM_001258355.1|NM_178849.2	NP_000448.3|NP_001245284.1|NP_849180.1	P41235	HNF4A_HUMAN	hepatocyte nuclear factor 4, alpha						blood coagulation (GO:0007596)|endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|glucose homeostasis (GO:0042593)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|ornithine metabolic process (GO:0006591)|phospholipid homeostasis (GO:0055091)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gastrulation (GO:0010470)|regulation of growth hormone receptor signaling pathway (GO:0060398)|regulation of insulin secretion (GO:0050796)|regulation of lipid metabolic process (GO:0019216)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|sex differentiation (GO:0007548)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|fatty acid binding (GO:0005504)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(7)|lung(17)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	34		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			CTTCCATTGTAGATGCCAAGG	0.587																																					.	Colon(79;2 1269 8820 14841 52347)	Atlas-SNP	.											.	HNF4A	150	.	0			c.827-2A>T						.						26	20	22					20																	43052656		2194	4289	6483	SO:0001630	splice_region_variant	3172	exon8			CATTGTAGATGCC	X76930	CCDS13330.1, CCDS13331.1, CCDS42876.1, CCDS46604.1, CCDS46605.1, CCDS68131.1, CCDS74728.1	20q13.12	2014-09-17			ENSG00000101076	ENSG00000101076		"Nuclear hormone receptors"	5024	protein-coding gene	gene with protein product		600281		TCF14, MODY, MODY1		7926813, 9048927	Standard	NM_001030003		Approved	NR2A1, HNF4	uc010zwo.1	P41235	OTTHUMG00000032531	ENST00000316099.4:c.893-1A>T	chr20.hg19:g.43052656A>T		99.0	0.0		123.0	45.0	NM_001030004	A5JW41|B2RPP8|O00659|O00723|Q14540|Q5QPB8|Q6B4V5|Q6B4V6|Q6B4V7|Q92653|Q92654|Q92655|Q99864|Q9NQH0	Splice_Site	SNP	ENST00000316099.4	hg19	CCDS13330.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.358626	0.82243	.	.	ENSG00000101076	ENST00000316673;ENST00000457232;ENST00000316099;ENST00000443598;ENST00000338692;ENST00000415691	.	.	.	5.4	5.4	0.78164	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4152	0.74960	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	HNF4A	42486070	1.000000	0.71417	1.000000	0.80357	0.865000	0.49528	9.339000	0.96797	2.034000	0.60081	0.460000	0.39030	.	.	.		0.587	HNF4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079363.3		Intron	T	43052656	A	T	43052656	5	4	368	1	0	0	0	0	0	0	1	0	7262	434	15	4	974	4	HNF4A	20	43052656	Splice_Site	SNP	A	TCGA-ZP-A9D2-01A-11D-A382-10		43052656	19972864	54	51125										
TBX1	6899	hgsc.bcm.edu	37	chr22	19754071	19754071	+	Intron	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	cccgctgcccggcgcgcccgGaggccggcccagtcccccga	14	22	0	0			TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr22:19754071G>T	ENST00000329705.7	+	8	1138				TBX1_ENST00000359500.3_Intron|TBX1_ENST00000332710.4_Missense_Mutation_p.G390V	NM_080646.1	NP_542377.1	O43435	TBX1_HUMAN	T-box 1						angiogenesis (GO:0001525)|anterior/posterior pattern specification (GO:0009952)|aorta morphogenesis (GO:0035909)|artery morphogenesis (GO:0048844)|blood vessel development (GO:0001568)|blood vessel morphogenesis (GO:0048514)|blood vessel remodeling (GO:0001974)|cell fate specification (GO:0001708)|cell proliferation (GO:0008283)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to retinoic acid (GO:0071300)|cochlea morphogenesis (GO:0090103)|coronary artery morphogenesis (GO:0060982)|determination of left/right symmetry (GO:0007368)|ear morphogenesis (GO:0042471)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic viscerocranium morphogenesis (GO:0048703)|enamel mineralization (GO:0070166)|epithelial cell differentiation (GO:0030855)|face morphogenesis (GO:0060325)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|lymph vessel development (GO:0001945)|mesenchymal cell apoptotic process (GO:0097152)|mesoderm development (GO:0007498)|middle ear morphogenesis (GO:0042474)|muscle cell fate commitment (GO:0042693)|muscle organ development (GO:0007517)|muscle organ morphogenesis (GO:0048644)|muscle tissue morphogenesis (GO:0060415)|negative regulation of cell differentiation (GO:0045596)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|otic vesicle morphogenesis (GO:0071600)|outer ear morphogenesis (GO:0042473)|outflow tract morphogenesis (GO:0003151)|outflow tract septum morphogenesis (GO:0003148)|parathyroid gland development (GO:0060017)|pattern specification process (GO:0007389)|pharyngeal system development (GO:0060037)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of tongue muscle cell differentiation (GO:2001037)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of organ morphogenesis (GO:2000027)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retinoic acid receptor signaling pathway (GO:0048384)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|social behavior (GO:0035176)|soft palate development (GO:0060023)|thymus development (GO:0048538)|thyroid gland development (GO:0030878)|tongue morphogenesis (GO:0043587)|transcription, DNA-templated (GO:0006351)|vagus nerve morphogenesis (GO:0021644)	nucleus (GO:0005634)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|lung(3)|ovary(2)	8	Colorectal(54;0.0993)	all_lung(157;3.05e-06)				ggcgcgcccggaggccggccc	0.781																																					p.G390V		Atlas-SNP	.											.	TBX1	62	.	0			c.G1169T						.						1	1	1					22																	19754071		789	1895	2684	SO:0001627	intron_variant	6899	exon9			CGCCCGGAGGCCG	AF012131	CCDS13765.1, CCDS13766.1, CCDS13767.1	22q11.21	2014-09-17			ENSG00000184058	ENSG00000184058		"T-boxes"	11592	protein-coding gene	gene with protein product		602054	"velocardiofacial syndrome"	VCF		9268629, 23000736	Standard	NM_080646		Approved	CATCH22	uc002zqa.1	O43435	OTTHUMG00000150421	ENST00000329705.7:c.1009+546G>T	chr22.hg19:g.19754071G>T		387.0	1.0		458.0	182.0	NM_080647	C6G493|C6G494|O43436|Q96RJ2	Missense_Mutation	SNP	ENST00000329705.7	hg19	CCDS13766.1	.	.	.	.	.	.	.	.	.	.	G	13.27	2.188036	0.38609	.	.	ENSG00000184058	ENST00000332710	D	0.85339	-1.97	2.85	1.75	0.24633	.	2.560210	0.02131	U	0.056401	T	0.77491	0.4138	L	0.36672	1.1	0.80722	D	1	P	0.35575	0.51	B	0.23275	0.045	T	0.58662	-0.7597	10	0.20046	T	0.44	.	11.1907	0.48683	0.0:0.1889:0.811:0.0	.	390	D9ZGG0	.	V	390	ENSP00000331791:G390V	ENSP00000331791:G390V	G	+	2	0	TBX1	18134071	0.711000	0.27906	0.332000	0.25469	0.892000	0.51952	1.189000	0.32114	0.477000	0.27464	0.416000	0.27883	GGA	.	.		0.781	TBX1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318033.1	NM_080647		T	19754071	G	T	19754071	1	4	368	0	1	0	0	0	0	0	0	0	15665	1174	41	3		3	TBX1	22	19754071	Intron	SNP	G	TCGA-ZP-A9D2-01A-11D-A382-10		19754071	31550495	55	51126										
C22orf15	150248	hgsc.bcm.edu	37	chr22	24106453	24106453	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	ccatgtcctcccagcgaccaTtgctctcctggctgaggatg	10	15	1	1	rs553969002		TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr22:24106453T>C	ENST00000402217.3	+	3	372	c.119T>C	c.(118-120)aTt>aCt	p.I40T	C22orf15_ENST00000305199.5_Missense_Mutation_p.I40T|C22orf15_ENST00000382821.3_Missense_Mutation_p.I40T	NM_182520.2	NP_872326.2	Q8WYQ4	CV015_HUMAN	chromosome 22 open reading frame 15	40										breast(1)|pancreas(1)	2		Medulloblastoma(6;6.27e-05)|all_neural(6;0.00518)				CCAGCGACCATTGCTCTCCTG	0.642													T|||	1	0.000199681	0	0	5008	,	,		20227	0		0	False		,,,				2504	0.001				p.I40T		Atlas-SNP	.											.	C22orf15	5	.	0			c.T119C						.						54	63	60					22																	24106453		692	1591	2283	SO:0001583	missense	150248	exon3			CGACCATTGCTCT	AB050773	CCDS13814.2	22q11.23	2012-11-13			ENSG00000169314	ENSG00000169314			15558	protein-coding gene	gene with protein product							Standard	NM_182520		Approved	FLJ36561, N27C7-3	uc011aja.2	Q8WYQ4	OTTHUMG00000150740	ENST00000402217.3:c.119T>C	chr22.hg19:g.24106453T>C	ENSP00000384965:p.Ile40Thr	76.0	0.0		83.0	28.0	NM_182520	Q6ICJ7	Missense_Mutation	SNP	ENST00000402217.3	hg19	CCDS13814.2	.	.	.	.	.	.	.	.	.	.	T	11.36	1.617206	0.28801	.	.	ENSG00000169314	ENST00000336186;ENST00000402217;ENST00000305199;ENST00000382821	T	0.43294	0.95	2.79	2.79	0.32731	.	0.638862	0.13251	N	0.402042	T	0.41351	0.1155	M	0.73962	2.25	0.09310	N	1	B;P;P	0.50819	0.447;0.939;0.939	B;B;B	0.41174	0.266;0.349;0.349	T	0.42224	-0.9464	10	0.72032	D	0.01	-11.1421	7.4919	0.27466	0.0:0.0:0.0:1.0	.	40;40;40	Q8WYQ4;C9JMV7;Q8WYQ4-2	CV015_HUMAN;.;.	T	40	ENSP00000384965:I40T	ENSP00000305096:I40T	I	+	2	0	C22orf15	22436453	0.062000	0.20869	0.013000	0.15412	0.063000	0.16089	0.812000	0.27211	1.540000	0.49301	0.454000	0.30748	ATT	.	.		0.642	C22orf15-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319887.2	NM_182520		C	24106453	T	C	24106453	3	2	368	1	0	0	0	0	1	0	0	0	2138	1493	52	2	129	2	C22orf15	22	24106453	Missense_Mutation	SNP	T	TCGA-ZP-A9D2-01A-11D-A382-10	4352382	24106453	27198113	56	51127										
NEFH	4744	hgsc.bcm.edu	37	chr22	29885571	29885572	+	In_Frame_Ins	INS	-	-	CCCCTGAGAAGGCCAAGT													0.0178571428571429	1	1	0.571212121212121	0	0.612012987012987	1	1	0	aacgaaggaggaagcaaagtINScccctgagaaggccaagtcc							TCGA-ZP-A9D2-01A-11D-A382-10	TCGA-ZP-A9D2-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0eb7de5-8ea1-4f7c-82b5-c216979bef5b	517ff09a-3831-4085-b380-60a157b3840f	g.chr22:29885571_29885572insCCCCTGAGAAGGCCAAGT	ENST00000310624.6	+	4	1975_1976	c.1942_1943insCCCCTGAGAAGGCCAAGT	c.(1942-1944)tcc>tCCCCTGAGAAGGCCAAGTcc	p.648_648S>SPEKAKS		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	654	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.			Missing (in Ref. 1; CAA33366 and 5; AC000035). {ECO:0000305}.	axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						GGAAGCAAAGTCCCCTGAGAAG	0.569																																					p.S648delinsSPEKAKS		Atlas-INDEL	.											.	NEFH	178	.	0			c.1942_1943insCCCCTGAGAAGGCCAAGT						.																																			SO:0001652	inframe_insertion	4744	exon4			.		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1943_1960dupCCCCTGAGAAGGCCAAGT	chr22.hg19:g.29885571_29885572insCCCCTGAGAAGGCCAAGT	Exception_encountered	241.0	0.0		266.0	39.0	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Ins	INS	ENST00000310624.6	hg19	CCDS13858.1																																																																																			.	.		0.569	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		CCCCTGAGAAGGCCAAGT	29885572	-	CCCCTGAGAAGGCCAAGT	29885571	7	5	368	1	0	1	1	0	0	0	0	0	10323	1667	58	0	1956	0	NEFH	22	29885571	In_Frame_Ins	INS	-	TCGA-ZP-A9D2-01A-11D-A382-10	5779118	29885571	21418995	57	51128										
PLEKHO1	51177	hgsc.bcm.edu	37	chr1	150131451	150131451	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	aaactggaggagactcaggaGcttctggcagaggttcaggg	16	7	3	2			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr1:150131451G>A	ENST00000369124.4	+	6	1241	c.963G>A	c.(961-963)gaG>gaA	p.E321E	PLEKHO1_ENST00000025469.6_Silent_p.E287E|PLEKHO1_ENST00000369126.1_Silent_p.E138E	NM_016274.4	NP_057358.2	Q53GL0	PKHO1_HUMAN	pleckstrin homology domain containing, family O member 1	321	Negative regulator of AP-1 activity.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|skin(2)	22	Lung NSC(24;7.78e-28)|Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGACTCAGGAGCTTCTGGCAG	0.642																																					p.E321E		Atlas-SNP	.											.	PLEKHO1	37	.	0			c.G963A						.						46	52	50					1																	150131451		2203	4300	6503	SO:0001819	synonymous_variant	51177	exon6			TCAGGAGCTTCTG	AF073836	CCDS945.1	1q21.2	2013-01-10			ENSG00000023902	ENSG00000023902		"Pleckstrin homology (PH) domain containing"	24310	protein-coding gene	gene with protein product		608335				10799509	Standard	NM_016274		Approved	CKIP-1, OC120	uc001ett.3	Q53GL0	OTTHUMG00000012510	ENST00000369124.4:c.963G>A	chr1.hg19:g.150131451G>A		279.0	0.0		313.0	16.0	NM_016274	Q336K5|Q8IZ51|Q9NRV3|Q9UL48	Silent	SNP	ENST00000369124.4	hg19	CCDS945.1																																																																																			.	.		0.642	PLEKHO1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034962.1	NM_016274		A	150131451	G	A	150131451	2	1	369	1	0	0	0	0	0	0	0	1	12093	962	34	3		3	PLEKHO1	1	150131451	Silent	SNP	G	TCGA-ZP-A9D4-01A-11D-A36X-10		150131451	99119170	1	51129										
CCDC19	25790	hgsc.bcm.edu	37	chr1	159847189	159847189	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	ctgcatggccctcaagcgtgCgatctccttctctttctccc	7	17	4	0			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr1:159847189C>T	ENST00000368099.4	-	9	1172	c.1108G>A	c.(1108-1110)Gca>Aca	p.A370T	CCDC19_ENST00000426543.2_Missense_Mutation_p.A285T|CCDC19_ENST00000476696.1_5'UTR	NM_012337.2	NP_036469.2														endometrium(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	26	all_hematologic(112;0.0597)		BRCA - Breast invasive adenocarcinoma(70;0.151)			CTCAAGCGTGCGATCTCCTTC	0.537																																					p.A370T		Atlas-SNP	.											.	CCDC19	79	.	0			c.G1108A						.						314	257	276					1																	159847189		2203	4300	6503	SO:0001583	missense	25790	exon9			AGCGTGCGATCTC																												ENST00000368099.4:c.1108G>A	chr1.hg19:g.159847189C>T	ENSP00000357079:p.Ala370Thr	146.0	0.0		154.0	33.0	NM_012337		Missense_Mutation	SNP	ENST00000368099.4	hg19	CCDS30914.1	.	.	.	.	.	.	.	.	.	.	c	13.57	2.277087	0.40294	.	.	ENSG00000213085	ENST00000368099;ENST00000426543	T;T	0.11277	2.79;2.79	4.57	0.434	0.16539	.	0.517167	0.20680	N	0.087663	T	0.02807	0.0084	L	0.47716	1.5	0.30694	N	0.750993	B;B	0.13145	0.007;0.007	B;B	0.15870	0.014;0.008	T	0.43540	-0.9385	9	.	.	.	-2.3368	7.9394	0.29950	0.0:0.6248:0.0:0.3752	.	370;370	A8K884;Q9UL16	.;CCD19_HUMAN	T	370;285	ENSP00000357079:A370T;ENSP00000403044:A285T	.	A	-	1	0	CCDC19	158113813	0.011000	0.17503	0.710000	0.30468	0.961000	0.63080	0.102000	0.15272	-0.003000	0.14444	0.586000	0.80456	GCA	.	.		0.537	CCDC19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085979.1			T	159847189	C	T	159847189	3	4	369	1	0	0	0	0	1	0	0	0	2797	768	27	1	563	1	CCDC19	1	159847189	Missense_Mutation	SNP	C	TCGA-ZP-A9D4-01A-11D-A36X-10	9715738	159847189	89403432	2	51130										
DNAH6	1768	hgsc.bcm.edu	37	chr2	85039487	85039487	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	ttctctggaaacactcaacaAagccatcgctggatttgtgg	9	10	2	0			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr2:85039487A>G	ENST00000237449.6	+	72	11770	c.11762A>G	c.(11761-11763)aAa>aGa	p.K3921R	DNAH6_ENST00000389394.3_Missense_Mutation_p.K3921R			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	3921					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						ACACTCAACAAAGCCATCGCT	0.448																																					p.K3921R		Atlas-SNP	.											.	DNAH6	194	.	0			c.A11762G						.						110	102	105					2																	85039487		692	1591	2283	SO:0001583	missense	1768	exon73			TCAACAAAGCCAT	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.11762A>G	chr2.hg19:g.85039487A>G	ENSP00000237449:p.Lys3921Arg	137.0	0.0		147.0	62.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	hg19	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	A	18.13	3.555032	0.65425	.	.	ENSG00000115423	ENST00000389394;ENST00000237449	T;T	0.08896	3.04;3.04	5.7	4.56	0.56223	Dynein heavy chain (1);	0.000000	0.56097	D	0.000025	T	0.15046	0.0363	L	0.60845	1.875	0.80722	D	1	P	0.44659	0.84	P	0.50754	0.649	T	0.00565	-1.1668	10	0.44086	T	0.13	.	9.1923	0.37207	0.9153:0.0:0.0847:0.0	.	3921	Q9C0G6	DYH6_HUMAN	R	3921	ENSP00000374045:K3921R;ENSP00000237449:K3921R	ENSP00000237449:K3921R	K	+	2	0	DNAH6	84892998	1.000000	0.71417	0.998000	0.56505	0.571000	0.35966	4.794000	0.62482	2.178000	0.69098	0.477000	0.44152	AAA	.	.		0.448	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		G	85039487	A	G	85039487	3	3	369	1	0	0	0	0	1	0	0	0	4607	14	1	2	12048	2	DNAH6	2	85039487	Missense_Mutation	SNP	A	TCGA-ZP-A9D4-01A-11D-A36X-10		85039487	158159886	3	51131										
GPAT2	150763	hgsc.bcm.edu	37	chr2	96690055	96690055	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	agggcccctggggcggcactCtgcctgccagcagcccccgc	14	19	1	0			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr2:96690055C>G	ENST00000434632.1	-	17	2159	c.1700G>C	c.(1699-1701)aGa>aCa	p.R567T	GPAT2_ENST00000377137.3_Missense_Mutation_p.R567T|FAHD2CP_ENST00000607780.1_RNA|GPAT2_ENST00000453542.1_Missense_Mutation_p.R496T|GPAT2_ENST00000359548.4_Missense_Mutation_p.R567T			Q6NUI2	GPAT2_HUMAN	glycerol-3-phosphate acyltransferase 2, mitochondrial	567					CDP-diacylglycerol biosynthetic process (GO:0016024)|glycerol-3-phosphate metabolic process (GO:0006072)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			NS(1)|breast(1)|cervix(1)|endometrium(4)|large_intestine(1)|lung(5)|skin(3)	16						GGGCGGCACTCTGCCTGCCAG	0.642																																					p.R567T		Atlas-SNP	.											.	GPAT2	46	.	0			c.G1700C						.						9	11	11					2																	96690055		1847	3954	5801	SO:0001583	missense	150763	exon16			GGCACTCTGCCTG	BC042847	CCDS42714.1	2q11.2	2010-05-04			ENSG00000186281	ENSG00000186281			27168	protein-coding gene	gene with protein product	"cancer/testis antigen 123"					12477932	Standard	NM_207328		Approved	CT123	uc010yuf.1	Q6NUI2	OTTHUMG00000155208	ENST00000434632.1:c.1700G>C	chr2.hg19:g.96690055C>G	ENSP00000389395:p.Arg567Thr	85.0	0.0		98.0	6.0	NM_207328	Q6P2E4|Q6ZNI3|Q6ZNI5|Q6ZWJ4	Missense_Mutation	SNP	ENST00000434632.1	hg19	CCDS42714.1	.	.	.	.	.	.	.	.	.	.	c	15.88	2.962803	0.53507	.	.	ENSG00000186281	ENST00000359548;ENST00000434632;ENST00000453542;ENST00000377137	T;T;T;T	0.78126	-1.14;-1.14;-0.17;-1.15	5.2	4.32	0.51571	.	0.148103	0.40554	N	0.001071	T	0.81254	0.4784	M	0.65498	2.005	0.27417	N	0.954412	D;P;P;P;D	0.56035	0.974;0.763;0.469;0.554;0.974	P;B;B;B;P	0.53861	0.647;0.288;0.158;0.218;0.736	T	0.75340	-0.3352	10	0.62326	D	0.03	.	9.7275	0.40342	0.0:0.9037:0.0:0.0963	.	496;567;573;567;496	E9PE95;Q6NUI2-3;Q6NUI2-4;Q6NUI2;B4DNZ9	.;.;.;GPAT2_HUMAN;.	T	567;567;496;567	ENSP00000352547:R567T;ENSP00000389395:R567T;ENSP00000393770:R496T;ENSP00000366341:R567T	ENSP00000352547:R567T	R	-	2	0	GPAT2	96053782	0.011000	0.17503	0.987000	0.45799	0.982000	0.71751	1.312000	0.33574	1.197000	0.43143	0.637000	0.83480	AGA	.	.		0.642	GPAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338786.1	NM_207328		G	96690055	C	G	96690055	3	3	369	1	0	0	0	0	1	0	0	0	6597	913	32	4	715	4	GPAT2	2	96690055	Missense_Mutation	SNP	C	TCGA-ZP-A9D4-01A-11D-A36X-10	11650568	96690055	146509318	4	51132										
GALNT13	114805	hgsc.bcm.edu	37	chr2	155295175	155295175	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	gatgtttctagactcaatggAcctgtaatcatgttaaaatg	8	6	3	1			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr2:155295175A>G	ENST00000392825.3	+	12	2034	c.1467A>G	c.(1465-1467)ggA>ggG	p.G489G	GALNT13_ENST00000409237.1_Silent_p.G489G|AC009227.2_ENST00000434635.1_RNA|GALNT13_ENST00000487047.1_3'UTR	NM_052917.2	NP_443149.2	Q8IUC8	GLT13_HUMAN	polypeptide N-acetylgalactosaminyltransferase 13	489	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(6)|lung(37)|ovary(3)|pancreas(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	65						GACTCAATGGACCTGTAATCA	0.323																																					p.G489G		Atlas-SNP	.											.	GALNT13	170	.	0			c.A1467G						.						128	132	131					2																	155295175		2203	4300	6503	SO:0001819	synonymous_variant	114805	exon12			CAATGGACCTGTA	AB067505	CCDS2199.1	2q24.1	2014-03-13	2014-03-13		ENSG00000144278	ENSG00000144278	2.4.1.41	"Glycosyltransferase family 2 domain containing"	23242	protein-coding gene	gene with protein product	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13", "polypeptide GalNAc transferase 13"	608369	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13 (GalNAc-T13)"			11572484, 12407114	Standard	XM_005246267		Approved	KIAA1918, GalNAc-T13	uc002tyr.4	Q8IUC8	OTTHUMG00000131917	ENST00000392825.3:c.1467A>G	chr2.hg19:g.155295175A>G		92.0	0.0		87.0	35.0	NM_052917	Q08ER7|Q68VI8|Q6ZWG1|Q96PX0|Q9UIE5	Silent	SNP	ENST00000392825.3	hg19	CCDS2199.1	.	.	.	.	.	.	.	.	.	.	A	10.53	1.377026	0.24857	.	.	ENSG00000144278	ENST00000450838;ENST00000422126	.	.	.	5.55	-1.18	0.09617	.	.	.	.	.	T	0.40040	0.1101	.	.	.	0.80722	D	1	B	0.09022	0.002	B	0.04013	0.001	T	0.25293	-1.0136	7	0.66056	D	0.02	.	2.1258	0.03738	0.2784:0.1605:0.4057:0.1555	.	469	Q8IUC8-2	.	A	75;28	.	ENSP00000391469:T28A	T	+	1	0	GALNT13	155003421	0.472000	0.25870	0.997000	0.53966	0.980000	0.70556	-0.109000	0.10840	-0.142000	0.11354	-0.899000	0.02877	ACC	.	.		0.323	GALNT13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254870.2	NM_052917		G	155295175	A	G	155295175	2	3	369	1	0	0	0	0	0	0	0	1	6219	262	10	2		2	GALNT13	2	155295175	Silent	SNP	A	TCGA-ZP-A9D4-01A-11D-A36X-10	58605120	155295175	87904198	5	51133										
TTN	7273	hgsc.bcm.edu	37	chr2	179399862	179399862	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	ggacaattccaaactcaccaCgcccaagatcttcagcaatc	5	15	3	1	rs376403708		TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr2:179399862C>T	ENST00000591111.1	-	308	96781	c.96557G>A	c.(96556-96558)cGt>cAt	p.R32186H	TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R24887H|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000415561.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R24954H|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R33827H|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R24762H|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R31259H			Q8WZ42	TITIN_HUMAN	titin	32186	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AAACTCACCACGCCCAAGATC	0.408													C|||	1	0.000199681	0	0	5008	,	,		20558	0		0	False		,,,				2504	0.001				p.R33827H		Atlas-SNP	.											.	TTN	18412	.	0			c.G101480A						.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	0,3806		0,0,1903	117	113	114		74861,74660,93776,74285	4.8	1	2		114	1,8237		0,1,4118	no	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	29,29,29,29	0,1,6021	TT,TC,CC		0.0121,0.0,0.0083	benign,benign,benign,benign	24954/27119,24887/27052,31259/33424,24762/26927	179399862	1,12043	1903	4119	6022	SO:0001583	missense	7273	exon358			TCACCACGCCCAA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.96557G>A	chr2.hg19:g.179399862C>T	ENSP00000465570:p.Arg32186His	62.0	0.0		65.0	22.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	15.39	2.819595	0.50633	0.0	1.21E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24	5.72	4.85	0.62838	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.60907	0.2305	L	0.56199	1.76	0.54753	D	0.999981	B;B;B;B	0.22146	0.065;0.065;0.065;0.065	B;B;B;B	0.17722	0.019;0.019;0.019;0.019	T	0.61222	-0.7106	9	0.87932	D	0	.	10.7451	0.46177	0.0:0.8546:0.0:0.1454	.	24762;24887;24954;32186	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	H	31259;24762;24954;24887;24759	ENSP00000343764:R31259H;ENSP00000434586:R24762H;ENSP00000340554:R24954H;ENSP00000352154:R24887H	ENSP00000340554:R24954H	R	-	2	0	TTN	179108108	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	4.102000	0.57776	1.407000	0.46875	0.557000	0.71058	CGT	.	.		0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179399862	C	T	179399862	3	4	369	1	0	0	0	0	1	0	0	0	16750	536	19	1	6519	1	TTN	2	179399862	Missense_Mutation	SNP	C	TCGA-ZP-A9D4-01A-11D-A36X-10	24104687	179399862	63799511	6	51134										
FSIP2	401024	hgsc.bcm.edu	37	chr2	186672932	186672932	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	ttcgaattctgaatttcaacCtcaagtagaggaagaagtat	8	6	3	3			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr2:186672932C>T	ENST00000424728.1	+	17	18899	c.18899C>T	c.(18898-18900)cCt>cTt	p.P6300L	FSIP2_ENST00000343098.5_Missense_Mutation_p.P6389L			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	6300										NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						GAATTTCAACCTCAAGTAGAG	0.303																																					p.P6389L		Atlas-SNP	.											.	FSIP2	251	.	0			c.C19166T						.						43	41	41					2																	186672932		1811	4067	5878	SO:0001583	missense	401024	exon17			TTCAACCTCAAGT	AK092099	CCDS54426.1	2q32.1	2010-06-18			ENSG00000188738	ENSG00000188738			21675	protein-coding gene	gene with protein product		615796				14702039	Standard	NM_173651		Approved	FLJ34780	uc002upl.3	Q5CZC0	OTTHUMG00000153874	ENST00000424728.1:c.18899C>T	chr2.hg19:g.186672932C>T	ENSP00000401306:p.Pro6300Leu	347.0	0.0		326.0	140.0	NM_173651	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Missense_Mutation	SNP	ENST00000424728.1	hg19		.	.	.	.	.	.	.	.	.	.	C	16.31	3.087744	0.55968	.	.	ENSG00000188738	ENST00000343098;ENST00000424728	T;T	0.51817	0.69;0.69	5.21	3.37	0.38596	.	0.449576	0.19458	N	0.113770	T	0.49541	0.1563	L	0.49126	1.545	0.40431	D	0.979945	.	.	.	.	.	.	T	0.53151	-0.8479	8	0.72032	D	0.01	.	7.3416	0.26640	0.0:0.7386:0.17:0.0913	.	.	.	.	L	6389;6300	ENSP00000344403:P6389L;ENSP00000401306:P6300L	ENSP00000344403:P6389L	P	+	2	0	FSIP2	186381177	0.055000	0.20627	0.997000	0.53966	0.936000	0.57629	0.619000	0.24388	1.417000	0.47077	0.591000	0.81541	CCT	.	.		0.303	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651		T	186672932	C	T	186672932	3	4	369	1	0	0	0	0	1	0	0	0	6083	681	24	3	19232	3	FSIP2	2	186672932	Missense_Mutation	SNP	C	TCGA-ZP-A9D4-01A-11D-A36X-10	7273070	186672932	56526441	7	51135										
DNAH7	56171	hgsc.bcm.edu	37	chr2	196619175	196619175	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	ctgctgggcaccggtcaggaAggcttgtgtgaagaagaagc	16	8	1	3			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr2:196619175A>G	ENST00000312428.6	-	63	11750	c.11650T>C	c.(11650-11652)Ttc>Ctc	p.F3884L	DNAH7_ENST00000409063.1_Missense_Mutation_p.F367L	NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	3884					cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						CCGGTCAGGAAGGCTTGTGTG	0.468																																					p.F3884L		Atlas-SNP	.											.	DNAH7	512	.	0			c.T11650C						.						99	100	100					2																	196619175		1919	4118	6037	SO:0001583	missense	56171	exon63			TCAGGAAGGCTTG	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.11650T>C	chr2.hg19:g.196619175A>G	ENSP00000311273:p.Phe3884Leu	138.0	0.0		157.0	65.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	hg19	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	A	32	5.186620	0.94885	.	.	ENSG00000118997	ENST00000312428;ENST00000409063	T;T	0.14266	2.52;2.52	5.55	5.55	0.83447	Dynein heavy chain (1);	0.000000	0.85682	D	0.000000	T	0.47857	0.1468	M	0.92077	3.27	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.59653	-0.7414	10	0.66056	D	0.02	.	15.517	0.75833	1.0:0.0:0.0:0.0	.	3884	Q8WXX0	DYH7_HUMAN	L	3884;367	ENSP00000311273:F3884L;ENSP00000386912:F367L	ENSP00000311273:F3884L	F	-	1	0	DNAH7	196327420	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	8.747000	0.91610	2.326000	0.78906	0.533000	0.62120	TTC	.	.		0.468	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		G	196619175	A	G	196619175	3	3	369	1	0	0	0	0	1	0	0	0	4608	72	3	2	436	2	DNAH7	2	196619175	Missense_Mutation	SNP	A	TCGA-ZP-A9D4-01A-11D-A36X-10	9946243	196619175	46580198	8	51136										
MFF	56947	hgsc.bcm.edu	37	chr2	228194472	228194472	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	ctgtatttaaatgagtaaagGaacaagcagtgacacatcac	8	7	1	2	rs145010660	byFrequency	TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr2:228194472G>T	ENST00000353339.3	+	3	452	c.11G>T	c.(10-12)gGa>gTa	p.G4V	MFF_ENST00000476924.1_Intron|MFF_ENST00000349901.7_Intron|MFF_ENST00000409565.1_Intron|MFF_ENST00000304593.9_Intron|MFF_ENST00000524634.1_Intron|MFF_ENST00000354503.6_Intron|MFF_ENST00000409616.1_5'UTR|MFF_ENST00000392059.1_Missense_Mutation_p.G4V|MFF_ENST00000337110.7_Intron	NM_001277061.1	NP_001263990.1	Q9GZY8	MFF_HUMAN	mitochondrial fission factor	4					mitochondrial fission (GO:0000266)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial fusion (GO:0008053)|mitochondrion morphogenesis (GO:0070584)|peroxisome fission (GO:0016559)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein homooligomerization (GO:0051260)|protein targeting to mitochondrion (GO:0006626)|regulation of mitochondrion organization (GO:0010821)|regulation of peroxisome organization (GO:1900063)|release of cytochrome c from mitochondria (GO:0001836)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|integral component of mitochondrial membrane (GO:0032592)|mitochondrial outer membrane (GO:0005741)|peroxisome (GO:0005777)|synapse (GO:0045202)	protein homodimerization activity (GO:0042803)			breast(3)|endometrium(2)|kidney(3)|large_intestine(7)|lung(4)|stomach(2)	21						ATGAGTAAAGGAACAAGCAGT	0.358																																					p.G4V		Atlas-SNP	.											.	MFF	48	.	0			c.G11T						.						121	114	117					2																	228194472		2203	4300	6503	SO:0001583	missense	56947	exon3			GTAAAGGAACAAG	AF258660	CCDS2465.1, CCDS63139.1, CCDS63140.1, CCDS63141.1, CCDS63142.1, CCDS74662.1	2q36	2008-05-29	2008-05-29	2008-05-29	ENSG00000168958	ENSG00000168958			24858	protein-coding gene	gene with protein product		614785	"chromosome 2 open reading frame 33"	C2orf33		18353969	Standard	NM_001277061		Approved	GL004	uc002voy.4	Q9GZY8	OTTHUMG00000133180	ENST00000353339.3:c.11G>T	chr2.hg19:g.228194472G>T	ENSP00000302037:p.Gly4Val	268.0	0.0		283.0	98.0	NM_020194	Q567U1|Q658R6|Q9BVZ1|Q9H690|Q9NRG8	Missense_Mutation	SNP	ENST00000353339.3	hg19	CCDS2465.1	.	.	.	.	.	.	.	.	.	.	G	13.21	2.170092	0.38315	.	.	ENSG00000168958	ENST00000353339;ENST00000436237;ENST00000443428;ENST00000392059	T;T;T;T	0.38077	1.51;1.16;1.48;1.51	5.97	4.15	0.48705	.	0.224259	0.31636	N	0.007317	T	0.17323	0.0416	N	0.08118	0	0.43203	D	0.995053	B	0.17667	0.023	B	0.17722	0.019	T	0.06409	-1.0828	9	.	.	.	-1.3011	8.8122	0.34974	0.0815:0.1512:0.7673:0.0	.	4	Q9GZY8	MFF_HUMAN	V	4	ENSP00000302037:G4V;ENSP00000411386:G4V;ENSP00000391829:G4V;ENSP00000375912:G4V	.	G	+	2	0	MFF	227902716	1.000000	0.71417	0.998000	0.56505	0.959000	0.62525	2.047000	0.41269	0.833000	0.34828	0.650000	0.86243	GGA	.	G|0.999;C|0.001		0.358	MFF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256887.2	NM_020194		T	228194472	G	T	228194472	3	4	369	1	0	0	0	0	1	0	0	0	9528	1174	41	3	13	3	MFF	2	228194472	Missense_Mutation	SNP	G	TCGA-ZP-A9D4-01A-11D-A36X-10	31575297	228194472	15004901	9	51137										
ANKMY1	51281	hgsc.bcm.edu	37	chr2	241421602	241421602	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	gcctgcagacacacttactgCccctgctccttcacatccag	6	18	1	1			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr2:241421602C>G	ENST00000272972.3	-	15	2830	c.2616G>C	c.(2614-2616)ggG>ggC	p.G872G	ANKMY1_ENST00000361678.4_Silent_p.G648G|ANKMY1_ENST00000373318.2_Silent_p.G651G|ANKMY1_ENST00000401804.1_Silent_p.G961G|ANKMY1_ENST00000406958.1_Silent_p.G633G|ANKMY1_ENST00000403283.1_Silent_p.G774G|ANKMY1_ENST00000391987.1_Silent_p.G872G|ANKMY1_ENST00000373320.4_Silent_p.G642G	NM_016552.2	NP_057636.2	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1	872							metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	30		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.03e-30)|all cancers(36;4.78e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.45e-14)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.8e-06)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.01)|Colorectal(34;0.0101)|COAD - Colon adenocarcinoma(134;0.0476)		ACACTTACTGCCCCTGCTCCT	0.617																																					p.G872G		Atlas-SNP	.											.	ANKMY1	112	.	0			c.G2616C						.						106	98	100					2																	241421602		2203	4300	6503	SO:0001819	synonymous_variant	51281	exon15			TTACTGCCCCTGC	AB034636	CCDS2535.1, CCDS2536.1, CCDS63184.1, CCDS63185.1, CCDS74681.1	2q37.3	2013-01-10			ENSG00000144504	ENSG00000144504		"Zinc fingers, MYND-type", "Ankyrin repeat domain containing"	20987	protein-coding gene	gene with protein product							Standard	XM_005247020		Approved	FLJ20499, ZMYND13	uc002vyz.1	Q9P2S6	OTTHUMG00000133355	ENST00000272972.3:c.2616G>C	chr2.hg19:g.241421602C>G		86.0	0.0		67.0	16.0	NM_016552	B2RB78|Q4ZFV3|Q8IYX5|Q8NDK5|Q9H0V8|Q9NX10	Silent	SNP	ENST00000272972.3	hg19	CCDS2536.1																																																																																			.	.		0.617	ANKMY1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257187.2	NM_017844		G	241421602	C	G	241421602	2	3	369	1	0	0	0	0	0	0	0	1	634	726	26	4		4	ANKMY1	2	241421602	Silent	SNP	C	TCGA-ZP-A9D4-01A-11D-A36X-10	13227130	241421602	1777771	10	51138										
GOLGA4	2803	hgsc.bcm.edu	37	chr3	37340443	37340443	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	ataaggaacaatgtacactaTtaactagtgaaaaagaagct	7	5	0	2			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr3:37340443T>C	ENST00000361924.2	+	8	1308	c.934T>C	c.(934-936)Tta>Cta	p.L312L	GOLGA4_ENST00000435830.2_3'UTR|GOLGA4_ENST00000356847.4_Silent_p.L334L|GOLGA4_ENST00000444882.1_Intron	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	312	Glu-rich.				Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						ATGTACACTATTAACTAGTGA	0.353																																					p.L334L		Atlas-SNP	.											.	GOLGA4	173	.	0			c.T1000C						.						111	116	114					3																	37340443		2203	4300	6503	SO:0001819	synonymous_variant	2803	exon9			ACACTATTAACTA	U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"golgin 245"	602509	"golgi autoantigen, golgin subfamily a, 4"			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.934T>C	chr3.hg19:g.37340443T>C		463.0	0.0		449.0	172.0	NM_001172713	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Silent	SNP	ENST00000361924.2	hg19	CCDS2666.1																																																																																			.	.		0.353	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078		C	37340443	T	C	37340443	2	2	369	1	0	0	0	0	0	0	0	1	6563	1490	52	2		2	GOLGA4	3	37340443	Silent	SNP	T	TCGA-ZP-A9D4-01A-11D-A36X-10		37340443	160681987	11	51139										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266107	41266107	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	gtcttacctggactctggaaTccattctggtgccactacca	8	13	3	0	rs121913416		TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr3:41266107T>G	ENST00000349496.5	+	3	384	c.104T>G	c.(103-105)aTc>aGc	p.I35S	CTNNB1_ENST00000453024.1_Missense_Mutation_p.I28S|CTNNB1_ENST00000396185.3_Missense_Mutation_p.I35S|CTNNB1_ENST00000396183.3_Missense_Mutation_p.I35S|CTNNB1_ENST00000405570.1_Missense_Mutation_p.I35S	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	35			I -> S (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.I35S(20)|p.I35T(13)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.I35_S37>T(1)|p.A13_R151del(1)|p.D32_H36>D(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.I35_K170del(1)|p.H24_G38del(1)|p.S29_H36del(1)|p.I35_T41del(1)|p.I35N(1)|p.I35_G38del(1)|p.I35K(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.D32fs*9(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.GIHS34?(1)|p.A5_I35del(1)|p.D32_H36del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GACTCTGGAATCCATTCTGGT	0.493		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.I35S	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,NS,carcinoma,0,1	CTNNB1	4904	.	169	Deletion - In frame(107)|Substitution - Missense(35)|Complex - deletion inframe(17)|Unknown(7)|Deletion - Frameshift(3)	liver(118)|large_intestine(19)|salivary_gland(12)|stomach(7)|soft_tissue(2)|small_intestine(2)|endometrium(2)|skin(2)|adrenal_gland(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|pituitary(1)|kidney(1)	c.T104G						.						95	80	85					3																	41266107		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	CTGGAATCCATTC	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.104T>G	chr3.hg19:g.41266107T>G	ENSP00000344456:p.Ile35Ser	183.0	0.0		126.0	51.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.188620	0.78789	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.51817	0.69;0.69;0.69;0.69;0.69;0.69;0.69;0.69;0.69	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.69548	0.3123	M	0.79614	2.46	0.80722	D	1	D	0.76494	0.999	D	0.71414	0.973	T	0.73949	-0.3821	10	0.87932	D	0	-3.5499	16.0677	0.80897	0.0:0.0:0.0:1.0	.	35	P35222	CTNB1_HUMAN	S	28;35;35;35;35;28;35;35;35	ENSP00000400508:I28S;ENSP00000385604:I35S;ENSP00000412219:I35S;ENSP00000379486:I35S;ENSP00000344456:I35S;ENSP00000411226:I28S;ENSP00000379488:I35S;ENSP00000409302:I35S;ENSP00000401599:I35S	ENSP00000344456:I35S	I	+	2	0	CTNNB1	41241111	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.040000	0.89188	2.201000	0.70794	0.533000	0.62120	ATC	.	.		0.493	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41266107	T	G	41266107	3	3	369	1	0	0	0	0	1	0	0	0	4018	1435	50	5	110	5	CTNNB1	3	41266107	Missense_Mutation	SNP	T	TCGA-ZP-A9D4-01A-11D-A36X-10	3925664	41266107	156756323	12	51140										
B4GALT4	8702	hgsc.bcm.edu	37	chr3	118948707	118948707	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	cacttactgaggtaaggagaCacagaagggcagttgtcaag	13	7	1	3			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr3:118948707C>T	ENST00000483209.1	-	3	881	c.240G>A	c.(238-240)gtG>gtA	p.V80V	B4GALT4-AS1_ENST00000470790.1_RNA|B4GALT4_ENST00000359213.3_Silent_p.V80V|B4GALT4_ENST00000460321.1_Intron|B4GALT4_ENST00000393765.2_Silent_p.V80V|B4GALT4_ENST00000471675.1_Silent_p.V33V|B4GALT4_ENST00000467604.1_Silent_p.V80V			O60513	B4GT4_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 4	80					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|membrane lipid metabolic process (GO:0006643)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)|metal ion binding (GO:0046872)|N-acetyllactosamine synthase activity (GO:0003945)			breast(2)|endometrium(1)|large_intestine(1)|lung(6)|skin(2)|stomach(2)	14				GBM - Glioblastoma multiforme(114;0.222)	N-Acetyl-D-glucosamine(DB00141)	GGTAAGGAGACACAGAAGGGC	0.368																																					p.V80V		Atlas-SNP	.											.	B4GALT4	30	.	0			c.G240A						.						136	125	129					3																	118948707		2203	4300	6503	SO:0001819	synonymous_variant	8702	exon4			AGGAGACACAGAA	AF022367	CCDS2986.1	3q13.3	2013-02-19			ENSG00000121578	ENSG00000121578		"Beta 4-glycosyltransferases"	927	protein-coding gene	gene with protein product		604015				9597550	Standard	NM_003778		Approved	beta4Gal-T4	uc003eci.3	O60513	OTTHUMG00000159358	ENST00000483209.1:c.240G>A	chr3.hg19:g.118948707C>T		60.0	0.0		50.0	21.0	NM_212543	Q68D68|Q9BSW3|Q9C078	Silent	SNP	ENST00000483209.1	hg19	CCDS2986.1																																																																																			.	.		0.368	B4GALT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354925.2	NM_003778		T	118948707	C	T	118948707	2	4	369	1	0	0	0	0	0	0	0	1	1273	465	17	3		3	B4GALT4	3	118948707	Silent	SNP	C	TCGA-ZP-A9D4-01A-11D-A36X-10	77682600	118948707	79073723	13	51141										
HGD	3081	hgsc.bcm.edu	37	chr3	120389301	120389301	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	ggatcaggatcaacttcatcCcagttgtgagtgacttggcc	11	10	3	2			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr3:120389301C>A	ENST00000283871.5	-	4	714	c.255G>T	c.(253-255)tgG>tgT	p.W85C	HGD_ENST00000488183.1_5'UTR	NM_000187.3	NP_000178.2	Q93099	HGD_HUMAN	homogentisate 1,2-dioxygenase	85					cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	homogentisate 1,2-dioxygenase activity (GO:0004411)|metal ion binding (GO:0046872)			cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(2)	25				GBM - Glioblastoma multiforme(114;0.158)		CAACTTCATCCCAGTTGTGAG	0.418																																					p.W85C		Atlas-SNP	.											.	HGD	65	.	0			c.G255T						.						150	147	148					3																	120389301		2203	4296	6499	SO:0001583	missense	3081	exon4			TTCATCCCAGTTG		CCDS3000.1	3q	2010-04-27	2010-04-27		ENSG00000113924	ENSG00000113924	1.13.11.5		4892	protein-coding gene	gene with protein product	"homogentisate oxidase"	607474	"homogentisate 1,2-dioxygenase (homogentisate oxidase)"	AKU		8188241	Standard	NM_000187		Approved	HGO	uc003edw.3	Q93099	OTTHUMG00000159441	ENST00000283871.5:c.255G>T	chr3.hg19:g.120389301C>A	ENSP00000283871:p.Trp85Cys	123.0	0.0		120.0	50.0	NM_000187	A8K417|B2R8Z0	Missense_Mutation	SNP	ENST00000283871.5	hg19	CCDS3000.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.007814	0.75046	.	.	ENSG00000113924	ENST00000283871;ENST00000476082	D;D	0.98968	-5.28;-5.28	6.06	6.06	0.98353	Cupin, RmlC-type (1);	0.000000	0.85682	D	0.000000	D	0.98807	0.9598	L	0.60904	1.88	0.80722	D	1	D	0.76494	0.999	D	0.72338	0.977	D	0.99218	1.0878	10	0.44086	T	0.13	-12.3701	18.1221	0.89574	0.0:1.0:0.0:0.0	.	85	Q93099	HGD_HUMAN	C	85;44	ENSP00000283871:W85C;ENSP00000419560:W44C	ENSP00000283871:W85C	W	-	3	0	HGD	121871991	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.498000	0.73679	2.871000	0.98454	0.655000	0.94253	TGG	.	.		0.418	HGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355410.1			A	120389301	C	A	120389301	3	1	369	1	0	0	0	0	1	0	0	0	7093	624	22	3	1126	3	HGD	3	120389301	Missense_Mutation	SNP	C	TCGA-ZP-A9D4-01A-11D-A36X-10	1440594	120389301	77633129	14	51142										
POLQ	10721	hgsc.bcm.edu	37	chr3	121258426	121258426	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	ctacttttattcctacttccTgaaacagactctgaattgag	5	10	1	4			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr3:121258426T>C	ENST00000264233.5	-	4	613	c.485A>G	c.(484-486)cAg>cGg	p.Q162R		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	162	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		TCCTACTTCCTGAAACAGACT	0.373								DNA polymerases (catalytic subunits)																													p.Q162R	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.A485G						.						82	79	80					3																	121258426		2203	4300	6503	SO:0001583	missense	10721	exon4			ACTTCCTGAAACA	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.485A>G	chr3.hg19:g.121258426T>C	ENSP00000264233:p.Gln162Arg	238.0	0.0		214.0	83.0	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	hg19	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	T	19.88	3.909861	0.72983	.	.	ENSG00000051341	ENST00000264233;ENST00000393672	T	0.15017	2.46	6.06	4.89	0.63831	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.203846	0.52532	D	0.000071	T	0.17831	0.0428	N	0.25144	0.715	0.43550	D	0.99585	B	0.29301	0.241	B	0.40009	0.316	T	0.07158	-1.0787	10	0.52906	T	0.07	.	13.5722	0.61853	0.0:0.0:0.1297:0.8702	.	162	O75417	DPOLQ_HUMAN	R	162;297	ENSP00000264233:Q162R	ENSP00000264233:Q162R	Q	-	2	0	POLQ	122741116	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.932000	0.70121	1.087000	0.41251	0.528000	0.53228	CAG	.	.		0.373	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		C	121258426	T	C	121258426	3	2	369	1	0	0	0	0	1	0	0	0	12217	1580	55	2	7395	2	POLQ	3	121258426	Missense_Mutation	SNP	T	TCGA-ZP-A9D4-01A-11D-A36X-10	869125	121258426	76764004	15	51143										
KCTD8	386617	hgsc.bcm.edu	37	chr4	44449630	44449630	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	agatcttgtcgtcgcggtacTggttgacgaaggcggcggtg	17	8	1	2			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr4:44449630T>C	ENST00000360029.3	-	1	1194	c.911A>G	c.(910-912)cAg>cGg	p.Q304R	AC131951.1_ENST00000584757.1_RNA	NM_198353.2	NP_938167.1	Q6ZWB6	KCTD8_HUMAN	potassium channel tetramerization domain containing 8	304					protein homooligomerization (GO:0051260)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)				central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(5)|lung(19)|ovary(1)|prostate(3)|upper_aerodigestive_tract(4)	41						GTCGCGGTACTGGTTGACGAA	0.612										HNSCC(17;0.042)																											p.Q304R		Atlas-SNP	.											.	KCTD8	96	.	0			c.A911G						.						30	27	28					4																	44449630		2203	4299	6502	SO:0001583	missense	386617	exon1			CGGTACTGGTTGA	AK123347	CCDS3467.1	4p13	2013-06-20	2013-06-20		ENSG00000183783	ENSG00000183783			22394	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 8"				Standard	NM_198353		Approved		uc003gwu.3	Q6ZWB6	OTTHUMG00000099409	ENST00000360029.3:c.911A>G	chr4.hg19:g.44449630T>C	ENSP00000353129:p.Gln304Arg	89.0	0.0		66.0	38.0	NM_198353	A2RU39	Missense_Mutation	SNP	ENST00000360029.3	hg19	CCDS3467.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.12|15.12	2.740103|2.740103	0.49045|0.49045	.|.	.|.	ENSG00000183783|ENSG00000183783	ENST00000360029|ENST00000515268	T|.	0.38560|.	1.13|.	4.2|4.2	4.2|4.2	0.49525|0.49525	.|.	0.076891|.	0.53938|.	D|.	0.000059|.	T|T	0.57932|0.57932	0.2087|0.2087	L|L	0.43152|0.43152	1.355|1.355	0.46798|0.46798	D|D	0.999205|0.999205	B|.	0.20052|.	0.041|.	B|.	0.17098|.	0.017|.	T|T	0.55431|0.55431	-0.8142|-0.8142	10|5	0.45353|.	T|.	0.12|.	.|.	12.6153|12.6153	0.56573|0.56573	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	304|.	Q6ZWB6|.	KCTD8_HUMAN|.	R|G	304|1	ENSP00000353129:Q304R|.	ENSP00000353129:Q304R|.	Q|S	-|-	2|1	0|0	KCTD8|KCTD8	44144387|44144387	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	5.929000|5.929000	0.70096|0.70096	1.769000|1.769000	0.52152|0.52152	0.482000|0.482000	0.46254|0.46254	CAG|AGT	.	.		0.612	KCTD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216868.1			C	44449630	T	C	44449630	3	2	369	1	0	0	0	0	1	0	0	0	8124	1580	55	2	518	2	KCTD8	4	44449630	Missense_Mutation	SNP	T	TCGA-ZP-A9D4-01A-11D-A36X-10		44449630	146704646	16	51144										
KIT	3815	hgsc.bcm.edu	37	chr4	55564533	55564533	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	tccgctgtcctctcacagacCcagaagtgaccaattattcc	6	15	1	3			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr4:55564533C>T	ENST00000288135.5	+	3	518	c.421C>T	c.(421-423)Cca>Tca	p.P141S		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	141	Ig-like C2-type 2.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TCTCACAGACCCAGAAGTGAC	0.512		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																												p.P141S		Atlas-SNP	.	yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	.	KIT	7396	.	0			c.C421T						.						51	50	50					4																	55564533		2203	4300	6503	SO:0001583	missense	3815	exon3	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	ACAGACCCAGAAG	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.421C>T	chr4.hg19:g.55564533C>T	ENSP00000288135:p.Pro141Ser	136.0	0.0		101.0	31.0	NM_000222	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	hg19	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	C	17.76	3.469049	0.63625	.	.	ENSG00000157404	ENST00000288135;ENST00000412167;ENST00000536403	D;D	0.84370	-1.84;-1.82	5.63	5.63	0.86233	Immunoglobulin-like fold (1);	0.099447	0.44688	D	0.000423	D	0.92522	0.7625	M	0.78637	2.42	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.93048	0.6463	10	0.87932	D	0	.	17.8639	0.88790	0.0:1.0:0.0:0.0	.	141;141	P10721-2;P10721	.;KIT_HUMAN	S	141	ENSP00000288135:P141S;ENSP00000390987:P141S	ENSP00000288135:P141S	P	+	1	0	KIT	55259290	1.000000	0.71417	0.991000	0.47740	0.273000	0.26683	5.302000	0.65733	2.657000	0.90304	0.561000	0.74099	CCA	.	.		0.512	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			T	55564533	C	T	55564533	3	4	369	1	0	0	0	0	1	0	0	0	8338	623	22	3	431	3	KIT	4	55564533	Missense_Mutation	SNP	C	TCGA-ZP-A9D4-01A-11D-A36X-10	11114903	55564533	135589743	17	51145										
SLC4A4	8671	hgsc.bcm.edu	37	chr4	72205022	72205022	+	Intron	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	cttggggagagaggaagagcCcggagctccactttcctcag	14	11	1	2			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr4:72205022C>T	ENST00000264485.5	+	4	370				SLC4A4_ENST00000351898.6_Intron|SLC4A4_ENST00000340595.3_Silent_p.A19A|SLC4A4_ENST00000514331.1_Intron|SLC4A4_ENST00000425175.1_Intron|SLC4A4_ENST00000512686.1_Silent_p.A19A	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4						bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	58			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)		Sodium bicarbonate(DB01390)	GAGGAAGAGCCCGGAGCTCCA	0.498																																					p.A19A		Atlas-SNP	.											.	SLC4A4	269	.	0			c.C57T						.						182	208	200					4																	72205022		2203	4300	6503	SO:0001627	intron_variant	8671	exon1			AAGAGCCCGGAGC	AF007216	CCDS3549.1, CCDS43236.1, CCDS47071.1	4q13.3	2013-07-19	2013-07-19		ENSG00000080493	ENSG00000080493		"Solute carriers"	11030	protein-coding gene	gene with protein product		603345	"solute carrier family 4, sodium bicarbonate cotransporter, member 4"	SLC4A5		9235899, 9651366	Standard	NM_001098484		Approved	NBC1, HNBC1, NBC2, pNBC, hhNMC	uc010iic.3	Q9Y6R1	OTTHUMG00000129907	ENST00000264485.5:c.254-65C>T	chr4.hg19:g.72205022C>T		179.0	0.0		156.0	60.0	NM_003759	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Silent	SNP	ENST00000264485.5	hg19	CCDS43236.1																																																																																			.	.		0.498	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759		T	72205022	C	T	72205022	1	4	369	0	1	0	0	0	0	0	0	0	14671	610	22	3		3	SLC4A4	4	72205022	Intron	SNP	C	TCGA-ZP-A9D4-01A-11D-A36X-10	16640489	72205022	118949254	18	51146										
HHIP	64399	hgsc.bcm.edu	37	chr4	145580921	145580921	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	gaaggttatgtgaagatactTacccctgaaggagaaatttt	10	5	0	4			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr4:145580921T>C	ENST00000296575.3	+	4	1417	c.762T>C	c.(760-762)ctT>ctC	p.L254L	HHIP_ENST00000511314.1_3'UTR|HHIP_ENST00000434550.2_Silent_p.L254L|HHIP-AS1_ENST00000512359.1_RNA	NM_022475.2	NP_071920.1	Q96QV1	HHIP_HUMAN	hedgehog interacting protein	254					carbohydrate metabolic process (GO:0005975)|dorsal/ventral pattern formation (GO:0009953)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|negative regulation of signal transduction (GO:0009968)|negative regulation of smoothened signaling pathway (GO:0045879)|neuroblast proliferation (GO:0007405)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|skeletal system morphogenesis (GO:0048705)|smoothened signaling pathway (GO:0007224)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	hedgehog family protein binding (GO:0097108)|oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	33	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0185)		TGAAGATACTTACCCCTGAAG	0.423																																					p.L254L		Atlas-SNP	.											.	HHIP	100	.	0			c.T762C						.						97	106	103					4																	145580921		2203	4300	6503	SO:0001819	synonymous_variant	64399	exon4			GATACTTACCCCT	AK024645	CCDS3762.1	4q31.21-q31.3	2008-08-29	2001-11-29		ENSG00000164161	ENSG00000164161			14866	protein-coding gene	gene with protein product		606178	"hedgehog-interacting protein"			11435703, 11731473	Standard	NM_022475		Approved	HIP, FLJ20992	uc003ijs.2	Q96QV1	OTTHUMG00000161428	ENST00000296575.3:c.762T>C	chr4.hg19:g.145580921T>C		197.0	0.0		167.0	66.0	NM_022475	Q6PK09|Q8NCI7|Q9BXK3|Q9H1J4|Q9H7E7	Silent	SNP	ENST00000296575.3	hg19	CCDS3762.1																																																																																			.	.		0.423	HHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364887.2			C	145580921	T	C	145580921	2	2	369	1	0	0	0	0	0	0	0	1	7101	1741	61	2		2	HHIP	4	145580921	Silent	SNP	T	TCGA-ZP-A9D4-01A-11D-A36X-10	73375899	145580921	45573355	19	51147										
DDX60	55601	hgsc.bcm.edu	37	chr4	169209405	169209405	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	agtcagaaaggtgaattaaaTtcagattccaaaattcaaaa	6	5	3	3			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr4:169209405T>C	ENST00000393743.3	-	9	1394	c.1103A>G	c.(1102-1104)aAt>aGt	p.N368S		NM_017631.5	NP_060101.3	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	368					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|single-stranded RNA binding (GO:0003727)			breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|urinary_tract(4)	63		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0485)		GTGAATTAAATTCAGATTCCA	0.259																																					p.N368S		Atlas-SNP	.											.	DDX60	304	.	0			c.A1103G						.						46	53	50					4																	169209405		2166	4260	6426	SO:0001583	missense	55601	exon9			ATTAAATTCAGAT	AK001649	CCDS34097.1	4q32.3	2010-02-17			ENSG00000137628	ENSG00000137628			25942	protein-coding gene	gene with protein product		613974				12477932	Standard	NM_017631		Approved	FLJ20035	uc003irp.3	Q8IY21	OTTHUMG00000161350	ENST00000393743.3:c.1103A>G	chr4.hg19:g.169209405T>C	ENSP00000377344:p.Asn368Ser	738.0	1.0		669.0	256.0	NM_017631	Q6PK35|Q9NVE3	Missense_Mutation	SNP	ENST00000393743.3	hg19	CCDS34097.1	.	.	.	.	.	.	.	.	.	.	T	17.68	3.450481	0.63290	.	.	ENSG00000137628	ENST00000393743	T	0.20069	2.1	4.86	4.86	0.63082	.	0.282994	0.29964	N	0.010753	T	0.26593	0.0650	M	0.66939	2.045	0.33731	D	0.618275	P	0.48911	0.917	B	0.43950	0.437	T	0.43294	-0.9400	10	0.25751	T	0.34	.	13.7386	0.62833	0.0:0.0:0.0:1.0	.	368	Q8IY21	DDX60_HUMAN	S	368	ENSP00000377344:N368S	ENSP00000377344:N368S	N	-	2	0	DDX60	169445980	0.995000	0.38212	0.999000	0.59377	0.984000	0.73092	2.990000	0.49401	1.959000	0.56917	0.377000	0.23210	AAT	.	.		0.259	DDX60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364622.1	NM_017631		C	169209405	T	C	169209405	3	2	369	1	0	0	0	0	1	0	0	0	4380	1493	52	2	4155	2	DDX60	4	169209405	Missense_Mutation	SNP	T	TCGA-ZP-A9D4-01A-11D-A36X-10	23628484	169209405	21944871	20	51148										
BRD9	65980	hgsc.bcm.edu	37	chr5	892720	892720	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	cacaaagcgccgccgcctcaCcctcgtaggacgagcgccac	10	19	1	0			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr5:892720C>T	ENST00000467963.1	-	1	219		c.e1+1		BRD9_ENST00000435709.2_5'Flank|BRD9_ENST00000388890.4_5'Flank|BRD9_ENST00000483173.1_5'Flank|BRD9_ENST00000323510.4_5'Flank|TRIP13_ENST00000166345.3_5'Flank	NM_023924.4	NP_076413.3	Q9H8M2	BRD9_HUMAN	bromodomain containing 9						chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		lysine-acetylated histone binding (GO:0070577)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(3)	29			Epithelial(17;0.00202)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00815)|Lung(60;0.185)			CGCCGCCTCACCCTCGTAGGA	0.761																																					.		Atlas-SNP	.											.	BRD9	113	.	0			c.52+1G>A						.						6	8	7					5																	892720		658	1547	2205	SO:0001630	splice_region_variant	65980	exon2			GCCTCACCCTCGT	AK023503	CCDS34127.1, CCDS34128.1, CCDS34127.2, CCDS34128.2	5p15.33	2008-02-05			ENSG00000028310	ENSG00000028310			25818	protein-coding gene	gene with protein product						12477932	Standard	NM_023924		Approved	FLJ13441	uc003jbq.3	Q9H8M2	OTTHUMG00000159258	ENST00000467963.1:c.52+1G>A	chr5.hg19:g.892720C>T		89.0	0.0		198.0	8.0	NM_023924	A6NFY8|B4DMQ2|B4DR93|Q2XUS1|Q6UWU9|Q8IUS4|Q9H5Q5|Q9H7R9	Splice_Site	SNP	ENST00000467963.1	hg19	CCDS34127.2	.	.	.	.	.	.	.	.	.	.	C	10.38	1.333052	0.24167	.	.	ENSG00000028310	ENST00000467963	.	.	.	3.21	2.3	0.28687	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.0584	0.42259	0.0:0.7918:0.2082:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	BRD9	945720	1.000000	0.71417	0.922000	0.36590	0.954000	0.61252	2.642000	0.46596	0.645000	0.30675	0.591000	0.81541	.	.	.		0.761	BRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354113.1	NM_023924	Intron	T	892720	C	T	892720	5	4	369	1	0	0	0	0	0	0	1	0	1509	521	18	3	1804	3	BRD9	5	892720	Splice_Site	SNP	C	TCGA-ZP-A9D4-01A-11D-A36X-10		892720	180022540	21	51149										
TRIP13	9319	hgsc.bcm.edu	37	chr5	912081	912081	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	gcagcagccatcttcaaaatCtacctctcttgtttggaaga	7	11	4	1			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr5:912081C>T	ENST00000166345.3	+	10	1346	c.990C>T	c.(988-990)atC>atT	p.I330I		NM_004237.3	NP_004228.1	Q15645	PCH2_HUMAN	thyroid hormone receptor interactor 13	330					double-strand break repair (GO:0006302)|female meiosis I (GO:0007144)|male meiosis I (GO:0007141)|oocyte maturation (GO:0001556)|oogenesis (GO:0048477)|reciprocal meiotic recombination (GO:0007131)|regulation of RNA biosynthetic process (GO:2001141)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)|transcription from RNA polymerase II promoter (GO:0006366)	male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)	ATP binding (GO:0005524)|transcription cofactor activity (GO:0003712)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	18			Epithelial(17;0.00147)|OV - Ovarian serous cystadenocarcinoma(19;0.00271)|all cancers(22;0.00622)|Lung(60;0.165)			TCTTCAAAATCTACCTCTCTT	0.408																																					p.I330I		Atlas-SNP	.											.	TRIP13	41	.	0			c.C990T						.						170	148	155					5																	912081		2203	4300	6503	SO:0001819	synonymous_variant	9319	exon10			CAAAATCTACCTC	L40384	CCDS3858.1	5p15	2010-04-21			ENSG00000071539	ENSG00000071539		"ATPases / AAA-type"	12307	protein-coding gene	gene with protein product	"thyroid receptor interacting protein 13"	604507				7776974	Standard	NM_004237		Approved	16E1BP	uc003jbr.3	Q15645	OTTHUMG00000090349	ENST00000166345.3:c.990C>T	chr5.hg19:g.912081C>T		99.0	0.0		200.0	25.0	NM_004237	C9K0T3|D3DTC0|O15324	Silent	SNP	ENST00000166345.3	hg19	CCDS3858.1																																																																																			.	.		0.408	TRIP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206721.2	NM_004237		T	912081	C	T	912081	2	4	369	1	0	0	0	0	0	0	0	1	16572	903	32	3		3	TRIP13	5	912081	Silent	SNP	C	TCGA-ZP-A9D4-01A-11D-A36X-10	19361	912081	180003179	22	51150										
TERT	7015	hgsc.bcm.edu	37	chr5	1294294	1294294	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	cagcgccacgcctgggcctcTtgggcaacggcagacttcgg	14	15	1	1			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr5:1294294T>G	ENST00000310581.5	-	2	764	c.707A>C	c.(706-708)aAg>aCg	p.K236T	TERT_ENST00000334602.6_Missense_Mutation_p.K236T|TERT_ENST00000508104.2_Missense_Mutation_p.K236T|TERT_ENST00000296820.5_Missense_Mutation_p.K236T|TERT_ENST00000522877.1_5'Flank	NM_001193376.1|NM_198253.2	NP_001180305.1|NP_937983.2	O14746	TERT_HUMAN	telomerase reverse transcriptase	236	Linker.				DNA strand elongation (GO:0022616)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|replicative senescence (GO:0090399)|telomere formation via telomerase (GO:0032203)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|telomerase holoenzyme complex (GO:0005697)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|telomerase activity (GO:0003720)|telomeric DNA binding (GO:0042162)|telomeric RNA binding (GO:0070034)|telomeric template RNA reverse transcriptase activity (GO:0003721)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(3)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	41	all_cancers(3;3.17e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.87e-10)		Epithelial(17;0.00105)|all cancers(22;0.00178)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)		Zidovudine(DB00495)	CCTGGGCCTCTTGGGCAACGG	0.751									TERT Mutation-Associated Haematological Disorders;Pulmonary Fibrosis, Idiopathic;Congenital Dyskeratosis																												p.K236T		Atlas-SNP	.											.	TERT	2594	.	0			c.A707C						.						7	8	8					5																	1294294		2142	4134	6276	SO:0001583	missense	7015	exon2	Familial Cancer Database	;Hamman-Rich syndrome, Fibrocystic Pulmonary Dysplasia;Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita	GGCCTCTTGGGCA	AF015950	CCDS3861.2, CCDS54831.1	5p15.33	2014-09-17			ENSG00000164362	ENSG00000164362			11730	protein-coding gene	gene with protein product		187270				9252327	Standard	NM_198253		Approved	TRT, TP2, TCS1, hEST2, EST2	uc003jcb.1	O14746	OTTHUMG00000090357	ENST00000310581.5:c.707A>C	chr5.hg19:g.1294294T>G	ENSP00000309572:p.Lys236Thr	338.0	2.0		743.0	544.0	NM_001193376	O14783|Q2XS35|Q8N6C3|Q8NG38|Q8NG46	Missense_Mutation	SNP	ENST00000310581.5	hg19	CCDS3861.2	.	.	.	.	.	.	.	.	.	.	T	13.41	2.229911	0.39399	.	.	ENSG00000164362	ENST00000310581;ENST00000296820;ENST00000334602;ENST00000508104	D;D;D;D	0.97232	-4.27;-4.3;-4.2;-4.3	3.34	3.34	0.38264	.	0.400740	0.23504	N	0.047464	D	0.95153	0.8429	M	0.66939	2.045	0.35939	D	0.833101	P;P;P	0.40332	0.713;0.59;0.59	B;B;B	0.40410	0.328;0.176;0.176	D	0.95694	0.8743	10	0.66056	D	0.02	-25.129	7.0682	0.25164	0.0:0.0:0.2311:0.7689	.	236;236;236	O14746-3;O14746;Q8NG38	.;TERT_HUMAN;.	T	236	ENSP00000309572:K236T;ENSP00000296820:K236T;ENSP00000334346:K236T;ENSP00000426042:K236T	ENSP00000296820:K236T	K	-	2	0	TERT	1347294	0.014000	0.17966	0.393000	0.26258	0.059000	0.15707	0.559000	0.23485	1.476000	0.48215	0.379000	0.24179	AAG	.	.		0.751	TERT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206729.2			G	1294294	T	G	1294294	3	3	369	1	0	0	0	0	1	0	0	0	15779	1609	56	5	2751	5	TERT	5	1294294	Missense_Mutation	SNP	T	TCGA-ZP-A9D4-01A-11D-A36X-10	382213	1294294	179620966	23	51151										
OSMR	9180	hgsc.bcm.edu	37	chr5	38921880	38921880	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	gtaggtcccaataccacaagCacagtcattagcacaggtaa	8	11	1	0			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr5:38921880C>T	ENST00000274276.3	+	12	2151	c.1749C>T	c.(1747-1749)agC>agT	p.S583S		NM_003999.2	NP_003990.1	Q99650	OSMR_HUMAN	oncostatin M receptor	583	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	oncostatin-M receptor complex (GO:0005900)	growth factor binding (GO:0019838)|oncostatin-M receptor activity (GO:0004924)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(8)|lung(20)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	46	all_lung(31;0.000365)					ATACCACAAGCACAGTCATTA	0.443																																					p.S583S		Atlas-SNP	.											.	OSMR	133	.	0			c.C1749T						.						174	160	165					5																	38921880		2203	4300	6503	SO:0001819	synonymous_variant	9180	exon12			CACAAGCACAGTC	U60805	CCDS3928.1, CCDS54847.1	5p13.2	2013-02-11			ENSG00000145623	ENSG00000145623		"Fibronectin type III domain containing"	8507	protein-coding gene	gene with protein product		601743				8999038	Standard	NM_001168355		Approved	OSMRB	uc003jln.2	Q99650	OTTHUMG00000090811	ENST00000274276.3:c.1749C>T	chr5.hg19:g.38921880C>T		175.0	0.0		155.0	75.0	NM_003999	Q6P4E8|Q96QJ6	Silent	SNP	ENST00000274276.3	hg19	CCDS3928.1																																																																																			.	.		0.443	OSMR-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000207609.2	NM_003999		T	38921880	C	T	38921880	2	4	369	1	0	0	0	0	0	0	0	1	11301	709	25	3		3	OSMR	5	38921880	Silent	SNP	C	TCGA-ZP-A9D4-01A-11D-A36X-10	37627586	38921880	141993380	24	51152										
MRPS30	10884	hgsc.bcm.edu	37	chr5	44809645	44809645	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	cctcagcccacacaacccggCcctggccgctgccgccctcg	9	23	1	0			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr5:44809645C>T	ENST00000507110.1	+	1	619	c.581C>T	c.(580-582)gCc>gTc	p.A194V	RP11-53O19.1_ENST00000508945.1_RNA|RP11-53O19.1_ENST00000508123.1_RNA|RP11-53O19.1_ENST00000514597.1_RNA|RP11-53O19.1_ENST00000503179.1_RNA|RP11-53O19.1_ENST00000503452.1_RNA|RP11-53O19.1_ENST00000505401.1_RNA|RP11-53O19.1_ENST00000505637.1_RNA|RP11-53O19.1_ENST00000505302.1_RNA	NM_016640.3	NP_057724.2	Q9NP92	RT30_HUMAN	mitochondrial ribosomal protein S30	194					apoptotic process (GO:0006915)|translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(2)|lung(11)|prostate(1)	20	Lung NSC(6;8.08e-07)					CACAACCCGGCCCTGGCCGCT	0.642																																					p.A194V		Atlas-SNP	.											.	MRPS30	90	.	0			c.C581T						.						35	42	39					5																	44809645		2182	4272	6454	SO:0001583	missense	10884	exon1			ACCCGGCCCTGGC	AF146192	CCDS3951.1	5q11	2012-09-13		2001-11-09	ENSG00000112996	ENSG00000112996		"Mitochondrial ribosomal proteins / small subunits"	8769	protein-coding gene	gene with protein product		611991		PDCD9		10640817, 11279123	Standard	NM_016640		Approved	PAP	uc003joh.3	Q9NP92	OTTHUMG00000096967	ENST00000507110.1:c.581C>T	chr5.hg19:g.44809645C>T	ENSP00000424328:p.Ala194Val	125.0	0.0		120.0	52.0	NM_016640	Q96I91|Q96Q19|Q9H0P8|Q9NSF9|Q9NZ76	Missense_Mutation	SNP	ENST00000507110.1	hg19	CCDS3951.1	.	.	.	.	.	.	.	.	.	.	C	6.515	0.463283	0.12402	.	.	ENSG00000112996	ENST00000507110	T	0.17054	2.3	4.89	-5.07	0.02938	.	1.231740	0.05330	N	0.528128	T	0.04907	0.0132	N	0.00972	-1.085	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.44190	-0.9344	10	0.10377	T	0.69	-0.9645	10.8884	0.46981	0.0:0.167:0.1097:0.7233	.	194	Q9NP92	RT30_HUMAN	V	194	ENSP00000424328:A194V	ENSP00000424328:A194V	A	+	2	0	MRPS30	44845402	0.000000	0.05858	0.003000	0.11579	0.465000	0.32709	-0.950000	0.03889	-0.904000	0.03876	-0.254000	0.11334	GCC	.	.		0.642	MRPS30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214033.2	NM_016640		T	44809645	C	T	44809645	3	4	369	1	0	0	0	0	1	0	0	0	9849	739	26	3	583	3	MRPS30	5	44809645	Missense_Mutation	SNP	C	TCGA-ZP-A9D4-01A-11D-A36X-10	5887765	44809645	136105615	25	51153										
GZMK	3003	hgsc.bcm.edu	37	chr5	54320628	54320628	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	tgctgacagcagcccactgcCaatatcggtgagtcctccac	9	15	0	2			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr5:54320628C>T	ENST00000231009.2	+	2	275	c.205C>T	c.(205-207)Caa>Taa	p.Q69*	CTD-2313F11.1_ENST00000608929.1_RNA|CTD-2313F11.1_ENST00000596137.1_RNA|ESM1_ENST00000598310.1_5'Flank|CTD-2313F11.1_ENST00000595218.1_RNA|CTD-2313F11.1_ENST00000371487.3_RNA|CTD-2313F11.1_ENST00000609699.1_RNA|CTD-2313F11.1_ENST00000607910.1_RNA|CTD-2313F11.1_ENST00000608466.1_RNA|CTD-2313F11.1_ENST00000596909.2_RNA	NM_002104.2	NP_002095.1	P49863	GRAK_HUMAN	granzyme K (granzyme 3; tryptase II)	69	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(4)	15		Lung NSC(810;4.08e-05)|Breast(144;0.0433)|Prostate(74;0.183)				AGCCCACTGCCAATATCGGTG	0.458																																					p.Q69X		Atlas-SNP	.											.	GZMK	39	.	0			c.C205T						.						47	49	48					5																	54320628		2203	4300	6503	SO:0001587	stop_gained	3003	exon2			CACTGCCAATATC	BC035802	CCDS3964.1	5q11.2	2008-05-15	2005-08-17		ENSG00000113088	ENSG00000113088			4711	protein-coding gene	gene with protein product		600784	"granzyme K (serine protease, granzyme 3; tryptase II)"			7758581	Standard	NM_002104		Approved	TRYP2, PRSS	uc003jpl.1	P49863	OTTHUMG00000097009	ENST00000231009.2:c.205C>T	chr5.hg19:g.54320628C>T	ENSP00000231009:p.Gln69*	109.0	0.0		86.0	27.0	NM_002104	B2R563	Nonsense_Mutation	SNP	ENST00000231009.2	hg19	CCDS3964.1	.	.	.	.	.	.	.	.	.	.	c	15.41	2.826578	0.50739	.	.	ENSG00000113088	ENST00000231009	.	.	.	4.55	-0.331	0.12679	.	1.286500	0.05059	N	0.479504	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	.	3.4567	0.07518	0.4411:0.2962:0.0:0.2627	.	.	.	.	X	69	.	ENSP00000231009:Q69X	Q	+	1	0	GZMK	54356385	0.001000	0.12720	0.021000	0.16686	0.012000	0.07955	-0.894000	0.04123	-0.079000	0.12707	-0.903000	0.02851	CAA	.	.		0.458	GZMK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214098.1	NM_002104		T	54320628	C	T	54320628	4	4	369	1	0	0	0	0	0	1	0	0	6927	595	21	3	211	3	GZMK	5	54320628	Nonsense_Mutation	SNP	C	TCGA-ZP-A9D4-01A-11D-A36X-10	9510983	54320628	126594632	26	51154										
ANKHD1	54882	hgsc.bcm.edu	37	chr5	139908468	139908468	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	gcaacagtgatttcttctgtGacaagcacttgtagttccct	8	10	2	2			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr5:139908468G>A	ENST00000360839.2	+	29	6091	c.5937G>A	c.(5935-5937)gtG>gtA	p.V1979V	ANKHD1_ENST00000297183.6_Silent_p.V1979V|ANKHD1-EIF4EBP3_ENST00000532219.1_Silent_p.V1979V|ANKHD1_ENST00000544120.1_Silent_p.V362V|SNORD45_ENST00000363181.1_RNA	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	1979	Ser-rich.					cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTTCTTCTGTGACAAGCACTT	0.493																																					p.V1979V		Atlas-SNP	.											.	ANKHD1	233	.	0			c.G5937A						.						156	153	154					5																	139908468		2203	4300	6503	SO:0001819	synonymous_variant	54882	exon29			TTCTGTGACAAGC	AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503		"Ankyrin repeat domain containing"	24714	protein-coding gene	gene with protein product		610500				10470851, 11230166, 16098192	Standard	NM_017747		Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.5937G>A	chr5.hg19:g.139908468G>A		49.0	0.0		27.0	22.0	NM_017747	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Silent	SNP	ENST00000360839.2	hg19	CCDS4225.1	.	.	.	.	.	.	.	.	.	.	G	2.662	-0.279626	0.05642	.	.	ENSG00000131503	ENST00000435794;ENST00000432301	.	.	.	5.3	4.43	0.53597	.	.	.	.	.	T	0.69708	0.3141	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68689	-0.5342	4	.	.	.	.	13.8855	0.63706	0.0736:0.0:0.9264:0.0	.	.	.	.	N	470;430	.	.	D	+	1	0	ANKHD1	139888652	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	2.506000	0.45433	1.247000	0.43917	-0.142000	0.14014	GAC	.	.		0.493	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747		A	139908468	G	A	139908468	2	1	369	1	0	0	0	0	0	0	0	1	628	1277	45	3		3	ANKHD1	5	139908468	Silent	SNP	G	TCGA-ZP-A9D4-01A-11D-A36X-10	85587840	139908468	41006792	27	51155										
HAVCR1	26762	hgsc.bcm.edu	37	chr5	156482260	156482260	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	tttcatgtcattgaaccaccCacggtgctcaacacggcaac	7	14	3	1			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr5:156482260C>T	ENST00000339252.3	-	2	863	c.331G>A	c.(331-333)Ggg>Agg	p.G111R	HAVCR1_ENST00000523175.1_Missense_Mutation_p.G111R|HAVCR1_ENST00000522693.1_Missense_Mutation_p.G111R|HAVCR1_ENST00000425854.1_Missense_Mutation_p.G111R|HAVCR1_ENST00000544197.1_Missense_Mutation_p.G111R	NM_012206.2	NP_036338.2	Q96D42	HAVR1_HUMAN	hepatitis A virus cellular receptor 1	0	Ig-like V-type.				viral process (GO:0016032)	integral component of membrane (GO:0016021)	virus receptor activity (GO:0001618)			endometrium(3)|large_intestine(2)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TTGAACCACCCACGGTGCTCA	0.408																																					p.G111R		Atlas-SNP	.											.	HAVCR1	84	.	0			c.G331A						.						91	79	83					5																	156482260		1981	4175	6156	SO:0001583	missense	26762	exon3			ACCACCCACGGTG	AF043724	CCDS43392.1	5q33.2	2014-01-14			ENSG00000113249	ENSG00000113249		"Immunoglobulin superfamily / V-set domain containing"	17866	protein-coding gene	gene with protein product	"T-cell immunoglobulin mucin family member 1"	606518				9658108, 11725301	Standard	NM_012206		Approved	HAVCR-1, TIM-1, TIM1, HAVCR, TIMD1	uc021ygj.1	Q96D42	OTTHUMG00000163466	ENST00000339252.3:c.331G>A	chr5.hg19:g.156482260C>T	ENSP00000344844:p.Gly111Arg	118.0	0.0		94.0	29.0	NM_001099414	O43656	Missense_Mutation	SNP	ENST00000339252.3	hg19	CCDS43392.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.063285	0.76187	.	.	ENSG00000113249	ENST00000522693;ENST00000523175;ENST00000339252;ENST00000425854;ENST00000544197;ENST00000518745	T;T;T;T;T;T	0.58797	0.31;0.31;0.31;0.31;0.31;0.31	5.78	5.78	0.91487	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.82508	0.5052	M	0.92459	3.31	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.85830	0.1391	10	0.66056	D	0.02	-26.0765	18.7919	0.91976	0.0:1.0:0.0:0.0	.	111;111	F1CME6;Q96D42	.;HAVR1_HUMAN	R	111	ENSP00000428524:G111R;ENSP00000427898:G111R;ENSP00000344844:G111R;ENSP00000403333:G111R;ENSP00000440258:G111R;ENSP00000428422:G111R	ENSP00000344844:G111R	G	-	1	0	HAVCR1	156414838	0.783000	0.28701	0.368000	0.25939	0.345000	0.29048	2.404000	0.44539	2.729000	0.93468	0.650000	0.86243	GGG	.	.		0.408	HAVCR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373698.1			T	156482260	C	T	156482260	3	4	369	1	0	0	0	0	1	0	0	0	6982	594	21	3	791	3	HAVCR1	5	156482260	Missense_Mutation	SNP	C	TCGA-ZP-A9D4-01A-11D-A36X-10	16573792	156482260	24433000	28	51156										
FAM184A	79632	hgsc.bcm.edu	37	chr6	119297186	119297186	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	aattgcagctgcatgttgatGgttgagttctgagcgcaagg	14	6	1	3			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr6:119297186G>A	ENST00000338891.7	-	12	2922	c.2479C>T	c.(2479-2481)Cat>Tat	p.H827Y	FAM184A_ENST00000521531.1_Missense_Mutation_p.H827Y|RP11-351A11.1_ENST00000518570.1_RNA|FAM184A_ENST00000368475.4_Missense_Mutation_p.H707Y|FAM184A_ENST00000352896.5_Missense_Mutation_p.H707Y	NM_024581.4	NP_078857.5	Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A	827						extracellular space (GO:0005615)				breast(2)|central_nervous_system(2)|endometrium(2)|kidney(5)|large_intestine(19)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(5)	52						GCATGTTGATGGTTGAGTTCT	0.348																																					p.H827Y		Atlas-SNP	.											.	FAM184A	109	.	0			c.C2479T						.						92	84	87					6																	119297186		1867	4109	5976	SO:0001583	missense	79632	exon12			GTTGATGGTTGAG	BC009055	CCDS43499.1, CCDS43500.1, CCDS75508.1	6q22.31	2008-08-14	2008-08-14	2008-08-14	ENSG00000111879	ENSG00000111879			20991	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 60"	C6orf60		11230166	Standard	NM_024581		Approved	FLJ13942	uc003pyj.3	Q8NB25	OTTHUMG00000015471	ENST00000338891.7:c.2479C>T	chr6.hg19:g.119297186G>A	ENSP00000342604:p.His827Tyr	46.0	0.0		46.0	15.0	NM_024581	B9DI75|F8W8D6|Q5TBS9|Q7Z323|Q96GY8|Q9H0J8|Q9H851	Missense_Mutation	SNP	ENST00000338891.7	hg19	CCDS43499.1	.	.	.	.	.	.	.	.	.	.	G	17.06	3.292181	0.59976	.	.	ENSG00000111879	ENST00000338891;ENST00000352896;ENST00000368475;ENST00000521531	T;T;T;T	0.27256	2.41;2.35;1.7;1.68	5.21	5.21	0.72293	.	0.105878	0.64402	D	0.000005	T	0.21718	0.0523	M	0.69823	2.125	0.80722	D	1	B;B;B	0.31040	0.305;0.176;0.108	B;B;B	0.33960	0.112;0.09;0.173	T	0.03619	-1.1019	9	.	.	.	-6.4031	18.7445	0.91787	0.0:0.0:1.0:0.0	.	827;707;827	Q8NB25-2;F8W8D6;Q8NB25	.;.;F184A_HUMAN	Y	827;707;707;827	ENSP00000342604:H827Y;ENSP00000326608:H707Y;ENSP00000357460:H707Y;ENSP00000430442:H827Y	.	H	-	1	0	FAM184A	119338885	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	7.163000	0.77524	2.437000	0.82529	0.563000	0.77884	CAT	.	.		0.348	FAM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042009.3	NM_024581		A	119297186	G	A	119297186	3	1	369	1	0	0	0	0	1	0	0	0	5516	1348	47	3	971	3	FAM184A	6	119297186	Missense_Mutation	SNP	G	TCGA-ZP-A9D4-01A-11D-A36X-10		119297186	51817881	29	51157										
FUT10	84750	hgsc.bcm.edu	37	chr8	33318937	33318937	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	ggctgtgacgcacaggcaagAtgccaaaagcttcctcctct	10	13	1	2			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr8:33318937A>G	ENST00000327671.5	-	2	665	c.34T>C	c.(34-36)Tct>Cct	p.S12P	FUT10_ENST00000524021.1_5'UTR|FUT10_ENST00000518672.1_Intron|FUT10_ENST00000335589.3_5'UTR	NM_032664.3	NP_116053.3	Q6P4F1	FUT10_HUMAN	fucosyltransferase 10 (alpha (1,3) fucosyltransferase)	12					embryo development (GO:0009790)|fertilization (GO:0009566)|fucosylation (GO:0036065)|hemopoiesis (GO:0030097)|L-fucose catabolic process (GO:0042355)|nervous system development (GO:0007399)|protein folding (GO:0006457)|protein glycosylation (GO:0006486)|protein targeting (GO:0006605)|wound healing (GO:0042060)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)			cervix(1)|endometrium(1)|large_intestine(7)|liver(1)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2)	29				KIRC - Kidney renal clear cell carcinoma(67;0.129)|Kidney(114;0.154)		CACAGGCAAGATGCCAAAAGC	0.557																																					p.S12P		Atlas-SNP	.											.	FUT10	62	.	0			c.T34C						.						197	140	159					8																	33318937		2203	4300	6503	SO:0001583	missense	84750	exon2			GGCAAGATGCCAA	AJ512465	CCDS6088.1	8p12	2013-02-26			ENSG00000172728	ENSG00000172728		"Fucosyltransferases"	19234	protein-coding gene	gene with protein product							Standard	NM_032664		Approved		uc003xje.3	Q6P4F1	OTTHUMG00000163954	ENST00000327671.5:c.34T>C	chr8.hg19:g.33318937A>G	ENSP00000332757:p.Ser12Pro	57.0	0.0		23.0	15.0	NM_032664	A8KAC8|Q70GG3|Q8IVI6|Q8IVI7|Q8IVJ3|Q8TE43|Q9BSR3	Missense_Mutation	SNP	ENST00000327671.5	hg19	CCDS6088.1	.	.	.	.	.	.	.	.	.	.	A	14.06	2.423874	0.43020	.	.	ENSG00000172728	ENST00000327671;ENST00000380081	T	0.39997	1.05	5.79	4.61	0.57282	.	3.111010	0.00963	N	0.003130	T	0.46889	0.1416	M	0.62723	1.935	0.80722	D	1	B;B;B	0.13145	0.007;0.003;0.004	B;B;B	0.14578	0.006;0.006;0.011	T	0.13388	-1.0511	10	0.33940	T	0.23	.	10.0117	0.41990	0.8302:0.1698:0.0:0.0	.	12;12;12	B4DLS4;Q6P4F1-5;Q6P4F1	.;.;FUT10_HUMAN	P	12	ENSP00000332757:S12P	ENSP00000332757:S12P	S	-	1	0	FUT10	33438479	1.000000	0.71417	0.951000	0.38953	0.951000	0.60555	3.848000	0.55903	1.016000	0.39470	0.524000	0.50904	TCT	.	.		0.557	FUT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376540.1	NM_032664		G	33318937	A	G	33318937	3	3	369	1	0	0	0	0	1	0	0	0	6110	333	12	2	1421	2	FUT10	8	33318937	Missense_Mutation	SNP	A	TCGA-ZP-A9D4-01A-11D-A36X-10		33318937	113045085	30	51158										
RB1CC1	9821	hgsc.bcm.edu	37	chr8	53573155	53573155	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	ggttagaaaataaatacataCacaaaaggaagggggccagg	12	5	0	1			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr8:53573155C>T	ENST00000025008.5	-	12	2213		c.e12+1		RB1CC1_ENST00000539297.1_Splice_Site|RB1CC1_ENST00000521611.1_Intron|RB1CC1_ENST00000435644.2_Splice_Site	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1						autophagic vacuole assembly (GO:0000045)|cell cycle (GO:0007049)|heart development (GO:0007507)|JNK cascade (GO:0007254)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell size (GO:0045793)|positive regulation of protein phosphorylation (GO:0001934)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)				NS(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(19)|ovary(8)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	60		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				TAAATACATACACAAAAGGAA	0.333																																					.	GBM(180;1701 2102 13475 42023 52570)	Atlas-SNP	.											.	RB1CC1	163	.	0			c.1689+1G>A						.						40	47	45					8																	53573155		2201	4294	6495	SO:0001630	splice_region_variant	9821	exon13			TACATACACAAAA	AB059622	CCDS34892.1, CCDS47856.1	8q11	2014-06-13				ENSG00000023287			15574	protein-coding gene	gene with protein product	"200 kDa FAK family kinase-interacting protein", "phosphatase 1, regulatory subunit 131"	606837				11850849, 7724523, 18443221	Standard	NM_014781		Approved	KIAA0203, Cc1, DRAGOU14, FIP200, ATG17, PPP1R131	uc003xre.4	Q8TDY2		ENST00000025008.5:c.1689+1G>A	chr8.hg19:g.53573155C>T		515.0	0.0		294.0	205.0	NM_014781	Q86YR4|Q8WVU9|Q92601	Splice_Site	SNP	ENST00000025008.5	hg19	CCDS34892.1	.	.	.	.	.	.	.	.	.	.	C	18.68	3.676302	0.67928	.	.	ENSG00000023287	ENST00000025008;ENST00000435644;ENST00000539297	.	.	.	5.2	4.31	0.51392	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.9447	0.71020	0.0:0.8557:0.1443:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	RB1CC1	53735708	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	5.342000	0.65970	1.302000	0.44855	0.460000	0.39030	.	.	.		0.333	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378011.1	NM_014781	Intron	T	53573155	C	T	53573155	5	4	369	1	0	0	0	0	0	0	1	0	13114	492	17	3	3146	3	RB1CC1	8	53573155	Splice_Site	SNP	C	TCGA-ZP-A9D4-01A-11D-A36X-10	20254218	53573155	92790867	31	51159										
KIAA1797	54914	hgsc.bcm.edu	37	chr9	20986401	20986401	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	tgcagcaccgtgagaaagagGtgttggcctggatgattctg	15	7	1	3	rs376770371		TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr9:20986401G>T	ENST00000380249.1	+	42	5207	c.4843G>T	c.(4843-4845)Gtg>Ttg	p.V1615L	FOCAD_ENST00000605086.1_Missense_Mutation_p.V1051L|FOCAD_ENST00000338382.6_Missense_Mutation_p.V1615L	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	1615						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)											TGAGAAAGAGGTGTTGGCCTG	0.517																																					p.V1615L		Atlas-SNP	.											.	.	.	.	0			c.G4843T						.						134	100	111					9																	20986401		2203	4300	6503	SO:0001583	missense	54914	exon42			AAAGAGGTGTTGG	AB058700	CCDS34993.1	9p21	2012-03-23	2012-03-23	2012-03-23	ENSG00000188352	ENSG00000188352			23377	protein-coding gene	gene with protein product		614606	"KIAA1797"	KIAA1797		22427331	Standard	XM_006716794		Approved	FLJ20375	uc003zog.1	Q5VW36	OTTHUMG00000066930	ENST00000380249.1:c.4843G>T	chr9.hg19:g.20986401G>T	ENSP00000369599:p.Val1615Leu	47.0	0.0		42.0	15.0	NM_017794	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Missense_Mutation	SNP	ENST00000380249.1	hg19	CCDS34993.1	.	.	.	.	.	.	.	.	.	.	G	8.894	0.954781	0.18431	.	.	ENSG00000188352	ENST00000380249;ENST00000338382	T;T	0.18657	2.2;2.2	5.72	-5.02	0.02982	.	0.403128	0.27168	N	0.020605	T	0.05960	0.0155	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21211	-1.0252	10	0.18710	T	0.47	-26.0131	2.003	0.03471	0.3732:0.1014:0.329:0.1964	.	1615	Q5VW36	K1797_HUMAN	L	1615	ENSP00000369599:V1615L;ENSP00000344307:V1615L	ENSP00000344307:V1615L	V	+	1	0	KIAA1797	20976401	0.050000	0.20438	0.000000	0.03702	0.836000	0.47400	-0.031000	0.12287	-1.328000	0.02261	-1.166000	0.01754	GTG	.	.		0.517	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794		T	20986401	G	T	20986401	3	4	369	1	0	0	0	0	1	0	0	0	8267	1261	44	3	4997	3	KIAA1797	9	20986401	Missense_Mutation	SNP	G	TCGA-ZP-A9D4-01A-11D-A36X-10		20986401	120227030	32	51160										
SVEP1	79987	hgsc.bcm.edu	37	chr9	113252044	113252044	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	aggtggggtgaaagctggatGaacgtggactgacacctatt	15	6	0	3			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr9:113252044G>T	ENST00000401783.2	-	9	2152	c.1816C>A	c.(1816-1818)Cat>Aat	p.H606N	SVEP1_ENST00000302728.8_Missense_Mutation_p.H606N|SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000374469.1_Missense_Mutation_p.H583N|SVEP1_ENST00000374461.1_Missense_Mutation_p.H583N	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	606	HYR 1. {ECO:0000255|PROSITE- ProRule:PRU00113}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						AAAGCTGGATGAACGTGGACT	0.388																																					p.H606N		Atlas-SNP	.											.	SVEP1	326	.	0			c.C1816A						.						160	154	156					9																	113252044		1929	4141	6070	SO:0001583	missense	79987	exon9			CTGGATGAACGTG	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.1816C>A	chr9.hg19:g.113252044G>T	ENSP00000384917:p.His606Asn	121.0	0.0		132.0	39.0	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	hg19	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	G	9.930	1.214531	0.22289	.	.	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728;ENST00000374461	T;T;T;T	0.21031	2.03;2.03;2.03;2.03	4.85	2.8	0.32819	Hyalin (2);	0.297330	0.34676	N	0.003767	T	0.08403	0.0209	N	0.05124	-0.11	0.25917	N	0.983168	B;B;B	0.27625	0.183;0.116;0.095	B;B;B	0.27887	0.084;0.054;0.032	T	0.27020	-1.0086	10	0.23302	T	0.38	.	5.7906	0.18359	0.1069:0.0:0.4527:0.4404	.	606;606;606	E9PBN8;Q4LDE5;Q4LDE5-2	.;SVEP1_HUMAN;.	N	606;583;606;583	ENSP00000384917:H606N;ENSP00000363593:H583N;ENSP00000304118:H606N;ENSP00000363585:H583N	ENSP00000304118:H606N	H	-	1	0	SVEP1	112291865	1.000000	0.71417	0.757000	0.31301	0.733000	0.41908	3.422000	0.52749	1.045000	0.40225	0.563000	0.77884	CAT	.	.		0.388	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	113252044	G	T	113252044	3	4	369	1	0	0	0	0	1	0	0	0	15435	1290	45	3	9059	3	SVEP1	9	113252044	Missense_Mutation	SNP	G	TCGA-ZP-A9D4-01A-11D-A36X-10	92265643	113252044	27961387	33	51161										
DBC1	1620	hgsc.bcm.edu	37	chr9	121929597	121929597	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	acgaagaggaatagaactggCcgccctgtgtgtaggactgg	15	8	0	2			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr9:121929597C>T	ENST00000265922.3	-	8	2512	c.2051G>A	c.(2050-2052)gGc>gAc	p.G684D	BRINP1_ENST00000482797.1_Intron	NM_014618.2	NP_055433.2	O60477	BRNP1_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 1	684					cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell cycle (GO:0045786)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	cytoplasm (GO:0005737)		p.G684D(1)|p.G684V(1)									ATAGAACTGGCCGCCCTGTGT	0.577																																					p.G684D		Atlas-SNP	.											DBC1,brain,glioma,0,2	DBC1	194	.	2	Substitution - Missense(2)	lung(1)|central_nervous_system(1)	c.G2051A						.						144	137	139					9																	121929597		2203	4300	6503	SO:0001583	missense	1620	exon8			AACTGGCCGCCCT	AF027734	CCDS6822.1	9q32-q33	2013-08-06	2013-08-06	2013-07-31	ENSG00000078725	ENSG00000078725			2687	protein-coding gene	gene with protein product		602865	"deleted in bladder cancer chromosome region candidate 1", "deleted in bladder cancer 1"	DBCCR1, DBC1		9175739, 10444335, 15193422	Standard	NM_014618		Approved	FAM5A	uc004bkc.2	O60477	OTTHUMG00000021020	ENST00000265922.3:c.2051G>A	chr9.hg19:g.121929597C>T	ENSP00000265922:p.Gly684Asp	151.0	0.0		163.0	8.0	NM_014618	Q6IPV6|Q6P1A0|Q8WU22	Missense_Mutation	SNP	ENST00000265922.3	hg19	CCDS6822.1	.	.	.	.	.	.	.	.	.	.	C	9.952	1.220446	0.22457	.	.	ENSG00000078725	ENST00000373969;ENST00000265922	T	0.13420	2.59	5.73	4.84	0.62591	.	0.158127	0.56097	N	0.000025	T	0.10637	0.0260	N	0.22421	0.69	0.50813	D	0.999896	B	0.06786	0.001	B	0.04013	0.001	T	0.10800	-1.0614	10	0.28530	T	0.3	-25.2604	14.8292	0.70135	0.0:0.9312:0.0:0.0688	.	684	O60477	DBC1_HUMAN	D	684	ENSP00000265922:G684D	ENSP00000265922:G684D	G	-	2	0	DBC1	120969418	0.996000	0.38824	0.997000	0.53966	0.985000	0.73830	2.512000	0.45485	1.577000	0.49804	0.650000	0.86243	GGC	.	.		0.577	BRINP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055440.2	NM_014618		T	121929597	C	T	121929597	3	4	369	1	0	0	0	0	1	0	0	0	4249	739	26	3	238	3	DBC1	9	121929597	Missense_Mutation	SNP	C	TCGA-ZP-A9D4-01A-11D-A36X-10	8677553	121929597	19283834	34	51162										
MEGF9	1955	hgsc.bcm.edu	37	chr9	123370235	123370235	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	ttcacatttattgcagttcgGgcctatgtaaccatctttac	6	10	2	0			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr9:123370235G>C	ENST00000373930.3	-	5	1252	c.1141C>G	c.(1141-1143)Ccg>Gcg	p.P381A	MEGF9_ENST00000426959.1_Missense_Mutation_p.P418A	NM_001080497.2	NP_001073966.2	Q9H1U4	MEGF9_HUMAN	multiple EGF-like-domains 9	381	Laminin EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00460}.					integral component of membrane (GO:0016021)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|upper_aerodigestive_tract(1)	16						TTGCAGTTCGGGCCTATGTAA	0.393																																					p.P381A		Atlas-SNP	.											.	MEGF9	33	.	0			c.C1141G						.						134	126	128					9																	123370235		1889	4106	5995	SO:0001583	missense	1955	exon5			AGTTCGGGCCTAT	AB011542	CCDS48010.1, CCDS48010.2	9q32-q33.3	2008-07-21	2006-03-31	2006-03-31	ENSG00000106780	ENSG00000106780			3234	protein-coding gene	gene with protein product		604268	"EGF-like-domain, multiple 5"	EGFL5		9693030	Standard	NM_001080497		Approved		uc022bms.1	Q9H1U4	OTTHUMG00000021039	ENST00000373930.3:c.1141C>G	chr9.hg19:g.123370235G>C	ENSP00000363040:p.Pro381Ala	129.0	0.0		131.0	44.0	NM_001080497	B7Z315|O75098	Missense_Mutation	SNP	ENST00000373930.3	hg19	CCDS48010.2	.	.	.	.	.	.	.	.	.	.	G	9.138	1.012992	0.19277	.	.	ENSG00000106780	ENST00000373930;ENST00000426959	T;T	0.61040	0.14;0.14	5.23	1.96	0.26148	.	0.761100	0.11916	N	0.517196	T	0.35770	0.0943	N	0.24115	0.695	0.30392	N	0.780949	P	0.38280	0.625	B	0.34931	0.192	T	0.25606	-1.0127	10	0.13853	T	0.58	3.9453	6.9123	0.24342	0.0838:0.0:0.6122:0.3041	.	418	C9J1K8	.	A	381;418	ENSP00000363040:P381A;ENSP00000392666:P418A	ENSP00000363040:P381A	P	-	1	0	MEGF9	122410056	0.997000	0.39634	0.979000	0.43373	0.804000	0.45430	2.584000	0.46102	0.650000	0.30769	0.557000	0.71058	CCG	.	.		0.393	MEGF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055513.1	NM_001080497		C	123370235	G	C	123370235	3	2	369	1	0	0	0	0	1	0	0	0	9473	1232	43	4	675	4	MEGF9	9	123370235	Missense_Mutation	SNP	G	TCGA-ZP-A9D4-01A-11D-A36X-10	1440638	123370235	17843196	35	51163										
STRBP	55342	hgsc.bcm.edu	37	chr9	125920368	125920368	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	ggtccatctccagcactttgTaaatctggccaaaggctgat	9	11	2	1			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr9:125920368T>C	ENST00000348403.5	-	11	1397	c.968A>G	c.(967-969)tAc>tGc	p.Y323C	STRBP_ENST00000447404.2_Missense_Mutation_p.Y323C|STRBP_ENST00000360998.3_Missense_Mutation_p.Y309C	NM_018387.4	NP_060857.2	Q96SI9	STRBP_HUMAN	spermatid perinuclear RNA binding protein	323	DZF. {ECO:0000255|PROSITE- ProRule:PRU01040}.				cellular component movement (GO:0006928)|mechanosensory behavior (GO:0007638)|multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(6)|prostate(1)|skin(2)	26						CAGCACTTTGTAAATCTGGCC	0.373																																					p.Y323C		Atlas-SNP	.											.	STRBP	73	.	0			c.A968G						.						115	115	115					9																	125920368		2203	4300	6503	SO:0001583	missense	55342	exon11			ACTTTGTAAATCT	AK002169	CCDS6851.1, CCDS55337.1	9q33.1-q33.3	2008-08-29	2001-11-28		ENSG00000165209	ENSG00000165209			16462	protein-coding gene	gene with protein product		611138	"spermatid perinuclear RNA-binding protein", "interleukin enhancer binding factor 3-like"	ILF3L			Standard	NM_018387		Approved	FLJ11307, SPNR	uc004bns.3	Q96SI9	OTTHUMG00000020636	ENST00000348403.5:c.968A>G	chr9.hg19:g.125920368T>C	ENSP00000321347:p.Tyr323Cys	85.0	0.0		68.0	21.0	NM_018387	Q32NB9|Q9BUE1|Q9BXG4|Q9H0B4|Q9H7V1|Q9NUK4	Missense_Mutation	SNP	ENST00000348403.5	hg19	CCDS6851.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.225443	0.79576	.	.	ENSG00000165209	ENST00000447404;ENST00000348403;ENST00000360998	T;T;T	0.41758	0.99;0.99;0.99	5.29	5.29	0.74685	DZF (2);	0.061386	0.64402	D	0.000002	T	0.44582	0.1300	L	0.48642	1.525	0.80722	D	1	B	0.29136	0.234	B	0.37451	0.25	T	0.46020	-0.9221	10	0.66056	D	0.02	-9.6521	15.2158	0.73264	0.0:0.0:0.0:1.0	.	323	Q96SI9	STRBP_HUMAN	C	323;323;309	ENSP00000415968:Y323C;ENSP00000321347:Y323C;ENSP00000354271:Y309C	ENSP00000321347:Y323C	Y	-	2	0	STRBP	124960189	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	5.975000	0.70475	1.993000	0.58246	0.460000	0.39030	TAC	.	.		0.373	STRBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053982.1			C	125920368	T	C	125920368	3	2	369	1	0	0	0	0	1	0	0	0	15342	1638	57	2	1086	2	STRBP	9	125920368	Missense_Mutation	SNP	T	TCGA-ZP-A9D4-01A-11D-A36X-10	2550133	125920368	15293063	36	51164										
TOR1B	27348	hgsc.bcm.edu	37	chr9	132566402	132566402	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	ttggacagcatctagccacgGaagtgattttcaaggcgctg	12	9	2	1			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr9:132566402G>C	ENST00000259339.2	+	2	310	c.250G>C	c.(250-252)Gaa>Caa	p.E84Q	TOR1B_ENST00000486372.1_3'UTR	NM_014506.1	NP_055321.1	O14657	TOR1B_HUMAN	torsin family 1, member B (torsin B)	84					ATP catabolic process (GO:0006200)|chaperone mediated protein folding requiring cofactor (GO:0051085)|endoplasmic reticulum organization (GO:0007029)|nuclear membrane organization (GO:0071763)|protein homooligomerization (GO:0051260)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear envelope (GO:0005635)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			endometrium(3)|kidney(1)|large_intestine(1)|lung(7)	12		Ovarian(14;0.0586)				TCTAGCCACGGAAGTGATTTT	0.478																																					p.E84Q		Atlas-SNP	.											.	TOR1B	20	.	0			c.G250C						.						80	78	79					9																	132566402		2203	4300	6503	SO:0001583	missense	27348	exon2			GCCACGGAAGTGA	AF007872	CCDS6929.1	9q34	2008-07-21			ENSG00000136816	ENSG00000136816			11995	protein-coding gene	gene with protein product		608050				9288096, 10644435	Standard	NM_014506		Approved	DQ1, MGC4386	uc004byk.1	O14657	OTTHUMG00000020795	ENST00000259339.2:c.250G>C	chr9.hg19:g.132566402G>C	ENSP00000259339:p.Glu84Gln	97.0	0.0		109.0	45.0	NM_014506		Missense_Mutation	SNP	ENST00000259339.2	hg19	CCDS6929.1	.	.	.	.	.	.	.	.	.	.	G	12.25	1.880702	0.33255	.	.	ENSG00000136816	ENST00000259339;ENST00000437263	T	0.32988	1.43	5.1	4.19	0.49359	.	0.378995	0.31279	N	0.007940	T	0.19005	0.0456	N	0.25957	0.775	0.27298	N	0.957659	B	0.20459	0.045	B	0.25405	0.06	T	0.23976	-1.0173	10	0.12103	T	0.63	.	8.3606	0.32357	0.179:0.0:0.821:0.0	.	84	O14657	TOR1B_HUMAN	Q	84	ENSP00000259339:E84Q	ENSP00000259339:E84Q	E	+	1	0	TOR1B	131606223	0.692000	0.27719	0.986000	0.45419	0.987000	0.75469	1.268000	0.33062	1.132000	0.42129	0.561000	0.74099	GAA	.	.		0.478	TOR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054615.1	NM_014506		C	132566402	G	C	132566402	3	2	369	1	0	0	0	0	1	0	0	0	16389	1175	41	4	256	4	TOR1B	9	132566402	Missense_Mutation	SNP	G	TCGA-ZP-A9D4-01A-11D-A36X-10	6646034	132566402	8647029	37	51165										
RET	5979	hgsc.bcm.edu	37	chr10	43609005	43609005	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	gggctacgtctgccctcaggGggcagcattgttgggggaca	17	10	2	0			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr10:43609005G>A	ENST00000355710.3	+	10	1993	c.1761G>A	c.(1759-1761)cgG>cgA	p.R587R	RET_ENST00000340058.5_Splice_Site_p.R587R	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	587		Breakpoint for translocation to form the TRIM27/RET oncogene.			activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to retinoic acid (GO:0071300)|embryonic epithelial tube formation (GO:0001838)|enteric nervous system development (GO:0048484)|homophilic cell adhesion (GO:0007156)|innervation (GO:0060384)|lymphocyte migration into lymphoid organs (GO:0097021)|MAPK cascade (GO:0000165)|membrane protein proteolysis (GO:0033619)|neural crest cell migration (GO:0001755)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch morphogenesis (GO:0061146)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell migration (GO:0030335)|positive regulation of cell size (GO:0045793)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of neuron maturation (GO:0014042)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior midgut development (GO:0007497)|protein phosphorylation (GO:0006468)|regulation of axonogenesis (GO:0050770)|regulation of cell adhesion (GO:0030155)|response to drug (GO:0042493)|response to pain (GO:0048265)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ureter maturation (GO:0035799)|ureteric bud development (GO:0001657)	endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		CCDC6/RET(4)|KIF5B/RET(79)	NS(2)|adrenal_gland(26)|breast(5)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|lung(27)|ovary(5)|prostate(3)|skin(1)|thyroid(504)|upper_aerodigestive_tract(1)|urinary_tract(1)	607		Ovarian(717;0.0423)			Cabozantinib(DB08875)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	TGCCCTCAGGGGGCAGCATTG	0.652		1	"T, Mis, N, F"	"H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6"	"medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC"	"medullary thyroid,  papillary thyroid, pheochromocytoma"	Hirschsprung disease		Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma																												p.R587R	Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149)	Atlas-SNP	.	yes	Dom	yes	Multiple endocrine neoplasia 2A/2B	10	10q11.2	5979	ret proto-oncogene	yes	"E, O"	.	RET	916	.	0			c.G1761A						.						16	18	17					10																	43609005		2199	4295	6494	SO:0001630	splice_region_variant	5979	exon10	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	CTCAGGGGGCAGC	BC004257	CCDS7200.1, CCDS53525.1	10q11.2	2014-09-17	2007-02-16		ENSG00000165731	ENSG00000165731		"Cadherins / Cadherin-related"	9967	protein-coding gene	gene with protein product	"cadherin-related family member 16"	164761	"multiple endocrine neoplasia and medullary thyroid carcinoma 1", "Hirschsprung disease 1"	HSCR1, MEN2A, MTC1, MEN2B		2687772, 1611909	Standard	NM_020975		Approved	PTC, CDHF12, RET51, CDHR16	uc001jal.3	P07949	OTTHUMG00000018024	ENST00000355710.3:c.1760-1G>A	chr10.hg19:g.43609005G>A		22.0	0.0		35.0	19.0	NM_020630	A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Silent	SNP	ENST00000355710.3	hg19	CCDS7200.1																																																																																			.	.		0.652	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	NM_020975	Silent	A	43609005	G	A	43609005	5	1	369	1	0	0	0	0	0	0	1	0	13250	1246	43	3	1799	3	RET	10	43609005	Splice_Site	SNP	G	TCGA-ZP-A9D4-01A-11D-A36X-10		43609005	91925742	38	51166										
TIAL1	7073	hgsc.bcm.edu	37	chr10	121339462	121339462	+	Silent	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	cgtaccagtttgttataaaaAgatacaaaaccatagccttt	5	8	0	1			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr10:121339462A>C	ENST00000436547.2	-	6	476	c.432T>G	c.(430-432)tcT>tcG	p.S144S	TIAL1_ENST00000463089.2_5'Flank|TIAL1_ENST00000369093.2_Silent_p.S161S|TIAL1_ENST00000369092.4_Silent_p.S21S	NM_003252.3	NP_003243.1	Q01085	TIAR_HUMAN	TIA1 cytotoxic granule-associated RNA binding protein-like 1	144	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				apoptotic process (GO:0006915)|defense response (GO:0006952)|germ cell development (GO:0007281)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell division (GO:0017145)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(3)|ovary(1)	13		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.00239)|BRCA - Breast invasive adenocarcinoma(275;0.0932)		TGTTATAAAAAGATACAAAAC	0.333																																					p.S161S		Atlas-SNP	.											.	TIAL1	47	.	0			c.T483G						.						63	66	65					10																	121339462		2203	4300	6503	SO:0001819	synonymous_variant	7073	exon6			ATAAAAAGATACA	AL833106	CCDS7613.1, CCDS31295.1	10q	2013-02-12	2001-11-28		ENSG00000151923	ENSG00000151923		"RNA binding motif (RRM) containing"	11804	protein-coding gene	gene with protein product		603413	"TIA1 cytotoxic granule-associated RNA-binding protein-like 1"			1326761	Standard	XM_005270108		Approved	TIAR	uc001lej.1	Q01085	OTTHUMG00000019156	ENST00000436547.2:c.432T>G	chr10.hg19:g.121339462A>C		144.0	0.0		130.0	40.0	NM_001033925	A8K3T0|A8K4L9	Silent	SNP	ENST00000436547.2	hg19	CCDS7613.1																																																																																			.	.		0.333	TIAL1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050672.2	NM_022333, NM_003252		C	121339462	A	C	121339462	2	2	369	1	0	0	0	0	0	0	0	1	15904	59	3	5		5	TIAL1	10	121339462	Silent	SNP	A	TCGA-ZP-A9D4-01A-11D-A36X-10	77730457	121339462	14195285	39	51167										
SIGIRR	59307	hgsc.bcm.edu	37	chr11	406869	406869	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	gccgggcctccagagcagcaAggtcaccaggtggcggtgct	16	13	1	1			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr11:406869A>T	ENST00000431843.2	-	8	1159	c.853T>A	c.(853-855)Ttg>Atg	p.L285M	SIGIRR_ENST00000531205.1_Missense_Mutation_p.L285M|SIGIRR_ENST00000332725.3_Missense_Mutation_p.L285M|SIGIRR_ENST00000397632.3_Missense_Mutation_p.L285M|SIGIRR_ENST00000382520.2_Missense_Mutation_p.L285M|SIGIRR_ENST00000529486.1_5'Flank	NM_001135054.1	NP_001128526.1	Q6IA17	SIGIR_HUMAN	single immunoglobulin and toll-interleukin 1 receptor (TIR) domain	285	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				acute-phase response (GO:0006953)|negative regulation of chemokine biosynthetic process (GO:0045079)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				cervix(2)|endometrium(1)|liver(1)|lung(5)|prostate(2)|skin(1)|urinary_tract(1)	13		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CAGAGCAGCAAGGTCACCAGG	0.741																																					p.L285M		Atlas-SNP	.											.	SIGIRR	22	.	0			c.T853A						.						5	7	6					11																	406869		1994	4025	6019	SO:0001583	missense	59307	exon8			GCAGCAAGGTCAC		CCDS31325.1	11p15.5	2013-01-11	2005-10-10					"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	30575	protein-coding gene	gene with protein product	"single immunoglobulin domain IL1R1 related"	605478				10346978	Standard	NM_021805		Approved	TIR8	uc001lpe.1	Q6IA17		ENST00000431843.2:c.853T>A	chr11.hg19:g.406869A>T	ENSP00000403104:p.Leu285Met	52.0	0.0		54.0	23.0	NM_001135053	Q3KQY2|Q6UXI3|Q9H733	Missense_Mutation	SNP	ENST00000431843.2	hg19	CCDS31325.1	.	.	.	.	.	.	.	.	.	.	a	18.97	3.734864	0.69189	.	.	ENSG00000185187	ENST00000431843;ENST00000397632;ENST00000332725;ENST00000531205;ENST00000382520;ENST00000528209	T;T;T;T;T;T	0.23950	1.88;1.88;1.88;1.88;1.88;1.88	3.42	1.04	0.20106	Toll/interleukin-1 receptor homology (TIR) domain (3);	0.321095	0.27375	N	0.019645	T	0.20088	0.0483	L	0.27053	0.805	0.34564	D	0.712687	P;P	0.48503	0.828;0.911	P;P	0.49752	0.542;0.621	T	0.23154	-1.0196	10	0.40728	T	0.16	.	5.3158	0.15854	0.3932:0.1507:0.456:0.0	.	285;285	C9JFX4;Q6IA17	.;SIGIR_HUMAN	M	285;285;285;285;285;181	ENSP00000403104:L285M;ENSP00000380756:L285M;ENSP00000333656:L285M;ENSP00000433022:L285M;ENSP00000371960:L285M;ENSP00000435135:L181M	ENSP00000333656:L285M	L	-	1	2	SIGIRR	396869	0.136000	0.22515	0.996000	0.52242	0.979000	0.70002	-0.270000	0.08584	0.352000	0.24053	0.397000	0.26171	TTG	.	.		0.741	SIGIRR-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383884.3	NM_021805		T	406869	A	T	406869	3	4	369	1	0	0	0	0	1	0	0	0	14319	69	3	4	391	4	SIGIRR	11	406869	Missense_Mutation	SNP	A	TCGA-ZP-A9D4-01A-11D-A36X-10		406869	134599647	40	51168										
MICAL2	9645	hgsc.bcm.edu	37	chr11	12281400	12281400	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	agacactcccaccgaaagttCttgcgcagtggccgccattg	10	14	1	1			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr11:12281400C>G	ENST00000256194.4	+	26	3578	c.3290C>G	c.(3289-3291)tCt>tGt	p.S1097C	MICAL2_ENST00000342902.5_Missense_Mutation_p.S1076C|RP11-265D17.2_ENST00000527288.1_RNA|MICAL2_ENST00000527546.1_Missense_Mutation_p.S907C|MICAL2_ENST00000537344.1_Missense_Mutation_p.S907C|MICAL2_ENST00000379612.3_Missense_Mutation_p.S871C	NM_001282663.1|NM_014632.2	NP_001269592.1|NP_055447.1	O94851	MICA2_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 2	1097					actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|heart development (GO:0007507)|heart looping (GO:0001947)|oxidation-reduction process (GO:0055114)|positive regulation of transcription via serum response element binding (GO:0010735)|sulfur oxidation (GO:0019417)	nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|NADPH:sulfur oxidoreductase activity (GO:0043914)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	47				Epithelial(150;0.00552)		ACCGAAAGTTCTTGCGCAGTG	0.587																																					p.S1097C		Atlas-SNP	.											.	MICAL2	114	.	0			c.C3290G						.						48	49	49					11																	12281400		2201	4294	6495	SO:0001583	missense	9645	exon26			AAAGTTCTTGCGC	AB018293	CCDS7809.1, CCDS60726.1, CCDS60727.1, CCDS60728.1	11p15.3	2014-08-12	2013-03-26		ENSG00000133816	ENSG00000133816			24693	protein-coding gene	gene with protein product		608881				12110185	Standard	XM_005253249		Approved	KIAA0750	uc001mjz.3	O94851	OTTHUMG00000165744	ENST00000256194.4:c.3290C>G	chr11.hg19:g.12281400C>G	ENSP00000256194:p.Ser1097Cys	258.0	0.0		224.0	76.0	NM_014632	B4DGZ0|B7Z849|D3DQW5|G3XAC8|Q5KTR3|Q5KTR4|Q7Z3A8	Missense_Mutation	SNP	ENST00000256194.4	hg19	CCDS7809.1	.	.	.	.	.	.	.	.	.	.	C	14.24	2.475762	0.44044	.	.	ENSG00000133816	ENST00000537344;ENST00000544073;ENST00000256194;ENST00000527546;ENST00000342902;ENST00000379612	T;T;T;T;T	0.62232	0.04;0.05;0.04;0.05;0.11	5.37	4.45	0.53987	.	1.018760	0.07827	N	0.960726	T	0.66187	0.2764	N	0.19112	0.55	0.26663	N	0.971875	D;D;P;D;D;D	0.69078	0.997;0.996;0.697;0.996;0.983;0.983	P;P;B;P;B;P	0.61592	0.781;0.891;0.338;0.784;0.436;0.533	T	0.60398	-0.7271	10	0.72032	D	0.01	.	13.1459	0.59461	0.0:0.9223:0.0:0.0777	.	440;1076;907;850;871;1097	B4DYS3;G3XAC8;B7Z849;Q5KTR3;Q5KTR4;O94851	.;.;.;.;.;MICA2_HUMAN	C	907;440;1097;907;1076;871	ENSP00000441689:S907C;ENSP00000256194:S1097C;ENSP00000433965:S907C;ENSP00000344894:S1076C;ENSP00000368932:S871C	ENSP00000256194:S1097C	S	+	2	0	MICAL2	12237976	0.993000	0.37304	0.996000	0.52242	0.040000	0.13550	1.488000	0.35551	2.492000	0.84095	0.591000	0.81541	TCT	.	.		0.587	MICAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385993.1	NM_014632		G	12281400	C	G	12281400	3	3	369	1	0	0	0	0	1	0	0	0	9579	913	32	4	3384	4	MICAL2	11	12281400	Missense_Mutation	SNP	C	TCGA-ZP-A9D4-01A-11D-A36X-10	11874531	12281400	122725116	41	51169										
SIK2	23235	hgsc.bcm.edu	37	chr11	111592590	111592590	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	agcaggaaagcgtctccactCtccctgccagcgtgcatccc	9	17	2	0			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr11:111592590C>T	ENST00000304987.3	+	13	2154	c.1981C>T	c.(1981-1983)Ctc>Ttc	p.L661F		NM_015191.1	NP_056006.1	Q9H0K1	SIK2_HUMAN	salt-inducible kinase 2	661					insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of insulin receptor signaling pathway (GO:0046626)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	30						CGTCTCCACTCTCCCTGCCAG	0.567																																					p.L661F		Atlas-SNP	.											.	SIK2	89	.	0			c.C1981T						.						72	68	70					11																	111592590		2201	4297	6498	SO:0001583	missense	23235	exon13			TCCACTCTCCCTG	AB018324	CCDS8347.1	11q23.1	2008-12-23	2008-12-23	2008-12-23	ENSG00000170145	ENSG00000170145			21680	protein-coding gene	gene with protein product		608973	"SNF1-like kinase 2"	SNF1LK2		15067358	Standard	NM_015191		Approved	KIAA0781, QIK, DKFZp434K1115, LOH11CR1I	uc001plt.3	Q9H0K1	OTTHUMG00000150644	ENST00000304987.3:c.1981C>T	chr11.hg19:g.111592590C>T	ENSP00000305976:p.Leu661Phe	52.0	0.0		45.0	15.0	NM_015191	A8K5B8|B0YJ94|O94878|Q17RV0|Q6AZE2|Q76N03|Q8NCV7|Q96CZ8	Missense_Mutation	SNP	ENST00000304987.3	hg19	CCDS8347.1	.	.	.	.	.	.	.	.	.	.	C	5.131	0.209869	0.09757	.	.	ENSG00000170145	ENST00000304987	T	0.72282	-0.64	5.89	2.53	0.30540	.	0.361014	0.32301	N	0.006285	T	0.39358	0.1075	N	0.04203	-0.255	0.24952	N	0.991789	B	0.02656	0.0	B	0.04013	0.001	T	0.20405	-1.0276	10	0.09084	T	0.74	.	5.7945	0.18379	0.0:0.4523:0.3839:0.1638	.	661	Q9H0K1	SIK2_HUMAN	F	661	ENSP00000305976:L661F	ENSP00000305976:L661F	L	+	1	0	SIK2	111097800	0.999000	0.42202	0.030000	0.17652	0.188000	0.23474	3.828000	0.55753	0.812000	0.34326	-0.302000	0.09304	CTC	.	.		0.567	SIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319352.3	NM_015191		T	111592590	C	T	111592590	3	4	369	1	0	0	0	0	1	0	0	0	14333	913	32	3	2031	3	SIK2	11	111592590	Missense_Mutation	SNP	C	TCGA-ZP-A9D4-01A-11D-A36X-10	99311190	111592590	23413926	42	51170										
HMBS	3145	hgsc.bcm.edu	37	chr11	118963733	118963733	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	catccatgtccctgcccaggTaccaaagctggagggcgagg	13	13	0	0			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr11:118963733T>C	ENST00000278715.3	+	13	1063		c.e13+2		HMBS_ENST00000392841.1_Splice_Site|HMBS_ENST00000537841.1_Splice_Site|HMBS_ENST00000543090.1_Splice_Site|HMBS_ENST00000442944.2_Splice_Site|HMBS_ENST00000542729.1_Splice_Site|HMBS_ENST00000544387.1_Splice_Site	NM_000190.3	NP_000181.2	P08397	HEM3_HUMAN	hydroxymethylbilane synthase						heme biosynthetic process (GO:0006783)|peptidyl-pyrromethane cofactor linkage (GO:0018160)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	hydroxymethylbilane synthase activity (GO:0004418)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|urinary_tract(1)	15	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.72e-05)		CCTGCCCAGGTACCAAAGCTG	0.517																																					.		Atlas-SNP	.											.	HMBS	27	.	0			c.741+2T>C						.						77	77	77					11																	118963733		2200	4295	6495	SO:0001630	splice_region_variant	3145	exon12			CCCAGGTACCAAA	X04808	CCDS8409.1, CCDS41726.1, CCDS58186.1, CCDS58187.1	11q23.3	2013-07-10			ENSG00000256269	ENSG00000256269	2.5.1.61		4982	protein-coding gene	gene with protein product		609806	"uroporphyrinogen I synthase", "porphobilinogen deaminase", "porphyria, acute; Chester type"	PBGD, UPS, PORC		8432552, 17298217	Standard	NM_001258208		Approved		uc001puz.1	P08397	OTTHUMG00000168295	ENST00000278715.3:c.912+2T>C	chr11.hg19:g.118963733T>C		149.0	0.0		135.0	63.0	NM_001258209	A8K2L0|G3V1P4|G5EA58|P08396|Q16012	Splice_Site	SNP	ENST00000278715.3	hg19	CCDS8409.1	.	.	.	.	.	.	.	.	.	.	t	19.14	3.770737	0.69992	.	.	ENSG00000256269;ENSG00000256269;ENSG00000256269;ENSG00000256269;ENSG00000256269;ENSG00000256269;ENSG00000149397	ENST00000278715;ENST00000537841;ENST00000542729;ENST00000544387;ENST00000543090;ENST00000392841;ENST00000442944	.	.	.	4.8	4.8	0.61643	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.1242	0.53907	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	CTD-2589C9.4;HMBS	118468943	1.000000	0.71417	0.991000	0.47740	0.959000	0.62525	6.106000	0.71511	2.132000	0.65825	0.454000	0.30748	.	.	.		0.517	HMBS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399188.1	NM_000190	Intron	C	118963733	T	C	118963733	5	2	369	1	0	0	0	0	0	0	1	0	7228	1652	57	2	964	2	HMBS	11	118963733	Splice_Site	SNP	T	TCGA-ZP-A9D4-01A-11D-A36X-10	7371143	118963733	16042783	43	51171										
CLSTN3	9746	hgsc.bcm.edu	37	chr12	7293899	7293899	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	gttccccacagtcacactctAtaccgacggcatctccttcg	6	17	3	0			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr12:7293899A>G	ENST00000266546.6	+	9	1835	c.1385A>G	c.(1384-1386)tAt>tGt	p.Y462C	CLSTN3_ENST00000537408.1_Missense_Mutation_p.Y474C	NM_014718.3	NP_055533.2	Q9BQT9	CSTN3_HUMAN	calsyntenin 3	462					homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(7)|prostate(1)|skin(1)	33						GTCACACTCTATACCGACGGC	0.577											OREG0021650	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y462C		Atlas-SNP	.											.	CLSTN3	84	.	0			c.A1385G						.						348	256	287					12																	7293899		2203	4300	6503	SO:0001583	missense	9746	exon9			CACTCTATACCGA	AB018269	CCDS8575.1	12p13.31	2011-07-01			ENSG00000139182	ENSG00000139182		"Cadherins / Cadherin-related"	18371	protein-coding gene	gene with protein product	"cadherin-related family member 14"	611324				12498782	Standard	NM_014718		Approved	CSTN3, KIAA0726, CDHR14	uc001qsr.3	Q9BQT9	OTTHUMG00000168167	ENST00000266546.6:c.1385A>G	chr12.hg19:g.7293899A>G	ENSP00000266546:p.Tyr462Cys	178.0	0.0	640	155.0	65.0	NM_014718	D3DUT6|O94831|Q2T9J5|Q5UE57	Missense_Mutation	SNP	ENST00000266546.6	hg19	CCDS8575.1	.	.	.	.	.	.	.	.	.	.	A	19.33	3.807145	0.70797	.	.	ENSG00000139182	ENST00000266546;ENST00000537408	D;D	0.88354	-2.37;-2.37	5.38	5.38	0.77491	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.000000	0.85682	D	0.000000	D	0.93112	0.7807	M	0.72894	2.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.93496	0.6840	10	0.87932	D	0	-18.0968	10.5888	0.45298	0.9249:0.0:0.0751:0.0	.	474;462	Q5UE57;Q9BQT9	.;CSTN3_HUMAN	C	462;474	ENSP00000266546:Y462C;ENSP00000440679:Y474C	ENSP00000266546:Y462C	Y	+	2	0	CLSTN3	7185166	1.000000	0.71417	0.702000	0.30337	0.813000	0.45954	8.962000	0.93254	2.033000	0.60031	0.374000	0.22700	TAT	.	.		0.577	CLSTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398560.2	NM_014718		G	7293899	A	G	7293899	3	3	369	1	0	0	0	0	1	0	0	0	3565	449	16	2	1419	2	CLSTN3	12	7293899	Missense_Mutation	SNP	A	TCGA-ZP-A9D4-01A-11D-A36X-10		7293899	126557996	44	51172										
TRPC4	7223	hgsc.bcm.edu	37	chr13	38211276	38211276	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	acattgttcactgagaccggGaatgctcaggtcaccccgtg	11	12	3	1			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr13:38211276G>T	ENST00000379705.3	-	11	3555	c.2698C>A	c.(2698-2700)Ccc>Acc	p.P900T	TRPC4_ENST00000379679.1_Missense_Mutation_p.P727T|TRPC4_ENST00000379681.3_Missense_Mutation_p.P905T|TRPC4_ENST00000447043.1_Missense_Mutation_p.P759T|TRPC4_ENST00000426868.2_3'UTR|TRPC4_ENST00000355779.2_Missense_Mutation_p.P759T|TRPC4_ENST00000358477.2_Missense_Mutation_p.P816T|TRPC4_ENST00000338947.5_Missense_Mutation_p.P727T|TRPC4_ENST00000379673.2_Missense_Mutation_p.P751T			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	900	Binds to ITPR1, ITPR2 and ITPR3.				axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|gamma-aminobutyric acid secretion (GO:0014051)|ion transmembrane transport (GO:0034220)|oligodendrocyte differentiation (GO:0048709)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|calcium channel complex (GO:0034704)|caveola (GO:0005901)|cell surface (GO:0009986)|cortical cytoskeleton (GO:0030863)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			NS(2)|breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(26)|lung(30)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	83				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		CTGAGACCGGGAATGCTCAGG	0.468																																					p.P905T		Atlas-SNP	.											.	TRPC4	389	.	0			c.C2713A						.						117	102	107					13																	38211276		2203	4300	6503	SO:0001583	missense	7223	exon11			GACCGGGAATGCT	U40983	CCDS9365.1, CCDS45035.1, CCDS45036.1, CCDS45038.1, CCDS45039.1	13q13.3	2013-01-10			ENSG00000133107	ENSG00000133107		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	12336	protein-coding gene	gene with protein product		603651				8646775, 16382100	Standard	NM_016179		Approved	HTRP4, TRP4	uc010abx.3	Q9UBN4	OTTHUMG00000016752	ENST00000379705.3:c.2698C>A	chr13.hg19:g.38211276G>T	ENSP00000369027:p.Pro900Thr	102.0	0.0		95.0	45.0	NM_003306	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Missense_Mutation	SNP	ENST00000379705.3	hg19	CCDS9365.1	.	.	.	.	.	.	.	.	.	.	G	8.875	0.950159	0.18431	.	.	ENSG00000133107	ENST00000379705;ENST00000379681;ENST00000338947;ENST00000379679;ENST00000355779;ENST00000358477;ENST00000379673;ENST00000447043	T;T;T;T;T;T;T;T	0.70282	-0.08;-0.08;0.12;0.12;0.24;-0.19;-0.47;0.24	5.43	4.54	0.55810	.	0.174545	0.41194	D	0.000932	T	0.65565	0.2703	N	0.08118	0	0.25714	N	0.985445	B;B;D;B;B;B	0.57899	0.004;0.013;0.981;0.152;0.043;0.018	B;B;D;B;B;B	0.70487	0.015;0.022;0.969;0.058;0.079;0.011	T	0.56498	-0.7969	10	0.21540	T	0.41	-20.4477	11.7376	0.51773	0.0:0.1688:0.7113:0.1198	.	759;751;905;727;816;900	Q9UBN4-3;Q9UBN4-4;Q9UBN4-5;Q9UBN4-6;Q9UBN4-2;Q9UBN4	.;.;.;.;.;TRPC4_HUMAN	T	900;905;727;727;759;816;751;759	ENSP00000369027:P900T;ENSP00000369003:P905T;ENSP00000342580:P727T;ENSP00000369001:P727T;ENSP00000348025:P759T;ENSP00000351264:P816T;ENSP00000368995:P751T;ENSP00000414316:P759T	ENSP00000342580:P727T	P	-	1	0	TRPC4	37109276	0.976000	0.34144	0.919000	0.36401	0.508000	0.34012	2.533000	0.45667	2.687000	0.91594	0.655000	0.94253	CCC	.	.		0.468	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306		T	38211276	G	T	38211276	3	4	369	1	0	0	0	0	1	0	0	0	16595	1174	41	3	239	3	TRPC4	13	38211276	Missense_Mutation	SNP	G	TCGA-ZP-A9D4-01A-11D-A36X-10		38211276	76958602	45	51173										
HERC2	8924	hgsc.bcm.edu	37	chr15	28419719	28419729	+	Frame_Shift_Del	DEL	CGTGCCATTGC	CGTGCCATTGC	-													0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	ggcttcctgttaaccgtggtCgtgccattgccctgctggcc					rs373351931		TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	CGTGCCATTGC	CGTGCCATTGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr15:28419719_28419729delCGTGCCATTGC	ENST00000261609.7	-	65	9977_9987	c.9869_9879delGCAATGGCACG	c.(9868-9879)ggcaatggcacgfs	p.GNGT3290fs		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		TAACCGTGGTCGTGCCATTGCCCTGCTGGCC	0.498																																					p.3290_3294del		Atlas-INDEL	.											.	HERC2	501	.	0			c.9870_9880del						.																																			SO:0001589	frameshift_variant	8924	exon65			.	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.9869_9879delGCAATGGCACG	chr15.hg19:g.28419719_28419729delCGTGCCATTGC	ENSP00000261609:p.Gly3290fs	463.0	0.0		397.0	59.0	NM_004667		Frame_Shift_Del	DEL	ENST00000261609.7	hg19	CCDS10021.1																																																																																			.	.		0.498	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		-	28419729	CGTGCCATTGC	-	28419719	7	5	369	1	0	1	0	1	0	0	0	0	7067	871	31	0	4741	0	HERC2	15	28419719	Frame_Shift_Del	DEL	CGTGCCATTGC	TCGA-ZP-A9D4-01A-11D-A36X-10		28419719	74111673	46	51174										
ACTC1	70	hgsc.bcm.edu	37	chr15	35084698	35084698	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	ccagatccagacgcatgatgGcatggggcaaagcgtagccc	13	12	0	3			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr15:35084698G>T	ENST00000290378.4	-	4	1182	c.527C>A	c.(526-528)gCc>gAc	p.A176D	ACTC1_ENST00000557860.1_5'UTR|RP11-814P5.1_ENST00000503496.1_RNA|RP11-814P5.1_ENST00000558707.1_RNA	NM_005159.4	NP_005150.1	P68032	ACTC_HUMAN	actin, alpha, cardiac muscle 1	176					actin filament-based movement (GO:0030048)|actin-myosin filament sliding (GO:0033275)|actomyosin structure organization (GO:0031032)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cardiac muscle contraction (GO:0060048)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|heart contraction (GO:0060047)|muscle filament sliding (GO:0030049)|negative regulation of apoptotic process (GO:0043066)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|skeletal muscle thin filament assembly (GO:0030240)	actin filament (GO:0005884)|actomyosin, actin portion (GO:0042643)|blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|I band (GO:0031674)|membrane (GO:0016020)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|myosin binding (GO:0017022)			central_nervous_system(1)|endometrium(5)|kidney(1)|lung(14)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	31		all_lung(180;2.3e-08)		all cancers(64;5.83e-19)|GBM - Glioblastoma multiforme(113;1.98e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0244)		ACGCATGATGGCATGGGGCAA	0.547																																					p.A176D		Atlas-SNP	.											.	ACTC1	75	.	0			c.C527A						.						154	134	141					15																	35084698		2201	4298	6499	SO:0001583	missense	70	exon4			ATGATGGCATGGG	BC009978	CCDS10041.1	15q14	2014-09-17	2006-08-24	2006-08-24	ENSG00000159251	ENSG00000159251			143	protein-coding gene	gene with protein product		102540	"actin, alpha, cardiac muscle"	ACTC		1639426	Standard	NM_005159		Approved	CMD1R	uc001ziu.1	P68032	OTTHUMG00000129675	ENST00000290378.4:c.527C>A	chr15.hg19:g.35084698G>T	ENSP00000290378:p.Ala176Asp	179.0	0.0		179.0	20.0	NM_005159	P04270	Missense_Mutation	SNP	ENST00000290378.4	hg19	CCDS10041.1	.	.	.	.	.	.	.	.	.	.	G	18.23	3.578764	0.65878	.	.	ENSG00000159251	ENST00000290378;ENST00000544062	D	0.97850	-4.57	4.99	4.99	0.66335	.	0.000000	0.52532	U	0.000080	D	0.99155	0.9708	H	0.99074	4.42	0.58432	D	0.999999	P	0.44816	0.844	P	0.52646	0.705	D	0.99066	1.0832	10	0.87932	D	0	.	18.8258	0.92117	0.0:0.0:1.0:0.0	.	176	P68032	ACTC_HUMAN	D	176;141	ENSP00000290378:A176D	ENSP00000290378:A176D	A	-	2	0	ACTC1	32871990	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.657000	0.98554	2.755000	0.94549	0.591000	0.81541	GCC	.	.		0.547	ACTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251876.3	NM_005159		T	35084698	G	T	35084698	3	4	369	1	0	0	0	0	1	0	0	0	195	1203	42	3	622	3	ACTC1	15	35084698	Missense_Mutation	SNP	G	TCGA-ZP-A9D4-01A-11D-A36X-10	6664979	35084698	67446694	47	51175										
SPATA5L1	79029	hgsc.bcm.edu	37	chr15	45694823	45694823	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	1	1	1	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	gcactgcctggcctcggcggGacggagcggacggctttgtg	18	12	0	0			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr15:45694823G>C	ENST00000305560.6	+	1	295	c.196G>C	c.(196-198)Gac>Cac	p.D66H	GATM_ENST00000458245.5_5'Flank|SPATA5L1_ENST00000559860.1_Missense_Mutation_p.D66H	NM_024063.2	NP_076968.2	Q9BVQ7	SPA5L_HUMAN	spermatogenesis associated 5-like 1	66						cytoplasm (GO:0005737)	ATP binding (GO:0005524)			kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	14		Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;7.31e-17)|GBM - Glioblastoma multiforme(94;6.28e-07)		GCCTCGGCGGGACGGAGCGGA	0.741																																					p.D66H		Atlas-SNP	.											.	SPATA5L1	40	.	0			c.G196C						.						4	5	5					15																	45694823		2027	4067	6094	SO:0001583	missense	79029	exon1			CGGCGGGACGGAG	AK023232	CCDS10123.1	15q15.1	2010-04-21			ENSG00000171763	ENSG00000171763		"ATPases / AAA-type"	28762	protein-coding gene	gene with protein product						12477932	Standard	NM_024063		Approved	MGC5347, FLJ12286	uc001zve.3	Q9BVQ7	OTTHUMG00000131425	ENST00000305560.6:c.196G>C	chr15.hg19:g.45694823G>C	ENSP00000305494:p.Asp66His	60.0	0.0		64.0	22.0	NM_024063	C9JHR5|Q9H8W7|Q9HA41	Missense_Mutation	SNP	ENST00000305560.6	hg19	CCDS10123.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.530409	0.85706	.	.	ENSG00000171763	ENST00000305560	D	0.94966	-3.57	4.87	2.99	0.34606	.	0.058275	0.64402	D	0.000002	D	0.95931	0.8675	M	0.71581	2.175	0.42303	D	0.992184	D	0.76494	0.999	D	0.66716	0.946	D	0.95171	0.8290	10	0.87932	D	0	-22.7009	9.6755	0.40039	0.1701:0.0:0.8299:0.0	.	66	Q9BVQ7	SPA5L_HUMAN	H	66	ENSP00000305494:D66H	ENSP00000305494:D66H	D	+	1	0	SPATA5L1	43482115	1.000000	0.71417	0.999000	0.59377	0.986000	0.74619	6.712000	0.74681	0.657000	0.30906	0.557000	0.71058	GAC	.	.		0.741	SPATA5L1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254218.1	NM_024063		C	45694823	G	C	45694823	3	2	369	1	0	0	0	0	1	0	0	0	15027	1174	41	4	198	4	SPATA5L1	15	45694823	Missense_Mutation	SNP	G	TCGA-ZP-A9D4-01A-11D-A36X-10	10610125	45694823	56836569	48	51176										
TLN2	83660	hgsc.bcm.edu	37	chr15	63069030	63069030	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	ggaagccgtggatgacatcaTggtgacgctgaacgaagctg	15	8	1	3			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr15:63069030T>C	ENST00000561311.1	+	42	5665	c.5435T>C	c.(5434-5436)aTg>aCg	p.M1812T	TLN2_ENST00000472902.1_Missense_Mutation_p.M205T|TLN2_ENST00000306829.6_Missense_Mutation_p.M1812T			Q9Y4G6	TLN2_HUMAN	talin 2	1812					cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						GATGACATCATGGTGACGCTG	0.562																																					p.M1812T		Atlas-SNP	.											.	TLN2	253	.	0			c.T5435C						.						108	87	94					15																	63069030		2203	4300	6503	SO:0001583	missense	83660	exon40			ACATCATGGTGAC	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.5435T>C	chr15.hg19:g.63069030T>C	ENSP00000453508:p.Met1812Thr	76.0	0.0		85.0	38.0	NM_015059	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	hg19	CCDS32261.1	.	.	.	.	.	.	.	.	.	.	T	9.670	1.146443	0.21288	.	.	ENSG00000171914	ENST00000306829	T	0.14640	2.49	5.48	5.48	0.80851	.	0.079544	0.85682	D	0.000000	T	0.08891	0.0220	N	0.16233	0.39	0.48395	D	0.999644	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.16070	-1.0415	10	0.09084	T	0.74	-32.1648	15.2464	0.73509	0.0:0.0:0.0:1.0	.	856;1812	G1UI21;Q9Y4G6	.;TLN2_HUMAN	T	1812	ENSP00000303476:M1812T	ENSP00000303476:M1812T	M	+	2	0	TLN2	60856083	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.215000	0.72206	2.076000	0.62316	0.460000	0.39030	ATG	.	.		0.562	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			C	63069030	T	C	63069030	3	2	369	1	0	0	0	0	1	0	0	0	15963	1464	51	2	5593	2	TLN2	15	63069030	Missense_Mutation	SNP	T	TCGA-ZP-A9D4-01A-11D-A36X-10	17374207	63069030	39462362	49	51177										
HCN4	10021	hgsc.bcm.edu	37	chr15	73660429	73660429	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	cgggactccgtgccacccgcGgccgccgagggggagggcga	19	15	0	0			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr15:73660429G>A	ENST00000261917.3	-	1	1176	c.183C>T	c.(181-183)gcC>gcT	p.A61A		NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	61					blood circulation (GO:0008015)|cation transport (GO:0006812)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)	cAMP binding (GO:0030552)|cation channel activity (GO:0005261)|identical protein binding (GO:0042802)|intracellular cAMP activated cation channel activity (GO:0005222)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(13)|liver(1)|lung(18)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				COAD - Colon adenocarcinoma(1;0.142)		TGCCACCCGCGGCCGCCGAGG	0.781																																					p.A61A		Atlas-SNP	.											.	HCN4	150	.	0			c.C183T						.						1	1	1					15																	73660429		662	1712	2374	SO:0001819	synonymous_variant	10021	exon1			ACCCGCGGCCGCC	AJ132429	CCDS10248.1	15q24.1	2011-07-05			ENSG00000138622	ENSG00000138622		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	16882	protein-coding gene	gene with protein product		605206				10228147, 10430953, 16382102	Standard	NM_005477		Approved		uc002avp.3	Q9Y3Q4	OTTHUMG00000137563	ENST00000261917.3:c.183C>T	chr15.hg19:g.73660429G>A		377.0	1.0		410.0	180.0	NM_005477	Q9UMQ7	Silent	SNP	ENST00000261917.3	hg19	CCDS10248.1																																																																																			.	.		0.781	HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268900.2	NM_005477		A	73660429	G	A	73660429	2	1	369	1	0	0	0	0	0	0	0	1	7008	1103	39	1		1	HCN4	15	73660429	Silent	SNP	G	TCGA-ZP-A9D4-01A-11D-A36X-10	10591399	73660429	28870963	50	51178										
XYLT1	64131	hgsc.bcm.edu	37	chr16	17235129	17235129	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	gaaccagtccgaaccgccatCcacggcaatgccctctggga	10	16	1	0			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr16:17235129C>T	ENST00000261381.6	-	7	1552	c.1468G>A	c.(1468-1470)Gat>Aat	p.D490N	CTD-2576D5.4_ENST00000567344.1_RNA	NM_022166.3	NP_071449.1	Q86Y38	XYLT1_HUMAN	xylosyltransferase I	490					cellular response to heat (GO:0034605)|chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						GAACCGCCATCCACGGCAATG	0.567																																					p.D490N		Atlas-SNP	.											.	XYLT1	147	.	0			c.G1468A						.						106	108	108					16																	17235129		2197	4300	6497	SO:0001583	missense	64131	exon7			CGCCATCCACGGC	AJ277441	CCDS10569.1	16p12	2013-02-25			ENSG00000103489	ENSG00000103489	2.4.2.26	"Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	15516	protein-coding gene	gene with protein product	"protein xylosyltransferase 1"	608124				11099377	Standard	NM_022166		Approved	XT-I, PXYLT1	uc002dfa.3	Q86Y38	OTTHUMG00000129975	ENST00000261381.6:c.1468G>A	chr16.hg19:g.17235129C>T	ENSP00000261381:p.Asp490Asn	98.0	0.0		86.0	42.0	NM_022166	Q9H1B6	Missense_Mutation	SNP	ENST00000261381.6	hg19	CCDS10569.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.184988	0.78677	.	.	ENSG00000103489	ENST00000261381	T	0.11604	2.76	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.29976	0.0750	L	0.52126	1.63	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.00060	-1.2164	10	0.40728	T	0.16	-27.5973	19.2967	0.94126	0.0:1.0:0.0:0.0	.	490	Q86Y38	XYLT1_HUMAN	N	490	ENSP00000261381:D490N	ENSP00000261381:D490N	D	-	1	0	XYLT1	17142630	1.000000	0.71417	0.986000	0.45419	0.080000	0.17528	5.972000	0.70448	2.797000	0.96272	0.555000	0.69702	GAT	.	.		0.567	XYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252241.2	NM_022166		T	17235129	C	T	17235129	3	4	369	1	0	0	0	0	1	0	0	0	17478	855	30	3	1435	3	XYLT1	16	17235129	Missense_Mutation	SNP	C	TCGA-ZP-A9D4-01A-11D-A36X-10		17235129	73119624	51	51179										
IRX6	79190	hgsc.bcm.edu	37	chr16	55362676	55362676	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	ctggaagacctggaggaagaGgaggaggaggaggaggaagc	21	4	0	2			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr16:55362676G>A	ENST00000290552.7	+	5	2118	c.786G>A	c.(784-786)gaG>gaA	p.E262E	RP11-26L20.3_ENST00000558730.2_RNA	NM_024335.2	NP_077311.2	P78412	IRX6_HUMAN	iroquois homeobox 6	262					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(5)|endometrium(3)|kidney(2)|large_intestine(6)|liver(2)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	33						Tggaggaagaggaggaggagg	0.622																																					p.E262E		Atlas-SNP	.											.	IRX6	66	.	0			c.G786A						.						33	38	36					16																	55362676		2195	4295	6490	SO:0001819	synonymous_variant	79190	exon5			GGAAGAGGAGGAG	AF319966	CCDS32449.1	16q12.2	2011-06-20	2007-07-13	2003-01-10		ENSG00000159387		"Homeoboxes / TALE class"	14675	protein-coding gene	gene with protein product		606196	"iroquois homeobox protein 7", "iroquois homeobox protein 6"	IRX7			Standard	NM_024335		Approved	IRX-3	uc002ehy.3	P78412		ENST00000290552.7:c.786G>A	chr16.hg19:g.55362676G>A		75.0	0.0		87.0	6.0	NM_024335	B2RN06|Q7Z2K0	Silent	SNP	ENST00000290552.7	hg19	CCDS32449.1																																																																																			.	.		0.622	IRX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417445.4	NM_024335		A	55362676	G	A	55362676	2	1	369	1	0	0	0	0	0	0	0	1	7857	991	35	3		3	IRX6	16	55362676	Silent	SNP	G	TCGA-ZP-A9D4-01A-11D-A36X-10	38127547	55362676	34992077	52	51180										
COLEC12	81035	hgsc.bcm.edu	37	chr18	334824	334824	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	gggccaggagggccggggggGcccttggggcctggcatgcc	22	12	0	0			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr18:334824G>T	ENST00000400256.3	-	6	1941	c.1734C>A	c.(1732-1734)ggC>ggA	p.G578G		NM_130386.2	NP_569057	Q5KU26	COL12_HUMAN	collectin sub-family member 12	578	Collagen-like 3.				carbohydrate mediated signaling (GO:0009756)|defense response (GO:0006952)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)|phagocytosis, recognition (GO:0006910)|protein homooligomerization (GO:0051260)|receptor-mediated endocytosis (GO:0006898)	collagen trimer (GO:0005581)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galactose binding (GO:0005534)|low-density lipoprotein particle binding (GO:0030169)|metal ion binding (GO:0046872)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	46		all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426)				GGCCGGGGGGGCCCTTGGGGC	0.697																																					p.G578G		Atlas-SNP	.											.	COLEC12	121	.	0			c.C1734A						.						18	19	19					18																	334824		2199	4287	6486	SO:0001819	synonymous_variant	81035	exon6			GGGGGGGCCCTTG	AB038518	CCDS32782.1	18p11.32	2013-09-19			ENSG00000158270	ENSG00000158270		"Collectins"	16016	protein-coding gene	gene with protein product		607621				11162630	Standard	NM_130386		Approved	SRCL, CL-P1, SCARA4	uc002kkm.3	Q5KU26	OTTHUMG00000178145	ENST00000400256.3:c.1734C>A	chr18.hg19:g.334824G>T		61.0	0.0		62.0	30.0	NM_130386	Q6P9F2|Q8TCR2|Q8WZA4|Q9BY85|Q9BYH7	Silent	SNP	ENST00000400256.3	hg19	CCDS32782.1																																																																																			.	.		0.697	COLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440746.1			T	334824	G	T	334824	2	4	369	1	0	0	0	0	0	0	0	1	3714	1190	42	3		3	COLEC12	18	334824	Silent	SNP	G	TCGA-ZP-A9D4-01A-11D-A36X-10		334824	77742424	53	51181										
TSHZ3	57616	hgsc.bcm.edu	37	chr19	31770531	31770531	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	ggggagttctggtagctgggGcaggccctggcgagctcctt	18	10	1	0			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr19:31770531G>C	ENST00000240587.4	-	2	495	c.168C>G	c.(166-168)tgC>tgG	p.C56W		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	56					in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					GGTAGCTGGGGCAGGCCCTGG	0.592																																					p.C56W		Atlas-SNP	.											.	TSHZ3	549	.	0			c.C168G						.						33	35	35					19																	31770531		1964	4132	6096	SO:0001583	missense	57616	exon2			GCTGGGGCAGGCC	AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	30700	protein-coding gene	gene with protein product	"teashirt 3"	614119	"zinc finger protein 537", "teashirt family zinc finger 3"	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.168C>G	chr19.hg19:g.31770531G>C	ENSP00000240587:p.Cys56Trp	49.0	0.0		42.0	12.0	NM_020856	Q9H0G6|Q9P254	Missense_Mutation	SNP	ENST00000240587.4	hg19	CCDS12421.2	.	.	.	.	.	.	.	.	.	.	G	13.06	2.123830	0.37436	.	.	ENSG00000121297	ENST00000240587	T	0.11495	2.77	5.92	2.26	0.28386	.	0.301733	0.26474	U	0.024173	T	0.06645	0.0170	N	0.14661	0.345	0.52099	D	0.999949	P	0.47034	0.889	B	0.43018	0.405	T	0.36089	-0.9762	10	0.51188	T	0.08	-26.241	7.1481	0.25595	0.2178:0.0:0.6577:0.1245	.	56	Q63HK5	TSH3_HUMAN	W	56	ENSP00000240587:C56W	ENSP00000240587:C56W	C	-	3	2	TSHZ3	36462371	1.000000	0.71417	0.995000	0.50966	0.862000	0.49288	0.713000	0.25794	0.847000	0.35167	0.650000	0.86243	TGC	.	.		0.592	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856		C	31770531	G	C	31770531	3	2	369	1	0	0	0	0	1	0	0	0	16640	1195	42	4	3081	4	TSHZ3	19	31770531	Missense_Mutation	SNP	G	TCGA-ZP-A9D4-01A-11D-A36X-10		31770531	27358452	54	51182										
ZNF382	84911	hgsc.bcm.edu	37	chr19	37117613	37117613	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	agaagccctctgcctacaacAaatatgggaaattcctctgc	7	12	2	1			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr19:37117613A>G	ENST00000292928.2	+	5	927	c.814A>G	c.(814-816)Aaa>Gaa	p.K272E	ZNF382_ENST00000439428.1_Missense_Mutation_p.K271E|ZNF382_ENST00000423582.1_Missense_Mutation_p.K223E|ZNF382_ENST00000435416.1_Missense_Mutation_p.K271E|CTD-3234P18.2_ENST00000585467.1_lincRNA	NM_001256838.1|NM_032825.4	NP_001243767.1|NP_116214.2	Q96SR6	ZN382_HUMAN	zinc finger protein 382	272					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	34	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			TGCCTACAACAAATATGGGAA	0.393																																					p.K272E		Atlas-SNP	.											.	ZNF382	87	.	0			c.A814G						.						68	70	69					19																	37117613		2203	4296	6499	SO:0001583	missense	84911	exon5			TACAACAAATATG	AF513816	CCDS33004.1, CCDS58659.1	19q13.13	2013-01-08			ENSG00000161298	ENSG00000161298		"Zinc fingers, C2H2-type", "-"	17409	protein-coding gene	gene with protein product		609516					Standard	NM_032825		Approved	FLJ14686, KS1	uc010efb.4	Q96SR6	OTTHUMG00000048153	ENST00000292928.2:c.814A>G	chr19.hg19:g.37117613A>G	ENSP00000292928:p.Lys272Glu	91.0	0.0		102.0	42.0	NM_032825	A3KMP6|A8MT55|C9K0V5|Q53ZY8|Q5JPJ2	Missense_Mutation	SNP	ENST00000292928.2	hg19	CCDS33004.1	.	.	.	.	.	.	.	.	.	.	A	3.921	-0.018131	0.07681	.	.	ENSG00000161298	ENST00000423582;ENST00000292928;ENST00000439428;ENST00000435416	T;T;T;T	0.26518	1.73;1.73;1.73;1.73	4.59	3.49	0.39957	.	0.000000	0.42821	D	0.000658	T	0.03915	0.0110	N	0.00205	-1.85	0.20307	N	0.999919	B;B;B	0.24823	0.112;0.112;0.068	B;B;B	0.22880	0.042;0.042;0.019	T	0.43212	-0.9405	10	0.02654	T	1	.	4.3939	0.11353	0.6949:0.2022:0.1028:0.0	.	271;271;272	Q96SR6-2;Q96SR6-3;Q96SR6	.;.;ZN382_HUMAN	E	223;272;271;271	ENSP00000389722:K223E;ENSP00000292928:K272E;ENSP00000407593:K271E;ENSP00000410113:K271E	ENSP00000292928:K272E	K	+	1	0	ZNF382	41809453	0.000000	0.05858	0.996000	0.52242	0.891000	0.51852	0.192000	0.17096	2.065000	0.61736	0.383000	0.25322	AAA	.	.		0.393	ZNF382-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109562.2	NM_032825		G	37117613	A	G	37117613	3	3	369	1	0	0	0	0	1	0	0	0	17888	131	5	2	824	2	ZNF382	19	37117613	Missense_Mutation	SNP	A	TCGA-ZP-A9D4-01A-11D-A36X-10	5347082	37117613	22011370	55	51183										
ZNF569	148266	hgsc.bcm.edu	37	chr19	37904717	37904717	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	tgatcaataagatttgatttCtggctgaaggacttctcaca	8	7	3	4			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr19:37904717C>A	ENST00000316950.6	-	6	1400	c.843G>T	c.(841-843)caG>caT	p.Q281H	ZNF569_ENST00000392149.2_Missense_Mutation_p.Q281H|ZNF569_ENST00000392150.2_Missense_Mutation_p.Q122H	NM_152484.2	NP_689697.2	Q5MCW4	ZN569_HUMAN	zinc finger protein 569	281					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(5)|endometrium(4)|large_intestine(16)|lung(11)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	40			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GATTTGATTTCTGGCTGAAGG	0.358																																					p.Q281H		Atlas-SNP	.											.	ZNF569	101	.	0			c.G843T						.						77	81	80					19																	37904717		2203	4300	6503	SO:0001583	missense	148266	exon6			TGATTTCTGGCTG	AL833408	CCDS12503.1	19q13.12	2013-09-20			ENSG00000196437	ENSG00000196437		"Zinc fingers, C2H2-type", "-"	24737	protein-coding gene	gene with protein product		613904				12477932	Standard	NM_152484		Approved	FLJ32053, ZAP1	uc002ogi.3	Q5MCW4	OTTHUMG00000048172	ENST00000316950.6:c.843G>T	chr19.hg19:g.37904717C>A	ENSP00000325018:p.Gln281His	56.0	0.0		62.0	24.0	NM_152484	A8K1S2|Q15925|Q17RR6|Q96MQ2	Missense_Mutation	SNP	ENST00000316950.6	hg19	CCDS12503.1	.	.	.	.	.	.	.	.	.	.	C	10.02	1.236321	0.22626	.	.	ENSG00000196437	ENST00000316950;ENST00000392150	T;T	0.07327	3.2;3.2	3.97	0.39	0.16275	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.35805	N	0.002963	T	0.08133	0.0203	N	0.05510	-0.035	0.09310	N	1	B;D	0.69078	0.016;0.997	B;D	0.79108	0.024;0.992	T	0.34004	-0.9846	10	0.18276	T	0.48	.	5.9243	0.19101	0.3342:0.5695:0.0:0.0963	.	122;281	Q17RR6;Q5MCW4	.;ZN569_HUMAN	H	281;122	ENSP00000325018:Q281H;ENSP00000375993:Q122H	ENSP00000325018:Q281H	Q	-	3	2	ZNF569	42596557	0.000000	0.05858	0.862000	0.33874	0.991000	0.79684	-1.281000	0.02802	0.073000	0.16731	0.655000	0.94253	CAG	.	.		0.358	ZNF569-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109594.2	NM_152484		A	37904717	C	A	37904717	3	1	369	1	0	0	0	0	1	0	0	0	18015	912	32	3	1221	3	ZNF569	19	37904717	Missense_Mutation	SNP	C	TCGA-ZP-A9D4-01A-11D-A36X-10	787104	37904717	21224266	56	51184										
FBXO17	115290	hgsc.bcm.edu	37	chr19	39437164	39437164	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	gtccagcagctcctgccacaCcccttccatcaccaggtcca	6	20	1	0	rs546215787		TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr19:39437164C>G	ENST00000292852.4	-	4	846	c.505G>C	c.(505-507)Gtg>Ctg	p.V169L	FBXO17_ENST00000595329.1_Missense_Mutation_p.V169L|SARS2_ENST00000448145.2_Missense_Mutation_p.V4L|CTC-360G5.8_ENST00000599996.1_Missense_Mutation_p.G73A	NM_024907.5	NP_079183.4	Q96EF6	FBX17_HUMAN	F-box protein 17	169	FBA. {ECO:0000255|PROSITE- ProRule:PRU00482}.					SCF ubiquitin ligase complex (GO:0019005)	glycoprotein binding (GO:0001948)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)	7	all_cancers(60;8.37e-07)|all_lung(34;3.71e-07)|Lung NSC(34;4.17e-07)|all_epithelial(25;1.13e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			TCCTGCCACACCCCTTCCATC	0.612																																					p.V178L		Atlas-SNP	.											.	FBXO17	42	.	0			c.G532C						.						83	66	72					19																	39437164		2203	4300	6503	SO:0001583	missense	115290	exon4			GCCACACCCCTTC	AF386743	CCDS12526.1	19q13.2	2010-07-02	2004-06-15	2004-06-16		ENSG00000269190		"F-boxes /  "other""	18754	protein-coding gene	gene with protein product	"F-box only protein 26"	609094	"F-box only protein 17"	FBXO26			Standard	NM_148169		Approved	FBG4, FLJ25205, MGC9379, FLJ11798, Fbx17		Q96EF6		ENST00000292852.4:c.505G>C	chr19.hg19:g.39437164C>G	ENSP00000292852:p.Val169Leu	161.0	0.0		140.0	62.0	NM_148169	Q96LQ4	Missense_Mutation	SNP	ENST00000292852.4	hg19	CCDS12526.1	.	.	.	.	.	.	.	.	.	.	C	0.565	-0.843601	0.02671	.	.	ENSG00000104835	ENST00000448145;ENST00000392076;ENST00000292852	T;T	0.23754	1.89;1.89	4.25	-2.18	0.07037	Galactose-binding domain-like (1);F-box associated (FBA) domain (2);	0.321927	0.21695	N	0.070509	T	0.04272	0.0118	N	0.00656	-1.285	.	.	.	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.40175	-0.9577	9	0.02654	T	1	.	4.0976	0.09998	0.0:0.3549:0.3384:0.3066	.	4;169	E7EX87;Q96EF6	.;FBX17_HUMAN	L	4;178;169	ENSP00000399330:V4L;ENSP00000292852:V169L	ENSP00000292852:V169L	V	-	1	0	FBXO17	44129004	0.000000	0.05858	0.357000	0.25798	0.769000	0.43574	-0.882000	0.04174	-0.053000	0.13289	0.455000	0.32223	GTG	.	.		0.612	FBXO17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463273.1	NM_024907		G	39437164	C	G	39437164	3	3	369	1	0	0	0	0	1	0	0	0	5738	507	18	4	343	4	FBXO17	19	39437164	Missense_Mutation	SNP	C	TCGA-ZP-A9D4-01A-11D-A36X-10	1532447	39437164	19691819	57	51185										
ZNF223	7766	hgsc.bcm.edu	37	chr19	44570689	44570689	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	aaacctttcaaatgtgaacaAtgtgggagaggcttcagatg	11	6	2	3			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr19:44570689A>G	ENST00000434772.3	+	5	963	c.708A>G	c.(706-708)caA>caG	p.Q236Q	ZNF223_ENST00000591793.1_Silent_p.Q346Q	NM_013361.4	NP_037493.3	Q9UK11	ZN223_HUMAN	zinc finger protein 223	236					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18		Prostate(69;0.0352)				AATGTGAACAATGTGGGAGAG	0.418																																					p.Q236Q		Atlas-SNP	.											.	ZNF223	61	.	0			c.A708G						.						147	145	146					19																	44570689		2203	4300	6503	SO:0001819	synonymous_variant	7766	exon5			TGAACAATGTGGG	AF187989	CCDS12635.1	19q13.2	2013-01-08				ENSG00000178386		"Zinc fingers, C2H2-type", "-"	13016	protein-coding gene	gene with protein product							Standard	XM_006723365		Approved		uc002oyf.1	Q9UK11		ENST00000434772.3:c.708A>G	chr19.hg19:g.44570689A>G		107.0	0.0		94.0	45.0	NM_013361	Q15736|Q8TBJ3|Q9HCA9	Silent	SNP	ENST00000434772.3	hg19	CCDS12635.1																																																																																			.	.		0.418	ZNF223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460469.2			G	44570689	A	G	44570689	2	3	369	1	0	0	0	0	0	0	0	1	17792	98	4	2		2	ZNF223	19	44570689	Silent	SNP	A	TCGA-ZP-A9D4-01A-11D-A36X-10	5133525	44570689	14558294	58	51186										
ZNF227	7770	hgsc.bcm.edu	37	chr19	44739935	44739935	+	Nonsense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	cttcagccacaattcaccatTaatatgccatcggagagtcc	6	13	2	1			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr19:44739935T>G	ENST00000313040.7	+	6	1557	c.1352T>G	c.(1351-1353)tTa>tGa	p.L451*	ZNF227_ENST00000589005.1_Nonsense_Mutation_p.L400*|ZNF227_ENST00000391961.2_Nonsense_Mutation_p.L400*	NM_182490.1	NP_872296.1	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	451					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(2)|stomach(1)|urinary_tract(1)	24		Prostate(69;0.0435)				AATTCACCATTAATATGCCAT	0.468																																					p.L451X		Atlas-SNP	.											.	ZNF227	62	.	0			c.T1352G						.						93	91	92					19																	44739935		2203	4300	6503	SO:0001587	stop_gained	7770	exon6			CACCATTAATATG	AK092253	CCDS12636.1, CCDS74388.1	19q13.32	2013-01-08						"Zinc fingers, C2H2-type", "-"	13020	protein-coding gene	gene with protein product							Standard	XM_005259232		Approved		uc002oyu.3	Q86WZ6		ENST00000313040.7:c.1352T>G	chr19.hg19:g.44739935T>G	ENSP00000321049:p.Leu451*	101.0	0.0		68.0	24.0	NM_182490	B3KRU7|B7Z5P9	Nonsense_Mutation	SNP	ENST00000313040.7	hg19	CCDS12636.1	.	.	.	.	.	.	.	.	.	.	T	36	5.891761	0.97074	.	.	ENSG00000131115	ENST00000313040;ENST00000328297;ENST00000391961;ENST00000418980;ENST00000377916	.	.	.	4.02	2.96	0.34315	.	.	.	.	.	.	.	.	.	.	.	0.25863	N	0.983792	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.9013	0.13777	0.0:0.1013:0.2011:0.6976	.	.	.	.	X	451;408;400;430;152	.	ENSP00000321049:L451X	L	+	2	0	ZNF227	49431775	0.002000	0.14202	0.005000	0.12908	0.981000	0.71138	1.338000	0.33873	0.673000	0.31224	0.460000	0.39030	TTA	.	.		0.468	ZNF227-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460720.1	NM_182490		G	44739935	T	G	44739935	4	3	369	1	0	0	0	0	0	1	0	0	17796	1764	61	5	1366	5	ZNF227	19	44739935	Nonsense_Mutation	SNP	T	TCGA-ZP-A9D4-01A-11D-A36X-10	169246	44739935	14389048	59	51187										
HAS1	3036	hgsc.bcm.edu	37	chr19	52222514	52222514	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	aggctgtgtacatgacctcgCgcttgccgccccagcgctgc	12	16	0	1			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr19:52222514C>T	ENST00000222115.1	-	2	681	c.647G>A	c.(646-648)cGc>cAc	p.R216H	HAS1_ENST00000594621.1_Missense_Mutation_p.R70H|HAS1_ENST00000601714.1_Missense_Mutation_p.R223H|HAS1_ENST00000540069.2_Missense_Mutation_p.R215H	NM_001523.2	NP_001514.2	Q92839	HYAS1_HUMAN	hyaluronan synthase 1	216					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|negative regulation of fibroblast migration (GO:0010764)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronan synthase activity (GO:0050501)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	40		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00102)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		CATGACCTCGCGCTTGCCGCC	0.657																																					p.R216H	NSCLC(132;636 2450 45807 47979)	Atlas-SNP	.											.	HAS1	61	.	0			c.G647A						.						43	37	39					19																	52222514		2202	4298	6500	SO:0001583	missense	3036	exon2			ACCTCGCGCTTGC	U59269	CCDS12838.1, CCDS74436.1	19q13.3-q13.4	2013-02-22			ENSG00000105509	ENSG00000105509	2.4.1.212	"Glycosyltransferase family 2 domain containing"	4818	protein-coding gene	gene with protein product		601463		HAS		9169154	Standard	XM_005258834		Approved		uc002pxo.1	Q92839		ENST00000222115.1:c.647G>A	chr19.hg19:g.52222514C>T	ENSP00000222115:p.Arg216His	56.0	0.0		64.0	27.0	NM_001523	Q14470|Q9NS49	Missense_Mutation	SNP	ENST00000222115.1	hg19	CCDS12838.1	.	.	.	.	.	.	.	.	.	.	.	28.2	4.900084	0.92035	.	.	ENSG00000105509	ENST00000540069;ENST00000222115;ENST00000376737;ENST00000376738	T;T	0.59224	0.28;0.28	3.79	3.79	0.43588	.	0.000000	0.64402	D	0.000001	T	0.79690	0.4489	M	0.91972	3.26	0.58432	D	0.999997	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.84857	0.0817	10	0.87932	D	0	-20.6314	13.4921	0.61402	0.0:1.0:0.0:0.0	.	215;216;215	G3V1S7;Q92839;Q8IYH3	.;HAS1_HUMAN;.	H	215;216;70;70	ENSP00000445021:R215H;ENSP00000222115:R216H	ENSP00000222115:R216H	R	-	2	0	HAS1	56914326	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.424000	0.80242	1.812000	0.52913	0.423000	0.28283	CGC	.	.		0.657	HAS1-005	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466953.1	NM_001523		T	52222514	C	T	52222514	3	4	369	1	0	0	0	0	1	0	0	0	6970	768	27	1	1105	1	HAS1	19	52222514	Missense_Mutation	SNP	C	TCGA-ZP-A9D4-01A-11D-A36X-10	7482579	52222514	6906469	60	51188										
ZNF813	126017	hgsc.bcm.edu	37	chr19	53995222	53995222	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	tcatactggagagaaaccttAcaagtgtaatgaatgtggca	10	6	1	2			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr19:53995222A>T	ENST00000396403.4	+	4	1864	c.1736A>T	c.(1735-1737)tAc>tTc	p.Y579F	ZNF813_ENST00000396421.4_Intron	NM_001004301.3	NP_001004301.2	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	579					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)		GAGAAACCTTACAAGTGTAAT	0.373																																					p.Y579F		Atlas-SNP	.											.	ZNF813	81	.	0			c.A1736T						.						41	43	42					19																	53995222		2199	4298	6497	SO:0001583	missense	126017	exon4			AACCTTACAAGTG	AK091460	CCDS46172.1	19q13.41	2013-01-08			ENSG00000198346	ENSG00000198346		"Zinc fingers, C2H2-type", "-"	33257	protein-coding gene	gene with protein product							Standard	NM_001004301		Approved	FLJ16542	uc002qbu.2	Q6ZN06	OTTHUMG00000158309	ENST00000396403.4:c.1736A>T	chr19.hg19:g.53995222A>T	ENSP00000379684:p.Tyr579Phe	174.0	0.0		144.0	60.0	NM_001004301		Missense_Mutation	SNP	ENST00000396403.4	hg19	CCDS46172.1	.	.	.	.	.	.	.	.	.	.	a	11.10	1.538031	0.27475	.	.	ENSG00000198346	ENST00000396403	T	0.18338	2.22	1.28	-0.352	0.12598	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.15132	0.0365	N	0.13299	0.325	0.09310	N	0.999994	P	0.45768	0.866	P	0.55112	0.769	T	0.21245	-1.0251	9	0.42905	T	0.14	.	5.0799	0.14651	0.3851:0.0:0.0:0.6149	.	579	Q6ZN06	ZN813_HUMAN	F	579	ENSP00000379684:Y579F	ENSP00000379684:Y579F	Y	+	2	0	ZNF813	58687034	0.000000	0.05858	0.147000	0.22382	0.094000	0.18550	-0.643000	0.05421	0.383000	0.24910	0.158000	0.16466	TAC	.	.		0.373	ZNF813-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350638.1	NM_001004301		T	53995222	A	T	53995222	3	4	369	1	0	0	0	0	1	0	0	0	18190	391	14	4	1746	4	ZNF813	19	53995222	Missense_Mutation	SNP	A	TCGA-ZP-A9D4-01A-11D-A36X-10	1772708	53995222	5133761	61	51189										
PSMG1	8624	hgsc.bcm.edu	37	chr21	40550541	40550541	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	cgacatgtgagaatagttatCtgcatgttcttccttggaca	9	8	2	1			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr21:40550541C>G	ENST00000331573.3	-	5	954	c.489G>C	c.(487-489)caG>caC	p.Q163H	PSMG1_ENST00000380900.2_Missense_Mutation_p.Q142H	NM_001261824.1|NM_003720.3	NP_001248753.1|NP_003711.1	O95456	PSMG1_HUMAN	proteasome (prosome, macropain) assembly chaperone 1	163					cerebellar granule cell precursor proliferation (GO:0021930)|proteasome assembly (GO:0043248)|proteasome core complex assembly (GO:0080129)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)				autonomic_ganglia(1)|endometrium(2)|large_intestine(1)|lung(1)|skin(1)|urinary_tract(2)	8		Prostate(19;8.44e-08)				GAATAGTTATCTGCATGTTCT	0.348																																					p.Q163H		Atlas-SNP	.											.	PSMG1	11	.	0			c.G489C						.						88	88	88					21																	40550541		2203	4300	6503	SO:0001583	missense	8624	exon5			AGTTATCTGCATG	AJ006291	CCDS13660.1, CCDS13661.1	21q22.3	2007-10-23	2007-10-23	2007-10-23	ENSG00000183527	ENSG00000183527			3043	protein-coding gene	gene with protein product		605296	"Down syndrome critical region gene 2"	DSCR2		10872820, 17189198	Standard	NM_003720		Approved	c21-LRP, LRPC21, PAC1	uc002yxi.4	O95456	OTTHUMG00000066034	ENST00000331573.3:c.489G>C	chr21.hg19:g.40550541C>G	ENSP00000329915:p.Gln163His	131.0	0.0		159.0	72.0	NM_003720	B5BUN2|Q6FHA3|Q6FHD3|Q6S713	Missense_Mutation	SNP	ENST00000331573.3	hg19	CCDS13660.1	.	.	.	.	.	.	.	.	.	.	C	15.22	2.768698	0.49680	.	.	ENSG00000183527	ENST00000331573;ENST00000380900	T;T	0.29917	1.55;1.55	5.5	-0.945	0.10388	.	0.295226	0.37348	N	0.002123	T	0.39384	0.1076	M	0.72479	2.2	0.32517	N	0.536789	P;D	0.54047	0.955;0.964	P;P	0.55785	0.66;0.784	T	0.48958	-0.8988	10	0.59425	D	0.04	-20.6822	6.0761	0.19915	0.1254:0.3692:0.0:0.5055	.	142;163	O95456-2;O95456	.;PSMG1_HUMAN	H	163;142	ENSP00000329915:Q163H;ENSP00000370286:Q142H	ENSP00000329915:Q163H	Q	-	3	2	PSMG1	39472411	0.994000	0.37717	0.213000	0.23690	0.882000	0.50991	0.248000	0.18198	-0.248000	0.09583	-0.251000	0.11542	CAG	.	.		0.348	PSMG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141404.2	NM_003720		G	40550541	C	G	40550541	3	3	369	1	0	0	0	0	1	0	0	0	12723	912	32	4	389	4	PSMG1	21	40550541	Missense_Mutation	SNP	C	TCGA-ZP-A9D4-01A-11D-A36X-10		40550541	7579354	62	51190										
SCUBE1	80274	hgsc.bcm.edu	37	chr22	43634957	43634957	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	ctccgttattgactgcgcacGtctctggggagggaaagaga	14	9	1	2			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chr22:43634957G>A	ENST00000360835.4	-	7	857	c.731C>T	c.(730-732)aCg>aTg	p.T244M	Z82214.2_ENST00000419643.1_RNA|SCUBE1_ENST00000290460.7_Missense_Mutation_p.T274M	NM_173050.3	NP_766638.2	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1	244	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|post-embryonic development (GO:0009791)|protein homooligomerization (GO:0051260)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extrinsic component of plasma membrane (GO:0019897)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)	p.T244M(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(4)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_neural(38;0.0414)|Ovarian(80;0.07)				GACTGCGCACGTCTCTGGGGA	0.582																																					p.T244M		Atlas-SNP	.											SCUBE1,NS,carcinoma,0,1	SCUBE1	105	.	1	Substitution - Missense(1)	lung(1)	c.C731T						.						48	43	45					22																	43634957		2203	4300	6503	SO:0001583	missense	80274	exon7			GCGCACGTCTCTG		CCDS14048.1	22q13	2008-07-01			ENSG00000159307	ENSG00000159307			13441	protein-coding gene	gene with protein product		611746				11087664	Standard	NM_173050		Approved		uc003bdt.2	Q8IWY4	OTTHUMG00000150679	ENST00000360835.4:c.731C>T	chr22.hg19:g.43634957G>A	ENSP00000354080:p.Thr244Met	153.0	0.0		124.0	44.0	NM_173050	Q5R336	Missense_Mutation	SNP	ENST00000360835.4	hg19	CCDS14048.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.8|25.8	4.671195|4.671195	0.88348|0.88348	.|.	.|.	ENSG00000159307|ENSG00000159307	ENST00000381243|ENST00000360835;ENST00000434132;ENST00000290460	.|D;D	.|0.88741	.|-2.05;-2.42	5.57|5.57	5.57|5.57	0.84162|0.84162	.|Epidermal growth factor-like (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.93360|0.93360	0.7883|0.7883	L|L	0.53249|0.53249	1.67|1.67	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.83275	.|0.97;0.996	D|D	0.93418|0.93418	0.6774|0.6774	6|10	0.87932|0.62326	D|D	0|0.03	.|.	19.1674|19.1674	0.93562|0.93562	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|274;244	.|B1AH90;Q8IWY4	.|.;SCUB1_HUMAN	C|M	37|244;244;274	.|ENSP00000354080:T244M;ENSP00000290460:T274M	ENSP00000370642:R37C|ENSP00000290460:T274M	R|T	-|-	1|2	0|0	SCUBE1|SCUBE1	41964901|41964901	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.644000|0.644000	0.38419|0.38419	7.806000|7.806000	0.86020|0.86020	2.630000|2.630000	0.89119|0.89119	0.655000|0.655000	0.94253|0.94253	CGT|ACG	.	.		0.582	SCUBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319582.3	NM_173050		A	43634957	G	A	43634957	3	1	369	1	0	0	0	0	1	0	0	0	13959	1145	40	1	2299	1	SCUBE1	22	43634957	Missense_Mutation	SNP	G	TCGA-ZP-A9D4-01A-11D-A36X-10		43634957	7669609	63	51191										
FRMPD4	9758	hgsc.bcm.edu	37	chrX	12632900	12632900	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	cattctatttgtctccaggtGgcccctctgaaggcaagctg	10	12	3	1			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chrX:12632900G>A	ENST00000380682.1	+	4	828	c.322G>A	c.(322-324)Ggc>Agc	p.G108S	7SK_ENST00000606842.1_RNA	NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	108	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				positive regulation of synapse structural plasticity (GO:0051835)	cytoskeleton (GO:0005856)|dendritic spine (GO:0043197)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						GTCTCCAGGTGGCCCCTCTGA	0.507																																					p.G108S		Atlas-SNP	.											.	FRMPD4	214	.	0			c.G322A						.						107	103	104					X																	12632900		2203	4300	6503	SO:0001583	missense	9758	exon4			CCAGGTGGCCCCT	AB002314	CCDS35201.1	Xp22.31	2006-02-09	2006-02-09	2006-02-09	ENSG00000169933	ENSG00000169933			29007	protein-coding gene	gene with protein product		300838	"PDZ domain containing 10"	PDZK10, PDZD10		9205841	Standard	NM_014728		Approved	KIAA0316	uc004cuz.2	Q14CM0	OTTHUMG00000021138	ENST00000380682.1:c.322G>A	chrX.hg19:g.12632900G>A	ENSP00000370057:p.Gly108Ser	177.0	0.0		134.0	55.0	NM_014728	A8K0X9|O15032	Missense_Mutation	SNP	ENST00000380682.1	hg19	CCDS35201.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.962069	0.74016	.	.	ENSG00000169933	ENST00000380682;ENST00000429478;ENST00000304087	T	0.29142	1.58	5.4	5.4	0.78164	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.53818	0.1820	L	0.58101	1.795	0.58432	D	0.999999	D;D	0.76494	0.999;0.972	D;P	0.77004	0.989;0.888	T	0.54807	-0.8238	10	0.59425	D	0.04	.	18.3276	0.90259	0.0:0.0:1.0:0.0	.	100;108	B7ZLE1;Q14CM0	.;FRPD4_HUMAN	S	108;99;97	ENSP00000370057:G108S	ENSP00000304583:G97S	G	+	1	0	FRMPD4	12542821	1.000000	0.71417	1.000000	0.80357	0.013000	0.08279	9.221000	0.95188	2.268000	0.75426	0.594000	0.82650	GGC	.	.		0.507	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055771.1	XM_045712		A	12632900	G	A	12632900	3	1	369	1	0	0	0	0	1	0	0	0	6067	1348	47	3	336	3	FRMPD4	23	12632900	Missense_Mutation	SNP	G	TCGA-ZP-A9D4-01A-11D-A36X-10		12632900	142637660	64	51192										
ATRX	546	hgsc.bcm.edu	37	chrX	76938720	76938720	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0923076923076923	6	1	1.33545310015898	2.52252252252252	0.908108108108108	1	1	0	tcattacattcttcatctgaAttagatgttacagggttagt	7	6	4	2			TCGA-ZP-A9D4-01A-11D-A36X-10	TCGA-ZP-A9D4-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a6d2530-b2f0-4021-988f-4a0f41cae737	e029bef5-a63c-42bb-9902-0acc5f1bb090	g.chrX:76938720A>G	ENST00000373344.5	-	9	2242	c.2028T>C	c.(2026-2028)aaT>aaC	p.N676N	ATRX_ENST00000395603.3_Silent_p.N638N|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	676					ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						CTTCATCTGAATTAGATGTTA	0.373			"Mis, F, N"		"Pancreatic neuroendocrine tumors, paediatric GBM"		ATR-X (alpha thalassemia/mental retardation) syndrome																														p.N676N		Atlas-SNP	.		Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	.	ATRX	833	.	1	Unknown(1)	bone(1)	c.T2028C						.						134	134	134					X																	76938720		2203	4293	6496	SO:0001819	synonymous_variant	546	exon9			ATCTGAATTAGAT	U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"RAD54 homolog (S. cerevisiae)"	300032	"alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)", "Juberg-Marsidi syndrome"	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.2028T>C	chrX.hg19:g.76938720A>G		82.0	0.0		100.0	37.0	NM_000489	D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Silent	SNP	ENST00000373344.5	hg19	CCDS14434.1																																																																																			.	.		0.373	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		G	76938720	A	G	76938720	2	3	369	1	0	0	0	0	0	0	0	1	1208	98	4	2		2	ATRX	23	76938720	Silent	SNP	A	TCGA-ZP-A9D4-01A-11D-A36X-10	64305820	76938720	78331840	65	51193										
ARID1A	8289	hgsc.bcm.edu	37	chr1	27106649	27106649	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	ttgcctgcctgtcctggacgGactcctacactgggcagttt	11	13	0	0			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr1:27106649G>A	ENST00000324856.7	+	20	6631	c.6260G>A	c.(6259-6261)gGa>gAa	p.G2087E	ARID1A_ENST00000457599.2_Missense_Mutation_p.G1870E|ARID1A_ENST00000374152.2_Missense_Mutation_p.G1704E|ARID1A_ENST00000540690.1_Missense_Mutation_p.G415E	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	2087			G -> R (found in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:22009941}.		androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)	p.G2087E(1)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		GTCCTGGACGGACTCCTACAC	0.587			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.G2087E		Atlas-SNP	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	ARID1A,NS,adenocarcinoma,0,2	ARID1A	842	.	1	Substitution - Missense(1)	liver(1)	c.G6260A						.						89	87	88					1																	27106649		2203	4300	6503	SO:0001583	missense	8289	exon20			TGGACGGACTCCT	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.6260G>A	chr1.hg19:g.27106649G>A	ENSP00000320485:p.Gly2087Glu	125.0	1.0		104.0	28.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Missense_Mutation	SNP	ENST00000324856.7	hg19	CCDS285.1	.	.	.	.	.	.	.	.	.	.	G	18.01	3.528439	0.64860	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000374152;ENST00000540690	T;T;T;T	0.56611	0.45;0.45;0.45;0.45	5.07	5.07	0.68467	.	0.051909	0.85682	D	0.000000	T	0.76054	0.3934	M	0.83953	2.67	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	T	0.79291	-0.1864	10	0.87932	D	0	-4.2604	19.0485	0.93032	0.0:0.0:1.0:0.0	.	1704;2087;1870	O14497-3;O14497;O14497-2	.;ARI1A_HUMAN;.	E	2087;1870;1704;415	ENSP00000320485:G2087E;ENSP00000387636:G1870E;ENSP00000363267:G1704E;ENSP00000442437:G415E	ENSP00000320485:G2087E	G	+	2	0	ARID1A	26979236	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.413000	0.97351	2.814000	0.96858	0.585000	0.79938	GGA	.	.		0.587	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		A	27106649	G	A	27106649	3	1	370	1	0	0	0	0	1	0	0	0	913	1174	41	3	6338	3	ARID1A	1	27106649	Missense_Mutation	SNP	G	TCGA-ZS-A9CD-01A-11D-A36X-10		27106649	222143972	1	51194										
CSMD2	114784	hgsc.bcm.edu	37	chr1	34204787	34204787	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	cagaccacgctgccctccttCaggacgcaggtgatggtctc	11	15	2	2			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr1:34204787C>T	ENST00000373381.4	-	15	2498	c.2322G>A	c.(2320-2322)ctG>ctA	p.L774L		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	734	CUB 5. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				TGCCCTCCTTCAGGACGCAGG	0.617																																					p.L734L		Atlas-SNP	.											.	CSMD2	946	.	0			c.G2202A						.						54	49	50					1																	34204787		2203	4300	6503	SO:0001819	synonymous_variant	114784	exon15			CTCCTTCAGGACG	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.2322G>A	chr1.hg19:g.34204787C>T		100.0	0.0		83.0	22.0	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Silent	SNP	ENST00000373381.4	hg19																																																																																				.	.		0.617	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896		T	34204787	C	T	34204787	2	4	370	1	0	0	0	0	0	0	0	1	3947	813	29	3		3	CSMD2	1	34204787	Silent	SNP	C	TCGA-ZS-A9CD-01A-11D-A36X-10	7098138	34204787	215045834	2	51195										
KCNC4	3749	hgsc.bcm.edu	37	chr1	110766436	110766436	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	gtcacccatgtactgcaagtCtgaggagacttccccccggg	11	14	2	2			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr1:110766436C>T	ENST00000369787.3	+	2	1556	c.1529C>T	c.(1528-1530)tCt>tTt	p.S510F	KCNC4_ENST00000438661.2_Missense_Mutation_p.S510F|KCNC4_ENST00000412512.2_Intron|KCNC4_ENST00000413138.3_Missense_Mutation_p.S510F	NM_004978.4	NP_004969.2	Q03721	KCNC4_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 4	510					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of neurotransmitter secretion (GO:0046928)|synaptic transmission (GO:0007268)	axon terminus (GO:0043679)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(2)|lung(11)|ovary(1)|skin(2)	32		all_cancers(81;9.88e-06)|all_epithelial(167;3.23e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0238)|all cancers(265;0.0693)|Epithelial(280;0.0748)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.135)		TACTGCAAGTCTGAGGAGACT	0.607																																					p.S510F		Atlas-SNP	.											.	KCNC4	113	.	0			c.C1529T						.						71	78	75					1																	110766436		2203	4300	6503	SO:0001583	missense	3749	exon2			GCAAGTCTGAGGA	BC101769	CCDS821.1, CCDS44193.1	1p21	2012-07-05			ENSG00000116396	ENSG00000116396		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6236	protein-coding gene	gene with protein product		176265	"chromosome 1 open reading frame 30"	C1orf30		1920536, 1740329, 16382104	Standard	NM_004978		Approved	Kv3.4, HKSHIIIC	uc001dzh.3	Q03721	OTTHUMG00000011037	ENST00000369787.3:c.1529C>T	chr1.hg19:g.110766436C>T	ENSP00000358802:p.Ser510Phe	114.0	0.0		118.0	31.0	NM_001039574	Q3MIM4|Q5TBI6	Missense_Mutation	SNP	ENST00000369787.3	hg19	CCDS821.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.305965	0.81247	.	.	ENSG00000116396	ENST00000369787;ENST00000413138;ENST00000438661	D;D;D	0.97378	-4.36;-4.36;-4.36	4.89	4.89	0.63831	.	2.911490	0.01276	N	0.009589	D	0.98077	0.9366	L	0.57536	1.79	0.80722	D	1	D;D;D	0.71674	0.997;0.998;0.961	D;D;P	0.67382	0.929;0.951;0.875	D	0.90954	0.4807	10	0.62326	D	0.03	.	18.0014	0.89198	0.0:1.0:0.0:0.0	.	510;510;510	Q03721;Q03721-3;Q03721-2	KCNC4_HUMAN;.;.	F	510	ENSP00000358802:S510F;ENSP00000388029:S510F;ENSP00000393655:S510F	ENSP00000358802:S510F	S	+	2	0	KCNC4	110567959	1.000000	0.71417	0.942000	0.38095	0.990000	0.78478	7.818000	0.86416	2.422000	0.82143	0.462000	0.41574	TCT	.	.		0.607	KCNC4-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052146.2	NM_001039574		T	110766436	C	T	110766436	3	4	370	1	0	0	0	0	1	0	0	0	8026	913	32	3	1535	3	KCNC4	1	110766436	Missense_Mutation	SNP	C	TCGA-ZS-A9CD-01A-11D-A36X-10	76561649	110766436	138484185	3	51196										
ADAM30	11085	hgsc.bcm.edu	37	chr1	120436590	120436591	+	Frame_Shift_Ins	INS	-	-	T													0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	agtatggattgcccggttacINStttttttgtttcttgacact							TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr1:120436590_120436591insT	ENST00000369400.1	-	1	2527_2528	c.2369_2370insA	c.(2368-2370)aagfs	p.K790fs		NM_021794.3	NP_068566.2	Q9UKF2	ADA30_HUMAN	ADAM metallopeptidase domain 30	790					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(16)|ovary(2)|skin(2)	38	all_cancers(5;7.07e-10)|all_epithelial(5;1.62e-10)|all_neural(166;0.153)|Breast(55;0.234)	all_lung(203;1.55e-06)|Lung NSC(69;1.04e-05)|all_epithelial(167;0.00138)		Lung(183;0.0204)|LUSC - Lung squamous cell carcinoma(189;0.117)		TGCCCGGTTACTTTTTTTGTTT	0.356																																					p.K790fs		Atlas-INDEL	.											.	ADAM30	88	.	0			c.2370_2371insA						.																																			SO:0001589	frameshift_variant	11085	exon1			.	AF171932	CCDS907.1	1p12	2012-05-16	2005-08-18		ENSG00000134249	ENSG00000134249		"ADAM metallopeptidase domain containing"	208	protein-coding gene	gene with protein product		604779	"a disintegrin and metalloproteinase domain 30"				Standard	NM_021794		Approved	svph4	uc001eij.3	Q9UKF2	OTTHUMG00000012176	ENST00000369400.1:c.2370dupA	chr1.hg19:g.120436597_120436597dupT	ENSP00000358407:p.Lys790fs	70.0	0.0		74.0	17.0	NM_021794	A8K8W8|Q5T3X6|Q9UKF1	Frame_Shift_Ins	INS	ENST00000369400.1	hg19	CCDS907.1																																																																																			.	.		0.356	ADAM30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033678.1	NM_021794		T	120436591	-	T	120436590	7	5	370	1	0	1	1	0	0	0	0	0	248	564	20	0	6	0	ADAM30	1	120436590	Frame_Shift_Ins	INS	-	TCGA-ZS-A9CD-01A-11D-A36X-10	9670154	120436590	128814031	4	51197										
LCE1F	353137	hgsc.bcm.edu	37	chr1	152749007	152749007	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	gctccggaggctgctgtggcTccagctctgggggctgctgc	17	13	1	0	rs544759833	byFrequency	TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr1:152749007T>A	ENST00000334371.2	+	1	160	c.160T>A	c.(160-162)Tcc>Acc	p.S54T		NM_178354.2	NP_848131.1	Q5T754	LCE1F_HUMAN	late cornified envelope 1F	54					keratinization (GO:0031424)					kidney(1)|large_intestine(2)|lung(7)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGCTGTGGCTCCAGCTCTGG	0.682																																					p.S54T		Atlas-SNP	.											.	LCE1F	42	.	0			c.T160A						.						37	40	39					1																	152749007		2202	4300	6502	SO:0001583	missense	353137	exon1			TGTGGCTCCAGCT		CCDS1023.1	1q21.3	2008-02-05			ENSG00000240386	ENSG00000240386		"Late cornified envelopes"	29467	protein-coding gene	gene with protein product		612608				11698679	Standard	NM_178354		Approved	LEP6	uc010pdv.2	Q5T754	OTTHUMG00000012403	ENST00000334371.2:c.160T>A	chr1.hg19:g.152749007T>A	ENSP00000334187:p.Ser54Thr	320.0	0.0		285.0	17.0	NM_178354		Missense_Mutation	SNP	ENST00000334371.2	hg19	CCDS1023.1	.	.	.	.	.	.	.	.	.	.	T	8.025	0.760389	0.15914	.	.	ENSG00000240386	ENST00000334371	T	0.04360	3.64	2.56	-2.1	0.07210	.	.	.	.	.	T	0.01800	0.0057	L	0.59436	1.845	0.09310	N	0.999992	B	0.20988	0.05	B	0.15870	0.014	T	0.42616	-0.9441	9	0.87932	D	0	.	6.7639	0.23556	0.0:0.5552:0.0:0.4448	.	54	Q5T754	LCE1F_HUMAN	T	54	ENSP00000334187:S54T	ENSP00000334187:S54T	S	+	1	0	LCE1F	151015631	0.024000	0.19004	0.207000	0.23584	0.986000	0.74619	0.132000	0.15891	-0.478000	0.06823	-0.380000	0.06706	TCC	.	.		0.682	LCE1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034523.2	NM_178354		A	152749007	T	A	152749007	3	1	370	1	0	0	0	0	1	0	0	0	8673	1551	54	4	162	4	LCE1F	1	152749007	Missense_Mutation	SNP	T	TCGA-ZS-A9CD-01A-11D-A36X-10	32312417	152749007	96501614	5	51198										
DUSP27	92235	hgsc.bcm.edu	37	chr1	167095804	167095804	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	ctcggagagcacctgggacgCatggaacgagaggctgctgg	17	10	0	2			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr1:167095804C>T	ENST00000361200.2	+	6	1602	c.1436C>T	c.(1435-1437)gCa>gTa	p.A479V	DUSP27_ENST00000443333.1_Missense_Mutation_p.A479V|DUSP27_ENST00000485151.1_Intron|DUSP27_ENST00000271385.5_Missense_Mutation_p.A479V			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	479					protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						ACCTGGGACGCATGGAACGAG	0.642																																					p.A479V		Atlas-SNP	.											.	DUSP27	235	.	0			c.C1436T						.						31	31	31					1																	167095804		2203	4300	6503	SO:0001583	missense	92235	exon5			GGGACGCATGGAA	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.1436C>T	chr1.hg19:g.167095804C>T	ENSP00000354483:p.Ala479Val	262.0	0.0		249.0	101.0	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	hg19	CCDS30932.1	.	.	.	.	.	.	.	.	.	.	C	11.23	1.577097	0.28092	.	.	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.02656	4.21;4.21;4.21	5.27	-1.26	0.09376	.	0.976965	0.08432	N	0.946804	T	0.00608	0.0020	N	0.08118	0	0.23506	N	0.997539	B	0.02656	0.0	B	0.01281	0.0	T	0.45731	-0.9241	10	0.54805	T	0.06	-4.8606	10.0593	0.42263	0.0:0.3425:0.0:0.6575	.	479	Q5VZP5	DUS27_HUMAN	V	479	ENSP00000354483:A479V;ENSP00000271385:A479V;ENSP00000404874:A479V	ENSP00000271385:A479V	A	+	2	0	DUSP27	165362428	0.999000	0.42202	0.323000	0.25347	0.357000	0.29423	2.544000	0.45761	-0.541000	0.06257	-0.796000	0.03273	GCA	.	.		0.642	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426		T	167095804	C	T	167095804	3	4	370	1	0	0	0	0	1	0	0	0	4826	710	25	3	1454	3	DUSP27	1	167095804	Missense_Mutation	SNP	C	TCGA-ZS-A9CD-01A-11D-A36X-10	14346797	167095804	82154817	6	51199										
APOB	338	hgsc.bcm.edu	37	chr2	21236228	21236228	+	Frame_Shift_Del	DEL	A	A	-													0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	tgatacaacttgggaatggtAaaagtagggacttggaactc							TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr2:21236228delA	ENST00000233242.1	-	25	4147	c.4020delT	c.(4018-4020)tttfs	p.F1340fs		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	1340					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGGGAATGGTAAAAGTAGGGA	0.488																																					p.T1341fs		Atlas-INDEL	.											.	APOB	761	.	0			c.4021delA						.						153	147	149					2																	21236228		2203	4300	6503	SO:0001589	frameshift_variant	338	exon25			.	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.4020delT	chr2.hg19:g.21236228delA	ENSP00000233242:p.Phe1340fs	122.0	0.0		136.0	26.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Frame_Shift_Del	DEL	ENST00000233242.1	hg19	CCDS1703.1																																																																																			.	.		0.488	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			-	21236228	A	-	21236228	7	5	370	1	0	1	0	1	0	0	0	0	785	359	13	0	9691	0	APOB	2	21236228	Frame_Shift_Del	DEL	A	TCGA-ZS-A9CD-01A-11D-A36X-10		21236228	221963145	7	51200										
TTC7A	57217	hgsc.bcm.edu	37	chr2	47184111	47184111	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	ggagaacaagcccctgtatcAgatgcggctgctgtcggagg	15	10	1	2			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr2:47184111A>G	ENST00000319190.5	+	3	850	c.482A>G	c.(481-483)cAg>cGg	p.Q161R	TTC7A_ENST00000409245.1_Missense_Mutation_p.Q127R|TTC7A_ENST00000394850.2_Missense_Mutation_p.Q161R|TTC7A_ENST00000461601.1_3'UTR|RP11-15I20.1_ENST00000607950.1_RNA|TTC7A_ENST00000263737.6_5'UTR	NM_020458.2	NP_065191.2	Q9ULT0	TTC7A_HUMAN	tetratricopeptide repeat domain 7A	161					cellular iron ion homeostasis (GO:0006879)|hemopoiesis (GO:0030097)					breast(4)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			CCCCTGTATCAGATGCGGCTG	0.577																																					p.Q161R		Atlas-SNP	.											.	TTC7A	80	.	0			c.A482G						.						121	118	119					2																	47184111		2203	4300	6503	SO:0001583	missense	57217	exon3			TGTATCAGATGCG	AB032966	CCDS33193.1, CCDS74510.1, CCDS74511.1	2p16.3	2013-01-10	2004-06-02	2004-06-02	ENSG00000068724	ENSG00000068724		"Tetratricopeptide (TTC) repeat domain containing"	19750	protein-coding gene	gene with protein product		609332	"tetratricopeptide repeat domain 7"	TTC7		10574461	Standard	XM_005264439		Approved	KIAA1140	uc002rvo.3	Q9ULT0	OTTHUMG00000153121	ENST00000319190.5:c.482A>G	chr2.hg19:g.47184111A>G	ENSP00000316699:p.Gln161Arg	124.0	0.0		128.0	26.0	NM_020458	Q6PIX4|Q8ND67|Q9BUS3	Missense_Mutation	SNP	ENST00000319190.5	hg19	CCDS33193.1	.	.	.	.	.	.	.	.	.	.	A	5.672	0.308568	0.10733	.	.	ENSG00000068724	ENST00000409245;ENST00000319190;ENST00000394850	T;T;T	0.28454	2.02;2.03;1.61	5.84	5.84	0.93424	Tetratricopeptide-like helical (1);	0.311397	0.33515	N	0.004839	T	0.19248	0.0462	N	0.26042	0.785	0.80722	D	1	B;B;B	0.18610	0.029;0.015;0.0	B;B;B	0.12837	0.006;0.008;0.002	T	0.12116	-1.0560	10	0.13853	T	0.58	-24.2038	9.1628	0.37032	0.7413:0.0:0.0:0.2587	.	161;161;127	Q2T9J9;Q9ULT0;G5E9G4	.;TTC7A_HUMAN;.	R	127;161;161	ENSP00000386307:Q127R;ENSP00000316699:Q161R;ENSP00000378320:Q161R	ENSP00000316699:Q161R	Q	+	2	0	TTC7A	47037615	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.223000	0.51231	2.234000	0.73211	0.459000	0.35465	CAG	.	.		0.577	TTC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329667.2	XM_372927		G	47184111	A	G	47184111	3	3	370	1	0	0	0	0	1	0	0	0	16727	188	7	2	492	2	TTC7A	2	47184111	Missense_Mutation	SNP	A	TCGA-ZS-A9CD-01A-11D-A36X-10	25947883	47184111	196015262	8	51201										
CNGA3	1261	hgsc.bcm.edu	37	chr2	99013428	99013428	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	ccgaagccaagaaggccctgGaggagaaaggacggcagatc	15	10	0	3	rs376992789		TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr2:99013428G>A	ENST00000272602.2	+	7	1834	c.1795G>A	c.(1795-1797)Gag>Aag	p.E599K	CNGA3_ENST00000393504.1_Missense_Mutation_p.E599K|CNGA3_ENST00000436404.2_Missense_Mutation_p.E581K|CNGA3_ENST00000409937.1_Missense_Mutation_p.E603K			Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3	599					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to magnesium ion (GO:0032026)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|photoreceptor outer segment membrane (GO:0042622)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(17)|ovary(5)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	49						GAAGGCCCTGGAGGAGAAAGG	0.592																																					p.E599K		Atlas-SNP	.											.	CNGA3	118	.	0			c.G1795A						.	G	LYS/GLU,LYS/GLU	2,4404	4.2+/-10.8	0,2,2201	39	41	40		1741,1795	5.4	1	2		40	0,8600		0,0,4300	no	missense,missense	CNGA3	NM_001079878.1,NM_001298.2	56,56	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	probably-damaging,probably-damaging	581/677,599/695	99013428	2,13004	2203	4300	6503	SO:0001583	missense	1261	exon8			GCCCTGGAGGAGA	S76069	CCDS2034.1, CCDS42719.1	2q11.2	2013-01-08			ENSG00000144191	ENSG00000144191		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2150	protein-coding gene	gene with protein product		600053		CNCG3, ACHM2		7532814, 9517456, 16382102	Standard	NM_001298		Approved	CCNC1, CCNCa, CNG3	uc002syt.3	Q16281	OTTHUMG00000130561	ENST00000272602.2:c.1795G>A	chr2.hg19:g.99013428G>A	ENSP00000272602:p.Glu599Lys	102.0	0.0		88.0	28.0	NM_001298	E9PF93|Q4VAP7|Q53RD2|Q6ZNA7|Q9UP64	Missense_Mutation	SNP	ENST00000272602.2	hg19	CCDS2034.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.055037	0.75960	4.54E-4	0.0	ENSG00000144191	ENST00000393504;ENST00000436404;ENST00000272602;ENST00000409937	D;D;D;D	0.96587	-4.06;-4.06;-4.06;-4.06	5.42	5.42	0.78866	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.97983	0.9336	M	0.85299	2.745	0.80722	D	1	D;P;B	0.58620	0.983;0.944;0.255	P;P;B	0.61477	0.889;0.76;0.095	D	0.97873	1.0287	10	0.49607	T	0.09	.	18.154	0.89686	0.0:0.0:1.0:0.0	.	603;581;599	E9PF93;Q4VAP7;Q16281	.;.;CNGA3_HUMAN	K	599;581;599;603	ENSP00000377140:E599K;ENSP00000410070:E581K;ENSP00000272602:E599K;ENSP00000386761:E603K	ENSP00000272602:E599K	E	+	1	0	CNGA3	98379860	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.263000	0.95617	2.826000	0.97356	0.563000	0.77884	GAG	.	.		0.592	CNGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252986.1	NM_001298		A	99013428	G	A	99013428	3	1	370	1	0	0	0	0	1	0	0	0	3600	1175	41	3	1821	3	CNGA3	2	99013428	Missense_Mutation	SNP	G	TCGA-ZS-A9CD-01A-11D-A36X-10	51829317	99013428	144185945	9	51202										
REV1	51455	hgsc.bcm.edu	37	chr2	100058822	100058822	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	tatattgcttggacctggcaGaggatcctcaggtctgcata	11	9	2	1			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr2:100058822G>A	ENST00000258428.3	-	5	688	c.460C>T	c.(460-462)Ctg>Ttg	p.L154L	REV1_ENST00000393445.3_Silent_p.L154L|REV1_ENST00000465835.1_5'UTR	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)	154					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|error-prone translesion synthesis (GO:0042276)|response to UV (GO:0009411)	nucleoplasm (GO:0005654)	damaged DNA binding (GO:0003684)|deoxycytidyl transferase activity (GO:0017125)|DNA-directed DNA polymerase activity (GO:0003887)|magnesium ion binding (GO:0000287)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(12)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GGACCTGGCAGAGGATCCTCA	0.443								Direct reversal of damage																													p.L154L		Atlas-SNP	.											.	REV1	100	.	0			c.C460T						.						104	93	97					2																	100058822		2203	4300	6503	SO:0001819	synonymous_variant	51455	exon5			CTGGCAGAGGATC	AF206019	CCDS2045.1, CCDS42722.1	2q11.1-q11.2	2012-05-18	2012-05-18	2006-11-07	ENSG00000135945	ENSG00000135945		"DNA polymerases"	14060	protein-coding gene	gene with protein product		606134	"REV1 (yeast homolog)- like", "REV1-like (yeast)", "REV1 homolog (S. cerevisiae)"	REV1L		10536157	Standard	XM_005263968		Approved		uc002tad.3	Q9UBZ9	OTTHUMG00000130636	ENST00000258428.3:c.460C>T	chr2.hg19:g.100058822G>A		141.0	0.0		122.0	38.0	NM_001037872	O95941|Q53SI7|Q9C0J4|Q9NUP2	Silent	SNP	ENST00000258428.3	hg19	CCDS2045.1																																																																																			.	.		0.443	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253123.2	NM_016316		A	100058822	G	A	100058822	2	1	370	1	0	0	0	0	0	0	0	1	13254	933	33	3		3	REV1	2	100058822	Silent	SNP	G	TCGA-ZS-A9CD-01A-11D-A36X-10	1045394	100058822	143140551	10	51203										
BAZ2B	29994	hgsc.bcm.edu	37	chr2	160181399	160181399	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	ttcttataaccaggaacaagTttcaagtttacaggaagtag	8	6	2	0			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr2:160181399T>C	ENST00000392783.2	-	36	6771	c.6276A>G	c.(6274-6276)aaA>aaG	p.K2092K	BAZ2B_ENST00000392782.1_Silent_p.K2056K|BAZ2B_ENST00000355831.2_Silent_p.K2058K|BAZ2B_ENST00000343439.5_Silent_p.K1992K	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	2092	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						CAGGAACAAGTTTCAAGTTTA	0.328																																					p.K2092K		Atlas-SNP	.											.	BAZ2B	196	.	0			c.A6276G						.						65	61	62					2																	160181399		1801	4066	5867	SO:0001819	synonymous_variant	29994	exon36			AACAAGTTTCAAG	AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636		"Zinc fingers, PHD-type"	963	protein-coding gene	gene with protein product		605683				10662543	Standard	XM_005246488		Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.6276A>G	chr2.hg19:g.160181399T>C		379.0	0.0		349.0	14.0	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Silent	SNP	ENST00000392783.2	hg19	CCDS2209.2																																																																																			.	.		0.328	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2			C	160181399	T	C	160181399	2	2	370	1	0	0	0	0	0	0	0	1	1332	1722	60	2		2	BAZ2B	2	160181399	Silent	SNP	T	TCGA-ZS-A9CD-01A-11D-A36X-10	60122577	160181399	83017974	11	51204										
LRP2	4036	hgsc.bcm.edu	37	chr2	170002368	170002368	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	tttattttgtttccatacttCtcccttttccttagatatcc	2	11	1	1			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr2:170002368C>G	ENST00000263816.3	-	70	13162	c.12877G>C	c.(12877-12879)Gaa>Caa	p.E4293Q		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	4293					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	TTCCATACTTCTCCCTTTTCC	0.408																																					p.E4293Q		Atlas-SNP	.											.	LRP2	751	.	0			c.G12877C						.						93	87	89					2																	170002368		2203	4300	6503	SO:0001583	missense	4036	exon70			ATACTTCTCCCTT		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.12877G>C	chr2.hg19:g.170002368C>G	ENSP00000263816:p.Glu4293Gln	119.0	0.0		95.0	19.0	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	hg19	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.453537	0.84209	.	.	ENSG00000081479	ENST00000263816	D	0.91011	-2.77	5.33	5.33	0.75918	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.000000	0.85682	D	0.000000	D	0.93025	0.7780	L	0.52266	1.64	0.80722	D	1	D	0.71674	0.998	P	0.59357	0.856	D	0.92338	0.5879	10	0.44086	T	0.13	.	19.397	0.94611	0.0:1.0:0.0:0.0	.	4293	P98164	LRP2_HUMAN	Q	4293	ENSP00000263816:E4293Q	ENSP00000263816:E4293Q	E	-	1	0	LRP2	169710614	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	5.929000	0.70096	2.665000	0.90641	0.655000	0.94253	GAA	.	.		0.408	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		G	170002368	C	G	170002368	3	3	370	1	0	0	0	0	1	0	0	0	8965	922	32	4	1130	4	LRP2	2	170002368	Missense_Mutation	SNP	C	TCGA-ZS-A9CD-01A-11D-A36X-10	9820969	170002368	73197005	12	51205										
FASTKD2	22868	hgsc.bcm.edu	37	chr2	207639082	207639082	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	tctatctattcttcatacttActcttctctcaatcatgtct	1	12	9	0			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr2:207639082A>C	ENST00000236980.6	+	7	1736	c.1388A>C	c.(1387-1389)tAc>tCc	p.Y463S	FASTKD2_ENST00000403094.3_Missense_Mutation_p.Y463S|FASTKD2_ENST00000402774.3_Missense_Mutation_p.Y463S	NM_014929.3	NP_055744.2	Q9NYY8	FAKD2_HUMAN	FAST kinase domains 2	463					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(2)	21				LUSC - Lung squamous cell carcinoma(261;0.0718)|Epithelial(149;0.119)|Lung(261;0.138)		CTTCATACTTACTCTTCTCTC	0.318																																					p.Y463S		Atlas-SNP	.											.	FASTKD2	49	.	0			c.A1388C						.						115	119	118					2																	207639082		2202	4298	6500	SO:0001583	missense	22868	exon7			ATACTTACTCTTC	BC001544	CCDS2371.1	2q33.3	2008-02-05	2006-07-07	2006-07-07	ENSG00000118246	ENSG00000118246			29160	protein-coding gene	gene with protein product		612322	"KIAA0971"	KIAA0971			Standard	NM_014929		Approved		uc002vbx.3	Q9NYY8	OTTHUMG00000132917	ENST00000236980.6:c.1388A>C	chr2.hg19:g.207639082A>C	ENSP00000236980:p.Tyr463Ser	82.0	0.0		108.0	27.0	NM_001136193	Q9NVX6|Q9Y2H7	Missense_Mutation	SNP	ENST00000236980.6	hg19	CCDS2371.1	.	.	.	.	.	.	.	.	.	.	A	14.39	2.520380	0.44866	.	.	ENSG00000118246	ENST00000236980;ENST00000402774;ENST00000403094	T;T;T	0.45276	0.9;0.9;0.9	5.99	4.83	0.62350	FAST kinase leucine-rich (1);	0.201998	0.44483	N	0.000452	T	0.62502	0.2433	M	0.73598	2.24	0.49130	D	0.999754	D;D	0.89917	0.976;1.0	P;D	0.87578	0.87;0.998	T	0.64407	-0.6415	10	0.59425	D	0.04	-8.1288	11.0657	0.47974	0.9268:0.0:0.0732:0.0	.	463;463	Q9NYY8-2;Q9NYY8	.;FAKD2_HUMAN	S	463	ENSP00000236980:Y463S;ENSP00000385990:Y463S;ENSP00000384929:Y463S	ENSP00000236980:Y463S	Y	+	2	0	FASTKD2	207347327	1.000000	0.71417	0.466000	0.27168	0.164000	0.22412	5.038000	0.64177	1.083000	0.41159	0.533000	0.62120	TAC	.	.		0.318	FASTKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256428.2	NM_014929		C	207639082	A	C	207639082	3	2	370	1	0	0	0	0	1	0	0	0	5694	391	14	5	1410	5	FASTKD2	2	207639082	Missense_Mutation	SNP	A	TCGA-ZS-A9CD-01A-11D-A36X-10	37636714	207639082	35560291	13	51206										
DOCK10	55619	hgsc.bcm.edu	37	chr2	225750511	225750511	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	tgagtcagctggaagtagcgCtttttgaatgactaaataaa	10	5	1	3			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr2:225750511C>T	ENST00000258390.7	-	7	691	c.624G>A	c.(622-624)aaG>aaA	p.K208K	DOCK10_ENST00000409592.3_Silent_p.K202K	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	208	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		GGAAGTAGCGCTTTTTGAATG	0.318																																					p.K208K		Atlas-SNP	.											.	DOCK10	308	.	0			c.G624A						.						92	85	87					2																	225750511		1822	4099	5921	SO:0001819	synonymous_variant	55619	exon7			GTAGCGCTTTTTG	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"Pleckstrin homology (PH) domain containing"	23479	protein-coding gene	gene with protein product	"zizimin3"	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.624G>A	chr2.hg19:g.225750511C>T		108.0	0.0		91.0	28.0	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Silent	SNP	ENST00000258390.7	hg19	CCDS46528.1																																																																																			.	.		0.318	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1			T	225750511	C	T	225750511	2	4	370	1	0	0	0	0	0	0	0	1	4687	796	28	3		3	DOCK10	2	225750511	Silent	SNP	C	TCGA-ZS-A9CD-01A-11D-A36X-10	18111429	225750511	17448862	14	51207										
DIS3L2	129563	hgsc.bcm.edu	37	chr2	233114009	233114009	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	gcagcctcaaccccatgtccGacaagctgaccttctctgtg	8	16	2	1			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr2:233114009G>A	ENST00000409307.1	+	11	1378	c.1378G>A	c.(1378-1380)Gac>Aac	p.D460N	DIS3L2_ENST00000325385.7_Missense_Mutation_p.D460N|DIS3L2_ENST00000273009.6_Missense_Mutation_p.D460N					DIS3 like 3'-5' exoribonuclease 2											breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(2)|urinary_tract(1)	40		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)		CCCCATGTCCGACAAGCTGAC	0.517																																					p.D460N		Atlas-SNP	.											.	DIS3L2	77	.	0			c.G1378A						.						78	85	82					2																	233114009		2194	4291	6485	SO:0001583	missense	129563	exon12			ATGTCCGACAAGC	BC026166	CCDS42834.1, CCDS58752.1, CCDS58753.1	2q37.1	2014-09-17	2014-03-05		ENSG00000144535	ENSG00000144535			28648	protein-coding gene	gene with protein product		614184	"family with sequence similarity 6, member A", "DIS3 mitotic control homolog (S. cerevisiae)-like 2"	FAM6A		22306653, 23503588	Standard	NM_152383		Approved	FLJ36974, MGC42174	uc010fxz.3	Q8IYB7	OTTHUMG00000153385	ENST00000409307.1:c.1378G>A	chr2.hg19:g.233114009G>A	ENSP00000386799:p.Asp460Asn	85.0	0.0		65.0	4.0	NM_152383		Missense_Mutation	SNP	ENST00000409307.1	hg19	CCDS42834.1	.	.	.	.	.	.	.	.	.	.	G	32	5.185256	0.94885	.	.	ENSG00000144535	ENST00000273009;ENST00000542873;ENST00000325385;ENST00000431466;ENST00000409307;ENST00000424049	T;T;T;T	0.36699	1.24;1.24;1.24;1.24	5.8	5.8	0.92144	Ribonuclease II/R (2);	0.000000	0.85682	D	0.000000	T	0.67097	0.2857	M	0.85099	2.735	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.71002	-0.4718	10	0.87932	D	0	-24.1311	20.0706	0.97721	0.0:0.0:1.0:0.0	.	460	Q8IYB7	DI3L2_HUMAN	N	460;460;460;460;460;95	ENSP00000273009:D460N;ENSP00000315569:D460N;ENSP00000386799:D460N;ENSP00000415419:D95N	ENSP00000273009:D460N	D	+	1	0	DIS3L2	232822253	1.000000	0.71417	0.982000	0.44146	0.981000	0.71138	9.164000	0.94755	2.744000	0.94065	0.655000	0.94253	GAC	.	.		0.517	DIS3L2-015	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330988.1	NM_152383		A	233114009	G	A	233114009	3	1	370	1	0	0	0	0	1	0	0	0	4539	1058	37	1	1420	1	DIS3L2	2	233114009	Missense_Mutation	SNP	G	TCGA-ZS-A9CD-01A-11D-A36X-10	7363498	233114009	10085364	15	51208										
FGD5	152273	hgsc.bcm.edu	37	chr3	14860691	14860691	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	gaacaaatgcagcaacgggcGgctgccctgtgtagacaggg	15	10	0	1	rs368711724	byFrequency	TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr3:14860691G>T	ENST00000285046.5	+	1	223	c.113G>T	c.(112-114)cGg>cTg	p.R38L	FGD5_ENST00000543601.1_5'Flank	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	38					actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			NS(2)|breast(2)|endometrium(3)|kidney(5)|large_intestine(10)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(1)	54						AGCAACGGGCGGCTGCCCTGT	0.612																																					p.R38L		Atlas-SNP	.											.	FGD5	248	.	0			c.G113T						.						29	31	30					3																	14860691		692	1591	2283	SO:0001583	missense	152273	exon1			ACGGGCGGCTGCC	AK097276	CCDS46767.1	3p25.1	2013-01-10			ENSG00000154783	ENSG00000154783		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	19117	protein-coding gene	gene with protein product		614788					Standard	NM_152536		Approved	ZFYVE23, FLJ39957, FLJ00274	uc003bzc.3	Q6ZNL6	OTTHUMG00000155556	ENST00000285046.5:c.113G>T	chr3.hg19:g.14860691G>T	ENSP00000285046:p.Arg38Leu	259.0	0.0		199.0	64.0	NM_152536	B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	Missense_Mutation	SNP	ENST00000285046.5	hg19	CCDS46767.1	.	.	.	.	.	.	.	.	.	.	G	13.63	2.293278	0.40594	.	.	ENSG00000154783	ENST00000285046	T	0.75704	-0.96	5.76	1.25	0.21368	.	0.302725	0.27609	N	0.018607	T	0.50905	0.1643	N	0.14661	0.345	0.28045	N	0.933587	B	0.27166	0.17	B	0.20577	0.03	T	0.44817	-0.9303	10	0.72032	D	0.01	-15.0555	4.8283	0.13427	0.623:0.1655:0.2114:0.0	.	38	Q6ZNL6	FGD5_HUMAN	L	38	ENSP00000285046:R38L	ENSP00000285046:R38L	R	+	2	0	FGD5	14835695	0.302000	0.24454	0.910000	0.35882	0.549000	0.35272	0.396000	0.20867	-0.002000	0.14469	0.591000	0.81541	CGG	.	.		0.612	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340628.1	NM_152536		T	14860691	G	T	14860691	3	4	370	1	0	0	0	0	1	0	0	0	5844	1116	39	1	115	1	FGD5	3	14860691	Missense_Mutation	SNP	G	TCGA-ZS-A9CD-01A-11D-A36X-10		14860691	183161739	16	51209										
BTD	686	hgsc.bcm.edu	37	chr3	15686574	15686574	+	Missense_Mutation	SNP	C	C	A													0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	gatgatgtatgacaatttcaCcctggtccctgtctggggaa					rs397514405		TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr3:15686574C>A	ENST00000303498.5	+	4	1320	c.1211C>A	c.(1210-1212)aCc>aAc	p.T404N	BTD_ENST00000383778.4_Missense_Mutation_p.T384N|BTD_ENST00000437172.1_Missense_Mutation_p.T406N|BTD_ENST00000449107.1_Missense_Mutation_p.T406N	NM_000060.2|NM_001281723.1	NP_000051.1|NP_001268652.1	P43251	BTD_HUMAN	biotinidase	404					biotin metabolic process (GO:0006768)|central nervous system development (GO:0007417)|epidermis development (GO:0008544)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|nucleolus (GO:0005730)|perikaryon (GO:0043204)	biotin carboxylase activity (GO:0004075)|biotinidase activity (GO:0047708)			breast(2)|endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	18						GACAATTTCACCCTGGTCCCT	0.498																																					p.T404N		Atlas-SNP	.											.	BTD	49	.	0			c.C1211A	GRCh37	CM021516	BTD	M		.						166	159	161					3																	15686574		2203	4300	6503	SO:0001583	missense	686	exon4			ATTTCACCCTGGT	AF018631	CCDS2628.1, CCDS63563.1, CCDS63564.1, CCDS63565.1	3p25	2007-03-26			ENSG00000169814	ENSG00000169814	3.5.1.12		1122	protein-coding gene	gene with protein product		609019				8001986	Standard	NM_001281723		Approved		uc003cah.3	P43251	OTTHUMG00000129861	ENST00000303498.5:c.1211C>A	chr3.hg19:g.15686574C>A	ENSP00000306477:p.Thr404Asn	99.0	0.0		121.0	27.0	NM_000060	A6NHF2|B2R865|B4DFX1|B4DLJ9|B7Z7C9|F8W1Q3|Q96EM9	Missense_Mutation	SNP	ENST00000303498.5	hg19	CCDS2628.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.569398	0.86439	.	.	ENSG00000169814	ENST00000449107;ENST00000303498;ENST00000437172;ENST00000383778	D;D;D;D	0.87650	-2.28;-2.28;-2.28;-2.28	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	D	0.93200	0.7834	M	0.72479	2.2	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.92466	0.5981	10	0.46703	T	0.11	-44.3738	19.5597	0.95367	0.0:1.0:0.0:0.0	.	406;406;404	A6NHF2;B4DLJ9;P43251	.;.;BTD_HUMAN	N	406;404;406;384	ENSP00000388212:T406N;ENSP00000306477:T404N;ENSP00000400995:T406N;ENSP00000373288:T384N	ENSP00000306477:T404N	T	+	2	0	BTD	15661578	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.940000	0.70187	2.641000	0.89580	0.561000	0.74099	ACC	.	.		0.498	BTD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252103.2	NM_000060		A	15686574	C	A	15686574	3	1	370	1	0	0	0	0	1	0	0	0	1552	507	18	3	1225	3	BTD	3	15686574	Missense_Mutation	SNP	C	TCGA-ZS-A9CD-01A-11D-A36X-10	825883	15686574	182335856	17	51210	268	2								
BTD	686	hgsc.bcm.edu	37	chr3	15686579	15686579	+	Missense_Mutation	SNP	G	G	T													0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	tgtatgacaatttcaccctgGtccctgtctggggaaaggaa							TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr3:15686579G>T	ENST00000303498.5	+	4	1325	c.1216G>T	c.(1216-1218)Gtc>Ttc	p.V406F	BTD_ENST00000383778.4_Missense_Mutation_p.V386F|BTD_ENST00000437172.1_Missense_Mutation_p.V408F|BTD_ENST00000449107.1_Missense_Mutation_p.V408F	NM_000060.2|NM_001281723.1	NP_000051.1|NP_001268652.1	P43251	BTD_HUMAN	biotinidase	406					biotin metabolic process (GO:0006768)|central nervous system development (GO:0007417)|epidermis development (GO:0008544)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|nucleolus (GO:0005730)|perikaryon (GO:0043204)	biotin carboxylase activity (GO:0004075)|biotinidase activity (GO:0047708)			breast(2)|endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	18						TTTCACCCTGGTCCCTGTCTG	0.498																																					p.V406F		Atlas-SNP	.											.	BTD	49	.	0			c.G1216T						.						166	158	161					3																	15686579		2203	4300	6503	SO:0001583	missense	686	exon4			ACCCTGGTCCCTG	AF018631	CCDS2628.1, CCDS63563.1, CCDS63564.1, CCDS63565.1	3p25	2007-03-26			ENSG00000169814	ENSG00000169814	3.5.1.12		1122	protein-coding gene	gene with protein product		609019				8001986	Standard	NM_001281723		Approved		uc003cah.3	P43251	OTTHUMG00000129861	ENST00000303498.5:c.1216G>T	chr3.hg19:g.15686579G>T	ENSP00000306477:p.Val406Phe	96.0	0.0		122.0	26.0	NM_000060	A6NHF2|B2R865|B4DFX1|B4DLJ9|B7Z7C9|F8W1Q3|Q96EM9	Missense_Mutation	SNP	ENST00000303498.5	hg19	CCDS2628.1	.	.	.	.	.	.	.	.	.	.	G	19.73	3.881859	0.72294	.	.	ENSG00000169814	ENST00000449107;ENST00000303498;ENST00000437172;ENST00000383778	D;D;D;D	0.87650	-2.28;-2.28;-2.28;-2.28	5.58	4.69	0.59074	.	0.182959	0.47455	D	0.000228	D	0.91683	0.7371	M	0.80847	2.515	0.48395	D	0.999647	D;D;D	0.65815	0.995;0.995;0.995	P;P;P	0.62382	0.901;0.901;0.901	D	0.90986	0.4831	10	0.45353	T	0.12	-39.4077	10.9369	0.47251	0.1436:0.0:0.8564:0.0	.	408;408;406	A6NHF2;B4DLJ9;P43251	.;.;BTD_HUMAN	F	408;406;408;386	ENSP00000388212:V408F;ENSP00000306477:V406F;ENSP00000400995:V408F;ENSP00000373288:V386F	ENSP00000306477:V406F	V	+	1	0	BTD	15661583	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	3.260000	0.51523	2.641000	0.89580	0.561000	0.74099	GTC	.	.		0.498	BTD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252103.2	NM_000060		T	15686579	G	T	15686579	3	4	370	1	0	0	0	0	1	0	0	0	1552	1261	44	3	1230	3	BTD	3	15686579	Missense_Mutation	SNP	G	TCGA-ZS-A9CD-01A-11D-A36X-10	5	15686579	182335851	18	51211	268	2								
PDCD6IP	10015	hgsc.bcm.edu	37	chr3	33883512	33883512	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	ggcatccagactgttgatcaGttgattaaagaactgcctga	10	8	1	5			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr3:33883512G>A	ENST00000307296.3	+	10	1682	c.1305G>A	c.(1303-1305)caG>caA	p.Q435Q	PDCD6IP_ENST00000457054.2_Silent_p.Q440Q			Q8WUM4	PDC6I_HUMAN	programmed cell death 6 interacting protein	435	Interaction with CHMP4A, CHMP4B and CHMP4C.|Interaction with EIAV p9.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell division (GO:0051301)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)			central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|skin(1)|stomach(1)	23						CTGTTGATCAGTTGATTAAAG	0.388																																					p.Q440Q		Atlas-SNP	.											.	PDCD6IP	62	.	0			c.G1320A						.						87	85	86					3																	33883512		2203	4300	6503	SO:0001819	synonymous_variant	10015	exon10			TGATCAGTTGATT	BC020066	CCDS2660.1, CCDS54561.1	3p22.3	2012-08-30	2001-11-29		ENSG00000170248	ENSG00000170248			8766	protein-coding gene	gene with protein product	"ALG-2 interacting protein X"	608074	"programmed cell death 6-interacting protein"			9880530	Standard	NM_001162429		Approved	Alix, AIP1, Hp95	uc003cfy.4	Q8WUM4	OTTHUMG00000130751	ENST00000307296.3:c.1305G>A	chr3.hg19:g.33883512G>A		362.0	0.0		301.0	80.0	NM_001162429	C5MQH7|E9PFU1|Q6NUS1|Q9BX86|Q9NUN0|Q9P2H2|Q9UKL5	Silent	SNP	ENST00000307296.3	hg19	CCDS2660.1																																																																																			.	.		0.388	PDCD6IP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253251.2			A	33883512	G	A	33883512	2	1	370	1	0	0	0	0	0	0	0	1	11633	1020	36	3		3	PDCD6IP	3	33883512	Silent	SNP	G	TCGA-ZS-A9CD-01A-11D-A36X-10	18196933	33883512	164138918	19	51212										
RAD54L2	23132	hgsc.bcm.edu	37	chr3	51671348	51671348	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	caacctcattgagtactggtGcatggtggactttgtgcgcc	12	10	1	1			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr3:51671348G>A	ENST00000409535.2	+	10	1636	c.1511G>A	c.(1510-1512)tGc>tAc	p.C504Y	RAD54L2_ENST00000296477.3_Missense_Mutation_p.C198Y	NM_015106.2	NP_055921.2	Q9Y4B4	ARIP4_HUMAN	RAD54-like 2 (S. cerevisiae)	504	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|transcription cofactor activity (GO:0003712)			NS(2)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|liver(2)|lung(9)|ovary(4)|skin(2)	31				BRCA - Breast invasive adenocarcinoma(193;0.000102)|Kidney(197;0.000758)|KIRC - Kidney renal clear cell carcinoma(197;0.000896)		GAGTACTGGTGCATGGTGGAC	0.557																																					p.C504Y		Atlas-SNP	.											RAD54L2,NS,carcinoma,0,1	RAD54L2	94	.	0			c.G1511A						.						90	73	79					3																	51671348		2203	4300	6503	SO:0001583	missense	23132	exon10			ACTGGTGCATGGT	AB018352	CCDS33765.2	3p21.2	2006-01-17			ENSG00000164080	ENSG00000164080			29123	protein-coding gene	gene with protein product						9872452	Standard	NM_015106		Approved	KIAA0809, SRISNF2L	uc011bdt.2	Q9Y4B4	OTTHUMG00000152936	ENST00000409535.2:c.1511G>A	chr3.hg19:g.51671348G>A	ENSP00000386520:p.Cys504Tyr	123.0	0.0		98.0	19.0	NM_015106	Q8TB57|Q9BV54	Missense_Mutation	SNP	ENST00000409535.2	hg19	CCDS33765.2	.	.	.	.	.	.	.	.	.	.	G	24.6	4.551771	0.86127	.	.	ENSG00000164080	ENST00000409535;ENST00000296477	D;D	0.93247	-3.19;-3.19	5.31	5.31	0.75309	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.85682	D	0.000000	D	0.96537	0.8870	M	0.75150	2.29	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96990	0.9721	10	0.87932	D	0	-12.8036	17.9697	0.89110	0.0:0.0:1.0:0.0	.	504;95	Q9Y4B4;B3KV54	ARIP4_HUMAN;.	Y	504;198	ENSP00000386520:C504Y;ENSP00000296477:C198Y	ENSP00000296477:C198Y	C	+	2	0	RAD54L2	51646388	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.807000	0.99171	2.490000	0.84030	0.561000	0.74099	TGC	.	.		0.557	RAD54L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328700.2	NM_015106		A	51671348	G	A	51671348	3	1	370	1	0	0	0	0	1	0	0	0	13009	1319	46	3	1545	3	RAD54L2	3	51671348	Missense_Mutation	SNP	G	TCGA-ZS-A9CD-01A-11D-A36X-10	17787836	51671348	146351082	20	51213										
ROBO2	6092	hgsc.bcm.edu	37	chr3	77612353	77612353	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	tcagtaaaaactatgatttaAgtgacctgccagggccacca	8	10	1	2			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr3:77612353A>G	ENST00000461745.1	+	11	2455	c.1555A>G	c.(1555-1557)Agt>Ggt	p.S519G	ROBO2_ENST00000332191.8_Missense_Mutation_p.S519G|ROBO2_ENST00000487694.3_Missense_Mutation_p.S535G	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	519					apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)			NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		CTATGATTTAAGTGACCTGCC	0.458																																					p.S519G		Atlas-SNP	.											.	ROBO2	527	.	0			c.A1555G						.						65	62	63					3																	77612353		1874	4105	5979	SO:0001583	missense	6092	exon11			GATTTAAGTGACC	AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10250	protein-coding gene	gene with protein product		602431	"roundabout (axon guidance receptor, Drosophila) homolog 2"			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.1555A>G	chr3.hg19:g.77612353A>G	ENSP00000417164:p.Ser519Gly	84.0	0.0		93.0	22.0	NM_002942	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	hg19	CCDS43109.1	.	.	.	.	.	.	.	.	.	.	A	16.40	3.112578	0.56398	.	.	ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000343019;ENST00000461745;ENST00000332191;ENST00000398467	D;D;D	0.82526	-1.62;-1.62;-1.62	6.07	6.07	0.98685	Fibronectin, type III (1);Immunoglobulin-like fold (1);	0.566176	0.15431	N	0.262703	T	0.77212	0.4097	L	0.28344	0.845	0.24281	N	0.995207	B;B;B	0.11235	0.0;0.004;0.0	B;B;B	0.18263	0.0;0.021;0.0	T	0.76044	-0.3103	9	0.54805	T	0.06	.	16.6406	0.85098	1.0:0.0:0.0:0.0	.	535;519;519	Q19AB5;F8W703;Q9HCK4	.;.;ROBO2_HUMAN	G	535;535;539;519;519;240	ENSP00000417335:S535G;ENSP00000417164:S519G;ENSP00000327536:S519G	ENSP00000327536:S519G	S	+	1	0	ROBO2	77695043	1.000000	0.71417	0.641000	0.29422	0.906000	0.53458	8.919000	0.92770	2.326000	0.78906	0.533000	0.62120	AGT	.	.		0.458	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		G	77612353	A	G	77612353	3	3	370	1	0	0	0	0	1	0	0	0	13529	72	3	2	1599	2	ROBO2	3	77612353	Missense_Mutation	SNP	A	TCGA-ZS-A9CD-01A-11D-A36X-10	25941005	77612353	120410077	21	51214										
EPHA3	2042	hgsc.bcm.edu	37	chr3	89480491	89480491	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	gtcctggaggatgacccagaAgctgcttatacaacaagagt	11	9	0	3			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr3:89480491A>G	ENST00000336596.2	+	13	2553	c.2328A>G	c.(2326-2328)gaA>gaG	p.E776E	EPHA3_ENST00000494014.1_Silent_p.E776E	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	776	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		ATGACCCAGAAGCTGCTTATA	0.393										TSP Lung(6;0.00050)																											p.E776E		Atlas-SNP	.											.	EPHA3	501	.	0			c.A2328G						.						104	99	101					3																	89480491		2203	4300	6503	SO:0001819	synonymous_variant	2042	exon13			CCCAGAAGCTGCT	M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3387	protein-coding gene	gene with protein product		179611	"EphA3"	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.2328A>G	chr3.hg19:g.89480491A>G		143.0	0.0		133.0	16.0	NM_005233	Q9H2V3|Q9H2V4	Silent	SNP	ENST00000336596.2	hg19	CCDS2922.1																																																																																			.	.		0.393	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		G	89480491	A	G	89480491	2	3	370	1	0	0	0	0	0	0	0	1	5170	69	3	2		2	EPHA3	3	89480491	Silent	SNP	A	TCGA-ZS-A9CD-01A-11D-A36X-10	11868138	89480491	108541939	22	51215										
KALRN	8997	hgsc.bcm.edu	37	chr3	124160836	124160836	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	gctgaggtgtttctcaagtaCatccacaggaacaacgtcag	10	10	2	1			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr3:124160836C>T	ENST00000240874.3	+	19	3394	c.3237C>T	c.(3235-3237)taC>taT	p.Y1079Y	KALRN_ENST00000360013.3_Silent_p.Y1079Y|KALRN_ENST00000460856.1_Silent_p.Y1070Y	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1079					apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						TTCTCAAGTACATCCACAGGA	0.587																																					p.Y1079Y		Atlas-SNP	.											.	KALRN	556	.	0			c.C3237T						.						66	59	62					3																	124160836		2203	4300	6503	SO:0001819	synonymous_variant	8997	exon19			CAAGTACATCCAC	U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	4814	protein-coding gene	gene with protein product	"serine/threonine kinase with Dbl and pleckstrin homology domains"	604605	"huntingtin-associated protein interacting protein (duo)"	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000240874.3:c.3237C>T	chr3.hg19:g.124160836C>T		404.0	0.0		405.0	93.0	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000240874.3	hg19	CCDS3027.1	.	.	.	.	.	.	.	.	.	.	C	10.04	1.242283	0.22796	.	.	ENSG00000160145	ENST00000354186	.	.	.	5.22	5.22	0.72569	.	.	.	.	.	T	0.75133	0.3808	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.72626	-0.4236	4	.	.	.	.	19.3361	0.94319	0.0:1.0:0.0:0.0	.	.	.	.	I	1048	.	.	T	+	2	0	KALRN	125643526	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.120000	0.50430	2.878000	0.98634	0.650000	0.86243	ACA	.	.		0.587	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947		T	124160836	C	T	124160836	2	4	370	1	0	0	0	0	0	0	0	1	7984	489	17	3		3	KALRN	3	124160836	Silent	SNP	C	TCGA-ZS-A9CD-01A-11D-A36X-10	34680345	124160836	73861594	23	51216										
KALRN	8997	hgsc.bcm.edu	37	chr3	124210191	124210191	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	cctcagagctgggtgtgaccGagcacgtggagggcgatccc	16	12	1	2			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr3:124210191G>A	ENST00000240874.3	+	31	4760	c.4603G>A	c.(4603-4605)Gag>Aag	p.E1535K	KALRN_ENST00000360013.3_Missense_Mutation_p.E1535K|KALRN_ENST00000460856.1_Missense_Mutation_p.E1526K	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1535	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						GGGTGTGACCGAGCACGTGGA	0.567																																					p.E1535K		Atlas-SNP	.											.	KALRN	556	.	0			c.G4603A						.						72	65	67					3																	124210191		2203	4300	6503	SO:0001583	missense	8997	exon31			GTGACCGAGCACG	U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	4814	protein-coding gene	gene with protein product	"serine/threonine kinase with Dbl and pleckstrin homology domains"	604605	"huntingtin-associated protein interacting protein (duo)"	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000240874.3:c.4603G>A	chr3.hg19:g.124210191G>A	ENSP00000240874:p.Glu1535Lys	97.0	0.0		95.0	27.0	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Missense_Mutation	SNP	ENST00000240874.3	hg19	CCDS3027.1	.	.	.	.	.	.	.	.	.	.	G	34	5.316292	0.95655	.	.	ENSG00000160145	ENST00000460856;ENST00000240874;ENST00000360013	T;T;T	0.29655	1.56;1.56;1.56	5.12	5.12	0.69794	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.85682	D	0.000000	T	0.66703	0.2816	M	0.93062	3.375	0.80722	D	1	D;P;D	0.89917	0.999;0.929;1.0	D;P;D	0.85130	0.994;0.802;0.997	T	0.75714	-0.3221	10	0.87932	D	0	.	18.7502	0.91810	0.0:0.0:1.0:0.0	.	1526;1535;1535	C9IZQ6;O60229;O60229-2	.;KALRN_HUMAN;.	K	1526;1535;1535	ENSP00000418611:E1526K;ENSP00000240874:E1535K;ENSP00000353109:E1535K	ENSP00000240874:E1535K	E	+	1	0	KALRN	125692881	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.651000	0.98493	2.664000	0.90586	0.655000	0.94253	GAG	.	.		0.567	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947		A	124210191	G	A	124210191	3	1	370	1	0	0	0	0	1	0	0	0	7984	1059	37	1	4725	1	KALRN	3	124210191	Missense_Mutation	SNP	G	TCGA-ZS-A9CD-01A-11D-A36X-10	49355	124210191	73812239	24	51217										
AP2M1	1173	hgsc.bcm.edu	37	chr3	183898987	183899008	+	Frame_Shift_Del	DEL	AAGGCACAGCTGATGAAACAAG	AAGGCACAGCTGATGAAACAAG	-													0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	tgttattgaaaagcagggcaAaggcacagctgatgaaacaa							TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	AAGGCACAGCTGATGAAACAAG	AAGGCACAGCTGATGAAACAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr3:183898987_183899008delAAGGCACAGCTGATGAAACAAG	ENST00000292807.5	+	7	828_849	c.680_701delAAGGCACAGCTGATGAAACAAG	c.(679-702)aaaggcacagctgatgaaacaagcfs	p.KGTADETS227fs	AP2M1_ENST00000439647.1_Frame_Shift_Del_p.KGTADETS225fs|AP2M1_ENST00000411763.2_Frame_Shift_Del_p.KGTADETS252fs|EIF2B5_ENST00000444495.1_Intron|AP2M1_ENST00000461733.1_3'UTR|AP2M1_ENST00000382456.3_Frame_Shift_Del_p.KGTADETS225fs	NM_004068.3	NP_004059.2	Q96CW1	AP2M1_HUMAN	adaptor-related protein complex 2, mu 1 subunit	227	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of protein localization to plasma membrane (GO:1903077)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(1)	18	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.92e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			AAGCAGGGCAAAGGCACAGCTGATGAAACAAGCAAGAGGTGC	0.527																																					p.225_232del		Atlas-INDEL	.											.	AP2M1	35	.	0			c.673_694del						.																																			SO:0001589	frameshift_variant	1173	exon6			.	U36188	CCDS43177.1, CCDS43178.1	3q28	2008-07-18			ENSG00000161203	ENSG00000161203			564	protein-coding gene	gene with protein product	"clathrin-associated/assembly/adaptor protein, medium 1", "plasma membrane adaptor AP-2 50kDA protein", "clathrin coat adaptor protein AP50", "clathrin adaptor complex AP2, mu subunit", "HA2 50 kDA subunit", "clathrin assembly protein complex 2 medium chain", "AP-2 mu 2 chain"	601024		CLAPM1		8595912	Standard	NM_004068		Approved	AP50, mu2	uc003fmw.3	Q96CW1	OTTHUMG00000156822	ENST00000292807.5:c.680_701delAAGGCACAGCTGATGAAACAAG	chr3.hg19:g.183898987_183899008delAAGGCACAGCTGATGAAACAAG	ENSP00000292807:p.Lys227fs	256.0	0.0		160.0	18.0	NM_001025205	A6NE12|D3DNT1|P20172|P53679	Frame_Shift_Del	DEL	ENST00000292807.5	hg19	CCDS43177.1																																																																																			.	.		0.527	AP2M1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346013.1	NM_004068		-	183899008	AAGGCACAGCTGATGAAACAAG	-	183898987	7	5	370	1	0	1	0	1	0	0	0	0	742	14	1	0	699	0	AP2M1	3	183898987	Frame_Shift_Del	DEL	AAGGCACAGCTGATGAAACAAG	TCGA-ZS-A9CD-01A-11D-A36X-10	59688796	183898987	14123443	25	51218										
ZNF732	654254	hgsc.bcm.edu	37	chr4	265506	265506	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	tctccagtatgaatactcttAtgtttattaagggttgcgga	9	6	2	1			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr4:265506A>C	ENST00000419098.1	-	4	1150	c.1140T>G	c.(1138-1140)caT>caG	p.H380Q		NM_001137608.1	NP_001131080.1	B4DXR9	ZN732_HUMAN	zinc finger protein 732	380					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|lung(2)	3						GAATACTCTTATGTTTATTAA	0.383																																					p.H379Q		Atlas-SNP	.											.	ZNF732	117	.	0			c.T1137G						.						56	51	53					4																	265506		692	1591	2283	SO:0001583	missense	654254	exon3			ACTCTTATGTTTA	AK302099	CCDS46990.1	4p16.3	2014-02-12	2009-07-22		ENSG00000186777	ENSG00000186777		"Zinc fingers, C2H2-type", "-"	37138	protein-coding gene	gene with protein product							Standard	NM_001137608		Approved	FLJ59067	uc011buu.1	B4DXR9	OTTHUMG00000159883	ENST00000419098.1:c.1140T>G	chr4.hg19:g.265506A>C	ENSP00000415774:p.His380Gln	104.0	0.0		101.0	8.0	NM_001137608		Missense_Mutation	SNP	ENST00000419098.1	hg19	CCDS46990.1	.	.	.	.	.	.	.	.	.	.	A	6.225	0.409720	0.11812	.	.	ENSG00000186777	ENST00000419098	D	0.86865	-2.18	0.977	0.977	0.19733	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94076	0.8101	H	0.95645	3.7	0.23555	N	0.997428	D	0.89917	1.0	D	0.97110	1.0	D	0.84316	0.0513	9	0.87932	D	0	.	5.7319	0.18045	1.0:0.0:0.0:0.0	.	380	B4DXR9	ZN732_HUMAN	Q	380	ENSP00000415774:H380Q	ENSP00000415774:H380Q	H	-	3	2	ZNF732	255506	0.184000	0.23200	0.030000	0.17652	0.027000	0.11550	0.295000	0.19065	0.338000	0.23692	0.329000	0.21502	CAT	.	.		0.383	ZNF732-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000357937.2	NM_001137608		C	265506	A	C	265506	3	2	370	1	0	0	0	0	1	0	0	0	18138	446	16	5	621	5	ZNF732	4	265506	Missense_Mutation	SNP	A	TCGA-ZS-A9CD-01A-11D-A36X-10		265506	190888770	26	51219										
HTT	3064	hgsc.bcm.edu	37	chr4	3208260	3208260	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	ctccgagcacttaacgtggcTcattgtaaatcacattcaag	7	11	3	0			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr4:3208260T>G	ENST00000355072.5	+	43	5901	c.5756T>G	c.(5755-5757)cTc>cGc	p.L1919R		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	1919					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		TTAACGTGGCTCATTGTAAAT	0.463																																					p.L1919R		Atlas-SNP	.											.	HTT	221	.	0			c.T5756G						.						104	100	101					4																	3208260		1964	4160	6124	SO:0001583	missense	3064	exon43			CGTGGCTCATTGT	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.5756T>G	chr4.hg19:g.3208260T>G	ENSP00000347184:p.Leu1919Arg	131.0	0.0		129.0	43.0	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	hg19	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	T	28.6	4.937643	0.92458	.	.	ENSG00000197386	ENST00000355072	T	0.14391	2.51	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.40145	0.1105	M	0.78637	2.42	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.32693	-0.9897	10	0.87932	D	0	.	15.806	0.78513	0.0:0.0:0.0:1.0	.	1919	P42858	HD_HUMAN	R	1919	ENSP00000347184:L1919R	ENSP00000347184:L1919R	L	+	2	0	HTT	3178058	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.934000	0.87649	2.196000	0.70406	0.533000	0.62120	CTC	.	.		0.463	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		G	3208260	T	G	3208260	3	3	370	1	0	0	0	0	1	0	0	0	7466	1551	54	5	5926	5	HTT	4	3208260	Missense_Mutation	SNP	T	TCGA-ZS-A9CD-01A-11D-A36X-10	2942754	3208260	187946016	27	51220										
PCDH7	5099	hgsc.bcm.edu	37	chr4	30724272	30724272	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	ttaacatcaaagacgagaacGacaacgtgccgtccattgaa	8	10	1	3			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr4:30724272G>A	ENST00000361762.2	+	1	2236	c.1228G>A	c.(1228-1230)Gac>Aac	p.D410N	PCDH7_ENST00000543491.1_Missense_Mutation_p.D410N	NM_002589.2	NP_002580.2	O60245	PCDH7_HUMAN	protocadherin 7	410	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D363H(1)|p.D410H(1)		NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(8)|liver(1)|lung(26)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	55						AGACGAGAACGACAACGTGCC	0.637																																					p.D410N		Atlas-SNP	.											PCDH7_ENST00000361762,NS,carcinoma,0,1	PCDH7	215	.	2	Substitution - Missense(2)	lung(2)	c.G1228A						.						43	46	45					4																	30724272		2202	4300	6502	SO:0001583	missense	5099	exon1			GAGAACGACAACG	AB006755	CCDS33971.1, CCDS75116.1	4p15	2014-06-13	2007-02-12			ENSG00000169851		"Cadherins / Protocadherins : Non-clustered"	8659	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 120"	602988	"BH-protocadherin (brain-heart)"			9615233	Standard	NM_002589		Approved	BH-Pcdh, PPP1R120	uc021xnd.1	O60245		ENST00000361762.2:c.1228G>A	chr4.hg19:g.30724272G>A	ENSP00000355243:p.Asp410Asn	303.0	0.0		306.0	89.0	NM_032457	O60246|O60247|Q4W5C4	Missense_Mutation	SNP	ENST00000361762.2	hg19	CCDS33971.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.5|20.5	3.995379|3.995379	0.74703|0.74703	.|.	.|.	ENSG00000169851|ENSG00000169851	ENST00000361762;ENST00000543491;ENST00000333135|ENST00000511884	T;T|.	0.53640|.	0.61;0.61|.	5.24|5.24	5.24|5.24	0.73138|0.73138	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);|.	.|.	.|.	.|.	.|.	D|D	0.87386|0.87386	0.6164|0.6164	H|H	0.94658|0.94658	3.565|3.565	0.58432|0.58432	D|D	0.999999|0.999999	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.91635|.	0.999;0.999;0.998|.	D|D	0.90947|0.90947	0.4802|0.4802	9|5	0.87932|.	D|.	0|.	.|.	18.8233|18.8233	0.92106|0.92106	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	410;363;410|.	F5GWJ1;O60245-3;O60245|.	.;.;PCDH7_HUMAN|.	N|Q	410;410;363|99	ENSP00000355243:D410N;ENSP00000441802:D410N|.	ENSP00000330302:D363N|.	D|R	+|+	1|2	0|0	PCDH7|PCDH7	30333370|30333370	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.516000|0.516000	0.34256|0.34256	9.869000|9.869000	0.99810|0.99810	2.453000|2.453000	0.82957|0.82957	0.655000|0.655000	0.94253|0.94253	GAC|CGA	.	.		0.637	PCDH7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360366.1	NM_032457, NM_002589		A	30724272	G	A	30724272	3	1	370	1	0	0	0	0	1	0	0	0	11525	1058	37	1	1230	1	PCDH7	4	30724272	Missense_Mutation	SNP	G	TCGA-ZS-A9CD-01A-11D-A36X-10	27516012	30724272	160430004	28	51221										
TMEM33	55161	hgsc.bcm.edu	37	chr4	41946817	41946817	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	tcttttgttttaggcaagggGctcaaatagtttacctctgc	9	8	3	0			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr4:41946817G>C	ENST00000504986.1	+	5	769	c.404G>C	c.(403-405)gGc>gCc	p.G135A	TMEM33_ENST00000325094.5_Missense_Mutation_p.G135A|TMEM33_ENST00000513702.1_Missense_Mutation_p.G135A	NM_018126.2	NP_060596.2	P57088	TMM33_HUMAN	transmembrane protein 33	135						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)				endometrium(1)|large_intestine(3)|lung(4)|ovary(1)	9						TAGGCAAGGGGCTCAAATAGT	0.338																																					p.G135A		Atlas-SNP	.											.	TMEM33	17	.	0			c.G404C						.						74	72	73					4																	41946817		2203	4299	6502	SO:0001583	missense	55161	exon5			CAAGGGGCTCAAA	BC000948	CCDS3464.1	4p14	2008-02-05			ENSG00000109133	ENSG00000109133			25541	protein-coding gene	gene with protein product						12477932	Standard	NM_018126		Approved	FLJ10525	uc003gwi.2	P57088	OTTHUMG00000099381	ENST00000504986.1:c.404G>C	chr4.hg19:g.41946817G>C	ENSP00000422473:p.Gly135Ala	105.0	0.0		73.0	21.0	NM_018126	B3KSS8|Q9H953	Missense_Mutation	SNP	ENST00000504986.1	hg19	CCDS3464.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.4|26.4	4.738667|4.738667	0.89573|0.89573	.|.	.|.	ENSG00000109133|ENSG00000109133	ENST00000513558|ENST00000504986;ENST00000508448;ENST00000513702;ENST00000325094	.|.	.|.	.|.	5.12|5.12	5.12|5.12	0.69794|0.69794	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.70736|0.70736	0.3258|0.3258	M|M	0.84585|0.84585	2.705|2.705	0.80722|0.80722	D|D	1|1	.|B	.|0.29936	.|0.262	.|B	.|0.31686	.|0.134	T|T	0.69709|0.69709	-0.5072|-0.5072	5|9	.|0.14252	.|T	.|0.57	-12.5872|-12.5872	18.584|18.584	0.91182|0.91182	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|135	.|P57088	.|TMM33_HUMAN	P|A	69|135	.|.	.|ENSP00000441455:G135A	A|G	+|+	1|2	0|0	TMEM33|TMEM33	41641574|41641574	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	7.653000|7.653000	0.83643|0.83643	2.399000|2.399000	0.81585|0.81585	0.655000|0.655000	0.94253|0.94253	GCT|GGC	.	.		0.338	TMEM33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216834.2	NM_018126		C	41946817	G	C	41946817	3	2	370	1	0	0	0	0	1	0	0	0	16171	1203	42	4	422	4	TMEM33	4	41946817	Missense_Mutation	SNP	G	TCGA-ZS-A9CD-01A-11D-A36X-10	11222545	41946817	149207459	29	51222										
ODAM	54959	hgsc.bcm.edu	37	chr4	71067172	71067172	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	tttttaaaaaatctgacagaTaccattctatgctcaatttg	4	7	3	2			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr4:71067172T>C	ENST00000396094.2	+	7	578	c.530T>C	c.(529-531)aTa>aCa	p.I177T		NM_017855.3	NP_060325.3	A1E959	ODAM_HUMAN	odontogenic, ameloblast asssociated	177	Gln-rich.				biomineral tissue development (GO:0031214)|odontogenesis of dentin-containing tooth (GO:0042475)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|fibril (GO:0043205)|nucleus (GO:0005634)				NS(1)|breast(2)|endometrium(2)|large_intestine(2)|lung(8)|ovary(3)|skin(2)	20						ATCTGACAGATACCATTCTAT	0.249																																					p.I177T		Atlas-SNP	.											.	ODAM	38	.	0			c.T530C						.						36	38	38					4																	71067172		2197	4292	6489	SO:0001630	splice_region_variant	54959	exon7			GACAGATACCATT	AK000520	CCDS3536.2	4q13.3	2010-11-23			ENSG00000109205	ENSG00000109205			26043	protein-coding gene	gene with protein product		614843				14647039	Standard	NM_017855		Approved	APin, FLJ20513	uc003hfc.3	A1E959	OTTHUMG00000129406	ENST00000396094.2:c.529-1T>C	chr4.hg19:g.71067172T>C		681.0	1.0		618.0	152.0	NM_017855	Q8WWE5|Q9NWZ9	Missense_Mutation	SNP	ENST00000396094.2	hg19	CCDS3536.2	.	.	.	.	.	.	.	.	.	.	T	10.49	1.365660	0.24684	.	.	ENSG00000109205	ENST00000396094;ENST00000510709	T	0.52526	0.66	4.93	4.93	0.64822	.	0.536654	0.16291	N	0.220914	T	0.40956	0.1138	L	0.47716	1.5	0.33479	D	0.587191	P	0.36535	0.557	B	0.34242	0.178	T	0.59563	-0.7431	10	0.72032	D	0.01	-3.7397	10.8896	0.46988	0.0:0.0:0.0:1.0	.	177	A1E959	ODAM_HUMAN	T	177;163	ENSP00000379401:I177T	ENSP00000379401:I177T	I	+	2	0	ODAM	71101761	0.992000	0.36948	1.000000	0.80357	0.410000	0.31052	3.370000	0.52372	2.074000	0.62210	0.377000	0.23210	ATA	.	.		0.249	ODAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251562.1	NM_017855	Missense_Mutation	C	71067172	T	C	71067172	5	2	370	1	0	0	0	0	0	0	1	0	10833	1420	49	2	556	2	ODAM	4	71067172	Splice_Site	SNP	T	TCGA-ZS-A9CD-01A-11D-A36X-10	29120355	71067172	120087104	30	51223										
ALB	213	hgsc.bcm.edu	37	chr4	74276080	74276096	+	Frame_Shift_Del	DEL	AAGTGTGCCAGTCTCCA	AAGTGTGCCAGTCTCCA	-													0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	cgtctgccaaacagagactcAagtgtgccagtctccaaaaa					rs373929336		TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	AAGTGTGCCAGTCTCCA	AAGTGTGCCAGTCTCCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr4:74276080_74276096delAAGTGTGCCAGTCTCCA	ENST00000503124.1	+	4	424_440	c.217_233delAAGTGTGCCAGTCTCCA	c.(217-234)aagtgtgccagtctccaafs	p.KCASLQ73fs	ALB_ENST00000415165.2_Intron|ALB_ENST00000295897.4_Frame_Shift_Del_p.KCASLQ223fs|ALB_ENST00000401494.3_Frame_Shift_Del_p.KCASLQ108fs|ALB_ENST00000505649.1_3'UTR|ALB_ENST00000509063.1_Frame_Shift_Del_p.KCASLQ223fs			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			ACAGAGACTCAAGTGTGCCAGTCTCCAAAAATTTGGA	0.35																																					p.222_228del		Atlas-INDEL	.											.	ALB	132	.	0			c.666_682del						.																																			SO:0001589	frameshift_variant	213	exon6			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.217_233delAAGTGTGCCAGTCTCCA	chr4.hg19:g.74276080_74276096delAAGTGTGCCAGTCTCCA	ENSP00000421027:p.Lys73fs	371.0	0.0		298.0	40.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Frame_Shift_Del	DEL	ENST00000503124.1	hg19																																																																																				.	.		0.35	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		-	74276096	AAGTGTGCCAGTCTCCA	-	74276080	7	5	370	1	0	1	0	1	0	0	0	0	486	131	5	0	689	0	ALB	4	74276080	Frame_Shift_Del	DEL	AAGTGTGCCAGTCTCCA	TCGA-ZS-A9CD-01A-11D-A36X-10	3208908	74276080	116878196	31	51224										
CCDC158	339965	hgsc.bcm.edu	37	chr4	77303825	77303825	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	cgagcactgctagctttctcAgtaagtcctgttatttcaac	7	11	2	0			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr4:77303825A>G	ENST00000388914.3	-	7	1004	c.852T>C	c.(850-852)acT>acC	p.T284T	CCDC158_ENST00000434846.2_Silent_p.T284T	NM_001042784.1	NP_001036249.1	Q5M9N0	CD158_HUMAN	coiled-coil domain containing 158	284										breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(1)	56						TAGCTTTCTCAGTAAGTCCTG	0.353																																					p.T284T		Atlas-SNP	.											.	CCDC158	114	.	0			c.T852C						.						149	140	143					4																	77303825		1869	4103	5972	SO:0001819	synonymous_variant	339965	exon7			TTTCTCAGTAAGT	BC035224	CCDS43242.1	4q21.1	2009-04-06			ENSG00000163749	ENSG00000163749			26374	protein-coding gene	gene with protein product						12477932	Standard	NM_001042784		Approved	FLJ25770	uc003hkb.4	Q5M9N0	OTTHUMG00000160916	ENST00000388914.3:c.852T>C	chr4.hg19:g.77303825A>G		57.0	0.0		65.0	21.0	NM_001042784	Q8IYQ1|Q8N7D4|Q8N7E3	Silent	SNP	ENST00000388914.3	hg19	CCDS43242.1																																																																																			.	.		0.353	CCDC158-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362694.2	NM_001042784		G	77303825	A	G	77303825	2	3	370	1	0	0	0	0	0	0	0	1	2792	175	7	2		2	CCDC158	4	77303825	Silent	SNP	A	TCGA-ZS-A9CD-01A-11D-A36X-10	3027745	77303825	113850451	32	51225										
STC2	8614	hgsc.bcm.edu	37	chr5	172752987	172752987	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	gccacaccccacatcgccagCgttgaccaaacagtgctgga	9	16	0	1			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr5:172752987C>T	ENST00000265087.4	-	2	1487	c.178G>A	c.(178-180)Gct>Act	p.A60T	STC2_ENST00000520593.1_5'Flank	NM_003714.2	NP_003705.1	O76061	STC2_HUMAN	stanniocalcin 2	60					cellular calcium ion homeostasis (GO:0006874)|cellular response to hypoxia (GO:0071456)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of gene expression (GO:0010629)|negative regulation of multicellular organism growth (GO:0040015)|regulation of hormone biosynthetic process (GO:0046885)|regulation of store-operated calcium entry (GO:2001256)|response to oxidative stress (GO:0006979)|response to peptide hormone (GO:0043434)|response to vitamin D (GO:0033280)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|heme binding (GO:0020037)|protein homodimerization activity (GO:0042803)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(3)	25	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|Ovarian(839;0.223)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			ACATCGCCAGCGTTGACCAAA	0.453																																					p.A60T		Atlas-SNP	.											.	STC2	59	.	0			c.G178A						.						165	176	172					5																	172752987		2203	4300	6503	SO:0001583	missense	8614	exon2			CGCCAGCGTTGAC	AB012664	CCDS4388.1	5q35.2	2004-05-17			ENSG00000113739	ENSG00000113739			11374	protein-coding gene	gene with protein product		603665				9723890, 9753616	Standard	NM_003714		Approved	STC-2	uc003mco.1	O76061	OTTHUMG00000130542	ENST00000265087.4:c.178G>A	chr5.hg19:g.172752987C>T	ENSP00000265087:p.Ala60Thr	172.0	0.0		147.0	30.0	NM_003714		Missense_Mutation	SNP	ENST00000265087.4	hg19	CCDS4388.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.0|25.0	4.588007|4.588007	0.86851|0.86851	.|.	.|.	ENSG00000113739|ENSG00000113739	ENST00000265087|ENST00000520648	.|.	.|.	.|.	5.6|5.6	4.73|4.73	0.59995|0.59995	.|.	0.049807|.	0.85682|.	D|.	0.000000|.	T|T	0.76062|0.76062	0.3935|0.3935	M|M	0.78637|0.78637	2.42|2.42	0.58432|0.58432	D|D	0.999999|0.999999	P|.	0.37330|.	0.59|.	B|.	0.32465|.	0.146|.	T|T	0.77515|0.77515	-0.2559|-0.2559	9|5	0.62326|.	D|.	0.03|.	-4.6472|-4.6472	16.5284|16.5284	0.84344|0.84344	0.0:0.8691:0.1309:0.0|0.0:0.8691:0.1309:0.0	.|.	60|.	O76061|.	STC2_HUMAN|.	T|H	60|13	.|.	ENSP00000265087:A60T|.	A|R	-|-	1|2	0|0	STC2|STC2	172685593|172685593	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	3.711000|3.711000	0.54868|0.54868	1.352000|1.352000	0.45808|0.45808	0.655000|0.655000	0.94253|0.94253	GCT|CGC	.	.		0.453	STC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252965.1	NM_003714		T	172752987	C	T	172752987	3	4	370	1	0	0	0	0	1	0	0	0	15291	768	27	1	742	1	STC2	5	172752987	Missense_Mutation	SNP	C	TCGA-ZS-A9CD-01A-11D-A36X-10		172752987	8162273	33	51226										
TBC1D22B	55633	hgsc.bcm.edu	37	chr6	37250093	37250093	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	gactgtccgggagaaaacccGcctagaaaaattccgtcaac	9	12	1	2			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr6:37250093G>T	ENST00000373491.3	+	4	700	c.554G>T	c.(553-555)cGc>cTc	p.R185L		NM_017772.2	NP_060242.2	Q9NU19	TB22B_HUMAN	TBC1 domain family, member 22B	185							Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|prostate(1)	15			OV - Ovarian serous cystadenocarcinoma(102;0.241)			GAGAAAACCCGCCTAGAAAAA	0.572																																					p.R185L		Atlas-SNP	.											TBC1D22B,NS,carcinoma,0,1	TBC1D22B	37	.	0			c.G554T						.						35	40	38					6																	37250093		2203	4300	6503	SO:0001583	missense	55633	exon4			AAACCCGCCTAGA	AK096340	CCDS4832.1	6p21.2	2005-01-05	2005-01-05	2005-01-05	ENSG00000065491	ENSG00000065491			21602	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 197"	C6orf197			Standard	NM_017772		Approved	FLJ20337, dJ744I24.2	uc003onn.3	Q9NU19	OTTHUMG00000014619	ENST00000373491.3:c.554G>T	chr6.hg19:g.37250093G>T	ENSP00000362590:p.Arg185Leu	104.0	0.0		133.0	42.0	NM_017772	A8KA28|Q32MQ8|Q5VUK9|Q6P4C3|Q7Z6P7|Q9BPV6|Q9BUT5|Q9NXB6	Missense_Mutation	SNP	ENST00000373491.3	hg19	CCDS4832.1	.	.	.	.	.	.	.	.	.	.	G	34	5.339675	0.95783	.	.	ENSG00000065491	ENST00000373491	T	0.20738	2.05	5.91	5.91	0.95273	Rab-GAP/TBC domain (1);	0.000000	0.85682	D	0.000000	T	0.35624	0.0938	M	0.76574	2.34	0.80722	D	1	D	0.57899	0.981	P	0.55871	0.786	T	0.10776	-1.0615	10	0.87932	D	0	.	19.07	0.93130	0.0:0.0:1.0:0.0	.	185	Q9NU19	TB22B_HUMAN	L	185	ENSP00000362590:R185L	ENSP00000362590:R185L	R	+	2	0	TBC1D22B	37358071	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.430000	0.97488	2.793000	0.96121	0.655000	0.94253	CGC	.	.		0.572	TBC1D22B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040402.1	NM_017772		T	37250093	G	T	37250093	3	4	370	1	0	0	0	0	1	0	0	0	15627	1087	38	1	568	1	TBC1D22B	6	37250093	Missense_Mutation	SNP	G	TCGA-ZS-A9CD-01A-11D-A36X-10		37250093	133864974	34	51227										
EPHA7	2045	hgsc.bcm.edu	37	chr6	93969086	93969086	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	ccttacctgcaccaatcacaCgctcaattttaatacaggag	5	13	2	0			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr6:93969086C>G	ENST00000369303.4	-	10	2094	c.1910G>C	c.(1909-1911)cGt>cCt	p.R637P		NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	637	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|ephrin receptor signaling pathway (GO:0048013)|negative chemotaxis (GO:0050919)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cell-cell adhesion (GO:0022407)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of protein autophosphorylation (GO:0031952)|retinal ganglion cell axon guidance (GO:0031290)	dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|chemorepellent activity (GO:0045499)|GPI-linked ephrin receptor activity (GO:0005004)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(1)|central_nervous_system(7)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|lung(43)|ovary(8)|pancreas(1)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(13)|urinary_tract(1)	112		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		ACCAATCACACGCTCAATTTT	0.433																																					p.R637P		Atlas-SNP	.											.	EPHA7	251	.	0			c.G1910C						.						164	148	153					6																	93969086		2203	4300	6503	SO:0001583	missense	2045	exon10			ATCACACGCTCAA	L36642	CCDS5031.1, CCDS75494.1	6q16.3	2013-02-11	2004-10-28		ENSG00000135333	ENSG00000135333		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3390	protein-coding gene	gene with protein product		602190	"EphA7"			9267020	Standard	NM_004440		Approved	Hek11	uc003poe.3	Q15375	OTTHUMG00000015228	ENST00000369303.4:c.1910G>C	chr6.hg19:g.93969086C>G	ENSP00000358309:p.Arg637Pro	210.0	0.0		194.0	77.0	NM_004440	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Missense_Mutation	SNP	ENST00000369303.4	hg19	CCDS5031.1	.	.	.	.	.	.	.	.	.	.	C	16.27	3.077084	0.55753	.	.	ENSG00000135333	ENST00000369303	T	0.63913	-0.07	5.9	5.9	0.94986	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.73233	0.3561	L	0.57536	1.79	0.80722	D	1	D;D;D	0.76494	0.995;0.999;0.999	P;D;D	0.68039	0.717;0.925;0.955	T	0.74179	-0.3749	10	0.87932	D	0	.	20.2821	0.98520	0.0:1.0:0.0:0.0	.	633;632;637	Q15375-4;Q15375-2;Q15375	.;.;EPHA7_HUMAN	P	637	ENSP00000358309:R637P	ENSP00000358309:R637P	R	-	2	0	EPHA7	94025807	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.089000	0.71384	2.786000	0.95864	0.563000	0.77884	CGT	.	.		0.433	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1			G	93969086	C	G	93969086	3	3	370	1	0	0	0	0	1	0	0	0	5174	536	19	4	1118	4	EPHA7	6	93969086	Missense_Mutation	SNP	C	TCGA-ZS-A9CD-01A-11D-A36X-10	56718993	93969086	77145981	35	51228										
FUT9	10690	hgsc.bcm.edu	37	chr6	96651187	96651187	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	tctgtgctgaaaatgaaaaaCttcttttccaccaaaactga	5	9	2	3	rs534420311		TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr6:96651187C>T	ENST00000302103.5	+	3	482	c.156C>T	c.(154-156)aaC>aaT	p.N52N		NM_006581.3	NP_006572.2	Q9Y231	FUT9_HUMAN	fucosyltransferase 9 (alpha (1,3) fucosyltransferase)	52					carbohydrate metabolic process (GO:0005975)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|nervous system development (GO:0007399)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)	p.N52N(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|liver(2)|lung(10)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(2)	34		all_cancers(76;4.77e-07)|Acute lymphoblastic leukemia(125;4.01e-09)|all_hematologic(75;1.25e-06)|all_epithelial(107;0.00279)|Colorectal(196;0.0356)		BRCA - Breast invasive adenocarcinoma(108;0.08)		AAATGAAAAACTTCTTTTCCA	0.423													C|||	1	0.000199681	0	0	5008	,	,		18806	0.001		0	False		,,,				2504	0				p.N52N	Melanoma(98;1369 1476 6592 22940 26587)	Atlas-SNP	.											FUT9,NS,carcinoma,0,1	FUT9	79	.	1	Substitution - coding silent(1)	prostate(1)	c.C156T						.						102	95	97					6																	96651187		2203	4300	6503	SO:0001819	synonymous_variant	10690	exon3			GAAAAACTTCTTT	AB023021	CCDS5033.1	6q16	2013-02-26			ENSG00000172461	ENSG00000172461		"Fucosyltransferases"	4020	protein-coding gene	gene with protein product		606865				10386598, 10575236	Standard	NM_006581		Approved	Fuc-TIX	uc003pop.4	Q9Y231	OTTHUMG00000015236	ENST00000302103.5:c.156C>T	chr6.hg19:g.96651187C>T		101.0	0.0		126.0	8.0	NM_006581	Q5T0W4	Silent	SNP	ENST00000302103.5	hg19	CCDS5033.1																																																																																			.	.		0.423	FUT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041554.2	NM_006581		T	96651187	C	T	96651187	2	4	370	1	0	0	0	0	0	0	0	1	6119	564	20	3		3	FUT9	6	96651187	Silent	SNP	C	TCGA-ZS-A9CD-01A-11D-A36X-10	2682101	96651187	74463880	36	51229										
FUT9	10690	hgsc.bcm.edu	37	chr6	96652040	96652040	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	gggaatcacatgcatgtttgGcttgcgatcatgtgaaaagg	13	6	2	1			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr6:96652040G>C	ENST00000302103.5	+	3	1335	c.1009G>C	c.(1009-1011)Gct>Cct	p.A337P		NM_006581.3	NP_006572.2	Q9Y231	FUT9_HUMAN	fucosyltransferase 9 (alpha (1,3) fucosyltransferase)	337					carbohydrate metabolic process (GO:0005975)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|nervous system development (GO:0007399)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|liver(2)|lung(10)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(2)	34		all_cancers(76;4.77e-07)|Acute lymphoblastic leukemia(125;4.01e-09)|all_hematologic(75;1.25e-06)|all_epithelial(107;0.00279)|Colorectal(196;0.0356)		BRCA - Breast invasive adenocarcinoma(108;0.08)		TGCATGTTTGGCTTGCGATCA	0.338																																					p.A337P	Melanoma(98;1369 1476 6592 22940 26587)	Atlas-SNP	.											.	FUT9	79	.	0			c.G1009C						.						88	88	88					6																	96652040		2203	4300	6503	SO:0001583	missense	10690	exon3			TGTTTGGCTTGCG	AB023021	CCDS5033.1	6q16	2013-02-26			ENSG00000172461	ENSG00000172461		"Fucosyltransferases"	4020	protein-coding gene	gene with protein product		606865				10386598, 10575236	Standard	NM_006581		Approved	Fuc-TIX	uc003pop.4	Q9Y231	OTTHUMG00000015236	ENST00000302103.5:c.1009G>C	chr6.hg19:g.96652040G>C	ENSP00000302599:p.Ala337Pro	127.0	0.0		120.0	10.0	NM_006581	Q5T0W4	Missense_Mutation	SNP	ENST00000302103.5	hg19	CCDS5033.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.938587	0.73557	.	.	ENSG00000172461	ENST00000302103	T	0.26810	1.71	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.55114	0.1900	M	0.91510	3.215	0.80722	D	1	D	0.71674	0.998	D	0.79108	0.992	T	0.64871	-0.6305	10	0.62326	D	0.03	-13.338	18.3764	0.90437	0.0:0.0:1.0:0.0	.	337	Q9Y231	FUT9_HUMAN	P	337	ENSP00000302599:A337P	ENSP00000302599:A337P	A	+	1	0	FUT9	96758761	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	6.354000	0.73036	2.586000	0.87340	0.467000	0.42956	GCT	.	.		0.338	FUT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041554.2	NM_006581		C	96652040	G	C	96652040	3	2	370	1	0	0	0	0	1	0	0	0	6119	1203	42	4	1011	4	FUT9	6	96652040	Missense_Mutation	SNP	G	TCGA-ZS-A9CD-01A-11D-A36X-10	853	96652040	74463027	37	51230										
ATG5	9474	hgsc.bcm.edu	37	chr6	106740950	106740951	+	Missense_Mutation	DNP	GA	GA	AT													0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	aagagctgaacttgatgcaaGaagatcaaatagcaaaccaa							TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr6:106740950_106740951GA>AT	ENST00000369076.3	-	4	590_591	c.267_268TC>AT	c.(265-270)ctTCtt>ctATtt	p.L90F	ATG5_ENST00000369070.1_Missense_Mutation_p.L12F|ATG5_ENST00000343245.3_Missense_Mutation_p.L90F|ATG5_ENST00000360666.4_Intron	NM_004849.2	NP_004840.1	Q9H1Y0	ATG5_HUMAN	autophagy related 5	90					apoptotic process (GO:0006915)|autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|blood vessel remodeling (GO:0001974)|heart contraction (GO:0060047)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of type I interferon production (GO:0032480)|negative stranded viral RNA replication (GO:0039689)|otolith development (GO:0048840)|post-translational protein modification (GO:0043687)|regulation of cilium assembly (GO:1902017)|regulation of cytokine secretion involved in immune response (GO:0002739)|response to drug (GO:0042493)|response to fungus (GO:0009620)|vasodilation (GO:0042311)|ventricular cardiac muscle cell development (GO:0055015)	autophagic vacuole (GO:0005776)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|membrane (GO:0016020)|pre-autophagosomal structure membrane (GO:0034045)				endometrium(1)|large_intestine(5)|lung(1)|prostate(1)	8	Breast(9;0.0296)	all_cancers(87;0.000301)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0612)|Lung NSC(302;0.216)	BRCA - Breast invasive adenocarcinoma(8;0.00802)	OV - Ovarian serous cystadenocarcinoma(136;0.128)|Epithelial(106;0.159)|all cancers(137;0.18)		CTTGATGCAAGAAGATCAAATA	0.287																																					p.L90F|p.L89L		Atlas-SNP	.											.	ATG5	23	.	0			c.C268T|c.T267A						.																																			SO:0001583	missense	9474	exon4			ATGCAAGAAGATC|TGCAAGAAGATCA	Y11588	CCDS5055.1, CCDS69159.1, CCDS75498.1	6q21	2014-02-12	2012-06-06	2005-09-11	ENSG00000057663	ENSG00000057663			589	protein-coding gene	gene with protein product		604261	"APG5 (autophagy 5, S. cerevisiae)-like", "APG5 autophagy 5-like (S. cerevisiae)", "ATG5 autophagy related 5 homolog (S. cerevisiae)"	APG5L		9563500, 11349150, 15778222	Standard	NM_001286111		Approved	ASP, APG5, hAPG5	uc003prf.3	Q9H1Y0	OTTHUMG00000016193	ENST00000369076.3:c.267_268delinsAT	chr6.hg19:g.106740950_106740951delinsAT	ENSP00000358072:p.Leu90Phe	299.0|298.0	0.0		367.0|365.0	21.0	NM_004849	O60875|Q5JVR2|Q68DI4|Q9H2B8|Q9HCZ7	Missense_Mutation|Silent	SNP	ENST00000369076.3	hg19	CCDS5055.1																																																																																			.	.		0.287	ATG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043476.1	NM_004849		AT	106740951	GA	AT	106740950	3	1	370	1	0	0	0	0	1	0	0	0	1100	942	33	3	579	3	ATG5	6	106740950	Missense_Mutation	DNP	GA	TCGA-ZS-A9CD-01A-11D-A36X-10	10088910	106740950	64374117	38	51231										
FNDC1	84624	hgsc.bcm.edu	37	chr6	159653741	159653741	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	catctcggctgctgcccaccCagccacacctgagctctcca	7	20	2	1			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr6:159653741C>T	ENST00000297267.9	+	11	2397	c.2197C>T	c.(2197-2199)Cag>Tag	p.Q733*	FNDC1_ENST00000340366.6_Nonsense_Mutation_p.Q670*	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	733	Ser-rich.				cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		GCTGCCCACCCAGCCACACCT	0.632																																					p.Q733X		Atlas-SNP	.											.	FNDC1	250	.	0			c.C2197T						.						25	30	29					6																	159653741		2068	4201	6269	SO:0001587	stop_gained	84624	exon11			CCCACCCAGCCAC	AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"Fibronectin type III domain containing"	21184	protein-coding gene	gene with protein product		609991	"fibronectin type III domain containing 2"	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.2197C>T	chr6.hg19:g.159653741C>T	ENSP00000297267:p.Gln733*	97.0	0.0		83.0	13.0	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Nonsense_Mutation	SNP	ENST00000297267.9	hg19	CCDS47512.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	37|37	6.112551|6.112551	0.97296|0.97296	.|.	.|.	ENSG00000164694|ENSG00000164694	ENST00000329629|ENST00000297267;ENST00000340366	.|.	.|.	.|.	3.83|3.83	0.145|0.145	0.14829|0.14829	.|.	.|0.956115	.|0.08612	.|N	.|0.919835	T|.	0.03136|.	0.0092|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.40251|.	-0.9573|.	3|.	.|0.02654	.|T	.|1	-3.4001|-3.4001	4.5935|4.5935	0.12319|0.12319	0.2677:0.3004:0.4319:0.0|0.2677:0.3004:0.4319:0.0	.|.	.|.	.|.	.|.	L|X	628|733;670	.|.	.|ENSP00000297267:Q733X	P|Q	+|+	2|1	0|0	FNDC1|FNDC1	159573731|159573731	0.000000|0.000000	0.05858|0.05858	0.003000|0.003000	0.11579|0.11579	0.054000|0.054000	0.15201|0.15201	0.030000|0.030000	0.13688|0.13688	0.189000|0.189000	0.20188|0.20188	0.655000|0.655000	0.94253|0.94253	CCA|CAG	.	.		0.632	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532		T	159653741	C	T	159653741	4	4	370	1	0	0	0	0	0	1	0	0	5976	595	21	3	2239	3	FNDC1	6	159653741	Nonsense_Mutation	SNP	C	TCGA-ZS-A9CD-01A-11D-A36X-10	52912791	159653741	11461326	39	51232										
TBP	6908	hgsc.bcm.edu	37	chr6	170871004	170871004	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	gagcaacaaaggcagcagcaGcaacaacaacagcagcagca	10	12	0	0			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr6:170871004G>A	ENST00000392092.2	+	3	459	c.180G>A	c.(178-180)caG>caA	p.Q60Q	TBP_ENST00000230354.6_Silent_p.Q60Q|TBP_ENST00000540980.1_Silent_p.Q40Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	60	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		Ggcagcagcagcaacaacaac	0.542																																					p.Q60Q		Atlas-SNP	.											.	TBP	58	.	0			c.G180A						.						43	45	44					6																	170871004		2203	4300	6503	SO:0001819	synonymous_variant	6908	exon3			GCAGCAGCAACAA	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"General transcription factors"	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.180G>A	chr6.hg19:g.170871004G>A		68.0	0.0		58.0	5.0	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	hg19	CCDS5315.1																																																																																			.	.		0.542	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194		A	170871004	G	A	170871004	2	1	370	1	0	0	0	0	0	0	0	1	15659	962	34	3		3	TBP	6	170871004	Silent	SNP	G	TCGA-ZS-A9CD-01A-11D-A36X-10	11217263	170871004	244063	40	51233										
NEUROD6	63974	hgsc.bcm.edu	37	chr7	31378068	31378068	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	aggtttcttcttgcttcaggGaaaatatcccattatagtta	7	7	3	0			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr7:31378068G>A	ENST00000297142.3	-	2	1137	c.815C>T	c.(814-816)tCc>tTc	p.S272F		NM_022728.2	NP_073565.2	Q96NK8	NDF6_HUMAN	neuronal differentiation 6	272					cell differentiation (GO:0030154)|dentate gyrus development (GO:0021542)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	32						TTGCTTCAGGGAAAATATCCC	0.478																																					p.S272F		Atlas-SNP	.											.	NEUROD6	84	.	0			c.C815T						.						73	74	74					7																	31378068		2203	4300	6503	SO:0001583	missense	63974	exon2			TTCAGGGAAAATA	AF248954	CCDS5434.1	7p15.1	2013-05-21	2012-02-22		ENSG00000164600	ENSG00000164600		"Basic helix-loop-helix proteins"	13804	protein-coding gene	gene with protein product		611513	"neurogenic differentiation 6"			12357074	Standard	NM_022728		Approved	Atoh2, NEX1M, Math-2, bHLHa2, Nex1	uc003tch.4	Q96NK8	OTTHUMG00000022865	ENST00000297142.3:c.815C>T	chr7.hg19:g.31378068G>A	ENSP00000297142:p.Ser272Phe	90.0	0.0		79.0	29.0	NM_022728	Q548T9|Q9H3H6	Missense_Mutation	SNP	ENST00000297142.3	hg19	CCDS5434.1	.	.	.	.	.	.	.	.	.	.	G	17.26	3.343885	0.61073	.	.	ENSG00000164600	ENST00000297142	T	0.74002	-0.8	5.14	5.14	0.70334	Neurogenic differentiation factor, domain of unknown function (1);	0.000000	0.85682	D	0.000000	D	0.87605	0.6219	M	0.83118	2.625	0.80722	D	1	D	0.63880	0.993	D	0.81914	0.995	D	0.89465	0.3739	10	0.87932	D	0	-18.6607	18.6029	0.91255	0.0:0.0:1.0:0.0	.	272	Q96NK8	NDF6_HUMAN	F	272	ENSP00000297142:S272F	ENSP00000297142:S272F	S	-	2	0	NEUROD6	31344593	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.414000	0.97362	2.379000	0.81126	0.650000	0.86243	TCC	.	.		0.478	NEUROD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215050.1	NM_022728		A	31378068	G	A	31378068	3	1	370	1	0	0	0	0	1	0	0	0	10360	1174	41	3	202	3	NEUROD6	7	31378068	Missense_Mutation	SNP	G	TCGA-ZS-A9CD-01A-11D-A36X-10		31378068	127760595	41	51234										
WBSCR16	81554	hgsc.bcm.edu	37	chr7	74470082	74470082	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	ctgggttgaactccgtcaagCcaaagagagtgggtggaatc	14	8	1	2			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr7:74470082C>A	ENST00000329959.4	-	9	1212	c.1157G>T	c.(1156-1158)gGc>gTc	p.G386V	WBSCR16_ENST00000503250.2_Missense_Mutation_p.G386V	NM_030798.3	NP_110425.2	Q96I51	WBS16_HUMAN	Williams-Beuren syndrome chromosome region 16	386							poly(A) RNA binding (GO:0044822)			kidney(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	4						CTCCGTCAAGCCAAAGAGAGT	0.522																																					p.G386V		Atlas-SNP	.											.	WBSCR16	16	.	0			c.G1157T						.						38	43	41					7																	74470082		2203	4297	6500	SO:0001583	missense	81554	exon9			GTCAAGCCAAAGA	AF410455	CCDS5577.1, CCDS64683.1, CCDS64684.1	7q11.23	2008-08-14			ENSG00000174374	ENSG00000274523			14948	protein-coding gene	gene with protein product						12073013	Standard	NM_030798		Approved		uc003ubr.3	Q96I51	OTTHUMG00000130373	ENST00000329959.4:c.1157G>T	chr7.hg19:g.74470082C>A	ENSP00000333799:p.Gly386Val	592.0	0.0		541.0	90.0	NM_030798	D3DXK0|F5GX55|F5H6C7|Q548B1|Q8IW88|Q8N572|Q9H0G7	Missense_Mutation	SNP	ENST00000329959.4	hg19	CCDS5577.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.510955	0.85389	.	.	ENSG00000174374	ENST00000503250;ENST00000329959	D;D	0.82893	-1.66;-1.66	4.96	4.96	0.65561	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.85682	D	0.000000	D	0.92828	0.7719	M	0.91196	3.185	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.988	D	0.94137	0.7393	10	0.59425	D	0.04	-25.7576	16.7688	0.85531	0.0:1.0:0.0:0.0	.	386;386	F5H6C7;Q96I51	.;WBS16_HUMAN	V	386	ENSP00000437702:G386V;ENSP00000333799:G386V	ENSP00000333799:G386V	G	-	2	0	WBSCR16	74108018	1.000000	0.71417	0.869000	0.34112	0.890000	0.51754	7.578000	0.82498	2.264000	0.75181	0.462000	0.41574	GGC	.	.		0.522	WBSCR16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252740.1	NM_030798		A	74470082	C	A	74470082	3	1	370	1	0	0	0	0	1	0	0	0	17278	739	26	3	249	3	WBSCR16	7	74470082	Missense_Mutation	SNP	C	TCGA-ZS-A9CD-01A-11D-A36X-10	43092014	74470082	84668581	42	51235										
GIGYF1	64599	hgsc.bcm.edu	37	chr7	100281944	100281944	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	cctgttgcttcttcagccgcTcctggtccatgtttccctgc	8	16	2	0			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr7:100281944T>C	ENST00000275732.5	-	14	2855	c.1646A>G	c.(1645-1647)gAg>gGg	p.E549G	GIGYF1_ENST00000471340.2_5'Flank	NM_022574.4	NP_072096.2	O75420	PERQ1_HUMAN	GRB10 interacting GYF protein 1	549	Gln-rich.				insulin-like growth factor receptor signaling pathway (GO:0048009)					central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)					CTTCAGCCGCTCCTGGTCCAT	0.662																																					p.E549G		Atlas-SNP	.											.	GIGYF1	113	.	0			c.A1646G						.						22	22	22					7																	100281944		2201	4296	6497	SO:0001583	missense	64599	exon14			AGCCGCTCCTGGT	AF053356	CCDS34708.1	7q22	2008-02-11	2008-02-11	2008-02-11	ENSG00000146830	ENSG00000146830			9126	protein-coding gene	gene with protein product	"GYF domain containing 1"	612064	"PERQ amino acid rich, with GYF domain 1"	PERQ1		9799793, 12771153	Standard	NM_022574		Approved	GYF1	uc003uwg.1	O75420	OTTHUMG00000157036	ENST00000275732.5:c.1646A>G	chr7.hg19:g.100281944T>C	ENSP00000275732:p.Glu549Gly	48.0	0.0		56.0	22.0	NM_022574	Q6Y7W7|Q8WZ38	Missense_Mutation	SNP	ENST00000275732.5	hg19	CCDS34708.1	.	.	.	.	.	.	.	.	.	.	.	14.62	2.588489	0.46110	.	.	ENSG00000146830	ENST00000539430;ENST00000275732	D	0.84589	-1.87	4.52	4.52	0.55395	.	0.068034	0.56097	D	0.000025	T	0.81202	0.4773	L	0.54323	1.7	0.47153	D	0.999334	B	0.21071	0.051	B	0.19148	0.024	T	0.78492	-0.2183	10	0.45353	T	0.12	-31.8772	11.8296	0.52288	0.0:0.0:0.0:1.0	.	549	O75420	PERQ1_HUMAN	G	268;549	ENSP00000275732:E549G	ENSP00000275732:E549G	E	-	2	0	GIGYF1	100119880	1.000000	0.71417	1.000000	0.80357	0.707000	0.40811	4.012000	0.57131	1.907000	0.55213	0.260000	0.18958	GAG	.	.		0.662	GIGYF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347205.2	NM_022574		C	100281944	T	C	100281944	3	2	370	1	0	0	0	0	1	0	0	0	6385	1551	54	2	1505	2	GIGYF1	7	100281944	Missense_Mutation	SNP	T	TCGA-ZS-A9CD-01A-11D-A36X-10	25811862	100281944	58856719	43	51236										
KCNU1	157855	hgsc.bcm.edu	37	chr8	36664901	36664901	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	attggtttgtaggtttaaggTtcctaagagccttgcgcctg	12	7	0	1			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr8:36664901T>C	ENST00000399881.3	+	6	626	c.589T>C	c.(589-591)Ttc>Ctc	p.F197L		NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	197					multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		AGGTTTAAGGTTCCTAAGAGC	0.453																																					p.F197L		Atlas-SNP	.											.	KCNU1	359	.	0			c.T589C						.						145	146	146					8																	36664901		1869	4104	5973	SO:0001583	missense	157855	exon6			TTAAGGTTCCTAA	BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.589T>C	chr8.hg19:g.36664901T>C	ENSP00000382770:p.Phe197Leu	103.0	0.0		72.0	27.0	NM_001031836		Missense_Mutation	SNP	ENST00000399881.3	hg19	CCDS55220.1	.	.	.	.	.	.	.	.	.	.	T	27.5	4.839801	0.91117	.	.	ENSG00000215262	ENST00000523973;ENST00000399881	T;T	0.54675	0.56;0.56	5.03	5.03	0.67393	Ion transport (1);	0.000000	0.39341	U	0.001397	T	0.55369	0.1916	N	0.16037	0.36	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.62567	-0.6827	10	0.87932	D	0	-4.7666	12.2942	0.54836	0.0:0.0:0.0:1.0	.	197	A8MYU2	KCNU1_HUMAN	L	197	ENSP00000429951:F197L;ENSP00000382770:F197L	ENSP00000382770:F197L	F	+	1	0	KCNU1	36784059	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	6.259000	0.72494	1.900000	0.55004	0.528000	0.53228	TTC	.	.		0.453	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836		C	36664901	T	C	36664901	3	2	370	1	0	0	0	0	1	0	0	0	8102	1725	60	2	611	2	KCNU1	8	36664901	Missense_Mutation	SNP	T	TCGA-ZS-A9CD-01A-11D-A36X-10		36664901	109699121	44	51237										
APBA1	320	hgsc.bcm.edu	37	chr9	72131800	72131800	+	Silent	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	ctctcgtcctcggggtcctgCgcgcgctccgcatcgtagcc	12	18	1	0			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr9:72131800C>G	ENST00000265381.4	-	2	549	c.327G>C	c.(325-327)gcG>gcC	p.A109A		NM_001163.3	NP_001154.2	Q02410	APBA1_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 1	109					axon cargo transport (GO:0008088)|cell adhesion (GO:0007155)|gamma-aminobutyric acid secretion (GO:0014051)|glutamate secretion (GO:0014047)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein complex assembly (GO:0006461)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synaptic vesicle (GO:0008021)	beta-amyloid binding (GO:0001540)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(4)|kidney(2)|large_intestine(12)|lung(13)|prostate(3)|skin(3)	37						CGGGGTCCTGCGCGCGCTCCG	0.726																																					p.A109A		Atlas-SNP	.											.	APBA1	96	.	0			c.G327C						.						16	15	15					9																	72131800		2199	4281	6480	SO:0001819	synonymous_variant	320	exon2			GTCCTGCGCGCGC	AF029106	CCDS6630.1	9q13-q21	2008-07-18	2008-07-18		ENSG00000107282	ENSG00000107282			578	protein-coding gene	gene with protein product		602414		MINT1		7678331, 7719031	Standard	NM_001163		Approved	D9S411E, X11	uc004ahh.2	Q02410	OTTHUMG00000019984	ENST00000265381.4:c.327G>C	chr9.hg19:g.72131800C>G		27.0	0.0		20.0	9.0	NM_001163	O14914|O60570|Q5VYR8	Silent	SNP	ENST00000265381.4	hg19	CCDS6630.1																																																																																			.	.		0.726	APBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052589.2	NM_001163		G	72131800	C	G	72131800	2	3	370	1	0	0	0	0	0	0	0	1	756	755	27	4		4	APBA1	9	72131800	Silent	SNP	C	TCGA-ZS-A9CD-01A-11D-A36X-10		72131800	69081631	45	51238										
YME1L1	10730	hgsc.bcm.edu	37	chr10	27406578	27406578	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	catcttttgtgtaatatgcaAtaatggcatgaccagattca	7	7	2	2			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr10:27406578A>C	ENST00000326799.3	-	16	1965	c.1817T>G	c.(1816-1818)aTt>aGt	p.I606S	YME1L1_ENST00000375972.3_Missense_Mutation_p.I516S|YME1L1_ENST00000376016.3_Missense_Mutation_p.I549S	NM_139312.2	NP_647473.1	Q96TA2	YMEL1_HUMAN	YME1-like 1 ATPase	606					cell proliferation (GO:0008283)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|mitochondrion organization (GO:0007005)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	23						GTAATATGCAATAATGGCATG	0.383																																					p.I606S		Atlas-SNP	.											.	YME1L1	71	.	0			c.T1817G						.						324	273	291					10																	27406578		2203	4300	6503	SO:0001583	missense	10730	exon16			TATGCAATAATGG	AJ132637	CCDS7151.1, CCDS7152.1, CCDS58072.1	10p14	2013-06-10	2013-06-10		ENSG00000136758	ENSG00000136758		"ATPases / AAA-type"	12843	protein-coding gene	gene with protein product		607472	"YME1 (S.cerevisiae)-like 1", "YME1-like 1 (S. cerevisiae)"			22262461	Standard	NM_139312		Approved		uc001itj.3	Q96TA2	OTTHUMG00000017853	ENST00000326799.3:c.1817T>G	chr10.hg19:g.27406578A>C	ENSP00000318480:p.Ile606Ser	100.0	0.0		115.0	14.0	NM_139312	B4DNM1|D3DRV8|D3DRV9|Q5T8D9|Q9H1Q0|Q9UMR9	Missense_Mutation	SNP	ENST00000326799.3	hg19	CCDS7152.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.052336	0.75960	.	.	ENSG00000136758	ENST00000376016;ENST00000326799;ENST00000375969;ENST00000375972;ENST00000546122	D;D;D	0.86230	-2.09;-2.09;-2.09	5.49	5.49	0.81192	Peptidase M41 (1);Peptidase M41, FtsH (2);	0.050151	0.85682	D	0.000000	D	0.88463	0.6443	L	0.55743	1.74	0.80722	D	1	P;B;B	0.47191	0.891;0.082;0.1	P;B;B	0.49012	0.598;0.037;0.098	D	0.89807	0.3979	10	0.87932	D	0	-26.4193	15.8844	0.79232	1.0:0.0:0.0:0.0	.	516;549;606	B4DNM1;Q96TA2-2;Q96TA2	.;.;YMEL1_HUMAN	S	549;606;606;516;352	ENSP00000365184:I549S;ENSP00000318480:I606S;ENSP00000365139:I516S	ENSP00000318480:I606S	I	-	2	0	YME1L1	27446584	1.000000	0.71417	1.000000	0.80357	0.391000	0.30476	9.236000	0.95360	2.218000	0.71995	0.533000	0.62120	ATT	.	.		0.383	YME1L1-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047306.1	NM_139312		C	27406578	A	C	27406578	3	2	370	1	0	0	0	0	1	0	0	0	17502	101	4	5	524	5	YME1L1	10	27406578	Missense_Mutation	SNP	A	TCGA-ZS-A9CD-01A-11D-A36X-10		27406578	108128169	46	51239										
LIPF	8513	hgsc.bcm.edu	37	chr10	90438430	90438430	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	tttctatgatatcagaagatAaaaagtagttctggatttaa	7	3	3	3			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr10:90438430A>T	ENST00000238983.4	+	10	1235	c.1189A>T	c.(1189-1191)Aaa>Taa	p.K397*	LIPF_ENST00000608620.1_Nonsense_Mutation_p.K364*|LIPF_ENST00000355843.2_Nonsense_Mutation_p.K374*|LIPF_ENST00000394375.3_Nonsense_Mutation_p.K407*	NM_004190.3	NP_004181.1	P07098	LIPG_HUMAN	lipase, gastric	397					lipid catabolic process (GO:0016042)|malate metabolic process (GO:0006108)|triglyceride metabolic process (GO:0006641)	extracellular region (GO:0005576)|mitochondrion (GO:0005739)	lipid binding (GO:0008289)|malate dehydrogenase activity (GO:0016615)|triglyceride lipase activity (GO:0004806)			NS(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(6)	13		Colorectal(252;0.0161)		Colorectal(12;3.91e-05)|COAD - Colon adenocarcinoma(12;5.43e-05)	Orlistat(DB01083)	ATCAGAAGATAAAAAGTAGTT	0.328																																					p.K407X		Atlas-SNP	.											.	LIPF	62	.	0			c.A1219T						.						40	43	42					10																	90438430		2203	4299	6502	SO:0001587	stop_gained	8513	exon11			GAAGATAAAAAGT	X05997	CCDS7389.1, CCDS55718.1, CCDS55719.1, CCDS65896.1	10q23	2005-10-30			ENSG00000182333	ENSG00000182333	3.1.1.3		6622	protein-coding gene	gene with protein product		601980				3304425, 9186906	Standard	NM_004190		Approved	HGL, HLAL	uc010qmt.2	P07098	OTTHUMG00000018695	ENST00000238983.4:c.1189A>T	chr10.hg19:g.90438430A>T	ENSP00000238983:p.Lys397*	64.0	0.0		81.0	23.0	NM_001198829	B7Z723|F5H1P4|Q2M1P6|Q5VXI7|Q5VXI8|Q658L8	Nonsense_Mutation	SNP	ENST00000238983.4	hg19	CCDS7389.1	.	.	.	.	.	.	.	.	.	.	A	12.93	2.085316	0.36758	.	.	ENSG00000182333	ENST00000394375;ENST00000238983;ENST00000355843	.	.	.	5.13	-8.19	0.01049	.	1.055910	0.07417	N	0.893362	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.23891	T	0.37	-0.0855	1.3157	0.02107	0.2742:0.0913:0.2683:0.3662	.	.	.	.	X	407;397;364	.	ENSP00000238983:K397X	K	+	1	0	LIPF	90428410	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.123000	0.10611	-1.687000	0.01437	-1.139000	0.01908	AAA	.	.		0.328	LIPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049256.1			T	90438430	A	T	90438430	4	4	370	1	0	0	0	0	0	1	0	0	8831	363	13	4	1223	4	LIPF	10	90438430	Nonsense_Mutation	SNP	A	TCGA-ZS-A9CD-01A-11D-A36X-10	63031852	90438430	45096317	47	51240										
ERLIN1	1147	hgsc.bcm.edu	37	chr10	101945277	101945277	+	IGR	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	cacatgccgctcacctgtagTacacagccagatggccctcc	8	17	1	1			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr10:101945277T>A	ENST00000370397.7	-	0	3625				ERLIN1_ENST00000421367.2_Missense_Mutation_p.Y36F|ERLIN1_ENST00000407654.3_Missense_Mutation_p.Y36F|CHUK_ENST00000590930.1_5'Flank	NM_001278.3	NP_001269.3	O15111	IKKA_HUMAN	conserved helix-loop-helix ubiquitous kinase						anatomical structure morphogenesis (GO:0009653)|cellular response to tumor necrosis factor (GO:0071356)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|morphogenesis of an epithelial sheet (GO:0002011)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hydroperoxide (GO:0033194)|response to lipopolysaccharide (GO:0032496)|response to toxic substance (GO:0009636)|response to virus (GO:0009615)|Rho protein signal transduction (GO:0007266)|skeletal muscle contraction (GO:0003009)|striated muscle cell differentiation (GO:0051146)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|scaffold protein binding (GO:0097110)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(9)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	27		Colorectal(252;0.117)		Epithelial(162;2.05e-10)|all cancers(201;1.91e-08)	Acetylcysteine(DB06151)|Aminosalicylic Acid(DB00233)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	TCACCTGTAGTACACAGCCAG	0.562																																					p.Y36F	Ovarian(159;52 1904 10536 35305 37148)	Atlas-SNP	.											.	.	.	.	0			c.A107T						.						159	144	149					10																	101945277		2203	4300	6503	SO:0001628	intergenic_variant	10613	exon1			CTGTAGTACACAG	AF009225	CCDS7488.1	10q24-q25	2008-08-01			ENSG00000213341	ENSG00000213341			1974	protein-coding gene	gene with protein product		600664		TCF16		7558004, 16902410	Standard	XR_246062		Approved	IKK1, IKK-alpha, IkBKA, NFKBIKA, IKKA	uc001kqp.3	O15111	OTTHUMG00000018899		chr10.hg19:g.101945277T>A		149.0	0.0		129.0	27.0	NM_006459	O14666|Q13132|Q5W0I4|Q92467	Missense_Mutation	SNP	ENST00000370397.7	hg19	CCDS7488.1	.	.	.	.	.	.	.	.	.	.	T	26.9	4.785579	0.90282	.	.	ENSG00000107566	ENST00000421367;ENST00000407654;ENST00000370408	D;D;D	0.94417	-3.42;-3.42;-3.42	4.68	4.68	0.58851	.	0.000000	0.64402	U	0.000002	D	0.95579	0.8563	M	0.88241	2.94	0.80722	D	1	B	0.25351	0.124	B	0.37387	0.248	D	0.94725	0.7904	10	0.48119	T	0.1	-0.8814	12.424	0.55536	0.0:0.0:0.0:1.0	.	36	D3DR65	.	F	36	ENSP00000410964:Y36F;ENSP00000384900:Y36F;ENSP00000359436:Y36F	ENSP00000359436:Y36F	Y	-	2	0	ERLIN1	101935267	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.798000	0.85924	2.097000	0.63578	0.374000	0.22700	TAC	.	.		0.562	CHUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049836.1	NM_001278		A	101945277	T	A	101945277	1	1	370	0	1	0	0	0	0	0	0	0	5234	1638	57	4		4	ERLIN1	10	101945277	IGR	SNP	T	TCGA-ZS-A9CD-01A-11D-A36X-10	11506847	101945277	33589470	48	51241										
C10orf88	80007	hgsc.bcm.edu	37	chr10	124712495	124712495	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	cacacctcaggtaaaggaagCaggggttttcatctttgttg	11	8	3	0			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr10:124712495C>T	ENST00000481909.1	-	2	442	c.218G>A	c.(217-219)tGc>tAc	p.C73Y	C10orf88_ENST00000368891.5_5'UTR	NM_024942.3	NP_079218.2	Q9H8K7	CJ088_HUMAN	chromosome 10 open reading frame 88	73										breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)	18		all_neural(114;0.0765)|Lung NSC(174;0.163)|all_lung(145;0.205)		Colorectal(40;0.0686)|COAD - Colon adenocarcinoma(40;0.0735)		GTAAAGGAAGCAGGGGTTTTC	0.413																																					p.C73Y		Atlas-SNP	.											.	C10orf88	33	.	0			c.G218A						.						69	67	67					10																	124712495		2203	4300	6503	SO:0001583	missense	80007	exon2			AGGAAGCAGGGGT	AK023552	CCDS7632.1	10q26.13	2012-11-09			ENSG00000119965	ENSG00000119965			25822	protein-coding gene	gene with protein product						12477932	Standard	NM_024942		Approved	FLJ13490, Em:AC073585.5	uc001lgw.2	Q9H8K7	OTTHUMG00000019190	ENST00000481909.1:c.218G>A	chr10.hg19:g.124712495C>T	ENSP00000419126:p.Cys73Tyr	154.0	0.0		129.0	28.0	NM_024942	Q0P6C6|Q8N597	Missense_Mutation	SNP	ENST00000481909.1	hg19	CCDS7632.1	.	.	.	.	.	.	.	.	.	.	C	14.25	2.480527	0.44044	.	.	ENSG00000119965	ENST00000481909	.	.	.	4.64	4.64	0.57946	.	0.000000	0.64402	U	0.000018	T	0.79161	0.4399	M	0.79475	2.455	0.50039	D	0.99984	D	0.89917	1.0	D	0.91635	0.999	T	0.82643	-0.0356	9	0.87932	D	0	.	15.3099	0.74023	0.0:1.0:0.0:0.0	.	73	Q9H8K7	CJ088_HUMAN	Y	73	.	ENSP00000419126:C73Y	C	-	2	0	C10orf88	124702485	1.000000	0.71417	1.000000	0.80357	0.229000	0.25112	3.072000	0.50049	2.098000	0.63641	0.555000	0.69702	TGC	.	.		0.413	C10orf88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050807.1	NM_024942		T	124712495	C	T	124712495	3	4	370	1	0	0	0	0	1	0	0	0	1624	710	25	3	1139	3	C10orf88	10	124712495	Missense_Mutation	SNP	C	TCGA-ZS-A9CD-01A-11D-A36X-10	22767218	124712495	10822252	49	51242										
FAM196A	642938	hgsc.bcm.edu	37	chr10	128973669	128973669	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	gggactaggctggttccccaGccccggcggggtgtgagtct	17	12	1	1			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr10:128973669G>A	ENST00000522781.1	-	4	1546	c.991C>T	c.(991-993)Ctg>Ttg	p.L331L	FAM196A_ENST00000424811.2_Silent_p.L331L|DOCK1_ENST00000280333.6_Intron	NM_001039762.2	NP_001034851.1	Q6ZSG2	F196A_HUMAN	family with sequence similarity 196, member A	331										breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						TGGTTCCCCAGCCCCGGCGGG	0.622																																					p.L331L		Atlas-SNP	.											.	FAM196A	55	.	0			c.C991T						.						82	91	88					10																	128973669		2203	4300	6503	SO:0001819	synonymous_variant	642938	exon4			TCCCCAGCCCCGG		CCDS31312.1	10q26.2	2009-09-11	2009-09-11	2009-09-11		ENSG00000188916			33859	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 141"	C10orf141			Standard	NM_001039762		Approved	FLJ45557	uc001ljv.1	Q6ZSG2		ENST00000522781.1:c.991C>T	chr10.hg19:g.128973669G>A		64.0	0.0		66.0	14.0	NM_001039762	B2RNT4|B7ZME7	Silent	SNP	ENST00000522781.1	hg19	CCDS31312.1																																																																																			.	.		0.622	FAM196A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050978.2	NM_001039762		A	128973669	G	A	128973669	2	1	370	1	0	0	0	0	0	0	0	1	5533	962	34	3		3	FAM196A	10	128973669	Silent	SNP	G	TCGA-ZS-A9CD-01A-11D-A36X-10	4261174	128973669	6561078	50	51243										
TRIM5	85363	hgsc.bcm.edu	37	chr11	5686301	5686301	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	ggaaagcactacatttaactCcttcctctaaccctataacc	3	14	1	0			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr11:5686301C>A	ENST00000380034.3	-	8	1476	c.1220G>T	c.(1219-1221)gGa>gTa	p.G407V	TRIM5_ENST00000396853.4_Intron|TRIM5_ENST00000380027.1_Intron|TRIM5_ENST00000396855.3_Intron|TRIM5_ENST00000483835.1_Intron|TRIM5_ENST00000305836.5_Missense_Mutation_p.G407V|TRIM5_ENST00000396847.3_3'UTR	NM_033034.2|NM_033092.2	NP_149023.2|NP_149083.2	Q9C035	TRIM5_HUMAN	tripartite motif containing 5	407	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				activation of innate immune response (GO:0002218)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein K63-linked ubiquitination (GO:0070534)|protein trimerization (GO:0070206)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|signaling pattern recognition receptor activity (GO:0008329)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	21		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)|Lung NSC(207;0.138)|all_lung(207;0.221)		Epithelial(150;7.21e-09)|BRCA - Breast invasive adenocarcinoma(625;0.139)		ACATTTAACTCCTTCCTCTAA	0.408																																					p.G407V		Atlas-SNP	.											.	TRIM5	111	.	0			c.G1220T						.						120	121	121					11																	5686301		2201	4297	6498	SO:0001583	missense	85363	exon8			TTAACTCCTTCCT	AF220025	CCDS31392.1, CCDS31393.1, CCDS31394.1	11p15	2014-06-03	2011-01-25		ENSG00000132256	ENSG00000132256		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16276	protein-coding gene	gene with protein product	"tripartite motif protein TRIM5", "tripartite motif protein TRIM"	608487	"tripartite motif-containing 5"			11331580	Standard	NM_033034		Approved	RNF88, TRIM5alpha	uc001mbm.2	Q9C035	OTTHUMG00000066893	ENST00000380034.3:c.1220G>T	chr11.hg19:g.5686301C>A	ENSP00000369373:p.Gly407Val	91.0	0.0		70.0	19.0	NM_033034	A6NGQ1|A8WFA8|D3DQS8|D3DQS9|G3GJY1|Q2MLV4|Q2MLV8|Q2MLV9|Q2MLW1|Q2MLW3|Q2MLW4|Q2MLW6|Q2MLW7|Q2MLX1|Q2MLX2|Q2MLX3|Q2MLX5|Q2MLY3|Q2MLY4|Q2V6Q6|Q6GX26|Q8WU46|Q96SR5|Q9C031|Q9C032|Q9C033|Q9C034	Missense_Mutation	SNP	ENST00000380034.3	hg19	CCDS31393.1	.	.	.	.	.	.	.	.	.	.	C	6.154	0.396588	0.11638	.	.	ENSG00000132256	ENST00000305836;ENST00000380034	T;T	0.63580	-0.05;-0.05	3.93	-7.86	0.01187	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	4.960520	0.00496	N	0.000152	T	0.61337	0.2339	L	0.58302	1.8	0.09310	N	1	B	0.30361	0.277	B	0.39339	0.297	T	0.58329	-0.7655	10	0.41790	T	0.15	.	9.7748	0.40612	0.0:0.4862:0.3399:0.1739	.	407	Q9C035	TRIM5_HUMAN	V	407	ENSP00000307031:G407V;ENSP00000369373:G407V	ENSP00000307031:G407V	G	-	2	0	TRIM5	5642877	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.917000	0.01575	-2.805000	0.00350	-2.258000	0.00281	GGA	.	.		0.408	TRIM5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000143360.3	NM_033034		A	5686301	C	A	5686301	3	1	370	1	0	0	0	0	1	0	0	0	16540	855	30	3	355	3	TRIM5	11	5686301	Missense_Mutation	SNP	C	TCGA-ZS-A9CD-01A-11D-A36X-10		5686301	129320215	51	51244										
NAV2	89797	hgsc.bcm.edu	37	chr11	19955146	19955147	+	Missense_Mutation	DNP	GG	GG	CT													0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	agtcgcatgctcaccaccgtGggccctgcttccagcagccc							TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr11:19955146_19955147GG>CT	ENST00000396087.3	+	8	1524_1525	c.1425_1426GG>CT	c.(1423-1428)gtGGgc>gtCTgc	p.G476C	NAV2_ENST00000349880.4_Missense_Mutation_p.G453C|NAV2_ENST00000527559.2_Missense_Mutation_p.G405C|NAV2_ENST00000540292.1_Missense_Mutation_p.G407C|NAV2_ENST00000360655.4_Missense_Mutation_p.G389C|NAV2_ENST00000396085.1_Missense_Mutation_p.G453C	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	476					glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						TCACCACCGTGGGCCCTGCTTC	0.614																																					p.V475V|p.G476C		Atlas-SNP	.											.	NAV2	255	.	0			c.G1425C|c.G1426T						.																																			SO:0001583	missense	89797	exon8			CACCGTGGGCCCT|ACCGTGGGCCCTG	AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 2", "retinoic acid inducible gene in neuroblastoma 1", "helicase, APC down-regulated 1"	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	Exception_encountered	chr11.hg19:g.19955146_19955147delinsCT	ENSP00000379396:p.Gly476Cys	133.0|132.0	0.0		129.0	41.0|42.0	NM_001244963	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Silent|Missense_Mutation	SNP	ENST00000396087.3	hg19	CCDS58126.1																																																																																			.	.		0.614	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117		CT	19955147	GG	CT	19955146	3	2	370	1	0	0	0	0	1	0	0	0	10193	1335	47	4	1461	4	NAV2	11	19955146	Missense_Mutation	DNP	GG	TCGA-ZS-A9CD-01A-11D-A36X-10	14268845	19955146	115051370	52	51245										
OR4C15	81309	hgsc.bcm.edu	37	chr11	55322138	55322138	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	gtacttcttcttgggcttccTgtccttcctggatgcgtgct	10	12	2	0			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr11:55322138T>A	ENST00000314644.2	+	1	356	c.356T>A	c.(355-357)cTg>cAg	p.L119Q		NM_001001920.1	NP_001001920.1	Q8NGM1	OR4CF_HUMAN	olfactory receptor, family 4, subfamily C, member 15	65						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(31)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(5)	56						TTGGGCTTCCTGTCCTTCCTG	0.468										HNSCC(20;0.049)																											p.L119Q		Atlas-SNP	.											.	OR4C15	145	.	0			c.T356A						.						187	150	162					11																	55322138		2201	4296	6497	SO:0001583	missense	81309	exon1			GCTTCCTGTCCTT	BK004319	CCDS31501.1	11q11	2012-08-09			ENSG00000181939	ENSG00000181939		"GPCR / Class A : Olfactory receptors"	15171	protein-coding gene	gene with protein product							Standard	NM_001001920		Approved		uc010rig.2	Q8NGM1	OTTHUMG00000166714	ENST00000314644.2:c.356T>A	chr11.hg19:g.55322138T>A	ENSP00000324958:p.Leu119Gln	40.0	0.0		44.0	9.0	NM_001001920	Q6IFE2	Missense_Mutation	SNP	ENST00000314644.2	hg19	CCDS31501.1	.	.	.	.	.	.	.	.	.	.	T	19.03	3.748846	0.69533	.	.	ENSG00000181939	ENST00000314644	T	0.00520	6.85	5.0	5.0	0.66597	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.04724	0.0128	H	0.99712	4.72	0.37817	D	0.928254	D	0.89917	1.0	D	0.91635	0.999	T	0.01242	-1.1408	9	0.87932	D	0	.	12.6919	0.56980	0.0:0.0:0.0:1.0	.	65	Q8NGM1	OR4CF_HUMAN	Q	119	ENSP00000324958:L119Q	ENSP00000324958:L119Q	L	+	2	0	OR4C15	55078714	0.668000	0.27493	0.986000	0.45419	0.663000	0.39108	5.063000	0.64332	2.105000	0.64084	0.317000	0.21355	CTG	.	.		0.468	OR4C15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391164.1	NM_001001920		A	55322138	T	A	55322138	3	1	370	1	0	0	0	0	1	0	0	0	11057	1580	55	4	358	4	OR4C15	11	55322138	Missense_Mutation	SNP	T	TCGA-ZS-A9CD-01A-11D-A36X-10	35366992	55322138	79684378	53	51246										
SERPING1	710	hgsc.bcm.edu	37	chr11	57367761	57367761	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	agatttctccctgaagctctAccacgccttctcagcaatga	6	14	3	3	rs281875168		TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr11:57367761A>C	ENST00000278407.4	+	3	688	c.461A>C	c.(460-462)tAc>tCc	p.Y154S	SERPING1_ENST00000340687.6_Missense_Mutation_p.Y154S|SERPING1_ENST00000403558.1_Missense_Mutation_p.Y188S|SERPING1_ENST00000378323.4_Missense_Mutation_p.Y159S|SERPING1_ENST00000378324.2_Missense_Mutation_p.Y102S	NM_000062.2	NP_000053.2	P05155	IC1_HUMAN	serpin peptidase inhibitor, clade G (C1 inhibitor), member 1	154			Y -> C (in HAE; dbSNP:rs281875168). {ECO:0000269|PubMed:22994404}.		blood circulation (GO:0008015)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|complement activation, classical pathway (GO:0006958)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(11)|pancreas(2)|prostate(1)|urinary_tract(1)	27						CTGAAGCTCTACCACGCCTTC	0.542																																					p.Y154S		Atlas-SNP	.											SERPING1,bladder,carcinoma,0,1	SERPING1	57	.	0			c.A461C						.						109	111	110					11																	57367761		2201	4296	6497	SO:0001583	missense	710	exon2			AGCTCTACCACGC	X54486	CCDS7962.1	11q12.1	2014-09-17	2008-07-31		ENSG00000149131	ENSG00000149131		"Serine (or cysteine) peptidase inhibitors"	1228	protein-coding gene	gene with protein product	"plasma protease C1 inhibitor", "angioedema, hereditary"	606860	"serine (or cysteine) proteinase inhibitor, clade G (C1 inhibitor), member 1, (angioedema, hereditary)"	C1NH		2026152, 24172014	Standard	NM_000062		Approved	C1IN, C1-INH, HAE1, HAE2	uc001nkp.1	P05155	OTTHUMG00000150304	ENST00000278407.4:c.461A>C	chr11.hg19:g.57367761A>C	ENSP00000278407:p.Tyr154Ser	134.0	1.0		98.0	22.0	NM_001032295	A6NMU0|A8KAI9|B2R6L5|B4E1F0|B4E1H2|Q16304|Q547W3|Q59EI5|Q7Z455|Q96FE0|Q9UC49|Q9UCF9	Missense_Mutation	SNP	ENST00000278407.4	hg19	CCDS7962.1	.	.	.	.	.	.	.	.	.	.	A	18.13	3.555873	0.65425	.	.	ENSG00000149131	ENST00000405496;ENST00000278407;ENST00000340687;ENST00000378323;ENST00000378324;ENST00000403558	D;D;D;D;D;D	0.96334	-3.98;-2.57;-2.57;-2.57;-2.57;-2.57	5.94	5.94	0.96194	Serpin domain (3);	0.068425	0.64402	D	0.000011	D	0.98210	0.9408	M	0.88842	2.985	0.53688	D	0.999973	D;D;D;D	0.89917	0.992;1.0;0.992;0.992	D;D;D;D	0.97110	0.922;1.0;0.922;0.922	D	0.99050	1.0827	10	0.87932	D	0	.	12.7897	0.57526	1.0:0.0:0.0:0.0	.	159;188;154;154	B4E1F0;E9PGN7;E9KL26;P05155	.;.;.;IC1_HUMAN	S	154;154;154;159;102;188	ENSP00000384561:Y154S;ENSP00000278407:Y154S;ENSP00000341861:Y154S;ENSP00000367574:Y159S;ENSP00000367575:Y102S;ENSP00000384420:Y188S	ENSP00000278407:Y154S	Y	+	2	0	SERPING1	57124337	1.000000	0.71417	1.000000	0.80357	0.409000	0.31022	3.475000	0.53136	2.279000	0.76181	0.459000	0.35465	TAC	.	.		0.542	SERPING1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317465.1	NM_000062		C	57367761	A	C	57367761	3	2	370	1	0	0	0	0	1	0	0	0	14131	391	14	5	467	5	SERPING1	11	57367761	Missense_Mutation	SNP	A	TCGA-ZS-A9CD-01A-11D-A36X-10	2045623	57367761	77638755	54	51247										
OSBP	5007	hgsc.bcm.edu	37	chr11	59345631	59345631	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	ctgatactcacggtaaaggaTtccttttccacagcatgacc	7	12	1	2			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr11:59345631T>A	ENST00000263847.1	-	12	2530	c.2051A>T	c.(2050-2052)aAt>aTt	p.N684I		NM_002556.2	NP_002547.1	P22059	OSBP1_HUMAN	oxysterol binding protein	684					lipid transport (GO:0006869)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	oxysterol binding (GO:0008142)			NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		all_epithelial(135;0.000236)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)		CGGTAAAGGATTCCTTTTCCA	0.483																																					p.N684I		Atlas-SNP	.											.	OSBP	57	.	0			c.A2051T						.						237	183	201					11																	59345631		2201	4295	6496	SO:0001583	missense	5007	exon12			AAAGGATTCCTTT	AF185696	CCDS7974.1	11q12-q13	2013-01-10			ENSG00000110048	ENSG00000110048		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	8503	protein-coding gene	gene with protein product		167040					Standard	NM_002556		Approved	OSBP1	uc001noc.1	P22059	OTTHUMG00000167422	ENST00000263847.1:c.2051A>T	chr11.hg19:g.59345631T>A	ENSP00000263847:p.Asn684Ile	124.0	0.0		90.0	35.0	NM_002556	Q6P524	Missense_Mutation	SNP	ENST00000263847.1	hg19	CCDS7974.1	.	.	.	.	.	.	.	.	.	.	T	15.26	2.781262	0.49891	.	.	ENSG00000110048	ENST00000263847;ENST00000378235	T	0.32988	1.43	5.72	5.72	0.89469	.	0.045544	0.85682	D	0.000000	T	0.48003	0.1476	M	0.80422	2.495	0.58432	D	0.999996	P	0.37276	0.589	P	0.46208	0.507	T	0.49312	-0.8953	10	0.49607	T	0.09	-25.2278	14.9838	0.71330	0.0:0.0:0.0:1.0	.	684	P22059	OSBP1_HUMAN	I	684;284	ENSP00000263847:N684I	ENSP00000263847:N684I	N	-	2	0	OSBP	59102207	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	5.979000	0.70508	2.183000	0.69458	0.528000	0.53228	AAT	.	.		0.483	OSBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394555.1			A	59345631	T	A	59345631	3	1	370	1	0	0	0	0	1	0	0	0	11282	1493	52	4	384	4	OSBP	11	59345631	Missense_Mutation	SNP	T	TCGA-ZS-A9CD-01A-11D-A36X-10	1977870	59345631	75660885	55	51248										
CD6	923	hgsc.bcm.edu	37	chr11	60739363	60739363	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	gctcttcttcgggatcactgGattgctgacggcagccctct	11	13	4	1			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr11:60739363G>T	ENST00000313421.7	+	1	212	c.26G>T	c.(25-27)gGa>gTa	p.G9V	CD6_ENST00000352009.5_Missense_Mutation_p.G9V|CD6_ENST00000346437.4_Missense_Mutation_p.G9V|CD6_ENST00000344028.5_Missense_Mutation_p.G9V|CD6_ENST00000545105.1_3'UTR|CD6_ENST00000452451.2_Missense_Mutation_p.G9V	NM_006725.4	NP_006716.3	P30203	CD6_HUMAN	CD6 molecule	9					cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	scavenger receptor activity (GO:0005044)			endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)	18						GGGATCACTGGATTGCTGACG	0.642																																					p.G9V	Pancreas(169;904 2017 4767 38890 42505)	Atlas-SNP	.											.	CD6	122	.	0			c.G26T						.						73	63	66					11																	60739363		2203	4299	6502	SO:0001583	missense	923	exon1			TCACTGGATTGCT		CCDS7999.1, CCDS58137.1, CCDS58138.1	11q12.2	2006-03-28	2006-03-28		ENSG00000013725	ENSG00000013725		"CD molecules"	1691	protein-coding gene	gene with protein product		186720	"CD6 antigen"			9013954	Standard	NM_006725		Approved	Tp120	uc001nqq.3	P30203	OTTHUMG00000167823	ENST00000313421.7:c.26G>T	chr11.hg19:g.60739363G>T	ENSP00000323280:p.Gly9Val	48.0	0.0		37.0	14.0	NM_006725	A4KAD4|A4KAD5|Q9UMF2|Q9Y4K7|Q9Y4K8|Q9Y4K9|Q9Y4L0	Missense_Mutation	SNP	ENST00000313421.7	hg19	CCDS7999.1	.	.	.	.	.	.	.	.	.	.	G	16.03	3.008037	0.54361	.	.	ENSG00000013725	ENST00000344028;ENST00000346437;ENST00000313421;ENST00000542157;ENST00000433107;ENST00000452451;ENST00000352009	T;T;T;T;T;T;T	0.01981	4.76;4.77;4.52;4.66;4.85;4.7;4.72	3.7	3.7	0.42460	.	15.212100	0.00166	N	0.000006	T	0.08313	0.0207	L	0.27053	0.805	0.40311	D	0.978718	D;D;D;D;D	0.89917	1.0;1.0;1.0;0.993;0.964	D;D;D;P;P	0.91635	0.998;0.999;0.999;0.804;0.706	T	0.20940	-1.0260	10	0.59425	D	0.04	.	11.2533	0.49039	0.0:0.0:1.0:0.0	.	9;9;9;9;9	E7ER04;P30203-5;P30203-4;P30203;Q8N4Q7	.;.;.;CD6_HUMAN;.	V	9	ENSP00000344108:G9V;ENSP00000345566:G9V;ENSP00000323280:G9V;ENSP00000440055:G9V;ENSP00000410638:G9V;ENSP00000390676:G9V;ENSP00000340628:G9V	ENSP00000323280:G9V	G	+	2	0	CD6	60495939	0.888000	0.30383	0.423000	0.26634	0.009000	0.06853	2.530000	0.45641	2.348000	0.79779	0.655000	0.94253	GGA	.	.		0.642	CD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396449.1	NM_006725		T	60739363	G	T	60739363	3	4	370	1	0	0	0	0	1	0	0	0	3030	1174	41	3	28	3	CD6	11	60739363	Missense_Mutation	SNP	G	TCGA-ZS-A9CD-01A-11D-A36X-10	1393732	60739363	74267153	56	51249										
CNTN1	1272	hgsc.bcm.edu	37	chr12	41312465	41312465	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	tgaggaagacaaaggatttgGaccaatttttgaagagcagc	12	5	0	4			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr12:41312465G>T	ENST00000551295.2	+	4	236	c.119G>T	c.(118-120)gGa>gTa	p.G40V	CNTN1_ENST00000360099.3_Missense_Mutation_p.G40V|CNTN1_ENST00000547849.1_Missense_Mutation_p.G40V|CNTN1_ENST00000348761.2_Missense_Mutation_p.G29V|CNTN1_ENST00000347616.1_Missense_Mutation_p.G40V|CNTN1_ENST00000547702.1_Missense_Mutation_p.G40V	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	40					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(21)|lung(49)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				AAAGGATTTGGACCAATTTTT	0.368																																					p.G40V		Atlas-SNP	.											.	CNTN1	207	.	0			c.G119T						.						71	77	75					12																	41312465		2203	4300	6503	SO:0001583	missense	1272	exon4			GATTTGGACCAAT	Z21488	CCDS8737.1, CCDS8738.1, CCDS58225.1	12q11-q12	2014-01-30				ENSG00000018236		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing", "Endogenous ligands"	2171	protein-coding gene	gene with protein product	"glycoprotein gP135"	600016				7959734, 8586965	Standard	NM_001843		Approved	F3, GP135	uc031qgz.1	Q12860		ENST00000551295.2:c.119G>T	chr12.hg19:g.41312465G>T	ENSP00000447006:p.Gly40Val	286.0	0.0		320.0	70.0	NM_001256063	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Missense_Mutation	SNP	ENST00000551295.2	hg19	CCDS8737.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.817016	0.90790	.	.	ENSG00000018236	ENST00000547702;ENST00000551424;ENST00000551295;ENST00000548005;ENST00000552248;ENST00000547849;ENST00000552913;ENST00000347616;ENST00000360099;ENST00000348761	T;T;T;T;T;T;T;T	0.67171	-0.25;0.16;0.91;0.91;-0.25;0.16;-0.25;0.12	5.36	5.36	0.76844	Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.68860	0.3047	N	0.08118	0	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.75938	-0.3141	10	0.59425	D	0.04	.	19.4779	0.94996	0.0:0.0:1.0:0.0	.	40;29;40	Q12860-3;Q12860-2;Q12860	.;.;CNTN1_HUMAN	V	40;40;40;40;40;40;40;40;40;29	ENSP00000448004:G40V;ENSP00000447006:G40V;ENSP00000447862:G40V;ENSP00000447860:G40V;ENSP00000448653:G40V;ENSP00000325660:G40V;ENSP00000353213:G40V;ENSP00000261160:G29V	ENSP00000325660:G40V	G	+	2	0	CNTN1	39598732	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.989000	0.93506	2.682000	0.91365	0.585000	0.79938	GGA	.	.		0.368	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	NM_001843		T	41312465	G	T	41312465	3	4	370	1	0	0	0	0	1	0	0	0	3642	1174	41	3	129	3	CNTN1	12	41312465	Missense_Mutation	SNP	G	TCGA-ZS-A9CD-01A-11D-A36X-10		41312465	92539430	57	51250										
KRT73	319101	hgsc.bcm.edu	37	chr12	53012005	53012005	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	ggtgacctgatggataccccCgggcgggcacaacgacggac	15	13	0	2	rs199866943		TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr12:53012005C>A	ENST00000305748.3	-	1	338	c.304G>T	c.(304-306)Ggg>Tgg	p.G102W	RP11-641A6.2_ENST00000552364.1_RNA	NM_175068.2	NP_778238.1	Q86Y46	K2C73_HUMAN	keratin 73	102	Gly-rich.|Head.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)	p.G102R(1)|p.G102W(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44				BRCA - Breast invasive adenocarcinoma(357;0.189)		TGGATACCCCCGGGCGGGCAC	0.632																																					p.G102W		Atlas-SNP	.											KRT73,colon,carcinoma,0,1	KRT73	101	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G304T						.						109	115	113					12																	53012005		2203	4300	6503	SO:0001583	missense	319101	exon1			TACCCCCGGGCGG	AJ508776	CCDS8834.1	12q13.13	2013-06-25			ENSG00000186049	ENSG00000186049		"-", "Intermediate filaments type II, keratins (basic)"	28928	protein-coding gene	gene with protein product		608247				12648212, 16831889	Standard	NM_175068		Approved	KRT6IRS3, K6IRS3	uc001sas.3	Q86Y46	OTTHUMG00000169746	ENST00000305748.3:c.304G>T	chr12.hg19:g.53012005C>A	ENSP00000307014:p.Gly102Trp	163.0	0.0		120.0	38.0	NM_175068	Q32MB2	Missense_Mutation	SNP	ENST00000305748.3	hg19	CCDS8834.1	.	.	.	.	.	.	.	.	.	.	C	12.29	1.892215	0.33442	.	.	ENSG00000186049	ENST00000305748	D	0.92495	-3.05	4.64	3.75	0.43078	.	0.000000	0.53938	D	0.000055	D	0.97040	0.9033	H	0.95260	3.645	0.31888	N	0.61763	D	0.89917	1.0	D	0.91635	0.999	D	0.97057	0.9768	10	0.87932	D	0	.	13.7729	0.63036	0.0:0.9237:0.0:0.0763	.	102	Q86Y46	K2C73_HUMAN	W	102	ENSP00000307014:G102W	ENSP00000307014:G102W	G	-	1	0	KRT73	51298272	0.013000	0.17824	0.801000	0.32222	0.004000	0.04260	2.627000	0.46469	1.276000	0.44395	-0.123000	0.14984	GGG	.	C|1.000;T|0.000		0.632	KRT73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405700.1	NM_175068		A	53012005	C	A	53012005	3	1	370	1	0	0	0	0	1	0	0	0	8495	652	23	1	1354	1	KRT73	12	53012005	Missense_Mutation	SNP	C	TCGA-ZS-A9CD-01A-11D-A36X-10	11699540	53012005	80839890	58	51251										
KRT79	338785	hgsc.bcm.edu	37	chr12	53225249	53225249	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	agctctgagtccagcctcccCcgctcgctctgaagtctgtc	9	17	3	2			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr12:53225249C>A	ENST00000330553.5	-	2	673	c.639G>T	c.(637-639)cgG>cgT	p.R213R		NM_175834.2	NP_787028.1	Q5XKE5	K2C79_HUMAN	keratin 79	213	Coil 1B.|Rod.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	enzyme binding (GO:0019899)|structural molecule activity (GO:0005198)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						CCAGCCTCCCCCGCTCGCTCT	0.612																																					p.R213R		Atlas-SNP	.											.	KRT79	78	.	0			c.G639T						.						112	112	112					12																	53225249		2203	4300	6503	SO:0001819	synonymous_variant	338785	exon2			CCTCCCCCGCTCG	AJ564105	CCDS8839.1	12q13.13	2014-02-12	2007-07-03		ENSG00000185640	ENSG00000185640		"-", "Intermediate filaments type II, keratins (basic)"	28930	protein-coding gene	gene with protein product	"keratin 6-like"	611160				11683385	Standard	NM_175834		Approved	K6L, KRT6L	uc001sbb.3	Q5XKE5	OTTHUMG00000169878	ENST00000330553.5:c.639G>T	chr12.hg19:g.53225249C>A		81.0	0.0		61.0	19.0	NM_175834	Q6P465|Q7Z793	Silent	SNP	ENST00000330553.5	hg19	CCDS8839.1																																																																																			.	.		0.612	KRT79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406376.1	NM_175834		A	53225249	C	A	53225249	2	1	370	1	0	0	0	0	0	0	0	1	8501	610	22	3		3	KRT79	12	53225249	Silent	SNP	C	TCGA-ZS-A9CD-01A-11D-A36X-10	213244	53225249	80626646	59	51252										
E2F7	144455	hgsc.bcm.edu	37	chr12	77444515	77444515	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	gtccacagcactgtccccaaCaacatcaagctacagagggc	8	15	1	1			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr12:77444515C>A	ENST00000322886.7	-	4	614	c.379G>T	c.(379-381)Gtt>Ttt	p.V127F	E2F7_ENST00000416496.2_Missense_Mutation_p.V127F	NM_203394.2	NP_976328.2	Q96AV8	E2F7_HUMAN	E2F transcription factor 7	127					chorionic trophoblast cell differentiation (GO:0060718)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|hepatocyte differentiation (GO:0070365)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokinesis (GO:0032466)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|identical protein binding (GO:0042802)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(15)|lung(14)|ovary(3)|upper_aerodigestive_tract(2)	42						CTGTCCCCAACAACATCAAGC	0.483																																					p.V127F		Atlas-SNP	.											.	E2F7	201	.	0			c.G379T						.						92	87	89					12																	77444515		2203	4300	6503	SO:0001583	missense	144455	exon4			CCCCAACAACATC	BC016658	CCDS9016.1	12q21.1	2008-02-05				ENSG00000165891			23820	protein-coding gene	gene with protein product		612046				12893818	Standard	NM_203394		Approved		uc001sym.4	Q96AV8	OTTHUMG00000169969	ENST00000322886.7:c.379G>T	chr12.hg19:g.77444515C>A	ENSP00000323246:p.Val127Phe	59.0	0.0		39.0	12.0	NM_203394	A6NC74|B2RMR7|B3KTZ5|B3KUP8|B5MED9	Missense_Mutation	SNP	ENST00000322886.7	hg19	CCDS9016.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.68|17.68	3.448734|3.448734	0.63178|0.63178	.|.	.|.	ENSG00000165891|ENSG00000165891	ENST00000551058|ENST00000322886;ENST00000416496;ENST00000550669	.|T;T;T	.|0.19105	.|2.43;2.17;2.18	5.7|5.7	4.8|4.8	0.61643|0.61643	.|.	.|0.371732	.|0.30028	.|N	.|0.010582	T|T	0.26159|0.26159	0.0638|0.0638	L|L	0.44542|0.44542	1.39|1.39	0.29557|0.29557	N|N	0.850913|0.850913	.|P;P	.|0.49961	.|0.925;0.93	.|P;P	.|0.48141	.|0.568;0.467	T|T	0.05852|0.05852	-1.0860|-1.0860	5|10	.|0.29301	.|T	.|0.29	-7.3522|-7.3522	15.8342|15.8342	0.78787|0.78787	0.0:0.8639:0.1361:0.0|0.0:0.8639:0.1361:0.0	.|.	.|127;127	.|F8VSE7;Q96AV8	.|.;E2F7_HUMAN	F|F	4|127	.|ENSP00000323246:V127F;ENSP00000393639:V127F;ENSP00000448245:V127F	.|ENSP00000323246:V127F	L|V	-|-	3|1	2|0	E2F7|E2F7	75968646|75968646	0.959000|0.959000	0.32827|0.32827	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	3.328000|3.328000	0.52052|0.52052	1.394000|1.394000	0.46624|0.46624	0.650000|0.650000	0.86243|0.86243	TTG|GTT	.	.		0.483	E2F7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406716.1	XM_084871		A	77444515	C	A	77444515	3	1	370	1	0	0	0	0	1	0	0	0	4874	478	17	3	2396	3	E2F7	12	77444515	Missense_Mutation	SNP	C	TCGA-ZS-A9CD-01A-11D-A36X-10	24219266	77444515	56407380	60	51253										
STAB2	55576	hgsc.bcm.edu	37	chr12	104155082	104155082	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	cttctcatttccctagacggAgaccaggtttgttgatggaa	10	9	1	3			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr12:104155082A>C	ENST00000388887.2	+	66	7457	c.7253A>C	c.(7252-7254)gAg>gCg	p.E2418A	RP11-341G23.4_ENST00000551299.1_RNA|RP11-341G23.4_ENST00000550029.1_RNA	NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						CCCTAGACGGAGACCAGGTTT	0.522																																					p.E2418A		Atlas-SNP	.											.	STAB2	370	.	0			c.A7253C						.						150	129	136					12																	104155082		2203	4300	6503	SO:0001583	missense	55576	exon66			AGACGGAGACCAG	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"hyaluronic acid receptor for endocytosis"	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.7253A>C	chr12.hg19:g.104155082A>C	ENSP00000373539:p.Glu2418Ala	85.0	0.0		83.0	22.0	NM_017564		Missense_Mutation	SNP	ENST00000388887.2	hg19	CCDS31888.1	.	.	.	.	.	.	.	.	.	.	A	5.927	0.355088	0.11239	.	.	ENSG00000136011	ENST00000388887	D	0.91740	-2.9	4.95	4.95	0.65309	FAS1 domain (4);	0.357304	0.25230	N	0.032167	D	0.86527	0.5954	N	0.17800	0.525	0.35374	D	0.789317	P	0.46859	0.885	P	0.48770	0.589	D	0.85232	0.1033	10	0.08179	T	0.78	.	10.7619	0.46270	0.841:0.159:0.0:0.0	.	2418	Q8WWQ8	STAB2_HUMAN	A	2418	ENSP00000373539:E2418A	ENSP00000373539:E2418A	E	+	2	0	STAB2	102679212	1.000000	0.71417	0.996000	0.52242	0.455000	0.32408	4.033000	0.57282	1.855000	0.53841	0.533000	0.62120	GAG	.	.		0.522	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			C	104155082	A	C	104155082	3	2	370	1	0	0	0	0	1	0	0	0	15253	304	11	5	7515	5	STAB2	12	104155082	Missense_Mutation	SNP	A	TCGA-ZS-A9CD-01A-11D-A36X-10	26710567	104155082	29696813	61	51254										
TDG	6996	hgsc.bcm.edu	37	chr12	104378700	104378700	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	gacctacagcttgcccaaggTatgttactgtcctcattcct	7	13	1	0			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr12:104378700T>A	ENST00000392872.3	+	8	1198		c.e8+2		TDG_ENST00000544861.1_Splice_Site|TDG_ENST00000542036.1_Splice_Site|AC078819.1_ENST00000401157.1_RNA|TDG_ENST00000266775.9_Splice_Site	NM_003211.4	NP_003202.3	Q13569	TDG_HUMAN	thymine-DNA glycosylase						base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|chromatin modification (GO:0016568)|depyrimidination (GO:0045008)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|embryo development (GO:0009790)|mismatch repair (GO:0006298)|negative regulation of chromatin binding (GO:0035562)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression, epigenetic (GO:0040029)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|double-stranded DNA binding (GO:0003690)|mismatched DNA binding (GO:0030983)|protein homodimerization activity (GO:0042803)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|RNA polymerase II transcription cofactor activity (GO:0001104)|structure-specific DNA binding (GO:0043566)			large_intestine(2)|lung(14)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(302;0.00114)		TTGCCCAAGGTATGTTACTGT	0.313								Base excision repair (BER), DNA glycosylases																													.		Atlas-SNP	.											.	TDG	43	.	0			c.964+2T>A						.						119	112	115					12																	104378700		2203	4300	6503	SO:0001630	splice_region_variant	6996	exon8			CCAAGGTATGTTA	U51166	CCDS9095.1	12q24.1	2014-05-14			ENSG00000139372	ENSG00000139372	3.2.2.29		11700	protein-coding gene	gene with protein product	"G/T mismatch-specific thymine DNA glycosylase"	601423				8662714, 9299239	Standard	NM_003211		Approved		uc001tkg.3	Q13569	OTTHUMG00000168418	ENST00000392872.3:c.964+2T>A	chr12.hg19:g.104378700T>A		116.0	0.0		151.0	43.0	NM_003211	Q8IUZ6|Q8IZM3	Splice_Site	SNP	ENST00000392872.3	hg19	CCDS9095.1	.	.	.	.	.	.	.	.	.	.	T	19.61	3.860203	0.71834	.	.	ENSG00000139372	ENST00000392872;ENST00000266775;ENST00000544861;ENST00000542036	.	.	.	5.99	5.99	0.97316	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.4943	0.84223	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	TDG	102902830	1.000000	0.71417	0.940000	0.37924	0.735000	0.41995	8.040000	0.89188	2.291000	0.77112	0.533000	0.62120	.	.	.		0.313	TDG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399673.2		Intron	A	104378700	T	A	104378700	5	1	370	1	0	0	0	0	0	0	1	0	15740	1652	57	4	996	4	TDG	12	104378700	Splice_Site	SNP	T	TCGA-ZS-A9CD-01A-11D-A36X-10	223618	104378700	29473195	62	51255										
NOC4L	79050	hgsc.bcm.edu	37	chr12	132636036	132636036	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	ctgccctgcccagccacctcCccgcctacctggtggccgcc	9	23	0	0	rs554287010	byFrequency	TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr12:132636036C>T	ENST00000330579.1	+	12	1122	c.1081C>T	c.(1081-1083)Ccc>Tcc	p.P361S	NOC4L_ENST00000535343.1_3'UTR|NOC4L_ENST00000538784.1_5'UTR	NM_024078.1	NP_076983.1	Q9BVI4	NOC4L_HUMAN	nucleolar complex associated 4 homolog (S. cerevisiae)	361					rRNA processing (GO:0006364)	integral component of membrane (GO:0016021)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(2)|large_intestine(1)|lung(7)|skin(2)	14	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.2e-08)|Epithelial(86;3.34e-07)|all cancers(50;1.97e-05)		CAGCCACCTCCCCGCCTACCT	0.706																																					p.P361S		Atlas-SNP	.											NOC4L,mucosal,malignant_melanoma,0,1	NOC4L	31	.	0			c.C1081T						.						16	20	19					12																	132636036		2178	4284	6462	SO:0001583	missense	79050	exon12			CACCTCCCCGCCT		CCDS9277.1	12q24.33	2011-08-12			ENSG00000184967	ENSG00000184967			28461	protein-coding gene	gene with protein product		612819				12446671	Standard	NM_024078		Approved	MGC3162, NET49, UTP19	uc001ujz.1	Q9BVI4	OTTHUMG00000168260	ENST00000330579.1:c.1081C>T	chr12.hg19:g.132636036C>T	ENSP00000328854:p.Pro361Ser	36.0	0.0		25.0	6.0	NM_024078	Q8N2S5|Q96I14	Missense_Mutation	SNP	ENST00000330579.1	hg19	CCDS9277.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.990210	0.74589	.	.	ENSG00000184967	ENST00000330579	T	0.23552	1.9	5.33	4.44	0.53790	CCAAT-binding factor (1);	0.000000	0.85682	D	0.000000	T	0.43077	0.1231	L	0.53617	1.68	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.18085	-1.0348	10	0.19590	T	0.45	-27.0096	13.6021	0.62026	0.0:0.9239:0.0:0.0761	.	361	Q9BVI4	NOC4L_HUMAN	S	361	ENSP00000328854:P361S	ENSP00000328854:P361S	P	+	1	0	NOC4L	131201989	1.000000	0.71417	0.874000	0.34290	0.498000	0.33706	5.399000	0.66314	1.251000	0.43983	0.561000	0.74099	CCC	.	.		0.706	NOC4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398999.1	NM_024078		T	132636036	C	T	132636036	3	4	370	1	0	0	0	0	1	0	0	0	10524	623	22	3	1127	3	NOC4L	12	132636036	Missense_Mutation	SNP	C	TCGA-ZS-A9CD-01A-11D-A36X-10	28257336	132636036	1215859	63	51256										
ATP8A2	51761	hgsc.bcm.edu	37	chr13	26594029	26594029	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	gtgtgcttcactttcagatgGgtatgctttttctcaagaag	10	7	3	2			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr13:26594029G>T	ENST00000381655.2	+	37	3615	c.3473G>T	c.(3472-3474)gGg>gTg	p.G1158V	ATP8A2_ENST00000255283.8_Missense_Mutation_p.G1093V	NM_016529.4	NP_057613.4	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8A, member 2	1118					aging (GO:0007568)|axonogenesis (GO:0007409)|detection of light stimulus involved in visual perception (GO:0050908)|eating behavior (GO:0042755)|inner ear morphogenesis (GO:0042472)|involuntary skeletal muscle contraction (GO:0003011)|negative regulation of cell proliferation (GO:0008285)|neurofilament cytoskeleton organization (GO:0060052)|neuromuscular process controlling posture (GO:0050884)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phospholipid translocation (GO:0061092)|response to auditory stimulus (GO:0010996)|retina layer formation (GO:0010842)|skin development (GO:0043588)	cell projection (GO:0042995)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(17)|lung(31)|ovary(4)|skin(3)|stomach(1)|urinary_tract(1)	72		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		CTTTCAGATGGGTATGCTTTT	0.438																																					p.G1158V		Atlas-SNP	.											.	ATP8A2	181	.	0			c.G3473T						.						104	97	99					13																	26594029		1919	4138	6057	SO:0001583	missense	51761	exon37			CAGATGGGTATGC	AL137256	CCDS41873.1	13q12	2010-04-20	2010-03-31		ENSG00000132932	ENSG00000132932	3.6.3.1	"ATPases / P-type"	13533	protein-coding gene	gene with protein product		605870	"ATPase, aminophospholipid transporter-like, Class I, type 8A, member 2", "ATPase, aminophospholipid transporter-like, class I, type 8A, member 2"			11015572, 19778899	Standard	NM_016529		Approved	ATPIB, ML-1	uc001uqk.3	Q9NTI2	OTTHUMG00000016611	ENST00000381655.2:c.3473G>T	chr13.hg19:g.26594029G>T	ENSP00000371070:p.Gly1158Val	109.0	0.0		68.0	21.0	NM_016529	Q9H527|Q9NPU6|Q9NTL2|Q9NYM3	Missense_Mutation	SNP	ENST00000381655.2	hg19	CCDS41873.1	.	.	.	.	.	.	.	.	.	.	G	19.32	3.804283	0.70682	.	.	ENSG00000132932	ENST00000381655;ENST00000255283;ENST00000544544	T;T	0.78246	-0.25;-1.16	4.81	4.81	0.61882	.	0.270973	0.35096	N	0.003446	D	0.90027	0.6886	M	0.88031	2.925	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.91977	0.5591	10	0.87932	D	0	.	18.0766	0.89428	0.0:0.0:1.0:0.0	.	1093;1118	B7Z880;Q9NTI2	.;AT8A2_HUMAN	V	1158;1093;938	ENSP00000371070:G1158V;ENSP00000255283:G1093V	ENSP00000255283:G1093V	G	+	2	0	ATP8A2	25492029	1.000000	0.71417	0.987000	0.45799	0.894000	0.52154	6.910000	0.75741	2.507000	0.84556	0.555000	0.69702	GGG	.	.		0.438	ATP8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044236.2	NM_016529		T	26594029	G	T	26594029	3	4	370	1	0	0	0	0	1	0	0	0	1193	1232	43	3	3619	3	ATP8A2	13	26594029	Missense_Mutation	SNP	G	TCGA-ZS-A9CD-01A-11D-A36X-10		26594029	88575849	64	51257										
ELF1	1997	hgsc.bcm.edu	37	chr13	41507803	41507803	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	agcaaccagctgtgaactgcGaggagaaaaggtcaccacag	12	10	1	2	rs538458962	byFrequency	TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr13:41507803G>A	ENST00000239882.3	-	9	1932	c.1618C>T	c.(1618-1620)Cgc>Tgc	p.R540C	ELF1_ENST00000498824.1_5'UTR|ELF1_ENST00000442101.1_Missense_Mutation_p.R516C	NM_172373.3	NP_758961.1	P32519	ELF1_HUMAN	E74-like factor 1 (ets domain transcription factor)	540					cell differentiation (GO:0030154)|negative regulation of T cell receptor signaling pathway (GO:0050860)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine production (GO:0001817)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37		Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367)		all cancers(112;1.87e-08)|Epithelial(112;8.45e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000202)|GBM - Glioblastoma multiforme(144;0.00266)|BRCA - Breast invasive adenocarcinoma(63;0.072)		TGTGAACTGCGAGGAGAAAAG	0.463													G|||	3	0.000599042	0	0	5008	,	,		21812	0		0	False		,,,				2504	0.0031				p.R540C		Atlas-SNP	.											.	ELF1	65	.	0			c.C1618T						.						95	89	91					13																	41507803		2203	4300	6503	SO:0001583	missense	1997	exon9			AACTGCGAGGAGA	M82882	CCDS9374.1	13q13	2008-07-18			ENSG00000120690	ENSG00000120690			3316	protein-coding gene	gene with protein product		189973				1545787	Standard	NM_001145353		Approved		uc001uxs.3	P32519	OTTHUMG00000016783	ENST00000239882.3:c.1618C>T	chr13.hg19:g.41507803G>A	ENSP00000239882:p.Arg540Cys	90.0	0.0		72.0	22.0	NM_172373	B4E2I5|E9PDQ9|Q8N6F6|Q9UDE1	Missense_Mutation	SNP	ENST00000239882.3	hg19	CCDS9374.1	.	.	.	.	.	.	.	.	.	.	G	15.06	2.720088	0.48728	.	.	ENSG00000120690	ENST00000442101;ENST00000379498;ENST00000239882	T;T	0.20463	2.07;2.07	5.23	4.33	0.51752	.	0.333731	0.31461	N	0.007611	T	0.16557	0.0398	L	0.27053	0.805	0.40465	D	0.980284	D;D	0.69078	0.993;0.997	B;P	0.46339	0.427;0.513	T	0.01007	-1.1483	10	0.56958	D	0.05	.	8.0336	0.30480	0.0:0.1271:0.5628:0.3101	.	516;540	E9PDQ9;P32519	.;ELF1_HUMAN	C	516;282;540	ENSP00000405580:R516C;ENSP00000239882:R540C	ENSP00000239882:R540C	R	-	1	0	ELF1	40405803	0.999000	0.42202	1.000000	0.80357	0.967000	0.64934	2.365000	0.44196	2.438000	0.82558	0.591000	0.81541	CGC	.	.		0.463	ELF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044654.3	NM_172373		A	41507803	G	A	41507803	3	1	370	1	0	0	0	0	1	0	0	0	5055	1058	37	1	245	1	ELF1	13	41507803	Missense_Mutation	SNP	G	TCGA-ZS-A9CD-01A-11D-A36X-10	14913774	41507803	73662075	65	51258										
ITGBL1	9358	hgsc.bcm.edu	37	chr13	102235651	102235651	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	catggggacacctgtgaatgTgatgagagggactgtagagc	16	6	0	4			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr13:102235651T>C	ENST00000376180.3	+	6	1032	c.813T>C	c.(811-813)tgT>tgC	p.C271C	ITGBL1_ENST00000376162.3_Silent_p.C178C|ITGBL1_ENST00000545560.2_Silent_p.C130C	NM_001271756.1|NM_004791.1	NP_001258685.1|NP_004782.1	O95965	ITGBL_HUMAN	integrin, beta-like 1 (with EGF-like repeat domains)	271	Cysteine-rich tandem repeats.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)				breast(1)|large_intestine(6)|lung(16)|ovary(1)|prostate(4)|skin(3)	31	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					CCTGTGAATGTGATGAGAGGG	0.502																																					p.C271C		Atlas-SNP	.											ITGBL1,bladder,carcinoma,0,1	ITGBL1	83	.	0			c.T813C						.						261	248	252					13																	102235651		2203	4300	6503	SO:0001819	synonymous_variant	9358	exon6			TGAATGTGATGAG	AF072752	CCDS9499.1, CCDS61361.1, CCDS61362.1, CCDS73594.1	13q33	2008-07-18			ENSG00000198542	ENSG00000198542			6164	protein-coding gene	gene with protein product	"ten integrin EGF-like repeat domains protein", "ITGBL1, integrin beta-like 1"	604234				10051402	Standard	NM_004791		Approved	TIED, OSCP	uc001vpb.4	O95965	OTTHUMG00000017296	ENST00000376180.3:c.813T>C	chr13.hg19:g.102235651T>C		146.0	0.0		104.0	26.0	NM_004791	A8K5M5|B3KTP1|B4DQ02|Q8N172|Q9NPR0	Silent	SNP	ENST00000376180.3	hg19	CCDS9499.1																																																																																			.	.		0.502	ITGBL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045669.2	NM_004791		C	102235651	T	C	102235651	2	2	370	1	0	0	0	0	0	0	0	1	7911	1702	59	2		2	ITGBL1	13	102235651	Silent	SNP	T	TCGA-ZS-A9CD-01A-11D-A36X-10	60727848	102235651	12934227	66	51259										
AP4S1	11154	hgsc.bcm.edu	37	chr14	31554030	31554030	+	Intron	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	cctggagccccagcagacttGcttttctccagacagttcat	8	14	2	2			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr14:31554030G>T	ENST00000542754.2	+	5	699				AP4S1_ENST00000554345.1_Missense_Mutation_p.C117F|AP4S1_ENST00000334725.4_3'UTR|AP4S1_ENST00000216366.4_Missense_Mutation_p.C141F|AP4S1_ENST00000313566.6_Intron|AP4S1_ENST00000554609.1_Intron	NM_001128126.2|NM_001254728.1	NP_001121598.1|NP_001241657.1	Q9Y587	AP4S1_HUMAN	adaptor-related protein complex 4, sigma 1 subunit							coated pit (GO:0005905)|Golgi apparatus (GO:0005794)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			lung(1)	1	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.221)	GBM - Glioblastoma multiforme(265;0.00553)		CAGCAGACTTGCTTTTCTCCA	0.438																																					p.C141F	Pancreas(128;620 2365 4508 44145)	Atlas-SNP	.											.	AP4S1	23	.	0			c.G422T						.						74	76	75					14																	31554030		2203	4300	6503	SO:0001627	intron_variant	11154	exon6			AGACTTGCTTTTC	AB030654	CCDS9642.1, CCDS45093.1, CCDS58309.1, CCDS58310.1	14q12	2012-06-29			ENSG00000100478	ENSG00000100478			575	protein-coding gene	gene with protein product		607243				10436028, 21620353	Standard	NM_007077		Approved	CLA20, AP47B, SPG52	uc001wqw.4	Q9Y587	OTTHUMG00000140202	ENST00000542754.2:c.306+4240G>T	chr14.hg19:g.31554030G>T		350.0	0.0		330.0	25.0	NM_007077	G3V2N8|Q6IAQ4|Q86U36|Q9BVE7	Missense_Mutation	SNP	ENST00000542754.2	hg19	CCDS45093.1	.	.	.	.	.	.	.	.	.	.	G	13.26	2.184710	0.38609	.	.	ENSG00000100478	ENST00000216366;ENST00000554345	.	.	.	4.05	2.07	0.26955	.	6.477130	0.00718	N	0.000868	T	0.36908	0.0984	.	.	.	0.09310	N	0.999999	P;P	0.50528	0.828;0.936	B;P	0.44990	0.371;0.466	T	0.36648	-0.9739	8	0.33940	T	0.23	.	10.515	0.44885	0.0:0.4249:0.5751:0.0	.	117;141	G3V2N8;Q9Y587-2	.;.	F	141;117	.	ENSP00000216366:C141F	C	+	2	0	AP4S1	30623781	0.108000	0.22018	0.004000	0.12327	0.128000	0.20619	1.182000	0.32029	0.572000	0.29383	0.655000	0.94253	TGC	.	.		0.438	AP4S1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409723.1			T	31554030	G	T	31554030	1	4	370	0	1	0	0	0	0	0	0	0	754	1319	46	3		3	AP4S1	14	31554030	Intron	SNP	G	TCGA-ZS-A9CD-01A-11D-A36X-10		31554030	75795510	67	51260										
ACTN1	87	hgsc.bcm.edu	37	chr14	69358837	69358837	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	gccgcagcttggtctgcagcGtgttgaagttgatctccagc	13	11	2	2			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr14:69358837G>A	ENST00000193403.6	-	10	1402	c.1019C>T	c.(1018-1020)aCg>aTg	p.T340M	ACTN1_ENST00000376839.3_Missense_Mutation_p.T275M|ACTN1_ENST00000554508.1_5'Flank|ACTN1_ENST00000538545.2_Missense_Mutation_p.T340M|ACTN1_ENST00000394419.4_Missense_Mutation_p.T340M|ACTN1_ENST00000438964.2_Missense_Mutation_p.T340M	NM_001102.3	NP_001093.1	P12814	ACTN1_HUMAN	actinin, alpha 1	340	Interaction with DDN.				actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|negative regulation of cellular component movement (GO:0051271)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of apoptotic process (GO:0042981)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|double-stranded RNA binding (GO:0003725)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|vinculin binding (GO:0017166)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(9)|prostate(2)|urinary_tract(1)	27				BRCA - Breast invasive adenocarcinoma(234;0.00605)|all cancers(60;0.00846)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		GGTCTGCAGCGTGTTGAAGTT	0.637																																					p.T340M		Atlas-SNP	.											.	ACTN1	77	.	0			c.C1019T						.						91	81	85					14																	69358837		2203	4300	6503	SO:0001583	missense	87	exon10			TGCAGCGTGTTGA	M95178	CCDS9792.1, CCDS45129.1, CCDS45130.1	14q24.1	2014-08-08			ENSG00000072110	ENSG00000072110		"EF-hand domain containing"	163	protein-coding gene	gene with protein product		102575				2349951	Standard	NM_001102		Approved		uc001xkm.3	P12814	OTTHUMG00000171386	ENST00000193403.6:c.1019C>T	chr14.hg19:g.69358837G>A	ENSP00000193403:p.Thr340Met	128.0	0.0		96.0	11.0	NM_001102	B3V8S3|B4DHH3|B7TY16|Q1HE25|Q9BTN1	Missense_Mutation	SNP	ENST00000193403.6	hg19	CCDS9792.1	.	.	.	.	.	.	.	.	.	.	G	28.6	4.935430	0.92458	.	.	ENSG00000072110	ENST00000193403;ENST00000394419;ENST00000438964;ENST00000376839;ENST00000538545	T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67	4.77	4.77	0.60923	.	0.000000	0.85682	D	0.000000	T	0.76407	0.3983	M	0.92649	3.33	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;P;D	0.79108	0.983;0.992;0.904;0.972	D	0.83383	0.0013	10	0.87932	D	0	.	17.9951	0.89181	0.0:0.0:1.0:0.0	.	340;340;340;340	B7TY16;P12814-2;Q1HE25;P12814	.;.;.;ACTN1_HUMAN	M	340;340;340;275;340	ENSP00000193403:T340M;ENSP00000377941:T340M;ENSP00000414272:T340M;ENSP00000366035:T275M;ENSP00000439828:T340M	ENSP00000193403:T340M	T	-	2	0	ACTN1	68428590	1.000000	0.71417	0.999000	0.59377	0.986000	0.74619	9.631000	0.98424	2.464000	0.83262	0.643000	0.83706	ACG	.	.		0.637	ACTN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413233.3	NM_001102		A	69358837	G	A	69358837	3	1	370	1	0	0	0	0	1	0	0	0	204	1145	40	1	1777	1	ACTN1	14	69358837	Missense_Mutation	SNP	G	TCGA-ZS-A9CD-01A-11D-A36X-10	37804807	69358837	37990703	68	51261										
PTPN21	11099	hgsc.bcm.edu	37	chr14	88967666	88967666	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	tccatagccatccattctctCtacctcctgcatgtacagca	4	16	2	0			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr14:88967666C>T	ENST00000556564.1	-	7	918	c.634G>A	c.(634-636)Gag>Aag	p.E212K	RP11-507K2.2_ENST00000555444.1_RNA|PTPN21_ENST00000328736.3_Missense_Mutation_p.E212K|PTPN21_ENST00000554628.1_5'UTR	NM_007039.3	NP_008970.2	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type 21	212	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|liver(1)|lung(7)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						TCCATTCTCTCTACCTCCTGC	0.448																																					p.E212K		Atlas-SNP	.											.	PTPN21	113	.	0			c.G634A						.						177	179	179					14																	88967666		2203	4300	6503	SO:0001583	missense	11099	exon7			TTCTCTCTACCTC	X79510	CCDS9884.1	14q31	2011-06-09				ENSG00000070778		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9651	protein-coding gene	gene with protein product		603271				7519780	Standard	NM_007039		Approved	PTPD1, PTPRL10	uc001xwv.4	Q16825		ENST00000556564.1:c.634G>A	chr14.hg19:g.88967666C>T	ENSP00000452414:p.Glu212Lys	234.0	0.0		191.0	54.0	NM_007039		Missense_Mutation	SNP	ENST00000556564.1	hg19	CCDS9884.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.837863	0.91117	.	.	ENSG00000070778	ENST00000328736;ENST00000556564	T;T	0.77229	-1.08;-1.08	5.34	5.34	0.76211	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);FERM conserved site (1);	0.000000	0.85682	D	0.000000	T	0.77532	0.4144	N	0.10733	0.035	0.50313	D	0.999862	D	0.89917	1.0	D	0.87578	0.998	T	0.78406	-0.2216	10	0.28530	T	0.3	.	18.6691	0.91504	0.0:1.0:0.0:0.0	.	212	Q16825	PTN21_HUMAN	K	212	ENSP00000330276:E212K;ENSP00000452414:E212K	ENSP00000330276:E212K	E	-	1	0	PTPN21	88037419	1.000000	0.71417	0.988000	0.46212	0.778000	0.44026	7.248000	0.78268	2.511000	0.84671	0.655000	0.94253	GAG	.	.		0.448	PTPN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410303.1			T	88967666	C	T	88967666	3	4	370	1	0	0	0	0	1	0	0	0	12801	922	32	3	2942	3	PTPN21	14	88967666	Missense_Mutation	SNP	C	TCGA-ZS-A9CD-01A-11D-A36X-10	19608829	88967666	18381874	69	51262										
DISP2	85455	hgsc.bcm.edu	37	chr15	40660759	40660759	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	agcgctggctgctggcactcTgtcaccgggcccggaatcag	14	14	3	0			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr15:40660759T>C	ENST00000267889.3	+	8	2533	c.2446T>C	c.(2446-2448)Tgt>Cgt	p.C816R	RP11-64K12.4_ENST00000558421.1_RNA	NM_033510.1	NP_277045.1	A7MBM2	DISP2_HUMAN	dispatched homolog 2 (Drosophila)	816					smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)	30		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.39e-06)|Colorectal(105;0.0114)|READ - Rectum adenocarcinoma(2;0.0649)|BRCA - Breast invasive adenocarcinoma(123;0.0798)|Lung(196;0.15)|LUAD - Lung adenocarcinoma(183;0.247)		GCTGGCACTCTGTCACCGGGC	0.672																																					p.C816R		Atlas-SNP	.											.	DISP2	86	.	0			c.T2446C						.						35	41	39					15																	40660759		2201	4296	6497	SO:0001583	missense	85455	exon8			GCACTCTGTCACC	AB051529	CCDS10056.1	15q14	2004-01-15			ENSG00000140323	ENSG00000140323			19712	protein-coding gene	gene with protein product		607503				11214970, 10619433	Standard	NM_033510		Approved	DISPB, KIAA1742, HsT16908	uc001zlk.1	A7MBM2	OTTHUMG00000129983	ENST00000267889.3:c.2446T>C	chr15.hg19:g.40660759T>C	ENSP00000267889:p.Cys816Arg	63.0	0.0		58.0	11.0	NM_033510	Q6AHW3|Q9C0C1	Missense_Mutation	SNP	ENST00000267889.3	hg19	CCDS10056.1	.	.	.	.	.	.	.	.	.	.	T	16.38	3.106032	0.56291	.	.	ENSG00000140323	ENST00000267889	T	0.32023	1.47	5.29	5.29	0.74685	.	0.044253	0.85682	D	0.000000	T	0.59487	0.2197	M	0.83483	2.645	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.65747	-0.6093	10	0.72032	D	0.01	-30.1226	15.3877	0.74714	0.0:0.0:0.0:1.0	.	816	A7MBM2	DISP2_HUMAN	R	816	ENSP00000267889:C816R	ENSP00000267889:C816R	C	+	1	0	DISP2	38448051	1.000000	0.71417	0.146000	0.22360	0.697000	0.40408	7.862000	0.87013	2.224000	0.72417	0.459000	0.35465	TGT	.	.		0.672	DISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252249.1	NM_033510		C	40660759	T	C	40660759	3	2	370	1	0	0	0	0	1	0	0	0	4542	1580	55	2	2476	2	DISP2	15	40660759	Missense_Mutation	SNP	T	TCGA-ZS-A9CD-01A-11D-A36X-10		40660759	61870633	70	51263										
PLA2G4F	255189	hgsc.bcm.edu	37	chr15	42434382	42434382	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	gtccccaaaggccttctcctCagctgtttgtcgctccacac	7	17	2	0			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr15:42434382C>T	ENST00000382396.4	-	20	2436	c.2350G>A	c.(2350-2352)Gag>Aag	p.E784K	PLA2G4F_ENST00000397272.3_Missense_Mutation_p.E786K			Q68DD2	PA24F_HUMAN	phospholipase A2, group IVF	784	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid secretion (GO:0050482)|cellular response to antibiotic (GO:0071236)|cellular response to organic cyclic compound (GO:0071407)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	calcium-dependent phospholipase A2 activity (GO:0047498)|lysophospholipase activity (GO:0004622)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32		all_cancers(109;4.82e-12)|all_epithelial(112;5.64e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(94;8.97e-07)		GCCTTCTCCTCAGCTGTTTGT	0.572																																					p.E784K		Atlas-SNP	.											.	PLA2G4F	75	.	0			c.G2350A						.						67	58	61					15																	42434382		2203	4299	6502	SO:0001583	missense	255189	exon20			TCTCCTCAGCTGT		CCDS32204.1	15q15.1	2008-09-19				ENSG00000168907	3.1.1.4		27396	protein-coding gene	gene with protein product						14702039, 15866882	Standard	NM_213600		Approved	PLA2G4F/Z	uc001zoz.3	Q68DD2		ENST00000382396.4:c.2350G>A	chr15.hg19:g.42434382C>T	ENSP00000371833:p.Glu784Lys	112.0	0.0		92.0	29.0	NM_213600	Q6ZMC8	Missense_Mutation	SNP	ENST00000382396.4	hg19	CCDS32204.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.132183	0.77662	.	.	ENSG00000168907	ENST00000290497;ENST00000397272;ENST00000382396;ENST00000443825	T;T	0.04551	3.6;3.6	5.21	5.21	0.72293	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (2);	0.377447	0.24652	N	0.036716	T	0.07683	0.0193	L	0.50333	1.59	0.46749	D	0.99918	B;B;B	0.30937	0.11;0.301;0.11	B;B;B	0.25884	0.016;0.064;0.011	T	0.16158	-1.0412	10	0.56958	D	0.05	-17.3755	19.1295	0.93399	0.0:1.0:0.0:0.0	.	571;786;784	A2RRC4;C9J281;Q68DD2	.;.;PA24F_HUMAN	K	780;786;784;784	ENSP00000380442:E786K;ENSP00000371833:E784K	ENSP00000290497:E780K	E	-	1	0	PLA2G4F	40221674	0.908000	0.30866	0.999000	0.59377	0.991000	0.79684	2.722000	0.47269	2.616000	0.88540	0.655000	0.94253	GAG	.	.		0.572	PLA2G4F-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000420463.1	NM_213600		T	42434382	C	T	42434382	3	4	370	1	0	0	0	0	1	0	0	0	12015	835	29	3	203	3	PLA2G4F	15	42434382	Missense_Mutation	SNP	C	TCGA-ZS-A9CD-01A-11D-A36X-10	1773623	42434382	60097010	71	51264										
ADAL	161823	hgsc.bcm.edu	37	chr15	43643187	43643187	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	tcagacagttccatcttatgAccagcaccatttcggattct	6	12	3	2			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr15:43643187A>G	ENST00000562188.1	+	9	837	c.821A>G	c.(820-822)gAc>gGc	p.D274G	ADAL_ENST00000422466.2_Missense_Mutation_p.D274G|ADAL_ENST00000428046.3_Missense_Mutation_p.D247G			Q6DHV7	ADAL_HUMAN	adenosine deaminase-like	274					adenosine catabolic process (GO:0006154)|drug metabolic process (GO:0017144)|inosine biosynthetic process (GO:0046103)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	adenosine deaminase activity (GO:0004000)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|lung(2)|prostate(1)|skin(1)	7		all_cancers(109;7.96e-11)|all_epithelial(112;2.96e-09)|Lung NSC(122;8.91e-07)|all_lung(180;8.8e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;9.31e-07)		CCATCTTATGACCAGCACCAT	0.408																																					p.D247G		Atlas-SNP	.											.	ADAL	48	.	0			c.A740G						.						422	342	366					15																	43643187		690	1590	2280	SO:0001583	missense	161823	exon11			CTTATGACCAGCA		CCDS32214.1, CCDS53936.1	15q15.3	2014-08-08			ENSG00000168803	ENSG00000168803			31853	protein-coding gene	gene with protein product							Standard	NM_001012969		Approved		uc010udo.2	Q6DHV7	OTTHUMG00000176646	ENST00000562188.1:c.821A>G	chr15.hg19:g.43643187A>G	ENSP00000456242:p.Asp274Gly	138.0	0.0		144.0	20.0	NM_001159280	A6NHZ3|B4DQM8	Missense_Mutation	SNP	ENST00000562188.1	hg19		.	.	.	.	.	.	.	.	.	.	A	13.50	2.256922	0.39896	.	.	ENSG00000168803	ENST00000422466;ENST00000428046	D;D	0.95482	-3.72;-3.72	5.69	2.09	0.27110	Adenosine/AMP deaminase (1);	.	.	.	.	D	0.91240	0.7239	L	0.38175	1.15	0.36743	D	0.882344	B;P	0.45957	0.12;0.869	B;P	0.45167	0.06;0.472	D	0.86794	0.1987	9	0.35671	T	0.21	-2.5682	4.8897	0.13721	0.7085:0.0:0.1541:0.1374	.	247;274	B4DQM8;Q6DHV7	.;ADAL_HUMAN	G	274;247	ENSP00000398744:D274G;ENSP00000413074:D247G	ENSP00000398744:D274G	D	+	2	0	ADAL	41430479	1.000000	0.71417	0.910000	0.35882	0.369000	0.29798	4.265000	0.58865	0.099000	0.17552	-0.344000	0.07964	GAC	.	.		0.408	ADAL-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432960.1	XM_091156		G	43643187	A	G	43643187	3	3	370	1	0	0	0	0	1	0	0	0	233	275	10	2	887	2	ADAL	15	43643187	Missense_Mutation	SNP	A	TCGA-ZS-A9CD-01A-11D-A36X-10	1208805	43643187	58888205	72	51265										
SORD	6652	hgsc.bcm.edu	37	chr15	45361208	45361208	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	tgcaagccggaagtcaccatCgagtgcacgggggcagaggc	16	11	1	1			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr15:45361208C>G	ENST00000267814.9	+	7	924	c.744C>G	c.(742-744)atC>atG	p.I248M	SORD_ENST00000558580.1_Missense_Mutation_p.I227M	NM_003104.5	NP_003095.2	Q00796	DHSO_HUMAN	sorbitol dehydrogenase	248					fructose biosynthetic process (GO:0046370)|glucose metabolic process (GO:0006006)|L-xylitol catabolic process (GO:0051160)|L-xylitol metabolic process (GO:0051164)|sorbitol catabolic process (GO:0006062)|sperm motility (GO:0030317)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|motile cilium (GO:0031514)	carbohydrate binding (GO:0030246)|L-iditol 2-dehydrogenase activity (GO:0003939)|NAD binding (GO:0051287)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(3)|lung(4)	9		all_cancers(109;3.43e-12)|all_epithelial(112;2.33e-10)|Lung NSC(122;6.01e-07)|all_lung(180;4.38e-06)|Melanoma(134;0.0122)		all cancers(107;1.6e-18)|GBM - Glioblastoma multiforme(94;4.95e-07)|COAD - Colon adenocarcinoma(120;0.0704)|Colorectal(133;0.0706)		AAGTCACCATCGAGTGCACGG	0.587																																					p.I248M		Atlas-SNP	.											.	SORD	24	.	0			c.C744G						.						43	43	43					15																	45361208		2198	4298	6496	SO:0001583	missense	6652	exon7			CACCATCGAGTGC		CCDS10116.1	15q15-q21.1	2012-10-02			ENSG00000140263	ENSG00000140263	1.1.1.14		11184	protein-coding gene	gene with protein product		182500				7782086	Standard	NM_003104		Approved		uc001zul.4	Q00796	OTTHUMG00000131265	ENST00000267814.9:c.744C>G	chr15.hg19:g.45361208C>G	ENSP00000267814:p.Ile248Met	273.0	0.0		297.0	42.0	NM_003104	B2R655|B7Z3A6|J3JZZ5|Q16682|Q9UMD6	Missense_Mutation	SNP	ENST00000267814.9	hg19	CCDS10116.1	.	.	.	.	.	.	.	.	.	.	C	11.85	1.761955	0.31228	.	.	ENSG00000140263	ENST00000267814	T	0.47528	0.84	4.74	-6.57	0.01842	Alcohol dehydrogenase, C-terminal (1);NAD(P)-binding domain (1);	0.165302	0.51477	N	0.000089	T	0.48804	0.1520	M	0.62723	1.935	0.35602	D	0.807937	P;P	0.46064	0.872;0.604	P;P	0.53912	0.737;0.545	T	0.60469	-0.7257	10	0.62326	D	0.03	-8.2986	9.4171	0.38528	0.0:0.145:0.222:0.633	.	169;248	B4DKI2;Q00796	.;DHSO_HUMAN	M	248	ENSP00000267814:I248M	ENSP00000267814:I248M	I	+	3	3	SORD	43148500	0.003000	0.15002	0.571000	0.28486	0.286000	0.27126	-1.412000	0.02476	-1.233000	0.02551	-1.219000	0.01604	ATC	.	.		0.587	SORD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254033.3			G	45361208	C	G	45361208	3	3	370	1	0	0	0	0	1	0	0	0	14948	874	31	4	770	4	SORD	15	45361208	Missense_Mutation	SNP	C	TCGA-ZS-A9CD-01A-11D-A36X-10	1718021	45361208	57170184	73	51266										
STOML1	9399	hgsc.bcm.edu	37	chr15	74281023	74281023	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	ggccttggtcatggcgttctGggctgtcatgcgtgtggctg	17	9	3	0			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr15:74281023G>C	ENST00000316900.5	-	4	635	c.511C>G	c.(511-513)Cag>Gag	p.Q171E	STOML1_ENST00000359750.4_Missense_Mutation_p.Q171E|STOML1_ENST00000316911.6_Missense_Mutation_p.Q121E|STOML1_ENST00000564777.1_Missense_Mutation_p.Q121E|STOML1_ENST00000541638.1_Missense_Mutation_p.Q129E|STOML1_ENST00000561656.1_Missense_Mutation_p.Q84E	NM_001256672.1|NM_001256675.1|NM_001256677.1|NM_004809.4	NP_001243601.1|NP_001243604.1|NP_001243606.1|NP_004800.2	Q9UBI4	STML1_HUMAN	stomatin (EPB72)-like 1	171						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	8						ATGGCGTTCTGGGCTGTCATG	0.597																																					p.Q171E		Atlas-SNP	.											.	STOML1	22	.	0			c.C511G						.						114	100	105					15																	74281023		2198	4297	6495	SO:0001583	missense	9399	exon4			CGTTCTGGGCTGT	Y16522	CCDS10254.1, CCDS58381.1, CCDS58382.1, CCDS58383.1, CCDS58384.1, CCDS58385.1	15q24-q25	2008-07-18			ENSG00000067221	ENSG00000067221			14560	protein-coding gene	gene with protein product	"stomatin-like 1", "stomatin (EBP72)-like 1"	608326				9931417	Standard	NM_004809		Approved	hUNC-24, SLP-1, STORP, FLJ36370	uc002awe.4	Q9UBI4	OTTHUMG00000137608	ENST00000316900.5:c.511C>G	chr15.hg19:g.74281023G>C	ENSP00000319323:p.Gln171Glu	73.0	0.0		80.0	19.0	NM_001256672	B3KQN0|B4DUU5|B4DXM9|E7ESC0|H3BRP3|O95675|Q4PNR4|Q6FGL8|Q8WYI7|Q9UMB9|Q9UMC0|Q9Y6H9	Missense_Mutation	SNP	ENST00000316900.5	hg19	CCDS10254.1	.	.	.	.	.	.	.	.	.	.	G	19.28	3.796685	0.70567	.	.	ENSG00000067221	ENST00000316900;ENST00000316911;ENST00000541638;ENST00000359750	D;D;D;D	0.93811	-3.29;-3.29;-3.29;-3.29	4.34	4.34	0.51931	.	0.229694	0.45867	D	0.000335	D	0.94301	0.8169	M	0.87900	2.915	0.51233	D	0.999913	B;P;B;P;B;B	0.39424	0.112;0.673;0.342;0.673;0.112;0.112	B;B;B;B;B;B	0.40702	0.119;0.338;0.202;0.338;0.119;0.119	D	0.95488	0.8566	10	0.72032	D	0.01	-12.8463	15.6083	0.76692	0.0:0.0:1.0:0.0	.	129;171;121;171;171;171	B4DUU5;E7ESC0;Q9UBI4-2;Q4PNR4;Q53HB6;Q9UBI4	.;.;.;.;.;STML1_HUMAN	E	171;121;129;171	ENSP00000319323:Q171E;ENSP00000319384:Q121E;ENSP00000442478:Q129E;ENSP00000352788:Q171E	ENSP00000319323:Q171E	Q	-	1	0	STOML1	72068076	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.483000	0.90442	2.250000	0.74265	0.655000	0.94253	CAG	.	.		0.597	STOML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269022.1	NM_004809		C	74281023	G	C	74281023	3	2	370	1	0	0	0	0	1	0	0	0	15328	1357	47	4	701	4	STOML1	15	74281023	Missense_Mutation	SNP	G	TCGA-ZS-A9CD-01A-11D-A36X-10	28919815	74281023	28250369	74	51267										
WDR73	84942	hgsc.bcm.edu	37	chr15	85186706	85186707	+	Frame_Shift_Del	DEL	GG	GG	-													0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	ggaaagatgctggtgtcagcGgggggcacaaaggtccaccc					rs376622127		TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr15:85186706_85186707delGG	ENST00000434634.2	-	8	1191_1192	c.1131_1132delCC	c.(1129-1134)ccccgcfs	p.R378fs	SCAND2P_ENST00000348993.5_RNA|WDR73_ENST00000398528.3_5'UTR	NM_032856.2	NP_116245.2	Q6P4I2	WDR73_HUMAN	WD repeat domain 73	378										cervix(1)|large_intestine(1)|lung(1)	3						TGGTGTCAGCGGGGGGCACAAA	0.545																																					p.378_378del		Atlas-INDEL	.											WDR73,NS,carcinoma,0,1	WDR73	15	.	0			c.1132_1133del						.																																			SO:0001589	frameshift_variant	84942	exon8			.	AK027200	CCDS45339.1	15q25.2	2013-01-09				ENSG00000177082		"WD repeat domain containing"	25928	protein-coding gene	gene with protein product						12477932	Standard	NM_032856		Approved	FLJ14888, HSPC264	uc002bkw.2	Q6P4I2		ENST00000434634.2:c.1131_1132delCC	chr15.hg19:g.85186710_85186711delGG	ENSP00000387982:p.Arg378fs	78.0	0.0		87.0	28.0	NM_032856	Q96JZ1|Q9P0B7	Frame_Shift_Del	DEL	ENST00000434634.2	hg19	CCDS45339.1																																																																																			.	.		0.545	WDR73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418195.1	NM_032856		-	85186707	GG	-	85186706	7	5	370	1	0	1	0	1	0	0	0	0	17338	1116	39	0	8	0	WDR73	15	85186706	Frame_Shift_Del	DEL	GG	TCGA-ZS-A9CD-01A-11D-A36X-10	10905683	85186706	17344686	75	51268										
ACAN	176	hgsc.bcm.edu	37	chr15	89398123	89398123	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	cccactggcgcagcaacagaGgaaagtacagaaggcccttc	11	13	0	2	rs191404107	byFrequency	TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr15:89398123G>C	ENST00000561243.1	+	11	2307	c.2307G>C	c.(2305-2307)gaG>gaC	p.E769D	ACAN_ENST00000352105.7_Missense_Mutation_p.E769D|ACAN_ENST00000439576.2_Missense_Mutation_p.E769D|ACAN_ENST00000559004.1_Missense_Mutation_p.E769D			P16112	PGCA_HUMAN	aggrecan	768	KS.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			CAGCAACAGAGGAAAGTACAG	0.542																																					p.E769D		Atlas-SNP	.											.	ACAN	220	.	0			c.G2307C						.						24	26	25					15																	89398123		1925	4122	6047	SO:0001583	missense	176	exon12			AACAGAGGAAAGT	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	319	protein-coding gene	gene with protein product	"aggrecan proteoglycan"	155760	"chondroitin sulfate proteoglycan 1", "aggrecan 1"	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.2307G>C	chr15.hg19:g.89398123G>C	ENSP00000453342:p.Glu769Asp	177.0	0.0		135.0	11.0	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	hg19	CCDS53970.1	.	.	.	.	.	.	.	.	.	.	G	14.47	2.545535	0.45280	.	.	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	T;T	0.02763	4.42;4.17	5.53	0.232	0.15381	.	0.261462	0.20140	N	0.098393	T	0.09024	0.0223	M	0.71581	2.175	0.33456	D	0.584303	D;D	0.76494	0.999;0.999	D;D	0.63793	0.918;0.918	T	0.12811	-1.0533	10	0.44086	T	0.13	-23.5224	7.3096	0.26467	0.4742:0.0:0.5258:0.0	.	769;769	E7ENV9;E7EX88	.;.	D	769	ENSP00000387356:E769D;ENSP00000341615:E769D	ENSP00000268134:E769D	E	+	3	2	ACAN	87199127	1.000000	0.71417	0.781000	0.31783	0.682000	0.39822	1.386000	0.34419	0.158000	0.19367	0.655000	0.94253	GAG	.	G|0.999;A|0.001		0.542	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135		C	89398123	G	C	89398123	3	2	370	1	0	0	0	0	1	0	0	0	117	991	35	4	2349	4	ACAN	15	89398123	Missense_Mutation	SNP	G	TCGA-ZS-A9CD-01A-11D-A36X-10	4211417	89398123	13133269	76	51269										
C16orf68	79091	hgsc.bcm.edu	37	chr16	8722963	8722963	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	agcccgcacgatatcatcagAataggtaaatagaggtgtga	11	7	2	3			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr16:8722963A>C	ENST00000381920.3	+	3	768	c.510A>C	c.(508-510)agA>agC	p.R170S	METTL22_ENST00000561758.1_Missense_Mutation_p.R114S	NM_024109.2	NP_077014.2	Q9BUU2	MET22_HUMAN	methyltransferase like 22	170						nucleus (GO:0005634)	methyltransferase activity (GO:0008168)			large_intestine(5)|lung(4)	9						ATATCATCAGAATAGGTAAAT	0.547																																					p.R170S		Atlas-SNP	.											.	METTL22	23	.	0			c.A510C						.						173	180	178					16																	8722963		2115	4230	6345	SO:0001583	missense	79091	exon3			CATCAGAATAGGT	AK022495	CCDS10533.2	16p13.2	2014-07-15	2011-03-03	2011-03-03	ENSG00000067365	ENSG00000067365			28368	protein-coding gene	gene with protein product		615261	"chromosome 16 open reading frame 68"	C16orf68		24140279	Standard	XM_005255570		Approved	FLJ12433,MGC2654	uc002cyz.3	Q9BUU2	OTTHUMG00000129694	ENST00000381920.3:c.510A>C	chr16.hg19:g.8722963A>C	ENSP00000371345:p.Arg170Ser	66.0	0.0		43.0	11.0	NM_024109	B2RD29|D3DUF2|Q6XYB4|Q9HA03	Missense_Mutation	SNP	ENST00000381920.3	hg19	CCDS10533.2	.	.	.	.	.	.	.	.	.	.	A	9.913	1.210067	0.22289	.	.	ENSG00000067365	ENST00000381920;ENST00000163678	T;T	0.52057	2.29;0.68	5.24	1.78	0.24846	.	0.410464	0.22993	N	0.053180	T	0.25901	0.0631	N	0.16368	0.405	0.25797	N	0.984553	P	0.35124	0.485	B	0.28553	0.091	T	0.11867	-1.0570	10	0.72032	D	0.01	-12.9404	7.3646	0.26766	0.7433:0.0:0.2567:0.0	.	170	Q9BUU2	MET22_HUMAN	S	170	ENSP00000371345:R170S;ENSP00000163678:R170S	ENSP00000163678:R170S	R	+	3	2	METTL22	8630464	0.999000	0.42202	0.429000	0.26710	0.029000	0.11900	2.122000	0.41987	0.031000	0.15407	-0.379000	0.06801	AGA	.	.		0.547	METTL22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251901.1	NM_024109		C	8722963	A	C	8722963	3	2	370	1	0	0	0	0	1	0	0	0	1829	243	9	5	516	5	C16orf68	16	8722963	Missense_Mutation	SNP	A	TCGA-ZS-A9CD-01A-11D-A36X-10		8722963	81631790	77	51270										
GRIN2A	2903	hgsc.bcm.edu	37	chr16	10274102	10274102	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	gccccgccgcctgctcggggCcccacagtgttcgaagttcg	13	17	0	0			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr16:10274102C>A	ENST00000396573.2	-	3	476	c.167G>T	c.(166-168)gGc>gTc	p.G56V	GRIN2A_ENST00000404927.2_Missense_Mutation_p.G56V|GRIN2A_ENST00000396575.2_Missense_Mutation_p.G56V|GRIN2A_ENST00000562109.1_Missense_Mutation_p.G56V|GRIN2A_ENST00000330684.3_Missense_Mutation_p.G56V	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	56					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CTGCTCGGGGCCCCACAGTGT	0.667																																					p.G56V		Atlas-SNP	.											.	GRIN2A	366	.	0			c.G167T						.						57	62	61					16																	10274102		2197	4300	6497	SO:0001583	missense	2903	exon3			TCGGGGCCCCACA		CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.167G>T	chr16.hg19:g.10274102C>A	ENSP00000379818:p.Gly56Val	84.0	0.0		76.0	15.0	NM_000833	O00669|Q17RZ6	Missense_Mutation	SNP	ENST00000396573.2	hg19	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	C	14.24	2.477121	0.44044	.	.	ENSG00000183454	ENST00000396573;ENST00000404927;ENST00000330684;ENST00000396575	D;D;D;D	0.88431	-2.38;-2.38;-2.38;-2.38	4.54	4.54	0.55810	.	0.350805	0.25114	N	0.033040	T	0.81955	0.4932	L	0.36672	1.1	0.80722	D	1	P;B;B	0.50272	0.933;0.164;0.099	B;B;B	0.39706	0.307;0.035;0.056	T	0.80910	-0.1171	9	.	.	.	.	11.1048	0.48197	0.0:0.7956:0.2044:0.0	.	56;56;56	Q547U9;Q17RZ6;Q12879	.;.;NMDE1_HUMAN	V	56	ENSP00000379818:G56V;ENSP00000385872:G56V;ENSP00000332549:G56V;ENSP00000379820:G56V	.	G	-	2	0	GRIN2A	10181603	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.489000	0.45285	2.088000	0.63022	0.561000	0.74099	GGC	.	.		0.667	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			A	10274102	C	A	10274102	3	1	370	1	0	0	0	0	1	0	0	0	6788	739	26	3	4275	3	GRIN2A	16	10274102	Missense_Mutation	SNP	C	TCGA-ZS-A9CD-01A-11D-A36X-10	1551139	10274102	80080651	78	51271										
C16orf58	64755	hgsc.bcm.edu	37	chr16	31519395	31519395	+	Splice_Site	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	ccccagacgaccgagctgacCtgcacggaatcccacagctg	10	17	0	2			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr16:31519395C>T	ENST00000327237.2	-	1	339	c.300G>A	c.(298-300)caG>caA	p.Q100Q	C16orf58_ENST00000570164.1_Splice_Site_p.Q100Q|C16orf58_ENST00000430477.2_5'UTR|RP11-452L6.7_ENST00000569782.1_RNA|C16orf58_ENST00000567994.1_Splice_Site_p.Q55Q			Q96GQ5	RUS1_HUMAN	chromosome 16 open reading frame 58	100						integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)	14						CCGAGCTGACCTGCACGGAAT	0.672																																					p.P100P		Atlas-SNP	.											.	C16orf58	28	.	0			c.A300A						.																																			SO:0001630	splice_region_variant	64755	exon1			GCTGACCTGCACG	AK023930	CCDS10715.1	16p11.2	2013-03-04			ENSG00000140688	ENSG00000140688			25848	protein-coding gene	gene with protein product							Standard	NM_022744		Approved	FLJ13868	uc002eci.3	Q96GQ5	OTTHUMG00000132466	ENST00000327237.2:c.300+1G>A	chr16.hg19:g.31519395C>T		194.0	0.0		155.0	33.0	NM_022744	Q53GL8|Q8NAJ4|Q9BVY3|Q9H887	Silent	SNP	ENST00000327237.2	hg19	CCDS10715.1																																																																																			.	.		0.672	C16orf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255629.2	NM_022744	Silent	T	31519395	C	T	31519395	5	4	370	1	0	0	0	0	0	0	1	0	1824	695	24	3	1158	3	C16orf58	16	31519395	Splice_Site	SNP	C	TCGA-ZS-A9CD-01A-11D-A36X-10	21245293	31519395	58835358	79	51272										
FHOD1	29109	hgsc.bcm.edu	37	chr16	67281173	67281173	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	tgcgcgcccaagggcagcgcCccgtccaggctgcaggtggg	17	15	0	0			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr16:67281173C>A	ENST00000258201.4	-	1	388	c.141G>T	c.(139-141)ggG>ggT	p.G47G	SLC9A5_ENST00000299798.11_5'Flank	NM_013241.2	NP_037373.2	Q9Y613	FHOD1_HUMAN	formin homology 2 domain containing 1	47					positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			breast(4)|endometrium(3)|kidney(3)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	34		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000691)|Epithelial(162;0.00462)|all cancers(182;0.0434)		AGGGCAGCGCCCCGTCCAGGC	0.701																																					p.G47G		Atlas-SNP	.											.	FHOD1	86	.	0			c.G141T						.						19	21	21					16																	67281173		2194	4297	6491	SO:0001819	synonymous_variant	29109	exon1			CAGCGCCCCGTCC	AF113615	CCDS10834.1	16q22	2008-02-22			ENSG00000135723	ENSG00000135723			17905	protein-coding gene	gene with protein product		606881				10352228, 16112087	Standard	NM_013241		Approved	FHOS	uc002esl.3	Q9Y613	OTTHUMG00000137521	ENST00000258201.4:c.141G>T	chr16.hg19:g.67281173C>A		84.0	0.0		75.0	15.0	NM_013241	Q59F76|Q6Y1F2|Q76MS8|Q8N521	Silent	SNP	ENST00000258201.4	hg19	CCDS10834.1																																																																																			.	.		0.701	FHOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268844.2			A	67281173	C	A	67281173	2	1	370	1	0	0	0	0	0	0	0	1	5890	610	22	3		3	FHOD1	16	67281173	Silent	SNP	C	TCGA-ZS-A9CD-01A-11D-A36X-10	35761778	67281173	23073580	80	51273										
MYH3	4621	hgsc.bcm.edu	37	chr17	10543991	10543991	+	Silent	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	tcagggattgcactggcattCagcactcggtatctgcattg	11	10	3	0			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr17:10543991C>A	ENST00000583535.1	-	20	2265	c.2178G>T	c.(2176-2178)ctG>ctT	p.L726L	MYH3_ENST00000226209.7_Silent_p.L726L	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	726	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						cactggcattcagcactcggt	0.443																																					p.L726L		Atlas-SNP	.											.	MYH3	227	.	0			c.G2178T						.						97	84	88					17																	10543991		2203	4300	6503	SO:0001819	synonymous_variant	4621	exon20			GGCATTCAGCACT		CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"Myosins / Myosin superfamily : Class II"	7573	protein-coding gene	gene with protein product	"myosin, skeletal, heavy chain, embryonic 1", "muscle embryonic myosin heavy chain 3"	160720	"myosin, heavy polypeptide 3, skeletal muscle, embryonic"			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.2178G>T	chr17.hg19:g.10543991C>A		64.0	0.0		60.0	16.0	NM_002470	Q15492	Silent	SNP	ENST00000583535.1	hg19	CCDS11157.1																																																																																			.	.		0.443	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470		A	10543991	C	A	10543991	2	1	370	1	0	0	0	0	0	0	0	1	10045	813	29	3		3	MYH3	17	10543991	Silent	SNP	C	TCGA-ZS-A9CD-01A-11D-A36X-10		10543991	70651219	81	51274										
KIAA0100	9703	hgsc.bcm.edu	37	chr17	26970319	26970319	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	cacttctccaaagcacaatgCcacatagtgtctgcccagaa	6	14	2	1			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr17:26970319C>A	ENST00000528896.2	-	4	333	c.259G>T	c.(259-261)Gca>Tca	p.A87S	KIAA0100_ENST00000389003.3_5'UTR|KIAA0100_ENST00000544884.1_5'UTR	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	87						extracellular region (GO:0005576)				breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68	Lung NSC(42;0.00431)					AAGCACAATGCCACATAGTGT	0.512																																					p.A87S		Atlas-SNP	.											.	KIAA0100	175	.	0			c.G259T						.						101	101	101					17																	26970319		2203	4300	6503	SO:0001583	missense	9703	exon4			ACAATGCCACATA	D43947	CCDS32595.1	17q11.2	2012-11-29			ENSG00000007202	ENSG00000007202			28960	protein-coding gene	gene with protein product	"cancer/testis antigen 101", "breast cancer overexpressed gene 1"	610664				16289875	Standard	NM_014680		Approved	DKFZp686M0843, MGC111488, BCOX1, CT101, BCOX	uc002hbu.3	Q14667	OTTHUMG00000166587	ENST00000528896.2:c.259G>T	chr17.hg19:g.26970319C>A	ENSP00000436773:p.Ala87Ser	90.0	0.0		80.0	23.0	NM_014680	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Missense_Mutation	SNP	ENST00000528896.2	hg19	CCDS32595.1	.	.	.	.	.	.	.	.	.	.	C	13.10	2.137767	0.37728	.	.	ENSG00000007202	ENST00000005905;ENST00000389003;ENST00000528896	T	0.25579	1.79	5.66	5.66	0.87406	FMP27, N-terminal (1);	0.050292	0.85682	D	0.000000	T	0.29783	0.0744	L	0.32530	0.975	0.80722	D	1	D;P	0.55605	0.972;0.58	P;B	0.51550	0.673;0.223	T	0.01033	-1.1474	10	0.19590	T	0.45	.	16.8925	0.86091	0.0:1.0:0.0:0.0	.	87;87	F6XS94;Q14667	.;K0100_HUMAN	S	87	ENSP00000436773:A87S	ENSP00000005905:A87S	A	-	1	0	KIAA0100	23994446	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	5.200000	0.65158	2.672000	0.90937	0.655000	0.94253	GCA	.	.		0.512	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680		A	26970319	C	A	26970319	3	1	370	1	0	0	0	0	1	0	0	0	8163	739	26	3	6592	3	KIAA0100	17	26970319	Missense_Mutation	SNP	C	TCGA-ZS-A9CD-01A-11D-A36X-10	16426328	26970319	54224891	82	51275										
C17orf50	146853	hgsc.bcm.edu	37	chr17	34091295	34091295	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	cggacagcggcttctggggcTggctcggccccttagcgctg	16	14	1	0			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr17:34091295T>A	ENST00000285023.4	+	2	315	c.283T>A	c.(283-285)Tgg>Agg	p.W95R	C17orf50_ENST00000588628.1_Missense_Mutation_p.L102Q|C17orf50_ENST00000586491.1_Intron	NM_145272.3	NP_660315.2	Q8WW18	CQ050_HUMAN	chromosome 17 open reading frame 50	95													Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CTTCTGGGGCTGGCTCGGCCC	0.756																																					p.W95R		Atlas-SNP	.											.	C17orf50	4	.	0			c.T283A						.						2	3	2					17																	34091295		974	2250	3224	SO:0001583	missense	146853	exon2			TGGGGCTGGCTCG	BC021727	CCDS42298.1	17q12	2014-05-06			ENSG00000154768	ENSG00000270806			29581	protein-coding gene	gene with protein product							Standard	NM_145272		Approved		uc002hjx.3	Q8WW18	OTTHUMG00000188389	ENST00000285023.4:c.283T>A	chr17.hg19:g.34091295T>A	ENSP00000285023:p.Trp95Arg	92.0	0.0		62.0	16.0	NM_145272	Q6Q621	Missense_Mutation	SNP	ENST00000285023.4	hg19	CCDS42298.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.133117	0.77662	.	.	ENSG00000154768	ENST00000285023	T	0.59638	0.25	5.16	5.16	0.70880	.	0.000000	0.38837	N	0.001552	T	0.61451	0.2348	L	0.27053	0.805	0.33353	D	0.57136	D	0.67145	0.996	D	0.65573	0.936	T	0.72808	-0.4181	10	0.87932	D	0	-17.7624	11.3888	0.49802	0.0:0.0:0.0:1.0	.	95	Q8WW18	CQ050_HUMAN	R	95	ENSP00000285023:W95R	ENSP00000285023:W95R	W	+	1	0	C17orf50	31115408	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	2.583000	0.46094	1.943000	0.56356	0.460000	0.39030	TGG	.	.		0.756	C17orf50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449132.1	NM_145272		A	34091295	T	A	34091295	3	1	370	1	0	0	0	0	1	0	0	0	1863	1580	55	4	289	4	C17orf50	17	34091295	Missense_Mutation	SNP	T	TCGA-ZS-A9CD-01A-11D-A36X-10	7120976	34091295	47103915	83	51276										
ARHGAP27	201176	hgsc.bcm.edu	37	chr17	43474146	43474146	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	tccaggcccacggggcccagGgcgggcgcggctgccgcggg	20	16	0	0			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr17:43474146G>A	ENST00000428638.1	-	12	1961	c.1962C>T	c.(1960-1962)gcC>gcT	p.A654A	ARHGAP27_ENST00000528384.1_Silent_p.A286A|ARHGAP27_ENST00000442348.1_Silent_p.A627A|ARHGAP27_ENST00000532038.1_Silent_p.A432A|CTB-39G8.3_ENST00000592389.1_RNA|ARHGAP27_ENST00000455881.1_Silent_p.A313A|ARHGAP27_ENST00000532891.2_Silent_p.A632A|ARHGAP27_ENST00000376922.2_Silent_p.A313A|ARHGAP27_ENST00000582826.1_5'Flank			Q6ZUM4	RHG27_HUMAN	Rho GTPase activating protein 27	654					positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of Rac GTPase activity (GO:0032855)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|SH3 domain binding (GO:0017124)			endometrium(4)|large_intestine(9)|lung(3)|skin(1)	17	Renal(3;0.0405)					CGGGGCCCAGGGCGGGCGCGG	0.711																																					p.A313A		Atlas-SNP	.											.	ARHGAP27	37	.	0			c.C939T						.						15	19	18					17																	43474146		2197	4275	6472	SO:0001819	synonymous_variant	201176	exon12			GCCCAGGGCGGGC	AK125535	CCDS11498.1, CCDS74082.1	17q21.31	2013-01-10			ENSG00000159314	ENSG00000159314		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	31813	protein-coding gene	gene with protein product		610591	"SH3 domain containing 20"	SH3D20		15147912	Standard	NM_199282		Approved	CAMGAP1, FLJ43547, SH3P20	uc002iix.3	Q6ZUM4	OTTHUMG00000166982	ENST00000428638.1:c.1962C>T	chr17.hg19:g.43474146G>A		80.0	0.0		60.0	11.0	NM_199282	A4FU35|A8K3N5|C9JTF3|Q494U0|Q6NWZ8|Q8WY58	Silent	SNP	ENST00000428638.1	hg19																																																																																				.	.		0.711	ARHGAP27-202	KNOWN	basic	protein_coding	protein_coding		NM_199282		A	43474146	G	A	43474146	2	1	370	1	0	0	0	0	0	0	0	1	876	1219	43	3		3	ARHGAP27	17	43474146	Silent	SNP	G	TCGA-ZS-A9CD-01A-11D-A36X-10	9382851	43474146	37721064	84	51277										
HN1	51155	hgsc.bcm.edu	37	chr17	73132208	73132208	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	cagtcagagctaacccaagaCgaggctggacttgccgccag	12	13	1	2			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr17:73132208C>T	ENST00000409753.3	-	5	739	c.454G>A	c.(454-456)Gtc>Atc	p.V152I	HN1_ENST00000482348.1_Missense_Mutation_p.V106I|HN1_ENST00000392566.2_Missense_Mutation_p.V106I|HN1_ENST00000481647.1_Missense_Mutation_p.V106I|HN1_ENST00000405458.3_Missense_Mutation_p.V106I|HN1_ENST00000470924.1_Missense_Mutation_p.V106I|HN1_ENST00000476258.1_Missense_Mutation_p.V106I|RP11-649A18.5_ENST00000584339.1_RNA|HN1_ENST00000356033.4_Silent_p.S145S	NM_016185.2	NP_057269.1	Q9UK76	HN1_HUMAN	hematological and neurological expressed 1	152					developmental process (GO:0032502)	nucleus (GO:0005634)			HN1/USH1G(2)	breast(1)	1	all_lung(278;0.14)|Lung NSC(278;0.168)					TAACCCAAGACGAGGCTGGAC	0.587																																					p.V152I		Atlas-SNP	.											.	HN1	17	.	0			c.G454A						.						80	77	78					17																	73132208		2203	4300	6503	SO:0001583	missense	51155	exon5			CCAAGACGAGGCT	AF086910	CCDS32729.1, CCDS45771.1, CCDS45772.1	17q25.1	2013-09-20			ENSG00000189159	ENSG00000189159			14569	protein-coding gene	gene with protein product	"androgen-regulated protein 2"					15094197	Standard	NM_001002032		Approved	ARM2, HN1A	uc002jnb.1	Q9UK76	OTTHUMG00000154521	ENST00000409753.3:c.454G>A	chr17.hg19:g.73132208C>T	ENSP00000387059:p.Val152Ile	310.0	0.0		251.0	66.0	NM_016185	B2R6K3|Q53FG7|Q7Z2D2|Q7Z2F0	Missense_Mutation	SNP	ENST00000409753.3	hg19	CCDS45771.1	.	.	.	.	.	.	.	.	.	.	C	18.27	3.586138	0.66105	.	.	ENSG00000189159	ENST00000405458;ENST00000409753;ENST00000392566	.	.	.	5.87	5.87	0.94306	.	.	.	.	.	T	0.46560	0.1399	.	.	.	0.44908	D	0.997929	P	0.35527	0.507	B	0.24155	0.051	T	0.41910	-0.9482	7	0.34782	T	0.22	-42.9835	18.3821	0.90454	0.0:1.0:0.0:0.0	.	152	Q9UK76	HN1_HUMAN	I	106;152;106	.	ENSP00000440912:V106I	V	-	1	0	HN1	70643803	0.998000	0.40836	0.967000	0.41034	0.905000	0.53344	4.949000	0.63596	2.773000	0.95371	0.643000	0.83706	GTC	.	.		0.587	HN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000335692.1	NM_001002032		T	73132208	C	T	73132208	3	4	370	1	0	0	0	0	1	0	0	0	7258	536	19	1	114	1	HN1	17	73132208	Missense_Mutation	SNP	C	TCGA-ZS-A9CD-01A-11D-A36X-10	29658062	73132208	8063002	85	51278										
C19orf21	126353	hgsc.bcm.edu	37	chr19	757270	757270	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	gcccaccagggacgtccaacAtgggcactccgcccagagga	12	16	0	1			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr19:757270A>G	ENST00000215582.6	+	2	427	c.324A>G	c.(322-324)acA>acG	p.T108T		NM_173481.2	NP_775752.1	Q8IVT2	MISP_HUMAN	mitotic spindle positioning	108					mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											GACGTCCAACATGGGCACTCC	0.677																																					p.T108T		Atlas-SNP	.											.	C19orf21	56	.	0			c.A324G						.						57	49	52					19																	757270		2203	4300	6503	SO:0001819	synonymous_variant	126353	exon2			TCCAACATGGGCA	BC052236	CCDS12042.1	19p13.3	2014-06-25	2013-05-03	2013-05-03	ENSG00000099812	ENSG00000099812			27000	protein-coding gene	gene with protein product	"mitotic interactor and substrate of Plk1"	615289	"chromosome 19 open reading frame 21"	C19orf21		23574715, 23509069, 24475924	Standard	NM_173481		Approved	DKFZp686H18209, Caprice		Q8IVT2	OTTHUMG00000181786	ENST00000215582.6:c.324A>G	chr19.hg19:g.757270A>G		191.0	0.0		148.0	41.0	NM_173481		Silent	SNP	ENST00000215582.6	hg19	CCDS12042.1																																																																																			.	.		0.677	MISP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457600.2	NM_173481		G	757270	A	G	757270	2	3	370	1	0	0	0	0	0	0	0	1	1915	204	8	2		2	C19orf21	19	757270	Silent	SNP	A	TCGA-ZS-A9CD-01A-11D-A36X-10		757270	58371713	86	51279										
MUM1	84939	hgsc.bcm.edu	37	chr19	1371003	1371003	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	acctgcagggcgtctaccagGaggtgggggccaaggtgctc	17	11	1	0			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr19:1371003G>A	ENST00000415183.3	+	11	1941	c.1915G>A	c.(1915-1917)Gag>Aag	p.E639K	MUM1_ENST00000311401.5_Missense_Mutation_p.E570K|MUM1_ENST00000344663.3_Missense_Mutation_p.E639K|MUM1_ENST00000591806.1_Missense_Mutation_p.E639K			Q2TAK8	MUM1_HUMAN	melanoma associated antigen (mutated) 1	638					chromatin organization (GO:0006325)|DNA repair (GO:0006281)	nucleus (GO:0005634)	nucleosome binding (GO:0031491)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CGTCTACCAGGAGGTGGGGGC	0.647																																					p.E639K		Atlas-SNP	.											.	MUM1	54	.	0			c.G1915A						.						59	42	48					19																	1371003		2185	4281	6466	SO:0001583	missense	84939	exon12			TACCAGGAGGTGG	AK075241	CCDS12062.1	19p13.3	2008-02-05				ENSG00000160953			29641	protein-coding gene	gene with protein product						11042152, 7644523	Standard	NM_032853		Approved	MUM-1	uc002lrz.2	Q2TAK8		ENST00000415183.3:c.1915G>A	chr19.hg19:g.1371003G>A	ENSP00000394925:p.Glu639Lys	75.0	0.0		86.0	7.0	NM_032853	A1L489|B5ME02|B7ZLY8|J3KQD6|Q13109|Q5XKB9|Q8N2I4|Q96A67	Missense_Mutation	SNP	ENST00000415183.3	hg19		.	.	.	.	.	.	.	.	.	.	G	19.44	3.828326	0.71143	.	.	ENSG00000160953	ENST00000344663;ENST00000311401;ENST00000415183	T;T;T	0.50813	0.73;0.73;0.73	4.82	1.23	0.21249	.	1.190750	0.05791	N	0.610350	T	0.55970	0.1954	L	0.59436	1.845	0.09310	N	1	P;P;P;B	0.49783	0.675;0.675;0.928;0.43	B;B;P;B	0.47402	0.241;0.145;0.546;0.085	T	0.57688	-0.7768	10	0.66056	D	0.02	.	15.5375	0.76016	0.0:0.556:0.444:0.0	.	639;639;570;638	B7ZLY8;D6W5Y8;Q2TAK8-2;Q2TAK8	.;.;.;MUM1_HUMAN	K	639;570;639	ENSP00000345789:E639K;ENSP00000309135:E570K;ENSP00000394925:E639K	ENSP00000309135:E570K	E	+	1	0	MUM1	1322003	0.357000	0.24938	0.000000	0.03702	0.479000	0.33129	1.229000	0.32600	0.132000	0.18615	0.462000	0.41574	GAG	.	.		0.647	MUM1-016	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000449510.1	NM_032853		A	1371003	G	A	1371003	3	1	370	1	0	0	0	0	1	0	0	0	9994	1175	41	3	1957	3	MUM1	19	1371003	Missense_Mutation	SNP	G	TCGA-ZS-A9CD-01A-11D-A36X-10	613733	1371003	57757980	87	51280										
FUT3	2525	hgsc.bcm.edu	37	chr19	5844157	5844157	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	cagcgtctccatcatggtccCcttgggcaggggcttgtggg	15	12	2	0			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr19:5844157C>T	ENST00000303225.6	-	3	1328	c.694G>A	c.(694-696)Ggg>Agg	p.G232R	FUT3_ENST00000589918.1_Missense_Mutation_p.G232R|FUT3_ENST00000589620.1_Missense_Mutation_p.G232R|FUT3_ENST00000593144.1_5'Flank|FUT3_ENST00000458379.2_Missense_Mutation_p.G232R	NM_000149.3	NP_000140	P21217	FUT3_HUMAN	fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group)	232					cell-cell recognition (GO:0009988)|fucosylation (GO:0036065)|macromolecule glycosylation (GO:0043413)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(1)	14						ATCATGGTCCCCTTGGGCAGG	0.607																																					p.G232R	Esophageal Squamous(82;745 1728 24593 44831)	Atlas-SNP	.											.	FUT3	30	.	0			c.G694A						.						87	85	86					19																	5844157		2201	4299	6500	SO:0001583	missense	2525	exon3			TGGTCCCCTTGGG		CCDS12153.1	19p13.3	2014-07-19	2006-01-12		ENSG00000171124	ENSG00000171124	2.4.1.65	"CD molecules", "Blood group antigens", "Fucosyltransferases"	4014	protein-coding gene	gene with protein product		111100	"fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group included)"	LE		1977660, 1740457	Standard	NM_000149		Approved	CD174	uc002mdk.2	P21217	OTTHUMG00000180614	ENST00000303225.6:c.694G>A	chr19.hg19:g.5844157C>T	ENSP00000305603:p.Gly232Arg	228.0	0.0		203.0	59.0	NM_001097640	B5U7U9|B5U7V0|Q32NE7|Q99448|Q99449	Missense_Mutation	SNP	ENST00000303225.6	hg19	CCDS12153.1	.	.	.	.	.	.	.	.	.	.	C	2.355	-0.348033	0.05208	.	.	ENSG00000171124	ENST00000303225;ENST00000458379	T;T	0.27104	1.69;1.69	2.29	-3.59	0.04583	.	4.706620	0.00508	N	0.000179	T	0.17152	0.0412	L	0.29908	0.895	0.09310	N	1	B;B;B;B	0.10296	0.003;0.003;0.003;0.003	B;B;B;B	0.15052	0.012;0.012;0.012;0.012	T	0.13683	-1.0500	10	0.29301	T	0.29	.	4.39	0.11335	0.0:0.2092:0.1964:0.5944	.	232;232;232;232	B3W6H0;A8K737;B3GVC1;P21217	.;.;.;FUT3_HUMAN	R	232	ENSP00000305603:G232R;ENSP00000416443:G232R	ENSP00000305603:G232R	G	-	1	0	FUT3	5795157	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-0.590000	0.05760	-0.658000	0.05366	0.194000	0.17425	GGG	.	.		0.607	FUT3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452204.1	NM_000149		T	5844157	C	T	5844157	3	4	370	1	0	0	0	0	1	0	0	0	6113	623	22	3	395	3	FUT3	19	5844157	Missense_Mutation	SNP	C	TCGA-ZS-A9CD-01A-11D-A36X-10	4473154	5844157	53284826	88	51281										
PEPD	5184	hgsc.bcm.edu	37	chr19	33892756	33892756	+	Nonsense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	ggaagcgaagcagtaatactCaccgcccatgtcgaacaggc	11	12	1	0			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr19:33892756C>A	ENST00000244137.7	-	12	871	c.838G>T	c.(838-840)Gag>Tag	p.E280*	PEPD_ENST00000436370.3_Nonsense_Mutation_p.E216*|PEPD_ENST00000397032.4_Nonsense_Mutation_p.E239*	NM_000285.3	NP_000276.2	P12955	PEPD_HUMAN	peptidase D	280					cellular amino acid metabolic process (GO:0006520)|collagen catabolic process (GO:0030574)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)	aminopeptidase activity (GO:0004177)|dipeptidase activity (GO:0016805)|manganese ion binding (GO:0030145)|metallocarboxypeptidase activity (GO:0004181)			endometrium(3)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)	17	Esophageal squamous(110;0.137)					CAGTAATACTCACCGCCCATG	0.622																																					p.E280X		Atlas-SNP	.											.	PEPD	48	.	0			c.G838T						.						61	70	67					19																	33892756		2111	4221	6332	SO:0001587	stop_gained	5184	exon12			AATACTCACCGCC	BC015027	CCDS42544.1, CCDS54244.1, CCDS54245.1	19q13.11	2008-02-05				ENSG00000124299	3.4.13.9		8840	protein-coding gene	gene with protein product	"prolidase"	613230				2925654, 1972707	Standard	NM_000285		Approved		uc002nur.4	P12955		ENST00000244137.7:c.838G>T	chr19.hg19:g.33892756C>A	ENSP00000244137:p.Glu280*	106.0	0.0		100.0	24.0	NM_000285	A8K3Z1|A8K416|A8K696|A8MX47|B4DDB7|B4DGJ1|E9PCE8|Q8TBN9|Q9BT75	Nonsense_Mutation	SNP	ENST00000244137.7	hg19	CCDS42544.1	.	.	.	.	.	.	.	.	.	.	C	37	6.590919	0.97688	.	.	ENSG00000124299	ENST00000244137;ENST00000397032;ENST00000436370	.	.	.	5.38	5.38	0.77491	.	0.203246	0.50627	D	0.000110	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-34.7746	17.702	0.88298	0.0:1.0:0.0:0.0	.	.	.	.	X	280;239;216	.	ENSP00000244137:E280X	E	-	1	0	PEPD	38584596	1.000000	0.71417	0.944000	0.38274	0.842000	0.47809	6.909000	0.75735	2.507000	0.84556	0.462000	0.41574	GAG	.	.		0.622	PEPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451432.3	NM_000285		A	33892756	C	A	33892756	4	1	370	1	0	0	0	0	0	1	0	0	11737	835	29	3	659	3	PEPD	19	33892756	Nonsense_Mutation	SNP	C	TCGA-ZS-A9CD-01A-11D-A36X-10	28048599	33892756	25236227	89	51282										
SCN1B	6324	hgsc.bcm.edu	37	chr19	35521747	35521747	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	ggggaggctgctggccttagTggtcggcgcggcactgggtg	21	9	0	0			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr19:35521747T>C	ENST00000262631.5	+	1	160	c.23T>C	c.(22-24)gTg>gCg	p.V8A	SCN1B_ENST00000595652.1_Missense_Mutation_p.V8A|SCN1B_ENST00000415950.3_Missense_Mutation_p.V8A	NM_001037.4	NP_001028.1	Q07699	SCN1B_HUMAN	sodium channel, voltage-gated, type I, beta subunit	8					axon guidance (GO:0007411)|cardiac conduction (GO:0061337)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|corticospinal neuron axon guidance (GO:0021966)|locomotion (GO:0040011)|membrane depolarization (GO:0051899)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane depolarization during Purkinje myocyte cell action potential (GO:0086047)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to pyrethroid (GO:0046684)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	extracellular region (GO:0005576)|intercalated disc (GO:0014704)|node of Ranvier (GO:0033268)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	sodium channel inhibitor activity (GO:0019871)|sodium channel regulator activity (GO:0017080)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)|voltage-gated sodium channel activity involved in Purkinje myocyte action potential (GO:0086062)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(3)	11	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)		Valproic Acid(DB00313)|Zonisamide(DB00909)	CTGGCCTTAGTGGTCGGCGCG	0.806																																					p.V8A		Atlas-SNP	.											.	SCN1B	32	.	0			c.T23C						.						1	1	1					19																	35521747		421	969	1390	SO:0001583	missense	6324	exon1			CCTTAGTGGTCGG		CCDS12441.1, CCDS46047.1	19q13.12	2014-09-17	2012-02-28		ENSG00000105711	ENSG00000105711		"Sodium channels", "Voltage-gated ion channels / Sodium channels", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10586	protein-coding gene	gene with protein product		600235	"sodium channel, voltage-gated, type I, beta polypeptide", "sodium channel, voltage-gated, type I, beta"			8394762	Standard	NM_001037		Approved		uc002nxo.2	Q07699	OTTHUMG00000182472	ENST00000262631.5:c.23T>C	chr19.hg19:g.35521747T>C	ENSP00000262631:p.Val8Ala	170.0	0.0		126.0	11.0	NM_001037	Q5TZZ4|Q6TN97	Missense_Mutation	SNP	ENST00000262631.5	hg19	CCDS12441.1	.	.	.	.	.	.	.	.	.	.	t	12.94	2.088307	0.36855	.	.	ENSG00000105711	ENST00000262631;ENST00000415950	D;D	0.97976	-4.64;-2.51	3.17	2.01	0.26516	.	0.421766	0.18829	U	0.130014	D	0.92381	0.7582	N	0.19112	0.55	0.23700	N	0.997074	B;B;B	0.30211	0.0;0.019;0.273	B;B;B	0.32980	0.001;0.003;0.156	D	0.85048	0.0927	10	0.18710	T	0.47	-4.242	5.7753	0.18275	0.2365:0.0:0.0:0.7635	.	8;8;8	B4DI92;Q07699;Q07699-2	.;SCN1B_HUMAN;.	A	8	ENSP00000262631:V8A;ENSP00000396915:V8A	ENSP00000262631:V8A	V	+	2	0	SCN1B	40213587	0.991000	0.36638	0.998000	0.56505	0.438000	0.31896	0.798000	0.27014	1.210000	0.43336	0.248000	0.18094	GTG	.	.		0.806	SCN1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461567.1			C	35521747	T	C	35521747	3	2	370	1	0	0	0	0	1	0	0	0	13930	1696	59	2	25	2	SCN1B	19	35521747	Missense_Mutation	SNP	T	TCGA-ZS-A9CD-01A-11D-A36X-10	1628991	35521747	23607236	90	51283										
MARK4	57787	hgsc.bcm.edu	37	chr19	45790827	45790827	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	gcaccgcggggagtgggagtCgagggctgcccccctccagc	17	15	0	0			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr19:45790827C>T	ENST00000262891.4	+	13	1730	c.1399C>T	c.(1399-1401)Cga>Tga	p.R467*	MARK4_ENST00000300843.4_Nonsense_Mutation_p.R467*	NM_001199867.1	NP_001186796.1	Q96L34	MARK4_HUMAN	MAP/microtubule affinity-regulating kinase 4	467					microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|nervous system development (GO:0007399)|positive regulation of programmed cell death (GO:0043068)|protein phosphorylation (GO:0006468)	centrosome (GO:0005813)|microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|gamma-tubulin binding (GO:0043015)|microtubule binding (GO:0008017)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)|ubiquitin binding (GO:0043130)			NS(1)|biliary_tract(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	31		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0102)		GAGTGGGAGTCGAGGGCTGCC	0.711																																					p.R467X		Atlas-SNP	.											.	MARK4	132	.	0			c.C1399T						.						27	33	31					19																	45790827		2184	4295	6479	SO:0001587	stop_gained	57787	exon13			GGGAGTCGAGGGC	AB049127	CCDS12658.1, CCDS56097.1	19q13.32	2014-04-07	2002-06-12	2002-06-14	ENSG00000007047	ENSG00000007047	2.7.11.1		13538	protein-coding gene	gene with protein product		606495	"MAP/microtubule affinity-regulating kinase like 1"	MARKL1		23400999, 11326310, 9108484	Standard	NM_001199867		Approved	Nbla00650, FLJ90097, KIAA1860, PAR-1D	uc002paz.2	Q96L34	OTTHUMG00000181769	ENST00000262891.4:c.1399C>T	chr19.hg19:g.45790827C>T	ENSP00000262891:p.Arg467*	416.0	0.0		371.0	86.0	NM_001199867	Q8NG37|Q96JG7|Q96SQ2|Q9BYD8	Nonsense_Mutation	SNP	ENST00000262891.4	hg19	CCDS56097.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	36|36	5.697991|5.697991	0.96802|0.96802	.|.	.|.	ENSG00000007047|ENSG00000007047	ENST00000262891;ENST00000300843|ENST00000262893	.|.	.|.	.|.	5.06|5.06	4.01|4.01	0.46588|0.46588	.|.	0.092055|.	0.44902|.	D|.	0.000406|.	.|T	.|0.66848	.|0.2831	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.77156	.|-0.2691	.|4	0.09338|0.59425	T|D	0.73|0.04	.|.	12.5646|12.5646	0.56301|0.56301	0.1675:0.8325:0.0:0.0|0.1675:0.8325:0.0:0.0	.|.	.|.	.|.	.|.	X|L	467|431	.|.	ENSP00000262891:R467X|ENSP00000262893:S431L	R|S	+|+	1|2	2|0	MARK4|MARK4	50482667|50482667	0.991000|0.991000	0.36638|0.36638	0.328000|0.328000	0.25416|0.25416	0.675000|0.675000	0.39556|0.39556	1.747000|1.747000	0.38298|0.38298	1.348000|1.348000	0.45733|0.45733	0.591000|0.591000	0.81541|0.81541	CGA|TCG	.	.		0.711	MARK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457537.1	NM_031417		T	45790827	C	T	45790827	4	4	370	1	0	0	0	0	0	1	0	0	9324	876	31	1	1449	1	MARK4	19	45790827	Nonsense_Mutation	SNP	C	TCGA-ZS-A9CD-01A-11D-A36X-10	10269080	45790827	13338156	91	51284										
VN1R2	317701	hgsc.bcm.edu	37	chr19	53761659	53761659	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	ctctttaccctaccccttttGctttgtatccaataaatatc	2	13	1	0			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr19:53761659G>T	ENST00000341702.3	+	1	115	c.31G>T	c.(31-33)Gct>Tct	p.A11S		NM_173856.2	NP_776255.2	Q8NFZ6	VN1R2_HUMAN	vomeronasal 1 receptor 2	11					response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(134;0.00301)		taccccttttgctttgtatcc	0.532																																					p.A11S		Atlas-SNP	.											.	VN1R2	71	.	0			c.G31T						.						8	7	8					19																	53761659		1678	3053	4731	SO:0001583	missense	317701	exon1			CCTTTTGCTTTGT	AF370359	CCDS12862.1	19q13.42	2012-08-22			ENSG00000196131	ENSG00000196131		"Vomeronasal receptors / Type 1", "GPCR / Unclassified : Vomeronasal receptors, type 1"	19872	protein-coding gene	gene with protein product						12123587	Standard	NM_173856		Approved	V1RL2	uc002qbi.2	Q8NFZ6		ENST00000341702.3:c.31G>T	chr19.hg19:g.53761659G>T	ENSP00000351244:p.Ala11Ser	59.0	0.0		58.0	13.0	NM_173856	A1L411|Q8TDU4	Missense_Mutation	SNP	ENST00000341702.3	hg19	CCDS12862.1	.	.	.	.	.	.	.	.	.	.	-	3.417	-0.118937	0.06838	.	.	ENSG00000196131	ENST00000341702	T	0.10960	2.82	.	.	.	.	.	.	.	.	T	0.06188	0.0160	N	0.08118	0	0.09310	N	1	P	0.38711	0.643	B	0.41691	0.364	T	0.34725	-0.9817	7	0.87932	D	0	.	.	.	.	.	11	Q8NFZ6	VN1R2_HUMAN	S	11	ENSP00000351244:A11S	ENSP00000351244:A11S	A	+	1	0	VN1R2	58453471	0.121000	0.22262	0.230000	0.23976	0.230000	0.25150	0.170000	0.16663	0.119000	0.18210	0.121000	0.15741	GCT	.	.		0.532	VN1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464285.1	NM_173856		T	53761659	G	T	53761659	3	4	370	1	0	0	0	0	1	0	0	0	17194	1319	46	3	33	3	VN1R2	19	53761659	Missense_Mutation	SNP	G	TCGA-ZS-A9CD-01A-11D-A36X-10	7970832	53761659	5367324	92	51285										
LILRA2	11027	hgsc.bcm.edu	37	chr19	55087301	55087301	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	ctatgacagaccctctctctCggtgcagccggtccccacag	9	17	2	2			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr19:55087301C>A	ENST00000251377.3	+	7	1113	c.980C>A	c.(979-981)tCg>tAg	p.S327*	LILRA2_ENST00000391738.3_Nonsense_Mutation_p.S327*|LILRB1_ENST00000418536.2_Intron|LILRB1_ENST00000396321.2_Intron|LILRA2_ENST00000251376.3_Nonsense_Mutation_p.S327*|LILRA2_ENST00000391737.1_Nonsense_Mutation_p.S315*|LILRB1_ENST00000448689.1_Intron			Q8N149	LIRA2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 2	327	Ig-like C2-type 4.				defense response (GO:0006952)|immune system process (GO:0002376)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(33)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	50				GBM - Glioblastoma multiforme(193;0.0963)		CCCTCTCTCTCGGTGCAGCCG	0.602																																					p.S327X		Atlas-SNP	.											.	LILRA2	99	.	0			c.C980A						.						52	47	49					19																	55087301		2203	4300	6503	SO:0001587	stop_gained	11027	exon6			CTCTCTCGGTGCA	U82275	CCDS12900.1, CCDS46179.1, CCDS74453.1	19q13.4	2013-01-11			ENSG00000239998	ENSG00000239998		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6603	protein-coding gene	gene with protein product		604812				9079806, 9548455	Standard	XM_005258452		Approved	LIR-7, ILT1, CD85h, LIR7		Q8N149	OTTHUMG00000065703	ENST00000251377.3:c.980C>A	chr19.hg19:g.55087301C>A	ENSP00000251377:p.Ser327*	84.0	0.0		102.0	25.0	NM_001130917	O75020	Nonsense_Mutation	SNP	ENST00000251377.3	hg19	CCDS46179.1	.	.	.	.	.	.	.	.	.	.	C	11.19	1.566946	0.28003	.	.	ENSG00000239998	ENST00000439534;ENST00000251377;ENST00000391738;ENST00000251376;ENST00000391737	.	.	.	2.06	-3.81	0.04294	.	2.015420	0.02866	N	0.130973	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	3.4375	0.07452	0.0:0.345:0.2092:0.4458	.	.	.	.	X	327;327;327;327;315	.	ENSP00000251376:S327X	S	+	2	0	LILRA2	59779113	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-1.663000	0.01968	-0.829000	0.04268	-1.540000	0.00911	TCG	.	.		0.602	LILRA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140813.2			A	55087301	C	A	55087301	4	1	370	1	0	0	0	0	0	1	0	0	8794	893	31	1	1002	1	LILRA2	19	55087301	Nonsense_Mutation	SNP	C	TCGA-ZS-A9CD-01A-11D-A36X-10	1325642	55087301	4041682	93	51286			1	72		2	2	18	N	C_A	5.381561e-05
LILRA2	11027	hgsc.bcm.edu	37	chr19	55087318	55087318	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	tctcggtgcagccggtccccAcagtagccccaggaaagaac	11	15	1	1			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr19:55087318A>G	ENST00000251377.3	+	7	1130	c.997A>G	c.(997-999)Aca>Gca	p.T333A	LILRA2_ENST00000391738.3_Missense_Mutation_p.T333A|LILRB1_ENST00000418536.2_Intron|LILRB1_ENST00000396321.2_Intron|LILRA2_ENST00000251376.3_Missense_Mutation_p.T333A|LILRA2_ENST00000391737.1_Missense_Mutation_p.T321A|LILRB1_ENST00000448689.1_Intron			Q8N149	LIRA2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 2	333	Ig-like C2-type 4.				defense response (GO:0006952)|immune system process (GO:0002376)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(33)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	50				GBM - Glioblastoma multiforme(193;0.0963)		GCCGGTCCCCACAGTAGCCCC	0.597																																					p.T333A		Atlas-SNP	.											.	LILRA2	99	.	0			c.A997G						.						62	56	58					19																	55087318		2203	4300	6503	SO:0001583	missense	11027	exon6			GTCCCCACAGTAG	U82275	CCDS12900.1, CCDS46179.1, CCDS74453.1	19q13.4	2013-01-11			ENSG00000239998	ENSG00000239998		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6603	protein-coding gene	gene with protein product		604812				9079806, 9548455	Standard	XM_005258452		Approved	LIR-7, ILT1, CD85h, LIR7		Q8N149	OTTHUMG00000065703	ENST00000251377.3:c.997A>G	chr19.hg19:g.55087318A>G	ENSP00000251377:p.Thr333Ala	93.0	0.0		110.0	27.0	NM_001130917	O75020	Missense_Mutation	SNP	ENST00000251377.3	hg19	CCDS46179.1	.	.	.	.	.	.	.	.	.	.	A	8.482	0.860049	0.17178	.	.	ENSG00000239998	ENST00000251377;ENST00000391738;ENST00000251376;ENST00000391737	T;T;T;T	0.03386	3.95;3.95;3.95;3.95	2.19	0.944	0.19537	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	2.403190	0.02094	N	0.053344	T	0.09905	0.0243	M	0.82517	2.595	0.09310	N	1	B;B;B	0.32302	0.363;0.363;0.167	B;B;B	0.39152	0.217;0.292;0.196	T	0.34825	-0.9813	9	.	.	.	.	3.5932	0.07997	0.7234:0.0:0.2766:0.0	.	321;333;333	A8MZH0;Q8N149;Q8N149-2	.;LIRA2_HUMAN;.	A	333;333;333;321	ENSP00000251377:T333A;ENSP00000375618:T333A;ENSP00000251376:T333A;ENSP00000375617:T321A	.	T	+	1	0	LILRA2	59779130	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.210000	0.01227	0.191000	0.20236	0.416000	0.27883	ACA	.	.		0.597	LILRA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140813.2			G	55087318	A	G	55087318	3	3	370	1	0	0	0	0	1	0	0	0	8794	159	6	2	1019	2	LILRA2	19	55087318	Missense_Mutation	SNP	A	TCGA-ZS-A9CD-01A-11D-A36X-10	17	55087318	4041665	94	51287			1	72		2	2	18	N	C_A	5.381561e-05
ZNRF3	84133	hgsc.bcm.edu	37	chr22	29445468	29445469	+	Frame_Shift_Ins	INS	-	-	GGCCA													0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	gcctggccgctcaccgctgcINSggcctggagcaccgggccta					rs34671303	byFrequency	TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chr22:29445468_29445469insGGCCA	ENST00000544604.2	+	8	1474_1475	c.1299_1300insGGCCA	c.(1300-1302)ggcfs	p.-434fs	ZNRF3_ENST00000402174.1_Frame_Shift_Ins_p.-334fs|ZNRF3_ENST00000332811.4_Frame_Shift_Ins_p.-334fs|ZNRF3_ENST00000406323.3_Frame_Shift_Ins_p.-334fs	NM_001206998.1	NP_001193927.1	Q9ULT6	ZNRF3_HUMAN	zinc and ring finger 3						canonical Wnt signaling pathway (GO:0060070)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of non-canonical Wnt signaling pathway (GO:2000051)|protein ubiquitination (GO:0016567)|stem cell proliferation (GO:0072089)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	integral component of plasma membrane (GO:0005887)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(4)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	28						CTCACCGCTGCGGCCTGGAGCA	0.678																																					p.C433fs		Atlas-INDEL	.											ZNRF3,caecum,carcinoma,0,1	ZNRF3	75	.	0			c.1299_1300insGGCCA						.																																			SO:0001589	frameshift_variant	84133	exon8			.	AB051436	CCDS42999.1, CCDS56225.1	22q12.1	2013-01-09			ENSG00000183579	ENSG00000183579		"RING-type (C3HC4) zinc fingers"	18126	protein-coding gene	gene with protein product		612062				10574461	Standard	NM_032173		Approved	KIAA1133, BK747E2.3, FLJ22057, RNF203	uc003aeg.3	Q9ULT6	OTTHUMG00000151009	Exception_encountered	chr22.hg19:g.29445468_29445469insGGCCA	ENSP00000443824:p.Gly434fs	57.0	0.0		53.0	11.0	NM_001206998	B3KU18|Q6ICH1|Q6NTF8|Q8WU18	Frame_Shift_Ins	INS	ENST00000544604.2	hg19	CCDS56225.1																																																																																			.	.		0.678	ZNRF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320943.2	XM_290972		GGCCA	29445469	-	GGCCA	29445468	7	5	370	1	0	1	1	0	0	0	0	0	18228	776	27	0	1025	0	ZNRF3	22	29445468	Frame_Shift_Ins	INS	-	TCGA-ZS-A9CD-01A-11D-A36X-10		29445468	21859098	95	51288										
CXorf22	170063	hgsc.bcm.edu	37	chrX	35969436	35969436	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	tagcccagagcccataaattGggtggccatcatacaagatg	10	10	1	2			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chrX:35969436G>C	ENST00000297866.5	+	5	911	c.845G>C	c.(844-846)tGg>tCg	p.W282S		NM_152632.3	NP_689845.2	Q6ZTR5	CX022_HUMAN	chromosome X open reading frame 22	282										breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(3)	44						CCCATAAATTGGGTGGCCATC	0.398																																					p.W282S		Atlas-SNP	.											.	CXorf22	272	.	0			c.G845C						.						49	45	47					X																	35969436		2202	4300	6502	SO:0001583	missense	170063	exon5			TAAATTGGGTGGC	BC027936	CCDS14237.2	Xp21.1	2014-08-07			ENSG00000165164	ENSG00000165164			28546	protein-coding gene	gene with protein product						12477932	Standard	NM_152632		Approved	MGC34831	uc004ddj.3	Q6ZTR5	OTTHUMG00000021350	ENST00000297866.5:c.845G>C	chrX.hg19:g.35969436G>C	ENSP00000297866:p.Trp282Ser	242.0	0.0		201.0	110.0	NM_152632	Q5JRM8|Q8N6X8	Missense_Mutation	SNP	ENST00000297866.5	hg19	CCDS14237.2	.	.	.	.	.	.	.	.	.	.	G	16.46	3.128588	0.56721	.	.	ENSG00000165164	ENST00000297866	T	0.18810	2.19	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.50222	0.1603	M	0.77103	2.36	0.58432	D	0.999998	D	0.89917	1.0	D	0.83275	0.996	T	0.52320	-0.8591	10	0.66056	D	0.02	-20.477	17.7748	0.88504	0.0:0.0:1.0:0.0	.	282	Q6ZTR5	CX022_HUMAN	S	282	ENSP00000297866:W282S	ENSP00000297866:W282S	W	+	2	0	CXorf22	35879357	1.000000	0.71417	1.000000	0.80357	0.458000	0.32498	6.957000	0.76019	2.416000	0.81992	0.513000	0.50165	TGG	.	.		0.398	CXorf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056216.2	NM_152632		C	35969436	G	C	35969436	3	2	370	1	0	0	0	0	1	0	0	0	4104	1357	47	4	863	4	CXorf22	23	35969436	Missense_Mutation	SNP	G	TCGA-ZS-A9CD-01A-11D-A36X-10		35969436	119301124	96	51289										
MAOB	4129	hgsc.bcm.edu	37	chrX	43698217	43698217	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	tctgggttggtccaacatagGatcctccaaggtccacatat	9	11	1	0			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chrX:43698217G>A	ENST00000378069.4	-	3	323	c.176C>T	c.(175-177)tCc>tTc	p.S59F	MAOB_ENST00000538942.1_Missense_Mutation_p.S43F|MAOB_ENST00000536181.1_Missense_Mutation_p.S43F|MAOB_ENST00000487544.1_5'UTR	NM_000898.4	NP_000889.3	P27338	AOFB_HUMAN	monoamine oxidase B	59					negative regulation of serotonin secretion (GO:0014063)|positive regulation of dopamine metabolic process (GO:0045964)|response to aluminum ion (GO:0010044)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|primary amine oxidase activity (GO:0008131)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(2)|skin(5)	21					Amantadine(DB00915)|Amphetamine(DB00182)|Dopamine(DB00988)|Ephedra(DB01363)|Flavin adenine dinucleotide(DB03147)|Furazolidone(DB00614)|Isocarboxazid(DB01247)|Linezolid(DB00601)|Methamphetamine(DB01577)|Moclobemide(DB01171)|Nandrolone decanoate(DB08804)|Nicotine(DB00184)|Pargyline(DB01626)|Phenelzine(DB00780)|Phentermine(DB00191)|Procaine(DB00721)|Rasagiline(DB01367)|Selegiline(DB01037)|Sertraline(DB01104)|Tranylcypromine(DB00752)|Zonisamide(DB00909)	TCCAACATAGGATCCTCCAAG	0.368																																					p.S59F		Atlas-SNP	.											.	MAOB	52	.	0			c.C176T						.						128	110	116					X																	43698217		2203	4300	6503	SO:0001583	missense	4129	exon3			ACATAGGATCCTC		CCDS14261.1	Xp11.4-p11.3	2008-02-05			ENSG00000069535	ENSG00000069535	1.4.3.4		6834	protein-coding gene	gene with protein product		309860					Standard	NM_000898		Approved		uc004dfz.4	P27338	OTTHUMG00000021388	ENST00000378069.4:c.176C>T	chrX.hg19:g.43698217G>A	ENSP00000367309:p.Ser59Phe	78.0	0.0		86.0	4.0	NM_000898	B2R6R3|B7Z5H3|D3DWC3|Q7Z6S2	Missense_Mutation	SNP	ENST00000378069.4	hg19	CCDS14261.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.237024	0.79800	.	.	ENSG00000069535	ENST00000378069;ENST00000536181;ENST00000538942	D;D;D	0.93076	-3.16;-3.16;-3.16	5.13	5.13	0.70059	Amine oxidase (1);	0.110356	0.64402	D	0.000008	D	0.95940	0.8678	L	0.58810	1.83	0.46678	D	0.999158	D;D;D	0.89917	1.0;0.976;0.999	D;P;D	0.85130	0.997;0.864;0.993	D	0.96283	0.9208	10	0.62326	D	0.03	-7.0208	17.9488	0.89046	0.0:0.0:1.0:0.0	.	43;59;59	B7Z5H3;Q8TBI1;P27338	.;.;AOFB_HUMAN	F	59;43;43	ENSP00000367309:S59F;ENSP00000441613:S43F;ENSP00000442240:S43F	ENSP00000367309:S59F	S	-	2	0	MAOB	43583161	1.000000	0.71417	0.995000	0.50966	0.829000	0.46940	9.187000	0.94912	2.259000	0.74868	0.513000	0.50165	TCC	.	.		0.368	MAOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056303.1	NM_000898		A	43698217	G	A	43698217	3	1	370	1	0	0	0	0	1	0	0	0	9235	1174	41	3	1438	3	MAOB	23	43698217	Missense_Mutation	SNP	G	TCGA-ZS-A9CD-01A-11D-A36X-10	7728781	43698217	111572343	97	51290										
AR	367	hgsc.bcm.edu	37	chrX	66766368	66766368	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	gggggtggtggcggcggcggCggcggcggcggcggcggcgg	29	10	0	0			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chrX:66766368C>T	ENST00000374690.3	+	1	1904	c.1380C>T	c.(1378-1380)ggC>ggT	p.G460G	AR_ENST00000396044.3_Silent_p.G460G|AR_ENST00000504326.1_Silent_p.G460G|AR_ENST00000513847.1_3'UTR	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	458	Modulating.|Poly-Gly.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	gcggcggcggcggcggcggcg	0.756									Androgen Insensitivity Syndrome																												p.G460G		Atlas-SNP	.											.	AR	249	.	0			c.C1380T						.						1	1	1					X																	66766368		414	1064	1478	SO:0001819	synonymous_variant	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	CGGCGGCGGCGGC	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.1380C>T	chrX.hg19:g.66766368C>T		162.0	0.0		322.0	66.0	NM_000044	A2RUN2|B1AKD7|Q9UD95	Silent	SNP	ENST00000374690.3	hg19	CCDS14387.1																																																																																			.	.		0.756	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		T	66766368	C	T	66766368	2	4	370	1	0	0	0	0	0	0	0	1	836	755	27	1		1	AR	23	66766368	Silent	SNP	C	TCGA-ZS-A9CD-01A-11D-A36X-10	23068151	66766368	88504192	98	51291										
SPRY3	10251	hgsc.bcm.edu	37	chrX	155004358	155004358	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0612244897959184	6	1	1.20823244552058	0.939736346516008	1.28145865434001	0.118881118881119	0.692854020979022	0	gtgtgcagaaagatctcttcTggtagtgcacccttccccaa	9	12	2	2			TCGA-ZS-A9CD-01A-11D-A36X-10	TCGA-ZS-A9CD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	58e384ba-b93a-45d0-af93-821c3717e9ec	bf3a7873-31f2-4a59-9c3e-61836f34ab07	g.chrX:155004358T>G	ENST00000302805.2	+	2	1256	c.825T>G	c.(823-825)tcT>tcG	p.S275S		NM_005840.1	NP_005831.1	O43610	SPY3_HUMAN	sprouty homolog 3 (Drosophila)	275					multicellular organismal development (GO:0007275)|regulation of signal transduction (GO:0009966)	cytoplasm (GO:0005737)|membrane (GO:0016020)						all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					AGATCTCTTCTGGTAGTGCAC	0.547																																					p.S275S		Atlas-SNP	.											.	SPRY3	52	.	0			c.T825G						.						130	127	128					X																	155004358		2203	4296	6499	SO:0001819	synonymous_variant	10251	exon2			CTCTTCTGGTAGT	AF041038	CCDS14769.4	Xq28 and Yq12	2008-02-05	2001-11-28		ENSG00000168939	ENSG00000168939		"Pseudoautosomal regions / PAR2"	11271	protein-coding gene	gene with protein product	"antagonist of FGF signaling"	300531	"sprouty (Drosophila) homolog 2"			9458049	Standard	NM_005840		Approved	HSPRY3	uc004fnq.1	O43610	OTTHUMG00000022675	ENST00000302805.2:c.825T>G	chrX.hg19:g.155004358T>G		133.0	0.0		160.0	35.0	NM_005840	A8K0H8	Silent	SNP	ENST00000302805.2	hg19	CCDS14769.4																																																																																			.	.		0.547	SPRY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058823.2	NM_005840		G	155004358	T	G	155004358	2	3	370	1	0	0	0	0	0	0	0	1	15122	1567	55	5		5	SPRY3	23	155004358	Silent	SNP	T	TCGA-ZS-A9CD-01A-11D-A36X-10	88237990	155004358	266202	99	51292										
TCEA3	6920	hgsc.bcm.edu	37	chr1	23720511	23720511	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	acttcatgtccgtgctcttgAgctcttggtagatatgtgac	10	9	3	3			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr1:23720511A>C	ENST00000450454.2	-	8	786	c.680T>G	c.(679-681)cTc>cGc	p.L227R		NM_003196.1	NP_003187.1	O75764	TCEA3_HUMAN	transcription elongation factor A (SII), 3	227	TFIIS central. {ECO:0000255|PROSITE- ProRule:PRU00651}.				regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|urinary_tract(1)	7		Colorectal(325;3.46e-05)|Lung NSC(340;4.16e-05)|all_lung(284;6.68e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.0054)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.6e-25)|Colorectal(126;8.32e-08)|COAD - Colon adenocarcinoma(152;4.29e-06)|GBM - Glioblastoma multiforme(114;9e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00424)|STAD - Stomach adenocarcinoma(196;0.0145)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0963)|LUSC - Lung squamous cell carcinoma(448;0.198)		CGTGCTCTTGAGCTCTTGGTA	0.627																																					p.L227R		Atlas-SNP	.											.	TCEA3	20	.	0			c.T680G						.						61	62	62					1																	23720511		1968	4135	6103	SO:0001583	missense	6920	exon8			CTCTTGAGCTCTT	AJ223473	CCDS44086.1	1p36.11	2011-01-25			ENSG00000204219	ENSG00000204219			11615	protein-coding gene	gene with protein product		604128				9790746	Standard	NM_003196		Approved	TFIIS.H	uc021oig.1	O75764	OTTHUMG00000003233	ENST00000450454.2:c.680T>G	chr1.hg19:g.23720511A>C	ENSP00000406293:p.Leu227Arg	78.0	0.0		66.0	27.0	NM_003196	A8K2K7|Q5DR83	Missense_Mutation	SNP	ENST00000450454.2	hg19	CCDS44086.1	.	.	.	.	.	.	.	.	.	.	A	15.79	2.937894	0.52972	.	.	ENSG00000204219	ENST00000450454	T	0.47177	0.85	5.46	5.46	0.80206	Transcription elongation factor S-IIM (1);Transcription elongation factor S-II, central domain (4);	0.360158	0.29438	N	0.012141	T	0.60547	0.2277	M	0.82193	2.58	0.80722	D	1	P	0.36222	0.544	B	0.43680	0.427	T	0.65751	-0.6092	10	0.62326	D	0.03	-14.8948	14.7441	0.69477	1.0:0.0:0.0:0.0	.	227	O75764	TCEA3_HUMAN	R	227	ENSP00000406293:L227R	ENSP00000406293:L227R	L	-	2	0	TCEA3	23593098	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.199000	0.72112	2.232000	0.73038	0.529000	0.55759	CTC	.	.		0.627	TCEA3-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008911.2	NM_003196		C	23720511	A	C	23720511	3	2	371	1	0	0	0	0	1	0	0	0	15684	304	11	5	382	5	TCEA3	1	23720511	Missense_Mutation	SNP	A	TCGA-ZS-A9CE-01A-11D-A36X-10		23720511	225530110	1	51293										
FUBP1	8880	hgsc.bcm.edu	37	chr1	78422295	78422295	+	Frame_Shift_Del	DEL	G	G	-													0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	ttgtagttggtgcacctgcaGgggctgctggtggtggctgt							TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr1:78422295delG	ENST00000370768.2	-	17	1748	c.1667delC	c.(1666-1668)cctfs	p.P556fs	FUBP1_ENST00000370767.1_Frame_Shift_Del_p.P556fs|FUBP1_ENST00000436586.2_Frame_Shift_Del_p.P577fs	NM_003902.3	NP_003893.2	Q96AE4	FUBP1_HUMAN	far upstream element (FUSE) binding protein 1	556	Pro-rich.				positive regulation of gene expression (GO:0010628)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)			central_nervous_system(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(3)	17						TGCACCTGCAGGGGCTGCTGG	0.423			"F, N"		oligodendroglioma																																p.P556fs		Atlas-INDEL	.		Rec	yes		1	1p13.1	8880	far upstream element (FUSE) binding protein 1		O	.	FUBP1	112	.	0			c.1668delT						.						153	144	147					1																	78422295		2203	4300	6503	SO:0001589	frameshift_variant	8880	exon17			.	U05040	CCDS683.1	1p31.1	2008-02-05			ENSG00000162613	ENSG00000162613			4004	protein-coding gene	gene with protein product		603444		FUBP		8125259	Standard	XM_005271309		Approved	FBP	uc001dii.3	Q96AE4	OTTHUMG00000040799	ENST00000370768.2:c.1667delC	chr1.hg19:g.78422295delG	ENSP00000359804:p.Pro556fs	81.0	0.0		84.0	37.0	NM_003902	Q12828	Frame_Shift_Del	DEL	ENST00000370768.2	hg19	CCDS683.1																																																																																			.	.		0.423	FUBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098030.3	NM_003902		-	78422295	G	-	78422295	7	5	371	1	0	1	0	1	0	0	0	0	6100	1000	35	0	283	0	FUBP1	1	78422295	Frame_Shift_Del	DEL	G	TCGA-ZS-A9CE-01A-11D-A36X-10	54701784	78422295	170828326	2	51294										
FUBP1	8880	hgsc.bcm.edu	37	chr1	78429310	78429310	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	tggcacaataaaattaaattCctgtagtccaccaggtggtc	8	9	0	0			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr1:78429310C>A	ENST00000370768.2	-	13	1213	c.1132G>T	c.(1132-1134)Gaa>Taa	p.E378*	FUBP1_ENST00000370767.1_Nonsense_Mutation_p.E378*|FUBP1_ENST00000436586.2_Nonsense_Mutation_p.E399*	NM_003902.3	NP_003893.2	Q96AE4	FUBP1_HUMAN	far upstream element (FUSE) binding protein 1	378	Gly-rich.|KH 4. {ECO:0000255|PROSITE- ProRule:PRU00117}.				positive regulation of gene expression (GO:0010628)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)			central_nervous_system(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(3)	17						AAATTAAATTCCTGTAGTCCA	0.408			"F, N"		oligodendroglioma																																p.E378X		Atlas-SNP	.		Rec	yes		1	1p13.1	8880	far upstream element (FUSE) binding protein 1		O	.,1	FUBP1	112	.	0			c.G1132T						.						81	83	82					1																	78429310		2203	4300	6503	SO:0001587	stop_gained	8880	exon13			TAAATTCCTGTAG	U05040	CCDS683.1	1p31.1	2008-02-05			ENSG00000162613	ENSG00000162613			4004	protein-coding gene	gene with protein product		603444		FUBP		8125259	Standard	XM_005271309		Approved	FBP	uc001dii.3	Q96AE4	OTTHUMG00000040799	ENST00000370768.2:c.1132G>T	chr1.hg19:g.78429310C>A	ENSP00000359804:p.Glu378*	281.0	0.0		324.0	128.0	NM_003902	Q12828	Nonsense_Mutation	SNP	ENST00000370768.2	hg19	CCDS683.1	.	.	.	.	.	.	.	.	.	.	C	38	6.918572	0.97936	.	.	ENSG00000162613	ENST00000370773;ENST00000370767;ENST00000370768;ENST00000394922;ENST00000436586	.	.	.	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	-23.7575	20.2241	0.98333	0.0:1.0:0.0:0.0	.	.	.	.	X	377;378;378;377;399	.	ENSP00000294623:E377X	E	-	1	0	FUBP1	78201898	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.487000	0.81328	2.785000	0.95823	0.655000	0.94253	GAA	.	.		0.408	FUBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098030.3	NM_003902		A	78429310	C	A	78429310	4	1	371	1	0	0	0	0	0	1	0	0	6100	864	30	3	834	3	FUBP1	1	78429310	Nonsense_Mutation	SNP	C	TCGA-ZS-A9CE-01A-11D-A36X-10	7015	78429310	170821311	3	51295										
PDZK1	5174	hgsc.bcm.edu	37	chr1	145747212	145747212	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	aagatggagacagagttcttAggatcaatggtgtctttgtg	13	4	3	3			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr1:145747212A>G	ENST00000344770.2	+	2	242	c.169A>G	c.(169-171)Agg>Ggg	p.R57G	PDZK1_ENST00000451928.2_Missense_Mutation_p.R57G|PDZK1_ENST00000417171.1_Missense_Mutation_p.R57G	NM_002614.4	NP_002605.2	Q5T2W1	NHRF3_HUMAN	PDZ domain containing 1	57	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				carnitine transport (GO:0015879)|cell proliferation (GO:0008283)|drug transport (GO:0015893)|establishment of protein localization to plasma membrane (GO:0090002)|positive regulation of ion transmembrane transport (GO:0034767)|positive regulation of protein targeting to membrane (GO:0090314)|regulation of anion transport (GO:0044070)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|transporter activity (GO:0005215)			NS(1)|endometrium(1)|large_intestine(1)|lung(3)|pancreas(1)	7	all_hematologic(18;0.00473)|Acute lymphoblastic leukemia(18;0.0786)		KIRC - Kidney renal clear cell carcinoma(6;0.0764)|Kidney(552;0.118)|Colorectal(543;0.229)			CAGAGTTCTTAGGATCAATGG	0.512																																					p.R57G		Atlas-SNP	.											.	PDZK1	15	.	0			c.A169G						.						130	129	129					1																	145747212		2203	4300	6503	SO:0001583	missense	5174	exon3			GTTCTTAGGATCA	AF012281	CCDS72859.1, CCDS72860.1	1q21	2009-08-21			ENSG00000174827	ENSG00000174827			8821	protein-coding gene	gene with protein product		603831				9461128	Standard	NM_002614		Approved	PDZD1, NHERF3	uc001eoo.2	Q5T2W1	OTTHUMG00000013735	ENST00000344770.2:c.169A>G	chr1.hg19:g.145747212A>G	ENSP00000342143:p.Arg57Gly	163.0	0.0		217.0	87.0	NM_002614	B4DPB9|E7EU02|O60450|Q5T5P6|Q9BQ41	Missense_Mutation	SNP	ENST00000344770.2	hg19	CCDS924.1	.	.	.	.	.	.	.	.	.	.	A	11.93	1.785461	0.31593	.	.	ENSG00000174827	ENST00000443667;ENST00000417171;ENST00000451928;ENST00000344770	T;T;T;T	0.41758	0.99;1.76;1.76;1.76	5.82	0.29	0.15728	PDZ/DHR/GLGF (4);	0.356446	0.35320	N	0.003286	T	0.14356	0.0347	N	0.04820	-0.15	0.09310	N	1	B;B	0.28783	0.002;0.222	B;P	0.44990	0.052;0.466	T	0.35001	-0.9806	10	0.72032	D	0.01	-1.1169	8.3043	0.32034	0.485:0.3899:0.0:0.1251	.	57;57	E7EU02;Q5T2W1	.;NHRF3_HUMAN	G	57	ENSP00000409291:R57G;ENSP00000394485:R57G;ENSP00000403422:R57G;ENSP00000342143:R57G	ENSP00000342143:R57G	R	+	1	2	PDZK1	144458569	0.604000	0.26932	0.220000	0.23810	0.052000	0.14988	1.319000	0.33655	0.075000	0.16796	0.533000	0.62120	AGG	.	.		0.512	PDZK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038502.2	NM_002614		G	145747212	A	G	145747212	3	3	371	1	0	0	0	0	1	0	0	0	11716	411	15	2	171	2	PDZK1	1	145747212	Missense_Mutation	SNP	A	TCGA-ZS-A9CE-01A-11D-A36X-10	67317902	145747212	103503409	4	51296										
HRNR	388697	hgsc.bcm.edu	37	chr1	152192560	152192561	+	Nonsense_Mutation	DNP	GG	GG	TT													0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	gacccatgctgaccatagctGgaagatgaacctgcactaga					rs146581615		TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr1:152192560_152192561GG>TT	ENST00000368801.2	-	3	1619_1620	c.1544_1545CC>AA	c.(1543-1545)tCC>tAA	p.S515*	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	515					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GACCATAGCTGGAAGATGAACC	0.584																																					p.S515S|p.S515Y		Atlas-SNP	.											.	HRNR	403	.	0			c.C1545A|c.C1544A						.																																			SO:0001587	stop_gained	388697	exon3			ATAGCTGGAAGAT|TAGCTGGAAGATG	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"EF-hand domain containing"	20846	protein-coding gene	gene with protein product	"filaggrin family member 3"						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.1544_1545delinsTT	chr1.hg19:g.152192560_152192561delinsTT	ENSP00000357791:p.Ser515*	89.0	0.0		107.0|106.0	45.0|46.0	NM_001009931	Q5DT20|Q5U1F4	Silent|Missense_Mutation	SNP	ENST00000368801.2	hg19	CCDS30859.1																																																																																			.	.|G|1.000;A|0.000		0.584	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868		TT	152192561	GG	TT	152192560	4	4	371	1	0	0	0	0	0	1	0	0	7368	1335	47	3	7011	3	HRNR	1	152192560	Nonsense_Mutation	DNP	GG	TCGA-ZS-A9CE-01A-11D-A36X-10	6445348	152192560	97058061	5	51297										
FLG2	388698	hgsc.bcm.edu	37	chr1	152327802	152327802	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	gagccagacccatgttgtccAaagccagcggactgacctga	11	13	0	3			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr1:152327802A>T	ENST00000388718.5	-	3	2532	c.2460T>A	c.(2458-2460)ttT>ttA	p.F820L	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	820	Ser-rich.				establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CATGTTGTCCAAAGCCAGCGG	0.522																																					p.F820L		Atlas-SNP	.											.	FLG2	431	.	0			c.T2460A						.						291	286	288					1																	152327802		2203	4300	6503	SO:0001583	missense	388698	exon3			TTGTCCAAAGCCA	AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"EF-hand domain containing"	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.2460T>A	chr1.hg19:g.152327802A>T	ENSP00000373370:p.Phe820Leu	109.0	0.0		162.0	82.0	NM_001014342	Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	hg19	CCDS30861.1	.	.	.	.	.	.	.	.	.	.	A	9.626	1.135104	0.21123	.	.	ENSG00000143520	ENST00000388718	T	0.20881	2.04	4.72	2.21	0.28008	.	.	.	.	.	T	0.03520	0.0101	L	0.39020	1.185	0.09310	N	1	B	0.21225	0.053	B	0.17098	0.017	T	0.42699	-0.9436	9	0.11182	T	0.66	.	1.5429	0.02559	0.5537:0.1772:0.098:0.1711	.	820	Q5D862	FILA2_HUMAN	L	820	ENSP00000373370:F820L	ENSP00000373370:F820L	F	-	3	2	FLG2	150594426	0.000000	0.05858	0.016000	0.15963	0.071000	0.16799	0.291000	0.18994	0.797000	0.33971	0.529000	0.55759	TTT	.	.		0.522	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		T	152327802	A	T	152327802	3	4	371	1	0	0	0	0	1	0	0	0	5931	127	5	4	4719	4	FLG2	1	152327802	Missense_Mutation	SNP	A	TCGA-ZS-A9CE-01A-11D-A36X-10	135242	152327802	96922819	6	51298										
C1orf104	23623	hgsc.bcm.edu	37	chr1	155290828	155290828	+	Intron	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	tagaccgatggacctgggcaCgaggggcggggcaggacaag	19	9	0	1			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr1:155290828C>A	ENST00000368352.5	+	1	65				RUSC1-AS1_ENST00000543656.1_RNA|RUSC1_ENST00000368347.4_5'Flank|RUSC1-AS1_ENST00000446880.1_RNA|RUSC1-AS1_ENST00000450199.1_RNA|RUSC1-AS1_ENST00000443642.1_RNA|RUSC1_ENST00000368354.3_Intron	NM_001105203.1	NP_001098673.1	Q9BVN2	RUSC1_HUMAN	RUN and SH3 domain containing 1						positive regulation of signal transduction (GO:0009967)|protein polyubiquitination (GO:0000209)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(2)|skin(1)|urinary_tract(1)	21	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;1.55e-10)|all cancers(21;4.15e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)			GACCTGGGCACGAGGGGCGGG	0.642																																					p.R151L		Atlas-SNP	.											.	.	.	.	0			c.G452T						.						51	61	58					1																	155290828		2026	4156	6182	SO:0001627	intron_variant	284618	exon2			TGGGCACGAGGGG	AB026894	CCDS1112.1, CCDS41410.1, CCDS41411.1, CCDS41412.1	1q21-q22	2011-04-28			ENSG00000160753	ENSG00000160753			17153	protein-coding gene	gene with protein product						10760598	Standard	NM_001105203		Approved	NESCA	uc001fkj.2	Q9BVN2	OTTHUMG00000013910	ENST00000368352.5:c.-87+46C>A	chr1.hg19:g.155290828C>A		194.0	0.0		295.0	92.0	NM_001039517	B3KWM9|Q5T9U9|Q5T9V0|Q5T9V1|Q5T9V2|Q9UPY4|Q9Y4T5	Missense_Mutation	SNP	ENST00000368352.5	hg19	CCDS41410.1																																																																																			.	.		0.642	RUSC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039071.1			A	155290828	C	A	155290828	1	1	371	0	1	0	0	0	0	0	0	0	1980	536	19	1		1	C1orf104	1	155290828	Intron	SNP	C	TCGA-ZS-A9CE-01A-11D-A36X-10	2963026	155290828	93959793	7	51299										
GON4L	54856	hgsc.bcm.edu	37	chr1	155720493	155720493	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	cttcacaggcagtgtggaagAgctgcatgagttctcgaaaa	12	8	2	2			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr1:155720493A>C	ENST00000368331.1	-	32	6656	c.6608T>G	c.(6607-6609)cTc>cGc	p.L2203R	GON4L_ENST00000271883.5_Missense_Mutation_p.L2202R|GON4L_ENST00000437809.1_Missense_Mutation_p.L2202R	NM_001282858.1|NM_001282860.1	NP_001269787.1|NP_001269789.1	Q3T8J9	GON4L_HUMAN	gon-4-like (C. elegans)	2203					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	45	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					AGTGTGGAAGAGCTGCATGAG	0.488																																					p.L2202R		Atlas-SNP	.											.	GON4L	392	.	0			c.T6605G						.						48	48	48					1																	155720493		1939	4134	6073	SO:0001583	missense	54856	exon32			TGGAAGAGCTGCA	AB046826	CCDS1121.1, CCDS44242.1, CCDS60296.1	1q22	2013-10-31	2006-11-08	2006-02-16	ENSG00000116580	ENSG00000116580			25973	protein-coding gene	gene with protein product		610393	"gon-4 homolog (C.elegans)"	GON4		16545939, 21454521	Standard	XM_005245283		Approved	FLJ20203, GON-4	uc001fly.1	Q3T8J9	OTTHUMG00000014106	ENST00000368331.1:c.6608T>G	chr1.hg19:g.155720493A>C	ENSP00000357315:p.Leu2203Arg	219.0	0.0		367.0	61.0	NM_001037533	B7ZBL4|Q14C93|Q3T8J8|Q5VYZ5|Q5W0D5|Q6AWA6|Q6P1Q6|Q7Z3L3|Q8IY79|Q9BQI1|Q9HCG6	Missense_Mutation	SNP	ENST00000368331.1	hg19		.	.	.	.	.	.	.	.	.	.	-	21.5	4.165463	0.78339	.	.	ENSG00000116580	ENST00000437809;ENST00000368331;ENST00000271883	T;T;T	0.37235	1.21;1.21;1.21	4.88	4.88	0.63580	SANT domain, DNA binding (1);Homeodomain-related (1);Homeodomain-like (1);	0.000000	0.64402	D	0.000014	T	0.53190	0.1781	M	0.79123	2.44	0.47778	D	0.999512	D;D	0.89917	0.999;1.0	D;D	0.87578	0.996;0.998	T	0.60934	-0.7164	10	0.87932	D	0	.	14.3576	0.66748	1.0:0.0:0.0:0.0	.	2203;2202	Q3T8J9;Q3T8J9-3	GON4L_HUMAN;.	R	2202;2203;2202	ENSP00000396117:L2202R;ENSP00000357315:L2203R;ENSP00000271883:L2202R	ENSP00000271883:L2202R	L	-	2	0	GON4L	153987117	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.624000	0.74243	2.052000	0.61016	0.449000	0.29647	CTC	.	.		0.488	GON4L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_032292		C	155720493	A	C	155720493	3	2	371	1	0	0	0	0	1	0	0	0	6580	304	11	5	121	5	GON4L	1	155720493	Missense_Mutation	SNP	A	TCGA-ZS-A9CE-01A-11D-A36X-10	429665	155720493	93530128	8	51300										
CRP	1401	hgsc.bcm.edu	37	chr1	159683527	159683527	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	accgaaggaatcctgctcctGccccaagatgatgcttgctt	9	13	0	2			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr1:159683527G>A	ENST00000255030.5	-	2	566	c.463C>T	c.(463-465)Cag>Tag	p.Q155*	CRP_ENST00000343919.2_Intron|CRP_ENST00000368112.1_Intron|CRP_ENST00000368111.1_Intron|CRP_ENST00000437342.1_5'UTR|CRP_ENST00000368110.1_Intron|CRP_ENST00000473196.1_5'UTR	NM_000567.2	NP_000558.2	P02741	CRP_HUMAN	C-reactive protein, pentraxin-related	155	Pentaxin.				acute-phase response (GO:0006953)|aging (GO:0007568)|cellular response to calcium ion (GO:0071277)|complement activation, classical pathway (GO:0006958)|defense response to Gram-positive bacterium (GO:0050830)|inflammatory response (GO:0006954)|negative regulation of lipid storage (GO:0010888)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|opsonization (GO:0008228)|positive regulation of dendrite development (GO:1900006)|protein polymerization (GO:0051258)|regulation of interleukin-8 secretion (GO:2000482)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to lead ion (GO:0010288)|wound healing (GO:0042060)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|growth cone (GO:0030426)	calcium ion binding (GO:0005509)|cholesterol binding (GO:0015485)|choline binding (GO:0033265)|complement component C1q binding (GO:0001849)|low-density lipoprotein particle binding (GO:0030169)			breast(1)|endometrium(3)|kidney(1)|lung(15)|ovary(1)|skin(1)	22	all_hematologic(112;0.0429)				inhaled insulin(DB05278)	TCCTGCTCCTGCCCCAAGATG	0.537																																					p.Q155X		Atlas-SNP	.											.	CRP	49	.	0			c.C463T						.						245	245	245					1																	159683527		2203	4300	6503	SO:0001587	stop_gained	1401	exon2			GCTCCTGCCCCAA	M11725	CCDS30911.1	1q23.2	2013-05-13			ENSG00000132693	ENSG00000132693			2367	protein-coding gene	gene with protein product	"pentraxin 1"	123260				3840479, 6857266	Standard	NM_000567		Approved	PTX1	uc001ftw.3	P02741	OTTHUMG00000035344	ENST00000255030.5:c.463C>T	chr1.hg19:g.159683527G>A	ENSP00000255030:p.Gln155*	79.0	0.0		149.0	44.0	NM_000567	A8K078|D3DVD9|D3DVE0|Q08AK3|Q8WW75	Nonsense_Mutation	SNP	ENST00000255030.5	hg19	CCDS30911.1	.	.	.	.	.	.	.	.	.	.	G	37	6.373874	0.97515	.	.	ENSG00000132693	ENST00000255030	.	.	.	4.34	4.34	0.51931	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-20.5758	14.3656	0.66803	0.0:0.0:1.0:0.0	.	.	.	.	X	155	.	ENSP00000255030:Q155X	Q	-	1	0	CRP	157950151	1.000000	0.71417	0.988000	0.46212	0.995000	0.86356	5.769000	0.68865	1.935000	0.56089	0.650000	0.86243	CAG	.	.		0.537	CRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085553.1	NM_000567		A	159683527	G	A	159683527	4	1	371	1	0	0	0	0	0	1	0	0	3897	1328	46	3	215	3	CRP	1	159683527	Nonsense_Mutation	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10	3963034	159683527	89567094	9	51301										
PRRX1	5396	hgsc.bcm.edu	37	chr1	170705233	170705233	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	atgtgccaacaatagccctgCacagggcatcaacatggcca	9	13	1	0			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr1:170705233C>T	ENST00000239461.6	+	4	957	c.644C>T	c.(643-645)gCa>gTa	p.A215V	PRRX1_ENST00000367760.3_3'UTR|PRRX1_ENST00000476867.2_3'UTR	NM_022716.2	NP_073207.1	P54821	PRRX1_HUMAN	paired related homeobox 1	215					artery morphogenesis (GO:0048844)|cartilage development (GO:0051216)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic limb morphogenesis (GO:0030326)|inner ear morphogenesis (GO:0042472)|middle ear morphogenesis (GO:0042474)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|palate development (GO:0060021)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smoothened signaling pathway (GO:0045880)	nucleolus (GO:0005730)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)			large_intestine(2)|ovary(1)	3	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					AATAGCCCTGCACAGGGCATC	0.488																																					p.A215V		Atlas-SNP	.											.	PRRX1	81	.	0			c.C644T						.						168	170	169					1																	170705233		2203	4300	6503	SO:0001583	missense	5396	exon4			GCCCTGCACAGGG	M95929	CCDS1290.1, CCDS1291.1	1q24.3	2011-06-20	2003-11-12	2003-11-14	ENSG00000116132	ENSG00000116132		"Homeoboxes / PRD class"	9142	protein-coding gene	gene with protein product		167420	"paired mesoderm homeo box 1"	PMX1		1509260	Standard	NM_006902		Approved	PHOX1	uc001ghf.3	P54821	OTTHUMG00000035231	ENST00000239461.6:c.644C>T	chr1.hg19:g.170705233C>T	ENSP00000239461:p.Ala215Val	336.0	0.0		547.0	88.0	NM_022716	B5BUM7|O60807	Missense_Mutation	SNP	ENST00000239461.6	hg19	CCDS1290.1	.	.	.	.	.	.	.	.	.	.	C	16.51	3.142891	0.57044	.	.	ENSG00000116132	ENST00000239461;ENST00000476867	D;T	0.91521	-2.86;-1.3	6.06	6.06	0.98353	.	0.271361	0.41396	D	0.000897	T	0.81113	0.4755	L	0.50333	1.59	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.74405	-0.3676	10	0.17832	T	0.49	.	13.4416	0.61117	0.0:0.9249:0.0:0.0751	.	215	P54821	PRRX1_HUMAN	V	215;60	ENSP00000239461:A215V;ENSP00000451225:A60V	ENSP00000356734:A215V	A	+	2	0	PRRX1	168971857	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.579000	0.67457	2.871000	0.98454	0.655000	0.94253	GCA	.	.		0.488	PRRX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085236.3	NM_006902		T	170705233	C	T	170705233	3	4	371	1	0	0	0	0	1	0	0	0	12624	710	25	3	717	3	PRRX1	1	170705233	Missense_Mutation	SNP	C	TCGA-ZS-A9CE-01A-11D-A36X-10	11021706	170705233	78545388	10	51302										
RNPEP	6051	hgsc.bcm.edu	37	chr1	201958548	201958548	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	agctgtgatgagtgctagcaCctgggagaagagaggtccaa	15	7	0	4			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr1:201958548C>A	ENST00000295640.4	+	3	669	c.626C>A	c.(625-627)aCc>aAc	p.T209N	RNPEP_ENST00000367286.3_Missense_Mutation_p.T209N|RNPEP_ENST00000471105.1_Intron	NM_020216.3	NP_064601.3	Q9H4A4	AMPB_HUMAN	arginyl aminopeptidase (aminopeptidase B)	209				STW -> RPG (in Ref. 1; CAC12957). {ECO:0000305}.	leukotriene biosynthetic process (GO:0019370)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|epoxide hydrolase activity (GO:0004301)|metalloexopeptidase activity (GO:0008235)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|large_intestine(4)|lung(6)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21				KIRC - Kidney renal clear cell carcinoma(1967;3.23e-08)|Colorectal(1306;0.005)		AGTGCTAGCACCTGGGAGAAG	0.468																																					p.T209N	GBM(19;39 479 7473 13131 19462)	Atlas-SNP	.											.	RNPEP	39	.	0			c.C626A						.						125	120	122					1																	201958548		2203	4300	6503	SO:0001583	missense	6051	exon3			CTAGCACCTGGGA	BC001064	CCDS1418.1	1q32	2008-02-05			ENSG00000176393	ENSG00000176393	3.4.11.6		10078	protein-coding gene	gene with protein product		602675				9533033, 10467730	Standard	NM_020216		Approved		uc001gxd.3	Q9H4A4	OTTHUMG00000035866	ENST00000295640.4:c.626C>A	chr1.hg19:g.201958548C>A	ENSP00000295640:p.Thr209Asn	131.0	0.0		231.0	43.0	NM_020216	Q9BVM9|Q9H1D4|Q9NPT7	Missense_Mutation	SNP	ENST00000295640.4	hg19	CCDS1418.1	.	.	.	.	.	.	.	.	.	.	C	6.307	0.424713	0.11987	.	.	ENSG00000176393	ENST00000295640;ENST00000367286;ENST00000447312	T;T;T	0.04194	3.68;3.68;3.68	5.7	2.75	0.32379	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.442398	0.23604	N	0.046405	T	0.03011	0.0089	L	0.27053	0.805	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.47636	-0.9102	10	0.13853	T	0.58	-17.253	4.5691	0.12202	0.2793:0.5118:0.1352:0.0737	.	209	Q9H4A4	AMPB_HUMAN	N	209;209;78	ENSP00000295640:T209N;ENSP00000356255:T209N;ENSP00000389602:T78N	ENSP00000295640:T209N	T	+	2	0	RNPEP	200225171	0.103000	0.21917	0.479000	0.27329	0.996000	0.88848	0.277000	0.18734	0.307000	0.22880	0.655000	0.94253	ACC	.	.		0.468	RNPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087345.1	NM_020216		A	201958548	C	A	201958548	3	1	371	1	0	0	0	0	1	0	0	0	13524	507	18	3	636	3	RNPEP	1	201958548	Missense_Mutation	SNP	C	TCGA-ZS-A9CE-01A-11D-A36X-10	31253315	201958548	47292073	11	51303										
MYBPH	4608	hgsc.bcm.edu	37	chr1	203144856	203144856	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	ctcctctggactgcaggcagGgccctcggaggtgttttttt	13	11	1	0			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr1:203144856G>A	ENST00000255416.4	-	1	85	c.28C>T	c.(28-30)Cct>Tct	p.P10S		NM_004997.2	NP_004988.2	Q13203	MYBPH_HUMAN	myosin binding protein H	10					cell adhesion (GO:0007155)|regulation of striated muscle contraction (GO:0006942)	myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			endometrium(5)|large_intestine(6)|lung(7)|skin(1)|urinary_tract(1)	20			BRCA - Breast invasive adenocarcinoma(75;0.153)	Colorectal(1306;0.0306)		CTGCAGGCAGGGCCCTCGGAG	0.627																																					p.P10S	NSCLC(32;174 1025 14462 23899 42933)	Atlas-SNP	.											.	MYBPH	41	.	0			c.C28T						.						60	70	67					1																	203144856		2203	4300	6503	SO:0001583	missense	4608	exon1			AGGCAGGGCCCTC	BC044226	CCDS30975.1	1q32.1	2013-02-11	2001-11-28		ENSG00000133055	ENSG00000133055		"Myosin binding proteins", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7552	protein-coding gene	gene with protein product		160795	"myosin-binding protein H"			8486381	Standard	NM_004997		Approved		uc001gzh.1	Q13203	OTTHUMG00000042121	ENST00000255416.4:c.28C>T	chr1.hg19:g.203144856G>A	ENSP00000255416:p.Pro10Ser	62.0	0.0		109.0	14.0	NM_004997	Q16886|Q86YC5	Missense_Mutation	SNP	ENST00000255416.4	hg19	CCDS30975.1	.	.	.	.	.	.	.	.	.	.	G	4.088	0.014266	0.07959	.	.	ENSG00000133055	ENST00000255416	T	0.49720	0.77	5.02	-2.09	0.07232	.	0.998285	0.08105	N	0.997094	T	0.23410	0.0566	N	0.14661	0.345	0.09310	N	1	B	0.11235	0.004	B	0.09377	0.004	T	0.19549	-1.0302	10	0.16420	T	0.52	.	3.672	0.08277	0.2589:0.0:0.3427:0.3985	.	10	Q13203	MYBPH_HUMAN	S	10	ENSP00000255416:P10S	ENSP00000255416:P10S	P	-	1	0	MYBPH	201411479	0.000000	0.05858	0.000000	0.03702	0.123000	0.20343	-0.539000	0.06113	-0.417000	0.07461	0.462000	0.41574	CCT	.	.		0.627	MYBPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100264.1	NM_004997		A	203144856	G	A	203144856	3	1	371	1	0	0	0	0	1	0	0	0	10023	1232	43	3	1445	3	MYBPH	1	203144856	Missense_Mutation	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10	1186308	203144856	46105765	12	51304										
C1orf116	79098	hgsc.bcm.edu	37	chr1	207196069	207196069	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	gcttctctagagcttctttaCgtgcttttctctgctcttgc	7	12	4	1	rs376328889		TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr1:207196069C>T	ENST00000359470.5	-	4	1289	c.1040G>A	c.(1039-1041)cGt>cAt	p.R347H	C1orf116_ENST00000461135.2_Missense_Mutation_p.R101H	NM_023938.5	NP_076427.2	Q9BW04	SARG_HUMAN	chromosome 1 open reading frame 116	347						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(4)|stomach(1)	29	Prostate(682;0.19)					AGCTTCTTTACGTGCTTTTCT	0.567																																					p.R347H		Atlas-SNP	.											.	C1orf116	64	.	0			c.G1040A						.	C	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	63	65	64		302,1040	5.6	0.7	1		64	0,8600		0,0,4300	no	missense,missense	C1orf116	NM_001083924.1,NM_023938.5	29,29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	101/356,347/602	207196069	1,13005	2203	4300	6503	SO:0001583	missense	79098	exon4			TCTTTACGTGCTT		CCDS1475.1, CCDS44306.1	1q32.1	2012-06-26			ENSG00000182795	ENSG00000182795			28667	protein-coding gene	gene with protein product	"specifically androgen-regulated gene"	611680				15525603, 9389513	Standard	NM_023938		Approved	SARG, FLJ36507, MGC2742, MGC4309	uc001hfd.2	Q9BW04	OTTHUMG00000036580	ENST00000359470.5:c.1040G>A	chr1.hg19:g.207196069C>T	ENSP00000352447:p.Arg347His	47.0	0.0		104.0	28.0	NM_023938	C9JV41|Q658X3	Missense_Mutation	SNP	ENST00000359470.5	hg19	CCDS1475.1	.	.	.	.	.	.	.	.	.	.	C	19.40	3.820390	0.71028	2.27E-4	0.0	ENSG00000182795	ENST00000359470;ENST00000461135	T;T	0.13196	2.61;2.61	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.38321	0.1036	M	0.66939	2.045	0.31573	N	0.656102	D	0.89917	1.0	D	0.91635	0.999	T	0.35871	-0.9771	10	0.87932	D	0	-21.9504	18.0883	0.89464	0.0:1.0:0.0:0.0	.	347	Q9BW04	SARG_HUMAN	H	347;101	ENSP00000352447:R347H;ENSP00000436862:R101H	ENSP00000352447:R347H	R	-	2	0	C1orf116	205262692	0.386000	0.25180	0.724000	0.30704	0.390000	0.30446	2.433000	0.44793	2.608000	0.88229	0.655000	0.94253	CGT	.	.		0.567	C1orf116-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088973.1	NM_024115		T	207196069	C	T	207196069	3	4	371	1	0	0	0	0	1	0	0	0	1991	536	19	1	769	1	C1orf116	1	207196069	Missense_Mutation	SNP	C	TCGA-ZS-A9CE-01A-11D-A36X-10	4051213	207196069	42054552	13	51305										
ZP4	57829	hgsc.bcm.edu	37	chr1	238050802	238050802	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	atccaagagcagtggtggcgAggtcacgttccgagacacag	14	10	1	2			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr1:238050802A>G	ENST00000366570.4	-	5	771	c.613T>C	c.(613-615)Tcg>Ccg	p.S205P	RP11-193H5.1_ENST00000450451.1_RNA	NM_021186.3	NP_067009.1	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4	205	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				acrosomal vesicle exocytosis (GO:0060478)|binding of sperm to zona pellucida (GO:0007339)|intracellular signal transduction (GO:0035556)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of humoral immune response (GO:0002922)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of T cell proliferation (GO:0042102)|protein kinase A signaling (GO:0010737)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	acrosin binding (GO:0032190)|signal transducer activity (GO:0004871)			breast(6)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(42)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	73	Ovarian(103;0.103)	all_cancers(173;0.00175)|all_epithelial(177;0.162)|all_neural(198;0.164)|Melanoma(53;0.211)|Prostate(94;0.214)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			AGTGGTGGCGAGGTCACGTTC	0.527																																					p.S205P	NSCLC(166;160 2029 11600 18754 19936)	Atlas-SNP	.											.	ZP4	161	.	0			c.T613C						.						147	131	136					1																	238050802		2203	4300	6503	SO:0001583	missense	57829	exon5			GTGGCGAGGTCAC	U05781	CCDS1615.1	1q43	2013-01-17			ENSG00000116996	ENSG00000116996		"Zona pellucida glycoproteins"	15770	protein-coding gene	gene with protein product		613514				7841460	Standard	NM_021186		Approved	ZPB	uc001hym.3	Q12836	OTTHUMG00000039586	ENST00000366570.4:c.613T>C	chr1.hg19:g.238050802A>G	ENSP00000355529:p.Ser205Pro	187.0	0.0		305.0	44.0	NM_021186	B2RAE1	Missense_Mutation	SNP	ENST00000366570.4	hg19	CCDS1615.1	.	.	.	.	.	.	.	.	.	.	A	3.188	-0.166527	0.06461	.	.	ENSG00000116996	ENST00000366570	D	0.82984	-1.67	4.86	-0.897	0.10553	Zona pellucida sperm-binding protein (3);	0.914034	0.09291	N	0.822324	T	0.80675	0.4668	M	0.80028	2.48	0.09310	N	1	B	0.21753	0.06	B	0.32211	0.142	T	0.66520	-0.5903	10	0.30854	T	0.27	-2.2422	2.5405	0.04724	0.3095:0.0:0.3073:0.3832	.	205	Q12836	ZP4_HUMAN	P	205	ENSP00000355529:S205P	ENSP00000355529:S205P	S	-	1	0	ZP4	236117425	0.017000	0.18338	0.000000	0.03702	0.022000	0.10575	0.485000	0.22324	-0.019000	0.14055	-0.327000	0.08410	TCG	.	.		0.527	ZP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095476.1			G	238050802	A	G	238050802	3	3	371	1	0	0	0	0	1	0	0	0	18233	304	11	2	1041	2	ZP4	1	238050802	Missense_Mutation	SNP	A	TCGA-ZS-A9CE-01A-11D-A36X-10	30854733	238050802	11199819	14	51306										
RGS7	6000	hgsc.bcm.edu	37	chr1	241094018	241094018	+	Splice_Site	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	aatgagagatggcactgaccAtaatctgtgttttccggctc	10	9	1	3			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr1:241094018A>T	ENST00000407727.1	-	5	383	c.384T>A	c.(382-384)taT>taA	p.Y128*	RGS7_ENST00000366562.4_Splice_Site_p.Y128*|RGS7_ENST00000446183.2_Splice_Site_p.Y44*|RGS7_ENST00000401882.1_Intron|RGS7_ENST00000366563.1_Splice_Site_p.Y128*|RGS7_ENST00000331110.7_Splice_Site_p.Y102*|RGS7_ENST00000366565.1_Splice_Site_p.Y128*|RGS7_ENST00000348120.2_Intron|RGS7_ENST00000366564.1_Splice_Site_p.Y128*			P49802	RGS7_HUMAN	regulator of G-protein signaling 7	128					G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite terminus (GO:0044292)|heterotrimeric G-protein complex (GO:0005834)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta-subunit binding (GO:0031681)|GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(51)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			GGCACTGACCATAATCTGTGT	0.368																																					p.Y128X		Atlas-SNP	.											RGS7,NS,carcinoma,0,1	RGS7	308	.	0			c.T384A						.						133	148	143					1																	241094018		2203	4300	6503	SO:0001630	splice_region_variant	6000	exon6			CTGACCATAATCT	BC022009	CCDS31071.1, CCDS60457.1, CCDS60458.1, CCDS60459.1	1q43	2008-02-05	2007-08-14		ENSG00000182901	ENSG00000182901		"Regulators of G-protein signaling"	10003	protein-coding gene	gene with protein product		602517	"regulator of G-protein signalling 7"			8548815	Standard	XM_005273218		Approved		uc001hyv.2	P49802	OTTHUMG00000040107	ENST00000407727.1:c.385+1T>A	chr1.hg19:g.241094018A>T		274.0	0.0		451.0	131.0	NM_002924	Q5T3H4|Q8TD66|Q8TD67|Q8WW09|Q9UNU7|Q9Y6B9	Nonsense_Mutation	SNP	ENST00000407727.1	hg19		.	.	.	.	.	.	.	.	.	.	A	39	7.875008	0.98537	.	.	ENSG00000182901	ENST00000331110;ENST00000366565;ENST00000366564;ENST00000366563;ENST00000446183;ENST00000366562;ENST00000407727	.	.	.	5.83	-3.09	0.05331	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-24.5967	11.3762	0.49730	0.5851:0.0:0.4149:0.0	.	.	.	.	X	102;128;128;128;44;128;128	.	ENSP00000331485:Y102X	Y	-	3	2	RGS7	239160641	1.000000	0.71417	0.989000	0.46669	0.892000	0.51952	0.940000	0.28992	-0.509000	0.06532	-0.256000	0.11100	TAT	.	.		0.368	RGS7-204	KNOWN	basic	protein_coding	protein_coding		NM_002924	Nonsense_Mutation	T	241094018	A	T	241094018	5	4	371	1	0	0	0	0	0	0	1	0	13325	231	8	4	1131	4	RGS7	1	241094018	Splice_Site	SNP	A	TCGA-ZS-A9CE-01A-11D-A36X-10	3043216	241094018	8156603	15	51307										
OR2L3	391192	hgsc.bcm.edu	37	chr1	248224067	248224067	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	attggccttttcctcttcatCctcattgttttcattttcct	3	12	4	0			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr1:248224067C>T	ENST00000359959.3	+	1	84	c.84C>T	c.(82-84)atC>atT	p.I28I	OR2L13_ENST00000366478.2_Intron	NM_001004687.1	NP_001004687.1	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L, member 3	28						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|large_intestine(7)|lung(28)|prostate(1)|skin(1)|urinary_tract(1)	41	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)			TCCTCTTCATCCTCATTGTTT	0.398																																					p.I28I		Atlas-SNP	.											.	OR2L3	97	.	0			c.C84T						.						238	236	237					1																	248224067		2203	4300	6503	SO:0001819	synonymous_variant	391192	exon1			CTTCATCCTCATT	AB065950	CCDS31104.1	1q44	2012-08-09			ENSG00000198128	ENSG00000198128		"GPCR / Class A : Olfactory receptors"	15009	protein-coding gene	gene with protein product							Standard	NM_001004687		Approved		uc001idx.1	Q8NG85	OTTHUMG00000040195	ENST00000359959.3:c.84C>T	chr1.hg19:g.248224067C>T		112.0	0.0		237.0	72.0	NM_001004687	B9EH44	Silent	SNP	ENST00000359959.3	hg19	CCDS31104.1																																																																																			.	.		0.398	OR2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096852.1	NM_001004687		T	248224067	C	T	248224067	2	4	371	1	0	0	0	0	0	0	0	1	11017	845	30	3		3	OR2L3	1	248224067	Silent	SNP	C	TCGA-ZS-A9CE-01A-11D-A36X-10	7130049	248224067	1026554	16	51308										
OR2T2	401992	hgsc.bcm.edu	37	chr1	248616329	248616329	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	gataccatctacatctgtatCactgtccccaagatgctcca	5	14	3	1			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr1:248616329C>T	ENST00000342927.3	+	1	253	c.231C>T	c.(229-231)atC>atT	p.I77I		NM_001004136.1	NP_001004136.1	Q6IF00	OR2T2_HUMAN	olfactory receptor, family 2, subfamily T, member 2	77						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(21)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	37	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			ACATCTGTATCACTGTCCCCA	0.522																																					p.I77I		Atlas-SNP	.											.	OR2T2	73	.	0			c.C231T						.						130	147	141					1																	248616329		2203	4297	6500	SO:0001819	synonymous_variant	401992	exon1			CTGTATCACTGTC	BK004462	CCDS31116.1	1q44	2012-08-09	2002-11-13	2002-11-15	ENSG00000196240	ENSG00000196240		"GPCR / Class A : Olfactory receptors"	14725	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily T, member 2 pseudogene"	OR2T2P		14983052	Standard	NM_001004136		Approved		uc001iek.1	Q6IF00	OTTHUMG00000040480	ENST00000342927.3:c.231C>T	chr1.hg19:g.248616329C>T		873.0	0.0		1360.0	94.0	NM_001004136	B2RNM1|B9EH01	Silent	SNP	ENST00000342927.3	hg19	CCDS31116.1																																																																																			.	.		0.522	OR2T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097421.1	NM_001004136		T	248616329	C	T	248616329	2	4	371	1	0	0	0	0	0	0	0	1	11029	816	29	3		3	OR2T2	1	248616329	Silent	SNP	C	TCGA-ZS-A9CE-01A-11D-A36X-10	392262	248616329	634292	17	51309										
NBAS	51594	hgsc.bcm.edu	37	chr2	15427254	15427254	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	aaacttcccagcgggagacaCtgtaacgttgtgccagagaa	11	10	0	2			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr2:15427254C>T	ENST00000281513.5	-	42	5106	c.5081G>A	c.(5080-5082)aGt>aAt	p.S1694N	NBAS_ENST00000441750.1_Missense_Mutation_p.S1574N	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	1694					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				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						GCGGGAGACACTGTAACGTTG	0.463																																					p.S1694N		Atlas-SNP	.											.	NBAS	246	.	0			c.G5081A						.						139	134	135					2																	15427254		2203	4300	6503	SO:0001583	missense	51594	exon42			GAGACACTGTAAC	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.5081G>A	chr2.hg19:g.15427254C>T	ENSP00000281513:p.Ser1694Asn	113.0	0.0		149.0	75.0	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	hg19	CCDS1685.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.350|0.350	-0.945593|-0.945593	0.02304|0.02304	.|.	.|.	ENSG00000151779|ENSG00000151779	ENST00000441750;ENST00000281513|ENST00000442506	T;T|.	0.10192|.	2.9;3.08|.	5.55|5.55	-0.432|-0.432	0.12291|0.12291	.|.	0.502900|.	0.27996|.	N|.	0.017010|.	T|T	0.44286|0.44286	0.1286|0.1286	M|M	0.65975|0.65975	2.015|2.015	0.09310|0.09310	N|N	0.999994|0.999994	B;B|.	0.21753|.	0.06;0.001|.	B;B|.	0.22386|.	0.039;0.002|.	T|T	0.40327|0.40327	-0.9569|-0.9569	10|5	0.87932|.	D|.	0|.	.|.	7.1774|7.1774	0.25753|0.25753	0.0:0.4423:0.1133:0.4444|0.0:0.4423:0.1133:0.4444	.|.	1574;1694|.	A2RRP1-2;A2RRP1|.	.;NBAS_HUMAN|.	N|M	1574;1694|742	ENSP00000413201:S1574N;ENSP00000281513:S1694N|.	ENSP00000281513:S1694N|.	S|V	-|-	2|1	0|0	NBAS|NBAS	15344705|15344705	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.488000|0.488000	0.33401|0.33401	-0.084000|-0.084000	0.11268|0.11268	-0.034000|-0.034000	0.13713|0.13713	-0.137000|-0.137000	0.14449|0.14449	AGT|GTG	.	.		0.463	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		T	15427254	C	T	15427254	3	4	371	1	0	0	0	0	1	0	0	0	10195	565	20	3	2078	3	NBAS	2	15427254	Missense_Mutation	SNP	C	TCGA-ZS-A9CE-01A-11D-A36X-10		15427254	227772119	18	51310										
PLB1	151056	hgsc.bcm.edu	37	chr2	28761188	28761188	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	acggttctcctctcacagaaTgggcttgcggcgggcggcgt	15	12	2	1			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr2:28761188T>C	ENST00000327757.5	+	10	602	c.558T>C	c.(556-558)aaT>aaC	p.N186N	PLB1_ENST00000422425.2_Silent_p.N197N	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	186	4 X 308-326 AA approximate repeats.				glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(31)|ovary(6)|prostate(1)|skin(7)|stomach(2)	69	Acute lymphoblastic leukemia(172;0.155)					TCTCACAGAATGGGCTTGCGG	0.657																																					p.N197N		Atlas-SNP	.											.	PLB1	255	.	0			c.T591C						.						49	46	47					2																	28761188		2203	4300	6503	SO:0001819	synonymous_variant	151056	exon10			ACAGAATGGGCTT		CCDS33168.1, CCDS54340.1	2p23.3	2014-03-14			ENSG00000163803	ENSG00000163803	3.1.1.4, 3.1.1.5		30041	protein-coding gene	gene with protein product		610179				12150957	Standard	NM_153021		Approved	PLB, FLJ30866	uc002rmb.2	Q6P1J6	OTTHUMG00000152014	ENST00000327757.5:c.558T>C	chr2.hg19:g.28761188T>C		41.0	0.0		46.0	18.0	NM_001170585	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Silent	SNP	ENST00000327757.5	hg19	CCDS33168.1	.	.	.	.	.	.	.	.	.	.	T	0.598	-0.830236	0.02734	.	.	ENSG00000163803	ENST00000404858	.	.	.	5.0	-9.99	0.00435	.	.	.	.	.	T	0.16041	0.0386	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.08371	-1.0725	4	.	.	.	3.165	3.4752	0.07582	0.12:0.4363:0.2466:0.1971	.	.	.	.	T	196	.	.	M	+	2	0	PLB1	28614692	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-2.415000	0.01036	-3.088000	0.00248	-3.471000	0.00035	ATG	.	.		0.657	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2			C	28761188	T	C	28761188	2	2	371	1	0	0	0	0	0	0	0	1	12033	1461	51	2		2	PLB1	2	28761188	Silent	SNP	T	TCGA-ZS-A9CE-01A-11D-A36X-10	13333934	28761188	214438185	19	51311										
PLEKHH2	130271	hgsc.bcm.edu	37	chr2	43927267	43927267	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	gatgaactgaataaaaaattTcaatcccagagactcgatta	6	7	1	3			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr2:43927267T>C	ENST00000282406.4	+	8	1280	c.1170T>C	c.(1168-1170)ttT>ttC	p.F390F		NM_172069.3	NP_742066.2	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	390					negative regulation of actin filament depolymerization (GO:0030835)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	actin binding (GO:0003779)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(24)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	56		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				ATAAAAAATTTCAATCCCAGA	0.403																																					p.F390F		Atlas-SNP	.											PLEKHH2,NS,carcinoma,0,1	PLEKHH2	156	.	0			c.T1170C						.						55	55	55					2																	43927267		2203	4300	6503	SO:0001819	synonymous_variant	130271	exon8			AAAATTTCAATCC	AB095948	CCDS1812.1	2p22	2013-01-10			ENSG00000152527	ENSG00000152527		"Pleckstrin homology (PH) domain containing"	30506	protein-coding gene	gene with protein product		612723					Standard	NM_172069		Approved	KIAA2028, PLEKHH1L	uc010yny.2	Q8IVE3	OTTHUMG00000128657	ENST00000282406.4:c.1170T>C	chr2.hg19:g.43927267T>C		136.0	0.0		176.0	78.0	NM_172069	Q5JPJ6|Q6P4Q1|Q8N3Q3	Silent	SNP	ENST00000282406.4	hg19	CCDS1812.1																																																																																			.	.		0.403	PLEKHH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250537.1	NM_172069		C	43927267	T	C	43927267	2	2	371	1	0	0	0	0	0	0	0	1	12086	1780	62	2		2	PLEKHH2	2	43927267	Silent	SNP	T	TCGA-ZS-A9CE-01A-11D-A36X-10	15166079	43927267	199272106	20	51312										
PLEK	5341	hgsc.bcm.edu	37	chr2	68622843	68622843	+	Silent	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	gaggaagagaacctttttgaGatcatcacagcagatgaagt	11	6	2	4			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr2:68622843G>A	ENST00000234313.7	+	9	1127	c.948G>A	c.(946-948)gaG>gaA	p.E316E		NM_002664.2	NP_002655.2	P08567	PLEK_HUMAN	pleckstrin	316	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton reorganization (GO:0031532)|blood coagulation (GO:0007596)|cell projection organization (GO:0030030)|cortical actin cytoskeleton organization (GO:0030866)|hematopoietic progenitor cell differentiation (GO:0002244)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of calcium-mediated signaling (GO:0050849)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of inositol phosphate biosynthetic process (GO:0010920)|phosphatidylinositol metabolic process (GO:0046488)|phospholipase C-inhibiting G-protein coupled receptor signaling pathway (GO:0030845)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of inositol-polyphosphate 5-phosphatase activity (GO:0010925)|positive regulation of integrin activation (GO:0033625)|positive regulation of platelet activation (GO:0010572)|protein kinase C signaling (GO:0070528)|protein secretion by platelet (GO:0070560)|regulation of cell diameter (GO:0060305)|ruffle organization (GO:0031529)|thrombin receptor signaling pathway (GO:0070493)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|membrane (GO:0016020)|ruffle membrane (GO:0032587)	phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)			autonomic_ganglia(1)|endometrium(3)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	24		Ovarian(717;0.0129)		STAD - Stomach adenocarcinoma(1183;0.00159)|READ - Rectum adenocarcinoma(193;0.0419)		ACCTTTTTGAGATCATCACAG	0.542																																					p.E316E		Atlas-SNP	.											.	PLEK	64	.	0			c.G948A						.						156	140	145					2																	68622843		2203	4300	6503	SO:0001819	synonymous_variant	5341	exon9			TTTTGAGATCATC	X07743	CCDS1887.1	2p13.3	2013-01-10			ENSG00000115956	ENSG00000115956		"Pleckstrin homology (PH) domain containing"	9070	protein-coding gene	gene with protein product		173570				2897630, 12054651	Standard	NM_002664		Approved	P47	uc002sen.4	P08567	OTTHUMG00000129562	ENST00000234313.7:c.948G>A	chr2.hg19:g.68622843G>A		172.0	0.0		242.0	50.0	NM_002664	B2R9E8|Q53SU8|Q6FGM8|Q6FGQ1|Q8WV81	Silent	SNP	ENST00000234313.7	hg19	CCDS1887.1																																																																																			.	.		0.542	PLEK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251755.1	NM_002664		A	68622843	G	A	68622843	2	1	371	1	0	0	0	0	0	0	0	1	12062	933	33	3		3	PLEK	2	68622843	Silent	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10	24695576	68622843	174576530	21	51313										
ATP6V1B1	525	hgsc.bcm.edu	37	chr2	71190004	71190004	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	tggtcatactgacggacatgAgttcctatgcagaggccttg	12	9	1	3			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr2:71190004A>C	ENST00000234396.4	+	9	956	c.883A>C	c.(883-885)Agt>Cgt	p.S295R	ATP6V1B1_ENST00000412314.1_Missense_Mutation_p.S295R|RN7SL160P_ENST00000468558.2_RNA|AC007040.11_ENST00000606025.1_Intron	NM_001692.3	NP_001683.2	P15313	VATB1_HUMAN	ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B1	295					ATP hydrolysis coupled proton transport (GO:0015991)|ATP metabolic process (GO:0046034)|calcium ion homeostasis (GO:0055074)|cellular iron ion homeostasis (GO:0006879)|excretion (GO:0007588)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|ossification (GO:0001503)|pH reduction (GO:0045851)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|regulation of pH (GO:0006885)|sensory perception of sound (GO:0007605)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lateral plasma membrane (GO:0016328)|microvillus (GO:0005902)|proton-transporting V-type ATPase, V1 domain (GO:0033180)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	ATP binding (GO:0005524)|hydrogen ion transmembrane transporter activity (GO:0015078)|hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances (GO:0016820)			endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|prostate(1)|skin(1)	19						GACGGACATGAGTTCCTATGC	0.592																																					p.S295R		Atlas-SNP	.											.	ATP6V1B1	66	.	0			c.A883C						.						135	120	125					2																	71190004		2203	4300	6503	SO:0001583	missense	525	exon9			GACATGAGTTCCT	AF107466	CCDS1912.1	2p13	2010-04-21	2008-07-31	2002-05-10	ENSG00000116039	ENSG00000116039	3.6.3.14	"ATPases / V-type"	853	protein-coding gene	gene with protein product	"Renal tubular acidosis with deafness"	192132	"vacuolar proton pump 3"	VPP3, ATP6B1		9916796, 2527371	Standard	XM_005264368		Approved	VATB, RTA1B, Vma2	uc002shj.3	P15313	OTTHUMG00000129711	ENST00000234396.4:c.883A>C	chr2.hg19:g.71190004A>C	ENSP00000234396:p.Ser295Arg	45.0	0.0		63.0	28.0	NM_001692	Q53FY0|Q6P4H6	Missense_Mutation	SNP	ENST00000234396.4	hg19	CCDS1912.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.538771	0.85917	.	.	ENSG00000116039	ENST00000234396;ENST00000483246;ENST00000412314	D;D	0.82803	-1.65;-1.65	5.41	5.41	0.78517	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.92938	0.7753	H	0.94964	3.605	0.80722	D	1	P;D;D	0.64830	0.89;0.994;0.99	D;D;D	0.69654	0.948;0.965;0.936	D	0.94567	0.7767	10	0.87932	D	0	-9.6708	13.3939	0.60838	1.0:0.0:0.0:0.0	.	270;295;295	B4DWH7;C9JL73;P15313	.;.;VATB1_HUMAN	R	295;270;295	ENSP00000234396:S295R;ENSP00000388353:S295R	ENSP00000234396:S295R	S	+	1	0	ATP6V1B1	71043512	1.000000	0.71417	0.998000	0.56505	0.937000	0.57800	9.332000	0.96446	2.066000	0.61787	0.528000	0.53228	AGT	.	.		0.592	ATP6V1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251920.2	NM_001692		C	71190004	A	C	71190004	3	2	371	1	0	0	0	0	1	0	0	0	1178	304	11	5	917	5	ATP6V1B1	2	71190004	Missense_Mutation	SNP	A	TCGA-ZS-A9CE-01A-11D-A36X-10	2567161	71190004	172009369	22	51314										
ACVR2A	92	hgsc.bcm.edu	37	chr2	148684705	148684706	+	In_Frame_Ins	INS	-	-	AGGTTA													0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	gggatcacgacgcagaagccINSaggttatcagctggatgtgt							TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr2:148684705_148684706insAGGTTA	ENST00000241416.7	+	11	2040_2041	c.1404_1405insAGGTTA	c.(1405-1407)agg>AGGTTAagg	p.469_469R>RLR	ACVR2A_ENST00000404590.1_In_Frame_Ins_p.469_469R>RLR|ACVR2A_ENST00000535787.1_In_Frame_Ins_p.361_361R>RLR|ACVR2A_ENST00000495775.1_3'UTR	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	469	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		ACGCAGAAGCCAGGTTATCAGC	0.421																																					p.A468delinsARL		Atlas-INDEL	.											.	ACVR2A	125	.	0			c.1404_1405insAGGTTA						.																																			SO:0001652	inframe_insertion	92	exon11			.		CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"activin A receptor, type II"	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.1405_1410dupAGGTTA	chr2.hg19:g.148684706_148684711dupAGGTTA	Exception_encountered	142.0	0.0		67.0	26.0	NM_001616	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	In_Frame_Ins	INS	ENST00000241416.7	hg19	CCDS33301.1																																																																																			.	.		0.421	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616		AGGTTA	148684706	-	AGGTTA	148684705	7	5	371	1	0	1	1	0	0	0	0	0	223	581	21	0	1446	0	ACVR2A	2	148684705	In_Frame_Ins	INS	-	TCGA-ZS-A9CE-01A-11D-A36X-10	77494701	148684705	94514668	23	51315										
TTN	7273	hgsc.bcm.edu	37	chr2	179422457	179422457	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	tctgccttgatgcggaattgGtattcttctcctgtggtcag	11	9	4	1			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr2:179422457G>T	ENST00000591111.1	-	278	82925	c.82701C>A	c.(82699-82701)taC>taA	p.Y27567*	TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Nonsense_Mutation_p.Y20335*|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Nonsense_Mutation_p.Y29208*|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Nonsense_Mutation_p.Y20268*|TTN_ENST00000460472.2_Nonsense_Mutation_p.Y20143*|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Nonsense_Mutation_p.Y26640*|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	27567	Fibronectin type-III 100. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGCGGAATTGGTATTCTTCTC	0.413																																					p.Y29208X		Atlas-SNP	.											.	TTN	18412	.	0			c.C87624A						.						340	335	336					2																	179422457		1956	4143	6099	SO:0001587	stop_gained	7273	exon328			GAATTGGTATTCT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.82701C>A	chr2.hg19:g.179422457G>T	ENSP00000465570:p.Tyr27567*	116.0	0.0		67.0	49.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Nonsense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	66	91.457916	0.99996	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	.	.	.	5.96	0.939	0.19506	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	6.4651	0.21977	0.3623:0.0:0.5216:0.1161	.	.	.	.	X	26640;20143;20335;20268;20140	.	ENSP00000340554:Y20335X	Y	-	3	2	TTN	179130703	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	0.847000	0.27696	0.430000	0.26230	0.655000	0.94253	TAC	.	.		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179422457	G	T	179422457	4	4	371	1	0	0	0	0	0	1	0	0	16750	1256	44	3	20495	3	TTN	2	179422457	Nonsense_Mutation	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10	30737752	179422457	63776916	24	51316										
EPHA4	2043	hgsc.bcm.edu	37	chr2	222321452	222321452	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	ctttgatatctgtgttcctgGcagctgtccgaactatacga	9	10	1	1			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr2:222321452G>T	ENST00000281821.2	-	7	1525	c.1484C>A	c.(1483-1485)gCc>gAc	p.A495D	EPHA4_ENST00000409938.1_Missense_Mutation_p.A495D|EPHA4_ENST00000409854.1_Missense_Mutation_p.A495D|EPHA4_ENST00000392071.4_Missense_Mutation_p.A444D	NM_004438.3	NP_004429.1	P54764	EPHA4_HUMAN	EPH receptor A4	495	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult walking behavior (GO:0007628)|cell adhesion (GO:0007155)|corticospinal tract morphogenesis (GO:0021957)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|glial cell migration (GO:0008347)|motor neuron axon guidance (GO:0008045)|negative regulation of axon regeneration (GO:0048681)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001108)|protein autophosphorylation (GO:0046777)|regulation of astrocyte differentiation (GO:0048710)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rap GTPase activity (GO:0032317)	axon (GO:0030424)|axon terminus (GO:0043679)|axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|DH domain binding (GO:0097161)|GPI-linked ephrin receptor activity (GO:0005004)|PH domain binding (GO:0042731)|protein kinase activity (GO:0004672)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		TGTGTTCCTGGCAGCTGTCCG	0.478																																					p.A495D		Atlas-SNP	.											.	EPHA4	263	.	0			c.C1484A						.						139	122	128					2																	222321452		2203	4300	6503	SO:0001583	missense	2043	exon7			TTCCTGGCAGCTG	L36645	CCDS2447.1	2q36.3	2013-02-11	2004-10-28		ENSG00000116106	ENSG00000116106	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3388	protein-coding gene	gene with protein product		602188	"EphA4"	TYRO1		9267020	Standard	NM_004438		Approved	Hek8	uc002vmq.3	P54764	OTTHUMG00000133142	ENST00000281821.2:c.1484C>A	chr2.hg19:g.222321452G>T	ENSP00000281821:p.Ala495Asp	106.0	0.0		134.0	51.0	NM_004438	A8K2P1|B2R601|B7Z6Q8|Q2M380	Missense_Mutation	SNP	ENST00000281821.2	hg19	CCDS2447.1	.	.	.	.	.	.	.	.	.	.	G	14.01	2.408452	0.42715	.	.	ENSG00000116106	ENST00000281821;ENST00000409854;ENST00000409938;ENST00000392071	T;T;T;T	0.56444	0.46;0.46;0.46;0.46	5.91	5.02	0.67125	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.161120	0.56097	D	0.000023	T	0.39627	0.1085	N	0.10837	0.055	0.44611	D	0.997587	B	0.25235	0.121	B	0.30943	0.122	T	0.30679	-0.9970	10	0.52906	T	0.07	.	17.1291	0.86722	0.0:0.1265:0.8735:0.0	.	495	P54764	EPHA4_HUMAN	D	495;495;495;444	ENSP00000281821:A495D;ENSP00000386276:A495D;ENSP00000386829:A495D;ENSP00000375923:A444D	ENSP00000281821:A495D	A	-	2	0	EPHA4	222029696	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.429000	0.73387	1.481000	0.48307	-0.176000	0.13171	GCC	.	.		0.478	EPHA4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256836.3			T	222321452	G	T	222321452	3	4	371	1	0	0	0	0	1	0	0	0	5171	1203	42	3	1520	3	EPHA4	2	222321452	Missense_Mutation	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10	42898995	222321452	20877921	25	51317										
SNED1	25992	hgsc.bcm.edu	37	chr2	242007187	242007187	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	cattccccctaggaccccgcCctgtggaaggcttcgaggtc	11	16	0	0			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr2:242007187C>T	ENST00000310397.8	+	22	3019	c.3019C>T	c.(3019-3021)Cct>Tct	p.P1007S	SNED1_ENST00000401884.1_Missense_Mutation_p.P1007S|SNED1_ENST00000405547.3_Missense_Mutation_p.P1007S|SNED1_ENST00000342631.6_Missense_Mutation_p.P1007S	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	1007	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	24		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		AGGACCCCGCCCTGTGGAAGG	0.642																																					p.P1007S		Atlas-SNP	.											.	SNED1	76	.	0			c.C3019T						.						39	44	43					2																	242007187		2021	4154	6175	SO:0001583	missense	25992	exon22			CCCCGCCCTGTGG	AK074062	CCDS46562.1	2q37.3	2014-01-28			ENSG00000162804	ENSG00000162804		"Fibronectin type III domain containing"	24696	protein-coding gene	gene with protein product						12477932	Standard	NM_001080437		Approved	FLJ00133, SST3, Snep	uc002wah.1	Q8TER0	OTTHUMG00000151803	ENST00000310397.8:c.3019C>T	chr2.hg19:g.242007187C>T	ENSP00000308893:p.Pro1007Ser	107.0	0.0		143.0	30.0	NM_001080437	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Missense_Mutation	SNP	ENST00000310397.8	hg19	CCDS46562.1	.	.	.	.	.	.	.	.	.	.	C	18.78	3.697501	0.68386	.	.	ENSG00000162804	ENST00000401884;ENST00000405547;ENST00000310397;ENST00000342631	T;T;T;T	0.58652	0.32;0.32;0.32;0.32	4.92	4.92	0.64577	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.52532	D	0.000076	T	0.64735	0.2625	L	0.34521	1.04	0.41155	D	0.986051	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.977;0.999;0.986	T	0.59279	-0.7484	10	0.16896	T	0.51	.	16.2939	0.82762	0.0:1.0:0.0:0.0	.	1007;1007;1007	Q8TER0-5;B5MEF5;Q8TER0	.;.;SNED1_HUMAN	S	1007	ENSP00000384871:P1007S;ENSP00000386007:P1007S;ENSP00000308893:P1007S;ENSP00000342992:P1007S	ENSP00000308893:P1007S	P	+	1	0	SNED1	241655860	0.996000	0.38824	0.994000	0.49952	0.445000	0.32107	3.953000	0.56699	2.275000	0.75901	0.491000	0.48974	CCT	.	.		0.642	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482		T	242007187	C	T	242007187	3	4	371	1	0	0	0	0	1	0	0	0	14860	623	22	3	3105	3	SNED1	2	242007187	Missense_Mutation	SNP	C	TCGA-ZS-A9CE-01A-11D-A36X-10	19685735	242007187	1192186	26	51318										
SEMA3F	6405	hgsc.bcm.edu	37	chr3	50197097	50197097	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	ctctgggcttccctactgacCggggcctggccatccttccc	10	18	1	1	rs1046953	byFrequency	TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr3:50197097C>A	ENST00000002829.3	+	2	526	c.42C>A	c.(40-42)acC>acA	p.T14T	SEMA3F_ENST00000413852.1_Intron|SEMA3F_ENST00000434342.1_Silent_p.T14T	NM_004186.3	NP_004177.3	Q13275	SEM3F_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F	14					axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|negative regulation of axon extension involved in axon guidance (GO:0048843)|nerve development (GO:0021675)|neural crest cell migration (GO:0001755)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sympathetic ganglion development (GO:0061549)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	extracellular space (GO:0005615)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|receptor activity (GO:0004872)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(2)	17				BRCA - Breast invasive adenocarcinoma(193;0.00013)|KIRC - Kidney renal clear cell carcinoma(197;0.00599)|Kidney(197;0.00688)		CCCTACTGACCGGGGCCTGGC	0.617																																					p.T14T		Atlas-SNP	.											.	SEMA3F	62	.	0			c.C42A						.						60	57	58					3																	50197097		2203	4300	6503	SO:0001819	synonymous_variant	6405	exon2			ACTGACCGGGGCC	U33920	CCDS2811.1	3p21.3	2013-01-11			ENSG00000001617	ENSG00000001617		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10728	protein-coding gene	gene with protein product	"sema IV"	601124				8786119, 8649831	Standard	NM_004186		Approved	SEMAK, Sema4	uc003cyj.3	Q13275	OTTHUMG00000156806	ENST00000002829.3:c.42C>A	chr3.hg19:g.50197097C>A		48.0	0.0		37.0	18.0	NM_004186	C9JQ85|Q13274|Q13372|Q15704|Q6GTR4	Silent	SNP	ENST00000002829.3	hg19	CCDS2811.1																																																																																			.	C|0.626;T|0.374		0.617	SEMA3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345929.1	NM_004186		A	50197097	C	A	50197097	2	1	371	1	0	0	0	0	0	0	0	1	14044	639	23	1		1	SEMA3F	3	50197097	Silent	SNP	C	TCGA-ZS-A9CE-01A-11D-A36X-10		50197097	147825333	27	51319										
SFMBT1	51460	hgsc.bcm.edu	37	chr3	52966136	52966137	+	Frame_Shift_Ins	INS	-	-	G													0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	aaccaacgtgatgaagaaatINSggatccaagtaatacaacca							TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr3:52966136_52966137insG	ENST00000394752.3	-	6	1023_1024	c.641_642insC	c.(640-642)ccafs	p.P214fs	SFMBT1_ENST00000394750.1_Frame_Shift_Ins_p.P214fs|SFMBT1_ENST00000358080.2_Frame_Shift_Ins_p.P214fs|SFMBT1_ENST00000296295.6_Frame_Shift_Ins_p.P214fs	NM_016329.3	NP_057413.2	Q9UHJ3	SMBT1_HUMAN	Scm-like with four mbt domains 1	214					cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|negative regulation of muscle organ development (GO:0048635)|negative regulation of transcription, DNA-templated (GO:0045892)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|transcription corepressor activity (GO:0003714)			breast(2)|endometrium(3)|kidney(3)|large_intestine(8)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	24				BRCA - Breast invasive adenocarcinoma(193;9.91e-05)|Kidney(197;0.000644)|KIRC - Kidney renal clear cell carcinoma(197;0.000792)|OV - Ovarian serous cystadenocarcinoma(275;0.113)		GATGAAGAAATGGATCCAAGTA	0.401																																					p.P214fs		Atlas-INDEL	.											.	SFMBT1	53	.	0			c.642_643insC						.																																			SO:0001589	frameshift_variant	51460	exon6			.	AF168132	CCDS2867.1	3p21.31	2013-01-10			ENSG00000163935	ENSG00000163935		"Sterile alpha motif (SAM) domain containing"	20255	protein-coding gene	gene with protein product		607319				10661410	Standard	NM_016329		Approved	RU1, DKFZp434L243, SFMBT	uc003dgh.3	Q9UHJ3	OTTHUMG00000159052	ENST00000394752.3:c.642dupC	chr3.hg19:g.52966138_52966138dupG	ENSP00000378235:p.Pro214fs	82.0	0.0		84.0	39.0	NM_016329	Q402F7|Q96C73|Q9Y4Q9	Frame_Shift_Ins	INS	ENST00000394752.3	hg19	CCDS2867.1																																																																																			.	.		0.401	SFMBT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353040.3	NM_016329		G	52966137	-	G	52966136	7	5	371	1	0	1	1	0	0	0	0	0	14172	1451	51	0	2022	0	SFMBT1	3	52966136	Frame_Shift_Ins	INS	-	TCGA-ZS-A9CE-01A-11D-A36X-10	2769039	52966136	145056294	28	51320										
BBX	56987	hgsc.bcm.edu	37	chr3	107492029	107492029	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	tctgacattgagagcgtcatAtataccattgaagccgtcgc	9	10	2	3			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr3:107492029A>T	ENST00000325805.8	+	11	1748	c.1461A>T	c.(1459-1461)atA>atT	p.I487I	BBX_ENST00000402543.1_Silent_p.I487I|BBX_ENST00000416476.2_Intron|BBX_ENST00000415149.2_Silent_p.I487I|BBX_ENST00000406780.1_Silent_p.I487I			Q8WY36	BBX_HUMAN	bobby sox homolog (Drosophila)	487	Lys-rich.				bone development (GO:0060348)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(18)|ovary(4)|pancreas(1)|skin(2)	49			OV - Ovarian serous cystadenocarcinoma(3;0.112)			AGAGCGTCATATATACCATTG	0.463																																					p.I487I		Atlas-SNP	.											.	BBX	156	.	0			c.A1461T						.						76	80	79					3																	107492029		2203	4300	6503	SO:0001819	synonymous_variant	56987	exon11			CGTCATATATACC	AF168718	CCDS2950.1, CCDS46881.1, CCDS63712.1	3q13.1	2008-07-18			ENSG00000114439	ENSG00000114439			14422	protein-coding gene	gene with protein product	"x 001 protein"					11680820	Standard	NM_001142568		Approved	MDS001, HSPC339, HBP2	uc010hpr.4	Q8WY36	OTTHUMG00000150360	ENST00000325805.8:c.1461A>T	chr3.hg19:g.107492029A>T		382.0	0.0		374.0	87.0	NM_001142568	A2RRM7|Q2TAJ1|Q7L3J8|Q7LBY8|Q8NDB0|Q8WY35|Q9H0J6	Silent	SNP	ENST00000325805.8	hg19	CCDS46881.1																																																																																			.	.		0.463	BBX-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317820.1	NM_020235		T	107492029	A	T	107492029	2	4	371	1	0	0	0	0	0	0	0	1	1343	439	16	4		4	BBX	3	107492029	Silent	SNP	A	TCGA-ZS-A9CE-01A-11D-A36X-10	54525893	107492029	90530401	29	51321										
MYH15	22989	hgsc.bcm.edu	37	chr3	108133217	108133217	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	gttcttcctcatactgctctCgtagaaggtcacagtcacgc	8	13	5	1			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr3:108133217C>T	ENST00000273353.3	-	31	4123	c.4067G>A	c.(4066-4068)cGa>cAa	p.R1356Q		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	1356						cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						ATACTGCTCTCGTAGAAGGTC	0.502																																					p.R1356Q		Atlas-SNP	.											.	MYH15	223	.	0			c.G4067A						.						116	109	111					3																	108133217		2048	4202	6250	SO:0001583	missense	22989	exon31			TGCTCTCGTAGAA	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"Myosins / Myosin superfamily : Class II"	31073	protein-coding gene	gene with protein product		609929	"myosin, heavy polypeptide 15"			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.4067G>A	chr3.hg19:g.108133217C>T	ENSP00000273353:p.Arg1356Gln	54.0	0.0		55.0	24.0	NM_014981		Missense_Mutation	SNP	ENST00000273353.3	hg19	CCDS43127.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.949644	0.73787	.	.	ENSG00000144821	ENST00000273353	D	0.82711	-1.64	5.58	-2.93	0.05598	Myosin tail (1);	.	.	.	.	T	0.78874	0.4352	M	0.64170	1.965	0.09310	N	1	P	0.41102	0.738	B	0.42282	0.382	T	0.70241	-0.4926	9	0.62326	D	0.03	.	7.3104	0.26471	0.1054:0.4429:0.0:0.4517	.	1356	Q9Y2K3	MYH15_HUMAN	Q	1356	ENSP00000273353:R1356Q	ENSP00000273353:R1356Q	R	-	2	0	MYH15	109615907	0.002000	0.14202	0.000000	0.03702	0.416000	0.31233	0.489000	0.22387	-0.398000	0.07679	0.655000	0.94253	CGA	.	.		0.502	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988		T	108133217	C	T	108133217	3	4	371	1	0	0	0	0	1	0	0	0	10043	884	31	1	1821	1	MYH15	3	108133217	Missense_Mutation	SNP	C	TCGA-ZS-A9CE-01A-11D-A36X-10	641188	108133217	89889213	30	51322										
HPS3	84343	hgsc.bcm.edu	37	chr3	148884845	148884845	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	ttatatgtggtccttcatttGacatagcttccattattccg	6	9	1	1			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr3:148884845G>C	ENST00000296051.2	+	15	2754	c.2614G>C	c.(2614-2616)Gac>Cac	p.D872H	HPS3_ENST00000460120.1_Missense_Mutation_p.D707H	NM_032383.3	NP_115759.2	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3	872					organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	34			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			TCCTTCATTTGACATAGCTTC	0.393									Hermansky-Pudlak syndrome																												p.D872H		Atlas-SNP	.											.	HPS3	104	.	0			c.G2614C						.						144	144	144					3																	148884845		2203	4300	6503	SO:0001583	missense	84343	exon15	Familial Cancer Database	HPS, HPS1-8	TCATTTGACATAG	AY033141	CCDS3140.1	3q24	2014-06-18			ENSG00000163755	ENSG00000163755			15597	protein-coding gene	gene with protein product		606118				11455388	Standard	NM_032383		Approved	SUTAL	uc003ewu.1	Q969F9	OTTHUMG00000159548	ENST00000296051.2:c.2614G>C	chr3.hg19:g.148884845G>C	ENSP00000296051:p.Asp872His	80.0	0.0		49.0	16.0	NM_032383	A8K6G6|Q8WTV6|Q96AP1|Q96MR3|Q9H608	Missense_Mutation	SNP	ENST00000296051.2	hg19	CCDS3140.1	.	.	.	.	.	.	.	.	.	.	G	17.98	3.520603	0.64747	.	.	ENSG00000163755	ENST00000296051;ENST00000460120	T;T	0.64991	-0.13;-0.13	5.82	5.82	0.92795	.	0.286046	0.44688	D	0.000428	T	0.72890	0.3517	L	0.53249	1.67	0.80722	D	1	D;D	0.71674	0.995;0.998	D;D	0.65773	0.938;0.922	T	0.74337	-0.3698	10	0.72032	D	0.01	-21.4224	12.8002	0.57582	0.1173:0.0:0.8827:0.0	.	707;872	G5E9V4;Q969F9	.;HPS3_HUMAN	H	872;707	ENSP00000296051:D872H;ENSP00000418230:D707H	ENSP00000296051:D872H	D	+	1	0	HPS3	150367535	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.076000	0.41548	2.762000	0.94881	0.650000	0.86243	GAC	.	.		0.393	HPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356151.1	NM_032383		C	148884845	G	C	148884845	3	2	371	1	0	0	0	0	1	0	0	0	7349	1290	45	4	2672	4	HPS3	3	148884845	Missense_Mutation	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10	40751628	148884845	49137585	31	51323										
KCNAB1	7881	hgsc.bcm.edu	37	chr3	156170702	156170702	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	ttctaggaacatgggtgacaTttggaggtcaaatttcagat	11	5	3	2			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr3:156170702T>C	ENST00000490337.1	+	3	398	c.334T>C	c.(334-336)Ttt>Ctt	p.F112L	KCNAB1_ENST00000389634.5_Missense_Mutation_p.F94L|KCNAB1_ENST00000389636.5_Missense_Mutation_p.F112L|KCNAB1_ENST00000302490.8_Missense_Mutation_p.F94L|KCNAB1_ENST00000471742.1_Missense_Mutation_p.F101L	NM_172160.2	NP_751892.1	Q14722	KCAB1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, beta member 1	112					learning or memory (GO:0007611)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	28			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			ATGGGTGACATTTGGAGGTCA	0.353																																					p.F112L		Atlas-SNP	.											.	KCNAB1	176	.	0			c.T334C						.						111	124	120					3																	156170702		2203	4300	6503	SO:0001583	missense	7881	exon3			GTGACATTTGGAG	U33428	CCDS3174.1, CCDS3175.1, CCDS33882.1	3q26.1	2006-11-29			ENSG00000169282	ENSG00000169282		"Potassium channels", "Aldo-keto reductases"	6228	protein-coding gene	gene with protein product		601141				8838324, 7499366	Standard	NM_172160		Approved	AKR6A3, KCNA1B, hKvBeta3, Kvb1.3, hKvb3	uc003far.2	Q14722	OTTHUMG00000158552	ENST00000490337.1:c.334T>C	chr3.hg19:g.156170702T>C	ENSP00000419952:p.Phe112Leu	117.0	0.0		102.0	59.0	NM_172160	A8K9H8|A8KAD4|B3KPZ4|Q13031|Q13302|Q16547|Q6PI60|Q99869	Missense_Mutation	SNP	ENST00000490337.1	hg19	CCDS3174.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.519012	0.85495	.	.	ENSG00000169282	ENST00000472028;ENST00000490337;ENST00000389636;ENST00000471742;ENST00000475456;ENST00000302490;ENST00000389634	T;T;T;T;T;T;T	0.24723	1.84;1.84;1.84;1.84;1.84;1.84;1.84	5.71	5.71	0.89125	NADP-dependent oxidoreductase domain (3);	0.000000	0.85682	D	0.000000	T	0.49592	0.1566	M	0.83384	2.64	0.80722	D	1	B;P;D;P;P	0.56968	0.402;0.859;0.978;0.755;0.794	P;P;P;P;P	0.60117	0.539;0.654;0.869;0.579;0.704	T	0.54820	-0.8236	10	0.59425	D	0.04	-15.6506	12.396	0.55384	0.0:0.0:0.0:1.0	.	112;94;94;101;112	B7Z8E5;F8W6W4;B3KPZ4;Q14722-3;Q14722	.;.;.;.;KCAB1_HUMAN	L	30;112;112;101;55;94;94	ENSP00000420755:F30L;ENSP00000419952:F112L;ENSP00000374287:F112L;ENSP00000418956:F101L;ENSP00000420221:F55L;ENSP00000305858:F94L;ENSP00000374285:F94L	ENSP00000305858:F94L	F	+	1	0	KCNAB1	157653396	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.161000	0.71868	2.171000	0.68590	0.528000	0.53228	TTT	.	.		0.353	KCNAB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351411.1	NM_003471		C	156170702	T	C	156170702	3	2	371	1	0	0	0	0	1	0	0	0	8018	1493	52	2	815	2	KCNAB1	3	156170702	Missense_Mutation	SNP	T	TCGA-ZS-A9CE-01A-11D-A36X-10	7285857	156170702	41851728	32	51324										
MECOM	2122	hgsc.bcm.edu	37	chr3	169099207	169099207	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	cttcactggatgtggcaggaGagcatggctcttgaatattg	13	7	2	2			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr3:169099207G>T	ENST00000494292.1	-	2	240	c.143C>A	c.(142-144)tCt>tAt	p.S48Y	MECOM_ENST00000485957.1_5'UTR	NM_004991.3	NP_004982.2	Q13465	MDS1_HUMAN	MDS1 and EVI1 complex locus	48					regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	85						TGTGGCAGGAGAGCATGGCTC	0.483																																					p.S48Y		Atlas-SNP	.											.	MECOM	216	.	0			c.C143A						.						75	77	76					3																	169099207		1926	4129	6055	SO:0001583	missense	2122	exon2			GCAGGAGAGCATG	S82592, AF164154	CCDS3205.1, CCDS54669.1, CCDS54670.1	3q26.2	2013-01-08	2009-08-07	2009-08-07	ENSG00000085276	ENSG00000085276		"Zinc fingers, C2H2-type"	3498	protein-coding gene	gene with protein product		165215	"myelodysplasia syndrome 1", "ecotropic viral integration site 1"	MDS1, EVI1		2115646, 8171026, 8643684	Standard	NM_001105077		Approved	MDS1-EVI1, PRDM3	uc011bpj.1	Q03112	OTTHUMG00000158596	ENST00000494292.1:c.143C>A	chr3.hg19:g.169099207G>T	ENSP00000417899:p.Ser48Tyr	76.0	0.0		88.0	47.0	NM_004991	Q13466|Q6FH90	Missense_Mutation	SNP	ENST00000494292.1	hg19		.	.	.	.	.	.	.	.	.	.	G	14.19	2.462122	0.43736	.	.	ENSG00000085276	ENST00000494292;ENST00000486748	T;T	0.57595	0.39;0.39	5.92	5.92	0.95590	.	0.000000	0.64402	D	0.000011	T	0.73024	0.3534	M	0.72894	2.215	0.80722	D	1	D;P	0.67145	0.996;0.642	D;B	0.66979	0.948;0.199	T	0.73968	-0.3815	10	0.87932	D	0	.	20.3343	0.98733	0.0:0.0:1.0:0.0	.	48;48	Q13465;Q03112-3	MDS1_HUMAN;.	Y	48;72	ENSP00000417899:S48Y;ENSP00000419537:S72Y	ENSP00000419537:S72Y	S	-	2	0	MECOM	170581901	1.000000	0.71417	1.000000	0.80357	0.004000	0.04260	8.072000	0.89496	2.822000	0.97130	0.650000	0.86243	TCT	.	.		0.483	MECOM-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000351517.3	NM_005241, NM_004991		T	169099207	G	T	169099207	3	4	371	1	0	0	0	0	1	0	0	0	9431	942	33	3	3650	3	MECOM	3	169099207	Missense_Mutation	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10	12928505	169099207	28923223	33	51325										
GPR160	26996	hgsc.bcm.edu	37	chr3	169802764	169802764	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	aattgaaaagcctatatcaaTaatgatttgttaatattatt	4	3	1	2			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr3:169802764T>C	ENST00000355897.5	+	4	1612	c.1004T>C	c.(1003-1005)aTa>aCa	p.I335T	RP11-379K17.12_ENST00000599781.1_RNA	NM_014373.2	NP_055188.1	Q9UJ42	GP160_HUMAN	G protein-coupled receptor 160	335						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			breast(1)|cervix(1)|kidney(1)|large_intestine(3)|lung(2)	8	all_cancers(22;3.26e-22)|all_epithelial(15;5.71e-27)|all_lung(20;8.41e-17)|Lung NSC(18;3.49e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)			CCTATATCAATAATGATTTGT	0.289																																					p.I335T		Atlas-SNP	.											.	GPR160	26	.	0			c.T1004C						.						30	31	31					3																	169802764		2099	4250	6349	SO:0001583	missense	26996	exon4			TATCAATAATGAT	AB083583	CCDS3211.1	3q26.2-q27	2012-08-21			ENSG00000173890	ENSG00000173890		"GPCR / Class A : Orphans"	23693	protein-coding gene	gene with protein product						12044878	Standard	NM_014373		Approved	GPCR150, GPCR1	uc003fgi.3	Q9UJ42	OTTHUMG00000158776	ENST00000355897.5:c.1004T>C	chr3.hg19:g.169802764T>C	ENSP00000348161:p.Ile335Thr	197.0	0.0		216.0	61.0	NM_014373	D3DNQ2	Missense_Mutation	SNP	ENST00000355897.5	hg19	CCDS3211.1	.	.	.	.	.	.	.	.	.	.	T	5.062	0.197098	0.09599	.	.	ENSG00000173890	ENST00000355897	.	.	.	5.74	4.58	0.56647	.	0.689522	0.14402	N	0.321859	T	0.26774	0.0655	N	0.19112	0.55	0.09310	N	0.999994	B	0.23185	0.081	B	0.18561	0.022	T	0.16070	-1.0415	9	0.42905	T	0.14	.	7.2209	0.25985	0.1303:0.0704:0.0:0.7994	.	335	Q9UJ42	GP160_HUMAN	T	335	.	ENSP00000348161:I335T	I	+	2	0	GPR160	171285458	0.998000	0.40836	0.057000	0.19452	0.019000	0.09904	2.684000	0.46951	1.014000	0.39417	0.533000	0.62120	ATA	.	.		0.289	GPR160-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352167.1	NM_014373		C	169802764	T	C	169802764	3	2	371	1	0	0	0	0	1	0	0	0	6672	1406	49	2	1006	2	GPR160	3	169802764	Missense_Mutation	SNP	T	TCGA-ZS-A9CE-01A-11D-A36X-10	703557	169802764	28219666	34	51326										
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178936092	178936092	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	tcctctctctgaaatcactgAgcaggagaaagattttctat	7	9	4	4	rs121913274		TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr3:178936092A>C	ENST00000263967.3	+	10	1791	c.1634A>C	c.(1633-1635)gAg>gCg	p.E545A		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	545	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		E -> A (in CWS5 and HCC; also found in a glioblastoma multiforme sample). {ECO:0000269|PubMed:15608678, ECO:0000269|PubMed:15924253, ECO:0000269|PubMed:23246288}.|E -> G (in KERSEB; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:17673550}.|E -> K (in MCAP, KERSEB, CRC and BC; shows an increase in lipid kinase activity; oncogenic in vivo; occurs in the interface between the PI3K helical domain and the nSH2 (N-terminal SH2) region of the p85 regulatory subunit and may reduce the inhibitory effect of p85; requires interaction with RAS to induce cellular transformation; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.E545A(96)|p.E545G(78)|p.E545V(4)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	GAAATCACTGAGCAGGAGAAA	0.353	E545A(AGS_STOMACH)|E545G(KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											p.E545A	Colon(199;1504 1750 3362 26421 31210 32040)	Atlas-SNP	.		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	PIK3CA_ENST00000263967,NS,carcinoma,+1,211	PIK3CA	8460	.	178	Substitution - Missense(178)	breast(40)|large_intestine(39)|ovary(30)|endometrium(17)|skin(9)|urinary_tract(8)|upper_aerodigestive_tract(4)|central_nervous_system(4)|oesophagus(4)|stomach(4)|liver(4)|thyroid(3)|soft_tissue(3)|haematopoietic_and_lymphoid_tissue(2)|lung(2)|NS(1)|eye(1)|pancreas(1)|prostate(1)|pituitary(1)	c.A1634C						.						61	61	61					3																	178936092		1813	4072	5885	SO:0001583	missense	5290	exon10			TCACTGAGCAGGA		CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1634A>C	chr3.hg19:g.178936092A>C	ENSP00000263967:p.Glu545Ala	462.0	0.0		416.0	208.0	NM_006218	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	hg19	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.555316	0.86231	.	.	ENSG00000121879	ENST00000263967	T	0.62105	0.05	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.71074	0.3297	L	0.43757	1.38	0.80722	D	1	D	0.67145	0.996	D	0.65140	0.932	T	0.69109	-0.5232	10	0.34782	T	0.22	-25.7963	16.1026	0.81194	1.0:0.0:0.0:0.0	.	545	P42336	PK3CA_HUMAN	A	545	ENSP00000263967:E545A	ENSP00000263967:E545A	E	+	2	0	PIK3CA	180418786	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	8.962000	0.93254	2.198000	0.70561	0.383000	0.25322	GAG	.	.		0.353	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			C	178936092	A	C	178936092	3	2	371	1	0	0	0	0	1	0	0	0	11922	304	11	5	1668	5	PIK3CA	3	178936092	Missense_Mutation	SNP	A	TCGA-ZS-A9CE-01A-11D-A36X-10	9133328	178936092	19086338	35	51327										
BOD1L	259282	hgsc.bcm.edu	37	chr4	13589344	13589344	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	tggttcatcttctgaagagaGataatgctgctttctttttc	8	7	4	3			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr4:13589344G>A	ENST00000040738.5	-	16	8467	c.8332C>T	c.(8332-8334)Ctc>Ttc	p.L2778F		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	2778						nucleus (GO:0005634)	DNA binding (GO:0003677)										TCTGAAGAGAGATAATGCTGC	0.303																																					p.L2778F		Atlas-SNP	.											.	.	.	.	0			c.C8332T						.						34	35	35					4																	13589344		2197	4288	6485	SO:0001583	missense	259282	exon16			AAGAGAGATAATG	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.8332C>T	chr4.hg19:g.13589344G>A	ENSP00000040738:p.Leu2778Phe	440.0	1.0		365.0	103.0	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	hg19	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	G	9.511	1.105790	0.20632	.	.	ENSG00000038219	ENST00000040738	T	0.07800	3.16	4.99	-0.115	0.13560	.	1.416370	0.04550	N	0.389728	T	0.05640	0.0148	N	0.24115	0.695	0.09310	N	1	P	0.34462	0.454	B	0.31614	0.133	T	0.33240	-0.9876	10	0.56958	D	0.05	1.5412	2.1752	0.03860	0.1739:0.28:0.4029:0.1432	.	2778	Q8NFC6	BOD1L_HUMAN	F	2778	ENSP00000040738:L2778F	ENSP00000040738:L2778F	L	-	1	0	BOD1L	13198442	0.330000	0.24705	0.007000	0.13788	0.962000	0.63368	0.870000	0.28010	-0.042000	0.13535	-0.165000	0.13383	CTC	.	.		0.303	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		A	13589344	G	A	13589344	3	1	371	1	0	0	0	0	1	0	0	0	1483	942	33	3	867	3	BOD1L	4	13589344	Missense_Mutation	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10		13589344	177564932	36	51328										
FBXW7	55294	hgsc.bcm.edu	37	chr4	153245454	153245454	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	ccacttgttaacgactggtgCcctgttaacgtgtgaatgca	10	10	0	1			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr4:153245454C>T	ENST00000281708.4	-	11	2966	c.1737G>A	c.(1735-1737)ggG>ggA	p.G579G	FBXW7_ENST00000263981.5_Silent_p.G499G|FBXW7_ENST00000296555.5_Silent_p.G461G|FBXW7_ENST00000603841.1_Silent_p.G579G|FBXW7_ENST00000393956.3_Silent_p.G403G|FBXW7_ENST00000603548.1_Silent_p.G579G	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	579					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.G579_Q581>E(1)|p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				ACGACTGGTGCCCTGTTAACG	0.413			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																p.G579G		Atlas-SNP	.		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	.	FBXW7	2157	.	2	Unknown(1)|Complex - deletion inframe(1)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	c.G1737A						.						150	124	133					4																	153245454		2203	4300	6503	SO:0001819	synonymous_variant	55294	exon11			CTGGTGCCCTGTT	AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1737G>A	chr4.hg19:g.153245454C>T		150.0	0.0		154.0	28.0	NM_033632	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Silent	SNP	ENST00000281708.4	hg19	CCDS3777.1																																																																																			.	.		0.413	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			T	153245454	C	T	153245454	2	4	371	1	0	0	0	0	0	0	0	1	5777	726	26	3		3	FBXW7	4	153245454	Silent	SNP	C	TCGA-ZS-A9CE-01A-11D-A36X-10	139656110	153245454	37908822	37	51329										
RXFP3	51289	hgsc.bcm.edu	37	chr5	33937613	33937613	+	Frame_Shift_Del	DEL	G	G	-													0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	cgtttcccggacaagttgctGggccgcgacaggcagttctg							TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr5:33937613delG	ENST00000330120.3	+	1	1123	c.768delG	c.(766-768)ctgfs	p.L256fs		NM_016568.3	NP_057652.1	Q9NSD7	RL3R1_HUMAN	relaxin/insulin-like family peptide receptor 3	256					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled peptide receptor activity (GO:0008528)|G-protein coupled receptor activity (GO:0004930)			endometrium(4)|large_intestine(9)|lung(24)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)	42						ACAAGTTGCTGGGCCGCGACA	0.632																																					p.L256fs		Atlas-INDEL	.											.	RXFP3	114	.	0			c.767delT						.						46	37	40					5																	33937613		2201	4299	6500	SO:0001589	frameshift_variant	51289	exon1			.	D88437	CCDS3900.1	5p15.1-p14	2012-08-08	2006-05-09	2006-03-15	ENSG00000182631	ENSG00000182631		"GPCR / Class A : Relaxin family peptide receptors"	24883	protein-coding gene	gene with protein product		609445	"relaxin 3 receptor 1", "relaxin family peptide receptor 3"	RLN3R1		15956688, 16507880	Standard	NM_016568		Approved	SALPR, GPCR135, RXFPR3	uc003jic.2	Q9NSD7	OTTHUMG00000090685	ENST00000330120.3:c.768delG	chr5.hg19:g.33937613delG	ENSP00000328708:p.Leu256fs	109.0	0.0		117.0	50.0	NM_016568	Q14DA5	Frame_Shift_Del	DEL	ENST00000330120.3	hg19	CCDS3900.1																																																																																			.	.		0.632	RXFP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207369.1	NM_016568		-	33937613	G	-	33937613	7	5	371	1	0	1	0	1	0	0	0	0	13776	1335	47	0	770	0	RXFP3	5	33937613	Frame_Shift_Del	DEL	G	TCGA-ZS-A9CE-01A-11D-A36X-10		33937613	146977647	38	51330										
GPR98	84059	hgsc.bcm.edu	37	chr5	90074291	90074291	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	aaaagcttctatgagtttcaGctcactgcagtcagtgaggg	11	8	4	2			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr5:90074291G>A	ENST00000405460.2	+	63	12810	c.12714G>A	c.(12712-12714)caG>caA	p.Q4238Q	GPR98_ENST00000425867.2_5'Flank	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	4238	Calx-beta 28. {ECO:0000305|PubMed:11606593}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		ATGAGTTTCAGCTCACTGCAG	0.463																																					p.Q4238Q		Atlas-SNP	.											.	GPR98	605	.	0			c.G12714A						.																																			SO:0001819	synonymous_variant	84059	exon63			GTTTCAGCTCACT	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.12714G>A	chr5.hg19:g.90074291G>A		126.0	0.0		168.0	86.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	hg19	CCDS47246.1																																																																																			.	.		0.463	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		A	90074291	G	A	90074291	2	1	371	1	0	0	0	0	0	0	0	1	6730	962	34	3		3	GPR98	5	90074291	Silent	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10	56136678	90074291	90840969	39	51331										
PAM	5066	hgsc.bcm.edu	37	chr5	102326066	102326066	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	tctagaccctaagaataaccTggtgattttccacagaggtg	9	9	1	4			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr5:102326066T>C	ENST00000438793.3	+	15	2044	c.1574T>C	c.(1573-1575)cTg>cCg	p.L525P	PAM_ENST00000304400.7_Missense_Mutation_p.L525P|PAM_ENST00000455264.2_Missense_Mutation_p.L525P|PAM_ENST00000274392.9_Missense_Mutation_p.L428P|PAM_ENST00000346918.2_Missense_Mutation_p.L525P|PAM_ENST00000379787.4_5'UTR|PAM_ENST00000348126.2_Missense_Mutation_p.L418P	NM_000919.3|NM_001177306.1|NM_138766.2	NP_000910.2|NP_001170777.1|NP_620121.1	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase	525	Peptidyl-alpha-hydroxyglycine alpha- amidating lyase. {ECO:0000250}.				central nervous system development (GO:0007417)|heart development (GO:0007507)|lactation (GO:0007595)|limb development (GO:0060173)|long-chain fatty acid metabolic process (GO:0001676)|maternal process involved in female pregnancy (GO:0060135)|odontogenesis (GO:0042476)|ovulation cycle process (GO:0022602)|peptide amidation (GO:0001519)|protein amidation (GO:0018032)|protein homooligomerization (GO:0051260)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of protein secretion (GO:0050708)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to pH (GO:0009268)|toxin metabolic process (GO:0009404)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)|trans-Golgi network (GO:0005802)	calcium ion binding (GO:0005509)|copper ion binding (GO:0005507)|L-ascorbic acid binding (GO:0031418)|peptidylamidoglycolate lyase activity (GO:0004598)|peptidylglycine monooxygenase activity (GO:0004504)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	25		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)	AAGAATAACCTGGTGATTTTC	0.383																																					p.L525P		Atlas-SNP	.											.	PAM	180	.	0			c.T1574C						.						59	58	58					5																	102326066		2203	4300	6503	SO:0001583	missense	5066	exon15			ATAACCTGGTGAT	AB095007	CCDS4092.1, CCDS4093.1, CCDS4094.1, CCDS43348.1, CCDS54885.1	5q	2008-02-05			ENSG00000145730	ENSG00000145730	1.14.17.3		8596	protein-coding gene	gene with protein product	"peptidyl-alpha-hydroxyglycine alpha-amidating lyase", "peptidylglycine alpha-hydroxylating monooxygenase"	170270				2357221	Standard	NM_000919		Approved	PAL, PHM	uc003knt.3	P19021	OTTHUMG00000128729	ENST00000438793.3:c.1574T>C	chr5.hg19:g.102326066T>C	ENSP00000396493:p.Leu525Pro	127.0	0.0		188.0	91.0	NM_138822	A6NMR0|A8K293|O43211|O95080|Q16252|Q16253|Q54A45|Q86U53|Q8WVC7|Q9UCG0	Missense_Mutation	SNP	ENST00000438793.3	hg19	CCDS54885.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.189769	0.78789	.	.	ENSG00000145730	ENST00000438793;ENST00000346918;ENST00000348126;ENST00000304400;ENST00000274392;ENST00000455264	D;D;D;D;D;D	0.93019	-3.15;-3.15;-3.15;-3.15;-3.15;-3.15	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	D	0.94381	0.8193	L	0.33093	0.98	0.80722	D	1	D;P;D;D;P;D;D	0.89917	1.0;0.702;1.0;1.0;0.85;1.0;1.0	D;P;D;D;P;D;D	0.97110	1.0;0.45;1.0;1.0;0.697;1.0;1.0	D	0.94606	0.7800	10	0.49607	T	0.09	-12.2412	15.1757	0.72910	0.0:0.0:0.0:1.0	.	428;98;525;525;525;525;418	F8WE90;Q13749;P19021;P19021-4;P19021-3;P19021-5;P19021-2	.;.;AMD_HUMAN;.;.;.;.	P	525;525;418;525;428;525	ENSP00000396493:L525P;ENSP00000282992:L525P;ENSP00000314638:L418P;ENSP00000306100:L525P;ENSP00000274392:L428P;ENSP00000403461:L525P	ENSP00000274392:L428P	L	+	2	0	PAM	102353965	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	6.669000	0.74462	2.075000	0.62263	0.454000	0.30748	CTG	.	.		0.383	PAM-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250640.2	NM_000919		C	102326066	T	C	102326066	3	2	371	1	0	0	0	0	1	0	0	0	11421	1580	55	2	1632	2	PAM	5	102326066	Missense_Mutation	SNP	T	TCGA-ZS-A9CE-01A-11D-A36X-10	12251775	102326066	78589194	40	51332										
FTMT	94033	hgsc.bcm.edu	37	chr5	121187669	121187669	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	aggcggcgctatgctgtcctGcttcaggctcctctccaggc	12	15	2	0			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr5:121187669G>A	ENST00000321339.1	+	1	20	c.11G>A	c.(10-12)tGc>tAc	p.C4Y		NM_177478.1	NP_803431.1	Q8N4E7	FTMT_HUMAN	ferritin mitochondrial	4					cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)|positive regulation of cell proliferation (GO:0008284)|positive regulation of lyase activity (GO:0051349)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of transferase activity (GO:0051347)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ferric iron binding (GO:0008199)|ferroxidase activity (GO:0004322)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	33		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	Epithelial(69;0.000171)|OV - Ovarian serous cystadenocarcinoma(64;0.000188)|all cancers(49;0.0027)		ATGCTGTCCTGCTTCAGGCTC	0.697																																					p.C4Y		Atlas-SNP	.											.	FTMT	71	.	0			c.G11A						.						31	36	34					5																	121187669		2201	4297	6498	SO:0001583	missense	94033	exon1			TGTCCTGCTTCAG	BC034419	CCDS4128.1	5q23.1	2008-02-05			ENSG00000181867	ENSG00000181867			17345	protein-coding gene	gene with protein product		608847				11323407	Standard	NM_177478		Approved	MtF	uc003kss.3	Q8N4E7	OTTHUMG00000128912	ENST00000321339.1:c.11G>A	chr5.hg19:g.121187669G>A	ENSP00000313691:p.Cys4Tyr	37.0	0.0		35.0	15.0	NM_177478		Missense_Mutation	SNP	ENST00000321339.1	hg19	CCDS4128.1	.	.	.	.	.	.	.	.	.	.	G	7.698	0.692553	0.15039	.	.	ENSG00000181867	ENST00000321339	T	0.64803	-0.12	3.1	1.28	0.21552	.	.	.	.	.	T	0.40247	0.1109	N	0.14661	0.345	0.19575	N	0.999967	B	0.06786	0.001	B	0.04013	0.001	T	0.26815	-1.0092	9	0.51188	T	0.08	.	4.8436	0.13503	0.2928:0.0:0.7072:0.0	.	4	Q8N4E7	FTMT_HUMAN	Y	4	ENSP00000313691:C4Y	ENSP00000313691:C4Y	C	+	2	0	FTMT	121215568	0.007000	0.16637	0.057000	0.19452	0.125000	0.20455	0.115000	0.15540	0.324000	0.23333	0.650000	0.86243	TGC	.	.		0.697	FTMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250884.1	NM_177478		A	121187669	G	A	121187669	3	1	371	1	0	0	0	0	1	0	0	0	6093	1319	46	3	13	3	FTMT	5	121187669	Missense_Mutation	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10	18861603	121187669	59727591	41	51333										
PCDHB14	56122	hgsc.bcm.edu	37	chr5	140604578	140604579	+	Missense_Mutation	DNP	GC	GC	AA													0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	aggaccggcacctgcccctcGcctccttggtctccatcaac							TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr5:140604578_140604579GC>AA	ENST00000239449.4	+	1	1501_1502	c.1501_1502GC>AA	c.(1501-1503)GCc>AAc	p.A501N	PCDHB14_ENST00000515856.2_Missense_Mutation_p.A348N	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	501	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(21)|ovary(2)|prostate(3)|skin(6)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCTGCCCCTCGCCTCCTTGGTC	0.649																																					p.A501T|p.A501D	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											.	PCDHB14	132	.	0			c.G1501A|c.C1502A						.																																			SO:0001583	missense	56122	exon1			CCCCTCGCCTCCT|CCCTCGCCTCCTT	AF152493	CCDS4256.1	5q31	2010-01-26			ENSG00000120327	ENSG00000120327		"Cadherins / Protocadherins : Clustered"	8685	other	protocadherin		606340				10380929	Standard	NM_018934		Approved	PCDH-BETA14	uc003ljb.3	Q9Y5E9	OTTHUMG00000129619	Exception_encountered	chr5.hg19:g.140604578_140604579delinsAA	ENSP00000239449:p.Ala501Asn	88.0|87.0	0.0		160.0|161.0	51.0|52.0	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Missense_Mutation	SNP	ENST00000239449.4	hg19	CCDS4256.1																																																																																			.	.		0.649	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934		AA	140604579	GC	AA	140604578	3	1	371	1	0	0	0	0	1	0	0	0	11548	1087	38	1	1503	1	PCDHB14	5	140604578	Missense_Mutation	DNP	GC	TCGA-ZS-A9CE-01A-11D-A36X-10	19416909	140604578	40310682	42	51334										
PCDHGB4	8641	hgsc.bcm.edu	37	chr5	140769171	140769171	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	ccgacggctctgcgctcttcGatatggtgccgcacgctgca	12	15	2	0			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr5:140769171G>A	ENST00000519479.1	+	1	1720	c.1720G>A	c.(1720-1722)Gat>Aat	p.D574N	PCDHGB1_ENST00000523390.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_003736.2|NM_018925.2|NM_032098.1	NP_003727.1|NP_061748.1|NP_115269.1	Q9UN71	PCDGG_HUMAN	protocadherin gamma subfamily B, 4	574	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(9)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(2)	37			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGCGCTCTTCGATATGGTGCC	0.647																																					p.D574N		Atlas-SNP	.											.	PCDHGB4	125	.	0			c.G1720A						.						38	47	44					5																	140769171		2182	4278	6460	SO:0001583	missense	8641	exon1			CTCTTCGATATGG	AF152520	CCDS54928.1, CCDS75337.1	5q31	2010-01-26				ENSG00000253953		"Cadherins / Protocadherins : Clustered"	8711	other	protocadherin	"fibroblast cadherin FIB2", "cadherin 20"	603058				10380929	Standard	NM_003736		Approved	FIB2, CDH20, PCDH-GAMMA-B4		Q9UN71		ENST00000519479.1:c.1720G>A	chr5.hg19:g.140769171G>A	ENSP00000428288:p.Asp574Asn	61.0	0.0		108.0	33.0	NM_032098	O15099|Q2M267|Q9UN64	Missense_Mutation	SNP	ENST00000519479.1	hg19	CCDS54928.1	.	.	.	.	.	.	.	.	.	.	.	25.5	4.645136	0.87859	.	.	ENSG00000253953	ENST00000519479	T	0.37584	1.19	5.05	4.18	0.49190	Cadherin-like (1);	.	.	.	.	T	0.62744	0.2453	M	0.82323	2.585	0.30511	N	0.769447	D;D	0.89917	1.0;0.999	D;D	0.71656	0.974;0.942	T	0.68096	-0.5499	9	0.87932	D	0	.	14.83	0.70139	0.0:0.0:0.8547:0.1453	.	574;574	Q9UN71-2;Q9UN71	.;PCDGG_HUMAN	N	574	ENSP00000428288:D574N	ENSP00000428288:D574N	D	+	1	0	PCDHGB4	140749355	1.000000	0.71417	0.999000	0.59377	0.940000	0.58332	3.828000	0.55753	1.242000	0.43836	0.563000	0.77884	GAT	.	.		0.647	PCDHGB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374745.1	NM_003736		A	140769171	G	A	140769171	3	1	371	1	0	0	0	0	1	0	0	0	11574	1058	37	1	1722	1	PCDHGB4	5	140769171	Missense_Mutation	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10	164593	140769171	40146089	43	51335										
IL12B	3593	hgsc.bcm.edu	37	chr5	158750101	158750101	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	atcagtggaccaaattccatCttcctttttgtgaagcagca	7	10	2	1			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr5:158750101C>T	ENST00000231228.2	-	3	780	c.325G>A	c.(325-327)Gat>Aat	p.D109N		NM_002187.2	NP_002178.2	P29460	IL12B_HUMAN	interleukin 12B	109					cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|defense response to Gram-negative bacterium (GO:0050829)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|interferon-gamma biosynthetic process (GO:0042095)|natural killer cell activation (GO:0030101)|natural killer cell activation involved in immune response (GO:0002323)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of cell adhesion (GO:0045785)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of mononuclear cell proliferation (GO:0032946)|positive regulation of natural killer cell activation (GO:0032816)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|positive regulation of natural killer cell proliferation (GO:0032819)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NK T cell activation (GO:0051135)|positive regulation of NK T cell proliferation (GO:0051142)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of tissue remodeling (GO:0034105)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat4 protein (GO:0042520)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|regulation of cytokine biosynthetic process (GO:0042035)|regulation of tyrosine phosphorylation of Stat1 protein (GO:0042510)|response to UV-B (GO:0010224)|sensory perception of pain (GO:0019233)|sexual reproduction (GO:0019953)|T-helper 1 type immune response (GO:0042088)|T-helper cell differentiation (GO:0042093)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|interleukin-12 complex (GO:0043514)|interleukin-23 complex (GO:0070743)|membrane (GO:0016020)	cytokine receptor activity (GO:0004896)|identical protein binding (GO:0042802)|interleukin-12 alpha subunit binding (GO:0042164)|interleukin-12 receptor binding (GO:0005143)|protein heterodimerization activity (GO:0046982)			cervix(1)|endometrium(1)|large_intestine(5)|lung(4)	11	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CAAATTCCATCTTCCTTTTTG	0.418																																					p.D109N		Atlas-SNP	.											.	IL12B	30	.	0			c.G325A						.						80	79	80					5																	158750101		2203	4300	6503	SO:0001583	missense	3593	exon3			TTCCATCTTCCTT	M65290	CCDS4346.1	5q31.1-q33.1	2014-09-17	2014-04-04		ENSG00000113302	ENSG00000113302		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5970	protein-coding gene	gene with protein product	"natural killer cell stimulatory factor-2", "cytotoxic lymphocyte maturation factor 2, p40", "interleukin 12, p40", "natural killer cell stimulatory factor, 40 kD subunit", "interleukin-12 beta chain", "IL12, subunit p40"	161561	"interleukin 12B (natural killer cell stimulatory factor 2, cytotoxic lymphocyte maturation factor 2, p40)"	NKSF2		1673147	Standard	NM_002187		Approved	CLMF, IL-12B, NKSF, CLMF2	uc003lxr.1	P29460	OTTHUMG00000130307	ENST00000231228.2:c.325G>A	chr5.hg19:g.158750101C>T	ENSP00000231228:p.Asp109Asn	114.0	0.0		185.0	66.0	NM_002187		Missense_Mutation	SNP	ENST00000231228.2	hg19	CCDS4346.1	.	.	.	.	.	.	.	.	.	.	C	8.729	0.916122	0.17907	.	.	ENSG00000113302	ENST00000231228	T	0.17691	2.26	5.85	3.61	0.41365	.	0.368200	0.31450	N	0.007630	T	0.10078	0.0247	L	0.29908	0.895	0.32343	N	0.559463	B	0.02656	0.0	B	0.04013	0.001	T	0.15694	-1.0428	10	0.18276	T	0.48	-12.2537	5.4784	0.16708	0.1765:0.6917:0.0:0.1318	.	109	P29460	IL12B_HUMAN	N	109	ENSP00000231228:D109N	ENSP00000231228:D109N	D	-	1	0	IL12B	158682679	0.972000	0.33761	0.998000	0.56505	0.967000	0.64934	0.632000	0.24583	1.132000	0.42129	0.655000	0.94253	GAT	.	.		0.418	IL12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252652.2	NM_002187		T	158750101	C	T	158750101	3	4	371	1	0	0	0	0	1	0	0	0	7634	913	32	3	681	3	IL12B	5	158750101	Missense_Mutation	SNP	C	TCGA-ZS-A9CE-01A-11D-A36X-10	17980930	158750101	22165159	44	51336										
IL12B	3593	hgsc.bcm.edu	37	chr5	158750231	158750231	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	ccagagcctaagacctcactGctctggtccaaggtccaggt	10	14	2	2			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr5:158750231G>C	ENST00000231228.2	-	3	650	c.195C>G	c.(193-195)agC>agG	p.S65R		NM_002187.2	NP_002178.2	P29460	IL12B_HUMAN	interleukin 12B	65	Ig-like C2-type.				cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|defense response to Gram-negative bacterium (GO:0050829)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|interferon-gamma biosynthetic process (GO:0042095)|natural killer cell activation (GO:0030101)|natural killer cell activation involved in immune response (GO:0002323)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of cell adhesion (GO:0045785)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of mononuclear cell proliferation (GO:0032946)|positive regulation of natural killer cell activation (GO:0032816)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|positive regulation of natural killer cell proliferation (GO:0032819)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NK T cell activation (GO:0051135)|positive regulation of NK T cell proliferation (GO:0051142)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of tissue remodeling (GO:0034105)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat4 protein (GO:0042520)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|regulation of cytokine biosynthetic process (GO:0042035)|regulation of tyrosine phosphorylation of Stat1 protein (GO:0042510)|response to UV-B (GO:0010224)|sensory perception of pain (GO:0019233)|sexual reproduction (GO:0019953)|T-helper 1 type immune response (GO:0042088)|T-helper cell differentiation (GO:0042093)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|interleukin-12 complex (GO:0043514)|interleukin-23 complex (GO:0070743)|membrane (GO:0016020)	cytokine receptor activity (GO:0004896)|identical protein binding (GO:0042802)|interleukin-12 alpha subunit binding (GO:0042164)|interleukin-12 receptor binding (GO:0005143)|protein heterodimerization activity (GO:0046982)			cervix(1)|endometrium(1)|large_intestine(5)|lung(4)	11	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			AGACCTCACTGCTCTGGTCCA	0.527																																					p.S65R		Atlas-SNP	.											.	IL12B	30	.	0			c.C195G						.						96	86	89					5																	158750231		2203	4300	6503	SO:0001583	missense	3593	exon3			CTCACTGCTCTGG	M65290	CCDS4346.1	5q31.1-q33.1	2014-09-17	2014-04-04		ENSG00000113302	ENSG00000113302		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5970	protein-coding gene	gene with protein product	"natural killer cell stimulatory factor-2", "cytotoxic lymphocyte maturation factor 2, p40", "interleukin 12, p40", "natural killer cell stimulatory factor, 40 kD subunit", "interleukin-12 beta chain", "IL12, subunit p40"	161561	"interleukin 12B (natural killer cell stimulatory factor 2, cytotoxic lymphocyte maturation factor 2, p40)"	NKSF2		1673147	Standard	NM_002187		Approved	CLMF, IL-12B, NKSF, CLMF2	uc003lxr.1	P29460	OTTHUMG00000130307	ENST00000231228.2:c.195C>G	chr5.hg19:g.158750231G>C	ENSP00000231228:p.Ser65Arg	107.0	0.0		154.0	39.0	NM_002187		Missense_Mutation	SNP	ENST00000231228.2	hg19	CCDS4346.1	.	.	.	.	.	.	.	.	.	.	G	3.733	-0.055067	0.07362	.	.	ENSG00000113302	ENST00000231228	T	0.21361	2.01	5.96	-3.56	0.04626	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.576284	0.21928	N	0.067062	T	0.10594	0.0259	L	0.37561	1.115	0.09310	N	1	B	0.17038	0.02	B	0.11329	0.006	T	0.28106	-1.0054	10	0.17832	T	0.49	-8.388	4.5596	0.12154	0.3787:0.0:0.3263:0.295	.	65	P29460	IL12B_HUMAN	R	65	ENSP00000231228:S65R	ENSP00000231228:S65R	S	-	3	2	IL12B	158682809	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-1.286000	0.02788	-0.563000	0.06078	-0.122000	0.15005	AGC	.	.		0.527	IL12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252652.2	NM_002187		C	158750231	G	C	158750231	3	2	371	1	0	0	0	0	1	0	0	0	7634	1310	46	4	811	4	IL12B	5	158750231	Missense_Mutation	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10	130	158750231	22165029	45	51337										
PRELID1	27166	hgsc.bcm.edu	37	chr5	176732966	176732966	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	ggtctcctctagcttatttgGtgtctccagagctgtccagg	11	11	3	1			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr5:176732966G>C	ENST00000303204.4	+	3	625	c.413G>C	c.(412-414)gGt>gCt	p.G138A	MXD3_ENST00000427908.2_3'UTR|PRELID1_ENST00000503216.1_Missense_Mutation_p.G138A|RAB24_ENST00000303251.6_5'Flank|RAB24_ENST00000393611.2_5'Flank|RAB24_ENST00000303270.6_5'Flank			Q9Y255	PRLD1_HUMAN	PRELI domain containing 1	138	PRELI/MSF1. {ECO:0000255|PROSITE- ProRule:PRU00158}.				apoptotic process (GO:0006915)|immune response (GO:0006955)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mitochondrial membrane potential (GO:0010917)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|phospholipid transport (GO:0015914)|positive regulation of cellular respiration (GO:1901857)|positive regulation of endopeptidase activity (GO:0010950)|positive regulation of phospholipid transport (GO:2001140)|positive regulation of T cell apoptotic process (GO:0070234)|regulation of membrane lipid distribution (GO:0097035)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of T cell differentiation (GO:0045580)	mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)				endometrium(1)|kidney(2)|lung(2)|prostate(1)|stomach(1)	7	all_cancers(89;2.49e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGCTTATTTGGTGTCTCCAGA	0.582																																					p.G138A		Atlas-SNP	.											.	PRELID1	10	.	0			c.G413C						.						61	58	59					5																	176732966		2203	4300	6503	SO:0001583	missense	27166	exon3			TATTTGGTGTCTC	BC013748	CCDS4415.1, CCDS64328.1	5q35.3	2010-01-18			ENSG00000169230	ENSG00000169230			30255	protein-coding gene	gene with protein product	"protein of relevant evolutionary and lymphoid interest", "px19-like protein"	605733				10784606, 14640972	Standard	NM_013237		Approved	CGI-106, PX19, PRELI	uc003mfx.4	Q9Y255	OTTHUMG00000130847	ENST00000303204.4:c.413G>C	chr5.hg19:g.176732966G>C	ENSP00000302114:p.Gly138Ala	51.0	0.0		89.0	27.0	NM_013237	B2R5F7|D6RD25|Q549N2|Q9UI13|Q9UJS9	Missense_Mutation	SNP	ENST00000303204.4	hg19	CCDS4415.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	28.0|28.0	4.879958|4.879958	0.91740|0.91740	.|.	.|.	ENSG00000169230|ENSG00000169230	ENST00000303204;ENST00000503216|ENST00000503853	T;T|.	0.19105|.	2.17;2.17|.	4.48|4.48	4.48|4.48	0.54585|0.54585	PRELI/MSF1 (2);|.	0.050772|.	0.85682|.	N|.	0.000000|.	T|T	0.78622|0.78622	0.4312|0.4312	M|M	0.83852|0.83852	2.665|2.665	0.80722|0.80722	D|D	1|1	D;D|.	0.76494|.	0.997;0.999|.	D;D|.	0.79108|.	0.971;0.992|.	T|T	0.81378|0.81378	-0.0960|-0.0960	10|5	0.52906|.	T|.	0.07|.	-4.9142|-4.9142	17.3571|17.3571	0.87340|0.87340	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	138;138|.	D6RD25;Q9Y255|.	.;PRLD1_HUMAN|.	A|C	138|86	ENSP00000302114:G138A;ENSP00000427097:G138A|.	ENSP00000302114:G138A|.	G|W	+|+	2|3	0|0	PRELID1|PRELID1	176665572|176665572	1.000000|1.000000	0.71417|0.71417	0.950000|0.950000	0.38849|0.38849	0.988000|0.988000	0.76386|0.76386	7.184000|7.184000	0.77705|0.77705	2.332000|2.332000	0.79248|0.79248	0.561000|0.561000	0.74099|0.74099	GGT|TGG	.	.		0.582	PRELID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253414.1	NM_013237		C	176732966	G	C	176732966	3	2	371	1	0	0	0	0	1	0	0	0	12483	1261	44	4	423	4	PRELID1	5	176732966	Missense_Mutation	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10	17982735	176732966	4182294	46	51338										
SCUBE3	222663	hgsc.bcm.edu	37	chr6	35196493	35196493	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	ctatgatggattccacctggCacatgacggacacaactgtc	9	12	0	2			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr6:35196493C>T	ENST00000274938.7	+	3	311	c.311C>T	c.(310-312)gCa>gTa	p.A104V	SCUBE3_ENST00000394681.1_Missense_Mutation_p.A104V	NM_152753.2	NP_689966.2			signal peptide, CUB domain, EGF-like 3											breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(12)|lung(11)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	37						TTCCACCTGGCACATGACGGA	0.498																																					p.A104V		Atlas-SNP	.											.	SCUBE3	99	.	0			c.C311T						.						222	162	182					6																	35196493		2203	4300	6503	SO:0001583	missense	222663	exon3			ACCTGGCACATGA	AF452494.1	CCDS4800.1	6p21.3	2008-02-05	2004-05-19	2004-05-21		ENSG00000146197			13655	protein-coding gene	gene with protein product		614708	"CUB domain and EGF-like repeat containing 3"	CEGF3		12270931	Standard	NM_152753		Approved	FLJ34743	uc003okf.1	Q8IX30		ENST00000274938.7:c.311C>T	chr6.hg19:g.35196493C>T	ENSP00000274938:p.Ala104Val	128.0	0.0		142.0	24.0	NM_152753		Missense_Mutation	SNP	ENST00000274938.7	hg19	CCDS4800.1	.	.	.	.	.	.	.	.	.	.	C	35	5.478243	0.96291	.	.	ENSG00000146197	ENST00000394681;ENST00000274938	D;D	0.95035	-3.59;-3.59	5.31	5.31	0.75309	EGF-like region, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.94666	0.8280	L	0.28608	0.87	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.80764	0.994;0.992	D	0.94280	0.7519	10	0.45353	T	0.12	.	19.1881	0.93653	0.0:1.0:0.0:0.0	.	104;104	Q8IX30-2;Q8IX30	.;SCUB3_HUMAN	V	104	ENSP00000378174:A104V;ENSP00000274938:A104V	ENSP00000274938:A104V	A	+	2	0	SCUBE3	35304471	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.614000	0.82996	2.758000	0.94735	0.655000	0.94253	GCA	.	.		0.498	SCUBE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040275.1	NM_152753		T	35196493	C	T	35196493	3	4	371	1	0	0	0	0	1	0	0	0	13961	710	25	3	321	3	SCUBE3	6	35196493	Missense_Mutation	SNP	C	TCGA-ZS-A9CE-01A-11D-A36X-10		35196493	135918574	47	51339										
SYNE1	23345	hgsc.bcm.edu	37	chr6	152560752	152560752	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	gccatcagctctgtatggaaCtgggtttccttttggactgc	11	10	2	0			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr6:152560752C>G	ENST00000367255.5	-	108	20584	c.19983G>C	c.(19981-19983)caG>caC	p.Q6661H	SYNE1_ENST00000448038.1_Missense_Mutation_p.Q6590H|SYNE1_ENST00000356820.4_Missense_Mutation_p.Q1185H|SYNE1_ENST00000341594.5_Missense_Mutation_p.Q6273H|SYNE1_ENST00000265368.4_Missense_Mutation_p.Q6661H|SYNE1_ENST00000423061.1_Missense_Mutation_p.Q6590H	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	6661					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		CTGTATGGAACTGGGTTTCCT	0.453										HNSCC(10;0.0054)																											p.Q6661H		Atlas-SNP	.											.	SYNE1	3227	.	0			c.G19983C						.						127	108	114					6																	152560752		2203	4300	6503	SO:0001583	missense	23345	exon108			ATGGAACTGGGTT	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.19983G>C	chr6.hg19:g.152560752C>G	ENSP00000356224:p.Gln6661His	109.0	0.0		109.0	58.0	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	15.48	2.845628	0.51164	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820	T;T;T;T;T;T	0.35973	1.28;1.28;1.28;1.28;1.28;1.28	5.7	-0.503	0.12000	.	0.103551	0.42682	D	0.000666	T	0.43523	0.1251	M	0.72894	2.215	0.42632	D	0.99338	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.48958	-0.8988	10	0.62326	D	0.03	.	12.3799	0.55301	0.0:0.4863:0.0:0.5137	.	6661;6661;6590	Q8NF91;E7EQI5;Q8NF91-4	SYNE1_HUMAN;.;.	H	6661;6590;6661;6590;6273;1185	ENSP00000356224:Q6661H;ENSP00000396024:Q6590H;ENSP00000265368:Q6661H;ENSP00000390975:Q6590H;ENSP00000341887:Q6273H;ENSP00000349276:Q1185H	ENSP00000265368:Q6661H	Q	-	3	2	SYNE1	152602445	0.002000	0.14202	0.137000	0.22149	0.948000	0.59901	-0.142000	0.10311	-0.421000	0.07416	-0.880000	0.02959	CAG	.	.		0.453	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		G	152560752	C	G	152560752	3	3	371	1	0	0	0	0	1	0	0	0	15460	564	20	4	6639	4	SYNE1	6	152560752	Missense_Mutation	SNP	C	TCGA-ZS-A9CE-01A-11D-A36X-10	117364259	152560752	18554315	48	51340										
SLC22A3	6581	hgsc.bcm.edu	37	chr6	160819023	160819023	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	tttctcagtttgaccttgtcTgtgtcaatgcgtggatgctg	11	8	3	1			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr6:160819023T>A	ENST00000275300.2	+	2	594	c.442T>A	c.(442-444)Tgt>Agt	p.C148S	SLC22A3_ENST00000392145.1_Missense_Mutation_p.C148S	NM_021977.3	NP_068812.1	O75751	S22A3_HUMAN	solute carrier family 22 (organic cation transporter), member 3	148					dopamine transport (GO:0015872)|drug transmembrane transport (GO:0006855)|histamine uptake (GO:0051615)|organic cation transport (GO:0015695)|quaternary ammonium group transport (GO:0015697)|regulation of appetite (GO:0032098)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dopamine transmembrane transporter activity (GO:0005329)|organic cation transmembrane transporter activity (GO:0015101)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|toxin transporter activity (GO:0019534)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27		Breast(66;0.00028)|Ovarian(120;0.0308)|Prostate(117;0.218)		OV - Ovarian serous cystadenocarcinoma(65;9.47e-17)|BRCA - Breast invasive adenocarcinoma(81;9.75e-06)	Adefovir Dipivoxil(DB00718)|Amphetamine(DB00182)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Colchicine(DB01394)|Desipramine(DB01151)|Dopamine(DB00988)|Estradiol(DB00783)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Imipramine(DB00458)|Irinotecan(DB00762)|Lamivudine(DB00709)|Melphalan(DB01042)|Metformin(DB00331)|Methamphetamine(DB01577)|Nicotine(DB00184)|Norepinephrine(DB00368)|Oxaliplatin(DB00526)|Phenoxybenzamine(DB00925)|Prazosin(DB00457)|Procainamide(DB01035)|Progesterone(DB00396)|Testosterone(DB00624)|Vincristine(DB00541)	TGACCTTGTCTGTGTCAATGC	0.458																																					p.C148S		Atlas-SNP	.											SLC22A3,colon,carcinoma,0,1	SLC22A3	58	.	0			c.T442A						.						248	223	232					6																	160819023		2203	4300	6503	SO:0001583	missense	6581	exon2			CTTGTCTGTGTCA	AF078749	CCDS5277.1	6q25.3	2013-07-18	2013-07-18		ENSG00000146477	ENSG00000146477		"Solute carriers"	10967	protein-coding gene	gene with protein product		604842	"solute carrier family 22 (extraneuronal monoamine transporter), member 3"			9632645, 9933568	Standard	NM_021977		Approved	OCT3, EMT	uc003qti.4	O75751	OTTHUMG00000015953	ENST00000275300.2:c.442T>A	chr6.hg19:g.160819023T>A	ENSP00000275300:p.Cys148Ser	68.0	0.0		69.0	19.0	NM_021977	Q5SYN6|Q9UP02	Missense_Mutation	SNP	ENST00000275300.2	hg19	CCDS5277.1	.	.	.	.	.	.	.	.	.	.	T	18.97	3.736153	0.69189	.	.	ENSG00000146477	ENST00000275300;ENST00000392145	T;T	0.81078	-1.45;-1.45	5.31	5.31	0.75309	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.90208	0.6939	M	0.92555	3.32	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	D	0.92606	0.6095	10	0.87932	D	0	.	13.8388	0.63426	0.0:0.0:0.0:1.0	.	148	O75751	S22A3_HUMAN	S	148	ENSP00000275300:C148S;ENSP00000375989:C148S	ENSP00000275300:C148S	C	+	1	0	SLC22A3	160739013	1.000000	0.71417	0.998000	0.56505	0.540000	0.34992	5.479000	0.66813	2.008000	0.58898	0.454000	0.30748	TGT	.	.		0.458	SLC22A3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042953.1	NM_021977		A	160819023	T	A	160819023	3	1	371	1	0	0	0	0	1	0	0	0	14470	1580	55	4	448	4	SLC22A3	6	160819023	Missense_Mutation	SNP	T	TCGA-ZS-A9CE-01A-11D-A36X-10	8258271	160819023	10296044	49	51341										
GNA12	2768	hgsc.bcm.edu	37	chr7	2771229	2771229	+	Silent	SNP	C	C	G	0	1	0	0	1	0	1	1	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	atgaacaggatggacgtgatCccgtcgaagcactggaacca	12	10	0	2			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr7:2771229C>G	ENST00000275364.3	-	4	894	c.732G>C	c.(730-732)ggG>ggC	p.G244G	GNA12_ENST00000407653.1_Silent_p.G168G|GNA12_ENST00000491117.1_5'UTR|GNA12_ENST00000544127.1_Silent_p.G151G|AMZ1_ENST00000489665.1_Intron|GNA12_ENST00000407904.3_Silent_p.G185G|GNA12_ENST00000396960.3_Silent_p.G96G	NM_007353.2	NP_031379.2	Q03113	GNA12_HUMAN	guanine nucleotide binding protein (G protein) alpha 12	244					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|embryonic digit morphogenesis (GO:0042733)|G-protein coupled receptor signaling pathway (GO:0007186)|in utero embryonic development (GO:0001701)|platelet activation (GO:0030168)|regulation of cell shape (GO:0008360)|regulation of fibroblast migration (GO:0010762)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|regulation of TOR signaling (GO:0032006)|response to drug (GO:0042493)|Rho protein signal transduction (GO:0007266)	brush border membrane (GO:0031526)|focal adhesion (GO:0005925)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	D5 dopamine receptor binding (GO:0031752)|G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			endometrium(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;1.02e-13)		TGGACGTGATCCCGTCGAAGC	0.567																																					p.G244G		Atlas-SNP	.											.	GNA12	35	.	0			c.G732C						.						122	109	113					7																	2771229		2203	4300	6503	SO:0001819	synonymous_variant	2768	exon4			CGTGATCCCGTCG	L01694	CCDS5335.1, CCDS64584.1, CCDS64583.1	7p22.3	2006-07-08			ENSG00000146535	ENSG00000146535			4380	protein-coding gene	gene with protein product		604394				8423800, 16247467	Standard	NM_007353		Approved	gep	uc003smu.3	Q03113	OTTHUMG00000023064	ENST00000275364.3:c.732G>C	chr7.hg19:g.2771229C>G		87.0	0.0		119.0	5.0	NM_007353	A4D204|B3KXS2|B7Z3F7|Q2T9L1|Q5PPR5|Q86UM8|Q8TD71|Q9UDU9	Silent	SNP	ENST00000275364.3	hg19	CCDS5335.1																																																																																			.	.		0.567	GNA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241608.1	NM_007353		G	2771229	C	G	2771229	2	3	371	1	0	0	0	0	0	0	0	1	6508	842	30	4		4	GNA12	7	2771229	Silent	SNP	C	TCGA-ZS-A9CE-01A-11D-A36X-10		2771229	156367434	50	51342										
AUTS2	26053	hgsc.bcm.edu	37	chr7	70255042	70255042	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	gtctccctacgtgcggacccCggtggtggagagtgccaggc	16	13	1	1			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr7:70255042C>T	ENST00000342771.4	+	19	3161	c.2840C>T	c.(2839-2841)cCg>cTg	p.P947L	AUTS2_ENST00000406775.2_Missense_Mutation_p.P923L	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	947										breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		GTGCGGACCCCGGTGGTGGAG	0.731																																					p.P947L		Atlas-SNP	.											.	AUTS2	173	.	0			c.C2840T						.						9	12	11					7																	70255042		2164	4256	6420	SO:0001583	missense	26053	exon19			GGACCCCGGTGGT	AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321			14262	protein-coding gene	gene with protein product		607270				12160723	Standard	XM_005250257		Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.2840C>T	chr7.hg19:g.70255042C>T	ENSP00000344087:p.Pro947Leu	161.0	0.0		178.0	111.0	NM_015570	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Missense_Mutation	SNP	ENST00000342771.4	hg19	CCDS5539.1	.	.	.	.	.	.	.	.	.	.	C	18.45	3.627642	0.66901	.	.	ENSG00000158321	ENST00000406775;ENST00000342771	T;T	0.29397	1.57;1.57	4.28	4.28	0.50868	.	0.369254	0.31438	N	0.007652	T	0.32823	0.0842	L	0.46157	1.445	0.80722	D	1	P;D;D	0.57257	0.89;0.979;0.979	B;P;P	0.45449	0.128;0.481;0.481	T	0.10847	-1.0612	9	.	.	.	-19.4334	16.9403	0.86216	0.0:1.0:0.0:0.0	.	399;923;947	B4DLG0;Q8WXX7-2;Q8WXX7	.;.;AUTS2_HUMAN	L	923;947	ENSP00000385263:P923L;ENSP00000344087:P947L	.	P	+	2	0	AUTS2	69892978	0.994000	0.37717	0.739000	0.30968	0.985000	0.73830	3.221000	0.51215	2.223000	0.72356	0.655000	0.94253	CCG	.	.		0.731	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2			T	70255042	C	T	70255042	3	4	371	1	0	0	0	0	1	0	0	0	1225	652	23	1	3059	1	AUTS2	7	70255042	Missense_Mutation	SNP	C	TCGA-ZS-A9CE-01A-11D-A36X-10	67483813	70255042	88883621	51	51343										
ZNF394	84124	hgsc.bcm.edu	37	chr7	99091247	99091247	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	actttgtctaaatctttcccCacattcaagacatttgtaag	4	10	3	1			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr7:99091247C>T	ENST00000337673.6	-	3	1794	c.1591G>A	c.(1591-1593)Ggg>Agg	p.G531R	ZNF789_ENST00000493485.1_Intron|ZNF789_ENST00000494186.1_Intron|ZNF394_ENST00000426306.2_3'UTR|ZNF394_ENST00000394177.3_5'Flank	NM_032164.2	NP_115540.2	Q53GI3	ZN394_HUMAN	zinc finger protein 394	531					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(5)|stomach(1)|urinary_tract(1)	16	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					AATCTTTCCCCACATTCAAGA	0.453																																					p.G531R	Ovarian(24;589 697 9939 12704 40742)	Atlas-SNP	.											.	ZNF394	48	.	0			c.G1591A						.						182	177	178					7																	99091247		2203	4300	6503	SO:0001583	missense	84124	exon3			TTTCCCCACATTC	BC025241	CCDS5666.1	7q22.1	2014-01-28			ENSG00000160908	ENSG00000160908		"Zinc fingers, C2H2-type", "-", "-", "-"	18832	protein-coding gene	gene with protein product							Standard	NM_032164		Approved	ZKSCAN14, FLJ12298, ZSCAN46	uc003uqs.3	Q53GI3	OTTHUMG00000154660	ENST00000337673.6:c.1591G>A	chr7.hg19:g.99091247C>T	ENSP00000337363:p.Gly531Arg	170.0	0.0		224.0	73.0	NM_032164	A4D281|Q05DA6|Q6P5X9|Q8TB27|Q9HA37|Q9UD51	Missense_Mutation	SNP	ENST00000337673.6	hg19	CCDS5666.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.369226	0.82463	.	.	ENSG00000160908	ENST00000337673	T	0.07444	3.19	3.58	3.58	0.41010	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.48286	D	0.000191	T	0.21841	0.0526	L	0.50847	1.595	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.00662	-1.1621	10	0.59425	D	0.04	.	13.493	0.61407	0.0:1.0:0.0:0.0	.	531	Q53GI3	ZN394_HUMAN	R	531	ENSP00000337363:G531R	ENSP00000337363:G531R	G	-	1	0	ZNF394	98929183	0.997000	0.39634	1.000000	0.80357	0.999000	0.98932	2.862000	0.48388	2.292000	0.77174	0.655000	0.94253	GGG	.	.		0.453	ZNF394-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336498.1	NM_032164		T	99091247	C	T	99091247	3	4	371	1	0	0	0	0	1	0	0	0	17895	594	21	3	98	3	ZNF394	7	99091247	Missense_Mutation	SNP	C	TCGA-ZS-A9CE-01A-11D-A36X-10	28836205	99091247	60047416	52	51344										
ACTL6B	51412	hgsc.bcm.edu	37	chr7	100247666	100247666	+	Silent	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	cagtccagaggatacgcggtGagcacagccgtcttgcataa	12	11	1	2			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr7:100247666G>C	ENST00000160382.5	-	5	568	c.462C>G	c.(460-462)ctC>ctG	p.L154L		NM_016188.4	NP_057272.1	O94805	ACL6B_HUMAN	actin-like 6B	154					chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|nervous system development (GO:0007399)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	structural constituent of cytoskeleton (GO:0005200)|transcription coactivator activity (GO:0003713)			endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|skin(1)	13	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)					GATACGCGGTGAGCACAGCCG	0.592																																					p.L154L		Atlas-SNP	.											.	ACTL6B	47	.	0			c.C462G						.						171	126	141					7																	100247666		2203	4300	6503	SO:0001819	synonymous_variant	51412	exon5			CGCGGTGAGCACA	AB015906	CCDS5702.1	7q22	2008-02-01	2004-07-12	2004-07-14	ENSG00000077080	ENSG00000077080			160	protein-coding gene	gene with protein product		612458	"actin-like 6"	ACTL6		9799793	Standard	NM_016188		Approved	BAF53B	uc003uvy.3	O94805	OTTHUMG00000159661	ENST00000160382.5:c.462C>G	chr7.hg19:g.100247666G>C		38.0	0.0		41.0	27.0	NM_016188	A4D2D0|O75421	Silent	SNP	ENST00000160382.5	hg19	CCDS5702.1																																																																																			.	.		0.592	ACTL6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356745.1	NM_016188		C	100247666	G	C	100247666	2	2	371	1	0	0	0	0	0	0	0	1	199	1277	45	4		4	ACTL6B	7	100247666	Silent	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10	1156419	100247666	58890997	53	51345										
CTTNBP2	83992	hgsc.bcm.edu	37	chr7	117431601	117431602	+	Missense_Mutation	DNP	GG	GG	TC													0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	aaggagtttgggagagccctGgcttttttggagggatagga							TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr7:117431601_117431602GG>TC	ENST00000160373.3	-	4	1739_1740	c.1648_1649CC>GA	c.(1648-1650)CCa>GAa	p.P550E	CTTNBP2_ENST00000487820.1_5'Flank	NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	550	Pro-rich.				brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)				breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		GGAGAGCCCTGGCTTTTTTGGA	0.515																																					p.P550Q|p.P550A		Atlas-SNP	.											.	CTTNBP2	200	.	0			c.C1649A|c.C1648G						.																																			SO:0001583	missense	83992	exon4			AGCCCTGGCTTTT|GCCCTGGCTTTTT		CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"Ankyrin repeat domain containing"	15679	protein-coding gene	gene with protein product		609772	"cortactin binding protein 2"	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.1648_1649delinsTC	chr7.hg19:g.117431601_117431602delinsTC	ENSP00000160373:p.Pro550Glu	249.0|248.0	0.0		242.0|237.0	162.0|161.0	NM_033427	O43389|Q7LG11|Q9C0A5	Missense_Mutation	SNP	ENST00000160373.3	hg19	CCDS5774.1																																																																																			.	.		0.515	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		TC	117431602	GG	TC	117431601	3	4	371	1	0	0	0	0	1	0	0	0	4047	1348	47	3	3422	3	CTTNBP2	7	117431601	Missense_Mutation	DNP	GG	TCGA-ZS-A9CE-01A-11D-A36X-10	17183935	117431601	41707062	54	51346										
RP1	6101	hgsc.bcm.edu	37	chr8	55534746	55534746	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	caggaagggagccatttaaaCcaggaaattatgacatccaa	9	8	0	1			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr8:55534746C>T	ENST00000220676.1	+	3	833	c.685C>T	c.(685-687)Cca>Tca	p.P229S		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	229	Doublecortin 2. {ECO:0000255|PROSITE- ProRule:PRU00072}.				axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			GCCATTTAAACCAGGAAATTA	0.483																																					p.P229S	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.C685T						.						81	80	80					8																	55534746		2203	4300	6503	SO:0001583	missense	6101	exon3			TTTAAACCAGGAA	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.685C>T	chr8.hg19:g.55534746C>T	ENSP00000220676:p.Pro229Ser	90.0	0.0		110.0	48.0	NM_006269		Missense_Mutation	SNP	ENST00000220676.1	hg19	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	C	15.92	2.974338	0.53720	.	.	ENSG00000104237	ENST00000427058;ENST00000220676	D	0.86956	-2.19	5.55	4.67	0.58626	Doublecortin domain (4);	0.000000	0.64402	D	0.000018	D	0.89815	0.6824	M	0.62209	1.925	0.31032	N	0.717321	P;D	0.69078	0.926;0.997	P;P	0.59643	0.454;0.861	D	0.88702	0.3216	10	0.66056	D	0.02	.	9.3112	0.37905	0.0:0.6506:0.2773:0.072	.	39;229	E7EVW9;P56715	.;RP1_HUMAN	S	39;229	ENSP00000220676:P229S	ENSP00000220676:P229S	P	+	1	0	RP1	55697299	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.982000	0.29539	1.328000	0.45358	0.655000	0.94253	CCA	.	.		0.483	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		T	55534746	C	T	55534746	3	4	371	1	0	0	0	0	1	0	0	0	13547	507	18	3	691	3	RP1	8	55534746	Missense_Mutation	SNP	C	TCGA-ZS-A9CE-01A-11D-A36X-10		55534746	90829276	55	51347										
JPH1	56704	hgsc.bcm.edu	37	chr8	75233276	75233276	+	Frame_Shift_Del	DEL	G	G	-													0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	accatgtgaccactccccccGgtacatccacttgcccttcg							TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr8:75233276delG	ENST00000342232.4	-	1	287	c.247delC	c.(247-249)cggfs	p.R83fs		NM_020647.2	NP_065698.1	Q9HDC5	JPH1_HUMAN	junctophilin 1	83	Gly-rich.				calcium ion transport into cytosol (GO:0060402)|muscle organ development (GO:0007517)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	24	Breast(64;0.00576)		BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.0728)|all cancers(69;0.176)			CACTCCCCCCGGTACATCCAC	0.672																																					p.R83fs		Atlas-INDEL	.											.	JPH1	77	.	0			c.248delG						.						98	57	71					8																	75233276		2203	4300	6503	SO:0001589	frameshift_variant	56704	exon1			.	AB042634	CCDS6217.1	8q21	2008-07-03			ENSG00000104369	ENSG00000104369			14201	protein-coding gene	gene with protein product		605266				10891348, 10949023	Standard	XM_005251273		Approved	JP-1	uc003yae.3	Q9HDC5	OTTHUMG00000164524	ENST00000342232.4:c.247delC	chr8.hg19:g.75233276delG	ENSP00000344488:p.Arg83fs	156.0	0.0		191.0	71.0	NM_020647	B2RTZ0	Frame_Shift_Del	DEL	ENST00000342232.4	hg19	CCDS6217.1																																																																																			.	.		0.672	JPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379102.1			-	75233276	G	-	75233276	7	5	371	1	0	1	0	1	0	0	0	0	7969	1115	39	0	1758	0	JPH1	8	75233276	Frame_Shift_Del	DEL	G	TCGA-ZS-A9CE-01A-11D-A36X-10	19698530	75233276	71130746	56	51348										
GDAP1	54332	hgsc.bcm.edu	37	chr8	75274160	75274160	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	ctgagctgaagaaacttgctGaagaaaacccagatttacaa	8	8	0	6			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr8:75274160G>A	ENST00000220822.7	+	4	606	c.526G>A	c.(526-528)Gaa>Aaa	p.E176K	GDAP1_ENST00000434412.2_Missense_Mutation_p.E108K|GDAP1_ENST00000521096.1_3'UTR	NM_001040875.2|NM_018972.2	NP_001035808.1|NP_061845.2	Q8TB36	GDAP1_HUMAN	ganglioside induced differentiation associated protein 1	176	GST C-terminal.				cell death (GO:0008219)|mitochondrial fission (GO:0000266)|protein targeting to mitochondrion (GO:0006626)|response to retinoic acid (GO:0032526)	integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	Breast(64;0.00769)	Myeloproliferative disorder(644;0.0122)	BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.104)|all cancers(69;0.234)			GAAACTTGCTGAAGAAAACCC	0.373																																					p.E176K		Atlas-SNP	.											.	GDAP1	36	.	0			c.G526A						.						122	113	116					8																	75274160		2203	4300	6503	SO:0001583	missense	54332	exon4			CTTGCTGAAGAAA		CCDS34911.1, CCDS47877.1	8q13.3	2014-09-17	2012-02-09						15968	protein-coding gene	gene with protein product		606598	"Charcot-Marie-Tooth neuropathy 4A"	CMT4A		8268915, 11743579	Standard	NM_018972		Approved	CMT4	uc003yah.3	Q8TB36		ENST00000220822.7:c.526G>A	chr8.hg19:g.75274160G>A	ENSP00000220822:p.Glu176Lys	99.0	0.0		105.0	22.0	NM_018972	A8K957|E7FJF3|E7FJF4	Missense_Mutation	SNP	ENST00000220822.7	hg19	CCDS34911.1	.	.	.	.	.	.	.	.	.	.	G	14.99	2.699585	0.48307	.	.	ENSG00000104381	ENST00000220822;ENST00000434412	D;D	0.99032	-5.34;-5.35	5.27	4.36	0.52297	Glutathione S-transferase/chloride channel, C-terminal (1);	0.117788	0.56097	D	0.000029	D	0.96577	0.8883	N	0.20986	0.625	0.33581	D	0.599901	B	0.12630	0.006	B	0.25759	0.063	D	0.96035	0.9020	10	0.24483	T	0.36	-7.7737	15.9536	0.79861	0.0:0.2176:0.7824:0.0	.	176	Q8TB36	GDAP1_HUMAN	K	176;108	ENSP00000220822:E176K;ENSP00000417006:E108K	ENSP00000220822:E176K	E	+	1	0	GDAP1	75436715	0.993000	0.37304	1.000000	0.80357	0.998000	0.95712	2.481000	0.45215	2.758000	0.94735	0.561000	0.74099	GAA	.	.		0.373	GDAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379061.1	NM_018972		A	75274160	G	A	75274160	3	1	371	1	0	0	0	0	1	0	0	0	6315	1291	45	3	540	3	GDAP1	8	75274160	Missense_Mutation	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10	40884	75274160	71089862	57	51349										
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110420351	110420351	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	gatattacagaacaaaccaaAggaaaacccaacttggagac	7	9	0	2			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr8:110420351A>G	ENST00000378402.5	+	18	1991	c.1887A>G	c.(1885-1887)aaA>aaG	p.K629K		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	629					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			AACAAACCAAAGGAAAACCCA	0.408										HNSCC(38;0.096)																											p.K629K		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.A1887G						.						119	118	118					8																	110420351		1912	4123	6035	SO:0001819	synonymous_variant	93035	exon18			AACCAAAGGAAAA	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.1887A>G	chr8.hg19:g.110420351A>G		119.0	0.0		108.0	21.0	NM_177531	Q567P2|Q9UF27	Silent	SNP	ENST00000378402.5	hg19	CCDS47911.1																																																																																			.	.		0.408	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		G	110420351	A	G	110420351	2	3	371	1	0	0	0	0	0	0	0	1	11981	69	3	2		2	PKHD1L1	8	110420351	Silent	SNP	A	TCGA-ZS-A9CE-01A-11D-A36X-10	35146191	110420351	35943671	58	51350										
MELK	9833	hgsc.bcm.edu	37	chr9	36643018	36643018	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	ttcacctcgatgatgattgcGtaacagaactttctgtacat	7	9	2	3	rs374744271		TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr9:36643018G>A	ENST00000298048.2	+	11	1043	c.859G>A	c.(859-861)Gta>Ata	p.V287I	MELK_ENST00000536860.1_Missense_Mutation_p.V239I|MELK_ENST00000545008.1_Missense_Mutation_p.V216I|MELK_ENST00000538311.1_Missense_Mutation_p.V93I|MELK_ENST00000536329.1_Missense_Mutation_p.V216I|MELK_ENST00000541717.1_Missense_Mutation_p.V287I|MELK_ENST00000536987.1_Missense_Mutation_p.V156I|MELK_ENST00000543751.1_Missense_Mutation_p.V255I	NM_014791.3	NP_055606.1	Q14680	MELK_HUMAN	maternal embryonic leucine zipper kinase	287	UBA-like.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|hemopoiesis (GO:0030097)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|neural precursor cell proliferation (GO:0061351)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)	cell cortex (GO:0005938)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)	29		Acute lymphoblastic leukemia(2;1.09e-08)|all_hematologic(2;8.15e-06)	STAD - Stomach adenocarcinoma(86;0.228)			TGATGATTGCGTAACAGAACT	0.338																																					p.V287I	Ovarian(82;980 1317 7225 14391 18624)	Atlas-SNP	.											.	MELK	74	.	0			c.G859A						.						90	84	86					9																	36643018		2203	4300	6503	SO:0001583	missense	9833	exon11			GATTGCGTAACAG	D79997	CCDS6606.1, CCDS59123.1, CCDS59124.1, CCDS59125.1, CCDS59126.1, CCDS59127.1, CCDS59128.1	9p13.1	2008-02-05			ENSG00000165304	ENSG00000165304			16870	protein-coding gene	gene with protein product		607025				8724849, 9136115	Standard	NM_001256689		Approved	KIAA0175	uc003zzn.4	Q14680	OTTHUMG00000019906	ENST00000298048.2:c.859G>A	chr9.hg19:g.36643018G>A	ENSP00000298048:p.Val287Ile	390.0	0.0		444.0	180.0	NM_014791	A6P3A7|A6P3A8|B1AMQ6|B7Z1E6|B7Z5M5|B7Z6Q7|B7Z6R8|B7Z6Y0|B7Z7Q1|D3DRP8|F5H0Y0|F5H2R4|F5H689|Q7L3C3	Missense_Mutation	SNP	ENST00000298048.2	hg19	CCDS6606.1	.	.	.	.	.	.	.	.	.	.	G	8.088	0.773782	0.16051	.	.	ENSG00000165304	ENST00000298048;ENST00000538311;ENST00000536987;ENST00000545008;ENST00000536860;ENST00000536329;ENST00000541717;ENST00000543751	T;T;T;T;T;T;T;T	0.24908	1.85;2.08;1.83;1.85;1.85;1.85;1.85;1.85	5.46	-3.5	0.04710	Protein kinase-like domain (1);	0.482604	0.24274	N	0.039965	T	0.11707	0.0285	L	0.27053	0.805	0.27893	N	0.939243	B;B;B;B;B;B;B	0.12013	0.0;0.004;0.0;0.001;0.005;0.002;0.0	B;B;B;B;B;B;B	0.13407	0.002;0.009;0.002;0.003;0.005;0.002;0.001	T	0.37686	-0.9695	10	0.09843	T	0.71	-0.1289	7.6197	0.28179	0.5406:0.0:0.3482:0.1112	.	207;216;239;287;216;255;287	B7Z1G6;F5H2R4;F5H0Y0;F5H689;A6P3A8;A6P3A7;Q14680	.;.;.;.;.;.;MELK_HUMAN	I	287;93;156;216;239;216;287;255	ENSP00000298048:V287I;ENSP00000438226:V93I;ENSP00000439184:V156I;ENSP00000445452:V216I;ENSP00000439792:V239I;ENSP00000443550:V216I;ENSP00000437804:V287I;ENSP00000441596:V255I	ENSP00000298048:V287I	V	+	1	0	MELK	36633018	0.001000	0.12720	0.344000	0.25628	0.984000	0.73092	-0.551000	0.06027	-0.836000	0.04229	-0.133000	0.14855	GTA	.	.		0.338	MELK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052428.3	NM_014791		A	36643018	G	A	36643018	3	1	371	1	0	0	0	0	1	0	0	0	9479	1145	40	1	897	1	MELK	9	36643018	Missense_Mutation	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10		36643018	104570413	59	51351										
SPTAN1	6709	hgsc.bcm.edu	37	chr9	131329101	131329101	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	aggtcctagaccgataccacCgcttcaaggaactctcaacc	7	15	2	1			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr9:131329101C>T	ENST00000372731.4	+	2	192	c.82C>T	c.(82-84)Cgc>Tgc	p.R28C	SPTAN1_ENST00000358161.5_Missense_Mutation_p.R28C|SPTAN1_ENST00000372739.3_Missense_Mutation_p.R28C	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	28					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						CCGATACCACCGCTTCAAGGA	0.488																																					p.R28C	NSCLC(120;833 1744 2558 35612 37579)	Atlas-SNP	.											.	SPTAN1	266	.	0			c.C82T						.						106	105	105					9																	131329101		2203	4300	6503	SO:0001583	missense	6709	exon2			TACCACCGCTTCA	M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"EF-hand domain containing"	11273	protein-coding gene	gene with protein product	"alpha-fodrin"	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.82C>T	chr9.hg19:g.131329101C>T	ENSP00000361816:p.Arg28Cys	153.0	0.0		177.0	76.0	NM_003127	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Missense_Mutation	SNP	ENST00000372731.4	hg19	CCDS6905.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.625175	0.87560	.	.	ENSG00000197694	ENST00000358161;ENST00000372731;ENST00000372739;ENST00000372719	T;T;T	0.36520	1.25;1.25;1.25	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.59183	0.2175	M	0.72479	2.2	0.80722	D	1	D;D;D;D;D	0.89917	0.999;1.0;0.998;1.0;0.999	P;D;P;D;D	0.77004	0.898;0.989;0.88;0.978;0.922	T	0.60347	-0.7281	10	0.72032	D	0.01	.	14.5719	0.68218	0.1549:0.8451:0.0:0.0	.	28;28;28;28;28	A6NG51;B4DTV8;Q13813-3;Q13813-2;Q13813	.;.;.;.;SPTA2_HUMAN	C	28	ENSP00000350882:R28C;ENSP00000361816:R28C;ENSP00000361824:R28C	ENSP00000350882:R28C	R	+	1	0	SPTAN1	130368922	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.801000	0.69115	2.829000	0.97493	0.655000	0.94253	CGC	.	.		0.488	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127		T	131329101	C	T	131329101	3	4	371	1	0	0	0	0	1	0	0	0	15132	652	23	1	84	1	SPTAN1	9	131329101	Missense_Mutation	SNP	C	TCGA-ZS-A9CE-01A-11D-A36X-10	94686083	131329101	9884330	60	51352										
LARP4B	23185	hgsc.bcm.edu	37	chr10	860959	860959	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	agaagccggcaccgagggctCtctggagaccactacaggaa	13	12	1	2			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr10:860959C>T	ENST00000316157.3	-	15	1787	c.1747G>A	c.(1747-1749)Gag>Aag	p.E583K	LARP4B_ENST00000469487.1_5'UTR	NM_015155.1	NP_055970.1	Q92615	LAR4B_HUMAN	La ribonucleoprotein domain family, member 4B	583					positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(2)|skin(2)|urinary_tract(2)	38						ACCGAGGGCTCTCTGGAGACC	0.572																																					p.E583K		Atlas-SNP	.											.	LARP4B	110	.	0			c.G1747A						.						87	81	83					10																	860959		2203	4300	6503	SO:0001583	missense	23185	exon16			AGGGCTCTCTGGA	D86971	CCDS31131.1	10p15.3	2011-08-24	2009-06-09	2009-06-09	ENSG00000107929	ENSG00000107929		"La ribonucleoprotein domain containing"	28987	protein-coding gene	gene with protein product			"KIAA0217", "La ribonucleoprotein domain family, member 5"	KIAA0217, LARP5		9039502, 20573744	Standard	NM_015155		Approved		uc031ptb.1	Q92615	OTTHUMG00000017534	ENST00000316157.3:c.1747G>A	chr10.hg19:g.860959C>T	ENSP00000326128:p.Glu583Lys	51.0	0.0		56.0	10.0	NM_015155	A7MD20|Q5T3R3|Q5T3R4|Q5T3R5|Q68CY4	Missense_Mutation	SNP	ENST00000316157.3	hg19	CCDS31131.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.4|20.4	3.986474|3.986474	0.74589|0.74589	.|.	.|.	ENSG00000107929|ENSG00000107929	ENST00000316157|ENST00000448368	T|T	0.32272|0.40225	1.46|1.04	5.85|5.85	5.85|5.85	0.93711|0.93711	.|.	0.100150|.	0.64402|.	D|.	0.000003|.	T|T	0.46347|0.46347	0.1388|0.1388	L|L	0.34521|0.34521	1.04|1.04	0.58432|0.58432	D|D	0.999998|0.999998	P|.	0.48294|.	0.908|.	B|.	0.43950|.	0.437|.	T|T	0.13202|0.13202	-1.0518|-1.0518	10|6	0.36615|.	T|.	0.2|.	-5.2101|-5.2101	17.945|17.945	0.89036|0.89036	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	583|.	Q92615|.	LAR4B_HUMAN|.	K|K	583|148	ENSP00000326128:E583K|ENSP00000394545:R148K	ENSP00000326128:E583K|.	E|R	-|-	1|2	0|0	LARP4B|LARP4B	850959|850959	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.112000|0.112000	0.19704|0.19704	4.867000|4.867000	0.63013|0.63013	2.773000|2.773000	0.95371|0.95371	0.609000|0.609000	0.83330|0.83330	GAG|AGA	.	.		0.572	LARP4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046395.2	NM_015155		T	860959	C	T	860959	3	4	371	1	0	0	0	0	1	0	0	0	8640	922	32	3	481	3	LARP4B	10	860959	Missense_Mutation	SNP	C	TCGA-ZS-A9CE-01A-11D-A36X-10		860959	134673788	61	51353										
DDX50	79009	hgsc.bcm.edu	37	chr10	70706321	70706321	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	gctcaggaagtcgacaagatGgtagaagacgaagtgggaat	15	5	1	3			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr10:70706321G>T	ENST00000373585.3	+	15	2256	c.2149G>T	c.(2149-2151)Ggt>Tgt	p.G717C		NM_024045.1	NP_076950.1	Q9BQ39	DDX50_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 50	717	Arg-rich.					membrane (GO:0016020)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	29						TCGACAAGATGGTAGAAGACG	0.522																																					p.G717C		Atlas-SNP	.											.	DDX50	65	.	0			c.G2149T						.						78	79	79					10																	70706321		2203	4300	6503	SO:0001583	missense	79009	exon15			CAAGATGGTAGAA	AF334103	CCDS7283.1	10q22.2	2010-09-30			ENSG00000107625	ENSG00000107625		"DEAD-boxes"	17906	protein-coding gene	gene with protein product		610373				11891046	Standard	NM_024045		Approved	GU2, MGC3199, GUB, RH-II/GuB	uc001jou.3	Q9BQ39	OTTHUMG00000018362	ENST00000373585.3:c.2149G>T	chr10.hg19:g.70706321G>T	ENSP00000362687:p.Gly717Cys	97.0	0.0		73.0	19.0	NM_024045	Q5VX37|Q8WV76|Q9BWI8	Missense_Mutation	SNP	ENST00000373585.3	hg19	CCDS7283.1	.	.	.	.	.	.	.	.	.	.	G	14.40	2.523119	0.44866	.	.	ENSG00000107625	ENST00000373585;ENST00000541832	T	0.21734	1.99	4.93	2.91	0.33838	.	0.758008	0.12998	N	0.421861	T	0.13586	0.0329	N	0.08118	0	0.43283	D	0.995258	D	0.59767	0.986	P	0.48368	0.575	T	0.06499	-1.0823	10	0.48119	T	0.1	-7.767	7.3991	0.26954	0.2091:0.0:0.7909:0.0	.	717	Q9BQ39	DDX50_HUMAN	C	717;691	ENSP00000362687:G717C	ENSP00000362687:G717C	G	+	1	0	DDX50	70376327	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	2.841000	0.48223	1.107000	0.41642	0.467000	0.42956	GGT	.	.		0.522	DDX50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048363.1	NM_024045		T	70706321	G	T	70706321	3	4	371	1	0	0	0	0	1	0	0	0	4370	1348	47	3	2207	3	DDX50	10	70706321	Missense_Mutation	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10	69845362	70706321	64828426	62	51354										
MRPS16	51021	hgsc.bcm.edu	37	chr10	75010634	75010634	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	gtttctgtagcctctgtatcTgtagcttctgcatctgtttt	8	9	5	0			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr10:75010634T>C	ENST00000372945.3	-	3	600	c.390A>G	c.(388-390)acA>acG	p.T130T	MRPS16_ENST00000416782.2_Intron|MRPS16_ENST00000479005.1_5'UTR|DNAJC9-AS1_ENST00000513954.1_RNA|MRPS16_ENST00000372940.3_Intron|RP11-152N13.5_ENST00000457758.1_RNA|TTC18_ENST00000493787.1_5'Flank|DNAJC9-AS1_ENST00000440197.2_RNA|RP11-152N13.5_ENST00000457147.1_RNA|RP11-152N13.5_ENST00000394864.2_RNA|DNAJC9_ENST00000372950.4_5'Flank	NM_016065.3	NP_057149.1	Q9Y3D3	RT16_HUMAN	mitochondrial ribosomal protein S16	130					translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)	structural constituent of ribosome (GO:0003735)			large_intestine(2)|lung(2)	4	Prostate(51;0.0119)					CCTCTGTATCTGTAGCTTCTG	0.443																																					p.T130T		Atlas-SNP	.											.	MRPS16	12	.	0			c.A390G						.						209	188	195					10																	75010634		2203	4300	6503	SO:0001819	synonymous_variant	51021	exon3			TGTATCTGTAGCT	AB051351	CCDS7323.1	10q22.1	2012-09-13			ENSG00000182180	ENSG00000182180		"Mitochondrial ribosomal proteins / small subunits"	14048	protein-coding gene	gene with protein product		609204				10810093	Standard	NM_016065		Approved	CGI-132	uc001jts.1	Q9Y3D3	OTTHUMG00000018454	ENST00000372945.3:c.390A>G	chr10.hg19:g.75010634T>C		34.0	0.0		30.0	14.0	NM_016065	B4E032|Q96Q60	Silent	SNP	ENST00000372945.3	hg19	CCDS7323.1																																																																																			.	.		0.443	MRPS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048616.1			C	75010634	T	C	75010634	2	2	371	1	0	0	0	0	0	0	0	1	9835	1567	55	2		2	MRPS16	10	75010634	Silent	SNP	T	TCGA-ZS-A9CE-01A-11D-A36X-10	4304313	75010634	60524113	63	51355										
CCDC147	159686	hgsc.bcm.edu	37	chr10	106153114	106153120	+	Frame_Shift_Del	DEL	TTAAAGA	TTAAAGA	-													0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	taacagatatgaagagaaagTtaaagattatgatccatcag					rs371289437		TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	TTAAAGA	TTAAAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr10:106153114_106153120delTTAAAGA	ENST00000369704.3	+	11	1689_1695	c.1555_1561delTTAAAGA	c.(1555-1563)ttaaagattfs	p.LKI519fs		NM_001008723.1	NP_001008723.1	Q5T655	CC147_HUMAN		519						extracellular space (GO:0005615)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	52		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;7.55e-10)|all cancers(201;3.37e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0189)		GAAGAGAAAGTTAAAGATTATGATCCA	0.372																																					p.518_520del		Atlas-INDEL	.											.	CCDC147	137	.	0			c.1554_1560del						.																																			SO:0001589	frameshift_variant	159686	exon11			.																												ENST00000369704.3:c.1555_1561delTTAAAGA	chr10.hg19:g.106153114_106153120delTTAAAGA	ENSP00000358718:p.Leu519fs	198.0	0.0		174.0	29.0	NM_001008723	D3DRA6|Q8NA27	Frame_Shift_Del	DEL	ENST00000369704.3	hg19	CCDS31282.1																																																																																			.	.		0.372	CCDC147-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050216.1			-	106153120	TTAAAGA	-	106153114	7	5	371	1	0	1	0	1	0	0	0	0	2783	1722	60	0	1597	0	CCDC147	10	106153114	Frame_Shift_Del	DEL	TTAAAGA	TCGA-ZS-A9CE-01A-11D-A36X-10	31142480	106153114	29381633	64	51356										
FAM175B	23172	hgsc.bcm.edu	37	chr10	126523308	126523319	+	In_Frame_Del	DEL	CTTCCAATTATG	CTTCCAATTATG	-													0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	tcgacctcaagctgtgggctCttccaattatgcttccacca					rs142891578		TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	CTTCCAATTATG	CTTCCAATTATG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr10:126523308_126523319delCTTCCAATTATG	ENST00000298492.5	+	9	1061_1072	c.1016_1027delCTTCCAATTATG	c.(1015-1029)tcttccaattatgct>tct	p.SNYA340del		NM_032182.3	NP_115558.3	Q15018	F175B_HUMAN	family with sequence similarity 175, member B	340					cellular response to freezing (GO:0071497)	BRISC complex (GO:0070552)|cytoplasm (GO:0005737)	polyubiquitin binding (GO:0031593)			NS(1)	1						GCTGTGGGCTCTTCCAATTATGCTTCCACCAG	0.514																																					p.339_342del		Atlas-INDEL	.											.	FAM175B	39	.	0			c.1015_1026del						.																																			SO:0001651	inframe_deletion	23172	exon9			.	D63877	CCDS31308.2	10q26.2	2013-01-24	2008-07-02	2008-07-02	ENSG00000165660	ENSG00000165660			28975	protein-coding gene	gene with protein product	"Abraxas brother"	611144	"KIAA0157"	KIAA0157		8590280	Standard	NM_032182		Approved	Em:AC068896.4, ABRO1	uc001lib.4	Q15018	OTTHUMG00000019218	ENST00000298492.5:c.1016_1027delCTTCCAATTATG	chr10.hg19:g.126523308_126523319delCTTCCAATTATG	ENSP00000298492:p.Ser340_Ala343del	115.0	0.0		125.0	30.0	NM_032182	B4DKR2|Q96H11	In_Frame_Del	DEL	ENST00000298492.5	hg19	CCDS31308.2																																																																																			.	.		0.514	FAM175B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050891.2	NM_032182		-	126523319	CTTCCAATTATG	-	126523308	7	5	371	1	0	1	0	1	0	0	0	0	5503	913	32	0	1050	0	FAM175B	10	126523308	In_Frame_Del	DEL	CTTCCAATTATG	TCGA-ZS-A9CE-01A-11D-A36X-10	20370194	126523308	9011439	65	51357										
IFITM3	10410	hgsc.bcm.edu	37	chr11	320637	320637	+	Frame_Shift_Del	DEL	G	G	-													0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	agggtgttgaacagggaccaGacgacatggtcgggcacgga							TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr11:320637delG	ENST00000399808.4	-	1	413	c.177delC	c.(175-177)gtcfs	p.V59fs	RP11-326C3.10_ENST00000534271.1_RNA|RP11-326C3.14_ENST00000602809.1_lincRNA|RP11-326C3.11_ENST00000602756.1_RNA|IFITM3_ENST00000602735.1_Frame_Shift_Del_p.V38fs|RP11-326C3.11_ENST00000508004.2_RNA|RP11-326C3.11_ENST00000602429.1_RNA|IFITM3_ENST00000526811.1_Frame_Shift_Del_p.V38fs	NM_021034.2	NP_066362.2	Q01628	IFM3_HUMAN	interferon induced transmembrane protein 3	59					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|immune response (GO:0006955)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral genome replication (GO:0045071)|negative regulation of viral transcription (GO:0032897)|response to interferon-alpha (GO:0035455)|response to interferon-beta (GO:0035456)|response to interferon-gamma (GO:0034341)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)				central_nervous_system(7)|endometrium(7)|kidney(2)|large_intestine(1)|lung(1)	18		all_cancers(49;2e-09)|all_epithelial(84;3.36e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;8.85e-28)|Epithelial(43;5.52e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		ACAGGGACCAGACGACATGGT	0.632																																					p.W60fs		Atlas-INDEL	.											.	IFITM3	132	.	0			c.178delT						.						95	100	98					11																	320637		2087	4198	6285	SO:0001589	frameshift_variant	10410	exon1			.	X57352	CCDS41585.1	11p15.5	2011-05-24	2011-05-24		ENSG00000142089	ENSG00000142089			5414	protein-coding gene	gene with protein product		605579	"interferon induced transmembrane protein 3 (1-8U)"			1906403, 16326387	Standard	NM_021034		Approved	1-8U	uc001lpa.2	Q01628		ENST00000399808.4:c.177delC	chr11.hg19:g.320637delG	ENSP00000382707:p.Val59fs	53.0	0.0		78.0	28.0	NM_021034	Q53Y76|Q96HK8|Q96J15	Frame_Shift_Del	DEL	ENST00000399808.4	hg19	CCDS41585.1																																																																																			.	.		0.632	IFITM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384765.1	NM_021034		-	320637	G	-	320637	7	5	371	1	0	1	0	1	0	0	0	0	7537	929	33	0	232	0	IFITM3	11	320637	Frame_Shift_Del	DEL	G	TCGA-ZS-A9CE-01A-11D-A36X-10		320637	134685879	66	51358										
C11orf41	25758	hgsc.bcm.edu	37	chr11	33682552	33682552	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	atgagctcccgagccagtggGcagattcggtgagacccttg	14	11	0	3			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr11:33682552G>A	ENST00000321505.4	+	19	5440	c.5260G>A	c.(5260-5262)Gca>Aca	p.A1754T	KIAA1549L_ENST00000389726.3_Missense_Mutation_p.A1760T			Q6ZVL6	K154L_HUMAN	KIAA1549-like	1754						integral component of membrane (GO:0016021)											GAGCCAGTGGGCAGATTCGGT	0.483																																					p.A1754T		Atlas-SNP	.											.	.	.	.	0			c.G5260A						.						27	31	30					11																	33682552		1912	4125	6037	SO:0001583	missense	25758	exon19			CAGTGGGCAGATT	U10991	CCDS44565.1, CCDS44565.2	11p13	2012-08-09	2012-08-09	2012-08-09	ENSG00000110427	ENSG00000110427			24836	protein-coding gene	gene with protein product		612297	"chromosome 11 open reading frame 69", "chromosome 11 open reading frame 41"	C11orf69, C11orf41			Standard	NM_012194		Approved	G2, MGC34830	uc021qfs.1	Q6ZVL6	OTTHUMG00000150410	ENST00000321505.4:c.5260G>A	chr11.hg19:g.33682552G>A	ENSP00000315295:p.Ala1754Thr	56.0	0.0		86.0	16.0	NM_012194	B0QYU0	Missense_Mutation	SNP	ENST00000321505.4	hg19	CCDS44565.2	.	.	.	.	.	.	.	.	.	.	G	23.4	4.416191	0.83449	.	.	ENSG00000110427	ENST00000321505;ENST00000389726;ENST00000536568	.	.	.	4.97	4.97	0.65823	.	0.000000	0.56097	D	0.000021	T	0.46814	0.1412	L	0.27053	0.805	0.43029	D	0.99459	D	0.62365	0.991	P	0.50192	0.634	T	0.47548	-0.9109	9	0.49607	T	0.09	-12.8074	10.9809	0.47494	0.0862:0.0:0.9138:0.0	.	1760	E9PAT2	.	T	1754;1760;1593	.	ENSP00000315295:A1754T	A	+	1	0	C11orf41	33639128	1.000000	0.71417	0.998000	0.56505	0.971000	0.66376	6.211000	0.72182	2.308000	0.77769	0.491000	0.48974	GCA	.	.		0.483	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194		A	33682552	G	A	33682552	3	1	371	1	0	0	0	0	1	0	0	0	1642	1203	42	3	5352	3	C11orf41	11	33682552	Missense_Mutation	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10	33361915	33682552	101323964	67	51359										
VWF	7450	hgsc.bcm.edu	37	chr12	6230347	6230347	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	gcccagaactcaccaataatCgagaaggagcgtttctggca	10	11	2	2			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr12:6230347C>T	ENST00000261405.5	-	3	467	c.213G>A	c.(211-213)tcG>tcA	p.S71S	VWF_ENST00000572068.1_Silent_p.S108S|VWF_ENST00000545906.1_5'Flank	NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	71	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	CACCAATAATCGAGAAGGAGC	0.567																																					p.S71S		Atlas-SNP	.											.	VWF	338	.	0			c.G213A						.						62	61	61					12																	6230347		2203	4300	6503	SO:0001819	synonymous_variant	7450	exon3			AATAATCGAGAAG		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"Endogenous ligands"	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.213G>A	chr12.hg19:g.6230347C>T		72.0	0.0		95.0	35.0	NM_000552	Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	hg19	CCDS8539.1																																																																																			.	.		0.567	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		T	6230347	C	T	6230347	2	4	371	1	0	0	0	0	0	0	0	1	17261	871	31	1		1	VWF	12	6230347	Silent	SNP	C	TCGA-ZS-A9CE-01A-11D-A36X-10		6230347	127621548	68	51360										
KCNJ8	3764	hgsc.bcm.edu	37	chr12	21918723	21918740	+	In_Frame_Del	DEL	AGAATTGTTCCTTCGGAT	AGAATTGTTCCTTCGGAT	-													0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	acctttggtaccatgagggaAgaattgttccttcggataga					rs142014286		TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	AGAATTGTTCCTTCGGAT	AGAATTGTTCCTTCGGAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr12:21918723_21918740delAGAATTGTTCCTTCGGAT	ENST00000240662.2	-	3	1537_1554	c.1192_1209delATCCGAAGGAACAATTCT	c.(1192-1209)atccgaaggaacaattctdel	p.IRRNNS398del	RP11-59N23.1_ENST00000542489.1_RNA	NM_004982.3	NP_004973.1	Q15842	KCNJ8_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 8	398					defense response to virus (GO:0051607)|heart development (GO:0007507)|kidney development (GO:0001822)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|response to exogenous dsRNA (GO:0043330)|response to lipopolysaccharide (GO:0032496)|response to pH (GO:0009268)|synaptic transmission (GO:0007268)|vasodilation (GO:0042311)	ATP-sensitive potassium channel complex (GO:0008282)|mitochondrion (GO:0005739)|myofibril (GO:0030016)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATP-activated inward rectifier potassium channel activity (GO:0015272)|inward rectifier potassium channel activity (GO:0005242)	p.R399*(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	28					Gliquidone(DB01251)|Glisoxepide(DB01289)|Glyburide(DB01016)|Levosimendan(DB00922)|Phenformin(DB00914)|Thiamylal(DB01154)|Yohimbine(DB01392)	CCATGAGGGAAGAATTGTTCCTTCGGATAGAATTGTTC	0.413																																					p.398_404del		Atlas-INDEL	.											.	KCNJ8	59	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.1193_1210del						.																																			SO:0001651	inframe_deletion	3764	exon3			.	BC000544	CCDS8692.1	12p12.1	2011-07-05			ENSG00000121361	ENSG00000121361		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6269	protein-coding gene	gene with protein product		600935				8595887, 16382105	Standard	NM_004982		Approved	Kir6.1	uc001rff.4	Q15842	OTTHUMG00000169093	ENST00000240662.2:c.1192_1209delATCCGAAGGAACAATTCT	chr12.hg19:g.21918723_21918740delAGAATTGTTCCTTCGGAT	ENSP00000240662:p.Ile398_Ser403del	105.0	0.0		115.0	21.0	NM_004982	O00657	In_Frame_Del	DEL	ENST00000240662.2	hg19	CCDS8692.1																																																																																			.	.		0.413	KCNJ8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402226.1	NM_004982		-	21918740	AGAATTGTTCCTTCGGAT	-	21918723	7	5	371	1	0	1	0	1	0	0	0	0	8065	59	3	0	69	0	KCNJ8	12	21918723	In_Frame_Del	DEL	AGAATTGTTCCTTCGGAT	TCGA-ZS-A9CE-01A-11D-A36X-10	15688376	21918723	111933172	69	51361										
KRT6A	3853	hgsc.bcm.edu	37	chr12	52885513	52885513	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	ccttgttctgctgctccaggAaccgcacctgaaagagagac	10	13	1	3			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr12:52885513A>G	ENST00000330722.6	-	2	616	c.548T>C	c.(547-549)tTc>tCc	p.F183S		NM_005554.3	NP_005545.1	P02538	K2C6A_HUMAN	keratin 6A	183	Coil 1A.|Rod.				cell differentiation (GO:0030154)|positive regulation of cell proliferation (GO:0008284)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	39				BRCA - Breast invasive adenocarcinoma(357;0.189)		CTGCTCCAGGAACCGCACCTG	0.542																																					p.F183S		Atlas-SNP	.											.	KRT6A	89	.	0			c.T548C						.						52	52	52					12																	52885513		2203	4300	6503	SO:0001583	missense	3853	exon2			TCCAGGAACCGCA	BC014152, L42593, L42610	CCDS41786.1	12q13.13	2013-01-16			ENSG00000205420	ENSG00000205420		"-", "Intermediate filaments type II, keratins (basic)"	6443	protein-coding gene	gene with protein product		148041	"keratin 6C", "keratin 6D"	KRT6C, KRT6D		1713141, 16831889	Standard	NM_005554		Approved	CK6C, K6C, CK6D, K6D	uc001sam.3	P02538	OTTHUMG00000169597	ENST00000330722.6:c.548T>C	chr12.hg19:g.52885513A>G	ENSP00000369317:p.Phe183Ser	88.0	0.0		128.0	23.0	NM_005554	A4QPC1|P48667|Q08AR4|Q6NT67|Q96CL4	Missense_Mutation	SNP	ENST00000330722.6	hg19	CCDS41786.1	.	.	.	.	.	.	.	.	.	.	a	27.4	4.824552	0.90955	.	.	ENSG00000205420	ENST00000330722;ENST00000452121	T	0.70282	-0.47	5.26	5.26	0.73747	Filament (1);	0.000000	0.64402	D	0.000011	D	0.85401	0.5688	M	0.87827	2.91	0.58432	D	0.999994	D	0.71674	0.998	D	0.69479	0.964	D	0.88313	0.2957	10	0.87932	D	0	.	15.478	0.75501	1.0:0.0:0.0:0.0	.	183	P02538	K2C6A_HUMAN	S	183;139	ENSP00000369317:F183S	ENSP00000369317:F183S	F	-	2	0	KRT6A	51171780	1.000000	0.71417	0.998000	0.56505	0.964000	0.63967	9.139000	0.94554	2.116000	0.64780	0.459000	0.35465	TTC	.	.		0.542	KRT6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404978.2	NM_005554		G	52885513	A	G	52885513	3	3	371	1	0	0	0	0	1	0	0	0	8489	246	9	2	1178	2	KRT6A	12	52885513	Missense_Mutation	SNP	A	TCGA-ZS-A9CE-01A-11D-A36X-10	30966790	52885513	80966382	70	51362										
OR6C65	403282	hgsc.bcm.edu	37	chr12	55794617	55794617	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	catggcccaagtatttttttTaattcttttgggatcaacag	7	7	2	0			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr12:55794617T>C	ENST00000379665.2	+	1	404	c.305T>C	c.(304-306)tTa>tCa	p.L102S		NM_001005518.1	NP_001005518.1	A6NJZ3	O6C65_HUMAN	olfactory receptor, family 6, subfamily C, member 65	102						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|large_intestine(3)|lung(9)	15						GTATTTTTTTTAATTCTTTTG	0.363																																					p.L102S		Atlas-SNP	.											.	OR6C65	44	.	0			c.T305C						.						79	86	84					12																	55794617		2203	4300	6503	SO:0001583	missense	403282	exon1			TTTTTTTAATTCT		CCDS31821.1	12q13.2	2013-09-23			ENSG00000205328	ENSG00000205328		"GPCR / Class A : Olfactory receptors"	31295	protein-coding gene	gene with protein product							Standard	NM_001005518		Approved		uc010spl.2	A6NJZ3	OTTHUMG00000169955	ENST00000379665.2:c.305T>C	chr12.hg19:g.55794617T>C	ENSP00000368986:p.Leu102Ser	74.0	0.0		88.0	40.0	NM_001005518	B2RNH9	Missense_Mutation	SNP	ENST00000379665.2	hg19	CCDS31821.1	.	.	.	.	.	.	.	.	.	.	T	1.469	-0.560334	0.03939	.	.	ENSG00000205328	ENST00000379665	T	0.00498	6.97	3.56	0.865	0.19074	GPCR, rhodopsin-like superfamily (1);	0.578922	0.12857	U	0.433443	T	0.00328	0.0010	N	0.16368	0.405	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.40194	-0.9576	10	0.45353	T	0.12	.	8.2769	0.31877	0.1302:0.0:0.1326:0.7372	.	102	A6NJZ3	O6C65_HUMAN	S	102	ENSP00000368986:L102S	ENSP00000368986:L102S	L	+	2	0	OR6C65	54080884	0.000000	0.05858	0.103000	0.21229	0.275000	0.26752	0.111000	0.15458	0.097000	0.17492	-2.434000	0.00213	TTA	.	.		0.363	OR6C65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406674.1			C	55794617	T	C	55794617	3	2	371	1	0	0	0	0	1	0	0	0	11204	1764	61	2	307	2	OR6C65	12	55794617	Missense_Mutation	SNP	T	TCGA-ZS-A9CE-01A-11D-A36X-10	2909104	55794617	78057278	71	51363										
METAP2	10988	hgsc.bcm.edu	37	chr12	95867968	95867968	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	cgggcaacatggcgggtgtgGaggaggtagcggcctccggg	21	9	0	0			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr12:95867968G>A	ENST00000323666.5	+	1	242	c.13G>A	c.(13-15)Gag>Aag	p.E5K	METAP2_ENST00000546753.1_Missense_Mutation_p.E5K|METAP2_ENST00000261220.9_Missense_Mutation_p.E5K|METAP2_ENST00000551840.1_Missense_Mutation_p.E5K|METAP2_ENST00000550777.1_Missense_Mutation_p.E5K	NM_006838.3	NP_006829.1			methionyl aminopeptidase 2											endometrium(3)|large_intestine(2)|lung(7)|prostate(1)	13						GGCGGGTGTGGAGGAGGTAGC	0.642																																					p.E5K		Atlas-SNP	.											.	METAP2	28	.	0			c.G13A						.						33	41	38					12																	95867968		2203	4299	6502	SO:0001583	missense	10988	exon1			GGTGTGGAGGAGG	U13261	CCDS9052.1	12q22	2014-09-04			ENSG00000111142		3.4.11.18		16672	protein-coding gene	gene with protein product	"Peptidase M"	601870				7644482, 8858118	Standard	NM_006838		Approved	MNPEP, p67, MAP2	uc001tec.3	P50579	OTTHUMG00000170280	ENST00000323666.5:c.13G>A	chr12.hg19:g.95867968G>A	ENSP00000325312:p.Glu5Lys	186.0	0.0		196.0	80.0	NM_006838		Missense_Mutation	SNP	ENST00000323666.5	hg19	CCDS9052.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.113422	0.77210	.	.	ENSG00000111142	ENST00000323666;ENST00000546753;ENST00000261220;ENST00000549502;ENST00000553151;ENST00000550777;ENST00000551840	.	.	.	5.19	5.19	0.71726	.	0.616940	0.15964	N	0.236096	T	0.52709	0.1751	N	0.08118	0	0.38205	D	0.940312	B;B;B;D;B	0.56035	0.005;0.149;0.116;0.974;0.079	B;B;B;D;B	0.67725	0.006;0.08;0.031;0.953;0.043	T	0.60052	-0.7338	9	0.46703	T	0.11	1.1894	14.6031	0.68456	0.0:0.0:1.0:0.0	.	5;5;5;5;5	B4DUX5;F8VRR3;G3XA91;F8VQZ7;P50579	.;.;.;.;AMPM2_HUMAN	K	5	.	ENSP00000261220:E5K	E	+	1	0	METAP2	94392099	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	3.102000	0.50291	2.583000	0.87209	0.561000	0.74099	GAG	.	.		0.642	METAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408296.1	NM_006838		A	95867968	G	A	95867968	3	1	371	1	0	0	0	0	1	0	0	0	9496	1175	41	3	15	3	METAP2	12	95867968	Missense_Mutation	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10	40073351	95867968	37983927	72	51364										
GRK1	6011	hgsc.bcm.edu	37	chr13	114322307	114322307	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	ctagggaaagggggcttcggGgaggtgtcggcctgccagat	19	8	0	1			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr13:114322307G>A	ENST00000335678.6	+	1	838	c.606G>A	c.(604-606)ggG>ggA	p.G202G		NM_002929.2	NP_002920.1	Q15835	RK_HUMAN	G protein-coupled receptor kinase 1	202	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of apoptotic process (GO:0043066)|photoreceptor cell morphogenesis (GO:0008594)|phototransduction, visible light (GO:0007603)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)|protein autophosphorylation (GO:0046777)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|protein kinase activity (GO:0004672)|rhodopsin kinase activity (GO:0050254)			ovary(2)	2	Lung NSC(43;0.0113)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.00696)|all_epithelial(44;0.00347)|all_lung(25;0.0221)|Breast(118;0.0411)|Lung NSC(25;0.0839)	all cancers(43;0.234)			GGGGCTTCGGGGAGGTGTCGG	0.597																																					p.G202G		Atlas-SNP	.											.	GRK1	41	.	0			c.G606A						.						19	21	20					13																	114322307		2004	4179	6183	SO:0001819	synonymous_variant	6011	exon1			CTTCGGGGAGGTG			13q34	2013-09-02	2004-03-23	2004-03-24	ENSG00000185974	ENSG00000185974	2.7.11.14		10013	protein-coding gene	gene with protein product		180381	"rhodopsin kinase"	RHOK		8812493, 15057823	Standard	NM_002929		Approved	GPRK1, RK	uc010tkf.2	Q15835	OTTHUMG00000185528	ENST00000335678.6:c.606G>A	chr13.hg19:g.114322307G>A		159.0	0.0		232.0	63.0	NM_002929	Q53X14	Silent	SNP	ENST00000335678.6	hg19																																																																																				.	.		0.597	GRK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470655.1	NM_002929		A	114322307	G	A	114322307	2	1	371	1	0	0	0	0	0	0	0	1	6799	1219	43	3		3	GRK1	13	114322307	Silent	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10		114322307	847571	73	51365										
FAM179B	23116	hgsc.bcm.edu	37	chr14	45475303	45475303	+	Missense_Mutation	SNP	G	G	T													0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	gtctaaatgggacaaagcctGttcctcccataccaagggga							TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr14:45475303G>T	ENST00000361577.3	+	5	2951	c.2737G>T	c.(2737-2739)Gtt>Ttt	p.V913F	KLHL28_ENST00000553817.1_Intron|FAM179B_ENST00000361462.2_Missense_Mutation_p.V913F|FAM179B_ENST00000382233.2_Missense_Mutation_p.V913F	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	913										endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						GACAAAGCCTGTTCCTCCCAT	0.453																																					p.V913F		Atlas-SNP	.											.	FAM179B	115	.	0			c.G2737T						.						130	129	129					14																	45475303		2203	4300	6503	SO:0001583	missense	23116	exon5			AAGCCTGTTCCTC	AB007883	CCDS9681.1	14q21.3	2008-07-21	2008-07-21	2008-07-21	ENSG00000198718	ENSG00000198718			19959	protein-coding gene	gene with protein product			"KIAA0423"	KIAA0423			Standard	XM_005267451		Approved		uc001wvv.3	Q9Y4F4	OTTHUMG00000140264	ENST00000361577.3:c.2737G>T	chr14.hg19:g.45475303G>T	ENSP00000355045:p.Val913Phe	116.0	0.0		146.0	28.0	NM_015091	Q68D66|Q6PG27	Missense_Mutation	SNP	ENST00000361577.3	hg19	CCDS9681.1	.	.	.	.	.	.	.	.	.	.	G	17.00	3.276104	0.59649	.	.	ENSG00000198718	ENST00000429476;ENST00000361577;ENST00000361462;ENST00000382233	T;T;T	0.42513	2.38;2.36;0.97	5.39	5.39	0.77823	Armadillo-type fold (1);	0.198337	0.32488	N	0.006035	T	0.37461	0.1004	L	0.29908	0.895	0.45883	D	0.998731	B;B;B	0.23249	0.01;0.01;0.082	B;B;B	0.25140	0.007;0.007;0.058	T	0.20405	-1.0276	10	0.66056	D	0.02	-9.8358	18.8028	0.92025	0.0:0.0:1.0:0.0	.	913;913;913	G3XAE9;Q9Y4F4;Q9Y4F4-2	.;F179B_HUMAN;.	F	913	ENSP00000355045:V913F;ENSP00000354917:V913F;ENSP00000371668:V913F	ENSP00000354917:V913F	V	+	1	0	FAM179B	44545053	1.000000	0.71417	0.994000	0.49952	0.979000	0.70002	5.052000	0.64263	2.538000	0.85594	0.558000	0.71614	GTT	.	.		0.453	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781		T	45475303	G	T	45475303	3	4	371	1	0	0	0	0	1	0	0	0	5511	1377	48	3	2755	3	FAM179B	14	45475303	Missense_Mutation	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10		45475303	61874237	74	51366	269	2								
FAM179B	23116	hgsc.bcm.edu	37	chr14	45475307	45475307	+	Missense_Mutation	SNP	C	C	T													0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	aaatgggacaaagcctgttcCtcccataccaaggggaataa							TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr14:45475307C>T	ENST00000361577.3	+	5	2955	c.2741C>T	c.(2740-2742)cCt>cTt	p.P914L	KLHL28_ENST00000553817.1_Intron|FAM179B_ENST00000361462.2_Missense_Mutation_p.P914L|FAM179B_ENST00000382233.2_Missense_Mutation_p.P914L	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	914										endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						AAGCCTGTTCCTCCCATACCA	0.448																																					p.P914L		Atlas-SNP	.											.	FAM179B	115	.	0			c.C2741T						.						129	129	129					14																	45475307		2203	4300	6503	SO:0001583	missense	23116	exon5			CTGTTCCTCCCAT	AB007883	CCDS9681.1	14q21.3	2008-07-21	2008-07-21	2008-07-21	ENSG00000198718	ENSG00000198718			19959	protein-coding gene	gene with protein product			"KIAA0423"	KIAA0423			Standard	XM_005267451		Approved		uc001wvv.3	Q9Y4F4	OTTHUMG00000140264	ENST00000361577.3:c.2741C>T	chr14.hg19:g.45475307C>T	ENSP00000355045:p.Pro914Leu	119.0	0.0		148.0	28.0	NM_015091	Q68D66|Q6PG27	Missense_Mutation	SNP	ENST00000361577.3	hg19	CCDS9681.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	26.4|26.4	4.737453|4.737453	0.89482|0.89482	.|.	.|.	ENSG00000198718|ENSG00000198718	ENST00000557250|ENST00000429476;ENST00000361577;ENST00000361462;ENST00000382233	.|T;T;T	.|0.38077	.|2.32;2.29;1.16	5.39|5.39	5.39|5.39	0.77823|0.77823	.|Armadillo-type fold (1);	.|0.170595	.|0.40728	.|N	.|0.001040	T|T	0.50051|0.50051	0.1593|0.1593	L|L	0.27053|0.27053	0.805|0.805	0.58432|0.58432	D|D	0.999997|0.999997	.|D;D;D	.|0.89917	.|0.974;0.974;1.0	.|P;P;D	.|0.91635	.|0.731;0.731;0.999	T|T	0.53968|0.53968	-0.8363|-0.8363	5|10	.|0.87932	.|D	.|0	-16.3962|-16.3962	18.8028|18.8028	0.92025|0.92025	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|914;914;914	.|G3XAE9;Q9Y4F4;Q9Y4F4-2	.|.;F179B_HUMAN;.	F|L	106|914	.|ENSP00000355045:P914L;ENSP00000354917:P914L;ENSP00000371668:P914L	.|ENSP00000354917:P914L	L|P	+|+	1|2	0|0	FAM179B|FAM179B	44545057|44545057	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.982000|0.982000	0.71751|0.71751	5.371000|5.371000	0.66150|0.66150	2.538000|2.538000	0.85594|0.85594	0.558000|0.558000	0.71614|0.71614	CTC|CCT	.	.		0.448	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781		T	45475307	C	T	45475307	3	4	371	1	0	0	0	0	1	0	0	0	5511	681	24	3	2759	3	FAM179B	14	45475307	Missense_Mutation	SNP	C	TCGA-ZS-A9CE-01A-11D-A36X-10	4	45475307	61874233	75	51367	269	2								
PNMA1	9240	hgsc.bcm.edu	37	chr14	74180325	74180325	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	atcccccggcaccagtcttcCaacagtgtcatcgccatttt	6	16	2	0			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr14:74180325C>T	ENST00000316836.3	-	1	803	c.18G>A	c.(16-18)ttG>ttA	p.L6L		NM_006029.4	NP_006020.4	Q8ND90	PNMA1_HUMAN	paraneoplastic Ma antigen 1	6					inflammatory response to antigenic stimulus (GO:0002437)|positive regulation of apoptotic process (GO:0043065)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleolus (GO:0005730)				breast(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|prostate(1)|urinary_tract(2)	13				BRCA - Breast invasive adenocarcinoma(234;0.00331)|KIRC - Kidney renal clear cell carcinoma(182;0.0797)		accagtcttccaacagtgtca	0.522																																					p.L6L		Atlas-SNP	.											.	PNMA1	29	.	0			c.G18A						.						86	94	91					14																	74180325		2203	4300	6503	SO:0001819	synonymous_variant	9240	exon1			GTCTTCCAACAGT	AF037364	CCDS9818.1	14q24.3	2012-02-09	2012-02-09		ENSG00000176903	ENSG00000176903		"Paraneoplastic Ma antigens"	9158	protein-coding gene	gene with protein product		604010	"paraneoplastic antigen MA1"			10050892	Standard	NM_006029		Approved	MA1	uc001xor.1	Q8ND90	OTTHUMG00000169183	ENST00000316836.3:c.18G>A	chr14.hg19:g.74180325C>T		74.0	0.0		92.0	38.0	NM_006029	A8K4L5|O95144|Q8NG07	Silent	SNP	ENST00000316836.3	hg19	CCDS9818.1																																																																																			.	.		0.522	PNMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402774.1	NM_006029		T	74180325	C	T	74180325	2	4	371	1	0	0	0	0	0	0	0	1	12162	593	21	3		3	PNMA1	14	74180325	Silent	SNP	C	TCGA-ZS-A9CE-01A-11D-A36X-10	28705018	74180325	33169215	76	51368										
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105413228	105413228	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	gtcagtggtcttaagatcccCttgcatggaggggaagctcc	13	10	2	1			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr14:105413228C>G	ENST00000333244.5	-	7	8679	c.8560G>C	c.(8560-8562)Ggg>Cgg	p.G2854R	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2854						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				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)			TTAAGATCCCCTTGCATGGAG	0.632																																					p.G2854R		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G8560C						.						133	152	146					14																	105413228		1970	4154	6124	SO:0001583	missense	113146	exon7			GATCCCCTTGCAT	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.8560G>C	chr14.hg19:g.105413228C>G	ENSP00000353114:p.Gly2854Arg	133.0	0.0		168.0	30.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	hg19	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	c	13.86	2.363340	0.41902	.	.	ENSG00000185567	ENST00000333244	T	0.03358	3.96	3.07	3.07	0.35406	.	.	.	.	.	T	0.09024	0.0223	M	0.93197	3.39	0.09310	N	1	P	0.41784	0.762	B	0.39379	0.298	T	0.25779	-1.0122	9	0.14252	T	0.57	.	8.136	0.31054	0.0:0.8829:0.0:0.1171	.	2854	Q8IVF2	AHNK2_HUMAN	R	2854	ENSP00000353114:G2854R	ENSP00000353114:G2854R	G	-	1	0	AHNAK2	104484273	.	.	0.001000	0.08648	0.010000	0.07245	.	.	1.569000	0.49696	0.306000	0.20318	GGG	.	.		0.632	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		G	105413228	C	G	105413228	3	3	371	1	0	0	0	0	1	0	0	0	415	681	24	4	8831	4	AHNAK2	14	105413228	Missense_Mutation	SNP	C	TCGA-ZS-A9CE-01A-11D-A36X-10	31232903	105413228	1936312	77	51369										
TLN2	83660	hgsc.bcm.edu	37	chr15	62948248	62948248	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	ctctgatcagaatgtagattCgagagaccccgtgcagctga	11	10	2	5			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr15:62948248C>T	ENST00000561311.1	+	7	853	c.623C>T	c.(622-624)tCg>tTg	p.S208L	TLN2_ENST00000306829.6_Missense_Mutation_p.S208L			Q9Y4G6	TLN2_HUMAN	talin 2	208	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						AATGTAGATTCGAGAGACCCC	0.458																																					p.S208L		Atlas-SNP	.											TLN2,NS,carcinoma,0,3	TLN2	253	.	0			c.C623T						.						115	98	104					15																	62948248		2203	4300	6503	SO:0001583	missense	83660	exon5			TAGATTCGAGAGA	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.623C>T	chr15.hg19:g.62948248C>T	ENSP00000453508:p.Ser208Leu	91.0	0.0		106.0	41.0	NM_015059	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	hg19	CCDS32261.1	.	.	.	.	.	.	.	.	.	.	C	33	5.289973	0.95546	.	.	ENSG00000171914	ENST00000306829	T	0.75154	-0.91	5.47	5.47	0.80525	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.000000	0.85682	D	0.000000	D	0.87233	0.6126	M	0.81497	2.545	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87633	0.2517	10	0.56958	D	0.05	-9.4264	18.6826	0.91551	0.0:1.0:0.0:0.0	.	208	Q9Y4G6	TLN2_HUMAN	L	208	ENSP00000303476:S208L	ENSP00000303476:S208L	S	+	2	0	TLN2	60735540	1.000000	0.71417	0.876000	0.34364	0.913000	0.54294	7.768000	0.85345	2.723000	0.93209	0.655000	0.94253	TCG	.	.		0.458	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			T	62948248	C	T	62948248	3	4	371	1	0	0	0	0	1	0	0	0	15963	893	31	1	641	1	TLN2	15	62948248	Missense_Mutation	SNP	C	TCGA-ZS-A9CE-01A-11D-A36X-10		62948248	39583144	78	51370										
HERC1	8925	hgsc.bcm.edu	37	chr15	64048942	64048942	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	aaagtgcagtactgtccagcTtcaatctataaacaaagaat	6	8	2	1			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr15:64048942T>G	ENST00000443617.2	-	5	1314	c.1227A>C	c.(1225-1227)gaA>gaC	p.E409D		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	409					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						ACTGTCCAGCTTCAATCTATA	0.388																																					p.E409D		Atlas-SNP	.											.	HERC1	624	.	0			c.A1227C						.						16	15	15					15																	64048942		1822	4083	5905	SO:0001583	missense	8925	exon5			TCCAGCTTCAATC	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.1227A>C	chr15.hg19:g.64048942T>G	ENSP00000390158:p.Glu409Asp	32.0	0.0		57.0	22.0	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	hg19	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.185179	0.78677	.	.	ENSG00000103657	ENST00000443617	D	0.85013	-1.93	5.38	5.38	0.77491	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.85682	U	0.000000	D	0.89339	0.6687	L	0.51422	1.61	0.58432	D	0.999999	D;D	0.76494	0.996;0.999	D;D	0.80764	0.99;0.994	D	0.86906	0.2057	10	0.22706	T	0.39	.	15.6888	0.77434	0.0:0.0:0.0:1.0	.	409;409	C9JUT5;Q15751	.;HERC1_HUMAN	D	409	ENSP00000390158:E409D	ENSP00000390158:E409D	E	-	3	2	HERC1	61835995	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.305000	0.51873	2.167000	0.68274	0.454000	0.30748	GAA	.	.		0.388	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		G	64048942	T	G	64048942	3	3	371	1	0	0	0	0	1	0	0	0	7066	1606	56	5	13654	5	HERC1	15	64048942	Missense_Mutation	SNP	T	TCGA-ZS-A9CE-01A-11D-A36X-10	1100694	64048942	38482450	79	51371										
MAN2A2	4122	hgsc.bcm.edu	37	chr15	91448887	91448887	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	aaggcttcgacatctcctacGacccgcacgactgggatgct	10	14	1	0			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr15:91448887G>T	ENST00000559717.1	+	4	928	c.469G>T	c.(469-471)Gac>Tac	p.D157Y	MAN2A2_ENST00000360468.3_Missense_Mutation_p.D157Y|MAN2A2_ENST00000431652.2_5'Flank			P49641	MA2A2_HUMAN	mannosidase, alpha, class 2A, member 2	157					cellular protein metabolic process (GO:0044267)|mannose metabolic process (GO:0006013)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|lung(13)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)			CATCTCCTACGACCCGCACGA	0.597																																					p.D157Y		Atlas-SNP	.											.	MAN2A2	99	.	0			c.G469T						.						98	71	80					15																	91448887		2198	4298	6496	SO:0001583	missense	4122	exon3			TCCTACGACCCGC	L28821	CCDS32332.1	15q25	2011-06-30			ENSG00000196547	ENSG00000196547			6825	protein-coding gene	gene with protein product		600988				8524845	Standard	NM_006122		Approved	MANA2X, HsT19662	uc002bqc.3	P49641		ENST00000559717.1:c.469G>T	chr15.hg19:g.91448887G>T	ENSP00000452948:p.Asp157Tyr	110.0	0.0		106.0	22.0	NM_006122	A6NH12|A8K1E8|Q13754	Missense_Mutation	SNP	ENST00000559717.1	hg19	CCDS32332.1	.	.	.	.	.	.	.	.	.	.	G	14.30	2.495236	0.44352	.	.	ENSG00000196547	ENST00000360468	T	0.25414	1.8	4.71	0.573	0.17363	Glycoside hydrolase/deacetylase, beta/alpha-barrel (1);Glycoside hydrolase, family 38, core (1);	0.504438	0.24379	N	0.039036	T	0.29061	0.0722	L	0.46157	1.445	0.80722	D	1	P;B	0.43392	0.805;0.273	P;P	0.49887	0.625;0.524	T	0.03566	-1.1024	10	0.72032	D	0.01	-8.4821	8.8564	0.35231	0.5095:0.0:0.4905:0.0	.	157;157	P49641-1;P49641	.;MA2A2_HUMAN	Y	157	ENSP00000353655:D157Y	ENSP00000353655:D157Y	D	+	1	0	MAN2A2	89249891	0.983000	0.35010	0.980000	0.43619	0.507000	0.33981	1.970000	0.40520	0.002000	0.14630	-0.330000	0.08379	GAC	.	.		0.597	MAN2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418246.5	NM_006122		T	91448887	G	T	91448887	3	4	371	1	0	0	0	0	1	0	0	0	9224	1058	37	1	479	1	MAN2A2	15	91448887	Missense_Mutation	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10	27399945	91448887	11082505	80	51372										
C16orf11	146325	hgsc.bcm.edu	37	chr16	613785	613785	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	cctgcctgagtcgtggaagcCggggatgggaggggacccaa	18	10	0	1			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr16:613785C>T	ENST00000409413.3	+	2	770	c.491C>T	c.(490-492)cCg>cTg	p.P164L		NM_145270.2	NP_660313.1	P0CG20	PRR35_HUMAN		164	Pro-rich.									central_nervous_system(1)|endometrium(1)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	10						TCGTGGAAGCCGGGGATGGGA	0.736																																					p.P164L		Atlas-SNP	.											.	C16orf11	27	.	0			c.C491T						.						4	6	5					16																	613785		1789	3951	5740	SO:0001583	missense	146325	exon2			GGAAGCCGGGGAT																												ENST00000409413.3:c.491C>T	chr16.hg19:g.613785C>T	ENSP00000386499:p.Pro164Leu	65.0	0.0		70.0	18.0	NM_145270	B8ZZ27|Q8N233|Q96AX3|Q96S23	Missense_Mutation	SNP	ENST00000409413.3	hg19	CCDS45365.1	.	.	.	.	.	.	.	.	.	.	C	0.998	-0.691966	0.03303	.	.	ENSG00000161992	ENST00000409413	T	0.08546	3.08	4.96	-2.6	0.06190	.	0.467553	0.18396	N	0.142490	T	0.02380	0.0073	N	0.04959	-0.14	0.21020	N	0.999809	B	0.06786	0.001	B	0.04013	0.001	T	0.43147	-0.9409	10	0.02654	T	1	.	5.1659	0.15084	0.2177:0.3768:0.0:0.4055	.	164	P0CG20	CP011_HUMAN	L	164	ENSP00000386499:P164L	ENSP00000386499:P164L	P	+	2	0	C16orf11	553786	0.004000	0.15560	0.017000	0.16124	0.005000	0.04900	0.332000	0.19751	-0.364000	0.08088	-1.119000	0.02030	CCG	.	.		0.736	C16orf11-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000333913.1			T	613785	C	T	613785	3	4	371	1	0	0	0	0	1	0	0	0	1812	652	23	1	493	1	C16orf11	16	613785	Missense_Mutation	SNP	C	TCGA-ZS-A9CE-01A-11D-A36X-10		613785	89740968	81	51373										
TNRC6A	27327	hgsc.bcm.edu	37	chr16	24788418	24788441	+	In_Frame_Del	DEL	CAGCAGCAGCCACAGCCGCAGCCG	CAGCAGCAGCCACAGCCGCAGCCG	-													0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	agccgcagcagcagcagccaCagcagcagccacagccgcag					rs201560222|rs71156436|rs10593507|rs60829899|rs11644562|rs71383714	byFrequency	TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	CAGCAGCAGCCACAGCCGCAGCCG	CAGCAGCAGCCACAGCCGCAGCCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr16:24788418_24788441delCAGCAGCAGCCACAGCCGCAGCCG	ENST00000395799.3	+	5	457_480	c.328_351delCAGCAGCAGCCACAGCCGCAGCCG	c.(328-351)cagcagcagccacagccgcagccgdel	p.QQQPQPQP110del	TNRC6A_ENST00000315183.7_In_Frame_Del_p.QQQPQPQP110del	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	110	Gln-rich.|Interaction with argonaute family proteins.				cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.P117P(1)		breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		gcagcagccacagcagcagccacagccgcagccgcagcagcagc	0.58																																					p.109_117del		Atlas-INDEL	.											.	TNRC6A	171	.	1	Substitution - coding silent(1)	endometrium(1)	c.327_350del						.																																			SO:0001651	inframe_deletion	27327	exon5			.	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"Trinucleotide (CAG) repeat containing"	11969	protein-coding gene	gene with protein product		610739	"trinucleotide repeat containing 6"	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.328_351delCAGCAGCAGCCACAGCCGCAGCCG	chr16.hg19:g.24788418_24788441delCAGCAGCAGCCACAGCCGCAGCCG	ENSP00000379144:p.Gln110_Pro117del	62.0	0.0		88.0	33.0	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	In_Frame_Del	DEL	ENST00000395799.3	hg19	CCDS10624.2																																																																																			.	.		0.58	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		-	24788441	CAGCAGCAGCCACAGCCGCAGCCG	-	24788418	7	5	371	1	0	1	0	1	0	0	0	0	16355	479	17	0	346	0	TNRC6A	16	24788418	In_Frame_Del	DEL	CAGCAGCAGCCACAGCCGCAGCCG	TCGA-ZS-A9CE-01A-11D-A36X-10	24174633	24788418	65566335	82	51374										
TBX6	6911	hgsc.bcm.edu	37	chr16	30100136	30100136	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	taggtgtatgcggggttggtActtgtgcatggagtgcagga	18	4	0	0			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr16:30100136A>C	ENST00000395224.2	-	5	705	c.646T>G	c.(646-648)Tac>Gac	p.Y216D	TBX6_ENST00000279386.2_Missense_Mutation_p.Y216D|TBX6_ENST00000553607.1_Missense_Mutation_p.Y216D	NM_004608.3	NP_004599.2	O95947	TBX6_HUMAN	T-box 6	216					anatomical structure morphogenesis (GO:0009653)|cell fate specification (GO:0001708)|mesoderm development (GO:0007498)|mesoderm formation (GO:0001707)|negative regulation of neuron maturation (GO:0014043)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction involved in regulation of gene expression (GO:0023019)|somite rostral/caudal axis specification (GO:0032525)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)	9						CGGGGTTGGTACTTGTGCATG	0.632																																					p.Y216D		Atlas-SNP	.											.	TBX6	29	.	0			c.T646G						.						91	99	96					16																	30100136		2197	4300	6497	SO:0001583	missense	6911	exon5			GTTGGTACTTGTG	AJ007989	CCDS10670.1	16p11.2	2008-02-05			ENSG00000149922	ENSG00000149922		"T-boxes"	11605	protein-coding gene	gene with protein product		602427				9888994, 9933572	Standard	NM_004608		Approved		uc010veh.2	O95947	OTTHUMG00000132115	ENST00000395224.2:c.646T>G	chr16.hg19:g.30100136A>C	ENSP00000378650:p.Tyr216Asp	97.0	0.0		151.0	62.0	NM_004608	Q8TAS4|Q9HA44	Missense_Mutation	SNP	ENST00000395224.2	hg19	CCDS10670.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.582649	0.86748	.	.	ENSG00000149922	ENST00000395224;ENST00000279386;ENST00000553607	D;D;D	0.96136	-3.92;-3.92;-3.92	6.04	6.04	0.98038	p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.98507	0.9502	H	0.96460	3.825	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99655	1.0992	10	0.87932	D	0	.	15.5711	0.76337	1.0:0.0:0.0:0.0	.	216;216	O95947;Q9HA44	TBX6_HUMAN;.	D	216	ENSP00000378650:Y216D;ENSP00000279386:Y216D;ENSP00000461223:Y216D	ENSP00000279386:Y216D	Y	-	1	0	TBX6	30007637	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.281000	0.95811	2.317000	0.78254	0.460000	0.39030	TAC	.	.		0.632	TBX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255157.2	NM_004608, NM_080758		C	30100136	A	C	30100136	3	2	371	1	0	0	0	0	1	0	0	0	15677	391	14	5	684	5	TBX6	16	30100136	Missense_Mutation	SNP	A	TCGA-ZS-A9CE-01A-11D-A36X-10	5311718	30100136	60254617	83	51375										
PHKB	5257	hgsc.bcm.edu	37	chr16	47699867	47699867	+	Intron	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	ccccaggtcggttgtacgccGtgcagcaagtcttttaagta	11	11	1	0	rs527426323		TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr16:47699867G>A	ENST00000323584.5	+	25	2451				PHKB_ENST00000455779.1_Intron|PHKB_ENST00000299167.8_Missense_Mutation_p.R784H|PHKB_ENST00000566044.1_Missense_Mutation_p.R777H	NM_000293.2	NP_000284.1	Q93100	KPBB_HUMAN	phosphorylase kinase, beta						carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|liver(1)|lung(18)|ovary(1)|skin(1)	41		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				GTTGTACGCCGTGCAGCAAGT	0.458													G|||	1	0.000199681	8e-04	0	5008	,	,		18021	0		0	False		,,,				2504	0				p.R777H		Atlas-SNP	.											.	PHKB	298	.	0			c.G2330A						.						91	90	90					16																	47699867		1895	4118	6013	SO:0001627	intron_variant	5257	exon26			TACGCCGTGCAGC		CCDS10729.1, CCDS42161.1	16q12-q13	2009-07-10			ENSG00000102893	ENSG00000102893	2.7.11.19		8927	protein-coding gene	gene with protein product		172490					Standard	NM_000293		Approved		uc002eev.4	Q93100	OTTHUMG00000133102	ENST00000323584.5:c.2427+981G>A	chr16.hg19:g.47699867G>A		88.0	0.0		102.0	13.0	NM_001031835	Q8N4T5	Missense_Mutation	SNP	ENST00000323584.5	hg19	CCDS10729.1	.	.	.	.	.	.	.	.	.	.	G	11.96	1.794128	0.31777	.	.	ENSG00000102893	ENST00000299167	.	.	.	5.21	-2.05	0.07321	.	.	.	.	.	T	0.22627	0.0546	N	0.10874	0.06	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.13415	-1.0510	8	0.18710	T	0.47	.	1.4003	0.02269	0.3662:0.0968:0.3418:0.1953	.	25;777	B3KVX5;Q93100-4	.;.	H	777	.	ENSP00000299167:R777H	R	+	2	0	PHKB	46257368	0.998000	0.40836	0.993000	0.49108	0.996000	0.88848	0.554000	0.23407	-0.116000	0.11893	0.650000	0.86243	CGT	.	.		0.458	PHKB-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000430413.1			A	47699867	G	A	47699867	1	1	371	0	1	0	0	0	0	0	0	0	11854	1145	40	1		1	PHKB	16	47699867	Intron	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10	17599731	47699867	42654886	84	51376										
MMP2	4313	hgsc.bcm.edu	37	chr16	55522498	55522498	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	gctgaaggacagccctgcaaGtttccattccgcttccaggg	11	13	0	1			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr16:55522498G>T	ENST00000219070.4	+	6	1385	c.876G>T	c.(874-876)aaG>aaT	p.K292N	MMP2_ENST00000437642.2_Missense_Mutation_p.K242N|MMP2_ENST00000570308.1_Missense_Mutation_p.K216N|MMP2_ENST00000543485.1_Missense_Mutation_p.K216N	NM_004530.4	NP_004521.1	P08253	MMP2_HUMAN	matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)	292	Collagen-binding.|Fibronectin type-II 2. {ECO:0000255|PROSITE-ProRule:PRU00479}.				angiogenesis (GO:0001525)|blood vessel maturation (GO:0001955)|bone trabecula formation (GO:0060346)|cellular protein metabolic process (GO:0044267)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|positive regulation of innate immune response (GO:0045089)|proteolysis (GO:0006508)|response to hypoxia (GO:0001666)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|sarcomere (GO:0030017)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|liver(2)|lung(23)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	58		Renal(780;0.00183)|Breast(268;0.00354)|Hepatocellular(780;0.00826)|all_neural(199;0.0189)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0185)|all cancers(182;7.16e-45)|Epithelial(162;5.26e-37)|GBM - Glioblastoma multiforme(240;9e-08)|Kidney(780;0.00227)|BRCA - Breast invasive adenocarcinoma(181;0.00786)	Captopril(DB01197)|Marimastat(DB00786)	AGCCCTGCAAGTTTCCATTCC	0.612																																					p.K292N		Atlas-SNP	.											.	MMP2	119	.	0			c.G876T						.						81	66	71					16																	55522498		2198	4300	6498	SO:0001583	missense	4313	exon6			CTGCAAGTTTCCA		CCDS10752.1, CCDS45487.1	16q13-q21	2008-02-05	2005-08-08		ENSG00000087245	ENSG00000087245	3.4.24.24		7166	protein-coding gene	gene with protein product		120360	"matrix metalloproteinase 2 (gelatinase A, 72kD gelatinase, 72kD type IV collagenase)", "matrix metalloproteinase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)"	CLG4, CLG4A			Standard	NM_004530		Approved	TBE-1	uc002ehz.4	P08253	OTTHUMG00000133202	ENST00000219070.4:c.876G>T	chr16.hg19:g.55522498G>T	ENSP00000219070:p.Lys292Asn	64.0	0.0		91.0	40.0	NM_004530	B2R6U1|B4DWH3|E9PE45|Q9UCJ8	Missense_Mutation	SNP	ENST00000219070.4	hg19	CCDS10752.1	.	.	.	.	.	.	.	.	.	.	G	11.63	1.696211	0.30052	.	.	ENSG00000087245	ENST00000219070;ENST00000543485;ENST00000437642	T;T;T	0.51071	0.72;0.72;0.72	4.93	2.93	0.34026	Peptidase M10, metallopeptidase (1);Fibronectin, type II, collagen-binding (5);Kringle-like fold (1);Peptidase, metallopeptidase (1);	0.000000	0.85682	D	0.000000	T	0.56992	0.2023	L	0.53561	1.675	0.80722	D	1	D;D	0.89917	0.989;1.0	P;D	0.75484	0.907;0.986	T	0.52185	-0.8609	10	0.19147	T	0.46	.	9.8941	0.41306	0.2851:0.0:0.7149:0.0	.	242;292	E9PE45;P08253	.;MMP2_HUMAN	N	292;216;242	ENSP00000219070:K292N;ENSP00000444143:K216N;ENSP00000394237:K242N	ENSP00000219070:K292N	K	+	3	2	MMP2	54079999	1.000000	0.71417	1.000000	0.80357	0.743000	0.42351	2.205000	0.42770	1.204000	0.43247	-0.374000	0.07098	AAG	.	.		0.612	MMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256913.3			T	55522498	G	T	55522498	3	4	371	1	0	0	0	0	1	0	0	0	9667	1020	36	3	905	3	MMP2	16	55522498	Missense_Mutation	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10	7822631	55522498	34832255	85	51377										
SLC12A4	6560	hgsc.bcm.edu	37	chr16	67985897	67985897	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	agctgtcttggcacagatgtCaaactggtcccgggacaggg	14	10	2	1			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr16:67985897C>A	ENST00000316341.3	-	8	1101	c.961G>T	c.(961-963)Gac>Tac	p.D321Y	SLC12A4_ENST00000572037.1_Missense_Mutation_p.D273Y|SLC12A4_ENST00000537830.2_Missense_Mutation_p.D315Y|SLC12A4_ENST00000541864.2_Missense_Mutation_p.D290Y|SLC12A4_ENST00000422611.2_Missense_Mutation_p.D323Y|SLC12A4_ENST00000572010.1_5'Flank|SLC12A4_ENST00000576616.1_Missense_Mutation_p.D321Y|SLC12A4_ENST00000338335.3_Missense_Mutation_p.D321Y	NM_001145961.1|NM_005072.4	NP_001139433.1|NP_005063.1	Q9UP95	S12A4_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 4	321					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(2)|ovary(2)|prostate(4)|skin(2)|urinary_tract(3)	29		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)	Bumetanide(DB00887)|Potassium Chloride(DB00761)	GCACAGATGTCAAACTGGTCC	0.587																																					p.D323Y		Atlas-SNP	.											SLC12A4,bladder,carcinoma,0,1	SLC12A4	81	.	0			c.G967T						.						100	70	80					16																	67985897		2198	4300	6498	SO:0001583	missense	6560	exon7			AGATGTCAAACTG		CCDS10855.1, CCDS54030.1, CCDS54031.1, CCDS54032.1	16q22.1	2013-07-18	2013-07-18		ENSG00000124067	ENSG00000124067		"Solute carriers"	10913	protein-coding gene	gene with protein product		604119				8663127	Standard	NM_005072		Approved	KCC1	uc010ceu.2	Q9UP95	OTTHUMG00000137535	ENST00000316341.3:c.961G>T	chr16.hg19:g.67985897C>A	ENSP00000318557:p.Asp321Tyr	89.0	0.0		113.0	46.0	NM_001145962	B4DF69|B4DR04|B4DZ82|B7ZAV0|F5H066|F5H0S9|F5H3C0|O60632|O75893|Q13953|Q96LD5	Missense_Mutation	SNP	ENST00000316341.3	hg19	CCDS10855.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.113518	0.77210	.	.	ENSG00000124067	ENST00000422611;ENST00000541864;ENST00000537830;ENST00000338335;ENST00000316341	T;T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28;-0.28	5.0	5.0	0.66597	.	0.043142	0.85682	D	0.000000	D	0.83871	0.5348	M	0.86953	2.85	0.80722	D	1	D;P;D;P;B;B	0.63046	0.991;0.711;0.992;0.905;0.079;0.021	P;B;D;P;B;B	0.67548	0.847;0.287;0.952;0.583;0.094;0.015	D	0.86387	0.1733	10	0.59425	D	0.04	.	18.6574	0.91459	0.0:1.0:0.0:0.0	.	323;321;290;315;321;321	F5H3C0;B4DF30;F5H066;F5H0S9;Q9UP95-2;Q9UP95	.;.;.;.;.;S12A4_HUMAN	Y	323;290;315;321;321	ENSP00000395983:D323Y;ENSP00000438334:D290Y;ENSP00000445962:D315Y;ENSP00000343374:D321Y;ENSP00000318557:D321Y	ENSP00000318557:D321Y	D	-	1	0	SLC12A4	66543398	1.000000	0.71417	0.995000	0.50966	0.805000	0.45488	6.030000	0.70903	2.499000	0.84300	0.467000	0.42956	GAC	.	.		0.587	SLC12A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268864.4	NM_005072		A	67985897	C	A	67985897	3	1	371	1	0	0	0	0	1	0	0	0	14400	826	29	3	2364	3	SLC12A4	16	67985897	Missense_Mutation	SNP	C	TCGA-ZS-A9CE-01A-11D-A36X-10	12463399	67985897	22368856	86	51378										
HAS3	3038	hgsc.bcm.edu	37	chr16	69143870	69143870	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	gtgcatcatgcagaagtgggGaggcaagcgcgaggtcatgt	17	7	2	1			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr16:69143870G>A	ENST00000306560.1	+	2	728	c.572G>A	c.(571-573)gGa>gAa	p.G191E	HAS3_ENST00000569188.1_Missense_Mutation_p.G191E|HAS3_ENST00000219322.3_Missense_Mutation_p.G191E	NM_005329.2	NP_005320.2	O00219	HYAS3_HUMAN	hyaluronan synthase 3	191					carbohydrate metabolic process (GO:0005975)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|positive regulation of hyaluranon cable assembly (GO:1900106)|positive regulation of transcription, DNA-templated (GO:0045893)|small molecule metabolic process (GO:0044281)	hyaluranon cable (GO:0036117)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronan synthase activity (GO:0050501)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|urinary_tract(2)	16		Ovarian(137;0.101)		OV - Ovarian serous cystadenocarcinoma(108;0.0694)		CAGAAGTGGGGAGGCAAGCGC	0.647																																					p.G191E		Atlas-SNP	.											.	HAS3	61	.	0			c.G572A						.						79	63	68					16																	69143870		2198	4300	6498	SO:0001583	missense	3038	exon2			AGTGGGGAGGCAA	BC021853	CCDS10870.1, CCDS10871.1	16q22.1	2013-02-22			ENSG00000103044	ENSG00000103044	2.4.1.212	"Glycosyltransferase family 2 domain containing"	4820	protein-coding gene	gene with protein product		602428				9169154, 9083017	Standard	NM_005329		Approved		uc010cfh.3	O00219	OTTHUMG00000137562	ENST00000306560.1:c.572G>A	chr16.hg19:g.69143870G>A	ENSP00000304440:p.Gly191Glu	73.0	0.0		93.0	40.0	NM_138612	A8K5T5|Q8WTZ0|Q9NYP0	Missense_Mutation	SNP	ENST00000306560.1	hg19	CCDS10871.1	.	.	.	.	.	.	.	.	.	.	G	32	5.126065	0.94429	.	.	ENSG00000103044	ENST00000219322;ENST00000306560	D;T	0.85258	-1.96;0.22	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	D	0.94241	0.8151	M	0.90977	3.165	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.983;1.0	D	0.95038	0.8175	10	0.72032	D	0.01	-8.2812	18.9466	0.92625	0.0:0.0:1.0:0.0	.	191;191	O00219;O00219-2	HAS3_HUMAN;.	E	191	ENSP00000219322:G191E;ENSP00000304440:G191E	ENSP00000219322:G191E	G	+	2	0	HAS3	67701371	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.723000	0.98772	2.593000	0.87608	0.561000	0.74099	GGA	.	.		0.647	HAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268898.2	NM_138612		A	69143870	G	A	69143870	3	1	371	1	0	0	0	0	1	0	0	0	6972	1174	41	3	574	3	HAS3	16	69143870	Missense_Mutation	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10	1157973	69143870	21210883	87	51379										
ATAD5	79915	hgsc.bcm.edu	37	chr17	29187555	29187555	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	atgagtattcaaaaaatctgGagaagaccaataggaagtca	9	5	3	3			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr17:29187555G>T	ENST00000321990.4	+	10	3439	c.3061G>T	c.(3061-3063)Gag>Tag	p.E1021*	CTD-2349P21.11_ENST00000580873.1_RNA|RNU6-298P_ENST00000390888.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	1021					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				AAAAAATCTGGAGAAGACCAA	0.348																																					p.E1021X		Atlas-SNP	.											.	ATAD5	150	.	0			c.G3061T						.						60	62	61					17																	29187555		2203	4299	6502	SO:0001587	stop_gained	79915	exon10			AATCTGGAGAAGA		CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"ATPases / AAA-type"	25752	protein-coding gene	gene with protein product	"enhanced level of genomic instability 1 homolog (S. cerevisiae)"	609534	"chromosome 17 open reading frame 41"	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.3061G>T	chr17.hg19:g.29187555G>T	ENSP00000313171:p.Glu1021*	439.0	0.0		614.0	240.0	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Nonsense_Mutation	SNP	ENST00000321990.4	hg19	CCDS11260.1	.	.	.	.	.	.	.	.	.	.	G	37	6.623947	0.97714	.	.	ENSG00000176208	ENST00000321990	.	.	.	4.37	-0.165	0.13355	.	1.095080	0.06861	N	0.799166	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12430	T	0.62	.	5.0443	0.14475	0.321:0.1811:0.4979:0.0	.	.	.	.	X	1021	.	ENSP00000313171:E1021X	E	+	1	0	ATAD5	26211681	0.755000	0.28372	0.001000	0.08648	0.026000	0.11368	0.142000	0.16096	-0.014000	0.14175	0.585000	0.79938	GAG	.	.		0.348	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857		T	29187555	G	T	29187555	4	4	371	1	0	0	0	0	0	1	0	0	1076	1175	41	3	3099	3	ATAD5	17	29187555	Nonsense_Mutation	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10		29187555	52007655	88	51380										
PLEKHH3	79990	hgsc.bcm.edu	37	chr17	40824222	40824223	+	Frame_Shift_Ins	INS	-	-	G													0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	tcttgggtagccgggagcccINSggggggacctgcagggcccg							TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr17:40824222_40824223insG	ENST00000591022.1	-	7	1344_1345	c.957_958insC	c.(955-960)cccgggfs	p.G320fs	PLEKHH3_ENST00000412503.1_Frame_Shift_Ins_p.G320fs|PLEKHH3_ENST00000293349.6_Frame_Shift_Ins_p.G320fs|PLEKHH3_ENST00000456950.2_5'UTR	NM_024927.4	NP_079203	Q7Z736	PKHH3_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 3	320	MyTH4. {ECO:0000255|PROSITE- ProRule:PRU00359}.				signal transduction (GO:0007165)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)				endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)|skin(2)	13		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.14)		GCCGGGAGCCCGGGGGGACCTG	0.678																																					p.G320fs		Atlas-INDEL	.											.	PLEKHH3	49	.	0			c.958_959insC						.																																			SO:0001589	frameshift_variant	79990	exon7			.	BC052978	CCDS11434.1	17q21.2	2013-01-11				ENSG00000068137		"Pleckstrin homology (PH) domain containing"	26105	protein-coding gene	gene with protein product						12477932	Standard	NM_024927		Approved	FLJ21019	uc002iau.3	Q7Z736		ENST00000591022.1:c.958dupC	chr17.hg19:g.40824228_40824228dupG	ENSP00000468678:p.Gly320fs	65.0	0.0		74.0	29.0	NM_024927	C9JQ76|Q59H20|Q96B28|Q9H7D6|Q9NT18	Frame_Shift_Ins	INS	ENST00000591022.1	hg19	CCDS11434.1																																																																																			.	.		0.678	PLEKHH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452332.1	NM_024927		G	40824223	-	G	40824222	7	5	371	1	0	1	1	0	0	0	0	0	12087	652	23	0	1451	0	PLEKHH3	17	40824222	Frame_Shift_Ins	INS	-	TCGA-ZS-A9CE-01A-11D-A36X-10	11636667	40824222	40370988	89	51381										
COIL	8161	hgsc.bcm.edu	37	chr17	55027539	55027539	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	cagtctgtgatgacagccctGggcctggacgacctcttcct	11	14	2	2			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr17:55027539G>A	ENST00000240316.4	-	2	1098	c.1064C>T	c.(1063-1065)cCa>cTa	p.P355L		NM_004645.2	NP_004636.1	P38432	COIL_HUMAN	coilin	355						Cajal body (GO:0015030)|cytoplasm (GO:0005737)|female germ cell nucleus (GO:0001674)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	disulfide oxidoreductase activity (GO:0015036)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)			NS(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|urinary_tract(1)	15	Breast(9;6.15e-08)					TGACAGCCCTGGGCCTGGACG	0.572																																					p.P355L		Atlas-SNP	.											.	COIL	49	.	0			c.C1064T						.						67	67	67					17																	55027539		2203	4300	6503	SO:0001583	missense	8161	exon2			AGCCCTGGGCCTG	U06632	CCDS11592.1	17q22	2012-10-02			ENSG00000121058	ENSG00000121058			2184	protein-coding gene	gene with protein product		600272				7971277	Standard	NM_004645		Approved	CLN80, p80-coilin	uc002iuu.3	P38432	OTTHUMG00000178126	ENST00000240316.4:c.1064C>T	chr17.hg19:g.55027539G>A	ENSP00000240316:p.Pro355Leu	47.0	0.0		61.0	18.0	NM_004645	B2R931	Missense_Mutation	SNP	ENST00000240316.4	hg19	CCDS11592.1	.	.	.	.	.	.	.	.	.	.	G	1.678	-0.507165	0.04231	.	.	ENSG00000121058	ENST00000240316	.	.	.	5.8	2.74	0.32292	.	0.941871	0.09014	N	0.861077	T	0.41766	0.1173	L	0.60455	1.87	0.09310	N	0.999999	B	0.25390	0.125	B	0.23419	0.046	T	0.32981	-0.9886	9	0.21540	T	0.41	-2.1439	7.1941	0.25843	0.1406:0.0:0.7215:0.1379	.	355	P38432	COIL_HUMAN	L	355	.	ENSP00000240316:P355L	P	-	2	0	COIL	52382538	0.062000	0.20869	0.001000	0.08648	0.037000	0.13140	2.034000	0.41145	0.381000	0.24851	0.552000	0.68991	CCA	.	.		0.572	COIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440618.1			A	55027539	G	A	55027539	3	1	371	1	0	0	0	0	1	0	0	0	3667	1348	47	3	690	3	COIL	17	55027539	Missense_Mutation	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10	14203317	55027539	26167671	90	51382										
TEX2	55852	hgsc.bcm.edu	37	chr17	62238222	62238222	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	aggctctttacctagtttggTcaaattcattttggtctcga	8	8	4	0			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr17:62238222T>C	ENST00000583097.1	-	8	2915	c.2743A>G	c.(2743-2745)Acc>Gcc	p.T915A	TEX2_ENST00000258991.3_Missense_Mutation_p.T922A|TEX2_ENST00000584379.1_Missense_Mutation_p.T915A			Q8IWB9	TEX2_HUMAN	testis expressed 2	915					signal transduction (GO:0007165)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)				breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(8;1.33e-10)	READ - Rectum adenocarcinoma(1115;0.0689)		CCTAGTTTGGTCAAATTCATT	0.413																																					p.T922A		Atlas-SNP	.											.	TEX2	89	.	0			c.A2764G						.						147	152	150					17																	62238222		2203	4300	6503	SO:0001583	missense	55852	exon8			GTTTGGTCAAATT	AB051525	CCDS11658.1, CCDS74131.1	17q23.3	2007-03-13	2007-03-13			ENSG00000136478			30884	protein-coding gene	gene with protein product	"transmembrane protein 96"		"testis expressed sequence 2"			11214970	Standard	XM_005257507		Approved	HT008, TMEM96, KIAA1738	uc002jee.3	Q8IWB9		ENST00000583097.1:c.2743A>G	chr17.hg19:g.62238222T>C	ENSP00000462665:p.Thr915Ala	117.0	0.0		115.0	41.0	NM_018469	Q6AHZ5|Q8N3L0|Q9C0C5	Missense_Mutation	SNP	ENST00000583097.1	hg19		.	.	.	.	.	.	.	.	.	.	T	12.35	1.910663	0.33721	.	.	ENSG00000136478	ENST00000258991	T	0.41400	1.0	5.84	5.84	0.93424	.	0.099080	0.64402	D	0.000001	T	0.33818	0.0876	L	0.33485	1.01	0.50313	D	0.999862	B;B	0.19706	0.038;0.023	B;B	0.26517	0.07;0.032	T	0.12400	-1.0549	10	0.35671	T	0.21	-19.7321	11.3176	0.49401	0.1357:0.0:0.0:0.8643	.	922;915	Q8IWB9-2;Q8IWB9	.;TEX2_HUMAN	A	922	ENSP00000258991:T922A	ENSP00000258991:T922A	T	-	1	0	TEX2	59591954	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.025000	0.49681	2.234000	0.73211	0.459000	0.35465	ACC	.	.		0.413	TEX2-003	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000443745.1	NM_018469		C	62238222	T	C	62238222	3	2	371	1	0	0	0	0	1	0	0	0	15796	1667	58	2	660	2	TEX2	17	62238222	Missense_Mutation	SNP	T	TCGA-ZS-A9CE-01A-11D-A36X-10	7210683	62238222	18956988	91	51383										
HELZ	9931	hgsc.bcm.edu	37	chr17	65103749	65103749	+	Nonsense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	tggtggcatttcagctagttCccgtgtttcactttgatcac	9	10	3	1			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr17:65103749C>A	ENST00000358691.5	-	31	4943	c.4777G>T	c.(4777-4779)Gaa>Taa	p.E1593*	HELZ_ENST00000580168.1_Nonsense_Mutation_p.E1594*	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	1593						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					TCAGCTAGTTCCCGTGTTTCA	0.423																																					p.E1593X		Atlas-SNP	.											.	HELZ	160	.	0			c.G4777T						.						101	97	98					17																	65103749		1927	4128	6055	SO:0001587	stop_gained	9931	exon31			CTAGTTCCCGTGT	D29677	CCDS42374.1	17q24.2	2013-01-18			ENSG00000198265	ENSG00000198265		"Zinc fingers, CCCH-type domain containing"	16878	protein-coding gene	gene with protein product	"down-regulated in human cancers"	606699				10471385, 12691822	Standard	NM_014877		Approved	KIAA0054, HUMORF5, DHRC	uc002jfx.4	P42694	OTTHUMG00000179555	ENST00000358691.5:c.4777G>T	chr17.hg19:g.65103749C>A	ENSP00000351524:p.Glu1593*	163.0	0.0		187.0	84.0	NM_014877	I6L9H4	Nonsense_Mutation	SNP	ENST00000358691.5	hg19	CCDS42374.1	.	.	.	.	.	.	.	.	.	.	C	45	11.662574	0.99588	.	.	ENSG00000198265	ENST00000358691	.	.	.	5.08	5.08	0.68730	.	0.161243	0.52532	D	0.000077	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	-14.7503	18.4879	0.90836	0.0:1.0:0.0:0.0	.	.	.	.	X	1593	.	ENSP00000351524:E1593X	E	-	1	0	HELZ	62534211	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.784000	0.68990	2.368000	0.80403	0.478000	0.44815	GAA	.	.		0.423	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		A	65103749	C	A	65103749	4	1	371	1	0	0	0	0	0	1	0	0	7058	864	30	3	1063	3	HELZ	17	65103749	Nonsense_Mutation	SNP	C	TCGA-ZS-A9CE-01A-11D-A36X-10	2865527	65103749	16091461	92	51384										
JMJD6	23210	hgsc.bcm.edu	37	chr17	74721921	74721921	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	cagacagctgtaaagcatctGccctttccacgttatcctga	7	13	1	2	rs367636744		TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr17:74721921G>A	ENST00000397625.4	-	2	260	c.146C>T	c.(145-147)gCa>gTa	p.A49V	JMJD6_ENST00000445478.2_Missense_Mutation_p.A49V|METTL23_ENST00000590964.1_5'Flank|METTL23_ENST00000586752.1_5'Flank|METTL23_ENST00000588302.1_5'Flank|METTL23_ENST00000586738.1_5'Flank|METTL23_ENST00000341249.6_5'Flank|METTL23_ENST00000586200.1_5'Flank|METTL23_ENST00000588783.1_5'Flank|METTL23_ENST00000589977.1_5'Flank|METTL23_ENST00000591571.1_5'Flank|METTL23_ENST00000588822.1_5'Flank|JMJD6_ENST00000585429.1_Missense_Mutation_p.A49V	NM_015167.2	NP_055982.2	Q6NYC1	JMJD6_HUMAN	jumonji domain containing 6	49					cell surface receptor signaling pathway (GO:0007166)|erythrocyte development (GO:0048821)|heart development (GO:0007507)|histone H3-R2 demethylation (GO:0070078)|histone H4-R3 demethylation (GO:0070079)|kidney development (GO:0001822)|lung development (GO:0030324)|macrophage activation (GO:0042116)|mRNA processing (GO:0006397)|peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine (GO:0018395)|recognition of apoptotic cell (GO:0043654)|regulation of mRNA splicing, via spliceosome (GO:0048024)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|RNA splicing (GO:0008380)|sprouting angiogenesis (GO:0002040)|T cell differentiation in thymus (GO:0033077)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone demethylase activity (H3-R2 specific) (GO:0033746)|histone demethylase activity (H4-R3 specific) (GO:0033749)|identical protein binding (GO:0042802)|iron ion binding (GO:0005506)|peptidyl-lysine 5-dioxygenase activity (GO:0070815)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			endometrium(2)|kidney(5)|large_intestine(2)|lung(3)|ovary(2)|skin(2)	16						TAAAGCATCTGCCCTTTCCAC	0.468																																					p.A49V		Atlas-SNP	.											.	JMJD6	57	.	0			c.C146T						.						66	61	63					17																	74721921		1852	4096	5948	SO:0001583	missense	23210	exon2			GCATCTGCCCTTT	AB011157	CCDS42383.1, CCDS42384.1	17q25	2007-11-20	2007-02-16	2007-02-16	ENSG00000070495	ENSG00000070495			19355	protein-coding gene	gene with protein product		604914	"phosphatidylserine receptor"	PTDSR		11877474	Standard	NM_015167		Approved	PTDSR1, KIAA0585	uc002jsn.1	Q6NYC1	OTTHUMG00000169267	ENST00000397625.4:c.146C>T	chr17.hg19:g.74721921G>A	ENSP00000380750:p.Ala49Val	52.0	0.0		71.0	5.0	NM_001081461	B3KMN8|B4DGX1|Q86VY0|Q8IUM5|Q9Y4E2	Missense_Mutation	SNP	ENST00000397625.4	hg19	CCDS42384.1	.	.	.	.	.	.	.	.	.	.	G	1.946	-0.442318	0.04604	.	.	ENSG00000070495	ENST00000445478;ENST00000344991;ENST00000397625	T;T	0.68181	-0.31;-0.31	5.5	4.33	0.51752	.	0.162754	0.53938	D	0.000046	T	0.25195	0.0612	N	0.00237	-1.79	0.47994	D	0.999565	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.08055	0.0;0.001;0.003	T	0.48234	-0.9053	10	0.02654	T	1	-16.5806	11.6802	0.51453	0.1518:0.0:0.8482:0.0	.	49;49;49	B2WTI3;Q6NYC1;Q6NYC1-3	.;JMJD6_HUMAN;.	V	49	ENSP00000394085:A49V;ENSP00000380750:A49V	ENSP00000302916:A49V	A	-	2	0	JMJD6	72233516	1.000000	0.71417	0.941000	0.38009	0.078000	0.17371	5.165000	0.64959	2.568000	0.86640	0.555000	0.69702	GCA	.	.		0.468	JMJD6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403211.1	NM_015167		A	74721921	G	A	74721921	3	1	371	1	0	0	0	0	1	0	0	0	7962	1319	46	3	1126	3	JMJD6	17	74721921	Missense_Mutation	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10	9618172	74721921	6473289	93	51385										
TNRC6C	57690	hgsc.bcm.edu	37	chr17	76087679	76087679	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	cccccctggagcagaaccctAgcaagcatggtacgtctgag	11	14	1	2			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr17:76087679A>G	ENST00000588061.1	+	16	4688	c.3961A>G	c.(3961-3963)Agc>Ggc	p.S1321G	TNRC6C_ENST00000544502.1_Missense_Mutation_p.S1318G|TNRC6C_ENST00000335749.4_Missense_Mutation_p.S1318G|TNRC6C_ENST00000301624.4_Missense_Mutation_p.S1321G|TNRC6C_ENST00000588847.1_Missense_Mutation_p.S1318G|TNRC6C_ENST00000541771.1_Missense_Mutation_p.S1321G			Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C	1321	Silencing domain; interaction with CNOT1 and PAN3.				embryonic hemopoiesis (GO:0035162)|endoderm formation (GO:0001706)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of gene silencing by miRNA (GO:0060964)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			GCAGAACCCTAGCAAGCATGG	0.552																																					p.S1321G		Atlas-SNP	.											.	TNRC6C	173	.	0			c.A3961G						.						30	32	31					17																	76087679		2007	4165	6172	SO:0001583	missense	57690	exon15			AACCCTAGCAAGC	AL834429	CCDS45798.1, CCDS45799.1	17q25.3	2012-10-04			ENSG00000078687	ENSG00000078687		"Trinucleotide (CAG) repeat containing"	29318	protein-coding gene	gene with protein product		610741					Standard	NM_018996		Approved	KIAA1582, FLJ20015	uc002juf.2	Q9HCJ0	OTTHUMG00000132642	ENST00000588061.1:c.3961A>G	chr17.hg19:g.76087679A>G	ENSP00000468647:p.Ser1321Gly	62.0	0.0		68.0	25.0	NM_018996	G3XAB8|Q86UE5|Q8N3D8|Q96MU9	Missense_Mutation	SNP	ENST00000588061.1	hg19	CCDS45798.1	.	.	.	.	.	.	.	.	.	.	A	12.89	2.074641	0.36566	.	.	ENSG00000078687	ENST00000455761;ENST00000395801;ENST00000335749;ENST00000301624;ENST00000541771;ENST00000544502	T;T;T;T	0.16324	2.35;2.35;2.35;2.35	5.97	2.48	0.30137	.	0.184288	0.64402	N	0.000013	T	0.09949	0.0244	N	0.24115	0.695	0.29309	N	0.868151	B;B	0.09022	0.002;0.0	B;B	0.09377	0.004;0.002	T	0.28870	-1.0030	10	0.20046	T	0.44	-8.5714	8.6295	0.33911	0.7047:0.0:0.2953:0.0	.	1318;1321	G3XAB8;Q9HCJ0	.;TNR6C_HUMAN	G	1321;1318;1318;1321;1321;1318	ENSP00000336783:S1318G;ENSP00000301624:S1321G;ENSP00000440310:S1321G;ENSP00000442421:S1318G	ENSP00000301624:S1321G	S	+	1	0	TNRC6C	73599274	0.822000	0.29219	0.851000	0.33527	0.928000	0.56348	1.431000	0.34925	0.139000	0.18822	-0.417000	0.06048	AGC	.	.		0.552	TNRC6C-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395947.1	NM_018996		G	76087679	A	G	76087679	3	3	371	1	0	0	0	0	1	0	0	0	16357	420	15	2	4007	2	TNRC6C	17	76087679	Missense_Mutation	SNP	A	TCGA-ZS-A9CE-01A-11D-A36X-10	1365758	76087679	5107531	94	51386										
EMILIN2	84034	hgsc.bcm.edu	37	chr18	2891712	2891712	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	gccctgccaggagtgtcaggGtcaggagatgaacgggtcat	16	9	3	2			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr18:2891712G>A	ENST00000254528.3	+	4	1746	c.1587G>A	c.(1585-1587)ggG>ggA	p.G529G		NM_032048.2	NP_114437.2	Q9BXX0	EMIL2_HUMAN	elastin microfibril interfacer 2	529					cell adhesion (GO:0007155)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix constituent conferring elasticity (GO:0030023)			breast(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(4)	48				READ - Rectum adenocarcinoma(2;0.1)		GAGTGTCAGGGTCAGGAGATG	0.532																																					p.G529G		Atlas-SNP	.											.	EMILIN2	97	.	0			c.G1587A						.						70	72	71					18																	2891712		2203	4300	6503	SO:0001819	synonymous_variant	84034	exon4			GTCAGGGTCAGGA	AF270513	CCDS11828.1	18p11.3	2008-02-05			ENSG00000132205	ENSG00000132205		"EMI domain containing"	19881	protein-coding gene	gene with protein product		608928					Standard	NM_032048		Approved	FLJ33200, FOAP-10	uc002kln.3	Q9BXX0	OTTHUMG00000128525	ENST00000254528.3:c.1587G>A	chr18.hg19:g.2891712G>A		82.0	0.0		96.0	26.0	NM_032048	B2RMY3|Q8NBH3|Q96JQ4	Silent	SNP	ENST00000254528.3	hg19	CCDS11828.1																																																																																			.	.		0.532	EMILIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250337.2	NM_032048		A	2891712	G	A	2891712	2	1	371	1	0	0	0	0	0	0	0	1	5096	1248	44	3		3	EMILIN2	18	2891712	Silent	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10		2891712	75185536	95	51387										
ANKRD12	23253	hgsc.bcm.edu	37	chr18	9258165	9258165	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	aggtcatttcacatgaaaaaGaaaacaaactggagagtttg	9	5	2	3			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr18:9258165G>C	ENST00000262126.4	+	9	5140	c.4900G>C	c.(4900-4902)Gaa>Caa	p.E1634Q	RP11-888D10.4_ENST00000609701.1_RNA|ANKRD12_ENST00000400020.3_Missense_Mutation_p.E1611Q|ANKRD12_ENST00000383440.2_Missense_Mutation_p.E1611Q	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	1634						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						ACATGAAAAAGAAAACAAACT	0.353																																					p.E1634Q		Atlas-SNP	.											.	ANKRD12	167	.	0			c.G4900C						.						59	57	58					18																	9258165		2203	4300	6503	SO:0001583	missense	23253	exon9			GAAAAAGAAAACA	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.4900G>C	chr18.hg19:g.9258165G>C	ENSP00000262126:p.Glu1634Gln	80.0	0.0		92.0	46.0	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Missense_Mutation	SNP	ENST00000262126.4	hg19	CCDS11843.1	.	.	.	.	.	.	.	.	.	.	G	10.69	1.422350	0.25639	.	.	ENSG00000101745	ENST00000383440;ENST00000262126	T;T	0.57107	0.42;0.42	5.29	5.29	0.74685	.	0.362158	0.27749	N	0.018011	T	0.41971	0.1182	L	0.29908	0.895	0.42281	D	0.992097	B;B	0.34103	0.437;0.31	B;B	0.34779	0.189;0.134	T	0.40905	-0.9538	10	0.48119	T	0.1	-10.7309	12.6308	0.56657	0.0762:0.0:0.9238:0.0	.	1611;1634	Q6UB98-2;Q6UB98	.;ANR12_HUMAN	Q	1611;1634	ENSP00000372932:E1611Q;ENSP00000262126:E1634Q	ENSP00000262126:E1634Q	E	+	1	0	ANKRD12	9248165	1.000000	0.71417	0.989000	0.46669	0.460000	0.32559	5.503000	0.66962	2.619000	0.88677	0.655000	0.94253	GAA	.	.		0.353	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		C	9258165	G	C	9258165	3	2	371	1	0	0	0	0	1	0	0	0	640	943	33	4	4930	4	ANKRD12	18	9258165	Missense_Mutation	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10	6366453	9258165	68819083	96	51388										
FHOD3	80206	hgsc.bcm.edu	37	chr18	34326998	34326998	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	tcaaggcaattgcaaaacatGaaatgaaaccagttttaaaa	6	6	1	2			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr18:34326998G>T	ENST00000359247.4	+	20	3556	c.3556G>T	c.(3556-3558)Gaa>Taa	p.E1186*	FHOD3_ENST00000257209.4_Nonsense_Mutation_p.E1203*|FHOD3_ENST00000590592.1_Nonsense_Mutation_p.E1378*|FHOD3_ENST00000445677.1_Nonsense_Mutation_p.E1165*|FHOD3_ENST00000592128.1_Nonsense_Mutation_p.E182*|FHOD3_ENST00000591635.1_Nonsense_Mutation_p.E399*	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	1186	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)				NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				TGCAAAACATGAAATGAAACC	0.363																																					p.E1203X		Atlas-SNP	.											FHOD3,NS,carcinoma,0,1	FHOD3	210	.	0			c.G3607T						.						95	92	93					18																	34326998		2203	4300	6503	SO:0001587	stop_gained	80206	exon21			AAACATGAAATGA	AK091899	CCDS32816.1, CCDS62418.1, CCDS62419.1	18q12	2007-08-02				ENSG00000134775			26178	protein-coding gene	gene with protein product		609691				11214970	Standard	NM_025135		Approved	FHOS2, KIAA1695, FLJ22297, FLJ22717	uc021uiv.1	Q2V2M9		ENST00000359247.4:c.3556G>T	chr18.hg19:g.34326998G>T	ENSP00000352186:p.Glu1186*	217.0	0.0		190.0	40.0	NM_025135	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Nonsense_Mutation	SNP	ENST00000359247.4	hg19		.	.	.	.	.	.	.	.	.	.	G	42	9.676315	0.99236	.	.	ENSG00000134775	ENST00000257209;ENST00000359247;ENST00000445677	.	.	.	5.67	4.79	0.61399	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	13.1176	0.59309	0.0776:0.0:0.9224:0.0	.	.	.	.	X	1203;1186;1165	.	ENSP00000257209:E1203X	E	+	1	0	FHOD3	32580996	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.869000	0.99810	1.404000	0.46819	0.462000	0.41574	GAA	.	.		0.363	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114		T	34326998	G	T	34326998	4	4	371	1	0	0	0	0	0	1	0	0	5891	1291	45	3	3689	3	FHOD3	18	34326998	Nonsense_Mutation	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10	25068833	34326998	43750250	97	51389										
SERPINB4	6318	hgsc.bcm.edu	37	chr18	61305147	61305147	+	Nonsense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	aaaggccttgtgtaggacttTagatactgagagaccgtggc	13	7	0	3			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr18:61305147T>A	ENST00000341074.5	-	8	1094	c.979A>T	c.(979-981)Aaa>Taa	p.K327*	SERPINB4_ENST00000356424.6_Nonsense_Mutation_p.K275*	NM_002974.2	NP_002965.1	P48594	SPB4_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 4	327					negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	enzyme binding (GO:0019899)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	42						TGTAGGACTTTAGATACTGAG	0.502																																					p.K327X		Atlas-SNP	.											.	SERPINB4	89	.	0			c.A979T						.						130	120	123					18																	61305147		2203	4300	6503	SO:0001587	stop_gained	6318	exon8			GGACTTTAGATAC	X89015	CCDS11986.1	18q21.33	2014-02-18	2005-08-18		ENSG00000206073	ENSG00000206073		"Serine (or cysteine) peptidase inhibitors"	10570	protein-coding gene	gene with protein product	"squamous cell carcinoma antigen 2"	600518	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 4"	SCCA2		7724531, 14630915, 24172014	Standard	NM_175041		Approved	PI11, LEUPIN, SCCA-2, SCCA1		P48594	OTTHUMG00000060405	ENST00000341074.5:c.979A>T	chr18.hg19:g.61305147T>A	ENSP00000343445:p.Lys327*	92.0	0.0		107.0	56.0	NM_002974	A8K847	Nonsense_Mutation	SNP	ENST00000341074.5	hg19	CCDS11986.1	.	.	.	.	.	.	.	.	.	.	t	17.04	3.288069	0.59976	.	.	ENSG00000206073	ENST00000341074;ENST00000356424	.	.	.	4.51	2.08	0.27032	.	0.333204	0.21587	N	0.072149	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.4414	0.32818	0.0:0.2432:0.0:0.7568	.	.	.	.	X	327;275	.	ENSP00000343445:K327X	K	-	1	0	SERPINB4	59456127	0.000000	0.05858	0.001000	0.08648	0.024000	0.10985	-0.170000	0.09897	0.338000	0.23692	-0.308000	0.09152	AAA	.	.		0.502	SERPINB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133794.2	NM_175041		A	61305147	T	A	61305147	4	1	371	1	0	0	0	0	0	1	0	0	14118	1763	61	4	197	4	SERPINB4	18	61305147	Nonsense_Mutation	SNP	T	TCGA-ZS-A9CE-01A-11D-A36X-10	26978149	61305147	16772101	98	51390										
PCSK4	92840	hgsc.bcm.edu	37	chr19	1490287	1490287	+	5'Flank	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	cccaccccacagcccgggggCggacaagggccagggccaag	15	17	0	0			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr19:1490287C>T	ENST00000233596.3	+	0	0				PCSK4_ENST00000587784.1_Intron|PCSK4_ENST00000300954.5_Missense_Mutation_p.R20H	NM_138393.1	NP_612402.1	Q96HR9	REEP6_HUMAN	receptor accessory protein 6						regulation of intracellular transport (GO:0032386)	apical part of cell (GO:0045177)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				lung(1)|ovary(1)	2		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AGCCCGGGGGCGGACAAGGGC	0.741																																					p.R20H		Atlas-SNP	.											.	PCSK4	44	.	0			c.G59A						.						5	7	6					19																	1490287		2114	4156	6270	SO:0001631	upstream_gene_variant	54760	exon1			CGGGGGCGGACAA	BC008201	CCDS12070.1	19p13.3	2012-12-20	2006-02-08	2006-02-07	ENSG00000115255	ENSG00000115255		"Receptor accessory proteins"	30078	protein-coding gene	gene with protein product	"polyposis locus protein 1-like 1", "deleted in polyposis 1-like 1"	609346	"chromosome 19 open reading frame 32"	C19orf32		16271481, 15550249	Standard	NM_138393		Approved	DP1L1, FLJ25383	uc002ltc.3	Q96HR9	OTTHUMG00000180072		chr19.hg19:g.1490287C>T	Exception_encountered	48.0	0.0		34.0	14.0	NM_017573	B2RE01|D6W5Z0|Q96LM0	Missense_Mutation	SNP	ENST00000233596.3	hg19	CCDS12070.1	.	.	.	.	.	.	.	.	.	.	C	6.172	0.399835	0.11696	.	.	ENSG00000115257	ENST00000300954	T	0.69175	-0.38	3.31	0.995	0.19838	.	1.617810	0.04195	N	0.329028	T	0.37100	0.0991	N	0.08118	0	0.09310	N	1	P	0.46277	0.875	B	0.32211	0.142	T	0.30001	-0.9993	10	0.15499	T	0.54	.	4.8057	0.13319	0.2108:0.6684:0.0:0.1208	.	20	Q6UW60	PCSK4_HUMAN	H	20	ENSP00000300954:R20H	ENSP00000300954:R20H	R	-	2	0	PCSK4	1441287	0.067000	0.21026	0.088000	0.20740	0.016000	0.09150	0.437000	0.21543	0.053000	0.16036	0.313000	0.20887	CGC	.	.		0.741	REEP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449623.1	NM_138393		T	1490287	C	T	1490287	1	4	371	0	1	0	0	0	0	0	0	0	11611	768	27	1		1	PCSK4	19	1490287	5'Flank	SNP	C	TCGA-ZS-A9CE-01A-11D-A36X-10		1490287	57638696	99	51391										
GATAD2A	54815	hgsc.bcm.edu	37	chr19	19607000	19607000	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	ccgcgtcgccaatgttcccaAcaccagcctgctcgtcaaca	7	18	1	0			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr19:19607000A>G	ENST00000360315.3	+	7	1208	c.896A>G	c.(895-897)aAc>aGc	p.N299S	GATAD2A_ENST00000252577.5_Missense_Mutation_p.N299S|GATAD2A_ENST00000429563.2_Missense_Mutation_p.N126S|GATAD2A_ENST00000537887.1_Intron|GATAD2A_ENST00000358713.3_Missense_Mutation_p.N299S|GATAD2A_ENST00000404158.1_Missense_Mutation_p.N299S	NM_017660.3	NP_060130.3	Q86YP4	P66A_HUMAN	GATA zinc finger domain containing 2A	299					anterior neuropore closure (GO:0021506)|blood vessel development (GO:0001568)|DNA methylation (GO:0006306)|embryonic body morphogenesis (GO:0010172)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|neural fold formation (GO:0001842)|programmed cell death (GO:0012501)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|NuRD complex (GO:0016581)	protein binding, bridging (GO:0030674)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	13						AATGTTCCCAACACCAGCCTG	0.652																																					p.N299S		Atlas-SNP	.											.	GATAD2A	81	.	0			c.A896G						.						113	89	97					19																	19607000		2203	4300	6503	SO:0001583	missense	54815	exon7			TTCCCAACACCAG	AL390164	CCDS12402.2	19p13.11	2013-01-25			ENSG00000167491	ENSG00000167491		"GATA zinc finger domain containing"	29989	protein-coding gene	gene with protein product	"p66 alpha"	614997				12183469	Standard	NM_017660		Approved	p66alpha	uc010xqt.2	Q86YP4	OTTHUMG00000152541	ENST00000360315.3:c.896A>G	chr19.hg19:g.19607000A>G	ENSP00000353463:p.Asn299Ser	54.0	0.0		56.0	19.0	NM_017660	B5MC40|Q7L3J2|Q96F28|Q9NPU2|Q9NXS1	Missense_Mutation	SNP	ENST00000360315.3	hg19	CCDS12402.2	.	.	.	.	.	.	.	.	.	.	A	13.85	2.360410	0.41801	.	.	ENSG00000167491	ENST00000360315;ENST00000252577;ENST00000404158;ENST00000358713;ENST00000429563	T;T;T;T	0.44083	1.5;1.54;1.5;0.93	5.65	2.48	0.30137	.	0.042391	0.85682	N	0.000000	T	0.30665	0.0772	L	0.43923	1.385	0.80722	D	1	B;B;B	0.20261	0.043;0.043;0.043	B;B;B	0.15870	0.014;0.014;0.014	T	0.06356	-1.0831	10	0.24483	T	0.36	-1.2984	8.4933	0.33112	0.7771:0.0:0.2229:0.0	.	126;318;299	B4DKZ7;B5MC40;Q86YP4	.;.;P66A_HUMAN	S	299;299;318;299;126	ENSP00000353463:N299S;ENSP00000252577:N299S;ENSP00000351552:N299S;ENSP00000388416:N126S	ENSP00000252577:N299S	N	+	2	0	GATAD2A	19468000	0.986000	0.35501	0.994000	0.49952	0.995000	0.86356	2.251000	0.43187	0.115000	0.18071	0.533000	0.62120	AAC	.	.		0.652	GATAD2A-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326671.4	NM_017660		G	19607000	A	G	19607000	3	3	371	1	0	0	0	0	1	0	0	0	6268	43	2	2	918	2	GATAD2A	19	19607000	Missense_Mutation	SNP	A	TCGA-ZS-A9CE-01A-11D-A36X-10	18116713	19607000	39521983	100	51392										
ZNF99	7652	hgsc.bcm.edu	37	chr19	22941385	22941385	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	ccagtatgaattatcttatgTtttctaagggctgagaaacg	9	6	2	2			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr19:22941385T>A	ENST00000596209.1	-	4	1416	c.1326A>T	c.(1324-1326)aaA>aaT	p.K442N	ZNF99_ENST00000397104.3_Missense_Mutation_p.K351N	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	442					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				TTATCTTATGTTTTCTAAGGG	0.358																																					p.K442N		Atlas-SNP	.											.	ZNF99	273	.	0			c.A1326T						.						57	59	58					19																	22941385		2029	4215	6244	SO:0001583	missense	7652	exon4			CTTATGTTTTCTA	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"Zinc fingers, C2H2-type", "-"	13175	protein-coding gene	gene with protein product		603981	"zinc finger protein 99 (F8281)", "chromosome 19 open reading frame 9"	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.1326A>T	chr19.hg19:g.22941385T>A	ENSP00000472969:p.Lys442Asn	58.0	0.0		73.0	32.0	NM_001080409	M0R335	Missense_Mutation	SNP	ENST00000596209.1	hg19	CCDS59369.1	.	.	.	.	.	.	.	.	.	.	N	1.143	-0.648896	0.03506	.	.	ENSG00000213973	ENST00000397104	T	0.20598	2.06	1.28	-2.55	0.06288	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.11239	0.0274	N	0.25485	0.75	0.09310	N	1	B	0.17465	0.022	B	0.26517	0.07	T	0.39099	-0.9630	9	0.19590	T	0.45	.	2.6546	0.05008	0.4804:0.2932:0.0:0.2264	.	351	A8MXY4	ZNF99_HUMAN	N	351	ENSP00000380293:K351N	ENSP00000380293:K351N	K	-	3	2	ZNF99	22733225	0.000000	0.05858	0.002000	0.10522	0.036000	0.12997	-5.051000	0.00156	-1.146000	0.02854	-0.560000	0.04181	AAA	.	.		0.358	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124		A	22941385	T	A	22941385	3	1	371	1	0	0	0	0	1	0	0	0	18219	1722	60	4	2071	4	ZNF99	19	22941385	Missense_Mutation	SNP	T	TCGA-ZS-A9CE-01A-11D-A36X-10	3334385	22941385	36187598	101	51393										
ZNF91	7644	hgsc.bcm.edu	37	chr19	23545201	23545201	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	atgttgggttttgtgtaaacGgatgcaaaatgacttgacac	11	5	0	2	rs377229432		TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr19:23545201G>A	ENST00000300619.7	-	4	785	c.580C>T	c.(580-582)Cgt>Tgt	p.R194C	ZNF91_ENST00000397082.2_Missense_Mutation_p.R162C|ZNF91_ENST00000599743.1_Intron	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	194					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				TTGTGTAAACGGATGCAAAAT	0.308																																					p.R194C		Atlas-SNP	.											.	ZNF91	349	.	0			c.C580T						.	G	CYS/ARG	2,4120		0,2,2059	74	76	75		580		0.1	19		75	1,8489		0,1,4244	no	missense	ZNF91	NM_003430.2	180	0,3,6303	AA,AG,GG		0.0118,0.0485,0.0238	possibly-damaging	194/1192	23545201	3,12609	2061	4245	6306	SO:0001583	missense	7644	exon4			GTAAACGGATGCA	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"Zinc fingers, C2H2-type", "-"	13166	protein-coding gene	gene with protein product		603971	"zinc finger protein 91 (HPF7, HTF10)"			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.580C>T	chr19.hg19:g.23545201G>A	ENSP00000300619:p.Arg194Cys	119.0	0.0		159.0	8.0	NM_003430	A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	hg19	CCDS42541.1	.	.	.	.	.	.	.	.	.	.	G	1.656	-0.512791	0.04200	4.85E-4	1.18E-4	ENSG00000167232	ENST00000300619;ENST00000397082	T;T	0.16073	2.37;2.37	.	.	.	Zinc finger, C2H2 (1);	.	.	.	.	T	0.06826	0.0174	L	0.28014	0.82	0.09310	N	1	P;B	0.43578	0.811;0.319	B;B	0.14578	0.011;0.002	T	0.29971	-0.9994	8	0.52906	T	0.07	.	3.8088	0.08788	0.0:0.0:0.5804:0.4195	.	162;194	Q05481-2;Q05481	.;ZNF91_HUMAN	C	194;162	ENSP00000300619:R194C;ENSP00000380272:R162C	ENSP00000300619:R194C	R	-	1	0	ZNF91	23337041	0.000000	0.05858	0.078000	0.20375	0.020000	0.10135	-3.047000	0.00630	0.064000	0.16427	0.064000	0.15345	CGT	.	.		0.308	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430		A	23545201	G	A	23545201	3	1	371	1	0	0	0	0	1	0	0	0	18215	1116	39	1	2999	1	ZNF91	19	23545201	Missense_Mutation	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10	603816	23545201	35583782	102	51394										
C19orf48	84798	hgsc.bcm.edu	37	chr19	51301638	51301638	+	Frame_Shift_Del	DEL	G	G	-													0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	ctggtggcctggcgggccctGgcaccatggagagcagcctg							TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr19:51301638delG	ENST00000598463.1	-	5	1166	c.68delC	c.(67-69)ccafs	p.P23fs	C19orf48_ENST00000595794.1_5'Flank|SNORD88B_ENST00000408454.1_RNA|C19orf48_ENST00000596655.1_Frame_Shift_Del_p.P23fs|C19orf48_ENST00000391812.1_Frame_Shift_Del_p.P23fs|SNORD88A_ENST00000408314.1_RNA|C19orf48_ENST00000345523.4_Frame_Shift_Del_p.P23fs			Q6RUI8	CS048_HUMAN	chromosome 19 open reading frame 48	23										endometrium(1)|kidney(1)|lung(1)|ovary(1)	4		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00531)|GBM - Glioblastoma multiforme(134;0.0145)		GGCGGGCCCTGGCACCATGGA	0.622																																					p.P23fs		Atlas-INDEL	.											.	C19orf48	11	.	0			c.69delA						.						85	83	84					19																	51301638		2203	4300	6503	SO:0001589	frameshift_variant	84798	exon5			.	BC037227	CCDS12803.1	19q13.33	2012-10-26			ENSG00000167747	ENSG00000167747			29667	protein-coding gene	gene with protein product	"multidrug resistance-related protein"					12452007	Standard	NM_001290154		Approved	MGC13170	uc002ptg.3	Q6RUI8		ENST00000598463.1:c.68delC	chr19.hg19:g.51301638delG	ENSP00000471463:p.Pro23fs	51.0	0.0		72.0	21.0	NM_199249		Frame_Shift_Del	DEL	ENST00000598463.1	hg19	CCDS12803.1																																																																																			.	.		0.622	C19orf48-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464107.1	NM_032712		-	51301638	G	-	51301638	7	5	371	1	0	1	0	1	0	0	0	0	1933	1348	47	0	289	0	C19orf48	19	51301638	Frame_Shift_Del	DEL	G	TCGA-ZS-A9CE-01A-11D-A36X-10	27756437	51301638	7827345	103	51395										
SSTR4	6754	hgsc.bcm.edu	37	chr20	23017238	23017238	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	ccagcaggaagccctgcaacCagaacccggccgcaagcgca	11	17	0	1			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr20:23017238C>A	ENST00000255008.3	+	1	1182	c.1118C>A	c.(1117-1119)cCa>cAa	p.P373Q	RP4-753D10.3_ENST00000440921.1_RNA	NM_001052.2	NP_001043.2	P31391	SSR4_HUMAN	somatostatin receptor 4	373					arachidonic acid metabolic process (GO:0019369)|cell migration (GO:0016477)|cellular response to glucocorticoid stimulus (GO:0071385)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP metabolic process (GO:0030815)|negative regulation of cell proliferation (GO:0008285)|positive regulation of MAPK cascade (GO:0043410)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)	p.P373Q(1)		breast(1)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)	32	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)					GCCCTGCAACCAGAACCCGGC	0.667																																					p.P373Q	Esophageal Squamous(15;850 1104 16640)	Atlas-SNP	.											SSTR4,NS,carcinoma,0,1	SSTR4	83	.	1	Substitution - Missense(1)	lung(1)	c.C1118A						.						40	48	45					20																	23017238		2081	4203	6284	SO:0001583	missense	6754	exon1			TGCAACCAGAACC		CCDS42856.1	20p11.21	2014-07-11			ENSG00000132671	ENSG00000132671		"GPCR / Class A : Somatostatin receptors"	11333	protein-coding gene	gene with protein product		182454				8483934	Standard	NM_001052		Approved		uc002wsr.2	P31391	OTTHUMG00000032054	ENST00000255008.3:c.1118C>A	chr20.hg19:g.23017238C>A	ENSP00000255008:p.Pro373Gln	61.0	0.0		66.0	13.0	NM_001052	Q17RM1|Q17RM3|Q9UIY1	Missense_Mutation	SNP	ENST00000255008.3	hg19	CCDS42856.1	.	.	.	.	.	.	.	.	.	.	C	3.375	-0.127528	0.06753	.	.	ENSG00000132671	ENST00000255008	T	0.65178	-0.14	3.92	1.89	0.25635	.	1.730700	0.03659	N	0.242347	T	0.49779	0.1577	N	0.22421	0.69	0.09310	N	0.999998	B	0.12630	0.006	B	0.12837	0.008	T	0.38607	-0.9653	10	0.51188	T	0.08	.	6.9321	0.24447	0.1725:0.7314:0.0:0.0962	.	373	P31391	SSR4_HUMAN	Q	373	ENSP00000255008:P373Q	ENSP00000255008:P373Q	P	+	2	0	SSTR4	22965238	0.049000	0.20398	0.067000	0.19924	0.002000	0.02628	1.327000	0.33746	0.284000	0.22305	-0.140000	0.14226	CCA	.	.		0.667	SSTR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078308.1			A	23017238	C	A	23017238	3	1	371	1	0	0	0	0	1	0	0	0	15215	594	21	3	1120	3	SSTR4	20	23017238	Missense_Mutation	SNP	C	TCGA-ZS-A9CE-01A-11D-A36X-10		23017238	40008282	104	51396										
CABLES2	81928	hgsc.bcm.edu	37	chr20	60967986	60967986	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	gggcactcaccatgtacgacGcaaagatgaggacacgtttg	12	10	1	2			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr20:60967986G>A	ENST00000279101.5	-	7	982	c.974C>T	c.(973-975)gCg>gTg	p.A325V		NM_031215.2	NP_112492.2	Q9BTV7	CABL2_HUMAN	Cdk5 and Abl enzyme substrate 2	325					cell cycle (GO:0007049)|cell division (GO:0051301)|regulation of cell cycle (GO:0051726)|regulation of cell division (GO:0051302)		cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			endometrium(2)|kidney(1)|lung(6)|pancreas(1)|skin(1)	11	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			CATGTACGACGCAAAGATGAG	0.647																																					p.A325V		Atlas-SNP	.											.	CABLES2	30	.	0			c.C974T						.						150	130	137					20																	60967986		2203	4300	6503	SO:0001583	missense	81928	exon7			TACGACGCAAAGA	BC003122	CCDS33503.1	20q13.33	2004-01-09	2004-01-09	2004-01-09	ENSG00000149679	ENSG00000149679			16143	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 150"	C20orf150		12477932	Standard	NM_031215		Approved	dJ908M14.2, ik3-2	uc002ycv.2	Q9BTV7	OTTHUMG00000032912	ENST00000279101.5:c.974C>T	chr20.hg19:g.60967986G>A	ENSP00000279101:p.Ala325Val	52.0	0.0		73.0	4.0	NM_031215	Q5JWL0|Q9BYK0	Missense_Mutation	SNP	ENST00000279101.5	hg19	CCDS33503.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.20|19.20	3.781958|3.781958	0.70222|0.70222	.|.	.|.	ENSG00000149679|ENSG00000149679	ENST00000370560;ENST00000279101|ENST00000453274	T|.	0.18016|.	2.24|.	5.05|5.05	5.05|5.05	0.67936|0.67936	Cyclin-like (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.75845|0.75845	0.3905|0.3905	M|M	0.72894|0.72894	2.215|2.215	0.80722|0.80722	D|D	1|1	D|.	0.56746|.	0.977|.	P|.	0.47075|.	0.536|.	T|T	0.75590|0.75590	-0.3265|-0.3265	10|5	0.27082|.	T|.	0.32|.	-23.5783|-23.5783	18.778|18.778	0.91920|0.91920	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	325|.	Q9BTV7|.	CABL2_HUMAN|.	V|C	113;325|119	ENSP00000279101:A325V|.	ENSP00000279101:A325V|.	A|R	-|-	2|1	0|0	CABLES2|CABLES2	60401381|60401381	1.000000|1.000000	0.71417|0.71417	0.695000|0.695000	0.30226|0.30226	0.121000|0.121000	0.20230|0.20230	9.633000|9.633000	0.98432|0.98432	2.522000|2.522000	0.85027|0.85027	0.655000|0.655000	0.94253|0.94253	GCG|CGT	.	.		0.647	CABLES2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080027.2	XM_037265		A	60967986	G	A	60967986	3	1	371	1	0	0	0	0	1	0	0	0	2532	1087	38	1	478	1	CABLES2	20	60967986	Missense_Mutation	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10	37950748	60967986	2057534	105	51397										
SEC14L2	23541	hgsc.bcm.edu	37	chr22	30803523	30803523	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	ctgttctcagcctccaaacaGgacctgctgaggaccaagat	9	13	1	2			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr22:30803523G>A	ENST00000312932.9	+	5	614	c.354G>A	c.(352-354)caG>caA	p.Q118Q	SEC14L2_ENST00000403484.1_Silent_p.Q44Q|SEC14L2_ENST00000402592.3_Intron|RP4-539M6.19_ENST00000439838.1_5'Flank|SEC14L2_ENST00000405717.3_Silent_p.Q118Q|SEC14L2_ENST00000459728.1_3'UTR	NM_012429.3	NP_036561.1	O76054	S14L2_HUMAN	SEC14-like 2 (S. cerevisiae)	118	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cholesterol biosynthetic process (GO:0045540)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	phospholipid binding (GO:0005543)|transporter activity (GO:0005215)|vitamin E binding (GO:0008431)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|urinary_tract(1)	10					Vitamin E(DB00163)	CCTCCAAACAGGACCTGCTGA	0.552																																					p.Q118Q		Atlas-SNP	.											.	SEC14L2	24	.	0			c.G354A						.						141	126	131					22																	30803523		2203	4300	6503	SO:0001819	synonymous_variant	23541	exon5			CAAACAGGACCTG	AL096881	CCDS13876.1, CCDS46685.1, CCDS56228.1	22q12.2	2010-08-19	2001-11-28		ENSG00000100003	ENSG00000100003			10699	protein-coding gene	gene with protein product	"supernatant protein factor"	607558	"SEC14 (S. cerevisiae)-like 2"	C22orf6		10591208	Standard	NM_033382		Approved	TAP, SPF, KIAA1186, KIAA1658	uc003ahr.3	O76054	OTTHUMG00000151024	ENST00000312932.9:c.354G>A	chr22.hg19:g.30803523G>A		58.0	0.0		90.0	33.0	NM_012429	B7Z8Q1|F5H3U4|Q53EQ2|Q6PD61|Q9ULN4	Silent	SNP	ENST00000312932.9	hg19	CCDS13876.1																																																																																			.	.		0.552	SEC14L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321018.4	NM_012429		A	30803523	G	A	30803523	2	1	371	1	0	0	0	0	0	0	0	1	13997	991	35	3		3	SEC14L2	22	30803523	Silent	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10		30803523	20501043	106	51398										
SLC5A4	6527	hgsc.bcm.edu	37	chr22	32627060	32627060	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	aggtaccacacatgctaccaTatctggggaagaattcagaa	9	9	2	2			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr22:32627060T>C	ENST00000266086.4	-	10	1035	c.1024A>G	c.(1024-1026)Atg>Gtg	p.M342V	RP1-90G24.10_ENST00000434942.1_RNA	NM_014227.2	NP_055042.1	Q9NY91	SC5A4_HUMAN	solute carrier family 5 (glucose activated ion channel), member 4	342					carbohydrate transport (GO:0008643)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(15)|pancreas(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						CATGCTACCATATCTGGGGAA	0.453																																					p.M342V		Atlas-SNP	.											.	SLC5A4	82	.	0			c.A1024G						.						106	77	87					22																	32627060		2203	4300	6503	SO:0001583	missense	6527	exon10			CTACCATATCTGG	U41897	CCDS13903.1	22q12.3	2013-07-19	2013-07-19		ENSG00000100191	ENSG00000100191		"Solute carriers"	11039	protein-coding gene	gene with protein product			"solute carrier family 5 (low affinity glucose cotransporter), member 4"			9501190, 12354616	Standard	NM_014227		Approved	SAAT1, SGLT3, DJ90G24.4	uc003ami.3	Q9NY91	OTTHUMG00000150007	ENST00000266086.4:c.1024A>G	chr22.hg19:g.32627060T>C	ENSP00000266086:p.Met342Val	82.0	0.0		102.0	17.0	NM_014227	O15279	Missense_Mutation	SNP	ENST00000266086.4	hg19	CCDS13903.1	.	.	.	.	.	.	.	.	.	.	.	3.782	-0.045464	0.07452	.	.	ENSG00000100191	ENST00000266086	D	0.87729	-2.29	4.86	1.53	0.23141	.	0.511737	0.22153	N	0.063885	T	0.68449	0.3002	N	0.05306	-0.075	0.22226	N	0.999274	B	0.02656	0.0	B	0.01281	0.0	T	0.58696	-0.7591	10	0.54805	T	0.06	.	3.5866	0.07973	0.0:0.2693:0.1918:0.5389	.	342	Q9NY91	SC5A4_HUMAN	V	342	ENSP00000266086:M342V	ENSP00000266086:M342V	M	-	1	0	SLC5A4	30957060	0.860000	0.29831	0.217000	0.23759	0.017000	0.09413	1.566000	0.36396	0.398000	0.25338	-0.280000	0.10049	ATG	.	.		0.453	SLC5A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315724.1	NM_014227		C	32627060	T	C	32627060	3	2	371	1	0	0	0	0	1	0	0	0	14682	1406	49	2	979	2	SLC5A4	22	32627060	Missense_Mutation	SNP	T	TCGA-ZS-A9CE-01A-11D-A36X-10	1823537	32627060	18677506	107	51399										
SREBF2	6721	hgsc.bcm.edu	37	chr22	42266958	42266958	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	accacactgaagacagatggCagccctgttatggctgcggt	12	11	0	3			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chr22:42266958C>T	ENST00000361204.4	+	4	952	c.786C>T	c.(784-786)ggC>ggT	p.G262G		NM_004599.2	NP_004590.2	Q12772	SRBP2_HUMAN	sterol regulatory element binding transcription factor 2	262	Interaction with LMNA. {ECO:0000250}.				cellular lipid metabolic process (GO:0044255)|cellular response to laminar fluid shear stress (GO:0071499)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cholesterol homeostasis (GO:2000188)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|response to low-density lipoprotein particle (GO:0055098)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SREBP-SCAP-Insig complex (GO:0032937)	E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(6)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	38						AGACAGATGGCAGCCCTGTTA	0.537																																					p.G262G		Atlas-SNP	.											.	SREBF2	99	.	0			c.C786T						.						168	156	160					22																	42266958		2203	4300	6503	SO:0001819	synonymous_variant	6721	exon4			AGATGGCAGCCCT	U02031	CCDS14023.1	22q13.2	2013-05-21			ENSG00000198911	ENSG00000198911		"Basic helix-loop-helix proteins"	11290	protein-coding gene	gene with protein product		600481				7903453	Standard	NM_004599		Approved	SREBP2, bHLHd2	uc003bbi.3	Q12772	OTTHUMG00000151261	ENST00000361204.4:c.786C>T	chr22.hg19:g.42266958C>T		98.0	0.0		113.0	44.0	NM_004599	Q05BD5|Q6GTH7|Q86V36|Q9UH04	Silent	SNP	ENST00000361204.4	hg19	CCDS14023.1																																																																																			.	.		0.537	SREBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321956.1	NM_004599		T	42266958	C	T	42266958	2	4	371	1	0	0	0	0	0	0	0	1	15157	697	25	3		3	SREBF2	22	42266958	Silent	SNP	C	TCGA-ZS-A9CE-01A-11D-A36X-10	9639898	42266958	9037608	108	51400										
USP9X	8239	hgsc.bcm.edu	37	chrX	41022048	41022048	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	tttcttaatttgcagaccatGaagattatgacccacaaact	5	9	1	4			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chrX:41022048G>T	ENST00000324545.8	+	15	2536	c.1903G>T	c.(1903-1905)Gaa>Taa	p.E635*	USP9X_ENST00000378308.2_Nonsense_Mutation_p.E635*	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	635					axon extension (GO:0048675)|BMP signaling pathway (GO:0030509)|cerebellar cortex structural organization (GO:0021698)|chromosome segregation (GO:0007059)|female gamete generation (GO:0007292)|gene expression (GO:0010467)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|protein deubiquitination (GO:0016579)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)	co-SMAD binding (GO:0070410)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						TGCAGACCATGAAGATTATGA	0.363																																					p.E635X	Ovarian(172;1807 2695 35459 49286)	Atlas-SNP	.											.	USP9X	385	.	0			c.G1903T						.						132	123	126					X																	41022048		2185	4293	6478	SO:0001587	stop_gained	8239	exon15			GACCATGAAGATT	X98296	CCDS43930.1, CCDS55403.1	Xp11.4	2010-08-03	2006-02-14		ENSG00000124486	ENSG00000124486		"Ubiquitin-specific peptidases"	12632	protein-coding gene	gene with protein product		300072	"ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila)", "ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila)", "ubiquitin specific peptidase 9, X-linked (fat facets-like, Drosophila)"			8922996	Standard	NM_001039590		Approved	DFFRX, FAF	uc004dfb.3	Q93008	OTTHUMG00000021367	ENST00000324545.8:c.1903G>T	chrX.hg19:g.41022048G>T	ENSP00000316357:p.Glu635*	210.0	0.0		237.0	111.0	NM_001039591	O75550|Q8WWT3|Q8WX12	Nonsense_Mutation	SNP	ENST00000324545.8	hg19	CCDS43930.1	.	.	.	.	.	.	.	.	.	.	G	40	8.171626	0.98688	.	.	ENSG00000124486	ENST00000378308;ENST00000324545	.	.	.	5.32	5.32	0.75619	.	0.100122	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10902	T	0.67	.	18.3466	0.90324	0.0:0.0:1.0:0.0	.	.	.	.	X	635	.	ENSP00000316357:E635X	E	+	1	0	USP9X	40906992	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	5.069000	0.64370	2.360000	0.80028	0.422000	0.28245	GAA	.	.		0.363	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652		T	41022048	G	T	41022048	4	4	371	1	0	0	0	0	0	1	0	0	17105	1291	45	3	1957	3	USP9X	23	41022048	Nonsense_Mutation	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10		41022048	114248512	109	51401										
CASK	8573	hgsc.bcm.edu	37	chrX	41394032	41394032	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	atgtgtcttctcccaacaccAtgtgcgcctatgtcatttag	7	12	3	0			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chrX:41394032A>G	ENST00000378163.1	-	24	2718	c.2244T>C	c.(2242-2244)caT>caC	p.H748H	CASK_ENST00000442742.2_Silent_p.H720H|CASK_ENST00000318588.9_Silent_p.H743H|CASK_ENST00000378166.4_Silent_p.H743H|CASK_ENST00000421587.2_Silent_p.H719H|CASK_ENST00000361962.4_Silent_p.H731H|CASK_ENST00000378158.1_Silent_p.H731H			O14936	CSKP_HUMAN	calcium/calmodulin-dependent serine protein kinase (MAGUK family)	748	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				calcium ion import (GO:0070509)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of wound healing (GO:0061045)|nucleotide phosphorylation (GO:0046939)|positive regulation of calcium ion import (GO:0090280)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	actin cytoskeleton (GO:0015629)|basement membrane (GO:0005604)|basolateral plasma membrane (GO:0016323)|cell-cell junction (GO:0005911)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nuclear lamina (GO:0005652)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	ATP binding (GO:0005524)|guanylate kinase activity (GO:0004385)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(5)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|ovary(3)|prostate(1)|stomach(1)	32						TCCCAACACCATGTGCGCCTA	0.368																																					p.H743H	NSCLC(42;104 1086 3090 27189 35040)	Atlas-SNP	.											.	CASK	93	.	0			c.T2229C						.						266	207	227					X																	41394032		2203	4300	6503	SO:0001819	synonymous_variant	8573	exon24			AACACCATGTGCG	AF035582	CCDS14257.1, CCDS48094.1, CCDS48095.1	Xp11.4	2010-02-09			ENSG00000147044	ENSG00000147044			1497	protein-coding gene	gene with protein product		300172	"trinucleotide repeat containing 8"	TNRC8		9722958	Standard	NM_003688		Approved	LIN2, CAGH39, FGS4	uc004dfl.4	O14936	OTTHUMG00000021378	ENST00000378163.1:c.2244T>C	chrX.hg19:g.41394032A>G		88.0	0.0		115.0	55.0	NM_003688	A6NES1|B7ZKY0|O43215|Q17RI4|Q59HA0|Q5VT16|Q5VT17|Q5VT18|Q5VT19|Q66T42|Q9BYH6|Q9NYB2|Q9NYB3	Silent	SNP	ENST00000378163.1	hg19																																																																																				.	.		0.368	CASK-007	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000056285.1	NM_003688		G	41394032	A	G	41394032	2	3	371	1	0	0	0	0	0	0	0	1	2667	214	8	2		2	CASK	23	41394032	Silent	SNP	A	TCGA-ZS-A9CE-01A-11D-A36X-10	371984	41394032	113876528	110	51402										
TSPYL2	64061	hgsc.bcm.edu	37	chrX	53115089	53115089	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	gctgatgaccacgaaaccacTgacaacaatgagagtgcaga	10	10	0	5			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chrX:53115089T>A	ENST00000375442.4	+	6	1647	c.1515T>A	c.(1513-1515)acT>acA	p.T505T		NM_022117.3	NP_071400.1	Q9H2G4	TSYL2_HUMAN	TSPY-like 2	505	Asn-rich.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell cycle (GO:0007049)|cellular protein metabolic process (GO:0044267)|chromatin modification (GO:0016568)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA replication (GO:0008156)|nucleosome assembly (GO:0006334)|regulation of protein kinase activity (GO:0045859)|regulation of signal transduction (GO:0009966)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	rDNA binding (GO:0000182)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(1)	19						acgaaaccactgacaacaatg	0.453																																					p.T505T		Atlas-SNP	.											.	TSPYL2	53	.	0			c.T1515A						.						241	173	196					X																	53115089		2203	4300	6503	SO:0001819	synonymous_variant	64061	exon6			AACCACTGACAAC	AF273046	CCDS14350.1	Xp11	2014-06-09			ENSG00000184205	ENSG00000184205			24358	protein-coding gene	gene with protein product		300564				11318608, 11395479	Standard	NM_022117		Approved	SE20-4, HRIHFB2216, CTCL, DENTT, CDA1, CINAP, TSPX	uc004drw.3	Q9H2G4	OTTHUMG00000021597	ENST00000375442.4:c.1515T>A	chrX.hg19:g.53115089T>A		182.0	0.0		203.0	46.0	NM_022117	O94799|Q96DG7|Q9BZW6	Silent	SNP	ENST00000375442.4	hg19	CCDS14350.1																																																																																			.	.		0.453	TSPYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056718.1	NM_022117		A	53115089	T	A	53115089	2	1	371	1	0	0	0	0	0	0	0	1	16675	1567	55	4		4	TSPYL2	23	53115089	Silent	SNP	T	TCGA-ZS-A9CE-01A-11D-A36X-10	11721057	53115089	102155471	111	51403										
TRO	7216	hgsc.bcm.edu	37	chrX	54955093	54955093	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	accgcgaggcagtggagatgGaagtccaagctgcagctgtg	16	9	0	1			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chrX:54955093G>A	ENST00000173898.7	+	12	2048	c.1936G>A	c.(1936-1938)Gaa>Aaa	p.E646K	TRO_ENST00000420798.2_Missense_Mutation_p.E177K|TRO_ENST00000375022.4_Missense_Mutation_p.E646K|TRO_ENST00000399736.1_Missense_Mutation_p.E249K|TRO_ENST00000319167.8_Missense_Mutation_p.E646K|SNORA11_ENST00000408823.1_RNA|TRO_ENST00000375041.2_Missense_Mutation_p.E249K	NM_001039705.2	NP_001034794.1	Q12816	TROP_HUMAN	trophinin	646					embryo implantation (GO:0007566)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|skin(2)|urinary_tract(1)	37						AGTGGAGATGGAAGTCCAAgc	0.547																																					p.E646K		Atlas-SNP	.											.	TRO	246	.	0			c.G1936A						.						43	49	47					X																	54955093		2136	4246	6382	SO:0001583	missense	7216	exon12			GAGATGGAAGTCC	U04811	CCDS43958.1, CCDS43959.1, CCDS59527.1, CCDS59528.1, CCDS59529.1	Xp11.22-p11.21	2008-02-05			ENSG00000067445	ENSG00000067445			12326	protein-coding gene	gene with protein product		300132				9533028, 11454705	Standard	NM_001039705		Approved	MAGE-D3, KIAA1114, MAGED3	uc004dtq.4	Q12816	OTTHUMG00000021640	ENST00000173898.7:c.1936G>A	chrX.hg19:g.54955093G>A	ENSP00000173898:p.Glu646Lys	222.0	0.0		261.0	123.0	NM_016157	B1AKE9|B1AKF1|F5GY27|Q96SX2|Q9NU89|Q9UPN8	Missense_Mutation	SNP	ENST00000173898.7	hg19	CCDS43959.1	.	.	.	.	.	.	.	.	.	.	G	13.52	2.261909	0.39995	.	.	ENSG00000067445	ENST00000173898;ENST00000319167;ENST00000375022;ENST00000399736;ENST00000319179;ENST00000420798;ENST00000375041	T;T;T;T;T;T	0.08984	3.68;3.43;3.43;3.26;3.03;3.37	2.99	1.16	0.20824	.	.	.	.	.	T	0.06781	0.0173	L	0.41492	1.28	0.25762	N	0.984937	B;B;B;B	0.28082	0.2;0.008;0.01;0.2	B;B;B;B	0.19391	0.025;0.004;0.006;0.025	T	0.31194	-0.9952	9	0.66056	D	0.02	.	5.4075	0.16330	0.1309:0.2047:0.6644:0.0	.	249;249;646;646	B1AKE9;B1AKF1;Q96SX2;Q12816	.;.;.;TROP_HUMAN	K	646;646;646;249;249;177;249	ENSP00000173898:E646K;ENSP00000318278:E646K;ENSP00000364162:E646K;ENSP00000382641:E249K;ENSP00000405126:E177K;ENSP00000364181:E249K	ENSP00000173898:E646K	E	+	1	0	TRO	54971818	1.000000	0.71417	0.998000	0.56505	0.834000	0.47266	1.455000	0.35190	0.179000	0.19938	0.544000	0.68410	GAA	.	.		0.547	TRO-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056837.3	NM_016157		A	54955093	G	A	54955093	3	1	371	1	0	0	0	0	1	0	0	0	16589	1175	41	3	1978	3	TRO	23	54955093	Missense_Mutation	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10	1840004	54955093	100315467	112	51404										
ZXDB	158586	hgsc.bcm.edu	37	chrX	57618959	57618960	+	Missense_Mutation	DNP	GG	GG	TT													0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	cggccccgatctccgcccccGgccccgccgcggccttcgcg							TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chrX:57618959_57618960GG>TT	ENST00000374888.1	+	1	691_692	c.478_479GG>TT	c.(478-480)GGc>TTc	p.G160F		NM_007157.3	NP_009088.1	P98169	ZXDB_HUMAN	zinc finger, X-linked, duplicated B	160					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(2)|skin(6)	27						ctccgcccccggccccgccgcg	0.738																																					p.G160C|p.G160V		Atlas-SNP	.											.	ZXDB	51	.	0			c.G478T|c.G479T						.																																			SO:0001583	missense	158586	exon1			GCCCCCGGCCCCG|CCCCCGGCCCCGC	L14788	CCDS35313.1	Xp11.1	2013-01-08			ENSG00000198455	ENSG00000198455		"Zinc fingers, C2H2-type"	13199	protein-coding gene	gene with protein product		300236				8268913	Standard	NM_007157		Approved	ZNF905	uc004dvd.3	P98169	OTTHUMG00000021685	Exception_encountered	chrX.hg19:g.57618959_57618960delinsTT	ENSP00000364023:p.Gly160Phe	107.0|108.0	0.0		172.0|176.0	67.0|64.0	NM_007157	A8K151|Q9UBB3	Missense_Mutation	SNP	ENST00000374888.1	hg19	CCDS35313.1																																																																																			.	.		0.738	ZXDB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056922.1	NM_007157		TT	57618960	GG	TT	57618959	3	4	371	1	0	0	0	0	1	0	0	0	18266	1116	39	1	480	1	ZXDB	23	57618959	Missense_Mutation	DNP	GG	TCGA-ZS-A9CE-01A-11D-A36X-10	2663866	57618959	97651601	113	51405										
HDX	139324	hgsc.bcm.edu	37	chrX	83723670	83723670	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	acatatctctaatattcaccAtttgtgaatttggcatattt	4	7	2	1	rs138694491		TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chrX:83723670A>G	ENST00000297977.5	-	3	1172	c.1061T>C	c.(1060-1062)aTg>aCg	p.M354T	HDX_ENST00000373177.2_Missense_Mutation_p.M354T|HDX_ENST00000506585.2_Missense_Mutation_p.M296T	NM_001177479.1|NM_144657.4	NP_001170950.1|NP_653258.2	Q7Z353	HDX_HUMAN	highly divergent homeobox	354						nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(6)|kidney(2)|large_intestine(12)|liver(1)|lung(19)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						AATATTCACCATTTGTGAATT	0.403																																					p.M354T	Pancreas(53;231 1169 36156 43751 51139)	Atlas-SNP	.											.	HDX	124	.	0			c.T1061C						.						132	112	119					X																	83723670		2203	4300	6503	SO:0001583	missense	139324	exon3			TTCACCATTTGTG	BX538112	CCDS35342.1, CCDS55456.1	Xq21.1	2012-03-09	2007-07-13	2007-07-13	ENSG00000165259	ENSG00000165259		"Homeoboxes / POU class"	26411	protein-coding gene	gene with protein product			"chromosome X open reading frame 43"	CXorf43			Standard	NM_144657		Approved	FLJ30678	uc004eek.2	Q7Z353	OTTHUMG00000021926	ENST00000297977.5:c.1061T>C	chrX.hg19:g.83723670A>G	ENSP00000297977:p.Met354Thr	164.0	0.0		181.0	18.0	NM_144657	A8K1Y5|B7ZL18|Q5JZB4|Q96NK7	Missense_Mutation	SNP	ENST00000297977.5	hg19	CCDS35342.1	.	.	.	.	.	.	.	.	.	.	A	7.336	0.619977	0.14193	.	.	ENSG00000165259	ENST00000297977;ENST00000373177;ENST00000506585	T;T;T	0.32272	1.49;1.46;1.49	5.43	5.43	0.79202	.	0.285652	0.33854	N	0.004499	T	0.25005	0.0607	L	0.34521	1.04	0.45502	D	0.998464	B	0.30482	0.281	B	0.24006	0.05	T	0.04294	-1.0962	10	0.62326	D	0.03	-1.1798	14.5132	0.67802	1.0:0.0:0.0:0.0	.	354	Q7Z353	HDX_HUMAN	T	354;296;354	ENSP00000297977:M354T;ENSP00000362272:M296T;ENSP00000423670:M354T	ENSP00000297977:M354T	M	-	2	0	HDX	83610326	1.000000	0.71417	1.000000	0.80357	0.272000	0.26649	5.849000	0.69465	1.807000	0.52817	0.339000	0.21740	ATG	.	A|1.000;T|0.000		0.403	HDX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057379.2	NM_144657		G	83723670	A	G	83723670	3	3	371	1	0	0	0	0	1	0	0	0	7035	217	8	2	1043	2	HDX	23	83723670	Missense_Mutation	SNP	A	TCGA-ZS-A9CE-01A-11D-A36X-10	26104711	83723670	71546890	114	51406										
LUZP4	51213	hgsc.bcm.edu	37	chrX	114524334	114524334	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	gatgcagggaagatggcttcGtttcggaagctaacgctttc	13	8	0	1			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chrX:114524334G>A	ENST00000371920.3	+	1	16	c.9G>A	c.(7-9)tcG>tcA	p.S3S	LUZP4_ENST00000451986.2_5'UTR	NM_016383.3	NP_057467.1	Q9P127	LUZP4_HUMAN	leucine zipper protein 4	3						nucleus (GO:0005634)				endometrium(1)|large_intestine(2)|lung(4)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	14						AGATGGCTTCGTTTCGGAAGC	0.532																																					p.S3S		Atlas-SNP	.											.	LUZP4	51	.	0			c.G9A						.						108	85	93					X																	114524334		2203	4300	6503	SO:0001819	synonymous_variant	51213	exon1			GGCTTCGTTTCGG	AF124430	CCDS14567.1	Xq24	2009-03-25			ENSG00000102021	ENSG00000102021			24971	protein-coding gene	gene with protein product	"cancer/testis antigen 28"	300616				12032826, 11051238	Standard	XM_005268343		Approved	HOM-TES-85, CT-8, CT28	uc004eqa.3	Q9P127	OTTHUMG00000022234	ENST00000371920.3:c.9G>A	chrX.hg19:g.114524334G>A		108.0	0.0		141.0	56.0	NM_016383	B3KSD6	Silent	SNP	ENST00000371920.3	hg19	CCDS14567.1																																																																																			.	.		0.532	LUZP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057972.1	NM_016383		A	114524334	G	A	114524334	2	1	371	1	0	0	0	0	0	0	0	1	9097	1132	40	1		1	LUZP4	23	114524334	Silent	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10	30800664	114524334	40746226	115	51407										
IL13RA1	3597	hgsc.bcm.edu	37	chrX	117895239	117895239	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	taacagccaaactgagacacAtaatgttttctacgtaaggt	7	8	1	1			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chrX:117895239A>G	ENST00000371666.3	+	6	882	c.815A>G	c.(814-816)cAt>cGt	p.H272R	IL13RA1_ENST00000481868.1_3'UTR|IL13RA1_ENST00000371642.1_Missense_Mutation_p.H272R	NM_001560.2	NP_001551.1	P78552	I13R1_HUMAN	interleukin 13 receptor, alpha 1	272	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of immunoglobulin production (GO:0002639)	interleukin-13 receptor complex (GO:0005898)|plasma membrane (GO:0005886)	interleukin-13 receptor activity (GO:0016515)			endometrium(2)|kidney(1)|large_intestine(2)|lung(7)	12						ACTGAGACACATAATGTTTTC	0.294																																					p.H272R		Atlas-SNP	.											.	IL13RA1	41	.	0			c.A815G						.						112	112	112					X																	117895239		2203	4299	6502	SO:0001583	missense	3597	exon6			AGACACATAATGT	U62858	CCDS14573.1	Xq24	2008-02-05			ENSG00000131724	ENSG00000131724		"Interleukins and interleukin receptors", "CD molecules"	5974	protein-coding gene	gene with protein product	"IL13 receptor alpha-1 chain", "CD213a1 antigen"	300119				8910586, 9013879	Standard	NM_001560		Approved	IL-13Ra, NR4, CD213a1	uc004eqs.3	P78552	OTTHUMG00000022258	ENST00000371666.3:c.815A>G	chrX.hg19:g.117895239A>G	ENSP00000360730:p.His272Arg	158.0	0.0		188.0	45.0	NM_001560	O95646|Q5JSL4|Q99656|Q9UDY5	Missense_Mutation	SNP	ENST00000371666.3	hg19	CCDS14573.1	.	.	.	.	.	.	.	.	.	.	A	9.706	1.155782	0.21454	.	.	ENSG00000131724	ENST00000371666;ENST00000371642	D;D	0.85411	-1.98;-1.98	5.43	-3.62	0.04543	Fibronectin, type III (1);Immunoglobulin-like fold (1);	2.123750	0.01469	N	0.016214	T	0.75874	0.3909	L	0.38531	1.155	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.57159	-0.7859	10	0.21540	T	0.41	1.2789	5.311	0.15831	0.3829:0.2803:0.3369:0.0	.	272;272;272	Q5JSL4;P78552;Q9UDY5	.;I13R1_HUMAN;.	R	272	ENSP00000360730:H272R;ENSP00000360705:H272R	ENSP00000360705:H272R	H	+	2	0	IL13RA1	117779267	0.000000	0.05858	0.000000	0.03702	0.212000	0.24457	-0.143000	0.10296	-1.205000	0.02645	-0.467000	0.05162	CAT	.	.		0.294	IL13RA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058009.1	NM_001560		G	117895239	A	G	117895239	3	3	371	1	0	0	0	0	1	0	0	0	7638	217	8	2	837	2	IL13RA1	23	117895239	Missense_Mutation	SNP	A	TCGA-ZS-A9CE-01A-11D-A36X-10	3370905	117895239	37375321	116	51408										
ZCCHC12	170261	hgsc.bcm.edu	37	chrX	117959257	117959257	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	cagccggcggctgaatgcacCcttgccgccttgggcccatt	12	16	0	1			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chrX:117959257C>A	ENST00000310164.2	+	4	557	c.50C>A	c.(49-51)cCc>cAc	p.P17H		NM_173798.2	NP_776159.1	Q6PEW1	ZCH12_HUMAN	zinc finger, CCHC domain containing 12	17					BMP signaling pathway (GO:0030509)|transcription, DNA-templated (GO:0006351)	nuclear speck (GO:0016607)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(2)	22						CTGAATGCACCCTTGCCGCCT	0.532																																					p.P17H		Atlas-SNP	.											.	ZCCHC12	60	.	0			c.C50A						.						75	66	69					X																	117959257		2203	4300	6503	SO:0001583	missense	170261	exon4			ATGCACCCTTGCC	AK122676	CCDS14574.1	Xq24	2013-10-11			ENSG00000174460	ENSG00000174460		"Zinc fingers, CCHC domain containing", "Paraneoplastic Ma antigens"	27273	protein-coding gene	gene with protein product	"paraneoplastic Ma antigen family member 7A"	300701				21739307, 19578717	Standard	NM_173798		Approved	FLJ16123, SIZN, SIZN1, PNMA7A	uc004equ.3	Q6PEW1	OTTHUMG00000022261	ENST00000310164.2:c.50C>A	chrX.hg19:g.117959257C>A	ENSP00000308921:p.Pro17His	160.0	0.0		174.0	68.0	NM_173798	B3KV48|Q6PID5|Q8N1C1	Missense_Mutation	SNP	ENST00000310164.2	hg19	CCDS14574.1	.	.	.	.	.	.	.	.	.	.	C	6.239	0.412172	0.11812	.	.	ENSG00000174460	ENST00000310164	T	0.10099	2.91	3.05	0.0604	0.14336	.	0.480580	0.15659	N	0.250988	T	0.08758	0.0217	L	0.44542	1.39	0.19945	N	0.999942	B	0.10296	0.003	B	0.12156	0.007	T	0.26087	-1.0113	10	0.56958	D	0.05	-1.0646	5.7737	0.18267	0.208:0.3904:0.4016:0.0	.	17	Q6PEW1	ZCH12_HUMAN	H	17	ENSP00000308921:P17H	ENSP00000308921:P17H	P	+	2	0	ZCCHC12	117843285	0.156000	0.22821	0.176000	0.23000	0.732000	0.41865	0.553000	0.23391	-0.102000	0.12197	0.529000	0.55759	CCC	.	.		0.532	ZCCHC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058014.1	NM_173798		A	117959257	C	A	117959257	3	1	371	1	0	0	0	0	1	0	0	0	17596	623	22	3	52	3	ZCCHC12	23	117959257	Missense_Mutation	SNP	C	TCGA-ZS-A9CE-01A-11D-A36X-10	64018	117959257	37311303	117	51409										
MAGEA1	4100	hgsc.bcm.edu	37	chrX	152482654	152482654	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0769230769230769	9	1	1.13547280744733	2.46019108280255	0.894614939200926	0.410983981693364	1	0	gcctttgtgactggctccctGgctcgatatttgaggagcag	13	10	0	2			TCGA-ZS-A9CE-01A-11D-A36X-10	TCGA-ZS-A9CE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c5e17d28-a154-47f9-a251-47f16437c16f	0e32e986-dd29-487a-85a2-5df371bbb9a4	g.chrX:152482654G>A	ENST00000356661.5	-	3	575	c.357C>T	c.(355-357)gcC>gcT	p.A119A		NM_004988.4	NP_004979.3	P43355	MAGA1_HUMAN	melanoma antigen family A, 1 (directs expression of antigen MZ2-E)	119	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone deacetylase binding (GO:0042826)			breast(1)|central_nervous_system(7)|kidney(2)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CTGGCTCCCTGGCTCGATATT	0.488																																					p.A119A		Atlas-SNP	.											.	MAGEA1	57	.	0			c.C357T						.						123	123	123					X																	152482654		2203	4300	6503	SO:0001819	synonymous_variant	4100	exon3			CTCCCTGGCTCGA		CCDS76051.1	Xq28	2010-05-26			ENSG00000198681	ENSG00000198681			6796	protein-coding gene	gene with protein product	"melanoma-associated antigen 1", "melanoma-associated antigen MZ2-E", "melanoma antigen MAGE-1", "melanoma antigen family A 1", "cancer/testis antigen family 1, member 1"	300016		MAGE1		1840703	Standard	NM_004988		Approved	MGC9326, CT1.1	uc004fhf.2	P43355	OTTHUMG00000024192	ENST00000356661.5:c.357C>T	chrX.hg19:g.152482654G>A		302.0	0.0		363.0	153.0	NM_004988	B2RC81|O00346	Silent	SNP	ENST00000356661.5	hg19	CCDS14720.1																																																																																			.	.		0.488	MAGEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060940.1	NM_004988		A	152482654	G	A	152482654	2	1	371	1	0	0	0	0	0	0	0	1	9172	1335	47	3		3	MAGEA1	23	152482654	Silent	SNP	G	TCGA-ZS-A9CE-01A-11D-A36X-10	34523397	152482654	2787906	118	51410										
PTCHD2	57540	hgsc.bcm.edu	37	chr1	11596435	11596435	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	aggccgtgcggcacgtgggcGtggccatcgtctccagtgcc	16	14	1	0			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr1:11596435G>C	ENST00000294484.6	+	21	4009	c.3871G>C	c.(3871-3873)Gtg>Ctg	p.V1291L	PTCHD2_ENST00000389575.3_Missense_Mutation_p.V1291L|PTCHD2_ENST00000304391.6_Missense_Mutation_p.R177P	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	1291					cholesterol homeostasis (GO:0042632)|regulation of lipid transport (GO:0032368)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hedgehog receptor activity (GO:0008158)			NS(3)|breast(2)|endometrium(9)|kidney(4)|large_intestine(5)|lung(34)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	76	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		GCACGTGGGCGTGGCCATCGT	0.667																																					p.V1291L		Atlas-SNP	.											.	PTCHD2	193	.	0			c.G3871C						.						80	83	82					1																	11596435		2197	4276	6473	SO:0001583	missense	57540	exon21			GTGGGCGTGGCCA	AB037758	CCDS41247.1	1p36.22	2010-02-17			ENSG00000204624	ENSG00000204624			29251	protein-coding gene	gene with protein product		611251				15738394	Standard	NM_020780		Approved	KIAA1337, DISP3	uc001ash.4	Q9P2K9	OTTHUMG00000002074	ENST00000294484.6:c.3871G>C	1.37:g.11596435G>C	ENSP00000294484:p.Val1291Leu	29.0	0.0		47.0	25.0	NM_020780	Q5VTU9|Q9UJD6	Missense_Mutation	SNP	ENST00000294484.6	37	CCDS41247.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.40|18.40	3.615180|3.615180	0.66672|0.66672	.|.	.|.	ENSG00000204624|ENSG00000204624	ENST00000304391|ENST00000294484;ENST00000389575	.|D;D	.|0.91521	.|-2.86;-1.88	4.89|4.89	4.89|4.89	0.63831|0.63831	.|Membrane transport protein, MMPL type (1);	.|0.000000	.|0.64402	.|D	.|0.000005	D|D	0.91801|0.91801	0.7406|0.7406	L|L	0.38531|0.38531	1.155|1.155	0.58432|0.58432	D|D	0.999992|0.999992	.|D	.|0.89917	.|1.0	.|D	.|0.79784	.|0.993	D|D	0.88490|0.88490	0.3075|0.3075	6|10	0.87932|0.11182	D|T	0|0.66	-26.0944|-26.0944	17.0791|17.0791	0.86593|0.86593	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1291	.|Q9P2K9	.|PTHD2_HUMAN	P|L	177|1291	.|ENSP00000294484:V1291L;ENSP00000374226:V1291L	ENSP00000303400:R177P|ENSP00000294484:V1291L	R|V	+|+	2|1	0|0	PTCHD2|PTCHD2	11519022|11519022	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	6.270000|6.270000	0.72563|0.72563	2.256000|2.256000	0.74724|0.74724	0.655000|0.655000	0.94253|0.94253	CGT|GTG	.	.		0.667	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561		C	11596435	G	C	11596435	3	2	372	1	0	0	0	0	1	0	0	0	12745	1145	40	4	3949	4	PTCHD2	1	11596435	Missense_Mutation	SNP	G	TCGA-ZS-A9CF-01A-11D-A382-10		11596435	237654186	1	51411										
CCDC76	54482	hgsc.bcm.edu	37	chr1	100605738	100605738	+	Splice_Site	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	agttttatttttgtatatagGttccaatttcttctctatct	4	6	3	0			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr1:100605738G>C	ENST00000370141.2	+	5	331	c.325G>C	c.(325-327)Gtt>Ctt	p.V109L	TRMT13_ENST00000370143.1_Intron|TRMT13_ENST00000370139.1_Splice_Site_p.V78L	NM_019083.2	NP_061956.2	Q9NUP7	TRM13_HUMAN	tRNA methyltransferase 13 homolog (S. cerevisiae)	109					tRNA processing (GO:0008033)		metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)										TTGTATATAGGTTCCAATTTC	0.333																																					p.V109L		Atlas-SNP	.											.	.	.	.	0			c.G325C						.						44	43	44					1																	100605738		2200	4298	6498	SO:0001630	splice_region_variant	54482	exon5			ATATAGGTTCCAA	BC075811	CCDS765.1	1p21.2	2012-06-07	2012-06-07	2012-06-07	ENSG00000122435	ENSG00000122435			25502	protein-coding gene	gene with protein product			"coiled-coil domain containing 76"	CCDC76		11799066	Standard	NM_019083		Approved	FLJ10287, FLJ11219	uc001dsv.3	Q9NUP7	OTTHUMG00000010841	ENST00000370141.2:c.325-1G>C	1.37:g.100605738G>C		69.0	0.0		72.0	28.0	NM_019083	Q5VVL0|Q9NW65	Missense_Mutation	SNP	ENST00000370141.2	37	CCDS765.1	.	.	.	.	.	.	.	.	.	.	G	15.03	2.711719	0.48517	.	.	ENSG00000122435	ENST00000370141;ENST00000370139	T;T	0.45276	0.97;0.9	5.66	5.66	0.87406	.	0.108658	0.64402	D	0.000006	T	0.25494	0.0620	M	0.61703	1.905	0.49483	D	0.999797	B;P	0.39391	0.1;0.671	B;B	0.32393	0.031;0.145	T	0.07809	-1.0753	9	.	.	.	-21.0263	14.3978	0.67022	0.0:0.0:0.853:0.147	.	109;109	B4DQS9;Q9NUP7	.;TRM13_HUMAN	L	109;78	ENSP00000359160:V109L;ENSP00000359158:V78L	.	V	+	1	0	CCDC76	100378326	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.302000	0.51849	2.672000	0.90937	0.650000	0.86243	GTT	.	.		0.333	TRMT13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029919.1	NM_019083	Missense_Mutation	C	100605738	G	C	100605738	5	2	372	1	0	0	0	0	0	0	1	0	2852	1275	44	4	343	4	CCDC76	1	100605738	Splice_Site	SNP	G	TCGA-ZS-A9CF-01A-11D-A382-10	89009303	100605738	148644883	2	51412										
F5	2153	hgsc.bcm.edu	37	chr1	169521852	169521852	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	cccaaaatcccatcttctttCatattgggattcactgtatg	5	11	4	0			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr1:169521852C>A	ENST00000367797.3	-	8	1440	c.1239G>T	c.(1237-1239)atG>atT	p.M413I	F5_ENST00000367796.3_Missense_Mutation_p.M413I|F5_ENST00000546081.1_Missense_Mutation_p.M276I	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	413	F5/8 type A 2.|Plastocyanin-like 3.		M -> T (in dbSNP:rs6033). {ECO:0000269|PubMed:10391209, ECO:0000269|Ref.3}.		blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	CATCTTCTTTCATATTGGGAT	0.358																																					p.M413I		Atlas-SNP	.											F5,larynx,carcinoma,-2,1	F5	301	1	0			c.G1239T						.						154	154	154					1																	169521852		2203	4300	6503	SO:0001583	missense	2153	exon8			TTCTTTCATATTG	M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.1239G>T	1.37:g.169521852C>A	ENSP00000356771:p.Met413Ile	120.0	0.0		180.0	48.0	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	37	CCDS1281.1	.	.	.	.	.	.	.	.	.	.	C	4.952	0.176775	0.09443	.	.	ENSG00000198734	ENST00000367797;ENST00000367796;ENST00000546081	D;D;D	0.98914	-5.23;-5.23;-5.23	5.95	-0.944	0.10392	Cupredoxin (2);	1.658480	0.02698	N	0.111473	D	0.90239	0.6948	N	0.17082	0.46	0.21740	N	0.99957	B	0.02656	0.0	B	0.01281	0.0	D	0.88693	0.3210	9	0.27785	T	0.31	0.7786	5.4661	0.16644	0.0598:0.2597:0.376:0.3044	.	413	P12259	FA5_HUMAN	I	413;413;276	ENSP00000356771:M413I;ENSP00000356770:M413I;ENSP00000439664:M276I	ENSP00000356770:M413I	M	-	3	0	F5	167788476	0.000000	0.05858	0.000000	0.03702	0.548000	0.35241	-0.226000	0.09139	-0.443000	0.07180	-0.165000	0.13383	ATG	.	.		0.358	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130		A	169521852	C	A	169521852	3	1	372	1	0	0	0	0	1	0	0	0	5350	826	29	3	5507	3	F5	1	169521852	Missense_Mutation	SNP	C	TCGA-ZS-A9CF-01A-11D-A382-10	68916114	169521852	79728769	3	51413										
ZBTB37	84614	hgsc.bcm.edu	37	chr1	173840092	173840092	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	gttagagttcttggagcagtAcacatcaaaactgaaaatct	8	7	3	2			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr1:173840092A>G	ENST00000367701.5	+	2	920	c.729A>G	c.(727-729)gtA>gtG	p.V243V	ZBTB37_ENST00000432989.1_Silent_p.V243V|ZBTB37_ENST00000427304.1_Silent_p.V243V|ZBTB37_ENST00000367702.1_Silent_p.V243V|ZBTB37_ENST00000367704.1_Silent_p.V243V			Q5TC79	ZBT37_HUMAN	zinc finger and BTB domain containing 37	243					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(4)	13						TTGGAGCAGTACACATCAAAA	0.517																																					p.V243V		Atlas-SNP	.											.	ZBTB37	38	.	0			c.A729G						.						93	95	94					1																	173840092		2203	4300	6503	SO:0001819	synonymous_variant	84614	exon3			AGCAGTACACATC	AK057310	CCDS1312.1, CCDS44278.1	1q24.2	2013-01-08			ENSG00000185278	ENSG00000185278		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	28365	protein-coding gene	gene with protein product						12477932	Standard	NM_032522		Approved	MGC2629, ZNF908	uc009wwp.1	Q5TC79	OTTHUMG00000037274	ENST00000367701.5:c.729A>G	1.37:g.173840092A>G		146.0	0.0		172.0	54.0	NM_032522	Q5TC80|Q96M87|Q9BQ88	Silent	SNP	ENST00000367701.5	37	CCDS44278.1																																																																																			.	.		0.517	ZBTB37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090729.2	NM_032522		G	173840092	A	G	173840092	2	3	372	1	0	0	0	0	0	0	0	1	17553	378	14	2		2	ZBTB37	1	173840092	Silent	SNP	A	TCGA-ZS-A9CF-01A-11D-A382-10	4318240	173840092	75410529	4	51414										
C1orf106	55765	hgsc.bcm.edu	37	chr1	200870236	200870236	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	tccagcgctgcctggtcgagCggcggcgcaatagcgagcca	15	14	0	0			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr1:200870236C>T	ENST00000367342.4	+	5	924	c.724C>T	c.(724-726)Cgg>Tgg	p.R242W	C1orf106_ENST00000413687.2_Missense_Mutation_p.R157W	NM_018265.3	NP_060735.3	Q3KP66	CA106_HUMAN	chromosome 1 open reading frame 106	242										endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(2)	21						CCTGGTCGAGCGGCGGCGCAA	0.667																																					p.R256W		Atlas-SNP	.											.	C1orf106	59	.	0			c.C766T						.						6	8	7					1																	200870236		1819	3508	5327	SO:0001583	missense	55765	exon5			GTCGAGCGGCGGC	AK001763	CCDS44292.1	1q32.1	2011-02-15			ENSG00000163362	ENSG00000163362			25599	protein-coding gene	gene with protein product						14702039	Standard	NM_018265		Approved	FLJ10901	uc001gvo.4	Q3KP66	OTTHUMG00000035789	ENST00000367342.4:c.724C>T	1.37:g.200870236C>T	ENSP00000356311:p.Arg242Trp	57.0	0.0		75.0	27.0	NM_018265	B4E1K9|E9PFY0|Q9NV65|Q9NVI0	Missense_Mutation	SNP	ENST00000367342.4	37		.	.	.	.	.	.	.	.	.	.	C	14.98	2.697800	0.48307	.	.	ENSG00000163362	ENST00000367342;ENST00000413687	T;T	0.45276	0.9;0.92	4.15	2.08	0.27032	.	0.601193	0.16332	N	0.219076	T	0.39145	0.1067	L	0.51422	1.61	0.09310	N	1	D	0.69078	0.997	P	0.50231	0.635	T	0.19516	-1.0303	9	.	.	.	-9.3204	3.3503	0.07150	0.205:0.5733:0.0:0.2217	.	242	Q3KP66	CA106_HUMAN	W	242;157	ENSP00000356311:R242W;ENSP00000392105:R157W	.	R	+	1	2	C1orf106	199136859	0.291000	0.24352	0.184000	0.23157	0.043000	0.13939	0.608000	0.24223	0.854000	0.35336	0.460000	0.39030	CGG	.	.		0.667	C1orf106-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000087057.2	NM_018265		T	200870236	C	T	200870236	3	4	372	1	0	0	0	0	1	0	0	0	1982	759	27	1	742	1	C1orf106	1	200870236	Missense_Mutation	SNP	C	TCGA-ZS-A9CF-01A-11D-A382-10	27030144	200870236	48380385	5	51415										
TSNAX	7257	hgsc.bcm.edu	37	chr1	231700450	231700450	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	agccagtttttacgtcaggtTtatgatgggttttcattcat	9	6	3	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr1:231700450T>C	ENST00000366639.4	+	6	830	c.672T>C	c.(670-672)gtT>gtC	p.V224V	TSNAX-DISC1_ENST00000602962.1_Intron	NM_005999.2	NP_005990.1	Q99598	TSNAX_HUMAN	translin-associated factor X	224					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|sequence-specific DNA binding (GO:0043565)			endometrium(1)|kidney(1)|large_intestine(2)|lung(5)	9		all_cancers(173;0.0395)|Acute lymphoblastic leukemia(190;3.76e-06)|Prostate(94;0.116)				TACGTCAGGTTTATGATGGGT	0.428																																					p.V224V		Atlas-SNP	.											.	TSNAX	14	.	0			c.T672C						.						210	197	202					1																	231700450		2203	4300	6503	SO:0001819	synonymous_variant	7257	exon6			TCAGGTTTATGAT	X95073	CCDS1596.1	1q42.2	2008-02-05			ENSG00000116918	ENSG00000116918			12380	protein-coding gene	gene with protein product		602964				9013868	Standard	NM_005999		Approved	TRAX	uc001huw.3	Q99598	OTTHUMG00000039486	ENST00000366639.4:c.672T>C	1.37:g.231700450T>C		240.0	0.0		241.0	105.0	NM_005999	B1APC6	Silent	SNP	ENST00000366639.4	37	CCDS1596.1																																																																																			.	.		0.428	TSNAX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095267.2	NM_005999		C	231700450	T	C	231700450	2	2	372	1	0	0	0	0	0	0	0	1	16646	1828	64	2		2	TSNAX	1	231700450	Silent	SNP	T	TCGA-ZS-A9CF-01A-11D-A382-10	30830214	231700450	17550171	6	51416										
SMYD3	64754	hgsc.bcm.edu	37	chr1	246498775	246498775	+	Splice_Site	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	tgtggtctggccaagcttttTtctattaaaacaagagtggg	11	6	2	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr1:246498775T>C	ENST00000388985.4	-	3	229	c.230A>G	c.(229-231)aAa>aGa	p.K77R	SMYD3_ENST00000403792.3_Splice_Site_p.K77R|SMYD3_ENST00000490107.1_Splice_Site_p.K18R|SMYD3_ENST00000541742.1_Splice_Site_p.K18R			Q9H7B4	SMYD3_HUMAN	SET and MYND domain containing 3	77	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				cellular response to dexamethasone stimulus (GO:0071549)|establishment of protein localization (GO:0045184)|myotube cell development (GO:0014904)|negative regulation of protein kinase activity (GO:0006469)|nucleosome assembly (GO:0006334)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding (GO:0001162)			breast(3)|large_intestine(5)|lung(8)|skin(1)	17	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)		CCAAGCTTTTTTCTATTAAAA	0.378																																					p.K77R		Atlas-SNP	.											.	SMYD3	77	.	0			c.A230G						.						108	111	110					1																	246498775		2203	4300	6503	SO:0001630	splice_region_variant	64754	exon3			GCTTTTTTCTATT	AK023594	CCDS31083.1	1q44	2011-07-01	2003-05-14	2003-05-16	ENSG00000185420	ENSG00000185420		"Zinc fingers, MYND-type", "Chromatin-modifying enzymes / K-methyltransferases"	15513	protein-coding gene	gene with protein product		608783	"zinc finger, MYND domain containing 1"	ZNFN3A1, ZMYND1			Standard	NM_022743		Approved	KMT3E	uc001ibl.3	Q9H7B4	OTTHUMG00000040508	ENST00000388985.4:c.229-1A>G	1.37:g.246498775T>C		62.0	0.0		87.0	45.0	NM_001167740	A8K0P0|B1AN38|Q86TL8|Q8N5Z6|Q96AI5	Missense_Mutation	SNP	ENST00000388985.4	37	CCDS53486.1	.	.	.	.	.	.	.	.	.	.	T	8.661	0.900561	0.17686	.	.	ENSG00000185420	ENST00000541742;ENST00000490107;ENST00000388985;ENST00000453676;ENST00000403792;ENST00000455277	T;T;T;T;T	0.14516	2.5;2.5;2.5;2.5;2.5	5.41	3.09	0.35607	SET domain (2);Zinc finger, MYND-type (3);	0.237642	0.34879	N	0.003611	T	0.06735	0.0172	N	0.10972	0.075	0.41608	D	0.988891	B	0.24882	0.113	B	0.24269	0.052	T	0.36768	-0.9734	10	0.28530	T	0.3	-4.4062	7.8345	0.29362	0.0:0.2301:0.0:0.7699	.	77	Q9H7B4	SMYD3_HUMAN	R	18;18;77;18;77;18	ENSP00000444184:K18R;ENSP00000419184:K18R;ENSP00000373637:K77R;ENSP00000408122:K18R;ENSP00000385380:K77R	ENSP00000373637:K77R	K	-	2	0	SMYD3	244565398	1.000000	0.71417	1.000000	0.80357	0.212000	0.24457	3.123000	0.50453	0.449000	0.26747	-0.256000	0.11100	AAA	.	.		0.378	SMYD3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_022743	Missense_Mutation	C	246498775	T	C	246498775	5	2	372	1	0	0	0	0	0	0	1	0	14838	1855	64	2	1096	2	SMYD3	1	246498775	Splice_Site	SNP	T	TCGA-ZS-A9CF-01A-11D-A382-10	14798325	246498775	2751846	7	51417										
PXDN	7837	hgsc.bcm.edu	37	chr2	1653379	1653379	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	gttgttcacgcgccggtgggCggtacagcccgacaggtttg	16	11	1	0	rs374347969		TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr2:1653379C>T	ENST00000252804.4	-	17	2223	c.2173G>A	c.(2173-2175)Gcc>Acc	p.A725T		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	725					extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		CGCCGGTGGGCGGTACAGCCC	0.592																																					p.A725T		Atlas-SNP	.											.	PXDN	255	.	0			c.G2173A						.	C	THR/ALA	0,4178		0,0,2089	76	82	80		2173	5.6	0.4	2		80	1,8431		0,1,4215	no	missense	PXDN	NM_012293.1	58	0,1,6304	TT,TC,CC		0.0119,0.0,0.0079	benign	725/1480	1653379	1,12609	2089	4216	6305	SO:0001583	missense	7837	exon17			GGTGGGCGGTACA	AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"Immunoglobulin superfamily / I-set domain containing"	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.2173G>A	2.37:g.1653379C>T	ENSP00000252804:p.Ala725Thr	172.0	0.0		169.0	70.0	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Missense_Mutation	SNP	ENST00000252804.4	37	CCDS46221.1	.	.	.	.	.	.	.	.	.	.	C	11.74	1.729138	0.30684	0.0	1.19E-4	ENSG00000130508	ENST00000252804	T	0.61742	0.08	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.47746	0.1462	L	0.47078	1.49	0.53005	D	0.999962	B	0.33288	0.406	B	0.28709	0.093	T	0.41752	-0.9491	10	0.26408	T	0.33	-47.2078	12.9957	0.58646	0.0:0.9264:0.0:0.0736	.	725	Q92626	PXDN_HUMAN	T	725	ENSP00000252804:A725T	ENSP00000252804:A725T	A	-	1	0	PXDN	1632386	1.000000	0.71417	0.399000	0.26333	0.102000	0.19082	5.982000	0.70532	2.661000	0.90470	0.558000	0.71614	GCC	.	.		0.592	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455		T	1653379	C	T	1653379	3	4	372	1	0	0	0	0	1	0	0	0	12862	768	27	1	2294	1	PXDN	2	1653379	Missense_Mutation	SNP	C	TCGA-ZS-A9CF-01A-11D-A382-10		1653379	241545994	8	51418										
PROM2	150696	hgsc.bcm.edu	37	chr2	95941842	95941842	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	ctggcctgtgagcgcgcggcCctcatggtcttcctgctgct	13	15	2	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr2:95941842C>A	ENST00000317620.9	+	3	592	c.459C>A	c.(457-459)gcC>gcA	p.A153A	PROM2_ENST00000463580.1_Intron|PROM2_ENST00000317668.4_Silent_p.A153A|PROM2_ENST00000403131.2_Silent_p.A153A|PROM2_ENST00000542147.1_Silent_p.A153A	NM_001165978.1	NP_001159450.1	Q8N271	PROM2_HUMAN	prominin 2	153					negative regulation of caveolin-mediated endocytosis (GO:2001287)|negative regulation of pinocytosis (GO:0048550)|positive regulation of cell projection organization (GO:0031346)|positive regulation of protein phosphorylation (GO:0001934)|regulation of Cdc42 GTPase activity (GO:0043088)	cell projection (GO:0042995)|cell surface (GO:0009986)|cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|microspike (GO:0044393)|microvillus (GO:0005902)|prominosome (GO:0071914)	cholesterol binding (GO:0015485)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	32						AGCGCGCGGCCCTCATGGTCT	0.697																																					p.A153A		Atlas-SNP	.											.	PROM2	78	.	0			c.C459A						.						43	54	51					2																	95941842		2203	4300	6503	SO:0001819	synonymous_variant	150696	exon3			CGCGGCCCTCATG	AF245303	CCDS2012.1	2q11.1	2008-02-05			ENSG00000155066	ENSG00000155066			20685	protein-coding gene	gene with protein product						12514187	Standard	NM_001165978		Approved		uc002sui.3	Q8N271	OTTHUMG00000130393	ENST00000317620.9:c.459C>A	2.37:g.95941842C>A		108.0	0.0		84.0	38.0	NM_001165977	A8K2V1|Q2HIX6|Q8NB84|Q8TAE2	Silent	SNP	ENST00000317620.9	37	CCDS2012.1																																																																																			.	.		0.697	PROM2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252771.1	NM_144707		A	95941842	C	A	95941842	2	1	372	1	0	0	0	0	0	0	0	1	12568	610	22	3		3	PROM2	2	95941842	Silent	SNP	C	TCGA-ZS-A9CF-01A-11D-A382-10	94288463	95941842	147257531	9	51419										
GLI2	2736	hgsc.bcm.edu	37	chr2	121745822	121745822	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	tcagtggcagtgggggcggcGggcccgcggggctgctgccg	22	12	1	0			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr2:121745822G>A	ENST00000452319.1	+	14	2392	c.2332G>A	c.(2332-2334)Ggg>Agg	p.G778R	GLI2_ENST00000314490.11_Missense_Mutation_p.G450R|GLI2_ENST00000361492.4_Missense_Mutation_p.G778R					GLI family zinc finger 2											NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				Tgggggcggcgggcccgcggg	0.697																																					p.G778R		Atlas-SNP	.											.	GLI2	187	.	0			c.G2332A						.						8	10	9					2																	121745822		2147	4228	6375	SO:0001583	missense	2736	exon13			GGCGGCGGGCCCG		CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"Zinc fingers, C2H2-type"	4318	protein-coding gene	gene with protein product	"tax-responsive element-2 holding protein", "tax helper protein 1", "tax helper protein 2"	165230	"GLI-Kruppel family member GLI2", "glioma-associated oncogene family zinc finger 2"			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.2332G>A	2.37:g.121745822G>A	ENSP00000390436:p.Gly778Arg	791.0	0.0		695.0	304.0	NM_005270		Missense_Mutation	SNP	ENST00000452319.1	37	CCDS33283.1	.	.	.	.	.	.	.	.	.	.	G	10.30	1.312850	0.23908	.	.	ENSG00000074047	ENST00000452319;ENST00000361492;ENST00000314490	D;D;D	0.93426	-3.22;-3.22;-3.22	4.17	3.2	0.36748	.	0.675275	0.15638	N	0.252034	D	0.94460	0.8217	M	0.75777	2.31	0.09310	N	1	D;D;D;D	0.89917	1.0;1.0;0.996;1.0	D;D;P;D	0.85130	0.994;0.997;0.766;0.934	D	0.85080	0.0945	10	0.13853	T	0.58	.	3.4888	0.07630	0.233:0.0:0.5561:0.211	.	778;433;433;450	P10070;P10070-2;P10070-4;P10070-3	GLI2_HUMAN;.;.;.	R	778;778;450	ENSP00000390436:G778R;ENSP00000354586:G778R;ENSP00000312694:G450R	ENSP00000312694:G450R	G	+	1	0	GLI2	121462292	0.992000	0.36948	0.032000	0.17829	0.059000	0.15707	2.119000	0.41958	0.959000	0.37980	0.561000	0.74099	GGG	.	.		0.697	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270		A	121745822	G	A	121745822	3	1	372	1	0	0	0	0	1	0	0	0	6446	1116	39	1	2382	1	GLI2	2	121745822	Missense_Mutation	SNP	G	TCGA-ZS-A9CF-01A-11D-A382-10	25803980	121745822	121453551	10	51420										
LCT	3938	hgsc.bcm.edu	37	chr2	136570094	136570094	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	ggtctggggccacacatggtTcacgtgttgggagaagcctc	15	10	2	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr2:136570094T>A	ENST00000264162.2	-	7	2150	c.2140A>T	c.(2140-2142)Aac>Tac	p.N714Y	Y_RNA_ENST00000363794.1_RNA	NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	714	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	CACACATGGTTCACGTGTTGG	0.537																																					p.N714Y		Atlas-SNP	.											.	LCT	309	.	0			c.A2140T						.						103	99	101					2																	136570094		2203	4300	6503	SO:0001583	missense	3938	exon7			CATGGTTCACGTG	X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.2140A>T	2.37:g.136570094T>A	ENSP00000264162:p.Asn714Tyr	203.0	0.0		264.0	83.0	NM_002299	Q4ZG58	Missense_Mutation	SNP	ENST00000264162.2	37	CCDS2178.1	.	.	.	.	.	.	.	.	.	.	T	18.16	3.561772	0.65538	.	.	ENSG00000115850	ENST00000264162;ENST00000455227	T	0.53206	0.63	5.66	3.86	0.44501	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.273821	0.40064	N	0.001181	T	0.45357	0.1338	L	0.28740	0.885	0.36344	D	0.859649	P	0.51791	0.948	P	0.51229	0.663	T	0.56220	-0.8015	10	0.87932	D	0	-27.613	11.5005	0.50435	0.0:0.8532:0.0:0.1468	.	714	P09848	LPH_HUMAN	Y	714;146	ENSP00000264162:N714Y	ENSP00000264162:N714Y	N	-	1	0	LCT	136286564	1.000000	0.71417	0.065000	0.19835	0.746000	0.42486	4.897000	0.63231	0.734000	0.32515	-0.242000	0.12053	AAC	.	.		0.537	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299		A	136570094	T	A	136570094	3	1	372	1	0	0	0	0	1	0	0	0	8702	1783	62	4	3687	4	LCT	2	136570094	Missense_Mutation	SNP	T	TCGA-ZS-A9CF-01A-11D-A382-10	14824272	136570094	106629279	11	51421										
UBR3	130507	hgsc.bcm.edu	37	chr2	170936401	170936401	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	aattataacaccatttttcaGtactaccacagaaaaacctg	3	10	1	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr2:170936401G>C	ENST00000272793.5	+	37	5327	c.5277G>C	c.(5275-5277)caG>caC	p.Q1759H	UBR3_ENST00000392631.1_Missense_Mutation_p.Q580H|UBR3_ENST00000418381.1_Missense_Mutation_p.Q1759H			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	1759					embryo development (GO:0009790)|in utero embryonic development (GO:0001701)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)|suckling behavior (GO:0001967)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1)	33						CCATTTTTCAGTACTACCACA	0.388																																					p.Q1759H		Atlas-SNP	.											.	UBR3	182	.	0			c.G5277C						.						118	109	112					2																	170936401		2203	4300	6503	SO:0001583	missense	130507	exon37			TTTTCAGTACTAC	AL834144	CCDS2238.2	2q31.1	2008-06-23	2008-06-23	2007-11-29	ENSG00000144357	ENSG00000144357		"Ubiquitin protein ligase E3 component n-recognins"	30467	protein-coding gene	gene with protein product		613831	"zinc finger protein 650"	ZNF650		17462990	Standard	NM_172070		Approved	KIAA2024, DKFZp434P117, FLJ37422	uc010zdi.2	Q6ZT12	OTTHUMG00000132229	ENST00000272793.5:c.5277G>C	2.37:g.170936401G>C	ENSP00000272793:p.Gln1759His	132.0	0.0		145.0	64.0	NM_172070	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Missense_Mutation	SNP	ENST00000272793.5	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.16|19.16	3.774315|3.774315	0.69992|0.69992	.|.	.|.	ENSG00000144357|ENSG00000144357	ENST00000272793;ENST00000442603;ENST00000418381;ENST00000392631;ENST00000439681|ENST00000392632	T;T;T;T|.	0.49432|.	0.78;0.78;0.78;0.78|.	5.66|5.66	4.78|4.78	0.61160|0.61160	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.62804|0.62804	0.2458|0.2458	L|L	0.60455|0.60455	1.87|1.87	0.40880|0.40880	D|D	0.983983|0.983983	D;D;D|.	0.76494|.	0.99;0.999;0.98|.	D;D;D|.	0.85130|.	0.979;0.997;0.965|.	T|T	0.61594|0.61594	-0.7031|-0.7031	10|5	0.46703|.	T|.	0.11|.	.|.	10.2773|10.2773	0.43519|0.43519	0.1471:0.0:0.8529:0.0|0.1471:0.0:0.8529:0.0	.|.	1759;580;1788|.	Q6ZT12;Q6ZT12-2;E7EVK3|.	UBR3_HUMAN;.;.|.	H|T	1759;1788;1759;580;459|821	ENSP00000272793:Q1759H;ENSP00000396068:Q1759H;ENSP00000376408:Q580H;ENSP00000389097:Q459H|.	ENSP00000272793:Q1759H|.	Q|S	+|+	3|2	2|0	UBR3|UBR3	170644647|170644647	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.503000|5.503000	0.66962|0.66962	2.653000|2.653000	0.90120|0.90120	0.650000|0.650000	0.86243|0.86243	CAG|AGT	.	.		0.388	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070		C	170936401	G	C	170936401	3	2	372	1	0	0	0	0	1	0	0	0	16918	1020	36	4	5423	4	UBR3	2	170936401	Missense_Mutation	SNP	G	TCGA-ZS-A9CF-01A-11D-A382-10	34366307	170936401	72262972	12	51422										
AGPS	8540	hgsc.bcm.edu	37	chr2	178257523	178257523	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	cacaaggcggtagccatggcGgaggcggcggctgcagcggg	20	11	0	0			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr2:178257523G>T	ENST00000264167.4	+	1	152	c.6G>T	c.(4-6)gcG>gcT	p.A2A	AGPS_ENST00000409888.1_Silent_p.A2A|NFE2L2_ENST00000464747.1_5'Flank|AC074286.1_ENST00000397057.2_RNA	NM_003659.3	NP_003650.1	O00116	ADAS_HUMAN	alkylglycerone phosphate synthase	2	Poly-Ala.				cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|lipid biosynthetic process (GO:0008610)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	alkylglycerone-phosphate synthase activity (GO:0008609)|FAD binding (GO:0071949)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0018)|Epithelial(96;0.00919)|all cancers(119;0.0358)			TAGCCATGGCGGAGGCGGCGG	0.771																																					p.A2A		Atlas-SNP	.											.	AGPS	56	.	0			c.G6T						.						3	3	3					2																	178257523		1265	2959	4224	SO:0001819	synonymous_variant	8540	exon1			CATGGCGGAGGCG	Y09443	CCDS2275.1	2q	2008-02-05			ENSG00000018510	ENSG00000018510	2.5.1.26		327	protein-coding gene	gene with protein product		603051				9187299, 9553082	Standard	NM_003659		Approved	ADHAPS, ADAS, ALDHPSY, ADPS, ADAP-S	uc002ull.2	O00116	OTTHUMG00000132530	ENST00000264167.4:c.6G>T	2.37:g.178257523G>T		66.0	0.0		61.0	23.0	NM_003659	A5D8U9|Q2TU35	Silent	SNP	ENST00000264167.4	37	CCDS2275.1																																																																																			.	.		0.771	AGPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255730.2			T	178257523	G	T	178257523	2	4	372	1	0	0	0	0	0	0	0	1	394	1103	39	1		1	AGPS	2	178257523	Silent	SNP	G	TCGA-ZS-A9CF-01A-11D-A382-10	7321122	178257523	64941850	13	51423										
OSBPL6	114880	hgsc.bcm.edu	37	chr2	179197657	179197657	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	ctgcgacatcatcggttgtaTcgtcagaatgaaattgtgag	11	7	2	3			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr2:179197657T>C	ENST00000190611.4	+	8	922	c.546T>C	c.(544-546)taT>taC	p.Y182Y	OSBPL6_ENST00000357080.4_Silent_p.Y182Y|OSBPL6_ENST00000409045.3_Silent_p.Y182Y|OSBPL6_ENST00000409631.1_Silent_p.Y182Y|OSBPL6_ENST00000392505.2_Silent_p.Y182Y|OSBPL6_ENST00000315022.2_Silent_p.Y161Y|OSBPL6_ENST00000359685.3_Silent_p.Y182Y	NM_032523.3	NP_115912.1	Q9BZF3	OSBL6_HUMAN	oxysterol binding protein-like 6	182					lipid transport (GO:0006869)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(18)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			ATCGGTTGTATCGTCAGAATG	0.408																																					p.Y182Y		Atlas-SNP	.											.	OSBPL6	178	.	0			c.T546C						.						161	151	154					2																	179197657		2203	4300	6503	SO:0001819	synonymous_variant	114880	exon8			GTTGTATCGTCAG	AF392448	CCDS2277.1, CCDS2278.1, CCDS56150.1, CCDS56151.1, CCDS56152.1	2q32.1	2008-05-27			ENSG00000079156	ENSG00000079156		"Oxysterol binding proteins"	16388	protein-coding gene	gene with protein product	"OSBP-related protein 6"	606734				11483621	Standard	NM_001201480		Approved	ORP6	uc002uly.3	Q9BZF3	OTTHUMG00000132579	ENST00000190611.4:c.546T>C	2.37:g.179197657T>C		167.0	0.0		200.0	79.0	NM_001201482	B4DTW1|C4AMC0|C4AME4|D3DPF6|D3DPF7|Q4ZG68|Q53T68|Q59H61|Q7Z4Q1|Q86V84|Q8N9T0|Q96SR1	Silent	SNP	ENST00000190611.4	37	CCDS2277.1																																																																																			.	.		0.408	OSBPL6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334393.2	NM_032523		C	179197657	T	C	179197657	2	2	372	1	0	0	0	0	0	0	0	1	11290	1442	50	2		2	OSBPL6	2	179197657	Silent	SNP	T	TCGA-ZS-A9CF-01A-11D-A382-10	940134	179197657	64001716	14	51424										
TTN	7273	hgsc.bcm.edu	37	chr2	179479290	179479290	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	cttctcttactatcaacaatAgtcactgtggatttcttagg	6	9	4	0			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr2:179479290A>T	ENST00000591111.1	-	211	44252	c.44028T>A	c.(44026-44028)acT>acA	p.T14676T	RP11-171I2.4_ENST00000605334.1_lincRNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000359218.5_Silent_p.T7377T|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000460472.2_Silent_p.T7252T|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000589042.1_Silent_p.T16317T|TTN_ENST00000342175.6_Silent_p.T7444T|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342992.6_Silent_p.T13749T			Q8WZ42	TITIN_HUMAN	titin	14676	Ig-like 96.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TATCAACAATAGTCACTGTGG	0.418																																					p.T16317T		Atlas-SNP	.											.	TTN	18412	.	0			c.T48951A						.						113	106	108					2																	179479290		1931	4127	6058	SO:0001819	synonymous_variant	7273	exon261			AACAATAGTCACT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.44028T>A	2.37:g.179479290A>T		87.0	0.0		106.0	40.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				.	.		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179479290	A	T	179479290	2	4	372	1	0	0	0	0	0	0	0	1	16750	407	15	4		4	TTN	2	179479290	Silent	SNP	A	TCGA-ZS-A9CF-01A-11D-A382-10	281633	179479290	63720083	15	51425										
BARD1	580	hgsc.bcm.edu	37	chr2	215674279	215674279	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	ggctgccggttcctcggctgCcgattatccggcatcgtccc	12	16	0	0			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr2:215674279C>A	ENST00000260947.4	-	1	149	c.15G>T	c.(13-15)cgG>cgT	p.R5R	AC072062.1_ENST00000607412.1_RNA|BARD1_ENST00000449967.2_5'UTR|BARD1_ENST00000471787.1_5'UTR	NM_000465.2|NM_001282543.1|NM_001282545.1|NM_001282548.1	NP_000456.2|NP_001269472.1|NP_001269474.1|NP_001269477.1	Q99728	BARD1_HUMAN	BRCA1 associated RING domain 1	5					cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mRNA 3'-end processing (GO:0031441)|negative regulation of protein export from nucleus (GO:0046826)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein catabolic process (GO:0045732)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of phosphorylation (GO:0042325)|tissue homeostasis (GO:0001894)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	kinase binding (GO:0019900)|ligase activity (GO:0016874)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(14)|prostate(4)|upper_aerodigestive_tract(1)	35		Renal(323;0.0243)		Epithelial(149;3.2e-06)|all cancers(144;0.000461)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		TCCTCGGCTGCCGATTATCCG	0.677									Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																												p.R5R		Atlas-SNP	.											.	BARD1	138	.	0			c.G15T						.																																			SO:0001819	synonymous_variant	580	exon1	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	CGGCTGCCGATTA		CCDS2397.1, CCDS74645.1, CCDS74646.1, CCDS74647.1, CCDS74648.1	2q34-q35	2013-01-10			ENSG00000138376	ENSG00000138376		"Ankyrin repeat domain containing"	952	protein-coding gene	gene with protein product		601593				8944023, 9425226, 15159397	Standard	NM_001282548		Approved		uc002veu.2	Q99728	OTTHUMG00000133016	ENST00000260947.4:c.15G>T	2.37:g.215674279C>A		93.0	0.0		123.0	46.0	NM_000465	F6MDH7|F6MDH8|F6MDH9|O43574|Q53SS5	Silent	SNP	ENST00000260947.4	37	CCDS2397.1																																																																																			.	.		0.677	BARD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256602.1	NM_000465		A	215674279	C	A	215674279	2	1	372	1	0	0	0	0	0	0	0	1	1312	726	26	3		3	BARD1	2	215674279	Silent	SNP	C	TCGA-ZS-A9CF-01A-11D-A382-10	36194989	215674279	27525094	16	51426										
ACCN4	55515	hgsc.bcm.edu	37	chr2	220396805	220396805	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	atccaccagctggggttcggGgtgtccccaggcttccagac	13	14	0	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr2:220396805G>A	ENST00000347842.3	+	3	1205	c.1191G>A	c.(1189-1191)ggG>ggA	p.G397G	ASIC4_ENST00000473709.1_3'UTR|ASIC4_ENST00000358078.4_Silent_p.G397G	NM_182847.2	NP_878267.2	Q96FT7	ASIC4_HUMAN	acid-sensing (proton-gated) ion channel family member 4	397					ion transmembrane transport (GO:0034220)|sodium ion transmembrane transport (GO:0035725)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)	ion channel activity (GO:0005216)|sodium channel activity (GO:0005272)|sodium ion transmembrane transporter activity (GO:0015081)										TGGGGTTCGGGGTGTCCCCAG	0.622																																					p.G397G		Atlas-SNP	.											.	.	.	.	0			c.G1191A						.						67	73	71					2																	220396805		2203	4300	6503	SO:0001819	synonymous_variant	55515	exon3			GTTCGGGGTGTCC	AJ271643	CCDS2442.1	2q36.1	2012-02-22	2012-02-22	2012-02-22	ENSG00000072182	ENSG00000072182		"Ion channels / Acid-sensing (proton-gated) ion channels"	21263	protein-coding gene	gene with protein product		606715	"amiloride-sensitive cation channel 4, pituitary", "amiloride-sensitive cation channel family member 4, pituitary"	ACCN4		10852210	Standard	NM_182847		Approved	BNAC4	uc002vma.3	Q96FT7	OTTHUMG00000058928	ENST00000347842.3:c.1191G>A	2.37:g.220396805G>A		173.0	0.0		144.0	25.0	NM_182847	Q53SB7|Q6GMS1|Q6PIN9|Q9NQA4	Silent	SNP	ENST00000347842.3	37	CCDS2442.1																																																																																			.	.		0.622	ASIC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000130263.1	NM_018674		A	220396805	G	A	220396805	2	1	372	1	0	0	0	0	0	0	0	1	131	1219	43	3		3	ACCN4	2	220396805	Silent	SNP	G	TCGA-ZS-A9CF-01A-11D-A382-10	4722526	220396805	22802568	17	51427										
ITPR1	3708	hgsc.bcm.edu	37	chr3	4716014	4716014	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	ctctgataaagagaagaataAgcttacgtttgaggtaactc	9	6	1	4			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr3:4716014A>T	ENST00000443694.2	+	19	2540	c.2540A>T	c.(2539-2541)aAg>aTg	p.K847M	ITPR1_ENST00000357086.4_Missense_Mutation_p.K862M|ITPR1_ENST00000423119.2_Missense_Mutation_p.K862M|ITPR1_ENST00000456211.2_Missense_Mutation_p.K847M|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000302640.8_Missense_Mutation_p.K847M|ITPR1_ENST00000354582.6_Missense_Mutation_p.K862M			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	862					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	GAGAAGAATAAGCTTACGTTT	0.378																																					p.K862M		Atlas-SNP	.											.	ITPR1	659	.	0			c.A2585T						.						125	118	120					3																	4716014		1834	4085	5919	SO:0001583	missense	3708	exon22			AGAATAAGCTTAC	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"Ion channels / Inositol triphosphate receptors"	6180	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 94"	147265	"spinocerebellar ataxia 15", "spinocerebellar ataxia 16", "spinocerebellar ataxia 29"	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.2540A>T	3.37:g.4716014A>T	ENSP00000401671:p.Lys847Met	112.0	0.0		121.0	11.0	NM_001099952	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	37	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.445075	0.83993	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000357086;ENST00000456211;ENST00000443694	D;D;D;D;D;D	0.92495	-3.04;-3.05;-3.04;-3.04;-3.04;-3.04	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	D	0.95887	0.8661	M	0.84082	2.675	0.80722	D	1	P;D;P	0.89917	0.956;1.0;0.94	P;D;B	0.74023	0.706;0.982;0.379	D	0.95141	0.8264	10	0.33940	T	0.23	.	15.7832	0.78281	1.0:0.0:0.0:0.0	.	847;862;862	E7EPX7;Q14643;G5E9P1	.;ITPR1_HUMAN;.	M	862;847;862;862;862;847;847	ENSP00000306253:K847M;ENSP00000346595:K862M;ENSP00000405934:K862M;ENSP00000349597:K862M;ENSP00000397885:K847M;ENSP00000401671:K847M	ENSP00000306253:K847M	K	+	2	0	ITPR1	4691014	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.676000	0.91199	2.302000	0.77476	0.533000	0.62120	AAG	.	.		0.378	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		T	4716014	A	T	4716014	3	4	372	1	0	0	0	0	1	0	0	0	7929	72	3	4	2663	4	ITPR1	3	4716014	Missense_Mutation	SNP	A	TCGA-ZS-A9CF-01A-11D-A382-10		4716014	193306416	18	51428										
SCN11A	11280	hgsc.bcm.edu	37	chr3	38962724	38962724	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	ttcttcacagagcgtagcaaGgcccccacgatgaccttcag	9	14	3	2			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr3:38962724G>T	ENST00000302328.3	-	6	933	c.735C>A	c.(733-735)gcC>gcA	p.A245A	SCN11A_ENST00000450244.1_Silent_p.A245A|SCN11A_ENST00000456224.3_Silent_p.A245A|SCN11A_ENST00000444237.2_Silent_p.A245A	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	245					cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.A245A(1)		NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AGCGTAGCAAGGCCCCCACGA	0.542																																					p.A245A		Atlas-SNP	.											SCN11A,NS,carcinoma,0,1	SCN11A	296	1	1	Substitution - coding silent(1)	kidney(1)	c.C735A						.						102	99	100					3																	38962724		2203	4300	6503	SO:0001819	synonymous_variant	11280	exon6			TAGCAAGGCCCCC	AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10583	protein-coding gene	gene with protein product		604385	"sodium channel, voltage-gated, type XI, alpha polypeptide", "sodium channel, voltage-gated, type XII, alpha"	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.735C>A	3.37:g.38962724G>T		161.0	1.0		206.0	78.0	NM_014139	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Silent	SNP	ENST00000302328.3	37	CCDS33737.1																																																																																			.	.		0.542	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139		T	38962724	G	T	38962724	2	4	372	1	0	0	0	0	0	0	0	1	13928	987	35	3		3	SCN11A	3	38962724	Silent	SNP	G	TCGA-ZS-A9CF-01A-11D-A382-10	34246710	38962724	159059706	19	51429										
XIRP1	165904	hgsc.bcm.edu	37	chr3	39228541	39228541	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	catacttggcaagacagagcTcccctggccctcgggcctcc	10	17	0	2			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr3:39228541T>A	ENST00000340369.3	-	2	2624	c.2396A>T	c.(2395-2397)gAg>gTg	p.E799V	XIRP1_ENST00000421646.1_Intron|XIRP1_ENST00000396251.1_Missense_Mutation_p.E799V	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	799					cardiac muscle cell development (GO:0055013)|negative regulation of cell proliferation (GO:0008285)|regulation of membrane potential (GO:0042391)|sarcomere organization (GO:0045214)	fascia adherens (GO:0005916)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(14)|lung(22)|ovary(4)|pancreas(1)|prostate(2)|skin(6)	71				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		AAGACAGAGCTCCCCTGGCCC	0.612																																					p.E799V		Atlas-SNP	.											.	XIRP1	173	.	0			c.A2396T						.						64	65	65					3																	39228541		2203	4300	6503	SO:0001583	missense	165904	exon2			CAGAGCTCCCCTG	AW755250	CCDS2683.1, CCDS56245.1	3p21.33	2008-02-05	2007-06-27	2007-06-27	ENSG00000168334	ENSG00000168334			14301	protein-coding gene	gene with protein product		609777	"cardiomyopathy associated 1"	CMYA1		12203715, 15454575	Standard	NM_001198621		Approved	DKFZp451D042, Xin	uc003cjk.2	Q702N8	OTTHUMG00000131297	ENST00000340369.3:c.2396A>T	3.37:g.39228541T>A	ENSP00000343140:p.Glu799Val	130.0	0.0		169.0	15.0	NM_001198621	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Missense_Mutation	SNP	ENST00000340369.3	37	CCDS2683.1	.	.	.	.	.	.	.	.	.	.	T	16.43	3.120362	0.56613	.	.	ENSG00000168334	ENST00000396251;ENST00000340369	T;T	0.05513	3.43;3.82	4.11	2.85	0.33270	.	0.334304	0.29431	N	0.012178	T	0.08758	0.0217	L	0.51422	1.61	0.80722	D	1	P;P	0.50943	0.94;0.892	P;B	0.46144	0.505;0.406	T	0.06679	-1.0813	10	0.62326	D	0.03	.	8.9432	0.35742	0.0:0.0:0.1861:0.8139	.	799;799	Q702N8;Q702N8-2	XIRP1_HUMAN;.	V	799	ENSP00000379550:E799V;ENSP00000343140:E799V	ENSP00000343140:E799V	E	-	2	0	XIRP1	39203545	0.002000	0.14202	1.000000	0.80357	0.976000	0.68499	1.002000	0.29796	1.873000	0.54277	0.460000	0.39030	GAG	.	.		0.612	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522		A	39228541	T	A	39228541	3	1	372	1	0	0	0	0	1	0	0	0	17444	1551	54	4	3139	4	XIRP1	3	39228541	Missense_Mutation	SNP	T	TCGA-ZS-A9CF-01A-11D-A382-10	265817	39228541	158793889	20	51430										
SCAP	22937	hgsc.bcm.edu	37	chr3	47459072	47459072	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	agagcggccacagaccgcccGgtgccggggctcgggctgag	18	14	0	3			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr3:47459072G>A	ENST00000265565.5	-	17	3104	c.2692C>T	c.(2692-2694)Cgg>Tgg	p.R898W	SCAP_ENST00000441517.2_Missense_Mutation_p.R642W|SCAP_ENST00000545718.1_Missense_Mutation_p.R505W	NM_012235.2	NP_036367.2	Q12770	SCAP_HUMAN	SREBF chaperone	898	Interaction with SREBF2. {ECO:0000250}.				aging (GO:0007568)|cholesterol metabolic process (GO:0008203)|negative regulation of cholesterol biosynthetic process (GO:0045541)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|regulation of fatty acid biosynthetic process (GO:0042304)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)	unfolded protein binding (GO:0051082)			endometrium(4)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	26				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)		CAGACCGCCCGGTGCCGGGGC	0.662																																					p.R898W	Pancreas(149;978 1908 29304 37806 46700)	Atlas-SNP	.											.	SCAP	88	.	0			c.C2692T						.						7	9	8					3																	47459072		2121	4188	6309	SO:0001583	missense	22937	exon17			CCGCCCGGTGCCG	BC020987	CCDS2755.2	3p21.31	2013-01-10			ENSG00000114650	ENSG00000114650		"WD repeat domain containing"	30634	protein-coding gene	gene with protein product	"SREBP cleavage activating protein"	601510				8898195, 8724849, 10570913	Standard	XM_005264967		Approved	KIAA0199	uc003crh.1	Q12770	OTTHUMG00000125539	ENST00000265565.5:c.2692C>T	3.37:g.47459072G>A	ENSP00000265565:p.Arg898Trp	252.0	0.0		231.0	113.0	NM_012235	Q8N2E0|Q8WUA1	Missense_Mutation	SNP	ENST00000265565.5	37	CCDS2755.2	.	.	.	.	.	.	.	.	.	.	G	21.7	4.194997	0.78902	.	.	ENSG00000114650	ENST00000360832;ENST00000265565;ENST00000441517;ENST00000545718	T;T;T	0.80994	-1.44;-1.4;0.73	4.85	4.85	0.62838	.	0.000000	0.64402	D	0.000017	D	0.84014	0.5379	L	0.29908	0.895	0.48135	D	0.999594	D;D	0.89917	1.0;1.0	D;D	0.74674	0.984;0.965	D	0.84074	0.0381	10	0.41790	T	0.15	-31.6416	17.7353	0.88391	0.0:0.0:1.0:0.0	.	642;898	F8W921;Q12770	.;SCAP_HUMAN	W	524;898;642;505	ENSP00000265565:R898W;ENSP00000416847:R642W;ENSP00000438956:R505W	ENSP00000265565:R898W	R	-	1	2	SCAP	47434076	0.976000	0.34144	0.998000	0.56505	0.538000	0.34931	0.923000	0.28757	2.513000	0.84729	0.561000	0.74099	CGG	.	.		0.662	SCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246872.2	NM_012235		A	47459072	G	A	47459072	3	1	372	1	0	0	0	0	1	0	0	0	13892	1115	39	1	1175	1	SCAP	3	47459072	Missense_Mutation	SNP	G	TCGA-ZS-A9CF-01A-11D-A382-10	8230531	47459072	150563358	21	51431										
OR5H14	403273	hgsc.bcm.edu	37	chr3	97869095	97869095	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	tcctttattaaatcccatgaTctacagcctgagaaacaagc	5	11	1	2			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr3:97869095T>C	ENST00000437310.1	+	1	926	c.866T>C	c.(865-867)aTc>aCc	p.I289T	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005514.1	NP_001005514.1	A6NHG9	O5H14_HUMAN	olfactory receptor, family 5, subfamily H, member 14	289						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	31						AATCCCATGATCTACAGCCTG	0.348																																					p.I289T		Atlas-SNP	.											.	OR5H14	56	.	0			c.T866C						.						45	44	44					3																	97869095		2202	4296	6498	SO:0001583	missense	403273	exon1			CCATGATCTACAG		CCDS33798.1	3q11.2	2013-09-23			ENSG00000236032	ENSG00000236032		"GPCR / Class A : Olfactory receptors"	31286	protein-coding gene	gene with protein product							Standard	NM_001005514		Approved		uc003dsg.1	A6NHG9	OTTHUMG00000160079	ENST00000437310.1:c.866T>C	3.37:g.97869095T>C	ENSP00000401706:p.Ile289Thr	162.0	0.0		172.0	70.0	NM_001005514	B9EH15	Missense_Mutation	SNP	ENST00000437310.1	37	CCDS33798.1	.	.	.	.	.	.	.	.	.	.	T	11.56	1.675075	0.29783	.	.	ENSG00000236032	ENST00000437310	T	0.57273	0.41	2.49	2.49	0.30216	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47852	D	0.000212	T	0.75635	0.3876	H	0.96720	3.87	0.26098	N	0.980854	D	0.62365	0.991	P	0.60949	0.881	T	0.68872	-0.5294	10	0.87932	D	0	.	8.4219	0.32705	0.0:0.0:0.0:1.0	.	289	A6NHG9	O5H14_HUMAN	T	289	ENSP00000401706:I289T	ENSP00000401706:I289T	I	+	2	0	OR5H14	99351785	1.000000	0.71417	0.996000	0.52242	0.133000	0.20885	6.893000	0.75649	1.132000	0.42129	0.164000	0.16699	ATC	.	.		0.348	OR5H14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359112.1			C	97869095	T	C	97869095	3	2	372	1	0	0	0	0	1	0	0	0	11169	1435	50	2	868	2	OR5H14	3	97869095	Missense_Mutation	SNP	T	TCGA-ZS-A9CF-01A-11D-A382-10	50410023	97869095	100153335	22	51432										
MED12L	116931	hgsc.bcm.edu	37	chr3	150876484	150876484	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	tgttcatttaaggaaggaatGttagaaaaacacgaatattt	8	3	1	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr3:150876484G>A	ENST00000474524.1	+	6	773	c.735G>A	c.(733-735)atG>atA	p.M245I	MED12L_ENST00000422248.2_Missense_Mutation_p.M245I|MED12L_ENST00000309237.4_Missense_Mutation_p.M245I|MED12L_ENST00000273432.4_Missense_Mutation_p.M245I	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	245						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			AGGAAGGAATGTTAGAAAAAC	0.308																																					p.M245I		Atlas-SNP	.											.	MED12L	271	.	0			c.G735A						.						72	69	70					3																	150876484		2203	4300	6503	SO:0001583	missense	116931	exon6			AGGAATGTTAGAA	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.735G>A	3.37:g.150876484G>A	ENSP00000417235:p.Met245Ile	135.0	0.0		190.0	109.0	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Missense_Mutation	SNP	ENST00000474524.1	37	CCDS33876.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.543570	0.86022	.	.	ENSG00000144893	ENST00000422248;ENST00000309237;ENST00000474524;ENST00000273432	T;T;T;T	0.61274	0.45;0.43;0.31;0.12	5.07	5.07	0.68467	.	0.046152	0.85682	D	0.000000	T	0.69797	0.3151	L	0.58101	1.795	0.34666	D	0.723237	B;B;B;P	0.44281	0.073;0.131;0.206;0.831	B;B;B;P	0.54664	0.024;0.039;0.059;0.758	T	0.79112	-0.1937	10	0.87932	D	0	-18.1091	18.4436	0.90676	0.0:0.0:1.0:0.0	.	245;245;245;245	F8WAE6;Q86YW9;Q86YW9-2;Q86YW9-3	.;MD12L_HUMAN;.;.	I	245	ENSP00000403308:M245I;ENSP00000310760:M245I;ENSP00000417235:M245I;ENSP00000273432:M245I	ENSP00000273432:M245I	M	+	3	0	MED12L	152359174	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	8.194000	0.89721	2.519000	0.84933	0.467000	0.42956	ATG	.	.		0.308	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002		A	150876484	G	A	150876484	3	1	372	1	0	0	0	0	1	0	0	0	9438	1377	48	3	757	3	MED12L	3	150876484	Missense_Mutation	SNP	G	TCGA-ZS-A9CF-01A-11D-A382-10	53007389	150876484	47145946	23	51433										
UGT2B7	7364	hgsc.bcm.edu	37	chr4	69962260	69962260	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	tgtctgtgaaatggacttcaGtaattttgctaatacaactg	8	6	2	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr4:69962260G>T	ENST00000508661.1	+	1	49	c.22G>T	c.(22-24)Gta>Tta	p.V8L	UGT2B7_ENST00000509763.1_Intron|UGT2B7_ENST00000305231.7_Missense_Mutation_p.V8L			P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B7	8					androgen metabolic process (GO:0008209)|cellular glucuronidation (GO:0052695)|lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)			autonomic_ganglia(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38					Atorvastatin(DB01076)|Carbamazepine(DB00564)|Chenodeoxycholic acid(DB06777)|Codeine(DB00318)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Diclofenac(DB00586)|Epirubicin(DB00445)|Etodolac(DB00749)|Ezetimibe(DB00973)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naproxen(DB00788)|Oxazepam(DB00842)|Pitavastatin(DB08860)|Silodosin(DB06207)|Simvastatin(DB00641)|Suprofen(DB00870)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zidovudine(DB00495)	ATGGACTTCAGTAATTTTGCT	0.403																																					p.V8L		Atlas-SNP	.											.	UGT2B7	79	.	0			c.G22T						.						127	126	126					4																	69962260		2203	4300	6503	SO:0001583	missense	7364	exon1			ACTTCAGTAATTT	BC030974	CCDS3526.1	4q13	2008-02-05	2005-07-20		ENSG00000171234	ENSG00000171234		"UDP glucuronosyltransferases"	12554	protein-coding gene	gene with protein product		600068	"UDP glycosyltransferase 2 family, polypeptide B7"			2159463, 7835904	Standard	NM_001074		Approved	UGT2B9	uc003heg.4	P16662	OTTHUMG00000129404	ENST00000508661.1:c.22G>T	4.37:g.69962260G>T	ENSP00000427659:p.Val8Leu	81.0	0.0		103.0	30.0	NM_001074	B2R810|Q6GTW0	Missense_Mutation	SNP	ENST00000508661.1	37		.	.	.	.	.	.	.	.	.	.	G	9.040	0.989448	0.18966	.	.	ENSG00000171234	ENST00000305231;ENST00000508661	T;T	0.59502	0.26;0.9	2.54	-5.08	0.02929	.	0.760929	0.10779	U	0.635043	T	0.36663	0.0975	N	0.17082	0.46	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.12837	0.003;0.008	T	0.23511	-1.0186	9	.	.	.	.	14.6506	0.68794	0.0:0.1845:0.8155:0.0	.	8;8	E9PBP8;P16662	.;UD2B7_HUMAN	L	8	ENSP00000304811:V8L;ENSP00000427659:V8L	.	V	+	1	0	UGT2B7	69996849	.	.	0.000000	0.03702	0.007000	0.05969	.	.	-1.053000	0.03218	0.313000	0.20887	GTA	.	.		0.403	UGT2B7-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000362103.1	NM_001074		T	69962260	G	T	69962260	3	4	372	1	0	0	0	0	1	0	0	0	16977	1029	36	3	24	3	UGT2B7	4	69962260	Missense_Mutation	SNP	G	TCGA-ZS-A9CF-01A-11D-A382-10		69962260	121192016	24	51434										
IGJ	3512	hgsc.bcm.edu	37	chr4	71522068	71522068	+	Frame_Shift_Del	DEL	G	G	-													0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	agtcaggatagcaggcatctGgggttaaggctgtttccacc							TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr4:71522068delG	ENST00000254801.4	-	4	627	c.458delC	c.(457-459)ccafs	p.P153fs	IGJ_ENST00000543780.1_Frame_Shift_Del_p.P169fs|ENAM_ENST00000472903.1_Intron	NM_144646.3	NP_653247.1	P01591	IGJ_HUMAN	immunoglobulin J polypeptide, linker protein for immunoglobulin alpha and mu polypeptides	153					adaptive immune response (GO:0002250)|antibacterial humoral response (GO:0019731)|glomerular filtration (GO:0003094)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of respiratory burst (GO:0060267)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|dimeric IgA immunoglobulin complex (GO:0071750)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|monomeric IgA immunoglobulin complex (GO:0071748)|pentameric IgM immunoglobulin complex (GO:0071756)|secretory dimeric IgA immunoglobulin complex (GO:0071752)|secretory IgA immunoglobulin complex (GO:0071751)	antigen binding (GO:0003823)|IgA binding (GO:0019862)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)	7			Lung(101;0.235)			GCAGGCATCTGGGGTTAAGGC	0.423																																					p.P153fs		Atlas-Indel	.											.	IGJ	13	.	0			c.459delA						.						131	112	118					4																	71522068		2203	4300	6503	SO:0001589	frameshift_variant	3512	exon4			.	M12759	CCDS3545.1	4q21	2012-10-02			ENSG00000132465	ENSG00000132465		"Immunoglobulins / IGJ linker"	5713	protein-coding gene	gene with protein product	"immunoglobulin J chain", "IgJ chain"	147790				3016707, 2984306	Standard	NM_144646		Approved	IGCJ, JCH	uc003hfn.4	P01591	OTTHUMG00000129909	ENST00000254801.4:c.458delC	4.37:g.71522068delG	ENSP00000254801:p.Pro153fs	196.0	0.0		211.0	97.0	NM_144646		Frame_Shift_Del	DEL	ENST00000254801.4	37	CCDS3545.1																																																																																			.	.		0.423	IGJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252160.1	NM_144646		-	71522068	G	-	71522068	7	5	372	1	0	1	0	1	0	0	0	0	7601	1348	47	0	25	0	IGJ	4	71522068	Frame_Shift_Del	DEL	G	TCGA-ZS-A9CF-01A-11D-A382-10	1559808	71522068	119632208	25	51435										
ALB	213	hgsc.bcm.edu	37	chr4	74274521	74274524	+	Splice_Site	DEL	AAGT	AAGT	-													0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	atgaagagacatttttgaaaAagtaagtaatcagatgttta					rs17853494		TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	AAGT	AAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr4:74274521_74274524delAAGT	ENST00000295897.4	+	4	570_571	c.481_482delAAGT	c.(481-483)aag>g	p.K161fs	ALB_ENST00000503124.1_Intron|ALB_ENST00000401494.3_Intron|ALB_ENST00000509063.1_Splice_Site_p.K161fs|ALB_ENST00000415165.2_Intron|ALB_ENST00000505649.1_3'UTR	NM_000477.5	NP_000468.1	Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			ATTTTTGAAAAAGTAAGTAATCAG	0.348																																					p.160_161del		Atlas-Indel	.											.	ALB	132	.	0			c.480_482del						.																																			SO:0001630	splice_region_variant	213	exon4			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000295897.4:c.482+1AAGT>-	4.37:g.74274525_74274528delAAGT		87.0	0.0		77.0	28.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	In_Frame_Del	DEL	ENST00000295897.4	37	CCDS3555.1																																																																																			.	.		0.348	ALB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252173.3	NM_000477	Frame_Shift_Del	-	74274524	AAGT	-	74274521	8	5	372	1	0	1	0	1	0	0	1	0	486	28	1	0	495	0	ALB	4	74274521	Splice_Site	DEL	AAGT	TCGA-ZS-A9CF-01A-11D-A382-10	2752453	74274521	116879755	26	51436										
AFP	174	hgsc.bcm.edu	37	chr4	74303922	74303922	+	Missense_Mutation	SNP	G	G	C	1	0	0	1	0	1	1	1	0	1	1	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	tttttgcccagtttgttcaaGaagccacttacaaggaagta	8	8	1	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr4:74303922G>C	ENST00000395792.2	+	3	269	c.169G>C	c.(169-171)Gaa>Caa	p.E57Q	AFP_ENST00000226359.2_Missense_Mutation_p.E57Q	NM_001134.1	NP_001125.1	P02771	FETA_HUMAN	alpha-fetoprotein	57	Albumin 1. {ECO:0000255|PROSITE- ProRule:PRU00769}.				ovulation from ovarian follicle (GO:0001542)|progesterone metabolic process (GO:0042448)|SMAD protein signal transduction (GO:0060395)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	metal ion binding (GO:0046872)			breast(1)|endometrium(2)|large_intestine(3)|lung(13)|ovary(1)|skin(1)|urinary_tract(1)	22	Breast(15;0.00102)		Epithelial(6;2.42e-05)|all cancers(17;0.000268)|OV - Ovarian serous cystadenocarcinoma(6;0.000324)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GTTTGTTCAAGAAGCCACTTA	0.393									Alpha-Fetoprotein, Hereditary Persistence of																												p.E57Q		Atlas-SNP	.											.	AFP	60	.	0			c.G169C						.						127	126	126					4																	74303922		2203	4300	6503	SO:0001583	missense	174	exon3	Familial Cancer Database	HPAFP	GTTCAAGAAGCCA	V01514	CCDS3556.1	4q13.3	2012-05-16			ENSG00000081051	ENSG00000081051			317	protein-coding gene	gene with protein product		104150		HPAFP			Standard	NM_001134		Approved	FETA	uc003hgz.1	P02771	OTTHUMG00000130011	ENST00000395792.2:c.169G>C	4.37:g.74303922G>C	ENSP00000379138:p.Glu57Gln	131.0	0.0		125.0	55.0	NM_001134	B2RBU3	Missense_Mutation	SNP	ENST00000395792.2	37	CCDS3556.1	.	.	.	.	.	.	.	.	.	.	G	13.57	2.276271	0.40294	.	.	ENSG00000081051	ENST00000395792;ENST00000226359	T;T	0.39056	1.1;1.1	5.29	3.57	0.40892	Serum albumin-like (1);Serum albumin, N-terminal (3);	0.637984	0.16311	N	0.219982	T	0.32675	0.0837	L	0.42245	1.32	0.24510	N	0.994213	P	0.41393	0.748	B	0.44315	0.446	T	0.16158	-1.0412	10	0.02654	T	1	-3.1533	7.615	0.28152	0.1883:0.0:0.8117:0.0	.	57	P02771	FETA_HUMAN	Q	57	ENSP00000379138:E57Q;ENSP00000226359:E57Q	ENSP00000226359:E57Q	E	+	1	0	AFP	74522786	0.071000	0.21146	0.301000	0.25044	0.317000	0.28152	0.970000	0.29383	0.807000	0.34208	0.655000	0.94253	GAA	.	.		0.393	AFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252284.3			C	74303922	G	C	74303922	3	2	372	1	0	0	0	0	1	0	0	0	363	943	33	4	179	4	AFP	4	74303922	Missense_Mutation	SNP	G	TCGA-ZS-A9CF-01A-11D-A382-10	29401	74303922	116850354	27	51437										
GUCY1A3	2982	hgsc.bcm.edu	37	chr4	156618268	156618268	+	Frame_Shift_Del	DEL	C	C	-													0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	agtatttgcaaactgattttCccagaggtgagtgcgtgctc							TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr4:156618268delC	ENST00000296518.7	+	3	458	c.249delC	c.(247-249)ttcfs	p.F83fs	GUCY1A3_ENST00000506455.1_Frame_Shift_Del_p.F83fs|GUCY1A3_ENST00000455639.2_Frame_Shift_Del_p.F83fs|GUCY1A3_ENST00000513574.1_Frame_Shift_Del_p.F83fs|GUCY1A3_ENST00000515602.1_3'UTR|GUCY1A3_ENST00000511507.1_Frame_Shift_Del_p.F83fs|GUCY1A3_ENST00000393832.3_5'UTR|GUCY1A3_ENST00000511108.1_Frame_Shift_Del_p.F83fs			Q02108	GCYA3_HUMAN	guanylate cyclase 1, soluble, alpha 3	83					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of cGMP biosynthetic process (GO:0030828)|regulation of blood pressure (GO:0008217)|relaxation of vascular smooth muscle (GO:0060087)|response to defense-related host nitric oxide production (GO:0052565)	guanylate cyclase complex, soluble (GO:0008074)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)|receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|liver(2)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.17)		AACTGATTTTCCCAGAGGTGA	0.368																																					p.F83fs		Atlas-Indel	.											.	GUCY1A3	133	.	0			c.248delT						.						112	114	113					4																	156618268		2203	4300	6503	SO:0001589	frameshift_variant	2982	exon3			.		CCDS34085.1, CCDS54812.1	4q31.3-q33	2008-03-18				ENSG00000164116	4.6.1.2		4685	protein-coding gene	gene with protein product		139396		GUC1A3		1352257	Standard	NM_001130687		Approved	GC-SA3	uc003iow.3	Q02108		ENST00000296518.7:c.249delC	4.37:g.156618268delC	ENSP00000296518:p.Phe83fs	96.0	0.0		112.0	49.0	NM_001130682	D3DP19|D6RDW3|O43843|Q8TAH3	Frame_Shift_Del	DEL	ENST00000296518.7	37	CCDS34085.1																																																																																			.	.		0.368	GUCY1A3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365786.2			-	156618268	C	-	156618268	7	5	372	1	0	1	0	1	0	0	0	0	6903	854	30	0	251	0	GUCY1A3	4	156618268	Frame_Shift_Del	DEL	C	TCGA-ZS-A9CF-01A-11D-A382-10	82314346	156618268	34536008	28	51438										
CASP3	836	hgsc.bcm.edu	37	chr4	185550584	185550584	+	Frame_Shift_Del	DEL	A	A	-													0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	aaattcaagcttgtcggcatActgtttcagcatggcacaaa					rs137982553		TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr4:185550584delA	ENST00000308394.4	-	8	938	c.676delT	c.(676-678)tatfs	p.Y226fs	CASP3_ENST00000393585.2_3'UTR|CASP3_ENST00000393588.4_3'UTR|CASP3_ENST00000517513.1_3'UTR|CASP3_ENST00000523916.1_Frame_Shift_Del_p.Y226fs	NM_004346.3	NP_004337.2	P42574	CASP3_HUMAN	caspase 3, apoptosis-related cysteine peptidase	226					activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|B cell homeostasis (GO:0001782)|cell fate commitment (GO:0045165)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|erythrocyte differentiation (GO:0030218)|execution phase of apoptosis (GO:0097194)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|glial cell apoptotic process (GO:0034349)|heart development (GO:0007507)|hippo signaling (GO:0035329)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|keratinocyte differentiation (GO:0030216)|negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of apoptotic process (GO:0043066)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|neuron apoptotic process (GO:0051402)|neuron differentiation (GO:0030182)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet formation (GO:0030220)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|proteolysis (GO:0006508)|regulation of apoptotic DNA fragmentation (GO:1902510)|regulation of apoptotic process (GO:0042981)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|release of cytochrome c from mitochondria (GO:0001836)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)|response to wounding (GO:0009611)|sensory perception of sound (GO:0007605)|T cell homeostasis (GO:0043029)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	aspartic-type endopeptidase activity (GO:0004190)|cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type endopeptidase activity involved in apoptotic process (GO:0097153)|cysteine-type endopeptidase activity involved in execution phase of apoptosis (GO:0097200)|peptidase activity (GO:0008233)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|skin(1)	12		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Colorectal(36;0.00139)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.057)|all_hematologic(60;0.0592)		all cancers(43;2.05e-27)|Epithelial(43;4.27e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.04e-11)|Colorectal(24;2e-05)|STAD - Stomach adenocarcinoma(60;2.35e-05)|GBM - Glioblastoma multiforme(59;4.94e-05)|COAD - Colon adenocarcinoma(29;0.00017)|BRCA - Breast invasive adenocarcinoma(30;0.000218)|LUSC - Lung squamous cell carcinoma(40;0.00904)|READ - Rectum adenocarcinoma(43;0.161)	Minocycline(DB01017)	TTGTCGGCATACTGTTTCAGC	0.413																																					p.Y226fs		Atlas-Indel	.											.	CASP3	27	.	0			c.677delA						.						88	82	84					4																	185550584		2203	4300	6503	SO:0001589	frameshift_variant	836	exon7			.	BC016926	CCDS3836.1	4q34	2008-02-05	2005-08-17		ENSG00000164305	ENSG00000164305		"Caspases"	1504	protein-coding gene	gene with protein product		600636	"caspase 3, apoptosis-related cysteine protease"			8780721	Standard	NM_004346		Approved	CPP32, CPP32B, Yama, apopain	uc003iwi.3	P42574	OTTHUMG00000133681	ENST00000308394.4:c.676delT	4.37:g.185550584delA	ENSP00000311032:p.Tyr226fs	125.0	0.0		186.0	110.0	NM_032991	A8K5M2|D3DP53|Q96AN1|Q96KP2	Frame_Shift_Del	DEL	ENST00000308394.4	37	CCDS3836.1																																																																																			.	.		0.413	CASP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257885.2	NM_004346		-	185550584	A	-	185550584	7	5	372	1	0	1	0	1	0	0	0	0	2674	391	14	0	161	0	CASP3	4	185550584	Frame_Shift_Del	DEL	A	TCGA-ZS-A9CF-01A-11D-A382-10	28932316	185550584	5603692	29	51439	270	2								
CASP3	836	hgsc.bcm.edu	37	chr4	185550586	185550586	+	Missense_Mutation	SNP	T	T	G													0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	attcaagcttgtcggcatacTgtttcagcatggcacaaagc							TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr4:185550586T>G	ENST00000308394.4	-	8	936	c.674A>C	c.(673-675)cAg>cCg	p.Q225P	CASP3_ENST00000393585.2_3'UTR|CASP3_ENST00000393588.4_3'UTR|CASP3_ENST00000517513.1_3'UTR|CASP3_ENST00000523916.1_Missense_Mutation_p.Q225P	NM_004346.3	NP_004337.2	P42574	CASP3_HUMAN	caspase 3, apoptosis-related cysteine peptidase	225					activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|B cell homeostasis (GO:0001782)|cell fate commitment (GO:0045165)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|erythrocyte differentiation (GO:0030218)|execution phase of apoptosis (GO:0097194)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|glial cell apoptotic process (GO:0034349)|heart development (GO:0007507)|hippo signaling (GO:0035329)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|keratinocyte differentiation (GO:0030216)|negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of apoptotic process (GO:0043066)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|neuron apoptotic process (GO:0051402)|neuron differentiation (GO:0030182)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet formation (GO:0030220)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|proteolysis (GO:0006508)|regulation of apoptotic DNA fragmentation (GO:1902510)|regulation of apoptotic process (GO:0042981)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|release of cytochrome c from mitochondria (GO:0001836)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)|response to wounding (GO:0009611)|sensory perception of sound (GO:0007605)|T cell homeostasis (GO:0043029)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	aspartic-type endopeptidase activity (GO:0004190)|cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type endopeptidase activity involved in apoptotic process (GO:0097153)|cysteine-type endopeptidase activity involved in execution phase of apoptosis (GO:0097200)|peptidase activity (GO:0008233)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|skin(1)	12		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Colorectal(36;0.00139)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.057)|all_hematologic(60;0.0592)		all cancers(43;2.05e-27)|Epithelial(43;4.27e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.04e-11)|Colorectal(24;2e-05)|STAD - Stomach adenocarcinoma(60;2.35e-05)|GBM - Glioblastoma multiforme(59;4.94e-05)|COAD - Colon adenocarcinoma(29;0.00017)|BRCA - Breast invasive adenocarcinoma(30;0.000218)|LUSC - Lung squamous cell carcinoma(40;0.00904)|READ - Rectum adenocarcinoma(43;0.161)	Minocycline(DB01017)	GTCGGCATACTGTTTCAGCAT	0.418																																					p.Q225P		Atlas-SNP	.											.	CASP3	27	.	0			c.A674C						.						86	80	82					4																	185550586		2203	4300	6503	SO:0001583	missense	836	exon8			GCATACTGTTTCA	BC016926	CCDS3836.1	4q34	2008-02-05	2005-08-17		ENSG00000164305	ENSG00000164305		"Caspases"	1504	protein-coding gene	gene with protein product		600636	"caspase 3, apoptosis-related cysteine protease"			8780721	Standard	NM_004346		Approved	CPP32, CPP32B, Yama, apopain	uc003iwi.3	P42574	OTTHUMG00000133681	ENST00000308394.4:c.674A>C	4.37:g.185550586T>G	ENSP00000311032:p.Gln225Pro	123.0	0.0		186.0	112.0	NM_004346	A8K5M2|D3DP53|Q96AN1|Q96KP2	Missense_Mutation	SNP	ENST00000308394.4	37	CCDS3836.1	.	.	.	.	.	.	.	.	.	.	T	8.731	0.916737	0.17907	.	.	ENSG00000164305	ENST00000308394;ENST00000523916	T;T	0.21361	2.01;2.01	5.69	-4.3	0.03710	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase non-catalytic subunit p10 (1);Peptidase C14, caspase precursor p45, core (1);	0.941225	0.08994	N	0.864032	T	0.27765	0.0683	M	0.81802	2.56	0.09310	N	1	B	0.26577	0.153	B	0.33295	0.161	T	0.44498	-0.9324	10	0.54805	T	0.06	.	10.4944	0.44768	0.7169:0.0612:0.0:0.2219	.	225	P42574	CASP3_HUMAN	P	225	ENSP00000311032:Q225P;ENSP00000428929:Q225P	ENSP00000311032:Q225P	Q	-	2	0	CASP3	185787580	0.004000	0.15560	0.000000	0.03702	0.142000	0.21351	1.060000	0.30530	-0.998000	0.03446	-1.530000	0.00923	CAG	.	.		0.418	CASP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257885.2	NM_004346		G	185550586	T	G	185550586	3	3	372	1	0	0	0	0	1	0	0	0	2674	1580	55	5	163	5	CASP3	4	185550586	Missense_Mutation	SNP	T	TCGA-ZS-A9CF-01A-11D-A382-10	2	185550586	5603690	30	51440	270	2								
C1QTNF3	114899	hgsc.bcm.edu	37	chr5	34043130	34043130	+	Intron	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	ctattcttgccaccactttaTtagttcttccgctcacctcc	3	16	3	0			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr5:34043130T>G	ENST00000231338.7	-	1	172				C1QTNF3_ENST00000382065.3_Missense_Mutation_p.N34T|RP11-1084J3.4_ENST00000382079.3_Intron	NM_030945.3	NP_112207.1	Q9BXJ4	C1QT3_HUMAN	C1q and tumor necrosis factor related protein 3						cellular triglyceride homeostasis (GO:0035356)|fat cell differentiation (GO:0045444)|negative regulation of gene expression (GO:0010629)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-6 secretion (GO:1900165)|negative regulation of monocyte chemotactic protein-1 production (GO:0071638)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of adiponectin secretion (GO:0070165)|positive regulation of cytokine secretion (GO:0050715)|protein trimerization (GO:0070206)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|prostate(3)|stomach(1)|urinary_tract(1)	17	all_lung(31;0.0207)					CACCACTTTATTAGTTCTTCC	0.502																																					p.N34T		Atlas-SNP	.											.	C1QTNF3	31	.	0			c.A101C						.						174	174	174					5																	34043130		2203	4300	6503	SO:0001627	intron_variant	114899	exon1			ACTTTATTAGTTC	AF329837	CCDS3904.1, CCDS34141.1	5p13	2009-05-20			ENSG00000082196	ENSG00000082196			14326	protein-coding gene	gene with protein product	"cartonectin"	612045				18421280	Standard	NM_030945		Approved	CTRP3, Cors, Corcs, 2310005P21Rik, Cors-26	uc003jio.3	Q9BXJ4	OTTHUMG00000090735	ENST00000231338.7:c.84+16A>C	5.37:g.34043130T>G		86.0	0.0		57.0	29.0	NM_181435	Q0VAN4|Q542Y2|Q6MZN1|Q96KY1	Missense_Mutation	SNP	ENST00000231338.7	37	CCDS3904.1	.	.	.	.	.	.	.	.	.	.	T	14.50	2.555014	0.45487	.	.	ENSG00000082196	ENST00000382065	D	0.85171	-1.95	5.77	5.77	0.91146	.	.	.	.	.	T	0.80199	0.4579	.	.	.	0.80722	D	1	B	0.09022	0.002	B	0.12156	0.007	T	0.75797	-0.3191	8	0.51188	T	0.08	.	11.4399	0.50090	0.0:0.07:0.0:0.93	.	34	Q0VAN4	.	T	34	ENSP00000371497:N34T	ENSP00000371497:N34T	N	-	2	0	C1QTNF3	34078887	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.010000	0.64004	2.326000	0.78906	0.533000	0.62120	AAT	.	.		0.502	C1QTNF3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000207469.1	NM_030945		G	34043130	T	G	34043130	1	3	372	0	1	0	0	0	0	0	0	0	1966	1493	52	5		5	C1QTNF3	5	34043130	Intron	SNP	T	TCGA-ZS-A9CF-01A-11D-A382-10		34043130	146872130	31	51441										
NRG2	9542	hgsc.bcm.edu	37	chr5	139266992	139266992	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	cttgccatccttgaaccaacGgtaggaaggctggggattac	12	10	0	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr5:139266992G>T	ENST00000361474.1	-	2	1029	c.805C>A	c.(805-807)Cgt>Agt	p.R269S	NRG2_ENST00000340391.3_Missense_Mutation_p.R66S|NRG2_ENST00000545385.1_Missense_Mutation_p.R269S|NRG2_ENST00000394770.1_Missense_Mutation_p.R269S|NRG2_ENST00000518130.1_5'UTR|NRG2_ENST00000541337.1_Missense_Mutation_p.R269S|NRG2_ENST00000289409.4_Missense_Mutation_p.R269S|NRG2_ENST00000358522.3_Missense_Mutation_p.R269S|NRG2_ENST00000289422.7_Missense_Mutation_p.R269S	NM_004883.2	NP_004874.1	O14511	NRG2_HUMAN	neuregulin 2	269	Ig-like C2-type.				embryo development (GO:0009790)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)	p.R269C(1)		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)			TTGAACCAACGGTAGGAAGGC	0.557																																					p.R269S		Atlas-SNP	.											NRG2,NS,carcinoma,0,1	NRG2	69	1	1	Substitution - Missense(1)	breast(1)	c.C805A						.						158	128	139					5																	139266992		2203	4300	6503	SO:0001583	missense	9542	exon2			ACCAACGGTAGGA		CCDS4217.1, CCDS54910.1	5q23-q33	2013-01-11			ENSG00000158458	ENSG00000158458		"Immunoglobulin superfamily / I-set domain containing"	7998	protein-coding gene	gene with protein product	"neural- and thymus-derived activator for ErbB kinases", "divergent of neuregulin-1"	603818				9168114, 9168115	Standard	NM_004883		Approved	Don-1, NTAK, HRG2	uc003lev.2	O14511	OTTHUMG00000129241	ENST00000361474.1:c.805C>A	5.37:g.139266992G>T	ENSP00000354910:p.Arg269Ser	128.0	0.0		129.0	66.0	NM_013982		Missense_Mutation	SNP	ENST00000361474.1	37	CCDS4217.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.994199	0.74703	.	.	ENSG00000158458	ENST00000541337;ENST00000289422;ENST00000361474;ENST00000446269;ENST00000545385;ENST00000394770;ENST00000340391;ENST00000289409;ENST00000358522;ENST00000544729;ENST00000378238	T;T;T;T;T;T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01;-0.01;-0.01;-0.01;-0.01;-0.01	5.64	4.72	0.59763	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.215756	0.34291	N	0.004096	T	0.52386	0.1731	N	0.05280	-0.08	0.39275	D	0.964464	P;P;P;P	0.51240	0.881;0.579;0.943;0.583	P;B;P;B	0.55508	0.697;0.261;0.777;0.425	T	0.59284	-0.7483	10	0.49607	T	0.09	-24.2851	11.0045	0.47626	0.0:0.0:0.7288:0.2712	.	269;269;269;269	O14511-2;O14511;O14511-4;O14511-3	.;NRG2_HUMAN;.;.	S	269;269;269;269;269;269;66;269;269;177;269	ENSP00000444235:R269S;ENSP00000289422:R269S;ENSP00000354910:R269S;ENSP00000438753:R269S;ENSP00000378251:R269S;ENSP00000342660:R66S;ENSP00000289409:R269S;ENSP00000351323:R269S;ENSP00000367483:R269S	ENSP00000289409:R269S	R	-	1	0	NRG2	139247176	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	3.612000	0.54142	2.654000	0.90174	0.563000	0.77884	CGT	.	.		0.557	NRG2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251340.1	NM_013982		T	139266992	G	T	139266992	3	4	372	1	0	0	0	0	1	0	0	0	10657	1116	39	1	1874	1	NRG2	5	139266992	Missense_Mutation	SNP	G	TCGA-ZS-A9CF-01A-11D-A382-10	105223862	139266992	41648268	32	51442										
FBXO38	81545	hgsc.bcm.edu	37	chr5	147813252	147813252	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	tcactatgaccaattgtggaAtcacagatctagtgctaaaa	7	8	3	2			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr5:147813252A>T	ENST00000340253.5	+	17	2977	c.2809A>T	c.(2809-2811)Atc>Ttc	p.I937F	FBXO38_ENST00000296701.6_Missense_Mutation_p.I692F|FBXO38_ENST00000394370.3_Missense_Mutation_p.I862F|FBXO38_ENST00000513826.1_Missense_Mutation_p.I692F|CTD-2283N19.1_ENST00000520980.2_RNA			Q6PIJ6	FBX38_HUMAN	F-box protein 38	937					cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)			ATG4C/FBXO38(2)	NS(1)|breast(2)|endometrium(7)|kidney(5)|large_intestine(9)|lung(15)|ovary(5)|prostate(2)|skin(2)|stomach(2)|urinary_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAATTGTGGAATCACAGATCT	0.323																																					p.I862F		Atlas-SNP	.											.	FBXO38	115	.	0			c.A2584T						.						146	150	149					5																	147813252		2203	4300	6503	SO:0001583	missense	81545	exon17			TGTGGAATCACAG	BC005873	CCDS43384.1, CCDS64285.1	5q33.1	2008-02-05			ENSG00000145868	ENSG00000145868		"F-boxes /  "other""	28844	protein-coding gene	gene with protein product		608533				12477932	Standard	NM_030793		Approved	MOKA, SP329, FLJ13962, Fbx38	uc003lpg.2	Q6PIJ6	OTTHUMG00000129929	ENST00000340253.5:c.2809A>T	5.37:g.147813252A>T	ENSP00000342023:p.Ile937Phe	170.0	0.0		107.0	100.0	NM_030793	Q6PK72|Q7Z2U0|Q86VN3|Q9BXY6|Q9H837|Q9HC40	Missense_Mutation	SNP	ENST00000340253.5	37		.	.	.	.	.	.	.	.	.	.	A	21.7	4.190941	0.78789	.	.	ENSG00000145868	ENST00000340253;ENST00000296701;ENST00000394370;ENST00000513826	T;T;T;T	0.46819	0.86;0.94;0.91;0.94	5.16	5.16	0.70880	.	0.047356	0.85682	D	0.000000	T	0.57961	0.2089	L	0.32530	0.975	0.35264	D	0.779825	P;D;D	0.89917	0.899;0.999;1.0	B;D;D	0.83275	0.39;0.986;0.996	T	0.69285	-0.5185	10	0.66056	D	0.02	-12.7874	14.1172	0.65161	1.0:0.0:0.0:0.0	.	692;862;937	Q6PIJ6-3;Q6PIJ6-2;Q6PIJ6	.;.;FBX38_HUMAN	F	937;692;862;692	ENSP00000342023:I937F;ENSP00000296701:I692F;ENSP00000377895:I862F;ENSP00000426410:I692F	ENSP00000296701:I692F	I	+	1	0	FBXO38	147793445	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.142000	0.77339	2.069000	0.61940	0.460000	0.39030	ATC	.	.		0.323	FBXO38-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000252185.2	NM_030793		T	147813252	A	T	147813252	3	4	372	1	0	0	0	0	1	0	0	0	5754	101	4	4	2871	4	FBXO38	5	147813252	Missense_Mutation	SNP	A	TCGA-ZS-A9CF-01A-11D-A382-10	8546260	147813252	33102008	33	51443										
CSF1R	1436	hgsc.bcm.edu	37	chr5	149435893	149435893	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	acgttacgcgctgccacgtcCcggtggatgcactgagggaa	14	12	0	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr5:149435893C>T	ENST00000286301.3	-	18	2622	c.2331G>A	c.(2329-2331)cgG>cgA	p.R777R		NM_005211.3	NP_005202.2	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor	777	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		Missing (in HDLS). {ECO:0000269|PubMed:22197934}.		cell proliferation (GO:0008283)|cell-cell junction maintenance (GO:0045217)|cellular response to cytokine stimulus (GO:0071345)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cytokine-mediated signaling pathway (GO:0019221)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary gland duct morphogenesis (GO:0060603)|monocyte differentiation (GO:0030224)|multicellular organismal development (GO:0007275)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell motility (GO:2000147)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of bone resorption (GO:0045124)|regulation of cell shape (GO:0008360)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|macrophage colony-stimulating factor receptor activity (GO:0005011)|protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(38)|kidney(2)|large_intestine(6)|liver(3)|lung(23)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	93			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Imatinib(DB00619)|Sunitinib(DB01268)	CTGCCACGTCCCGGTGGATGC	0.577																																					p.R777R		Atlas-SNP	.											.	CSF1R	250	.	0			c.G2331A						.						96	85	89					5																	149435893		2203	4300	6503	SO:0001819	synonymous_variant	1436	exon18			CACGTCCCGGTGG	U63963	CCDS4302.1	5q32	2013-01-11	2008-08-01		ENSG00000182578	ENSG00000182578		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	2433	protein-coding gene	gene with protein product		164770	"McDonough feline sarcoma viral (v-fms) oncogene homolog"	FMS		1611909	Standard	NM_005211		Approved	C-FMS, CSFR, CD115	uc003lrm.3	P07333	OTTHUMG00000130050	ENST00000286301.3:c.2331G>A	5.37:g.149435893C>T		129.0	0.0		64.0	52.0	NM_005211	B5A955|D3DQG2|Q6LDW5|Q6LDY4|Q86VW7	Silent	SNP	ENST00000286301.3	37	CCDS4302.1																																																																																			.	.		0.577	CSF1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252329.2	NM_005211		T	149435893	C	T	149435893	2	4	372	1	0	0	0	0	0	0	0	1	3934	610	22	3		3	CSF1R	5	149435893	Silent	SNP	C	TCGA-ZS-A9CF-01A-11D-A382-10	1622641	149435893	31479367	34	51444										
GRIA1	2890	hgsc.bcm.edu	37	chr5	153054114	153054114	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	agagtggcgccaatgtgacaGgtttccagctggtgaactac	13	9	0	3			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr5:153054114G>A	ENST00000285900.5	+	6	1097	c.754G>A	c.(754-756)Ggt>Agt	p.G252S	GRIA1_ENST00000521843.2_Missense_Mutation_p.G183S|GRIA1_ENST00000448073.4_Missense_Mutation_p.G262S|GRIA1_ENST00000340592.5_Missense_Mutation_p.G252S|GRIA1_ENST00000518783.1_Missense_Mutation_p.G262S|GRIA1_ENST00000518142.1_Missense_Mutation_p.G172S	NM_000827.3|NM_001258019.1	NP_000818.2|NP_001244948.1	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1	252					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|axonal spine (GO:0044308)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|neuron spine (GO:0044309)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|PDZ domain binding (GO:0030165)			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)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Perampanel(DB08883)|Sevoflurane(DB01236)	CAATGTGACAGGTTTCCAGCT	0.507																																					p.G262S		Atlas-SNP	.											.	GRIA1	321	.	0			c.G784A						.						200	197	198					5																	153054114		2203	4300	6503	SO:0001583	missense	2890	exon6			GTGACAGGTTTCC		CCDS4322.1, CCDS47318.1, CCDS58986.1, CCDS58987.1, CCDS58988.1, CCDS58989.1	5q33	2012-08-29			ENSG00000155511	ENSG00000155511		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4571	protein-coding gene	gene with protein product		138248		GLUR1		1652753, 1319477	Standard	NM_000827		Approved	GluA1, GLURA	uc011dcy.2	P42261	OTTHUMG00000130148	ENST00000285900.5:c.754G>A	5.37:g.153054114G>A	ENSP00000285900:p.Gly252Ser	309.0	0.0		330.0	135.0	NM_001258021	B7Z2S0|B7Z2W8|B7Z3F6|B7Z9G9|D3DQI4|E7ESV8|Q2NKM6	Missense_Mutation	SNP	ENST00000285900.5	37	CCDS4322.1	.	.	.	.	.	.	.	.	.	.	G	20.0	3.930250	0.73327	.	.	ENSG00000155511	ENST00000285900;ENST00000544403;ENST00000518142;ENST00000537037;ENST00000340592;ENST00000521843;ENST00000544794;ENST00000518783;ENST00000448073	D;D;D;D;D;D;D	0.85339	-1.97;-1.97;-1.97;-1.97;-1.97;-1.97;-1.97	5.56	4.69	0.59074	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.90755	0.7098	M	0.66378	2.025	0.80722	D	1	P;P;P;P;P;D	0.61697	0.938;0.938;0.954;0.938;0.924;0.99	D;D;D;D;P;D	0.74674	0.921;0.921;0.963;0.921;0.872;0.984	D	0.91520	0.5234	10	0.87932	D	0	.	13.4661	0.61254	0.0752:0.0:0.9248:0.0	.	262;262;172;262;252;252	E7ESV8;B7Z9G9;B7Z3F6;B7Z2W8;P42261-2;P42261	.;.;.;.;.;GRIA1_HUMAN	S	252;252;172;206;252;183;183;262;262	ENSP00000285900:G252S;ENSP00000427920:G172S;ENSP00000339343:G252S;ENSP00000427864:G183S;ENSP00000442108:G183S;ENSP00000428994:G262S;ENSP00000415569:G262S	ENSP00000285900:G252S	G	+	1	0	GRIA1	153034307	1.000000	0.71417	1.000000	0.80357	0.488000	0.33401	9.640000	0.98453	1.350000	0.45770	-0.136000	0.14681	GGT	.	.		0.507	GRIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252456.3			A	153054114	G	A	153054114	3	1	372	1	0	0	0	0	1	0	0	0	6776	1000	35	3	776	3	GRIA1	5	153054114	Missense_Mutation	SNP	G	TCGA-ZS-A9CF-01A-11D-A382-10	3618221	153054114	27861146	35	51445										
DOCK2	1794	hgsc.bcm.edu	37	chr5	169101345	169101345	+	Nonsense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	caggtgcagtccatgatgtaCgatctgatggagtggaggtc	15	7	1	2	rs35393134	byFrequency	TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr5:169101345C>G	ENST00000256935.8	+	6	446	c.366C>G	c.(364-366)taC>taG	p.Y122*		NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	122					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CCATGATGTACGATCTGATGG	0.473																																					p.Y122X		Atlas-SNP	.											.	DOCK2	389	.	0			c.C366G						.						155	141	145					5																	169101345		2203	4300	6503	SO:0001587	stop_gained	1794	exon6			GATGTACGATCTG	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.366C>G	5.37:g.169101345C>G	ENSP00000256935:p.Tyr122*	124.0	0.0		110.0	59.0	NM_004946	Q2M3I0|Q96AK7	Nonsense_Mutation	SNP	ENST00000256935.8	37	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.336496	0.81801	.	.	ENSG00000134516	ENST00000256935	.	.	.	5.27	-3.53	0.04667	.	0.118746	0.64402	D	0.000010	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.597	0.61996	0.0:0.3685:0.0:0.6315	.	.	.	.	X	122	.	ENSP00000256935:Y122X	Y	+	3	2	DOCK2	169033923	0.001000	0.12720	0.971000	0.41717	0.925000	0.55904	-1.732000	0.01851	-0.653000	0.05401	-1.056000	0.02311	TAC	.	C|0.978;T|0.022		0.473	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		G	169101345	C	G	169101345	4	3	372	1	0	0	0	0	0	1	0	0	4689	547	19	4	388	4	DOCK2	5	169101345	Nonsense_Mutation	SNP	C	TCGA-ZS-A9CF-01A-11D-A382-10	16047231	169101345	11813915	36	51446										
HRH2	3274	hgsc.bcm.edu	37	chr5	175112488	175112488	+	IGR	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	atttgttcattcattcatttGcaaacattcatccaattccc	2	11	4	0			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr5:175112488G>A	ENST00000231683.2	+	0	3095				HRH2_ENST00000377291.2_Missense_Mutation_p.A385T	NM_022304.2	NP_071640.1	P25021	HRH2_HUMAN	histamine receptor H2						digestive tract development (GO:0048565)|epithelial cell morphogenesis (GO:0003382)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|gastrin-induced gastric acid secretion (GO:0001698)|gland development (GO:0048732)|histamine-induced gastric acid secretion (GO:0001697)|immune response (GO:0006955)|memory (GO:0007613)|positive regulation of vasoconstriction (GO:0045907)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	histamine receptor activity (GO:0004969)			breast(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(10)|ovary(1)	22	all_cancers(89;0.00805)|Renal(175;0.000269)|Lung NSC(126;0.00419)|all_lung(126;0.00711)	Medulloblastoma(196;0.0208)|all_neural(177;0.0277)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)	Colorectal(1;0.0154)|COAD - Colon adenocarcinoma(1;0.149)	Amitriptyline(DB00321)|Asenapine(DB06216)|Betazole(DB00272)|Cimetidine(DB00501)|Doxepin(DB01142)|Epinastine(DB00751)|Famotidine(DB00927)|Histamine Phosphate(DB00667)|Loxapine(DB00408)|Methantheline(DB00940)|Nizatidine(DB00585)|Olanzapine(DB00334)|Ranitidine(DB00863)|Roxatidine acetate(DB08806)|Tolazoline(DB00797)	tcattcattTGcaaacattca	0.398																																					p.A385T		Atlas-SNP	.											.	HRH2	108	.	0			c.G1153A						.						108	90	96					5																	175112488		692	1591	2283	SO:0001628	intergenic_variant	3274	exon3			TCATTTGCAAACA		CCDS4395.1, CCDS47344.1	5q35	2012-08-08			ENSG00000113749	ENSG00000113749		"GPCR / Class A : Histamine receptors"	5183	protein-coding gene	gene with protein product		142703				1714721	Standard	NM_022304		Approved		uc003mdc.4	P25021	OTTHUMG00000130660		5.37:g.175112488G>A		235.0	0.0		183.0	85.0	NM_001131055	B5BUP7|Q14464|Q7Z5R9	Missense_Mutation	SNP	ENST00000231683.2	37	CCDS4395.1	.	.	.	.	.	.	.	.	.	.	G	9.890	1.203903	0.22121	.	.	ENSG00000113749	ENST00000377291	T	0.64438	-0.1	2.53	0.676	0.17958	.	.	.	.	.	T	0.47395	0.1443	.	.	.	0.09310	N	0.999998	B	0.09022	0.002	B	0.08055	0.003	T	0.43048	-0.9415	8	0.87932	D	0	.	4.9524	0.14021	0.305:0.0:0.695:0.0	.	385	Q7Z5R9	.	T	385	ENSP00000366506:A385T	ENSP00000366506:A385T	A	+	1	0	HRH2	175045094	0.070000	0.21116	0.012000	0.15200	0.247000	0.25773	0.440000	0.21592	0.171000	0.19730	0.491000	0.48974	GCA	.	.		0.398	HRH2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253151.1			A	175112488	G	A	175112488	1	1	372	0	1	0	0	0	0	0	0	0	7365	1319	46	3		3	HRH2	5	175112488	IGR	SNP	G	TCGA-ZS-A9CF-01A-11D-A382-10	6011143	175112488	5802772	37	51447										
BAT2	7916	hgsc.bcm.edu	37	chr6	31593819	31593819	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	gttttccccgtgtggcgggcCcccgaggctcagggccacca	14	16	1	0			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr6:31593819C>T	ENST00000376033.2	+	9	1096	c.862C>T	c.(862-864)Ccc>Tcc	p.P288S	PRRC2A_ENST00000469577.1_3'UTR|SNORA38_ENST00000363946.1_RNA|PRRC2A_ENST00000376007.4_Missense_Mutation_p.P288S	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	288	4 X 57 AA type A repeats.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						TGTGGCGGGCCCCCGAGGCTC	0.502																																					p.P288S		Atlas-SNP	.											.	PRRC2A	152	.	0			c.C862T						.						54	61	58					6																	31593819		1508	2707	4215	SO:0001583	missense	7916	exon9			GCGGGCCCCCGAG	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"HLA-B associated transcript 2"	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.862C>T	6.37:g.31593819C>T	ENSP00000365201:p.Pro288Ser	112.0	0.0		169.0	61.0	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	37	CCDS4708.1	.	.	.	.	.	.	.	.	.	.	C	6.017	0.371466	0.11409	.	.	ENSG00000204469	ENST00000424184;ENST00000435052;ENST00000376007;ENST00000376033	T;T	0.02103	4.45;4.45	4.96	4.09	0.47781	.	0.000000	0.49916	D	0.000131	T	0.01124	0.0037	L	0.34521	1.04	0.46774	D	0.999191	B	0.26483	0.15	B	0.23419	0.046	T	0.52480	-0.8570	10	0.87932	D	0	-4.446	13.6421	0.62257	0.1564:0.8436:0.0:0.0	.	288	P48634	PRC2A_HUMAN	S	288	ENSP00000365175:P288S;ENSP00000365201:P288S	ENSP00000365175:P288S	P	+	1	0	PRRC2A	31701798	1.000000	0.71417	0.970000	0.41538	0.181000	0.23173	2.954000	0.49113	1.310000	0.45006	-0.181000	0.13052	CCC	.	.		0.502	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686		T	31593819	C	T	31593819	3	4	372	1	0	0	0	0	1	0	0	0	1319	623	22	3	892	3	BAT2	6	31593819	Missense_Mutation	SNP	C	TCGA-ZS-A9CF-01A-11D-A382-10		31593819	139521248	38	51448										
VARS	7407	hgsc.bcm.edu	37	chr6	31760169	31760169	+	Splice_Site	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	cagctccaccctcgcctcacCtcccctggaggtggctgctg	10	19	1	0			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr6:31760169C>G	ENST00000375663.3	-	5	1226	c.786G>C	c.(784-786)gaG>gaC	p.E262D	VARS_ENST00000444930.2_5'UTR	NM_006295.2	NP_006286.1	P26640	SYVC_HUMAN	valyl-tRNA synthetase	262					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	30					L-Valine(DB00161)	CTCGCCTCACCTCCCCTGGAG	0.537																																					p.E262D		Atlas-SNP	.											.	VARS	76	.	0			c.G786C						.						128	126	127					6																	31760169		2203	4300	6503	SO:0001630	splice_region_variant	7407	exon5			CCTCACCTCCCCT	BC012808	CCDS34412.1	6p21.3	2011-07-01		2005-07-05	ENSG00000204394	ENSG00000204394	6.1.1.9	"Aminoacyl tRNA synthetases / Class I"	12651	protein-coding gene	gene with protein product	"valine tRNA ligase 1, cytoplasmic"	192150	"valyl-tRNA synthetase 2"	VARS2		15779907	Standard	XM_005249362		Approved		uc003nxe.3	P26640	OTTHUMG00000031286	ENST00000375663.3:c.786+1G>C	6.37:g.31760169C>G		87.0	0.0		235.0	44.0	NM_006295	B0V1N1|B4DZ61|Q5JQ90|Q96E77|Q9UQM2	Missense_Mutation	SNP	ENST00000375663.3	37	CCDS34412.1	.	.	.	.	.	.	.	.	.	.	C	13.49	2.254204	0.39896	.	.	ENSG00000204394	ENST00000375663	T	0.04809	3.55	4.72	4.72	0.59763	.	0.106857	0.41396	D	0.000894	T	0.03477	0.0100	L	0.55834	1.745	0.80722	D	1	P	0.46395	0.877	B	0.40741	0.339	T	0.52343	-0.8588	9	.	.	.	-9.7875	15.4962	0.75653	0.0:1.0:0.0:0.0	.	262	P26640	SYVC_HUMAN	D	262	ENSP00000364815:E262D	.	E	-	3	2	VARS	31868148	1.000000	0.71417	1.000000	0.80357	0.099000	0.18886	4.185000	0.58330	2.315000	0.78130	0.313000	0.20887	GAG	.	.		0.537	VARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076619.2	NM_006295	Missense_Mutation	G	31760169	C	G	31760169	5	3	372	1	0	0	0	0	0	0	1	0	17138	695	24	4	3112	4	VARS	6	31760169	Splice_Site	SNP	C	TCGA-ZS-A9CF-01A-11D-A382-10	166350	31760169	139354898	39	51449										
TRERF1	55809	hgsc.bcm.edu	37	chr6	42214272	42214272	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	tttctttctagggaggtccaCttgtccgaacctacaacaaa	7	11	2	0			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr6:42214272C>G	ENST00000372922.4	-	14	3229	c.2667G>C	c.(2665-2667)aaG>aaC	p.K889N	TRERF1_ENST00000340840.2_Missense_Mutation_p.K806N|TRERF1_ENST00000354325.2_Missense_Mutation_p.K806N|TRERF1_ENST00000541110.1_Missense_Mutation_p.K909N|TRERF1_ENST00000372917.4_Missense_Mutation_p.K806N	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	889	Interacts with CREBBP.|SANT. {ECO:0000255|PROSITE- ProRule:PRU00624}.				cholesterol catabolic process (GO:0006707)|homeostatic process (GO:0042592)|multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone biosynthetic process (GO:0046885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|steroid biosynthetic process (GO:0006694)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			GGGAGGTCCACTTGTCCGAAC	0.373																																					p.K889N		Atlas-SNP	.											.	TRERF1	124	.	0			c.G2667C						.						104	103	103					6																	42214272		2203	4300	6503	SO:0001583	missense	55809	exon14			GGTCCACTTGTCC	AF297872	CCDS4867.1, CCDS75455.1	6p21.1-p12.1	2012-09-25			ENSG00000124496	ENSG00000124496			18273	protein-coding gene	gene with protein product		610322	"breast cancer anti-estrogen resistance 2"	BCAR2		11349124	Standard	XM_005249223		Approved	TReP-132, HSA277276, RAPA, dJ139D8.5	uc003osd.2	Q96PN7	OTTHUMG00000014698	ENST00000372922.4:c.2667G>C	6.37:g.42214272C>G	ENSP00000362013:p.Lys889Asn	83.0	0.0		89.0	40.0	NM_033502	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Missense_Mutation	SNP	ENST00000372922.4	37	CCDS4867.1	.	.	.	.	.	.	.	.	.	.	C	14.54	2.566756	0.45694	.	.	ENSG00000124496	ENST00000541110;ENST00000372917;ENST00000372922;ENST00000340840;ENST00000354325	T;T;T;T;T	0.12569	2.82;2.67;2.85;2.67;2.67	5.17	2.4	0.29515	SANT domain, DNA binding (1);Homeodomain-like (1);SANT, eukarya (1);	0.000000	0.56097	D	0.000032	T	0.11879	0.0289	M	0.64170	1.965	0.49299	D	0.999774	B;B;B;B;P	0.37370	0.241;0.155;0.155;0.241;0.592	B;B;B;B;P	0.48598	0.177;0.086;0.086;0.177;0.583	T	0.02009	-1.1230	10	0.59425	D	0.04	-24.6629	7.6482	0.28334	0.0:0.6625:0.0:0.3375	.	806;909;889;645;645	Q96PN7-4;Q05GC8;Q96PN7;Q96PN7-2;Q96PN7-3	.;.;TREF1_HUMAN;.;.	N	909;806;889;806;806	ENSP00000439689:K909N;ENSP00000362008:K806N;ENSP00000362013:K889N;ENSP00000339438:K806N;ENSP00000346285:K806N	ENSP00000339438:K806N	K	-	3	2	TRERF1	42322250	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	0.472000	0.22116	0.697000	0.31718	-0.136000	0.14681	AAG	.	.		0.373	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2	NM_033502		G	42214272	C	G	42214272	3	3	372	1	0	0	0	0	1	0	0	0	16490	564	20	4	955	4	TRERF1	6	42214272	Missense_Mutation	SNP	C	TCGA-ZS-A9CF-01A-11D-A382-10	10454103	42214272	128900795	40	51450										
CUL9	23113	hgsc.bcm.edu	37	chr6	43192005	43192005	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	taggccccaggcctcctcagGgccagaggcagaagaggagg	16	12	1	3			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr6:43192005G>T	ENST00000252050.4	+	41	7460	c.7376G>T	c.(7375-7377)gGg>gTg	p.G2459V	CUL9_ENST00000354495.3_Missense_Mutation_p.G2349V|RP3-330M21.5_ENST00000500590.1_RNA|CUL9_ENST00000372647.2_Missense_Mutation_p.G2431V	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	2459					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						GCCTCCTCAGGGCCAGAGGCA	0.607																																					p.G2459V		Atlas-SNP	.											.	CUL9	248	.	0			c.G7376T						.						72	63	66					6																	43192005		2203	4300	6503	SO:0001583	missense	23113	exon41			CCTCAGGGCCAGA	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"parkin-like cytoplasmic p53 binding protein", "p53-associated parkin-like cytoplasmic protein"	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.7376G>T	6.37:g.43192005G>T	ENSP00000252050:p.Gly2459Val	105.0	0.0		128.0	25.0	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Missense_Mutation	SNP	ENST00000252050.4	37	CCDS4890.1	.	.	.	.	.	.	.	.	.	.	G	2.295	-0.361602	0.05103	.	.	ENSG00000112659	ENST00000252050;ENST00000354495;ENST00000372647	T;T;T	0.16457	2.34;2.34;2.34	5.69	1.36	0.22044	.	1.421260	0.04262	N	0.340529	T	0.03651	0.0104	N	0.24115	0.695	0.19575	N	0.999962	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.09377	0.004;0.002;0.002	T	0.41070	-0.9529	10	0.72032	D	0.01	-14.3347	2.0522	0.03573	0.2099:0.1552:0.4763:0.1586	.	2349;2431;2459	Q8IWT3-3;E9PEZ1;Q8IWT3	.;.;CUL9_HUMAN	V	2459;2349;2431	ENSP00000252050:G2459V;ENSP00000346490:G2349V;ENSP00000361730:G2431V	ENSP00000252050:G2459V	G	+	2	0	CUL9	43299983	0.079000	0.21365	0.018000	0.16275	0.182000	0.23217	0.664000	0.25068	0.742000	0.32697	0.561000	0.74099	GGG	.	.		0.607	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		T	43192005	G	T	43192005	3	4	372	1	0	0	0	0	1	0	0	0	4063	1232	43	3	7534	3	CUL9	6	43192005	Missense_Mutation	SNP	G	TCGA-ZS-A9CF-01A-11D-A382-10	977733	43192005	127923062	41	51451										
IRAK1BP1	134728	hgsc.bcm.edu	37	chr6	79577582	79577582	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	gccgtctagattacatcacgCagagcctccagcagcagggc	11	14	2	2			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr6:79577582C>T	ENST00000369940.2	+	1	394	c.289C>T	c.(289-291)Cag>Tag	p.Q97*		NM_001010844.2	NP_001010844.1	Q5VVH5	IKBP1_HUMAN	interleukin-1 receptor-associated kinase 1 binding protein 1	97					I-kappaB kinase/NF-kappaB signaling (GO:0007249)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(3)	12		all_cancers(76;0.0398)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)		BRCA - Breast invasive adenocarcinoma(397;0.21)		TTACATCACGCAGAGCCTCCA	0.637																																					p.Q97X		Atlas-SNP	.											.	IRAK1BP1	18	.	0			c.C289T						.						15	14	14					6																	79577582		2200	4294	6494	SO:0001587	stop_gained	134728	exon1			ATCACGCAGAGCC	AI478629	CCDS34488.1	6q14-q15	2006-04-12				ENSG00000146243			17368	protein-coding gene	gene with protein product		615375				11096118	Standard	XM_005248654		Approved	AIP70, SIMPL	uc003pim.4	Q5VVH5		ENST00000369940.2:c.289C>T	6.37:g.79577582C>T	ENSP00000358956:p.Gln97*	179.0	0.0		389.0	305.0	NM_001010844		Nonsense_Mutation	SNP	ENST00000369940.2	37	CCDS34488.1	.	.	.	.	.	.	.	.	.	.	C	37	6.505076	0.97620	.	.	ENSG00000146243	ENST00000369940	.	.	.	4.45	4.45	0.53987	.	0.070462	0.64402	D	0.000016	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-5.7051	14.6281	0.68638	0.0:1.0:0.0:0.0	.	.	.	.	X	97	.	.	Q	+	1	0	IRAK1BP1	79634301	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.345000	0.59360	2.282000	0.76494	0.561000	0.74099	CAG	.	.		0.637	IRAK1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041296.2	XM_059729		T	79577582	C	T	79577582	4	4	372	1	0	0	0	0	0	1	0	0	7831	711	25	3	291	3	IRAK1BP1	6	79577582	Nonsense_Mutation	SNP	C	TCGA-ZS-A9CF-01A-11D-A382-10	36385577	79577582	91537485	42	51452										
KIAA1009	22832	hgsc.bcm.edu	37	chr6	84925113	84925113	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	ctggcaaaaaattgttctttCtcctcttgttcttctaatgt	5	9	5	0			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr6:84925113C>T	ENST00000403245.3	-	5	504	c.390G>A	c.(388-390)gaG>gaA	p.E130E	KIAA1009_ENST00000257766.4_Silent_p.E54E	NM_014895.2	NP_055710.2														breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	43		all_cancers(76;1.5e-06)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00258)		BRCA - Breast invasive adenocarcinoma(397;0.089)		ATTGTTCTTTCTCCTCTTGTT	0.348																																					p.E130E		Atlas-SNP	.											KIAA1009,NS,carcinoma,0,1	KIAA1009	119	1	0			c.G390A						.						114	105	108					6																	84925113		2203	4300	6503	SO:0001819	synonymous_variant	22832	exon5			TTCTTTCTCCTCT																												ENST00000403245.3:c.390G>A	6.37:g.84925113C>T		49.0	0.0		42.0	36.0	NM_014895		Silent	SNP	ENST00000403245.3	37	CCDS34494.2																																																																																			.	.		0.348	KIAA1009-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317315.1			T	84925113	C	T	84925113	2	4	372	1	0	0	0	0	0	0	0	1	8212	912	32	3		3	KIAA1009	6	84925113	Silent	SNP	C	TCGA-ZS-A9CF-01A-11D-A382-10	5347531	84925113	86189954	43	51453										
PCLO	27445	hgsc.bcm.edu	37	chr7	82583509	82583509	+	Missense_Mutation	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	atcagcactagctctaccatCtggtggggcagtccgatcta	10	12	4	0			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr7:82583509C>T	ENST00000333891.9	-	5	7097	c.6760G>A	c.(6760-6762)Gat>Aat	p.D2254N	PCLO_ENST00000423517.2_Missense_Mutation_p.D2254N	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.D2254N(2)|p.D2185N(1)		breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						GCTCTACCATCTGGTGGGGCA	0.388																																					p.D2254N		Atlas-SNP	.											Q9Y6V0-3,NS,carcinoma,0,3	PCLO	1506	3	3	Substitution - Missense(3)	cervix(3)	c.G6760A						.						73	71	71					7																	82583509		1867	4093	5960	SO:0001583	missense	27445	exon5			TACCATCTGGTGG	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.6760G>A	7.37:g.82583509C>T	ENSP00000334319:p.Asp2254Asn	60.0	0.0		64.0	35.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	C	7.938	0.742113	0.15642	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.15952	2.38;2.38	5.7	4.8	0.61643	.	.	.	.	.	T	0.12347	0.0300	N	0.22421	0.69	0.09310	N	1	B;B	0.30973	0.302;0.302	B;B	0.33620	0.109;0.167	T	0.12604	-1.0541	9	0.87932	D	0	.	5.7004	0.17879	0.1293:0.6293:0.159:0.0824	.	2254;2254	Q9Y6V0-5;Q9Y6V0-6	.;.	N	2185;2254;2254	ENSP00000334319:D2254N;ENSP00000388393:D2254N	ENSP00000334319:D2254N	D	-	1	0	PCLO	82421445	0.000000	0.05858	0.534000	0.28014	0.449000	0.32228	0.323000	0.19593	2.690000	0.91761	0.603000	0.83216	GAT	.	.		0.388	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		T	82583509	C	T	82583509	3	4	372	1	0	0	0	0	1	0	0	0	11592	913	32	3	8769	3	PCLO	7	82583509	Missense_Mutation	SNP	C	TCGA-ZS-A9CF-01A-11D-A382-10		82583509	76555154	44	51454										
PHYHIP	9796	hgsc.bcm.edu	37	chr8	22085742	22085742	+	Missense_Mutation	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	ttggaattcttattctccttCttgttaaggtcaatgaagta	7	6	4	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr8:22085742C>G	ENST00000321613.3	-	3	585	c.129G>C	c.(127-129)aaG>aaC	p.K43N	PHYHIP_ENST00000454243.2_Missense_Mutation_p.K43N	NM_001099335.1	NP_001092805.1	Q92561	PHYIP_HUMAN	phytanoyl-CoA 2-hydroxylase interacting protein	43	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.									endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|upper_aerodigestive_tract(1)	10				Colorectal(74;0.0152)|COAD - Colon adenocarcinoma(73;0.0629)		TATTCTCCTTCTTGTTAAGGT	0.527																																					p.K43N		Atlas-SNP	.											.	PHYHIP	24	.	0			c.G129C						.						122	123	123					8																	22085742		1987	4168	6155	SO:0001583	missense	9796	exon2			CTCCTTCTTGTTA	D87463	CCDS43723.1	8p21.2	2010-02-17	2006-01-09		ENSG00000168490	ENSG00000168490			16865	protein-coding gene	gene with protein product		608511	"phytanoyl-CoA hydroxylase interacting protein", "DYRK1A interacting protein 3"	DYRK1AP3		9039502, 10686344	Standard	NM_014759		Approved	KIAA0273, PAHX-AP	uc003xbj.4	Q92561	OTTHUMG00000163776	ENST00000321613.3:c.129G>C	8.37:g.22085742C>G	ENSP00000320017:p.Lys43Asn	143.0	0.0		74.0	64.0	NM_014759	D3DSR1|Q8N4I9	Missense_Mutation	SNP	ENST00000321613.3	37	CCDS43723.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.690058	0.88735	.	.	ENSG00000168490	ENST00000321613;ENST00000454243;ENST00000456132	T;T	0.42513	0.97;0.97	5.67	4.79	0.61399	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.061993	0.64402	D	0.000007	T	0.52597	0.1744	L	0.42245	1.32	0.45318	D	0.998312	D	0.63880	0.993	P	0.61397	0.888	T	0.54344	-0.8308	10	0.59425	D	0.04	-29.4667	13.3462	0.60575	0.0:0.923:0.0:0.077	.	43	Q92561	PHYIP_HUMAN	N	43	ENSP00000320017:K43N;ENSP00000415491:K43N	ENSP00000320017:K43N	K	-	3	2	PHYHIP	22141687	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.071000	0.57556	1.404000	0.46819	0.511000	0.50034	AAG	.	.		0.527	PHYHIP-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000375388.1	NM_014759		G	22085742	C	G	22085742	3	3	372	1	0	0	0	0	1	0	0	0	11875	912	32	4	879	4	PHYHIP	8	22085742	Missense_Mutation	SNP	C	TCGA-ZS-A9CF-01A-11D-A382-10		22085742	124278280	45	51455										
RNF19A	25897	hgsc.bcm.edu	37	chr8	101276968	101276968	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	accacctgctatggccaaatTccgtttgtgctttgaaacat	7	11	0	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr8:101276968T>G	ENST00000519449.1	-	7	1553	c.1237A>C	c.(1237-1239)Aat>Cat	p.N413H	RNF19A_ENST00000341084.2_Missense_Mutation_p.N413H|RNF19A_ENST00000523255.1_5'UTR	NM_001280539.1|NM_015435.3	NP_001267468.1|NP_056250.3	Q9NV58	RN19A_HUMAN	ring finger protein 19A, RBR E3 ubiquitin protein ligase	413					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	30	all_cancers(14;3.5e-05)|all_epithelial(15;8.91e-08)|Lung NSC(17;0.000615)|all_lung(17;0.00166)		Epithelial(11;3.06e-11)|all cancers(13;5.78e-09)|OV - Ovarian serous cystadenocarcinoma(57;2.24e-05)|STAD - Stomach adenocarcinoma(118;0.0525)			ATGGCCAAATTCCGTTTGTGC	0.378																																					p.N413H		Atlas-SNP	.											.	RNF19A	67	.	0			c.A1237C						.						240	212	222					8																	101276968		2203	4300	6503	SO:0001583	missense	25897	exon7			CCAAATTCCGTTT	AB029316	CCDS6286.1	8q22	2013-10-03	2013-10-03	2007-08-20		ENSG00000034677		"RING-type (C3HC4) zinc fingers"	13432	protein-coding gene	gene with protein product		607119	"ring finger protein 19", "ring finger protein 19A", "ring finger protein 19A, E3 ubiquitin protein ligase"	RNF19		11237715, 10976766	Standard	NM_183419		Approved	dorfin, DKFZp566B1346	uc003yjj.1	Q9NV58		ENST00000519449.1:c.1237A>C	8.37:g.101276968T>G	ENSP00000428968:p.Asn413His	97.0	0.0		128.0	55.0	NM_015435	A3KCU9|Q52LG1|Q9H5H9|Q9H8M8|Q9UFG0|Q9UFX6|Q9Y4Y1	Missense_Mutation	SNP	ENST00000519449.1	37	CCDS6286.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.503574	0.85176	.	.	ENSG00000034677	ENST00000519449;ENST00000341084	D;D	0.85171	-1.95;-1.95	5.17	5.17	0.71159	.	0.143656	0.64402	D	0.000009	D	0.90466	0.7014	M	0.61703	1.905	0.58432	D	0.999994	D	0.89917	1.0	D	0.68192	0.956	D	0.91056	0.4882	10	0.56958	D	0.05	.	15.0318	0.71713	0.0:0.0:0.0:1.0	.	413	Q9NV58	RN19A_HUMAN	H	413	ENSP00000428968:N413H;ENSP00000342667:N413H	ENSP00000342667:N413H	N	-	1	0	RNF19A	101346144	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.655000	0.83696	2.089000	0.63090	0.529000	0.55759	AAT	.	.		0.378	RNF19A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380004.1	NM_015435		G	101276968	T	G	101276968	3	3	372	1	0	0	0	0	1	0	0	0	13485	1783	62	5	1299	5	RNF19A	8	101276968	Missense_Mutation	SNP	T	TCGA-ZS-A9CF-01A-11D-A382-10	79191226	101276968	45087054	46	51456										
NCALD	83988	hgsc.bcm.edu	37	chr8	102701577	102701577	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	tcgggtcgcactgcaggaggCgcacaatggacgggtcgctt	16	11	0	0			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr8:102701577C>A	ENST00000311028.3	-	7	920	c.542G>T	c.(541-543)cGc>cTc	p.R181L	NCALD_ENST00000521599.1_Missense_Mutation_p.R181L|NCALD_ENST00000395923.1_Missense_Mutation_p.R181L|NCALD_ENST00000522951.1_Intron|KB-1107E3.1_ENST00000518749.1_RNA|NCALD_ENST00000220931.6_Missense_Mutation_p.R181L|NCALD_ENST00000519508.2_Missense_Mutation_p.R181L	NM_001040624.1|NM_001040626.1	NP_001035714.1|NP_001035716.1	P61601	NCALD_HUMAN	neurocalcin delta	181					calcium-mediated signaling (GO:0019722)|regulation of systemic arterial blood pressure (GO:0003073)|synaptic transmission (GO:0007268)|vesicle-mediated transport (GO:0016192)	clathrin coat of trans-Golgi network vesicle (GO:0030130)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|clathrin binding (GO:0030276)|tubulin binding (GO:0015631)			endometrium(1)|large_intestine(2)|lung(4)|prostate(1)	8	all_cancers(14;8.94e-08)|all_epithelial(15;7.03e-10)|Lung NSC(17;1.36e-05)|all_lung(17;2.7e-05)		all cancers(13;1.09e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000699)			CTGCAGGAGGCGCACAATGGA	0.562																																					p.R181L		Atlas-SNP	.											NCALD,right_upper_lobe,carcinoma,0,1	NCALD	16	1	0			c.G542T						.						51	46	48					8																	102701577		2203	4300	6503	SO:0001583	missense	83988	exon6			AGGAGGCGCACAA	AF052142	CCDS6292.1	8q22.3	2014-08-12			ENSG00000104490	ENSG00000104490		"EF-hand domain containing"	7655	protein-coding gene	gene with protein product		606722				11267673	Standard	XM_006716672		Approved		uc003ykk.3	P61601	OTTHUMG00000164876	ENST00000311028.3:c.542G>T	8.37:g.102701577C>A	ENSP00000310587:p.Arg181Leu	154.0	0.0		133.0	51.0	NM_001040627	P29554|Q8IYC3|Q9H0W2	Missense_Mutation	SNP	ENST00000311028.3	37	CCDS6292.1	.	.	.	.	.	.	.	.	.	.	C	18.10	3.547493	0.65311	.	.	ENSG00000104490	ENST00000395923;ENST00000311028;ENST00000220931;ENST00000521599;ENST00000519508	T;T;T;T;T	0.68181	-0.31;-0.31;-0.31;-0.31;-0.31	5.6	5.6	0.85130	EF-hand-like domain (1);	.	.	.	.	T	0.62696	0.2449	L	0.42686	1.345	0.80722	D	1	B	0.12630	0.006	B	0.12156	0.007	T	0.55471	-0.8136	9	0.36615	T	0.2	.	19.9733	0.97292	0.0:1.0:0.0:0.0	.	181	P61601	NCALD_HUMAN	L	181	ENSP00000379256:R181L;ENSP00000310587:R181L;ENSP00000220931:R181L;ENSP00000428105:R181L;ENSP00000430476:R181L	ENSP00000220931:R181L	R	-	2	0	NCALD	102770753	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	7.771000	0.85420	2.804000	0.96469	0.655000	0.94253	CGC	.	.		0.562	NCALD-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380732.2			A	102701577	C	A	102701577	3	1	372	1	0	0	0	0	1	0	0	0	10210	768	27	1	43	1	NCALD	8	102701577	Missense_Mutation	SNP	C	TCGA-ZS-A9CF-01A-11D-A382-10	1424609	102701577	43662445	47	51457										
ZFPM2	23414	hgsc.bcm.edu	37	chr8	106331209	106331209	+	Splice_Site	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	gcaaaccccggcagatcaaaCgtaagtttgcgcgcggggcc	13	13	1	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr8:106331209C>A	ENST00000407775.2	+	1	290	c.40C>A	c.(40-42)Cgg>Agg	p.R14R	ZFPM2_ENST00000520492.1_5'Flank	NM_012082.3	NP_036214.2	Q8WW38	FOG2_HUMAN	zinc finger protein, FOG family member 2	14					blood coagulation (GO:0007596)|embryonic organ development (GO:0048568)|gonadal mesoderm development (GO:0007506)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of female gonad development (GO:2000195)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(4)|breast(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(11)|liver(2)|lung(48)|ovary(4)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	99			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			GCAGATCAAACGTAAGTTTGC	0.711																																					p.R14R		Atlas-SNP	.											.	ZFPM2	219	.	0			c.C40A						.						5	7	6					8																	106331209		1557	3525	5082	SO:0001630	splice_region_variant	23414	exon1			ATCAAACGTAAGT	AF119334	CCDS47908.1	8q23	2013-01-10	2012-11-27		ENSG00000169946	ENSG00000169946		"Zinc fingers, C2H2-type", "Zinc fingers, C2HC-type containing"	16700	protein-coding gene	gene with protein product		603693	"zinc finger protein, multitype 2"			9927675, 10438528	Standard	NM_012082		Approved	FOG2, hFOG-2, ZNF89B, ZC2HC11B	uc003ymd.3	Q8WW38	OTTHUMG00000164818	ENST00000407775.2:c.40+1C>A	8.37:g.106331209C>A		331.0	0.0		345.0	169.0	NM_012082	Q32MA6|Q9NPL7|Q9NPS4|Q9UNI5	Silent	SNP	ENST00000407775.2	37	CCDS47908.1																																																																																			.	.		0.711	ZFPM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380614.1		Silent	A	106331209	C	A	106331209	5	1	372	1	0	0	0	0	0	0	1	0	17673	550	19	1	42	1	ZFPM2	8	106331209	Splice_Site	SNP	C	TCGA-ZS-A9CF-01A-11D-A382-10	3629632	106331209	40032813	48	51458										
GLDC	2731	hgsc.bcm.edu	37	chr9	6610207	6610208	+	Frame_Shift_Ins	INS	-	-	GT													0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	tcacctgtagcacagctgcaINSgtgcctctgcggctgcagtc					rs142181803	byFrequency	TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr9:6610207_6610208insGT	ENST00000321612.6	-	4	769_770	c.619_620insAC	c.(619-621)ctgfs	p.L207fs		NM_000170.2	NP_000161.2	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)	207					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|glycine dehydrogenase (decarboxylating) activity (GO:0004375)|lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)			cervix(1)|endometrium(2)|large_intestine(5)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)	GCACAGCTGCAGTGCCTCTGCG	0.525																																					p.L207fs		Atlas-Indel	.											.	GLDC	118	.	0			c.620_621insAC						.																																			SO:0001589	frameshift_variant	2731	exon4			.	D90239	CCDS34987.1	9p22	2014-09-17	2006-05-22		ENSG00000178445	ENSG00000178445	1.4.4.2		4313	protein-coding gene	gene with protein product	"glycine cleavage system protein P", "glycine decarboxylase"	238300	"glycine dehydrogenase (decarboxylating; glycine decarboxylase, glycine cleavage system protein P)"			1993704, 1996985	Standard	NM_000170		Approved	GCSP, NKH	uc003zkc.3	P23378	OTTHUMG00000019524	ENST00000321612.6:c.618_619dupAC	9.37:g.6610208_6610209dupGT	ENSP00000370737:p.Leu207fs	110.0	0.0		87.0	32.0	NM_000170	Q2M2F8	Frame_Shift_Ins	INS	ENST00000321612.6	37	CCDS34987.1																																																																																			.	.		0.525	GLDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051674.2	NM_000170		GT	6610208	-	GT	6610207	7	5	372	1	0	1	1	0	0	0	0	0	6441	188	7	0	2530	0	GLDC	9	6610207	Frame_Shift_Ins	INS	-	TCGA-ZS-A9CF-01A-11D-A382-10		6610207	134603224	49	51459										
NTRK2	4915	hgsc.bcm.edu	37	chr9	87635185	87635185	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	gagcatcatgtacaggaaatTcacgacggaaagcgacgtct	11	9	3	0			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr9:87635185T>G	ENST00000323115.4	+	16	2542	c.2189T>G	c.(2188-2190)tTc>tGc	p.F730C	NTRK2_ENST00000376214.1_Missense_Mutation_p.F746C|NTRK2_ENST00000376213.1_Missense_Mutation_p.F730C|NTRK2_ENST00000277120.3_Missense_Mutation_p.F746C			Q16620	NTRK2_HUMAN	neurotrophic tyrosine kinase, receptor, type 2	730	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of adenylate cyclase activity (GO:0007190)|aging (GO:0007568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|central nervous system neuron development (GO:0021954)|cerebral cortex development (GO:0021987)|circadian rhythm (GO:0007623)|feeding behavior (GO:0007631)|glutamate secretion (GO:0014047)|learning (GO:0007612)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mechanoreceptor differentiation (GO:0042490)|negative regulation of anoikis (GO:2000811)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular junction development (GO:0007528)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peripheral nervous system neuron development (GO:0048935)|positive regulation of axonogenesis (GO:0050772)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|regulation of dendrite development (GO:0050773)|regulation of neurotransmitter secretion (GO:0046928)|regulation of protein kinase B signaling (GO:0051896)|regulation of Rac GTPase activity (GO:0032314)|response to auditory stimulus (GO:0010996)|retinal rod cell development (GO:0046548)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vasculogenesis (GO:0001570)	cell surface (GO:0009986)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endosome (GO:0005768)|excitatory synapse (GO:0060076)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|receptor complex (GO:0043235)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|brain-derived neurotrophic factor binding (GO:0048403)|brain-derived neurotrophic factor-activated receptor activity (GO:0060175)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	46					Amitriptyline(DB00321)	TACAGGAAATTCACGACGGAA	0.552										TSP Lung(25;0.17)																											p.F746C		Atlas-SNP	.											.	NTRK2	331	.	0			c.T2237G						.						136	125	129					9																	87635185		2203	4300	6503	SO:0001583	missense	4915	exon20			GGAAATTCACGAC	AF410902	CCDS6671.1, CCDS35050.1, CCDS35051.1, CCDS35052.1, CCDS35053.1	9q22.1	2013-01-11			ENSG00000148053	ENSG00000148053	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing"	8032	protein-coding gene	gene with protein product		600456				7789988	Standard	NM_001018065		Approved	TRKB	uc004anz.1	Q16620	OTTHUMG00000020120	ENST00000323115.4:c.2189T>G	9.37:g.87635185T>G	ENSP00000314586:p.Phe730Cys	176.0	0.0		136.0	71.0	NM_006180	B1ANZ4|B4DFV9|Q16675|Q59GJ1|Q8WXJ5|Q8WXJ6|Q8WXJ7	Missense_Mutation	SNP	ENST00000323115.4	37	CCDS35050.1	.	.	.	.	.	.	.	.	.	.	T	27.7	4.853418	0.91355	.	.	ENSG00000148053	ENST00000376214;ENST00000376213;ENST00000277120;ENST00000323115	D;D;D;D	0.89810	-2.57;-2.57;-2.57;-2.57	6.16	6.16	0.99307	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.94896	0.8350	M	0.83852	2.665	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	D	0.95318	0.8418	10	0.87932	D	0	.	16.8061	0.85666	0.0:0.0:0.0:1.0	.	730;746	Q16620;Q16620-4	NTRK2_HUMAN;.	C	746;730;746;730	ENSP00000365387:F746C;ENSP00000365386:F730C;ENSP00000277120:F746C;ENSP00000314586:F730C	ENSP00000277120:F746C	F	+	2	0	NTRK2	86825005	1.000000	0.71417	1.000000	0.80357	0.820000	0.46376	8.033000	0.88852	2.367000	0.80283	0.528000	0.53228	TTC	.	.		0.552	NTRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052882.1			G	87635185	T	G	87635185	3	3	372	1	0	0	0	0	1	0	0	0	10716	1783	62	5	2378	5	NTRK2	9	87635185	Missense_Mutation	SNP	T	TCGA-ZS-A9CF-01A-11D-A382-10	81024978	87635185	53578246	50	51460										
OR1K1	392392	hgsc.bcm.edu	37	chr9	125563246	125563246	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	cactgtcatgtacactgtagTcacccccatgctgaacccca	6	16	2	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr9:125563246T>C	ENST00000277309.2	+	1	877	c.845T>C	c.(844-846)gTc>gCc	p.V282A		NM_080859.1	NP_543135.1	Q8NGR3	OR1K1_HUMAN	olfactory receptor, family 1, subfamily K, member 1	282						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(8)|lung(2)|ovary(1)|skin(4)|stomach(1)	17						TACACTGTAGTCACCCCCATG	0.577																																					p.V282A		Atlas-SNP	.											.	OR1K1	34	.	0			c.T845C						.						101	89	93					9																	125563246		2203	4300	6503	SO:0001583	missense	392392	exon1			CTGTAGTCACCCC	AL359512	CCDS35132.1	9q33	2013-09-20			ENSG00000165204	ENSG00000165204		"GPCR / Class A : Olfactory receptors"	8212	protein-coding gene	gene with protein product							Standard	NM_080859		Approved	hg99, MNAB	uc011lze.2	Q8NGR3	OTTHUMG00000020625	ENST00000277309.2:c.845T>C	9.37:g.125563246T>C	ENSP00000277309:p.Val282Ala	55.0	0.0		52.0	22.0	NM_080859	B9EH41|Q4VXB7|Q96R23	Missense_Mutation	SNP	ENST00000277309.2	37	CCDS35132.1	.	.	.	.	.	.	.	.	.	.	T	15.62	2.888832	0.52014	.	.	ENSG00000165204	ENST00000277309	T	0.00296	8.24	4.02	4.02	0.46733	GPCR, rhodopsin-like superfamily (1);	0.220885	0.22557	U	0.058513	T	0.00666	0.0022	M	0.91354	3.2	0.09310	N	0.999995	P	0.41673	0.759	P	0.53760	0.734	T	0.03807	-1.1002	10	0.72032	D	0.01	.	12.0785	0.53657	0.0:0.0:0.0:1.0	.	282	Q8NGR3	OR1K1_HUMAN	A	282	ENSP00000277309:V282A	ENSP00000277309:V282A	V	+	2	0	OR1K1	124603067	0.022000	0.18835	0.310000	0.25168	0.896000	0.52359	1.906000	0.39887	1.683000	0.51011	0.460000	0.39030	GTC	.	.		0.577	OR1K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053958.1			C	125563246	T	C	125563246	3	2	372	1	0	0	0	0	1	0	0	0	10971	1667	58	2	847	2	OR1K1	9	125563246	Missense_Mutation	SNP	T	TCGA-ZS-A9CF-01A-11D-A382-10	37928061	125563246	15650185	51	51461										
RABGAP1	23637	hgsc.bcm.edu	37	chr9	125719407	125719407	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	gtatctactcttaatagtgaAgattttgtcttggtttccag	8	6	3	2			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr9:125719407A>G	ENST00000373647.4	+	2	203	c.69A>G	c.(67-69)gaA>gaG	p.E23E		NM_012197.3	NP_036329.3	Q9Y3P9	RBGP1_HUMAN	RAB GTPase activating protein 1	23					cell cycle (GO:0007049)|positive regulation of GTPase activity (GO:0043547)|regulation of GTP catabolic process (GO:0033124)	centrosome (GO:0005813)|cytosol (GO:0005829)|microtubule associated complex (GO:0005875)	DNA binding (GO:0003677)|GTPase activator activity (GO:0005096)|Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)|tubulin binding (GO:0015631)			breast(3)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|prostate(4)|stomach(3)|upper_aerodigestive_tract(1)	41						TTAATAGTGAAGATTTTGTCT	0.383																																					p.E23E		Atlas-SNP	.											.	RABGAP1	164	.	0			c.A69G						.						108	93	98					9																	125719407		1568	3582	5150	SO:0001819	synonymous_variant	23637	exon2			TAGTGAAGATTTT	AJ011679	CCDS6848.2	9q34.11	2013-07-09			ENSG00000011454	ENSG00000011454			17155	protein-coding gene	gene with protein product	"rab6 GTPase activating protein (GAP and centrosome-associated)", "TBC1 domain family, member 11"	615882				10202141	Standard	NM_012197		Approved	GAPCenA, TBC1D11	uc011lzh.2	Q9Y3P9	OTTHUMG00000020633	ENST00000373647.4:c.69A>G	9.37:g.125719407A>G		102.0	0.0		121.0	59.0	NM_012197	B9A6L2|Q05CW2|Q6ZMY1|Q9HA28|Q9P0E2|Q9UG67	Silent	SNP	ENST00000373647.4	37	CCDS6848.2																																																																																			.	.		0.383	RABGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053976.3	NM_012197		G	125719407	A	G	125719407	2	3	372	1	0	0	0	0	0	0	0	1	12979	69	3	2		2	RABGAP1	9	125719407	Silent	SNP	A	TCGA-ZS-A9CF-01A-11D-A382-10	156161	125719407	15494024	52	51462										
FPGS	2356	hgsc.bcm.edu	37	chr9	130565239	130565239	+	Silent	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	agccacctgcgcgccgctctAttcctggcagcggcgtctgc	12	17	2	0			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr9:130565239A>T	ENST00000373247.2	+	1	86	c.36A>T	c.(34-36)ctA>ctT	p.L12L	FPGS_ENST00000373225.3_5'Flank|FPGS_ENST00000393706.2_Silent_p.L12L|FPGS_ENST00000373245.1_Silent_p.L12L|FPGS_ENST00000460181.1_3'UTR	NM_004957.4	NP_004948.4	Q05932	FOLC_HUMAN	folylpolyglutamate synthase	12					brain development (GO:0007420)|folic acid metabolic process (GO:0046655)|liver development (GO:0001889)|nucleobase-containing compound metabolic process (GO:0006139)|one-carbon metabolic process (GO:0006730)|organ regeneration (GO:0031100)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|tetrahydrofolylpolyglutamate synthase activity (GO:0004326)			endometrium(2)|kidney(1)|lung(3)|ovary(1)	7					Methotrexate(DB00563)|Pralatrexate(DB06813)|Raltitrexed(DB00293)	GCGCCGCTCTATTCCTGGCAG	0.771																																					p.L12L		Atlas-SNP	.											.	FPGS	30	.	0			c.A36T						.						1	2	2					9																	130565239		1058	2288	3346	SO:0001819	synonymous_variant	2356	exon1			CGCTCTATTCCTG		CCDS35148.1, CCDS35149.1, CCDS75905.1	9q34.11	2013-09-19			ENSG00000136877	ENSG00000136877	6.3.2.17		3824	protein-coding gene	gene with protein product		136510					Standard	NM_004957		Approved		uc004bsg.1	Q05932	OTTHUMG00000020716	ENST00000373247.2:c.36A>T	9.37:g.130565239A>T		44.0	0.0		47.0	29.0	NM_004957	B3KPW4|B7Z2Z3|F5H0K6|Q5JU19|Q5JU22|Q6P2P6	Silent	SNP	ENST00000373247.2	37	CCDS35148.1																																																																																			.	.		0.771	FPGS-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054251.1			T	130565239	A	T	130565239	2	4	372	1	0	0	0	0	0	0	0	1	6044	436	16	4		4	FPGS	9	130565239	Silent	SNP	A	TCGA-ZS-A9CF-01A-11D-A382-10	4845832	130565239	10648192	53	51463										
GDF2	2658	hgsc.bcm.edu	37	chr10	48416487	48416487	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	gggaccccactcaggttaagGctgcgcaggaaatccacctt	11	13	1	0			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr10:48416487G>A	ENST00000249598.1	-	1	366	c.207C>T	c.(205-207)agC>agT	p.S69S		NM_016204.1	NP_057288.1	Q9UK05	GDF2_HUMAN	growth differentiation factor 2	69					activin receptor signaling pathway (GO:0032924)|angiogenesis (GO:0001525)|blood vessel morphogenesis (GO:0048514)|BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|cellular iron ion homeostasis (GO:0006879)|cellular response to BMP stimulus (GO:0071773)|growth (GO:0040007)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of DNA replication (GO:0008156)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|ossification (GO:0001503)|osteoblast differentiation (GO:0001649)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(2)|large_intestine(3)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	28						TCAGGTTAAGGCTGCGCAGGA	0.572																																					p.S69S		Atlas-SNP	.											.	GDF2	77	.	0			c.C207T						.						83	77	79					10																	48416487		2203	4300	6503	SO:0001819	synonymous_variant	2658	exon1			GTTAAGGCTGCGC	AF156891	CCDS73118.1	10q11.22	2014-05-06			ENSG00000128802	ENSG00000263761		"Endogenous ligands"	4217	protein-coding gene	gene with protein product		605120				10849432	Standard	NM_016204		Approved	BMP-9, BMP9	uc001jfa.1	Q9UK05	OTTHUMG00000188320	ENST00000249598.1:c.207C>T	10.37:g.48416487G>A		145.0	0.0		124.0	63.0	NM_016204	Q5VSQ9|Q9Y571	Silent	SNP	ENST00000249598.1	37	CCDS7219.1																																																																																			.	.		0.572	GDF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047891.1	NM_016204		A	48416487	G	A	48416487	2	1	372	1	0	0	0	0	0	0	0	1	6322	1194	42	3		3	GDF2	10	48416487	Silent	SNP	G	TCGA-ZS-A9CF-01A-11D-A382-10		48416487	87118260	54	51464										
ATAD1	84896	hgsc.bcm.edu	37	chr10	89544307	89544307	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	cagccaatttctgagattctCcataccacttatcggtcagt	6	12	3	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr10:89544307C>A	ENST00000308448.7	-	5	881	c.503G>T	c.(502-504)gGa>gTa	p.G168V	ATAD1_ENST00000495903.1_5'Flank|ATAD1_ENST00000328142.3_Missense_Mutation_p.G168V|ATAD1_ENST00000541004.1_Missense_Mutation_p.G168V|ATAD1_ENST00000400215.3_Missense_Mutation_p.G110V	NM_032810.2	NP_116199.2	Q8NBU5	ATAD1_HUMAN	ATPase family, AAA domain containing 1	168					ATP catabolic process (GO:0006200)|learning (GO:0007612)|memory (GO:0007613)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|positive regulation of receptor internalization (GO:0002092)	cell junction (GO:0030054)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			kidney(1)|large_intestine(4)|lung(4)|ovary(1)	10		all_cancers(4;6.78e-12)|Prostate(4;3.56e-12)|all_epithelial(4;5.58e-09)|Melanoma(5;0.0273)|Breast(4;0.0424)|all_hematologic(4;0.0846)|Colorectal(252;0.207)|Glioma(4;0.217)|all_neural(4;0.224)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00131)|GBM - Glioblastoma multiforme(1;1.1e-32)|Lung(2;1.4e-05)|LUSC - Lung squamous cell carcinoma(2;2.69e-05)|Colorectal(12;7.09e-05)|COAD - Colon adenocarcinoma(12;0.000261)|STAD - Stomach adenocarcinoma(243;0.235)		CTGAGATTCTCCATACCACTT	0.433																																					p.G168V		Atlas-SNP	.											.	ATAD1	32	.	0			c.G503T						.						145	134	138					10																	89544307		2203	4300	6503	SO:0001583	missense	84896	exon5			GATTCTCCATACC	AL834370	CCDS7386.1	10q23.31	2010-04-21		2007-02-08	ENSG00000138138	ENSG00000138138		"ATPases / AAA-type"	25903	protein-coding gene	gene with protein product		614452				12477932	Standard	NM_032810		Approved	FLJ14600	uc001kez.1	Q8NBU5	OTTHUMG00000018685	ENST00000308448.7:c.503G>T	10.37:g.89544307C>A	ENSP00000339017:p.Gly168Val	89.0	0.0		106.0	45.0	NM_032810	D3DR26|Q6DKG1|Q6P4B9|Q8N3G1|Q8WYR9|Q969Y3	Missense_Mutation	SNP	ENST00000308448.7	37	CCDS7386.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.381743	0.82792	.	.	ENSG00000138138	ENST00000308448;ENST00000328142;ENST00000400215;ENST00000541004	D;D;D;D	0.95137	-3.62;-3.62;-3.62;-3.62	5.35	4.44	0.53790	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.98635	0.9543	H	0.99454	4.575	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99651	1.0991	9	.	.	.	-20.4245	16.3117	0.82873	0.0:0.8674:0.1325:0.0	.	110;168	B4E2J1;Q8NBU5	.;ATAD1_HUMAN	V	168;168;110;168	ENSP00000339017:G168V;ENSP00000339016:G168V;ENSP00000412968:G110V;ENSP00000445500:G168V	.	G	-	2	0	ATAD1	89534287	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.487000	0.81328	1.365000	0.46057	0.563000	0.77884	GGA	.	.		0.433	ATAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049235.1	NM_032810		A	89544307	C	A	89544307	3	1	372	1	0	0	0	0	1	0	0	0	1070	855	30	3	606	3	ATAD1	10	89544307	Missense_Mutation	SNP	C	TCGA-ZS-A9CF-01A-11D-A382-10	41127820	89544307	45990440	55	51465										
C10orf12	26148	hgsc.bcm.edu	37	chr10	98743503	98743504	+	Frame_Shift_Ins	INS	-	-	G													0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	caccgtggtagatgaacagcINScaaagtttatggaatggtgt							TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr10:98743503_98743504insG	ENST00000286067.2	+	1	2463_2464	c.2356_2357insG	c.(2356-2358)ccafs	p.P786fs		NM_015652.2	NP_056467.2	Q8N655	CJ012_HUMAN	chromosome 10 open reading frame 12	786										NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(3)|prostate(2)|skin(2)|stomach(4)	45		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		AGATGAACAGCCAAAGTTTATG	0.49																																					p.P786fs		Atlas-Indel	.											.	C10orf12	94	.	0			c.2356_2357insG						.																																			SO:0001589	frameshift_variant	26148	exon1			.	BC024315	CCDS7452.1	10q24.2	2014-03-11			ENSG00000155640	ENSG00000155640			23420	protein-coding gene	gene with protein product						24550272	Standard	NM_015652		Approved	DKFZP564P1916, FLJ13022	uc001kmv.3	Q8N655	OTTHUMG00000018840	Exception_encountered	10.37:g.98743503_98743504insG	ENSP00000286067:p.Pro786fs	199.0	0.0		193.0	16.0	NM_015652	Q9H945|Q9Y457	Frame_Shift_Ins	INS	ENST00000286067.2	37	CCDS7452.1																																																																																			.	.		0.49	C10orf12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049627.1	NM_015652		G	98743504	-	G	98743503	7	5	372	1	0	1	1	0	0	0	0	0	1591	739	26	0	2358	0	C10orf12	10	98743503	Frame_Shift_Ins	INS	-	TCGA-ZS-A9CF-01A-11D-A382-10	9199196	98743503	36791244	56	51466										
PAX2	5076	hgsc.bcm.edu	37	chr10	102584454	102584454	+	Silent	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	ggttacccccctcacgtgccCcccactggccagggaagcta	10	18	1	0			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr10:102584454C>A	ENST00000428433.1	+	9	1588	c.1038C>A	c.(1036-1038)ccC>ccA	p.P346P	PAX2_ENST00000355243.3_Silent_p.P323P|PAX2_ENST00000556085.1_Silent_p.P322P|PAX2_ENST00000370296.2_Silent_p.P346P|PAX2_ENST00000361791.3_Silent_p.P323P	NM_003987.3|NM_003990.3	NP_003978|NP_003981.2	Q02962	PAX2_HUMAN	paired box 2	346					aging (GO:0007568)|axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye development (GO:0043010)|cell fate determination (GO:0001709)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucose stimulus (GO:0071333)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cochlea development (GO:0090102)|cochlea morphogenesis (GO:0090103)|glial cell differentiation (GO:0010001)|inner ear morphogenesis (GO:0042472)|mesenchymal to epithelial transition (GO:0060231)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|mesodermal cell fate specification (GO:0007501)|mesonephric duct development (GO:0072177)|mesonephric tubule formation (GO:0072172)|mesonephros development (GO:0001823)|metanephric collecting duct development (GO:0072205)|metanephric distal convoluted tubule development (GO:0072221)|metanephric epithelium development (GO:0072207)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchyme development (GO:0072075)|metanephric nephron tubule formation (GO:0072289)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic process involved in metanephric collecting duct development (GO:1900215)|negative regulation of apoptotic process involved in metanephric nephron tubule development (GO:1900218)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of cytolysis (GO:0045918)|negative regulation of mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis (GO:0072305)|negative regulation of mesenchymal cell apoptotic process involved in metanephros development (GO:1900212)|negative regulation of programmed cell death (GO:0043069)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct formation (GO:0072179)|neural tube closure (GO:0001843)|optic chiasma development (GO:0061360)|optic cup morphogenesis involved in camera-type eye development (GO:0002072)|optic nerve development (GO:0021554)|optic nerve morphogenesis (GO:0021631)|optic nerve structural organization (GO:0021633)|pancreas development (GO:0031016)|paramesonephric duct development (GO:0061205)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0072108)|positive regulation of metanephric DCT cell differentiation (GO:2000594)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of optic nerve formation (GO:2000597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephric field specification (GO:0039003)|pronephros development (GO:0048793)|protein kinase B signaling (GO:0043491)|reactive oxygen species metabolic process (GO:0072593)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of metanephros size (GO:0035566)|response to nutrient levels (GO:0031667)|retinal pigment epithelium development (GO:0003406)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|ureter development (GO:0072189)|ureter maturation (GO:0035799)|ureter morphogenesis (GO:0072197)|urogenital system development (GO:0001655)|vestibulocochlear nerve formation (GO:0021650)|visual perception (GO:0007601)	centriolar satellite (GO:0034451)|lysosome (GO:0005764)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|protein complex (GO:0043234)|protein-DNA complex (GO:0032993)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|superoxide-generating NADPH oxidase activity (GO:0016175)|transcription regulatory region DNA binding (GO:0044212)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	18		Colorectal(252;0.234)		Epithelial(162;1.32e-08)|all cancers(201;7.32e-07)		CTCACGTGCCCCCCACTGGCC	0.607																																					p.P346P		Atlas-SNP	.											.	PAX2	83	.	0			c.C1038A						.						97	93	94					10																	102584454		2203	4300	6503	SO:0001819	synonymous_variant	5076	exon9			CGTGCCCCCCACT		CCDS7499.1, CCDS41561.1	10q24.31	2011-06-20	2007-07-12		ENSG00000075891	ENSG00000075891		"Paired boxes", "Homeoboxes / PRD class"	8616	protein-coding gene	gene with protein product		167409	"paired box gene 2"			8431641, 7981748	Standard	NM_003990		Approved		uc001krk.4	Q02962	OTTHUMG00000018913	ENST00000428433.1:c.1038C>A	10.37:g.102584454C>A		61.0	0.0		51.0	16.0	NM_003987	Q15105|Q15110|Q15837|Q5SZP2|Q5SZP3	Silent	SNP	ENST00000428433.1	37	CCDS53569.1																																																																																			.	.		0.607	PAX2-202	KNOWN	basic|CCDS	protein_coding	protein_coding				A	102584454	C	A	102584454	2	1	372	1	0	0	0	0	0	0	0	1	11488	610	22	3		3	PAX2	10	102584454	Silent	SNP	C	TCGA-ZS-A9CF-01A-11D-A382-10	3840951	102584454	32950293	57	51467										
TNNI2	7136	hgsc.bcm.edu	37	chr11	1862321	1862321	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	agttcaagcggcccccactgCggagggtgcgcatgtcggcc	15	14	1	0			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr11:1862321C>T	ENST00000381906.1	+	7	406	c.337C>T	c.(337-339)Cgg>Tgg	p.R113W	TNNI2_ENST00000252898.7_Missense_Mutation_p.R113W|TNNI2_ENST00000381905.3_Missense_Mutation_p.R113W|TNNI2_ENST00000381911.1_Missense_Mutation_p.R113W	NM_001145829.1	NP_001139301.1	P48788	TNNI2_HUMAN	troponin I type 2 (skeletal, fast)	113	Involved in binding TNC and actin.				muscle filament sliding (GO:0030049)|positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|nucleus (GO:0005634)|troponin complex (GO:0005861)	troponin T binding (GO:0031014)			lung(8)|prostate(1)|urinary_tract(1)	10		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00136)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		GCCCCCACTGCGGAGGGTGCG	0.637																																					p.R113W		Atlas-SNP	.											TNNI2,NS,carcinoma,-1,1	TNNI2	24	1	0			c.C337T						.						33	33	33					11																	1862321		2201	4299	6500	SO:0001583	missense	7136	exon5			CCACTGCGGAGGG	L21715	CCDS31333.1, CCDS53594.1	11p15.5	2014-09-17	2005-09-12		ENSG00000130598	ENSG00000130598			11946	protein-coding gene	gene with protein product	"troponin I, fast-twitch skeletal muscle isoform", "troponin I fast twitch 2"	191043	"troponin I, skeletal, fast", "arthrogryposis multiplex congenita, distal, type 2B"	AMCD2B		9016781, 12592607	Standard	NM_001145829		Approved	FSSV, DA2B	uc010qxe.1	P48788	OTTHUMG00000012253	ENST00000381906.1:c.337C>T	11.37:g.1862321C>T	ENSP00000371331:p.Arg113Trp	102.0	0.0		86.0	39.0	NM_001145841	A6NIV8|A6NJU5	Missense_Mutation	SNP	ENST00000381906.1	37	CCDS31333.1	.	.	.	.	.	.	.	.	.	.	c	11.00	1.509196	0.27036	.	.	ENSG00000130598	ENST00000381911;ENST00000381906;ENST00000252898;ENST00000381905	D;D;D;D	0.95171	-3.63;-3.63;-3.63;-3.63	2.92	0.872	0.19113	.	0.173313	0.47455	D	0.000221	D	0.96081	0.8723	M	0.70842	2.15	0.42989	D	0.994481	D;D	0.89917	1.0;1.0	P;D	0.81914	0.905;0.995	D	0.95126	0.8251	10	0.72032	D	0.01	-0.4131	11.8296	0.52288	0.4576:0.5424:0.0:0.0	.	113;113	A6NIV8;P48788	.;TNNI2_HUMAN	W	113	ENSP00000371336:R113W;ENSP00000371331:R113W;ENSP00000252898:R113W;ENSP00000371330:R113W	ENSP00000252898:R113W	R	+	1	2	TNNI2	1818897	1.000000	0.71417	0.024000	0.17045	0.035000	0.12851	1.116000	0.31221	0.223000	0.20920	0.313000	0.20887	CGG	.	.		0.637	TNNI2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034046.2	NM_003282		T	1862321	C	T	1862321	3	4	372	1	0	0	0	0	1	0	0	0	16342	759	27	1	374	1	TNNI2	11	1862321	Missense_Mutation	SNP	C	TCGA-ZS-A9CF-01A-11D-A382-10		1862321	133144195	58	51468										
KCNA4	3739	hgsc.bcm.edu	37	chr11	30033969	30033969	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	tcttctcagaccgctgtcgcCtcctcctccgactaccccgg	7	20	2	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr11:30033969C>T	ENST00000328224.6	-	2	1490	c.257G>A	c.(256-258)aGg>aAg	p.R86K	KCNA4_ENST00000526518.1_5'Flank	NM_002233.3	NP_002224.1	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 4	86				RRRRQ -> EEEAT (in Ref. 1; AAA60034). {ECO:0000305}.	potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	potassium ion binding (GO:0030955)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(39)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	78					Dalfampridine(DB06637)	CCGCTGTCGCCTCCTCCTCCG	0.637																																					p.R86K		Atlas-SNP	.											.	KCNA4	158	.	0			c.G257A						.						43	45	45					11																	30033969		2056	4201	6257	SO:0001583	missense	3739	exon2			TGTCGCCTCCTCC	M55514	CCDS41629.1	11p14	2012-07-05	2002-07-10			ENSG00000182255		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6222	protein-coding gene	gene with protein product		176266	"potassium voltage-gated channel, shaker-related subfamily, member 4-like"	KCNA4L		2263489, 16382104	Standard	NM_002233		Approved	Kv1.4, HK1, HPCN2	uc001msk.3	P22459		ENST00000328224.6:c.257G>A	11.37:g.30033969C>T	ENSP00000328511:p.Arg86Lys	54.0	0.0		46.0	18.0	NM_002233		Missense_Mutation	SNP	ENST00000328224.6	37	CCDS41629.1	.	.	.	.	.	.	.	.	.	.	C	7.643	0.681305	0.14907	.	.	ENSG00000182255	ENST00000328224	D	0.96396	-4.0	4.84	2.95	0.34219	.	7.853160	0.00710	U	0.000828	D	0.90645	0.7066	N	0.08118	0	0.30678	N	0.752597	B	0.02656	0.0	B	0.01281	0.0	T	0.83218	-0.0070	10	0.30078	T	0.28	.	5.8313	0.18582	0.0:0.6302:0.1569:0.2129	.	86	P22459	KCNA4_HUMAN	K	86	ENSP00000328511:R86K	ENSP00000328511:R86K	R	-	2	0	KCNA4	29990545	0.083000	0.21467	0.859000	0.33776	0.082000	0.17680	0.824000	0.27379	0.462000	0.27095	-0.254000	0.11334	AGG	.	.		0.637	KCNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388074.2	NM_002233		T	30033969	C	T	30033969	3	4	372	1	0	0	0	0	1	0	0	0	8014	681	24	3	1708	3	KCNA4	11	30033969	Missense_Mutation	SNP	C	TCGA-ZS-A9CF-01A-11D-A382-10	28171648	30033969	104972547	59	51469										
ELF5	2001	hgsc.bcm.edu	37	chr11	34527248	34527248	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	ccacgacatcaggggatcgcAgaaggatgcattaggcagga	14	9	1	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr11:34527248A>G	ENST00000312319.2	-	2	308	c.79T>C	c.(79-81)Tgc>Cgc	p.C27R	ELF5_ENST00000532417.1_Missense_Mutation_p.C17R|ELF5_ENST00000429939.2_Missense_Mutation_p.C17R|ELF5_ENST00000528709.1_5'UTR|ELF5_ENST00000257832.2_Missense_Mutation_p.C17R	NM_001243081.1|NM_198381.1	NP_001230010.1|NP_938195.1	Q9UKW6	ELF5_HUMAN	E74-like factor 5 (ets domain transcription factor)	27					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|ectoderm development (GO:0007398)|mammary gland epithelial cell differentiation (GO:0060644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			large_intestine(4)|skin(1)	5		Acute lymphoblastic leukemia(5;0.0087)|all_hematologic(20;0.0384)				AGGGGATCGCAGAAGGATGCA	0.537																																					p.C27R	Melanoma(61;202 1660 4348 21594)	Atlas-SNP	.											ELF5,colon,carcinoma,+1,1	ELF5	21	1	0			c.T79C						.						191	141	158					11																	34527248		2202	4298	6500	SO:0001583	missense	2001	exon2			GATCGCAGAAGGA	AF049703	CCDS7892.1, CCDS7893.1, CCDS58129.1, CCDS73273.1	11p13-p12	2008-05-14			ENSG00000135374	ENSG00000135374			3320	protein-coding gene	gene with protein product		605169				9840936	Standard	NM_001422		Approved		uc001mvp.2	Q9UKW6	OTTHUMG00000166451	ENST00000312319.2:c.79T>C	11.37:g.34527248A>G	ENSP00000311010:p.Cys27Arg	134.0	0.0		116.0	48.0	NM_198381	A6XAE6|A8K452|O95175|Q8N2K9|Q96QY3|Q9UKW5	Missense_Mutation	SNP	ENST00000312319.2	37	CCDS7892.1	.	.	.	.	.	.	.	.	.	.	A	12.74	2.028165	0.35797	.	.	ENSG00000135374	ENST00000257832;ENST00000312319;ENST00000429939;ENST00000532417	T;T;T;T	0.33654	2.54;2.51;1.86;1.4	5.38	4.25	0.50352	Sterile alpha motif/pointed domain (1);	3.120010	0.01230	U	0.008336	T	0.46308	0.1386	N	0.19112	0.55	0.54753	D	0.999988	P;D;D	0.64830	0.486;0.994;0.989	B;D;P	0.77004	0.032;0.989;0.55	T	0.44390	-0.9331	10	0.17369	T	0.5	.	8.8694	0.35307	0.9144:0.0:0.0856:0.0	.	17;17;27	A6XAE6;Q9UKW6-3;Q9UKW6	.;.;ELF5_HUMAN	R	17;27;17;17	ENSP00000257832:C17R;ENSP00000311010:C27R;ENSP00000407589:C17R;ENSP00000436386:C17R	ENSP00000257832:C17R	C	-	1	0	ELF5	34483824	1.000000	0.71417	0.998000	0.56505	0.164000	0.22412	4.990000	0.63876	0.882000	0.36016	0.454000	0.30748	TGC	.	.		0.537	ELF5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389845.1	NM_198381		G	34527248	A	G	34527248	3	3	372	1	0	0	0	0	1	0	0	0	5059	188	7	2	742	2	ELF5	11	34527248	Missense_Mutation	SNP	A	TCGA-ZS-A9CF-01A-11D-A382-10	4493279	34527248	100479268	60	51470										
OR8H2	390151	hgsc.bcm.edu	37	chr11	55872886	55872886	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	ctcaatggcccatgatcgctAtgcagcgatctgcagtcctc	9	14	2	1	rs570097222		TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr11:55872886A>T	ENST00000313503.1	+	1	368	c.368A>T	c.(367-369)tAt>tTt	p.Y123F		NM_001005200.1	NP_001005200.1	Q8N162	OR8H2_HUMAN	olfactory receptor, family 8, subfamily H, member 2	123						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(38)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	61	Esophageal squamous(21;0.00693)					CATGATCGCTATGCAGCGATC	0.463										HNSCC(53;0.14)																											p.Y123F		Atlas-SNP	.											.	OR8H2	117	.	0			c.A368T						.						191	189	190					11																	55872886		2201	4296	6497	SO:0001583	missense	390151	exon1			ATCGCTATGCAGC	AB065657	CCDS31518.1	11q11	2012-08-09			ENSG00000181767	ENSG00000181767		"GPCR / Class A : Olfactory receptors"	15308	protein-coding gene	gene with protein product							Standard	NM_001005200		Approved		uc010riy.2	Q8N162	OTTHUMG00000166832	ENST00000313503.1:c.368A>T	11.37:g.55872886A>T	ENSP00000323982:p.Tyr123Phe	128.0	0.0		107.0	47.0	NM_001005200	Q6IFC1	Missense_Mutation	SNP	ENST00000313503.1	37	CCDS31518.1	.	.	.	.	.	.	.	.	.	.	a	11.60	1.687283	0.29962	.	.	ENSG00000181767	ENST00000313503	T	0.02050	4.48	3.35	0.598	0.17512	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47852	D	0.000204	T	0.07728	0.0194	M	0.69523	2.12	0.26686	N	0.971448	D	0.89917	1.0	D	0.71414	0.973	T	0.04961	-1.0915	10	0.56958	D	0.05	.	6.2726	0.20963	0.6782:0.1639:0.0:0.1579	.	123	Q8N162	OR8H2_HUMAN	F	123	ENSP00000323982:Y123F	ENSP00000323982:Y123F	Y	+	2	0	OR8H2	55629462	0.166000	0.22962	0.835000	0.33067	0.012000	0.07955	0.884000	0.28214	0.440000	0.26502	-0.724000	0.03597	TAT	.	.		0.463	OR8H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391540.1	NM_001005200		T	55872886	A	T	55872886	3	4	372	1	0	0	0	0	1	0	0	0	11247	449	16	4	370	4	OR8H2	11	55872886	Missense_Mutation	SNP	A	TCGA-ZS-A9CF-01A-11D-A382-10	21345638	55872886	79133630	61	51471										
PIWIL4	143689	hgsc.bcm.edu	37	chr11	94308255	94308255	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	ctttatggatttgagtatctGtaccagagaaaaattggcac	9	6	1	2			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr11:94308255G>C	ENST00000299001.6	+	3	468	c.257G>C	c.(256-258)tGt>tCt	p.C86S	RP11-867G2.8_ENST00000537874.1_RNA|RP11-867G2.8_ENST00000536540.1_RNA	NM_152431.2	NP_689644.2	Q7Z3Z4	PIWL4_HUMAN	piwi-like RNA-mediated gene silencing 4	86					cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|piP-body (GO:0071547)	piRNA binding (GO:0034584)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|urinary_tract(2)	30		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				TTGAGTATCTGTACCAGAGAA	0.353																																					p.C86S		Atlas-SNP	.											.	PIWIL4	70	.	0			c.G257C						.						120	125	123					11																	94308255		2201	4298	6499	SO:0001583	missense	143689	exon3			GTATCTGTACCAG	AB079366	CCDS31656.1	11q12	2013-02-15	2013-02-15			ENSG00000134627		"Argonaute/PIWI family"	18444	protein-coding gene	gene with protein product		610315	"piwi-like 4 (Drosophila)"			12906857	Standard	NM_152431		Approved	FLJ36156, HIWI2, Miwi2	uc001pfa.3	Q7Z3Z4		ENST00000299001.6:c.257G>C	11.37:g.94308255G>C	ENSP00000299001:p.Cys86Ser	150.0	0.0		199.0	81.0	NM_152431	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Missense_Mutation	SNP	ENST00000299001.6	37	CCDS31656.1	.	.	.	.	.	.	.	.	.	.	G	6.716	0.500749	0.12822	.	.	ENSG00000134627	ENST00000299001;ENST00000545603	T;T	0.12465	2.68;2.68	4.6	3.61	0.41365	.	0.501088	0.20304	N	0.094967	T	0.09291	0.0229	L	0.43152	1.355	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.17107	-1.0380	10	0.13108	T	0.6	-17.7313	4.5016	0.11867	0.2839:0.0:0.7161:0.0	.	86	Q7Z3Z4	PIWL4_HUMAN	S	86;17	ENSP00000299001:C86S;ENSP00000440499:C17S	ENSP00000299001:C86S	C	+	2	0	PIWIL4	93947903	0.929000	0.31497	0.997000	0.53966	0.227000	0.25037	1.372000	0.34261	2.398000	0.81561	0.650000	0.86243	TGT	.	.		0.353	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396388.1	NM_152431		C	94308255	G	C	94308255	3	2	372	1	0	0	0	0	1	0	0	0	11969	1377	48	4	267	4	PIWIL4	11	94308255	Missense_Mutation	SNP	G	TCGA-ZS-A9CF-01A-11D-A382-10	38435369	94308255	40698261	62	51472										
AMOTL1	154810	hgsc.bcm.edu	37	chr11	94602440	94602440	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	cacccacctcagcactgtccTccatagcctccactacggca	5	20	1	0			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr11:94602440T>C	ENST00000433060.2	+	12	2707	c.2566T>C	c.(2566-2568)Tcc>Ccc	p.S856P	AMOTL1_ENST00000317837.9_Missense_Mutation_p.S443P|AMOTL1_ENST00000317829.8_Missense_Mutation_p.S806P	NM_130847.2	NP_570899.1	Q8IY63	AMOL1_HUMAN	angiomotin like 1	856					establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|hippo signaling (GO:0035329)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|tight junction (GO:0005923)	identical protein binding (GO:0042802)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	36		Acute lymphoblastic leukemia(157;2.38e-05)|all_hematologic(158;0.00824)				AGCACTGTCCTCCATAGCCTC	0.607																																					p.S856P		Atlas-SNP	.											.	AMOTL1	95	.	0			c.T2566C						.						26	33	31					11																	94602440		2157	4265	6422	SO:0001583	missense	154810	exon12			CTGTCCTCCATAG	AF453742	CCDS44712.1, CCDS73368.1	11q21	2008-07-18				ENSG00000166025			17811	protein-coding gene	gene with protein product	"junction-enriched and associated protein"	614657				11733531	Standard	XM_005273798		Approved	JEAP	uc001pfb.3	Q8IY63		ENST00000433060.2:c.2566T>C	11.37:g.94602440T>C	ENSP00000387739:p.Ser856Pro	122.0	0.0		114.0	5.0	NM_130847	Q63HK7|Q8NDN0|Q8TEN8|Q8WXD1|Q96CM5	Missense_Mutation	SNP	ENST00000433060.2	37	CCDS44712.1	.	.	.	.	.	.	.	.	.	.	T	10.20	1.283514	0.23392	.	.	ENSG00000166025	ENST00000317829;ENST00000317837;ENST00000433060	T;T;T	0.38722	2.29;1.12;2.3	5.48	3.53	0.40419	.	0.351400	0.27797	N	0.017810	T	0.09379	0.0231	N	0.00237	-1.79	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36163	-0.9759	10	0.02654	T	1	-2.9307	8.6656	0.34118	0.0:0.7062:0.0:0.2938	.	806;856	Q8IY63-2;Q8IY63	.;AMOL1_HUMAN	P	806;443;856	ENSP00000320968:S806P;ENSP00000323474:S443P;ENSP00000387739:S856P	ENSP00000320968:S806P	S	+	1	0	AMOTL1	94242088	0.083000	0.21467	0.003000	0.11579	0.255000	0.26057	1.126000	0.31344	0.683000	0.31428	-0.337000	0.08149	TCC	.	.		0.607	AMOTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396474.3	NM_130847		C	94602440	T	C	94602440	3	2	372	1	0	0	0	0	1	0	0	0	583	1551	54	2	2612	2	AMOTL1	11	94602440	Missense_Mutation	SNP	T	TCGA-ZS-A9CF-01A-11D-A382-10	294185	94602440	40404076	63	51473										
GLI1	2735	hgsc.bcm.edu	37	chr12	57865281	57865281	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	ggggcagggaagatgcccccGcccaggaaccttcctaccag	13	15	0	1	rs368469814		TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr12:57865281G>A	ENST00000228682.2	+	12	2849	c.2758G>A	c.(2758-2760)Gcc>Acc	p.A920T	GLI1_ENST00000546141.1_Missense_Mutation_p.A879T|GLI1_ENST00000543426.1_Missense_Mutation_p.A792T	NM_005269.2	NP_005260.1	P08151	GLI1_HUMAN	GLI family zinc finger 1	920					cerebellar cortex morphogenesis (GO:0021696)|digestive tract morphogenesis (GO:0048546)|dorsal/ventral pattern formation (GO:0009953)|epidermal cell differentiation (GO:0009913)|lung development (GO:0030324)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|notochord regression (GO:0060032)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|regulation of smoothened signaling pathway (GO:0008589)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|spermatogenesis (GO:0007283)|ventral midline development (GO:0007418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|primary cilium (GO:0072372)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription regulatory region DNA binding (GO:0044212)			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)			AGATGCCCCCGCCCAGGAACC	0.562																																					p.A920T	Pancreas(157;841 1936 10503 41495 50368)	Atlas-SNP	.											.	GLI1	141	.	0			c.G2758A						.	G	THR/ALA,THR/ALA,THR/ALA	0,4406		0,0,2203	34	38	36		2374,2635,2758	1.1	0.6	12		36	2,8598	1.2+/-3.3	0,2,4298	no	missense,missense,missense	GLI1	NM_001160045.1,NM_001167609.1,NM_005269.2	58,58,58	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign,benign,benign	792/979,879/1066,920/1107	57865281	2,13004	2203	4300	6503	SO:0001583	missense	2735	exon12			GCCCCCGCCCAGG		CCDS8940.1, CCDS53806.1, CCDS53807.1	12q13.2-q13.3	2013-01-25	2009-03-05	2005-01-14		ENSG00000111087		"Zinc fingers, C2H2-type"	4317	protein-coding gene	gene with protein product		165220	"glioma-associated oncogene homolog 1 (zinc finger protein)", "glioma-associated oncogene family zinc finger 1"	GLI		2850480	Standard	NM_005269		Approved		uc001snx.3	P08151		ENST00000228682.2:c.2758G>A	12.37:g.57865281G>A	ENSP00000228682:p.Ala920Thr	87.0	0.0		113.0	33.0	NM_005269	D0EUY3|E9PQQ9|F5H6H8|Q8TDN9	Missense_Mutation	SNP	ENST00000228682.2	37	CCDS8940.1	.	.	.	.	.	.	.	.	.	.	G	2.388	-0.340469	0.05243	0.0	2.33E-4	ENSG00000111087	ENST00000543426;ENST00000228682;ENST00000546141;ENST00000528467;ENST00000443131	T;T;T;T	0.12465	2.79;2.68;2.75;2.75	4.53	1.09	0.20402	.	0.811582	0.10385	N	0.681045	T	0.04998	0.0134	N	0.08118	0	0.09310	N	1	B	0.24426	0.103	B	0.14023	0.01	T	0.43702	-0.9375	10	0.08599	T	0.76	.	4.156	0.10261	0.3576:0.1672:0.4752:0.0	.	920	P08151	GLI1_HUMAN	T	792;920;879;879;388	ENSP00000437607:A792T;ENSP00000228682:A920T;ENSP00000441006:A879T;ENSP00000434408:A879T	ENSP00000228682:A920T	A	+	1	0	GLI1	56151548	0.000000	0.05858	0.562000	0.28370	0.204000	0.24138	-0.167000	0.09940	0.096000	0.17463	-0.234000	0.12200	GCC	.	.		0.562	GLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394197.1	NM_005269		A	57865281	G	A	57865281	3	1	372	1	0	0	0	0	1	0	0	0	6445	1087	38	1	2800	1	GLI1	12	57865281	Missense_Mutation	SNP	G	TCGA-ZS-A9CF-01A-11D-A382-10		57865281	75986614	64	51474										
MYBPC1	4604	hgsc.bcm.edu	37	chr12	102045035	102045035	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	ctctgaagattttgacacctCtgactgatcagactgtaaat	7	9	3	6			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr12:102045035C>T	ENST00000550270.1	+	14	1315	c.1315C>T	c.(1315-1317)Ctg>Ttg	p.L439L	MYBPC1_ENST00000553190.1_Silent_p.L439L|MYBPC1_ENST00000545503.2_Silent_p.L439L|RP11-755O11.2_ENST00000552081.1_RNA|MYBPC1_ENST00000550501.1_Intron|MYBPC1_ENST00000536007.1_Silent_p.L420L|MYBPC1_ENST00000441232.1_Silent_p.L439L|MYBPC1_ENST00000360610.2_Silent_p.L439L|MYBPC1_ENST00000549145.1_Silent_p.L452L|MYBPC1_ENST00000361685.2_Silent_p.L464L|MYBPC1_ENST00000547509.1_Silent_p.L425L|MYBPC1_ENST00000547405.1_Silent_p.L413L|MYBPC1_ENST00000361466.2_Silent_p.L464L|MYBPC1_ENST00000392934.3_Silent_p.L426L|MYBPC1_ENST00000541119.1_Silent_p.L427L|RP11-755O11.2_ENST00000547027.1_RNA|MYBPC1_ENST00000452455.2_Silent_p.L439L|MYBPC1_ENST00000551300.1_Silent_p.L340L			Q00872	MYPC1_HUMAN	myosin binding protein C, slow type	439	Ig-like C2-type 4.				cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myofibril (GO:0030016)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	57						TTTGACACCTCTGACTGATCA	0.413																																					p.L464L		Atlas-SNP	.											.	MYBPC1	235	.	0			c.C1390T						.						131	136	135					12																	102045035		2203	4300	6503	SO:0001819	synonymous_variant	4604	exon16			ACACCTCTGACTG		CCDS9083.1, CCDS9084.1, CCDS9085.1, CCDS55877.1, CCDS58268.1, CCDS58269.1, CCDS58270.1, CCDS58271.1, CCDS58272.1, CCDS58273.1	12q23.2	2013-02-11	2001-11-28		ENSG00000196091	ENSG00000196091		"Myosin binding proteins", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7549	protein-coding gene	gene with protein product		160794	"myosin-binding protein C, slow-type"			8375400, 16918501	Standard	NM_002465		Approved		uc010svs.2	Q00872	OTTHUMG00000170274	ENST00000550270.1:c.1315C>T	12.37:g.102045035C>T		150.0	0.0		133.0	53.0	NM_206819	B4DKR5|B7Z8G8|B7ZL02|B7ZL09|B7ZL10|E7ESM5|E7EWS6|G3XAE8|Q15497|Q17RR7|Q569K7|Q86T48|Q86TC8|Q8N3L2	Silent	SNP	ENST00000550270.1	37	CCDS9085.1																																																																																			.	.		0.413	MYBPC1-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000408806.1			T	102045035	C	T	102045035	2	4	372	1	0	0	0	0	0	0	0	1	10020	912	32	3		3	MYBPC1	12	102045035	Silent	SNP	C	TCGA-ZS-A9CF-01A-11D-A382-10	44179754	102045035	31806860	65	51475										
SPRY2	10253	hgsc.bcm.edu	37	chr13	80911241	80911241	+	Frame_Shift_Del	DEL	G	G	-													0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	caaaggcactgcttgtcgcaGatccagtctgatggcagagg							TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr13:80911241delG	ENST00000377102.1	-	2	1577	c.600delC	c.(598-600)atcfs	p.I200fs	SPRY2_ENST00000540649.1_Frame_Shift_Del_p.I200fs|SPRY2_ENST00000377104.3_Frame_Shift_Del_p.I200fs			O43597	SPY2_HUMAN	sprouty homolog 2 (Drosophila)	200	Cys-rich.|SPR. {ECO:0000255|PROSITE- ProRule:PRU00572}.				bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment of mitotic spindle orientation (GO:0000132)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inner ear morphogenesis (GO:0042472)|lung growth (GO:0060437)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of Ras GTPase activity (GO:0034261)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|sensory perception of sound (GO:0007605)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase inhibitor activity (GO:0030291)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)	12	Medulloblastoma(90;0.18)	Acute lymphoblastic leukemia(28;0.218)|Breast(118;0.244)		GBM - Glioblastoma multiforme(99;0.0318)		GCTTGTCGCAGATCCAGTCTG	0.512																																					p.C201fs		Atlas-Indel	.											SPRY2,NS,carcinoma,+2,1	SPRY2	28	1	0			c.601delT						.						111	95	100					13																	80911241		2203	4300	6503	SO:0001589	frameshift_variant	10253	exon2			.	AF039843	CCDS9463.1	13q31.1	2008-05-14	2001-11-28		ENSG00000136158	ENSG00000136158			11270	protein-coding gene	gene with protein product		602466	"sprouty (Drosophila) homolog 2"			9458049	Standard	NM_005842		Approved	hSPRY2	uc001vlj.3	O43597	OTTHUMG00000017140	ENST00000377102.1:c.600delC	13.37:g.80911241delG	ENSP00000366306:p.Ile200fs	152.0	0.0		123.0	51.0	NM_005842	B2R9J9|Q5T6Z7	Frame_Shift_Del	DEL	ENST00000377102.1	37	CCDS9463.1																																																																																			.	.		0.512	SPRY2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045387.1			-	80911241	G	-	80911241	7	5	372	1	0	1	0	1	0	0	0	0	15121	932	33	0	351	0	SPRY2	13	80911241	Frame_Shift_Del	DEL	G	TCGA-ZS-A9CF-01A-11D-A382-10		80911241	34258637	66	51476										
COL4A1	1282	hgsc.bcm.edu	37	chr13	110807652	110807652	+	Nonsense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	tcacaaaagagtagccgatcCacagcgaggaccacccgctg	10	14	1	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr13:110807652C>T	ENST00000375820.4	-	50	4854	c.4733G>A	c.(4732-4734)tGg>tAg	p.W1578*		NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	1578	Collagen IV NC1. {ECO:0000255|PROSITE- ProRule:PRU00736}.				axon guidance (GO:0007411)|basement membrane organization (GO:0071711)|blood vessel morphogenesis (GO:0048514)|brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)|patterning of blood vessels (GO:0001569)|renal tubule morphogenesis (GO:0061333)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)|platelet-derived growth factor binding (GO:0048407)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	105	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			GTAGCCGATCCACAGCGAGGA	0.612																																					p.W1578X		Atlas-SNP	.											COL4A1_ENST00000375815,NS,carcinoma,-1,2	COL4A1	372	2	0			c.G4733A						.						62	60	61					13																	110807652		2203	4300	6503	SO:0001587	stop_gained	1282	exon50			CCGATCCACAGCG	J04217	CCDS9511.1	13q34	2013-09-05			ENSG00000187498	ENSG00000187498		"Collagens"	2202	protein-coding gene	gene with protein product		120130				3691802	Standard	NM_001845		Approved		uc001vqw.4	P02462	OTTHUMG00000017342	ENST00000375820.4:c.4733G>A	13.37:g.110807652C>T	ENSP00000364979:p.Trp1578*	200.0	1.0		164.0	89.0	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Nonsense_Mutation	SNP	ENST00000375820.4	37	CCDS9511.1	.	.	.	.	.	.	.	.	.	.	C	46	12.191043	0.99645	.	.	ENSG00000187498	ENST00000375815;ENST00000375820;ENST00000397198	.	.	.	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.0031	0.92841	0.0:1.0:0.0:0.0	.	.	.	.	X	1221;1578;1227	.	ENSP00000364973:W1221X	W	-	2	0	COL4A1	109605653	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	7.525000	0.81892	2.479000	0.83701	0.609000	0.83330	TGG	.	.		0.612	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3			T	110807652	C	T	110807652	4	4	372	1	0	0	0	0	0	1	0	0	3691	595	21	3	288	3	COL4A1	13	110807652	Nonsense_Mutation	SNP	C	TCGA-ZS-A9CF-01A-11D-A382-10	29896411	110807652	4362226	67	51477										
OR4M1	441670	hgsc.bcm.edu	37	chr14	20248678	20248678	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	gtatttcctgttggctaatcTggccctccttgatatttggt	9	9	1	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr14:20248678T>C	ENST00000315957.4	+	1	278	c.197T>C	c.(196-198)cTg>cCg	p.L66P		NM_001005500.1	NP_001005500.1	Q8NGD0	OR4M1_HUMAN	olfactory receptor, family 4, subfamily M, member 1	66						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(32)|prostate(1)|skin(2)	42	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TTGGCTAATCTGGCCCTCCTT	0.418																																					p.L66P		Atlas-SNP	.											OR4M1,NS,carcinoma,-1,1	OR4M1	104	1	0			c.T197C						.						309	326	320					14																	20248678		2203	4300	6503	SO:0001583	missense	441670	exon1			CTAATCTGGCCCT		CCDS32021.1	14q11.2	2013-09-23			ENSG00000176299	ENSG00000176299		"GPCR / Class A : Olfactory receptors"	14735	protein-coding gene	gene with protein product							Standard	NM_001005500		Approved		uc010tku.2	Q8NGD0	OTTHUMG00000170599	ENST00000315957.4:c.197T>C	14.37:g.20248678T>C	ENSP00000319654:p.Leu66Pro	147.0	0.0		144.0	59.0	NM_001005500	B9EH18|Q6IFA3	Missense_Mutation	SNP	ENST00000315957.4	37	CCDS32021.1	.	.	.	.	.	.	.	.	.	.	.	14.18	2.459442	0.43736	.	.	ENSG00000176299	ENST00000315957	T	0.00591	6.35	4.2	4.2	0.49525	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36703	N	0.002460	T	0.05318	0.0141	H	0.97962	4.115	0.49687	D	0.999815	D	0.89917	1.0	D	0.75484	0.986	T	0.00367	-1.1785	10	0.87932	D	0	-6.2105	11.5315	0.50614	0.0:0.0:0.0:1.0	.	66	Q8NGD0	OR4M1_HUMAN	P	66	ENSP00000319654:L66P	ENSP00000319654:L66P	L	+	2	0	OR4M1	19318518	0.914000	0.31030	0.974000	0.42286	0.937000	0.57800	5.599000	0.67592	1.894000	0.54839	0.330000	0.21533	CTG	.	.		0.418	OR4M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409770.1			C	20248678	T	C	20248678	3	2	372	1	0	0	0	0	1	0	0	0	11084	1580	55	2	199	2	OR4M1	14	20248678	Missense_Mutation	SNP	T	TCGA-ZS-A9CF-01A-11D-A382-10		20248678	87100862	68	51478										
RORA	6095	hgsc.bcm.edu	37	chr15	60824052	60824052	+	Splice_Site	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	ggaataatttcaatttgagcTgcaacagaagcacgcaacca	8	9	1	2			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr15:60824052T>A	ENST00000335670.6	-	3	297		c.e3-2		CTD-2501E16.2_ENST00000560280.1_RNA|RP11-219B17.1_ENST00000559902.1_RNA|RP11-219B17.1_ENST00000559824.1_RNA|RORA_ENST00000261523.5_Splice_Site|RP11-219B17.1_ENST00000559203.1_RNA|RP11-219B17.1_ENST00000558235.1_RNA|RORA_ENST00000449337.2_Splice_Site|RP11-219B17.1_ENST00000558140.1_RNA|RORA_ENST00000309157.4_Splice_Site|RORA_ENST00000560004.1_Splice_Site	NM_134261.2	NP_599023.1	P35398	RORA_HUMAN	RAR-related orphan receptor A						angiogenesis (GO:0001525)|cellular response to hypoxia (GO:0071456)|cellular response to sterol (GO:0036315)|cerebellar granule cell precursor proliferation (GO:0021930)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|circadian regulation of gene expression (GO:0032922)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|muscle cell differentiation (GO:0042692)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|nitric oxide biosynthetic process (GO:0006809)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of cholesterol homeostasis (GO:2000188)|regulation of glucose metabolic process (GO:0010906)|regulation of macrophage activation (GO:0043030)|regulation of smoothened signaling pathway (GO:0008589)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription involved in cell fate commitment (GO:0060850)|regulation of transcription, DNA-templated (GO:0006355)|T-helper 17 cell differentiation (GO:0072539)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)|xenobiotic metabolic process (GO:0006805)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	direct ligand regulated sequence-specific DNA binding transcription factor activity (GO:0098531)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|oxysterol binding (GO:0008142)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator binding (GO:0001223)|transcription corepressor binding (GO:0001222)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	21						CAATTTGAGCTGCAACAGAAG	0.358																																					.		Atlas-SNP	.											.	RORA	114	.	0			c.272-2A>T						.						108	97	101					15																	60824052		2203	4300	6503	SO:0001630	splice_region_variant	6095	exon4			TTGAGCTGCAACA	U04897	CCDS10177.1, CCDS10178.1, CCDS10179.1, CCDS45271.1	15q21-q22	2013-01-16			ENSG00000069667	ENSG00000069667		"Nuclear hormone receptors"	10258	protein-coding gene	gene with protein product		600825				7926749	Standard	NM_134261		Approved	RZRA, ROR1, ROR2, ROR3, NR1F1	uc002agv.3	P35398	OTTHUMG00000132769	ENST00000335670.6:c.197-2A>T	15.37:g.60824052T>A		165.0	0.0		185.0	84.0	NM_002943	P35397|P35399|P45445|Q495X4|Q96H83	Splice_Site	SNP	ENST00000335670.6	37	CCDS10177.1	.	.	.	.	.	.	.	.	.	.	T	19.78	3.891081	0.72524	.	.	ENSG00000069667	ENST00000335670;ENST00000449337;ENST00000309157;ENST00000261523	.	.	.	5.8	5.8	0.92144	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3317	0.74219	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	RORA	58611344	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.206000	0.71126	0.528000	0.53228	.	.	.		0.358	RORA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256142.2		Intron	A	60824052	T	A	60824052	5	1	372	1	0	0	0	0	0	0	1	0	13543	1594	55	4	1412	4	RORA	15	60824052	Splice_Site	SNP	T	TCGA-ZS-A9CF-01A-11D-A382-10		60824052	41707340	69	51479										
HERC1	8925	hgsc.bcm.edu	37	chr15	63966786	63966786	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	tttcagccagaacttttggtAtcagcaacagctcagcatat	7	10	3	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr15:63966786A>T	ENST00000443617.2	-	38	7688	c.7601T>A	c.(7600-7602)aTa>aAa	p.I2534K	RP11-317G6.1_ENST00000559303.2_RNA	NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	2534					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						AACTTTTGGTATCAGCAACAG	0.473																																					p.I2534K		Atlas-SNP	.											.	HERC1	624	.	0			c.T7601A						.						69	67	68					15																	63966786		1996	4175	6171	SO:0001583	missense	8925	exon38			TTTGGTATCAGCA	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.7601T>A	15.37:g.63966786A>T	ENSP00000390158:p.Ile2534Lys	182.0	0.0		173.0	85.0	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	37	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.560882	0.86335	.	.	ENSG00000103657	ENST00000443617	T	0.29917	1.55	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.32852	0.0843	N	0.24115	0.695	0.80722	D	1	D	0.54964	0.969	P	0.50352	0.638	T	0.11518	-1.0584	10	0.87932	D	0	.	16.2631	0.82557	1.0:0.0:0.0:0.0	.	2534	Q15751	HERC1_HUMAN	K	2534	ENSP00000390158:I2534K	ENSP00000390158:I2534K	I	-	2	0	HERC1	61753839	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	9.339000	0.96797	2.239000	0.73571	0.528000	0.53228	ATA	.	.		0.473	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		T	63966786	A	T	63966786	3	4	372	1	0	0	0	0	1	0	0	0	7066	449	16	4	7148	4	HERC1	15	63966786	Missense_Mutation	SNP	A	TCGA-ZS-A9CF-01A-11D-A382-10	3142734	63966786	38564606	70	51480										
SEMA7A	8482	hgsc.bcm.edu	37	chr15	74706891	74706891	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	ccggggtagcctctcacctgTagttaggtaaagcacatgaa	11	10	1	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr15:74706891T>C	ENST00000261918.4	-	10	1839	c.1291A>G	c.(1291-1293)Aca>Gca	p.T431A	SEMA7A_ENST00000543145.2_Missense_Mutation_p.T417A|SEMA7A_ENST00000542748.1_Missense_Mutation_p.T266A	NM_003612.3	NP_003603.1	O75326	SEM7A_HUMAN	semaphorin 7A, GPI membrane anchor (John Milton Hagen blood group)	431	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon extension (GO:0048675)|axon guidance (GO:0007411)|immune response (GO:0006955)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|olfactory lobe development (GO:0021988)|osteoblast differentiation (GO:0001649)|positive regulation of axon extension (GO:0045773)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of protein phosphorylation (GO:0001934)|regulation of inflammatory response (GO:0050727)	anchored component of membrane (GO:0031225)|external side of plasma membrane (GO:0009897)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(3)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(3)|lung(12)|upper_aerodigestive_tract(1)	30						CTCTCACCTGTAGTTAGGTAA	0.483																																					p.T431A		Atlas-SNP	.											.	SEMA7A	58	.	0			c.A1291G						.						111	117	115					15																	74706891		2197	4296	6493	SO:0001583	missense	8482	exon10			CACCTGTAGTTAG	AF069493	CCDS10262.1, CCDS53958.1, CCDS53959.1	15q22.3-q23	2014-07-18	2006-02-23		ENSG00000138623	ENSG00000138623		"Semaphorins", "CD molecules", "Blood group antigens", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10741	protein-coding gene	gene with protein product	"John Milton Hagen blood group", "H-Sema K1"	607961	"sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A", "sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A (JMH blood group)"	SEMAL		9721204	Standard	NM_003612		Approved	H-Sema-L, CD108	uc002axv.3	O75326	OTTHUMG00000139000	ENST00000261918.4:c.1291A>G	15.37:g.74706891T>C	ENSP00000261918:p.Thr431Ala	247.0	0.0		192.0	86.0	NM_003612	B4DDP7|F5H1S0|Q1XE81|Q1XE82|Q1XE83|Q1XE84|Q3MIY5	Missense_Mutation	SNP	ENST00000261918.4	37	CCDS10262.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.089903	0.76756	.	.	ENSG00000138623	ENST00000261918;ENST00000543145;ENST00000542748	T;T;T	0.33216	1.42;1.42;1.42	5.46	5.46	0.80206	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.54581	0.1867	M	0.76727	2.345	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.69654	0.941;0.965	T	0.59337	-0.7473	10	0.87932	D	0	.	14.0647	0.64821	0.0:0.0:0.0:1.0	.	417;431	F5H1S0;O75326	.;SEM7A_HUMAN	A	431;417;266	ENSP00000261918:T431A;ENSP00000438966:T417A;ENSP00000441493:T266A	ENSP00000261918:T431A	T	-	1	0	SEMA7A	72493944	1.000000	0.71417	1.000000	0.80357	0.676000	0.39594	5.083000	0.64456	2.211000	0.71520	0.454000	0.30748	ACA	.	.		0.483	SEMA7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272904.3	NM_003612		C	74706891	T	C	74706891	3	2	372	1	0	0	0	0	1	0	0	0	14058	1638	57	2	729	2	SEMA7A	15	74706891	Missense_Mutation	SNP	T	TCGA-ZS-A9CF-01A-11D-A382-10	10740105	74706891	27824501	71	51481			1	73		2	2	23	N	T_G	7.319628e-05
SEMA7A	8482	hgsc.bcm.edu	37	chr15	74706913	74706913	+	Silent	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	gttaggtaaagcacatgaaaGgtctccccgtggctggcttg	13	9	1	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr15:74706913G>T	ENST00000261918.4	-	10	1817	c.1269C>A	c.(1267-1269)acC>acA	p.T423T	SEMA7A_ENST00000543145.2_Silent_p.T409T|SEMA7A_ENST00000542748.1_Silent_p.T258T	NM_003612.3	NP_003603.1	O75326	SEM7A_HUMAN	semaphorin 7A, GPI membrane anchor (John Milton Hagen blood group)	423	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon extension (GO:0048675)|axon guidance (GO:0007411)|immune response (GO:0006955)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|olfactory lobe development (GO:0021988)|osteoblast differentiation (GO:0001649)|positive regulation of axon extension (GO:0045773)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of protein phosphorylation (GO:0001934)|regulation of inflammatory response (GO:0050727)	anchored component of membrane (GO:0031225)|external side of plasma membrane (GO:0009897)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(3)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(3)|lung(12)|upper_aerodigestive_tract(1)	30						GCACATGAAAGGTCTCCCCGT	0.517																																					p.T423T		Atlas-SNP	.											.	SEMA7A	58	.	0			c.C1269A						.						114	119	117					15																	74706913		2197	4296	6493	SO:0001819	synonymous_variant	8482	exon10			ATGAAAGGTCTCC	AF069493	CCDS10262.1, CCDS53958.1, CCDS53959.1	15q22.3-q23	2014-07-18	2006-02-23		ENSG00000138623	ENSG00000138623		"Semaphorins", "CD molecules", "Blood group antigens", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10741	protein-coding gene	gene with protein product	"John Milton Hagen blood group", "H-Sema K1"	607961	"sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A", "sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A (JMH blood group)"	SEMAL		9721204	Standard	NM_003612		Approved	H-Sema-L, CD108	uc002axv.3	O75326	OTTHUMG00000139000	ENST00000261918.4:c.1269C>A	15.37:g.74706913G>T		261.0	0.0		202.0	91.0	NM_003612	B4DDP7|F5H1S0|Q1XE81|Q1XE82|Q1XE83|Q1XE84|Q3MIY5	Silent	SNP	ENST00000261918.4	37	CCDS10262.1																																																																																			.	.		0.517	SEMA7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272904.3	NM_003612		T	74706913	G	T	74706913	2	4	372	1	0	0	0	0	0	0	0	1	14058	987	35	3		3	SEMA7A	15	74706913	Silent	SNP	G	TCGA-ZS-A9CF-01A-11D-A382-10	22	74706913	27824479	72	51482			1	73		2	2	23	N	T_G	7.319628e-05
CSK	1445	hgsc.bcm.edu	37	chr15	75094691	75094691	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	gcccctgaaggacgtcgtccCtcgggtggagaagggctaca	15	12	0	2			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr15:75094691C>A	ENST00000220003.9	+	13	1919	c.1190C>A	c.(1189-1191)cCt>cAt	p.P397H	CSK_ENST00000567571.1_Missense_Mutation_p.P397H|CSK_ENST00000439220.2_Missense_Mutation_p.P397H|CSK_ENST00000309470.9_Missense_Mutation_p.P397H	NM_004383.2	NP_004374.1	P41240	CSK_HUMAN	c-src tyrosine kinase	397	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adherens junction organization (GO:0034332)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cellular response to peptide hormone stimulus (GO:0071375)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of bone resorption (GO:0045779)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of Golgi to plasma membrane protein transport (GO:0042997)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of kinase activity (GO:0033673)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|negative regulation of phagocytosis (GO:0050765)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|positive regulation of MAP kinase activity (GO:0043406)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060368)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein C-terminus binding (GO:0008022)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(1)|lung(2)	3						GACGTCGTCCCTCGGGTGGAG	0.662																																					p.P397H		Atlas-SNP	.											.	CSK	43	.	0			c.C1190A						.						50	58	55					15																	75094691		2197	4296	6493	SO:0001583	missense	1445	exon14			TCGTCCCTCGGGT		CCDS10269.1	15q24.1	2013-02-14			ENSG00000103653	ENSG00000103653	2.7.10.1	"SH2 domain containing"	2444	protein-coding gene	gene with protein product		124095				1377109	Standard	NM_004383		Approved		uc010bka.3	P41240	OTTHUMG00000142814	ENST00000220003.9:c.1190C>A	15.37:g.75094691C>A	ENSP00000220003:p.Pro397His	48.0	0.0		50.0	25.0	NM_001127190	Q2M3N2|Q6FGZ6	Missense_Mutation	SNP	ENST00000220003.9	37	CCDS10269.1	.	.	.	.	.	.	.	.	.	.	C	19.80	3.894076	0.72639	.	.	ENSG00000103653	ENST00000220003;ENST00000439220;ENST00000451345;ENST00000309470	D;D;D	0.82255	-1.59;-1.59;-1.59	4.28	4.28	0.50868	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.72558	0.3475	N	0.11064	0.09	0.80722	D	1	D	0.54397	0.966	P	0.47015	0.534	T	0.73344	-0.4012	10	0.26408	T	0.33	-8.9995	15.6577	0.77155	0.0:1.0:0.0:0.0	.	397	P41240	CSK_HUMAN	H	397;397;346;397	ENSP00000220003:P397H;ENSP00000414764:P397H;ENSP00000438808:P397H	ENSP00000220003:P397H	P	+	2	0	CSK	72881744	0.220000	0.23631	1.000000	0.80357	0.995000	0.86356	1.549000	0.36212	2.218000	0.71995	0.563000	0.77884	CCT	.	.		0.662	CSK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286398.2	NM_004383		A	75094691	C	A	75094691	3	1	372	1	0	0	0	0	1	0	0	0	3945	681	24	3	1236	3	CSK	15	75094691	Missense_Mutation	SNP	C	TCGA-ZS-A9CF-01A-11D-A382-10	387778	75094691	27436701	73	51483										
CES1	1066	hgsc.bcm.edu	37	chr16	55853489	55853489	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	agctcctcttccgtcttctgTcgcaggcagtgaaccatgac	9	14	3	2			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr16:55853489T>C	ENST00000361503.4	-	7	991	c.861A>G	c.(859-861)cgA>cgG	p.R287R	CES1_ENST00000566555.1_5'Flank|CES1_ENST00000360526.3_Silent_p.R288R|CES1_ENST00000422046.2_Silent_p.R287R			P23141	EST1_HUMAN	carboxylesterase 1	287					epithelial cell differentiation (GO:0030855)|metabolic process (GO:0008152)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)	carboxylic ester hydrolase activity (GO:0052689)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)								all cancers(182;0.13)|Epithelial(162;0.137)	Benzocaine(DB01086)|Capecitabine(DB01101)|Ciclesonide(DB01410)|Clopidogrel(DB00758)|Cyclandelate(DB04838)|Dabigatran etexilate(DB06695)|Indomethacin(DB00328)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Mycophenolate mofetil(DB00688)|Oseltamivir(DB00198)|Probucol(DB01599)|Rufinamide(DB06201)|Tamoxifen(DB00675)|Trandolapril(DB00519)	CCGTCTTCTGTCGCAGGCAGT	0.498																																					p.R288R	NSCLC(162;1801 2756 42904 52896)	Atlas-SNP	.											CES1_ENST00000360526,NS,adenoma,-1,1	CES1	78	1	0			c.A864G						.						141	140	140					16																	55853489		2198	4300	6498	SO:0001819	synonymous_variant	1066	exon7			CTTCTGTCGCAGG	BC012418	CCDS32450.1, CCDS45488.1, CCDS45489.1	16q22.2	2010-10-12	2010-10-12		ENSG00000198848	ENSG00000198848	3.1.1.1	"Carboxylesterases"	1863	protein-coding gene	gene with protein product	"human monocyte/macrophage serine esterase 1"	114835	"carboxylesterase 1 (monocyte/macrophage serine esterase 1)"			2070086, 20931200	Standard	XM_005255774		Approved	HMSE, CES2, HMSE1, SES1, CEH, CES1A1, CES1A2	uc002eil.3	P23141		ENST00000361503.4:c.861A>G	16.37:g.55853489T>C		71.0	2.0		88.0	7.0	NM_001025195	A6NIM1|A8K3K8|A8K844|E9PAU8|P82127|Q00015|Q13657|Q14062|Q16737|Q16788|Q549X7|Q549X8|Q86UK2|Q96EE8|Q9UC52|Q9UDG8|Q9UK77|Q9ULY2	Silent	SNP	ENST00000361503.4	37	CCDS45488.1																																																																																			.	.		0.498	CES1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000433285.1	NM_001266		C	55853489	T	C	55853489	2	2	372	1	0	0	0	0	0	0	0	1	3271	1654	58	2		2	CES1	16	55853489	Silent	SNP	T	TCGA-ZS-A9CF-01A-11D-A382-10		55853489	34501264	74	51484										
MYH1	4619	hgsc.bcm.edu	37	chr17	10404770	10404770	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	gcttctctgctttggcccggGaggcccgctctgcctcgatt	12	15	2	0			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr17:10404770G>A	ENST00000226207.5	-	27	3489	c.3395C>T	c.(3394-3396)tCc>tTc	p.S1132F	RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	1132					muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						TTTGGCCCGGGAGGCCCGCTC	0.567																																					p.S1132F		Atlas-SNP	.											MYH1,NS,carcinoma,-1,1	MYH1	403	1	0			c.C3395T						.						39	44	42					17																	10404770		2203	4295	6498	SO:0001583	missense	4619	exon27			GCCCGGGAGGCCC		CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"Myosins / Myosin superfamily : Class II"	7567	protein-coding gene	gene with protein product	"myosin heavy chain IIx/d"	160730	"myosin, heavy polypeptide 1, skeletal muscle, adult"			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.3395C>T	17.37:g.10404770G>A	ENSP00000226207:p.Ser1132Phe	98.0	0.0		62.0	49.0	NM_005963	Q14CA4|Q9Y622	Missense_Mutation	SNP	ENST00000226207.5	37	CCDS11155.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.054564	0.75960	.	.	ENSG00000109061	ENST00000226207	T	0.78924	-1.22	5.3	5.3	0.74995	Myosin tail (1);	0.000000	0.42964	U	0.000628	T	0.73418	0.3584	L	0.37697	1.125	0.58432	D	0.999999	P	0.38535	0.635	B	0.38921	0.285	T	0.76822	-0.2817	10	0.72032	D	0.01	.	19.3291	0.94278	0.0:0.0:1.0:0.0	.	1132	P12882	MYH1_HUMAN	F	1132	ENSP00000226207:S1132F	ENSP00000226207:S1132F	S	-	2	0	MYH1	10345495	1.000000	0.71417	0.991000	0.47740	0.994000	0.84299	7.916000	0.87491	2.641000	0.89580	0.650000	0.86243	TCC	.	.		0.567	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963		A	10404770	G	A	10404770	3	1	372	1	0	0	0	0	1	0	0	0	10038	1174	41	3	2480	3	MYH1	17	10404770	Missense_Mutation	SNP	G	TCGA-ZS-A9CF-01A-11D-A382-10		10404770	70790440	75	51485										
MYH2	4620	hgsc.bcm.edu	37	chr17	10438678	10438678	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	tggtcatcagcttgttcaaaTtctcctgtaaaaccaggaaa	7	9	4	0			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr17:10438678T>C	ENST00000245503.5	-	18	2363	c.1979A>G	c.(1978-1980)aAt>aGt	p.N660S	RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA|MYH2_ENST00000532183.2_Intron|MYH2_ENST00000397183.2_Missense_Mutation_p.N660S|CTC-297N7.11_ENST00000587182.2_RNA	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	660	Myosin motor.				Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|plasma membrane repair (GO:0001778)|response to activity (GO:0014823)	A band (GO:0031672)|actomyosin contractile ring (GO:0005826)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|protein complex (GO:0043234)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(99)|ovary(6)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(4)	176						CTTGTTCAAATTCTCCTGTAA	0.388																																					p.N660S		Atlas-SNP	.											.	MYH2	390	.	0			c.A1979G						.						79	77	77					17																	10438678		2203	4300	6503	SO:0001583	missense	4620	exon18			TTCAAATTCTCCT		CCDS11156.1	17p13.1	2014-02-04	2006-09-29		ENSG00000125414	ENSG00000125414		"Myosins / Myosin superfamily : Class II"	7572	protein-coding gene	gene with protein product		160740	"myosin, heavy polypeptide 2, skeletal muscle, adult", "inclusion body myopathy 3, autosomal dominant"	IBM3		7545970, 11889243	Standard	NM_001100112		Approved	MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A	uc010coi.3	Q9UKX2	OTTHUMG00000130363	ENST00000245503.5:c.1979A>G	17.37:g.10438678T>C	ENSP00000245503:p.Asn660Ser	147.0	0.0		68.0	58.0	NM_017534	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Missense_Mutation	SNP	ENST00000245503.5	37	CCDS11156.1	.	.	.	.	.	.	.	.	.	.	T	17.08	3.298973	0.60195	.	.	ENSG00000125414	ENST00000245503;ENST00000397183	T;T	0.68624	-0.34;-0.34	4.97	4.97	0.65823	Myosin head, motor domain (2);	0.000000	0.41605	U	0.000841	T	0.45438	0.1342	N	0.02973	-0.45	0.54753	D	0.999985	B	0.20459	0.045	B	0.31101	0.124	T	0.41787	-0.9489	10	0.23302	T	0.38	.	14.8132	0.70010	0.0:0.0:0.0:1.0	.	660	Q9UKX2	MYH2_HUMAN	S	660	ENSP00000245503:N660S;ENSP00000380367:N660S	ENSP00000245503:N660S	N	-	2	0	MYH2	10379403	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	7.848000	0.86902	2.086000	0.62901	0.533000	0.62120	AAT	.	.		0.388	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534		C	10438678	T	C	10438678	3	2	372	1	0	0	0	0	1	0	0	0	10044	1493	52	2	3938	2	MYH2	17	10438678	Missense_Mutation	SNP	T	TCGA-ZS-A9CF-01A-11D-A382-10	33908	10438678	70756532	76	51486										
MYOCD	93649	hgsc.bcm.edu	37	chr17	12649346	12649346	+	Missense_Mutation	SNP	C	C	A	0	1	1	0	1	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	tggacaaactggtgtctcttCtttcaaaccaggcccactcc	7	14	3	0			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr17:12649346C>A	ENST00000343344.4	+	9	1082	c.1082C>A	c.(1081-1083)tCt>tAt	p.S361Y	AC005358.1_ENST00000609971.1_Missense_Mutation_p.S265Y|MYOCD_ENST00000425538.1_Missense_Mutation_p.S361Y|MYOCD_ENST00000395988.1_3'UTR			Q8IZQ8	MYCD_HUMAN	myocardin	361					cardiac muscle cell differentiation (GO:0055007)|cardiac ventricle development (GO:0003231)|cardiocyte differentiation (GO:0035051)|cell growth involved in cardiac muscle cell development (GO:0061049)|cellular component maintenance (GO:0043954)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hypoxia (GO:0071456)|digestive tract development (GO:0048565)|ductus arteriosus closure (GO:0097070)|hepatic stellate cell activation (GO:0035733)|lung alveolus development (GO:0048286)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of skeletal muscle cell differentiation (GO:2001015)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cardiac vascular smooth muscle cell differentiation (GO:2000724)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cell growth by extracellular stimulus (GO:0001560)|regulation of histone acetylation (GO:0035065)|regulation of myoblast differentiation (GO:0045661)|regulation of smooth muscle cell differentiation (GO:0051150)|response to hypoxia (GO:0001666)|smooth muscle cell differentiation (GO:0051145)|urinary bladder development (GO:0060157)|uterus development (GO:0060065)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(2)|lung(33)|ovary(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	70				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)		GGTGTCTCTTCTTTCAAACCA	0.408																																					p.S361Y		Atlas-SNP	.											.	MYOCD	291	.	0			c.C1082A						.						127	122	124					17																	12649346		2203	4300	6503	SO:0001583	missense	93649	exon9			TCTCTTCTTTCAA	AF532596	CCDS11163.1, CCDS54091.1	17p11.2	2004-03-01			ENSG00000141052	ENSG00000141052			16067	protein-coding gene	gene with protein product		606127				11439182, 12397177	Standard	XM_005256863		Approved	MYCD	uc002gno.2	Q8IZQ8	OTTHUMG00000058767	ENST00000343344.4:c.1082C>A	17.37:g.12649346C>A	ENSP00000341835:p.Ser361Tyr	105.0	0.0		65.0	52.0	NM_001146312	Q5UBU5|Q8N7Q1	Missense_Mutation	SNP	ENST00000343344.4	37	CCDS11163.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.239249	0.79800	.	.	ENSG00000141052	ENST00000395982;ENST00000425538;ENST00000343344;ENST00000395988;ENST00000443061	T;T	0.50277	0.75;0.79	5.71	5.71	0.89125	.	0.224226	0.48767	D	0.000174	T	0.56906	0.2017	L	0.27053	0.805	0.54753	D	0.999988	D;D;D;D	0.76494	0.999;0.998;0.998;0.997	D;D;D;D	0.70487	0.962;0.969;0.969;0.931	T	0.59268	-0.7486	10	0.66056	D	0.02	-12.2496	16.78	0.85561	0.0:1.0:0.0:0.0	.	80;265;361;361	E9PEP9;Q8IZQ8-2;Q8IZQ8-3;Q8IZQ8	.;.;.;MYCD_HUMAN	Y	80;361;361;265;66	ENSP00000341835:S361Y;ENSP00000400148:S66Y	ENSP00000341835:S361Y	S	+	2	0	MYOCD	12590071	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	3.642000	0.54367	2.704000	0.92352	0.561000	0.74099	TCT	.	.		0.408	MYOCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129950.1	NM_153604		A	12649346	C	A	12649346	3	1	372	1	0	0	0	0	1	0	0	0	10096	913	32	3	1116	3	MYOCD	17	12649346	Missense_Mutation	SNP	C	TCGA-ZS-A9CF-01A-11D-A382-10	2210668	12649346	68545864	77	51487										
LGALS9	3965	hgsc.bcm.edu	37	chr17	25975942	25975942	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	gaatactaccatcgcctgagGaacctgcccaccatcaacag	7	15	1	1	rs373192382		TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr17:25975942G>T	ENST00000395473.2	+	11	2470	c.1002G>T	c.(1000-1002)agG>agT	p.R334S	LGALS9_ENST00000413914.2_3'UTR|LGALS9_ENST00000310394.5_Missense_Mutation_p.R290S|LGALS9_ENST00000302228.5_Missense_Mutation_p.R302S|LGALS9_ENST00000313648.6_3'UTR	NM_009587.2	NP_033665.1	O00182	LEG9_HUMAN	lectin, galactoside-binding, soluble, 9	334	Galectin 2. {ECO:0000255|PROSITE- ProRule:PRU00639}.				positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)|galactose binding (GO:0005534)|signal transducer activity (GO:0004871)			endometrium(3)|large_intestine(2)|lung(12)|skin(1)	18	Lung NSC(42;0.0103)		BRCA - Breast invasive adenocarcinoma(3;0.0141)	UCEC - Uterine corpus endometrioid carcinoma (53;0.155)		ATCGCCTGAGGAACCTGCCCA	0.602																																					p.R334S	Melanoma(106;677 1527 28724 29571 46552)|Ovarian(193;263 2088 2118 29005 43023)	Atlas-SNP	.											.	LGALS9	29	.	0			c.G1002T						.						281	250	261					17																	25975942		2203	4300	6503	SO:0001583	missense	3965	exon11			CCTGAGGAACCTG	AB006782	CCDS11222.1, CCDS32592.1	17q11.2	2013-03-28	2008-07-25		ENSG00000168961	ENSG00000168961		"Lectins, galactoside-binding"	6570	protein-coding gene	gene with protein product	"galectin 9"	601879				9045665	Standard	NM_009587		Approved	LGALS9A	uc002gzp.3	O00182	OTTHUMG00000179831	ENST00000395473.2:c.1002G>T	17.37:g.25975942G>T	ENSP00000378856:p.Arg334Ser	1057.0	0.0		892.0	401.0	NM_009587	A7VJG6|O14532|O75028|Q3B8N1|Q53FQ0|Q9NQ58	Missense_Mutation	SNP	ENST00000395473.2	37	CCDS11222.1	.	.	.	.	.	.	.	.	.	.	G	7.798	0.713065	0.15306	.	.	ENSG00000168961	ENST00000395473;ENST00000302228;ENST00000310394	T;T;T	0.10477	2.87;2.87;2.87	4.73	-4.61	0.03380	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	0.752729	0.11972	N	0.511684	T	0.03434	0.0099	N	0.12443	0.215	0.09310	N	0.999992	B;B;B	0.17667	0.002;0.023;0.023	B;B;B	0.18561	0.004;0.022;0.022	T	0.43475	-0.9389	10	0.15066	T	0.55	.	0.1677	0.00110	0.325:0.2375:0.1964:0.2411	.	245;302;334	B4DJD7;Q3B8N1;O00182	.;.;LEG9_HUMAN	S	334;302;290	ENSP00000378856:R334S;ENSP00000306228:R302S;ENSP00000312259:R290S	ENSP00000306228:R302S	R	+	3	2	LGALS9	23000069	0.000000	0.05858	0.855000	0.33649	0.001000	0.01503	-0.383000	0.07398	-0.460000	0.07003	-1.136000	0.01936	AGG	.	.		0.602	LGALS9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255583.1	NM_009587		T	25975942	G	T	25975942	3	4	372	1	0	0	0	0	1	0	0	0	8757	1165	41	3	1044	3	LGALS9	17	25975942	Missense_Mutation	SNP	G	TCGA-ZS-A9CF-01A-11D-A382-10	13326596	25975942	55219268	78	51488										
FNDC8	54752	hgsc.bcm.edu	37	chr17	33448911	33448911	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	acttcttggaggatgataccAtcaacctactgtaagtcaca	7	10	3	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr17:33448911A>G	ENST00000158009.5	+	1	314	c.199A>G	c.(199-201)Atc>Gtc	p.I67V	RAD51D_ENST00000394589.4_5'Flank|RAD51D_ENST00000590016.1_5'Flank|RAD51D_ENST00000345365.6_5'Flank|RAD51L3-RFFL_ENST00000593039.1_5'Flank|RAD51D_ENST00000360276.3_5'Flank|RAD51D_ENST00000335858.7_5'Flank|RAD51D_ENST00000357906.3_5'Flank|RAD51D_ENST00000460118.2_5'Flank|RAD51D_ENST00000590380.1_5'Flank	NM_017559.2	NP_060029.1	Q8TC99	FNDC8_HUMAN	fibronectin type III domain containing 8	67						nucleus (GO:0005634)				breast(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)	11		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.022)		GGATGATACCATCAACCTACT	0.512																																					p.I67V		Atlas-SNP	.											FNDC8,NS,carcinoma,-1,1	FNDC8	28	1	0			c.A199G						.						100	92	95					17																	33448911		2203	4300	6503	SO:0001583	missense	54752	exon1			GATACCATCAACC	BC024002	CCDS11290.1	17q12	2013-02-11			ENSG00000073598	ENSG00000073598		"Fibronectin type III domain containing"	25286	protein-coding gene	gene with protein product						12477932	Standard	XM_005257993		Approved	DKFZp434H2215	uc002hix.3	Q8TC99	OTTHUMG00000132932	ENST00000158009.5:c.199A>G	17.37:g.33448911A>G	ENSP00000158009:p.Ile67Val	137.0	1.0		103.0	44.0	NM_017559	B2R9G6|Q9UFC2	Missense_Mutation	SNP	ENST00000158009.5	37	CCDS11290.1	.	.	.	.	.	.	.	.	.	.	A	10.83	1.460184	0.26248	.	.	ENSG00000073598	ENST00000158009	T	0.31510	1.49	4.68	2.28	0.28536	.	0.409342	0.21140	N	0.079492	T	0.16685	0.0401	N	0.24115	0.695	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.12142	-1.0559	10	0.46703	T	0.11	-9.6888	3.7095	0.08414	0.7087:0.0:0.1022:0.1891	.	67	Q8TC99	FNDC8_HUMAN	V	67	ENSP00000158009:I67V	ENSP00000158009:I67V	I	+	1	0	FNDC8	30473024	0.072000	0.21174	0.093000	0.20910	0.162000	0.22319	1.579000	0.36536	0.903000	0.36546	0.454000	0.30748	ATC	.	.		0.512	FNDC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256459.2	NM_017559		G	33448911	A	G	33448911	3	3	372	1	0	0	0	0	1	0	0	0	5982	217	8	2	201	2	FNDC8	17	33448911	Missense_Mutation	SNP	A	TCGA-ZS-A9CF-01A-11D-A382-10	7472969	33448911	47746299	79	51489										
NBR1	4077	hgsc.bcm.edu	37	chr17	41346472	41346472	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	aggcaaaaaatgttgccagtGagagggagctctacatccca	11	9	1	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr17:41346472G>A	ENST00000422280.1	+	13	2089	c.1630G>A	c.(1630-1632)Gag>Aag	p.E544K	NBR1_ENST00000589872.1_Missense_Mutation_p.E544K|NBR1_ENST00000542611.1_Missense_Mutation_p.E523K|NBR1_ENST00000389312.4_Missense_Mutation_p.E544K|NBR1_ENST00000341165.6_Missense_Mutation_p.E544K|NBR1_ENST00000590996.1_Missense_Mutation_p.E544K	NM_031858.2	NP_114064.1	Q14596	NBR1_HUMAN	neighbor of BRCA1 gene 1	544	ATG8 family protein-binding.				macroautophagy (GO:0016236)|negative regulation of osteoblast differentiation (GO:0045668)|protein oligomerization (GO:0051259)|regulation of bone mineralization (GO:0030500)|regulation of stress-activated MAPK cascade (GO:0032872)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)	mitogen-activated protein kinase binding (GO:0051019)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(1)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	24		Breast(137;0.00086)		BRCA - Breast invasive adenocarcinoma(366;0.0934)		TGTTGCCAGTGAGAGGGAGCT	0.507																																					p.E544K		Atlas-SNP	.											.	NBR1	55	.	0			c.G1630A						.						156	158	157					17																	41346472		1984	4148	6132	SO:0001583	missense	4077	exon13			GCCAGTGAGAGGG	X76952	CCDS45694.1	17q21.31	2008-02-01	2005-02-15	2005-02-16		ENSG00000188554			6746	protein-coding gene	gene with protein product		166945	"membrane component, chromosome 17, surface marker 2 (ovarian carcinoma antigen CA125)"	M17S2		8069304	Standard	XM_006721903		Approved	CA125, KIAA0049, 1A1-3B	uc010whv.2	Q14596		ENST00000422280.1:c.1630G>A	17.37:g.41346472G>A	ENSP00000411250:p.Glu544Lys	293.0	1.0		256.0	115.0	NM_031862	Q13173|Q15026|Q5J7Q8|Q96GB6|Q9NRF7	Missense_Mutation	SNP	ENST00000422280.1	37	CCDS45694.1	.	.	.	.	.	.	.	.	.	.	G	13.45	2.241125	0.39598	.	.	ENSG00000188554	ENST00000422280;ENST00000542611;ENST00000341165;ENST00000389312;ENST00000389311	T;T;T;T	0.45668	1.49;0.89;1.49;1.49	5.91	3.94	0.45596	.	.	.	.	.	T	0.33059	0.0850	L	0.33485	1.01	0.44092	D	0.99685	B;B;B;B	0.14438	0.005;0.01;0.008;0.005	B;B;B;B	0.18871	0.006;0.014;0.023;0.006	T	0.09465	-1.0673	9	0.54805	T	0.06	-6.7715	11.6268	0.51151	0.1445:0.0:0.8555:0.0	.	544;523;544;544	A8K1U0;B7Z5R6;Q14596-2;Q14596	.;.;.;NBR1_HUMAN	K	544;523;544;544;544	ENSP00000411250:E544K;ENSP00000437545:E523K;ENSP00000343479:E544K;ENSP00000373963:E544K	ENSP00000343479:E544K	E	+	1	0	NBR1	38599998	1.000000	0.71417	0.779000	0.31741	0.468000	0.32798	4.110000	0.57831	0.862000	0.35528	-0.140000	0.14226	GAG	.	.		0.507	NBR1-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453461.1	NM_005899		A	41346472	G	A	41346472	3	1	372	1	0	0	0	0	1	0	0	0	10209	1291	45	3	1676	3	NBR1	17	41346472	Missense_Mutation	SNP	G	TCGA-ZS-A9CF-01A-11D-A382-10	7897561	41346472	39848738	80	51490										
TOB1	10140	hgsc.bcm.edu	37	chr17	48940589	48940589	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	attaggagaaagagcagaggTtttctgctgttgttgctgct	13	5	1	3			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr17:48940589T>A	ENST00000268957.3	-	3	1218	c.790A>T	c.(790-792)Acc>Tcc	p.T264S	TOB1_ENST00000499247.2_Missense_Mutation_p.T264S|TOB1_ENST00000509385.1_5'Flank	NM_001243877.1	NP_001230806.1	P50616	TOB1_HUMAN	transducer of ERBB2, 1	264					negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell proliferation (GO:0008285)|negative regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060212)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of translation (GO:0017148)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of signal transduction (GO:0009967)|SMAD protein import into nucleus (GO:0007184)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	receptor tyrosine kinase binding (GO:0030971)|SH3/SH2 adaptor activity (GO:0005070)|transcription corepressor activity (GO:0003714)			breast(1)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13			BRCA - Breast invasive adenocarcinoma(22;1.09e-08)			AGAGCAGAGGTTTTctgctgt	0.537																																					p.T264S	NSCLC(144;643 1919 24513 29423 40686)	Atlas-SNP	.											.	TOB1	40	.	0			c.A790T						.						50	48	48					17																	48940589		2203	4300	6503	SO:0001583	missense	10140	exon2			CAGAGGTTTTCTG	D38305	CCDS11576.1	17q21.33	2012-08-14			ENSG00000141232	ENSG00000141232			11979	protein-coding gene	gene with protein product		605523		TROB1		8632892, 17785442	Standard	NM_005749		Approved	TOB, TROB	uc002isw.3	P50616	OTTHUMG00000162277	ENST00000268957.3:c.790A>T	17.37:g.48940589T>A	ENSP00000268957:p.Thr264Ser	98.0	0.0		111.0	24.0	NM_005749	B2R9T0|D3DTY3|Q4KMQ0	Missense_Mutation	SNP	ENST00000268957.3	37	CCDS11576.1	.	.	.	.	.	.	.	.	.	.	T	7.267	0.606423	0.14002	.	.	ENSG00000141232	ENST00000499247;ENST00000268957	T;T	0.41758	0.99;0.99	6.06	5.0	0.66597	.	0.394592	0.29522	N	0.011913	T	0.19087	0.0458	N	0.08118	0	0.34169	D	0.669623	B	0.14012	0.009	B	0.10450	0.005	T	0.21484	-1.0244	10	0.07325	T	0.83	.	8.0231	0.30421	0.0:0.0679:0.1362:0.7958	.	264	P50616	TOB1_HUMAN	S	264	ENSP00000427695:T264S;ENSP00000268957:T264S	ENSP00000268957:T264S	T	-	1	0	TOB1	46295588	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.298000	0.33412	1.123000	0.41961	0.528000	0.53228	ACC	.	.		0.537	TOB1-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000368364.1			A	48940589	T	A	48940589	3	1	372	1	0	0	0	0	1	0	0	0	16362	1725	60	4	251	4	TOB1	17	48940589	Missense_Mutation	SNP	T	TCGA-ZS-A9CF-01A-11D-A382-10	7594117	48940589	32254621	81	51491										
KIF19	124602	hgsc.bcm.edu	37	chr17	72349069	72349069	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	ccagcacctgcagaacagcgCcctccctcccctcagcacag	7	21	1	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr17:72349069C>G	ENST00000389916.4	+	15	2228	c.2090C>G	c.(2089-2091)gCc>gGc	p.A697G	AC103809.2_ENST00000599136.1_5'Flank	NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	697					ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						CAGAACAGCGCCCTCCCTCCC	0.597																																					p.A697G		Atlas-SNP	.											.	KIF19	102	.	0			c.C2090G						.						64	71	69					17																	72349069		2014	4178	6192	SO:0001583	missense	124602	exon15			ACAGCGCCCTCCC	AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"Kinesins"	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.2090C>G	17.37:g.72349069C>G	ENSP00000374566:p.Ala697Gly	99.0	0.0		135.0	34.0	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Missense_Mutation	SNP	ENST00000389916.4	37	CCDS32718.2	.	.	.	.	.	.	.	.	.	.	C	13.10	2.136354	0.37728	.	.	ENSG00000196169	ENST00000389916	T	0.70516	-0.49	5.08	1.68	0.24146	.	.	.	.	.	T	0.44456	0.1294	N	0.08118	0	0.09310	N	1	B	0.17667	0.023	B	0.14023	0.01	T	0.24368	-1.0162	9	0.25106	T	0.35	.	4.183	0.10385	0.0:0.5076:0.2367:0.2556	.	697	Q2TAC6	KIF19_HUMAN	G	697	ENSP00000374566:A697G	ENSP00000374566:A697G	A	+	2	0	KIF19	69860664	0.000000	0.05858	0.128000	0.21923	0.069000	0.16628	0.483000	0.22292	0.471000	0.27319	0.456000	0.33151	GCC	.	.		0.597	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209		G	72349069	C	G	72349069	3	3	372	1	0	0	0	0	1	0	0	0	8291	739	26	4	2148	4	KIF19	17	72349069	Missense_Mutation	SNP	C	TCGA-ZS-A9CF-01A-11D-A382-10	23408480	72349069	8846141	82	51492										
EVPL	2125	hgsc.bcm.edu	37	chr17	74004527	74004527	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	cccacactcctggtcggcctGgtcccgggccctctgcagct	11	19	1	0			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr17:74004527G>C	ENST00000301607.3	-	22	5012	c.4759C>G	c.(4759-4761)Cag>Gag	p.Q1587E	EVPL_ENST00000586740.1_Missense_Mutation_p.Q1609E|TEN1-CDK3_ENST00000567351.1_RNA	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	1587	Central fibrous rod domain.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						TGGTCGGCCTGGTCCCGGGCC	0.701																																					p.Q1587E		Atlas-SNP	.											.	EVPL	155	.	0			c.C4759G						.						6	7	7					17																	74004527		2151	4211	6362	SO:0001583	missense	2125	exon22			CGGCCTGGTCCCG	U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.4759C>G	17.37:g.74004527G>C	ENSP00000301607:p.Gln1587Glu	65.0	0.0		183.0	82.0	NM_001988	A0AUV5	Missense_Mutation	SNP	ENST00000301607.3	37	CCDS11737.1	.	.	.	.	.	.	.	.	.	.	G	4.116	0.019660	0.08006	.	.	ENSG00000167880	ENST00000301607	T	0.63255	-0.03	5.17	5.17	0.71159	.	0.758911	0.12398	N	0.472409	T	0.60327	0.2260	M	0.63428	1.95	0.09310	N	1	B;B	0.17465	0.022;0.01	B;B	0.10450	0.005;0.004	T	0.49051	-0.8979	10	0.20046	T	0.44	-32.1298	15.0738	0.72059	0.0:0.1422:0.8578:0.0	.	1609;1587	B7ZLH8;Q92817	.;EVPL_HUMAN	E	1587	ENSP00000301607:Q1587E	ENSP00000301607:Q1587E	Q	-	1	0	EVPL	71516122	1.000000	0.71417	0.814000	0.32528	0.848000	0.48234	3.515000	0.53429	2.413000	0.81919	0.561000	0.74099	CAG	.	.		0.701	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988		C	74004527	G	C	74004527	3	2	372	1	0	0	0	0	1	0	0	0	5294	1357	47	4	1346	4	EVPL	17	74004527	Missense_Mutation	SNP	G	TCGA-ZS-A9CF-01A-11D-A382-10	1655458	74004527	7190683	83	51493										
KIAA1632	57724	hgsc.bcm.edu	37	chr18	43505857	43505857	+	Nonsense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	aaaggcagttctttaaacaaGtatagagaaaccttattaaa	6	5	1	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr18:43505857G>C	ENST00000282041.5	-	14	2599	c.2565C>G	c.(2563-2565)taC>taG	p.Y855*		NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	855					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)					NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						CTTTAAACAAGTATAGAGAAA	0.303																																					p.Y855X		Atlas-SNP	.											.	EPG5	199	.	0			c.C2565G						.						60	54	56					18																	43505857		1818	4075	5893	SO:0001587	stop_gained	57724	exon14			AAACAAGTATAGA	AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"KIAA1632"	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.2565C>G	18.37:g.43505857G>C	ENSP00000282041:p.Tyr855*	187.0	0.0		229.0	155.0	NM_020964	A2BDF3|Q9H8C8	Nonsense_Mutation	SNP	ENST00000282041.5	37	CCDS11926.2	.	.	.	.	.	.	.	.	.	.	G	40	8.299130	0.98750	.	.	ENSG00000152223	ENST00000282041	.	.	.	5.47	2.72	0.32119	.	1.157670	0.05983	N	0.644630	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.6092	7.4008	0.26962	0.3981:0.0:0.6019:0.0	.	.	.	.	X	855	.	ENSP00000282041:Y855X	Y	-	3	2	EPG5	41759855	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	3.046000	0.49846	0.384000	0.24942	0.650000	0.86243	TAC	.	.		0.303	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		C	43505857	G	C	43505857	4	2	372	1	0	0	0	0	0	1	0	0	8258	1024	36	4	5298	4	KIAA1632	18	43505857	Nonsense_Mutation	SNP	G	TCGA-ZS-A9CF-01A-11D-A382-10		43505857	34571391	84	51494										
ABCA7	10347	hgsc.bcm.edu	37	chr19	1062215	1062215	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	gcacctcagcatgggatactGccctcaatccgatgccatct	8	15	3	0			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr19:1062215G>T	ENST00000263094.6	+	42	5846	c.5615G>T	c.(5614-5616)tGc>tTc	p.C1872F	ABCA7_ENST00000433129.1_Missense_Mutation_p.C1872F|ABCA7_ENST00000435683.2_Missense_Mutation_p.C1734F	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1872	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ATGGGATACTGCCCTCAATCC	0.682																																					p.C1872F		Atlas-SNP	.											.	ABCA7	174	.	0			c.G5615T						.						107	115	112					19																	1062215		2203	4300	6503	SO:0001583	missense	10347	exon42			GATACTGCCCTCA	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"ATP binding cassette transporters / subfamily A"	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.5615G>T	19.37:g.1062215G>T	ENSP00000263094:p.Cys1872Phe	106.0	0.0		67.0	30.0	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	37	CCDS12055.1	.	.	.	.	.	.	.	.	.	.	G	16.43	3.120353	0.56613	.	.	ENSG00000064687	ENST00000263094;ENST00000433129	D;D	0.93488	-3.23;-3.23	3.61	3.61	0.41365	ATPase, AAA+ type, core (1);ABC transporter-like (2);	.	.	.	.	D	0.96297	0.8792	M	0.81942	2.565	0.58432	D	0.999991	D;D	0.89917	1.0;0.999	D;D	0.75484	0.986;0.986	D	0.96820	0.9603	9	0.87932	D	0	.	13.98	0.64299	0.0:0.0:1.0:0.0	.	997;1872	D6W5Y0;Q8IZY2	.;ABCA7_HUMAN	F	1872	ENSP00000263094:C1872F;ENSP00000414062:C1872F	ENSP00000263094:C1872F	C	+	2	0	ABCA7	1013215	1.000000	0.71417	1.000000	0.80357	0.238000	0.25445	9.186000	0.94906	1.859000	0.53934	0.555000	0.69702	TGC	.	.		0.682	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112		T	1062215	G	T	1062215	3	4	372	1	0	0	0	0	1	0	0	0	37	1319	46	3	5777	3	ABCA7	19	1062215	Missense_Mutation	SNP	G	TCGA-ZS-A9CF-01A-11D-A382-10		1062215	58066768	85	51495										
GNA15	2769	hgsc.bcm.edu	37	chr19	3155884	3155884	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	atccattgtttcgagaacgtGatcgccctcatctacctggc	8	13	2	2			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr19:3155884G>T	ENST00000262958.3	+	5	936	c.678G>T	c.(676-678)gtG>gtT	p.V226V	AC005264.2_ENST00000587587.1_RNA	NM_002068.2	NP_002059.2	P30679	GNA15_HUMAN	guanine nucleotide binding protein (G protein), alpha 15 (Gq class)	226					activation of phospholipase C activity (GO:0007202)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			large_intestine(5)|lung(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;7.04e-05)|OV - Ovarian serous cystadenocarcinoma(105;5.08e-113)|Epithelial(107;6.19e-111)|all cancers(105;6.19e-103)|BRCA - Breast invasive adenocarcinoma(158;0.00145)|STAD - Stomach adenocarcinoma(1328;0.184)		TCGAGAACGTGATCGCCCTCA	0.592																																					p.V226V		Atlas-SNP	.											.	GNA15	40	.	0			c.G678T						.						192	150	164					19																	3155884		2203	4300	6503	SO:0001819	synonymous_variant	2769	exon5			GAACGTGATCGCC		CCDS12104.1	19p13.3	2008-07-16				ENSG00000060558			4383	protein-coding gene	gene with protein product		139314				1302014	Standard	NM_002068		Approved	GNA16	uc002lxf.2	P30679		ENST00000262958.3:c.678G>T	19.37:g.3155884G>T		109.0	0.0		79.0	46.0	NM_002068	E9KL40|E9KL47|O75247|Q53XK2	Silent	SNP	ENST00000262958.3	37	CCDS12104.1																																																																																			.	.		0.592	GNA15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452320.2	NM_002068		T	3155884	G	T	3155884	2	4	372	1	0	0	0	0	0	0	0	1	6511	1277	45	3		3	GNA15	19	3155884	Silent	SNP	G	TCGA-ZS-A9CF-01A-11D-A382-10	2093669	3155884	55973099	86	51496										
SLC27A1	376497	hgsc.bcm.edu	37	chr19	17597668	17597668	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	ggccaaggcgggcatggaggCcgcgctgctcaacgtgaacc	16	13	1	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr19:17597668C>A	ENST00000252595.7	+	2	561	c.464C>A	c.(463-465)gCc>gAc	p.A155D	SLC27A1_ENST00000442725.1_Missense_Mutation_p.A155D|CTD-3131K8.2_ENST00000596643.1_lincRNA|SLC27A1_ENST00000598424.1_5'UTR	NM_198580.1	NP_940982.1	Q6PCB7	S27A1_HUMAN	solute carrier family 27 (fatty acid transporter), member 1	155					adiponectin-activated signaling pathway (GO:0033211)|cardiolipin biosynthetic process (GO:0032049)|cellular lipid metabolic process (GO:0044255)|fatty acid metabolic process (GO:0006631)|long-chain fatty acid transport (GO:0015909)|medium-chain fatty acid transport (GO:0001579)|negative regulation of phospholipid biosynthetic process (GO:0071072)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phosphatidylglycerol biosynthetic process (GO:0006655)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylserine biosynthetic process (GO:0006659)|positive regulation of heat generation (GO:0031652)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|response to cold (GO:0009409)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	fatty acid transporter activity (GO:0015245)|nucleotide binding (GO:0000166)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						GGCATGGAGGCCGCGCTGCTC	0.706																																					p.A155D		Atlas-SNP	.											.	SLC27A1	97	.	0			c.C464A						.						15	18	17					19																	17597668		2185	4272	6457	SO:0001583	missense	376497	exon2			TGGAGGCCGCGCT	BC059399	CCDS32953.1	19p13.11	2013-07-15			ENSG00000130304	ENSG00000130304		"Acyl-CoA synthetase family", "Solute carriers"	10995	protein-coding gene	gene with protein product		600691				10873384	Standard	NM_198580		Approved	FATP1, FATP, MGC71751, FLJ00336, ACSVL5	uc002ngu.1	Q6PCB7	OTTHUMG00000182878	ENST00000252595.7:c.464C>A	19.37:g.17597668C>A	ENSP00000252595:p.Ala155Asp	75.0	0.0		40.0	20.0	NM_198580	A6NIH2|B7Z662	Missense_Mutation	SNP	ENST00000252595.7	37	CCDS32953.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.116454	0.77323	.	.	ENSG00000130304	ENST00000442725;ENST00000252595;ENST00000300969	T;T	0.43294	0.95;0.95	4.92	4.92	0.64577	AMP-dependent synthetase/ligase (1);	0.055037	0.64402	D	0.000001	T	0.70613	0.3244	M	0.91872	3.25	0.80722	D	1	D	0.61080	0.989	D	0.71656	0.974	T	0.77451	-0.2583	10	0.54805	T	0.06	.	15.6336	0.76933	0.0:1.0:0.0:0.0	.	155	Q6PCB7	S27A1_HUMAN	D	155;155;17	ENSP00000413424:A155D;ENSP00000252595:A155D	ENSP00000252595:A155D	A	+	2	0	SLC27A1	17458668	1.000000	0.71417	0.998000	0.56505	0.475000	0.33008	7.288000	0.78691	2.287000	0.76781	0.561000	0.74099	GCC	.	.		0.706	SLC27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464145.1	NM_198580		A	17597668	C	A	17597668	3	1	372	1	0	0	0	0	1	0	0	0	14540	739	26	3	470	3	SLC27A1	19	17597668	Missense_Mutation	SNP	C	TCGA-ZS-A9CF-01A-11D-A382-10	14441784	17597668	41531315	87	51497										
MEGF8	1954	hgsc.bcm.edu	37	chr19	42830443	42830443	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	gcactggttttggccttggcCgtgctggggtcgctgtcccc	15	13	0	0			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr19:42830443C>T	ENST00000251268.6	+	1	48	c.48C>T	c.(46-48)gcC>gcT	p.A16A	MEGF8_ENST00000334370.4_Silent_p.A16A	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	16					BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)			breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				TGGCCTTGGCCGTGCTGGGGT	0.697											OREG0025502	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A16A		Atlas-SNP	.											.	MEGF8	358	.	0			c.C48T						.						23	27	26					19																	42830443		1995	4141	6136	SO:0001819	synonymous_variant	1954	exon1			CTTGGCCGTGCTG	AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"HBV pre s2 binding protein 1"	604267	"EGF-like-domain, multiple 4", "chromosome 19 open reading frame 49"	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.48C>T	19.37:g.42830443C>T		337.0	0.0	911	267.0	127.0	NM_001271938	A8KAY0|O75097	Silent	SNP	ENST00000251268.6	37																																																																																				.	.		0.697	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410		T	42830443	C	T	42830443	2	4	372	1	0	0	0	0	0	0	0	1	9472	639	23	1		1	MEGF8	19	42830443	Silent	SNP	C	TCGA-ZS-A9CF-01A-11D-A382-10	25232775	42830443	16298540	88	51498										
CACNG8	59283	hgsc.bcm.edu	37	chr19	54485510	54485510	+	Nonsense_Mutation	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	tggccgtcaacatctacatcGagcgcagccgcgaggcgcac	12	15	2	0			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr19:54485510G>T	ENST00000270458.2	+	4	788	c.685G>T	c.(685-687)Gag>Tag	p.E229*	MIR935_ENST00000401179.1_RNA	NM_031895.5	NP_114101	Q8WXS5	CCG8_HUMAN	calcium channel, voltage-dependent, gamma subunit 8	229					calcium ion transport (GO:0006816)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			kidney(1)|large_intestine(3)|lung(8)|urinary_tract(1)	13	all_cancers(19;0.0385)|all_epithelial(19;0.0207)|all_lung(19;0.145)|Lung NSC(19;0.168)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.162)		CATCTACATCGAGCGCAGCCG	0.677																																					p.E229X		Atlas-SNP	.											.	CACNG8	29	.	0			c.G685T						.						36	27	30					19																	54485510		2200	4300	6500	SO:0001587	stop_gained	59283	exon4			TACATCGAGCGCA	AF288388	CCDS33104.1	19q13.4	2008-05-02			ENSG00000142408	ENSG00000142408		"Calcium channel subunits"	13628	protein-coding gene	gene with protein product		606900				11170751	Standard	NM_031895		Approved		uc002qcs.2	Q8WXS5	OTTHUMG00000064908	ENST00000270458.2:c.685G>T	19.37:g.54485510G>T	ENSP00000270458:p.Glu229*	75.0	0.0		34.0	29.0	NM_031895	Q9BXT0|Q9BY23	Nonsense_Mutation	SNP	ENST00000270458.2	37	CCDS33104.1	.	.	.	.	.	.	.	.	.	.	.	37	6.371487	0.97511	.	.	ENSG00000142408	ENST00000270458	.	.	.	1.82	1.82	0.25136	.	0.085246	0.45867	U	0.000329	.	.	.	.	.	.	0.80722	D	1.000000	.	.	.	.	.	.	.	.	.	.	0.23891	T	0.37	.	9.2411	0.37498	0.0:0.0:1.0:0.0	.	.	.	.	X	229	.	ENSP00000270458:E229X	E	+	1	0	CACNG8	59177322	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.630000	0.90987	0.998000	0.38996	0.281000	0.19383	GAG	.	.		0.677	CACNG8-001	KNOWN	non_ATG_start|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139361.3			T	54485510	G	T	54485510	4	4	372	1	0	0	0	0	0	1	0	0	2565	1059	37	1	699	1	CACNG8	19	54485510	Nonsense_Mutation	SNP	G	TCGA-ZS-A9CF-01A-11D-A382-10	11655067	54485510	4643473	89	51499										
ZIM2	23619	hgsc.bcm.edu	37	chr19	57286539	57286539	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	tgtctgttgaggtgtggcatGagatagaaggcttcagcaca	14	6	2	3			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr19:57286539G>T	ENST00000391708.3	-	12	1643	c.1101C>A	c.(1099-1101)ctC>ctA	p.L367L	AC006115.3_ENST00000597946.1_RNA|ZIM2_ENST00000599935.1_Silent_p.L367L|ZIM2_ENST00000221722.5_Silent_p.L367L|ZIM2_ENST00000593711.1_Silent_p.L367L|AC006115.3_ENST00000595954.1_RNA|ZIM2_ENST00000601070.1_Silent_p.L367L|AC006115.3_ENST00000594400.1_RNA	NM_001146326.1|NM_001146327.1	NP_001139798.1|NP_001139799.1	Q9NZV7	ZIM2_HUMAN	zinc finger, imprinted 2	367					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.L367L(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(20)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0314)		GGTGTGGCATGAGATAGAAGG	0.478																																					p.L367L		Atlas-SNP	.											ZIM2,bladder,carcinoma,0,2	ZIM2	511	2	1	Substitution - coding silent(1)	urinary_tract(1)	c.C1101A						.						128	111	117					19																	57286539		2203	4300	6503	SO:0001819	synonymous_variant	23619	exon11			TGGCATGAGATAG	AF166122	CCDS33123.1	19q13.4	2012-10-31				ENSG00000269699		"Zinc fingers, C2H2-type"	12875	protein-coding gene	gene with protein product							Standard	NM_015363		Approved	ZNF656		Q9NZV7		ENST00000391708.3:c.1101C>A	19.37:g.57286539G>T		90.0	0.0		70.0	59.0	NM_015363	Q2M3K1	Silent	SNP	ENST00000391708.3	37	CCDS33123.1																																																																																			.	.		0.478	ZIM2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416094.2			T	57286539	G	T	57286539	2	4	372	1	0	0	0	0	0	0	0	1	17699	1277	45	3		3	ZIM2	19	57286539	Silent	SNP	G	TCGA-ZS-A9CF-01A-11D-A382-10	2801029	57286539	1842444	90	51500										
ASXL1	171023	hgsc.bcm.edu	37	chr20	31024023	31024023	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	atggaagcagccccagttctTtaagggctttgaaggagcct	12	9	1	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr20:31024023T>C	ENST00000375687.4	+	13	3932	c.3508T>C	c.(3508-3510)Tta>Cta	p.L1170L	ASXL1_ENST00000306058.5_Silent_p.L1165L	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	1170					bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						CCCCAGTTCTTTAAGGGCTTT	0.517			"F, N, Mis"		"MDS, CMML"																																p.L1170L		Atlas-SNP	.		Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	.	ASXL1	1114	.	0			c.T3508C						.						64	67	66					20																	31024023		2203	4300	6503	SO:0001819	synonymous_variant	171023	exon12			AGTTCTTTAAGGG	AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456			18318	protein-coding gene	gene with protein product		612990	"additional sex combs like 1 (Drosophila)"			12657473	Standard	NM_015338		Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.3508T>C	20.37:g.31024023T>C		118.0	0.0		79.0	37.0	NM_015338	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Silent	SNP	ENST00000375687.4	37	CCDS13201.1																																																																																			.	.		0.517	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338		C	31024023	T	C	31024023	2	2	372	1	0	0	0	0	0	0	0	1	1066	1838	64	2		2	ASXL1	20	31024023	Silent	SNP	T	TCGA-ZS-A9CF-01A-11D-A382-10		31024023	32001497	91	51501										
BPIL3	128859	hgsc.bcm.edu	37	chr20	31622067	31622067	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	gtgggcatcttccaatgtgtGtccacaggcatgaccgtcac	11	12	2	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr20:31622067G>A	ENST00000349552.1	+	3	273	c.273G>A	c.(271-273)gtG>gtA	p.V91V		NM_174897.2	NP_777557.1	Q8NFQ5	BPIB6_HUMAN	BPI fold containing family B, member 6	91						extracellular region (GO:0005576)	lipid binding (GO:0008289)										TCCAATGTGTGTCCACAGGCA	0.562																																					p.V91V		Atlas-SNP	.											.	.	.	.	0			c.G273A						.						158	122	134					20																	31622067		2203	4300	6503	SO:0001819	synonymous_variant	128859	exon3			ATGTGTGTCCACA	AF465767	CCDS13211.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000167104	ENSG00000167104		"BPI fold containing"	16504	protein-coding gene	gene with protein product		614110	"bactericidal/permeability-increasing protein-like 3"	BPIL3		12185532, 21787333	Standard	NM_174897		Approved	LPLUNC6	uc010zuc.2	Q8NFQ5	OTTHUMG00000032238	ENST00000349552.1:c.273G>A	20.37:g.31622067G>A		81.0	0.0		46.0	20.0	NM_174897		Silent	SNP	ENST00000349552.1	37	CCDS13211.1																																																																																			.	.		0.562	BPIFB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078658.2	NM_174897		A	31622067	G	A	31622067	2	1	372	1	0	0	0	0	0	0	0	1	1495	1364	48	3		3	BPIL3	20	31622067	Silent	SNP	G	TCGA-ZS-A9CF-01A-11D-A382-10	598044	31622067	31403453	92	51502										
C20orf152	140894	hgsc.bcm.edu	37	chr20	34568456	34568456	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	cagaggatgagatccaggccGtctgtaacatcttgcaggtt	12	9	2	2			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr20:34568456G>A	ENST00000373973.3	+	4	492	c.319G>A	c.(319-321)Gtc>Atc	p.V107I	CNBD2_ENST00000349339.1_Missense_Mutation_p.V107I|CNBD2_ENST00000538900.1_Missense_Mutation_p.V107I			Q96M20	CNBD2_HUMAN	cyclic nucleotide binding domain containing 2	107																	GATCCAGGCCGTCTGTAACAT	0.542																																					p.V107I		Atlas-SNP	.											C20orf152,NS,carcinoma,-1,1	.	.	1	0			c.G319A						.						104	86	92					20																	34568456		2203	4300	6503	SO:0001583	missense	140894	exon4			CAGGCCGTCTGTA	AL359828	CCDS13270.1, CCDS56189.1	20q11.23	2012-11-15	2012-11-15	2012-11-15	ENSG00000149646	ENSG00000149646			16145	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 152", "cyclic nucleotide (cNMP) binding domain containing 1"	C20orf152, CNMPD1		11780052	Standard	NM_080834		Approved	dJ954P9.1	uc002xer.1	Q96M20	OTTHUMG00000032371	ENST00000373973.3:c.319G>A	20.37:g.34568456G>A	ENSP00000363084:p.Val107Ile	147.0	0.0		109.0	40.0	NM_080834	Q14C79|Q5JWY7|Q5T3S1|Q9BR36|Q9BWY5	Missense_Mutation	SNP	ENST00000373973.3	37		.	.	.	.	.	.	.	.	.	.	G	10.41	1.343799	0.24339	.	.	ENSG00000149646	ENST00000373973;ENST00000349339;ENST00000538900	D;D;D	0.83419	-1.72;-1.72;-1.72	5.15	4.21	0.49690	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);	0.218004	0.31601	N	0.007375	T	0.67859	0.2938	N	0.22421	0.69	0.21220	N	0.999758	B;B	0.20164	0.019;0.042	B;B	0.11329	0.004;0.006	T	0.50180	-0.8858	10	0.13108	T	0.6	-15.3993	8.5119	0.33222	0.1669:0.6557:0.1774:0.0	.	107;107	Q96M20;Q96M20-2	CT152_HUMAN;.	I	107	ENSP00000363084:V107I;ENSP00000340954:V107I;ENSP00000442729:V107I	ENSP00000340954:V107I	V	+	1	0	C20orf152	34031870	0.308000	0.24509	0.187000	0.23214	0.003000	0.03518	0.809000	0.27168	1.163000	0.42636	-0.165000	0.13383	GTC	.	.		0.542	CNBD2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000078960.2	NM_080834		A	34568456	G	A	34568456	3	1	372	1	0	0	0	0	1	0	0	0	2094	1145	40	1	333	1	C20orf152	20	34568456	Missense_Mutation	SNP	G	TCGA-ZS-A9CF-01A-11D-A382-10	2946389	34568456	28457064	93	51503										
NFATC2	4773	hgsc.bcm.edu	37	chr20	50139710	50139710	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	ccgagtttctcctctcgcccTgctcgcagggccccaggaac	10	18	2	0			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr20:50139710T>G	ENST00000396009.3	-	2	1289	c.1070A>C	c.(1069-1071)cAg>cCg	p.Q357P	NFATC2_ENST00000371564.3_Missense_Mutation_p.Q357P|NFATC2_ENST00000610033.1_Missense_Mutation_p.Q138P|NFATC2_ENST00000609943.1_Missense_Mutation_p.Q337P|NFATC2_ENST00000609507.1_Missense_Mutation_p.Q138P|NFATC2_ENST00000414705.1_Missense_Mutation_p.Q337P	NM_001258297.1|NM_173091.3	NP_001245226.1|NP_775114.1	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	357					B cell receptor signaling pathway (GO:0050853)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear transcription factor complex (GO:0044798)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)		EWSR1/NFATC2(9)	breast(2)|endometrium(7)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	53	Hepatocellular(150;0.248)					CCTCTCGCCCTGCTCGCAGGG	0.677																																					p.Q357P		Atlas-SNP	.											.	NFATC2	112	.	0			c.A1070C						.						57	69	65					20																	50139710		2203	4300	6503	SO:0001583	missense	4773	exon2			TCGCCCTGCTCGC	U43342, U43341	CCDS13437.1, CCDS33488.1, CCDS46614.1, CCDS68156.1, CCDS68157.1	20q13.2	2009-11-24			ENSG00000101096	ENSG00000101096		"Nuclear factor of activated T-cells"	7776	protein-coding gene	gene with protein product		600490				8202141	Standard	NM_012340		Approved	NF-ATP, NFATp, NFAT1	uc002xwd.4	Q13469	OTTHUMG00000032747	ENST00000396009.3:c.1070A>C	20.37:g.50139710T>G	ENSP00000379330:p.Gln357Pro	133.0	0.0		95.0	51.0	NM_012340	B5B2N8|B5B2N9|B5B2P0|B5B2P2|B5B2P3|Q13468|Q5TFW7|Q5TFW8|Q9NPX6|Q9NQH3|Q9UJR2	Missense_Mutation	SNP	ENST00000396009.3	37	CCDS13437.1	.	.	.	.	.	.	.	.	.	.	T	16.10	3.027888	0.54790	.	.	ENSG00000101096	ENST00000371564;ENST00000396009;ENST00000371567;ENST00000414705	T;T;T	0.16597	2.33;2.33;2.35	5.8	5.8	0.92144	.	0.314770	0.31577	N	0.007403	T	0.32971	0.0847	L	0.41492	1.28	0.54753	D	0.999989	D;D;D;D	0.76494	0.999;0.997;0.999;0.999	D;P;D;D	0.65874	0.939;0.889;0.939;0.939	T	0.02471	-1.1154	10	0.66056	D	0.02	-18.6322	16.1448	0.81559	0.0:0.0:0.0:1.0	.	337;337;357;357	B5B2N9;B5B2P2;Q13469;B5B2N8	.;.;NFAC2_HUMAN;.	P	357;357;138;337	ENSP00000360619:Q357P;ENSP00000379330:Q357P;ENSP00000396471:Q337P	ENSP00000360619:Q357P	Q	-	2	0	NFATC2	49573117	1.000000	0.71417	1.000000	0.80357	0.479000	0.33129	3.308000	0.51896	2.214000	0.71695	0.374000	0.22700	CAG	.	.		0.677	NFATC2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079730.2	NM_012340		G	50139710	T	G	50139710	3	3	372	1	0	0	0	0	1	0	0	0	10371	1580	55	5	1791	5	NFATC2	20	50139710	Missense_Mutation	SNP	T	TCGA-ZS-A9CF-01A-11D-A382-10	15571254	50139710	12885810	94	51504										
NCAM2	4685	hgsc.bcm.edu	37	chr21	22782603	22782603	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	ttgtattacagatgcccccaAgtttatatcaaaccaaacaa	4	10	1	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr21:22782603A>T	ENST00000400546.1	+	10	1454	c.1205A>T	c.(1204-1206)aAg>aTg	p.K402M	NCAM2_ENST00000284894.7_Missense_Mutation_p.K260M	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	402	Ig-like C2-type 5.				axonal fasciculation (GO:0007413)|neuron cell-cell adhesion (GO:0007158)|sensory perception of smell (GO:0007608)	axon (GO:0030424)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(4)|cervix(2)|endometrium(8)|kidney(6)|large_intestine(22)|liver(4)|lung(49)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	108		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		GATGCCCCCAAGTTTATATCA	0.284																																					p.K402M		Atlas-SNP	.											.	NCAM2	220	.	0			c.A1205T						.						30	28	29					21																	22782603		1792	4049	5841	SO:0001583	missense	4685	exon10			CCCCCAAGTTTAT		CCDS42910.1	21q21	2013-02-11			ENSG00000154654	ENSG00000154654		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7657	protein-coding gene	gene with protein product		602040				9226371	Standard	NM_004540		Approved	NCAM21, MGC51008	uc002yld.2	O15394	OTTHUMG00000078121	ENST00000400546.1:c.1205A>T	21.37:g.22782603A>T	ENSP00000383392:p.Lys402Met	247.0	0.0		328.0	127.0	NM_004540	A8MQ06|B7Z841|Q7Z7F2	Missense_Mutation	SNP	ENST00000400546.1	37	CCDS42910.1	.	.	.	.	.	.	.	.	.	.	A	16.94	3.259852	0.59321	.	.	ENSG00000154654	ENST00000400546;ENST00000284894	T;T	0.31769	1.48;1.48	4.77	4.77	0.60923	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.044865	0.85682	D	0.000000	T	0.46658	0.1404	M	0.81802	2.56	0.80722	D	1	P;P	0.41131	0.739;0.739	P;P	0.49637	0.617;0.518	T	0.51865	-0.8651	10	0.87932	D	0	-18.6622	10.2864	0.43570	0.8345:0.1654:0.0:0.0	.	260;402	B7Z5K2;O15394	.;NCAM2_HUMAN	M	402;260	ENSP00000383392:K402M;ENSP00000284894:K260M	ENSP00000284894:K260M	K	+	2	0	NCAM2	21704474	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	3.153000	0.50685	1.888000	0.54679	0.482000	0.46254	AAG	.	.		0.284	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540		T	22782603	A	T	22782603	3	4	372	1	0	0	0	0	1	0	0	0	10212	72	3	4	1243	4	NCAM2	21	22782603	Missense_Mutation	SNP	A	TCGA-ZS-A9CF-01A-11D-A382-10		22782603	25347292	95	51505										
SYNJ1	8867	hgsc.bcm.edu	37	chr21	34018849	34018849	+	Missense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	aagtaccaaggccggaacttGaagatggctggagatgctga	14	7	0	4			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr21:34018849G>A	ENST00000322229.7	-	23	3100	c.3101C>T	c.(3100-3102)tCa>tTa	p.S1034L	SYNJ1_ENST00000433931.2_Missense_Mutation_p.S1073L|SYNJ1_ENST00000382491.3_Missense_Mutation_p.S1029L|SYNJ1_ENST00000382499.2_Missense_Mutation_p.S1073L|SYNJ1_ENST00000357345.3_Missense_Mutation_p.S1034L			O43426	SYNJ1_HUMAN	synaptojanin 1	1034	Poly-Ser.|Pro-rich.				cell death (GO:0008219)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of synaptic vesicle uncoating (GO:1903390)|regulation of synaptic vesicle membrane organization (GO:1901632)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)	cytosol (GO:0005829)	inositol-polyphosphate 5-phosphatase activity (GO:0004445)|nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|lung(11)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	57						GCCGGAACTTGAAGATGGCTG	0.498																																					p.S1073L		Atlas-SNP	.											.	SYNJ1	253	.	0			c.C3218T						.						133	126	128					21																	34018849		2203	4300	6503	SO:0001583	missense	8867	exon24			GAACTTGAAGATG	AF009040	CCDS33539.1, CCDS33540.1, CCDS33539.2, CCDS33540.2, CCDS54483.1	21q22.2	2008-06-23			ENSG00000159082	ENSG00000159082			11503	protein-coding gene	gene with protein product		604297				9428629, 10773674	Standard	NM_203446		Approved	INPP5G	uc002yqh.2	O43426	OTTHUMG00000064926	ENST00000322229.7:c.3101C>T	21.37:g.34018849G>A	ENSP00000322234:p.Ser1034Leu	169.0	0.0		145.0	60.0	NM_203446	O43425|O94984|Q4KMR1	Missense_Mutation	SNP	ENST00000322229.7	37	CCDS54484.1	.	.	.	.	.	.	.	.	.	.	G	14.91	2.675994	0.47886	.	.	ENSG00000159082	ENST00000382491;ENST00000357345;ENST00000382499;ENST00000433931;ENST00000322229	D;D;D;D;D	0.93906	-2.42;-3.31;-3.31;-2.5;-2.47	5.42	5.42	0.78866	.	0.183657	0.48767	D	0.000168	D	0.88224	0.6379	L	0.27053	0.805	0.20074	N	0.999934	B;B;B;B;B	0.12013	0.0;0.001;0.001;0.005;0.001	B;B;B;B;B	0.09377	0.002;0.002;0.004;0.004;0.004	T	0.78836	-0.2047	10	0.45353	T	0.12	.	13.5147	0.61533	0.0748:0.0:0.9252:0.0	.	1029;1073;1034;1034;1034	B9EGN3;C9JFZ1;O43426-2;O43426;O43426-4	.;.;.;SYNJ1_HUMAN;.	L	1029;1034;1073;1073;1034	ENSP00000371931:S1029L;ENSP00000349903:S1034L;ENSP00000371939:S1073L;ENSP00000409667:S1073L;ENSP00000322234:S1034L	ENSP00000322234:S1034L	S	-	2	0	SYNJ1	32940720	0.613000	0.27009	0.626000	0.29213	0.995000	0.86356	3.760000	0.55235	2.529000	0.85273	0.655000	0.94253	TCA	.	.		0.498	SYNJ1-201	KNOWN	basic|CCDS	protein_coding	protein_coding				A	34018849	G	A	34018849	3	1	372	1	0	0	0	0	1	0	0	0	15467	1294	45	3	1681	3	SYNJ1	21	34018849	Missense_Mutation	SNP	G	TCGA-ZS-A9CF-01A-11D-A382-10	11236246	34018849	14111046	96	51506										
KRTAP10-9	386676	hgsc.bcm.edu	37	chr21	46047778	46047778	+	Silent	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	tgctgcagaccctcctcctcTgtgtccctcctctgccgccc	7	21	2	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr21:46047778T>G	ENST00000397911.3	+	1	739	c.690T>G	c.(688-690)tcT>tcG	p.S230S	TSPEAR_ENST00000323084.4_Intron|KRTAP10-9_ENST00000484861.1_Intron	NM_198690.2	NP_941963.2	P60411	KR109_HUMAN	keratin associated protein 10-9	230	25 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9						CCTCCTCCTCTGTGTCCCTCC	0.687																																					p.S230S		Atlas-SNP	.											.	KRTAP10-9	24	.	0			c.T690G						.						111	130	124					21																	46047778		2203	4300	6503	SO:0001819	synonymous_variant	386676	exon1			CTCCTCTGTGTCC	AJ566386	CCDS42961.1	21q22.3	2007-10-05			ENSG00000221837	ENSG00000221837		"Keratin associated proteins"	22971	protein-coding gene	gene with protein product				KRTAP18-9			Standard	NM_198690		Approved	KAP10.9, KAP18.9	uc002zfp.4	P60411	OTTHUMG00000057637	ENST00000397911.3:c.690T>G	21.37:g.46047778T>G		63.0	0.0		64.0	29.0	NM_198690	A2RRG1|A6NIR9|Q70LJ1	Silent	SNP	ENST00000397911.3	37	CCDS42961.1																																																																																			.	.		0.687	KRTAP10-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128040.1			G	46047778	T	G	46047778	2	3	372	1	0	0	0	0	0	0	0	1	8525	1567	55	5		5	KRTAP10-9	21	46047778	Silent	SNP	T	TCGA-ZS-A9CF-01A-11D-A382-10	12028929	46047778	2082117	97	51507										
PRAME	23532	hgsc.bcm.edu	37	chr22	22890574	22890574	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	gaggacaggggttggcactaAgccagaccatgctgggccgc	16	11	0	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chr22:22890574A>C	ENST00000398741.1	-	6	1751	c.1445T>G	c.(1444-1446)cTt>cGt	p.L482R	PRAME_ENST00000398743.2_Missense_Mutation_p.L482R|PRAME_ENST00000402697.1_Missense_Mutation_p.L482R|PRAME_ENST00000424204.2_Missense_Mutation_p.L466R|PRAME_ENST00000405655.3_Missense_Mutation_p.L482R|PRAME_ENST00000485532.1_5'Flank|PRAME_ENST00000543184.1_Missense_Mutation_p.L482R|PRAME_ENST00000539862.1_Missense_Mutation_p.L466R	NM_206955.1	NP_996838.1	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma	482	Mediates interaction with RARA.				apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	retinoic acid receptor binding (GO:0042974)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05)		READ - Rectum adenocarcinoma(21;0.0649)		GTTGGCACTAAGCCAGACCAT	0.587																																					p.L482R	Melanoma(73;1707 1838 15168 27201)	Atlas-SNP	.											.	PRAME	78	.	0			c.T1445G						.						118	111	113					22																	22890574		2203	4300	6503	SO:0001583	missense	23532	exon6			GCACTAAGCCAGA	U65011	CCDS13801.1	22q11.22	2013-01-17			ENSG00000185686	ENSG00000185686		"-"	9336	protein-coding gene	gene with protein product	"cancer/testis antigen 130"	606021		MAPE		9047241, 10591208	Standard	XM_006725402		Approved	CT130	uc002zwj.3	P78395	OTTHUMG00000151172	ENST00000398741.1:c.1445T>G	22.37:g.22890574A>C	ENSP00000381726:p.Leu482Arg	128.0	0.0		86.0	37.0	NM_206954	B2R6Y7|O43481|Q8IXN8	Missense_Mutation	SNP	ENST00000398741.1	37	CCDS13801.1	.	.	.	.	.	.	.	.	.	.	A	12.82	2.052525	0.36181	.	.	ENSG00000185686	ENST00000398743;ENST00000543184;ENST00000398741;ENST00000405655;ENST00000539862;ENST00000402697;ENST00000424204	T;T;T;T;T;T;T	0.51574	0.7;0.7;0.7;0.7;0.7;0.7;0.7	3.68	3.68	0.42216	.	0.466193	0.21690	N	0.070584	T	0.56455	0.1986	L	0.43923	1.385	0.09310	N	1	D	0.76494	0.999	D	0.72625	0.978	T	0.42949	-0.9421	10	0.87932	D	0	.	9.0179	0.36182	1.0:0.0:0.0:0.0	.	482	P78395	PRAME_HUMAN	R	482;482;482;482;466;482;466	ENSP00000381728:L482R;ENSP00000445675:L482R;ENSP00000381726:L482R;ENSP00000384343:L482R;ENSP00000445097:L466R;ENSP00000385198:L482R;ENSP00000407342:L466R	ENSP00000381726:L482R	L	-	2	0	PRAME	21220574	1.000000	0.71417	0.137000	0.22149	0.004000	0.04260	1.168000	0.31859	1.902000	0.55061	0.523000	0.50628	CTT	.	.		0.587	PRAME-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321644.1	NM_206953		C	22890574	A	C	22890574	3	2	372	1	0	0	0	0	1	0	0	0	12436	72	3	5	88	5	PRAME	22	22890574	Missense_Mutation	SNP	A	TCGA-ZS-A9CF-01A-11D-A382-10		22890574	28413992	98	51508										
MAGEB1	4112	hgsc.bcm.edu	37	chrX	30269467	30269467	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	aaccaccaagatgaaagtccTcgagtttttggccaagatga	9	9	0	4			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chrX:30269467T>C	ENST00000378981.3	+	4	1178	c.857T>C	c.(856-858)cTc>cCc	p.L286P	MAGEB1_ENST00000397548.2_Missense_Mutation_p.L286P|MAGEB1_ENST00000397550.1_Missense_Mutation_p.L286P	NM_002363.4	NP_002354.2	P43366	MAGB1_HUMAN	melanoma antigen family B, 1	286	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.									NS(2)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(8)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	32						ATGAAAGTCCTCGAGTTTTTG	0.507																																					p.L286P		Atlas-SNP	.											.	MAGEB1	76	.	0			c.T857C						.						135	113	121					X																	30269467		2202	4300	6502	SO:0001583	missense	4112	exon3			AAGTCCTCGAGTT		CCDS14222.1	Xp21.3	2009-03-17			ENSG00000214107	ENSG00000214107			6808	protein-coding gene	gene with protein product	"DSS/AHC critical interval MAGE superfamily 10", "cancer/testis antigen family 3, member 1"	300097				7761436, 9441743	Standard	NM_002363		Approved	MAGEL1, MAGE-Xp, DAM10, MGC9322, CT3.1	uc004dce.3	P43366	OTTHUMG00000021322	ENST00000378981.3:c.857T>C	X.37:g.30269467T>C	ENSP00000368264:p.Leu286Pro	94.0	0.0		93.0	6.0	NM_177415	B2RC79|O00601|O75862|Q6FHJ0|Q96CW8	Missense_Mutation	SNP	ENST00000378981.3	37	CCDS14222.1	.	.	.	.	.	.	.	.	.	.	T	10.11	1.261556	0.23051	.	.	ENSG00000214107	ENST00000378981;ENST00000397550;ENST00000397548	T;T;T	0.11169	2.8;2.8;2.8	3.86	3.86	0.44501	.	0.000000	0.64402	D	0.000003	T	0.42787	0.1218	H	0.97186	3.955	0.21416	N	0.999699	D	0.89917	1.0	D	0.83275	0.996	T	0.47420	-0.9119	10	0.87932	D	0	.	8.1385	0.31069	0.0:0.0:0.0:1.0	.	286	P43366	MAGB1_HUMAN	P	286	ENSP00000368264:L286P;ENSP00000380683:L286P;ENSP00000380681:L286P	ENSP00000368264:L286P	L	+	2	0	MAGEB1	30179388	0.142000	0.22610	0.004000	0.12327	0.069000	0.16628	3.262000	0.51538	1.737000	0.51674	0.417000	0.27973	CTC	.	.		0.507	MAGEB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056160.1	NM_002363		C	30269467	T	C	30269467	3	2	372	1	0	0	0	0	1	0	0	0	9181	1551	54	2	859	2	MAGEB1	23	30269467	Missense_Mutation	SNP	T	TCGA-ZS-A9CF-01A-11D-A382-10		30269467	125001093	99	51509										
FAM47B	170062	hgsc.bcm.edu	37	chrX	34962125	34962125	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	gtccgcggccttttgagagtCggatgccccatctccgcctg	12	15	1	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chrX:34962125C>T	ENST00000329357.5	+	1	1213	c.1177C>T	c.(1177-1179)Cgg>Tgg	p.R393W		NM_152631.2	NP_689844.2	Q8NA70	FA47B_HUMAN	family with sequence similarity 47, member B	393										breast(3)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	71						TTTTGAGAGTCGGATGCCCCA	0.587																																					p.R393W		Atlas-SNP	.											.	FAM47B	209	.	0			c.C1177T						.						54	49	51					X																	34962125		2202	4300	6502	SO:0001583	missense	170062	exon1			GAGAGTCGGATGC	BC035026	CCDS14236.1	Xp21.1	2004-08-09			ENSG00000189132	ENSG00000189132			26659	protein-coding gene	gene with protein product						14702039	Standard	NM_152631		Approved	FLJ35782	uc004ddi.2	Q8NA70	OTTHUMG00000021345	ENST00000329357.5:c.1177C>T	X.37:g.34962125C>T	ENSP00000328307:p.Arg393Trp	77.0	0.0		89.0	85.0	NM_152631	Q5JQN5|Q6PIG3	Missense_Mutation	SNP	ENST00000329357.5	37	CCDS14236.1	.	.	.	.	.	.	.	.	.	.	C	5.961	0.361232	0.11296	.	.	ENSG00000189132	ENST00000329357	T	0.16196	2.36	0.703	-0.729	0.11158	.	.	.	.	.	T	0.16214	0.0390	M	0.65498	2.005	0.09310	N	1	B	0.22414	0.069	B	0.12156	0.007	T	0.27468	-1.0073	8	0.66056	D	0.02	.	.	.	.	.	393	Q8NA70	FA47B_HUMAN	W	393	ENSP00000328307:R393W	ENSP00000328307:R393W	R	+	1	2	FAM47B	34872046	0.410000	0.25376	0.000000	0.03702	0.005000	0.04900	1.109000	0.31135	-0.345000	0.08325	0.418000	0.28097	CGG	.	.		0.587	FAM47B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056211.1	NM_152631		T	34962125	C	T	34962125	3	4	372	1	0	0	0	0	1	0	0	0	5578	875	31	1	1179	1	FAM47B	23	34962125	Missense_Mutation	SNP	C	TCGA-ZS-A9CF-01A-11D-A382-10	4692658	34962125	120308435	100	51510										
DRP2	1821	hgsc.bcm.edu	37	chrX	100496749	100496750	+	Missense_Mutation	DNP	CG	CG	TT													0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	tgtgggagaagttgacagccCgctgtgtggaccagcaccgt					rs369730985|rs368516281		TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	C|G	C|G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chrX:100496749_100496750CG>TT	ENST00000395209.3	+	7	1179_1180	c.652_653CG>TT	c.(652-654)CGc>TTc	p.R218F	DRP2_ENST00000538510.1_Missense_Mutation_p.R218F|DRP2_ENST00000541709.1_Missense_Mutation_p.R140F|DRP2_ENST00000402866.1_Missense_Mutation_p.R218F	NM_001939.2	NP_001930.2	Q13474	DRP2_HUMAN	dystrophin related protein 2	218					central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(3)|prostate(1)|skin(2)|urinary_tract(2)	31						GTTGACAGCCCGCTGTGTGGAC	0.559																																					p.R218C|p.R218L		Atlas-SNP	.											.	DRP2	98	.	0			c.C652T|c.G653T						.																																			SO:0001583	missense	1821	exon7			ACAGCCCGCTGTG|CAGCCCGCTGTGT	U43519	CCDS14480.2, CCDS55465.1	Xq22	2008-02-05			ENSG00000102385	ENSG00000102385			3032	protein-coding gene	gene with protein product		300052				8640231	Standard	NM_001939		Approved		uc004egz.2	Q13474	OTTHUMG00000022020	Exception_encountered	X.37:g.100496749_100496750delinsTT	ENSP00000378635:p.Arg218Phe	66.0	0.0		51.0	48.0	NM_001939	A6ZKI5|A8K1B0|B1B1F3|B4DIZ0	Missense_Mutation	SNP	ENST00000395209.3	37	CCDS14480.2																																																																																			.	.		0.559	DRP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057522.3	NM_001939		TT	100496750	CG	TT	100496749	3	4	372	1	0	0	0	0	1	0	0	0	4766	652	23	1	670	1	DRP2	23	100496749	Missense_Mutation	DNP	CG	TCGA-ZS-A9CF-01A-11D-A382-10	65534624	100496749	54773811	101	51511										
SERPINA7	6906	hgsc.bcm.edu	37	chrX	105279299	105279299	+	Nonsense_Mutation	SNP	G	G	A	1	0	0	1	0	1	1	0	1	1	0	1	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	ctggtgcatcatgggcacttGaacagtggtggtcttgtcta	13	8	3	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chrX:105279299G>A	ENST00000327674.4	-	2	1035	c.700C>T	c.(700-702)Caa>Taa	p.Q234*	SERPINA7_ENST00000487487.1_5'Flank|SERPINA7_ENST00000372563.1_Nonsense_Mutation_p.Q234*			P05543	THBG_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 7	234					aging (GO:0007568)|negative regulation of endopeptidase activity (GO:0010951)|post-embryonic development (GO:0009791)|regulation of proteolysis (GO:0030162)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to peptide hormone (GO:0043434)|response to prostaglandin E (GO:0034695)|response to vitamin A (GO:0033189)|thyroid hormone transport (GO:0070327)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	hormone binding (GO:0042562)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(14)|ovary(1)|skin(3)	24					Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	ATGGGCACTTGAACAGTGGTG	0.433																																					p.Q234X		Atlas-SNP	.											.	SERPINA7	72	.	0			c.C700T						.						224	189	201					X																	105279299		2203	4300	6503	SO:0001587	stop_gained	6906	exon3			GCACTTGAACAGT	M14091	CCDS14518.1	Xq21-q22	2014-02-18	2005-08-18		ENSG00000123561	ENSG00000123561		"Serine (or cysteine) peptidase inhibitors"	11583	protein-coding gene	gene with protein product	"thyroxin-binding globulin", "thyroxine-binding globulin", "alpha-1 antiproteinase, antitrypsin"	314200	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 7"	TBG		24172014	Standard	NM_000354		Approved		uc004eme.2	P05543	OTTHUMG00000022144	ENST00000327674.4:c.700C>T	X.37:g.105279299G>A	ENSP00000329374:p.Gln234*	81.0	0.0		86.0	75.0	NM_000354	D3DUX1	Nonsense_Mutation	SNP	ENST00000327674.4	37	CCDS14518.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.530213	0.85706	.	.	ENSG00000123561	ENST00000327674;ENST00000372563	.	.	.	4.41	0.112	0.14623	.	0.663946	0.14010	N	0.347545	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.5034	0.27530	0.0:0.1452:0.2693:0.5855	.	.	.	.	X	234	.	ENSP00000329374:Q234X	Q	-	1	0	SERPINA7	105165955	0.227000	0.23707	0.045000	0.18777	0.248000	0.25809	0.533000	0.23082	0.066000	0.16515	-0.209000	0.12711	CAA	.	.		0.433	SERPINA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057790.1	NM_000354		A	105279299	G	A	105279299	4	1	372	1	0	0	0	0	0	1	0	0	14109	1299	45	3	559	3	SERPINA7	23	105279299	Nonsense_Mutation	SNP	G	TCGA-ZS-A9CF-01A-11D-A382-10	4782550	105279299	49991261	102	51512										
ZDHHC9	51114	hgsc.bcm.edu	37	chrX	128957708	128957708	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	cccggggaggccggaagatcTtgcatgtgtaacagtatttc	13	9	1	1			TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chrX:128957708T>A	ENST00000357166.6	-	5	825	c.434A>T	c.(433-435)aAg>aTg	p.K145M	AL359542.1_ENST00000582964.1_RNA|ZDHHC9_ENST00000371064.3_Missense_Mutation_p.K145M|ZDHHC9_ENST00000491039.1_5'UTR	NM_016032.3	NP_057116.2	Q9Y397	ZDHC9_HUMAN	zinc finger, DHHC-type containing 9	145					peptidyl-L-cysteine S-palmitoylation (GO:0018230)|protein palmitoylation (GO:0018345)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)|palmitoyltransferase complex (GO:0002178)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|Ras palmitoyltransferase activity (GO:0043849)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)	19						CCGGAAGATCTTGCATGTGTA	0.512																																					p.K145M		Atlas-SNP	.											.	ZDHHC9	41	.	0			c.A434T						.						143	133	136					X																	128957708		2203	4300	6503	SO:0001583	missense	51114	exon4			AAGATCTTGCATG	AF151847	CCDS35395.1	Xq26.1	2008-02-05			ENSG00000188706	ENSG00000188706		"Zinc fingers, DHHC-type"	18475	protein-coding gene	gene with protein product		300646	"zinc finger, DHHC-type containing 10", "chromosome X open reading frame 11"	ZDHHC10, CXorf11		10810093	Standard	NM_001008222		Approved	ZNF379, CGI-89, ZNF380	uc004euw.3	Q9Y397	OTTHUMG00000022375	ENST00000357166.6:c.434A>T	X.37:g.128957708T>A	ENSP00000349689:p.Lys145Met	54.0	0.0		50.0	45.0	NM_001008222	B4F6G2|D3DTF9|Q59EK4|Q5JSW5|Q8WWS7|Q9BPY4|Q9NSP0|Q9NVL0|Q9NVR6	Missense_Mutation	SNP	ENST00000357166.6	37	CCDS35395.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	21.0|21.0	4.084348|4.084348	0.76642|0.76642	.|.	.|.	ENSG00000188706|ENSG00000188706	ENST00000357166;ENST00000371064;ENST00000406492|ENST00000433917	T;T;T|.	0.26810|.	1.71;1.71;1.71|.	5.66|5.66	5.66|5.66	0.87406|0.87406	Zinc finger, DHHC-type, palmitoyltransferase (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.73148|.	0.3550|.	M|M	0.71581|0.71581	2.175|2.175	0.80722|0.80722	D|D	1|1	D|.	0.56035|.	0.974|.	D|.	0.65233|.	0.933|.	T|.	0.73464|.	-0.3974|.	10|.	0.25106|.	T|.	0.35|.	-15.1815|-15.1815	14.5407|14.5407	0.67990|0.67990	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	145|.	Q9Y397|.	ZDHC9_HUMAN|.	M|X	145|105	ENSP00000349689:K145M;ENSP00000360103:K145M;ENSP00000383991:K145M|.	ENSP00000349689:K145M|.	K|R	-|-	2|1	0|2	ZDHHC9|ZDHHC9	128785389|128785389	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.922000|0.922000	0.55478|0.55478	7.667000|7.667000	0.83888|0.83888	1.894000|1.894000	0.54839|0.54839	0.483000|0.483000	0.47432|0.47432	AAG|AGA	.	.		0.512	ZDHHC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058213.1	NM_016032		A	128957708	T	A	128957708	3	1	372	1	0	0	0	0	1	0	0	0	17637	1609	56	4	688	4	ZDHHC9	23	128957708	Missense_Mutation	SNP	T	TCGA-ZS-A9CF-01A-11D-A382-10	23678409	128957708	26312852	103	51513										
SLC6A8	6535	hgsc.bcm.edu	37	chrX	152959837	152959837	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0776699029126214	8	1	1.64173228346457	1.26287098728044	1.8241469816273	0.193027325346615	0.751940625889747	0	cagctgtttgactactactcGgccagcggcaccaccctgct	9	16	0	1	rs1060453		TCGA-ZS-A9CF-01A-11D-A382-10	TCGA-ZS-A9CF-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2b7e988c-761a-40aa-bbf0-23064aa3a82c	5feaeaff-2fb4-4cfd-a652-27e3146e3877	g.chrX:152959837G>C	ENST00000253122.5	+	10	1907	c.1431G>C	c.(1429-1431)tcG>tcC	p.S477S	SLC6A8_ENST00000430077.2_Silent_p.S362S|SLC6A8_ENST00000485324.1_3'UTR	NM_001142805.1|NM_005629.3	NP_001136277.1|NP_005620.1	P48029	SC6A8_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 8	477					cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|creatine transmembrane transport (GO:1902598)|creatine transport (GO:0015881)|muscle contraction (GO:0006936)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	creatine transmembrane transporter activity (GO:0005308)|creatine:sodium symporter activity (GO:0005309)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)	13	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)				Creatine(DB00148)	ACTACTACTCGGCCAGCGGCA	0.652																																					p.S477S		Atlas-SNP	.											.	SLC6A8	34	.	0			c.G1431C						.						60	57	58					X																	152959837		2203	4300	6503	SO:0001819	synonymous_variant	6535	exon10			CTACTCGGCCAGC		CCDS14726.1, CCDS48190.1	Xq28	2013-07-19	2013-07-19		ENSG00000130821	ENSG00000130821		"Solute carriers"	11055	protein-coding gene	gene with protein product	"creatine transporter"	300036	"solute carrier family 6 (neurotransmitter transporter, creatine), member 8"			7774949	Standard	NM_001142805		Approved	CRTR, CT1	uc004fib.3	P48029	OTTHUMG00000024208	ENST00000253122.5:c.1431G>C	X.37:g.152959837G>C		81.0	0.0		81.0	78.0	NM_005629	B2KY47|B4DIA3|E9PFC0|Q13032|Q66I36	Silent	SNP	ENST00000253122.5	37	CCDS14726.1	.	.	.	.	.	.	.	.	.	.	g	4.576	0.106970	0.08780	.	.	ENSG00000130821	ENST00000442457	.	.	.	4.57	-9.13	0.00704	.	.	.	.	.	T	0.43765	0.1262	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51849	-0.8653	4	.	.	.	.	5.6539	0.17633	0.1448:0.346:0.4228:0.0865	.	.	.	.	P	162	.	.	R	+	2	0	SLC6A8	152613031	0.000000	0.05858	0.469000	0.27204	0.924000	0.55760	-4.544000	0.00218	-3.055000	0.00258	-1.177000	0.01723	CGG	.	.		0.652	SLC6A8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061003.1			C	152959837	G	C	152959837	2	2	372	1	0	0	0	0	0	0	0	1	14705	1103	39	4		4	SLC6A8	23	152959837	Silent	SNP	G	TCGA-ZS-A9CF-01A-11D-A382-10	24002129	152959837	2310723	104	51514										
HSPG2	3339	hgsc.bcm.edu	37	chr1	22178363	22178363	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	ccgttgctggcccggcagacGtactgtcccgcatcggcagg	14	15	0	1	rs552716935		TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr1:22178363G>A	ENST00000374695.3	-	54	7006	c.6927C>T	c.(6925-6927)taC>taT	p.Y2309Y	HSPG2_ENST00000430507.1_3'UTR	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2309	Ig-like C2-type 8.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	CCCGGCAGACGTACTGTCCCG	0.672													g|||	1	0.000199681	0	0	5008	,	,		17636	0.001		0	False		,,,				2504	0				p.Y2309Y		Atlas-SNP	.											.	HSPG2	311	.	0			c.C6927T						.						27	28	28					1																	22178363		2202	4300	6502	SO:0001819	synonymous_variant	3339	exon54			GCAGACGTACTGT	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"Proteoglycans / Extracellular Matrix : Other", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5273	protein-coding gene	gene with protein product	"perlecan proteoglycan"	142461	"Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.6927C>T	chr1.hg19:g.22178363G>A		102.0	0.0		82.0	4.0	NM_005529	Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	hg19	CCDS30625.1																																																																																			.	.		0.672	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		A	22178363	G	A	22178363	2	1	373	1	0	0	0	0	0	0	0	1	7439	1140	40	1		1	HSPG2	1	22178363	Silent	SNP	G	TCGA-ZS-A9CG-01A-11D-A36X-10		22178363	227072258	1	51515										
HSPG2	3339	hgsc.bcm.edu	37	chr1	22216583	22216583	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	tgaatctgagccccatccgcAttcccttccgagcccacatc	6	18	1	2			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr1:22216583A>T	ENST00000374695.3	-	6	544	c.465T>A	c.(463-465)aaT>aaA	p.N155K		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	155	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	CCCCATCCGCATTCCCTTCCG	0.612																																					p.N155K		Atlas-SNP	.											.	HSPG2	311	.	0			c.T465A						.						176	153	161					1																	22216583		2203	4300	6503	SO:0001583	missense	3339	exon6			ATCCGCATTCCCT	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"Proteoglycans / Extracellular Matrix : Other", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5273	protein-coding gene	gene with protein product	"perlecan proteoglycan"	142461	"Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.465T>A	chr1.hg19:g.22216583A>T	ENSP00000363827:p.Asn155Lys	160.0	0.0		125.0	15.0	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	hg19	CCDS30625.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.28|10.28	1.306944|1.306944	0.23821|0.23821	.|.	.|.	ENSG00000142798|ENSG00000142798	ENST00000412328|ENST00000374695;ENST00000439717	T|T;T	0.50001|0.76060	0.76|-0.99;0.76	5.44|5.44	-5.27|-5.27	0.02763|0.02763	.|SEA (2);	.|0.000000	.|0.42294	.|D	.|0.000728	T|T	0.68842|0.68842	0.3045|0.3045	L|L	0.29908|0.29908	0.895|0.895	0.27704|0.27704	N|N	0.945691|0.945691	B|D	0.34015|0.57257	0.435|0.979	B|P	0.30572|0.54270	0.117|0.747	T|T	0.71381|0.71381	-0.4610|-0.4610	8|10	.|0.66056	.|D	.|0.02	.|.	14.7541|14.7541	0.69549|0.69549	0.7515:0.0:0.2485:0.0|0.7515:0.0:0.2485:0.0	.|.	78|155	Q5SZI5|P98160	.|PGBM_HUMAN	K|K	78|155;121	ENSP00000405412:M78K|ENSP00000363827:N155K;ENSP00000395884:N121K	.|ENSP00000363827:N155K	M|N	-|-	2|3	0|2	HSPG2|HSPG2	22089170|22089170	0.000000|0.000000	0.05858|0.05858	0.007000|0.007000	0.13788|0.13788	0.150000|0.150000	0.21749|0.21749	-0.554000|-0.554000	0.06006|0.06006	-1.324000|-1.324000	0.02272|0.02272	-0.242000|-0.242000	0.12053|0.12053	ATG|AAT	.	.		0.612	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		T	22216583	A	T	22216583	3	4	373	1	0	0	0	0	1	0	0	0	7439	214	8	4	13078	4	HSPG2	1	22216583	Missense_Mutation	SNP	A	TCGA-ZS-A9CG-01A-11D-A36X-10	38220	22216583	227034038	2	51516										
NES	10763	hgsc.bcm.edu	37	chr1	156639240	156639240	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	agagcactcccctcctcctcCtgaaaggggctccctcggtc	9	18	0	2			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr1:156639240C>T	ENST00000368223.3	-	4	4872	c.4740G>A	c.(4738-4740)caG>caA	p.Q1580Q		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin	1580	Tail.				brain development (GO:0007420)|cell projection morphogenesis (GO:0048858)|central nervous system development (GO:0007417)|embryonic camera-type eye development (GO:0031076)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of catalytic activity (GO:0043086)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein binding (GO:0032091)|positive regulation of intermediate filament depolymerization (GO:0030844)|positive regulation of neural precursor cell proliferation (GO:2000179)|stem cell proliferation (GO:0072089)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	intermediate filament binding (GO:0019215)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(30)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(4)	64	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CCTCCTCCTCCTGAAAGGGGC	0.592																																					p.Q1580Q		Atlas-SNP	.											.	NES	196	.	0			c.G4740A						.						86	78	81					1																	156639240		2203	4300	6503	SO:0001819	synonymous_variant	10763	exon4			CTCCTCCTGAAAG	X65964	CCDS1151.1	1q23	2013-01-16			ENSG00000132688	ENSG00000132688		"Intermediate filaments type IV"	7756	protein-coding gene	gene with protein product		600915				1478958, 9104587	Standard	NM_006617		Approved	FLJ21841	uc001fpq.3	P48681	OTTHUMG00000034299	ENST00000368223.3:c.4740G>A	chr1.hg19:g.156639240C>T		113.0	0.0		121.0	6.0	NM_006617	O00552|Q3LIF5|Q5SYZ6	Silent	SNP	ENST00000368223.3	hg19	CCDS1151.1																																																																																			.	.		0.592	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	NM_006617		T	156639240	C	T	156639240	2	4	373	1	0	0	0	0	0	0	0	1	10346	680	24	3		3	NES	1	156639240	Silent	SNP	C	TCGA-ZS-A9CG-01A-11D-A36X-10	134422657	156639240	92611381	3	51517										
SPTA1	6708	hgsc.bcm.edu	37	chr1	158648295	158648295	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	ttcacctcattttgcttagaCtgaattaagggtaggtcagg	10	7	3	2			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr1:158648295C>A	ENST00000368147.4	-	6	888	c.708G>T	c.(706-708)caG>caT	p.Q236H		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	236					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TTTGCTTAGACTGAATTAAGG	0.403																																					p.Q236H		Atlas-SNP	.											.	SPTA1	720	.	0			c.G708T						.						73	69	70					1																	158648295		1872	4104	5976	SO:0001583	missense	6708	exon6			CTTAGACTGAATT	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.708G>T	chr1.hg19:g.158648295C>A	ENSP00000357129:p.Gln236His	73.0	0.0		83.0	28.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	C	11.44	1.638245	0.29157	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.53206	0.63;0.63	4.66	2.78	0.32641	.	0.956614	0.08483	N	0.939112	T	0.28234	0.0697	L	0.33245	0.995	0.09310	N	1	B	0.29301	0.241	B	0.42495	0.389	T	0.50947	-0.8767	10	0.46703	T	0.11	.	9.663	0.39967	0.0:0.8288:0.0:0.1712	.	236	P02549	SPTA1_HUMAN	H	236	ENSP00000357130:Q236H;ENSP00000357129:Q236H	ENSP00000357129:Q236H	Q	-	3	2	SPTA1	156914919	0.629000	0.27146	0.003000	0.11579	0.004000	0.04260	1.691000	0.37721	0.688000	0.31529	0.650000	0.86243	CAG	.	.		0.403	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		A	158648295	C	A	158648295	3	1	373	1	0	0	0	0	1	0	0	0	15131	564	20	3	6739	3	SPTA1	1	158648295	Missense_Mutation	SNP	C	TCGA-ZS-A9CG-01A-11D-A36X-10	2009055	158648295	90602326	4	51518										
SLAMF8	56833	hgsc.bcm.edu	37	chr1	159802783	159802783	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	caacatcagcgaaataacctAtagctggcgacgggagacaa	10	10	1	1			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr1:159802783A>G	ENST00000289707.5	+	3	634	c.485A>G	c.(484-486)tAt>tGt	p.Y162C	C1orf204_ENST00000491974.1_5'Flank|SLAMF8_ENST00000368104.4_Missense_Mutation_p.Y53C|SLAMF8_ENST00000471286.1_3'UTR	NM_020125.2	NP_064510.1	Q9P0V8	SLAF8_HUMAN	SLAM family member 8	162	Ig-like C2-type.				cellular response to drug (GO:0035690)|defense response to bacterium (GO:0042742)|phagosome acidification (GO:0090383)|regulation of kinase activity (GO:0043549)|regulation of NAD(P)H oxidase activity (GO:0033860)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			endometrium(2)|large_intestine(4)|lung(6)	12	all_hematologic(112;0.0597)					GAAATAACCTATAGCTGGCGA	0.532																																					p.Y162C		Atlas-SNP	.											.	SLAMF8	30	.	0			c.A485G						.						103	102	102					1																	159802783		2203	4300	6503	SO:0001583	missense	56833	exon3			TAACCTATAGCTG	AF146761	CCDS1188.1	1q23.1	2013-01-11			ENSG00000158714	ENSG00000158714		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	21391	protein-coding gene	gene with protein product		606620				11313408	Standard	NM_020125		Approved	BLAME, SBBI42, CD353	uc001fue.4	Q9P0V8	OTTHUMG00000035433	ENST00000289707.5:c.485A>G	chr1.hg19:g.159802783A>G	ENSP00000289707:p.Tyr162Cys	163.0	0.0		194.0	94.0	NM_020125	Q32MC6|Q5VU15	Missense_Mutation	SNP	ENST00000289707.5	hg19	CCDS1188.1	.	.	.	.	.	.	.	.	.	.	A	14.26	2.483628	0.44147	.	.	ENSG00000158714	ENST00000289707;ENST00000368104	T;T	0.58506	0.33;0.33	4.6	4.6	0.57074	Immunoglobulin-like (1);	0.151754	0.45606	D	0.000346	T	0.67813	0.2933	M	0.77820	2.39	0.41646	D	0.989108	D	0.89917	1.0	D	0.91635	0.999	T	0.73421	-0.3988	10	0.87932	D	0	-12.1505	10.3147	0.43729	1.0:0.0:0.0:0.0	.	162	Q9P0V8	SLAF8_HUMAN	C	162;53	ENSP00000289707:Y162C;ENSP00000357084:Y53C	ENSP00000289707:Y162C	Y	+	2	0	SLAMF8	158069407	0.995000	0.38212	0.973000	0.42090	0.400000	0.30750	4.345000	0.59360	1.927000	0.55829	0.528000	0.53228	TAT	.	.		0.532	SLAMF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085983.1	NM_020125		G	159802783	A	G	159802783	3	3	373	1	0	0	0	0	1	0	0	0	14385	449	16	2	495	2	SLAMF8	1	159802783	Missense_Mutation	SNP	A	TCGA-ZS-A9CG-01A-11D-A36X-10	1154488	159802783	89447838	5	51519										
FAM5C	339479	hgsc.bcm.edu	37	chr1	190067645	190067645	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	ataacactgcaggggtaggtCcaacttagtccgctcccagt	10	12	0	0			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr1:190067645C>A	ENST00000367462.3	-	8	2035	c.1804G>T	c.(1804-1806)Gac>Tac	p.D602Y	BRINP3_ENST00000534846.1_Missense_Mutation_p.D500Y	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	602					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)											AGGGGTAGGTCCAACTTAGTC	0.468																																					p.D602Y		Atlas-SNP	.											FAM5C,NS,carcinoma,0,1	FAM5C	343	.	0			c.G1804T						.						213	220	218					1																	190067645		2203	4300	6503	SO:0001583	missense	339479	exon8			GTAGGTCCAACTT	AB111893	CCDS1373.1	1q31.1	2013-09-18	2013-09-18	2013-09-18	ENSG00000162670	ENSG00000162670			22393	protein-coding gene	gene with protein product			"family with sequence similarity 5, member C"	FAM5C		16018821, 15193423	Standard	NM_199051		Approved	DBCCR1L, DBCCR1L1	uc001gse.1	Q76B58	OTTHUMG00000035533	ENST00000367462.3:c.1804G>T	chr1.hg19:g.190067645C>A	ENSP00000356432:p.Asp602Tyr	104.0	0.0		162.0	45.0	NM_199051	B3KVP1|B7Z260|O95726|Q2M330	Missense_Mutation	SNP	ENST00000367462.3	hg19	CCDS1373.1	.	.	.	.	.	.	.	.	.	.	C	17.85	3.489771	0.64074	.	.	ENSG00000162670	ENST00000367462;ENST00000534846	T;T	0.23552	2.15;1.9	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.45994	0.1370	M	0.68952	2.095	0.80722	D	1	D;D	0.63046	0.992;0.986	P;P	0.57548	0.823;0.552	T	0.41945	-0.9480	10	0.87932	D	0	.	17.1246	0.86710	0.0:1.0:0.0:0.0	.	500;602	B7Z260;Q76B58	.;FAM5C_HUMAN	Y	602;500	ENSP00000356432:D602Y;ENSP00000438022:D500Y	ENSP00000356432:D602Y	D	-	1	0	FAM5C	188334268	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.734000	0.84928	2.645000	0.89757	0.585000	0.79938	GAC	.	.		0.468	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086278.1	NM_199051		A	190067645	C	A	190067645	3	1	373	1	0	0	0	0	1	0	0	0	5602	855	30	3	500	3	FAM5C	1	190067645	Missense_Mutation	SNP	C	TCGA-ZS-A9CG-01A-11D-A36X-10	30264862	190067645	59182976	6	51520										
GPR25	2848	hgsc.bcm.edu	37	chr1	200842406	200842406	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	tggataccttcgtgctgcacCtggcggcagctgacctgggc	14	13	0	1			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr1:200842406C>T	ENST00000304244.2	+	1	324	c.241C>T	c.(241-243)Ctg>Ttg	p.L81L		NM_005298.2	NP_005289.2	O00155	GPR25_HUMAN	G protein-coupled receptor 25	81					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			large_intestine(1)|lung(2)|ovary(1)|skin(1)	5						CGTGCTGCACCTGGCGGCAGC	0.751																																					p.L81L		Atlas-SNP	.											.	GPR25	23	.	0			c.C241T						.						7	7	7					1																	200842406		2082	3984	6066	SO:0001819	synonymous_variant	2848	exon1			CTGCACCTGGCGG	U91939	CCDS1405.1	1q32.1	2012-08-21			ENSG00000170128	ENSG00000170128		"GPCR / Class A : Orphans"	4480	protein-coding gene	gene with protein product		602174				9020062	Standard	NM_005298		Approved		uc001gvn.2	O00155	OTTHUMG00000035788	ENST00000304244.2:c.241C>T	chr1.hg19:g.200842406C>T		92.0	0.0		101.0	50.0	NM_005298	A0AVJ5	Silent	SNP	ENST00000304244.2	hg19	CCDS1405.1																																																																																			.	.		0.751	GPR25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087056.1	NM_005298		T	200842406	C	T	200842406	2	4	373	1	0	0	0	0	0	0	0	1	6691	680	24	3		3	GPR25	1	200842406	Silent	SNP	C	TCGA-ZS-A9CG-01A-11D-A36X-10	10774761	200842406	48408215	7	51521										
IKBKE	9641	hgsc.bcm.edu	37	chr1	206658535	206658535	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	cctttgtgccccacagctagCggaggtcctctccagatgct	10	15	1	1			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr1:206658535C>T	ENST00000367120.3	+	15	1881	c.1508C>T	c.(1507-1509)gCg>gTg	p.A503V	IKBKE_ENST00000537984.1_Missense_Mutation_p.A418V	NM_001193322.1|NM_014002.3	NP_001180251.1|NP_054721.1	Q14164	IKKE_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase epsilon	503	Interaction with DDX3X.				immune response (GO:0006955)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of type I interferon production (GO:0032480)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein phosphorylation (GO:0006468)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|NF-kappaB-inducing kinase activity (GO:0004704)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|ovary(3)|skin(2)	32	Breast(84;0.137)					CCACAGCTAGCGGAGGTCCTC	0.627																																					p.A503V		Atlas-SNP	.											.	IKBKE	77	.	0			c.C1508T						.						44	43	43					1																	206658535		2203	4300	6503	SO:0001583	missense	9641	exon15			AGCTAGCGGAGGT	AB016590	CCDS30996.1, CCDS53464.1, CCDS73019.1	1q31	2014-05-06			ENSG00000143466				14552	protein-coding gene	gene with protein product		605048				10421793, 10882136	Standard	NM_001193321		Approved	IKKE, IKK-i, KIAA0151	uc001hdz.2	Q14164	OTTHUMG00000184613	ENST00000367120.3:c.1508C>T	chr1.hg19:g.206658535C>T	ENSP00000356087:p.Ala503Val	180.0	0.0		194.0	45.0	NM_001193322	D3DT78|Q3B754|Q3KR43|Q5JTS6	Missense_Mutation	SNP	ENST00000367120.3	hg19	CCDS30996.1	.	.	.	.	.	.	.	.	.	.	C	14.90	2.672830	0.47781	.	.	ENSG00000143466	ENST00000367120;ENST00000537984	T;T	0.17054	2.3;2.3	5.24	2.13	0.27403	.	0.924949	0.09269	N	0.825439	T	0.08846	0.0219	N	0.12182	0.205	0.09310	N	1	B;B	0.14438	0.01;0.005	B;B	0.08055	0.002;0.003	T	0.28267	-1.0049	10	0.38643	T	0.18	1.0507	4.6448	0.12566	0.2017:0.5885:0.1222:0.0876	.	418;503	Q3B754;Q14164	.;IKKE_HUMAN	V	503;418	ENSP00000356087:A503V;ENSP00000444529:A418V	ENSP00000356087:A503V	A	+	2	0	IKBKE	204725158	0.014000	0.17966	0.095000	0.20976	0.696000	0.40369	0.091000	0.15046	1.199000	0.43173	0.563000	0.77884	GCG	.	.		0.627	IKBKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088484.1			T	206658535	C	T	206658535	3	4	373	1	0	0	0	0	1	0	0	0	7621	768	27	1	1558	1	IKBKE	1	206658535	Missense_Mutation	SNP	C	TCGA-ZS-A9CG-01A-11D-A36X-10	5816129	206658535	42592086	8	51522										
ALMS1	7840	hgsc.bcm.edu	37	chr2	73613037	73613037	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	atggccgggcgagctggaggAggaggaggaggaggaggagg	25	4	0	0	rs61156725|rs72319667|rs3074417	byFrequency	TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr2:73613037A>T	ENST00000264448.6	+	1	152	c.41A>T	c.(40-42)gAg>gTg	p.E14V	ALMS1_ENST00000377715.1_Missense_Mutation_p.E14V|ALMS1_ENST00000409009.1_Missense_Mutation_p.E14V	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	14	Glu-rich.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.E27_E28delEE(1)		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						GAGCTggaggaggaggaggag	0.697																																					p.E14V		Atlas-SNP	.											.	ALMS1	384	.	1	Deletion - In frame(1)	ovary(1)	c.A41T						.						3	4	4					2																	73613037		1515	3244	4759	SO:0001583	missense	7840	exon1			TGGAGGAGGAGGA	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.41A>T	chr2.hg19:g.73613037A>T	ENSP00000264448:p.Glu14Val	145.0	0.0		197.0	29.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	A	15.37	2.813706	0.50527	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.26660	2.37;2.58;1.72	3.19	3.19	0.36642	.	0.259523	0.20097	U	0.099311	T	0.31358	0.0794	N	0.19112	0.55	0.24255	N	0.995306	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.02698	-1.1122	10	0.87932	D	0	.	8.1308	0.31027	1.0:0.0:0.0:0.0	.	14;14	B8ZZJ3;Q8TCU4	.;ALMS1_HUMAN	V	14	ENSP00000386627:E14V;ENSP00000264448:E14V;ENSP00000366944:E14V	ENSP00000264448:E14V	E	+	2	0	ALMS1	73466545	1.000000	0.71417	1.000000	0.80357	0.821000	0.46438	3.230000	0.51286	1.682000	0.51000	0.397000	0.26171	GAG	.	.		0.697	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		T	73613037	A	T	73613037	3	4	373	1	0	0	0	0	1	0	0	0	535	304	11	4	43	4	ALMS1	2	73613037	Missense_Mutation	SNP	A	TCGA-ZS-A9CG-01A-11D-A36X-10		73613037	169586336	9	51523			1	74		2	2	29	N	G_A	7.778297e-05
ALMS1	7840	hgsc.bcm.edu	37	chr2	73613065	73613065	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	gaggaggaggaggaggaggaGgaggaagaggaggaggctgc	25	2	0	1			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr2:73613065G>A	ENST00000264448.6	+	1	180	c.69G>A	c.(67-69)gaG>gaA	p.E23E	ALMS1_ENST00000377715.1_Silent_p.E23E|ALMS1_ENST00000409009.1_Silent_p.E23E	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	23	Glu-rich.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				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						aggaggaggaggaggaagagg	0.687																																					p.E23E		Atlas-SNP	.											.	ALMS1	384	.	0			c.G69A						.						6	9	8					2																	73613065		1849	3831	5680	SO:0001819	synonymous_variant	7840	exon1			GGAGGAGGAGGAA	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.69G>A	chr2.hg19:g.73613065G>A		543.0	0.0		460.0	26.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	hg19	CCDS42697.1																																																																																			.	.		0.687	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		A	73613065	G	A	73613065	2	1	373	1	0	0	0	0	0	0	0	1	535	991	35	3		3	ALMS1	2	73613065	Silent	SNP	G	TCGA-ZS-A9CG-01A-11D-A36X-10	28	73613065	169586308	10	51524			1	74		2	2	29	N	G_A	7.778297e-05
SESTD1	91404	hgsc.bcm.edu	37	chr2	180008343	180008343	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	attaccttctgttgaatctcTtctaactgtgtgcgcttgct	7	10	3	1			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr2:180008343T>A	ENST00000428443.3	-	9	1141	c.825A>T	c.(823-825)gaA>gaT	p.E275D		NM_178123.4	NP_835224.3	Q86VW0	SESD1_HUMAN	SEC14 and spectrin domains 1	275							phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(3)	30			OV - Ovarian serous cystadenocarcinoma(117;0.0344)|Epithelial(96;0.0531)|all cancers(119;0.147)			GTTGAATCTCTTCTAACTGTG	0.373																																					p.E275D		Atlas-SNP	.											.	SESTD1	66	.	0			c.A825T						.						144	139	141					2																	180008343		2203	4300	6503	SO:0001583	missense	91404	exon9			AATCTCTTCTAAC	AK096232	CCDS33338.1	2q31.3	2014-01-28			ENSG00000187231	ENSG00000187231			18379	protein-coding gene	gene with protein product						12837271	Standard	NM_178123		Approved	DKFZp434O0515, Solo	uc002uni.4	Q86VW0	OTTHUMG00000154554	ENST00000428443.3:c.825A>T	chr2.hg19:g.180008343T>A	ENSP00000415332:p.Glu275Asp	77.0	0.0		78.0	28.0	NM_178123	Q53R38|Q53SP3|Q5GM69|Q8N6M1|Q96LQ2	Missense_Mutation	SNP	ENST00000428443.3	hg19	CCDS33338.1	.	.	.	.	.	.	.	.	.	.	T	13.04	2.117028	0.37339	.	.	ENSG00000187231	ENST00000428443	T	0.35789	1.29	6.07	1.15	0.20763	.	0.086607	0.85682	D	0.000000	T	0.12305	0.0299	N	0.03608	-0.345	0.45502	D	0.998462	B	0.02656	0.0	B	0.04013	0.001	T	0.10154	-1.0642	9	.	.	.	-26.6991	4.9016	0.13777	0.1875:0.5082:0.0:0.3043	.	275	Q86VW0	SESD1_HUMAN	D	275	ENSP00000415332:E275D	.	E	-	3	2	SESTD1	179716588	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.802000	0.27069	0.202000	0.20498	-0.250000	0.11733	GAA	.	.		0.373	SESTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335916.2	NM_178123		A	180008343	T	A	180008343	3	1	373	1	0	0	0	0	1	0	0	0	14142	1606	56	4	1305	4	SESTD1	2	180008343	Missense_Mutation	SNP	T	TCGA-ZS-A9CG-01A-11D-A36X-10	106395278	180008343	63191030	11	51525										
NDUFS1	4719	hgsc.bcm.edu	37	chr2	206994823	206994823	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	gatacttaccttgataaataAtgaaacaatcctttggcaaa	5	7	0	2			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr2:206994823A>C	ENST00000233190.6	-	15	1963	c.1697T>G	c.(1696-1698)aTt>aGt	p.I566S	NDUFS1_ENST00000440274.1_Missense_Mutation_p.I530S|NDUFS1_ENST00000449699.1_Missense_Mutation_p.I566S|NDUFS1_ENST00000423725.1_Missense_Mutation_p.I509S|NDUFS1_ENST00000455934.2_Missense_Mutation_p.I580S|NDUFS1_ENST00000457011.1_Missense_Mutation_p.I450S|NDUFS1_ENST00000432169.1_Missense_Mutation_p.I455S	NM_005006.6	NP_004997.4	P28331	NDUS1_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 1, 75kDa (NADH-coenzyme Q reductase)	566					apoptotic mitochondrial changes (GO:0008637)|ATP metabolic process (GO:0046034)|cellular metabolic process (GO:0044237)|cellular respiration (GO:0045333)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|reactive oxygen species metabolic process (GO:0072593)|regulation of mitochondrial membrane potential (GO:0051881)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial respiratory chain complex I (GO:0005747)	2 iron, 2 sulfur cluster binding (GO:0051537)|4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(15)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						TTGATAAATAATGAAACAATC	0.398																																					p.I580S		Atlas-SNP	.											.	NDUFS1	82	.	0			c.T1739G						.						94	93	93					2																	206994823		2203	4300	6503	SO:0001583	missense	4719	exon15			TAAATAATGAAAC		CCDS2366.1, CCDS56162.1, CCDS56163.1, CCDS56164.1, CCDS56165.1	2q33-q34	2011-07-04	2002-08-29		ENSG00000023228	ENSG00000023228	1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7707	protein-coding gene	gene with protein product	"complex I 75kDa subunit", "NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial"	157655	"NADH dehydrogenase (ubiquinone) Fe-S protein 1 (75kD) (NADH-coenzyme Q reductase)"			1935949	Standard	NM_005006		Approved	CI-75k	uc010ziq.2	P28331	OTTHUMG00000132892	ENST00000233190.6:c.1697T>G	chr2.hg19:g.206994823A>C	ENSP00000233190:p.Ile566Ser	108.0	0.0		109.0	47.0	NM_001199984	B4DIN9|B4DJA0|B4DPG1|B4DUC1|E7ENF3|Q53TR8|Q8N1C4|Q8TCC9	Missense_Mutation	SNP	ENST00000233190.6	hg19	CCDS2366.1	.	.	.	.	.	.	.	.	.	.	a	23.7	4.452591	0.84209	.	.	ENSG00000023228	ENST00000233190;ENST00000423725;ENST00000457011;ENST00000440274;ENST00000455934;ENST00000449699;ENST00000432169	D;D;D;D;D;D;D	0.91011	-2.77;-2.77;-2.77;-2.77;-2.77;-2.77;-2.77	5.7	5.7	0.88788	Molybdopterin oxidoreductase (1);	0.045982	0.85682	D	0.000000	D	0.95130	0.8422	M	0.81802	2.56	0.80722	D	1	P;D;D;D	0.61697	0.503;0.989;0.99;0.99	P;D;D;P	0.67103	0.536;0.949;0.924;0.868	D	0.95660	0.8714	10	0.87932	D	0	0.681	15.9596	0.79918	1.0:0.0:0.0:0.0	.	455;530;580;566	B4DPG1;E7ENF3;B4DJA0;P28331	.;.;.;NDUS1_HUMAN	S	566;509;450;530;580;566;455	ENSP00000233190:I566S;ENSP00000397760:I509S;ENSP00000400976:I450S;ENSP00000409766:I530S;ENSP00000392709:I580S;ENSP00000399912:I566S;ENSP00000409689:I455S	ENSP00000233190:I566S	I	-	2	0	NDUFS1	206703068	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	9.003000	0.93577	2.171000	0.68590	0.402000	0.26972	ATT	.	.		0.398	NDUFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256391.4	NM_005006		C	206994823	A	C	206994823	3	2	373	1	0	0	0	0	1	0	0	0	10300	101	4	5	506	5	NDUFS1	2	206994823	Missense_Mutation	SNP	A	TCGA-ZS-A9CG-01A-11D-A36X-10	26986480	206994823	36204550	12	51526										
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41266103	41266103	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	aacagtcttacctggactctGgaatccattctggtgccact	8	12	3	0	rs121913399|rs121913416		TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr3:41266103G>A	ENST00000349496.5	+	3	380	c.100G>A	c.(100-102)Gga>Aga	p.G34R	CTNNB1_ENST00000396183.3_Missense_Mutation_p.G34R|CTNNB1_ENST00000453024.1_Missense_Mutation_p.G27R|CTNNB1_ENST00000405570.1_Missense_Mutation_p.G34R|CTNNB1_ENST00000396185.3_Missense_Mutation_p.G34R	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	34			G -> E (in PTR). {ECO:0000269|PubMed:10192393}.|G -> R (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|G -> V (in hepatoblastoma; dbSNP:rs28931589). {ECO:0000269|PubMed:9927029}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.G34R(87)|p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.D32_H36>D(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.S33_G34insGTS(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.GIHS34?(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.D32fs*9(1)|p.A5_T40del(1)|p.S29_H36del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.S33_G34insGI(1)|p.A5_I35del(1)|p.D32_H36del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CCTGGACTCTGGAATCCATTC	0.488		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.G34R	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	CTNNB1,gallbladder,other,-1,1	CTNNB1	4904	.	220	Deletion - In frame(105)|Substitution - Missense(87)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)|Insertion - In frame(2)	liver(126)|large_intestine(21)|central_nervous_system(19)|pancreas(15)|endometrium(11)|stomach(10)|skin(4)|pituitary(4)|soft_tissue(2)|small_intestine(2)|adrenal_gland(1)|haematopoietic_and_lymphoid_tissue(1)|bone(1)|lung(1)|ovary(1)|kidney(1)	c.G100A						.						92	77	82					3																	41266103		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	GACTCTGGAATCC	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.100G>A	chr3.hg19:g.41266103G>A	ENSP00000344456:p.Gly34Arg	193.0	0.0		159.0	113.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.745738	0.89663	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.52526	0.66;0.66;0.66;0.66;0.66;0.66;0.66;0.66;0.66	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.72053	0.3413	M	0.79258	2.445	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74188	-0.3746	10	0.87932	D	0	-31.2232	19.9596	0.97236	0.0:0.0:1.0:0.0	.	34	P35222	CTNB1_HUMAN	R	27;34;34;34;34;27;34;34;34	ENSP00000400508:G27R;ENSP00000385604:G34R;ENSP00000412219:G34R;ENSP00000379486:G34R;ENSP00000344456:G34R;ENSP00000411226:G27R;ENSP00000379488:G34R;ENSP00000409302:G34R;ENSP00000401599:G34R	ENSP00000344456:G34R	G	+	1	0	CTNNB1	41241107	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.726000	0.93360	0.655000	0.94253	GGA	.	.		0.488	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		A	41266103	G	A	41266103	3	1	373	1	0	0	0	0	1	0	0	0	4018	1349	47	3	106	3	CTNNB1	3	41266103	Missense_Mutation	SNP	G	TCGA-ZS-A9CG-01A-11D-A36X-10		41266103	156756327	13	51527										
BAP1	8314	hgsc.bcm.edu	37	chr3	52437545	52437545	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	agcgtatgcagtcaacacgcAgcaggctgtcatcctctcca	9	14	3	0			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr3:52437545A>T	ENST00000460680.1	-	13	2087	c.1616T>A	c.(1615-1617)cTg>cAg	p.L539Q	BAP1_ENST00000296288.5_Missense_Mutation_p.L521Q	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		GTCAACACGCAGCAGGCTGTC	0.622			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.L539Q	GBM(101;493 1458 7992 21037 25532)	Atlas-SNP	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.	BAP1	371	.	0			c.T1616A						.						80	73	75					3																	52437545		2203	4300	6503	SO:0001583	missense	8314	exon13			ACACGCAGCAGGC	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.1616T>A	chr3.hg19:g.52437545A>T	ENSP00000417132:p.Leu539Gln	119.0	0.0		110.0	17.0	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Missense_Mutation	SNP	ENST00000460680.1	hg19	CCDS2853.1	.	.	.	.	.	.	.	.	.	.	A	19.71	3.877709	0.72294	.	.	ENSG00000163930	ENST00000460680;ENST00000296288;ENST00000478368	T;T;T	0.61627	0.13;0.09;0.24	5.94	5.94	0.96194	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (1);	0.066216	0.64402	D	0.000007	T	0.64427	0.2597	L	0.29908	0.895	0.53688	D	0.999978	D	0.71674	0.998	P	0.62014	0.897	T	0.66999	-0.5781	10	0.59425	D	0.04	.	16.3932	0.83546	1.0:0.0:0.0:0.0	.	539	Q92560	BAP1_HUMAN	Q	539;521;40	ENSP00000417132:L539Q;ENSP00000296288:L521Q;ENSP00000420647:L40Q	ENSP00000296288:L521Q	L	-	2	0	BAP1	52412585	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.336000	0.79245	2.267000	0.75376	0.533000	0.62120	CTG	.	.		0.622	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			T	52437545	A	T	52437545	3	4	373	1	0	0	0	0	1	0	0	0	1311	188	7	4	593	4	BAP1	3	52437545	Missense_Mutation	SNP	A	TCGA-ZS-A9CG-01A-11D-A36X-10	11171442	52437545	145584885	14	51528										
ALB	213	hgsc.bcm.edu	37	chr4	74274521	74274524	+	Splice_Site	DEL	AAGT	AAGT	-													0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	atgaagagacatttttgaaaAagtaagtaatcagatgttta					rs17853494		TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	AAGT	AAGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr4:74274521_74274524delAAGT	ENST00000295897.4	+	4	570_571	c.481_482delAAGT	c.(481-483)aag>g	p.K161fs	ALB_ENST00000415165.2_Intron|ALB_ENST00000505649.1_3'UTR|ALB_ENST00000509063.1_Splice_Site_p.K161fs|ALB_ENST00000401494.3_Intron|ALB_ENST00000503124.1_Intron	NM_000477.5	NP_000468.1	Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			ATTTTTGAAAAAGTAAGTAATCAG	0.348																																					p.160_161del		Atlas-INDEL	.											.	ALB	132	.	0			c.480_482del						.																																			SO:0001630	splice_region_variant	213	exon4			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000295897.4:c.482+1AAGT>-	chr4.hg19:g.74274525_74274528delAAGT		115.0	0.0		102.0	30.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	In_Frame_Del	DEL	ENST00000295897.4	hg19	CCDS3555.1																																																																																			.	.		0.348	ALB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252173.3	NM_000477	Frame_Shift_Del	-	74274524	AAGT	-	74274521	8	5	373	1	0	1	0	1	0	0	1	0	486	28	1	0	495	0	ALB	4	74274521	Splice_Site	DEL	AAGT	TCGA-ZS-A9CG-01A-11D-A36X-10		74274521	116879755	15	51529										
SHROOM3	57619	hgsc.bcm.edu	37	chr4	77680796	77680796	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	actgaacaaaatcaaagagaTgccagcagaagtgaatgagg	11	6	1	5			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr4:77680796T>C	ENST00000296043.6	+	9	6250	c.5297T>C	c.(5296-5298)aTg>aCg	p.M1766T	RP11-359D14.2_ENST00000452412.1_RNA|RP11-359D14.3_ENST00000449007.1_RNA	NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	1766	ASD2. {ECO:0000255|PROSITE- ProRule:PRU00638}.				actin cytoskeleton organization (GO:0030036)|apical protein localization (GO:0045176)|cell morphogenesis (GO:0000902)|cellular pigment accumulation (GO:0043482)|columnar/cuboidal epithelial cell development (GO:0002066)|neural tube closure (GO:0001843)|pattern specification process (GO:0007389)|regulation of cell shape (GO:0008360)	adherens junction (GO:0005912)|apical junction complex (GO:0043296)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)				NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(29)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	60			Lung(101;0.0903)			ATCAAAGAGATGCCAGCAGAA	0.443																																					p.M1766T		Atlas-SNP	.											.	SHROOM3	134	.	0			c.T5297C						.						123	105	111					4																	77680796		2203	4300	6503	SO:0001583	missense	57619	exon9			AAGAGATGCCAGC	AB055660	CCDS3579.2	4q21.1	2009-11-25			ENSG00000138771	ENSG00000138771			30422	protein-coding gene	gene with protein product		604570				10589677, 16615870	Standard	NM_020859		Approved	ShrmL, SHRM, KIAA1481, APXL3	uc011cbx.2	Q8TF72	OTTHUMG00000157075	ENST00000296043.6:c.5297T>C	chr4.hg19:g.77680796T>C	ENSP00000296043:p.Met1766Thr	238.0	0.0		215.0	81.0	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Missense_Mutation	SNP	ENST00000296043.6	hg19	CCDS3579.2	.	.	.	.	.	.	.	.	.	.	T	12.11	1.839965	0.32513	.	.	ENSG00000138771	ENST00000296043	T	0.29142	1.58	5.43	4.22	0.49857	Apx/shroom, ASD2 (2);	0.181335	0.48286	D	0.000184	T	0.37128	0.0992	L	0.61218	1.895	0.36958	D	0.893176	P	0.38148	0.62	B	0.43728	0.429	T	0.47195	-0.9136	10	0.87932	D	0	-29.4575	10.5268	0.44954	0.1441:0.0:0.0:0.8559	.	1766	Q8TF72	SHRM3_HUMAN	T	1766	ENSP00000296043:M1766T	ENSP00000296043:M1766T	M	+	2	0	SHROOM3	77899820	1.000000	0.71417	0.959000	0.39883	0.018000	0.09664	6.210000	0.72176	1.037000	0.40024	0.528000	0.53228	ATG	.	.		0.443	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859		C	77680796	T	C	77680796	3	2	373	1	0	0	0	0	1	0	0	0	14310	1464	51	2	5331	2	SHROOM3	4	77680796	Missense_Mutation	SNP	T	TCGA-ZS-A9CG-01A-11D-A36X-10	3406275	77680796	113473480	16	51530										
DSPP	1834	hgsc.bcm.edu	37	chr4	88537513	88537513	+	Missense_Mutation	SNP	A	A	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	gacagcagtgacagcaatgaAagcagcgacagcagtgacag	13	9	0	3	rs112275895		TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr4:88537513A>C	ENST00000282478.7	+	4	3732	c.3699A>C	c.(3697-3699)gaA>gaC	p.E1233D	DSPP_ENST00000399271.1_Missense_Mutation_p.E1233D|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1233	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			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)		acagcaatgaaagcagcgaca	0.547																																					p.E1233D		Atlas-SNP	.											.	DSPP	174	.	0			c.A3699C						.																																			SO:0001583	missense	1834	exon5			CAATGAAAGCAGC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3699A>C	chr4.hg19:g.88537513A>C	ENSP00000282478:p.Glu1233Asp	274.0	0.0		386.0	73.0	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	hg19	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	A	0.010	-1.785366	0.00628	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.88741	-2.42;-2.42	2.61	-5.21	0.02815	.	.	.	.	.	T	0.57213	0.2038	N	0.01048	-1.04	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.57347	-0.7827	9	0.02654	T	1	.	0.7125	0.00926	0.2623:0.1881:0.1298:0.4197	.	1233	Q9NZW4	DSPP_HUMAN	D	1233	ENSP00000382213:E1233D;ENSP00000282478:E1233D	ENSP00000282478:E1233D	E	+	3	2	DSPP	88756537	0.003000	0.15002	0.000000	0.03702	0.000000	0.00434	-2.769000	0.00780	-2.252000	0.00699	-3.496000	0.00033	GAA	.	A|0.500;C|0.500		0.547	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		C	88537513	A	C	88537513	3	2	373	1	0	0	0	0	1	0	0	0	4784	11	1	5	3713	5	DSPP	4	88537513	Missense_Mutation	SNP	A	TCGA-ZS-A9CG-01A-11D-A36X-10	10856717	88537513	102616763	17	51531										
NFKB1	4790	hgsc.bcm.edu	37	chr4	103528819	103528819	+	Missense_Mutation	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	attgtagggtgatgcccatgTggacagtactacctacgatg	12	8	0	1			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr4:103528819T>G	ENST00000505458.1	+	19	2412	c.2135T>G	c.(2134-2136)gTg>gGg	p.V712G	NFKB1_ENST00000600343.1_Missense_Mutation_p.V532G|NFKB1_ENST00000394820.4_Missense_Mutation_p.V712G|NFKB1_ENST00000226574.4_Missense_Mutation_p.V713G			P19838	NFKB1_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 1	712	Interaction with CFLAR.				apoptotic process (GO:0006915)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of calcidiol 1-monooxygenase activity (GO:0010956)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of cytokine production (GO:0001818)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-12 biosynthetic process (GO:0045083)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|response to copper ion (GO:0046688)|response to oxidative stress (GO:0006979)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I-kappaB/NF-kappaB complex (GO:0033256)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleic acid binding transcription factor activity (GO:0001071)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			biliary_tract(1)|breast(4)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	27		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.59e-08)	Acetylsalicylic acid(DB00945)|Pranlukast(DB01411)|Thalidomide(DB01041)|Triflusal(DB08814)	GATGCCCATGTGGACAGTACT	0.547																																					p.V713G		Atlas-SNP	.											.	NFKB1	78	.	0			c.T2138G						.						187	166	173					4																	103528819		2203	4300	6503	SO:0001583	missense	4790	exon19			CCCATGTGGACAG	M58603	CCDS3657.1, CCDS54783.1	4q24	2013-01-10	2008-07-28		ENSG00000109320	ENSG00000109320		"Ankyrin repeat domain containing"	7794	protein-coding gene	gene with protein product		164011				1992489	Standard	NM_003998		Approved	KBF1, p105, NFKB-p50, p50, NF-kappaB, NFkappaB, NF-kB1	uc011cep.2	P19838	OTTHUMG00000161080	ENST00000505458.1:c.2135T>G	chr4.hg19:g.103528819T>G	ENSP00000424790:p.Val712Gly	77.0	0.0		68.0	23.0	NM_003998	A8K5Y5|B3KVE8|Q68D84|Q86V43|Q8N4X7|Q9NZC0	Missense_Mutation	SNP	ENST00000505458.1	hg19	CCDS54783.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.411002	0.83340	.	.	ENSG00000109320	ENST00000226574;ENST00000394820;ENST00000505458	T;T;T	0.42900	0.96;0.96;0.96	5.15	5.15	0.70609	Ankyrin repeat-containing domain (3);	0.000000	0.64402	D	0.000001	T	0.72269	0.3439	M	0.92923	3.36	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.91635	0.999;0.997;0.994	T	0.80455	-0.1375	10	0.87932	D	0	.	15.0022	0.71483	0.0:0.0:0.0:1.0	.	532;712;713	B3KVE8;P19838;P19838-2	.;NFKB1_HUMAN;.	G	713;712;712	ENSP00000226574:V713G;ENSP00000378297:V712G;ENSP00000424790:V712G	ENSP00000226574:V713G	V	+	2	0	NFKB1	103747857	1.000000	0.71417	0.908000	0.35775	0.985000	0.73830	6.868000	0.75516	1.942000	0.56320	0.533000	0.62120	GTG	.	.		0.547	NFKB1-003	KNOWN	alternative_5_UTR|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363411.1			G	103528819	T	G	103528819	3	3	373	1	0	0	0	0	1	0	0	0	10384	1696	59	5	2208	5	NFKB1	4	103528819	Missense_Mutation	SNP	T	TCGA-ZS-A9CG-01A-11D-A36X-10	14991306	103528819	87625457	18	51532										
CASP3	836	hgsc.bcm.edu	37	chr4	185552301	185552301	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	tgccacagtccagttctgtaCcacggcaggcctgggtgtta	12	12	1	0			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr4:185552301C>T	ENST00000308394.4	-	7	756	c.494G>A	c.(493-495)gGt>gAt	p.G165D	CASP3_ENST00000517513.1_Intron|CASP3_ENST00000393588.4_Intron|CASP3_ENST00000523916.1_Missense_Mutation_p.G165D|CASP3_ENST00000393585.2_Intron	NM_004346.3	NP_004337.2	P42574	CASP3_HUMAN	caspase 3, apoptosis-related cysteine peptidase	165					activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|B cell homeostasis (GO:0001782)|cell fate commitment (GO:0045165)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|erythrocyte differentiation (GO:0030218)|execution phase of apoptosis (GO:0097194)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|glial cell apoptotic process (GO:0034349)|heart development (GO:0007507)|hippo signaling (GO:0035329)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|keratinocyte differentiation (GO:0030216)|negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of apoptotic process (GO:0043066)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|neuron apoptotic process (GO:0051402)|neuron differentiation (GO:0030182)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet formation (GO:0030220)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|proteolysis (GO:0006508)|regulation of apoptotic DNA fragmentation (GO:1902510)|regulation of apoptotic process (GO:0042981)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|release of cytochrome c from mitochondria (GO:0001836)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)|response to wounding (GO:0009611)|sensory perception of sound (GO:0007605)|T cell homeostasis (GO:0043029)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	aspartic-type endopeptidase activity (GO:0004190)|cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type endopeptidase activity involved in apoptotic process (GO:0097153)|cysteine-type endopeptidase activity involved in execution phase of apoptosis (GO:0097200)|peptidase activity (GO:0008233)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|skin(1)	12		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Colorectal(36;0.00139)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.057)|all_hematologic(60;0.0592)		all cancers(43;2.05e-27)|Epithelial(43;4.27e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.04e-11)|Colorectal(24;2e-05)|STAD - Stomach adenocarcinoma(60;2.35e-05)|GBM - Glioblastoma multiforme(59;4.94e-05)|COAD - Colon adenocarcinoma(29;0.00017)|BRCA - Breast invasive adenocarcinoma(30;0.000218)|LUSC - Lung squamous cell carcinoma(40;0.00904)|READ - Rectum adenocarcinoma(43;0.161)	Minocycline(DB01017)	CAGTTCTGTACCACGGCAGGC	0.378																																					p.G165D		Atlas-SNP	.											.	CASP3	27	.	0			c.G494A						.						75	66	69					4																	185552301		2203	4300	6503	SO:0001583	missense	836	exon7			TCTGTACCACGGC	BC016926	CCDS3836.1	4q34	2008-02-05	2005-08-17		ENSG00000164305	ENSG00000164305		"Caspases"	1504	protein-coding gene	gene with protein product		600636	"caspase 3, apoptosis-related cysteine protease"			8780721	Standard	NM_004346		Approved	CPP32, CPP32B, Yama, apopain	uc003iwi.3	P42574	OTTHUMG00000133681	ENST00000308394.4:c.494G>A	chr4.hg19:g.185552301C>T	ENSP00000311032:p.Gly165Asp	124.0	0.0		104.0	42.0	NM_004346	A8K5M2|D3DP53|Q96AN1|Q96KP2	Missense_Mutation	SNP	ENST00000308394.4	hg19	CCDS3836.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.519618	0.85495	.	.	ENSG00000164305	ENST00000308394;ENST00000523916	T;T	0.57107	0.42;0.42	5.54	5.54	0.83059	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase precursor p45, core (2);Peptidase C14, ICE, catalytic subunit p20 (1);	0.000000	0.85682	D	0.000000	D	0.84884	0.5571	H	0.99026	4.405	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90970	0.4819	10	0.87932	D	0	.	19.4811	0.95009	0.0:1.0:0.0:0.0	.	165	P42574	CASP3_HUMAN	D	165	ENSP00000311032:G165D;ENSP00000428929:G165D	ENSP00000311032:G165D	G	-	2	0	CASP3	185789295	1.000000	0.71417	0.982000	0.44146	0.595000	0.36748	6.014000	0.70784	2.619000	0.88677	0.491000	0.48974	GGT	.	.		0.378	CASP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257885.2	NM_004346		T	185552301	C	T	185552301	3	4	373	1	0	0	0	0	1	0	0	0	2674	507	18	3	347	3	CASP3	4	185552301	Missense_Mutation	SNP	C	TCGA-ZS-A9CG-01A-11D-A36X-10	82023482	185552301	5601975	19	51533										
HEATR7B2	133558	hgsc.bcm.edu	37	chr5	41057463	41057463	+	Splice_Site	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	gtcagtatttgttttaggctCtaaagtggaaactcccacag	9	8	2	0			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr5:41057463C>T	ENST00000399564.4	-	8	1207		c.e8-1		MROH2B_ENST00000506092.2_Intron	NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B																		GTTTTAGGCTCTAAAGTGGAA	0.433																																					.		Atlas-SNP	.											HEATR7B2,bladder,carcinoma,0,1	.	.	.	0			c.757-1G>A						.						37	35	36					5																	41057463		1862	4115	5977	SO:0001630	splice_region_variant	133558	exon9			TAGGCTCTAAAGT		CCDS47202.1	5p13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000171495	ENSG00000171495		"maestro heat-like repeat containing"	26857	protein-coding gene	gene with protein product			"HEAT repeat family member 7B2"	HEATR7B2		12477932	Standard	NM_173489		Approved	DKFZp781F0822, FLJ40243	uc003jmj.4	Q7Z745	OTTHUMG00000162151	ENST00000399564.4:c.757-1G>A	chr5.hg19:g.41057463C>T		102.0	0.0		88.0	31.0	NM_173489	Q68DM1|Q7Z4U4|Q8N7X3	Splice_Site	SNP	ENST00000399564.4	hg19	CCDS47202.1	.	.	.	.	.	.	.	.	.	.	C	9.903	1.207524	0.22205	.	.	ENSG00000171495	ENST00000399564	.	.	.	5.21	5.21	0.72293	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4504	0.67382	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	HEATR7B2	41093220	1.000000	0.71417	0.993000	0.49108	0.070000	0.16714	3.256000	0.51492	2.873000	0.98535	0.561000	0.74099	.	.	.		0.433	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489	Intron	T	41057463	C	T	41057463	5	4	373	1	0	0	0	0	0	0	1	0	7044	927	32	3	4141	3	HEATR7B2	5	41057463	Splice_Site	SNP	C	TCGA-ZS-A9CG-01A-11D-A36X-10		41057463	139857797	20	51534										
C5orf36	285600	hgsc.bcm.edu	37	chr5	93775757	93775757	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	gtttccagaagcaagttccaGttacaacgtggctgggataa	11	8	0	1			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr5:93775757G>T	ENST00000513200.3	-	13	2499	c.2427C>A	c.(2425-2427)aaC>aaA	p.N809K	KIAA0825_ENST00000312498.7_Missense_Mutation_p.N809K|KIAA0825_ENST00000427991.2_Missense_Mutation_p.N809K	NM_001145678.1	NP_001139150.1	Q8IV33	K0825_HUMAN	KIAA0825	809										breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|pancreas(1)|prostate(1)|skin(1)	13						GCAAGTTCCAGTTACAACGTG	0.433																																					p.N809K		Atlas-SNP	.											.	KIAA0825	172	.	0			c.C2427A						.						180	153	161					5																	93775757		692	1591	2283	SO:0001583	missense	285600	exon14			GTTCCAGTTACAA	BX648338	CCDS4070.1	5q15	2011-02-23	2011-02-23	2011-02-23	ENSG00000185261	ENSG00000185261			28532	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 36"	C5orf36		12477932	Standard	NM_173665		Approved	DKFZp686F0372, MGC34713	uc011cuk.2	Q8IV33	OTTHUMG00000131331	ENST00000513200.3:c.2427C>A	chr5.hg19:g.93775757G>T	ENSP00000424618:p.Asn809Lys	357.0	1.0		343.0	115.0	NM_001145678	O94914|Q6ZNN2	Missense_Mutation	SNP	ENST00000513200.3	hg19		.	.	.	.	.	.	.	.	.	.	G	12.18	1.860379	0.32884	.	.	ENSG00000185261	ENST00000513200;ENST00000427991;ENST00000312498	T;T;T	0.52295	0.67;0.67;0.67	5.55	-0.0279	0.13924	.	0.000000	0.64402	D	0.000001	T	0.32675	0.0837	L	0.41961	1.31	0.32503	N	0.538582	B	0.27997	0.197	B	0.28465	0.09	T	0.19647	-1.0299	10	0.35671	T	0.21	.	5.3213	0.15883	0.6002:0.1434:0.2565:0.0	.	809	Q8IV33	K0825_HUMAN	K	809	ENSP00000424618:N809K;ENSP00000400288:N809K;ENSP00000312205:N809K	ENSP00000312205:N809K	N	-	3	2	KIAA0825	93801513	1.000000	0.71417	0.994000	0.49952	0.969000	0.65631	1.635000	0.37134	-0.171000	0.10797	-0.670000	0.03821	AAC	.	.		0.433	KIAA0825-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000254102.5	NM_173665		T	93775757	G	T	93775757	3	4	373	1	0	0	0	0	1	0	0	0	2297	1020	36	3	1432	3	C5orf36	5	93775757	Missense_Mutation	SNP	G	TCGA-ZS-A9CG-01A-11D-A36X-10	52718294	93775757	87139503	21	51535										
WDR36	134430	hgsc.bcm.edu	37	chr5	110443041	110443041	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	tatcattgcttgccatcaagGtaagctatcttgctcaacct	6	11	4	0	rs77756277|rs140155952		TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr5:110443041G>C	ENST00000513710.2	+	12	1401	c.1397G>C	c.(1396-1398)gGt>gCt	p.G466A	WDR36_ENST00000505303.1_Missense_Mutation_p.G410A|WDR36_ENST00000506538.2_Missense_Mutation_p.G466A			Q8NI36	WDR36_HUMAN	WD repeat domain 36	466					regulation of axon extension (GO:0030516)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|rRNA processing (GO:0006364)|visual perception (GO:0007601)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(9)|kidney(4)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(142;2.72e-05)|all_epithelial(76;4.4e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0418)|Ovarian(225;0.0443)|Colorectal(57;0.0465)|all_lung(232;0.0508)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.39e-08)|Epithelial(69;1.82e-07)|all cancers(49;2.04e-05)|COAD - Colon adenocarcinoma(37;0.111)		TGCCATCAAGGTAAGCTATCT	0.358																																					p.G466A		Atlas-SNP	.											.	WDR36	111	.	0			c.G1397C						.						90	86	87					5																	110443041		2202	4299	6501	SO:0001583	missense	134430	exon12			ATCAAGGTAAGCT	AF385437	CCDS4102.1	5q22.2	2013-01-09			ENSG00000134987	ENSG00000134987		"WD repeat domain containing"	30696	protein-coding gene	gene with protein product		609669	"glaucoma 1, open angle, G"	GLC1G		15590835, 15677485	Standard	NM_139281		Approved	TA-WDRP, UTP21	uc003kpd.3	Q8NI36	OTTHUMG00000128790	ENST00000513710.2:c.1397G>C	chr5.hg19:g.110443041G>C	ENSP00000424628:p.Gly466Ala	182.0	0.0		176.0	58.0	NM_139281	A2RUS4|Q68E02|Q8N1Q2	Missense_Mutation	SNP	ENST00000513710.2	hg19	CCDS4102.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.335782	0.81801	.	.	ENSG00000134987	ENST00000506538;ENST00000513710;ENST00000505303	T;T;T	0.69435	-0.4;-0.4;0.17	4.91	4.91	0.64330	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);	0.144850	0.64402	D	0.000006	T	0.77948	0.4207	M	0.88775	2.98	0.80722	D	1	D	0.59767	0.986	P	0.52031	0.688	T	0.82754	-0.0301	10	0.87932	D	0	-11.6593	11.9142	0.52755	0.0807:0.0:0.9193:0.0	.	466	Q8NI36	WDR36_HUMAN	A	466;466;410	ENSP00000423067:G466A;ENSP00000424628:G466A;ENSP00000422158:G410A	ENSP00000422158:G410A	G	+	2	0	WDR36	110470940	1.000000	0.71417	0.994000	0.49952	0.978000	0.69477	6.518000	0.73764	2.436000	0.82500	0.467000	0.42956	GGT	.	G|1.000;A|0.000		0.358	WDR36-008	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000373504.3	NM_139281		C	110443041	G	C	110443041	3	2	373	1	0	0	0	0	1	0	0	0	17305	1261	44	4	1443	4	WDR36	5	110443041	Missense_Mutation	SNP	G	TCGA-ZS-A9CG-01A-11D-A36X-10	16667284	110443041	70472219	22	51536										
TRPC7	57113	hgsc.bcm.edu	37	chr5	135692611	135692611	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	gagaagcgcgtgccgtcctcGtcgtaggcatagaagtcgtc	14	11	0	2			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr5:135692611G>A	ENST00000513104.1	-	2	747	c.465C>T	c.(463-465)gaC>gaT	p.D155D	TRPC7_ENST00000355180.3_Silent_p.D155D|TRPC7_ENST00000426057.2_Silent_p.D155D	NM_020389.2	NP_065122.1	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel, subfamily C, member 7	155					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|manganese ion transport (GO:0006828)|platelet activation (GO:0030168)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(3)	46			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TGCCGTCCTCGTCGTAGGCAT	0.662																																					p.D155D		Atlas-SNP	.											.	TRPC7	126	.	0			c.C465T						.						123	131	128					5																	135692611		2203	4300	6503	SO:0001819	synonymous_variant	57113	exon2			GTCCTCGTCGTAG	AJ272034	CCDS47267.1, CCDS47267.2, CCDS54905.1, CCDS54906.1	5q31.2	2011-12-14			ENSG00000069018	ENSG00000069018		"Voltage-gated ion channels / Transient receptor potential cation channels"	20754	protein-coding gene	gene with protein product						11805119, 16382100	Standard	NM_020389		Approved		uc003lbn.2	Q9HCX4	OTTHUMG00000162035	ENST00000513104.1:c.465C>T	chr5.hg19:g.135692611G>A		70.0	0.0		76.0	29.0	NM_001167576	A1A4Z4|F5H5U9|Q70T26|Q8IWP7	Silent	SNP	ENST00000513104.1	hg19	CCDS47267.2	.	.	.	.	.	.	.	.	.	.	G	9.575	1.121972	0.20877	.	.	ENSG00000069018	ENST00000352189;ENST00000378459;ENST00000502753	.	.	.	5.27	-1.0	0.10196	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-29.8234	10.075	0.42355	0.589:0.0:0.411:0.0	.	.	.	.	X	155	.	.	R	-	1	2	TRPC7	135720510	0.747000	0.28283	0.983000	0.44433	0.998000	0.95712	-0.005000	0.12855	-0.097000	0.12307	0.655000	0.94253	CGA	.	.		0.662	TRPC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366975.1	NM_020389		A	135692611	G	A	135692611	2	1	373	1	0	0	0	0	0	0	0	1	16599	1136	40	1		1	TRPC7	5	135692611	Silent	SNP	G	TCGA-ZS-A9CG-01A-11D-A36X-10	25249570	135692611	45222649	23	51537										
PCDHB3	56132	hgsc.bcm.edu	37	chr5	140480417	140480418	+	Frame_Shift_Ins	INS	-	-	G													0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	ggtagaggaactggccgcgaINSggggggcccaagttgtgtcc							TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr5:140480417_140480418insG	ENST00000231130.2	+	1	184_185	c.184_185insG	c.(184-186)aggfs	p.R62fs	AC005754.7_ENST00000607216.1_RNA	NM_018937.2	NP_061760.1	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3	62	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	72			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACTGGCCGCGAGGGGGGCCCAA	0.5																																					p.R62fs		Atlas-INDEL	.											.	PCDHB3	208	.	0			c.184_185insG						.																																			SO:0001589	frameshift_variant	56132	exon1			.	AF152496	CCDS4245.1	5q31	2010-01-26			ENSG00000113205	ENSG00000113205		"Cadherins / Protocadherins : Clustered"	8688	other	protocadherin		606329				10380929	Standard	NM_018937		Approved	PCDH-BETA3	uc003lio.3	Q9Y5E6	OTTHUMG00000129622	ENST00000231130.2:c.190dupG	chr5.hg19:g.140480423_140480423dupG	ENSP00000231130:p.Arg62fs	250.0	0.0		257.0	55.0	NM_018937	B2R8P2	Frame_Shift_Ins	INS	ENST00000231130.2	hg19	CCDS4245.1																																																																																			.	.		0.5	PCDHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251817.2	NM_018937		G	140480418	-	G	140480417	7	5	373	1	0	1	1	0	0	0	0	0	11552	295	11	0	186	0	PCDHB3	5	140480417	Frame_Shift_Ins	INS	-	TCGA-ZS-A9CG-01A-11D-A36X-10	4787806	140480417	40434843	24	51538										
POU4F3	5459	hgsc.bcm.edu	37	chr5	145719608	145719608	+	Silent	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	aagctgggggtgacccaggcGgacgtgggcgcggctctggc	20	11	1	1			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr5:145719608G>A	ENST00000230732.4	+	2	707	c.618G>A	c.(616-618)gcG>gcA	p.A206A	CTC-359M8.1_ENST00000515598.1_RNA	NM_002700.2	NP_002691.1	Q15319	PO4F3_HUMAN	POU class 4 homeobox 3	206	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.				auditory receptor cell differentiation (GO:0042491)|axon extension (GO:0048675)|inner ear morphogenesis (GO:0042472)|neuromuscular process controlling balance (GO:0050885)|neuron apoptotic process (GO:0051402)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retinal ganglion cell axon guidance (GO:0031290)|sensory perception of sound (GO:0007605)|vestibulocochlear nerve development (GO:0021562)|visual perception (GO:0007601)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGACCCAGGCGGACGTGGGCG	0.647																																					p.A206A		Atlas-SNP	.											.	POU4F3	47	.	0			c.G618A						.						39	44	42					5																	145719608		2203	4300	6503	SO:0001819	synonymous_variant	5459	exon2			CCAGGCGGACGTG	U10060	CCDS4281.1	5q32	2011-06-20	2007-07-13		ENSG00000091010	ENSG00000091010		"Homeoboxes / POU class"	9220	protein-coding gene	gene with protein product		602460	"POU domain class 4, transcription factor 3"	DFNA15		9506947	Standard	NM_002700		Approved	BRN3C	uc003loa.2	Q15319	OTTHUMG00000129684	ENST00000230732.4:c.618G>A	chr5.hg19:g.145719608G>A		98.0	0.0		105.0	38.0	NM_002700	O60557|Q2M3F8	Silent	SNP	ENST00000230732.4	hg19	CCDS4281.1																																																																																			.	.		0.647	POU4F3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251887.2	NM_002700		A	145719608	G	A	145719608	2	1	373	1	0	0	0	0	0	0	0	1	12289	1103	39	1		1	POU4F3	5	145719608	Silent	SNP	G	TCGA-ZS-A9CG-01A-11D-A36X-10	5239191	145719608	35195652	25	51539										
TCERG1	10915	hgsc.bcm.edu	37	chr5	145838662	145838663	+	In_Frame_Ins	INS	-	-	GCCCAG													0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	aggcccaggcccaggcccagINSgcccaggcccaagcccaagc							TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr5:145838662_145838663insGCCCAG	ENST00000296702.5	+	4	692_693	c.654_655insGCCCAG	c.(655-657)gcc>GCCCAGgcc	p.219_219A>AQA	TCERG1_ENST00000394421.2_In_Frame_Ins_p.219_219A>AQA	NM_006706.3	NP_006697.2	O14776	TCRG1_HUMAN	transcription elongation regulator 1	219	Ala/Gln-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(18)|lung(9)|ovary(2)|prostate(3)|skin(1)	46		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			cccaggcccaggcccaggccca	0.728																																					p.Q218delinsQAQ		Atlas-INDEL	.											.	TCERG1	148	.	0			c.654_655insGCCCAG						.																																			SO:0001652	inframe_insertion	10915	exon4			.	AF017789	CCDS4282.1, CCDS43379.1	5q31	2010-01-25	2002-01-24	2002-01-25	ENSG00000113649	ENSG00000113649			15630	protein-coding gene	gene with protein product	"transcription factor CA150", "co-activator of 150 kDa", "TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD", "TATA box-binding protein-associated factor 2S"	605409	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"	TAF2S		9315662, 11003711	Standard	XM_005268365		Approved	CA150, Urn1	uc003lob.3	O14776	OTTHUMG00000129683	ENST00000296702.5:c.655_660dupGCCCAG	chr5.hg19:g.145838663_145838668dupGCCCAG	ENSP00000296702:p.GlnAla241dup	156.0	0.0		147.0	18.0	NM_006706	Q2NKN2|Q59EA1	In_Frame_Ins	INS	ENST00000296702.5	hg19	CCDS4282.1																																																																																			.	.		0.728	TCERG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251886.1	NM_001040006		GCCCAG	145838663	-	GCCCAG	145838662	7	5	373	1	0	1	1	0	0	0	0	0	15700	991	35	0	668	0	TCERG1	5	145838662	In_Frame_Ins	INS	-	TCGA-ZS-A9CG-01A-11D-A36X-10	119054	145838662	35076598	26	51540										
DCDC2	51473	hgsc.bcm.edu	37	chr6	24291202	24291202	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	acttgtcaaaaagtaactcaCtgtaaggcagtttcttaaac	6	8	3	0			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr6:24291202C>A	ENST00000378454.3	-	5	963	c.662G>T	c.(661-663)aGt>aTt	p.S221I		NM_001195610.1|NM_016356.3	NP_001182539.1|NP_057440.2	Q9UHG0	DCDC2_HUMAN	doublecortin domain containing 2	221	Doublecortin 2. {ECO:0000255|PROSITE- ProRule:PRU00072}.		S -> G (in dbSNP:rs2274305). {ECO:0000269|PubMed:10574461, ECO:0000269|PubMed:10601354, ECO:0000269|PubMed:15489334}.		cellular defense response (GO:0006968)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|neuron migration (GO:0001764)|visual learning (GO:0008542)					breast(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32		Ovarian(999;0.101)				AAGTAACTCACTGTAAGGCAG	0.408																																					p.S221I		Atlas-SNP	.											.	DCDC2	53	.	0			c.G662T						.						126	117	120					6																	24291202		2203	4300	6503	SO:0001583	missense	51473	exon6			AACTCACTGTAAG	AB032980	CCDS4550.1	6p22.1	2008-02-05			ENSG00000146038	ENSG00000146038			18141	protein-coding gene	gene with protein product		605755				10601354, 10574461	Standard	NM_001195610		Approved	RU2, KIAA1154, DCDC2A	uc003ndx.3	Q9UHG0	OTTHUMG00000016275	ENST00000378454.3:c.662G>T	chr6.hg19:g.24291202C>A	ENSP00000367715:p.Ser221Ile	118.0	0.0		136.0	21.0	NM_001195610	Q5VTR8|Q5VTR9|Q86W35|Q9UFD1|Q9UHG1|Q9ULR6	Missense_Mutation	SNP	ENST00000378454.3	hg19	CCDS4550.1	.	.	.	.	.	.	.	.	.	.	C	9.230	1.035561	0.19590	.	.	ENSG00000146038	ENST00000378454	D	0.93763	-3.28	5.48	4.59	0.56863	Doublecortin domain (4);	0.345140	0.33496	N	0.004848	D	0.84915	0.5578	L	0.43152	1.355	0.80722	D	1	B	0.17038	0.02	B	0.18561	0.022	T	0.80953	-0.1152	10	0.22706	T	0.39	-24.4174	15.5503	0.76145	0.0:0.8298:0.1702:0.0	.	221	Q9UHG0	DCDC2_HUMAN	I	221	ENSP00000367715:S221I	ENSP00000367715:S221I	S	-	2	0	DCDC2	24399181	1.000000	0.71417	0.995000	0.50966	0.700000	0.40528	2.512000	0.45485	1.337000	0.45525	0.650000	0.86243	AGT	.	.		0.408	DCDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043604.1	NM_016356		A	24291202	C	A	24291202	3	1	373	1	0	0	0	0	1	0	0	0	4287	565	20	3	792	3	DCDC2	6	24291202	Missense_Mutation	SNP	C	TCGA-ZS-A9CG-01A-11D-A36X-10		24291202	146823865	27	51541										
ABCF1	23	hgsc.bcm.edu	37	chr6	30558377	30558377	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	attgccagctgtgggtggtgGaggagcagagtgttagccaa	17	6	0	1			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr6:30558377G>A	ENST00000326195.8	+	25	2549	c.2437G>A	c.(2437-2439)Gag>Aag	p.E813K	ABCF1_ENST00000376545.3_Missense_Mutation_p.E775K|ABCF1_ENST00000396515.4_Missense_Mutation_p.E206K	NM_001025091.1	NP_001020262.1	Q8NE71	ABCF1_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 1	813	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				inflammatory response (GO:0006954)|positive regulation of translation (GO:0045727)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)|ribosome (GO:0005840)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|translation activator activity (GO:0008494)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|skin(2)	21						GTGGGTGGTGGAGGAGCAGAG	0.537																																					p.E813K		Atlas-SNP	.											.	ABCF1	61	.	0			c.G2437A						.						326	349	341					6																	30558377		1511	2708	4219	SO:0001583	missense	23	exon25			GTGGTGGAGGAGC	AF027302	CCDS34380.1, CCDS34381.1	6p21.33	2012-03-14			ENSG00000204574	ENSG00000204574		"ATP binding cassette transporters / subfamily F"	70	protein-coding gene	gene with protein product		603429		ABC50		9790762	Standard	NM_001025091		Approved	EST123147	uc003nql.3	Q8NE71	OTTHUMG00000031094	ENST00000326195.8:c.2437G>A	chr6.hg19:g.30558377G>A	ENSP00000313603:p.Glu813Lys	215.0	0.0		225.0	85.0	NM_001025091	A2BF75|O14897|Q69YP6	Missense_Mutation	SNP	ENST00000326195.8	hg19	CCDS34380.1	.	.	.	.	.	.	.	.	.	.	g	34	5.349085	0.95830	.	.	ENSG00000204574	ENST00000326195;ENST00000376545;ENST00000455943;ENST00000396515	D;D;T	0.91407	-2.66;-2.84;0.95	5.49	5.49	0.81192	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.000000	0.85682	D	0.000000	D	0.84597	0.5507	L	0.28115	0.83	0.80722	D	1	P;P;P	0.46784	0.884;0.884;0.781	B;P;B	0.44946	0.41;0.465;0.235	D	0.87504	0.2435	10	0.66056	D	0.02	-34.6475	18.1562	0.89692	0.0:0.0:1.0:0.0	.	206;775;813	Q5STZ7;Q2L6I2;Q8NE71	.;.;ABCF1_HUMAN	K	813;775;501;206	ENSP00000313603:E813K;ENSP00000365728:E775K;ENSP00000379772:E206K	ENSP00000313603:E813K	E	+	1	0	ABCF1	30666356	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.166000	0.94766	2.595000	0.87683	0.645000	0.84053	GAG	.	.		0.537	ABCF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076137.3			A	30558377	G	A	30558377	3	1	373	1	0	0	0	0	1	0	0	0	65	1175	41	3	2535	3	ABCF1	6	30558377	Missense_Mutation	SNP	G	TCGA-ZS-A9CG-01A-11D-A36X-10	6267175	30558377	140556690	28	51542										
MUT	4594	hgsc.bcm.edu	37	chr6	49407923	49407923	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	caacagtttttagtacctggAaaagagggcctatgtccaca	9	9	0	1	rs1136145		TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr6:49407923A>T	ENST00000274813.3	-	11	2079	c.1952T>A	c.(1951-1953)tTc>tAc	p.F651Y		NM_000255.3	NP_000246.2	P22033	MUTA_HUMAN	methylmalonyl CoA mutase	651	B12-binding. {ECO:0000255|PROSITE- ProRule:PRU00666}.				cellular lipid metabolic process (GO:0044255)|cobalamin metabolic process (GO:0009235)|fatty acid beta-oxidation (GO:0006635)|homocysteine metabolic process (GO:0050667)|post-embryonic development (GO:0009791)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	cobalamin binding (GO:0031419)|metal ion binding (GO:0046872)|methylmalonyl-CoA mutase activity (GO:0004494)|modified amino acid binding (GO:0072341)			endometrium(2)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	30	Lung NSC(77;0.0376)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TAGTACCTGGAAAAGAGGGCC	0.368																																					p.F651Y		Atlas-SNP	.											.	MUT	70	.	0			c.T1952A						.						124	121	122					6																	49407923		2203	4300	6503	SO:0001583	missense	4594	exon11			ACCTGGAAAAGAG		CCDS4924.1	6p21	2012-10-02	2010-04-30		ENSG00000146085	ENSG00000146085	5.4.99.2		7526	protein-coding gene	gene with protein product		609058	"methylmalonyl Coenzyme A mutase"			2907507, 9503014	Standard	NM_000255		Approved		uc003ozg.4	P22033	OTTHUMG00000014814	ENST00000274813.3:c.1952T>A	chr6.hg19:g.49407923A>T	ENSP00000274813:p.Phe651Tyr	56.0	0.0		72.0	25.0	NM_000255	A8K953|Q5SYZ3|Q96B11|Q9UD64	Missense_Mutation	SNP	ENST00000274813.3	hg19	CCDS4924.1	.	.	.	.	.	.	.	.	.	.	A	27.4	4.824281	0.90955	.	.	ENSG00000146085	ENST00000274813;ENST00000540138	D	0.96200	-3.94	5.68	5.68	0.88126	Cobalamin (vitamin B12)-binding (4);Methylmalonyl-CoA mutase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98061	0.9361	M	0.92317	3.295	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99305	1.0902	10	0.87932	D	0	-21.6676	15.1058	0.72322	1.0:0.0:0.0:0.0	.	651	P22033	MUTA_HUMAN	Y	651;98	ENSP00000274813:F651Y	ENSP00000274813:F651Y	F	-	2	0	MUT	49515882	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	8.962000	0.93254	2.161000	0.67846	0.482000	0.46254	TTC	.	.		0.368	MUT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040854.1			T	49407923	A	T	49407923	3	4	373	1	0	0	0	0	1	0	0	0	10000	246	9	4	312	4	MUT	6	49407923	Missense_Mutation	SNP	A	TCGA-ZS-A9CG-01A-11D-A36X-10	18849546	49407923	121707144	29	51543										
DDX43	55510	hgsc.bcm.edu	37	chr6	74121953	74121953	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	1	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	catggcctcattcagttcatCgcctcgcacaatcttatttg	6	13	4	0			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr6:74121953C>A	ENST00000370336.4	+	11	1464	c.1306C>A	c.(1306-1308)Cgc>Agc	p.R436S	DDX43_ENST00000479773.1_3'UTR	NM_018665.2	NP_061135.2	Q9NXZ2	DDX43_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 43	436	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)			NS(1)|breast(2)|central_nervous_system(1)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	24						TTCAGTTCATCGCCTCGCACA	0.323																																					p.R436S		Atlas-SNP	.											DDX43,middle_lobe,carcinoma,0,1	DDX43	69	.	0			c.C1306A						.						189	172	178					6																	74121953		2203	4300	6503	SO:0001583	missense	55510	exon11			GTTCATCGCCTCG		CCDS4977.1	6q13	2014-01-21			ENSG00000080007	ENSG00000080007		"DEAD-boxes"	18677	protein-coding gene	gene with protein product	"cancer/testis antigen 13"	606286				10919659	Standard	NM_018665		Approved	HAGE, DKFZp434H2114, CT13	uc003pgw.3	Q9NXZ2	OTTHUMG00000015033	ENST00000370336.4:c.1306C>A	chr6.hg19:g.74121953C>A	ENSP00000359361:p.Arg436Ser	126.0	0.0		119.0	65.0	NM_018665	B4E0C8|Q6NXR1	Missense_Mutation	SNP	ENST00000370336.4	hg19	CCDS4977.1	.	.	.	.	.	.	.	.	.	.	C	14.71	2.616994	0.46736	.	.	ENSG00000080007	ENST00000370336	T	0.15139	2.45	5.22	3.38	0.38709	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.15435	0.0372	N	0.17872	0.535	0.80722	D	1	D	0.76494	0.999	D	0.75484	0.986	T	0.03739	-1.1008	10	0.51188	T	0.08	.	14.0177	0.64533	0.2909:0.7091:0.0:0.0	.	436	Q9NXZ2	DDX43_HUMAN	S	436	ENSP00000359361:R436S	ENSP00000359361:R436S	R	+	1	0	DDX43	74178674	1.000000	0.71417	0.988000	0.46212	0.032000	0.12392	4.059000	0.57470	0.645000	0.30675	0.561000	0.74099	CGC	.	.		0.323	DDX43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041219.3	NM_018665		A	74121953	C	A	74121953	3	1	373	1	0	0	0	0	1	0	0	0	4365	884	31	1	1348	1	DDX43	6	74121953	Missense_Mutation	SNP	C	TCGA-ZS-A9CG-01A-11D-A36X-10	24714030	74121953	96993114	30	51544										
FILIP1	27145	hgsc.bcm.edu	37	chr6	76022223	76022223	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	gtgattcctgggagagcgaaGgacagtgccggtggaaacct	16	8	0	2			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr6:76022223G>A	ENST00000237172.7	-	5	3655	c.3325C>T	c.(3325-3327)Ctt>Ttt	p.L1109F	FILIP1_ENST00000498523.1_5'UTR|FILIP1_ENST00000393004.2_Missense_Mutation_p.L1109F|FILIP1_ENST00000370020.1_Missense_Mutation_p.L1010F	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	1109										breast(3)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)	80						GGAGAGCGAAGGACAGTGCCG	0.542																																					p.L1109F		Atlas-SNP	.											.	FILIP1	173	.	0			c.C3325T						.						221	166	184					6																	76022223		2203	4300	6503	SO:0001583	missense	27145	exon5			AGCGAAGGACAGT	AB033101	CCDS4984.1, CCDS75480.1	6q14.1	2008-02-05			ENSG00000118407	ENSG00000118407			21015	protein-coding gene	gene with protein product		607307				10574462	Standard	XM_005248713		Approved	FILIP, KIAA1275	uc003pia.3	Q7Z7B0	OTTHUMG00000015056	ENST00000237172.7:c.3325C>T	chr6.hg19:g.76022223G>A	ENSP00000237172:p.Leu1109Phe	231.0	0.0		228.0	85.0	NM_015687	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Missense_Mutation	SNP	ENST00000237172.7	hg19	CCDS4984.1	.	.	.	.	.	.	.	.	.	.	G	18.71	3.682928	0.68157	.	.	ENSG00000118407	ENST00000393004;ENST00000237172;ENST00000370020	T;T;T	0.20881	2.05;2.04;2.05	5.86	5.86	0.93980	.	0.055829	0.64402	D	0.000001	T	0.33352	0.0860	L	0.59436	1.845	0.51767	D	0.999936	D;D;D	0.71674	0.998;0.987;0.985	P;P;P	0.62560	0.904;0.753;0.79	T	0.00496	-1.1705	10	0.35671	T	0.21	-7.7723	20.1865	0.98220	0.0:0.0:1.0:0.0	.	1109;1109;1109	A8K2G7;Q7Z7B0;Q7Z7B0-2	.;FLIP1_HUMAN;.	F	1109;1109;1010	ENSP00000376728:L1109F;ENSP00000237172:L1109F;ENSP00000359037:L1010F	ENSP00000237172:L1109F	L	-	1	0	FILIP1	76078943	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	3.296000	0.51802	2.775000	0.95449	0.655000	0.94253	CTT	.	.		0.542	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179		A	76022223	G	A	76022223	3	1	373	1	0	0	0	0	1	0	0	0	5902	1000	35	3	324	3	FILIP1	6	76022223	Missense_Mutation	SNP	G	TCGA-ZS-A9CG-01A-11D-A36X-10	1900270	76022223	95092844	31	51545										
PRDM1	639	hgsc.bcm.edu	37	chr6	106552764	106552764	+	Silent	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	gaactctgcccaaagaatgtCccaaagagagagtacagcgt	10	10	1	3			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr6:106552764C>T	ENST00000369096.4	+	5	963	c.729C>T	c.(727-729)gtC>gtT	p.V243V	PRDM1_ENST00000369089.3_Silent_p.V109V|PRDM1_ENST00000369091.2_Silent_p.V207V	NM_001198.3	NP_001189.2	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain	243					cell fate commitment (GO:0045165)|eye photoreceptor cell development (GO:0042462)|germ cell development (GO:0007281)|intestinal epithelial cell development (GO:0060576)|maternal placenta development (GO:0001893)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gene expression (GO:0010628)|post-embryonic development (GO:0009791)|transcription, DNA-templated (GO:0006351)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(59)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(5)|urinary_tract(2)	94	Breast(9;0.022)	all_cancers(87;2.2e-31)|all_epithelial(87;2.03e-21)|Acute lymphoblastic leukemia(125;4.99e-11)|all_lung(197;7.55e-09)|all_hematologic(75;5.82e-08)|Lung NSC(302;1.28e-06)|Colorectal(196;0.0112)|Ovarian(999;0.0365)		all cancers(137;1.83e-46)|Epithelial(106;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(136;1.99e-20)|GBM - Glioblastoma multiforme(226;3.72e-11)|BRCA - Breast invasive adenocarcinoma(108;1.38e-05)		CAAAGAATGTCCCAAAGAGAG	0.453			"D, N, Mis, F, S"		DLBCL																																p.V243V		Atlas-SNP	.		Rec	yes		6	6q21	639	"PR domain containing 1, with ZNF domain"		L	.	PRDM1	195	.	0			c.C729T						.						198	212	207					6																	106552764		2203	4300	6503	SO:0001819	synonymous_variant	639	exon5			GAATGTCCCAAAG		CCDS5054.2, CCDS34505.1	6q21	2013-01-08			ENSG00000057657	ENSG00000057657		"Zinc fingers, C2H2-type"	9346	protein-coding gene	gene with protein product		603423		BLIMP1		1851123	Standard	NM_001198		Approved	PRDI-BF1	uc003prd.2	O75626	OTTHUMG00000015299	ENST00000369096.4:c.729C>T	chr6.hg19:g.106552764C>T		167.0	0.0		112.0	41.0	NM_001198	B2REA6|E1P5E0|Q86WM7	Silent	SNP	ENST00000369096.4	hg19	CCDS5054.2																																																																																			.	.		0.453	PRDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041661.3			T	106552764	C	T	106552764	2	4	373	1	0	0	0	0	0	0	0	1	12462	842	30	3		3	PRDM1	6	106552764	Silent	SNP	C	TCGA-ZS-A9CG-01A-11D-A36X-10	30530541	106552764	64562303	32	51546										
ADCY1	107	hgsc.bcm.edu	37	chr7	45750131	45750131	+	Silent	SNP	C	C	T	0	1	1	0	1	0	1	0	1	1	0	1	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	gctggctgttttctaggcatCaatgttggccctgtggtggc	14	9	2	0			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr7:45750131C>T	ENST00000297323.7	+	19	2959	c.2937C>T	c.(2935-2937)atC>atT	p.I979I		NM_021116.2	NP_066939.1	Q08828	ADCY1_HUMAN	adenylate cyclase 1 (brain)	979					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|axonogenesis (GO:0007409)|cellular response to glucagon stimulus (GO:0071377)|circadian rhythm (GO:0007623)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of circadian rhythm (GO:0042752)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(33)|ovary(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	71					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	TTCTAGGCATCAATGTTGGCC	0.577																																					p.I979I		Atlas-SNP	.											.	ADCY1	187	.	0			c.C2937T						.						88	83	85					7																	45750131		2203	4300	6503	SO:0001819	synonymous_variant	107	exon19			AGGCATCAATGTT	L05500	CCDS34631.1, CCDS75593.1	7p13-p12	2013-02-04			ENSG00000164742	ENSG00000164742	4.6.1.1	"Adenylate cyclases"	232	protein-coding gene	gene with protein product		103072				8314585	Standard	NM_021116		Approved	AC1	uc003tne.4	Q08828	OTTHUMG00000155420	ENST00000297323.7:c.2937C>T	chr7.hg19:g.45750131C>T		109.0	0.0		95.0	38.0	NM_021116	A4D2L8|Q75MI1	Silent	SNP	ENST00000297323.7	hg19	CCDS34631.1																																																																																			.	.		0.577	ADCY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340055.2	NM_021116		T	45750131	C	T	45750131	2	4	373	1	0	0	0	0	0	0	0	1	292	816	29	3		3	ADCY1	7	45750131	Silent	SNP	C	TCGA-ZS-A9CG-01A-11D-A36X-10		45750131	113388532	33	51547										
SEMA3D	223117	hgsc.bcm.edu	37	chr7	84651739	84651739	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	acattacatcgtactggccaTcttctgcaatgacatgatcc	6	12	2	2			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr7:84651739T>A	ENST00000284136.6	-	11	1425	c.1382A>T	c.(1381-1383)gAt>gTt	p.D461V	SEMA3D_ENST00000484038.1_5'UTR	NM_152754.2	NP_689967.2	O95025	SEM3D_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	461	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(1)|breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(19)|lung(29)|ovary(3)|pancreas(1)|prostate(4)|skin(2)	73						GTACTGGCCATCTTCTGCAAT	0.378																																					p.D461V	Ovarian(63;442 1191 17318 29975 31528)	Atlas-SNP	.											.	SEMA3D	177	.	0			c.A1382T						.						252	224	234					7																	84651739		2203	4300	6503	SO:0001583	missense	223117	exon11			TGGCCATCTTCTG	BC029590	CCDS34676.1	7q21.11	2013-01-11			ENSG00000153993	ENSG00000153993		"Semaphorins", "Immunoglobulin superfamily / V-set domain containing"	10726	protein-coding gene	gene with protein product		609907					Standard	NM_152754		Approved	coll-2, Sema-Z2	uc003uic.3	O95025	OTTHUMG00000154569	ENST00000284136.6:c.1382A>T	chr7.hg19:g.84651739T>A	ENSP00000284136:p.Asp461Val	117.0	0.0		139.0	56.0	NM_152754	A6NK46|Q6UW77|Q8NCQ1	Missense_Mutation	SNP	ENST00000284136.6	hg19	CCDS34676.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.481672	0.84747	.	.	ENSG00000153993	ENST00000284136	T	0.15952	2.38	5.67	5.67	0.87782	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.45895	0.1365	M	0.89287	3.02	0.80722	D	1	D	0.57899	0.981	P	0.59889	0.865	T	0.55829	-0.8079	10	0.87932	D	0	.	15.9171	0.79527	0.0:0.0:0.0:1.0	.	461	O95025	SEM3D_HUMAN	V	461	ENSP00000284136:D461V	ENSP00000284136:D461V	D	-	2	0	SEMA3D	84489675	1.000000	0.71417	1.000000	0.80357	0.854000	0.48673	8.040000	0.89188	2.152000	0.67230	0.455000	0.32223	GAT	.	.		0.378	SEMA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336084.2	NM_152754		A	84651739	T	A	84651739	3	1	373	1	0	0	0	0	1	0	0	0	14042	1435	50	4	979	4	SEMA3D	7	84651739	Missense_Mutation	SNP	T	TCGA-ZS-A9CG-01A-11D-A36X-10	38901608	84651739	74486924	34	51548										
ABCB1	5243	hgsc.bcm.edu	37	chr7	87195498	87195498	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	acccagtgaaaaatgttgccAttgactgaaagaacattcca	7	9	0	4			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr7:87195498A>T	ENST00000265724.3	-	8	1007	c.590T>A	c.(589-591)aTg>aAg	p.M197K	ABCB1_ENST00000543898.1_Missense_Mutation_p.M133K	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	197	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				drug transmembrane transport (GO:0006855)|G2/M transition of mitotic cell cycle (GO:0000086)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|stem cell proliferation (GO:0072089)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(14)|kidney(9)|large_intestine(14)|lung(48)|ovary(4)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	111	Esophageal squamous(14;0.00164)				Acebutolol(DB01193)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Adenosine triphosphate(DB00171)|ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Albendazole(DB00518)|Alfentanil(DB00802)|Alitretinoin(DB00523)|Amantadine(DB00915)|Aminohippurate(DB00345)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Amsacrine(DB00276)|Apixaban(DB06605)|Arsenic trioxide(DB01169)|Astemizole(DB00637)|Atazanavir(DB01072)|Atenolol(DB00335)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzocaine(DB01086)|Bepridil(DB01244)|Betamethasone(DB00443)|Biperiden(DB00810)|Boceprevir(DB08873)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Bromocriptine(DB01200)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Canagliflozin(DB08907)|Candesartan(DB00796)|Captopril(DB01197)|Carbamazepine(DB00564)|Carfilzomib(DB08889)|Carvedilol(DB01136)|Caspofungin(DB00520)|Chloroquine(DB00608)|Chlorpromazine(DB00477)|Chlorpropamide(DB00672)|Chlorprothixene(DB01239)|Cilazapril(DB01340)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisplatin(DB00515)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Clofazimine(DB00845)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabigatran etexilate(DB06695)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dipyridamole(DB00975)|Docetaxel(DB01248)|Domperidone(DB01184)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Dronedarone(DB04855)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Etravirine(DB06414)|Ezetimibe(DB00973)|Felodipine(DB01023)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fidaxomicin(DB08874)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluticasone furoate(DB08906)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gemcitabine(DB00441)|Glyburide(DB01016)|Gramicidin D(DB00027)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Imatinib(DB00619)|Imipramine(DB00458)|Indacaterol(DB05039)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketoconazole(DB01026)|Lamivudine(DB00709)|Lamotrigine(DB00555)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lenalidomide(DB00480)|Levetiracetam(DB01202)|Levofloxacin(DB01137)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Liothyronine(DB00279)|Liotrix(DB01583)|Lisinopril(DB00722)|Lomitapide(DB08827)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Mannitol(DB00742)|Maprotiline(DB00934)|Mebendazole(DB00643)|Mefloquine(DB00358)|Megestrol acetate(DB00351)|Meprobamate(DB00371)|Methadone(DB00333)|Methotrexate(DB00563)|Methylprednisolone(DB00959)|Metoprolol(DB00264)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mitomycin(DB00305)|Mitoxantrone(DB01204)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nadolol(DB01203)|Naloxone(DB01183)|Naltrexone(DB00704)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Neostigmine(DB01400)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nizatidine(DB00585)|Norethindrone(DB00717)|Olanzapine(DB00334)|Omeprazole(DB00338)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paroxetine(DB00715)|Pazopanib(DB06589)|Perindopril(DB00790)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Pitavastatin(DB08860)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pravastatin(DB00175)|Prazosin(DB00457)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Progesterone(DB00396)|Promethazine(DB01069)|Propafenone(DB01182)|Propranolol(DB00571)|Protriptyline(DB00344)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reboxetine(DB00234)|Regorafenib(DB08896)|Reserpine(DB00206)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Roxithromycin(DB00778)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Scopolamine(DB00747)|Selegiline(DB01037)|Sertraline(DB01104)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|SOFOSBUVIR(DB08934)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Streptozocin(DB00428)|Sulfinpyrazone(DB01138)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telaprevir(DB05521)|Telmisartan(DB00966)|Temsirolimus(DB06287)|Terazosin(DB01162)|Testosterone(DB00624)|Ticagrelor(DB08816)|Timolol(DB00373)|Tolvaptan(DB06212)|Topotecan(DB01030)|Toremifene(DB00539)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Vecuronium(DB01339)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voacamine(DB04877)|Zidovudine(DB00495)	AAATGTTGCCATTGACTGAAA	0.383																																					p.M197K		Atlas-SNP	.											.	ABCB1	263	.	0			c.T590A						.						155	142	147					7																	87195498		2203	4300	6503	SO:0001583	missense	5243	exon8			GTTGCCATTGACT	M14758	CCDS5608.1	7q21.12	2012-03-14	2004-05-12		ENSG00000085563	ENSG00000085563		"CD molecules", "ATP binding cassette transporters / subfamily B"	40	protein-coding gene	gene with protein product	"multidrug resistance protein 1"	171050	"colchicin sensitivity"	PGY1, MDR1, CLCS		3027054	Standard	NM_000927		Approved	P-gp, CD243, GP170, ABC20	uc003uiz.2	P08183	OTTHUMG00000023393	ENST00000265724.3:c.590T>A	chr7.hg19:g.87195498A>T	ENSP00000265724:p.Met197Lys	207.0	0.0		164.0	57.0	NM_000927	A8K294|B5AK60|Q12755|Q14812	Missense_Mutation	SNP	ENST00000265724.3	hg19	CCDS5608.1	.	.	.	.	.	.	.	.	.	.	A	14.09	2.430786	0.43122	.	.	ENSG00000085563	ENST00000265724;ENST00000543898	D;D	0.89939	-2.59;-2.59	5.86	5.86	0.93980	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.888482	0.10114	N	0.714267	D	0.90438	0.7006	M	0.73430	2.235	0.21290	N	0.999733	B;B	0.31949	0.348;0.012	B;B	0.37692	0.256;0.035	D	0.84162	0.0429	10	0.62326	D	0.03	-0.0156	12.5051	0.55977	0.8752:0.0:0.0:0.1248	.	133;197	B5AK60;P08183	.;MDR1_HUMAN	K	197;133	ENSP00000265724:M197K;ENSP00000444095:M133K	ENSP00000265724:M197K	M	-	2	0	ABCB1	87033434	0.800000	0.28916	0.667000	0.29798	0.998000	0.95712	3.388000	0.52509	2.240000	0.73641	0.533000	0.62120	ATG	.	.		0.383	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2	NM_000927		T	87195498	A	T	87195498	3	4	373	1	0	0	0	0	1	0	0	0	40	217	8	4	3340	4	ABCB1	7	87195498	Missense_Mutation	SNP	A	TCGA-ZS-A9CG-01A-11D-A36X-10	2543759	87195498	71943165	35	51549										
PSMC2	5701	hgsc.bcm.edu	37	chr7	103008217	103008217	+	Nonsense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	tgagtgttgaaagagatatcAgatttgaactgttagcacga	11	4	1	5			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr7:103008217A>T	ENST00000435765.1	+	12	1516	c.1105A>T	c.(1105-1107)Aga>Tga	p.R369*	SLC26A5_ENST00000356767.4_Intron|SLC26A5_ENST00000339444.6_Intron|PSMC2_ENST00000292644.3_Nonsense_Mutation_p.R369*|SLC26A5_ENST00000393735.2_Intron|PSMC2_ENST00000544811.1_Nonsense_Mutation_p.R232*	NM_002803.3	NP_002794.1	P35998	PRS7_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 2	369					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|osteoblast differentiation (GO:0001649)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	21						AAGAGATATCAGATTTGAACT	0.363																																					p.R369X		Atlas-SNP	.											.	PSMC2	38	.	0			c.A1105T						.						104	106	105					7																	103008217		2203	4300	6503	SO:0001587	stop_gained	5701	exon11			GATATCAGATTTG	D11094	CCDS5731.1	7q22.1-q22.3	2010-04-21			ENSG00000161057	ENSG00000161057		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9548	protein-coding gene	gene with protein product	"proteasome 26S subunit, ATPase, 2", "mammalian suppressor of sgv-1 of yeast", "protease 26S subunit 7", "putative protein product of Nbla10058"	154365				9473509, 1377363	Standard	NM_002803		Approved	MSS1, S7, Nbla10058	uc003vbs.3	P35998	OTTHUMG00000157206	ENST00000435765.1:c.1105A>T	chr7.hg19:g.103008217A>T	ENSP00000391211:p.Arg369*	107.0	0.0		101.0	25.0	NM_002803	A4D0Q1|B7Z5E2|Q3LIA5|Q9UDI3	Nonsense_Mutation	SNP	ENST00000435765.1	hg19	CCDS5731.1	.	.	.	.	.	.	.	.	.	.	A	27.3	4.815698	0.90790	.	.	ENSG00000161057	ENST00000435765;ENST00000292644;ENST00000544811	.	.	.	5.1	-0.64	0.11493	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.7382	15.3517	0.74393	0.4118:0.5882:0.0:0.0	.	.	.	.	X	369;369;232	.	ENSP00000292644:R369X	R	+	1	2	PSMC2	102795453	0.969000	0.33509	0.994000	0.49952	0.997000	0.91878	1.142000	0.31540	-0.359000	0.08150	0.524000	0.50904	AGA	.	.		0.363	PSMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347922.1	NM_002803		T	103008217	A	T	103008217	4	4	373	1	0	0	0	0	0	1	0	0	12698	180	7	4	1147	4	PSMC2	7	103008217	Nonsense_Mutation	SNP	A	TCGA-ZS-A9CG-01A-11D-A36X-10	15812719	103008217	56130446	36	51550										
SMO	6608	hgsc.bcm.edu	37	chr7	128852200	128852200	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	gtgcaccggcccccgtggcaTgggctcatggccgccgacag	15	16	1	0			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr7:128852200T>A	ENST00000249373.3	+	12	2552	c.2272T>A	c.(2272-2274)Tgg>Agg	p.W758R	RP11-286H14.8_ENST00000466717.1_RNA	NM_005631.4	NP_005622.1	Q99835	SMO_HUMAN	smoothened, frizzled class receptor	758					adenohypophysis development (GO:0021984)|anterior/posterior pattern specification (GO:0009952)|atrial septum morphogenesis (GO:0060413)|axon extension involved in axon guidance (GO:0048846)|canonical Wnt signaling pathway (GO:0060070)|cardioblast differentiation (GO:0010002)|cell fate specification (GO:0001708)|cellular response to cholesterol (GO:0071397)|central nervous system neuron differentiation (GO:0021953)|cerebellar cortex morphogenesis (GO:0021696)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|detection of cell density by contact stimulus involved in contact inhibition (GO:0060248)|determination of left/right asymmetry in lateral mesoderm (GO:0003140)|determination of left/right symmetry (GO:0007368)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic neurocranium morphogenesis (GO:0048702)|embryonic viscerocranium morphogenesis (GO:0048703)|epithelial-mesenchymal cell signaling (GO:0060684)|exocrine pancreas development (GO:0031017)|facial nerve development (GO:0021561)|floor plate formation (GO:0021508)|forebrain morphogenesis (GO:0048853)|gonad development (GO:0008406)|hair follicle morphogenesis (GO:0031069)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|mammary gland epithelial cell differentiation (GO:0060644)|mesenchymal to epithelial transition involved in metanephric renal vesicle formation (GO:0072285)|midgut development (GO:0007494)|multicellular organism growth (GO:0035264)|muscle cell fate commitment (GO:0042693)|myoblast migration (GO:0051451)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA binding (GO:0043392)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of gene expression (GO:0010629)|negative regulation of hair follicle development (GO:0051799)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neuron fate commitment (GO:0048663)|neuron projection regeneration (GO:0031102)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|otolith morphogenesis (GO:0032474)|pancreas morphogenesis (GO:0061113)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gene expression (GO:0010628)|positive regulation of hh target transcription factor activity (GO:0007228)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to nucleus (GO:0034504)|protein stabilization (GO:0050821)|regulation of heart morphogenesis (GO:2000826)|regulation of stem cell maintenance (GO:2000036)|renal system development (GO:0072001)|semicircular canal morphogenesis (GO:0048752)|skeletal muscle fiber development (GO:0048741)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021910)|somite development (GO:0061053)|spermatogenesis (GO:0007283)|thalamus development (GO:0021794)|type B pancreatic cell development (GO:0003323)|vasculogenesis (GO:0001570)|ventral midline determination (GO:0007371)	ciliary membrane (GO:0060170)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	drug binding (GO:0008144)|G-protein coupled receptor activity (GO:0004930)|patched binding (GO:0005113)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			biliary_tract(1)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(14)|liver(1)|lung(11)|pancreas(2)|prostate(1)|skin(20)|upper_aerodigestive_tract(3)|urinary_tract(1)	64					Fluocinonide(DB01047)|Vismodegib(DB08828)	CCCCGTGGCATGGGCTCATGG	0.637			Mis		skin basal cell																																p.W758R		Atlas-SNP	.		Dom	yes		7	7q31-q32	6608	smoothened homolog (Drosophila)		E	.	SMO	145	.	0			c.T2272A						.						39	43	42					7																	128852200		2202	4300	6502	SO:0001583	missense	6608	exon12			GTGGCATGGGCTC	U84401	CCDS5811.1	7q32.1	2014-01-29	2014-01-29	2003-01-17	ENSG00000128602	ENSG00000128602		"GPCR / Class F : Frizzled receptors"	11119	protein-coding gene	gene with protein product	"frizzled family member 11"	601500	"smoothened (Drosophila) homolog", "smoothened homolog (Drosophila)", "smoothened, seven transmembrane spanning receptor", "smoothened, frizzled family receptor"	SMOH		9628830	Standard	NM_005631		Approved	FZD11	uc003vor.3	Q99835	OTTHUMG00000158421	ENST00000249373.3:c.2272T>A	chr7.hg19:g.128852200T>A	ENSP00000249373:p.Trp758Arg	147.0	0.0		120.0	44.0	NM_005631	A4D1K5	Missense_Mutation	SNP	ENST00000249373.3	hg19	CCDS5811.1	.	.	.	.	.	.	.	.	.	.	T	6.709	0.499503	0.12762	.	.	ENSG00000128602	ENST00000249373	T	0.75050	-0.9	5.24	5.24	0.73138	.	0.297293	0.33959	N	0.004389	T	0.57198	0.2037	N	0.19112	0.55	0.36123	D	0.845578	B	0.02656	0.0	B	0.04013	0.001	T	0.59144	-0.7509	10	0.31617	T	0.26	.	8.6726	0.34159	0.1819:0.0:0.0:0.8181	.	758	Q99835	SMO_HUMAN	R	758	ENSP00000249373:W758R	ENSP00000249373:W758R	W	+	1	0	SMO	128639436	0.968000	0.33430	0.999000	0.59377	0.170000	0.22686	1.966000	0.40481	1.973000	0.57446	0.482000	0.46254	TGG	.	.		0.637	SMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350986.1	NM_005631		A	128852200	T	A	128852200	3	1	373	1	0	0	0	0	1	0	0	0	14815	1464	51	4	2318	4	SMO	7	128852200	Missense_Mutation	SNP	T	TCGA-ZS-A9CG-01A-11D-A36X-10	25843983	128852200	30286463	37	51551										
DGKI	9162	hgsc.bcm.edu	37	chr7	137154301	137154301	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	aaaggcagaactcaccatctAggaagcaccaccgaggagag	11	11	2	2			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr7:137154301A>G	ENST00000288490.5	-	25	2492	c.2492T>C	c.(2491-2493)cTa>cCa	p.L831P	DGKI_ENST00000453654.2_Missense_Mutation_p.L531P|DGKI_ENST00000446122.1_Missense_Mutation_p.L813P|DGKI_ENST00000424189.2_Missense_Mutation_p.L834P	NM_004717.2	NP_004708.1	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	831					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|positive regulation of Ras protein signal transduction (GO:0046579)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of Rap GTPase activity (GO:0032317)	cytoplasm (GO:0005737)|guanyl-nucleotide exchange factor complex (GO:0032045)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(46)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	84						CTCACCATCTAGGAAGCACCA	0.512																																					p.L831P		Atlas-SNP	.											.	DGKI	335	.	0			c.T2492C						.						121	107	112					7																	137154301		2203	4300	6503	SO:0001583	missense	9162	exon25			CCATCTAGGAAGC	AF061936	CCDS5845.1	7q32.3-q33	2013-01-10			ENSG00000157680	ENSG00000157680		"Ankyrin repeat domain containing"	2855	protein-coding gene	gene with protein product		604072				9830018	Standard	NM_004717		Approved	DGK-IOTA	uc003vtt.3	O75912	OTTHUMG00000155697	ENST00000288490.5:c.2492T>C	chr7.hg19:g.137154301A>G	ENSP00000288490:p.Leu831Pro	131.0	0.0		109.0	44.0	NM_004717	A4D1Q9|Q9NZ49	Missense_Mutation	SNP	ENST00000288490.5	hg19	CCDS5845.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.449593	0.84101	.	.	ENSG00000157680	ENST00000453654;ENST00000540376;ENST00000424189;ENST00000288490;ENST00000446122	T;T;T	0.38560	1.48;1.13;1.34	5.65	5.65	0.86999	.	0.000000	0.64402	D	0.000001	T	0.65595	0.2706	M	0.76170	2.325	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.993;0.999	T	0.69491	-0.5131	10	0.72032	D	0.01	.	15.8828	0.79216	1.0:0.0:0.0:0.0	.	531;831	E9PFX6;O75912	.;DGKI_HUMAN	P	531;779;834;831;813	ENSP00000392161:L531P;ENSP00000288490:L831P;ENSP00000399131:L813P	ENSP00000288490:L831P	L	-	2	0	DGKI	136804841	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.816000	0.75247	2.152000	0.67230	0.533000	0.62120	CTA	.	.		0.512	DGKI-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341286.3	NM_004717		G	137154301	A	G	137154301	3	3	373	1	0	0	0	0	1	0	0	0	4473	420	15	2	745	2	DGKI	7	137154301	Missense_Mutation	SNP	A	TCGA-ZS-A9CG-01A-11D-A36X-10	8302101	137154301	21984362	38	51552										
WDR60	55112	hgsc.bcm.edu	37	chr7	158715203	158715203	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	tgtgtgggatatttggcagcCttcagggccacagaaagttc	13	8	1	1			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr7:158715203C>A	ENST00000407559.3	+	16	2215	c.2057C>A	c.(2056-2058)cCt>cAt	p.P686H		NM_018051.4	NP_060521.4	Q8WVS4	WDR60_HUMAN	WD repeat domain 60	686					cell projection organization (GO:0030030)	cilium (GO:0005929)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(3)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(4)|lung(16)|ovary(2)	35	Ovarian(565;0.152)	all_cancers(7;1.25e-09)|all_epithelial(9;0.000894)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)|STAD - Stomach adenocarcinoma(7;0.18)		ATTTGGCAGCCTTCAGGGCCA	0.547																																					p.P686H		Atlas-SNP	.											.	WDR60	94	.	0			c.C2057A						.						69	69	69					7																	158715203		2120	4221	6341	SO:0001583	missense	55112	exon16			GGCAGCCTTCAGG		CCDS47757.1	7q36.3	2013-11-15			ENSG00000126870	ENSG00000126870		"WD repeat domain containing"	21862	protein-coding gene	gene with protein product		615462				23910462	Standard	NM_018051		Approved	FLJ10300, FAP163	uc003woe.4	Q8WVS4	OTTHUMG00000151443	ENST00000407559.3:c.2057C>A	chr7.hg19:g.158715203C>A	ENSP00000384290:p.Pro686His	140.0	0.0		115.0	47.0	NM_018051	Q9NW58	Missense_Mutation	SNP	ENST00000407559.3	hg19	CCDS47757.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.430714	0.83776	.	.	ENSG00000126870	ENST00000407559	T	0.66460	-0.21	5.27	5.27	0.74061	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.83603	0.5290	M	0.85859	2.78	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.86409	0.1747	10	0.87932	D	0	-18.3572	16.3685	0.83344	0.0:1.0:0.0:0.0	.	169;686	A4D230;Q8WVS4	.;WDR60_HUMAN	H	686	ENSP00000384290:P686H	ENSP00000384290:P686H	P	+	2	0	WDR60	158407964	1.000000	0.71417	0.967000	0.41034	0.982000	0.71751	5.995000	0.70631	2.439000	0.82584	0.591000	0.81541	CCT	.	.		0.547	WDR60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322668.1	NM_018051		A	158715203	C	A	158715203	3	1	373	1	0	0	0	0	1	0	0	0	17326	681	24	3	2119	3	WDR60	7	158715203	Missense_Mutation	SNP	C	TCGA-ZS-A9CG-01A-11D-A36X-10	21560902	158715203	423460	39	51553										
RHOBTB2	23221	hgsc.bcm.edu	37	chr8	22865129	22865129	+	Silent	SNP	C	C	G	0	1	1	0	1	0	1	1	0	1	1	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	attgctgagctgctcgaggtCtttgatctgcgcatgatggt	13	8	2	3			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr8:22865129C>G	ENST00000251822.6	+	5	1908	c.1371C>G	c.(1369-1371)gtC>gtG	p.V457V	RP11-875O11.1_ENST00000523884.1_RNA|RHOBTB2_ENST00000519685.1_Silent_p.V479V|RHOBTB2_ENST00000522948.1_Silent_p.V464V|RP11-875O11.1_ENST00000502083.2_RNA	NM_015178.2	NP_055993.2	Q9BYZ6	RHBT2_HUMAN	Rho-related BTB domain containing 2	457					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	31		Prostate(55;0.0513)|Breast(100;0.214)		Colorectal(74;0.0157)|COAD - Colon adenocarcinoma(73;0.064)		TGCTCGAGGTCTTTGATCTGC	0.567																																					p.V479V		Atlas-SNP	.											.	RHOBTB2	67	.	0			c.C1437G						.						132	125	128					8																	22865129		2203	4300	6503	SO:0001819	synonymous_variant	23221	exon7			CGAGGTCTTTGAT	AF315385	CCDS6034.1, CCDS55210.1, CCDS55211.1	8p21.2	2013-01-08			ENSG00000008853	ENSG00000008853		"BTB/POZ domain containing"	18756	protein-coding gene	gene with protein product		607352				11222756	Standard	NM_001160036		Approved	KIAA0717, DBC2	uc011kzp.1	Q9BYZ6	OTTHUMG00000097827	ENST00000251822.6:c.1371C>G	chr8.hg19:g.22865129C>G		94.0	0.0		55.0	32.0	NM_001160036	A8K9Z8|D3DSR8|E9PBU2|E9PEI7|O94825|Q8N4A8|Q9BZK6	Silent	SNP	ENST00000251822.6	hg19	CCDS6034.1																																																																																			.	.		0.567	RHOBTB2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000215101.2			G	22865129	C	G	22865129	2	3	373	1	0	0	0	0	0	0	0	1	13349	900	32	4		4	RHOBTB2	8	22865129	Silent	SNP	C	TCGA-ZS-A9CG-01A-11D-A36X-10		22865129	123498893	40	51554										
C8orf80	389643	hgsc.bcm.edu	37	chr8	27888861	27888861	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	ggactgcttaaaagcatctaTgtgaggcatcagagctgaac	11	8	2	3			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr8:27888861T>C	ENST00000413272.2	-	15	1949	c.1807A>G	c.(1807-1809)Ata>Gta	p.I603V	NUGGC_ENST00000341513.6_Missense_Mutation_p.I603V	NM_001010906.1	NP_001010906.1	Q68CJ6	SLIP_HUMAN	nuclear GTPase, germinal center associated	603					cellular response to DNA damage stimulus (GO:0006974)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)										AAAGCATCTATGTGAGGCATC	0.438																																					p.I603V		Atlas-SNP	.											.	.	.	.	0			c.A1807G						.						102	103	103					8																	27888861		1884	4118	6002	SO:0001583	missense	389643	exon15			CATCTATGTGAGG	AB075870	CCDS47833.1	8p21.1	2012-06-07	2012-06-07	2012-06-07	ENSG00000189233	ENSG00000189233			33550	protein-coding gene	gene with protein product	"speckled-like pattern in the germinal center"		"chromosome 8 open reading frame 80"	C8orf80		19734146	Standard	NM_001010906		Approved	HMFN0672, SLIP-GC	uc003xgm.4	Q68CJ6	OTTHUMG00000155970	ENST00000413272.2:c.1807A>G	chr8.hg19:g.27888861T>C	ENSP00000408697:p.Ile603Val	131.0	0.0		57.0	10.0	NM_001010906	Q6ZP73	Missense_Mutation	SNP	ENST00000413272.2	hg19	CCDS47833.1	.	.	.	.	.	.	.	.	.	.	T	9.032	0.987417	0.18889	.	.	ENSG00000189233	ENST00000413272;ENST00000341513	T;T	0.35236	1.32;1.32	5.23	1.26	0.21427	.	0.221629	0.39083	N	0.001475	T	0.19167	0.0460	L	0.27053	0.805	0.27229	N	0.959447	B	0.31077	0.307	B	0.28385	0.089	T	0.11446	-1.0587	10	0.25751	T	0.34	-13.9874	5.3838	0.16206	0.0:0.0912:0.3449:0.564	.	603	Q68CJ6	SLIP_HUMAN	V	603	ENSP00000408697:I603V;ENSP00000345031:I603V	ENSP00000345031:I603V	I	-	1	0	C8orf80	27944780	0.972000	0.33761	0.851000	0.33527	0.255000	0.26057	0.183000	0.16919	0.304000	0.22809	-0.291000	0.09656	ATA	.	.		0.438	NUGGC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342494.1	NM_001010906		C	27888861	T	C	27888861	3	2	373	1	0	0	0	0	1	0	0	0	2441	1464	51	2	603	2	C8orf80	8	27888861	Missense_Mutation	SNP	T	TCGA-ZS-A9CG-01A-11D-A36X-10	5023732	27888861	118475161	41	51555										
MCM4	4173	hgsc.bcm.edu	37	chr8	48883070	48883070	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	gacatgtctctgattatttaGggaattttgcttcagctctt	8	7	3	1			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr8:48883070G>A	ENST00000262105.2	+	11	1643		c.e11-1		MCM4_ENST00000523944.1_Splice_Site|MCM4_ENST00000518680.1_Splice_Site	NM_005914.3	NP_005905.2	P33991	MCM4_HUMAN	minichromosome maintenance complex component 4						DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|single-stranded DNA binding (GO:0003697)			biliary_tract(1)|breast(1)|endometrium(7)|kidney(4)|large_intestine(5)|lung(16)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	44		all_cancers(86;0.026)|all_epithelial(80;0.000748)|Lung NSC(129;0.00327)|all_lung(136;0.00354)				TGATTATTTAGGGAATTTTGC	0.398																																					.		Atlas-SNP	.											.	MCM4	97	.	0			c.1435-1G>A						.						99	102	101					8																	48883070		2203	4300	6503	SO:0001630	splice_region_variant	4173	exon12			TATTTAGGGAATT		CCDS6143.1	8q12-q13	2008-02-05	2007-04-04		ENSG00000104738	ENSG00000104738			6947	protein-coding gene	gene with protein product		602638	"MCM4 minichromosome maintenance deficient 4 (S. cerevisiae)"	CDC21		7601140	Standard	NM_005914		Approved	CDC54, hCdc21, P1-Cdc21, MGC33310	uc003xql.2	P33991	OTTHUMG00000164205	ENST00000262105.2:c.1435-1G>A	chr8.hg19:g.48883070G>A		114.0	0.0		246.0	12.0	NM_182746	Q8NEH1|Q99658	Splice_Site	SNP	ENST00000262105.2	hg19	CCDS6143.1	.	.	.	.	.	.	.	.	.	.	G	19.86	3.905243	0.72868	.	.	ENSG00000104738	ENST00000523944;ENST00000262105;ENST00000396826;ENST00000429229;ENST00000520637	.	.	.	6.17	6.17	0.99709	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MCM4	49045623	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	9.397000	0.97276	2.941000	0.99782	0.655000	0.94253	.	.	.		0.398	MCM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377791.1	NM_005914	Intron	A	48883070	G	A	48883070	5	1	373	1	0	0	0	0	0	0	1	0	9398	1014	35	3	1476	3	MCM4	8	48883070	Splice_Site	SNP	G	TCGA-ZS-A9CG-01A-11D-A36X-10	20994209	48883070	97480952	42	51556										
ATAD2	29028	hgsc.bcm.edu	37	chr8	124369923	124369923	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	gactgcactcattggcaagtGctctggcaaccagagtcttt	10	11	3	1			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr8:124369923G>A	ENST00000287394.5	-	12	1543	c.1436C>T	c.(1435-1437)gCa>gTa	p.A479V	ATAD2_ENST00000534257.1_5'Flank|ATAD2_ENST00000521903.1_5'UTR	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	479					ATP catabolic process (GO:0006200)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	48	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			ATTGGCAAGTGCTCTGGCAAC	0.388																																					p.A479V		Atlas-SNP	.											.	ATAD2	160	.	0			c.C1436T						.						97	87	90					8																	124369923		2203	4300	6503	SO:0001583	missense	29028	exon12			GCAAGTGCTCTGG	BC019909	CCDS6343.1	8q24.13	2014-01-21		2007-02-08	ENSG00000156802	ENSG00000156802		"ATPases / AAA-type"	30123	protein-coding gene	gene with protein product		611941				12477932	Standard	NM_014109		Approved	PRO2000, DKFZp667N1320, MGC5254, MGC29843, CT137	uc003yqh.4	Q6PL18	OTTHUMG00000165090	ENST00000287394.5:c.1436C>T	chr8.hg19:g.124369923G>A	ENSP00000287394:p.Ala479Val	137.0	0.0		237.0	42.0	NM_014109	Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	Missense_Mutation	SNP	ENST00000287394.5	hg19	CCDS6343.1	.	.	.	.	.	.	.	.	.	.	G	36	5.700017	0.96802	.	.	ENSG00000156802	ENST00000287394	D	0.96011	-3.88	5.77	5.77	0.91146	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.97192	0.9082	L	0.54863	1.705	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.994;0.999	D	0.97172	0.9845	10	0.66056	D	0.02	-21.5766	20.3626	0.98863	0.0:0.0:1.0:0.0	.	309;479	Q6PL18-2;Q6PL18	.;ATAD2_HUMAN	V	479	ENSP00000287394:A479V	ENSP00000287394:A479V	A	-	2	0	ATAD2	124439104	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.851000	0.86920	2.885000	0.99019	0.655000	0.94253	GCA	.	.		0.388	ATAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381766.2	NM_014109		A	124369923	G	A	124369923	3	1	373	1	0	0	0	0	1	0	0	0	1071	1319	46	3	2804	3	ATAD2	8	124369923	Missense_Mutation	SNP	G	TCGA-ZS-A9CG-01A-11D-A36X-10	75486853	124369923	21994099	43	51557										
BAI1	575	hgsc.bcm.edu	37	chr8	143624960	143624960	+	Splice_Site	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	actgcccagaccccgcctgcAgaagatcatgcacacccgga	9	17	1	3			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr8:143624960A>G	ENST00000517894.1	+	30	5343		c.e30-1		BAI1_ENST00000323289.5_Splice_Site			O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1						axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)|signal transduction (GO:0007165)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(28)|ovary(4)|pancreas(1)|prostate(7)	57	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					CCCCGCCTGCAGAAGATCATG	0.687																																					.		Atlas-SNP	.											.	BAI1	146	.	0			c.4450-2A>G						.						22	27	26					8																	143624960		2056	4186	6242	SO:0001630	splice_region_variant	575	exon29			GCCTGCAGAAGAT	AB005297	CCDS64985.1	8q24.3	2014-08-08			ENSG00000181790	ENSG00000181790		"-", "GPCR / Class B : Orphans"	943	protein-coding gene	gene with protein product		602682				9533023	Standard	NM_001702		Approved		uc003ywm.3	O14514	OTTHUMG00000164732	ENST00000517894.1:c.4450-1A>G	chr8.hg19:g.143624960A>G		429.0	0.0		784.0	258.0	NM_001702		Splice_Site	SNP	ENST00000517894.1	hg19		.	.	.	.	.	.	.	.	.	.	A	19.75	3.885718	0.72410	.	.	ENSG00000181790	ENST00000517894;ENST00000323289	.	.	.	4.42	4.42	0.53409	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.8463	0.57831	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	BAI1	143621962	1.000000	0.71417	0.994000	0.49952	0.957000	0.61999	8.617000	0.90927	1.635000	0.50512	0.459000	0.35465	.	.	.		0.687	BAI1-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379963.3	NM_001702	Intron	G	143624960	A	G	143624960	5	3	373	1	0	0	0	0	0	0	1	0	1298	202	7	2	4562	2	BAI1	8	143624960	Splice_Site	SNP	A	TCGA-ZS-A9CG-01A-11D-A36X-10	19255037	143624960	2739062	44	51558										
WNK2	65268	hgsc.bcm.edu	37	chr9	96070795	96070795	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	tgaagcccacgctcaaccagCtgaagcagacccagaagctg	10	14	1	4			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr9:96070795C>T	ENST00000297954.4	+	28	6556	c.6556C>T	c.(6556-6558)Ctg>Ttg	p.L2186L	WNK2_ENST00000395475.2_3'UTR|WNK2_ENST00000427277.2_Silent_p.L1761L|WNK2_ENST00000356055.3_3'UTR|WNK2_ENST00000349097.3_Silent_p.L1798L|WNK2_ENST00000395477.2_Silent_p.L2149L	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	2186					intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						GCTCAACCAGCTGAAGCAGAC	0.677																																					p.L2149L		Atlas-SNP	.											.	WNK2	277	.	0			c.C6445T						.						57	43	47					9																	96070795		2201	4294	6495	SO:0001819	synonymous_variant	65268	exon27			AACCAGCTGAAGC	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"serologically defined colon cancer antigen 43"	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.6556C>T	chr9.hg19:g.96070795C>T		267.0	0.0		263.0	37.0	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Silent	SNP	ENST00000297954.4	hg19		.	.	.	.	.	.	.	.	.	.	C	10.14	1.268853	0.23136	.	.	ENSG00000165238	ENST00000411624	.	.	.	5.55	3.61	0.41365	.	.	.	.	.	T	0.58878	0.2153	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53078	-0.8489	4	.	.	.	.	9.0476	0.36356	0.0:0.7656:0.0:0.2344	.	.	.	.	V	1640	.	.	A	+	2	0	WNK2	95110616	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.147000	0.50639	0.622000	0.30249	0.655000	0.94253	GCT	.	.		0.677	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648		T	96070795	C	T	96070795	2	4	373	1	0	0	0	0	0	0	0	1	17393	796	28	3		3	WNK2	9	96070795	Silent	SNP	C	TCGA-ZS-A9CG-01A-11D-A36X-10		96070795	45142636	45	51559										
CELF2	10659	hgsc.bcm.edu	37	chr10	11330509	11330509	+	Missense_Mutation	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	gcgccctgggagccctcacgAgtcccggtgagtgtgggggg	19	12	1	1			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr10:11330509A>G	ENST00000379261.4	+	9	1041	c.949A>G	c.(949-951)Agt>Ggt	p.S317G	CELF2_ENST00000315874.4_Missense_Mutation_p.S293G|CELF2_ENST00000399850.3_Missense_Mutation_p.S293G|CELF2_ENST00000450189.1_Missense_Mutation_p.S324G|CELF2_ENST00000542579.1_Missense_Mutation_p.S324G|CELF2_ENST00000608830.1_Missense_Mutation_p.S293G|CELF2_ENST00000609692.1_Missense_Mutation_p.S293G|CELF2_ENST00000537122.1_Missense_Mutation_p.S206G|CELF2_ENST00000354440.2_Missense_Mutation_p.S293G|CELF2_ENST00000427450.1_Missense_Mutation_p.S293G|CELF2_ENST00000416382.2_Missense_Mutation_p.S317G|CELF2_ENST00000354897.3_Missense_Mutation_p.S293G|CELF2_ENST00000417956.2_Missense_Mutation_p.S293G	NM_001025077.2	NP_001020248.1	O95319	CELF2_HUMAN	CUGBP, Elav-like family member 2	317	Ala-rich.				mRNA processing (GO:0006397)|regulation of heart contraction (GO:0008016)|RNA processing (GO:0006396)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(5)|prostate(1)|skin(1)	16						AGCCCTCACGAGTCCCGGTGA	0.657																																					p.S324G		Atlas-SNP	.											.	CELF2	78	.	0			c.A970G						.						26	29	28					10																	11330509		2046	4189	6235	SO:0001583	missense	10659	exon9			CTCACGAGTCCCG	U69546	CCDS41488.1, CCDS44354.1, CCDS44355.1, CCDS44356.1	10p13	2013-02-12	2010-02-19	2010-02-19	ENSG00000048740	ENSG00000048740		"RNA binding motif (RRM) containing"	2550	protein-coding gene	gene with protein product		602538	"CUG triplet repeat, RNA-binding protein 2", "CUG triplet repeat, RNA binding protein 2"	CUGBP2		7869393, 9887331	Standard	NM_006561		Approved	Etr-3, NAPOR-2, BRUNOL3	uc001ikl.4	O95319	OTTHUMG00000017668	ENST00000379261.4:c.949A>G	chr10.hg19:g.11330509A>G	ENSP00000368563:p.Ser317Gly	43.0	0.0		36.0	15.0	NM_006561	B7ZAN9|Q7KYU4|Q8N499|Q92950|Q96NW9|Q96RQ5|Q96RQ6|Q9UL67	Missense_Mutation	SNP	ENST00000379261.4	hg19	CCDS44354.1	.	.	.	.	.	.	.	.	.	.	A	16.42	3.119646	0.56613	.	.	ENSG00000048740	ENST00000379261;ENST00000416382;ENST00000450189;ENST00000542579;ENST00000399850;ENST00000417956;ENST00000315874;ENST00000354440;ENST00000354897;ENST00000427450;ENST00000537122;ENST00000538632	T;T;T;T;T;T;T;T;T;T	0.47177	0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85	4.72	4.72	0.59763	.	0.135911	0.64402	D	0.000004	T	0.61825	0.2378	L	0.56124	1.755	0.80722	D	1	B;B;P;B;P;B;B	0.52577	0.002;0.003;0.954;0.001;0.779;0.012;0.002	B;B;D;B;B;B;B	0.63597	0.004;0.005;0.916;0.003;0.191;0.027;0.004	T	0.64774	-0.6328	10	0.62326	D	0.03	-12.4685	14.2274	0.65868	1.0:0.0:0.0:0.0	.	301;317;89;312;324;312;317	B4DDE7;B4DS31;B4DMB0;B2RA86;E9PC62;O95319-3;O95319	.;.;.;.;.;.;CELF2_HUMAN	G	317;317;324;324;293;293;293;293;293;293;206;123	ENSP00000368563:S317G;ENSP00000406451:S317G;ENSP00000389951:S324G;ENSP00000443926:S324G;ENSP00000382743:S293G;ENSP00000404834:S293G;ENSP00000315328:S293G;ENSP00000346426:S293G;ENSP00000388530:S293G;ENSP00000438884:S206G	ENSP00000315328:S293G	S	+	1	0	CELF2	11370515	1.000000	0.71417	0.961000	0.40146	0.806000	0.45545	8.359000	0.90093	1.770000	0.52166	0.377000	0.23210	AGT	.	.		0.657	CELF2-201	KNOWN	basic|CCDS	protein_coding	protein_coding				G	11330509	A	G	11330509	3	3	373	1	0	0	0	0	1	0	0	0	3218	304	11	2	1061	2	CELF2	10	11330509	Missense_Mutation	SNP	A	TCGA-ZS-A9CG-01A-11D-A36X-10		11330509	124204238	46	51560										
PARG	8505	hgsc.bcm.edu	37	chr10	51028218	51028218	+	Silent	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	atctcctacttaccaacagtGagtttcctttcagtaaggaa	6	10	2	1			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr10:51028218G>T	ENST00000402038.3	-	13	1313	c.1314C>A	c.(1312-1314)ctC>ctA	p.L438L		NM_003631.2	NP_003622.2	Q86W56	PARG_HUMAN	poly (ADP-ribose) glycohydrolase	923	A-domain.				carbohydrate metabolic process (GO:0005975)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	poly(ADP-ribose) glycohydrolase activity (GO:0004649)			endometrium(5)|kidney(2)|lung(1)|ovary(2)	10				Epithelial(53;0.213)		TACCAACAGTGAGTTTCCTTT	0.428																																					p.L923L		Atlas-SNP	.											.	PARG	46	.	0			c.C2769A						.						128	106	112					10																	51028218		692	1591	2283	SO:0001819	synonymous_variant	8505	exon17			AACAGTGAGTTTC	AF005043	CCDS73130.1	10q11.23	2012-04-20			ENSG00000227345	ENSG00000227345	3.2.1.143		8605	protein-coding gene	gene with protein product		603501				9115250, 10449915	Standard	NM_003631		Approved		uc001jif.3	Q86W56	OTTHUMG00000018201	ENST00000402038.3:c.1314C>A	chr10.hg19:g.51028218G>T		142.0	0.0		134.0	10.0	NM_003631	A5YBK3|B2RC24|B4DIU5|B4DYR4|I6RUV3|Q6E4P6|Q6E4P7|Q7Z742|Q9Y4W7	Silent	SNP	ENST00000402038.3	hg19		.	.	.	.	.	.	.	.	.	.	G	8.675	0.903845	0.17760	.	.	ENSG00000227345	ENST00000432127	.	.	.	6.03	1.95	0.26073	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	-8.0507	0.9853	0.01445	0.1591:0.3564:0.1386:0.3458	.	.	.	.	X	139	.	.	S	-	2	0	PARG	50698224	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	0.937000	0.28951	0.080000	0.16959	-0.302000	0.09304	TCA	.	.		0.428	PARG-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048011.2	NM_003631		T	51028218	G	T	51028218	2	4	373	1	0	0	0	0	0	0	0	1	11457	1277	45	3		3	PARG	10	51028218	Silent	SNP	G	TCGA-ZS-A9CG-01A-11D-A36X-10	39697709	51028218	84506529	47	51561										
CHUK	1147	hgsc.bcm.edu	37	chr10	101980381	101980381	+	Frame_Shift_Del	DEL	T	T	-													0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	tgaagaactatgttttcaggTtttagatctcgatgtataat							TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr10:101980381delT	ENST00000370397.7	-	5	524	c.438delA	c.(436-438)aaafs	p.K146fs		NM_001278.3	NP_001269.3	O15111	IKKA_HUMAN	conserved helix-loop-helix ubiquitous kinase	146	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				anatomical structure morphogenesis (GO:0009653)|cellular response to tumor necrosis factor (GO:0071356)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|morphogenesis of an epithelial sheet (GO:0002011)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hydroperoxide (GO:0033194)|response to lipopolysaccharide (GO:0032496)|response to toxic substance (GO:0009636)|response to virus (GO:0009615)|Rho protein signal transduction (GO:0007266)|skeletal muscle contraction (GO:0003009)|striated muscle cell differentiation (GO:0051146)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|scaffold protein binding (GO:0097110)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(9)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	27		Colorectal(252;0.117)		Epithelial(162;2.05e-10)|all cancers(201;1.91e-08)	Acetylcysteine(DB06151)|Aminosalicylic Acid(DB00233)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	TGTTTTCAGGTTTTAGATCTC	0.318																																					p.P147fs	Ovarian(159;52 1904 10536 35305 37148)	Atlas-INDEL	.											.	CHUK	71	.	0			c.439delC						.						105	103	103					10																	101980381		2203	4299	6502	SO:0001589	frameshift_variant	1147	exon5			.	AF009225	CCDS7488.1	10q24-q25	2008-08-01			ENSG00000213341	ENSG00000213341			1974	protein-coding gene	gene with protein product		600664		TCF16		7558004, 16902410	Standard	XR_246062		Approved	IKK1, IKK-alpha, IkBKA, NFKBIKA, IKKA	uc001kqp.3	O15111	OTTHUMG00000018899	ENST00000370397.7:c.438delA	chr10.hg19:g.101980381delT	ENSP00000359424:p.Lys146fs	99.0	0.0		101.0	45.0	NM_001278	O14666|Q13132|Q5W0I4|Q92467	Frame_Shift_Del	DEL	ENST00000370397.7	hg19	CCDS7488.1																																																																																			.	.		0.318	CHUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049836.1	NM_001278		-	101980381	T	-	101980381	7	5	373	1	0	1	0	1	0	0	0	0	3418	1722	60	0	1867	0	CHUK	10	101980381	Frame_Shift_Del	DEL	T	TCGA-ZS-A9CG-01A-11D-A36X-10	50952163	101980381	33554366	48	51562										
TACC2	10579	hgsc.bcm.edu	37	chr10	123903126	123903126	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	catgcgggtcttcctccctcGgctgcagaacacatagtttc	9	14	1	1	rs145822203	byFrequency	TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr10:123903126G>C	ENST00000369005.1	+	7	6079	c.5739G>C	c.(5737-5739)tcG>tcC	p.S1913S	TACC2_ENST00000513429.1_Intron|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000515273.1_Intron|TACC2_ENST00000369001.1_Intron|TACC2_ENST00000493951.1_3'UTR|TACC2_ENST00000515603.1_Intron|TACC2_ENST00000334433.3_Silent_p.S1913S|TACC2_ENST00000369000.1_Intron|TACC2_ENST00000453444.2_Intron	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	1913					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				TTCCTCCCTCGGCTGCAGAAC	0.562											OREG0020589	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S1913S		Atlas-SNP	.											.	TACC2	271	.	0			c.G5739C						.						102	89	93					10																	123903126		2203	4300	6503	SO:0001819	synonymous_variant	10579	exon7			TCCCTCGGCTGCA	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.5739G>C	chr10.hg19:g.123903126G>C		89.0	0.0	1530	67.0	18.0	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Silent	SNP	ENST00000369005.1	hg19	CCDS7626.1																																																																																			.	G|0.999;A|0.001		0.562	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1			C	123903126	G	C	123903126	2	2	373	1	0	0	0	0	0	0	0	1	15517	1103	39	4		4	TACC2	10	123903126	Silent	SNP	G	TCGA-ZS-A9CG-01A-11D-A36X-10	21922745	123903126	11631621	49	51563										
TACC2	10579	hgsc.bcm.edu	37	chr10	123969922	123969922	+	Silent	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	gtttccccaggatgtggttcTgagacagtccctgtccctga	11	12	1	2			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr10:123969922T>C	ENST00000369005.1	+	9	6322	c.5982T>C	c.(5980-5982)tcT>tcC	p.S1994S	TACC2_ENST00000513429.1_Silent_p.S140S|TACC2_ENST00000358010.1_Silent_p.S140S|TACC2_ENST00000360561.3_Silent_p.S72S|TACC2_ENST00000515273.1_Silent_p.S1998S|TACC2_ENST00000368999.1_Silent_p.S72S|TACC2_ENST00000369001.1_5'UTR|TACC2_ENST00000493951.1_3'UTR|TACC2_ENST00000515603.1_Silent_p.S1949S|TACC2_ENST00000334433.3_Silent_p.S1994S|TACC2_ENST00000369000.1_5'UTR|TACC2_ENST00000260733.3_Silent_p.S72S|TACC2_ENST00000369004.3_Silent_p.S72S|TACC2_ENST00000453444.2_Silent_p.S1998S	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	1994	Pro-rich.				astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				GATGTGGTTCTGAGACAGTCC	0.562																																					p.S1994S		Atlas-SNP	.											.	TACC2	271	.	0			c.T5982C						.						132	102	112					10																	123969922		2203	4300	6503	SO:0001819	synonymous_variant	10579	exon9			TGGTTCTGAGACA	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.5982T>C	chr10.hg19:g.123969922T>C		175.0	0.0		159.0	60.0	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Silent	SNP	ENST00000369005.1	hg19	CCDS7626.1																																																																																			.	.		0.562	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1			C	123969922	T	C	123969922	2	2	373	1	0	0	0	0	0	0	0	1	15517	1567	55	2		2	TACC2	10	123969922	Silent	SNP	T	TCGA-ZS-A9CG-01A-11D-A36X-10	66796	123969922	11564825	50	51564										
LDHAL6A	160287	hgsc.bcm.edu	37	chr11	18500385	18500385	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	tgcaaaagagtgcagaaacaCtttgggaaattcagaaggag	12	5	1	3			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr11:18500385C>T	ENST00000280706.2	+	7	1764	c.967C>T	c.(967-969)Ctt>Ttt	p.L323F	LDHAL6A_ENST00000396213.3_Missense_Mutation_p.L323F|TSG101_ENST00000536719.1_Intron	NM_144972.4	NP_659409.2	Q6ZMR3	LDH6A_HUMAN	lactate dehydrogenase A-like 6A	323					cellular carbohydrate metabolic process (GO:0044262)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	L-lactate dehydrogenase activity (GO:0004459)			large_intestine(3)|lung(9)|urinary_tract(1)	13						TGCAGAAACACTTTGGGAAAT	0.378																																					p.L323F		Atlas-SNP	.											.	LDHAL6A	35	.	0			c.C967T						.						144	156	152					11																	18500385		2199	4293	6492	SO:0001583	missense	160287	exon7			GAAACACTTTGGG	AK131523	CCDS7841.1	11p15.1	2011-01-27			ENSG00000166800	ENSG00000166800			28335	protein-coding gene	gene with protein product						12477932	Standard	NM_001144071		Approved	MGC23940, LDH6A	uc001mop.1	Q6ZMR3	OTTHUMG00000167724	ENST00000280706.2:c.967C>T	chr11.hg19:g.18500385C>T	ENSP00000280706:p.Leu323Phe	66.0	0.0		68.0	23.0	NM_144972	D3DQY5	Missense_Mutation	SNP	ENST00000280706.2	hg19	CCDS7841.1	.	.	.	.	.	.	.	.	.	.	C	11.78	1.739520	0.30774	.	.	ENSG00000166800	ENST00000396213;ENST00000280706	D;D	0.83163	-1.69;-1.69	4.06	3.14	0.36123	Lactate/malate dehydrogenase, C-terminal (1);Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal (2);	0.000000	0.53938	U	0.000048	D	0.92397	0.7587	H	0.97186	3.955	0.49389	D	0.999784	D	0.71674	0.998	D	0.68765	0.96	D	0.91182	0.4977	10	0.87932	D	0	.	7.1979	0.25864	0.0:0.79:0.0:0.21	.	323	Q6ZMR3	LDH6A_HUMAN	F	323	ENSP00000379516:L323F;ENSP00000280706:L323F	ENSP00000280706:L323F	L	+	1	0	LDHAL6A	18456961	0.253000	0.23982	0.050000	0.19076	0.049000	0.14656	0.345000	0.19979	0.699000	0.31761	0.555000	0.69702	CTT	.	.		0.378	LDHAL6A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395904.1	NM_144972		T	18500385	C	T	18500385	3	4	373	1	0	0	0	0	1	0	0	0	8708	565	20	3	993	3	LDHAL6A	11	18500385	Missense_Mutation	SNP	C	TCGA-ZS-A9CG-01A-11D-A36X-10		18500385	116506131	51	51565										
ACCSL	390110	hgsc.bcm.edu	37	chr11	44074236	44074242	+	Frame_Shift_Del	DEL	TCTATGG	TCTATGG	-													0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	cttcctggtccctgctccctTctatggtggctttgccttta							TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	TCTATGG	TCTATGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr11:44074236_44074242delTCTATGG	ENST00000378832.1	+	6	853_859	c.797_803delTCTATGG	c.(796-804)ttctatggtfs	p.FYG266fs		NM_001031854.2	NP_001027025.2	Q4AC99	1A1L2_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)-like	266					biosynthetic process (GO:0009058)		catalytic activity (GO:0003824)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(14)|ovary(5)|pancreas(1)|skin(2)	34						CCTGCTCCCTTCTATGGTGGCTTTGCC	0.551																																					p.266_268del		Atlas-INDEL	.											.	ACCSL	57	.	0			c.796_802del						.																																			SO:0001589	frameshift_variant	390110	exon6			.		CCDS41636.1	11p11.2	2008-11-26			ENSG00000205126	ENSG00000205126			34391	protein-coding gene	gene with protein product							Standard	NM_001031854		Approved		uc001mxw.1	Q4AC99	OTTHUMG00000166426	ENST00000378832.1:c.797_803delTCTATGG	chr11.hg19:g.44074236_44074242delTCTATGG	ENSP00000368109:p.Phe266fs	81.0	0.0		67.0	14.0	NM_001031854		Frame_Shift_Del	DEL	ENST00000378832.1	hg19	CCDS41636.1																																																																																			.	.		0.551	ACCSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389717.1	NM_001031854		-	44074242	TCTATGG	-	44074236	7	5	373	1	0	1	0	1	0	0	0	0	134	1783	62	0	819	0	ACCSL	11	44074236	Frame_Shift_Del	DEL	TCTATGG	TCGA-ZS-A9CG-01A-11D-A36X-10	25573851	44074236	90932280	52	51566										
CBL	867	hgsc.bcm.edu	37	chr11	119168164	119168165	+	Frame_Shift_Ins	INS	-	-	CATCTAT													0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	taatattcagtcccaggcgcINScatctatcaccgagagcagc					rs587778157		TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr11:119168164_119168165insCATCTAT	ENST00000264033.4	+	14	2600_2601	c.2224_2225insCATCTAT	c.(2224-2226)ccafs	p.-744fs		NM_005188.3	NP_005179.2	P22681	CBL_HUMAN	Cbl proto-oncogene, E3 ubiquitin protein ligase						cell surface receptor signaling pathway (GO:0007166)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|flotillin complex (GO:0016600)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ephrin receptor binding (GO:0046875)|ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(194)|kidney(3)|large_intestine(9)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	251		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)		GTCCCAGGCGCCATCTATCACC	0.406			"T, Mis S, O"	MLL	"AML, JMML, MDS"				Noonan syndrome;CBL gene-associated Juvenile Myelomonocytic Leukemia and Developmental Anomalies																												p.P742fs		Atlas-INDEL	.		"Dom, Rec"	yes		11	11q23.3	867	Cas-Br-M (murine) ecotropic retroviral transforming		L	.	CBL	408	.	0			c.2224_2225insCATCTAT						.																																			SO:0001589	frameshift_variant	867	exon14	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CBL-associated JMML	.	X57110	CCDS8418.1	11q23.3	2014-09-17	2012-02-23		ENSG00000110395	ENSG00000110395		"RING-type (C3HC4) zinc fingers"	1541	protein-coding gene	gene with protein product	"oncogene CBL2"	165360	"Cas-Br-M (murine) ecotropic retroviral transforming sequence"	CBL2		2013228	Standard	NM_005188		Approved	RNF55, c-Cbl	uc001pwe.4	P22681	OTTHUMG00000166170	ENST00000264033.4:c.2225_2231dupCATCTAT	chr11.hg19:g.119168165_119168171dupCATCTAT	ENSP00000264033:p.Ile744fs	122.0	0.0		93.0	14.0	NM_005188	A3KMP8	Frame_Shift_Ins	INS	ENST00000264033.4	hg19	CCDS8418.1																																																																																			.	.		0.406	CBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388219.4	NM_005188		CATCTAT	119168165	-	CATCTAT	119168164	7	5	373	1	0	1	1	0	0	0	0	0	2702	739	26	0	2278	0	CBL	11	119168164	Frame_Shift_Ins	INS	-	TCGA-ZS-A9CG-01A-11D-A36X-10	75093928	119168164	15838352	53	51567										
UBASH3B	84959	hgsc.bcm.edu	37	chr11	122671897	122671897	+	Splice_Site	SNP	T	T	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	actgtattttacccctaaggTttacaacaagaaaatcactt	4	9	1	1			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr11:122671897T>G	ENST00000284273.5	+	11	1827	c.1452T>G	c.(1450-1452)ggT>ggG	p.G484G		NM_032873.4	NP_116262.2	Q8TF42	UBS3B_HUMAN	ubiquitin associated and SH3 domain containing B	484	Protein tyrosine phosphatase. {ECO:0000250}.				negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein kinase activity (GO:0006469)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(11)|prostate(1)|skin(2)|stomach(2)	26		Breast(109;0.00254)|Medulloblastoma(222;0.00877)|Lung NSC(97;0.0183)|all_lung(97;0.0186)|all_neural(223;0.0381)|all_hematologic(192;0.104)		BRCA - Breast invasive adenocarcinoma(274;1.37e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0463)		ACCCCTAAGGTTTACAACAAG	0.408																																					p.G484G		Atlas-SNP	.											.	UBASH3B	73	.	0			c.T1452G						.						96	96	96					11																	122671897		2202	4299	6501	SO:0001630	splice_region_variant	84959	exon11			CTAAGGTTTACAA	AB075839	CCDS31694.1	11q24.1	2010-04-28	2010-04-28		ENSG00000154127	ENSG00000154127			29884	protein-coding gene	gene with protein product	"SH3 domain-containing 70 kDa protein, suppressor of T-cell receptor signaling 1, nm23-phosphorylated unknown substrate"	609201				11853319, 12370296	Standard	NM_032873		Approved	KIAA1959, STS-1	uc001pyi.4	Q8TF42	OTTHUMG00000166025	ENST00000284273.5:c.1451-1T>G	chr11.hg19:g.122671897T>G		113.0	0.0		121.0	49.0	NM_032873	Q53GT5|Q53GT8|Q8NBV7|Q96IG9|Q96NZ2	Silent	SNP	ENST00000284273.5	hg19	CCDS31694.1																																																																																			.	.		0.408	UBASH3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387499.1	NM_032873	Silent	G	122671897	T	G	122671897	5	3	373	1	0	0	0	0	0	0	1	0	16855	1739	60	5	1494	5	UBASH3B	11	122671897	Splice_Site	SNP	T	TCGA-ZS-A9CG-01A-11D-A36X-10	3503733	122671897	12334619	54	51568										
NECAP1	25977	hgsc.bcm.edu	37	chr12	8248299	8248299	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	agacttcagcactgcctccaGgtaatgggcatagtgaaact	10	10	1	2			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr12:8248299G>A	ENST00000339754.5	+	7	857	c.779G>A	c.(778-780)aGc>aAc	p.S260N		NM_015509.3	NP_056324.2	Q8NC96	NECP1_HUMAN	NECAP endocytosis associated 1	260					endocytosis (GO:0006897)|protein transport (GO:0015031)	clathrin vesicle coat (GO:0030125)|coated pit (GO:0005905)|plasma membrane (GO:0005886)				cervix(1)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10				Kidney(36;0.0915)		ACTGCCTCCAGGTAATGGGCA	0.448																																					p.S260N		Atlas-SNP	.											.	NECAP1	21	.	0			c.G779A						.						90	83	86					12																	8248299		2203	4300	6503	SO:0001630	splice_region_variant	25977	exon7			CCTCCAGGTAATG	AK074923	CCDS8589.1	12p13.31	2012-05-02			ENSG00000089818	ENSG00000089818			24539	protein-coding gene	gene with protein product		611623				14555962, 15494011	Standard	NM_015509		Approved	DKFZP566B183	uc001qtx.2	Q8NC96	OTTHUMG00000168568	ENST00000339754.5:c.779+1G>A	chr12.hg19:g.8248299G>A		48.0	0.0		44.0	16.0	NM_015509	Q2NL73|Q5XG95|Q6NWY6|Q8N153|Q8NCB0|Q9BU52|Q9Y407	Missense_Mutation	SNP	ENST00000339754.5	hg19	CCDS8589.1	.	.	.	.	.	.	.	.	.	.	G	14.14	2.446102	0.43429	.	.	ENSG00000089818	ENST00000545179;ENST00000339754;ENST00000540291	T	0.32023	1.47	4.62	3.73	0.42828	.	0.108036	0.64402	D	0.000010	T	0.31199	0.0789	M	0.62723	1.935	0.80722	D	1	P	0.43352	0.804	B	0.42851	0.4	T	0.04522	-1.0945	10	0.33141	T	0.24	.	8.6992	0.34316	0.103:0.0:0.897:0.0	.	260	Q8NC96	NECP1_HUMAN	N	260;260;118	ENSP00000341737:S260N	ENSP00000341737:S260N	S	+	2	0	NECAP1	8139566	1.000000	0.71417	1.000000	0.80357	0.310000	0.27922	4.271000	0.58902	1.162000	0.42619	0.591000	0.81541	AGC	.	.		0.448	NECAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400244.1	NM_015509	Missense_Mutation	A	8248299	G	A	8248299	5	1	373	1	0	0	0	0	0	0	1	0	10316	1014	35	3	805	3	NECAP1	12	8248299	Splice_Site	SNP	G	TCGA-ZS-A9CG-01A-11D-A36X-10		8248299	125603596	55	51569										
CCDC60	160777	hgsc.bcm.edu	37	chr12	119909936	119909936	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	attccagccagccgaaaagaTctcagaaatccactatgggg	9	11	1	2			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr12:119909936T>A	ENST00000327554.2	+	3	773	c.308T>A	c.(307-309)aTc>aAc	p.I103N	RP11-768F21.1_ENST00000509470.2_lincRNA|CCDC60_ENST00000546345.1_3'UTR	NM_178499.3	NP_848594.2	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60	103										endometrium(4)|kidney(3)|large_intestine(8)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)		GCCGAAAAGATCTCAGAAATC	0.438																																					p.I103N		Atlas-SNP	.											.	CCDC60	84	.	0			c.T308A						.						167	173	171					12																	119909936		2203	4300	6503	SO:0001583	missense	160777	exon3			AAAAGATCTCAGA	BC040553	CCDS9190.1	12q24.23	2006-02-03			ENSG00000183273	ENSG00000183273			28610	protein-coding gene	gene with protein product						12477932	Standard	NM_178499		Approved	MGC39827	uc001txe.3	Q8IWA6	OTTHUMG00000168943	ENST00000327554.2:c.308T>A	chr12.hg19:g.119909936T>A	ENSP00000333374:p.Ile103Asn	161.0	0.0		139.0	43.0	NM_178499		Missense_Mutation	SNP	ENST00000327554.2	hg19	CCDS9190.1	.	.	.	.	.	.	.	.	.	.	T	10.72	1.429850	0.25726	.	.	ENSG00000183273	ENST00000327554	T	0.23950	1.88	5.22	-2.85	0.05734	.	2.298030	0.01590	N	0.021516	T	0.19565	0.0470	L	0.36672	1.1	0.09310	N	1	P	0.40834	0.73	B	0.39258	0.295	T	0.25117	-1.0141	9	.	.	.	0.0784	5.1906	0.15207	0.493:0.0849:0.0:0.4221	.	103	Q8IWA6	CCD60_HUMAN	N	103	ENSP00000333374:I103N	.	I	+	2	0	CCDC60	118394319	0.000000	0.05858	0.000000	0.03702	0.212000	0.24457	-0.186000	0.09670	-0.032000	0.13758	0.334000	0.21626	ATC	.	.		0.438	CCDC60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401680.1	NM_178499		A	119909936	T	A	119909936	3	1	373	1	0	0	0	0	1	0	0	0	2833	1435	50	4	318	4	CCDC60	12	119909936	Missense_Mutation	SNP	T	TCGA-ZS-A9CG-01A-11D-A36X-10	111661637	119909936	13941959	56	51570										
ACIN1	22985	hgsc.bcm.edu	37	chr14	23549129	23549129	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	ctaattcctcaatttttagaGggaggggctgagcagatctg	12	7	2	3			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr14:23549129G>A	ENST00000262710.1	-	6	1916	c.1589C>T	c.(1588-1590)cCt>cTt	p.P530L	ACIN1_ENST00000605057.1_Missense_Mutation_p.P472L|ACIN1_ENST00000457657.1_Missense_Mutation_p.P490L|ACIN1_ENST00000555352.1_5'Flank|ACIN1_ENST00000555053.1_Missense_Mutation_p.P530L	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	530					apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		AATTTTTAGAGGGAGGGGCTG	0.488																																					p.P530L		Atlas-SNP	.											.	ACIN1	147	.	0			c.C1589T						.						121	128	126					14																	23549129		2203	4300	6503	SO:0001583	missense	22985	exon6			TTTAGAGGGAGGG	AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 152"	604562	"apoptotic chromatin condensation inducer in the nucleus"	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.1589C>T	chr14.hg19:g.23549129G>A	ENSP00000262710:p.Pro530Leu	92.0	0.0		66.0	27.0	NM_001164814	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Missense_Mutation	SNP	ENST00000262710.1	hg19	CCDS9587.1	.	.	.	.	.	.	.	.	.	.	G	10.37	1.330399	0.24167	.	.	ENSG00000100813	ENST00000262710;ENST00000457657;ENST00000555053	T;T;T	0.24538	1.85;1.85;1.85	5.42	3.62	0.41486	.	0.183676	0.26919	N	0.021827	T	0.14960	0.0361	N	0.24115	0.695	0.45342	D	0.998339	P;P;P	0.44734	0.763;0.651;0.842	B;B;B	0.37144	0.242;0.122;0.196	T	0.03175	-1.1064	10	0.87932	D	0	-0.5614	8.0748	0.30710	0.1796:0.0:0.8204:0.0	.	530;530;490	G3V3M7;Q9UKV3;E7EQT4	.;ACINU_HUMAN;.	L	530;490;530	ENSP00000262710:P530L;ENSP00000405677:P490L;ENSP00000451328:P530L	ENSP00000262710:P530L	P	-	2	0	ACIN1	22618969	0.943000	0.32029	0.984000	0.44739	0.723000	0.41478	1.933000	0.40153	0.871000	0.35750	-0.142000	0.14014	CCT	.	.		0.488	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977		A	23549129	G	A	23549129	3	1	373	1	0	0	0	0	1	0	0	0	142	1000	35	3	2639	3	ACIN1	14	23549129	Missense_Mutation	SNP	G	TCGA-ZS-A9CG-01A-11D-A36X-10		23549129	83800411	57	51571										
HECTD1	25831	hgsc.bcm.edu	37	chr14	31613412	31613412	+	Missense_Mutation	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	cttcaaaagtacaattaggtTttctaaagctgtcttcatta	5	7	4	0			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr14:31613412T>A	ENST00000399332.1	-	17	3171	c.2683A>T	c.(2683-2685)Aac>Tac	p.N895Y	HECTD1_ENST00000553700.1_Missense_Mutation_p.N895Y|RNU6-541P_ENST00000384709.1_RNA	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	895					neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		ACAATTAGGTTTTCTAAAGCT	0.318																																					p.N895Y		Atlas-SNP	.											.	HECTD1	159	.	0			c.A2683T						.						43	42	42					14																	31613412		1813	4069	5882	SO:0001583	missense	25831	exon17			TTAGGTTTTCTAA	AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"Ankyrin repeat domain containing"	20157	protein-coding gene	gene with protein product			"HECT domain containing 1"			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.2683A>T	chr14.hg19:g.31613412T>A	ENSP00000382269:p.Asn895Tyr	247.0	0.0		235.0	35.0	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Missense_Mutation	SNP	ENST00000399332.1	hg19	CCDS41939.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.380244	0.82682	.	.	ENSG00000092148	ENST00000553700;ENST00000261312;ENST00000399332;ENST00000553957;ENST00000556224	T;T;T;T	0.64991	-0.13;-0.13;1.51;-0.13	5.66	5.66	0.87406	Armadillo-type fold (1);	0.000000	0.85682	U	0.000000	T	0.59128	0.2171	L	0.34521	1.04	0.80722	D	1	D;D	0.58970	0.984;0.971	P;P	0.47299	0.527;0.543	T	0.64253	-0.6451	10	0.66056	D	0.02	-10.7488	15.8889	0.79276	0.0:0.0:0.0:1.0	.	895;895	D3DS86;Q9ULT8	.;HECD1_HUMAN	Y	895;895;895;369;895	ENSP00000450697:N895Y;ENSP00000382269:N895Y;ENSP00000451860:N369Y;ENSP00000452015:N895Y	ENSP00000261312:N895Y	N	-	1	0	HECTD1	30683163	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.160000	0.64929	2.143000	0.66587	0.533000	0.62120	AAC	.	.		0.318	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			A	31613412	T	A	31613412	3	1	373	1	0	0	0	0	1	0	0	0	7048	1841	64	4	5257	4	HECTD1	14	31613412	Missense_Mutation	SNP	T	TCGA-ZS-A9CG-01A-11D-A36X-10	8064283	31613412	75736128	58	51572										
NID2	22795	hgsc.bcm.edu	37	chr14	52535631	52535631	+	Missense_Mutation	SNP	C	C	G	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	gtctgggtgcagcgccgcggCccgcaacattagcaacggca	14	14	1	0			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr14:52535631C>G	ENST00000216286.5	-	1	81	c.82G>C	c.(82-84)Gcc>Ccc	p.A28P	NID2_ENST00000541773.1_Intron	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	28					basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					AGCGCCGCGGCCCGCAACATT	0.687																																					p.A28P		Atlas-SNP	.											.	NID2	201	.	0			c.G82C						.						50	47	48					14																	52535631		2203	4300	6503	SO:0001583	missense	22795	exon1			CCGCGGCCCGCAA	AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.82G>C	chr14.hg19:g.52535631C>G	ENSP00000216286:p.Ala28Pro	276.0	0.0		225.0	83.0	NM_007361	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	hg19	CCDS9706.1	.	.	.	.	.	.	.	.	.	.	C	14.82	2.648681	0.47258	.	.	ENSG00000087303	ENST00000216286;ENST00000316204;ENST00000395707	T	0.23348	1.91	4.66	2.81	0.32909	.	0.613341	0.17065	N	0.188403	T	0.23094	0.0558	L	0.49350	1.555	0.21627	N	0.999619	P;P	0.48407	0.91;0.61	B;B	0.44315	0.446;0.193	T	0.07366	-1.0776	10	0.34782	T	0.22	.	6.0297	0.19673	0.3268:0.5812:0.0:0.092	.	30;28	Q5CZI2;Q14112	.;NID2_HUMAN	P	28;28;30	ENSP00000216286:A28P	ENSP00000216286:A28P	A	-	1	0	NID2	51605381	0.003000	0.15002	0.010000	0.14722	0.161000	0.22273	0.952000	0.29149	0.964000	0.38108	-0.385000	0.06624	GCC	.	.		0.687	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1			G	52535631	C	G	52535631	3	3	373	1	0	0	0	0	1	0	0	0	10424	739	26	4	4133	4	NID2	14	52535631	Missense_Mutation	SNP	C	TCGA-ZS-A9CG-01A-11D-A36X-10	20922219	52535631	54813909	59	51573										
YLPM1	56252	hgsc.bcm.edu	37	chr14	75265439	75265439	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	ggagcagggagagaggaccaCctcgagggcctggcagtcga	18	10	0	1			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr14:75265439C>T	ENST00000325680.7	+	5	3563	c.3439C>T	c.(3439-3441)Cct>Tct	p.P1147S	YLPM1_ENST00000238571.3_Missense_Mutation_p.P952S|YLPM1_ENST00000552421.1_Intron	NM_019589.2	NP_062535.2	P49750	YLPM1_HUMAN	YLP motif containing 1	952	Arg-rich.				regulation of telomere maintenance (GO:0032204)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	62			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		GAGAGGACCACCTCGAGGGCC	0.572																																					p.P1147S		Atlas-SNP	.											.	YLPM1	298	.	0			c.C3439T						.						48	52	51					14																	75265439		1891	4116	6007	SO:0001583	missense	56252	exon5			GGACCACCTCGAG	AK090435	CCDS45135.1	14q24.3	2014-06-13	2004-07-15	2004-07-15	ENSG00000119596	ENSG00000119596			17798	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 169"		"chromosome 14 open reading frame 170"	C14orf170		7596406	Standard	NM_019589		Approved	ZAP, PPP1R169	uc001xqj.4	P49750	OTTHUMG00000172503	ENST00000325680.7:c.3439C>T	chr14.hg19:g.75265439C>T	ENSP00000324463:p.Pro1147Ser	152.0	0.0		163.0	61.0	NM_019589	P49752|Q96I64|Q9P1V7	Missense_Mutation	SNP	ENST00000325680.7	hg19	CCDS45135.1	.	.	.	.	.	.	.	.	.	.	C	12.69	2.013265	0.35511	.	.	ENSG00000119596	ENST00000325680;ENST00000238571;ENST00000423680	.	.	.	5.56	4.66	0.58398	.	0.502190	0.20108	N	0.099079	T	0.39253	0.1071	L	0.58101	1.795	0.29458	N	0.857975	B	0.20671	0.047	B	0.18561	0.022	T	0.34129	-0.9841	9	0.30854	T	0.27	-6.9576	5.0184	0.14349	0.1321:0.5925:0.1956:0.0798	.	1147	P49750-4	.	S	1147;952;860	.	ENSP00000238571:P952S	P	+	1	0	YLPM1	74335192	0.358000	0.24947	0.855000	0.33649	0.950000	0.60333	0.637000	0.24659	1.321000	0.45227	0.551000	0.68910	CCT	.	.		0.572	YLPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404451.1	NM_019589		T	75265439	C	T	75265439	3	4	373	1	0	0	0	0	1	0	0	0	17501	507	18	3	3457	3	YLPM1	14	75265439	Missense_Mutation	SNP	C	TCGA-ZS-A9CG-01A-11D-A36X-10	22729808	75265439	32084101	60	51574										
BCL11B	64919	hgsc.bcm.edu	37	chr14	99640842	99640842	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	gggcccgggccgcccaggtgCggggtgctgcctccgctggc	19	16	0	0			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr14:99640842C>T	ENST00000357195.3	-	4	2340	c.2331G>A	c.(2329-2331)ccG>ccA	p.P777P	BCL11B_ENST00000443726.2_Silent_p.P583P|BCL11B_ENST00000345514.2_Silent_p.P706P	NM_001282237.1|NM_138576.2	NP_001269166.1|NP_612808.1	Q9C0K0	BC11B_HUMAN	B-cell CLL/lymphoma 11B (zinc finger protein)	777					alpha-beta T cell differentiation (GO:0046632)|epithelial cell morphogenesis (GO:0003382)|keratinocyte development (GO:0003334)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|odontogenesis of dentin-containing tooth (GO:0042475)|olfactory bulb axon guidance (GO:0071678)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive T cell selection (GO:0043368)|post-embryonic camera-type eye development (GO:0031077)|regulation of keratinocyte proliferation (GO:0010837)|regulation of lipid metabolic process (GO:0019216)|regulation of neuron differentiation (GO:0045664)|striatal medium spiny neuron differentiation (GO:0021773)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|thymus development (GO:0048538)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.P777P(1)		NS(3)|breast(1)|central_nervous_system(9)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(9)|prostate(2)|skin(2)	34		Melanoma(154;0.0866)|all_epithelial(191;0.241)		COAD - Colon adenocarcinoma(157;0.103)		cgcccAGGTGCGGGGTGCTGC	0.746			T	TLX3	T-ALL																																p.P777P		Atlas-SNP	.		Dom	yes		14	14q32.1	64919	B-cell CLL/lymphoma 11B  (CTIP2)		L	BCL11B,brain,glioma,0,1	BCL11B	108	.	1	Substitution - coding silent(1)	central_nervous_system(1)	c.G2331A						.						3	3	3					14																	99640842		1615	3348	4963	SO:0001819	synonymous_variant	64919	exon4			CAGGTGCGGGGTG	AJ404614	CCDS9949.1, CCDS9950.1	14q32	2013-01-08			ENSG00000127152	ENSG00000127152		"Zinc fingers, C2H2-type"	13222	protein-coding gene	gene with protein product		606558		ZNF856B		11719382, 16950772	Standard	NM_138576		Approved	CTIP-2, CTIP2, hRIT1-alpha	uc001yga.3	Q9C0K0	OTTHUMG00000028967	ENST00000357195.3:c.2331G>A	chr14.hg19:g.99640842C>T		21.0	1.0		25.0	8.0	NM_138576	Q9H162	Silent	SNP	ENST00000357195.3	hg19	CCDS9950.1																																																																																			.	.		0.746	BCL11B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000072332.2	NM_138576		T	99640842	C	T	99640842	2	4	373	1	0	0	0	0	0	0	0	1	1364	755	27	1		1	BCL11B	14	99640842	Silent	SNP	C	TCGA-ZS-A9CG-01A-11D-A36X-10	24375403	99640842	7708698	61	51575										
BMF	90427	hgsc.bcm.edu	37	chr15	40398071	40398071	+	Missense_Mutation	SNP	G	G	T	1	0	0	1	0	1	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	gctgggggaggctgggctgaGagtctgggtagctttgtctt	19	6	2	1			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr15:40398071G>T	ENST00000354670.4	-	3	451	c.217C>A	c.(217-219)Ctc>Atc	p.L73I	BMF_ENST00000220446.4_Missense_Mutation_p.L73I|BMF_ENST00000558057.1_5'Flank|BMF_ENST00000561282.1_Missense_Mutation_p.L73I|BMF_ENST00000397573.1_Missense_Mutation_p.L73I|BMF_ENST00000561360.1_Missense_Mutation_p.L73I|BMF_ENST00000558774.1_Missense_Mutation_p.L73I|BMF_ENST00000431415.3_Missense_Mutation_p.L73I|BMF_ENST00000559701.1_Missense_Mutation_p.L73I	NM_001003940.1	NP_001003940.1	Q96LC9	BMF_HUMAN	Bcl2 modifying factor	73	Interaction with DLC2. {ECO:0000250}.				anoikis (GO:0043276)|apoptotic process (GO:0006915)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of apoptotic signaling pathway (GO:2001234)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of protein homooligomerization (GO:0032464)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)	acrosomal vesicle (GO:0001669)|cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)				endometrium(2)|large_intestine(2)|lung(1)|ovary(1)	6		all_cancers(109;4.18e-18)|all_epithelial(112;6.15e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.29e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0516)		GCTGGGCTGAGAGTCTGGGTA	0.607																																					p.L73I		Atlas-SNP	.											.	BMF	18	.	0			c.C217A						.						73	78	76					15																	40398071		2203	4300	6503	SO:0001583	missense	90427	exon3			GGCTGAGAGTCTG	BC060783	CCDS10052.1, CCDS32196.1, CCDS45223.1	15q14	2014-03-07			ENSG00000104081	ENSG00000104081			24132	protein-coding gene	gene with protein product		606266				11546872	Standard	NM_001003943		Approved	FLJ00065	uc001zkw.4	Q96LC9	OTTHUMG00000129875	ENST00000354670.4:c.217C>A	chr15.hg19:g.40398071G>T	ENSP00000346697:p.Leu73Ile	104.0	0.0		89.0	36.0	NM_001003943	Q2M396|Q6NT30|Q6NT56|Q6P9F6|Q7Z7D4|Q7Z7D5|Q9H7K7	Missense_Mutation	SNP	ENST00000354670.4	hg19	CCDS10052.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.501362	0.85176	.	.	ENSG00000104081	ENST00000354670;ENST00000397573;ENST00000431415;ENST00000220446	.	.	.	5.12	5.12	0.69794	.	0.000000	0.64402	D	0.000005	T	0.68348	0.2991	L	0.34521	1.04	0.48762	D	0.999707	D;D;D	0.67145	0.996;0.996;0.996	D;D;D	0.80764	0.986;0.994;0.994	T	0.71537	-0.4563	9	0.87932	D	0	-6.6255	18.7373	0.91759	0.0:0.0:1.0:0.0	.	73;73;73	Q96LC9;Q96LC9-3;Q96LC9-2	BMF_HUMAN;.;.	I	73	.	ENSP00000220446:L73I	L	-	1	0	BMF	38185363	1.000000	0.71417	1.000000	0.80357	0.888000	0.51559	4.687000	0.61708	2.664000	0.90586	0.561000	0.74099	CTC	.	.		0.607	BMF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252119.1	NM_033503		T	40398071	G	T	40398071	3	4	373	1	0	0	0	0	1	0	0	0	1454	942	33	3	349	3	BMF	15	40398071	Missense_Mutation	SNP	G	TCGA-ZS-A9CG-01A-11D-A36X-10		40398071	62133321	62	51576										
UNC13C	440279	hgsc.bcm.edu	37	chr15	54305886	54305886	+	Silent	SNP	A	A	G	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	attgaaacagaactttctgaActacgagggcacgtcaatgc	9	9	2	3			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr15:54305886A>G	ENST00000260323.11	+	1	786	c.786A>G	c.(784-786)gaA>gaG	p.E262E	UNC13C_ENST00000545554.1_Silent_p.E262E|UNC13C_ENST00000537900.1_Silent_p.E262E	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	262					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		AACTTTCTGAACTACGAGGGC	0.453																																					p.E262E		Atlas-SNP	.											.	UNC13C	674	.	0			c.A786G						.						85	84	84					15																	54305886		1969	4160	6129	SO:0001819	synonymous_variant	440279	exon1			TTCTGAACTACGA	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.786A>G	chr15.hg19:g.54305886A>G		91.0	0.0		75.0	25.0	NM_001080534	Q0P613|Q8ND48|Q96NP3	Silent	SNP	ENST00000260323.11	hg19	CCDS45264.1																																																																																			.	.		0.453	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		G	54305886	A	G	54305886	2	3	373	1	0	0	0	0	0	0	0	1	17001	40	2	2		2	UNC13C	15	54305886	Silent	SNP	A	TCGA-ZS-A9CG-01A-11D-A36X-10	13907815	54305886	48225506	63	51577										
LRRK1	79705	hgsc.bcm.edu	37	chr15	101593240	101593240	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	gtaccagggccagcctgtggCcgtcaagcgcttccacatca	11	15	2	0			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr15:101593240C>T	ENST00000388948.3	+	25	4162	c.3803C>T	c.(3802-3804)gCc>gTc	p.A1268V	LRRK1_ENST00000284395.5_Missense_Mutation_p.A1265V|RP11-505E24.2_ENST00000559857.1_RNA	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1											breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			CAGCCTGTGGCCGTCAAGCGC	0.597																																					p.A1268V		Atlas-SNP	.											.	LRRK1	310	.	0			c.C3803T						.						41	50	47					15																	101593240		2088	4234	6322	SO:0001583	missense	79705	exon25			CTGTGGCCGTCAA	AB058693	CCDS42086.1	15q26.3	2007-01-29			ENSG00000154237	ENSG00000154237			18608	protein-coding gene	gene with protein product		610986				11347906, 14654223	Standard	XM_005254979		Approved	FLJ23119, KIAA1790, Roco1, RIPK6	uc002bwr.3	Q38SD2	OTTHUMG00000165514	ENST00000388948.3:c.3803C>T	chr15.hg19:g.101593240C>T	ENSP00000373600:p.Ala1268Val	160.0	0.0		129.0	42.0	NM_024652		Missense_Mutation	SNP	ENST00000388948.3	hg19	CCDS42086.1	.	.	.	.	.	.	.	.	.	.	C	18.69	3.678435	0.68042	.	.	ENSG00000154237	ENST00000388948;ENST00000284395	D;D	0.97976	-4.64;-4.64	5.12	4.2	0.49525	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.061192	0.64402	N	0.000004	D	0.97739	0.9258	M	0.78049	2.395	0.49687	D	0.999812	P	0.47034	0.889	P	0.50825	0.651	D	0.97871	1.0286	10	0.87932	D	0	.	13.8433	0.63453	0.0:0.9257:0.0:0.0743	.	1268	Q38SD2	LRRK1_HUMAN	V	1268;1265	ENSP00000373600:A1268V;ENSP00000284395:A1265V	ENSP00000284395:A1265V	A	+	2	0	LRRK1	99410763	1.000000	0.71417	0.637000	0.29366	0.134000	0.20937	7.600000	0.82769	1.281000	0.44480	0.650000	0.86243	GCC	.	.		0.597	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652		T	101593240	C	T	101593240	3	4	373	1	0	0	0	0	1	0	0	0	9041	739	26	3	3897	3	LRRK1	15	101593240	Missense_Mutation	SNP	C	TCGA-ZS-A9CG-01A-11D-A36X-10	47287354	101593240	938152	64	51578										
RHOT2	89941	hgsc.bcm.edu	37	chr16	723032	723032	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	tcaccggccgagttttgccgCaagcaccggctacccgctcc	10	18	1	0			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr16:723032C>T	ENST00000315082.4	+	18	1746	c.1632C>T	c.(1630-1632)cgC>cgT	p.R544R	RHBDL1_ENST00000352681.3_5'Flank	NM_138769.2	NP_620124.1	Q8IXI1	MIRO2_HUMAN	ras homolog family member T2	544	Miro 2.				cellular homeostasis (GO:0019725)|mitochondrial outer membrane permeabilization (GO:0097345)|mitochondrion transport along microtubule (GO:0047497)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(2)|kidney(3)|lung(4)|ovary(1)|pancreas(2)|prostate(1)	13		Hepatocellular(780;0.0218)				AGTTTTGCCGCAAGCACCGGC	0.667																																					p.R544R		Atlas-SNP	.											.	RHOT2	35	.	0			c.C1632T						.						56	53	54					16																	723032		2191	4294	6485	SO:0001819	synonymous_variant	89941	exon18			TTGCCGCAAGCAC	BC014942	CCDS10417.1	16p13.3	2013-01-10	2012-02-27	2004-03-24	ENSG00000140983	ENSG00000140983		"EF-hand domain containing"	21169	protein-coding gene	gene with protein product	"mitochondrial Rho (MIRO) GTPase 2"	613889	"chromosome 16 open reading frame 39", "ras homolog gene family, member T2"	C16orf39, ARHT2		12482879	Standard	NM_138769		Approved	MIRO-2	uc002cip.3	Q8IXI1	OTTHUMG00000121139	ENST00000315082.4:c.1632C>T	chr16.hg19:g.723032C>T		121.0	0.0		111.0	37.0	NM_138769	A2IDC2|Q8NF53|Q96C13|Q96S17|Q9BT60|Q9H7M8	Silent	SNP	ENST00000315082.4	hg19	CCDS10417.1																																																																																			.	.		0.667	RHOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241617.1	NM_138769		T	723032	C	T	723032	2	4	373	1	0	0	0	0	0	0	0	1	13359	697	25	3		3	RHOT2	16	723032	Silent	SNP	C	TCGA-ZS-A9CG-01A-11D-A36X-10		723032	89631721	65	51579										
NAT15	79903	hgsc.bcm.edu	37	chr16	3534783	3534783	+	Missense_Mutation	SNP	C	C	A	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	gtctaccgccaggcccacagCctgctctgcagcttcctgcc	9	19	2	0			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr16:3534783C>A	ENST00000407558.4	+	7	960	c.657C>A	c.(655-657)agC>agA	p.S219R	NAA60_ENST00000572942.1_Missense_Mutation_p.A120D|NAA60_ENST00000424546.2_Missense_Mutation_p.S226R|NAA60_ENST00000575076.1_Missense_Mutation_p.S219R|NAA60_ENST00000570819.1_Missense_Mutation_p.A120D|NAA60_ENST00000610180.1_Missense_Mutation_p.S219R|NAA60_ENST00000577013.1_Missense_Mutation_p.S111R|NAA60_ENST00000570551.1_3'UTR|NAA60_ENST00000576916.1_Missense_Mutation_p.S111R|NAA60_ENST00000360862.5_Missense_Mutation_p.S154R|NAA60_ENST00000414063.2_Missense_Mutation_p.S219R|NAA60_ENST00000573580.1_Missense_Mutation_p.S154R|NAA60_ENST00000608722.1_Missense_Mutation_p.S219R|LA16c-306E5.3_ENST00000574423.2_RNA|NAA60_ENST00000421765.3_Missense_Mutation_p.P144T|NAA60_ENST00000608993.1_Missense_Mutation_p.S154R|NAA60_ENST00000572584.1_Missense_Mutation_p.S219R			Q9H7X0	NAA60_HUMAN	N(alpha)-acetyltransferase 60, NatF catalytic subunit	219					cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|histone H4 acetylation (GO:0043967)|N-terminal peptidyl-methionine acetylation (GO:0017196)|nucleosome assembly (GO:0006334)	Golgi membrane (GO:0000139)	H4 histone acetyltransferase activity (GO:0010485)|peptide alpha-N-acetyltransferase activity (GO:0004596)			breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(1)	7						AGGCCCACAGCCTGCTCTGCA	0.637																																					p.S219R		Atlas-SNP	.											.	NAA60	21	.	0			c.C657A						.						18	23	21					16																	3534783		2071	4210	6281	SO:0001583	missense	79903	exon6			CCACAGCCTGCTC		CCDS45396.1	16p13.3	2012-07-13	2011-08-02	2011-08-02	ENSG00000122390	ENSG00000122390	2.3.1.48, 2.3.1.88	"N(alpha)-acetyltransferase subunits"	25875	protein-coding gene	gene with protein product		614246	"N-acetyltransferase 15 (GCN5-related, putative)"	NAT15		12975309, 21750686	Standard	NM_001083600		Approved	FLJ14154	uc010btm.3	Q9H7X0	OTTHUMG00000150268	ENST00000407558.4:c.657C>A	chr16.hg19:g.3534783C>A	ENSP00000385903:p.Ser219Arg	123.0	0.0		100.0	40.0	NM_001083600	B3KRQ0|B4DLZ0|B4DPZ8|B4DYC4|D3DUC2|E7EQ65|Q6IA31|Q6UX26	Missense_Mutation	SNP	ENST00000407558.4	hg19	CCDS45396.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.9|21.9	4.213467|4.213467	0.79352|0.79352	.|.	.|.	ENSG00000122390|ENSG00000122390	ENST00000421765|ENST00000424546;ENST00000407558;ENST00000414063;ENST00000360862	.|T;T;T;T	.|0.49139	.|0.79;0.83;0.83;0.83	5.84|5.84	4.7|4.7	0.59300|0.59300	.|.	.|0.144746	.|0.64402	.|D	.|0.000008	T|T	0.33030|0.33030	0.0849|0.0849	N|N	0.24115|0.24115	0.695|0.695	0.38529|0.38529	D|D	0.948918|0.948918	.|B	.|0.19583	.|0.037	.|B	.|0.17098	.|0.017	T|T	0.17258|0.17258	-1.0375|-1.0375	6|10	0.02654|0.41790	T|T	1|0.15	-2.0563|-2.0563	11.2831|11.2831	0.49206|0.49206	0.0:0.8468:0.0:0.1532|0.0:0.8468:0.0:0.1532	.|.	.|219	.|Q9H7X0	.|NAA60_HUMAN	T|R	144|226;219;219;154	.|ENSP00000401237:S226R;ENSP00000385903:S219R;ENSP00000393224:S219R;ENSP00000354108:S154R	ENSP00000405873:P144T|ENSP00000354108:S154R	P|S	+|+	1|3	0|2	NAA60|NAA60	3474784|3474784	0.999000|0.999000	0.42202|0.42202	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	0.733000|0.733000	0.26087|0.26087	2.768000|2.768000	0.95171|0.95171	0.561000|0.561000	0.74099|0.74099	CCT|AGC	.	.		0.637	NAA60-001	KNOWN	NMD_exception|non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317235.2	NM_024845		A	3534783	C	A	3534783	3	1	373	1	0	0	0	0	1	0	0	0	10185	738	26	3	675	3	NAT15	16	3534783	Missense_Mutation	SNP	C	TCGA-ZS-A9CG-01A-11D-A36X-10	2811751	3534783	86819970	66	51580										
RPH3AL	9501	hgsc.bcm.edu	37	chr17	63676	63676	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	ctggaggggcctgctggagcTgcgtcagcagcgggggctcg	20	11	1	0			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr17:63676T>A	ENST00000331302.7	-	10	1222	c.915A>T	c.(913-915)gcA>gcT	p.A305A	RPH3AL_ENST00000536489.2_Silent_p.A276A|RPH3AL_ENST00000323434.8_Silent_p.A276A|RPH3AL_ENST00000576001.1_5'Flank	NM_001190411.1|NM_006987.3	NP_001177340.1|NP_008918.1	Q9UNE2	RPH3L_HUMAN	rabphilin 3A-like (without C2 domains)	305					exocytosis (GO:0006887)|glucose homeostasis (GO:0042593)|intracellular protein transport (GO:0006886)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|positive regulation of protein secretion (GO:0050714)|regulation of calcium ion-dependent exocytosis (GO:0017158)|response to drug (GO:0042493)	cytoplasm (GO:0005737)|secretory granule membrane (GO:0030667)	cytoskeletal protein binding (GO:0008092)|metal ion binding (GO:0046872)			NS(2)|breast(1)|kidney(1)|large_intestine(1)|skin(1)	6				UCEC - Uterine corpus endometrioid carcinoma (25;0.023)|all cancers(1;4.96e-06)|Epithelial(1;2.86e-05)|BRCA - Breast invasive adenocarcinoma(1;0.00453)|OV - Ovarian serous cystadenocarcinoma(1;0.0716)|LUAD - Lung adenocarcinoma(1115;0.102)|COAD - Colon adenocarcinoma(4;0.107)		CTGCTGGAGCTGCGTCAGCAG	0.642																																					p.A305A		Atlas-SNP	.											.	RPH3AL	18	.	0			c.A915T						.						22	26	25					17																	63676		2203	4299	6502	SO:0001819	synonymous_variant	9501	exon10			TGGAGCTGCGTCA		CCDS10994.1, CCDS54059.1	17p13.3	2014-07-02			ENSG00000181031	ENSG00000181031		"Synaptotagmins"	10296	protein-coding gene	gene with protein product		604881				10395805	Standard	NM_006987		Approved	Noc2	uc021tmx.1	Q9UNE2	OTTHUMG00000090273	ENST00000331302.7:c.915A>T	chr17.hg19:g.63676T>A		83.0	0.0		54.0	12.0	NM_006987	D3DTG7|Q9BSB3	Silent	SNP	ENST00000331302.7	hg19	CCDS10994.1																																																																																			.	.		0.642	RPH3AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206597.2	NM_006987		A	63676	T	A	63676	2	1	373	1	0	0	0	0	0	0	0	1	13567	1567	55	4		4	RPH3AL	17	63676	Silent	SNP	T	TCGA-ZS-A9CG-01A-11D-A36X-10		63676	81131534	67	51581										
POLR2A	5430	hgsc.bcm.edu	37	chr17	7406937	7406937	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	tgagcaagaagctggtgattGtgaatggggatgacccacta	14	6	0	5			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr17:7406937G>T	ENST00000322644.6	+	19	3466	c.3067G>T	c.(3067-3069)Gtg>Ttg	p.V1023L		NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	1023					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA-directed RNA polymerase activity (GO:0003968)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(17)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	50		Prostate(122;0.173)				GCTGGTGATTGTGAATGGGGA	0.552																																					p.V1023L		Atlas-SNP	.											.	POLR2A	157	.	0			c.G3067T						.						81	72	75					17																	7406937		2203	4300	6503	SO:0001583	missense	5430	exon19			GTGATTGTGAATG			17p13.1	2013-01-21	2002-08-29		ENSG00000181222	ENSG00000181222	2.7.7.6	"RNA polymerase subunits"	9187	protein-coding gene	gene with protein product	"DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit", "RNA polymerase II subunit B1"	180660	"polymerase (RNA) II (DNA directed) polypeptide A (220kD)"	POLR2			Standard	NM_000937		Approved	POLRA, RPB1	uc002ghf.4	P24928	OTTHUMG00000177594	ENST00000322644.6:c.3067G>T	chr17.hg19:g.7406937G>T	ENSP00000314949:p.Val1023Leu	155.0	0.0		93.0	4.0	NM_000937	A6NN93|B9EH88|Q6NX41	Missense_Mutation	SNP	ENST00000322644.6	hg19	CCDS32548.1	.	.	.	.	.	.	.	.	.	.	G	32	5.113410	0.94339	.	.	ENSG00000181222	ENST00000535204;ENST00000322644	T	0.68331	-0.32	5.91	5.91	0.95273	RNA polymerase Rpb1, domain 6 (1);RNA polymerase Rpb1, domain 5 (1);	0.000000	0.85682	D	0.000000	D	0.83335	0.5232	M	0.87617	2.895	0.80722	D	1	P	0.39551	0.678	P	0.54706	0.759	D	0.84392	0.0555	10	0.87932	D	0	-12.7046	19.07	0.93130	0.0:0.0:1.0:0.0	.	1023	P24928	RPB1_HUMAN	L	979;1023	ENSP00000314949:V1023L	ENSP00000314949:V1023L	V	+	1	0	SLC35G6	7347661	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.740000	0.91579	2.793000	0.96121	0.655000	0.94253	GTG	.	.		0.552	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	NM_000937		T	7406937	G	T	7406937	3	4	373	1	0	0	0	0	1	0	0	0	12223	1377	48	3	3141	3	POLR2A	17	7406937	Missense_Mutation	SNP	G	TCGA-ZS-A9CG-01A-11D-A36X-10	7343261	7406937	73788273	68	51582										
ZNF18	7566	hgsc.bcm.edu	37	chr17	11882000	11882000	+	Silent	SNP	G	G	T	1	0	0	0	0	1	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	gcttgacaggaagcatgcagGagctcctggtccctgtgatt	13	10	0	2			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr17:11882000G>T	ENST00000322748.3	-	9	1528	c.924C>A	c.(922-924)ctC>ctA	p.L308L	RP11-1096G20.5_ENST00000580270.1_RNA|ZNF18_ENST00000580306.2_Silent_p.L308L|ZNF18_ENST00000454073.3_Silent_p.L307L	NM_144680.2	NP_653281.2	P17022	ZNF18_HUMAN	zinc finger protein 18	308					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)	14				Colorectal(4;3.33e-05)|COAD - Colon adenocarcinoma(4;0.000494)|READ - Rectum adenocarcinoma(10;0.233)		AAGCATGCAGGAGCTCCTGGT	0.463																																					p.L308L		Atlas-SNP	.											.	ZNF18	42	.	0			c.C924A						.						117	124	122					17																	11882000		2201	4287	6488	SO:0001819	synonymous_variant	7566	exon9			ATGCAGGAGCTCC	X52342	CCDS32568.1	17p12	2013-01-09	2006-05-10		ENSG00000154957	ENSG00000154957		"Zinc fingers, C2H2-type", "-", "-", "-"	12969	protein-coding gene	gene with protein product		194524	"zinc finger protein 18 (KOX 11)"			15702252	Standard	XM_005256786		Approved	ZKSCAN6, KOX11, HDSG1, Zfp535, ZNF535, ZSCAN38	uc002gng.1	P17022	OTTHUMG00000178307	ENST00000322748.3:c.924C>A	chr17.hg19:g.11882000G>T		43.0	0.0		54.0	16.0	NM_144680	Q5QHQ3|Q8IYC4|Q8NAH6	Silent	SNP	ENST00000322748.3	hg19	CCDS32568.1																																																																																			.	.		0.463	ZNF18-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441450.2	XM_085596		T	11882000	G	T	11882000	2	4	373	1	0	0	0	0	0	0	0	1	17762	1161	41	3		3	ZNF18	17	11882000	Silent	SNP	G	TCGA-ZS-A9CG-01A-11D-A36X-10	4475063	11882000	69313210	69	51583										
SYNRG	11276	hgsc.bcm.edu	37	chr17	35937549	35937549	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	1	0	1	0	1	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	tggtggtaccacttacacatCcatctacagcaaccccgtta	6	14	1	0			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr17:35937549C>T	ENST00000339208.6	-	7	892	c.752G>A	c.(751-753)gGa>gAa	p.G251E	SYNRG_ENST00000346661.4_Missense_Mutation_p.G251E|SYNRG_ENST00000502449.2_Intron|SYNRG_ENST00000394378.2_Intron|SYNRG_ENST00000345615.4_Intron|SYNRG_ENST00000591288.1_Intron|SYNRG_ENST00000588194.1_Intron|SYNRG_ENST00000585472.1_Intron	NM_001163544.1|NM_001163545.1|NM_007247.4	NP_001157016.1|NP_001157017.1|NP_009178.3	Q9UMZ2	SYNRG_HUMAN	synergin, gamma	251					endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)	AP-1 adaptor complex (GO:0030121)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						ACTTACACATCCATCTACAGC	0.438																																					p.G251E		Atlas-SNP	.											.	SYNRG	101	.	0			c.G752A						.						265	261	262					17																	35937549		2203	4300	6503	SO:0001583	missense	11276	exon7			ACACATCCATCTA	AF169548	CCDS11321.1, CCDS11322.1, CCDS11322.2, CCDS54113.1, CCDS54114.1, CCDS59284.1, CCDS59285.1	17q12	2014-04-16	2009-07-20	2009-07-20	ENSG00000006114	ENSG00000275066			557	protein-coding gene	gene with protein product	"gamma-synergin", "adaptor-related protein complex 1 gamma subunit-binding protein 1"	607291	"AP1 gamma subunit binding protein 1"	AP1GBP1		10477754	Standard	XM_005256980		Approved	SYNG, MGC104959	uc010wdf.2	Q9UMZ2	OTTHUMG00000188473	ENST00000339208.6:c.752G>A	chr17.hg19:g.35937549C>T	ENSP00000343610:p.Gly251Glu	183.0	0.0		166.0	61.0	NM_007247	A8MWU4|B7ZKZ2|B7ZKZ3|Q17RI2|Q5BKU5|Q6ZT17	Missense_Mutation	SNP	ENST00000339208.6	hg19	CCDS11321.1	.	.	.	.	.	.	.	.	.	.	C	16.65	3.181501	0.57800	.	.	ENSG00000006114	ENST00000346661;ENST00000345615;ENST00000394379	T;T	0.55588	1.64;0.51	5.46	5.46	0.80206	.	0.234208	0.37530	N	0.002055	T	0.42698	0.1214	L	0.45581	1.43	0.45762	D	0.998652	P;B;B	0.36683	0.565;0.197;0.197	B;B;B	0.33690	0.168;0.119;0.119	T	0.41610	-0.9499	10	0.02654	T	1	-12.4824	17.4774	0.87662	0.0:1.0:0.0:0.0	.	352;251;251	A8MYE0;Q9UMZ2-5;Q9UMZ2	.;.;SYNRG_HUMAN	E	251;251;352	ENSP00000005279:G251E;ENSP00000315722:G251E	ENSP00000315722:G251E	G	-	2	0	SYNRG	33011662	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.506000	0.35747	2.543000	0.85770	0.591000	0.81541	GGA	.	.		0.438	SYNRG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256811.2	NM_007247		T	35937549	C	T	35937549	3	4	373	1	0	0	0	0	1	0	0	0	15475	855	30	3	3329	3	SYNRG	17	35937549	Missense_Mutation	SNP	C	TCGA-ZS-A9CG-01A-11D-A36X-10	24055549	35937549	45257661	70	51584										
ACSF2	80221	hgsc.bcm.edu	37	chr17	48539553	48539553	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	ccccttccacaggtgggctgCaaggcccttgtgttccccaa	10	16	0	0			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr17:48539553C>T	ENST00000300441.4	+	5	620	c.516C>T	c.(514-516)tgC>tgT	p.C172C	ACSF2_ENST00000502667.1_Silent_p.C159C|ACSF2_ENST00000541920.1_Silent_p.C12C|ACSF2_ENST00000427954.2_Silent_p.C197C|ACSF2_ENST00000504392.1_Silent_p.C129C	NM_025149.4	NP_079425.3	Q96CM8	ACSF2_HUMAN	acyl-CoA synthetase family member 2	172					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ligase activity (GO:0016874)			endometrium(7)|kidney(3)|large_intestine(1)|lung(1)|stomach(1)	13	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			AGGTGGGCTGCAAGGCCCTTG	0.577																																					p.C172C		Atlas-SNP	.											.	ACSF2	46	.	0			c.C516T						.						60	59	59					17																	48539553		2203	4300	6503	SO:0001819	synonymous_variant	80221	exon5			GGGCTGCAAGGCC	AK024573, BC012053	CCDS11567.1, CCDS74103.1, CCDS74104.1, CCDS74105.1	17q21.33	2007-10-17			ENSG00000167107	ENSG00000167107		"Acyl-CoA synthetase family"	26101	protein-coding gene	gene with protein product		610465				17762044	Standard	NM_001288968		Approved	FLJ20920, ACSMW	uc002iqu.2	Q96CM8	OTTHUMG00000162128	ENST00000300441.4:c.516C>T	chr17.hg19:g.48539553C>T		63.0	0.0		51.0	26.0	NM_025149	B4DFQ6|B4DHT5|B4DUF5|Q9H7G2	Silent	SNP	ENST00000300441.4	hg19	CCDS11567.1	.	.	.	.	.	.	.	.	.	.	C	29.5	5.012272	0.93346	.	.	ENSG00000167107	ENST00000506582	.	.	.	5.59	4.62	0.57501	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-18.9535	10.0108	0.41986	0.0:0.7889:0.0:0.2111	.	.	.	.	X	145	.	ENSP00000424842:Q145X	Q	+	1	0	ACSF2	45894552	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	0.829000	0.27449	1.362000	0.46000	-0.126000	0.14955	CAA	.	.		0.577	ACSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367423.3	NM_025149		T	48539553	C	T	48539553	2	4	373	1	0	0	0	0	0	0	0	1	175	718	25	3		3	ACSF2	17	48539553	Silent	SNP	C	TCGA-ZS-A9CG-01A-11D-A36X-10	12602004	48539553	32655657	71	51585										
LAMA1	284217	hgsc.bcm.edu	37	chr18	6993751	6993751	+	Splice_Site	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	actcgctaacatcctagtgaGctggtggaaaaataaagtct	9	8	1	1			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr18:6993751G>A	ENST00000389658.3	-	35	4990	c.4897C>T	c.(4897-4899)Ctc>Ttc	p.L1633F		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1633	Domain II and I.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				ATCCTAGTGAGCTGGTGGAAA	0.403																																					p.L1633F		Atlas-SNP	.											.	LAMA1	458	.	0			c.C4897T						.						133	124	127					18																	6993751		2203	4300	6503	SO:0001630	splice_region_variant	284217	exon35			TAGTGAGCTGGTG	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.4897-1C>T	chr18.hg19:g.6993751G>A		72.0	0.0		52.0	23.0	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	hg19	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	G	12.93	2.084710	0.36758	.	.	ENSG00000101680	ENST00000389658	T	0.10860	2.83	5.76	5.76	0.90799	Laminin I (1);	0.369922	0.26418	N	0.024485	T	0.17831	0.0428	M	0.62723	1.935	0.33205	D	0.552676	D	0.57899	0.981	P	0.52159	0.691	T	0.11324	-1.0592	10	0.28530	T	0.3	.	8.1009	0.30857	0.0793:0.0:0.7619:0.1588	.	1633	P25391	LAMA1_HUMAN	F	1633	ENSP00000374309:L1633F	ENSP00000374309:L1633F	L	-	1	0	LAMA1	6983751	0.999000	0.42202	0.998000	0.56505	0.053000	0.15095	1.590000	0.36654	2.882000	0.98803	0.655000	0.94253	CTC	.	.		0.403	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	Missense_Mutation	A	6993751	G	A	6993751	5	1	373	1	0	0	0	0	0	0	1	0	8614	985	34	3	4446	3	LAMA1	18	6993751	Splice_Site	SNP	G	TCGA-ZS-A9CG-01A-11D-A36X-10		6993751	71083497	72	51586										
LAMA3	3909	hgsc.bcm.edu	37	chr18	21437935	21437935	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	gagtgtgtgacccagggaccGgggcttgcctctgcaaggta	16	10	1	1			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr18:21437935G>C	ENST00000313654.9	+	33	4505	c.4264G>C	c.(4264-4266)Ggg>Cgg	p.G1422R	LAMA3_ENST00000399516.3_Missense_Mutation_p.G1422R	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	1422	Domain III B.|Laminin EGF-like 12. {ECO:0000255|PROSITE-ProRule:PRU00460}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					CCCAGGGACCGGGGCTTGCCT	0.527																																					p.G1422R		Atlas-SNP	.											LAMA3,NS,carcinoma,0,3	LAMA3	397	.	0			c.G4264C						.						97	97	97					18																	21437935		2033	4180	6213	SO:0001583	missense	3909	exon33			GGGACCGGGGCTT	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"Laminins"	6483	protein-coding gene	gene with protein product		600805	"laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.4264G>C	chr18.hg19:g.21437935G>C	ENSP00000324532:p.Gly1422Arg	82.0	0.0		82.0	41.0	NM_001127717	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	hg19	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.562706	0.86335	.	.	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000416669	T;T	0.75821	-0.97;-0.97	5.43	5.43	0.79202	EGF-like, laminin (3);	.	.	.	.	D	0.90906	0.7142	H	0.95151	3.63	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.994	D	0.93103	0.6510	9	0.87932	D	0	.	19.6064	0.95583	0.0:0.0:1.0:0.0	.	1422;1422	Q6VU67;Q16787	.;LAMA3_HUMAN	R	1422;1422;1420	ENSP00000324532:G1422R;ENSP00000382432:G1422R	ENSP00000324532:G1422R	G	+	1	0	LAMA3	19691933	1.000000	0.71417	0.529000	0.27951	0.839000	0.47603	7.352000	0.79404	2.710000	0.92621	0.561000	0.74099	GGG	.	.		0.527	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		C	21437935	G	C	21437935	3	2	373	1	0	0	0	0	1	0	0	0	8616	1116	39	4	4394	4	LAMA3	18	21437935	Missense_Mutation	SNP	G	TCGA-ZS-A9CG-01A-11D-A36X-10	14444184	21437935	56639313	73	51587										
MEX3D	399664	hgsc.bcm.edu	37	chr19	1556821	1556821	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	ctcacgcttggccatctccaCgtcctccttccggccggtca	8	19	3	0			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr19:1556821C>T	ENST00000402693.4	-	2	696	c.697G>A	c.(697-699)Gtg>Atg	p.V233M	MEX3D_ENST00000388824.6_Missense_Mutation_p.V233M|AC027307.1_ENST00000410788.1_RNA|AC027307.2_ENST00000581992.1_RNA	NM_203304.3	NP_976049.3	Q86XN8	MEX3D_HUMAN	mex-3 RNA binding family member D	233	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.				mRNA destabilization (GO:0061157)|mRNA localization resulting in posttranscriptional regulation of gene expression (GO:0010609)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	AU-rich element binding (GO:0017091)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(1)|lung(3)	4		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCCATCTCCACGTCCTCCTTC	0.672																																					p.V233M		Atlas-SNP	.											MEX3D,NS,carcinoma,0,1	MEX3D	11	.	0			c.G697A						.						32	33	33					19																	1556821		2201	4287	6488	SO:0001583	missense	399664	exon2			TCTCCACGTCCTC	AB107353	CCDS32865.2	19p13.3	2013-08-21	2013-08-21	2007-07-18	ENSG00000181588	ENSG00000181588		"RING-type (C3HC4) zinc fingers", "Mex-3 homologs"	16734	protein-coding gene	gene with protein product	"bcl-2 ARE RNA binding protein"	611009	"ring finger and KH domain containing 1", "mex-3 homolog D (C. elegans)"	RKHD1		17267406	Standard	NM_203304		Approved	Tino, KIAA2031, OK/SW-cl.4, RNF193	uc010dsn.3	Q86XN8	OTTHUMG00000150369	ENST00000402693.4:c.697G>A	chr19.hg19:g.1556821C>T	ENSP00000384398:p.Val233Met	197.0	0.0		131.0	45.0	NM_203304	A0PJL8|A1L023|E9PAL6|Q71M49	Missense_Mutation	SNP	ENST00000402693.4	hg19	CCDS32865.2	.	.	.	.	.	.	.	.	.	.	C	24.2	4.506728	0.85282	.	.	ENSG00000181588	ENST00000355663;ENST00000402693;ENST00000388824	T;T	0.45668	0.89;0.89	4.63	4.63	0.57726	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.000000	0.64402	D	0.000001	T	0.66137	0.2759	M	0.79123	2.44	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.72181	-0.4368	10	0.87932	D	0	-25.3952	16.4484	0.83959	0.0:1.0:0.0:0.0	.	233	Q86XN8	MEX3D_HUMAN	M	123;233;233	ENSP00000384398:V233M;ENSP00000373476:V233M	ENSP00000347885:V123M	V	-	1	0	MEX3D	1507821	1.000000	0.71417	0.999000	0.59377	0.886000	0.51366	5.608000	0.67654	2.125000	0.65367	0.491000	0.48974	GTG	.	.		0.672	MEX3D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317870.2	NM_203304		T	1556821	C	T	1556821	3	4	373	1	0	0	0	0	1	0	0	0	9521	536	19	1	1325	1	MEX3D	19	1556821	Missense_Mutation	SNP	C	TCGA-ZS-A9CG-01A-11D-A36X-10		1556821	57572162	74	51588										
THOP1	7064	hgsc.bcm.edu	37	chr19	2811648	2811648	+	Missense_Mutation	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	gcaggtggctacgacgcccaGtactacgggtacctgtggag	15	11	0	0			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr19:2811648G>C	ENST00000307741.6	+	12	2027	c.1824G>C	c.(1822-1824)caG>caC	p.Q608H	THOP1_ENST00000395212.4_Missense_Mutation_p.Q119H|THOP1_ENST00000586677.1_Missense_Mutation_p.Q487H	NM_003249.3	NP_003240.1	P52888	THOP1_HUMAN	thimet oligopeptidase 1	608					intracellular signal transduction (GO:0035556)|peptide metabolic process (GO:0006518)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)			NS(1)|central_nervous_system(1)|endometrium(1)|lung(8)|ovary(2)|skin(1)	14				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACGACGCCCAGTACTACGGGT	0.617																																					p.Q608H		Atlas-SNP	.											.	THOP1	49	.	0			c.G1824C						.						120	82	95					19																	2811648		2202	4300	6502	SO:0001583	missense	7064	exon12			CGCCCAGTACTAC		CCDS12095.1	19p13.3	2008-02-05				ENSG00000172009	3.4.24.15		11793	protein-coding gene	gene with protein product		601117				9790774	Standard	NM_003249		Approved		uc002lwj.3	P52888		ENST00000307741.6:c.1824G>C	chr19.hg19:g.2811648G>C	ENSP00000304467:p.Gln608His	134.0	0.0		89.0	28.0	NM_003249	B3KSE2|Q9UCB3	Missense_Mutation	SNP	ENST00000307741.6	hg19	CCDS12095.1	.	.	.	.	.	.	.	.	.	.	G	19.21	3.783844	0.70222	.	.	ENSG00000172009	ENST00000307741;ENST00000395212	T;T	0.11930	3.15;2.73	4.81	3.77	0.43336	Neurolysin/Thimet oligopeptidase, domain 2 (1);	0.000000	0.85682	D	0.000000	T	0.35278	0.0926	M	0.76170	2.325	0.80722	D	1	D;P;D	0.89917	1.0;0.936;1.0	D;P;D	0.77557	0.99;0.601;0.99	T	0.11792	-1.0573	10	0.72032	D	0.01	-56.0146	11.8645	0.52486	0.0874:0.0:0.9125:0.0	.	487;119;608	B4DU96;B3KSE2;P52888	.;.;THOP1_HUMAN	H	608;119	ENSP00000304467:Q608H;ENSP00000378638:Q119H	ENSP00000304467:Q608H	Q	+	3	2	THOP1	2762648	1.000000	0.71417	0.998000	0.56505	0.772000	0.43724	6.347000	0.73004	1.006000	0.39211	0.561000	0.74099	CAG	.	.		0.617	THOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451587.2			C	2811648	G	C	2811648	3	2	373	1	0	0	0	0	1	0	0	0	15886	1020	36	4	1870	4	THOP1	19	2811648	Missense_Mutation	SNP	G	TCGA-ZS-A9CG-01A-11D-A36X-10	1254827	2811648	56317335	75	51589										
ANKRD24	170961	hgsc.bcm.edu	37	chr19	4216727	4216727	+	Missense_Mutation	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	aggtccccagagaagaggggGcagcctgtggggagagtgag	20	7	0	4			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr19:4216727G>T	ENST00000600132.1	+	18	1846	c.1570G>T	c.(1570-1572)Gca>Tca	p.A524S	ANKRD24_ENST00000262970.5_Missense_Mutation_p.A614S|ANKRD24_ENST00000318934.4_Missense_Mutation_p.A524S	NM_133475.1	NP_597732.1	Q8TF21	ANR24_HUMAN	ankyrin repeat domain 24	524										endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)	21				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0233)|STAD - Stomach adenocarcinoma(1328;0.181)		AGAAGAGGGGGCAGCCTGTGG	0.617																																					p.A524S		Atlas-SNP	.											.	ANKRD24	180	.	0			c.G1570T						.						18	22	20					19																	4216727		2024	4168	6192	SO:0001583	missense	170961	exon18			GAGGGGGCAGCCT	AB075861	CCDS45925.1	19p13.3	2013-01-10				ENSG00000089847		"Ankyrin repeat domain containing"	29424	protein-coding gene	gene with protein product						11853319	Standard	NM_133475		Approved	KIAA1981	uc010dtt.1	Q8TF21		ENST00000600132.1:c.1570G>T	chr19.hg19:g.4216727G>T	ENSP00000471252:p.Ala524Ser	131.0	0.0		84.0	30.0	NM_133475	O75268|O95781	Missense_Mutation	SNP	ENST00000600132.1	hg19	CCDS45925.1	.	.	.	.	.	.	.	.	.	.	g	15.37	2.812659	0.50527	.	.	ENSG00000089847	ENST00000318934;ENST00000262970	T;T	0.30714	1.52;1.52	3.78	-0.895	0.10560	.	.	.	.	.	T	0.12518	0.0304	N	0.08118	0	0.09310	N	1	B;B	0.24426	0.063;0.103	B;B	0.25140	0.026;0.058	T	0.35748	-0.9776	9	0.15952	T	0.53	-0.1779	5.1988	0.15252	0.3618:0.1459:0.4923:0.0	.	524;614	Q8TF21;Q8TF21-2	ANR24_HUMAN;.	S	524;614	ENSP00000321731:A524S;ENSP00000262970:A614S	ENSP00000262970:A614S	A	+	1	0	ANKRD24	4167727	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	0.119000	0.15626	-0.158000	0.11040	-0.642000	0.03964	GCA	.	.		0.617	ANKRD24-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458188.1	XM_114000		T	4216727	G	T	4216727	3	4	373	1	0	0	0	0	1	0	0	0	653	1203	42	3	1636	3	ANKRD24	19	4216727	Missense_Mutation	SNP	G	TCGA-ZS-A9CG-01A-11D-A36X-10	1405079	4216727	54912256	76	51590										
COL5A3	50509	hgsc.bcm.edu	37	chr19	10089907	10089907	+	Silent	SNP	T	T	A	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	cctagaggtcccacttctccTgtctttccctggtgaggaag	10	13	2	2			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr19:10089907T>A	ENST00000264828.3	-	39	2860	c.2775A>T	c.(2773-2775)acA>acT	p.T925T		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	925	Collagen-like 4.|Triple-helical region.				axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			CCACTTCTCCTGTCTTTCCCT	0.607																																					p.T925T		Atlas-SNP	.											.	COL5A3	243	.	0			c.A2775T						.						43	47	46					19																	10089907		2203	4299	6502	SO:0001819	synonymous_variant	50509	exon39			TTCTCCTGTCTTT	AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573		"Collagens"	14864	protein-coding gene	gene with protein product		120216				10722718	Standard	NM_015719		Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.2775A>T	chr19.hg19:g.10089907T>A		205.0	0.0		179.0	23.0	NM_015719	Q9NZQ6	Silent	SNP	ENST00000264828.3	hg19	CCDS12222.1																																																																																			.	.		0.607	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719		A	10089907	T	A	10089907	2	1	373	1	0	0	0	0	0	0	0	1	3700	1567	55	4		4	COL5A3	19	10089907	Silent	SNP	T	TCGA-ZS-A9CG-01A-11D-A36X-10	5873180	10089907	49039076	77	51591										
RASGRP4	115727	hgsc.bcm.edu	37	chr19	38912788	38912788	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	1	1	0	1	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	ttccggtgcattcctggtggGacttcctgtgggcacagccc	13	13	0	0			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr19:38912788G>A	ENST00000587738.1	-	2	99	c.29C>T	c.(28-30)tCc>tTc	p.S10F	RASGRP4_ENST00000293062.9_Missense_Mutation_p.S10F|RASGRP4_ENST00000586305.1_Missense_Mutation_p.S10F|RASGRP4_ENST00000587753.1_Missense_Mutation_p.S10F|RASGRP4_ENST00000433821.2_Missense_Mutation_p.S10F|RASGRP4_ENST00000454404.2_Missense_Mutation_p.S10F|RASGRP4_ENST00000426920.2_Missense_Mutation_p.S10F			Q8TDF6	GRP4_HUMAN	RAS guanyl releasing protein 4	10					activation of phospholipase C activity (GO:0007202)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|myeloid cell differentiation (GO:0030099)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|response to extracellular stimulus (GO:0009991)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|GTP-dependent protein binding (GO:0030742)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			cervix(1)|kidney(1)|large_intestine(4)|lung(12)|pancreas(1)|prostate(3)|skin(1)	23	all_cancers(60;4.21e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			TTCCTGGTGGGACTTCCTGTG	0.602																																					p.S10F		Atlas-SNP	.											.	RASGRP4	54	.	0			c.C29T						.						33	38	36					19																	38912788		1921	4128	6049	SO:0001583	missense	115727	exon2			TGGTGGGACTTCC	AY048119	CCDS46068.1, CCDS54262.1, CCDS54263.1, CCDS54264.1	19q13.1	2013-01-10						"EF-hand domain containing"	18958	protein-coding gene	gene with protein product		607320				11956218	Standard	NM_170604		Approved		uc021uub.1	Q8TDF6		ENST00000587738.1:c.29C>T	chr19.hg19:g.38912788G>A	ENSP00000465772:p.Ser10Phe	41.0	0.0		43.0	13.0	NM_001146206	A6H8M4|C0LTP2|C0LTP3|C0LTP4|C0LTP5|C0LTP7|C9J416|C9JHZ1|Q8N858|Q96QN5|Q96QN6|Q96QN7	Missense_Mutation	SNP	ENST00000587738.1	hg19	CCDS46068.1	.	.	.	.	.	.	.	.	.	.	G	15.99	2.995087	0.54041	.	.	ENSG00000171777	ENST00000433821;ENST00000293062;ENST00000426920;ENST00000405332;ENST00000454404	T;T;T;T	0.33654	1.4;1.4;1.4;1.4	4.07	2.93	0.34026	.	0.827806	0.10518	N	0.665357	T	0.49915	0.1585	L	0.56769	1.78	0.39437	D	0.967186	D;D;D;D;D;D;D	0.61697	0.984;0.984;0.99;0.976;0.99;0.986;0.976	P;P;P;P;P;P;P	0.57371	0.819;0.75;0.527;0.556;0.804;0.748;0.459	T	0.54748	-0.8247	10	0.72032	D	0.01	-23.1122	11.5958	0.50972	0.0:0.1823:0.8177:0.0	.	10;10;10;10;10;10;10	C0LTP5;C0LTP7;C0LTP2;C0LTP4;C0LTP3;Q8TDF6-2;Q8TDF6	.;.;.;.;.;.;GRP4_HUMAN	F	10	ENSP00000411878:S10F;ENSP00000293062:S10F;ENSP00000445966:S10F;ENSP00000416463:S10F	ENSP00000293062:S10F	S	-	2	0	RASGRP4	43604628	1.000000	0.71417	1.000000	0.80357	0.625000	0.37756	3.129000	0.50500	2.284000	0.76573	0.462000	0.41574	TCC	.	.		0.602	RASGRP4-013	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460540.1	NM_170604		A	38912788	G	A	38912788	3	1	373	1	0	0	0	0	1	0	0	0	13092	1174	41	3	2056	3	RASGRP4	19	38912788	Missense_Mutation	SNP	G	TCGA-ZS-A9CG-01A-11D-A36X-10	28822881	38912788	20216195	78	51592										
PNKP	11284	hgsc.bcm.edu	37	chr19	50368637	50368637	+	Missense_Mutation	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	cccccagagagccctccaacCccggcttcaactcctgggtc	8	20	1	1			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr19:50368637C>T	ENST00000322344.3	-	4	354	c.245G>A	c.(244-246)gGg>gAg	p.G82E	PNKP_ENST00000600910.1_Missense_Mutation_p.G82E|PNKP_ENST00000600573.1_Missense_Mutation_p.G82E|PNKP_ENST00000596014.1_Missense_Mutation_p.G82E|PNKP_ENST00000595792.1_5'Flank	NM_007254.3	NP_009185.2	Q96T60	PNKP_HUMAN	polynucleotide kinase 3'-phosphatase	82	FHA.				dephosphorylation (GO:0016311)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide phosphorylation (GO:0046939)|nucleotide-excision repair, DNA damage removal (GO:0000718)|polynucleotide 3' dephosphorylation (GO:0098506)|response to oxidative stress (GO:0006979)|response to radiation (GO:0009314)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|damaged DNA binding (GO:0003684)|double-stranded DNA binding (GO:0003690)|endonuclease activity (GO:0004519)|nucleotide kinase activity (GO:0019201)|polynucleotide 3'-phosphatase activity (GO:0046403)|purine nucleotide binding (GO:0017076)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|urinary_tract(1)	19		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0118)|OV - Ovarian serous cystadenocarcinoma(262;0.0134)		GCCCTCCAACCCCGGCTTCAA	0.637								Other BER factors																													p.G82E		Atlas-SNP	.											.	PNKP	71	.	0			c.G245A						.						40	40	40					19																	50368637		2203	4300	6503	SO:0001583	missense	11284	exon4			TCCAACCCCGGCT	AF126486	CCDS12783.1	19q13.3-q13.4	2008-02-05				ENSG00000039650			9154	protein-coding gene	gene with protein product		605610				10446192, 10446193	Standard	NM_007254		Approved	PNK	uc002pqj.3	Q96T60		ENST00000322344.3:c.245G>A	chr19.hg19:g.50368637C>T	ENSP00000323511:p.Gly82Glu	177.0	0.0		120.0	13.0	NM_007254	Q9BUL2|Q9P1V2|Q9UKU8|Q9UNF8|Q9UNI0	Missense_Mutation	SNP	ENST00000322344.3	hg19	CCDS12783.1	.	.	.	.	.	.	.	.	.	.	C	17.84	3.487137	0.63962	.	.	ENSG00000039650	ENST00000322344	T	0.24538	1.85	4.66	3.62	0.41486	SMAD/FHA domain (1);	0.191569	0.44285	N	0.000472	T	0.28863	0.0716	L	0.46157	1.445	0.20403	N	0.999904	D;D	0.55800	0.973;0.957	P;P	0.50934	0.654;0.472	T	0.06373	-1.0830	10	0.46703	T	0.11	-31.6012	8.3291	0.32175	0.0:0.8918:0.0:0.1082	.	43;82	Q9BUL2;Q96T60	.;PNKP_HUMAN	E	82	ENSP00000323511:G82E	ENSP00000323511:G82E	G	-	2	0	PNKP	55060449	0.308000	0.24509	0.026000	0.17262	0.903000	0.53119	2.428000	0.44749	1.172000	0.42781	0.561000	0.74099	GGG	.	.		0.637	PNKP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465830.1	NM_007254		T	50368637	C	T	50368637	3	4	373	1	0	0	0	0	1	0	0	0	12156	623	22	3	1376	3	PNKP	19	50368637	Missense_Mutation	SNP	C	TCGA-ZS-A9CG-01A-11D-A36X-10	11455849	50368637	8760346	79	51593										
BRSK1	84446	hgsc.bcm.edu	37	chr19	55815053	55815053	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	agaccccccccggaagcgtgTggattctcccatgctgagcc	11	16	1	2			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr19:55815053T>C	ENST00000309383.1	+	12	1422	c.1145T>C	c.(1144-1146)gTg>gCg	p.V382A	BRSK1_ENST00000590333.1_Missense_Mutation_p.V398A|BRSK1_ENST00000326848.7_Missense_Mutation_p.V77A	NM_032430.1	NP_115806.1	Q8TDC3	BRSK1_HUMAN	BR serine/threonine kinase 1	382					axonogenesis (GO:0007409)|cellular response to DNA damage stimulus (GO:0006974)|centrosome duplication (GO:0051298)|establishment of cell polarity (GO:0030010)|G2 DNA damage checkpoint (GO:0031572)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|protein phosphorylation (GO:0006468)|response to UV (GO:0009411)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|gamma-tubulin binding (GO:0043015)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(15)|ovary(2)|prostate(2)|skin(6)|stomach(1)	48		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0474)		CGGAAGCGTGTGGATTCTCCC	0.592																																					p.V382A		Atlas-SNP	.											.	BRSK1	192	.	0			c.T1145C						.						60	70	67					19																	55815053		2203	4300	6503	SO:0001583	missense	84446	exon12			AGCGTGTGGATTC	AB058714	CCDS12921.1	19q13.4	2008-02-05				ENSG00000160469			18994	protein-coding gene	gene with protein product		609235				14976552	Standard	NM_032430		Approved	KIAA1811	uc002qkg.3	Q8TDC3		ENST00000309383.1:c.1145T>C	chr19.hg19:g.55815053T>C	ENSP00000310649:p.Val382Ala	307.0	1.0		285.0	98.0	NM_032430	F1DG44|Q5J5B5|Q8NDD0|Q8NDR4|Q8TDC2|Q96AV4|Q96JL4	Missense_Mutation	SNP	ENST00000309383.1	hg19	CCDS12921.1	.	.	.	.	.	.	.	.	.	.	.	23.3	4.404568	0.83230	.	.	ENSG00000160469	ENST00000309383;ENST00000543410;ENST00000326848	T;T	0.73047	-0.71;1.36	3.96	3.96	0.45880	.	0.000000	0.64402	D	0.000008	T	0.82157	0.4976	M	0.80616	2.505	0.47153	D	0.99933	D;D	0.67145	0.993;0.996	P;D	0.65684	0.867;0.937	D	0.84200	0.0450	10	0.56958	D	0.05	.	12.2704	0.54702	0.0:0.0:0.0:1.0	.	382;398	Q8TDC3;Q8TDC3-2	BRSK1_HUMAN;.	A	382;77;77	ENSP00000310649:V382A;ENSP00000320853:V77A	ENSP00000310649:V382A	V	+	2	0	BRSK1	60506865	1.000000	0.71417	0.998000	0.56505	0.939000	0.58152	7.479000	0.81095	1.813000	0.52934	0.459000	0.35465	GTG	.	.		0.592	BRSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452787.1	NM_032430		C	55815053	T	C	55815053	3	2	373	1	0	0	0	0	1	0	0	0	1525	1696	59	2	1191	2	BRSK1	19	55815053	Missense_Mutation	SNP	T	TCGA-ZS-A9CG-01A-11D-A36X-10	5446416	55815053	3313930	80	51594										
PTGIS	5740	hgsc.bcm.edu	37	chr20	48130860	48130860	+	Missense_Mutation	SNP	G	G	A	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	gatactctcgagctctccgcGgacagcagccagggcttcag	12	14	3	0			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr20:48130860G>A	ENST00000244043.4	-	7	957	c.928C>T	c.(928-930)Cgc>Tgc	p.R310C	PTGIS_ENST00000478971.1_5'UTR	NM_000961.3	NP_000952.1	Q16647	PTGIS_HUMAN	prostaglandin I2 (prostacyclin) synthase	310					apoptotic signaling pathway (GO:0097190)|arachidonic acid metabolic process (GO:0019369)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cyclooxygenase pathway (GO:0019371)|icosanoid metabolic process (GO:0006690)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|positive regulation of angiogenesis (GO:0045766)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)|prostaglandin-I synthase activity (GO:0008116)			endometrium(1)|kidney(1)|large_intestine(7)|lung(6)|ovary(3)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(12;2.37e-05)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Epoprostenol(DB01240)|Phenylbutazone(DB00812)	AGCTCTCCGCGGACAGCAGCC	0.587																																					p.R310C		Atlas-SNP	.											.	PTGIS	60	.	0			c.C928T						.						56	52	53					20																	48130860		2203	4300	6503	SO:0001583	missense	5740	exon7			CTCCGCGGACAGC		CCDS13419.1	20q13	2013-11-18			ENSG00000124212	ENSG00000124212	5.3.99.4	"Cytochrome P450s"	9603	protein-coding gene	gene with protein product	"cytochrome P450, family 8, subfamily A, polypeptide 1"	601699				8812456	Standard	NM_000961		Approved	PGIS, CYP8A1	uc002xut.3	Q16647	OTTHUMG00000033077	ENST00000244043.4:c.928C>T	chr20.hg19:g.48130860G>A	ENSP00000244043:p.Arg310Cys	73.0	0.0		70.0	23.0	NM_000961	Q3MII8|Q9HAX2|Q9HAX3|Q9HAX4	Missense_Mutation	SNP	ENST00000244043.4	hg19	CCDS13419.1	.	.	.	.	.	.	.	.	.	.	G	16.72	3.202544	0.58234	.	.	ENSG00000124212	ENST00000244043	T	0.01705	4.68	4.1	3.15	0.36227	.	0.577942	0.15393	N	0.264738	T	0.02455	0.0075	M	0.72894	2.215	0.27370	N	0.955721	P	0.41080	0.737	B	0.30105	0.111	T	0.37731	-0.9693	10	0.48119	T	0.1	-2.1553	9.6497	0.39890	0.105:0.0:0.895:0.0	.	310	Q16647	PTGIS_HUMAN	C	310	ENSP00000244043:R310C	ENSP00000244043:R310C	R	-	1	0	PTGIS	47564267	0.718000	0.27976	0.185000	0.23176	0.212000	0.24457	1.708000	0.37899	0.843000	0.35070	0.561000	0.74099	CGC	.	.		0.587	PTGIS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080496.2			A	48130860	G	A	48130860	3	1	373	1	0	0	0	0	1	0	0	0	12765	1116	39	1	590	1	PTGIS	20	48130860	Missense_Mutation	SNP	G	TCGA-ZS-A9CG-01A-11D-A36X-10		48130860	14894660	81	51595										
PRPF6	57473	hgsc.bcm.edu	37	chr20	62612631	62612631	+	Intron	SNP	G	G	T	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	aagaaaccgttcctagggatGcccgcgcccctcggctacgt	11	15	0	1			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr20:62612631G>T	ENST00000450537.1	-	2	56				ZNF512B_ENST00000217130.3_Intron|PRPF6_ENST00000535781.1_Missense_Mutation_p.M11I|SAMD10_ENST00000498830.1_5'Flank|SAMD10_ENST00000369886.3_5'Flank			Q96KM6	Z512B_HUMAN	zinc finger protein 512B						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(4)|skin(1)	33	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					TCCTAGGGATGCCCGCGCCCC	0.677																																					p.M11I		Atlas-SNP	.											.	PRPF6	88	.	0			c.G33T						.						23	22	22					20																	62612631		2191	4290	6481	SO:0001627	intron_variant	24148	exon1			AGGGATGCCCGCG	AB033022	CCDS13548.1	20q13.33	2011-02-09			ENSG00000196700	ENSG00000196700			29212	protein-coding gene	gene with protein product						10574462	Standard	NM_020713		Approved	GM632, MGC149845, MGC149846	uc002yhl.2	Q96KM6	OTTHUMG00000033008	ENST00000450537.1:c.5-13323C>A	chr20.hg19:g.62612631G>T		195.0	0.0		145.0	48.0	NM_012469	Q08AK9|Q9ULM4	Missense_Mutation	SNP	ENST00000450537.1	hg19	CCDS13548.1	.	.	.	.	.	.	.	.	.	.	G	18.50	3.637670	0.67130	.	.	ENSG00000101161	ENST00000266079;ENST00000535781	T;T	0.77750	-1.1;-1.12	4.46	4.46	0.54185	.	0.000000	0.85682	D	0.000000	T	0.72112	0.3420	L	0.43152	1.355	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.12156	0.007;0.002	T	0.69022	-0.5255	10	0.41790	T	0.15	-31.8364	16.6876	0.85312	0.0:0.0:1.0:0.0	.	11;11	O94906-2;O94906	.;PRP6_HUMAN	I	11	ENSP00000266079:M11I;ENSP00000446216:M11I	ENSP00000266079:M11I	M	+	3	0	PRPF6	62083075	1.000000	0.71417	1.000000	0.80357	0.868000	0.49771	7.953000	0.87836	2.017000	0.59298	0.491000	0.48974	ATG	.	.		0.677	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713		T	62612631	G	T	62612631	1	4	373	0	1	0	0	0	0	0	0	0	12586	1319	46	3		3	PRPF6	20	62612631	Intron	SNP	G	TCGA-ZS-A9CG-01A-11D-A36X-10	14481771	62612631	412889	82	51596										
APOBEC3G	60489	hgsc.bcm.edu	37	chr22	39476966	39476966	+	Missense_Mutation	SNP	A	A	T	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	cgaacttaagtaccacccagAgatgagattcttccactggt	8	11	1	2			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr22:39476966A>T	ENST00000407997.3	+	3	557	c.200A>T	c.(199-201)gAg>gTg	p.E67V	APOBEC3G_ENST00000461827.1_3'UTR|APOBEC3G_ENST00000452957.2_Missense_Mutation_p.E67V	NM_021822.3	NP_068594.1	Q9HC16	ABC3G_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3G	67	CMP/dCMP deaminase zinc-binding 1.				base conversion or substitution editing (GO:0016553)|cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)|negative regulation of viral genome replication (GO:0045071)|negative regulation of viral process (GO:0048525)|positive regulation of defense response to virus by host (GO:0002230)|viral process (GO:0016032)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|ribonucleoprotein complex (GO:0030529)	cytidine deaminase activity (GO:0004126)|deoxycytidine deaminase activity (GO:0047844)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			central_nervous_system(1)|large_intestine(4)|lung(5)|skin(1)|stomach(1)	12	Melanoma(58;0.04)					TACCACCCAGAGATGAGATTC	0.572																																					p.E67V		Atlas-SNP	.											.	APOBEC3G	69	.	0			c.A200T						.						55	51	52					22																	39476966		2203	4300	6503	SO:0001583	missense	60489	exon3			ACCCAGAGATGAG	AF182420	CCDS13984.1	22q13.1-q13.2	2008-05-15			ENSG00000239713	ENSG00000239713		"Apolipoprotein B mRNA editing enzymes"	17357	protein-coding gene	gene with protein product		607113				11863358	Standard	NM_021822		Approved	CEM15, MDS019, dJ494G10.1, FLJ12740, bK150C2.7		Q9HC16	OTTHUMG00000151081	ENST00000407997.3:c.200A>T	chr22.hg19:g.39476966A>T	ENSP00000385057:p.Glu67Val	97.0	0.0		78.0	29.0	NM_021822	B2RDR9|Q45F02|Q5TF77|Q7Z2N1|Q7Z2N4|Q9H9H8	Missense_Mutation	SNP	ENST00000407997.3	hg19	CCDS13984.1	.	.	.	.	.	.	.	.	.	.	.	12.71	2.018764	0.35606	.	.	ENSG00000239713	ENST00000452957;ENST00000407997	D;D	0.94897	-3.55;-3.55	2.34	1.29	0.21616	APOBEC-like, N-terminal (1);	.	.	.	.	D	0.96806	0.8957	H	0.95004	3.61	0.09310	N	1	D	0.55605	0.972	P	0.59825	0.864	D	0.90297	0.4327	9	0.87932	D	0	.	4.0427	0.09758	0.8182:0.0:0.1818:0.0	.	67	Q9HC16	ABC3G_HUMAN	V	67	ENSP00000413376:E67V;ENSP00000385057:E67V	ENSP00000385057:E67V	E	+	2	0	APOBEC3G	37806912	0.557000	0.26546	0.005000	0.12908	0.008000	0.06430	2.245000	0.43133	0.329000	0.23460	0.374000	0.22700	GAG	.	.		0.572	APOBEC3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321219.1	NM_021822		T	39476966	A	T	39476966	3	4	373	1	0	0	0	0	1	0	0	0	794	304	11	4	210	4	APOBEC3G	22	39476966	Missense_Mutation	SNP	A	TCGA-ZS-A9CG-01A-11D-A36X-10		39476966	11827600	83	51597										
CYP2D6	1565	hgsc.bcm.edu	37	chr22	42525162	42525162	+	Silent	SNP	G	G	C	1	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	cgcctctgctcgcgccacgcGggcccatagcgcgccaggaa	13	18	1	0	rs369043970		TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chr22:42525162G>C	ENST00000360608.5	-	3	492	c.378C>G	c.(376-378)ccC>ccG	p.P126P	NDUFA6-AS1_ENST00000416037.2_RNA|CYP2D6_ENST00000359033.4_Intron|NDUFA6-AS1_ENST00000608491.1_RNA|NDUFA6-AS1_ENST00000608288.1_RNA|CYP2D6_ENST00000389970.3_Silent_p.P126P|NDUFA6-AS1_ENST00000439129.1_RNA	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	126					alkaloid catabolic process (GO:0009822)|alkaloid metabolic process (GO:0009820)|coumarin metabolic process (GO:0009804)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|isoquinoline alkaloid metabolic process (GO:0033076)|monoterpenoid metabolic process (GO:0016098)|negative regulation of binding (GO:0051100)|negative regulation of cellular organofluorine metabolic process (GO:0090350)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(4)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21					Abiraterone(DB05812)|Acebutolol(DB01193)|Acetaminophen(DB00316)|Ajmaline(DB01426)|Almotriptan(DB00918)|Alogliptin(DB06203)|Alprenolol(DB00866)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amoxapine(DB00543)|Amphetamine(DB00182)|Amprenavir(DB00701)|Amsacrine(DB00276)|Antipyrine(DB01435)|Aprindine(DB01429)|Arformoterol(DB01274)|Aripiprazole(DB01238)|Artemether(DB06697)|Asenapine(DB06216)|Astemizole(DB00637)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzatropine(DB00245)|Benzyl alcohol(DB06770)|Bepridil(DB01244)|Betaxolol(DB00195)|Bicalutamide(DB01128)|Biperiden(DB00810)|Bisoprolol(DB00612)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Buspirone(DB00490)|Caffeine(DB00201)|Captopril(DB01197)|Carbinoxamine(DB00748)|Carteolol(DB00521)|Carvedilol(DB01136)|Celecoxib(DB00482)|Cephalexin(DB00567)|Cevimeline(DB00185)|Chlordiazepoxide(DB00475)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Cisapride(DB00604)|Citalopram(DB00215)|Clemastine(DB00283)|Clevidipine(DB04920)|Clomipramine(DB01242)|Clonidine(DB00575)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Codeine(DB00318)|Cyclobenzaprine(DB00924)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Darifenacin(DB00496)|Debrisoquin(DB04840)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dihydrocodeine(DB01551)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronedarone(DB04855)|Duloxetine(DB00476)|Efavirenz(DB00625)|Eletriptan(DB00216)|Encainide(DB01228)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erlotinib(DB00530)|Escitalopram(DB01175)|Ethylmorphine(DB01466)|Etoricoxib(DB01628)|Felodipine(DB01023)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fingolimod(DB08868)|Flecainide(DB01195)|Flunarizine(DB04841)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Galantamine(DB00674)|Gefitinib(DB00317)|Glutethimide(DB01437)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Halothane(DB01159)|Histamine Phosphate(DB00667)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Hydroxychloroquine(DB01611)|Hydroxyurea(DB01005)|Hydroxyzine(DB00557)|Idarubicin(DB01177)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Ipratropium bromide(DB00332)|Irbesartan(DB01029)|Isoniazid(DB00951)|Itraconazole(DB01167)|Ketoconazole(DB01026)|L-DOPA(DB01235)|Labetalol(DB00598)|Lansoprazole(DB00448)|Lercanidipine(DB00528)|Levomilnacipran(DB08918)|Lidocaine(DB00281)|Lisuride(DB00589)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Lovastatin(DB00227)|Lumefantrine(DB06708)|Maprotiline(DB00934)|Mefloquine(DB00358)|Mepyramine(DB06691)|Mequitazine(DB01071)|Mesoridazine(DB00933)|Methadone(DB00333)|Methamphetamine(DB01577)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Methylnaltrexone(DB06800)|Methylphenidate(DB00422)|Methyprylon(DB01107)|Metoclopramide(DB01233)|Metoprolol(DB00264)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midodrine(DB00211)|Mifepristone(DB00834)|Minaprine(DB00805)|Mirabegron(DB08893)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Morphine(DB00295)|Nateglinide(DB00731)|Nebivolol(DB04861)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niacin(DB00627)|Nicardipine(DB00622)|Nicergoline(DB00699)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitrofural(DB00336)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxamniquine(DB01096)|Oxprenolol(DB01580)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Paliperidone(DB01267)|Palonosetron(DB00377)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Pergolide(DB01186)|Perhexiline(DB01074)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenformin(DB00914)|Phentermine(DB00191)|Pimozide(DB01100)|Pindolol(DB00960)|Pioglitazone(DB01132)|Piperazine(DB00592)|Pipotiazine(DB01621)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Primaquine(DB01087)|Procainamide(DB01035)|Prochlorperazine(DB00433)|Progesterone(DB00396)|Proguanil(DB01131)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Pyrimethamine(DB00205)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranitidine(DB00863)|Ranolazine(DB00243)|Reboxetine(DB00234)|Remoxipride(DB00409)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivastigmine(DB00989)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertindole(DB06144)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tamsulosin(DB00706)|Tapentadol(DB06204)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Terbinafine(DB00857)|Tetrabenazine(DB04844)|Theophylline(DB00277)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Timolol(DB00373)|Tiotropium(DB01409)|Tipranavir(DB00932)|Tolterodine(DB01036)|Trabectedin(DB05109)|Tramadol(DB00193)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Trospium(DB00209)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)|Vinblastine(DB00570)|Vinorelbine(DB00361)|Yohimbine(DB01392)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Ziprasidone(DB00246)|Zolpidem(DB00425)	CGCGCCACGCGGGCCCATAGC	0.682																																					p.P126P		Atlas-SNP	.											.	CYP2D6	104	.	0			c.C378G						.						20	24	23					22																	42525162		2021	4167	6188	SO:0001819	synonymous_variant	1565	exon3			CCACGCGGGCCCA	M20403	CCDS33657.1, CCDS46721.1	22q13.1	2014-09-17	2003-01-14		ENSG00000100197	ENSG00000100197		"Cytochrome P450s"	2625	protein-coding gene	gene with protein product		124030	"cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolizing), polypeptide 6", "cytochrome P450, family 2, subfamily D, polypeptide 7 pseudogene 2", "cytochrome P450, subfamily II (debrisoquine, sparteine, etc., -metabolising), polypeptide 7 pseudogene 2", "cytochrome P450, family 2, subfamily D, polypeptide 8 pseudogene 2", "cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolising), polypeptide 8 pseudogene 2"	CYP2DL1, CYP2D7P2, CYP2D7BP, CYP2D8P2, CYP2D7AP		8449513	Standard	NM_000106		Approved	CPD6, P450-DB1, CYP2D, P450C2D	uc003bce.3	P10635	OTTHUMG00000150918	ENST00000360608.5:c.378C>G	chr22.hg19:g.42525162G>C		58.0	0.0		73.0	21.0	NM_000106	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Silent	SNP	ENST00000360608.5	hg19	CCDS46721.1																																																																																			.	.		0.682	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1			C	42525162	G	C	42525162	2	2	373	1	0	0	0	0	0	0	0	1	4171	1103	39	4		4	CYP2D6	22	42525162	Silent	SNP	G	TCGA-ZS-A9CG-01A-11D-A36X-10	3048196	42525162	8779404	84	51598										
PPP2R3B	28227	hgsc.bcm.edu	37	chrX	306923	306923	+	Missense_Mutation	SNP	T	T	C	0	0	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	ccgcacctgcaggaaggagcTcctccgcagctcggcgcagg	14	16	0	0			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chrX:306923T>C	ENST00000390665.3	-	6	883	c.865A>G	c.(865-867)Agc>Ggc	p.S289G		NM_013239.4	NP_037371.2	Q9Y5P8	P2R3B_HUMAN	protein phosphatase 2, regulatory subunit B'', beta	289					cell cycle arrest (GO:0007050)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|phosphoprotein phosphatase activity (GO:0004721)|protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			endometrium(5)|lung(5)|skin(1)	11		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				AGGAAGGAGCTCCTCCGCAGC	0.697																																					p.S289G		Atlas-SNP	.											.	PPP2R3B	43	.	0			c.A865G						.						16	23	20					X																	306923		1945	4111	6056	SO:0001583	missense	28227	exon6			AGGAGCTCCTCCG	AF215840	CCDS14104.1	Xp22.3 and Yp11.3	2013-01-10	2010-06-18		ENSG00000167393	ENSG00000167393		"Pseudoautosomal regions / PAR1", "Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "EF-hand domain containing"	13417	protein-coding gene	gene with protein product		300339	"protein phosphatase 2 (formerly 2A), regulatory subunit B'', beta"	PPP2R3L		11173861	Standard	NM_013239		Approved	PPP2R3LY, PR48	uc004cpg.3	Q9Y5P8	OTTHUMG00000021052	ENST00000390665.3:c.865A>G	chrX.hg19:g.306923T>C	ENSP00000375080:p.Ser289Gly	59.0	0.0		46.0	10.0	NM_013239	Q6P4G9|Q7RTT1|Q96H01	Missense_Mutation	SNP	ENST00000390665.3	hg19	CCDS14104.1	.	.	.	.	.	.	.	.	.	.	T	7.489	0.650265	0.14516	.	.	ENSG00000167393	ENST00000390665	T	0.50277	0.75	1.18	1.18	0.20946	.	0.325715	0.30260	U	0.010030	T	0.55768	0.1941	M	0.68317	2.08	0.09310	N	0.999997	D;P	0.54964	0.969;0.915	P;P	0.57846	0.828;0.616	T	0.47169	-0.9138	10	0.87932	D	0	.	7.6049	0.28097	0.0:0.0:0.0:1.0	.	128;289	B4DE79;Q9Y5P8	.;P2R3B_HUMAN	G	289	ENSP00000375080:S289G	ENSP00000375080:S289G	S	-	1	0	PPP2R3B	226923	1.000000	0.71417	0.981000	0.43875	0.000000	0.00434	4.098000	0.57748	0.405000	0.25532	0.000000	0.15137	AGC	.	.		0.697	PPP2R3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055577.2	NM_013239		C	306923	T	C	306923	3	2	373	1	0	0	0	0	1	0	0	0	12401	1551	54	2	894	2	PPP2R3B	23	306923	Missense_Mutation	SNP	T	TCGA-ZS-A9CG-01A-11D-A36X-10		306923	154963637	85	51599										
AR	367	hgsc.bcm.edu	37	chrX	66766365	66766365	+	Silent	SNP	C	C	T	0	1	0	0	0	0	0	0	0	0	0	0	0.0348837209302326	3	1	0.706609972941631	1.31227566403446	0.574120603015075	1	1	0	ggtgggggtggtggcggcggCggcggcggcggcggcggcgg	29	9	0	0			TCGA-ZS-A9CG-01A-11D-A36X-10	TCGA-ZS-A9CG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d44d787d-1a49-474d-9dca-07f1930ff316	823b073f-c65b-4652-8dfc-2957727cbb77	g.chrX:66766365C>T	ENST00000374690.3	+	1	1901	c.1377C>T	c.(1375-1377)ggC>ggT	p.G459G	AR_ENST00000513847.1_3'UTR|AR_ENST00000396044.3_Silent_p.G459G|AR_ENST00000504326.1_Silent_p.G459G	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	457	Modulating.|Poly-Gly.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	gtggcggcggcggcggcggcg	0.756									Androgen Insensitivity Syndrome																												p.G459G		Atlas-SNP	.											.	AR	249	.	0			c.C1377T						.																																			SO:0001819	synonymous_variant	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	CGGCGGCGGCGGC	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.1377C>T	chrX.hg19:g.66766365C>T		193.0	0.0		472.0	86.0	NM_000044	A2RUN2|B1AKD7|Q9UD95	Silent	SNP	ENST00000374690.3	hg19	CCDS14387.1																																																																																			.	.		0.756	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		T	66766365	C	T	66766365	2	4	373	1	0	0	0	0	0	0	0	1	836	755	27	1		1	AR	23	66766365	Silent	SNP	C	TCGA-ZS-A9CG-01A-11D-A36X-10	66459442	66766365	88504195	86	51600										
